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	G	C	tCw	wGa	tC	Ga	tC_mutation	tC_mutation_to_G	tC_mutation_to_T	APOBEC_mutation	APOBEC_mutation_to_G	APOBEC_mutation_to_T	[tCw_to_G+tCw_to_T]_per_mut	tCw_to_G+tCw_to_T	BH_Fisher_p-value_tCw	APOBEC_enrich	tCw_to_G_enrich	tCw_to_T_enrich	p-value_GvT_skew	BH_p-value_GvT_skew	APOBEC_MutLoad_MinEstimate	"CONTEXT(+/-20)"	g_counts	c_counts	tcw_counts	wga_counts	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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_CancerGermlineMut	i_CGC_CancerMolecularGenetics	i_CGC_CancerSomaticMut	i_CGC_CancerSyndrome	i_CGC_Chr	i_CGC_ChrBand	i_CGC_GeneID	i_CGC_Name	i_CGC_OtherGermlineMut	i_CGC_TissueType	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_AccessionNumbers	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_EnzymeIDs	i_HGNC_Genefamilydescription	i_HGNC_HGNCID	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_NameSynonyms	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_PrimaryIDs	i_HGNC_PubmedIDs	i_HGNC_RecordType	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_SecondaryIDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP_NR	i_dbNSFP_GERP_RS	i_dbNSFP_GERP_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos1coor	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	newbase	end	tum_allele1	tum_allele2	start	effect_idx	newbase_idx	pat_idx	is_coding	is_flank	is_indel	is_ins	is_del	is_missense	is_nonsense	is_splice	is_silent	gene_idx	context_and_effect	context65	categ_idx	trackpos	categ	gene	chr	pos	type	classification	ref_allele	patient	DistBetween_Mutations	Distance_to_LT_end	Distance_to_RT_end	Strain_Mutation_ID	Dataset_Mutation_ID	Complex_ID	Complex_Size	StrainCluster_ID	Dataset_Cluster_ID	Distance_Between_Clusters	Cluster_Size_Mutations	Cluster_Size_Complexes	Cluster_Length	Cluster_Coordination	Content_of_non_coordinated_cluster	Cluster_Pvalue
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056344	27056344	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgccatgggcggcctctcttAtacacagcaggtagatggtg	13	10	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:27056344A>G	ENST00000324856.7	+	2	1711	c.1340A>G	c.(1339-1341)tAt>tGt	p.Y447C	ARID1A_ENST00000457599.2_Missense_Mutation_p.Y447C|ARID1A_ENST00000374152.2_Missense_Mutation_p.Y64C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	447					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		GGCCTCTCTTATACACAGCAG	0.552			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											34	38	36					1																	27056344		2203	4300	6503	26928931	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1340A>G	1.37:g.27056344A>G	ENSP00000320485:p.Tyr447Cys		26928931	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.431272	0.43122	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	T;T;T;T	0.65364	2.76;2.37;-0.15;2.84	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.996	T	0.70096	-0.4966	10	0.39692	T	0.17	-4.8274	16.4127	0.83723	1.0:0.0:0.0:0.0	.	447;447;101	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	C	447;447;64;64	ENSP00000320485:Y447C;ENSP00000387636:Y447C;ENSP00000432473:Y64C;ENSP00000363267:Y64C	ENSP00000320485:Y447C	Y	+	2	0	ARID1A	26928931	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.631000	0.90991	2.279000	0.76181	0.528000	0.53228	TAT		0.552	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27056344	A	G	27056344	3	3	1	1	0	0	0	0	1	0	0	0	913	449	16	4	1346	4	ARID1A	1	27056344	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10		27056344	222194277	1	1										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27059168	27059168	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tttgtttttcttgttgtaggAgctatctcaagattcatttg	8	5	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:27059168A>G	ENST00000324856.7	+	4	2176	c.1805A>G	c.(1804-1806)gAg>gGg	p.E602G	ARID1A_ENST00000457599.2_Splice_Site_p.E602G|ARID1A_ENST00000374152.2_Splice_Site_p.E219G	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	602					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		TTGTTGTAGGAGCTATCTCAA	0.468			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											128	110	116					1																	27059168		2203	4300	6503	26931755	SO:0001630	splice_region_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1804-1A>G	1.37:g.27059168A>G			26931755	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494532	0.64186	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.03272	4.15;3.99;4.06	5.7	5.7	0.88788	.	0.113436	0.64402	D	0.000018	T	0.12475	0.0303	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.986;0.994;0.986	T	0.34229	-0.9837	10	0.14252	T	0.57	-14.2407	15.9492	0.79820	1.0:0.0:0.0:0.0	.	602;602;256	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	G	602;602;219	ENSP00000320485:E602G;ENSP00000387636:E602G;ENSP00000363267:E219G	ENSP00000320485:E602G	E	+	2	0	ARID1A	26931755	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.251000	0.89838	2.182000	0.69389	0.402000	0.26972	GAG		0.468	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	Missense_Mutation	G	27059168	A	G	27059168	5	3	1	1	0	0	0	0	0	0	1	0	913	318	11	4	1819	4	ARID1A	1	27059168	Splice_Site	SNP	A	TCGA-AF-2687-01A-02D-1733-10	2824	27059168	222191453	2	2										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27099905	27099905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggatgggtgacccctacagtCgtgctgccggccctgggcta	15	13	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:27099905C>T	ENST00000324856.7	+	15	4155	c.3784C>T	c.(3784-3786)Cgt>Tgt	p.R1262C	ARID1A_ENST00000457599.2_Missense_Mutation_p.R1262C|ARID1A_ENST00000540690.1_5'UTR|ARID1A_ENST00000374152.2_Missense_Mutation_p.R879C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1262					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		CCCCTACAGTCGTGCTGCCGG	0.592			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											64	61	62					1																	27099905		2203	4300	6503	26972492	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3784C>T	1.37:g.27099905C>T	ENSP00000320485:p.Arg1262Cys		26972492	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.00|15.00	2.702186|2.702186	0.48307|0.48307	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152|ENST00000430799	T;T;T|T	0.03441|0.03553	4.07;3.96;3.93|3.89	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.12178|0.12178	0.0296|0.0296	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;1.0|.	P;P;P;P|.	0.60682|.	0.804;0.759;0.878;0.759|.	T|T	0.00303|0.00303	-1.1833|-1.1833	10|7	0.56958|0.87932	D|D	0.05|0	-0.9968|-0.9968	18.5413|18.5413	0.91029|0.91029	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	879;1262;1262;915|.	O14497-3;O14497;O14497-2;Q4LE49|.	.;ARI1A_HUMAN;.;.|.	C|L	1262;1262;879|158	ENSP00000320485:R1262C;ENSP00000387636:R1262C;ENSP00000363267:R879C|ENSP00000390317:S158L	ENSP00000320485:R1262C|ENSP00000390317:S158L	R|S	+|+	1|2	0|0	ARID1A|ARID1A	26972492|26972492	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	4.352000|4.352000	0.59404|0.59404	2.627000|2.627000	0.88993|0.88993	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.592	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27099905	C	T	27099905	3	4	1	1	0	0	0	0	1	0	0	0	913	884	31	1	3842	1	ARID1A	1	27099905	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	40737	27099905	222150716	3	3										
TEKT2	27285	hgsc.bcm.edu	37	chr1	36553586	36553586	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttccctagggacgcactggaCgccctgtgcaagcacctggc	12	15	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:36553586C>T	ENST00000207457.3	+	10	1219	c.1092C>T	c.(1090-1092)gaC>gaT	p.D364D	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	364					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACGCACTGGACGCCCTGTGCA	0.637																																																0			1											38	29	32					1																	36553586		2203	4300	6503	36326173	SO:0001819	synonymous_variant	27285			AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.1092C>T	1.37:g.36553586C>T			36326173	A6NIS6|O60638	Silent	SNP	ENST00000207457.3	37	CCDS401.1																																																																																				0.637	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		T	36553586	C	T	36553586	2	4	1	1	0	0	0	0	0	0	0	1	15792	535	19	1		1	TEKT2	1	36553586	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	9453681	36553586	212697035	4	4										
PRPF38A	84950	hgsc.bcm.edu	37	chr1	52876804	52876804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cagagtttgaattgatgcatGttgatgagtttattgatgaa	11	2	0	7			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:52876804G>A	ENST00000257181.9	+	4	616	c.430G>A	c.(430-432)Gtt>Att	p.V144I	snoU13_ENST00000458879.1_RNA|PRPF38A_ENST00000474048.1_Intron	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	144					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						ATTGATGCATGTTGATGAGTT	0.358																																																0			1											140	128	132					1																	52876804		2203	4300	6503	52649392	SO:0001583	missense	84950			AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.430G>A	1.37:g.52876804G>A	ENSP00000257181:p.Val144Ile		52649392	Q96JW1|Q9BVZ8	Missense_Mutation	SNP	ENST00000257181.9	37	CCDS567.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.621127	0.66787	.	.	ENSG00000134748	ENST00000257181	.	.	.	4.57	4.57	0.56435	.	0.055210	0.64402	D	0.000001	T	0.32010	0.0815	N	0.10945	0.07	0.80722	D	1	B	0.33583	0.418	B	0.32393	0.145	T	0.17837	-1.0356	9	0.08381	T	0.77	-11.342	17.5428	0.87853	0.0:0.0:1.0:0.0	.	144	Q8NAV1	PR38A_HUMAN	I	144	.	ENSP00000257181:V144I	V	+	1	0	PRPF38A	52649392	1.000000	0.71417	0.987000	0.45799	0.904000	0.53231	7.684000	0.84104	2.380000	0.81148	0.563000	0.77884	GTT		0.358	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		A	52876804	G	A	52876804	3	1	1	1	0	0	0	0	1	0	0	0	12601	1377	48	3	444	3	PRPF38A	1	52876804	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	16323218	52876804	196373817	5	5										
LRRC40	55631	hgsc.bcm.edu	37	chr1	70650578	70650578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtttgtaatttcttcagggaGtattttcagtttattatggc	9	4	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:70650578G>A	ENST00000370952.3	-	4	506	c.427C>T	c.(427-429)Ctc>Ttc	p.L143F		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	143						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TCTTCAGGGAGTATTTTCAGT	0.303																																																0			1											141	142	142					1																	70650578		2202	4300	6502	70423166	SO:0001583	missense	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.427C>T	1.37:g.70650578G>A	ENSP00000359990:p.Leu143Phe		70423166	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.051028	0.36181	.	.	ENSG00000066557	ENST00000370952	T	0.70045	-0.45	5.98	5.07	0.68467	.	0.120183	0.56097	N	0.000024	T	0.70937	0.3281	M	0.75777	2.31	0.41135	D	0.985913	D	0.76494	0.999	D	0.71414	0.973	T	0.74453	-0.3660	10	0.46703	T	0.11	.	7.8188	0.29276	0.1398:0.0:0.7267:0.1335	.	143	Q9H9A6	LRC40_HUMAN	F	143	ENSP00000359990:L143F	ENSP00000359990:L143F	L	-	1	0	LRRC40	70423166	0.848000	0.29623	0.961000	0.40146	0.241000	0.25554	1.141000	0.31528	1.554000	0.49487	-0.122000	0.15005	CTC		0.303	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		A	70650578	G	A	70650578	3	1	1	1	0	0	0	0	1	0	0	0	9027	1029	36	3	1429	3	LRRC40	1	70650578	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	17773774	70650578	178600043	6	6										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82456643	82456643	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gaagacctctctccctccagGaggagtgagaatgaggacat	12	10	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:82456643G>C	ENST00000370728.1	+	25	4839	c.4194G>C	c.(4192-4194)agG>agC	p.R1398S	LPHN2_ENST00000370717.2_Missense_Mutation_p.R1413S|LPHN2_ENST00000359929.3_Missense_Mutation_p.R1342S|LPHN2_ENST00000370721.1_Missense_Mutation_p.R1323S|LPHN2_ENST00000319517.6_Missense_Mutation_p.R1342S|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000370727.1_Missense_Mutation_p.R1370S|LPHN2_ENST00000370725.1_Missense_Mutation_p.R1413S|LPHN2_ENST00000370730.1_Missense_Mutation_p.R1355S|LPHN2_ENST00000370723.1_Missense_Mutation_p.R1400S|LPHN2_ENST00000335786.5_Missense_Mutation_p.R1355S|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000271029.4_Missense_Mutation_p.R1370S|LPHN2_ENST00000394879.1_Missense_Mutation_p.R1400S|LPHN2_ENST00000469377.2_3'UTR			O95490	LPHN2_HUMAN	latrophilin 2	1398					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTCCCTCCAGGAGGAGTGAGA	0.498																																																0			1											73	69	71					1																	82456643		2203	4300	6503	82229231	SO:0001583	missense	23266			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4194G>C	1.37:g.82456643G>C	ENSP00000359763:p.Arg1398Ser		82229231	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	4.128|4.128|4.128	0.021945|0.021945|0.021945	0.08006|0.08006|0.08006	.|.|.	.|.|.	ENSG00000117114|ENSG00000117114|ENSG00000117114	ENST00000402328|ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	.|.|T;T;T;T;T;T;T;T;T;T;T;T	.|.|0.67523	.|.|-0.24;-0.27;-0.26;-0.2;-0.2;-0.16;-0.22;-0.22;-0.2;-0.16;-0.2;-0.26	5.15|5.15|5.15	3.29|3.29|3.29	0.37713|0.37713|0.37713	.|.|.	.|.|0.207171	.|.|0.39615	.|.|N	.|.|0.001305	T|T|T	0.32556|0.32556|0.32556	0.0833|0.0833|0.0833	L|L|L	0.29908|0.29908|0.29908	0.895|0.895|0.895	0.37169|0.37169|0.37169	D|D|D	0.902975|0.902975|0.902975	.|.|B;B	.|.|0.33000	.|.|0.171;0.393	.|.|B;B	.|.|0.28916	.|.|0.062;0.096	T|T|T	0.13229|0.13229|0.13229	-1.0517|-1.0517|-1.0517	5|5|10	.|.|0.42905	.|.|T	.|.|0.14	.|.|.	8.5952|8.5952|8.5952	0.33712|0.33712|0.33712	0.2315:0.0:0.7685:0.0|0.2315:0.0:0.7685:0.0|0.2315:0.0:0.7685:0.0	.|.|.	.|.|1342;322	.|.|O95490-2;B3KVU1	.|.|.;.	Q|A|S	410|1290|1323;1398;1355;1370;1413;1400;1342;1342;1413;1400;1370;1355	.|.|ENSP00000359756:R1323S;ENSP00000359763:R1398S;ENSP00000359765:R1355S;ENSP00000359762:R1370S;ENSP00000359760:R1413S;ENSP00000359758:R1400S;ENSP00000353006:R1342S;ENSP00000322270:R1342S;ENSP00000359752:R1413S;ENSP00000378344:R1400S;ENSP00000271029:R1370S;ENSP00000337306:R1355S	.|.|ENSP00000271029:R1370S	E|G|R	+|+|+	1|2|3	0|0|2	LPHN2|LPHN2|LPHN2	82229231|82229231|82229231	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	1.639000|1.639000|1.639000	0.37176|0.37176|0.37176	0.584000|0.584000|0.584000	0.29591|0.29591|0.29591	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAG|GGA|AGG		0.498	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		C	82456643	G	C	82456643	3	2	1	1	0	0	0	0	1	0	0	0	8945	1165	41	5	4100	5	LPHN2	1	82456643	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	11806065	82456643	166793978	7	7										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85397191	85397191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gatttgggcaaaggttgcaaAcatgtcatcaccgttgacca	10	9	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:85397191A>G	ENST00000370608.3	-	12	1463	c.1396T>C	c.(1396-1398)Ttt>Ctt	p.F466L	MCOLN2_ENST00000284027.5_Missense_Mutation_p.F438L	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	466					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		AAGGTTGCAAACATGTCATCA	0.383																																																0			1											72	75	74					1																	85397191		2203	4300	6503	85169779	SO:0001583	missense	255231			AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.1396T>C	1.37:g.85397191A>G	ENSP00000359640:p.Phe466Leu		85169779	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	37	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.852208	0.91355	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.74315	-0.83;-0.83	4.93	4.93	0.64822	Polycystin cation channel, PKD1/PKD2 (1);	0.048293	0.85682	D	0.000000	T	0.71736	0.3375	M	0.80982	2.52	0.80722	D	1	P	0.45715	0.865	P	0.45753	0.492	T	0.74191	-0.3745	10	0.35671	T	0.21	-49.2802	14.9003	0.70672	1.0:0.0:0.0:0.0	.	466	Q8IZK6	MCLN2_HUMAN	L	466;438	ENSP00000359640:F466L;ENSP00000284027:F438L	ENSP00000284027:F438L	F	-	1	0	MCOLN2	85169779	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	1.993000	0.58246	0.528000	0.53228	TTT		0.383	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		G	85397191	A	G	85397191	3	3	1	1	0	0	0	0	1	0	0	0	9426	43	2	4	316	4	MCOLN2	1	85397191	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	2940548	85397191	163853430	8	8										
SORT1	6272	hgsc.bcm.edu	37	chr1	109897121	109897121	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctaaagattcttcctccacgActtcctccagacacctctgc	4	17	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:109897121A>T	ENST00000256637.6	-	5	634	c.576T>A	c.(574-576)agT>agA	p.S192R	SORT1_ENST00000538502.1_Missense_Mutation_p.S56R|SORT1_ENST00000482236.1_5'UTR	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	192					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		TTCCTCCACGACTTCCTCCAG	0.428																																																0			1											142	133	136					1																	109897121		2203	4300	6503	109698644	SO:0001583	missense	6272			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.576T>A	1.37:g.109897121A>T	ENSP00000256637:p.Ser192Arg		109698644	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876317	0.51801	.	.	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.22743	1.94;1.94	5.11	-2.43	0.06522	VPS10 (1);	0.256528	0.46758	D	0.000272	T	0.04907	0.0132	L	0.43152	1.355	0.23381	N	0.997794	P;P	0.41393	0.748;0.707	B;B	0.35859	0.154;0.212	T	0.40608	-0.9554	10	0.30854	T	0.27	-16.3554	9.3142	0.37924	0.2524:0.0:0.6116:0.136	.	56;192	B4DWI3;Q99523	.;SORT_HUMAN	R	192;56	ENSP00000256637:S192R;ENSP00000438597:S56R	ENSP00000256637:S192R	S	-	3	2	SORT1	109698644	0.266000	0.24112	0.962000	0.40283	0.972000	0.66771	0.007000	0.13174	-0.361000	0.08125	-0.290000	0.09829	AGT		0.428	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959		T	109897121	A	T	109897121	3	4	1	1	0	0	0	0	1	0	0	0	14972	272	10	5	1983	5	SORT1	1	109897121	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	24499930	109897121	139353500	9	9										
NBPF7	343505	hgsc.bcm.edu	37	chr1	120381827	120381827	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccagaagaatgtttagagcaTcctgccattcatcttgagaa	8	9	2	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:120381827T>C								REG4 (27544 upstream) : ADAM30 (54328 downstream)														p.D273V(1)									GTTTAGAGCATCCTGCCATTC	0.408																																																1	Substitution - Missense(1)	ovary(1)	1											156	158	157					1																	120381827		2137	4260	6397	120183350	SO:0001628	intergenic_variant	343505																															1.37:g.120381827T>C			120183350		Missense_Mutation	SNP		37																																																																																				0	0.408									C	120381827	T	C	120381827	1	2	1	0	1	0	0	0	0	0	0	0	10229	1435	50	4		4	NBPF7	1	120381827	IGR	SNP	T	TCGA-AF-2687-01A-02D-1733-10	10484706	120381827	128868794	10	10										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858597	149858597	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gctcgtcccgcgctggcctcCagttcccggtagggcgagtg	15	15	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:149858597C>T	ENST00000331380.2	+	1	73	c.73C>T	c.(73-75)Cag>Tag	p.Q25*	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	25						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Q25*(1)		NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CGCTGGCCTCCAGTTCCCGGT	0.647																																																1	Substitution - Nonsense(1)	ovary(1)	1											69	75	73					1																	149858597		2203	4299	6502	148125221	SO:0001587	stop_gained	8338			AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.73C>T	1.37:g.149858597C>T	ENSP00000332194:p.Gln25*		148125221	Q6DRA7|Q8IUE5	Nonsense_Mutation	SNP	ENST00000331380.2	37	CCDS937.1	.	.	.	.	.	.	.	.	.	.	C	31	5.077244	0.94000	.	.	ENSG00000184260	ENST00000331380	.	.	.	5.81	5.81	0.92471	.	0.000000	0.42053	D	0.000761	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6409	0.91396	0.0:1.0:0.0:0.0	.	.	.	.	X	25	.	ENSP00000332194:Q25X	Q	+	1	0	HIST2H2AC	148125221	1.000000	0.71417	0.959000	0.39883	0.936000	0.57629	7.596000	0.82721	2.745000	0.94114	0.655000	0.94253	CAG		0.647	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		T	149858597	C	T	149858597	4	4	1	1	0	0	0	0	0	1	0	0	7199	595	21	3	75	3	HIST2H2AC	1	149858597	Nonsense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	29476770	149858597	99392024	11	11										
CD5L	922	hgsc.bcm.edu	37	chr1	157803129	157803129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cccagggccatagcatttccGgtctctgaaggagggagaga	14	10	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:157803129G>A	ENST00000368174.4	-	5	988	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	298	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.R298W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TAGCATTTCCGGTCTCTGAAG	0.577																																																1	Substitution - Missense(1)	endometrium(1)	1											113	115	114					1																	157803129		2203	4300	6503	156069753	SO:0001583	missense	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.892C>T	1.37:g.157803129G>A	ENSP00000357156:p.Arg298Trp		156069753	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.319847	0.23994	.	.	ENSG00000073754	ENST00000368174	T	0.36157	1.27	4.84	0.107	0.14544	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.518270	0.17576	N	0.169301	T	0.37732	0.1014	M	0.63843	1.955	0.09310	N	1	D	0.89917	1.0	D	0.66847	0.947	T	0.28004	-1.0057	10	0.72032	D	0.01	.	11.7445	0.51811	0.0:0.0:0.3041:0.6959	.	298	O43866	CD5L_HUMAN	W	298	ENSP00000357156:R298W	ENSP00000357156:R298W	R	-	1	2	CD5L	156069753	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.587000	0.05780	0.182000	0.20032	-0.274000	0.10170	CGG		0.577	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157803129	G	A	157803129	3	1	1	1	0	0	0	0	1	0	0	0	3033	1115	39	1	159	1	CD5L	1	157803129	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	7944532	157803129	91447492	12	12										
DNM3	26052	hgsc.bcm.edu	37	chr1	172017862	172017862	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tctggtaatacaagaattaaTcaacactgtgaagaagtgta	8	5	2	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:172017862T>C	ENST00000355305.5	+	10	1464	c.1307T>C	c.(1306-1308)aTc>aCc	p.I436T	DNM3_ENST00000520906.1_Missense_Mutation_p.I436T|DNM3_ENST00000367731.1_Missense_Mutation_p.I436T|DNM3_ENST00000367733.2_Missense_Mutation_p.I436T|DNM3_ENST00000358155.4_Missense_Mutation_p.I436T			Q9UQ16	DYN3_HUMAN	dynamin 3	436					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CAAGAATTAATCAACACTGTG	0.363																																																0			1											132	128	129					1																	172017862		1865	4112	5977	170284485	SO:0001583	missense	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1307T>C	1.37:g.172017862T>C	ENSP00000347457:p.Ile436Thr		170284485	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		.	.	.	.	.	.	.	.	.	.	T	15.43	2.829887	0.50845	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	N	0.20610	0.595	0.58432	D	0.999997	B;B;B;B	0.16396	0.0;0.017;0.004;0.0	B;B;B;B	0.15052	0.004;0.012;0.012;0.004	T	0.36939	-0.9727	10	0.23891	T	0.37	.	15.0317	0.71713	0.0:0.0:0.0:1.0	.	436;436;436;436	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	T	436;436;436;436;436;436;326	ENSP00000350876:I436T;ENSP00000356707:I436T;ENSP00000347457:I436T;ENSP00000356705:I436T;ENSP00000429701:I436T;ENSP00000429416:I326T	ENSP00000347457:I436T	I	+	2	0	DNM3	170284485	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.250000	0.72435	2.137000	0.66172	0.460000	0.39030	ATC		0.363	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		C	172017862	T	C	172017862	3	2	1	1	0	0	0	0	1	0	0	0	4684	1435	50	4	1345	4	DNM3	1	172017862	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	14214733	172017862	77232759	13	13										
CENPF	1063	hgsc.bcm.edu	37	chr1	214813303	214813303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaccatgttaagagatcttcAagaaaaaataaatcagcaag	6	6	3	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:214813303A>G	ENST00000366955.3	+	12	1790	c.1622A>G	c.(1621-1623)cAa>cGa	p.Q541R		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAGATCTTCAAGAAAAAATA	0.338																																					Colon(80;575 1284 11000 14801 43496)											0			1											80	93	88					1																	214813303		2200	4299	6499	212879926	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1622A>G	1.37:g.214813303A>G	ENSP00000355922:p.Gln541Arg		212879926	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	8.712	0.912341	0.17907	.	.	ENSG00000117724	ENST00000366955	T	0.03441	3.93	5.16	5.16	0.70880	.	0.470539	0.15821	N	0.243000	T	0.01940	0.0061	.	.	.	0.28203	N	0.927262	P	0.40050	0.7	B	0.31547	0.132	T	0.38329	-0.9666	9	0.10377	T	0.69	.	9.7776	0.40630	0.9222:0.0:0.0778:0.0	.	541	P49454	CENPF_HUMAN	R	541	ENSP00000355922:Q541R	ENSP00000355922:Q541R	Q	+	2	0	CENPF	212879926	0.996000	0.38824	0.998000	0.56505	0.262000	0.26303	2.741000	0.47426	2.069000	0.61940	0.477000	0.44152	CAA		0.338	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214813303	A	G	214813303	3	3	1	1	0	0	0	0	1	0	0	0	3237	130	5	4	1664	4	CENPF	1	214813303	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	42795441	214813303	34437318	14	14										
PRSS38	339501	hgsc.bcm.edu	37	chr1	228003502	228003502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcctggtggtggcccctcccCgggtcgcagcattggtccac	13	16	0	0	rs373059773		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:228003502C>T	ENST00000366757.3	+	1	109	c.85C>T	c.(85-87)Cgg>Tgg	p.R29W		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	29						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						GGCCCCTCCCCGGGTCGCAGC	0.692																																																0			1						C	TRP/ARG	0,4406		0,0,2203	25	27	26		85	-2.9	0	1		26	1,8599		0,1,4299	no	missense	PRSS38	NM_183062.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	29/327	228003502	1,13005	2203	4300	6503	226070125	SO:0001583	missense	0				CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.85C>T	1.37:g.228003502C>T	ENSP00000355719:p.Arg29Trp		226070125	Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	37	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	C	7.688	0.690509	0.15039	0.0	1.16E-4	ENSG00000185888	ENST00000366757	D	0.88896	-2.44	2.28	-2.94	0.05581	.	1.699720	0.04118	N	0.315778	T	0.72137	0.3423	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.59495	-0.7444	10	0.46703	T	0.11	.	2.3008	0.04162	0.1727:0.3624:0.3403:0.1246	.	29	A1L453	PRS38_HUMAN	W	29	ENSP00000355719:R29W	ENSP00000355719:R29W	R	+	1	2	PRSS38	226070125	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.441000	0.06879	-0.701000	0.05063	-1.516000	0.00938	CGG		0.692	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228003502	C	T	228003502	3	4	1	1	0	0	0	0	1	0	0	0	12661	643	23	1	87	1	PRSS38	1	228003502	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	13190199	228003502	21247119	15	15										
PLD5	200150	hgsc.bcm.edu	37	chr1	242383405	242383405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aagcggtcatgttcatgtacGtcacctcggctcctaggagt	11	11	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr1:242383405G>A	ENST00000536534.2	-	5	861	c.620C>T	c.(619-621)aCg>aTg	p.T207M	PLD5_ENST00000427495.1_Missense_Mutation_p.T145M|PLD5_ENST00000442594.2_Missense_Mutation_p.T115M			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	207						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.T115M(3)|p.T207M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GTTCATGTACGTCACCTCGGC	0.557																																																4	Substitution - Missense(4)	lung(2)|ovary(1)|large_intestine(1)	1											131	118	123					1																	242383405		2203	4300	6503	240450028	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.620C>T	1.37:g.242383405G>A	ENSP00000440896:p.Thr207Met		240450028	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226328	0.39300	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.13778	2.56;2.56;2.56	5.52	4.6	0.57074	.	0.238118	0.43747	D	0.000527	T	0.07548	0.0190	N	0.17474	0.49	0.33978	D	0.647606	B;B;B	0.33694	0.421;0.297;0.421	B;B;B	0.21360	0.034;0.015;0.023	T	0.14420	-1.0473	10	0.54805	T	0.06	-20.8238	10.7734	0.46336	0.0909:0.0:0.9091:0.0	.	115;207;145	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	M	145;115;207	ENSP00000401285:T145M;ENSP00000414188:T115M;ENSP00000440896:T207M	ENSP00000401285:T145M	T	-	2	0	PLD5	240450028	0.983000	0.35010	0.999000	0.59377	0.995000	0.86356	1.828000	0.39111	2.591000	0.87537	0.655000	0.94253	ACG		0.557	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		A	242383405	G	A	242383405	3	1	1	1	0	0	0	0	1	0	0	0	12080	1145	40	1	1014	1	PLD5	1	242383405	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	14379903	242383405	6867216	16	16										
ALK	238	hgsc.bcm.edu	37	chr2	29519893	29519893	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	caaggacacgtttcccctcaAgactccacgaatgagccagg	9	14	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:29519893A>G	ENST00000389048.3	-	9	2584	c.1678T>C	c.(1678-1680)Ttg>Ctg	p.L560L	ALK_ENST00000431873.1_Intron|ALK_ENST00000498037.1_5'UTR	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	560	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.		L -> F (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TTTCCCCTCAAGACTCCACGA	0.542			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	0			2											128	103	112					2																	29519893		2203	4300	6503	29373397	SO:0001819	synonymous_variant	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1678T>C	2.37:g.29519893A>G			29373397	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29519893	A	G	29519893	2	3	1	1	0	0	0	0	0	0	0	1	525	69	3	4		4	ALK	2	29519893	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10		29519893	213679480	17	17										
EIF2AK2	5610	hgsc.bcm.edu	37	chr2	37374945	37374945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aacctgctgaaagatcaccaGccatttcttcttcccgtatc	5	14	3	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:37374945G>T	ENST00000233057.4	-	3	327	c.5C>A	c.(4-6)gCt>gAt	p.A2D	EIF2AK2_ENST00000405334.1_Missense_Mutation_p.A2D|EIF2AK2_ENST00000395127.2_Missense_Mutation_p.A2D	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	2					activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)	p.A2G(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				AAGATCACCAGCCATTTCTTC	0.403																																																1	Substitution - Missense(1)	ovary(1)	2											97	100	99					2																	37374945		2203	4300	6503	37228449	SO:0001583	missense	5610			BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 83"	176871	"protein kinase, interferon-inducible double stranded RNA dependent"	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.5C>A	2.37:g.37374945G>T	ENSP00000233057:p.Ala2Asp		37228449	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Missense_Mutation	SNP	ENST00000233057.4	37	CCDS1786.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155562	0.38021	.	.	ENSG00000055332	ENST00000233057;ENST00000395127;ENST00000405334;ENST00000379156;ENST00000411537;ENST00000390013	T;T;T	0.80304	-1.14;-1.14;-1.36	5.32	3.46	0.39613	.	0.377447	0.22605	N	0.057911	D	0.85927	0.5811	L	0.52905	1.665	0.34413	D	0.69656	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.997	D	0.88891	0.3346	10	0.87932	D	0	-1.7891	11.0115	0.47665	0.0:0.0:0.6616:0.3384	.	2;2;2;2	Q8IW76;B7ZKK7;P19525;E9PC80	.;.;E2AK2_HUMAN;.	D	2	ENSP00000233057:A2D;ENSP00000378559:A2D;ENSP00000385014:A2D	ENSP00000233057:A2D	A	-	2	0	EIF2AK2	37228449	0.964000	0.33143	0.664000	0.29753	0.056000	0.15407	1.681000	0.37618	0.684000	0.31448	0.650000	0.86243	GCT		0.403	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		T	37374945	G	T	37374945	3	4	1	1	0	0	0	0	1	0	0	0	5008	971	34	2	1710	2	EIF2AK2	2	37374945	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	7855052	37374945	205824428	18	18										
MSH2	4436	hgsc.bcm.edu	37	chr2	47690183	47690183	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tttgcaggtggaaaaccatgAattccttgtaaaaccttcat	7	8	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:47690183A>G	ENST00000233146.2	+	9	1623	c.1400A>G	c.(1399-1401)gAa>gGa	p.E467G	MSH2_ENST00000543555.1_Missense_Mutation_p.E401G|MSH2_ENST00000406134.1_Missense_Mutation_p.E467G	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	467					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAAAACCATGAATTCCTTGTA	0.318			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	2											74	74	74					2																	47690183		2203	4300	6503	47543687	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1400A>G	2.37:g.47690183A>G	ENSP00000233146:p.Glu467Gly		47543687	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.868864	0.72065	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000422810;ENST00000413880	D;D;D	0.87256	-2.23;-2.23;-2.23	5.4	4.21	0.49690	DNA mismatch repair protein MutS, core (3);	0.000000	0.85682	D	0.000000	D	0.93539	0.7938	M	0.86502	2.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.81914	0.99;0.986;0.995	D	0.93689	0.7005	10	0.87932	D	0	-24.2812	12.3126	0.54938	0.8583:0.1417:0.0:0.0	.	401;467;467	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	G	467;401;467;467;467;467;117;253	ENSP00000233146:E467G;ENSP00000442697:E401G;ENSP00000384199:E467G	ENSP00000233146:E467G	E	+	2	0	MSH2	47543687	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	8.647000	0.91057	0.854000	0.35336	0.383000	0.25322	GAA		0.318	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			G	47690183	A	G	47690183	3	3	1	1	0	0	0	0	1	0	0	0	9900	246	9	4	1434	4	MSH2	2	47690183	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	10315238	47690183	195509190	19	19										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51254920	51254920	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agggtgagcttgagcgccgcGgcgcgcagttccgggggcag	20	11	0	2	rs201180707		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:51254920G>T	ENST00000406316.2	-	2	1968	c.492C>A	c.(490-492)gcC>gcA	p.A164A	NRXN1_ENST00000405581.1_Silent_p.A164A|NRXN1_ENST00000406859.3_Silent_p.A164A|NRXN1_ENST00000404971.1_Silent_p.A164A|NRXN1_ENST00000401669.2_Silent_p.A164A|NRXN1_ENST00000402717.3_Silent_p.A164A|NRXN1_ENST00000405472.3_Silent_p.A164A	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	164	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TGAGCGCCGCGGCGCGCAGTT	0.677																																																0			2											21	27	25					2																	51254920		2066	4201	6267	51108424	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.492C>A	2.37:g.51254920G>T			51108424	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.677	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	51254920	G	T	51254920	2	4	1	1	0	0	0	0	0	0	0	1	10696	1103	39	2		2	NRXN1	2	51254920	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	3564737	51254920	191944453	20	20										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55536106	55536106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tctggcgttcccgattaataTctttcttagactttatcaat	5	9	4	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:55536106T>C	ENST00000436346.1	-	25	5067	c.4226A>G	c.(4225-4227)gAt>gGt	p.D1409G	CCDC88A_ENST00000413716.2_Missense_Mutation_p.D1408G|CCDC88A_ENST00000263630.8_Missense_Mutation_p.D1409G|CCDC88A_ENST00000336838.6_Missense_Mutation_p.D1408G|AC012358.8_ENST00000366287.4_RNA|CCDC88A_ENST00000422883.2_Missense_Mutation_p.D32G	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1409					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.D1409G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CCGATTAATATCTTTCTTAGA	0.353																																																1	Substitution - Missense(1)	ovary(1)	2											90	89	89					2																	55536106		2203	4300	6503	55389610	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4226A>G	2.37:g.55536106T>C	ENSP00000410608:p.Asp1409Gly		55389610	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.64|16.64	3.180626|3.180626	0.57800|0.57800	.|.	.|.	ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000444458	T;T;T;T;T;T|.	0.45276|.	2.47;2.7;2.7;0.9;2.48;1.43|.	4.75|4.75	4.75|4.75	0.60458|0.60458	.|.	0.000000|.	0.49305|.	U|.	0.000143|.	T|T	0.55033|0.55033	0.1895|0.1895	L|L	0.44542|0.44542	1.39|1.39	0.34414|0.34414	D|D	0.696689|0.696689	B;P;B;P;B;P;P|.	0.48162|.	0.325;0.493;0.361;0.906;0.177;0.493;0.493|.	B;B;B;B;B;B;B|.	0.43386|.	0.275;0.234;0.118;0.418;0.141;0.234;0.234|.	T|T	0.64976|0.64976	-0.6280|-0.6280	10|5	0.66056|.	D|.	0.02|.	-12.3101|-12.3101	14.5506|14.5506	0.68065|0.68065	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1408;1409;1354;32;1409;1408;1408|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.	.;.;.;.;GRDN_HUMAN;.;.|.	G|V	1408;1409;1409;32;454;1408;584|34	ENSP00000338728:D1408G;ENSP00000263630:D1409G;ENSP00000410608:D1409G;ENSP00000390012:D454G;ENSP00000404431:D1408G;ENSP00000405080:D584G|.	ENSP00000263630:D1409G|.	D|I	-|-	2|1	0|0	CCDC88A|CCDC88A	55389610|55389610	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.828000|5.828000	0.69307|0.69307	1.890000|1.890000	0.54733|0.54733	0.482000|0.482000	0.46254|0.46254	GAT|ATA		0.353	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55536106	T	C	55536106	3	2	1	1	0	0	0	0	1	0	0	0	2869	1435	50	4	1421	4	CCDC88A	2	55536106	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	4281186	55536106	187663267	21	21										
DYSF	8291	hgsc.bcm.edu	37	chr2	71795140	71795140	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cagatacgggtcaagctgtgGtttgggctctcagtggatga	15	7	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:71795140G>A	ENST00000258104.3	+	25	2848	c.2571G>A	c.(2569-2571)tgG>tgA	p.W857*	DYSF_ENST00000409366.1_Nonsense_Mutation_p.W858*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.W858*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.W889*|DYSF_ENST00000410020.3_Nonsense_Mutation_p.W875*|DYSF_ENST00000410041.1_Nonsense_Mutation_p.W875*|DYSF_ENST00000413539.2_Nonsense_Mutation_p.W888*|DYSF_ENST00000429174.2_Nonsense_Mutation_p.W857*|DYSF_ENST00000409762.1_Nonsense_Mutation_p.W874*|DYSF_ENST00000409582.3_Nonsense_Mutation_p.W874*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.W844*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	857					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCAAGCTGTGGTTTGGGCTCT	0.572																																																0			2											163	150	154					2																	71795140		2203	4300	6503	71648648	SO:0001587	stop_gained	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2571G>A	2.37:g.71795140G>A	ENSP00000258104:p.Trp857*		71648648	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Nonsense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	44	10.652870	0.99445	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	4.97	4.06	0.47325	.	0.147984	0.52532	D	0.000069	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6246	12.8666	0.57944	0.0:0.1654:0.8346:0.0	.	.	.	.	X	888;874;874;857;857;889;858;844;858;875;875	.	ENSP00000258104:W857X	W	+	3	0	DYSF	71648648	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	9.869000	0.99810	1.046000	0.40249	0.549000	0.68633	TGG		0.572	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71795140	G	A	71795140	4	1	1	1	0	0	0	0	0	1	0	0	4870	1270	44	3	2861	3	DYSF	2	71795140	Nonsense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	16259034	71795140	171404233	22	22										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85532500	85532500	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtcaagcaggaaccggcaccCcccagcctgagccctgcagt	11	17	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:85532500C>A	ENST00000282111.3	+	8	1238	c.963C>A	c.(961-963)ccC>ccA	p.P321P		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	321	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						AACCGGCACCCCCCAGCCTGA	0.662																																																0			2											46	45	45					2																	85532500		2203	4300	6503	85386011	SO:0001819	synonymous_variant	83439			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.963C>A	2.37:g.85532500C>A			85386011	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	37	CCDS1971.1																																																																																				0.662	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		A	85532500	C	A	85532500	2	1	1	1	0	0	0	0	0	0	0	1	15736	610	22	2		2	TCF7L1	2	85532500	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	13737360	85532500	157666873	23	23										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96944664	96944664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggtgacgatctcagcattgaAgtggtcatgcatacagtggt	13	7	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:96944664A>G	ENST00000323853.5	-	37	5283	c.5206T>C	c.(5206-5208)Ttc>Ctc	p.F1736L	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1736	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.		F -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCAGCATTGAAGTGGTCATGC	0.488																																																0			2											138	120	126					2																	96944664		2203	4300	6503	96308391	SO:0001583	missense	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5206T>C	2.37:g.96944664A>G	ENSP00000317123:p.Phe1736Leu		96308391	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143590	0.57044	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	T	0.34275	1.37	5.58	4.35	0.52113	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24431	0.0592	N	0.21142	0.635	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.04781	-1.0927	10	0.35671	T	0.21	-19.9737	11.7332	0.51750	0.8528:0.1472:0.0:0.0	.	1736	O75643	U520_HUMAN	L	1736;195;319	ENSP00000317123:F1736L	ENSP00000317123:F1736L	F	-	1	0	SNRNP200	96308391	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.516000	0.67055	2.246000	0.74042	0.533000	0.62120	TTC		0.488	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		G	96944664	A	G	96944664	3	3	1	1	0	0	0	0	1	0	0	0	14889	72	3	4	1240	4	SNRNP200	2	96944664	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	11412164	96944664	146254709	24	24										
IL18R1	8809	hgsc.bcm.edu	37	chr2	102984374	102984374	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gttcacttgcacatgagattGaaacaaccaccaaaagctgg	8	10	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:102984374G>T	ENST00000409599.1	+	4	504	c.148G>T	c.(148-150)Gaa>Taa	p.E50*	IL18R1_ENST00000233957.1_Nonsense_Mutation_p.E50*|IL18R1_ENST00000334376.3_Nonsense_Mutation_p.E50*			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	50	Ig-like C2-type 1.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.E50K(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						ACATGAGATTGAAACAACCAC	0.428																																																1	Substitution - Missense(1)	ovary(1)	2											127	119	122					2																	102984374		2203	4300	6503	102350806	SO:0001587	stop_gained	8809			U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.148G>T	2.37:g.102984374G>T	ENSP00000387211:p.Glu50*		102350806	B2R9Y5|Q52LC9	Nonsense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.758981	0.89843	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957;ENST00000334376	.	.	.	5.23	-2.35	0.06684	.	1.535540	0.03512	N	0.219759	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	1.1998	0.01882	0.4375:0.1533:0.2534:0.1558	.	.	.	.	X	50	.	ENSP00000233957:E50X	E	+	1	0	IL18R1	102350806	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.520000	0.06252	-0.265000	0.09352	0.563000	0.77884	GAA		0.428	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		T	102984374	G	T	102984374	4	4	1	1	0	0	0	0	0	1	0	0	7668	1291	45	2	154	2	IL18R1	2	102984374	Nonsense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	6039710	102984374	140214999	25	25										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163302673	163302673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gatttacatatgttgttctgAagtttattaaaatatctatg	6	3	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:163302673A>G	ENST00000332142.5	-	7	1508	c.1409T>C	c.(1408-1410)tTc>tCc	p.F470S	KCNH7_ENST00000328032.4_Missense_Mutation_p.F463S	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	470					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.F470C(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGTTGTTCTGAAGTTTATTAA	0.358																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	ovary(1)	2											99	92	94					2																	163302673		2203	4300	6503	163010919	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1409T>C	2.37:g.163302673A>G	ENSP00000331727:p.Phe470Ser		163010919	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.474598	0.84640	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.96011	-3.88;-3.88	5.7	5.7	0.88788	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98308	0.9439	M	0.93197	3.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.986;0.999	D	0.99544	1.0964	10	0.87932	D	0	.	15.9661	0.79970	1.0:0.0:0.0:0.0	.	463;470	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	S	470;463	ENSP00000331727:F470S;ENSP00000333781:F463S	ENSP00000333781:F463S	F	-	2	0	KCNH7	163010919	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.182000	0.69389	0.528000	0.53228	TTC		0.358	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		G	163302673	A	G	163302673	3	3	1	1	0	0	0	0	1	0	0	0	8058	246	9	4	2287	4	KCNH7	2	163302673	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	60318299	163302673	79896700	26	26										
TTN	7273	hgsc.bcm.edu	37	chr2	179406125	179406125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cttcagtaaggccagtggagCggtaccgtgtcattgtcaca	12	10	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:179406125C>T	ENST00000591111.1	-	300	92980	c.92756G>A	c.(92755-92757)cGc>cAc	p.R30919H	TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R23687H|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R32560H|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R29992H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R23620H|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R23495H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000588244.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30919	Fibronectin type-III 125. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCAGTGGAGCGGTACCGTGT	0.493																																																0			2											120	113	115					2																	179406125		1961	4157	6118	179114371	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.92756G>A	2.37:g.179406125C>T	ENSP00000465570:p.Arg30919His		179114371	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	33	5.276394	0.95459	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.72	5.72	0.89469	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73118	0.3546	M	0.68593	2.085	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.74512	-0.3641	9	0.87932	D	0	.	19.8706	0.96849	0.0:1.0:0.0:0.0	.	23495;23620;23687;30919	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	29992;23495;23687;23620;23492	ENSP00000343764:R29992H;ENSP00000434586:R23495H;ENSP00000340554:R23687H;ENSP00000352154:R23620H	ENSP00000340554:R23687H	R	-	2	0	TTN	179114371	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	7.814000	0.86154	2.692000	0.91855	0.561000	0.74099	CGC		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179406125	C	T	179406125	3	4	1	1	0	0	0	0	1	0	0	0	16775	768	27	1	10352	1	TTN	2	179406125	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	16103452	179406125	63793248	27	27										
SESTD1	91404	hgsc.bcm.edu	37	chr2	180008366	180008366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	taactgtgtgcgcttgctacGttgcctacaaacttcctggt	9	11	0	0	rs144405691		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:180008366G>A	ENST00000428443.3	-	9	1118	c.802C>T	c.(802-804)Cgt>Tgt	p.R268C		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	268							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			CGCTTGCTACGTTGCCTACAA	0.383																																																0			2						G	CYS/ARG	0,4406		0,0,2203	161	157	158		802	5.2	1	2	dbSNP_134	158	1,8599	1.2+/-3.3	0,1,4299	no	missense	SESTD1	NM_178123.4	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	268/697	180008366	1,13005	2203	4300	6503	179716611	SO:0001583	missense	91404			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.802C>T	2.37:g.180008366G>A	ENSP00000415332:p.Arg268Cys		179716611	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745304	0.89663	0.0	1.16E-4	ENSG00000187231	ENST00000428443	T	0.50548	0.74	6.07	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.51432	0.1674	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.52793	-0.8528	9	.	.	.	-8.5108	16.5444	0.84410	0.0:0.0:0.8684:0.1316	.	268	Q86VW0	SESD1_HUMAN	C	268	ENSP00000415332:R268C	.	R	-	1	0	SESTD1	179716611	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	5.164000	0.64954	1.513000	0.48852	0.655000	0.94253	CGT		0.383	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	180008366	G	A	180008366	3	1	1	1	0	0	0	0	1	0	0	0	14164	1145	40	1	1328	1	SESTD1	2	180008366	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	602241	180008366	63191007	28	28										
GLS	2744	hgsc.bcm.edu	37	chr2	191819355	191819355	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gaacagcgggactatgattcTagaacagcactccatgtagc	10	10	1	2	rs1058592		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:191819355T>A	ENST00000320717.3	+	16	2016	c.1758T>A	c.(1756-1758)tcT>tcA	p.S586S	GLS_ENST00000409428.1_Silent_p.S91S	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	586					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	ACTATGATTCTAGAACAGCAC	0.358																																																0			2											84	87	86					2																	191819355		2203	4300	6503	191527600	SO:0001819	synonymous_variant	27165			AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.1758T>A	2.37:g.191819355T>A			191527600	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Silent	SNP	ENST00000320717.3	37	CCDS2308.1																																																																																				0.358	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			A	191819355	T	A	191819355	2	1	1	1	0	0	0	0	0	0	0	1	6483	1509	53	5		5	GLS	2	191819355	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	11810989	191819355	51380018	29	29										
EEF1B2	1933	hgsc.bcm.edu	37	chr2	207027530	207027530	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aagatgataaagttggaacaGatatgctggaggagcagatc	13	4	0	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:207027530G>C	ENST00000392222.2	+	6	976	c.601G>C	c.(601-603)Gat>Cat	p.D201H	SNORD51_ENST00000384320.2_RNA|SNORA41_ENST00000384675.1_RNA|EEF1B2_ENST00000392221.1_Missense_Mutation_p.D201H|EEF1B2_ENST00000236957.5_Missense_Mutation_p.D201H	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	201					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)			breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						AGTTGGAACAGATATGCTGGA	0.388																																																0			2											56	57	56					2																	207027530		2201	4280	6481	206735775	SO:0001583	missense	1933			X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.601G>C	2.37:g.207027530G>C	ENSP00000376056:p.Asp201His		206735775	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139362	0.77775	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222	.	.	.	5.2	5.2	0.72013	Translation elongation factor EF1B/ribosomal protein S6 (1);Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange (3);	0.045735	0.85682	D	0.000000	D	0.83658	0.5302	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	D	0.86261	0.1655	9	0.87932	D	0	-12.1904	18.7341	0.91748	0.0:0.0:1.0:0.0	.	201	P24534	EF1B_HUMAN	H	201	.	ENSP00000236957:D201H	D	+	1	0	EEF1B2	206735775	1.000000	0.71417	0.980000	0.43619	0.643000	0.38383	9.869000	0.99810	2.435000	0.82474	0.655000	0.94253	GAT		0.388	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663		C	207027530	G	C	207027530	3	2	1	1	0	0	0	0	1	0	0	0	4936	942	33	5	623	5	EEF1B2	2	207027530	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	15208175	207027530	36171843	30	30										
USP37	57695	hgsc.bcm.edu	37	chr2	219418412	219418412	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cggctttgtttcgctccactGggtcgaagcaccacattttt	9	12	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:219418412G>A	ENST00000258399.3	-	5	604	c.192C>T	c.(190-192)ccC>ccT	p.P64P	USP37_ENST00000454775.1_Silent_p.P64P|USP37_ENST00000338465.5_Silent_p.P64P|USP37_ENST00000418019.1_Silent_p.P64P|USP37_ENST00000415516.1_5'UTR	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	64					G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TCGCTCCACTGGGTCGAAGCA	0.358																																																0			2											102	97	99					2																	219418412		2203	4300	6503	219126656	SO:0001819	synonymous_variant	57695			AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.192C>T	2.37:g.219418412G>A			219126656	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Silent	SNP	ENST00000258399.3	37	CCDS2418.1																																																																																				0.358	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		A	219418412	G	A	219418412	2	1	1	1	0	0	0	0	0	0	0	1	17108	1335	47	3		3	USP37	2	219418412	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	12390882	219418412	23780961	31	31										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220396778	220396778	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atccacagccaggaggagccGccctacatccaccagctggg	11	16	0	0	rs572070268		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:220396778G>A	ENST00000347842.3	+	3	1178	c.1164G>A	c.(1162-1164)ccG>ccA	p.P388P	ASIC4_ENST00000473709.1_3'UTR|ASIC4_ENST00000358078.4_Silent_p.P388P	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	388					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										AGGAGGAGCCGCCCTACATCC	0.602													G|||	1	0.000199681	8e-04	0	5008	,	,		17929	0		0	False		,,,				2504	0															0			2											81	88	86					2																	220396778		2203	4300	6503	220105022	SO:0001819	synonymous_variant	55515			AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1164G>A	2.37:g.220396778G>A			220105022	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Silent	SNP	ENST00000347842.3	37	CCDS2442.1																																																																																				0.602	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		A	220396778	G	A	220396778	2	1	1	1	0	0	0	0	0	0	0	1	131	1074	38	1		1	ACCN4	2	220396778	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	978366	220396778	22802595	32	32										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225266122	225266122	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	caccccccagatgggcagctGactgtccaggctgtagaact	11	14	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:225266122G>A	ENST00000409685.3	-	1	629	c.364C>T	c.(364-366)Cag>Tag	p.Q122*	FAM124B_ENST00000243806.2_Nonsense_Mutation_p.Q122*|FAM124B_ENST00000389874.3_Nonsense_Mutation_p.Q122*	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	122								p.Q122*(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		ATGGGCAGCTGACTGTCCAGG	0.562																																																1	Substitution - Nonsense(1)	ovary(1)	2											54	52	53					2																	225266122		2203	4300	6503	224974366	SO:0001587	stop_gained	79843			AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.364C>T	2.37:g.225266122G>A	ENSP00000386895:p.Gln122*		224974366	A6NNC7|Q8NBZ4|Q8TAV7	Nonsense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	G	39	7.645591	0.98409	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	.	.	.	5.79	4.9	0.64082	.	0.348682	0.34555	N	0.003861	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-14.2537	16.8416	0.85971	0.0:0.1286:0.8714:0.0	.	.	.	.	X	122	.	ENSP00000243806:Q122X	Q	-	1	0	FAM124B	224974366	1.000000	0.71417	0.923000	0.36655	0.971000	0.66376	4.565000	0.60836	1.426000	0.47256	0.655000	0.94253	CAG		0.562	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		A	225266122	G	A	225266122	4	1	1	1	0	0	0	0	0	1	0	0	5442	1299	45	3	1102	3	FAM124B	2	225266122	Nonsense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	4869344	225266122	17933251	33	33										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238245107	238245107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tggtggtcaccggcttcgtcGtagtcaccggcttcgttgtc	13	12	2	0	rs150907698	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr2:238245107G>A	ENST00000295550.4	-	40	9088	c.8636C>T	c.(8635-8637)aCg>aTg	p.T2879M	COL6A3_ENST00000472056.1_Missense_Mutation_p.T2272M|COL6A3_ENST00000346358.4_Missense_Mutation_p.T2679M|COL6A3_ENST00000409809.1_Missense_Mutation_p.T2673M|COL6A3_ENST00000347401.3_Missense_Mutation_p.T2678M|COL6A3_ENST00000353578.4_Missense_Mutation_p.T2673M	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2879	Nonhelical region.|Thr-rich.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CGGCTTCGTCGTAGTCACCGG	0.458													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		18430	0		0	False		,,,				2504	0.001															0			2						G	MET/THR,MET/THR,MET/THR	6,4400	11.4+/-27.6	0,6,2197	165	155	158		8636,6815,8018	3.7	0.2	2	dbSNP_134	158	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	81,81,81	0,22,6481	AA,AG,GG		0.186,0.1362,0.1692	probably-damaging,probably-damaging,probably-damaging	2879/3178,2272/2571,2673/2972	238245107	22,12984	2203	4300	6503	237909846	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8636C>T	2.37:g.238245107G>A	ENSP00000295550:p.Thr2879Met		237909846	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	1.784	-0.481114	0.04383	0.001362	0.00186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.89343	-2.5;-2.48;-2.47;-2.46;-2.47;-2.46	3.68	3.68	0.42216	.	.	.	.	.	D	0.92828	0.7719	M	0.78049	2.395	0.09310	N	0.999992	D;D;D	0.89917	0.999;1.0;0.999	P;P;P	0.60886	0.761;0.88;0.761	D	0.85291	0.1067	9	0.87932	D	0	.	11.2673	0.49118	0.0:0.0:1.0:0.0	.	2272;2673;2879	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	M	2879;2678;2673;2272;2673;2679	ENSP00000295550:T2879M;ENSP00000315609:T2678M;ENSP00000315873:T2673M;ENSP00000418285:T2272M;ENSP00000386844:T2673M;ENSP00000295546:T2679M	ENSP00000295550:T2879M	T	-	2	0	COL6A3	237909846	0.962000	0.33011	0.178000	0.23040	0.016000	0.09150	3.023000	0.49666	1.749000	0.51849	0.563000	0.77884	ACG		0.458	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238245107	G	A	238245107	3	1	1	1	0	0	0	0	1	0	0	0	3707	1145	40	1	917	1	COL6A3	2	238245107	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	12978985	238245107	4954266	34	34										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365330	37365330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cttagggaaaagtgtgaacaAgaaaaagaaacattgttgaa	10	3	0	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:37365330A>G	ENST00000361924.2	+	14	2327	c.1953A>G	c.(1951-1953)caA>caG	p.Q651Q	GOLGA4_ENST00000356847.4_Silent_p.Q673Q|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	651	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AGTGTGAACAAGAAAAAGAAA	0.368																																																0			3											52	53	53					3																	37365330		2203	4300	6503	37340334	SO:0001819	synonymous_variant	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1953A>G	3.37:g.37365330A>G			37340334	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	37	CCDS2666.1																																																																																				0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37365330	A	G	37365330	2	3	1	1	0	0	0	0	0	0	0	1	6575	69	3	4		4	GOLGA4	3	37365330	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10		37365330	160657100	35	35										
CCR9	10803	hgsc.bcm.edu	37	chr3	45943249	45943249	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tatgtttttgtgggtgagagAttccgccgggatctcgtgaa	14	6	1	3	rs199573914		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:45943249A>G	ENST00000357632.2	+	3	1149	c.969A>G	c.(967-969)agA>agG	p.R323R	LZTFL1_ENST00000536047.1_Intron|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000355983.2_Silent_p.R311R|CCR9_ENST00000422395.1_3'UTR|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Silent_p.R311R	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	323					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TGGGTGAGAGATTCCGCCGGG	0.517																																																0			3											107	101	103					3																	45943249		2203	4300	6503	45918253	SO:0001819	synonymous_variant	10803			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.969A>G	3.37:g.45943249A>G			45918253	Q4VBM3|Q549E0|Q9UQQ6	Silent	SNP	ENST00000357632.2	37	CCDS2732.1																																																																																				0.517	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			G	45943249	A	G	45943249	2	3	1	1	0	0	0	0	0	0	0	1	2954	330	12	4		4	CCR9	3	45943249	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	8577919	45943249	152079181	36	36										
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50382648	50382648	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttcagcttctccaggttctcAtgctgctggttccacctgcc	8	15	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:50382648A>G	ENST00000231749.3	-	2	1380	c.108T>C	c.(106-108)caT>caC	p.H36H	ZMYND10_ENST00000360165.3_Silent_p.H36H|ZMYND10-AS1_ENST00000440013.1_RNA|NPRL2_ENST00000493465.1_5'Flank|ZMYND10_ENST00000490675.1_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	36					inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CCAGGTTCTCATGCTGCTGGT	0.587										TSP Lung(30;0.18)																																						0			3											142	113	123					3																	50382648		2203	4300	6503	50357652	SO:0001819	synonymous_variant	51364			U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"Zinc fingers, MYND-type"	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.108T>C	3.37:g.50382648A>G			50357652	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Silent	SNP	ENST00000231749.3	37	CCDS2825.1																																																																																				0.587	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		G	50382648	A	G	50382648	2	3	1	1	0	0	0	0	0	0	0	1	17744	214	8	4		4	ZMYND10	3	50382648	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	4439399	50382648	147639782	37	37										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51517770	51517770	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	accatgtcctgcccactgccAtgttccttttcccactgctc	5	18	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:51517770A>C	ENST00000335891.5	-	1	84	c.75T>G	c.(73-75)caT>caG	p.H25Q				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	25					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		GCCCACTGCCATGTTCCTTTT	0.428																																																0			3											148	133	138					3																	51517770		1925	4128	6053	51492810	SO:0001583	missense	9730			AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.75T>G	3.37:g.51517770A>C	ENSP00000338857:p.His25Gln		51492810	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	A	15.37	2.813450	0.50527	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.56444	0.46;0.9	5.77	4.61	0.57282	.	0.141403	0.64402	D	0.000005	T	0.33876	0.0878	N	0.21617	0.685	0.23449	N	0.997657	B	0.21905	0.062	B	0.19391	0.025	T	0.19095	-1.0316	10	0.06625	T	0.88	-17.2361	11.5994	0.50993	0.9294:0.0:0.0706:0.0	.	25	Q9Y4B6	VPRBP_HUMAN	Q	25	ENSP00000338857:H25Q;ENSP00000421724:H25Q	ENSP00000338857:H25Q	H	-	3	2	VPRBP	51492810	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.630000	0.46494	1.005000	0.39183	0.533000	0.62120	CAT		0.428	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		C	51517770	A	C	51517770	3	2	1	1	0	0	0	0	1	0	0	0	17225	214	8	4	4377	4	VPRBP	3	51517770	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	1135122	51517770	146504660	38	38										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89391237	89391237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcagcatcacaactaatcagGctggtgagtacatactagat	8	9	3	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:89391237G>T	ENST00000336596.2	+	5	1528	c.1303G>T	c.(1303-1305)Gct>Tct	p.A435S	EPHA3_ENST00000494014.1_Missense_Mutation_p.A435S|EPHA3_ENST00000452448.2_Missense_Mutation_p.A435S	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	435	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.A435S(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AACTAATCAGGCTGGTGAGTA	0.443										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	lung(1)	3											54	45	48					3																	89391237		2203	4300	6503	89473927	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1303G>T	3.37:g.89391237G>T	ENSP00000337451:p.Ala435Ser		89473927	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253478	0.80135	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.54675	0.56;0.56;0.56	5.53	5.53	0.82687	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71013	0.3290	M	0.63843	1.955	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.75020	0.985;0.945	T	0.68085	-0.5502	9	.	.	.	.	19.8407	0.96681	0.0:0.0:1.0:0.0	.	435;435	P29320;P29320-2	EPHA3_HUMAN;.	S	435	ENSP00000337451:A435S;ENSP00000399926:A435S;ENSP00000419190:A435S	.	A	+	1	0	EPHA3	89473927	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.951000	0.87819	2.763000	0.94921	0.563000	0.77884	GCT		0.443	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89391237	G	T	89391237	3	4	1	1	0	0	0	0	1	0	0	0	5181	1203	42	2	1321	2	EPHA3	3	89391237	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	37873467	89391237	108631193	39	39										
ST3GAL6	10402	hgsc.bcm.edu	37	chr3	98510736	98510736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccatcacattggcgttttacAtatgtcacgaagttcaccta	6	11	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:98510736A>G	ENST00000483910.1	+	9	1097	c.808A>G	c.(808-810)Ata>Gta	p.I270V	ST3GAL6_ENST00000394162.1_Missense_Mutation_p.I270V|ST3GAL6_ENST00000462152.1_3'UTR|ST3GAL6_ENST00000265261.6_Missense_Mutation_p.I152V	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	270					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)	p.I270V(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						GGCGTTTTACATATGTCACGA	0.393																																																1	Substitution - Missense(1)	ovary(1)	3											182	170	174					3																	98510736		2203	4300	6503	99993426	SO:0001583	missense	10402			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.808A>G	3.37:g.98510736A>G	ENSP00000417376:p.Ile270Val		99993426	B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	37	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.351896	0.41700	.	.	ENSG00000064225	ENST00000483910;ENST00000265261;ENST00000394162	T;T;T	0.29655	1.56;1.56;1.56	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.34687	0.0906	L	0.43646	1.37	0.45690	D	0.998606	B;B	0.34103	0.34;0.437	B;B	0.44224	0.237;0.444	T	0.08638	-1.0712	10	0.20519	T	0.43	-28.8281	13.9197	0.63923	1.0:0.0:0.0:0.0	.	152;270	F8W6U0;Q9Y274	.;SIA10_HUMAN	V	270;152;270	ENSP00000417376:I270V;ENSP00000265261:I152V;ENSP00000377717:I270V	ENSP00000265261:I152V	I	+	1	0	ST3GAL6	99993426	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	2.628000	0.46477	2.181000	0.69327	0.533000	0.62120	ATA		0.393	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		G	98510736	A	G	98510736	3	3	1	1	0	0	0	0	1	0	0	0	15258	217	8	4	838	4	ST3GAL6	3	98510736	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	9119499	98510736	99511694	40	40										
TFDP2	7029	hgsc.bcm.edu	37	chr3	141692894	141692894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agattttctcacttacctccAgattctgacattcctgagca	5	12	2	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:141692894A>G	ENST00000489671.1	-	8	1089	c.659T>C	c.(658-660)cTg>cCg	p.L220P	TFDP2_ENST00000317104.7_Missense_Mutation_p.L144P|TFDP2_ENST00000310282.6_Missense_Mutation_p.L160P|TFDP2_ENST00000486111.1_Missense_Mutation_p.L160P|TFDP2_ENST00000467072.1_Missense_Mutation_p.L160P|TFDP2_ENST00000495310.1_Missense_Mutation_p.L123P|TFDP2_ENST00000477292.1_Missense_Mutation_p.L84P|TFDP2_ENST00000479040.1_Missense_Mutation_p.L159P|TFDP2_ENST00000397991.4_Missense_Mutation_p.L192P|TFDP2_ENST00000499676.2_Missense_Mutation_p.L160P			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	220	Dimerization. {ECO:0000255}.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						ACTTACCTCCAGATTCTGACA	0.308																																																0			3											87	81	83					3																	141692894		1843	4118	5961	143175584	SO:0001583	missense	7029			U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.659T>C	3.37:g.141692894A>G	ENSP00000420616:p.Leu220Pro		143175584	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Missense_Mutation	SNP	ENST00000489671.1	37	CCDS54650.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533007	0.85812	.	.	ENSG00000114126	ENST00000499676;ENST00000489671;ENST00000486111;ENST00000477292;ENST00000495310;ENST00000467072;ENST00000317104;ENST00000310282;ENST00000479040;ENST00000397991;ENST00000467667;ENST00000478006;ENST00000497579	T;T;T;T;T;T;T;T;T;T;T;T	0.57752	1.36;1.32;1.36;0.42;0.38;1.36;1.38;1.36;1.36;1.33;1.08;1.09	5.77	5.77	0.91146	Transcription factor DP, C-terminal (1);	0.000000	0.64402	D	0.000005	T	0.79411	0.4441	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.84772	0.0768	10	0.87932	D	0	-3.6025	16.0985	0.81148	1.0:0.0:0.0:0.0	.	123;220;160	B7Z8L5;Q14188;Q14188-5	.;TFDP2_HUMAN;.	P	160;220;160;84;123;160;144;160;159;192;160;134;159	ENSP00000439782:L160P;ENSP00000420616:L220P;ENSP00000420599:L160P;ENSP00000418971:L84P;ENSP00000419036:L123P;ENSP00000418590:L160P;ENSP00000315668:L144P;ENSP00000309622:L160P;ENSP00000417585:L159P;ENSP00000381078:L192P;ENSP00000417726:L160P;ENSP00000417220:L159P	ENSP00000309622:L160P	L	-	2	0	TFDP2	143175584	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.170000	0.94795	2.197000	0.70478	0.455000	0.32223	CTG		0.308	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		G	141692894	A	G	141692894	3	3	1	1	0	0	0	0	1	0	0	0	15837	188	7	4	705	4	TFDP2	3	141692894	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	43182158	141692894	56329536	41	41										
MED12L	116931	hgsc.bcm.edu	37	chr3	151067973	151067973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcctgaaaattctaaataagAagagcaccacagagacaggg	9	8	1	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:151067973A>G	ENST00000474524.1	+	15	2310	c.2272A>G	c.(2272-2274)Aag>Gag	p.K758E	MED12L_ENST00000491549.1_3'UTR|MED12L_ENST00000273432.4_Missense_Mutation_p.K618E|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	758						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.K758E(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCTAAATAAGAAGAGCACCAC	0.443																																																1	Substitution - Missense(1)	ovary(1)	3											99	103	102					3																	151067973		2203	4300	6503	152550663	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2272A>G	3.37:g.151067973A>G	ENSP00000417235:p.Lys758Glu		152550663	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.909136	0.92107	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.69806	-0.25;-0.43	5.81	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.78704	0.4325	M	0.65975	2.015	0.80722	D	1	D;B	0.89917	1.0;0.384	D;B	0.87578	0.998;0.159	T	0.79787	-0.1656	10	0.87932	D	0	-31.5076	11.1202	0.48284	0.9279:0.0:0.0721:0.0	.	618;758	F8WAE6;Q86YW9	.;MD12L_HUMAN	E	758;618	ENSP00000417235:K758E;ENSP00000273432:K618E	ENSP00000273432:K618E	K	+	1	0	MED12L	152550663	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.474000	0.90413	1.051000	0.40369	0.455000	0.32223	AAG		0.443	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151067973	A	G	151067973	3	3	1	1	0	0	0	0	1	0	0	0	9459	247	9	4	2330	4	MED12L	3	151067973	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	9375079	151067973	46954457	42	42										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952125	178952125	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaaatggattggatcttccaCacaattaaacagcatgcatt	6	8	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:178952125C>A	ENST00000263967.3	+	21	3337	c.3180C>A	c.(3178-3180)caC>caA	p.H1060Q	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1060	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1060H(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GGATCTTCCACACAATTAAAC	0.388		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - coding silent(1)	thyroid(1)	3											92	83	86					3																	178952125		1907	4136	6043	180434819	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3180C>A	3.37:g.178952125C>A	ENSP00000263967:p.His1060Gln		180434819	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018411	0.54576	.	.	ENSG00000121879	ENST00000263967	T	0.80738	-1.41	6.08	5.04	0.67666	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.85682	D	0.000000	D	0.91811	0.7409	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92964	0.6391	10	0.87932	D	0	-9.2959	12.6212	0.56603	0.0:0.8609:0.0:0.1391	.	1060	P42336	PK3CA_HUMAN	Q	1060	ENSP00000263967:H1060Q	ENSP00000263967:H1060Q	H	+	3	2	PIK3CA	180434819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.727000	0.54984	2.894000	0.99253	0.591000	0.81541	CAC		0.388	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178952125	C	A	178952125	3	1	1	1	0	0	0	0	1	0	0	0	11944	477	17	2	3258	2	PIK3CA	3	178952125	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	27884152	178952125	19070305	43	43										
CPN2	1370	hgsc.bcm.edu	37	chr3	194063287	194063287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gatgatgtttttcgtatatgGcgggatgtccagtgggacgg	16	5	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr3:194063287G>A	ENST00000323830.3	-	2	234	c.145C>T	c.(145-147)Cca>Tca	p.P49S	CPN2_ENST00000429275.1_Missense_Mutation_p.P49S	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	49	LRRNT.				protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		TTCGTATATGGCGGGATGTCC	0.547																																																0			3											134	126	129					3																	194063287		2203	4300	6503	195544982	SO:0001583	missense	221184			J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.145C>T	3.37:g.194063287G>A	ENSP00000319464:p.Pro49Ser		195544982	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.151219	0.00325	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.23950	1.88;1.88	5.19	4.3	0.51218	Leucine-rich repeat-containing N-terminal (1);	0.213797	0.23852	N	0.043928	T	0.16171	0.0389	L	0.33753	1.03	0.09310	N	1	B	0.21381	0.055	B	0.18263	0.021	T	0.26815	-1.0092	10	0.06494	T	0.89	.	10.5023	0.44813	0.0784:0.1697:0.7519:0.0	.	49	P22792	CPN2_HUMAN	S	49	ENSP00000319464:P49S;ENSP00000402232:P49S	ENSP00000319464:P49S	P	-	1	0	CPN2	195544982	0.000000	0.05858	0.036000	0.18154	0.012000	0.07955	0.697000	0.25556	1.299000	0.44798	0.561000	0.74099	CCA		0.547	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		A	194063287	G	A	194063287	3	1	1	1	0	0	0	0	1	0	0	0	3816	1203	42	3	1496	3	CPN2	3	194063287	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	15111162	194063287	3959143	44	44										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-													0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tggagtgccacctgctcacaCacgtgcccatgtggagtgcc					rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																																1	Substitution - Missense(1)	pancreas(1)	4																																								1378622	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs		1378594	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388622	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	1388594	7	5	1	1	0	1	0	1	0	0	0	0	3883	478	17	0	297	0	CRIPAK	4	1388594	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	TCGA-AF-2687-01A-02D-1733-10		1388594	189765682	45	45										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6064099	6064099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcctggagcagggcgtaggcGcgttgcagggcctggtactc	17	11	0	0	rs149678000		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:6064099G>A	ENST00000282924.5	-	10	1985	c.1500C>T	c.(1498-1500)cgC>cgT	p.R500R	JAKMIP1_ENST00000457227.2_5'Flank|JAKMIP1_ENST00000410077.2_Silent_p.R335R|JAKMIP1_ENST00000409831.1_Silent_p.R500R|JAKMIP1_ENST00000409021.3_Silent_p.R500R|JAKMIP1_ENST00000409371.3_Silent_p.R315R	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	500	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGGCGTAGGCGCGTTGCAGGG	0.642													G|||	1	0.000199681	0	0	5008	,	,		14934	0		0.001	False		,,,				2504	0															0			4						G	,	1,4399		0,1,2199	40	46	44		1500,1500	-4.8	0.9	4	dbSNP_134	44	2,8588		0,2,4293	no	coding-synonymous,coding-synonymous	JAKMIP1	NM_001099433.1,NM_144720.3	,	0,3,6492	AA,AG,GG		0.0233,0.0227,0.0231	,	500/832,500/627	6064099	3,12987	2200	4295	6495	6115000	SO:0001819	synonymous_variant	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1500C>T	4.37:g.6064099G>A			6115000	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	37	CCDS3385.1																																																																																				0.642	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		A	6064099	G	A	6064099	2	1	1	1	0	0	0	0	0	0	0	1	7961	1074	38	1		1	JAKMIP1	4	6064099	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	4675505	6064099	185090177	46	46										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6598866	6598866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tccaggcctggacgggcttcTacacgtcccgcagctcactg	11	16	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:6598866T>C	ENST00000285599.3	+	8	1120	c.1084T>C	c.(1084-1086)Tac>Cac	p.Y362H	MAN2B2_ENST00000504248.1_Missense_Mutation_p.Y311H	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	362					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						GACGGGCTTCTACACGTCCCG	0.632																																																0			4											94	103	100					4																	6598866		2203	4300	6503	6649767	SO:0001583	missense	23324			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1084T>C	4.37:g.6598866T>C	ENSP00000285599:p.Tyr362His		6649767	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.663321	0.88251	.	.	ENSG00000013288	ENST00000285599;ENST00000504248	D;D	0.87179	-2.22;-2.22	5.13	5.13	0.70059	Glycoside hydrolase, family 38, central domain (2);	0.250811	0.39759	N	0.001262	D	0.95069	0.8403	H	0.94264	3.515	0.51233	D	0.999911	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.989;0.986	D	0.96263	0.9192	10	0.87932	D	0	-19.2869	14.099	0.65042	0.0:0.0:0.0:1.0	.	311;362;362	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	H	362;311	ENSP00000285599:Y362H;ENSP00000423129:Y311H	ENSP00000285599:Y362H	Y	+	1	0	MAN2B2	6649767	1.000000	0.71417	0.932000	0.37286	0.946000	0.59487	6.493000	0.73658	1.925000	0.55765	0.448000	0.29417	TAC		0.632	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		C	6598866	T	C	6598866	3	2	1	1	0	0	0	0	1	0	0	0	9247	1522	53	4	1114	4	MAN2B2	4	6598866	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	534767	6598866	184555410	47	47										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110415907	110415907	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atggctaagccttttggctaTggctatccaacacttcagcc	8	12	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:110415907T>C	ENST00000265175.5	+	6	1438	c.1383T>C	c.(1381-1383)taT>taC	p.Y461Y	SEC24B_ENST00000504968.2_Silent_p.Y492Y|SEC24B_ENST00000399100.2_Silent_p.Y426Y	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	461					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CTTTTGGCTATGGCTATCCAA	0.512																																																0			4											111	115	114					4																	110415907		2127	4279	6406	110635356	SO:0001819	synonymous_variant	10427			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.1383T>C	4.37:g.110415907T>C			110635356	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	CCDS47124.1																																																																																				0.512	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			C	110415907	T	C	110415907	2	2	1	1	0	0	0	0	0	0	0	1	14032	1471	51	4		4	SEC24B	4	110415907	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	103817041	110415907	80738369	48	48										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143007404	143007404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	attttgttcctgaaaatgtgAaatatctgaaggggaaaaaa	9	3	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:143007404A>G	ENST00000513000.1	-	25	2813	c.2380T>C	c.(2380-2382)Tca>Cca	p.S794P	INPP4B_ENST00000262992.4_Missense_Mutation_p.S794P|INPP4B_ENST00000308502.4_Missense_Mutation_p.S794P|INPP4B_ENST00000509777.1_Missense_Mutation_p.S794P|INPP4B_ENST00000508116.1_Missense_Mutation_p.S794P	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	794					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TGAAAATGTGAAATATCTGAA	0.318																																																0			4											43	46	45					4																	143007404		2201	4298	6499	143226854	SO:0001583	missense	8821			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2380T>C	4.37:g.143007404A>G	ENSP00000425487:p.Ser794Pro		143226854	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	A	5.493	0.276032	0.10403	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.29142	1.92;1.92;1.92;1.92;1.92;1.93;1.58;1.59	5.45	4.29	0.51040	.	0.305004	0.31092	N	0.008264	T	0.09774	0.0240	N	0.02225	-0.63	0.37499	D	0.916702	B	0.06786	0.001	B	0.06405	0.002	T	0.24440	-1.0160	10	0.12766	T	0.61	.	4.7558	0.13082	0.8169:0.0:0.1831:0.0	.	794	O15327	INP4B_HUMAN	P	794;794;794;665;794;794;609;609;794;665	ENSP00000425487:S794P;ENSP00000262992:S794P;ENSP00000308441:S794P;ENSP00000423954:S794P;ENSP00000422793:S794P;ENSP00000426207:S609P;ENSP00000427250:S794P;ENSP00000421065:S665P	ENSP00000262992:S794P	S	-	1	0	INPP4B	143226854	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.903000	0.63272	2.371000	0.80710	0.533000	0.62120	TCA		0.318	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		G	143007404	A	G	143007404	3	3	1	1	0	0	0	0	1	0	0	0	7774	246	9	4	406	4	INPP4B	4	143007404	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	32591497	143007404	48146872	49	49										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148944515	148944515	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcgaagagacaaggccagagAaccaagaggcccgtggccgt	14	11	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:148944515A>G	ENST00000336498.3	+	19	2057	c.1818A>G	c.(1816-1818)agA>agG	p.R606R	ARHGAP10_ENST00000414545.2_Silent_p.R255R	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		AAGGCCAGAGAACCAAGAGGC	0.512																																																0			4											93	96	95					4																	148944515		2203	4300	6503	149163965	SO:0001819	synonymous_variant	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.1818A>G	4.37:g.148944515A>G			149163965	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000336498.3	37	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	A	10.07	1.248474	0.22880	.	.	ENSG00000071205	ENST00000507661	.	.	.	5.72	1.67	0.24075	.	.	.	.	.	T	0.46229	0.1382	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31943	-0.9925	4	.	.	.	.	3.7872	0.08705	0.2908:0.0:0.4567:0.2525	.	.	.	.	D	284	.	.	N	+	1	0	ARHGAP10	149163965	0.999000	0.42202	0.980000	0.43619	0.957000	0.61999	0.652000	0.24888	0.750000	0.32877	-0.242000	0.12053	AAC		0.512	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		G	148944515	A	G	148944515	2	3	1	1	0	0	0	0	0	0	0	1	862	243	9	4		4	ARHGAP10	4	148944515	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	5937111	148944515	42209761	50	50										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247367	153247367	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaccctaagagtggcatctcGagaaccgctaacaactctgc	8	13	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:153247367G>A	ENST00000281708.4	-	10	2664	c.1435C>T	c.(1435-1437)Cga>Tga	p.R479*	FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R479*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R479*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.R303*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.R399*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.R361*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	479					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R479*(4)|p.R479G(3)|p.R240*(2)|p.R479R(2)|p.R399*(2)|p.R399R(1)|p.?(1)|p.R361R(1)|p.R361*(1)|p.R240R(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GTGGCATCTCGAGAACCGCTA	0.398			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	18	Substitution - Nonsense(9)|Substitution - coding silent(5)|Substitution - Missense(3)|Unknown(1)	lung(10)|large_intestine(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(1)	4											83	78	79					4																	153247367		2203	4299	6502	153466817	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1435C>T	4.37:g.153247367G>A	ENSP00000281708:p.Arg479*		153466817	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	38	6.707523	0.97780	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	5.72	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7081	15.6805	0.77364	0.0:0.0:0.8491:0.1508	.	.	.	.	X	479;361;399;303	.	ENSP00000263981:R399X	R	-	1	2	FBXW7	153466817	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.541000	0.73865	1.492000	0.48499	0.650000	0.86243	CGA		0.398	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153247367	G	A	153247367	4	1	1	1	0	0	0	0	0	1	0	0	5788	1066	37	1	700	1	FBXW7	4	153247367	Nonsense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	4302852	153247367	37906909	51	51										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160274960	160274960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agcacaaagtataacaggcaAaatcaaagtagagagagcct	9	7	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:160274960A>G	ENST00000264431.4	+	22	4349	c.3930A>G	c.(3928-3930)caA>caG	p.Q1310Q		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1310					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		ATAACAGGCAAAATCAAAGTA	0.468																																																0			4											96	96	96					4																	160274960		1884	4119	6003	160494410	SO:0001819	synonymous_variant	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3930A>G	4.37:g.160274960A>G			160494410	D3DP27	Silent	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	A	0.665	-0.804093	0.02819	.	.	ENSG00000109756	ENST00000505026	.	.	.	6.11	0.296	0.15757	.	.	.	.	.	T	0.57504	0.2058	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49457	-0.8938	4	.	.	.	.	10.0017	0.41933	0.2446:0.1078:0.6476:0.0	.	.	.	.	E	245	.	.	K	+	1	0	RAPGEF2	160494410	0.311000	0.24536	0.992000	0.48379	0.129000	0.20672	-0.713000	0.05007	-0.276000	0.09206	-0.250000	0.11733	AAA		0.468	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		G	160274960	A	G	160274960	2	3	1	1	0	0	0	0	0	0	0	1	13081	11	1	4		4	RAPGEF2	4	160274960	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	7027593	160274960	30879316	52	52										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164272326	164272326	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	catgtgtgttacctgctccaGaaagaccttctcaagagaac	8	11	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:164272326G>A	ENST00000515560.1	+	4	2423	c.901G>A	c.(901-903)Gaa>Aaa	p.E301K	NPY5R_ENST00000506953.1_Missense_Mutation_p.E301K|NPY5R_ENST00000338566.3_Missense_Mutation_p.E301K			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	301					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				ACCTGCTCCAGAAAGACCTTC	0.428																																					Melanoma(139;1287 1774 9781 19750 25599)											0			4											90	91	91					4																	164272326		2203	4300	6503	164491776	SO:0001583	missense	4889			BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.901G>A	4.37:g.164272326G>A	ENSP00000423917:p.Glu301Lys		164491776	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	37	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	G	1.121	-0.655396	0.03480	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.70282	-0.47;-0.47;-0.47	4.49	0.231	0.15377	GPCR, rhodopsin-like superfamily (1);	0.907354	0.09072	N	0.852674	T	0.35653	0.0939	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30909	-0.9962	10	0.05721	T	0.95	.	0.8019	0.01077	0.1892:0.2374:0.3346:0.2388	.	301	Q15761	NPY5R_HUMAN	K	301	ENSP00000339377:E301K;ENSP00000423917:E301K;ENSP00000423474:E301K	ENSP00000339377:E301K	E	+	1	0	NPY5R	164491776	0.000000	0.05858	0.197000	0.23402	0.346000	0.29079	0.343000	0.19944	0.177000	0.19895	-0.373000	0.07131	GAA		0.428	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		A	164272326	G	A	164272326	3	1	1	1	0	0	0	0	1	0	0	0	10641	943	33	3	903	3	NPY5R	4	164272326	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	3997366	164272326	26881950	53	53										
TKTL2	84076	hgsc.bcm.edu	37	chr4	164394568	164394568	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggtagggtgtctctccaagtCgctgtgaagtttcctcaggt	13	9	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr4:164394568C>A	ENST00000280605.3	-	1	479	c.319G>T	c.(319-321)Gac>Tac	p.D107Y		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	107						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CTCTCCAAGTCGCTGTGAAGT	0.542																																																0			4											128	97	107					4																	164394568		2203	4300	6503	164614018	SO:0001583	missense	84076			BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.319G>T	4.37:g.164394568C>A	ENSP00000280605:p.Asp107Tyr		164614018	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746987	0.30955	.	.	ENSG00000151005	ENST00000280605	T	0.21734	1.99	4.26	1.53	0.23141	Transketolase, N-terminal (1);	0.062570	0.64402	D	0.000010	T	0.35219	0.0924	M	0.63208	1.945	0.51012	D	0.999904	D	0.71674	0.998	D	0.71184	0.972	T	0.05305	-1.0893	10	0.62326	D	0.03	-4.4881	5.7769	0.18283	0.0:0.6495:0.1627:0.1878	.	107	Q9H0I9	TKTL2_HUMAN	Y	107	ENSP00000280605:D107Y	ENSP00000280605:D107Y	D	-	1	0	TKTL2	164614018	0.977000	0.34250	0.000000	0.03702	0.338000	0.28826	1.332000	0.33805	0.310000	0.22990	0.561000	0.74099	GAC		0.542	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		A	164394568	C	A	164394568	3	1	1	1	0	0	0	0	1	0	0	0	15975	884	31	2	1565	2	TKTL2	4	164394568	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	122242	164394568	26759708	54	54										
TERT	7015	hgsc.bcm.edu	37	chr5	1253913	1253913	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cctccagggcagtcagcgtcGtccccgggagcttccgactc	12	17	1	0	rs199422306		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:1253913G>A	ENST00000310581.5	-	16	3386	c.3329C>T	c.(3328-3330)aCg>aTg	p.T1110M	TERT_ENST00000334602.6_Missense_Mutation_p.T1047M|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1110	CTE.		T -> M (in idiopathic pulmonary fibrosis susceptibility; impaired telomerase activity). {ECO:0000269|PubMed:17392301}.		DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	AGTCAGCGTCGTCCCCGGGAG	0.657									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																																							0			5	GRCh37	CM072077	TERT	M							23	32	28					5																	1253913		2182	4261	6443	1306913	SO:0001583	missense	7015	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3329C>T	5.37:g.1253913G>A	ENSP00000309572:p.Thr1110Met		1306913	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	g	10.34	1.323502	0.24080	.	.	ENSG00000164362	ENST00000310581;ENST00000334602	D;D	0.96587	-4.06;-3.97	3.83	2.0	0.26442	.	0.947994	0.08865	N	0.882461	D	0.90689	0.7079	L	0.29908	0.895	0.09310	A	2.39116e-07	P;D	0.53619	0.929;0.961	B;B	0.37601	0.202;0.254	D	0.86117	0.1566	9	0.46703	T	0.11	-9.6301	5.2556	0.15546	0.1162:0.2098:0.6741:0.0	.	1047;1110	O14746-3;O14746	.;TERT_HUMAN	M	1110;1047	ENSP00000309572:T1110M;ENSP00000334346:T1047M	ENSP00000309572:T1110M	T	-	2	0	TERT	1306913	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.012000	0.12699	0.390000	0.25115	0.561000	0.74099	ACG		0.657	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1253913	G	A	1253913	3	1	1	1	0	0	0	0	1	0	0	0	15803	1145	40	1	73	1	TERT	5	1253913	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10		1253913	179661347	55	55										
TERT	7015	hgsc.bcm.edu	37	chr5	1293484	1293484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcatcttccacgtcagctccTgcagcgagagcttggcatgc	10	14	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:1293484T>C	ENST00000310581.5	-	2	1574	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	TERT_ENST00000508104.2_Missense_Mutation_p.Q506R|TERT_ENST00000334602.6_Missense_Mutation_p.Q506R|TERT_ENST00000522877.1_5'Flank|TERT_ENST00000296820.5_Missense_Mutation_p.Q506R	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	506	QFP motif.|RNA-interacting domain 2.|Required for oligomerization.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CGTCAGCTCCTGCAGCGAGAG	0.657									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																																							0			5											52	51	51					5																	1293484		2202	4300	6502	1346484	SO:0001583	missense	7015	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.1517A>G	5.37:g.1293484T>C	ENSP00000309572:p.Gln506Arg		1346484	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	T	0.024	-1.386745	0.01194	.	.	ENSG00000164362	ENST00000310581;ENST00000296820;ENST00000334602;ENST00000508104	D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07	4.47	-1.08	0.09936	Telomerase ribonucleoprotein complex - RNA-binding domain (2);	0.606170	0.16981	N	0.191720	T	0.67674	0.2918	N	0.25286	0.73	0.09310	N	1	B;B;B	0.13145	0.002;0.002;0.007	B;B;B	0.17433	0.007;0.014;0.018	T	0.50171	-0.8859	10	0.20046	T	0.44	-14.7581	2.6866	0.05109	0.1123:0.2681:0.1143:0.5053	.	506;506;506	O14746-3;O14746;Q8NG38	.;TERT_HUMAN;.	R	506	ENSP00000309572:Q506R;ENSP00000296820:Q506R;ENSP00000334346:Q506R;ENSP00000426042:Q506R	ENSP00000296820:Q506R	Q	-	2	0	TERT	1346484	0.029000	0.19370	0.025000	0.17156	0.008000	0.06430	-0.464000	0.06688	-0.488000	0.06726	-1.489000	0.00976	CAG		0.657	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			C	1293484	T	C	1293484	3	2	1	1	0	0	0	0	1	0	0	0	15803	1580	55	4	1941	4	TERT	5	1293484	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	39571	1293484	179621776	56	56										
APC	324	hgsc.bcm.edu	37	chr5	112175212	112175216	+	Frame_Shift_Del	DEL	AAAAG	AAAAG	-													0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	accctgcaaatagcagaaatAaaagaaaagattggaactag					rs121913224		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	AAAAG	AAAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:112175212_112175216delAAAAG	ENST00000457016.1	+	16	4301_4305	c.3921_3925delAAAAG	c.(3919-3927)ataaaagaafs	p.KE1308fs	APC_ENST00000257430.4_Frame_Shift_Del_p.KE1308fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Del_p.KE1308fs			P25054	APC_HUMAN	adenomatous polyposis coli	1308	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*6(51)|p.E1309fs*4(42)|p.E1309*(25)|p.I1307fs*6(12)|p.K1308*(6)|p.I1307fs*7(2)|p.I1311fs*4(2)|p.K1308fs*6(1)|p.I1307fs*13(1)|p.?(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1309K(1)|p.K1308E(1)|p.K1308fs*4(1)|p.I1307fs*14(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGCAGAAATAAAAGAAAAGATTGG	0.424		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	150	Deletion - Frameshift(61)|Insertion - Frameshift(54)|Substitution - Nonsense(31)|Substitution - Missense(2)|Unknown(1)|Complex - frameshift(1)	large_intestine(145)|stomach(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|skin(1)	5	GRCh37	CD040160|CD084022|CD941590|CD972006|CM086765|CM920052	APC	D|M																																				112203115	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3921_3925delAAAAG	5.37:g.112175217_112175221delAAAAG	ENSP00000413133:p.Lys1308fs		112203111	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.424	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175216	AAAAG	-	112175212	7	5	1	1	0	1	0	1	0	0	0	0	763	352	13	0	3979	0	APC	5	112175212	Frame_Shift_Del	DEL	AAAAG	TCGA-AF-2687-01A-02D-1733-10	110881728	112175212	68740048	57	57										
APC	324	hgsc.bcm.edu	37	chr5	112175696	112175696	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agagagagagtggacctaagCaagctgcagtaaatgctgca	13	7	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:112175696C>T	ENST00000457016.1	+	16	4785	c.4405C>T	c.(4405-4407)Caa>Taa	p.Q1469*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1469*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1469*			P25054	APC_HUMAN	adenomatous polyposis coli	1469	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1469*(6)|p.A1470fs*17(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGACCTAAGCAAGCTGCAGT	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	10	Substitution - Nonsense(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	large_intestine(6)|soft_tissue(2)|thyroid(1)|skin(1)	5											81	78	79					5																	112175696		2202	4300	6502	112203595	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4405C>T	5.37:g.112175696C>T	ENSP00000413133:p.Gln1469*		112203595	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.347607	0.98772	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.16	6.16	0.99307	.	0.300318	0.37530	N	0.002053	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.1458	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	1469	.	.	Q	+	1	0	APC	112203595	1.000000	0.71417	0.997000	0.53966	0.718000	0.41266	6.223000	0.72257	2.937000	0.99478	0.650000	0.86243	CAA		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175696	C	T	112175696	4	4	1	1	0	0	0	0	0	1	0	0	763	711	25	3	4463	3	APC	5	112175696	Nonsense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	484	112175696	68739564	58	58										
PHF15	23338	hgsc.bcm.edu	37	chr5	133900193	133900193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtcctgcccaggtcagcatcGgctgcccagagaagatggag	14	12	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:133900193G>A	ENST00000402835.1	+	8	1117	c.862G>A	c.(862-864)Ggc>Agc	p.G288S	PHF15_ENST00000361895.2_Missense_Mutation_p.G288S|PHF15_ENST00000395003.1_Missense_Mutation_p.G288S|PHF15_ENST00000282605.4_Missense_Mutation_p.G288S																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGTCAGCATCGGCTGCCCAGA	0.597																																																0			5											43	36	39					5																	133900193		2203	4297	6500	133928092	SO:0001583	missense	23338																														ENST00000402835.1:c.862G>A	5.37:g.133900193G>A	ENSP00000384671:p.Gly288Ser		133928092		Missense_Mutation	SNP	ENST00000402835.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.410597	0.96072	.	.	ENSG00000043143	ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000402835;ENST00000395003	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.37705	0.1013	M	0.64567	1.98	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.995;0.988;0.995	D;D;D;P;D	0.75484	0.984;0.986;0.953;0.815;0.953	T	0.06917	-1.0800	10	0.72032	D	0.01	.	19.3177	0.94223	0.0:0.0:1.0:0.0	.	288;288;288;288;304	Q9NQC1;B5MBX1;D3DQA3;Q9NQC1-3;B3KPL2	JADE2_HUMAN;.;.;.;.	S	288;304;288;288;288;288;288	ENSP00000282605:G288S;ENSP00000354425:G288S;ENSP00000384671:G288S;ENSP00000378451:G288S	ENSP00000282605:G288S	G	+	1	0	PHF15	133928092	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.471000	0.97696	2.554000	0.86153	0.655000	0.94253	GGC		0.597	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			A	133900193	G	A	133900193	3	1	1	1	0	0	0	0	1	0	0	0	11857	1116	39	1	888	1	PHF15	5	133900193	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	21724497	133900193	47015067	59	59										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140230003	140230003	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgtgccctggacgaaacggaCgcaccgcgccagcgcctact	12	17	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:140230003C>T	ENST00000532602.1	+	1	2956	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.D641D|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	641	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAAACGGACGCACCGCGCC	0.682																																					Melanoma(55;1800 1972 14909)											0			5											59	61	60					5																	140230003		2197	4272	6469	140210187	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1923C>T	5.37:g.140230003C>T			140210187	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.682	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140230003	C	T	140230003	2	4	1	1	0	0	0	0	0	0	0	1	11562	535	19	1		1	PCDHA9	5	140230003	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	6329810	140230003	40685257	60	60										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236912	140236912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atgagctggtggtgaccgcgCgggacgggggctcgcctccg	19	12	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:140236912C>T	ENST00000307360.5	+	1	1279	c.1279C>T	c.(1279-1281)Cgg>Tgg	p.R427W	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.R427W|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	427	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGACCGCGCGGGACGGGGG	0.647																																																0			5											107	103	104					5																	140236912		2197	4274	6471	140217096	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1279C>T	5.37:g.140236912C>T	ENSP00000304234:p.Arg427Trp		140217096	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	c	1.577	-0.532706	0.04112	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.54866	4.63;0.55	3.96	-3.24	0.05094	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.29158	0.0725	N	0.25825	0.765	0.09310	N	1	P;P;B	0.41748	0.761;0.589;0.048	B;B;B	0.34779	0.189;0.16;0.052	T	0.19549	-1.0302	9	0.87932	D	0	.	2.8682	0.05608	0.4522:0.2977:0.1017:0.1485	.	427;427;427	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	W	427	ENSP00000421030:R427W;ENSP00000304234:R427W	ENSP00000304234:R427W	R	+	1	2	PCDHA10	140217096	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.579000	0.02123	-0.455000	0.07054	-0.231000	0.12243	CGG		0.647	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140236912	C	T	140236912	3	4	1	1	0	0	0	0	1	0	0	0	11551	759	27	1	1281	1	PCDHA10	5	140236912	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	6909	140236912	40678348	61	61										
ZNF354A	6940	hgsc.bcm.edu	37	chr5	178139770	178139770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgtgaattctctgatgataaCgaagggatgagctagactta	11	5	1	5			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:178139770C>T	ENST00000335815.2	-	5	1306	c.1109G>A	c.(1108-1110)cGt>cAt	p.R370H		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	370					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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)	all cancers(165;0.185)		CTGATGATAACGAAGGGATGA	0.403																																																0			5											73	76	75					5																	178139770		2203	4297	6500	178072376	SO:0001583	missense	6940			AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"Zinc fingers, C2H2-type", "-"	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1109G>A	5.37:g.178139770C>T	ENSP00000337122:p.Arg370His		178072376	Q9UNJ8	Missense_Mutation	SNP	ENST00000335815.2	37	CCDS4438.1	.	.	.	.	.	.	.	.	.	.	C	8.925	0.961965	0.18583	.	.	ENSG00000169131	ENST00000335815	T	0.40225	1.04	4.96	4.03	0.46877	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33496	N	0.004846	T	0.34366	0.0895	L	0.48218	1.51	0.30333	N	0.786431	B	0.25719	0.132	B	0.22386	0.039	T	0.35649	-0.9780	10	0.56958	D	0.05	-24.7023	10.0683	0.42317	0.2004:0.7996:0.0:0.0	.	370	O60765	Z354A_HUMAN	H	370	ENSP00000337122:R370H	ENSP00000337122:R370H	R	-	2	0	ZNF354A	178072376	0.053000	0.20554	1.000000	0.80357	0.985000	0.73830	-0.022000	0.12480	2.741000	0.93983	0.655000	0.94253	CGT		0.403	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649		T	178139770	C	T	178139770	3	4	1	1	0	0	0	0	1	0	0	0	17903	536	19	1	712	1	ZNF354A	5	178139770	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	37902858	178139770	2775490	62	62										
SQSTM1	8878	hgsc.bcm.edu	37	chr5	179263547	179263547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	caagaactatgacatcggagCggctctggacaccatccagt	10	12	1	2	rs201239306		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr5:179263547C>T	ENST00000389805.4	+	8	1455	c.1277C>T	c.(1276-1278)gCg>gTg	p.A426V	C5orf45_ENST00000403396.2_3'UTR|SQSTM1_ENST00000402874.3_Missense_Mutation_p.A342V|C5orf45_ENST00000523267.1_5'Flank|SQSTM1_ENST00000360718.5_Missense_Mutation_p.A342V|SQSTM1_ENST00000510187.1_Missense_Mutation_p.R343W|SQSTM1_ENST00000376929.3_Missense_Mutation_p.A342V	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	426	Interaction with NTRK1. {ECO:0000250}.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACATCGGAGCGGCTCTGGAC	0.557													C|||	1	0.000199681	0	0.0014	5008	,	,		15597	0		0	False		,,,				2504	0															0			5											153	142	146					5																	179263547		2203	4300	6503	179196153	SO:0001583	missense	8878			U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"Paget disease of bone 3", "oxidative stress induced like"	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.1277C>T	5.37:g.179263547C>T	ENSP00000374455:p.Ala426Val		179196153	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Missense_Mutation	SNP	ENST00000389805.4	37	CCDS34317.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	17.93|17.93	3.510234|3.510234	0.64522|0.64522	.|.	.|.	ENSG00000161011|ENSG00000161011	ENST00000376929;ENST00000389805;ENST00000454378;ENST00000402874;ENST00000360718|ENST00000510187	D;D;D;D|T	0.89050|0.22134	-2.46;-2.46;-2.46;-2.46|1.97	4.53|4.53	4.53|4.53	0.55603|0.55603	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);UBA-like (1);|.	0.167892|.	0.52532|.	N|.	0.000077|.	T|T	0.24851|0.24851	0.0603|0.0603	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D|P	0.89917|0.36616	1.0|0.561	D|B	0.64506|0.29942	0.926|0.109	T|T	0.19582|0.19582	-1.0301|-1.0301	10|9	0.54805|0.87932	T|D	0.06|0	-10.1183|-10.1183	17.2546|17.2546	0.87052|0.87052	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	426|343	Q13501|E7EMC7	SQSTM_HUMAN|.	V|W	342;426;282;342;342|343	ENSP00000366128:A342V;ENSP00000374455:A426V;ENSP00000385553:A342V;ENSP00000353944:A342V|ENSP00000424477:R343W	ENSP00000353944:A342V|ENSP00000424477:R343W	A|R	+|+	2|1	0|2	SQSTM1|SQSTM1	179196153|179196153	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.164000|0.164000	0.22412|0.22412	4.753000|4.753000	0.62183|0.62183	2.033000|2.033000	0.60031|0.60031	0.462000|0.462000	0.41574|0.41574	GCG|CGG		0.557	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			T	179263547	C	T	179263547	3	4	1	1	0	0	0	0	1	0	0	0	15169	768	27	1	1307	1	SQSTM1	5	179263547	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	1123777	179263547	1651713	63	63										
MYLK4	340156	hgsc.bcm.edu	37	chr6	2749440	2749440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aacacttcactttctccaccTcttccctgcactgaaaaaag	3	15	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:2749440T>C	ENST00000274643.7	-	2	431	c.89A>G	c.(88-90)gAg>gGg	p.E30G	MYLK4_ENST00000268446.5_Missense_Mutation_p.E30G	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	30			E -> Q (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.			extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				TTTCTCCACCTCTTCCCTGCA	0.393																																																0			6											142	146	145					6																	2749440		2203	4300	6503	2694439	SO:0001583	missense	340156				CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"caMLCK like"						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.89A>G	6.37:g.2749440T>C	ENSP00000274643:p.Glu30Gly		2694439	A2RUC0|Q5TAW2	Missense_Mutation	SNP	ENST00000274643.7	37	CCDS34330.1	.	.	.	.	.	.	.	.	.	.	T	17.12	3.308459	0.60305	.	.	ENSG00000145949	ENST00000268446;ENST00000274643	T;T	0.68479	0.0;-0.33	5.65	5.65	0.86999	.	.	.	.	.	T	0.29288	0.0729	N	0.08118	0	0.27050	N	0.963809	B	0.23058	0.079	B	0.21917	0.037	T	0.16394	-1.0404	9	0.33940	T	0.23	.	13.2505	0.60050	0.0:0.0:0.0:1.0	.	30	Q86YV6	MYLK4_HUMAN	G	30	ENSP00000268446:E30G;ENSP00000274643:E30G	ENSP00000268446:E30G	E	-	2	0	MYLK4	2694439	0.964000	0.33143	0.877000	0.34402	0.887000	0.51463	3.020000	0.49643	2.149000	0.67028	0.533000	0.62120	GAG		0.393	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418		C	2749440	T	C	2749440	3	2	1	1	0	0	0	0	1	0	0	0	10089	1551	54	4	1121	4	MYLK4	6	2749440	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10		2749440	168365627	64	64										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327918	16327918	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgctgctgctgatgctgatgCtgctgctgctgctgctgctg	14	11	0	2	rs28555263	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:16327918C>A	ENST00000244769.4	-	8	1560	c.624G>T	c.(622-624)caG>caT	p.Q208H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q208H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	208	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gatgctgatgctgctgctgct	0.662													C|||	649	0.129593	0.1437	0.1153	5008	,	,		12912	0.2044		0.0318	False		,,,				2504	0.1442															0			6											5	8	7					6																	16327918		1579	3505	5084	16435897	SO:0001583	missense	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.624G>T	6.37:g.16327918C>A	ENSP00000244769:p.Gln208His		16435897	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	5.901	0.350402	0.11182	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56103	0.48;0.48	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	P	0.39520	0.676	B	0.36030	0.216	T	0.18493	-1.0335	8	0.13108	T	0.6	.	.	.	.	rs28555263	208	P54253	ATX1_HUMAN	H	208	ENSP00000244769:Q208H;ENSP00000416360:Q208H	ENSP00000244769:Q208H	Q	-	3	2	ATXN1	16435897	0.129000	0.22400	0.018000	0.16275	0.062000	0.15995	1.183000	0.32041	0.132000	0.18615	0.134000	0.15878	CAG		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327918	C	A	16327918	3	1	1	1	0	0	0	0	1	0	0	0	1210	796	28	2	1831	2	ATXN1	6	16327918	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	13578478	16327918	154787149	65	65										
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868570	31868570	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgcaggagtggagggggtagAggaggtgggggtgggggctt	26	3	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:31868570A>G	ENST00000375527.2	-	2	688	c.513T>C	c.(511-513)ccT>ccC	p.P171P	C2_ENST00000452323.2_5'Flank|C2_ENST00000469372.1_Intron	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	171	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						GAGGGGGTAGAGGAGGTGGGG	0.622																																																0			6											21	25	24					6																	31868570		2196	4278	6474	31976549	SO:0001819	synonymous_variant	221527			BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19066	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 46"	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.513T>C	6.37:g.31868570A>G			31976549	B0UY00|Q5JQ98	Silent	SNP	ENST00000375527.2	37	CCDS4727.1																																																																																				0.622	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		G	31868570	A	G	31868570	2	3	1	1	0	0	0	0	0	0	0	1	17564	291	11	4		4	ZBTB12	6	31868570	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	15540652	31868570	139246497	66	66										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33154591	33154591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	caatggccagctcctggacaTcaccctgcaaagacatgaga	9	13	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:33154591T>C	ENST00000374708.4	-	5	869	c.611A>G	c.(610-612)gAt>gGt	p.D204G	COL11A2_ENST00000395194.1_Missense_Mutation_p.D204G|COL11A2_ENST00000395197.1_Missense_Mutation_p.D204G|COL11A2_ENST00000374712.1_Missense_Mutation_p.D204G|COL11A2_ENST00000357486.1_Missense_Mutation_p.D204G|COL11A2_ENST00000341947.2_Missense_Mutation_p.D204G|COL11A2_ENST00000374713.1_Missense_Mutation_p.D204G|COL11A2_ENST00000361917.1_Missense_Mutation_p.D204G|COL11A2_ENST00000374714.1_Missense_Mutation_p.D204G	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	204	Laminin G-like.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.D204V(1)		biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CTCCTGGACATCACCCTGCAA	0.542																																					Melanoma(1;90 116 3946 5341 17093)											1	Substitution - Missense(1)	ovary(1)	6											123	118	119					6																	33154591		2203	4300	6503	33262569	SO:0001583	missense	1302			U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.611A>G	6.37:g.33154591T>C	ENSP00000363840:p.Asp204Gly		33262569	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956661	0.73902	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917;ENST00000457788;ENST00000395194	T;T;T;T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	4.21	4.21	0.49690	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.067864	0.56097	D	0.000035	D	0.87245	0.6129	M	0.90870	3.155	0.45227	D	0.998233	D;D;D;D	0.76494	0.999;0.964;0.964;0.997	D;P;P;D	0.87578	0.998;0.619;0.619;0.992	D	0.88980	0.3407	10	0.56958	D	0.05	.	11.5471	0.50700	0.0:0.0:0.0:1.0	.	204;204;204;204	Q7Z6C3;P13942-8;P13942-6;P13942	.;.;.;COBA2_HUMAN	G	204	ENSP00000363840:D204G;ENSP00000339915:D204G;ENSP00000350079:D204G;ENSP00000363846:D204G;ENSP00000363845:D204G;ENSP00000378623:D204G;ENSP00000363844:D204G;ENSP00000355123:D204G;ENSP00000405520:D204G;ENSP00000378620:D204G	ENSP00000339915:D204G	D	-	2	0	COL11A2	33262569	1.000000	0.71417	0.982000	0.44146	0.819000	0.46315	6.689000	0.74562	1.896000	0.54893	0.363000	0.22086	GAT		0.542	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			C	33154591	T	C	33154591	3	2	1	1	0	0	0	0	1	0	0	0	3674	1435	50	4	4922	4	COL11A2	6	33154591	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	1286021	33154591	137960476	67	67										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39832277	39832277	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atcgaccgcatcaattccatGgctgcggtgagtggctgccc	12	13	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:39832277G>T	ENST00000398904.2	+	4	509	c.327G>T	c.(325-327)atG>atT	p.M109I	DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000538976.1_Missense_Mutation_p.M109I|DAAM2_ENST00000274867.4_Missense_Mutation_p.M109I			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	109	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCAATTCCATGGCTGCGGTGA	0.602																																																0			6											55	56	56					6																	39832277		1990	4168	6158	39940255	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.327G>T	6.37:g.39832277G>T	ENSP00000381876:p.Met109Ile		39940255	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.037499	0.75617	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.89196	-2.48;-2.48;-2.48	5.89	5.89	0.94794	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	T	0.81517	0.4839	L	0.46157	1.445	0.80722	D	1	B;P	0.34462	0.4;0.454	B;B	0.34931	0.121;0.192	T	0.79652	-0.1714	10	0.21014	T	0.42	.	19.0281	0.92941	0.0:0.0:1.0:0.0	.	109;109	G5EA45;Q86T65	.;DAAM2_HUMAN	I	109	ENSP00000274867:M109I;ENSP00000381876:M109I;ENSP00000437808:M109I	ENSP00000274867:M109I	M	+	3	0	DAAM2	39940255	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.869000	0.99810	2.793000	0.96121	0.561000	0.74099	ATG		0.602	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39832277	G	T	39832277	3	4	1	1	0	0	0	0	1	0	0	0	4222	1348	47	2	337	2	DAAM2	6	39832277	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	6677686	39832277	131282790	68	68										
FRS3	10817	hgsc.bcm.edu	37	chr6	41740590	41740590	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctcagcggggtggctattgcGggtgatgatgacaggctctt	16	8	2	3	rs545980178		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:41740590G>A	ENST00000373018.3	-	5	612	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	FRS3_ENST00000259748.2_Missense_Mutation_p.R121C	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	121					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)	p.R121C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGCTATTGCGGGTGATGATG	0.547													G|||	1	0.000199681	8e-04	0	5008	,	,		16216	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	6											124	125	125					6																	41740590		2203	4300	6503	41848568	SO:0001583	missense	10817			AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.361C>T	6.37:g.41740590G>A	ENSP00000362109:p.Arg121Cys		41848568	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	37	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337540	0.81911	.	.	ENSG00000137218	ENST00000373018;ENST00000259748;ENST00000426290	D;D	0.82711	-1.64;-1.64	5.46	3.49	0.39957	.	0.207707	0.33875	N	0.004468	D	0.86847	0.6031	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.86363	0.1718	10	0.52906	T	0.07	-37.7643	12.373	0.55265	0.0:0.0:0.6461:0.3539	.	121	O43559	FRS3_HUMAN	C	121;121;145	ENSP00000362109:R121C;ENSP00000259748:R121C	ENSP00000259748:R121C	R	-	1	0	FRS3	41848568	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	4.032000	0.57274	2.573000	0.86826	0.655000	0.94253	CGC		0.547	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		A	41740590	G	A	41740590	3	1	1	1	0	0	0	0	1	0	0	0	6081	1116	39	1	1129	1	FRS3	6	41740590	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	1908313	41740590	129374477	69	69										
GPR115	221393	hgsc.bcm.edu	37	chr6	47682260	47682260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgatcattgaagccacagtgTggtcccgggtggttgtgacg	15	8	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:47682260T>C	ENST00000283303.2	+	6	1537	c.1279T>C	c.(1279-1281)Tgg>Cgg	p.W427R	RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Missense_Mutation_p.W484R|GPR115_ENST00000327753.3_Missense_Mutation_p.W427R	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	427					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						AGCCACAGTGTGGTCCCGGGT	0.488																																					GBM(22;431 510 9010 26644 32828)											0			6											181	157	165					6																	47682260		2203	4300	6503	47790219	SO:0001583	missense	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1279T>C	6.37:g.47682260T>C	ENSP00000283303:p.Trp427Arg		47790219	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Missense_Mutation	SNP	ENST00000283303.2	37	CCDS4922.2	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111825	0.56398	.	.	ENSG00000153294	ENST00000371220;ENST00000327753;ENST00000283303	T;T;T	0.36699	1.24;1.24;1.24	5.45	5.45	0.79879	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000002	T	0.56485	0.1988	M	0.82923	2.615	0.53005	D	0.999969	D	0.89917	1.0	D	0.97110	1.0	T	0.64550	-0.6381	10	0.87932	D	0	-11.894	14.9854	0.71345	0.0:0.0:0.0:1.0	.	427	Q8IZF3	GP115_HUMAN	R	484;427;427	ENSP00000360264:W484R;ENSP00000328319:W427R;ENSP00000283303:W427R	ENSP00000283303:W427R	W	+	1	0	GPR115	47790219	1.000000	0.71417	0.995000	0.50966	0.353000	0.29299	7.969000	0.87988	2.197000	0.70478	0.533000	0.62120	TGG		0.488	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		C	47682260	T	C	47682260	3	2	1	1	0	0	0	0	1	0	0	0	6652	1696	59	4	1297	4	GPR115	6	47682260	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	5941670	47682260	123432807	70	70										
TINAG	27283	hgsc.bcm.edu	37	chr6	54214666	54214666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atctaacaggatctatcaatGttctcctccatacagagtct	5	11	5	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:54214666G>A	ENST00000259782.4	+	7	1148	c.1052G>A	c.(1051-1053)tGt>tAt	p.C351Y		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	351					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			ATCTATCAATGTTCTCCTCCA	0.418																																																0			6											119	113	115					6																	54214666		2203	4300	6503	54322625	SO:0001583	missense	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1052G>A	6.37:g.54214666G>A	ENSP00000259782:p.Cys351Tyr		54322625	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.629364	0.67015	.	.	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.86865	-2.18	5.87	5.87	0.94306	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.88012	0.6323	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88777	0.3268	10	0.59425	D	0.04	.	13.3137	0.60394	0.0:0.1585:0.8415:0.0	.	351	Q9UJW2	TINAG_HUMAN	Y	210;351;30	ENSP00000259782:C351Y	ENSP00000259782:C351Y	C	+	2	0	TINAG	54322625	1.000000	0.71417	0.980000	0.43619	0.928000	0.56348	3.633000	0.54295	2.785000	0.95823	0.591000	0.81541	TGT		0.418	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		A	54214666	G	A	54214666	3	1	1	1	0	0	0	0	1	0	0	0	15960	1377	48	3	1078	3	TINAG	6	54214666	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	6532406	54214666	116900401	71	71										
BACH2	60468	hgsc.bcm.edu	37	chr6	90718472	90718472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cacagagaatatcctttttcCgctggtcattgaggcccagg	10	11	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:90718472C>T	ENST00000257749.4	-	6	799	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	BACH2_ENST00000343122.3_Missense_Mutation_p.R31Q|BACH2_ENST00000537989.1_Missense_Mutation_p.R31Q	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	31						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		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)		ATCCTTTTTCCGCTGGTCATT	0.542																																																0			6											160	150	153					6																	90718472		2203	4300	6503	90775193	SO:0001583	missense	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.92G>A	6.37:g.90718472C>T	ENSP00000257749:p.Arg31Gln		90775193	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	37	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	C	35	5.496452	0.96355	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122;ENST00000406998;ENST00000453877	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.33	5.33	0.75918	BTB/POZ (1);BTB/POZ fold (2);	0.061018	0.64402	D	0.000002	T	0.53932	0.1827	M	0.92026	3.265	0.58432	D	0.999996	D	0.89917	1.0	D	0.66602	0.945	T	0.66156	-0.5994	10	0.87932	D	0	-1.7635	19.0228	0.92921	0.0:1.0:0.0:0.0	.	31	Q9BYV9	BACH2_HUMAN	Q	31	ENSP00000257749:R31Q;ENSP00000437473:R31Q;ENSP00000345642:R31Q;ENSP00000384145:R31Q;ENSP00000397668:R31Q	ENSP00000257749:R31Q	R	-	2	0	BACH2	90775193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.416000	0.80143	2.507000	0.84556	0.591000	0.81541	CGG		0.542	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		T	90718472	C	T	90718472	3	4	1	1	0	0	0	0	1	0	0	0	1285	652	23	1	2449	1	BACH2	6	90718472	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	36503806	90718472	80396595	72	72										
RPF2	84154	hgsc.bcm.edu	37	chr6	111312960	111312960	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atattcttaggaaaaatattAcaagaccttttgaggatcag	7	5	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:111312960A>G	ENST00000441448.2	+	4	297	c.205A>G	c.(205-207)Aca>Gca	p.T69A		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	69	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						GAAAAATATTACAAGACCTTT	0.214																																																0			6											18	19	19					6																	111312960		2107	4189	6296	111419653	SO:0001583	missense	84154			AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"ribosomal processing factor 2 homolog (S. cerevisiae)"		"brix domain containing 1"	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.205A>G	6.37:g.111312960A>G	ENSP00000402338:p.Thr69Ala		111419653	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	37	CCDS5088.1	.	.	.	.	.	.	.	.	.	.	a	14.74	2.626060	0.46840	.	.	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.21932	1.98;1.98;1.98	5.54	5.54	0.83059	Brix domain (3);	0.104603	0.64402	D	0.000004	T	0.10551	0.0258	L	0.38838	1.175	0.49483	D	0.999795	B;B	0.22003	0.063;0.063	B;B	0.19666	0.026;0.026	T	0.03364	-1.1044	10	0.62326	D	0.03	-44.472	15.3605	0.74469	1.0:0.0:0.0:0.0	.	69;69	A8K800;Q9H7B2	.;RPF2_HUMAN	A	69;30;36	ENSP00000402338:T69A;ENSP00000357857:T30A;ENSP00000414026:T36A	ENSP00000357857:T30A	T	+	1	0	RPF2	111419653	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.912000	0.75753	2.101000	0.63845	0.379000	0.24179	ACA		0.214	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194		G	111312960	A	G	111312960	3	3	1	1	0	0	0	0	1	0	0	0	13584	391	14	4	219	4	RPF2	6	111312960	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	20594488	111312960	59802107	73	73										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127797201	127797201	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccacgttcctccgcagcagcTccgtctcgtcttccaccagc	7	20	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:127797201T>C	ENST00000525778.1	-	6	2715	c.1970A>G	c.(1969-1971)gAg>gGg	p.E657G	SOGA3_ENST00000465909.2_Missense_Mutation_p.E657G|SOGA3_ENST00000481848.2_Missense_Mutation_p.E657G|SOGA3_ENST00000368268.2_Missense_Mutation_p.E657G|SOGA3_ENST00000556132.1_Missense_Mutation_p.E657G|SOGA3_ENST00000474293.2_5'Flank			Q5TF21	SOGA3_HUMAN	SOGA family member 3	657					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CCGCAGCAGCTCCGTCTCGTC	0.642																																																0			6											51	57	55					6																	127797201		2188	4286	6474	127838894	SO:0001583	missense	387104			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1970A>G	6.37:g.127797201T>C	ENSP00000434570:p.Glu657Gly		127838894		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279154	0.80692	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.39406	1.08;1.08;1.08;1.09	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	M	0.77313	2.365	0.80722	D	1	D	0.61080	0.989	D	0.70935	0.971	T	0.63028	-0.6728	10	0.56958	D	0.05	-24.3048	15.1046	0.72310	0.0:0.0:0.0:1.0	.	657	Q5TF21	CF174_HUMAN	G	657	ENSP00000451768:E657G;ENSP00000357251:E657G;ENSP00000434570:E657G;ENSP00000435559:E657G	ENSP00000435559:E657G	E	-	2	0	C6orf174	127838894	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	7.994000	0.88315	1.979000	0.57680	0.459000	0.35465	GAG		0.642	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		C	127797201	T	C	127797201	3	2	1	1	0	0	0	0	1	0	0	0	2351	1551	54	4	881	4	C6orf174	6	127797201	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	16484241	127797201	43317866	74	74										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143090798	143090798	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttttttgcttggacctcagaAgagccagcgtggtcttggtg	13	8	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:143090798A>G	ENST00000367604.1	-	4	5717	c.5078T>C	c.(5077-5079)cTt>cCt	p.L1693P	HIVEP2_ENST00000367603.2_Missense_Mutation_p.L1693P|HIVEP2_ENST00000012134.2_Missense_Mutation_p.L1693P			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1693					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GGACCTCAGAAGAGCCAGCGT	0.473																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											0			6											148	137	141					6																	143090798		1889	4126	6015	143132491	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5078T>C	6.37:g.143090798A>G	ENSP00000356576:p.Leu1693Pro		143132491	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.576320	0.65878	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.12984	2.63;2.63;2.63	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.35307	0.0927	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.33879	-0.9851	10	0.87932	D	0	-21.3117	16.4025	0.83647	1.0:0.0:0.0:0.0	.	1693	P31629	ZEP2_HUMAN	P	1693	ENSP00000356576:L1693P;ENSP00000356575:L1693P;ENSP00000012134:L1693P	ENSP00000012134:L1693P	L	-	2	0	HIVEP2	143132491	1.000000	0.71417	0.999000	0.59377	0.908000	0.53690	9.261000	0.95576	2.268000	0.75426	0.533000	0.62120	CTT		0.473	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			G	143090798	A	G	143090798	3	3	1	1	0	0	0	0	1	0	0	0	7208	72	3	4	2286	4	HIVEP2	6	143090798	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	15293597	143090798	28024269	75	75										
ULBP3	79465	hgsc.bcm.edu	37	chr6	150386726	150386726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaagaggaggaacttccgtcCatcgaagctgaactgccaag	11	10	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:150386726C>T	ENST00000367339.2	-	3	464	c.436G>A	c.(436-438)Gga>Aga	p.G146R	ULBP3_ENST00000438272.2_Missense_Mutation_p.G146R			Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3	146	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)|viral process (GO:0016032)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			central_nervous_system(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	9		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)		AACTTCCGTCCATCGAAGCTG	0.532																																																0			6											140	130	133					6																	150386726		2203	4300	6503	150428419	SO:0001583	missense	79465			AF304379	CCDS5225.1	6q25	2008-04-11			ENSG00000131019	ENSG00000131019			14895	protein-coding gene	gene with protein product		605699				11239445, 11827464	Standard	NM_024518		Approved	RAET1N	uc003qns.3	Q9BZM4	OTTHUMG00000015811	ENST00000367339.2:c.436G>A	6.37:g.150386726C>T	ENSP00000356308:p.Gly146Arg		150428419	Q5VY82|Q8IZX5|Q8TE75	Missense_Mutation	SNP	ENST00000367339.2	37	CCDS5225.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.233739	0.39498	.	.	ENSG00000131019	ENST00000399812;ENST00000253335;ENST00000367339;ENST00000438272	T;T	0.02916	4.11;4.11	3.34	2.47	0.30058	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.06554	0.0168	M	0.82433	2.59	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.18272	-1.0342	9	0.87932	D	0	-4.1369	6.3937	0.21601	0.0:0.8626:0.0:0.1374	.	146;146	Q5VY82;Q9BZM4	.;N2DL3_HUMAN	R	97;146;146;146	ENSP00000356308:G146R;ENSP00000403562:G146R	ENSP00000253335:G146R	G	-	1	0	ULBP3	150428419	0.000000	0.05858	0.014000	0.15608	0.009000	0.06853	-0.039000	0.12124	0.970000	0.38263	0.491000	0.48974	GGA		0.532	ULBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042678.2			T	150386726	C	T	150386726	3	4	1	1	0	0	0	0	1	0	0	0	17014	603	21	3	305	3	ULBP3	6	150386726	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	7295928	150386726	20728341	76	76										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152461139	152461139	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atgtcagtgctgagttccagAcgctggagctgttccaactc	11	11	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:152461139A>G	ENST00000367255.5	-	140	26005	c.25404T>C	c.(25402-25404)cgT>cgC	p.R8468R	SYNE1_ENST00000423061.1_Silent_p.R8420R|SYNE1_ENST00000539504.1_Silent_p.R623R|SYNE1_ENST00000341594.5_Silent_p.R8080R|SYNE1_ENST00000265368.4_Silent_p.R8468R|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Silent_p.R8420R|SYNE1_ENST00000354674.4_Silent_p.R646R|SYNE1_ENST00000356820.4_Silent_p.R2992R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8468			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGAGTTCCAGACGCTGGAGCT	0.562										HNSCC(10;0.0054)																																						0			6											118	96	104					6																	152461139		2203	4300	6503	152502832	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25404T>C	6.37:g.152461139A>G			152502832	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.562	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152461139	A	G	152461139	2	3	1	1	0	0	0	0	0	0	0	1	15484	262	10	4		4	SYNE1	6	152461139	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	2074413	152461139	18653928	77	77										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152655269	152655269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agcacaggttgttagactgaCggcacaaatcgagccactga	11	10	0	3	rs140492158		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:152655269C>T	ENST00000367255.5	-	77	13269	c.12668G>A	c.(12667-12669)cGt>cAt	p.R4223H	SYNE1_ENST00000423061.1_Missense_Mutation_p.R4152H|SYNE1_ENST00000341594.5_Missense_Mutation_p.R4088H|SYNE1_ENST00000265368.4_Missense_Mutation_p.R4223H|SYNE1_ENST00000448038.1_Missense_Mutation_p.R4152H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4223			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R4223H(1)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTTAGACTGACGGCACAAATC	0.373										HNSCC(10;0.0054)			C|||	1	0.000199681	0	0	5008	,	,		16701	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	6						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	217	191	200		12455,12668	-0.9	0.5	6	dbSNP_134	200	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SYNE1	NM_033071.3,NM_182961.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	4152/8750,4223/8798	152655269	1,13005	2203	4300	6503	152696962	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12668G>A	6.37:g.152655269C>T	ENSP00000356224:p.Arg4223His		152696962	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	6.162	0.398168	0.11696	0.0	1.16E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	5.71	-0.854	0.10705	.	0.513023	0.17921	N	0.157481	T	0.04588	0.0125	N	0.04508	-0.205	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.0;0.0;0.001	T	0.27365	-1.0076	10	0.31617	T	0.26	.	3.2606	0.06848	0.483:0.2691:0.0609:0.187	.	4223;4223;4152	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	H	4223;4152;4223;4152;4088	ENSP00000356224:R4223H;ENSP00000396024:R4152H;ENSP00000265368:R4223H;ENSP00000390975:R4152H;ENSP00000341887:R4088H	ENSP00000265368:R4223H	R	-	2	0	SYNE1	152696962	0.769000	0.28531	0.527000	0.27925	0.214000	0.24535	1.310000	0.33551	-0.355000	0.08199	-2.290000	0.00267	CGT		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152655269	C	T	152655269	3	4	1	1	0	0	0	0	1	0	0	0	15484	536	19	1	14078	1	SYNE1	6	152655269	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	194130	152655269	18459798	78	78										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159460321	159460321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgagtagcaggaggttgggcCgggggagcttatctgcaacc	17	8	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr6:159460321C>T	ENST00000367066.3	-	8	939	c.608G>A	c.(607-609)cGg>cAg	p.R203Q	TAGAP_ENST00000338313.5_Missense_Mutation_p.R203Q|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.R25Q|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	203	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GAGGTTGGGCCGGGGGAGCTT	0.498																																																0			6											70	69	69					6																	159460321		2203	4300	6503	159380309	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.608G>A	6.37:g.159460321C>T	ENSP00000356033:p.Arg203Gln		159380309	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	c	9.642	1.139243	0.21205	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000338313	T;T;T	0.18810	2.19;2.19;2.19	5.87	-1.71	0.08133	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.556823	0.17586	N	0.168933	T	0.04679	0.0127	L	0.45285	1.41	0.09310	N	1	B;B	0.32753	0.232;0.383	B;B	0.23150	0.019;0.044	T	0.26224	-1.0109	10	0.51188	T	0.08	-2.5662	6.9761	0.24677	0.0:0.4524:0.3099:0.2377	.	203;203	Q8N103-4;Q8N103	.;TAGAP_HUMAN	Q	203;25;203	ENSP00000356033:R203Q;ENSP00000322650:R25Q;ENSP00000340217:R203Q	ENSP00000322650:R25Q	R	-	2	0	TAGAP	159380309	0.010000	0.17322	0.006000	0.13384	0.016000	0.09150	0.407000	0.21049	-0.328000	0.08539	-1.616000	0.00795	CGG		0.498	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159460321	C	T	159460321	3	4	1	1	0	0	0	0	1	0	0	0	15576	652	23	1	1617	1	TAGAP	6	159460321	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	6805052	159460321	11654746	79	79										
CARD11	84433	hgsc.bcm.edu	37	chr7	2984152	2984152	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttcatcaggaagtgcgtgagGccctcgtggccttcctccac	11	14	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:2984152G>A	ENST00000396946.4	-	5	781	c.378C>T	c.(376-378)ggC>ggT	p.G126G	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	126					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		AGTGCGTGAGGCCCTCGTGGC	0.622			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	0			7											59	55	56					7																	2984152		2203	4300	6503	2950678	SO:0001819	synonymous_variant	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.378C>T	7.37:g.2984152G>A			2950678	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																				0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2984152	G	A	2984152	2	1	1	1	0	0	0	0	0	0	0	1	2651	1190	42	3		3	CARD11	7	2984152	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10		2984152	156154511	80	80										
SDK1	221935	hgsc.bcm.edu	37	chr7	4088987	4088987	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgccctgccacagtgcccacCgcgcccccgcagaacgtgca	10	20	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:4088987C>T	ENST00000404826.2	+	18	2749	c.2610C>T	c.(2608-2610)acC>acT	p.T870T	SDK1_ENST00000389531.3_Silent_p.T870T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	870					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CAGTGCCCACCGCGCCCCCGC	0.572																																																0			7											57	53	54					7																	4088987		2203	4300	6503	4055513	SO:0001819	synonymous_variant	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2610C>T	7.37:g.4088987C>T			4055513	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.572	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4088987	C	T	4088987	2	4	1	1	0	0	0	0	0	0	0	1	14005	639	23	1		1	SDK1	7	4088987	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	1104835	4088987	155049676	81	81										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21675538	21675538	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtatgtagaatatttcattgAgcaagtgttaagctggcaaa	10	4	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:21675538A>G	ENST00000409508.3	+	26	4581	c.4550A>G	c.(4549-4551)gAg>gGg	p.E1517G	DNAH11_ENST00000328843.6_Missense_Mutation_p.E1522G|DNAH11_ENST00000465593.1_3'UTR	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1522	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TATTTCATTGAGCAAGTGTTA	0.348									Kartagener syndrome																																							0			7											58	55	56					7																	21675538		1841	4087	5928	21642063	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4550A>G	7.37:g.21675538A>G	ENSP00000475939:p.Glu1517Gly		21642063	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	A	15.30	2.793743	0.50102	.	.	ENSG00000105877	ENST00000328843	T	0.62941	-0.01	5.56	5.56	0.83823	Dynein heavy chain, domain-2 (1);	0.277370	0.32952	N	0.005449	T	0.56920	0.2018	.	.	.	0.42527	D	0.993028	P	0.35793	0.521	B	0.35182	0.197	T	0.60742	-0.7203	9	0.51188	T	0.08	.	14.6877	0.69062	1.0:0.0:0.0:0.0	.	1522	Q96DT5	DYH11_HUMAN	G	1522	ENSP00000330671:E1522G	ENSP00000330671:E1522G	E	+	2	0	DNAH11	21642063	0.998000	0.40836	0.981000	0.43875	0.844000	0.47949	2.570000	0.45981	2.098000	0.63641	0.528000	0.53228	GAG		0.348	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21675538	A	G	21675538	3	3	1	1	0	0	0	0	1	0	0	0	4610	304	11	4	4667	4	DNAH11	7	21675538	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	17586551	21675538	137463125	82	82										
MRPL32	64983	hgsc.bcm.edu	37	chr7	42972035	42972035	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttcgccgtggtctgcggcccGgggagtgcttcgaaactact	14	12	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:42972035G>C	ENST00000223324.2	+	1	237	c.50G>C	c.(49-51)cGg>cCg	p.R17P	PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	17				SPWSAARGVLRNYWERLLRKLPQSRPGFPSPPW -> RRGL RPGECFETTGSDCYGSFRRAGRAFPVLRGV (in Ref. 3). {ECO:0000305}.	translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						TCTGCGGCCCGGGGAGTGCTT	0.652																																																0			7											41	43	42					7																	42972035		2203	4300	6503	42938560	SO:0001583	missense	64983			AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"Mitochondrial ribosomal proteins / large subunits"	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.50G>C	7.37:g.42972035G>C	ENSP00000223324:p.Arg17Pro		42938560	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.995990	0.35226	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.7	1.78	0.24846	.	0.902335	0.09563	N	0.785302	T	0.32194	0.0821	L	0.48642	1.525	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.28332	-1.0047	9	0.36615	T	0.2	-2.4544	3.964	0.09423	0.1423:0.1316:0.5974:0.1287	.	17	Q9BYC8	RM32_HUMAN	P	17	.	ENSP00000223324:R17P	R	+	2	0	MRPL32	42938560	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.591000	0.23969	0.045000	0.15804	0.585000	0.79938	CGG		0.652	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903		C	42972035	G	C	42972035	3	2	1	1	0	0	0	0	1	0	0	0	9825	1116	39	5	52	5	MRPL32	7	42972035	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	21296497	42972035	116166628	83	83										
EGFR	1956	hgsc.bcm.edu	37	chr7	55268969	55268969	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agacatggacgacgtggtggAtgccgacgagtacctcatcc	13	11	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:55268969A>G	ENST00000275493.2	+	25	3212	c.3035A>G	c.(3034-3036)gAt>gGt	p.D1012G	EGFR_ENST00000454757.2_Missense_Mutation_p.D959G|EGFR_ENST00000455089.1_Missense_Mutation_p.D967G|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1012					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GACGTGGTGGATGCCGACGAG	0.547		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											162	146	152					7																	55268969		2203	4300	6503	55236463	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3035A>G	7.37:g.55268969A>G	ENSP00000275493:p.Asp1012Gly		55236463	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838817	0.91117	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.76839	-1.04;-1.05;-1.04	5.65	5.65	0.86999	Protein kinase-like domain (1);	0.042476	0.85682	D	0.000000	D	0.89529	0.6741	M	0.88241	2.94	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.988;0.995	D	0.91207	0.4996	10	0.66056	D	0.02	.	15.0093	0.71539	1.0:0.0:0.0:0.0	.	967;1012	Q504U8;P00533	.;EGFR_HUMAN	G	967;882;1012;959	ENSP00000415559:D967G;ENSP00000275493:D1012G;ENSP00000395243:D959G	ENSP00000275493:D1012G	D	+	2	0	EGFR	55236463	1.000000	0.71417	0.532000	0.27989	0.969000	0.65631	9.192000	0.94947	2.281000	0.76405	0.528000	0.53228	GAT		0.547	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55268969	A	G	55268969	3	3	1	1	0	0	0	0	1	0	0	0	4978	333	12	4	3397	4	EGFR	7	55268969	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	12296934	55268969	103869694	84	84										
RSBN1L	222194	hgsc.bcm.edu	37	chr7	77408253	77408253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggaagaacctgtgaatgttaAtattcctgaaaagactacag	9	6	0	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:77408253A>G	ENST00000334955.8	+	8	2336	c.2309A>G	c.(2308-2310)aAt>aGt	p.N770S	RSBN1L_ENST00000445288.1_Missense_Mutation_p.N500S	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	770						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTGAATGTTAATATTCCTGAA	0.308																																																0			7											66	63	64					7																	77408253		1833	4082	5915	77246189	SO:0001583	missense	222194			AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.2309A>G	7.37:g.77408253A>G	ENSP00000334040:p.Asn770Ser		77246189	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	A	3.416	-0.119113	0.06838	.	.	ENSG00000187257	ENST00000334955;ENST00000445288	.	.	.	5.84	-1.03	0.10102	.	0.651240	0.15720	N	0.247966	T	0.20007	0.0481	N	0.16478	0.41	0.20403	N	0.999907	B	0.06786	0.001	B	0.04013	0.001	T	0.20874	-1.0262	9	0.16896	T	0.51	-0.0225	6.2127	0.20638	0.5177:0.2885:0.1937:0.0	.	770	Q6PCB5	RSBNL_HUMAN	S	770;500	.	ENSP00000334040:N770S	N	+	2	0	RSBN1L	77246189	0.543000	0.26434	0.074000	0.20217	0.971000	0.66376	1.206000	0.32321	-0.157000	0.11059	-0.389000	0.06534	AAT		0.308	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		G	77408253	A	G	77408253	3	3	1	1	0	0	0	0	1	0	0	0	13734	101	4	4	2339	4	RSBN1L	7	77408253	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	22139284	77408253	81730410	85	85										
FEZF1	389549	hgsc.bcm.edu	37	chr7	121943236	121943236	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gacagatgaacacacctgcgTgtgaatgatcttgtgcctgc	11	10	1	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:121943236T>C	ENST00000442488.2	-	2	998	c.931A>G	c.(931-933)Acg>Gcg	p.T311A	FEZF1_ENST00000427185.2_Missense_Mutation_p.T261A|FEZF1-AS1_ENST00000428449.1_RNA|FEZF1_ENST00000331178.4_Missense_Mutation_p.T307A|FEZF1-AS1_ENST00000437317.1_RNA	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	311					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						CACACCTGCGTGTGAATGATC	0.463																																																0			7											143	136	139					7																	121943236		2203	4300	6503	121730472	SO:0001583	missense	389549			AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"Zinc fingers, C2H2-type"	22788	protein-coding gene	gene with protein product		613301	"zinc finger protein 312B"	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.931A>G	7.37:g.121943236T>C	ENSP00000411145:p.Thr311Ala		121730472	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878317	0.91740	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.26518	1.73;1.73;1.73	5.23	5.23	0.72850	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.76494	0.999;0.998	D;D	0.85130	0.997;0.994	T	0.49532	-0.8930	10	0.87932	D	0	-18.979	15.4555	0.75311	0.0:0.0:0.0:1.0	.	311;261	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	A	311;307;261	ENSP00000411145:T311A;ENSP00000332777:T307A;ENSP00000392727:T261A	ENSP00000332777:T307A	T	-	1	0	FEZF1	121730472	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.953000	0.87836	2.103000	0.63969	0.529000	0.55759	ACG		0.463	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613		C	121943236	T	C	121943236	3	2	1	1	0	0	0	0	1	0	0	0	5844	1696	59	4	508	4	FEZF1	7	121943236	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	44534983	121943236	37195427	86	86										
SMO	6608	hgsc.bcm.edu	37	chr7	128850334	128850334	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttggaactggcatcgccatgAgcacctgggtctggaccaag	13	11	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:128850334A>G	ENST00000249373.3	+	9	1877	c.1597A>G	c.(1597-1599)Agc>Ggc	p.S533G	RP11-286H14.8_ENST00000466717.1_RNA	NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	533					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CATCGCCATGAGCACCTGGGT	0.617			Mis		skin basal cell						OREG0018305	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	0			7											126	109	115					7																	128850334		2203	4300	6503	128637570	SO:0001583	missense	54498			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1597A>G	7.37:g.128850334A>G	ENSP00000249373:p.Ser533Gly	1568	128637570	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	37	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.223080	0.79464	.	.	ENSG00000128602	ENST00000249373	D	0.81579	-1.51	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.83436	0.5254	L	0.31752	0.955	0.80722	D	1	D;D	0.63046	0.992;0.992	D;D	0.76071	0.987;0.987	T	0.81861	-0.0738	10	0.29301	T	0.29	.	15.2066	0.73183	1.0:0.0:0.0:0.0	.	533;533	A4D1K5;Q99835	.;SMO_HUMAN	G	533	ENSP00000249373:S533G	ENSP00000249373:S533G	S	+	1	0	SMO	128637570	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.031000	0.93731	2.199000	0.70637	0.418000	0.28097	AGC		0.617	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		G	128850334	A	G	128850334	3	3	1	1	0	0	0	0	1	0	0	0	14837	304	11	4	1631	4	SMO	7	128850334	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	6907098	128850334	30288329	87	87										
PODXL	5420	hgsc.bcm.edu	37	chr7	131189266	131189266	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gcagctcctctgttagccgcTgctagagtggggaaggtgac	15	10	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:131189266T>C	ENST00000378555.3	-	9	1728	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R	PODXL_ENST00000322985.9_Splice_Site_p.Q462R|PODXL_ENST00000541194.1_Splice_Site_p.Q496R|PODXL_ENST00000537928.1_Splice_Site_p.Q462R			O00592	PODXL_HUMAN	podocalyxin-like	494					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TGTTAGCCGCTGCTAGAGTGG	0.547																																																0			7											107	96	100					7																	131189266		2203	4300	6503	130839806	SO:0001630	splice_region_variant	5420				CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1480-1A>G	7.37:g.131189266T>C			130839806	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.950193	0.73787	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.49847	0.1581	M	0.72118	2.19	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.53143	-0.8480	10	0.87932	D	0	-26.2341	13.2059	0.59795	0.0:0.0:0.0:1.0	.	462;494	O00592-2;O00592	.;PODXL_HUMAN	R	496;462;452;494;462	ENSP00000440518:Q496R;ENSP00000442655:Q462R;ENSP00000367817:Q494R;ENSP00000319782:Q462R	ENSP00000319782:Q462R	Q	-	2	0	PODXL	130839806	1.000000	0.71417	1.000000	0.80357	0.413000	0.31143	5.901000	0.69861	2.060000	0.61445	0.454000	0.30748	CAG		0.547	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	Missense_Mutation	C	131189266	T	C	131189266	5	2	1	1	0	0	0	0	0	0	1	0	12211	1594	55	4	199	4	PODXL	7	131189266	Splice_Site	SNP	T	TCGA-AF-2687-01A-02D-1733-10	2338932	131189266	27949397	88	88										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143096856	143096856	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgcatgcggggtgcacctgaGggcctggggctggcccgcgc	19	13	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:143096856G>A	ENST00000275815.3	-	4	809	c.723C>T	c.(721-723)ccC>ccT	p.P241P		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	241	Cys-rich.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GTGCACCTGAGGGCCTGGGGC	0.677																																																0			7											28	29	29					7																	143096856		2203	4300	6503	142806978	SO:0001819	synonymous_variant	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.723C>T	7.37:g.143096856G>A			142806978	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																				0.677	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143096856	G	A	143096856	2	1	1	1	0	0	0	0	0	0	0	1	5178	987	35	3		3	EPHA1	7	143096856	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	11907590	143096856	16041807	89	89										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154876013	154876013	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cattggcgtgttcgtgctctGctggatccccttctttctca	9	13	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr7:154876013G>T	ENST00000287907.2	+	2	1466	c.890G>T	c.(889-891)tGc>tTc	p.C297F	HTR5A_ENST00000486819.1_3'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	297					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	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)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TTCGTGCTCTGCTGGATCCCC	0.612																																																0			7											232	187	202					7																	154876013		2203	4300	6503	154506946	SO:0001583	missense	3361				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.890G>T	7.37:g.154876013G>T	ENSP00000287907:p.Cys297Phe		154506946	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294084	0.81025	.	.	ENSG00000157219	ENST00000287907	T	0.52295	0.67	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.79493	0.4455	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86965	0.2094	10	0.87932	D	0	.	18.1526	0.89679	0.0:0.0:1.0:0.0	.	297	P47898	5HT5A_HUMAN	F	297	ENSP00000287907:C297F	ENSP00000287907:C297F	C	+	2	0	HTR5A	154506946	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	9.438000	0.97539	2.274000	0.75844	0.655000	0.94253	TGC		0.612	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154876013	G	T	154876013	3	4	1	1	0	0	0	0	1	0	0	0	7471	1319	46	2	896	2	HTR5A	7	154876013	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	11779157	154876013	4262650	90	90										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885717	88885717	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aagctacctatgaacagcgaCgctgggagcagcacggcaca	12	12	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr8:88885717C>T	ENST00000319675.3	-	1	579	c.483G>A	c.(481-483)gcG>gcA	p.A161A		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	161								p.A161A(2)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TGAACAGCGACGCTGGGAGCA	0.567																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	8											101	94	96					8																	88885717		2203	4300	6503	88954833	SO:0001819	synonymous_variant	0			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.483G>A	8.37:g.88885717C>T			88954833		Silent	SNP	ENST00000319675.3	37	CCDS6245.1																																																																																				0.567	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		T	88885717	C	T	88885717	2	4	1	1	0	0	0	0	0	0	0	1	4278	523	19	1		1	DCAF4L2	8	88885717	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10		88885717	57478305	91	91										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885751	88885751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cggcacagcttggagtatctGcaagtcccacgaagcacagc	11	13	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr8:88885751G>A	ENST00000319675.3	-	1	545	c.449C>T	c.(448-450)gCa>gTa	p.A150V		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	150										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TGGAGTATCTGCAAGTCCCAC	0.542																																																0			8											95	89	91					8																	88885751		2203	4300	6503	88954867	SO:0001583	missense	0			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.449C>T	8.37:g.88885751G>A	ENSP00000316496:p.Ala150Val		88954867		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.659387	0.29515	.	.	ENSG00000176566	ENST00000319675	T	0.70631	-0.5	1.68	0.726	0.18248	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.098022	0.64402	D	0.000001	T	0.68155	0.2970	M	0.63843	1.955	0.33247	D	0.557971	P	0.41498	0.752	P	0.48770	0.589	T	0.72121	-0.4386	10	0.66056	D	0.02	.	3.4871	0.07624	0.2692:0.0:0.7308:0.0	.	150	Q8NA75	DC4L2_HUMAN	V	150	ENSP00000316496:A150V	ENSP00000316496:A150V	A	-	2	0	DCAF4L2	88954867	1.000000	0.71417	0.018000	0.16275	0.030000	0.12068	3.432000	0.52824	0.922000	0.37019	0.467000	0.42956	GCA		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885751	G	A	88885751	3	1	1	1	0	0	0	0	1	0	0	0	4278	1319	46	3	742	3	DCAF4L2	8	88885751	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	34	88885751	57478271	92	92										
NUDCD1	84955	hgsc.bcm.edu	37	chr8	110293376	110293376	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gttactgtcaaatcatcttcAgtctgttgccagtaatacag	7	9	5	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr8:110293376A>G	ENST00000239690.4	-	6	1223	c.849T>C	c.(847-849)acT>acC	p.T283T	NUDCD1_ENST00000427660.2_Silent_p.T254T	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			AATCATCTTCAGTCTGTTGCC	0.358																																																0			8											111	100	104					8																	110293376		2203	4300	6503	110362552	SO:0001819	synonymous_variant	84955			AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.849T>C	8.37:g.110293376A>G			110362552		Silent	SNP	ENST00000239690.4	37	CCDS6312.1																																																																																				0.358	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		G	110293376	A	G	110293376	2	3	1	1	0	0	0	0	0	0	0	1	10753	175	7	4		4	NUDCD1	8	110293376	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	21407625	110293376	36070646	93	93										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133187813	133187813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtagacaagaaatgaagaaaGgatgagtgtcaggaaaccga	13	4	1	5			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr8:133187813G>A	ENST00000388996.4	-	5	1240	c.820C>T	c.(820-822)Ctt>Ttt	p.L274F	KCNQ3_ENST00000521134.1_Missense_Mutation_p.L154F|KCNQ3_ENST00000519445.1_Missense_Mutation_p.L274F	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	274					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	AATGAAGAAAGGATGAGTGTC	0.488																																																0			8											114	110	111					8																	133187813		2203	4300	6503	133256995	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.820C>T	8.37:g.133187813G>A	ENSP00000373648:p.Leu274Phe		133256995	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765315	0.31228	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.97279	-4.32;-4.32;-4.32	5.39	3.61	0.41365	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.93697	0.7986	N	0.17674	0.51	0.46437	D	0.999049	D;D	0.52996	0.957;0.957	P;P	0.53490	0.727;0.727	D	0.90538	0.4500	10	0.02654	T	1	-15.3411	10.4712	0.44638	0.2194:0.0:0.7806:0.0	.	274;274	E7ET42;O43525	.;KCNQ3_HUMAN	F	274;154;274;263;153	ENSP00000373648:L274F;ENSP00000429799:L154F;ENSP00000428790:L274F	ENSP00000373648:L274F	L	-	1	0	KCNQ3	133256995	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	4.198000	0.58419	0.762000	0.33152	-0.140000	0.14226	CTT		0.488	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133187813	G	A	133187813	3	1	1	1	0	0	0	0	1	0	0	0	8105	1000	35	3	1842	3	KCNQ3	8	133187813	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	22894437	133187813	13176209	94	94										
KCNK9	51305	hgsc.bcm.edu	37	chr8	140630763	140630763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	actgcaggtccgggacgtccGccttgtacctgggccggctg	15	14	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr8:140630763G>A	ENST00000520439.1	-	2	926	c.863C>T	c.(862-864)gCg>gTg	p.A288V	KCNK9_ENST00000303015.1_Missense_Mutation_p.A288V|KCNK9_ENST00000523477.1_5'Flank	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	288					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A288V(1)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGGGACGTCCGCCTTGTACCT	0.667																																																1	Substitution - Missense(1)	ovary(1)	8											48	53	51					8																	140630763		2203	4300	6503	140699945	SO:0001583	missense	51305			AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.863C>T	8.37:g.140630763G>A	ENSP00000430676:p.Ala288Val		140699945	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	37	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676779	0.47886	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.17528	2.27;2.27;2.27	5.53	3.67	0.42095	.	1.078660	0.07116	N	0.843000	T	0.22282	0.0537	M	0.63843	1.955	0.26385	N	0.976664	B	0.26876	0.162	B	0.25759	0.063	T	0.42258	-0.9462	10	0.15066	T	0.55	.	14.9469	0.71039	0.0:0.2816:0.7184:0.0	.	288	Q9NPC2	KCNK9_HUMAN	V	288	ENSP00000429847:A288V;ENSP00000302166:A288V;ENSP00000430676:A288V	ENSP00000302166:A288V	A	-	2	0	KCNK9	140699945	0.997000	0.39634	0.905000	0.35620	0.886000	0.51366	3.277000	0.51654	0.624000	0.30286	0.591000	0.81541	GCG		0.667	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		A	140630763	G	A	140630763	3	1	1	1	0	0	0	0	1	0	0	0	8093	1087	38	1	265	1	KCNK9	8	140630763	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	7442950	140630763	5733259	95	95										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6015511	6015511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttcctctgcttgcctccgcaCcatacagcttggattgatca	7	14	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:6015511C>T	ENST00000259569.5	-	1	107	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	RANBP6_ENST00000485372.1_5'UTR	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	33					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TGCCTCCGCACCATACAGCTT	0.502																																																0			9											80	86	84					9																	6015511		2203	4300	6503	6005511	SO:0001583	missense	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.97G>A	9.37:g.6015511C>T	ENSP00000259569:p.Val33Met		6005511	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	37	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.119300	0.56505	.	.	ENSG00000137040	ENST00000259569	T	0.73258	-0.73	4.54	3.64	0.41730	Armadillo-like helical (1);Armadillo-type fold (1);	0.146513	0.45606	D	0.000359	T	0.72795	0.3505	L	0.55481	1.735	0.45899	D	0.99874	P	0.48640	0.913	P	0.52514	0.701	T	0.73600	-0.3931	10	0.48119	T	0.1	-3.4988	11.0944	0.48134	0.0:0.9087:0.0:0.0913	.	33	O60518	RNBP6_HUMAN	M	33	ENSP00000259569:V33M	ENSP00000259569:V33M	V	-	1	0	RANBP6	6005511	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.048000	0.49862	1.515000	0.48885	0.561000	0.74099	GTG		0.502	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		T	6015511	C	T	6015511	3	4	1	1	0	0	0	0	1	0	0	0	13068	507	18	3	3224	3	RANBP6	9	6015511	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10		6015511	135197920	96	96										
GNA14	9630	hgsc.bcm.edu	37	chr9	80039058	80039058	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaagcttcaggataaagtctCtggcagctctgacatcctgt	9	10	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:80039058C>T	ENST00000341700.6	-	7	1418	c.905G>A	c.(904-906)aGa>aAa	p.R302K	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	302					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R302K(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						GATAAAGTCTCTGGCAGCTCT	0.408																																																1	Substitution - Missense(1)	ovary(1)	9											141	133	136					9																	80039058		2203	4300	6503	79228878	SO:0001583	missense	9630			AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.905G>A	9.37:g.80039058C>T	ENSP00000365807:p.Arg302Lys		79228878	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.251015	0.39797	.	.	ENSG00000156049	ENST00000341700	D	0.87809	-2.3	6.07	6.07	0.98685	.	0.090958	0.85682	D	0.000000	T	0.79046	0.4380	N	0.17838	0.53	0.33830	D	0.630088	B	0.06786	0.001	B	0.15870	0.014	T	0.77443	-0.2586	10	0.30854	T	0.27	.	14.418	0.67163	0.0:0.9293:0.0:0.0707	.	302	O95837	GNA14_HUMAN	K	302	ENSP00000365807:R302K	ENSP00000365807:R302K	R	-	2	0	GNA14	79228878	0.439000	0.25610	1.000000	0.80357	0.997000	0.91878	0.864000	0.27926	2.884000	0.98904	0.655000	0.94253	AGA		0.408	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			T	80039058	C	T	80039058	3	4	1	1	0	0	0	0	1	0	0	0	6522	913	32	3	166	3	GNA14	9	80039058	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	74023547	80039058	61174373	97	97										
SLC28A3	64078	hgsc.bcm.edu	37	chr9	86903016	86903016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	attttaggtttttctgtctcAggccaaaagagtttagcagc	9	7	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:86903016A>G	ENST00000376238.4	-	12	1276	c.1227T>C	c.(1225-1227)ccT>ccC	p.P409P	SLC28A3_ENST00000537648.1_Silent_p.P340P|RP11-380F14.2_ENST00000419815.1_RNA	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	409					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	TTTCTGTCTCAGGCCAAAAGA	0.453																																					Ovarian(106;425 1539 34835 42413 43572)											0			9											155	160	158					9																	86903016		2203	4300	6503	86092836	SO:0001819	synonymous_variant	64078			AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1227T>C	9.37:g.86903016A>G			86092836	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Silent	SNP	ENST00000376238.4	37	CCDS6670.1																																																																																				0.453	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		G	86903016	A	G	86903016	2	3	1	1	0	0	0	0	0	0	0	1	14570	175	7	4		4	SLC28A3	9	86903016	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	6863958	86903016	54310415	98	98										
ECM2	1842	hgsc.bcm.edu	37	chr9	95285114	95285114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agtcagtttgaaaaatgataAgcagaaaaaaacaaaacaaa	6	4	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:95285114A>G	ENST00000344604.5	-	2	184	c.35T>C	c.(34-36)cTt>cCt	p.L12P	ECM2_ENST00000375540.1_Missense_Mutation_p.L12P|CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Missense_Mutation_p.L12P	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	12					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						AAAAATGATAAGCAGAAAAAA	0.333																																																0			9											46	49	48					9																	95285114		2202	4300	6502	94324935	SO:0001583	missense	1842			AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"matrix glycoprotein SC1/ECM2"	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.35T>C	9.37:g.95285114A>G	ENSP00000344758:p.Leu12Pro		94324935	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729281	0.69074	.	.	ENSG00000106823	ENST00000444490;ENST00000344604;ENST00000375540;ENST00000395534	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.28	4.28	0.50868	.	0.303544	0.27340	N	0.019818	T	0.42063	0.1186	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.76494	0.998;0.998;0.997;0.999	D;P;P;D	0.66351	0.909;0.831;0.831;0.943	T	0.39800	-0.9596	10	0.87932	D	0	.	13.5504	0.61728	1.0:0.0:0.0:0.0	.	12;12;12;12	Q5T9F3;O94769;B4DK93;O94769-2	.;ECM2_HUMAN;.;.	P	12	ENSP00000393971:L12P;ENSP00000344758:L12P;ENSP00000364690:L12P;ENSP00000378905:L12P	ENSP00000344758:L12P	L	-	2	0	ECM2	94324935	1.000000	0.71417	0.602000	0.28890	0.943000	0.58893	5.725000	0.68507	1.948000	0.56530	0.528000	0.53228	CTT		0.333	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		G	95285114	A	G	95285114	3	3	1	1	0	0	0	0	1	0	0	0	4909	72	3	4	2100	4	ECM2	9	95285114	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	8382098	95285114	45928317	99	99										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98211430	98211430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctcccgcgccctgctgggccTcgtagtgccgaagctcctcg	12	18	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:98211430T>C	ENST00000331920.6	-	22	4024	c.3725A>G	c.(3724-3726)gAg>gGg	p.E1242G	PTCH1_ENST00000418258.1_Missense_Mutation_p.E1091G|PTCH1_ENST00000429896.2_Missense_Mutation_p.E1091G|PTCH1_ENST00000375274.2_Missense_Mutation_p.E1241G|PTCH1_ENST00000421141.1_Missense_Mutation_p.E1091G|PTCH1_ENST00000437951.1_Missense_Mutation_p.E1176G|PTCH1_ENST00000430669.2_Missense_Mutation_p.E1176G	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1242			E -> K (in squamous cell carcinoma). {ECO:0000269|PubMed:11286632}.		brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CTGCTGGGCCTCGTAGTGCCG	0.627																																																0			9											28	29	28					9																	98211430		2203	4300	6503	97251251	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.3725A>G	9.37:g.98211430T>C	ENSP00000332353:p.Glu1242Gly		97251251	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251085	0.22880	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000375284;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.90844	-2.74;-2.73;-2.72;-2.72;-2.73;-2.72;-2.74	5.89	4.76	0.60689	.	0.413534	0.29239	N	0.012727	D	0.87059	0.6083	L	0.51422	1.61	0.36425	D	0.864542	B;B;B	0.25904	0.034;0.137;0.085	B;B;B	0.25140	0.025;0.058;0.026	D	0.87463	0.2409	10	0.49607	T	0.09	-18.1029	11.3938	0.49830	0.0:0.0702:0.0:0.9297	.	1176;1241;1242	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	G	1242;1176;1091;1091;1176;34;1091;1241	ENSP00000332353:E1242G;ENSP00000389744:E1176G;ENSP00000399981:E1091G;ENSP00000396135:E1091G;ENSP00000410287:E1176G;ENSP00000414823:E1091G;ENSP00000364423:E1241G	ENSP00000332353:E1242G	E	-	2	0	PTCH1	97251251	1.000000	0.71417	0.591000	0.28745	0.111000	0.19643	3.222000	0.51223	2.250000	0.74265	0.533000	0.62120	GAG		0.627	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98211430	T	C	98211430	3	2	1	1	0	0	0	0	1	0	0	0	12764	1551	54	4	626	4	PTCH1	9	98211430	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	2926316	98211430	43002001	100	100										
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670815	131670815	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcaagctggagctgatccccGacgtgaccatcccgcccagc	10	17	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:131670815G>T	ENST00000259324.5	+	3	1895	c.1372G>T	c.(1372-1374)Gac>Tac	p.D458Y	LRRC8A_ENST00000372599.3_Missense_Mutation_p.D458Y|LRRC8A_ENST00000372600.4_Missense_Mutation_p.D458Y	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	458					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						GCTGATCCCCGACGTGACCAT	0.622																																																0			9											24	23	24					9																	131670815		2203	4297	6500	130710636	SO:0001583	missense	56262			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1372G>T	9.37:g.131670815G>T	ENSP00000259324:p.Asp458Tyr		130710636	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.224303	0.58668	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.23950	1.88;1.88;1.88	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.42131	0.1189	L	0.35723	1.085	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.06752	-1.0809	10	0.34782	T	0.22	.	18.4034	0.90525	0.0:0.0:1.0:0.0	.	458	Q8IWT6	LRC8A_HUMAN	Y	458	ENSP00000361682:D458Y;ENSP00000361680:D458Y;ENSP00000259324:D458Y	ENSP00000259324:D458Y	D	+	1	0	LRRC8A	130710636	1.000000	0.71417	0.943000	0.38184	0.900000	0.52787	9.869000	0.99810	2.595000	0.87683	0.561000	0.74099	GAC		0.622	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131670815	G	T	131670815	3	4	1	1	0	0	0	0	1	0	0	0	9050	1058	37	2	1374	2	LRRC8A	9	131670815	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	33459385	131670815	9542616	101	101										
BRD3	8019	hgsc.bcm.edu	37	chr9	136905313	136905313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cttcttcttcttctccttctCcttcttctccttcttcttct	0	17	10	0	rs202054855		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:136905313C>T	ENST00000303407.7	-	9	1671	c.1486G>A	c.(1486-1488)Gag>Aag	p.E496K	BRD3_ENST00000357885.2_Missense_Mutation_p.E496K|BRD3_ENST00000371834.2_Missense_Mutation_p.E496K|BRD3_ENST00000473349.1_Intron	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	496	Lys-rich.				chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		ttctccttctccttcttctcc	0.557			T	C15orf55	lethal midline carcinoma of young people																																		Dom	yes		9	9q34	8019	bromodomain containing 3		E	0			9											54	36	42					9																	136905313		2196	4294	6490	135895134	SO:0001583	missense	8019				CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"RING3-like"	601541	"bromodomain-containing 3"			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.1486G>A	9.37:g.136905313C>T	ENSP00000305918:p.Glu496Lys		135895134	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Missense_Mutation	SNP	ENST00000303407.7	37	CCDS6980.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.286555	0.40494	.	.	ENSG00000169925	ENST00000303407;ENST00000540795;ENST00000371834;ENST00000357885	T;T;T	0.32753	1.44;1.44;1.44	4.71	3.81	0.43845	.	0.317725	0.27764	N	0.017941	T	0.10252	0.0251	N	0.01168	-0.975	0.48395	D	0.999644	P;B	0.37330	0.59;0.319	B;B	0.38500	0.275;0.023	T	0.23511	-1.0186	10	0.02654	T	1	-9.7665	12.1789	0.54202	0.0:0.9156:0.0:0.0844	.	496;496	Q15059-2;Q15059	.;BRD3_HUMAN	K	496;175;496;496	ENSP00000305918:E496K;ENSP00000360900:E496K;ENSP00000350557:E496K	ENSP00000305918:E496K	E	-	1	0	BRD3	135895134	1.000000	0.71417	0.981000	0.43875	0.958000	0.62258	7.482000	0.81143	1.099000	0.41499	0.561000	0.74099	GAG		0.557	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371		T	136905313	C	T	136905313	3	4	1	1	0	0	0	0	1	0	0	0	1506	864	30	3	710	3	BRD3	9	136905313	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	5234498	136905313	4308118	102	102										
TUBB2C	10383	hgsc.bcm.edu	37	chr9	140137892	140137892	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agggcatggacgagatggagTtcaccgaggccgagagcaac	16	9	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr9:140137892T>C	ENST00000340384.4	+	4	1370	c.1222T>C	c.(1222-1224)Ttc>Ctc	p.F408L		NM_006088.5	NP_006079.1	P68371	TBB4B_HUMAN	tubulin, beta 4B class IVb	408					'de novo' posttranslational protein folding (GO:0051084)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|unfolded protein binding (GO:0051082)	p.F408I(1)								Albendazole(DB00518)|Mebendazole(DB00643)	CGAGATGGAGTTCACCGAGGC	0.617																																																1	Substitution - Missense(1)	ovary(1)	9											101	98	99					9																	140137892		2203	4297	6500	139257713	SO:0001583	missense	10383			BC019359	CCDS7039.1	9q34.3	2011-10-10	2011-10-10	2011-10-10	ENSG00000188229	ENSG00000188229		"Tubulins"	20771	protein-coding gene	gene with protein product	"class IVb beta-tubulin"	602660	"tubulin, beta 2C"	TUBB2C		3999141	Standard	NM_006088		Approved	Beta2	uc004cmh.1	P68371	OTTHUMG00000131783	ENST00000340384.4:c.1222T>C	9.37:g.140137892T>C	ENSP00000341289:p.Phe408Leu		139257713	A2BFA2|P05217	Missense_Mutation	SNP	ENST00000340384.4	37	CCDS7039.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852037	0.71719	.	.	ENSG00000188229	ENST00000340384	D	0.86694	-2.16	5.57	5.57	0.84162	.	0.062592	0.64402	N	0.000006	D	0.94857	0.8338	M	0.92691	3.335	0.58432	D	0.999998	D	0.71674	0.998	D	0.85130	0.997	D	0.95892	0.8908	10	0.87932	D	0	.	14.5794	0.68274	0.0:0.0:0.0:1.0	.	408	P68371	TBB4B_HUMAN	L	408	ENSP00000341289:F408L	ENSP00000341289:F408L	F	+	1	0	TUBB2C	139257713	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.152000	0.71812	2.122000	0.65172	0.533000	0.62120	TTC		0.617	TUBB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254715.1	NM_006088		C	140137892	T	C	140137892	3	2	1	1	0	0	0	0	1	0	0	0	16796	1725	60	4	1236	4	TUBB2C	9	140137892	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	3232579	140137892	1075539	103	103										
WDR37	22884	hgsc.bcm.edu	37	chr10	1130478	1130478	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgctcgggactgcatcagccGgtgagtcgcacacggacctg	14	13	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:1130478G>A	ENST00000358220.1	+	6	676	c.532G>A	c.(532-534)Gat>Aat	p.D178N	WDR37_ENST00000263150.4_Splice_Site_p.D178N|WDR37_ENST00000381329.1_Splice_Site_p.D178N			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	178										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		TGCATCAGCCGGTGAGTCGCA	0.602																																																0			10											60	55	57					10																	1130478		2203	4300	6503	1120478	SO:0001630	splice_region_variant	22884			AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.532+1G>A	10.37:g.1130478G>A			1120478	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	37	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420664	0.83559	.	.	ENSG00000047056	ENST00000358220;ENST00000381329;ENST00000263150;ENST00000436154	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	H	0.98849	4.35	0.80722	D	1	D;D;D	0.89917	0.996;0.999;1.0	P;P;D	0.69142	0.767;0.845;0.962	D	0.98294	1.0515	10	0.72032	D	0.01	.	19.4706	0.94962	0.0:0.0:1.0:0.0	.	178;178;178	A8K976;Q9Y2I8;E7EQ49	.;WDR37_HUMAN;.	N	178;178;178;145	ENSP00000350954:D178N;ENSP00000370730:D178N;ENSP00000263150:D178N;ENSP00000404346:D145N	ENSP00000263150:D178N	D	+	1	0	WDR37	1120478	1.000000	0.71417	0.999000	0.59377	0.031000	0.12232	8.991000	0.93514	2.689000	0.91719	0.650000	0.86243	GAT		0.602	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023	Missense_Mutation	A	1130478	G	A	1130478	5	1	1	1	0	0	0	0	0	0	1	0	17331	1130	39	1	550	1	WDR37	10	1130478	Splice_Site	SNP	G	TCGA-AF-2687-01A-02D-1733-10		1130478	134404269	104	104										
RET	5979	hgsc.bcm.edu	37	chr10	43623706	43623706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cggcaaaattaatggacacgTttgatagttaacatttcttt	7	6	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:43623706T>C	ENST00000355710.3	+	20	3566	c.3334T>C	c.(3334-3336)Ttt>Ctt	p.F1112L		NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	1112			F -> Y (in a bladder transitional cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AATGGACACGTTTGATAGTTA	0.423		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	0			10											120	108	112					10																	43623706		2203	4300	6503	42943712	SO:0001583	missense	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.3334T>C	10.37:g.43623706T>C	ENSP00000347942:p.Phe1112Leu		42943712	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.818388	0.32145	.	.	ENSG00000165731	ENST00000355710	T	0.75589	-0.95	5.72	4.58	0.56647	.	0.221862	0.48767	D	0.000179	T	0.59918	0.2229	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.52373	-0.8584	10	0.32370	T	0.25	.	13.1087	0.59261	0.0:0.0:0.1339:0.8661	.	1112	P07949	RET_HUMAN	L	1112	ENSP00000347942:F1112L	ENSP00000347942:F1112L	F	+	1	0	RET	42943712	1.000000	0.71417	0.971000	0.41717	0.991000	0.79684	1.735000	0.38176	0.984000	0.38629	-0.418000	0.06021	TTT		0.423	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		C	43623706	T	C	43623706	3	2	1	1	0	0	0	0	1	0	0	0	13272	1725	60	4	3444	4	RET	10	43623706	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	42493228	43623706	91911041	105	105										
AGAP4	119016	hgsc.bcm.edu	37	chr10	46321476	46321476	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtgggcatctcgggccatgaCgtccaccccgtaccagatca	11	15	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:46321476C>T	ENST00000448048.2	-	7	2004	c.1879G>A	c.(1879-1881)Gtc>Atc	p.V627I	AGAP4_ENST00000430779.2_5'Flank	NM_133446.2	NP_597703.2	Q96P64	AGAP4_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	627					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.V627I(1)		central_nervous_system(1)|lung(1)|ovary(1)	3						CGGGCCATGACGTCCACCCCG	0.672																																																1	Substitution - Missense(1)	ovary(1)	10											1	1	1					10																	46321476		214	382	596	45641482	SO:0001583	missense	119016			AF411132	CCDS7215.1	10q11.21	2014-06-19	2008-09-22	2008-09-22	ENSG00000188234	ENSG00000188234		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	23459	protein-coding gene	gene with protein product			"centaurin, gamma-like family, member 1", "ArfGAP with GTPase domain, ankyrin repeat and PH domain 8", "centaurin, gamma-like family, member 5"	CTGLF1, AGAP8, CTGLF5		12477932	Standard	XM_005271797		Approved	Em:AC012044.1, MRIP2	uc001jcx.4	Q96P64	OTTHUMG00000018088	ENST00000448048.2:c.1879G>A	10.37:g.46321476C>T	ENSP00000392513:p.Val627Ile		45641482		Missense_Mutation	SNP	ENST00000448048.2	37	CCDS7215.1	.	.	.	.	.	.	.	.	.	.	c	2.318	-0.356320	0.05138	.	.	ENSG00000188234	ENST00000448048;ENST00000342551	T	0.65916	-0.18	.	.	.	Ankyrin repeat-containing domain (4);	0.223555	0.38436	N	0.001698	T	0.39306	0.1073	N	0.17922	0.545	0.24802	N	0.992697	B;B	0.12630	0.006;0.003	B;B	0.16289	0.015;0.01	T	0.15263	-1.0443	9	0.33141	T	0.24	.	5.89	0.18904	0.0:0.9992:0.0:8.0E-4	.	650;627	C9JRW4;Q96P64	.;AGAP4_HUMAN	I	627;403	ENSP00000392513:V627I	ENSP00000343438:V403I	V	-	1	0	AGAP4	45641482	0.956000	0.32656	0.271000	0.24616	0.274000	0.26718	0.179000	0.16840	0.107000	0.17824	0.109000	0.15622	GTC		0.672	AGAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047799.1	NM_133446		T	46321476	C	T	46321476	3	4	1	1	0	0	0	0	1	0	0	0	370	536	19	1	116	1	AGAP4	10	46321476	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	2697770	46321476	89213271	106	106										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	68940231	68940231	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aggcgtttctctagtgatggTcgtatttcctcctcagttac	9	10	2	1	rs564004112		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:68940231T>C	ENST00000433211.2	-	7	1065	c.891A>G	c.(889-891)cgA>cgG	p.R297R	CTNNA3_ENST00000545309.1_Silent_p.R297R|CTNNA3_ENST00000373744.4_Silent_p.R297R	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						CTAGTGATGGTCGTATTTCCT	0.448																																																0			10											147	133	138					10																	68940231		2203	4300	6503	68610237	SO:0001819	synonymous_variant	29119			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.891A>G	10.37:g.68940231T>C			68610237		Silent	SNP	ENST00000433211.2	37	CCDS7269.1																																																																																				0.448	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		C	68940231	T	C	68940231	2	2	1	1	0	0	0	0	0	0	0	1	4020	1654	58	4		4	CTNNA3	10	68940231	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	22618755	68940231	66594516	107	107										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720772	89720772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tagcatttgcagtatagagcGtgcagataatgacaaggaat	11	5	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:89720772G>A	ENST00000371953.3	+	8	2280	c.923G>A	c.(922-924)cGt>cAt	p.R308H	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	308	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.R308fs*9(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.R308fs*3(1)|p.W274_F341del(1)|p.R308fs*7(1)|p.R308fs*4(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGTATAGAGCGTGCAGATAAT	0.338		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	57	Whole gene deletion(37)|Deletion - Frameshift(15)|Deletion - In frame(2)|Unknown(2)|Insertion - Frameshift(1)	prostate(16)|central_nervous_system(12)|endometrium(6)|skin(6)|lung(4)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|urinary_tract(2)|soft_tissue(1)	10											105	102	103					10																	89720772		2203	4299	6502	89710752	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.923G>A	10.37:g.89720772G>A	ENSP00000361021:p.Arg308His		89710752	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798663	0.70567	.	.	ENSG00000171862	ENST00000371953	D	0.94537	-3.45	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.167826	0.53938	D	0.000054	D	0.91050	0.7184	L	0.38175	1.15	0.58432	D	0.999999	B	0.13145	0.007	B	0.08055	0.003	D	0.87089	0.2171	9	.	.	.	-1.1912	18.5632	0.91108	0.0:0.0:1.0:0.0	.	308	P60484	PTEN_HUMAN	H	308	ENSP00000361021:R308H	.	R	+	2	0	PTEN	89710752	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.647000	0.74354	2.399000	0.81585	0.591000	0.81541	CGT		0.338	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89720772	G	A	89720772	3	1	1	1	0	0	0	0	1	0	0	0	12772	1145	40	1	953	1	PTEN	10	89720772	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	20780541	89720772	45813975	108	108										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105920864	105920864	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	taatctttgaattgttttctTtcttcttcagtccacacagc	4	10	5	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr10:105920864T>C	ENST00000357060.3	-	27	3586	c.3471A>G	c.(3469-3471)gaA>gaG	p.E1157E	WDR96_ENST00000428666.1_Silent_p.E1158E	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ATTGTTTTCTTTCTTCTTCAG	0.323																																																0			10											111	102	105					10																	105920864		2203	4299	6502	105910854	SO:0001819	synonymous_variant	80217																														ENST00000357060.3:c.3471A>G	10.37:g.105920864T>C			105910854		Silent	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	8.932	0.963616	0.18583	.	.	ENSG00000197748	ENST00000457071;ENST00000434629	.	.	.	5.69	4.56	0.56223	.	.	.	.	.	T	0.59838	0.2223	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56335	-0.7996	4	.	.	.	.	9.2713	0.37673	0.0:0.1471:0.0:0.8529	.	.	.	.	R	6;518	.	.	K	-	2	0	WDR96	105910854	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.109000	0.31135	0.986000	0.38683	0.533000	0.62120	AAA		0.323	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	105920864	T	C	105920864	2	2	1	1	0	0	0	0	0	0	0	1	1622	1838	64	4		4	C10orf79	10	105920864	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	16200092	105920864	29613883	109	109										
CDHR5	53841	hgsc.bcm.edu	37	chr11	621658	621658	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atgacggtggagttcactttCgtgtcctggggagggagagg	18	6	1	2	rs140067219		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:621658C>T	ENST00000358353.3	-	6	733	c.411G>A	c.(409-411)acG>acA	p.T137T	CDHR5_ENST00000529337.1_5'Flank|CDHR5_ENST00000397542.2_Silent_p.T137T|CDHR5_ENST00000349570.7_Silent_p.T137T			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.T137T(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						AGTTCACTTTCGTGTCCTGGG	0.627													c|||	1	0.000199681	8e-04	0	5008	,	,		15813	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11							,,	1,4405	2.1+/-5.4	0,1,2202	118	97	104		411,411,411	-7.8	0.4	11	dbSNP_134	104	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	137/840,137/846,137/652	621658	1,13005	2203	4300	6503	611658	SO:0001819	synonymous_variant	0			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.411G>A	11.37:g.621658C>T			611658	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																				0.627	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		T	621658	C	T	621658	2	4	1	1	0	0	0	0	0	0	0	1	3128	871	31	1		1	CDHR5	11	621658	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10		621658	134384858	110	110										
ANO3	63982	hgsc.bcm.edu	37	chr11	26620415	26620415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tctctcataggaaacacttcGtccccagtttgaagccaagt	7	12	2	1	rs199929076		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:26620415G>A	ENST00000256737.3	+	16	2393	c.1541G>A	c.(1540-1542)cGt>cAt	p.R514H	ANO3_ENST00000531568.1_Missense_Mutation_p.R368H|ANO3_ENST00000537978.1_Missense_Mutation_p.R498H|ANO3_ENST00000525139.1_Missense_Mutation_p.R498H	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	514					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						GAAACACTTCGTCCCCAGTTT	0.393													G|||	1	0.000199681	0	0	5008	,	,		16761	0		0.001	False		,,,				2504	0															0			11											67	60	62					11																	26620415		2203	4299	6502	26576991	SO:0001583	missense	63982			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1541G>A	11.37:g.26620415G>A	ENSP00000256737:p.Arg514His		26576991	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	37	CCDS31447.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	28.4	4.920671	0.92249	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.97	5.97	0.96955	.	0.120935	0.64402	D	0.000013	D	0.83344	0.5234	M	0.92317	3.295	0.80722	D	1	P;P	0.48350	0.909;0.779	P;B	0.47162	0.54;0.392	D	0.86997	0.2114	10	0.87932	D	0	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	416;514	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	H	498;498;514;416;368	ENSP00000440737:R498H;ENSP00000432576:R498H;ENSP00000256737:R514H;ENSP00000432394:R368H	ENSP00000256737:R514H	R	+	2	0	ANO3	26576991	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.867000	0.87062	2.834000	0.97654	0.650000	0.86243	CGT		0.393	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26620415	G	A	26620415	3	1	1	1	0	0	0	0	1	0	0	0	698	1145	40	1	1603	1	ANO3	11	26620415	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	25998757	26620415	108386101	111	111										
CHST1	8534	hgsc.bcm.edu	37	chr11	45672345	45672345	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctctcctcgcacagtcgctcGgccagcccggcctctgccag	10	20	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:45672345G>A	ENST00000308064.2	-	4	799	c.129C>T	c.(127-129)gcC>gcT	p.A43A	RP11-495O11.1_ENST00000525563.1_RNA|CHST1_ENST00000533673.1_5'Flank	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	43					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		ACAGTCGCTCGGCCAGCCCGG	0.662																																																0			11											62	63	62					11																	45672345		2203	4299	6502	45628921	SO:0001819	synonymous_variant	8534			U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"Sulfotransferases, membrane-bound"	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.129C>T	11.37:g.45672345G>A			45628921	D3DQP2	Silent	SNP	ENST00000308064.2	37	CCDS7913.1																																																																																				0.662	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654		A	45672345	G	A	45672345	2	1	1	1	0	0	0	0	0	0	0	1	3403	1103	39	1		1	CHST1	11	45672345	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	19051930	45672345	89334171	112	112										
LRP4	4038	hgsc.bcm.edu	37	chr11	46903378	46903378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggtcagattagaagagataaTgacttggcggcctgaggcat	14	6	1	5			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:46903378T>C	ENST00000378623.1	-	20	2931	c.2689A>G	c.(2689-2691)Att>Gtt	p.I897V		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	897					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAAGAGATAATGACTTGGCGG	0.522																																																0			11											98	90	93					11																	46903378		2201	4299	6500	46859954	SO:0001583	missense	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.2689A>G	11.37:g.46903378T>C	ENSP00000367888:p.Ile897Val		46859954	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.524894	0.85600	.	.	ENSG00000134569	ENST00000378623	D	0.96011	-3.88	5.94	5.94	0.96194	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95185	0.8439	L	0.49640	1.575	0.58432	D	0.999999	B	0.29188	0.236	B	0.41174	0.349	D	0.93997	0.7272	10	0.52906	T	0.07	.	16.4075	0.83691	0.0:0.0:0.0:1.0	.	897	O75096	LRP4_HUMAN	V	897	ENSP00000367888:I897V	ENSP00000367888:I897V	I	-	1	0	LRP4	46859954	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	6.148000	0.71788	2.275000	0.75901	0.528000	0.53228	ATT		0.522	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		C	46903378	T	C	46903378	3	2	1	1	0	0	0	0	1	0	0	0	8988	1464	51	4	3104	4	LRP4	11	46903378	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	1231033	46903378	88103138	113	113										
MARK2	2011	hgsc.bcm.edu	37	chr11	63667404	63667404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gattgcagactttggcttcaGcaatgaattcacctttggga	10	8	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:63667404G>A	ENST00000509502.2	+	8	954	c.491G>A	c.(490-492)aGc>aAc	p.S164N	MARK2_ENST00000513765.2_Missense_Mutation_p.S164N|MARK2_ENST00000408948.3_Missense_Mutation_p.S164N|MARK2_ENST00000350490.7_Missense_Mutation_p.S197N|MARK2_ENST00000425897.2_Missense_Mutation_p.S164N|MARK2_ENST00000402010.2_Missense_Mutation_p.S197N|MARK2_ENST00000413835.2_Missense_Mutation_p.S197N|MARK2_ENST00000377809.4_Missense_Mutation_p.S197N|MARK2_ENST00000361128.5_Missense_Mutation_p.S197N|MARK2_ENST00000315032.8_Missense_Mutation_p.S197N|MARK2_ENST00000508192.1_Missense_Mutation_p.S197N|MARK2_ENST00000502399.3_Missense_Mutation_p.S197N|MARK2_ENST00000377810.3_Missense_Mutation_p.S164N	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2									p.S164N(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						TTTGGCTTCAGCAATGAATTC	0.488																																																1	Substitution - Missense(1)	ovary(1)	11											157	151	153					11																	63667404		2201	4297	6498	63423980	SO:0001583	missense	2011			BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.491G>A	11.37:g.63667404G>A	ENSP00000423974:p.Ser164Asn		63423980		Missense_Mutation	SNP	ENST00000509502.2	37	CCDS41665.1	.	.	.	.	.	.	.	.	.	.	g	34	5.327907	0.95733	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	T;T;T;T;T;T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69097	0.3073	H	0.95187	3.635	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.993;1.0;1.0	D;D;D;D;D;D	0.87578	0.995;0.995;0.988;0.98;0.997;0.998	T	0.78324	-0.2248	10	0.87932	D	0	.	18.3171	0.90225	0.0:0.0:1.0:0.0	.	164;164;197;197;197;197	E7ETY4;Q7KZI7-14;Q7KZI7-15;Q7KZI7-5;Q7KZI7;Q7KZI7-16	.;.;.;.;MARK2_HUMAN;.	N	197;197;197;197;164;197;197;197;197;164;164;164;164	ENSP00000385751:S197N;ENSP00000326632:S197N;ENSP00000367040:S197N;ENSP00000389184:S197N;ENSP00000367041:S164N;ENSP00000425765:S197N;ENSP00000355091:S197N;ENSP00000294247:S197N;ENSP00000423974:S164N;ENSP00000421075:S164N;ENSP00000386128:S164N;ENSP00000415494:S164N	ENSP00000326632:S197N	S	+	2	0	MARK2	63423980	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.654000	0.98509	2.858000	0.98145	0.651000	0.88453	AGC		0.488	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		A	63667404	G	A	63667404	3	1	1	1	0	0	0	0	1	0	0	0	9343	971	34	3	620	3	MARK2	11	63667404	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	16764026	63667404	71339112	114	114										
KRTAP5-10	387273	hgsc.bcm.edu	37	chr11	71276922	71276951	+	In_Frame_Del	DEL	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	-													0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccaaggggggctgtggctccTgtgggggctccaaggggggc					rs78111049|rs7933459|rs369128313|rs199839459|rs76397897|rs111317671|rs527935556	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:71276922_71276951delTGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	ENST00000398531.1	+	1	314_343	c.289_318delTGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	c.(289-318)tgtgggggctccaaggggggctgtggttctdel	p.CGGSKGGCGS127del	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	127	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						CTGTGGCTCCTGTGGGGGCTCCAAGGGGGGCTGTGGTTCTTGTGGGGGCT	0.678																																																0			11																																								70954599	SO:0001651	inframe_deletion	387273			AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"Keratin associated proteins"	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.289_318delTGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	11.37:g.71276922_71276951delTGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	ENSP00000381542:p.Cys127_Ser136del		70954570	B9EHA4	In_Frame_Del	DEL	ENST00000398531.1	37	CCDS41684.1																																																																																				0.678	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2			-	71276951	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	-	71276922	7	5	1	1	0	1	0	1	0	0	0	0	8581	1580	55	0	291	0	KRTAP5-10	11	71276922	In_Frame_Del	DEL	TGTGGGGGCTCCAAGGGGGGCTGTGGTTCT	TCGA-AF-2687-01A-02D-1733-10	7609518	71276922	63729594	115	115										
UVRAG	7405	hgsc.bcm.edu	37	chr11	75852039	75852039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cttggacttctccaaagaaaAcaagaaaaaaggagaggatc	9	7	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:75852039A>G	ENST00000356136.3	+	15	1923	c.1682A>G	c.(1681-1683)aAc>aGc	p.N561S	UVRAG_ENST00000533454.1_Missense_Mutation_p.N189S|UVRAG_ENST00000532130.1_Missense_Mutation_p.N189S|UVRAG_ENST00000528420.1_Missense_Mutation_p.N460S|UVRAG_ENST00000539288.1_Missense_Mutation_p.N189S|UVRAG_ENST00000531818.1_Missense_Mutation_p.N189S|UVRAG_ENST00000538870.1_Missense_Mutation_p.N117S	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	561					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						TCCAAAGAAAACAAGAAAAAA	0.547																																																0			11											48	48	48					11																	75852039		2200	4292	6492	75529687	SO:0001583	missense	7405			X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1682A>G	11.37:g.75852039A>G	ENSP00000348455:p.Asn561Ser		75529687	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.364931	0.24684	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288;ENST00000538870	T	0.43294	0.95	5.6	-0.844	0.10741	.	0.595355	0.18974	N	0.126076	T	0.20536	0.0494	N	0.12182	0.205	0.24433	N	0.994562	B;B	0.16603	0.018;0.0	B;B	0.12156	0.007;0.0	T	0.22138	-1.0225	10	0.18276	T	0.48	-5.8299	10.5467	0.45064	0.5223:0.0:0.4777:0.0	.	117;561	B7Z6A0;Q9P2Y5	.;UVRAG_HUMAN	S	561;460;189;189;189;189;117	ENSP00000348455:N561S	ENSP00000348455:N561S	N	+	2	0	UVRAG	75529687	0.000000	0.05858	0.974000	0.42286	0.951000	0.60555	-0.348000	0.07740	-0.157000	0.11059	-0.250000	0.11733	AAC		0.547	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		G	75852039	A	G	75852039	3	3	1	1	0	0	0	0	1	0	0	0	17148	43	2	4	1740	4	UVRAG	11	75852039	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	4575117	75852039	59154477	116	116										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110450666	110450666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctgccctgatgagggaccggGcattccggaaacatggctgg	15	11	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:110450666G>A	ENST00000260283.4	-	16	3288	c.3004C>T	c.(3004-3006)Ccc>Tcc	p.P1002S	ARHGAP20_ENST00000527598.1_Missense_Mutation_p.P966S|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.P966S|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.P545S|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.P976S|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.P976S|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.P979S	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	1002					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GAGGGACCGGGCATTCCGGAA	0.507																																																0			11											61	59	60					11																	110450666		2201	4298	6499	109955876	SO:0001583	missense	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.3004C>T	11.37:g.110450666G>A	ENSP00000260283:p.Pro1002Ser		109955876	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	4.977	0.181538	0.09495	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.08634	3.07;3.07;3.12;3.07;3.08;3.07;3.08	5.9	2.23	0.28157	.	0.406304	0.25217	N	0.032271	T	0.07773	0.0195	L	0.60455	1.87	0.09310	N	1	P;B;P	0.43287	0.802;0.451;0.587	B;B;B	0.38156	0.266;0.137;0.266	T	0.24119	-1.0169	10	0.26408	T	0.33	.	6.8606	0.24064	0.2042:0.2133:0.5825:0.0	.	976;1002;979	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	S	1002;976;545;979;966;976;966	ENSP00000260283:P1002S;ENSP00000349660:P976S;ENSP00000437905:P545S;ENSP00000432076:P979S;ENSP00000436319:P966S;ENSP00000436522:P976S;ENSP00000431399:P966S	ENSP00000260283:P1002S	P	-	1	0	ARHGAP20	109955876	0.482000	0.25948	0.296000	0.24974	0.155000	0.21991	1.737000	0.38197	1.518000	0.48934	0.650000	0.86243	CCC		0.507	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		A	110450666	G	A	110450666	3	1	1	1	0	0	0	0	1	0	0	0	870	1203	42	3	575	3	ARHGAP20	11	110450666	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	34598627	110450666	24555850	117	117										
CBL	867	hgsc.bcm.edu	37	chr11	119148966	119148966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aggatgtaaagattgagcccTgtggacacctcatgtgcaca	11	9	1	2	rs387906665		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:119148966T>C	ENST00000264033.4	+	8	1562	c.1186T>C	c.(1186-1188)Tgt>Cgt	p.C396R		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	396	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E366_Q409del(13)|p.C396R(3)|p.?(1)|p.E366_K477del(1)|p.C396G(1)|p.E369_Q409del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GATTGAGCCCTGTGGACACCT	0.383			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	20	Deletion - In frame(15)|Substitution - Missense(4)|Unknown(1)	haematopoietic_and_lymphoid_tissue(20)	11											126	117	120					11																	119148966		2199	4295	6494	118654176	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1186T>C	11.37:g.119148966T>C	ENSP00000264033:p.Cys396Arg		118654176	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.362648	0.61403	.	.	ENSG00000110395	ENST00000264033	D	0.92149	-2.98	5.52	5.52	0.82312	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.97958	0.9328	H	0.99668	4.69	0.80722	D	1	D	0.62365	0.991	D	0.65010	0.931	D	0.99679	1.0998	10	0.87932	D	0	-27.6918	15.9527	0.79855	0.0:0.0:0.0:1.0	.	396	P22681	CBL_HUMAN	R	396	ENSP00000264033:C396R	ENSP00000264033:C396R	C	+	1	0	CBL	118654176	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.655000	0.83696	2.227000	0.72691	0.455000	0.32223	TGT		0.383	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119148966	T	C	119148966	3	2	1	1	0	0	0	0	1	0	0	0	2706	1580	55	4	1216	4	CBL	11	119148966	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	8698300	119148966	15857550	118	118										
STT3A	3703	hgsc.bcm.edu	37	chr11	125478127	125478127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttgaagttcttttccggagcGtcatctctctggtaggcttt	10	9	4	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr11:125478127G>A	ENST00000529196.1	+	10	1110	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	STT3A_ENST00000531491.1_Missense_Mutation_p.V210I|STT3A_ENST00000392708.4_Missense_Mutation_p.V302I			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	302					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TTTCCGGAGCGTCATCTCTCT	0.478																																																0			11											121	115	117					11																	125478127		2201	4299	6500	124983337	SO:0001583	missense	3703			BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.904G>A	11.37:g.125478127G>A	ENSP00000436962:p.Val302Ile		124983337	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	37	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.905799	0.33628	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	L	0.29908	0.895	0.80722	D	1	B;B;B	0.18166	0.009;0.026;0.014	B;B;B	0.18263	0.008;0.021;0.021	T	0.45833	-0.9234	9	0.14656	T	0.56	-22.0069	19.7105	0.96095	0.0:0.0:1.0:0.0	.	210;210;302	B4DJ24;E9PNQ1;P46977	.;.;STT3A_HUMAN	I	302;302;210	.	ENSP00000376472:V302I	V	+	1	0	STT3A	124983337	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.004000	0.88535	2.760000	0.94817	0.655000	0.94253	GTC		0.478	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		A	125478127	G	A	125478127	3	1	1	1	0	0	0	0	1	0	0	0	15372	1145	40	1	934	1	STT3A	11	125478127	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	6329161	125478127	9528389	119	119										
A2ML1	144568	hgsc.bcm.edu	37	chr12	9020926	9020926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgagcaaccgacttcacctcGatccttgactctcactattc	5	15	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:9020926G>A	ENST00000299698.7	+	31	4214	c.4034G>A	c.(4033-4035)cGa>cAa	p.R1345Q	A2ML1_ENST00000539547.1_Missense_Mutation_p.R854Q	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.R1345Q(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ACTTCACCTCGATCCTTGACT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	12											156	154	155					12																	9020926		1978	4161	6139	8912193	SO:0001583	missense	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.4034G>A	12.37:g.9020926G>A	ENSP00000299698:p.Arg1345Gln		8912193		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	G	5.355	0.250736	0.10130	.	.	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.42513	0.97;0.97;0.97	3.69	-0.271	0.12922	Alpha-macroglobulin, receptor-binding (2);	4.993110	0.00691	N	0.000724	T	0.31513	0.0799	L	0.41573	1.285	0.09310	N	1	B	0.26318	0.146	B	0.17433	0.018	T	0.05419	-1.0886	10	0.23302	T	0.38	.	4.3132	0.10981	0.3687:0.0:0.4769:0.1544	.	1345	A8K2U0	A2ML1_HUMAN	Q	1345;1345;895;854	ENSP00000299698:R1345Q;ENSP00000443174:R895Q;ENSP00000438292:R854Q	ENSP00000299698:R1345Q	R	+	2	0	A2ML1	8912193	0.000000	0.05858	0.235000	0.24058	0.127000	0.20565	-0.162000	0.10012	-0.060000	0.13132	0.561000	0.74099	CGA		0.488	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		A	9020926	G	A	9020926	3	1	1	1	0	0	0	0	1	0	0	0	5	1058	37	1	4156	1	A2ML1	12	9020926	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10		9020926	124830969	120	120										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18552754	18552754	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atggacattttctcaaccttTagaggctcttgggcttttga	9	8	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:18552754T>A	ENST00000266497.5	+	14	2203	c.2165T>A	c.(2164-2166)tTa>tAa	p.L722*	PIK3C2G_ENST00000433979.1_Nonsense_Mutation_p.L722*|PIK3C2G_ENST00000538779.1_Nonsense_Mutation_p.L763*			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	722	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.L722S(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCTCAACCTTTAGAGGCTCTT	0.413																																																1	Substitution - Missense(1)	central_nervous_system(1)	12											65	64	64					12																	18552754		1832	4089	5921	18444021	SO:0001587	stop_gained	5288			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2165T>A	12.37:g.18552754T>A	ENSP00000266497:p.Leu722*		18444021	A1L3U0	Nonsense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	38	7.195019	0.98129	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	.	.	.	5.08	2.67	0.31697	.	0.364736	0.22279	N	0.062143	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3184	5.0597	0.14551	0.0:0.1586:0.1551:0.6863	.	.	.	.	X	722;722;763	.	ENSP00000266497:L722X	L	+	2	0	PIK3C2G	18444021	0.981000	0.34729	0.987000	0.45799	0.730000	0.41778	1.859000	0.39418	0.384000	0.24942	0.477000	0.44152	TTA		0.413	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18552754	T	A	18552754	4	1	1	1	0	0	0	0	0	1	0	0	11942	1764	61	5	2219	5	PIK3C2G	12	18552754	Nonsense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	9531828	18552754	115299141	121	121										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20766516	20766516	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gagcaacttgctcagcacacAgctcaccttccaggccattc	7	16	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:20766516A>T	ENST00000359062.3	+	3	1191	c.1151A>T	c.(1150-1152)cAg>cTg	p.Q384L	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	384					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CTCAGCACACAGCTCACCTTC	0.542																																																0			12											109	101	104					12																	20766516		2203	4300	6503	20657783	SO:0001583	missense	5139				CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1151A>T	12.37:g.20766516A>T	ENSP00000351957:p.Gln384Leu		20657783	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.952671	0.92660	.	.	ENSG00000172572	ENST00000359062	T	0.56103	0.48	5.87	5.87	0.94306	.	2.091460	0.01485	N	0.016845	T	0.76183	0.3952	L	0.61218	1.895	0.58432	D	0.999999	D	0.64830	0.994	D	0.75020	0.985	T	0.53655	-0.8408	10	0.59425	D	0.04	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	384	Q14432	PDE3A_HUMAN	L	384	ENSP00000351957:Q384L	ENSP00000351957:Q384L	Q	+	2	0	PDE3A	20657783	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.340000	0.90044	2.371000	0.80710	0.533000	0.62120	CAG		0.542	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20766516	A	T	20766516	3	4	1	1	0	0	0	0	1	0	0	0	11668	188	7	5	1161	5	PDE3A	12	20766516	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	2213762	20766516	113085379	122	122										
RAB5B	5869	hgsc.bcm.edu	37	chr12	56383809	56383809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggacacagctgggcaggagcGatatcacagcttagccccca	12	13	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:56383809G>A	ENST00000360299.5	+	3	463	c.242G>A	c.(241-243)cGa>cAa	p.R81Q	RAB5B_ENST00000553116.1_Missense_Mutation_p.R81Q|RAB5B_ENST00000448789.2_Missense_Mutation_p.R81Q	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	81					antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			GGGCAGGAGCGATATCACAGC	0.507																																																0			12											149	123	132					12																	56383809		2203	4300	6503	54670076	SO:0001583	missense	5869				CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"RAB, member RAS oncogene"	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.242G>A	12.37:g.56383809G>A	ENSP00000353444:p.Arg81Gln		54670076	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Missense_Mutation	SNP	ENST00000360299.5	37	CCDS8900.1	.	.	.	.	.	.	.	.	.	.	G	34	5.368666	0.95900	.	.	ENSG00000111540	ENST00000553116;ENST00000360299;ENST00000548068;ENST00000551459;ENST00000448789	T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17	4.81	4.81	0.61882	Small GTP-binding protein domain (1);	0.000000	0.49305	D	0.000157	T	0.79540	0.4463	L	0.54908	1.71	0.80722	D	1	P;D	0.65815	0.928;0.995	P;P	0.48921	0.595;0.588	T	0.82766	-0.0295	10	0.87932	D	0	-2.6971	17.1784	0.86848	0.0:0.0:1.0:0.0	.	81;81	B4DKD7;P61020	.;RAB5B_HUMAN	Q	81	ENSP00000450168:R81Q;ENSP00000353444:R81Q;ENSP00000447895:R81Q;ENSP00000449554:R81Q;ENSP00000391319:R81Q	ENSP00000353444:R81Q	R	+	2	0	RAB5B	54670076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.750000	0.85110	2.676000	0.91093	0.585000	0.79938	CGA		0.507	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			A	56383809	G	A	56383809	3	1	1	1	0	0	0	0	1	0	0	0	12986	1058	37	1	248	1	RAB5B	12	56383809	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	35617293	56383809	77468086	123	123										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816730	75816730	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aaccaggaatattttgtactCgatgtggcagacgtgacaaa	10	7	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:75816730C>A	ENST00000550916.1	+	4	678	c.631C>A	c.(631-633)Cga>Aga	p.R211R	GLIPR1L2_ENST00000435775.1_3'UTR|GLIPR1L2_ENST00000320460.4_Silent_p.R211R|GLIPR1L2_ENST00000441218.1_Silent_p.R146R|GLIPR1L2_ENST00000378692.3_Silent_p.R104R	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	211						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						ATTTTGTACTCGATGTGGCAG	0.328																																																0			12											160	157	158					12																	75816730		2203	4300	6503	74102997	SO:0001819	synonymous_variant	144321			BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.631C>A	12.37:g.75816730C>A			74102997	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	37	CCDS58258.1																																																																																				0.328	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		A	75816730	C	A	75816730	2	1	1	1	0	0	0	0	0	0	0	1	6463	876	31	2		2	GLIPR1L2	12	75816730	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	19432921	75816730	58035165	124	124										
UTP20	27340	hgsc.bcm.edu	37	chr12	101745962	101745962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgggacagatcaatcaaaaaCtgggtgtcaggtgtggtcaa	13	7	4	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:101745962C>T	ENST00000261637.4	+	39	5188	c.5014C>T	c.(5014-5016)Ctg>Ttg	p.L1672L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1672					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAATCAAAAACTGGGTGTCAG	0.338																																																0			12											144	144	144					12																	101745962		2203	4300	6503	100270093	SO:0001819	synonymous_variant	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5014C>T	12.37:g.101745962C>T			100270093	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																				0.338	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101745962	C	T	101745962	2	4	1	1	0	0	0	0	0	0	0	1	17139	564	20	3		3	UTP20	12	101745962	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	25929232	101745962	32105933	125	125										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112601455	112601455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgatggagcccaggccggccCgcacggccgtcacgcactcc	13	18	1	1	rs181634938	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:112601455C>T	ENST00000430131.2	-	73	12667	c.11522G>A	c.(11521-11523)cGg>cAg	p.R3841Q	HECTD4_ENST00000377560.5_Missense_Mutation_p.R4091Q|HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Missense_Mutation_p.R4117Q			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3841	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CAGGCCGGCCCGCACGGCCGT	0.677													C|||	2	0.000399361	0	0.0029	5008	,	,		17305	0		0	False		,,,				2504	0															0			12						C	GLN/ARG	0,3200		0,0,1600	9	14	12		12272	5.7	1	12		12	1,6265		0,1,3132	no	missense	C12orf51	NM_001109662.2	43	0,1,4732	TT,TC,CC		0.016,0.0,0.0106	possibly-damaging	4091/4247	112601455	1,9465	1600	3133	4733	111085838	SO:0001583	missense	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11522G>A	12.37:g.112601455C>T	ENSP00000404379:p.Arg3841Gln		111085838	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	C	34	5.388529	0.95988	0.0	1.6E-4	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.49139	0.79;0.79;0.79	5.73	5.73	0.89815	HECT (4);	.	.	.	.	T	0.54983	0.1892	L	0.39898	1.24	0.58432	D	0.999998	D	0.69078	0.997	D	0.72982	0.979	T	0.60821	-0.7187	9	0.66056	D	0.02	.	19.8984	0.96975	0.0:1.0:0.0:0.0	.	3841	Q9Y4D8	K0614_HUMAN	Q	4091;3841;4117;306	ENSP00000366783:R4091Q;ENSP00000404379:R3841Q;ENSP00000449784:R4117Q	ENSP00000366783:R4091Q	R	-	2	0	C12orf51	111085838	1.000000	0.71417	0.965000	0.40720	0.808000	0.45660	7.310000	0.78947	2.713000	0.92767	0.655000	0.94253	CGG		0.677	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112601455	C	T	112601455	3	4	1	1	0	0	0	0	1	0	0	0	1700	652	23	1	480	1	C12orf51	12	112601455	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	10855493	112601455	21250440	126	126										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926889	112926889	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtgcggtctcagaggtcaggGatggtccagacagaagcaca	15	9	2	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:112926889G>A	ENST00000351677.2	+	13	1707	c.1509G>A	c.(1507-1509)ggG>ggA	p.G503G		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	507	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						AGAGGTCAGGGATGGTCCAGA	0.463			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12																																								111411272	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1509G>A	12.37:g.112926889G>A			111411272	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.463	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			A	112926889	G	A	112926889	2	1	1	1	0	0	0	0	0	0	0	1	12815	1161	41	3		3	PTPN11	12	112926889	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	325434	112926889	20925006	127	127										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130898850	130898850	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aggcggtctcgcccgtaatcGtctgcgagcaagtgggggtg	17	10	2	0	rs149347862	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr12:130898850G>A	ENST00000261655.4	-	14	2635	c.2472C>T	c.(2470-2472)gaC>gaT	p.D824D		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	824					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.D824D(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GCCCGTAATCGTCTGCGAGCA	0.572													G|||	23	0.00459265	0.0166	0.0014	5008	,	,		18348	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	prostate(1)	12						G		58,4348	55.5+/-91.7	0,58,2145	52	58	56		2472	-2	0.2	12	dbSNP_134	56	0,8600		0,0,4300	yes	coding-synonymous-near-splice	RIMBP2	NM_015347.4		0,58,6445	AA,AG,GG		0.0,1.3164,0.4459		824/1053	130898850	58,12948	2203	4300	6503	129464803	SO:0001630	splice_region_variant	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2471-1C>T	12.37:g.130898850G>A			129464803	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																				0.572	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	Silent	A	130898850	G	A	130898850	5	1	1	1	0	0	0	0	0	0	1	0	13400	1159	40	1	710	1	RIMBP2	12	130898850	Splice_Site	SNP	G	TCGA-AF-2687-01A-02D-1733-10	17971961	130898850	2953045	128	128										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671795	25671795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	caacacagacagtgggtccaCgtcctgcagctgctgctgct	11	14	0	1	rs113416318	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr13:25671795C>T	ENST00000281589.3	+	1	1496	c.1459C>T	c.(1459-1461)Cgt>Tgt	p.R487C		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	487					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AGTGGGTCCACGTCctgcagc	0.522													c|||	175	0.0349441	0.0537	0.0403	5008	,	,		21647	0.0119		0.0159	False		,,,				2504	0.0491															0			13																																								24569795	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1459C>T	13.37:g.25671795C>T	ENSP00000281589:p.Arg487Cys		24569795	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.862076	0.51482	.	.	ENSG00000151846	ENST00000281589	T	0.31247	1.5	0.875	0.875	0.19130	.	0.135300	0.32190	U	0.006459	T	0.29556	0.0737	L	0.59436	1.845	0.58432	D	0.999997	D	0.58970	0.984	P	0.45660	0.489	T	0.12630	-1.0540	10	0.72032	D	0.01	.	7.5489	0.27783	0.0:1.0:0.0:0.0	.	487	Q9H361	PABP3_HUMAN	C	487	ENSP00000281589:R487C	ENSP00000281589:R487C	R	+	1	0	PABPC3	24569795	1.000000	0.71417	0.944000	0.38274	0.640000	0.38277	4.773000	0.62331	0.759000	0.33084	0.313000	0.20887	CGT		0.522	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		T	25671795	C	T	25671795	3	4	1	1	0	0	0	0	1	0	0	0	11396	536	19	1	1461	1	PABPC3	13	25671795	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10		25671795	89498083	129	129										
MYH7	4625	hgsc.bcm.edu	37	chr14	23898994	23898994	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgcctcccaccttcagtgccGtctggctccgcctgctcctc	8	20	2	0	rs2231126	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:23898994G>A	ENST00000355349.3	-	12	1290	c.1128C>T	c.(1126-1128)gaC>gaT	p.D376D		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	376	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CTTCAGTGCCGTCTGGCTCCG	0.517													g|||	782	0.15615	0.4206	0.0764	5008	,	,		18741	0.0198		0.0785	False		,,,				2504	0.0757															0			14								1653,2753	506.6+/-366.4	311,1031,861	77	72	74		1128	-4.2	0.9	14	dbSNP_98	74	746,7854	178.2+/-227.6	35,676,3589	no	coding-synonymous	MYH7	NM_000257.2		346,1707,4450	AA,AG,GG		8.6744,37.517,18.4453		376/1936	23898994	2399,10607	2203	4300	6503	22968834	SO:0001819	synonymous_variant	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1128C>T	14.37:g.23898994G>A			22968834	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																				0.517	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23898994	G	A	23898994	2	1	1	1	0	0	0	0	0	0	0	1	10069	1136	40	1		1	MYH7	14	23898994	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10		23898994	83450546	130	130										
DHRS4L2	317749	hgsc.bcm.edu	37	chr14	24459529	24459529	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtgacgggcactgtgtgccaTgtggggaaggcggaggaccg	20	8	0	1	rs563512511		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:24459529T>C	ENST00000335125.6	+	2	393	c.267T>C	c.(265-267)caT>caC	p.H89H	DHRS4L2_ENST00000558753.1_Silent_p.H89H|DHRS4L2_ENST00000545240.1_Silent_p.H89H|DHRS4L2_ENST00000382755.4_Silent_p.H87H|DHRS4L2_ENST00000534993.1_5'UTR|DHRS4L2_ENST00000397071.1_Silent_p.H89H|DHRS4L2_ENST00000537912.1_Silent_p.H89H|DHRS4L2_ENST00000543805.1_5'UTR	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	87						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)	p.H89Q(1)		breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		CTGTGTGCCATGTGGGGAAGG	0.677													t|||	1	0.000199681	0	0	5008	,	,		14991	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	ovary(1)	14											33	37	36					14																	24459529		2200	4298	6498	23529369	SO:0001819	synonymous_variant	317749				CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	19731	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 3"	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.267T>C	14.37:g.24459529T>C			23529369	Q3YLD4	Silent	SNP	ENST00000335125.6	37	CCDS9606.2																																																																																				0.677	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4			C	24459529	T	C	24459529	2	2	1	1	0	0	0	0	0	0	0	1	4505	1461	51	4		4	DHRS4L2	14	24459529	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	560535	24459529	82890011	131	131										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917280	26917280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttccagtaatggttaccttcCgattccttgtgccaggtacg	9	11	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:26917280C>T	ENST00000539517.2	-	5	1726	c.1409G>A	c.(1408-1410)cGg>cAg	p.R470Q	NOVA1_ENST00000267422.7_Missense_Mutation_p.R348Q|NOVA1_ENST00000465357.2_Missense_Mutation_p.R446Q	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	473	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GGTTACCTTCCGATTCCTTGT	0.453																																																0			14											163	135	145					14																	26917280		2203	4300	6503	25987120	SO:0001583	missense	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.1409G>A	14.37:g.26917280C>T	ENSP00000438875:p.Arg470Gln		25987120	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	37	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340276	0.60963	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422	T;T;T	0.35236	1.32;1.32;1.32	6.04	5.11	0.69529	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.64402	D	0.000005	T	0.70579	0.3240	H	0.94964	3.605	0.58432	D	0.999995	P;D;D	0.89917	0.687;1.0;1.0	B;D;D	0.97110	0.282;1.0;1.0	T	0.78755	-0.2080	10	0.87932	D	0	-2.001	16.1653	0.81750	0.1339:0.8661:0.0:0.0	.	473;446;470	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	Q	446;470;348	ENSP00000447391:R446Q;ENSP00000438875:R470Q;ENSP00000267422:R348Q	ENSP00000267422:R348Q	R	-	2	0	NOVA1	25987120	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.995000	0.70631	2.873000	0.98535	0.563000	0.77884	CGG		0.453	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		T	26917280	C	T	26917280	3	4	1	1	0	0	0	0	1	0	0	0	10585	652	23	1	118	1	NOVA1	14	26917280	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	2457751	26917280	80432260	132	132										
CDKL1	8814	hgsc.bcm.edu	37	chr14	50807788	50807788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gatacagctgatccacatccGattttcctggccacagaggc	9	13	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:50807788G>A	ENST00000216378.2	-	6	1264	c.620C>T	c.(619-621)tCg>tTg	p.S207L	CDKL1_ENST00000395834.1_Missense_Mutation_p.S207L|CDKL1_ENST00000356146.1_5'UTR	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	206	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					ATCCACATCCGATTTTCCTGG	0.547																																																0			14											107	94	98					14																	50807788		2203	4300	6503	49877538	SO:0001583	missense	8814			AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"Cyclin-dependent kinases"	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000216378.2:c.620C>T	14.37:g.50807788G>A	ENSP00000216378:p.Ser207Leu		49877538	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	37		.	.	.	.	.	.	.	.	.	.	G	28.2	4.896047	0.91962	.	.	ENSG00000100490	ENST00000395834;ENST00000216378	T;T	0.50813	0.73;0.73	5.01	5.01	0.66863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.69602	0.3129	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.72633	-0.4234	9	0.87932	D	0	.	19.1942	0.93681	0.0:0.0:1.0:0.0	.	878;206	Q00532-2;Q00532	.;CDKL1_HUMAN	L	207	ENSP00000379176:S207L;ENSP00000216378:S207L	ENSP00000216378:S207L	S	-	2	0	CDKL1	49877538	1.000000	0.71417	0.985000	0.45067	0.632000	0.37999	9.720000	0.98763	2.708000	0.92522	0.655000	0.94253	TCG		0.547	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1			A	50807788	G	A	50807788	3	1	1	1	0	0	0	0	1	0	0	0	3159	1059	37	1	476	1	CDKL1	14	50807788	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	23890508	50807788	56541752	133	133										
DPF3	8110	hgsc.bcm.edu	37	chr14	73181173	73181173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtggtcttcctgagaggcggCgtcgtgcctcctcctgcccc	13	16	1	1	rs61742824	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:73181173C>T	ENST00000556509.1	-	6	561	c.562G>A	c.(562-564)Gcc>Acc	p.A188T	DPF3_ENST00000541685.1_Missense_Mutation_p.A188T|DPF3_ENST00000546183.1_Missense_Mutation_p.A198T|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	188					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TGAGAGGCGGCGTCGTGCCTC	0.627													C|||	101	0.0201677	0.0741	0.0029	5008	,	,		18051	0		0.001	False		,,,				2504	0															0			14						C	THR/ALA	261,3911		10,241,1835	79	92	88		562	1.8	0.2	14	dbSNP_129	88	2,8424		0,2,4211	yes	missense	DPF3	NM_012074.3	58	10,243,6046	TT,TC,CC		0.0237,6.256,2.0876	benign	188/358	73181173	263,12335	2086	4213	6299	72250926	SO:0001583	missense	8110			U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.562G>A	14.37:g.73181173C>T	ENSP00000450518:p.Ala188Thr		72250926	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	C	13.94	2.385909	0.42308	0.06256	2.37E-4	ENSG00000205683	ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.90563	-2.69;-0.15;-0.16	4.9	1.8	0.24995	.	.	.	.	.	T	0.40522	0.1120	L	0.31752	0.955	0.33049	D	0.532449	B;B;B	0.24317	0.101;0.066;0.0	B;B;B	0.20384	0.029;0.013;0.0	T	0.65063	-0.6259	9	0.21540	T	0.41	.	8.509	0.33206	0.0:0.5953:0.3235:0.0813	.	198;188;188	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	T	188;187;188;198	ENSP00000450518:A188T;ENSP00000441640:A188T;ENSP00000444662:A198T	ENSP00000381791:A243T	A	-	1	0	DPF3	72250926	0.998000	0.40836	0.240000	0.24138	0.976000	0.68499	2.465000	0.45075	0.555000	0.29079	0.561000	0.74099	GCC		0.627	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			T	73181173	C	T	73181173	3	4	1	1	0	0	0	0	1	0	0	0	4729	768	27	1	527	1	DPF3	14	73181173	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	22373385	73181173	34168367	134	134										
GOLGA5	9950	hgsc.bcm.edu	37	chr14	93303792	93303792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gagtttttgtaattatatatAtggtaagtaaatttatttga	7	0	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:93303792A>G	ENST00000163416.2	+	12	2369	c.2113A>G	c.(2113-2115)Atg>Gtg	p.M705V	GOLGA5_ENST00000355976.2_Intron	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	705					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		AATTATATATATGGTAAGTAA	0.343			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	0			14											75	86	83					14																	93303792		2203	4300	6503	92373545	SO:0001583	missense	440270			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.2113A>G	14.37:g.93303792A>G	ENSP00000163416:p.Met705Val		92373545	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196276	0.78902	.	.	ENSG00000066455	ENST00000163416;ENST00000439315	T	0.38401	1.14	5.4	5.4	0.78164	.	0.000000	0.56097	D	0.000021	T	0.44222	0.1283	L	0.39397	1.21	0.80722	D	1	D	0.60160	0.987	P	0.55112	0.769	T	0.31447	-0.9943	10	0.45353	T	0.12	-21.6805	14.6183	0.68565	1.0:0.0:0.0:0.0	.	705	Q8TBA6	GOGA5_HUMAN	V	705;614	ENSP00000163416:M705V	ENSP00000163416:M705V	M	+	1	0	GOLGA5	92373545	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	8.568000	0.90741	2.032000	0.59987	0.528000	0.53228	ATG		0.343	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			G	93303792	A	G	93303792	3	3	1	1	0	0	0	0	1	0	0	0	6576	449	16	4	2155	4	GOLGA5	14	93303792	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	20122619	93303792	14045748	135	135										
IFI27	3429	hgsc.bcm.edu	37	chr14	94582135	94582135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcttccctgcagttgtggctGtgcccatggtgctcagtgcc	12	13	2	0	rs200845428		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr14:94582135G>A	ENST00000555744.1	+	4	318	c.130G>A	c.(130-132)Gtg>Atg	p.V44M	IFI27_ENST00000298902.5_Missense_Mutation_p.V44M|IFI27_ENST00000448882.1_Missense_Mutation_p.V47M|IFI27_ENST00000444961.1_Missense_Mutation_p.V47M|IFI27_ENST00000557634.1_Missense_Mutation_p.V34M|IFI27_ENST00000557098.1_5'UTR			P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27	44					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)				breast(1)|lung(3)	4				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)		AGTTGTGGCTGTGCCCATGGT	0.642																																					GBM(128;797 1667 20895 29868 47129)											0			14											14	13	14					14																	94582135		2189	4282	6471	93651888	SO:0001583	missense	3429			X67325	CCDS32148.1	14q32.12	2012-10-02			ENSG00000165949	ENSG00000165949			5397	protein-coding gene	gene with protein product		600009				8358738	Standard	NM_005532		Approved	P27, FAM14D	uc021sba.1	P40305	OTTHUMG00000171303	ENST00000555744.1:c.130G>A	14.37:g.94582135G>A	ENSP00000451956:p.Val44Met		93651888	Q53YA6|Q6IEC1|Q96BK3	Missense_Mutation	SNP	ENST00000555744.1	37	CCDS32148.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.513727	0.27123	.	.	ENSG00000165949	ENST00000554448;ENST00000444961;ENST00000448882;ENST00000554800;ENST00000556544;ENST00000298902;ENST00000557634;ENST00000555744	T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;1.29	3.38	2.49	0.30216	.	0.202210	0.41712	D	0.000826	T	0.47284	0.1437	M	0.87827	2.91	0.09310	N	1	P	0.47034	0.889	P	0.48552	0.581	T	0.44636	-0.9315	10	0.66056	D	0.02	.	6.6799	0.23115	0.131:0.0:0.869:0.0	.	44	P40305	IFI27_HUMAN	M	44;47;47;44;44;44;34;44	ENSP00000451370:V44M;ENSP00000413536:V47M;ENSP00000410901:V47M;ENSP00000451875:V44M;ENSP00000298902:V44M;ENSP00000452560:V34M;ENSP00000451956:V44M	ENSP00000298902:V44M	V	+	1	0	IFI27	93651888	0.095000	0.21747	0.009000	0.14445	0.015000	0.08874	2.609000	0.46317	0.996000	0.38943	-0.379000	0.06801	GTG		0.642	IFI27-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412889.1	NM_005532		A	94582135	G	A	94582135	3	1	1	1	0	0	0	0	1	0	0	0	7533	1377	48	3	140	3	IFI27	14	94582135	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	1278343	94582135	12767405	136	136										
DLL4	54567	hgsc.bcm.edu	37	chr15	41228533	41228533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	actgtgcccgtaacccttgcGcccacggtggcacttgccat	10	16	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr15:41228533G>A	ENST00000249749.5	+	9	1624	c.1348G>A	c.(1348-1350)Gcc>Acc	p.A450T		NM_019074.3	NP_061947.1	Q9NR61	DLL4_HUMAN	delta-like 4 (Drosophila)	450	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac atrium morphogenesis (GO:0003209)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|dorsal aorta morphogenesis (GO:0035912)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of neural precursor cell proliferation (GO:2000179)|regulation of neural retina development (GO:0061074)|regulation of neurogenesis (GO:0050767)|signal transduction (GO:0007165)|ventral spinal cord interneuron fate commitment (GO:0060579)|ventricular trabecula myocardium morphogenesis (GO:0003222)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			breast(3)|large_intestine(1)	4		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		TAACCCTTGCGCCCACGGTGG	0.637																																																0			15											34	37	36					15																	41228533		2171	4259	6430	39015825	SO:0001583	missense	54567			AF253468	CCDS45232.1	15q14	2008-07-03	2001-12-03			ENSG00000128917			2910	protein-coding gene	gene with protein product		605185	"delta-like 4 homolog (Drosophila)"			10837024	Standard	NM_019074		Approved		uc001zng.2	Q9NR61		ENST00000249749.5:c.1348G>A	15.37:g.41228533G>A	ENSP00000249749:p.Ala450Thr		39015825	Q3KP23|Q9NQT9	Missense_Mutation	SNP	ENST00000249749.5	37	CCDS45232.1	.	.	.	.	.	.	.	.	.	.	G	7.221	0.597358	0.13875	.	.	ENSG00000128917	ENST00000249749	T	0.61392	0.11	5.85	4.92	0.64577	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.522071	0.23510	N	0.047419	T	0.46288	0.1385	L	0.53617	1.68	0.40207	D	0.977583	B	0.09022	0.002	B	0.08055	0.003	T	0.39396	-0.9616	10	0.18710	T	0.47	.	5.4299	0.16448	0.0757:0.1167:0.6337:0.1739	.	450	Q9NR61	DLL4_HUMAN	T	450	ENSP00000249749:A450T	ENSP00000249749:A450T	A	+	1	0	DLL4	39015825	1.000000	0.71417	0.920000	0.36463	0.118000	0.20060	3.285000	0.51716	1.453000	0.47775	0.655000	0.94253	GCC		0.637	DLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418859.1			A	41228533	G	A	41228533	3	1	1	1	0	0	0	0	1	0	0	0	4579	1087	38	1	1382	1	DLL4	15	41228533	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10		41228533	61302859	137	137										
SNX33	257364	hgsc.bcm.edu	37	chr15	75942728	75942728	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	aggccatcagtcattccttcCagatggacccccccttttgc	7	16	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr15:75942728C>T	ENST00000308527.5	+	1	2482	c.1285C>T	c.(1285-1287)Cag>Tag	p.Q429*	IMP3_ENST00000314852.2_5'Flank|IMP3_ENST00000565349.1_5'Flank	NM_153271.1	NP_695003.1	Q8WV41	SNX33_HUMAN	sorting nexin 33	429	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038)	cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	19						TCATTCCTTCCAGATGGACCC	0.572																																																0			15											116	105	108					15																	75942728		2197	4294	6491	73729783	SO:0001587	stop_gained	257364			AK091291	CCDS10283.1	15q23	2008-04-18	2008-03-25	2008-03-25	ENSG00000173548	ENSG00000173548			28468	protein-coding gene	gene with protein product			"SH3 and PX domain containing 3"	SH3PX3		16374509, 16782399, 18353773	Standard	NM_153271		Approved	MGC32065, SH3PXD3C, SNX30	uc002bau.3	Q8WV41	OTTHUMG00000142835	ENST00000308527.5:c.1285C>T	15.37:g.75942728C>T	ENSP00000311427:p.Gln429*		73729783	B1NM17	Nonsense_Mutation	SNP	ENST00000308527.5	37	CCDS10283.1	.	.	.	.	.	.	.	.	.	.	C	48	14.517368	0.99799	.	.	ENSG00000173548	ENST00000308527	.	.	.	5.48	5.48	0.80851	.	0.176896	0.51477	D	0.000081	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-14.3268	18.3366	0.90290	0.0:1.0:0.0:0.0	.	.	.	.	X	429	.	ENSP00000311427:Q429X	Q	+	1	0	SNX33	73729783	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.440000	0.52886	2.586000	0.87340	0.561000	0.74099	CAG		0.572	SNX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286471.1	NM_153271		T	75942728	C	T	75942728	4	4	1	1	0	0	0	0	0	1	0	0	14940	595	21	3	1287	3	SNX33	15	75942728	Nonsense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	34714195	75942728	26588664	138	138										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1252441	1252441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgagaagatcccgcatgtggTcggggagcatggtgaggacc	17	9	0	3	rs4984636	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:1252441T>C	ENST00000348261.5	+	9	2239	c.1991T>C	c.(1990-1992)gTc>gCc	p.V664A	CACNA1H_ENST00000565831.1_Missense_Mutation_p.V664A|CACNA1H_ENST00000358590.4_Missense_Mutation_p.V664A	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	664			V -> A (in dbSNP:rs4984636). {ECO:0000269|PubMed:11751928, ECO:0000269|PubMed:12891677, ECO:0000269|PubMed:9670923}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGCATGTGGTCGGGGAGCAT	0.682													T|||	530	0.105831	0.0091	0.1744	5008	,	,		16513	0.002		0.2863	False		,,,				2504	0.1094															0			16						T	ALA/VAL,ALA/VAL	178,3466		11,156,1655	4	5	5		1991,1991	4.5	0.2	16	dbSNP_111	5	1823,5663		248,1327,2168	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	64,64	259,1483,3823	CC,CT,TT		24.3521,4.8847,17.9784	possibly-damaging,possibly-damaging	664/2348,664/2354	1252441	2001,9129	1822	3743	5565	1192442	SO:0001583	missense	8912			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1991T>C	16.37:g.1252441T>C	ENSP00000334198:p.Val664Ala		1192442	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	287	0.13141025641025642	8	0.016260162601626018	63	0.17403314917127072	1	0.0017482517482517483	215	0.2836411609498681	T	17.49	3.403103	0.62288	0.048847	0.243521	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96619	-4.07;-4.01	4.47	4.47	0.54385	.	157.429000	0.00166	N	0.000000	T	0.00178	0.0005	L	0.50333	1.59	0.36796	P	0.11489499999999997	P;D	0.53151	0.571;0.958	B;P	0.46026	0.288;0.501	T	0.54669	-0.8259	9	0.51188	T	0.08	.	13.0686	0.59048	0.0:0.0:0.0:1.0	rs4984636;rs57010276;rs4984636	664;664	O95180-2;O95180	.;CAC1H_HUMAN	A	664	ENSP00000334198:V664A;ENSP00000351401:V664A	ENSP00000334198:V664A	V	+	2	0	CACNA1H	1192442	1.000000	0.71417	0.174000	0.22961	0.858000	0.48976	4.766000	0.62279	1.864000	0.54056	0.533000	0.62120	GTC		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		C	1252441	T	C	1252441	3	2	1	1	0	0	0	0	1	0	0	0	2551	1667	58	4	2021	4	CACNA1H	16	1252441	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10		1252441	89102312	139	139										
ABCA3	21	hgsc.bcm.edu	37	chr16	2369796	2369796	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	catggtactccatgatggccCggtccacagcatgctgcacg	11	14	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:2369796C>A	ENST00000301732.5	-	8	1359	c.659G>T	c.(658-660)cGg>cTg	p.R220L	ABCA3_ENST00000382381.3_Missense_Mutation_p.R220L	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	220					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CATGATGGCCCGGTCCACAGC	0.647																																																0			16											108	87	94					16																	2369796		2198	4300	6498	2309797	SO:0001583	missense	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.659G>T	16.37:g.2369796C>A	ENSP00000301732:p.Arg220Leu		2309797	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	9.974	1.226211	0.22542	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.90324	-2.65	5.18	-2.37	0.06643	.	0.328711	0.31809	N	0.007026	D	0.86331	0.5907	M	0.75884	2.315	0.09310	N	1	P;B;B	0.34934	0.476;0.008;0.166	B;B;B	0.34093	0.175;0.048;0.173	T	0.79107	-0.1939	10	0.72032	D	0.01	.	6.7053	0.23246	0.1169:0.4771:0.0:0.406	.	220;282;220	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	L	220;282	ENSP00000301732:R220L	ENSP00000301732:R220L	R	-	2	0	ABCA3	2309797	0.007000	0.16637	0.019000	0.16419	0.013000	0.08279	0.395000	0.20850	-0.230000	0.09840	-0.136000	0.14681	CGG		0.647	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2369796	C	A	2369796	3	1	1	1	0	0	0	0	1	0	0	0	33	652	23	2	4559	2	ABCA3	16	2369796	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	1117355	2369796	87984957	140	140										
CORO7	79585	hgsc.bcm.edu	37	chr16	4411003	4411003	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agcctgaaggtcccagatgcGaacagtgaggtcataggagg	15	8	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:4411003G>T	ENST00000251166.4	-	19	2003	c.1858C>A	c.(1858-1860)Cgc>Agc	p.R620S	CORO7_ENST00000574025.1_Missense_Mutation_p.R535S|CORO7_ENST00000537233.2_Missense_Mutation_p.R602S|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.R620S|CORO7_ENST00000539968.1_Missense_Mutation_p.R400S|CORO7-PAM16_ENST00000572274.1_5'Flank|CORO7_ENST00000423908.2_3'UTR	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	620					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						TCCCAGATGCGAACAGTGAGG	0.637																																																0			16											95	85	88					16																	4411003		2196	4300	6496	4351004	SO:0001583	missense	79585			AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.1858C>A	16.37:g.4411003G>T	ENSP00000251166:p.Arg620Ser		4351004	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660401	0.67586	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968	T;T	0.67345	-0.26;-0.26	5.17	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.056297	0.64402	D	0.000001	T	0.76688	0.4022	M	0.72576	2.205	0.80722	D	1	D;P;D;D;D	0.71674	0.998;0.956;0.991;0.975;0.995	D;P;P;P;D	0.69142	0.94;0.733;0.878;0.878;0.962	T	0.75878	-0.3162	10	0.51188	T	0.08	-14.2097	8.1675	0.31235	0.0872:0.0:0.7622:0.1506	.	535;602;400;620;601	P57737-2;B4DFD6;B3KUH7;P57737;B4DKU9	.;.;.;CORO7_HUMAN;.	S	620;535;400	ENSP00000251166:R620S;ENSP00000446221:R400S	ENSP00000251166:R620S	R	-	1	0	CORO7	4351004	1.000000	0.71417	0.839000	0.33178	0.745000	0.42441	2.912000	0.48782	0.991000	0.38814	0.455000	0.32223	CGC		0.637	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535		T	4411003	G	T	4411003	3	4	1	1	0	0	0	0	1	0	0	0	3765	1058	37	2	959	2	CORO7	16	4411003	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	2041207	4411003	85943750	141	141										
NOD2	64127	hgsc.bcm.edu	37	chr16	50745482	50745482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcctgcacctgggcagactgGctctgtggggcctgggcatg	16	12	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:50745482G>A	ENST00000300589.2	+	4	1765	c.1660G>A	c.(1660-1662)Gct>Act	p.A554T	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	554	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				GGGCAGACTGGCTCTGTGGGG	0.632																																																0			16											33	35	34					16																	50745482		2198	4300	6498	49302983	SO:0001583	missense	64127			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1660G>A	16.37:g.50745482G>A	ENSP00000300589:p.Ala554Thr		49302983	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188469	0.57909	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	D	0.89617	-2.54	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000012	D	0.95348	0.8490	M	0.91818	3.245	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.96101	0.9069	10	0.87932	D	0	.	14.1217	0.65192	0.0:0.0:1.0:0.0	.	338;527;554	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	T	527;554	ENSP00000300589:A554T	ENSP00000300589:A554T	A	+	1	0	NOD2	49302983	1.000000	0.71417	0.998000	0.56505	0.044000	0.14063	8.484000	0.90445	2.399000	0.81585	0.556000	0.70494	GCT		0.632	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50745482	G	A	50745482	3	1	1	1	0	0	0	0	1	0	0	0	10548	1203	42	3	1674	3	NOD2	16	50745482	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	46334479	50745482	39609271	142	142										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55703563	55703563	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tggctctgggacagtacaacCgggagggggctgccaccgtt	16	11	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:55703563C>T	ENST00000379906.2	+	2	616	c.361C>T	c.(361-363)Cgg>Tgg	p.R121W	SLC6A2_ENST00000414754.3_Missense_Mutation_p.R121W|SLC6A2_ENST00000219833.8_Missense_Mutation_p.R121W|SLC6A2_ENST00000568943.1_Missense_Mutation_p.R121W|SLC6A2_ENST00000567238.1_5'Flank|SLC6A2_ENST00000561820.1_Missense_Mutation_p.R121W|SLC6A2_ENST00000566163.1_Missense_Mutation_p.R121W	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	121					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	ACAGTACAACCGGGAGGGGGC	0.547																																																0			16											69	61	63					16																	55703563		2198	4300	6498	54261064	SO:0001583	missense	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.361C>T	16.37:g.55703563C>T	ENSP00000369237:p.Arg121Trp		54261064	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487423	0.44249	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	T;T;T	0.78126	-1.15;-1.15;-1.15	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.92251	0.7542	H	0.97540	4.025	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94268	0.7508	10	0.87932	D	0	.	14.9552	0.71107	0.1428:0.8572:0.0:0.0	.	121;121	Q96KH8;P23975	.;SC6A2_HUMAN	W	121	ENSP00000394956:R121W;ENSP00000369237:R121W;ENSP00000219833:R121W	ENSP00000219833:R121W	R	+	1	2	SLC6A2	54261064	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.758000	0.26447	2.778000	0.95560	0.655000	0.94253	CGG		0.547	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			T	55703563	C	T	55703563	3	4	1	1	0	0	0	0	1	0	0	0	14720	643	23	1	367	1	SLC6A2	16	55703563	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	4958081	55703563	34651190	143	143										
KIAA0895L	653319	hgsc.bcm.edu	37	chr16	67212282	67212282	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gaacggctgcttgcggaacaGcacgctgtgcaggctggcca	15	12	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:67212282G>C	ENST00000290881.7	-	6	1899	c.973C>G	c.(973-975)Ctg>Gtg	p.L325V	KIAA0895L_ENST00000563902.1_Missense_Mutation_p.L325V|KIAA0895L_ENST00000561621.1_Missense_Mutation_p.L325V|KIAA0895L_ENST00000563831.2_5'UTR			Q68EN5	K895L_HUMAN	KIAA0895-like	325										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						TTGCGGAACAGCACGCTGTGC	0.706																																																0			16											8	10	10					16																	67212282		2049	4166	6215	65769783	SO:0001583	missense	653319			AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.973C>G	16.37:g.67212282G>C	ENSP00000290881:p.Leu325Val		65769783	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Missense_Mutation	SNP	ENST00000290881.7	37	CCDS42177.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301998	0.81136	.	.	ENSG00000196123	ENST00000290881	.	.	.	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.78672	0.4320	M	0.78223	2.4	0.54753	D	0.999984	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.996;0.999;0.994	T	0.80331	-0.1427	9	0.52906	T	0.07	-14.6329	15.1423	0.72620	0.0:0.0:1.0:0.0	.	325;325;170	Q68EN5-2;Q68EN5;Q68EN5-3	.;K895L_HUMAN;.	V	325	.	ENSP00000290881:L325V	L	-	1	2	KIAA0895L	65769783	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.344000	0.59354	2.510000	0.84645	0.585000	0.79938	CTG		0.706	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715		C	67212282	G	C	67212282	3	2	1	1	0	0	0	0	1	0	0	0	8219	962	34	5	454	5	KIAA0895L	16	67212282	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	11508719	67212282	23142471	144	144										
THAP11	57215	hgsc.bcm.edu	37	chr16	67876826	67876826	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cagcagcagcagcagcaacaGcagcagcagcagcagcagca	12	14	0	0	rs3982383|rs377516180|rs111586870	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:67876826G>A	ENST00000303596.1	+	1	614	c.369G>A	c.(367-369)caG>caA	p.Q123Q	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	123	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		agcagcaacagcagcagcagc	0.687													G|||	927	0.185104	0.3585	0.1686	5008	,	,		13659	0.0298		0.1372	False		,,,				2504	0.1718															0			16											21	31	28					16																	67876826		2013	3937	5950	66434327	SO:0001819	synonymous_variant	57215			AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"THAP (C2CH-type zinc finger) domain containing"	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.369G>A	16.37:g.67876826G>A			66434327	A4UCT5|A8K002|O94795	Silent	SNP	ENST00000303596.1	37	CCDS10847.1																																																																																				0.687	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457		A	67876826	G	A	67876826	2	1	1	1	0	0	0	0	0	0	0	1	15882	962	34	3		3	THAP11	16	67876826	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	664544	67876826	22477927	145	145										
CDH1	999	hgsc.bcm.edu	37	chr16	68844147	68844147	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gggaatgcagttgaggatccAatggagattttgatcacggt	14	5	1	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:68844147A>G	ENST00000261769.5	+	6	926	c.735A>G	c.(733-735)ccA>ccG	p.P245P	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Silent_p.P245P	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	245	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TTGAGGATCCAATGGAGATTT	0.488			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	4	Unknown(4)	breast(4)	16											162	149	154					16																	68844147		2198	4300	6498	67401648	SO:0001819	synonymous_variant	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.735A>G	16.37:g.68844147A>G			67401648	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																				0.488	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68844147	A	G	68844147	2	3	1	1	0	0	0	0	0	0	0	1	3101	117	5	4		4	CDH1	16	68844147	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	967321	68844147	21510606	146	146										
CDH1	999	hgsc.bcm.edu	37	chr16	68844172	68844172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agattttgatcacggtaaccGatcagaatgacaacaagccc	8	10	2	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:68844172G>A	ENST00000261769.5	+	6	951	c.760G>A	c.(760-762)Gat>Aat	p.D254N	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.D254N	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	254	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(4)|p.D254H(1)|p.D254Y(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACGGTAACCGATCAGAATGA	0.468			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	6	Unknown(4)|Substitution - Missense(2)	breast(6)	16											150	141	144					16																	68844172		2198	4300	6498	67401673	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.760G>A	16.37:g.68844172G>A	ENSP00000261769:p.Asp254Asn		67401673	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818611	0.90790	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	D;D	0.88509	-2.39;-2.39	5.22	5.22	0.72569	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.51477	D	0.000098	D	0.95720	0.8608	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.96300	0.9220	10	0.66056	D	0.02	.	17.9295	0.88992	0.0:0.0:1.0:0.0	.	254;254	Q9UII8;P12830	.;CADH1_HUMAN	N	254	ENSP00000261769:D254N;ENSP00000414946:D254N	ENSP00000261769:D254N	D	+	1	0	CDH1	67401673	1.000000	0.71417	0.952000	0.39060	0.499000	0.33736	9.476000	0.97823	2.592000	0.87571	0.557000	0.71058	GAT		0.468	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68844172	G	A	68844172	3	1	1	1	0	0	0	0	1	0	0	0	3101	1058	37	1	782	1	CDH1	16	68844172	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	25	68844172	21510581	147	147										
CALB2	794	hgsc.bcm.edu	37	chr16	71417308	71417308	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctgaagaaggcgaaccggccGtacgatgagcccaagctcca	12	13	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:71417308G>A	ENST00000302628.4	+	6	515	c.438G>A	c.(436-438)ccG>ccA	p.P146P	CALB2_ENST00000349553.5_Silent_p.P146P	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	146					cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				CGAACCGGCCGTACGATGAGC	0.547																																																0			16											118	90	99					16																	71417308		2198	4300	6498	69974809	SO:0001819	synonymous_variant	794			X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"EF-hand domain containing"	1435	protein-coding gene	gene with protein product	"calretinin"	114051	"calbindin 2, 29kDa (calretinin)"			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.438G>A	16.37:g.71417308G>A			69974809	A8K4Y1|Q53HD2|Q96BK4	Silent	SNP	ENST00000302628.4	37	CCDS10899.1																																																																																				0.547	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740		A	71417308	G	A	71417308	2	1	1	1	0	0	0	0	0	0	0	1	2580	1132	40	1		1	CALB2	16	71417308	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	2573136	71417308	18937445	148	148										
ACSF3	197322	hgsc.bcm.edu	37	chr16	89178630	89178630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gcacgcccaggatttcttgcGtgcagtttgtgaagaaaaaa	11	8	1	2	rs200352879		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:89178630G>A	ENST00000317447.4	+	5	1330	c.953G>A	c.(952-954)cGt>cAt	p.R318H	ACSF3_ENST00000378345.4_Missense_Mutation_p.R53H|ACSF3_ENST00000406948.3_Missense_Mutation_p.R318H|CTD-2555A7.3_ENST00000562782.1_RNA	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	318					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		GATTTCTTGCGTGCAGTTTGT	0.423																																																0			16											146	153	151					16																	89178630		2198	4300	6498	87706131	SO:0001583	missense	197322			AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"Acyl-CoA synthetase family"	27288	protein-coding gene	gene with protein product	"malonyl-CoA synthetase"	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.953G>A	16.37:g.89178630G>A	ENSP00000320646:p.Arg318His		87706131	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Missense_Mutation	SNP	ENST00000317447.4	37	CCDS10974.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.288568	0.23478	.	.	ENSG00000176715	ENST00000537895;ENST00000317447;ENST00000540697;ENST00000406948;ENST00000378345;ENST00000544543;ENST00000538340	T;T;T;T;T;T;T	0.55588	2.78;0.72;2.78;0.72;1.03;0.81;0.51	4.49	2.51	0.30379	AMP-dependent synthetase/ligase (1);	0.174789	0.49916	N	0.000125	T	0.46328	0.1387	L	0.55103	1.725	0.35667	D	0.813029	B	0.23806	0.091	B	0.28232	0.087	T	0.53913	-0.8371	10	0.44086	T	0.13	-10.3346	9.5942	0.39565	0.1697:0.0:0.8303:0.0	.	318	Q4G176	ACSF3_HUMAN	H	53;318;53;318;53;53;93	ENSP00000439201:R53H;ENSP00000320646:R318H;ENSP00000445397:R53H;ENSP00000384627:R318H;ENSP00000367596:R53H;ENSP00000442781:R53H;ENSP00000445870:R93H	ENSP00000320646:R318H	R	+	2	0	ACSF3	87706131	1.000000	0.71417	0.922000	0.36590	0.026000	0.11368	1.180000	0.32005	0.897000	0.36392	0.558000	0.71614	CGT		0.423	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917		A	89178630	G	A	89178630	3	1	1	1	0	0	0	0	1	0	0	0	176	1145	40	1	963	1	ACSF3	16	89178630	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	17761322	89178630	1176123	149	149										
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89935986	89935986	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gtgctgcagatgaagatgccTtctaagaaatttggacacat	10	7	1	4			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr16:89935986T>C	ENST00000378247.3	+	14	1861	c.1818T>C	c.(1816-1818)ccT>ccC	p.P606P	SPIRE2_ENST00000393062.2_Intron	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	606					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TGAAGATGCCTTCTAAGAAAT	0.532																																																0			16											118	97	104					16																	89935986		2198	4300	6498	88463487	SO:0001819	synonymous_variant	84501			AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"spire homolog 2 (Drosophila)", "spire family actin nucleation factor 2"			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1818T>C	16.37:g.89935986T>C			88463487	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Silent	SNP	ENST00000378247.3	37	CCDS32516.1																																																																																				0.532	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		C	89935986	T	C	89935986	2	2	1	1	0	0	0	0	0	0	0	1	15111	1596	56	4		4	SPIRE2	16	89935986	Silent	SNP	T	TCGA-AF-2687-01A-02D-1733-10	757356	89935986	418767	150	150										
TP53	7157	hgsc.bcm.edu	37	chr17	7577102	7577102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cctctgtgcgccggtctctcCcaggacaggcacaaacacgc	10	17	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:7577102C>T	ENST00000269305.4	-	8	1025	c.836G>A	c.(835-837)gGg>gAg	p.G279E	TP53_ENST00000445888.2_Missense_Mutation_p.G279E|TP53_ENST00000359597.4_Missense_Mutation_p.G279E|TP53_ENST00000420246.2_Missense_Mutation_p.G279E|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G279E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	279	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).|G -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G279E(32)|p.0?(8)|p.G279V(4)|p.?(2)|p.G279fs*65(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.G279_R280delGR(1)|p.F270_D281del12(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.G279fs*26(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGGTCTCTCCCAGGACAGGC	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	60	Substitution - Missense(36)|Deletion - Frameshift(8)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(2)	upper_aerodigestive_tract(16)|urinary_tract(8)|oesophagus(7)|breast(5)|bone(5)|haematopoietic_and_lymphoid_tissue(4)|skin(4)|large_intestine(3)|central_nervous_system(3)|ovary(2)|stomach(1)|lung(1)|liver(1)	17											75	65	68					17																	7577102		2203	4300	6503	7517827	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.836G>A	17.37:g.7577102C>T	ENSP00000269305:p.Gly279Glu		7517827	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753775	0.89753	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99898	-7.61;-7.61;-7.61;-7.61;-7.61;-7.61	5.13	4.16	0.48862	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.90425	3.115	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.999;0.991;0.999;1.0	D	0.96457	0.9338	10	0.87932	D	0	-22.6503	11.5187	0.50539	0.0:0.9131:0.0:0.0869	.	279;279;279;279	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	E	279;279;279;279;279;268;147	ENSP00000352610:G279E;ENSP00000269305:G279E;ENSP00000398846:G279E;ENSP00000391127:G279E;ENSP00000391478:G279E;ENSP00000425104:G147E	ENSP00000269305:G279E	G	-	2	0	TP53	7517827	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.862000	0.69560	1.390000	0.46547	0.462000	0.41574	GGG		0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577102	C	T	7577102	3	4	1	1	0	0	0	0	1	0	0	0	16421	623	22	3	450	3	TP53	17	7577102	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10		7577102	73618108	151	151			1	1		4	4	2765	N	T_C	8.15226e-07
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	1	1	0	0	0	0	1	0	0	0	16421	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	436	7577538	73617672	152	152			1	1		4	4	2765	N	T_C	8.15226e-07
TP53	7157	hgsc.bcm.edu	37	chr17	7578273	7578273	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccttccactcggataagatgCtgaggaggggccagacctaa	12	11	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:7578273C>A	ENST00000269305.4	-	6	765	c.576G>T	c.(574-576)caG>caT	p.Q192H	TP53_ENST00000445888.2_Missense_Mutation_p.Q192H|TP53_ENST00000359597.4_Missense_Mutation_p.Q192H|TP53_ENST00000420246.2_Missense_Mutation_p.Q192H|TP53_ENST00000413465.2_Missense_Mutation_p.Q192H|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.Q192H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	192	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> L (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(6)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.Q192H(3)|p.P191fs*53(2)|p.Q192Q(2)|p.P191fs*15(1)|p.Q192>XXXXXXXXX(1)|p.Q192del(1)|p.P191fs*6(1)|p.P98_E105>Q(1)|p.P191_Q192delPQ(1)|p.P59_E66>Q(1)|p.A189fs*53(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGATAAGATGCTGAGGAGGGG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	36	Whole gene deletion(8)|Deletion - In frame(6)|Unknown(6)|Complex - deletion inframe(5)|Deletion - Frameshift(4)|Substitution - Missense(3)|Substitution - coding silent(2)|Complex - frameshift(1)|Complex - insertion inframe(1)	breast(6)|biliary_tract(5)|skin(4)|bone(4)|stomach(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|lung(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|liver(1)|large_intestine(1)	17											93	83	87					17																	7578273		2203	4300	6503	7518998	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.576G>T	17.37:g.7578273C>A	ENSP00000269305:p.Gln192His		7518998	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	8.951	0.968192	0.18659	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99760	-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66	5.41	2.22	0.28083	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.242461	0.43260	N	0.000594	D	0.99542	0.9836	M	0.70903	2.155	0.45216	D	0.99822	B;B;B;B;B;B;D	0.76494	0.186;0.022;0.12;0.057;0.027;0.027;0.999	B;B;B;B;B;B;D	0.72075	0.094;0.036;0.112;0.055;0.061;0.091;0.976	D	0.99466	1.0944	10	0.87932	D	0	-22.6404	7.338	0.26621	0.424:0.4986:0.0:0.0773	.	153;192;192;99;192;192;192	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	192;192;192;192;192;192;181;99;60;99;60	ENSP00000410739:Q192H;ENSP00000352610:Q192H;ENSP00000269305:Q192H;ENSP00000398846:Q192H;ENSP00000391127:Q192H;ENSP00000391478:Q192H;ENSP00000425104:Q60H;ENSP00000423862:Q99H	ENSP00000269305:Q192H	Q	-	3	2	TP53	7518998	0.457000	0.25752	0.975000	0.42487	0.036000	0.12997	-0.237000	0.08990	0.312000	0.23038	0.655000	0.94253	CAG		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578273	C	A	7578273	3	1	1	1	0	0	0	0	1	0	0	0	16421	796	28	2	718	2	TP53	17	7578273	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	735	7578273	73616937	153	153			1	1		4	4	2765	N	T_C	8.15226e-07
TP53	7157	hgsc.bcm.edu	37	chr17	7579866	7579866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ataggtctgaaaatgtttccTgactcagagggggctcgacg	13	8	2	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:7579866T>A	ENST00000269305.4	-	2	236	c.47A>T	c.(46-48)cAg>cTg	p.Q16L	TP53_ENST00000445888.2_Missense_Mutation_p.Q16L|TP53_ENST00000359597.4_Missense_Mutation_p.Q16L|TP53_ENST00000420246.2_Missense_Mutation_p.Q16L|TP53_ENST00000413465.2_Missense_Mutation_p.Q16L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.Q16L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	16	Interaction with HRMT1L2.|Transcription activation (acidic).		Q -> L (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.Q16L(2)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AAATGTTTCCTGACTCAGAGG	0.602		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	11	Whole gene deletion(8)|Substitution - Missense(2)|Deletion - Frameshift(1)	bone(4)|central_nervous_system(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)	17											50	46	47					17																	7579866		2203	4300	6503	7520591	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.47A>T	17.37:g.7579866T>A	ENSP00000269305:p.Gln16Leu		7520591	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	19.50	3.839456	0.71488	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D;D	0.99503	-5.55;-6.03;-5.75;-6.03;-6.03;-5.75;-5.75;-4.43;-2.49	5.36	5.36	0.76844	p53 transactivation domain (1);	0.302055	0.34245	N	0.004123	D	0.99420	0.9795	M	0.81942	2.565	0.48135	D	0.999595	D;D;D;P;D;D;D	0.89917	1.0;0.998;0.981;0.77;1.0;0.999;0.997	D;D;D;P;D;D;D	0.80764	0.993;0.985;0.969;0.537;0.991;0.982;0.994	D	0.98662	1.0684	10	0.87932	D	0	-30.4841	12.0477	0.53489	0.0:0.0:0.0:1.0	.	16;16;16;16;16;16;16	E7EMR6;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	L	16	ENSP00000410739:Q16L;ENSP00000352610:Q16L;ENSP00000269305:Q16L;ENSP00000398846:Q16L;ENSP00000391127:Q16L;ENSP00000391478:Q16L;ENSP00000423862:Q16L;ENSP00000424104:Q16L;ENSP00000426252:Q16L	ENSP00000269305:Q16L	Q	-	2	0	TP53	7520591	1.000000	0.71417	0.999000	0.59377	0.498000	0.33706	4.667000	0.61561	2.171000	0.68590	0.459000	0.35465	CAG		0.602	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7579866	T	A	7579866	3	1	1	1	0	0	0	0	1	0	0	0	16421	1580	55	5	1263	5	TP53	17	7579866	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	1593	7579866	73615344	154	154			1	1		4	4	2765	N	T_C	8.15226e-07
TOP3A	7156	hgsc.bcm.edu	37	chr17	18210248	18210248	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ggcagtacttttcaatttctGcttcaaagaggacaagaggg	11	7	3	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:18210248G>T	ENST00000321105.5	-	4	561	c.347C>A	c.(346-348)gCa>gAa	p.A116E	TOP3A_ENST00000542570.1_Missense_Mutation_p.A21E|TOP3A_ENST00000582230.1_5'Flank	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	116	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TTCAATTTCTGCTTCAAAGAG	0.438																																																0			17											87	84	85					17																	18210248		2203	4300	6503	18150973	SO:0001583	missense	7156			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.347C>A	17.37:g.18210248G>T	ENSP00000321636:p.Ala116Glu		18150973	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.65|18.65	3.670133|3.670133	0.67814|0.67814	.|.	.|.	ENSG00000177302|ENSG00000177302	ENST00000321105;ENST00000542570|ENST00000412083	T;T|.	0.21734|.	1.99;2.76|.	5.84|5.84	5.84|5.84	0.93424|0.93424	DNA topoisomerase, type IA, core domain (1);Toprim domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86159|0.86159	0.5866|0.5866	M|M	0.90759|0.90759	3.145|3.145	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	D|D	0.87704|0.87704	0.2562|0.2562	10|5	0.87932|.	D|.	0|.	-13.5484|-13.5484	20.1342|20.1342	0.98015|0.98015	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	21;116|.	B4DK80;Q13472|.	.;TOP3A_HUMAN|.	E|R	116;21|95	ENSP00000321636:A116E;ENSP00000442336:A21E|.	ENSP00000321636:A116E|.	A|S	-|-	2|3	0|2	TOP3A|TOP3A	18150973|18150973	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.377000|9.377000	0.97184|0.97184	2.754000|2.754000	0.94517|0.94517	0.655000|0.655000	0.94253|0.94253	GCA|AGC		0.438	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			T	18210248	G	T	18210248	3	4	1	1	0	0	0	0	1	0	0	0	16407	1319	46	2	2722	2	TOP3A	17	18210248	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	10630382	18210248	62984962	155	155										
SPAG5	10615	hgsc.bcm.edu	37	chr17	26919703	26919703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gataggtttctcagatacagCagcaacttctgaaaacctgt	8	9	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:26919703C>T	ENST00000321765.5	-	3	891	c.559G>A	c.(559-561)Gct>Act	p.A187T		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	187					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)		p.A187T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TCAGATACAGCAGCAACTTCT	0.463																																																1	Substitution - Missense(1)	central_nervous_system(1)	17											116	114	115					17																	26919703		2203	4300	6503	23943830	SO:0001583	missense	10615			AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.559G>A	17.37:g.26919703C>T	ENSP00000323300:p.Ala187Thr		23943830	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	C	4.241	0.043621	0.08196	.	.	ENSG00000076382	ENST00000321765	T	0.23950	1.88	5.89	-2.61	0.06171	.	1.259610	0.05317	N	0.525941	T	0.12817	0.0311	N	0.11560	0.145	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.28586	-1.0039	10	0.41790	T	0.15	7.1699	5.4205	0.16398	0.1327:0.3823:0.0:0.485	.	187	Q96R06	SPAG5_HUMAN	T	187	ENSP00000323300:A187T	ENSP00000323300:A187T	A	-	1	0	SPAG5	23943830	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.435000	0.06931	-0.719000	0.04942	-0.150000	0.13652	GCT		0.463	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		T	26919703	C	T	26919703	3	4	1	1	0	0	0	0	1	0	0	0	15020	710	25	3	3110	3	SPAG5	17	26919703	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	8709455	26919703	54275507	156	156										
CDK12	51755	hgsc.bcm.edu	37	chr17	37676317	37676317	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gacttccttaaagatgtcgaActcagcaaaatggctcctcc	7	12	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:37676317A>G	ENST00000447079.4	+	11	3105	c.3072A>G	c.(3070-3072)gaA>gaG	p.E1024E	CDK12_ENST00000430627.2_Silent_p.E1024E	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1024					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						AAGATGTCGAACTCAGCAAAA	0.473			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0			17											131	111	118					17																	37676317		2203	4300	6503	34929843	SO:0001819	synonymous_variant	0			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3072A>G	17.37:g.37676317A>G			34929843	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																				0.473	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		G	37676317	A	G	37676317	2	3	1	1	0	0	0	0	0	0	0	1	3134	40	2	4		4	CDK12	17	37676317	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	10756614	37676317	43518893	157	157										
NMT1	4836	hgsc.bcm.edu	37	chr17	43182230	43182230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tccctgctgctttgcagaaaGggtttgatgtgttcaatgca	11	8	1	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:43182230G>A	ENST00000592782.1	+	12	1467	c.1336G>A	c.(1336-1338)Ggg>Agg	p.G446R	NMT1_ENST00000258960.2_Missense_Mutation_p.G446R			P30419	NMT1_HUMAN	N-myristoyltransferase 1	446					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				TTTGCAGAAAGGGTTTGATGT	0.502																																																0			17											147	145	146					17																	43182230		2203	4300	6503	40537756	SO:0001583	missense	4836				CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"alternative, short form NMT-S", "myristoyl-CoA:protein N-myristoyltransferase", "long form, NMT-L"	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.1336G>A	17.37:g.43182230G>A	ENSP00000468424:p.Gly446Arg		40537756	A8K7C1|Q9UE09	Missense_Mutation	SNP	ENST00000592782.1	37	CCDS11494.1	.	.	.	.	.	.	.	.	.	.	G	34	5.336026	0.95758	.	.	ENSG00000136448	ENST00000258960	T	0.45276	0.9	5.93	5.93	0.95920	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68439	0.3001	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.69606	-0.5100	10	0.72032	D	0.01	-21.4263	20.3437	0.98782	0.0:0.0:1.0:0.0	.	446	P30419	NMT1_HUMAN	R	446	ENSP00000258960:G446R	ENSP00000258960:G446R	G	+	1	0	NMT1	40537756	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.760000	0.98935	2.815000	0.96918	0.561000	0.74099	GGG		0.502	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079		A	43182230	G	A	43182230	3	1	1	1	0	0	0	0	1	0	0	0	10534	1000	35	3	1378	3	NMT1	17	43182230	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	5505913	43182230	38012980	158	158										
SKAP1	8631	hgsc.bcm.edu	37	chr17	46265270	46265270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	accatcgcttctgccactccGatccaaagaaactatgatct	5	14	2	2	rs368601769		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:46265270G>A	ENST00000336915.6	-	6	446	c.377C>T	c.(376-378)tCg>tTg	p.S126L	RP11-456D7.1_ENST00000582246.1_RNA|SKAP1_ENST00000584924.1_Missense_Mutation_p.S126L	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	126	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						CTGCCACTCCGATCCAAAGAA	0.413																																																0			17						G	LEU/SER,LEU/SER	0,4406		0,0,2203	113	97	103		377,377	6	1	17		103	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SKAP1	NM_001075099.1,NM_003726.3	145,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	126/359,126/360	46265270	1,13005	2203	4300	6503	43620269	SO:0001583	missense	8631			Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.377C>T	17.37:g.46265270G>A	ENSP00000338171:p.Ser126Leu		43620269	D3DTV1|O15268	Missense_Mutation	SNP	ENST00000336915.6	37	CCDS32674.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.452544	0.43531	0.0	1.16E-4	ENSG00000141293	ENST00000336915	T	0.13307	2.6	6.04	6.04	0.98038	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.199846	0.45126	D	0.000384	T	0.26991	0.0661	L	0.38838	1.175	0.47778	D	0.999511	P;D	0.89917	0.602;1.0	B;P	0.62649	0.022;0.905	T	0.00501	-1.1702	10	0.21014	T	0.42	-3.0535	20.1899	0.98228	0.0:0.0:1.0:0.0	.	126;126	Q86WV1-2;Q86WV1	.;SKAP1_HUMAN	L	126	ENSP00000338171:S126L	ENSP00000338171:S126L	S	-	2	0	SKAP1	43620269	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	5.318000	0.65829	2.873000	0.98535	0.563000	0.77884	TCG		0.413	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		A	46265270	G	A	46265270	3	1	1	1	0	0	0	0	1	0	0	0	14392	1059	37	1	730	1	SKAP1	17	46265270	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	3083040	46265270	34929940	159	159										
ZNF652	22834	hgsc.bcm.edu	37	chr17	47394440	47394440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttacgcttaggtggctctacActcttcctacgacctcttgt	7	13	3	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:47394440A>G	ENST00000362063.2	-	2	966	c.648T>C	c.(646-648)agT>agC	p.S216S	ZNF652_ENST00000430262.2_Silent_p.S216S	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S216R(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			GTGGCTCTACACTCTTCCTAC	0.517																																																1	Substitution - Missense(1)	ovary(1)	17											118	104	109					17																	47394440		2203	4300	6503	44749439	SO:0001819	synonymous_variant	22834			AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"Zinc fingers, C2H2-type"	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.648T>C	17.37:g.47394440A>G			44749439	A4QPD9|Q5H9Q0	Silent	SNP	ENST00000362063.2	37	CCDS32677.1																																																																																				0.517	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		G	47394440	A	G	47394440	2	3	1	1	0	0	0	0	0	0	0	1	18104	156	6	4		4	ZNF652	17	47394440	Silent	SNP	A	TCGA-AF-2687-01A-02D-1733-10	1129170	47394440	33800770	160	160										
ACE	1636	hgsc.bcm.edu	37	chr17	61561265	61561265	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atgaagccctgtgcaaggagGcaggctatgagggcccactg	15	10	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:61561265G>T	ENST00000290866.4	+	11	1666	c.1642G>T	c.(1642-1644)Gca>Tca	p.A548S	ACE_ENST00000421982.2_5'Flank|ACE_ENST00000490216.2_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000428043.1_Missense_Mutation_p.A548S|ACE_ENST00000413513.3_5'Flank|ACE_ENST00000577647.1_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	548	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GTGCAAGGAGGCAGGCTATGA	0.617																																																0			17											88	74	79					17																	61561265		2203	4300	6503	58914997	SO:0001583	missense	1636			J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1642G>T	17.37:g.61561265G>T	ENSP00000290866:p.Ala548Ser		58914997	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.877816	0.91664	.	.	ENSG00000159640	ENST00000290866;ENST00000428043	T;T	0.44482	0.92;0.92	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	L	0.52126	1.63	0.80722	D	1	D;B	0.65815	0.995;0.051	D;P	0.79784	0.993;0.447	T	0.52223	-0.8604	10	0.31617	T	0.26	-15.5179	19.8372	0.96661	0.0:0.0:1.0:0.0	.	548;548	P12821-2;P12821	.;ACE_HUMAN	S	548	ENSP00000290866:A548S;ENSP00000397593:A548S	ENSP00000290866:A548S	A	+	1	0	ACE	58914997	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.765000	0.98953	2.695000	0.91970	0.462000	0.41574	GCA		0.617	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			T	61561265	G	T	61561265	3	4	1	1	0	0	0	0	1	0	0	0	136	1203	42	2	1684	2	ACE	17	61561265	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	14166825	61561265	19633945	161	161										
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73481572	73481572	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcagcgtcctgaaggagcagCtggaggcagtgctggaagga	17	8	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:73481572C>T	ENST00000314256.7	+	3	482	c.88C>T	c.(88-90)Ctg>Ttg	p.L30L	KIAA0195_ENST00000375248.5_Silent_p.L40L|KIAA0195_ENST00000579208.1_Intron	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	30						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAAGGAGCAGCTGGAGGCAGT	0.657																																																0			17											93	91	92					17																	73481572		2203	4300	6503	70993167	SO:0001819	synonymous_variant	9772				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.88C>T	17.37:g.73481572C>T			70993167	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																				0.657	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		T	73481572	C	T	73481572	2	4	1	1	0	0	0	0	0	0	0	1	8181	796	28	3		3	KIAA0195	17	73481572	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	11920307	73481572	7713638	162	162										
FBF1	85302	hgsc.bcm.edu	37	chr17	73922457	73922457	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cccatcatcaaacaacaattCttctttttttcggatggggg	7	10	4	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr17:73922457C>T	ENST00000586717.1	-	10	877	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	FBF1_ENST00000389570.4_Missense_Mutation_p.E202K|FBF1_ENST00000319129.5_Missense_Mutation_p.E202K			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	202					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						AACAACAATTCTTCTTTTTTT	0.507																																																0			17											33	34	34					17																	73922457		1881	4105	5986	71434052	SO:0001583	missense	85302			AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.604G>A	17.37:g.73922457C>T	ENSP00000465132:p.Glu202Lys		71434052	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		.	.	.	.	.	.	.	.	.	.	C	12.16	1.854282	0.32791	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.24151	1.87;1.87	4.88	3.91	0.45181	.	.	.	.	.	T	0.30792	0.0776	M	0.61703	1.905	0.22896	N	0.998595	B;B;B	0.33694	0.29;0.17;0.421	B;B;B	0.37601	0.107;0.165;0.254	T	0.19844	-1.0293	9	0.66056	D	0.02	-1.3408	11.1053	0.48199	0.0:0.9121:0.0:0.0879	.	216;202;202	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	K	202;202;202;215	ENSP00000374221:E202K;ENSP00000324292:E202K	ENSP00000324292:E202K	E	-	1	0	FBF1	71434052	0.480000	0.25933	0.056000	0.19401	0.376000	0.30014	1.677000	0.37576	1.038000	0.40049	0.655000	0.94253	GAA		0.507	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		T	73922457	C	T	73922457	3	4	1	1	0	0	0	0	1	0	0	0	5714	922	32	3	2877	3	FBF1	17	73922457	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	440885	73922457	7272753	163	163										
USP14	9097	hgsc.bcm.edu	37	chr18	198092	198092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgacaccttctaaaaagaaaAgtttaatcgatcagttcttc	5	9	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr18:198092A>G	ENST00000261601.7	+	9	812	c.721A>G	c.(721-723)Agt>Ggt	p.S241G	USP14_ENST00000400266.3_Missense_Mutation_p.S230G|USP14_ENST00000383589.2_Missense_Mutation_p.S195G|USP14_ENST00000582707.1_Missense_Mutation_p.S206G	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	241	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				TAAAAAGAAAAGTTTAATCGA	0.318																																																0			18											71	73	72					18																	198092		2203	4300	6503	188092	SO:0001583	missense	9097			U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"Ubiquitin-specific peptidases"	12612	protein-coding gene	gene with protein product		607274	"ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.721A>G	18.37:g.198092A>G	ENSP00000261601:p.Ser241Gly		188092	J3QRZ5|Q53XY5	Missense_Mutation	SNP	ENST00000261601.7	37	CCDS32780.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.846315	0.71603	.	.	ENSG00000101557	ENST00000261601;ENST00000383589;ENST00000400266	T;T	0.35973	1.28;1.28	6.17	6.17	0.99709	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.037204	0.85682	D	0.000000	T	0.44644	0.1303	M	0.76170	2.325	0.80722	D	1	B;B;B	0.14805	0.011;0.011;0.006	B;B;B	0.23150	0.044;0.023;0.03	T	0.34030	-0.9845	10	0.56958	D	0.05	-15.6353	16.8222	0.85835	1.0:0.0:0.0:0.0	.	230;206;241	B7Z4N8;A6NJA2;P54578	.;.;UBP14_HUMAN	G	241;206;230	ENSP00000261601:S241G;ENSP00000383125:S230G	ENSP00000261601:S241G	S	+	1	0	USP14	188092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	AGT		0.318	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151		G	198092	A	G	198092	3	3	1	1	0	0	0	0	1	0	0	0	17085	72	3	4	755	4	USP14	18	198092	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10		198092	77879156	164	164										
COLEC12	81035	hgsc.bcm.edu	37	chr18	335079	335079	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cctttgccgccacgctctccGgggggaccagctggtccaat	12	16	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr18:335079G>T	ENST00000400256.3	-	6	1686	c.1479C>A	c.(1477-1479)ccC>ccA	p.P493P		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	493	Collagen-like 2.				carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)	p.P493P(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CACGCTCTCCGGGGGGACCAG	0.672																																																1	Substitution - coding silent(1)	lung(1)	18											29	32	31					18																	335079		2188	4272	6460	325079	SO:0001819	synonymous_variant	81035			AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1479C>A	18.37:g.335079G>T			325079	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	37	CCDS32782.1																																																																																				0.672	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	335079	G	T	335079	2	4	1	1	0	0	0	0	0	0	0	1	3718	1103	39	2		2	COLEC12	18	335079	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	136987	335079	77742169	165	165										
SALL3	27164	hgsc.bcm.edu	37	chr18	76754048	76754048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccagtgcgtcatctgccaccGggtgctgagctgccagagcg	14	14	2	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr18:76754048G>A	ENST00000537592.2	+	2	2057	c.2057G>A	c.(2056-2058)cGg>cAg	p.R686Q	SALL3_ENST00000536229.3_Missense_Mutation_p.R553Q|SALL3_ENST00000575389.2_Missense_Mutation_p.R686Q	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	686					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ATCTGCCACCGGGTGCTGAGC	0.612																																																0			18											27	27	27					18																	76754048		2197	4296	6493	74855036	SO:0001583	missense	27164			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2057G>A	18.37:g.76754048G>A	ENSP00000441823:p.Arg686Gln		74855036	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.913697	0.52439	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.07567	3.18	4.89	4.89	0.63831	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000100	T	0.29256	0.0728	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.01853	-1.1260	10	0.72032	D	0.01	-44.546	18.4468	0.90686	0.0:0.0:1.0:0.0	.	418;686	F5GXY4;Q9BXA9	.;SALL3_HUMAN	Q	686;686;418	ENSP00000441823:R686Q	ENSP00000299466:R686Q	R	+	2	0	SALL3	74855036	1.000000	0.71417	0.994000	0.49952	0.902000	0.53008	9.731000	0.98807	2.430000	0.82344	0.655000	0.94253	CGG		0.612	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76754048	G	A	76754048	3	1	1	1	0	0	0	0	1	0	0	0	13849	1116	39	1	2063	1	SALL3	18	76754048	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	76418969	76754048	1323200	166	166										
DAPK3	1613	hgsc.bcm.edu	37	chr19	3964314	3964314	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cttgtgcgcgatgccgaagtCgatgagcttgattcgtgggt	15	8	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr19:3964314C>T	ENST00000545797.2	-	4	724	c.481G>A	c.(481-483)Gac>Aac	p.D161N	DAPK3_ENST00000301264.3_Missense_Mutation_p.D161N|MIR637_ENST00000385000.1_RNA			O43293	DAPK3_HUMAN	death-associated protein kinase 3	161	Activation segment. {ECO:0000250|UniProtKB:O96017}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in an ovarian mucinous carcinoma sample; somatic mutation; greatly reduces kinase acivity, increases cell proliferation and cell survival). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21487036}.		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)	p.D161N(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGCCGAAGTCGATGAGCTTG	0.627																																																1	Substitution - Missense(1)	ovary(1)	19											223	133	163					19																	3964314		2203	4300	6503	3915314	SO:0001583	missense	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.481G>A	19.37:g.3964314C>T	ENSP00000442973:p.Asp161Asn		3915314	A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	37	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	C	34	5.332717	0.95733	.	.	ENSG00000167657	ENST00000301264;ENST00000545797;ENST00000442766	D;D	0.92965	-3.14;-3.14	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97439	0.9162	H	0.95780	3.72	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98444	1.0588	10	0.87932	D	0	.	18.3495	0.90333	0.0:1.0:0.0:0.0	.	161	O43293	DAPK3_HUMAN	N	161;161;16	ENSP00000301264:D161N;ENSP00000442973:D161N	ENSP00000301264:D161N	D	-	1	0	DAPK3	3915314	1.000000	0.71417	0.999000	0.59377	0.676000	0.39594	7.584000	0.82572	2.581000	0.87130	0.561000	0.74099	GAC		0.627	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		T	3964314	C	T	3964314	3	4	1	1	0	0	0	0	1	0	0	0	4243	884	31	1	907	1	DAPK3	19	3964314	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10		3964314	55164669	167	167										
FSD1	79187	hgsc.bcm.edu	37	chr19	4307965	4307965	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	actctgcaggccatggacagCgaggactttcctcaggtggg	14	11	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr19:4307965C>T	ENST00000221856.6	+	4	477	c.330C>T	c.(328-330)agC>agT	p.S110S	FSD1_ENST00000597590.1_Silent_p.S110S|FSD1_ENST00000598010.1_3'UTR	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	110	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		CCATGGACAGCGAGGACTTTC	0.562																																																0			19											55	47	50					19																	4307965		2203	4300	6503	4258965	SO:0001819	synonymous_variant	79187			AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.330C>T	19.37:g.4307965C>T			4258965	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																				0.562	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		T	4307965	C	T	4307965	2	4	1	1	0	0	0	0	0	0	0	1	6089	767	27	1		1	FSD1	19	4307965	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	343651	4307965	54821018	168	168										
MAST1	1777	hgsc.bcm.edu	37	chr19	12984570	12984570	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tgcgcgatgcaagtcggccgGcaacatccctctatcgccgc	11	16	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr19:12984570G>A	ENST00000222219.3	-	0	1955				AC020934.1_ENST00000578125.1_RNA|MAST1_ENST00000251472.4_Missense_Mutation_p.G1200D	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal						apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						AAGTCGGCCGGCAACATCCCT	0.692																																																0			19											34	36	35					19																	12984570		2203	4297	6500	12845570	SO:0001628	intergenic_variant	23332			AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115			19.37:g.12984570G>A			12845570	B2RD06|B7Z4K6|O43910	Missense_Mutation	SNP	ENST00000222219.3	37	CCDS12284.1	.	.	.	.	.	.	.	.	.	.	g	21.7	4.186387	0.78789	.	.	ENSG00000105613	ENST00000251472	T	0.41758	0.99	4.69	4.69	0.59074	.	0.070116	0.56097	D	0.000027	T	0.62527	0.2435	M	0.66939	2.045	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.64947	-0.6287	10	0.54805	T	0.06	-31.9496	15.4844	0.75555	0.0:0.0:1.0:0.0	.	1200	Q9Y2H9	MAST1_HUMAN	D	1200	ENSP00000251472:G1200D	ENSP00000251472:G1200D	G	+	2	0	MAST1	12845570	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	9.652000	0.98499	2.320000	0.78422	0.552000	0.68991	GGC		0.692	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			A	12984570	G	A	12984570	1	1	1	0	1	0	0	0	0	0	0	0	9354	1203	42	3		3	MAST1	19	12984570	IGR	SNP	G	TCGA-AF-2687-01A-02D-1733-10	8676605	12984570	46144413	169	169										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31040254	31040254	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gggtcttctccaagcccaggAccccttggcgggcctgccaa	12	16	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr19:31040254A>T	ENST00000355537.3	+	4	3875	c.3728A>T	c.(3727-3729)gAc>gTc	p.D1243V		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1243					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CAAGCCCAGGACCCCTTGGCG	0.642																																																0			19											21	22	22					19																	31040254		2202	4297	6499	35732094	SO:0001583	missense	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3728A>T	19.37:g.31040254A>T	ENSP00000347730:p.Asp1243Val		35732094	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	8.860	0.946818	0.18356	.	.	ENSG00000198597	ENST00000355537	T	0.10192	2.9	5.18	5.18	0.71444	.	0.393945	0.30383	N	0.009758	T	0.09024	0.0223	N	0.19112	0.55	0.58432	D	0.999999	B;B	0.27559	0.001;0.181	B;B	0.24974	0.001;0.057	T	0.14309	-1.0477	10	0.72032	D	0.01	-26.5127	15.0402	0.71785	1.0:0.0:0.0:0.0	.	1243;1243	A7E228;O15090	.;ZN536_HUMAN	V	1243	ENSP00000347730:D1243V	ENSP00000347730:D1243V	D	+	2	0	ZNF536	35732094	1.000000	0.71417	0.993000	0.49108	0.477000	0.33069	3.508000	0.53378	1.944000	0.56390	0.528000	0.53228	GAC		0.642	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31040254	A	T	31040254	3	4	1	1	0	0	0	0	1	0	0	0	18013	275	10	5	3738	5	ZNF536	19	31040254	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	18055684	31040254	28088729	170	170										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46443951	46443951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gttggccacggggcctgccaCgttggcgtagctgatgttga	16	10	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr19:46443951C>T	ENST00000263257.5	-	4	843	c.649G>A	c.(649-651)Gtg>Atg	p.V217M		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	217					regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		GGGCCTGCCACGTTGGCGTAG	0.706																																																0			19											53	29	37					19																	46443951		2161	4226	6387	51135791	SO:0001583	missense	4858			U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.649G>A	19.37:g.46443951C>T	ENSP00000263257:p.Val217Met		51135791	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	37	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237545	0.39598	.	.	ENSG00000104967	ENST00000263257	T	0.50277	0.75	3.15	3.15	0.36227	.	0.253661	0.32736	N	0.005715	T	0.33265	0.0857	L	0.46157	1.445	0.33894	D	0.637687	P	0.50443	0.935	B	0.36534	0.227	T	0.53229	-0.8468	10	0.51188	T	0.08	-13.6904	7.4493	0.27229	0.2581:0.7419:0.0:0.0	.	217	Q9UNW9	NOVA2_HUMAN	M	217	ENSP00000263257:V217M	ENSP00000263257:V217M	V	-	1	0	NOVA2	51135791	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	0.843000	0.27640	1.608000	0.50180	0.484000	0.47621	GTG		0.706	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		T	46443951	C	T	46443951	3	4	1	1	0	0	0	0	1	0	0	0	10586	536	19	1	833	1	NOVA2	19	46443951	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	15403697	46443951	12685032	171	171										
TGM3	7053	hgsc.bcm.edu	37	chr20	2293561	2293561	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cagtttgaagaagacattctCagcatctgcctctcaatctt	6	11	4	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:2293561C>T	ENST00000381458.5	+	5	621	c.558C>T	c.(556-558)ctC>ctT	p.L186L		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	186					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	AAGACATTCTCAGCATCTGCC	0.478																																																0			20											192	180	184					20																	2293561		2203	4300	6503	2241561	SO:0001819	synonymous_variant	7053			L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.558C>T	20.37:g.2293561C>T			2241561	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Silent	SNP	ENST00000381458.5	37	CCDS33435.1																																																																																				0.478	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2293561	C	T	2293561	2	4	1	1	0	0	0	0	0	0	0	1	15870	813	29	3		3	TGM3	20	2293561	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10		2293561	60731959	172	172										
CD93	22918	hgsc.bcm.edu	37	chr20	23066171	23066171	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ccccacaggctacattggccGcagaggcaaagggcacagcc	12	15	0	1	rs138932459		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:23066171G>T	ENST00000246006.4	-	1	806	c.659C>A	c.(658-660)gCg>gAg	p.A220E		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	220			A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)	p.A220V(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					TACATTGGCCGCAGAGGCAAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											78	79	79					20																	23066171		2203	4300	6503	23014171	SO:0001583	missense	22918			U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.659C>A	20.37:g.23066171G>T	ENSP00000246006:p.Ala220Glu		23014171	O00274	Missense_Mutation	SNP	ENST00000246006.4	37	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	3.784	-0.045138	0.07452	.	.	ENSG00000125810	ENST00000246006;ENST00000413585	T	0.43688	0.94	5.52	-2.56	0.06268	.	2.092740	0.02000	N	0.046191	T	0.20820	0.0501	L	0.29908	0.895	0.09310	N	1	B	0.33135	0.399	B	0.20577	0.03	T	0.07693	-1.0759	10	0.06236	T	0.91	-1.4651	2.4339	0.04478	0.4712:0.1171:0.2978:0.1139	.	220	Q9NPY3	C1QR1_HUMAN	E	220	ENSP00000246006:A220E	ENSP00000246006:A220E	A	-	2	0	CD93	23014171	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.298000	0.19120	-0.106000	0.12110	-1.261000	0.01458	GCG		0.617	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23066171	G	T	23066171	3	4	1	1	0	0	0	0	1	0	0	0	3053	1087	38	2	1307	2	CD93	20	23066171	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	20772610	23066171	39959349	173	173										
HCK	3055	hgsc.bcm.edu	37	chr20	30689235	30689235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgctgctggaaaaaccgtccGgaggagcggccgaccttcga	14	13	0	0	rs144688972	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:30689235G>A	ENST00000520553.1	+	13	1677	c.1431G>A	c.(1429-1431)ccG>ccA	p.P477P	HCK_ENST00000538448.1_Silent_p.P477P|HCK_ENST00000375862.2_Silent_p.P497P|HCK_ENST00000534862.1_Silent_p.P478P|HCK_ENST00000375852.2_Silent_p.P498P|HCK_ENST00000518730.1_Silent_p.P476P	NM_001172129.1|NM_001172130.1|NM_001172131.1|NM_002110.3	NP_001165600.1|NP_001165601.1|NP_001165602.1|NP_002101.2	P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	498	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	AAAACCGTCCGGAGGAGCGGC	0.572													G|||	2	0.000399361	0	0	5008	,	,		18525	0		0.001	False		,,,				2504	0.001															0			20						G	,,,,,	0,4406		0,0,2203	57	48	51		1431,1491,1428,1434,1431,1494	-9.8	0.1	20	dbSNP_134	51	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HCK	NM_001172129.1,NM_001172130.1,NM_001172131.1,NM_001172132.1,NM_001172133.1,NM_002110.3	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	477/506,497/526,476/505,478/507,477/506,498/527	30689235	1,13005	2203	4300	6503	30152896	SO:0001819	synonymous_variant	3055			AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"SH2 domain containing"	4840	protein-coding gene	gene with protein product		142370	"hemopoietic cell kinase"			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000520553.1:c.1431G>A	20.37:g.30689235G>A			30152896	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Silent	SNP	ENST00000520553.1	37	CCDS54455.1																																																																																				0.572	HCK-006	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000375751.1			A	30689235	G	A	30689235	2	1	1	1	0	0	0	0	0	0	0	1	7015	1103	39	1		1	HCK	20	30689235	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	7623064	30689235	32336285	174	174										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023473	31023473	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	attgaaaagctgaaaatcaaCggagactctgaagcactgag	10	7	2	5	rs200471411		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:31023473C>T	ENST00000375687.4	+	13	3382	c.2958C>T	c.(2956-2958)aaC>aaT	p.N986N	ASXL1_ENST00000306058.5_Silent_p.N981N	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	986					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TGAAAATCAACGGAGACTCTG	0.517			"F, N, Mis"		"MDS, CMML"								C|||	1	0.000199681	0	0	5008	,	,		24193	0		0.001	False		,,,				2504	0						Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20											87	71	76					20																	31023473		2203	4300	6503	30487134	SO:0001819	synonymous_variant	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2958C>T	20.37:g.31023473C>T			30487134	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																				0.517	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31023473	C	T	31023473	2	4	1	1	0	0	0	0	0	0	0	1	1067	535	19	1		1	ASXL1	20	31023473	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	334238	31023473	32002047	175	175										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31652531	31652531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cccaagtcccgtgccccagcCaaggtgccccccaagaagga	10	18	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:31652531C>T	ENST00000375494.3	+	8	804	c.804C>T	c.(802-804)gcC>gcT	p.A268A		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	268					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GTGCCCCAGCCAAGGTGCCCC	0.587																																																0			20											81	72	75					20																	31652531		2203	4300	6503	31116192	SO:0001819	synonymous_variant	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.804C>T	20.37:g.31652531C>T			31116192	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																				0.587	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		T	31652531	C	T	31652531	2	4	1	1	0	0	0	0	0	0	0	1	2103	581	21	3		3	C20orf185	20	31652531	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	629058	31652531	31372989	176	176										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46264690	46264690	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gggaaccacagcttttccagCagctctctcagtgccctgca	9	15	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:46264690C>A	ENST00000371998.3	+	12	1751	c.1560C>A	c.(1558-1560)agC>agA	p.S520R	NCOA3_ENST00000341724.6_Missense_Mutation_p.S530R|NCOA3_ENST00000372004.3_Missense_Mutation_p.S520R|NCOA3_ENST00000371997.3_Missense_Mutation_p.S530R			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	520	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTTTTCCAGCAGCTCTCTCA	0.458																																																0			20											65	65	65					20																	46264690		2203	4300	6503	45698097	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.1560C>A	20.37:g.46264690C>A	ENSP00000361066:p.Ser520Arg		45698097	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461440	0.63513	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.72	0.461	0.16689	.	0.000000	0.85682	D	0.000000	T	0.36853	0.0982	M	0.74258	2.255	0.54753	D	0.999982	D;D;D;D;D;D	0.89917	0.996;1.0;0.996;0.997;0.999;0.997	D;D;D;D;D;D	0.91635	0.954;0.999;0.954;0.954;0.979;0.947	T	0.10894	-1.0610	10	0.72032	D	0.01	-14.7172	10.1955	0.43051	0.0:0.6738:0.0:0.3262	.	520;530;524;520;520;520	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	R	520;530;520;520;530	ENSP00000342123:S530R;ENSP00000361073:S520R;ENSP00000361066:S520R;ENSP00000361065:S530R	ENSP00000345671:S520R	S	+	3	2	NCOA3	45698097	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	1.283000	0.33237	0.083000	0.17047	0.655000	0.94253	AGC		0.458	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		A	46264690	C	A	46264690	3	1	1	1	0	0	0	0	1	0	0	0	10261	709	25	2	1628	2	NCOA3	20	46264690	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	14612159	46264690	16760830	177	177										
TMEM189	387521	hgsc.bcm.edu	37	chr20	48741643	48741643	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tcatctgcccgaggcttctcGcccgtcaggccctggatgag	12	15	4	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:48741643G>A	ENST00000371652.4	-	6	861	c.765C>T	c.(763-765)ggC>ggT	p.G255G	TMEM189_ENST00000371650.5_Silent_p.G252G|TMEM189_ENST00000371656.2_Silent_p.G180G|TMEM189-UBE2V1_ENST00000341698.2_Intron|TMEM189_ENST00000557021.1_Intron	NM_199129.2	NP_954580			transmembrane protein 189											breast(1)|endometrium(2)|large_intestine(3)|lung(2)	8			BRCA - Breast invasive adenocarcinoma(9;3.02e-07)			GAGGCTTCTCGCCCGTCAGGC	0.572																																					GBM(75;703 1202 5766 12781 15082)											0			20											84	71	76					20																	48741643		2203	4300	6503	48175050	SO:0001819	synonymous_variant	387521			AF155120	CCDS13428.1, CCDS54473.1	20q13.13	2007-07-30			ENSG00000240849	ENSG00000240849			16735	protein-coding gene	gene with protein product		610994				11076860	Standard	NM_199129		Approved	Kua		A5PLL7	OTTHUMG00000152625	ENST00000371652.4:c.765C>T	20.37:g.48741643G>A			48175050		Silent	SNP	ENST00000371652.4	37	CCDS13428.1																																																																																				0.572	TMEM189-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080529.1	NM_199129		A	48741643	G	A	48741643	2	1	1	1	0	0	0	0	0	0	0	1	16150	1074	38	1		1	TMEM189	20	48741643	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	2476953	48741643	14283877	178	178										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60927304	60927304	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cctccccggcccacctctccGttctccaggggcacgatgcg	10	20	2	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:60927304G>A	ENST00000252999.3	-	4	747	c.681C>T	c.(679-681)aaC>aaT	p.N227N	RP11-157P1.5_ENST00000456721.2_RNA|LAMA5_ENST00000370677.3_Silent_p.N227N|RP11-157P1.5_ENST00000477848.1_RNA|RP11-157P1.5_ENST00000487421.1_RNA|RP11-157P1.5_ENST00000478167.1_RNA|LAMA5_ENST00000370692.3_Silent_p.N227N	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	227	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ccacctctccGTTCTCCAGGG	0.692																																																0			20											47	43	44					20																	60927304		2202	4293	6495	60360699	SO:0001819	synonymous_variant	3911			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.681C>T	20.37:g.60927304G>A			60360699	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																				0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60927304	G	A	60927304	2	1	1	1	0	0	0	0	0	0	0	1	8631	1136	40	1		1	LAMA5	20	60927304	Silent	SNP	G	TCGA-AF-2687-01A-02D-1733-10	12185661	60927304	2098216	179	179										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62059776	62059776	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	agcagctccagctggttcagCggggggataagtctggggca	17	9	2	0	rs147453497	byFrequency	TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr20:62059776C>T	ENST00000359125.2	-	10	1335	c.1161G>A	c.(1159-1161)ccG>ccA	p.P387P	KCNQ2_ENST00000354587.3_Silent_p.P377P|KCNQ2_ENST00000344462.4_Silent_p.P387P|KCNQ2_ENST00000370224.1_Silent_p.P377P|KCNQ2_ENST00000359689.1_Silent_p.P387P|KCNQ2_ENST00000360480.3_Silent_p.P377P|KCNQ2_ENST00000357249.2_Silent_p.P387P	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	387					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCTGGTTCAGCGGGGGGATAA	0.627																																																0			20						C	,,,	1,4399		0,1,2199	31	29	30		1131,1161,1161,1161	-8.6	0	20	dbSNP_134	30	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3	,,,	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	,,,	377/845,387/855,387/873,387/842	62059776	2,12992	2200	4297	6497	61530220	SO:0001819	synonymous_variant	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1161G>A	20.37:g.62059776C>T			61530220	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																				0.627	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		T	62059776	C	T	62059776	2	4	1	1	0	0	0	0	0	0	0	1	8104	755	27	1		1	KCNQ2	20	62059776	Silent	SNP	C	TCGA-AF-2687-01A-02D-1733-10	1132472	62059776	965744	180	180										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28338453	28338453	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gcgtagacgaggtagcccacCttgccgccgccggagtagag	15	13	0	2			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr21:28338453C>A	ENST00000284987.5	-	1	379	c.258G>T	c.(256-258)aaG>aaT	p.K86N		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	86					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GGTAGCCCACCTTGCCGCCGC	0.701																																					Esophageal Squamous(53;683 1080 10100 14424 45938)											0			21											49	47	48					21																	28338453		2186	4290	6476	27260324	SO:0001583	missense	11096			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.258G>T	21.37:g.28338453C>A	ENSP00000284987:p.Lys86Asn		27260324	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424517	0.62733	.	.	ENSG00000154736	ENST00000284987	T	0.06449	3.3	4.32	-0.058	0.13799	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.07773	0.0195	M	0.65498	2.005	0.36072	D	0.842185	B	0.28324	0.207	B	0.32583	0.148	T	0.12915	-1.0529	10	0.40728	T	0.16	.	6.2098	0.20623	0.0:0.5686:0.1433:0.2881	.	86	Q9UNA0	ATS5_HUMAN	N	86	ENSP00000284987:K86N	ENSP00000284987:K86N	K	-	3	2	ADAMTS5	27260324	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	0.660000	0.25009	0.085000	0.17107	0.563000	0.77884	AAG		0.701	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28338453	C	A	28338453	3	1	1	1	0	0	0	0	1	0	0	0	269	680	24	2	2566	2	ADAMTS5	21	28338453	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10		28338453	19791442	181	181										
XKR3	150165	hgsc.bcm.edu	37	chr22	17265234	17265234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	atcatcattgctgatctggaTggccagtatattgcagcgaa	10	8	3	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr22:17265234T>C	ENST00000331428.5	-	4	757	c.655A>G	c.(655-657)Atc>Gtc	p.I219V		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTGATCTGGATGGCCAGTATA	0.403																																																0			22											16	16	16					22																	17265234		1465	3478	4943	15645234	SO:0001583	missense	150165			AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.655A>G	22.37:g.17265234T>C	ENSP00000331704:p.Ile219Val		15645234	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	.	.	.	.	.	.	.	.	.	.	.	14.99	2.699176	0.48307	.	.	ENSG00000172967	ENST00000331428	T	0.62788	-0.0	0.771	0.771	0.18504	.	0.132226	0.47455	U	0.000232	T	0.43590	0.1254	L	0.46157	1.445	0.33829	D	0.630067	P	0.39551	0.678	B	0.34824	0.19	T	0.48958	-0.8988	10	0.16420	T	0.52	.	5.862	0.18754	0.0:0.0:0.0:1.0	.	219	Q5GH77	XKR3_HUMAN	V	219	ENSP00000331704:I219V	ENSP00000331704:I219V	I	-	1	0	XKR3	15645234	1.000000	0.71417	0.841000	0.33234	0.121000	0.20230	5.073000	0.64395	0.630000	0.30394	0.246000	0.17985	ATC		0.403	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		C	17265234	T	C	17265234	3	2	1	1	0	0	0	0	1	0	0	0	17472	1464	51	4	728	4	XKR3	22	17265234	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10		17265234	34039332	182	182										
CCDC157	550631	hgsc.bcm.edu	37	chr22	30772726	30772726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cacaccagccccaggagcggCccatgtagcctgtggcccag	12	17	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr22:30772726C>T	ENST00000405659.1	+	12	2960	c.2251C>T	c.(2251-2253)Ccc>Tcc	p.P751S	RP1-130H16.16_ENST00000332468.4_RNA|CCDC157_ENST00000338306.3_Missense_Mutation_p.P751S			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	751										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CCAGGAGCGGCCCATGTAGCC	0.632																																																0			22											15	16	15					22																	30772726		2143	4227	6370	29102726	SO:0001583	missense	550631			BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.2251C>T	22.37:g.30772726C>T	ENSP00000385357:p.Pro751Ser		29102726	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046728	0.75846	.	.	ENSG00000187860	ENST00000405659;ENST00000338306	T;T	0.37411	1.2;1.2	4.57	3.47	0.39725	.	0.089550	0.42420	D	0.000720	T	0.33469	0.0864	L	0.29908	0.895	0.80722	D	1	P	0.50156	0.932	P	0.50352	0.638	T	0.08764	-1.0706	10	0.87932	D	0	-21.4883	9.3481	0.38120	0.2134:0.7866:0.0:0.0	.	751	Q569K6	CC157_HUMAN	S	751	ENSP00000385357:P751S;ENSP00000343087:P751S	ENSP00000343087:P751S	P	+	1	0	CCDC157	29102726	0.012000	0.17670	0.700000	0.30305	0.809000	0.45718	0.886000	0.28241	2.527000	0.85204	0.555000	0.69702	CCC		0.632	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		T	30772726	C	T	30772726	3	4	1	1	0	0	0	0	1	0	0	0	2795	739	26	3	2289	3	CCDC157	22	30772726	Missense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	13507492	30772726	20531840	183	183										
GRAP2	9402	hgsc.bcm.edu	37	chr22	40367005	40367005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	tggtggaggtcctggatagcTccaacccatcctggtggacc	13	12	0	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr22:40367005T>C	ENST00000344138.4	+	8	1173	c.910T>C	c.(910-912)Tcc>Ccc	p.S304P	GRAP2_ENST00000407075.3_Missense_Mutation_p.S304P|GRAP2_ENST00000540310.1_Missense_Mutation_p.S238P|GRAP2_ENST00000399090.2_Missense_Mutation_p.S191P|GRAP2_ENST00000543252.1_Missense_Mutation_p.S252P|GRAP2_ENST00000544756.1_Missense_Mutation_p.S232P	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	304	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)	p.S304P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CCTGGATAGCTCCAACCCATC	0.632																																																1	Substitution - Missense(1)	central_nervous_system(1)	22											80	70	73					22																	40367005		2203	4300	6503	38696951	SO:0001583	missense	9402			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.910T>C	22.37:g.40367005T>C	ENSP00000339186:p.Ser304Pro		38696951	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.036069	0.75617	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.53640	0.61;1.51;0.61;0.61;0.61;0.61	5.45	3.26	0.37387	Src homology-3 domain (4);	0.454387	0.27876	N	0.017489	T	0.50871	0.1641	L	0.41027	1.25	0.53688	D	0.999976	P;D;B;B;P	0.55385	0.918;0.971;0.182;0.239;0.928	P;P;B;B;P	0.56434	0.698;0.798;0.267;0.122;0.798	T	0.43048	-0.9415	10	0.49607	T	0.09	-25.2361	10.6026	0.45375	0.2571:0.0:0.0:0.7429	.	191;304;238;278;304	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	P	304;252;278;238;232;191;304	ENSP00000339186:S304P;ENSP00000446350:S252P;ENSP00000444734:S238P;ENSP00000442195:S232P;ENSP00000382040:S191P;ENSP00000385607:S304P	ENSP00000339186:S304P	S	+	1	0	GRAP2	38696951	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.397000	0.52572	0.319000	0.23209	0.455000	0.32223	TCC		0.632	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		C	40367005	T	C	40367005	3	2	1	1	0	0	0	0	1	0	0	0	6775	1551	54	4	936	4	GRAP2	22	40367005	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10	9594279	40367005	10937561	184	184										
EP300	2033	hgsc.bcm.edu	37	chr22	41573425	41573425	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cccagggtaaggcagcaggcCaggtgacccctccaacccct	11	17	0	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chr22:41573425C>T	ENST00000263253.7	+	31	6929	c.5710C>T	c.(5710-5712)Cag>Tag	p.Q1904*	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1904					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GGCAGCAGGCCAGGTGACCCC	0.627			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											76	69	71					22																	41573425		2203	4300	6503	39903371	SO:0001587	stop_gained	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.5710C>T	22.37:g.41573425C>T	ENSP00000263253:p.Gln1904*		39903371	B1AKC2	Nonsense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	52	19.991127	0.99926	.	.	ENSG00000100393	ENST00000263253	.	.	.	5.47	5.47	0.80525	.	0.000000	0.46145	D	0.000301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-5.8439	19.3276	0.94268	0.0:1.0:0.0:0.0	.	.	.	.	X	1904	.	ENSP00000263253:Q1904X	Q	+	1	0	EP300	39903371	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.831000	0.55776	2.573000	0.86826	0.561000	0.74099	CAG		0.627	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41573425	C	T	41573425	4	4	1	1	0	0	0	0	0	1	0	0	5161	595	21	3	5832	3	EP300	22	41573425	Nonsense_Mutation	SNP	C	TCGA-AF-2687-01A-02D-1733-10	1206420	41573425	9731141	185	185										
NHS	4810	hgsc.bcm.edu	37	chrX	17750348	17750348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cacaaggggctgaggcattgTccccactctctccatgctcc	9	16	1	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:17750348T>C	ENST00000380060.3	+	8	4995	c.4657T>C	c.(4657-4659)Tcc>Ccc	p.S1553P	NHS_ENST00000398097.3_Missense_Mutation_p.S1397P	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1574					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TGAGGCATTGTCCCCACTCTC	0.592																																																0			X											104	88	93					X																	17750348		2203	4300	6503	17660269	SO:0001583	missense	4810				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.4657T>C	X.37:g.17750348T>C	ENSP00000369400:p.Ser1553Pro		17660269	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.929282	0.52759	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.49432	0.78;0.78	5.69	5.69	0.88448	.	0.250624	0.42053	D	0.000771	T	0.58878	0.2153	M	0.62723	1.935	0.21740	N	0.999562	D;D;D;D	0.64830	0.958;0.958;0.958;0.994	P;P;P;P	0.58454	0.563;0.563;0.563;0.839	T	0.55879	-0.8071	10	0.42905	T	0.14	-14.2251	10.9059	0.47079	0.1423:0.0:0.0:0.8577	.	1574;1395;1397;1553	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	P	1553;1397;1395	ENSP00000369400:S1553P;ENSP00000381170:S1397P	ENSP00000369397:S1395P	S	+	1	0	NHS	17660269	0.328000	0.24687	0.998000	0.56505	0.929000	0.56500	0.812000	0.27211	2.025000	0.59659	0.486000	0.48141	TCC		0.592	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		C	17750348	T	C	17750348	3	2	1	1	0	0	0	0	1	0	0	0	10442	1667	58	4	4792	4	NHS	23	17750348	Missense_Mutation	SNP	T	TCGA-AF-2687-01A-02D-1733-10		17750348	137520212	186	186										
RLIM	51132	hgsc.bcm.edu	37	chrX	73811648	73811648	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cacctgatgagcctgatgatGagcttccttcattactgcct	8	12	1	5	rs200629905		TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:73811648G>A	ENST00000332687.6	-	4	1720	c.1502C>T	c.(1501-1503)tCa>tTa	p.S501L	RLIM_ENST00000349225.2_Missense_Mutation_p.S501L	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	501	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S501L(3)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTGATGATGAGCTTCCTTC	0.488																																					Esophageal Squamous(169;1899 1923 14997 18818 32118)											3	Substitution - Missense(3)	prostate(2)|ovary(1)	X											45	38	40					X																	73811648		2203	4300	6503	73728373	SO:0001583	missense	51132			AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1502C>T	X.37:g.73811648G>A	ENSP00000328059:p.Ser501Leu		73728373	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	7.117	0.577275	0.13686	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.08984	3.03;3.03	5.41	4.55	0.56014	.	0.666655	0.15400	N	0.264373	T	0.10121	0.0248	L	0.49126	1.545	0.38573	D	0.949983	B	0.02656	0.0	B	0.01281	0.0	T	0.08764	-1.0706	10	0.23891	T	0.37	-0.2985	13.4694	0.61273	0.0772:0.0:0.9228:0.0	.	501	Q9NVW2	RNF12_HUMAN	L	501	ENSP00000328059:S501L;ENSP00000253571:S501L	ENSP00000328059:S501L	S	-	2	0	RLIM	73728373	0.997000	0.39634	0.969000	0.41365	0.831000	0.47069	2.664000	0.46783	1.072000	0.40860	-0.192000	0.12808	TCA		0.488	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811648	G	A	73811648	3	1	1	1	0	0	0	0	1	0	0	0	13427	1294	45	3	376	3	RLIM	23	73811648	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	56061300	73811648	81458912	187	187										
TMEM164	84187	hgsc.bcm.edu	37	chrX	109388058	109388058	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ttggagatttactacattcaGcatgttatgctctacgtggt	9	7	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:109388058G>C	ENST00000372073.1	+	5	876	c.540G>C	c.(538-540)caG>caC	p.Q180H	TMEM164_ENST00000288381.4_Missense_Mutation_p.Q141H|TMEM164_ENST00000372068.2_Missense_Mutation_p.Q180H|TMEM164_ENST00000372072.3_Missense_Mutation_p.Q31H			Q5U3C3	TM164_HUMAN	transmembrane protein 164	180						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|skin(1)	14						ACTACATTCAGCATGTTATGC	0.463																																																0			X											197	145	163					X																	109388058		2203	4300	6503	109274714	SO:0001583	missense	84187			AK094127	CCDS14550.2, CCDS55475.1	Xq22.3	2008-02-05			ENSG00000157600	ENSG00000157600			26217	protein-coding gene	gene with protein product						12477932	Standard	NM_032227		Approved	FLJ22679, RP13-360B22.2	uc004eom.3	Q5U3C3	OTTHUMG00000022192	ENST00000372073.1:c.540G>C	X.37:g.109388058G>C	ENSP00000361143:p.Gln180His		109274714	B3KSQ8|F5H2P2	Missense_Mutation	SNP	ENST00000372073.1	37	CCDS14550.2	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429886	0.62844	.	.	ENSG00000157600	ENST00000372072;ENST00000372073;ENST00000372068;ENST00000288381;ENST00000501872	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	5.41	2.23	0.28157	.	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	M	0.73962	2.25	0.58432	D	0.999999	P;D	0.64830	0.933;0.994	P;P	0.55011	0.479;0.766	T	0.65014	-0.6271	10	0.52906	T	0.07	-7.5233	8.8417	0.35146	0.3051:0.0:0.6949:0.0	.	141;180	Q9H617;Q5U3C3	.;TM164_HUMAN	H	31;180;180;141;141	ENSP00000384075:Q31H;ENSP00000361143:Q180H;ENSP00000361138:Q180H;ENSP00000288381:Q141H	ENSP00000288381:Q141H	Q	+	3	2	TMEM164	109274714	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.674000	0.46867	0.495000	0.27882	0.600000	0.82982	CAG		0.463	TMEM164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057898.1	NM_032227		C	109388058	G	C	109388058	3	2	1	1	0	0	0	0	1	0	0	0	16118	962	34	5	554	5	TMEM164	23	109388058	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	35576410	109388058	45882502	188	188										
XPNPEP2	7512	hgsc.bcm.edu	37	chrX	128888545	128888545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	ctcgggggcagagatcgtggAcaagttccgagggtgaagag	18	7	0	3			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:128888545A>G	ENST00000371106.3	+	12	1397	c.1205A>G	c.(1204-1206)gAc>gGc	p.D402G		NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	402						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						GAGATCGTGGACAAGTTCCGA	0.582																																																0			X											61	40	48					X																	128888545		2200	4291	6491	128716226	SO:0001583	missense	7512			U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.1205A>G	X.37:g.128888545A>G	ENSP00000360147:p.Asp402Gly		128716226	A0AV16|O75994	Missense_Mutation	SNP	ENST00000371106.3	37	CCDS14613.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.790060	0.50102	.	.	ENSG00000122121	ENST00000371106	T	0.78003	-1.14	5.62	5.62	0.85841	Peptidase M24, structural domain (3);	0.290766	0.41500	D	0.000879	T	0.79317	0.4425	M	0.62209	1.925	0.50313	D	0.999861	B	0.33171	0.4	B	0.40410	0.328	T	0.80355	-0.1417	10	0.72032	D	0.01	-6.4372	13.7259	0.62759	1.0:0.0:0.0:0.0	.	402	O43895	XPP2_HUMAN	G	402	ENSP00000360147:D402G	ENSP00000360147:D402G	D	+	2	0	XPNPEP2	128716226	0.990000	0.36364	0.036000	0.18154	0.133000	0.20885	6.026000	0.70873	1.885000	0.54596	0.412000	0.27726	GAC		0.582	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399		G	128888545	A	G	128888545	3	3	1	1	0	0	0	0	1	0	0	0	17483	275	10	4	1251	4	XPNPEP2	23	128888545	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	19500487	128888545	26382015	189	189										
LDOC1	23641	hgsc.bcm.edu	37	chrX	140271175	140271175	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	cgcggtgccgcatcaggagcGcgtgcagcagcagcaccaac	14	15	1	0			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:140271175G>A	ENST00000370526.2	-	1	135	c.32C>T	c.(31-33)gCg>gTg	p.A11V	LDOC1_ENST00000460721.1_5'UTR	NM_012317.2	NP_036449.1	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	11					negative regulation of cell proliferation (GO:0008285)	nucleus (GO:0005634)				endometrium(6)|large_intestine(1)|lung(6)|ovary(1)	14	Acute lymphoblastic leukemia(192;7.65e-05)					CATCAGGAGCGCGTGCAGCAG	0.667																																																0			X											27	22	24					X																	140271175		2203	4296	6499	140098841	SO:0001583	missense	23641			AB019527	CCDS14672.1	Xq27	2008-02-05			ENSG00000182195	ENSG00000182195			6548	protein-coding gene	gene with protein product		300402		BCUR1		10403563, 15716091, 16093683	Standard	NM_012317		Approved	Mar7, Mart7	uc004fbj.3	O95751	OTTHUMG00000022558	ENST00000370526.2:c.32C>T	X.37:g.140271175G>A	ENSP00000359557:p.Ala11Val		140098841	Q6IAR6	Missense_Mutation	SNP	ENST00000370526.2	37	CCDS14672.1	.	.	.	.	.	.	.	.	.	.	.	23.0	4.361048	0.82353	.	.	ENSG00000182195	ENST00000370526	T	0.24908	1.83	3.61	3.61	0.41365	.	0.000000	0.41823	D	0.000801	T	0.34279	0.0892	L	0.36672	1.1	0.29195	N	0.875582	D	0.71674	0.998	D	0.65443	0.935	T	0.04855	-1.0922	10	0.39692	T	0.17	-11.5154	9.7936	0.40722	0.0:0.0:1.0:0.0	.	11	O95751	LDOC1_HUMAN	V	11	ENSP00000359557:A11V	ENSP00000359557:A11V	A	-	2	0	LDOC1	140098841	1.000000	0.71417	0.912000	0.35992	0.819000	0.46315	4.063000	0.57499	2.060000	0.61445	0.287000	0.19450	GCG		0.667	LDOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058592.1	NM_012317		A	140271175	G	A	140271175	3	1	1	1	0	0	0	0	1	0	0	0	8731	1087	38	1	412	1	LDOC1	23	140271175	Missense_Mutation	SNP	G	TCGA-AF-2687-01A-02D-1733-10	11382630	140271175	14999385	190	190										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151815599	151815599	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0366492146596859	7	1	0.549737525347281	1.55497185741088	0.496267614067303	0.0405594405594406	0.274902874902875	0	gaatcgcgtgtttcagcttcAcccagatggaacggtgcggt	13	10	2	1			TCGA-AF-2687-01A-02D-1733-10	TCGA-AF-2687-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3d727a51-b21c-4088-8124-90c2481c7dc2	31b94086-e0f6-4a2b-84db-466c50fa904e	g.chrX:151815599A>G	ENST00000370306.2	+	4	517	c.497A>G	c.(496-498)cAc>cGc	p.H166R		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	166					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTCAGCTTCACCCAGATGGA	0.522																																																0			X											210	147	168					X																	151815599		2203	4300	6503	151566255	SO:0001583	missense	55879			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.497A>G	X.37:g.151815599A>G	ENSP00000359329:p.His166Arg		151566255	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018978	0.54576	.	.	ENSG00000147402	ENST00000370306	T	0.79141	-1.24	5.19	5.19	0.71726	Neurotransmitter-gated ion-channel ligand-binding (3);	0.155258	0.30639	N	0.009196	T	0.77618	0.4157	L	0.33189	0.99	0.43857	D	0.996455	D	0.54047	0.964	P	0.55055	0.767	T	0.79569	-0.1749	10	0.62326	D	0.03	.	11.968	0.53047	1.0:0.0:0.0:0.0	.	166	Q9UN88	GBRT_HUMAN	R	166	ENSP00000359329:H166R	ENSP00000359329:H166R	H	+	2	0	GABRQ	151566255	1.000000	0.71417	0.988000	0.46212	0.173000	0.22820	7.273000	0.78527	1.729000	0.51567	0.441000	0.28932	CAC		0.522	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		G	151815599	A	G	151815599	3	3	1	1	0	0	0	0	1	0	0	0	6194	159	6	4	511	4	GABRQ	23	151815599	Missense_Mutation	SNP	A	TCGA-AF-2687-01A-02D-1733-10	11544424	151815599	3454961	191	191										
PAX7	5081	hgsc.bcm.edu	37	chr1	19018317	19018317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	actgaagcgcaagcagcgacGcagtcggaccacattcacgg	12	13	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:19018317G>A	ENST00000375375.3	+	5	1254	c.656G>A	c.(655-657)cGc>cAc	p.R219H	PAX7_ENST00000400661.3_Missense_Mutation_p.R217H|PAX7_ENST00000420770.2_Missense_Mutation_p.R219H	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	219					anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R219H(1)	PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		AAGCAGCGACGCAGTCGGACC	0.637			T	FOXO1A	alveolar rhabdomyosarcoma																																		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	1	Substitution - Missense(1)	large_intestine(1)	1											40	33	35					1																	19018317		2202	4300	6502	18890904	SO:0001583	missense	5081			X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709		"Paired boxes", "Homeoboxes / PRD class"	8621	protein-coding gene	gene with protein product		167410	"paired box gene 7"			7981748, 8431641	Standard	NM_001135254		Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000375375.3:c.656G>A	1.37:g.19018317G>A	ENSP00000364524:p.Arg219His		18890904	E9PFV9|Q0VA99|Q2PJS5	Missense_Mutation	SNP	ENST00000375375.3	37	CCDS186.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091474	0.76756	.	.	ENSG00000009709	ENST00000375375;ENST00000420770;ENST00000400661	D;D;D	0.96885	-4.16;-4.16;-4.16	4.98	4.98	0.66077	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98896	0.9626	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	0.994;1.0;1.0	P;D;D	0.77004	0.824;0.927;0.989	D	0.99552	1.0966	10	0.87932	D	0	.	16.8192	0.85741	0.0:0.0:1.0:0.0	.	219;217;219	E9PFV9;P23759-2;P23759	.;.;PAX7_HUMAN	H	219;219;217	ENSP00000364524:R219H;ENSP00000403389:R219H;ENSP00000383502:R217H	ENSP00000364524:R219H	R	+	2	0	PAX7	18890904	1.000000	0.71417	0.960000	0.40013	0.195000	0.23768	9.823000	0.99369	2.313000	0.78055	0.655000	0.94253	CGC		0.637	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584		A	19018317	G	A	19018317	3	1	2	1	0	0	0	0	1	0	0	0	11515	1087	38	1	674	1	PAX7	1	19018317	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		19018317	230232304	1	192										
PLA2G5	5322	hgsc.bcm.edu	37	chr1	20416369	20416369	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tcctacaaatacagattcgcGtggggcgtggtcacctgcgg	13	11	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:20416369G>A	ENST00000375108.3	+	4	541	c.273G>A	c.(271-273)gcG>gcA	p.A91A	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	91					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)	p.A91A(1)		NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		ACAGATTCGCGTGGGGCGTGG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	1											100	82	88					1																	20416369		2203	4300	6503	20288956	SO:0001819	synonymous_variant	5322			U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.273G>A	1.37:g.20416369G>A			20288956	Q8N435	Silent	SNP	ENST00000375108.3	37	CCDS202.1																																																																																				0.587	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929		A	20416369	G	A	20416369	2	1	2	1	0	0	0	0	0	0	0	1	12038	1132	40	1		1	PLA2G5	1	20416369	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	1398052	20416369	228834252	2	193										
PIK3R3	8503	hgsc.bcm.edu	37	chr1	46511590	46511590	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tatccccagagaagacttacAccacagagcaagcatagcat	7	12	0	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:46511590A>G	ENST00000262741.5	-	9	1876	c.1187T>C	c.(1186-1188)gTg>gCg	p.V396A	PIK3R3_ENST00000340332.6_Splice_Site_p.V301A|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000420542.1_Splice_Site_p.V396A|PIK3R3_ENST00000540385.1_Splice_Site_p.V442A|PIK3R3_ENST00000354242.4_Splice_Site_p.V337A|PIK3R3_ENST00000423209.1_Splice_Site_p.V337A|PIK3R3_ENST00000372006.1_Splice_Site_p.V396A|RP4-533D7.4_ENST00000450004.1_RNA	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	396	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)	p.V396A(1)		endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	GAAGACTTACACCACAGAGCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											164	151	155					1																	46511590		2203	4300	6503	46284177	SO:0001630	splice_region_variant	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.1187+1T>C	1.37:g.46511590A>G			46284177	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	37	CCDS529.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.901574	0.92035	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000354242;ENST00000340332;ENST00000540385;ENST00000423209	D;D;D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5	6.08	6.08	0.98989	SH2 motif (5);	0.054304	0.64402	D	0.000001	D	0.93268	0.7855	M	0.62209	1.925	0.80722	D	1	P;P;P;D	0.56521	0.756;0.84;0.745;0.976	P;P;P;D	0.71870	0.503;0.666;0.65;0.975	D	0.92685	0.6161	9	.	.	.	-8.1552	16.6438	0.85155	1.0:0.0:0.0:0.0	.	442;429;337;396	F6TDL0;Q7Z3W2;Q92569-2;Q92569	.;.;.;P55G_HUMAN	A	396;396;396;337;301;442;337	ENSP00000361075:V396A;ENSP00000262741:V396A;ENSP00000412546:V396A;ENSP00000346188:V337A;ENSP00000342484:V301A;ENSP00000439913:V442A;ENSP00000391431:V337A	.	V	-	2	0	PIK3R3	46284177	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.339000	0.96797	2.333000	0.79357	0.533000	0.62120	GTG		0.363	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	Missense_Mutation	G	46511590	A	G	46511590	5	3	2	1	0	0	0	0	0	0	1	0	11951	173	6	4	206	4	PIK3R3	1	46511590	Splice_Site	SNP	A	TCGA-AF-2689-01A-01W-0831-10	26095221	46511590	202739031	3	194										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99771528	99771528	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	accttcagcaataccttgccGcgagccaataccccatctgt	6	16	2	0	rs202142961		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:99771528G>A	ENST00000370185.3	+	7	1751	c.1254G>A	c.(1252-1254)ccG>ccA	p.P418P	LPPR4_ENST00000370184.1_Silent_p.P260P|LPPR4_ENST00000457765.1_Silent_p.P360P	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		418					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.P418P(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ATACCTTGCCGCGAGCCAATA	0.498																																																2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	1											54	56	55					1																	99771528		2203	4300	6503	99544116	SO:0001819	synonymous_variant	9890																														ENST00000370185.3:c.1254G>A	1.37:g.99771528G>A			99544116	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Silent	SNP	ENST00000370185.3	37	CCDS757.1																																																																																				0.498	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			A	99771528	G	A	99771528	2	1	2	1	0	0	0	0	0	0	0	1	8956	1074	38	1		1	LPPR4	1	99771528	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	53259938	99771528	149479093	4	195										
GPR89A	653519	hgsc.bcm.edu	37	chr1	145765381	145765381	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aaacttaccattatctgtgcTaatagcaggacaatgacatt	6	8	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:145765381T>C	ENST00000313835.9	-	13	1292	c.1149A>G	c.(1147-1149)ttA>ttG	p.L383L	GPR89A_ENST00000454423.3_Silent_p.L263L|GPR89A_ENST00000462900.2_Silent_p.L358L|GPR89A_ENST00000534502.1_Silent_p.L358L			B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A	383					intracellular pH reduction (GO:0051452)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|regulation of anion transport (GO:0044070)|signal transduction (GO:0007165)	Golgi cisterna membrane (GO:0032580)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)|voltage-gated anion channel activity (GO:0008308)	p.L383L(1)		breast(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			TTATCTGTGCTAATAGCAGGA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	1											213	233	226					1																	145765381		2203	4300	6503	144476738	SO:0001819	synonymous_variant	653519			AB097024	CCDS72857.1, CCDS72858.1	1q21.1	2008-12-17	2007-06-06	2007-06-06	ENSG00000117262	ENSG00000117262			31984	protein-coding gene	gene with protein product		612821					Standard	NM_001097612		Approved	UNQ192	uc001eot.2	B7ZAQ6	OTTHUMG00000013738	ENST00000313835.9:c.1149A>G	1.37:g.145765381T>C			144476738	A6NN37|B2RUV3|B3KMN3|B4DLT3|B4DXE7|Q53FQ9|Q5T2V8|Q5T5P5|Q659E2|Q6NVY5|Q9P0S4|Q9Y302	Silent	SNP	ENST00000313835.9	37	CCDS41377.1																																																																																				0.323	GPR89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038507.2	NM_001097612		C	145765381	T	C	145765381	2	2	2	1	0	0	0	0	0	0	0	1	6738	1519	53	4		4	GPR89A	1	145765381	Silent	SNP	T	TCGA-AF-2689-01A-01W-0831-10	45993853	145765381	103485240	5	196										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173506165	173506165	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gaattccattgttacgctgtTtttcaaagctactctaaaca	5	9	2	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:173506165T>G	ENST00000367714.3	-	14	1993	c.1571A>C	c.(1570-1572)aAa>aCa	p.K524T	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Missense_Mutation_p.K422T	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	524					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.K524T(1)									GTTACGCTGTTTTTCAAAGCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											115	118	117					1																	173506165		2203	4300	6503	171772788	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1571A>C	1.37:g.173506165T>G	ENSP00000356687:p.Lys524Thr		171772788	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527872	0.44969	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.24908	1.83;1.83	5.52	4.33	0.51752	.	0.000000	0.64402	D	0.000008	T	0.12603	0.0306	L	0.60455	1.87	0.23309	N	0.997932	P	0.42409	0.779	B	0.39840	0.311	T	0.04870	-1.0921	10	0.38643	T	0.18	-32.4035	10.0974	0.42484	0.0:0.0:0.1804:0.8196	.	524	Q5TAH2	S9A11_HUMAN	T	524;422	ENSP00000356687:K524T;ENSP00000445437:K422T	ENSP00000356687:K524T	K	-	2	0	SLC9A11	171772788	0.999000	0.42202	1.000000	0.80357	0.846000	0.48090	2.372000	0.44257	2.094000	0.63399	0.416000	0.27883	AAA		0.333	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		G	173506165	T	G	173506165	3	3	2	1	0	0	0	0	1	0	0	0	14748	1841	64	4	1863	4	SLC9A11	1	173506165	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10	27740784	173506165	75744456	6	197										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205896666	205896666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	cagccagagtgacagaaagcGcacagcaaatgacatgaatt	10	9	0	5			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr1:205896666G>A	ENST00000367135.3	-	10	1282	c.1169C>T	c.(1168-1170)gCg>gTg	p.A390V	SLC26A9_ENST00000367134.2_Missense_Mutation_p.A390V|SLC26A9_ENST00000340781.4_Missense_Mutation_p.A390V	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	390					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)	p.A390V(1)		NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			GACAGAAAGCGCACAGCAAAT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	76	75					1																	205896666		2203	4300	6503	204163289	SO:0001583	missense	115019			AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.1169C>T	1.37:g.205896666G>A	ENSP00000356103:p.Ala390Val		204163289	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	G	33	5.279698	0.95489	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.93366	-3.21;-3.21;-3.21	5.09	5.09	0.68999	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.95484	0.8533	M	0.84511	2.7	0.58432	D	0.999995	D;D	0.69078	0.992;0.997	P;P	0.49922	0.488;0.626	D	0.96247	0.9180	10	0.87932	D	0	.	18.4557	0.90720	0.0:0.0:1.0:0.0	.	390;390	Q7LBE3;B1AVM8	S26A9_HUMAN;.	V	390	ENSP00000341682:A390V;ENSP00000356103:A390V;ENSP00000356102:A390V	ENSP00000341682:A390V	A	-	2	0	SLC26A9	204163289	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.414000	0.97362	2.525000	0.85131	0.655000	0.94253	GCG		0.527	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		A	205896666	G	A	205896666	3	1	2	1	0	0	0	0	1	0	0	0	14561	1087	38	1	1550	1	SLC26A9	1	205896666	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	32390501	205896666	43353955	7	198										
ATP6V1E2	90423	hgsc.bcm.edu	37	chr2	46739441	46739441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ccaggaggaggtcttgtggcCggcagcgtacaatcatcaca	13	11	3	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr2:46739441C>T	ENST00000306448.4	-	2	1523	c.410G>A	c.(409-411)cGg>cAg	p.R137Q	ATP6V1E2_ENST00000522587.1_Missense_Mutation_p.R137Q	NM_080653.3	NP_542384.1	Q96A05	VATE2_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E2	137					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.R137Q(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.151)			GTCTTGTGGCCGGCAGCGTAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	2											93	91	92					2																	46739441		2203	4300	6503	46592945	SO:0001583	missense	90423			BC008981	CCDS1826.1	2p21	2011-02-10	2006-01-13	2002-06-21	ENSG00000250565	ENSG00000250565		"ATPases / V-type"	18125	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD-like 2", "ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 2"	ATP6EL2, ATP6V1EL2		12036578	Standard	NM_080653		Approved	MGC9341, VMA4, ATP6E1	uc002ruy.3	Q96A05	OTTHUMG00000128819	ENST00000306448.4:c.410G>A	2.37:g.46739441C>T	ENSP00000304891:p.Arg137Gln		46592945		Missense_Mutation	SNP	ENST00000306448.4	37	CCDS1826.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183964	0.94885	.	.	ENSG00000250565	ENST00000306448;ENST00000522587	.	.	.	4.37	4.37	0.52481	.	0.048550	0.64402	D	0.000001	T	0.79673	0.4486	M	0.88775	2.98	0.80722	D	1	D	0.76494	0.999	D	0.65010	0.931	T	0.83156	-0.0101	9	0.87932	D	0	-22.3678	12.7449	0.57276	0.0:1.0:0.0:0.0	.	137	Q96A05	VATE2_HUMAN	Q	137	.	ENSP00000304891:R137Q	R	-	2	0	ATP6V1E2	46592945	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	5.022000	0.64078	2.713000	0.92767	0.655000	0.94253	CGG		0.542	ATP6V1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250753.1	NM_080653		T	46739441	C	T	46739441	3	4	2	1	0	0	0	0	1	0	0	0	1185	652	23	1	274	1	ATP6V1E2	2	46739441	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10		46739441	196459932	8	199										
MYRIP	25924	hgsc.bcm.edu	37	chr3	40275432	40275432	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	agaggagttgatagcaggatCtacagggccctgggagtccc	15	9	1	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:40275432C>T	ENST00000302541.6	+	12	2330	c.1988C>T	c.(1987-1989)tCt>tTt	p.S663F	MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000444716.1_Missense_Mutation_p.S663F|MYRIP_ENST00000396217.3_Missense_Mutation_p.S574F|MYRIP_ENST00000425621.1_Intron|MYRIP_ENST00000539167.1_Missense_Mutation_p.S476F	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	663	Actin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)	p.S663F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		ATAGCAGGATCTACAGGGCCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	76	78					3																	40275432		2203	4300	6503	40250436	SO:0001583	missense	25924			AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1988C>T	3.37:g.40275432C>T	ENSP00000301972:p.Ser663Phe		40250436	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410877	0.62399	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000396217;ENST00000539167	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.79	4.92	0.64577	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.063145	0.64402	D	0.000004	T	0.52008	0.1708	L	0.58101	1.795	0.36284	D	0.855967	D;D	0.60160	0.983;0.987	P;D	0.63703	0.899;0.917	T	0.60510	-0.7249	9	.	.	.	.	12.6195	0.56595	0.0:0.9203:0.0:0.0797	.	574;663	Q32M42;Q8NFW9	.;MYRIP_HUMAN	F	663;663;574;476	ENSP00000398665:S663F;ENSP00000301972:S663F;ENSP00000379519:S574F;ENSP00000438297:S476F	.	S	+	2	0	MYRIP	40250436	1.000000	0.71417	0.683000	0.30040	0.917000	0.54804	6.710000	0.74670	1.458000	0.47871	-0.136000	0.14681	TCT		0.512	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		T	40275432	C	T	40275432	3	4	2	1	0	0	0	0	1	0	0	0	10130	913	32	3	2030	3	MYRIP	3	40275432	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10		40275432	157746998	9	200										
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42916263	42916263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gggtgggtgcagccctcagcCgcagcgtctcctccaccacg	13	17	2	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:42916263C>T	ENST00000316161.4	-	1	1370	c.1046G>A	c.(1045-1047)cGg>cAg	p.R349Q	KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.R349Q|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	349					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)	p.R349Q(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		AGCCCTCAGCCGCAGCGTCTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	3											51	49	50					3																	42916263		2203	4300	6503	42891267	SO:0001583	missense	1582			AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"Cytochrome P450s"	2653	protein-coding gene	gene with protein product		602172	"cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1046G>A	3.37:g.42916263C>T	ENSP00000318867:p.Arg349Gln		42891267	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604933	0.66445	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	D;D	0.97480	-4.4;-4.4	5.27	5.27	0.74061	.	0.078391	0.51477	D	0.000099	D	0.98918	0.9633	H	0.94503	3.545	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99675	1.0997	10	0.87932	D	0	-20.635	17.6592	0.88187	0.0:1.0:0.0:0.0	.	349;349	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	Q	349	ENSP00000404499:R349Q;ENSP00000318867:R349Q	ENSP00000318867:R349Q	R	-	2	0	CYP8B1	42891267	0.949000	0.32298	0.296000	0.24974	0.015000	0.08874	7.724000	0.84798	2.456000	0.83038	0.561000	0.74099	CGG		0.587	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		T	42916263	C	T	42916263	3	4	2	1	0	0	0	0	1	0	0	0	4204	652	23	1	463	1	CYP8B1	3	42916263	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	2640831	42916263	155106167	10	201										
TGM4	7047	hgsc.bcm.edu	37	chr3	44943361	44943361	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gacacagaaaggaacctcacGgtggacacctatgtgaatga	11	9	1	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:44943361G>A	ENST00000296125.4	+	8	977	c.909G>A	c.(907-909)acG>acA	p.T303T	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	303					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T303T(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GGAACCTCACGGTGGACACCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	3											127	117	121					3																	44943361		2203	4300	6503	44918365	SO:0001819	synonymous_variant	7047			BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.909G>A	3.37:g.44943361G>A			44918365	Q16707|Q96QN4	Silent	SNP	ENST00000296125.4	37	CCDS2723.1																																																																																				0.542	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44943361	G	A	44943361	2	1	2	1	0	0	0	0	0	0	0	1	15871	1103	39	1		1	TGM4	3	44943361	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	2027098	44943361	153079069	11	202										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48608296	48608296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ctgttcccagcccctcacccGctctccactagggcctggct	8	20	2	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:48608296G>A	ENST00000328333.8	-	94	7377	c.7270C>T	c.(7270-7272)Cgg>Tgg	p.R2424W	COL7A1_ENST00000454817.1_Missense_Mutation_p.R2392W	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2424	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R2424W(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCCTCACCCGCTCTCCACTA	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	3											34	29	31					3																	48608296		2202	4300	6502	48583300	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7270C>T	3.37:g.48608296G>A	ENSP00000332371:p.Arg2424Trp		48583300	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	G	9.142	1.014011	0.19277	.	.	ENSG00000114270	ENST00000328333;ENST00000454817;ENST00000422991	D;D;D	0.96334	-3.98;-3.98;-3.98	5.24	3.36	0.38483	.	0.000000	0.41396	D	0.000897	D	0.97791	0.9275	M	0.83483	2.645	0.44834	D	0.997842	D	0.89917	1.0	D	0.76071	0.987	D	0.98036	1.0379	10	0.66056	D	0.02	.	12.5534	0.56240	0.0:0.0:0.5423:0.4577	.	2424	Q02388	CO7A1_HUMAN	W	2424;2392;89	ENSP00000332371:R2424W;ENSP00000412569:R2392W;ENSP00000391608:R89W	ENSP00000332371:R2424W	R	-	1	2	COL7A1	48583300	0.980000	0.34600	1.000000	0.80357	0.284000	0.27059	0.318000	0.19504	1.174000	0.42811	0.655000	0.94253	CGG		0.667	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48608296	G	A	48608296	3	1	2	1	0	0	0	0	1	0	0	0	3710	1086	38	1	1664	1	COL7A1	3	48608296	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	3664935	48608296	149414134	12	203										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111950220	111950220	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tacagtactatttgtgctgaCaagagacgcctgttggccag	11	9	0	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:111950220C>G	ENST00000305815.5	-	13	1812	c.1560G>C	c.(1558-1560)ttG>ttC	p.L520F	SLC9C1_ENST00000487372.1_Missense_Mutation_p.L472F	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	520					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.L520F(1)									TTTGTGCTGACAAGAGACGCC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											148	142	144					3																	111950220		2203	4300	6503	113432910	SO:0001583	missense	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1560G>C	3.37:g.111950220C>G	ENSP00000306627:p.Leu520Phe		113432910	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.678413	0.29783	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;D	0.81579	-1.48;-1.51	5.44	0.279	0.15677	.	0.321128	0.21091	N	0.080309	T	0.77994	0.4214	L	0.32530	0.975	0.09310	N	0.999997	D;D	0.63880	0.991;0.993	D;P	0.69654	0.965;0.855	T	0.65590	-0.6131	10	0.62326	D	0.03	-6.3067	1.6981	0.02866	0.1461:0.4578:0.1424:0.2536	.	472;520	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	F	520;472	ENSP00000306627:L520F;ENSP00000420688:L472F	ENSP00000306627:L520F	L	-	3	2	SLC9A10	113432910	0.016000	0.18221	0.065000	0.19835	0.520000	0.34377	-1.058000	0.03482	0.044000	0.15775	-0.351000	0.07748	TTG		0.358	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		G	111950220	C	G	111950220	3	3	2	1	0	0	0	0	1	0	0	0	14747	477	17	5	2041	5	SLC9A10	3	111950220	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	63341924	111950220	86072210	13	204										
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170198432	170198432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tttgcctggaaggcccagccGgattctcatggtgtaataat	11	9	1	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:170198432G>A	ENST00000231706.5	-	7	1954	c.1639C>T	c.(1639-1641)Cgg>Tgg	p.R547W	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	547					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.R547W(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			AGGCCCAGCCGGATTCTCATG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											97	96	96					3																	170198432		2203	4300	6503	171681126	SO:0001583	missense	57709			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1639C>T	3.37:g.170198432G>A	ENSP00000231706:p.Arg547Trp		171681126	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	37	CCDS33892.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.105603	0.56291	.	.	ENSG00000013293	ENST00000231706	D	0.88509	-2.39	5.51	5.51	0.81932	.	0.363497	0.31859	N	0.006950	D	0.87501	0.6193	L	0.56769	1.78	0.58432	D	0.999995	P	0.51537	0.946	B	0.40565	0.333	D	0.87203	0.2242	10	0.36615	T	0.2	.	19.3998	0.94623	0.0:0.0:1.0:0.0	.	547	Q8TBB6	S7A14_HUMAN	W	547	ENSP00000231706:R547W	ENSP00000231706:R547W	R	-	1	2	SLC7A14	171681126	1.000000	0.71417	0.999000	0.59377	0.556000	0.35491	6.400000	0.73252	2.579000	0.87056	0.591000	0.81541	CGG		0.507	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170198432	G	A	170198432	3	1	2	1	0	0	0	0	1	0	0	0	14733	1115	39	1	684	1	SLC7A14	3	170198432	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	58248212	170198432	27823998	14	205										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173999082	173999082	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	acccccattcacattcaacaAccagggtatagccagataag	6	13	2	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr3:173999082A>T	ENST00000457714.1	+	7	2890	c.2461A>T	c.(2461-2463)Acc>Tcc	p.T821S	NLGN1_ENST00000545397.1_Missense_Mutation_p.T821S|NLGN1_ENST00000361589.4_Missense_Mutation_p.T821S|NLGN1_ENST00000401917.3_Missense_Mutation_p.T861S	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	838					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.T821S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ACATTCAACAACCAGGGTATA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											45	44	44					3																	173999082		2203	4300	6503	175481776	SO:0001583	missense	22871			AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.2461A>T	3.37:g.173999082A>T	ENSP00000392500:p.Thr821Ser		175481776	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813831	0.50527	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.73363	-0.69;-0.69;-0.69;-0.74	5.6	4.37	0.52481	.	0.166402	0.52532	D	0.000075	D	0.82733	0.5101	M	0.62723	1.935	0.53688	D	0.999972	D	0.56035	0.974	D	0.67725	0.953	D	0.84690	0.0722	10	0.87932	D	0	.	13.2655	0.60131	0.8686:0.1314:0.0:0.0	.	821	Q8N2Q7-2	.	S	821;821;821;861	ENSP00000392500:T821S;ENSP00000354541:T821S;ENSP00000441108:T821S;ENSP00000385750:T861S	ENSP00000354541:T821S	T	+	1	0	NLGN1	175481776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.262000	0.72514	2.254000	0.74563	0.482000	0.46254	ACC		0.418	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		T	173999082	A	T	173999082	3	4	2	1	0	0	0	0	1	0	0	0	10492	43	2	5	2479	5	NLGN1	3	173999082	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	3800650	173999082	24023348	15	206										
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95506883	95506883	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tgcccagatcactgggactgAacattgtaagtgaacttcta	9	9	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr4:95506883A>G	ENST00000317968.4	+	6	1014	c.878A>G	c.(877-879)gAa>gGa	p.E293G	PDLIM5_ENST00000538141.1_Missense_Mutation_p.E170G|PDLIM5_ENST00000514743.1_Missense_Mutation_p.E190G|PDLIM5_ENST00000437932.1_Missense_Mutation_p.E184G|PDLIM5_ENST00000318007.5_Missense_Mutation_p.E170G|PDLIM5_ENST00000542407.1_Missense_Mutation_p.E171G|PDLIM5_ENST00000380180.3_Missense_Mutation_p.E190G|PDLIM5_ENST00000450793.1_Missense_Mutation_p.E190G|PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000508216.1_Missense_Mutation_p.E190G	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	293					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)	p.E293G(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		ACTGGGACTGAACATTGTAAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	74	77					4																	95506883		2203	4300	6503	95725906	SO:0001583	missense	10611			AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.878A>G	4.37:g.95506883A>G	ENSP00000321746:p.Glu293Gly		95725906	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.4|28.4	4.917481|4.917481	0.92249|0.92249	.|.	.|.	ENSG00000163110|ENSG00000163110	ENST00000437932;ENST00000380180;ENST00000318007;ENST00000450793;ENST00000538141;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000508216;ENST00000514743|ENST00000513341	T;T;T;T;T;T;T;T;T;T|.	0.69685|.	-0.07;0.95;0.86;1.0;0.55;0.1;-0.07;-0.42;0.95;-0.3|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.050975|.	0.85682|.	D|.	0.000000|.	T|T	0.72779|0.72779	0.3503|0.3503	M|M	0.68593|0.68593	2.085|2.085	0.80722|0.80722	D|D	1|1	D;D;P;D;P;D|.	0.89917|.	0.994;0.999;0.773;0.995;0.932;1.0|.	D;D;B;D;P;D|.	0.80764|.	0.968;0.922;0.437;0.948;0.638;0.994|.	T|T	0.72717|0.72717	-0.4209|-0.4209	10|5	0.62326|.	D|.	0.03|.	.|.	15.5463|15.5463	0.76104|0.76104	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	190;190;293;184;190;170|.	E9PBF5;D6RB78;Q96HC4;Q96HC4-4;Q96HC4-2;Q96HC4-3|.	.;.;PDLI5_HUMAN;.;.;.|.	G|D	184;190;170;190;170;293;190;171;190;190|152	ENSP00000398469:E184G;ENSP00000369527:E190G;ENSP00000322021:E170G;ENSP00000401579:E190G;ENSP00000439795:E170G;ENSP00000321746:E293G;ENSP00000424297:E190G;ENSP00000442187:E171G;ENSP00000426804:E190G;ENSP00000424360:E190G|.	ENSP00000321746:E293G|.	E|N	+|+	2|1	0|0	PDLIM5|PDLIM5	95725906|95725906	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.995000|0.995000	0.86356|0.86356	8.905000|8.905000	0.92613|0.92613	2.120000|2.120000	0.65058|0.65058	0.528000|0.528000	0.53228|0.53228	GAA|AAC		0.458	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			G	95506883	A	G	95506883	3	3	2	1	0	0	0	0	1	0	0	0	11714	246	9	4	958	4	PDLIM5	4	95506883	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10		95506883	95647393	16	207										
GZMK	3003	hgsc.bcm.edu	37	chr5	54329599	54329599	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tttcttccttccagggtgacTcagggggccccttgatctgt	11	12	3	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr5:54329599T>A	ENST00000231009.2	+	5	710	c.640T>A	c.(640-642)Tca>Aca	p.S214T	CTD-2313F11.1_ENST00000596137.1_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000609792.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	214	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S214T(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CCAGGGTGACTCAGGGGGCCC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	68	70					5																	54329599		2203	4300	6503	54365356	SO:0001583	missense	3003			BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"granzyme K (serine protease, granzyme 3; tryptase II)"			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.640T>A	5.37:g.54329599T>A	ENSP00000231009:p.Ser214Thr		54365356	B2R563	Missense_Mutation	SNP	ENST00000231009.2	37	CCDS3964.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.144348	0.77888	.	.	ENSG00000113088	ENST00000231009	D	0.96491	-4.03	5.28	4.08	0.47627	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000001	D	0.98137	0.9385	M	0.91920	3.255	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.98066	1.0396	10	0.87932	D	0	.	9.4908	0.38958	0.1582:0.0:0.0:0.8418	.	214	P49863	GRAK_HUMAN	T	214	ENSP00000231009:S214T	ENSP00000231009:S214T	S	+	1	0	GZMK	54365356	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	4.088000	0.57678	0.963000	0.38082	0.533000	0.62120	TCA		0.458	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104		A	54329599	T	A	54329599	3	1	2	1	0	0	0	0	1	0	0	0	6939	1551	54	5	658	5	GZMK	5	54329599	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10		54329599	126585661	17	208										
PSD2	84249	hgsc.bcm.edu	37	chr5	139192982	139192982	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	cagagctgctgcggggcaccCagtacagcagcctcgactcc	12	16	0	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr5:139192982C>T	ENST00000274710.3	+	3	665	c.460C>T	c.(460-462)Cag>Tag	p.Q154*		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	154					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.Q154*(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGGGCACCCAGTACAGCAG	0.637																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											42	46	45					5																	139192982		2203	4300	6503	139173166	SO:0001587	stop_gained	84249			AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.460C>T	5.37:g.139192982C>T	ENSP00000274710:p.Gln154*		139173166	D3DQD3|Q8N3J8	Nonsense_Mutation	SNP	ENST00000274710.3	37	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	37	6.509314	0.97624	.	.	ENSG00000146005	ENST00000274710	.	.	.	4.52	3.36	0.38483	.	0.249733	0.34088	N	0.004274	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	3.6945	0.08358	0.0:0.6882:0.0:0.3118	.	.	.	.	X	154	.	ENSP00000274710:Q154X	Q	+	1	0	PSD2	139173166	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.255000	0.65462	2.214000	0.71695	0.462000	0.41574	CAG		0.637	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139192982	C	T	139192982	4	4	2	1	0	0	0	0	0	1	0	0	12681	595	21	3	466	3	PSD2	5	139192982	Nonsense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	84863383	139192982	41722278	18	209										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147820739	147820739	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tctgacttcccttggctgagGtcattacgagctgcagagcc	11	12	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr5:147820739G>A	ENST00000340253.5	+	21	3495	c.3327G>A	c.(3325-3327)agG>agA	p.R1109R	FBXO38_ENST00000513826.1_Silent_p.R864R|FBXO38_ENST00000296701.6_Silent_p.R864R|FBXO38_ENST00000394370.3_Silent_p.R1034R			Q6PIJ6	FBX38_HUMAN	F-box protein 38	1109					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R1109R(1)	ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGGCTGAGGTCATTACGAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	5											240	198	212					5																	147820739		2203	4300	6503	147800932	SO:0001819	synonymous_variant	81545			BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.3327G>A	5.37:g.147820739G>A			147800932	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Silent	SNP	ENST00000340253.5	37																																																																																					0.438	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		A	147820739	G	A	147820739	2	1	2	1	0	0	0	0	0	0	0	1	5765	1252	44	3		3	FBXO38	5	147820739	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	8627757	147820739	33094521	19	210										
DCDC2	51473	hgsc.bcm.edu	37	chr6	24278380	24278380	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tttttccctttcctcttcagGggctgaggagatgagttgtc	11	9	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr6:24278380G>A	ENST00000378454.3	-	7	1120	c.819C>T	c.(817-819)ccC>ccT	p.P273P		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	273					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)			p.P273P(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TCCTCTTCAGGGGCTGAGGAG	0.358																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	6											136	127	130					6																	24278380		2203	4300	6503	24386359	SO:0001819	synonymous_variant	51473			AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.819C>T	6.37:g.24278380G>A			24386359	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1																																																																																				0.358	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		A	24278380	G	A	24278380	2	1	2	1	0	0	0	0	0	0	0	1	4291	1219	43	3		3	DCDC2	6	24278380	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10		24278380	146836687	20	211										
PEX3	8504	hgsc.bcm.edu	37	chr6	143792159	143792159	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ctggttgttcttttgcgggtCcagttaaacataattggtgg	12	6	1	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr6:143792159C>T	ENST00000367591.4	+	5	456	c.393C>T	c.(391-393)gtC>gtT	p.V131V		NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	131	Interaction with PEX19.				peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.V131V(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		TTTTGCGGGTCCAGTTAAACA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	6											145	138	140					6																	143792159		2203	4300	6503	143833852	SO:0001819	synonymous_variant	8504			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.393C>T	6.37:g.143792159C>T			143833852	Q6FGP5	Silent	SNP	ENST00000367591.4	37	CCDS5199.1																																																																																				0.368	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1			T	143792159	C	T	143792159	2	4	2	1	0	0	0	0	0	0	0	1	11778	842	30	3		3	PEX3	6	143792159	Silent	SNP	C	TCGA-AF-2689-01A-01W-0831-10	119513779	143792159	27322908	21	212										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100085867	100085867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ctaacacccagctctctgtcTccttcgatgagtcctgcccc	6	18	2	1	rs202132246		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr7:100085867T>C	ENST00000300179.2	+	4	682	c.523T>C	c.(523-525)Tcc>Ccc	p.S175P	NYAP1_ENST00000423930.1_Missense_Mutation_p.S175P|NYAP1_ENST00000454988.1_Missense_Mutation_p.S118P	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	175	Involved in CYFIP1- and NCKAP1-binding. {ECO:0000250}.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.S175P(1)									GCTCTCTGTCTCCTTCGATGA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	7											84	93	90					7																	100085867		2203	4300	6503	99923803	SO:0001583	missense	222950			AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.523T>C	7.37:g.100085867T>C	ENSP00000300179:p.Ser175Pro		99923803	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.635852	0.67130	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.67171	-0.25;-0.25;-0.25	5.32	5.32	0.75619	.	0.000000	0.50627	D	0.000111	T	0.79240	0.4412	M	0.67700	2.07	0.48040	D	0.999579	D	0.89917	1.0	D	0.85130	0.997	T	0.79848	-0.1630	10	0.48119	T	0.1	-23.7526	13.2221	0.59894	0.0:0.0:0.0:1.0	.	175	Q6ZVC0	CG051_HUMAN	P	175;175;118	ENSP00000300179:S175P;ENSP00000411861:S175P;ENSP00000394424:S118P	ENSP00000300179:S175P	S	+	1	0	C7orf51	99923803	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	4.187000	0.58344	2.013000	0.59113	0.334000	0.21626	TCC		0.652	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		C	100085867	T	C	100085867	3	2	2	1	0	0	0	0	1	0	0	0	2406	1551	54	4	533	4	C7orf51	7	100085867	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10		100085867	59052796	22	213										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112112275	112112275	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tggttcttccattggttaggAacgggattttccaacagaaa	10	7	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr7:112112275A>G	ENST00000403825.3	+	10	1304	c.1043A>G	c.(1042-1044)gAa>gGa	p.E348G	IFRD1_ENST00000535603.1_Splice_Site_p.E298G|IFRD1_ENST00000005558.4_Splice_Site_p.E348G	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	348					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)		p.E348G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						ATTGGTTAGGAACGGGATTTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											113	113	113					7																	112112275		2203	4300	6503	111899511	SO:0001630	splice_region_variant	3475			Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1042-1A>G	7.37:g.112112275A>G			111899511	B7Z5G1|O75234|Q5U013|Q9BVE4	Missense_Mutation	SNP	ENST00000403825.3	37	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.197436	0.58126	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000536259;ENST00000535603;ENST00000421296;ENST00000462155	T;T;T	0.49432	0.78;0.78;0.8	5.93	5.93	0.95920	.	0.097095	0.64402	D	0.000001	T	0.37237	0.0996	L	0.35487	1.065	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.21759	-1.0236	10	0.11485	T	0.65	-18.5924	16.3789	0.83431	1.0:0.0:0.0:0.0	.	348;348	A4D0U1;O00458	.;IFRD1_HUMAN	G	348;348;83;298;83;11	ENSP00000005558:E348G;ENSP00000384477:E348G;ENSP00000439188:E298G	ENSP00000005558:E348G	E	+	2	0	IFRD1	111899511	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.981000	0.93465	2.267000	0.75376	0.533000	0.62120	GAA		0.373	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	Missense_Mutation	G	112112275	A	G	112112275	5	3	2	1	0	0	0	0	0	0	1	0	7574	260	9	4	1081	4	IFRD1	7	112112275	Splice_Site	SNP	A	TCGA-AF-2689-01A-01W-0831-10	12026408	112112275	47026388	23	214										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113522320	113522320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttaatgaagaatattacctgTattctttggattctcaaagt	6	5	2	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr7:113522320T>C	ENST00000284601.3	-	2	906	c.838A>G	c.(838-840)Aca>Gca	p.T280A		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	280					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.T280A(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATATTACCTGTATTCTTTGGA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	41	40					7																	113522320		2188	4277	6465	113309556	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.838A>G	7.37:g.113522320T>C	ENSP00000284601:p.Thr280Ala		113309556	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	9.368	1.069695	0.20147	.	.	ENSG00000154415	ENST00000284601	T	0.16743	2.32	5.92	2.16	0.27623	.	0.613719	0.17499	N	0.172069	T	0.10252	0.0251	L	0.36672	1.1	0.22240	N	0.999269	B	0.06786	0.001	B	0.08055	0.003	T	0.29212	-1.0019	10	0.25106	T	0.35	.	1.8772	0.03220	0.1605:0.146:0.1145:0.5789	.	280	Q16821	PPR3A_HUMAN	A	280	ENSP00000284601:T280A	ENSP00000284601:T280A	T	-	1	0	PPP1R3A	113309556	0.870000	0.30015	0.446000	0.26920	0.510000	0.34073	0.864000	0.27926	0.447000	0.26695	0.459000	0.35465	ACA		0.254	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113522320	T	C	113522320	3	2	2	1	0	0	0	0	1	0	0	0	12405	1638	57	4	2542	4	PPP1R3A	7	113522320	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10	1410045	113522320	45616343	24	215										
FAM71F1	84691	hgsc.bcm.edu	37	chr7	128359089	128359089	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gaccctaggattcttgtcacGcactgcctggtacccaagaa	9	13	2	1	rs144120466		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr7:128359089G>A	ENST00000315184.5	+	3	692	c.639G>A	c.(637-639)acG>acA	p.T213T	FAM71F1_ENST00000469348.1_3'UTR|FAM71F1_ENST00000485070.1_Silent_p.T114T	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	213								p.T213T(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TTCTTGTCACGCACTGCCTGG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	7						G		0,4406		0,0,2203	123	112	115		639	1	1	7	dbSNP_134	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAM71F1	NM_032599.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		213/345	128359089	1,13005	2203	4300	6503	128146325	SO:0001819	synonymous_variant	84691			AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"family with sequence similarity 137, member A"	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.639G>A	7.37:g.128359089G>A			128146325	Q8IY75|Q8NA48	Silent	SNP	ENST00000315184.5	37	CCDS5804.1																																																																																				0.532	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599		A	128359089	G	A	128359089	2	1	2	1	0	0	0	0	0	0	0	1	5631	1074	38	1		1	FAM71F1	7	128359089	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	14836769	128359089	30779574	25	216										
NOM1	64434	hgsc.bcm.edu	37	chr7	156754863	156754863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	agattcggtttatgctagagAcgatgttggccctgaagaac	12	7	0	4			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr7:156754863A>G	ENST00000275820.3	+	5	1666	c.1651A>G	c.(1651-1653)Acg>Gcg	p.T551A		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	551	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T551A(1)		endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TATGCTAGAGACGATGTTGGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	7											197	204	201					7																	156754863		2203	4300	6503	156447624	SO:0001583	missense	64434			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1651A>G	7.37:g.156754863A>G	ENSP00000275820:p.Thr551Ala		156447624	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125668	0.77436	.	.	ENSG00000146909	ENST00000275820	T	0.23552	1.9	4.52	4.52	0.55395	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	U	0.000000	T	0.50463	0.1617	M	0.85299	2.745	0.58432	D	0.999999	P	0.46621	0.881	P	0.59288	0.855	T	0.53830	-0.8383	10	0.38643	T	0.18	-25.9397	13.8879	0.63719	1.0:0.0:0.0:0.0	.	551	Q5C9Z4	NOM1_HUMAN	A	551	ENSP00000275820:T551A	ENSP00000275820:T551A	T	+	1	0	NOM1	156447624	1.000000	0.71417	0.957000	0.39632	0.986000	0.74619	8.561000	0.90715	1.676000	0.50930	0.444000	0.29173	ACG		0.448	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		G	156754863	A	G	156754863	3	3	2	1	0	0	0	0	1	0	0	0	10561	275	10	4	1669	4	NOM1	7	156754863	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	28395774	156754863	2383800	26	217										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72969251	72969251	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tcttttatgtctacttgggcAcctaaaaaaaaacactatgt	5	8	2	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr8:72969251A>C	ENST00000262209.4	-	10	1302	c.1095T>G	c.(1093-1095)ggT>ggG	p.G365G		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	365					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.G365G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTACTTGGGCACCTAAAAAAA	0.274																																																1	Substitution - coding silent(1)	large_intestine(1)	8											25	24	24					8																	72969251		2200	4295	6495	73131805	SO:0001630	splice_region_variant	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1094-1T>G	8.37:g.72969251A>C			73131805	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																				0.274	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	Silent	C	72969251	A	C	72969251	5	2	2	1	0	0	0	0	0	0	1	0	16617	173	6	4	2336	4	TRPA1	8	72969251	Splice_Site	SNP	A	TCGA-AF-2689-01A-01W-0831-10		72969251	73394771	27	218										
MMP16	4325	hgsc.bcm.edu	37	chr8	89179995	89179995	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aagtaggcatgtgccaaaaaTcctccctctccatcaaaggg	8	12	2	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr8:89179995T>C	ENST00000286614.6	-	4	893	c.612A>G	c.(610-612)ggA>ggG	p.G204G	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	204					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G204G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GTGCCAAAAATCCTCCCTCTC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	8											98	85	89					8																	89179995		2203	4300	6503	89249111	SO:0001819	synonymous_variant	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.612A>G	8.37:g.89179995T>C			89249111	B2RAN7|Q14824|Q52H48	Silent	SNP	ENST00000286614.6	37	CCDS6246.1																																																																																				0.443	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		C	89179995	T	C	89179995	2	2	2	1	0	0	0	0	0	0	0	1	9685	1422	50	4		4	MMP16	8	89179995	Silent	SNP	T	TCGA-AF-2689-01A-01W-0831-10	16210744	89179995	57184027	28	219										
ENPP2	5168	hgsc.bcm.edu	37	chr8	120581486	120581486	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttaacttacaaggaggaaagAggaatccgtaggacatctgc	11	7	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr8:120581486A>G	ENST00000075322.6	-	21	2100	c.2042T>C	c.(2041-2043)cTc>cCc	p.L681P	ENPP2_ENST00000259486.6_Missense_Mutation_p.L733P|ENPP2_ENST00000522826.1_Missense_Mutation_p.L706P|ENPP2_ENST00000427067.2_Missense_Mutation_p.L702P|ENPP2_ENST00000522167.1_Missense_Mutation_p.L316P	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	681					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.L733P(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGGAGGAAAGAGGAATCCGTA	0.443																																					Melanoma(20;305 879 2501 4818 31020)											1	Substitution - Missense(1)	large_intestine(1)	8											170	162	165					8																	120581486		2203	4300	6503	120650667	SO:0001583	missense	5168			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2042T>C	8.37:g.120581486A>G	ENSP00000075322:p.Leu681Pro		120650667	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093265	0.76756	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45	5.37	5.37	0.77165	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.85682	D	0.000000	D	0.90762	0.7100	M	0.87827	2.91	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.92444	0.5964	10	0.87932	D	0	.	15.386	0.74703	1.0:0.0:0.0:0.0	.	219;706;681;733;316	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	P	733;702;316;706;681	ENSP00000259486:L733P;ENSP00000403315:L702P;ENSP00000429476:L316P;ENSP00000428291:L706P;ENSP00000075322:L681P	ENSP00000075322:L681P	L	-	2	0	ENPP2	120650667	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.524000	0.90579	2.038000	0.60285	0.533000	0.62120	CTC		0.443	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			G	120581486	A	G	120581486	3	3	2	1	0	0	0	0	1	0	0	0	5143	304	11	4	569	4	ENPP2	8	120581486	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	31401491	120581486	25782536	29	220										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32630351	32630351	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttcctcttcatctgcaagatCaccatctcccccttctgggg	6	16	6	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr9:32630351C>A	ENST00000242310.4	-	1	5316	c.5227G>T	c.(5227-5229)Gat>Tat	p.D1743Y		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1743					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.D1743Y(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCTGCAAGATCACCATCTCCC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	9											242	219	227					9																	32630351		2203	4300	6503	32620351	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5227G>T	9.37:g.32630351C>A	ENSP00000418379:p.Asp1743Tyr		32620351	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.964477	0.53507	.	.	ENSG00000122728	ENST00000242310	T	0.11495	2.77	1.16	1.16	0.20824	.	0.092799	0.64402	D	0.000001	T	0.19765	0.0475	L	0.56769	1.78	0.46564	D	0.999109	D	0.71674	0.998	P	0.59288	0.855	T	0.01039	-1.1472	10	0.62326	D	0.03	.	8.1579	0.31180	0.0:1.0:0.0:0.0	.	1743	Q8IZX4	TAF1L_HUMAN	Y	1743	ENSP00000418379:D1743Y	ENSP00000418379:D1743Y	D	-	1	0	TAF1L	32620351	1.000000	0.71417	0.876000	0.34364	0.344000	0.29017	3.306000	0.51881	0.507000	0.28148	0.195000	0.17529	GAT		0.488	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32630351	C	A	32630351	3	1	2	1	0	0	0	0	1	0	0	0	15562	826	29	2	257	2	TAF1L	9	32630351	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10		32630351	108583080	30	221										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119382680	119382680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gtcatcgatcacatccccttTccctgagcaccagtaggaac	7	15	2	1	rs370185624		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr9:119382680T>C	ENST00000313400.4	-	18	3215	c.3115A>G	c.(3115-3117)Aaa>Gaa	p.K1039E	ASTN2_ENST00000361477.3_Missense_Mutation_p.K91E|ASTN2_ENST00000373996.3_Missense_Mutation_p.K1035E|ASTN2_ENST00000288520.5_Missense_Mutation_p.K140E|ASTN2_ENST00000341734.4_Missense_Mutation_p.K91E|ASTN2_ENST00000358637.4_Missense_Mutation_p.K91E|ASTN2_ENST00000361209.2_Missense_Mutation_p.K988E			O75129	ASTN2_HUMAN	astrotactin 2	1039					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.K988E(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						ACATCCCCTTTCCCTGAGCAC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	9						T	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	1,4405	2.1+/-5.4	0,1,2202	188	169	175		271,271,2962,418,271,271	6.1	1	9		175	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	ASTN2	NM_001184734.1,NM_001184735.1,NM_014010.4,NM_198186.3,NM_198187.3,NM_198188.2	56,56,56,56,56,56	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	91/376,91/195,988/1289,140/441,91/403,91/396	119382680	1,13005	2203	4300	6503	118422501	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3115A>G	9.37:g.119382680T>C	ENSP00000314038:p.Lys1039Glu		118422501	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	T	18.08	3.544356	0.65198	2.27E-4	0.0	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477;ENST00000358637	T;T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38	6.08	6.08	0.98989	.	0.099528	0.64402	D	0.000002	T	0.30854	0.0778	L	0.38838	1.175	0.51012	D	0.9999	B;P;P;B;P;B;P;P	0.43094	0.373;0.728;0.734;0.372;0.799;0.216;0.525;0.728	B;B;B;B;B;B;B;B	0.38378	0.081;0.199;0.187;0.114;0.255;0.19;0.115;0.272	T	0.03576	-1.1023	9	.	.	.	-14.9714	16.6438	0.85155	0.0:0.0:0.0:1.0	.	91;91;762;988;1039;1035;91;140	B7ZKP4;B7ZKP5;A2A2T8;O75129-2;O75129;O75129-3;O75129-6;O75129-4	.;.;.;.;ASTN2_HUMAN;.;.;.	E	1039;1035;140;91;762;988;91;91	ENSP00000314038:K1039E;ENSP00000363108:K1035E;ENSP00000288520:K140E;ENSP00000339925:K91E;ENSP00000363098:K762E;ENSP00000354504:K988E;ENSP00000355116:K91E;ENSP00000351460:K91E	.	K	-	1	0	ASTN2	118422501	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.665000	0.83852	2.333000	0.79357	0.533000	0.62120	AAA		0.527	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		C	119382680	T	C	119382680	3	2	2	1	0	0	0	0	1	0	0	0	1066	1792	62	4	1047	4	ASTN2	9	119382680	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10	86752329	119382680	21830751	31	222										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50946053	50946053	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tggaagtagttggccggtgtGgagcagttgaccacgatcca	15	8	0	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr10:50946053G>A	ENST00000374103.4	-	19	2542	c.2457C>T	c.(2455-2457)tcC>tcT	p.S819S	OGDHL_ENST00000490844.1_5'UTR|OGDHL_ENST00000419399.1_Silent_p.S762S|OGDHL_ENST00000432695.1_Silent_p.S610S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	819					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.S819S(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						TGGCCGGTGTGGAGCAGTTGA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	10											251	232	238					10																	50946053		2203	4300	6503	50616059	SO:0001819	synonymous_variant	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2457C>T	10.37:g.50946053G>A			50616059	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																				0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50946053	G	A	50946053	2	1	2	1	0	0	0	0	0	0	0	1	10871	1335	47	3		3	OGDHL	10	50946053	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10		50946053	84588694	32	223										
HELLS	3070	hgsc.bcm.edu	37	chr10	96353345	96353345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	attaatctgactgcagcagaTacagttatcatttatgatag	7	6	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr10:96353345T>C	ENST00000348459.5	+	18	2166	c.2061T>C	c.(2059-2061)gaT>gaC	p.D687D	HELLS_ENST00000371332.4_Silent_p.D733D|HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000394045.1_Silent_p.D589D|RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific									p.D687D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		CTGCAGCAGATACAGTTATCA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	10											121	113	116					10																	96353345		2203	4300	6503	96343335	SO:0001819	synonymous_variant	3070			AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.2061T>C	10.37:g.96353345T>C			96343335		Silent	SNP	ENST00000348459.5	37	CCDS7434.1																																																																																				0.363	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		C	96353345	T	C	96353345	2	2	2	1	0	0	0	0	0	0	0	1	7067	1403	49	4		4	HELLS	10	96353345	Silent	SNP	T	TCGA-AF-2689-01A-01W-0831-10	45407292	96353345	39181402	33	224										
GBF1	8729	hgsc.bcm.edu	37	chr10	104121552	104121552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gagatgaaggagatggcactGgaggccattgtgcagctctg	16	7	1	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr10:104121552G>A	ENST00000369983.3	+	14	1826	c.1566G>A	c.(1564-1566)ctG>ctA	p.L522L		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	522					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.L522L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		AGATGGCACTGGAGGCCATTG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	10											139	122	128					10																	104121552		2203	4300	6503	104111542	SO:0001819	synonymous_variant	8729			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.1566G>A	10.37:g.104121552G>A			104111542	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																				0.468	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			A	104121552	G	A	104121552	2	1	2	1	0	0	0	0	0	0	0	1	6291	1335	47	3		3	GBF1	10	104121552	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	7768207	104121552	31413195	34	225										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45245965	45245965	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	atgttctggaggcctcactgGaatctgcgaaggtggaagcc	14	9	3	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr11:45245965G>A	ENST00000530656.1	+	7	1042	c.1042G>A	c.(1042-1044)Gaa>Aaa	p.E348K	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000263765.4_Missense_Mutation_p.E348K|PRDM11_ENST00000424263.2_Missense_Mutation_p.E314K|PRDM11_ENST00000528980.1_Intron			Q9NQV5	PRD11_HUMAN	PR domain containing 11	348							methyltransferase activity (GO:0008168)	p.E348K(1)		endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GGCCTCACTGGAATCTGCGAA	0.517																																					NSCLC(118;1511 1736 6472 36603 43224)											1	Substitution - Missense(1)	large_intestine(1)	11											136	140	139					11																	45245965		2203	4299	6502	45202541	SO:0001583	missense	56981			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.1042G>A	11.37:g.45245965G>A	ENSP00000435976:p.Glu348Lys		45202541	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	37		.	.	.	.	.	.	.	.	.	.	G	24.7	4.560611	0.86335	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.50277	0.75;0.75;0.75	5.41	5.41	0.78517	.	0.000000	0.56097	D	0.000027	T	0.59998	0.2235	L	0.29908	0.895	0.47476	D	0.999436	D	0.71674	0.998	D	0.80764	0.994	T	0.63625	-0.6595	10	0.87932	D	0	-25.2056	19.2758	0.94031	0.0:0.0:1.0:0.0	.	348	Q9NQV5	PRD11_HUMAN	K	348;348;314	ENSP00000263765:E348K;ENSP00000435976:E348K;ENSP00000394314:E314K	ENSP00000263765:E348K	E	+	1	0	PRDM11	45202541	1.000000	0.71417	0.972000	0.41901	0.690000	0.40134	8.599000	0.90856	2.569000	0.86673	0.558000	0.71614	GAA		0.517	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		A	45245965	G	A	45245965	3	1	2	1	0	0	0	0	1	0	0	0	12486	1175	41	3	1068	3	PRDM11	11	45245965	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		45245965	89760551	35	226										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118772693	118772693	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ccggagctgcatgggatcttGaacatccatgggcccccgca	12	14	1	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr11:118772693G>A	ENST00000334801.3	-	6	2723	c.1759C>T	c.(1759-1761)Caa>Taa	p.Q587*	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	587					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.Q587*(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		ATGGGATCTTGAACATCCATG	0.642																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											36	37	37					11																	118772693		2200	4295	6495	118277903	SO:0001587	stop_gained	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1759C>T	11.37:g.118772693G>A	ENSP00000335320:p.Gln587*		118277903	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Nonsense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	46	12.284320	0.99653	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	.	.	.	4.73	4.73	0.59995	.	0.000000	0.41712	D	0.000823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7137	17.4781	0.87666	0.0:0.0:1.0:0.0	.	.	.	.	X	587;550;587;587	.	ENSP00000335320:Q587X	Q	-	1	0	BCL9L	118277903	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	2.858000	0.48356	2.465000	0.83290	0.313000	0.20887	CAA		0.642	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118772693	G	A	118772693	4	1	2	1	0	0	0	0	0	1	0	0	1383	1299	45	3	2752	3	BCL9L	11	118772693	Nonsense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	73526728	118772693	16233823	36	227										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	2	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10		25398281	108453614	37	228										
TPH2	121278	hgsc.bcm.edu	37	chr12	72425471	72425471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aatgaaccaatatctggggaTttgatgcctggaactatgtt	10	6	1	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr12:72425471T>C	ENST00000333850.3	+	11	1610	c.1469T>C	c.(1468-1470)aTt>aCt	p.I490T		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	490					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.I490T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	TATCTGGGGATTTGATGCCTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											147	147	147					12																	72425471		2203	4299	6502	70711738	SO:0001583	missense	121278			AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1469T>C	12.37:g.72425471T>C	ENSP00000329093:p.Ile490Thr		70711738	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	37	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.361693	0.61403	.	.	ENSG00000139287	ENST00000333850	D	0.99557	-6.16	5.86	5.86	0.93980	.	0.055324	0.64402	D	0.000001	D	0.98002	0.9342	N	0.14661	0.345	0.58432	D	0.999999	P	0.45594	0.862	B	0.41917	0.37	D	0.99862	1.1084	10	0.87932	D	0	.	16.2526	0.82494	0.0:0.0:0.0:1.0	.	490	Q8IWU9	TPH2_HUMAN	T	490	ENSP00000329093:I490T	ENSP00000329093:I490T	I	+	2	0	TPH2	70711738	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	8.040000	0.89188	2.241000	0.73720	0.482000	0.46254	ATT		0.423	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		C	72425471	T	C	72425471	3	2	2	1	0	0	0	0	1	0	0	0	16442	1493	52	4	1511	4	TPH2	12	72425471	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10	47027190	72425471	61426424	38	229										
ANO4	121601	hgsc.bcm.edu	37	chr12	101430924	101430924	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tgaagctgcgtttcccctgcAtgaggtattgtgctgtcttt	11	9	1	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr12:101430924A>C	ENST00000392977.3	+	10	1103	c.893A>C	c.(892-894)cAt>cCt	p.H298P	RP11-350G24.1_ENST00000549036.1_RNA|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.H263P			Q32M45	ANO4_HUMAN	anoctamin 4	298					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.H263P(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TTTCCCCTGCATGAGGTATTG	0.353										HNSCC(74;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											360	311	328					12																	101430924		2203	4300	6503	99955055	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.893A>C	12.37:g.101430924A>C	ENSP00000376703:p.His298Pro		99955055	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	A	23.9	4.473143	0.84640	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.73363	-0.74;-0.74	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89729	0.6799	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	D	0.92335	0.5877	10	0.87932	D	0	.	16.1172	0.81314	1.0:0.0:0.0:0.0	.	298;263	Q32M45;Q32M45-2	ANO4_HUMAN;.	P	263;298	ENSP00000376705:H263P;ENSP00000376703:H298P	ENSP00000376703:H298P	H	+	2	0	ANO4	99955055	1.000000	0.71417	0.981000	0.43875	0.973000	0.67179	8.894000	0.92506	2.266000	0.75297	0.533000	0.62120	CAT		0.353	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		C	101430924	A	C	101430924	3	2	2	1	0	0	0	0	1	0	0	0	699	217	8	4	818	4	ANO4	12	101430924	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	29005453	101430924	32420971	39	230										
P2RX7	5027	hgsc.bcm.edu	37	chr12	121603968	121603968	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	cttccgagaaacaggcgataAtttttcagatgtggcaattc	9	8	1	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr12:121603968A>G	ENST00000546057.1	+	7	865	c.722A>G	c.(721-723)aAt>aGt	p.N241S	P2RX7_ENST00000535250.1_Missense_Mutation_p.N151S|P2RX7_ENST00000541446.1_5'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.N71S|P2RX7_ENST00000377162.2_Intron|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	241					apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)	p.N241S(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACAGGCGATAATTTTTCAGAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											254	256	255					12																	121603968		2203	4300	6503	120088351	SO:0001583	missense	5027			Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.722A>G	12.37:g.121603968A>G	ENSP00000442349:p.Asn241Ser		120088351	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.254522	0.39896	.	.	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250	T;T;T	0.04234	3.67;3.67;3.67	5.38	2.92	0.33932	.	0.665278	0.14804	N	0.297471	T	0.06234	0.0161	L	0.57536	1.79	0.41357	D	0.987409	B;B;B	0.22909	0.037;0.077;0.01	B;B;B	0.23716	0.017;0.048;0.04	T	0.20405	-1.0276	10	0.33940	T	0.23	.	6.8597	0.24060	0.7675:0.1512:0.0813:0.0	.	71;151;241	F8W951;F5H7E8;Q99572	.;.;P2RX7_HUMAN	S	241;71;151	ENSP00000442349:N241S;ENSP00000330696:N71S;ENSP00000442572:N151S	ENSP00000330696:N71S	N	+	2	0	P2RX7	120088351	0.072000	0.21174	0.693000	0.30195	0.990000	0.78478	1.869000	0.39519	0.306000	0.22856	0.460000	0.39030	AAT		0.493	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		G	121603968	A	G	121603968	3	3	2	1	0	0	0	0	1	0	0	0	11376	101	4	4	748	4	P2RX7	12	121603968	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	20173044	121603968	12247927	40	231										
SGCG	6445	hgsc.bcm.edu	37	chr13	23869602	23869602	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	agtggagacaccccttgtcaGagccgacccgtttcaagacc	10	14	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr13:23869602G>T	ENST00000218867.3	+	6	678	c.554G>T	c.(553-555)aGa>aTa	p.R185I	SGCG_ENST00000545013.1_Missense_Mutation_p.R185I|SGCG_ENST00000537476.1_Missense_Mutation_p.R185I	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	185					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.R185I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CCCCTTGTCAGAGCCGACCCG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	13											144	146	146					13																	23869602		2203	4300	6503	22767602	SO:0001583	missense	6445			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.554G>T	13.37:g.23869602G>T	ENSP00000218867:p.Arg185Ile		22767602	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	37	CCDS9299.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295704	0.23564	.	.	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.95137	-3.62;-3.62;-3.62	4.6	-1.05	0.10036	.	0.321642	0.37483	N	0.002076	D	0.92420	0.7594	M	0.86502	2.82	0.52501	D	0.999956	P	0.34562	0.457	B	0.33799	0.17	D	0.84963	0.0878	10	0.72032	D	0.01	-15.8157	4.6131	0.12413	0.302:0.2919:0.4061:0.0	.	185	Q13326	SGCG_HUMAN	I	185	ENSP00000218867:R185I;ENSP00000444100:R185I;ENSP00000442232:R185I	ENSP00000218867:R185I	R	+	2	0	SGCG	22767602	0.933000	0.31639	0.045000	0.18777	0.346000	0.29079	0.184000	0.16939	-0.549000	0.06191	-0.310000	0.09108	AGA		0.413	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		T	23869602	G	T	23869602	3	4	2	1	0	0	0	0	1	0	0	0	14240	942	33	2	572	2	SGCG	13	23869602	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		23869602	91300276	41	232										
UBR1	197131	hgsc.bcm.edu	37	chr15	43307955	43307955	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tgtcatacatgagtttatgaGtttcaatgaagtttttctgt	8	4	3	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr15:43307955G>C	ENST00000290650.4	-	29	3218	c.3140C>G	c.(3139-3141)aCt>aGt	p.T1047S	UBR1_ENST00000568782.1_5'UTR|UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1047					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T1047S(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GAGTTTATGAGTTTCAATGAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											192	182	186					15																	43307955		2203	4299	6502	41095247	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3140C>G	15.37:g.43307955G>C	ENSP00000290650:p.Thr1047Ser		41095247	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226781	0.58668	.	.	ENSG00000159459	ENST00000290650	T	0.39787	1.06	5.65	5.65	0.86999	.	0.106370	0.64402	D	0.000003	T	0.26557	0.0649	N	0.17474	0.49	0.80722	D	1	B;B	0.34200	0.02;0.441	B;B	0.24848	0.019;0.056	T	0.08269	-1.0730	10	0.11182	T	0.66	-11.2637	19.9142	0.97043	0.0:0.0:1.0:0.0	.	1047;1047	B4DYL2;Q8IWV7	.;UBR1_HUMAN	S	1047	ENSP00000290650:T1047S	ENSP00000290650:T1047S	T	-	2	0	UBR1	41095247	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.263000	0.95617	2.941000	0.99782	0.655000	0.94253	ACT		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43307955	G	C	43307955	3	2	2	1	0	0	0	0	1	0	0	0	16941	1029	36	5	2185	5	UBR1	15	43307955	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		43307955	59223437	42	233										
LBXCOR1	390598	hgsc.bcm.edu	37	chr15	68122580	68122580	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	cgatgatttggaaacgaggaAatcctatccagaccaaagga	10	8	0	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr15:68122580A>T	ENST00000380035.2	+	4	2517	c.2459A>T	c.(2458-2460)aAa>aTa	p.K820I	RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000554054.1_Missense_Mutation_p.K792I|SKOR1_ENST00000389002.1_Missense_Mutation_p.K776I|SKOR1_ENST00000341418.5_Missense_Mutation_p.K723I|SKOR1_ENST00000554240.1_Missense_Mutation_p.K781I			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	820					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)	p.K776I(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GAAACGAGGAAATCCTATCCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	78	82					15																	68122580		2200	4298	6498	65909634	SO:0001583	missense	390598				CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"SKI transcriptional corepressors"	21326	protein-coding gene	gene with protein product	"transcriptional corepressor CORL1", "functional smad suppressing element 15", "corepressor for LBX1"	611273	"Lbxcor1 homolog (mouse)"	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2459A>T	15.37:g.68122580A>T	ENSP00000369374:p.Lys820Ile		65909634	A6NIP4|A6NJY0|Q2VWA5	Missense_Mutation	SNP	ENST00000380035.2	37		.	.	.	.	.	.	.	.	.	.	A	23.9	4.473075	0.84640	.	.	ENSG00000188779	ENST00000341418;ENST00000554240;ENST00000554054;ENST00000380035;ENST00000389002	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	5.79	4.66	0.58398	.	0.131887	0.50627	D	0.000107	T	0.52885	0.1762	L	0.32530	0.975	0.39226	D	0.963584	D	0.63880	0.993	P	0.61940	0.896	T	0.57353	-0.7826	10	0.66056	D	0.02	-16.7565	10.7214	0.46042	0.9248:0.0:0.0752:0.0	.	776	P84550-3	.	I	723;781;792;820;776	ENSP00000343200:K723I;ENSP00000451193:K781I;ENSP00000452361:K792I;ENSP00000369374:K820I;ENSP00000373654:K776I	ENSP00000343200:K723I	K	+	2	0	SKOR1	65909634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.591000	0.61019	1.020000	0.39573	0.533000	0.62120	AAA		0.522	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807		T	68122580	A	T	68122580	3	4	2	1	0	0	0	0	1	0	0	0	8677	14	1	5	2345	5	LBXCOR1	15	68122580	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	24814625	68122580	34408812	43	234										
CDH8	1006	hgsc.bcm.edu	37	chr16	61854885	61854885	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	catcagaagtgatttcaaaaAgtgctgttccatctccatcg	7	10	3	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr16:61854885A>T	ENST00000577390.1	-	6	1922	c.968T>A	c.(967-969)cTt>cAt	p.L323H	CDH8_ENST00000584337.1_Missense_Mutation_p.L323H|CDH8_ENST00000299345.6_Missense_Mutation_p.L323H|CDH8_ENST00000577730.1_Missense_Mutation_p.L323H	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	323	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.L323H(1)|p.L323P(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GATTTCAAAAAGTGCTGTTCC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	16											172	138	149					16																	61854885		2203	4300	6503	60412386	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.968T>A	16.37:g.61854885A>T	ENSP00000462701:p.Leu323His		60412386	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.003550	0.74932	.	.	ENSG00000150394	ENST00000299345	T	0.03745	3.82	6.16	6.16	0.99307	Cadherin (4);Cadherin-like (1);	0.181883	0.49305	D	0.000155	T	0.09905	0.0243	L	0.33093	0.98	0.37111	D	0.90036	P;B	0.48764	0.915;0.006	P;B	0.60789	0.879;0.017	T	0.45963	-0.9225	10	0.23891	T	0.37	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	139;323	Q3LID3;P55286	.;CADH8_HUMAN	H	323	ENSP00000299345:L323H	ENSP00000299345:L323H	L	-	2	0	CDH8	60412386	0.696000	0.27757	0.998000	0.56505	0.980000	0.70556	5.886000	0.69743	2.367000	0.80283	0.528000	0.53228	CTT		0.403	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61854885	A	T	61854885	3	4	2	1	0	0	0	0	1	0	0	0	3122	72	3	5	1459	5	CDH8	16	61854885	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10		61854885	28499868	44	235										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70599160	70599160	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttgtccagctggaacagaatGaggcagcttttaggtaagca	12	7	0	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr16:70599160G>A	ENST00000302516.5	+	19	2867	c.2656G>A	c.(2656-2658)Gag>Aag	p.E886K		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	886					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.E886K(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				GGAACAGAATGAGGCAGCTTT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	16											79	78	78					16																	70599160		2198	4300	6498	69156661	SO:0001583	missense	23450			AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2656G>A	16.37:g.70599160G>A	ENSP00000305790:p.Glu886Lys		69156661	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	G	36	5.955745	0.97145	.	.	ENSG00000189091	ENST00000302516	T	0.61859	0.07	5.96	5.96	0.96718	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81597	0.4856	M	0.90082	3.085	0.80722	D	1	D	0.63880	0.993	D	0.68765	0.96	D	0.84104	0.0397	10	0.87932	D	0	.	20.422	0.99049	0.0:0.0:1.0:0.0	.	886	Q15393	SF3B3_HUMAN	K	886	ENSP00000305790:E886K	ENSP00000305790:E886K	E	+	1	0	SF3B3	69156661	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.789000	0.99068	2.832000	0.97577	0.655000	0.94253	GAG		0.527	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		A	70599160	G	A	70599160	3	1	2	1	0	0	0	0	1	0	0	0	14189	1291	45	3	2726	3	SF3B3	16	70599160	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	8744275	70599160	19755593	45	236										
TP53	7157	hgsc.bcm.edu	37	chr17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gggcaccaccacactatgtcGaaaagtgtttctgtcatcca	8	12	2	0	rs397516436		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	large_intestine(89)|breast(45)|lung(37)|upper_aerodigestive_tract(30)|central_nervous_system(18)|skin(16)|oesophagus(15)|stomach(14)|ovary(14)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(9)|biliary_tract(8)|liver(8)|soft_tissue(5)|endometrium(5)|bone(4)|prostate(3)|thyroid(1)|pancreas(1)|autonomic_ganglia(1)	17	GRCh37	CM951226	TP53	M							132	118	123					17																	7578212		2203	4300	6503	7518937	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.637C>T	17.37:g.7578212G>A	ENSP00000269305:p.Arg213*		7518937	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578212	G	A	7578212	4	1	2	1	0	0	0	0	0	1	0	0	16421	1066	37	1	657	1	TP53	17	7578212	Nonsense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		7578212	73616998	46	237										
KRT20	54474	hgsc.bcm.edu	37	chr17	39038874	39038874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gcattatcaatttgcaggacAcaccgagcattttgcagttg	9	9	1	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr17:39038874A>G	ENST00000167588.3	-	2	464	c.423T>C	c.(421-423)tgT>tgC	p.C141C		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	141	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.C141C(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				TTTGCAGGACACACCGAGCAT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	17											128	118	122					17																	39038874		2203	4300	6503	36292400	SO:0001819	synonymous_variant	54474			BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.423T>C	17.37:g.39038874A>G			36292400	B2R6W7	Silent	SNP	ENST00000167588.3	37	CCDS11379.1																																																																																				0.318	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			G	39038874	A	G	39038874	2	3	2	1	0	0	0	0	0	0	0	1	8479	157	6	4		4	KRT20	17	39038874	Silent	SNP	A	TCGA-AF-2689-01A-01W-0831-10	31460662	39038874	42156336	47	238										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10291152	10291152	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tgcttggttcccgttttctaGacgtccattcacttcccggt	8	13	2	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:10291152G>C	ENST00000340748.4	-	4	554	c.319C>G	c.(319-321)Cta>Gta	p.L107V	DNMT1_ENST00000540357.1_Missense_Mutation_p.L107V|DNMT1_ENST00000359526.4_Missense_Mutation_p.L107V			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	107	Interaction with DMAP1.|Interaction with DNMT3A.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.L107V(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CCGTTTTCTAGACGTCCATTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	19											129	125	126					19																	10291152		2203	4300	6503	10152152	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.319C>G	19.37:g.10291152G>C	ENSP00000345739:p.Leu107Val		10152152	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	g	11.78	1.740070	0.30865	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748	T;T;T	0.29142	1.9;1.58;1.58	5.65	3.35	0.38373	.	1.024130	0.07797	N	0.955835	T	0.19366	0.0465	N	0.19112	0.55	0.09310	N	1	P;P;P	0.40794	0.729;0.729;0.61	B;B;B	0.39027	0.288;0.288;0.15	T	0.11397	-1.0589	10	0.33940	T	0.23	.	4.8236	0.13405	0.1721:0.4721:0.3558:0.0	.	107;107;107	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	V	107	ENSP00000352516:L107V;ENSP00000440457:L107V;ENSP00000345739:L107V	ENSP00000345739:L107V	L	-	1	2	DNMT1	10152152	0.146000	0.22672	0.111000	0.21465	0.990000	0.78478	0.908000	0.28545	1.371000	0.46172	0.650000	0.86243	CTA		0.517	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		C	10291152	G	C	10291152	3	2	2	1	0	0	0	0	1	0	0	0	4686	933	33	5	4731	5	DNMT1	19	10291152	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10		10291152	48837831	48	239										
CALR	811	hgsc.bcm.edu	37	chr19	13051137	13051137	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aagattgacaacagccaggtGgagtccggctccttggaaga	13	9	0	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:13051137G>C	ENST00000316448.5	+	5	646	c.573G>C	c.(571-573)gtG>gtC	p.V191V		NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	191	4 X approximate repeats.|N-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)	p.V191V(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	ACAGCCAGGTGGAGTCCGGCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	19											99	106	104					19																	13051137		2203	4300	6503	12912137	SO:0001819	synonymous_variant	811			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.573G>C	19.37:g.13051137G>C			12912137	Q6IAT4|Q9UDG2	Silent	SNP	ENST00000316448.5	37	CCDS12288.1																																																																																				0.507	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		C	13051137	G	C	13051137	2	2	2	1	0	0	0	0	0	0	0	1	2598	1335	47	5		5	CALR	19	13051137	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10	2759985	13051137	46077846	49	240										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16962243	16962243	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttcacaggaaacgggccgtgCgagatgcacagcgtgcagaa	14	10	1	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:16962243C>T	ENST00000248054.5	+	6	768	c.747C>T	c.(745-747)tgC>tgT	p.C249C	SIN3B_ENST00000596802.1_Silent_p.C249C|SIN3B_ENST00000379803.1_Silent_p.C249C					SIN3 transcription regulator family member B									p.C249C(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACGGGCCGTGCGAGATGCACA	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	19											81	80	81					19																	16962243		2203	4300	6503	16823243	SO:0001819	synonymous_variant	23309			AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.747C>T	19.37:g.16962243C>T			16823243		Silent	SNP	ENST00000248054.5	37																																																																																					0.647	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		T	16962243	C	T	16962243	2	4	2	1	0	0	0	0	0	0	0	1	14363	776	27	1		1	SIN3B	19	16962243	Silent	SNP	C	TCGA-AF-2689-01A-01W-0831-10	3911106	16962243	42166740	50	241										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37904605	37904605	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aggtttctccccagtatgaaCtttctgatgtgcaatgaggc	10	9	2	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:37904605C>A	ENST00000316950.6	-	6	1512	c.955G>T	c.(955-957)Gtt>Ttt	p.V319F	ZNF569_ENST00000392149.2_Missense_Mutation_p.V319F|ZNF569_ENST00000392150.2_Missense_Mutation_p.V160F	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V319F(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGTATGAACTTTCTGATGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											132	131	131					19																	37904605		2203	4300	6503	42596445	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.955G>T	19.37:g.37904605C>A	ENSP00000325018:p.Val319Phe		42596445	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789238	0.49997	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	T;T	0.09911	2.93;2.93	3.97	0.537	0.17144	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34223	N	0.004145	T	0.20700	0.0498	M	0.69463	2.115	0.30014	N	0.81494	B;D	0.67145	0.44;0.996	B;D	0.79108	0.255;0.992	T	0.13602	-1.0503	10	0.87932	D	0	.	0.5092	0.00592	0.1849:0.3455:0.1803:0.2893	.	160;319	Q17RR6;Q5MCW4	.;ZN569_HUMAN	F	319;160	ENSP00000325018:V319F;ENSP00000375993:V160F	ENSP00000325018:V319F	V	-	1	0	ZNF569	42596445	0.000000	0.05858	1.000000	0.80357	0.999000	0.98932	-0.475000	0.06599	0.412000	0.25729	0.655000	0.94253	GTT		0.388	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		A	37904605	C	A	37904605	3	1	2	1	0	0	0	0	1	0	0	0	18039	565	20	2	1109	2	ZNF569	19	37904605	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	20942362	37904605	21224378	51	242										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52004667	52004667	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ctctctctggtgtctctgatGctcagggtacaatccttgtt	9	11	4	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:52004667G>T	ENST00000291707.3	-	1	376	c.321C>A	c.(319-321)agC>agA	p.S107R	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	107	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.S107R(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGTCTCTGATGCTCAGGGTAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											167	149	155					19																	52004667		2203	4300	6503	56696479	SO:0001583	missense	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.321C>A	19.37:g.52004667G>T	ENSP00000291707:p.Ser107Arg		56696479	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	12.08	1.830289	0.32329	.	.	ENSG00000254521	ENST00000291707	T	0.64618	-0.11	2.42	1.3	0.21679	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59528	0.2200	M	0.64676	1.99	0.22541	N	0.999003	D	0.71674	0.998	P	0.46885	0.53	T	0.50866	-0.8777	9	0.51188	T	0.08	.	6.6415	0.22911	0.0:0.3009:0.6991:0.0	.	107	Q96PQ1	SIG12_HUMAN	R	107	ENSP00000291707:S107R	ENSP00000291707:S107R	S	-	3	2	SIGLEC12	56696479	0.305000	0.24481	0.349000	0.25694	0.135000	0.20990	0.149000	0.16243	0.194000	0.20326	0.395000	0.25975	AGC		0.493	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		T	52004667	G	T	52004667	3	4	2	1	0	0	0	0	1	0	0	0	14345	1310	46	2	1571	2	SIGLEC12	19	52004667	Missense_Mutation	SNP	G	TCGA-AF-2689-01A-01W-0831-10	14100062	52004667	7124316	52	243										
ZNF160	90338	hgsc.bcm.edu	37	chr19	53571637	53571637	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gatgggtggttaggcttgaaCgaacactgaaggctttccca	13	8	0	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:53571637C>G	ENST00000429604.1	-	7	2565	c.2150G>C	c.(2149-2151)cGt>cCt	p.R717P	ZNF160_ENST00000601421.1_Missense_Mutation_p.R681P|ZNF160_ENST00000418871.1_Missense_Mutation_p.R717P|ZNF160_ENST00000599056.1_Missense_Mutation_p.R717P	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	717					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R717P(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TAGGCTTGAACGAACACTGAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											161	142	148					19																	53571637		2203	4300	6503	58263449	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.2150G>C	19.37:g.53571637C>G	ENSP00000406201:p.Arg717Pro		58263449	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	C	4.492	0.091275	0.08632	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.07688	3.17;3.17	2.21	-4.43	0.03568	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02807	0.0084	N	0.10645	0.015	0.09310	N	1	P	0.52061	0.95	B	0.40134	0.32	T	0.24657	-1.0154	9	0.39692	T	0.17	.	0.8491	0.01168	0.3943:0.2656:0.1307:0.2093	.	717	Q9HCG1	ZN160_HUMAN	P	717	ENSP00000406201:R717P;ENSP00000409597:R717P	ENSP00000409597:R717P	R	-	2	0	ZNF160	58263449	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.989000	0.00319	-1.232000	0.02554	-0.314000	0.08810	CGT		0.443	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		G	53571637	C	G	53571637	3	3	2	1	0	0	0	0	1	0	0	0	17778	536	19	5	310	5	ZNF160	19	53571637	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	1566970	53571637	5557346	53	244										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56370508	56370508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aactttcatattattgacaaCgtggacttggtggtttctgc	9	7	2	1	rs201393247		TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr19:56370508C>T	ENST00000301295.6	+	3	2171	c.1749C>T	c.(1747-1749)aaC>aaT	p.N583N	NLRP4_ENST00000587891.1_Silent_p.N508N|NLRP4_ENST00000346986.5_Silent_p.N583N	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	583					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.N583N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TTATTGACAACGTGGACTTGG	0.418													C|||	1	0.000199681	0	0	5008	,	,		20296	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	82	75	77		1749	-6.9	0	19		77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NLRP4	NM_134444.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		583/995	56370508	2,13004	2203	4300	6503	61062320	SO:0001819	synonymous_variant	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1749C>T	19.37:g.56370508C>T			61062320	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																				0.418	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56370508	C	T	56370508	2	4	2	1	0	0	0	0	0	0	0	1	10510	535	19	1		1	NLRP4	19	56370508	Silent	SNP	C	TCGA-AF-2689-01A-01W-0831-10	2798871	56370508	2758475	54	245										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61542512	61542512	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ccatcgctgtcactatcggaGgtgtcatcgtggtcatcccc	10	14	3	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chr20:61542512G>A	ENST00000266070.4	-	3	778	c.453C>T	c.(451-453)acC>acT	p.T151T	DIDO1_ENST00000266071.5_Silent_p.T151T|DIDO1_ENST00000395335.2_Silent_p.T151T|DIDO1_ENST00000370371.4_Silent_p.T151T|DIDO1_ENST00000370366.1_Silent_p.T151T|DIDO1_ENST00000354665.4_Silent_p.T151T|DIDO1_ENST00000395343.1_Silent_p.T151T|DIDO1_ENST00000395340.1_Silent_p.T151T|DIDO1_ENST00000370368.1_Silent_p.T151T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	151					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.T151T(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CACTATCGGAGGTGTCATCGT	0.572																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											1	Substitution - coding silent(1)	large_intestine(1)	20											95	71	79					20																	61542512		2203	4300	6503	61012957	SO:0001819	synonymous_variant	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.453C>T	20.37:g.61542512G>A			61012957	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																				0.572	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61542512	G	A	61542512	2	1	2	1	0	0	0	0	0	0	0	1	4533	987	35	3		3	DIDO1	20	61542512	Silent	SNP	G	TCGA-AF-2689-01A-01W-0831-10		61542512	1483008	55	246										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21534689	21534689	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ttgaaaaagcgacctcagagCatgcttacctcagcaccagc	8	13	2	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:21534689C>G	ENST00000379510.3	+	9	933	c.897C>G	c.(895-897)agC>agG	p.S299R	CNKSR2_ENST00000543067.1_Intron|CNKSR2_ENST00000279451.4_Missense_Mutation_p.S299R|CNKSR2_ENST00000425654.2_Missense_Mutation_p.S299R	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	299					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.S299R(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						GACCTCAGAGCATGCTTACCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											112	97	102					X																	21534689		2203	4300	6503	21444610	SO:0001583	missense	22866			AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.897C>G	X.37:g.21534689C>G	ENSP00000368824:p.Ser299Arg		21444610	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	37	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752354	0.69533	.	.	ENSG00000149970	ENST00000425654;ENST00000279451;ENST00000379510	T;T;T	0.38722	1.12;1.12;1.12	5.25	5.25	0.73442	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.56688	0.2002	M	0.62723	1.935	0.80722	D	1	D;P	0.62365	0.991;0.93	P;P	0.56612	0.802;0.67	T	0.54846	-0.8232	10	0.33940	T	0.23	-22.4144	17.8997	0.88900	0.0:1.0:0.0:0.0	.	299;299	B7ZLJ1;Q8WXI2	.;CNKR2_HUMAN	R	299	ENSP00000397906:S299R;ENSP00000279451:S299R;ENSP00000368824:S299R	ENSP00000279451:S299R	S	+	3	2	CNKSR2	21444610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.754000	0.68743	2.160000	0.67779	0.594000	0.82650	AGC		0.438	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		G	21534689	C	G	21534689	3	3	2	1	0	0	0	0	1	0	0	0	3613	709	25	5	931	5	CNKSR2	23	21534689	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10		21534689	133735871	56	247										
RBM10	8241	hgsc.bcm.edu	37	chrX	47044541	47044541	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tccagcctatcagctccctgCgagatgacgagaggcgggag	14	12	1	3			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:47044541C>T	ENST00000377604.3	+	18	2780	c.2038C>T	c.(2038-2040)Cga>Tga	p.R680*	RBM10_ENST00000345781.6_Nonsense_Mutation_p.R603*|RBM10_ENST00000329236.7_Nonsense_Mutation_p.R602*	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	680					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.R680*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CAGCTCCCTGCGAGATGACGA	0.567																																					Melanoma(171;120 2705 19495 39241)											1	Substitution - Nonsense(1)	large_intestine(1)	X											53	48	50					X																	47044541		2203	4300	6503	46929485	SO:0001587	stop_gained	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.2038C>T	X.37:g.47044541C>T	ENSP00000366829:p.Arg680*		46929485	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Nonsense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	40	8.407096	0.98799	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	.	.	.	5.72	2.84	0.33178	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6775	12.4108	0.55466	0.4736:0.5264:0.0:0.0	.	.	.	.	X	680;602;603	.	ENSP00000328848:R602X	R	+	1	2	RBM10	46929485	0.448000	0.25681	0.805000	0.32314	0.921000	0.55340	0.184000	0.16939	0.205000	0.20568	0.594000	0.82650	CGA		0.567	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47044541	C	T	47044541	4	4	2	1	0	0	0	0	0	1	0	0	13148	760	27	1	2104	1	RBM10	23	47044541	Nonsense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	25509852	47044541	108226019	57	248										
RBM3	5935	hgsc.bcm.edu	37	chrX	48434980	48434980	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	tggatatggacgttccagagActataatggcaggtgggtag	15	5	0	1			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:48434980A>T	ENST00000376759.3	+	5	464	c.401A>T	c.(400-402)gAc>gTc	p.D134V	RBM3_ENST00000354480.2_Missense_Mutation_p.T107S|RBM3_ENST00000430348.2_Missense_Mutation_p.T107S|RBM3_ENST00000376755.1_Missense_Mutation_p.D134V|AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000466764.1_3'UTR	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3	134	Gly-rich.				positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)	p.T107S(1)|p.D134V(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						CGTTCCAGAGACTATAATGGC	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	X											69	64	66					X																	48434980		2195	4277	6472	48319924	SO:0001583	missense	5935			BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"RNA binding motif (RRM) containing"	9900	protein-coding gene	gene with protein product		300027	"RNA binding motif protein 3"			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.401A>T	X.37:g.48434980A>T	ENSP00000365950:p.Asp134Val		48319924		Missense_Mutation	SNP	ENST00000376759.3	37	CCDS14301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.44|16.44	3.125220|3.125220	0.56721|0.56721	.|.	.|.	ENSG00000102317|ENSG00000102317	ENST00000376759;ENST00000376755|ENST00000430348;ENST00000354480	T;T|.	0.19532|.	2.14;2.14|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.267553|.	0.29775|.	U|.	0.011224|.	T|T	0.40171|0.40171	0.1106|0.1106	L|L	0.36672|0.36672	1.1|1.1	0.20074|0.20074	N|N	0.999932|0.999932	D|.	0.59357|.	0.985|.	B|.	0.42422|.	0.387|.	T|T	0.28650|0.28650	-1.0037|-1.0037	9|5	.|.	.|.	.|.	-6.744|-6.744	12.1034|12.1034	0.53798|0.53798	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	134|.	P98179|.	RBM3_HUMAN|.	V|S	134|107	ENSP00000365950:D134V;ENSP00000365946:D134V|.	.|.	D|T	+|+	2|1	0|0	RBM3|RBM3	48319924|48319924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	6.434000|6.434000	0.73408|0.73408	1.831000|1.831000	0.53308|0.53308	0.486000|0.486000	0.48141|0.48141	GAC|ACT		0.512	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743		T	48434980	A	T	48434980	3	4	2	1	0	0	0	0	1	0	0	0	13166	275	10	5	415	5	RBM3	23	48434980	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	1390439	48434980	106835580	58	249										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53642763	53642763	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	gctgatgtctcatgagctcaTcgacagcactccccaggttg	10	13	2	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:53642763T>A	ENST00000342160.3	-	21	2448	c.1991A>T	c.(1990-1992)gAt>gTt	p.D664V	HUWE1_ENST00000218328.8_Missense_Mutation_p.D664V|HUWE1_ENST00000262854.6_Missense_Mutation_p.D664V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	664					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.D664V(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CATGAGCTCATCGACAGCACT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											194	137	156					X																	53642763		2203	4300	6503	53659488	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.1991A>T	X.37:g.53642763T>A	ENSP00000340648:p.Asp664Val		53659488	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.734909	0.89482	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.63913	-0.07;-0.07;-0.07	5.75	5.75	0.90469	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-type fold (1);	0.061437	0.64402	D	0.000008	T	0.80226	0.4584	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.83400	0.0022	10	0.87932	D	0	.	13.9463	0.64086	0.0:0.0:0.0:1.0	.	664	Q7Z6Z7	HUWE1_HUMAN	V	664	ENSP00000340648:D664V;ENSP00000262854:D664V;ENSP00000218328:D664V	ENSP00000218328:D664V	D	-	2	0	HUWE1	53659488	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.628000	0.83189	1.939000	0.56221	0.441000	0.28932	GAT		0.448	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53642763	T	A	53642763	3	1	2	1	0	0	0	0	1	0	0	0	7482	1435	50	5	11385	5	HUWE1	23	53642763	Missense_Mutation	SNP	T	TCGA-AF-2689-01A-01W-0831-10	5207783	53642763	101627797	59	250										
WNK3	65267	hgsc.bcm.edu	37	chrX	54224990	54224991	+	Frame_Shift_Ins	INS	-	-	T													0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ggcccaggaaatgaagggagINStgagagtccttgtggcaagg							TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:54224990_54224991insT	ENST00000375159.2	-	23	5168_5169	c.5169_5170insA	c.(5167-5172)tcactcfs	p.L1724fs	WNK3_ENST00000375169.3_Frame_Shift_Ins_p.L1667fs|WNK3_ENST00000354646.2_Frame_Shift_Ins_p.L1724fs			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1724					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1724fs*20(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AATGAAGGGAGTGAGAGTCCTT	0.49																																																1	Insertion - Frameshift(1)	large_intestine(1)	X																																								54241716	SO:0001589	frameshift_variant	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.5170dupA	X.37:g.54224991_54224991dupT	ENSP00000364301:p.Leu1724fs		54241715	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Frame_Shift_Ins	INS	ENST00000375159.2	37	CCDS14357.1																																																																																				0.49	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54224991	-	T	54224990	7	5	2	1	0	1	1	0	0	0	0	0	17419	1029	36	0	236	0	WNK3	23	54224990	Frame_Shift_Ins	INS	-	TCGA-AF-2689-01A-01W-0831-10	582227	54224990	101045570	60	251										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128982	83128982	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	aaggagagtcagaaagatgaAaaaaaggataaaaaagattc	10	2	1	5			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:83128982A>G	ENST00000329312.4	+	4	1303	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	422					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E421E(3)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						AGAAAGATGAAAAAAAGGATA	0.338																																																3	Substitution - coding silent(3)	large_intestine(3)	X											20	16	17					X																	83128982		2186	4262	6448	83015638	SO:0001819	synonymous_variant	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1266A>G	X.37:g.83128982A>G			83015638	A0AVQ8|Q5JQQ9	Silent	SNP	ENST00000329312.4	37	CCDS35341.1																																																																																				0.338	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		G	83128982	A	G	83128982	2	3	2	1	0	0	0	0	0	0	0	1	4147	11	1	4		4	CYLC1	23	83128982	Silent	SNP	A	TCGA-AF-2689-01A-01W-0831-10	28903992	83128982	72141578	61	252										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123695614	123695614	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	ctgacacacacagtgccaacCattttgatccagggtacatc	7	13	0	2			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:123695614C>A	ENST00000371130.3	-	14	2404	c.2341G>T	c.(2341-2343)Ggt>Tgt	p.G781C	TENM1_ENST00000422452.2_Missense_Mutation_p.G781C	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	781	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G783C(1)									CAGTGCCAACCATTTTGATCC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											199	154	169					X																	123695614		2203	4300	6503	123523295	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.2341G>T	X.37:g.123695614C>A	ENSP00000360171:p.Gly781Cys		123523295	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671819	0.88348	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.14640	2.49;2.49	5.39	5.39	0.77823	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.999;0.96	T	0.41910	-0.9482	10	0.72032	D	0.01	.	18.4118	0.90554	0.0:1.0:0.0:0.0	.	780;781;781	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	C	781	ENSP00000360171:G781C;ENSP00000403954:G781C	ENSP00000360171:G781C	G	-	1	0	ODZ1	123523295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.772000	0.85439	2.376000	0.81061	0.594000	0.82650	GGT		0.488	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123695614	C	A	123695614	3	1	2	1	0	0	0	0	1	0	0	0	10865	594	21	2	5933	2	ODZ1	23	123695614	Missense_Mutation	SNP	C	TCGA-AF-2689-01A-01W-0831-10	40566632	123695614	31574946	62	253										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128633741	128633741	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0634920634920635	4	1	0.817057291666667	1.08940972222222	0.754206730769231	0.545454545454546	1	0	atcttactcagccccaagtaAatctttatttcctttttagg	4	10	3	0			TCGA-AF-2689-01A-01W-0831-10	TCGA-AF-2689-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8d3fb086-a5f4-4044-95bf-23595663672e	05c78132-6673-4e34-a7cb-d90f30cf1de2	g.chrX:128633741A>C	ENST00000371122.4	-	10	1374	c.1245T>G	c.(1243-1245)atT>atG	p.I415M	SMARCA1_ENST00000371123.1_Missense_Mutation_p.I415M|SMARCA1_ENST00000371121.3_Missense_Mutation_p.I415M	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	415					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.I415M(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						GCCCCAAGTAAATCTTTATTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	X											112	116	115					X																	128633741		2203	4297	6500	128461422	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.1245T>G	X.37:g.128633741A>C	ENSP00000360163:p.Ile415Met		128461422	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	A	16.27	3.077238	0.55753	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.28	5.28	0.74379	SNF2-related (1);	0.081974	0.47093	D	0.000245	T	0.79112	0.4391	L	0.56769	1.78	0.44508	D	0.997451	P;P;P;P	0.44429	0.835;0.835;0.802;0.74	P;P;P;P	0.49477	0.612;0.612;0.477;0.457	T	0.80386	-0.1404	10	0.62326	D	0.03	-6.5305	9.6497	0.39890	0.8424:0.0:0.0:0.1576	.	394;415;415;415	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	M	415;415;415;394	ENSP00000360162:I415M;ENSP00000360164:I415M;ENSP00000360163:I415M;ENSP00000404275:I394M	ENSP00000360162:I415M	I	-	3	3	SMARCA1	128461422	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.324000	0.43831	1.738000	0.51689	0.417000	0.27973	ATT		0.308	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		C	128633741	A	C	128633741	3	2	2	1	0	0	0	0	1	0	0	0	14805	10	1	4	1979	4	SMARCA1	23	128633741	Missense_Mutation	SNP	A	TCGA-AF-2689-01A-01W-0831-10	4938127	128633741	26636819	63	254										
CSMD2	114784	hgsc.bcm.edu	37	chr1	33992805	33992805	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	accatacgtactcaaggcttGggtgagcggtggctcccggg	15	11	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:33992805G>A	ENST00000373381.4	-	65	10401	c.10225C>T	c.(10225-10227)Caa>Taa	p.Q3409*		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Q3265*(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CTCAAGGCTTGGGTGAGCGGT	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											100	94	96					1																	33992805		2203	4300	6503	33765392	SO:0001587	stop_gained	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.10225C>T	1.37:g.33992805G>A	ENSP00000362479:p.Gln3409*		33765392	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Nonsense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	51	18.017117	0.99897	.	.	ENSG00000121904	ENST00000373381	.	.	.	5.41	4.43	0.53597	.	0.353980	0.27831	N	0.017669	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	9.9737	0.41770	0.0:0.0:0.7073:0.2927	.	.	.	.	X	3409	.	ENSP00000241312:Q3265X	Q	-	1	0	CSMD2	33765392	0.998000	0.40836	0.915000	0.36163	0.145000	0.21501	3.056000	0.49923	2.562000	0.86427	0.655000	0.94253	CAA		0.517	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	33992805	G	A	33992805	4	1	3	1	0	0	0	0	0	1	0	0	3951	1357	47	3	694	3	CSMD2	1	33992805	Nonsense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		33992805	215257816	1	255										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504566	70504566	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aggaagccacgaacgaccggAtaagatgctgggaccagagc	14	10	0	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:70504566A>T	ENST00000035383.5	+	19	2975	c.2945A>T	c.(2944-2946)gAt>gTt	p.D982V	LRRC7_ENST00000310961.5_Missense_Mutation_p.D987V|LRRC7_ENST00000415775.2_Missense_Mutation_p.D266V	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	982						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.D982V(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						GAACGACCGGATAAGATGCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	62	64					1																	70504566		2203	4300	6503	70277154	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2945A>T	1.37:g.70504566A>T	ENSP00000035383:p.Asp982Val		70277154	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.339864	0.24339	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.38401	1.14;1.23;2.31	5.69	5.69	0.88448	.	0.165122	0.51477	D	0.000089	T	0.42653	0.1212	L	0.50333	1.59	0.80722	D	1	D;D;D	0.76494	0.991;0.999;0.998	P;D;P	0.68192	0.798;0.956;0.905	T	0.21895	-1.0232	10	0.33940	T	0.23	.	15.1202	0.72438	1.0:0.0:0.0:0.0	.	266;982;982	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	V	987;982;266;805	ENSP00000309245:D987V;ENSP00000035383:D982V;ENSP00000394867:D266V	ENSP00000035383:D982V	D	+	2	0	LRRC7	70277154	1.000000	0.71417	0.086000	0.20670	0.069000	0.16628	8.664000	0.91139	2.174000	0.68829	0.460000	0.39030	GAT		0.458	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70504566	A	T	70504566	3	4	3	1	0	0	0	0	1	0	0	0	9049	333	12	5	3019	5	LRRC7	1	70504566	Missense_Mutation	SNP	A	TCGA-AF-2691-01A-01W-0831-10	36511761	70504566	178746055	2	256										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75708640	75708640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tagcttttgtcttttgtgtaCaaaagttgcatttccacata	6	7	1	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:75708640C>A	ENST00000370855.5	-	8	515	c.402G>T	c.(400-402)ttG>ttT	p.L134F	SLC44A5_ENST00000370859.3_Missense_Mutation_p.L134F|SLC44A5_ENST00000469525.1_5'UTR|SLC44A5_ENST00000535611.1_Missense_Mutation_p.L4F	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	134					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L134F(1)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						CTTTTGTGTACAAAAGTTGCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	138	138					1																	75708640		2203	4300	6503	75481228	SO:0001583	missense	204962			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.402G>T	1.37:g.75708640C>A	ENSP00000359892:p.Leu134Phe		75481228	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	37	CCDS667.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.190055	0.21954	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535611;ENST00000535790	T;T;T	0.28255	1.62;1.62;2.48	5.07	-2.77	0.05877	.	2.259400	0.01762	N	0.030633	T	0.08358	0.0208	L	0.50333	1.59	0.09310	N	1	B;B;B;B;B	0.17852	0.011;0.024;0.011;0.02;0.02	B;B;B;B;B	0.18263	0.014;0.009;0.009;0.021;0.021	T	0.11227	-1.0596	10	0.10111	T	0.7	7.2797	6.1512	0.20313	0.0:0.3033:0.247:0.4497	.	128;173;134;134;173	B7Z5Y4;B7Z470;Q8NCS7;Q8NCS7-2;F5GYS0	.;.;CTL5_HUMAN;.;.	F	134;173;134;4;127	ENSP00000359896:L134F;ENSP00000359892:L134F;ENSP00000443090:L4F	ENSP00000359892:L134F	L	-	3	2	SLC44A5	75481228	0.000000	0.05858	0.000000	0.03702	0.724000	0.41520	-0.865000	0.04250	-0.468000	0.06922	-0.137000	0.14449	TTG		0.398	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		A	75708640	C	A	75708640	3	1	3	1	0	0	0	0	1	0	0	0	14676	477	17	2	1936	2	SLC44A5	1	75708640	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	5204074	75708640	173541981	3	257										
NRAS	4893	hgsc.bcm.edu	37	chr1	115258748	115258748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tgcgcttttcccaacaccacCtgctccaaccaccaccagtt	4	19	0	0	rs121913250		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:115258748C>A	ENST00000369535.4	-	2	287	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	12			G -> C (in leukemia). {ECO:0000269|PubMed:2998510}.|G -> D (in KNEN). {ECO:0000269|PubMed:22499344}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12S(133)|p.G12C(81)|p.G12R(18)|p.G12N(2)|p.G12P(1)|p.G12Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		CCAACACCACCTGCTCCAACC	0.493	G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	236	Substitution - Missense(236)	haematopoietic_and_lymphoid_tissue(149)|skin(29)|upper_aerodigestive_tract(21)|large_intestine(13)|thyroid(8)|prostate(6)|lung(4)|soft_tissue(2)|urinary_tract(1)|NS(1)|kidney(1)|pancreas(1)	1											203	181	189					1																	115258748		2203	4300	6503	115060271	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.34G>T	1.37:g.115258748C>A	ENSP00000358548:p.Gly12Cys		115060271	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208516	0.95069	.	.	ENSG00000213281	ENST00000369535	T	0.79141	-1.24	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000025	D	0.85826	0.5787	M	0.89904	3.07	0.80722	D	1	P	0.39480	0.675	P	0.49276	0.605	D	0.87171	0.2221	10	0.72032	D	0.01	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	12	P01111	RASN_HUMAN	C	12	ENSP00000358548:G12C	ENSP00000358548:G12C	G	-	1	0	NRAS	115060271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT		0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		A	115258748	C	A	115258748	3	1	3	1	0	0	0	0	1	0	0	0	10671	681	24	2	551	2	NRAS	1	115258748	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	39550108	115258748	133991873	4	258										
OR10X1	128367	hgsc.bcm.edu	37	chr1	158548822	158548822	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gggggtaatgacagtataagGgactgctatgagtgtgtcat	15	4	1	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:158548822G>T	ENST00000368150.1	-	1	867	c.868C>A	c.(868-870)Cct>Act	p.P290T		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P290T(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					ACAGTATAAGGGACTGCTATG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	112	111					1																	158548822		2203	4300	6503	156815446	SO:0001583	missense	128367			BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"GPCR / Class A : Olfactory receptors"	14995	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily X, member 1"	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.868C>A	1.37:g.158548822G>T	ENSP00000357132:p.Pro290Thr		156815446	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	G	1.803	-0.476599	0.04414	.	.	ENSG00000186400	ENST00000368150	T	0.00051	8.81	4.5	3.51	0.40186	.	0.000000	0.48286	D	0.000184	T	0.00039	0.0001	N	0.00392	-1.555	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56129	-0.8030	10	0.02654	T	1	.	7.2998	0.26413	0.0934:0.0:0.7359:0.1707	.	290	Q8NGY0	O10X1_HUMAN	T	290	ENSP00000357132:P290T	ENSP00000357132:P290T	P	-	1	0	OR10X1	156815446	0.000000	0.05858	0.641000	0.29422	0.995000	0.86356	0.061000	0.14366	2.473000	0.83533	0.563000	0.77884	CCT		0.443	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		T	158548822	G	T	158548822	3	4	3	1	0	0	0	0	1	0	0	0	10953	1232	43	2	107	2	OR10X1	1	158548822	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	43290074	158548822	90701799	5	259										
C1orf114	57821	hgsc.bcm.edu	37	chr1	169364428	169364428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctctgccattttttccatccGtttccttcttaaccatctgt	3	14	3	0	rs370391570		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:169364428G>A	ENST00000367806.3	-	6	1539	c.1387C>T	c.(1387-1389)Cgg>Tgg	p.R463W	CCDC181_ENST00000367805.3_Missense_Mutation_p.R462W|BLZF1_ENST00000329281.2_Intron|CCDC181_ENST00000545005.1_Missense_Mutation_p.R462W	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	463						nucleus (GO:0005634)		p.R462W(1)									TTTTCCATCCGTTTCCTTCTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG,	0,4406		0,0,2203	127	121	123		1384,	5.2	1	1		123	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	BLZF1,C1orf114	NM_021179.1,NM_003666.2	101,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	462/509,	169364428	1,13005	2203	4300	6503	167631052	SO:0001583	missense	57821			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1387C>T	1.37:g.169364428G>A	ENSP00000356780:p.Arg463Trp		167631052	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		.	.	.	.	.	.	.	.	.	.	G	18.43	3.622097	0.66787	0.0	1.16E-4	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005	T;T;T	0.26810	1.71;1.71;1.71	6.07	5.16	0.70880	.	0.234953	0.43110	D	0.000601	T	0.34774	0.0909	M	0.61703	1.905	0.39929	D	0.974262	D;D	0.89917	1.0;1.0	D;D	0.63703	0.917;0.917	T	0.38222	-0.9671	9	0.87932	D	0	-2.1492	13.6219	0.62143	0.0:0.0:0.5805:0.4195	.	463;462	Q5TID7;Q5TID7-3	CA114_HUMAN;.	W	462;463;462	ENSP00000356779:R462W;ENSP00000356780:R463W;ENSP00000442297:R462W	ENSP00000356779:R462W	R	-	1	2	C1orf114	167631052	1.000000	0.71417	0.966000	0.40874	0.737000	0.42083	3.041000	0.49807	1.553000	0.49476	0.655000	0.94253	CGG		0.388	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		A	169364428	G	A	169364428	3	1	3	1	0	0	0	0	1	0	0	0	1993	1144	40	1	146	1	C1orf114	1	169364428	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	10815606	169364428	79886193	6	260										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204401488	204401488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ccagattatggatgaaaaaaTtgagctttgtggctacactg	10	6	0	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:204401488T>C	ENST00000367187.3	-	28	4551	c.3995A>G	c.(3994-3996)aAt>aGt	p.N1332S	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Missense_Mutation_p.N1304S	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1332	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.N1332S(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			GATGAAAAAATTGAGCTTTGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	67	70					1																	204401488		2203	4300	6503	202668111	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3995A>G	1.37:g.204401488T>C	ENSP00000356155:p.Asn1332Ser		202668111	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.593717	0.86953	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.81330	-1.48;-1.48	6.08	4.96	0.65561	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.257228	0.42053	D	0.000777	D	0.89757	0.6807	M	0.86028	2.79	0.47341	D	0.999397	D;B	0.89917	1.0;0.208	D;B	0.85130	0.997;0.03	D	0.90477	0.4457	10	0.87932	D	0	.	11.6762	0.51432	0.0:0.0691:0.0:0.9309	.	1304;1332	F5GWN5;O00750	.;P3C2B_HUMAN	S	1332;1304	ENSP00000356155:N1332S;ENSP00000400561:N1304S	ENSP00000356155:N1332S	N	-	2	0	PIK3C2B	202668111	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.040000	0.89188	1.134000	0.42165	0.533000	0.62120	AAT		0.507	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204401488	T	C	204401488	3	2	3	1	0	0	0	0	1	0	0	0	11941	1493	52	4	937	4	PIK3C2B	1	204401488	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10	35037060	204401488	44849133	7	261										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205899064	205899064	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gtaggaggggatggtcagtcCgaagatgtacttgagcaccg	16	7	1	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:205899064C>T	ENST00000367135.3	-	6	786	c.673G>A	c.(673-675)Gga>Aga	p.G225R	SLC26A9_ENST00000367134.2_Missense_Mutation_p.G225R|SLC26A9_ENST00000340781.4_Missense_Mutation_p.G225R	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	225					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)	p.G225R(1)		NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			ATGGTCAGTCCGAAGATGTAC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	71	74					1																	205899064		2203	4300	6503	204165687	SO:0001583	missense	115019			AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.673G>A	1.37:g.205899064C>T	ENSP00000356103:p.Gly225Arg		204165687	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.514953	0.85389	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.94758	-3.51;-3.51;-3.51	5.6	5.6	0.85130	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97945	0.9324	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98609	1.0662	10	0.87932	D	0	.	19.1973	0.93695	0.0:1.0:0.0:0.0	.	225;225	Q7LBE3;B1AVM8	S26A9_HUMAN;.	R	225	ENSP00000341682:G225R;ENSP00000356103:G225R;ENSP00000356102:G225R	ENSP00000341682:G225R	G	-	1	0	SLC26A9	204165687	1.000000	0.71417	0.920000	0.36463	0.437000	0.31866	5.957000	0.70323	2.653000	0.90120	0.561000	0.74099	GGA		0.587	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205899064	C	T	205899064	3	4	3	1	0	0	0	0	1	0	0	0	14561	661	23	1	2062	1	SLC26A9	1	205899064	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	1497576	205899064	43351557	8	262										
CD55	1604	hgsc.bcm.edu	37	chr1	207504512	207504512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	taattcaaggggaacgtgacCattatggatatagacagtct	10	6	2	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:207504512C>T	ENST00000367064.3	+	6	982	c.724C>T	c.(724-726)Cat>Tat	p.H242Y	CD55_ENST00000391920.4_Missense_Mutation_p.H242Y|CD55_ENST00000391921.4_Missense_Mutation_p.H178Y|CD55_ENST00000314754.8_Missense_Mutation_p.H242Y|CD55_ENST00000367062.4_Missense_Mutation_p.H242Y|CD55_ENST00000367065.5_Missense_Mutation_p.H242Y|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367063.2_Missense_Mutation_p.H242Y|CD55_ENST00000367067.4_3'UTR	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	242	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)	p.H242Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	GGAACGTGACCATTATGGATA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											161	147	152					1																	207504512		2203	4300	6503	205571135	SO:0001583	missense	1604			BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"CD molecules", "Blood group antigens"	2665	protein-coding gene	gene with protein product		125240	"decay accelerating factor for complement (CD55, Cromer blood group system)"	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.724C>T	1.37:g.207504512C>T	ENSP00000356031:p.His242Tyr		205571135	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Missense_Mutation	SNP	ENST00000367064.3	37	CCDS31006.1	.	.	.	.	.	.	.	.	.	.	C	2.464	-0.323525	0.05350	.	.	ENSG00000196352	ENST00000367064;ENST00000367063;ENST00000391921;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	T;T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	5.13	-7.5	0.01351	Complement control module (2);Sushi/SCR/CCP (3);	2.529520	0.01294	N	0.010122	T	0.40015	0.1100	N	0.12502	0.225	0.09310	N	0.999998	P;P;P;D;P	0.56035	0.873;0.953;0.484;0.974;0.795	B;B;B;P;P	0.47102	0.335;0.44;0.258;0.537;0.47	T	0.50346	-0.8839	10	0.33940	T	0.23	.	0.2036	0.00148	0.2226:0.2084:0.235:0.3341	.	178;242;242;242;242	B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.;.;.;DAF_HUMAN;.	Y	242;242;178;178;242;242;242;242	ENSP00000356031:H242Y;ENSP00000356030:H242Y;ENSP00000375788:H178Y;ENSP00000316333:H242Y;ENSP00000356032:H242Y;ENSP00000375787:H242Y;ENSP00000356029:H242Y	ENSP00000316333:H242Y	H	+	1	0	CD55	205571135	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.496000	0.06436	-1.429000	0.01987	-0.979000	0.02580	CAT		0.323	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574		T	207504512	C	T	207504512	3	4	3	1	0	0	0	0	1	0	0	0	3030	594	21	3	746	3	CD55	1	207504512	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	1605448	207504512	41746109	9	263										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233518135	233518135	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tcacagtcatctgccaagggAggtctcacccaagaagcaca	9	13	4	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr1:233518135A>T	ENST00000366624.3	+	10	3050	c.2789A>T	c.(2788-2790)gAg>gTg	p.E930V	MLK4_ENST00000366622.1_Missense_Mutation_p.E376V	NM_032435.2	NP_115811.2												p.E930V(1)									CTGCCAAGGGAGGTCTCACCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	91	94					1																	233518135		2203	4300	6503	231584758	SO:0001583	missense	84451																														ENST00000366624.3:c.2789A>T	1.37:g.233518135A>T	ENSP00000355583:p.Glu930Val		231584758		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	A	8.760	0.923431	0.18056	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.75050	-0.9;3.17	4.64	2.24	0.28232	.	0.715684	0.10475	U	0.670255	T	0.58836	0.2150	N	0.14661	0.345	0.09310	N	1	D;B	0.55172	0.97;0.139	P;B	0.47981	0.563;0.027	T	0.46925	-0.9156	10	0.33141	T	0.24	.	3.5314	0.07778	0.5874:0.1995:0.2131:0.0	.	377;930	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	V	930;376	ENSP00000355583:E930V;ENSP00000355581:E376V	ENSP00000355581:E376V	E	+	2	0	RP5-862P8.2	231584758	0.783000	0.28701	0.001000	0.08648	0.055000	0.15305	1.874000	0.39568	0.268000	0.21939	0.383000	0.25322	GAG		0.587	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233518135	A	T	233518135	3	4	3	1	0	0	0	0	1	0	0	0	8280	304	11	5	2827	5	KIAA1804	1	233518135	Missense_Mutation	SNP	A	TCGA-AF-2691-01A-01W-0831-10	26013623	233518135	15732486	10	264										
ADI1	55256	hgsc.bcm.edu	37	chr2	3504621	3504621	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aagcggtgatagatccccgcGgggagcgtcaccatgtctcc	13	13	2	2	rs562498332		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr2:3504621G>A	ENST00000327435.6	-	3	632	c.384C>T	c.(382-384)ccC>ccT	p.P128P	ADI1_ENST00000382093.5_Silent_p.P122P	NM_018269.3	NP_060739.2			acireductone dioxygenase 1									p.P128P(1)		breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		AGATCCCCGCGGGGAGCGTCA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	2											172	134	147					2																	3504621		2203	4300	6503	3483628	SO:0001819	synonymous_variant	55256				CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.384C>T	2.37:g.3504621G>A			3483628		Silent	SNP	ENST00000327435.6	37	CCDS1653.1																																																																																				0.617	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269		A	3504621	G	A	3504621	2	1	3	1	0	0	0	0	0	0	0	1	315	1103	39	1		1	ADI1	2	3504621	Silent	SNP	G	TCGA-AF-2691-01A-01W-0831-10		3504621	239694752	11	265										
IL1F9	56300	hgsc.bcm.edu	37	chr2	113742478	113742478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gaaacccttccttttctaccGtgccaagactggtaggacct	8	13	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr2:113742478G>A	ENST00000259205.4	+	5	431	c.362G>A	c.(361-363)cGt>cAt	p.R121H	IL36G_ENST00000376489.2_Missense_Mutation_p.R86H	NM_019618.2	NP_062564.1	Q9NZH8	IL36G_HUMAN	interleukin 36, gamma	121					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular space (GO:0005615)		p.R121H(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						CTTTTCTACCGTGCCAAGACT	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											145	130	135					2																	113742478		2203	4300	6503	113458949	SO:0001583	missense	56300			AF200492	CCDS2108.1, CCDS62992.1	2q12-q21	2011-07-14	2011-06-06	2011-06-06	ENSG00000136688	ENSG00000136688		"Interleukins and interleukin receptors"	15741	protein-coding gene	gene with protein product	"interleukin-1 homolog 1", "interleukin 1-related protein 2", "interleukin-1 epsilon"	605542	"interleukin 1 family, member 9"	IL1F9		10860666, 10744718, 11991722, 11991723	Standard	NM_019618		Approved	IL-1H1, IL-1RP2, IL-1F9, IL1H1, IL1E	uc002tio.1	Q9NZH8	OTTHUMG00000131336	ENST00000259205.4:c.362G>A	2.37:g.113742478G>A	ENSP00000259205:p.Arg121His		113458949	Q56B91|Q6UVX7|Q7RTZ9	Missense_Mutation	SNP	ENST00000259205.4	37	CCDS2108.1	.	.	.	.	.	.	.	.	.	.	G	1.244	-0.620440	0.03636	.	.	ENSG00000136688	ENST00000376489;ENST00000259205	T;T	0.21734	1.99;1.99	4.7	-0.563	0.11778	.	0.447148	0.21593	N	0.072074	T	0.06690	0.0171	N	0.04373	-0.215	0.09310	N	0.999999	B;B	0.13145	0.004;0.007	B;B	0.13407	0.0;0.009	T	0.30621	-0.9972	10	0.20046	T	0.44	-10.2763	3.2889	0.06942	0.4651:0.0:0.3516:0.1832	.	86;121	Q9NZH8-2;Q9NZH8	.;IL36G_HUMAN	H	86;121	ENSP00000365672:R86H;ENSP00000259205:R121H	ENSP00000259205:R121H	R	+	2	0	IL36G	113458949	0.000000	0.05858	0.065000	0.19835	0.035000	0.12851	-0.972000	0.03802	-0.166000	0.10890	0.561000	0.74099	CGT		0.512	IL36G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330713.2	NM_019618		A	113742478	G	A	113742478	3	1	3	1	0	0	0	0	1	0	0	0	7678	1145	40	1	376	1	IL1F9	2	113742478	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	110237857	113742478	129456895	12	266										
PPIG	9360	hgsc.bcm.edu	37	chr2	170493428	170493428	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gagaatgtgatataactaaaGgtaaacacagttataatagc	8	4	0	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr2:170493428G>T	ENST00000260970.3	+	14	1880	c.1660G>T	c.(1660-1662)Ggt>Tgt	p.G554C	PPIG_ENST00000409714.3_Missense_Mutation_p.G539C|PPIG_ENST00000448752.2_Missense_Mutation_p.G554C	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	554	Arg/Ser-rich (RS domain).				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.G554C(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	TATAACTAAAGGTAAACACAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	92	93					2																	170493428		2203	4300	6503	170201674	SO:0001583	missense	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1660G>T	2.37:g.170493428G>T	ENSP00000260970:p.Gly554Cys		170201674	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.468248	0.43839	.	.	ENSG00000138398	ENST00000260970;ENST00000409714;ENST00000448752	T;T;T	0.16743	2.32;2.32;2.32	5.74	-1.34	0.09143	.	0.642536	0.16893	N	0.195231	T	0.22126	0.0533	N	0.24115	0.695	0.26645	N	0.972206	B;D;B	0.76494	0.221;0.999;0.221	B;D;B	0.64042	0.159;0.921;0.159	T	0.16689	-1.0394	10	0.72032	D	0.01	0.3236	12.1594	0.54096	0.655:0.0:0.345:0.0	.	539;539;554	E9PG73;Q2NKQ6;Q13427	.;.;PPIG_HUMAN	C	554;539;554	ENSP00000260970:G554C;ENSP00000386245:G539C;ENSP00000407083:G554C	ENSP00000260970:G554C	G	+	1	0	PPIG	170201674	1.000000	0.71417	0.925000	0.36789	0.974000	0.67602	0.810000	0.27183	-0.623000	0.05618	-0.136000	0.14681	GGT		0.403	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			T	170493428	G	T	170493428	3	4	3	1	0	0	0	0	1	0	0	0	12358	1000	35	2	1706	2	PPIG	2	170493428	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	56750950	170493428	72705945	13	267										
C3orf32	51066	hgsc.bcm.edu	37	chr3	8672496	8672496	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cgttaatcgtattaccttgaCcagtgacgagtgagggacct	11	9	0	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr3:8672496C>G	ENST00000317371.4	-	13	1679	c.454G>C	c.(454-456)Gtc>Ctc	p.V152L	SSUH2_ENST00000415132.1_Missense_Mutation_p.V152L|SSUH2_ENST00000544814.1_Missense_Mutation_p.V174L|SSUH2_ENST00000341795.3_Missense_Mutation_p.V152L			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	152						cytoplasm (GO:0005737)		p.V152L(1)									ATTACCTTGACCAGTGACGAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	93	101					3																	8672496		2203	4300	6503	8647496	SO:0001583	missense	51066			AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 32"	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.454G>C	3.37:g.8672496C>G	ENSP00000324551:p.Val152Leu		8647496	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346498	0.61073	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814	T;T;T;T	0.51325	0.76;0.76;0.71;0.76	5.72	5.72	0.89469	.	0.119039	0.56097	D	0.000028	T	0.56848	0.2013	M	0.70595	2.14	0.35091	D	0.764289	D;D	0.57571	0.98;0.976	P;P	0.50405	0.606;0.64	T	0.66077	-0.6013	10	0.32370	T	0.25	-47.1844	15.3754	0.74602	0.0:1.0:0.0:0.0	.	174;152	F5H2S5;Q9Y2M2	.;CC032_HUMAN	L	152;152;152;174	ENSP00000339150:V152L;ENSP00000324551:V152L;ENSP00000410757:V152L;ENSP00000439378:V174L	ENSP00000324551:V152L	V	-	1	0	C3orf32	8647496	1.000000	0.71417	0.996000	0.52242	0.333000	0.28666	4.666000	0.61554	2.699000	0.92147	0.591000	0.81541	GTC		0.522	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		G	8672496	C	G	8672496	3	3	3	1	0	0	0	0	1	0	0	0	2228	507	18	5	635	5	C3orf32	3	8672496	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10		8672496	189349934	14	268										
CRELD1	78987	hgsc.bcm.edu	37	chr3	9985616	9985616	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	catcttaactgatttaacccCtgaaacaacccgacgctgga	6	13	1	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr3:9985616C>G	ENST00000383811.3	+	9	1647				CRELD1_ENST00000326434.5_Missense_Mutation_p.P360R|CRELD1_ENST00000489674.1_Intron|CRELD1_ENST00000452070.1_Intron|CRELD1_ENST00000397170.3_Intron	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1						cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.P360R(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						gatttaacccctgaaacaacc	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	105	107					3																	9985616		2203	4300	6503	9960616	SO:0001627	intron_variant	78987			AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"atrioventricular septal defect 2"	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.1048+417C>G	3.37:g.9985616C>G			9960616	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Missense_Mutation	SNP	ENST00000383811.3	37	CCDS2593.1	.	.	.	.	.	.	.	.	.	.	C	8.253	0.809504	0.16537	.	.	ENSG00000163703	ENST00000326434	T	0.63255	-0.03	3.28	1.44	0.22558	.	3.505800	0.02289	N	0.070138	T	0.46927	0.1418	.	.	.	0.09310	N	1	B	0.19817	0.039	B	0.19391	0.025	T	0.22730	-1.0208	8	.	.	.	.	5.7999	0.18408	0.0:0.7687:0.0:0.2313	.	360	Q96HD1-2	.	R	360	ENSP00000321856:P360R	.	P	+	2	0	CRELD1	9960616	0.002000	0.14202	0.000000	0.03702	0.023000	0.10783	1.012000	0.29924	0.239000	0.21243	0.591000	0.81541	CCT		0.468	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513		G	9985616	C	G	9985616	1	3	3	0	1	0	0	0	0	0	0	0	3872	681	24	5		5	CRELD1	3	9985616	Intron	SNP	C	TCGA-AF-2691-01A-01W-0831-10	1313120	9985616	188036814	15	269										
SETD2	29072	hgsc.bcm.edu	37	chr3	47084094	47084094	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aatcttcccttctggatctcGagctgtcttccagttgggag	10	11	4	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr3:47084094G>A	ENST00000409792.3	-	17	7237	c.7195C>T	c.(7195-7197)Cga>Tga	p.R2399*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2399	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.R1896*(2)|p.R2399*(2)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCTGGATCTCGAGCTGTCTTC	0.453			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	4	Substitution - Nonsense(4)	large_intestine(2)|breast(2)	3											113	112	112					3																	47084094		2203	4300	6503	47059098	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7195C>T	3.37:g.47084094G>A	ENSP00000386759:p.Arg2399*		47059098	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	48	14.190842	0.99783	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.51	3.7	0.42460	.	0.000000	0.43110	D	0.000617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4304	0.44405	0.0695:0.0:0.796:0.1346	.	.	.	.	X	2399	.	ENSP00000386759:R2399X	R	-	1	2	SETD2	47059098	1.000000	0.71417	0.995000	0.50966	0.974000	0.67602	3.171000	0.50824	0.685000	0.31468	-0.182000	0.12963	CGA		0.453	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47084094	G	A	47084094	4	1	3	1	0	0	0	0	0	1	0	0	14168	1066	37	1	519	1	SETD2	3	47084094	Nonsense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	37098478	47084094	150938336	16	270										
OSTalpha	200931	hgsc.bcm.edu	37	chr3	195955768	195955768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tgggcctgtttctcgtccccGacggcatctatgacccagca	10	15	2	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr3:195955768G>A	ENST00000296327.5	+	6	819	c.610G>A	c.(610-612)Gac>Aac	p.D204N		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	204					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)	p.D204N(1)								Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	TCTCGTCCCCGACGGCATCTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	103	108					3																	195955768		2203	4300	6503	197440165	SO:0001583	missense	200931				CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"Solute carriers"	29955	protein-coding gene	gene with protein product	"organic solute transporter, alpha subunit"	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.610G>A	3.37:g.195955768G>A	ENSP00000296327:p.Asp204Asn		197440165	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	37	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622018	0.66787	.	.	ENSG00000163959	ENST00000296327	T	0.40225	1.04	6.07	6.07	0.98685	.	0.000000	0.51477	D	0.000091	T	0.42562	0.1208	L	0.42581	1.335	0.80722	D	1	D	0.58970	0.984	P	0.46172	0.506	T	0.09058	-1.0692	10	0.14656	T	0.56	.	19.6321	0.95713	0.0:0.0:1.0:0.0	.	204	Q86UW1	OSTA_HUMAN	N	204	ENSP00000296327:D204N	ENSP00000296327:D204N	D	+	1	0	AC069257.9	197440165	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	6.403000	0.73264	2.884000	0.98904	0.655000	0.94253	GAC		0.522	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672		A	195955768	G	A	195955768	3	1	3	1	0	0	0	0	1	0	0	0	11331	1058	37	1	632	1	OSTalpha	3	195955768	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	148871674	195955768	2066662	17	271										
MAP9	79884	hgsc.bcm.edu	37	chr4	156268950	156268950	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aattatcaaaacacttttgcGaacacagttctgcttggagg	8	8	2	0	rs373425298		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr4:156268950G>A	ENST00000311277.4	-	14	2192	c.1929C>T	c.(1927-1929)ttC>ttT	p.F643F	AC097467.2_ENST00000595760.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000512269.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000593486.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000609254.1_RNA|MAP9_ENST00000515654.1_Silent_p.F619F|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000597955.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000608544.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	643					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)		p.F643F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		ACACTTTTGCGAACACAGTTC	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G		0,4406		0,0,2203	94	91	92		1929	2.5	0.4	4		92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP9	NM_001039580.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		643/648	156268950	1,13005	2203	4300	6503	156488400	SO:0001819	synonymous_variant	79884			AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1929C>T	4.37:g.156268950G>A			156488400	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Silent	SNP	ENST00000311277.4	37	CCDS35493.1																																																																																				0.343	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		A	156268950	G	A	156268950	2	1	3	1	0	0	0	0	0	0	0	1	9300	1049	37	1		1	MAP9	4	156268950	Silent	SNP	G	TCGA-AF-2691-01A-01W-0831-10		156268950	34885326	18	272										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13751296	13751296	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ttatctcaggggtgtaggctGggttaggcaatttggtggta	16	4	1	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr5:13751296G>C	ENST00000265104.4	-	65	11206	c.11102C>G	c.(11101-11103)cCa>cGa	p.P3701R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3701	AAA 5. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P3701R(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GGTGTAGGCTGGGTTAGGCAA	0.418									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											175	159	164					5																	13751296		2203	4300	6503	13804296	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.11102C>G	5.37:g.13751296G>C	ENSP00000265104:p.Pro3701Arg		13804296	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.680119	0.88542	.	.	ENSG00000039139	ENST00000265104	T	0.35605	1.3	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.78635	0.4314	H	0.99286	4.5	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87571	0.2478	10	0.87932	D	0	.	19.9403	0.97159	0.0:0.0:1.0:0.0	.	3701	Q8TE73	DYH5_HUMAN	R	3701	ENSP00000265104:P3701R	ENSP00000265104:P3701R	P	-	2	0	DNAH5	13804296	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.343000	0.97047	2.712000	0.92718	0.650000	0.86243	CCA		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13751296	G	C	13751296	3	2	3	1	0	0	0	0	1	0	0	0	4615	1348	47	5	2832	5	DNAH5	5	13751296	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		13751296	167163964	19	273										
APC	324	hgsc.bcm.edu	37	chr5	112175328	112175328	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ttctagtttatcttcagaatCagccaggcacaaagctgttg	8	9	4	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr5:112175328C>G	ENST00000457016.1	+	16	4417	c.4037C>G	c.(4036-4038)tCa>tGa	p.S1346*	APC_ENST00000508376.2_Nonsense_Mutation_p.S1346*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1346*			P25054	APC_HUMAN	adenomatous polyposis coli	1346	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1346*(14)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTTCAGAATCAGCCAGGCAC	0.483		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	16	Substitution - Nonsense(14)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(14)|soft_tissue(1)|skin(1)	5											59	63	61					5																	112175328		2202	4300	6502	112203227	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4037C>G	5.37:g.112175328C>G	ENSP00000413133:p.Ser1346*		112203227	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.934355	0.99008	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.386425	0.26734	N	0.022770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.3113	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1346	.	.	S	+	2	0	APC	112203227	0.997000	0.39634	0.940000	0.37924	0.981000	0.71138	5.272000	0.65559	2.861000	0.98227	0.655000	0.94253	TCA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175328	C	G	112175328	4	3	3	1	0	0	0	0	0	1	0	0	763	838	29	5	4095	5	APC	5	112175328	Nonsense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	98424032	112175328	68739932	20	274										
FAT2	2196	hgsc.bcm.edu	37	chr5	150922845	150922845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ggtgacatctgcgttctgacCttcatctgcatcataggcca	9	12	5	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr5:150922845C>T	ENST00000261800.5	-	9	7855	c.7843G>A	c.(7843-7845)Ggt>Agt	p.G2615S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2615	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G2615S(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGTTCTGACCTTCATCTGCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											219	215	216					5																	150922845		2203	4300	6503	150903038	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7843G>A	5.37:g.150922845C>T	ENSP00000261800:p.Gly2615Ser		150903038	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249683	0.80024	.	.	ENSG00000086570	ENST00000261800	T	0.64618	-0.11	5.36	5.36	0.76844	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000005	D	0.85915	0.5808	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89427	0.3714	10	0.56958	D	0.05	.	19.0961	0.93251	0.0:1.0:0.0:0.0	.	2615	Q9NYQ8	FAT2_HUMAN	S	2615	ENSP00000261800:G2615S	ENSP00000261800:G2615S	G	-	1	0	FAT2	150903038	1.000000	0.71417	0.973000	0.42090	0.969000	0.65631	7.755000	0.85180	2.506000	0.84524	0.462000	0.41574	GGT		0.463	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150922845	C	T	150922845	3	4	3	1	0	0	0	0	1	0	0	0	5709	681	24	3	5266	3	FAT2	5	150922845	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	38747517	150922845	29992415	21	275										
C6orf81	221481	hgsc.bcm.edu	37	chr6	35704997	35704997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tctacaaggccatcaaggctGgcataaaatgcaaaccaccc	7	13	2	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:35704997G>A	ENST00000373866.3	+	1	134	c.112G>A	c.(112-114)Ggc>Agc	p.G38S	ARMC12_ENST00000288065.2_Missense_Mutation_p.G38S|ARMC12_ENST00000373869.3_Missense_Mutation_p.G38S|RP3-510O8.4_ENST00000452048.1_RNA			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	38						nucleus (GO:0005634)		p.G38S(1)									CATCAAGGCTGGCATAAAATG	0.622											OREG0017379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	6											116	106	110					6																	35704997		2203	4300	6503	35812975	SO:0001583	missense	221481			AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"Armadillo repeat containing"	21099	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 81"	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.112G>A	6.37:g.35704997G>A	ENSP00000362973:p.Gly38Ser	857	35812975	Q8NEB2|Q96LL8	Missense_Mutation	SNP	ENST00000373866.3	37		.	.	.	.	.	.	.	.	.	.	G	21.0	4.083624	0.76642	.	.	ENSG00000157343	ENST00000373869;ENST00000288065;ENST00000373866	T;T;T	0.53857	0.6;0.6;0.6	4.86	4.86	0.63082	.	0.000000	0.49916	D	0.000139	T	0.49508	0.1561	L	0.32530	0.975	0.37317	D	0.909396	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.45775	-0.9238	10	0.25751	T	0.34	-2.1982	13.5383	0.61659	0.0:0.0:1.0:0.0	.	38;38	Q5T9G4-3;Q5T9G4-2	.;.	S	38	ENSP00000362976:G38S;ENSP00000288065:G38S;ENSP00000362973:G38S	ENSP00000288065:G38S	G	+	1	0	C6orf81	35812975	1.000000	0.71417	0.897000	0.35233	0.793000	0.44817	4.957000	0.63652	2.261000	0.74972	0.449000	0.29647	GGC		0.622	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028		A	35704997	G	A	35704997	3	1	3	1	0	0	0	0	1	0	0	0	2378	1348	47	3	114	3	C6orf81	6	35704997	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		35704997	135410070	22	276										
NFYA	4800	hgsc.bcm.edu	37	chr6	41057388	41057388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gcaggtgcagggccagcaggGccagacccagcagatcatca	14	13	2	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:41057388G>T	ENST00000341376.6	+	5	581	c.380G>T	c.(379-381)gGc>gTc	p.G127V	OARD1_ENST00000480585.1_Intron|NFYA_ENST00000353205.5_Missense_Mutation_p.G98V	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	127	Gln-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G127V(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGCCAGCAGGGCCAGACCCAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	65	66					6																	41057388		2203	4300	6503	41165366	SO:0001583	missense	4800				CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.380G>T	6.37:g.41057388G>T	ENSP00000345702:p.Gly127Val		41165366	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	37	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637267	0.67130	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.988;0.994	T	0.61352	-0.7080	9	0.24483	T	0.36	-0.1332	18.4308	0.90624	0.0:0.0:1.0:0.0	.	98;127	P23511-2;P23511	.;NFYA_HUMAN	V	127;98	.	ENSP00000345702:G127V	G	+	2	0	NFYA	41165366	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.425000	0.97467	2.831000	0.97527	0.650000	0.86243	GGC		0.537	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			T	41057388	G	T	41057388	3	4	3	1	0	0	0	0	1	0	0	0	10420	1203	42	2	394	2	NFYA	6	41057388	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	5352391	41057388	130057679	23	277										
UBR2	23304	hgsc.bcm.edu	37	chr6	42571414	42571414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gtatgcagtagaaatattaaCctgggaaaaagaaagtgaat	10	3	0	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:42571414C>T	ENST00000372899.1	+	5	878	c.620C>T	c.(619-621)aCc>aTc	p.T207I	UBR2_ENST00000372901.1_Missense_Mutation_p.T207I|UBR2_ENST00000372903.2_Missense_Mutation_p.T207I	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	207					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T207I(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GAAATATTAACCTGGGAAAAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	6											113	118	117					6																	42571414		2203	4299	6502	42679392	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.620C>T	6.37:g.42571414C>T	ENSP00000361990:p.Thr207Ile		42679392	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106793	0.37145	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73258	-0.73;0.25;0.25	5.58	5.58	0.84498	.	0.214637	0.47093	D	0.000258	T	0.48114	0.1482	N	0.17723	0.515	0.80722	D	1	B;B	0.28998	0.23;0.12	B;B	0.34536	0.05;0.185	T	0.49021	-0.8982	10	0.20519	T	0.43	-2.3523	19.62	0.95651	0.0:1.0:0.0:0.0	.	207;207	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	I	207	ENSP00000361994:T207I;ENSP00000361990:T207I;ENSP00000361992:T207I	ENSP00000361990:T207I	T	+	2	0	UBR2	42679392	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.225000	0.78051	2.627000	0.88993	0.650000	0.86243	ACC		0.318	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		T	42571414	C	T	42571414	3	4	3	1	0	0	0	0	1	0	0	0	16942	507	18	3	638	3	UBR2	6	42571414	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	1514026	42571414	128543653	24	278										
CUL9	23113	hgsc.bcm.edu	37	chr6	43166413	43166413	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	actgattcgatccctggttgGgggcccatctgcagaactac	11	12	1	2	rs397840127|rs3215697	byFrequency	TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:43166413G>T	ENST00000252050.4	+	12	2954	c.2870G>T	c.(2869-2871)gGg>gTg	p.G957V	CUL9_ENST00000354495.3_Missense_Mutation_p.G847V|CUL9_ENST00000372647.2_Missense_Mutation_p.G957V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	957					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.G957V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TCCCTGGTTGGGGGCCCATCT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	116	114					6																	43166413		2203	4300	6503	43274391	SO:0001583	missense	23113			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2870G>T	6.37:g.43166413G>T	ENSP00000252050:p.Gly957Val		43274391	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.816426	0.70912	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72942	-0.7;-0.7;-0.6	5.28	4.35	0.52113	Armadillo-type fold (1);	0.147667	0.44483	D	0.000446	T	0.73450	0.3588	L	0.54323	1.7	0.58432	D	0.999998	D;D;D	0.76494	0.995;0.999;0.999	D;D;D	0.68621	0.909;0.925;0.959	T	0.74064	-0.3785	10	0.48119	T	0.1	-32.7779	12.4476	0.55659	0.0:0.1689:0.8311:0.0	.	847;957;957	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	V	957;847;957	ENSP00000252050:G957V;ENSP00000346490:G847V;ENSP00000361730:G957V	ENSP00000252050:G957V	G	+	2	0	CUL9	43274391	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.439000	0.52878	2.463000	0.83235	0.555000	0.69702	GGG		0.622	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43166413	G	T	43166413	3	4	3	1	0	0	0	0	1	0	0	0	4067	1232	43	2	2912	2	CUL9	6	43166413	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	594999	43166413	127948654	25	279										
GPR116	221395	hgsc.bcm.edu	37	chr6	46847725	46847725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ccttttcacacaccagactgActgtgtccccttcaaagatg	6	14	2	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:46847725A>G	ENST00000283296.7	-	9	1154	c.866T>C	c.(865-867)gTc>gCc	p.V289A	GPR116_ENST00000456426.2_Intron|GPR116_ENST00000265417.7_Missense_Mutation_p.V289A|GPR116_ENST00000362015.4_Missense_Mutation_p.V289A	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	289	Ig-like 1.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V289A(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CACCAGACTGACTGTGTCCCC	0.403																																					NSCLC(59;410 1274 8751 36715 50546)											1	Substitution - Missense(1)	large_intestine(1)	6											132	115	120					6																	46847725		2203	4300	6503	46955684	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.866T>C	6.37:g.46847725A>G	ENSP00000283296:p.Val289Ala		46955684	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.775438	0.49786	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000265417	T;T;T	0.65732	-0.17;-0.17;-0.17	5.9	5.9	0.94986	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.111000	0.39909	N	0.001233	T	0.69788	0.3150	M	0.62154	1.92	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.75020	0.985;0.985	T	0.74813	-0.3537	10	0.87932	D	0	-13.1872	12.715	0.57109	1.0:0.0:0.0:0.0	.	289;289	A8K0D8;Q8IZF2	.;GP116_HUMAN	A	289	ENSP00000283296:V289A;ENSP00000354563:V289A;ENSP00000265417:V289A	ENSP00000265417:V289A	V	-	2	0	GPR116	46955684	0.836000	0.29430	0.511000	0.27724	0.176000	0.22953	4.472000	0.60189	2.254000	0.74563	0.482000	0.46254	GTC		0.403	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		G	46847725	A	G	46847725	3	3	3	1	0	0	0	0	1	0	0	0	6653	275	10	4	3226	4	GPR116	6	46847725	Missense_Mutation	SNP	A	TCGA-AF-2691-01A-01W-0831-10	3681312	46847725	124267342	26	280										
CRISP1	167	hgsc.bcm.edu	37	chr6	49808641	49808641	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agtgacaaacgtagagatatCgaggtgatccttgttggcgg	14	6	0	3	rs267601065		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:49808641C>T	ENST00000335847.4	-	6	604	c.503G>A	c.(502-504)cGa>cAa	p.R168Q	CRISP1_ENST00000507853.1_Missense_Mutation_p.R168Q|CRISP1_ENST00000505118.1_Missense_Mutation_p.R168Q|CRISP1_ENST00000329411.5_Missense_Mutation_p.R168Q|CRISP1_ENST00000355791.2_Missense_Mutation_p.R168Q|CRISP1_ENST00000536021.1_Missense_Mutation_p.R168Q	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	168	SCP.				binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)	p.R168Q(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					GTAGAGATATCGAGGTGATCC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											103	92	96					6																	49808641		2203	4300	6503	49916600	SO:0001583	missense	167			D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.503G>A	6.37:g.49808641C>T	ENSP00000338276:p.Arg168Gln		49916600	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	37	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	C	9.913	1.210049	0.22289	.	.	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18	4.8	-2.5	0.06384	CAP domain (3);	2.898410	0.01360	N	0.012197	T	0.01124	0.0037	N	0.11284	0.12	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.44251	-0.9340	9	.	.	.	.	5.1795	0.15152	0.0:0.159:0.2845:0.5565	.	168;168	P54107-2;P54107	.;CRIS1_HUMAN	Q	168	ENSP00000425020:R168Q;ENSP00000338276:R168Q;ENSP00000348044:R168Q;ENSP00000331317:R168Q;ENSP00000427589:R168Q;ENSP00000441798:R168Q	.	R	-	2	0	CRISP1	49916600	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.080000	0.11339	-0.771000	0.04608	-0.812000	0.03155	CGA		0.348	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		T	49808641	C	T	49808641	3	4	3	1	0	0	0	0	1	0	0	0	3885	884	31	1	258	1	CRISP1	6	49808641	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	2960916	49808641	121306426	27	281										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152652802	152652802	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	taactcctccaagttggtgaCtgacacttggattttccttt	7	10	0	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:152652802C>A	ENST00000367255.5	-	78	13619	c.13018G>T	c.(13018-13020)Gtc>Ttc	p.V4340F	SYNE1_ENST00000341594.5_Missense_Mutation_p.V4205F|SYNE1_ENST00000448038.1_Missense_Mutation_p.V4269F|SYNE1_ENST00000265368.4_Missense_Mutation_p.V4340F|SYNE1_ENST00000423061.1_Missense_Mutation_p.V4269F	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4340					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V4340F(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AAGTTGGTGACTGACACTTGG	0.453										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											153	142	146					6																	152652802		2203	4300	6503	152694495	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.13018G>T	6.37:g.152652802C>A	ENSP00000356224:p.Val4340Phe		152694495	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	9.400	1.077651	0.20227	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36	5.84	2.15	0.27550	.	0.113042	0.39083	N	0.001465	T	0.23289	0.0563	L	0.60455	1.87	0.80722	D	1	P;P;P;P	0.47962	0.903;0.498;0.498;0.631	P;B;B;B	0.45037	0.467;0.232;0.232;0.387	T	0.03139	-1.1068	10	0.56958	D	0.05	.	10.8306	0.46659	0.0:0.7588:0.0:0.2412	.	4340;4340;4340;4269	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	F	4340;4269;4340;4269;4205	ENSP00000356224:V4340F;ENSP00000396024:V4269F;ENSP00000265368:V4340F;ENSP00000390975:V4269F;ENSP00000341887:V4205F	ENSP00000265368:V4340F	V	-	1	0	SYNE1	152694495	0.095000	0.21747	0.165000	0.22776	0.989000	0.77384	0.650000	0.24858	0.113000	0.18004	0.655000	0.94253	GTC		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152652802	C	A	152652802	3	1	3	1	0	0	0	0	1	0	0	0	15484	565	20	2	13724	2	SYNE1	6	152652802	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	102844161	152652802	18462265	28	282										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168298993	168298993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aaacctacgtggaaggccagCgcatctcagaaaccaccatg	9	13	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr6:168298993C>T	ENST00000447894.2	+	11	1426	c.1426C>T	c.(1426-1428)Cgc>Tgc	p.R476C	MLLT4_ENST00000351017.4_Missense_Mutation_p.R476C|MLLT4_ENST00000400822.3_Missense_Mutation_p.R475C|MLLT4_ENST00000344191.4_Missense_Mutation_p.R476C|MLLT4_ENST00000392108.3_Missense_Mutation_p.R476C|MLLT4_ENST00000366806.2_Missense_Mutation_p.R476C|MLLT4_ENST00000392112.1_Missense_Mutation_p.R460C			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	476	FHA.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.R460C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		GGAAGGCCAGCGCATCTCAGA	0.532			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	1	Substitution - Missense(1)	large_intestine(1)	6											100	85	90					6																	168298993		2203	4300	6503	168041842	SO:0001583	missense	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1426C>T	6.37:g.168298993C>T	ENSP00000404595:p.Arg476Cys		168041842	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.263277|5.263277	0.95399|0.95399	.|.	.|.	ENSG00000130396|ENSG00000130396	ENST00000423229|ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.|D;D;D;D;D;D;D	.|0.89746	.|-2.56;-2.56;-2.56;-2.56;-2.56;-2.56;-2.56	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93374|0.93374	0.7887|0.7887	M|M	0.70842|0.70842	2.15|2.15	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.997;0.999;0.998;0.998	.|D;D;D;D	.|0.68943	.|0.961;0.912;0.954;0.941	D|D	0.93623|0.93623	0.6949|0.6949	5|10	.|0.87932	.|D	.|0	-14.2475|-14.2475	19.5218|19.5218	0.95187|0.95187	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;475;476;460	.|Q96C95;P55196-5;P55196-6;P55196-2	.|.;.;.;.	V|C	174|476;476;476;476;460;476;475;476	.|ENSP00000341118:R476C;ENSP00000252692:R476C;ENSP00000375956:R476C;ENSP00000355771:R476C;ENSP00000375960:R460C;ENSP00000383623:R475C;ENSP00000404595:R476C	.|ENSP00000345834:R476C	A|R	+|+	2|1	0|0	MLLT4|MLLT4	168041842|168041842	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.618000|7.618000	0.83043|0.83043	2.609000|2.609000	0.88269|0.88269	0.650000|0.650000	0.86243|0.86243	GCG|CGC		0.532	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168298993	C	T	168298993	3	4	3	1	0	0	0	0	1	0	0	0	9659	768	27	1	1468	1	MLLT4	6	168298993	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	15646191	168298993	2816074	29	283										
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92761049	92761049	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agtcctacaaattgcaagacCtctcggagttgtttttttag	8	8	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr7:92761049C>A	ENST00000318238.4	-	5	5452	c.4236G>T	c.(4234-4236)gaG>gaT	p.E1412D	SAMD9L_ENST00000411955.1_Missense_Mutation_p.E1412D|SAMD9L_ENST00000437805.1_Missense_Mutation_p.E1412D	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1412					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.E1412D(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			ATTGCAAGACCTCTCGGAGTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											147	148	148					7																	92761049		2203	4300	6503	92598985	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4236G>T	7.37:g.92761049C>A	ENSP00000326247:p.Glu1412Asp		92598985	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	C	7.886	0.731350	0.15507	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.24723	1.84;1.84;1.84	5.22	1.61	0.23674	.	0.449320	0.22432	N	0.060122	T	0.19927	0.0479	L	0.59436	1.845	0.19300	N	0.999974	P	0.36412	0.552	B	0.33042	0.157	T	0.11470	-1.0586	10	0.41790	T	0.15	-19.5054	5.1827	0.15169	0.1562:0.4406:0.0:0.4033	.	1412	Q8IVG5	SAM9L_HUMAN	D	1412;1412;1412;234	ENSP00000326247:E1412D;ENSP00000405760:E1412D;ENSP00000408796:E1412D	ENSP00000326247:E1412D	E	-	3	2	SAMD9L	92598985	0.000000	0.05858	0.951000	0.38953	0.074000	0.17049	-0.693000	0.05121	0.126000	0.18424	-0.373000	0.07131	GAG		0.403	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92761049	C	A	92761049	3	1	3	1	0	0	0	0	1	0	0	0	13864	680	24	2	522	2	SAMD9L	7	92761049	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10		92761049	66377614	30	284										
TRIM35	23087	hgsc.bcm.edu	37	chr8	27151776	27151776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctccactctcaagaactcgcGaagcttatcaaactcctgcc	5	16	2	1	rs369635979		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr8:27151776G>A	ENST00000305364.4	-	3	666	c.583C>T	c.(583-585)Cgc>Tgc	p.R195C	TRIM35_ENST00000521253.1_Missense_Mutation_p.R163C	NM_171982.3	NP_741983.2	Q9UPQ4	TRI35_HUMAN	tripartite motif containing 35	195					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R195C(1)		breast(1)|endometrium(6)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	14		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)		AAGAACTCGCGAAGCTTATCA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	CYS/ARG	0,4406		0,0,2203	59	52	54		583	5.8	0.1	8		54	1,8599	1.2+/-3.3	0,1,4299	no	missense	TRIM35	NM_171982.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	195/494	27151776	1,13005	2203	4300	6503	27207693	SO:0001583	missense	23087			AB029021	CCDS6056.2	8p21.2	2013-01-09	2011-01-25		ENSG00000104228	ENSG00000104228		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16285	protein-coding gene	gene with protein product			"tripartite motif-containing 35"			11331580, 14662771, 12692137	Standard	XM_005273451		Approved	KIAA1098, MAIR, HLS5	uc003xfl.1	Q9UPQ4	OTTHUMG00000102047	ENST00000305364.4:c.583C>T	8.37:g.27151776G>A	ENSP00000301924:p.Arg195Cys		27207693	Q86XQ0|Q8WVA4	Missense_Mutation	SNP	ENST00000305364.4	37	CCDS6056.2	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425368	0.62733	0.0	1.16E-4	ENSG00000104228	ENST00000305364;ENST00000521253	T;T	0.68331	-0.22;-0.32	5.82	5.82	0.92795	.	.	.	.	.	T	0.74245	0.3691	L	0.56769	1.78	0.35117	D	0.766649	D;D	0.89917	1.0;0.999	P;P	0.54706	0.759;0.642	T	0.81854	-0.0741	9	0.72032	D	0.01	.	15.5931	0.76554	0.0:0.0:1.0:0.0	.	163;195	E5RGB3;Q9UPQ4	.;TRI35_HUMAN	C	195;163	ENSP00000301924:R195C;ENSP00000428770:R163C	ENSP00000301924:R195C	R	-	1	0	TRIM35	27207693	1.000000	0.71417	0.076000	0.20297	0.281000	0.26958	8.210000	0.89753	2.756000	0.94617	0.561000	0.74099	CGC		0.577	TRIM35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219848.2	NM_171982		A	27151776	G	A	27151776	3	1	3	1	0	0	0	0	1	0	0	0	16549	1058	37	1	914	1	TRIM35	8	27151776	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		27151776	119212246	31	285										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121209172	121209172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gcattcgatgtgggctcagaGaagacacgaattggtataat	12	6	1	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr8:121209172G>T	ENST00000297848.3	+	6	849	c.579G>T	c.(577-579)gaG>gaT	p.E193D	COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.E193D|COL14A1_ENST00000537875.1_Missense_Mutation_p.E193D|COL14A1_ENST00000247781.3_Missense_Mutation_p.E193D	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.E193D(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TGGGCTCAGAGAAGACACGAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											164	154	157					8																	121209172		2203	4300	6503	121278353	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.579G>T	8.37:g.121209172G>T	ENSP00000297848:p.Glu193Asp		121278353		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.97|15.97	2.988782|2.988782	0.53934|0.53934	.|.	.|.	ENSG00000187955|ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	D;D;D;D;D|.	0.82893|.	-1.66;-1.66;-1.66;-1.66;-1.66|.	5.43|5.43	3.48|3.48	0.39840|0.39840	von Willebrand factor, type A (3);|.	0.267459|0.267459	0.42053|0.42053	D|D	0.000778|0.000778	T|.	0.10852|.	0.0265|.	N|N	0.00387|0.00387	-1.565|-1.565	0.33246|0.33246	D|D	0.557834|0.557834	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|.	0.10268|.	-1.0637|.	10|.	0.15499|0.42905	T|T	0.54|0.14	.|.	9.1228|9.1228	0.36797|0.36797	0.0787:0.0:0.6989:0.2224|0.0787:0.0:0.6989:0.2224	.|.	193|.	Q05707|.	COEA1_HUMAN|.	D|X	193;193;193;193;6|45	ENSP00000443974:E193D;ENSP00000311809:E193D;ENSP00000297848:E193D;ENSP00000247781:E193D;ENSP00000409461:E6D|.	ENSP00000247781:E193D|ENSP00000429123:E45X	E|E	+|+	3|1	2|0	COL14A1|COL14A1	121278353|121278353	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	1.281000|1.281000	0.33214|0.33214	1.504000|1.504000	0.48704|0.48704	0.650000|0.650000	0.86243|0.86243	GAG|GAA		0.388	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121209172	G	T	121209172	3	4	3	1	0	0	0	0	1	0	0	0	3677	933	33	2	597	2	COL14A1	8	121209172	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	94057396	121209172	25154850	32	286										
ADCY8	114	hgsc.bcm.edu	37	chr8	131916038	131916038	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	attctgtttccccacgatatTatcaaagggcagttcagggc	9	10	3	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr8:131916038T>C	ENST00000286355.5	-	7	3983	c.1891A>G	c.(1891-1893)Aat>Gat	p.N631D	ADCY8_ENST00000377928.3_Missense_Mutation_p.N631D	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	631					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.N631D(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CCCACGATATTATCAAAGGGC	0.507										HNSCC(32;0.087)																																						1	Substitution - Missense(1)	large_intestine(1)	8											107	94	99					8																	131916038		2203	4300	6503	131985220	SO:0001583	missense	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1891A>G	8.37:g.131916038T>C	ENSP00000286355:p.Asn631Asp		131985220		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.085180	0.76642	.	.	ENSG00000155897	ENST00000286355;ENST00000377928;ENST00000522949	T;T;T	0.81415	-1.49;-1.49;-1.33	6.08	6.08	0.98989	.	0.085300	0.85682	D	0.000000	D	0.85796	0.5780	M	0.62723	1.935	0.41718	D	0.98949	D;B	0.63046	0.992;0.116	P;B	0.57152	0.814;0.085	D	0.85721	0.1325	10	0.42905	T	0.14	.	15.8323	0.78764	0.0:0.0:0.0:1.0	.	631;631	E7EVL1;P40145	.;ADCY8_HUMAN	D	631;631;246	ENSP00000286355:N631D;ENSP00000367161:N631D;ENSP00000428010:N246D	ENSP00000286355:N631D	N	-	1	0	ADCY8	131985220	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.314000	0.78988	2.333000	0.79357	0.482000	0.46254	AAT		0.507	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			C	131916038	T	C	131916038	3	2	3	1	0	0	0	0	1	0	0	0	300	1754	61	4	1912	4	ADCY8	8	131916038	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10	10706866	131916038	14447984	33	287										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8518185	8518185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agcacaggttcgctgggaggCccccgcccaatgttattgac	12	13	0	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr9:8518185C>T	ENST00000381196.4	-	18	1749	c.1206G>A	c.(1204-1206)ggG>ggA	p.G402G	PTPRD_ENST00000397617.3_Silent_p.G392G|PTPRD_ENST00000540109.1_Silent_p.G402G|PTPRD_ENST00000356435.5_Silent_p.G402G|PTPRD_ENST00000397606.3_Silent_p.G392G|PTPRD_ENST00000397611.3_Silent_p.G399G|PTPRD_ENST00000537002.1_Silent_p.G399G|PTPRD_ENST00000360074.4_Silent_p.G389G|PTPRD_ENST00000358503.5_Silent_p.G389G|PTPRD_ENST00000355233.5_Silent_p.G402G|PTPRD_ENST00000486161.1_Silent_p.G402G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	402	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G402G(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		CGCTGGGAGGCCCCCGCCCAA	0.537										TSP Lung(15;0.13)																																						1	Substitution - coding silent(1)	large_intestine(1)	9											138	134	135					9																	8518185		2203	4300	6503	8508185	SO:0001819	synonymous_variant	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1206G>A	9.37:g.8518185C>T			8508185	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	CCDS43786.1																																																																																				0.537	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8518185	C	T	8518185	2	4	3	1	0	0	0	0	0	0	0	1	12836	726	26	3		3	PTPRD	9	8518185	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10		8518185	132695246	34	288										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101788194	101788194	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gatgttccccagggccctgaGggacagcctggagttgatgg	16	10	0	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr9:101788194G>T	ENST00000375001.3	+	16	2412	c.1989G>T	c.(1987-1989)gaG>gaT	p.E663D		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	663	Collagen-like 1.|Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.E663D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				AGGGCCCTGAGGGACAGCCTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	9											75	66	69					9																	101788194		2203	4300	6503	100828015	SO:0001583	missense	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1989G>T	9.37:g.101788194G>T	ENSP00000364140:p.Glu663Asp		100828015	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.770986	0.31320	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.93712	-3.27	4.58	-1.27	0.09347	.	0.587826	0.16489	N	0.212195	T	0.82075	0.4958	N	0.17312	0.475	0.26422	N	0.976083	B	0.18610	0.029	B	0.17098	0.017	T	0.68265	-0.5454	10	0.21014	T	0.42	-7.5686	3.7584	0.08595	0.3961:0.0:0.4292:0.1747	.	663	P39059	COFA1_HUMAN	D	663;633	ENSP00000364140:E663D	ENSP00000364140:E663D	E	+	3	2	COL15A1	100828015	0.997000	0.39634	0.773000	0.31616	0.988000	0.76386	0.294000	0.19047	-0.050000	0.13356	0.491000	0.48974	GAG		0.582	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101788194	G	T	101788194	3	4	3	1	0	0	0	0	1	0	0	0	3678	991	35	2	2051	2	COL15A1	9	101788194	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	93270009	101788194	39425237	35	289										
MPP7	143098	hgsc.bcm.edu	37	chr10	28343023	28343023	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	taaccagctcactggcacccAatgggtctctgtctctaatt	7	13	3	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:28343023A>T	ENST00000375732.1	-	17	1961	c.1702T>A	c.(1702-1704)Tgg>Agg	p.W568R	MPP7_ENST00000540098.1_Missense_Mutation_p.W568R|MPP7_ENST00000375719.3_Missense_Mutation_p.W568R|MPP7_ENST00000337532.5_Missense_Mutation_p.W568R			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	568					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)	p.W568R(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						ACTGGCACCCAATGGGTCTCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											82	82	82					10																	28343023		2203	4300	6503	28383029	SO:0001583	missense	143098			BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.1702T>A	10.37:g.28343023A>T	ENSP00000364884:p.Trp568Arg		28383029	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302382	0.81136	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	5.36	5.36	0.76844	.	0.059758	0.64402	D	0.000001	T	0.59197	0.2176	M	0.90595	3.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69109	-0.5232	10	0.87932	D	0	.	15.3574	0.74437	1.0:0.0:0.0:0.0	.	568	Q5T2T1	MPP7_HUMAN	R	568	ENSP00000364884:W568R;ENSP00000337907:W568R;ENSP00000438693:W568R;ENSP00000364871:W568R	ENSP00000337907:W568R	W	-	1	0	MPP7	28383029	1.000000	0.71417	0.973000	0.42090	0.964000	0.63967	9.339000	0.96797	2.022000	0.59522	0.482000	0.46254	TGG		0.338	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		T	28343023	A	T	28343023	3	4	3	1	0	0	0	0	1	0	0	0	9769	130	5	5	32	5	MPP7	10	28343023	Missense_Mutation	SNP	A	TCGA-AF-2691-01A-01W-0831-10		28343023	107191724	36	290										
RET	5979	hgsc.bcm.edu	37	chr10	43597793	43597793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctgacttctctctgcagaccGcggctttcccctgctcaccg	8	18	3	2	rs76397662	byFrequency	TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:43597793G>A	ENST00000355710.3	+	3	573	c.341G>A	c.(340-342)cGc>cAc	p.R114H	RET_ENST00000340058.5_Missense_Mutation_p.R114H	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	114			R -> C (in HSCR1). {ECO:0000269|PubMed:22174939}.|R -> H (in CCHS and HSCR1). {ECO:0000269|PubMed:12086152, ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:22174939}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R114H(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCTGCAGACCGCGGCTTTCCC	0.627		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	7	0.00139776	0	0	5008	,	,		20443	0.006		0	False		,,,				2504	0.001				Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	1	Substitution - Missense(1)	large_intestine(1)	10	GRCh37	CM023441	RET	M	rs76397662						103	92	96					10																	43597793		2203	4300	6503	42917799	SO:0001583	missense	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.341G>A	10.37:g.43597793G>A	ENSP00000347942:p.Arg114His		42917799	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	8.828	0.939278	0.18281	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	T;T	0.78707	-1.08;-1.2	4.82	4.82	0.62117	.	0.581302	0.19338	N	0.116724	T	0.52175	0.1718	N	0.08118	0	0.24599	A	0.00621181	B;B	0.13145	0.001;0.007	B;B	0.06405	0.0;0.002	T	0.64032	-0.6502	9	0.45353	T	0.12	.	13.4102	0.60938	0.0:0.0:1.0:0.0	.	114;114	P07949;P07949-2	RET_HUMAN;.	H	114	ENSP00000347942:R114H;ENSP00000344798:R114H	ENSP00000344798:R114H	R	+	2	0	RET	42917799	0.652000	0.27349	0.587000	0.28692	0.010000	0.07245	2.402000	0.44521	2.214000	0.71695	0.655000	0.94253	CGC		0.627	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43597793	G	A	43597793	3	1	3	1	0	0	0	0	1	0	0	0	13272	1087	38	1	351	1	RET	10	43597793	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	15254770	43597793	91936954	37	291										
DNAJC12	56521	hgsc.bcm.edu	37	chr10	69571294	69571294	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aaacccaccgtcttcactgaGtcattcaaagcttcccactg	5	15	4	1	rs377051523		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:69571294G>A	ENST00000225171.2	-	3	437	c.285C>T	c.(283-285)gaC>gaT	p.D95D	DNAJC12_ENST00000339758.7_Silent_p.D95D|RNU6-1250P_ENST00000391218.1_RNA|DNAJC12_ENST00000483798.2_Silent_p.D125D	NM_021800.2	NP_068572.1	Q9UKB3	DJC12_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 12	95								p.D95D(1)		breast(2)|kidney(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	12						TCTTCACTGAGTCATTCAAAG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	10											193	153	167					10																	69571294		2203	4300	6503	69241300	SO:0001819	synonymous_variant	56521			AF176012	CCDS7271.1, CCDS7272.1	10q21.3	2011-09-02			ENSG00000108176	ENSG00000108176		"Heat shock proteins / DNAJ (HSP40)"	28908	protein-coding gene	gene with protein product	"J domain protein 1"	606060				10760603	Standard	NM_021800		Approved	JDP1	uc001jnb.3	Q9UKB3	OTTHUMG00000018339	ENST00000225171.2:c.285C>T	10.37:g.69571294G>A			69241300	Q5JVQ1|Q9UKB2	Silent	SNP	ENST00000225171.2	37	CCDS7271.1																																																																																				0.502	DNAJC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048291.1	NM_021800		A	69571294	G	A	69571294	2	1	3	1	0	0	0	0	0	0	0	1	4642	1020	36	3		3	DNAJC12	10	69571294	Silent	SNP	G	TCGA-AF-2691-01A-01W-0831-10	25973501	69571294	65963453	38	292										
PPP1R3C	5507	hgsc.bcm.edu	37	chr10	93390322	93390322	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cagatcccacgctggttcttCtgggaggtcggagaagacat	13	10	2	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:93390322C>A	ENST00000238994.5	-	2	400	c.316G>T	c.(316-318)Gaa>Taa	p.E106*		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C									p.E106*(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				GCTGGTTCTTCTGGGAGGTCG	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											86	88	88					10																	93390322		2203	4300	6503	93380302	SO:0001587	stop_gained	5507			Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9293	protein-coding gene	gene with protein product	"Phosphatase 1, regulatory inhibitor subunit 5", "protein targeting to glycogen"	602999	"protein phosphatase 1, regulatory (inhibitor) subunit 3C"	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.316G>T	10.37:g.93390322C>A	ENSP00000238994:p.Glu106*		93380302		Nonsense_Mutation	SNP	ENST00000238994.5	37	CCDS7416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.497069|5.497069	0.96355|0.96355	.|.	.|.	ENSG00000119938|ENSG00000119938	ENST00000500094|ENST00000238994;ENST00000438999	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.099447	.|0.64402	.|D	.|0.000002	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|0.16420	.|T	.|0.52	.|-23.8977	20.04|20.04	0.97581|0.97581	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|X	-1|106	.|.	.|ENSP00000238994:E106X	.|E	-|-	.|1	.|0	PPP1R3C|PPP1R3C	93380302|93380302	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	7.381000|7.381000	0.79718|0.79718	2.733000|2.733000	0.93635|0.93635	0.655000|0.655000	0.94253|0.94253	.|GAA		0.488	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398		A	93390322	C	A	93390322	4	1	3	1	0	0	0	0	0	1	0	0	12407	922	32	2	641	2	PPP1R3C	10	93390322	Nonsense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	23819028	93390322	42144425	39	293										
ZDHHC6	64429	hgsc.bcm.edu	37	chr10	114200336	114200336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agctatggttgttcctaaagCtaatcccaaggcaaacaagg	9	9	0	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:114200336C>T	ENST00000369405.3	-	5	1060	c.637G>A	c.(637-639)Gct>Act	p.A213T	ZDHHC6_ENST00000369404.3_Missense_Mutation_p.A209T	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	213					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.A213T(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		GTTCCTAAAGCTAATCCCAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											158	145	149					10																	114200336		2203	4300	6503	114190326	SO:0001583	missense	64429			AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"Zinc fingers, DHHC-type"	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.637G>A	10.37:g.114200336C>T	ENSP00000358413:p.Ala213Thr		114190326	D3DRB6|Q53G45|Q96IV7|Q9H605	Missense_Mutation	SNP	ENST00000369405.3	37	CCDS7574.1	.	.	.	.	.	.	.	.	.	.	C	36	5.749561	0.96890	.	.	ENSG00000023041	ENST00000369405;ENST00000369404	T;T	0.25414	1.8;1.8	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.41259	0.1151	L	0.28608	0.87	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.70935	0.922;0.971	T	0.03981	-1.0987	10	0.34782	T	0.22	-7.9332	20.3065	0.98633	0.0:1.0:0.0:0.0	.	209;213	Q9H6R6-2;Q9H6R6	.;ZDHC6_HUMAN	T	213;209	ENSP00000358413:A213T;ENSP00000358412:A209T	ENSP00000358412:A209T	A	-	1	0	ZDHHC6	114190326	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	2.809000	0.96659	0.650000	0.86243	GCT		0.438	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494		T	114200336	C	T	114200336	3	4	3	1	0	0	0	0	1	0	0	0	17658	797	28	3	632	3	ZDHHC6	10	114200336	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	20810014	114200336	21334411	40	294										
PNLIP	5406	hgsc.bcm.edu	37	chr10	118321070	118321070	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gcagatggttaaatttatttGgtataacaatgtgatcaacc	8	5	1	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr10:118321070G>A	ENST00000369221.2	+	12	1284	c.1256G>A	c.(1255-1257)tGg>tAg	p.W419*		NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	419	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)	p.W419*(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	AAATTTATTTGGTATAACAAT	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											140	135	137					10																	118321070		2203	4300	6503	118311060	SO:0001587	stop_gained	5406			BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.1256G>A	10.37:g.118321070G>A	ENSP00000358223:p.Trp419*		118311060	Q5VSQ2	Nonsense_Mutation	SNP	ENST00000369221.2	37	CCDS7594.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822981	0.71028	.	.	ENSG00000175535	ENST00000369221	.	.	.	5.99	5.99	0.97316	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2471	0.93906	0.0:0.0:1.0:0.0	.	.	.	.	X	419	.	ENSP00000358223:W419X	W	+	2	0	PNLIP	118311060	1.000000	0.71417	0.992000	0.48379	0.106000	0.19336	6.756000	0.74919	2.847000	0.97988	0.655000	0.94253	TGG		0.383	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936		A	118321070	G	A	118321070	4	1	3	1	0	0	0	0	0	1	0	0	12180	1357	47	3	1298	3	PNLIP	10	118321070	Nonsense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	4120734	118321070	17213677	41	295										
NAT10	55226	hgsc.bcm.edu	37	chr11	34140023	34140023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	acccagcctgtgggtgtgttGgtggactgctgtaagactct	14	9	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr11:34140023G>T	ENST00000257829.3	+	8	959	c.753G>T	c.(751-753)ttG>ttT	p.L251F	NAT10_ENST00000527971.1_Missense_Mutation_p.L251F|NAT10_ENST00000531159.2_Missense_Mutation_p.L179F	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	251						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)	p.L251F(1)		endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TGGGTGTGTTGGTGGACTGCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											110	103	106					11																	34140023		2202	4298	6500	34096599	SO:0001583	missense	55226			AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.753G>T	11.37:g.34140023G>T	ENSP00000257829:p.Leu251Phe		34096599	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	37	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.649050	0.67358	.	.	ENSG00000135372	ENST00000257829;ENST00000531159;ENST00000527971	T;T	0.45276	0.9;0.93	5.29	2.18	0.27775	.	0.147232	0.42682	D	0.000665	T	0.53206	0.1782	M	0.88512	2.96	0.58432	D	0.999999	P	0.49783	0.928	P	0.50231	0.635	T	0.54970	-0.8213	10	0.66056	D	0.02	-12.0696	5.4514	0.16566	0.0701:0.1247:0.5476:0.2576	.	251	Q9H0A0	NAT10_HUMAN	F	251;179;251	ENSP00000257829:L251F;ENSP00000433011:L179F	ENSP00000257829:L251F	L	+	3	2	NAT10	34096599	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	0.777000	0.26718	0.570000	0.29347	0.555000	0.69702	TTG		0.522	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		T	34140023	G	T	34140023	3	4	3	1	0	0	0	0	1	0	0	0	10204	1339	47	2	779	2	NAT10	11	34140023	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		34140023	100866493	42	296										
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122669731	122669731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctgcgttcagactgcacacaAtatcttgaaaggtaagactt	8	9	2	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr11:122669731A>G	ENST00000284273.5	+	10	1814	c.1439A>G	c.(1438-1440)aAt>aGt	p.N480S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	480	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.N480S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ACTGCACACAATATCTTGAAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											115	103	107					11																	122669731		2202	4299	6501	122174941	SO:0001583	missense	84959			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1439A>G	11.37:g.122669731A>G	ENSP00000284273:p.Asn480Ser		122174941	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.708622	0.30322	.	.	ENSG00000154127	ENST00000284273	T	0.28666	1.6	6.07	4.92	0.64577	Histidine phosphatase superfamily, clade-1 (1);	0.086335	0.85682	D	0.000000	T	0.15825	0.0381	N	0.17312	0.475	0.51767	D	0.999938	P	0.37423	0.594	B	0.32393	0.145	T	0.03910	-1.0993	10	0.07482	T	0.82	-0.6699	13.0746	0.59079	0.8657:0.1343:0.0:0.0	.	480	Q8TF42	UBS3B_HUMAN	S	480	ENSP00000284273:N480S	ENSP00000284273:N480S	N	+	2	0	UBASH3B	122174941	1.000000	0.71417	0.990000	0.47175	0.968000	0.65278	8.704000	0.91351	1.081000	0.41110	0.533000	0.62120	AAT		0.438	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		G	122669731	A	G	122669731	3	3	3	1	0	0	0	0	1	0	0	0	16880	101	4	4	1477	4	UBASH3B	11	122669731	Missense_Mutation	SNP	A	TCGA-AF-2691-01A-01W-0831-10	88529708	122669731	12336785	43	297										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	3	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10		25398284	108453611	44	298										
ASB8	140461	hgsc.bcm.edu	37	chr12	48543494	48543494	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ttgatgactctgacctctgcGccataatccagaaggatgct	9	11	2	4			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr12:48543494G>A	ENST00000317697.3	-	4	691	c.522C>T	c.(520-522)ggC>ggT	p.G174G	ASB8_ENST00000539528.1_3'UTR|ASB8_ENST00000536549.1_Silent_p.G174G|ASB8_ENST00000537754.1_5'UTR|ASB8_ENST00000536953.1_3'UTR	NM_024095.3	NP_077000.1	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box containing 8	174					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.G174G(1)		breast(1)|kidney(2)|large_intestine(2)|lung(5)|soft_tissue(1)	11						TGACCTCTGCGCCATAATCCA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											76	73	74					12																	48543494		2203	4300	6503	46829761	SO:0001819	synonymous_variant	140461			AK024908	CCDS8761.1	12q13.12	2013-01-10	2011-01-25			ENSG00000177981		"Ankyrin repeat domain containing"	17183	protein-coding gene	gene with protein product		615053	"ankyrin repeat and SOCS box-containing 8"			12076535	Standard	NM_024095		Approved	MGC5540, FLJ21255	uc001rrh.3	Q9H765		ENST00000317697.3:c.522C>T	12.37:g.48543494G>A			46829761	A8K1P2|Q547Q2	Silent	SNP	ENST00000317697.3	37	CCDS8761.1																																																																																				0.532	ASB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396497.1			A	48543494	G	A	48543494	2	1	3	1	0	0	0	0	0	0	0	1	1030	1074	38	1		1	ASB8	12	48543494	Silent	SNP	G	TCGA-AF-2691-01A-01W-0831-10	23145210	48543494	85308401	45	299										
LRRC10	376132	hgsc.bcm.edu	37	chr12	70004051	70004051	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	atcaatcacctccaggaaggGcatgtgaagcagcacagtgg	12	10	2	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr12:70004051G>T	ENST00000361484.3	-	1	891	c.568C>A	c.(568-570)Ccc>Acc	p.P190T		NM_201550.2	NP_963844.2	Q5BKY1	LRC10_HUMAN	leucine rich repeat containing 10	190					cardiac muscle cell development (GO:0055013)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sarcomere (GO:0030017)		p.P190T(1)		large_intestine(2)|lung(6)	8	all_cancers(2;2.83e-105)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;1.98e-18)|GBM - Glioblastoma multiforme(2;7.43e-12)|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)			TCCAGGAAGGGCATGTGAAGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12											91	81	84					12																	70004051		2203	4300	6503	68290318	SO:0001583	missense	376132			AK095935	CCDS31856.1	12q15	2009-09-08				ENSG00000198812			20264	protein-coding gene	gene with protein product		610846				14751244	Standard	NM_201550		Approved	HRLRRP, LRRC10A	uc001svc.3	Q5BKY1		ENST00000361484.3:c.568C>A	12.37:g.70004051G>T	ENSP00000355166:p.Pro190Thr		68290318	Q6ZVY4	Missense_Mutation	SNP	ENST00000361484.3	37	CCDS31856.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029477	0.75504	.	.	ENSG00000198812	ENST00000361484	T	0.23950	1.88	5.63	5.63	0.86233	.	0.098837	0.64402	D	0.000001	T	0.41650	0.1168	M	0.63428	1.95	0.51482	D	0.999925	D	0.63880	0.993	P	0.56343	0.796	T	0.10800	-1.0614	10	0.08837	T	0.75	.	20.0471	0.97613	0.0:0.0:1.0:0.0	.	190	Q5BKY1	LRC10_HUMAN	T	190	ENSP00000355166:P190T	ENSP00000355166:P190T	P	-	1	0	LRRC10	68290318	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.488000	0.73637	2.815000	0.96918	0.561000	0.74099	CCC		0.587	LRRC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403834.1	NM_201550		T	70004051	G	T	70004051	3	4	3	1	0	0	0	0	1	0	0	0	8996	1203	42	2	269	2	LRRC10	12	70004051	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	21460557	70004051	63847844	46	300										
CCDC63	160762	hgsc.bcm.edu	37	chr12	111342486	111342486	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gaggctgagatcccgccaccCttcatcaaccctttctgggg	10	15	3	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr12:111342486C>G	ENST00000308208.5	+	11	1679	c.1437C>G	c.(1435-1437)ccC>ccG	p.P479P	CCDC63_ENST00000552694.1_Silent_p.P400P|CCDC63_ENST00000545036.1_Silent_p.P439P	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	479								p.P479P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TCCCGCCACCCTTCATCAACC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	12											75	70	72					12																	111342486		2203	4300	6503	109826869	SO:0001819	synonymous_variant	160762			AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1437C>G	12.37:g.111342486C>G			109826869	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	37	CCDS9151.1																																																																																				0.597	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		G	111342486	C	G	111342486	2	3	3	1	0	0	0	0	0	0	0	1	2840	668	24	5		5	CCDC63	12	111342486	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10	41338435	111342486	22509409	47	301										
SCARB1	949	hgsc.bcm.edu	37	chr12	125284769	125284769	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gcgttgaggaagtgaggatgGgagagaaacaagggggcacc	19	5	0	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr12:125284769G>T	ENST00000415380.2	-	8	1154	c.1029C>A	c.(1027-1029)tcC>tcA	p.S343S	SCARB1_ENST00000540495.1_Silent_p.S306S|SCARB1_ENST00000339570.5_Silent_p.S343S|SCARB1_ENST00000376788.1_Silent_p.S243S|SCARB1_ENST00000541205.1_Silent_p.S302S|SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000546215.1_Silent_p.S343S|SCARB1_ENST00000544327.1_Silent_p.S289S|SCARB1_ENST00000261693.6_Silent_p.S343S			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	343					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.S343S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	AGTGAGGATGGGAGAGAAACA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	12											86	83	84					12																	125284769		2203	4300	6503	123850722	SO:0001819	synonymous_variant	949			Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.1029C>A	12.37:g.125284769G>T			123850722	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Silent	SNP	ENST00000415380.2	37																																																																																					0.602	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		T	125284769	G	T	125284769	2	4	3	1	0	0	0	0	0	0	0	1	13918	1219	43	2		2	SCARB1	12	125284769	Silent	SNP	G	TCGA-AF-2691-01A-01W-0831-10	13942283	125284769	8567126	48	302										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46541918	46541918	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gtctctccttttgtctcgttCtctctctcgttctcgttctc	5	15	6	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr13:46541918C>A	ENST00000242848.4	-	15	4390	c.4042G>T	c.(4042-4044)Gaa>Taa	p.E1348*	ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.E1348*|ZC3H13_ENST00000378921.2_Nonsense_Mutation_p.E304*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1348							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.E1348*(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		ttgtctcgttctctctctcgt	0.473																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Nonsense(1)	large_intestine(1)	13											274	196	223					13																	46541918		2203	4299	6502	45439919	SO:0001587	stop_gained	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.4042G>T	13.37:g.46541918C>A	ENSP00000242848:p.Glu1348*		45439919	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	C	46	12.303638	0.99655	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	.	.	.	5.0	5.0	0.66597	.	0.128939	0.33631	N	0.004720	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	14.4519	0.67392	0.0:0.852:0.148:0.0	.	.	.	.	X	1348;304;1348	.	ENSP00000242848:E1348X	E	-	1	0	ZC3H13	45439919	1.000000	0.71417	0.998000	0.56505	0.932000	0.56968	2.661000	0.46758	2.319000	0.78375	0.591000	0.81541	GAA		0.473	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46541918	C	A	46541918	4	1	3	1	0	0	0	0	0	1	0	0	17604	922	32	2	664	2	ZC3H13	13	46541918	Nonsense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10		46541918	68627960	49	303										
SPTB	6710	hgsc.bcm.edu	37	chr14	65263288	65263288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tcattacctgggccacgaggCgctggttttcactgagccag	12	12	2	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr14:65263288C>T	ENST00000389721.5	-	10	1360	c.1328G>A	c.(1327-1329)cGc>cAc	p.R443H	SPTB_ENST00000556626.1_Missense_Mutation_p.R443H|SPTB_ENST00000389720.3_Missense_Mutation_p.R443H|SPTB_ENST00000389722.3_Missense_Mutation_p.R443H|SPTB_ENST00000542895.1_Missense_Mutation_p.R443H	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	443					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.R443H(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GGCCACGAGGCGCTGGTTTTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	14											73	73	73					14																	65263288		2203	4300	6503	64333041	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.1328G>A	14.37:g.65263288C>T	ENSP00000374371:p.Arg443His		64333041	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546756	0.86022	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	5.81	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.58680	0.2139	M	0.69463	2.115	0.53005	D	0.999965	P;D	0.56746	0.752;0.977	P;P	0.53224	0.458;0.721	T	0.63479	-0.6628	10	0.62326	D	0.03	.	14.0503	0.64732	0.0:0.9265:0.0:0.0735	.	443;447	P11277;Q59FP5	SPTB1_HUMAN;.	H	447;443;443;443;443;443	ENSP00000374372:R443H;ENSP00000451752:R443H;ENSP00000374371:R443H;ENSP00000443882:R443H;ENSP00000374370:R443H	ENSP00000374370:R443H	R	-	2	0	SPTB	64333041	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.953000	0.63624	1.474000	0.48178	-0.137000	0.14449	CGC		0.587	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65263288	C	T	65263288	3	4	3	1	0	0	0	0	1	0	0	0	15157	768	27	1	5831	1	SPTB	14	65263288	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10		65263288	42086252	50	304										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610318	81610318	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cgacttcatatgcatggcccCaatctcattctatgctctgt	6	13	4	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr14:81610318C>A	ENST00000541158.2	+	11	2238	c.1916C>A	c.(1915-1917)cCa>cAa	p.P639Q	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Missense_Mutation_p.P639Q			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	639			P -> A (in TTNs). {ECO:0000269|PubMed:11434721}.|P -> S (in HTNA; gain of function). {ECO:0000269|PubMed:10199795}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.P639Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGCATGGCCCCAATCTCATTC	0.453			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	1	Substitution - Missense(1)	large_intestine(1)	14											187	171	177					14																	81610318		2203	4300	6503	80680071	SO:0001583	missense	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1916C>A	14.37:g.81610318C>A	ENSP00000441235:p.Pro639Gln		80680071	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835497	0.71373	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.80393	-1.37;-1.37	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.93933	0.8058	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96321	0.9236	10	0.87932	D	0	.	18.4246	0.90605	0.0:1.0:0.0:0.0	.	639	F5GYU5	.	Q	639;286;639	ENSP00000441235:P639Q;ENSP00000298171:P639Q	ENSP00000298171:P639Q	P	+	2	0	TSHR	80680071	1.000000	0.71417	0.988000	0.46212	0.943000	0.58893	7.818000	0.86416	2.350000	0.79820	0.561000	0.74099	CCA		0.453	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		A	81610318	C	A	81610318	3	1	3	1	0	0	0	0	1	0	0	0	16662	594	21	2	2091	2	TSHR	14	81610318	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	16347030	81610318	25739222	51	305										
WARS	7453	hgsc.bcm.edu	37	chr14	100803478	100803478	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	acacgtccacatcacagttgCccccaaactgcctgtgctcc	6	18	1	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr14:100803478C>A	ENST00000355338.2	-	10	1793	c.1175G>T	c.(1174-1176)gGc>gTc	p.G392V	RP11-638I2.9_ENST00000556212.1_RNA|WARS_ENST00000358655.4_Missense_Mutation_p.G351V|WARS_ENST00000557135.1_Missense_Mutation_p.G392V|RP11-638I2.8_ENST00000557226.1_RNA|WARS_ENST00000556645.1_Missense_Mutation_p.G351V|WARS_ENST00000344102.5_Missense_Mutation_p.G351V|WARS_ENST00000392882.2_Missense_Mutation_p.G392V	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	392					angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)	p.G392V(1)		breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	ATCACAGTTGCCCCCAAACTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	14											296	250	266					14																	100803478		2203	4300	6503	99873231	SO:0001583	missense	7453			M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"Aminoacyl tRNA synthetases / Class I"	12729	protein-coding gene	gene with protein product	"tryptophan tRNA ligase 1, cytoplasmic"	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.1175G>T	14.37:g.100803478C>A	ENSP00000347495:p.Gly392Val		99873231	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Missense_Mutation	SNP	ENST00000355338.2	37	CCDS9960.1	.	.	.	.	.	.	.	.	.	.	C	32	5.108232	0.94292	.	.	ENSG00000140105	ENST00000392882;ENST00000358655;ENST00000355338;ENST00000344102;ENST00000557135;ENST00000556645	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83152	-0.0103	10	0.72032	D	0.01	-5.3317	20.1169	0.97940	0.0:1.0:0.0:0.0	.	392	P23381	SYWC_HUMAN	V	392;351;392;351;392;351	ENSP00000376620:G392V;ENSP00000351481:G351V;ENSP00000347495:G392V;ENSP00000339485:G351V;ENSP00000451460:G392V;ENSP00000451887:G351V	ENSP00000339485:G351V	G	-	2	0	WARS	99873231	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.980000	0.70516	2.835000	0.97688	0.591000	0.81541	GGC		0.557	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1	NM_004184		A	100803478	C	A	100803478	3	1	3	1	0	0	0	0	1	0	0	0	17289	739	26	2	248	2	WARS	14	100803478	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	19193160	100803478	6546062	52	306										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42742302	42742302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cacttttttgaagctctgcaTccaagctagcactctcaaag	6	12	2	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr15:42742302T>C	ENST00000263805.4	-	2	2425	c.2099A>G	c.(2098-2100)gAt>gGt	p.D700G	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	700					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D700G(1)									AAGCTCTGCATCCAAGCTAGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	15											118	119	118					15																	42742302		2203	4299	6502	40529594	SO:0001583	missense	64397			AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.2099A>G	15.37:g.42742302T>C	ENSP00000263805:p.Asp700Gly		40529594	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.382639	0.42207	.	.	ENSG00000103994	ENST00000263805	T	0.42900	0.96	5.52	5.52	0.82312	.	0.524948	0.20820	N	0.085081	T	0.46347	0.1388	M	0.63843	1.955	0.80722	D	1	P;B	0.43231	0.801;0.189	B;B	0.42625	0.393;0.112	T	0.45279	-0.9272	10	0.42905	T	0.14	-18.3465	15.9235	0.79592	0.0:0.0:0.0:1.0	.	483;700	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	G	700	ENSP00000263805:D700G	ENSP00000263805:D700G	D	-	2	0	ZFP106	40529594	1.000000	0.71417	0.989000	0.46669	0.965000	0.64279	4.088000	0.57678	2.218000	0.71995	0.528000	0.53228	GAT		0.453	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		C	42742302	T	C	42742302	3	2	3	1	0	0	0	0	1	0	0	0	17676	1435	50	4	3624	4	ZFP106	15	42742302	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10		42742302	59789090	53	307										
ZNF597	146434	hgsc.bcm.edu	37	chr16	3490874	3490874	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agggacctctgggcagggtgCagagtcacgcactcctcttg	14	12	3	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr16:3490874C>A	ENST00000301744.4	-	3	328	c.93G>T	c.(91-93)ctG>ctT	p.L31L	NAA60_ENST00000407558.4_5'Flank|NAA60_ENST00000424546.2_5'Flank|NAA60_ENST00000573580.1_5'Flank|NAA60_ENST00000608722.1_5'Flank	NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	31	KRAB.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L31L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						GGGCAGGGTGCAGAGTCACGC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	16											94	81	86					16																	3490874		2197	4300	6497	3430875	SO:0001819	synonymous_variant	146434			AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"Zinc fingers, C2H2-type", "-"	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.93G>T	16.37:g.3490874C>A			3430875		Silent	SNP	ENST00000301744.4	37	CCDS10505.1																																																																																				0.498	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		A	3490874	C	A	3490874	2	1	3	1	0	0	0	0	0	0	0	1	18066	697	25	2		2	ZNF597	16	3490874	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10		3490874	86863879	54	308										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48138174	48138174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctgctgcagaaagttctctgCgtgaaacggcagcctcacat	10	12	2	2			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr16:48138174C>T	ENST00000311303.3	-	20	3124	c.2779G>A	c.(2779-2781)Gca>Aca	p.A927T	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Intron	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	927	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A927T(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AAGTTCTCTGCGTGAAACGGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	16											170	160	164					16																	48138174		2201	4300	6501	46695675	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2779G>A	16.37:g.48138174C>T	ENSP00000311030:p.Ala927Thr		46695675	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050415	0.55218	.	.	ENSG00000140798	ENST00000311303;ENST00000449939	D	0.89681	-2.55	5.55	3.61	0.41365	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.308605	0.37857	N	0.001905	T	0.80639	0.4661	L	0.31526	0.94	0.80722	D	1	B	0.31989	0.35	B	0.34180	0.177	T	0.73742	-0.3887	10	0.18710	T	0.47	.	8.941	0.35729	0.0:0.8273:0.0:0.1727	.	927	Q96J65	MRP9_HUMAN	T	927;845	ENSP00000311030:A927T	ENSP00000311030:A927T	A	-	1	0	ABCC12	46695675	0.939000	0.31865	0.327000	0.25402	0.960000	0.62799	1.982000	0.40638	1.336000	0.45506	0.655000	0.94253	GCA		0.488	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48138174	C	T	48138174	3	4	3	1	0	0	0	0	1	0	0	0	52	768	27	1	1340	1	ABCC12	16	48138174	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	44647300	48138174	42216579	55	309										
TP53	7157	hgsc.bcm.edu	37	chr17	7577530	7577530	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cagtgtgatgatggtgaggaTgggcctccggttcatgccgc	16	9	1	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr17:7577530T>A	ENST00000269305.4	-	7	940	c.751A>T	c.(751-753)Atc>Ttc	p.I251F	TP53_ENST00000445888.2_Missense_Mutation_p.I251F|TP53_ENST00000420246.2_Missense_Mutation_p.I251F|TP53_ENST00000413465.2_Missense_Mutation_p.I251F|TP53_ENST00000455263.2_Missense_Mutation_p.I251F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.I251F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	251	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in sporadic cancers; somatic mutation).|I -> M (in LFS; germline mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|I -> T (in sporadic cancers; somatic mutation).|I -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I251F(9)|p.0?(8)|p.I251fs*94(6)|p.I251L(5)|p.I251_T253delILT(4)|p.I251del(2)|p.I251V(2)|p.P250_L252delPIL(2)|p.I251fs*12(1)|p.P250_T253delPILT(1)|p.P250_I251insXXXXXX(1)|p.P250_I251insX(1)|p.P250_I251insXXXXXXX(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.R249_I251delRPI(1)|p.I251fs*13(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGTGAGGATGGGCCTCCGG	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	47	Substitution - Missense(16)|Deletion - In frame(11)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - In frame(3)|Insertion - Frameshift(2)	stomach(9)|breast(7)|large_intestine(6)|haematopoietic_and_lymphoid_tissue(5)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|liver(3)|urinary_tract(2)|lung(2)|oesophagus(2)|skin(1)	17											153	111	126					17																	7577530		2203	4300	6503	7518255	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.751A>T	17.37:g.7577530T>A	ENSP00000269305:p.Ile251Phe		7518255	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175686	0.78564	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99854	-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.82323	2.585	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.992;0.999;0.997;1.0	D	0.96557	0.9412	10	0.87932	D	0	-1.7057	12.3101	0.54924	0.0:0.0:0.0:1.0	.	251;251;251;251;251	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	F	251;251;251;251;251;251;240;119	ENSP00000410739:I251F;ENSP00000352610:I251F;ENSP00000269305:I251F;ENSP00000398846:I251F;ENSP00000391127:I251F;ENSP00000391478:I251F;ENSP00000425104:I119F	ENSP00000269305:I251F	I	-	1	0	TP53	7518255	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	7.824000	0.86668	2.074000	0.62210	0.379000	0.24179	ATC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577530	T	A	7577530	3	1	3	1	0	0	0	0	1	0	0	0	16421	1464	51	5	539	5	TP53	17	7577530	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10		7577530	73617680	56	310										
CDH19	28513	hgsc.bcm.edu	37	chr18	64197181	64197181	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	acttgcacatacagtgggatCgaagagatctgttctatatt	9	7	2	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr18:64197181C>G	ENST00000540086.1	-	9	1605	c.1359G>C	c.(1357-1359)tcG>tcC	p.S453S	CDH19_ENST00000262150.2_Silent_p.S453S	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	561	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S453S(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				ACAGTGGGATCGAAGAGATCT	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	18											107	103	104					18																	64197181		2203	4300	6503	62348161	SO:0001819	synonymous_variant	28513			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.1359G>C	18.37:g.64197181C>G			62348161	O15098	Silent	SNP	ENST00000540086.1	37	CCDS59325.1																																																																																				0.313	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		G	64197181	C	G	64197181	2	3	3	1	0	0	0	0	0	0	0	1	3110	871	31	5		5	CDH19	18	64197181	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10		64197181	13880067	57	311										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36332649	36332649	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gttgaatgttggtttggtccGagccaagggcgttggtggct	17	6	0	1	rs386833926		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr19:36332649G>T	ENST00000378910.5	-	20	2782	c.2783C>A	c.(2782-2784)tCg>tAg	p.S928*	NPHS1_ENST00000353632.6_Nonsense_Mutation_p.S928*	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	928	Ig-like C2-type 8.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.S928*(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGTTTGGTCCGAGCCAAGGGC	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											195	145	162					19																	36332649		2203	4300	6503	41024489	SO:0001587	stop_gained	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2783C>A	19.37:g.36332649G>T	ENSP00000368190:p.Ser928*		41024489	A6NDH2|C3RX61	Nonsense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	G	41	8.838174	0.98972	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	.	.	.	5.4	5.4	0.78164	.	0.283025	0.33813	N	0.004532	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2146	10.2195	0.43188	0.0898:0.0:0.9102:0.0	.	.	.	.	X	928	.	ENSP00000343634:S928X	S	-	2	0	NPHS1	41024489	0.891000	0.30450	0.984000	0.44739	0.764000	0.43329	2.019000	0.41001	2.567000	0.86603	0.558000	0.71614	TCG		0.587	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36332649	G	T	36332649	4	4	3	1	0	0	0	0	0	1	0	0	10613	1059	37	2	982	2	NPHS1	19	36332649	Nonsense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		36332649	22796334	58	312										
RYR1	6261	hgsc.bcm.edu	37	chr19	39075643	39075643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gaggcattggggacgagatcGaggaccccgcgggtgacgaa	18	9	0	2	rs372418113		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr19:39075643G>A	ENST00000359596.3	+	102	14707	c.14707G>A	c.(14707-14709)Gag>Aag	p.E4903K	RYR1_ENST00000355481.4_Missense_Mutation_p.E4898K|RYR1_ENST00000360985.3_Missense_Mutation_p.E4898K			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4903					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.E4903K(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGACGAGATCGAGGACCCCGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	239	187	204		14707,14692	5.1	1	19		204	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	4903/5039,4898/5034	39075643	1,13005	2203	4300	6503	43767483	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14707G>A	19.37:g.39075643G>A	ENSP00000352608:p.Glu4903Lys		43767483	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.815596	0.70912	0.0	1.16E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.92299	-3.01;-3.01;-3.01	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.64402	U	0.000002	D	0.95680	0.8595	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	D	0.95774	0.8811	10	0.66056	D	0.02	.	18.3248	0.90250	0.0:0.0:1.0:0.0	.	4898;4903	P21817-2;P21817	.;RYR1_HUMAN	K	4903;4898;4898	ENSP00000352608:E4903K;ENSP00000347667:E4898K;ENSP00000354254:E4898K	ENSP00000347667:E4898K	E	+	1	0	RYR1	43767483	1.000000	0.71417	0.991000	0.47740	0.927000	0.56198	9.656000	0.98514	2.658000	0.90341	0.449000	0.29647	GAG		0.562	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39075643	G	A	39075643	3	1	3	1	0	0	0	0	1	0	0	0	13805	1059	37	1	15113	1	RYR1	19	39075643	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	2742994	39075643	20053340	59	313										
SARS2	54938	hgsc.bcm.edu	37	chr19	39416935	39416935	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tgcctcagctcctgccatgtCgagatctggggtggatataa	12	10	2	1	rs144229840	byFrequency	TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr19:39416935C>G	ENST00000221431.6	-	2	432	c.273G>C	c.(271-273)tcG>tcC	p.S91S	SARS2_ENST00000594171.1_5'UTR|SARS2_ENST00000448145.2_Silent_p.S91S|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.D161H|SARS2_ENST00000430193.3_Silent_p.S91S|SARS2_ENST00000600042.1_Silent_p.S91S	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)	p.S91S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCTGCCATGTCGAGATCTGGG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											50	42	45					19																	39416935		2203	4300	6503	44108775	SO:0001819	synonymous_variant	54938			AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.273G>C	19.37:g.39416935C>G			44108775	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1																																																																																				0.612	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		G	39416935	C	G	39416935	2	3	3	1	0	0	0	0	0	0	0	1	13882	871	31	5		5	SARS2	19	39416935	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10	341292	39416935	19712048	60	314										
TSKS	60385	hgsc.bcm.edu	37	chr19	50243068	50243068	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tgagcccccctgttttggggGggttcctgcactgctgcctc	13	14	0	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr19:50243068G>T	ENST00000246801.3	-	11	1826	c.1744C>A	c.(1744-1746)Ccc>Acc	p.P582T	TSKS_ENST00000358830.3_Missense_Mutation_p.P382T	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	582					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.P582T(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		TGTTTTGGGGGGGTTCCTGCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											99	99	99					19																	50243068		2203	4300	6503	54934880	SO:0001583	missense	60385			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1744C>A	19.37:g.50243068G>T	ENSP00000246801:p.Pro582Thr		54934880	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.421361	0.25639	.	.	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	.	0.145674	0.31963	N	0.006784	T	0.45074	0.1324	N	0.24115	0.695	0.35190	D	0.773322	D	0.71674	0.998	D	0.68943	0.961	T	0.57900	-0.7731	10	0.66056	D	0.02	-15.0189	14.4234	0.67200	0.0:0.0:1.0:0.0	.	582	Q9UJT2	TSKS_HUMAN	T	582;382	ENSP00000246801:P582T;ENSP00000351691:P382T	ENSP00000246801:P582T	P	-	1	0	TSKS	54934880	0.995000	0.38212	0.964000	0.40570	0.014000	0.08584	2.845000	0.48254	2.471000	0.83476	0.609000	0.83330	CCC		0.542	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50243068	G	T	50243068	3	4	3	1	0	0	0	0	1	0	0	0	16666	1232	43	2	38	2	TSKS	19	50243068	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	10826133	50243068	8885915	61	315										
ZNF175	7728	hgsc.bcm.edu	37	chr19	52090211	52090211	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gaaagtttgaagctgaacctAgaagtgaacggtcagaatga	12	5	1	6			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr19:52090211A>T	ENST00000262259.2	+	5	985	c.627A>T	c.(625-627)ctA>ctT	p.L209L	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	209					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L209L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		AGCTGAACCTAGAAGTGAACG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	19											83	78	80					19																	52090211		2203	4299	6502	56782023	SO:0001819	synonymous_variant	7728			D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.627A>T	19.37:g.52090211A>T			56782023	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																				0.463	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		T	52090211	A	T	52090211	2	4	3	1	0	0	0	0	0	0	0	1	17784	407	15	5		5	ZNF175	19	52090211	Silent	SNP	A	TCGA-AF-2691-01A-01W-0831-10	1847143	52090211	7038772	62	316										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62303953	62303953	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	ctgaaggggacagtcgtgatCtttgacgaagctcacaacgt	12	9	2	3			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr20:62303953C>T	ENST00000360203.5	+	9	1069	c.744C>T	c.(742-744)atC>atT	p.I248I	RTEL1_ENST00000318100.4_Silent_p.I248I|RTEL1_ENST00000508582.2_Silent_p.I272I|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.I248I|RTEL1_ENST00000370018.3_Silent_p.I248I					regulator of telomere elongation helicase 1									p.I248I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			CAGTCGTGATCTTTGACGAAG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	20											92	67	75					20																	62303953		2203	4300	6503	61774397	SO:0001819	synonymous_variant	51750			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.744C>T	20.37:g.62303953C>T			61774397		Silent	SNP	ENST00000360203.5	37																																																																																					0.557	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		T	62303953	C	T	62303953	2	4	3	1	0	0	0	0	0	0	0	1	13757	903	32	3		3	RTEL1	20	62303953	Silent	SNP	C	TCGA-AF-2691-01A-01W-0831-10		62303953	721567	63	317										
ISX	91464	hgsc.bcm.edu	37	chr22	35463236	35463236	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	atggacagaccagaagggccAggtgaagagggccccggaga	17	9	0	5			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr22:35463236A>T	ENST00000308700.6	+	1	1108	c.156A>T	c.(154-156)ccA>ccT	p.P52P	ISX_ENST00000404699.2_Silent_p.P52P|RP1-272J12.1_ENST00000448318.4_RNA	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	52					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.P52P(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						CAGAAGGGCCAGGTGAAGAGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	22											32	34	33					22																	35463236		2202	4299	6501	33793236	SO:0001819	synonymous_variant	91464			AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"Homeoboxes / PRD class"	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.156A>T	22.37:g.35463236A>T			33793236	Q68DJ5	Silent	SNP	ENST00000308700.6	37	CCDS33640.1																																																																																				0.577	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494		T	35463236	A	T	35463236	2	4	3	1	0	0	0	0	0	0	0	1	7886	175	7	5		5	ISX	22	35463236	Silent	SNP	A	TCGA-AF-2691-01A-01W-0831-10		35463236	15841330	64	318										
MCM5	4174	hgsc.bcm.edu	37	chr22	35808565	35808565	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	agttccgtcgcctggctgccCtcccaaatgtctatgaggtc	10	14	1	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr22:35808565C>A	ENST00000216122.4	+	8	1136	c.982C>A	c.(982-984)Ctc>Atc	p.L328I	MCM5_ENST00000382011.5_Missense_Mutation_p.L285I|MCM5_ENST00000465557.1_3'UTR	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	328					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.L328I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CCTGGCTGCCCTCCCAAATGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											81	75	77					22																	35808565		2203	4300	6503	34138565	SO:0001583	missense	4174				CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.982C>A	22.37:g.35808565C>A	ENSP00000216122:p.Leu328Ile		34138565	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.189897	0.21954	.	.	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000444582	T;T	0.06449	3.3;3.3	5.62	4.52	0.55395	.	0.454514	0.24993	N	0.033964	T	0.07458	0.0188	L	0.39245	1.2	0.23406	N	0.997743	B;B;B;B	0.21071	0.01;0.051;0.051;0.01	B;B;B;B	0.22386	0.039;0.039;0.039;0.039	T	0.16867	-1.0388	10	0.52906	T	0.07	-28.1623	13.257	0.60085	0.2738:0.7262:0.0:0.0	.	328;328;285;328	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	I	328;285;237	ENSP00000216122:L328I;ENSP00000371441:L285I	ENSP00000216122:L328I	L	+	1	0	MCM5	34138565	0.471000	0.25862	0.959000	0.39883	0.100000	0.18952	0.946000	0.29069	2.651000	0.90000	0.561000	0.74099	CTC		0.612	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			A	35808565	C	A	35808565	3	1	3	1	0	0	0	0	1	0	0	0	9420	681	24	2	1008	2	MCM5	22	35808565	Missense_Mutation	SNP	C	TCGA-AF-2691-01A-01W-0831-10	345329	35808565	15496001	65	319										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45929716	45929716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	caacacagtgggctctttccGctgccagcgggacagcagct	12	14	1	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chr22:45929716G>A	ENST00000327858.6	+	7	817	c.722G>A	c.(721-723)cGc>cAc	p.R241H	FBLN1_ENST00000348697.2_Missense_Mutation_p.R241H|FBLN1_ENST00000442170.2_Missense_Mutation_p.R241H|FBLN1_ENST00000262722.7_Missense_Mutation_p.R241H|FBLN1_ENST00000402984.3_Missense_Mutation_p.R279H|FBLN1_ENST00000340923.5_Missense_Mutation_p.R241H	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	241	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.R241H(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GGCTCTTTCCGCTGCCAGCGG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	22											112	115	114					22																	45929716		2203	4300	6503	44308380	SO:0001583	missense	2192				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.722G>A	22.37:g.45929716G>A	ENSP00000331544:p.Arg241His		44308380	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.016401	0.93404	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923;ENST00000451475	D;D;D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04;-3.04;-3.04	5.19	5.19	0.71726	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.000000	0.85682	D	0.000000	D	0.92964	0.7761	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.999	D	0.90238	0.4284	10	0.15066	T	0.55	.	18.6997	0.91615	0.0:0.0:1.0:0.0	.	279;241;241;241	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	H	241;279;241;241;241;241;161	ENSP00000262723:R241H;ENSP00000385521:R279H;ENSP00000262722:R241H;ENSP00000331544:R241H;ENSP00000393812:R241H;ENSP00000342212:R241H;ENSP00000415160:R161H	ENSP00000262722:R241H	R	+	2	0	FBLN1	44308380	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.217000	0.72218	2.412000	0.81896	0.305000	0.20034	CGC		0.587	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		A	45929716	G	A	45929716	3	1	3	1	0	0	0	0	1	0	0	0	5717	1087	38	1	748	1	FBLN1	22	45929716	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	10121151	45929716	5374850	66	320										
ZNF645	158506	hgsc.bcm.edu	37	chrX	22292316	22292316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	gtcaccttgtccaccaacgcGgagtccacctccttcaaccc	6	19	2	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:22292316G>T	ENST00000323684.1	+	1	1252	c.1208G>T	c.(1207-1209)cGg>cTg	p.R403L		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	403					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R403L(1)		cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						CCACCAACGCGGAGTCCACCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X																																								22202237	SO:0001583	missense	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.1208G>T	X.37:g.22292316G>T	ENSP00000323348:p.Arg403Leu		22202237	A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	G	9.237	1.037232	0.19669	.	.	ENSG00000175809	ENST00000323684	T	0.32023	1.47	2.34	-0.0796	0.13710	.	0.427893	0.23192	U	0.050891	T	0.13030	0.0316	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.15206	-1.0445	10	0.62326	D	0.03	.	5.3193	0.15872	0.6682:0.0:0.3318:0.0	.	403	Q8N7E2	ZN645_HUMAN	L	403	ENSP00000323348:R403L	ENSP00000323348:R403L	R	+	2	0	ZNF645	22202237	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	2.456000	0.44997	-0.109000	0.12044	-0.340000	0.08031	CGG		0.458	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		T	22292316	G	T	22292316	3	4	3	1	0	0	0	0	1	0	0	0	18100	1116	39	2	1210	2	ZNF645	23	22292316	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10		22292316	132978244	67	321										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86869032	86869032	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	actgattgcaggacacctccGcatcccagcccataggtaag	9	14	0	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:86869032G>A	ENST00000373119.4	+	2	720	c.575G>A	c.(574-576)cGc>cAc	p.R192H	KLHL4_ENST00000373114.4_Missense_Mutation_p.R192H	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	192	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R192H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GGACACCTCCGCATCCCAGCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	X											110	97	101					X																	86869032		2203	4300	6503	86755688	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.575G>A	X.37:g.86869032G>A	ENSP00000362211:p.Arg192His		86755688	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	g	11.45	1.642508	0.29246	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.68903	-0.36;-0.36	5.14	0.425	0.16473	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.721802	0.12544	N	0.459631	T	0.55401	0.1918	L	0.60957	1.885	0.09310	N	1	B;B	0.33044	0.395;0.343	B;B	0.29785	0.107;0.104	T	0.51301	-0.8723	10	0.62326	D	0.03	.	4.5665	0.12189	0.4719:0.3108:0.2173:0.0	.	192;192	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	H	192	ENSP00000362211:R192H;ENSP00000362206:R192H	ENSP00000362206:R192H	R	+	2	0	KLHL4	86755688	1.000000	0.71417	0.113000	0.21522	0.703000	0.40648	1.773000	0.38563	0.379000	0.24794	0.502000	0.49764	CGC		0.368	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			A	86869032	G	A	86869032	3	1	3	1	0	0	0	0	1	0	0	0	8412	1087	38	1	581	1	KLHL4	23	86869032	Missense_Mutation	SNP	G	TCGA-AF-2691-01A-01W-0831-10	64576716	86869032	68401528	68	322										
ARHGEF6	9459	hgsc.bcm.edu	37	chrX	135862981	135862981	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cggatcacagatggtcttttTaggggactctaaaactccca	9	10	3	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:135862981T>A	ENST00000250617.6	-	1	1266	c.61A>T	c.(61-63)Aaa>Taa	p.K21*		NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	21	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K21*(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					ATGGTCTTTTTAGGGGACTCT	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											117	110	112					X																	135862981		2203	4300	6503	135690647	SO:0001587	stop_gained	9459			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.61A>T	X.37:g.135862981T>A	ENSP00000250617:p.Lys21*		135690647	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Nonsense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	T	48	14.733252	0.99808	.	.	ENSG00000129675	ENST00000250617	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4762	0.75481	0.0:0.0:0.0:1.0	.	.	.	.	X	21	.	ENSP00000250617:K21X	K	-	1	0	ARHGEF6	135690647	1.000000	0.71417	0.996000	0.52242	0.855000	0.48748	7.698000	0.84413	2.039000	0.60335	0.417000	0.27973	AAA		0.463	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		A	135862981	T	A	135862981	4	1	3	1	0	0	0	0	0	1	0	0	910	1763	61	5	2357	5	ARHGEF6	23	135862981	Nonsense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10	48993949	135862981	19407579	69	323										
CXorf66	347487	hgsc.bcm.edu	37	chrX	139040347	139040347	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	tcttctaaggtagttcaattTtgtctgcattgattcaacag	7	7	5	1			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:139040347T>C	ENST00000370540.1	-	2	141	c.118A>G	c.(118-120)Aaa>Gaa	p.K40E		NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN	chromosome X open reading frame 66	40						integral component of membrane (GO:0016021)		p.K40E(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						TAGTTCAATTTTGTCTGCATT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	X											151	143	146					X																	139040347		2203	4300	6503	138868013	SO:0001583	missense	347487				CCDS35411.1	Xq27.1	2014-05-30			ENSG00000203933	ENSG00000203933			33743	protein-coding gene	gene with protein product	"secreted glycoprotein, X-linked"					24709545	Standard	NM_001013403		Approved	RP11-35F15.2, SGPX	uc004fbb.3	Q5JRM2	OTTHUMG00000022539	ENST00000370540.1:c.118A>G	X.37:g.139040347T>C	ENSP00000359571:p.Lys40Glu		138868013		Missense_Mutation	SNP	ENST00000370540.1	37	CCDS35411.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.260093	0.39995	.	.	ENSG00000203933	ENST00000370540	T	0.49720	0.77	3.56	2.36	0.29203	.	.	.	.	.	T	0.50463	0.1617	L	0.34521	1.04	0.09310	N	1	D	0.76494	0.999	D	0.67725	0.953	T	0.28459	-1.0043	8	.	.	.	-11.2112	6.115	0.20122	0.0:0.0:0.261:0.739	.	40	Q5JRM2	CX066_HUMAN	E	40	ENSP00000359571:K40E	.	K	-	1	0	CXorf66	138868013	0.000000	0.05858	0.001000	0.08648	0.093000	0.18481	-0.031000	0.12287	0.555000	0.29079	0.430000	0.28490	AAA		0.313	CXorf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058572.1	NM_001013403		C	139040347	T	C	139040347	3	2	3	1	0	0	0	0	1	0	0	0	4124	1850	64	4	975	4	CXorf66	23	139040347	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10	3177366	139040347	16230213	70	324										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140994556	140994556	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	cctctttctcctacactttaTtgagtcttttccagagttcc	4	13	3	2	rs61701368		TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:140994556T>C	ENST00000285879.4	+	4	1652	c.1366T>C	c.(1366-1368)Ttg>Ctg	p.L456L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	456								p.L456L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTACACTTTATTGAGTCTTTT	0.483										HNSCC(15;0.026)																																						1	Substitution - coding silent(1)	large_intestine(1)	X						A		6,3828		1,0,4,1631,566	94	104	101		1366	-0.3	0	X	dbSNP_129	101	2,6720		0,0,2,2428,1864	no	coding-synonymous	MAGEC1	NM_005462.4		1,0,6,4059,2430	CC,CT,C,TT,T		0.0298,0.1565,0.0758		456/1143	140994556	8,10548	2202	4294	6496	140822222	SO:0001819	synonymous_variant	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1366T>C	X.37:g.140994556T>C			140822222	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	37	CCDS35417.1																																																																																				0.483	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		C	140994556	T	C	140994556	2	2	3	1	0	0	0	0	0	0	0	1	9210	1490	52	4		4	MAGEC1	23	140994556	Silent	SNP	T	TCGA-AF-2691-01A-01W-0831-10	1954209	140994556	14276004	71	325										
GAB3	139716	hgsc.bcm.edu	37	chrX	153940899	153940899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.381714285714286	0.954285714285714	0.238571428571429	1	1	0	aggggagcggctgcaggcagTcaacaaaaacatcatcaaat	11	9	3	0			TCGA-AF-2691-01A-01W-0831-10	TCGA-AF-2691-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	0a041965-3054-4091-9dae-8b6b40cc7a03	0dc37a16-724e-44fe-a593-b1efde8ccf36	g.chrX:153940899T>G	ENST00000369575.3	-	4	702	c.671A>C	c.(670-672)gAc>gCc	p.D224A	GAB3_ENST00000496390.1_Intron|GAB3_ENST00000424127.2_Missense_Mutation_p.D225A	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	224					macrophage differentiation (GO:0030225)			p.D224A(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTGCAGGCAGTCAACAAAAAC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	X											81	78	79					X																	153940899		2203	4300	6503	153594093	SO:0001583	missense	139716			AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"Pleckstrin homology (PH) domain containing"	17515	protein-coding gene	gene with protein product	"DOS/Gab family member 3", "Gab3 scaffolding protein"	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.671A>C	X.37:g.153940899T>G	ENSP00000358588:p.Asp224Ala		153594093	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.057261	0.55325	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.33654	1.4;1.4;1.4	5.53	5.53	0.82687	.	0.044671	0.85682	D	0.000000	T	0.59689	0.2212	M	0.77616	2.38	0.80722	D	1	D;P;P	0.89917	1.0;0.911;0.911	D;P;P	0.83275	0.996;0.609;0.609	T	0.61715	-0.7006	10	0.44086	T	0.13	-1.5326	12.3926	0.55366	0.0:0.0:0.0:1.0	.	225;225;224	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	A	224;225;225	ENSP00000358588:D224A;ENSP00000358581:D225A;ENSP00000399588:D225A	ENSP00000358581:D225A	D	-	2	0	GAB3	153594093	1.000000	0.71417	0.222000	0.23844	0.485000	0.33311	5.108000	0.64609	1.831000	0.53308	0.412000	0.27726	GAC		0.537	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		G	153940899	T	G	153940899	3	3	3	1	0	0	0	0	1	0	0	0	6169	1667	58	4	1117	4	GAB3	23	153940899	Missense_Mutation	SNP	T	TCGA-AF-2691-01A-01W-0831-10	12946343	153940899	1329661	72	326										
RPE65	6121	hgsc.bcm.edu	37	chr1	68910558	68910558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cccgtacgtaagcatcagtgCggatgaacctgaaggacatt	11	10	1	2	rs61752870		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr1:68910558C>T	ENST00000262340.5	-	4	307	c.254G>A	c.(253-255)cGc>cAc	p.R85H		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	85			R -> H (in RP20; uncertain pathological significance). {ECO:0000269|PubMed:11095629}.		cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)	p.R85H(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						AGCATCAGTGCGGATGAACCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM005348	RPE65	M	rs61752870	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	72	64	67	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	254	5	1	1	dbSNP_129	67	0,8600		0,0,4300	no	missense	RPE65	NM_000329.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	85/534	68910558	1,13005	2203	4300	6503	68683146	SO:0001583	missense	6121			U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.254G>A	1.37:g.68910558C>T	ENSP00000262340:p.Arg85His		68683146	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	37	CCDS643.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130505	0.77549	2.27E-4	0.0	ENSG00000116745	ENST00000262340	D	0.95588	-3.75	5.03	5.03	0.67393	.	0.212817	0.46758	D	0.000264	D	0.92662	0.7668	M	0.79805	2.47	0.58432	D	0.999999	P	0.46952	0.887	B	0.31495	0.131	D	0.94072	0.7336	10	0.59425	D	0.04	-0.0031	18.5413	0.91029	0.0:1.0:0.0:0.0	rs61752870	85	Q16518	RPE65_HUMAN	H	85	ENSP00000262340:R85H	ENSP00000262340:R85H	R	-	2	0	RPE65	68683146	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.645000	0.54389	2.615000	0.88500	0.655000	0.94253	CGC		0.458	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		T	68910558	C	T	68910558	3	4	4	1	0	0	0	0	1	0	0	0	13582	768	27	1	1391	1	RPE65	1	68910558	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		68910558	180340063	1	327										
DPYD	1806	hgsc.bcm.edu	37	chr1	97544573	97544573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	taagggtacgcctctctttgGttcataaggtgttgtcctgg	12	8	2	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr1:97544573G>A	ENST00000370192.3	-	23	3137	c.3037C>T	c.(3037-3039)Cca>Tca	p.P1013S		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	1013					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.P1013S(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	CCTCTCTTTGGTTCATAAGGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											238	220	226					1																	97544573		2203	4300	6503	97317161	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.3037C>T	1.37:g.97544573G>A	ENSP00000359211:p.Pro1013Ser		97317161	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.638102	0.87760	.	.	ENSG00000188641	ENST00000370192	D	0.91792	-2.91	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.88894	0.6561	M	0.68317	2.08	0.80722	D	1	P	0.38048	0.616	B	0.34452	0.183	D	0.89670	0.3883	10	0.52906	T	0.07	-9.9722	19.6731	0.95918	0.0:0.0:1.0:0.0	.	1013	Q12882	DPYD_HUMAN	S	1013	ENSP00000359211:P1013S	ENSP00000359211:P1013S	P	-	1	0	DPYD	97317161	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.813000	0.99286	2.735000	0.93741	0.561000	0.74099	CCA		0.443	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97544573	G	A	97544573	3	1	4	1	0	0	0	0	1	0	0	0	4756	1261	44	3	44	3	DPYD	1	97544573	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	28634015	97544573	151706048	2	328										
C4BPA	722	hgsc.bcm.edu	37	chr1	207287484	207287484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cactttatcatttgctgcccCgatggatattacgttgactg	8	10	1	1			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr1:207287484C>T	ENST00000367070.3	+	3	376	c.182C>T	c.(181-183)cCg>cTg	p.P61L		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	61	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.P61L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TTTGCTGCCCCGATGGATATT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											196	178	184					1																	207287484		2203	4300	6503	205354107	SO:0001583	missense	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.182C>T	1.37:g.207287484C>T	ENSP00000356037:p.Pro61Leu		205354107	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.137057	0.56936	.	.	ENSG00000123838	ENST00000367070;ENST00000421786	T;T	0.64803	-0.12;-0.12	5.25	3.39	0.38822	Complement control module (2);Sushi/SCR/CCP (3);	0.244990	0.29376	N	0.012321	T	0.57814	0.2079	L	0.41573	1.285	0.09310	N	0.999997	D	0.60575	0.988	P	0.55455	0.776	T	0.48647	-0.9017	10	0.08599	T	0.76	.	8.3139	0.32088	0.0:0.8217:0.0:0.1783	.	61	P04003	C4BPA_HUMAN	L	61	ENSP00000356037:P61L;ENSP00000403386:P61L	ENSP00000356037:P61L	P	+	2	0	C4BPA	205354107	0.000000	0.05858	0.008000	0.14137	0.001000	0.01503	0.309000	0.19332	0.911000	0.36747	-0.150000	0.13652	CCG		0.468	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207287484	C	T	207287484	3	4	4	1	0	0	0	0	1	0	0	0	2255	652	23	1	188	1	C4BPA	1	207287484	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	109742911	207287484	41963137	3	329										
ARPP21	10777	hgsc.bcm.edu	37	chr3	35780947	35780947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	agcagcccagctatgtaatcGcctctacaggccagcagctt	9	14	1	0	rs151173813	byFrequency	TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr3:35780947G>A	ENST00000187397.4	+	17	2239	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T	ARPP21_ENST00000337271.5_Missense_Mutation_p.A576T|ARPP21_ENST00000417925.1_Missense_Mutation_p.A596T|ARPP21_ENST00000444190.1_Missense_Mutation_p.A576T|ARPP21_ENST00000458225.1_Missense_Mutation_p.A596T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	595	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.A595T(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						CTATGTAATCGCCTCTACAGG	0.627													G|||	7	0.00139776	0	0.0029	5008	,	,		15714	0		0.003	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	3						G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	58	59	58		1783	4.1	0.4	3	dbSNP_134	58	37,8563	25.7+/-73.6	0,37,4263	yes	missense	ARPP21	NM_016300.4	58	0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076	benign	595/813	35780947	40,12966	2203	4300	6503	35755951	SO:0001583	missense	10777			AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1783G>A	3.37:g.35780947G>A	ENSP00000187397:p.Ala595Thr		35755951	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	11.71	1.719677	0.30503	6.81E-4	0.004302	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.96	4.14	0.48551	.	0.068903	0.56097	N	0.000036	T	0.19127	0.0459	L	0.31476	0.935	0.31779	N	0.631164	B;B;B;B	0.32543	0.067;0.375;0.011;0.067	B;B;B;B	0.28385	0.023;0.089;0.006;0.023	T	0.19418	-1.0306	10	0.12103	T	0.63	-7.922	10.8408	0.46715	0.1502:0.0:0.8498:0.0	.	596;118;595;576	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	T	596;576;576;595;596	ENSP00000414351:A596T;ENSP00000337792:A576T;ENSP00000405276:A576T;ENSP00000187397:A595T;ENSP00000412326:A596T	ENSP00000187397:A595T	A	+	1	0	ARPP21	35755951	1.000000	0.71417	0.406000	0.26421	0.573000	0.36030	4.374000	0.59543	1.499000	0.48617	0.655000	0.94253	GCC		0.627	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		A	35780947	G	A	35780947	3	1	4	1	0	0	0	0	1	0	0	0	979	1087	38	1	1854	1	ARPP21	3	35780947	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10		35780947	162241483	4	330										
SIDT1	54847	hgsc.bcm.edu	37	chr3	113329934	113329934	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cacccagacatcaatgccagCgcctactctgcctatgcctc	6	18	2	1	rs145430934	byFrequency	TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr3:113329934C>T	ENST00000264852.4	+	18	2526	c.1800C>T	c.(1798-1800)agC>agT	p.S600S	SIDT1_ENST00000463226.1_3'UTR|SIDT1_ENST00000393830.3_Silent_p.S600S	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	600					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)	p.S600S(1)		breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TCAATGCCAGCGCCTACTCTG	0.577													C|||	4	0.000798722	0	0	5008	,	,		16525	0.004		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						C		1,4405	2.1+/-5.4	0,1,2202	187	160	169		1800	-2.5	1	3	dbSNP_134	169	0,8600		0,0,4300	no	coding-synonymous	SIDT1	NM_017699.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		600/828	113329934	1,13005	2203	4300	6503	114812624	SO:0001819	synonymous_variant	54847			AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1800C>T	3.37:g.113329934C>T			114812624	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																				0.577	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		T	113329934	C	T	113329934	2	4	4	1	0	0	0	0	0	0	0	1	14339	767	27	1		1	SIDT1	3	113329934	Silent	SNP	C	TCGA-AF-2692-01A-01W-0831-10	77548987	113329934	84692496	5	331										
IGSF11	152404	hgsc.bcm.edu	37	chr3	118624539	118624539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	agacagggcactgatgttccGgatggtgactgttccctgga	14	9	0	3			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr3:118624539G>A	ENST00000393775.2	-	5	912	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	IGSF11_ENST00000489689.1_Missense_Mutation_p.R203W|IGSF11_ENST00000441144.2_Missense_Mutation_p.R202W|IGSF11_ENST00000491903.1_Missense_Mutation_p.R203W|IGSF11_ENST00000354673.2_Missense_Mutation_p.R202W|IGSF11_ENST00000425327.2_Missense_Mutation_p.R202W	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	203	Ig-like C2-type.				cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R202W(2)|p.R203W(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTGATGTTCCGGATGGTGACT	0.473																																																3	Substitution - Missense(3)	breast(2)|large_intestine(1)	3											108	104	105					3																	118624539		2203	4300	6503	120107229	SO:0001583	missense	152404			AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"Immunoglobulin superfamily / I-set domain containing"	16669	protein-coding gene	gene with protein product	"cancer/testis antigen 119"	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.607C>T	3.37:g.118624539G>A	ENSP00000377370:p.Arg203Trp		120107229	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Missense_Mutation	SNP	ENST00000393775.2	37	CCDS46891.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.958571	0.74016	.	.	ENSG00000144847	ENST00000425327;ENST00000393775;ENST00000489689;ENST00000354673;ENST00000441144;ENST00000491903	T;T;D;T;D;T	0.84298	3.99;3.99;-1.83;3.99;-1.79;3.99	5.22	4.35	0.52113	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.158514	0.53938	N	0.000045	D	0.88451	0.6440	L	0.56199	1.76	0.44295	D	0.997164	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.71656	0.962;0.96;0.941;0.962;0.974	D	0.88339	0.2973	10	0.72032	D	0.01	.	8.1314	0.31029	0.0761:0.0:0.6718:0.252	.	203;202;202;203;203	C9JBA5;Q5DX21-3;Q5DX21-2;C9JMW0;Q5DX21	.;.;.;.;IGS11_HUMAN	W	202;203;203;202;202;203	ENSP00000406092:R202W;ENSP00000377370:R203W;ENSP00000420486:R203W;ENSP00000346700:R202W;ENSP00000401240:R202W;ENSP00000417413:R203W	ENSP00000346700:R202W	R	-	1	2	IGSF11	120107229	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.290000	0.59019	1.573000	0.49748	0.655000	0.94253	CGG		0.473	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2			A	118624539	G	A	118624539	3	1	4	1	0	0	0	0	1	0	0	0	7619	1115	39	1	700	1	IGSF11	3	118624539	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	5294605	118624539	79397891	6	332										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121411009	121411009	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gcagttcagcaatagctactTggattgcctcttccttgcca	8	12	2	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr3:121411009T>C	ENST00000340645.5	-	14	7312	c.7187A>G	c.(7186-7188)cAa>cGa	p.Q2396R	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q2401R	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2396					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.Q2396R(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AATAGCTACTTGGATTGCCTC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											85	86	86					3																	121411009		2203	4300	6503	122893699	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7187A>G	3.37:g.121411009T>C	ENSP00000341848:p.Gln2396Arg		122893699	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	9.799	1.179999	0.21787	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.14144	2.53;2.53	5.9	4.7	0.59300	.	0.343560	0.25324	N	0.031487	T	0.15565	0.0375	L	0.44542	1.39	0.22982	N	0.998477	P;D;D	0.53312	0.949;0.958;0.959	P;P;B	0.53649	0.461;0.731;0.331	T	0.17684	-1.0361	10	0.16896	T	0.51	.	4.3299	0.11059	0.2141:0.0931:0.0:0.6928	.	2401;2401;2396	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	R	2396;2401	ENSP00000341848:Q2396R;ENSP00000377275:Q2401R	ENSP00000341848:Q2396R	Q	-	2	0	GOLGB1	122893699	0.001000	0.12720	1.000000	0.80357	0.790000	0.44656	0.872000	0.28037	2.254000	0.74563	0.460000	0.39030	CAA		0.423	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121411009	T	C	121411009	3	2	4	1	0	0	0	0	1	0	0	0	6585	1812	63	4	2628	4	GOLGB1	3	121411009	Missense_Mutation	SNP	T	TCGA-AF-2692-01A-01W-0831-10	2786470	121411009	76611421	7	333										
CHCHD6	84303	hgsc.bcm.edu	37	chr3	126676391	126676391	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cgctgcgtgagcgccgcccaCaaggtaaggccttgcctgcc	13	16	0	1	rs1071658		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr3:126676391C>T	ENST00000290913.3	+	7	792	c.699C>T	c.(697-699)caC>caT	p.H233H	CHCHD6_ENST00000508789.1_Silent_p.H234H	NM_032343.2	NP_115719.1	Q9BRQ6	MIC25_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 6	233					cellular response to DNA damage stimulus (GO:0006974)|cristae formation (GO:0042407)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.H233H(1)		endometrium(2)|large_intestine(3)|lung(3)	8						GCGCCGCCCACAAGGTAAGGC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											32	23	26					3																	126676391		2193	4291	6484	128159081	SO:0001819	synonymous_variant	84303			BC006123	CCDS3041.1	3q21.3	2012-04-17			ENSG00000159685	ENSG00000159685		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28184	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 23", "coiled-coil-helix cristae morphology 1"	615634				17624330, 22228767	Standard	NM_032343		Approved	MGC13016, PPP1R23, CHCM1	uc003ejf.2	Q9BRQ6	OTTHUMG00000159601	ENST00000290913.3:c.699C>T	3.37:g.126676391C>T			128159081	D6R9U0|D6RIB4|H8Y0Y7	Silent	SNP	ENST00000290913.3	37	CCDS3041.1	.	.	.	.	.	.	.	.	.	.	C	6.701	0.497937	0.12762	.	.	ENSG00000159685	ENST00000513253	.	.	.	4.22	2.08	0.27032	.	.	.	.	.	T	0.54224	0.1845	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50857	-0.8778	4	.	.	.	-9.0088	7.1958	0.25851	0.1676:0.5365:0.2959:0.0	.	.	.	.	I	164	.	.	T	+	2	0	CHCHD6	128159081	0.995000	0.38212	0.994000	0.49952	0.667000	0.39255	0.454000	0.21827	1.914000	0.55421	0.467000	0.42956	ACA		0.602	CHCHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356432.1	NM_032343		T	126676391	C	T	126676391	2	4	4	1	0	0	0	0	0	0	0	1	3326	477	17	3		3	CHCHD6	3	126676391	Silent	SNP	C	TCGA-AF-2692-01A-01W-0831-10	5265382	126676391	71346039	8	334										
MTTP	4547	hgsc.bcm.edu	37	chr4	100532497	100532497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gtgtgtcatcaggtagtcccCgttcggcatctacttacagc	10	12	3	0	rs148696330		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr4:100532497C>T	ENST00000265517.5	+	14	2079	c.1876C>T	c.(1876-1878)Cgt>Tgt	p.R626C	MTTP_ENST00000511045.1_Missense_Mutation_p.R653C|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.R626C			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	626	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.R626C(1)|p.R626S(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	AGGTAGTCCCCGTTCGGCATC	0.443																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4						C	CYS/ARG	0,4406		0,0,2203	229	215	220		1876	4.7	0.1	4	dbSNP_134	220	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MTTP	NM_000253.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	626/895	100532497	1,13005	2203	4300	6503	100751520	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1876C>T	4.37:g.100532497C>T	ENSP00000265517:p.Arg626Cys		100751520	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345403	0.41498	0.0	1.16E-4	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.62788	-0.0;0.01;0.01	5.62	4.7	0.59300	Lipid transport protein, N-terminal (1);	0.300723	0.38548	N	0.001652	T	0.35422	0.0931	N	0.08118	0	0.09310	N	0.999999	P;D	0.56968	0.807;0.978	B;B	0.36989	0.238;0.232	T	0.26849	-1.0091	10	0.56958	D	0.05	-29.3378	8.1716	0.31258	0.0:0.6198:0.2805:0.0997	.	653;626	E9PBP6;P55157	.;MTP_HUMAN	C	653;626;626	ENSP00000427679:R653C;ENSP00000400821:R626C;ENSP00000265517:R626C	ENSP00000265517:R626C	R	+	1	0	MTTP	100751520	0.017000	0.18338	0.062000	0.19696	0.003000	0.03518	1.337000	0.33862	1.229000	0.43630	0.655000	0.94253	CGT		0.443	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			T	100532497	C	T	100532497	3	4	4	1	0	0	0	0	1	0	0	0	9994	652	23	1	1930	1	MTTP	4	100532497	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		100532497	90621779	9	335										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9122872	9122872	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cgacagaggcaggatcccacGgcgctgccatctgtgtgcgt	14	13	1	1			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:9122872G>A	ENST00000382496.5	-	14	2342	c.1677C>T	c.(1675-1677)gcC>gcT	p.A559A		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	559	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.A559A(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						AGGATCCCACGGCGCTGCCAT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	5											59	61	60					5																	9122872		2203	4300	6503	9175872	SO:0001819	synonymous_variant	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1677C>T	5.37:g.9122872G>A			9175872	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																				0.632	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			A	9122872	G	A	9122872	2	1	4	1	0	0	0	0	0	0	0	1	14074	1103	39	1		1	SEMA5A	5	9122872	Silent	SNP	G	TCGA-AF-2692-01A-01W-0831-10		9122872	171792388	10	336										
AGXT2	64902	hgsc.bcm.edu	37	chr5	35014171	35014171	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	acaatgtcaggcaggacatcGtgggtttggaagccccagaa	13	9	1	1	rs116605914	byFrequency	TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:35014171G>A	ENST00000231420.6	-	10	1217	c.1017C>T	c.(1015-1017)caC>caT	p.H339H		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	339					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)	p.H339H(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	GCAGGACATCGTGGGTTTGGA	0.507													G|||	3	0.000599042	8e-04	0	5008	,	,		19243	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						G		1,4405	2.1+/-5.4	0,1,2202	145	122	130		1017	-8.9	0	5	dbSNP_132	130	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	AGXT2	NM_031900.3		0,28,6475	AA,AG,GG		0.314,0.0227,0.2153		339/515	35014171	28,12978	2203	4300	6503	35049928	SO:0001819	synonymous_variant	64902			AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"beta-alanine-pyruvate aminotransferase", "beta-ALAAT II"	612471	"alanine-glyoxylate aminotransferase 2"			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.1017C>T	5.37:g.35014171G>A			35049928	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Silent	SNP	ENST00000231420.6	37	CCDS3908.1																																																																																				0.507	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900		A	35014171	G	A	35014171	2	1	4	1	0	0	0	0	0	0	0	1	405	1136	40	1		1	AGXT2	5	35014171	Silent	SNP	G	TCGA-AF-2692-01A-01W-0831-10	25891299	35014171	145901089	11	337										
APC	324	hgsc.bcm.edu	37	chr5	112173429	112173429	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gctcaagaacctcattcattCaaagcacaaaatgattgcta	5	10	4	2	rs137854570		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:112173429C>G	ENST00000457016.1	+	16	2518	c.2138C>G	c.(2137-2139)tCa>tGa	p.S713*	APC_ENST00000257430.4_Nonsense_Mutation_p.S713*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.S713*			P25054	APC_HUMAN	adenomatous polyposis coli	713	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S713*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCATTCATTCAAAGCACAAA	0.448		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5	GRCh37	CM910032	APC	M	rs137854570						109	100	103					5																	112173429		2202	4300	6502	112201328	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2138C>G	5.37:g.112173429C>G	ENSP00000413133:p.Ser713*		112201328	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.146713	0.97324	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.17	6.17	0.99709	.	0.058606	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.279	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	713;695;713;713;713	.	ENSP00000257430:S713X	S	+	2	0	APC	112201328	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCA		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173429	C	G	112173429	4	3	4	1	0	0	0	0	0	1	0	0	763	838	29	5	2196	5	APC	5	112173429	Nonsense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	77159258	112173429	68741831	12	338										
ZNF608	57507	hgsc.bcm.edu	37	chr5	124080180	124080180	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	aggtgctggtgctggtactaTtgctgtttgggttgccgctg	16	7	0	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:124080180T>C	ENST00000306315.5	-	1	938	c.503A>G	c.(502-504)aAt>aGt	p.N168S	ZNF608_ENST00000504926.1_5'UTR	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	168							metal ion binding (GO:0046872)	p.N168S(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		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)		GCTGGTACTATTGCTGTTTGG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	5											48	53	51					5																	124080180		2203	4300	6503	124108079	SO:0001583	missense	57507			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.503A>G	5.37:g.124080180T>C	ENSP00000307746:p.Asn168Ser		124108079	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.746876	0.00669	.	.	ENSG00000168916	ENST00000306315;ENST00000509799;ENST00000513986	T	0.42131	0.98	4.76	0.788	0.18601	.	0.657055	0.14012	N	0.347362	T	0.24044	0.0582	L	0.29908	0.895	0.34397	D	0.694884	B	0.02656	0.0	B	0.06405	0.002	T	0.33854	-0.9852	10	0.07990	T	0.79	-3.4663	7.2493	0.26140	0.0:0.0741:0.2745:0.6514	.	168	Q9ULD9	ZN608_HUMAN	S	168	ENSP00000307746:N168S	ENSP00000307746:N168S	N	-	2	0	ZNF608	124108079	0.982000	0.34865	0.039000	0.18376	0.129000	0.20672	0.749000	0.26320	-0.034000	0.13713	-0.313000	0.08912	AAT		0.622	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		C	124080180	T	C	124080180	3	2	4	1	0	0	0	0	1	0	0	0	18073	1493	52	4	4071	4	ZNF608	5	124080180	Missense_Mutation	SNP	T	TCGA-AF-2692-01A-01W-0831-10	11906751	124080180	56835080	13	339										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202400	140202400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ggatgtgaatgataatacccCagagatggccataaccaccc	9	11	0	3			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:140202400C>T	ENST00000529859.1	+	1	1040	c.1040C>T	c.(1039-1041)cCa>cTa	p.P347L	PCDHA5_ENST00000529619.1_Missense_Mutation_p.P347L|PCDHA5_ENST00000378126.3_Missense_Mutation_p.P347L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	347	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.P347L(2)|p.P347Q(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATAATACCCCAGAGATGGCC	0.453																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	5											80	74	76					5																	140202400		2203	4300	6503	140182584	SO:0001583	missense	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1040C>T	5.37:g.140202400C>T	ENSP00000436557:p.Pro347Leu		140182584	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969672	0.74246	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	D;D;D	0.88124	-2.34;-2.34;-2.34	3.97	3.97	0.46021	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96950	0.9004	H	0.99900	4.915	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99441	1.0938	9	0.87932	D	0	.	16.4	0.83637	0.0:1.0:0.0:0.0	.	347;347;347	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	L	347	ENSP00000433416:P347L;ENSP00000436557:P347L;ENSP00000367366:P347L	ENSP00000367366:P347L	P	+	2	0	PCDHA5	140182584	1.000000	0.71417	0.417000	0.26559	0.986000	0.74619	7.812000	0.86109	1.900000	0.55004	0.655000	0.94253	CCA		0.453	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140202400	C	T	140202400	3	4	4	1	0	0	0	0	1	0	0	0	11558	594	21	3	1042	3	PCDHA5	5	140202400	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	16122220	140202400	40712860	14	340										
UNC5A	90249	hgsc.bcm.edu	37	chr5	176295869	176295869	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gggagcacagcctggtggtgCgacaggcccgccttgctgac	16	13	0	1			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr5:176295869C>T	ENST00000329542.4	+	5	899	c.625C>T	c.(625-627)Cga>Tga	p.R209*	UNC5A_ENST00000261961.3_Nonsense_Mutation_p.R169*	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	209	Ig-like C2-type.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R209*(1)		endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	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)			CCTGGTGGTGCGACAGGCCCG	0.662																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											91	69	76					5																	176295869		2203	4299	6502	176228475	SO:0001587	stop_gained	90249			AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.625C>T	5.37:g.176295869C>T	ENSP00000332737:p.Arg209*		176228475	B2RXE6|Q8TF26|Q96GP4	Nonsense_Mutation	SNP	ENST00000329542.4	37	CCDS34299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.000354|8.000354	0.98602|0.98602	.|.	.|.	ENSG00000113763|ENSG00000113763	ENST00000509580|ENST00000329542;ENST00000261961	.|.	.|.	.|.	4.52|4.52	4.52|4.52	0.55395|0.55395	.|.	.|0.095070	.|0.45361	.|D	.|0.000370	T|.	0.26376|.	0.0644|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.27839|.	-1.0062|.	3|.	.|0.02654	.|T	.|1	-14.733|-14.733	11.3407|11.3407	0.49531|0.49531	0.3186:0.6814:0.0:0.0|0.3186:0.6814:0.0:0.0	.|.	.|.	.|.	.|.	V|X	174|209;169	.|.	.|ENSP00000261961:R169X	A|R	+|+	2|1	0|2	UNC5A|UNC5A	176228475|176228475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.176000|2.176000	0.42500|0.42500	2.068000|2.068000	0.61886|0.61886	0.561000|0.561000	0.74099|0.74099	GCG|CGA		0.662	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		T	176295869	C	T	176295869	4	4	4	1	0	0	0	0	0	1	0	0	17031	760	27	1	643	1	UNC5A	5	176295869	Nonsense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	36093469	176295869	4619391	15	341										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31779179	31779179	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gacatgtcgttctccttgacCtcctttatctaaaccatagg	6	12	2	1			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr6:31779179C>A	ENST00000375654.4	-	2	760	c.571G>T	c.(571-573)Ggt>Tgt	p.G191C	HSPA1L_ENST00000417199.3_Missense_Mutation_p.G191C	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	191					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)	p.G191C(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TCTCCTTGACCTCCTTTATCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	89	92					6																	31779179		2203	4300	6503	31887158	SO:0001583	missense	3305			D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.571G>T	6.37:g.31779179C>A	ENSP00000364805:p.Gly191Cys		31887158	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	37	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	C	6.318	0.426862	0.11987	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653;ENST00000424494	T;T	0.01034	5.42;5.42	4.66	1.59	0.23543	.	.	.	.	.	T	0.02688	0.0081	H	0.95365	3.66	0.09310	N	1	D	0.55172	0.97	P	0.61658	0.892	T	0.22521	-1.0214	9	0.48119	T	0.1	.	8.2366	0.31629	0.0:0.697:0.0:0.303	.	191	P34931	HS71L_HUMAN	C	191;191;136;81	ENSP00000364805:G191C;ENSP00000387691:G191C	ENSP00000364804:G136C	G	-	1	0	HSPA1L	31887158	0.191000	0.23288	0.022000	0.16811	0.658000	0.38924	1.678000	0.37586	0.548000	0.28955	0.460000	0.39030	GGT		0.453	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			A	31779179	C	A	31779179	3	1	4	1	0	0	0	0	1	0	0	0	7431	681	24	2	1358	2	HSPA1L	6	31779179	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		31779179	139335888	16	342										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43306183	43306187	+	Frame_Shift_Del	DEL	TACTT	TACTT	-													0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	tgtggactcaatttgatcacTactttacttggagtttcact							TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	TACTT	TACTT	TACTT	-	TACTT	TACTT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr6:43306183_43306187delTACTT	ENST00000361428.2	-	10	5626_5630	c.5549_5553delAAGTA	c.(5548-5553)aaagtafs	p.KV1850fs	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1850					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.K1850fs*24(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			ATTTGATCACTACTTTACTTGGAGT	0.4																																																1	Deletion - Frameshift(1)	large_intestine(1)	6																																								43414165	SO:0001589	frameshift_variant	24149			AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.5549_5553delAAGTA	6.37:g.43306188_43306192delTACTT	ENSP00000354964:p.Lys1850fs		43414161	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	37	CCDS4895.2																																																																																				0.4	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		-	43306187	TACTT	-	43306183	7	5	4	1	0	1	0	1	0	0	0	0	17875	1509	53	0	1290	0	ZNF318	6	43306183	Frame_Shift_Del	DEL	TACTT	TCGA-AF-2692-01A-01W-0831-10	11527004	43306183	127808884	17	343										
TAS2R5	54429	hgsc.bcm.edu	37	chr7	141490397	141490397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ccagagcagccgttggcttcGctatcttagtatcttctggg	11	11	3	1	rs142235954		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr7:141490397G>A	ENST00000247883.4	+	1	381	c.236G>A	c.(235-237)cGc>cAc	p.R79H		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	79					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.R79H(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					CGTTGGCTTCGCTATCTTAGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	79	76	77		236	-7.9	0	7	dbSNP_134	77	0,8600		0,0,4300	no	missense	TAS2R5	NM_018980.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	79/300	141490397	1,13005	2203	4300	6503	141136866	SO:0001583	missense	54429			AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.236G>A	7.37:g.141490397G>A	ENSP00000247883:p.Arg79His		141136866	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	.	.	.	.	.	.	.	.	.	.	G	7.008	0.556251	0.13436	2.27E-4	0.0	ENSG00000127366	ENST00000247883	T	0.00824	5.65	4.46	-7.93	0.01156	.	.	.	.	.	T	0.00754	0.0025	N	0.25890	0.77	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.45702	-0.9243	9	0.51188	T	0.08	.	6.9954	0.24779	0.6225:0.0:0.1491:0.2284	.	79	Q9NYW4	TA2R5_HUMAN	H	79	ENSP00000247883:R79H	ENSP00000247883:R79H	R	+	2	0	TAS2R5	141136866	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-1.024000	0.03603	-1.779000	0.01280	-0.291000	0.09656	CGC		0.507	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1			A	141490397	G	A	141490397	3	1	4	1	0	0	0	0	1	0	0	0	15622	1087	38	1	238	1	TAS2R5	7	141490397	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10		141490397	17648266	18	344										
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8747632	8747632	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ttagaacagagaatgtgcacGgtgtagtgcagtccaggcca	13	8	0	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr8:8747632G>C	ENST00000276282.6	-	1	3523	c.2937C>G	c.(2935-2937)acC>acG	p.T979T		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	979								p.T979T(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GAATGTGCACGGTGTAGTGCA	0.488																																					Melanoma(103;1201 2045 17515 28966)											1	Substitution - coding silent(1)	large_intestine(1)	8											113	99	104					8																	8747632		2203	4300	6503	8785042	SO:0001819	synonymous_variant	9258			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2937C>G	8.37:g.8747632G>C			8785042	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																				0.488	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8747632	G	C	8747632	2	2	4	1	0	0	0	0	0	0	0	1	9551	1103	39	5		5	MFHAS1	8	8747632	Silent	SNP	G	TCGA-AF-2692-01A-01W-0831-10		8747632	137616390	19	345										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114901049	114901050	+	Frame_Shift_Ins	INS	-	-	A													0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ggaaacccacctccacacttINSaccagccgacgtagacccca							TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr10:114901049_114901050insA	ENST00000355995.4	+	6	1166_1167	c.659_660insA	c.(658-663)ttaccafs	p.P221fs	TCF7L2_ENST00000534894.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000543371.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000369397.4_Frame_Shift_Ins_p.P198fs|TCF7L2_ENST00000536810.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000352065.5_Frame_Shift_Ins_p.P198fs|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000545257.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000349937.2_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000355717.4_Frame_Shift_Ins_p.P245fs|TCF7L2_ENST00000538897.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000369395.1_Frame_Shift_Ins_p.P246fs			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	221	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P221fs*107(1)|p.P198fs*107(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCTCCACACTTACCAGCCGACG	0.589			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	2	Insertion - Frameshift(2)	large_intestine(2)	10																																								114891040	SO:0001589	frameshift_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.660dupA	10.37:g.114901050_114901050dupA	ENSP00000348274:p.Pro221fs		114891039	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Ins	INS	ENST00000355995.4	37																																																																																					0.589	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114901050	-	A	114901049	7	5	4	1	0	1	1	0	0	0	0	0	15737	1764	61	0	826	0	TCF7L2	10	114901049	Frame_Shift_Ins	INS	-	TCGA-AF-2692-01A-01W-0831-10		114901049	20633698	20	346										
C10orf120	399814	hgsc.bcm.edu	37	chr10	124459193	124459193	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ggggcttgatcctgaaaggaAgagttggtattaaatattct	12	4	1	3			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr10:124459193A>T	ENST00000329446.4	-	1	145	c.114T>A	c.(112-114)tcT>tcA	p.S38S		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	38								p.S38S(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				CCTGAAAGGAAGAGTTGGTAT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	10											126	113	117					10																	124459193		2203	4300	6503	124449183	SO:0001819	synonymous_variant	399814				CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.114T>A	10.37:g.124459193A>T			124449183	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	.	.	.	.	.	.	.	.	.	.	A	4.833	0.154868	0.09236	.	.	ENSG00000183559	ENST00000432000	.	.	.	4.29	-0.95	0.10372	.	.	.	.	.	T	0.30947	0.0781	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30650	-0.9971	4	.	.	.	-0.0053	7.499	0.27507	0.5942:0.0:0.4058:0.0	.	.	.	.	H	31	.	.	L	-	2	0	C10orf120	124449183	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.401000	0.07232	-0.268000	0.09312	-0.290000	0.09829	CTT		0.443	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912		T	124459193	A	T	124459193	2	4	4	1	0	0	0	0	0	0	0	1	1594	59	3	5		5	C10orf120	10	124459193	Silent	SNP	A	TCGA-AF-2692-01A-01W-0831-10	9558144	124459193	11075554	21	347										
MRGPRX2	117194	hgsc.bcm.edu	37	chr11	19076997	19076997	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	acatctccggggtgccctgaCggaagcatccttcactgtga	11	13	2	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:19076997C>T	ENST00000329773.2	-	2	1040	c.953G>A	c.(952-954)cGt>cAt	p.R318H		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	318					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.R318H(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						GGTGCCCTGACGGAAGCATCC	0.557																																					GBM(198;1966 2199 4849 37227 49954)											1	Substitution - Missense(1)	large_intestine(1)	11											64	65	65					11																	19076997		2199	4293	6492	19033573	SO:0001583	missense	117194				CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"GPCR / Class A : Orphans"	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.953G>A	11.37:g.19076997C>T	ENSP00000333800:p.Arg318His		19033573	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	.	.	.	.	.	.	.	.	.	.	.	11.30	1.598442	0.28445	.	.	ENSG00000183695	ENST00000329773	T	0.06218	3.33	4.71	2.81	0.32909	.	1.118960	0.06776	N	0.784366	T	0.05502	0.0145	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38001	-0.9681	10	0.49607	T	0.09	.	7.7248	0.28753	0.0:0.19:0.6313:0.1787	.	318	Q96LB1	MRGX2_HUMAN	H	318	ENSP00000333800:R318H	ENSP00000333800:R318H	R	-	2	0	MRGPRX2	19033573	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.732000	0.04904	0.882000	0.36016	-0.171000	0.13296	CGT		0.557	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030		T	19076997	C	T	19076997	3	4	4	1	0	0	0	0	1	0	0	0	9797	536	19	1	43	1	MRGPRX2	11	19076997	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		19076997	115929519	22	348										
E2F8	79733	hgsc.bcm.edu	37	chr11	19251430	19251430	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cccaggggctggatgagggaCggtgctgtcagctccatctc	15	12	2	1	rs140189421	byFrequency	TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:19251430C>T	ENST00000527884.1	-	10	1696	c.1464G>A	c.(1462-1464)ccG>ccA	p.P488P	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Silent_p.P488P	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	488					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P488P(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGATGAGGGACGGTGCTGTCA	0.592													C|||	5	0.000998403	0	0.0014	5008	,	,		16089	0		0.003	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	11						C		4,4394	8.1+/-20.4	0,4,2195	123	131	128		1464	-5.9	0	11	dbSNP_134	128	17,8569	13.3+/-46.6	0,17,4276	no	coding-synonymous	E2F8	NM_024680.2		0,21,6471	TT,TC,CC		0.198,0.091,0.1617		488/868	19251430	21,12963	2199	4293	6492	19208006	SO:0001819	synonymous_variant	79733				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1464G>A	11.37:g.19251430C>T			19208006	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Silent	SNP	ENST00000527884.1	37	CCDS7849.1																																																																																				0.592	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		T	19251430	C	T	19251430	2	4	4	1	0	0	0	0	0	0	0	1	4884	523	19	1		1	E2F8	11	19251430	Silent	SNP	C	TCGA-AF-2692-01A-01W-0831-10	174433	19251430	115755086	23	349										
WT1	7490	hgsc.bcm.edu	37	chr11	32421575	32421575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gttgtgtggttatcgctctcGtaccctgtgctgtggctgca	13	10	1	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:32421575G>A	ENST00000379079.2	-	6	654	c.381C>T	c.(379-381)taC>taT	p.Y127Y	WT1_ENST00000448076.3_Silent_p.Y339Y|WT1_ENST00000332351.3_Silent_p.Y339Y|WT1_ENST00000530998.1_Silent_p.Y110Y	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	271					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.E272fs*5(1)|p.Y271Y(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TATCGCTCTCGTACCCTGTGC	0.522			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	2	Substitution - coding silent(1)|Insertion - Frameshift(1)	large_intestine(1)|kidney(1)	11	GRCh37	CM952245	WT1	M							249	210	223					11																	32421575		2202	4299	6501	32378151	SO:0001819	synonymous_variant	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.381C>T	11.37:g.32421575G>A			32378151	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000379079.2	37	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	G	7.368	0.626271	0.14257	.	.	ENSG00000184937	ENST00000527882	.	.	.	5.98	-6.17	0.02091	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2127	0.86935	0.6937:0.0:0.3063:0.0	.	.	.	.	X	30	.	.	R	-	1	2	WT1	32378151	0.965000	0.33210	0.790000	0.31976	0.796000	0.44982	0.107000	0.15375	-1.253000	0.02488	0.650000	0.86243	CGA		0.522	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		A	32421575	G	A	32421575	2	1	4	1	0	0	0	0	0	0	0	1	17448	1140	40	1		1	WT1	11	32421575	Silent	SNP	G	TCGA-AF-2692-01A-01W-0831-10	13170145	32421575	102584941	24	350										
MS4A5	64232	hgsc.bcm.edu	37	chr11	60197173	60197173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ttcaagcaccgcacacagtcCggtgtttctggtatttcctc	8	13	2	0	rs34799130	byFrequency	TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:60197173C>T	ENST00000300190.2	+	1	112	c.26C>T	c.(25-27)cCg>cTg	p.P9L	MS4A5_ENST00000534071.1_3'UTR	NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	9						integral component of membrane (GO:0016021)		p.P9L(1)		large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						GCACACAGTCCGGTGTTTCTG	0.423													C|||	74	0.0147764	0.0295	0.0043	5008	,	,		19704	0.002		0	False		,,,				2504	0.0307															1	Substitution - Missense(1)	large_intestine(1)	11						C	LEU/PRO	116,4290	89.2+/-127.9	2,112,2089	117	117	117		26	4.7	0.2	11	dbSNP_126	117	1,8599		0,1,4299	yes	missense	MS4A5	NM_023945.2	98	2,113,6388	TT,TC,CC		0.0116,2.6328,0.8996	probably-damaging	9/201	60197173	117,12889	2203	4300	6503	59953749	SO:0001583	missense	64232			AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.26C>T	11.37:g.60197173C>T	ENSP00000300190:p.Pro9Leu		59953749	Q9BZH1	Missense_Mutation	SNP	ENST00000300190.2	37	CCDS7987.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	C	22.0	4.236109	0.79800	0.026328	1.16E-4	ENSG00000166930	ENST00000300190	T	0.13307	2.6	4.66	4.66	0.58398	.	0.773994	0.12613	N	0.453732	T	0.10337	0.0253	L	0.36672	1.1	0.20489	N	0.999891	D	0.89917	1.0	D	0.70227	0.968	T	0.03008	-1.1083	10	0.66056	D	0.02	-11.3906	13.2445	0.60016	0.0:1.0:0.0:0.0	rs34799130	9	Q9H3V2	MS4A5_HUMAN	L	9	ENSP00000300190:P9L	ENSP00000300190:P9L	P	+	2	0	MS4A5	59953749	0.119000	0.22226	0.158000	0.22627	0.662000	0.39071	3.127000	0.50484	2.578000	0.87016	0.467000	0.42956	CCG		0.423	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1			T	60197173	C	T	60197173	3	4	4	1	0	0	0	0	1	0	0	0	9893	652	23	1	28	1	MS4A5	11	60197173	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	27775598	60197173	74809343	25	351										
USP28	57646	hgsc.bcm.edu	37	chr11	113674554	113674554	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gagttctaggcctgttaggaGatacacagacacttttcgga	11	8	1	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:113674554G>A	ENST00000003302.4	-	22	2772	c.2704C>T	c.(2704-2706)Ctc>Ttc	p.L902F	USP28_ENST00000545540.1_Missense_Mutation_p.L745F|USP28_ENST00000544967.1_Missense_Mutation_p.L578F|USP28_ENST00000260188.5_Missense_Mutation_p.L870F	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	902					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.L902F(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		CCTGTTAGGAGATACACAGAC	0.353																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											1	Substitution - Missense(1)	large_intestine(1)	11											103	102	102					11																	113674554		2201	4296	6497	113179764	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2704C>T	11.37:g.113674554G>A	ENSP00000003302:p.Leu902Phe		113179764	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815807	0.90790	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	T;T;T;T	0.58210	0.86;0.94;0.35;0.94	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.69378	0.3104	L	0.47016	1.485	0.80722	D	1	D;D;D	0.89917	1.0;0.974;1.0	D;P;D	0.91635	0.998;0.677;0.999	T	0.69281	-0.5186	10	0.72032	D	0.01	-15.1787	20.2617	0.98447	0.0:0.0:1.0:0.0	.	745;902;578	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	F	902;870;578;745	ENSP00000003302:L902F;ENSP00000260188:L870F;ENSP00000442431:L578F;ENSP00000444991:L745F	ENSP00000003302:L902F	L	-	1	0	USP28	113179764	1.000000	0.71417	0.962000	0.40283	0.982000	0.71751	7.400000	0.79949	2.793000	0.96121	0.655000	0.94253	CTC		0.353	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			A	113674554	G	A	113674554	3	1	4	1	0	0	0	0	1	0	0	0	17098	942	33	3	545	3	USP28	11	113674554	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	53477381	113674554	21331962	26	352										
CXCR5	643	hgsc.bcm.edu	37	chr11	118764840	118764840	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	agtcagccaaggccatcacaAcaactccctgccacgttgca	7	16	2	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:118764840A>T	ENST00000292174.4	+	2	763	c.587A>T	c.(586-588)aAc>aTc	p.N196I	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	196					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)	p.N196I(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GGCCATCACAACAACTCCCTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11											75	62	67					11																	118764840		2200	4295	6495	118270050	SO:0001583	missense	643			X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.587A>T	11.37:g.118764840A>T	ENSP00000292174:p.Asn196Ile		118270050	Q14811	Missense_Mutation	SNP	ENST00000292174.4	37	CCDS8402.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.559880	0.27827	.	.	ENSG00000160683	ENST00000292174	T	0.72615	-0.67	3.96	3.96	0.45880	GPCR, rhodopsin-like superfamily (1);	0.513580	0.17725	U	0.164100	T	0.69106	0.3074	L	0.29908	0.895	0.43924	D	0.996577	D	0.71674	0.998	D	0.68943	0.961	T	0.63625	-0.6595	10	0.18710	T	0.47	.	6.153	0.20322	0.8383:0.0:0.1617:0.0	.	196	P32302	CXCR5_HUMAN	I	196	ENSP00000292174:N196I	ENSP00000292174:N196I	N	+	2	0	CXCR5	118270050	0.626000	0.27120	0.731000	0.30826	0.181000	0.23173	4.114000	0.57858	1.649000	0.50652	0.260000	0.18958	AAC		0.567	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		T	118764840	A	T	118764840	3	4	4	1	0	0	0	0	1	0	0	0	4100	43	2	5	593	5	CXCR5	11	118764840	Missense_Mutation	SNP	A	TCGA-AF-2692-01A-01W-0831-10	5090286	118764840	16241676	27	353										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294082	124294082	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ctttggatctgccctctgcaGaaggaatacagaggatgttg	12	8	2	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr11:124294082G>T	ENST00000356130.3	-	1	707	c.686C>A	c.(685-687)tCt>tAt	p.S229Y		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S229Y(1)		endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GCCCTCTGCAGAAGGAATACA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	72	74					11																	124294082		2201	4299	6500	123799292	SO:0001583	missense	283162			AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.686C>A	11.37:g.124294082G>T	ENSP00000348449:p.Ser229Tyr		123799292	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	g	15.71	2.913426	0.52439	.	.	ENSG00000198657	ENST00000356130	T	0.00337	8.05	4.14	4.14	0.48551	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000088	T	0.01421	0.0046	H	0.96015	3.755	0.29995	N	0.816578	D	0.89917	1.0	D	0.79108	0.992	T	0.02925	-1.1093	10	0.72032	D	0.01	.	17.3176	0.87228	0.0:0.0:1.0:0.0	.	229	Q96RC9	OR8B4_HUMAN	Y	229	ENSP00000348449:S229Y	ENSP00000348449:S229Y	S	-	2	0	OR8B4	123799292	0.055000	0.20627	0.995000	0.50966	0.901000	0.52897	2.163000	0.42377	2.610000	0.88304	0.655000	0.94253	TCT		0.438	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		T	124294082	G	T	124294082	3	4	4	1	0	0	0	0	1	0	0	0	11260	942	33	2	245	2	OR8B4	11	124294082	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	5529242	124294082	10712434	28	354										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	4	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		25398284	108453611	29	355										
CCDC91	55297	hgsc.bcm.edu	37	chr12	28459710	28459710	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cacactcatctggatatctcActttttccattgggtttaac	5	11	3	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr12:28459710A>G	ENST00000545336.1	+	8	722	c.303A>G	c.(301-303)tcA>tcG	p.S101S	CCDC91_ENST00000306172.5_Silent_p.S71S|CCDC91_ENST00000539107.1_Silent_p.S101S|CCDC91_ENST00000381256.1_Silent_p.S101S|CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000381259.1_Silent_p.S101S			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	101					protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S101S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TGGATATCTCACTTTTTCCAT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	12											85	88	87					12																	28459710		2203	4299	6502	28350977	SO:0001819	synonymous_variant	55297			AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"GGA binding partner"					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.303A>G	12.37:g.28459710A>G			28350977	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Silent	SNP	ENST00000545336.1	37	CCDS8716.1																																																																																				0.348	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318		G	28459710	A	G	28459710	2	3	4	1	0	0	0	0	0	0	0	1	2876	146	6	4		4	CCDC91	12	28459710	Silent	SNP	A	TCGA-AF-2692-01A-01W-0831-10	3061426	28459710	105392185	30	356										
C14orf106	55320	hgsc.bcm.edu	37	chr14	45693604	45693604	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	tttgttccttttcaaggttaGatatttttattttccggttg	7	5	1	1			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr14:45693604G>A	ENST00000310806.4	-	11	2644	c.2186C>T	c.(2185-2187)tCt>tTt	p.S729F		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	729					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.S729F(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TTCAAGGTTAGATATTTTTAT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	14											68	70	69					14																	45693604		2203	4300	6503	44763354	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2186C>T	14.37:g.45693604G>A	ENSP00000309790:p.Ser729Phe		44763354	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	G	2.872	-0.233674	0.05983	.	.	ENSG00000129534	ENST00000310806	T	0.17528	2.27	5.72	2.88	0.33553	.	0.817444	0.11446	N	0.563318	T	0.14700	0.0355	L	0.36672	1.1	0.09310	N	1	B	0.29805	0.257	B	0.26969	0.075	T	0.17501	-1.0367	10	0.56958	D	0.05	-0.015	10.609	0.45410	0.0735:0.2515:0.675:0.0	.	729	Q6P0N0	M18BP_HUMAN	F	729	ENSP00000309790:S729F	ENSP00000309790:S729F	S	-	2	0	MIS18BP1	44763354	0.138000	0.22547	0.001000	0.08648	0.009000	0.06853	1.657000	0.37366	0.140000	0.18849	-1.872000	0.00552	TCT		0.318	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45693604	G	A	45693604	3	1	4	1	0	0	0	0	1	0	0	0	1742	942	33	3	1240	3	C14orf106	14	45693604	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10		45693604	61655936	31	357										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11725301	11725301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ataagcaatgtgaggaatgaAgtcaagagccagggtctggt	14	5	2	3			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr17:11725301A>G	ENST00000262442.4	+	46	8840	c.8772A>G	c.(8770-8772)gaA>gaG	p.E2924E	DNAH9_ENST00000454412.2_Silent_p.E2924E	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2924	AAA 4. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E2924E(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		TGAGGAATGAAGTCAAGAGCC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	17											84	77	79					17																	11725301		2203	4300	6503	11666026	SO:0001819	synonymous_variant	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.8772A>G	17.37:g.11725301A>G			11666026	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.463	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11725301	A	G	11725301	2	3	4	1	0	0	0	0	0	0	0	1	4619	69	3	4		4	DNAH9	17	11725301	Silent	SNP	A	TCGA-AF-2692-01A-01W-0831-10		11725301	69469909	32	358										
ANKRD40	91369	hgsc.bcm.edu	37	chr17	48777056	48777056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ccccagggggaagcaatggaGgtgagccatctgcagggggt	18	9	1	1	rs185905249		TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr17:48777056G>A	ENST00000285243.6	-	3	751	c.482C>T	c.(481-483)cCt>cTt	p.P161L	Y_RNA_ENST00000364470.1_RNA	NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	161	Pro-rich.							p.P161L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			AAGCAATGGAGGTGAGCCATC	0.592													G|||	1	0.000199681	0	0	5008	,	,		16765	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											59	67	65					17																	48777056		2203	4300	6503	46132055	SO:0001583	missense	91369			BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"Ankyrin repeat domain containing"	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.482C>T	17.37:g.48777056G>A	ENSP00000285243:p.Pro161Leu		46132055	Q96E32	Missense_Mutation	SNP	ENST00000285243.6	37	CCDS11572.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	4.710	0.131969	0.08981	.	.	ENSG00000154945	ENST00000285243	T	0.23950	1.88	4.54	2.55	0.30701	.	0.444056	0.24105	N	0.041517	T	0.11024	0.0269	N	0.12182	0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.12142	-1.0559	10	0.35671	T	0.21	-1.3393	2.6978	0.05140	0.3325:0.0:0.4648:0.2028	.	161	Q6AI12	ANR40_HUMAN	L	161	ENSP00000285243:P161L	ENSP00000285243:P161L	P	-	2	0	ANKRD40	46132055	0.011000	0.17503	0.454000	0.27019	0.236000	0.25371	1.052000	0.30429	1.263000	0.44181	0.650000	0.86243	CCT		0.592	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855		A	48777056	G	A	48777056	3	1	4	1	0	0	0	0	1	0	0	0	669	1000	35	3	636	3	ANKRD40	17	48777056	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	37051755	48777056	32418154	33	359										
SCPEP1	59342	hgsc.bcm.edu	37	chr17	55058472	55058472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ttgactggcccacagaggagGgcaaggaagtatgggattat	15	6	0	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr17:55058472G>A	ENST00000262288.3	+	2	161	c.106G>A	c.(106-108)Ggc>Agc	p.G36S	SCPEP1_ENST00000571898.1_3'UTR|RP5-1107A17.4_ENST00000572877.1_RNA	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	36					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)	p.G36S(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					CACAGAGGAGGGCAAGGAAGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											122	100	107					17																	55058472		2203	4300	6503	52413471	SO:0001583	missense	59342			AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"retinoid inducible serine carboxypeptidase"					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.106G>A	17.37:g.55058472G>A	ENSP00000262288:p.Gly36Ser		52413471	Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	37	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.387829	0.61956	.	.	ENSG00000121064	ENST00000262288	T	0.43688	0.94	5.84	4.87	0.63330	.	0.444283	0.25332	N	0.031426	T	0.33702	0.0872	L	0.51853	1.615	0.34270	D	0.680921	B	0.29378	0.243	B	0.27262	0.078	T	0.43196	-0.9406	10	0.21014	T	0.42	-25.108	8.9092	0.35543	0.08:0.191:0.729:0.0	.	36	Q9HB40	RISC_HUMAN	S	36	ENSP00000262288:G36S	ENSP00000262288:G36S	G	+	1	0	SCPEP1	52413471	0.980000	0.34600	0.957000	0.39632	0.366000	0.29705	1.765000	0.38481	1.482000	0.48325	0.655000	0.94253	GGC		0.488	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626		A	55058472	G	A	55058472	3	1	4	1	0	0	0	0	1	0	0	0	13972	1232	43	3	112	3	SCPEP1	17	55058472	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	6281416	55058472	26136738	34	360										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35661430	35661430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gagaagtttaggactttctgCcgtgccagtgggagaggtca	15	7	2	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chr22:35661430C>T	ENST00000216106.5	+	5	1177	c.1049C>T	c.(1048-1050)gCc>gTc	p.A350V	HMGXB4_ENST00000444518.2_Missense_Mutation_p.A241V	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	350					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)	p.A350V(1)		breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGACTTTCTGCCGTGCCAGTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	22											95	97	96					22																	35661430		2203	4300	6503	33991430	SO:0001583	missense	10042			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1049C>T	22.37:g.35661430C>T	ENSP00000216106:p.Ala350Val		33991430	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	37	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	C	2.139	-0.397253	0.04899	.	.	ENSG00000100281	ENST00000420166;ENST00000444518;ENST00000455359;ENST00000216106	T;T;T;T	0.46063	0.88;2.2;0.89;2.2	5.22	1.98	0.26296	.	1.792470	0.01925	N	0.040780	T	0.28001	0.0690	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.25882	-1.0119	10	0.46703	T	0.11	4.1168	9.2195	0.37368	0.0:0.7812:0.0:0.2188	.	350	Q9UGU5	HMGX4_HUMAN	V	241;241;241;350	ENSP00000401658:A241V;ENSP00000398302:A241V;ENSP00000415500:A241V;ENSP00000216106:A350V	ENSP00000216106:A350V	A	+	2	0	HMGXB4	33991430	0.009000	0.17119	0.000000	0.03702	0.095000	0.18619	2.436000	0.44819	0.347000	0.23924	0.650000	0.86243	GCC		0.512	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		T	35661430	C	T	35661430	3	4	4	1	0	0	0	0	1	0	0	0	7260	739	26	3	1063	3	HMGXB4	22	35661430	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10		35661430	15643136	35	361										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128113	83128113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	ctttgaagaaagattccaagAaaaaaggaggttcatatgca	9	5	1	4			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chrX:83128113A>G	ENST00000329312.4	+	4	434	c.397A>G	c.(397-399)Aaa>Gaa	p.K133E		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	133					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.K132E(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						AGATTCCAAGAAAAAAGGAGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	X											25	22	23					X																	83128113		2195	4296	6491	83014769	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.397A>G	X.37:g.83128113A>G	ENSP00000331556:p.Lys133Glu		83014769	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	5.208	0.223955	0.09863	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.41400	1.0	4.67	0.985	0.19779	.	.	.	.	.	T	0.19525	0.0469	N	0.12746	0.255	0.09310	N	1	B;B	0.19331	0.035;0.035	B;B	0.19391	0.025;0.025	T	0.30707	-0.9969	9	0.08599	T	0.76	-0.2071	5.9568	0.19277	0.6429:0.0:0.3571:0.0	.	133;133	P35663;F5H4V5	CYLC1_HUMAN;.	E	133	ENSP00000331556:K133E	ENSP00000331556:K133E	K	+	1	0	CYLC1	83014769	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.314000	0.19432	-0.020000	0.14032	0.486000	0.48141	AAA		0.323	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		G	83128113	A	G	83128113	3	3	4	1	0	0	0	0	1	0	0	0	4147	247	9	4	411	4	CYLC1	23	83128113	Missense_Mutation	SNP	A	TCGA-AF-2692-01A-01W-0831-10		83128113	72142447	36	362										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96502815	96502815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	cccaagcagaaaatcaacacGataagtttgtggaaaagatg	9	7	1	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chrX:96502815G>A	ENST00000324765.8	+	23	3168	c.2821G>A	c.(2821-2823)Gat>Aat	p.D941N	DIAPH2_ENST00000373049.4_Missense_Mutation_p.D941N|DIAPH2_ENST00000373054.4_Missense_Mutation_p.D937N|DIAPH2_ENST00000373061.3_Missense_Mutation_p.D941N|DIAPH2_ENST00000355827.4_Missense_Mutation_p.D941N			O60879	DIAP2_HUMAN	diaphanous-related formin 2	941	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)	p.D941N(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						AAATCAACACGATAAGTTTGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	X											149	125	133					X																	96502815		2203	4299	6502	96389471	SO:0001583	missense	1730			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2821G>A	X.37:g.96502815G>A	ENSP00000321348:p.Asp941Asn		96389471	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	37	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134506	0.77662	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.66	5.66	0.87406	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.74642	0.3743	M	0.87827	2.91	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79165	-0.1916	10	0.87932	D	0	.	19.0056	0.92849	0.0:0.0:1.0:0.0	.	941;941	O60879;O60879-2	DIAP2_HUMAN;.	N	941;937;941;941;941;948	ENSP00000362152:D941N;ENSP00000362145:D937N;ENSP00000348082:D941N;ENSP00000362140:D941N;ENSP00000321348:D941N	ENSP00000321348:D941N	D	+	1	0	DIAPH2	96389471	1.000000	0.71417	0.963000	0.40424	0.504000	0.33889	9.041000	0.93788	2.523000	0.85059	0.594000	0.82650	GAT		0.353	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		A	96502815	G	A	96502815	3	1	4	1	0	0	0	0	1	0	0	0	4530	1058	37	1	2911	1	DIAPH2	23	96502815	Missense_Mutation	SNP	G	TCGA-AF-2692-01A-01W-0831-10	13374702	96502815	58767745	37	363										
OCRL	4952	hgsc.bcm.edu	37	chrX	128691337	128691337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gggttcagggggactggatcAgagagcgccgctttgaaatc	16	8	2	2			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chrX:128691337A>G	ENST00000371113.4	+	5	439	c.274A>G	c.(274-276)Aga>Gga	p.R92G	OCRL_ENST00000486673.1_3'UTR|OCRL_ENST00000357121.5_Missense_Mutation_p.R92G	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	92	PH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.R92G(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						GGACTGGATCAGAGAGCGCCG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											89	85	86					X																	128691337		2203	4300	6503	128519018	SO:0001583	missense	4952			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.274A>G	X.37:g.128691337A>G	ENSP00000360154:p.Arg92Gly		128519018	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585569	0.28268	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94046	-3.34;-3.34	5.57	1.85	0.25348	.	0.591091	0.17807	N	0.161345	T	0.79724	0.4495	N	0.04508	-0.205	0.25112	N	0.990706	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.66304	-0.5957	10	0.23302	T	0.38	.	3.0202	0.06073	0.5182:0.0:0.2906:0.1913	.	92;92	Q01968-2;Q01968	.;OCRL_HUMAN	G	92	ENSP00000360154:R92G;ENSP00000349635:R92G	ENSP00000349635:R92G	R	+	1	2	OCRL	128519018	0.700000	0.27796	1.000000	0.80357	0.993000	0.82548	0.551000	0.23361	0.241000	0.21283	0.486000	0.48141	AGA		0.428	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128691337	A	G	128691337	3	3	4	1	0	0	0	0	1	0	0	0	10854	180	7	4	292	4	OCRL	23	128691337	Missense_Mutation	SNP	A	TCGA-AF-2692-01A-01W-0831-10	32188522	128691337	26579223	38	364										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138908951	138908951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	3	1	0.923076923076923	4	0.666666666666667	1	1	0	gattgccaacaaacactgtgCgtgtgccaactcgtttctct	8	12	1	0			TCGA-AF-2692-01A-01W-0831-10	TCGA-AF-2692-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	88efe19b-b28e-47c6-a3e2-631755629880	a7cba55c-dc39-41d1-b5fc-a704b5dbb460	g.chrX:138908951C>T	ENST00000327569.3	-	2	166	c.68G>A	c.(67-69)cGc>cAc	p.R23H	ATP11C_ENST00000361648.2_Missense_Mutation_p.R23H|ATP11C_ENST00000370543.1_Missense_Mutation_p.R23H|ATP11C_ENST00000359686.2_Missense_Mutation_p.R23H|ATP11C_ENST00000370557.1_Missense_Mutation_p.R20H	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	23					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R23H(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					AAACACTGTGCGTGTGCCAAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											138	114	122					X																	138908951		2203	4300	6503	138736617	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.68G>A	X.37:g.138908951C>T	ENSP00000332756:p.Arg23His		138736617	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789372	0.90367	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.83216	0.5206	M	0.92691	3.335	0.53005	D	0.999966	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87329	0.2323	10	0.87932	D	0	.	14.6521	0.68805	0.0:1.0:0.0:0.0	.	23;23	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	H	20;23;23;23;23	ENSP00000359588:R20H;ENSP00000355165:R23H;ENSP00000332756:R23H;ENSP00000359574:R23H;ENSP00000352715:R23H	ENSP00000332756:R23H	R	-	2	0	ATP11C	138736617	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.969000	0.76092	2.430000	0.82344	0.544000	0.68410	CGC		0.388	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		T	138908951	C	T	138908951	3	4	4	1	0	0	0	0	1	0	0	0	1122	768	27	1	3509	1	ATP11C	23	138908951	Missense_Mutation	SNP	C	TCGA-AF-2692-01A-01W-0831-10	10217614	138908951	16361609	39	365										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105551	27105551	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gctccttgtagaatatttccGacgatgcctgattgagatct	9	9	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:27105551G>A	ENST00000324856.7	+	20	5533	c.5162G>A	c.(5161-5163)cGa>cAa	p.R1721Q	ARID1A_ENST00000374152.2_Missense_Mutation_p.R1338Q|ARID1A_ENST00000540690.1_Missense_Mutation_p.R49Q|ARID1A_ENST00000457599.2_Missense_Mutation_p.R1504Q	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1721					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		GAATATTTCCGACGATGCCTG	0.443			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											183	201	195					1																	27105551		2203	4300	6503	26978138	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5162G>A	1.37:g.27105551G>A	ENSP00000320485:p.Arg1721Gln		26978138	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.138378	0.77775	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.12774	4.19;4.07;4.02;2.65	4.71	4.71	0.59529	.	0.060827	0.64402	D	0.000007	T	0.37625	0.1010	M	0.71206	2.165	0.49389	D	0.999786	P;P;D	0.76494	0.95;0.917;0.999	P;P;D	0.77557	0.498;0.459;0.99	T	0.05989	-1.0852	10	0.42905	T	0.14	-6.2012	18.208	0.89860	0.0:0.0:1.0:0.0	.	1338;1721;1504	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	Q	1721;1504;1338;49	ENSP00000320485:R1721Q;ENSP00000387636:R1504Q;ENSP00000363267:R1338Q;ENSP00000442437:R49Q	ENSP00000320485:R1721Q	R	+	2	0	ARID1A	26978138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.084000	0.94076	2.622000	0.88805	0.591000	0.81541	CGA		0.443	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27105551	G	A	27105551	3	1	5	1	0	0	0	0	1	0	0	0	913	1058	37	1	5240	1	ARID1A	1	27105551	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		27105551	222145070	1	366										
RBBP4	5928	hgsc.bcm.edu	37	chr1	33123108	33123108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acaaaaccatcttgttatagCcagtgtgcagctccctaatg	7	11	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:33123108C>A	ENST00000373493.5	+	3	404	c.245C>A	c.(244-246)gCc>gAc	p.A82D	RBBP4_ENST00000524393.1_Intron|RBBP4_ENST00000373485.1_Missense_Mutation_p.A82D|RBBP4_ENST00000544435.1_Intron|RBBP4_ENST00000458695.2_Missense_Mutation_p.A47D|RBBP4_ENST00000414241.3_Missense_Mutation_p.A81D	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	82					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)	p.A82D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CTTGTTATAGCCAGTGTGCAG	0.433																																																1	Substitution - Missense(1)	ovary(1)	1											126	105	112					1																	33123108		2203	4300	6503	32895695	SO:0001583	missense	5928			BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"WD repeat domain containing"	9887	protein-coding gene	gene with protein product		602923	"retinoblastoma-binding protein 4"			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.245C>A	1.37:g.33123108C>A	ENSP00000362592:p.Ala82Asp		32895695	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Missense_Mutation	SNP	ENST00000373493.5	37	CCDS366.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265493	0.95399	.	.	ENSG00000162521	ENST00000414241;ENST00000373493;ENST00000373485;ENST00000458695;ENST00000490500;ENST00000445722	T;T;T;T	0.71934	-0.58;-0.61;-0.5;-0.56	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.88865	0.6553	H	0.96943	3.91	0.80722	D	1	D;P	0.56035	0.974;0.955	P;P	0.61592	0.644;0.891	D	0.92463	0.5979	10	0.87932	D	0	.	18.1598	0.89705	0.0:1.0:0.0:0.0	.	81;82	Q09028-2;Q09028	.;RBBP4_HUMAN	D	81;82;82;47;47;47	ENSP00000398242:A81D;ENSP00000362592:A82D;ENSP00000362584:A82D;ENSP00000396057:A47D	ENSP00000362584:A82D	A	+	2	0	RBBP4	32895695	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.692000	0.84203	2.607000	0.88179	0.561000	0.74099	GCC		0.433	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610		A	33123108	C	A	33123108	3	1	5	1	0	0	0	0	1	0	0	0	13138	739	26	2	255	2	RBBP4	1	33123108	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	6017557	33123108	216127513	2	367										
MPL	4352	hgsc.bcm.edu	37	chr1	43805162	43805162	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagaggcctcactcagcctcTgctctggaccagtctccatg	9	16	5	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:43805162T>C	ENST00000372470.3	+	4	654	c.612T>C	c.(610-612)tcT>tcC	p.S204S	MPL_ENST00000413998.2_Silent_p.S204S	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	204	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	ACTCAGCCTCTGCTCTGGACC	0.572			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	0			1											86	83	84					1																	43805162		2203	4300	6503	43577749	SO:0001819	synonymous_variant	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.612T>C	1.37:g.43805162T>C			43577749	Q5JUZ0	Silent	SNP	ENST00000372470.3	37	CCDS483.1																																																																																				0.572	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		C	43805162	T	C	43805162	2	2	5	1	0	0	0	0	0	0	0	1	9760	1567	55	4		4	MPL	1	43805162	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	10682054	43805162	205445459	3	368										
C1orf168	199920	hgsc.bcm.edu	37	chr1	57189325	57189325	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcttttctaagttttgcttcTtggttttgaagaaatttcta	6	5	4	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:57189325T>C	ENST00000343433.6	-	17	1990	c.1910A>G	c.(1909-1911)aAg>aGg	p.K637R	C1orf168_ENST00000484327.1_5'Flank	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	637										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						GTTTTGCTTCTTGGTTTTGAA	0.313																																																0			1											54	52	52					1																	57189325		2201	4296	6497	56961913	SO:0001583	missense	199920			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1910A>G	1.37:g.57189325T>C	ENSP00000345972:p.Lys637Arg		56961913	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.155752	0.78114	.	.	ENSG00000187889	ENST00000343433	T	0.37584	1.19	4.74	4.74	0.60224	.	0.000000	0.53938	D	0.000049	T	0.54565	0.1866	M	0.68317	2.08	0.33587	D	0.600617	D	0.76494	0.999	D	0.66351	0.943	T	0.68907	-0.5285	10	0.66056	D	0.02	-11.5604	12.1494	0.54042	0.0:0.0:0.0:1.0	.	637	Q5VWT5	CA168_HUMAN	R	637	ENSP00000345972:K637R	ENSP00000345972:K637R	K	-	2	0	C1orf168	56961913	1.000000	0.71417	0.992000	0.48379	0.924000	0.55760	1.813000	0.38962	2.119000	0.64992	0.533000	0.62120	AAG		0.313	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		C	57189325	T	C	57189325	3	2	5	1	0	0	0	0	1	0	0	0	2018	1609	56	4	292	4	C1orf168	1	57189325	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	13384163	57189325	192061296	4	369										
ST6GALNAC3	256435	hgsc.bcm.edu	37	chr1	76877830	76877830	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cccaccaaaggttatgaagaAgatgtcggccgcatgaccat	10	11	0	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:76877830A>G	ENST00000328299.3	+	3	499	c.351A>G	c.(349-351)gaA>gaG	p.E117E	ST6GALNAC3_ENST00000464140.1_3'UTR	NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	117					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)	p.E117E(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						GTTATGAAGAAGATGTCGGCC	0.448																																																1	Substitution - coding silent(1)	ovary(1)	1											128	116	120					1																	76877830		2203	4300	6503	76650418	SO:0001819	synonymous_variant	256435				CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"Sialyltransferases"	19343	protein-coding gene	gene with protein product	"ST6GALNAC III"	610133	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.351A>G	1.37:g.76877830A>G			76650418	Q6PCE0|Q6UX29|Q8N259	Silent	SNP	ENST00000328299.3	37	CCDS672.1																																																																																				0.448	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996		G	76877830	A	G	76877830	2	3	5	1	0	0	0	0	0	0	0	1	15264	69	3	4		4	ST6GALNAC3	1	76877830	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	19688505	76877830	172372791	5	370										
CHIA	27159	hgsc.bcm.edu	37	chr1	111861256	111861256	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccacctctggtgctggtcctGctgggccctatgccaaggag	13	14	1	0	rs549528699		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:111861256G>T	ENST00000369740.1	+	9	974	c.871G>T	c.(871-873)Gct>Tct	p.A291S	CHIA_ENST00000343320.6_Missense_Mutation_p.A291S|CHIA_ENST00000451398.2_Missense_Mutation_p.A130S|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Missense_Mutation_p.A130S|CHIA_ENST00000430615.1_Missense_Mutation_p.A183S|CHIA_ENST00000353665.6_Missense_Mutation_p.A130S	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	291					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGCTGGTCCTGCTGGGCCCTA	0.537													G|||	1	0.000199681	0	0	5008	,	,		19581	0		0	False		,,,				2504	0.001															0			1											144	139	141					1																	111861256		2203	4300	6503	111662779	SO:0001583	missense	27159			AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.871G>T	1.37:g.111861256G>T	ENSP00000358755:p.Ala291Ser		111662779	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466533	0.63625	.	.	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.05855	3.38;3.38;3.38;3.38;3.38;3.38;3.38;3.38	4.84	1.57	0.23409	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.176583	0.34507	N	0.003915	T	0.09598	0.0236	L	0.51914	1.62	0.45822	D	0.998694	P	0.35011	0.48	P	0.57911	0.829	T	0.05386	-1.0888	10	0.37606	T	0.19	-6.1937	13.709	0.62656	0.0:0.4607:0.5393:0.0	.	291	Q9BZP6	CHIA_HUMAN	S	235;130;291;291;130;130;130;183	ENSP00000387671:A235S;ENSP00000436946:A130S;ENSP00000358755:A291S;ENSP00000341828:A291S;ENSP00000390476:A130S;ENSP00000338970:A130S;ENSP00000433309:A130S;ENSP00000391132:A183S	ENSP00000341828:A291S	A	+	1	0	CHIA	111662779	0.993000	0.37304	0.998000	0.56505	0.910000	0.53928	2.085000	0.41634	0.521000	0.28445	0.563000	0.77884	GCT		0.537	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111861256	G	T	111861256	3	4	5	1	0	0	0	0	1	0	0	0	3348	1319	46	2	901	2	CHIA	1	111861256	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	34983426	111861256	137389365	6	371										
KCND3	3752	hgsc.bcm.edu	37	chr1	112329627	112329627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaatccggctaaagttggaaAcaatcacagggactggcagg	12	8	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:112329627A>G	ENST00000315987.2	-	3	1687	c.1208T>C	c.(1207-1209)gTt>gCt	p.V403A	KCND3_ENST00000302127.4_Missense_Mutation_p.V403A|KCND3_ENST00000369697.1_Missense_Mutation_p.V403A	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	403					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AAAGTTGGAAACAATCACAGG	0.537																																																0			1											126	116	120					1																	112329627		2203	4300	6503	112131150	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.1208T>C	1.37:g.112329627A>G	ENSP00000319591:p.Val403Ala		112131150	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.808423	0.90707	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.97279	-4.32;-4.32;-4.32	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.97961	0.9329	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	D	0.99180	1.0867	10	0.87932	D	0	.	14.3685	0.66823	1.0:0.0:0.0:0.0	.	403;403	Q14D71;Q9UK17	.;KCND3_HUMAN	A	403	ENSP00000358711:V403A;ENSP00000319591:V403A;ENSP00000306923:V403A	ENSP00000306923:V403A	V	-	2	0	KCND3	112131150	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	1.942000	0.56320	0.459000	0.35465	GTT		0.537	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		G	112329627	A	G	112329627	3	3	5	1	0	0	0	0	1	0	0	0	8041	43	2	4	783	4	KCND3	1	112329627	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	468371	112329627	136920994	7	372										
LCE1D	353134	hgsc.bcm.edu	37	chr1	152770576	152770576	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcggggggctccagctgctgCggtgggggcagcagccagca	19	12	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:152770576C>T	ENST00000326233.6	+	2	349	c.306C>T	c.(304-306)tgC>tgT	p.C102C		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	102	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCAGCTGCTGCGGTGGGGGCA	0.637																																																0			1											44	40	41					1																	152770576		2018	3691	5709	151037200	SO:0001819	synonymous_variant	353134				CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"Late cornified envelopes"	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.306C>T	1.37:g.152770576C>T			151037200		Silent	SNP	ENST00000326233.6	37	CCDS1025.1																																																																																				0.637	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352		T	152770576	C	T	152770576	2	4	5	1	0	0	0	0	0	0	0	1	8684	776	27	1		1	LCE1D	1	152770576	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	40440949	152770576	96480045	8	373										
PKLR	5313	hgsc.bcm.edu	37	chr1	155264373	155264373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agccacgtcgctggctttccGcacaaaggaggcaaagacga	12	12	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:155264373G>A	ENST00000342741.4	-	6	903	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	PKLR_ENST00000392414.3_Missense_Mutation_p.R258W	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	289					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CTGGCTTTCCGCACAAAGGAG	0.622																																																0			1											89	79	82					1																	155264373		2203	4300	6503	153530997	SO:0001583	missense	5313			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.865C>T	1.37:g.155264373G>A	ENSP00000339933:p.Arg289Trp		153530997	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	37	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390328	0.82902	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99793	-6.77;-6.77	4.48	3.55	0.40652	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.99885	0.9945	H	0.99545	4.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.96676	0.9500	10	0.87932	D	0	-24.4399	11.7498	0.51841	0.0:0.0:0.8221:0.1779	.	289;280	P30613;B1AVT1	KPYR_HUMAN;.	W	314;258;289;203	ENSP00000376214:R258W;ENSP00000339933:R289W	ENSP00000271946:R203W	R	-	1	2	PKLR	153530997	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	5.185000	0.65076	1.210000	0.43336	0.467000	0.42956	CGG		0.622	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		A	155264373	G	A	155264373	3	1	5	1	0	0	0	0	1	0	0	0	12007	1086	38	1	883	1	PKLR	1	155264373	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	2493797	155264373	93986248	9	374										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155408817	155408817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gactatccacagagtcatccCcagaagcaactaatcttgga	7	12	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:155408817C>T	ENST00000368346.3	-	5	5768	c.5129G>A	c.(5128-5130)gGg>gAg	p.G1710E	ASH1L_ENST00000392403.3_Missense_Mutation_p.G1710E			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1710	Ser-rich.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AGAGTCATCCCCAGAAGCAAC	0.433																																																0			1											53	54	53					1																	155408817		2203	4300	6503	153675441	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5129G>A	1.37:g.155408817C>T	ENSP00000357330:p.Gly1710Glu		153675441	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	11.72	1.723576	0.30593	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.87729	-2.29;-2.29	5.2	3.13	0.36017	.	1.032010	0.07649	N	0.931665	T	0.60287	0.2257	N	0.08118	0	0.26863	N	0.967914	B;B	0.16603	0.01;0.018	B;B	0.23150	0.02;0.044	T	0.56517	-0.7966	10	0.59425	D	0.04	.	8.6753	0.34176	0.4993:0.408:0.0927:0.0	.	1710;1710	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	E	1710	ENSP00000357330:G1710E;ENSP00000376204:G1710E	ENSP00000357330:G1710E	G	-	2	0	ASH1L	153675441	0.986000	0.35501	0.666000	0.29783	0.983000	0.72400	1.864000	0.39469	0.613000	0.30089	0.563000	0.77884	GGG		0.433	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155408817	C	T	155408817	3	4	5	1	0	0	0	0	1	0	0	0	1042	623	22	3	3861	3	ASH1L	1	155408817	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	144444	155408817	93841804	10	375										
RGS4	5999	hgsc.bcm.edu	37	chr1	163044228	163044228	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgatggagaaggattcctacCgccgcttcctcaagtctcga	10	12	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:163044228C>A	ENST00000367909.6	+	5	836	c.496C>A	c.(496-498)Cgc>Agc	p.R166S	RGS4_ENST00000421743.2_Missense_Mutation_p.R263S|RGS4_ENST00000527809.1_Missense_Mutation_p.R148S|RGS4_ENST00000367906.3_Missense_Mutation_p.R148S|RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000367908.4_3'UTR|RGS4_ENST00000531057.1_Intron	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	166	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.R166C(1)|p.R263S(1)|p.R166S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						GGATTCCTACCGCCGCTTCCT	0.502																																					Ovarian(76;1257 1738 3039 6086)											3	Substitution - Missense(3)	lung(2)|ovary(1)	1											233	249	243					1																	163044228		2203	4300	6503	161310852	SO:0001583	missense	5999			BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.496C>A	1.37:g.163044228C>A	ENSP00000356885:p.Arg166Ser		161310852	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	37	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.729493	0.89390	.	.	ENSG00000117152	ENST00000421743;ENST00000367909;ENST00000527809;ENST00000367906	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	4.84	4.84	0.62591	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.058915	0.64402	D	0.000002	T	0.02649	0.0080	N	0.17800	0.525	0.47905	D	0.999542	P;D	0.64830	0.929;0.994	P;P	0.61275	0.746;0.886	T	0.58589	-0.7610	9	0.66056	D	0.02	.	15.4794	0.75514	0.0:1.0:0.0:0.0	.	166;263	P49798;A7XA59	RGS4_HUMAN;.	S	263;166;148;148	ENSP00000397181:R263S;ENSP00000356885:R166S;ENSP00000433261:R148S;ENSP00000356882:R148S	ENSP00000356882:R148S	R	+	1	0	RGS4	161310852	0.990000	0.36364	0.998000	0.56505	0.991000	0.79684	4.564000	0.60830	2.501000	0.84356	0.591000	0.81541	CGC		0.502	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		A	163044228	C	A	163044228	3	1	5	1	0	0	0	0	1	0	0	0	13344	652	23	2	809	2	RGS4	1	163044228	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	7635411	163044228	86206393	11	376										
XCL2	6846	hgsc.bcm.edu	37	chr1	168511319	168511319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agtgaggctcacacaggtccTcctatgtgagacttcactcc	9	13	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:168511319T>C	ENST00000367819.2	-	2	120	c.88A>G	c.(88-90)Agg>Ggg	p.R30G		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	30					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					ACACAGGTCCTCCTATGTGAG	0.453																																																0			1											119	93	102					1																	168511319		2197	4275	6472	166777943	SO:0001583	missense	6846			BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"Endogenous ligands"	10646	protein-coding gene	gene with protein product		604828	"small inducible cytokine subfamily C, member 2"	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.88A>G	1.37:g.168511319T>C	ENSP00000356793:p.Arg30Gly		166777943		Missense_Mutation	SNP	ENST00000367819.2	37	CCDS1273.1	.	.	.	.	.	.	.	.	.	.	T	9.123	1.009467	0.19277	.	.	ENSG00000143185	ENST00000367819	T	0.04406	3.63	2.49	2.49	0.30216	Chemokine interleukin-8-like domain (2);	0.673392	0.14425	N	0.320416	T	0.01061	0.0035	N	0.16478	0.41	0.20703	N	0.999865	B	0.19073	0.033	B	0.22880	0.042	T	0.47315	-0.9127	9	0.28530	T	0.3	-4.923	6.7626	0.23548	0.0:0.0:0.0:1.0	.	30	Q9UBD3	XCL2_HUMAN	G	30	ENSP00000356793:R30G	ENSP00000356793:R30G	R	-	1	2	XCL2	166777943	0.002000	0.14202	0.008000	0.14137	0.039000	0.13416	1.131000	0.31406	1.135000	0.42183	0.164000	0.16699	AGG		0.453	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175		C	168511319	T	C	168511319	3	2	5	1	0	0	0	0	1	0	0	0	17464	1550	54	4	264	4	XCL2	1	168511319	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5467091	168511319	80739302	12	377										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171511137	171511137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagtgatttcaatgagaggcGagagagggatgaaaaaaaaa	13	3	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:171511137G>T	ENST00000338920.4	+	16	4763	c.4526G>T	c.(4525-4527)cGa>cTa	p.R1509L	PRRC2C_ENST00000392078.3_Missense_Mutation_p.R1511L|PRRC2C_ENST00000426496.2_Missense_Mutation_p.R1509L|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R1511L	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1509					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AATGAGAGGCGAGAGAGGGAT	0.398																																																0			1											66	70	69					1																	171511137		2203	4300	6503	169777761	SO:0001583	missense	0			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4526G>T	1.37:g.171511137G>T	ENSP00000343629:p.Arg1509Leu		169777761	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.41|13.41	2.228966|2.228966	0.39399|0.39399	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.05925	.|3.39;3.37;3.37;3.37	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.42294	.|D	.|0.000738	.|T	.|0.21718	.|0.0523	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	.|T	.|0.00928	.|-1.1511	.|10	.|0.87932	.|D	.|0	.|.	19.7924|19.7924	0.96464|0.96464	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1509	.|Q9Y520-4	.|.	X|L	57|1511;1510;1509;1511;1509;1266	.|ENSP00000375928:R1511L;ENSP00000410219:R1509L;ENSP00000356716:R1511L;ENSP00000343629:R1509L	.|ENSP00000343629:R1509L	E|R	+|+	1|2	0|0	PRRC2C|PRRC2C	169777761|169777761	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.997000|0.997000	0.91878|0.91878	9.461000|9.461000	0.97646|0.97646	2.660000|2.660000	0.90430|0.90430	0.650000|0.650000	0.86243|0.86243	GAG|CGA		0.398	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171511137	G	T	171511137	3	4	5	1	0	0	0	0	1	0	0	0	1322	1058	37	2	4584	2	BAT2L2	1	171511137	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	2999818	171511137	77739484	13	378										
ASTN1	460	hgsc.bcm.edu	37	chr1	176926878	176926878	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aattcttactgcagcccccgTtatctttgctgcagtcgcgc	8	14	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:176926878T>A	ENST00000367654.3	-	11	2058	c.1847A>T	c.(1846-1848)aAc>aTc	p.N616I	ASTN1_ENST00000424564.2_Missense_Mutation_p.N608I|ASTN1_ENST00000361833.2_Missense_Mutation_p.N608I|ASTN1_ENST00000367657.3_Missense_Mutation_p.N608I|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	616	EGF-like 2.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GCAGCCCCCGTTATCTTTGCT	0.527																																																0			1											73	70	71					1																	176926878		2203	4300	6503	175193501	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1847A>T	1.37:g.176926878T>A	ENSP00000356626:p.Asn616Ile		175193501	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.851243	0.91355	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.20463	2.07;2.48;2.48;2.07	5.58	5.58	0.84498	Epidermal growth factor-like (1);	0.041188	0.85682	D	0.000000	T	0.35770	0.0943	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.997	D;D;D	0.85130	0.997;0.994;0.994	T	0.15235	-1.0444	10	0.87932	D	0	-36.9469	15.4147	0.74956	0.0:0.0:0.0:1.0	.	616;608;608	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	I	608;608;616;608;608	ENSP00000356629:N608I;ENSP00000354536:N608I;ENSP00000356626:N616I;ENSP00000395041:N608I	ENSP00000354536:N608I	N	-	2	0	ASTN1	175193501	1.000000	0.71417	0.777000	0.31699	0.985000	0.73830	7.555000	0.82223	2.117000	0.64856	0.460000	0.39030	AAC		0.527	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176926878	T	A	176926878	3	1	5	1	0	0	0	0	1	0	0	0	1065	1725	60	5	2117	5	ASTN1	1	176926878	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5415741	176926878	72323743	14	379										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186106681	186106681	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagagcctgcagtgtcacctGtggaaaaggcatccaaaaga	12	9	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:186106681G>C	ENST00000271588.4	+	88	13863	c.13634G>C	c.(13633-13635)tGt>tCt	p.C4545S	HMCN1_ENST00000367492.2_Missense_Mutation_p.C4545S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4545	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGTGTCACCTGTGGAAAAGGC	0.463																																																0			1											70	69	70					1																	186106681		2203	4300	6503	184373304	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13634G>C	1.37:g.186106681G>C	ENSP00000271588:p.Cys4545Ser		184373304	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	30	5.051235	0.93740	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.96459	-4.02;-4.02	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.98963	0.9647	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99282	1.0896	10	0.22706	T	0.39	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	4545	Q96RW7	HMCN1_HUMAN	S	4545	ENSP00000271588:C4545S;ENSP00000356462:C4545S	ENSP00000271588:C4545S	C	+	2	0	HMCN1	184373304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.414000	0.97362	2.729000	0.93468	0.650000	0.86243	TGT		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186106681	G	C	186106681	3	2	5	1	0	0	0	0	1	0	0	0	7241	1377	48	5	13984	5	HMCN1	1	186106681	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	9179803	186106681	63143940	15	380										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202699086	202699086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctcactggagaggccctctcTttccaggcgtctcttcagtt	9	14	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:202699086T>C	ENST00000367265.3	-	26	5410	c.4246A>G	c.(4246-4248)Aga>Gga	p.R1416G	KDM5B_ENST00000367264.2_Missense_Mutation_p.R1452G	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1416					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AGGCCCTCTCTTTCCAGGCGT	0.468																																																0			1											102	97	99					1																	202699086		2203	4300	6503	200965709	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.4246A>G	1.37:g.202699086T>C	ENSP00000356234:p.Arg1416Gly		200965709	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.984736	0.53934	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.86865	-2.18;-1.99;-2.17	5.34	5.34	0.76211	.	0.113338	0.64402	D	0.000013	D	0.90031	0.6887	M	0.63843	1.955	0.44345	D	0.997238	D;D	0.63880	0.993;0.979	D;P	0.63033	0.91;0.628	D	0.88218	0.2895	10	0.30078	T	0.28	-16.9285	9.7879	0.40688	0.0:0.0769:0.0:0.9231	.	1452;1416	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	G	1416;1258;1452;1258	ENSP00000356234:R1416G;ENSP00000356233:R1452G;ENSP00000235790:R1258G	ENSP00000235790:R1258G	R	-	1	2	KDM5B	200965709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.182000	0.58310	2.013000	0.59113	0.528000	0.53228	AGA		0.468	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		C	202699086	T	C	202699086	3	2	5	1	0	0	0	0	1	0	0	0	8155	1617	56	4	396	4	KDM5B	1	202699086	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	16592405	202699086	46551535	16	381										
RAB7L1	8934	hgsc.bcm.edu	37	chr1	205740629	205740629	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caagagcaggcagggcaccgGctctccattgggtagtgtga	15	10	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:205740629G>T	ENST00000367139.3	-	4	652	c.349C>A	c.(349-351)Ccg>Acg	p.P117T	RAB7L1_ENST00000235932.4_Missense_Mutation_p.P117T|RAB7L1_ENST00000437324.2_Missense_Mutation_p.P45T|RAB7L1_ENST00000414729.1_Missense_Mutation_p.P117T|RAB7L1_ENST00000446390.2_Missense_Mutation_p.P93T|RAB7L1_ENST00000468887.1_Intron	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		117					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CAGGGCACCGGCTCTCCATTG	0.493																																					Pancreas(25;658 872 27763 34889 38531)											0			1											269	259	262					1																	205740629		2203	4300	6503	204007252	SO:0001583	missense	8934																														ENST00000367139.3:c.349C>A	1.37:g.205740629G>T	ENSP00000356107:p.Pro117Thr		204007252	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	37	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881427	0.51801	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	T;T;T;T;T	0.79352	-1.26;-1.26;-0.4;-1.26;-1.26	5.41	5.41	0.78517	Small GTP-binding protein domain (1);	0.192953	0.45867	D	0.000331	T	0.75503	0.3858	L	0.29908	0.895	0.28008	N	0.935021	D;P	0.54772	0.968;0.566	P;B	0.50314	0.637;0.378	T	0.70945	-0.4734	10	0.40728	T	0.16	-9.7494	16.9603	0.86271	0.0:0.0:1.0:0.0	.	93;117	B4E1K3;O14966	.;RAB7L_HUMAN	T	117;117;45;93;117	ENSP00000356107:P117T;ENSP00000235932:P117T;ENSP00000416613:P45T;ENSP00000389899:P93T;ENSP00000402910:P117T	ENSP00000235932:P117T	P	-	1	0	RAB7L1	204007252	1.000000	0.71417	0.573000	0.28510	0.908000	0.53690	4.869000	0.63028	2.517000	0.84864	0.460000	0.39030	CCG		0.493	RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1			T	205740629	G	T	205740629	3	4	5	1	0	0	0	0	1	0	0	0	12992	1203	42	2	274	2	RAB7L1	1	205740629	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	3041543	205740629	43509992	17	382										
IL19	29949	hgsc.bcm.edu	37	chr1	207014388	207014388	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	actgcaggcaggaagccaccAatgccaccagagtcatccat	9	14	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:207014388A>G	ENST00000270218.6	+	6	1342	c.403A>G	c.(403-405)Aat>Gat	p.N135D	IL19_ENST00000340758.2_Missense_Mutation_p.N173D	NM_013371.3	NP_037503.2	Q9UHD0	IL19_HUMAN	interleukin 19	135					apoptotic process (GO:0006915)|immune response (GO:0006955)|interleukin-6 biosynthetic process (GO:0042226)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|reactive oxygen species metabolic process (GO:0072593)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			central_nervous_system(2)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7			BRCA - Breast invasive adenocarcinoma(75;0.211)			GGAAGCCACCAATGCCACCAG	0.522																																																0			1											126	95	105					1																	207014388		2203	4300	6503	205081011	SO:0001583	missense	29949			AF192498	CCDS1468.1, CCDS1469.1	1q32.2	2008-07-18			ENSG00000142224	ENSG00000142224		"Interleukins and interleukin receptors"	5990	protein-coding gene	gene with protein product	"melanoma differentiation associated protein-like protein"	605687				11196675	Standard	NM_153758		Approved	IL-19, MDA1, ZMDA1, IL-10C, NG.1	uc001heo.3	Q9UHD0	OTTHUMG00000036387	ENST00000270218.6:c.403A>G	1.37:g.207014388A>G	ENSP00000270218:p.Asn135Asp		205081011	B6VEV9|Q5VUT3|Q96QR4|Q9NUA0	Missense_Mutation	SNP	ENST00000270218.6	37	CCDS1469.1	.	.	.	.	.	.	.	.	.	.	A	8.518	0.868077	0.17250	.	.	ENSG00000142224	ENST00000340758;ENST00000270218	T;T	0.17370	2.28;2.28	5.71	3.19	0.36642	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.561477	0.21175	N	0.078911	T	0.21631	0.0521	M	0.63428	1.95	0.30750	N	0.745213	B;P	0.42296	0.444;0.775	B;P	0.47744	0.255;0.556	T	0.04413	-1.0953	10	0.37606	T	0.19	.	5.5965	0.17329	0.7374:0.173:0.0897:0.0	.	135;173	Q9UHD0;Q5VUT3	IL19_HUMAN;.	D	173;135	ENSP00000343000:N173D;ENSP00000270218:N135D	ENSP00000270218:N135D	N	+	1	0	IL19	205081011	0.078000	0.21339	0.971000	0.41717	0.311000	0.27955	0.448000	0.21726	2.182000	0.69389	0.482000	0.46254	AAT		0.522	IL19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088567.2	NM_153758		G	207014388	A	G	207014388	3	3	5	1	0	0	0	0	1	0	0	0	7670	130	5	4	535	4	IL19	1	207014388	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	1273759	207014388	42236233	18	383										
USH2A	7399	hgsc.bcm.edu	37	chr1	216591941	216591941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gttgcaaaccatttactgtgCgataataaaacatggtctct	7	8	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:216591941C>T	ENST00000307340.3	-	3	952	c.566G>A	c.(565-567)cGc>cAc	p.R189H	USH2A_ENST00000366942.3_Missense_Mutation_p.R189H|USH2A_ENST00000366943.2_Missense_Mutation_p.R189H	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	189					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTTACTGTGCGATAATAAAA	0.363										HNSCC(13;0.011)																																						0			1											129	123	125					1																	216591941		2203	4300	6503	214658564	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.566G>A	1.37:g.216591941C>T	ENSP00000305941:p.Arg189His		214658564	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120714	0.77436	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.74315	-0.83;-0.83;-0.83	5.62	3.76	0.43208	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.43579	U	0.000557	D	0.83147	0.5191	M	0.65975	2.015	0.37858	D	0.929605	D;P	0.89917	1.0;0.798	D;B	0.73380	0.98;0.229	D	0.85453	0.1162	10	0.87932	D	0	.	11.9499	0.52948	0.0:0.8597:0.0:0.1403	.	189;189	O75445-2;O75445	.;USH2A_HUMAN	H	189	ENSP00000305941:R189H;ENSP00000355910:R189H;ENSP00000355909:R189H	ENSP00000305941:R189H	R	-	2	0	USH2A	214658564	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	1.593000	0.36686	0.729000	0.32403	0.655000	0.94253	CGC		0.363	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216591941	C	T	216591941	3	4	5	1	0	0	0	0	1	0	0	0	17076	768	27	1	15336	1	USH2A	1	216591941	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	9577553	216591941	32658680	19	384										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228475488	228475488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgtgctgtcatctgtggctgCgcccgtgaagtggtgctatg	15	9	2	1	rs375877740		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:228475488C>T	ENST00000422127.1	+	36	9682	c.9638C>T	c.(9637-9639)gCg>gTg	p.A3213V	OBSCN_ENST00000359599.6_Missense_Mutation_p.A2060V|OBSCN_ENST00000366707.4_Missense_Mutation_p.A332V|OBSCN_ENST00000570156.2_Missense_Mutation_p.A3642V|OBSCN_ENST00000366709.4_Missense_Mutation_p.A332V|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3213V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3213	Ig-like 32.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCTGTGGCTGCGCCCGTGAAG	0.632																																																0			1						C	VAL/ALA,VAL/ALA	0,4368		0,0,2184	73	83	80		9638,9638	3.2	0	1		80	1,8565		0,1,4282	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	64,64	0,1,6466	TT,TC,CC		0.0117,0.0,0.0077	possibly-damaging,possibly-damaging	3213/7969,3213/6621	228475488	1,12933	2184	4283	6467	226542111	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9638C>T	1.37:g.228475488C>T	ENSP00000409493:p.Ala3213Val		226542111	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677575	0.47886	0.0	1.17E-4	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;3.56;-0.43	5.06	3.16	0.36331	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.345259	0.26227	N	0.025598	T	0.74374	0.3708	M	0.65320	2	0.09310	N	1	P;D	0.89917	0.814;1.0	P;D	0.73380	0.49;0.98	T	0.63857	-0.6542	10	0.17369	T	0.5	.	10.2947	0.43616	0.0:0.7901:0.136:0.074	.	3213;3213	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	3213;3213;332;332;2060	ENSP00000284548:A3213V;ENSP00000409493:A3213V;ENSP00000355668:A332V;ENSP00000355670:A332V;ENSP00000352613:A2060V	ENSP00000284548:A3213V	A	+	2	0	OBSCN	226542111	0.023000	0.18921	0.001000	0.08648	0.030000	0.12068	0.791000	0.26915	0.522000	0.28464	0.561000	0.74099	GCG		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228475488	C	T	228475488	3	4	5	1	0	0	0	0	1	0	0	0	10843	768	27	1	9776	1	OBSCN	1	228475488	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	11883547	228475488	20775133	20	385										
GALNT2	2590	hgsc.bcm.edu	37	chr1	230372430	230372430	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggacggggctctcttggggaAaattgagaaagtgcgagttc	16	6	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:230372430A>C	ENST00000366672.4	+	6	638	c.566A>C	c.(565-567)aAa>aCa	p.K189T	GALNT2_ENST00000541865.1_Missense_Mutation_p.K99T|GALNT2_ENST00000543760.1_Missense_Mutation_p.K151T	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	189	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CTCTTGGGGAAAATTGAGAAA	0.408																																																0			1											101	102	102					1																	230372430		2203	4300	6503	228439053	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.566A>C	1.37:g.230372430A>C	ENSP00000355632:p.Lys189Thr		228439053	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053716	0.55218	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.60548	0.18;0.18;0.18	5.3	5.3	0.74995	Glycosyl transferase, family 2 (1);	0.043508	0.85682	D	0.000000	T	0.54498	0.1862	L	0.52905	1.665	0.80722	D	1	P;B	0.42961	0.795;0.188	P;B	0.44477	0.451;0.172	T	0.55711	-0.8098	10	0.40728	T	0.16	.	8.8658	0.35284	0.9146:0.0:0.0854:0.0	.	189;151	Q10471;G3V1S6	GALT2_HUMAN;.	T	151;189;70;99	ENSP00000445017:K151T;ENSP00000355632:K189T;ENSP00000444346:K99T	ENSP00000355632:K189T	K	+	2	0	GALNT2	228439053	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.149000	0.71795	1.996000	0.58369	0.459000	0.35465	AAA		0.408	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		C	230372430	A	C	230372430	3	2	5	1	0	0	0	0	1	0	0	0	6233	14	1	4	588	4	GALNT2	1	230372430	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	1896942	230372430	18878191	21	386										
RYR2	6262	hgsc.bcm.edu	37	chr1	237778016	237778016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tccggaggaggagagtgacaCgctggagaaagagctcagtg	17	7	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:237778016C>T	ENST00000366574.2	+	37	5905	c.5588C>T	c.(5587-5589)aCg>aTg	p.T1863M	RYR2_ENST00000360064.6_Missense_Mutation_p.T1861M|RYR2_ENST00000542537.1_Missense_Mutation_p.T1847M	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1863	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGAGTGACACGCTGGAGAAA	0.542																																																0			1											55	57	56					1																	237778016		2041	4192	6233	235844639	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5588C>T	1.37:g.237778016C>T	ENSP00000355533:p.Thr1863Met		235844639	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	3.546	-0.092632	0.07053	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.72835	-0.69;-0.69;-0.69	5.62	-2.98	0.05513	.	1.479610	0.04626	N	0.402749	T	0.46034	0.1372	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.18561	0.022	T	0.29150	-1.0021	10	0.51188	T	0.08	.	3.2066	0.06667	0.1124:0.2428:0.112:0.5327	.	1863	Q92736	RYR2_HUMAN	M	1863;1861;1847	ENSP00000355533:T1863M;ENSP00000353174:T1861M;ENSP00000443798:T1847M	ENSP00000353174:T1861M	T	+	2	0	RYR2	235844639	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.422000	0.07043	-0.524000	0.06400	0.650000	0.86243	ACG		0.542	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237778016	C	T	237778016	3	4	5	1	0	0	0	0	1	0	0	0	13806	536	19	1	5734	1	RYR2	1	237778016	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	7405586	237778016	11472605	22	387										
PLD5	200150	hgsc.bcm.edu	37	chr1	242383406	242383406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agcggtcatgttcatgtacgTcacctcggctcctaggagtt	11	11	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:242383406T>C	ENST00000536534.2	-	5	860	c.619A>G	c.(619-621)Acg>Gcg	p.T207A	PLD5_ENST00000442594.2_Missense_Mutation_p.T115A|PLD5_ENST00000427495.1_Missense_Mutation_p.T145A			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	207						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			TTCATGTACGTCACCTCGGCT	0.552																																																0			1											131	118	122					1																	242383406		2203	4300	6503	240450029	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.619A>G	1.37:g.242383406T>C	ENSP00000440896:p.Thr207Ala		240450029	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	T	12.33	1.905769	0.33628	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.13196	2.61;2.61;2.61	5.52	5.52	0.82312	.	0.238118	0.43747	D	0.000527	T	0.09642	0.0237	N	0.17474	0.49	0.32535	N	0.534433	B;B;B	0.24920	0.114;0.07;0.114	B;B;B	0.24394	0.053;0.024;0.036	T	0.08472	-1.0720	10	0.41790	T	0.15	-20.8238	12.0198	0.53337	0.0:0.0:0.0:1.0	.	115;207;145	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	A	145;115;207	ENSP00000401285:T145A;ENSP00000414188:T115A;ENSP00000440896:T207A	ENSP00000401285:T145A	T	-	1	0	PLD5	240450029	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.781000	0.47750	2.093000	0.63338	0.533000	0.62120	ACG		0.552	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		C	242383406	T	C	242383406	3	2	5	1	0	0	0	0	1	0	0	0	12080	1667	58	4	1015	4	PLD5	1	242383406	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	4605390	242383406	6867215	23	388										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247654838	247654838	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcactacatggcagtcatgCgcccacatctctgcctgcag	9	15	2	0	rs370367058		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:247654838C>T	ENST00000522351.1	+	0	469							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R137C(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-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)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GGCAGTCATGCGCCCACATCT	0.597																																																1	Substitution - Missense(1)	breast(1)	1						C	CYS/ARG	0,4406		0,0,2203	113	85	94		409	1.9	0.5	1		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	OR2W5	NM_001004698.2	180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	137/321	247654838	2,13004	2203	4300	6503	245721461			441932					1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247654838C>T			245721461	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																					0.597	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		T	247654838	C	T	247654838	1	4	5	0	1	0	0	0	0	0	0	0	11065	768	27	1		1	OR2W5	1	247654838	RNA	SNP	C	TCGA-AF-2693-01A-02D-1733-10	5271432	247654838	1595783	24	389										
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366766	248366766	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tttgccaccctctaagatacAccaatctcatgagccctaaa	4	14	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:248366766A>G	ENST00000456743.1	+	1	435	c.397A>G	c.(397-399)Acc>Gcc	p.T133A		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCTAAGATACACCAATCTCAT	0.423																																																0			1											222	222	222					1																	248366766		2203	4300	6503	246433389	SO:0001583	missense	127062				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.397A>G	1.37:g.248366766A>G	ENSP00000389625:p.Thr133Ala		246433389	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	A	7.199	0.593186	0.13875	.	.	ENSG00000228198	ENST00000456743	T	0.19250	2.16	2.55	-5.09	0.02920	GPCR, rhodopsin-like superfamily (1);	0.669759	0.11450	U	0.562904	T	0.10465	0.0256	N	0.25647	0.755	0.09310	N	1	B	0.16396	0.017	B	0.23275	0.045	T	0.27773	-1.0064	10	0.54805	T	0.06	.	1.6802	0.02830	0.4627:0.1774:0.2449:0.115	.	133	Q8NG83	OR2M3_HUMAN	A	133	ENSP00000389625:T133A	ENSP00000389625:T133A	T	+	1	0	OR2M3	246433389	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-10.897000	0.00005	-1.107000	0.03004	-0.842000	0.03052	ACC		0.423	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		G	248366766	A	G	248366766	3	3	5	1	0	0	0	0	1	0	0	0	11042	159	6	4	399	4	OR2M3	1	248366766	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	711928	248366766	883855	25	390										
OR2M4	26245	hgsc.bcm.edu	37	chr1	248403107	248403107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	accctctcatttatagcctcCgcaacaaagaagtgttcagg	7	12	2	1	rs531102387		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:248403107C>T	ENST00000306687.1	+	1	877	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	293					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R293C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TTATAGCCTCCGCAACAAAGA	0.438													c|||	1	0.000199681	0	0	5008	,	,		18194	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											79	73	75					1																	248403107		2203	4300	6503	246469730	SO:0001583	missense	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.877C>T	1.37:g.248403107C>T	ENSP00000306688:p.Arg293Cys		246469730	Q15611|Q8NG82	Missense_Mutation	SNP	ENST00000306687.1	37	CCDS31108.1	.	.	.	.	.	.	.	.	.	.	c	8.596	0.885645	0.17540	.	.	ENSG00000171180	ENST00000306687	T	0.40476	1.03	3.34	-0.264	0.12950	.	0.000000	0.37304	N	0.002142	T	0.50888	0.1642	H	0.98027	4.13	0.09310	N	1	B	0.25667	0.131	B	0.21151	0.033	T	0.56080	-0.8038	10	0.72032	D	0.01	.	3.39	0.07285	0.4765:0.2975:0.0:0.2259	.	293	Q96R27	OR2M4_HUMAN	C	293	ENSP00000306688:R293C	ENSP00000306688:R293C	R	+	1	0	OR2M4	246469730	0.000000	0.05858	0.070000	0.20053	0.811000	0.45836	0.091000	0.15046	0.175000	0.19841	0.543000	0.68304	CGC		0.438	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		T	248403107	C	T	248403107	3	4	5	1	0	0	0	0	1	0	0	0	11043	652	23	1	879	1	OR2M4	1	248403107	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	36341	248403107	847514	26	391										
C2orf44	80304	hgsc.bcm.edu	37	chr2	24261804	24261804	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cacctgtgaagagtcttctgAgcgctgtcccaaatataaga	9	10	2	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:24261804A>G	ENST00000295148.4	-	2	618	c.561T>C	c.(559-561)gcT>gcC	p.A187A	C2orf44_ENST00000406895.3_Silent_p.A187A	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	187									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGTCTTCTGAGCGCTGTCCC	0.557			T	ALK	NSCLC																																		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	0			2											53	48	50					2																	24261804		2203	4300	6503	24115308	SO:0001819	synonymous_variant	80304			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.561T>C	2.37:g.24261804A>G			24115308	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																				0.557	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		G	24261804	A	G	24261804	2	3	5	1	0	0	0	0	0	0	0	1	2174	291	11	4		4	C2orf44	2	24261804	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10		24261804	218937569	27	392										
PLB1	151056	hgsc.bcm.edu	37	chr2	28851975	28851975	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctgcagctcccaagggctttCgtcaacgtggtggaggtcat	13	11	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:28851975C>T	ENST00000327757.5	+	53	3785	c.3741C>T	c.(3739-3741)ttC>ttT	p.F1247F	PLB1_ENST00000422425.2_Silent_p.F1236F|PLB1_ENST00000541605.1_Silent_p.F212F	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1247	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CAAGGGCTTTCGTCAACGTGG	0.597																																																0			2											85	68	74					2																	28851975		2203	4300	6503	28705479	SO:0001819	synonymous_variant	151056				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3741C>T	2.37:g.28851975C>T			28705479	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	6.396	0.441236	0.12164	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.75	-1.99	0.07457	.	.	.	.	.	T	0.34077	0.0885	.	.	.	0.22620	N	0.998929	.	.	.	.	.	.	T	0.33727	-0.9857	4	.	.	.	-25.1842	10.4716	0.44640	0.0:0.4002:0.0:0.5998	.	.	.	.	L	1235	.	.	S	+	2	0	PLB1	28705479	0.000000	0.05858	0.002000	0.10522	0.808000	0.45660	-0.824000	0.04438	-0.803000	0.04415	0.561000	0.74099	TCG		0.597	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			T	28851975	C	T	28851975	2	4	5	1	0	0	0	0	0	0	0	1	12055	883	31	1		1	PLB1	2	28851975	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	4590171	28851975	214347398	28	393										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32654233	32654233	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtggtgagcttcattttctCcaaattggaggaacctgtga	12	7	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:32654233C>T	ENST00000421745.2	+	11	3026	c.2892C>T	c.(2890-2892)ctC>ctT	p.L964L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	964					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCATTTTCTCCAAATTGGAG	0.333																																					Pancreas(94;175 1509 16028 18060 45422)											0			2											67	64	65					2																	32654233		2202	4298	6500	32507737	SO:0001819	synonymous_variant	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2892C>T	2.37:g.32654233C>T			32507737	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																				0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32654233	C	T	32654233	2	4	5	1	0	0	0	0	0	0	0	1	1439	842	30	3		3	BIRC6	2	32654233	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	3802258	32654233	210545140	29	394										
REL	5966	hgsc.bcm.edu	37	chr2	61144021	61144021	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tttctattcagtccctgaaaAacagctgaatgatattgaag	7	7	2	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:61144021A>G	ENST00000295025.8	+	5	724	c.404A>G	c.(403-405)aAa>aGa	p.K135R	REL_ENST00000394479.3_Missense_Mutation_p.K135R	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	135	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			GTCCCTGAAAAACAGCTGAAT	0.373			A		Hodgkin Lymphoma																																		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	0			2											135	126	129					2																	61144021		2203	4300	6503	60997525	SO:0001583	missense	5966			M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.404A>G	2.37:g.61144021A>G	ENSP00000295025:p.Lys135Arg		60997525	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.691014	0.48097	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.44881	0.91;0.91	5.82	1.98	0.26296	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.373499	0.28465	N	0.015245	T	0.26666	0.0652	N	0.13168	0.305	0.22531	N	0.999019	B;B	0.29481	0.007;0.245	B;B	0.31101	0.003;0.124	T	0.12167	-1.0558	10	0.33141	T	0.24	-19.9427	13.8012	0.63202	0.6049:0.3951:0.0:0.0	.	135;135	Q17RU2;Q04864	.;REL_HUMAN	R	135	ENSP00000295025:K135R;ENSP00000377989:K135R	ENSP00000295025:K135R	K	+	2	0	REL	60997525	1.000000	0.71417	0.978000	0.43139	0.996000	0.88848	3.333000	0.52090	0.066000	0.16515	0.482000	0.46254	AAA		0.373	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908		G	61144021	A	G	61144021	3	3	5	1	0	0	0	0	1	0	0	0	13252	14	1	4	422	4	REL	2	61144021	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	28489788	61144021	182055352	30	395										
GKN1	56287	hgsc.bcm.edu	37	chr2	69206108	69206108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttgatgcactggtcaaggaaAagaaggtaaaaataaaaggc	11	4	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:69206108A>G	ENST00000377938.2	+	4	415	c.352A>G	c.(352-354)Aag>Gag	p.K118E		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	118	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						GGTCAAGGAAAAGAAGGTAAA	0.398																																																0			2											66	61	63					2																	69206108		2203	4300	6503	69059612	SO:0001583	missense	56287			AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"BRICHOS domain containing"	23217	protein-coding gene	gene with protein product	"BRICHOS domain containing 1"	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.352A>G	2.37:g.69206108A>G	ENSP00000367172:p.Lys118Glu		69059612	Q8IUA9	Missense_Mutation	SNP	ENST00000377938.2	37	CCDS1891.2	.	.	.	.	.	.	.	.	.	.	A	12.17	1.856858	0.32791	.	.	ENSG00000169605	ENST00000377938	T	0.79653	-1.29	5.55	1.7	0.24286	BRICHOS (2);	0.482216	0.22022	N	0.065703	T	0.79441	0.4446	M	0.68952	2.095	0.20307	N	0.999912	P	0.40144	0.704	B	0.42462	0.388	T	0.70741	-0.4789	10	0.56958	D	0.05	-3.6789	11.8499	0.52405	0.5661:0.4339:0.0:0.0	.	118	Q9NS71	GKN1_HUMAN	E	118	ENSP00000367172:K118E	ENSP00000367172:K118E	K	+	1	0	GKN1	69059612	0.999000	0.42202	0.361000	0.25849	0.564000	0.35744	1.836000	0.39191	0.144000	0.18951	0.529000	0.55759	AAG		0.398	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617		G	69206108	A	G	69206108	3	3	5	1	0	0	0	0	1	0	0	0	6444	15	1	4	366	4	GKN1	2	69206108	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	8062087	69206108	173993265	31	396										
DQX1	165545	hgsc.bcm.edu	37	chr2	74746786	74746786	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gttcaattcgttgcatgagtTctaggagttctccccgaagt	10	9	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:74746786T>A	ENST00000404568.3	-	10	1922	c.1703A>T	c.(1702-1704)gAa>gTa	p.E568V	DQX1_ENST00000393951.2_Missense_Mutation_p.E568V	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	568						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TTGCATGAGTTCTAGGAGTTC	0.517																																																0			2											140	136	137					2																	74746786		2203	4300	6503	74600294	SO:0001583	missense	165545			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1703A>T	2.37:g.74746786T>A	ENSP00000384621:p.Glu568Val		74600294	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	T	22.6	4.312198	0.81358	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	T;T	0.03272	3.99;3.99	5.6	4.37	0.52481	Domain of unknown function DUF1605 (1);	0.072484	0.52532	D	0.000064	T	0.12347	0.0300	M	0.62723	1.935	0.46874	D	0.999235	D	0.69078	0.997	D	0.65874	0.939	T	0.00775	-1.1571	10	0.45353	T	0.12	-15.8884	10.5168	0.44894	0.0:0.0:0.1624:0.8376	.	568	Q8TE96	DQX1_HUMAN	V	568	ENSP00000377523:E568V;ENSP00000384621:E568V	ENSP00000377523:E568V	E	-	2	0	DQX1	74600294	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.732000	0.68563	2.119000	0.64992	0.482000	0.46254	GAA		0.517	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		A	74746786	T	A	74746786	3	1	5	1	0	0	0	0	1	0	0	0	4762	1783	62	5	462	5	DQX1	2	74746786	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5540678	74746786	168452587	32	397										
ANKRD23	200539	hgsc.bcm.edu	37	chr2	97507799	97507799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccccgacctcccactcacctTaaccaggggctcaggtttcc	7	19	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:97507799T>C	ENST00000318357.4	-	3	339	c.298A>G	c.(298-300)Aag>Gag	p.K100E	ANKRD23_ENST00000418232.1_Missense_Mutation_p.K100E|ANKRD23_ENST00000476975.1_5'UTR|ANKRD23_ENST00000331001.2_Missense_Mutation_p.K100E	NM_144994.7	NP_659431.5	Q86SG2	ANR23_HUMAN	ankyrin repeat domain 23	100					fatty acid metabolic process (GO:0006631)|response to mechanical stimulus (GO:0009612)	I band (GO:0031674)|intercalated disc (GO:0014704)|nucleus (GO:0005634)	titin binding (GO:0031432)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)	9						CCACTCACCTTAACCAGGGGC	0.567																																																0			2											76	79	78					2																	97507799		2203	4300	6503	96871526	SO:0001583	missense	200539				CCDS2027.1	2q11.2	2013-01-10			ENSG00000163126	ENSG00000163126		"Ankyrin repeat domain containing"	24470	protein-coding gene	gene with protein product	"diabetes related ankyrin repeat protein"	610736				12456686	Standard	NM_144994		Approved	DARP, FLJ32449, MARP3	uc002sxa.3	Q86SG2	OTTHUMG00000130534	ENST00000318357.4:c.298A>G	2.37:g.97507799T>C	ENSP00000321679:p.Lys100Glu		96871526	Q711K7|Q8NAJ7	Missense_Mutation	SNP	ENST00000318357.4	37	CCDS2027.1	.	.	.	.	.	.	.	.	.	.	T	8.832	0.940081	0.18281	.	.	ENSG00000163126	ENST00000318357;ENST00000418232;ENST00000331001	T;T;T	0.66815	-0.23;-0.23;-0.11	4.49	0.711	0.18162	.	0.572709	0.14581	N	0.310849	T	0.31796	0.0808	N	0.03983	-0.305	0.53688	D	0.999979	B;B	0.28971	0.229;0.0	B;B	0.30572	0.117;0.002	T	0.35251	-0.9796	10	0.02654	T	1	-7.3166	3.2878	0.06937	0.0:0.3535:0.2619:0.3846	.	100;100	Q86SG2-2;Q86SG2	.;ANR23_HUMAN	E	100	ENSP00000321679:K100E;ENSP00000398987:K100E;ENSP00000333108:K100E	ENSP00000321679:K100E	K	-	1	0	ANKRD23	96871526	0.392000	0.25229	0.629000	0.29254	0.633000	0.38033	0.354000	0.20146	0.294000	0.22547	0.454000	0.30748	AAG		0.567	ANKRD23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252956.1	NM_144994		C	97507799	T	C	97507799	3	2	5	1	0	0	0	0	1	0	0	0	652	1763	61	4	647	4	ANKRD23	2	97507799	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	22761013	97507799	145691574	33	398										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98804463	98804463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaacaagaagacagtccatgCaaaatattgcagcaggtttg	10	7	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:98804463C>A	ENST00000477737.1	+	10	1541	c.1337C>A	c.(1336-1338)gCa>gAa	p.A446E	VWA3B_ENST00000435344.1_Missense_Mutation_p.A446E|VWA3B_ENST00000451075.2_Missense_Mutation_p.A296E	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	446										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ACAGTCCATGCAAAATATTGC	0.478																																																0			2											82	80	81					2																	98804463		1935	4148	6083	98170895	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1337C>A	2.37:g.98804463C>A	ENSP00000417955:p.Ala446Glu		98170895	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240018	0.79912	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.27890	1.64;3.02;2.37	4.76	4.76	0.60689	.	0.000000	0.56097	D	0.000035	T	0.49881	0.1583	L	0.47716	1.5	0.31642	N	0.647958	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.57219	-0.7849	10	0.72032	D	0.01	.	16.8999	0.86110	0.0:1.0:0.0:0.0	.	296;446;446	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	E	446;446;296	ENSP00000401959:A446E;ENSP00000417955:A446E;ENSP00000389463:A296E	ENSP00000388158:A446E	A	+	2	0	VWA3B	98170895	0.999000	0.42202	1.000000	0.80357	0.947000	0.59692	5.259000	0.65485	2.336000	0.79503	0.460000	0.39030	GCA		0.478	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98804463	C	A	98804463	3	1	5	1	0	0	0	0	1	0	0	0	17281	710	25	2	1371	2	VWA3B	2	98804463	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	1296664	98804463	144394910	34	399										
IL1RL1	9173	hgsc.bcm.edu	37	chr2	102959786	102959786	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aagaatagctgacgtgaaggAagaggatttattgctgcagt	13	4	0	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:102959786A>G	ENST00000233954.1	+	8	1152	c.881A>G	c.(880-882)gAa>gGa	p.E294G	IL1RL1_ENST00000404917.2_Missense_Mutation_p.E177G|IL1RL1_ENST00000311734.2_Missense_Mutation_p.E294G|IL1RL1_ENST00000409584.1_Missense_Mutation_p.E280G	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	294	Ig-like C2-type 3.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						GACGTGAAGGAAGAGGATTTA	0.438																																																0			2											210	193	199					2																	102959786		2203	4300	6503	102326218	SO:0001583	missense	9173			D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5998	protein-coding gene	gene with protein product	"homolog of mouse growth stimulation-expressed"	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.881A>G	2.37:g.102959786A>G	ENSP00000233954:p.Glu294Gly		102326218	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.717141	0.30413	.	.	ENSG00000115602	ENST00000233954;ENST00000404917;ENST00000311734;ENST00000409584	T;T;T;T	0.14516	4.02;4.02;4.02;2.5	5.19	5.19	0.71726	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.630980	0.16451	N	0.213845	T	0.25606	0.0623	M	0.75447	2.3	0.58432	D	0.999996	D;D;P	0.55172	0.97;0.962;0.858	P;B;B	0.49853	0.624;0.441;0.345	T	0.01516	-1.1335	10	0.49607	T	0.09	.	11.3494	0.49579	1.0:0.0:0.0:0.0	.	177;294;294	B4E0I3;Q01638-2;Q01638	.;.;ILRL1_HUMAN	G	294;177;294;280	ENSP00000233954:E294G;ENSP00000384822:E177G;ENSP00000310371:E294G;ENSP00000386618:E280G	ENSP00000233954:E294G	E	+	2	0	IL1RL1	102326218	0.821000	0.29204	0.152000	0.22495	0.075000	0.17131	2.936000	0.48971	2.180000	0.69256	0.477000	0.44152	GAA		0.438	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232		G	102959786	A	G	102959786	3	3	5	1	0	0	0	0	1	0	0	0	7684	246	9	4	907	4	IL1RL1	2	102959786	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	4155323	102959786	140239587	35	400										
CCNT2	905	hgsc.bcm.edu	37	chr2	135711084	135711084	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcacaccaggaatggcctcaAcatcaagactcagcaaggac	8	13	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:135711084A>G	ENST00000264157.5	+	9	1089	c.1059A>G	c.(1057-1059)caA>caG	p.Q353Q	CCNT2_ENST00000537343.1_Silent_p.Q178Q|CCNT2_ENST00000295238.6_Silent_p.Q353Q	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	353					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		aatggcctcaacaTCAAGACT	0.428																																																0			2											109	99	102					2																	135711084		2203	4300	6503	135427554	SO:0001819	synonymous_variant	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1059A>G	2.37:g.135711084A>G			135427554	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Silent	SNP	ENST00000264157.5	37	CCDS2174.1																																																																																				0.428	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		G	135711084	A	G	135711084	2	3	5	1	0	0	0	0	0	0	0	1	2941	40	2	4		4	CCNT2	2	135711084	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	32751298	135711084	107488289	36	401										
PPIG	9360	hgsc.bcm.edu	37	chr2	170493347	170493347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctaaacagttagaatcaaagAgtaatgagcatgatcacagt	8	6	2	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:170493347A>G	ENST00000260970.3	+	14	1799	c.1579A>G	c.(1579-1581)Agt>Ggt	p.S527G	PPIG_ENST00000448752.2_Missense_Mutation_p.S527G|PPIG_ENST00000409714.3_Missense_Mutation_p.S512G	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	527					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.S527G(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AGAATCAAAGAGTAATGAGCA	0.333																																																1	Substitution - Missense(1)	ovary(1)	2											55	54	54					2																	170493347		2203	4300	6503	170201593	SO:0001583	missense	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1579A>G	2.37:g.170493347A>G	ENSP00000260970:p.Ser527Gly		170201593	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094862	0.36952	.	.	ENSG00000138398	ENST00000260970;ENST00000409714;ENST00000448752	T;T;T	0.18338	2.22;2.22;2.22	5.74	5.74	0.90152	.	0.211109	0.49305	D	0.000152	T	0.11110	0.0271	N	0.19112	0.55	0.35355	D	0.787679	B;P;B	0.39782	0.043;0.688;0.043	B;B;B	0.28849	0.027;0.095;0.027	T	0.17228	-1.0376	10	0.49607	T	0.09	-14.9731	16.0351	0.80621	1.0:0.0:0.0:0.0	.	512;512;527	E9PG73;Q2NKQ6;Q13427	.;.;PPIG_HUMAN	G	527;512;527	ENSP00000260970:S527G;ENSP00000386245:S512G;ENSP00000407083:S527G	ENSP00000260970:S527G	S	+	1	0	PPIG	170201593	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.777000	0.55364	2.186000	0.69663	0.533000	0.62120	AGT		0.333	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170493347	A	G	170493347	3	3	5	1	0	0	0	0	1	0	0	0	12358	304	11	4	1625	4	PPIG	2	170493347	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	34782263	170493347	72706026	37	402										
PPIG	9360	hgsc.bcm.edu	37	chr2	170493409	170493409	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgcgcacaatccaggagtagAgaatgtgatataactaaagg	11	7	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:170493409A>G	ENST00000260970.3	+	14	1861	c.1641A>G	c.(1639-1641)agA>agG	p.R547R	PPIG_ENST00000448752.2_Silent_p.R547R|PPIG_ENST00000409714.3_Silent_p.R532R	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	547	Arg/Ser-rich (RS domain).				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.R547R(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CCAGGAGTAGAGAATGTGATA	0.388																																																1	Substitution - coding silent(1)	ovary(1)	2											84	81	82					2																	170493409		2203	4300	6503	170201655	SO:0001819	synonymous_variant	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1641A>G	2.37:g.170493409A>G			170201655	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																				0.388	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170493409	A	G	170493409	2	3	5	1	0	0	0	0	0	0	0	1	12358	301	11	4		4	PPIG	2	170493409	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	62	170493409	72705964	38	403										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171056662	171056662	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tttttctaccctgtttaggaTatggatgaagaaattgaggc	10	5	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:171056662T>C	ENST00000408978.4	+	3	332	c.189T>C	c.(187-189)gaT>gaC	p.D63D	MYO3B_ENST00000409044.3_Silent_p.D63D|MYO3B_ENST00000334231.6_Silent_p.D72D|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	63	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CTGTTTAGGATATGGATGAAG	0.353																																																0			2											91	89	90					2																	171056662		1856	4112	5968	170764908	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.189T>C	2.37:g.171056662T>C			170764908	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103198	0.37145	.	.	ENSG00000071909	ENST00000442690	.	.	.	5.52	0.219	0.15274	.	.	.	.	.	T	0.56848	0.2013	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49485	-0.8935	4	.	.	.	.	9.4898	0.38953	0.0:0.288:0.0:0.712	.	.	.	.	H	63	.	.	Y	+	1	0	MYO3B	170764908	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	0.805000	0.27112	-0.125000	0.11703	-0.274000	0.10170	TAT		0.353	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			C	171056662	T	C	171056662	2	2	5	1	0	0	0	0	0	0	0	1	10107	1403	49	4		4	MYO3B	2	171056662	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	563253	171056662	72142711	39	404										
CIR1	9541	hgsc.bcm.edu	37	chr2	175213553	175213553	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgctgtcctccctagaactcTcgtgttttaagaacctgggc	9	12	1	2	rs200766128		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:175213553T>C	ENST00000342016.3	-	10	1117	c.1025A>G	c.(1024-1026)gAg>gGg	p.E342G	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	342	Lys/Ser-rich.				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E342G(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						CCTAGAACTCTCGTGTTTTAA	0.443																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											159	159	159					2																	175213553		2203	4300	6503	174921799	SO:0001583	missense	7335			AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"recepin", "CBF1 interacting corepressor"	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.1025A>G	2.37:g.175213553T>C	ENSP00000339723:p.Glu342Gly		174921799	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Missense_Mutation	SNP	ENST00000342016.3	37	CCDS2256.1	.	.	.	.	.	.	.	.	.	.	T	9.932	1.215039	0.22373	.	.	ENSG00000138433	ENST00000342016	.	.	.	6.16	5.01	0.66863	.	0.277370	0.34531	N	0.003885	T	0.53384	0.1793	L	0.56769	1.78	0.34740	D	0.730643	B;B	0.17465	0.022;0.012	B;B	0.17433	0.018;0.005	T	0.61173	-0.7116	9	0.59425	D	0.04	.	10.7341	0.46115	0.0:0.0721:0.0:0.9279	.	342;342	A0PJI7;Q86X95	.;CIR1_HUMAN	G	342	.	ENSP00000339723:E342G	E	-	2	0	CIR1	174921799	1.000000	0.71417	0.425000	0.26659	0.026000	0.11368	2.277000	0.43417	1.152000	0.42452	0.528000	0.53228	GAG		0.443	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882		C	175213553	T	C	175213553	3	2	5	1	0	0	0	0	1	0	0	0	3438	1551	54	4	331	4	CIR1	2	175213553	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	4156891	175213553	67985820	40	405										
PLEKHA3	65977	hgsc.bcm.edu	37	chr2	179350384	179350384	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttaggctggcagcctcgttgGtttgttttagataatggaat	12	5	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:179350384G>A	ENST00000234453.5	+	2	459	c.57G>A	c.(55-57)tgG>tgA	p.W19*	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	19	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AGCCTCGTTGGTTTGTTTTAG	0.358																																																0			2											114	113	113					2																	179350384		2203	4300	6503	179058630	SO:0001587	stop_gained	65977			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.57G>A	2.37:g.179350384G>A	ENSP00000234453:p.Trp19*		179058630	Q4ZG69|Q86TQ1|Q9NXT3	Nonsense_Mutation	SNP	ENST00000234453.5	37	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	35	5.502460	0.96371	.	.	ENSG00000116095	ENST00000234453	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3514	18.6285	0.91350	0.0:0.0:1.0:0.0	.	.	.	.	X	19	.	ENSP00000234453:W19X	W	+	3	0	PLEKHA3	179058630	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.864000	0.99589	2.380000	0.81148	0.563000	0.77884	TGG		0.358	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		A	179350384	G	A	179350384	4	1	5	1	0	0	0	0	0	1	0	0	12088	1270	44	3	63	3	PLEKHA3	2	179350384	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	4136831	179350384	63848989	41	406										
AOX1	316	hgsc.bcm.edu	37	chr2	201527647	201527647	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaatactttgtttatggagcTgcctgttccgaggttgaaat	11	6	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:201527647T>C	ENST00000374700.2	+	31	3739	c.3498T>C	c.(3496-3498)gcT>gcC	p.A1166A	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1166					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TTTATGGAGCTGCCTGTTCCG	0.468																																																0			2											160	150	153					2																	201527647		2203	4300	6503	201235892	SO:0001819	synonymous_variant	316			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3498T>C	2.37:g.201527647T>C			201235892	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																				0.468	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		C	201527647	T	C	201527647	2	2	5	1	0	0	0	0	0	0	0	1	729	1567	55	4		4	AOX1	2	201527647	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	22177263	201527647	41671726	42	407										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204354499	204354499	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgctgattagttactaagggTttagtatcttctagtacaga	9	5	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:204354499T>A	ENST00000319170.5	-	4	839	c.540A>T	c.(538-540)aaA>aaT	p.K180N	RAPH1_ENST00000439222.1_Missense_Mutation_p.K180N|RAPH1_ENST00000308091.4_Missense_Mutation_p.K180N|RAPH1_ENST00000419464.1_Missense_Mutation_p.K180N|RAPH1_ENST00000374493.3_Missense_Mutation_p.K180N|RAPH1_ENST00000374488.2_Missense_Mutation_p.K180N|RAPH1_ENST00000374489.2_Missense_Mutation_p.K180N|RAPH1_ENST00000418114.1_Missense_Mutation_p.K180N|RAPH1_ENST00000453034.1_Missense_Mutation_p.K180N|RAPH1_ENST00000457812.1_Missense_Mutation_p.K180N|RAPH1_ENST00000423104.1_Missense_Mutation_p.K180N	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	180					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTACTAAGGGTTTAGTATCTT	0.473																																																0			2											128	119	122					2																	204354499		2203	4300	6503	204062744	SO:0001583	missense	65059			AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.540A>T	2.37:g.204354499T>A	ENSP00000316543:p.Lys180Asn		204062744	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	T	8.544	0.874019	0.17395	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201	T;T;T;T;T;T;T;T;T;T;T	0.48201	0.87;0.86;0.84;0.86;0.87;0.83;0.87;0.87;0.86;0.82;0.87	5.33	0.726	0.18248	.	0.000000	0.45606	D	0.000359	T	0.44052	0.1275	L	0.34521	1.04	0.39761	D	0.97202	P;P;D	0.60575	0.646;0.948;0.988	B;B;P	0.57204	0.173;0.431;0.815	T	0.27365	-1.0076	10	0.23302	T	0.38	-17.4432	8.4847	0.33065	0.0:0.4304:0.0:0.5696	.	180;180;180	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	N	180	ENSP00000392854:K180N;ENSP00000316543:K180N;ENSP00000363617:K180N;ENSP00000363613:K180N;ENSP00000363612:K180N;ENSP00000311293:K180N;ENSP00000411138:K180N;ENSP00000390578:K180N;ENSP00000397751:K180N;ENSP00000406662:K180N;ENSP00000396711:K180N	ENSP00000311293:K180N	K	-	3	2	RAPH1	204062744	0.988000	0.35896	0.578000	0.28575	0.164000	0.22412	0.065000	0.14466	0.233000	0.21120	-0.973000	0.02599	AAA		0.473	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204354499	T	A	204354499	3	1	5	1	0	0	0	0	1	0	0	0	13087	1722	60	5	3427	5	RAPH1	2	204354499	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	2826852	204354499	38844874	43	408										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209190290	209190290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctgggatcctgacatccctCctgagtctctgccctgtgat	9	15	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:209190290C>T	ENST00000264380.4	+	20	2913	c.2755C>T	c.(2755-2757)Cct>Tct	p.P919S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	919					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TGACATCCCTCCTGAGTCTCT	0.522																																																0			2											74	68	70					2																	209190290		2203	4300	6503	208898535	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2755C>T	2.37:g.209190290C>T	ENSP00000264380:p.Pro919Ser		208898535	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.556806	0.00138	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.26373	1.74;1.9	6.07	2.19	0.27852	.	0.716341	0.13266	N	0.400875	T	0.08935	0.0221	N	0.04043	-0.29	0.26934	N	0.966409	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37865	-0.9687	10	0.05721	T	0.95	-0.6125	6.2846	0.21027	0.0:0.6143:0.1232:0.2624	.	919;863	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	S	919;495;863	ENSP00000264380:P919S;ENSP00000405736:P863S	ENSP00000264380:P919S	P	+	1	0	PIKFYVE	208898535	0.000000	0.05858	0.004000	0.12327	0.120000	0.20174	-0.051000	0.11885	0.407000	0.25591	-0.143000	0.13931	CCT		0.522	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209190290	C	T	209190290	3	4	5	1	0	0	0	0	1	0	0	0	11955	855	30	3	2840	3	PIKFYVE	2	209190290	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	4835791	209190290	34009083	44	409										
SPAG16	79582	hgsc.bcm.edu	37	chr2	214228834	214228834	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agaaacattgaagaaactgcAaagaggacatagttaccatg	9	6	0	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:214228834A>G	ENST00000331683.5	+	8	892	c.797A>G	c.(796-798)cAa>cGa	p.Q266R	SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000272898.7_Missense_Mutation_p.Q266R|SPAG16_ENST00000413312.1_Missense_Mutation_p.Q235R|SPAG16_ENST00000447990.1_Missense_Mutation_p.Q266R|SPAG16_ENST00000374309.3_Missense_Mutation_p.Q172R	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	266					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		AAGAAACTGCAAAGAGGACAT	0.289																																																0			2											28	28	28					2																	214228834		2201	4273	6474	213937079	SO:0001583	missense	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.797A>G	2.37:g.214228834A>G	ENSP00000332592:p.Gln266Arg		213937079	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.687834	0.29962	.	.	ENSG00000144451	ENST00000331683;ENST00000413312;ENST00000272898;ENST00000447990;ENST00000374309	T;T	0.57273	0.5;0.41	4.83	4.83	0.62350	.	0.418505	0.24452	N	0.038420	T	0.34483	0.0899	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.19200	0.009;0.017;0.034;0.009;0.0	B;B;B;B;B	0.15870	0.007;0.011;0.014;0.003;0.0	T	0.32375	-0.9909	10	0.72032	D	0.01	.	11.0856	0.48084	1.0:0.0:0.0:0.0	.	172;117;235;206;266	B4DYB5;Q8N0X2-2;Q8N0X2-3;Q4G1A2;Q8N0X2	.;.;.;.;SPG16_HUMAN	R	266;235;266;266;172	ENSP00000332592:Q266R;ENSP00000363428:Q172R	ENSP00000272898:Q266R	Q	+	2	0	SPAG16	213937079	0.884000	0.30299	0.086000	0.20670	0.002000	0.02628	2.666000	0.46799	1.940000	0.56252	0.528000	0.53228	CAA		0.289	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		G	214228834	A	G	214228834	3	3	5	1	0	0	0	0	1	0	0	0	15017	130	5	4	843	4	SPAG16	2	214228834	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	5038544	214228834	28970539	45	410										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713758	218713758	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcagggagtctttcttcttCaccttagcatacaggctccc	8	13	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:218713758C>T	ENST00000171887.4	-	17	1559	c.1107G>A	c.(1105-1107)gtG>gtA	p.V369V	TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Silent_p.V369V|TNS1_ENST00000419504.1_Silent_p.V369V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	369					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		CTTTCTTCTTCACCTTAGCAT	0.582																																																0			2											139	134	136					2																	218713758		2203	4300	6503	218422003	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1107G>A	2.37:g.218713758C>T			218422003	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.582	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218713758	C	T	218713758	2	4	5	1	0	0	0	0	0	0	0	1	16382	813	29	3		3	TNS1	2	218713758	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	4484924	218713758	24485615	46	411										
AGFG1	3267	hgsc.bcm.edu	37	chr2	228418450	228418450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcagcatttggacaaacaaAgccagtagtaaccccttttg	8	10	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:228418450A>G	ENST00000310078.8	+	12	1828	c.1568A>G	c.(1567-1569)aAg>aGg	p.K523R	AGFG1_ENST00000373671.3_Missense_Mutation_p.K483R|AGFG1_ENST00000409171.1_Missense_Mutation_p.K521R|AGFG1_ENST00000409315.1_Missense_Mutation_p.K502R|AGFG1_ENST00000409979.2_Missense_Mutation_p.K545R	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	523					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K523R(1)|p.T522fs*3(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						GGACAAACAAAGCCAGTAGTA	0.348																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|central_nervous_system(1)	2											102	109	107					2																	228418450		2203	4300	6503	228126694	SO:0001583	missense	3267				CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1568A>G	2.37:g.228418450A>G	ENSP00000312059:p.Lys523Arg		228126694	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	37	CCDS2467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.500134|4.500134	0.85176|0.85176	.|.	.|.	ENSG00000173744|ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171|ENST00000458212	T;T;T;T;T|.	0.32272|.	1.6;1.61;1.46;1.66;1.66|.	5.75|5.75	4.58|4.58	0.56647|0.56647	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69088|0.69088	0.3072|0.3072	M|M	0.62723|0.62723	1.935|1.935	0.46356|0.46356	D|D	0.999|0.999	D;B;D;D|.	0.76494|.	0.998;0.392;0.997;0.999|.	D;B;D;P|.	0.80764|.	0.994;0.124;0.98;0.874|.	T|T	0.66925|0.66925	-0.5800|-0.5800	10|5	0.26408|.	T|.	0.33|.	.|.	13.0852|13.0852	0.59135|0.59135	0.8659:0.1341:0.0:0.0|0.8659:0.1341:0.0:0.0	.|.	483;521;545;523|.	P52594-2;P52594-3;E9PHX7;P52594|.	.;.;.;AGFG1_HUMAN|.	R|G	545;530;523;502;483;521|93	ENSP00000387282:K545R;ENSP00000312059:K523R;ENSP00000387154:K502R;ENSP00000362775:K483R;ENSP00000387218:K521R|.	ENSP00000312059:K523R|.	K|S	+|+	2|1	0|0	AGFG1|AGFG1	228126694|228126694	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.641000|6.641000	0.74324|0.74324	0.983000|0.983000	0.38602|0.38602	0.482000|0.482000	0.46254|0.46254	AAG|AGC		0.348	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		G	228418450	A	G	228418450	3	3	5	1	0	0	0	0	1	0	0	0	380	72	3	4	1690	4	AGFG1	2	228418450	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	9704692	228418450	14780923	47	412										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234869684	234869684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggaaggaagacagaaatggcCgggacgagatggacatagaa	16	5	0	4	rs200707338		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:234869684C>T	ENST00000324695.4	+	12	1667	c.1627C>T	c.(1627-1629)Cgg>Tgg	p.R543W	TRPM8_ENST00000433712.2_Missense_Mutation_p.R231W	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	543					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CAGAAATGGCCGGGACGAGAT	0.488																																																0			2											61	56	57					2																	234869684		2203	4300	6503	234534423	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1627C>T	2.37:g.234869684C>T	ENSP00000323926:p.Arg543Trp		234534423	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231806	0.39399	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.64438	-0.1;-0.1	5.65	3.26	0.37387	.	0.255433	0.35262	N	0.003332	T	0.51176	0.1659	N	0.19112	0.55	0.35794	D	0.822651	D;D	0.56968	0.975;0.978	P;P	0.46758	0.526;0.518	T	0.62397	-0.6863	10	0.72032	D	0.01	-32.9589	11.976	0.53091	0.5493:0.4507:0.0:0.0	.	231;543	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	W	543;231	ENSP00000323926:R543W;ENSP00000404423:R231W	ENSP00000323926:R543W	R	+	1	2	TRPM8	234534423	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	1.329000	0.33770	0.412000	0.25729	-0.262000	0.10625	CGG		0.488	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234869684	C	T	234869684	3	4	5	1	0	0	0	0	1	0	0	0	16632	643	23	1	1669	1	TRPM8	2	234869684	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	6451234	234869684	8329689	48	413										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489860	237489860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccaggagaagcacagcagccGgaagatcatcttctcctacg	10	13	3	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:237489860G>A	ENST00000272928.3	+	2	1062	c.752G>A	c.(751-753)cGg>cAg	p.R251Q		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	251					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										CACAGCAGCCGGAAGATCATC	0.572																																																0			2											123	103	110					2																	237489860		2203	4300	6503	237154599	SO:0001583	missense	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.752G>A	2.37:g.237489860G>A	ENSP00000272928:p.Arg251Gln		237154599	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.262677	0.39995	.	.	ENSG00000144476	ENST00000272928	T	0.71817	-0.6	5.8	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.121195	0.56097	D	0.000028	T	0.65059	0.2655	M	0.62723	1.935	0.41896	D	0.990391	B	0.27316	0.175	B	0.21151	0.033	T	0.63611	-0.6598	9	.	.	.	.	13.3954	0.60849	0.1478:0.0:0.8522:0.0	.	251	P25106	CXCR7_HUMAN	Q	251	ENSP00000272928:R251Q	.	R	+	2	0	CXCR7	237154599	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.686000	0.84128	1.457000	0.47850	0.655000	0.94253	CGG		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		A	237489860	G	A	237489860	3	1	5	1	0	0	0	0	1	0	0	0	4102	1116	39	1	754	1	CXCR7	2	237489860	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	2620176	237489860	5709513	49	414										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238277613	238277613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gccgtatggcgtccagcaccGgggcctgggatctgtaggtt	16	11	1	0	rs146629310		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:238277613G>A	ENST00000295550.4	-	10	4945	c.4493C>T	c.(4492-4494)cCg>cTg	p.P1498L	COL6A3_ENST00000472056.1_Missense_Mutation_p.P891L|COL6A3_ENST00000409809.1_Missense_Mutation_p.P1292L|COL6A3_ENST00000353578.4_Missense_Mutation_p.P1292L|COL6A3_ENST00000346358.4_Missense_Mutation_p.P1298L|COL6A3_ENST00000347401.3_Missense_Mutation_p.P1297L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1498	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		GTCCAGCACCGGGGCCTGGGA	0.537																																																0			2						G	LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	50	51	51		3875,2672,4493	1.1	0	2	dbSNP_134	51	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	98,98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	1292/2972,891/2571,1498/3178	238277613	1,13005	2203	4300	6503	237942352	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4493C>T	2.37:g.238277613G>A	ENSP00000295550:p.Pro1498Leu		237942352	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	5.325	0.245290	0.10077	0.0	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.36	1.13	0.20643	von Willebrand factor, type A (3);	1.137570	0.06774	N	0.784062	T	0.69052	0.3068	N	0.11064	0.09	0.09310	N	1	B;B;B	0.25441	0.093;0.039;0.126	B;B;B	0.22753	0.032;0.01;0.041	T	0.55786	-0.8086	10	0.40728	T	0.16	.	10.5123	0.44868	0.0:0.2462:0.5122:0.2416	.	891;1292;1498	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	L	1498;1297;1292;891;1292;1298	ENSP00000295550:P1498L;ENSP00000315609:P1297L;ENSP00000315873:P1292L;ENSP00000418285:P891L;ENSP00000386844:P1292L;ENSP00000295546:P1298L	ENSP00000295550:P1498L	P	-	2	0	COL6A3	237942352	0.000000	0.05858	0.000000	0.03702	0.299000	0.27559	0.797000	0.26999	0.195000	0.20347	0.655000	0.94253	CCG		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238277613	G	A	238277613	3	1	5	1	0	0	0	0	1	0	0	0	3707	1116	39	1	5180	1	COL6A3	2	238277613	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	787753	238277613	4921760	50	415										
VHL	7428	hgsc.bcm.edu	37	chr3	10191600	10191600	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cccaaatgtgcagaaagaccTggagcggctgacacaggagc	13	11	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:10191600T>C	ENST00000256474.2	+	3	1433	c.593T>C	c.(592-594)cTg>cCg	p.L198P	VHL_ENST00000345392.2_Missense_Mutation_p.L157P|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	198			L -> Q (in pheochromocytoma). {ECO:0000269|PubMed:12000816}.|L -> R (in ECY2 and VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L198fs*11(1)|p.L198P(1)|p.P192fs*3(1)|p.K196fs*4(1)|p.K196fs*17(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAGAAAGACCTGGAGCGGCTG	0.488		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	5	Deletion - Frameshift(4)|Substitution - Missense(1)	kidney(4)|adrenal_gland(1)	3	GRCh37	CM020982|CM941392	VHL	M							71	63	66					3																	10191600		2203	4300	6503	10166600	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.593T>C	3.37:g.10191600T>C	ENSP00000256474:p.Leu198Pro		10166600	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164919	0.78339	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99816	-6.91;-6.91	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.082264	0.51477	D	0.000097	D	0.99667	0.9876	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.958;0.994	D	0.97146	0.9828	10	0.87932	D	0	-3.5946	12.9354	0.58311	0.0:0.0:0.0:1.0	.	157;198	P40337-2;P40337	.;VHL_HUMAN	P	198;157;116	ENSP00000256474:L198P;ENSP00000344757:L157P	ENSP00000256474:L198P	L	+	2	0	VHL	10166600	1.000000	0.71417	0.942000	0.38095	0.928000	0.56348	5.558000	0.67319	2.209000	0.71365	0.533000	0.62120	CTG		0.488	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10191600	T	C	10191600	3	2	5	1	0	0	0	0	1	0	0	0	17202	1580	55	4	603	4	VHL	3	10191600	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10		10191600	187830830	51	416										
RFTN1	23180	hgsc.bcm.edu	37	chr3	16358606	16358606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaacacagtttcccatgtctCcagctttggaagactggtct	8	11	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:16358606C>T	ENST00000334133.4	-	10	1738	c.1466G>A	c.(1465-1467)gGa>gAa	p.G489E	RP11-415F23.2_ENST00000607464.1_RNA|RFTN1_ENST00000483671.1_5'UTR|RFTN1_ENST00000432519.1_Missense_Mutation_p.G453E|OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000606098.1_Intron|OXNAD1_ENST00000544043.1_Intron|OXNAD1_ENST00000435829.2_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	489					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)	p.G489V(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						TCCCATGTCTCCAGCTTTGGA	0.493																																																1	Substitution - Missense(1)	ovary(1)	3											134	125	128					3																	16358606		2203	4300	6503	16333610	SO:0001583	missense	23180			D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1466G>A	3.37:g.16358606C>T	ENSP00000334153:p.Gly489Glu		16333610	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808249	0.31961	.	.	ENSG00000131378	ENST00000432519;ENST00000334133	T;T	0.42513	0.97;1.06	5.43	1.49	0.22878	.	1.797300	0.02497	N	0.090031	T	0.49047	0.1534	L	0.57536	1.79	0.29821	N	0.83087	P;P	0.52842	0.775;0.956	B;P	0.51016	0.436;0.656	T	0.23726	-1.0180	10	0.72032	D	0.01	-8.4003	3.0083	0.06035	0.1457:0.5567:0.1409:0.1567	.	453;489	G3XAJ6;Q14699	.;RFTN1_HUMAN	E	453;489	ENSP00000403926:G453E;ENSP00000334153:G489E	ENSP00000334153:G489E	G	-	2	0	RFTN1	16333610	0.003000	0.15002	0.001000	0.08648	0.019000	0.09904	0.103000	0.15292	0.054000	0.16065	0.563000	0.77884	GGA		0.493	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		T	16358606	C	T	16358606	3	4	5	1	0	0	0	0	1	0	0	0	13295	855	30	3	274	3	RFTN1	3	16358606	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	6167006	16358606	181663824	52	417										
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21462734	21462734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagcaaacagcacaggagtgTgggcggtccgaatgggtcca	16	9	0	0	rs113211928		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:21462734T>C	ENST00000281523.2	-	8	1678	c.1160A>G	c.(1159-1161)cAc>cGc	p.H387R		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	387			H -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						CACAGGAGTGTGGGCGGTCCG	0.468																																																0			3											41	39	40					3																	21462734		2203	4300	6503	21437738	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1160A>G	3.37:g.21462734T>C	ENSP00000281523:p.His387Arg		21437738		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	T	13.27	2.187296	0.38609	.	.	ENSG00000151789	ENST00000281523	T	0.34072	1.38	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.46157	1.445	0.50313	D	0.999865	D	0.59357	0.985	P	0.51974	0.686	T	0.30851	-0.9964	10	0.44086	T	0.13	-35.4295	16.1268	0.81402	0.0:0.0:0.0:1.0	.	387	Q9H6B1	Z385D_HUMAN	R	387	ENSP00000281523:H387R	ENSP00000281523:H387R	H	-	2	0	ZNF385D	21437738	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.158000	0.71851	2.213000	0.71641	0.455000	0.32223	CAC		0.468	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		C	21462734	T	C	21462734	3	2	5	1	0	0	0	0	1	0	0	0	17917	1696	59	4	31	4	ZNF385D	3	21462734	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5104128	21462734	176559696	53	418										
MLH1	4292	hgsc.bcm.edu	37	chr3	37092043	37092043	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aacacattgtctataaagccTtgcgctcacacattctgcct	5	13	3	0	rs63749875		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:37092043T>C	ENST00000231790.2	+	19	2386	c.2170T>C	c.(2170-2172)Ttg>Ctg	p.L724L	MLH1_ENST00000536378.1_Intron|MLH1_ENST00000435176.1_Silent_p.L626L|MLH1_ENST00000458205.2_Silent_p.L483L|MLH1_ENST00000455445.2_Silent_p.L483L|MLH1_ENST00000539477.1_Silent_p.L483L	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	724			L -> M (in HNPCC2). {ECO:0000269|PubMed:15365995}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CTATAAAGCCTTGCGCTCACA	0.448		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	1	Whole gene deletion(1)	ovary(1)	3	GRCh37	CM042744	MLH1	M	rs63749875						122	112	115					3																	37092043		2203	4300	6503	37067047	SO:0001819	synonymous_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.2170T>C	3.37:g.37092043T>C			37067047	B4DI13|B4DQ11|E9PCU2	Silent	SNP	ENST00000231790.2	37	CCDS2663.1																																																																																				0.448	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		C	37092043	T	C	37092043	2	2	5	1	0	0	0	0	0	0	0	1	9647	1606	56	4		4	MLH1	3	37092043	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	15629309	37092043	160930387	54	419										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38101313	38101313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccccagaagattactacaccGatacagtgccgtttcactct	6	14	2	2	rs149190717	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:38101313G>A	ENST00000308059.6	+	3	664	c.643G>A	c.(643-645)Gat>Aat	p.D215N	DLEC1_ENST00000346219.3_Missense_Mutation_p.D215N|DLEC1_ENST00000452631.2_Missense_Mutation_p.D215N					deleted in lung and esophageal cancer 1									p.D215N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TTACTACACCGATACAGTGCC	0.493													G|||	20	0.00399361	0.0129	0.0043	5008	,	,		20302	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	skin(1)	3						G	ASN/ASP,ASN/ASP	30,3834		0,30,1902	190	185	186		643,643	2	0	3	dbSNP_134	186	4,8292		0,4,4144	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	23,23	0,34,6046	AA,AG,GG		0.0482,0.7764,0.2796	probably-damaging,probably-damaging	215/1756,215/1779	38101313	34,12126	1932	4148	6080	38076317	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.643G>A	3.37:g.38101313G>A	ENSP00000308597:p.Asp215Asn		38076317		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	8	0.003663003663003663	5	0.01016260162601626	3	0.008287292817679558	0	0.0	0	0.0	G	9.656	1.142794	0.21205	0.007764	4.82E-4	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05319	3.47;3.46;3.7	4.99	2.01	0.26516	.	0.782790	0.12264	N	0.484423	T	0.04907	0.0132	M	0.72894	2.215	0.09310	N	1	P;B;P	0.34546	0.456;0.171;0.456	B;B;B	0.24701	0.055;0.023;0.055	T	0.30736	-0.9968	10	0.26408	T	0.33	-5.4822	7.9747	0.30149	0.0:0.3352:0.4919:0.1729	.	215;215;215	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	N	215	ENSP00000308597:D215N;ENSP00000315914:D215N;ENSP00000410427:D215N	ENSP00000308597:D215N	D	+	1	0	DLEC1	38076317	0.348000	0.24861	0.002000	0.10522	0.430000	0.31655	1.177000	0.31969	0.207000	0.20607	0.655000	0.94253	GAT		0.493	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38101313	G	A	38101313	3	1	5	1	0	0	0	0	1	0	0	0	4563	1058	37	1	653	1	DLEC1	3	38101313	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	1009270	38101313	159921117	55	420										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266161	41266161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagtggtaaaggcaatcctgAggaagaggatgtggatacct	15	5	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:41266161A>G	ENST00000349496.5	+	3	438	c.158A>G	c.(157-159)gAg>gGg	p.E53G	CTNNB1_ENST00000396183.3_Missense_Mutation_p.E53G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.E53G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.E53G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.E46G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	53					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGCAATCCTGAGGAAGAGGAT	0.478		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	111	Deletion - In frame(88)|Complex - deletion inframe(16)|Unknown(7)	liver(82)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											73	67	69					3																	41266161		2203	4300	6503	41241165	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.158A>G	3.37:g.41266161A>G	ENSP00000344456:p.Glu53Gly		41241165	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.303529	0.60195	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.91	5.91	0.95273	.	0.092424	0.64402	D	0.000001	T	0.42944	0.1225	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23547	-1.0185	10	0.54805	T	0.06	-0.5071	16.3453	0.83126	1.0:0.0:0.0:0.0	.	53	P35222	CTNB1_HUMAN	G	46;53;53;53;53;46;53;53;53	ENSP00000400508:E46G;ENSP00000385604:E53G;ENSP00000412219:E53G;ENSP00000379486:E53G;ENSP00000344456:E53G;ENSP00000411226:E46G;ENSP00000379488:E53G;ENSP00000409302:E53G;ENSP00000401599:E53G	ENSP00000344456:E53G	E	+	2	0	CTNNB1	41241165	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	GAG		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266161	A	G	41266161	3	3	5	1	0	0	0	0	1	0	0	0	4022	304	11	4	164	4	CTNNB1	3	41266161	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	3164848	41266161	156756269	56	421										
SETD2	29072	hgsc.bcm.edu	37	chr3	47161980	47161980	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaatctttcttttcattcacAgctaaagtgtccttaatgga	5	8	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:47161980A>G	ENST00000409792.3	-	3	4188	c.4146T>C	c.(4144-4146)gcT>gcC	p.A1382A		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1382					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.A879A(2)|p.A1382A(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTTCATTCACAGCTAAAGTGT	0.363			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	3	Substitution - coding silent(3)	kidney(3)	3											64	65	65					3																	47161980		2203	4300	6503	47136984	SO:0001819	synonymous_variant	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4146T>C	3.37:g.47161980A>G			47136984	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.363	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47161980	A	G	47161980	2	3	5	1	0	0	0	0	0	0	0	1	14168	175	7	4		4	SETD2	3	47161980	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	5895819	47161980	150860450	57	422										
GRM2	2912	hgsc.bcm.edu	37	chr3	51749544	51749544	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gccctggccaccctctttgtGctgggtgtctttgtgcggca	13	13	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:51749544G>A	ENST00000395052.3	+	4	1989	c.1755G>A	c.(1753-1755)gtG>gtA	p.V585V	GRM2_ENST00000442933.2_Intron|GRM2_ENST00000475478.1_3'UTR	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	585					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCCTCTTTGTGCTGGGTGTCT	0.627																																																0			3											79	76	77					3																	51749544		2203	4300	6503	51724584	SO:0001819	synonymous_variant	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.1755G>A	3.37:g.51749544G>A			51724584	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Silent	SNP	ENST00000395052.3	37	CCDS2834.1																																																																																				0.627	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			A	51749544	G	A	51749544	2	1	5	1	0	0	0	0	0	0	0	1	6818	1306	46	3		3	GRM2	3	51749544	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	4587564	51749544	146272886	58	423										
DUSP7	1849	hgsc.bcm.edu	37	chr3	52084905	52084905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaagtagagctgctcactcgAcgcgtggttgtcgcacgggc	14	11	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:52084905A>G	ENST00000495880.1	-	3	1369	c.1186T>C	c.(1186-1188)Tcg>Ccg	p.S396P	DUSP7_ENST00000296483.6_Missense_Mutation_p.S345P			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	396					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGCTCACTCGACGCGTGGTTG	0.597																																																0			3											167	130	142					3																	52084905		2203	4300	6503	52059945	SO:0001583	missense	1849			X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.1186T>C	3.37:g.52084905A>G	ENSP00000417183:p.Ser396Pro		52059945	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	37	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	a	1.283	-0.609654	0.03690	.	.	ENSG00000164086	ENST00000495880;ENST00000296483	T;T	0.02421	4.3;4.3	5.75	4.89	0.63831	.	0.165531	0.53938	N	0.000043	T	0.01387	0.0045	N	0.02247	-0.625	0.23661	N	0.997172	B	0.02656	0.0	B	0.06405	0.002	T	0.45338	-0.9268	10	0.02654	T	1	.	14.5032	0.67737	0.0713:0.0:0.9287:0.0	.	396	Q16829	DUS7_HUMAN	P	396;345	ENSP00000417183:S396P;ENSP00000296483:S345P	ENSP00000296483:S345P	S	-	1	0	DUSP7	52059945	1.000000	0.71417	0.883000	0.34634	0.481000	0.33189	5.699000	0.68310	1.452000	0.47756	-0.138000	0.14375	TCG		0.597	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947		G	52084905	A	G	52084905	3	3	5	1	0	0	0	0	1	0	0	0	4841	275	10	4	77	4	DUSP7	3	52084905	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	335361	52084905	145937525	59	424										
PTPRG	5793	hgsc.bcm.edu	37	chr3	62189578	62189578	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctaaaaagcctatgtcccgCggggaccgattttctgaaga	10	10	2	2	rs371158794		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:62189578C>T	ENST00000474889.1	+	12	2486	c.2109C>T	c.(2107-2109)cgC>cgT	p.R703R	PTPRG_ENST00000295874.10_Silent_p.R703R	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	703					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R703R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CTATGTCCCGCGGGGACCGAT	0.542																																																1	Substitution - coding silent(1)	ovary(1)	3																																								62164618	SO:0001819	synonymous_variant	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.2109C>T	3.37:g.62189578C>T			62164618	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																				0.542	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		T	62189578	C	T	62189578	2	4	5	1	0	0	0	0	0	0	0	1	12839	755	27	1		1	PTPRG	3	62189578	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	10104673	62189578	135832852	60	425										
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113517280	113517280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agacctggcagaaattgtacAgcttgtgggaaaggtgagtt	14	5	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:113517280A>G	ENST00000273398.3	+	12	1589	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.Q461R	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	494					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GAAATTGTACAGCTTGTGGGA	0.423																																																0			3											76	78	77					3																	113517280		2203	4300	6503	114999970	SO:0001583	missense	523			L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1481A>G	3.37:g.113517280A>G	ENSP00000273398:p.Gln494Arg		114999970	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018282	0.75275	.	.	ENSG00000114573	ENST00000545842;ENST00000273398;ENST00000538620	D;D	0.81739	-1.53;-1.53	4.93	4.93	0.64822	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);ATPase, F1 complex beta subunit/V1 complex, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88310	0.6402	M	0.74258	2.255	0.80722	D	1	D	0.67145	0.996	D	0.72075	0.976	D	0.87567	0.2475	10	0.34782	T	0.22	-9.3633	14.8767	0.70498	1.0:0.0:0.0:0.0	.	494	P38606	VATA_HUMAN	R	211;494;461	ENSP00000273398:Q494R;ENSP00000439874:Q461R	ENSP00000273398:Q494R	Q	+	2	0	ATP6V1A	114999970	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.886000	0.92447	1.983000	0.57843	0.459000	0.35465	CAG		0.423	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		G	113517280	A	G	113517280	3	3	5	1	0	0	0	0	1	0	0	0	1178	188	7	4	1523	4	ATP6V1A	3	113517280	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	51327702	113517280	84505150	61	426										
GAP43	2596	hgsc.bcm.edu	37	chr3	115439655	115439655	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctcagaagctgtagatgaaAccaaacctaaggaaagtgcc	9	9	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:115439655A>G	ENST00000305124.6	+	3	1009	c.643A>G	c.(643-645)Acc>Gcc	p.T215A	GAP43_ENST00000393780.3_Missense_Mutation_p.T251A	NM_002045.3	NP_002036.1	P17677	NEUM_HUMAN	growth associated protein 43	215					axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		TGTAGATGAAACCAAACCTAA	0.438																																																0			3											197	207	204					3																	115439655		2203	4300	6503	116922345	SO:0001583	missense	2596				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020			4140	protein-coding gene	gene with protein product	"neuron growth-associated protein 43", "neuromodulin", "nerve growth-related peptide GAP43", "axonal membrane protein GAP-43", "protein F1", "calmodulin-binding protein P-57", "neural phosphoprotein B-50"	162060				3272162, 8231732	Standard	NM_002045		Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000305124.6:c.643A>G	3.37:g.115439655A>G	ENSP00000305010:p.Thr215Ala		116922345	A8K0Y4	Missense_Mutation	SNP	ENST00000305124.6	37	CCDS33830.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082186	0.36758	.	.	ENSG00000172020	ENST00000305124;ENST00000393780	T;T	0.58506	0.33;0.33	5.7	4.55	0.56014	Neuromodulin (GAP-43), C-terminal (1);	0.226724	0.36444	N	0.002599	T	0.47210	0.1433	L	0.33485	1.01	0.41085	D	0.985558	B;B	0.25048	0.117;0.117	B;B	0.29524	0.103;0.044	T	0.41734	-0.9492	10	0.46703	T	0.11	-3.9186	10.8563	0.46800	0.9254:0.0:0.0746:0.0	.	251;215	A8K0Y4;P17677	.;NEUM_HUMAN	A	215;251	ENSP00000305010:T215A;ENSP00000377372:T251A	ENSP00000305010:T215A	T	+	1	0	GAP43	116922345	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.868000	0.56055	1.002000	0.39104	0.482000	0.46254	ACC		0.438	GAP43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258216.2	NM_002045		G	115439655	A	G	115439655	3	3	5	1	0	0	0	0	1	0	0	0	6255	43	2	4	795	4	GAP43	3	115439655	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	1922375	115439655	82582775	62	427										
CD80	941	hgsc.bcm.edu	37	chr3	119256010	119256010	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tccagttgaaggtctgattcActcttaaatgtccatacttg	7	9	3	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:119256010A>G	ENST00000264246.3	-	4	1036	c.674T>C	c.(673-675)gTg>gCg	p.V225A	CD80_ENST00000383669.3_Missense_Mutation_p.V225A|CD80_ENST00000478182.1_Missense_Mutation_p.V225A|CD80_ENST00000383668.3_Intron	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	225	Ig-like C2-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.V225E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	GGTCTGATTCACTCTTAAATG	0.373																																					Melanoma(132;135 1764 1806 5833 14593)											1	Substitution - Missense(1)	ovary(1)	3											203	192	196					3																	119256010		2203	4300	6503	120738700	SO:0001583	missense	941				CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.674T>C	3.37:g.119256010A>G	ENSP00000264246:p.Val225Ala		120738700	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	37	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598053	0.66332	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669	T;T;T	0.75367	-0.93;-0.93;-0.93	5.19	5.19	0.71726	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000295	D	0.84611	0.5510	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	D	0.83873	0.0275	10	0.33141	T	0.24	-18.903	11.3641	0.49662	1.0:0.0:0.0:0.0	.	225;225	Q5DTB0;P33681	.;CD80_HUMAN	A	225	ENSP00000264246:V225A;ENSP00000418364:V225A;ENSP00000373165:V225A	ENSP00000264246:V225A	V	-	2	0	CD80	120738700	0.888000	0.30383	0.788000	0.31933	0.047000	0.14425	3.987000	0.56944	2.175000	0.68902	0.528000	0.53228	GTG		0.373	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		G	119256010	A	G	119256010	3	3	5	1	0	0	0	0	1	0	0	0	3044	159	6	4	204	4	CD80	3	119256010	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	3816355	119256010	78766420	63	428										
FBXO40	51725	hgsc.bcm.edu	37	chr3	121345659	121345659	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttgtagagcacaaaactgacCcgattcttttgactagcatg	8	9	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:121345659C>A	ENST00000338040.4	+	4	2446	c.2032C>A	c.(2032-2034)Ccg>Acg	p.P678T		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	678					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P678T(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CAAAACTGACCCGATTCTTTT	0.478																																																1	Substitution - Missense(1)	ovary(1)	3											115	111	113					3																	121345659		2203	4300	6503	122828349	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.2032C>A	3.37:g.121345659C>A	ENSP00000337510:p.Pro678Thr		122828349	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035186	0.93575	.	.	ENSG00000163833	ENST00000338040	T	0.35973	1.28	6.17	6.17	0.99709	.	0.050909	0.85682	D	0.000000	T	0.61085	0.2319	M	0.68593	2.085	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.59225	-0.7494	10	0.66056	D	0.02	-15.0266	18.3732	0.90420	0.0:1.0:0.0:0.0	.	678	Q9UH90	FBX40_HUMAN	T	678	ENSP00000337510:P678T	ENSP00000337510:P678T	P	+	1	0	FBXO40	122828349	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.973000	0.56845	2.941000	0.99782	0.655000	0.94253	CCG		0.478	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		A	121345659	C	A	121345659	3	1	5	1	0	0	0	0	1	0	0	0	5768	623	22	2	2042	2	FBXO40	3	121345659	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2089649	121345659	76676771	64	429										
UROC1	131669	hgsc.bcm.edu	37	chr3	126228489	126228489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgatggcggcagccactttcGtctggcaggggtactgctca	14	11	2	1	rs556450823	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:126228489G>A	ENST00000290868.2	-	3	343	c.290C>T	c.(289-291)aCg>aTg	p.T97M	UROC1_ENST00000383579.3_Missense_Mutation_p.T97M	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	97					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		AGCCACTTTCGTCTGGCAGGG	0.612													G|||	2	0.000399361	0	0	5008	,	,		16032	0		0	False		,,,				2504	0.002															0			3											42	30	34					3																	126228489		2128	4118	6246	127711179	SO:0001583	missense	131669			AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.290C>T	3.37:g.126228489G>A	ENSP00000290868:p.Thr97Met		127711179	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	37	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037377	0.35989	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.44482	0.92;0.92	5.13	2.36	0.29203	Urocanase domain (2);	0.216752	0.47093	N	0.000253	T	0.62962	0.2471	M	0.85299	2.745	0.48395	D	0.999646	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.954	T	0.63646	-0.6590	10	0.87932	D	0	-1.7954	7.8133	0.29243	0.2743:0.0:0.7257:0.0	.	97;97	E9PE13;Q96N76	.;HUTU_HUMAN	M	97	ENSP00000290868:T97M;ENSP00000373073:T97M	ENSP00000290868:T97M	T	-	2	0	UROC1	127711179	1.000000	0.71417	0.497000	0.27552	0.013000	0.08279	3.002000	0.49496	0.562000	0.29204	-0.339000	0.08088	ACG		0.612	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		A	126228489	G	A	126228489	3	1	5	1	0	0	0	0	1	0	0	0	17068	1145	40	1	1996	1	UROC1	3	126228489	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	4882830	126228489	71793941	65	430										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142455330	142455330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gttaccataactattgaaaaCgaaaacttggatatactgca	6	7	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:142455330C>T	ENST00000476941.1	+	2	768	c.282C>T	c.(280-282)aaC>aaT	p.N94N	TRPC1_ENST00000273482.6_Silent_p.N94N	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	94					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CTATTGAAAACGAAAACTTGG	0.363																																																0			3											174	175	174					3																	142455330		2203	4300	6503	143938020	SO:0001819	synonymous_variant	7220			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.282C>T	3.37:g.142455330C>T			143938020	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																				0.363	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		T	142455330	C	T	142455330	2	4	5	1	0	0	0	0	0	0	0	1	16618	535	19	1		1	TRPC1	3	142455330	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	16226841	142455330	55567100	66	431										
SKIL	6498	hgsc.bcm.edu	37	chr3	170110052	170110052	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttttaaatcacatagttggcAgaactgaggcagagattgga	11	5	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:170110052A>G	ENST00000458537.3	+	6	2611	c.1902A>G	c.(1900-1902)gcA>gcG	p.A634A	SKIL_ENST00000413427.2_Silent_p.A588A|SKIL_ENST00000259119.4_Silent_p.A634A|SKIL_ENST00000426052.2_Silent_p.A614A	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	634					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CATAGTTGGCAGAACTGAGGC	0.363																																																0			3											86	90	89					3																	170110052		2203	4300	6503	171592746	SO:0001819	synonymous_variant	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.1902A>G	3.37:g.170110052A>G			171592746	A6NGT1|B4DT50|O00464|P12756|Q07501	Silent	SNP	ENST00000458537.3	37	CCDS33890.1																																																																																				0.363	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		G	170110052	A	G	170110052	2	3	5	1	0	0	0	0	0	0	0	1	14395	175	7	4		4	SKIL	3	170110052	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	27654722	170110052	27912378	67	432										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172065127	172065127	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ataagagacctgttgcctgcTgcacagtattgctgtagact	10	9	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:172065127T>A	ENST00000336824.4	+	21	2589	c.2490T>A	c.(2488-2490)gcT>gcA	p.A830A	FNDC3B_ENST00000416957.1_Silent_p.A830A|FNDC3B_ENST00000415807.2_Silent_p.A830A	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	830	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TGTTGCCTGCTGCACAGTATT	0.443																																																0			3											97	91	93					3																	172065127		2203	4300	6503	173547821	SO:0001819	synonymous_variant	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2490T>A	3.37:g.172065127T>A			173547821	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																				0.443	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	172065127	T	A	172065127	2	1	5	1	0	0	0	0	0	0	0	1	5989	1567	55	5		5	FNDC3B	3	172065127	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	1955075	172065127	25957303	68	433										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952076	178952076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtatttcatgaaacaaatgaAtgatgcacatcatggtggct	9	6	2	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:178952076A>G	ENST00000263967.3	+	21	3288	c.3131A>G	c.(3130-3132)aAt>aGt	p.N1044S	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1044	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N1044S(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAACAAATGAATGATGCACAT	0.373		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	3											99	89	92					3																	178952076		1910	4124	6034	180434770	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3131A>G	3.37:g.178952076A>G	ENSP00000263967:p.Asn1044Ser		180434770	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813104	0.50527	.	.	ENSG00000121879	ENST00000263967	T	0.81078	-1.45	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.39566	1.225	0.80722	D	1	P	0.45078	0.85	B	0.39339	0.297	T	0.71708	-0.4511	10	0.19590	T	0.45	-24.648	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1044	P42336	PK3CA_HUMAN	S	1044	ENSP00000263967:N1044S	ENSP00000263967:N1044S	N	+	2	0	PIK3CA	180434770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	AAT		0.373	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952076	A	G	178952076	3	3	5	1	0	0	0	0	1	0	0	0	11944	101	4	4	3209	4	PIK3CA	3	178952076	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	6886949	178952076	19070354	69	434										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910747	184910747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gattcaacattcgattccccAcaaatccaaaacagttgcct	4	13	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:184910747A>G	ENST00000231887.3	-	7	1514	c.1439T>C	c.(1438-1440)gTg>gCg	p.V480A	EHHADH_ENST00000456310.1_Missense_Mutation_p.V384A|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	480	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TCGATTCCCCACAAATCCAAA	0.418																																																0			3											108	109	108					3																	184910747		2203	4300	6503	186393441	SO:0001583	missense	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1439T>C	3.37:g.184910747A>G	ENSP00000231887:p.Val480Ala		186393441	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703750	0.68501	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.91124	-2.79;-2.79	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);3-hydroxyacyl-CoA dehydrogenase, conserved site (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.117554	0.56097	D	0.000023	D	0.93897	0.8047	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	D	0.65010	0.931	D	0.93489	0.6834	10	0.44086	T	0.13	-29.7634	16.3483	0.83171	1.0:0.0:0.0:0.0	.	480	Q08426	ECHP_HUMAN	A	480;384	ENSP00000231887:V480A;ENSP00000387746:V384A	ENSP00000231887:V480A	V	-	2	0	EHHADH	186393441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.845000	0.69437	2.254000	0.74563	0.533000	0.62120	GTG		0.418	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			G	184910747	A	G	184910747	3	3	5	1	0	0	0	0	1	0	0	0	4993	159	6	4	736	4	EHHADH	3	184910747	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	5958671	184910747	13111683	70	435										
TRA2B	6434	hgsc.bcm.edu	37	chr3	185643399	185643399	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtataatgccttcgggagctTcttctggatctagacctgca	10	10	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:185643399T>C	ENST00000453386.2	-	3	461	c.186A>G	c.(184-186)agA>agG	p.R62R	TRA2B_ENST00000471134.1_5'Flank|TRA2B_ENST00000382191.4_5'UTR	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	62	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						TTCGGGAGCTTCTTCTGGATC	0.458																																																0			3											94	92	93					3																	185643399		2203	4300	6503	187126093	SO:0001819	synonymous_variant	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"RNA binding motif (RRM) containing"	10781	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 156"	602719	"splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.186A>G	3.37:g.185643399T>C			187126093	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Silent	SNP	ENST00000453386.2	37	CCDS33905.1																																																																																				0.458	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		C	185643399	T	C	185643399	2	2	5	1	0	0	0	0	0	0	0	1	16474	1780	62	4		4	TRA2B	3	185643399	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	732652	185643399	12379031	71	436										
ETV5	2119	hgsc.bcm.edu	37	chr3	185783741	185783741	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgtttgaatccctgagggggCgggggagctgcagggacaat	18	7	0	2	rs370362112		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:185783741C>T	ENST00000306376.5	-	8	1017	c.771G>A	c.(769-771)ccG>ccA	p.P257P	ETV5_ENST00000480706.1_5'Flank|ETV5_ENST00000434744.1_Silent_p.P257P|ETV5_ENST00000537818.1_Silent_p.P299P	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	257					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			CCTGAGGGGGCGGGGGAGCTG	0.587			T	"TMPRSS2, SCL45A3"	Prostate																																		Dom	yes		3	3q28	2119	ets variant gene 5		E	0			3						C		0,4406		0,0,2203	55	63	60		771	-10.6	0.8	3		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ETV5	NM_004454.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		257/511	185783741	1,13005	2203	4300	6503	187266435	SO:0001819	synonymous_variant	2119			BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.771G>A	3.37:g.185783741C>T			187266435	A6NH46|B7Z7D7|Q6IBN5	Silent	SNP	ENST00000306376.5	37	CCDS33906.1																																																																																				0.587	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		T	185783741	C	T	185783741	2	4	5	1	0	0	0	0	0	0	0	1	5295	755	27	1		1	ETV5	3	185783741	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	140342	185783741	12238689	72	437										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgcctgctcacacgtgccgaTgcggagtgcccgcctgctca	12	17	2	0	rs71614970	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1389005T>C	ENST00000324803.4	+	1	3666	c.706T>C	c.(706-708)Tgc>Cgc	p.C236R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	236					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACGTGCCGATGCGGAGTGCC	0.672													t|||	859	0.171526	0.1059	0.245	5008	,	,		14444	0.0437		0.2913	False		,,,				2504	0.2168															0			4											163	133	143					4																	1389005		2188	4292	6480	1379005	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.706T>C	4.37:g.1389005T>C	ENSP00000323978:p.Cys236Arg		1379005	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	1.791	-0.479438	0.04383	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.18338	2.22	1.11	-2.23	0.06930	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32214	-0.9915	9	0.46703	T	0.11	.	2.6743	0.05077	0.0:0.3283:0.2597:0.412	.	236	Q8N1N5	CRPAK_HUMAN	R	236;178	ENSP00000323978:C236R	ENSP00000323978:C236R	C	+	1	0	CRIPAK	1379005	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.211000	0.09332	-0.571000	0.06014	-0.530000	0.04314	TGC		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1389005	T	C	1389005	3	2	5	1	0	0	0	0	1	0	0	0	3883	1464	51	4	708	4	CRIPAK	4	1389005	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10		1389005	189765271	73	438										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1962766	1962766	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcttgtgatttccagggagAatttgttaacgagtacgttg	12	5	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1962766A>G	ENST00000382895.3	+	20	3691	c.3260A>G	c.(3259-3261)gAa>gGa	p.E1087G	WHSC1_ENST00000382891.5_Missense_Mutation_p.E1087G|WHSC1_ENST00000382892.2_Missense_Mutation_p.E1087G|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382888.3_Missense_Mutation_p.E435G|WHSC1_ENST00000508803.1_Missense_Mutation_p.E1087G	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1087	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		TTCCAGGGAGAATTTGTTAAC	0.522			T	IGH@	MM																																		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	0			4											264	217	233					4																	1962766		2203	4300	6503	1932564	SO:0001583	missense	7468			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.3260A>G	4.37:g.1962766A>G	ENSP00000372351:p.Glu1087Gly		1932564	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961782	0.92791	.	.	ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	5.51	5.51	0.81932	SET domain (3);	0.000000	0.53938	D	0.000049	D	0.91050	0.7184	M	0.63428	1.95	0.80722	D	1	B;D	0.89917	0.036;1.0	B;D	0.87578	0.054;0.998	D	0.91719	0.5387	10	0.62326	D	0.03	.	15.6239	0.76833	1.0:0.0:0.0:0.0	.	435;1087	A2A2T2;O96028	.;NSD2_HUMAN	G	1087;1087;1087;1087;435	ENSP00000423972:E1087G;ENSP00000372347:E1087G;ENSP00000372348:E1087G;ENSP00000372351:E1087G;ENSP00000372344:E435G	ENSP00000372344:E435G	E	+	2	0	WHSC1	1932564	1.000000	0.71417	0.963000	0.40424	0.966000	0.64601	9.123000	0.94387	2.105000	0.64084	0.533000	0.62120	GAA		0.522	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		G	1962766	A	G	1962766	3	3	5	1	0	0	0	0	1	0	0	0	17402	246	9	4	3402	4	WHSC1	4	1962766	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	573761	1962766	189191510	74	439										
TNIP2	79155	hgsc.bcm.edu	37	chr4	2744248	2744248	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcgtctggctctcgagaatcCtggagaaaaggcaagggtgt	15	8	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:2744248C>T	ENST00000315423.7	-	6	1113		c.e6-1		TNIP2_ENST00000505186.1_Splice_Site|TNIP2_ENST00000510267.1_Splice_Site|TNIP2_ENST00000503235.1_Splice_Site	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTCGAGAATCCTGGAGAAAAG	0.572																																																0			4											30	32	32					4																	2744248		2203	4300	6503	2714046	SO:0001630	splice_region_variant	79155			BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.1027-1G>A	4.37:g.2744248C>T			2714046		Splice_Site	SNP	ENST00000315423.7	37	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.683216	0.29872	.	.	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	.	.	.	4.02	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.219	0.73296	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TNIP2	2714046	1.000000	0.71417	0.994000	0.49952	0.218000	0.24690	4.261000	0.58841	2.252000	0.74401	0.561000	0.74099	.		0.572	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	Intron	T	2744248	C	T	2744248	5	4	5	1	0	0	0	0	0	0	1	0	16354	695	24	3	267	3	TNIP2	4	2744248	Splice_Site	SNP	C	TCGA-AF-2693-01A-02D-1733-10	781482	2744248	188410028	75	440										
STK32B	55351	hgsc.bcm.edu	37	chr4	5468461	5468461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaactgcgatcccacatttgAgcttgaagagatgattctag	10	8	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:5468461A>G	ENST00000282908.5	+	10	1363	c.941A>G	c.(940-942)gAg>gGg	p.E314G	STK32B_ENST00000512636.1_Missense_Mutation_p.E237G|STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000510398.1_Missense_Mutation_p.E267G	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CCCACATTTGAGCTTGAAGAG	0.448																																																0			4											81	72	75					4																	5468461		2203	4300	6503	5519362	SO:0001583	missense	55351			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.941A>G	4.37:g.5468461A>G	ENSP00000282908:p.Glu314Gly		5519362		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740065	0.89573	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.24908	1.83;1.83;1.83	5.17	5.17	0.71159	Protein kinase-like domain (1);	0.000000	0.42420	U	0.000712	T	0.55033	0.1895	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62666	-0.6806	10	0.72032	D	0.01	.	13.8534	0.63510	1.0:0.0:0.0:0.0	.	314	Q9NY57	ST32B_HUMAN	G	314;237;267	ENSP00000282908:E314G;ENSP00000423209:E237G;ENSP00000420984:E267G	ENSP00000282908:E314G	E	+	2	0	STK32B	5519362	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.923000	0.87546	1.952000	0.56665	0.472000	0.43445	GAG		0.448	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		G	5468461	A	G	5468461	3	3	5	1	0	0	0	0	1	0	0	0	15337	304	11	4	979	4	STK32B	4	5468461	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	2724213	5468461	185685815	76	441										
C4orf35	85438	hgsc.bcm.edu	37	chr4	71201243	71201243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctcaataacctctgaagtcTctggcacactaaaggacagc	7	12	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:71201243T>C	ENST00000273936.5	+	1	561	c.487T>C	c.(487-489)Tct>Cct	p.S163P		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	163					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CTCTGAAGTCTCTGGCACACT	0.413																																																0			4											55	57	57					4																	71201243		2201	4298	6499	71235832	SO:0001583	missense	85438			AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"casein-like phosphoprotein"		"chromosome 4 open reading frame 35"	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.487T>C	4.37:g.71201243T>C	ENSP00000273936:p.Ser163Pro		71235832	B2RCB5|Q86UE0|Q96M17	Missense_Mutation	SNP	ENST00000273936.5	37	CCDS3539.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.917136	0.52546	.	.	ENSG00000145309	ENST00000273936	T	0.36878	1.23	4.16	2.95	0.34219	.	0.385300	0.19291	N	0.117890	T	0.40619	0.1124	L	0.34521	1.04	0.21064	N	0.999799	D	0.61080	0.989	D	0.63957	0.92	T	0.09185	-1.0686	10	0.40728	T	0.16	-20.455	6.9084	0.24321	0.2047:0.0:0.0:0.7953	.	163	Q96KC9	CABS1_HUMAN	P	163	ENSP00000273936:S163P	ENSP00000273936:S163P	S	+	1	0	CABS1	71235832	0.970000	0.33590	0.357000	0.25798	0.011000	0.07611	1.197000	0.32211	0.904000	0.36572	0.533000	0.62120	TCT		0.413	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122		C	71201243	T	C	71201243	3	2	5	1	0	0	0	0	1	0	0	0	2271	1551	54	4	489	4	C4orf35	4	71201243	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	65732782	71201243	119953033	77	442										
C4orf35	85438	hgsc.bcm.edu	37	chr4	71201261	71201261	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctctggcacactaaaggacAgcagtgctggtgttgctgac	12	10	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:71201261A>G	ENST00000273936.5	+	1	579	c.505A>G	c.(505-507)Agc>Ggc	p.S169G		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	169					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ACTAAAGGACAGCAGTGCTGG	0.443																																																0			4											54	57	56					4																	71201261		2197	4299	6496	71235850	SO:0001583	missense	85438			AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"casein-like phosphoprotein"		"chromosome 4 open reading frame 35"	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.505A>G	4.37:g.71201261A>G	ENSP00000273936:p.Ser169Gly		71235850	B2RCB5|Q86UE0|Q96M17	Missense_Mutation	SNP	ENST00000273936.5	37	CCDS3539.1	.	.	.	.	.	.	.	.	.	.	A	8.414	0.844917	0.16963	.	.	ENSG00000145309	ENST00000273936	T	0.28255	1.62	4.72	2.19	0.27852	.	0.272907	0.26601	N	0.023478	T	0.14184	0.0343	N	0.14661	0.345	0.09310	N	1	B	0.16802	0.019	B	0.17433	0.018	T	0.15838	-1.0423	10	0.30078	T	0.28	-28.786	3.6126	0.08066	0.7008:0.0:0.1094:0.1898	.	169	Q96KC9	CABS1_HUMAN	G	169	ENSP00000273936:S169G	ENSP00000273936:S169G	S	+	1	0	CABS1	71235850	0.015000	0.18098	0.001000	0.08648	0.025000	0.11179	2.358000	0.44134	0.366000	0.24427	-0.333000	0.08304	AGC		0.443	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122		G	71201261	A	G	71201261	3	3	5	1	0	0	0	0	1	0	0	0	2271	188	7	4	507	4	C4orf35	4	71201261	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	18	71201261	119953015	78	443										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74019691	74019691	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agcagcaatctggctacttcCacatgtccagcacttccagc	7	15	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:74019691C>T	ENST00000358602.4	-	6	1256	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	ANKRD17_ENST00000514252.1_5'Flank|ANKRD17_ENST00000509867.2_Silent_p.V267V|ANKRD17_ENST00000330838.6_Silent_p.V380V	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	380					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGGCTACTTCCACATGTCCAG	0.428																																																0			4											139	129	133					4																	74019691		2203	4300	6503	74238555	SO:0001819	synonymous_variant	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.1140G>A	4.37:g.74019691C>T			74238555	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																				0.428	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		T	74019691	C	T	74019691	2	4	5	1	0	0	0	0	0	0	0	1	646	581	21	3		3	ANKRD17	4	74019691	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2818430	74019691	117134585	79	444										
SFRP2	6423	hgsc.bcm.edu	37	chr4	154702675	154702675	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cccttctgccaccgcttcacCgaggtgatcaccagctcccc	7	20	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:154702675C>T	ENST00000274063.4	-	3	1100	c.816G>A	c.(814-816)tcG>tcA	p.S272S		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	272	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S272S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				ACCGCTTCACCGAGGTGATCA	0.592																																																1	Substitution - coding silent(1)	ovary(1)	4											133	101	111					4																	154702675		2203	4300	6503	154922125	SO:0001819	synonymous_variant	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.816G>A	4.37:g.154702675C>T			154922125	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1																																																																																				0.592	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			T	154702675	C	T	154702675	2	4	5	1	0	0	0	0	0	0	0	1	14199	639	23	1		1	SFRP2	4	154702675	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	80682984	154702675	36451601	80	445										
ADCY2	108	hgsc.bcm.edu	37	chr5	7520992	7520992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgtctgcaacaccgggaggcAaggagcacctggtctggcag	15	11	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:7520992A>G	ENST00000338316.4	+	3	639	c.550A>G	c.(550-552)Aag>Gag	p.K184E		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	184					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						ACCGGGAGGCAAGGAGCACCT	0.612																																																0			5											161	109	127					5																	7520992		2203	4300	6503	7573992	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.550A>G	5.37:g.7520992A>G	ENSP00000342952:p.Lys184Glu		7573992	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	A	1.318	-0.600199	0.03744	.	.	ENSG00000078295	ENST00000338316;ENST00000541993	T	0.75821	-0.97	5.65	0.2	0.15181	.	0.221927	0.44902	D	0.000403	T	0.51075	0.1653	N	0.20986	0.625	0.29339	N	0.866129	B	0.06786	0.001	B	0.09377	0.004	T	0.36648	-0.9739	10	0.07990	T	0.79	.	7.4678	0.27332	0.5178:0.4078:0.0745:0.0	.	184	Q08462	ADCY2_HUMAN	E	184;35	ENSP00000342952:K184E	ENSP00000342952:K184E	K	+	1	0	ADCY2	7573992	0.764000	0.28473	0.704000	0.30370	0.556000	0.35491	1.342000	0.33919	-0.178000	0.10672	0.528000	0.53228	AAG		0.612	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7520992	A	G	7520992	3	3	5	1	0	0	0	0	1	0	0	0	294	131	5	4	560	4	ADCY2	5	7520992	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10		7520992	173394268	81	446										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23523448	23523448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	atgtggatggaaaagataaaTcctgggccaactggatgagg	14	5	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:23523448T>C	ENST00000296682.3	+	9	1113	c.931T>C	c.(931-933)Tcc>Ccc	p.S311P		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	311	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AAAAGATAAATCCTGGGCCAA	0.433										HNSCC(3;0.000094)																																						0			5											131	126	128					5																	23523448		2203	4300	6503	23559205	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.931T>C	5.37:g.23523448T>C	ENSP00000296682:p.Ser311Pro		23559205	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	t	8.521	0.868829	0.17322	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.42131	0.98	3.72	2.39	0.29439	SET domain (2);	0.219316	0.23420	N	0.048377	T	0.36248	0.0960	L	0.48260	1.515	0.09310	N	1	P	0.51791	0.948	P	0.46049	0.502	T	0.24404	-1.0161	10	0.87932	D	0	-13.217	6.4452	0.21871	0.0:0.0:0.252:0.748	.	311	Q9NQV7	PRDM9_HUMAN	P	311;105	ENSP00000296682:S311P	ENSP00000253473:S105P	S	+	1	0	PRDM9	23559205	0.125000	0.22332	0.022000	0.16811	0.058000	0.15608	0.541000	0.23207	1.631000	0.50456	0.483000	0.47432	TCC		0.433	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		C	23523448	T	C	23523448	3	2	5	1	0	0	0	0	1	0	0	0	12497	1435	50	4	961	4	PRDM9	5	23523448	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	16002456	23523448	157391812	82	447										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37177738	37177738	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cttaccctttttgttcagtcGatttttcctccataattgtc	4	11	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:37177738G>A	ENST00000508244.1	-	29	5978	c.5885C>T	c.(5884-5886)tCg>tTg	p.S1962L	C5orf42_ENST00000425232.2_Missense_Mutation_p.S1962L|C5orf42_ENST00000274258.7_Missense_Mutation_p.S842L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1962						integral component of membrane (GO:0016021)		p.S842L(1)|p.S1962L(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTGTTCAGTCGATTTTTCCTC	0.378																																																2	Substitution - Missense(2)	skin(2)	5											223	210	214					5																	37177738		2203	4300	6503	37213495	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5885C>T	5.37:g.37177738G>A	ENSP00000421690:p.Ser1962Leu		37213495	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	10.83	1.460971	0.26248	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.23950	1.9;1.9;1.88;1.88	4.9	-1.53	0.08611	.	1.786580	0.03831	N	0.269106	T	0.16642	0.0400	N	0.25647	0.755	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.09377	0.004;0.004	T	0.17868	-1.0355	10	0.30078	T	0.28	.	4.5409	0.12056	0.4453:0.0:0.4079:0.1467	.	1962;842	E9PH94;Q9H799	.;CE042_HUMAN	L	1962;1962;842;1010;842	ENSP00000421690:S1962L;ENSP00000389014:S1962L;ENSP00000274258:S842L;ENSP00000424223:S1010L	ENSP00000274258:S842L	S	-	2	0	C5orf42	37213495	0.001000	0.12720	0.000000	0.03702	0.041000	0.13682	0.142000	0.16096	-0.613000	0.05694	-1.623000	0.00790	TCG		0.378	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37177738	G	A	37177738	3	1	5	1	0	0	0	0	1	0	0	0	2307	1059	37	1	3800	1	C5orf42	5	37177738	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	13654290	37177738	143737522	83	448										
C5orf44	80006	hgsc.bcm.edu	37	chr5	64957892	64957892	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cttaggctccaggttatggaGatgttaggttgtctttggag	14	5	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:64957892G>A	ENST00000399438.3	+	11	1258	c.913G>A	c.(913-915)Gat>Aat	p.D305N	TRAPPC13_ENST00000438419.2_Missense_Mutation_p.D305N|TRAPPC13_ENST00000231526.4_Missense_Mutation_p.D299N|TRAPPC13_ENST00000545191.1_Missense_Mutation_p.D306N|TRAPPC13_ENST00000505553.1_Missense_Mutation_p.D299N	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	305																	AGGTTATGGAGATGTTAGGTT	0.378																																																0			5											179	165	170					5																	64957892		1886	4103	5989	64993648	SO:0001583	missense	80006				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"Trs65-related"		"chromosome 5 open reading frame 44"	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.913G>A	5.37:g.64957892G>A	ENSP00000382367:p.Asp305Asn		64993648	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Missense_Mutation	SNP	ENST00000399438.3	37	CCDS47222.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554460	0.86231	.	.	ENSG00000113597	ENST00000399438;ENST00000438419;ENST00000231526;ENST00000505553;ENST00000545191	.	.	.	5.35	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.67776	0.2929	L	0.52823	1.66	0.80722	D	1	D;P;D;D	0.58620	0.983;0.922;0.983;0.972	P;P;P;P	0.59595	0.86;0.781;0.86;0.728	T	0.71563	-0.4555	9	0.72032	D	0.01	-25.4577	14.0851	0.64951	0.072:0.0:0.928:0.0	.	299;299;305;305	A5PLN9-4;A5PLN9-2;A5PLN9-5;A5PLN9	.;.;.;CE044_HUMAN	N	305;305;299;299;306	.	ENSP00000231526:D299N	D	+	1	0	C5orf44	64993648	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	9.156000	0.94705	1.493000	0.48517	0.557000	0.71058	GAT		0.378	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941		A	64957892	G	A	64957892	3	1	5	1	0	0	0	0	1	0	0	0	2309	942	33	3	955	3	C5orf44	5	64957892	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	27780154	64957892	115957368	84	449										
GPR98	84059	hgsc.bcm.edu	37	chr5	90074423	90074423	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cttcgagtgtcagaagcacaGagggtatagtatgaaatgct	12	6	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:90074423G>A	ENST00000405460.2	+	63	12942	c.12846G>A	c.(12844-12846)caG>caA	p.Q4282Q	GPR98_ENST00000425867.2_5'Flank	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4282	Calx-beta 29. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CAGAAGCACAGAGGGTATAGT	0.383																																																0			5											45	43	43					5																	90074423		1918	4127	6045	90110179	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12846G>A	5.37:g.90074423G>A			90110179	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																				0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90074423	G	A	90074423	2	1	5	1	0	0	0	0	0	0	0	1	6742	933	33	3		3	GPR98	5	90074423	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	25116531	90074423	90840837	85	450										
SPATA9	83890	hgsc.bcm.edu	37	chr5	94994411	94994411	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctctgcttattagcaagaagCttggggtaatctgaaatgtc	10	7	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:94994411C>T	ENST00000274432.8	-	5	822	c.681G>A	c.(679-681)aaG>aaA	p.K227K	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	227					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		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)		TAGCAAGAAGCTTGGGGTAAT	0.408																																																0			5											93	93	93					5																	94994411		2203	4299	6502	95020167	SO:0001819	synonymous_variant	83890			AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.681G>A	5.37:g.94994411C>T			95020167	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	37	CCDS4076.1																																																																																				0.408	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		T	94994411	C	T	94994411	2	4	5	1	0	0	0	0	0	0	0	1	15055	796	28	3		3	SPATA9	5	94994411	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	4919988	94994411	85920849	86	451										
APC	324	hgsc.bcm.edu	37	chr5	112173346	112173346	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aatgcatgtggaactttgtgGaatctctcagcaagaaatcc	9	8	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112173346G>A	ENST00000457016.1	+	16	2435	c.2055G>A	c.(2053-2055)tgG>tgA	p.W685*	APC_ENST00000508376.2_Nonsense_Mutation_p.W685*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.W685*			P25054	APC_HUMAN	adenomatous polyposis coli	685	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.W685*(2)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAACTTTGTGGAATCTCTCAG	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(2)|Unknown(1)	large_intestine(1)|lung(1)|skin(1)	5	GRCh37	CM931177	APC	M							95	96	95					5																	112173346		2202	4300	6502	112201245	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2055G>A	5.37:g.112173346G>A	ENSP00000413133:p.Trp685*		112201245	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	36	5.886725	0.97068	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.3726	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	X	685;667;685;685;685	.	ENSP00000257430:W685X	W	+	3	0	APC	112201245	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	TGG		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112173346	G	A	112173346	4	1	5	1	0	0	0	0	0	1	0	0	763	1183	41	3	2113	3	APC	5	112173346	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	17178935	112173346	68741914	87	452										
APC	324	hgsc.bcm.edu	37	chr5	112175257	112175257	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gctgaagatcctgtgagcgaAgttccagcagtgtcacagca	12	10	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112175257A>G	ENST00000457016.1	+	16	4346	c.3966A>G	c.(3964-3966)gaA>gaG	p.E1322E	APC_ENST00000508376.2_Silent_p.E1322E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.E1322E			P25054	APC_HUMAN	adenomatous polyposis coli	1322	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.V1320fs*8(1)|p.K1192fs*3(1)|p.?(1)|p.E1322fs*8(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGTGAGCGAAGTTCCAGCAG	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CI931064	APC	I							61	63	62					5																	112175257		2202	4300	6502	112203156	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3966A>G	5.37:g.112175257A>G			112203156	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175257	A	G	112175257	2	3	5	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112175257	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	1911	112175257	68740003	88	453										
APC	324	hgsc.bcm.edu	37	chr5	112175456	112175456	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcatgtttagcagatgtactTctgtcagttcacttgatagt	8	7	4	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112175456T>C	ENST00000457016.1	+	16	4545	c.4165T>C	c.(4165-4167)Tct>Cct	p.S1389P	APC_ENST00000508376.2_Missense_Mutation_p.S1389P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1389P			P25054	APC_HUMAN	adenomatous polyposis coli	1389	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1389fs*5(3)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGATGTACTTCTGTCAGTTC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											106	100	102					5																	112175456		2202	4300	6502	112203355	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4165T>C	5.37:g.112175456T>C	ENSP00000413133:p.Ser1389Pro		112203355	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065285	0.76187	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.94537	-3.45;-3.45;-3.45	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.96460	0.8845	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96010	0.9001	9	.	.	.	-15.765	16.4957	0.84242	0.0:0.0:0.0:1.0	.	1391;1389	Q4LE70;P25054	.;APC_HUMAN	P	1389	ENSP00000413133:S1389P;ENSP00000257430:S1389P;ENSP00000427089:S1389P	.	S	+	1	0	APC	112203355	1.000000	0.71417	0.991000	0.47740	0.920000	0.55202	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	TCT		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175456	T	C	112175456	3	2	5	1	0	0	0	0	1	0	0	0	763	1783	62	4	4223	4	APC	5	112175456	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	199	112175456	68739804	89	454										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114469752	114469752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccgatattcaagaacatagcTatcagctttatccttttctg	5	10	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:114469752T>C	ENST00000282369.3	-	8	1460	c.1339A>G	c.(1339-1341)Agc>Ggc	p.S447G	TRIM36_ENST00000513154.1_Missense_Mutation_p.S435G|TRIM36_ENST00000514154.1_Missense_Mutation_p.S292G	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	447	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S447C(1)		breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		AGAACATAGCTATCAGCTTTA	0.358																																																1	Substitution - Missense(1)	lung(1)	5											121	112	115					5																	114469752		2202	4300	6502	114497651	SO:0001583	missense	55521			AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.1339A>G	5.37:g.114469752T>C	ENSP00000282369:p.Ser447Gly		114497651	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	T	9.403	1.078465	0.20227	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.52526	0.66;0.66;0.66	5.63	4.48	0.54585	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.472746	0.24681	N	0.036478	T	0.30355	0.0762	N	0.22421	0.69	0.80722	D	1	B;B	0.14012	0.003;0.009	B;B	0.17979	0.01;0.02	T	0.08597	-1.0714	10	0.10636	T	0.68	.	11.0049	0.47629	0.0:0.0724:0.0:0.9276	.	435;447	E9PFI8;Q9NQ86	.;TRI36_HUMAN	G	447;435;292	ENSP00000282369:S447G;ENSP00000423934:S435G;ENSP00000424259:S292G	ENSP00000282369:S447G	S	-	1	0	TRIM36	114497651	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	2.842000	0.48230	2.145000	0.66743	0.533000	0.62120	AGC		0.358	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		C	114469752	T	C	114469752	3	2	5	1	0	0	0	0	1	0	0	0	16550	1522	53	4	859	4	TRIM36	5	114469752	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	2294296	114469752	66445508	90	455										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229951	140229951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgcgagcatcccgttccgcgTggggctgtacacgggcgaga	16	13	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140229951T>C	ENST00000532602.1	+	1	2904	c.1871T>C	c.(1870-1872)gTg>gCg	p.V624A	PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.V624A|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGTTCCGCGTGGGGCTGTAC	0.667																																					Melanoma(55;1800 1972 14909)											0			5											69	73	72					5																	140229951		2197	4274	6471	140210135	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1871T>C	5.37:g.140229951T>C	ENSP00000436042:p.Val624Ala		140210135	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.842564	0.51057	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.59772	0.24;0.24	4.05	4.05	0.47172	Cadherin (4);Cadherin-like (1);	0.382752	0.15065	U	0.282541	D	0.83608	0.5291	H	0.97415	4	0.23872	N	0.996605	D;D	0.67145	0.985;0.996	D;D	0.76071	0.928;0.987	T	0.76940	-0.2773	10	0.87932	D	0	.	12.9417	0.58348	0.0:0.0:0.0:1.0	.	624;624	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	A	624	ENSP00000436042:V624A;ENSP00000367362:V624A	ENSP00000367362:V624A	V	+	2	0	PCDHA9	140210135	0.996000	0.38824	1.000000	0.80357	0.186000	0.23388	1.923000	0.40055	1.579000	0.49836	0.260000	0.18958	GTG		0.667	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		C	140229951	T	C	140229951	3	2	5	1	0	0	0	0	1	0	0	0	11562	1696	59	4	1873	4	PCDHA9	5	140229951	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	25760199	140229951	40685309	91	456										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256623	140256623	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaggtgtacgcgctgcagccGctagaccacgaggagctgga	15	11	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140256623G>A	ENST00000398631.2	+	1	1566	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	522	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTGCAGCCGCTAGACCACG	0.692																																					Pancreas(113;759 1672 13322 24104 50104)											0			5											78	85	82					5																	140256623		2203	4298	6501	140236807	SO:0001819	synonymous_variant	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1566G>A	5.37:g.140256623G>A			140236807	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																				0.692	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256623	G	A	140256623	2	1	5	1	0	0	0	0	0	0	0	1	11553	1074	38	1		1	PCDHA12	5	140256623	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	26672	140256623	40658637	92	457										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515027	140515027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtctgaacaatggagactgCgctagcaaaaacgccacaga	11	10	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140515027C>T	ENST00000231134.5	+	1	228	c.11C>T	c.(10-12)gCg>gTg	p.A4V		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	4					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGGAGACTGCGCTAGCAAAA	0.458																																																0			5											88	78	81					5																	140515027		2203	4300	6503	140495211	SO:0001583	missense	26167			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.11C>T	5.37:g.140515027C>T	ENSP00000231134:p.Ala4Val		140495211	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753099	0.69648	.	.	ENSG00000113209	ENST00000231134	T	0.51071	0.72	5.38	4.46	0.54185	.	.	.	.	.	T	0.45418	0.1341	L	0.57536	1.79	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.22556	-1.0213	9	0.30078	T	0.28	.	14.0354	0.64642	0.212:0.788:0.0:0.0	.	4	Q9Y5E4	PCDB5_HUMAN	V	4	ENSP00000231134:A4V	ENSP00000231134:A4V	A	+	2	0	PCDHB5	140495211	0.000000	0.05858	0.557000	0.28306	0.970000	0.65996	0.631000	0.24568	2.687000	0.91594	0.561000	0.74099	GCG		0.458	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		T	140515027	C	T	140515027	3	4	5	1	0	0	0	0	1	0	0	0	11576	768	27	1	13	1	PCDHB5	5	140515027	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	258404	140515027	40400233	93	458										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140553439	140553439	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gttgatgtaacagatataaaCgataatcgacccgagctgct	9	8	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140553439C>T	ENST00000231137.3	+	1	1197	c.1023C>T	c.(1021-1023)aaC>aaT	p.N341N		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	341	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGATATAAACGATAATCGAC	0.443																																																0			5											46	47	46					5																	140553439		2203	4300	6503	140533623	SO:0001819	synonymous_variant	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1023C>T	5.37:g.140553439C>T			140533623	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																				0.443	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		T	140553439	C	T	140553439	2	4	5	1	0	0	0	0	0	0	0	1	11578	535	19	1		1	PCDHB7	5	140553439	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	38412	140553439	40361821	94	459										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140870546	140870546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctcagccccccagcgtctccCtcgctctgctcctcctggct	7	22	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140870546C>T	ENST00000252087.1	+	1	1739	c.1739C>T	c.(1738-1740)cCt>cTt	p.P580L	PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	580	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCGTCTCCCTCGCTCTGCT	0.587																																																0			5											61	55	57					5																	140870546		2203	4300	6503	140850730	SO:0001583	missense	56097			AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1739C>T	5.37:g.140870546C>T	ENSP00000252087:p.Pro580Leu		140850730	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465826	0.43839	.	.	ENSG00000240764	ENST00000252087	T	0.21031	2.03	5.45	4.55	0.56014	Cadherin (2);Cadherin-like (1);	0.363922	0.23902	N	0.043431	T	0.40670	0.1126	M	0.62154	1.92	0.54753	D	0.999986	D;P	0.76494	0.999;0.825	D;P	0.70935	0.971;0.492	T	0.10405	-1.0631	10	0.66056	D	0.02	.	11.6309	0.51173	0.0:0.7849:0.1385:0.0766	.	580;580	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	L	580	ENSP00000252087:P580L	ENSP00000252087:P580L	P	+	2	0	PCDHGC5	140850730	0.676000	0.27567	1.000000	0.80357	0.999000	0.98932	0.973000	0.29422	2.833000	0.97629	0.655000	0.94253	CCT		0.587	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		T	140870546	C	T	140870546	3	4	5	1	0	0	0	0	1	0	0	0	11602	681	24	3	1741	3	PCDHGC5	5	140870546	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	317107	140870546	40044714	95	460										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149324228	149324228	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tccacctcctctgctgtcacCtcgcccatggctgggaatcc	8	18	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:149324228C>A	ENST00000255266.5	-	1	128	c.9G>T	c.(7-9)gaG>gaT	p.E3D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	3					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTGCTGTCACCTCGCCCATGG	0.552																																																0			5											32	28	29					5																	149324228		2203	4300	6503	149304421	SO:0001583	missense	5145				CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.9G>T	5.37:g.149324228C>A	ENSP00000255266:p.Glu3Asp		149304421	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.603535	0.28534	.	.	ENSG00000132915	ENST00000255266	T	0.63744	-0.06	5.79	-0.951	0.10369	.	0.200405	0.43747	D	0.000527	T	0.48333	0.1494	L	0.46157	1.445	0.30985	N	0.722104	B	0.11235	0.004	B	0.11329	0.006	T	0.42498	-0.9448	10	0.33940	T	0.23	.	8.7182	0.34425	0.0:0.3758:0.0:0.6242	.	3	P16499	PDE6A_HUMAN	D	3	ENSP00000255266:E3D	ENSP00000255266:E3D	E	-	3	2	PDE6A	149304421	0.194000	0.23325	0.972000	0.41901	0.524000	0.34500	-0.600000	0.05693	-0.090000	0.12462	-0.254000	0.11334	GAG		0.552	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149324228	C	A	149324228	3	1	5	1	0	0	0	0	1	0	0	0	11676	680	24	2	2661	2	PDE6A	5	149324228	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	8453682	149324228	31591032	96	461										
KCNIP1	30820	hgsc.bcm.edu	37	chr5	170162792	170162792	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	atcatgaggtctctccagctGtttcaaaatgtcatgtaact	7	9	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:170162792G>A	ENST00000411494.1	+	9	666	c.666G>A	c.(664-666)ctG>ctA	p.L222L	KCNIP1_ENST00000328939.4_Silent_p.L211L|KCNIP1_ENST00000434108.1_Silent_p.L236L|KCNIP1_ENST00000390656.4_Silent_p.L211L|KCNIP1_ENST00000520740.1_Silent_p.L183L|KCNIP1_ENST00000377360.4_Silent_p.L220L			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	222	Interaction with KCND2. {ECO:0000250}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCTCCAGCTGTTTCAAAATG	0.473																																																0			5											135	123	127					5																	170162792		2203	4300	6503	170095370	SO:0001819	synonymous_variant	30820			AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.666G>A	5.37:g.170162792G>A			170095370	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Silent	SNP	ENST00000411494.1	37	CCDS34286.1																																																																																				0.473	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			A	170162792	G	A	170162792	2	1	5	1	0	0	0	0	0	0	0	1	8060	1364	48	3		3	KCNIP1	5	170162792	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	20838564	170162792	10752468	97	462										
HK3	3101	hgsc.bcm.edu	37	chr5	176314614	176314614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtctcctccagcaggcgccGgtgggcagccagacgggcag	17	14	1	1	rs376532514		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:176314614G>A	ENST00000292432.5	-	11	1529	c.1438C>T	c.(1438-1440)Cgg>Tgg	p.R480W		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	480	Hexokinase type-1 2.|Regulatory.		R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)	p.R480W(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			AGCAGGCGCCGGTGGGCAGCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	TRP/ARG	0,4406		0,0,2203	32	32	32		1438	1.4	1	5		32	1,8599	1.2+/-3.3	0,1,4299	no	missense	HK3	NM_002115.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	480/924	176314614	1,13005	2203	4300	6503	176247220	SO:0001583	missense	84376				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1438C>T	5.37:g.176314614G>A	ENSP00000292432:p.Arg480Trp		176247220	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.929608	0.34096	0.0	1.16E-4	ENSG00000160883	ENST00000292432	D	0.98296	-4.85	4.43	1.43	0.22495	Hexokinase, N-terminal (1);	0.319071	0.22897	N	0.054307	D	0.98005	0.9343	M	0.78801	2.425	0.33245	D	0.5578	D	0.64830	0.994	P	0.58820	0.846	D	0.97198	0.9862	10	0.59425	D	0.04	-16.9109	6.465	0.21977	0.0881:0.0:0.5593:0.3525	.	480	P52790	HXK3_HUMAN	W	480	ENSP00000292432:R480W	ENSP00000292432:R480W	R	-	1	2	HK3	176247220	0.997000	0.39634	0.966000	0.40874	0.008000	0.06430	2.526000	0.45607	-0.045000	0.13468	-1.334000	0.01262	CGG		0.662	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			A	176314614	G	A	176314614	3	1	5	1	0	0	0	0	1	0	0	0	7213	1115	39	1	1369	1	HK3	5	176314614	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	6151822	176314614	4600646	98	463										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954921	30954921	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aactctgactccagcacaacCtccagtggggccagcacagc	9	16	1	1	rs548248760	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:30954921C>G	ENST00000376296.3	+	2	1210	c.969C>G	c.(967-969)acC>acG	p.T323T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	323	28 X 15 AA approximate tandem repeats.|Ser-rich.		T -> P (in dbSNP:rs41288679). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAGCACAACCTCCAGTGGGG	0.627													c|||	32	0.00638978	0.0083	0.0144	5008	,	,		22635	0.001		0.005	False		,,,				2504	0.0051															0			6																																								31062900	SO:0001819	synonymous_variant	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.969C>G	6.37:g.30954921C>G			31062900	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																				0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		G	30954921	C	G	30954921	2	3	5	1	0	0	0	0	0	0	0	1	10007	668	24	5		5	MUC21	6	30954921	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10		30954921	140160146	99	464										
RNF8	9025	hgsc.bcm.edu	37	chr6	37358529	37358529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctccaaagcaaagagattgTtctgaagaccgtgctctaag	9	9	3	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:37358529T>C	ENST00000373479.4	+	8	1646	c.1453T>C	c.(1453-1455)Ttc>Ctc	p.F485L	RNF8_ENST00000469731.1_Silent_p.C416C	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	485					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						AAAGAGATTGTTCTGAAGACC	0.502																																																0			6											113	110	111					6																	37358529		2203	4300	6503	37466507	SO:0001583	missense	9025			AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"RING-type (C3HC4) zinc fingers"	10071	protein-coding gene	gene with protein product		611685	"ring finger protein (C3HC4 type) 8", "ring finger protein 8"			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1453T>C	6.37:g.37358529T>C	ENSP00000362578:p.Phe485Leu		37466507	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Missense_Mutation	SNP	ENST00000373479.4	37	CCDS4834.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.530486	0.27387	.	.	ENSG00000112130	ENST00000373479;ENST00000498460	D	0.84442	-1.85	5.02	3.85	0.44370	.	0.700839	0.13829	N	0.359888	T	0.60470	0.2271	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54951	-0.8216	9	0.23302	T	0.38	.	7.5659	0.27879	0.0:0.0965:0.0:0.9035	.	485	O76064	RNF8_HUMAN	L	485;176	ENSP00000362578:F485L	ENSP00000362578:F485L	F	+	1	0	RNF8	37466507	0.003000	0.15002	0.860000	0.33809	0.569000	0.35902	1.059000	0.30517	1.033000	0.39918	0.533000	0.62120	TTC		0.502	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2			C	37358529	T	C	37358529	3	2	5	1	0	0	0	0	1	0	0	0	13537	1734	60	4	1483	4	RNF8	6	37358529	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	6403608	37358529	133756538	100	465										
TJAP1	93643	hgsc.bcm.edu	37	chr6	43466758	43466758	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaatgactagtgccgcccctGctaagaaaccctaccgtaag	9	13	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:43466758G>C	ENST00000372445.5	+	4	395	c.19G>C	c.(19-21)Gct>Cct	p.A7P	TJAP1_ENST00000372452.1_Missense_Mutation_p.A7P|TJAP1_ENST00000372449.1_Missense_Mutation_p.A7P|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Missense_Mutation_p.A7P|TJAP1_ENST00000259751.1_Missense_Mutation_p.A7P|TJAP1_ENST00000438588.2_Missense_Mutation_p.A7P|TJAP1_ENST00000372444.2_Missense_Mutation_p.A7P	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	7					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TGCCGCCCCTGCTAAGAAACC	0.582																																																0			6											84	70	75					6																	43466758		2203	4300	6503	43574736	SO:0001583	missense	93643			AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.19G>C	6.37:g.43466758G>C	ENSP00000361522:p.Ala7Pro		43574736	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835493	0.50951	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.31	4.36	0.52297	.	0.275252	0.35708	N	0.003033	T	0.21062	0.0507	L	0.40543	1.245	0.40092	D	0.976269	B;P;P	0.45212	0.0;0.853;0.853	B;B;B	0.42882	0.002;0.401;0.401	T	0.10636	-1.0621	10	0.59425	D	0.04	-5.8652	5.9438	0.19207	0.0992:0.0:0.582:0.3188	.	7;7;7	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	P	7	ENSP00000361521:A7P;ENSP00000361522:A7P;ENSP00000407080:A7P;ENSP00000390981:A7P;ENSP00000259751:A7P;ENSP00000361530:A7P;ENSP00000361527:A7P;ENSP00000408769:A7P	ENSP00000259751:A7P	A	+	1	0	TJAP1	43574736	0.896000	0.30565	1.000000	0.80357	0.999000	0.98932	2.092000	0.41700	2.495000	0.84180	0.655000	0.94253	GCT		0.582	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		C	43466758	G	C	43466758	3	2	5	1	0	0	0	0	1	0	0	0	15967	1319	46	5	21	5	TJAP1	6	43466758	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	6108229	43466758	127648309	101	466										
DST	667	hgsc.bcm.edu	37	chr6	56483974	56483974	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcgtagctgatctttaaaacCatctgcctgaattttcagtg	8	9	3	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:56483974C>A	ENST00000370765.6	-	23	4965	c.4858G>T	c.(4858-4860)Ggt>Tgt	p.G1620C	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	6360					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCTTTAAAACCATCTGCCTGA	0.353																																																0			6											171	166	168					6																	56483974		2202	4299	6501	56591933	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4858G>T	6.37:g.56483974C>A	ENSP00000359801:p.Gly1620Cys		56591933	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566457	0.45694	.	.	ENSG00000151914	ENST00000370765	T	0.39592	1.07	5.35	4.25	0.50352	.	.	.	.	.	T	0.39332	0.1074	.	.	.	0.20074	N	0.999932	D	0.63880	0.993	P	0.56514	0.8	T	0.40327	-0.9569	7	0.56958	D	0.05	.	7.7125	0.28686	0.0:0.7506:0.0:0.2494	.	1620	Q03001-3	.	C	1620	ENSP00000359801:G1620C	ENSP00000359801:G1620C	G	-	1	0	DST	56591933	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.311000	0.43717	2.661000	0.90470	0.650000	0.86243	GGT		0.353	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		A	56483974	C	A	56483974	3	1	5	1	0	0	0	0	1	0	0	0	4794	594	21	2	15545	2	DST	6	56483974	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	13017216	56483974	114631093	102	467										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93965716	93965716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agcagcaattcctctcagcaTtcctactaactgaatgactg	6	12	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:93965716T>C	ENST00000369303.4	-	13	2396	c.2212A>G	c.(2212-2214)Atg>Gtg	p.M738V		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	738	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CCTCTCAGCATTCCTACTAAC	0.403																																																0			6											135	130	132					6																	93965716		2203	4300	6503	94022437	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2212A>G	6.37:g.93965716T>C	ENSP00000358309:p.Met738Val		94022437	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569161	0.86439	.	.	ENSG00000135333	ENST00000369303	T	0.61040	0.14	5.75	5.75	0.90469	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	L	0.29908	0.895	0.80722	D	1	P;D;D	0.55385	0.825;0.964;0.971	P;P;P	0.51615	0.629;0.546;0.675	T	0.56153	-0.8026	10	0.72032	D	0.01	.	16.0455	0.80717	0.0:0.0:0.0:1.0	.	734;733;738	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	V	738	ENSP00000358309:M738V	ENSP00000358309:M738V	M	-	1	0	EPHA7	94022437	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.189000	0.69895	0.460000	0.39030	ATG		0.403	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			C	93965716	T	C	93965716	3	2	5	1	0	0	0	0	1	0	0	0	5185	1493	52	4	804	4	EPHA7	6	93965716	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	37481742	93965716	77149351	103	468										
AKD1	221264	hgsc.bcm.edu	37	chr6	109854526	109854526	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttttgttttagtttccacttTtcaatttgggcaggaaggag	10	5	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:109854526T>C	ENST00000424296.2	-	28	3574	c.3498A>G	c.(3496-3498)gaA>gaG	p.E1166E	AK9_ENST00000341338.6_Silent_p.E245E|AK9_ENST00000355283.1_Silent_p.E245E	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1166	Adenylate kinase 2.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.E245E(1)									GTTTCCACTTTTCAATTTGGG	0.358																																																1	Substitution - coding silent(1)	ovary(1)	6											169	151	157					6																	109854526		2203	4300	6503	109961219	SO:0001819	synonymous_variant	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3498A>G	6.37:g.109854526T>C			109961219	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	T	8.653	0.898716	0.17686	.	.	ENSG00000155085	ENST00000470564;ENST00000491875	.	.	.	5.16	-0.0333	0.13901	.	.	.	.	.	T	0.34077	0.0885	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.22941	-1.0202	4	.	.	.	.	4.5933	0.12317	0.1325:0.2279:0.0:0.6396	.	.	.	.	R	4;101	.	.	K	-	2	0	AKD1	109961219	0.456000	0.25744	0.472000	0.27241	0.889000	0.51656	0.241000	0.18065	0.047000	0.15862	0.448000	0.29417	AAA		0.358	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		C	109854526	T	C	109854526	2	2	5	1	0	0	0	0	0	0	0	1	460	1838	64	4		4	AKD1	6	109854526	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	15888810	109854526	61260541	104	469										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121638667	121638667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caatgatgaatcactatcagAgcaattgtctgtgcggtaac	9	8	3	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:121638667A>G	ENST00000398212.2	-	3	518	c.469T>C	c.(469-471)Tct>Cct	p.S157P	TBC1D32_ENST00000275159.6_Missense_Mutation_p.S157P	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	157					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCACTATCAGAGCAATTGTCT	0.318																																																0			6											296	270	278					6																	121638667		1862	4091	5953	121680366	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.469T>C	6.37:g.121638667A>G	ENSP00000381270:p.Ser157Pro		121680366	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870427	0.51588	.	.	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.25414	1.8;1.8;1.8	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	M	0.62016	1.91	0.54753	D	0.999987	P	0.47762	0.9	B	0.43194	0.411	T	0.02805	-1.1108	10	0.51188	T	0.08	-0.0535	15.0687	0.72017	1.0:0.0:0.0:0.0	.	157	Q96NH3	BROMI_HUMAN	P	157	ENSP00000275159:S157P;ENSP00000381270:S157P;ENSP00000397993:S157P	ENSP00000275159:S157P	S	-	1	0	C6orf170	121680366	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.050000	0.89445	2.013000	0.59113	0.533000	0.62120	TCT		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121638667	A	G	121638667	3	3	5	1	0	0	0	0	1	0	0	0	2350	304	11	4	3424	4	C6orf170	6	121638667	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	11784141	121638667	49476400	105	470										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161491657	161491657	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tagttttctgaatttccagaTcccatgtggggttcagatta	9	7	2	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:161491657T>C	ENST00000392142.4	+	4	1873	c.1725T>C	c.(1723-1725)gaT>gaC	p.D575D	MAP3K4_ENST00000348824.7_Silent_p.D575D|MAP3K4_ENST00000366919.2_Silent_p.D575D|MAP3K4_ENST00000366920.2_Silent_p.D575D	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	575					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AATTTCCAGATCCCATGTGGG	0.428																																																0			6											123	122	123					6																	161491657		2203	4300	6503	161411647	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.1725T>C	6.37:g.161491657T>C			161411647	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.428	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			C	161491657	T	C	161491657	2	2	5	1	0	0	0	0	0	0	0	1	9282	1432	50	4		4	MAP3K4	6	161491657	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	39852990	161491657	9623410	106	471										
MAD1L1	8379	hgsc.bcm.edu	37	chr7	1855715	1855715	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagcctgcaggctacgccacGgtctggcggctgaagagctc	15	13	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:1855715G>A	ENST00000406869.1	-	19	2705	c.2148C>T	c.(2146-2148)acC>acT	p.T716T	MAD1L1_ENST00000402746.1_Silent_p.T624T|MAD1L1_ENST00000399654.2_Silent_p.T716T|MAD1L1_ENST00000265854.7_Silent_p.T716T			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	716					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GCTACGCCACGGTCTGGCGGC	0.692																																																0			7											21	27	25					7																	1855715		2055	4208	6263	1822241	SO:0001819	synonymous_variant	8379			U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.2148C>T	7.37:g.1855715G>A			1822241	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1																																																																																				0.692	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	1855715	G	A	1855715	2	1	5	1	0	0	0	0	0	0	0	1	9177	1103	39	1		1	MAD1L1	7	1855715	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10		1855715	157282948	107	472										
GLI3	2737	hgsc.bcm.edu	37	chr7	42004760	42004760	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cattcaccatgctgccagctGactcatttggcgctaccggc	9	15	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:42004760G>T	ENST00000395925.3	-	15	3995	c.3911C>A	c.(3910-3912)tCa>tAa	p.S1304*	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1304			S -> P (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCTGCCAGCTGACTCATTTGG	0.637									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											40	40	40					7																	42004760		2203	4300	6503	41971285	SO:0001587	stop_gained	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3911C>A	7.37:g.42004760G>T	ENSP00000379258:p.Ser1304*		41971285	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Nonsense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	39	7.552695	0.98355	.	.	ENSG00000106571	ENST00000395925	.	.	.	5.65	2.4	0.29515	.	1.424740	0.03942	N	0.287122	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	6.0097	0.19569	0.2297:0.0:0.5534:0.2169	.	.	.	.	X	1304	.	ENSP00000379258:S1304X	S	-	2	0	GLI3	41971285	0.001000	0.12720	0.161000	0.22692	0.066000	0.16364	0.915000	0.28638	0.721000	0.32231	0.655000	0.94253	TCA		0.637	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42004760	G	T	42004760	4	4	5	1	0	0	0	0	0	1	0	0	6459	1294	45	2	835	2	GLI3	7	42004760	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	40149045	42004760	117133903	108	473										
EGFR	1956	hgsc.bcm.edu	37	chr7	55259522	55259522	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acagattttgggctggccaaActgctgggtgcggaagagaa	15	7	0	2	rs397517130		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:55259522A>G	ENST00000275493.2	+	21	2757	c.2580A>G	c.(2578-2580)aaA>aaG	p.K860K	EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Silent_p.K815K|EGFR_ENST00000454757.2_Silent_p.K807K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	860	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGCTGGCCAAACTGCTGGGTG	0.552		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											103	97	99					7																	55259522		2203	4300	6503	55227016	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2580A>G	7.37:g.55259522A>G			55227016	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.552	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55259522	A	G	55259522	2	3	5	1	0	0	0	0	0	0	0	1	4978	40	2	4		4	EGFR	7	55259522	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	13254762	55259522	103879141	109	474										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72884712	72884712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgtgccaataggagtcctgcGcatgactagtttggccttgg	13	9	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:72884712G>A	ENST00000339594.4	-	8	3033	c.2695C>T	c.(2695-2697)Cgc>Tgc	p.R899C	BAZ1B_ENST00000404251.1_Missense_Mutation_p.R899C	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	899					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GGAGTCCTGCGCATGACTAGT	0.423																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											0			7											190	161	171					7																	72884712		2203	4300	6503	72522648	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2695C>T	7.37:g.72884712G>A	ENSP00000342434:p.Arg899Cys		72522648	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.915905	0.73098	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.63580	-0.05;-0.05	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.74030	0.3663	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74003	-0.3804	10	0.46703	T	0.11	-15.9366	12.7402	0.57249	0.0:0.0:0.8358:0.1641	.	899	Q9UIG0	BAZ1B_HUMAN	C	899	ENSP00000342434:R899C;ENSP00000385442:R899C	ENSP00000342434:R899C	R	-	1	0	BAZ1B	72522648	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	4.869000	0.63028	2.440000	0.82611	0.557000	0.71058	CGC		0.423	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		A	72884712	G	A	72884712	3	1	5	1	0	0	0	0	1	0	0	0	1331	1087	38	1	1804	1	BAZ1B	7	72884712	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	17625190	72884712	86253951	110	475										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726163	91726163	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agaacaaggtcgaaacttagAgcttcaggtacttcttgaat	9	7	2	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:91726163A>G	ENST00000359028.2	+	41	10127	c.9902A>G	c.(9901-9903)gAg>gGg	p.E3301G	AKAP9_ENST00000358100.2_Missense_Mutation_p.E3247G|AKAP9_ENST00000356239.3_Missense_Mutation_p.E3297G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3301			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CGAAACTTAGAGCTTCAGGTA	0.433			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											107	104	105					7																	91726163		2203	4300	6503	91564099	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9902A>G	7.37:g.91726163A>G	ENSP00000351922:p.Glu3301Gly		91564099	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	15.36	2.811806	0.50527	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.05580	3.52;3.52;3.59;3.42	5.56	3.21	0.36854	.	0.170707	0.28192	N	0.016253	T	0.06416	0.0165	L	0.42245	1.32	0.40521	D	0.98083	B;B;B;B;B	0.30542	0.284;0.197;0.125;0.197;0.197	B;B;B;B;B	0.30251	0.113;0.09;0.041;0.09;0.09	T	0.37009	-0.9724	10	0.33141	T	0.24	.	9.4705	0.38839	0.8543:0.0:0.1457:0.0	.	572;3301;3301;3297;3289	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	G	3297;3301;3247;3301;1143	ENSP00000348573:E3297G;ENSP00000351922:E3301G;ENSP00000350813:E3247G;ENSP00000378042:E1143G	ENSP00000348573:E3297G	E	+	2	0	AKAP9	91564099	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.894000	0.63206	0.496000	0.27904	0.533000	0.62120	GAG		0.433	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91726163	A	G	91726163	3	3	5	1	0	0	0	0	1	0	0	0	459	304	11	4	10052	4	AKAP9	7	91726163	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	18841451	91726163	67412500	111	476										
PON3	5446	hgsc.bcm.edu	37	chr7	94993256	94993256	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctcccttgggctgtagaaaAgaacataagtccagcgaaga	10	10	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:94993256A>T	ENST00000265627.5	-	6	624	c.614T>A	c.(613-615)cTt>cAt	p.L205H	PON3_ENST00000451904.1_Missense_Mutation_p.L205H|PON3_ENST00000427422.1_Missense_Mutation_p.L205H|PON1_ENST00000542556.1_Intron	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	205					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GCTGTAGAAAAGAACATAAGT	0.443																																																0			7											182	187	185					7																	94993256		2203	4300	6503	94831192	SO:0001583	missense	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.614T>A	7.37:g.94993256A>T	ENSP00000265627:p.Leu205His		94831192	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.875033	0.72180	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.47177	0.85;0.85	5.27	4.12	0.48240	Six-bladed beta-propeller, TolB-like (1);	0.387835	0.28442	N	0.015332	T	0.61540	0.2355	M	0.66939	2.045	0.09310	N	0.999999	D;D	0.69078	0.997;0.996	P;P	0.61874	0.87;0.895	T	0.55755	-0.8091	10	0.87932	D	0	-2.1494	10.806	0.46518	0.9247:0.0:0.0753:0.0	.	253;205	B4E2I0;Q15166	.;PON3_HUMAN	H	205	ENSP00000265627:L205H;ENSP00000413276:L205H	ENSP00000265627:L205H	L	-	2	0	PON3	94831192	0.999000	0.42202	0.022000	0.16811	0.325000	0.28411	6.606000	0.74159	0.958000	0.37956	0.533000	0.62120	CTT		0.443	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		T	94993256	A	T	94993256	3	4	5	1	0	0	0	0	1	0	0	0	12281	72	3	5	466	5	PON3	7	94993256	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	3267093	94993256	64145407	112	477										
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95665046	95665046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgaggaaggtacagtctacaCggcttgtcgtcatggaaggt	14	7	2	1	rs551953723		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:95665046C>T	ENST00000324972.6	+	13	1590	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M	DYNC1I1_ENST00000359388.4_Missense_Mutation_p.T429M|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.T429M|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.T446M|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.T449M|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.T449M	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	466					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			ACAGTCTACACGGCTTGTCGT	0.448													C|||	1	0.000199681	0	0	5008	,	,		22007	0		0.001	False		,,,				2504	0															0			7											344	281	302					7																	95665046		2203	4300	6503	95502982	SO:0001583	missense	1780			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1397C>T	7.37:g.95665046C>T	ENSP00000320130:p.Thr466Met		95502982	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922266	0.33908	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.06218	3.33;3.33;3.33;3.33;3.33;3.33	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.050263	0.85682	D	0.000000	T	0.08313	0.0207	L	0.52364	1.645	0.58432	D	0.999992	P;P;P;B;P	0.45672	0.624;0.741;0.741;0.425;0.864	B;B;B;B;B	0.35182	0.097;0.197;0.197;0.097;0.133	T	0.13548	-1.0505	10	0.49607	T	0.09	-20.8872	19.0933	0.93238	0.0:1.0:0.0:0.0	.	449;446;449;466;429	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	M	449;466;429;446;429;449	ENSP00000392337:T449M;ENSP00000320130:T466M;ENSP00000438377:T429M;ENSP00000398118:T446M;ENSP00000352348:T429M;ENSP00000412444:T449M	ENSP00000320130:T466M	T	+	2	0	DYNC1I1	95502982	0.997000	0.39634	0.971000	0.41717	0.492000	0.33523	3.645000	0.54389	2.830000	0.97506	0.585000	0.79938	ACG		0.448	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		T	95665046	C	T	95665046	3	4	5	1	0	0	0	0	1	0	0	0	4853	536	19	1	1443	1	DYNC1I1	7	95665046	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	671790	95665046	63473617	113	478										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518303	113518303	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttacaaatattttctgatttCgtagaaataggttggctagc	8	5	1	2	rs150965727		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:113518303C>T	ENST00000284601.3	-	4	2912	c.2844G>A	c.(2842-2844)acG>acA	p.T948T		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	948					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.T948T(3)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTTCTGATTTCGTAGAAATAG	0.378																																																3	Substitution - coding silent(3)	skin(3)	7						C		0,4406		0,0,2203	86	86	86	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2844	-8.2	0	7	dbSNP_134	86	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PPP1R3A	NM_002711.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		948/1123	113518303	1,13003	2203	4299	6502	113305539	SO:0001819	synonymous_variant	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2844G>A	7.37:g.113518303C>T			113305539	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	37	CCDS5759.1																																																																																				0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113518303	C	T	113518303	2	4	5	1	0	0	0	0	0	0	0	1	12405	871	31	1		1	PPP1R3A	7	113518303	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	17853257	113518303	45620360	114	479										
NPBWR1	2831	hgsc.bcm.edu	37	chr8	53852612	53852612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttgtctacgcggtgatctgcGccgtgggtctggcgggcaac	16	11	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:53852612G>A	ENST00000331251.3	+	1	1622	c.145G>A	c.(145-147)Gcc>Acc	p.A49T		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	49					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)	p.A49T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GGTGATCTGCGCCGTGGGTCT	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	8											33	30	31					8																	53852612		2202	4298	6500	54015165	SO:0001583	missense	2831			BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"GPCR / Class A : Neuropeptide receptors : W/B"	4522	protein-coding gene	gene with protein product		600730	"G protein-coupled receptor 7"	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.145G>A	8.37:g.53852612G>A	ENSP00000330284:p.Ala49Thr		54015165	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	G	36	5.903824	0.97087	.	.	ENSG00000183729	ENST00000331251	T	0.37235	1.21	4.74	4.74	0.60224	.	0.115150	0.36815	N	0.002381	T	0.38558	0.1045	N	0.08118	0	0.58432	D	0.999998	D	0.76494	0.999	P	0.62435	0.902	T	0.49826	-0.8898	10	0.52906	T	0.07	.	17.9109	0.88934	0.0:0.0:1.0:0.0	.	49	P48145	NPBW1_HUMAN	T	49	ENSP00000330284:A49T	ENSP00000330284:A49T	A	+	1	0	NPBWR1	54015165	1.000000	0.71417	0.987000	0.45799	0.935000	0.57460	7.403000	0.79983	2.457000	0.83068	0.655000	0.94253	GCC		0.697	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285		A	53852612	G	A	53852612	3	1	5	1	0	0	0	0	1	0	0	0	10599	1087	38	1	147	1	NPBWR1	8	53852612	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		53852612	92511410	115	480										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70964378	70964378	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tctgagaagattttcccacaGatgctgcatgagcagccatc	9	11	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:70964378G>T	ENST00000276594.2	-	8	1851	c.1650C>A	c.(1648-1650)atC>atA	p.I550I		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	550					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TTTTCCCACAGATGCTGCATG	0.478																																					NSCLC(129;99 1813 5906 40656 46114)											0			8											120	113	116					8																	70964378		2203	4300	6503	71126932	SO:0001819	synonymous_variant	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1650C>A	8.37:g.70964378G>T			71126932	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																				0.478	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70964378	G	T	70964378	2	4	5	1	0	0	0	0	0	0	0	1	12489	932	33	2		2	PRDM14	8	70964378	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	17111766	70964378	75399644	116	481										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70978671	70978671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggggaagcgggcacagttgaCataggacatccagttccccg	14	11	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:70978671C>T	ENST00000276594.2	-	5	1183	c.982G>A	c.(982-984)Gtc>Atc	p.V328I		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	328	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.V328I(1)		NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GCACAGTTGACATAGGACATC	0.428																																					NSCLC(129;99 1813 5906 40656 46114)											1	Substitution - Missense(1)	ovary(1)	8											128	125	126					8																	70978671		2203	4300	6503	71141225	SO:0001583	missense	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.982G>A	8.37:g.70978671C>T	ENSP00000276594:p.Val328Ile		71141225	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682484	0.88542	.	.	ENSG00000147596	ENST00000276594	T	0.78595	-1.19	5.89	5.89	0.94794	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.83968	0.5369	L	0.41492	1.28	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78909	-0.2018	10	0.22109	T	0.4	-29.9487	20.2618	0.98447	0.0:1.0:0.0:0.0	.	328	Q9GZV8	PRD14_HUMAN	I	328	ENSP00000276594:V328I	ENSP00000276594:V328I	V	-	1	0	PRDM14	71141225	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	7.481000	0.81124	2.793000	0.96121	0.655000	0.94253	GTC		0.428	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70978671	C	T	70978671	3	4	5	1	0	0	0	0	1	0	0	0	12489	478	17	3	749	3	PRDM14	8	70978671	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	14293	70978671	75385351	117	482										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92998451	92998451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctcggcgtcactgtaccgccGgatccagtaattcaattctt	8	13	3	0	rs200248598		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:92998451G>A	ENST00000523629.1	-	9	1634	c.1180C>T	c.(1180-1182)Cgg>Tgg	p.R394W	RUNX1T1_ENST00000518844.1_Missense_Mutation_p.R367W|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.R357W|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.R357W|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.R394W|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.R357W|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.R405W|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.R367W	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	394					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R357W(1)|p.R405W(1)|p.R394W(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CTGTACCGCCGGATCCAGTAA	0.517													G|||	1	0.000199681	0	0	5008	,	,		14722	0		0.001	False		,,,				2504	0															3	Substitution - Missense(3)	lung(3)	8											119	120	120					8																	92998451		2203	4300	6503	93067627	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1180C>T	8.37:g.92998451G>A	ENSP00000428543:p.Arg394Trp		93067627	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	29.1	4.978612	0.92982	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.67	5.67	0.87782	NHR2-like (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.996	T	0.79711	-0.1689	10	0.87932	D	0	-16.5075	14.5933	0.68386	0.0:0.0:0.8542:0.1458	.	405;394;367	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	W	394;367;394;357;357;357;405;367	ENSP00000428543:R394W;ENSP00000379520:R367W;ENSP00000265814:R394W;ENSP00000353504:R357W;ENSP00000390137:R357W;ENSP00000428742:R357W;ENSP00000402257:R405W;ENSP00000430728:R367W	ENSP00000265814:R394W	R	-	1	2	RUNX1T1	93067627	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.515000	0.60489	2.677000	0.91161	0.655000	0.94253	CGG		0.517	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	92998451	G	A	92998451	3	1	5	1	0	0	0	0	1	0	0	0	13784	1115	39	1	650	1	RUNX1T1	8	92998451	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	22019780	92998451	53365571	118	483										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94809683	94809683	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctctttcaagtacttactgtCctcttctttttggaggtata	6	9	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:94809683C>T	ENST00000453321.3	+	20	2143	c.2085C>T	c.(2083-2085)gtC>gtT	p.V695V	TMEM67_ENST00000409623.3_Silent_p.V614V	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	695					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)	p.V685V(1)		breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TACTTACTGTCCTCTTCTTTT	0.299																																																1	Substitution - coding silent(1)	ovary(1)	8											111	106	108					8																	94809683		2203	4300	6503	94878859	SO:0001819	synonymous_variant	91147			BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2085C>T	8.37:g.94809683C>T			94878859	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	37	CCDS6258.2																																																																																				0.299	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		T	94809683	C	T	94809683	2	4	5	1	0	0	0	0	0	0	0	1	16235	842	30	3		3	TMEM67	8	94809683	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	1811232	94809683	51554339	119	484										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113241027	113241027	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caaatcctgcaaatataagtGcaaaaaaaggcacaagaata	6	7	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113241027G>T	ENST00000297405.5	-	70	11166	c.10922C>A	c.(10921-10923)gCa>gAa	p.A3641E	CSMD3_ENST00000343508.3_Missense_Mutation_p.A3601E|CSMD3_ENST00000455883.2_Missense_Mutation_p.A3472E|CSMD3_ENST00000352409.3_Missense_Mutation_p.A3571E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3641						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAATATAAGTGCAAAAAAAGG	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											79	82	81					8																	113241027		2203	4297	6500	113310203	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10922C>A	8.37:g.113241027G>T	ENSP00000297405:p.Ala3641Glu		113310203	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227201	0.95173	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.40476	1.39;1.38;1.45;1.03;1.42	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	T	0.66829	0.2829	M	0.73217	2.22	0.80722	D	1	D;D;P	0.89917	1.0;0.999;0.845	D;D;P	0.87578	0.998;0.995;0.458	T	0.67741	-0.5592	10	0.87932	D	0	.	20.14	0.98056	0.0:0.0:1.0:0.0	.	3472;3641;3601	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	3601;3641;2911;3472;3571	ENSP00000345799:A3601E;ENSP00000297405:A3641E;ENSP00000341558:A2911E;ENSP00000412263:A3472E;ENSP00000343124:A3571E	ENSP00000297405:A3641E	A	-	2	0	CSMD3	113310203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.837000	0.97791	0.591000	0.81541	GCA		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113241027	G	T	113241027	3	4	5	1	0	0	0	0	1	0	0	0	3952	1319	46	2	209	2	CSMD3	8	113241027	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	18431344	113241027	33122995	120	485										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113275951	113275951	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aggatagctcatagcctggaGaacagatgtagctaatacta	10	7	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113275951G>T	ENST00000297405.5	-	61	10023	c.9779C>A	c.(9778-9780)tCt>tAt	p.S3260Y	CSMD3_ENST00000343508.3_Missense_Mutation_p.S3220Y|CSMD3_ENST00000455883.2_Missense_Mutation_p.S3091Y|CSMD3_ENST00000352409.3_Missense_Mutation_p.S3190Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3260	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATAGCCTGGAGAACAGATGTA	0.473										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											108	91	97					8																	113275951		2203	4300	6503	113345127	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9779C>A	8.37:g.113275951G>T	ENSP00000297405:p.Ser3260Tyr		113345127	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.985315	0.35036	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.76	5.76	0.90799	Complement control module (2);Sushi/SCR/CCP (3);	0.194332	0.37261	N	0.002175	T	0.69744	0.3145	N	0.25789	0.76	0.80722	D	1	P;D;D	0.71674	0.951;0.961;0.998	P;P;D	0.69479	0.864;0.905;0.964	T	0.67979	-0.5530	10	0.38643	T	0.18	.	19.9759	0.97304	0.0:0.0:1.0:0.0	.	3091;3260;3220	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	3220;3260;2530;3091;3190	ENSP00000345799:S3220Y;ENSP00000297405:S3260Y;ENSP00000341558:S2530Y;ENSP00000412263:S3091Y;ENSP00000343124:S3190Y	ENSP00000297405:S3260Y	S	-	2	0	CSMD3	113345127	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.942000	0.63547	2.713000	0.92767	0.655000	0.94253	TCT		0.473	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113275951	G	T	113275951	3	4	5	1	0	0	0	0	1	0	0	0	3952	942	33	2	1388	2	CSMD3	8	113275951	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	34924	113275951	33088071	121	486										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113392655	113392655	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttagatacagattattagacGtactattcaaaagatggggt	9	4	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113392655G>A	ENST00000297405.5	-	38	6306	c.6062C>T	c.(6061-6063)aCg>aTg	p.T2021M	CSMD3_ENST00000343508.3_Missense_Mutation_p.T1981M|CSMD3_ENST00000455883.2_Missense_Mutation_p.T1917M|CSMD3_ENST00000352409.3_Missense_Mutation_p.T1951M	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2021	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T2021K(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTATTAGACGTACTATTCAA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	ovary(1)	8											105	112	110					8																	113392655		2203	4292	6495	113461831	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6062C>T	8.37:g.113392655G>A	ENSP00000297405:p.Thr2021Met		113461831	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263582	0.80358	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	5.64	5.64	0.86602	CUB (5);	0.000000	0.64402	D	0.000001	T	0.56717	0.2004	M	0.90252	3.1	0.52099	D	0.999941	D;P;D	0.89917	1.0;0.955;1.0	D;P;D	0.97110	0.999;0.816;1.0	T	0.62891	-0.6758	10	0.52906	T	0.07	.	19.2842	0.94065	0.0:0.0:1.0:0.0	.	1917;2021;1981	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	M	1981;2021;1291;1917;1951	ENSP00000345799:T1981M;ENSP00000297405:T2021M;ENSP00000341558:T1291M;ENSP00000412263:T1917M;ENSP00000343124:T1951M	ENSP00000297405:T2021M	T	-	2	0	CSMD3	113461831	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.573000	0.82421	2.654000	0.90174	0.591000	0.81541	ACG		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113392655	G	A	113392655	3	1	5	1	0	0	0	0	1	0	0	0	3952	1145	40	1	5197	1	CSMD3	8	113392655	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	116704	113392655	32971367	122	487										
ADCY8	114	hgsc.bcm.edu	37	chr8	132051814	132051814	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaggcctgctgccaggatctGggtggtcatggccacccagg	16	12	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:132051814G>A	ENST00000286355.5	-	1	2858	c.766C>T	c.(766-768)Cag>Tag	p.Q256*	ADCY8_ENST00000377928.3_Nonsense_Mutation_p.Q256*	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	256					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.Q256*(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCCAGGATCTGGGTGGTCATG	0.642										HNSCC(32;0.087)																																						1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	8											46	41	43					8																	132051814		2203	4300	6503	132120996	SO:0001587	stop_gained	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.766C>T	8.37:g.132051814G>A	ENSP00000286355:p.Gln256*		132120996		Nonsense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	54	22.537047	0.99949	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	18.2863	0.90115	0.0:0.0:1.0:0.0	.	.	.	.	X	256	.	ENSP00000286355:Q256X	Q	-	1	0	ADCY8	132120996	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.444000	0.97578	2.580000	0.87095	0.455000	0.32223	CAG		0.642	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132051814	G	A	132051814	4	1	5	1	0	0	0	0	0	1	0	0	300	1357	47	3	3061	3	ADCY8	8	132051814	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	18659159	132051814	14312208	123	488										
MLLT3	4300	hgsc.bcm.edu	37	chr9	20414187	20414187	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttgtgatccctggaaggttcTttgaaggcacttttatgttc	10	7	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:20414187T>C	ENST00000380338.4	-	5	943	c.657A>G	c.(655-657)aaA>aaG	p.K219K	MLLT3_ENST00000475957.1_5'UTR|MIR4473_ENST00000583731.1_RNA|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.K216K	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	219					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TGGAAGGTTCTTTGAAGGCAC	0.388			T	MLL	ALL																																		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	0			9											256	272	267					9																	20414187		2203	4300	6503	20404187	SO:0001819	synonymous_variant	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.657A>G	9.37:g.20414187T>C			20404187	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				0.388	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		C	20414187	T	C	20414187	2	2	5	1	0	0	0	0	0	0	0	1	9658	1606	56	4		4	MLLT3	9	20414187	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10		20414187	120799244	124	489										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79966342	79966342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggagatgtagaaaaagccatGgtgaagtaacacagaaggat	13	4	0	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:79966342G>A	ENST00000360280.3	+	53	7659	c.7399G>A	c.(7399-7401)Ggt>Agt	p.G2467S	VPS13A_ENST00000357409.5_Missense_Mutation_p.G2467S|VPS13A_ENST00000376634.4_Missense_Mutation_p.G2467S|VPS13A_ENST00000376636.3_Missense_Mutation_p.G2428S	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2467					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAAAAGCCATGGTGAAGTAAC	0.473																																																0			9											164	159	161					9																	79966342		2203	4300	6503	79156162	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7399G>A	9.37:g.79966342G>A	ENSP00000353422:p.Gly2467Ser		79156162	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938545	0.73557	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.46819	1.03;0.86;0.94;1.03	5.19	5.19	0.71726	.	0.061993	0.64402	D	0.000005	T	0.63674	0.2531	M	0.72894	2.215	0.80722	D	1	P;D;D;D	0.71674	0.753;0.997;0.998;0.998	P;P;D;D	0.62955	0.511;0.908;0.909;0.909	T	0.58691	-0.7592	10	0.10377	T	0.69	.	18.6648	0.91485	0.0:0.0:1.0:0.0	.	2428;2467;2467;2467	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	S	2467;2428;2467;2467	ENSP00000365821:G2467S;ENSP00000365823:G2428S;ENSP00000353422:G2467S;ENSP00000349985:G2467S	ENSP00000349985:G2467S	G	+	1	0	VPS13A	79156162	1.000000	0.71417	0.993000	0.49108	0.754000	0.42855	7.778000	0.85637	2.563000	0.86464	0.555000	0.69702	GGT		0.473	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79966342	G	A	79966342	3	1	5	1	0	0	0	0	1	0	0	0	17229	1348	47	3	7609	3	VPS13A	9	79966342	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	59552155	79966342	61247089	125	490										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88247913	88247913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aggtaaggacagtaagaggaAgactgcagtccttcttcatt	11	7	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:88247913A>G	ENST00000357081.3	-	14	1823	c.1679T>C	c.(1678-1680)cTt>cCt	p.L560P	AGTPBP1_ENST00000376109.3_Missense_Mutation_p.L572P|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.L398P|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.L520P|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	560					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGTAAGAGGAAGACTGCAGTC	0.433																																																0			9											123	115	118					9																	88247913		2203	4300	6503	87437733	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1679T>C	9.37:g.88247913A>G	ENSP00000349592:p.Leu560Pro		87437733	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	A	3.894	-0.023389	0.07634	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.46063	2.21;2.21;2.18;0.88	5.93	3.45	0.39498	.	0.519691	0.19812	N	0.105516	T	0.15478	0.0373	N	0.03115	-0.41	0.09310	N	0.999994	B;B;B;B	0.10296	0.002;0.0;0.003;0.001	B;B;B;B	0.15484	0.001;0.001;0.013;0.001	T	0.05022	-1.0911	10	0.30854	T	0.27	-11.8214	1.2715	0.02022	0.3626:0.349:0.1186:0.1698	.	572;560;398;520	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	P	560;520;572;398	ENSP00000349592:L560P;ENSP00000365251:L520P;ENSP00000365277:L572P;ENSP00000402804:L398P	ENSP00000349592:L560P	L	-	2	0	AGTPBP1	87437733	0.995000	0.38212	0.988000	0.46212	0.312000	0.27988	1.181000	0.32017	2.271000	0.75665	0.533000	0.62120	CTT		0.433	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88247913	A	G	88247913	3	3	5	1	0	0	0	0	1	0	0	0	400	72	3	4	2053	4	AGTPBP1	9	88247913	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	8281571	88247913	52965518	126	491										
CDK20	23552	hgsc.bcm.edu	37	chr9	90582504	90582504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgggggcaggtccccctagaCgctgaggaatcggcagctca	15	12	1	2	rs376253655		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:90582504C>T	ENST00000325303.8	-	8	1219	c.914G>A	c.(913-915)cGt>cAt	p.R305H	CDK20_ENST00000605159.1_Missense_Mutation_p.V275I|CDK20_ENST00000336654.5_Missense_Mutation_p.R297H|CDK20_ENST00000375871.4_Missense_Mutation_p.V243I|CDK20_ENST00000375883.3_Missense_Mutation_p.R284H	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20	305					cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						TCCCCCTAGACGCTGAGGAAT	0.612																																																0			9						C	HIS/ARG,ILE/VAL,ILE/VAL,HIS/ARG,HIS/ARG	1,4267		0,1,2133	31	29	30		914,823,727,851,890	4.7	1	9		30	0,8326		0,0,4163	no	missense,missense,missense,missense,missense	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	29,29,29,29,29	0,1,6296	TT,TC,CC		0.0,0.0234,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	305/347,275/276,243/244,284/326,297/339	90582504	1,12593	2134	4163	6297	89772324	SO:0001583	missense	0			AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"Cyclin-dependent kinases"	21420	protein-coding gene	gene with protein product		610076	"cell cycle related kinase"	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.914G>A	9.37:g.90582504C>T	ENSP00000322343:p.Arg305His		89772324	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	23.7|23.7	4.446060|4.446060	0.84101|0.84101	2.34E-4|2.34E-4	0.0|0.0	ENSG00000156345|ENSG00000156345	ENST00000375883;ENST00000336654;ENST00000325303;ENST00000286878|ENST00000375871	T;T;T|T	0.69561|0.64438	-0.08;-0.24;-0.41|-0.1	4.7|4.7	4.7|4.7	0.59300|0.59300	Protein kinase-like domain (1);|.	0.065878|.	0.64402|.	D|.	0.000018|.	T|T	0.47377|0.47377	0.1442|0.1442	.|.	.|.	.|.	0.23636|0.23636	N|N	0.997237|0.997237	D;D;D|B	0.89917|0.30482	1.0;1.0;0.999|0.281	D;D;P|B	0.70935|0.19666	0.971;0.935;0.885|0.026	T|T	0.31530|0.31530	-0.9940|-0.9940	9|8	0.72032|0.30854	D|T	0.01|0.27	-17.2466|-17.2466	13.5185|13.5185	0.61553|0.61553	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	297;284;305|243	A2A390;E7EQ88;Q8IZL9|Q8IZL9-2	.;.;CDK20_HUMAN|.	H|I	284;297;305;284|243	ENSP00000365043:R284H;ENSP00000338975:R297H;ENSP00000322343:R305H|ENSP00000365031:V243I	ENSP00000286878:R284H|ENSP00000365031:V243I	R|V	-|-	2|1	0|0	CDK20|CDK20	89772324|89772324	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.785000|0.785000	0.44390|0.44390	4.951000|4.951000	0.63610|0.63610	2.335000|2.335000	0.79485|0.79485	0.561000|0.561000	0.74099|0.74099	CGT|GTC		0.612	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119		T	90582504	C	T	90582504	3	4	5	1	0	0	0	0	1	0	0	0	3143	536	19	1	130	1	CDK20	9	90582504	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2334591	90582504	50630927	127	492										
S1PR3	1903	hgsc.bcm.edu	37	chr9	91616968	91616968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcaaggctcagtggttcatcGtgttggctgtgctcaactcc	11	11	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:91616968G>A	ENST00000375846.3	+	1	5548	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	S1PR3_ENST00000358157.2_Missense_Mutation_p.V285M			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	285					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.V285M(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GTGGTTCATCGTGTTGGCTGT	0.597																																																1	Substitution - Missense(1)	endometrium(1)	9											119	73	89					9																	91616968		2203	4300	6503	90806788	SO:0001583	missense	1903			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.853G>A	9.37:g.91616968G>A	ENSP00000365006:p.Val285Met		90806788	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	37	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.620387	0.28801	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.72615	-0.67;-0.67	4.85	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.894418	0.09595	N	0.781019	T	0.60702	0.2289	L	0.46885	1.475	0.20764	N	0.999852	B	0.19817	0.039	B	0.14023	0.01	T	0.47548	-0.9109	10	0.34782	T	0.22	.	7.2013	0.25883	0.3589:0.0:0.6411:0.0	.	285	Q99500	S1PR3_HUMAN	M	285	ENSP00000350878:V285M;ENSP00000365006:V285M	ENSP00000350878:V285M	V	+	1	0	S1PR3	90806788	0.197000	0.23362	0.991000	0.47740	0.713000	0.41058	2.807000	0.47955	0.199000	0.20427	0.313000	0.20887	GTG		0.597	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		A	91616968	G	A	91616968	3	1	5	1	0	0	0	0	1	0	0	0	13832	1145	40	1	855	1	S1PR3	9	91616968	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	1034464	91616968	49596463	128	493										
SEMA4D	10507	hgsc.bcm.edu	37	chr9	91996163	91996163	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caggcgcagtaggggtcccgCgccagcacacagtcctcgca	13	16	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:91996163C>T	ENST00000450295.1	-	14	2321	c.1545G>A	c.(1543-1545)gcG>gcA	p.A515A	SEMA4D_ENST00000420987.1_Silent_p.A515A|SEMA4D_ENST00000438547.2_Silent_p.A515A|SEMA4D_ENST00000422704.2_Silent_p.A515A|SEMA4D_ENST00000455551.2_Silent_p.A515A|SEMA4D_ENST00000339861.4_Silent_p.A515A|SEMA4D_ENST00000356444.2_Silent_p.A515A|SEMA4D_ENST00000343780.4_Silent_p.A515A			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	515	PSI.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGGGGTCCCGCGCCAGCACAC	0.687																																																0			9											34	35	34					9																	91996163		2202	4299	6501	91185983	SO:0001819	synonymous_variant	10507			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.1545G>A	9.37:g.91996163C>T			91185983	B2RPM6|Q7Z5S4|Q8N8B0	Silent	SNP	ENST00000450295.1	37	CCDS6685.1																																																																																				0.687	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		T	91996163	C	T	91996163	2	4	5	1	0	0	0	0	0	0	0	1	14071	755	27	1		1	SEMA4D	9	91996163	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	379195	91996163	49217268	129	494										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117070032	117070032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcactcatggtggacagacgTgtctcaagcccatcacggcc	10	14	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:117070032T>C	ENST00000356083.3	+	59	5582	c.5191T>C	c.(5191-5193)Tgt>Cgt	p.C1731R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1731	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGGACAGACGTGTCTCAAGCC	0.607																																																0			9											212	156	175					9																	117070032		2203	4300	6503	116109853	SO:0001583	missense	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.5191T>C	9.37:g.117070032T>C	ENSP00000348385:p.Cys1731Arg		116109853	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167610	0.57476	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.88046	-2.33	5.6	4.46	0.54185	Fibrillar collagen, C-terminal (3);	.	.	.	.	D	0.95262	0.8463	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;0.983	D;D	0.97110	1.0;0.924	D	0.95146	0.8268	9	0.62326	D	0.03	.	11.0616	0.47950	0.0:0.0:0.156:0.844	.	46;1731	Q9HAA3;Q8IZC6	.;CORA1_HUMAN	R	1731;1738	ENSP00000348385:C1731R	ENSP00000348385:C1731R	C	+	1	0	COL27A1	116109853	1.000000	0.71417	0.968000	0.41197	0.965000	0.64279	6.293000	0.72731	0.947000	0.37659	0.459000	0.35465	TGT		0.607	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		C	117070032	T	C	117070032	3	2	5	1	0	0	0	0	1	0	0	0	3691	1696	59	4	5425	4	COL27A1	9	117070032	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	25073869	117070032	24143399	130	495										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137622201	137622201	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cccagtgaggactactacacGccctcaccgtatgatgacct	8	15	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:137622201G>A	ENST00000371817.3	+	7	1458	c.1044G>A	c.(1042-1044)acG>acA	p.T348T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	348	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.T348T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ACTACTACACGCCCTCACCGT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	9											126	114	118					9																	137622201		2203	4300	6503	136762022	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1044G>A	9.37:g.137622201G>A			136762022	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137622201	G	A	137622201	2	1	5	1	0	0	0	0	0	0	0	1	3702	1074	38	1		1	COL5A1	9	137622201	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	20552169	137622201	3591230	131	496										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139390675	139390675	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cggggtgaggaaggggtgctCaggcacctgtagctggtggc	20	8	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:139390675C>A	ENST00000277541.6	-	34	7591	c.7516G>T	c.(7516-7518)Gag>Tag	p.E2506*		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2506					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E2507*(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AAGGGGTGCTCAGGCACCTGT	0.682			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	9											20	28	25					9																	139390675		2098	4192	6290	138510496	SO:0001587	stop_gained	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7516G>T	9.37:g.139390675C>A	ENSP00000277541:p.Glu2506*		138510496	Q59ED8|Q5SXM3	Nonsense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	48	14.592525	0.99802	.	.	ENSG00000148400	ENST00000277541	.	.	.	5.24	5.24	0.73138	.	0.050760	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.1647	0.89721	0.0:1.0:0.0:0.0	.	.	.	.	X	2506	.	ENSP00000277541:E2506X	E	-	1	0	NOTCH1	138510496	1.000000	0.71417	0.995000	0.50966	0.954000	0.61252	7.664000	0.83830	2.616000	0.88540	0.462000	0.41574	GAG		0.682	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139390675	C	A	139390675	4	1	5	1	0	0	0	0	0	1	0	0	10578	835	29	2	155	2	NOTCH1	9	139390675	Nonsense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	1768474	139390675	1822756	132	497										
CDC123	8872	hgsc.bcm.edu	37	chr10	12291612	12291612	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttccgttgcacaaacagtgaAgtgacagtccagcccagccc	9	14	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:12291612A>G	ENST00000281141.4	+	12	1159	c.879A>G	c.(877-879)gaA>gaG	p.E293E	RP11-186N15.3_ENST00000421657.1_RNA|CDC123_ENST00000455773.3_3'UTR|CDC123_ENST00000378900.2_Silent_p.E252E	NM_006023.2	NP_006014.2	O75794	CD123_HUMAN	cell division cycle 123	293					cell cycle arrest (GO:0007050)|cell division (GO:0051301)|positive regulation of cell proliferation (GO:0008284)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12						CAAACAGTGAAGTGACAGTCC	0.433																																																0			10											112	103	106					10																	12291612		2203	4300	6503	12331618	SO:0001819	synonymous_variant	8872			BC001600	CCDS7090.1	10p13	2013-01-17	2013-01-17	2006-11-06	ENSG00000151465	ENSG00000151465			16827	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 7", "cell division cycle 123 homolog (S. cerevisiae)"	C10orf7		15319434	Standard	NM_006023		Approved	D123	uc001ill.3	O75794	OTTHUMG00000017680	ENST00000281141.4:c.879A>G	10.37:g.12291612A>G			12331618	A8JZZ7|Q14107|Q5T0L4|Q5T0L5|Q5T0L7|Q5T0L8|Q5T0L9	Silent	SNP	ENST00000281141.4	37	CCDS7090.1																																																																																				0.433	CDC123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046801.1	NM_006023		G	12291612	A	G	12291612	2	3	5	1	0	0	0	0	0	0	0	1	3061	69	3	4		4	CDC123	10	12291612	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10		12291612	123243135	133	498										
FAM107B	83641	hgsc.bcm.edu	37	chr10	14563961	14563961	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttctgctttattacttggtcTcgttttcttttttccatcac	4	10	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:14563961T>C	ENST00000378470.1	-	3	472	c.186A>G	c.(184-186)cgA>cgG	p.R62R	FAM107B_ENST00000181796.2_Silent_p.R237R|FAM107B_ENST00000378465.3_Silent_p.R62R|FAM107B_ENST00000378462.1_Silent_p.R62R|FAM107B_ENST00000378467.4_Silent_p.R62R|FAM107B_ENST00000378458.2_Silent_p.R62R|FAM107B_ENST00000496330.1_Silent_p.R62R|FAM107B_ENST00000478076.1_Silent_p.R62R|FAM107B_ENST00000468747.1_Silent_p.R62R|FAM107B_ENST00000479731.1_Silent_p.R62R	NM_001282695.1|NM_001282696.1|NM_001282697.1|NM_001282698.1|NM_001282700.1|NM_001282701.1|NM_001282702.1|NM_001282703.1	NP_001269624.1|NP_001269625.1|NP_001269626.1|NP_001269627.1|NP_001269629.1|NP_001269630.1|NP_001269631.1|NP_001269632.1	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	62					sensory perception of sound (GO:0007605)					breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTACTTGGTCTCGTTTTCTTT	0.398																																																0			10											189	177	181					10																	14563961		2203	4300	6503	14603967	SO:0001819	synonymous_variant	83641			AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 45"	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000378470.1:c.186A>G	10.37:g.14563961T>C			14603967	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Silent	SNP	ENST00000378470.1	37																																																																																					0.398	FAM107B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046899.1	NM_031453		C	14563961	T	C	14563961	2	2	5	1	0	0	0	0	0	0	0	1	5406	1538	54	4		4	FAM107B	10	14563961	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	2272349	14563961	120970786	134	499										
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27687573	27687573	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cataaccctgggaccataatCtgaaaaataattctcctcta	4	11	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:27687573C>T	ENST00000438700.3	-	4	2071	c.1954G>A	c.(1954-1956)Gat>Aat	p.D652N		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	652					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GGACCATAATCTGAAAAATAA	0.358																																																0			10											58	57	58					10																	27687573		2203	4300	6503	27727579	SO:0001583	missense	374308			AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1954G>A	10.37:g.27687573C>T	ENSP00000417658:p.Asp652Asn		27727579	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.362020	0.24684	.	.	ENSG00000182077	ENST00000438700	D	0.84944	-1.92	4.19	-0.192	0.13248	.	1.226220	0.05626	N	0.580749	T	0.78155	0.4239	L	0.39633	1.23	0.09310	N	1	B	0.23249	0.082	B	0.29663	0.105	T	0.57997	-0.7714	10	0.18710	T	0.47	-0.0831	5.9062	0.19002	0.0:0.449:0.308:0.243	.	652	Q3KNS1	PTHD3_HUMAN	N	652	ENSP00000417658:D652N	ENSP00000417658:D652N	D	-	1	0	PTCHD3	27727579	0.020000	0.18652	0.014000	0.15608	0.770000	0.43624	1.126000	0.31344	-0.246000	0.09611	0.484000	0.47621	GAT		0.358	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		T	27687573	C	T	27687573	3	4	5	1	0	0	0	0	1	0	0	0	12768	913	32	3	353	3	PTCHD3	10	27687573	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	13123612	27687573	107847174	135	500										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38345270	38345270	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aatcggaacttgctcaacatCagagatcacatacaggggaa	9	9	3	1	rs267602486		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:38345270C>T	ENST00000458705.2	+	5	2373	c.2215C>T	c.(2215-2217)Cag>Tag	p.Q739*	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000374618.3_Nonsense_Mutation_p.Q740*|ZNF33A_ENST00000432900.2_Nonsense_Mutation_p.Q746*|ZNF33A_ENST00000307441.9_Nonsense_Mutation_p.Q739*			Q06730	ZN33A_HUMAN	zinc finger protein 33A	739					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q739*(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						TGCTCAACATCAGAGATCACA	0.388																																																1	Substitution - Nonsense(1)	skin(1)	10											105	100	102					10																	38345270		2203	4300	6503	38385276	SO:0001587	stop_gained	7581			D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2215C>T	10.37:g.38345270C>T	ENSP00000387713:p.Gln739*		38385276	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Nonsense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.028792	0.54790	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	.	.	.	1.92	1.92	0.25849	.	0.000000	0.32343	N	0.006233	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	9.4078	0.38473	0.0:1.0:0.0:0.0	.	.	.	.	X	740;746;739;739	.	ENSP00000304268:Q739X	Q	+	1	0	ZNF33A	38385276	0.000000	0.05858	0.993000	0.49108	0.337000	0.28794	0.276000	0.18716	1.044000	0.40200	0.313000	0.20887	CAG		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		T	38345270	C	T	38345270	4	4	5	1	0	0	0	0	0	1	0	0	17893	827	29	3	2232	3	ZNF33A	10	38345270	Nonsense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	10657697	38345270	97189477	136	501										
AGAP4	119016	hgsc.bcm.edu	37	chr10	46321475	46321475	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgtgggcatctcgggccatgAcgtccaccccgtaccagatc	11	16	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:46321475A>G	ENST00000448048.2	-	7	2005	c.1880T>C	c.(1879-1881)gTc>gCc	p.V627A	AGAP4_ENST00000430779.2_5'Flank	NM_133446.2	NP_597703.2	Q96P64	AGAP4_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	627					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(1)|lung(1)|ovary(1)	3						TCGGGCCATGACGTCCACCCC	0.672																																																0			10											1	1	1					10																	46321475		216	377	593	45641481	SO:0001583	missense	119016			AF411132	CCDS7215.1	10q11.21	2014-06-19	2008-09-22	2008-09-22	ENSG00000188234	ENSG00000188234		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	23459	protein-coding gene	gene with protein product			"centaurin, gamma-like family, member 1", "ArfGAP with GTPase domain, ankyrin repeat and PH domain 8", "centaurin, gamma-like family, member 5"	CTGLF1, AGAP8, CTGLF5		12477932	Standard	XM_005271797		Approved	Em:AC012044.1, MRIP2	uc001jcx.4	Q96P64	OTTHUMG00000018088	ENST00000448048.2:c.1880T>C	10.37:g.46321475A>G	ENSP00000392513:p.Val627Ala		45641481		Missense_Mutation	SNP	ENST00000448048.2	37	CCDS7215.1	.	.	.	.	.	.	.	.	.	.	a	9.177	1.022587	0.19433	.	.	ENSG00000188234	ENST00000448048;ENST00000342551	T	0.68479	-0.33	.	.	.	Ankyrin repeat-containing domain (4);	0.223555	0.38436	N	0.001698	T	0.47967	0.1474	L	0.31294	0.92	0.27716	N	0.945282	B;B	0.15141	0.012;0.007	B;B	0.23150	0.044;0.029	T	0.37361	-0.9709	9	0.52906	T	0.07	.	4.5362	0.12032	0.9994:0.0:6.0E-4:0.0	.	650;627	C9JRW4;Q96P64	.;AGAP4_HUMAN	A	627;403	ENSP00000392513:V627A	ENSP00000343438:V403A	V	-	2	0	AGAP4	45641481	0.987000	0.35691	0.263000	0.24496	0.266000	0.26442	6.064000	0.71169	0.093000	0.17368	0.092000	0.15492	GTC		0.672	AGAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047799.1	NM_133446		G	46321475	A	G	46321475	3	3	5	1	0	0	0	0	1	0	0	0	370	275	10	4	115	4	AGAP4	10	46321475	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	7976205	46321475	89213272	137	502										
PRKG1	5592	hgsc.bcm.edu	37	chr10	53822295	53822295	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctttcattgtttctctttgcAggtaaatgtcactcgtgaag	8	8	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:53822295A>G	ENST00000401604.2	+	7	989		c.e7-1		PRKG1_ENST00000373975.2_Splice_Site|PRKG1_ENST00000373985.1_Splice_Site|PRKG1_ENST00000373980.4_Splice_Site			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I						actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.?(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTCTCTTTGCAGGTAAATGTC	0.393																																																1	Unknown(1)	ovary(1)	10											63	61	62					10																	53822295		2203	4300	6503	53492301	SO:0001630	splice_region_variant	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.796-1A>G	10.37:g.53822295A>G			53492301	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Splice_Site	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.722065	0.68959	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0391	0.64663	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRKG1	53492301	1.000000	0.71417	0.932000	0.37286	0.784000	0.44337	8.793000	0.91862	2.202000	0.70862	0.533000	0.62120	.		0.393	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron	G	53822295	A	G	53822295	5	3	5	1	0	0	0	0	0	0	1	0	12556	202	7	4	1135	4	PRKG1	10	53822295	Splice_Site	SNP	A	TCGA-AF-2693-01A-02D-1733-10	7500820	53822295	81712452	138	503										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720711	89720711	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caggaccagaggaaacctcaGaaaaagtagaaaatggaagt	11	6	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:89720711G>A	ENST00000371953.3	+	8	2219	c.862G>A	c.(862-864)Gaa>Aaa	p.E288K	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	288	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.S287fs*1(1)|p.E288K(1)|p.E288fs*9(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGAAACCTCAGAAAAAGTAGA	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	56	Whole gene deletion(37)|Deletion - Frameshift(12)|Deletion - In frame(2)|Substitution - Nonsense(2)|Unknown(2)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|skin(6)|endometrium(4)|lung(4)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|urinary_tract(2)|vulva(1)|soft_tissue(1)	10											56	59	58					10																	89720711		2202	4296	6498	89710691	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.862G>A	10.37:g.89720711G>A	ENSP00000361021:p.Glu288Lys		89710691	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.317240	0.60524	.	.	ENSG00000171862	ENST00000371953	D	0.84800	-1.9	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.146381	0.64402	D	0.000011	T	0.78451	0.4285	N	0.24115	0.695	0.58432	D	0.999999	B	0.23185	0.081	B	0.28385	0.089	T	0.72646	-0.4230	9	.	.	.	-13.8205	18.5632	0.91108	0.0:0.0:1.0:0.0	.	288	P60484	PTEN_HUMAN	K	288	ENSP00000361021:E288K	.	E	+	1	0	PTEN	89710691	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.369000	0.97156	2.399000	0.81585	0.591000	0.81541	GAA		0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89720711	G	A	89720711	3	1	5	1	0	0	0	0	1	0	0	0	12772	943	33	3	892	3	PTEN	10	89720711	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	35898416	89720711	45814036	139	504										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720745	89720745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tggaagtctatgtgatcaagAaatcgatagcatttgcagta	10	5	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:89720745A>G	ENST00000371953.3	+	8	2253	c.896A>G	c.(895-897)gAa>gGa	p.E299G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	299	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TGTGATCAAGAAATCGATAGC	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											95	93	94					10																	89720745		2203	4298	6501	89710725	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.896A>G	10.37:g.89720745A>G	ENSP00000361021:p.Glu299Gly		89710725	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643976	0.67244	.	.	ENSG00000171862	ENST00000371953	D	0.94828	-3.53	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.222866	0.46442	D	0.000294	D	0.90463	0.7013	L	0.36672	1.1	0.58432	D	0.999997	B	0.02656	0.0	B	0.04013	0.001	D	0.86672	0.1911	9	.	.	.	-14.8198	14.9228	0.70854	1.0:0.0:0.0:0.0	.	299	P60484	PTEN_HUMAN	G	299	ENSP00000361021:E299G	.	E	+	2	0	PTEN	89710725	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.724000	0.61972	1.942000	0.56320	0.482000	0.46254	GAA		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720745	A	G	89720745	3	3	5	1	0	0	0	0	1	0	0	0	12772	246	9	4	926	4	PTEN	10	89720745	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	34	89720745	45814002	140	505										
STAMBPL1	57559	hgsc.bcm.edu	37	chr10	90676486	90676486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aattgtgccaaagcagtctgCgggaccagactattgtgaca	11	9	1	2	rs140820995	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:90676486C>T	ENST00000371926.3	+	8	1911	c.953C>T	c.(952-954)gCg>gTg	p.A318V	STAMBPL1_ENST00000371924.1_Missense_Mutation_p.A318V|STAMBPL1_ENST00000371922.1_Missense_Mutation_p.A152V|STAMBPL1_ENST00000371927.3_Missense_Mutation_p.A318V	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	318	MPN.					membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.A318E(1)		breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		AAGCAGTCTGCGGGACCAGAC	0.373																																																1	Substitution - Missense(1)	ovary(1)	10						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	163	151	155		953	6.1	1	10	dbSNP_134	155	7,8593	5.7+/-21.5	0,7,4293	yes	missense	STAMBPL1	NM_020799.2	64	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging	318/437	90676486	8,12998	2203	4300	6503	90666466	SO:0001583	missense	57559			AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"associated molecule with the SH3 domain of STAM (AMSH) like protein", "associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.953C>T	10.37:g.90676486C>T	ENSP00000360994:p.Ala318Val		90666466	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.720747	0.68959	2.27E-4	8.14E-4	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924;ENST00000371922	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	6.07	6.07	0.98685	.	0.065128	0.64402	D	0.000014	T	0.43765	0.1262	L	0.53561	1.675	0.38881	D	0.956903	P;D	0.61697	0.863;0.99	B;B	0.32762	0.052;0.152	T	0.57659	-0.7773	10	0.72032	D	0.01	-3.199	14.7776	0.69740	0.0:0.8559:0.1441:0.0	.	318;318	Q96FJ0-2;Q96FJ0	.;STALP_HUMAN	V	318;318;318;152	ENSP00000360994:A318V;ENSP00000360995:A318V;ENSP00000360992:A318V;ENSP00000360990:A152V	ENSP00000360990:A152V	A	+	2	0	STAMBPL1	90666466	0.999000	0.42202	0.973000	0.42090	0.988000	0.76386	3.946000	0.56644	2.885000	0.99019	0.650000	0.86243	GCG		0.373	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799		T	90676486	C	T	90676486	3	4	5	1	0	0	0	0	1	0	0	0	15290	768	27	1	979	1	STAMBPL1	10	90676486	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	955741	90676486	44858261	141	506										
CYP2C19	1557	hgsc.bcm.edu	37	chr10	96535288	96535288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccttgtggaggagttgagaaAaaccaagggtgggtgaacat	15	5	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:96535288A>G	ENST00000371321.3	+	3	555	c.473A>G	c.(472-474)aAa>aGa	p.K158R	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	158					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	GAGTTGAGAAAAACCAAGGGT	0.507																																																0			10											159	154	156					10																	96535288		2203	4300	6503	96525278	SO:0001583	missense	1557			M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"Cytochrome P450s"	2621	protein-coding gene	gene with protein product		124020	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.473A>G	10.37:g.96535288A>G	ENSP00000360372:p.Lys158Arg		96525278	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040661	0.35989	.	.	ENSG00000165841	ENST00000371321	T	0.70516	-0.49	3.9	2.71	0.32032	.	0.699906	0.12222	U	0.488301	T	0.73853	0.3640	M	0.63169	1.94	0.09310	N	1	P	0.45569	0.861	P	0.51079	0.658	T	0.62793	-0.6779	10	0.87932	D	0	.	7.8523	0.29462	0.8935:0.0:0.1065:0.0	.	158	P33261	CP2CJ_HUMAN	R	158	ENSP00000360372:K158R	ENSP00000360372:K158R	K	+	2	0	CYP2C19	96525278	0.000000	0.05858	0.129000	0.21949	0.444000	0.32077	0.278000	0.18753	0.466000	0.27193	0.333000	0.21579	AAA		0.507	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769		G	96535288	A	G	96535288	3	3	5	1	0	0	0	0	1	0	0	0	4172	14	1	4	483	4	CYP2C19	10	96535288	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	5858802	96535288	38999459	142	507										
TAF5	6877	hgsc.bcm.edu	37	chr10	105138095	105138095	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	atgagaccatgttggattttCgaacaagtaaatttgttctg	9	5	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:105138095C>T	ENST00000369839.3	+	3	924	c.901C>T	c.(901-903)Cga>Tga	p.R301*	TAF5_ENST00000351396.4_Nonsense_Mutation_p.R301*	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	301					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GTTGGATTTTCGAACAAGTAA	0.398																																																0			10											137	127	130					10																	105138095		2203	4300	6503	105128085	SO:0001587	stop_gained	6877			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"WD repeat domain containing"	11539	protein-coding gene	gene with protein product		601787	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.901C>T	10.37:g.105138095C>T	ENSP00000358854:p.Arg301*		105128085	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Nonsense_Mutation	SNP	ENST00000369839.3	37	CCDS7547.1	.	.	.	.	.	.	.	.	.	.	C	36	5.860507	0.97036	.	.	ENSG00000148835	ENST00000369839;ENST00000351396	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7494	19.8062	0.96532	0.0:1.0:0.0:0.0	.	.	.	.	X	301	.	ENSP00000311024:R301X	R	+	1	2	TAF5	105128085	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.781000	0.68964	2.676000	0.91093	0.555000	0.69702	CGA		0.398	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1			T	105138095	C	T	105138095	4	4	5	1	0	0	0	0	0	1	0	0	15567	876	31	1	911	1	TAF5	10	105138095	Nonsense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	8602807	105138095	30396652	143	508										
VWA2	340706	hgsc.bcm.edu	37	chr10	116032537	116032537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggaacttgctctgaaataccTtctgcacagagggttgcctg	11	10	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:116032537T>C	ENST00000392982.3	+	6	660	c.410T>C	c.(409-411)cTt>cCt	p.L137P	VWA2_ENST00000603594.1_Missense_Mutation_p.L137P			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	137	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.L137R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CTGAAATACCTTCTGCACAGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	10											112	109	110					10																	116032537		2203	4300	6503	116022527	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.410T>C	10.37:g.116032537T>C	ENSP00000376708:p.Leu137Pro		116022527	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	T	14.42	2.530212	0.45073	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.83837	-1.77	4.83	3.67	0.42095	von Willebrand factor, type A (3);	0.341394	0.27323	N	0.019887	D	0.90099	0.6907	M	0.87547	2.89	0.53005	D	0.999964	D;D	0.69078	0.997;0.996	D;D	0.67103	0.949;0.914	D	0.88651	0.3182	10	0.48119	T	0.1	.	9.2493	0.37545	0.1612:0.0:0.0:0.8388	.	137;137	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	P	137	ENSP00000376708:L137P	ENSP00000298715:L137P	L	+	2	0	VWA2	116022527	1.000000	0.71417	0.998000	0.56505	0.371000	0.29859	5.402000	0.66332	0.656000	0.30886	0.533000	0.62120	CTT		0.537	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		C	116032537	T	C	116032537	3	2	5	1	0	0	0	0	1	0	0	0	17279	1609	56	4	428	4	VWA2	10	116032537	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	10894442	116032537	19502210	144	509										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123263319	123263319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctcacttatctcttggaaacTcccattttgggtcctctgga	7	12	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:123263319T>C	ENST00000358487.5	-	10	1696	c.1424A>G	c.(1423-1425)gAg>gGg	p.E475G	FGFR2_ENST00000360144.3_Missense_Mutation_p.E387G|FGFR2_ENST00000351936.6_Missense_Mutation_p.E473G|FGFR2_ENST00000369061.4_Missense_Mutation_p.E363G|FGFR2_ENST00000357555.5_Missense_Mutation_p.E386G|FGFR2_ENST00000356226.4_Missense_Mutation_p.E358G|FGFR2_ENST00000369056.1_Missense_Mutation_p.E476G|FGFR2_ENST00000457416.2_Missense_Mutation_p.E476G|FGFR2_ENST00000346997.2_Missense_Mutation_p.E473G|FGFR2_ENST00000369060.4_Missense_Mutation_p.E359G|FGFR2_ENST00000369059.1_Missense_Mutation_p.E361G|FGFR2_ENST00000478859.1_Missense_Mutation_p.E247G	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	475					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCTTGGAAACTCCCATTTTGG	0.488		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											76	75	76					10																	123263319		2203	4300	6503	123253309	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1424A>G	10.37:g.123263319T>C	ENSP00000351276:p.Glu475Gly		123253309	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837995	0.91117	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.043220	0.85682	D	0.000000	D	0.96700	0.8923	M	0.88450	2.955	0.80722	D	1	D;D;D;P;D;D;D;P	0.89917	0.997;0.999;1.0;0.887;1.0;0.999;1.0;0.826	P;D;D;P;D;D;D;B	0.97110	0.885;0.946;1.0;0.561;0.931;0.946;0.987;0.282	D	0.97317	0.9941	10	0.87932	D	0	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	492;474;386;358;475;387;476;378	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	G	386;476;363;475;358;359;361;67;473;476;473;387;476;476;384	ENSP00000350166:E386G;ENSP00000358057:E363G;ENSP00000351276:E475G;ENSP00000348559:E358G;ENSP00000358056:E359G;ENSP00000358055:E361G;ENSP00000404219:E67G;ENSP00000263451:E473G;ENSP00000410294:E476G;ENSP00000309878:E473G;ENSP00000353262:E387G;ENSP00000358052:E476G;ENSP00000358054:E476G;ENSP00000337665:E384G	ENSP00000337665:E384G	E	-	2	0	FGFR2	123253309	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	7.985000	0.88162	2.302000	0.77476	0.533000	0.62120	GAG		0.488	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		C	123263319	T	C	123263319	3	2	5	1	0	0	0	0	1	0	0	0	5885	1551	54	4	1181	4	FGFR2	10	123263319	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	7230782	123263319	12271428	145	510										
MKI67	4288	hgsc.bcm.edu	37	chr10	129901237	129901237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaactcttctggatatttttAgaggttttccactgtcaggt	9	7	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:129901237A>G	ENST00000368654.3	-	13	9242	c.8867T>C	c.(8866-8868)cTa>cCa	p.L2956P	MKI67_ENST00000368653.3_Missense_Mutation_p.L2596P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2956					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGATATTTTTAGAGGTTTTCC	0.483																																																0			10											90	97	94					10																	129901237		2203	4300	6503	129791227	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.8867T>C	10.37:g.129901237A>G	ENSP00000357643:p.Leu2956Pro		129791227	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.147707	0.37923	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01981	4.55;4.52	3.91	-3.12	0.05282	.	1.287800	0.06003	N	0.648194	T	0.03695	0.0105	L	0.27053	0.805	0.09310	N	0.999996	B;D;D	0.89917	0.101;0.998;1.0	B;D;D	0.71184	0.046;0.962;0.972	T	0.36163	-0.9759	10	0.25751	T	0.34	.	0.2359	0.00186	0.3813:0.1613:0.2314:0.226	.	2955;2596;2956	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	P	2956;2596;2955	ENSP00000357643:L2956P;ENSP00000357642:L2596P	ENSP00000357642:L2596P	L	-	2	0	MKI67	129791227	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.006000	0.03671	-0.490000	0.06707	-0.379000	0.06801	CTA		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129901237	A	G	129901237	3	3	5	1	0	0	0	0	1	0	0	0	9628	420	15	4	915	4	MKI67	10	129901237	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	6637918	129901237	5633510	146	511										
IGF2	3481	hgsc.bcm.edu	37	chr11	2154760	2154760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccctcaccggaagcacggtcGgaggggtcgacacgtccctc	13	16	1	0	rs143785521		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:2154760G>A	ENST00000416167.2	-	3	1459	c.293C>T	c.(292-294)cCg>cTg	p.P98L	IGF2_ENST00000434045.2_Missense_Mutation_p.P154L|IGF2_ENST00000418738.2_Missense_Mutation_p.P98L|IGF2_ENST00000300632.5_Missense_Mutation_p.P98L|IGF2_ENST00000381406.4_Missense_Mutation_p.P101L|IGF2_ENST00000381392.1_Missense_Mutation_p.P101L|IGF2_ENST00000381389.1_Missense_Mutation_p.P98L|MIR483_ENST00000385070.1_RNA|IGF2_ENST00000381395.1_Missense_Mutation_p.P98L			P01344	IGF2_HUMAN	insulin-like growth factor 2	98					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|exocrine pancreas development (GO:0031017)|female pregnancy (GO:0007565)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nicotine (GO:0035094)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|striated muscle cell differentiation (GO:0051146)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	growth factor activity (GO:0008083)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protein serine/threonine kinase activator activity (GO:0043539)|receptor activator activity (GO:0030546)			central_nervous_system(1)|kidney(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	6		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		AAGCACGGTCGGAGGGGTCGA	0.637																																																0			11							LEU/PRO,LEU/PRO,LEU/PRO	0,4404		0,0,2202	41	37	38		293,293,461	-0.9	0	11	dbSNP_134	38	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense,missense	IGF2	NM_000612.4,NM_001007139.4,NM_001127598.1	98,98,98	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	98/181,98/181,154/237	2154760	1,12997	2202	4297	6499	2111336	SO:0001583	missense	3481			M29645, AK025719	CCDS7728.1, CCDS44517.1	11p15.5	2014-09-16	2014-09-16		ENSG00000167244	ENSG00000167244			5466	protein-coding gene	gene with protein product	"somatomedin A"	147470	"chromosome 11 open reading frame 43"	C11orf43		2450353, 3167054	Standard	NM_000612		Approved	FLJ44734, IGF-II	uc009ydf.3	P01344	OTTHUMG00000009395	ENST00000416167.2:c.293C>T	11.37:g.2154760G>A	ENSP00000414497:p.Pro98Leu		2111336	B3KX48|B7WP08|C9JAF2|E3UN45|P78449|Q14299|Q1WM26|Q9UC68|Q9UC69	Missense_Mutation	SNP	ENST00000416167.2	37	CCDS7728.1	.	.	.	.	.	.	.	.	.	.	G	5.251	0.231857	0.09969	0.0	1.16E-4	ENSG00000167244	ENST00000381395;ENST00000381406;ENST00000416167;ENST00000300632;ENST00000381319;ENST00000434045;ENST00000381392;ENST00000381389;ENST00000418738;ENST00000337883;ENST00000381379	D;D;D;D;D;D;D;D;D	0.91740	-2.86;-2.83;-2.86;-2.86;-2.9;-2.83;-2.86;-2.86;-2.86	3.16	-0.938	0.10412	Insulin-like growth factor II E-peptide, C-terminal (1);	0.140501	0.48286	U	0.000182	T	0.82047	0.4952	L	0.27053	0.805	0.37648	D	0.922316	B;B	0.12013	0.005;0.005	B;B	0.04013	0.001;0.001	T	0.66893	-0.5808	10	0.45353	T	0.12	-10.0653	4.4442	0.11589	0.3124:0.0:0.5136:0.1739	.	154;98	C9JAF2;P01344	.;IGF2_HUMAN	L	98;101;98;98;101;154;101;98;98;98;101	ENSP00000370802:P98L;ENSP00000370813:P101L;ENSP00000414497:P98L;ENSP00000300632:P98L;ENSP00000391826:P154L;ENSP00000370799:P101L;ENSP00000370796:P98L;ENSP00000402047:P98L;ENSP00000338297:P98L	ENSP00000300632:P98L	P	-	2	0	IGF2	2111336	1.000000	0.71417	0.011000	0.14972	0.962000	0.63368	2.245000	0.43133	-0.228000	0.09869	0.450000	0.29827	CCG		0.637	IGF2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026053.2	NM_000612		A	2154760	G	A	2154760	3	1	5	1	0	0	0	0	1	0	0	0	7593	1116	39	1	257	1	IGF2	11	2154760	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		2154760	132851756	147	512										
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703580	4703580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtggcagatggccacataaCggtcaaaggccatggccagc	14	11	1	1	rs201184158		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:4703580C>T	ENST00000396950.3	-	2	601	c.362G>A	c.(361-363)cGt>cAt	p.R121H		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	121					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GGCCACATAACGGTCAAAGGC	0.537																																																0			11											60	49	52					11																	4703580		2201	4298	6499	4660156	SO:0001583	missense	81285			AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.362G>A	11.37:g.4703580C>T	ENSP00000380153:p.Arg121His		4660156	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	37	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415059	0.83449	.	.	ENSG00000167332	ENST00000396950	T	0.77489	-1.1	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000632	D	0.90300	0.6966	H	0.94734	3.575	0.44337	D	0.99722	D	0.89917	1.0	D	0.91635	0.999	D	0.91843	0.5485	10	0.72032	D	0.01	.	11.3906	0.49811	0.0:0.9131:0.0:0.0869	.	121	Q9H255	O51E2_HUMAN	H	121	ENSP00000380153:R121H	ENSP00000380153:R121H	R	-	2	0	OR51E2	4660156	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.693000	0.68264	2.613000	0.88420	0.655000	0.94253	CGT		0.537	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		T	4703580	C	T	4703580	3	4	5	1	0	0	0	0	1	0	0	0	11126	536	19	1	604	1	OR51E2	11	4703580	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2548820	4703580	130302936	148	513										
OVCH2	341277	hgsc.bcm.edu	37	chr11	7720314	7720314	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cacctctggagctctttctcCgattacctgggaaaggaaaa	9	11	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:7720314C>T	ENST00000534193.2	-	0	934				OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		GCTCTTTCTCCGATTACCTGG	0.448																																																0			11											52	53	53					11																	7720314		1838	4080	5918	7676890			341277			BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"ovochymase 2"			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7720314C>T			7676890		Missense_Mutation	SNP	ENST00000534193.2	37		.	.	.	.	.	.	.	.	.	.	C	0.013	-1.615665	0.00828	.	.	ENSG00000183378	ENST00000454689	D	0.86230	-2.09	4.32	-8.65	0.00870	.	1.683680	0.03838	N	0.270061	T	0.75903	0.3913	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64664	-0.6354	10	0.09590	T	0.72	0.9161	12.8624	0.57922	0.1019:0.6899:0.0:0.2082	.	303	Q7RTZ1	OVCH2_HUMAN	Q	303	ENSP00000407158:R303Q	ENSP00000407158:R303Q	R	-	2	0	OVCH2	7676890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.087000	0.00610	-2.862000	0.00326	-0.813000	0.03139	CGG		0.448	OVCH2-001	KNOWN	non_canonical_polymorphism|not_organism_supported|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000383929.7	NM_198185		T	7720314	C	T	7720314	1	4	5	0	1	0	0	0	0	0	0	0	11355	652	23	1		1	OVCH2	11	7720314	RNA	SNP	C	TCGA-AF-2693-01A-02D-1733-10	3016734	7720314	127286202	149	514										
COMMD9	29099	hgsc.bcm.edu	37	chr11	36296289	36296289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtgacagctgagatggaggGtttgtctccgcataggctgg	17	7	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:36296289G>A	ENST00000263401.5	-	6	506	c.490C>T	c.(490-492)Ccc>Tcc	p.P164S	COMMD9_ENST00000533308.1_5'Flank|COMMD9_ENST00000532705.1_Missense_Mutation_p.T152I|LINC00610_ENST00000355500.1_lincRNA|COMMD9_ENST00000452374.2_Missense_Mutation_p.P122S	NM_014186.3	NP_054905.2	Q9P000	COMD9_HUMAN	COMM domain containing 9	164	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	5	all_lung(20;0.211)	all_hematologic(20;0.107)				GAGATGGAGGGTTTGTCTCCG	0.542																																																0			11											151	124	133					11																	36296289		2202	4298	6500	36252865	SO:0001583	missense	29099			AY542164	CCDS7900.1, CCDS44571.1	11p13	2008-02-05			ENSG00000110442	ENSG00000110442			25014	protein-coding gene	gene with protein product		612299				15799966	Standard	NM_014186		Approved	HSPC166, FLJ31106	uc001mwn.4	Q9P000	OTTHUMG00000166333	ENST00000263401.5:c.490C>T	11.37:g.36296289G>A	ENSP00000263401:p.Pro164Ser		36252865	E9PAN2|Q96FI2|Q9H0R0	Missense_Mutation	SNP	ENST00000263401.5	37	CCDS7900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.847|9.847	1.192681|1.192681	0.21954|0.21954	.|.	.|.	ENSG00000110442|ENSG00000110442	ENST00000263401;ENST00000537683;ENST00000452374|ENST00000532705	T;T|.	0.09350|.	2.99;2.99|.	5.66|5.66	4.75|4.75	0.60458|0.60458	COMM domain (1);|.	0.290765|.	0.38605|.	N|.	0.001634|.	T|T	0.55924|0.55924	0.1951|0.1951	M|M	0.74258|0.74258	2.255|2.255	0.09310|0.09310	N|N	1|1	P;P|.	0.49783|.	0.928;0.669|.	B;B|.	0.44108|.	0.441;0.355|.	T|T	0.49173|0.49173	-0.8967|-0.8967	10|6	0.35671|0.34782	T|T	0.21|0.22	-18.0524|-18.0524	10.1884|10.1884	0.43011|0.43011	0.159:0.0:0.841:0.0|0.159:0.0:0.841:0.0	.|.	122;164|.	Q9P000-2;Q9P000|.	.;COMD9_HUMAN|.	S|I	164;164;122|152	ENSP00000263401:P164S;ENSP00000392510:P122S|.	ENSP00000263401:P164S|ENSP00000435599:T152I	P|T	-|-	1|2	0|0	COMMD9|COMMD9	36252865|36252865	0.985000|0.985000	0.35326|0.35326	0.362000|0.362000	0.25862|0.25862	0.810000|0.810000	0.45777|0.45777	3.175000|3.175000	0.50855|0.50855	1.386000|1.386000	0.46466|0.46466	0.655000|0.655000	0.94253|0.94253	CCC|ACC		0.542	COMMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389196.1	NM_014186		A	36296289	G	A	36296289	3	1	5	1	0	0	0	0	1	0	0	0	3729	1261	44	3	110	3	COMMD9	11	36296289	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	28575975	36296289	98710227	150	515										
SLC22A11	55867	hgsc.bcm.edu	37	chr11	64323797	64323797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caccagctggagcgaagctgAcacggagccgtgtgtggacg	16	11	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:64323797A>G	ENST00000301891.4	+	1	700	c.326A>G	c.(325-327)gAc>gGc	p.D109G	SLC22A11_ENST00000490834.1_3'UTR|SLC22A11_ENST00000377581.3_Missense_Mutation_p.D109G|SLC22A11_ENST00000377585.3_Missense_Mutation_p.D109G	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	109					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	AGCGAAGCTGACACGGAGCCG	0.682																																																0			11											46	52	50					11																	64323797		2201	4297	6498	64080373	SO:0001583	missense	55867			AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"Solute carriers"	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.326A>G	11.37:g.64323797A>G	ENSP00000301891:p.Asp109Gly		64080373	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Missense_Mutation	SNP	ENST00000301891.4	37	CCDS8074.1	.	.	.	.	.	.	.	.	.	.	A	4.244	0.044209	0.08196	.	.	ENSG00000168065	ENST00000301891;ENST00000377585;ENST00000377581	T;T;T	0.15487	2.42;2.42;2.42	3.97	-5.2	0.02823	Major facilitator superfamily domain (1);	0.488989	0.20471	U	0.091696	T	0.17874	0.0429	N	0.25332	0.735	0.09310	N	1	B;B;B;D	0.53619	0.027;0.009;0.034;0.961	B;B;B;P	0.56216	0.013;0.022;0.022;0.794	T	0.10291	-1.0636	10	0.25751	T	0.34	.	16.0505	0.80760	0.8333:0.1667:0.0:0.0	.	109;109;109;109	Q9NSA0-2;A6NCG2;Q9NSA0;B4DJH6	.;.;S22AB_HUMAN;.	G	109	ENSP00000301891:D109G;ENSP00000366809:D109G;ENSP00000366804:D109G	ENSP00000301891:D109G	D	+	2	0	SLC22A11	64080373	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.014000	0.13333	-0.693000	0.05121	-0.565000	0.04167	GAC		0.682	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484		G	64323797	A	G	64323797	3	3	5	1	0	0	0	0	1	0	0	0	14479	275	10	4	328	4	SLC22A11	11	64323797	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	28027508	64323797	70682719	151	516										
MRGPRD	116512	hgsc.bcm.edu	37	chr11	68748293	68748293	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaaggggttcctgtgcattcGaaagcccagcagccagatca	12	11	1	1	rs140992386		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:68748293G>A	ENST00000309106.3	-	1	162	c.163C>T	c.(163-165)Cga>Tga	p.R55*		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	55						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGTGCATTCGAAAGCCCAGC	0.597																																																0			11						G	stop/ARG	0,4400		0,0,2200	66	66	66		163	-5.3	0	11	dbSNP_134	66	1,8587	1.2+/-3.3	0,1,4293	yes	stop-gained	MRGPRD	NM_198923.2		0,1,6493	AA,AG,GG		0.0116,0.0,0.0077		55/322	68748293	1,12987	2200	4294	6494	68504869	SO:0001587	stop_gained	116512			AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"GPCR / Class A : Orphans"	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.163C>T	11.37:g.68748293G>A	ENSP00000310631:p.Arg55*		68504869	Q8NGK7	Nonsense_Mutation	SNP	ENST00000309106.3	37	CCDS31625.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520969	0.44866	0.0	1.16E-4	ENSG00000172938	ENST00000309106	.	.	.	5.17	-5.33	0.02713	.	0.603819	0.13615	U	0.374820	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3184	0.723	0.00944	0.3441:0.104:0.2356:0.3163	.	.	.	.	X	55	.	ENSP00000310631:R55X	R	-	1	2	MRGPRD	68504869	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.442000	0.06871	-0.996000	0.03455	-0.373000	0.07131	CGA		0.597	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923		A	68748293	G	A	68748293	4	1	5	1	0	0	0	0	0	1	0	0	9793	1066	37	1	805	1	MRGPRD	11	68748293	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	4424496	68748293	66258223	152	517										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76169374	76169374	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagcataatgcatctcttccAgtgcctgcagaaacaggaag	9	11	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:76169374A>G	ENST00000529032.1	+	4	393	c.393A>G	c.(391-393)ccA>ccG	p.P131P	C11orf30_ENST00000334736.3_Silent_p.P131P|C11orf30_ENST00000525038.1_Silent_p.P145P|C11orf30_ENST00000524490.1_Silent_p.P131P|C11orf30_ENST00000533248.1_Silent_p.P145P|C11orf30_ENST00000343878.3_Silent_p.P131P|C11orf30_ENST00000524767.1_Silent_p.P145P|C11orf30_ENST00000525919.1_Silent_p.P131P			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	131	Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CATCTCTTCCAGTGCCTGCAG	0.428																																																0			11											87	85	86					11																	76169374		2200	4292	6492	75847022	SO:0001819	synonymous_variant	56946			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.393A>G	11.37:g.76169374A>G			75847022	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	37	CCDS8244.1																																																																																				0.428	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		G	76169374	A	G	76169374	2	3	5	1	0	0	0	0	0	0	0	1	1640	175	7	4		4	C11orf30	11	76169374	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	7421081	76169374	58837142	153	518										
ATM	472	hgsc.bcm.edu	37	chr11	108236086	108236086	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtttcaacaaagtagctgaaCgtgtcttaatgagactacaa	8	7	2	2	rs587782292		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:108236086C>A	ENST00000452508.2	+	64	9211	c.9022C>A	c.(9022-9024)Cgt>Agt	p.R3008S	ATM_ENST00000525178.1_3'UTR|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.R3008S|C11orf65_ENST00000526725.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	3008			R -> C (in AT, T-prolymphocytic leukemia and mantle cell lymphoma). {ECO:0000269|PubMed:10706620, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:9334731, ECO:0000269|PubMed:9488043, ECO:0000269|PubMed:9872980}.|R -> H (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10397742}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R3008C(4)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AGTAGCTGAACGTGTCTTAAT	0.413			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	4	Substitution - Missense(4)	haematopoietic_and_lymphoid_tissue(4)	11	GRCh37	CM000656	ATM	M							127	124	125					11																	108236086		2201	4298	6499	107741296	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.9022C>A	11.37:g.108236086C>A	ENSP00000388058:p.Arg3008Ser		107741296	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011988	0.75046	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02121	4.44;4.44	5.22	5.22	0.72569	Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.110750	0.64402	D	0.000007	T	0.14098	0.0341	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.00083	-1.2103	10	0.87932	D	0	.	19.0354	0.92974	0.0:1.0:0.0:0.0	.	3008	Q13315	ATM_HUMAN	S	3008	ENSP00000278616:R3008S;ENSP00000388058:R3008S	ENSP00000278616:R3008S	R	+	1	0	ATM	107741296	1.000000	0.71417	0.998000	0.56505	0.549000	0.35272	5.681000	0.68175	2.726000	0.93360	0.650000	0.86243	CGT		0.413	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108236086	C	A	108236086	3	1	5	1	0	0	0	0	1	0	0	0	1110	536	19	2	9268	2	ATM	11	108236086	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	32066712	108236086	26770430	154	519										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108385374	108385374	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttgtgcttgtcctaggagaaAaggttttaaaaccttcccta	8	8	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:108385374A>G	ENST00000265843.4	-	6	970	c.860T>C	c.(859-861)tTt>tCt	p.F287S	EXPH5_ENST00000428840.1_Missense_Mutation_p.F211S|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000443411.1_Missense_Mutation_p.F99S|EXPH5_ENST00000525344.1_Missense_Mutation_p.F280S	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	287					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.F287S(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CCTAGGAGAAAAGGTTTTAAA	0.363																																																1	Substitution - Missense(1)	ovary(1)	11											95	90	92					11																	108385374		2201	4298	6499	107890584	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.860T>C	11.37:g.108385374A>G	ENSP00000265843:p.Phe287Ser		107890584	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.460487	0.63401	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.06294	3.92;3.83;3.69;3.92;3.73;3.32	5.67	5.67	0.87782	.	0.105878	0.42548	D	0.000685	T	0.19446	0.0467	M	0.69823	2.125	0.31610	N	0.651609	D	0.89917	1.0	D	0.85130	0.997	T	0.26710	-1.0095	10	0.66056	D	0.02	-20.0778	5.0773	0.14638	0.708:0.1762:0.1158:0.0	.	287	Q8NEV8	EXPH5_HUMAN	S	287;211;99;280;131;211;99	ENSP00000265843:F287S;ENSP00000391966:F211S;ENSP00000411390:F99S;ENSP00000432546:F280S;ENSP00000432683:F211S;ENSP00000446434:F99S	ENSP00000265843:F287S	F	-	2	0	EXPH5	107890584	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.272000	0.51616	2.154000	0.67381	0.533000	0.62120	TTT		0.363	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108385374	A	G	108385374	3	3	5	1	0	0	0	0	1	0	0	0	5335	14	1	4	5113	4	EXPH5	11	108385374	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	149288	108385374	26621142	155	520										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771916	118771916	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcctccagagaatccctgctGgccctggttgggaaactgtg	13	12	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:118771916G>A	ENST00000334801.3	-	6	3500	c.2536C>T	c.(2536-2538)Cag>Tag	p.Q846*	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	846					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AATCCCTGCTGGCCCTGGTTG	0.602																																																0			11											84	76	79					11																	118771916		2200	4295	6495	118277126	SO:0001587	stop_gained	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2536C>T	11.37:g.118771916G>A	ENSP00000335320:p.Gln846*		118277126	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Nonsense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	47	13.396728	0.99739	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	.	.	.	5.11	4.19	0.49359	.	0.000000	0.47455	D	0.000235	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-11.3315	4.6956	0.12802	0.0829:0.1513:0.6097:0.1561	.	.	.	.	X	846;809;139;846;846	.	ENSP00000335320:Q846X	Q	-	1	0	BCL9L	118277126	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.327000	0.52045	2.358000	0.79984	0.655000	0.94253	CAG		0.602	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118771916	G	A	118771916	4	1	5	1	0	0	0	0	0	1	0	0	1383	1357	47	3	1975	3	BCL9L	11	118771916	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	10386542	118771916	16234600	156	521										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440424	124440424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgctttacaacatcattatgTctcatcacacctgcctgctg	5	13	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:124440424T>C	ENST00000284287.3	+	1	532	c.460T>C	c.(460-462)Tct>Cct	p.S154P		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	154					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		CATCATTATGTCTCATCACAC	0.483																																																0			11											161	135	144					11																	124440424		2201	4299	6500	123945634	SO:0001583	missense	390275			BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.460T>C	11.37:g.124440424T>C	ENSP00000284287:p.Ser154Pro		123945634	Q6IEW7|Q96RC6	Missense_Mutation	SNP	ENST00000284287.3	37	CCDS31712.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598616	0.46318	.	.	ENSG00000196119	ENST00000284287	T	0.41065	1.01	5.03	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.309751	0.23364	N	0.048991	T	0.46698	0.1406	M	0.88031	2.925	0.29436	N	0.859502	B	0.21905	0.062	B	0.30316	0.114	T	0.56673	-0.7940	10	0.72032	D	0.01	.	2.3025	0.04165	0.1446:0.0825:0.2826:0.4903	.	154	Q8NGG7	OR8A1_HUMAN	P	154	ENSP00000284287:S154P	ENSP00000284287:S154P	S	+	1	0	OR8A1	123945634	0.028000	0.19301	0.921000	0.36526	0.670000	0.39368	-0.007000	0.12810	0.905000	0.36596	0.528000	0.53228	TCT		0.483	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		C	124440424	T	C	124440424	3	2	5	1	0	0	0	0	1	0	0	0	11256	1667	58	4	462	4	OR8A1	11	124440424	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5668508	124440424	10566092	157	522										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3147233	3147233	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgatcatcacctgctccacgAaggtctgctctttcggcaag	9	13	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:3147233A>T	ENST00000397122.2	+	9	895	c.610A>T	c.(610-612)Aag>Tag	p.K204*	TEAD4_ENST00000359864.2_Nonsense_Mutation_p.K333*|TEAD4_ENST00000358409.2_Nonsense_Mutation_p.K290*	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	333					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			CTGCTCCACGAAGGTCTGCTC	0.587																																																0			12											89	79	83					12																	3147233		2203	4300	6503	3017494	SO:0001587	stop_gained	7004			X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.610A>T	12.37:g.3147233A>T	ENSP00000380311:p.Lys204*		3017494	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Nonsense_Mutation	SNP	ENST00000397122.2	37	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	A	38	7.162676	0.98107	.	.	ENSG00000197905	ENST00000358409;ENST00000359864;ENST00000397122	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.6861	13.4969	0.61432	1.0:0.0:0.0:0.0	.	.	.	.	X	290;333;204	.	ENSP00000351184:K290X	K	+	1	0	TEAD4	3017494	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	9.295000	0.96095	1.773000	0.52216	0.533000	0.62120	AAG		0.587	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		T	3147233	A	T	3147233	4	4	5	1	0	0	0	0	0	1	0	0	15780	247	9	5	1031	5	TEAD4	12	3147233	Nonsense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10		3147233	130704662	158	523										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7586120	7586120	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agtcacggcttgtccaaaacGaaacatggcgaaagaaaatg	10	8	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:7586120G>T	ENST00000313599.3	-	3	352	c.295C>A	c.(295-297)Cgt>Agt	p.R99S	CD163L1_ENST00000416109.2_Missense_Mutation_p.R99S|CD163L1_ENST00000396630.1_Missense_Mutation_p.R99S			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	99	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TGTCCAAAACGAAACATGGCG	0.478																																																0			12											123	97	106					12																	7586120		2203	4300	6503	7477387	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.295C>A	12.37:g.7586120G>T	ENSP00000315945:p.Arg99Ser		7477387	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	0.382	-0.928373	0.02359	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630;ENST00000543276	T;T;T;T	0.33438	1.41;1.41;1.41;3.51	1.64	0.641	0.17759	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	2.179770	0.03610	U	0.234674	T	0.13586	0.0329	N	0.03917	-0.325	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.21895	-1.0232	10	0.07813	T	0.8	.	8.1402	0.31078	0.0:0.3695:0.6304:0.0	.	99;99	E7EVK4;Q9NR16	.;C163B_HUMAN	S	99;99;99;3	ENSP00000315945:R99S;ENSP00000393474:R99S;ENSP00000379871:R99S;ENSP00000442328:R3S	ENSP00000315945:R99S	R	-	1	0	CD163L1	7477387	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.362000	0.07602	0.156000	0.19299	-0.414000	0.06135	CGT		0.478	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7586120	G	T	7586120	3	4	5	1	0	0	0	0	1	0	0	0	2974	1058	37	2	4134	2	CD163L1	12	7586120	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	4438887	7586120	126265775	159	524										
C12orf40	283461	hgsc.bcm.edu	37	chr12	40114805	40114805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	atcagtttccacagttgcagTgcaattcagcccacattttg	7	11	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:40114805T>C	ENST00000324616.5	+	13	1865	c.1711T>C	c.(1711-1713)Tgc>Cgc	p.C571R		NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	571								p.C571G(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ACAGTTGCAGTGCAATTCAGC	0.383																																																1	Substitution - Missense(1)	ovary(1)	12											95	90	92					12																	40114805		1922	4136	6058	38401072	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1711T>C	12.37:g.40114805T>C	ENSP00000317671:p.Cys571Arg		38401072	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.976734	0.34848	.	.	ENSG00000180116	ENST00000324616	T	0.49720	0.77	4.95	0.83	0.18854	.	0.543405	0.18058	N	0.153036	T	0.37839	0.1018	L	0.32530	0.975	0.24512	N	0.994207	P	0.43701	0.815	P	0.48921	0.595	T	0.27088	-1.0084	10	0.72032	D	0.01	.	1.465	0.02404	0.2136:0.0941:0.159:0.5333	.	571	Q86WS4	CL040_HUMAN	R	571	ENSP00000317671:C571R	ENSP00000317671:C571R	C	+	1	0	C12orf40	38401072	0.000000	0.05858	0.077000	0.20336	0.012000	0.07955	-0.490000	0.06482	0.023000	0.15187	0.477000	0.44152	TGC		0.383	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		C	40114805	T	C	40114805	3	2	5	1	0	0	0	0	1	0	0	0	1690	1696	59	4	1761	4	C12orf40	12	40114805	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	32528685	40114805	93737090	160	525										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858556	42858556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cattgggctgtggctgaaagAggcttttatcaccaaacttg	11	8	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:42858556A>G	ENST00000455697.1	-	7	1565	c.1280T>C	c.(1279-1281)cTc>cCc	p.L427P	PRICKLE1_ENST00000445766.2_Missense_Mutation_p.L427P|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.L427P|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.L427P|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.L427P	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	427					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TGGCTGAAAGAGGCTTTTATC	0.438																																																0			12											70	73	72					12																	42858556		2203	4300	6503	41144823	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1280T>C	12.37:g.42858556A>G	ENSP00000401060:p.Leu427Pro		41144823	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669468	0.47677	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	5.76	4.62	0.57501	.	0.178326	0.52532	D	0.000078	T	0.40815	0.1132	N	0.08118	0	0.80722	D	1	B	0.12630	0.006	B	0.12156	0.007	T	0.17715	-1.0360	10	0.30078	T	0.28	-4.2574	11.811	0.52183	0.9316:0.0:0.0684:0.0	.	427	Q96MT3	PRIC1_HUMAN	P	427	ENSP00000401060:L427P;ENSP00000398947:L427P;ENSP00000448359:L427P;ENSP00000345064:L427P;ENSP00000449819:L427P	ENSP00000345064:L427P	L	-	2	0	PRICKLE1	41144823	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.910000	0.92685	1.119000	0.41883	0.528000	0.53228	CTC		0.438	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			G	42858556	A	G	42858556	3	3	5	1	0	0	0	0	1	0	0	0	12520	304	11	4	1223	4	PRICKLE1	12	42858556	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	2743751	42858556	90993339	161	526										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53875791	53875791	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcagggccagggatgacctcTgaaggaggtgggtccagtgg	18	8	2	2	rs552979863		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:53875791T>C	ENST00000267079.2	-	14	2640	c.2415A>G	c.(2413-2415)tcA>tcG	p.S805S	MAP3K12_ENST00000547035.1_Silent_p.S838S|MAP3K12_ENST00000547488.1_Silent_p.S838S	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	805					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GGATGACCTCTGAAGGAGGTG	0.562											OREG0021873	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			12											101	94	96					12																	53875791		2203	4300	6503	52162058	SO:0001819	synonymous_variant	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.2415A>G	12.37:g.53875791T>C		996	52162058	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	37	CCDS8860.1																																																																																				0.562	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		C	53875791	T	C	53875791	2	2	5	1	0	0	0	0	0	0	0	1	9276	1567	55	4		4	MAP3K12	12	53875791	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	11017235	53875791	79976104	162	527										
NACA	4666	hgsc.bcm.edu	37	chr12	57112396	57112464	+	In_Frame_Del	DEL	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	-													0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagtagctggacctccttttGgggagggaggagttgcagct					rs200360816|rs537859542|rs199568239|rs555857821|rs201572567|rs371165343	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENST00000454682.1	-	3	3131_3199	c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	c.(2848-2919)cctaaaggaggcccagctaccccatccccgaaatgggcccccacacccccagctgcaactcctccctcccca>cca	p.950_973PKGGPATPSPKWAPTPPAATPPSP>P	NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	950	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P959P(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						ACCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTAGGGGAGGGAG	0.647			T	BCL6	NHL																																		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	1	Substitution - coding silent(1)	prostate(1)	12																																								55398731	SO:0001651	inframe_deletion	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	12.37:g.57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENSP00000403817:p.Pro950_Ser972del		55398663		In_Frame_Del	DEL	ENST00000454682.1	37																																																																																					0.647	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		-	57112464	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	-	57112396	7	5	5	1	0	1	0	1	0	0	0	0	10163	1348	47	0	3346	0	NACA	12	57112396	In_Frame_Del	DEL	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	TCGA-AF-2693-01A-02D-1733-10	3236605	57112396	76739499	163	528										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112888165	112888165	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcaagattcagaacactggtGattactatgacctgtatgga	9	7	2	4	rs397507508|rs397507510		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:112888165G>T	ENST00000351677.2	+	3	379	c.181G>T	c.(181-183)Gat>Tat	p.D61Y	PTPN11_ENST00000392597.1_Missense_Mutation_p.D61Y	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	61	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		D -> G (in NS1). {ECO:0000269|PubMed:11704759, ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12161469, ECO:0000269|PubMed:12634870}.|D -> N (in NS1). {ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12634870}.|D -> V (in JMML; also in myelodysplastic syndrome). {ECO:0000269|PubMed:12717436}.|D -> Y (in JMML). {ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.D61Y(29)|p.D61H(3)|p.D61N(2)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GAACACTGGTGATTACTATGA	0.423			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	34	Substitution - Missense(34)	haematopoietic_and_lymphoid_tissue(34)	12	GRCh37	CD055729|CM021127	PTPN11	D|M							143	134	137					12																	112888165		2203	4300	6503	111372548	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.181G>T	12.37:g.112888165G>T	ENSP00000340944:p.Asp61Tyr		111372548	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132218	0.94473	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.96774	-4.12;-4.12	5.9	5.9	0.94986	.	0.046067	0.85682	D	0.000000	D	0.98451	0.9484	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.98880	1.0769	10	0.87932	D	0	.	20.2787	0.98501	0.0:0.0:1.0:0.0	.	61;61	Q06124-2;Q06124-3	.;.	Y	61	ENSP00000376376:D61Y;ENSP00000340944:D61Y	ENSP00000340944:D61Y	D	+	1	0	PTPN11	111372548	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.860000	0.99555	2.798000	0.96311	0.650000	0.86243	GAT		0.423	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112888165	G	T	112888165	3	4	5	1	0	0	0	0	1	0	0	0	12815	1290	45	2	191	2	PTPN11	12	112888165	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	55775769	112888165	20963730	164	529										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112888197	112888197	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctgtatggaggggagaaattTgccactttggctgagttggt	15	5	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:112888197T>C	ENST00000351677.2	+	3	411	c.213T>C	c.(211-213)ttT>ttC	p.F71F	PTPN11_ENST00000392597.1_Silent_p.F71F	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	71	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12717436}.|F -> L (in myelodysplastic syndrome). {ECO:0000269|PubMed:12634870, ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.F71L(5)|p.F71K(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGGAGAAATTTGCCACTTTGG	0.418			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)	12											154	142	146					12																	112888197		2203	4300	6503	111372580	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.213T>C	12.37:g.112888197T>C			111372580	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			C	112888197	T	C	112888197	2	2	5	1	0	0	0	0	0	0	0	1	12815	1809	63	4		4	PTPN11	12	112888197	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	32	112888197	20963698	165	530										
ACADS	35	hgsc.bcm.edu	37	chr12	121176678	121176678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcccggctgctgacctggcGcgctgccatgctgaaggata	14	13	0	2	rs199633532		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:121176678G>A	ENST00000242592.4	+	8	1140	c.989G>A	c.(988-990)cGc>cAc	p.R330H	RP11-173P15.7_ENST00000542620.1_RNA|ACADS_ENST00000411593.2_Missense_Mutation_p.R326H	NM_000017.2	NP_000008.1	P16219	ACADS_HUMAN	acyl-CoA dehydrogenase, C-2 to C-3 short chain	330					butyrate catabolic process (GO:0046359)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|protein homotetramerization (GO:0051289)|response to glucocorticoid (GO:0051384)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|butyryl-CoA dehydrogenase activity (GO:0004085)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)	p.R330H(2)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			Flavin adenine dinucleotide(DB03147)	CTGACCTGGCGCGCTGCCATG	0.642													G|||	1	0.000199681	0	0	5008	,	,		17348	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	prostate(1)|kidney(1)	12	GRCh37	CM067634	ACADS	M							46	52	50					12																	121176678		2203	4300	6503	119661061	SO:0001583	missense	35			M26393	CCDS9207.1	12q24.31	2012-07-13	2010-04-30		ENSG00000122971	ENSG00000122971	1.3.8.1		90	protein-coding gene	gene with protein product		606885	"acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain"			2565344	Standard	NM_000017		Approved	SCAD, ACAD3	uc001tza.4	P16219	OTTHUMG00000169203	ENST00000242592.4:c.989G>A	12.37:g.121176678G>A	ENSP00000242592:p.Arg330His		119661061	P78331	Missense_Mutation	SNP	ENST00000242592.4	37	CCDS9207.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357217	0.82243	.	.	ENSG00000122971	ENST00000242592;ENST00000411593	D;D	0.96619	-4.07;-4.07	4.63	4.63	0.57726	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.053187	0.64402	D	0.000001	D	0.96694	0.8921	L	0.33792	1.035	0.58432	D	0.999993	D;P;P	0.89917	1.0;0.737;0.737	D;B;B	0.80764	0.994;0.14;0.14	D	0.97682	1.0173	10	0.62326	D	0.03	.	17.5068	0.87748	0.0:0.0:1.0:0.0	.	326;330;330	E9PE82;E5KSD5;P16219	.;.;ACADS_HUMAN	H	330;326	ENSP00000242592:R330H;ENSP00000401045:R326H	ENSP00000242592:R330H	R	+	2	0	ACADS	119661061	1.000000	0.71417	0.916000	0.36221	0.916000	0.54674	7.185000	0.77714	2.125000	0.65367	0.561000	0.74099	CGC		0.642	ACADS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402861.1	NM_000017		A	121176678	G	A	121176678	3	1	5	1	0	0	0	0	1	0	0	0	114	1087	38	1	1019	1	ACADS	12	121176678	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	8288481	121176678	12675217	166	531										
CAMKK2	10645	hgsc.bcm.edu	37	chr12	121707359	121707359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tattgtcattttcattgtagGccaacttgacgacaccatag	7	9	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:121707359G>A	ENST00000324774.5	-	4	1373	c.545C>T	c.(544-546)gCc>gTc	p.A182V	CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000347034.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000402834.4_Missense_Mutation_p.A182V|CAMKK2_ENST00000392474.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000412367.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000538733.1_Missense_Mutation_p.A182V|CAMKK2_ENST00000446440.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000337174.3_Missense_Mutation_p.A182V|CAMKK2_ENST00000392473.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000404169.3_Missense_Mutation_p.A182V	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	182	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCATTGTAGGCCAACTTGAC	0.468																																																0			12											168	143	151					12																	121707359		2203	4300	6503	120191742	SO:0001583	missense	10645			AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.545C>T	12.37:g.121707359G>A	ENSP00000312741:p.Ala182Val		120191742	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	37	CCDS9216.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976640	0.92982	.	.	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473	T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.69	4.69	0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51041	0.1651	N	0.13198	0.31	0.80722	D	1	P;P;P;B;P;P;P	0.50710	0.778;0.907;0.808;0.421;0.924;0.938;0.808	P;P;P;B;P;P;P	0.55303	0.55;0.664;0.664;0.421;0.664;0.773;0.54	T	0.55231	-0.8173	10	0.45353	T	0.12	0.1016	17.5005	0.87730	0.0:0.0:1.0:0.0	.	182;182;182;182;182;182;182	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	V	182;182;182;182;182;182;182;165;182;182	ENSP00000376266:A182V;ENSP00000321230:A182V;ENSP00000445944:A182V;ENSP00000336634:A182V;ENSP00000312741:A182V;ENSP00000388368:A182V;ENSP00000384600:A182V;ENSP00000388273:A182V;ENSP00000376265:A182V	ENSP00000312741:A182V	A	-	2	0	CAMKK2	120191742	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.709000	0.91379	2.560000	0.86352	0.655000	0.94253	GCC		0.468	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226		A	121707359	G	A	121707359	3	1	5	1	0	0	0	0	1	0	0	0	2613	1203	42	3	1287	3	CAMKK2	12	121707359	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	530681	121707359	12144536	167	532										
RSRC2	65117	hgsc.bcm.edu	37	chr12	123006784	123006784	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gatacttctgactgctctttTttcttatctctatctggtga	6	9	5	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123006784T>C	ENST00000331738.7	-	2	214	c.69A>G	c.(67-69)aaA>aaG	p.K23K	RSRC2_ENST00000354654.2_5'UTR	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2	23							poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		ACTGCTCTTTTTTCTTATCTC	0.353																																																0			12											157	145	149					12																	123006784		2203	4300	6503	121572737	SO:0001819	synonymous_variant	65117			AF161432	CCDS31920.1	12q24.31	2007-02-13			ENSG00000111011	ENSG00000111011			30559	protein-coding gene	gene with protein product						17203224	Standard	NM_023012		Approved	FLJ11021	uc001ucr.3	Q7L4I2	OTTHUMG00000167572	ENST00000331738.7:c.69A>G	12.37:g.123006784T>C			121572737	Q6N040|Q6NW16|Q9H864	Silent	SNP	ENST00000331738.7	37	CCDS31920.1																																																																																				0.353	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	NM_023012		C	123006784	T	C	123006784	2	2	5	1	0	0	0	0	0	0	0	1	13752	1838	64	4		4	RSRC2	12	123006784	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	1299425	123006784	10845111	168	533										
HIP1R	9026	hgsc.bcm.edu	37	chr12	123340853	123340853	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acaagctgaaggaaaagcacAgtgagctcgtccatgtgcac	11	10	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123340853A>T	ENST00000253083.4	+	15	1488	c.1363A>T	c.(1363-1365)Agt>Tgt	p.S455C		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	455					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GGAAAAGCACAGTGAGCTCGT	0.662																																																0			12											112	104	107					12																	123340853		2203	4300	6503	121906806	SO:0001583	missense	9026			AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1363A>T	12.37:g.123340853A>T	ENSP00000253083:p.Ser455Cys		121906806	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039991	0.55003	.	.	ENSG00000130787	ENST00000253083	T	0.16897	2.31	4.84	2.49	0.30216	.	0.228496	0.52532	D	0.000075	T	0.26738	0.0654	M	0.71581	2.175	0.33198	D	0.551805	D;D;D	0.58620	0.967;0.967;0.983	P;P;P	0.51266	0.642;0.664;0.599	T	0.41752	-0.9491	10	0.87932	D	0	-4.7583	8.704	0.34343	0.8442:0.0:0.1558:0.0	.	455;455;443	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	C	455	ENSP00000253083:S455C	ENSP00000253083:S455C	S	+	1	0	HIP1R	121906806	1.000000	0.71417	0.889000	0.34880	0.471000	0.32888	3.539000	0.53604	0.239000	0.21243	0.459000	0.35465	AGT		0.662	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		T	123340853	A	T	123340853	3	4	5	1	0	0	0	0	1	0	0	0	7136	188	7	5	1421	5	HIP1R	12	123340853	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	334069	123340853	10511042	169	534										
SETD8	387893	hgsc.bcm.edu	37	chr12	123892040	123892040	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tggccctccttcccctccagCgtggatgcaactagagagac	10	15	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123892040C>T	ENST00000402868.3	+	8	1275	c.849C>T	c.(847-849)tgC>tgT	p.C283C	SETD8_ENST00000330479.4_Splice_Site_p.C283C			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	324	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TCCCCTCCAGCGTGGATGCAA	0.498																																																0			12											70	56	60					12																	123892040		2203	4300	6503	122457993	SO:0001630	splice_region_variant	387893			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.849-1C>T	12.37:g.123892040C>T			122457993	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																				0.498	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	Silent	T	123892040	C	T	123892040	5	4	5	1	0	0	0	0	0	0	1	0	14174	782	27	1	879	1	SETD8	12	123892040	Splice_Site	SNP	C	TCGA-AF-2693-01A-02D-1733-10	551187	123892040	9959855	170	535										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124352061	124352061	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tttgagaagtatgtgccctaTctcatggatgtgatagtgga	12	5	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:124352061T>C	ENST00000409039.3	+	41	6886	c.6861T>C	c.(6859-6861)taT>taC	p.Y2287Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2287	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ATGTGCCCTATCTCATGGATG	0.368																																																0			12											88	82	84					12																	124352061		1876	4098	5974	122918014	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6861T>C	12.37:g.124352061T>C			122918014	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.368	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124352061	T	C	124352061	2	2	5	1	0	0	0	0	0	0	0	1	4609	1442	50	4		4	DNAH10	12	124352061	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	460021	124352061	9499834	171	536										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125834441	125834441	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcaagatgtttgctttccctGaggccagggaagtggcagcc	13	10	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:125834441G>A	ENST00000299308.3	+	2	504	c.496G>A	c.(496-498)Gag>Aag	p.E166K	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	166						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		TGCTTTCCCTGAGGCCAGGGA	0.587																																																0			12											83	85	84					12																	125834441		2002	4195	6197	124400394	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.496G>A	12.37:g.125834441G>A	ENSP00000299308:p.Glu166Lys		124400394	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	35	5.447518	0.96205	.	.	ENSG00000139364	ENST00000299308	T	0.14391	2.51	5.34	5.34	0.76211	.	.	.	.	.	T	0.36744	0.0978	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.05209	-1.0899	9	0.19147	T	0.46	.	19.0585	0.93076	0.0:0.0:1.0:0.0	.	166	Q14DG7	T132B_HUMAN	K	166	ENSP00000299308:E166K	ENSP00000299308:E166K	E	+	1	0	TMEM132B	124400394	1.000000	0.71417	0.950000	0.38849	0.956000	0.61745	9.540000	0.98080	2.488000	0.83962	0.655000	0.94253	GAG		0.587	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		A	125834441	G	A	125834441	3	1	5	1	0	0	0	0	1	0	0	0	16085	1291	45	3	502	3	TMEM132B	12	125834441	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	1482380	125834441	8017454	172	537										
LATS2	26524	hgsc.bcm.edu	37	chr13	21549228	21549228	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcccaggccttggtgctaccTtcgctggcatcgttccaagg	11	14	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:21549228T>C	ENST00000382592.4	-	8	3453	c.3048A>G	c.(3046-3048)gaA>gaG	p.E1016E	LATS2_ENST00000542899.1_Silent_p.E1016E	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TGGTGCTACCTTCGCTGGCAT	0.542																																																0			13											253	221	232					13																	21549228		2203	4300	6503	20447228	SO:0001819	synonymous_variant	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.3048A>G	13.37:g.21549228T>C			20447228		Silent	SNP	ENST00000382592.4	37	CCDS9294.1																																																																																				0.542	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			C	21549228	T	C	21549228	2	2	5	1	0	0	0	0	0	0	0	1	8669	1606	56	4		4	LATS2	13	21549228	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10		21549228	93620650	173	538										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587388	39587388	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tttgaaccatttaaaggagtActcaagctggagagacctga	10	7	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:39587388A>G	ENST00000352251.3	-	11	2834	c.2001T>C	c.(1999-2001)agT>agC	p.S667S	PROSER1_ENST00000350125.3_Silent_p.S645S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	667	Ser-rich.																TTAAAGGAGTACTCAAGCTGG	0.458																																																0			13											123	115	117					13																	39587388		2203	4300	6503	38485388	SO:0001819	synonymous_variant	80209			AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.2001T>C	13.37:g.39587388A>G			38485388	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																				0.458	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		G	39587388	A	G	39587388	2	3	5	1	0	0	0	0	0	0	0	1	1725	388	14	4		4	C13orf23	13	39587388	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10	18038160	39587388	75582490	174	539										
RB1	5925	hgsc.bcm.edu	37	chr13	48951109	48951109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aagagtgaaggatataggatAcatctttaaagagaaatttg	10	2	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:48951109A>G	ENST00000267163.4	+	13	1409	c.1271A>G	c.(1270-1272)tAc>tGc	p.Y424C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	424	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GATATAGGATACATCTTTAAA	0.358		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											109	117	115					13																	48951109		2203	4299	6502	47849110	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1271A>G	13.37:g.48951109A>G	ENSP00000267163:p.Tyr424Cys		47849110	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338827	0.24253	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.87650	-2.28	5.93	-1.42	0.08913	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	1.054330	0.07280	N	0.870674	T	0.72431	0.3459	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.55805	-0.8083	10	0.37606	T	0.19	.	7.6705	0.28455	0.4623:0.0:0.4311:0.1067	.	424	P06400	RB_HUMAN	C	403;424	ENSP00000267163:Y424C	ENSP00000267163:Y424C	Y	+	2	0	RB1	47849110	0.282000	0.24268	0.050000	0.19076	0.982000	0.71751	1.045000	0.30341	-0.633000	0.05545	0.482000	0.46254	TAC		0.358	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48951109	A	G	48951109	3	3	5	1	0	0	0	0	1	0	0	0	13135	391	14	4	1321	4	RB1	13	48951109	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	9363721	48951109	66218769	175	540										
TDRD3	81550	hgsc.bcm.edu	37	chr13	61084006	61084006	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agaagcagcactgaacgtacTtcttacaagcaataaacaga	7	9	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:61084006T>A	ENST00000196169.3	+	9	1477	c.689T>A	c.(688-690)cTt>cAt	p.L230H	TDRD3_ENST00000377881.2_Missense_Mutation_p.L230H|TDRD3_ENST00000377894.2_Missense_Mutation_p.L230H|TDRD3_ENST00000535286.1_Missense_Mutation_p.L323H	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	230	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		CTGAACGTACTTCTTACAAGC	0.403																																					Colon(36;164 906 35820 50723)											0			13											124	118	120					13																	61084006		2203	4300	6503	59982007	SO:0001583	missense	81550			AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.689T>A	13.37:g.61084006T>A	ENSP00000196169:p.Leu230His		59982007	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327256	0.81690	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.99	5.99	0.97316	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.78978	0.4369	M	0.72353	2.195	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81070	-0.1099	10	0.87932	D	0	-18.2117	16.4943	0.84223	0.0:0.0:0.0:1.0	.	323;229;230	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	H	230;230;230;323	ENSP00000196169:L230H;ENSP00000367113:L230H;ENSP00000367126:L230H;ENSP00000440190:L323H	ENSP00000196169:L230H	L	+	2	0	TDRD3	59982007	1.000000	0.71417	0.999000	0.59377	0.723000	0.41478	7.474000	0.81024	2.291000	0.77112	0.533000	0.62120	CTT		0.403	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61084006	T	A	61084006	3	1	5	1	0	0	0	0	1	0	0	0	15771	1609	56	5	1002	5	TDRD3	13	61084006	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	12132897	61084006	54085872	176	541										
PSMA3	5684	hgsc.bcm.edu	37	chr14	58718854	58718854	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagtacagctattggaatcaGatgcaaagatggtgttgtct	11	6	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:58718854G>T	ENST00000216455.4	+	3	212	c.122G>T	c.(121-123)aGa>aTa	p.R41I	PSMA3_ENST00000412908.2_Missense_Mutation_p.R41I|PSMA3_ENST00000557508.1_5'UTR	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	41					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						ATTGGAATCAGATGCAAAGAT	0.294																																																0			14											118	118	118					14																	58718854		2203	4300	6503	57788607	SO:0001583	missense	5684				CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"Proteasome (prosome, macropain) subunits"	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.122G>T	14.37:g.58718854G>T	ENSP00000216455:p.Arg41Ile		57788607	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	37	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.419072	0.62622	.	.	ENSG00000100567	ENST00000216455;ENST00000412908	T;T	0.24350	1.86;1.86	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.986;0.992	T	0.68815	-0.5309	10	0.87932	D	0	-18.4014	19.7578	0.96301	0.0:0.0:1.0:0.0	.	41;41	P25788-2;P25788	.;PSA3_HUMAN	I	41	ENSP00000216455:R41I;ENSP00000390491:R41I	ENSP00000216455:R41I	R	+	2	0	PSMA3	57788607	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.420000	0.97426	2.748000	0.94277	0.655000	0.94253	AGA		0.294	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1	NM_002788		T	58718854	G	T	58718854	3	4	5	1	0	0	0	0	1	0	0	0	12702	942	33	2	132	2	PSMA3	14	58718854	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		58718854	48630686	177	542										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174536	63174536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagcctggatgggactgtgcTctagcggacttcgggcctcc	14	13	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:63174536T>C	ENST00000322893.7	-	11	2925	c.2657A>G	c.(2656-2658)gAg>gGg	p.E886G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	886					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGGACTGTGCTCTAGCGGACT	0.502																																																0			14											128	115	119					14																	63174536		2203	4300	6503	62244289	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2657A>G	14.37:g.63174536T>C	ENSP00000321427:p.Glu886Gly		62244289	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.522810	0.27211	.	.	ENSG00000140015	ENST00000322893	D	0.99060	-5.38	5.44	5.44	0.79542	.	0.278712	0.35772	N	0.002984	D	0.96275	0.8785	N	0.14661	0.345	0.80722	D	1	B	0.22683	0.073	B	0.24701	0.055	D	0.94546	0.7749	10	0.30854	T	0.27	.	15.6661	0.77230	0.0:0.0:0.0:1.0	.	886	Q8NCM2	KCNH5_HUMAN	G	886	ENSP00000321427:E886G	ENSP00000321427:E886G	E	-	2	0	KCNH5	62244289	1.000000	0.71417	0.998000	0.56505	0.529000	0.34654	4.510000	0.60455	2.285000	0.76669	0.533000	0.62120	GAG		0.502	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		C	63174536	T	C	63174536	3	2	5	1	0	0	0	0	1	0	0	0	8056	1551	54	4	313	4	KCNH5	14	63174536	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	4455682	63174536	44175004	178	543										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76905829	76905829	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgtccgacgccagcggcggcTttggcctggccctgggcacc	15	17	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:76905829T>C	ENST00000509242.1	+	3	231	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	ESRRB_ENST00000380887.2_Missense_Mutation_p.F45L|ESRRB_ENST00000556177.1_Missense_Mutation_p.F45L|ESRRB_ENST00000507951.1_3'UTR|ESRRB_ENST00000261532.7_Missense_Mutation_p.F45L	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	45					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		CAGCGGCGGCTTTGGCCTGGC	0.692																																																0			14											22	25	24					14																	76905829		2194	4280	6474	75975582	SO:0001583	missense	2103			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.133T>C	14.37:g.76905829T>C	ENSP00000422488:p.Phe45Leu		75975582	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.198223	0.79015	.	.	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000556177;ENST00000380887;ENST00000261532	D;D;D;D;D	0.92348	-3.01;-3.02;-3.0;-3.02;-2.99	5.13	5.13	0.70059	.	0.056855	0.64402	D	0.000001	D	0.84156	0.5410	N	0.08118	0	0.45806	D	0.998686	B;B	0.29552	0.128;0.248	B;B	0.29524	0.103;0.103	D	0.84119	0.0405	10	0.72032	D	0.01	.	14.9565	0.71116	0.0:0.0:0.0:1.0	.	45;50	Q5F0P7;E7EWD9	.;.	L	50;45;45;45;45	ENSP00000424992:F50L;ENSP00000422488:F45L;ENSP00000451658:F45L;ENSP00000370270:F45L;ENSP00000261532:F45L	ENSP00000261532:F45L	F	+	1	0	ESRRB	75975582	1.000000	0.71417	0.969000	0.41365	0.897000	0.52465	8.000000	0.88501	1.937000	0.56155	0.533000	0.62120	TTT		0.692	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			C	76905829	T	C	76905829	3	2	5	1	0	0	0	0	1	0	0	0	5274	1609	56	4	135	4	ESRRB	14	76905829	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	13731293	76905829	30443711	179	544										
TMEM63C	57156	hgsc.bcm.edu	37	chr14	77714714	77714714	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtgttcctgccagacaacggCgccttctttgtcaactacgt	9	13	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:77714714C>T	ENST00000298351.4	+	19	1770	c.1626C>T	c.(1624-1626)ggC>ggT	p.G542G		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	542					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		CAGACAACGGCGCCTTCTTTG	0.567																																																0			14											49	49	49					14																	77714714		2201	4299	6500	76784467	SO:0001819	synonymous_variant	57156				CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"		"chromosome 14 open reading frame 171"	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.1626C>T	14.37:g.77714714C>T			76784467	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	37	CCDS45141.1																																																																																				0.567	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1			T	77714714	C	T	77714714	2	4	5	1	0	0	0	0	0	0	0	1	16231	755	27	1		1	TMEM63C	14	77714714	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	808885	77714714	29634826	180	545										
OR4N4	283694	hgsc.bcm.edu	37	chr15	22383320	22383320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agtgatctttccattgatgaAtcctatgatttatacccttc	5	9	1	4			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:22383320A>G	ENST00000328795.4	+	1	939	c.848A>G	c.(847-849)aAt>aGt	p.N283S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N283I(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CCATTGATGAATCCTATGATT	0.403																																																1	Substitution - Missense(1)	ovary(1)	15											135	123	127					15																	22383320		2188	4259	6447	19884684	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.848A>G	15.37:g.22383320A>G	ENSP00000332500:p.Asn283Ser		19884684	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	13.68	2.309110	0.40895	.	.	ENSG00000183706	ENST00000328795	T	0.58652	0.32	3.2	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.61489	0.2351	L	0.60957	1.885	0.34131	D	0.665298	P	0.47350	0.894	P	0.51866	0.682	T	0.74022	-0.3798	10	0.87932	D	0	-4.4181	9.7407	0.40416	1.0:0.0:0.0:0.0	.	283	Q8N0Y3	OR4N4_HUMAN	S	283	ENSP00000332500:N283S	ENSP00000332500:N283S	N	+	2	0	OR4N4	19884684	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	8.318000	0.89990	1.454000	0.47793	0.332000	0.21555	AAT		0.403	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			G	22383320	A	G	22383320	3	3	5	1	0	0	0	0	1	0	0	0	11109	101	4	4	850	4	OR4N4	15	22383320	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10		22383320	80148072	181	546										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27188386	27188386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caccacggtgctgaccatgaCgaccctcagcatcagcgcca	9	17	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:27188386C>T	ENST00000335625.5	+	10	1790	c.902C>T	c.(901-903)aCg>aTg	p.T301M	GABRA5_ENST00000355395.5_Missense_Mutation_p.T301M|GABRA5_ENST00000400081.3_Missense_Mutation_p.T301M	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	301					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CTGACCATGACGACCCTCAGC	0.612																																																0			15											16	17	17					15																	27188386		2091	4208	6299	24771132	SO:0001583	missense	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.902C>T	15.37:g.27188386C>T	ENSP00000335592:p.Thr301Met		24771132	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	-	24.3	4.513029	0.85389	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	D;D;D	0.93811	-3.29;-3.29;-3.29	5.27	4.36	0.52297	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.046170	0.85682	D	0.000000	D	0.96093	0.8727	M	0.75150	2.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96360	0.9265	10	0.87932	D	0	.	13.2941	0.60286	0.0:0.9235:0.0:0.0765	.	301	P31644	GBRA5_HUMAN	M	301	ENSP00000335592:T301M;ENSP00000347557:T301M;ENSP00000382953:T301M	ENSP00000335592:T301M	T	+	2	0	GABRA5	24771132	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	7.600000	0.82769	1.359000	0.45940	0.651000	0.88453	ACG		0.612	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27188386	C	T	27188386	3	4	5	1	0	0	0	0	1	0	0	0	6183	536	19	1	932	1	GABRA5	15	27188386	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	4805066	27188386	75343006	182	547										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34527516	34527516	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcctcacattggactggtccCtgagtggggaagaaataaag	13	8	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:34527516C>T	ENST00000354181.3	-	25	3720		c.e25-1		SLC12A6_ENST00000558667.1_Splice_Site|SLC12A6_ENST00000458406.2_Splice_Site|SLC12A6_ENST00000560611.1_Splice_Site|SLC12A6_ENST00000397702.2_Splice_Site|SLC12A6_ENST00000560164.1_Splice_Site|SLC12A6_ENST00000397707.2_Splice_Site|SLC12A6_ENST00000451844.2_Splice_Site|SLC12A6_ENST00000558589.1_Splice_Site|SLC12A6_ENST00000290209.5_Splice_Site			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6						angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GGACTGGTCCCTGAGTGGGGA	0.403																																																0			15											77	70	72					15																	34527516		2201	4298	6499	32314808	SO:0001630	splice_region_variant	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.3228-1G>A	15.37:g.34527516C>T			32314808	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Splice_Site	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018194	0.54576	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3256	0.87246	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC12A6	32314808	1.000000	0.71417	0.999000	0.59377	0.382000	0.30200	7.307000	0.78920	2.617000	0.88574	0.561000	0.74099	.		0.403	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	Intron	T	34527516	C	T	34527516	5	4	5	1	0	0	0	0	0	0	1	0	14424	695	24	3	233	3	SLC12A6	15	34527516	Splice_Site	SNP	C	TCGA-AF-2693-01A-02D-1733-10	7339130	34527516	68003876	183	548										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058183	48058183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cgcatccccctcagtcgctgTgagcgttatggatcatgtaa	10	12	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:48058183T>C	ENST00000316364.5	+	14	1984	c.1545T>C	c.(1543-1545)tgT>tgC	p.C515C	SEMA6D_ENST00000354744.4_Silent_p.C515C|SEMA6D_ENST00000558014.1_Silent_p.C515C|SEMA6D_ENST00000355997.3_Silent_p.C515C|SEMA6D_ENST00000558816.1_Silent_p.C515C|SEMA6D_ENST00000389433.2_Silent_p.C515C|SEMA6D_ENST00000537942.1_Silent_p.C515C|SEMA6D_ENST00000389428.3_Silent_p.C515C|SEMA6D_ENST00000389432.2_Silent_p.C515C|SEMA6D_ENST00000358066.4_Silent_p.C515C|SEMA6D_ENST00000536845.2_Silent_p.C515C	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	515	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TCAGTCGCTGTGAGCGTTATG	0.418																																																0			15											229	210	217					15																	48058183		2198	4297	6495	45845475	SO:0001819	synonymous_variant	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1545T>C	15.37:g.48058183T>C			45845475	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																				0.418	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		C	48058183	T	C	48058183	2	2	5	1	0	0	0	0	0	0	0	1	14079	1702	59	4		4	SEMA6D	15	48058183	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	13530667	48058183	54473209	184	549										
COPS2	9318	hgsc.bcm.edu	37	chr15	49426216	49426216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agtggttcgtcttggacttcCagattcatcataattcttga	8	8	4	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:49426216C>T	ENST00000388901.5	-	8	878	c.805G>A	c.(805-807)Gga>Aga	p.G269R	COPS2_ENST00000542928.1_Missense_Mutation_p.G205R|COPS2_ENST00000299259.6_Missense_Mutation_p.G276R	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	269	PCI.				cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		CTTGGACTTCCAGATTCATCA	0.373																																					NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)											0			15											94	101	98					15																	49426216		2196	4295	6491	47213508	SO:0001583	missense	9318			AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.805G>A	15.37:g.49426216C>T	ENSP00000373553:p.Gly269Arg		47213508	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	ENST00000388901.5	37	CCDS32235.1	.	.	.	.	.	.	.	.	.	.	C	35	5.475641	0.96291	.	.	ENSG00000166200	ENST00000299259;ENST00000388901;ENST00000542928	T;T;T	0.75260	2.25;-0.92;2.25	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);PCI/PINT associated module (1);	0.000000	0.85682	D	0.000000	D	0.89622	0.6768	M	0.90019	3.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90636	0.4571	10	0.87932	D	0	-0.0025	20.3465	0.98790	0.0:1.0:0.0:0.0	.	205;277;269	B4DIH5;Q59EL2;P61201	.;.;CSN2_HUMAN	R	276;269;205	ENSP00000299259:G276R;ENSP00000373553:G269R;ENSP00000443664:G205R	ENSP00000299259:G276R	G	-	1	0	COPS2	47213508	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.818000	0.86416	2.798000	0.96311	0.655000	0.94253	GGA		0.373	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236		T	49426216	C	T	49426216	3	4	5	1	0	0	0	0	1	0	0	0	3739	603	21	3	550	3	COPS2	15	49426216	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	1368033	49426216	53105176	185	550										
STRA6	64220	hgsc.bcm.edu	37	chr15	74494576	74494576	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tagtcctctgtggccccgggGgaggtctggttccctgctgg	16	12	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:74494576G>A	ENST00000323940.5	-	2	278	c.33C>T	c.(31-33)tcC>tcT	p.S11S	RP11-60L3.1_ENST00000561332.1_RNA|RP11-60L3.1_ENST00000560148.1_RNA|STRA6_ENST00000432245.2_Silent_p.S11S|STRA6_ENST00000423167.2_Silent_p.S11S|STRA6_ENST00000395105.4_Silent_p.S11S|STRA6_ENST00000563965.1_Silent_p.S50S|STRA6_ENST00000574278.1_Silent_p.S26S|RP11-60L3.1_ENST00000558645.1_RNA|STRA6_ENST00000449139.2_Silent_p.S11S|STRA6_ENST00000535552.1_Silent_p.S48S|STRA6_ENST00000416286.3_Silent_p.S11S|STRA6_ENST00000574439.1_5'UTR	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	11					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						TGGCCCCGGGGGAGGTCTGGT	0.592																																																0			15											56	56	56					15																	74494576		2198	4297	6495	72281629	SO:0001819	synonymous_variant	64220			AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"retinol binding protein 4 receptor"	610745	"stimulated by retinoic acid gene 6 homolog (mouse)", "stimulated by retinoic acid 6 homolog (mouse)"			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.33C>T	15.37:g.74494576G>A			72281629	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Silent	SNP	ENST00000323940.5	37	CCDS10261.1																																																																																				0.592	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1			A	74494576	G	A	74494576	2	1	5	1	0	0	0	0	0	0	0	1	15361	1219	43	3		3	STRA6	15	74494576	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	25068360	74494576	28036816	186	551										
STARD5	80765	hgsc.bcm.edu	37	chr15	81605707	81605707	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaggtaaccgctgaggtcggTatggaagaatgtgaccaggt	16	6	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:81605707T>C	ENST00000302824.6	-	6	557	c.532A>G	c.(532-534)Acc>Gcc	p.T178A		NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	178	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						CTGAGGTCGGTATGGAAGAAT	0.552																																																0			15											192	164	173					15																	81605707		2203	4300	6503	79392762	SO:0001583	missense	80765			AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"StAR-related lipid transfer (START) domain containing"	18065	protein-coding gene	gene with protein product		607050	"START domain containing 5"			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.532A>G	15.37:g.81605707T>C	ENSP00000304032:p.Thr178Ala		79392762	P59094	Missense_Mutation	SNP	ENST00000302824.6	37	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.170144	0.57584	.	.	ENSG00000172345	ENST00000302824	T	0.77489	-1.1	5.07	3.91	0.45181	Lipid-binding START (3);START-like domain (1);	0.058138	0.64402	D	0.000002	D	0.85301	0.5665	M	0.84082	2.675	0.54753	D	0.999984	D	0.63046	0.992	P	0.60949	0.881	D	0.83511	0.0080	10	0.30078	T	0.28	-0.3983	11.2931	0.49263	0.1368:0.0:0.0:0.8632	.	178	Q9NSY2	STAR5_HUMAN	A	178	ENSP00000304032:T178A	ENSP00000304032:T178A	T	-	1	0	STARD5	79392762	1.000000	0.71417	0.992000	0.48379	0.058000	0.15608	5.177000	0.65032	0.833000	0.34828	0.459000	0.35465	ACC		0.552	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2			C	81605707	T	C	81605707	3	2	5	1	0	0	0	0	1	0	0	0	15299	1638	57	4	113	4	STARD5	15	81605707	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	7111131	81605707	20925685	187	552										
BNC1	646	hgsc.bcm.edu	37	chr15	83932792	83932792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggttggggttggcgctatggCgattccggctccttagggag	18	8	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:83932792C>T	ENST00000345382.2	-	4	1296	c.1211G>A	c.(1210-1212)cGc>cAc	p.R404H	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.R397H	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	404					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R404H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						GGCGCTATGGCGATTCCGGCT	0.527																																																1	Substitution - Missense(1)	ovary(1)	15											170	159	163					15																	83932792		2203	4300	6503	81723796	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1211G>A	15.37:g.83932792C>T	ENSP00000307041:p.Arg404His		81723796	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745100	0.89663	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.30981	1.51	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.61022	0.2314	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.65261	-0.6211	10	0.87932	D	0	-33.1899	19.4213	0.94723	0.0:1.0:0.0:0.0	.	397;404	F5GY04;Q01954	.;BNC1_HUMAN	H	404;397	ENSP00000307041:R404H	ENSP00000307041:R404H	R	-	2	0	BNC1	81723796	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.755000	0.85180	2.589000	0.87451	0.655000	0.94253	CGC		0.527	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		T	83932792	C	T	83932792	3	4	5	1	0	0	0	0	1	0	0	0	1475	768	27	1	1781	1	BNC1	15	83932792	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2327085	83932792	18598600	188	553										
PCSK6	5046	hgsc.bcm.edu	37	chr15	101938708	101938708	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagctggcactgtaaatgtcGatgtagttgggtctgatgcc	13	8	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:101938708G>A	ENST00000348070.1	-	8	893	c.894C>T	c.(892-894)atC>atT	p.I298I	PCSK6_ENST00000344273.2_Silent_p.I298I|PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000331826.7_Silent_p.I133I|PCSK6_ENST00000398181.2_Silent_p.I298I|PCSK6_ENST00000358417.3_Silent_p.I298I	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	299	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGTAAATGTCGATGTAGTTGG	0.597																																																0			15											85	91	89					15																	101938708		2091	4250	6341	99756231	SO:0001819	synonymous_variant	5046				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"subtilisin-like protease", "subtilisin-like proprotein convertase 4", "subtilisin/kexin-like protease PACE4"	167405	"paired basic amino acid cleaving system 4"	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.894C>T	15.37:g.101938708G>A			99756231	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Nonsense_Mutation	SNP	ENST00000348070.1	37																																																																																					0.597	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570		A	101938708	G	A	101938708	2	1	5	1	0	0	0	0	0	0	0	1	11635	1048	37	1		1	PCSK6	15	101938708	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	18005916	101938708	592684	189	554										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1306355	1306355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctggcgagcccggcctacgTggcccctggtgagtcccagc	14	17	0	1	rs1800984	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:1306355T>C	ENST00000211076.3	+	1	222	c.74T>C	c.(73-75)gTg>gCg	p.V25A	TPSD1_ENST00000397534.2_Missense_Mutation_p.V18A|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	25			V -> A (in dbSNP:rs1800984).	V -> G (in Ref. 1; AAD17861). {ECO:0000305}.		extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CCGGCCTACGTGGCCCCTGGT	0.721													-|||	3599	0.71865	0.7564	0.6542	5008	,	,		14753	0.9484		0.5577	False		,,,				2504	0.6421															0			16						T	ALA/VAL	3121,1271		1094,933,169	29	37	34		74	-3.1	0	16	dbSNP_89	34	4690,3906		1125,2440,733	no	missense	TPSD1	NM_012217.2	64	2219,3373,902	CC,CT,TT		45.4397,28.939,39.8599	benign	25/243	1306355	7811,5177	2196	4298	6494	1246356	SO:0001583	missense	23430			AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.74T>C	16.37:g.1306355T>C	ENSP00000211076:p.Val25Ala		1246356	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	1558	0.7133699633699634	388	0.7886178861788617	208	0.574585635359116	556	0.972027972027972	406	0.5356200527704486	-	0.855	-0.737258	0.03111	0.71061	0.545603	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.81247	-1.47;-1.47	2.55	-3.13	0.05266	.	0.813971	0.10635	N	0.651704	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	3.4489	0.07491	0.0:0.375:0.2043:0.4206	rs1800984;rs3865206;rs4083416	25	Q9BZJ3	TRYD_HUMAN	A	18;25	ENSP00000380668:V18A;ENSP00000211076:V25A	ENSP00000211076:V25A	V	+	2	0	TPSD1	1246356	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.814000	0.01723	-0.826000	0.04284	-1.137000	0.01932	GTG		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			C	1306355	T	C	1306355	3	2	5	1	0	0	0	0	1	0	0	0	16465	1696	59	4	76	4	TPSD1	16	1306355	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10		1306355	89048398	190	555										
EME2	197342	hgsc.bcm.edu	37	chr16	1823754	1823754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctgatggaggccctggaggCcctgggctgcgagtgccgca	17	13	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:1823754C>T	ENST00000568449.1	+	2	317	c.296C>T	c.(295-297)gCc>gTc	p.A99V	MRPS34_ENST00000397375.2_5'Flank|EME2_ENST00000307394.7_Missense_Mutation_p.A99V|NME3_ENST00000219302.3_5'Flank|MRPS34_ENST00000177742.3_5'Flank|NME3_ENST00000563498.1_5'Flank	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	99					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						GCCCTGGAGGCCCTGGGCTGC	0.741								Direct reversal of damage;Homologous recombination																																								0			16											5	4	4					16																	1823754		1791	3575	5366	1763755	SO:0001583	missense	197342			AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.296C>T	16.37:g.1823754C>T	ENSP00000457353:p.Ala99Val		1763755	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	37	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.255434	0.22965	.	.	ENSG00000197774	ENST00000307394;ENST00000454910	T	0.23147	1.92	3.56	2.57	0.30868	ERCC4 domain (2);	1.209980	0.06420	U	0.722101	T	0.16599	0.0399	.	.	.	0.09310	N	1	B	0.25850	0.136	B	0.24701	0.055	T	0.19549	-1.0302	9	0.29301	T	0.29	-1.3381	6.4619	0.21960	0.0:0.7682:0.0:0.2318	.	99	A4GXA9	EME2_HUMAN	V	99	ENSP00000303779:A99V	ENSP00000303779:A99V	A	+	2	0	EME2	1763755	0.001000	0.12720	0.231000	0.23993	0.792000	0.44763	1.611000	0.36879	1.707000	0.51288	0.306000	0.20318	GCC		0.741	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865		T	1823754	C	T	1823754	3	4	5	1	0	0	0	0	1	0	0	0	5102	739	26	3	302	3	EME2	16	1823754	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	517399	1823754	88530999	191	556										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27512525	27512525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tggttaccttcttcttgatgCcatcttgaatgacagtggtc	9	9	3	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:27512525C>T	ENST00000356183.4	-	12	2063	c.2048G>A	c.(2047-2049)gGc>gAc	p.G683D	GTF3C1_ENST00000561623.1_Missense_Mutation_p.G683D	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	683					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CTTCTTGATGCCATCTTGAAT	0.527																																																0			16											128	103	111					16																	27512525		2197	4300	6497	27420026	SO:0001583	missense	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2048G>A	16.37:g.27512525C>T	ENSP00000348510:p.Gly683Asp		27420026	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880473	0.91740	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.24908	1.83	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	M	0.67953	2.075	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.47971	-0.9075	10	0.51188	T	0.08	-13.1534	19.0541	0.93056	0.0:1.0:0.0:0.0	.	683;683	Q12789;Q12789-3	TF3C1_HUMAN;.	D	683;681	ENSP00000348510:G683D	ENSP00000348510:G683D	G	-	2	0	GTF3C1	27420026	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.256000	0.78350	2.655000	0.90218	0.655000	0.94253	GGC		0.527	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27512525	C	T	27512525	3	4	5	1	0	0	0	0	1	0	0	0	6893	739	26	3	4385	3	GTF3C1	16	27512525	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	25688771	27512525	62842228	192	557										
CYLD	1540	hgsc.bcm.edu	37	chr16	50811825	50811825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	actcacaaccacaatccaaaTcaaaaaatacatggtacatt	2	11	2	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:50811825T>C	ENST00000427738.3	+	7	1316	c.1111T>C	c.(1111-1113)Tca>Cca	p.S371P	CYLD_ENST00000564326.1_Missense_Mutation_p.S368P|CYLD_ENST00000568704.2_Missense_Mutation_p.S368P|CYLD_ENST00000540145.1_Missense_Mutation_p.S371P|CYLD_ENST00000311559.9_Missense_Mutation_p.S371P|CYLD_ENST00000566206.1_Missense_Mutation_p.S368P|CYLD_ENST00000398568.2_Missense_Mutation_p.S368P|CYLD_ENST00000569418.1_Missense_Mutation_p.S368P			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	371	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				ACAATCCAAATCAAAAAATAC	0.313			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											87	81	83					16																	50811825		1814	4061	5875	49369326	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1111T>C	16.37:g.50811825T>C	ENSP00000392025:p.Ser371Pro		49369326	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.272448	0.40194	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D	0.93906	-3.31;-3.31;-3.31	5.57	3.25	0.37280	.	0.283087	0.35870	N	0.002940	D	0.85327	0.5671	N	0.24115	0.695	0.42188	D	0.991711	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.09377	0.0;0.004;0.0;0.0	T	0.77953	-0.2394	10	0.35671	T	0.21	-6.4529	6.1147	0.20120	0.2678:0.072:0.0:0.6602	.	368;371;368;371	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	P	371;371;368;368	ENSP00000445447:S371P;ENSP00000308928:S371P;ENSP00000381574:S368P	ENSP00000308928:S371P	S	+	1	0	CYLD	49369326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.942000	0.40243	0.995000	0.38917	0.528000	0.53228	TCA		0.313	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			C	50811825	T	C	50811825	3	2	5	1	0	0	0	0	1	0	0	0	4149	1435	50	4	1133	4	CYLD	16	50811825	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	23299300	50811825	39542928	193	558										
CHD9	80205	hgsc.bcm.edu	37	chr16	53272297	53272297	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaaatgggtcttggcaaaacTattcaatcaattacattcct	6	8	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:53272297T>C	ENST00000398510.3	+	11	2763	c.2676T>C	c.(2674-2676)acT>acC	p.T892T	CHD9_ENST00000564845.1_Silent_p.T892T|CHD9_ENST00000447540.1_Silent_p.T892T|CHD9_ENST00000566029.1_Silent_p.T892T			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	892	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.T892T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TTGGCAAAACTATTCAATCAA	0.348																																																1	Substitution - coding silent(1)	kidney(1)	16											91	85	87					16																	53272297		1831	4084	5915	51829798	SO:0001819	synonymous_variant	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2676T>C	16.37:g.53272297T>C			51829798	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																					0.348	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		C	53272297	T	C	53272297	2	2	5	1	0	0	0	0	0	0	0	1	3338	1509	53	4		4	CHD9	16	53272297	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	2460472	53272297	37082456	194	559										
WWP2	11060	hgsc.bcm.edu	37	chr16	69971053	69971053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctggcgtttcacccgaggcgTggaagagcagaccaaagcct	13	12	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:69971053T>C	ENST00000359154.2	+	20	2251	c.2150T>C	c.(2149-2151)gTg>gCg	p.V717A	WWP2_ENST00000568684.1_Missense_Mutation_p.V278A|WWP2_ENST00000448661.1_Missense_Mutation_p.V717A|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.V601A|WWP2_ENST00000356003.2_Missense_Mutation_p.V717A	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	717	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACCCGAGGCGTGGAAGAGCAG	0.617																																																0			16											77	68	71					16																	69971053		2198	4300	6498	68528554	SO:0001583	missense	11060			BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2150T>C	16.37:g.69971053T>C	ENSP00000352069:p.Val717Ala		68528554	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	T	31	5.065869	0.93898	.	.	ENSG00000198373	ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	5.21	5.21	0.72293	HECT (4);	0.000000	0.85682	D	0.000000	T	0.81365	0.4807	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.84442	0.0583	9	.	.	.	.	15.3883	0.74723	0.0:0.0:0.0:1.0	.	717	O00308	WWP2_HUMAN	A	717;278;717;717;604;601	ENSP00000352069:V717A;ENSP00000396871:V717A;ENSP00000348283:V717A;ENSP00000445616:V601A	.	V	+	2	0	WWP2	68528554	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.997000	0.88414	2.077000	0.62373	0.533000	0.62120	GTG		0.617	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		C	69971053	T	C	69971053	3	2	5	1	0	0	0	0	1	0	0	0	17456	1696	59	4	2228	4	WWP2	16	69971053	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	16698756	69971053	20383700	195	560										
CDYL2	124359	hgsc.bcm.edu	37	chr16	80638362	80638362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggagctccagagctgcttgaGcatgaggcattccttctcgt	12	11	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:80638362G>A	ENST00000570137.2	-	7	1599	c.1444C>T	c.(1444-1446)Ctc>Ttc	p.L482F	CDYL2_ENST00000562812.1_Missense_Mutation_p.L483F|CDYL2_ENST00000563890.1_Missense_Mutation_p.L483F|CDYL2_ENST00000566173.1_Missense_Mutation_p.L483F	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	482						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						AGCTGCTTGAGCATGAGGCAT	0.542																																																0			16											135	129	131					16																	80638362		2203	4300	6503	79195863	SO:0001583	missense	124359			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"chromodomain Y-like protein 2"			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1444C>T	16.37:g.80638362G>A	ENSP00000476295:p.Leu482Phe		79195863	Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167966	0.78339	.	.	ENSG00000166446	ENST00000299564	T	0.65364	-0.15	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000002	T	0.81692	0.4876	M	0.91140	3.18	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.84662	0.0707	10	0.87932	D	0	.	11.0713	0.48006	0.0923:0.0:0.9077:0.0	.	482	Q8N8U2	CDYL2_HUMAN	F	482	ENSP00000299564:L482F	ENSP00000299564:L482F	L	-	1	0	CDYL2	79195863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.966000	0.40481	2.717000	0.92951	0.650000	0.86243	CTC		0.542	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		A	80638362	G	A	80638362	3	1	5	1	0	0	0	0	1	0	0	0	3192	971	34	3	80	3	CDYL2	16	80638362	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	10667309	80638362	9716391	196	561										
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84522896	84522896	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acacttgccttgcagcttcaTgtcagagagcagctgagcag	11	11	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:84522896T>C	ENST00000343629.6	-	4	699	c.517A>G	c.(517-519)Atg>Gtg	p.M173V	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.M146V	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	173						lysosomal membrane (GO:0005765)											TGCAGCTTCATGTCAGAGAGC	0.582																																																0			16											50	47	48					16																	84522896		2200	4300	6500	83080397	SO:0001583	missense	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.517A>G	16.37:g.84522896T>C	ENSP00000343635:p.Met173Val		83080397	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	t	11.55	1.672637	0.29693	.	.	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.09163	3.2;3.01	5.04	1.27	0.21489	.	0.465387	0.24879	N	0.034869	T	0.09335	0.0230	M	0.62723	1.935	0.23198	N	0.998133	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.28522	-1.0041	10	0.31617	T	0.26	-19.7902	2.5659	0.04783	0.1426:0.099:0.4438:0.3146	.	146;173	F5GWS3;Q6P9B6	.;K1609_HUMAN	V	173;146	ENSP00000343635:M173V;ENSP00000441997:M146V	ENSP00000343635:M173V	M	-	1	0	KIAA1609	83080397	0.412000	0.25392	0.992000	0.48379	0.784000	0.44337	-0.489000	0.06490	0.213000	0.20722	-0.332000	0.08345	ATG		0.582	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		C	84522896	T	C	84522896	3	2	5	1	0	0	0	0	1	0	0	0	8268	1464	51	4	873	4	KIAA1609	16	84522896	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	3884534	84522896	5831857	197	562										
ATP2A3	489	hgsc.bcm.edu	37	chr17	3844345	3844345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctccacgcgggcgaagcagcGggcggtgcggcaggcctggc	19	14	0	0	rs9895012	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:3844345G>A	ENST00000352011.3	-	14	2074	c.2020C>T	c.(2020-2022)Cgc>Tgc	p.R674C	ATP2A3_ENST00000397035.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000309890.7_Missense_Mutation_p.R674C|ATP2A3_ENST00000397041.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000359983.3_Missense_Mutation_p.R674C			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	674			R -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GCGAAGCAGCGGGCGGTGCGG	0.657													G|||	65	0.0129792	8e-04	0.0259	5008	,	,		13726	0.001		0.0408	False		,,,				2504	0.0041				GBM(32;29 774 15719 37967)											0			17	GRCh37	CM992303	ATP2A3	M	rs9895012	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	23,4383	29.0+/-57.7	0,23,2180	55	59	58		2020,2020,2020,2020,2020,2020,2020	-4.6	0.8	17	dbSNP_119	58	220,8368	86.3+/-148.7	1,218,4075	yes	missense,missense,missense,missense,missense,missense,missense	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	180,180,180,180,180,180,180	1,241,6255	AA,AG,GG		2.5617,0.522,1.8701	benign,benign,benign,benign,benign,benign,benign	674/1000,674/1053,674/1045,674/1044,674/1030,674/999,674/1030	3844345	243,12751	2203	4294	6497	3791094	SO:0001583	missense	489				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"ATPases / P-type"	813	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 3", "calcium pump 3"	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.2020C>T	17.37:g.3844345G>A	ENSP00000301387:p.Arg674Cys		3791094	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	37	CCDS11041.1	44	0.020146520146520148	0	0.0	13	0.03591160220994475	1	0.0017482517482517483	30	0.0395778364116095	G	11.91	1.778975	0.31502	0.00522	0.025617	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8;-3.8;-3.8	4.16	-4.62	0.03370	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.192116	0.45867	N	0.000325	T	0.78541	0.4299	M	0.70275	2.135	0.80722	D	1	B;B;B;B;B;B	0.12630	0.002;0.001;0.002;0.006;0.006;0.002	B;B;B;B;B;B	0.10450	0.0;0.001;0.001;0.003;0.005;0.001	T	0.70781	-0.4779	10	0.30854	T	0.27	.	11.1164	0.48262	0.5039:0.0:0.4961:0.0	rs9895012	674;674;674;674;674;674	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	C	674	ENSP00000380236:R674C;ENSP00000301387:R674C;ENSP00000353072:R674C;ENSP00000380234:R674C;ENSP00000312577:R674C;ENSP00000380229:R674C	ENSP00000312577:R674C	R	-	1	0	ATP2A3	3791094	0.817000	0.29147	0.759000	0.31340	0.917000	0.54804	1.124000	0.31320	-0.821000	0.04312	-0.459000	0.05422	CGC		0.657	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		A	3844345	G	A	3844345	3	1	5	1	0	0	0	0	1	0	0	0	1139	1116	39	1	1222	1	ATP2A3	17	3844345	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		3844345	77350865	198	563										
TP53	7157	hgsc.bcm.edu	37	chr17	7579591	7579591	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcttgggacggcaagggggaCtgtagatgggtgaaaagagc	19	5	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:7579591C>T	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	17	GRCh37	CS971912	TP53	S							141	137	138					17																	7579591		2203	4300	6503	7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>A	17.37:g.7579591C>T			7520316	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.702	0.498192	0.12762	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40380	D	0.979434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7579591	C	T	7579591	5	4	5	1	0	0	0	0	0	0	1	0	16421	579	20	3	1206	3	TP53	17	7579591	Splice_Site	SNP	C	TCGA-AF-2693-01A-02D-1733-10	3735246	7579591	73615619	199	564										
MYH3	4621	hgsc.bcm.edu	37	chr17	10542709	10542709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	catccaaggcctgctggtgcGcctcttggagggccttcttc	12	14	2	0	rs34088014	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:10542709G>A	ENST00000583535.1	-	24	3095	c.3008C>T	c.(3007-3009)gCg>gTg	p.A1003V	MYH3_ENST00000226209.7_Missense_Mutation_p.A1003V	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1003			A -> V (in dbSNP:rs34088014).		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CTGCTGGTGCGCCTCTTGGAG	0.443													G|||	109	0.0217652	0.0333	0.0086	5008	,	,		19720	0.003		0.0239	False		,,,				2504	0.0327															0			17						G	VAL/ALA	129,4277	93.9+/-132.6	2,125,2076	68	66	67		3008	5.5	1	17	dbSNP_126	67	177,8423	79.5+/-142.1	1,175,4124	yes	missense	MYH3	NM_002470.3	64	3,300,6200	AA,AG,GG		2.0581,2.9278,2.3528	benign	1003/1941	10542709	306,12700	2203	4300	6503	10483434	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.3008C>T	17.37:g.10542709G>A	ENSP00000464317:p.Ala1003Val		10483434	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	38	0.0173992673992674	14	0.028455284552845527	3	0.008287292817679558	1	0.0017482517482517483	20	0.026385224274406333	G	17.29	3.352176	0.61183	0.029278	0.020581	ENSG00000109063	ENST00000226209	D	0.83250	-1.7	5.54	5.54	0.83059	.	.	.	.	.	T	0.65709	0.2717	M	0.63843	1.955	0.54753	D	0.999988	B	0.15930	0.015	B	0.10450	0.005	T	0.72497	-0.4275	9	0.46703	T	0.11	.	19.8414	0.96690	0.0:0.0:1.0:0.0	rs34088014	1003	P11055	MYH3_HUMAN	V	1003	ENSP00000226209:A1003V	ENSP00000226209:A1003V	A	-	2	0	MYH3	10483434	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	6.734000	0.74801	2.763000	0.94921	0.650000	0.86243	GCG		0.443	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10542709	G	A	10542709	3	1	5	1	0	0	0	0	1	0	0	0	10066	1087	38	1	2886	1	MYH3	17	10542709	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	2963118	10542709	70652501	200	565										
NF1	4763	hgsc.bcm.edu	37	chr17	29528489	29528489	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgctggtaaattcactccatCgaatcatcaccaatgtaagt	6	10	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:29528489C>T	ENST00000358273.4	+	11	1629	c.1246C>T	c.(1246-1248)Cga>Tga	p.R416*	NF1_ENST00000356175.3_Nonsense_Mutation_p.R416*|NF1_ENST00000431387.4_Nonsense_Mutation_p.R416*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	416					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.R416*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTCACTCCATCGAATCATCAC	0.308			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	15	Whole gene deletion(8)|Unknown(6)|Substitution - Nonsense(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	17	GRCh37	CM992366	NF1	M							85	95	92					17																	29528489		2203	4294	6497	26552615	SO:0001587	stop_gained	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1246C>T	17.37:g.29528489C>T	ENSP00000351015:p.Arg416*		26552615	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751639	0.89753	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5894	0.61951	0.1554:0.8446:0.0:0.0	.	.	.	.	X	416;416;416;82	.	ENSP00000348498:R416X	R	+	1	2	NF1	26552615	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.539000	0.53604	2.408000	0.81797	0.484000	0.47621	CGA		0.308	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29528489	C	T	29528489	4	4	5	1	0	0	0	0	0	1	0	0	10387	876	31	1	1288	1	NF1	17	29528489	Nonsense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	18985780	29528489	51666721	201	566										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37882854	37882854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	atgtcggccaagattccgggAgttggtgtctgaattctccc	12	10	2	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:37882854A>G	ENST00000269571.5	+	24	3071	c.2912A>G	c.(2911-2913)gAg>gGg	p.E971G	ERBB2_ENST00000584601.1_Missense_Mutation_p.E941G|ERBB2_ENST00000406381.2_Missense_Mutation_p.E941G|ERBB2_ENST00000540147.1_Missense_Mutation_p.E941G|ERBB2_ENST00000584450.1_Missense_Mutation_p.E971G|ERBB2_ENST00000541774.1_Missense_Mutation_p.E956G|MIEN1_ENST00000474210.1_5'Flank|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000445658.2_Missense_Mutation_p.E695G			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	971	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.E971G(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	AGATTCCGGGAGTTGGTGTCT	0.612		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	1	Substitution - Missense(1)	ovary(1)	17											132	107	116					17																	37882854		2203	4300	6503	35136380	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2912A>G	17.37:g.37882854A>G	ENSP00000269571:p.Glu971Gly		35136380	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110891	0.56398	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.29	5.29	0.74685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.75568	0.3867	M	0.79011	2.435	0.80722	D	1	P;B;P	0.44309	0.832;0.108;0.832	P;B;P	0.49708	0.62;0.036;0.62	T	0.79706	-0.1691	9	0.87932	D	0	.	14.247	0.65995	1.0:0.0:0.0:0.0	.	695;956;971	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	G	941;956;695;971;941	ENSP00000385185:E941G;ENSP00000446466:E956G;ENSP00000404047:E695G;ENSP00000269571:E971G;ENSP00000443562:E941G	ENSP00000269571:E971G	E	+	2	0	ERBB2	35136380	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.523000	0.81856	2.003000	0.58678	0.533000	0.62120	GAG		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			G	37882854	A	G	37882854	3	3	5	1	0	0	0	0	1	0	0	0	5219	304	11	4	3006	4	ERBB2	17	37882854	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	8354365	37882854	43312356	202	567										
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39254148	39254152	+	Frame_Shift_Del	DEL	GGTGG	GGTGG	-													0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cagcagctggggcgacagcaGgtgggctggcagcacacaga					rs201246375		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGG	GGTGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:39254148_39254152delGGTGG	ENST00000333822.4	-	1	241_245	c.185_189delCCACC	c.(184-189)cccaccfs	p.PT62fs		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	62	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GGCGACAGCAGGTGGGCTGGCAGCA	0.649																																																0			17																																								36507678	SO:0001589	frameshift_variant	728224			AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.185_189delCCACC	17.37:g.39254148_39254152delGGTGG	ENSP00000328444:p.Pro62fs		36507674	A8MSH3	Frame_Shift_Del	DEL	ENST00000333822.4	37	CCDS45674.1																																																																																				0.649	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		-	39254152	GGTGG	-	39254148	7	5	5	1	0	1	0	1	0	0	0	0	8578	987	35	0	372	0	KRTAP4-8	17	39254148	Frame_Shift_Del	DEL	GGTGG	TCGA-AF-2693-01A-02D-1733-10	1371294	39254148	41941062	203	568										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45438838	45438838	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ttggatagcatgggtatcccTataaaccgtgaaattttaga	9	6	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:45438838T>C	ENST00000331493.2	+	10	1167	c.756T>C	c.(754-756)ccT>ccC	p.P252P	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	252						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGGGTATCCCTATAAACCGTG	0.353																																																0			17											181	177	178					17																	45438838		2203	4300	6503	42793837	SO:0001819	synonymous_variant	124989			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.756T>C	17.37:g.45438838T>C			42793837	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																				0.353	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		C	45438838	T	C	45438838	2	2	5	1	0	0	0	0	0	0	0	1	1870	1509	53	4		4	C17orf57	17	45438838	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	6184690	45438838	35756372	204	569										
LRRC59	55379	hgsc.bcm.edu	37	chr17	48462526	48462526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtttcttctcctgctcccgcTtggctgctttgagggcatca	10	13	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:48462526T>C	ENST00000225972.7	-	6	864	c.629A>G	c.(628-630)aAg>aGg	p.K210R	Y_RNA_ENST00000384097.1_RNA	NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	210						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CTGCTCCCGCTTGGCTGCTTT	0.552																																																0			17											182	177	178					17																	48462526		2203	4300	6503	45817525	SO:0001583	missense	55379			AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829			28817	protein-coding gene	gene with protein product		614854				12477932	Standard	NM_018509		Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.629A>G	17.37:g.48462526T>C	ENSP00000225972:p.Lys210Arg		45817525	B2RE83|D3DTX8|Q9P189	Missense_Mutation	SNP	ENST00000225972.7	37	CCDS11566.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775526	0.90195	.	.	ENSG00000108829	ENST00000225972	T	0.05199	3.48	5.87	5.87	0.94306	.	0.098404	0.64402	D	0.000001	T	0.12135	0.0295	L	0.53249	1.67	0.80722	D	1	P	0.51057	0.941	P	0.46917	0.531	T	0.02156	-1.1204	10	0.37606	T	0.19	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	210	Q96AG4	LRC59_HUMAN	R	210	ENSP00000225972:K210R	ENSP00000225972:K210R	K	-	2	0	LRRC59	45817525	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.976000	0.49289	2.371000	0.80710	0.533000	0.62120	AAG		0.552	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367117.2	NM_018509		C	48462526	T	C	48462526	3	2	5	1	0	0	0	0	1	0	0	0	9044	1609	56	4	302	4	LRRC59	17	48462526	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	3023688	48462526	32732684	205	570										
MSI2	124540	hgsc.bcm.edu	37	chr17	55478755	55478755	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgcagatggtcacaagaacaAagaaaatatttgtaggcggg	12	5	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:55478755A>G	ENST00000284073.2	+	6	537	c.328A>G	c.(328-330)Aag>Gag	p.K110E	MSI2_ENST00000416426.2_Missense_Mutation_p.K88E|MSI2_ENST00000579180.1_Missense_Mutation_p.K6E|MSI2_ENST00000322684.3_Missense_Mutation_p.K106E|MSI2_ENST00000442934.2_Missense_Mutation_p.K49E	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	110	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		CACAAGAACAAAGAAAATATT	0.448			T	HOXA9	CML																																		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	0			17											110	106	107					17																	55478755		2203	4300	6503	52833754	SO:0001583	missense	124540			BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	18585	protein-coding gene	gene with protein product		607897	"musashi homolog 2 (Drosophila)"			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.328A>G	17.37:g.55478755A>G	ENSP00000284073:p.Lys110Glu		52833754	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.823027	0.90873	.	.	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000322684;ENST00000442934	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	5.5	5.5	0.81552	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.64402	D	0.000001	D	0.93785	0.8013	L	0.39898	1.24	0.54753	D	0.999988	D;D;D	0.58268	0.982;0.964;0.97	D;P;P	0.67548	0.952;0.889;0.777	D	0.94583	0.7781	10	0.87932	D	0	.	15.9002	0.79369	1.0:0.0:0.0:0.0	.	88;106;110	B4DHE8;Q96DH6-2;Q96DH6	.;.;MSI2H_HUMAN	E	88;110;106;49	ENSP00000414671:K88E;ENSP00000284073:K110E;ENSP00000313616:K106E;ENSP00000392607:K49E	ENSP00000284073:K110E	K	+	1	0	MSI2	52833754	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.867000	0.92314	2.219000	0.72066	0.533000	0.62120	AAG		0.448	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			G	55478755	A	G	55478755	3	3	5	1	0	0	0	0	1	0	0	0	9906	15	1	4	400	4	MSI2	17	55478755	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	7016229	55478755	25716455	206	571										
MAP3K3	4215	hgsc.bcm.edu	37	chr17	61771046	61771046	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccacatctctgaacatggccGggacttcctgaggcgcattt	10	13	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:61771046G>T	ENST00000361733.3	+	16	2110	c.1790G>T	c.(1789-1791)cGg>cTg	p.R597L	MAP3K3_ENST00000579585.1_Missense_Mutation_p.R628L|MAP3K3_ENST00000361357.3_Missense_Mutation_p.R628L|MAP3K3_ENST00000584573.1_Missense_Mutation_p.R624L|MAP3K3_ENST00000577395.1_Missense_Mutation_p.R593L	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)	p.R597Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						GAACATGGCCGGGACTTCCTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											107	96	100					17																	61771046		2203	4300	6503	59124778	SO:0001583	missense	4215			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6855	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 3", "MAPK/ERK kinase kinase 3"	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1790G>T	17.37:g.61771046G>T	ENSP00000354485:p.Arg597Leu		59124778	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Missense_Mutation	SNP	ENST00000361733.3	37	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220934	0.79464	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	T;T	0.64618	-0.11;-0.11	4.95	3.98	0.46160	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73265	0.3565	L	0.57536	1.79	0.80722	D	1	D;D;P;B	0.61697	0.99;0.979;0.621;0.386	D;P;P;B	0.65010	0.931;0.879;0.527;0.392	T	0.76088	-0.3087	10	0.87932	D	0	.	13.4432	0.61125	0.0765:0.0:0.9235:0.0	.	593;565;597;628	Q1PBM3;Q96HN9;Q99759;Q99759-2	.;.;M3K3_HUMAN;.	L	628;597	ENSP00000354927:R628L;ENSP00000354485:R597L	ENSP00000354927:R628L	R	+	2	0	MAP3K3	59124778	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	1.085000	0.41206	0.561000	0.74099	CGG		0.567	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401		T	61771046	G	T	61771046	3	4	5	1	0	0	0	0	1	0	0	0	9281	1116	39	2	1949	2	MAP3K3	17	61771046	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	6292291	61771046	19424164	207	572										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67079367	67079367	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acccacctaagccttccagaCaccatgatggccacacggtc	7	17	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:67079367C>A	ENST00000284425.2	-	35	4635	c.4461G>T	c.(4459-4461)gtG>gtT	p.V1487V	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1487	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GCCTTCCAGACACCATGATGG	0.532																																																0			17											100	84	90					17																	67079367		2203	4300	6503	64590962	SO:0001819	synonymous_variant	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.4461G>T	17.37:g.67079367C>A			64590962	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																				0.532	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67079367	C	A	67079367	2	1	5	1	0	0	0	0	0	0	0	1	36	465	17	2		2	ABCA6	17	67079367	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	5308321	67079367	14115843	208	573										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67153002	67153002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gggtctttattcattatttcAtttccatacttcatttccag	4	9	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:67153002A>T	ENST00000269081.4	-	29	4335	c.3426T>A	c.(3424-3426)aaT>aaA	p.N1142K	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1142					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TCATTATTTCATTTCCATACT	0.264																																																0			17											27	27	27					17																	67153002		2200	4294	6494	64664597	SO:0001583	missense	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3426T>A	17.37:g.67153002A>T	ENSP00000269081:p.Asn1142Lys		64664597	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	A	0.298	-0.975616	0.02215	.	.	ENSG00000154263	ENST00000269081	D	0.86366	-2.11	3.28	-5.12	0.02893	.	0.766269	0.10439	N	0.674483	T	0.44180	0.1281	N	0.00125	-2.05	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59434	-0.7455	10	0.02654	T	1	.	2.9049	0.05718	0.1618:0.4537:0.1056:0.2789	.	134;1142	B4DPV2;Q8WWZ4	.;ABCAA_HUMAN	K	1142	ENSP00000269081:N1142K	ENSP00000269081:N1142K	N	-	3	2	ABCA10	64664597	0.000000	0.05858	0.019000	0.16419	0.992000	0.81027	-2.458000	0.01000	-0.692000	0.05128	0.460000	0.39030	AAT		0.264	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67153002	A	T	67153002	3	4	5	1	0	0	0	0	1	0	0	0	29	214	8	5	1253	5	ABCA10	17	67153002	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	73635	67153002	14042208	209	574										
PRPSAP1	5635	hgsc.bcm.edu	37	chr17	74309925	74309925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gatgattgcgatgcggcctcCaacatctccaactacagtta	8	12	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:74309925C>T	ENST00000446526.3	-	8	1274	c.829G>A	c.(829-831)Gga>Aga	p.G277R	PRPSAP1_ENST00000588364.1_5'Flank|PRPSAP1_ENST00000324684.4_Missense_Mutation_p.G174R	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	248					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						ATGCGGCCTCCAACATCTCCA	0.458																																																0			17											208	159	176					17																	74309925		2203	4300	6503	71821520	SO:0001583	missense	5635			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.829G>A	17.37:g.74309925C>T	ENSP00000414624:p.Gly277Arg		71821520	B2R6M4|Q96H06	Missense_Mutation	SNP	ENST00000446526.3	37	CCDS11743.2	.	.	.	.	.	.	.	.	.	.	C	19.42	3.825063	0.71143	.	.	ENSG00000161542	ENST00000446526;ENST00000324684;ENST00000435555	T;T;T	0.73681	-0.77;-0.77;-0.77	5.81	5.81	0.92471	.	0.106285	0.64402	D	0.000004	T	0.72882	0.3516	N	0.25789	0.76	0.80722	D	1	P;B	0.51653	0.947;0.439	P;B	0.54270	0.747;0.249	T	0.69247	-0.5195	10	0.26408	T	0.33	.	15.5584	0.76219	0.0:0.8628:0.1372:0.0	.	248;277	Q14558;Q14558-2	KPRA_HUMAN;.	R	277;174;174	ENSP00000414624:G277R;ENSP00000314973:G174R;ENSP00000392838:G174R	ENSP00000314973:G174R	G	-	1	0	PRPSAP1	71821520	1.000000	0.71417	0.935000	0.37517	0.986000	0.74619	5.965000	0.70387	2.746000	0.94184	0.591000	0.81541	GGA		0.458	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766		T	74309925	C	T	74309925	3	4	5	1	0	0	0	0	1	0	0	0	12615	603	21	3	340	3	PRPSAP1	17	74309925	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	7156923	74309925	6885285	210	575										
RNF213	57674	hgsc.bcm.edu	37	chr17	78291028	78291028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aatccaattccccgcggagcAtggctggaaggagtcgttgc	13	11	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:78291028A>G	ENST00000582970.1	+	16	2995	c.2852A>G	c.(2851-2853)cAt>cGt	p.H951R	CTD-2047H16.2_ENST00000576808.1_RNA|RNF213_ENST00000319921.4_Missense_Mutation_p.H951R|RNF213_ENST00000456466.1_Missense_Mutation_p.H951R|RNF213_ENST00000508628.2_Missense_Mutation_p.H1000R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	951					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCCGCGGAGCATGGCTGGAAG	0.572																																																0			17											88	82	84					17																	78291028		2203	4298	6501	75905623	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2852A>G	17.37:g.78291028A>G	ENSP00000464087:p.His951Arg		75905623	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	a	6.305	0.424450	0.11928	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.13538	2.58;2.58	3.71	-0.144	0.13440	.	1.326120	0.05384	N	0.537744	T	0.18676	0.0448	L	0.43152	1.355	0.09310	N	1	D;D	0.64830	0.962;0.994	P;P	0.54026	0.605;0.74	T	0.17776	-1.0358	10	0.38643	T	0.18	-7.7398	3.9507	0.09368	0.4237:0.1961:0.0:0.3802	.	951;951	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	R	951;1000;951;951	ENSP00000392123:H951R;ENSP00000324392:H951R	ENSP00000324392:H951R	H	+	2	0	RNF213	75905623	0.000000	0.05858	0.000000	0.03702	0.725000	0.41563	-0.165000	0.09968	-0.056000	0.13221	0.525000	0.51046	CAT		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78291028	A	G	78291028	3	3	5	1	0	0	0	0	1	0	0	0	13514	217	8	4	3061	4	RNF213	17	78291028	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	3981103	78291028	2904182	211	576										
DSC2	1824	hgsc.bcm.edu	37	chr18	28666673	28666673	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	catcgtgtcaggctcatcttTgtcagtagcacacacttgtc	8	12	4	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:28666673T>C	ENST00000280904.6	-	7	1251	c.808A>G	c.(808-810)Aaa>Gaa	p.K270E	DSC2_ENST00000251081.6_Missense_Mutation_p.K270E	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	270	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K270*(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			GGCTCATCTTTGTCAGTAGCA	0.453																																																1	Substitution - Nonsense(1)	ovary(1)	18											231	185	200					18																	28666673		2203	4300	6503	26920671	SO:0001583	missense	1825			X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.808A>G	18.37:g.28666673T>C	ENSP00000280904:p.Lys270Glu		26920671		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672223	0.29693	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.61040	0.14;0.14	5.61	1.79	0.24919	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.50017	0.1591	L	0.38692	1.165	0.09310	N	0.999999	P;P	0.41848	0.763;0.721	P;B	0.46208	0.507;0.373	T	0.34527	-0.9825	9	0.41790	T	0.15	.	6.549	0.22423	0.0:0.0989:0.2884:0.6127	.	270;270	Q02487;Q02487-2	DSC2_HUMAN;.	E	270;270;36;283	ENSP00000251081:K270E;ENSP00000280904:K270E	ENSP00000251081:K270E	K	-	1	0	DSC2	26920671	0.857000	0.29778	0.871000	0.34182	0.275000	0.26752	1.198000	0.32223	0.370000	0.24538	0.533000	0.62120	AAA		0.453	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28666673	T	C	28666673	3	2	5	1	0	0	0	0	1	0	0	0	4777	1821	63	4	1977	4	DSC2	18	28666673	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10		28666673	49410575	212	577										
DSG2	1829	hgsc.bcm.edu	37	chr18	29111211	29111211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	acactggactaccagcccatGcaaggtaagagagagtgaca	11	10	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:29111211G>A	ENST00000261590.8	+	9	1485	c.1276G>A	c.(1276-1278)Gca>Aca	p.A426T		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	426	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			ACCAGCCCATGCAAGGTAAGA	0.348																																																0			18											102	92	95					18																	29111211		1859	4095	5954	27365209	SO:0001583	missense	1829			Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1276G>A	18.37:g.29111211G>A	ENSP00000261590:p.Ala426Thr		27365209	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651336	0.47362	.	.	ENSG00000046604	ENST00000261590	T	0.54279	0.58	5.02	5.02	0.67125	Cadherin (4);Cadherin-like (1);	0.374516	0.22696	N	0.056741	T	0.30885	0.0779	N	0.03608	-0.345	0.58432	D	0.999999	P	0.39717	0.684	B	0.38378	0.272	T	0.38650	-0.9651	10	0.87932	D	0	.	12.3349	0.55060	0.0879:0.0:0.9121:0.0	.	426	Q14126	DSG2_HUMAN	T	426	ENSP00000261590:A426T	ENSP00000261590:A426T	A	+	1	0	DSG2	27365209	0.411000	0.25384	0.283000	0.24790	0.009000	0.06853	3.061000	0.49963	2.606000	0.88127	0.491000	0.48974	GCA		0.348	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		A	29111211	G	A	29111211	3	1	5	1	0	0	0	0	1	0	0	0	4788	1319	46	3	1310	3	DSG2	18	29111211	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	444538	29111211	48966037	213	578										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48603020	48603020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cttaaaaggtctttgatttgCgtcagtgtcatcgacagatg	10	7	3	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:48603020C>T	ENST00000342988.3	+	11	1859	c.1321C>T	c.(1321-1323)Cgt>Tgt	p.R441C	SMAD4_ENST00000588745.1_Missense_Mutation_p.R345C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R441C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	441	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.R441fs*16(1)|p.R441C(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CTTTGATTTGCGTCAGTGTCA	0.448																																																40	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)|Deletion - Frameshift(1)	pancreas(27)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											41	42	41					18																	48603020		2203	4300	6503	46857018	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1321C>T	18.37:g.48603020C>T	ENSP00000341551:p.Arg441Cys		46857018	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247024	0.80024	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.97430	-4.38;-4.38	6.03	6.03	0.97812	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98544	0.9514	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.64237	0.923	D	0.99143	1.0856	10	0.87932	D	0	.	19.3283	0.94273	0.0:1.0:0.0:0.0	.	441	Q13485	SMAD4_HUMAN	C	441	ENSP00000341551:R441C;ENSP00000381452:R441C	ENSP00000341551:R441C	R	+	1	0	SMAD4	46857018	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.556000	0.60775	2.861000	0.98227	0.655000	0.94253	CGT		0.448	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48603020	C	T	48603020	3	4	5	1	0	0	0	0	1	0	0	0	14797	768	27	1	1359	1	SMAD4	18	48603020	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	19491809	48603020	29474228	214	579										
SERPINB8	5271	hgsc.bcm.edu	37	chr18	61645698	61645698	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcaaagggaagcactgcagcCcagatgtcccaggtatgtgt	13	10	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:61645698C>T	ENST00000397985.2	+	2	412	c.156C>T	c.(154-156)gcC>gcT	p.A52A	SERPINB8_ENST00000397988.3_Silent_p.A52A|SERPINB8_ENST00000542677.1_Intron|HMSD_ENST00000481726.1_3'UTR|SERPINB8_ENST00000353706.2_Silent_p.A52A	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	52					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				GCACTGCAGCCCAGATGTCCC	0.507																																																0			18											92	82	85					18																	61645698		2203	4300	6503	59796678	SO:0001819	synonymous_variant	5271			L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.156C>T	18.37:g.61645698C>T			59796678	B4DTW2|Q7Z2V6|Q8N178	Silent	SNP	ENST00000397985.2	37	CCDS11991.1																																																																																				0.507	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848		T	61645698	C	T	61645698	2	4	5	1	0	0	0	0	0	0	0	1	14144	610	22	3		3	SERPINB8	18	61645698	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	13042678	61645698	16431550	215	580										
STK11	6794	hgsc.bcm.edu	37	chr19	1223020	1223020	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	catcctccggctgaagcaccAgtgcccatcccaccgagccc	8	20	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:1223020A>G	ENST00000326873.7	+	8	2130	c.957A>G	c.(955-957)ccA>ccG	p.P319P		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	319					activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.V320fs*16(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAAGCACCAGTGCCCATCC	0.652		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																												yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	21	Whole gene deletion(20)|Complex - frameshift(1)	cervix(15)|lung(2)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19	GRCh37	CX012582	STK11	X							34	41	39					19																	1223020		2095	4216	6311	1174020	SO:0001819	synonymous_variant	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.957A>G	19.37:g.1223020A>G			1174020	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																				0.652	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		G	1223020	A	G	1223020	2	3	5	1	0	0	0	0	0	0	0	1	15326	175	7	4		4	STK11	19	1223020	Silent	SNP	A	TCGA-AF-2693-01A-02D-1733-10		1223020	57905963	216	581										
KLHL26	55295	hgsc.bcm.edu	37	chr19	18779181	18779181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctacaccgacagcgaccgctCggtcagcagcaaggtctacc	10	16	2	0	rs148560244	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:18779181C>T	ENST00000300976.4	+	3	1064	c.974C>T	c.(973-975)tCg>tTg	p.S325L	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	325										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						AGCGACCGCTCGGTCAGCAGC	0.692													C|||	3	0.000599042	0.0023	0	5008	,	,		12999	0		0	False		,,,				2504	0															0			19						C	LEU/SER	4,4392		0,4,2194	16	16	16		974	4	0	19	dbSNP_134	16	0,8568		0,0,4284	no	missense	KLHL26	NM_018316.1	145	0,4,6478	TT,TC,CC		0.0,0.091,0.0309	benign	325/616	18779181	4,12960	2198	4284	6482	18640181	SO:0001583	missense	55295				CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"Kelch-like", "BTB/POZ domain containing"	25623	protein-coding gene	gene with protein product			"kelch-like 26 (Drosophila)"				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.974C>T	19.37:g.18779181C>T	ENSP00000300976:p.Ser325Leu		18640181	Q8TAP0|Q9NUX3	Missense_Mutation	SNP	ENST00000300976.4	37	CCDS12384.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.362170	0.24684	9.1E-4	0.0	ENSG00000167487	ENST00000300976	T	0.75821	-0.97	5.04	3.98	0.46160	Galactose oxidase, beta-propeller (1);	0.401657	0.26467	N	0.024220	T	0.55337	0.1914	N	0.12887	0.27	0.20563	N	0.99989	B	0.24576	0.106	B	0.17433	0.018	T	0.34625	-0.9821	9	.	.	.	.	14.3318	0.66561	0.0:0.8504:0.1496:0.0	.	325	Q53HC5	KLH26_HUMAN	L	325	ENSP00000300976:S325L	.	S	+	2	0	KLHL26	18640181	0.670000	0.27512	0.007000	0.13788	0.737000	0.42083	3.715000	0.54897	1.078000	0.41014	0.591000	0.81541	TCG		0.692	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		T	18779181	C	T	18779181	3	4	5	1	0	0	0	0	1	0	0	0	8402	893	31	1	984	1	KLHL26	19	18779181	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	17556161	18779181	40349802	217	582										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33450807	33450807	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcggcgatctggtacctaccGaggcctcagctgtgaggtgg	16	11	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:33450807G>A	ENST00000305768.5	-	3	392	c.304C>T	c.(304-306)Cgg>Tgg	p.R102W	CEP89_ENST00000590597.2_Splice_Site_p.R102W	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	102					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGTACCTACCGAGGCCTCAGC	0.587																																																0			19											98	79	85					19																	33450807		2203	4300	6503	38142647	SO:0001630	splice_region_variant	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.305+1C>T	19.37:g.33450807G>A			38142647	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.589173	0.28357	.	.	ENSG00000121289	ENST00000305768	T	0.33216	1.42	5.48	3.25	0.37280	.	0.317619	0.28382	N	0.015556	T	0.28200	0.0696	L	0.46157	1.445	0.34322	D	0.686742	B;B	0.22414	0.01;0.069	B;B	0.16289	0.007;0.015	T	0.43097	-0.9412	10	0.62326	D	0.03	-1.7133	14.057	0.64776	0.0:0.5783:0.4217:0.0	.	102;102	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	W	102	ENSP00000306105:R102W	ENSP00000306105:R102W	R	-	1	2	CEP89	38142647	0.935000	0.31712	0.697000	0.30258	0.024000	0.10985	1.735000	0.38176	1.276000	0.44395	0.655000	0.94253	CGG		0.587	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	Missense_Mutation	A	33450807	G	A	33450807	5	1	5	1	0	0	0	0	0	0	1	0	2765	1072	37	1	2115	1	CCDC123	19	33450807	Splice_Site	SNP	G	TCGA-AF-2693-01A-02D-1733-10	14671626	33450807	25678176	218	583										
SPINT2	10653	hgsc.bcm.edu	37	chr19	38780921	38780921	+	Splice_Site	DEL	G	G	-													0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctgcatgctccgctgcttccGtaagtctgcagcccctcagc							TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:38780921delG	ENST00000301244.7	+	5	988		c.e5+1		SPINT2_ENST00000454580.3_Splice_Site|SPINT2_ENST00000587090.1_Splice_Site|CTB-102L5.4_ENST00000591889.1_Splice_Site	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2						cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGCTGCTTCCGTAAGTCTGCA	0.572																																																0			19											34	36	35					19																	38780921		2203	4300	6503	43472761	SO:0001630	splice_region_variant	10653			U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"placental bikunin"	605124	"serine protease inhibitor, Kunitz type, 2"			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.553+1G>-	19.37:g.38780921delG			43472761	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Frame_Shift_Del	DEL	ENST00000301244.7	37	CCDS12510.1																																																																																				0.572	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2		Intron	-	38780921	G	-	38780921	8	5	5	1	0	1	0	1	0	0	1	0	15108	1159	40	0	572	0	SPINT2	19	38780921	Splice_Site	DEL	G	TCGA-AF-2693-01A-02D-1733-10	5330114	38780921	20348062	219	584										
RYR1	6261	hgsc.bcm.edu	37	chr19	38968461	38968461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcttcgacctcagcaaggtcCgggtcgtgacggtgaccatg	14	12	1	2	rs200546266		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:38968461C>T	ENST00000359596.3	+	30	4405	c.4405C>T	c.(4405-4407)Cgg>Tgg	p.R1469W	RYR1_ENST00000355481.4_Missense_Mutation_p.R1469W|RYR1_ENST00000360985.3_Missense_Mutation_p.R1469W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1469	6 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAGCAAGGTCCGGGTCGTGAC	0.667													C|||	1	0.000199681	0	0	5008	,	,		14060	0		0.001	False		,,,				2504	0															0			19						C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	63	50	55		4405,4405	3.3	1	19		55	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1469/5039,1469/5034	38968461	1,13005	2203	4300	6503	43660301	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4405C>T	19.37:g.38968461C>T	ENSP00000352608:p.Arg1469Trp		43660301	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.64	2.894071	0.52121	0.0	1.16E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.71103	-0.54;-0.54;-0.54	5.41	3.26	0.37387	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	U	0.000018	T	0.82130	0.4970	M	0.84326	2.69	0.47584	D	0.999464	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.82552	-0.0400	10	0.72032	D	0.01	.	7.7965	0.29150	0.143:0.7251:0.0:0.1319	.	1469;1469	P21817-2;P21817	.;RYR1_HUMAN	W	1469	ENSP00000352608:R1469W;ENSP00000347667:R1469W;ENSP00000354254:R1469W	ENSP00000347667:R1469W	R	+	1	2	RYR1	43660301	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.478000	0.45189	1.271000	0.44313	0.313000	0.20887	CGG		0.667	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38968461	C	T	38968461	3	4	5	1	0	0	0	0	1	0	0	0	13805	643	23	1	4523	1	RYR1	19	38968461	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	187540	38968461	20160522	220	585										
GSK3A	2931	hgsc.bcm.edu	37	chr19	42735003	42735003	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gactgccagtctgagctggtCggagtctcagttaaagctgg	14	9	2	1	rs372575967	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:42735003C>T	ENST00000222330.3	-	11	1522	c.1395G>A	c.(1393-1395)ccG>ccA	p.P465P	GSK3A_ENST00000398249.4_Silent_p.P383P	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	465					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CTGAGCTGGTCGGAGTCTCAG	0.567													C|||	23	0.00459265	0	0	5008	,	,		14554	0		0	False		,,,				2504	0.0235															0			19											84	68	74					19																	42735003		2198	4288	6486	47426843	SO:0001819	synonymous_variant	2931				CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.1395G>A	19.37:g.42735003C>T			47426843	O14959	Silent	SNP	ENST00000222330.3	37	CCDS12599.1																																																																																				0.567	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1			T	42735003	C	T	42735003	2	4	5	1	0	0	0	0	0	0	0	1	6844	871	31	1		1	GSK3A	19	42735003	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	3766542	42735003	16393980	221	586										
LIPE	3991	hgsc.bcm.edu	37	chr19	42930864	42930864	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcttcttgttgagctggaggTggctctcctggcccaggccc	14	13	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:42930864T>C	ENST00000244289.4	-	1	714	c.438A>G	c.(436-438)ccA>ccG	p.P146P	LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000594688.1_RNA|CTB-50E14.4_ENST00000596781.1_RNA|LIPE-AS1_ENST00000457234.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	146			P -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|P -> S (in dbSNP:rs34348028). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GAGCTGGAGGTGGCTCTCCTG	0.562																																																0			19											87	87	87					19																	42930864		2203	4300	6503	47622704	SO:0001819	synonymous_variant	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.438A>G	19.37:g.42930864T>C			47622704	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																				0.562	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		C	42930864	T	C	42930864	2	2	5	1	0	0	0	0	0	0	0	1	8845	1683	59	4		4	LIPE	19	42930864	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	195861	42930864	16198119	222	587										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48558305	48558305	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agtcagtggtagcccggatgGtctgagaaggaggcaataag	16	6	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:48558305G>T	ENST00000599921.1	-	15	1616	c.1259C>A	c.(1258-1260)aCc>aAc	p.T420N	PLA2G4C_ENST00000599111.1_Splice_Site_p.T430N|PLA2G4C_ENST00000354276.3_Splice_Site_p.T420N|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000413144.2_Splice_Site_p.T420N			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	420	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		AGCCCGGATGGTCTGAGAAGG	0.587																																																0			19											60	60	60					19																	48558305		2203	4300	6503	53250117	SO:0001630	splice_region_variant	8605			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1258-1C>A	19.37:g.48558305G>T			53250117	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658437	0.67586	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.12361	2.69;2.69	3.19	3.19	0.36642	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.084168	0.46145	U	0.000317	T	0.30792	0.0776	M	0.65498	2.005	0.34102	D	0.661925	D;D	0.89917	0.999;1.0	D;D	0.87578	0.993;0.998	T	0.39901	-0.9591	10	0.35671	T	0.21	-17.8502	10.1982	0.43067	0.0:0.0:1.0:0.0	.	430;420	B4DI40;Q9UP65	.;PA24C_HUMAN	N	420	ENSP00000346228:T420N;ENSP00000400036:T420N	ENSP00000346228:T420N	T	-	2	0	PLA2G4C	53250117	1.000000	0.71417	0.813000	0.32504	0.488000	0.33401	2.704000	0.47118	1.481000	0.48307	0.411000	0.27672	ACC		0.587	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		Missense_Mutation	T	48558305	G	T	48558305	5	4	5	1	0	0	0	0	0	0	1	0	12034	1275	44	2	382	2	PLA2G4C	19	48558305	Splice_Site	SNP	G	TCGA-AF-2693-01A-02D-1733-10	5627441	48558305	10570678	223	588										
KLK10	5655	hgsc.bcm.edu	37	chr19	51518084	51518084	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agcgtatgactttattgatcCaggacatgtatttgcagatc	9	7	0	3	rs78258028	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:51518084C>T	ENST00000309958.3	-	6	1021	c.803G>A	c.(802-804)tGg>tAg	p.W268*	KLK10_ENST00000391805.1_Nonsense_Mutation_p.W268*|KLK10_ENST00000358789.3_Nonsense_Mutation_p.W268*|CTB-147C22.9_ENST00000594512.1_RNA|CTC-518B2.12_ENST00000596286.1_RNA	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	268	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TTTATTGATCCAGGACATGTA	0.537													C|||	6	0.00119808	0	0	5008	,	,		20674	0.005		0	False		,,,				2504	0.001															0			19											146	133	138					19																	51518084		2203	4300	6503	56209896	SO:0001587	stop_gained	5655			AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.803G>A	19.37:g.51518084C>T	ENSP00000311746:p.Trp268*		56209896	A6NC12|Q53YL3|Q99920|Q9GZW9	Nonsense_Mutation	SNP	ENST00000309958.3	37	CCDS12817.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	c	20.2	3.954908	0.73902	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.52099	D	0.99994	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4099	0.74911	0.0:1.0:0.0:0.0	.	.	.	.	X	268	.	ENSP00000311746:W268X	W	-	2	0	KLK10	56209896	1.000000	0.71417	0.942000	0.38095	0.047000	0.14425	7.187000	0.77730	2.318000	0.78349	0.313000	0.20887	TGG		0.537	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		T	51518084	C	T	51518084	4	4	5	1	0	0	0	0	0	1	0	0	8419	595	21	3	31	3	KLK10	19	51518084	Nonsense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	2959779	51518084	7610899	224	589										
IGLON5	402665	hgsc.bcm.edu	37	chr19	51827033	51827033	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cggctgctcatcaacaccccCgaggagttctccatcctcat	7	17	4	0	rs200499741	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:51827033C>T	ENST00000270642.8	+	3	276	c.276C>T	c.(274-276)ccC>ccT	p.P92P		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	92	Ig-like C2-type 1.					extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						TCAACACCCCCGAGGAGTTCT	0.657													C|||	16	0.00319489	0	0.0014	5008	,	,		15965	0		0	False		,,,				2504	0.0153															0			19											34	41	39					19																	51827033		1975	4147	6122	56518845	SO:0001819	synonymous_variant	402665				CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.276C>T	19.37:g.51827033C>T			56518845		Silent	SNP	ENST00000270642.8	37	CCDS46158.1																																																																																				0.657	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372		T	51827033	C	T	51827033	2	4	5	1	0	0	0	0	0	0	0	1	7616	639	23	1		1	IGLON5	19	51827033	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	308949	51827033	7301950	225	590										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54314533	54314533	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggacatagtccctgtaggttTcctggggatctaggggagag	16	7	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:54314533T>C	ENST00000324134.6	-	3	548	c.380A>G	c.(379-381)gAa>gGa	p.E127G	NLRP12_ENST00000535162.1_Missense_Mutation_p.E127G|NLRP12_ENST00000345770.5_Missense_Mutation_p.E127G|NLRP12_ENST00000354278.3_Missense_Mutation_p.E127G|NLRP12_ENST00000391772.1_Missense_Mutation_p.E127G|NLRP12_ENST00000351894.4_Missense_Mutation_p.E127G|NLRP12_ENST00000391773.1_Missense_Mutation_p.E127G|NLRP12_ENST00000391775.3_Missense_Mutation_p.E127G	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	127					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CCTGTAGGTTTCCTGGGGATC	0.542																																																0			19											73	72	72					19																	54314533		2202	4295	6497	59006345	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.380A>G	19.37:g.54314533T>C	ENSP00000319377:p.Glu127Gly		59006345	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.551798	0.27739	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.75154	-0.84;-0.87;-0.9;-0.91;-0.89;-0.84;-0.88	4.47	2.31	0.28768	.	0.703660	0.12215	N	0.488905	T	0.64951	0.2645	L	0.57536	1.79	0.09310	N	1	B;P;P;P	0.40144	0.255;0.651;0.651;0.704	B;B;B;B	0.35859	0.104;0.15;0.212;0.197	T	0.55289	-0.8164	10	0.48119	T	0.1	.	4.8331	0.13451	0.3279:0.0:0.1697:0.5023	.	127;127;127;127	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	G	127	ENSP00000319377:E127G;ENSP00000438030:E127G;ENSP00000340473:E127G;ENSP00000346231:E127G;ENSP00000375655:E127G;ENSP00000375653:E127G;ENSP00000375652:E127G	ENSP00000319377:E127G	E	-	2	0	NLRP12	59006345	0.003000	0.15002	0.001000	0.08648	0.228000	0.25075	1.300000	0.33436	0.197000	0.20387	0.254000	0.18369	GAA		0.542	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		C	54314533	T	C	54314533	3	2	5	1	0	0	0	0	1	0	0	0	10505	1783	62	4	2933	4	NLRP12	19	54314533	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	2487500	54314533	4814450	226	591										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56443518	56443518	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caagtttgcccaggggatacGcgggaagtgcccctgggggg	18	10	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:56443518G>A	ENST00000342929.3	-	1	159	c.160C>T	c.(160-162)Cgt>Tgt	p.R54C	NLRP13_ENST00000588751.1_Missense_Mutation_p.R54C	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	54	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CAGGGGATACGCGGGAAGTGC	0.557																																																0			19											57	60	59					19																	56443518		2203	4300	6503	61135330	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.160C>T	19.37:g.56443518G>A	ENSP00000343891:p.Arg54Cys		61135330	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	G	1.292	-0.607384	0.03717	.	.	ENSG00000173572	ENST00000342929	T	0.53206	0.63	1.97	-3.94	0.04130	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.28134	0.0694	L	0.32530	0.975	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.12066	-1.0562	9	0.56958	D	0.05	.	0.3437	0.00338	0.3405:0.1354:0.1752:0.3489	.	54	Q86W25	NAL13_HUMAN	C	54	ENSP00000343891:R54C	ENSP00000343891:R54C	R	-	1	0	NLRP13	61135330	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.167000	0.03126	-2.817000	0.00345	-2.097000	0.00363	CGT		0.557	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		A	56443518	G	A	56443518	3	1	5	1	0	0	0	0	1	0	0	0	10506	1087	38	1	3013	1	NLRP13	19	56443518	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	2128985	56443518	2685465	227	592										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56466193	56466193	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	agacgacagaccagagcttcTccgagctgattgagcaaaag	11	10	1	5			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:56466193T>A	ENST00000291971.3	+	3	840	c.769T>A	c.(769-771)Tcc>Acc	p.S257T	NLRP8_ENST00000590542.1_Missense_Mutation_p.S257T	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	257	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCAGAGCTTCTCCGAGCTGAT	0.512																																																0			19											154	151	152					19																	56466193		2203	4300	6503	61158005	SO:0001583	missense	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.769T>A	19.37:g.56466193T>A	ENSP00000291971:p.Ser257Thr		61158005	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.024878	0.35701	.	.	ENSG00000179709	ENST00000291971	T	0.23552	1.9	2.04	0.977	0.19733	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.17916	0.0430	N	0.16368	0.405	0.09310	N	1	D;B	0.53312	0.959;0.242	P;B	0.48552	0.581;0.166	T	0.10847	-1.0612	9	0.44086	T	0.13	.	5.0815	0.14659	0.0:0.0:0.3094:0.6906	.	257;257	Q86W28-2;Q86W28	.;NALP8_HUMAN	T	257	ENSP00000291971:S257T	ENSP00000291971:S257T	S	+	1	0	NLRP8	61158005	0.000000	0.05858	0.003000	0.11579	0.028000	0.11728	0.109000	0.15417	0.219000	0.20840	0.421000	0.28195	TCC		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56466193	T	A	56466193	3	1	5	1	0	0	0	0	1	0	0	0	10514	1551	54	5	779	5	NLRP8	19	56466193	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	22675	56466193	2662790	228	593										
AURKC	6795	hgsc.bcm.edu	37	chr19	57744834	57744834	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctttgcacccacagataataGaggagttggcagatgccctg	11	10	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:57744834G>T	ENST00000302804.7	+	5	628	c.442G>T	c.(442-444)Gag>Tag	p.E148*	AURKC_ENST00000599062.1_Nonsense_Mutation_p.E145*|AURKC_ENST00000598785.1_Nonsense_Mutation_p.E114*|AURKC_ENST00000448930.1_Nonsense_Mutation_p.E114*|AURKC_ENST00000415300.2_Nonsense_Mutation_p.E129*	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> Q (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.E114*(1)|p.E148*(1)|p.E114Q(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		ACAGATAATAGAGGAGTTGGC	0.478																																																3	Substitution - Nonsense(2)|Substitution - Missense(1)	lung(3)	19											98	96	97					19																	57744834		2203	4300	6503	62436646	SO:0001587	stop_gained	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.442G>T	19.37:g.57744834G>T	ENSP00000302898:p.Glu148*		62436646	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Nonsense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	G	36	5.829037	0.96996	.	.	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	.	.	.	3.67	2.61	0.31194	.	0.050269	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-32.584	11.5835	0.50904	0.0:0.1816:0.8184:0.0	.	.	.	.	X	129;114;148	.	ENSP00000302898:E148X	E	+	1	0	AURKC	62436646	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.741000	0.47426	1.107000	0.41642	0.462000	0.41574	GAG		0.478	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		T	57744834	G	T	57744834	4	4	5	1	0	0	0	0	0	1	0	0	1225	943	33	2	465	2	AURKC	19	57744834	Nonsense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10	1278641	57744834	1384149	229	594										
PSMF1	9491	hgsc.bcm.edu	37	chr20	1115856	1115856	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggaaaaggctaatgtaagcaGtccccaccgggagttccccc	11	13	0	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:1115856G>T	ENST00000335877.6	+	4	634	c.458G>T	c.(457-459)aGt>aTt	p.S153I	PSMF1_ENST00000484891.1_3'UTR|PSMF1_ENST00000333082.3_Missense_Mutation_p.S153I|PSMF1_ENST00000381898.4_Missense_Mutation_p.S65I|PSMF1_ENST00000438768.2_Intron|PSMF1_ENST00000246015.4_Missense_Mutation_p.S153I	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	153					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						AATGTAAGCAGTCCCCACCGG	0.572																																																0			20											116	102	107					20																	1115856		2203	4300	6503	1063856	SO:0001583	missense	9491			D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"Proteasome (prosome, macropain) subunits"	9571	protein-coding gene	gene with protein product	"proteasome inhibitor hP131 subunit"					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.458G>T	20.37:g.1115856G>T	ENSP00000338039:p.Ser153Ile		1063856	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	37	CCDS13010.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.610|6.610	0.481018|0.481018	0.12581|0.12581	.|.	.|.	ENSG00000125818|ENSG00000125818	ENST00000435720|ENST00000333082;ENST00000381898;ENST00000381899;ENST00000454500;ENST00000246015;ENST00000335877	.|T;T;T;T;T	.|0.47177	.|1.34;0.85;1.38;1.33;1.34	5.22|5.22	2.09|2.09	0.27110|0.27110	.|.	.|0.522992	.|0.21889	.|N	.|0.067607	T|T	0.36110|0.36110	0.0955|0.0955	L|L	0.47716|0.47716	1.5|1.5	0.33144|0.33144	D|D	0.544744|0.544744	.|P;B;B;B	.|0.37636	.|0.603;0.119;0.201;0.257	.|B;B;B;B	.|0.37304	.|0.246;0.055;0.03;0.075	T|T	0.48127|0.48127	-0.9062|-0.9062	5|10	.|0.52906	.|T	.|0.07	0.1591|0.1591	5.0394|5.0394	0.14451|0.14451	0.2412:0.1597:0.5991:0.0|0.2412:0.1597:0.5991:0.0	.|.	.|65;65;153;153	.|F5H4Z3;B4DUJ0;Q5QPM7;Q92530	.|.;.;.;PSMF1_HUMAN	H|I	12|153;65;153;65;153;153	.|ENSP00000327704:S153I;ENSP00000371323:S65I;ENSP00000371324:S153I;ENSP00000246015:S153I;ENSP00000338039:S153I	.|ENSP00000246015:S153I	Q|S	+|+	3|2	2|0	PSMF1|PSMF1	1063856|1063856	0.995000|0.995000	0.38212|0.38212	0.969000|0.969000	0.41365|0.41365	0.032000|0.032000	0.12392|0.12392	2.256000|2.256000	0.43231|0.43231	0.750000|0.750000	0.32877|0.32877	-0.157000|-0.157000	0.13467|0.13467	CAG|AGT		0.572	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578		T	1115856	G	T	1115856	3	4	5	1	0	0	0	0	1	0	0	0	12744	1029	36	2	472	2	PSMF1	20	1115856	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		1115856	61909664	230	595										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13867033	13867033	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctcagattttcaggtctttcCgttagtctcactttttccac	5	12	4	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:13867033C>A	ENST00000284951.5	-	9	875	c.801G>T	c.(799-801)acG>acT	p.T267T	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Silent_p.T267T			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	267						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CAGGTCTTTCCGTTAGTCTCA	0.373																																																0			20											133	122	125					20																	13867033		1837	4094	5931	13815033	SO:0001819	synonymous_variant	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.801G>T	20.37:g.13867033C>A			13815033	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																					0.373	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13867033	C	A	13867033	2	1	5	1	0	0	0	0	0	0	0	1	14048	639	23	2		2	SEL1L2	20	13867033	Silent	SNP	C	TCGA-AF-2693-01A-02D-1733-10	12751177	13867033	49158487	231	596										
CTNNBL1	56259	hgsc.bcm.edu	37	chr20	36470761	36470761	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gttgacagactaatggagttGcattttaaatatctgggtgc	11	5	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:36470761G>A	ENST00000361383.6	+	13	1449	c.1332G>A	c.(1330-1332)ttG>ttA	p.L444L	CTNNBL1_ENST00000373469.1_Silent_p.L192L|CTNNBL1_ENST00000473857.1_3'UTR|CTNNBL1_ENST00000405275.2_Silent_p.L417L|CTNNBL1_ENST00000373473.1_Silent_p.L257L	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	444					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TAATGGAGTTGCATTTTAAAT	0.453																																					Ovarian(184;582 2038 3273 4106 42608)											0			20											161	128	139					20																	36470761		2203	4300	6503	35904175	SO:0001819	synonymous_variant	56259			AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"nuclear associated protein"	611537	"chromosome 20 open reading frame 33"	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.1332G>A	20.37:g.36470761G>A			35904175	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Silent	SNP	ENST00000361383.6	37	CCDS13298.1																																																																																				0.453	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877		A	36470761	G	A	36470761	2	1	5	1	0	0	0	0	0	0	0	1	4024	1310	46	3		3	CTNNBL1	20	36470761	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	22603728	36470761	26554759	232	597										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52192707	52192707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtgggctgagaaggagctaCtggaagaggtttcaattttg	16	4	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:52192707C>T	ENST00000371471.2	-	4	3021	c.2596G>A	c.(2596-2598)Gta>Ata	p.V866I	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.V866I			O75362	ZN217_HUMAN	zinc finger protein 217	866					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GAAGGAGCTACTGGAAGAGGT	0.532																																																0			20											88	84	85					20																	52192707		2203	4300	6503	51626114	SO:0001583	missense	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2596G>A	20.37:g.52192707C>T	ENSP00000360526:p.Val866Ile		51626114	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	C	6.156	0.397054	0.11638	.	.	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.07567	3.18;3.18	5.0	3.83	0.44106	.	1.781150	0.03171	N	0.170766	T	0.06416	0.0165	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.25222	-1.0138	10	0.11485	T	0.65	0.3058	10.1998	0.43075	0.0:0.8466:0.0:0.1534	.	866	O75362	ZN217_HUMAN	I	866;866;26	ENSP00000360526:V866I;ENSP00000304308:V866I	ENSP00000304308:V866I	V	-	1	0	ZNF217	51626114	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.035000	0.12205	2.304000	0.77564	0.650000	0.86243	GTA		0.532	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52192707	C	T	52192707	3	4	5	1	0	0	0	0	1	0	0	0	17811	565	20	3	558	3	ZNF217	20	52192707	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	15721946	52192707	10832813	233	598										
APP	351	hgsc.bcm.edu	37	chr21	27484438	27484438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caatctggggttcagccagcAggccagcattaccatcagtg	11	12	3	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:27484438A>G	ENST00000346798.3	-	2	116	c.83T>C	c.(82-84)cTg>cCg	p.L28P	APP_ENST00000348990.5_Missense_Mutation_p.L28P|APP_ENST00000358918.3_Missense_Mutation_p.L28P|APP_ENST00000354192.3_Intron|APP_ENST00000359726.3_Missense_Mutation_p.L28P|APP_ENST00000357903.3_Missense_Mutation_p.L28P|APP_ENST00000474136.1_5'UTR|APP_ENST00000448388.2_5'UTR|APP_ENST00000440126.3_Missense_Mutation_p.L23P|APP_ENST00000439274.2_Intron	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	28					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TTCAGCCAGCAGGCCAGCATT	0.488																																																0			21											119	106	111					21																	27484438		2203	4300	6503	26406309	SO:0001583	missense	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.83T>C	21.37:g.27484438A>G	ENSP00000284981:p.Leu28Pro		26406309	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.318766	0.81469	.	.	ENSG00000142192	ENST00000346798;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000440126	D;D;D;D;D;D	0.96427	-2.05;-4.01;-2.07;-1.91;-4.01;-2.09	5.44	5.44	0.79542	Amyloidogenic glycoprotein, heparin-binding (1);Amyloidogenic glycoprotein, extracellular (1);	0.000000	0.64402	D	0.000001	D	0.97476	0.9174	M	0.61703	1.905	0.80722	D	1	D;B;D;D;D	0.89917	1.0;0.111;0.999;0.996;0.998	D;B;D;D;D	0.91635	0.999;0.086;0.985;0.968;0.988	D	0.97603	1.0124	10	0.46703	T	0.11	-15.0248	15.1534	0.72720	1.0:0.0:0.0:0.0	.	28;23;28;28;28	P05067-2;B4DII8;P05067-4;P05067-8;P05067	.;.;.;.;A4_HUMAN	P	28;28;28;28;28;23	ENSP00000284981:L28P;ENSP00000345463:L28P;ENSP00000350578:L28P;ENSP00000351796:L28P;ENSP00000352760:L28P;ENSP00000387483:L23P	ENSP00000284981:L28P	L	-	2	0	APP	26406309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.051000	0.76627	2.047000	0.60756	0.533000	0.62120	CTG		0.488	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		G	27484438	A	G	27484438	3	3	5	1	0	0	0	0	1	0	0	0	815	188	7	4	2297	4	APP	21	27484438	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10		27484438	20645457	234	599										
SLC5A3	6526	hgsc.bcm.edu	37	chr21	35469094	35469094	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctgtaattgtgagccttctcAcaccacctcccacaaaggaa	6	14	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:35469094A>G	ENST00000381151.3	+	2	2109	c.1597A>G	c.(1597-1599)Aca>Gca	p.T533A	SLC5A3_ENST00000608209.1_Missense_Mutation_p.T533A|AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	533					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GAGCCTTCTCACACCACCTCC	0.468																																																0			21											80	69	73					21																	35469094		2203	4300	6503	34390964	SO:0001583	missense	6526				CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1597A>G	21.37:g.35469094A>G	ENSP00000370543:p.Thr533Ala		34390964	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389658	0.61956	.	.	ENSG00000198743	ENST00000381151	T	0.66280	-0.2	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.74688	0.3749	M	0.80422	2.495	0.48696	D	0.999697	D	0.54772	0.968	P	0.53401	0.725	T	0.79317	-0.1853	10	0.87932	D	0	.	15.1328	0.72539	1.0:0.0:0.0:0.0	.	533	P53794	SC5A3_HUMAN	A	533	ENSP00000370543:T533A	ENSP00000370543:T533A	T	+	1	0	SLC5A3	34390964	1.000000	0.71417	0.993000	0.49108	0.958000	0.62258	8.930000	0.92872	2.224000	0.72417	0.533000	0.62120	ACA		0.468	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			G	35469094	A	G	35469094	3	3	5	1	0	0	0	0	1	0	0	0	14703	159	6	4	1599	4	SLC5A3	21	35469094	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	7984656	35469094	12660801	235	600										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875779	46875779	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gaacattgccggtgtcggagCcgagatcctgaacgtggcca	14	11	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:46875779C>A	ENST00000359759.4	+	1	356	c.335C>A	c.(334-336)gCc>gAc	p.A112D	COL18A1_ENST00000355480.5_Missense_Mutation_p.A112D|COL18A1_ENST00000400337.2_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	112					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGTGTCGGAGCCGAGATCCTG	0.637																																																0			21											39	48	45					21																	46875779		2159	4258	6417	45700207	SO:0001583	missense	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.335C>A	21.37:g.46875779C>A	ENSP00000352798:p.Ala112Asp		45700207	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	10.38	1.335038	0.24253	.	.	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.53206	0.63;0.63	3.68	3.68	0.42216	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	0.274745	0.22560	N	0.058479	T	0.65123	0.2661	M	0.66939	2.045	0.33684	D	0.612495	D;D	0.69078	0.997;0.996	D;D	0.70935	0.971;0.951	T	0.77294	-0.2641	10	0.87932	D	0	.	14.3285	0.66537	0.0:1.0:0.0:0.0	.	112;112	P39060;P39060-1	COIA1_HUMAN;.	D	112	ENSP00000347665:A112D;ENSP00000352798:A112D	ENSP00000347665:A112D	A	+	2	0	COL18A1	45700207	0.583000	0.26757	0.989000	0.46669	0.092000	0.18411	0.017000	0.13399	1.781000	0.52344	0.313000	0.20887	GCC		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46875779	C	A	46875779	3	1	5	1	0	0	0	0	1	0	0	0	3681	739	26	2	451	2	COL18A1	21	46875779	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	11406685	46875779	1254116	236	601										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47552085	47552085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gagcagcaggtggccttcccGctgagccacaacctcacggc	12	16	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:47552085G>A	ENST00000300527.4	+	28	2783	c.2679G>A	c.(2677-2679)ccG>ccA	p.P893P		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	893	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGGCCTTCCCGCTGAGCCACA	0.682																																																0			21																																								46376513	SO:0001819	synonymous_variant	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2679G>A	21.37:g.47552085G>A			46376513	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																				0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			A	47552085	G	A	47552085	2	1	5	1	0	0	0	0	0	0	0	1	3706	1074	38	1		1	COL6A2	21	47552085	Silent	SNP	G	TCGA-AF-2693-01A-02D-1733-10	676306	47552085	577810	237	602										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12712556	12712556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggagagatccagttgctttcGagtatctctatgttcaggta	11	7	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12712556G>A	ENST00000380682.1	+	9	1422	c.916G>A	c.(916-918)Gag>Aag	p.E306K		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	306	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						AGTTGCTTTCGAGTATCTCTA	0.388																																																0			X											114	96	102					X																	12712556		2203	4300	6503	12622477	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.916G>A	X.37:g.12712556G>A	ENSP00000370057:p.Glu306Lys		12622477	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031547	0.93575	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.78816	-1.21	5.02	5.02	0.67125	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.87625	0.6224	M	0.73217	2.22	0.52501	D	0.999952	D;D	0.89917	1.0;0.995	D;P	0.83275	0.996;0.739	D	0.89078	0.3474	10	0.72032	D	0.01	.	17.7822	0.88527	0.0:0.0:1.0:0.0	.	298;306	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	K	306;297;295	ENSP00000370057:E306K	ENSP00000304583:E295K	E	+	1	0	FRMPD4	12622477	1.000000	0.71417	0.970000	0.41538	0.979000	0.70002	9.322000	0.96357	2.217000	0.71921	0.513000	0.50165	GAG		0.388	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		A	12712556	G	A	12712556	3	1	5	1	0	0	0	0	1	0	0	0	6078	1059	37	1	950	1	FRMPD4	23	12712556	Missense_Mutation	SNP	G	TCGA-AF-2693-01A-02D-1733-10		12712556	142558004	238	603										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12734595	12734595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccccaacccttggctatgaaAcgctactagatgagggtcct	9	13	0	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12734595A>G	ENST00000380682.1	+	15	2523	c.2017A>G	c.(2017-2019)Acg>Gcg	p.T673A		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	673					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TGGCTATGAAACGCTACTAGA	0.483																																																0			X											153	165	161					X																	12734595		2203	4300	6503	12644516	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2017A>G	X.37:g.12734595A>G	ENSP00000370057:p.Thr673Ala		12644516	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	12.42	1.931377	0.34096	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.28454	1.61	5.86	0.241	0.15494	.	0.047976	0.85682	D	0.000000	T	0.12050	0.0293	N	0.08118	0	0.20975	N	0.999818	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31668	-0.9935	10	0.13853	T	0.58	-25.4542	8.0093	0.30344	0.5427:0.3871:0.0701:0.0	.	665;673	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	A	673;664;662	ENSP00000370057:T673A	ENSP00000304583:T662A	T	+	1	0	FRMPD4	12644516	1.000000	0.71417	0.012000	0.15200	0.576000	0.36127	3.275000	0.51639	-0.006000	0.14370	0.486000	0.48141	ACG		0.483	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		G	12734595	A	G	12734595	3	3	5	1	0	0	0	0	1	0	0	0	6078	43	2	4	2075	4	FRMPD4	23	12734595	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	22039	12734595	142535965	239	604										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937997	12937997	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtgcttcaattaatatagatCgttttgcttttcaaaacttg	6	6	2	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12937997C>A	ENST00000218032.6	+	2	925	c.838C>A	c.(838-840)Cgt>Agt	p.R280S	TLR8_ENST00000311912.5_Missense_Mutation_p.R298S	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	280					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TAATATAGATCGTTTTGCTTT	0.408																																																0			X											109	90	97					X																	12937997		2203	4299	6502	12847918	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.838C>A	X.37:g.12937997C>A	ENSP00000218032:p.Arg280Ser		12847918	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	0.624	-0.820042	0.02755	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56941	0.43;0.43	5.03	2.18	0.27775	.	0.586022	0.14193	N	0.335229	T	0.28732	0.0712	N	0.12637	0.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16188	-1.0411	10	0.27082	T	0.32	.	4.6572	0.12624	0.2682:0.5243:0.1278:0.0797	.	280;298	Q9NR97;D1CS70	TLR8_HUMAN;.	S	280;298	ENSP00000218032:R280S;ENSP00000312082:R298S	ENSP00000218032:R280S	R	+	1	0	TLR8	12847918	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.355000	0.20163	0.098000	0.17522	-1.528000	0.00924	CGT		0.408	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12937997	C	A	12937997	3	1	5	1	0	0	0	0	1	0	0	0	15996	884	31	2	844	2	TLR8	23	12937997	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	203402	12937997	142332563	240	605										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18664127	18664127	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tgtttctccccactaactagAcggtggatgtgatggcagaa	11	9	1	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:18664127A>G	ENST00000379989.3	+	20	2999	c.2714A>G	c.(2713-2715)gAc>gGc	p.D905G	CDKL5_ENST00000379996.3_Splice_Site_p.D905G|RS1_ENST00000476595.1_Intron|RS1_ENST00000379984.3_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					cactaactagacggtggatgt	0.488																																																0			X											140	112	122					X																	18664127		2203	4300	6503	18574048	SO:0001630	splice_region_variant	6792			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2714-1A>G	X.37:g.18664127A>G			18574048	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752565	0.15778	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.68624	-0.34;-0.34	1.89	0.648	0.17801	.	0.326495	0.27577	N	0.018744	T	0.28167	0.0695	N	0.01168	-0.975	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.21008	-1.0258	9	.	.	.	.	4.4178	0.11465	0.6504:0.3496:0.0:0.0	.	905	O76039	CDKL5_HUMAN	G	905	ENSP00000369332:D905G;ENSP00000369325:D905G	.	D	+	2	0	CDKL5	18574048	0.389000	0.25205	0.165000	0.22776	0.063000	0.16089	0.479000	0.22228	0.105000	0.17753	0.340000	0.21749	GAC		0.488	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Missense_Mutation	G	18664127	A	G	18664127	5	3	5	1	0	0	0	0	0	0	1	0	3163	289	10	4	2784	4	CDKL5	23	18664127	Splice_Site	SNP	A	TCGA-AF-2693-01A-02D-1733-10	5726130	18664127	136606433	241	606										
ZFX	7543	hgsc.bcm.edu	37	chrX	24225594	24225594	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctggagaagatgacttaggTaagaagaagtgtttagacat	12	4	0	6			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:24225594T>G	ENST00000379177.1	+	7	1223		c.e7+2		ZFX_ENST00000338565.3_Intron|ZFX_ENST00000459724.1_Splice_Site|ZFX_ENST00000540034.1_Splice_Site|ZFX_ENST00000304543.5_Splice_Site|ZFX_ENST00000539115.1_Splice_Site|ZFX_ENST00000379188.3_Splice_Site	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked						death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						ATGACTTAGGTAAGAAGAAGT	0.393																																					Esophageal Squamous(20;306 562 7346 32868 37983)											0			X											129	116	120					X																	24225594		2203	4300	6503	24135515	SO:0001630	splice_region_variant	7543				CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"Zinc fingers, C2H2-type"	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.796+2T>G	X.37:g.24225594T>G			24135515	B9EG97|O43668|Q8WYJ8	Splice_Site	SNP	ENST00000379177.1	37	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.004629	0.54254	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000545937	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4962	0.67688	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZFX	24135515	1.000000	0.71417	0.997000	0.53966	0.818000	0.46254	7.655000	0.83696	1.871000	0.54225	0.481000	0.45027	.		0.393	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410	Intron	G	24225594	T	G	24225594	5	3	5	1	0	0	0	0	0	0	1	0	17700	1652	57	4	808	4	ZFX	23	24225594	Splice_Site	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5561467	24225594	131044966	242	607										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35988902	35988902	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	caggccaattttcacaaaagTtccaagatttaactatgtga	6	8	1	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:35988902T>C	ENST00000297866.5	+	11	1898	c.1832T>C	c.(1831-1833)gTt>gCt	p.V611A		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	611										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						TTCACAAAAGTTCCAAGATTT	0.279																																																0			X											40	35	37					X																	35988902		2202	4293	6495	35898823	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1832T>C	X.37:g.35988902T>C	ENSP00000297866:p.Val611Ala		35898823	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	0.238	-1.015474	0.02078	.	.	ENSG00000165164	ENST00000297866	T	0.16597	2.33	5.0	-1.55	0.08558	.	0.728208	0.13134	N	0.411214	T	0.08492	0.0211	N	0.17474	0.49	0.09310	N	1	B	0.18310	0.027	B	0.17098	0.017	T	0.41378	-0.9512	10	0.15499	T	0.54	-27.6915	8.8496	0.35192	0.0:0.5333:0.0:0.4667	.	611	Q6ZTR5	CX022_HUMAN	A	611	ENSP00000297866:V611A	ENSP00000297866:V611A	V	+	2	0	CXorf22	35898823	0.020000	0.18652	0.173000	0.22940	0.003000	0.03518	0.120000	0.15647	-0.429000	0.07329	-0.328000	0.08392	GTT		0.279	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35988902	T	C	35988902	3	2	5	1	0	0	0	0	1	0	0	0	4108	1725	60	4	1874	4	CXorf22	23	35988902	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	11763308	35988902	119281658	243	608										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53223695	53223695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ggtgggattgggcctcggagAgctgaggaggcgaggcactg	21	7	0	2			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:53223695A>G	ENST00000375401.3	-	23	4196	c.3664T>C	c.(3664-3666)Tct>Cct	p.S1222P	KDM5C_ENST00000375383.3_Missense_Mutation_p.S1181P|KDM5C_ENST00000452825.3_Missense_Mutation_p.S1155P|KDM5C_ENST00000404049.3_Missense_Mutation_p.S1221P|KDM5C_ENST00000375379.3_Missense_Mutation_p.S1222P	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1222					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.S1222P(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GGCCTCGGAGAGCTGAGGAGG	0.637			"N, F, S"		clear cell renal carcinoma																																		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	1	Substitution - Missense(1)	kidney(1)	X											135	76	96					X																	53223695		2202	4298	6500	53240420	SO:0001583	missense	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.3664T>C	X.37:g.53223695A>G	ENSP00000364550:p.Ser1222Pro		53240420	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	a	8.723	0.914794	0.17907	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	T;T;T;T;T	0.00932	5.53;5.53;5.53;5.53;5.53	4.08	4.08	0.47627	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.355088	0.26029	N	0.026761	T	0.01287	0.0042	L	0.46670	1.46	0.29529	N	0.852945	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.15484	0.013;0.009;0.006	T	0.16958	-1.0385	10	0.49607	T	0.09	-17.0743	10.1937	0.43041	1.0:0.0:0.0:0.0	.	1155;1221;1222	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	P	1155;1222;1221;1222;1181	ENSP00000445176:S1155P;ENSP00000364550:S1222P;ENSP00000385394:S1221P;ENSP00000364528:S1222P;ENSP00000364532:S1181P	ENSP00000364528:S1222P	S	-	1	0	KDM5C	53240420	0.509000	0.26163	0.991000	0.47740	0.741000	0.42261	0.219000	0.17641	1.522000	0.49001	0.427000	0.28365	TCT		0.637	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		G	53223695	A	G	53223695	3	3	5	1	0	0	0	0	1	0	0	0	8156	304	11	4	1132	4	KDM5C	23	53223695	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	17234793	53223695	102046865	244	609										
AR	367	hgsc.bcm.edu	37	chrX	66765185	66765185	+	Missense_Mutation	SNP	A	A	T													0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcagcagcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:66765185A>T	ENST00000374690.3	+	1	721	c.197A>T	c.(196-198)cAg>cTg	p.Q66L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q66L|AR_ENST00000504326.1_Missense_Mutation_p.Q66L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	66	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																																							0			X											4	8	7					X																	66765185		1431	2929	4360	66681910	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.197A>T	X.37:g.66765185A>T	ENSP00000363822:p.Gln66Leu		66681910	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.50	1.658247	0.29425	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.70986	-0.53;-0.53;-0.53	1.43	1.43	0.22495	.	2.785180	0.01967	U	0.043766	T	0.72112	0.3420	N	0.19112	0.55	0.19945	N	0.999949	P;P;P	0.49559	0.807;0.925;0.807	D;D;P	0.67900	0.932;0.954;0.728	T	0.59862	-0.7374	10	0.38643	T	0.18	.	4.8652	0.13604	1.0:0.0:0.0:0.0	.	66;66;64	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	66	ENSP00000363822:Q66L;ENSP00000421155:Q66L;ENSP00000379359:Q66L	ENSP00000363822:Q66L	Q	+	2	0	AR	66681910	0.019000	0.18553	0.911000	0.35937	0.616000	0.37450	-0.130000	0.10498	0.644000	0.30656	0.084000	0.15446	CAG		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765185	A	T	66765185	3	4	5	1	0	0	0	0	1	0	0	0	836	188	7	5	199	5	AR	23	66765185	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	13541490	66765185	88505375	245	610	1	2								
AR	367	hgsc.bcm.edu	37	chrX	66765188	66765188	+	Missense_Mutation	SNP	A	A	T													0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gcagcagcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:66765188A>T	ENST00000374690.3	+	1	724	c.200A>T	c.(199-201)cAg>cTg	p.Q67L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q67L|AR_ENST00000504326.1_Missense_Mutation_p.Q67L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	67	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																																							0			X											4	8	7					X																	66765188		1328	2795	4123	66681913	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.200A>T	X.37:g.66765188A>T	ENSP00000363822:p.Gln67Leu		66681913	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.39	1.924161	0.34002	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.59224	0.28;0.28;0.28	1.43	1.43	0.22495	.	1.958740	0.03276	U	0.185421	T	0.60483	0.2272	N	0.19112	0.55	0.19945	N	0.999946	P;P;P	0.49559	0.807;0.925;0.807	D;D;P	0.65140	0.932;0.932;0.728	T	0.51325	-0.8720	10	0.72032	D	0.01	.	4.8652	0.13604	1.0:0.0:0.0:0.0	.	67;67;65	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	67	ENSP00000363822:Q67L;ENSP00000421155:Q67L;ENSP00000379359:Q67L	ENSP00000363822:Q67L	Q	+	2	0	AR	66681913	0.407000	0.25352	0.994000	0.49952	0.753000	0.42808	0.127000	0.15790	0.644000	0.30656	0.084000	0.15446	CAG		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765188	A	T	66765188	3	4	5	1	0	0	0	0	1	0	0	0	836	188	7	5	202	5	AR	23	66765188	Missense_Mutation	SNP	A	TCGA-AF-2693-01A-02D-1733-10	3	66765188	88505372	246	611	1	2								
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73959989	73959989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ccttgtggacctgttctcgcTccatgtgctttcccttacat	7	14	1	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:73959989T>C	ENST00000055682.6	-	3	5014	c.4403A>G	c.(4402-4404)gAg>gGg	p.E1468G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1468					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.E1468G(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGTTCTCGCTCCATGTGCTT	0.473																																																1	Substitution - Missense(1)	ovary(1)	X											209	164	179					X																	73959989		2203	4300	6503	73876714	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4403A>G	X.37:g.73959989T>C	ENSP00000055682:p.Glu1468Gly		73876714	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	T	19.14	3.769015	0.69992	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.39997	1.05;1.05	5.36	5.36	0.76844	.	0.154190	0.56097	D	0.000022	T	0.43055	0.1230	L	0.29908	0.895	0.52099	D	0.999942	D	0.53312	0.959	P	0.50659	0.647	T	0.44112	-0.9349	10	0.87932	D	0	-10.3741	14.4375	0.67293	0.0:0.0:0.0:1.0	.	1468	Q5QGS0	K2022_HUMAN	G	1468	ENSP00000362567:E1468G;ENSP00000055682:E1468G	ENSP00000055682:E1468G	E	-	2	0	KIAA2022	73876714	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.698000	0.84413	1.789000	0.52484	0.441000	0.28932	GAG		0.473	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		C	73959989	T	C	73959989	3	2	5	1	0	0	0	0	1	0	0	0	8290	1551	54	4	155	4	KIAA2022	23	73959989	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	7194801	73959989	81310571	247	612										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698170	79698170	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	gtaaaaccaaaagacatcatTcatgttgtgaaagatcaact	6	7	3	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:79698170T>C	ENST00000308293.5	+	3	371	c.132T>C	c.(130-132)atT>atC	p.I44I	FAM46D_ENST00000538312.1_Silent_p.I44I	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	44										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						AAGACATCATTCATGTTGTGA	0.383																																																0			X											123	106	111					X																	79698170		2202	4298	6500	79584826	SO:0001819	synonymous_variant	169966			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.132T>C	X.37:g.79698170T>C			79584826	B2R9Q6|Q7Z3F6|Q8NHU1	Silent	SNP	ENST00000308293.5	37	CCDS14446.1																																																																																				0.383	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		C	79698170	T	C	79698170	2	2	5	1	0	0	0	0	0	0	0	1	5587	1771	62	4		4	FAM46D	23	79698170	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	5738181	79698170	75572390	248	613										
HMGN5	79366	hgsc.bcm.edu	37	chrX	80370223	80370223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	tcctcttttccttcttcctcTtcttttaaatcttctttctc	0	14	7	0			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:80370223T>C	ENST00000358130.2	-	7	1102	c.774A>G	c.(772-774)gaA>gaG	p.E258E	HMGN5_ENST00000491275.1_5'Flank	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	258					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						cttcttcctcttcttttaaat	0.343																																																0			X											240	213	222					X																	80370223		1620	2844	4464	80256879	SO:0001819	synonymous_variant	0			AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"High-mobility group / Canonical"	8013	protein-coding gene	gene with protein product		300385	"nucleosomal binding protein 1", "high-mobility group nucleosome binding domain 5"	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.774A>G	X.37:g.80370223T>C			80256879	Q5JSL1	Silent	SNP	ENST00000358130.2	37	CCDS14448.1																																																																																				0.343	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763		C	80370223	T	C	80370223	2	2	5	1	0	0	0	0	0	0	0	1	7259	1606	56	4		4	HMGN5	23	80370223	Silent	SNP	T	TCGA-AF-2693-01A-02D-1733-10	672053	80370223	74900337	249	614										
AGTR2	186	hgsc.bcm.edu	37	chrX	115304581	115304581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aaagagagagtatgtcttgcCggaaaagcagttctcttaga	11	6	2	3			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:115304581C>T	ENST00000371906.4	+	3	1238	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	350					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TATGTCTTGCCGGAAAAGCAG	0.438																																																0			X											93	87	89					X																	115304581		2203	4300	6503	115218609	SO:0001583	missense	186			AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.1048C>T	X.37:g.115304581C>T	ENSP00000360973:p.Arg350Trp		115218609	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	C	8.496	0.863090	0.17250	.	.	ENSG00000180772	ENST00000371906	T	0.38401	1.14	4.87	-0.991	0.10235	.	0.155918	0.40818	N	0.001015	T	0.15739	0.0379	N	0.08118	0	0.23249	N	0.998049	D	0.56968	0.978	B	0.40444	0.329	T	0.31308	-0.9948	10	0.66056	D	0.02	-4.2867	9.0441	0.36336	0.5143:0.3697:0.116:0.0	.	350	P50052	AGTR2_HUMAN	W	350	ENSP00000360973:R350W	ENSP00000360973:R350W	R	+	1	2	AGTR2	115218609	0.562000	0.26586	0.744000	0.31058	0.398000	0.30690	0.347000	0.20014	-0.146000	0.11274	0.506000	0.49869	CGG		0.438	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		T	115304581	C	T	115304581	3	4	5	1	0	0	0	0	1	0	0	0	402	643	23	1	1050	1	AGTR2	23	115304581	Missense_Mutation	SNP	C	TCGA-AF-2693-01A-02D-1733-10	34934358	115304581	39965979	250	615										
ACTRT1	139741	hgsc.bcm.edu	37	chrX	127185239	127185239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	aagccagctgttccacttccTtcatgagcctttcctccagc	6	16	1	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:127185239T>C	ENST00000371124.3	-	1	1143	c.947A>G	c.(946-948)aAg>aGg	p.K316R		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	316						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						TTCCACTTCCTTCATGAGCCT	0.493																																																0			X											127	92	104					X																	127185239		2203	4300	6503	127012920	SO:0001583	missense	139741			AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.947A>G	X.37:g.127185239T>C	ENSP00000360165:p.Lys316Arg		127012920	Q6X7C1|Q96L10	Missense_Mutation	SNP	ENST00000371124.3	37	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	T	5.618	0.298816	0.10622	.	.	ENSG00000123165	ENST00000371124	D	0.94650	-3.48	3.58	1.08	0.20341	.	0.219866	0.32952	N	0.005457	D	0.87795	0.6267	L	0.31207	0.915	0.24556	N	0.993994	B	0.21606	0.058	B	0.24701	0.055	T	0.79037	-0.1967	10	0.87932	D	0	.	3.6252	0.08111	0.1959:0.1171:0.0:0.687	.	316	Q8TDG2	ACTT1_HUMAN	R	316	ENSP00000360165:K316R	ENSP00000360165:K316R	K	-	2	0	ACTRT1	127012920	1.000000	0.71417	0.013000	0.15412	0.018000	0.09664	5.469000	0.66749	0.107000	0.17824	-0.323000	0.08544	AAG		0.493	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289		C	127185239	T	C	127185239	3	2	5	1	0	0	0	0	1	0	0	0	218	1609	56	4	187	4	ACTRT1	23	127185239	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	11880658	127185239	28085321	251	616										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135302951	135302951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	ctacttcctgtattgaagtgTctttcatgcttttttgtctg	7	8	3	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:135302951T>C	ENST00000316077.9	-	16	2679	c.2459A>G	c.(2458-2460)gAc>gGc	p.D820G	MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370661.1_Missense_Mutation_p.D785G|MAP7D3_ENST00000370663.5_Missense_Mutation_p.D802G	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	820					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TATTGAAGTGTCTTTCATGCT	0.358																																																0			X											184	169	174					X																	135302951		1831	4077	5908	135130617	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.2459A>G	X.37:g.135302951T>C	ENSP00000318086:p.Asp820Gly		135130617	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.614386	0.28712	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.20463	2.07;3.64;3.64;2.09	3.73	3.73	0.42828	.	.	.	.	.	T	0.23289	0.0563	N	0.24115	0.695	0.09310	N	1	D;D;D;D	0.71674	0.998;0.997;0.994;0.997	P;P;P;P	0.59487	0.81;0.858;0.725;0.858	T	0.08027	-1.0742	9	0.22109	T	0.4	-14.5836	8.0072	0.30332	0.0:0.0:0.0:1.0	.	802;779;820;785	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	G	785;820;802;779	ENSP00000359695:D785G;ENSP00000318086:D820G;ENSP00000359697:D802G;ENSP00000359694:D779G	ENSP00000318086:D820G	D	-	2	0	MAP7D3	135130617	0.004000	0.15560	0.022000	0.16811	0.013000	0.08279	0.427000	0.21379	1.706000	0.51276	0.430000	0.28490	GAC		0.358	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135302951	T	C	135302951	3	2	5	1	0	0	0	0	1	0	0	0	9299	1667	58	4	183	4	MAP7D3	23	135302951	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	8117712	135302951	19967609	252	617										
NAA10	8260	hgsc.bcm.edu	37	chrX	153195525	153195525	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	7	1	0.472413020263411	0	0.486874643332699	0.00579710144927537	0.0785829307568439	0	cctcgctgaggtccttgctgTccccaccactatcctcggca	8	18	0	1			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:153195525T>C	ENST00000464845.1	-	8	941	c.623A>G	c.(622-624)gAc>gGc	p.D208G	NAA10_ENST00000393710.3_5'Flank|NAA10_ENST00000393712.3_3'UTR|NAA10_ENST00000370015.4_3'UTR|NAA10_ENST00000370009.1_Missense_Mutation_p.D193G	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	208					DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						GTCCTTGCTGTCCCCACCACT	0.617																																					Ovarian(94;1099 1433 38814 45882 51063)											0			X											109	85	93					X																	153195525		2203	4300	6503	152848719	SO:0001583	missense	0			BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"N(alpha)-acetyltransferase subunits"	18704	protein-coding gene	gene with protein product		300013	"ARD1 homolog, N-acetyltransferase (S. cerevisiae)", "ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.623A>G	X.37:g.153195525T>C	ENSP00000417763:p.Asp208Gly		152848719	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	37	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376822	0.61735	.	.	ENSG00000102030	ENST00000464845;ENST00000370009	T;T	0.59638	0.25;0.26	5.35	5.35	0.76521	.	0.052011	0.85682	D	0.000000	T	0.50599	0.1625	L	0.43152	1.355	0.51233	D	0.99991	B;B	0.13594	0.008;0.008	B;B	0.11329	0.005;0.006	T	0.47711	-0.9096	10	0.49607	T	0.09	-39.9726	13.3468	0.60578	0.0:0.0:0.0:1.0	.	193;208	A6NM98;P41227	.;NAA10_HUMAN	G	208;193	ENSP00000417763:D208G;ENSP00000359026:D193G	ENSP00000359026:D193G	D	-	2	0	NAA10	152848719	1.000000	0.71417	0.951000	0.38953	0.962000	0.63368	7.282000	0.78630	1.794000	0.52575	0.425000	0.28330	GAC		0.617	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491		C	153195525	T	C	153195525	3	2	5	1	0	0	0	0	1	0	0	0	10146	1667	58	4	88	4	NAA10	23	153195525	Missense_Mutation	SNP	T	TCGA-AF-2693-01A-02D-1733-10	17892574	153195525	2075035	253	618										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6529509	6529509	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtagataaggaggaaggaCcctggttagggaaggcccaa	16	6	0	1	rs147140763		TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr1:6529509C>G	ENST00000400915.3	-	19	2169	c.2103G>C	c.(2101-2103)ggG>ggC	p.G701G	PLEKHG5_ENST00000537245.1_Splice_Site_p.G724G|PLEKHG5_ENST00000377740.3_Splice_Site_p.G722G|PLEKHG5_ENST00000377732.1_Splice_Site_p.G682G|PLEKHG5_ENST00000544978.1_Splice_Site_p.G645G|PLEKHG5_ENST00000340850.5_Splice_Site_p.G645G|PLEKHG5_ENST00000377737.2_Splice_Site_p.G645G|PLEKHG5_ENST00000400913.1_Splice_Site_p.G645G|PLEKHG5_ENST00000377728.3_Splice_Site_p.G645G|PLEKHG5_ENST00000535355.1_Splice_Site_p.G714G|PLEKHG5_ENST00000377725.1_Splice_Site_p.G645G|PLEKHG5_ENST00000377748.1_Splice_Site_p.G722G	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	701	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.G722G(1)		liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGAGGAAGGACCCTGGTTAGG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	98	96					1																	6529509		2203	4300	6503	6452096	SO:0001630	splice_region_variant	57449			AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2102-1G>C	1.37:g.6529509C>G			6452096	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	37	CCDS41241.1																																																																																				0.607	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	Silent	G	6529509	C	G	6529509	5	3	6	1	0	0	0	0	0	0	1	0	12104	521	18	5	1101	5	PLEKHG5	1	6529509	Splice_Site	SNP	C	TCGA-AF-3400-01A-01W-0831-10		6529509	242721112	1	619										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34102147	34102147	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggatcaaaacatgactcccgCgggttttctgggaaaaagaa	11	8	2	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr1:34102147C>T	ENST00000373380.1	-	9	1621	c.1401G>A	c.(1399-1401)ccG>ccA	p.P467P	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Silent_p.P1594P			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1554	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P1554P(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ATGACTCCCGCGGGTTTTCTG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	1											46	43	44					1																	34102147		2203	4300	6503	33874734	SO:0001819	synonymous_variant	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.1401G>A	1.37:g.34102147C>T			33874734	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																					0.562	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		T	34102147	C	T	34102147	2	4	6	1	0	0	0	0	0	0	0	1	3951	755	27	1		1	CSMD2	1	34102147	Silent	SNP	C	TCGA-AF-3400-01A-01W-0831-10	27572638	34102147	215148474	2	620										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198495825	198495825	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctccagccaatcagcatcaaGtgtactaatgactgatcctt	6	12	2	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr2:198495825G>C	ENST00000295049.4	-	5	1374	c.838C>G	c.(838-840)Ctt>Gtt	p.L280V		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	280					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)		p.L280V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TCAGCATCAAGTGTACTAATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											95	83	87					2																	198495825		2203	4300	6503	198204070	SO:0001583	missense	130132			AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.838C>G	2.37:g.198495825G>C	ENSP00000295049:p.Leu280Val		198204070	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	37	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263837	0.59431	.	.	ENSG00000162944	ENST00000295049	T	0.58652	0.32	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	L	0.60455	1.87	0.53688	D	0.999979	D	0.69078	0.997	D	0.64042	0.921	T	0.71404	-0.4603	10	0.87932	D	0	-19.4651	12.1565	0.54081	0.0786:0.0:0.9214:0.0	.	280	Q52LD8	RFTN2_HUMAN	V	280	ENSP00000295049:L280V	ENSP00000295049:L280V	L	-	1	0	RFTN2	198204070	1.000000	0.71417	0.954000	0.39281	0.734000	0.41952	5.566000	0.67372	2.691000	0.91804	0.655000	0.94253	CTT		0.358	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		C	198495825	G	C	198495825	3	2	6	1	0	0	0	0	1	0	0	0	13296	1029	36	5	687	5	RFTN2	2	198495825	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10		198495825	44703548	3	621										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220159774	220159774	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaagtggaactgcgtgagCgtgcgcgtctcctgggtctg	17	9	2	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr2:220159774C>T	ENST00000295718.2	-	19	2838	c.2598G>A	c.(2596-2598)acG>acA	p.T866T	MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000409251.3_Silent_p.T837T|PTPRN_ENST00000497977.1_Intron|PTPRN_ENST00000423636.2_Silent_p.T776T	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	866	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T866T(1)		breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		ACTGCGTGAGCGTGCGCGTCT	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	2											45	50	48					2																	220159774		2203	4300	6503	219868018	SO:0001819	synonymous_variant	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2598G>A	2.37:g.220159774C>T			219868018	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843079	0.32606	.	.	ENSG00000054356	ENST00000443981	.	.	.	5.2	-1.51	0.08664	.	.	.	.	.	T	0.42517	0.1206	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29027	-1.0025	4	.	.	.	.	3.37	0.07217	0.197:0.1932:0.4605:0.1494	.	.	.	.	H	69	.	.	R	-	2	0	PTPRN	219868018	0.745000	0.28261	0.995000	0.50966	0.998000	0.95712	-0.232000	0.09055	-0.153000	0.11137	0.650000	0.86243	CGC		0.682	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			T	220159774	C	T	220159774	2	4	6	1	0	0	0	0	0	0	0	1	12844	755	27	1		1	PTPRN	2	220159774	Silent	SNP	C	TCGA-AF-3400-01A-01W-0831-10	21663949	220159774	23039599	4	622										
APC	324	hgsc.bcm.edu	37	chr5	112175171	112175171	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	taggatgtaatcagacgacaCaggaagcagattctgctaat	10	7	2	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr5:112175171C>T	ENST00000457016.1	+	16	4260	c.3880C>T	c.(3880-3882)Cag>Tag	p.Q1294*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1294*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1294*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1294	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1294*(11)|p.T1293fs*2(1)|p.Q1294fs*6(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAGACGACACAGGAAGCAGA	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(11)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5	GRCh37	CM930027	APC	M							55	57	56					5																	112175171		2202	4300	6502	112203070	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3880C>T	5.37:g.112175171C>T	ENSP00000413133:p.Gln1294*		112203070	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.839479	0.97877	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	4.85	0.62838	.	0.122222	0.53938	D	0.000054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.559	13.8243	0.63342	0.2784:0.7216:0.0:0.0	.	.	.	.	X	1294	.	.	Q	+	1	0	APC	112203070	0.993000	0.37304	1.000000	0.80357	0.962000	0.63368	2.731000	0.47343	1.533000	0.49186	0.655000	0.94253	CAG		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175171	C	T	112175171	4	4	6	1	0	0	0	0	0	1	0	0	763	479	17	3	3938	3	APC	5	112175171	Nonsense_Mutation	SNP	C	TCGA-AF-3400-01A-01W-0831-10		112175171	68740089	5	623										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148407482	148407482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgcttggcactagactcacGgtcaggcaggcaggccagca	13	12	2	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr5:148407482G>A	ENST00000515425.1	-	11	1914	c.1813C>T	c.(1813-1815)Cgt>Tgt	p.R605C	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000394358.2_Missense_Mutation_p.R490C|SH3TC2_ENST00000512049.1_Missense_Mutation_p.R598C|SH3TC2_ENST00000538184.1_Missense_Mutation_p.R152C	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	605					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)		p.R490C(1)|p.R605C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTAGACTCACGGTCAGGCAGG	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	5											58	56	57					5																	148407482		2203	4300	6503	148387675	SO:0001583	missense	79628			AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1813C>T	5.37:g.148407482G>A	ENSP00000423660:p.Arg605Cys		148387675	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187842	0.38609	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	6.04	3.18	0.36537	Tetratricopeptide-like helical (1);	0.499855	0.22258	N	0.062451	T	0.61837	0.2379	L	0.27053	0.805	0.24165	N	0.995649	B;D;D;D	0.69078	0.176;0.997;0.997;0.997	B;P;P;P	0.53360	0.01;0.614;0.724;0.614	T	0.55237	-0.8172	10	0.62326	D	0.03	.	10.6601	0.45698	0.1334:0.1211:0.7455:0.0	.	490;598;605;605	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	C	152;605;598;490	ENSP00000441427:R152C;ENSP00000423660:R605C;ENSP00000421860:R598C;ENSP00000377886:R490C	ENSP00000377886:R490C	R	-	1	0	SH3TC2	148387675	1.000000	0.71417	0.621000	0.29145	0.380000	0.30137	6.560000	0.73950	1.568000	0.49683	0.563000	0.77884	CGT		0.602	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148407482	G	A	148407482	3	1	6	1	0	0	0	0	1	0	0	0	14299	1116	39	1	2081	1	SH3TC2	5	148407482	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	36232311	148407482	32507778	6	624										
SPARC	6678	hgsc.bcm.edu	37	chr5	151045924	151045924	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tagggtctggggtcttacccGtcaatggggtgctggtccag	16	9	3	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr5:151045924G>A	ENST00000231061.4	-	8	1045	c.732C>T	c.(730-732)gaC>gaT	p.D244D	SPARC_ENST00000537849.1_5'Flank	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	244					blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)	p.D244D(1)		central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		GGTCTTACCCGTCAATGGGGT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											77	72	74					5																	151045924		2203	4300	6503	151026117	SO:0001819	synonymous_variant	6678				CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"cysteine-rich protein", "osteonectin"	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.732C>T	5.37:g.151045924G>A			151026117	D3DQH9|Q6IBK4	Silent	SNP	ENST00000231061.4	37	CCDS4318.1																																																																																				0.572	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118		A	151045924	G	A	151045924	2	1	6	1	0	0	0	0	0	0	0	1	15034	1136	40	1		1	SPARC	5	151045924	Silent	SNP	G	TCGA-AF-3400-01A-01W-0831-10	2638442	151045924	29869336	7	625										
GPR31	2853	hgsc.bcm.edu	37	chr6	167570514	167570514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cactgtgcaggtaggtgaggCtgcccgtgacatccgaggta	15	10	0	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr6:167570514C>T	ENST00000366834.1	-	1	1303	c.806G>A	c.(805-807)aGc>aAc	p.S269N		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	269					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S269N(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		GTAGGTGAGGCTGCCCGTGAC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											87	85	86					6																	167570514		2203	4300	6503	167490504	SO:0001583	missense	2853			U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.806G>A	6.37:g.167570514C>T	ENSP00000355799:p.Ser269Asn		167490504	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	37	CCDS5299.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895753	0.52121	.	.	ENSG00000120436	ENST00000366834	T	0.72282	-0.64	3.54	3.54	0.40534	GPCR, rhodopsin-like superfamily (1);	0.164448	0.28958	N	0.013593	T	0.75162	0.3812	M	0.81112	2.525	0.24455	N	0.99447	D	0.63046	0.992	P	0.61477	0.889	T	0.67169	-0.5738	10	0.42905	T	0.14	-37.0518	13.854	0.63515	0.0:1.0:0.0:0.0	.	269	O00270	GPR31_HUMAN	N	269	ENSP00000355799:S269N	ENSP00000355799:S269N	S	-	2	0	GPR31	167490504	0.994000	0.37717	0.835000	0.33067	0.187000	0.23431	1.743000	0.38258	1.811000	0.52892	0.313000	0.20887	AGC		0.607	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		T	167570514	C	T	167570514	3	4	6	1	0	0	0	0	1	0	0	0	6707	797	28	3	156	3	GPR31	6	167570514	Missense_Mutation	SNP	C	TCGA-AF-3400-01A-01W-0831-10		167570514	3544553	8	626										
SGCE	8910	hgsc.bcm.edu	37	chr7	94257670	94257670	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgggatcattactaatctcGcctagataagaaacagagaa	8	7	2	3			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr7:94257670G>A	ENST00000265735.7	-	3	344	c.234C>T	c.(232-234)ggC>ggT	p.G78G	SGCE_ENST00000428696.2_Splice_Site_p.G78G|SGCE_ENST00000447873.1_Splice_Site_p.G78G|SGCE_ENST00000445866.2_Splice_Site_p.G78G|SGCE_ENST00000437425.2_Splice_Site_p.G37G|SGCE_ENST00000415788.2_Splice_Site_p.G114G	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	78				G -> S (in Ref. 3; AAM64204). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)	p.G78G(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	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)			TACTAATCTCGCCTAGATAAG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	7											54	53	53					7																	94257670		2203	4299	6502	94095606	SO:0001630	splice_region_variant	8910			AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.233-1C>T	7.37:g.94257670G>A			94095606	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Silent	SNP	ENST00000265735.7	37	CCDS5637.1																																																																																				0.333	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2		Silent	A	94257670	G	A	94257670	5	1	6	1	0	0	0	0	0	0	1	0	14239	1101	38	1	1267	1	SGCE	7	94257670	Splice_Site	SNP	G	TCGA-AF-3400-01A-01W-0831-10		94257670	64880993	9	627										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138836916	138836916	+	Silent	SNP	G	G	A													0	0	1	0	0	0	1	1	0	cttttcctccggatcttcttGaagatttccgtcagctcatc							TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr9:138836916G>A	ENST00000371756.3	-	7	1051	c.834C>T	c.(832-834)ttC>ttT	p.F278F	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	278					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.F278F(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		GGATCTTCTTGAAGATTTCCG	0.627																																					NSCLC(78;973 1398 27381 29552 42415)											1	Substitution - coding silent(1)	large_intestine(1)	9											155	137	143					9																	138836916		2203	4300	6503	137976737	SO:0001819	synonymous_variant	10422			AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.834C>T	9.37:g.138836916G>A			137976737	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	37	CCDS35177.1																																																																																				0.627	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		A	138836916	G	A	138836916	2	1	6	1	0	0	0	0	0	0	0	1	16874	1281	45	3		3	UBAC1	9	138836916	Silent	SNP	G	TCGA-AF-3400-01A-01W-0831-10		138836916	2376515	10	628	2	2								
UBAC1	10422	hgsc.bcm.edu	37	chr9	138836919	138836919	+	Silent	SNP	G	G	A													0	0	1	0	0	0	1	1	0	ttcctccggatcttcttgaaGatttccgtcagctcatctct							TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr9:138836919G>A	ENST00000371756.3	-	7	1048	c.831C>T	c.(829-831)atC>atT	p.I277I	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	277					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.I277I(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TCTTCTTGAAGATTTCCGTCA	0.617																																					NSCLC(78;973 1398 27381 29552 42415)											1	Substitution - coding silent(1)	large_intestine(1)	9											158	139	145					9																	138836919		2203	4300	6503	137976740	SO:0001819	synonymous_variant	10422			AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.831C>T	9.37:g.138836919G>A			137976740	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	37	CCDS35177.1																																																																																				0.617	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		A	138836919	G	A	138836919	2	1	6	1	0	0	0	0	0	0	0	1	16874	932	33	3		3	UBAC1	9	138836919	Silent	SNP	G	TCGA-AF-3400-01A-01W-0831-10	3	138836919	2376512	11	629	2	2								
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17191188	17191188	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgctaaagcctctgcttccAtctgtaatgcttcttctttg	6	11	4	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr11:17191188A>T	ENST00000265970.7	-	1	100	c.101T>A	c.(100-102)aTg>aAg	p.M34K	PIK3C2A_ENST00000540361.1_Intron|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	34	Interaction with clathrin; sufficient to induce clathrin assemby.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.M34K(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						CTCTGCTTCCATCTGTAATGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											194	188	190					11																	17191188		2200	4293	6493	17147764	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.101T>A	11.37:g.17191188A>T	ENSP00000265970:p.Met34Lys		17147764	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.905181	0.72868	.	.	ENSG00000011405	ENST00000265970;ENST00000544896;ENST00000532035	T	0.69040	-0.37	5.23	5.23	0.72850	.	0.094256	0.64402	D	0.000001	T	0.74869	0.3773	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.987	D;D	0.83275	0.996;0.942	T	0.78026	-0.2365	10	0.87932	D	0	-12.9962	15.112	0.72365	1.0:0.0:0.0:0.0	.	34;34	F5H5W9;O00443	.;P3C2A_HUMAN	K	34	ENSP00000265970:M34K	ENSP00000265970:M34K	M	-	2	0	PIK3C2A	17147764	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.519000	0.90563	1.980000	0.57719	0.397000	0.26171	ATG		0.423	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		T	17191188	A	T	17191188	3	4	6	1	0	0	0	0	1	0	0	0	11940	217	8	5	5087	5	PIK3C2A	11	17191188	Missense_Mutation	SNP	A	TCGA-AF-3400-01A-01W-0831-10		17191188	117815328	12	630										
SSRP1	6749	hgsc.bcm.edu	37	chr11	57100241	57100241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtcataacgaccacgaggaGtcagacactgcagctcccgg	11	13	2	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr11:57100241G>A	ENST00000278412.2	-	6	892	c.626C>T	c.(625-627)aCt>aTt	p.T209I		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	209					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T209I(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						ACCACGAGGAGTCAGACACTG	0.537																																					Colon(89;1000 1340 6884 23013 41819)											1	Substitution - Missense(1)	large_intestine(1)	11											84	80	81					11																	57100241		2201	4296	6497	56856817	SO:0001583	missense	6749			M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 80 kDa subunit"	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.626C>T	11.37:g.57100241G>A	ENSP00000278412:p.Thr209Ile		56856817	Q5BJG8	Missense_Mutation	SNP	ENST00000278412.2	37	CCDS7952.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.898389	0.72639	.	.	ENSG00000149136	ENST00000278412;ENST00000526696;ENST00000529002	T;T;T	0.58652	0.32;0.32;0.32	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.80380	0.4612	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.81346	-0.0974	10	0.62326	D	0.03	-18.3486	20.0291	0.97531	0.0:0.0:1.0:0.0	.	209	Q08945	SSRP1_HUMAN	I	209;112;112	ENSP00000278412:T209I;ENSP00000431154:T112I;ENSP00000434546:T112I	ENSP00000278412:T209I	T	-	2	0	SSRP1	56856817	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	9.103000	0.94232	2.838000	0.97847	0.561000	0.74099	ACT		0.537	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		A	57100241	G	A	57100241	3	1	6	1	0	0	0	0	1	0	0	0	15233	1029	36	3	1551	3	SSRP1	11	57100241	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	39909053	57100241	77906275	13	631										
MMP3	4314	hgsc.bcm.edu	37	chr11	102713560	102713560	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaggaacttctgcatttctcGgatttttttaacaacaggac	7	8	2	0	rs143174783		TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr11:102713560G>A	ENST00000299855.5	-	2	449	c.193C>T	c.(193-195)Cga>Tga	p.R65*		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	65					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R65*(1)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TGCATTTCTCGGATTTTTTTA	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	11						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	50	46	47		193	5.2	0.6	11	dbSNP_134	47	1,8597	1.2+/-3.3	0,1,4298	yes	stop-gained	MMP3	NM_002422.3		0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154		65/478	102713560	2,13002	2203	4299	6502	102218770	SO:0001587	stop_gained	4314			X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.193C>T	11.37:g.102713560G>A	ENSP00000299855:p.Arg65*		102218770	B2R8B8|Q3B7S0|Q6GRF8	Nonsense_Mutation	SNP	ENST00000299855.5	37	CCDS8323.1	.	.	.	.	.	.	.	.	.	.	G	38	7.053271	0.98029	2.27E-4	1.16E-4	ENSG00000149968	ENST00000299855	.	.	.	6.16	5.2	0.72013	.	1.509290	0.04732	N	0.421300	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4284	0.55561	0.0:0.0:0.7472:0.2528	.	.	.	.	X	65	.	ENSP00000299855:R65X	R	-	1	2	MMP3	102218770	0.000000	0.05858	0.592000	0.28758	0.981000	0.71138	0.760000	0.26475	2.937000	0.99478	0.650000	0.86243	CGA		0.448	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422		A	102713560	G	A	102713560	4	1	6	1	0	0	0	0	0	1	0	0	9696	1124	39	1	1276	1	MMP3	11	102713560	Nonsense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	45613319	102713560	32292956	14	632										
TECTA	7007	hgsc.bcm.edu	37	chr11	121028731	121028731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggccggcggcggcgtcttccGcaccttcgacggcgccttcc	14	18	1	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr11:121028731G>A	ENST00000392793.1	+	14	4758	c.4487G>A	c.(4486-4488)cGc>cAc	p.R1496H	TECTA_ENST00000264037.2_Missense_Mutation_p.R1496H			O75443	TECTA_HUMAN	tectorin alpha	1496	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.R1496H(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GGCGTCTTCCGCACCTTCGAC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											44	36	38					11																	121028731		2203	4299	6502	120533941	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4487G>A	11.37:g.121028731G>A	ENSP00000376543:p.Arg1496His		120533941		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769826	0.90020	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.59772	0.24;0.24	5.54	4.57	0.56435	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.64159	0.2573	L	0.38175	1.15	0.46437	D	0.999047	D	0.89917	1.0	D	0.91635	0.999	T	0.55335	-0.8157	10	0.10902	T	0.67	.	15.8438	0.78871	0.0:0.1358:0.8642:0.0	.	1496	O75443	TECTA_HUMAN	H	1496	ENSP00000376543:R1496H;ENSP00000264037:R1496H	ENSP00000264037:R1496H	R	+	2	0	TECTA	120533941	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.457000	0.66672	2.618000	0.88619	0.462000	0.41574	CGC		0.642	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121028731	G	A	121028731	3	1	6	1	0	0	0	0	1	0	0	0	15786	1087	38	1	4537	1	TECTA	11	121028731	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	18315171	121028731	13977785	15	633										
MYL6B	140465	hgsc.bcm.edu	37	chr12	56549214	56549214	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacctccagagctgaagtcgCggcgtgtggactttgagact	13	10	0	3	rs149424698		TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr12:56549214C>A	ENST00000553066.1	+	5	780	c.358C>A	c.(358-360)Cgg>Agg	p.R120R	MYL6_ENST00000548400.1_5'Flank|MYL6_ENST00000348108.4_5'Flank|MYL6B_ENST00000552568.1_Silent_p.R120R|MYL6_ENST00000551589.1_5'Flank|MYL6_ENST00000293422.5_5'Flank|MYL6_ENST00000548293.1_5'Flank|MYL6_ENST00000548580.1_5'Flank|MYL6_ENST00000536128.1_5'Flank|MYL6B_ENST00000550152.1_3'UTR|MYL6_ENST00000549566.1_5'Flank|MYL6_ENST00000549017.1_5'Flank|MYL6B_ENST00000550443.1_Silent_p.R120R|MYL6B_ENST00000207437.5_Silent_p.R120R|MYL6_ENST00000547408.1_5'Flank|RP11-603J24.14_ENST00000548731.1_RNA|MYL6_ENST00000547649.1_5'Flank|MYL6_ENST00000550697.1_5'Flank			P14649	MYL6B_HUMAN	myosin, light chain 6B, alkali, smooth muscle and non-muscle	120					metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle tissue development (GO:0007519)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|unconventional myosin complex (GO:0016461)	calcium ion binding (GO:0005509)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.R120R(1)		endometrium(2)|kidney(1)|large_intestine(4)	7			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			GCTGAAGTCGCGGCGTGTGGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	12											100	98	99					12																	56549214		2203	4300	6503	54835481	SO:0001819	synonymous_variant	140465			M31211	CCDS8905.1	12q13.2	2013-01-10	2006-09-29			ENSG00000196465		"Myosins / Light chain", "EF-hand domain containing"	29823	protein-coding gene	gene with protein product	"myosin light chain 1 slow a"	609930	"myosin, light polypeptide 6B, alkali, smooth muscle and non-muscle"			2602161, 2304459	Standard	NM_002475		Approved	MLC1SA	uc001sjs.3	P14649		ENST00000553066.1:c.358C>A	12.37:g.56549214C>A			54835481		Silent	SNP	ENST00000553066.1	37	CCDS8905.1																																																																																				0.522	MYL6B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407920.2	NM_002475		A	56549214	C	A	56549214	2	1	6	1	0	0	0	0	0	0	0	1	10082	759	27	2		2	MYL6B	12	56549214	Silent	SNP	C	TCGA-AF-3400-01A-01W-0831-10		56549214	77302681	16	634										
CLN5	1203	hgsc.bcm.edu	37	chr13	77570154	77570154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttccccatctccgacctgaaAtggatgcccctttctggtgt	8	14	2	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr13:77570154A>G	ENST00000377453.3	+	3	1896	c.604A>G	c.(604-606)Atg>Gtg	p.M202V	CLN5_ENST00000485938.1_3'UTR	NM_006493.2	NP_006484.1	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	153					brain development (GO:0007420)|cell death (GO:0008219)|glycosylation (GO:0070085)|lysosomal lumen acidification (GO:0007042)|neurogenesis (GO:0022008)|neuron maturation (GO:0042551)|protein catabolic process (GO:0030163)|signal peptide processing (GO:0006465)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|vacuolar lumen (GO:0005775)	mannose binding (GO:0005537)	p.M202V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		CCGACCTGAAATGGATGCCCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	13											180	164	169					13																	77570154		2203	4300	6503	76468155	SO:0001583	missense	1203				CCDS9456.1	13q21.2-q32	2014-09-17			ENSG00000102805	ENSG00000102805			2076	protein-coding gene	gene with protein product		608102				7942847, 8661106	Standard	NM_006493		Approved		uc001vkc.3	O75503	OTTHUMG00000017100	ENST00000377453.3:c.604A>G	13.37:g.77570154A>G	ENSP00000366673:p.Met202Val		76468155	B3KQK7	Missense_Mutation	SNP	ENST00000377453.3	37	CCDS9456.1	.	.	.	.	.	.	.	.	.	.	A	8.491	0.862124	0.17178	.	.	ENSG00000102805	ENST00000377453;ENST00000541907;ENST00000535238	D	0.87809	-2.3	5.54	4.33	0.51752	.	0.320592	0.41396	N	0.000889	T	0.77315	0.4112	L	0.38838	1.175	0.80722	D	1	B	0.13594	0.008	B	0.12156	0.007	T	0.65129	-0.6243	10	0.08179	T	0.78	-4.5739	8.2022	0.31432	0.7958:0.1338:0.0705:0.0	.	153	O75503	CLN5_HUMAN	V	202;153;68	ENSP00000366673:M202V	ENSP00000366673:M202V	M	+	1	0	CLN5	76468155	0.437000	0.25593	0.995000	0.50966	0.974000	0.67602	1.111000	0.31159	0.901000	0.36495	0.460000	0.39030	ATG		0.428	CLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045318.1	NM_006493		G	77570154	A	G	77570154	3	3	6	1	0	0	0	0	1	0	0	0	3550	101	4	4	614	4	CLN5	13	77570154	Missense_Mutation	SNP	A	TCGA-AF-3400-01A-01W-0831-10		77570154	37599724	17	635										
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24659659	24659659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggctggggtggaatctcccGggcgatgttcttggtgcgac	18	9	2	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr14:24659659G>A	ENST00000261789.4	-	5	1712	c.1354C>T	c.(1354-1356)Cgg>Tgg	p.R452W	TM9SF1_ENST00000556387.1_Missense_Mutation_p.R661W|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000396854.4_Missense_Mutation_p.R452W|TM9SF1_ENST00000528669.1_Missense_Mutation_p.R452W|IPO4_ENST00000354464.6_5'Flank|TM9SF1_ENST00000524835.1_Missense_Mutation_p.R365W|TM9SF1_ENST00000530611.1_Missense_Mutation_p.R661W	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	452					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.R452W(1)|p.R452R(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		GGAATCTCCCGGGCGATGTTC	0.542																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	14											132	111	118					14																	24659659		2203	4300	6503	23729499	SO:0001583	missense	10548			U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.1354C>T	14.37:g.24659659G>A	ENSP00000261789:p.Arg452Trp		23729499	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411296	0.83340	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000530611	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.83889	0.5352	H	0.98388	4.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88545	0.3112	10	0.87932	D	0	-12.3352	11.0074	0.47641	0.0:0.0:0.8139:0.1861	.	452;452	Q86SZ6;O15321	.;TM9S1_HUMAN	W	452;452;661;365;452;661	ENSP00000261789:R452W;ENSP00000432997:R452W;ENSP00000451949:R661W;ENSP00000434387:R365W;ENSP00000380063:R452W;ENSP00000433967:R661W	ENSP00000433967:R661W	R	-	1	2	TM9SF1;RP11-468E2.1	23729499	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.409000	0.52657	2.317000	0.78254	0.655000	0.94253	CGG		0.542	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		A	24659659	G	A	24659659	3	1	6	1	0	0	0	0	1	0	0	0	16016	1115	39	1	517	1	TM9SF1	14	24659659	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10		24659659	82689881	18	636										
NID2	22795	hgsc.bcm.edu	37	chr14	52520996	52520996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtccaacggggaagtgctgcCgatatggaaagcccacactc	12	12	0	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr14:52520996C>T	ENST00000216286.5	-	4	810	c.811G>A	c.(811-813)Ggc>Agc	p.G271S	NID2_ENST00000541773.1_Missense_Mutation_p.G218S	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	271	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)	p.G271S(1)		NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GAAGTGCTGCCGATATGGAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	14											50	50	50					14																	52520996		2203	4300	6503	51590746	SO:0001583	missense	22795			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.811G>A	14.37:g.52520996C>T	ENSP00000216286:p.Gly271Ser		51590746	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156747	0.78114	.	.	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.73897	-0.79;-0.79	5.52	4.64	0.57946	Nidogen, extracellular domain (3);	0.044478	0.85682	N	0.000000	T	0.81851	0.4910	L	0.50847	1.595	0.44462	D	0.997394	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.983;1.0;0.979	T	0.80926	-0.1164	10	0.37606	T	0.19	.	14.306	0.66384	0.0:0.9278:0.0:0.0722	.	218;273;271	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	S	271;218;273	ENSP00000216286:G271S;ENSP00000443730:G218S	ENSP00000216286:G271S	G	-	1	0	NID2	51590746	0.995000	0.38212	0.888000	0.34837	0.442000	0.32017	3.382000	0.52463	1.466000	0.48025	0.655000	0.94253	GGC		0.502	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52520996	C	T	52520996	3	4	6	1	0	0	0	0	1	0	0	0	10446	652	23	1	3392	1	NID2	14	52520996	Missense_Mutation	SNP	C	TCGA-AF-3400-01A-01W-0831-10	27861337	52520996	54828544	19	637										
RPS6KL1	83694	hgsc.bcm.edu	37	chr14	75378075	75378075	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgctcaccatgtggcacctGggtaggctctgggagcagca	14	12	2	0			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr14:75378075G>T	ENST00000555647.1	-	7	827	c.540C>A	c.(538-540)ccC>ccA	p.P180P	RPS6KL1_ENST00000554900.1_5'UTR|RPS6KL1_ENST00000557413.1_Silent_p.P180P|RPS6KL1_ENST00000354625.2_Silent_p.P149P|RPS6KL1_ENST00000358328.4_Silent_p.P180P			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	180	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P180P(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		TGTGGCACCTGGGTAGGCTCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	14											84	74	77					14																	75378075		2203	4300	6503	74447828	SO:0001819	synonymous_variant	83694			BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.540C>A	14.37:g.75378075G>T			74447828	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Silent	SNP	ENST00000555647.1	37	CCDS9834.2																																																																																				0.627	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1			T	75378075	G	T	75378075	2	4	6	1	0	0	0	0	0	0	0	1	13696	1335	47	2		2	RPS6KL1	14	75378075	Silent	SNP	G	TCGA-AF-3400-01A-01W-0831-10	22857079	75378075	31971465	20	638										
CYP46A1	10858	hgsc.bcm.edu	37	chr14	100182494	100182494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ctgaagagggagcccaggacGacgagggtctgctggacaac	16	10	1	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr14:100182494G>A	ENST00000261835.3	+	9	969	c.865G>A	c.(865-867)Gac>Aac	p.D289N	CYP46A1_ENST00000423126.2_Missense_Mutation_p.D192N|CYP46A1_ENST00000554176.1_Missense_Mutation_p.D136N	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	289					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.D289N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				AGCCCAGGACGACGAGGGTCT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	14											112	110	110					14																	100182494		2203	4300	6503	99252247	SO:0001583	missense	10858			AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"Cytochrome P450s"	2641	protein-coding gene	gene with protein product		604087	"cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.865G>A	14.37:g.100182494G>A	ENSP00000261835:p.Asp289Asn		99252247	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	37	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.80|13.80	2.344361|2.344361	0.41498|0.41498	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000261835;ENST00000423126;ENST00000554176;ENST00000556313|ENST00000380228	T;T;T;T|.	0.71222|.	-0.55;-0.55;-0.55;-0.55|.	4.77|4.77	4.77|4.77	0.60923|0.60923	.|.	0.393031|.	0.27604|.	N|.	0.018640|.	T|T	0.60650|0.60650	0.2285|0.2285	L|L	0.46885|0.46885	1.475|1.475	0.36038|0.36038	D|D	0.8399|0.8399	B;P|.	0.44344|.	0.104;0.833|.	B;B|.	0.39119|.	0.048;0.291|.	T|T	0.65957|0.65957	-0.6042|-0.6042	10|5	0.27785|.	T|.	0.31|.	.|.	13.6794|13.6794	0.62474|0.62474	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	136;289|.	Q8N2B0;Q9Y6A2|.	.;CP46A_HUMAN|.	N|Q	289;192;136;42|275	ENSP00000261835:D289N;ENSP00000405779:D192N;ENSP00000450553:D136N;ENSP00000451602:D42N|.	ENSP00000261835:D289N|.	D|R	+|+	1|2	0|0	CYP46A1|CYP46A1	99252247|99252247	1.000000|1.000000	0.71417|0.71417	0.729000|0.729000	0.30791|0.30791	0.626000|0.626000	0.37791|0.37791	6.110000|6.110000	0.71535|0.71535	2.371000|2.371000	0.80710|0.80710	0.561000|0.561000	0.74099|0.74099	GAC|CGA		0.512	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			A	100182494	G	A	100182494	3	1	6	1	0	0	0	0	1	0	0	0	4188	1058	37	1	899	1	CYP46A1	14	100182494	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	24804419	100182494	7167046	21	639										
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100594247	100594247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgttgatggaccccttacccGagtctttgagagctagaaag	11	9	1	3	rs143817747	byFrequency	TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr15:100594247G>A	ENST00000268070.4	-	16	2255	c.2150C>T	c.(2149-2151)tCg>tTg	p.S717L		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	717	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S717L(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	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)		CCCCTTACCCGAGTCTTTGAG	0.532													G|||	3	0.000599042	0	0	5008	,	,		17330	0		0.003	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15						G	LEU/SER	0,4406		0,0,2203	106	111	109		2150	5	0.4	15	dbSNP_134	109	8,8592	5.7+/-21.5	0,8,4292	yes	missense	ADAMTS17	NM_139057.2	145	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	benign	717/1096	100594247	8,12998	2203	4300	6503	98411770	SO:0001583	missense	170691			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2150C>T	15.37:g.100594247G>A	ENSP00000268070:p.Ser717Leu		98411770	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.53	3.844130	0.71488	0.0	9.3E-4	ENSG00000140470	ENST00000268070	T	0.52983	0.64	5.97	5.04	0.67666	ADAM-TS Spacer 1 (1);	0.147808	0.44902	D	0.000403	T	0.39226	0.1070	L	0.33668	1.02	0.50039	D	0.999847	D	0.53151	0.958	B	0.41917	0.37	T	0.15492	-1.0435	10	0.27785	T	0.31	.	16.5202	0.84312	0.0:0.0:0.868:0.132	.	717	Q8TE56	ATS17_HUMAN	L	717	ENSP00000268070:S717L	ENSP00000268070:S717L	S	-	2	0	ADAMTS17	98411770	1.000000	0.71417	0.435000	0.26784	0.881000	0.50899	9.235000	0.95353	1.511000	0.48818	0.655000	0.94253	TCG		0.532	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100594247	G	A	100594247	3	1	6	1	0	0	0	0	1	0	0	0	262	1059	37	1	1165	1	ADAMTS17	15	100594247	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10		100594247	1937145	22	640										
NDE1	54820	hgsc.bcm.edu	37	chr16	15790583	15790583	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	caggcactggagtccaaactCgcttcctgccggaacctcgt	10	15	0	0	rs534864382		TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr16:15790583C>T	ENST00000396353.2	+	9	1639	c.813C>T	c.(811-813)ctC>ctT	p.L271L	NDE1_ENST00000396354.1_Silent_p.L271L|NDE1_ENST00000396355.1_Silent_p.L271L|NDE1_ENST00000342673.5_Silent_p.L271L			Q9NXR1	NDE1_HUMAN	nudE neurodevelopment protein 1	271	Interaction with CENPF. {ECO:0000250}.				centrosome duplication (GO:0051298)|cerebral cortex development (GO:0021987)|establishment of chromosome localization (GO:0051303)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuroblast proliferation (GO:0007405)|neuron migration (GO:0001764)|vesicle transport along microtubule (GO:0047496)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole centrosome (GO:0031616)	microtubule binding (GO:0008017)	p.L271L(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						AGTCCAAACTCGCTTCCTGCC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	16											82	83	83					16																	15790583		2197	4300	6497	15698084	SO:0001819	synonymous_variant	54820			AF124431	CCDS10564.1	16p13.11	2013-08-06	2013-08-06		ENSG00000072864	ENSG00000072864			17619	protein-coding gene	gene with protein product		609449	"nudE nuclear distribution gene E homolog 1 (A. nidulans)", "nudE nuclear distribution E homolog 1 (A. nidulans)"			10940388, 12427674	Standard	NM_017668		Approved	nudE, FLJ20101, NDE	uc002dds.3	Q9NXR1	OTTHUMG00000129885	ENST00000396353.2:c.813C>T	16.37:g.15790583C>T			15698084	Q49AQ2	Silent	SNP	ENST00000396353.2	37																																																																																					0.542	NDE1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017668		T	15790583	C	T	15790583	2	4	6	1	0	0	0	0	0	0	0	1	10274	871	31	1		1	NDE1	16	15790583	Silent	SNP	C	TCGA-AF-3400-01A-01W-0831-10		15790583	74564170	23	641										
CES7	221223	hgsc.bcm.edu	37	chr16	55907805	55907805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcgatgcaggctgcgggttcGtaaatcgcagggatcccagc	15	11	0	0	rs570591787	byFrequency	TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr16:55907805G>A	ENST00000290567.9	-	2	339	c.218C>T	c.(217-219)aCg>aTg	p.T73M	CES5A_ENST00000541580.1_Intron|CES5A_ENST00000521992.1_Missense_Mutation_p.T102M|CES5A_ENST00000319165.9_Missense_Mutation_p.T73M|CES5A_ENST00000518005.1_De_novo_Start_OutOfFrame|CES5A_ENST00000520435.1_Missense_Mutation_p.T73M	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	73						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)	p.T73M(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						CTGCGGGTTCGTAAATCGCAG	0.587													G|||	4	0.000798722	0	0	5008	,	,		18885	0		0	False		,,,				2504	0.0041															1	Substitution - Missense(1)	large_intestine(1)	16											75	69	71					16																	55907805		2198	4300	6498	54465306	SO:0001583	missense	221223			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.218C>T	16.37:g.55907805G>A	ENSP00000290567:p.Thr73Met		54465306	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	g	16.13	3.037076	0.54896	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000290567;ENST00000520435	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.7	2.6	0.31112	Carboxylesterase, type B (1);	1.461070	0.04463	N	0.374715	T	0.62356	0.2421	N	0.11154	0.105	0.09310	N	1	D;D	0.65815	0.995;0.964	P;B	0.55545	0.778;0.417	T	0.55464	-0.8137	10	0.62326	D	0.03	.	8.3591	0.32348	0.0738:0.0:0.6368:0.2894	.	73;73	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	M	102;73;73;73	ENSP00000428864:T102M;ENSP00000324271:T73M;ENSP00000290567:T73M;ENSP00000428887:T73M	ENSP00000290567:T73M	T	-	2	0	CES5A	54465306	0.769000	0.28531	0.001000	0.08648	0.001000	0.01503	2.418000	0.44662	0.394000	0.25230	-0.119000	0.15052	ACG		0.587	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		A	55907805	G	A	55907805	3	1	6	1	0	0	0	0	1	0	0	0	3278	1145	40	1	1557	1	CES7	16	55907805	Missense_Mutation	SNP	G	TCGA-AF-3400-01A-01W-0831-10	40117222	55907805	34446948	24	642										
TP53	7157	hgsc.bcm.edu	37	chr17	7578265	7578265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaaatttccttccactcggAtaagatgctgaggaggggcc	12	10	0	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr17:7578265A>G	ENST00000269305.4	-	6	773	c.584T>C	c.(583-585)aTc>aCc	p.I195T	TP53_ENST00000445888.2_Missense_Mutation_p.I195T|TP53_ENST00000455263.2_Missense_Mutation_p.I195T|TP53_ENST00000420246.2_Missense_Mutation_p.I195T|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.I195T|TP53_ENST00000413465.2_Missense_Mutation_p.I195T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195T(69)|p.I195N(12)|p.I195S(10)|p.0?(8)|p.I195fs*14(5)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102S(2)|p.I102T(2)|p.I63T(2)|p.I63S(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.I102fs*14(1)|p.I195fs*12(1)|p.I195fs*50(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I63fs*14(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCCACTCGGATAAGATGCTG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	134	Substitution - Missense(99)|Whole gene deletion(8)|Insertion - Frameshift(7)|Deletion - In frame(6)|Complex - deletion inframe(6)|Unknown(5)|Deletion - Frameshift(2)|Complex - frameshift(1)	ovary(37)|breast(21)|large_intestine(18)|lung(10)|central_nervous_system(8)|biliary_tract(6)|haematopoietic_and_lymphoid_tissue(5)|skin(5)|stomach(4)|oesophagus(4)|bone(4)|endometrium(3)|urinary_tract(3)|upper_aerodigestive_tract(2)|liver(2)|pancreas(2)	17											100	89	93					17																	7578265		2203	4300	6503	7518990	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.584T>C	17.37:g.7578265A>G	ENSP00000269305:p.Ile195Thr		7518990	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324656	0.41197	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99823	-6.95;-6.95;-6.95;-6.95;-6.95;-6.95;-6.95;-6.95	5.41	3.21	0.36854	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	N	0.000004	D	0.99785	0.9910	M	0.90019	3.08	0.52099	D	0.999943	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.991;0.989;0.998;0.997;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.995;0.953;0.979;0.995;0.993;0.996	D	0.98429	1.0581	10	0.87932	D	0	-18.4587	8.2743	0.31864	0.8356:0.0:0.1644:0.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	T	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195T;ENSP00000352610:I195T;ENSP00000269305:I195T;ENSP00000398846:I195T;ENSP00000391127:I195T;ENSP00000391478:I195T;ENSP00000425104:I63T;ENSP00000423862:I102T	ENSP00000269305:I195T	I	-	2	0	TP53	7518990	1.000000	0.71417	0.946000	0.38457	0.026000	0.11368	9.287000	0.95975	0.456000	0.26937	-0.256000	0.11100	ATC		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578265	A	G	7578265	3	3	6	1	0	0	0	0	1	0	0	0	16421	333	12	4	710	4	TP53	17	7578265	Missense_Mutation	SNP	A	TCGA-AF-3400-01A-01W-0831-10		7578265	73616945	25	643										
PSME3	10197	hgsc.bcm.edu	37	chr17	40990741	40990741	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtcctcatatatgttttgaCctccaggtcaaaatgtgggt	10	8	2	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr17:40990741C>A	ENST00000590720.1	+	7	638				PSME3_ENST00000592169.1_Intron|PSME3_ENST00000293362.3_Missense_Mutation_p.D146E|PSME3_ENST00000545225.1_Intron|PSME3_ENST00000441946.2_Intron|PSME3_ENST00000541124.1_Intron			P61289	PSME3_HUMAN	proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)	p.D146E(1)		NS(1)|cervix(1)|large_intestine(3)|lung(1)	6		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		TATGTTTTGACCTCCAGGTCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17											81	83	82					17																	40990741		2203	4300	6503	38244267	SO:0001627	intron_variant	10197			U11292	CCDS11442.1, CCDS45689.1, CCDS59290.1	17q12-q21	2004-02-17				ENSG00000131467		"Proteasome (prosome, macropain) subunits"	9570	protein-coding gene	gene with protein product		605129				7951316	Standard	NM_005789		Approved	Ki, PA28-gamma, REG-GAMMA, PA28G	uc002ibq.4	P61289		ENST00000590720.1:c.406-7C>A	17.37:g.40990741C>A			38244267	A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9	Missense_Mutation	SNP	ENST00000590720.1	37	CCDS45689.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270662	0.40194	.	.	ENSG00000131467	ENST00000293362	T	0.21361	2.01	5.04	-0.551	0.11822	.	1.665370	0.03485	N	0.215691	T	0.11665	0.0284	.	.	.	0.09310	N	1	B	0.15141	0.012	B	0.11329	0.006	T	0.21999	-1.0229	9	0.24483	T	0.36	-23.7537	2.2556	0.04054	0.1154:0.4155:0.2486:0.2205	.	146	P61289-2	.	E	146	ENSP00000293362:D146E	ENSP00000293362:D146E	D	+	3	2	PSME3	38244267	0.000000	0.05858	0.000000	0.03702	0.330000	0.28571	0.046000	0.14035	0.044000	0.15775	0.655000	0.94253	GAC		0.453	PSME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452430.1	NM_176863		A	40990741	C	A	40990741	1	1	6	0	1	0	0	0	0	0	0	0	12742	506	18	2		2	PSME3	17	40990741	Intron	SNP	C	TCGA-AF-3400-01A-01W-0831-10	33412476	40990741	40204469	26	644										
RUNDC1	146923	hgsc.bcm.edu	37	chr17	41142452	41142452	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgcctccaggaaacagcaaAagtaagtgcagtttccagaa	9	10	0	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr17:41142452A>G	ENST00000361677.1	+	4	987	c.975A>G	c.(973-975)aaA>aaG	p.K325K		NM_173079.2	NP_775102	Q96C34	RUND1_HUMAN	RUN domain containing 1	325								p.K325K(1)		breast(1)|large_intestine(2)|lung(4)|prostate(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		GAAACAGCAAAAGTAAGTGCA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	17											63	64	64					17																	41142452		2203	4300	6503	38395978	SO:0001630	splice_region_variant	146923			AL831813	CCDS11448.1	17q21.31	2004-02-27				ENSG00000198863			25418	protein-coding gene	gene with protein product						12477932	Standard	NM_173079		Approved	DKFZp761H0421	uc002ici.1	Q96C34		ENST00000361677.1:c.976+1A>G	17.37:g.41142452A>G			38395978	Q6Y2K8|Q8IXT9|Q8N3W1	Silent	SNP	ENST00000361677.1	37	CCDS11448.1																																																																																				0.522	RUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452464.1	NM_173079	Silent	G	41142452	A	G	41142452	5	3	6	1	0	0	0	0	0	0	1	0	13779	28	1	4	989	4	RUNDC1	17	41142452	Splice_Site	SNP	A	TCGA-AF-3400-01A-01W-0831-10	151711	41142452	40052758	27	645										
USP29	57663	hgsc.bcm.edu	37	chr19	57641702	57641702	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccacctcttcccttgagcagTagtgcacctgttgggaaatg	10	12	1	1			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr19:57641702T>C	ENST00000254181.4	+	4	2113	c.1659T>C	c.(1657-1659)agT>agC	p.S553S	USP29_ENST00000598197.1_Silent_p.S553S	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	553	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.S553S(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTTGAGCAGTAGTGCACCTG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	19											130	140	136					19																	57641702		2203	4300	6503	62333514	SO:0001819	synonymous_variant	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1659T>C	19.37:g.57641702T>C			62333514		Silent	SNP	ENST00000254181.4	37	CCDS33124.1																																																																																				0.423	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			C	57641702	T	C	57641702	2	2	6	1	0	0	0	0	0	0	0	1	17099	1635	57	4		4	USP29	19	57641702	Silent	SNP	T	TCGA-AF-3400-01A-01W-0831-10		57641702	1487281	28	646										
SOX12	6666	hgsc.bcm.edu	37	chr20	306702	306702	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccacatcaagaggccgatgaAcgcattcatggtgtggtcgc	12	11	2	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chr20:306702A>G	ENST00000342665.2	+	1	464	c.134A>G	c.(133-135)aAc>aGc	p.N45S	RP5-1103G7.4_ENST00000414676.1_RNA|SOX12_ENST00000544632.1_Missense_Mutation_p.N45S|RP5-1103G7.4_ENST00000442637.1_RNA	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	45					cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.N45S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			AGGCCGATGAACGCATTCATG	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	20											27	22	23					20																	306702		2202	4298	6500	254702	SO:0001583	missense	6666			U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732		"SRY (sex determining region Y)-boxes"	11198	protein-coding gene	gene with protein product		601947	"SRY (sex determining region Y)-box 22"	SOX22		9215677	Standard	NM_006943		Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.134A>G	20.37:g.306702A>G	ENSP00000347646:p.Asn45Ser		254702	Q5D038|Q9NUD4	Missense_Mutation	SNP	ENST00000342665.2	37	CCDS12995.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.811277	0.70797	.	.	ENSG00000177732	ENST00000544632;ENST00000342665	D;D	0.93426	-3.22;-3.22	3.63	3.63	0.41609	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.50627	U	0.000104	D	0.95326	0.8483	M	0.68317	2.08	0.58432	D	0.999994	D	0.76494	0.999	D	0.81914	0.995	D	0.95131	0.8255	10	0.87932	D	0	.	10.2285	0.43241	1.0:0.0:0.0:0.0	.	45	O15370	SOX12_HUMAN	S	45	ENSP00000441671:N45S;ENSP00000347646:N45S	ENSP00000347646:N45S	N	+	2	0	SOX12	254702	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	8.240000	0.89813	1.513000	0.48852	0.260000	0.18958	AAC		0.721	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943		G	306702	A	G	306702	3	3	6	1	0	0	0	0	1	0	0	0	14980	43	2	4	136	4	SOX12	20	306702	Missense_Mutation	SNP	A	TCGA-AF-3400-01A-01W-0831-10		306702	62718818	29	647										
CAPN6	827	hgsc.bcm.edu	37	chrX	110496397	110496397	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaaatatcccagcgtatttTtctgttttttgagggtccca	8	8	1	2			TCGA-AF-3400-01A-01W-0831-10	TCGA-AF-3400-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1b98a28c-12c2-4694-9710-93b2d9db8bb9	ae4b6297-db40-4acc-b397-86583d13fddd	g.chrX:110496397T>G	ENST00000324068.1	-	4	512	c.345A>C	c.(343-345)gaA>gaC	p.E115D	CAPN6_ENST00000541758.1_5'UTR	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	115	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)	p.E115D(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						CAGCGTATTTTTCTGTTTTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											106	102	103					X																	110496397		2203	4300	6503	110383053	SO:0001583	missense	827			AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.345A>C	X.37:g.110496397T>G	ENSP00000317214:p.Glu115Asp		110383053	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	37	CCDS14555.1	.	.	.	.	.	.	.	.	.	.	t	3.849	-0.032208	0.07543	.	.	ENSG00000077274	ENST00000324068	D	0.88975	-2.45	5.97	-2.76	0.05896	Peptidase C2, calpain, catalytic domain (3);	0.461885	0.25101	N	0.033121	T	0.73598	0.3607	L	0.28115	0.83	0.44012	D	0.996723	B	0.06786	0.001	B	0.12156	0.007	T	0.50947	-0.8767	10	0.15499	T	0.54	.	2.8905	0.05675	0.1811:0.4832:0.1541:0.1816	.	115	Q9Y6Q1	CAN6_HUMAN	D	115	ENSP00000317214:E115D	ENSP00000317214:E115D	E	-	3	2	CAPN6	110383053	0.989000	0.36119	0.987000	0.45799	0.941000	0.58515	0.363000	0.20301	-0.545000	0.06224	-0.320000	0.08662	GAA		0.408	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			G	110496397	T	G	110496397	3	3	6	1	0	0	0	0	1	0	0	0	2636	1838	64	4	1620	4	CAPN6	23	110496397	Missense_Mutation	SNP	T	TCGA-AF-3400-01A-01W-0831-10		110496397	44774163	30	648										
KIAA0495	57212	broad.mit.edu	37	chr1	3662495	3662495	+	RNA	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	actgctggtatctttacttgGaaagcaggaaacactgaaag	10	7	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:3662495G>C	ENST00000452079.1	-	0	1391				TP73-AS1_ENST00000418088.1_RNA|TP73-AS1_ENST00000544565.1_RNA|TP73-AS1_ENST00000423764.1_RNA|TP73-AS1_ENST00000608600.1_RNA	NR_033711.1		Q9UF72	T73AS_HUMAN	TP73 antisense RNA 1							extracellular region (GO:0005576)											TCTTTACTTGGAAAGCAGGAA	0.592																																																0			1											65	73	71					1																	3662495		2068	4213	6281	3652355			57212					1p36.32	2014-01-20	2014-01-20	2014-01-20	ENSG00000227372	ENSG00000227372		"Long non-coding RNAs"	29052	non-coding RNA	RNA, long non-coding	"p53-dependent apoptosis modulator"		"KIAA0495"	KIAA0495		9455484, 20477830, 23726844	Standard	NR_033708		Approved	PDAM	uc009vlm.3	Q9UF72	OTTHUMG00000003414		1.37:g.3662495G>C			3652355		Missense_Mutation	SNP	ENST00000452079.1	37																																																																																					0.592	TP73-AS1-003	KNOWN	basic	antisense	antisense	OTTHUMT00000009558.1	NR_033708		C	3662495	G	C	3662495	1	2	7	0	1	0	0	0	0	0	0	0	8201	1165	41	5		5	KIAA0495	1	3662495	RNA	SNP	G	TCGA-AF-3913-01A-02W-1073-09		3662495	245588126	1	649										
CTRC	11330	broad.mit.edu	37	chr1	15768968	15768968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cccggacctaccgtgtggccGtgggaaagaacaacctggag	14	12	0	1	rs367979183		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:15768968G>A	ENST00000375949.4	+	4	282	c.256G>A	c.(256-258)Gtg>Atg	p.V86M	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_Silent_p.P22P	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	86	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.V86M(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCGTGTGGCCGTGGGAAAGAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	MET/VAL	0,4406		0,0,2203	132	87	102		256	2.5	1	1		102	1,8599		0,1,4299	no	missense	CTRC	NM_007272.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	86/269	15768968	1,13005	2203	4300	6503	15641555	SO:0001583	missense	11330			BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.256G>A	1.37:g.15768968G>A	ENSP00000365116:p.Val86Met		15641555	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	.	.	.	.	.	.	.	.	.	.	.	6.056	0.378699	0.11466	0.0	1.16E-4	ENSG00000162438	ENST00000375949	D	0.89552	-2.53	4.39	2.52	0.30459	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.239260	0.35436	N	0.003206	D	0.83142	0.5190	L	0.53729	1.69	0.80722	D	1	B;B	0.29612	0.251;0.039	B;B	0.23018	0.043;0.017	T	0.81104	-0.1084	10	0.59425	D	0.04	-11.4298	7.8498	0.29448	0.0:0.5931:0.3171:0.0898	.	86;86	A8MTQ9;Q99895	.;CTRC_HUMAN	M	86	ENSP00000365116:V86M	ENSP00000365116:V86M	V	+	1	0	CTRC	15641555	0.004000	0.15560	0.999000	0.59377	0.017000	0.09413	-0.006000	0.12833	1.204000	0.43247	-0.234000	0.12200	GTG		0.617	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		A	15768968	G	A	15768968	3	1	7	1	0	0	0	0	1	0	0	0	4033	1145	40	1	270	1	CTRC	1	15768968	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	12106473	15768968	233481653	2	650										
GJA4	2701	broad.mit.edu	37	chr1	35260477	35260477	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtggttggactcatctccctGgtgcttaacctgctggagtt	12	10	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:35260477G>A	ENST00000342280.4	+	2	751	c.663G>A	c.(661-663)ctG>ctA	p.L221L		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	221					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)		p.L221L(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TCATCTCCCTGGTGCTTAACC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	87	89					1																	35260477		2203	4300	6503	35033064	SO:0001819	synonymous_variant	2701			M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"Ion channels / Gap junction proteins (connexins)"	4278	protein-coding gene	gene with protein product	"connexin 37"	121012	"gap junction protein, alpha 4, 37kD (connexin 37)", "gap junction protein, alpha 4, 37kDa (connexin 37)"			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.663G>A	1.37:g.35260477G>A			35033064	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Silent	SNP	ENST00000342280.4	37	CCDS30669.1																																																																																				0.617	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		A	35260477	G	A	35260477	2	1	7	1	0	0	0	0	0	0	0	1	6423	1335	47	3		3	GJA4	1	35260477	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	19491509	35260477	213990144	3	651										
RIMS3	9783	broad.mit.edu	37	chr1	41101660	41101660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cctggcgtgtgacccggctcCgcatctccaccgcgatgcct	11	18	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:41101660C>T	ENST00000372684.3	-	4	756	c.287G>A	c.(286-288)cGg>cAg	p.R96Q	RIMS3_ENST00000372683.1_Missense_Mutation_p.R96Q	NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	96					calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)		p.R96Q(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GACCCGGCTCCGCATCTCCAC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	64	66					1																	41101660		2203	4300	6503	40874247	SO:0001583	missense	9783			BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016			21292	protein-coding gene	gene with protein product		611600				12620390, 10748113	Standard	NM_014747		Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.287G>A	1.37:g.41101660C>T	ENSP00000361769:p.Arg96Gln		40874247	D3DPV8|Q92511|X5D7U7	Missense_Mutation	SNP	ENST00000372684.3	37	CCDS30687.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.329311	0.81690	.	.	ENSG00000117016	ENST00000372684;ENST00000372683	T;T	0.37411	1.2;1.2	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	P	0.53593	0.73	T	0.24333	-1.0163	10	0.51188	T	0.08	-24.1876	15.9164	0.79521	0.0:1.0:0.0:0.0	.	96	Q9UJD0	RIMS3_HUMAN	Q	96	ENSP00000361769:R96Q;ENSP00000361768:R96Q	ENSP00000361768:R96Q	R	-	2	0	RIMS3	40874247	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.575000	0.82447	2.626000	0.88956	0.650000	0.86243	CGG		0.682	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019585.1	NM_014747		T	41101660	C	T	41101660	3	4	7	1	0	0	0	0	1	0	0	0	13406	652	23	1	659	1	RIMS3	1	41101660	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	5841183	41101660	208148961	4	652										
FPGT	8790	broad.mit.edu	37	chr1	74670203	74670203	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	acattgatttccccttaaatAtgaatcctggaattctggtt	6	8	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:74670203A>C	ENST00000609362.1	+	4	509	c.472A>C	c.(472-474)Atg>Ctg	p.M158L	FPGT_ENST00000467578.2_3'UTR|TNNI3K_ENST00000370891.2_Intron|FPGT_ENST00000370894.5_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.M171L|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	158					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.M158L(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						CCCCTTAAATATGAATCCTGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											109	112	111					1																	74670203		2203	4300	6503	74442791	SO:0001583	missense	8790			AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.472A>C	1.37:g.74670203A>C	ENSP00000476680:p.Met158Leu		74442791	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	CCDS663.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784334	0.70222	.	.	ENSG00000254685	ENST00000370898;ENST00000472069	T;T	0.31510	1.49;1.49	5.57	4.45	0.53987	L-fucokinase (1);	.	.	.	.	T	0.24812	0.0602	M	0.65975	2.015	0.80722	D	1	P	0.40681	0.727	P	0.48840	0.592	T	0.05305	-1.0893	9	0.13853	T	0.58	.	10.9181	0.47148	0.9269:0.0:0.0731:0.0	.	158	O14772	FPGT_HUMAN	L	158;156	ENSP00000359935:M158L;ENSP00000433499:M156L	ENSP00000359935:M158L	M	+	1	0	TNNI3K	74442791	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.175000	0.77632	2.116000	0.64780	0.482000	0.46254	ATG		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	74670203	A	C	74670203	3	2	7	1	0	0	0	0	1	0	0	0	6056	449	16	4	486	4	FPGT	1	74670203	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09	33568543	74670203	174580418	5	653										
EXTL2	2135	broad.mit.edu	37	chr1	101343241	101343241	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtttcaataagagatctgttCtgttgtacgtctgcattatg	9	6	4	1	rs200323785		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:101343241C>G	ENST00000370114.3	-	3	1660	c.224G>C	c.(223-225)aGa>aCa	p.R75T	EXTL2_ENST00000535414.1_Missense_Mutation_p.R62T|EXTL2_ENST00000370113.3_Missense_Mutation_p.R75T	NM_001033025.2|NM_001261440.1	NP_001028197.1|NP_001248369.1	Q9UBQ6	EXTL2_HUMAN	exostosin-like glycosyltransferase 2	75					heparan sulfate proteoglycan biosynthetic process (GO:0015012)|N-acetylglucosamine metabolic process (GO:0006044)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	alpha-1,4-N-acetylgalactosaminyltransferase activity (GO:0035248)|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.R75T(1)|p.R83T(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	14		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)		GAGATCTGTTCTGTTGTACGT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	1											131	130	130					1																	101343241		2203	4300	6503	101115829	SO:0001583	missense	2135			U76189	CCDS775.1, CCDS72831.1	1p21	2013-03-01	2013-03-01		ENSG00000162694	ENSG00000162694	2.4.1.223	"Exostosin glycosyltransferase family"	3516	protein-coding gene	gene with protein product	"alpha-1,4-N-acteylhexosaminyltransferase"	602411	"exostoses (multiple)-like 2"			9450183, 15831490	Standard	NM_001439		Approved		uc001dtk.2	Q9UBQ6	OTTHUMG00000011814	ENST00000370114.3:c.224G>C	1.37:g.101343241C>G	ENSP00000359132:p.Arg75Thr		101115829	B2R795|D3DT60	Missense_Mutation	SNP	ENST00000370114.3	37	CCDS775.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908908	0.92107	.	.	ENSG00000162694	ENST00000370114;ENST00000370113;ENST00000535414;ENST00000450240;ENST00000416479	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	5.61	5.61	0.85477	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.91713	0.7380	M	0.91872	3.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.92562	0.6059	10	0.87932	D	0	-27.9273	20.0018	0.97417	0.0:1.0:0.0:0.0	.	75;75	Q8N8F1;Q9UBQ6	.;EXTL2_HUMAN	T	75;75;62;83;62	ENSP00000359132:R75T;ENSP00000359131:R75T;ENSP00000444385:R62T;ENSP00000403363:R83T;ENSP00000392255:R62T	ENSP00000359131:R75T	R	-	2	0	EXTL2	101115829	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.445000	0.80570	2.793000	0.96121	0.655000	0.94253	AGA		0.398	EXTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032705.1	NM_001439		G	101343241	C	G	101343241	3	3	7	1	0	0	0	0	1	0	0	0	5339	913	32	5	780	5	EXTL2	1	101343241	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	26673038	101343241	147907380	6	654										
NRAS	4893	broad.mit.edu	37	chr1	115256528	115256528	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctcatggcactgtactcttcTtgtccagctgtatccagtat	7	12	3	0	rs121913255		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:115256528T>G	ENST00000369535.4	-	3	436	c.183A>C	c.(181-183)caA>caC	p.Q61H		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61H(100)|p.Q61Q(3)|p.Q61L(3)|p.Q61R(2)|p.Q61K(1)|p.Q61_E62>HK(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		TGTACTCTTCTTGTCCAGCTG	0.463	Q61H(ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61H(RD_SOFT_TISSUE)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	110	Substitution - Missense(106)|Substitution - coding silent(3)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(48)|skin(43)|soft_tissue(8)|thyroid(6)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|NS(1)	1											180	156	164					1																	115256528		2203	4300	6503	115058051	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.183A>C	1.37:g.115256528T>G	ENSP00000358548:p.Gln61His		115058051	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.585934	0.66105	.	.	ENSG00000213281	ENST00000369535	D	0.84146	-1.81	5.08	3.93	0.45458	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.87026	0.6075	H	0.94385	3.53	0.80722	D	1	B	0.30763	0.294	B	0.42087	0.375	D	0.89247	0.3588	10	0.72032	D	0.01	.	5.8174	0.18500	0.0:0.1721:0.0:0.8279	.	61	P01111	RASN_HUMAN	H	61	ENSP00000358548:Q61H	ENSP00000358548:Q61H	Q	-	3	2	NRAS	115058051	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.898000	0.28404	2.120000	0.65058	0.533000	0.62120	CAA		0.463	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		G	115256528	T	G	115256528	3	3	7	1	0	0	0	0	1	0	0	0	10671	1606	56	4	398	4	NRAS	1	115256528	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	13913287	115256528	133994093	7	655										
SPAG17	200162	broad.mit.edu	37	chr1	118558619	118558619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	caggatctgtggcctgaaagGataacaatggggtcaagtct	13	7	3	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:118558619G>T	ENST00000336338.5	-	29	4321	c.4256C>A	c.(4255-4257)tCc>tAc	p.S1419Y		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1419						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.S1419Y(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGCCTGAAAGGATAACAATGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	162	159					1																	118558619		2203	4300	6503	118360142	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4256C>A	1.37:g.118558619G>T	ENSP00000337804:p.Ser1419Tyr		118360142	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	7.908	0.735938	0.15574	.	.	ENSG00000155761	ENST00000336338	T	0.20069	2.1	4.98	2.04	0.26737	.	0.457000	0.24511	N	0.037884	T	0.08492	0.0211	L	0.56769	1.78	0.22156	N	0.999327	P	0.44044	0.825	B	0.39935	0.314	T	0.10823	-1.0613	10	0.56958	D	0.05	.	7.6275	0.28220	0.2821:0.0:0.7179:0.0	.	1419	Q6Q759	SPG17_HUMAN	Y	1419	ENSP00000337804:S1419Y	ENSP00000337804:S1419Y	S	-	2	0	SPAG17	118360142	1.000000	0.71417	0.313000	0.25210	0.331000	0.28603	1.873000	0.39558	0.140000	0.18849	0.460000	0.39030	TCC		0.413	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118558619	G	T	118558619	3	4	7	1	0	0	0	0	1	0	0	0	15018	1174	41	2	2495	2	SPAG17	1	118558619	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	3302091	118558619	130692002	8	656										
FLG2	388698	broad.mit.edu	37	chr1	152328756	152328756	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ccatgctgtccaaagccagaGgactgacctgagcctgaccc	10	15	0	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:152328756G>T	ENST00000388718.5	-	3	1578	c.1506C>A	c.(1504-1506)tcC>tcA	p.S502S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	502	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S502S(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAAAGCCAGAGGACTGACCTG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											232	231	232					1																	152328756		2203	4300	6503	150595380	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1506C>A	1.37:g.152328756G>T			150595380	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.522	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152328756	G	T	152328756	2	4	7	1	0	0	0	0	0	0	0	1	5942	987	35	2		2	FLG2	1	152328756	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	33770137	152328756	96921865	9	657										
LCE3D	84648	broad.mit.edu	37	chr1	152552262	152552262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtggtggttcaggaagcagcCgccctcggagctagggccac	16	12	1	0	rs145962377	byFrequency	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:152552262C>T	ENST00000368787.3	-	2	207	c.151G>A	c.(151-153)Ggc>Agc	p.G51S		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	51					keratinization (GO:0031424)			p.G51S(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGGAAGCAGCCGCCCTCGGAG	0.672													C|||	2	0.000399361	8e-04	0	5008	,	,		15382	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	46	55	52		151	1.7	0.4	1	dbSNP_134	52	5,8587	3.7+/-12.6	0,5,4291	no	missense	LCE3D	NM_032563.1	56	0,6,6493	TT,TC,CC		0.0582,0.0227,0.0462	benign	51/93	152552262	6,12992	2203	4296	6499	150818886	SO:0001583	missense	84648			BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"Late cornified envelopes"	16615	protein-coding gene	gene with protein product		612616	"small proline rich-like (epidermal differentiation complex) 6B"	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.151G>A	1.37:g.152552262C>T	ENSP00000357776:p.Gly51Ser		150818886	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	37	CCDS1014.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	11.02	1.516689	0.27123	2.27E-4	5.82E-4	ENSG00000163202	ENST00000368787	T	0.04603	3.59	3.6	1.68	0.24146	.	.	.	.	.	T	0.01189	0.0039	.	.	.	0.23978	N	0.996284	B	0.31968	0.349	B	0.21708	0.036	T	0.46898	-0.9158	8	0.87932	D	0	.	5.89	0.18904	0.0:0.7473:0.0:0.2527	.	51	Q9BYE3	LCE3D_HUMAN	S	51	ENSP00000357776:G51S	ENSP00000357776:G51S	G	-	1	0	LCE3D	150818886	0.235000	0.23794	0.421000	0.26609	0.937000	0.57800	0.305000	0.19254	0.326000	0.23384	0.655000	0.94253	GGC		0.672	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563		T	152552262	C	T	152552262	3	4	7	1	0	0	0	0	1	0	0	0	8694	652	23	1	131	1	LCE3D	1	152552262	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	223506	152552262	96698359	10	658										
UBAP2L	9898	broad.mit.edu	37	chr1	154224110	154224110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	caagccaggctccaagtagcCtgtataccagcacggccagg	11	14	0	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:154224110C>A	ENST00000361546.2	+	13	1687	c.1645C>A	c.(1645-1647)Ctg>Atg	p.L549M	UBAP2L_ENST00000428931.1_Missense_Mutation_p.L549M|UBAP2L_ENST00000343815.6_Missense_Mutation_p.L549M|UBAP2L_ENST00000271877.7_Missense_Mutation_p.L560M|AL590431.1_ENST00000517008.1_RNA			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	549					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.L549M(1)|p.L45M(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCCAAGTAGCCTGTATACCAG	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	1											77	79	78					1																	154224110		2203	4300	6503	152490734	SO:0001583	missense	9898			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1645C>A	1.37:g.154224110C>A	ENSP00000355343:p.Leu549Met		152490734	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101774	0.76983	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.16073	2.39;2.4;2.37;2.4	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	L	0.57536	1.79	0.58432	D	0.999999	D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.998	D;D;D;D;D	0.85130	0.99;0.997;0.996;0.996;0.994	T	0.02868	-1.1100	10	0.87932	D	0	-1.6432	17.817	0.88638	0.0:1.0:0.0:0.0	.	463;560;542;549;549	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	M	549;549;45;45;560;549	ENSP00000345308:L549M;ENSP00000389445:L549M;ENSP00000271877:L560M;ENSP00000355343:L549M	ENSP00000271877:L560M	L	+	1	2	UBAP2L	152490734	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.137000	0.77295	2.755000	0.94549	0.650000	0.86243	CTG		0.483	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		A	154224110	C	A	154224110	3	1	7	1	0	0	0	0	1	0	0	0	16878	680	24	2	1695	2	UBAP2L	1	154224110	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	1671848	154224110	95026511	11	659										
RAB25	57111	broad.mit.edu	37	chr1	156035800	156035800	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gccgcaccaccatcggggttGagttctccacccgcactgtg	11	16	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:156035800G>C	ENST00000361084.5	+	2	383	c.142G>C	c.(142-144)Gag>Cag	p.E48Q	RAB25_ENST00000487325.1_Intron	NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	48					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)	p.E52Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					CATCGGGGTTGAGTTCTCCAC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	68	67					1																	156035800		2157	4274	6431	154302424	SO:0001583	missense	57111			AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"RAB, member RAS oncogene"	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.142G>C	1.37:g.156035800G>C	ENSP00000354376:p.Glu48Gln		154302424	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Missense_Mutation	SNP	ENST00000361084.5	37	CCDS41413.1	.	.	.	.	.	.	.	.	.	.	G	35	5.424759	0.96111	.	.	ENSG00000132698	ENST00000361084	T	0.80994	-1.44	5.44	5.44	0.79542	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.87993	0.6318	M	0.71920	2.185	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.88360	0.2987	10	0.87932	D	0	.	18.0139	0.89232	0.0:0.0:1.0:0.0	.	48	P57735	RAB25_HUMAN	Q	48	ENSP00000354376:E48Q	ENSP00000354376:E48Q	E	+	1	0	RAB25	154302424	1.000000	0.71417	0.973000	0.42090	0.981000	0.71138	9.525000	0.98039	2.828000	0.97474	0.655000	0.94253	GAG		0.607	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1			C	156035800	G	C	156035800	3	2	7	1	0	0	0	0	1	0	0	0	12949	1291	45	5	148	5	RAB25	1	156035800	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	1811690	156035800	93214821	12	660										
CACNA1E	777	broad.mit.edu	37	chr1	181764147	181764147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggagttaccactcctccttgCggctgtcagcccaccgcctg	10	17	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:181764147C>T	ENST00000367573.2	+	46	6175	c.6175C>T	c.(6175-6177)Cgg>Tgg	p.R2059W	CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1623W|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R2040W|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R2016W|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1997W|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1948W|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R2010W	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2059					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R2016W(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTCCTCCTTGCGGCTGTCAGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	60	59					1																	181764147		1929	4130	6059	180030770	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6175C>T	1.37:g.181764147C>T	ENSP00000356545:p.Arg2059Trp		180030770	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729196	0.69074	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97138	-4.18;-4.17;-4.09;-4.17;-4.26;-4.08;-4.09	5.91	1.32	0.21799	.	0.562824	0.19394	N	0.115332	D	0.93432	0.7905	N	0.24115	0.695	0.46203	D	0.998923	D;D	0.56287	0.975;0.962	B;P	0.45428	0.436;0.48	D	0.90329	0.4350	10	0.87932	D	0	.	11.272	0.49144	0.6122:0.324:0.0:0.0638	.	1997;2016	Q15878-2;Q15878-3	.;.	W	2016;1997;2010;1948;1623;2040;2059	ENSP00000356542:R2016W;ENSP00000434814:R1997W;ENSP00000350183:R2010W;ENSP00000351101:R1948W;ENSP00000356539:R1623W;ENSP00000353222:R2040W;ENSP00000356545:R2059W	ENSP00000350183:R2010W	R	+	1	2	CACNA1E	180030770	0.998000	0.40836	0.997000	0.53966	0.986000	0.74619	0.444000	0.21661	-0.062000	0.13088	0.655000	0.94253	CGG		0.542	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181764147	C	T	181764147	3	4	7	1	0	0	0	0	1	0	0	0	2548	759	27	1	6224	1	CACNA1E	1	181764147	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	25728347	181764147	67486474	13	661										
CYB5R1	51706	broad.mit.edu	37	chr1	202935700	202935700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gggcggtgggcagggcaaagCggaacctcttggtgttgtgg	20	7	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:202935700C>T	ENST00000367249.4	-	3	268	c.194G>A	c.(193-195)cGc>cAc	p.R65H	CYB5R1_ENST00000497655.1_5'Flank	NM_016243.2	NP_057327.2	Q9UHQ9	NB5R1_HUMAN	cytochrome b5 reductase 1	65	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				sterol biosynthetic process (GO:0016126)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)	p.R65H(1)		breast(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(75;0.141)		Flavin adenine dinucleotide(DB03147)	CAGGGCAAAGCGGAACCTCTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											111	89	96					1																	202935700		2203	4300	6503	201202323	SO:0001583	missense	51706			AF169481	CCDS1431.1	1q32.1	2011-04-08		2005-07-13	ENSG00000159348	ENSG00000159348	1.6.2.2		13397	protein-coding gene	gene with protein product		608341	"NAD(P)H:quinone oxidoreductase type 3, polypeptide A2"	NQO3A2		12975309, 10611283	Standard	NM_016243		Approved	humb5R2	uc001gyt.2	Q9UHQ9	OTTHUMG00000041387	ENST00000367249.4:c.194G>A	1.37:g.202935700C>T	ENSP00000356218:p.Arg65His		201202323	A0PK21|B2R8E0|O95329|Q53F73|Q8NCL5|Q9UHJ1	Missense_Mutation	SNP	ENST00000367249.4	37	CCDS1431.1	.	.	.	.	.	.	.	.	.	.	C	37	6.325784	0.97476	.	.	ENSG00000159348	ENST00000367249	D	0.85702	-2.02	5.95	5.95	0.96441	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);Oxidoreductase, FAD-binding domain (1);	0.134163	0.49916	D	0.000122	D	0.94108	0.8111	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.94735	0.7913	10	0.87932	D	0	-0.0195	17.887	0.88858	0.0:1.0:0.0:0.0	.	65	Q9UHQ9	NB5R1_HUMAN	H	65	ENSP00000356218:R65H	ENSP00000356218:R65H	R	-	2	0	CYB5R1	201202323	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.707000	0.74654	2.824000	0.97209	0.655000	0.94253	CGC		0.607	CYB5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099155.1	NM_016243		T	202935700	C	T	202935700	3	4	7	1	0	0	0	0	1	0	0	0	4132	768	27	1	751	1	CYB5R1	1	202935700	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	21171553	202935700	46314921	14	662										
OPN3	23596	broad.mit.edu	37	chr1	241767754	241767754	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aggagaggtgctcctgcccaCgccagtgagtagagccagat	14	11	0	4	rs370046789		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr1:241767754C>T	ENST00000366554.2	-	2	607	c.501G>A	c.(499-501)gcG>gcA	p.A167A	OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_5'UTR	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	167			A -> V (in dbSNP:rs12072790).		detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.A167A(1)		endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			CTCCTGCCCACGCCAGTGAGT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		0,4406		0,0,2203	104	90	95		501	-10.5	0	1		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OPN3	NM_014322.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		167/403	241767754	1,13005	2203	4300	6503	239834377	SO:0001819	synonymous_variant	23596			AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"GPCR / Class A : Opsin receptors"	14007	protein-coding gene	gene with protein product	"panopsin", "protein phosphatase 1, regulatory subunit 116"	606695	"encephalopsin"	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691	ENST00000366554.2:c.501G>A	1.37:g.241767754C>T			239834377	Q8IX08|Q9Y344	Silent	SNP	ENST00000366554.2	37	CCDS31072.1																																																																																				0.547	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322		T	241767754	C	T	241767754	2	4	7	1	0	0	0	0	0	0	0	1	10912	523	19	1		1	OPN3	1	241767754	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	38832054	241767754	7482867	15	663										
ALLC	55821	broad.mit.edu	37	chr2	3730543	3730543	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tattgctagctaaaatccgaCgactggagttacttggttcc	9	9	0	0	rs201690293		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:3730543C>T	ENST00000252505.3	+	7	552	c.390C>T	c.(388-390)gaC>gaT	p.D130D		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	149					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)	p.D130D(1)		breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		TAAAATCCGACGACTGGAGTT	0.428										HNSCC(21;0.051)																																						1	Substitution - coding silent(1)	large_intestine(1)	2											124	125	125					2																	3730543		1893	4117	6010	3708418	SO:0001819	synonymous_variant	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.390C>T	2.37:g.3730543C>T			3708418	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Silent	SNP	ENST00000252505.3	37	CCDS46223.1																																																																																				0.428	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			T	3730543	C	T	3730543	2	4	7	1	0	0	0	0	0	0	0	1	534	535	19	1		1	ALLC	2	3730543	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09		3730543	239468830	16	664										
KCNK3	3777	broad.mit.edu	37	chr2	26950590	26950590	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aaggtgttctgcatgttctaCgcgctgctgggcatcccgct	12	12	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:26950590C>T	ENST00000302909.3	+	2	464	c.339C>T	c.(337-339)taC>taT	p.Y113Y		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	113					brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)	p.Y113Y(1)		endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	GCATGTTCTACGCGCTGCTGG	0.622																																					GBM(80;1457 1631 27100 45946)											1	Substitution - coding silent(1)	large_intestine(1)	2											127	121	123					2																	26950590		2203	4300	6503	26804094	SO:0001819	synonymous_variant	3777			AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6278	protein-coding gene	gene with protein product		603220				9312005, 9721223, 16382106	Standard	NM_002246		Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.339C>T	2.37:g.26950590C>T			26804094	Q53SU2	Silent	SNP	ENST00000302909.3	37	CCDS1727.1																																																																																				0.622	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		T	26950590	C	T	26950590	2	4	7	1	0	0	0	0	0	0	0	1	8088	547	19	1		1	KCNK3	2	26950590	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	23220047	26950590	216248783	17	665										
EIF2AK2	5610	broad.mit.edu	37	chr2	37353494	37353494	+	Frame_Shift_Del	DEL	G	G	-													0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tcaattctgtgttttgctttGaaaacttggccaaatccacc							TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:37353494delG	ENST00000233057.4	-	11	1168	c.846delC	c.(844-846)ttcfs	p.F282fs	EIF2AK2_ENST00000405334.1_Intron|EIF2AK2_ENST00000395127.2_Frame_Shift_Del_p.F282fs	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	282	Interaction with TRAF5.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)	p.F282fs*28(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				GTTTTGCTTTGAAAACTTGGC	0.308																																																1	Deletion - Frameshift(1)	large_intestine(1)	2											95	94	94					2																	37353494		2203	4300	6503	37206998	SO:0001589	frameshift_variant	5610			BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 83"	176871	"protein kinase, interferon-inducible double stranded RNA dependent"	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.846delC	2.37:g.37353494delG	ENSP00000233057:p.Phe282fs		37206998	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Frame_Shift_Del	DEL	ENST00000233057.4	37	CCDS1786.1																																																																																				0.308	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		-	37353494	G	-	37353494	7	5	7	1	0	1	0	1	0	0	0	0	5008	1281	45	0	837	0	EIF2AK2	2	37353494	Frame_Shift_Del	DEL	G	TCGA-AF-3913-01A-02W-1073-09	10402904	37353494	205845879	18	666										
KIAA1841	84542	broad.mit.edu	37	chr2	61361295	61361295	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gacaaactgagacccagagaCggcactgtgtctaagagcaa	11	10	1	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:61361295C>T	ENST00000295031.5	+	21	2429	c.2052C>T	c.(2050-2052)gaC>gaT	p.D684D		NM_032506.2	NP_115895.2	Q6NSI8	K1841_HUMAN	KIAA1841	0								p.D684D(1)		breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			gacccagagacggcactgtgt	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	2											152	139	144					2																	61361295		2203	4300	6503	61214799	SO:0001819	synonymous_variant	84542			BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000295031.5:c.2052C>T	2.37:g.61361295C>T			61214799	Q49AF0|Q6ZND0|Q96JI6	Silent	SNP	ENST00000295031.5	37	CCDS1867.1																																																																																				0.403	KIAA1841-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251580.1	NM_032506		T	61361295	C	T	61361295	2	4	7	1	0	0	0	0	0	0	0	1	8282	535	19	1		1	KIAA1841	2	61361295	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	24007801	61361295	181838078	19	667										
GTDC1	79712	broad.mit.edu	37	chr2	144764947	144764947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtcgtgcagtatcaaggccaCagtgtgtatcacactctgaa	10	10	3	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:144764947C>T	ENST00000392869.2	-	6	829	c.677G>A	c.(676-678)tGt>tAt	p.C226Y	GTDC1_ENST00000463875.2_Missense_Mutation_p.C97Y|GTDC1_ENST00000542155.1_Missense_Mutation_p.C226Y|GTDC1_ENST00000392867.3_Missense_Mutation_p.C226Y|GTDC1_ENST00000409214.1_Missense_Mutation_p.C226Y|GTDC1_ENST00000409298.1_Intron|GTDC1_ENST00000241391.5_Missense_Mutation_p.C226Y|GTDC1_ENST00000344850.4_Missense_Mutation_p.C226Y	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	226					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)	p.C226Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		ATCAAGGCCACAGTGTGTATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	105	106					2																	144764947		2203	4300	6503	144481417	SO:0001583	missense	79712			AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"Glycosyltransferase group 1 domain containing"	20887	protein-coding gene	gene with protein product	"mannosyltransferase-like"	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.677G>A	2.37:g.144764947C>T	ENSP00000376608:p.Cys226Tyr		144481417	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	CCDS33300.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512743	0.27123	.	.	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000463875	T;T;T;T;T;T;T	0.41758	1.0;1.0;0.99;1.0;0.99;1.0;1.0	5.42	0.99	0.19807	.	0.441905	0.24633	N	0.036864	T	0.31949	0.0813	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.18013	0.025;0.025;0.021;0.025	B;B;B;B	0.21708	0.036;0.036;0.011;0.036	T	0.24190	-1.0167	10	0.52906	T	0.07	-24.4104	7.8726	0.29576	0.0987:0.2903:0.611:0.0	.	226;226;226;226	G1UFN1;Q4AE62-2;Q4AE62;Q4AE62-3	.;.;GTDC1_HUMAN;.	Y	226;226;226;226;226;226;97	ENSP00000376608:C226Y;ENSP00000386581:C226Y;ENSP00000376606:C226Y;ENSP00000438323:C226Y;ENSP00000241391:C226Y;ENSP00000339750:C226Y;ENSP00000437964:C97Y	ENSP00000241391:C226Y	C	-	2	0	GTDC1	144481417	0.030000	0.19436	0.001000	0.08648	0.031000	0.12232	0.536000	0.23129	-0.052000	0.13311	-0.147000	0.13772	TGT		0.418	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659		T	144764947	C	T	144764947	3	4	7	1	0	0	0	0	1	0	0	0	6872	478	17	3	723	3	GTDC1	2	144764947	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	83403652	144764947	98434426	20	668										
FIGN	55137	broad.mit.edu	37	chr2	164466241	164466241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggcatggagggggcccaccaCtgcttcctgacacaaatgag	13	12	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:164466241C>T	ENST00000333129.3	-	3	2415	c.2101G>A	c.(2101-2103)Gtg>Atg	p.V701M	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'Flank	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	701					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)	p.V701M(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GGGCCCACCACTGCTTCCTGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	57	56					2																	164466241		2008	4179	6187	164174487	SO:0001583	missense	55137			AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.2101G>A	2.37:g.164466241C>T	ENSP00000333836:p.Val701Met		164174487	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	C	10.77	1.443462	0.25987	.	.	ENSG00000182263	ENST00000333129	D	0.98345	-4.88	5.89	5.89	0.94794	.	0.530996	0.20443	N	0.092260	D	0.97312	0.9121	L	0.45581	1.43	0.26513	N	0.974568	B	0.29253	0.239	B	0.35859	0.212	D	0.93003	0.6425	10	0.87932	D	0	-7.0114	20.2527	0.98410	0.0:1.0:0.0:0.0	.	701	Q5HY92	FIGN_HUMAN	M	701	ENSP00000333836:V701M	ENSP00000333836:V701M	V	-	1	0	FIGN	164174487	0.955000	0.32602	0.949000	0.38748	0.988000	0.76386	2.955000	0.49121	2.788000	0.95919	0.557000	0.71058	GTG		0.507	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164466241	C	T	164466241	3	4	7	1	0	0	0	0	1	0	0	0	5910	565	20	3	182	3	FIGN	2	164466241	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	19701294	164466241	78733132	21	669										
TTN	7273	broad.mit.edu	37	chr2	179428320	179428320	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ttgcacttggtccatctaacGccttccttatctcgtttttc	5	13	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:179428320G>A	ENST00000591111.1	-	276	77840	c.77616C>T	c.(77614-77616)ggC>ggT	p.G25872G	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Silent_p.G18640G|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.G27513G|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Silent_p.G24945G|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Silent_p.G18448G|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000359218.5_Silent_p.G18573G			Q8WZ42	TITIN_HUMAN	titin	25872	Fibronectin type-III 88. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G18640G(1)|p.G24943G(1)|p.G18448G(1)|p.G18573G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCATCTAACGCCTTCCTTAT	0.468																																																4	Substitution - coding silent(4)	large_intestine(4)	2											122	121	121					2																	179428320		1984	4163	6147	179136566	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.77616C>T	2.37:g.179428320G>A			179136566	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179428320	G	A	179428320	2	1	7	1	0	0	0	0	0	0	0	1	16775	1074	38	1		1	TTN	2	179428320	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	14962079	179428320	63771053	22	670										
PIKFYVE	200576	broad.mit.edu	37	chr2	209163489	209163489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cagagaccactgaggatgaaCgcaaaattcttctggtactg	10	9	2	3	rs61752183		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:209163489C>T	ENST00000264380.4	+	8	1194	c.1036C>T	c.(1036-1038)Cgc>Tgc	p.R346C	PIKFYVE_ENST00000407449.1_Missense_Mutation_p.R346C|PIKFYVE_ENST00000392202.3_Missense_Mutation_p.R249C|PIKFYVE_ENST00000308862.6_Missense_Mutation_p.R260C	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	346					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R346C(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TGAGGATGAACGCAAAATTCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	116	126					2																	209163489		2203	4300	6503	208871734	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.1036C>T	2.37:g.209163489C>T	ENSP00000264380:p.Arg346Cys		208871734	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769890	0.69992	.	.	ENSG00000115020	ENST00000392202;ENST00000264380;ENST00000407449;ENST00000308862;ENST00000452564	T;T;T	0.68181	1.44;-0.31;1.53	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.72309	0.3444	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.993;0.993;0.984;0.973;0.992	T	0.71830	-0.4474	10	0.45353	T	0.12	-12.4426	14.6352	0.68682	0.1456:0.8544:0.0:0.0	rs61752183	346;346;260;346;249	Q9Y2I7;E9PDH4;Q9Y2I7-3;Q08AR7;Q9Y2I7-2	FYV1_HUMAN;.;.;.;.	C	249;346;346;260;346	ENSP00000264380:R346C;ENSP00000384356:R346C;ENSP00000405736:R346C	ENSP00000264380:R346C	R	+	1	0	PIKFYVE	208871734	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.300000	0.43620	2.747000	0.94245	0.650000	0.86243	CGC		0.418	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209163489	C	T	209163489	3	4	7	1	0	0	0	0	1	0	0	0	11955	536	19	1	1062	1	PIKFYVE	2	209163489	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	29735169	209163489	34035884	23	671										
SLC19A3	80704	broad.mit.edu	37	chr2	228552899	228552899	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tacctgaatgctgactggcaAgttgagccctctctgatcta	9	11	2	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr2:228552899A>G	ENST00000258403.3	-	5	1368	c.1297T>C	c.(1297-1299)Ttg>Ctg	p.L433L	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Silent_p.L429L	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	433					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.L433L(1)		breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	CTGACTGGCAAGTTGAGCCCT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											156	139	145					2																	228552899		2203	4300	6503	228261143	SO:0001819	synonymous_variant	80704			AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1297T>C	2.37:g.228552899A>G			228261143		Silent	SNP	ENST00000258403.3	37	CCDS2468.1																																																																																				0.393	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			G	228552899	A	G	228552899	2	3	7	1	0	0	0	0	0	0	0	1	14467	69	3	4		4	SLC19A3	2	228552899	Silent	SNP	A	TCGA-AF-3913-01A-02W-1073-09	19389410	228552899	14646474	24	672										
WDR5B	54554	broad.mit.edu	37	chr3	122133553	122133553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aatgtaaaccaggttatcctCggaaccagacacaatccact	6	12	0	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr3:122133553C>T	ENST00000330689.4	-	1	1329	c.823G>A	c.(823-825)Gag>Aag	p.E275K	RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	275								p.E275K(1)		kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		AGGTTATCCTCGGAACCAGAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											139	132	134					3																	122133553		2203	4300	6503	123616243	SO:0001583	missense	54554			AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.823G>A	3.37:g.122133553C>T	ENSP00000330381:p.Glu275Lys		123616243	B2RCM9|Q9NUL4	Missense_Mutation	SNP	ENST00000330689.4	37	CCDS3012.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892951	0.91889	.	.	ENSG00000196981	ENST00000330689	T	0.59906	0.23	4.77	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68857	-0.5298	10	0.35671	T	0.21	.	15.7027	0.77555	0.0:1.0:0.0:0.0	.	275	Q86VZ2	WDR5B_HUMAN	K	275	ENSP00000330381:E275K	ENSP00000330381:E275K	E	-	1	0	WDR5B	123616243	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.838000	0.75359	2.644000	0.89710	0.561000	0.74099	GAG		0.408	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		T	122133553	C	T	122133553	3	4	7	1	0	0	0	0	1	0	0	0	17349	893	31	1	173	1	WDR5B	3	122133553	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		122133553	75888877	25	673										
COL6A6	131873	broad.mit.edu	37	chr3	130300575	130300575	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cagagactcaggtcagtgtgGcttttcaagtgaccaatgcc	11	10	3	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr3:130300575G>C	ENST00000358511.6	+	8	3749	c.3718G>C	c.(3718-3720)Gct>Cct	p.A1240P	COL6A6_ENST00000453409.2_Missense_Mutation_p.A1240P	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1240	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A1240P(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGTCAGTGTGGCTTTTCAAGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											97	97	97					3																	130300575		2008	4167	6175	131783265	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3718G>C	3.37:g.130300575G>C	ENSP00000351310:p.Ala1240Pro		131783265	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.581120	0.86748	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.38887	1.11;1.11	6.06	6.06	0.98353	von Willebrand factor, type A (2);	.	.	.	.	T	0.63674	0.2531	L	0.58101	1.795	0.42564	D	0.993151	D	0.89917	1.0	D	0.85130	0.997	T	0.60722	-0.7207	9	0.52906	T	0.07	.	19.3923	0.94587	0.0:0.0:1.0:0.0	.	1240	A6NMZ7	CO6A6_HUMAN	P	1240	ENSP00000351310:A1240P;ENSP00000399236:A1240P	ENSP00000351310:A1240P	A	+	1	0	COL6A6	131783265	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	6.472000	0.73567	2.882000	0.98803	0.655000	0.94253	GCT		0.443	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130300575	G	C	130300575	3	2	7	1	0	0	0	0	1	0	0	0	3709	1203	42	5	3748	5	COL6A6	3	130300575	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	8167022	130300575	67721855	26	674										
COL6A6	131873	broad.mit.edu	37	chr3	130345385	130345385	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggctttcctggtcctcgtggCttgcaggtttgtattttgac	12	9	0	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr3:130345385C>A	ENST00000358511.6	+	24	4966	c.4935C>A	c.(4933-4935)ggC>ggA	p.G1645G	COL6A6_ENST00000453409.2_Silent_p.G1645G	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1645	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G1645G(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GTCCTCGTGGCTTGCAGGTTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	3											160	160	160					3																	130345385		1874	4112	5986	131828075	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4935C>A	3.37:g.130345385C>A			131828075	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.408	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130345385	C	A	130345385	2	1	7	1	0	0	0	0	0	0	0	1	3709	784	28	2		2	COL6A6	3	130345385	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	44810	130345385	67677045	27	675										
SGCB	6443	broad.mit.edu	37	chr4	52899640	52899640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	taaacaagaggataatcacaCagatggctaaattgcccttt	7	8	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:52899640C>A	ENST00000381431.5	-	2	422	c.200G>T	c.(199-201)tGt>tTt	p.C67F	SGCB_ENST00000535450.1_Intron	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	67					cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.C67F(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			GATAATCACACAGATGGCTAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											162	149	154					4																	52899640		2203	4300	6503	52594397	SO:0001583	missense	6443			U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.200G>T	4.37:g.52899640C>A	ENSP00000370839:p.Cys67Phe		52594397	B7Z635|O00661	Missense_Mutation	SNP	ENST00000381431.5	37	CCDS3488.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.807856	0.50421	.	.	ENSG00000163069	ENST00000381431	D	0.94138	-3.36	5.29	5.29	0.74685	.	0.043261	0.85682	D	0.000000	D	0.94371	0.8190	L	0.50333	1.59	0.80722	D	1	D	0.55385	0.971	P	0.60541	0.876	D	0.91865	0.5502	10	0.12430	T	0.62	-16.2361	17.921	0.88966	0.0:1.0:0.0:0.0	.	67	Q16585	SGCB_HUMAN	F	67	ENSP00000370839:C67F	ENSP00000370839:C67F	C	-	2	0	SGCB	52594397	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	7.750000	0.85110	2.476000	0.83614	0.650000	0.86243	TGT		0.363	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			A	52899640	C	A	52899640	3	1	7	1	0	0	0	0	1	0	0	0	14237	478	17	2	776	2	SGCB	4	52899640	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		52899640	138254636	28	676										
DSPP	1834	broad.mit.edu	37	chr4	88533324	88533324	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tttgcatctcctagcaagatCaaatgtgtcagtacaggtat	8	8	3	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:88533324C>G	ENST00000282478.7	+	2	152	c.119C>G	c.(118-120)tCa>tGa	p.S40*	DSPP_ENST00000399271.1_Nonsense_Mutation_p.S40*|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	40					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.S40*(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		CTAGCAAGATCAAATGTGTCA	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											106	101	103					4																	88533324		1843	4082	5925	88752348	SO:0001587	stop_gained	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.119C>G	4.37:g.88533324C>G	ENSP00000282478:p.Ser40*		88752348	A8MUI0|O95815	Nonsense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747722	0.49257	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	.	.	.	4.89	-1.85	0.07784	.	1.492390	0.05048	N	0.477580	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	1.8005	9.0281	0.36243	0.0:0.4071:0.0:0.5929	.	.	.	.	X	40	.	ENSP00000282478:S40X	S	+	2	0	DSPP	88752348	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.142000	0.03203	-0.256000	0.09473	0.460000	0.39030	TCA		0.358	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88533324	C	G	88533324	4	3	7	1	0	0	0	0	0	1	0	0	4793	838	29	5	125	5	DSPP	4	88533324	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	35633684	88533324	102620952	29	677										
PRSS12	8492	broad.mit.edu	37	chr4	119204223	119204223	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctctggtaccagagtatgatAatctccaaccctaacagcat	6	12	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:119204223A>C	ENST00000296498.3	-	12	2365	c.2083T>G	c.(2083-2085)Tat>Gat	p.Y695D	PRSS12_ENST00000510903.1_5'UTR	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	695	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Y695D(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						AGAGTATGATAATCTCCAACC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											145	151	149					4																	119204223		2203	4300	6503	119423671	SO:0001583	missense	8492			AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2083T>G	4.37:g.119204223A>C	ENSP00000296498:p.Tyr695Asp		119423671	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	37	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.300484	0.60195	.	.	ENSG00000164099	ENST00000296498	D	0.93189	-3.18	5.88	3.43	0.39272	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.128903	0.53938	D	0.000050	D	0.94686	0.8286	L	0.49455	1.56	0.54753	D	0.999983	D	0.89917	1.0	D	0.97110	1.0	D	0.93506	0.6849	10	0.66056	D	0.02	.	10.4299	0.44400	0.8676:0.0:0.1324:0.0	.	695	P56730	NETR_HUMAN	D	695	ENSP00000296498:Y695D	ENSP00000296498:Y695D	Y	-	1	0	PRSS12	119423671	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	6.946000	0.75953	0.475000	0.27415	0.482000	0.46254	TAT		0.438	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			C	119204223	A	C	119204223	3	2	7	1	0	0	0	0	1	0	0	0	12649	362	13	4	552	4	PRSS12	4	119204223	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09	30670899	119204223	71950053	30	678										
FABP2	2169	broad.mit.edu	37	chr4	120241984	120241984	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgagctgcaagcttccttttCactatattaacacctgtaaa	5	10	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:120241984C>T	ENST00000274024.3	-	2	368	c.81G>A	c.(79-81)gtG>gtA	p.V27V		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	27					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)	p.V27V(1)		breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	GCTTCCTTTTCACTATATTAA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	4											61	66	65					4																	120241984		2203	4299	6502	120461432	SO:0001819	synonymous_variant	2169			J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"Fatty acid binding protein family"	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.81G>A	4.37:g.120241984C>T			120461432	Q2NKJ1	Silent	SNP	ENST00000274024.3	37	CCDS3712.1																																																																																				0.313	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134		T	120241984	C	T	120241984	2	4	7	1	0	0	0	0	0	0	0	1	5373	813	29	3		3	FABP2	4	120241984	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	1037761	120241984	70912292	31	679										
KIAA1712	80817	broad.mit.edu	37	chr4	175225427	175225427	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	caacaaagaaagaaaatcagTtctggtaagtcagaacctcc	7	9	3	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:175225427T>A	ENST00000503780.1	+	6	828	c.414T>A	c.(412-414)agT>agA	p.S138R	CEP44_ENST00000296519.4_Missense_Mutation_p.S138R|CEP44_ENST00000426172.1_Missense_Mutation_p.S138R|CEP44_ENST00000457424.2_Missense_Mutation_p.S138R	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	138						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)		p.S138R(1)		endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						AGAAAATCAGTTCTGGTAAGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	70	69					4																	175225427		2203	4300	6503	175462002	SO:0001583	missense	80817			AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.414T>A	4.37:g.175225427T>A	ENSP00000423153:p.Ser138Arg		175462002	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	37	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	T	6.711	0.499955	0.12762	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000503053;ENST00000426172;ENST00000296519	T;T;T;T;T	0.43294	0.98;0.96;0.95;0.96;0.98	5.01	5.01	0.66863	.	1.113100	0.06533	N	0.741830	T	0.39733	0.1089	L	0.34521	1.04	0.26684	N	0.971481	P;P	0.39157	0.662;0.513	B;B	0.40009	0.316;0.238	T	0.29882	-0.9997	10	0.30854	T	0.27	.	13.5906	0.61957	0.0:0.0:0.0:1.0	.	138;138	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	R	138	ENSP00000423153:S138R;ENSP00000389427:S138R;ENSP00000421128:S138R;ENSP00000408221:S138R;ENSP00000296519:S138R	ENSP00000296519:S138R	S	+	3	2	CEP44	175462002	0.003000	0.15002	0.098000	0.21074	0.282000	0.26991	1.191000	0.32138	1.998000	0.58463	0.379000	0.24179	AGT		0.338	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		A	175225427	T	A	175225427	3	1	7	1	0	0	0	0	1	0	0	0	8274	1722	60	5	428	5	KIAA1712	4	175225427	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	54983443	175225427	15928849	32	680										
FAT1	2195	broad.mit.edu	37	chr4	187535391	187535391	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tctgcacctgaacccaataaCgtgtaagtaatttcagcgtt	7	10	2	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr4:187535391C>T	ENST00000441802.2	-	12	9392	c.9183G>A	c.(9181-9183)acG>acA	p.T3061T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3061	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T3061T(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AACCCAATAACGTGTAAGTAA	0.383										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - coding silent(1)	large_intestine(1)	4											193	186	188					4																	187535391		1878	4107	5985	187772385	SO:0001819	synonymous_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9183G>A	4.37:g.187535391C>T			187772385		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.383	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187535391	C	T	187535391	2	4	7	1	0	0	0	0	0	0	0	1	5708	523	19	1		1	FAT1	4	187535391	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	12309964	187535391	3618885	33	681										
CDH9	1007	broad.mit.edu	37	chr5	26906107	26906107	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gttgttgttgacatctgtcaGcgtgatgttcactgtggtgg	14	6	3	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:26906107G>T	ENST00000231021.4	-	5	944	c.772C>A	c.(772-774)Ctg>Atg	p.L258M		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	258	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L258M(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ACATCTGTCAGCGTGATGTTC	0.463																																					Melanoma(8;187 585 15745 40864 52829)											1	Substitution - Missense(1)	large_intestine(1)	5											248	227	234					5																	26906107		2203	4300	6503	26941864	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.772C>A	5.37:g.26906107G>T	ENSP00000231021:p.Leu258Met		26941864	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.338216	0.81911	.	.	ENSG00000113100	ENST00000231021	T	0.56275	0.47	5.6	4.71	0.59529	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.76652	0.4017	M	0.93808	3.46	0.51482	D	0.99992	D	0.54047	0.964	P	0.61328	0.887	T	0.82448	-0.0452	9	.	.	.	.	14.1793	0.65564	0.077:0.0:0.923:0.0	.	258	Q9ULB4	CADH9_HUMAN	M	258	ENSP00000231021:L258M	.	L	-	1	2	CDH9	26941864	1.000000	0.71417	0.956000	0.39512	0.958000	0.62258	4.817000	0.62650	2.802000	0.96397	0.650000	0.86243	CTG		0.463	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26906107	G	T	26906107	3	4	7	1	0	0	0	0	1	0	0	0	3123	962	34	2	1629	2	CDH9	5	26906107	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		26906107	154009153	34	682										
C5orf42	65250	broad.mit.edu	37	chr5	37121812	37121812	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtagagttggtagctgtactGactcagataacagttcattc	10	7	2	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:37121812G>A	ENST00000508244.1	-	47	9023	c.8930C>T	c.(8929-8931)tCa>tTa	p.S2977L	C5orf42_ENST00000425232.2_Missense_Mutation_p.S2977L|C5orf42_ENST00000274258.7_Missense_Mutation_p.S1875L|C5orf42_ENST00000512288.1_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2977						integral component of membrane (GO:0016021)		p.S2977L(1)|p.S1875L(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TAGCTGTACTGACTCAGATAA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	5											310	272	285					5																	37121812		2203	4300	6503	37157569	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.8930C>T	5.37:g.37121812G>A	ENSP00000421690:p.Ser2977Leu		37157569	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	37	6.171485	0.97343	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.28	5.28	0.74379	.	0.239166	0.29403	N	0.012243	T	0.71048	0.3294	M	0.72118	2.19	0.24876	N	0.992258	D;D	0.89917	0.996;1.0	P;D	0.83275	0.906;0.996	T	0.65500	-0.6153	10	0.87932	D	0	.	14.4287	0.67233	0.0:0.0:1.0:0.0	.	2977;1875	E9PH94;Q9H799	.;CE042_HUMAN	L	2977;2977;1875;2043	ENSP00000421690:S2977L;ENSP00000389014:S2977L;ENSP00000274258:S1875L;ENSP00000424223:S2043L	ENSP00000274258:S1875L	S	-	2	0	C5orf42	37157569	0.996000	0.38824	0.293000	0.24932	0.925000	0.55904	5.045000	0.64220	2.470000	0.83445	0.591000	0.81541	TCA		0.448	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37121812	G	A	37121812	3	1	7	1	0	0	0	0	1	0	0	0	2307	1294	45	3	683	3	C5orf42	5	37121812	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	10215705	37121812	143793448	35	683										
LIFR	3977	broad.mit.edu	37	chr5	38482732	38482732	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctgtaatgctttacagttttCtggatttggaatatcagggt	10	5	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:38482732C>A	ENST00000263409.4	-	19	2791	c.2629G>T	c.(2629-2631)Gaa>Taa	p.E877*	LIFR_ENST00000453190.2_Nonsense_Mutation_p.E877*	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	877					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.E877*(2)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TTACAGTTTTCTGGATTTGGA	0.234			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	2	Substitution - Nonsense(2)	large_intestine(2)	5											41	51	48					5																	38482732		2183	4254	6437	38518489	SO:0001587	stop_gained	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2629G>T	5.37:g.38482732C>A	ENSP00000263409:p.Glu877*		38518489	Q6LCD9	Nonsense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	41	8.669285	0.98908	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	.	.	.	6.07	6.07	0.98685	.	0.217657	0.48767	D	0.000171	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-37.2953	20.6593	0.99626	0.0:1.0:0.0:0.0	.	.	.	.	X	877	.	ENSP00000263409:E877X	E	-	1	0	LIFR	38518489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.359000	0.66074	2.885000	0.99019	0.655000	0.94253	GAA		0.234	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38482732	C	A	38482732	4	1	7	1	0	0	0	0	0	1	0	0	8803	922	32	2	672	2	LIFR	5	38482732	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	1360920	38482732	142432528	36	684										
HEATR7B2	133558	broad.mit.edu	37	chr5	41007469	41007469	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctaggactgctgagtagagtCcataagttgtccccctcatc	9	12	1	2	rs200376875		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:41007469C>G	ENST00000399564.4	-	34	4146	c.3696G>C	c.(3694-3696)tgG>tgC	p.W1232C	MROH2B_ENST00000506092.2_Missense_Mutation_p.W787C	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1232								p.W1232C(1)									TGAGTAGAGTCCATAAGTTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	67	68					5																	41007469		1888	4110	5998	41043226	SO:0001583	missense	133558				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.3696G>C	5.37:g.41007469C>G	ENSP00000382476:p.Trp1232Cys		41043226	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359979	0.61403	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.04706	3.57;3.82	6.08	6.08	0.98989	Armadillo-type fold (1);	0.000000	0.64402	D	0.000019	T	0.22437	0.0541	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00007	-1.2504	10	0.87932	D	0	.	16.1635	0.81734	0.0:1.0:0.0:0.0	.	1232	Q7Z745	HTRB2_HUMAN	C	787;937;1232	ENSP00000441504:W787C;ENSP00000382476:W1232C	ENSP00000296803:W937C	W	-	3	0	HEATR7B2	41043226	0.991000	0.36638	0.943000	0.38184	0.708000	0.40852	3.458000	0.53014	2.894000	0.99253	0.655000	0.94253	TGG		0.438	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		G	41007469	C	G	41007469	3	3	7	1	0	0	0	0	1	0	0	0	7056	856	30	5	1097	5	HEATR7B2	5	41007469	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	2524737	41007469	139907791	37	685										
RASGRF2	5924	broad.mit.edu	37	chr5	80476046	80476046	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gagtttattatacggagaacGgctaccaatcgagttctgaa	10	7	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:80476046G>C	ENST00000265080.4	+	18	2806	c.2739G>C	c.(2737-2739)acG>acC	p.T913T		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	913					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T913T(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TACGGAGAACGGCTACCAATC	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	5											155	148	150					5																	80476046		2203	4300	6503	80511802	SO:0001819	synonymous_variant	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2739G>C	5.37:g.80476046G>C			80511802	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																				0.423	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		C	80476046	G	C	80476046	2	2	7	1	0	0	0	0	0	0	0	1	13110	1103	39	5		5	RASGRF2	5	80476046	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	39468577	80476046	100439214	38	686										
PPIP5K2	23262	broad.mit.edu	37	chr5	102484941	102484941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggtggaacgagacagtgaagGaaaagaagtaagataccctg	14	5	0	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:102484941G>A	ENST00000358359.3	+	8	1339	c.830G>A	c.(829-831)gGa>gAa	p.G277E	PPIP5K2_ENST00000414217.1_Missense_Mutation_p.G277E|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.G277E	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	277					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)	p.G277E(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GACAGTGAAGGAAAAGAAGTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	102	102					5																	102484941		2203	4300	6503	102512840	SO:0001583	missense	23262			AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.830G>A	5.37:g.102484941G>A	ENSP00000351126:p.Gly277Glu		102512840	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	37		.	.	.	.	.	.	.	.	.	.	G	33	5.198576	0.94997	.	.	ENSG00000145725	ENST00000321521;ENST00000507921;ENST00000358359;ENST00000451606;ENST00000414217	T;T;T	0.36520	1.29;1.25;1.29	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.70579	0.3240	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.993	T	0.78792	-0.2065	10	0.87932	D	0	.	19.0897	0.93221	0.0:0.0:1.0:0.0	.	199;277;277	D6RBU4;O43314-2;O43314	.;.;VIP2_HUMAN	E	277;199;277;277;277	ENSP00000313070:G277E;ENSP00000351126:G277E;ENSP00000416016:G277E	ENSP00000313070:G277E	G	+	2	0	PPIP5K2	102512840	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.809000	0.99208	2.569000	0.86673	0.655000	0.94253	GGA		0.408	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		A	102484941	G	A	102484941	3	1	7	1	0	0	0	0	1	0	0	0	12367	1174	41	3	856	3	PPIP5K2	5	102484941	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	22008895	102484941	78430319	39	687										
APC	324	broad.mit.edu	37	chr5	112175246	112175246	+	Frame_Shift_Del	DEL	C	C	-													0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gaactaggtcagctgaagatCctgtgagcgaagttccagca							TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:112175246delC	ENST00000457016.1	+	16	4335	c.3955delC	c.(3955-3957)cctfs	p.P1319fs	APC_ENST00000257430.4_Frame_Shift_Del_p.P1319fs|APC_ENST00000508376.2_Frame_Shift_Del_p.P1319fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1319	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.P1319fs*2(1)|p.P1319T(1)|p.K1192fs*3(1)|p.?(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGCTGAAGATCCTGTGAGCGA	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Deletion - Frameshift(3)|Substitution - Missense(1)|Unknown(1)	large_intestine(2)|soft_tissue(1)|liver(1)|skin(1)	5											61	63	62					5																	112175246		2202	4300	6502	112203145	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3955delC	5.37:g.112175246delC	ENSP00000413133:p.Pro1319fs		112203145	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175246	C	-	112175246	7	5	7	1	0	1	0	1	0	0	0	0	763	855	30	0	4013	0	APC	5	112175246	Frame_Shift_Del	DEL	C	TCGA-AF-3913-01A-02W-1073-09	9690305	112175246	68740014	40	688										
FTMT	94033	broad.mit.edu	37	chr5	121188017	121188017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtatttccttcaccagtcccGggaggagaccgagcacgcgg	13	13	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:121188017G>A	ENST00000321339.1	+	1	368	c.359G>A	c.(358-360)cGg>cAg	p.R120Q		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	120	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)	p.R120Q(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CACCAGTCCCGGGAGGAGACC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											59	57	57					5																	121188017		2203	4300	6503	121215916	SO:0001583	missense	94033			BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.359G>A	5.37:g.121188017G>A	ENSP00000313691:p.Arg120Gln		121215916		Missense_Mutation	SNP	ENST00000321339.1	37	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845465	0.32606	.	.	ENSG00000181867	ENST00000321339	T	0.61742	0.08	3.6	1.72	0.24424	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.757310	0.12053	N	0.503928	T	0.28234	0.0697	N	0.03084	-0.415	0.09310	N	0.999998	B	0.15473	0.013	B	0.14578	0.011	T	0.14476	-1.0471	10	0.35671	T	0.21	.	3.094	0.06303	0.2303:0.0:0.5471:0.2225	.	120	Q8N4E7	FTMT_HUMAN	Q	120	ENSP00000313691:R120Q	ENSP00000313691:R120Q	R	+	2	0	FTMT	121215916	0.669000	0.27502	0.066000	0.19879	0.944000	0.59088	3.858000	0.55979	0.455000	0.26910	0.655000	0.94253	CGG		0.582	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121188017	G	A	121188017	3	1	7	1	0	0	0	0	1	0	0	0	6104	1116	39	1	361	1	FTMT	5	121188017	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	9012771	121188017	59727243	41	689										
PCDHA12	56137	broad.mit.edu	37	chr5	140256339	140256339	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	atgagctggtggtgactgcgCgggatgggggctcgccttcg	19	9	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:140256339C>T	ENST00000398631.2	+	1	1282	c.1282C>T	c.(1282-1284)Cgg>Tgg	p.R428W	PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	428	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R428W(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGACTGCGCGGGATGGGGG	0.637																																					Pancreas(113;759 1672 13322 24104 50104)											1	Substitution - Missense(1)	large_intestine(1)	5											158	162	161					5																	140256339		2203	4300	6503	140236523	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1282C>T	5.37:g.140256339C>T	ENSP00000381628:p.Arg428Trp		140236523	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	C	9.650	1.141217	0.21205	.	.	ENSG00000251664	ENST00000398631	T	0.01804	4.63	4.96	-0.91	0.10511	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01940	0.0061	N	0.13327	0.33	0.09310	N	1	P;P	0.43094	0.586;0.799	B;P	0.49708	0.133;0.62	T	0.49908	-0.8889	9	0.87932	D	0	.	5.3836	0.16206	0.4642:0.3574:0.104:0.0744	.	428;428	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	W	428	ENSP00000381628:R428W	ENSP00000381628:R428W	R	+	1	2	PCDHA12	140236523	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.867000	0.00346	-0.080000	0.12685	-0.345000	0.07892	CGG		0.637	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140256339	C	T	140256339	3	4	7	1	0	0	0	0	1	0	0	0	11553	759	27	1	1284	1	PCDHA12	5	140256339	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	19068322	140256339	40658921	42	690										
RUFY1	80230	broad.mit.edu	37	chr5	179020615	179020615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gcagctggaagaagtcaaagCgattaatttacagatgtttc	10	6	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr5:179020615C>T	ENST00000319449.4	+	11	1394	c.1382C>T	c.(1381-1383)gCg>gTg	p.A461V	RUFY1_ENST00000393438.2_Missense_Mutation_p.A353V|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000437570.2_Missense_Mutation_p.A353V	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	461					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)	p.A353V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGTCAAAGCGATTAATTTA	0.478										HNSCC(44;0.11)																																						1	Substitution - Missense(1)	large_intestine(1)	5											98	103	101					5																	179020615		2203	4300	6503	178953221	SO:0001583	missense	80230			AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1382C>T	5.37:g.179020615C>T	ENSP00000325594:p.Ala461Val		178953221	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	37	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.57|11.57	1.678595|1.678595	0.29783|0.29783	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000319449;ENST00000437570;ENST00000393438;ENST00000360569|ENST00000508609	T;T;T|.	0.55052|.	0.54;0.6;0.6|.	4.95|4.95	3.11|3.11	0.35812|0.35812	.|.	0.377601|.	0.32386|.	N|.	0.006170|.	T|.	0.50411|.	0.1614|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	P|.	0.41748|.	0.761|.	B|.	0.35073|.	0.195|.	T|.	0.34054|.	-0.9844|.	10|.	0.44086|.	T|.	0.13|.	-2.9847|-2.9847	9.7858|9.7858	0.40675|0.40675	0.1396:0.7867:0.0:0.0736|0.1396:0.7867:0.0:0.0736	.|.	461|.	Q96T51|.	RUFY1_HUMAN|.	V|X	461;353;353;63|250	ENSP00000325594:A461V;ENSP00000390025:A353V;ENSP00000377087:A353V|.	ENSP00000325594:A461V|.	A|R	+|+	2|1	0|2	RUFY1|RUFY1	178953221|178953221	1.000000|1.000000	0.71417|0.71417	0.510000|0.510000	0.27712|0.27712	0.002000|0.002000	0.02628|0.02628	4.463000|4.463000	0.60128|0.60128	0.564000|0.564000	0.29238|0.29238	-0.291000|-0.291000	0.09656|0.09656	GCG|CGA		0.478	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		T	179020615	C	T	179020615	3	4	7	1	0	0	0	0	1	0	0	0	13775	768	27	1	1424	1	RUFY1	5	179020615	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	38764276	179020615	1894645	43	691										
ATF6B	1388	broad.mit.edu	37	chr6	32088833	32088833	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	agtgagggggctgggacatcCcacaggaggcatcctgaagg	17	9	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr6:32088833C>T	ENST00000375203.3	-	7	665	c.633G>A	c.(631-633)tgG>tgA	p.W211*	ATF6B_ENST00000375201.4_Nonsense_Mutation_p.W208*	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	211					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.W211*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						CTGGGACATCCCACAGGAGGC	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											47	47	47					6																	32088833		2203	4300	6503	32196811	SO:0001587	stop_gained	1388				CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.633G>A	6.37:g.32088833C>T	ENSP00000364349:p.Trp211*		32196811	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Nonsense_Mutation	SNP	ENST00000375203.3	37	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.903792	0.52333	.	.	ENSG00000213676	ENST00000375203;ENST00000375201	.	.	.	4.91	4.04	0.47022	.	1.443690	0.05030	U	0.474380	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-1.3233	9.1701	0.37076	0.0:0.8982:0.0:0.1018	.	.	.	.	X	211;208	.	ENSP00000364347:W208X	W	-	3	0	ATF6B	32196811	0.223000	0.23663	0.879000	0.34478	0.044000	0.14063	0.376000	0.20535	1.079000	0.41038	-0.136000	0.14681	TGG		0.542	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			T	32088833	C	T	32088833	4	4	7	1	0	0	0	0	0	1	0	0	1086	624	22	3	1526	3	ATF6B	6	32088833	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		32088833	139026234	44	692										
FRS3	10817	broad.mit.edu	37	chr6	41738472	41738472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ttttgaggtcaatcacggcgTaggagtctgagcttcgggca	14	8	3	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr6:41738472T>C	ENST00000373018.3	-	7	1615	c.1364A>G	c.(1363-1365)tAc>tGc	p.Y455C	FRS3_ENST00000259748.2_Missense_Mutation_p.Y455C	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	455					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)	p.Y455C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			AATCACGGCGTAGGAGTCTGA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	79	77					6																	41738472		2203	4300	6503	41846450	SO:0001583	missense	10817			AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.1364A>G	6.37:g.41738472T>C	ENSP00000362109:p.Tyr455Cys		41846450	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	37	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928711	0.73327	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	T;T	0.62364	0.03;0.03	5.59	5.59	0.84812	.	0.113339	0.64402	D	0.000007	T	0.74427	0.3715	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78861	-0.2037	10	0.87932	D	0	-23.1523	15.4379	0.75160	0.0:0.0:0.0:1.0	.	455	O43559	FRS3_HUMAN	C	455	ENSP00000362109:Y455C;ENSP00000259748:Y455C	ENSP00000259748:Y455C	Y	-	2	0	FRS3	41846450	1.000000	0.71417	0.983000	0.44433	0.997000	0.91878	6.213000	0.72194	2.137000	0.66172	0.533000	0.62120	TAC		0.647	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		C	41738472	T	C	41738472	3	2	7	1	0	0	0	0	1	0	0	0	6081	1638	57	4	118	4	FRS3	6	41738472	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	9649639	41738472	129376595	45	693										
GPR116	221395	broad.mit.edu	37	chr6	46849286	46849286	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gctttatgtattaactcaagTgatggtggtgtagtcttgac	11	5	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr6:46849286T>C	ENST00000283296.7	-	8	1008	c.720A>G	c.(718-720)tcA>tcG	p.S240S	GPR116_ENST00000265417.7_Silent_p.S240S|GPR116_ENST00000456426.2_Silent_p.S240S|GPR116_ENST00000362015.4_Silent_p.S240S	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	240	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S240S(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TTAACTCAAGTGATGGTGGTG	0.408																																					NSCLC(59;410 1274 8751 36715 50546)											1	Substitution - coding silent(1)	large_intestine(1)	6											329	259	283					6																	46849286		2203	4300	6503	46957245	SO:0001819	synonymous_variant	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.720A>G	6.37:g.46849286T>C			46957245	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																				0.408	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		C	46849286	T	C	46849286	2	2	7	1	0	0	0	0	0	0	0	1	6653	1683	59	4		4	GPR116	6	46849286	Silent	SNP	T	TCGA-AF-3913-01A-02W-1073-09	5110814	46849286	124265781	46	694										
PDE7B	27115	broad.mit.edu	37	chr6	136429871	136429871	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggattttctgttttctaggaGatatacgactaaggggtcag	12	5	3	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr6:136429871G>C	ENST00000308191.6	+	3	388	c.85G>C	c.(85-87)Gat>Cat	p.D29H	RP13-143G15.4_ENST00000591521.1_RNA|RP13-143G15.4_ENST00000417643.1_RNA|RP13-143G15.4_ENST00000585946.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	29					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.D29H(1)		breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	TTTTCTAGGAGATATACGACT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											108	106	107					6																	136429871		2203	4300	6503	136471564	SO:0001583	missense	27115			AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"Phosphodiesterases"	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.85G>C	6.37:g.136429871G>C	ENSP00000310661:p.Asp29His		136471564	Q5W154	Missense_Mutation	SNP	ENST00000308191.6	37	CCDS5175.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778530	0.90195	.	.	ENSG00000171408	ENST00000308191;ENST00000367787	T	0.72051	-0.62	6.07	6.07	0.98685	.	2.452900	0.01451	N	0.015503	T	0.79896	0.4525	L	0.50333	1.59	0.58432	D	0.999994	D;D	0.76494	0.999;0.994	P;D	0.64687	0.887;0.928	T	0.64575	-0.6375	10	0.62326	D	0.03	.	17.5619	0.87910	0.0:0.0:1.0:0.0	.	81;29	A1E5M1;Q9NP56	.;PDE7B_HUMAN	H	29;165	ENSP00000310661:D29H	ENSP00000310661:D29H	D	+	1	0	PDE7B	136471564	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.864000	0.69575	2.885000	0.99019	0.650000	0.86243	GAT		0.468	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1			C	136429871	G	C	136429871	3	2	7	1	0	0	0	0	1	0	0	0	11683	942	33	5	95	5	PDE7B	6	136429871	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	89580585	136429871	34685196	47	695										
HIVEP2	3097	broad.mit.edu	37	chr6	143090704	143090704	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gttacctgagtaaactgcttCcaagcacttgatgatgtaag	9	8	0	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr6:143090704C>A	ENST00000367604.1	-	4	5811	c.5172G>T	c.(5170-5172)tgG>tgT	p.W1724C	HIVEP2_ENST00000367603.2_Missense_Mutation_p.W1724C|HIVEP2_ENST00000012134.2_Missense_Mutation_p.W1724C			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1724					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W1724C(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TAAACTGCTTCCAAGCACTTG	0.408																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - Missense(1)	large_intestine(1)	6											99	90	93					6																	143090704		1859	4117	5976	143132397	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5172G>T	6.37:g.143090704C>A	ENSP00000356576:p.Trp1724Cys		143132397	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.666854	0.47677	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02974	4.09;4.09;4.09	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.13243	0.0321	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00865	-1.1535	10	0.66056	D	0.02	-11.9478	19.8109	0.96545	0.0:1.0:0.0:0.0	.	1724	P31629	ZEP2_HUMAN	C	1724	ENSP00000356576:W1724C;ENSP00000356575:W1724C;ENSP00000012134:W1724C	ENSP00000012134:W1724C	W	-	3	0	HIVEP2	143132397	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.561000	0.82288	2.679000	0.91253	0.655000	0.94253	TGG		0.408	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			A	143090704	C	A	143090704	3	1	7	1	0	0	0	0	1	0	0	0	7208	856	30	2	2192	2	HIVEP2	6	143090704	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	6660833	143090704	28024363	48	696										
DNAH11	8701	broad.mit.edu	37	chr7	21657267	21657267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cactcaacaaggaagtccgcGtctgggatgcttacacgggc	12	12	2	0	rs531283952		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:21657267G>T	ENST00000409508.3	+	23	4157	c.4126G>T	c.(4126-4128)Gtc>Ttc	p.V1376F	DNAH11_ENST00000328843.6_Missense_Mutation_p.V1381F	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1381	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V1381F(1)|p.V1381I(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GGAAGTCCGCGTCTGGGATGC	0.483									Kartagener syndrome																																							2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	7											55	55	55					7																	21657267		1887	4106	5993	21623792	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4126G>T	7.37:g.21657267G>T	ENSP00000475939:p.Val1376Phe		21623792	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	5.455	0.268998	0.10349	.	.	ENSG00000105877	ENST00000328843	T	0.60920	0.15	5.48	2.44	0.29823	Dynein heavy chain, domain-2 (1);	0.624196	0.14824	N	0.296281	T	0.42063	0.1186	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.15052	0.012	T	0.35226	-0.9797	9	0.59425	D	0.04	.	4.7959	0.13272	0.0847:0.1064:0.573:0.2359	.	1381	Q96DT5	DYH11_HUMAN	F	1381	ENSP00000330671:V1381F	ENSP00000330671:V1381F	V	+	1	0	DNAH11	21623792	0.000000	0.05858	0.055000	0.19348	0.034000	0.12701	0.206000	0.17375	0.705000	0.31890	-1.303000	0.01326	GTC		0.483	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21657267	G	T	21657267	3	4	7	1	0	0	0	0	1	0	0	0	4610	1145	40	2	4231	2	DNAH11	7	21657267	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		21657267	137481396	49	697										
ABCA13	154664	broad.mit.edu	37	chr7	48313935	48313935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggaaggaatttcagaagcttGtaaaaggtatttactttaac	9	4	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:48313935G>T	ENST00000435803.1	+	17	4696	c.4672G>T	c.(4672-4674)Gta>Tta	p.V1558L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1558					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.V1558L(1)|p.V1503L(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCAGAAGCTTGTAAAAGGTAT	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	7											56	58	58					7																	48313935		1800	4058	5858	48284481	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4672G>T	7.37:g.48313935G>T	ENSP00000411096:p.Val1558Leu		48284481	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	5.252	0.231921	0.09969	.	.	ENSG00000179869	ENST00000435803	D	0.86164	-2.08	5.37	-7.45	0.01374	.	0.965332	0.08456	N	0.943227	T	0.69495	0.3117	N	0.24115	0.695	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.55724	-0.8096	9	.	.	.	.	1.9345	0.03333	0.3895:0.3089:0.1649:0.1367	.	1558	Q86UQ4	ABCAD_HUMAN	L	1558	ENSP00000411096:V1558L	.	V	+	1	0	ABCA13	48284481	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.310000	0.08135	-1.488000	0.01847	-0.253000	0.11424	GTA		0.299	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48313935	G	T	48313935	3	4	7	1	0	0	0	0	1	0	0	0	31	1377	48	2	4567	2	ABCA13	7	48313935	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	26656668	48313935	110824728	50	698										
PCLO	27445	broad.mit.edu	37	chr7	82764531	82764531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgactgtactttggagcttgGaatatcaggttttgttgttg	12	4	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:82764531G>A	ENST00000333891.9	-	3	2672	c.2335C>T	c.(2335-2337)Cca>Tca	p.P779S	PCLO_ENST00000423517.2_Missense_Mutation_p.P779S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.P779S(2)|p.P725S(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGGAGCTTGGAATATCAGGT	0.453																																																3	Substitution - Missense(3)	large_intestine(3)	7											232	208	216					7																	82764531		1908	4134	6042	82602467	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2335C>T	7.37:g.82764531G>A	ENSP00000334319:p.Pro779Ser		82602467		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	0.127	-1.118461	0.01785	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.14893	2.47;2.47	5.83	3.04	0.35103	.	.	.	.	.	T	0.10766	0.0263	N	0.24115	0.695	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.001;0.005	T	0.31613	-0.9937	9	0.87932	D	0	.	3.4474	0.07486	0.1171:0.1258:0.5256:0.2314	.	779;779	Q9Y6V0-5;Q9Y6V0-6	.;.	S	725;779;779	ENSP00000334319:P779S;ENSP00000388393:P779S	ENSP00000334319:P779S	P	-	1	0	PCLO	82602467	0.000000	0.05858	0.000000	0.03702	0.160000	0.22226	0.436000	0.21526	0.370000	0.24538	-0.293000	0.09583	CCA		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82764531	G	A	82764531	3	1	7	1	0	0	0	0	1	0	0	0	11614	1174	41	3	13202	3	PCLO	7	82764531	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	34450596	82764531	76374132	51	699										
CALCR	799	broad.mit.edu	37	chr7	93116298	93116298	+	De_novo_Start_OutOfFrame	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	taaatgtgaacctcatttttGatttttgaagatctctttgt	6	5	2	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:93116298G>C	ENST00000394441.1	-	0	311				CALCR_ENST00000360249.4_De_novo_Start_OutOfFrame|CALCR_ENST00000359558.2_Nonsense_Mutation_p.S17*|MIR489_ENST00000384923.1_RNA|CALCR_ENST00000421592.1_De_novo_Start_OutOfFrame|CALCR_ENST00000426151.1_De_novo_Start_OutOfFrame	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor						adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.S17*(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CCTCATTTTTGATTTTTGAAG	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											82	88	86					7																	93116298		2202	4299	6501	92954234			799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.-5C>G	7.37:g.93116298G>C			92954234	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Nonsense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	G	37	6.614848	0.97705	.	.	ENSG00000004948	ENST00000359558	.	.	.	3.64	3.64	0.41730	.	.	.	.	.	.	.	.	.	.	.	0.44424	D	0.997342	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	11.1083	0.48216	0.0:0.0:1.0:0.0	.	.	.	.	X	17	.	ENSP00000352561:S17X	S	-	2	0	CALCR	92954234	0.298000	0.24417	0.067000	0.19924	0.113000	0.19764	2.548000	0.45794	2.315000	0.78130	0.650000	0.86243	TCA		0.299	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		C	93116298	G	C	93116298	1	2	7	1	0	1	0	0	0	0	0	0	2585	1294	45	5		5	CALCR	7	93116298	De_novo_Start_OutOfFrame	SNP	G	TCGA-AF-3913-01A-02W-1073-09	10351767	93116298	66022365	52	700										
SMURF1	57154	broad.mit.edu	37	chr7	98634740	98634740	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cagatgttgagggatgagctCattgaaccccttctgcagag	12	9	2	5			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:98634740C>T	ENST00000361125.1	-	16	2156	c.1837G>A	c.(1837-1839)Gag>Aag	p.E613K	AC004893.11_ENST00000468960.2_RNA|AC004893.11_ENST00000360902.1_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.E587K	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	613	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)	p.E613K(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			GGGATGAGCTCATTGAACCCC	0.517											OREG0018188	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	7											141	127	131					7																	98634740		2203	4300	6503	98472676	SO:0001583	missense	57154			AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1837G>A	7.37:g.98634740C>T	ENSP00000354621:p.Glu613Lys	1337	98472676	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	37	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	C	36	5.701949	0.96812	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.59502	0.26;0.26	5.43	5.43	0.79202	HECT (4);	0.000000	0.85682	D	0.000000	T	0.75700	0.3885	M	0.67625	2.065	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.74023	0.977;0.975;0.982	T	0.77327	-0.2629	10	0.87932	D	0	.	19.5914	0.95514	0.0:1.0:0.0:0.0	.	587;613;587	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	K	587;613	ENSP00000355326:E587K;ENSP00000354621:E613K	ENSP00000354621:E613K	E	-	1	0	SMURF1	98472676	1.000000	0.71417	0.255000	0.24374	0.966000	0.64601	7.701000	0.84566	2.720000	0.93068	0.591000	0.81541	GAG		0.517	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		T	98634740	C	T	98634740	3	4	7	1	0	0	0	0	1	0	0	0	14856	835	29	3	452	3	SMURF1	7	98634740	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	5518442	98634740	60503923	53	701										
SLC12A9	56996	broad.mit.edu	37	chr7	100456522	100456522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ccagcgtctttgctgtcctcTttaacggctgtacaggcatc	9	13	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:100456522T>C	ENST00000354161.3	+	6	948	c.823T>C	c.(823-825)Ttt>Ctt	p.F275L	SLC12A9_ENST00000540482.1_Missense_Mutation_p.F275L|SLC12A9_ENST00000275729.3_Missense_Mutation_p.F186L|SLC12A9_ENST00000415287.1_Missense_Mutation_p.F186L|SLC12A9_ENST00000428758.1_Missense_Mutation_p.F275L	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	275					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)	p.F275L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					TGCTGTCCTCTTTAACGGCTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	73	80					7																	100456522		2203	4300	6503	100294458	SO:0001583	missense	56996			AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.823T>C	7.37:g.100456522T>C	ENSP00000275730:p.Phe275Leu		100294458	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	T	31	5.066537	0.93898	.	.	ENSG00000146828	ENST00000540482;ENST00000418037;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000416675	D;D;D;D;D;D;D	0.98762	-5.12;-5.12;-5.12;-5.12;-5.12;-5.12;-5.12	5.04	5.04	0.67666	Amino acid permease domain (1);	0.066872	0.64402	N	0.000014	D	0.99345	0.9770	H	0.95224	3.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98786	1.0734	10	0.87932	D	0	.	12.7139	0.57103	0.0:0.0:0.0:1.0	.	186;275	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	L	275;11;275;186;186;275;83	ENSP00000443702:F275L;ENSP00000406560:F11L;ENSP00000408301:F275L;ENSP00000275729:F186L;ENSP00000413796:F186L;ENSP00000275730:F275L;ENSP00000410692:F83L	ENSP00000275729:F186L	F	+	1	0	SLC12A9	100294458	1.000000	0.71417	0.924000	0.36721	0.987000	0.75469	7.850000	0.86915	1.879000	0.54435	0.391000	0.25812	TTT		0.597	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		C	100456522	T	C	100456522	3	2	7	1	0	0	0	0	1	0	0	0	14427	1609	56	4	841	4	SLC12A9	7	100456522	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	1821782	100456522	58682141	54	702										
MKLN1	4289	broad.mit.edu	37	chr7	131151088	131151088	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tcttgctctccaaagatgagAttagatgacttctggtcact	8	9	4	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr7:131151088A>G	ENST00000352689.6	+	15	1882	c.1842A>G	c.(1840-1842)agA>agG	p.R614R	MKLN1_ENST00000498778.1_3'UTR|MKLN1_ENST00000421797.2_Silent_p.R522R	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	614					signal transduction (GO:0007165)	cytoplasm (GO:0005737)		p.R614R(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					CAAAGATGAGATTAGATGACT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	7											142	143	143					7																	131151088		2203	4300	6503	130801628	SO:0001819	synonymous_variant	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1842A>G	7.37:g.131151088A>G			130801628	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Silent	SNP	ENST00000352689.6	37	CCDS34754.1																																																																																				0.343	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		G	131151088	A	G	131151088	2	3	7	1	0	0	0	0	0	0	0	1	9633	330	12	4		4	MKLN1	7	131151088	Silent	SNP	A	TCGA-AF-3913-01A-02W-1073-09	30694566	131151088	27987575	55	703										
AGPAT6	137964	broad.mit.edu	37	chr8	41470394	41470394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgcacgggggactcatgggtGtgattcagagagccatggtg	17	7	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:41470394G>T	ENST00000396987.3	+	8	1753	c.826G>T	c.(826-828)Gtg>Ttg	p.V276L	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	276					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.V276L(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			ACTCATGGGTGTGATTCAGAG	0.547											OREG0018739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											120	85	97					8																	41470394		2203	4300	6503	41589551	SO:0001583	missense	137964			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.826G>T	8.37:g.41470394G>T	ENSP00000380184:p.Val276Leu	901	41589551	Q86V89	Missense_Mutation	SNP	ENST00000396987.3	37	CCDS6117.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971851	0.74246	.	.	ENSG00000158669	ENST00000396987	D	0.92397	-3.03	5.3	5.3	0.74995	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.85579	0.5729	N	0.13043	0.29	0.80722	D	1	B	0.09022	0.002	B	0.15484	0.013	T	0.79550	-0.1757	10	0.27082	T	0.32	.	18.1301	0.89598	0.0:0.0:1.0:0.0	.	276	Q86UL3	GPAT4_HUMAN	L	276	ENSP00000380184:V276L	ENSP00000380184:V276L	V	+	1	0	AGPAT6	41589551	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	3.911000	0.56378	2.769000	0.95229	0.655000	0.94253	GTG		0.547	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		T	41470394	G	T	41470394	3	4	7	1	0	0	0	0	1	0	0	0	391	1377	48	2	852	2	AGPAT6	8	41470394	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		41470394	104893628	56	704										
ANK1	286	broad.mit.edu	37	chr8	41530174	41530174	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gccccctccaacttccactcGtgacctgtggcatcagagtc	8	17	1	2	rs61753678		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:41530174G>A	ENST00000347528.4	-	38	4877	c.4794C>T	c.(4792-4794)caC>caT	p.H1598H	ANK1_ENST00000379758.2_Silent_p.H1598H|ANK1_ENST00000396942.1_Silent_p.H1598H|ANK1_ENST00000265709.8_Silent_p.H1639H|ANK1_ENST00000289734.7_Silent_p.H1598H|ANK1_ENST00000352337.4_Silent_p.H1598H|ANK1_ENST00000396945.1_Silent_p.H1598H	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1598	55 kDa regulatory domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.H1598H(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	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)			ACTTCCACTCGTGACCTGTGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	8											88	89	89					8																	41530174		2203	4300	6503	41649331	SO:0001819	synonymous_variant	286			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4794C>T	8.37:g.41530174G>A			41649331	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1																																																																																				0.597	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41530174	G	A	41530174	2	1	7	1	0	0	0	0	0	0	0	1	620	1136	40	1		1	ANK1	8	41530174	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	59780	41530174	104833848	57	705										
PRKDC	5591	broad.mit.edu	37	chr8	48855841	48855841	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tttgtgtgggcacaccacttTaacaagacttcaaatagaga	8	8	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:48855841T>C	ENST00000314191.2	-	10	950	c.894A>G	c.(892-894)ttA>ttG	p.L298L	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Silent_p.L298L	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	298					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.L298L(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	CACACCACTTTAACAAGACTT	0.433								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											2	Substitution - coding silent(2)	large_intestine(2)	8											71	69	70					8																	48855841		1900	4117	6017	49018394	SO:0001819	synonymous_variant	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.894A>G	8.37:g.48855841T>C			49018394	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Silent	SNP	ENST00000314191.2	37																																																																																					0.433	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		C	48855841	T	C	48855841	2	2	7	1	0	0	0	0	0	0	0	1	12555	1751	61	4		4	PRKDC	8	48855841	Silent	SNP	T	TCGA-AF-3913-01A-02W-1073-09	7325667	48855841	97508181	58	706										
ST18	9705	broad.mit.edu	37	chr8	53028937	53028937	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ttctgttctatgagtttgttCtcctcctctatcgtctttaa	5	10	5	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:53028937C>T	ENST00000276480.7	-	25	3584	c.2901G>A	c.(2899-2901)gaG>gaA	p.E967E		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	967					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E967E(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGAGTTTGTTCTCCTCCTCTA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	8											239	171	194					8																	53028937		2203	4300	6503	53191490	SO:0001819	synonymous_variant	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2901G>A	8.37:g.53028937C>T			53191490	Q17RY1	Silent	SNP	ENST00000276480.7	37	CCDS6149.1																																																																																				0.428	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028937	C	T	53028937	2	4	7	1	0	0	0	0	0	0	0	1	15251	912	32	3		3	ST18	8	53028937	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	4173096	53028937	93335085	59	707										
OSGIN2	734	broad.mit.edu	37	chr8	90936738	90936738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tttccttttttaggagcctaAaaggggatcgagttatgcca	10	7	0	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:90936738A>G	ENST00000297438.2	+	6	851	c.496A>G	c.(496-498)Aaa>Gaa	p.K166E	OSGIN2_ENST00000451899.2_Missense_Mutation_p.K210E	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	166					meiotic nuclear division (GO:0007126)			p.K166E(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TAGGAGCCTAAAAGGGGATCG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8											55	62	59					8																	90936738		2182	4291	6473	91005913	SO:0001583	missense	734			AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.496A>G	8.37:g.90936738A>G	ENSP00000297438:p.Lys166Glu		91005913		Missense_Mutation	SNP	ENST00000297438.2	37	CCDS6248.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.077494	0.36662	.	.	ENSG00000164823	ENST00000297438;ENST00000451899	T;T	0.25250	1.81;1.81	4.93	4.93	0.64822	.	0.099261	0.64402	D	0.000002	T	0.27731	0.0682	L	0.44542	1.39	0.80722	D	1	P;P	0.49090	0.919;0.855	P;P	0.47015	0.501;0.534	T	0.02345	-1.1173	10	0.19590	T	0.45	-19.184	14.872	0.70465	1.0:0.0:0.0:0.0	.	210;166	Q9Y236-2;Q9Y236	.;OSGI2_HUMAN	E	166;210	ENSP00000297438:K166E;ENSP00000396445:K210E	ENSP00000297438:K166E	K	+	1	0	OSGIN2	91005913	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	4.919000	0.63383	1.992000	0.58205	0.454000	0.30748	AAA		0.328	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		G	90936738	A	G	90936738	3	3	7	1	0	0	0	0	1	0	0	0	11321	15	1	4	650	4	OSGIN2	8	90936738	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09	37907801	90936738	55427284	60	708										
SPAG1	6674	broad.mit.edu	37	chr8	101196231	101196231	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aattgatgaagattacaaagAaaagacggtaatagacaagt	9	3	0	6			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:101196231A>C	ENST00000388798.2	+	6	727	c.536A>C	c.(535-537)gAa>gCa	p.E179A	Y_RNA_ENST00000362797.1_RNA|SPAG1_ENST00000251809.3_Missense_Mutation_p.E179A|SPAG1_ENST00000520643.1_Missense_Mutation_p.E179A|SPAG1_ENST00000520508.1_Missense_Mutation_p.E179A	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	179					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.E179A(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GATTACAAAGAAAAGACGGTA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	8											53	55	55					8																	101196231		2203	4287	6490	101265407	SO:0001583	missense	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.536A>C	8.37:g.101196231A>C	ENSP00000373450:p.Glu179Ala		101265407	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259556	0.59321	.	.	ENSG00000104450	ENST00000520643;ENST00000251809;ENST00000520508;ENST00000388798	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	5.66	4.5	0.54988	.	1.696240	0.02577	N	0.098466	T	0.20618	0.0496	M	0.69823	2.125	0.33453	D	0.583984	B;B	0.26318	0.146;0.138	B;B	0.23150	0.039;0.044	T	0.24693	-1.0153	10	0.45353	T	0.12	-14.6961	6.8595	0.24060	0.7713:0.1511:0.0776:0.0	.	179;179	Q07617;G3XAM3	SPAG1_HUMAN;.	A	179	ENSP00000427716:E179A;ENSP00000251809:E179A;ENSP00000428070:E179A;ENSP00000373450:E179A	ENSP00000251809:E179A	E	+	2	0	SPAG1	101265407	1.000000	0.71417	0.975000	0.42487	0.794000	0.44872	2.097000	0.41748	0.982000	0.38575	0.459000	0.35465	GAA		0.279	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101196231	A	C	101196231	3	2	7	1	0	0	0	0	1	0	0	0	15014	246	9	4	554	4	SPAG1	8	101196231	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09	10259493	101196231	45167791	61	709										
NUDCD1	84955	broad.mit.edu	37	chr8	110293397	110293397	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtctgttgccagtaatacagAggttctattgggaaaagaaa	11	5	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:110293397A>C	ENST00000239690.4	-	6	1202	c.828T>G	c.(826-828)ccT>ccG	p.P276P	NUDCD1_ENST00000427660.2_Silent_p.P247P	NM_032869.3	NP_116258.2			NudC domain containing 1									p.P276P(1)		breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			AGTAATACAGAGGTTCTATTG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	8											87	80	82					8																	110293397		2203	4300	6503	110362573	SO:0001819	synonymous_variant	84955			AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.828T>G	8.37:g.110293397A>C			110362573		Silent	SNP	ENST00000239690.4	37	CCDS6312.1																																																																																				0.338	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		C	110293397	A	C	110293397	2	2	7	1	0	0	0	0	0	0	0	1	10753	291	11	4		4	NUDCD1	8	110293397	Silent	SNP	A	TCGA-AF-3913-01A-02W-1073-09	9097166	110293397	36070625	62	710										
EXT1	2131	broad.mit.edu	37	chr8	119122509	119122509	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aataccagcatgtacttcctGagaggagggatggtgttgaa	13	6	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr8:119122509G>A	ENST00000378204.2	-	1	1583	c.777C>T	c.(775-777)ctC>ctT	p.L259L		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	259					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)	p.L259L(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TGTACTTCCTGAGAGGAGGGA	0.498			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																													yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	1	Substitution - coding silent(1)	large_intestine(1)	8											193	155	168					8																	119122509		2203	4300	6503	119191690	SO:0001819	synonymous_variant	2131	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.777C>T	8.37:g.119122509G>A			119191690	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	G	4.140	0.024308	0.08054	.	.	ENSG00000182197	ENST00000436216	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.1406	15.0861	0.72155	0.0:0.1413:0.8587:0.0	.	.	.	.	X	49	.	.	Q	-	1	0	EXT1	119191690	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.948000	0.49066	2.616000	0.88540	0.462000	0.41574	CAG		0.498	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		A	119122509	G	A	119122509	2	1	7	1	0	0	0	0	0	0	0	1	5336	1277	45	3		3	EXT1	8	119122509	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	8829112	119122509	27241513	63	711										
GLIS3	169792	broad.mit.edu	37	chr9	4118682	4118682	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gtaggatggtaatgagttagAgacactattgctggacatgg	14	4	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:4118682A>T	ENST00000324333.10	-	3	524	c.331T>A	c.(331-333)Tct>Act	p.S111T	GLIS3_ENST00000381971.3_Missense_Mutation_p.S266T	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	111	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.S111T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		AATGAGTTAGAGACACTATTG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											163	146	152					9																	4118682		2203	4300	6503	4108682	SO:0001583	missense	169792			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.331T>A	9.37:g.4118682A>T	ENSP00000325494:p.Ser111Thr		4108682	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	A	7.509	0.654300	0.14580	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.12147	2.74;2.71	5.59	4.41	0.53225	.	0.272854	0.25564	N	0.029811	T	0.09686	0.0238	L	0.39467	1.215	0.37025	D	0.896402	B;B	0.18310	0.027;0.006	B;B	0.13407	0.009;0.004	T	0.15378	-1.0439	10	0.09084	T	0.74	.	7.6424	0.28300	0.714:0.1462:0.0:0.1398	.	266;111	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	T	111;266	ENSP00000325494:S111T;ENSP00000371398:S266T	ENSP00000325494:S111T	S	-	1	0	GLIS3	4108682	1.000000	0.71417	0.996000	0.52242	0.862000	0.49288	2.315000	0.43752	0.904000	0.36572	0.533000	0.62120	TCT		0.562	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		T	4118682	A	T	4118682	3	4	7	1	0	0	0	0	1	0	0	0	6467	304	11	5	2028	5	GLIS3	9	4118682	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09		4118682	137094749	64	712										
KIAA1045	23349	broad.mit.edu	37	chr9	34977130	34977130	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gagcgggagcgagcccgagcCgccttcctggctcggggcag	18	14	0	0	rs374791324		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:34977130C>T	ENST00000242315.3	+	6	982	c.900C>T	c.(898-900)gcC>gcT	p.A300A	KIAA1045_ENST00000544237.1_Silent_p.A300A|KIAA1045_ENST00000476115.2_3'UTR	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	300							metal ion binding (GO:0046872)	p.A300A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			GAGCCCGAGCCGCCTTCCTGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9						C		0,3788		0,0,1894	45	50	49		900	0.4	0.9	9		49	2,8208		0,2,4103	no	coding-synonymous	KIAA1045	NM_015297.1		0,2,5997	TT,TC,CC		0.0244,0.0,0.0167		300/401	34977130	2,11996	1894	4105	5999	34967130	SO:0001819	synonymous_variant	23349			AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.900C>T	9.37:g.34977130C>T			34967130	B7Z253|Q58FE9|Q5T662	Silent	SNP	ENST00000242315.3	37	CCDS43796.1																																																																																				0.582	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592		T	34977130	C	T	34977130	2	4	7	1	0	0	0	0	0	0	0	1	8228	639	23	1		1	KIAA1045	9	34977130	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	30858448	34977130	106236301	65	713										
ZNF658	26149	broad.mit.edu	37	chr9	40774130	40774130	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	atttcccatgttcatcagaaAggtagaatttatcttctgtg	7	7	4	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:40774130A>T	ENST00000602553.1	-	5	1439	c.1145T>A	c.(1144-1146)cTt>cAt	p.L382H	ZNF658_ENST00000377626.3_Missense_Mutation_p.L382H|ZNF658_ENST00000441795.1_Missense_Mutation_p.L380H			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L382H(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TTCATCAGAAAGGTAGAATTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											210	211	211					9																	40774130		2203	4300	6503	40764130	SO:0001583	missense	26149			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1145T>A	9.37:g.40774130A>T	ENSP00000473484:p.Leu382His		40764130	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	a	5.269	0.234977	0.09969	.	.	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.15718	2.4;2.4	1.96	-0.601	0.11638	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05135	0.0137	N	0.03608	-0.345	0.09310	N	1	P;P	0.40032	0.699;0.574	B;B	0.34931	0.192;0.094	T	0.21895	-1.0232	9	0.56958	D	0.05	.	0.193	0.00136	0.2373:0.1586:0.2321:0.372	.	382;382	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	H	380;382	ENSP00000408462:L380H;ENSP00000366853:L382H	ENSP00000366853:L382H	L	-	2	0	ZNF658	40764130	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.015000	0.12634	-0.135000	0.11495	-0.940000	0.02684	CTT		0.398	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		T	40774130	A	T	40774130	3	4	7	1	0	0	0	0	1	0	0	0	18108	72	3	5	2038	5	ZNF658	9	40774130	Missense_Mutation	SNP	A	TCGA-AF-3913-01A-02W-1073-09	5797000	40774130	100439301	66	714										
C9orf103	414328	broad.mit.edu	37	chr9	86243847	86243847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gaggaaaatcgaaggaagatGggaaaaggcataccgctcaa	13	6	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:86243847G>A	ENST00000376419.4	+	3	145	c.141G>A	c.(139-141)atG>atA	p.M47I	IDNK_ENST00000376417.4_Missense_Mutation_p.M47I|IDNK_ENST00000405990.3_Nonsense_Mutation_p.W37*|IDNK_ENST00000277124.8_Start_Codon_SNP_p.M1I|IDNK_ENST00000454393.1_Missense_Mutation_p.M90I	NM_001001551.3	NP_001001551.2	Q5T6J7	GNTK_HUMAN	idnK, gluconokinase homolog (E. coli)	47					D-gluconate catabolic process (GO:0046177)		ATP binding (GO:0005524)|gluconokinase activity (GO:0046316)	p.M1I(1)									GAAGGAAGATGGGAAAAGGCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											251	188	210					9																	86243847		2203	4300	6503	85433667	SO:0001583	missense	414328			BC036421	CCDS35048.1, CCDS35048.2, CCDS59134.1	9q21.32	2012-03-30	2012-03-30	2012-03-30	ENSG00000148057	ENSG00000148057			31367	protein-coding gene	gene with protein product		611343	"chromosome 9 open reading frame 103"	C9orf103			Standard	NM_001001551		Approved	bA522I20.2	uc004amu.3	Q5T6J7	OTTHUMG00000020105	ENST00000376419.4:c.141G>A	9.37:g.86243847G>A	ENSP00000365601:p.Met47Ile		85433667	A5PLN6|Q5T6J6	Missense_Mutation	SNP	ENST00000376419.4	37	CCDS35048.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	13.59|13.59	2.282028|2.282028	0.40394|0.40394	.|.	.|.	ENSG00000148057|ENSG00000148057	ENST00000277124;ENST00000530832;ENST00000376417;ENST00000376419;ENST00000454393|ENST00000405990	T;T;T;T|.	0.68624|.	-0.34;1.31;1.31;1.31|.	4.7|4.7	4.7|4.7	0.59300|0.59300	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.73361|.	0.3577|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.79108|.	0.992|.	T|.	0.77088|.	-0.2717|.	9|.	0.87932|0.87932	D|D	0|0	-15.6057|-15.6057	13.4681|13.4681	0.61268|0.61268	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	47|.	Q5T6J7|.	GNTK_HUMAN|.	I|X	1;1;47;47;90|37	ENSP00000277124:M1I;ENSP00000365599:M47I;ENSP00000365601:M47I;ENSP00000403290:M90I|.	ENSP00000277124:M1I|ENSP00000385324:W37X	M|W	+|+	3|2	0|0	C9orf103|C9orf103	85433667|85433667	0.999000|0.999000	0.42202|0.42202	0.972000|0.972000	0.41901|0.41901	0.065000|0.065000	0.16274|0.16274	4.569000|4.569000	0.60865|0.60865	2.286000|2.286000	0.76751|0.76751	0.558000|0.558000	0.71614|0.71614	ATG|TGG		0.468	IDNK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052837.2	NM_001001551		A	86243847	G	A	86243847	3	1	7	1	0	0	0	0	1	0	0	0	2452	1348	47	3	5	3	C9orf103	9	86243847	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	45469717	86243847	54969584	67	715										
SYK	6850	broad.mit.edu	37	chr9	93637111	93637111	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aattttggaactgtgaaaaaGggctactaccaaatgaaaaa	8	5	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:93637111G>T	ENST00000375754.4	+	9	1309	c.1161G>T	c.(1159-1161)aaG>aaT	p.K387N	SYK_ENST00000375751.4_Missense_Mutation_p.K364N|SYK_ENST00000375746.1_Missense_Mutation_p.K387N|SYK_ENST00000375747.1_Missense_Mutation_p.K364N	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	387	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.K364N(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CTGTGAAAAAGGGCTACTACC	0.468			T	"ETV6, ITK"	"MDS, peripheral T-cell lymphoma"																																		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	1	Substitution - Missense(1)	large_intestine(1)	9											103	111	108					9																	93637111		2203	4300	6503	92676932	SO:0001583	missense	6850			L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"SH2 domain containing"	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1161G>T	9.37:g.93637111G>T	ENSP00000364907:p.Lys387Asn		92676932		Missense_Mutation	SNP	ENST00000375754.4	37	CCDS6688.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545791	0.65198	.	.	ENSG00000165025	ENST00000375754;ENST00000375751;ENST00000375747;ENST00000375746	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	4.29	2.44	0.29823	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.181985	0.47455	D	0.000235	T	0.71290	0.3322	M	0.73753	2.245	0.58432	D	0.999998	D;D	0.65815	0.971;0.995	P;D	0.67231	0.832;0.95	T	0.70288	-0.4913	10	0.54805	T	0.06	.	4.4892	0.11805	0.4444:0.0:0.5556:0.0	.	364;387	P43405-2;P43405	.;KSYK_HUMAN	N	387;364;364;387	ENSP00000364907:K387N;ENSP00000364904:K364N;ENSP00000364899:K364N;ENSP00000364898:K387N	ENSP00000364898:K387N	K	+	3	2	SYK	92676932	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.394000	0.34509	1.164000	0.42652	-0.137000	0.14449	AAG		0.468	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			T	93637111	G	T	93637111	3	4	7	1	0	0	0	0	1	0	0	0	15477	991	35	2	1191	2	SYK	9	93637111	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	7393264	93637111	47576320	68	716										
ANKS6	203286	broad.mit.edu	37	chr9	101513343	101513343	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aaaaatgggctgatatttctCaagtgataatttcttaagga	8	4	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:101513343C>G	ENST00000353234.4	-	13	2409	c.2362G>C	c.(2362-2364)Gag>Cag	p.E788Q	ANKS6_ENST00000540940.1_Missense_Mutation_p.E593Q|ANKS6_ENST00000375018.1_Missense_Mutation_p.E789Q|ANKS6_ENST00000375019.2_Missense_Mutation_p.E487Q			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	788	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.					cilium (GO:0005929)|cytoplasm (GO:0005737)		p.E788Q(1)		endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TGATATTTCTCAAGTGATAAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	9											98	93	94					9																	101513343		1813	4087	5900	100553164	SO:0001583	missense	203286			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.2362G>C	9.37:g.101513343C>G	ENSP00000297837:p.Glu788Gln		100553164	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	37	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.657537|4.657537	0.88154|0.88154	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.46819|.	0.86;0.86;0.86;0.86|.	5.91|5.91	5.91|5.91	0.95273|0.95273	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.67730|.	0.2924|.	L|L	0.45285|0.45285	1.41|1.41	0.51012|0.51012	D|D	0.999905|0.999905	D;D|.	0.76494|.	0.989;0.999|.	P;D|.	0.83275|.	0.883;0.996|.	T|.	0.62338|.	-0.6875|.	10|.	0.87932|.	D|.	0|.	-38.4283|-38.4283	17.7923|17.7923	0.88558|0.88558	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	789;788|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	Q|S	487;789;788;593|257	ENSP00000364159:E487Q;ENSP00000364158:E789Q;ENSP00000297837:E788Q;ENSP00000442189:E593Q|.	ENSP00000297837:E788Q|.	E|X	-|-	1|2	0|2	ANKS6|ANKS6	100553164|100553164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.081000|7.081000	0.76844|0.76844	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GAG|TGA		0.308	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		G	101513343	C	G	101513343	3	3	7	1	0	0	0	0	1	0	0	0	692	835	29	5	265	5	ANKS6	9	101513343	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	7876232	101513343	39700088	69	717										
KIAA0368	23392	broad.mit.edu	37	chr9	114156515	114156515	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gctgcttgcctcacgtgtggGttggggctgatgatatgttt	15	7	1	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr9:114156515G>C	ENST00000338205.5	-	25	3066	c.2847C>G	c.(2845-2847)aaC>aaG	p.N949K	KIAA0368_ENST00000374378.3_5'UTR|KIAA0368_ENST00000259335.4_Missense_Mutation_p.N1127K			Q5VYK3	ECM29_HUMAN	KIAA0368	955					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.N1127K(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TCACGTGTGGGTTGGGGCTGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											66	66	66					9																	114156515		1960	4147	6107	113196336	SO:0001583	missense	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2847C>G	9.37:g.114156515G>C	ENSP00000339889:p.Asn949Lys		113196336	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	G	12.88	2.071218	0.36566	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.68903	-0.36	5.68	0.679	0.17975	.	0.149513	0.56097	D	0.000023	T	0.41328	0.1154	N	0.17278	0.47	0.80722	D	1	B	0.16396	0.017	B	0.20184	0.028	T	0.33879	-0.9851	10	0.02654	T	1	.	9.4678	0.38824	0.4059:0.0:0.5941:0.0	.	424	B3KXF2	.	K	949;1127;424	ENSP00000259335:N1127K	ENSP00000259335:N1127K	N	-	3	2	KIAA0368	113196336	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.608000	0.36847	0.080000	0.16959	-0.140000	0.14226	AAC		0.463	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114156515	G	C	114156515	3	2	7	1	0	0	0	0	1	0	0	0	8192	1252	44	5	2772	5	KIAA0368	9	114156515	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	12643172	114156515	27056916	70	718										
PCDH15	65217	broad.mit.edu	37	chr10	55996623	55996623	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	attcctggcctatctgatggCggttgaatattccggtcctg	11	10	1	2	rs150450873		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:55996623C>T	ENST00000320301.6	-	9	1339	c.945G>A	c.(943-945)ccG>ccA	p.P315P	PCDH15_ENST00000437009.1_Silent_p.P315P|PCDH15_ENST00000395438.1_Silent_p.P315P|PCDH15_ENST00000395440.1_Silent_p.P315P|PCDH15_ENST00000414778.1_Silent_p.P320P|PCDH15_ENST00000395446.1_Silent_p.P315P|PCDH15_ENST00000395442.1_Silent_p.P315P|PCDH15_ENST00000395432.2_Silent_p.P278P|PCDH15_ENST00000395445.1_Silent_p.P315P|PCDH15_ENST00000395433.1_Silent_p.P293P|PCDH15_ENST00000373965.2_Silent_p.P315P|PCDH15_ENST00000373955.1_Silent_p.P315P|PCDH15_ENST00000373957.3_Silent_p.P293P|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395430.1_Silent_p.P315P|PCDH15_ENST00000361849.3_Silent_p.P315P	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	315	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.P320P(2)|p.P315P(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TATCTGATGGCGGTTGAATAT	0.378										HNSCC(58;0.16)																																						3	Substitution - coding silent(3)	large_intestine(3)	10											177	166	169					10																	55996623		2203	4300	6503	55666629	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.945G>A	10.37:g.55996623C>T			55666629	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.378	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55996623	C	T	55996623	2	4	7	1	0	0	0	0	0	0	0	1	11542	755	27	1		1	PCDH15	10	55996623	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09		55996623	79538124	71	719										
TET1	80312	broad.mit.edu	37	chr10	70450734	70450734	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ccgaagactgcttcagccacAccagctccactgaagaatga	8	14	1	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:70450734A>T	ENST00000373644.4	+	12	5783	c.5574A>T	c.(5572-5574)acA>acT	p.T1858T		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1858					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.T1858T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CTTCAGCCACACCAGCTCCAC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	10											84	78	80					10																	70450734		2203	4300	6503	70120740	SO:0001819	synonymous_variant	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5574A>T	10.37:g.70450734A>T			70120740	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Silent	SNP	ENST00000373644.4	37	CCDS7281.1																																																																																				0.542	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70450734	A	T	70450734	2	4	7	1	0	0	0	0	0	0	0	1	15808	146	6	5		5	TET1	10	70450734	Silent	SNP	A	TCGA-AF-3913-01A-02W-1073-09	14454111	70450734	65084013	72	720										
DLG5	9231	broad.mit.edu	37	chr10	79579711	79579711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgccggctggaatgcccaggCgagtaaggtgcccactcctg	14	13	0	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:79579711C>T	ENST00000372391.2	-	16	3473	c.3468G>A	c.(3466-3468)tcG>tcA	p.S1156S	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Silent_p.S816S	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1156					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)	p.S1156S(1)		breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AATGCCCAGGCGAGTAAGGTG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	10											62	70	68					10																	79579711		2203	4299	6502	79249717	SO:0001819	synonymous_variant	9231			U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.3468G>A	10.37:g.79579711C>T			79249717	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																				0.627	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			T	79579711	C	T	79579711	2	4	7	1	0	0	0	0	0	0	0	1	4569	755	27	1		1	DLG5	10	79579711	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	9128977	79579711	55955036	73	721										
BTAF1	9044	broad.mit.edu	37	chr10	93784547	93784547	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cggtttgggaaatggcagcaCttccgagagtggcacagagt	15	8	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:93784547C>A	ENST00000265990.6	+	35	5206	c.4898C>A	c.(4897-4899)aCt>aAt	p.T1633N	BTAF1_ENST00000544642.1_Missense_Mutation_p.T461N	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1633					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T1633N(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				AATGGCAGCACTTCCGAGAGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											104	94	98					10																	93784547		2203	4300	6503	93774527	SO:0001583	missense	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.4898C>A	10.37:g.93784547C>A	ENSP00000265990:p.Thr1633Asn		93774527	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738191	0.30774	.	.	ENSG00000095564	ENST00000265990;ENST00000544642;ENST00000538688	D;D	0.90261	-2.64;-2.59	5.95	5.95	0.96441	.	0.233433	0.43919	D	0.000514	D	0.87136	0.6102	L	0.40543	1.245	0.37125	D	0.900994	B	0.06786	0.001	B	0.08055	0.003	T	0.82796	-0.0280	10	0.14656	T	0.56	-15.4489	20.3697	0.98890	0.0:1.0:0.0:0.0	.	1633	O14981	BTAF1_HUMAN	N	1633;461;483	ENSP00000265990:T1633N;ENSP00000439924:T461N	ENSP00000265990:T1633N	T	+	2	0	BTAF1	93774527	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.995000	0.63908	2.811000	0.96726	0.655000	0.94253	ACT		0.418	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		A	93784547	C	A	93784547	3	1	7	1	0	0	0	0	1	0	0	0	1539	565	20	2	5036	2	BTAF1	10	93784547	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	14204836	93784547	41750200	74	722										
SLIT1	6585	broad.mit.edu	37	chr10	98807528	98807528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ccaccacgttggcctcacagCggcacttgtggggacagacc	12	15	1	1	rs373698645		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:98807528C>T	ENST00000266058.4	-	16	1798	c.1553G>A	c.(1552-1554)cGc>cAc	p.R518H	SLIT1_ENST00000371070.4_Missense_Mutation_p.R518H|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	518	LRRNT 3.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.R518H(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GGCCTCACAGCGGCACTTGTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	HIS/ARG	0,4406		0,0,2203	75	69	71		1553	4.7	1	10		71	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLIT1	NM_003061.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	518/1535	98807528	1,13005	2203	4300	6503	98797518	SO:0001583	missense	6585			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1553G>A	10.37:g.98807528C>T	ENSP00000266058:p.Arg518His		98797518	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360998	0.82353	0.0	1.16E-4	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867	D;D;D	0.95885	-3.84;-3.84;-3.84	4.73	4.73	0.59995	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.95551	0.8554	M	0.66439	2.03	0.80722	D	1	B;D	0.63046	0.377;0.992	B;P	0.49502	0.093;0.613	D	0.94662	0.7849	10	0.33141	T	0.24	.	17.8954	0.88886	0.0:1.0:0.0:0.0	.	528;518	E7EWQ8;O75093	.;SLIT1_HUMAN	H	518;528;518;511	ENSP00000266058:R518H;ENSP00000360109:R518H;ENSP00000315005:R511H	ENSP00000266058:R518H	R	-	2	0	SLIT1	98797518	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	7.097000	0.76967	2.448000	0.82819	0.462000	0.41574	CGC		0.647	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		T	98807528	C	T	98807528	3	4	7	1	0	0	0	0	1	0	0	0	14776	768	27	1	3139	1	SLIT1	10	98807528	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	5022981	98807528	36727219	75	723										
NOLC1	9221	broad.mit.edu	37	chr10	103912176	103912176	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	attgcctggaggatggcggaCgccggcattcgccgcgtggt	17	11	0	0	rs540452525	byFrequency	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:103912176C>T	ENST00000605788.1	+	1	244	c.9C>T	c.(7-9)gaC>gaT	p.D3D	NOLC1_ENST00000603742.1_5'UTR|NOLC1_ENST00000405356.1_Silent_p.D3D|NOLC1_ENST00000488254.2_Silent_p.D3D	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	3				D -> A (in Ref. 6; BAA04803). {ECO:0000305}.	cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)	p.D3D(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		GGATGGCGGACGCCGGCATTC	0.617													C|||	2	0.000399361	0	0	5008	,	,		17405	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	10											76	75	75					10																	103912176		2203	4300	6503	103902166	SO:0001819	synonymous_variant	9221			Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.9C>T	10.37:g.103912176C>T			103902166	Q15030|Q5VV70|Q9BUV3	De_novo_Start_OutOfFrame	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																				0.617	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		T	103912176	C	T	103912176	2	4	7	1	0	0	0	0	0	0	0	1	10560	535	19	1		1	NOLC1	10	103912176	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	5104648	103912176	31622571	76	724										
PDZD8	118987	broad.mit.edu	37	chr10	119042838	119042838	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gctgctgaatggctgagagtCtattagttggcttatttcat	11	6	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr10:119042838C>G	ENST00000334464.5	-	5	3645	c.3406G>C	c.(3406-3408)Gac>Cac	p.D1136H	PDZD8_ENST00000482496.1_5'Flank	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	1136					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.D1136H(1)		kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		GGCTGAGAGTCTATTAGTTGG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											161	152	155					10																	119042838		2203	4300	6503	119032828	SO:0001583	missense	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.3406G>C	10.37:g.119042838C>G	ENSP00000334642:p.Asp1136His		119032828	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.151119	0.38021	.	.	ENSG00000165650	ENST00000334464	D	0.86627	-2.15	5.81	4.9	0.64082	.	0.326990	0.33057	N	0.005339	T	0.81805	0.4900	N	0.19112	0.55	0.35923	D	0.831936	P	0.51351	0.944	P	0.49012	0.598	D	0.85825	0.1388	10	0.72032	D	0.01	-17.0826	9.8966	0.41322	0.0:0.7982:0.0:0.2018	.	1136	Q8NEN9	PDZD8_HUMAN	H	1136	ENSP00000334642:D1136H	ENSP00000334642:D1136H	D	-	1	0	PDZD8	119032828	0.846000	0.29590	1.000000	0.80357	0.993000	0.82548	1.676000	0.37565	2.746000	0.94184	0.655000	0.94253	GAC		0.383	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		G	119042838	C	G	119042838	3	3	7	1	0	0	0	0	1	0	0	0	11736	913	32	5	62	5	PDZD8	10	119042838	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	15130662	119042838	16491909	77	725										
PIK3C2A	5286	broad.mit.edu	37	chr11	17139085	17139085	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tactttttctgctactcctcCtaaaagctgtacaagtttcg	5	11	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr11:17139085C>G	ENST00000265970.7	-	18	3168	c.3169G>C	c.(3169-3171)Gga>Cga	p.G1057R	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.G677R|RNU6-593P_ENST00000364716.1_RNA	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1057					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.G1057R(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						GCTACTCCTCCTAAAAGCTGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											136	137	137					11																	17139085		2200	4293	6493	17095661	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3169G>C	11.37:g.17139085C>G	ENSP00000265970:p.Gly1057Arg		17095661	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.597470	0.87055	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80653	-1.4;-1.4	5.51	5.51	0.81932	Protein kinase-like domain (1);	0.050098	0.85682	D	0.000000	D	0.88078	0.6340	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	D	0.85440	0.1154	10	0.30078	T	0.28	-13.798	19.4111	0.94673	0.0:1.0:0.0:0.0	.	1057	O00443	P3C2A_HUMAN	R	1057;677	ENSP00000265970:G1057R;ENSP00000438687:G677R	ENSP00000265970:G1057R	G	-	1	0	PIK3C2A	17095661	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.142000	0.77339	2.597000	0.87782	0.591000	0.81541	GGA		0.403	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17139085	C	G	17139085	3	3	7	1	0	0	0	0	1	0	0	0	11940	690	24	5	1951	5	PIK3C2A	11	17139085	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		17139085	117867431	78	726										
APLNR	187	broad.mit.edu	37	chr11	57003486	57003486	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctgctgtgggaggtgcctgcGcacctgctctggccacagca	14	14	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr11:57003486G>A	ENST00000606794.1	-	1	1189	c.993C>T	c.(991-993)tgC>tgT	p.C331C		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	331					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.C331C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						AGGTGCCTGCGCACCTGCTCT	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	11											60	43	49					11																	57003486		2201	4296	6497	56760062	SO:0001819	synonymous_variant	187			U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"APJ (apelin) receptor"	600052	"angiotensin II receptor-like 1"	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.993C>T	11.37:g.57003486G>A			56760062		Silent	SNP	ENST00000606794.1	37	CCDS7950.1																																																																																				0.642	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161		A	57003486	G	A	57003486	2	1	7	1	0	0	0	0	0	0	0	1	777	1079	38	1		1	APLNR	11	57003486	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	39864401	57003486	78003030	79	727										
FAM90A1	55138	broad.mit.edu	37	chr12	8374624	8374624	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gcgtccgttttccagtctccGaaagagcactctgagaggct	11	12	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:8374624G>A	ENST00000538603.1	-	7	1747	c.1189C>T	c.(1189-1191)Cgg>Tgg	p.R397W	FAM90A1_ENST00000307435.6_Missense_Mutation_p.R397W	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	397							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R397W(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TCCAGTCTCCGAAAGAGCACT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											15	21	19					12																	8374624		2032	3877	5909	8265891	SO:0001583	missense	55138			AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1189C>T	12.37:g.8374624G>A	ENSP00000445418:p.Arg397Trp		8265891	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	11.43	1.636869	0.29157	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.13307	2.6;2.6	1.06	-0.512	0.11966	.	.	.	.	.	T	0.18882	0.0453	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.72625	0.978	T	0.14868	-1.0457	9	0.66056	D	0.02	-1.1302	3.7926	0.08727	0.0:0.0:0.4156:0.5844	.	397	Q86YD7	F90A1_HUMAN	W	397	ENSP00000307798:R397W;ENSP00000445418:R397W	ENSP00000307798:R397W	R	-	1	2	FAM90A1	8265891	0.010000	0.17322	0.003000	0.11579	0.021000	0.10359	-0.738000	0.04871	-0.140000	0.11394	0.205000	0.17691	CGG		0.632	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		A	8374624	G	A	8374624	3	1	7	1	0	0	0	0	1	0	0	0	5669	1057	37	1	209	1	FAM90A1	12	8374624	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		8374624	125477271	80	728										
SCN8A	6334	broad.mit.edu	37	chr12	52168085	52168085	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gatgttgctcaagtggacagCctatggcttcgtcaagttct	11	9	3	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:52168085C>A	ENST00000354534.6	+	20	3936	c.3758C>A	c.(3757-3759)gCc>gAc	p.A1253D	SCN8A_ENST00000545061.1_Missense_Mutation_p.A1253D	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1253					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.A1253D(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	AAGTGGACAGCCTATGGCTTC	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	12											190	191	191					12																	52168085		2199	4300	6499	50454352	SO:0001583	missense	6334			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.3758C>A	12.37:g.52168085C>A	ENSP00000346534:p.Ala1253Asp		50454352	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.938830	0.92526	.	.	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D	0.99105	-5.43;-4.64;-4.64	4.86	4.86	0.63082	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	M	0.89163	3.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.995	D	0.98818	1.0746	10	0.87932	D	0	.	18.564	0.91111	0.0:1.0:0.0:0.0	.	1253;1253	F8VWM7;Q9UQD0	.;SCN8A_HUMAN	D	1253;1253;1253;1166	ENSP00000346534:A1253D;ENSP00000440360:A1253D;ENSP00000347255:A1253D	ENSP00000346534:A1253D	A	+	2	0	SCN8A	50454352	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.593000	0.82686	2.684000	0.91462	0.561000	0.74099	GCC		0.488	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52168085	C	A	52168085	3	1	7	1	0	0	0	0	1	0	0	0	13961	739	26	2	3832	2	SCN8A	12	52168085	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	43793461	52168085	81683810	81	729										
STAT2	6773	broad.mit.edu	37	chr12	56750243	56750243	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	accagttctggtcttcaatcCagacagccaagtactgtcga	8	12	3	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:56750243C>T	ENST00000314128.4	-	2	136	c.113G>A	c.(112-114)tGg>tAg	p.W38*	STAT2_ENST00000418572.2_Nonsense_Mutation_p.W38*|STAT2_ENST00000557235.1_Nonsense_Mutation_p.W38*			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	38					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.W38*(1)		NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						GTCTTCAATCCAGACAGCCAA	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											94	92	93					12																	56750243		2203	4300	6503	55036510	SO:0001587	stop_gained	6773			BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"SH2 domain containing"	11363	protein-coding gene	gene with protein product		600556	"signal transducer and activator of transcription 2, 113kD"			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.113G>A	12.37:g.56750243C>T	ENSP00000315768:p.Trp38*		55036510	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Nonsense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750887	0.89753	.	.	ENSG00000170581	ENST00000314128;ENST00000557235;ENST00000553337;ENST00000418572	.	.	.	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7979	15.6427	0.77020	0.0:1.0:0.0:0.0	.	.	.	.	X	38	.	ENSP00000315768:W38X	W	-	2	0	STAT2	55036510	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.579000	0.74036	2.769000	0.95229	0.655000	0.94253	TGG		0.522	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419		T	56750243	C	T	56750243	4	4	7	1	0	0	0	0	0	1	0	0	15304	595	21	3	2534	3	STAT2	12	56750243	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	4582158	56750243	77101652	82	730										
NAB2	4665	broad.mit.edu	37	chr12	57485247	57485247	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggtacccggaaagggagcatGagcaatgggcatggcagccc	16	10	0	1	rs200872269		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:57485247G>A	ENST00000300131.3	+	2	801	c.423G>A	c.(421-423)atG>atA	p.M141I	NAB2_ENST00000554718.1_3'UTR|NAB2_ENST00000357680.4_Missense_Mutation_p.M141I|NAB2_ENST00000342556.6_Missense_Mutation_p.M141I	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	141					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.M141I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AAGGGAGCATGAGCAATGGGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12											69	72	71					12																	57485247		2203	4300	6503	55771514	SO:0001583	missense	4665			BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.423G>A	12.37:g.57485247G>A	ENSP00000300131:p.Met141Ile		55771514	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	.	.	.	.	.	.	.	.	.	.	G	9.613	1.131879	0.21041	.	.	ENSG00000166886	ENST00000300131;ENST00000342556;ENST00000357680	.	.	.	4.59	1.65	0.23941	.	0.410743	0.25380	N	0.031098	T	0.21590	0.0520	N	0.14661	0.345	0.34994	D	0.755284	B	0.02656	0.0	B	0.01281	0.0	T	0.08027	-1.0742	9	0.18276	T	0.48	-4.4298	1.7106	0.02891	0.1867:0.1624:0.4839:0.167	.	141	Q15742	NAB2_HUMAN	I	141	.	ENSP00000300131:M141I	M	+	3	0	NAB2	55771514	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.807000	0.27140	0.533000	0.28675	0.462000	0.41574	ATG		0.587	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		A	57485247	G	A	57485247	3	1	7	1	0	0	0	0	1	0	0	0	10162	1290	45	3	429	3	NAB2	12	57485247	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	735004	57485247	76366648	83	731										
SLC6A15	55117	broad.mit.edu	37	chr12	85257235	85257235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	taccttatcttcaatccatgCgttatagccaggaggactta	7	10	2	0	rs376347410		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:85257235C>T	ENST00000266682.5	-	11	2342	c.1801G>A	c.(1801-1803)Gca>Aca	p.A601T	SLC6A15_ENST00000309283.7_Missense_Mutation_p.A309T|SLC6A15_ENST00000552192.1_Missense_Mutation_p.A494T	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	601					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.A601T(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TCAATCCATGCGTTATAGCCA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	THR/ALA,THR/ALA	0,4406		0,0,2203	88	94	92		1480,1801	5.7	1	12		92	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	SLC6A15	NM_001146335.1,NM_182767.4	58,58	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	494/624,601/731	85257235	1,12997	2203	4296	6499	83781366	SO:0001583	missense	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1801G>A	12.37:g.85257235C>T	ENSP00000266682:p.Ala601Thr		83781366	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	33	5.207705	0.95033	0.0	1.16E-4	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000552192;ENST00000548267	T;T;T	0.74947	-0.89;-0.89;-0.89	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.85729	0.5764	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.975	D	0.85102	0.0958	10	0.51188	T	0.08	.	19.8516	0.96743	0.0:1.0:0.0:0.0	.	309;601	F8WJN6;Q9H2J7	.;S6A15_HUMAN	T	309;601;494;79	ENSP00000311645:A309T;ENSP00000266682:A601T;ENSP00000450145:A494T	ENSP00000266682:A601T	A	-	1	0	SLC6A15	83781366	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.395000	0.79876	2.685000	0.91497	0.585000	0.79938	GCA		0.299	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		T	85257235	C	T	85257235	3	4	7	1	0	0	0	0	1	0	0	0	14715	768	27	1	399	1	SLC6A15	12	85257235	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	27771988	85257235	48594660	84	732										
ANO4	121601	broad.mit.edu	37	chr12	101413842	101413842	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cacaacaaagaaacgttcttCaacaatgccacaagaagtag	6	10	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr12:101413842C>A	ENST00000392977.3	+	9	975	c.765C>A	c.(763-765)ttC>ttA	p.F255L	ANO4_ENST00000538618.1_3'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.F220L|ANO4_ENST00000299222.9_5'UTR			Q32M45	ANO4_HUMAN	anoctamin 4	255					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.F220L(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AAACGTTCTTCAACAATGCCA	0.289										HNSCC(74;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											84	83	84					12																	101413842		2203	4299	6502	99937973	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.765C>A	12.37:g.101413842C>A	ENSP00000376703:p.Phe255Leu		99937973	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	C	34	5.294507	0.95546	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.71222	-0.55;-0.55	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.87168	0.6110	M	0.89214	3.015	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.80764	0.993;0.994	D	0.88896	0.3349	10	0.87932	D	0	.	18.7759	0.91911	0.0:1.0:0.0:0.0	.	255;220	Q32M45;Q32M45-2	ANO4_HUMAN;.	L	220;255	ENSP00000376705:F220L;ENSP00000376703:F255L	ENSP00000376703:F255L	F	+	3	2	ANO4	99937973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.035000	0.76517	2.714000	0.92807	0.650000	0.86243	TTC		0.289	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101413842	C	A	101413842	3	1	7	1	0	0	0	0	1	0	0	0	699	825	29	2	686	2	ANO4	12	101413842	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	16156607	101413842	32438053	85	733										
ING1	3621	broad.mit.edu	37	chr13	111372025	111372025	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gctccaaggccaaggcggagCgagaggcgtcccctgccgac	15	15	0	1	rs368239053		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr13:111372025C>T	ENST00000375774.3	+	2	1477	c.1015C>T	c.(1015-1017)Cga>Tga	p.R339*	ING1_ENST00000375775.3_Nonsense_Mutation_p.R127*|ING1_ENST00000338450.7_Nonsense_Mutation_p.R152*|ING1_ENST00000333219.7_Nonsense_Mutation_p.R196*	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	339					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.R196*(3)|p.R339*(1)|p.R152*(1)		endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CAAGGCGGAGCGAGAGGCGTC	0.627																																																5	Substitution - Nonsense(5)	endometrium(3)|large_intestine(2)	13											102	71	81					13																	111372025		2203	4300	6503	110170026	SO:0001587	stop_gained	3621				CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.1015C>T	13.37:g.111372025C>T	ENSP00000364929:p.Arg339*		110170026	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Nonsense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461577	0.63513	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	.	.	.	5.41	-4.77	0.03219	.	0.047098	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-45.0616	23.0881	0.99979	0.1965:0.8034:0.0:0.0	.	.	.	.	X	152;196;127;339	.	ENSP00000328436:R196X	R	+	1	2	ING1	110170026	0.974000	0.33945	0.853000	0.33588	0.380000	0.30137	0.240000	0.18042	-1.095000	0.03050	-0.500000	0.04577	CGA		0.627	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		T	111372025	C	T	111372025	4	4	7	1	0	0	0	0	0	1	0	0	7756	760	27	1	1169	1	ING1	13	111372025	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		111372025	3797853	86	734										
FOXG1	2290	broad.mit.edu	37	chr14	29237487	29237488	+	Nonsense_Mutation	DNP	CC	CC	AG													0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aacggcaccacgtcggcctaCcccagccaccccatgcccta					rs531378284		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr14:29237487_29237488CC>AG	ENST00000313071.4	+	1	1201_1202	c.1002_1003CC>AG	c.(1000-1005)taCCcc>taAGcc	p.334_335YP>*A	FOXG1_ENST00000382535.3_Nonsense_Mutation_p.334_335YP>*A	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	334					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y334>?(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CGTCGGCCTACCCCAGCCACCC	0.658																																																1	Complex(1)	large_intestine(1)	14																																								28307239	SO:0001587	stop_gained	2290				CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	Exception_encountered	14.37:g.29237487_29237488delinsAG	ENSP00000339004:p.Y334_P335delins*A		28307238	A6NFY2|P55315|Q14488|Q86XT7	Nonsense_Mutation	DNP	ENST00000313071.4	37	CCDS9636.1																																																																																				0.658	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			AG	29237488	CC	AG	29237487	4	1	7	1	0	0	0	0	0	1	0	0	6026	518	18	2	1004	2	FOXG1	14	29237487	Nonsense_Mutation	DNP	CC	TCGA-AF-3913-01A-02W-1073-09		29237487	78112053	87	735										
SNW1	22938	broad.mit.edu	37	chr14	78205352	78205352	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gcctttgcaggtctggatcaTctgcattcataacctccttt	7	12	4	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr14:78205352T>C	ENST00000261531.7	-	4	445	c.383A>G	c.(382-384)gAt>gGt	p.D128G	SNW1_ENST00000555761.1_Missense_Mutation_p.D128G|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000554775.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	128					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)	p.D128G(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		GTCTGGATCATCTGCATTCAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											278	292	287					14																	78205352		2203	4300	6503	77275105	SO:0001583	missense	22938			AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"SKI interacting protein"	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.383A>G	14.37:g.78205352T>C	ENSP00000261531:p.Asp128Gly		77275105	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	37	CCDS9867.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.012927	0.35511	.	.	ENSG00000100603	ENST00000261531;ENST00000555761;ENST00000416259;ENST00000554324	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	L	0.31065	0.9	0.80722	D	1	B;B	0.14012	0.009;0.001	B;B	0.19666	0.026;0.003	T	0.44757	-0.9307	9	0.07175	T	0.84	.	15.8367	0.78805	0.0:0.0:0.0:1.0	.	128;128	G3V3A4;Q13573	.;SNW1_HUMAN	G	128	.	ENSP00000261531:D128G	D	-	2	0	SNW1	77275105	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.655000	0.83696	2.146000	0.66826	0.377000	0.23210	GAT		0.378	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		C	78205352	T	C	78205352	3	2	7	1	0	0	0	0	1	0	0	0	14916	1435	50	4	1271	4	SNW1	14	78205352	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	48967865	78205352	29144188	88	736										
AHNAK2	113146	broad.mit.edu	37	chr14	105419482	105419482	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggcccttgaggtccactttgGgcatcttcaaactgggcctc	11	13	2	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr14:105419482G>T	ENST00000333244.5	-	7	2425	c.2306C>A	c.(2305-2307)cCc>cAc	p.P769H	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	769						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.P769H(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GTCCACTTTGGGCATCTTCAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	14											116	128	124					14																	105419482		1873	4100	5973	104490527	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2306C>A	14.37:g.105419482G>T	ENSP00000353114:p.Pro769His		104490527	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	14.03	2.414075	0.42817	.	.	ENSG00000185567	ENST00000333244	T	0.02837	4.14	3.28	3.28	0.37604	.	.	.	.	.	T	0.18299	0.0439	M	0.92122	3.275	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.03933	-1.0991	9	0.72032	D	0.01	-7.189	8.3859	0.32499	0.1153:0.0:0.8847:0.0	.	769	Q8IVF2	AHNK2_HUMAN	H	769	ENSP00000353114:P769H	ENSP00000353114:P769H	P	-	2	0	AHNAK2	104490527	0.943000	0.32029	0.003000	0.11579	0.060000	0.15804	0.918000	0.28678	1.374000	0.46228	0.485000	0.47835	CCC		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105419482	G	T	105419482	3	4	7	1	0	0	0	0	1	0	0	0	415	1232	43	2	15085	2	AHNAK2	14	105419482	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	27214130	105419482	1930058	89	737										
RYR3	6263	broad.mit.edu	37	chr15	33944956	33944956	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gctacatggtctggggtggaGacattgtagccagttcccag	14	9	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:33944956G>C	ENST00000389232.4	+	32	4250	c.4180G>C	c.(4180-4182)Gac>Cac	p.D1394H	RYR3_ENST00000415757.3_Missense_Mutation_p.D1394H	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1394	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.D1394H(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGGGGTGGAGACATTGTAGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	15											96	97	97					15																	33944956		2023	4192	6215	31732248	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.4180G>C	15.37:g.33944956G>C	ENSP00000373884:p.Asp1394His		31732248	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.704921	0.68615	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.69561	-0.41;-0.41	5.52	5.52	0.82312	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.79919	0.4529	L	0.54323	1.7	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.77557	0.985;0.99	T	0.80377	-0.1408	10	0.87932	D	0	.	19.6435	0.95767	0.0:0.0:1.0:0.0	.	1394;1394	Q15413-2;Q15413	.;RYR3_HUMAN	H	1394	ENSP00000373884:D1394H;ENSP00000399610:D1394H	ENSP00000354735:D1394H	D	+	1	0	RYR3	31732248	1.000000	0.71417	0.995000	0.50966	0.606000	0.37113	9.646000	0.98474	2.866000	0.98385	0.650000	0.86243	GAC		0.527	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	33944956	G	C	33944956	3	2	7	1	0	0	0	0	1	0	0	0	13807	942	33	5	4306	5	RYR3	15	33944956	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		33944956	68586436	90	738										
SORD	6652	broad.mit.edu	37	chr15	45365703	45365703	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gttgaaaatcatgctcaagtGtgaccccagtgaccagaatc	9	10	2	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:45365703G>T	ENST00000267814.9	+	9	1229	c.1049G>T	c.(1048-1050)tGt>tTt	p.C350F	SORD_ENST00000559562.1_3'UTR|SORD_ENST00000558580.1_Missense_Mutation_p.C329F|RP11-109D20.2_ENST00000560967.1_RNA	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	350					fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)	p.C350F(1)		endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		ATGCTCAAGTGTGACCCCAGT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											39	49	46					15																	45365703		2093	4269	6362	43152995	SO:0001583	missense	6652				CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.1049G>T	15.37:g.45365703G>T	ENSP00000267814:p.Cys350Phe		43152995	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	37	CCDS10116.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085710	0.76642	.	.	ENSG00000140263	ENST00000267814	T	0.01947	4.54	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.07098	0.0180	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.988	T	0.46762	-0.9168	10	0.56958	D	0.05	-9.2148	18.2799	0.90096	0.0:0.0:1.0:0.0	.	271;350	B4DKI2;Q00796	.;DHSO_HUMAN	F	350	ENSP00000267814:C350F	ENSP00000267814:C350F	C	+	2	0	SORD	43152995	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	9.294000	0.96088	2.577000	0.86979	0.563000	0.77884	TGT		0.502	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3			T	45365703	G	T	45365703	3	4	7	1	0	0	0	0	1	0	0	0	14970	1377	48	2	1083	2	SORD	15	45365703	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	11420747	45365703	57165689	91	739										
MYO5C	55930	broad.mit.edu	37	chr15	52539205	52539205	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	catgagcaagtacagagagcTgcggaactaggaaacaaagc	12	8	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:52539205T>A	ENST00000261839.7	-	16	2049	c.1888A>T	c.(1888-1890)Agc>Tgc	p.S630C	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	630	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S630C(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TACAGAGAGCTGCGGAACTAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											104	104	104					15																	52539205		1994	4166	6160	50326497	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1888A>T	15.37:g.52539205T>A	ENSP00000261839:p.Ser630Cys		50326497	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.638286	0.87760	.	.	ENSG00000128833	ENST00000261839	T	0.19250	2.16	5.27	4.14	0.48551	Myosin head, motor domain (2);	0.085120	0.85682	D	0.000000	T	0.42765	0.1217	M	0.85710	2.77	0.80722	D	1	P	0.46706	0.883	P	0.54544	0.755	T	0.43327	-0.9398	10	0.66056	D	0.02	.	11.3127	0.49372	0.0:0.0721:0.0:0.9279	.	630	Q9NQX4	MYO5C_HUMAN	C	630	ENSP00000261839:S630C	ENSP00000261839:S630C	S	-	1	0	MYO5C	50326497	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.161000	0.64935	0.944000	0.37579	0.459000	0.35465	AGC		0.438	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52539205	T	A	52539205	3	1	7	1	0	0	0	0	1	0	0	0	10110	1580	55	5	3444	5	MYO5C	15	52539205	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	7173502	52539205	49992187	92	740										
UNC13C	440279	broad.mit.edu	37	chr15	54542626	54542626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aagtgtcaggacctgctaaaCgctgactgcttgcagagtga	12	9	1	3	rs531463822	byFrequency	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:54542626C>T	ENST00000260323.11	+	7	3432	c.3432C>T	c.(3430-3432)aaC>aaT	p.N1144N	UNC13C_ENST00000537900.1_Silent_p.N1142N|UNC13C_ENST00000545554.1_Silent_p.N1144N	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1144					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.N1144N(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACCTGCTAAACGCTGACTGCT	0.483													c|||	2	0.000399361	0	0.0014	5008	,	,		19452	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	15											66	68	68					15																	54542626		2174	4280	6454	52329918	SO:0001819	synonymous_variant	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3432C>T	15.37:g.54542626C>T			52329918	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																				0.483	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54542626	C	T	54542626	2	4	7	1	0	0	0	0	0	0	0	1	17026	535	19	1		1	UNC13C	15	54542626	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	2003421	54542626	47988766	93	741										
TLN2	83660	broad.mit.edu	37	chr15	62949993	62949993	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cgggatgacatcctgaatggCtctcaccctgtctccttcga	9	14	2	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:62949993C>T	ENST00000561311.1	+	8	914	c.684C>T	c.(682-684)ggC>ggT	p.G228G	TLN2_ENST00000306829.6_Silent_p.G228G			Q9Y4G6	TLN2_HUMAN	talin 2	228	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G228G(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TCCTGAATGGCTCTCACCCTG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	15											159	136	144					15																	62949993		2203	4300	6503	60737285	SO:0001819	synonymous_variant	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.684C>T	15.37:g.62949993C>T			60737285	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																				0.488	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	62949993	C	T	62949993	2	4	7	1	0	0	0	0	0	0	0	1	15987	784	28	3		3	TLN2	15	62949993	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09	8407367	62949993	39581399	94	742										
ADAMTSL3	57188	broad.mit.edu	37	chr15	84558897	84558897	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgctgaatgtgtggatatccGcttgaagagggtagttcctg	14	6	0	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr15:84558897G>C	ENST00000286744.5	+	11	1333	c.1109G>C	c.(1108-1110)cGc>cCc	p.R370P	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R370P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	370						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R370P(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GTGGATATCCGCTTGAAGAGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											190	168	175					15																	84558897		2203	4300	6503	82349901	SO:0001583	missense	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1109G>C	15.37:g.84558897G>C	ENSP00000286744:p.Arg370Pro		82349901	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790594	0.90367	.	.	ENSG00000156218	ENST00000286744	T	0.60672	0.17	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.73674	0.3617	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.76168	-0.3058	10	0.62326	D	0.03	.	18.304	0.90174	0.0:0.0:1.0:0.0	.	370;370	P82987-2;P82987	.;ATL3_HUMAN	P	370	ENSP00000286744:R370P	ENSP00000286744:R370P	R	+	2	0	ADAMTSL3	82349901	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.224000	0.95209	2.377000	0.81083	0.655000	0.94253	CGC		0.403	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		C	84558897	G	C	84558897	3	2	7	1	0	0	0	0	1	0	0	0	276	1087	38	5	1147	5	ADAMTSL3	15	84558897	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	21608904	84558897	17972495	95	743										
CACNG3	10368	broad.mit.edu	37	chr16	24366209	24366209	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	agtgtcacgctgctgttcttCggcgggctctgcgtggcagc	15	12	3	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr16:24366209C>T	ENST00000005284.3	+	3	1553	c.351C>T	c.(349-351)ttC>ttT	p.F117F		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	117					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.F117F(1)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		TGCTGTTCTTCGGCGGGCTCT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	16																																								24273710	SO:0001819	synonymous_variant	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.351C>T	16.37:g.24366209C>T			24273710		Silent	SNP	ENST00000005284.3	37	CCDS10620.1																																																																																				0.617	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24366209	C	T	24366209	2	4	7	1	0	0	0	0	0	0	0	1	2564	883	31	1		1	CACNG3	16	24366209	Silent	SNP	C	TCGA-AF-3913-01A-02W-1073-09		24366209	65988544	96	744										
TP53	7157	broad.mit.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	7	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		7578406	73616804	97	745										
C17orf48	56985	broad.mit.edu	37	chr17	10608461	10608461	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ctgttgtgtccttcagcttgGagatatcatcgatggatata	10	7	2	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr17:10608461G>C	ENST00000379774.4	+	2	309	c.218G>C	c.(217-219)gGa>gCa	p.G73A	ADPRM_ENST00000609540.1_Missense_Mutation_p.G73A	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	73							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)	p.G73A(1)									CTTCAGCTTGGAGATATCATC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	17											159	149	152					17																	10608461		2203	4300	6503	10549186	SO:0001583	missense	56985			BC070155	CCDS11159.2	17p13.1	2012-07-20	2012-07-20	2012-07-20	ENSG00000170222	ENSG00000170222	3.6.1.13, 3.6.1.16, 3.6.1.53		30925	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 48"	C17orf48		18352857	Standard	XM_005256738		Approved	MDS006	uc002gmt.3	Q3LIE5	OTTHUMG00000130366	ENST00000379774.4:c.218G>C	17.37:g.10608461G>C	ENSP00000369099:p.Gly73Ala		10549186	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	37	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126442	0.77549	.	.	ENSG00000170222	ENST00000379774	D	0.99946	-8.62	5.65	5.65	0.86999	Metallophosphoesterase domain (1);	0.050811	0.85682	D	0.000000	D	0.99947	0.9977	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95947	0.8951	10	0.87932	D	0	-12.9629	19.5221	0.95189	0.0:0.0:1.0:0.0	.	73	Q3LIE5	ADPRM_HUMAN	A	73	ENSP00000369099:G73A	ENSP00000369099:G73A	G	+	2	0	C17orf48	10549186	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	8.739000	0.91574	2.941000	0.99782	0.655000	0.94253	GGA		0.423	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		C	10608461	G	C	10608461	3	2	7	1	0	0	0	0	1	0	0	0	1864	1174	41	5	220	5	C17orf48	17	10608461	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	3030055	10608461	70586749	98	746										
ABCA8	10351	broad.mit.edu	37	chr17	66913554	66913554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tagaaacaaagaagagcccgCgcactttagcttcccttggg	10	11	0	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr17:66913554C>T	ENST00000269080.2	-	15	2103	c.1966G>A	c.(1966-1968)Gcg>Acg	p.A656T	ABCA8_ENST00000586539.1_Missense_Mutation_p.A696T|ABCA8_ENST00000430352.2_Missense_Mutation_p.A696T	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	656	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A656T(2)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GAAGAGCCCGCGCACTTTAGC	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	17											107	117	113					17																	66913554		2203	4300	6503	64425149	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.1966G>A	17.37:g.66913554C>T	ENSP00000269080:p.Ala656Thr		64425149	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431150	0.43122	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	T;T	0.62941	-0.01;-0.01	4.91	4.91	0.64330	ABC transporter-like (1);	0.000000	0.52532	D	0.000077	T	0.43523	0.1251	N	0.04655	-0.195	0.45139	D	0.998156	P;B;B;B;P	0.52061	0.95;0.394;0.314;0.163;0.599	B;B;B;B;B	0.42593	0.392;0.147;0.046;0.197;0.22	T	0.54105	-0.8343	10	0.45353	T	0.12	.	17.2483	0.87034	0.0:1.0:0.0:0.0	.	635;696;696;696;656	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	T	656;696;635	ENSP00000269080:A656T;ENSP00000402814:A696T	ENSP00000269080:A656T	A	-	1	0	ABCA8	64425149	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	3.277000	0.51654	2.554000	0.86153	0.549000	0.68633	GCG		0.408	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66913554	C	T	66913554	3	4	7	1	0	0	0	0	1	0	0	0	38	768	27	1	2875	1	ABCA8	17	66913554	Missense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09	56305093	66913554	14281656	99	747										
ZNF91	7644	broad.mit.edu	37	chr19	23543701	23543701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggttgagagtcgcttaaaagTtttgtcacattctttacatt	8	6	2	1	rs78293839		TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr19:23543701T>C	ENST00000300619.7	-	4	2285	c.2080A>G	c.(2080-2082)Act>Gct	p.T694A	ZNF91_ENST00000397082.2_Missense_Mutation_p.T662A|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	694					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T694A(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CGCTTAAAAGTTTTGTCACAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19											93	97	96					19																	23543701		2070	4250	6320	23335541	SO:0001583	missense	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2080A>G	19.37:g.23543701T>C	ENSP00000300619:p.Thr694Ala		23335541	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.096730	0.00034	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.03745	3.82;3.82	1.71	-3.43	0.04810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01695	0.0054	N	0.17674	0.51	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.11329	0.0;0.006	T	0.47699	-0.9097	9	0.02654	T	1	.	1.6096	0.02691	0.3397:0.3682:0.1678:0.1243	.	662;694	Q05481-2;Q05481	.;ZNF91_HUMAN	A	694;662	ENSP00000300619:T694A;ENSP00000380272:T662A	ENSP00000300619:T694A	T	-	1	0	ZNF91	23335541	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.129000	0.03244	-2.440000	0.00550	-3.411000	0.00038	ACT		0.343	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		C	23543701	T	C	23543701	3	2	7	1	0	0	0	0	1	0	0	0	18239	1725	60	4	1499	4	ZNF91	19	23543701	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09		23543701	35585282	100	748										
KIRREL2	84063	broad.mit.edu	37	chr19	36348303	36348303	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tggtggtgctgctgggggagGaagcccggctgccgtgtgct	20	9	0	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr19:36348303G>T	ENST00000360202.5	+	2	316	c.118G>T	c.(118-120)Gaa>Taa	p.E40*	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000262625.7_Nonsense_Mutation_p.E40*|KIRREL2_ENST00000347900.6_Intron|KIRREL2_ENST00000592409.1_Nonsense_Mutation_p.E40*	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	40	Ig-like C2-type 1.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)		p.E40*(2)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCTGGGGGAGGAAGCCCGGCT	0.647																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											48	57	54					19																	36348303		2199	4297	6496	41040143	SO:0001587	stop_gained	84063			AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.118G>T	19.37:g.36348303G>T	ENSP00000353331:p.Glu40*		41040143	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Nonsense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	G	38	6.838210	0.97877	.	.	ENSG00000126259	ENST00000262625;ENST00000360202;ENST00000341658	.	.	.	5.04	5.04	0.67666	.	0.000000	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-19.7951	14.3154	0.66446	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	ENSP00000262625:E40X	E	+	1	0	KIRREL2	41040143	0.568000	0.26635	0.992000	0.48379	0.997000	0.91878	1.180000	0.32005	2.525000	0.85131	0.650000	0.86243	GAA		0.647	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		T	36348303	G	T	36348303	4	4	7	1	0	0	0	0	0	1	0	0	8346	1175	41	2	124	2	KIRREL2	19	36348303	Nonsense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	12804602	36348303	22780680	101	749										
TBC1D17	79735	broad.mit.edu	37	chr19	50388006	50388006	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	tgctggaccccctgctctgcGacttcctgggtatgtctctc	10	15	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr19:50388006G>A	ENST00000221543.5	+	13	1734	c.1435G>A	c.(1435-1437)Gac>Aac	p.D479N	TBC1D17_ENST00000535102.2_Missense_Mutation_p.D446N	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	479	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)	p.D479N(1)		NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		CCTGCTCTGCGACTTCCTGGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											40	39	39					19																	50388006		2203	4300	6503	55079818	SO:0001583	missense	79735			AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1435G>A	19.37:g.50388006G>A	ENSP00000221543:p.Asp479Asn		55079818	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	37	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	G	9.855	1.194820	0.22037	.	.	ENSG00000104946	ENST00000221543;ENST00000535102	T;T	0.10860	2.83;2.83	4.23	4.23	0.50019	Rab-GAP/TBC domain (5);	0.124686	0.52532	D	0.000080	T	0.04048	0.0113	N	0.01761	-0.735	0.80722	D	1	B;B	0.24533	0.105;0.003	B;B	0.22386	0.039;0.013	T	0.40739	-0.9547	10	0.08837	T	0.75	-33.4833	14.5005	0.67719	0.0:0.0:1.0:0.0	.	446;479	F5H1W7;Q9HA65	.;TBC17_HUMAN	N	479;446	ENSP00000221543:D479N;ENSP00000446323:D446N	ENSP00000221543:D479N	D	+	1	0	TBC1D17	55079818	1.000000	0.71417	0.995000	0.50966	0.250000	0.25880	3.801000	0.55545	2.343000	0.79666	0.655000	0.94253	GAC		0.602	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		A	50388006	G	A	50388006	3	1	7	1	0	0	0	0	1	0	0	0	15645	1058	37	1	1485	1	TBC1D17	19	50388006	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	14039703	50388006	8740977	102	750										
MATN4	8785	broad.mit.edu	37	chr20	43933297	43933297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	atactggatcacgccaacgcGcgtggcgttgggacccacgt	13	13	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr20:43933297G>A	ENST00000372754.1	-	2	222	c.214C>T	c.(214-216)Cgc>Tgc	p.R72C	MATN4_ENST00000372756.1_Missense_Mutation_p.R72C|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000353917.5_Missense_Mutation_p.R72C|MATN4_ENST00000537548.1_Missense_Mutation_p.R72C|RBPJL_ENST00000372743.1_5'Flank|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000342716.4_Missense_Mutation_p.R72C|MATN4_ENST00000360607.6_Missense_Mutation_p.R72C			O95460	MATN4_HUMAN	matrilin 4	72	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)		p.R72C(1)|p.N69fs*3(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				ACGCCAACGCGCGTGGCGTTG	0.647																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|skin(1)	20											36	34	34					20																	43933297		2202	4299	6501	43366711	SO:0001583	missense	8785			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.214C>T	20.37:g.43933297G>A	ENSP00000361840:p.Arg72Cys		43366711	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	37		.	.	.	.	.	.	.	.	.	.	G	17.67	3.447297	0.63178	.	.	ENSG00000124159	ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	4.2	4.2	0.49525	.	0.000000	0.42964	D	0.000631	D	0.95172	0.8435	H	0.96916	3.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.95750	0.8791	10	0.87932	D	0	.	11.0291	0.47761	0.0:0.0:0.8142:0.1858	.	72;72;72	A6NNA4;O95460-4;O95460-2	.;.;.	C	72	ENSP00000361840:R72C;ENSP00000361842:R72C;ENSP00000243983:R72C;ENSP00000353819:R72C;ENSP00000343164:R72C;ENSP00000440328:R72C	ENSP00000255132:R72C	R	-	1	0	MATN4	43366711	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	3.380000	0.52448	2.161000	0.67846	0.462000	0.41574	CGC		0.647	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			A	43933297	G	A	43933297	3	1	7	1	0	0	0	0	1	0	0	0	9366	1087	38	1	1563	1	MATN4	20	43933297	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09		43933297	19092223	103	751										
ADNP	23394	broad.mit.edu	37	chr20	49507985	49507985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	taactccggctaagctgccaTgcatgggctcagctactcca	9	14	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr20:49507985T>C	ENST00000396029.3	-	5	3833	c.3266A>G	c.(3265-3267)cAt>cGt	p.H1089R	ADNP_ENST00000396032.3_Missense_Mutation_p.H1089R|ADNP_ENST00000371602.4_Missense_Mutation_p.H1089R|ADNP_ENST00000349014.3_Missense_Mutation_p.H1089R	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	1089					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H1089R(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						TAAGCTGCCATGCATGGGCTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20											106	81	90					20																	49507985		2203	4300	6503	48941392	SO:0001583	missense	23394			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.3266A>G	20.37:g.49507985T>C	ENSP00000379346:p.His1089Arg		48941392	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	T	9.795	1.179095	0.21787	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	5.87	5.87	0.94306	.	0.088722	0.49305	D	0.000156	T	0.31918	0.0812	N	0.08118	0	0.36542	D	0.871351	B	0.02656	0.0	B	0.04013	0.001	T	0.31392	-0.9945	9	0.39692	T	0.17	-2.0144	10.5936	0.45325	0.0:0.0714:0.0:0.9286	.	1089	Q9H2P0	ADNP_HUMAN	R	1089	.	ENSP00000342905:H1089R	H	-	2	0	ADNP	48941392	0.991000	0.36638	0.979000	0.43373	0.992000	0.81027	2.287000	0.43505	2.248000	0.74166	0.533000	0.62120	CAT		0.522	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		C	49507985	T	C	49507985	3	2	7	1	0	0	0	0	1	0	0	0	323	1464	51	4	46	4	ADNP	20	49507985	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	5574688	49507985	13517535	104	752										
NFATC2	4773	broad.mit.edu	37	chr20	50139944	50139944	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ggggtgccacgtgagatgagGgctgcggcgaggggctccgg	22	9	0	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr20:50139944G>T	ENST00000396009.3	-	2	1055	c.836C>A	c.(835-837)cCc>cAc	p.P279H	NFATC2_ENST00000609507.1_Missense_Mutation_p.P60H|NFATC2_ENST00000371564.3_Missense_Mutation_p.P279H|NFATC2_ENST00000609943.1_Missense_Mutation_p.P259H|NFATC2_ENST00000610033.1_Missense_Mutation_p.P60H|NFATC2_ENST00000414705.1_Missense_Mutation_p.P259H	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	279	3 X approximate SP repeats.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P279H(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTGAGATGAGGGCTGCGGCGA	0.711																																																1	Substitution - Missense(1)	large_intestine(1)	20											9	12	11					20																	50139944		2170	4223	6393	49573351	SO:0001583	missense	4773			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.836C>A	20.37:g.50139944G>T	ENSP00000379330:p.Pro279His		49573351	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130792	0.37630	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.79033	-1.23;-1.23;-1.23	5.22	4.27	0.50696	.	0.373507	0.30285	N	0.009980	T	0.66509	0.2796	L	0.28344	0.845	0.27851	N	0.940733	P;P;D;P	0.56521	0.855;0.85;0.976;0.947	B;B;P;P	0.46975	0.359;0.258;0.533;0.533	T	0.58301	-0.7660	10	0.16420	T	0.52	-19.4848	9.8161	0.40853	0.157:0.0:0.843:0.0	.	259;259;279;279	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	H	279;279;60;259	ENSP00000360619:P279H;ENSP00000379330:P279H;ENSP00000396471:P259H	ENSP00000360619:P279H	P	-	2	0	NFATC2	49573351	1.000000	0.71417	0.987000	0.45799	0.712000	0.41017	8.585000	0.90802	1.190000	0.43042	0.313000	0.20887	CCC		0.711	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		T	50139944	G	T	50139944	3	4	7	1	0	0	0	0	1	0	0	0	10393	1232	43	2	2025	2	NFATC2	20	50139944	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	631959	50139944	12885576	105	753										
PCK1	5105	broad.mit.edu	37	chr20	56140577	56140577	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aggcaaattcctctggccagGctttggagagaactccaggg	13	10	1	1			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr20:56140577G>T	ENST00000319441.4	+	10	1750	c.1586G>T	c.(1585-1587)gGc>gTc	p.G529V	PCK1_ENST00000543666.1_Missense_Mutation_p.G212V	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	529					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)	p.G529V(1)		endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CTCTGGCCAGGCTTTGGAGAG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	20											76	75	75					20																	56140577		2203	4300	6503	55573983	SO:0001583	missense	5105				CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1586G>T	20.37:g.56140577G>T	ENSP00000319814:p.Gly529Val		55573983	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866552	0.91511	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666	T;T	0.07444	3.19;3.19	5.69	5.69	0.88448	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.49609	0.1567	H	0.98333	4.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.70324	-0.4903	10	0.87932	D	0	-43.4742	19.8045	0.96525	0.0:0.0:1.0:0.0	.	212;529	B4DT64;P35558	.;PCKGC_HUMAN	V	211;529;212	ENSP00000319814:G529V;ENSP00000445767:G212V	ENSP00000319814:G529V	G	+	2	0	PCK1	55573983	1.000000	0.71417	0.908000	0.35775	0.987000	0.75469	9.731000	0.98807	2.676000	0.91093	0.655000	0.94253	GGC		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56140577	G	T	56140577	3	4	7	1	0	0	0	0	1	0	0	0	11612	1203	42	2	1620	2	PCK1	20	56140577	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	6000633	56140577	6884943	106	754										
COL6A2	1292	broad.mit.edu	37	chr21	47549221	47549221	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ccaacagttgctaaacgccaCggagctcacgcaggacccgg	11	15	1	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr21:47549221C>T	ENST00000300527.4	+	28	2565				COL6A2_ENST00000397763.1_Missense_Mutation_p.T858M|COL6A2_ENST00000409416.1_3'UTR|COL6A2_ENST00000310645.5_3'UTR|COL6A2_ENST00000357838.4_Missense_Mutation_p.T858M	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)		p.T858M(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CTAAACGCCACGGAGCTCACG	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	21											84	82	82					21																	47549221		2203	4300	6503	46373649	SO:0001627	intron_variant	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2462-2647C>T	21.37:g.47549221C>T			46373649	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.481435	0.44147	.	.	ENSG00000142173	ENST00000357838;ENST00000397763	D;D	0.90900	-2.75;-2.75	3.99	3.99	0.46301	.	.	.	.	.	D	0.90752	0.7097	.	.	.	0.80722	D	1	D	0.63880	0.993	P	0.50490	0.642	D	0.90374	0.4383	8	0.46703	T	0.11	.	12.0529	0.53518	0.0:0.8258:0.1742:0.0	.	858	P12110-2	.	M	858	ENSP00000350497:T858M;ENSP00000380870:T858M	ENSP00000350497:T858M	T	+	2	0	COL6A2	46373649	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.281000	0.43452	1.770000	0.52166	0.467000	0.42956	ACG		0.697	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			T	47549221	C	T	47549221	1	4	7	0	1	0	0	0	0	0	0	0	3706	536	19	1		1	COL6A2	21	47549221	Intron	SNP	C	TCGA-AF-3913-01A-02W-1073-09		47549221	580674	107	755										
GAL3ST1	9514	broad.mit.edu	37	chr22	30953352	30953352	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cagccccttagccatggactCccagggcttcttctgcggtg	11	15	2	0	rs138460948	byFrequency	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr22:30953352C>A	ENST00000402321.1	-	2	345	c.28G>T	c.(28-30)Gag>Tag	p.E10*	GAL3ST1_ENST00000406955.1_Nonsense_Mutation_p.E10*|GAL3ST1_ENST00000338911.5_Nonsense_Mutation_p.E10*|GAL3ST1_ENST00000443111.2_Nonsense_Mutation_p.E10*|GAL3ST1_ENST00000406361.1_Nonsense_Mutation_p.E10*|GAL3ST1_ENST00000401975.1_Nonsense_Mutation_p.E10*|GAL3ST1_ENST00000402369.1_Nonsense_Mutation_p.E10*			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	10					galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)	p.E10*(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						GCCATGGACTCCCAGGGCTTC	0.652																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											77	82	80					22																	30953352		2203	4300	6503	29283352	SO:0001587	stop_gained	9514			D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"Sulfotransferases, membrane-bound"	24240	protein-coding gene	gene with protein product	"cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.28G>T	22.37:g.30953352C>A	ENSP00000385735:p.Glu10*		29283352	Q96C63	Nonsense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	C	37	6.086896	0.97271	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111;ENST00000441967;ENST00000431313;ENST00000452827;ENST00000437282;ENST00000416358;ENST00000427899;ENST00000423299;ENST00000443136;ENST00000423371;ENST00000428682;ENST00000453479;ENST00000426220;ENST00000447224;ENST00000411821;ENST00000445645;ENST00000448604	.	.	.	5.84	1.11	0.20524	.	0.380754	0.27518	N	0.019020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-28.7184	6.9258	0.24414	0.0:0.306:0.442:0.252	.	.	.	.	X	10	.	ENSP00000343234:E10X	E	-	1	0	GAL3ST1	29283352	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	0.428000	0.21395	0.358000	0.24211	0.655000	0.94253	GAG		0.652	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861		A	30953352	C	A	30953352	4	1	7	1	0	0	0	0	0	1	0	0	6217	864	30	2	1251	2	GAL3ST1	22	30953352	Nonsense_Mutation	SNP	C	TCGA-AF-3913-01A-02W-1073-09		30953352	20351214	108	756										
GCAT	23464	broad.mit.edu	37	chr22	38212575	38212575	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	ttgctttctaccctcccaggCatctttgtcatcgggttcag	8	13	4	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr22:38212575C>T	ENST00000248924.6	+	9	1166	c.1110C>T	c.(1108-1110)ggC>ggT	p.G370G	GCAT_ENST00000323205.6_Splice_Site_p.G396G	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	370					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)	p.G370G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	CCCTCCCAGGCATCTTTGTCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	22											81	75	77					22																	38212575		2203	4300	6503	36542521	SO:0001630	splice_region_variant	23464			AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"2-amino-3-ketobutyrate coenzyme A ligase"	607422	"glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.1109-1C>T	22.37:g.38212575C>T			36542521	E2QC23|Q6ZWF1|Q96CA9	Silent	SNP	ENST00000248924.6	37	CCDS13957.1																																																																																				0.602	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	Silent	T	38212575	C	T	38212575	5	4	7	1	0	0	0	0	0	0	1	0	6304	724	25	3	1222	3	GCAT	22	38212575	Splice_Site	SNP	C	TCGA-AF-3913-01A-02W-1073-09	7259223	38212575	13091991	109	757										
ATF4	468	broad.mit.edu	37	chr22	39918282	39918282	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	taccaggggctctccaaataGgagcctcccatctccaggtg	10	14	2	0			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chr22:39918282G>T	ENST00000337304.2	+	2	1613	c.731G>T	c.(730-732)aGg>aTg	p.R244M	ATF4_ENST00000396680.1_Missense_Mutation_p.R244M|ATF4_ENST00000404241.2_Missense_Mutation_p.R244M	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	244					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R244M(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	TCTCCAAATAGGAGCCTCCCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	22											18	19	19					22																	39918282		2203	4297	6500	38248228	SO:0001583	missense	468			D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.731G>T	22.37:g.39918282G>T	ENSP00000336790:p.Arg244Met		38248228	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	G	3.871	-0.027951	0.07589	.	.	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.24908	1.83;1.83;1.83	3.64	-0.328	0.12690	.	2.266840	0.01429	N	0.014664	T	0.23886	0.0578	L	0.44542	1.39	0.09310	N	1	P	0.35600	0.511	B	0.32393	0.145	T	0.37174	-0.9717	10	0.87932	D	0	-9.0666	8.422	0.32707	0.501:0.0:0.499:0.0	.	244	P18848	ATF4_HUMAN	M	244	ENSP00000384587:R244M;ENSP00000336790:R244M;ENSP00000379912:R244M	ENSP00000336790:R244M	R	+	2	0	ATF4	38248228	0.000000	0.05858	0.001000	0.08648	0.309000	0.27889	0.688000	0.25422	0.076000	0.16826	0.313000	0.20887	AGG		0.532	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		T	39918282	G	T	39918282	3	4	7	1	0	0	0	0	1	0	0	0	1083	1000	35	2	737	2	ATF4	22	39918282	Missense_Mutation	SNP	G	TCGA-AF-3913-01A-02W-1073-09	1705707	39918282	11386284	110	758										
PRICKLE3	4007	broad.mit.edu	37	chrX	49034403	49034404	+	Frame_Shift_Ins	INS	-	-	T													0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	cctcgtagcaggcgcagcagINStgggggcggctctgacgcat							TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chrX:49034403_49034404insT	ENST00000376317.3	-	7	987_988	c.893_894insA	c.(892-894)cacfs	p.H298fs	PRICKLE3_ENST00000540849.1_Frame_Shift_Ins_p.H230fs|PRICKLE3_ENST00000538114.1_Intron|PRICKLE3_ENST00000536904.1_Frame_Shift_Ins_p.H217fs	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)	298	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.						zinc ion binding (GO:0008270)	p.H298fs*15(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						AGGCGCAGCAGTGGGGGCGGCT	0.624																																																1	Insertion - Frameshift(1)	large_intestine(1)	X																																								48921348	SO:0001589	frameshift_variant	4007			BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"LIM domain only 6"	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.894dupA	X.37:g.49034404_49034404dupT	ENSP00000365494:p.His298fs		48921347	B7Z8F2|O76007|Q53XR5	Frame_Shift_Ins	INS	ENST00000376317.3	37	CCDS14320.1																																																																																				0.624	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060811.1	NM_006150		T	49034404	-	T	49034403	7	5	7	1	0	1	1	0	0	0	0	0	12522	1020	36	0	965	0	PRICKLE3	23	49034403	Frame_Shift_Ins	INS	-	TCGA-AF-3913-01A-02W-1073-09		49034403	106236157	111	759										
WNK3	65267	broad.mit.edu	37	chrX	54263730	54263730	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	acatcagtctcacaagctgcGctgaaagataagaagttgtc	9	9	2	3			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chrX:54263730G>A	ENST00000375159.2	-	19	4268	c.4269C>T	c.(4267-4269)agC>agT	p.S1423S	WNK3_ENST00000375169.3_Silent_p.S1376S|WNK3_ENST00000354646.2_Silent_p.S1423S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1423					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S1423S(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						CACAAGCTGCGCTGAAAGATA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	X											85	72	76					X																	54263730		2203	4300	6503	54280455	SO:0001819	synonymous_variant	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4269C>T	X.37:g.54263730G>A			54280455	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	37	CCDS14357.1																																																																																				0.408	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		A	54263730	G	A	54263730	2	1	7	1	0	0	0	0	0	0	0	1	17419	1078	38	1		1	WNK3	23	54263730	Silent	SNP	G	TCGA-AF-3913-01A-02W-1073-09	5229327	54263730	101006830	112	760										
CPXCR1	53336	broad.mit.edu	37	chrX	88008496	88008496	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	aatgagcctcctaatgactgTagtacagacatagagtctcc	8	10	1	4			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chrX:88008496T>C	ENST00000276127.4	+	3	340	c.81T>C	c.(79-81)tgT>tgC	p.C27C	CPXCR1_ENST00000373111.1_Silent_p.C27C	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	27							metal ion binding (GO:0046872)	p.C27C(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						CTAATGACTGTAGTACAGACA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	X											38	33	35					X																	88008496		2203	4300	6503	87895152	SO:0001819	synonymous_variant	53336			AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.81T>C	X.37:g.88008496T>C			87895152	B2R9F9|D3DTE7|Q96RS3	Silent	SNP	ENST00000276127.4	37	CCDS14458.1																																																																																				0.433	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		C	88008496	T	C	88008496	2	2	7	1	0	0	0	0	0	0	0	1	3842	1644	57	4		4	CPXCR1	23	88008496	Silent	SNP	T	TCGA-AF-3913-01A-02W-1073-09	33744766	88008496	67262064	113	761										
LONRF3	79836	broad.mit.edu	37	chrX	118147049	118147049	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12280701754386	14	1	1.49333333333333	3.52	0.8448	0.722393472194293	1	0	gatcagaaatgttcaattctTtgctgatggccgctcagtgg	11	8	4	2			TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AF-3913-01A-02W-1073-09	TCGA-AF-3913-11A-01W-1073-09	g.chrX:118147049T>A	ENST00000371628.3	+	9	1890	c.1859T>A	c.(1858-1860)tTt>tAt	p.F620Y	LONRF3_ENST00000304778.7_Missense_Mutation_p.F579Y|LONRF3_ENST00000422289.2_Missense_Mutation_p.F364Y|LONRF3_ENST00000472173.1_3'UTR	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	620	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.F579Y(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GTTCAATTCTTTGCTGATGGC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											132	130	130					X																	118147049		2203	4300	6503	118031077	SO:0001583	missense	79836			AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.1859T>A	X.37:g.118147049T>A	ENSP00000360690:p.Phe620Tyr		118031077	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	T	33	5.193389	0.94960	.	.	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.88	5.88	0.94601	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.000000	0.85682	D	0.000000	T	0.58680	0.2139	L	0.51914	1.62	0.46654	D	0.999148	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.79108	0.988;0.982;0.992	T	0.59742	-0.7397	10	0.54805	T	0.06	-28.1277	14.2923	0.66286	0.0:0.0:0.0:1.0	.	364;579;620	B3KUN7;Q496Y0-2;Q496Y0	.;.;LONF3_HUMAN	Y	579;579;620;364	ENSP00000360691:F579Y;ENSP00000307732:F579Y;ENSP00000360690:F620Y;ENSP00000408894:F364Y	ENSP00000307732:F579Y	F	+	2	0	LONRF3	118031077	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	8.040000	0.89188	1.973000	0.57446	0.486000	0.48141	TTT		0.483	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		A	118147049	T	A	118147049	3	1	7	1	0	0	0	0	1	0	0	0	8925	1841	64	5	1893	5	LONRF3	23	118147049	Missense_Mutation	SNP	T	TCGA-AF-3913-01A-02W-1073-09	30138553	118147049	37123511	114	762										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2082231	2082231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cttgttctccctccctaggaCcttaagccagttatcgatgg	8	13	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:2082231C>T	ENST00000400921.2	+	6	824	c.141C>T	c.(139-141)gaC>gaT	p.D47D	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Silent_p.D47D	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	230	OPR.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	CTCCCTAGGACCTTAAGCCAG	0.567																																																0			1											66	60	62					1																	2082231		2203	4300	6503	2072091	SO:0001819	synonymous_variant	5590			BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.141C>T	1.37:g.2082231C>T			2072091	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																				0.567	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2082231	C	T	2082231	2	4	8	1	0	0	0	0	0	0	0	1	12551	506	18	3		3	PRKCZ	1	2082231	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10		2082231	247168390	1	763										
SLC2A1	6513	hgsc.bcm.edu	37	chr1	43392858	43392858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tttgaagtaggtgaagatgaAgaacagaaccaggagcacag	13	5	0	6			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:43392858A>G	ENST00000426263.3	-	10	1511	c.1333T>C	c.(1333-1335)Ttc>Ctc	p.F445L	SLC2A1_ENST00000475162.1_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	445					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)	p.F445L(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	GTGAAGATGAAGAACAGAACC	0.517																																																1	Substitution - Missense(1)	ovary(1)	1											86	68	74					1																	43392858		2203	4300	6503	43165445	SO:0001583	missense	6513			K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.1333T>C	1.37:g.43392858A>G	ENSP00000416293:p.Phe445Leu		43165445	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Missense_Mutation	SNP	ENST00000426263.3	37	CCDS477.1	.	.	.	.	.	.	.	.	.	.	A	10.45	1.354426	0.24512	.	.	ENSG00000117394	ENST00000426263;ENST00000372501;ENST00000397019	T	0.73789	-0.78	5.66	5.66	0.87406	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	L	0.31294	0.92	0.80722	D	1	B	0.14012	0.009	B	0.17979	0.02	T	0.58142	-0.7688	10	0.22706	T	0.39	.	13.8441	0.63457	1.0:0.0:0.0:0.0	.	445	P11166	GTR1_HUMAN	L	445;445;387	ENSP00000416293:F445L	ENSP00000361579:F445L	F	-	1	0	SLC2A1	43165445	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.978000	0.70501	2.166000	0.68216	0.454000	0.30748	TTC		0.517	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		G	43392858	A	G	43392858	3	3	8	1	0	0	0	0	1	0	0	0	14575	72	3	4	149	4	SLC2A1	1	43392858	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	41310627	43392858	205857763	2	764										
MPL	4352	hgsc.bcm.edu	37	chr1	43805059	43805059	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tttcctgaggtacgaactccGctatggccccagagatccca	9	14	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:43805059G>A	ENST00000372470.3	+	4	551	c.509G>A	c.(508-510)cGc>cAc	p.R170H	MPL_ENST00000413998.2_Missense_Mutation_p.R170H	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	170					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TACGAACTCCGCTATGGCCCC	0.572			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	0			1											80	73	75					1																	43805059		2203	4300	6503	43577646	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.509G>A	1.37:g.43805059G>A	ENSP00000361548:p.Arg170His		43577646	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.980277	0.53827	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	D;D	0.86432	-2.12;-2.12	5.55	4.44	0.53790	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.306681	0.38058	N	0.001831	D	0.88317	0.6404	L	0.32530	0.975	0.35985	D	0.836287	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.76575	0.988;0.973;0.925	D	0.89609	0.3840	10	0.52906	T	0.07	-20.9461	10.1702	0.42904	0.105:0.0:0.895:0.0	.	163;170;170	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	H	170	ENSP00000361548:R170H;ENSP00000414004:R170H	ENSP00000361546:R170H	R	+	2	0	MPL	43577646	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	2.294000	0.43567	2.617000	0.88574	0.555000	0.69702	CGC		0.572	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		A	43805059	G	A	43805059	3	1	8	1	0	0	0	0	1	0	0	0	9760	1087	38	1	523	1	MPL	1	43805059	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	412201	43805059	205445562	3	765										
L1TD1	54596	hgsc.bcm.edu	37	chr1	62675645	62675674	+	In_Frame_Del	DEL	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	-													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gatggaggatgatgaagataCctcagggctggaggaggagg					rs141196718|rs199552452|rs201629799|rs200503897|rs200931139|rs532563709|rs386631745|rs145231033|rs200789118	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:62675645_62675674delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	ENST00000498273.1	+	4	1494_1523	c.1199_1228delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	c.(1198-1230)acctcagggctggaggaggaggaggaagagccc>acc	p.SGLEEEEEEP401del	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	401	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						GATGAAGATACCTCAGGGCTggaggaggaggaggaagagccctcagggct	0.535																																																0			1							,	335,3925		13,309,1808					,	-4.7	0			50	405,7849		12,381,3734	no	coding,coding	L1TD1	NM_019079.4,NM_001164835.1	,	25,690,5542	A1A1,A1R,RR		4.9067,7.8638,5.9134	,	,		740,11774				62448262	SO:0001651	inframe_deletion	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1199_1228delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	1.37:g.62675645_62675674delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	ENSP00000419901:p.Ser401_Pro410del		62448233	Q8NDA1|Q9NUV8|Q9NV78	In_Frame_Del	DEL	ENST00000498273.1	37	CCDS619.1																																																																																				0.535	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		-	62675674	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	-	62675645	7	5	8	1	0	1	0	1	0	0	0	0	8611	507	18	0	1205	0	L1TD1	1	62675645	In_Frame_Del	DEL	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	TCGA-AF-4110-01A-02D-1733-10	18870586	62675645	186574976	4	766										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90400935	90400935	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aagtggacattctgccaaaaCaattgtttaaatgcataaag	7	6	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:90400935C>A	ENST00000337338.5	+	3	2715	c.2308C>A	c.(2308-2310)Caa>Aaa	p.Q770K	LRRC8D_ENST00000394593.3_Missense_Mutation_p.Q770K	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	770					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		TCTGCCAAAACAATTGTTTAA	0.423																																																0			1											96	94	95					1																	90400935		2203	4300	6503	90173523	SO:0001583	missense	55144			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.2308C>A	1.37:g.90400935C>A	ENSP00000338887:p.Gln770Lys		90173523	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	37	CCDS726.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.796115	0.31777	.	.	ENSG00000171492	ENST00000337338;ENST00000394593	T;T	0.56611	0.45;0.45	6.07	6.07	0.98685	.	0.137764	0.50627	D	0.000111	T	0.31544	0.0800	L	0.43152	1.355	0.45035	D	0.998057	B	0.19935	0.04	B	0.20184	0.028	T	0.06991	-1.0796	9	.	.	.	.	15.3709	0.74564	0.1393:0.8606:0.0:0.0	.	770	Q7L1W4	LRC8D_HUMAN	K	770	ENSP00000338887:Q770K;ENSP00000378093:Q770K	.	Q	+	1	0	LRRC8D	90173523	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.886000	0.56190	2.884000	0.98904	0.655000	0.94253	CAA		0.423	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90400935	C	A	90400935	3	1	8	1	0	0	0	0	1	0	0	0	9053	479	17	2	2310	2	LRRC8D	1	90400935	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	27725290	90400935	158849686	5	767										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060317	111060317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggacgccttcagtgtttgccCgaggatctgcagccccttgg	13	13	2	0	rs190117605		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:111060317C>T	ENST00000369771.2	-	1	1480	c.1093G>A	c.(1093-1095)Ggg>Agg	p.G365R		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	365					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	AGTGTTTGCCCGAGGATCTGC	0.557													C|||	1	0.000199681	0	0	5008	,	,		20618	0		0.001	False		,,,				2504	0															0			1											98	95	96					1																	111060317		2203	4300	6503	110861840	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1093G>A	1.37:g.111060317C>T	ENSP00000358786:p.Gly365Arg		110861840		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.76	3.211498	0.58343	.	.	ENSG00000143105	ENST00000369771	D	0.98701	-5.08	5.63	5.63	0.86233	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99287	0.9751	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99544	1.0964	10	0.87932	D	0	.	18.3064	0.90184	0.0:1.0:0.0:0.0	.	365	Q16322	KCA10_HUMAN	R	365	ENSP00000358786:G365R	ENSP00000358786:G365R	G	-	1	0	KCNA10	110861840	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	7.815000	0.86186	2.676000	0.91093	0.558000	0.71614	GGG		0.557	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060317	C	T	111060317	3	4	8	1	0	0	0	0	1	0	0	0	8023	652	23	1	446	1	KCNA10	1	111060317	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	20659382	111060317	138190304	6	768										
CD101	9398	hgsc.bcm.edu	37	chr1	117554415	117554415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gtttgcagccagtgacgtacAgctcaacaaactgggaccca	10	12	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:117554415A>G	ENST00000256652.4	+	3	726	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	CD101_ENST00000369470.1_Missense_Mutation_p.Q223R	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	223	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGTGACGTACAGCTCAACAAA	0.507																																																0			1											85	75	78					1																	117554415		2203	4300	6503	117355938	SO:0001583	missense	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.668A>G	1.37:g.117554415A>G	ENSP00000256652:p.Gln223Arg		117355938	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.338193	0.00224	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.64991	-0.13;-0.13	5.57	1.64	0.23874	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.608916	0.15180	N	0.276180	T	0.04497	0.0123	N	0.00146	-1.995	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44742	-0.9308	10	0.02654	T	1	-6.3817	5.4565	0.16594	0.2318:0.0:0.6273:0.1409	.	223	Q93033	IGSF2_HUMAN	R	223	ENSP00000256652:Q223R;ENSP00000358482:Q223R	ENSP00000256652:Q223R	Q	+	2	0	CD101	117355938	0.006000	0.16342	0.000000	0.03702	0.002000	0.02628	1.079000	0.30766	0.063000	0.16370	-0.202000	0.12741	CAG		0.507	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		G	117554415	A	G	117554415	3	3	8	1	0	0	0	0	1	0	0	0	2968	188	7	4	678	4	CD101	1	117554415	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	6494098	117554415	131696206	7	769										
BCL9	607	hgsc.bcm.edu	37	chr1	147086225	147086225	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cgagtcattttattcttttaGaatgtaattctgctgaccac	6	8	3	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:147086225G>T	ENST00000234739.3	+	6	1110		c.e6-1		BCL9_ENST00000473292.1_Splice_Site	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					TATTCTTTTAGAATGTAATTC	0.433			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	0			1											74	77	76					1																	147086225		2203	4300	6503	145552849	SO:0001630	splice_region_variant	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.371-1G>T	1.37:g.147086225G>T			145552849	Q5T489	Splice_Site	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.291838	0.80914	.	.	ENSG00000116128	ENST00000234739	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6982	0.96039	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BCL9	145552849	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.672000	0.74477	2.894000	0.99253	0.655000	0.94253	.		0.433	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	Intron	T	147086225	G	T	147086225	5	4	8	1	0	0	0	0	0	0	1	0	1382	956	33	2	380	2	BCL9	1	147086225	Splice_Site	SNP	G	TCGA-AF-4110-01A-02D-1733-10	29531810	147086225	102164396	8	770										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858598	149858598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctcgtcccgcgctggcctccAgttcccggtagggcgagtgc	14	16	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:149858598A>G	ENST00000331380.2	+	1	74	c.74A>G	c.(73-75)cAg>cGg	p.Q25R	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	25						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GCTGGCCTCCAGTTCCCGGTA	0.652																																																0			1											68	75	72					1																	149858598		2203	4299	6502	148125222	SO:0001583	missense	8338			AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.74A>G	1.37:g.149858598A>G	ENSP00000332194:p.Gln25Arg		148125222	Q6DRA7|Q8IUE5	Missense_Mutation	SNP	ENST00000331380.2	37	CCDS937.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.213734	0.58452	.	.	ENSG00000184260	ENST00000331380	T	0.66995	-0.24	5.81	4.66	0.58398	Histone-fold (2);Histone core (1);Histone H2A (3);	0.000000	0.42053	D	0.000761	T	0.78848	0.4348	H	0.95470	3.675	0.41055	D	0.985331	P	0.35793	0.521	P	0.50405	0.64	T	0.82303	-0.0524	10	0.87932	D	0	.	12.0124	0.53295	0.855:0.145:0.0:0.0	.	25	Q16777	H2A2C_HUMAN	R	25	ENSP00000332194:Q25R	ENSP00000332194:Q25R	Q	+	2	0	HIST2H2AC	148125222	1.000000	0.71417	0.989000	0.46669	0.940000	0.58332	6.119000	0.71590	0.995000	0.38917	0.533000	0.62120	CAG		0.652	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		G	149858598	A	G	149858598	3	3	8	1	0	0	0	0	1	0	0	0	7199	188	7	4	76	4	HIST2H2AC	1	149858598	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	2772373	149858598	99392023	9	771										
ECM1	1893	hgsc.bcm.edu	37	chr1	150485845	150485845	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	attatctgaggaacgtggctCtagtgtctggagacactgag	13	7	3	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:150485845C>G	ENST00000369047.4	+	10	1650	c.1525C>G	c.(1525-1527)Cta>Gta	p.L509V	ECM1_ENST00000369049.4_Missense_Mutation_p.L536V|LINC00568_ENST00000416894.1_lincRNA|ECM1_ENST00000346569.6_Missense_Mutation_p.L384V|ECM1_ENST00000470432.1_3'UTR	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	509					angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	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;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GAACGTGGCTCTAGTGTCTGG	0.542																																					Melanoma(156;1696 2560 11093 19685)											0			1											108	99	102					1																	150485845		2203	4300	6503	148752469	SO:0001583	missense	1893			U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.1525C>G	1.37:g.150485845C>G	ENSP00000358043:p.Leu509Val		148752469	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129237	0.37533	.	.	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	T;T;T	0.76578	-1.03;-1.03;-1.03	4.85	-1.24	0.09435	.	0.831604	0.10134	N	0.711736	T	0.37320	0.0999	L	0.35723	1.085	0.19945	N	0.999946	B;P;B	0.46859	0.228;0.885;0.02	B;B;B	0.41374	0.128;0.355;0.04	T	0.42932	-0.9422	10	0.02654	T	1	-1.118	6.1281	0.20189	0.0:0.2745:0.5154:0.2101	.	536;384;509	Q16610-4;Q16610-2;Q16610	.;.;ECM1_HUMAN	V	536;509;384	ENSP00000358045:L536V;ENSP00000358043:L509V;ENSP00000271630:L384V	ENSP00000271630:L384V	L	+	1	2	ECM1	148752469	0.016000	0.18221	0.960000	0.40013	0.880000	0.50808	-1.287000	0.02785	-0.065000	0.13021	0.563000	0.77884	CTA		0.542	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		G	150485845	C	G	150485845	3	3	8	1	0	0	0	0	1	0	0	0	4908	912	32	5	1563	5	ECM1	1	150485845	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	627247	150485845	98764776	10	772										
SMG5	23381	hgsc.bcm.edu	37	chr1	156230371	156230371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctagaggggaggtcaggcagTtcacaaccttcaagaagatc	12	9	3	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:156230371T>C	ENST00000361813.5	-	15	2298	c.2154A>G	c.(2152-2154)gaA>gaG	p.E718E	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	718					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.E718E(1)		NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					GGTCAGGCAGTTCACAACCTT	0.567																																																1	Substitution - coding silent(1)	ovary(1)	1											79	65	69					1																	156230371		2203	4300	6503	154496995	SO:0001819	synonymous_variant	23381			AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2154A>G	1.37:g.156230371T>C			154496995	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Silent	SNP	ENST00000361813.5	37	CCDS1137.1																																																																																				0.567	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		C	156230371	T	C	156230371	2	2	8	1	0	0	0	0	0	0	0	1	14833	1722	60	4		4	SMG5	1	156230371	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10	5744526	156230371	93020250	11	773										
RABIF	5877	hgsc.bcm.edu	37	chr1	202858154	202858154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cagcacccgggagccgcaacGctggcacagcaccgccttcc	11	19	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:202858154G>A	ENST00000367262.3	-	1	109	c.73C>T	c.(73-75)Cgt>Tgt	p.R25C		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	25					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			GAGCCGCAACGCTGGCACAGC	0.682																																																0			1											29	27	28					1																	202858154		2200	4299	6499	201124777	SO:0001583	missense	5877			S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.73C>T	1.37:g.202858154G>A	ENSP00000356231:p.Arg25Cys		201124777	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	37	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.063654	0.76187	.	.	ENSG00000183155	ENST00000367262	.	.	.	4.69	2.81	0.32909	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.000000	0.85682	D	0.000000	T	0.77025	0.4070	M	0.84511	2.7	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.76008	-0.3116	9	0.56958	D	0.05	-7.4854	8.1289	0.31016	0.0853:0.1589:0.7558:0.0	.	25	P47224	MSS4_HUMAN	C	25	.	ENSP00000356231:R25C	R	-	1	0	RABIF	201124777	1.000000	0.71417	0.956000	0.39512	0.996000	0.88848	5.978000	0.70501	0.575000	0.29434	0.655000	0.94253	CGT		0.682	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1			A	202858154	G	A	202858154	3	1	8	1	0	0	0	0	1	0	0	0	13006	1087	38	1	306	1	RABIF	1	202858154	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	46627783	202858154	46392467	12	774										
MFSD4	148808	hgsc.bcm.edu	37	chr1	205549974	205549974	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aagccttggtccaaccagacGttcccagggctgactccaaa	9	14	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:205549974G>A	ENST00000367147.4	+	3	708	c.615G>A	c.(613-615)acG>acA	p.T205T	MFSD4_ENST00000539267.1_Silent_p.T205T|MFSD4_ENST00000536357.1_Intron	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	205					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CCAACCAGACGTTCCCAGGGC	0.622																																																0			1											78	64	69					1																	205549974		2203	4300	6503	203816597	SO:0001819	synonymous_variant	148808			BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.615G>A	1.37:g.205549974G>A			203816597	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	37	CCDS1455.1																																																																																				0.622	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644		A	205549974	G	A	205549974	2	1	8	1	0	0	0	0	0	0	0	1	9563	1132	40	1		1	MFSD4	1	205549974	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	2691820	205549974	43700647	13	775										
USH2A	7399	hgsc.bcm.edu	37	chr1	215963508	215963508	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tggaataagttcagtctcacAgcattttactggcaccgggt	10	9	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr1:215963508A>G	ENST00000307340.3	-	51	10461	c.10075T>C	c.(10075-10077)Tgt>Cgt	p.C3359R	USH2A_ENST00000366943.2_Missense_Mutation_p.C3359R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3359					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCAGTCTCACAGCATTTTACT	0.388										HNSCC(13;0.011)																																						0			1											133	127	129					1																	215963508		2203	4300	6503	214030131	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.10075T>C	1.37:g.215963508A>G	ENSP00000305941:p.Cys3359Arg		214030131	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986175	0.74589	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.42513	0.97;0.97	5.76	5.76	0.90799	Fibronectin, type III (2);	0.000000	0.49305	D	0.000150	T	0.66218	0.2767	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.71424	-0.4597	10	0.87932	D	0	.	16.0843	0.81031	1.0:0.0:0.0:0.0	.	3359	O75445	USH2A_HUMAN	R	3359	ENSP00000305941:C3359R;ENSP00000355910:C3359R	ENSP00000305941:C3359R	C	-	1	0	USH2A	214030131	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.478000	0.90428	2.191000	0.70037	0.533000	0.62120	TGT		0.388	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	215963508	A	G	215963508	3	3	8	1	0	0	0	0	1	0	0	0	17076	188	7	4	5621	4	USH2A	1	215963508	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	10413534	215963508	33287113	14	776										
NRBP1	29959	hgsc.bcm.edu	37	chr2	27664625	27664625	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gaagagaccttgaacaagttCaattttgccaggaacagtac	9	8	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:27664625C>T	ENST00000233557.3	+	19	2386	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	KRTCAP3_ENST00000288873.3_5'Flank|KRTCAP3_ENST00000407293.1_5'Flank|KRTCAP3_ENST00000543753.1_5'Flank|NRBP1_ENST00000379852.3_Silent_p.F518F|NRBP1_ENST00000379863.3_Silent_p.F526F			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	518					ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					TGAACAAGTTCAATTTTGCCA	0.562																																																0			2											173	175	174					2																	27664625		2203	4300	6503	27518129	SO:0001819	synonymous_variant	29959			AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.1554C>T	2.37:g.27664625C>T			27518129	B3KV40|D6W558|Q53FZ5|Q96SU3	Silent	SNP	ENST00000233557.3	37	CCDS1753.1																																																																																				0.562	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		T	27664625	C	T	27664625	2	4	8	1	0	0	0	0	0	0	0	1	10673	825	29	3		3	NRBP1	2	27664625	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10		27664625	215534748	15	777										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29221082	29221082	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gctgggccccgggtgctcccGcctggaagcatcaactccag	13	16	1	0	rs201622059		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:29221082G>T	ENST00000379558.4	+	3	453	c.102G>T	c.(100-102)ccG>ccT	p.P34P	FAM179A_ENST00000403861.2_Silent_p.P34P	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	34										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGGTGCTCCCGCCTGGAAGCA	0.652																																																0			2											20	22	22					2																	29221082		1949	4142	6091	29074586	SO:0001819	synonymous_variant	165186			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.102G>T	2.37:g.29221082G>T			29074586	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																				0.652	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29221082	G	T	29221082	2	4	8	1	0	0	0	0	0	0	0	1	5521	1074	38	2		2	FAM179A	2	29221082	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	1556457	29221082	213978291	16	778										
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98123521	98123522	+	IGR	INS	-	-	G													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	catctagctctcaaacacctINSgcagcatctgaaataaatca							TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:98123521_98123522insG								AC159540.1 (32472 upstream) : ANKRD36B (40505 downstream)																							CTCAAACACCTGCAGCATCTGA	0.327																																																0			2																																								97489954	SO:0001628	intergenic_variant	57730																															2.37:g.98123522_98123522dupG			97489953		Frame_Shift_Ins	INS		37																																																																																				0	0.327									G	98123522	-	G	98123521	6	5	8	0	1	1	1	0	0	0	0	0	666	1580	55	0		0	ANKRD36B	2	98123521	IGR	INS	-	TCGA-AF-4110-01A-02D-1733-10	68902439	98123521	145075852	17	779										
LRP2	4036	hgsc.bcm.edu	37	chr2	170044659	170044659	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	agtcattatcctcatcacagAcgaaggttttactaatgcag	7	9	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:170044659A>G	ENST00000263816.3	-	49	9434	c.9149T>C	c.(9148-9150)gTc>gCc	p.V3050A		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3050	LDL-receptor class A 24. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CTCATCACAGACGAAGGTTTT	0.517																																																0			2											149	136	141					2																	170044659		2203	4300	6503	169752905	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.9149T>C	2.37:g.170044659A>G	ENSP00000263816:p.Val3050Ala		169752905	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	7.493	0.651109	0.14516	.	.	ENSG00000081479	ENST00000263816	D	0.95885	-3.84	5.68	-0.881	0.10607	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.728006	0.13884	N	0.356140	D	0.92747	0.7694	M	0.64260	1.97	0.09310	N	0.999999	B	0.29341	0.242	B	0.36766	0.232	T	0.81165	-0.1057	10	0.09338	T	0.73	.	10.3329	0.43833	0.6849:0.0:0.3151:0.0	.	3050	P98164	LRP2_HUMAN	A	3050	ENSP00000263816:V3050A	ENSP00000263816:V3050A	V	-	2	0	LRP2	169752905	0.997000	0.39634	0.004000	0.12327	0.479000	0.33129	3.878000	0.56130	-0.137000	0.11455	0.528000	0.53228	GTC		0.517	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170044659	A	G	170044659	3	3	8	1	0	0	0	0	1	0	0	0	8985	275	10	4	4942	4	LRP2	2	170044659	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	71921138	170044659	73154714	18	780										
TTN	7273	hgsc.bcm.edu	37	chr2	179495016	179495016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aacattggcagcttggaaatCcaccccacccgtctggtcca	8	15	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:179495016C>T	ENST00000591111.1	-	189	39534	c.39310G>A	c.(39310-39312)Gat>Aat	p.D13104N	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D14745N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D5680N|TTN_ENST00000342992.6_Missense_Mutation_p.D12177N|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D5805N|TTN_ENST00000342175.6_Missense_Mutation_p.D5872N|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13104					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTGGAAATCCACCCCACCC	0.393																																																0			2											84	88	87					2																	179495016		1860	4086	5946	179203261	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39310G>A	2.37:g.179495016C>T	ENSP00000465570:p.Asp13104Asn		179203261	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.21	3.059148	0.55325	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	6.04	6.04	0.98038	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43033	0.1229	L	0.57536	1.79	0.49213	D	0.999765	B;B;B;B	0.31383	0.321;0.321;0.321;0.321	B;B;B;B	0.33454	0.164;0.164;0.164;0.164	T	0.33929	-0.9849	9	0.87932	D	0	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	5680;5805;5872;13104	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	12177;5680;5872;5805;5680	ENSP00000343764:D12177N;ENSP00000434586:D5680N;ENSP00000340554:D5872N;ENSP00000352154:D5805N	ENSP00000340554:D5872N	D	-	1	0	TTN	179203261	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	6.044000	0.71012	2.873000	0.98535	0.563000	0.77884	GAT		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179495016	C	T	179495016	3	4	8	1	0	0	0	0	1	0	0	0	16775	855	30	3	63956	3	TTN	2	179495016	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	9450357	179495016	63704357	19	781										
TTN	7273	hgsc.bcm.edu	37	chr2	179669343	179669343	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acaacgctttgtaacggctgCgtaaacgtcggtgcttgagt	12	9	0	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:179669343C>T	ENST00000591111.1	-	2	251	c.27G>A	c.(25-27)acG>acA	p.T9T	TTN_ENST00000589042.1_Silent_p.T9T|TTN_ENST00000360870.5_Silent_p.T9T|TTN_ENST00000460472.2_Silent_p.T9T|TTN_ENST00000342992.6_Silent_p.T9T|TTN_ENST00000359218.5_Silent_p.T9T|TTN_ENST00000342175.6_Silent_p.T9T			Q8WZ42	TITIN_HUMAN	titin	32620	Ig-like 1.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAACGGCTGCGTAAACGTCG	0.448																																																0			2											125	103	110					2																	179669343		2203	4300	6503	179377588	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27G>A	2.37:g.179669343C>T			179377588	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179669343	C	T	179669343	2	4	8	1	0	0	0	0	0	0	0	1	16775	755	27	1		1	TTN	2	179669343	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	174327	179669343	63530030	20	782										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212293151	212293151	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	accatagctccaaacgtcacTctgatgggtgaatttcctgt	8	11	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:212293151T>A	ENST00000342788.4	-	22	3011	c.2701A>T	c.(2701-2703)Agt>Tgt	p.S901C	ERBB4_ENST00000436443.1_Missense_Mutation_p.S901C|ERBB4_ENST00000402597.1_Missense_Mutation_p.S891C	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	901	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CAAACGTCACTCTGATGGGTG	0.299										TSP Lung(8;0.080)																																						0			2											90	92	91					2																	212293151		2203	4294	6497	212001396	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2701A>T	2.37:g.212293151T>A	ENSP00000342235:p.Ser901Cys		212001396	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528108	0.85706	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	D;D;D	0.89485	-2.52;-2.52;-2.52	5.59	5.59	0.84812	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.036917	0.85682	D	0.000000	D	0.94443	0.8212	M	0.80508	2.5	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.77004	0.981;0.984;0.981;0.989	D	0.95116	0.8242	10	0.87932	D	0	.	15.7639	0.78110	0.0:0.0:0.0:1.0	.	891;891;901;901	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	C	901;901;891	ENSP00000342235:S901C;ENSP00000403204:S901C;ENSP00000385565:S891C	ENSP00000342235:S901C	S	-	1	0	ERBB4	212001396	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.865000	0.87049	2.125000	0.65367	0.528000	0.53228	AGT		0.299	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212293151	T	A	212293151	3	1	8	1	0	0	0	0	1	0	0	0	5222	1551	54	5	1253	5	ERBB4	2	212293151	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	32623808	212293151	30906222	21	783										
ACSL3	2181	hgsc.bcm.edu	37	chr2	223783820	223783820	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ccacgcctgcggcacatcatCactgttgatggaaagccacc	9	15	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:223783820C>A	ENST00000357430.3	+	7	1236	c.705C>A	c.(703-705)atC>atA	p.I235I	AC097461.4_ENST00000446709.1_RNA|ACSL3_ENST00000392066.3_Silent_p.I235I	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	235					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	GGCACATCATCACTGTTGATG	0.498			T	ETV1	prostate																																		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	0			2											119	101	107					2																	223783820		2203	4300	6503	223492064	SO:0001819	synonymous_variant	2181			D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"Acyl-CoA synthetase family"	3570	protein-coding gene	gene with protein product		602371	"fatty-acid-Coenzyme A ligase, long-chain 3"	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.705C>A	2.37:g.223783820C>A			223492064	Q60I92|Q8IUM9	Silent	SNP	ENST00000357430.3	37	CCDS2455.1																																																																																				0.498	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		A	223783820	C	A	223783820	2	1	8	1	0	0	0	0	0	0	0	1	178	816	29	2		2	ACSL3	2	223783820	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	11490669	223783820	19415553	22	784										
DGKD	8527	hgsc.bcm.edu	37	chr2	234296986	234296986	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tactttaagcttcgagggcgAacgctttactatgccaaaac	8	10	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:234296986A>G	ENST00000264057.2	+	2	252	c.240A>G	c.(238-240)cgA>cgG	p.R80R	AC019221.4_ENST00000442524.1_RNA|DGKD_ENST00000409813.3_Silent_p.R36R|DGKD_ENST00000489613.1_3'UTR	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	80	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TTCGAGGGCGAACGCTTTACT	0.512																																																0			2											106	100	102					2																	234296986		2203	4300	6503	233961725	SO:0001819	synonymous_variant	8527			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.240A>G	2.37:g.234296986A>G			233961725	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	37	CCDS2504.1																																																																																				0.512	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		G	234296986	A	G	234296986	2	3	8	1	0	0	0	0	0	0	0	1	4478	233	9	4		4	DGKD	2	234296986	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	10513166	234296986	8902387	23	785										
ILKAP	80895	hgsc.bcm.edu	37	chr2	239092718	239092718	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gcttgaaagtgtccaaaaggCatctcttcacggttttctct	8	10	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr2:239092718C>G	ENST00000254654.3	-	7	744	c.569G>C	c.(568-570)tGc>tCc	p.C190S		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	190	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		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)		GTCCAAAAGGCATCTCTTCAC	0.418																																																0			2											135	132	133					2																	239092718		2203	4300	6503	238757457	SO:0001583	missense	80895			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.569G>C	2.37:g.239092718C>G	ENSP00000254654:p.Cys190Ser		238757457	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983431	0.74474	.	.	ENSG00000132323	ENST00000254654;ENST00000450411;ENST00000457149	T;T;T	0.16457	2.34;2.34;2.34	5.42	5.42	0.78866	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.10035	0.0246	N	0.04880	-0.145	0.80722	D	1	B	0.28470	0.213	B	0.28139	0.086	T	0.30592	-0.9973	10	0.28530	T	0.3	0.0342	16.1473	0.81578	0.0:1.0:0.0:0.0	.	190	Q9H0C8	ILKAP_HUMAN	S	190;7;188	ENSP00000254654:C190S;ENSP00000406254:C7S;ENSP00000395301:C188S	ENSP00000254654:C190S	C	-	2	0	ILKAP	238757457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.247000	0.58750	2.549000	0.85964	0.655000	0.94253	TGC		0.418	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		G	239092718	C	G	239092718	3	3	8	1	0	0	0	0	1	0	0	0	7735	710	25	5	633	5	ILKAP	2	239092718	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	4795732	239092718	4106655	24	786										
FGD5	152273	hgsc.bcm.edu	37	chr3	14949172	14949172	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cctgcagaagctggtccacaTtgagcacagcgtccggggcc	13	14	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr3:14949172T>C	ENST00000285046.5	+	10	3400	c.3290T>C	c.(3289-3291)aTt>aCt	p.I1097T	FGD5_ENST00000543601.1_Missense_Mutation_p.I856T|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1097					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CTGGTCCACATTGAGCACAGC	0.627																																																0			3											51	57	55					3																	14949172		1987	4155	6142	14924176	SO:0001583	missense	152273			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3290T>C	3.37:g.14949172T>C	ENSP00000285046:p.Ile1097Thr		14924176	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861150	0.71949	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.35048	1.33;1.33	5.24	5.24	0.73138	Dbl homology (DH) domain (1);Pleckstrin homology-type (1);	0.000000	0.56097	D	0.000024	T	0.51669	0.1688	L	0.55990	1.75	0.54753	D	0.999988	D;D	0.71674	0.996;0.998	D;D	0.66602	0.945;0.945	T	0.53767	-0.8392	10	0.66056	D	0.02	-20.0142	11.5498	0.50715	0.0:0.0:0.0:1.0	.	856;1097	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	T	1097;856	ENSP00000285046:I1097T;ENSP00000445949:I856T	ENSP00000285046:I1097T	I	+	2	0	FGD5	14924176	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	5.447000	0.66606	1.979000	0.57680	0.482000	0.46254	ATT		0.627	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		C	14949172	T	C	14949172	3	2	8	1	0	0	0	0	1	0	0	0	5855	1493	52	4	3328	4	FGD5	3	14949172	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10		14949172	183073258	25	787										
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27436596	27436596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttatgatccaccctctctctGgatgagtaggctgttaaaaa	8	9	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr3:27436596G>A	ENST00000295736.5	-	19	2757	c.2687C>T	c.(2686-2688)cCa>cTa	p.P896L	SLC4A7_ENST00000440156.1_Missense_Mutation_p.P892L|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P772L|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P781L|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P777L|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P446L|SLC4A7_ENST00000437179.1_Missense_Mutation_p.P777L|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P905L|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P892L|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P888L	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	896					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.P896L(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CCCTCTCTCTGGATGAGTAGG	0.363																																																1	Substitution - Missense(1)	central_nervous_system(1)	3											61	60	60					3																	27436596		2203	4300	6503	27411600	SO:0001583	missense	9497			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2687C>T	3.37:g.27436596G>A	ENSP00000295736:p.Pro896Leu		27411600	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596990	0.46318	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	6.06	4.1	0.47936	Bicarbonate transporter, C-terminal (1);	0.308279	0.38217	N	0.001764	T	0.76111	0.3942	M	0.66560	2.04	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.26041	0.14;0.063;0.063;0.083;0.075;0.061;0.115;0.14;0.033	B;B;B;B;B;B;B;B;B	0.29176	0.099;0.063;0.063;0.099;0.099;0.096;0.06;0.099;0.063	T	0.76958	-0.2766	10	0.72032	D	0.01	.	12.6185	0.56590	0.0:0.0:0.4453:0.5547	.	892;777;888;892;905;446;772;896;777	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	L	447;896;772;905;892;777;888;777;892;781;446;792	ENSP00000411031:P447L;ENSP00000295736:P896L;ENSP00000416368:P772L;ENSP00000390394:P905L;ENSP00000414797:P892L;ENSP00000394252:P777L;ENSP00000406605:P888L;ENSP00000407382:P777L;ENSP00000406804:P892L;ENSP00000395336:P781L;ENSP00000373429:P446L;ENSP00000388703:P792L	ENSP00000295736:P896L	P	-	2	0	SLC4A7	27411600	1.000000	0.71417	0.986000	0.45419	0.573000	0.36030	2.202000	0.42743	1.560000	0.49568	0.655000	0.94253	CCA		0.363	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		A	27436596	G	A	27436596	3	1	8	1	0	0	0	0	1	0	0	0	14695	1348	47	3	985	3	SLC4A7	3	27436596	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	12487424	27436596	170585834	26	788										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365330	37365330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cttagggaaaagtgtgaacaAgaaaaagaaacattgttgaa	10	3	0	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr3:37365330A>G	ENST00000361924.2	+	14	2327	c.1953A>G	c.(1951-1953)caA>caG	p.Q651Q	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Silent_p.Q673Q	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	651	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AGTGTGAACAAGAAAAAGAAA	0.368																																																0			3											52	53	53					3																	37365330		2203	4300	6503	37340334	SO:0001819	synonymous_variant	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1953A>G	3.37:g.37365330A>G			37340334	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	37	CCDS2666.1																																																																																				0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37365330	A	G	37365330	2	3	8	1	0	0	0	0	0	0	0	1	6575	69	3	4		4	GOLGA4	3	37365330	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	9928734	37365330	160657100	27	789										
PCOLCE2	26577	hgsc.bcm.edu	37	chr3	142542457	142542457	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aggccacggtgggttttaaaCcttaattcaaagaagacata	9	7	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr3:142542457C>T	ENST00000295992.3	-	7	1172	c.866G>A	c.(865-867)gGt>gAt	p.G289D	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	289					positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						GGGTTTTAAACCTTAATTCAA	0.363																																																0			3											61	65	63					3																	142542457		2203	4300	6503	144025147	SO:0001630	splice_region_variant	26577			AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.866-1G>A	3.37:g.142542457C>T			144025147	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	.	.	.	.	.	.	.	.	.	.	C	5.938	0.357014	0.11239	.	.	ENSG00000163710	ENST00000295992	T	0.19105	2.17	5.41	4.55	0.56014	.	0.237201	0.49305	N	0.000146	T	0.10723	0.0262	N	0.22421	0.69	0.80722	D	1	B	0.21520	0.057	B	0.14023	0.01	T	0.11060	-1.0603	10	0.08381	T	0.77	.	6.1878	0.20508	0.1371:0.6555:0.1327:0.0747	.	289	Q9UKZ9	PCOC2_HUMAN	D	289	ENSP00000295992:G289D	ENSP00000295992:G289D	G	-	2	0	PCOLCE2	144025147	1.000000	0.71417	0.999000	0.59377	0.589000	0.36550	1.595000	0.36708	1.518000	0.48934	0.655000	0.94253	GGT		0.363	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363	Missense_Mutation	T	142542457	C	T	142542457	5	4	8	1	0	0	0	0	0	0	1	0	11626	521	18	3	393	3	PCOLCE2	3	142542457	Splice_Site	SNP	C	TCGA-AF-4110-01A-02D-1733-10	105177127	142542457	55479973	28	790										
FAT4	79633	hgsc.bcm.edu	37	chr4	126241591	126241591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctctgttactgcaactgattCcgattcaggtgacaatgctg	9	10	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr4:126241591C>T	ENST00000394329.3	+	1	4038	c.4025C>T	c.(4024-4026)tCc>tTc	p.S1342F		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1342	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCAACTGATTCCGATTCAGGT	0.393																																																0			4											139	132	134					4																	126241591		1893	4109	6002	126461041	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.4025C>T	4.37:g.126241591C>T	ENSP00000377862:p.Ser1342Phe		126461041	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121238	0.37436	.	.	ENSG00000196159	ENST00000394329	T	0.01887	4.58	4.83	3.98	0.46160	Cadherin (4);Cadherin-like (1);	0.000000	0.31624	U	0.007321	T	0.07638	0.0192	L	0.52573	1.65	0.80722	D	1	D	0.55385	0.971	P	0.62560	0.904	T	0.10776	-1.0615	10	0.59425	D	0.04	.	12.71	0.57083	0.0:0.9212:0.0:0.0788	.	1342	Q6V0I7	FAT4_HUMAN	F	1342	ENSP00000377862:S1342F	ENSP00000377862:S1342F	S	+	2	0	FAT4	126461041	1.000000	0.71417	0.536000	0.28039	0.877000	0.50540	4.537000	0.60643	1.262000	0.44165	0.655000	0.94253	TCC		0.393	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126241591	C	T	126241591	3	4	8	1	0	0	0	0	1	0	0	0	5711	855	30	3	4027	3	FAT4	4	126241591	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10		126241591	64912685	29	791										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138451837	138451837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctgaaattacaaattcatatCggcttctctggaagtggggt	10	7	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr4:138451837C>T	ENST00000344876.4	-	1	1792	c.1406G>A	c.(1405-1407)cGa>cAa	p.R469Q	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.R469Q|PCDH18_ENST00000507846.1_Missense_Mutation_p.R249Q	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	469	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					AAATTCATATCGGCTTCTCTG	0.428																																																0			4											125	123	124					4																	138451837		2203	4300	6503	138671287	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1406G>A	4.37:g.138451837C>T	ENSP00000355082:p.Arg469Gln		138671287	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.050864	0.36181	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.60672	0.17;0.17;0.17	5.93	5.08	0.68730	Cadherin (3);Cadherin-like (1);	0.216136	0.22434	N	0.060103	T	0.39860	0.1094	N	0.10945	0.07	0.80722	D	1	B;B;B	0.17667	0.005;0.003;0.023	B;B;B	0.14578	0.011;0.003;0.007	T	0.15492	-1.0435	10	0.29301	T	0.29	.	15.5028	0.75713	0.0:0.933:0.0:0.067	.	249;469;469	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	Q	469;469;249	ENSP00000355082:R469Q;ENSP00000390688:R469Q;ENSP00000425903:R249Q	ENSP00000355082:R469Q	R	-	2	0	PCDH18	138671287	0.999000	0.42202	0.987000	0.45799	0.993000	0.82548	3.974000	0.56852	1.479000	0.48272	0.563000	0.77884	CGA		0.428	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138451837	C	T	138451837	3	4	8	1	0	0	0	0	1	0	0	0	11544	884	31	1	2017	1	PCDH18	4	138451837	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	12210246	138451837	52702439	30	792										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13754367	13754367	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctttgctctgtccatctttcTttttcacctgccaagccact	4	15	4	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:13754367T>C	ENST00000265104.4	-	62	10604	c.10500A>G	c.(10498-10500)aaA>aaG	p.K3500K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3500					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K3500K(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCATCTTTCTTTTTCACCTG	0.413									Kartagener syndrome																																							1	Substitution - coding silent(1)	ovary(1)	5											119	116	117					5																	13754367		2203	4300	6503	13807367	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.10500A>G	5.37:g.13754367T>C			13807367	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13754367	T	C	13754367	2	2	8	1	0	0	0	0	0	0	0	1	4615	1606	56	4		4	DNAH5	5	13754367	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10		13754367	167160893	31	793										
ACTBL2	345651	hgsc.bcm.edu	37	chr5	56777934	56777934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ccgctcagcagtggtggtgaAgttatagcctcgctctgtca	12	11	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:56777934A>G	ENST00000423391.1	-	1	702	c.601T>C	c.(601-603)Ttc>Ctc	p.F201L	AC025470.1_ENST00000584598.1_RNA|CTD-2023N9.1_ENST00000506106.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	201						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		GTGGTGGTGAAGTTATAGCCT	0.542																																																0			5											102	83	89					5																	56777934		2203	4300	6503	56813691	SO:0001583	missense	345651				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.601T>C	5.37:g.56777934A>G	ENSP00000416706:p.Phe201Leu		56813691	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.045855	0.36085	.	.	ENSG00000169067	ENST00000423391	D	0.94497	-3.44	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000002	D	0.95300	0.8475	L	0.54908	1.71	0.45822	D	0.998693	B	0.25206	0.12	P	0.46758	0.526	D	0.94630	0.7821	10	0.87932	D	0	.	12.5346	0.56135	1.0:0.0:0.0:0.0	.	201	Q562R1	ACTBL_HUMAN	L	201	ENSP00000416706:F201L	ENSP00000416706:F201L	F	-	1	0	ACTBL2	56813691	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	9.131000	0.94446	2.057000	0.61298	0.533000	0.62120	TTC		0.542	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992		G	56777934	A	G	56777934	3	3	8	1	0	0	0	0	1	0	0	0	194	72	3	4	533	4	ACTBL2	5	56777934	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	43023567	56777934	124137326	32	794										
POC5	134359	hgsc.bcm.edu	37	chr5	74984855	74984855	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acctgcatcatttctgttttGaaatatagtcatggcttcaa	6	8	4	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:74984855G>A	ENST00000428202.2	-	9	1300	c.1111C>T	c.(1111-1113)Caa>Taa	p.Q371*	POC5_ENST00000514838.2_Nonsense_Mutation_p.Q343*|POC5_ENST00000510798.1_Nonsense_Mutation_p.Q254*|POC5_ENST00000380475.2_Nonsense_Mutation_p.Q254*|POC5_ENST00000446329.2_Nonsense_Mutation_p.Q346*	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	371					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTTCTGTTTTGAAATATAGTC	0.333																																																0			5											69	64	66					5																	74984855		1811	4066	5877	75020611	SO:0001587	stop_gained	0			AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1111C>T	5.37:g.74984855G>A	ENSP00000410216:p.Gln371*		75020611	B4DJG7|Q494X7|Q494X9|Q6P085	Nonsense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	G	37	6.350628	0.97498	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329	.	.	.	5.66	5.66	0.87406	.	0.266501	0.44097	D	0.000494	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-19.0937	19.7537	0.96281	0.0:0.0:1.0:0.0	.	.	.	.	X	371;343;254;254;346	.	ENSP00000369842:Q254X	Q	-	1	0	POC5	75020611	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.820000	0.62671	2.676000	0.91093	0.655000	0.94253	CAA		0.333	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		A	74984855	G	A	74984855	4	1	8	1	0	0	0	0	0	1	0	0	12208	1299	45	3	632	3	POC5	5	74984855	Nonsense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	18206921	74984855	105930405	33	795										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75866404	75866404	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tccctcctatcgtcactttaGaagtctggccttcattttcg	6	13	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:75866404G>C	ENST00000274364.6	+	4	600		c.e4-1		IQGAP2_ENST00000379730.3_Splice_Site	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CGTCACTTTAGAAGTCTGGCC	0.418																																																0			5											148	142	144					5																	75866404		2203	4300	6503	75902160	SO:0001630	splice_region_variant	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.304-1G>C	5.37:g.75866404G>C			75902160	A8K4V1|B7Z8A4|J3KR91	Splice_Site	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657727	0.47467	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7421	0.96237	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IQGAP2	75902160	1.000000	0.71417	0.924000	0.36721	0.221000	0.24807	6.242000	0.72376	2.666000	0.90696	0.650000	0.86243	.		0.418	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	Intron	C	75866404	G	C	75866404	5	2	8	1	0	0	0	0	0	0	1	0	7836	956	33	5	317	5	IQGAP2	5	75866404	Splice_Site	SNP	G	TCGA-AF-4110-01A-02D-1733-10	881549	75866404	105048856	34	796										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77471654	77471654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tattttgtaggacaatatacTgcacctccctagaaatcaaa	5	9	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:77471654T>C	ENST00000255194.6	-	10	1224	c.1049A>G	c.(1048-1050)cAg>cGg	p.Q350R	AP3B1_ENST00000519295.1_Missense_Mutation_p.Q301R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	350					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GACAATATACTGCACCTCCCT	0.308									Hermansky-Pudlak syndrome																																							0			5											139	146	144					5																	77471654		2202	4296	6498	77507410	SO:0001583	missense	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1049A>G	5.37:g.77471654T>C	ENSP00000255194:p.Gln350Arg		77507410	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.980124	0.74474	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.19806	2.12;2.12	4.82	4.82	0.62117	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.39937	0.1097	M	0.89287	3.02	0.80722	D	1	P	0.36086	0.536	B	0.42798	0.398	T	0.49021	-0.8982	10	0.87932	D	0	-11.1184	14.3773	0.66886	0.0:0.0:0.0:1.0	.	350	O00203	AP3B1_HUMAN	R	350;301;350;254	ENSP00000255194:Q350R;ENSP00000430597:Q301R	ENSP00000255194:Q350R	Q	-	2	0	AP3B1	77507410	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.698000	0.84413	1.797000	0.52628	0.383000	0.25322	CAG		0.308	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77471654	T	C	77471654	3	2	8	1	0	0	0	0	1	0	0	0	744	1580	55	4	2307	4	AP3B1	5	77471654	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	1605250	77471654	103443606	35	797										
CAMK4	814	hgsc.bcm.edu	37	chr5	110819926	110819926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gggggcacaggctgagctgaTgaaggtgcaagccttagaga	17	7	0	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:110819926T>C	ENST00000282356.4	+	11	1582	c.1184T>C	c.(1183-1185)aTg>aCg	p.M395T	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Missense_Mutation_p.M395T	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	395					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GCTGAGCTGATGAAGGTGCAA	0.507																																																0			5											63	66	65					5																	110819926		2202	4300	6502	110847825	SO:0001583	missense	814			D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1184T>C	5.37:g.110819926T>C	ENSP00000282356:p.Met395Thr		110847825	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.180397	0.38511	.	.	ENSG00000152495	ENST00000512453;ENST00000282356	T;T	0.65916	-0.18;-0.18	5.55	-7.1	0.01547	.	0.843495	0.10143	N	0.710635	T	0.29850	0.0746	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21724	-1.0237	10	0.17832	T	0.49	.	1.0194	0.01514	0.2558:0.1598:0.3567:0.2277	.	395	Q16566	KCC4_HUMAN	T	395	ENSP00000422634:M395T;ENSP00000282356:M395T	ENSP00000282356:M395T	M	+	2	0	CAMK4	110847825	0.000000	0.05858	0.001000	0.08648	0.228000	0.25075	-0.316000	0.08071	-0.593000	0.05844	0.482000	0.46254	ATG		0.507	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		C	110819926	T	C	110819926	3	2	8	1	0	0	0	0	1	0	0	0	2611	1464	51	4	1226	4	CAMK4	5	110819926	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	33348272	110819926	70095334	36	798										
APC	324	hgsc.bcm.edu	37	chr5	112163701	112163701	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctgaaagtgaagacttacagCaggtactatttagaatttca	8	6	1	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:112163701C>T	ENST00000457016.1	+	13	2004	c.1624C>T	c.(1624-1626)Cag>Tag	p.Q542*	CTC-554D6.1_ENST00000520401.1_Silent_p.S37S|APC_ENST00000508376.2_Nonsense_Mutation_p.Q542*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q542*			P25054	APC_HUMAN	adenomatous polyposis coli	542	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q542*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGACTTACAGCAGGTACTATT	0.418		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5	GRCh37	CM071554	APC	M							87	83	84					5																	112163701		2202	4300	6502	112191600	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1624C>T	5.37:g.112163701C>T	ENSP00000413133:p.Gln542*		112191600	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.719132	0.98450	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-7.6611	19.6223	0.95663	0.0:1.0:0.0:0.0	.	.	.	.	X	542;524;542;542;542	.	ENSP00000257430:Q542X	Q	+	1	0	APC	112191600	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.421000	0.80204	2.707000	0.92482	0.655000	0.94253	CAG		0.418	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112163701	C	T	112163701	4	4	8	1	0	0	0	0	0	1	0	0	763	711	25	3	1670	3	APC	5	112163701	Nonsense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	1343775	112163701	68751559	37	799										
APC	324	hgsc.bcm.edu	37	chr5	112175271	112175271	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gagcgaagttccagcagtgtCacagcaccctagaaccaaat	9	12	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:112175271C>A	ENST00000457016.1	+	16	4360	c.3980C>A	c.(3979-3981)tCa>tAa	p.S1327*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.S1327*|APC_ENST00000257430.4_Nonsense_Mutation_p.S1327*			P25054	APC_HUMAN	adenomatous polyposis coli	1327	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			AVSQHPR -> SSVHSTLE (in Ref. 1; AAA60353/ AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1327*(4)|p.K1192fs*3(1)|p.?(1)|p.V1326fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCAGCAGTGTCACAGCACCCT	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Substitution - Nonsense(4)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(5)|soft_tissue(1)|skin(1)	5											61	64	63					5																	112175271		2202	4300	6502	112203170	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3980C>A	5.37:g.112175271C>A	ENSP00000413133:p.Ser1327*		112203170	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	34	5.366503	0.95900	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.312416	0.32518	N	0.005998	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.4033	13.3889	0.60811	0.0:0.9279:0.0:0.0721	.	.	.	.	X	1327	.	.	S	+	2	0	APC	112203170	0.701000	0.27806	0.185000	0.23176	0.118000	0.20060	5.764000	0.68826	2.861000	0.98227	0.655000	0.94253	TCA		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175271	C	A	112175271	4	1	8	1	0	0	0	0	0	1	0	0	763	838	29	2	4038	2	APC	5	112175271	Nonsense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	11570	112175271	68739989	38	800										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125828621	125828621	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttcaagatacaaaataacttAcagaagttgcttgagaatgg	8	5	1	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:125828621A>G	ENST00000285689.3	+	14	1733	c.1272A>G	c.(1270-1272)ttA>ttG	p.L424L	GRAMD3_ENST00000515200.1_Silent_p.L402L|GRAMD3_ENST00000542322.1_Silent_p.L432L|GRAMD3_ENST00000513040.1_Silent_p.L439L|GRAMD3_ENST00000544396.1_Silent_p.L320L|RP11-517I3.1_ENST00000512500.1_RNA|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000543198.1_3'UTR|GRAMD3_ENST00000511134.1_Silent_p.L408L|GRAMD3_ENST00000502348.1_Silent_p.L315L	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	424						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		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)		AAAATAACTTACAGAAGTTGC	0.353																																																0			5											61	60	60					5																	125828621		2203	4300	6503	125856520	SO:0001819	synonymous_variant	65983			BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.1272A>G	5.37:g.125828621A>G			125856520	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Silent	SNP	ENST00000285689.3	37	CCDS4136.1																																																																																				0.353	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		G	125828621	A	G	125828621	2	3	8	1	0	0	0	0	0	0	0	1	6772	388	14	4		4	GRAMD3	5	125828621	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	13653350	125828621	55086639	39	801										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142661473	142661473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gtcacttttgatgaaacagaAgttttttgatatttccattt	6	5	1	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:142661473A>G	ENST00000343796.2	-	9	3308	c.2315T>C	c.(2314-2316)cTt>cCt	p.L772P	NR3C1_ENST00000424646.2_Missense_Mutation_p.L746P|NR3C1_ENST00000503201.1_Missense_Mutation_p.L772P|NR3C1_ENST00000415690.2_Intron|NR3C1_ENST00000394464.2_Missense_Mutation_p.L772P|NR3C1_ENST00000504572.1_Missense_Mutation_p.L773P|NR3C1_ENST00000231509.3_Missense_Mutation_p.L773P|NR3C1_ENST00000416954.2_Missense_Mutation_p.L375P|NR3C1_ENST00000394466.2_Missense_Mutation_p.L773P	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	772	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)	p.L773P(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	ATGAAACAGAAGTTTTTTGAT	0.318																																																1	Substitution - Missense(1)	ovary(1)	5											87	90	89					5																	142661473		2202	4300	6502	142641666	SO:0001583	missense	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2315T>C	5.37:g.142661473A>G	ENSP00000343205:p.Leu772Pro		142641666	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593056	0.66219	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	5.93	5.93	0.95920	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.97300	0.9117	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97948	1.0330	10	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	772;773	P04150;E5KQF6	GCR_HUMAN;.	P	772;772;588;746;773;773;773;375;772	ENSP00000377977:L772P;ENSP00000343205:L772P;ENSP00000405282:L746P;ENSP00000422518:L773P;ENSP00000377979:L773P;ENSP00000231509:L773P;ENSP00000404218:L375P;ENSP00000427672:L772P	ENSP00000231509:L773P	L	-	2	0	NR3C1	142641666	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.281000	0.76405	0.533000	0.62120	CTT		0.318	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			G	142661473	A	G	142661473	3	3	8	1	0	0	0	0	1	0	0	0	10661	72	3	4	74	4	NR3C1	5	142661473	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	16832852	142661473	38253787	40	802										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148697481	148697481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cttcaggatcctgcgcaaccGgcaggaggtggccatcttgg	14	12	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr5:148697481G>A	ENST00000296721.4	+	12	1555	c.1457G>A	c.(1456-1458)cGg>cAg	p.R486Q	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R486Q	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	486	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCGCAACCGGCAGGAGGTG	0.627																																																0			5											23	20	21					5																	148697481		2197	4299	6496	148677674	SO:0001583	missense	134265			AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.1457G>A	5.37:g.148697481G>A	ENSP00000296721:p.Arg486Gln		148677674	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043862	0.93685	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.11277	2.79;2.79	5.17	5.17	0.71159	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.178082	0.49305	D	0.000143	T	0.12092	0.0294	L	0.29908	0.895	0.29351	N	0.865348	P;P	0.52463	0.933;0.953	B;B	0.43052	0.345;0.406	T	0.01472	-1.1346	10	0.72032	D	0.01	-23.5609	18.853	0.92240	0.0:0.0:1.0:0.0	.	486;486	Q8TED9-2;Q8TED9	.;AF1L1_HUMAN	Q	486	ENSP00000296721:R486Q;ENSP00000424427:R486Q	ENSP00000296721:R486Q	R	+	2	0	AFAP1L1	148677674	0.967000	0.33354	0.999000	0.59377	0.998000	0.95712	3.990000	0.56965	2.700000	0.92200	0.561000	0.74099	CGG		0.627	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		A	148697481	G	A	148697481	3	1	8	1	0	0	0	0	1	0	0	0	354	1116	39	1	1503	1	AFAP1L1	5	148697481	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	6036008	148697481	32217779	41	803										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39824089	39824089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tgcagtgaccatggccccccGcaagaggagccaccatggcc	12	16	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:39824089G>A	ENST00000398904.2	+	2	193	c.11G>A	c.(10-12)cGc>cAc	p.R4H	DAAM2_ENST00000274867.4_Missense_Mutation_p.R4H|DAAM2_ENST00000538976.1_Missense_Mutation_p.R4H|DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000405961.3_Missense_Mutation_p.R4H			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	4					actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATGGCCCCCCGCAAGAGGAGC	0.617																																																0			6											20	23	22					6																	39824089		1992	4156	6148	39932067	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.11G>A	6.37:g.39824089G>A	ENSP00000381876:p.Arg4His		39932067	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.623445	0.87460	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976;ENST00000405961	D;D;D	0.81499	-1.5;-1.5;-1.5	5.92	5.05	0.67936	.	0.106857	0.64402	N	0.000012	T	0.80003	0.4544	M	0.66939	2.045	0.47737	D	0.999501	B;B;D	0.69078	0.003;0.002;0.997	B;B;P	0.52481	0.005;0.002;0.7	T	0.83021	-0.0167	10	0.66056	D	0.02	.	13.9184	0.63916	0.074:0.0:0.926:0.0	.	4;4;4	G5EA45;Q86T65;F2Z2Q2	.;DAAM2_HUMAN;.	H	4	ENSP00000274867:R4H;ENSP00000381876:R4H;ENSP00000437808:R4H	ENSP00000274867:R4H	R	+	2	0	DAAM2	39932067	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	6.243000	0.72384	1.499000	0.48617	0.655000	0.94253	CGC		0.617	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39824089	G	A	39824089	3	1	8	1	0	0	0	0	1	0	0	0	4222	1087	38	1	13	1	DAAM2	6	39824089	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10		39824089	131290978	42	804										
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44233393	44233393	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ccccctccccgcccccggcgGgcgcttccggaaagaggccc	12	22	0	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:44233393G>A	ENST00000275015.5	-	1	107	c.108C>T	c.(106-108)gcC>gcT	p.A36A		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	36					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			gcccccggcgggcgcTTCCGG	0.731																																																0			6											2	2	2					6																	44233393		1090	2156	3246	44341371	SO:0001819	synonymous_variant	4794			U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.108C>T	6.37:g.44233393G>A			44341371	Q5T9V9	Silent	SNP	ENST00000275015.5	37	CCDS34463.1																																																																																				0.731	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			A	44233393	G	A	44233393	2	1	8	1	0	0	0	0	0	0	0	1	10411	1219	43	3		3	NFKBIE	6	44233393	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	4409304	44233393	126881674	43	805										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46793169	46793169	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cctgagtttaactccattatCggacagcgcctggatttcag	9	11	1	1	rs146158038		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:46793169C>T	ENST00000230588.4	+	8	726	c.717C>T	c.(715-717)atC>atT	p.I239I		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	239	Metalloprotease.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			ACTCCATTATCGGACAGCGCC	0.428																																																0			6						C		0,4406		0,0,2203	139	122	128		717	0.9	1	6	dbSNP_134	128	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MEP1A	NM_005588.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		239/747	46793169	1,13005	2203	4300	6503	46901128	SO:0001819	synonymous_variant	4224				CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.717C>T	6.37:g.46793169C>T			46901128	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Silent	SNP	ENST00000230588.4	37	CCDS4918.1																																																																																				0.428	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46793169	C	T	46793169	2	4	8	1	0	0	0	0	0	0	0	1	9505	874	31	1		1	MEP1A	6	46793169	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	2559776	46793169	124321898	44	806										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76731915	76731915	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	caggagtgagagggaaaggcCcaagtgagacgttggcaaca	16	7	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:76731915C>G	ENST00000369950.3	-	6	773	c.584G>C	c.(583-585)gGg>gCg	p.G195A	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				AGGGAAAGGCCCAAGTGAGAC	0.383																																					Pancreas(37;839 1141 2599 26037)											0			6											150	134	139					6																	76731915		2203	4300	6503	76788635	SO:0001583	missense	3617			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.584G>C	6.37:g.76731915C>G	ENSP00000358966:p.Gly195Ala		76788635		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.977841	0.00452	.	.	ENSG00000112706	ENST00000369950	T	0.18174	2.23	5.2	-4.11	0.03928	.	3.564720	0.00802	N	0.001427	T	0.03263	0.0095	L	0.41236	1.265	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.30736	-0.9968	10	0.14252	T	0.57	.	4.2295	0.10596	0.0942:0.1515:0.4908:0.2635	.	195	Q17R60	IMPG1_HUMAN	A	195	ENSP00000358966:G195A	ENSP00000358966:G195A	G	-	2	0	IMPG1	76788635	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.582000	0.05814	-0.376000	0.07943	-0.355000	0.07637	GGG		0.383	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		G	76731915	C	G	76731915	3	3	8	1	0	0	0	0	1	0	0	0	7749	623	22	5	1857	5	IMPG1	6	76731915	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	29938746	76731915	94383152	45	807										
FYN	2534	hgsc.bcm.edu	37	chr6	112017653	112017653	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctacttttgtgtttccattcCaggtacctacaaacatccca	4	13	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:112017653C>A	ENST00000354650.3	-	10	1475	c.869G>T	c.(868-870)tGg>tTg	p.W290L	FYN_ENST00000368682.3_Missense_Mutation_p.W287L|FYN_ENST00000368678.4_Missense_Mutation_p.W287L|FYN_ENST00000538466.1_Missense_Mutation_p.W287L|FYN_ENST00000476769.2_5'UTR|FYN_ENST00000229470.5_Missense_Mutation_p.W238L|FYN_ENST00000368667.2_Missense_Mutation_p.W290L|FYN_ENST00000229471.4_Missense_Mutation_p.W235L|FYN_ENST00000356013.2_Missense_Mutation_p.W235L	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	GTTTCCATTCCAGGTACCTAC	0.398																																																0			6											102	90	94					6																	112017653		2203	4300	6503	112124346	SO:0001583	missense	2534			AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"SH2 domain containing"	4037	protein-coding gene	gene with protein product		137025	"FYN oncogene related to SRC, FGR, YES"			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.869G>T	6.37:g.112017653C>A	ENSP00000346671:p.Trp290Leu		112124346	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Missense_Mutation	SNP	ENST00000354650.3	37	CCDS5094.1	.	.	.	.	.	.	.	.	.	.	C	32	5.125707	0.94429	.	.	ENSG00000010810	ENST00000368682;ENST00000354650;ENST00000229471;ENST00000368667;ENST00000368678;ENST00000229470;ENST00000356013;ENST00000538466;ENST00000544792	T;T;T;T;T;T;T;T	0.81163	-1.46;1.84;-1.46;1.84;-1.46;1.84;-1.46;-1.46	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73133	0.3548	N	0.01742	-0.745	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.977;0.96;1.0	D	0.84793	0.0780	10	0.87932	D	0	.	19.7367	0.96208	0.0:1.0:0.0:0.0	.	290;235;287	P06241;P06241-3;E1P556	FYN_HUMAN;.;.	L	287;290;235;290;287;238;235;287;238	ENSP00000357671:W287L;ENSP00000346671:W290L;ENSP00000229471:W235L;ENSP00000357656:W290L;ENSP00000357667:W287L;ENSP00000229470:W238L;ENSP00000348295:W235L;ENSP00000440646:W287L	ENSP00000229470:W238L	W	-	2	0	FYN	112124346	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.787000	0.85759	2.656000	0.90262	0.655000	0.94253	TGG		0.398	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			A	112017653	C	A	112017653	3	1	8	1	0	0	0	0	1	0	0	0	6145	595	21	2	764	2	FYN	6	112017653	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	35285738	112017653	59097414	46	808										
PNLDC1	154197	hgsc.bcm.edu	37	chr6	160231096	160231096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atgatgatggacctgctgcaCctccatgagaagttcttcag	10	10	2	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:160231096C>A	ENST00000610273.1	+	10	960	c.789C>A	c.(787-789)caC>caA	p.H263Q	PNLDC1_ENST00000392167.3_Missense_Mutation_p.H274Q	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	263						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		ACCTGCTGCACCTCCATGAGA	0.453																																																0			6											121	108	112					6																	160231096		2203	4300	6503	160151086	SO:0001583	missense	154197			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.789C>A	6.37:g.160231096C>A	ENSP00000476448:p.His263Gln		160151086	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.557719	0.45590	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	T;T	0.26373	1.74;1.74	4.95	-0.543	0.11851	Ribonuclease H-like (1);	0.202450	0.34245	N	0.004125	T	0.15349	0.0370	M	0.66439	2.03	0.35373	D	0.789181	B;P	0.42941	0.151;0.794	B;P	0.45377	0.164;0.478	T	0.04481	-1.0948	10	0.39692	T	0.17	.	8.8362	0.35113	0.0:0.4946:0.0:0.5054	.	274;263	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	Q	263;274	ENSP00000275275:H263Q;ENSP00000376007:H274Q	ENSP00000275275:H263Q	H	+	3	2	PNLDC1	160151086	0.731000	0.28111	0.994000	0.49952	0.942000	0.58702	-0.600000	0.05693	0.029000	0.15352	-0.471000	0.05019	CAC		0.453	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		A	160231096	C	A	160231096	3	1	8	1	0	0	0	0	1	0	0	0	12179	506	18	2	823	2	PNLDC1	6	160231096	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	48213443	160231096	10883971	47	809										
THBS2	7058	hgsc.bcm.edu	37	chr6	169648555	169648555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	agcctttggccacgtacatcCggctcttttccgcctgcagg	10	15	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr6:169648555C>T	ENST00000366787.3	-	4	815	c.566G>A	c.(565-567)cGg>cAg	p.R189Q		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	189	Heparin-binding. {ECO:0000255}.|Laminin G-like.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R189P(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		CACGTACATCCGGCTCTTTTC	0.612																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Missense(1)	ovary(1)	6											101	104	103					6																	169648555		2203	4300	6503	169390480	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.566G>A	6.37:g.169648555C>T	ENSP00000355751:p.Arg189Gln		169390480	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223377	0.39300	.	.	ENSG00000186340	ENST00000366787	T	0.02216	4.39	4.5	3.6	0.41247	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.159155	0.28268	U	0.015970	T	0.00906	0.0030	L	0.41573	1.285	0.26483	N	0.975079	B	0.25772	0.134	B	0.17433	0.018	T	0.45963	-0.9225	10	0.45353	T	0.12	-39.3345	9.9005	0.41344	0.0:0.8357:0.0:0.1643	.	189	P35442	TSP2_HUMAN	Q	189	ENSP00000355751:R189Q	ENSP00000355751:R189Q	R	-	2	0	THBS2	169390480	1.000000	0.71417	1.000000	0.80357	0.347000	0.29111	2.330000	0.43885	2.204000	0.70986	0.563000	0.77884	CGG		0.612	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169648555	C	T	169648555	3	4	8	1	0	0	0	0	1	0	0	0	15893	652	23	1	3032	1	THBS2	6	169648555	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	9417459	169648555	1466512	48	810										
INTS1	26173	hgsc.bcm.edu	37	chr7	1522333	1522333	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tccagcagcgcctggaactcGctgtcgtcggcttcaggaag	13	13	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:1522333G>A	ENST00000404767.3	-	27	3637	c.3552C>T	c.(3550-3552)agC>agT	p.S1184S	INTS1_ENST00000389470.4_Silent_p.S1346S	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1184					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CCTGGAACTCGCTGTCGTCGG	0.647																																																0			7											52	61	58					7																	1522333		2069	4205	6274	1488859	SO:0001819	synonymous_variant	26173			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.3552C>T	7.37:g.1522333G>A			1488859	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																				0.647	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1522333	G	A	1522333	2	1	8	1	0	0	0	0	0	0	0	1	7796	1078	38	1		1	INTS1	7	1522333	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10		1522333	157616330	49	811										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726301	91726301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gccacccttgccctcagaggAcctactgaaagagctgcaga	10	14	1	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:91726301A>G	ENST00000359028.2	+	41	10265	c.10040A>G	c.(10039-10041)gAc>gGc	p.D3347G	AKAP9_ENST00000358100.2_Missense_Mutation_p.D3293G|AKAP9_ENST00000356239.3_Missense_Mutation_p.D3343G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3347					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CCCTCAGAGGACCTACTGAAA	0.468			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											60	62	61					7																	91726301		2203	4300	6503	91564237	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10040A>G	7.37:g.91726301A>G	ENSP00000351922:p.Asp3347Gly		91564237	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	7.484	0.649353	0.14516	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03496	4.0;4.0;4.0;3.91	5.04	5.04	0.67666	.	0.497819	0.16965	N	0.192356	T	0.07503	0.0189	M	0.70595	2.14	0.33799	D	0.626454	P;P;P;P;P	0.42692	0.611;0.787;0.501;0.634;0.634	B;B;B;B;B	0.38803	0.282;0.23;0.058;0.124;0.124	T	0.15122	-1.0448	10	0.49607	T	0.09	.	15.2346	0.73419	1.0:0.0:0.0:0.0	.	618;3347;3347;3343;3335	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	G	3343;3347;3293;3347;1189	ENSP00000348573:D3343G;ENSP00000351922:D3347G;ENSP00000350813:D3293G;ENSP00000378042:D1189G	ENSP00000348573:D3343G	D	+	2	0	AKAP9	91564237	1.000000	0.71417	0.979000	0.43373	0.195000	0.23768	4.109000	0.57824	2.240000	0.73641	0.533000	0.62120	GAC		0.468	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91726301	A	G	91726301	3	3	8	1	0	0	0	0	1	0	0	0	459	275	10	4	10190	4	AKAP9	7	91726301	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	90203968	91726301	67412362	50	812										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98547744	98547744	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctccgagcctttactggtcgTtttctctgcaacatgacatt	7	12	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:98547744T>C	ENST00000359863.4	+	37	5381	c.5172T>C	c.(5170-5172)cgT>cgC	p.R1724R	TRRAP_ENST00000446306.3_Silent_p.R1705R|TRRAP_ENST00000355540.3_Silent_p.R1706R	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1724			R -> H (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TTACTGGTCGTTTTCTCTGCA	0.418																																																0			7											112	109	110					7																	98547744		2203	4300	6503	98385680	SO:0001819	synonymous_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.5172T>C	7.37:g.98547744T>C			98385680	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	T	10.48	1.360886	0.24684	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.7	1.86	0.25419	.	.	.	.	.	T	0.53384	0.1793	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39800	-0.9596	4	.	.	.	.	5.7953	0.18383	0.1186:0.3345:0.0:0.5468	.	.	.	.	A	1446	.	.	V	+	2	0	TRRAP	98385680	0.882000	0.30256	0.998000	0.56505	0.997000	0.91878	-0.005000	0.12855	0.078000	0.16900	0.459000	0.35465	GTT		0.418	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		C	98547744	T	C	98547744	2	2	8	1	0	0	0	0	0	0	0	1	16641	1712	60	4		4	TRRAP	7	98547744	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10	6821443	98547744	60590919	51	813										
ZNF277	11179	hgsc.bcm.edu	37	chr7	111936290	111936290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	taatctctcaacagaagaacAagagaattattttttgttat	5	5	2	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:111936290A>G	ENST00000361822.3	+	4	518	c.389A>G	c.(388-390)cAa>cGa	p.Q130R	ZNF277_ENST00000450657.1_Missense_Mutation_p.Q130R	NM_021994.2	NP_068834.2	Q9NRM2	ZN277_HUMAN	zinc finger protein 277	130					cellular response to hydrogen peroxide (GO:0070301)|regulation of cellular senescence (GO:2000772)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			breast(4)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	15						ACAGAAGAACAAGAGAATTAT	0.313																																																0			7											57	62	60					7																	111936290		2198	4283	6481	111723526	SO:0001583	missense	11179			AF209198	CCDS5755.2	7q31.1	2012-10-05	2007-10-23	2007-10-23	ENSG00000198839	ENSG00000198839			13070	protein-coding gene	gene with protein product		605465	"zinc finger protein (C2H2 type) 277", "zinc finger protein 277 pseudogene"	ZNF277P		10860669, 16213364, 16395595	Standard	NM_021994		Approved	NRIF4	uc003vge.2	Q9NRM2	OTTHUMG00000150209	ENST00000361822.3:c.389A>G	7.37:g.111936290A>G	ENSP00000354501:p.Gln130Arg		111723526	Q75MZ2|Q75MZ3|Q8WY14	Missense_Mutation	SNP	ENST00000361822.3	37	CCDS5755.2	.	.	.	.	.	.	.	.	.	.	A	15.91	2.972404	0.53614	.	.	ENSG00000198839	ENST00000361822;ENST00000450657	T;T	0.31769	1.49;1.48	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.49406	0.1555	M	0.72479	2.2	0.80722	D	1	D;D	0.57257	0.979;0.96	P;P	0.54270	0.747;0.51	T	0.49643	-0.8918	10	0.56958	D	0.05	-19.3218	16.8222	0.85835	1.0:0.0:0.0:0.0	.	130;130	Q9NRM2;G5E9M4	ZN277_HUMAN;.	R	130	ENSP00000354501:Q130R;ENSP00000402292:Q130R	ENSP00000354501:Q130R	Q	+	2	0	ZNF277	111723526	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.792000	0.85828	2.371000	0.80710	0.533000	0.62120	CAA		0.313	ZNF277-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316843.2	NM_021994		G	111936290	A	G	111936290	3	3	8	1	0	0	0	0	1	0	0	0	17851	130	5	4	403	4	ZNF277	7	111936290	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	13388546	111936290	47202373	52	814										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138596010	138596010	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acatttatgacggatattgcCgtgtaaacgaaaggaccgga	11	7	0	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:138596010C>A	ENST00000422774.1	-	4	3075	c.3027G>T	c.(3025-3027)acG>acT	p.T1009T	KIAA1549_ENST00000440172.1_Silent_p.T1009T|KIAA1549_ENST00000242365.4_Silent_p.T959T			Q9HCM3	K1549_HUMAN	KIAA1549	1009						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CGGATATTGCCGTGTAAACGA	0.393			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	0			7											70	68	69					7																	138596010		1870	4101	5971	138246550	SO:0001819	synonymous_variant	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.3027G>T	7.37:g.138596010C>A			138246550	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																				0.393	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138596010	C	A	138596010	2	1	8	1	0	0	0	0	0	0	0	1	8265	639	23	2		2	KIAA1549	7	138596010	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	26659720	138596010	20542653	53	815										
KRBA1	84626	hgsc.bcm.edu	37	chr7	149423067	149423067	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tggccccccgaggaacccccAccagcttctcctcatccagc	7	21	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr7:149423067A>C	ENST00000485033.2	+	10	1390	c.1390A>C	c.(1390-1392)Acc>Ccc	p.T464P	KRBA1_ENST00000255992.10_Missense_Mutation_p.T464P|KRBA1_ENST00000319551.8_Missense_Mutation_p.T464P|KRBA1_ENST00000479560.1_3'UTR			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	522										breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGGAACCCCCACCAGCTTCTC	0.637																																																0			7											25	28	27					7																	149423067		1864	4105	5969	149054000	SO:0001583	missense	84626			AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.1390A>C	7.37:g.149423067A>C	ENSP00000420112:p.Thr464Pro		149054000	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37		.	.	.	.	.	.	.	.	.	.	A	6.602	0.479526	0.12581	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	T;T;T	0.35236	1.32;1.32;1.32	5.18	-2.3	0.06785	.	0.799813	0.10934	N	0.618074	T	0.15392	0.0371	N	0.12746	0.255	0.09310	N	1	B;B	0.18013	0.025;0.025	B;B	0.19946	0.027;0.027	T	0.17930	-1.0353	10	0.36615	T	0.2	-5.0205	1.1979	0.01878	0.3353:0.2774:0.0873:0.3001	.	464;464	E7ENE9;A5PL33	.;KRBA1_HUMAN	P	464	ENSP00000255992:T464P;ENSP00000317165:T464P;ENSP00000420112:T464P	ENSP00000255992:T464P	T	+	1	0	KRBA1	149054000	0.875000	0.30112	0.030000	0.17652	0.359000	0.29487	0.039000	0.13884	-0.708000	0.05015	-0.438000	0.05819	ACC		0.637	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534		C	149423067	A	C	149423067	3	2	8	1	0	0	0	0	1	0	0	0	8460	159	6	4	1428	4	KRBA1	7	149423067	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	10827057	149423067	9715596	54	816										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17612589	17612589	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ccacatcagaaaatgctgtgTaagtcatgtcttgggcttct	9	9	4	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:17612589T>C	ENST00000262102.6	-	2	952	c.728A>G	c.(727-729)tAc>tGc	p.Y243C	MTUS1_ENST00000381862.3_Missense_Mutation_p.Y243C|MTUS1_ENST00000519263.1_Missense_Mutation_p.Y243C|MTUS1_ENST00000381869.3_Missense_Mutation_p.Y243C	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	243					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AAATGCTGTGTAAGTCATGTC	0.408																																																0			8											187	166	173					8																	17612589		1917	4122	6039	17656869	SO:0001583	missense	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.728A>G	8.37:g.17612589T>C	ENSP00000262102:p.Tyr243Cys		17656869	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.324704	0.41197	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.21543	2.97;3.03;2.97;2.0	4.24	1.8	0.24995	.	0.777691	0.11551	N	0.552821	T	0.24122	0.0584	L	0.29908	0.895	0.09310	N	1	B;D;D	0.65815	0.043;0.995;0.995	B;P;P	0.60415	0.043;0.874;0.874	T	0.11012	-1.0605	9	.	.	.	-0.7227	3.7501	0.08563	0.1873:0.1028:0.0:0.7099	.	243;243;243	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	C	243	ENSP00000371293:Y243C;ENSP00000262102:Y243C;ENSP00000430167:Y243C;ENSP00000371286:Y243C	.	Y	-	2	0	MTUS1	17656869	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.077000	0.11394	0.387000	0.25024	0.533000	0.62120	TAC		0.408	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17612589	T	C	17612589	3	2	8	1	0	0	0	0	1	0	0	0	9995	1638	57	4	3459	4	MTUS1	8	17612589	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10		17612589	128751433	55	817										
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19192310	19192310	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctggaagaaagtggcagaaaAggaggaactggagcaaggat	16	4	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:19192310A>G	ENST00000265807.3	+	4	866	c.455A>G	c.(454-456)aAg>aGg	p.K152R	SH2D4A_ENST00000518040.1_Missense_Mutation_p.K107R|SH2D4A_ENST00000519207.1_Missense_Mutation_p.K152R	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	152					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		GTGGCAGAAAAGGAGGAACTG	0.468																																																0			8											98	93	95					8																	19192310		2203	4300	6503	19236590	SO:0001583	missense	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.455A>G	8.37:g.19192310A>G	ENSP00000265807:p.Lys152Arg		19236590	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508150	0.27036	.	.	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207;ENST00000523736	T;T;T;T	0.12672	3.07;2.66;3.07;3.07	5.28	0.0601	0.14334	.	1.068720	0.07144	N	0.847838	T	0.11110	0.0271	L	0.47190	1.495	0.09310	N	1	B;B	0.24823	0.047;0.112	B;B	0.19666	0.016;0.026	T	0.40365	-0.9567	10	0.22109	T	0.4	.	4.4713	0.11714	0.578:0.1604:0.2617:0.0	.	107;152	B4DDR1;Q9H788	.;SH24A_HUMAN	R	152;107;152;138	ENSP00000265807:K152R;ENSP00000429482:K107R;ENSP00000428684:K152R;ENSP00000428048:K138R	ENSP00000265807:K152R	K	+	2	0	SH2D4A	19236590	0.123000	0.22298	0.000000	0.03702	0.001000	0.01503	0.392000	0.20801	-0.219000	0.10003	-0.290000	0.09829	AAG		0.468	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		G	19192310	A	G	19192310	3	3	8	1	0	0	0	0	1	0	0	0	14272	72	3	4	515	4	SH2D4A	8	19192310	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	1579721	19192310	127171712	56	818										
TEX15	56154	hgsc.bcm.edu	37	chr8	30704086	30704086	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	taaatgtcaaatcctagaatTtctccatcttccttatttat	2	9	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:30704086T>G	ENST00000256246.2	-	1	2522	c.2448A>C	c.(2446-2448)gaA>gaC	p.E816D	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	816					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ATCCTAGAATTTCTCCATCTT	0.393																																																0			8											53	49	50					8																	30704086		2203	4297	6500	30823628	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2448A>C	8.37:g.30704086T>G	ENSP00000256246:p.Glu816Asp		30823628		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	4.775	0.144110	0.09134	.	.	ENSG00000133863	ENST00000256246	T	0.11277	2.79	5.73	3.31	0.37934	.	0.752485	0.12445	N	0.468270	T	0.06416	0.0165	N	0.19112	0.55	0.09310	N	1	P	0.41848	0.763	B	0.37144	0.242	T	0.32161	-0.9917	10	0.87932	D	0	.	3.7668	0.08626	0.1939:0.1096:0.0:0.6965	.	816	Q9BXT5	TEX15_HUMAN	D	816	ENSP00000256246:E816D	ENSP00000256246:E816D	E	-	3	2	TEX15	30823628	0.115000	0.22152	0.001000	0.08648	0.003000	0.03518	1.700000	0.37815	0.403000	0.25479	0.533000	0.62120	GAA		0.393	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30704086	T	G	30704086	3	3	8	1	0	0	0	0	1	0	0	0	15818	1838	64	4	5937	4	TEX15	8	30704086	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	11511776	30704086	115659936	57	819										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39613370	39613370	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gcataaataatagtggctctTggaatttgtaataaaaattt	7	3	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:39613370T>C	ENST00000265708.4	-	16	1777	c.1674A>G	c.(1672-1674)ccA>ccG	p.P558P	ADAM2_ENST00000347580.4_Silent_p.P539P|ADAM2_ENST00000521880.1_Intron|AC136365.1_ENST00000408091.1_RNA|ADAM2_ENST00000379853.2_Intron	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	558	Cys-rich.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		TAGTGGCTCTTGGAATTTGTA	0.303																																																0			8											68	71	70					8																	39613370		2202	4299	6501	39732527	SO:0001819	synonymous_variant	2515			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.1674A>G	8.37:g.39613370T>C			39732527	P78326|Q9UQQ8	Silent	SNP	ENST00000265708.4	37	CCDS34884.1																																																																																				0.303	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		C	39613370	T	C	39613370	2	2	8	1	0	0	0	0	0	0	0	1	241	1799	63	4		4	ADAM2	8	39613370	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10	8909284	39613370	106750652	58	820										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48776071	48776071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctttgggaaggcgagaatacAtcacgtctagaatcttatag	10	7	3	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:48776071A>G	ENST00000314191.2	-	43	5692	c.5636T>C	c.(5635-5637)aTg>aCg	p.M1879T	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Missense_Mutation_p.M1879T	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	1880					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GCGAGAATACATCACGTCTAG	0.338								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											0			8											169	166	167					8																	48776071		1847	4091	5938	48938624	SO:0001583	missense	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.5636T>C	8.37:g.48776071A>G	ENSP00000313420:p.Met1879Thr		48938624	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	A	24.4	4.527173	0.85706	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.30981	1.51;1.51	5.86	5.86	0.93980	NUC194 (1);Armadillo-type fold (1);	0.101148	0.64402	D	0.000003	T	0.49949	0.1587	M	0.71581	2.175	0.51767	D	0.999932	P;P	0.49696	0.927;0.927	P;P	0.54856	0.762;0.762	T	0.52578	-0.8557	10	0.72032	D	0.01	.	16.2668	0.82588	1.0:0.0:0.0:0.0	.	1879;1880	E7EUY0;P78527	.;PRKDC_HUMAN	T	1879	ENSP00000313420:M1879T;ENSP00000345182:M1879T	ENSP00000313420:M1879T	M	-	2	0	PRKDC	48938624	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.910000	0.92685	2.240000	0.73641	0.533000	0.62120	ATG		0.338	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		G	48776071	A	G	48776071	3	3	8	1	0	0	0	0	1	0	0	0	12555	217	8	4	6927	4	PRKDC	8	48776071	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	9162701	48776071	97587951	59	821										
MMP16	4325	hgsc.bcm.edu	37	chr8	89209459	89209459	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gcatggcagctagggcagacTgcatggtctctgcagagcgc	15	11	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr8:89209459T>C	ENST00000286614.6	-	2	490	c.209A>G	c.(208-210)cAg>cGg	p.Q70R	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	70					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	TAGGGCAGACTGCATGGTCTC	0.473																																																0			8											113	90	98					8																	89209459		2203	4300	6503	89278575	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.209A>G	8.37:g.89209459T>C	ENSP00000286614:p.Gln70Arg		89278575	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866877	0.51588	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	T;T	0.33865	1.39;1.39	6.08	6.08	0.98989	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.099857	0.64402	D	0.000001	T	0.27629	0.0679	N	0.13003	0.285	0.51012	D	0.999901	P;B	0.37083	0.581;0.046	B;B	0.42245	0.381;0.058	T	0.07616	-1.0763	10	0.11182	T	0.66	.	16.6512	0.85203	0.0:0.0:0.0:1.0	.	70;70	P51512-2;P51512	.;MMP16_HUMAN	R	70;87	ENSP00000286614:Q70R;ENSP00000429147:Q87R	ENSP00000286614:Q70R	Q	-	2	0	MMP16	89278575	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.186000	0.72026	2.333000	0.79357	0.482000	0.46254	CAG		0.473	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		C	89209459	T	C	89209459	3	2	8	1	0	0	0	0	1	0	0	0	9685	1580	55	4	1806	4	MMP16	8	89209459	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	40433388	89209459	57154563	60	822										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21968228	21968228	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tcagagcctctctggttcttTcaatcggggatgtctgcaga	11	10	5	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr9:21968228T>C	ENST00000304494.5	-	3	741	c.471A>G	c.(469-471)tgA>tgG	p.*157W	CDKN2A_ENST00000578845.2_Nonstop_Mutation_p.*106W|CDKN2A_ENST00000494262.1_Nonstop_Mutation_p.*106W|CDKN2A_ENST00000361570.3_3'UTR|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498628.2_Nonstop_Mutation_p.*106W|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000530628.2_3'UTR|CDKN2A_ENST00000498124.1_3'UTR|CDKN2A_ENST00000579122.1_Missense_Mutation_p.K133E	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	0					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(4)|p.0(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TCTGGTTCTTTCAATCGGGGA	0.557		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1320	Whole gene deletion(1316)|Unknown(4)	haematopoietic_and_lymphoid_tissue(277)|skin(165)|central_nervous_system(163)|lung(140)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|oesophagus(48)|upper_aerodigestive_tract(45)|ovary(33)|breast(30)|kidney(29)|pancreas(29)|thyroid(13)|biliary_tract(13)|NS(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											98	96	96					9																	21968228		2203	4300	6503	21958228	SO:0001578	stop_lost	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.471A>G	9.37:g.21968228T>C	ENSP00000307101:p.*157Cysext*13		21958228	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	T	1.489	-0.555047	0.03967	.	.	ENSG00000147889	ENST00000304494	.	.	.	2.65	0.029	0.14161	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.2576	0.06837	0.2383:0.0:0.2459:0.5158	.	.	.	.	W	157	.	.	X	-	3	0	CDKN2A	21958228	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.584000	0.05800	0.005000	0.14708	0.528000	0.53228	TGA		0.557	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		C	21968228	T	C	21968228	4	2	8	1	0	0	0	0	0	0	0	0	3167	1796	62	4	3	4	CDKN2A	9	21968228	Nonstop_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10		21968228	119245203	61	823										
ODF2	4957	hgsc.bcm.edu	37	chr9	131262506	131262506	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	caccttcctgactagctctcCcatccgctcccgatctcctc	4	21	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr9:131262506C>G	ENST00000434106.3	+	21	2825	c.2462C>G	c.(2461-2463)cCc>cGc	p.P821R	ODF2_ENST00000444119.2_Missense_Mutation_p.P797R|ODF2_ENST00000372807.5_Missense_Mutation_p.P816R|ODF2_ENST00000393527.3_Missense_Mutation_p.P797R|ODF2_ENST00000604420.1_Missense_Mutation_p.P821R|ODF2_ENST00000351030.3_Missense_Mutation_p.P816R	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	821					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						ACTAGCTCTCCCATCCGCTCC	0.552																																																0			9											210	173	185					9																	131262506		2203	4300	6503	130302327	SO:0001583	missense	4957			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2462C>G	9.37:g.131262506C>G	ENSP00000403453:p.Pro821Arg		130302327	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.124756	0.56613	.	.	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.31510	1.56;1.49;1.55	5.5	5.5	0.81552	.	0.146167	0.47093	D	0.000252	T	0.44726	0.1307	L	0.29908	0.895	0.80722	D	1	B;D;B;D	0.76494	0.001;0.999;0.018;0.998	B;D;B;D	0.66351	0.003;0.94;0.008;0.943	T	0.41610	-0.9499	10	0.87932	D	0	-17.391	18.3854	0.90465	0.0:1.0:0.0:0.0	.	816;166;821;797	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	R	816;821;797	ENSP00000342581:P816R;ENSP00000361882:P821R;ENSP00000307781:P797R	ENSP00000307781:P797R	P	+	2	0	ODF2	130302327	0.778000	0.28640	1.000000	0.80357	0.890000	0.51754	2.680000	0.46918	2.581000	0.87130	0.561000	0.74099	CCC		0.552	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			G	131262506	C	G	131262506	3	3	8	1	0	0	0	0	1	0	0	0	10858	623	22	5	2658	5	ODF2	9	131262506	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	109294278	131262506	9950925	62	824										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135982063	135982063	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttcccacgtcttcttcagacGgtggatggagttgctctgca	11	11	4	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr9:135982063G>T	ENST00000372050.3	-	8	1507	c.1486C>A	c.(1486-1488)Cgt>Agt	p.R496S	RALGDS_ENST00000542690.1_Missense_Mutation_p.R567S|RALGDS_ENST00000372047.3_Missense_Mutation_p.R484S|RALGDS_ENST00000393160.3_Missense_Mutation_p.R441S|RALGDS_ENST00000372062.3_Missense_Mutation_p.R467S|RALGDS_ENST00000393157.3_Missense_Mutation_p.R495S|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	496	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.		R -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTCTTCAGACGGTGGATGGAG	0.602			T	CIITA	"PMBL, Hodgkin Lymphona, "																																Melanoma(189;762 2088 15384 21931 52515)		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	0			9											63	54	57					9																	135982063		2200	4300	6500	134971884	SO:0001583	missense	5900			AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1486C>A	9.37:g.135982063G>T	ENSP00000361120:p.Arg496Ser		134971884	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.868390	0.51588	.	.	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000372051;ENST00000393157;ENST00000542690;ENST00000372062;ENST00000424572	T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	5.95	5.05	0.67936	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	D	0.87414	0.6171	H	0.96175	3.78	0.54753	D	0.999984	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;1.0;0.998;1.0;0.998;0.999;0.999;1.0	D	0.91482	0.5205	10	0.87932	D	0	.	15.3623	0.74487	0.0:0.0:0.8593:0.1407	.	567;467;496;484;441;495;484;496	F5H6M6;E7ER93;Q12967-2;Q8TEK9;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;.;.;GNDS_HUMAN	S	496;484;441;193;495;567;467;56	ENSP00000361120:R496S;ENSP00000361117:R484S;ENSP00000376867:R441S;ENSP00000376864:R495S;ENSP00000437518:R567S;ENSP00000361132:R467S;ENSP00000391814:R56S	ENSP00000361117:R484S	R	-	1	0	RALGDS	134971884	1.000000	0.71417	0.998000	0.56505	0.033000	0.12548	2.102000	0.41796	1.504000	0.48704	0.655000	0.94253	CGT		0.602	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		T	135982063	G	T	135982063	3	4	8	1	0	0	0	0	1	0	0	0	13053	1116	39	2	1302	2	RALGDS	9	135982063	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	4719557	135982063	5231368	63	825										
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cgagttacatacctgtgggcINStgtcatctttctcttcctcc					rs372921391|rs372038516	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	MRPL41_ENST00000371443.5_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0	0.0043	5008	,	,		18178	0		0.0099	False		,,,				2504	0															0			9							,	12,4252		0,12,2120					,	0.2	0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				139564449	SO:0001589	frameshift_variant	375775			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"Patatin-like phospholipase domain containing"	24768	protein-coding gene	gene with protein product		612122	"chromosome 9 open reading frame 111"	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs		139564448	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																				0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140444628	-	T	140444627	7	5	8	1	0	1	1	0	0	0	0	0	12201	797	28	0	4145	0	PNPLA7	9	140444627	Frame_Shift_Ins	INS	-	TCGA-AF-4110-01A-02D-1733-10	4462564	140444627	768804	64	826										
C1QL3	389941	hgsc.bcm.edu	37	chr10	16562533	16562533	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gccgtcccctccgcgcatcaGgacgtggtaggtgaagaagt	14	12	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:16562533G>A	ENST00000298943.3	-	1	1471	c.532C>T	c.(532-534)Ctg>Ttg	p.L178L		NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	178	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CCGCGCATCAGGACGTGGTAG	0.657																																																0			10											94	93	93					10																	16562533		2203	4300	6503	16602539	SO:0001819	synonymous_variant	389941				CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985			19359	protein-coding gene	gene with protein product		615227				21378161	Standard	NM_001010908		Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.532C>T	10.37:g.16562533G>A			16602539	A0PJY4|A0PJY5	Silent	SNP	ENST00000298943.3	37	CCDS31156.1																																																																																				0.657	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047003.1	XM_372305		A	16562533	G	A	16562533	2	1	8	1	0	0	0	0	0	0	0	1	1966	991	35	3		3	C1QL3	10	16562533	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10		16562533	118972214	65	827										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61062600	61062600	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gtttcaaaagcatcctttggCgaaatggcagtcctctggtc	10	10	2	0	rs114236655	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:61062600C>T	ENST00000373868.2	-	5	555	c.468G>A	c.(466-468)tcG>tcA	p.S156S	FAM13C_ENST00000442566.3_Silent_p.S156S|FAM13C_ENST00000435852.2_Silent_p.S156S|FAM13C_ENST00000510215.2_5'UTR|FAM13C_ENST00000468840.2_Silent_p.S73S|FAM13C_ENST00000422313.2_Silent_p.S156S|FAM13C_ENST00000419214.2_Silent_p.S156S|FAM13C_ENST00000373867.3_Silent_p.S73S|FAM13C_ENST00000277705.6_Silent_p.S156S	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	156										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CATCCTTTGGCGAAATGGCAG	0.358													C|||	39	0.00778754	0.0287	0.0014	5008	,	,		17975	0		0	False		,,,				2504	0															0			10						C	,,,	71,4335	65.3+/-102.7	2,67,2134	112	108	109		468,219,219,468	3.1	1	10	dbSNP_132	109	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM13C	NM_001001971.2,NM_001143773.1,NM_001166698.1,NM_198215.3	,,,	2,67,6434	TT,TC,CC		0.0,1.6114,0.5459	,,,	156/488,73/503,73/502,156/586	61062600	71,12935	2203	4300	6503	60732606	SO:0001819	synonymous_variant	220965			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.468G>A	10.37:g.61062600C>T			60732606	B7ZB77|Q5T631|Q6P2M3|Q99787	Silent	SNP	ENST00000373868.2	37	CCDS7255.1																																																																																				0.358	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			T	61062600	C	T	61062600	2	4	8	1	0	0	0	0	0	0	0	1	5470	755	27	1		1	FAM13C	10	61062600	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	44500067	61062600	74472147	66	828										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75550776	75550776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cttccacggagccgccagccGctgctgaatgggcatgtctg	13	14	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:75550776G>A	ENST00000605216.1	+	8	1202	c.985G>A	c.(985-987)Gct>Act	p.A329T	ZSWIM8_ENST00000398706.2_Missense_Mutation_p.A329T|ZSWIM8_ENST00000603114.1_Missense_Mutation_p.A329T|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.A329T|ZSWIM8_ENST00000604524.1_Missense_Mutation_p.A329T	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	329							zinc ion binding (GO:0008270)										GCCGCCAGCCGCTGCTGAATG	0.557																																																0			10											59	64	62					10																	75550776		2016	4184	6200	75220782	SO:0001583	missense	23053			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.985G>A	10.37:g.75550776G>A	ENSP00000474748:p.Ala329Thr		75220782	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.41|17.41	3.382929|3.382929	0.61845|0.61845	.|.	.|.	ENSG00000214655|ENSG00000214655	ENST00000398706|ENST00000433366	T|.	0.59364|.	0.27|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.000000|.	0.56097|.	U|.	0.000023|.	T|T	0.78175|0.78175	0.4242|0.4242	M|M	0.77616|0.77616	2.38|2.38	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.999;0.999;0.999|.	D;D;D|.	0.80764|.	0.99;0.994;0.99|.	T|T	0.77536|0.77536	-0.2551|-0.2551	10|5	0.66056|.	D|.	0.02|.	-3.4753|-3.4753	19.2662|19.2662	0.93985|0.93985	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	329;329;329|.	A7E2V4;A7E2V4-5;A7E2V4-4|.	K0913_HUMAN;.;.|.	T|H	329|51	ENSP00000381693:A329T|.	ENSP00000381693:A329T|.	A|R	+|+	1|2	0|0	KIAA0913|KIAA0913	75220782|75220782	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.982000|0.982000	0.71751|0.71751	8.953000|8.953000	0.93041|0.93041	2.789000|2.789000	0.95967|0.95967	0.591000|0.591000	0.81541|0.81541	GCT|CGC		0.557	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		A	75550776	G	A	75550776	3	1	8	1	0	0	0	0	1	0	0	0	8221	1087	38	1	1015	1	KIAA0913	10	75550776	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	14488176	75550776	59983971	67	829										
INA	9118	hgsc.bcm.edu	37	chr10	105046867	105046867	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gccaccttcgggaataccagGacttgctcaatgtcaaaatg	9	11	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:105046867G>T	ENST00000369849.4	+	2	1190	c.1141G>T	c.(1141-1143)Gac>Tac	p.D381Y		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	381	Coil 2.|Rod.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GGAATACCAGGACTTGCTCAA	0.468																																																0			10											121	100	107					10																	105046867		2203	4300	6503	105036857	SO:0001583	missense	9118			S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"Intermediate filaments type IV"	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.1141G>T	10.37:g.105046867G>T	ENSP00000358865:p.Asp381Tyr		105036857	B1AQK0|Q9BRC5	Missense_Mutation	SNP	ENST00000369849.4	37	CCDS7545.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442687	0.83993	.	.	ENSG00000148798	ENST00000369849	D	0.89485	-2.52	5.43	4.52	0.55395	Filament (1);	0.000000	0.85682	D	0.000000	D	0.96097	0.8728	H	0.96080	3.765	0.53688	D	0.999977	D	0.89917	1.0	D	0.97110	1.0	D	0.97183	0.9852	10	0.87932	D	0	.	13.8489	0.63485	0.0739:0.0:0.9261:0.0	.	381	Q16352	AINX_HUMAN	Y	381	ENSP00000358865:D381Y	ENSP00000358865:D381Y	D	+	1	0	INA	105036857	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.527000	0.98044	1.521000	0.48983	0.655000	0.94253	GAC		0.468	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727		T	105046867	G	T	105046867	3	4	8	1	0	0	0	0	1	0	0	0	7751	1174	41	2	1147	2	INA	10	105046867	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	29496091	105046867	30487880	68	830										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105204330	105204330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttcagctgggggatgcagagCgggccaaagccatttttgag	15	8	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:105204330C>T	ENST00000369797.3	+	35	5429	c.5335C>T	c.(5335-5337)Cgg>Tgg	p.R1779W		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1779					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.R1779W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GGATGCAGAGCGGGCCAAAGC	0.547																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											134	107	116					10																	105204330		2203	4300	6503	105194320	SO:0001583	missense	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5335C>T	10.37:g.105204330C>T	ENSP00000358812:p.Arg1779Trp		105194320	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210380	0.79240	.	.	ENSG00000148843	ENST00000369797	T	0.56275	0.47	5.57	4.65	0.58169	Tetratricopeptide-like helical (1);Suppressor of forked (1);Tetratricopeptide repeat-containing (1);	0.242285	0.39407	N	0.001369	T	0.77384	0.4122	M	0.89715	3.055	0.52501	D	0.999954	D	0.89917	1.0	D	0.78314	0.991	T	0.83241	-0.0058	10	0.87932	D	0	-20.5552	15.6725	0.77289	0.1383:0.8617:0.0:0.0	.	1779	Q14690	RRP5_HUMAN	W	1779	ENSP00000358812:R1779W	ENSP00000358812:R1779W	R	+	1	2	PDCD11	105194320	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	3.116000	0.50399	1.315000	0.45114	0.561000	0.74099	CGG		0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105204330	C	T	105204330	3	4	8	1	0	0	0	0	1	0	0	0	11648	759	27	1	5469	1	PDCD11	10	105204330	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	157463	105204330	30330417	69	831										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114901049	114901050	+	Frame_Shift_Ins	INS	-	-	A													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggaaacccacctccacacttINSaccagccgacgtagacccca							TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:114901049_114901050insA	ENST00000355995.4	+	6	1166_1167	c.659_660insA	c.(658-663)ttaccafs	p.P221fs	TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000369395.1_Frame_Shift_Ins_p.P246fs|TCF7L2_ENST00000369397.4_Frame_Shift_Ins_p.P198fs|TCF7L2_ENST00000352065.5_Frame_Shift_Ins_p.P198fs|TCF7L2_ENST00000349937.2_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000355717.4_Frame_Shift_Ins_p.P245fs|TCF7L2_ENST00000543371.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000536810.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000545257.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000534894.1_Frame_Shift_Ins_p.P221fs|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000538897.1_Frame_Shift_Ins_p.P221fs			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	221	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P221fs*107(1)|p.P198fs*107(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCTCCACACTTACCAGCCGACG	0.589			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	2	Insertion - Frameshift(2)	large_intestine(2)	10																																								114891040	SO:0001589	frameshift_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.660dupA	10.37:g.114901050_114901050dupA	ENSP00000348274:p.Pro221fs		114891039	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Ins	INS	ENST00000355995.4	37																																																																																					0.589	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114901050	-	A	114901049	7	5	8	1	0	1	1	0	0	0	0	0	15737	1764	61	0	826	0	TCF7L2	10	114901049	Frame_Shift_Ins	INS	-	TCGA-AF-4110-01A-02D-1733-10	9696719	114901049	20633698	70	832										
NRAP	4892	hgsc.bcm.edu	37	chr10	115356930	115356930	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acttgatactgtctggttttTtacggtacttggtctataag	9	6	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:115356930T>C	ENST00000359988.3	-	37	4590	c.4346A>G	c.(4345-4347)aAa>aGa	p.K1449R	NRAP_ENST00000369358.4_Missense_Mutation_p.K1457R|NRAP_ENST00000360478.3_Missense_Mutation_p.K1414R|NRAP_ENST00000369360.3_Missense_Mutation_p.K1422R	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GTCTGGTTTTTTACGGTACTT	0.448																																																0			10											276	250	259					10																	115356930		2203	4300	6503	115346920	SO:0001583	missense	65083				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.4346A>G	10.37:g.115356930T>C	ENSP00000353078:p.Lys1449Arg		115346920		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248405	0.39797	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350	T;T;T;T	0.16743	2.45;2.41;2.41;2.32	5.99	-0.506	0.11989	.	0.380721	0.32918	N	0.005481	T	0.10895	0.0266	L	0.34521	1.04	0.26122	N	0.98054	B;B;B;B	0.10296	0.003;0.0;0.0;0.0	B;B;B;B	0.10450	0.003;0.003;0.005;0.003	T	0.16512	-1.0400	10	0.52906	T	0.07	.	6.5573	0.22468	0.0:0.2468:0.1153:0.6379	.	607;1449;1414;1449	B1ANW7;A0AVL2;Q86VF7-4;Q86VF7	.;.;.;NRAP_HUMAN	R	1457;1422;1449;1414;607	ENSP00000358365:K1457R;ENSP00000358367:K1422R;ENSP00000353078:K1449R;ENSP00000353666:K1414R	ENSP00000353078:K1449R	K	-	2	0	NRAP	115346920	1.000000	0.71417	0.565000	0.28409	0.962000	0.63368	2.895000	0.48648	-0.316000	0.08690	-0.912000	0.02778	AAA		0.448	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		C	115356930	T	C	115356930	3	2	8	1	0	0	0	0	1	0	0	0	10669	1841	64	4	870	4	NRAP	10	115356930	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	455881	115356930	20177817	71	833										
PNLIPRP2	5408	hgsc.bcm.edu	37	chr10	118383592	118383592	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tttcttctgtacacaaatgaAaatccaaacaacttccaagt	3	10	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:118383592A>G	ENST00000298771.7	+	0	211				PNLIPRP2_ENST00000433618.4_RNA|PNLIPRP2_ENST00000537242.1_RNA	NR_103727.1		P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process (GO:0019376)|lipid digestion (GO:0044241)|phospholipid catabolic process (GO:0009395)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	acylglycerol lipase activity (GO:0047372)|calcium ion binding (GO:0005509)|galactolipase activity (GO:0047714)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		ACACAAATGAAAATCCAAACA	0.498																																																0			10											96	92	94					10																	118383592		1923	4144	6067	118373582			5408			M93284		10q26.12	2014-03-14				ENSG00000266200	3.1.1.3		9157	protein-coding gene	gene with protein product		604423				1379598	Standard	NM_005396		Approved	PLRP2	uc001lcq.3	P54317			10.37:g.118383592A>G			118373582	A8K627|Q6IB55	Missense_Mutation	SNP	ENST00000298771.7	37																																																																																					0.498	PNLIPRP2-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000050546.6	NM_005396		G	118383592	A	G	118383592	1	3	8	0	1	0	0	0	0	0	0	0	12182	14	1	4		4	PNLIPRP2	10	118383592	RNA	SNP	A	TCGA-AF-4110-01A-02D-1733-10	3026662	118383592	17151155	72	834										
MKI67	4288	hgsc.bcm.edu	37	chr10	129906140	129906140	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gccggttaagttctctgtcaGgtccagtttctgcactggag	12	10	3	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:129906140G>A	ENST00000368654.3	-	13	4339	c.3964C>T	c.(3964-3966)Ctg>Ttg	p.L1322L	MKI67_ENST00000368653.3_Silent_p.L962L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1322	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCTCTGTCAGGTCCAGTTTC	0.502																																																0			10											198	194	196					10																	129906140		2203	4300	6503	129796130	SO:0001819	synonymous_variant	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3964C>T	10.37:g.129906140G>A			129796130	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																				0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129906140	G	A	129906140	2	1	8	1	0	0	0	0	0	0	0	1	9628	991	35	3		3	MKI67	10	129906140	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	11522548	129906140	5628607	73	835										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135111468	135111468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tcacgtacctatcggcaaagCggtgtctgtgctgatgccag	12	11	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr10:135111468C>T	ENST00000252936.3	-	4	643	c.604G>A	c.(604-606)Gct>Act	p.A202T	TUBGCP2_ENST00000368563.2_Missense_Mutation_p.A202T|TUBGCP2_ENST00000470829.1_5'Flank|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000417178.2_Missense_Mutation_p.A72T|TUBGCP2_ENST00000543663.1_Missense_Mutation_p.A202T			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	202					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		ATCGGCAAAGCGGTGTCTGTG	0.537																																																0			10											164	139	147					10																	135111468		2203	4300	6503	134961458	SO:0001583	missense	10844			AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.604G>A	10.37:g.135111468C>T	ENSP00000252936:p.Ala202Thr		134961458	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Missense_Mutation	SNP	ENST00000252936.3	37	CCDS7676.1	.	.	.	.	.	.	.	.	.	.	C	8.006	0.756417	0.15846	.	.	ENSG00000130640	ENST00000252936;ENST00000417178;ENST00000368563;ENST00000543663	T;T;T;T	0.18657	2.46;2.2;2.46;2.49	5.24	3.37	0.38596	.	0.445404	0.27700	N	0.018219	T	0.08223	0.0205	N	0.04508	-0.205	0.09310	N	0.999999	B;B;B	0.12630	0.006;0.004;0.003	B;B;B	0.10450	0.005;0.002;0.002	T	0.36986	-0.9725	10	0.14252	T	0.57	-2.1915	7.5796	0.27957	0.0:0.672:0.0:0.328	.	202;202;202	F5H4L0;B7ZKL8;Q9BSJ2	.;.;GCP2_HUMAN	T	202;72;202;202	ENSP00000252936:A202T;ENSP00000395666:A72T;ENSP00000357551:A202T;ENSP00000446093:A202T	ENSP00000252936:A202T	A	-	1	0	TUBGCP2	134961458	0.020000	0.18652	0.062000	0.19696	0.357000	0.29423	0.260000	0.18424	0.697000	0.31718	0.561000	0.74099	GCT		0.537	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			T	135111468	C	T	135111468	3	4	8	1	0	0	0	0	1	0	0	0	16806	768	27	1	2160	1	TUBGCP2	10	135111468	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	5205328	135111468	423279	74	836										
IFITM3	10410	hgsc.bcm.edu	37	chr11	319855	319855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gatctatccataggcctggaAgatcagcactgggatgacga	12	9	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:319855A>G	ENST00000399808.4	-	2	621	c.385T>C	c.(385-387)Ttc>Ctc	p.F129L	RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.F108L|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.F108L|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	129	Interaction with VAPA.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.F129V(1)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TAGGCCTGGAAGATCAGCACT	0.587																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											68	70	70					11																	319855		2029	4178	6207	309855	SO:0001583	missense	10410			X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"interferon induced transmembrane protein 3 (1-8U)"			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.385T>C	11.37:g.319855A>G	ENSP00000382707:p.Phe129Leu		309855	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.348|0.348	-0.946328|-0.946328	0.02304|0.02304	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000399808;ENST00000526811|ENST00000270031	T;T|.	0.78126|.	-0.9;-1.15|.	2.58|2.58	-5.16|-5.16	0.02857|0.02857	.|.	.|0.215683	.|0.25981	.|U	.|0.027064	T|T	0.07503|0.07503	0.0189|0.0189	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.11665|0.11665	-1.0578|-1.0578	9|7	0.05833|0.51188	T|T	0.94|0.08	1.4325|1.4325	2.1432|2.1432	0.03780|0.03780	0.1561:0.2923:0.4058:0.1459|0.1561:0.2923:0.4058:0.1459	.|.	129|.	Q01628|.	IFM3_HUMAN|.	L|P	129;108|109	ENSP00000382707:F129L;ENSP00000432108:F108L|.	ENSP00000382707:F129L|ENSP00000372047:L109P	F|L	-|-	1|2	0|0	IFITM3|IFITM3	309855|309855	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-6.554000|-6.554000	0.00061|0.00061	-2.050000|-2.050000	0.00905|0.00905	-0.420000|-0.420000	0.06012|0.06012	TTC|CTT		0.587	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		G	319855	A	G	319855	3	3	8	1	0	0	0	0	1	0	0	0	7549	72	3	4	20	4	IFITM3	11	319855	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10		319855	134686661	75	837										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6530177	6530177	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	actacatcttctctccctttGggatcttgcatgtacatcct	5	13	3	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:6530177G>T	ENST00000527990.2	+	3	988	c.988G>T	c.(988-990)Ggg>Tgg	p.G330W	DNHD1_ENST00000254579.6_Missense_Mutation_p.G330W|DNHD1_ENST00000354685.3_Missense_Mutation_p.G330W			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	330					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.G330R(2)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTCTCCCTTTGGGATCTTGCA	0.517																																																2	Substitution - Missense(2)	ovary(2)	11											178	151	160					11																	6530177		2201	4296	6497	6486753	SO:0001583	missense	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.988G>T	11.37:g.6530177G>T	ENSP00000436180:p.Gly330Trp		6486753	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.689592	0.68271	.	.	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.19669	2.13;2.13;2.13	5.83	4.9	0.64082	.	0.317593	0.27464	N	0.019259	T	0.51346	0.1669	M	0.87381	2.88	0.36656	D	0.877663	D;D	0.89917	0.958;1.0	P;D	0.97110	0.665;1.0	T	0.66670	-0.5865	10	0.87932	D	0	.	13.3274	0.60467	0.0:0.0:0.8415:0.1585	.	330;330	Q96M86;Q96M86-4	DNHD1_HUMAN;.	W	330	ENSP00000254579:G330W;ENSP00000346716:G330W;ENSP00000436180:G330W	ENSP00000254579:G330W	G	+	1	0	DNHD1	6486753	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	5.429000	0.66495	1.418000	0.47098	0.650000	0.86243	GGG		0.517	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6530177	G	T	6530177	3	4	8	1	0	0	0	0	1	0	0	0	4679	1348	47	2	998	2	DNHD1	11	6530177	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	6210322	6530177	128476339	76	838										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735425	18735425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cactaaggtgcagagtggccGtggctgagccgtggtcattc	15	10	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:18735425G>A	ENST00000513874.1	-	14	2208	c.2069C>T	c.(2068-2070)aCg>aTg	p.T690M	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	690	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CAGAGTGGCCGTGGCTGAGCC	0.642																																																0			11											42	47	45					11																	18735425		2169	4258	6427	18692001	SO:0001583	missense	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2069C>T	11.37:g.18735425G>A	ENSP00000421191:p.Thr690Met		18692001	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101415	0.37048	.	.	ENSG00000179057	ENST00000513874	T	0.70164	-0.46	3.97	3.05	0.35203	.	0.000000	0.37906	U	0.001891	T	0.71879	0.3392	M	0.83774	2.66	0.09310	N	1	D	0.60575	0.988	P	0.53224	0.721	T	0.62623	-0.6815	10	0.37606	T	0.19	.	5.3709	0.16138	0.3017:0.0:0.6983:0.0	.	690	D6RGV7	.	M	690	ENSP00000421191:T690M	ENSP00000322422:T690M	T	-	2	0	IGSF22	18692001	0.013000	0.17824	0.013000	0.15412	0.811000	0.45836	1.572000	0.36461	0.891000	0.36235	0.442000	0.29010	ACG		0.642	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18735425	G	A	18735425	3	1	8	1	0	0	0	0	1	0	0	0	7621	1145	40	1	1951	1	IGSF22	11	18735425	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	12205248	18735425	116271091	77	839										
METT5D1	196074	hgsc.bcm.edu	37	chr11	28135029	28135029	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atgaagcccgggagcaaacaGatcaaactcaagcccaggag	11	11	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:28135029G>T	ENST00000407364.3	+	3	500	c.148G>T	c.(148-150)Gat>Tat	p.D50Y	METTL15_ENST00000379199.2_Missense_Mutation_p.D50Y|METTL15_ENST00000303459.6_Missense_Mutation_p.D50Y|METTL15_ENST00000403099.1_Missense_Mutation_p.D50Y|METTL15_ENST00000406787.3_Missense_Mutation_p.D50Y|METTL15_ENST00000342303.5_Missense_Mutation_p.D50Y			A6NJ78	MET15_HUMAN	methyltransferase like 15	50							methyltransferase activity (GO:0008168)	p.D50Y(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						GGAGCAAACAGATCAAACTCA	0.383																																																1	Substitution - Missense(1)	ovary(1)	11											52	59	57					11																	28135029		2202	4299	6501	28091605	SO:0001583	missense	196074			AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"methyltransferase 5 domain containing 1"	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.148G>T	11.37:g.28135029G>T	ENSP00000384369:p.Asp50Tyr		28091605	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	37	CCDS44559.1	.	.	.	.	.	.	.	.	.	.	G	3.329	-0.137051	0.06711	.	.	ENSG00000169519	ENST00000406787;ENST00000342303;ENST00000403099;ENST00000407364;ENST00000379199;ENST00000303459	T;T;T;T;T;T	0.46063	1.43;1.46;0.88;1.88;0.88;1.46	5.68	0.285	0.15705	.	1.560150	0.03265	N	0.183849	T	0.28466	0.0704	N	0.16478	0.41	0.09310	N	1	B;B;B	0.10296	0.0;0.0;0.003	B;B;B	0.08055	0.0;0.001;0.003	T	0.23190	-1.0195	10	0.46703	T	0.11	.	6.4548	0.21924	0.1468:0.0:0.3386:0.5146	.	50;50;50	A6NJ78;A6NJ78-2;A6NJ78-4	MET15_HUMAN;.;.	Y	50	ENSP00000385507:D50Y;ENSP00000342259:D50Y;ENSP00000385860:D50Y;ENSP00000384369:D50Y;ENSP00000368497:D50Y;ENSP00000307251:D50Y	ENSP00000307251:D50Y	D	+	1	0	METTL15	28091605	0.000000	0.05858	0.000000	0.03702	0.163000	0.22366	-0.901000	0.04093	0.089000	0.17243	-0.230000	0.12252	GAT		0.383	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636		T	28135029	G	T	28135029	3	4	8	1	0	0	0	0	1	0	0	0	9522	942	33	2	150	2	METT5D1	11	28135029	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	9399604	28135029	106871487	78	840										
OR5B21	219968	hgsc.bcm.edu	37	chr11	58275303	58275303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aactgagctgcacatccatcGtaggagatggccttgtcccc	10	13	0	2	rs146345059	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:58275303G>A	ENST00000360374.2	-	1	275	c.276C>T	c.(274-276)taC>taT	p.Y92Y		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACATCCATCGTAGGAGATGG	0.532													G|||	4	0.000798722	0	0.0058	5008	,	,		21630	0		0	False		,,,				2504	0															0			11						G		0,4402		0,0,2201	122	96	105		276	2.2	0.5	11	dbSNP_134	105	8,8582	6.4+/-24.3	0,8,4287	no	coding-synonymous	OR5B21	NM_001005218.1		0,8,6488	AA,AG,GG		0.0931,0.0,0.0616		92/310	58275303	8,12984	2201	4295	6496	58031879	SO:0001819	synonymous_variant	219968				CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.276C>T	11.37:g.58275303G>A			58031879		Silent	SNP	ENST00000360374.2	37	CCDS31552.1																																																																																				0.532	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		A	58275303	G	A	58275303	2	1	8	1	0	0	0	0	0	0	0	1	11182	1140	40	1		1	OR5B21	11	58275303	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	30140274	58275303	76731213	79	841										
VPS37C	55048	hgsc.bcm.edu	37	chr11	60901542	60901542	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tgctcctggcaccgctccacGagcttccggagctcctggta	11	16	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:60901542G>A	ENST00000301765.5	-	3	463	c.231C>T	c.(229-231)ctC>ctT	p.L77L		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	77					endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						ACCGCTCCACGAGCTTCCGGA	0.627																																																0			11											67	68	68					11																	60901542		2203	4299	6502	60658118	SO:0001819	synonymous_variant	55048			AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.231C>T	11.37:g.60901542G>A			60658118	Q8N3K4	Silent	SNP	ENST00000301765.5	37	CCDS31573.1																																																																																				0.627	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966		A	60901542	G	A	60901542	2	1	8	1	0	0	0	0	0	0	0	1	17247	1045	37	1		1	VPS37C	11	60901542	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	2626239	60901542	74104974	80	842										
ADAMTS15	170689	hgsc.bcm.edu	37	chr11	130343260	130343260	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cgggtccgctactccttctaTctgcccaaagagcctcggga	10	15	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr11:130343260T>C	ENST00000299164.2	+	8	2397	c.2397T>C	c.(2395-2397)taT>taC	p.Y799Y		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	799	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		ACTCCTTCTATCTGCCCAAAG	0.647																																																0			11											98	113	108					11																	130343260		2201	4296	6497	129848470	SO:0001819	synonymous_variant	170689			AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"ADAM metallopeptidases with thrombospondin type 1 motif"	16305	protein-coding gene	gene with protein product		607509	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.2397T>C	11.37:g.130343260T>C			129848470	Q32MI6	Silent	SNP	ENST00000299164.2	37	CCDS8488.1																																																																																				0.647	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		C	130343260	T	C	130343260	2	2	8	1	0	0	0	0	0	0	0	1	260	1442	50	4		4	ADAMTS15	11	130343260	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10	69441718	130343260	4663256	81	843										
PRB1	5542	hgsc.bcm.edu	37	chr12	11506416	11506417	+	Intron	INS	-	-	C													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	attgggaacttcgggacttgINStctccttgtgggggtggtcc							TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:11506416_11506417insC	ENST00000500254.2	-	4	351				PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			TTCGGGACTTGTCTCCTTGTGG	0.614																																																0			12																																								11397684	SO:0001627	intron_variant	5933				CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.314-92->G	12.37:g.11506416_11506417insC			11397683	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Frame_Shift_Ins	INS	ENST00000500254.2	37	CCDS8642.1																																																																																				0.614	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		C	11506417	-	C	11506416	6	5	8	0	1	1	1	0	0	0	0	0	12476	1368	48	0		0	PRB1	12	11506416	Intron	INS	-	TCGA-AF-4110-01A-02D-1733-10		11506416	122345479	82	844										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21377773	21377773	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atataattccacatcattttCgtaagttgtcataaatatat	3	6	2	0	rs368052440		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:21377773C>T	ENST00000256958.2	+	14	1961	c.1865C>T	c.(1864-1866)tCa>tTa	p.S622L		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	622					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	ACATCATTTTCGTAAGTTGTC	0.289																																																0			12						C	LEU/SER	0,4406		0,0,2203	93	91	91		1865	2.8	1	12		91	1,8599		0,1,4299	no	missense-near-splice	SLCO1B1	NM_006446.4	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	622/692	21377773	1,13005	2203	4300	6503	21269040	SO:0001630	splice_region_variant	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1865+1C>T	12.37:g.21377773C>T			21269040	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329494	0.24167	0.0	1.16E-4	ENSG00000134538	ENST00000256958	T	0.41065	1.01	3.66	2.76	0.32466	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.452872	0.21445	N	0.074438	T	0.28962	0.0719	N	0.20986	0.625	0.27379	N	0.955479	P	0.39391	0.671	B	0.38655	0.278	T	0.13388	-1.0511	10	0.66056	D	0.02	.	10.1303	0.42674	0.0:0.2185:0.7815:0.0	.	622	Q9Y6L6	SO1B1_HUMAN	L	622	ENSP00000256958:S622L	ENSP00000256958:S622L	S	+	2	0	SLCO1B1	21269040	1.000000	0.71417	0.994000	0.49952	0.339000	0.28857	2.021000	0.41020	0.726000	0.32339	-0.499000	0.04595	TCA		0.289	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	Missense_Mutation	T	21377773	C	T	21377773	5	4	8	1	0	0	0	0	0	0	1	0	14760	898	31	1	1915	1	SLCO1B1	12	21377773	Splice_Site	SNP	C	TCGA-AF-4110-01A-02D-1733-10	9871357	21377773	112474122	83	845										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	8	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	4020511	25398284	108453611	84	846										
FAM113B	91523	hgsc.bcm.edu	37	chr12	47629680	47629680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggcccgagagtcgaagggccGccccaggccaacagaaatca	13	14	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:47629680G>A	ENST00000546455.1	+	4	1565	c.834G>A	c.(832-834)ccG>ccA	p.P278P	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Silent_p.P278P			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	278	Pro-rich.						hydrolase activity (GO:0016787)										TCGAAGGGCCGCCCCAGGCCA	0.672																																																0			12											19	23	22					12																	47629680		2190	4264	6454	45915947	SO:0001819	synonymous_variant	91523			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.834G>A	12.37:g.47629680G>A			45915947	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																				0.672	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47629680	G	A	47629680	2	1	8	1	0	0	0	0	0	0	0	1	5418	1074	38	1		1	FAM113B	12	47629680	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	22231396	47629680	86222215	85	847										
TRPV4	59341	hgsc.bcm.edu	37	chr12	110221492	110221492	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tggtggccatcgcagcggggGttccccatgctgtccagagg	16	12	0	1	rs571407723		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:110221492G>C	ENST00000418703.2	-	15	2644	c.2550C>G	c.(2548-2550)aaC>aaG	p.N850K	TRPV4_ENST00000261740.2_Missense_Mutation_p.N850K|TRPV4_ENST00000346520.2_Missense_Mutation_p.N790K|TRPV4_ENST00000536838.1_Missense_Mutation_p.N816K|TRPV4_ENST00000541794.1_Missense_Mutation_p.N803K|TRPV4_ENST00000544971.1_Missense_Mutation_p.N743K|TRPV4_ENST00000392719.2_Missense_Mutation_p.N803K|TRPV4_ENST00000537083.1_Missense_Mutation_p.N790K	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	850					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						CGCAGCGGGGGTTCCCCATGC	0.652																																																0			12											68	57	60					12																	110221492		2203	4300	6503	108705875	SO:0001583	missense	59341			AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.2550C>G	12.37:g.110221492G>C	ENSP00000406191:p.Asn850Lys		108705875	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	37	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	G	9.557	1.117341	0.20795	.	.	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838	D;D;D;D;D;D;D;D	0.88354	-2.36;-2.36;-2.16;-2.37;-2.16;-2.37;-2.16;-2.36	5.39	0.116	0.14647	.	0.424674	0.24005	N	0.042436	T	0.72661	0.3488	N	0.08118	0	0.24486	N	0.994328	B;B;B;B;B	0.14012	0.0;0.0;0.0;0.0;0.009	B;B;B;B;B	0.15870	0.001;0.0;0.0;0.001;0.014	T	0.60271	-0.7296	10	0.33940	T	0.23	-4.5003	6.2548	0.20867	0.2267:0.3715:0.4018:0.0	.	790;850;743;803;816	Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5	.;TRPV4_HUMAN;.;.;.	K	850;850;803;790;743;790;803;816	ENSP00000406191:N850K;ENSP00000261740:N850K;ENSP00000376480:N803K;ENSP00000319003:N790K;ENSP00000443611:N743K;ENSP00000442738:N790K;ENSP00000442167:N803K;ENSP00000444336:N816K	ENSP00000261740:N850K	N	-	3	2	TRPV4	108705875	0.008000	0.16893	0.986000	0.45419	0.299000	0.27559	-0.034000	0.12225	-0.012000	0.14223	-1.080000	0.02220	AAC		0.652	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		C	110221492	G	C	110221492	3	2	8	1	0	0	0	0	1	0	0	0	16638	1252	44	5	69	5	TRPV4	12	110221492	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	62591812	110221492	23630403	86	848										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112888190	112888190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctatgacctgtatggaggggAgaaatttgccactttggctg	13	7	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:112888190A>G	ENST00000351677.2	+	3	404	c.206A>G	c.(205-207)gAg>gGg	p.E69G	PTPN11_ENST00000392597.1_Missense_Mutation_p.E69G	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	69	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		E -> K (in JMML; also in myelodysplastic syndrome). {ECO:0000269|PubMed:12717436}.|E -> Q (in NS1). {ECO:0000269|PubMed:12634870}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TATGGAGGGGAGAAATTTGCC	0.428			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12											152	141	145					12																	112888190		2203	4300	6503	111372573	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.206A>G	12.37:g.112888190A>G	ENSP00000340944:p.Glu69Gly		111372573	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	32	5.124235	0.94429	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.89270	-2.49;-2.49	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.94348	0.8183	M	0.76938	2.355	0.80722	D	1	P;D	0.89917	0.952;1.0	P;D	0.78314	0.672;0.991	D	0.94883	0.8041	10	0.87932	D	0	.	16.3291	0.83001	1.0:0.0:0.0:0.0	.	69;69	Q06124-2;Q06124-3	.;.	G	69	ENSP00000376376:E69G;ENSP00000340944:E69G	ENSP00000340944:E69G	E	+	2	0	PTPN11	111372573	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.332000	0.96446	2.257000	0.74773	0.528000	0.53228	GAG		0.428	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112888190	A	G	112888190	3	3	8	1	0	0	0	0	1	0	0	0	12815	304	11	4	216	4	PTPN11	12	112888190	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	2666698	112888190	20963705	87	849										
IQCD	115811	hgsc.bcm.edu	37	chr12	113645406	113645406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	caaacaggaaaccacggagcTctatcaggctgtcaataaaa	8	10	3	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:113645406T>C	ENST00000416617.2	-	2	756	c.566A>G	c.(565-567)gAg>gGg	p.E189G	IQCD_ENST00000546692.1_Missense_Mutation_p.E189G|IQCD_ENST00000299732.2_Missense_Mutation_p.E189G			Q96DY2	IQCD_HUMAN	IQ motif containing D	189										endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						ACCACGGAGCTCTATCAGGCT	0.478																																																0			12											100	95	97					12																	113645406		2203	4300	6503	112129789	SO:0001583	missense	115811			BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 10"					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.566A>G	12.37:g.113645406T>C	ENSP00000400669:p.Glu189Gly		112129789	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	37		.	.	.	.	.	.	.	.	.	.	T	20.3	3.963493	0.74016	.	.	ENSG00000166578	ENST00000299732;ENST00000416617;ENST00000546692;ENST00000392574	T;T;T	0.12361	2.69;2.69;2.69	5.25	5.25	0.73442	.	0.137587	0.47852	D	0.000205	T	0.37265	0.0997	M	0.74258	2.255	0.54753	D	0.999985	D;D	0.89917	0.999;1.0	D;D	0.72982	0.974;0.979	T	0.20773	-1.0265	10	0.87932	D	0	-29.2873	14.1294	0.65242	0.0:0.0:0.0:1.0	.	189;189	F8VZV9;Q96DY2-2	.;.	G	189	ENSP00000299732:E189G;ENSP00000400669:E189G;ENSP00000446623:E189G	ENSP00000299732:E189G	E	-	2	0	IQCD	112129789	0.993000	0.37304	0.044000	0.18714	0.004000	0.04260	4.086000	0.57664	1.977000	0.57605	0.460000	0.39030	GAG		0.478	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451		C	113645406	T	C	113645406	3	2	8	1	0	0	0	0	1	0	0	0	7826	1551	54	4	485	4	IQCD	12	113645406	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	757216	113645406	20206489	88	850										
EP400	57634	hgsc.bcm.edu	37	chr12	132554068	132554068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acagcagatcaccacccctgGcgcgcagcagaaggttgcct	11	15	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr12:132554068G>A	ENST00000333577.4	+	52	9120	c.9011G>A	c.(9010-9012)gGc>gAc	p.G3004D	EP400_ENST00000389562.2_Missense_Mutation_p.G2967D|EP400_ENST00000389561.2_Missense_Mutation_p.G2968D|EP400_ENST00000330386.6_Missense_Mutation_p.G2887D|EP400_ENST00000332482.4_Missense_Mutation_p.G2931D			Q96L91	EP400_HUMAN	E1A binding protein p400	3004					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		ACCACCCCTGGCGCGCAGCAG	0.652																																																0			12											74	75	75					12																	132554068		2203	4300	6503	131120021	SO:0001583	missense	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.9011G>A	12.37:g.132554068G>A	ENSP00000333602:p.Gly3004Asp		131120021	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	12.47	1.947282	0.34377	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90004	-2.58;-2.58;-2.6;-2.58;-2.57	5.01	5.01	0.66863	.	0.776328	0.12125	N	0.497365	D	0.90061	0.6896	N	0.19112	0.55	0.37178	D	0.903355	D;P;P;P	0.89917	1.0;0.763;0.763;0.763	D;P;P;P	0.83275	0.996;0.463;0.463;0.463	D	0.89882	0.4031	10	0.56958	D	0.05	.	13.1353	0.59405	0.0:0.2996:0.7004:0.0	.	3004;2968;2887;2967	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	D	3004;2968;2967;2931;2887;2968	ENSP00000333602:G3004D;ENSP00000374212:G2968D;ENSP00000374213:G2967D;ENSP00000331737:G2931D;ENSP00000330620:G2887D	ENSP00000330620:G2887D	G	+	2	0	EP400	131120021	.	.	0.995000	0.50966	0.006000	0.05464	.	.	2.295000	0.77249	0.491000	0.48974	GGC		0.652	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132554068	G	A	132554068	3	1	8	1	0	0	0	0	1	0	0	0	5162	1203	42	3	9098	3	EP400	12	132554068	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	18908662	132554068	1297827	89	851										
FLT1	2321	hgsc.bcm.edu	37	chr13	28893602	28893602	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	caatactccgtaagaccacaCgtcgctcttggtgctgtaga	9	12	1	2	rs142586121		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr13:28893602C>T	ENST00000282397.4	-	24	3495	c.3244G>A	c.(3244-3246)Gtg>Atg	p.V1082M	FLT1_ENST00000543394.1_Missense_Mutation_p.V105M|FLT1_ENST00000540678.1_Missense_Mutation_p.V300M	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1082	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TAAGACCACACGTCGCTCTTG	0.453																																																0			13						C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	88	78	81		3244	5.5	1	13	dbSNP_134	81	0,8600		0,0,4300	yes	missense	FLT1	NM_002019.4	21	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	1082/1339	28893602	2,13004	2203	4300	6503	27791602	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3244G>A	13.37:g.28893602C>T	ENSP00000282397:p.Val1082Met		27791602	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.008863	0.93346	4.54E-4	0.0	ENSG00000102755	ENST00000282397;ENST00000543394;ENST00000540678	D;D;D	0.88431	-2.38;-2.38;-2.38	5.49	5.49	0.81192	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94118	0.8114	M	0.67569	2.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94196	0.7445	10	0.87932	D	0	.	19.7347	0.96198	0.0:1.0:0.0:0.0	.	1082	P17948	VGFR1_HUMAN	M	1082;105;300	ENSP00000282397:V1082M;ENSP00000437841:V105M;ENSP00000443311:V300M	ENSP00000282397:V1082M	V	-	1	0	FLT1	27791602	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.746000	0.94184	0.655000	0.94253	GTG		0.453	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			T	28893602	C	T	28893602	3	4	8	1	0	0	0	0	1	0	0	0	5960	536	19	1	800	1	FLT1	13	28893602	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10		28893602	86276276	90	852										
BRCA2	675	hgsc.bcm.edu	37	chr13	32913406	32913406	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	agtatctttttgaaagttaaAgtacatgaaaatgtagaaaa	7	2	1	3	rs201431881		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr13:32913406A>G	ENST00000380152.3	+	11	5147	c.4914A>G	c.(4912-4914)aaA>aaG	p.K1638K	BRCA2_ENST00000544455.1_Silent_p.K1638K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1638	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGAAAGTTAAAGTACATGAAA	0.318			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1	0.000199681	8e-04	0	5008	,	,		19494	0		0	False		,,,				2504	0				Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											34	37	36					13																	32913406		2201	4297	6498	31811406	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.4914A>G	13.37:g.32913406A>G			31811406	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.318	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32913406	A	G	32913406	2	3	8	1	0	0	0	0	0	0	0	1	1502	69	3	4		4	BRCA2	13	32913406	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	4019804	32913406	82256472	91	853										
RB1	5925	hgsc.bcm.edu	37	chr13	48941672	48941672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acgaagaaatttatcttaaaAataaagatctagatgcaaga	6	4	2	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr13:48941672A>G	ENST00000267163.4	+	10	1120	c.982A>G	c.(982-984)Aat>Gat	p.N328D		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	328					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(7)|p.N328H(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTATCTTAAAAATAAAGATCT	0.299		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(7)|Substitution - Missense(1)	bone(11)|breast(5)|eye(2)|adrenal_gland(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											61	73	69					13																	48941672		2190	4283	6473	47839673	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.982A>G	13.37:g.48941672A>G	ENSP00000267163:p.Asn328Asp		47839673	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804433	0.31869	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92048	-2.96	5.43	5.43	0.79202	.	0.094778	0.64402	D	0.000001	D	0.87521	0.6198	L	0.44542	1.39	0.38926	D	0.957846	B	0.25007	0.116	B	0.19148	0.024	D	0.85192	0.1010	10	0.44086	T	0.13	.	10.3957	0.44198	0.8539:0.0:0.0:0.1461	.	328	P06400	RB_HUMAN	D	307;328	ENSP00000267163:N328D	ENSP00000267163:N328D	N	+	1	0	RB1	47839673	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.868000	0.63021	2.039000	0.60335	0.482000	0.46254	AAT		0.299	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48941672	A	G	48941672	3	3	8	1	0	0	0	0	1	0	0	0	13135	14	1	4	1020	4	RB1	13	48941672	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	16028266	48941672	66228206	92	854										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88329438	88329438	+	Missense_Mutation	SNP	G	G	C													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gtaaggcgcccaaaaaattcGctgagaccgacatgcgctcc					rs377281360		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr13:88329438G>C	ENST00000325089.6	+	2	2014	c.1795G>C	c.(1795-1797)Gct>Cct	p.A599P	SLITRK5_ENST00000400028.3_Missense_Mutation_p.A358P	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	599	LRRCT 2.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CAAAAAATTCGCTGAGACCGA	0.547																																																0			13											167	151	156					13																	88329438		2203	4300	6503	87127439	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1795G>C	13.37:g.88329438G>C	ENSP00000366283:p.Ala599Pro		87127439	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905879	0.52333	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.55760	0.67;0.5	5.47	5.47	0.80525	Cysteine-rich flanking region, C-terminal (1);	0.127931	0.51477	D	0.000097	T	0.66607	0.2806	M	0.79926	2.475	0.48040	D	0.99957	P;P	0.46912	0.886;0.754	P;B	0.50708	0.648;0.443	T	0.68969	-0.5269	9	.	.	.	-10.7401	16.8036	0.85620	0.0:0.0:1.0:0.0	.	358;599	B4DSH5;O94991	.;SLIK5_HUMAN	P	599;358	ENSP00000366283:A599P;ENSP00000442244:A358P	.	A	+	1	0	SLITRK5	87127439	0.986000	0.35501	0.998000	0.56505	0.984000	0.73092	1.896000	0.39789	2.554000	0.86153	0.555000	0.69702	GCT		0.547	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			C	88329438	G	C	88329438	3	2	8	1	0	0	0	0	1	0	0	0	14783	1087	38	5	1797	5	SLITRK5	13	88329438	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	39387766	88329438	26840440	93	855	3	2								
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88329444	88329444	+	Missense_Mutation	SNP	A	A	G													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cgcccaaaaaattcgctgagAccgacatgcgctccattaag							TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr13:88329444A>G	ENST00000325089.6	+	2	2020	c.1801A>G	c.(1801-1803)Acc>Gcc	p.T601A	SLITRK5_ENST00000400028.3_Missense_Mutation_p.T360A	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	601	LRRCT 2.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ATTCGCTGAGACCGACATGCG	0.552																																																0			13											168	152	158					13																	88329444		2203	4300	6503	87127445	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1801A>G	13.37:g.88329444A>G	ENSP00000366283:p.Thr601Ala		87127445	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	4.256	0.046544	0.08243	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.51817	0.69;0.73	5.47	5.47	0.80525	Cysteine-rich flanking region, C-terminal (1);	0.433164	0.24130	N	0.041274	T	0.33789	0.0875	N	0.24115	0.695	0.27793	N	0.942752	B;B	0.12630	0.006;0.002	B;B	0.14578	0.008;0.011	T	0.14811	-1.0459	9	.	.	.	-4.2483	13.4865	0.61369	1.0:0.0:0.0:0.0	.	360;601	B4DSH5;O94991	.;SLIK5_HUMAN	A	601;360	ENSP00000366283:T601A;ENSP00000442244:T360A	.	T	+	1	0	SLITRK5	87127445	0.997000	0.39634	0.969000	0.41365	0.976000	0.68499	2.911000	0.48774	2.065000	0.61736	0.454000	0.30748	ACC		0.552	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			G	88329444	A	G	88329444	3	3	8	1	0	0	0	0	1	0	0	0	14783	275	10	4	1803	4	SLITRK5	13	88329444	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	6	88329444	26840434	94	856	3	2								
RNASE11	122651	hgsc.bcm.edu	37	chr14	21052115	21052115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atcttctctaatgaggtaacActatggtattggcacctggg	10	8	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:21052115A>G	ENST00000610205.1	-	3	702	c.519T>C	c.(517-519)agT>agC	p.S173S	RNASE11_ENST00000555841.1_Silent_p.S173S|RNASE11_ENST00000553849.1_Silent_p.S173S|RNASE11_ENST00000398008.2_Silent_p.S173S|RNASE11_ENST00000398009.2_Silent_p.S173S|RNASE11_ENST00000432835.2_Silent_p.S173S	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	173						extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		ATGAGGTAACACTATGGTATT	0.443																																																0			14											105	88	94					14																	21052115		2203	4300	6503	20121955	SO:0001819	synonymous_variant	122651			BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"Ribonucleases, RNase A"	19269	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 6"	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.519T>C	14.37:g.21052115A>G			20121955		Silent	SNP	ENST00000610205.1	37	CCDS9553.1																																																																																				0.443	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250		G	21052115	A	G	21052115	2	3	8	1	0	0	0	0	0	0	0	1	13438	156	6	4		4	RNASE11	14	21052115	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10		21052115	86297425	95	857										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47530637	47530637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gctcagaacttcttaatggaCgaccatttttaaaccaacta	5	10	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:47530637C>T	ENST00000399232.2	-	7	1497	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	MDGA2_ENST00000357362.3_Missense_Mutation_p.R149H|MDGA2_ENST00000426342.1_Missense_Mutation_p.R149H|MDGA2_ENST00000439988.3_Missense_Mutation_p.R447H	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	378	Ig-like 4.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						TCTTAATGGACGACCATTTTT	0.408																																																0			14											142	127	132					14																	47530637		1885	4110	5995	46600387	SO:0001583	missense	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1133G>A	14.37:g.47530637C>T	ENSP00000382178:p.Arg378His		46600387	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	C	27.2	4.805483	0.90623	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.86	5.86	0.93980	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.48286	U	0.000185	T	0.78000	0.4215	L	0.48935	1.535	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.76838	-0.2811	10	0.51188	T	0.08	.	18.7657	0.91871	0.0:1.0:0.0:0.0	.	378	Q7Z553	MDGA2_HUMAN	H	378;149;447;149	ENSP00000400011:R378H;ENSP00000405456:R149H;ENSP00000382178:R447H;ENSP00000349925:R149H	ENSP00000349925:R149H	R	-	2	0	MDGA2	46600387	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.770000	0.85390	2.776000	0.95493	0.655000	0.94253	CGT		0.408	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47530637	C	T	47530637	3	4	8	1	0	0	0	0	1	0	0	0	9437	536	19	1	1781	1	MDGA2	14	47530637	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	26478522	47530637	59818903	96	858										
FCF1	51077	hgsc.bcm.edu	37	chr14	75200824	75200824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttgaccgggacctgaaaagaAgaatccgtaagattcctgga	11	8	0	5			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:75200824A>G	ENST00000341162.4	+	7	553	c.499A>G	c.(499-501)Aga>Gga	p.R167G	FCF1_ENST00000534938.2_Missense_Mutation_p.R155G|FCF1_ENST00000553615.1_Missense_Mutation_p.R152G	NM_015962.4	NP_057046.1	Q9Y324	FCF1_HUMAN	FCF1 rRNA-processing protein	167					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.0037)		CCTGAAAAGAAGAATCCGTAA	0.403																																																0			14											119	94	103					14																	75200824		2203	4300	6503	74270577	SO:0001583	missense	51077			AF132969	CCDS9832.1	14q24.2	2013-05-03	2013-05-03	2007-01-30	ENSG00000119616	ENSG00000119616			20220	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 111", "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)"	C14orf111		16762320	Standard	XR_245690		Approved	CGI-35, Bka, UTP24	uc001xqh.3	Q9Y324		ENST00000341162.4:c.499A>G	14.37:g.75200824A>G	ENSP00000344393:p.Arg167Gly		74270577	Q86TW8|Q8TBL8	Missense_Mutation	SNP	ENST00000341162.4	37	CCDS9832.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.438731	0.83885	.	.	ENSG00000119616	ENST00000341162;ENST00000534938;ENST00000553615	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.86226	0.5882	H	0.94306	3.52	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.74348	0.983;0.962	D	0.90109	0.4190	9	0.72032	D	0.01	.	15.1543	0.72726	1.0:0.0:0.0:0.0	.	167;152	Q9Y324;G3V5S9	FCF1_HUMAN;.	G	167;155;152	.	ENSP00000344393:R167G	R	+	1	2	FCF1	74270577	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.532000	0.67154	2.119000	0.64992	0.533000	0.62120	AGA		0.403	FCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413622.1	NM_015962		G	75200824	A	G	75200824	3	3	8	1	0	0	0	0	1	0	0	0	5796	64	3	4	525	4	FCF1	14	75200824	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	27670187	75200824	32148716	97	859										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90651019	90651019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aatggacagcgggtgctgccCgcaatgccagagaggactct	14	11	1	1	rs369202821		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:90651019C>T	ENST00000282146.4	+	2	1340	c.899C>T	c.(898-900)cCg>cTg	p.P300L		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	300					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GGGTGCTGCCCGCAATGCCAG	0.547													C|||	1	0.000199681	0	0	5008	,	,		20510	0		0.001	False		,,,				2504	0															0			14						C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	72	78	76		899	-9.4	0	14		76	0,8600		0,0,4300	no	missense	KCNK13	NM_022054.2	98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	300/409	90651019	1,13005	2203	4300	6503	89720772	SO:0001583	missense	56659			AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.899C>T	14.37:g.90651019C>T	ENSP00000282146:p.Pro300Leu		89720772	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	C	3.611	-0.079617	0.07141	2.27E-4	0.0	ENSG00000152315	ENST00000282146	T	0.11385	2.78	4.7	-9.39	0.00619	.	1.809910	0.03410	N	0.204657	T	0.07052	0.0179	L	0.29908	0.895	0.25356	N	0.988823	B	0.20368	0.044	B	0.15870	0.014	T	0.14117	-1.0484	10	0.27785	T	0.31	.	8.7398	0.34550	0.3889:0.2149:0.3962:0.0	.	300	Q9HB14	KCNKD_HUMAN	L	300	ENSP00000282146:P300L	ENSP00000282146:P300L	P	+	2	0	KCNK13	89720772	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.470000	0.06639	-2.445000	0.00547	-0.181000	0.13052	CCG		0.547	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		T	90651019	C	T	90651019	3	4	8	1	0	0	0	0	1	0	0	0	8082	652	23	1	905	1	KCNK13	14	90651019	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	15450195	90651019	16698521	98	860										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088768	94088768	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cgaaggatcctcaaagccagAggagctgccagagttctcct	11	12	2	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:94088768A>T	ENST00000393151.2	+	30	5189	c.5189A>T	c.(5188-5190)gAg>gTg	p.E1730V	UNC79_ENST00000555664.1_Missense_Mutation_p.E1730V|UNC79_ENST00000256339.4_Missense_Mutation_p.E1553V|UNC79_ENST00000553484.1_Missense_Mutation_p.E1752V			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1730					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCAAAGCCAGAGGAGCTGCCA	0.532																																																0			14											67	71	70					14																	94088768		2203	4300	6503	93158521	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5189A>T	14.37:g.94088768A>T	ENSP00000376858:p.Glu1730Val		93158521	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	A	4.465	0.086224	0.08583	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.20738	2.07;2.05;2.07;2.07	5.2	2.87	0.33458	.	0.224351	0.45361	D	0.000376	T	0.12178	0.0296	N	0.19112	0.55	0.29907	N	0.823938	B	0.30973	0.302	B	0.32289	0.143	T	0.11966	-1.0566	10	0.32370	T	0.25	-13.908	7.435	0.27150	0.6874:0.0:0.3126:0.0	.	1752	C9JQL1	.	V	1553;1730;1752;1730;1752	ENSP00000256339:E1553V;ENSP00000450868:E1730V;ENSP00000451360:E1752V;ENSP00000376858:E1730V	ENSP00000256339:E1553V	E	+	2	0	KIAA1409	93158521	1.000000	0.71417	0.623000	0.29173	0.102000	0.19082	1.374000	0.34283	0.825000	0.34637	0.254000	0.18369	GAG		0.532	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94088768	A	T	94088768	3	4	8	1	0	0	0	0	1	0	0	0	8251	304	11	5	4764	5	KIAA1409	14	94088768	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	3437749	94088768	13260772	99	861										
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102368208	102368208	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cggcagttggccaaatgtgtCtccagcccacacttccaggt	10	14	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr14:102368208C>T	ENST00000334743.5	+	9	1053	c.1005C>T	c.(1003-1005)gtC>gtT	p.V335V	PPP2R5C_ENST00000445439.3_Silent_p.V335V|PPP2R5C_ENST00000350249.3_Silent_p.V335V|PPP2R5C_ENST00000328724.5_Silent_p.V390V|PPP2R5C_ENST00000422945.2_Silent_p.V366V|PPP2R5C_ENST00000557095.1_Silent_p.V335V	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	335					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CCAAATGTGTCTCCAGCCCAC	0.448																																																0			14											57	61	60					14																	102368208		2203	4300	6503	101437961	SO:0001819	synonymous_variant	5527			L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1005C>T	14.37:g.102368208C>T			101437961	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Silent	SNP	ENST00000334743.5	37	CCDS9964.1																																																																																				0.448	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		T	102368208	C	T	102368208	2	4	8	1	0	0	0	0	0	0	0	1	12428	900	32	3		3	PPP2R5C	14	102368208	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	8279440	102368208	4981332	100	862										
FBN1	2200	hgsc.bcm.edu	37	chr15	48773887	48773887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttccttttttgccggagtagCccatatcacagtggcagata	9	10	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr15:48773887C>T	ENST00000316623.5	-	32	4384	c.3929G>A	c.(3928-3930)gGc>gAc	p.G1310D		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1310	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GCCGGAGTAGCCCATATCACA	0.373																																																0			15	GRCh37	CM077262	FBN1	M							138	135	136					15																	48773887		2198	4296	6494	46561179	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.3929G>A	15.37:g.48773887C>T	ENSP00000325527:p.Gly1310Asp		46561179	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640429	0.87859	.	.	ENSG00000166147	ENST00000316623	D	0.92397	-3.03	5.39	5.39	0.77823	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96818	0.8961	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97252	0.9898	10	0.87932	D	0	.	19.0959	0.93251	0.0:1.0:0.0:0.0	.	1310	P35555	FBN1_HUMAN	D	1310	ENSP00000325527:G1310D	ENSP00000325527:G1310D	G	-	2	0	FBN1	46561179	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	7.727000	0.84838	2.674000	0.91012	0.467000	0.42956	GGC		0.373	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48773887	C	T	48773887	3	4	8	1	0	0	0	0	1	0	0	0	5721	739	26	3	4826	3	FBN1	15	48773887	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10		48773887	53757505	101	863										
PTPLAD1	51495	hgsc.bcm.edu	37	chr15	65849211	65849211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tttgatcgttggctggatgaAtctgatgcggaaatggagct	14	5	1	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr15:65849211A>G	ENST00000261875.5	+	4	505	c.339A>G	c.(337-339)gaA>gaG	p.E113E	PTPLAD1_ENST00000565299.1_Silent_p.E151E|PTPLAD1_ENST00000568793.1_Silent_p.E88E|PTPLAD1_ENST00000566511.1_5'UTR|PTPLAD1_ENST00000569894.1_5'UTR|PTPLAD1_ENST00000566074.1_5'UTR|PTPLAD1_ENST00000562901.1_5'UTR|PTPLAD1_ENST00000442729.2_Intron	NM_016395.2	NP_057479.2	Q9P035	HACD3_HUMAN	protein tyrosine phosphatase-like A domain containing 1	113					activation of JUN kinase activity (GO:0007257)|fatty acid biosynthetic process (GO:0006633)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|positive regulation of GTPase activity (GO:0043547)|Rac protein signal transduction (GO:0016601)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)	GTPase activator activity (GO:0005096)|lyase activity (GO:0016829)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|pancreas(1)	5						GGCTGGATGAATCTGATGCGG	0.473																																																0			15											96	91	92					15																	65849211		1959	4161	6120	63636264	SO:0001819	synonymous_variant	51495				CCDS45282.1	15q22.2	2005-11-11				ENSG00000074696			24175	protein-coding gene	gene with protein product		615940				10747961, 11042152	Standard	NM_016395		Approved	B-ind1, HSPC121	uc002apc.3	Q9P035		ENST00000261875.5:c.339A>G	15.37:g.65849211A>G			63636264	A0PJA1|B4DRF4|Q280Z3|Q6PD63|Q8IUI5|Q8NC86|Q8NCB1|Q96T12|Q9NQA7	Silent	SNP	ENST00000261875.5	37	CCDS45282.1																																																																																				0.473	PTPLAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419739.1	NM_016395		G	65849211	A	G	65849211	2	3	8	1	0	0	0	0	0	0	0	1	12810	98	4	4		4	PTPLAD1	15	65849211	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	17075324	65849211	36682181	102	864										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30731533	30731533	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggcctggaaggtcgtgtctcTcgatatgaggcagacacatt	13	9	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr16:30731533T>C	ENST00000262518.4	+	19	3253	c.2868T>C	c.(2866-2868)tcT>tcC	p.S956S	SRCAP_ENST00000344771.4_Silent_p.S956S|SRCAP_ENST00000395059.2_Silent_p.S956S	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	956					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GTCGTGTCTCTCGATATGAGG	0.542																																																0			16											190	191	190					16																	30731533		2197	4300	6497	30639034	SO:0001819	synonymous_variant	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2868T>C	16.37:g.30731533T>C			30639034	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																				0.542	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30731533	T	C	30731533	2	2	8	1	0	0	0	0	0	0	0	1	15174	1538	54	4		4	SRCAP	16	30731533	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10		30731533	59623220	103	865										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31091794	31091794	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggatctttggagcggcacctGcgggagcatgaggagacaga	17	8	1	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr16:31091794G>A	ENST00000394979.2	+	1	4572	c.4149G>A	c.(4147-4149)ctG>ctA	p.L1383L	ZNF646_ENST00000300850.5_Silent_p.L1383L			O15015	ZN646_HUMAN	zinc finger protein 646	1383					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						AGCGGCACCTGCGGGAGCATG	0.677																																																0			16											31	35	33					16																	31091794		2197	4299	6496	30999295	SO:0001819	synonymous_variant	9726			AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.4149G>A	16.37:g.31091794G>A			30999295	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																					0.677	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		A	31091794	G	A	31091794	2	1	8	1	0	0	0	0	0	0	0	1	18101	1306	46	3		3	ZNF646	16	31091794	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	360261	31091794	59262959	104	866										
RBL2	5934	hgsc.bcm.edu	37	chr16	53498217	53498217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cactttttcttataagcctcCtgggaattttccatttatta	4	9	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr16:53498217C>A	ENST00000262133.6	+	12	1777	c.1640C>A	c.(1639-1641)cCt>cAt	p.P547H	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.P331H	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	547	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TATAAGCCTCCTGGGAATTTT	0.338																																																0			16											90	93	92					16																	53498217		2198	4300	6498	52055718	SO:0001583	missense	5934			X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1640C>A	16.37:g.53498217C>A	ENSP00000262133:p.Pro547His		52055718	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676974	0.47886	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.86865	-2.18;-2.18;-2.18	5.86	5.86	0.93980	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.050790	0.85682	D	0.000000	D	0.93766	0.8007	M	0.79475	2.455	0.45354	D	0.998345	D;D;P;D	0.89917	0.998;0.999;0.542;1.0	D;D;P;D	0.72338	0.947;0.976;0.489;0.977	D	0.93547	0.6883	10	0.66056	D	0.02	-15.6206	20.1996	0.98256	0.0:1.0:0.0:0.0	.	331;547;257;547	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	H	547;473;257;331	ENSP00000262133:P547H;ENSP00000443744:P473H;ENSP00000444685:P331H	ENSP00000262133:P547H	P	+	2	0	RBL2	52055718	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.599000	0.54045	2.776000	0.95493	0.650000	0.86243	CCT		0.338	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		A	53498217	C	A	53498217	3	1	8	1	0	0	0	0	1	0	0	0	13147	681	24	2	1686	2	RBL2	16	53498217	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	22406423	53498217	36856536	105	867										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89346415	89346415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctcagccactacggtggaaaCatccccaccgtttatgaccc	7	16	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr16:89346415C>T	ENST00000301030.4	-	9	6995	c.6535G>A	c.(6535-6537)Gtt>Att	p.V2179I	ANKRD11_ENST00000378330.2_Missense_Mutation_p.V2179I	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2179	Pro-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ACGGTGGAAACATCCCCACCG	0.632																																																0			16											18	23	21					16																	89346415		2106	4109	6215	87873916	SO:0001583	missense	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.6535G>A	16.37:g.89346415C>T	ENSP00000301030:p.Val2179Ile		87873916	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	c	10.42	1.344705	0.24426	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.38077	1.16;1.16	5.08	0.539	0.17156	.	0.977772	0.08335	N	0.961668	T	0.17066	0.0410	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28839	-1.0031	10	0.19147	T	0.46	.	6.9562	0.24572	0.0:0.5044:0.2584:0.2372	.	2179	Q6UB99	ANR11_HUMAN	I	2179	ENSP00000301030:V2179I;ENSP00000367581:V2179I	ENSP00000301030:V2179I	V	-	1	0	ANKRD11	87873916	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.190000	0.09615	0.537000	0.28751	0.450000	0.29827	GTT		0.632	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89346415	C	T	89346415	3	4	8	1	0	0	0	0	1	0	0	0	639	478	17	3	1476	3	ANKRD11	16	89346415	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	35848198	89346415	1008338	106	868										
TP53	7157	hgsc.bcm.edu	37	chr17	7578194	7578195	+	Frame_Shift_Ins	INS	-	-	C													0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acctcaggcggctcatagggINScaccaccacactatgtcgaa							TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr17:7578194_7578195insC	ENST00000269305.4	-	6	843_844	c.654_655insG	c.(652-657)gtgcccfs	p.P219fs	TP53_ENST00000455263.2_Frame_Shift_Ins_p.P219fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.P219fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.P219fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.P219fs|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Frame_Shift_Ins_p.P219fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	219	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> C (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in a sporadic cancer; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in a sporadic cancer; somatic mutation).|P -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(11)|p.0?(8)|p.V218del(5)|p.Y220fs*27(4)|p.P219S(4)|p.P219T(2)|p.D208fs*1(1)|p.V216fs*28(1)|p.V218fs*26(1)|p.T211fs*28(1)|p.V218_P219insX(1)|p.V218V(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.S215fs*27(1)|p.V218_Y220delVPY(1)|p.P219C(1)|p.V216_Y220delVVVPY(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCTCATAGGGCACCACCACAC	0.545		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	46	Unknown(11)|Deletion - In frame(9)|Deletion - Frameshift(9)|Whole gene deletion(8)|Substitution - Missense(7)|Insertion - In frame(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(6)|endometrium(6)|upper_aerodigestive_tract(5)|biliary_tract(5)|oesophagus(4)|bone(4)|central_nervous_system(3)|liver(3)|urinary_tract(2)|cervix(1)|vulva(1)|stomach(1)|soft_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	17	GRCh37	CM941330	TP53	M																																				7518920	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.655dupG	17.37:g.7578195_7578195dupC	ENSP00000269305:p.Pro219fs		7518919	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.545	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578195	-	C	7578194	7	5	8	1	0	1	1	0	0	0	0	0	16421	1203	42	0	639	0	TP53	17	7578194	Frame_Shift_Ins	INS	-	TCGA-AF-4110-01A-02D-1733-10		7578194	73617016	107	869										
MPRIP	23164	hgsc.bcm.edu	37	chr17	17061869	17061869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	aagaggagccgcgcacgggaGcggaggcgagagggccgctc	20	11	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr17:17061869G>T	ENST00000341712.4	+	14	1599	c.1599G>T	c.(1597-1599)gaG>gaT	p.E533D	MPRIP_ENST00000444976.1_Missense_Mutation_p.E495D|MPRIP_ENST00000395811.5_Missense_Mutation_p.E533D|MPRIP_ENST00000395804.3_Missense_Mutation_p.E533D			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	533						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GCGCACGGGAGCGGAGGCGAG	0.677																																																0			17											15	18	17					17																	17061869		2202	4298	6500	17002594	SO:0001583	missense	23164			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1599G>T	17.37:g.17061869G>T	ENSP00000342379:p.Glu533Asp		17002594	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.53|16.53	3.149821|3.149821	0.57151|0.57151	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712|ENST00000423885	T;T;T;T|.	0.26957|.	1.7;2.01;2.0;2.0|.	5.63|5.63	3.3|3.3	0.37823|0.37823	.|.	.|.	.|.	.|.	.|.	T|T	0.64405|0.64405	0.2595|0.2595	M|M	0.71581|0.71581	2.175|2.175	0.38798|0.38798	D|D	0.955146|0.955146	P;D|.	0.76494|.	0.939;0.999|.	P;D|.	0.77557|.	0.796;0.99|.	T|T	0.65861|0.65861	-0.6065|-0.6065	9|5	0.29301|.	T|.	0.29|.	.|.	9.0526|9.0526	0.36385|0.36385	0.3296:0.0:0.6704:0.0|0.3296:0.0:0.6704:0.0	.|.	533;533|.	Q6WCQ1-2;Q6WCQ1|.	.;MPRIP_HUMAN|.	D|I	495;533;533;533|20	ENSP00000400189:E495D;ENSP00000379156:E533D;ENSP00000379149:E533D;ENSP00000342379:E533D|.	ENSP00000342379:E533D|.	E|S	+|+	3|2	2|0	MPRIP|MPRIP	17002594|17002594	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.523000|0.523000	0.34469|0.34469	2.026000|2.026000	0.41069|0.41069	1.390000|1.390000	0.46547|0.46547	0.563000|0.563000	0.77884|0.77884	GAG|AGC		0.677	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		T	17061869	G	T	17061869	3	4	8	1	0	0	0	0	1	0	0	0	9773	962	34	2	1653	2	MPRIP	17	17061869	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	9483675	17061869	64133341	108	870										
KLHL10	317719	hgsc.bcm.edu	37	chr17	39998267	39998267	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggtatcgtcaggggttgctgCgagttcctcaagtcagagct	14	9	3	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr17:39998267C>T	ENST00000293303.4	+	2	540	c.387C>T	c.(385-387)tgC>tgT	p.C129C	KLHL10_ENST00000485613.1_3'UTR	NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	129					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)		p.C129C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				GGGGTTGCTGCGAGTTCCTCA	0.507																																																1	Substitution - coding silent(1)	breast(1)	17											122	113	116					17																	39998267		1995	4175	6170	37251793	SO:0001819	synonymous_variant	317719			AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.387C>T	17.37:g.39998267C>T			37251793	Q6NW28|Q96MC0	Silent	SNP	ENST00000293303.4	37	CCDS42340.1																																																																																				0.507	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		T	39998267	C	T	39998267	2	4	8	1	0	0	0	0	0	0	0	1	8387	776	27	1		1	KLHL10	17	39998267	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	22936398	39998267	41196943	109	871										
MARCH10	162333	hgsc.bcm.edu	37	chr17	60821765	60821765	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctgggaaccggcacctttgcAggccactgctgtttctgtct	11	13	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr17:60821765A>T	ENST00000311269.5	-	5	781	c.507T>A	c.(505-507)ccT>ccA	p.P169P	MARCH10_ENST00000583600.1_Silent_p.P207P|MARCH10_ENST00000544856.2_Silent_p.P168P|MARCH10_ENST00000456609.2_Silent_p.P169P	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	169					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						GCACCTTTGCAGGCCACTGCT	0.552																																																0			17											110	107	108					17																	60821765		2203	4300	6503	58175497	SO:0001819	synonymous_variant	162333			AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.507T>A	17.37:g.60821765A>T			58175497	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																				0.552	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		T	60821765	A	T	60821765	2	4	8	1	0	0	0	0	0	0	0	1	9329	175	7	5		5	MARCH10	17	60821765	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	20823498	60821765	20373445	110	872										
FASN	2194	hgsc.bcm.edu	37	chr17	80044289	80044289	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	agctccagctgcaggttcccGttgagctgaagcctgcaggc	13	13	0	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr17:80044289G>A	ENST00000306749.2	-	22	3791	c.3573C>T	c.(3571-3573)aaC>aaT	p.N1191N		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1191					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCAGGTTCCCGTTGAGCTGAA	0.687																																					Colon(59;314 1043 11189 28578 32273)											0			17											19	21	20					17																	80044289		2196	4287	6483	77637578	SO:0001819	synonymous_variant	2194			U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3573C>T	17.37:g.80044289G>A			77637578	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																				0.687	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80044289	G	A	80044289	2	1	8	1	0	0	0	0	0	0	0	1	5702	1136	40	1		1	FASN	17	80044289	Silent	SNP	G	TCGA-AF-4110-01A-02D-1733-10	19222524	80044289	1150921	111	873										
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39576651	39576651	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acttacatatgaagaacaagAtcttgtttggaagtttagat	8	4	1	4			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr18:39576651A>G	ENST00000262039.4	+	9	1027	c.941A>G	c.(940-942)gAt>gGt	p.D314G	PIK3C3_ENST00000398870.3_Missense_Mutation_p.D251G	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	314	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						GAAGAACAAGATCTTGTTTGG	0.269										TSP Lung(28;0.18)																											NSCLC(37;552 1060 2683 16430 37914)											0			18											79	86	83					18																	39576651		2202	4277	6479	37830649	SO:0001583	missense	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.941A>G	18.37:g.39576651A>G	ENSP00000262039:p.Asp314Gly		37830649	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370983	0.82573	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.64260	-0.09;-0.09	5.36	5.36	0.76844	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.67569	2.06	0.80722	D	1	B;P	0.38048	0.426;0.616	B;B	0.37091	0.074;0.241	T	0.62572	-0.6826	9	.	.	.	.	15.3393	0.74284	1.0:0.0:0.0:0.0	.	251;314	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	G	314;251	ENSP00000262039:D314G;ENSP00000381845:D251G	.	D	+	2	0	PIK3C3	37830649	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.852000	0.75430	2.027000	0.59764	0.383000	0.25322	GAT		0.269	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		G	39576651	A	G	39576651	3	3	8	1	0	0	0	0	1	0	0	0	11943	333	12	4	975	4	PIK3C3	18	39576651	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10		39576651	38500597	112	874										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43450590	43450590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggtccttccatggcagtttcCggtacgtgctatggaaagcg	13	10	0	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr18:43450590C>T	ENST00000282041.5	-	36	6201	c.6167G>A	c.(6166-6168)cGg>cAg	p.R2056Q	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2056			R -> W (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.R2056Q(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGGCAGTTTCCGGTACGTGCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	18											106	107	107					18																	43450590		1993	4170	6163	41704588	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.6167G>A	18.37:g.43450590C>T	ENSP00000282041:p.Arg2056Gln		41704588	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	8.527	0.870095	0.17322	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09817	2.94	6.03	-12.1	0.00011	.	.	.	.	.	T	0.05960	0.0155	N	0.03154	-0.405	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.58126	-0.7691	9	0.21014	T	0.42	-0.1748	29.0522	0.99999	0.0:0.8579:0.0:0.1421	.	2056	Q9HCE0	EPG5_HUMAN	Q	2056;931	ENSP00000282041:R2056Q	ENSP00000282041:R2056Q	R	-	2	0	EPG5	41704588	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-1.613000	0.02059	-2.940000	0.00297	-0.880000	0.02959	CGG		0.517	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		T	43450590	C	T	43450590	3	4	8	1	0	0	0	0	1	0	0	0	8270	652	23	1	1608	1	KIAA1632	18	43450590	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	3873939	43450590	34626658	113	875										
POLI	11201	hgsc.bcm.edu	37	chr18	51810308	51810308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atagtcctttagtgaagaagAttcatttaaaaaatgttcat	6	4	2	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr18:51810308A>G	ENST00000579534.1	+	7	1135	c.992A>G	c.(991-993)gAt>gGt	p.D331G	POLI_ENST00000579434.1_Missense_Mutation_p.D228G|POLI_ENST00000217800.5_Missense_Mutation_p.D205G|POLI_ENST00000406285.3_Missense_Mutation_p.D252G	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	331	DNA binding.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.D306V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AGTGAAGAAGATTCATTTAAA	0.279								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	kidney(1)	18											48	49	49					18																	51810308		2199	4289	6488	50064306	SO:0001583	missense	11201				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.992A>G	18.37:g.51810308A>G	ENSP00000462664:p.Asp331Gly		50064306	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	37	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	A	13.58	2.280632	0.40294	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.37584	1.19	5.5	5.5	0.81552	DNA polymerase, Y-family, little finger domain (2);	0.053964	0.64402	D	0.000001	T	0.62295	0.2416	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.971;0.985	T	0.64939	-0.6289	10	0.42905	T	0.14	-16.9681	14.8826	0.70545	1.0:0.0:0.0:0.0	.	251;331	B7Z780;Q9UNA4	.;POLI_HUMAN	G	252;331	ENSP00000385196:D252G	ENSP00000217800:D331G	D	+	2	0	POLI	50064306	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.580000	0.74040	2.213000	0.71641	0.528000	0.53228	GAT		0.279	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		G	51810308	A	G	51810308	3	3	8	1	0	0	0	0	1	0	0	0	12234	333	12	4	1018	4	POLI	18	51810308	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	8359718	51810308	26266940	114	876										
DSEL	92126	hgsc.bcm.edu	37	chr18	65180784	65180784	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gctaaccaatttccagctccAttctttaagatgaacttatc	4	11	1	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr18:65180784A>G	ENST00000310045.7	-	2	2565	c.1092T>C	c.(1090-1092)aaT>aaC	p.N364N	RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	354					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TTCCAGCTCCATTCTTTAAGA	0.423																																																0			18											111	111	111					18																	65180784		2203	4300	6503	63331764	SO:0001819	synonymous_variant	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.1092T>C	18.37:g.65180784A>G			63331764	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																				0.423	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65180784	A	G	65180784	2	3	8	1	0	0	0	0	0	0	0	1	4786	214	8	4		4	DSEL	18	65180784	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10	13370476	65180784	12896464	115	877										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72775977	72775977	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gccggccagttggtcaaggaCggtgtcacccaggtggtggt	17	10	2	0	rs527541602		TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr18:72775977C>T	ENST00000299687.5	+	8	6300	c.6300C>T	c.(6298-6300)gaC>gaT	p.D2100D		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TGGTCAAGGACGGTGTCACCC	0.657																																																0			18											36	42	40					18																	72775977		2145	4231	6376	70904965	SO:0001819	synonymous_variant	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6300C>T	18.37:g.72775977C>T			70904965	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.657	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72775977	C	T	72775977	2	4	8	1	0	0	0	0	0	0	0	1	17926	535	19	1		1	ZNF407	18	72775977	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	7595193	72775977	5301271	116	878										
GADD45GIP1	90480	hgsc.bcm.edu	37	chr19	13065203	13065203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggtccacctggtagcccaggAgctcctgggcctcagcctgc	13	16	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:13065203A>G	ENST00000316939.1	-	2	511	c.488T>C	c.(487-489)cTc>cCc	p.L163P		NM_052850.3	NP_443082.2	Q8TAE8	G45IP_HUMAN	growth arrest and DNA-damage-inducible, gamma interacting protein 1	163					cell cycle (GO:0007049)|viral process (GO:0016032)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				ovary(2)|prostate(1)|skin(1)	4						GTAGCCCAGGAGCTCCTGGGC	0.612																																																0			19											65	68	67					19																	13065203		2203	4300	6503	12926203	SO:0001583	missense	90480			AF479749	CCDS12290.1	19p13.2	2014-02-12				ENSG00000179271			29996	protein-coding gene	gene with protein product	"papillomavirus L2 interacting nuclear protein 1", "CKII beta binding protein 2", "CR6 interacting factor 1", "p53-responsive gene 6"	605162				10441517, 12482659	Standard	NM_052850		Approved	PLINP-1, MGC4667, MGC4758, CKBBP2, PRG6, Plinp1, CRIF1, CKbetaBP2	uc002mwb.4	Q8TAE8		ENST00000316939.1:c.488T>C	19.37:g.13065203A>G	ENSP00000323065:p.Leu163Pro		12926203	Q8IVM3|Q8TE51|Q969P9|Q9BSM6	Missense_Mutation	SNP	ENST00000316939.1	37	CCDS12290.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005444	0.35415	.	.	ENSG00000179271	ENST00000316939	.	.	.	5.02	1.23	0.21249	.	0.366329	0.23842	N	0.044034	T	0.21145	0.0509	N	0.08118	0	0.40449	D	0.980121	B	0.32939	0.391	B	0.28991	0.097	T	0.05582	-1.0876	9	0.62326	D	0.03	-12.5409	4.1128	0.10067	0.175:0.5209:0.0:0.3042	.	163	Q8TAE8	G45IP_HUMAN	P	163	.	ENSP00000323065:L163P	L	-	2	0	GADD45GIP1	12926203	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	1.486000	0.35530	0.503000	0.28060	-0.295000	0.09555	CTC		0.612	GADD45GIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452759.2	NM_052850		G	13065203	A	G	13065203	3	3	8	1	0	0	0	0	1	0	0	0	6203	304	11	4	184	4	GADD45GIP1	19	13065203	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10		13065203	46063780	117	879										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41383249	41383249	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acttgggctgccggttcttgCcgatcactctgtcaatctcc	9	14	5	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:41383249C>A	ENST00000301146.4	-	7	1548	c.1007G>T	c.(1006-1008)gGc>gTc	p.G336V	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.G285V	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	336						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.G336A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCGGTTCTTGCCGATCACTCT	0.522																																																1	Substitution - Missense(1)	ovary(1)	19											94	79	84					19																	41383249		2203	4298	6501	46075089	SO:0001583	missense	1549			NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1007G>T	19.37:g.41383249C>A	ENSP00000301146:p.Gly336Val		46075089	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868736	0.51588	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.18016	4.61;2.24	2.18	2.18	0.27775	.	0.131674	0.50627	U	0.000112	T	0.50326	0.1609	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.77557	0.99;0.976;0.969	T	0.64901	-0.6298	10	0.87932	D	0	.	11.4495	0.50145	0.0:1.0:0.0:0.0	.	336;285;336	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	V	336;285	ENSP00000301146:G336V;ENSP00000291764:G285V	ENSP00000291764:G285V	G	-	2	0	CYP2A7	46075089	0.998000	0.40836	0.117000	0.21633	0.656000	0.38851	5.118000	0.64673	1.215000	0.43411	0.184000	0.17185	GGC		0.522	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		A	41383249	C	A	41383249	3	1	8	1	0	0	0	0	1	0	0	0	4169	739	26	2	489	2	CYP2A7	19	41383249	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	28318046	41383249	17745734	118	880										
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43097788	43097788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tgtcatttctggtgacgttcCgcatcagcagggatgcattg	12	9	3	1	rs45440298	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:43097788C>T	ENST00000244336.5	-	2	430	c.329G>A	c.(328-330)cGg>cAg	p.R110Q	LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	110	Ig-like V-type.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GGTGACGTTCCGCATCAGCAG	0.443													.|||	2	0.000399361	0.0015	0	5008	,	,		23841	0		0	False		,,,				2504	0															0			19						C	GLN/ARG	34,4372	39.2+/-71.8	0,34,2169	302	274	283		329	-1.9	0	19	dbSNP_127	283	0,8600		0,0,4300	yes	missense	CEACAM8	NM_001816.3	43	0,34,6469	TT,TC,CC		0.0,0.7717,0.2614	benign	110/350	43097788	34,12972	2203	4300	6503	47789628	SO:0001583	missense	1088			D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.329G>A	19.37:g.43097788C>T	ENSP00000244336:p.Arg110Gln		47789628	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	0.017	-1.510913	0.00984	0.007717	0.0	ENSG00000124469	ENST00000244336	T	0.63096	-0.02	1.87	-1.87	0.07737	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13157	0.0319	N	0.00377	-1.585	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28170	-1.0052	9	0.02654	T	1	.	5.9523	0.19253	0.0:0.5434:0.0:0.4566	rs45440298	110	P31997	CEAM8_HUMAN	Q	110	ENSP00000244336:R110Q	ENSP00000244336:R110Q	R	-	2	0	CEACAM8	47789628	0.007000	0.16637	0.003000	0.11579	0.167000	0.22549	-0.142000	0.10311	-0.614000	0.05687	-0.752000	0.03492	CGG		0.443	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			T	43097788	C	T	43097788	3	4	8	1	0	0	0	0	1	0	0	0	3204	652	23	1	736	1	CEACAM8	19	43097788	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	1714539	43097788	16031195	119	881										
PLAUR	5329	hgsc.bcm.edu	37	chr19	44171781	44171781	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gcagaggtcctgtcccagggCgcactcttccacacggcaat	11	15	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:44171781C>A	ENST00000340093.3	-	2	347	c.118G>T	c.(118-120)Gcc>Tcc	p.A40S	PLAUR_ENST00000221264.4_Missense_Mutation_p.A40S|PLAUR_ENST00000339082.3_Missense_Mutation_p.A40S|PLAUR_ENST00000601723.1_Missense_Mutation_p.A40S	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	40	UPAR/Ly6 1.				attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)			endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TGTCCCAGGGCGCACTCTTCC	0.627																																																0			19											124	95	105					19																	44171781		2203	4300	6503	48863621	SO:0001583	missense	5329				CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"CD molecules"	9053	protein-coding gene	gene with protein product	"urokinase-type plasminogen activator (uPA) receptor", "urokinase plasminogen activator surface receptor"	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.118G>T	19.37:g.44171781C>A	ENSP00000339328:p.Ala40Ser		48863621	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816304	0.70912	.	.	ENSG00000011422	ENST00000339082;ENST00000340093;ENST00000221264	T;T;T	0.69306	-0.39;-0.39;-0.39	4.84	-5.3	0.02738	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);CD59 antigen (1);	1.117940	0.07006	N	0.824297	T	0.57548	0.2061	M	0.63843	1.955	0.09310	N	1	B;B;B;B	0.28801	0.223;0.004;0.004;0.097	B;B;B;B	0.31547	0.06;0.018;0.018;0.132	T	0.57154	-0.7860	10	0.62326	D	0.03	-3.7332	4.2334	0.10615	0.1223:0.2472:0.4749:0.1556	.	40;40;40;40	Q03405-3;Q03405;Q9UPI5;Q03405-2	.;UPAR_HUMAN;.;.	S	40	ENSP00000342049:A40S;ENSP00000339328:A40S;ENSP00000221264:A40S	ENSP00000221264:A40S	A	-	1	0	PLAUR	48863621	0.000000	0.05858	0.000000	0.03702	0.172000	0.22775	-1.180000	0.03088	-0.431000	0.07307	-0.305000	0.09177	GCC		0.627	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659		A	44171781	C	A	44171781	3	1	8	1	0	0	0	0	1	0	0	0	12054	768	27	2	1009	2	PLAUR	19	44171781	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	1073993	44171781	14957202	120	882										
DHX34	9704	hgsc.bcm.edu	37	chr19	47858534	47858534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cctcatgtcggccaccatcaAcatctcgctcttctccagct	5	18	5	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:47858534A>G	ENST00000328771.4	+	3	1293	c.944A>G	c.(943-945)aAc>aGc	p.N315S		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	315	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GCCACCATCAACATCTCGCTC	0.597																																																0			19											162	145	151					19																	47858534		2203	4300	6503	52550374	SO:0001583	missense	9704			D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.944A>G	19.37:g.47858534A>G	ENSP00000331907:p.Asn315Ser		52550374	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.116371	0.77323	.	.	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.23552	1.9	4.41	4.41	0.53225	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.64402	D	0.000011	T	0.51805	0.1696	M	0.81614	2.55	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.997	T	0.58092	-0.7697	10	0.72032	D	0.01	-1.5859	12.6586	0.56801	1.0:0.0:0.0:0.0	.	315;315	Q14147;B4E3G3	DHX34_HUMAN;.	S	315	ENSP00000331907:N315S	ENSP00000257252:N315S	N	+	2	0	DHX34	52550374	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.853000	0.92222	1.635000	0.50512	0.374000	0.22700	AAC		0.597	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		G	47858534	A	G	47858534	3	3	8	1	0	0	0	0	1	0	0	0	4518	43	2	4	950	4	DHX34	19	47858534	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	3686753	47858534	11270449	121	883										
CPT1C	126129	hgsc.bcm.edu	37	chr19	50212032	50212032	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ctactcaacagacggccactGcaaggggcacccggacccca	10	17	1	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:50212032G>A	ENST00000392518.4	+	14	1874	c.1502G>A	c.(1501-1503)tGc>tAc	p.C501Y	CPT1C_ENST00000323446.5_Missense_Mutation_p.C501Y|CPT1C_ENST00000405931.2_Missense_Mutation_p.C490Y|CPT1C_ENST00000598293.1_Missense_Mutation_p.C501Y|CPT1C_ENST00000354199.5_Missense_Mutation_p.C501Y	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	501					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GACGGCCACTGCAAGGGGCAC	0.607																																																0			19											109	101	104					19																	50212032		2203	4300	6503	54903844	SO:0001583	missense	126129			AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1502G>A	19.37:g.50212032G>A	ENSP00000376303:p.Cys501Tyr		54903844	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	37	CCDS12779.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.196177	0.78902	.	.	ENSG00000169169	ENST00000392518;ENST00000354199;ENST00000405931;ENST00000323446;ENST00000295404	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	4.42	4.42	0.53409	.	0.000000	0.53938	D	0.000057	D	0.93028	0.7781	M	0.64997	1.995	0.52501	D	0.999954	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.992;0.998;0.987;0.996	D	0.93735	0.7045	10	0.87932	D	0	-29.5414	14.5977	0.68419	0.0:0.0:1.0:0.0	.	372;501;490;501	C9IY45;Q8TCG5-3;Q8TCG5-2;Q8TCG5	.;.;.;CPT1C_HUMAN	Y	501;501;490;501;372	ENSP00000376303:C501Y;ENSP00000346138:C501Y;ENSP00000384465:C490Y;ENSP00000319343:C501Y	ENSP00000295404:C372Y	C	+	2	0	CPT1C	54903844	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.222000	0.95196	2.292000	0.77174	0.456000	0.33151	TGC		0.607	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		A	50212032	G	A	50212032	3	1	8	1	0	0	0	0	1	0	0	0	3839	1319	46	3	1548	3	CPT1C	19	50212032	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	2353498	50212032	8916951	122	884										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52004723	52004723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gaggtggaatcggtcccgagTctcctcctgcactgctcgag	13	13	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:52004723T>C	ENST00000291707.3	-	1	320	c.265A>G	c.(265-267)Act>Gct	p.T89A	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	89	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CGGTCCCGAGTCTCCTCCTGC	0.562																																																0			19											158	137	144					19																	52004723		2203	4300	6503	56696535	SO:0001583	missense	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.265A>G	19.37:g.52004723T>C	ENSP00000291707:p.Thr89Ala		56696535	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	14.03	2.413951	0.42817	.	.	ENSG00000254521	ENST00000291707	T	0.64991	-0.13	2.42	-0.0628	0.13779	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.58075	0.2097	M	0.81112	2.525	0.09310	N	1	B	0.28350	0.208	B	0.26202	0.067	T	0.56306	-0.8001	9	0.87932	D	0	.	4.1696	0.10324	0.0:0.4648:0.0:0.5352	.	89	Q96PQ1	SIG12_HUMAN	A	89	ENSP00000291707:T89A	ENSP00000291707:T89A	T	-	1	0	SIGLEC12	56696535	0.000000	0.05858	0.010000	0.14722	0.241000	0.25554	-0.856000	0.04290	0.101000	0.17610	0.325000	0.21440	ACT		0.562	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	52004723	T	C	52004723	3	2	8	1	0	0	0	0	1	0	0	0	14345	1667	58	4	1627	4	SIGLEC12	19	52004723	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	1792691	52004723	7124260	123	885										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54545034	54545034	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	cctaagcgggaggactcaccGagagagataccctttccata	10	12	1	2	rs148134957	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:54545034G>A	ENST00000338372.2	-	8	765	c.590C>T	c.(589-591)tCg>tTg	p.S197L	VSTM1_ENST00000425006.2_3'UTR|VSTM1_ENST00000366170.2_Splice_Site_p.S109L|VSTM1_ENST00000376626.1_Splice_Site_p.S166L	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	197					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	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)		AGGACTCACCGAGAGAGATAC	0.458													G|||	4	0.000798722	0.003	0	5008	,	,		16791	0		0	False		,,,				2504	0															0			19						G	LEU/SER	35,4371	39.2+/-71.8	0,35,2168	52	46	48		590	0.3	0.7	19	dbSNP_134	48	0,8600		0,0,4300	yes	missense-near-splice	VSTM1	NM_198481.3	145	0,35,6468	AA,AG,GG		0.0,0.7944,0.2691	benign	197/237	54545034	35,12971	2203	4300	6503	59236846	SO:0001630	splice_region_variant	284415			AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.591+1C>T	19.37:g.54545034G>A			59236846	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	37	CCDS12872.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	9.384	1.073832	0.20147	0.007944	0.0	ENSG00000189068	ENST00000419106;ENST00000338372;ENST00000376626;ENST00000366170	T;T;T;T	0.49139	2.52;6.75;6.5;0.79	2.43	0.27	0.15635	.	.	.	.	.	T	0.11623	0.0283	N	0.11560	0.145	0.58432	D	0.999997	B;P	0.34826	0.238;0.471	B;B	0.15870	0.014;0.014	T	0.15378	-1.0439	9	0.08837	T	0.75	.	4.7104	0.12870	0.3136:0.0:0.6864:0.0	.	166;197	D2DJS4;Q6UX27	.;VSTM1_HUMAN	L	87;197;166;109	ENSP00000409412:S87L;ENSP00000343366:S197L;ENSP00000365813:S166L;ENSP00000444153:S109L	ENSP00000343366:S197L	S	-	2	0	VSTM1	59236846	0.001000	0.12720	0.668000	0.29813	0.082000	0.17680	-0.148000	0.10219	0.157000	0.19338	-0.176000	0.13171	TCG		0.458	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	Missense_Mutation	A	54545034	G	A	54545034	5	1	8	1	0	0	0	0	0	0	1	0	17268	1072	37	1	128	1	VSTM1	19	54545034	Splice_Site	SNP	G	TCGA-AF-4110-01A-02D-1733-10	2540311	54545034	4583949	124	886										
ZSCAN5A	79149	hgsc.bcm.edu	37	chr19	56735071	56735071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ggcctggccttcccctggacGcatctggttcaccgaggagg	14	14	2	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr19:56735071G>A	ENST00000587340.1	-	5	1212	c.517C>T	c.(517-519)Cgt>Tgt	p.R173C	ZSCAN5A_ENST00000254165.3_Missense_Mutation_p.R56C|ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.R173C|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.R173C|ZSCAN5A_ENST00000587492.1_Missense_Mutation_p.R27C			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	173					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R173C(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCCCCTGGACGCATCTGGTTC	0.612																																																1	Substitution - Missense(1)	lung(1)	19											68	62	64					19																	56735071		2203	4300	6503	61426883	SO:0001583	missense	79149			AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.517C>T	19.37:g.56735071G>A	ENSP00000467631:p.Arg173Cys		61426883	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	.	.	.	.	.	.	.	.	.	.	g	6.634	0.485382	0.12641	.	.	ENSG00000131848	ENST00000391713;ENST00000254165	T;T	0.06449	3.33;3.3	2.81	-0.726	0.11170	.	.	.	.	.	T	0.03783	0.0107	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.41680	-0.9495	9	0.59425	D	0.04	.	3.0903	0.06291	0.2934:0.2313:0.4753:0.0	.	56;173	B4DX98;Q9BUG6	.;ZSA5A_HUMAN	C	173;56	ENSP00000375593:R173C;ENSP00000254165:R56C	ENSP00000254165:R56C	R	-	1	0	ZSCAN5A	61426883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.278000	0.08490	-0.051000	0.13334	-0.820000	0.03113	CGT		0.612	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		A	56735071	G	A	56735071	3	1	8	1	0	0	0	0	1	0	0	0	18277	1087	38	1	985	1	ZSCAN5A	19	56735071	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	2190037	56735071	2393912	125	887										
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20022260	20022260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttgatacacctgtcttgtccTctcaggatcctgtattagga	8	10	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr20:20022260T>C	ENST00000377340.2	-	10	1688	c.1657A>G	c.(1657-1659)Agg>Ggg	p.R553G	CRNKL1_ENST00000536226.1_Missense_Mutation_p.R392G|CRNKL1_ENST00000377327.4_Missense_Mutation_p.R541G	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	553	Mediates interaction with HSP90. {ECO:0000250|UniProtKB:P63154}.				mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TGTCTTGTCCTCTCAGGATCC	0.343																																																0			20											103	98	100					20																	20022260		2203	4300	6503	19970260	SO:0001583	missense	51340			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.1657A>G	20.37:g.20022260T>C	ENSP00000366557:p.Arg553Gly		19970260	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.235301	0.58886	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.35973	1.28;1.28;1.28	5.8	5.8	0.92144	Tetratricopeptide-like helical (1);	0.082885	0.85682	N	0.000000	T	0.53384	0.1793	M	0.90977	3.165	0.80722	D	1	P	0.46621	0.881	P	0.45856	0.495	T	0.65475	-0.6159	10	0.87932	D	0	-14.7932	12.406	0.55441	0.0:0.0:0.1789:0.8211	.	553	Q9BZJ0	CRNL1_HUMAN	G	541;553;392	ENSP00000366544:R541G;ENSP00000366557:R553G;ENSP00000440733:R392G	ENSP00000366544:R541G	R	-	1	2	CRNKL1	19970260	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.291000	0.65667	2.216000	0.71823	0.533000	0.62120	AGG		0.343	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			C	20022260	T	C	20022260	3	2	8	1	0	0	0	0	1	0	0	0	3897	1550	54	4	913	4	CRNKL1	20	20022260	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10		20022260	43003260	126	888										
RBM12	10137	hgsc.bcm.edu	37	chr20	34240767	34240767	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gggccggggccggggccaggCccaaaagctggtggcccacc	18	15	0	0	rs202158484	byFrequency	TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr20:34240767C>G	ENST00000374114.3	-	3	2741	c.2478G>C	c.(2476-2478)ggG>ggC	p.G826G	RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000359646.1_Silent_p.G826G|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000352393.4_Intron|RBM12_ENST00000374104.3_Silent_p.G826G|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	826	Gly-rich.|Pro-rich.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			cggggccaggCCCAAAAGCTG	0.622																																																0			20											12	14	13					20																	34240767		2148	4263	6411	33704181	SO:0001819	synonymous_variant	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.2478G>C	20.37:g.34240767C>G			33704181	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	37	CCDS13261.1																																																																																				0.622	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		G	34240767	C	G	34240767	2	3	8	1	0	0	0	0	0	0	0	1	13150	726	26	5		5	RBM12	20	34240767	Silent	SNP	C	TCGA-AF-4110-01A-02D-1733-10	14218507	34240767	28784753	127	889										
RBM39	9584	hgsc.bcm.edu	37	chr20	34312639	34312639	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tcagaaatcatcctcacatcTcgaacctagaaagaaaacac	4	12	4	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr20:34312639T>C	ENST00000253363.6	-	8	563	c.540A>G	c.(538-540)cgA>cgG	p.R180R	RBM39_ENST00000407261.4_Silent_p.R23R|RBM39_ENST00000528062.3_Silent_p.R158R|RBM39_ENST00000361162.6_Silent_p.R180R			Q14498	RBM39_HUMAN	RNA binding motif protein 39	180	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TCCTCACATCTCGAACCTAGA	0.368																																																0			20											99	93	95					20																	34312639		2203	4300	6503	33776053	SO:0001819	synonymous_variant	9584			L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.540A>G	20.37:g.34312639T>C			33776053	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Silent	SNP	ENST00000253363.6	37	CCDS13266.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.394321	0.25205	.	.	ENSG00000131051	ENST00000448303	T	0.16597	2.33	5.36	-3.6	0.04570	.	0.054147	0.64402	D	0.000001	T	0.20047	0.0482	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09930	-1.0652	7	0.87932	D	0	.	4.9901	0.14209	0.5845:0.0662:0.0838:0.2656	.	.	.	.	G	53	ENSP00000394824:R53G	ENSP00000394824:R53G	R	-	1	2	RBM39	33776053	0.997000	0.39634	0.996000	0.52242	0.944000	0.59088	0.401000	0.20948	-0.253000	0.09514	0.456000	0.33151	AGA		0.368	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		C	34312639	T	C	34312639	2	2	8	1	0	0	0	0	0	0	0	1	13170	1538	54	4		4	RBM39	20	34312639	Silent	SNP	T	TCGA-AF-4110-01A-02D-1733-10	71872	34312639	28712881	128	890										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44673751	44673751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	acgcctgctgcaggccatctCgagggatggcattgtgccct	13	13	1	0			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr20:44673751C>T	ENST00000454036.2	+	12	1659	c.1610C>T	c.(1609-1611)tCg>tTg	p.S537L	SLC12A5_ENST00000243964.3_Missense_Mutation_p.S514L	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	537					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CAGGCCATCTCGAGGGATGGC	0.622																																																0			20											69	70	70					20																	44673751		2203	4300	6503	44107158	SO:0001583	missense	57468			AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1610C>T	20.37:g.44673751C>T	ENSP00000387694:p.Ser537Leu		44107158	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.757435	0.69648	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	D;D	0.98996	-5.31;-5.31	4.32	4.32	0.51571	Amino acid permease domain (1);	0.243089	0.33364	N	0.004991	D	0.97564	0.9202	L	0.55103	1.725	0.80722	D	1	P;B	0.35363	0.497;0.035	B;B	0.33568	0.166;0.017	D	0.98922	1.0784	10	0.87932	D	0	.	15.5478	0.76123	0.0:1.0:0.0:0.0	.	537;514	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	L	537;514	ENSP00000387694:S537L;ENSP00000243964:S514L	ENSP00000243964:S514L	S	+	2	0	SLC12A5	44107158	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	7.304000	0.78882	2.225000	0.72522	0.313000	0.20887	TCG		0.622	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			T	44673751	C	T	44673751	3	4	8	1	0	0	0	0	1	0	0	0	14423	893	31	1	1712	1	SLC12A5	20	44673751	Missense_Mutation	SNP	C	TCGA-AF-4110-01A-02D-1733-10	10361112	44673751	18351769	129	891										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45789613	45789613	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	atcccagcattctgcaattcActtctaataagattcaattc	3	11	4	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chr22:45789613A>G	ENST00000357450.4	-	9	1445	c.1446T>C	c.(1444-1446)agT>agC	p.S482S	SMC1B_ENST00000404354.3_Silent_p.S482S	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	482					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTGCAATTCACTTCTAATAA	0.373																																																0			22											121	108	112					22																	45789613		1838	4085	5923	44168277	SO:0001819	synonymous_variant	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1446T>C	22.37:g.45789613A>G			44168277	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																				0.373	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		G	45789613	A	G	45789613	2	3	8	1	0	0	0	0	0	0	0	1	14819	156	6	4		4	SMC1B	22	45789613	Silent	SNP	A	TCGA-AF-4110-01A-02D-1733-10		45789613	5514953	130	892										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37026704	37026704	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tacgcttgtttgtcgccgtgAcgagtttttactccccaaaa	8	11	0	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chrX:37026704A>G	ENST00000358047.3	+	1	273	c.221A>G	c.(220-222)gAc>gGc	p.D74G		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	74										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TGTCGCCGTGACGAGTTTTTA	0.532																																																0			X											78	71	73					X																	37026704		2202	4300	6502	36936625	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.221A>G	X.37:g.37026704A>G	ENSP00000367913:p.Asp74Gly		36936625	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	A	9.225	1.034436	0.19590	.	.	ENSG00000198173	ENST00000358047	T	0.21543	2.0	0.502	0.502	0.16932	.	.	.	.	.	T	0.22044	0.0531	L	0.56769	1.78	0.09310	N	1	P	0.41313	0.745	B	0.43623	0.425	T	0.13872	-1.0493	8	0.32370	T	0.25	.	.	.	.	.	74	Q5HY64	FA47C_HUMAN	G	74	ENSP00000367913:D74G	ENSP00000367913:D74G	D	+	2	0	FAM47C	36936625	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.154000	0.16343	0.400000	0.25396	0.242000	0.17961	GAC		0.532	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		G	37026704	A	G	37026704	3	3	8	1	0	0	0	0	1	0	0	0	5590	275	10	4	223	4	FAM47C	23	37026704	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10		37026704	118243856	131	893										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99551325	99551325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	accaggggactctttgttgcGaccttccttcagaatggggc	12	11	2	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chrX:99551325G>A	ENST00000373034.4	-	6	5072	c.3397C>T	c.(3397-3399)Cgc>Tgc	p.R1133C	PCDH19_ENST00000255531.7_Missense_Mutation_p.R1086C|PCDH19_ENST00000464981.1_5'Flank|PCDH19_ENST00000420881.2_Missense_Mutation_p.R1085C	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1133					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TCTTTGTTGCGACCTTCCTTC	0.512																																																0			X											125	118	120					X																	99551325		2025	4167	6192	99437981	SO:0001583	missense	57575			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3397C>T	X.37:g.99551325G>A	ENSP00000362125:p.Arg1133Cys		99437981	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.768672	0.31320	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.54279	0.58;0.59;0.58	5.52	4.65	0.58169	.	0.188065	0.45867	N	0.000334	T	0.44829	0.1312	L	0.27053	0.805	0.80722	D	1	D;B;B	0.69078	0.997;0.007;0.004	P;B;B	0.50231	0.635;0.003;0.001	T	0.46359	-0.9197	10	0.87932	D	0	.	6.1926	0.20532	0.1553:0.0:0.6211:0.2237	.	1133;1086;1085	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	C	1085;1133;1086	ENSP00000400327:R1085C;ENSP00000362125:R1133C;ENSP00000255531:R1086C	ENSP00000255531:R1086C	R	-	1	0	PCDH19	99437981	1.000000	0.71417	0.805000	0.32314	0.923000	0.55619	2.070000	0.41491	1.082000	0.41137	0.600000	0.82982	CGC		0.512	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99551325	G	A	99551325	3	1	8	1	0	0	0	0	1	0	0	0	11545	1058	37	1	53	1	PCDH19	23	99551325	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	62524621	99551325	55719235	132	894										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128599877	128599877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	ttgaattcttgcttctccacGttcaatttgagccataattt	5	9	3	2			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chrX:128599877G>A	ENST00000371122.4	-	22	2890	c.2761C>T	c.(2761-2763)Cgt>Tgt	p.R921C	SMARCA1_ENST00000371123.1_Missense_Mutation_p.R909C|SMARCA1_ENST00000371121.3_Missense_Mutation_p.R909C	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	921					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						GCTTCTCCACGTTCAATTTGA	0.323																																																0			X											162	140	147					X																	128599877		2203	4300	6503	128427558	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.2761C>T	X.37:g.128599877G>A	ENSP00000360163:p.Arg921Cys		128427558	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631321	0.67015	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91843	-2.92;-2.92;-2.91;-2.91	5.73	4.86	0.63082	SLIDE (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000009	D	0.95878	0.8658	M	0.86028	2.79	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.68943	0.961;0.961;0.934;0.961	D	0.95903	0.8917	10	0.72032	D	0.01	-7.2706	13.0145	0.58749	0.0:0.0:0.7073:0.2927	.	900;921;909;921	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	C	909;909;921;900	ENSP00000360162:R909C;ENSP00000360164:R909C;ENSP00000360163:R921C;ENSP00000404275:R900C	ENSP00000360162:R909C	R	-	1	0	SMARCA1	128427558	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.160000	0.64929	1.154000	0.42482	0.600000	0.82982	CGT		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		A	128599877	G	A	128599877	3	1	8	1	0	0	0	0	1	0	0	0	14805	1145	40	1	415	1	SMARCA1	23	128599877	Missense_Mutation	SNP	G	TCGA-AF-4110-01A-02D-1733-10	29048552	128599877	26670683	133	895										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129377605	129377605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	tacaagatgaaatctaggcgAggcagccactggatttgatg	12	7	1	3			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chrX:129377605A>G	ENST00000370978.4	-	5	466	c.313T>C	c.(313-315)Tcg>Ccg	p.S105P		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	105	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						AATCTAGGCGAGGCAGCCACT	0.353																																																0			X											63	66	65					X																	129377605		2203	4300	6503	129205286	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.313T>C	X.37:g.129377605A>G	ENSP00000360017:p.Ser105Pro		129205286	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.581225	0.28180	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.25912	1.77;1.77	3.62	3.62	0.41486	.	.	.	.	.	T	0.29491	0.0735	L	0.39898	1.24	0.09310	N	1	B;P	0.42993	0.004;0.797	B;P	0.51101	0.021;0.659	T	0.07046	-1.0793	9	0.34782	T	0.22	.	7.8624	0.29517	1.0:0.0:0.0:0.0	.	105;105	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	P	105	ENSP00000360017:S105P;ENSP00000408521:S105P	ENSP00000066465:S105P	S	-	1	0	ZNF280C	129205286	0.006000	0.16342	0.013000	0.15412	0.011000	0.07611	1.588000	0.36633	1.441000	0.47550	0.412000	0.27726	TCG		0.353	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		G	129377605	A	G	129377605	3	3	8	1	0	0	0	0	1	0	0	0	17855	304	11	4	1960	4	ZNF280C	23	129377605	Missense_Mutation	SNP	A	TCGA-AF-4110-01A-02D-1733-10	777728	129377605	25892955	134	896										
CDR1	1038	hgsc.bcm.edu	37	chrX	139865857	139865857	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0373134328358209	5	1	0.614165890027959	2.03552123552124	0.419077901430843	1	1	0	gtcagtgtcttccagaaaaaTctacgtcttccaccaaatcc	5	13	4	1			TCGA-AF-4110-01A-02D-1733-10	TCGA-AF-4110-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2794481a-dadf-4ccc-a915-e5189600c7e4	97a7e45c-67dd-4039-b8ea-6f7a385986a2	g.chrX:139865857T>A	ENST00000370532.2	-	1	866	c.675A>T	c.(673-675)agA>agT	p.R225S		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	225										breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				TCCAGAAAAATCTACGTCTTC	0.443																																																0			X											119	113	115					X																	139865857		2203	4300	6503	139693523	SO:0001583	missense	1038				CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.675A>T	X.37:g.139865857T>A	ENSP00000359563:p.Arg225Ser		139693523	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.841546	0.51057	.	.	ENSG00000184258	ENST00000370532	.	.	.	4.58	1.97	0.26223	.	.	.	.	.	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.21606	0.058	B	0.16722	0.016	T	0.25152	-1.0140	7	.	.	.	.	3.8074	0.08783	0.1919:0.116:0.0:0.6921	.	225	P51861	CDR1_HUMAN	S	225	.	.	R	-	3	2	CDR1	139693523	0.000000	0.05858	0.001000	0.08648	0.184000	0.23303	0.560000	0.23500	0.664000	0.31047	0.345000	0.21793	AGA		0.443	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		A	139865857	T	A	139865857	3	1	8	1	0	0	0	0	1	0	0	0	3177	1432	50	5	117	5	CDR1	23	139865857	Missense_Mutation	SNP	T	TCGA-AF-4110-01A-02D-1733-10	10488252	139865857	15404703	135	897										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3415741	3415741	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	catccagccaggggcacagtGgcactgcccgtggacagggt	15	13	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:3415741G>A	ENST00000356575.4	-	24	3281	c.3055C>T	c.(3055-3057)Cac>Tac	p.H1019Y	MEGF6_ENST00000294599.4_Intron	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1019	EGF-like 18. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GGGGCACAGTGGCACTGCCCG	0.672																																					Ovarian(73;978 3658)											0			1											22	28	26					1																	3415741		1990	4156	6146	3405601	SO:0001583	missense	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3055C>T	1.37:g.3415741G>A	ENSP00000348982:p.His1019Tyr		3405601	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.552060	0.27739	.	.	ENSG00000162591	ENST00000356575	T	0.32515	1.45	4.94	4.94	0.65067	EGF-like, laminin (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.962540	0.08636	N	0.916288	T	0.31670	0.0804	L	0.49455	1.56	0.19945	N	0.999941	P	0.39862	0.692	B	0.36030	0.216	T	0.21484	-1.0244	10	0.48119	T	0.1	-17.9235	13.4438	0.61129	0.0:0.2845:0.7155:0.0	.	1019	O75095	MEGF6_HUMAN	Y	1019	ENSP00000348982:H1019Y	ENSP00000348982:H1019Y	H	-	1	0	MEGF6	3405601	0.002000	0.14202	0.997000	0.53966	0.843000	0.47879	0.231000	0.17872	2.440000	0.82611	0.549000	0.68633	CAC		0.672	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3415741	G	A	3415741	3	1	9	1	0	0	0	0	1	0	0	0	9492	1348	47	3	1626	3	MEGF6	1	3415741	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		3415741	245834880	1	898										
FAM131C	348487	hgsc.bcm.edu	37	chr1	16385031	16385031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccctcgggtccttgggccccGggcagccgccgccgatgctg	15	18	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:16385031G>A	ENST00000375662.4	-	7	927	c.744C>T	c.(742-744)ccC>ccT	p.P248P	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	248	Pro-rich.									large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGGGCCCCGGGCAGCCGCC	0.721																																																0			1											2	2	2					1																	16385031		1405	3126	4531	16257618	SO:0001819	synonymous_variant	348487				CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 117"	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.744C>T	1.37:g.16385031G>A			16257618	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																				0.721	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623		A	16385031	G	A	16385031	2	1	9	1	0	0	0	0	0	0	0	1	5457	1103	39	1		1	FAM131C	1	16385031	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	12969290	16385031	232865590	2	899										
IGSF21	84966	hgsc.bcm.edu	37	chr1	18703368	18703368	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctggacggcagcgctgagttCgacgggaaggagctggtgct	18	9	0	1	rs139607566		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:18703368C>T	ENST00000251296.1	+	8	1559	c.1176C>T	c.(1174-1176)ttC>ttT	p.F392F	IGSF21_ENST00000473951.1_3'UTR	NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	392	Ig-like 2.					extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		GCGCTGAGTTCGACGGGAAGG	0.652																																																0			1						C		1,4405	2.1+/-5.4	0,1,2202	45	45	45		1176	-3.6	0.2	1	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous	IGSF21	NM_032880.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		392/468	18703368	1,13005	2203	4300	6503	18575955	SO:0001819	synonymous_variant	84966			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.1176C>T	1.37:g.18703368C>T			18575955	Q8NBR8	Silent	SNP	ENST00000251296.1	37	CCDS184.1																																																																																				0.652	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		T	18703368	C	T	18703368	2	4	9	1	0	0	0	0	0	0	0	1	7620	883	31	1		1	IGSF21	1	18703368	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	2318337	18703368	230547253	3	900										
HMGCL	3155	hgsc.bcm.edu	37	chr1	24143201	24143201	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ttcaaatttggggtcaggacTgggtagttgatgccaggaaa	14	5	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:24143201T>C	ENST00000374490.3	-	4	355	c.312A>G	c.(310-312)ccA>ccG	p.P104P	HMGCL_ENST00000509389.1_5'UTR|HMGCL_ENST00000374483.4_Silent_p.P79P|HMGCL_ENST00000436439.2_Silent_p.P104P	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	104					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		GGGTCAGGACTGGGTAGTTGA	0.512																																																0			1											171	165	167					1																	24143201		2203	4300	6503	24015788	SO:0001819	synonymous_variant	3155			BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.312A>G	1.37:g.24143201T>C			24015788	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Silent	SNP	ENST00000374490.3	37	CCDS243.1																																																																																				0.512	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		C	24143201	T	C	24143201	2	2	9	1	0	0	0	0	0	0	0	1	7250	1567	55	4		4	HMGCL	1	24143201	Silent	SNP	T	TCGA-AF-5654-01A-01D-1657-10	5439833	24143201	225107420	4	901										
NT5C1A	84618	hgsc.bcm.edu	37	chr1	40125092	40125092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	acgaattgggcactccagccGcaggcctttggagtagaact	12	11	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:40125092G>A	ENST00000235628.1	-	6	807	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W		NM_032526.1	NP_115915.1	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	270					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|purine nucleobase metabolic process (GO:0006144)|purine nucleoside monophosphate catabolic process (GO:0009128)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			breast(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)	15	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			CACTCCAGCCGCAGGCCTTTG	0.587																																																0			1											45	49	48					1																	40125092		2203	4300	6503	39897679	SO:0001583	missense	84618			AF331801	CCDS440.1	1p34.3-p33	2008-07-18			ENSG00000116981	ENSG00000116981			17819	protein-coding gene	gene with protein product	"cytosolic 5' nucleotidase, type 1A", "AMP-specific 5'-NT", "cytosolic 5'-nucleotidase IA"	610525				11133996, 11690631	Standard	NM_032526		Approved	CN-I, CN-IA, CN1A, CN1, MGC119199, MGC119201	uc001cdq.1	Q9BXI3	OTTHUMG00000009244	ENST00000235628.1:c.808C>T	1.37:g.40125092G>A	ENSP00000235628:p.Arg270Trp		39897679	Q3SYB9|Q5TG98|Q9BWT8	Missense_Mutation	SNP	ENST00000235628.1	37	CCDS440.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.348561	0.61183	.	.	ENSG00000116981	ENST00000235628	.	.	.	5.26	0.84	0.18912	.	0.000000	0.85682	D	0.000000	T	0.82254	0.4997	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85637	0.1274	9	0.72032	D	0.01	-1.1619	16.1665	0.81759	0.0:0.0:0.4272:0.5728	.	270	Q9BXI3	5NT1A_HUMAN	W	270	.	ENSP00000235628:R270W	R	-	1	2	NT5C1A	39897679	1.000000	0.71417	0.991000	0.47740	0.774000	0.43823	2.870000	0.48451	0.275000	0.22094	-0.953000	0.02652	CGG		0.587	NT5C1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025626.1	NM_032526		A	40125092	G	A	40125092	3	1	9	1	0	0	0	0	1	0	0	0	10716	1086	38	1	302	1	NT5C1A	1	40125092	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	15981891	40125092	209125529	5	902										
GLIS1	148979	hgsc.bcm.edu	37	chr1	53975700	53975700	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gagaggaggccgggccccaaCctggagagaacagaggtgcc	17	11	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:53975700C>A	ENST00000312233.2	-	8	1925	c.1359G>T	c.(1357-1359)ggG>ggT	p.G453G		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CGGGCCCCAACCTGGAGAGAA	0.706																																																0			1											6	8	7					1																	53975700		2133	4200	6333	53748288	SO:0001630	splice_region_variant	148979			AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.1359-1G>T	1.37:g.53975700C>A			53748288		Silent	SNP	ENST00000312233.2	37	CCDS582.1																																																																																				0.706	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	Silent	A	53975700	C	A	53975700	5	1	9	1	0	0	0	0	0	0	1	0	6465	521	18	2	515	2	GLIS1	1	53975700	Splice_Site	SNP	C	TCGA-AF-5654-01A-01D-1657-10	13850608	53975700	195274921	6	903										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74507278	74507278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctctttctcgagcaacttgtGccatggctacaactcttact	6	13	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:74507278G>T	ENST00000395089.1	-	6	1336	c.1337C>A	c.(1336-1338)gCa>gAa	p.A446E	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.A446E			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	446										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						AGCAACTTGTGCCATGGCTAC	0.323																																																0			1											213	196	201					1																	74507278		1844	4094	5938	74279866	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1337C>A	1.37:g.74507278G>T	ENSP00000378524:p.Ala446Glu		74279866	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670663	0.47781	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.09817	2.94;2.94	5.77	4.64	0.57946	.	0.161766	0.29459	N	0.012094	T	0.07593	0.0191	L	0.32530	0.975	0.09310	N	0.999999	D	0.54047	0.964	P	0.55785	0.784	T	0.10965	-1.0607	10	0.56958	D	0.05	.	7.515	0.27596	0.1382:0.0:0.8618:0.0	.	446	A6PVS8	LRIQ3_HUMAN	E	446	ENSP00000378524:A446E;ENSP00000346414:A446E	ENSP00000346414:A446E	A	-	2	0	LRRIQ3	74279866	0.346000	0.24844	0.500000	0.27589	0.054000	0.15201	3.234000	0.51320	2.890000	0.99128	0.585000	0.79938	GCA		0.323	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		T	74507278	G	T	74507278	3	4	9	1	0	0	0	0	1	0	0	0	9059	1319	46	2	545	2	LRRIQ3	1	74507278	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	20531578	74507278	174743343	7	904										
DPYD	1806	hgsc.bcm.edu	37	chr1	97981479	97981479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tagttcaggcttggcagaaaCggaagctccatattgtgact	11	8	1	2	rs148994843		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:97981479C>T	ENST00000370192.3	-	13	1643	c.1543G>A	c.(1543-1545)Gtt>Att	p.V515I		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	515					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TTGGCAGAAACGGAAGCTCCA	0.353																																																0			1						C	ILE/VAL	0,4406		0,0,2203	64	60	62		1543	3.3	0.1	1	dbSNP_134	62	1,8597	1.2+/-3.3	0,1,4298	no	missense	DPYD	NM_000110.3	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	515/1026	97981479	1,13003	2203	4299	6502	97754067	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1543G>A	1.37:g.97981479C>T	ENSP00000359211:p.Val515Ile		97754067	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	0.057	-1.233118	0.01505	0.0	1.16E-4	ENSG00000188641	ENST00000370192	D	0.91945	-2.94	5.2	3.31	0.37934	.	0.126400	0.52532	N	0.000063	T	0.71392	0.3334	N	0.16066	0.365	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.60398	-0.7271	10	0.15066	T	0.55	-15.81	11.8376	0.52336	0.0:0.7925:0.0:0.2075	.	515	Q12882	DPYD_HUMAN	I	515	ENSP00000359211:V515I	ENSP00000359211:V515I	V	-	1	0	DPYD	97754067	0.921000	0.31238	0.060000	0.19600	0.001000	0.01503	1.930000	0.40124	0.299000	0.22661	-1.128000	0.01989	GTT		0.353	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	97981479	C	T	97981479	3	4	9	1	0	0	0	0	1	0	0	0	4756	536	19	1	1578	1	DPYD	1	97981479	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	23474201	97981479	151269142	8	905										
LPPR5	163404	hgsc.bcm.edu	37	chr1	99422193	99422193	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cggacagttcggcgcaccagCgggtttatatagcaacagtc	12	11	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:99422193C>T	ENST00000263177.4	-	2	563	c.342G>A	c.(340-342)ccG>ccA	p.P114P	LPPR5_ENST00000370188.3_Silent_p.P114P	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		114						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										GGCGCACCAGCGGGTTTATAT	0.363																																																0			1											70	73	72					1																	99422193		2202	4300	6502	99194781	SO:0001819	synonymous_variant	0																														ENST00000263177.4:c.342G>A	1.37:g.99422193C>T			99194781	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Silent	SNP	ENST00000263177.4	37	CCDS30778.1																																																																																				0.363	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			T	99422193	C	T	99422193	2	4	9	1	0	0	0	0	0	0	0	1	8957	755	27	1		1	LPPR5	1	99422193	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1440714	99422193	149828428	9	906										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206712	116206712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggtccgcattttggactctcGggaccggaattaccagggca	13	11	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:116206712G>A	ENST00000355485.2	+	4	906	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	VANGL1_ENST00000369509.1_Missense_Mutation_p.R212Q|VANGL1_ENST00000369510.4_Missense_Mutation_p.R210Q|VANGL1_ENST00000310260.3_Missense_Mutation_p.R212Q	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	212					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGGACTCTCGGGACCGGAAT	0.517																																																0			1											195	197	196					1																	116206712		2203	4300	6503	116008235	SO:0001583	missense	81839			AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.635G>A	1.37:g.116206712G>A	ENSP00000347672:p.Arg212Gln		116008235	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274091	0.40194	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.73	4.82	0.62117	.	0.120688	0.64402	D	0.000018	T	0.51449	0.1675	N	0.25890	0.77	0.39974	D	0.974838	B;B	0.15930	0.012;0.015	B;B	0.15052	0.007;0.012	T	0.50939	-0.8768	10	0.21014	T	0.42	2.8345	9.7263	0.40333	0.197:0.0:0.803:0.0	.	210;212	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	Q	212;210;212;212	ENSP00000347672:R212Q;ENSP00000358523:R210Q;ENSP00000310800:R212Q;ENSP00000358522:R212Q	ENSP00000310800:R212Q	R	+	2	0	VANGL1	116008235	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.819000	0.62664	1.582000	0.49881	-0.142000	0.14014	CGG		0.517	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116206712	G	A	116206712	3	1	9	1	0	0	0	0	1	0	0	0	17159	1116	39	1	645	1	VANGL1	1	116206712	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	16784519	116206712	133043909	10	907										
HFE2	148738	hgsc.bcm.edu	37	chr1	145415660	145415660	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gttttcccggctgcatggtcGtcccccggggttcttgcatt	12	13	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:145415660G>A	ENST00000336751.5	+	3	717	c.479G>A	c.(478-480)cGt>cAt	p.R160H	HFE2_ENST00000357836.5_Missense_Mutation_p.R47H|HFE2_ENST00000475797.1_Intron|HFE2_ENST00000497365.1_Intron	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN	hemochromatosis type 2 (juvenile)	160					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|iron ion homeostasis (GO:0055072)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGCATGGTCGTCCCCCGGGG	0.677																																																0			1											47	45	46					1																	145415660		2203	4300	6503	144127017	SO:0001583	missense	148738			AY372521	CCDS72877.1, CCDS72878.1, CCDS72879.1	1q21.2	2014-06-26			ENSG00000168509	ENSG00000168509			4887	protein-coding gene	gene with protein product	"repulsive guidance molecule c"	608374				10205270, 14647275	Standard	NM_213653		Approved	JH, HFE2A, RGMC, HJV, hemojuvelin, haemojuvelin	uc001eni.2	Q6ZVN8	OTTHUMG00000013748	ENST00000336751.5:c.479G>A	1.37:g.145415660G>A	ENSP00000337014:p.Arg160His		144127017	B1ALI7|Q2PQ63|Q6IMF6|Q8NAH2|Q8WVJ5	Missense_Mutation	SNP	ENST00000336751.5	37	CCDS910.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.119753	0.37436	.	.	ENSG00000168509	ENST00000357836;ENST00000336751	D;D	0.97455	-4.39;-4.39	4.86	3.93	0.45458	Repulsive guidance molecule, N-terminal (1);	0.397887	0.23706	N	0.045361	D	0.89649	0.6776	L	0.47716	1.5	0.23747	N	0.996954	B	0.20988	0.05	B	0.16289	0.015	D	0.84091	0.0390	10	0.42905	T	0.14	-19.0286	6.8206	0.23855	0.2116:0.0:0.7884:0.0	.	160	Q6ZVN8	RGMC_HUMAN	H	47;160	ENSP00000350495:R47H;ENSP00000337014:R160H	ENSP00000337014:R160H	R	+	2	0	HFE2	144127017	0.000000	0.05858	0.032000	0.17829	0.856000	0.48823	0.813000	0.27225	1.238000	0.43771	0.558000	0.71614	CGT		0.677	HFE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038527.1	NM_145277		A	145415660	G	A	145415660	3	1	9	1	0	0	0	0	1	0	0	0	7103	1145	40	1	485	1	HFE2	1	145415660	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	29208948	145415660	103834961	11	908										
LCE1B	353132	hgsc.bcm.edu	37	chr1	152785250	152785250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccagctgctgtggaggagggAgtggccagcactctggaggc	18	10	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:152785250A>G	ENST00000360090.3	+	1	804	c.328A>G	c.(328-330)Agt>Ggt	p.S110G		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	110	Gly-rich.				keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGGAGGAGGGAGTGGCCAGCA	0.617																																																0			1											35	43	40					1																	152785250		2199	4299	6498	151051874	SO:0001583	missense	353132			BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"Late cornified envelopes"	16611	protein-coding gene	gene with protein product		612604	"small proline rich-like (epidermal differentiation complex) 2A"	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.328A>G	1.37:g.152785250A>G	ENSP00000353203:p.Ser110Gly		151051874	A4IF40	Missense_Mutation	SNP	ENST00000360090.3	37	CCDS1027.1	.	.	.	.	.	.	.	.	.	.	A	1.511	-0.549572	0.03996	.	.	ENSG00000196734	ENST00000360090;ENST00000439693	T	0.02236	4.38	4.68	0.751	0.18392	.	0.862191	0.09496	N	0.794310	T	0.00608	0.0020	L	0.28274	0.84	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.48410	-0.9038	10	0.87932	D	0	.	2.7708	0.05334	0.5935:0.0:0.2167:0.1897	.	110	Q5T7P3	LCE1B_HUMAN	G	110;102	ENSP00000353203:S110G	ENSP00000353203:S110G	S	+	1	0	LCE1B	151051874	0.011000	0.17503	0.006000	0.13384	0.011000	0.07611	0.488000	0.22371	0.372000	0.24591	0.528000	0.53228	AGT		0.617	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349		G	152785250	A	G	152785250	3	3	9	1	0	0	0	0	1	0	0	0	8682	304	11	4	330	4	LCE1B	1	152785250	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	7369590	152785250	96465371	12	909										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154744734	154744734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgtgtaggagaaggccaggcGtgccgtccagaagaacttgt	15	8	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:154744734G>A	ENST00000271915.4	-	3	1480	c.1165C>T	c.(1165-1167)Cgc>Tgc	p.R389C	KCNN3_ENST00000358505.2_Missense_Mutation_p.R76C|KCNN3_ENST00000361147.4_Missense_Mutation_p.R84C	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	394					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	AAGGCCAGGCGTGCCGTCCAG	0.597																																																0			1											68	61	63					1																	154744734		2203	4300	6503	153011358	SO:0001583	missense	3782			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.1165C>T	1.37:g.154744734G>A	ENSP00000271915:p.Arg389Cys		153011358	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694787	0.88830	.	.	ENSG00000143603	ENST00000361147;ENST00000271915;ENST00000358505	D;D;D	0.98849	-5.18;-4.04;-5.17	4.69	4.69	0.59074	.	0.000000	0.56097	D	0.000033	D	0.98975	0.9651	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.99;0.921	D	0.99888	1.1127	10	0.87932	D	0	-18.6587	17.4259	0.87526	0.0:0.0:1.0:0.0	.	395;394;84	Q6JXY2;Q9UGI6;Q9UGI6-2	.;KCNN3_HUMAN;.	C	84;389;76	ENSP00000354764:R84C;ENSP00000271915:R389C;ENSP00000351295:R76C	ENSP00000271915:R389C	R	-	1	0	KCNN3	153011358	1.000000	0.71417	0.983000	0.44433	0.952000	0.60782	9.652000	0.98499	2.415000	0.81967	0.561000	0.74099	CGC		0.597	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154744734	G	A	154744734	3	1	9	1	0	0	0	0	1	0	0	0	8101	1145	40	1	1054	1	KCNN3	1	154744734	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1959484	154744734	94505887	13	910										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161967994	161967994	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaccagggtgcggtccgagcGttcaggtcgcttgtcacagc	15	12	2	0	rs34123330	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr1:161967994G>A	ENST00000294794.3	-	6	1518	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	OLFML2B_ENST00000367940.2_Silent_p.N366N	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	365					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.N365N(2)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CGGTCCGAGCGTTCAGGTCGC	0.612													G|||	14	0.00279553	0.0106	0	5008	,	,		18931	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	1						G		28,4378	34.3+/-65.2	0,28,2175	142	144	143		1095	-2	0	1	dbSNP_126	143	0,8600		0,0,4300	no	coding-synonymous	OLFML2B	NM_015441.1		0,28,6475	AA,AG,GG		0.0,0.6355,0.2153		365/751	161967994	28,12978	2203	4300	6503	160234618	SO:0001819	synonymous_variant	25903			BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.1095C>T	1.37:g.161967994G>A			160234618	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	37	CCDS1236.1																																																																																				0.612	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		A	161967994	G	A	161967994	2	1	9	1	0	0	0	0	0	0	0	1	10889	1136	40	1		1	OLFML2B	1	161967994	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	7223260	161967994	87282627	14	911										
APOB	338	hgsc.bcm.edu	37	chr2	21227488	21227488	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgcactgaagtcacggtgtgCaaatgttcctttagtcttag	10	8	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:21227488C>A	ENST00000233242.1	-	27	11975	c.11848G>T	c.(11848-11850)Gca>Tca	p.A3950S		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3950					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCACGGTGTGCAAATGTTCCT	0.348																																																0			2											167	159	162					2																	21227488		2203	4300	6503	21080993	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11848G>T	2.37:g.21227488C>A	ENSP00000233242:p.Ala3950Ser		21080993	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.283560	0.23392	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.19394	2.15	5.99	2.9	0.33743	.	0.882419	0.09750	N	0.760771	T	0.18964	0.0455	L	0.55103	1.725	0.18873	N	0.999987	B	0.14438	0.01	B	0.12156	0.007	T	0.37197	-0.9716	10	0.20046	T	0.44	.	6.1696	0.20410	0.2183:0.6065:0.0913:0.0839	.	3950	P04114	APOB_HUMAN	S	3950	ENSP00000233242:A3950S	ENSP00000233242:A3950S	A	-	1	0	APOB	21080993	0.978000	0.34361	0.156000	0.22583	0.610000	0.37248	0.251000	0.18257	0.357000	0.24183	0.655000	0.94253	GCA		0.348	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21227488	C	A	21227488	3	1	9	1	0	0	0	0	1	0	0	0	785	710	25	2	1855	2	APOB	2	21227488	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		21227488	221971885	15	912										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452464	43452465	+	Frame_Shift_Ins	INS	-	-	G													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gccgctctcctcgaagggccINSggcacagctcggtcttgtag							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:43452464_43452465insG	ENST00000282388.3	-	2	771_772	c.478_479insC	c.(478-480)cggfs	p.R160fs	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	160					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				CTCGAAGGGCCGGCACAGCTCG	0.649																																																0			2																																								43305969	SO:0001589	frameshift_variant	678			X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.479dupC	2.37:g.43452466_43452466dupG	ENSP00000282388:p.Arg160fs		43305968	Q53TB4|Q9BSJ3	Frame_Shift_Ins	INS	ENST00000282388.3	37	CCDS1811.1																																																																																				0.649	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		G	43452465	-	G	43452464	7	5	9	1	0	1	1	0	0	0	0	0	17686	652	23	0	1009	0	ZFP36L2	2	43452464	Frame_Shift_Ins	INS	-	TCGA-AF-5654-01A-01D-1657-10	22224976	43452464	199746909	16	913										
PAPOLG	64895	hgsc.bcm.edu	37	chr2	61021301	61021301	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cccatccatagatgggactcCtaagaggttgaaagacgtag	11	9	0	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:61021301C>T	ENST00000238714.3	+	19	2213	c.1964C>T	c.(1963-1965)cCt>cTt	p.P655L		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	655					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			GATGGGACTCCTAAGAGGTTG	0.368																																					GBM(183;1497 2932 21839 46797)											0			2											63	61	61					2																	61021301		2203	4300	6503	60874805	SO:0001583	missense	64895			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.1964C>T	2.37:g.61021301C>T	ENSP00000238714:p.Pro655Leu		60874805	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496375	0.64186	.	.	ENSG00000115421	ENST00000238714;ENST00000378104;ENST00000412217	.	.	.	6.03	6.03	0.97812	.	0.269734	0.42294	D	0.000729	T	0.60843	0.2300	L	0.48642	1.525	0.44092	D	0.996859	B;B;B	0.24317	0.061;0.101;0.001	B;B;B	0.29077	0.045;0.098;0.008	T	0.52924	-0.8510	9	0.28530	T	0.3	-16.3894	20.1519	0.98089	0.0:1.0:0.0:0.0	.	344;189;655	E9PEP5;Q53T81;Q9BWT3	.;.;PAPOG_HUMAN	L	655;344;323	.	ENSP00000238714:P655L	P	+	2	0	PAPOLG	60874805	0.395000	0.25254	0.577000	0.28562	0.927000	0.56198	4.504000	0.60414	2.861000	0.98227	0.655000	0.94253	CCT		0.368	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		T	61021301	C	T	61021301	3	4	9	1	0	0	0	0	1	0	0	0	11462	681	24	3	2038	3	PAPOLG	2	61021301	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	17568837	61021301	182178072	17	914										
TET3	200424	hgsc.bcm.edu	37	chr2	74329089	74329089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gagggcacgggcacggcaggAggaggctgcccggctgggcc	21	12	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:74329089A>G	ENST00000409262.3	+	9	4769	c.4769A>G	c.(4768-4770)gAg>gGg	p.E1590G		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1590					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCACGGCAGGAGGAGGCTGCC	0.657																																																0			2											13	16	15					2																	74329089		2005	4140	6145	74182597	SO:0001583	missense	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.4769A>G	2.37:g.74329089A>G	ENSP00000386869:p.Glu1590Gly		74182597	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.776968	0.49786	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	T	0.14640	2.49	5.18	5.18	0.71444	.	0.061993	0.64402	D	0.000004	T	0.26484	0.0647	M	0.67397	2.05	0.46044	D	0.998831	D	0.57257	0.979	P	0.51777	0.679	T	0.01541	-1.1329	10	0.62326	D	0.03	.	14.1531	0.65401	1.0:0.0:0.0:0.0	.	1590	O43151	TET3_HUMAN	G	1590;1474	ENSP00000386869:E1590G	ENSP00000233310:E1474G	E	+	2	0	TET3	74182597	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	6.964000	0.76061	2.186000	0.69663	0.533000	0.62120	GAG		0.657	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			G	74329089	A	G	74329089	3	3	9	1	0	0	0	0	1	0	0	0	15810	304	11	4	4803	4	TET3	2	74329089	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	13307788	74329089	168870284	18	915										
TRIM43	129868	hgsc.bcm.edu	37	chr2	96260179	96260179	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaagaggcagctgaggaacaCcgggtaagagatagctctgt	15	7	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:96260179C>G	ENST00000272395.2	+	2	544	c.408C>G	c.(406-408)caC>caG	p.H136Q		NM_001164464.1|NM_138800.1	NP_001157936.1|NP_620155.1	Q96BQ3	TRI43_HUMAN	tripartite motif containing 43	136						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|lung(7)|ovary(1)	12						CTGAGGAACACCGGGTAAGAG	0.488																																																0			2											41	42	42					2																	96260179		2201	4296	6497	95623906	SO:0001583	missense	129868			BK000505	CCDS2015.1	2q11	2014-02-17	2011-01-25		ENSG00000144015	ENSG00000144015		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19015	protein-coding gene	gene with protein product			"tripartite motif-containing 43"				Standard	NM_138800		Approved	TRIM43A	uc002suv.3	Q96BQ3	OTTHUMG00000130401	ENST00000272395.2:c.408C>G	2.37:g.96260179C>G	ENSP00000272395:p.His136Gln		95623906	Q53TJ7	Missense_Mutation	SNP	ENST00000272395.2	37	CCDS2015.1	.	.	.	.	.	.	.	.	.	.	.	4.671	0.124789	0.08931	.	.	ENSG00000144015	ENST00000272395	T	0.56103	0.48	1.22	1.22	0.21188	.	.	.	.	.	T	0.33381	0.0861	N	0.21282	0.65	0.09310	N	1	B	0.14805	0.011	B	0.19148	0.024	T	0.21177	-1.0253	9	0.45353	T	0.12	-0.0892	3.6351	0.08146	0.0:0.7443:0.0:0.2557	.	136	Q96BQ3	TRI43_HUMAN	Q	136	ENSP00000272395:H136Q	ENSP00000272395:H136Q	H	+	3	2	TRIM43	95623906	0.082000	0.21442	0.028000	0.17463	0.140000	0.21249	0.155000	0.16362	0.998000	0.38996	0.375000	0.23000	CAC		0.488	TRIM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252784.1	NM_138800		G	96260179	C	G	96260179	3	3	9	1	0	0	0	0	1	0	0	0	16558	506	18	5	410	5	TRIM43	2	96260179	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	21931090	96260179	146939194	19	916										
GCC2	9648	hgsc.bcm.edu	37	chr2	109086275	109086275	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aagaagcaatgaatacgcaaTtagaactttcagaacaactt	6	7	1	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:109086275T>C	ENST00000309863.6	+	6	1204	c.490T>C	c.(490-492)Tta>Cta	p.L164L	GCC2_ENST00000485546.1_3'UTR	NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	164					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GAATACGCAATTAGAACTTTC	0.338																																																0			2											86	91	89					2																	109086275		2203	4300	6503	108452707	SO:0001819	synonymous_variant	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.490T>C	2.37:g.109086275T>C			108452707	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																				0.338	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		C	109086275	T	C	109086275	2	2	9	1	0	0	0	0	0	0	0	1	6306	1490	52	4		4	GCC2	2	109086275	Silent	SNP	T	TCGA-AF-5654-01A-01D-1657-10	12826096	109086275	134113098	20	917										
BIN1	274	hgsc.bcm.edu	37	chr2	127811527	127811527	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cagggctcgtcacgggcgggAgggggtcaaagtccaggtcc	18	11	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:127811527A>G	ENST00000316724.5	-	13	1604	c.1193T>C	c.(1192-1194)cTc>cCc	p.L398P	BIN1_ENST00000409400.1_Intron|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000346226.3_Intron|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000357970.3_Missense_Mutation_p.L355P	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	398	Clathrin-binding.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CACGGGCGGGAGGGGGTCAAA	0.657																																																0			2											23	24	23					2																	127811527		2126	4152	6278	127527997	SO:0001583	missense	274			U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1193T>C	2.37:g.127811527A>G	ENSP00000316779:p.Leu398Pro		127527997	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911607	0.72983	.	.	ENSG00000136717	ENST00000357970;ENST00000316724	T;T	0.66638	-0.22;0.89	5.35	4.16	0.48862	.	0.467416	0.23427	N	0.048281	T	0.61135	0.2323	L	0.38175	1.15	0.80722	D	1	P;P	0.52692	0.955;0.877	B;P	0.48524	0.44;0.58	T	0.57201	-0.7852	10	0.35671	T	0.21	-7.2432	10.5812	0.45257	0.8552:0.0:0.0:0.1448	.	355;398	O00499-5;O00499	.;BIN1_HUMAN	P	355;398	ENSP00000350654:L355P;ENSP00000316779:L398P	ENSP00000316779:L398P	L	-	2	0	BIN1	127527997	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	4.564000	0.60830	0.845000	0.35118	0.369000	0.22263	CTC		0.657	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		G	127811527	A	G	127811527	3	3	9	1	0	0	0	0	1	0	0	0	1433	304	11	4	616	4	BIN1	2	127811527	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	18725252	127811527	115387846	21	918										
WDR33	55339	hgsc.bcm.edu	37	chr2	128463917	128463917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctaccgaccccttccaccacCccgtgaagctcctcgcctcg	6	22	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:128463917C>T	ENST00000322313.4	-	22	4149	c.3991G>A	c.(3991-3993)Ggt>Agt	p.G1331S		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1331					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTTCCACCACCCCGTGAAGCT	0.577																																																0			2											98	106	103					2																	128463917		2203	4300	6503	128180387	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3991G>A	2.37:g.128463917C>T	ENSP00000325377:p.Gly1331Ser		128180387	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.859715	0.51376	.	.	ENSG00000136709	ENST00000322313	D	0.96334	-3.98	5.47	5.47	0.80525	.	0.069516	0.56097	D	0.000021	D	0.96197	0.8760	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97540	1.0085	10	0.87932	D	0	-8.0291	19.6923	0.96007	0.0:1.0:0.0:0.0	.	1331	Q9C0J8	WDR33_HUMAN	S	1331	ENSP00000325377:G1331S	ENSP00000325377:G1331S	G	-	1	0	WDR33	128180387	1.000000	0.71417	0.702000	0.30337	0.070000	0.16714	6.039000	0.70972	2.712000	0.92718	0.650000	0.86243	GGT		0.577	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128463917	C	T	128463917	3	4	9	1	0	0	0	0	1	0	0	0	17327	623	22	3	23	3	WDR33	2	128463917	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	652390	128463917	114735456	22	919										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145162505	145162505	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	actgcgctgaaggtactcctCgatgctgactgcatgaccat	10	12	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:145162505C>T	ENST00000558170.2	-	5	1674	c.490G>A	c.(490-492)Gag>Aag	p.E164K	ZEB2_ENST00000539609.3_Missense_Mutation_p.E140K|ZEB2_ENST00000409487.3_Missense_Mutation_p.E164K|ZEB2_ENST00000303660.4_Missense_Mutation_p.E164K	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	164					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		AGGTACTCCTCGATGCTGACT	0.473																																					Melanoma(33;1235 1264 5755 16332)											0			2											99	83	88					2																	145162505		2203	4300	6503	144878975	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.490G>A	2.37:g.145162505C>T	ENSP00000454157:p.Glu164Lys		144878975	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.540109	0.65085	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46	5.62	5.62	0.85841	.	0.048286	0.85682	D	0.000000	T	0.77691	0.4168	L	0.49126	1.545	0.47123	D	0.999324	P;B;B;B	0.43519	0.809;0.167;0.052;0.052	B;B;B;B	0.37047	0.24;0.01;0.016;0.016	T	0.80730	-0.1252	10	0.66056	D	0.02	-11.8692	20.0114	0.97452	0.0:1.0:0.0:0.0	.	140;29;163;164	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	K	159;140;164;164;164;164	ENSP00000443792:E140K;ENSP00000302501:E164K;ENSP00000386854:E164K;ENSP00000395496:E164K;ENSP00000376601:E164K	ENSP00000302501:E164K	E	-	1	0	ZEB2	144878975	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.776000	0.85560	2.795000	0.96236	0.655000	0.94253	GAG		0.473	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		T	145162505	C	T	145162505	3	4	9	1	0	0	0	0	1	0	0	0	17663	893	31	1	3178	1	ZEB2	2	145162505	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	16698588	145162505	98036868	23	920										
TTN	7273	hgsc.bcm.edu	37	chr2	179431541	179431541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tagacgcaaatctgtaatgcGgcgtttattacattttatcc	7	8	1	1	rs55861600	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:179431541G>A	ENST00000591111.1	-	276	74619	c.74395C>T	c.(74395-74397)Cgc>Tgc	p.R24799C	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R26440C|TTN_ENST00000359218.5_Missense_Mutation_p.R17500C|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R17567C|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R23872C|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R17375C|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24799	Fibronectin type-III 80. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTGTAATGCGGCGTTTATTA	0.418													G|||	33	0.00658946	0.0219	0.0043	5008	,	,		16799	0.001		0	False		,,,				2504	0															0			2						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	99,3633		2,95,1769	66	66	66		52123,71614,52498,52699	4.9	1	2	dbSNP_129	66	1,8213		0,1,4106	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	180,180,180,180	2,96,5875	AA,AG,GG		0.0122,2.6527,0.8371	probably-damaging,probably-damaging,probably-damaging,probably-damaging	17375/26927,23872/33424,17500/27052,17567/27119	179431541	100,11846	1866	4107	5973	179139787	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74395C>T	2.37:g.179431541G>A	ENSP00000465570:p.Arg24799Cys		179139787	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	11.27	1.589985	0.28357	0.026527	1.22E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.75	4.87	0.63330	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.44435	0.1293	L	0.60012	1.86	0.53005	D	0.999962	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	P;P;P;P	0.60345	0.873;0.873;0.873;0.873	T	0.63107	-0.6711	9	0.87932	D	0	.	11.8922	0.52635	0.0:0.1318:0.7311:0.1371	rs55861600	17375;17500;17567;24799	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	23872;17375;17567;17500;17373	ENSP00000343764:R23872C;ENSP00000434586:R17375C;ENSP00000340554:R17567C;ENSP00000352154:R17500C	ENSP00000340554:R17567C	R	-	1	0	TTN	179139787	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.401000	0.52601	1.400000	0.46741	0.561000	0.74099	CGC		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179431541	G	A	179431541	3	1	9	1	0	0	0	0	1	0	0	0	16775	1116	39	1	28809	1	TTN	2	179431541	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	34269036	179431541	63767832	24	921										
TTN	7273	hgsc.bcm.edu	37	chr2	179436094	179436094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	attgtacttccatgctgtccCtggaggacagtgtgacaact	10	10	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:179436094C>T	ENST00000591111.1	-	276	70066	c.69842G>A	c.(69841-69843)aGg>aAg	p.R23281K	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R24922K|TTN_ENST00000359218.5_Missense_Mutation_p.R15982K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16049K|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R22354K|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R15857K|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23281	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATGCTGTCCCTGGAGGACAG	0.473																																																0			2											116	110	112					2																	179436094		1935	4166	6101	179144340	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69842G>A	2.37:g.179436094C>T	ENSP00000465570:p.Arg23281Lys		179144340	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	7.898	0.733740	0.15574	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	5.39	0.177	0.15054	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19644	0.0472	N	0.00611	-1.325	0.23712	N	0.997049	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.22906	-1.0203	9	0.87932	D	0	.	6.3835	0.21548	0.0:0.3952:0.138:0.4668	.	15857;15982;16049;23281	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	22354;15857;16049;15982;15855	ENSP00000343764:R22354K;ENSP00000434586:R15857K;ENSP00000340554:R16049K;ENSP00000352154:R15982K	ENSP00000340554:R16049K	R	-	2	0	TTN	179144340	1.000000	0.71417	0.232000	0.24009	0.479000	0.33129	2.271000	0.43364	-0.130000	0.11599	-0.312000	0.09012	AGG		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179436094	C	T	179436094	3	4	9	1	0	0	0	0	1	0	0	0	16775	681	24	3	33362	3	TTN	2	179436094	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	4553	179436094	63763279	25	922										
TTN	7273	hgsc.bcm.edu	37	chr2	179596497	179596497	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	actggtattcgccagcatctGcagctacaaacttgaggatc	9	11	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:179596497G>T	ENST00000591111.1	-	56	16378	c.16154C>A	c.(16153-16155)gCa>gAa	p.A5385E	TTN_ENST00000589042.1_Missense_Mutation_p.A5702E|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.A4458E|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12204	Ig-like 34.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCAGCATCTGCAGCTACAAA	0.483																																																0			2											109	110	110					2																	179596497		1953	4149	6102	179304742	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16154C>A	2.37:g.179596497G>T	ENSP00000465570:p.Ala5385Glu		179304742	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	8.246	0.807952	0.16467	.	.	ENSG00000155657	ENST00000342992	T	0.37411	1.2	5.93	5.05	0.67936	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.28665	0.0710	N	0.16037	0.36	0.22266	N	0.999241	B	0.18610	0.029	B	0.27608	0.081	T	0.34775	-0.9815	9	0.87932	D	0	.	15.416	0.74970	0.067:0.0:0.933:0.0	.	5385	Q8WZ42	TITIN_HUMAN	E	4458	ENSP00000343764:A4458E	ENSP00000343764:A4458E	A	-	2	0	TTN	179304742	0.527000	0.26306	0.945000	0.38365	0.993000	0.82548	3.662000	0.54510	1.504000	0.48704	0.655000	0.94253	GCA		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179596497	G	T	179596497	3	4	9	1	0	0	0	0	1	0	0	0	16775	1319	46	2	87644	2	TTN	2	179596497	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	160403	179596497	63602876	26	923										
CRYGB	1419	hgsc.bcm.edu	37	chr2	209010729	209010729	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccctggaaggccctgtcctcGtagaaggtgatctgaaaaat	11	10	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:209010729G>A	ENST00000260988.4	-	2	68	c.21C>T	c.(19-21)taC>taT	p.Y7Y		NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B	7	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		CCCTGTCCTCGTAGAAGGTGA	0.582																																																0			2											91	83	86					2																	209010729		2203	4300	6503	208718974	SO:0001819	synonymous_variant	1419				CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"crystallin, gamma 1-2"	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.21C>T	2.37:g.209010729G>A			208718974	Q17RB5|Q53ST2	Silent	SNP	ENST00000260988.4	37	CCDS2380.1																																																																																				0.582	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256473.2	NM_005210		A	209010729	G	A	209010729	2	1	9	1	0	0	0	0	0	0	0	1	3921	1140	40	1		1	CRYGB	2	209010729	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	29414232	209010729	34188644	27	924										
WNT10A	80326	hgsc.bcm.edu	37	chr2	219746977	219746977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cattgccaggcctgagccggCggcagatggaggtgtgtgtg	18	9	0	2	rs146460077	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:219746977C>T	ENST00000258411.3	+	2	841	c.208C>T	c.(208-210)Cgg>Tgg	p.R70W		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	70					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGAGCCGGCGGCAGATGGA	0.607													C|||	14	0.00279553	0	0.0014	5008	,	,		17871	0		0	False		,,,				2504	0.0133															0			2						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	92	86	88		208	0.7	1	2	dbSNP_134	88	17,8583	12.6+/-44.7	0,17,4283	yes	missense	WNT10A	NM_025216.2	101	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	probably-damaging	70/418	219746977	18,12988	2203	4300	6503	219455221	SO:0001583	missense	80326			AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"Wingless-type MMTV integration sites"	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.208C>T	2.37:g.219746977C>T	ENSP00000258411:p.Arg70Trp		219455221	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	18.64|18.64	3.667560|3.667560	0.67814|0.67814	2.27E-4|2.27E-4	0.001977|0.001977	ENSG00000135925|ENSG00000135925	ENST00000458582|ENST00000258411	.|T	.|0.77229	.|-1.08	4.82|4.82	0.679|0.679	0.17975|0.17975	.|.	.|0.068078	.|0.56097	.|D	.|0.000023	D|D	0.88206|0.88206	0.6374|0.6374	M|M	0.90705|0.90705	3.14|3.14	0.53688|0.53688	D|D	0.999973|0.999973	.|D	.|0.76494	.|0.999	.|D	.|0.67725	.|0.953	D|D	0.88678|0.88678	0.3200|0.3200	5|10	.|0.87932	.|D	.|0	.|.	13.6227|13.6227	0.62146|0.62146	0.5329:0.4671:0.0:0.0|0.5329:0.4671:0.0:0.0	.|.	.|70	.|Q9GZT5	.|WN10A_HUMAN	V|W	32|70	.|ENSP00000258411:R70W	.|ENSP00000258411:R70W	A|R	+|+	2|1	0|2	WNT10A|WNT10A	219455221|219455221	0.994000|0.994000	0.37717|0.37717	0.966000|0.966000	0.40874|0.40874	0.837000|0.837000	0.47467|0.47467	0.471000|0.471000	0.22100|0.22100	-0.183000|-0.183000	0.10585|0.10585	-0.475000|-0.475000	0.04921|0.04921	GCG|CGG		0.607	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		T	219746977	C	T	219746977	3	4	9	1	0	0	0	0	1	0	0	0	17422	759	27	1	214	1	WNT10A	2	219746977	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	10736248	219746977	23452396	28	925										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238275460	238275460	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aacgctgtggcgctgttggaCgctatctttccaacctcctc	9	14	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr2:238275460C>T	ENST00000295550.4	-	11	5822	c.5370G>A	c.(5368-5370)gcG>gcA	p.A1790A	COL6A3_ENST00000409809.1_Silent_p.A1584A|COL6A3_ENST00000472056.1_Silent_p.A1183A|COL6A3_ENST00000353578.4_Silent_p.A1584A|COL6A3_ENST00000346358.4_Silent_p.A1590A|COL6A3_ENST00000347401.3_Silent_p.A1589A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1790	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CGCTGTTGGACGCTATCTTTC	0.552																																																0			2											94	88	90					2																	238275460		2203	4300	6503	237940199	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5370G>A	2.37:g.238275460C>T			237940199	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238275460	C	T	238275460	2	4	9	1	0	0	0	0	0	0	0	1	3707	523	19	1		1	COL6A3	2	238275460	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	18528483	238275460	4923913	29	926										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33866733	33866733	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cggttttatctgccttaagtCgagagccgaccgtggacata	11	10	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr3:33866733C>T	ENST00000307296.3	+	5	894	c.517C>T	c.(517-519)Cga>Tga	p.R173*	PDCD6IP_ENST00000457054.2_Nonsense_Mutation_p.R173*			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	173	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TGCCTTAAGTCGAGAGCCGAC	0.413																																																0			3											122	131	128					3																	33866733		2203	4300	6503	33841737	SO:0001587	stop_gained	10015			BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.517C>T	3.37:g.33866733C>T	ENSP00000307387:p.Arg173*		33841737	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Nonsense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829656	0.91036	.	.	ENSG00000170248	ENST00000307296;ENST00000457054;ENST00000413073	.	.	.	5.6	3.76	0.43208	.	0.114916	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-8.0075	14.8691	0.70441	0.2753:0.7247:0.0:0.0	.	.	.	.	X	173;173;123	.	ENSP00000307387:R173X	R	+	1	2	PDCD6IP	33841737	1.000000	0.71417	0.911000	0.35937	0.562000	0.35680	2.168000	0.42424	0.679000	0.31345	-0.182000	0.12963	CGA		0.413	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			T	33866733	C	T	33866733	4	4	9	1	0	0	0	0	0	1	0	0	11655	876	31	1	535	1	PDCD6IP	3	33866733	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		33866733	164155697	30	927										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38348005	38348005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agatgggtggatctatcctgAcgctaagaagcgatcgctga	13	8	1	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr3:38348005A>G	ENST00000273173.4	+	1	579	c.488A>G	c.(487-489)gAc>gGc	p.D163G	RNU6-235P_ENST00000362644.1_RNA|SLC22A14_ENST00000448498.1_Missense_Mutation_p.D163G	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	163					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		ATCTATCCTGACGCTAAGAAG	0.488																																																0			3											122	111	115					3																	38348005		2203	4300	6503	38323009	SO:0001583	missense	9389			AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.488A>G	3.37:g.38348005A>G	ENSP00000273173:p.Asp163Gly		38323009	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.547736	0.27652	.	.	ENSG00000144671	ENST00000466887;ENST00000448498;ENST00000423219;ENST00000273173	T;T;T	0.66995	-0.24;-0.06;-0.06	5.06	0.934	0.19477	Major facilitator superfamily domain (1);	1.381930	0.04819	N	0.436565	T	0.50120	0.1597	N	0.19112	0.55	0.09310	N	1	B	0.22800	0.075	B	0.29524	0.103	T	0.41448	-0.9508	10	0.39692	T	0.17	.	2.0825	0.03638	0.4728:0.2968:0.0935:0.1369	.	163	Q9Y267	S22AE_HUMAN	G	31;163;163;163	ENSP00000442528:D31G;ENSP00000396283:D163G;ENSP00000273173:D163G	ENSP00000273173:D163G	D	+	2	0	SLC22A14	38323009	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	1.085000	0.30840	0.422000	0.26005	-0.290000	0.09829	GAC		0.488	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		G	38348005	A	G	38348005	3	3	9	1	0	0	0	0	1	0	0	0	14482	275	10	4	490	4	SLC22A14	3	38348005	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	4481272	38348005	159674425	31	928										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38750990	38750990	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ttttttttctgttgattgaaGttgtcaattatgaccccaac	6	7	2	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr3:38750990G>A	ENST00000449082.2	-	24	4259	c.4260C>T	c.(4258-4260)aaC>aaT	p.N1420N		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1420					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GTTGATTGAAGTTGTCAATTA	0.418																																																0			3											116	111	113					3																	38750990		2203	4300	6503	38725994	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4260C>T	3.37:g.38750990G>A			38725994	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.418	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38750990	G	A	38750990	2	1	9	1	0	0	0	0	0	0	0	1	13949	1020	36	3		3	SCN10A	3	38750990	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	402985	38750990	159271440	32	929										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53756425	53756425	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	acgttttactggctggttatCgtcctggtgtttctgaacac	10	9	1	1	rs200605154		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr3:53756425C>T	ENST00000350061.5	+	12	2101	c.1590C>T	c.(1588-1590)atC>atT	p.I530I	CACNA1D_ENST00000288139.4_Silent_p.I550I|CACNA1D_ENST00000422281.2_Silent_p.I530I	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	530					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCTGGTTATCGTCCTGGTGT	0.488													C|||	1	0.000199681	0	0	5008	,	,		18163	0		0.001	False		,,,				2504	0															0			3											173	138	150					3																	53756425		2203	4300	6503	53731465	SO:0001819	synonymous_variant	776			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.1590C>T	3.37:g.53756425C>T			53731465	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.07	1.249214	0.22880	.	.	ENSG00000157388	ENST00000481085	.	.	.	5.88	-6.2	0.02072	.	.	.	.	.	T	0.51856	0.1699	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55792	-0.8085	4	.	.	.	.	10.6351	0.45560	0.0859:0.4281:0.0:0.486	.	.	.	.	L	244	.	.	S	+	2	0	CACNA1D	53731465	0.720000	0.27996	0.904000	0.35570	0.984000	0.73092	-0.124000	0.10595	-1.064000	0.03172	-1.099000	0.02127	TCG		0.488	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53756425	C	T	53756425	2	4	9	1	0	0	0	0	0	0	0	1	2547	874	31	1		1	CACNA1D	3	53756425	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	15005435	53756425	144266005	33	930										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25821535	25821535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	taacttgatttgttcagcaaGttgcttctcaaggaggggat	11	6	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:25821535G>A	ENST00000399878.3	-	8	1440	c.1318C>T	c.(1318-1320)Ctt>Ttt	p.L440F	SEL1L3_ENST00000264868.5_Missense_Mutation_p.L405F|SEL1L3_ENST00000502949.1_Missense_Mutation_p.L287F	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	440						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TGTTCAGCAAGTTGCTTCTCA	0.403																																																0			4											65	60	62					4																	25821535		1895	4117	6012	25430633	SO:0001583	missense	0			BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1318C>T	4.37:g.25821535G>A	ENSP00000382767:p.Leu440Phe		25430633	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649742	0.29336	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.15487	2.63;2.63;2.42	5.95	5.95	0.96441	.	0.324362	0.30311	N	0.009904	T	0.19927	0.0479	L	0.60455	1.87	0.41146	D	0.985991	B	0.23540	0.087	B	0.15870	0.014	T	0.01570	-1.1322	10	0.31617	T	0.26	-18.8247	15.8933	0.79318	0.0:0.0:1.0:0.0	.	440	Q68CR1	SE1L3_HUMAN	F	440;405;287	ENSP00000382767:L440F;ENSP00000264868:L405F;ENSP00000425438:L287F	ENSP00000264868:L405F	L	-	1	0	SEL1L3	25430633	1.000000	0.71417	0.962000	0.40283	0.078000	0.17371	3.566000	0.53805	2.824000	0.97209	0.655000	0.94253	CTT		0.403	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25821535	G	A	25821535	3	1	9	1	0	0	0	0	1	0	0	0	14049	1029	36	3	2148	3	SEL1L3	4	25821535	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		25821535	165332741	34	931										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52938103	52938103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcttaaatctcttcaagctcAggaggatgcccgccacagaa	9	12	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:52938103A>G	ENST00000295213.4	+	6	913	c.539A>G	c.(538-540)cAg>cGg	p.Q180R	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Missense_Mutation_p.Q148R	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	180					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			CTTCAAGCTCAGGAGGATGCC	0.537																																																0			4											46	47	46					4																	52938103		2203	4300	6503	52632860	SO:0001583	missense	132671			BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.539A>G	4.37:g.52938103A>G	ENSP00000295213:p.Gln180Arg		52632860	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.350798	0.24512	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;D	0.86432	0.42;-2.12	5.12	5.12	0.69794	.	0.128971	0.64402	D	0.000020	D	0.91720	0.7382	M	0.70595	2.14	0.30220	N	0.796922	D;D;D	0.67145	0.969;0.969;0.996	P;P;D	0.75484	0.766;0.703;0.986	D	0.88649	0.3181	10	0.42905	T	0.14	-20.8417	11.2319	0.48918	1.0:0.0:0.0:0.0	.	148;180;180	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	R	180;148	ENSP00000295213:Q180R;ENSP00000415309:Q148R	ENSP00000295213:Q180R	Q	+	2	0	SPATA18	52632860	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	3.823000	0.55715	2.139000	0.66308	0.528000	0.53228	CAG		0.537	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		G	52938103	A	G	52938103	3	3	9	1	0	0	0	0	1	0	0	0	15042	188	7	4	561	4	SPATA18	4	52938103	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	27116568	52938103	138216173	35	932										
KDR	3791	hgsc.bcm.edu	37	chr4	55958864	55958864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctccaaggtcaggaagtcctTatacagatcttcaggagctg	10	10	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:55958864T>C	ENST00000263923.4	-	22	3284	c.2989A>G	c.(2989-2991)Aag>Gag	p.K997E	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	997	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGGAAGTCCTTATACAGATCT	0.443			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0			4											98	86	90					4																	55958864		2203	4300	6503	55653621	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2989A>G	4.37:g.55958864T>C	ENSP00000263923:p.Lys997Glu		55653621	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.116751	0.37339	.	.	ENSG00000128052	ENST00000263923	D	0.82711	-1.64	5.95	5.95	0.96441	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.69895	0.3162	N	0.17379	0.485	0.41100	D	0.985662	P	0.34724	0.465	B	0.35039	0.194	T	0.69591	-0.5104	10	0.06099	T	0.92	.	16.4092	0.83701	0.0:0.0:0.0:1.0	.	997	P35968	VGFR2_HUMAN	E	997	ENSP00000263923:K997E	ENSP00000263923:K997E	K	-	1	0	KDR	55653621	1.000000	0.71417	0.994000	0.49952	0.462000	0.32619	4.861000	0.62969	2.276000	0.75962	0.460000	0.39030	AAG		0.443	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			C	55958864	T	C	55958864	3	2	9	1	0	0	0	0	1	0	0	0	8160	1763	61	4	1117	4	KDR	4	55958864	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	3020761	55958864	135195412	36	933										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73986678	73986678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tccttggaagcaggctaaagTaagggcagtgttccgattgg	14	7	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:73986678T>C	ENST00000358602.4	-	20	3885	c.3769A>G	c.(3769-3771)Act>Gct	p.T1257A	ANKRD17_ENST00000330838.6_Missense_Mutation_p.T1006A|ANKRD17_ENST00000509867.2_Missense_Mutation_p.T1144A|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1257					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGGCTAAAGTAAGGGCAGTG	0.423																																																0			4											156	147	150					4																	73986678		2203	4300	6503	74205542	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.3769A>G	4.37:g.73986678T>C	ENSP00000351416:p.Thr1257Ala		74205542	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.668529	0.88348	.	.	ENSG00000132466	ENST00000358602;ENST00000330838;ENST00000509867	T;T;T	0.63580	-0.05;-0.05;-0.05	5.88	5.88	0.94601	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000002	T	0.63105	0.2483	N	0.12502	0.225	0.53005	D	0.999961	D;D;D;D;D	0.76494	0.999;0.996;0.996;0.997;0.997	D;D;D;D;D	0.83275	0.996;0.987;0.987;0.992;0.992	T	0.61312	-0.7088	10	0.16896	T	0.51	.	16.2881	0.82732	0.0:0.0:0.0:1.0	.	778;1256;1006;1257;1144	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	A	1257;1006;1144	ENSP00000351416:T1257A;ENSP00000332265:T1006A;ENSP00000427151:T1144A	ENSP00000332265:T1006A	T	-	1	0	ANKRD17	74205542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.036000	0.88901	2.227000	0.72691	0.528000	0.53228	ACT		0.423	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	73986678	T	C	73986678	3	2	9	1	0	0	0	0	1	0	0	0	646	1638	57	4	4102	4	ANKRD17	4	73986678	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	18027814	73986678	117167598	37	934										
TACR3	6870	hgsc.bcm.edu	37	chr4	104510879	104510879	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aggtatagggtgagcttatgAaacttgaagtggcggaggca	16	4	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:104510879A>G	ENST00000304883.2	-	5	1498	c.1358T>C	c.(1357-1359)tTc>tCc	p.F453S	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	453					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		TGAGCTTATGAAACTTGAAGT	0.473																																																0			4											123	122	122					4																	104510879		2203	4300	6503	104730328	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1358T>C	4.37:g.104510879A>G	ENSP00000303325:p.Phe453Ser		104730328	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386595	0.82902	.	.	ENSG00000169836	ENST00000304883	T	0.68331	-0.32	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000001	T	0.69708	0.3141	M	0.80847	2.515	0.44843	D	0.997859	B	0.18013	0.025	B	0.12837	0.008	T	0.69764	-0.5057	10	0.87932	D	0	.	15.0511	0.71872	1.0:0.0:0.0:0.0	.	453	P29371	NK3R_HUMAN	S	453	ENSP00000303325:F453S	ENSP00000303325:F453S	F	-	2	0	TACR3	104730328	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	4.786000	0.62425	2.145000	0.66743	0.533000	0.62120	TTC		0.473	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		G	104510879	A	G	104510879	3	3	9	1	0	0	0	0	1	0	0	0	15546	246	9	4	43	4	TACR3	4	104510879	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	30524201	104510879	86643397	38	935										
RRH	10692	hgsc.bcm.edu	37	chr4	110757206	110757206	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tacatcggcttgattctgggAgcctggatcaatggcctgtt	12	9	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:110757206A>G	ENST00000317735.4	+	4	475	c.441A>G	c.(439-441)ggA>ggG	p.G147G		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	147					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		TGATTCTGGGAGCCTGGATCA	0.453																																																0			4											204	186	192					4																	110757206		2203	4300	6503	110976655	SO:0001819	synonymous_variant	10692			AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"GPCR / Class A : Opsin receptors"	10450	protein-coding gene	gene with protein product	"peropsin"	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.441A>G	4.37:g.110757206A>G			110976655	A1A4V2|Q7RTS4	Silent	SNP	ENST00000317735.4	37	CCDS3687.1																																																																																				0.453	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583		G	110757206	A	G	110757206	2	3	9	1	0	0	0	0	0	0	0	1	13717	291	11	4		4	RRH	4	110757206	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	6246327	110757206	80397070	39	936										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153251901	153251901	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	taccttaggagatttgagttCtcctcgcctccagttagtat	8	10	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:153251901C>A	ENST00000281708.4	-	7	2334	c.1105G>T	c.(1105-1107)Gaa>Taa	p.E369*	FBXW7_ENST00000603548.1_Nonsense_Mutation_p.E369*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.E251*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.E369*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.E289*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.E193*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	369					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GATTTGAGTTCTCCTCGCCTC	0.383			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											334	286	302					4																	153251901		2203	4300	6503	153471351	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1105G>T	4.37:g.153251901C>A	ENSP00000281708:p.Glu369*		153471351	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	38	7.067783	0.98040	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	6.07	6.07	0.98685	.	0.042035	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-27.1765	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	369;251;289;193	.	ENSP00000263981:E289X	E	-	1	0	FBXW7	153471351	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.890000	0.99128	0.650000	0.86243	GAA		0.383	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153251901	C	A	153251901	4	1	9	1	0	0	0	0	0	1	0	0	5788	922	32	2	1042	2	FBXW7	4	153251901	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	42494695	153251901	37902375	40	937										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153271206	153271206	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aatattaccttgtatattctGagactttgcatggtttcttt	6	6	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:153271206G>C	ENST00000281708.4	-	3	1801	c.572C>G	c.(571-573)tCa>tGa	p.S191*	FBXW7_ENST00000603548.1_Nonsense_Mutation_p.S191*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.S73*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.S191*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.S111*|FBXW7_ENST00000393956.3_5'Flank	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	191					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)			NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGTATATTCTGAGACTTTGCA	0.294			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	0			4											23	24	23					4																	153271206		2190	4281	6471	153490656	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.572C>G	4.37:g.153271206G>C	ENSP00000281708:p.Ser191*		153490656	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	39	7.784023	0.98486	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981	.	.	.	6.17	6.17	0.99709	.	0.260649	0.39985	N	0.001211	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-13.3727	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	191;73;111	.	ENSP00000263981:S111X	S	-	2	0	FBXW7	153490656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.835000	0.92100	2.941000	0.99782	0.655000	0.94253	TCA		0.294	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153271206	G	C	153271206	4	2	9	1	0	0	0	0	0	1	0	0	5788	1294	45	5	1591	5	FBXW7	4	153271206	Nonsense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	19305	153271206	37883070	41	938										
SNX25	83891	hgsc.bcm.edu	37	chr4	186267728	186267728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aaaagtccagttgccttctcTtagcaagctgcctttcaaat	6	11	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr4:186267728T>C	ENST00000504273.1	+	13	2027	c.1733T>C	c.(1732-1734)cTt>cCt	p.L578P	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Missense_Mutation_p.L578P			Q9H3E2	SNX25_HUMAN	sorting nexin 25	578	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TTGCCTTCTCTTAGCAAGCTG	0.308																																																0			4											61	64	63					4																	186267728		2203	4298	6501	186504722	SO:0001583	missense	83891			AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1733T>C	4.37:g.186267728T>C	ENSP00000426255:p.Leu578Pro		186504722	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.851787	0.71719	.	.	ENSG00000109762	ENST00000504273;ENST00000264694;ENST00000264693	T;T	0.38240	1.15;1.15	5.43	5.43	0.79202	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.50922	0.1644	L	0.39245	1.2	0.80722	D	1	D;B;D	0.89917	1.0;0.45;1.0	D;B;D	0.97110	0.993;0.325;1.0	T	0.42548	-0.9445	10	0.33940	T	0.23	-14.4644	15.7735	0.78190	0.0:0.0:0.0:1.0	.	349;111;578	Q8N6K3;Q9H5Q8;Q9H3E2	.;.;SNX25_HUMAN	P	578;578;111	ENSP00000426255:L578P;ENSP00000264694:L578P	ENSP00000264693:L111P	L	+	2	0	SNX25	186504722	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.379000	0.79691	2.190000	0.69967	0.533000	0.62120	CTT		0.308	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		C	186267728	T	C	186267728	3	2	9	1	0	0	0	0	1	0	0	0	14933	1609	56	4	1779	4	SNX25	4	186267728	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	32996522	186267728	4886548	42	939										
RANBP3L	202151	hgsc.bcm.edu	37	chr5	36265126	36265126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtgtccaaatgtttttcttaCttttgcacaacttcgagctt	6	9	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr5:36265126C>T	ENST00000296604.3	-	6	900	c.415G>A	c.(415-417)Gta>Ata	p.V139I	RANBP3L_ENST00000515759.1_Missense_Mutation_p.V139I|RANBP3L_ENST00000502994.1_Missense_Mutation_p.V164I	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	139					intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GTTTTTCTTACTTTTGCACAA	0.358																																																0			5											147	151	149					5																	36265126		2203	4300	6503	36300883	SO:0001583	missense	202151			BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.415G>A	5.37:g.36265126C>T	ENSP00000296604:p.Val139Ile		36300883	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	37	CCDS3918.1	.	.	.	.	.	.	.	.	.	.	C	7.083	0.570688	0.13560	.	.	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759	T;T;T	0.23950	1.88;1.91;1.9	5.26	0.258	0.15578	.	1.075670	0.07187	N	0.854992	T	0.20618	0.0496	L	0.54323	1.7	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33292	-0.9874	10	0.22706	T	0.39	0.4999	3.0973	0.06314	0.3244:0.4117:0.0:0.2639	.	164;139	E9PGP9;Q86VV4	.;RNB3L_HUMAN	I	139;164;139	ENSP00000296604:V139I;ENSP00000421853:V164I;ENSP00000421149:V139I	ENSP00000296604:V139I	V	-	1	0	RANBP3L	36300883	0.002000	0.14202	0.003000	0.11579	0.508000	0.34012	-0.521000	0.06245	0.104000	0.17725	-0.188000	0.12872	GTA		0.358	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		T	36265126	C	T	36265126	3	4	9	1	0	0	0	0	1	0	0	0	13067	565	20	3	1018	3	RANBP3L	5	36265126	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		36265126	144650134	43	940										
RNF180	285671	hgsc.bcm.edu	37	chr5	63510221	63510221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gagcacctctcccctctggaCttcctgcactcagccaattt	6	17	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr5:63510221C>A	ENST00000389100.4	+	4	1140	c.1068C>A	c.(1066-1068)gaC>gaA	p.D356E	RNF180_ENST00000381081.2_Intron|RNF180_ENST00000296615.6_Missense_Mutation_p.D356E	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	356	Interaction with ZIC2. {ECO:0000250}.				adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		CCCCTCTGGACTTCCTGCACT	0.483																																																0			5											66	69	68					5																	63510221		2203	4300	6503	63545977	SO:0001583	missense	285671			AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"RING-type (C3HC4) zinc fingers"	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.1068C>A	5.37:g.63510221C>A	ENSP00000373752:p.Asp356Glu		63545977	Q0JSU3|Q495A8|Q8NBD1	Missense_Mutation	SNP	ENST00000389100.4	37	CCDS47219.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.080981	0.36758	.	.	ENSG00000164197	ENST00000296615;ENST00000389100	T	0.46063	0.88	5.85	3.83	0.44106	.	0.575312	0.19383	N	0.115619	T	0.30135	0.0755	L	0.56769	1.78	0.80722	D	1	B;P	0.38504	0.361;0.634	B;B	0.31101	0.115;0.124	T	0.26815	-1.0092	10	0.49607	T	0.09	-6.2583	2.5139	0.04663	0.2346:0.4876:0.0:0.2778	.	356;356	Q86T96;Q86T96-2	RN180_HUMAN;.	E	356	ENSP00000373752:D356E	ENSP00000296615:D356E	D	+	3	2	RNF180	63545977	0.995000	0.38212	1.000000	0.80357	0.948000	0.59901	0.598000	0.24074	1.472000	0.48140	0.650000	0.86243	GAC		0.483	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		A	63510221	C	A	63510221	3	1	9	1	0	0	0	0	1	0	0	0	13501	564	20	2	1078	2	RNF180	5	63510221	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	27245095	63510221	117405039	44	941										
APC	324	hgsc.bcm.edu	37	chr5	112175480	112175480	+	Nonsense_Mutation	SNP	G	G	T													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tcagttcacttgatagttttGagagtcgttcgattgccagc							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr5:112175480G>T	ENST00000457016.1	+	16	4569	c.4189G>T	c.(4189-4191)Gag>Tag	p.E1397*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1397*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1397*			P25054	APC_HUMAN	adenomatous polyposis coli	1397	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1399fs*9(18)|p.E1397*(8)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.E1397fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATAGTTTTGAGAGTCGTTC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Deletion - Frameshift(20)|Substitution - Nonsense(8)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(28)|soft_tissue(1)|skin(1)	5	GRCh37	CM992136	APC	M							104	98	100					5																	112175480		2202	4300	6502	112203379	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4189G>T	5.37:g.112175480G>T	ENSP00000413133:p.Glu1397*		112203379	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	41	8.742411	0.98937	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.111909	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.9405	20.4898	0.99202	0.0:0.0:1.0:0.0	.	.	.	.	X	1397	.	.	E	+	1	0	APC	112203379	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.281000	0.78621	2.941000	0.99782	0.655000	0.94253	GAG		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175480	G	T	112175480	4	4	9	1	0	0	0	0	0	1	0	0	763	1291	45	2	4247	2	APC	5	112175480	Nonsense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	48665259	112175480	68739780	45	942	4	2								
APC	324	hgsc.bcm.edu	37	chr5	112175483	112175483	+	Missense_Mutation	SNP	A	A	T													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gttcacttgatagttttgagAgtcgttcgattgccagctcc							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr5:112175483A>T	ENST00000457016.1	+	16	4572	c.4192A>T	c.(4192-4194)Agt>Tgt	p.S1398C	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1398C|APC_ENST00000508376.2_Missense_Mutation_p.S1398C			P25054	APC_HUMAN	adenomatous polyposis coli	1398	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1399fs*9(10)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGTTTTGAGAGTCGTTCGAT	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	13	Deletion - Frameshift(12)|Unknown(1)	large_intestine(11)|soft_tissue(1)|skin(1)	5	GRCh37	CD054298	APC	D							108	101	103					5																	112175483		2202	4300	6502	112203382	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4192A>T	5.37:g.112175483A>T	ENSP00000413133:p.Ser1398Cys		112203382	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.571877	0.65765	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90385	-2.66;-2.66;-2.66	6.17	6.17	0.99709	.	0.083847	0.85682	D	0.000000	D	0.93400	0.7895	L	0.55990	1.75	0.49915	D	0.999837	D;D	0.76494	0.999;0.999	D;D	0.64042	0.921;0.921	D	0.92710	0.6182	9	.	.	.	-20.8522	16.4957	0.84242	1.0:0.0:0.0:0.0	.	1400;1398	Q4LE70;P25054	.;APC_HUMAN	C	1398	ENSP00000413133:S1398C;ENSP00000257430:S1398C;ENSP00000427089:S1398C	.	S	+	1	0	APC	112203382	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.853000	0.69496	2.371000	0.80710	0.533000	0.62120	AGT		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175483	A	T	112175483	3	4	9	1	0	0	0	0	1	0	0	0	763	304	11	5	4250	5	APC	5	112175483	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	3	112175483	68739777	46	943	4	2								
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257074	140257074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tggtgtcgctggtggagaacGgccaggccccaaagacgtcg	16	11	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr5:140257074G>A	ENST00000398631.2	+	1	2017	c.2017G>A	c.(2017-2019)Ggc>Agc	p.G673S	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	673	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGAGAACGGCCAGGCCCC	0.672																																					Pancreas(113;759 1672 13322 24104 50104)											0			5											46	50	49					5																	140257074		2203	4298	6501	140237258	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.2017G>A	5.37:g.140257074G>A	ENSP00000381628:p.Gly673Ser		140237258	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.003103	0.35320	.	.	ENSG00000251664	ENST00000398631	T	0.48522	0.81	4.94	0.6	0.17524	Cadherin (3);	.	.	.	.	T	0.25717	0.0626	N	0.21240	0.645	0.09310	N	1	B;B	0.32302	0.363;0.106	B;B	0.18561	0.022;0.01	T	0.12915	-1.0529	9	0.17369	T	0.5	.	8.2282	0.31582	0.3619:0.0:0.6381:0.0	.	673;673	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	S	673	ENSP00000381628:G673S	ENSP00000381628:G673S	G	+	1	0	PCDHA12	140237258	0.008000	0.16893	0.001000	0.08648	0.037000	0.13140	0.923000	0.28757	-0.211000	0.10124	0.655000	0.94253	GGC		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140257074	G	A	140257074	3	1	9	1	0	0	0	0	1	0	0	0	11553	1116	39	1	2019	1	PCDHA12	5	140257074	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	28081591	140257074	40658186	47	944										
GPX5	2880	hgsc.bcm.edu	37	chr6	28501867	28501867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctgatggaatccctgtcatgCgctggtcccaccgggctacg	12	14	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:28501867C>T	ENST00000412168.2	+	5	678	c.589C>T	c.(589-591)Cgc>Tgc	p.R197C	GPX5_ENST00000442674.2_3'UTR	NM_001509.2	NP_001500.1	O75715	GPX5_HUMAN	glutathione peroxidase 5 (epididymal androgen-related protein)	197					lipid metabolic process (GO:0006629)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)			endometrium(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16					Glutathione(DB00143)	CCCTGTCATGCGCTGGTCCCA	0.512																																																0			6											87	88	88					6																	28501867		2203	4300	6503	28609846	SO:0001583	missense	2880			AJ005277	CCDS4652.1, CCDS4653.1	6p22.1	2008-02-05			ENSG00000224586	ENSG00000224586	1.11.1.9		4557	protein-coding gene	gene with protein product		603435				9639555	Standard	NM_001509		Approved		uc003nll.2	O75715	OTTHUMG00000016307	ENST00000412168.2:c.589C>T	6.37:g.28501867C>T	ENSP00000392398:p.Arg197Cys		28609846	A1A4Y0	Missense_Mutation	SNP	ENST00000412168.2	37	CCDS4652.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975619	0.74360	.	.	ENSG00000224586	ENST00000412168	T	0.05199	3.48	4.52	3.66	0.41972	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.27773	-1.0064	10	0.87932	D	0	-11.5047	11.2343	0.48931	0.0:0.91:0.0:0.09	.	197	O75715	GPX5_HUMAN	C	197	ENSP00000392398:R197C	ENSP00000392398:R197C	R	+	1	0	GPX5	28609846	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.253000	0.43205	1.504000	0.48704	0.655000	0.94253	CGC		0.512	GPX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043672.2			T	28501867	C	T	28501867	3	4	9	1	0	0	0	0	1	0	0	0	6764	768	27	1	607	1	GPX5	6	28501867	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		28501867	142613200	48	945										
UBD	10537	hgsc.bcm.edu	37	chr6	29523787	29523787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gggtctcagggattatacccGtcttagtctcgatcattgct	10	10	4	0	rs149806360	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:29523787G>A	ENST00000377050.4	-	2	591	c.368C>T	c.(367-369)aCg>aTg	p.T123M	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	123	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GATTATACCCGTCTTAGTCTC	0.493													G|||	2	0.000399361	0.0015	0	5008	,	,		20835	0		0	False		,,,				2504	0															0			6						G	MET/THR	7,3015		0,7,1504	162	133	143		368	5.2	0.6	6	dbSNP_134	143	2,5416		0,2,2707	yes	missense	UBD	NM_006398.3	81	0,9,4211	AA,AG,GG		0.0369,0.2316,0.1066	probably-damaging	123/166	29523787	9,8431	1511	2709	4220	29631766	SO:0001583	missense	10537			Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.368C>T	6.37:g.29523787G>A	ENSP00000366249:p.Thr123Met		29631766	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	37	CCDS4662.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152367	0.38021	0.002316	3.69E-4	ENSG00000213886	ENST00000377050	T	0.75260	-0.92	5.17	5.17	0.71159	Ubiquitin supergroup (1);Ubiquitin (2);	0.213437	0.23060	U	0.052395	T	0.79890	0.4524	M	0.65975	2.015	0.80722	D	1	D	0.71674	0.998	P	0.62740	0.906	T	0.82522	-0.0415	10	0.87932	D	0	-14.0727	14.1737	0.65527	0.0:0.0:1.0:0.0	.	123	O15205	UBD_HUMAN	M	123	ENSP00000366249:T123M	ENSP00000366249:T123M	T	-	2	0	UBD	29631766	0.151000	0.22747	0.552000	0.28243	0.045000	0.14185	2.670000	0.46833	2.390000	0.81377	0.609000	0.83330	ACG		0.493	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3			A	29523787	G	A	29523787	3	1	9	1	0	0	0	0	1	0	0	0	16883	1145	40	1	133	1	UBD	6	29523787	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1021920	29523787	141591280	49	946										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29576386	29576386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccacctcctcacctggcagaCgaaaggaaactggttcctcc	8	16	1	1	rs138809665		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:29576386C>T	ENST00000377034.4	-	16	2319	c.1984G>A	c.(1984-1986)Gtc>Atc	p.V662I	GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000377016.4_Missense_Mutation_p.V600I|GABBR1_ENST00000377012.4_Missense_Mutation_p.V545I|GABBR1_ENST00000355973.3_Missense_Mutation_p.V545I	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	662					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	ACCTGGCAGACGAAAGGAAAC	0.547																																																0			6						C	ILE/VAL,ILE/VAL,ILE/VAL	0,3022		0,0,1511	93	80	85		1984,1633,1798	4.6	1	6	dbSNP_134	85	1,5415		0,1,2707	no	missense,missense,missense	GABBR1	NM_001470.2,NM_021903.2,NM_021904.2	29,29,29	0,1,4218	TT,TC,CC		0.0185,0.0,0.0119	benign,benign,benign	662/962,545/845,600/900	29576386	1,8437	1511	2708	4219	29684365	SO:0001583	missense	10537			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1984G>A	6.37:g.29576386C>T	ENSP00000366233:p.Val662Ile		29684365	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.931|8.931	0.963426|0.963426	0.18583|0.18583	0.0|0.0	1.85E-4|1.85E-4	ENSG00000204681|ENSG00000204681	ENST00000485026|ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	.|D;D;D;D	.|0.88431	.|-2.38;-2.38;-2.38;-2.38	4.62|4.62	4.62|4.62	0.57501|0.57501	.|GPCR, family 3, C-terminal (2);	.|0.133902	.|0.49305	.|D	.|0.000157	T|T	0.55673|0.55673	0.1935|0.1935	N|N	0.10782|0.10782	0.045|0.045	0.80722|0.80722	D|D	1|1	.|B;P;B	.|0.40083	.|0.398;0.702;0.06	.|B;B;B	.|0.28638	.|0.035;0.092;0.04	T|T	0.71649|0.71649	-0.4529|-0.4529	5|10	.|0.02654	.|T	.|1	-10.4966|-10.4966	12.8253|12.8253	0.57716|0.57716	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|600;662;545	.|Q9UBS5-3;Q9UBS5;Q5SUJ9	.|.;GABR1_HUMAN;.	H|I	42|545;600;545;662	.|ENSP00000348248:V545I;ENSP00000366215:V600I;ENSP00000366211:V545I;ENSP00000366233:V662I	.|ENSP00000348248:V545I	R|V	-|-	2|1	0|0	GABBR1|GABBR1	29684365|29684365	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.928000|0.928000	0.56348|0.56348	3.371000|3.371000	0.52379|0.52379	2.391000|2.391000	0.81399|0.81399	0.557000|0.557000	0.71058|0.71058	CGT|GTC		0.547	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29576386	C	T	29576386	3	4	9	1	0	0	0	0	1	0	0	0	6174	536	19	1	933	1	GABBR1	6	29576386	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	52599	29576386	141538681	50	947										
SPACA1	81833	hgsc.bcm.edu	37	chr6	88763681	88763681	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tagtttcaaataggaatgtcGtcaaagaagtagaattcgga	10	4	2	2	rs373094172		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:88763681G>A	ENST00000237201.1	+	2	343	c.226G>A	c.(226-228)Gtc>Atc	p.V76I		NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	76					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		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;0.11)		TAGGAATGTCGTCAAAGAAGT	0.348																																																0			6						G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	87	85	86		226	1.9	0.4	6		86	0,8600		0,0,4300	no	missense	SPACA1	NM_030960.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	76/295	88763681	1,13005	2203	4300	6503	88820400	SO:0001583	missense	81833			AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.226G>A	6.37:g.88763681G>A	ENSP00000237201:p.Val76Ile		88820400		Missense_Mutation	SNP	ENST00000237201.1	37	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.341902	0.24339	2.27E-4	0.0	ENSG00000118434	ENST00000237201	T	0.21734	1.99	5.97	1.93	0.25924	.	0.811387	0.10979	N	0.612887	T	0.06462	0.0166	M	0.65975	2.015	0.09310	N	1	B	0.33494	0.414	B	0.21360	0.034	T	0.35325	-0.9793	10	0.56958	D	0.05	-6.9977	1.9497	0.03364	0.1539:0.1154:0.3434:0.3873	.	76	Q9HBV2	SACA1_HUMAN	I	76	ENSP00000237201:V76I	ENSP00000237201:V76I	V	+	1	0	SPACA1	88820400	0.792000	0.28813	0.363000	0.25875	0.182000	0.23217	0.669000	0.25142	0.388000	0.25054	0.650000	0.86243	GTC		0.348	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88763681	G	A	88763681	3	1	9	1	0	0	0	0	1	0	0	0	15009	1145	40	1	232	1	SPACA1	6	88763681	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	59187295	88763681	82351386	51	948										
GJA10	84694	hgsc.bcm.edu	37	chr6	90604409	90604409	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gatgcattccctatctctttGatcaggttctgggttttaca	8	9	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:90604409G>T	ENST00000369352.1	+	1	222	c.222G>T	c.(220-222)ttG>ttT	p.L74F		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	74					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		CTATCTCTTTGATCAGGTTCT	0.463																																																0			6											151	119	130					6																	90604409		2203	4300	6503	90661130	SO:0001583	missense	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.222G>T	6.37:g.90604409G>T	ENSP00000358358:p.Leu74Phe		90661130	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659346	0.47467	.	.	ENSG00000135355	ENST00000369352	D	0.99089	-5.41	4.8	3.93	0.45458	Connexin, N-terminal (2);	0.000000	0.64402	D	0.000002	D	0.98592	0.9529	M	0.71581	2.175	0.42198	D	0.991751	D	0.89917	1.0	D	0.97110	1.0	D	0.98239	1.0487	10	0.37606	T	0.19	.	8.2989	0.32001	0.0788:0.0:0.7672:0.1539	.	74	Q969M2	CXA10_HUMAN	F	74	ENSP00000358358:L74F	ENSP00000358358:L74F	L	+	3	2	GJA10	90661130	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.180000	0.42537	1.259000	0.44117	0.563000	0.77884	TTG		0.463	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90604409	G	T	90604409	3	4	9	1	0	0	0	0	1	0	0	0	6421	1281	45	2	224	2	GJA10	6	90604409	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1840728	90604409	80510658	52	949										
POPDC3	64208	hgsc.bcm.edu	37	chr6	105609486	105609486	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctcgggcaaaggttatgctgCgaacttgatatgcaatatga	11	7	0	2	rs202226180		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:105609486C>A	ENST00000254765.3	-	2	577	c.299G>T	c.(298-300)cGc>cTc	p.R100L	BVES-AS1_ENST00000580511.1_RNA|POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000369120.2_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	100					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)				NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				GGTTATGCTGCGAACTTGATA	0.448																																																0			6											169	181	177					6																	105609486		2203	4300	6503	105716179	SO:0001583	missense	64208			BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.299G>T	6.37:g.105609486C>A	ENSP00000254765:p.Arg100Leu		105716179	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	37	CCDS5052.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.779357	0.49891	.	.	ENSG00000132429	ENST00000254765	T	0.41065	1.01	5.72	-1.73	0.08081	.	0.263445	0.40469	N	0.001081	T	0.28200	0.0696	M	0.81112	2.525	0.48395	D	0.999643	B	0.31193	0.312	B	0.35114	0.196	T	0.18398	-1.0338	10	0.51188	T	0.08	-18.9645	10.9808	0.47492	0.0:0.5467:0.0:0.4533	.	100	Q9HBV1	POPD3_HUMAN	L	100	ENSP00000254765:R100L	ENSP00000254765:R100L	R	-	2	0	POPDC3	105716179	1.000000	0.71417	0.934000	0.37439	0.987000	0.75469	1.570000	0.36439	-0.737000	0.04824	-0.302000	0.09304	CGC		0.448	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361		A	105609486	C	A	105609486	3	1	9	1	0	0	0	0	1	0	0	0	12287	768	27	2	588	2	POPDC3	6	105609486	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	15005077	105609486	65505581	53	950										
ROS1	6098	hgsc.bcm.edu	37	chr6	117645564	117645564	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aagtatgaaacttgtttctgGtatccaaaaatcatctaata	5	6	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:117645564G>T	ENST00000368508.3	-	34	5770	c.5572C>A	c.(5572-5574)Cca>Aca	p.P1858T	ROS1_ENST00000368507.3_Missense_Mutation_p.P1852T|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1858					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CTTGTTTCTGGTATCCAAAAA	0.294			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	0			6											36	39	38					6																	117645564		2199	4282	6481	117752257	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.5572C>A	6.37:g.117645564G>T	ENSP00000357494:p.Pro1858Thr		117752257	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	3.590	-0.083761	0.07141	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70869	-0.51;-0.52	5.41	1.5	0.22942	.	0.215706	0.32473	N	0.006051	T	0.20373	0.0490	N	0.12182	0.205	0.80722	D	1	B	0.13145	0.007	B	0.12156	0.007	T	0.13150	-1.0520	10	0.09590	T	0.72	.	2.383	0.04358	0.1695:0.1429:0.5301:0.1574	.	1858	P08922	ROS1_HUMAN	T	1858;1852	ENSP00000357494:P1858T;ENSP00000357493:P1852T	ENSP00000357493:P1852T	P	-	1	0	ROS1	117752257	0.996000	0.38824	0.975000	0.42487	0.995000	0.86356	1.257000	0.32932	0.049000	0.15920	0.650000	0.86243	CCA		0.294	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			T	117645564	G	T	117645564	3	4	9	1	0	0	0	0	1	0	0	0	13568	1261	44	2	1511	2	ROS1	6	117645564	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	12036078	117645564	53469503	54	951										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119324168	119324168	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cattgctgacttcttatcctCttcatgttgaagccttaact	5	11	3	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:119324168C>T	ENST00000338891.7	-	9	2427	c.1984G>A	c.(1984-1986)Gag>Aag	p.E662K	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Missense_Mutation_p.E542K|FAM184A_ENST00000352896.5_Missense_Mutation_p.E542K|FAM184A_ENST00000521531.1_Missense_Mutation_p.E662K	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	662						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TTCTTATCCTCTTCATGTTGA	0.348																																																0			6											125	117	119					6																	119324168		1855	4097	5952	119365867	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1984G>A	6.37:g.119324168C>T	ENSP00000342604:p.Glu662Lys		119365867	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	35	5.457285	0.96223	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.97	5.97	0.96955	.	0.052158	0.85682	D	0.000000	T	0.45617	0.1351	L	0.48362	1.52	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.80764	0.991;0.994;0.994	T	0.04065	-1.0980	10	0.21014	T	0.42	-18.3092	20.4238	0.99064	0.0:1.0:0.0:0.0	.	662;542;662	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	K	662;542;542;662	ENSP00000342604:E662K;ENSP00000326608:E542K;ENSP00000357460:E542K;ENSP00000430442:E662K	ENSP00000342604:E662K	E	-	1	0	FAM184A	119365867	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.467000	0.73547	2.834000	0.97654	0.650000	0.86243	GAG		0.348	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119324168	C	T	119324168	3	4	9	1	0	0	0	0	1	0	0	0	5527	922	32	3	1478	3	FAM184A	6	119324168	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1678604	119324168	51790899	55	952										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151672397	151672397	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	actgaacctctgccagagaaCagagaggcccggggcgacac	13	13	1	3	rs377313534		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:151672397C>A	ENST00000253332.1	+	3	3060	c.2871C>A	c.(2869-2871)aaC>aaA	p.N957K	AKAP12_ENST00000359755.5_Missense_Mutation_p.N852K|AKAP12_ENST00000354675.6_Missense_Mutation_p.N859K|AKAP12_ENST00000402676.2_Missense_Mutation_p.N957K			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	957					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		TGCCAGAGAACAGAGAGGCCC	0.542																																					Melanoma(141;1616 1805 10049 24534 51979)											0			6						C	LYS/ASN,LYS/ASN	0,4406		0,0,2203	54	60	58		2871,2577	-0.7	0	6		58	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AKAP12	NM_005100.3,NM_144497.2	94,94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	957/1783,859/1685	151672397	1,13005	2203	4300	6503	151714090	SO:0001583	missense	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2871C>A	6.37:g.151672397C>A	ENSP00000253332:p.Asn957Lys		151714090	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	C	6.636	0.485830	0.12641	0.0	1.16E-4	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06068	3.35;3.35;3.36;3.36	5.06	-0.709	0.11237	.	1.377270	0.04726	N	0.420302	T	0.00815	0.0027	N	0.22421	0.69	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.38628	-0.9652	10	0.06236	T	0.91	.	0.3306	0.00317	0.2018:0.3041:0.2084:0.2857	.	852;859;957	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	K	957;957;859;852	ENSP00000384537:N957K;ENSP00000253332:N957K;ENSP00000346702:N859K;ENSP00000352794:N852K	ENSP00000253332:N957K	N	+	3	2	AKAP12	151714090	0.000000	0.05858	0.014000	0.15608	0.169000	0.22640	0.150000	0.16263	0.111000	0.17947	0.462000	0.41574	AAC		0.542	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			A	151672397	C	A	151672397	3	1	9	1	0	0	0	0	1	0	0	0	448	477	17	2	2910	2	AKAP12	6	151672397	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	32348229	151672397	19442670	56	953										
TCP1	6950	hgsc.bcm.edu	37	chr6	160206464	160206464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgtcttagcagcattaatcaGgcaatctcttcccagttcat	6	11	4	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:160206464G>A	ENST00000321394.7	-	5	722	c.442C>T	c.(442-444)Ctg>Ttg	p.L148L	TCP1_ENST00000392168.2_5'UTR|TCP1_ENST00000544255.1_Intron|TCP1_ENST00000420894.2_Silent_p.L148L|SNORA29_ENST00000384183.1_RNA	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	148					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		GCATTAATCAGGCAATCTCTT	0.353																																																0			6											196	172	180					6																	160206464		2203	4300	6503	160126454	SO:0001819	synonymous_variant	6950			X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"Heat Shock Proteins / Chaperonins"	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.442C>T	6.37:g.160206464G>A			160126454	E1P5B2|Q15556|Q5TCM3	Silent	SNP	ENST00000321394.7	37	CCDS5269.1																																																																																				0.353	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		A	160206464	G	A	160206464	2	1	9	1	0	0	0	0	0	0	0	1	15748	991	35	3		3	TCP1	6	160206464	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	8534067	160206464	10908603	57	954										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161510473	161510473	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gagcagacatccagtcagccGgtcatcgccaaagctttgca	10	13	2	1	rs368962247		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr6:161510473G>A	ENST00000392142.4	+	11	3091	c.2943G>A	c.(2941-2943)ccG>ccA	p.P981P	MAP3K4_ENST00000366920.2_Silent_p.P981P|MAP3K4_ENST00000348824.7_Silent_p.P981P|MAP3K4_ENST00000366919.2_Silent_p.P981P	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	981					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CCAGTCAGCCGGTCATCGCCA	0.463																																																0			6											131	131	131					6																	161510473		2203	4300	6503	161430463	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2943G>A	6.37:g.161510473G>A			161430463	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.463	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161510473	G	A	161510473	2	1	9	1	0	0	0	0	0	0	0	1	9282	1103	39	1		1	MAP3K4	6	161510473	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1304009	161510473	9604594	58	955										
CARD11	84433	hgsc.bcm.edu	37	chr7	2962846	2962846	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cgagtgcacgaagctccctcGcgcgttgccccccagcaggg	13	17	0	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:2962846G>A	ENST00000396946.4	-	16	2465	c.2062C>T	c.(2062-2064)Cga>Tga	p.R688*		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	688	PDZ.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		AAGCTCCCTCGCGCGTTGCCC	0.701			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	0			7											42	43	43					7																	2962846		2203	4298	6501	2929372	SO:0001587	stop_gained	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2062C>T	7.37:g.2962846G>A	ENSP00000380150:p.Arg688*		2929372	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	42	9.286587	0.99125	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	.	.	.	4.89	0.535	0.17133	.	0.309163	0.33217	N	0.005142	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-4.3815	7.4554	0.27264	0.0861:0.0:0.3307:0.5832	.	.	.	.	X	688;159	.	ENSP00000347695:R159X	R	-	1	2	CARD11	2929372	0.769000	0.28531	0.000000	0.03702	0.409000	0.31022	1.841000	0.39240	0.090000	0.17273	0.555000	0.69702	CGA		0.701	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2962846	G	A	2962846	4	1	9	1	0	0	0	0	0	1	0	0	2651	1095	38	1	1442	1	CARD11	7	2962846	Nonsense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		2962846	156175817	59	956										
RSPH10B	728194	hgsc.bcm.edu	37	chr7	6805370	6805370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	acaatcaagagggtacgtgtTggtacgagggagactgggta	16	5	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:6805370T>C	ENST00000403107.1	+	6	994	c.607T>C	c.(607-609)Tgg>Cgg	p.W203R	RSPH10B2_ENST00000359718.3_5'UTR|RSPH10B2_ENST00000463354.2_Intron|RSPH10B2_ENST00000433859.2_Missense_Mutation_p.W203R|RSPH10B2_ENST00000297186.3_Missense_Mutation_p.W203R|RSPH10B2_ENST00000404077.1_Missense_Mutation_p.W203R			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)	203										breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						GGGTACGTGTTGGTACGAGGG	0.428																																																0			7											26	33	31					7																	6805370		1993	4133	6126	6771895	SO:0001583	missense	728194				CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	ENST00000403107.1:c.607T>C	7.37:g.6805370T>C	ENSP00000384766:p.Trp203Arg		6771895	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000403107.1	37	CCDS43552.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298889	0.60195	.	.	ENSG00000169402	ENST00000403107;ENST00000404077;ENST00000297186;ENST00000433859;ENST00000540958	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	3.71	3.71	0.42584	.	0.068657	0.64402	D	0.000007	T	0.30008	0.0751	N	0.02802	-0.49	0.80722	D	1	D	0.67145	0.996	P	0.55667	0.781	T	0.25433	-1.0132	10	0.42905	T	0.14	.	10.5492	0.45079	0.0:0.0:0.0:1.0	.	203	B2RC85	R10B2_HUMAN	R	203;203;203;203;62	ENSP00000384766:W203R;ENSP00000386102:W203R;ENSP00000297186:W203R;ENSP00000416710:W203R	ENSP00000297186:W203R	W	+	1	0	RSPH10B2	6771895	1.000000	0.71417	0.798000	0.32154	0.816000	0.46133	7.049000	0.76613	1.563000	0.49615	0.314000	0.21332	TGG		0.428	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697		C	6805370	T	C	6805370	3	2	9	1	0	0	0	0	1	0	0	0	13740	1812	63	4	3314	4	RSPH10B	7	6805370	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	3842524	6805370	152333293	60	957										
PSPH	5723	hgsc.bcm.edu	37	chr7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cctcagctctgagtgggagaCcatcgctggaagaattttcc	11	11	2	3	rs77329757	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:56088902C>T	ENST00000395471.3	-	4	809	c.4G>A	c.(4-6)Gtc>Atc	p.V2I	PSPH_ENST00000275605.3_Missense_Mutation_p.V2I|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	2				V -> I (in Ref. 1; CAA71318). {ECO:0000305}.	cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAGTGGGAGACCATCGCTGGA	0.403																																																0			7											59	49	53					7																	56088902		2203	4300	6503	56056396	SO:0001583	missense	5723			Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.4G>A	7.37:g.56088902C>T	ENSP00000378854:p.Val2Ile		56056396	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870338	0.33069	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312;ENST00000424596;ENST00000413218;ENST00000416592	D;D;D;T;T	0.82619	-1.63;-1.63;-1.63;-1.11;-1.11	5.5	4.62	0.57501	.	0.498508	0.22451	N	0.059892	T	0.76586	0.4008	L	0.43152	1.355	0.25991	N	0.982243	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.004	T	0.62821	-0.6773	10	0.26408	T	0.33	-18.3475	13.3091	0.60370	0.0:0.9237:0.0:0.0763	.	2;2	Q53EY1;P78330	.;SERB_HUMAN	I	2	ENSP00000275605:V2I;ENSP00000378854:V2I;ENSP00000398653:V2I;ENSP00000399660:V2I;ENSP00000390952:V2I	ENSP00000275605:V2I	V	-	1	0	PSPH	56056396	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	1.602000	0.36783	1.325000	0.45301	0.591000	0.81541	GTC		0.403	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577		T	56088902	C	T	56088902	3	4	9	1	0	0	0	0	1	0	0	0	12751	507	18	3	693	3	PSPH	7	56088902	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	49283532	56088902	103049761	61	958										
ZNF138	7697	hgsc.bcm.edu	37	chr7	64292097	64292097	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aattcaaatagacacaagatAagacatactgaaaataaaca	4	6	1	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:64292097A>C	ENST00000359735.3	+	4	653	c.306A>C	c.(304-306)atA>atC	p.I102I	ZNF138_ENST00000440155.2_Silent_p.I133I|ZNF138_ENST00000430838.2_3'UTR|ZNF138_ENST00000397136.2_Silent_p.I102I|ZNF138_ENST00000307355.7_Silent_p.I159I|ZNF138_ENST00000494380.1_3'UTR|ZNF138_ENST00000440598.1_3'UTR|ZNF138_ENST00000437743.1_Silent_p.I127I	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138	102					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				GACACAAGATAAGACATACTG	0.274																																																0			7											41	43	42					7																	64292097		2202	4294	6496	63929532	SO:0001819	synonymous_variant	7697			U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"Zinc fingers, C2H2-type", "-"	12922	protein-coding gene	gene with protein product		604080	"zinc finger protein 138 (clone pHZ-32)"				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.306A>C	7.37:g.64292097A>C			63929532	B4DFX2|B4DP87|E9PHI7|E9PHK7	Silent	SNP	ENST00000359735.3	37																																																																																					0.274	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524		C	64292097	A	C	64292097	2	2	9	1	0	0	0	0	0	0	0	1	17766	352	13	4		4	ZNF138	7	64292097	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	8203195	64292097	94846566	62	959										
RHBDD2	57414	hgsc.bcm.edu	37	chr7	75511480	75511480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agtcctggttccgtggctccTgctgggtgcctcgtggctca	14	13	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:75511480T>C	ENST00000006777.6	+	2	647	c.512T>C	c.(511-513)cTg>cCg	p.L171P	RHBDD2_ENST00000318622.4_Missense_Mutation_p.L30P|RHBDD2_ENST00000468304.1_Intron|RHBDD2_ENST00000428119.1_Missense_Mutation_p.L30P	NM_001040456.1	NP_001035546.1	Q6NTF9	RHBD2_HUMAN	rhomboid domain containing 2	171						Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|lung(4)|prostate(1)	6						CCGTGGCTCCTGCTGGGTGCC	0.607																																																0			7											53	55	54					7																	75511480		2117	4237	6354	75349416	SO:0001583	missense	57414			AF226732	CCDS43602.1, CCDS43603.1	7q11	2008-09-04	2006-02-22	2006-02-22	ENSG00000005486	ENSG00000005486			23082	protein-coding gene	gene with protein product		615203	"rhomboid, veinlet-like 7 (Drosophila)"	RHBDL7		12838346	Standard	XM_005250511		Approved	NPD007	uc003udw.1	Q6NTF9	OTTHUMG00000156435	ENST00000006777.6:c.512T>C	7.37:g.75511480T>C	ENSP00000006777:p.Leu171Pro		75349416	Q7L534|Q9H5W6|Q9HBK7|Q9UDT2	Missense_Mutation	SNP	ENST00000006777.6	37	CCDS43602.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.386247	0.61956	.	.	ENSG00000005486	ENST00000006777;ENST00000413229;ENST00000318622;ENST00000428119	T;T;T	0.13538	2.58;2.58;2.58	5.51	5.51	0.81932	Peptidase S54, rhomboid domain (1);	0.334072	0.25135	N	0.032871	T	0.28764	0.0713	L	0.42245	1.32	0.58432	D	0.999997	D	0.89917	1.0	D	0.77004	0.989	T	0.01330	-1.1383	10	0.87932	D	0	-8.0455	12.0282	0.53384	0.0:0.0:0.1438:0.8562	.	171	Q6NTF9	RHBD2_HUMAN	P	171;216;30;30	ENSP00000006777:L171P;ENSP00000314144:L30P;ENSP00000391232:L30P	ENSP00000006777:L171P	L	+	2	0	RHBDD2	75349416	0.998000	0.40836	0.994000	0.49952	0.526000	0.34562	3.705000	0.54823	2.093000	0.63338	0.528000	0.53228	CTG		0.607	RHBDD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344176.1	NM_020684		C	75511480	T	C	75511480	3	2	9	1	0	0	0	0	1	0	0	0	13354	1580	55	4	518	4	RHBDD2	7	75511480	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	11219383	75511480	83627183	63	960										
PEX1	5189	hgsc.bcm.edu	37	chr7	92123679	92123679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agggcagggtcaatcaagtcAgggcgactagtagcagccaa	14	9	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:92123679A>G	ENST00000248633.4	-	19	3053	c.2958T>C	c.(2956-2958)ccT>ccC	p.P986P	PEX1_ENST00000438045.1_Silent_p.P664P|PEX1_ENST00000428214.1_Silent_p.P929P|AC007566.10_ENST00000441539.1_RNA|AC007566.10_ENST00000427458.1_RNA	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	986					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	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)			CAATCAAGTCAGGGCGACTAG	0.383																																																0			7											65	65	65					7																	92123679		2203	4300	6503	91961615	SO:0001819	synonymous_variant	5189			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.2958T>C	7.37:g.92123679A>G			91961615	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																				0.383	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92123679	A	G	92123679	2	3	9	1	0	0	0	0	0	0	0	1	11766	175	7	4		4	PEX1	7	92123679	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	16612199	92123679	67014984	64	961										
PSMC2	5701	hgsc.bcm.edu	37	chr7	103004631	103004631	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggcattgagcctcccaagggCgtgctgctctttggtccacc	12	14	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:103004631C>T	ENST00000435765.1	+	9	1044	c.633C>T	c.(631-633)ggC>ggT	p.G211G	SLC26A5_ENST00000339444.6_Intron|PSMC2_ENST00000292644.3_Silent_p.G211G|SLC26A5_ENST00000356767.4_Intron|PSMC2_ENST00000544811.1_Silent_p.G74G|SLC26A5_ENST00000393735.2_Intron	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2	211					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						CTCCCAAGGGCGTGCTGCTCT	0.493																																																0			7											107	93	98					7																	103004631		2203	4300	6503	102791867	SO:0001819	synonymous_variant	5701			D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.633C>T	7.37:g.103004631C>T			102791867	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Silent	SNP	ENST00000435765.1	37	CCDS5731.1																																																																																				0.493	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803		T	103004631	C	T	103004631	2	4	9	1	0	0	0	0	0	0	0	1	12720	755	27	1		1	PSMC2	7	103004631	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	10880952	103004631	56134032	65	962										
KCND2	3751	hgsc.bcm.edu	37	chr7	120385963	120385963	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccagcacctgctgttcacgaCgacacaaaaaaacttttcgc	6	14	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:120385963C>T	ENST00000331113.4	+	5	2562	c.1597C>T	c.(1597-1599)Cga>Tga	p.R533*	RP4-797C5.2_ENST00000450480.1_RNA	NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	533					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.R533*(2)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CTGTTCACGACGACACAAAAA	0.448																																																2	Substitution - Nonsense(2)	large_intestine(1)|central_nervous_system(1)	7											150	123	132					7																	120385963		2203	4300	6503	120173199	SO:0001587	stop_gained	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1597C>T	7.37:g.120385963C>T	ENSP00000333496:p.Arg533*		120173199	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Nonsense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.582337	0.65992	.	.	ENSG00000184408	ENST00000331113	.	.	.	6.06	0.749	0.18381	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8473	0.92212	0.7067:0.2933:0.0:0.0	.	.	.	.	X	533	.	.	R	+	1	2	KCND2	120173199	0.012000	0.17670	0.942000	0.38095	0.975000	0.68041	0.143000	0.16115	0.107000	0.17824	-0.791000	0.03333	CGA		0.448	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	120385963	C	T	120385963	4	4	9	1	0	0	0	0	0	1	0	0	8040	528	19	1	1615	1	KCND2	7	120385963	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	17381332	120385963	38752700	66	963										
SSPO	23145	hgsc.bcm.edu	37	chr7	149484798	149484798	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggctcgggcccgctgtggggCgctgctgcagccgctcttca	16	15	2	0	rs62490656	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:149484798C>T	ENST00000378016.2	+	0	3620							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGCTGTGGGGCGCTGCTGCAG	0.667													C|||	832	0.166134	0.0234	0.2147	5008	,	,		16879	0.1518		0.2495	False		,,,				2504	0.2536															0			7						C		177,3887		1,175,1856	7	10	9		3624	-2.7	0	7	dbSNP_129	9	1883,6435		211,1461,2487	no	coding-notMod3	SSPO	NM_198455.2		212,1636,4343	TT,TC,CC		22.6377,4.3553,16.6371			149484798	2060,10322	2032	4159	6191	149115731			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149484798C>T			149115731	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																					0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149484798	C	T	149484798	1	4	9	0	1	0	0	0	0	0	0	0	15228	768	27	1		1	SSPO	7	149484798	RNA	SNP	C	TCGA-AF-5654-01A-01D-1657-10	29098835	149484798	9653865	67	964										
DPP6	1804	hgsc.bcm.edu	37	chr7	154002599	154002599	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	catgaccacagccaaggagcCaagcgcttcggggaaatccg	12	13	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:154002599C>A	ENST00000377770.3	+	2	384				DPP6_ENST00000332007.3_Missense_Mutation_p.P7Q|DPP6_ENST00000406326.1_Intron|DPP6_ENST00000496611.1_3'UTR|DPP6_ENST00000404039.1_Intron|DPP6_ENST00000427557.1_Missense_Mutation_p.P7Q			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6						cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GCCAAGGAGCCAAGCGCTTCG	0.617																																					NSCLC(125;1384 1783 2490 7422 34254)											0			7											53	59	57					7																	154002599		1568	3579	5147	153633532	SO:0001627	intron_variant	1804			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.244-140700C>A	7.37:g.154002599C>A			153633532		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	C	11.25	1.581922	0.28180	.	.	ENSG00000130226	ENST00000332007;ENST00000427557	T;T	0.13307	2.6;2.6	5.01	4.03	0.46877	.	.	.	.	.	T	0.11153	0.0272	.	.	.	0.23787	N	0.996849	B;B;B	0.14805	0.0;0.011;0.0	B;B;B	0.14023	0.0;0.01;0.003	T	0.21655	-1.0239	8	0.44086	T	0.13	.	9.8419	0.41004	0.5797:0.4203:0.0:0.0	.	7;7;7	E9PDL2;B7Z1K3;P42658-2	.;.;.	Q	7	ENSP00000328226:P7Q;ENSP00000397303:P7Q	ENSP00000328226:P7Q	P	+	2	0	DPP6	153633532	0.941000	0.31946	0.508000	0.27688	0.802000	0.45316	3.145000	0.50623	1.007000	0.39238	0.462000	0.41574	CCA		0.617	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	154002599	C	A	154002599	1	1	9	0	1	0	0	0	0	0	0	0	4741	594	21	2		2	DPP6	7	154002599	Intron	SNP	C	TCGA-AF-5654-01A-01D-1657-10	4517801	154002599	5136064	68	965										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154863299	154863299	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tacaaggctgccaagttccgCgtgggctccaggaagaccaa	12	12	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr7:154863299C>T	ENST00000287907.2	+	1	1266	c.690C>T	c.(688-690)cgC>cgT	p.R230R	HTR5A-AS1_ENST00000543018.1_5'Flank|HTR5A-AS1_ENST00000493904.1_5'Flank|HTR5A-AS1_ENST00000395731.2_5'Flank	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	230					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	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)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	CCAAGTTCCGCGTGGGCTCCA	0.542																																																0			7											78	74	75					7																	154863299		2203	4300	6503	154494232	SO:0001819	synonymous_variant	3361				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.690C>T	7.37:g.154863299C>T			154494232	Q2M2D2	Silent	SNP	ENST00000287907.2	37	CCDS5936.1																																																																																				0.542	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154863299	C	T	154863299	2	4	9	1	0	0	0	0	0	0	0	1	7471	755	27	1		1	HTR5A	7	154863299	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	860700	154863299	4275364	69	966										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2796204	2796204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	catacatggggttttcaaacGatgcttgtccattgctgttt	9	8	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:2796204G>A	ENST00000520002.1	-	71	11156	c.10601C>T	c.(10600-10602)tCg>tTg	p.S3534L	CSMD1_ENST00000400186.3_Missense_Mutation_p.S3357L|CSMD1_ENST00000542608.1_Missense_Mutation_p.S3356L|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3534L|CSMD1_ENST00000537824.1_Missense_Mutation_p.S3533L|CSMD1_ENST00000602723.1_Missense_Mutation_p.S3357L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3534						integral component of membrane (GO:0016021)				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)		GTTTTCAAACGATGCTTGTCC	0.413																																																0			8											271	240	250					8																	2796204		1916	4116	6032	2783611	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10601C>T	8.37:g.2796204G>A	ENSP00000430733:p.Ser3534Leu		2783611	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	29.6	5.024079	0.93462	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.32753	1.44;1.58;1.6;1.44	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000003	T	0.51753	0.1693	L	0.44542	1.39	0.80722	D	1	D;P;D	0.89917	0.985;0.898;1.0	B;B;D	0.83275	0.265;0.241;0.996	T	0.47156	-0.9139	10	0.72032	D	0.01	.	20.3214	0.98679	0.0:0.0:1.0:0.0	.	3534;3534;3356	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	L	3357;3534;3395;3533;3356	ENSP00000383047:S3357L;ENSP00000430733:S3534L;ENSP00000441462:S3533L;ENSP00000446243:S3356L	ENSP00000320445:S3395L	S	-	2	0	CSMD1	2783611	1.000000	0.71417	0.802000	0.32245	0.852000	0.48524	7.827000	0.86722	2.804000	0.96469	0.655000	0.94253	TCG		0.413	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2796204	G	A	2796204	3	1	9	1	0	0	0	0	1	0	0	0	3950	1059	37	1	100	1	CSMD1	8	2796204	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		2796204	143567818	70	967										
FGL1	2267	hgsc.bcm.edu	37	chr8	17731885	17731885	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcacacctgttaaagttttcActgccatcagatcgtctctg	7	12	3	1	rs372364435		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:17731885A>T	ENST00000398056.2	-	6	1205	c.390T>A	c.(388-390)agT>agA	p.S130R	FGL1_ENST00000522444.1_Missense_Mutation_p.S130R|FGL1_ENST00000427924.1_Missense_Mutation_p.S130R|FGL1_ENST00000518650.1_Missense_Mutation_p.S130R|FGL1_ENST00000398054.1_Missense_Mutation_p.S130R|FGL1_ENST00000381840.2_Missense_Mutation_p.S130R|FGL1_ENST00000381841.2_Missense_Mutation_p.S130R			Q08830	FGL1_HUMAN	fibrinogen-like 1	130	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		TAAAGTTTTCACTGCCATCAG	0.373																																																0			8											127	118	121					8																	17731885		2203	4300	6503	17776165	SO:0001583	missense	2267			D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"Fibrinogen C domain containing"	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.390T>A	8.37:g.17731885A>T	ENSP00000381133:p.Ser130Arg		17776165	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Missense_Mutation	SNP	ENST00000398056.2	37	CCDS6004.1	.	.	.	.	.	.	.	.	.	.	A	9.546	1.114640	0.20795	.	.	ENSG00000104760	ENST00000221204;ENST00000398056;ENST00000521427;ENST00000522444;ENST00000381841;ENST00000427924;ENST00000398054;ENST00000381840;ENST00000518650	T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.11	-4.01	0.04045	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.487695	0.25801	N	0.028206	T	0.41351	0.1155	M	0.74389	2.26	0.39960	D	0.97465	B;B;D	0.76494	0.131;0.263;0.999	B;B;D	0.73708	0.038;0.147;0.981	T	0.37753	-0.9692	10	0.72032	D	0.01	.	8.5576	0.33492	0.3553:0.0:0.5316:0.1132	.	100;130;130	E7ERS0;Q8NG32;Q08830	.;.;FGL1_HUMAN	R	130;130;100;130;130;130;130;130;130	ENSP00000381133:S130R;ENSP00000429757:S130R;ENSP00000371263:S130R;ENSP00000401952:S130R;ENSP00000381131:S130R;ENSP00000371262:S130R;ENSP00000428430:S130R	ENSP00000221204:S130R	S	-	3	2	FGL1	17776165	0.072000	0.21174	0.783000	0.31826	0.333000	0.28666	-0.638000	0.05452	-0.953000	0.03645	-1.091000	0.02175	AGT		0.373	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467		T	17731885	A	T	17731885	3	4	9	1	0	0	0	0	1	0	0	0	5891	156	6	5	568	5	FGL1	8	17731885	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	14935681	17731885	128632137	71	968										
HR	55806	hgsc.bcm.edu	37	chr8	21984769	21984769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctcctcgacctcagggcagcCgcgtggacattcaaactgct	10	15	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:21984769C>T	ENST00000381418.4	-	3	2666	c.1186G>A	c.(1186-1188)Ggc>Agc	p.G396S	HR_ENST00000312841.8_Missense_Mutation_p.G396S	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	396					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.G396S(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		TCAGGGCAGCCGCGTGGACAT	0.662																																																1	Substitution - Missense(1)	prostate(1)	8											97	110	105					8																	21984769		2203	4300	6503	22040714	SO:0001583	missense	55806			AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1186G>A	8.37:g.21984769C>T	ENSP00000370826:p.Gly396Ser		22040714	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677511	0.47886	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.72615	-0.66;-0.67	6.04	4.22	0.49857	.	0.328139	0.26321	N	0.025057	T	0.47116	0.1428	N	0.16656	0.425	0.25412	N	0.988348	P;P	0.50943	0.94;0.901	B;B	0.36464	0.225;0.113	T	0.35051	-0.9804	10	0.28530	T	0.3	-3.0233	8.253	0.31737	0.0:0.8156:0.0:0.1844	.	396;396	O43593-2;O43593	.;HAIR_HUMAN	S	396	ENSP00000370826:G396S;ENSP00000326765:G396S	ENSP00000326765:G396S	G	-	1	0	HR	22040714	0.025000	0.19082	0.078000	0.20375	0.777000	0.43975	0.427000	0.21379	0.850000	0.35239	0.563000	0.77884	GGC		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			T	21984769	C	T	21984769	3	4	9	1	0	0	0	0	1	0	0	0	7368	652	23	1	2451	1	HR	8	21984769	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	4252884	21984769	124379253	72	969										
PNMA2	10687	hgsc.bcm.edu	37	chr8	26365183	26365183	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cccccaggtggttttcagtcGtctccctcatgattccagcg	9	15	3	1	rs202002019		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:26365183G>A	ENST00000522362.2	-	3	1983	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	363					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		GTTTTCAGTCGTCTCCCTCAT	0.473																																																0			8						G		0,4406		0,0,2203	97	99	99		1089	-8.6	0	8		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PNMA2	NM_007257.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		363/365	26365183	1,13005	2203	4300	6503	26421100	SO:0001819	synonymous_variant	10687				CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"Paraneoplastic Ma antigens"	9159	protein-coding gene	gene with protein product		603970	"paraneoplastic antigen MA2"			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.1089C>T	8.37:g.26365183G>A			26421100	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Silent	SNP	ENST00000522362.2	37	CCDS34868.1																																																																																				0.473	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375709.2	NM_007257		A	26365183	G	A	26365183	2	1	9	1	0	0	0	0	0	0	0	1	12185	1136	40	1		1	PNMA2	8	26365183	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	4380414	26365183	119998839	73	970										
TRIM35	23087	hgsc.bcm.edu	37	chr8	27145231	27145231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcgctccgcgtcatagaaagAcagctcgccctcctcacact	8	17	2	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:27145231A>G	ENST00000305364.4	-	6	1401	c.1318T>C	c.(1318-1320)Tct>Cct	p.S440P	TRIM35_ENST00000521253.1_3'UTR	NM_171982.3	NP_741983.2	Q9UPQ4	TRI35_HUMAN	tripartite motif containing 35	440	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	14		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)		TCATAGAAAGACAGCTCGCCC	0.692																																																0			8											53	49	50					8																	27145231		2202	4298	6500	27201148	SO:0001583	missense	23087			AB029021	CCDS6056.2	8p21.2	2013-01-09	2011-01-25		ENSG00000104228	ENSG00000104228		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16285	protein-coding gene	gene with protein product			"tripartite motif-containing 35"			11331580, 14662771, 12692137	Standard	XM_005273451		Approved	KIAA1098, MAIR, HLS5	uc003xfl.1	Q9UPQ4	OTTHUMG00000102047	ENST00000305364.4:c.1318T>C	8.37:g.27145231A>G	ENSP00000301924:p.Ser440Pro		27201148	Q86XQ0|Q8WVA4	Missense_Mutation	SNP	ENST00000305364.4	37	CCDS6056.2	.	.	.	.	.	.	.	.	.	.	A	20.8	4.046069	0.75846	.	.	ENSG00000104228	ENST00000305364;ENST00000380544	T	0.68903	-0.36	5.34	5.34	0.76211	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000002	D	0.85173	0.5636	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88450	0.3048	10	0.87932	D	0	.	11.7082	0.51610	1.0:0.0:0.0:0.0	.	440	Q9UPQ4	TRI35_HUMAN	P	440	ENSP00000301924:S440P	ENSP00000301924:S440P	S	-	1	0	TRIM35	27201148	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	5.083000	0.64456	2.021000	0.59480	0.379000	0.24179	TCT		0.692	TRIM35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219848.2	NM_171982		G	27145231	A	G	27145231	3	3	9	1	0	0	0	0	1	0	0	0	16549	275	10	4	167	4	TRIM35	8	27145231	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	780048	27145231	119218791	74	971										
TMEM64	169200	hgsc.bcm.edu	37	chr8	91643932	91643932	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gttgggtaatgagagatcagTaatctagaagagtagattaa	12	2	2	5			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:91643932T>A	ENST00000458549.2	-	2	976	c.799A>T	c.(799-801)Act>Tct	p.T267S	TMEM64_ENST00000519519.1_Missense_Mutation_p.T6S|TMEM64_ENST00000418210.2_Intron	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	267					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			GAGAGATCAGTAATCTAGAAG	0.378																																																0			8											100	95	97					8																	91643932		2203	4300	6503	91713108	SO:0001583	missense	169200			AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.799A>T	8.37:g.91643932T>A	ENSP00000414786:p.Thr267Ser		91713108	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Missense_Mutation	SNP	ENST00000458549.2	37	CCDS34920.2	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699960	0.68501	.	.	ENSG00000180694	ENST00000458549;ENST00000519519;ENST00000521852	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.50137	0.1598	L	0.31476	0.935	0.80722	D	1	P;D	0.52996	0.748;0.957	B;P	0.49752	0.319;0.621	T	0.41680	-0.9495	9	0.25106	T	0.35	.	16.2365	0.82377	0.0:0.0:0.0:1.0	.	6;267	Q6YI46-2;Q6YI46	.;TMM64_HUMAN	S	267;6;6	.	ENSP00000414786:T267S	T	-	1	0	TMEM64	91713108	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.992000	0.63889	2.238000	0.73509	0.477000	0.44152	ACT		0.378	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495		A	91643932	T	A	91643932	3	1	9	1	0	0	0	0	1	0	0	0	16232	1638	57	5	351	5	TMEM64	8	91643932	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	64498701	91643932	54720090	75	972										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116599698	116599698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tttgatggtggatatggcatGaccgtcctcttcgccgttgg	13	9	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:116599698G>T	ENST00000220888.5	-	4	2350	c.2191C>A	c.(2191-2193)Cat>Aat	p.H731N	TRPS1_ENST00000395715.3_Missense_Mutation_p.H744N|TRPS1_ENST00000519674.1_Missense_Mutation_p.H731N|TRPS1_ENST00000519076.1_Missense_Mutation_p.H485N|TRPS1_ENST00000520276.1_Missense_Mutation_p.H735N			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	731	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GATATGGCATGACCGTCCTCT	0.488									Langer-Giedion syndrome																																							0			8											171	175	174					8																	116599698		2022	4173	6195	116668873	SO:0001583	missense	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2191C>A	8.37:g.116599698G>T	ENSP00000220888:p.His731Asn		116668873	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	G	12.26	1.884571	0.33255	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	D;D;D;D;T	0.98345	-4.88;-4.85;-4.81;-4.86;0.97	5.86	5.86	0.93980	.	0.283862	0.40302	N	0.001128	D	0.96225	0.8769	L	0.29908	0.895	0.38317	D	0.943404	B;B;B	0.16802	0.019;0.011;0.019	B;B;B	0.15870	0.014;0.003;0.014	D	0.92986	0.6410	10	0.72032	D	0.01	.	20.2019	0.98263	0.0:0.0:1.0:0.0	.	735;731;744	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	N	744;731;485;735;731	ENSP00000379065:H744N;ENSP00000220888:H731N;ENSP00000428910:H485N;ENSP00000428680:H735N;ENSP00000429174:H731N	ENSP00000220888:H731N	H	-	1	0	TRPS1	116668873	0.990000	0.36364	0.121000	0.21740	0.730000	0.41778	5.746000	0.68681	2.776000	0.95493	0.655000	0.94253	CAT		0.488	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116599698	G	T	116599698	3	4	9	1	0	0	0	0	1	0	0	0	16633	1290	45	2	1666	2	TRPS1	8	116599698	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	24955766	116599698	29764324	76	973										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133142093	133142093	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcagatgatggttttcaaatCggaatacctgttgtcctcct	9	9	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr8:133142093C>A	ENST00000388996.4	-	15	2455	c.2035G>T	c.(2035-2037)Gat>Tat	p.D679Y	KCNQ3_ENST00000521134.1_Missense_Mutation_p.D559Y|KCNQ3_ENST00000519445.1_Missense_Mutation_p.D667Y	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	679					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTTTTCAAATCGGAATACCTG	0.532																																																0			8											142	119	127					8																	133142093		2203	4300	6503	133211275	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2035G>T	8.37:g.133142093C>A	ENSP00000373648:p.Asp679Tyr		133211275	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397623	0.62177	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99005	-5.3;-5.29;-5.32	5.42	5.42	0.78866	.	0.588749	0.18441	N	0.141130	D	0.97084	0.9047	N	0.08118	0	0.50632	D	0.999884	P;P	0.48407	0.91;0.91	P;P	0.48454	0.578;0.578	D	0.98128	1.0429	10	0.59425	D	0.04	-14.4265	18.1948	0.89818	0.0:1.0:0.0:0.0	.	667;679	E7ET42;O43525	.;KCNQ3_HUMAN	Y	679;559;667;656;558	ENSP00000373648:D679Y;ENSP00000429799:D559Y;ENSP00000428790:D667Y	ENSP00000373648:D679Y	D	-	1	0	KCNQ3	133211275	0.998000	0.40836	0.078000	0.20375	0.849000	0.48306	5.312000	0.65792	2.535000	0.85469	0.555000	0.69702	GAT		0.532	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133142093	C	A	133142093	3	1	9	1	0	0	0	0	1	0	0	0	8105	884	31	2	587	2	KCNQ3	8	133142093	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	16542395	133142093	13221929	77	974										
GLIS3	169792	hgsc.bcm.edu	37	chr9	4117899	4117899	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtcctcccctttgcgctggtCgatgtggaccttctcgatgt	11	13	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:4117899C>T	ENST00000324333.10	-	3	1307	c.1114G>A	c.(1114-1116)Gac>Aac	p.D372N	GLIS3_ENST00000381971.3_Missense_Mutation_p.D527N	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	372					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTGCGCTGGTCGATGTGGACC	0.602																																																0			9											126	111	116					9																	4117899		2203	4300	6503	4107899	SO:0001583	missense	169792			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.1114G>A	9.37:g.4117899C>T	ENSP00000325494:p.Asp372Asn		4107899	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114507	0.94339	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	D;D	0.88664	-2.41;-2.08	5.51	5.51	0.81932	Zinc finger, C2H2 (1);	0.000000	0.53938	D	0.000049	D	0.90160	0.6925	N	0.13098	0.295	0.80722	D	1	D;D;D;D;D	0.89917	0.996;1.0;1.0;0.999;1.0	P;D;D;D;D	0.83275	0.881;0.973;0.981;0.981;0.996	D	0.91787	0.5440	10	0.59425	D	0.04	.	19.4269	0.94746	0.0:1.0:0.0:0.0	.	35;40;40;527;372	Q1PHK4;Q1PHK2;Q1PHK3;Q8NEA6-2;Q8NEA6	.;.;.;.;GLIS3_HUMAN	N	372;527	ENSP00000325494:D372N;ENSP00000371398:D527N	ENSP00000325494:D372N	D	-	1	0	GLIS3	4107899	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.792000	0.85828	2.595000	0.87683	0.655000	0.94253	GAC		0.602	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		T	4117899	C	T	4117899	3	4	9	1	0	0	0	0	1	0	0	0	6467	884	31	1	1245	1	GLIS3	9	4117899	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		4117899	137095532	78	975										
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15433600	15433600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agaaaccattacaatagatcGagcctgcagacaagaaacat	7	9	0	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:15433600G>A	ENST00000380821.3	+	3	619	c.443G>A	c.(442-444)cGa>cAa	p.R148Q	SNAPC3_ENST00000461041.1_3'UTR|RNU6-319P_ENST00000516025.1_RNA	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	148					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		ACAATAGATCGAGCCTGCAGA	0.348																																																0			9											146	145	145					9																	15433600		2203	4300	6503	15423600	SO:0001583	missense	6619			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.443G>A	9.37:g.15433600G>A	ENSP00000370200:p.Arg148Gln		15423600	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.426737	0.83667	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.50548	0.74	5.39	5.39	0.77823	.	0.201144	0.46758	D	0.000264	T	0.66426	0.2788	M	0.67953	2.075	0.80722	D	1	D;P	0.76494	0.999;0.756	D;B	0.77557	0.99;0.106	T	0.68663	-0.5349	10	0.66056	D	0.02	-13.5248	14.6437	0.68745	0.0:0.0:1.0:0.0	.	119;148	B4DDR9;Q92966	.;SNPC3_HUMAN	Q	148;148;119;148	ENSP00000370200:R148Q	ENSP00000370185:R148Q	R	+	2	0	SNAPC3	15423600	1.000000	0.71417	0.952000	0.39060	0.973000	0.67179	5.246000	0.65411	2.520000	0.84964	0.655000	0.94253	CGA		0.348	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		A	15433600	G	A	15433600	3	1	9	1	0	0	0	0	1	0	0	0	14873	1058	37	1	453	1	SNAPC3	9	15433600	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	11315701	15433600	125779831	79	976										
MELK	9833	hgsc.bcm.edu	37	chr9	36651833	36651833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtttaaggctttcttctttcTcctgtggacaagccagtgct	9	10	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:36651833T>C	ENST00000298048.2	+	12	1196	c.1012T>C	c.(1012-1014)Tcc>Ccc	p.S338P	MELK_ENST00000536329.1_Missense_Mutation_p.S267P|MELK_ENST00000536860.1_Missense_Mutation_p.S290P|MELK_ENST00000543751.1_Missense_Mutation_p.S306P|MELK_ENST00000545008.1_Missense_Mutation_p.S267P|MELK_ENST00000536987.1_Missense_Mutation_p.S207P|MELK_ENST00000538311.1_Missense_Mutation_p.S144P|MELK_ENST00000541717.1_Missense_Mutation_p.S338P	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	338	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TTCTTCTTTCTCCTGTGGACA	0.488																																					Ovarian(82;980 1317 7225 14391 18624)											0			9											211	196	201					9																	36651833		2203	4300	6503	36641833	SO:0001583	missense	9833			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1012T>C	9.37:g.36651833T>C	ENSP00000298048:p.Ser338Pro		36641833	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.390663	0.62066	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.71934	-0.43;0.56;0.35;0.88;0.26;-0.61;-0.39;-0.43	5.63	3.18	0.36537	.	0.411874	0.28459	N	0.015274	T	0.62171	0.2406	N	0.25647	0.755	0.09310	N	1	P;P;B;B;P;P;B	0.52842	0.59;0.956;0.009;0.004;0.902;0.835;0.01	B;P;B;B;P;P;B	0.52554	0.391;0.702;0.028;0.011;0.548;0.514;0.013	T	0.51655	-0.8678	10	0.34782	T	0.22	-8.0493	6.7365	0.23413	0.1486:0.0:0.1536:0.6978	.	258;267;290;338;267;306;338	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	P	338;144;207;267;290;267;338;306	ENSP00000298048:S338P;ENSP00000438226:S144P;ENSP00000439184:S207P;ENSP00000445452:S267P;ENSP00000439792:S290P;ENSP00000443550:S267P;ENSP00000437804:S338P;ENSP00000441596:S306P	ENSP00000298048:S338P	S	+	1	0	MELK	36641833	0.094000	0.21725	0.902000	0.35471	0.951000	0.60555	0.793000	0.26944	2.145000	0.66743	0.533000	0.62120	TCC		0.488	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		C	36651833	T	C	36651833	3	2	9	1	0	0	0	0	1	0	0	0	9500	1551	54	4	1054	4	MELK	9	36651833	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	21218233	36651833	104561598	80	977										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84603895	84603895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	accctgtattcgtcacccacCgaaaaaaataatgacatcca	4	13	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:84603895C>T	ENST00000344803.2	+	1	209	c.162C>T	c.(160-162)acC>acT	p.T54T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	54					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CGTCACCCACCGAAAAAAATA	0.423																																																0			9											193	161	171					9																	84603895		1881	4103	5984	83793715	SO:0001819	synonymous_variant	0				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.162C>T	9.37:g.84603895C>T			83793715		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																				0.423	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84603895	C	T	84603895	2	4	9	1	0	0	0	0	0	0	0	1	5951	639	23	1		1	FLJ46321	9	84603895	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	47952062	84603895	56609536	81	978										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84606600	84606600	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atagagcctgttaacatctcAtttctcagccatgacattct	5	11	3	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:84606600A>T	ENST00000344803.2	+	4	1262	c.1215A>T	c.(1213-1215)tcA>tcT	p.S405S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	405					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTAACATCTCATTTCTCAGCC	0.458																																																0			9											95	82	86					9																	84606600		1852	4102	5954	83796420	SO:0001819	synonymous_variant	0				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.1215A>T	9.37:g.84606600A>T			83796420		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																				0.458	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84606600	A	T	84606600	2	4	9	1	0	0	0	0	0	0	0	1	5951	204	8	5		5	FLJ46321	9	84606600	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	2705	84606600	56606831	82	979										
ZNF189	7743	hgsc.bcm.edu	37	chr9	104171602	104171602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cctatctgtgcagacagtgtGgaaaaagctttagtcagctt	10	8	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr9:104171602G>A	ENST00000339664.2	+	3	1681	c.1552G>A	c.(1552-1554)Gga>Aga	p.G518R	ZNF189_ENST00000374861.3_Missense_Mutation_p.G504R|ZNF189_ENST00000259395.4_Missense_Mutation_p.G476R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	518					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CAGACAGTGTGGAAAAAGCTT	0.433																																																0			9											95	95	95					9																	104171602		2203	4300	6503	103211423	SO:0001583	missense	7743			AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1552G>A	9.37:g.104171602G>A	ENSP00000342019:p.Gly518Arg		103211423	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.701670	0.48307	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.21361	2.01;2.01;2.01	4.23	4.23	0.50019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46145	D	0.000306	T	0.47563	0.1452	M	0.81802	2.56	0.43930	D	0.996587	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.75020	0.985;0.985;0.948	T	0.50833	-0.8781	10	0.59425	D	0.04	.	14.9244	0.70866	0.0:0.0:1.0:0.0	.	503;504;518	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	R	504;518;476	ENSP00000363995:G504R;ENSP00000342019:G518R;ENSP00000259395:G476R	ENSP00000259395:G476R	G	+	1	0	ZNF189	103211423	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.694000	0.61760	2.635000	0.89317	0.563000	0.77884	GGA		0.433	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		A	104171602	G	A	104171602	3	1	9	1	0	0	0	0	1	0	0	0	17793	1349	47	3	1562	3	ZNF189	9	104171602	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	19565002	104171602	37041829	83	980										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28260161	28260161	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgaaccagaaatgtctttgcGgagggcagctgcttcttcct	11	10	2	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:28260161G>A	ENST00000305242.5	-	8	1110	c.1018C>T	c.(1018-1020)Cgc>Tgc	p.R340C	ARMC4_ENST00000239715.3_Missense_Mutation_p.R197C|ARMC4_ENST00000537576.1_Missense_Mutation_p.R32C|ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000480504.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	340					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R340C(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						ATGTCTTTGCGGAGGGCAGCT	0.418																																																1	Substitution - Missense(1)	prostate(1)	10											80	77	78					10																	28260161		2203	4300	6503	28300167	SO:0001583	missense	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1018C>T	10.37:g.28260161G>A	ENSP00000306410:p.Arg340Cys		28300167	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	g	8.100	0.776434	0.16051	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.22743	1.95;1.94;1.94;1.94	3.76	-2.77	0.05877	.	5.610880	0.00166	N	0.000010	T	0.14917	0.0360	L	0.36672	1.1	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24440	-1.0160	10	0.52906	T	0.07	-7.2146	0.53	0.00626	0.2141:0.1514:0.2409:0.3937	.	340	Q5T2S8	ARMC4_HUMAN	C	32;340;32;234;197	ENSP00000443208:R32C;ENSP00000306410:R340C;ENSP00000398155:R234C;ENSP00000239715:R197C	ENSP00000239715:R197C	R	-	1	0	ARMC4	28300167	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.841000	0.04359	-0.397000	0.07691	-0.848000	0.03037	CGC		0.418	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		A	28260161	G	A	28260161	3	1	9	1	0	0	0	0	1	0	0	0	954	1116	39	1	2168	1	ARMC4	10	28260161	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		28260161	107274586	84	981										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37431115	37431115	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	acacctgtaaagactggatgCgtggcaagagtaacatctaa	10	8	1	2	rs369621160		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:37431115C>T	ENST00000602533.1	+	7	1221	c.1122C>T	c.(1120-1122)tgC>tgT	p.C374C	ANKRD30A_ENST00000374660.1_Silent_p.C374C|ANKRD30A_ENST00000361713.1_Silent_p.C374C			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	430					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C374C(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AGACTGGATGCGTGGCAAGAG	0.393																																																1	Substitution - coding silent(1)	endometrium(1)	10						C		3,3727		0,3,1862	76	75	76		1122	0.1	0	10		76	0,8226		0,0,4113	no	coding-synonymous	ANKRD30A	NM_052997.2		0,3,5975	TT,TC,CC		0.0,0.0804,0.0251		374/1342	37431115	3,11953	1865	4113	5978	37471121	SO:0001819	synonymous_variant	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1122C>T	10.37:g.37431115C>T			37471121	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																					0.393	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37431115	C	T	37431115	2	4	9	1	0	0	0	0	0	0	0	1	658	776	27	1		1	ANKRD30A	10	37431115	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	9170954	37431115	98103632	85	982										
ANK3	288	hgsc.bcm.edu	37	chr10	61829033	61829033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aggtatcttttggtgaagtgGcctttatgggaagtttggat	14	3	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:61829033G>A	ENST00000280772.2	-	37	11797	c.11606C>T	c.(11605-11607)gCc>gTc	p.A3869V	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3869					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TGGTGAAGTGGCCTTTATGGG	0.398																																																0			10											301	296	298					10																	61829033		2203	4300	6503	61499039	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11606C>T	10.37:g.61829033G>A	ENSP00000280772:p.Ala3869Val		61499039	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278236	0.40294	.	.	ENSG00000151150	ENST00000280772	T	0.18016	2.24	5.07	5.07	0.68467	.	0.000000	0.41938	D	0.000796	T	0.27629	0.0679	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.06338	-1.0832	10	0.23302	T	0.38	.	18.8003	0.92013	0.0:0.0:1.0:0.0	.	3869	Q12955	ANK3_HUMAN	V	3869	ENSP00000280772:A3869V	ENSP00000280772:A3869V	A	-	2	0	ANK3	61499039	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.020000	0.76419	2.511000	0.84671	0.650000	0.86243	GCC		0.398	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61829033	G	A	61829033	3	1	9	1	0	0	0	0	1	0	0	0	622	1203	42	3	1868	3	ANK3	10	61829033	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	24397918	61829033	73705714	86	983										
TET1	80312	hgsc.bcm.edu	37	chr10	70426935	70426935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccctcttccaatggccgaccGgctatacacagagctcacag	8	16	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:70426935G>A	ENST00000373644.4	+	7	4804	c.4595G>A	c.(4594-4596)cGg>cAg	p.R1532Q		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1532					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						ATGGCCGACCGGCTATACACA	0.488																																																0			10											96	79	85					10																	70426935		2203	4300	6503	70096941	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4595G>A	10.37:g.70426935G>A	ENSP00000362748:p.Arg1532Gln		70096941	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.319987	0.23994	.	.	ENSG00000138336	ENST00000373644;ENST00000545846	T	0.22743	1.94	5.21	-1.09	0.09904	TET cysteine-rich domain (1);	0.875458	0.09976	N	0.731632	T	0.16938	0.0407	L	0.57536	1.79	0.09310	N	1	B	0.33413	0.411	B	0.24394	0.053	T	0.16630	-1.0396	10	0.48119	T	0.1	.	7.1581	0.25649	0.3526:0.1771:0.4703:0.0	.	1532	Q8NFU7	TET1_HUMAN	Q	1532;4	ENSP00000362748:R1532Q	ENSP00000362748:R1532Q	R	+	2	0	TET1	70096941	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.202000	0.17295	-0.004000	0.14419	0.585000	0.79938	CGG		0.488	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70426935	G	A	70426935	3	1	9	1	0	0	0	0	1	0	0	0	15808	1116	39	1	4617	1	TET1	10	70426935	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	8597902	70426935	65107812	87	984										
CDH23	414152	hgsc.bcm.edu	37	chr10	73491853	73491853	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aattacctggactacgagacCaagaccagctacatgatgaa	8	10	0	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:73491853C>G	ENST00000398786.2	-	1	97				CDH23_ENST00000224721.6_Silent_p.T1280T	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											ACTACGAGACCAAGACCAGCT	0.567																																																0			10											84	90	88					10																	73491853		2142	4239	6381	73161859	SO:0001627	intron_variant	64072			AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.4+5631G>C	10.37:g.73491853C>G			73161859		Silent	SNP	ENST00000398786.2	37	CCDS44430.1																																																																																				0.567	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375		G	73491853	C	G	73491853	1	3	9	0	1	0	0	0	0	0	0	0	3114	581	21	5		5	CDH23	10	73491853	Intron	SNP	C	TCGA-AF-5654-01A-01D-1657-10	3064918	73491853	62042894	88	985										
PTEN	5728	hgsc.bcm.edu	37	chr10	89693001	89693001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tggggaagtaaggaccagagAcaaaaaggtaagttattttt	12	3	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:89693001A>G	ENST00000371953.3	+	5	1842	c.485A>G	c.(484-486)gAc>gGc	p.D162G		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	162	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.D162G(1)|p.F56fs*2(1)|p.D162fs*8(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGGACCAGAGACAAAAAGGTA	0.358		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)|Substitution - Missense(1)|Insertion - Frameshift(1)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|thyroid(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											50	51	51					10																	89693001		2203	4300	6503	89682981	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.485A>G	10.37:g.89693001A>G	ENSP00000361021:p.Asp162Gly		89682981	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.546607	0.86022	.	.	ENSG00000171862	ENST00000371953	D	0.98512	-4.97	5.09	5.09	0.68999	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.98400	0.9468	M	0.71920	2.185	0.80722	D	1	D	0.61080	0.989	P	0.60117	0.869	D	0.98667	1.0686	9	.	.	.	-8.2651	14.8682	0.70434	1.0:0.0:0.0:0.0	.	162	P60484	PTEN_HUMAN	G	162	ENSP00000361021:D162G	.	D	+	2	0	PTEN	89682981	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.918000	0.92759	1.898000	0.54952	0.460000	0.39030	GAC		0.358	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89693001	A	G	89693001	3	3	9	1	0	0	0	0	1	0	0	0	12772	275	10	4	503	4	PTEN	10	89693001	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	16201148	89693001	45841746	89	986										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106160468	106160468	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agagagatatcctggggtctCagcttgttcggcgcaatgat	13	8	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:106160468C>A	ENST00000369704.3	+	13	1980	c.1846C>A	c.(1846-1848)Cag>Aag	p.Q616K	snoU13_ENST00000458914.1_RNA	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		616						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CCTGGGGTCTCAGCTTGTTCG	0.498																																																0			10											158	131	140					10																	106160468		2203	4300	6503	106150458	SO:0001583	missense	159686																														ENST00000369704.3:c.1846C>A	10.37:g.106160468C>A	ENSP00000358718:p.Gln616Lys		106150458	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	C	33	5.271062	0.95429	.	.	ENSG00000120051	ENST00000369704	T	0.46819	0.86	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	M	0.89840	3.065	0.80722	D	1	D	0.69078	0.997	P	0.61201	0.885	T	0.75022	-0.3464	10	0.37606	T	0.19	-23.587	19.645	0.95773	0.0:1.0:0.0:0.0	.	616	Q5T655	CC147_HUMAN	K	616	ENSP00000358718:Q616K	ENSP00000358718:Q616K	Q	+	1	0	CCDC147	106150458	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.647000	0.89833	0.655000	0.94253	CAG		0.498	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			A	106160468	C	A	106160468	3	1	9	1	0	0	0	0	1	0	0	0	2787	827	29	2	1896	2	CCDC147	10	106160468	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	16467467	106160468	29374279	90	987										
PDZD8	118987	hgsc.bcm.edu	37	chr10	119100490	119100490	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atgacaaaacaaagaacataCctgctacattctaacaacgt	4	10	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr10:119100490C>G	ENST00000334464.5	-	2	1235		c.e2+1			NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8						cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		AAAGAACATACCTGCTACATT	0.348																																																0			10											159	133	142					10																	119100490		2203	4300	6503	119090480	SO:0001630	splice_region_variant	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.995+1G>C	10.37:g.119100490C>G			119090480	Q86WE0|Q86WE5|Q9UFF1	Splice_Site	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507835	0.64410	.	.	ENSG00000165650	ENST00000334464	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6278	0.68635	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDZD8	119090480	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.089000	0.57685	2.608000	0.88229	0.585000	0.79938	.		0.348	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	Intron	G	119100490	C	G	119100490	5	3	9	1	0	0	0	0	0	0	1	0	11736	521	18	5	2484	5	PDZD8	10	119100490	Splice_Site	SNP	C	TCGA-AF-5654-01A-01D-1657-10	12940022	119100490	16434257	91	988										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6655209	6655209	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aggagggttgtcattctcgtCtgacagaaacaccttcacat	9	10	4	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:6655209C>G	ENST00000299441.3	-	4	2440	c.2029G>C	c.(2029-2031)Gac>Cac	p.D677H	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	677	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTCTCGTCTGACAGAAAC	0.562																																																0			11											77	77	77					11																	6655209		2201	4296	6497	6611785	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2029G>C	11.37:g.6655209C>G	ENSP00000299441:p.Asp677His		6611785	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607341	0.66558	.	.	ENSG00000166341	ENST00000299441	T	0.67698	-0.28	4.59	4.59	0.56863	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.44097	D	0.000486	D	0.88837	0.6545	H	0.98849	4.35	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.92904	0.6342	10	0.72032	D	0.01	.	14.721	0.69305	0.0:1.0:0.0:0.0	.	677	Q96JQ0	PCD16_HUMAN	H	677	ENSP00000299441:D677H	ENSP00000299441:D677H	D	-	1	0	DCHS1	6611785	1.000000	0.71417	0.996000	0.52242	0.613000	0.37349	6.756000	0.74919	2.397000	0.81536	0.561000	0.74099	GAC		0.562	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6655209	C	G	6655209	3	3	9	1	0	0	0	0	1	0	0	0	4293	913	32	5	7939	5	DCHS1	11	6655209	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		6655209	128351307	92	989										
SYT9	143425	hgsc.bcm.edu	37	chr11	7441758	7441758	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtaggtcacaatgagatcatCggcgtgtgtcaagtaggcaa	13	7	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:7441758C>T	ENST00000318881.6	+	6	1596	c.1359C>T	c.(1357-1359)atC>atT	p.I453I		NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	453	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ATGAGATCATCGGCGTGTGTC	0.443																																																0			11											172	150	157					11																	7441758		2201	4296	6497	7398334	SO:0001819	synonymous_variant	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1359C>T	11.37:g.7441758C>T			7398334		Silent	SNP	ENST00000318881.6	37	CCDS7778.1																																																																																				0.443	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		T	7441758	C	T	7441758	2	4	9	1	0	0	0	0	0	0	0	1	15520	874	31	1		1	SYT9	11	7441758	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	786549	7441758	127564758	93	990										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9172291	9172291	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gctggcatcagacttcctacGttctgaatcaagaagtattc	8	10	3	3	rs148317700		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:9172291G>A	ENST00000328194.3	-	14	2862	c.2542C>T	c.(2542-2544)Cgt>Tgt	p.R848C	DENND5A_ENST00000527700.1_Missense_Mutation_p.R191C|DENND5A_ENST00000530044.1_Missense_Mutation_p.R848C	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	848	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R848C(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GACTTCCTACGTTCTGAATCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	CYS/ARG	0,4402		0,0,2201	134	120	125		2542	5.5	1	11	dbSNP_134	125	1,8591		0,1,4295	yes	missense	DENND5A	NM_015213.3	180	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	848/1288	9172291	1,12993	2201	4296	6497	9128867	SO:0001583	missense	23258			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2542C>T	11.37:g.9172291G>A	ENSP00000328524:p.Arg848Cys		9128867	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.044212|4.044212	0.75732|0.75732	0.0|0.0	1.16E-4|1.16E-4	ENSG00000184014|ENSG00000184014	ENST00000328194;ENST00000530044;ENST00000527700|ENST00000524446	T;T;T|.	0.33438|.	1.41;1.41;1.41|.	5.53|5.53	5.53|5.53	0.82687|0.82687	RUN (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75831|0.75831	0.3903|0.3903	M|M	0.80616|0.80616	2.505|2.505	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.67725|.	0.953;0.939|.	T|T	0.76984|0.76984	-0.2756|-0.2756	10|5	0.87932|.	D|.	0|.	.|.	13.4783|13.4783	0.61322|0.61322	0.0:0.0:0.7382:0.2618|0.0:0.0:0.7382:0.2618	.|.	848;848|.	E9PS91;Q6IQ26|.	.;DEN5A_HUMAN|.	C|M	848;848;191|18	ENSP00000328524:R848C;ENSP00000435866:R848C;ENSP00000432549:R191C|.	ENSP00000328524:R848C|.	R|T	-|-	1|2	0|0	DENND5A|DENND5A	9128867|9128867	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	3.984000|3.984000	0.56923|0.56923	2.601000|2.601000	0.87937|0.87937	0.655000|0.655000	0.94253|0.94253	CGT|ACG		0.428	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		A	9172291	G	A	9172291	3	1	9	1	0	0	0	0	1	0	0	0	4447	1145	40	1	1361	1	DENND5A	11	9172291	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1730533	9172291	125834225	94	991										
RRAS2	22800	hgsc.bcm.edu	37	chr11	14300893	14300893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgaagggattctagaaaatgAcacaatggcagcctttcttg	10	7	2	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:14300893A>G	ENST00000256196.4	-	6	918	c.605T>C	c.(604-606)gTc>gCc	p.V202A	RRAS2_ENST00000529237.1_Missense_Mutation_p.V125A|RRAS2_ENST00000532814.1_Missense_Mutation_p.V125A|RRAS2_ENST00000414023.2_Missense_Mutation_p.V125A|RRAS2_ENST00000534746.1_Missense_Mutation_p.V125A|RRAS2_ENST00000526063.1_Missense_Mutation_p.V125A|RRAS2_ENST00000545643.1_Missense_Mutation_p.V208A|RRAS2_ENST00000537760.1_Missense_Mutation_p.V167A			P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2	202					osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|endometrium(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	12				Epithelial(150;0.203)		CTAGAAAATGACACAATGGCA	0.403																																																0			11											168	149	155					11																	14300893		2200	4294	6494	14257469	SO:0001583	missense	22800			M31468	CCDS7814.1, CCDS44544.1, CCDS53603.1	11p15.2	2014-05-09			ENSG00000133818	ENSG00000133818			17271	protein-coding gene	gene with protein product		600098				2108320, 8052619	Standard	NM_012250		Approved	TC21	uc001mlf.4	P62070	OTTHUMG00000165756	ENST00000256196.4:c.605T>C	11.37:g.14300893A>G	ENSP00000256196:p.Val202Ala		14257469	B2R9Z3|B7Z5Z2|B7Z6C4|B7Z7H6|P17082	Missense_Mutation	SNP	ENST00000256196.4	37	CCDS7814.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065728	0.55539	.	.	ENSG00000133818	ENST00000537760;ENST00000545643;ENST00000414023;ENST00000529237;ENST00000256196;ENST00000534746;ENST00000526063;ENST00000532814	T;T;T;T;T;T;T;T	0.71222	0.34;-0.26;-0.55;-0.55;-0.13;-0.55;-0.55;-0.55	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.74382	0.3709	N	0.19112	0.55	0.80722	D	1	B;D	0.64830	0.172;0.994	B;D	0.70716	0.05;0.97	T	0.76764	-0.2839	10	0.49607	T	0.09	.	16.3817	0.83467	1.0:0.0:0.0:0.0	.	208;202	B7Z5Z2;P62070	.;RRAS2_HUMAN	A	167;208;125;125;202;125;125;125	ENSP00000437547:V167A;ENSP00000441722:V208A;ENSP00000403282:V125A;ENSP00000433230:V125A;ENSP00000256196:V202A;ENSP00000437083:V125A;ENSP00000434104:V125A;ENSP00000431954:V125A	ENSP00000256196:V202A	V	-	2	0	RRAS2	14257469	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.274000	0.95731	2.276000	0.75962	0.454000	0.30748	GTC		0.403	RRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386035.1	NM_012250		G	14300893	A	G	14300893	3	3	9	1	0	0	0	0	1	0	0	0	13714	275	10	4	13	4	RRAS2	11	14300893	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	5128602	14300893	120705623	95	992										
SOX6	55553	hgsc.bcm.edu	37	chr11	16071410	16071410	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gggaagaggttctgggtgggAgacgttggggactttacagg	20	4	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:16071410A>G	ENST00000352083.6	-	11	1403	c.1326T>C	c.(1324-1326)tcT>tcC	p.S442S	SOX6_ENST00000527619.1_Silent_p.S404S|SOX6_ENST00000528252.1_Silent_p.S401S|SOX6_ENST00000528429.1_Silent_p.S442S|SOX6_ENST00000396356.3_Silent_p.S442S|SOX6_ENST00000316399.6_Silent_p.S442S			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	442					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						TCTGGGTGGGAGACGTTGGGG	0.512																																																0			11											235	241	239					11																	16071410		2200	4294	6494	16027986	SO:0001819	synonymous_variant	55553			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.1326T>C	11.37:g.16071410A>G			16027986	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Silent	SNP	ENST00000352083.6	37																																																																																					0.512	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		G	16071410	A	G	16071410	2	3	9	1	0	0	0	0	0	0	0	1	14992	291	11	4		4	SOX6	11	16071410	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	1770517	16071410	118935106	96	993										
SLC43A3	29015	hgsc.bcm.edu	37	chr11	57193533	57193533	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccttaaagtaatcttcattcTtgaagacaaacactagtgaa	5	8	3	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:57193533T>C	ENST00000395123.2	-	3	417	c.113A>G	c.(112-114)aAg>aGg	p.K38R	SLC43A3_ENST00000352187.1_Missense_Mutation_p.K38R|SLC43A3_ENST00000529554.1_Missense_Mutation_p.K38R|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000533524.1_Missense_Mutation_p.K38R|SLC43A3_ENST00000395124.1_Missense_Mutation_p.K38R	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	38					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						ATCTTCATTCTTGAAGACAAA	0.552																																																0			11											95	91	92					11																	57193533		2201	4296	6497	56950109	SO:0001583	missense	29015			AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.113A>G	11.37:g.57193533T>C	ENSP00000378555:p.Lys38Arg		56950109	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688833	0.68271	.	.	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005;ENST00000525474;ENST00000529112;ENST00000528187;ENST00000529494;ENST00000533245;ENST00000533235;ENST00000524863;ENST00000532795;ENST00000533051;ENST00000529896;ENST00000526621;ENST00000530316	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.70448	0.3225	M	0.86651	2.83	0.49798	D	0.999822	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.999;0.995	T	0.71377	-0.4611	10	0.25106	T	0.35	-15.2193	13.6946	0.62569	0.0:0.0:0.0:1.0	.	38;38;38	B4DV87;E7EQD2;Q8NBI5	.;.;S43A3_HUMAN	R	38	ENSP00000378555:K38R;ENSP00000378556:K38R;ENSP00000337561:K38R;ENSP00000436254:K38R;ENSP00000434515:K38R;ENSP00000435893:K38R;ENSP00000436055:K38R;ENSP00000434913:K38R;ENSP00000435273:K38R;ENSP00000433974:K38R;ENSP00000431762:K38R;ENSP00000435156:K38R;ENSP00000434569:K38R;ENSP00000435109:K38R;ENSP00000435490:K38R;ENSP00000431367:K38R;ENSP00000434710:K38R	ENSP00000337561:K38R	K	-	2	0	SLC43A3	56950109	1.000000	0.71417	0.909000	0.35828	0.049000	0.14656	6.465000	0.73538	2.057000	0.61298	0.459000	0.35465	AAG		0.552	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		C	57193533	T	C	57193533	3	2	9	1	0	0	0	0	1	0	0	0	14671	1609	56	4	1410	4	SLC43A3	11	57193533	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	41122123	57193533	77812983	97	994										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64674883	64674883	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcatcctcgtcatccgagtcCgagtctggggtgagatcaaa	12	11	3	1	rs200748453		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:64674883C>T	ENST00000377264.3	-	19	2788	c.2676G>A	c.(2674-2676)tcG>tcA	p.S892S	ATG2A_ENST00000421419.2_Silent_p.S892S	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	892					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CATCCGAGTCCGAGTCTGGGG	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		16120	0		0	False		,,,				2504	0															0			11											54	47	49					11																	64674883		2191	4291	6482	64431459	SO:0001819	synonymous_variant	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.2676G>A	11.37:g.64674883C>T			64431459	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	5.864	0.343495	0.11069	.	.	ENSG00000110046	ENST00000418259	.	.	.	4.33	-6.54	0.01860	.	.	.	.	.	T	0.43411	0.1246	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42344	-0.9457	4	.	.	.	.	4.3031	0.10933	0.1146:0.4647:0.1164:0.3043	.	.	.	.	R	694	.	.	G	-	1	0	ATG2A	64431459	0.017000	0.18338	0.759000	0.31340	0.468000	0.32798	-1.602000	0.02079	-1.495000	0.01831	-1.084000	0.02203	GGA		0.632	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		T	64674883	C	T	64674883	2	4	9	1	0	0	0	0	0	0	0	1	1094	639	23	1		1	ATG2A	11	64674883	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	7481350	64674883	70331633	98	995										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68575066	68575066	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	caggccggtgccaaacagcaCgccgctgaccacgttcttcg	11	16	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:68575066C>T	ENST00000265641.5	-	4	476	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	CPT1A_ENST00000376618.2_Missense_Mutation_p.V108M|CPT1A_ENST00000540367.1_Missense_Mutation_p.V108M|CPT1A_ENST00000539743.1_Missense_Mutation_p.V108M	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	108					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	CCAAACAGCACGCCGCTGACC	0.617																																																0			11											159	116	131					11																	68575066		2200	4294	6494	68331642	SO:0001583	missense	1374			L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.322G>A	11.37:g.68575066C>T	ENSP00000265641:p.Val108Met		68331642	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	37	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	C	9.438	1.087355	0.20390	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46	6.04	-5.37	0.02681	.	0.693653	0.14398	N	0.322103	T	0.72755	0.3500	M	0.80847	2.515	0.21290	N	0.99973	B;B;B	0.24132	0.068;0.07;0.098	B;B;B	0.25759	0.018;0.042;0.063	T	0.60546	-0.7242	10	0.32370	T	0.25	.	3.9711	0.09454	0.0818:0.3808:0.1611:0.3764	.	108;108;108	B2RAQ8;P50416;P50416-2	.;CPT1A_HUMAN;.	M	108	ENSP00000439084:V108M;ENSP00000365803:V108M;ENSP00000265641:V108M;ENSP00000446108:V108M	ENSP00000265641:V108M	V	-	1	0	CPT1A	68331642	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-1.387000	0.02535	-0.557000	0.06126	-0.219000	0.12488	GTG		0.617	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		T	68575066	C	T	68575066	3	4	9	1	0	0	0	0	1	0	0	0	3837	536	19	1	2103	1	CPT1A	11	68575066	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	3900183	68575066	66431450	99	996										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105797501	105797501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaattgttggaggtgtttggTggttctttacactcatcatt	11	5	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:105797501T>C	ENST00000530497.1	+	12	1882	c.1882T>C	c.(1882-1884)Tgg>Cgg	p.W628R	GRIA4_ENST00000393127.2_Missense_Mutation_p.W628R|GRIA4_ENST00000282499.5_Missense_Mutation_p.W628R|GRIA4_ENST00000525187.1_Missense_Mutation_p.W628R			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	628					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AGGTGTTTGGTGGTTCTTTAC	0.393																																																0			11											139	139	139					11																	105797501		2202	4298	6500	105302711	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1882T>C	11.37:g.105797501T>C	ENSP00000435775:p.Trp628Arg		105302711	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.579226	0.86645	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.6	5.6	0.85130	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000003	T	0.82033	0.4949	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.88285	0.2939	10	0.87932	D	0	.	16.0858	0.81049	0.0:0.0:0.0:1.0	.	628;628	P48058;G3V164	GRIA4_HUMAN;.	R	628	ENSP00000282499:W628R;ENSP00000376835:W628R;ENSP00000435775:W628R;ENSP00000432180:W628R	ENSP00000282499:W628R	W	+	1	0	GRIA4	105302711	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.997000	0.88414	2.264000	0.75181	0.533000	0.62120	TGG		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			C	105797501	T	C	105797501	3	2	9	1	0	0	0	0	1	0	0	0	6791	1696	59	4	1965	4	GRIA4	11	105797501	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	37222435	105797501	29209015	100	997										
HMBS	3145	hgsc.bcm.edu	37	chr11	118962859	118962859	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgcaccctgaggaatgcatgTatgctgtgggccaggtacac	13	10	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:118962859T>C	ENST00000278715.3	+	10	788	c.637T>C	c.(637-639)Tat>Cat	p.Y213H	HMBS_ENST00000544387.1_Missense_Mutation_p.Y213H|HMBS_ENST00000392841.1_Missense_Mutation_p.Y196H|HMBS_ENST00000542729.1_Missense_Mutation_p.Y196H|HMBS_ENST00000537841.1_Missense_Mutation_p.Y196H|HMBS_ENST00000442944.2_Missense_Mutation_p.Y196H|HMBS_ENST00000543090.1_Intron	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	213					heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		GGAATGCATGTATGCTGTGGG	0.532																																																0			11											104	89	94					11																	118962859		2200	4295	6495	118468069	SO:0001583	missense	3145			X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type"	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.637T>C	11.37:g.118962859T>C	ENSP00000278715:p.Tyr213His		118468069	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Missense_Mutation	SNP	ENST00000278715.3	37	CCDS8409.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.473863	0.63737	.	.	ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000149397	ENST00000278715;ENST00000537841;ENST00000542729;ENST00000546302;ENST00000544387;ENST00000392841;ENST00000442944	D;D;D;D;D;D;D	0.99680	-6.38;-6.38;-6.38;-6.38;-6.38;-6.38;-6.38	5.3	5.3	0.74995	Porphobilinogen deaminase, N-terminal (1);	0.112533	0.64402	D	0.000006	D	0.99351	0.9772	L	0.41027	1.25	0.80722	D	1	D;D;B;D	0.69078	0.996;0.996;0.003;0.997	P;P;B;D	0.69824	0.906;0.906;0.047;0.966	D	0.98914	1.0781	10	0.33940	T	0.23	-0.7086	14.5779	0.68262	0.0:0.0:0.0:1.0	.	196;196;213;213	P08397-2;G3V1P4;G5EA58;P08397	.;.;.;HEM3_HUMAN	H	213;196;196;187;213;196;196	ENSP00000278715:Y213H;ENSP00000444730:Y196H;ENSP00000443058:Y196H;ENSP00000445599:Y187H;ENSP00000438424:Y213H;ENSP00000376584:Y196H;ENSP00000392041:Y196H	ENSP00000392041:Y196H	Y	+	1	0	CTD-2589C9.4;HMBS	118468069	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.045000	0.76585	2.220000	0.72140	0.528000	0.53228	TAT		0.532	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190		C	118962859	T	C	118962859	3	2	9	1	0	0	0	0	1	0	0	0	7240	1638	57	4	675	4	HMBS	11	118962859	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	13165358	118962859	16043657	101	998										
KCNJ1	3758	hgsc.bcm.edu	37	chr11	128710086	128710086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agactagccttgctctttgcCgagaatgcccaaaaaagcga	9	11	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:128710086C>T	ENST00000392664.2	-	2	226	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	KCNJ1_ENST00000324036.3_Missense_Mutation_p.R18Q|KCNJ1_ENST00000392665.2_Missense_Mutation_p.R18Q|KCNJ1_ENST00000392666.1_Missense_Mutation_p.R18Q|KCNJ1_ENST00000440599.2_Missense_Mutation_p.R18Q	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	37					cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	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)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	TGCTCTTTGCCGAGAATGCCC	0.418																																																0			11											134	128	130					11																	128710086		2201	4297	6498	128215296	SO:0001583	missense	3758			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.110G>A	11.37:g.128710086C>T	ENSP00000376432:p.Arg37Gln		128215296	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	.	.	.	.	.	.	.	.	.	.	C	7.962	0.747129	0.15710	.	.	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664;ENST00000324003	D;D;D;D;D;D	0.94576	-2.6;-2.6;-2.6;-2.6;-2.56;-3.46	5.66	3.45	0.39498	.	0.436377	0.23407	N	0.048517	D	0.86535	0.5956	N	0.08118	0	0.18873	N	0.999983	B	0.06786	0.001	B	0.04013	0.001	T	0.77536	-0.2551	10	0.40728	T	0.16	.	12.4615	0.55734	0.0:0.8051:0.1217:0.0732	.	37	P48048	IRK1_HUMAN	Q	18;18;18;18;37;18	ENSP00000376433:R18Q;ENSP00000376434:R18Q;ENSP00000406320:R18Q;ENSP00000316233:R18Q;ENSP00000376432:R37Q;ENSP00000316136:R18Q	ENSP00000316136:R18Q	R	-	2	0	KCNJ1	128215296	0.285000	0.24296	0.261000	0.24466	0.098000	0.18820	3.278000	0.51662	1.404000	0.46819	0.455000	0.32223	CGG		0.418	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		T	128710086	C	T	128710086	3	4	9	1	0	0	0	0	1	0	0	0	8064	652	23	1	1069	1	KCNJ1	11	128710086	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	9747227	128710086	6296430	102	999										
KCNJ1	3758	hgsc.bcm.edu	37	chr11	128710105	128710105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccgagaatgcccaaaaaagcGagtgacgacccatttccgaa	9	12	0	2	rs139738175	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr11:128710105G>A	ENST00000392664.2	-	2	207	c.91C>T	c.(91-93)Cgc>Tgc	p.R31C	KCNJ1_ENST00000324036.3_Missense_Mutation_p.R12C|KCNJ1_ENST00000392665.2_Missense_Mutation_p.R12C|KCNJ1_ENST00000392666.1_Missense_Mutation_p.R12C|KCNJ1_ENST00000440599.2_Missense_Mutation_p.R12C	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	31					cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	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)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	CCAAAAAAGCGAGTGACGACC	0.398													G|||	2	0.000399361	0	0	5008	,	,		22652	0		0	False		,,,				2504	0.002															0			11						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4402		0,0,2201	119	114	115		91,34,34,34,34	4.6	0.1	11	dbSNP_134	115	2,8592	2.2+/-6.3	0,2,4295	no	missense,missense,missense,missense,missense	KCNJ1	NM_000220.2,NM_153764.1,NM_153765.1,NM_153766.1,NM_153767.2	180,180,180,180,180	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	31/392,12/373,12/373,12/373,12/373	128710105	2,12994	2201	4297	6498	128215315	SO:0001583	missense	3758			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.91C>T	11.37:g.128710105G>A	ENSP00000376432:p.Arg31Cys		128215315	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	.	.	.	.	.	.	.	.	.	.	G	4.534	0.099203	0.08681	0.0	2.33E-4	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664;ENST00000324003	D;D;D;D;D;D	0.94828	-2.66;-2.66;-2.66;-2.66;-2.6;-3.53	5.52	4.61	0.57282	.	2.062200	0.02849	U	0.128955	D	0.88883	0.6558	N	0.08118	0	0.09310	N	1	P	0.39116	0.66	B	0.32805	0.153	T	0.80264	-0.1455	10	0.39692	T	0.17	.	14.3601	0.66766	0.0711:0.0:0.9289:0.0	.	31	P48048	IRK1_HUMAN	C	12;12;12;12;31;12	ENSP00000376433:R12C;ENSP00000376434:R12C;ENSP00000406320:R12C;ENSP00000316233:R12C;ENSP00000376432:R31C;ENSP00000316136:R12C	ENSP00000316136:R12C	R	-	1	0	KCNJ1	128215315	0.969000	0.33509	0.053000	0.19242	0.052000	0.14988	4.470000	0.60175	1.344000	0.45657	0.455000	0.32223	CGC		0.398	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		A	128710105	G	A	128710105	3	1	9	1	0	0	0	0	1	0	0	0	8064	1058	37	1	1088	1	KCNJ1	11	128710105	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	19	128710105	6296411	103	1000										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	9	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		25398281	108453614	104	1001										
KRT73	319101	hgsc.bcm.edu	37	chr12	53005112	53005112	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctgctagctgcagctcctggAactagaggaaaaggaaccaa	11	10	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:53005112A>G	ENST00000305748.3	-	6	1020	c.986T>C	c.(985-987)tTc>tCc	p.F329S	RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	329	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGCTCCTGGAACTAGAGGAA	0.562																																																0			12											84	77	79					12																	53005112		2203	4300	6503	51291379	SO:0001630	splice_region_variant	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.985-1T>C	12.37:g.53005112A>G			51291379	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.463856	0.63513	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;T	0.88431	-2.38;-1.07	5.61	5.61	0.85477	Filament (1);	0.000000	0.56097	D	0.000036	D	0.92361	0.7576	M	0.66939	2.045	0.36753	D	0.882864	D	0.57257	0.979	P	0.62740	0.906	D	0.94415	0.7635	10	0.72032	D	0.01	.	11.2268	0.48888	0.8633:0.0:0.0:0.1367	.	329	Q86Y46	K2C73_HUMAN	S	329;74	ENSP00000307014:F329S;ENSP00000449081:F74S	ENSP00000307014:F329S	F	-	2	0	KRT73	51291379	0.985000	0.35326	1.000000	0.80357	0.626000	0.37791	0.784000	0.26816	2.276000	0.75962	0.454000	0.30748	TTC		0.562	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	Missense_Mutation	G	53005112	A	G	53005112	5	3	9	1	0	0	0	0	0	0	1	0	8507	260	9	4	652	4	KRT73	12	53005112	Splice_Site	SNP	A	TCGA-AF-5654-01A-01D-1657-10	27606831	53005112	80846783	105	1002										
SP7	121340	hgsc.bcm.edu	37	chr12	53722892	53722892	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agagctgtgccccttgggcaCtagtagcccagggtcctggg	15	12	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:53722892C>T	ENST00000536324.2	-	3	617	c.334G>A	c.(334-336)Gtg>Atg	p.V112M	SP7_ENST00000537210.2_Missense_Mutation_p.V94M|SP7_ENST00000303846.3_Missense_Mutation_p.V112M	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	112					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						CCCTTGGGCACTAGTAGCCCA	0.587																																																0			12											98	100	100					12																	53722892		1936	4147	6083	52009159	SO:0001583	missense	121340			AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.334G>A	12.37:g.53722892C>T	ENSP00000443827:p.Val112Met		52009159	B3KY26|Q3MJ72|Q7Z718	Missense_Mutation	SNP	ENST00000536324.2	37	CCDS44897.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.368998	0.42003	.	.	ENSG00000170374	ENST00000536324;ENST00000303846;ENST00000537210;ENST00000547755	T;T;T;T	0.49720	3.26;3.26;3.26;0.77	3.69	2.8	0.32819	.	0.269330	0.30193	N	0.010193	T	0.48314	0.1493	L	0.34521	1.04	0.31444	N	0.671607	D	0.58268	0.982	P	0.56434	0.798	T	0.55166	-0.8183	10	0.49607	T	0.09	.	10.8907	0.46994	0.0:0.9019:0.0:0.0981	.	112	Q8TDD2	SP7_HUMAN	M	112;112;94;94	ENSP00000443827:V112M;ENSP00000302812:V112M;ENSP00000441367:V94M;ENSP00000449355:V94M	ENSP00000302812:V112M	V	-	1	0	SP7	52009159	0.167000	0.22975	0.995000	0.50966	0.423000	0.31445	1.739000	0.38217	1.140000	0.42260	0.313000	0.20887	GTG		0.587	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53722892	C	T	53722892	3	4	9	1	0	0	0	0	1	0	0	0	15006	565	20	3	965	3	SP7	12	53722892	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	717780	53722892	80129003	106	1003										
COPZ1	22818	hgsc.bcm.edu	37	chr12	54737081	54737081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tctctatttctatgtgattgGcagctcctatgaaaatgagg	9	7	2	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:54737081G>A	ENST00000262061.2	+	4	279	c.242G>A	c.(241-243)gGc>gAc	p.G81D	COPZ1_ENST00000548753.1_5'UTR|COPZ1_ENST00000553231.1_Missense_Mutation_p.G58D|COPZ1_ENST00000552362.1_Missense_Mutation_p.G81D|RN7SL744P_ENST00000577604.1_RNA|COPZ1_ENST00000552218.1_Missense_Mutation_p.G81D|COPZ1_ENST00000551779.1_Missense_Mutation_p.G81D|COPZ1_ENST00000548281.1_Intron|RP11-968A15.8_ENST00000553061.1_RNA|COPZ1_ENST00000455864.2_Missense_Mutation_p.G58D|COPZ1_ENST00000549116.1_Intron|COPZ1_ENST00000549043.1_Missense_Mutation_p.G89D|COPZ1_ENST00000416254.2_Intron	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1	81					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						TATGTGATTGGCAGCTCCTAT	0.443																																																0			12											160	160	160					12																	54737081		2203	4300	6503	53023348	SO:0001583	missense	22818			AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"coatomer protein complex, subunit zeta"	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.242G>A	12.37:g.54737081G>A	ENSP00000262061:p.Gly81Asp		53023348	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	37	CCDS8877.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884857	0.91814	.	.	ENSG00000111481	ENST00000552848;ENST00000262061;ENST00000549043;ENST00000552218;ENST00000553231;ENST00000552362;ENST00000455864;ENST00000551779;ENST00000550713	.	.	.	5.34	5.34	0.76211	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.87704	0.6244	H	0.96489	3.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.91268	0.5042	9	0.87932	D	0	-12.5301	16.9051	0.86124	0.0:0.0:1.0:0.0	.	58;89;81	B4DDX8;F8VWL5;P61923	.;.;COPZ1_HUMAN	D	81;81;89;81;58;81;58;81;89	.	ENSP00000262061:G81D	G	+	2	0	COPZ1	53023348	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.820000	0.92003	2.668000	0.90789	0.655000	0.94253	GGC		0.443	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057		A	54737081	G	A	54737081	3	1	9	1	0	0	0	0	1	0	0	0	3747	1203	42	3	256	3	COPZ1	12	54737081	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1014189	54737081	79114814	107	1004										
GEFT	115557	hgsc.bcm.edu	37	chr12	58007244	58007244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cacctgaagaggagactttgTcccaagcccctgagagtgag	12	11	0	5			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:58007244T>C	ENST00000286494.4	+	4	890	c.430T>C	c.(430-432)Tcc>Ccc	p.S144P	AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.S183P	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	144						cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAGACTTTGTCCCAAGCCCC	0.532																																																0			12											98	101	100					12																	58007244		2203	4300	6503	56293511	SO:0001583	missense	0				CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.430T>C	12.37:g.58007244T>C	ENSP00000286494:p.Ser144Pro		56293511	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	.	.	.	.	.	.	.	.	.	.	t	16.35	3.098801	0.56183	.	.	ENSG00000240771	ENST00000333972;ENST00000300189;ENST00000286494	T;T	0.26373	1.74;1.74	3.89	1.4	0.22301	Dbl homology (DH) domain (1);	0.000000	0.37437	N	0.002083	T	0.32255	0.0823	L	0.43152	1.355	0.33573	D	0.598887	D;D;B	0.76494	0.999;0.997;0.027	D;P;B	0.74674	0.984;0.795;0.022	T	0.38112	-0.9676	10	0.37606	T	0.19	.	3.8732	0.09045	0.1898:0.1138:0.0:0.6964	.	183;144;18	F8W7Z4;Q86VW2;Q96M35	.;ARHGP_HUMAN;.	P	183;18;144	ENSP00000335560:S183P;ENSP00000286494:S144P	ENSP00000286494:S144P	S	+	1	0	ARHGEF25	56293511	0.880000	0.30214	0.894000	0.35097	0.970000	0.65996	0.794000	0.26958	1.556000	0.49512	0.374000	0.22700	TCC		0.532	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		C	58007244	T	C	58007244	3	2	9	1	0	0	0	0	1	0	0	0	6348	1667	58	4	666	4	GEFT	12	58007244	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	3270163	58007244	75844651	108	1005										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63544209	63544209	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	accagcatgtaggccgacgcAaacatgccgaacacctgcag	10	14	0	0	rs1042615	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:63544209A>G	ENST00000299178.2	-	1	513	c.408T>C	c.(406-408)ttT>ttC	p.F136F		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	136					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	AGGCCGACGCAAACATGCCGA	0.652													G|||	3259	0.650759	0.8525	0.6441	5008	,	,		18342	0.4583		0.5368	False		,,,				2504	0.6984															0			12						G		3636,770		1504,628,71	26	32	30		408	4.9	1	12	dbSNP_86	30	4976,3620		1454,2068,776	no	coding-synonymous	AVPR1A	NM_000706.3		2958,2696,847	GG,GA,AA		42.1126,17.4762,33.764		136/419	63544209	8612,4390	2203	4298	6501	61830476	SO:0001819	synonymous_variant	552			L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.408T>C	12.37:g.63544209A>G			61830476		Silent	SNP	ENST00000299178.2	37	CCDS8965.1																																																																																				0.652	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			G	63544209	A	G	63544209	2	3	9	1	0	0	0	0	0	0	0	1	1232	127	5	4		4	AVPR1A	12	63544209	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	5536965	63544209	70307686	109	1006										
NOS1	4842	hgsc.bcm.edu	37	chr12	117724058	117724058	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ttccagcctttccatgtgggCtttggagccaaatctgagtg	11	10	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:117724058C>T	ENST00000338101.4	-	5	1145	c.1141G>A	c.(1141-1143)Gcc>Acc	p.A381T	NOS1_ENST00000317775.6_Missense_Mutation_p.A381T|NOS1_ENST00000344089.3_Silent_p.K399K			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TCCATGTGGGCTTTGGAGCCA	0.517																																					Esophageal Squamous(162;1748 2599 51982 52956)											0			12											137	132	134					12																	117724058		2059	4213	6272	116208441	SO:0001583	missense	340719				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1141G>A	12.37:g.117724058C>T	ENSP00000337459:p.Ala381Thr		116208441		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.714793	0.68730	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.26223	1.75;1.75	5.14	4.25	0.50352	Nitric oxide synthase, oxygenase domain (3);	0.049306	0.85682	N	0.000000	T	0.31451	0.0797	M	0.71920	2.185	0.80722	D	1	B	0.15719	0.014	B	0.21708	0.036	T	0.17440	-1.0369	10	0.66056	D	0.02	-24.8012	13.3991	0.60872	0.0:0.9251:0.0:0.0749	.	381	P29475	NOS1_HUMAN	T	381	ENSP00000320758:A381T;ENSP00000337459:A381T	ENSP00000320758:A381T	A	-	1	0	NOS1	116208441	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.769000	0.62300	1.397000	0.46682	0.591000	0.81541	GCC		0.517	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117724058	C	T	117724058	3	4	9	1	0	0	0	0	1	0	0	0	10572	797	28	3	3259	3	NOS1	12	117724058	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	54179849	117724058	16127837	110	1007										
WSB2	55884	hgsc.bcm.edu	37	chr12	118490150	118490150	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggccaggggatcagtttgacGatgcagtgtccttgagacca	14	9	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:118490150G>A	ENST00000315436.3	-	2	288	c.147C>T	c.(145-147)atC>atT	p.I49I	WSB2_ENST00000535496.1_Silent_p.I51I|WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000542304.1_5'UTR|WSB2_ENST00000544233.1_5'UTR|WSB2_ENST00000441406.2_Silent_p.I66I	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	49					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCAGTTTGACGATGCAGTGTC	0.557																																																0			12											78	76	77					12																	118490150		2203	4300	6503	116974533	SO:0001819	synonymous_variant	55884			AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"WD repeat domain containing"	19222	protein-coding gene	gene with protein product			"WD repeat and SOCS box-containing 2"			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.147C>T	12.37:g.118490150G>A			116974533	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																				0.557	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639		A	118490150	G	A	118490150	2	1	9	1	0	0	0	0	0	0	0	1	17445	1048	37	1		1	WSB2	12	118490150	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	766092	118490150	15361745	111	1008										
WDR66	144406	hgsc.bcm.edu	37	chr12	122386916	122386916	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gttacttttaacccaacaaaTaataaagaattggtgagcaa	6	6	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:122386916T>A	ENST00000288912.4	+	8	2072	c.1218T>A	c.(1216-1218)aaT>aaA	p.N406K	WDR66_ENST00000397454.2_Missense_Mutation_p.N406K	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	406							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		ACCCAACAAATAATAAAGAAT	0.269																																					Esophageal Squamous(85;849 1794 49757 52143)											0			12											70	68	69					12																	122386916		1786	4041	5827	120871299	SO:0001583	missense	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.1218T>A	12.37:g.122386916T>A	ENSP00000288912:p.Asn406Lys		120871299	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430396	0.62844	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.63913	1.01;-0.07	5.69	0.748	0.18376	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.098691	0.64402	D	0.000002	T	0.56455	0.1986	M	0.66939	2.045	0.33095	D	0.538462	B	0.25521	0.128	B	0.26094	0.066	T	0.59915	-0.7364	10	0.66056	D	0.02	.	9.096	0.36640	0.0:0.2895:0.0:0.7105	.	406	Q8TBY9	WDR66_HUMAN	K	406	ENSP00000288912:N406K;ENSP00000380595:N406K	ENSP00000288912:N406K	N	+	3	2	WDR66	120871299	0.992000	0.36948	0.959000	0.39883	0.843000	0.47879	1.213000	0.32407	-0.099000	0.12263	-0.280000	0.10049	AAT		0.269	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		A	122386916	T	A	122386916	3	1	9	1	0	0	0	0	1	0	0	0	17357	1403	49	5	1244	5	WDR66	12	122386916	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	3896766	122386916	11464979	112	1009										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124838658	124838658	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cgtgggtgatggagccgcggTatgtgatggcgctgtccgag	19	8	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:124838658T>C	ENST00000405201.1	-	27	3674	c.3674A>G	c.(3673-3675)tAc>tGc	p.Y1225C	NCOR2_ENST00000356219.3_Missense_Mutation_p.Y1232C|NCOR2_ENST00000397355.1_Missense_Mutation_p.Y1216C|NCOR2_ENST00000404621.1_Missense_Mutation_p.Y1215C|NCOR2_ENST00000429285.2_Missense_Mutation_p.Y1215C|NCOR2_ENST00000404121.2_Missense_Mutation_p.Y786C			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1233					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GGAGCCGCGGTATGTGATGGC	0.617																																																0			12											43	50	48					12																	124838658		2145	4238	6383	123404611	SO:0001583	missense	9612			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3674A>G	12.37:g.124838658T>C	ENSP00000384018:p.Tyr1225Cys		123404611	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	T	14.15	2.450482	0.43531	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.36520	2.0;2.28;2.01;2.28;2.01;2.28;1.25	4.94	4.94	0.65067	.	0.066854	0.64402	D	0.000008	T	0.55321	0.1913	L	0.60455	1.87	0.49483	D	0.999793	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70935	0.971;0.953;0.971	T	0.58831	-0.7567	10	0.66056	D	0.02	-24.1613	14.6022	0.68447	0.0:0.0:0.0:1.0	.	1215;1216;1225	C9J0Q5;C9J239;C9JFD3	.;.;.	C	1225;1215;1232;1216;1224;786;1215;1233	ENSP00000384018:Y1225C;ENSP00000384202:Y1215C;ENSP00000348551:Y1232C;ENSP00000380513:Y1216C;ENSP00000385618:Y786C;ENSP00000400281:Y1215C;ENSP00000402808:Y1233C	ENSP00000348551:Y1232C	Y	-	2	0	NCOR2	123404611	1.000000	0.71417	0.957000	0.39632	0.464000	0.32679	4.176000	0.58269	1.852000	0.53769	0.459000	0.35465	TAC		0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		C	124838658	T	C	124838658	3	2	9	1	0	0	0	0	1	0	0	0	10267	1638	57	4	3954	4	NCOR2	12	124838658	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	2451742	124838658	9013237	113	1010										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126137055	126137055	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtcctggatgaccgagtcacCatcgcggagctgggagtgca	15	11	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr12:126137055C>A	ENST00000299308.3	+	8	1976	c.1968C>A	c.(1966-1968)acC>acA	p.T656T	TMEM132B_ENST00000535886.1_Silent_p.T168T	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	656						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		ACCGAGTCACCATCGCGGAGC	0.592																																																0			12											45	48	47					12																	126137055		2100	4239	6339	124703008	SO:0001819	synonymous_variant	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1968C>A	12.37:g.126137055C>A			124703008	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																				0.592	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		A	126137055	C	A	126137055	2	1	9	1	0	0	0	0	0	0	0	1	16085	581	21	2		2	TMEM132B	12	126137055	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1298397	126137055	7714840	114	1011										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20632767	20632767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	caaagagatgaagaacaaagCagttctttgcaaacctttaa	7	7	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr13:20632767C>T	ENST00000382874.2	+	16	2736	c.2546C>T	c.(2545-2547)gCa>gTa	p.A849V	ZMYM2_ENST00000382883.3_Missense_Mutation_p.A331V|ZMYM2_ENST00000382871.2_Missense_Mutation_p.A849V|ZMYM2_ENST00000382869.3_Missense_Mutation_p.A849V	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	849					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		AAGAACAAAGCAGTTCTTTGC	0.373																																																0			13											143	135	137					13																	20632767		1877	4112	5989	19530767	SO:0001583	missense	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.2546C>T	13.37:g.20632767C>T	ENSP00000372327:p.Ala849Val		19530767	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	C	32	5.122516	0.94429	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382883;ENST00000382870	T;T	0.57107	1.98;0.42	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.73133	0.3548	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.77156	-0.2691	10	0.72032	D	0.01	-0.7548	18.2277	0.89923	0.0:1.0:0.0:0.0	.	849	Q9UBW7	ZMYM2_HUMAN	V	849;849;847;847;331;227	ENSP00000372322:A849V;ENSP00000372336:A331V	ENSP00000372322:A849V	A	+	2	0	ZMYM2	19530767	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	7.445000	0.80570	2.378000	0.81104	0.585000	0.79938	GCA		0.373	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		T	20632767	C	T	20632767	3	4	9	1	0	0	0	0	1	0	0	0	17739	710	25	3	2596	3	ZMYM2	13	20632767	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		20632767	94537111	115	1012										
FLT1	2321	hgsc.bcm.edu	37	chr13	29001900	29001900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	caaacttaccattgacaattAgagtggcagtgaggttttta	9	6	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr13:29001900A>G	ENST00000282397.4	-	9	1516	c.1265T>C	c.(1264-1266)cTa>cCa	p.L422P	FLT1_ENST00000539099.1_Missense_Mutation_p.L422P|FLT1_ENST00000541932.1_Missense_Mutation_p.L422P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	422			L -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTGACAATTAGAGTGGCAGT	0.353																																																0			13											140	127	131					13																	29001900		2203	4300	6503	27899900	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1265T>C	13.37:g.29001900A>G	ENSP00000282397:p.Leu422Pro		27899900	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740481	0.69304	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	D;D;D	0.87571	-2.27;-2.27;-2.27	5.73	5.73	0.89815	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.96178	0.8754	H	0.97852	4.09	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97789	1.0237	10	0.87932	D	0	.	16.026	0.80545	1.0:0.0:0.0:0.0	.	422;422;422;422	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	P	422	ENSP00000282397:L422P;ENSP00000437631:L422P;ENSP00000442630:L422P	ENSP00000282397:L422P	L	-	2	0	FLT1	27899900	1.000000	0.71417	0.794000	0.32065	0.746000	0.42486	8.219000	0.89770	2.189000	0.69895	0.528000	0.53228	CTA		0.353	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			G	29001900	A	G	29001900	3	3	9	1	0	0	0	0	1	0	0	0	5960	420	15	4	3102	4	FLT1	13	29001900	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	8369133	29001900	86167978	116	1013										
BRCA2	675	hgsc.bcm.edu	37	chr13	32907503	32907503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atgcttttgaagcaccacttAcatttgcaaatgctgattca	6	9	1	2	rs80359315		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr13:32907503A>G	ENST00000380152.3	+	10	2121	c.1888A>G	c.(1888-1890)Aca>Gca	p.T630A	BRCA2_ENST00000544455.1_Missense_Mutation_p.T630A			P51587	BRCA2_HUMAN	breast cancer 2, early onset	630			T -> I (in ovarian cancer).		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AGCACCACTTACATTTGCAAA	0.313			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											36	37	37					13																	32907503		2181	4221	6402	31805503	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1888A>G	13.37:g.32907503A>G	ENSP00000369497:p.Thr630Ala		31805503	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	12.46	1.946032	0.34377	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00745	5.75;5.75	5.5	-1.97	0.07503	.	0.892392	0.09623	N	0.777347	T	0.00875	0.0029	M	0.70595	2.14	0.09310	N	1	B;P	0.39782	0.028;0.688	B;B	0.31946	0.006;0.138	T	0.41592	-0.9500	10	0.51188	T	0.08	.	1.409	0.02287	0.2725:0.1754:0.3809:0.1712	.	630;630	P51587;A1YBP1	BRCA2_HUMAN;.	A	630	ENSP00000369497:T630A;ENSP00000439902:T630A	ENSP00000369497:T630A	T	+	1	0	BRCA2	31805503	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.103000	0.15292	-0.138000	0.11434	-0.344000	0.07964	ACA		0.313	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32907503	A	G	32907503	3	3	9	1	0	0	0	0	1	0	0	0	1502	391	14	4	1922	4	BRCA2	13	32907503	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	3905603	32907503	82262375	117	1014										
ATP7B	540	hgsc.bcm.edu	37	chr13	52515241	52515241	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aatagccaccaggatggctgTctgtcctttcatctcgtggt	10	11	3	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr13:52515241T>C	ENST00000242839.4	-	16	3688	c.3532A>G	c.(3532-3534)Aca>Gca	p.T1178A	ATP7B_ENST00000344297.5_Missense_Mutation_p.T971A|ATP7B_ENST00000417240.2_Missense_Mutation_p.T389A|ATP7B_ENST00000400370.3_Missense_Mutation_p.T748A|ATP7B_ENST00000418097.2_Missense_Mutation_p.T1113A|ATP7B_ENST00000400366.3_Missense_Mutation_p.T1067A|ATP7B_ENST00000448424.2_Missense_Mutation_p.T1100A|ATP7B_ENST00000482841.1_5'UTR	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1178					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGGATGGCTGTCTGTCCTTTC	0.498									Wilson disease																																							0			13	GRCh37	CM061649	ATP7B	M							167	162	163					13																	52515241		2043	4184	6227	51413242	SO:0001583	missense	540	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3532A>G	13.37:g.52515241T>C	ENSP00000242839:p.Thr1178Ala		51413242	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.790957	0.70452	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05	5.0	5.0	0.66597	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.97676	0.9238	M	0.72353	2.195	0.80722	D	1	P;B;D;B;D;P;D;P	0.60575	0.859;0.134;0.988;0.383;0.988;0.885;0.988;0.908	D;B;D;B;D;P;D;D	0.75484	0.93;0.376;0.986;0.437;0.986;0.905;0.986;0.917	D	0.98487	1.0608	10	0.87932	D	0	-17.8217	15.1541	0.72726	0.0:0.0:0.0:1.0	.	1100;1130;1113;389;748;1067;971;1178	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	A	1178;1067;971;389;1100;748;1113	ENSP00000242839:T1178A;ENSP00000383217:T1067A;ENSP00000342559:T971A;ENSP00000390360:T389A;ENSP00000416738:T1100A;ENSP00000383221:T748A;ENSP00000393343:T1113A	ENSP00000242839:T1178A	T	-	1	0	ATP7B	51413242	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	7.776000	0.85560	2.225000	0.72522	0.533000	0.62120	ACA		0.498	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		C	52515241	T	C	52515241	3	2	9	1	0	0	0	0	1	0	0	0	1192	1667	58	4	889	4	ATP7B	13	52515241	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	19607738	52515241	62654637	118	1015										
COCH	1690	hgsc.bcm.edu	37	chr14	31354666	31354666	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tggagtaagaaaagggatccCcaaagtggtggtggtattta	14	4	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr14:31354666C>T	ENST00000396618.3	+	10	856	c.800C>T	c.(799-801)cCc>cTc	p.P267L	RP11-829H16.3_ENST00000555108.1_RNA|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000475087.1_Missense_Mutation_p.P267L|COCH_ENST00000216361.4_Missense_Mutation_p.P267L|COCH_ENST00000382493.4_Missense_Mutation_p.P118L|RP11-829H16.3_ENST00000468444.2_RNA|COCH_ENST00000460581.2_Missense_Mutation_p.P155L|RP11-829H16.3_ENST00000555421.1_RNA	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	267	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	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;0.00645)		AAAGGGATCCCCAAAGTGGTG	0.408																																																0			14											150	138	142					14																	31354666		2203	4300	6503	30424417	SO:0001583	missense	1690				CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.800C>T	14.37:g.31354666C>T	ENSP00000379862:p.Pro267Leu		30424417	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.982333|3.982333	0.74474|0.74474	.|.	.|.	ENSG00000100473|ENSG00000100473	ENST00000216361;ENST00000396618;ENST00000475087;ENST00000555881;ENST00000460581;ENST00000542225;ENST00000382493|ENST00000468826	D;D;D;D;D;D|D	0.84516|0.83837	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86|-1.77	5.6|5.6	5.6|5.6	0.85130|0.85130	von Willebrand factor, type A (3);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.91294|0.91294	0.7255|0.7255	M|M	0.83692|0.83692	2.655|2.655	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;0.999|.	D;D;D|.	0.97110|.	1.0;0.951;0.951|.	D|D	0.91086|0.91086	0.4903|0.4903	10|7	0.87932|.	D|.	0|.	-10.9833|-10.9833	19.6182|19.6182	0.95643|0.95643	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	118;267;267|.	E7EN67;Q96IU6;O43405|.	.;.;COCH_HUMAN|.	L|S	267;267;267;149;155;155;118|151	ENSP00000216361:P267L;ENSP00000379862:P267L;ENSP00000451528:P267L;ENSP00000452569:P149L;ENSP00000451713:P155L;ENSP00000371933:P118L|ENSP00000452284:P151S	ENSP00000216361:P267L|.	P|P	+|+	2|1	0|0	COCH|COCH	30424417|30424417	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.607000|5.607000	0.67648|0.67648	2.626000|2.626000	0.88956|0.88956	0.650000|0.650000	0.86243|0.86243	CCC|CCA		0.408	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		T	31354666	C	T	31354666	3	4	9	1	0	0	0	0	1	0	0	0	3662	623	22	3	834	3	COCH	14	31354666	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		31354666	75994874	119	1016										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356016	42356016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcggttggcagacaattttgTtacaaatattaaaaggaaag	10	4	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr14:42356016T>C	ENST00000298119.4	+	3	1377	c.188T>C	c.(187-189)gTt>gCt	p.V63A	LRFN5_ENST00000554171.1_Missense_Mutation_p.V63A|LRFN5_ENST00000554120.1_Missense_Mutation_p.V63A	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	63						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		GACAATTTTGTTACAAATATT	0.393										HNSCC(30;0.082)																																						0			14											52	50	51					14																	42356016		2203	4300	6503	41425766	SO:0001583	missense	145581			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.188T>C	14.37:g.42356016T>C	ENSP00000298119:p.Val63Ala		41425766	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499503	0.64298	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.53640	0.61;0.61;0.61	5.56	5.56	0.83823	.	0.000000	0.50627	D	0.000104	T	0.56558	0.1993	L	0.49126	1.545	0.58432	D	0.999996	P;P	0.42584	0.504;0.784	B;P	0.52343	0.356;0.696	T	0.59768	-0.7392	10	0.87932	D	0	.	13.6661	0.62396	0.0:0.0:0.0:1.0	.	63;63	G3V364;Q96NI6	.;LRFN5_HUMAN	A	63	ENSP00000298119:V63A;ENSP00000451897:V63A;ENSP00000451067:V63A	ENSP00000298119:V63A	V	+	2	0	LRFN5	41425766	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.098000	0.63641	0.528000	0.53228	GTT		0.393	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		C	42356016	T	C	42356016	3	2	9	1	0	0	0	0	1	0	0	0	8970	1725	60	4	190	4	LRFN5	14	42356016	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	11001350	42356016	64993524	120	1017										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58909440	58909440	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atagagctcaaagcatgcctGtttttaaggaagtaaaggta	10	5	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr14:58909440G>C	ENST00000556134.1	+	6	656	c.382G>C	c.(382-384)Gtt>Ctt	p.V128L	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Missense_Mutation_p.V143L|KIAA0586_ENST00000354386.6_Missense_Mutation_p.V196L|KIAA0586_ENST00000423743.3_Missense_Mutation_p.V99L|Y_RNA_ENST00000516389.1_RNA	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	128					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AAGCATGCCTGTTTTTAAGGA	0.348																																																0			14											40	38	39					14																	58909440		1836	4098	5934	57979193	SO:0001583	missense	9786			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.382G>C	14.37:g.58909440G>C	ENSP00000452351:p.Val128Leu		57979193	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500661	0.64298	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000554463;ENST00000555833;ENST00000261244;ENST00000546216	T;T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52;0.52	5.22	2.35	0.29111	.	0.672504	0.14027	N	0.346399	T	0.64670	0.2619	L	0.59436	1.845	0.29149	N	0.878496	B;B;D;D;B;B	0.76494	0.356;0.356;0.999;0.959;0.356;0.356	B;B;D;D;B;B	0.67103	0.127;0.127;0.944;0.949;0.127;0.127	T	0.58544	-0.7618	10	0.72032	D	0.01	.	9.9295	0.41514	0.2176:0.0:0.7824:0.0	.	3;3;196;143;128;99	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	L	196;128;99;58;58;143;3	ENSP00000346359:V196L;ENSP00000452351:V128L;ENSP00000399427:V99L;ENSP00000451831:V58L;ENSP00000450855:V58L;ENSP00000261244:V143L	ENSP00000261244:V143L	V	+	1	0	KIAA0586	57979193	1.000000	0.71417	0.991000	0.47740	0.876000	0.50452	1.603000	0.36794	0.701000	0.31803	0.563000	0.77884	GTT		0.348	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		C	58909440	G	C	58909440	3	2	9	1	0	0	0	0	1	0	0	0	8207	1377	48	5	445	5	KIAA0586	14	58909440	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	16553424	58909440	48440100	121	1018										
WDR25	79446	hgsc.bcm.edu	37	chr14	100848014	100848014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cacaggggccctgtcaacacCattcagtggtgtccagtcct	10	14	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr14:100848014C>T	ENST00000335290.6	+	2	979	c.753C>T	c.(751-753)acC>acT	p.T251T	WDR25_ENST00000402312.3_Silent_p.T251T|WDR25_ENST00000554998.1_Silent_p.T251T|WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000554175.1_Silent_p.T251T	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	251										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CTGTCAACACCATTCAGTGGT	0.438																																																0			14											53	51	51					14																	100848014		2203	4300	6503	99917767	SO:0001819	synonymous_variant	79446			BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"WD repeat domain containing"	21064	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 67"	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.753C>T	14.37:g.100848014C>T			99917767	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																				0.438	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		T	100848014	C	T	100848014	2	4	9	1	0	0	0	0	0	0	0	1	17322	581	21	3		3	WDR25	14	100848014	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	41938574	100848014	6501526	122	1019										
HERC2	8924	hgsc.bcm.edu	37	chr15	28459027	28459027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cttgaccgcccaggcgcaggCgaccatcgatgcctccaatc	10	17	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:28459027C>T	ENST00000261609.7	-	42	6755	c.6647G>A	c.(6646-6648)cGc>cAc	p.R2216H		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2216H(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CAGGCGCAGGCGACCATCGAT	0.577																																																1	Substitution - Missense(1)	ovary(1)	15											79	70	73					15																	28459027		2203	4300	6503	26132622	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6647G>A	15.37:g.28459027C>T	ENSP00000261609:p.Arg2216His		26132622		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566452	0.86439	.	.	ENSG00000128731	ENST00000261609	T	0.62105	0.05	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	M	0.79258	2.445	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.81972	-0.0688	10	0.72032	D	0.01	.	19.1711	0.93578	0.0:1.0:0.0:0.0	.	2216	O95714	HERC2_HUMAN	H	2216	ENSP00000261609:R2216H	ENSP00000261609:R2216H	R	-	2	0	HERC2	26132622	1.000000	0.71417	0.933000	0.37362	0.314000	0.28054	7.312000	0.78968	2.774000	0.95407	0.484000	0.47621	CGC		0.577	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28459027	C	T	28459027	3	4	9	1	0	0	0	0	1	0	0	0	7079	768	27	1	8065	1	HERC2	15	28459027	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		28459027	74072365	123	1020										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40582857	40582857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctttgtctccagctttttctTcatctctttggtgtcgctgc	7	12	4	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:40582857T>C	ENST00000260402.3	-	29	3379	c.3130A>G	c.(3130-3132)Aag>Gag	p.K1044E	PLCB2_ENST00000456256.2_Missense_Mutation_p.K1029E|PLCB2_ENST00000557821.1_Missense_Mutation_p.K1040E	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	1044					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		AGCTTTTTCTTCATCTCTTTG	0.587																																																0			15											198	201	200					15																	40582857		2020	4198	6218	38370149	SO:0001583	missense	5330				CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.3130A>G	15.37:g.40582857T>C	ENSP00000260402:p.Lys1044Glu		38370149	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	37	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.934465	0.73442	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.54479	0.57;0.57	4.3	4.3	0.51218	PLC-beta, C-terminal (1);	0.400928	0.24309	N	0.039649	T	0.66247	0.2770	L	0.54323	1.7	0.80722	D	1	D;P;D	0.76494	0.999;0.58;0.984	D;B;P	0.80764	0.994;0.39;0.803	T	0.68368	-0.5427	10	0.59425	D	0.04	.	12.7806	0.57474	0.0:0.0:0.0:1.0	.	1029;1040;1044	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	E	1044;1029	ENSP00000260402:K1044E;ENSP00000411991:K1029E	ENSP00000260402:K1044E	K	-	1	0	PLCB2	38370149	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.685000	0.54678	1.777000	0.52277	0.459000	0.35465	AAG		0.587	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			C	40582857	T	C	40582857	3	2	9	1	0	0	0	0	1	0	0	0	12059	1792	62	4	443	4	PLCB2	15	40582857	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	12123830	40582857	61948535	124	1021										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42529716	42529716	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggaagatgacagcaccaatcCaaaactgaattctcaggaga	9	9	1	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:42529716C>A	ENST00000389834.4	-	9	1046	c.782G>T	c.(781-783)tGg>tTg	p.W261L	TMEM87A_ENST00000448392.1_Missense_Mutation_p.W200L	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	261						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AGCACCAATCCAAAACTGAAT	0.433																																																0			15											98	89	92					15																	42529716		2203	4299	6502	40317008	SO:0001583	missense	25963			AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.782G>T	15.37:g.42529716C>A	ENSP00000374484:p.Trp261Leu		40317008	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	37	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	C	34	5.342950	0.95783	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.8	5.8	0.92144	.	0.062566	0.64402	D	0.000002	D	0.83732	0.5318	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.81665	-0.0830	9	0.34782	T	0.22	-6.4506	20.0566	0.97653	0.0:1.0:0.0:0.0	.	261;200	Q8NBN3;Q8NBN3-3	TM87A_HUMAN;.	L	261;200;237	.	ENSP00000374484:W261L	W	-	2	0	TMEM87A	40317008	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.802000	0.85969	2.750000	0.94351	0.467000	0.42956	TGG		0.433	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		A	42529716	C	A	42529716	3	1	9	1	0	0	0	0	1	0	0	0	16249	595	21	2	933	2	TMEM87A	15	42529716	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1946859	42529716	60001676	125	1022										
CEP152	22995	hgsc.bcm.edu	37	chr15	49031107	49031107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aggggtatgcagctgaatgcGgaagtgattcagaaccatta	13	6	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:49031107G>A	ENST00000380950.2	-	27	4659	c.4472C>T	c.(4471-4473)cCg>cTg	p.P1491L	CEP152_ENST00000399334.3_Missense_Mutation_p.P1435L	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1491					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AGCTGAATGCGGAAGTGATTC	0.438																																																0			15											125	121	122					15																	49031107		1896	4129	6025	46818399	SO:0001583	missense	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4472C>T	15.37:g.49031107G>A	ENSP00000370337:p.Pro1491Leu		46818399	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	G	0.246	-1.010368	0.02095	.	.	ENSG00000103995	ENST00000399334	T	0.48201	0.82	5.2	-6.83	0.01693	.	1.577130	0.04039	N	0.302827	T	0.15089	0.0364	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32134	-0.9918	10	0.02654	T	1	0.8222	6.1866	0.20500	0.3104:0.0:0.4548:0.2349	.	1435	O94986	CE152_HUMAN	L	1435	ENSP00000382271:P1435L	ENSP00000382271:P1435L	P	-	2	0	CEP152	46818399	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.766000	0.01797	-1.189000	0.02702	-2.041000	0.00417	CCG		0.438	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49031107	G	A	49031107	3	1	9	1	0	0	0	0	1	0	0	0	3254	1116	39	1	664	1	CEP152	15	49031107	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	6501391	49031107	53500285	126	1023										
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52885908	52885908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	catcaacaatgccgagaggaTcgaaacgatagttcaagaca	9	9	2	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:52885908T>C	ENST00000261844.7	-	10	2827	c.2675A>G	c.(2674-2676)gAt>gGt	p.D892G	FAM214A_ENST00000546305.2_Missense_Mutation_p.D899G|RP11-23N2.4_ENST00000562062.1_RNA	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	892																	GCCGAGAGGATCGAAACGATA	0.363																																																0			15											35	30	31					15																	52885908		1828	4052	5880	50673200	SO:0001583	missense	56204			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2675A>G	15.37:g.52885908T>C	ENSP00000261844:p.Asp892Gly		50673200	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.329264	0.81690	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T;T	0.39056	1.47;1.1;1.47	6.06	6.06	0.98353	.	0.046933	0.85682	D	0.000000	T	0.44891	0.1315	L	0.43152	1.355	0.58432	D	0.999998	B;B	0.29955	0.222;0.263	B;B	0.37989	0.171;0.262	T	0.41520	-0.9504	10	0.66056	D	0.02	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	899;892	F5H8G0;Q32MH5	.;K1370_HUMAN	G	892;892;891;899	ENSP00000261844:D892G;ENSP00000382153:D892G;ENSP00000443598:D899G	ENSP00000261844:D892G	D	-	2	0	KIAA1370	50673200	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.698000	0.84413	2.323000	0.78572	0.528000	0.53228	GAT		0.363	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		C	52885908	T	C	52885908	3	2	9	1	0	0	0	0	1	0	0	0	8247	1435	50	4	571	4	KIAA1370	15	52885908	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	3854801	52885908	49645484	127	1024										
POLG	5428	hgsc.bcm.edu	37	chr15	89870445	89870445	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tcattggccagatccatcaaCgacttcttcatctcccgctg	6	15	5	1	rs62640034	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr15:89870445C>G	ENST00000268124.5	-	7	1719	c.1386G>C	c.(1384-1386)tcG>tcC	p.S462S	POLG_ENST00000442287.2_Silent_p.S462S	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	462					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GATCCATCAACGACTTCTTCA	0.602								DNA polymerases (catalytic subunits)																													Colon(73;648 1203 11348 18386 27782)											0			15											95	90	92					15																	89870445		2200	4299	6499	87671449	SO:0001819	synonymous_variant	5428			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.1386G>C	15.37:g.89870445C>G			87671449	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																				0.602	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		G	89870445	C	G	89870445	2	3	9	1	0	0	0	0	0	0	0	1	12231	523	19	5		5	POLG	15	89870445	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	36984537	89870445	12660947	128	1025										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4797375	4797375	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ggaaaagccagcttctccagCagctcagggcctttcagaag	11	12	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:4797375C>T	ENST00000299320.5	+	9	1790	c.1312C>T	c.(1312-1314)Cag>Tag	p.Q438*	C16orf71_ENST00000590191.1_Nonsense_Mutation_p.Q455*|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	438										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCTTCTCCAGCAGCTCAGGGC	0.637																																																0			16											49	57	54					16																	4797375		2189	4286	6475	4737376	SO:0001587	stop_gained	146562			AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1312C>T	16.37:g.4797375C>T	ENSP00000299320:p.Gln438*		4737376	Q8NCV0	Nonsense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	.	.	.	.	.	.	.	.	.	.	C	39	7.342272	0.98224	.	.	ENSG00000166246	ENST00000299320;ENST00000411541	.	.	.	4.56	4.56	0.56223	.	0.348811	0.22057	N	0.065232	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-17.8458	13.0108	0.58729	0.0:1.0:0.0:0.0	.	.	.	.	X	438;193	.	ENSP00000299320:Q438X	Q	+	1	0	C16orf71	4737376	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	1.816000	0.38992	2.521000	0.84997	0.462000	0.41574	CAG		0.637	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		T	4797375	C	T	4797375	4	4	9	1	0	0	0	0	0	1	0	0	1834	711	25	3	1342	3	C16orf71	16	4797375	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		4797375	85557378	129	1026										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16232299	16232299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cttgtgttggatgaggccacGgcagccgtggacctggaaac	15	10	0	1	rs202222707		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:16232299G>A	ENST00000399410.3	+	30	4546	c.4371G>A	c.(4369-4371)acG>acA	p.T1457T	ABCC1_ENST00000349029.5_Silent_p.T1342T|ABCC1_ENST00000346370.5_Silent_p.T1401T|ABCC1_ENST00000351154.5_Silent_p.T1398T|ABCC1_ENST00000399408.2_Silent_p.T1467T|ABCC1_ENST00000345148.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1457	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	ATGAGGCCACGGCAGCCGTGG	0.607													G|||	1	0.000199681	8e-04	0	5008	,	,		15304	0		0	False		,,,				2504	0															0			16											46	51	49					16																	16232299		2078	4212	6290	16139800	SO:0001819	synonymous_variant	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4371G>A	16.37:g.16232299G>A			16139800	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																				0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16232299	G	A	16232299	2	1	9	1	0	0	0	0	0	0	0	1	49	1103	39	1		1	ABCC1	16	16232299	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	11434924	16232299	74122454	130	1027										
CES7	221223	hgsc.bcm.edu	37	chr16	55880487	55880487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tgctggtccaaaaatccaccCgcggttctttgagtctctgt	9	12	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:55880487C>T	ENST00000290567.9	-	13	1725	c.1604G>A	c.(1603-1605)cGg>cAg	p.R535Q	CES5A_ENST00000521992.1_Missense_Mutation_p.R564Q|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000319165.9_Missense_Mutation_p.R485Q|CES5A_ENST00000518005.1_Missense_Mutation_p.R429Q|CES5A_ENST00000520435.1_Missense_Mutation_p.R505Q	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	535						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AAAATCCACCCGCGGTTCTTT	0.532																																																0			16											212	208	210					16																	55880487		2198	4300	6498	54437988	SO:0001583	missense	0			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1604G>A	16.37:g.55880487C>T	ENSP00000290567:p.Arg535Gln		54437988	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	.	13.07	2.127442	0.37533	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.61	-0.403	0.12400	Carboxylesterase, type B (1);	1.250620	0.05566	N	0.570143	T	0.40886	0.1135	N	0.16790	0.44	0.09310	N	1	P;B	0.39404	0.672;0.007	B;B	0.31686	0.134;0.005	T	0.17776	-1.0358	10	0.11485	T	0.65	.	5.0479	0.14494	0.0:0.4453:0.1445:0.4102	.	535;485	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	Q	564;485;429;535;505;315	ENSP00000428864:R564Q;ENSP00000324271:R485Q;ENSP00000428571:R429Q;ENSP00000290567:R535Q;ENSP00000428887:R505Q	ENSP00000290567:R535Q	R	-	2	0	CES5A	54437988	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.075000	0.14686	-0.195000	0.10382	-0.119000	0.15052	CGG		0.532	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		T	55880487	C	T	55880487	3	4	9	1	0	0	0	0	1	0	0	0	3278	652	23	1	127	1	CES7	16	55880487	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	39648188	55880487	34474266	131	1028										
NIP7	51388	hgsc.bcm.edu	37	chr16	69375484	69375484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aagactgcagaaaagtagacCccatggcgattgtggtattt	11	7	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:69375484C>T	ENST00000254940.5	+	5	872	c.472C>T	c.(472-474)Ccc>Tcc	p.P158S	RP11-343C2.9_ENST00000563634.1_Intron|RP11-343C2.7_ENST00000564737.1_Intron|NIP7_ENST00000254941.6_Missense_Mutation_p.P111S|COG8_ENST00000306875.4_5'Flank|COG8_ENST00000562081.1_5'Flank	NM_016101.4	NP_057185.1	Q9Y221	NIP7_HUMAN	NIP7, nucleolar pre-rRNA processing protein	158	C-terminal domain.|PUA. {ECO:0000255|PROSITE- ProRule:PRU00161}.				ribosome assembly (GO:0042255)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Ovarian(137;0.101)				AAAAGTAGACCCCATGGCGAT	0.463																																																0			16											121	120	120					16																	69375484		2198	4300	6498	67932985	SO:0001583	missense	51388			AB112439	CCDS10877.1, CCDS56003.1	16q22.1	2013-03-04	2013-03-04		ENSG00000132603	ENSG00000132603			24328	protein-coding gene	gene with protein product			"nuclear import 7 homolog (S. cerevisiae)"			14660641, 22195017	Standard	NM_016101		Approved	CGI-37, FLJ10296, HSPC031, KD93	uc002exa.3	Q9Y221	OTTHUMG00000137568	ENST00000254940.5:c.472C>T	16.37:g.69375484C>T	ENSP00000254940:p.Pro158Ser		67932985	B2RD04|Q9NZZ0	Missense_Mutation	SNP	ENST00000254940.5	37	CCDS10877.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127556	0.94473	.	.	ENSG00000132603	ENST00000254940;ENST00000254941	.	.	.	5.44	5.44	0.79542	Pseudouridine synthase/archaeosine transglycosylase (2);PUA-like domain (1);	0.000000	0.85682	D	0.000000	D	0.82986	0.5156	M	0.90542	3.125	0.80722	D	1	D;P	0.53619	0.961;0.622	P;P	0.55391	0.775;0.498	D	0.86117	0.1566	9	0.66056	D	0.02	-17.3855	19.6311	0.95701	0.0:1.0:0.0:0.0	.	111;158	Q9Y221-2;Q9Y221	.;NIP7_HUMAN	S	158;111	.	ENSP00000254940:P158S	P	+	1	0	NIP7	67932985	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.710000	0.92621	0.561000	0.74099	CCC		0.463	NIP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268947.2	NM_016101		T	69375484	C	T	69375484	3	4	9	1	0	0	0	0	1	0	0	0	10452	623	22	3	490	3	NIP7	16	69375484	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	13494997	69375484	20979269	132	1029										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70913324	70913324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaagaactggccgcacaaccGtcactcgagggaggttcccc	12	14	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:70913324G>A	ENST00000393567.2	-	62	10583	c.10433C>T	c.(10432-10434)aCg>aTg	p.T3478M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3478					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.T3429M(1)|p.T3477M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCGCACAACCGTCACTCGAGG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	16											21	23	22					16																	70913324		1838	4084	5922	69470825	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.10433C>T	16.37:g.70913324G>A	ENSP00000377197:p.Thr3478Met		69470825	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.450914	0.43531	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01068	5.38	5.19	0.992	0.19819	.	0.000000	0.33792	U	0.004556	T	0.02767	0.0083	M	0.71581	2.175	0.47994	D	0.999567	D	0.60575	0.988	P	0.52424	0.698	T	0.54801	-0.8239	10	0.59425	D	0.04	.	7.517	0.27606	0.1654:0.2242:0.6104:0.0	.	3477	F8WD23	.	M	3478;3477	ENSP00000377197:T3478M	ENSP00000313052:T3477M	T	-	2	0	HYDIN	69470825	0.123000	0.22298	0.751000	0.31187	0.173000	0.22820	0.291000	0.18994	1.081000	0.41110	0.511000	0.50034	ACG		0.547	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70913324	G	A	70913324	3	1	9	1	0	0	0	0	1	0	0	0	7488	1145	40	1	5032	1	HYDIN	16	70913324	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1537840	70913324	19441429	133	1030										
HYDIN	54768	hgsc.bcm.edu	37	chr16	71094505	71094505	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gatattcccgaagtccacttGattgggatggacgtagataa	11	7	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:71094505G>T	ENST00000393567.2	-	18	2581	c.2431C>A	c.(2431-2433)Caa>Aaa	p.Q811K	HYDIN_ENST00000321489.5_Missense_Mutation_p.Q811K|HYDIN_ENST00000448089.2_Missense_Mutation_p.Q811K|HYDIN_ENST00000541601.1_Missense_Mutation_p.Q828K|HYDIN_ENST00000448691.1_Missense_Mutation_p.Q811K|HYDIN_ENST00000538248.1_Missense_Mutation_p.Q838K	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	811					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AAGTCCACTTGATTGGGATGG	0.483																																																0			16											2	2	2					16																	71094505		1641	3438	5079	69652006	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2431C>A	16.37:g.71094505G>T	ENSP00000377197:p.Gln811Lys		69652006	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.748482	0.00669	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601	T;T;T;T;T;T	0.03860	5.65;3.79;3.79;3.79;3.78;3.78	4.69	1.17	0.20885	.	0.263582	0.19123	U	0.122132	T	0.02494	0.0076	N	0.20483	0.58	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.001	T	0.48080	-0.9066	10	0.02654	T	1	.	7.3861	0.26882	0.0:0.2091:0.4695:0.3213	.	838;828;811;811	B4DRN4;F5H6V3;Q4G0P3-5;F8WD23	.;.;.;.	K	811;811;811;811;811;838;828	ENSP00000377197:Q811K;ENSP00000398544:Q811K;ENSP00000394826:Q811K;ENSP00000314736:Q811K;ENSP00000444970:Q838K;ENSP00000437341:Q828K	ENSP00000313052:Q811K	Q	-	1	0	HYDIN	69652006	0.000000	0.05858	0.059000	0.19551	0.012000	0.07955	-1.162000	0.03141	0.327000	0.23409	-0.248000	0.11899	CAA		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	71094505	G	T	71094505	3	4	9	1	0	0	0	0	1	0	0	0	7488	1299	45	2	13219	2	HYDIN	16	71094505	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	181181	71094505	19260248	134	1031										
BCAR1	9564	hgsc.bcm.edu	37	chr16	75276775	75276775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cggggtggcgggagggccggGgccaggccctgctggcttct	21	12	1	0	rs1035539	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:75276775G>A	ENST00000162330.5	-	2	352	c.226C>T	c.(226-228)Ccc>Tcc	p.P76S	BCAR1_ENST00000546196.1_Missense_Mutation_p.P47S|BCAR1_ENST00000542031.2_Missense_Mutation_p.P74S|BCAR1_ENST00000418647.3_Missense_Mutation_p.P122S|BCAR1_ENST00000420641.3_Missense_Mutation_p.P94S|BCAR1_ENST00000393422.2_Missense_Mutation_p.P94S|BCAR1_ENST00000538440.2_Missense_Mutation_p.P76S|BCAR1_ENST00000393420.6_Missense_Mutation_p.P76S|BCAR1_ENST00000535626.2_Intron	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	76	Pro-rich.		P -> S (in dbSNP:rs1035539). {ECO:0000269|PubMed:10639512, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GGAGGGCCGGGGCCAGGCCCT	0.692													G|||	2974	0.59385	0.3427	0.7622	5008	,	,		14078	0.629		0.6769	False		,,,				2504	0.6922															0			16						G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,,SER/PRO	1768,2620		372,1024,798	19	22	21		364,280,280,226,226,220,,226	4	0.1	16	dbSNP_86	21	5721,2867		1915,1891,488	no	missense,missense,missense,missense,missense,missense,intron,missense	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_014567.3	74,74,74,74,74,74,,74	2287,2915,1286	AA,AG,GG		33.3838,40.2917,42.2858	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging	122/917,94/889,94/889,76/889,76/871,74/869,,76/871	75276775	7489,5487	2194	4294	6488	73834276	SO:0001583	missense	9564			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"Cas scaffolding proteins"	971	protein-coding gene	gene with protein product	"Crk-associated substrate", "Cas scaffolding protein family member 1"	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.226C>T	16.37:g.75276775G>A	ENSP00000162330:p.Pro76Ser		73834276	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	1313	0.6011904761904762	190	0.3861788617886179	265	0.7320441988950276	345	0.6031468531468531	513	0.6767810026385225	G	4.260	0.047302	0.08243	0.402917	0.666162	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51	4.97	3.99	0.46301	Src homology-3 domain (1);	1.655160	0.04132	N	0.318187	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	1.999999999946489E-6	B;B;B;B;B;B;B	0.13594	0.0;0.008;0.003;0.001;0.0;0.003;0.0	B;B;B;B;B;B;B	0.12156	0.002;0.003;0.004;0.006;0.001;0.007;0.001	T	0.42682	-0.9437	9	0.17369	T	0.5	-8.8335	9.9141	0.41423	0.1013:0.0:0.8987:0.0	rs1035539;rs17855754;rs61029671	94;122;74;76;94;76;76	B4DIW5;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945	.;.;.;.;.;.;BCAR1_HUMAN	S	76;94;94;76;122;76;74;47	ENSP00000162330:P76S;ENSP00000377074:P94S;ENSP00000392708:P94S;ENSP00000443841:P76S;ENSP00000391669:P122S;ENSP00000377072:P76S;ENSP00000440415:P74S;ENSP00000442161:P47S	ENSP00000162330:P76S	P	-	1	0	BCAR1	73834276	0.726000	0.28059	0.109000	0.21407	0.115000	0.19883	3.618000	0.54188	1.200000	0.43188	0.655000	0.94253	CCC		0.692	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		A	75276775	G	A	75276775	3	1	9	1	0	0	0	0	1	0	0	0	1349	1232	43	3	2471	3	BCAR1	16	75276775	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	4182270	75276775	15077978	135	1032										
MON1B	22879	hgsc.bcm.edu	37	chr16	77225404	77225404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tggaggtcggaggagacactGctgccccggcccccgggggc	18	14	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:77225404G>A	ENST00000248248.3	+	2	372	c.22G>A	c.(22-24)Gct>Act	p.A8T	MON1B_ENST00000439557.2_Missense_Mutation_p.A8T|MON1B_ENST00000320859.6_Missense_Mutation_p.A8T|MON1B_ENST00000545553.1_Intron	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	8										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						AGGAGACACTGCTgccccggc	0.627																																																0			16											20	21	21					16																	77225404		2197	4299	6496	75782905	SO:0001583	missense	22879			BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.22G>A	16.37:g.77225404G>A	ENSP00000248248:p.Ala8Thr		75782905	B4DDZ0|O94949	Missense_Mutation	SNP	ENST00000248248.3	37	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248675	0.80024	.	.	ENSG00000103111	ENST00000248248;ENST00000320859;ENST00000439557	.	.	.	4.23	2.1	0.27182	.	0.788326	0.11011	N	0.609464	T	0.18130	0.0435	N	0.19112	0.55	0.27316	N	0.957162	B;B	0.29862	0.056;0.259	B;B	0.19666	0.01;0.026	T	0.15521	-1.0434	9	0.21540	T	0.41	-4.2425	4.7909	0.13248	0.1114:0.0:0.6778:0.2107	.	8;8	E7EW32;Q7L1V2	.;MON1B_HUMAN	T	8	.	ENSP00000248248:A8T	A	+	1	0	MON1B	75782905	0.101000	0.21875	1.000000	0.80357	0.963000	0.63663	0.408000	0.21065	1.117000	0.41842	0.448000	0.29417	GCT		0.627	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		A	77225404	G	A	77225404	3	1	9	1	0	0	0	0	1	0	0	0	9729	1319	46	3	24	3	MON1B	16	77225404	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1948629	77225404	13129349	136	1033										
VAT1L	57687	hgsc.bcm.edu	37	chr16	78011577	78011577	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agcgagaacaaggagcggatGccctttatccagtaactgag	12	9	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr16:78011577G>T	ENST00000302536.2	+	9	1398	c.1245G>T	c.(1243-1245)atG>atT	p.M415I		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	415							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						AGGAGCGGATGCCCTTTATCC	0.527																																																0			16											154	118	130					16																	78011577		2198	4300	6498	76569078	SO:0001583	missense	57687			AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.1245G>T	16.37:g.78011577G>T	ENSP00000303129:p.Met415Ile		76569078	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	37	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	G	9.930	1.214679	0.22289	.	.	ENSG00000171724	ENST00000302536	T	0.07216	3.21	4.97	4.0	0.46444	.	0.084915	0.85682	D	0.000000	T	0.05090	0.0136	N	0.08118	0	0.54753	D	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.38001	-0.9681	10	0.37606	T	0.19	-10.1573	13.3107	0.60378	0.0784:0.0:0.9216:0.0	.	415	Q9HCJ6	VAT1L_HUMAN	I	415	ENSP00000303129:M415I	ENSP00000303129:M415I	M	+	3	0	VAT1L	76569078	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.480000	0.60243	1.089000	0.41292	0.561000	0.74099	ATG		0.527	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		T	78011577	G	T	78011577	3	4	9	1	0	0	0	0	1	0	0	0	17170	1319	46	2	1279	2	VAT1L	16	78011577	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	786173	78011577	12343176	137	1034										
OR1A2	26189	hgsc.bcm.edu	37	chr17	3101437	3101437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gggtcggcgttttctctttgCcattactatgcatcattgtc	9	10	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr17:3101437C>T	ENST00000381951.1	+	1	625	c.625C>T	c.(625-627)Cca>Tca	p.P209S		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	209					positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						TTTCTCTTTGCCATTACTATG	0.438																																																0			17											244	204	218					17																	3101437		2203	4300	6503	3048187	SO:0001583	missense	26189			AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"GPCR / Class A : Olfactory receptors"	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.625C>T	17.37:g.3101437C>T	ENSP00000371377:p.Pro209Ser		3048187	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	37	CCDS11021.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392319	0.25118	.	.	ENSG00000172150	ENST00000381951	T	0.55930	0.49	4.09	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000156	T	0.55257	0.1909	L	0.50847	1.595	0.09310	N	1	D	0.55605	0.972	P	0.56216	0.794	T	0.50154	-0.8861	10	0.62326	D	0.03	.	5.9807	0.19405	0.0:0.6993:0.1965:0.1042	.	209	Q9Y585	OR1A2_HUMAN	S	209	ENSP00000371377:P209S	ENSP00000371377:P209S	P	+	1	0	OR1A2	3048187	0.000000	0.05858	0.612000	0.29024	0.055000	0.15305	-0.285000	0.08410	2.282000	0.76494	0.609000	0.83330	CCA		0.438	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352		T	3101437	C	T	3101437	3	4	9	1	0	0	0	0	1	0	0	0	10981	739	26	3	627	3	OR1A2	17	3101437	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		3101437	78093773	138	1035										
HAP1	9001	hgsc.bcm.edu	37	chr17	39888590	39888591	+	Frame_Shift_Ins	INS	-	-	CT													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gagctgcagtgttcaggtccINSctctctctctgcaggaccat							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr17:39888590_39888591insCT	ENST00000310778.5	-	3	614_615	c.605_606insAG	c.(604-606)aggfs	p.R202fs	RN7SL399P_ENST00000471648.2_RNA|JUP_ENST00000540235.1_Intron|HAP1_ENST00000393939.2_Frame_Shift_Ins_p.R202fs|HAP1_ENST00000347901.4_Frame_Shift_Ins_p.R202fs|HAP1_ENST00000341193.5_Frame_Shift_Ins_p.R210fs			P54257	HAP1_HUMAN	huntingtin-associated protein 1	202	HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TGTTCAGGTCCCTCTCTCTCTG	0.589																																																0			17																																								37142117	SO:0001589	frameshift_variant	9001			AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.604_605dupAG	17.37:g.39888599_39888600dupCT	ENSP00000309392:p.Arg202fs		37142116	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Frame_Shift_Ins	INS	ENST00000310778.5	37																																																																																					0.589	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		CT	39888591	-	CT	39888590	7	5	9	1	0	1	1	0	0	0	0	0	6974	622	22	0	1289	0	HAP1	17	39888590	Frame_Shift_Ins	INS	-	TCGA-AF-5654-01A-01D-1657-10	36787153	39888590	41306620	139	1036										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45384950	45384950	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tcctcatcaccatccacgacCgaaaagaattcgctaaattt	4	13	2	1	rs121918450		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr17:45384950C>T	ENST00000559488.1	+	14	2264	c.2248C>T	c.(2248-2250)Cga>Tga	p.R750*	ITGB3_ENST00000435993.2_Nonsense_Mutation_p.R703*|RP11-290H9.4_ENST00000575039.1_RNA|ITGB3_ENST00000560629.1_Missense_Mutation_p.P738L|RP11-290H9.4_ENST00000576345.1_RNA	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	750					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CATCCACGACCGAAAAGAATT	0.532													C|||	1	0.000199681	8e-04	0	5008	,	,		18650	0		0	False		,,,				2504	0															0			17	GRCh37	CM973033	ITGB3	M	rs121918450	C	stop/ARG	2,4404	4.2+/-10.8	0,2,2201	75	59	64	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2248	5.5	1	17	dbSNP_133	64	0,8600		0,0,4300	yes	stop-gained	ITGB3	NM_000212.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		750/789	45384950	2,13004	2203	4300	6503	42739949	SO:0001587	stop_gained	3690				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.2248C>T	17.37:g.45384950C>T	ENSP00000452786:p.Arg750*		42739949	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Nonsense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	39	7.667214	0.98422	4.54E-4	0.0	ENSG00000178852	ENST00000262017;ENST00000435993	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4681	0.90762	0.0:1.0:0.0:0.0	.	.	.	.	X	750;703	.	ENSP00000262017:R750X	R	+	1	2	C17orf57	42739949	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.061000	0.49963	2.720000	0.93068	0.557000	0.71058	CGA		0.532	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45384950	C	T	45384950	4	4	9	1	0	0	0	0	0	1	0	0	7916	644	23	1	2302	1	ITGB3	17	45384950	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	5496360	45384950	35810260	140	1037										
BAHCC1	57597	hgsc.bcm.edu	37	chr17	79428601	79428601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gacgggccggggctggcggcCggcgtgccctcccgcttcct	17	17	0	0	rs61738790	byFrequency	TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr17:79428601C>T	ENST00000307745.7	+	30	6912	c.6912C>T	c.(6910-6912)gcC>gcT	p.A2304A	RP11-1055B8.8_ENST00000572590.1_RNA																							GGCTGGCGGCCGGCGTGCCCT	0.701													C|||	304	0.0607029	0.1203	0.0504	5008	,	,		9369	0		0.0905	False		,,,				2504	0.0194															0			17						C		263,3537		5,253,1642	4	7	6		6741	-0.9	0	17	dbSNP_129	6	492,7332		15,462,3435	no	coding-synonymous	BAHCC1	NM_001080519.2		20,715,5077	TT,TC,CC		6.2883,6.9211,6.4952		2247/2552	79428601	755,10869	1900	3912	5812	77043196	SO:0001819	synonymous_variant	57597																														ENST00000307745.7:c.6912C>T	17.37:g.79428601C>T			77043196		Silent	SNP	ENST00000307745.7	37																																																																																					0.701	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	79428601	C	T	79428601	2	4	9	1	0	0	0	0	0	0	0	1	1297	639	23	1		1	BAHCC1	17	79428601	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	34043651	79428601	1766609	141	1038										
NARF	26502	hgsc.bcm.edu	37	chr17	80446002	80446002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cacgtaccagagccaggagcGtggcacacacagcctggaca	12	14	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr17:80446002G>A	ENST00000309794.11	+	11	1538	c.1340G>A	c.(1339-1341)cGt>cAt	p.R447H	NARF_ENST00000457415.3_Missense_Mutation_p.R493H|NARF_ENST00000345415.7_Missense_Mutation_p.R399H|NARF_ENST00000390006.4_Missense_Mutation_p.R388H	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	447						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			AGCCAGGAGCGTGGCACACAC	0.627																																																0			17											76	65	69					17																	80446002		2203	4300	6503	78039291	SO:0001583	missense	51444			BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.1340G>A	17.37:g.80446002G>A	ENSP00000309899:p.Arg447His		78039291	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Missense_Mutation	SNP	ENST00000309794.11	37	CCDS32777.1	.	.	.	.	.	.	.	.	.	.	.	5.889	0.348092	0.11126	.	.	ENSG00000141562	ENST00000390006;ENST00000374611;ENST00000309794;ENST00000345415	T;T;T	0.47177	0.85;0.85;0.85	5.19	-10.4	0.00318	Iron hydrogenase, small subunit-like (1);	2.114340	0.01730	N	0.028785	T	0.24661	0.0598	N	0.16790	0.44	0.20074	N	0.999938	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.33979	-0.9847	10	0.66056	D	0.02	-20.823	0.8901	0.01252	0.4179:0.1362:0.2135:0.2324	.	493;399;494;447	Q9UHQ1-2;Q9UHQ1-3;E9PH27;Q9UHQ1	.;.;.;NARF_HUMAN	H	388;494;447;399	ENSP00000374656:R388H;ENSP00000309899:R447H;ENSP00000283996:R399H	ENSP00000309899:R447H	R	+	2	0	NARF	78039291	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.523000	0.00442	-5.016000	0.00024	-2.255000	0.00281	CGT		0.627	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		A	80446002	G	A	80446002	3	1	9	1	0	0	0	0	1	0	0	0	10197	1145	40	1	1524	1	NARF	17	80446002	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	1017401	80446002	749208	142	1039										
CPLX4	339302	hgsc.bcm.edu	37	chr18	56964100	56964100	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atctaccattttccggagatCttcaggtaaatccacatcat	5	11	4	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr18:56964100C>T	ENST00000299721.3	-	3	499	c.313G>A	c.(313-315)Gat>Aat	p.D105N	CPLX4_ENST00000587244.1_Intron	NM_181654.3	NP_857637.1	Q7Z7G2	CPLX4_HUMAN	complexin 4	105					exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter secretion (GO:0046928)	cell junction (GO:0030054)|membrane (GO:0016020)|synapse (GO:0045202)				autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	16		Colorectal(73;0.175)				TTCCGGAGATCTTCAGGTAAA	0.358																																																0			18											94	85	88					18																	56964100		2203	4300	6503	55115080	SO:0001583	missense	339302			AY286502	CCDS11973.1	18q21.32	2005-08-02			ENSG00000166569	ENSG00000166569			24330	protein-coding gene	gene with protein product		609586				15911881	Standard	NM_181654		Approved	CPX-IV	uc002lhy.3	Q7Z7G2	OTTHUMG00000132756	ENST00000299721.3:c.313G>A	18.37:g.56964100C>T	ENSP00000299721:p.Asp105Asn		55115080	F1T0L6	Missense_Mutation	SNP	ENST00000299721.3	37	CCDS11973.1	.	.	.	.	.	.	.	.	.	.	C	31	5.083582	0.94050	.	.	ENSG00000166569	ENST00000299721	.	.	.	5.66	5.66	0.87406	.	0.043821	0.85682	D	0.000000	T	0.70474	0.3228	L	0.47716	1.5	0.80722	D	1	P	0.45348	0.856	P	0.53313	0.723	T	0.71899	-0.4453	9	0.72032	D	0.01	-17.5543	19.3422	0.94347	0.0:1.0:0.0:0.0	.	105	Q7Z7G2	CPLX4_HUMAN	N	105	.	ENSP00000299721:D105N	D	-	1	0	CPLX4	55115080	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	7.425000	0.80255	2.653000	0.90120	0.561000	0.74099	GAT		0.358	CPLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256127.1	NM_181654		T	56964100	C	T	56964100	3	4	9	1	0	0	0	0	1	0	0	0	3813	913	32	3	173	3	CPLX4	18	56964100	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10		56964100	21113148	143	1040										
APC2	10297	hgsc.bcm.edu	37	chr19	1455453	1455453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ccagcacatccgctcgctgaTggaggagcgcttcggcacct	12	15	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:1455453T>C	ENST00000535453.1	+	5	2306	c.593T>C	c.(592-594)aTg>aCg	p.M198T	CTB-25B13.12_ENST00000588225.1_RNA|APC2_ENST00000233607.2_Missense_Mutation_p.M198T|APC2_ENST00000238483.4_Intron			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCTCGCTGATGGAGGAGCGC	0.711																																																0			19											18	16	16					19																	1455453		2189	4292	6481	1406453	SO:0001583	missense	79085				CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.593T>C	19.37:g.1455453T>C	ENSP00000442954:p.Met198Thr		1406453	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000535453.1	37	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666417	0.88251	.	.	ENSG00000115266	ENST00000233607;ENST00000535453	D;D	0.90261	-2.64;-2.64	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	D	0.92890	0.7738	L	0.59436	1.845	0.80722	D	1	D;D	0.64830	0.993;0.994	P;D	0.65233	0.89;0.933	D	0.92886	0.6327	10	0.59425	D	0.04	-24.0879	11.4019	0.49875	0.0:0.0:0.0:1.0	.	197;198	O95996-3;O95996	.;APC2_HUMAN	T	198	ENSP00000233607:M198T;ENSP00000442954:M198T	ENSP00000233607:M198T	M	+	2	0	APC2	1406453	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.590000	0.82653	1.585000	0.49928	0.402000	0.26972	ATG		0.711	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		C	1455453	T	C	1455453	3	2	9	1	0	0	0	0	1	0	0	0	764	1464	51	4	611	4	APC2	19	1455453	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10		1455453	57673530	144	1041										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4157245	4157245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctcttgctccaccacaacccCagggccagtgatccaagtac	7	17	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:4157245C>T	ENST00000078445.2	+	3	557	c.410C>T	c.(409-411)cCa>cTa	p.P137L	CREB3L3_ENST00000595923.1_Missense_Mutation_p.P136L|CREB3L3_ENST00000602147.1_Missense_Mutation_p.P137L|CREB3L3_ENST00000602257.1_Missense_Mutation_p.P137L|CREB3L3_ENST00000252587.3_Missense_Mutation_p.P127L	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	137					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACAACCCCAGGGCCAGTG	0.642																																																0			19											89	93	92					19																	4157245		2203	4300	6503	4108245	SO:0001583	missense	84699				CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.410C>T	19.37:g.4157245C>T	ENSP00000078445:p.Pro137Leu		4108245	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	37	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	C	6.387	0.439565	0.12104	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	D;D	0.85171	-1.95;-1.95	4.75	0.915	0.19366	.	1.188910	0.06356	N	0.710757	T	0.73225	0.3560	N	0.21142	0.635	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.004;0.002	B;B;B;B	0.13407	0.009;0.001;0.004;0.002	T	0.57877	-0.7735	10	0.36615	T	0.2	.	3.4033	0.07331	0.2403:0.5142:0.0:0.2455	.	137;137;136;137	Q68CJ9-3;B7ZL69;Q68CJ9-2;Q68CJ9	.;.;.;CR3L3_HUMAN	L	137;137;127	ENSP00000078445:P137L;ENSP00000252587:P127L	ENSP00000078445:P137L	P	+	2	0	CREB3L3	4108245	0.000000	0.05858	0.003000	0.11579	0.031000	0.12232	-0.760000	0.04756	0.361000	0.24292	0.537000	0.68136	CCA		0.642	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4157245	C	T	4157245	3	4	9	1	0	0	0	0	1	0	0	0	3864	594	21	3	420	3	CREB3L3	19	4157245	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	2701792	4157245	54971738	145	1042										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066159	9066159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gtaaagacagcagggaagggAgagagctgggattttccaga	16	5	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:9066159A>G	ENST00000397910.4	-	3	21490	c.21287T>C	c.(21286-21288)cTc>cCc	p.L7096P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7098	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGGGAAGGGAGAGAGCTGGG	0.507																																																0			19											131	134	133					19																	9066159		2032	4174	6206	8927159	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21287T>C	19.37:g.9066159A>G	ENSP00000381008:p.Leu7096Pro		8927159	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	3.023	-0.201385	0.06219	.	.	ENSG00000181143	ENST00000397910	T	0.22134	1.97	2.32	-3.99	0.04069	.	.	.	.	.	T	0.06188	0.0160	N	0.02247	-0.625	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.29518	-1.0009	8	0.87932	D	0	.	0.571	0.00695	0.2502:0.3474:0.206:0.1964	.	7096	B5ME49	.	P	7096	ENSP00000381008:L7096P	ENSP00000381008:L7096P	L	-	2	0	MUC16	8927159	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.379000	0.07437	-0.909000	0.03852	0.330000	0.21533	CTC		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9066159	A	G	9066159	3	3	9	1	0	0	0	0	1	0	0	0	10003	304	11	4	22564	4	MUC16	19	9066159	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	4908914	9066159	50062824	146	1043										
MUC16	94025	hgsc.bcm.edu	37	chr19	9090251	9090251	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aaattgctgagctgtgctttCactggtccatgatgatgctt	10	8	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:9090251C>T	ENST00000397910.4	-	1	1767	c.1564G>A	c.(1564-1566)Gaa>Aaa	p.E522K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	522	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTGTGCTTTCACTGGTCCAT	0.552																																																0			19											97	95	96					19																	9090251		2114	4243	6357	8951251	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.1564G>A	19.37:g.9090251C>T	ENSP00000381008:p.Glu522Lys		8951251	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	9.220	1.033103	0.19590	.	.	ENSG00000181143	ENST00000397910	T	0.02682	4.2	1.45	-1.43	0.08884	.	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	.	.	.	P	0.34977	0.478	B	0.28916	0.096	T	0.45556	-0.9253	8	0.87932	D	0	.	3.2232	0.06723	0.2989:0.4052:0.2959:0.0	.	522	B5ME49	.	K	522	ENSP00000381008:E522K	ENSP00000381008:E522K	E	-	1	0	MUC16	8951251	0.000000	0.05858	0.000000	0.03702	0.582000	0.36321	-1.446000	0.02398	-0.300000	0.08895	0.313000	0.20887	GAA		0.552	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9090251	C	T	9090251	3	4	9	1	0	0	0	0	1	0	0	0	10003	835	29	3	42295	3	MUC16	19	9090251	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	24092	9090251	50038732	147	1044										
SLC27A1	376497	hgsc.bcm.edu	37	chr19	17608117	17608117	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctgctgaagcagccggtgcgCgaggcggagaggcgacaccg	18	12	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:17608117C>T	ENST00000252595.7	+	7	1147	c.1050C>T	c.(1048-1050)cgC>cgT	p.R350R	CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000442725.1_Silent_p.R350R|SLC27A1_ENST00000598424.1_Silent_p.R171R	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	350	Sufficient for oligomerization. {ECO:0000250}.				adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AGCCGGTGCGCGAGGCGGAGA	0.687																																																0			19											43	36	38					19																	17608117		2202	4298	6500	17469117	SO:0001819	synonymous_variant	376497			BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1050C>T	19.37:g.17608117C>T			17469117	A6NIH2|B7Z662	Silent	SNP	ENST00000252595.7	37	CCDS32953.1																																																																																				0.687	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		T	17608117	C	T	17608117	2	4	9	1	0	0	0	0	0	0	0	1	14562	755	27	1		1	SLC27A1	19	17608117	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	8517866	17608117	41520866	148	1045										
ZNF430	80264	hgsc.bcm.edu	37	chr19	21239944	21239944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	taagcagtcctcaacccttaCtacacataagataattcata	3	11	2	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:21239944C>T	ENST00000261560.5	+	5	1011	c.830C>T	c.(829-831)aCt>aTt	p.T277I	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	277					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						TCAACCCTTACTACACATAAG	0.393																																																0			19											56	61	59					19																	21239944		2203	4298	6501	21031784	SO:0001583	missense	80264			AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.830C>T	19.37:g.21239944C>T	ENSP00000261560:p.Thr277Ile		21031784	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	37	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.850157	0.00563	.	.	ENSG00000118620	ENST00000261560	T	0.07688	3.17	1.04	-0.505	0.11993	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06234	0.0161	N	0.17764	0.52	0.09310	N	1	B;P	0.36027	0.148;0.533	B;B	0.39379	0.051;0.298	T	0.41197	-0.9522	9	0.33940	T	0.23	.	8.6076	0.33782	0.0:0.3254:0.6746:0.0	.	276;277	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	I	277	ENSP00000261560:T277I	ENSP00000261560:T277I	T	+	2	0	ZNF430	21031784	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.685000	0.01930	-0.490000	0.06707	-0.485000	0.04761	ACT		0.393	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		T	21239944	C	T	21239944	3	4	9	1	0	0	0	0	1	0	0	0	17943	565	20	3	848	3	ZNF430	19	21239944	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	3631827	21239944	37889039	149	1046										
AP2A1	160	hgsc.bcm.edu	37	chr19	50303389	50303389	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gatgacgtccagggctatgcCgccaagaccgtctttgaggt	13	11	1	3	rs368042642		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:50303389C>T	ENST00000359032.5	+	11	1437	c.1437C>T	c.(1435-1437)gcC>gcT	p.A479A	AP2A1_ENST00000354293.5_Silent_p.A479A	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	479					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		AGGGCTATGCCGCCAAGACCG	0.617																																																0			19						C	,	0,4302		0,0,2151	69	77	74		1437,1437	-9.3	0.2	19		74	1,8483		0,1,4241	no	coding-synonymous,coding-synonymous	AP2A1	NM_014203.2,NM_130787.2	,	0,1,6392	TT,TC,CC		0.0118,0.0,0.0078	,	479/978,479/956	50303389	1,12785	2151	4242	6393	54995201	SO:0001819	synonymous_variant	160			AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.1437C>T	19.37:g.50303389C>T			54995201	Q96CI7|Q96PP6|Q96PP7|Q9H070	Silent	SNP	ENST00000359032.5	37	CCDS46148.1																																																																																				0.617	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			T	50303389	C	T	50303389	2	4	9	1	0	0	0	0	0	0	0	1	739	639	23	1		1	AP2A1	19	50303389	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	29063445	50303389	8825594	150	1047										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057342	53057342	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tatctggcaaaccatactagAattcatagtggagagaaaac	8	7	2	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr19:53057342A>G	ENST00000359798.4	+	5	1353	c.1173A>G	c.(1171-1173)agA>agG	p.R391R		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		ACCATACTAGAATTCATAGTG	0.383																																																0			19											104	110	108					19																	53057342		2190	4292	6482	57749154	SO:0001819	synonymous_variant	388558			CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1173A>G	19.37:g.53057342A>G			57749154	Q68CN7	Silent	SNP	ENST00000359798.4	37	CCDS46167.1																																																																																				0.383	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		G	53057342	A	G	53057342	2	3	9	1	0	0	0	0	0	0	0	1	18212	243	9	4		4	ZNF808	19	53057342	Silent	SNP	A	TCGA-AF-5654-01A-01D-1657-10	2753953	53057342	6071641	151	1048										
PAK7	57144	hgsc.bcm.edu	37	chr20	9561106	9561106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaatgaataatccagaggggAgctactcgaggctctctgat	12	8	1	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr20:9561106A>G	ENST00000378429.3	-	5	1222	c.676T>C	c.(676-678)Tcc>Ccc	p.S226P	RP5-986I17.2_ENST00000428769.1_RNA|PAK7_ENST00000353224.5_Missense_Mutation_p.S226P|PAK7_ENST00000378423.1_Missense_Mutation_p.S226P	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	226	Linker.|Poly-Ser.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TCCAGAGGGGAGCTACTCGAG	0.502																																																0			20											69	67	68					20																	9561106		2203	4300	6503	9509106	SO:0001583	missense	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.676T>C	20.37:g.9561106A>G	ENSP00000367686:p.Ser226Pro		9509106	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.435186	0.62955	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.29655	1.56;1.56;1.56	5.55	4.46	0.54185	.	0.279884	0.41605	N	0.000842	T	0.30885	0.0779	L	0.50333	1.59	0.40647	D	0.982006	P;P	0.48911	0.838;0.917	B;B	0.44315	0.367;0.446	T	0.04900	-1.0919	9	.	.	.	.	11.3927	0.49824	0.9294:0.0:0.0706:0.0	.	226;226	B0AZM9;Q9P286	.;PAK7_HUMAN	P	226;226;226;174	ENSP00000367686:S226P;ENSP00000322957:S226P;ENSP00000367679:S226P	.	S	-	1	0	PAK7	9509106	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	6.514000	0.73746	0.960000	0.38005	0.445000	0.29226	TCC		0.502	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9561106	A	G	9561106	3	3	9	1	0	0	0	0	1	0	0	0	11436	304	11	4	1511	4	PAK7	20	9561106	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10		9561106	53464414	152	1049										
MYH7B	26133	hgsc.bcm.edu	37	chr20	33589110	33589110	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cacgccgaggcccttaagggCgtgcgcaagcatgagcgccg	15	14	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr20:33589110C>T	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.G1888G			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CCCTTAAGGGCGTGCGCAAGC	0.667																																																0			20											31	40	37					20																	33589110		2122	4241	6363	33052771	SO:0001628	intergenic_variant	57644			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		20.37:g.33589110C>T			33052771	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																				0.667	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33589110	C	T	33589110	1	4	9	0	1	0	0	0	0	0	0	0	10070	755	27	1		1	MYH7B	20	33589110	IGR	SNP	C	TCGA-AF-5654-01A-01D-1657-10	24028004	33589110	29436410	153	1050										
TAF4	6874	hgsc.bcm.edu	37	chr20	60585127	60585127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cagctgaggaagtggtggtcGcccctggtaccgtgcgctga	16	11	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr20:60585127G>A	ENST00000252996.4	-	4	1735	c.1736C>T	c.(1735-1737)gCg>gTg	p.A579V	TAF4_ENST00000609045.1_5'UTR	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	579					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			AGTGGTGGTCGCCCCTGGTAC	0.627																																																0			20											94	75	81					20																	60585127		2203	4300	6503	60018522	SO:0001583	missense	6874			Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1736C>T	20.37:g.60585127G>A	ENSP00000252996:p.Ala579Val		60018522	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.865921	0.32977	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.27557	1.69;1.66	4.8	3.83	0.44106	.	0.769933	0.12453	N	0.467551	T	0.24084	0.0583	L	0.46157	1.445	0.44685	D	0.997672	P	0.44946	0.846	B	0.29353	0.101	T	0.06625	-1.0816	10	0.36615	T	0.2	-2.3747	14.8203	0.70068	0.0:0.1453:0.8547:0.0	.	579	O00268	TAF4_HUMAN	V	579;443	ENSP00000252996:A579V;ENSP00000399091:A443V	ENSP00000252996:A579V	A	-	2	0	TAF4	60018522	1.000000	0.71417	0.809000	0.32408	0.060000	0.15804	5.045000	0.64220	0.989000	0.38761	0.313000	0.20887	GCG		0.627	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60585127	G	A	60585127	3	1	9	1	0	0	0	0	1	0	0	0	15565	1087	38	1	1569	1	TAF4	20	60585127	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	26996017	60585127	2440393	154	1051										
SRMS	6725	hgsc.bcm.edu	37	chr20	62178671	62178671	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agagctgagggaaggggctgCaaggctcggcggggagcgtg	22	7	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr20:62178671C>A	ENST00000217188.1	-	1	186	c.146G>T	c.(145-147)tGc>tTc	p.C49F		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	49	N-terminal.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GAAGGGGCTGCAAGGCTCGGC	0.701																																																0			20											162	163	162					20																	62178671		2184	4254	6438	61649115	SO:0001583	missense	6725				CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.146G>T	20.37:g.62178671C>A	ENSP00000217188:p.Cys49Phe		61649115		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	.	.	.	.	.	.	.	.	.	.	C	2.442	-0.328477	0.05314	.	.	ENSG00000125508	ENST00000217188	T	0.40476	1.03	3.62	3.62	0.41486	.	1.940240	0.02556	N	0.096157	T	0.39200	0.1069	L	0.33339	1.005	0.21064	N	0.999793	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	10	0.56958	D	0.05	.	11.6539	0.51306	0.1782:0.8218:0.0:0.0	.	49	Q9H3Y6	SRMS_HUMAN	F	49	ENSP00000217188:C49F	ENSP00000217188:C49F	C	-	2	0	SRMS	61649115	0.047000	0.20315	0.034000	0.17996	0.097000	0.18754	2.689000	0.46993	1.722000	0.51474	0.436000	0.28706	TGC		0.701	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		A	62178671	C	A	62178671	3	1	9	1	0	0	0	0	1	0	0	0	15191	710	25	2	1352	2	SRMS	20	62178671	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1593544	62178671	846849	155	1052										
OLIG2	10215	hgsc.bcm.edu	37	chr21	34399549	34399549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcatgcacgacctcaacatcGccatggatggcctccgcgag	11	15	1	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr21:34399549G>A	ENST00000333337.3	+	1	1307	c.379G>A	c.(379-381)Gcc>Acc	p.A127T	AP000282.2_ENST00000454622.1_RNA|OLIG2_ENST00000382357.3_Missense_Mutation_p.A127T|AP000282.2_ENST00000420356.1_RNA			Q13516	OLIG2_HUMAN	oligodendrocyte lineage transcription factor 2	127	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				myelination (GO:0042552)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|positive regulation of oligodendrocyte differentiation (GO:0048714)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|thalamus development (GO:0021794)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|central_nervous_system(2)	3						CCTCAACATCGCCATGGATGG	0.607			T	TRA@	T-ALL																																		Dom	yes		21	21q22.11	10215	oligodendrocyte lineage transcription factor 2 (BHLHB1)		L	0			21											31	27	28					21																	34399549		2203	4300	6503	33321419	SO:0001583	missense	10215			U48250	CCDS13620.1	21q22.11	2013-05-21	2001-12-04	2001-12-07	ENSG00000205927	ENSG00000205927		"Basic helix-loop-helix proteins"	9398	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 2", "protein kinase C binding protein 2", "human protein kinase C-binding protein RACK17", "basic domain, helix-loop-helix protein, class B, 1"	606386	"protein kinase C binding protein 2"	PRKCBP2, BHLHB1		11526205	Standard	NM_005806		Approved	RACK17, OLIGO2, bHLHe19	uc002yqx.2	Q13516	OTTHUMG00000065032	ENST00000333337.3:c.379G>A	21.37:g.34399549G>A	ENSP00000331040:p.Ala127Thr		33321419	B3KRF3|Q05BP9|Q49AL3|Q86X04|Q9NZ14	Missense_Mutation	SNP	ENST00000333337.3	37	CCDS13620.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625834	0.87560	.	.	ENSG00000205927	ENST00000382357;ENST00000333337	D;D	0.98329	-4.87;-4.87	3.27	2.36	0.29203	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	U	0.000001	D	0.99026	0.9667	M	0.93462	3.42	0.52099	D	0.999945	D	0.89917	1.0	D	0.97110	1.0	D	0.99391	1.0925	10	0.87932	D	0	-0.0055	11.1574	0.48495	0.0:0.1892:0.8108:0.0	.	127	Q13516	OLIG2_HUMAN	T	127	ENSP00000371794:A127T;ENSP00000331040:A127T	ENSP00000331040:A127T	A	+	1	0	OLIG2	33321419	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.745000	0.85046	0.530000	0.28619	0.462000	0.41574	GCC		0.607	OLIG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139663.1	NM_005806		A	34399549	G	A	34399549	3	1	9	1	0	0	0	0	1	0	0	0	10892	1087	38	1	381	1	OLIG2	21	34399549	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10		34399549	13730346	156	1053										
TMEM50B	757	hgsc.bcm.edu	37	chr21	34832756	34832756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	accaaaaagaatccacatggAagcaataagtgacccaaaca	6	10	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr21:34832756A>G	ENST00000542230.2	-	5	551	c.337T>C	c.(337-339)Tcc>Ccc	p.S113P		NM_006134.6	NP_006125.2	P56557	TM50B_HUMAN	transmembrane protein 50B	113						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|ovary(1)|skin(1)	4						ATCCACATGGAAGCAATAAGT	0.343																																																0			21											80	73	75					21																	34832756		2203	4300	6503	33754626	SO:0001583	missense	757			AF045606	CCDS13625.1	21q22.1	2008-07-29	2005-06-02	2005-06-02	ENSG00000142188	ENSG00000142188			1280	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 4"	C21orf4			Standard	NR_040016		Approved		uc002yrs.2	P56557	OTTHUMG00000065286	ENST00000542230.2:c.337T>C	21.37:g.34832756A>G	ENSP00000439768:p.Ser113Pro		33754626	B2R4L4|D3DSF1|O60537|Q5PY47	Missense_Mutation	SNP	ENST00000542230.2	37	CCDS13625.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.795918	0.90453	.	.	ENSG00000142188	ENST00000542230;ENST00000440644	T	0.39592	1.07	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.67599	0.2910	M	0.84846	2.72	0.80722	D	1	D	0.61080	0.989	D	0.71656	0.974	T	0.73455	-0.3977	10	0.72032	D	0.01	-32.5255	14.8382	0.70201	1.0:0.0:0.0:0.0	.	113	P56557	TM50B_HUMAN	P	113	ENSP00000439768:S113P	ENSP00000371390:S113P	S	-	1	0	TMEM50B	33754626	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.529000	0.90602	2.197000	0.70478	0.528000	0.53228	TCC		0.343	TMEM50B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140080.5			G	34832756	A	G	34832756	3	3	9	1	0	0	0	0	1	0	0	0	16215	246	9	4	151	4	TMEM50B	21	34832756	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	433207	34832756	13297139	157	1054										
MORC3	23515	hgsc.bcm.edu	37	chr21	37734524	37734524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gacaaccggaaatgatccctCgggtaattaagccttctttt	8	10	1	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr21:37734524C>T	ENST00000400485.1	+	13	1526	c.1450C>T	c.(1450-1452)Cgg>Tgg	p.R484W	MORC3_ENST00000487909.1_3'UTR|AP000692.9_ENST00000397184.2_RNA	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	484					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						AATGATCCCTCGGGTAATTAA	0.393																																																0			21											49	48	49					21																	37734524		1800	4056	5856	36656394	SO:0001583	missense	23515			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1450C>T	21.37:g.37734524C>T	ENSP00000383333:p.Arg484Trp		36656394	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558398	0.65538	.	.	ENSG00000159256	ENST00000400485	T	0.15372	2.43	5.23	5.23	0.72850	.	1.692110	0.02406	N	0.081176	T	0.22589	0.0545	L	0.51422	1.61	0.29135	N	0.879388	D	0.56968	0.978	B	0.40410	0.328	T	0.33266	-0.9875	10	0.72032	D	0.01	-0.0279	11.721	0.51683	0.1764:0.8236:0.0:0.0	.	484	Q14149	MORC3_HUMAN	W	484	ENSP00000383333:R484W	ENSP00000383333:R484W	R	+	1	2	MORC3	36656394	0.794000	0.28838	0.994000	0.49952	0.809000	0.45718	3.336000	0.52113	2.613000	0.88420	0.563000	0.77884	CGG		0.393	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		T	37734524	C	T	37734524	3	4	9	1	0	0	0	0	1	0	0	0	9733	875	31	1	1500	1	MORC3	21	37734524	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	2901768	37734524	10395371	158	1055										
ADRBK2	157	hgsc.bcm.edu	37	chr22	26057588	26057588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atgaggaagaccgcctttgcAgaagtcgacaaatttatgat	10	7	0	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chr22:26057588A>G	ENST00000324198.6	+	4	502	c.310A>G	c.(310-312)Aga>Gga	p.R104G		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	104	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> K (in a lung bronchoalveolar carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	CCGCCTTTGCAGAAGTCGACA	0.333																																																0			22											149	128	135					22																	26057588		2203	4300	6503	24387588	SO:0001583	missense	157			X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.310A>G	22.37:g.26057588A>G	ENSP00000317578:p.Arg104Gly		24387588	Q9UGW9	Missense_Mutation	SNP	ENST00000324198.6	37	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	A	4.803	0.149335	0.09185	.	.	ENSG00000100077	ENST00000324198;ENST00000545323	T	0.01981	4.52	5.93	-0.622	0.11560	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.054895	0.64402	D	0.000002	T	0.03095	0.0091	L	0.44542	1.39	0.22601	N	0.998946	B;B	0.22276	0.067;0.036	B;B	0.32928	0.079;0.155	T	0.38802	-0.9644	10	0.25751	T	0.34	-24.8877	14.9226	0.70851	0.3343:0.6657:0.0:0.0	.	104;104	A8K869;P35626	.;ARBK2_HUMAN	G	104	ENSP00000317578:R104G	ENSP00000317578:R104G	R	+	1	2	ADRBK2	24387588	0.114000	0.22134	0.003000	0.11579	0.344000	0.29017	0.503000	0.22610	-0.488000	0.06726	0.533000	0.62120	AGA		0.333	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		G	26057588	A	G	26057588	3	3	9	1	0	0	0	0	1	0	0	0	344	180	7	4	324	4	ADRBK2	22	26057588	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10		26057588	25246978	159	1056										
FAM9A	171482	hgsc.bcm.edu	37	chrX	8766191	8766199	+	Splice_Site	DEL	CTGCAATAT	CTGCAATAT	-													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaatagctcctaaaacatacCtgcaatatgttctagcttca							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	CTGCAATAT	CTGCAATAT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:8766191_8766199delCTGCAATAT	ENST00000543214.1	-	5	500_508	c.365_373delATATTGCAG	c.(364-375)catattgcagct>cct	p.122_125HIAA>P	FAM9A_ENST00000381003.3_Splice_Site_p.122_125HIAA>P	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	122						nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				TAAAACATACCTGCAATATGTTCTAGCTT	0.321																																																0			X																																								8726199	SO:0001630	splice_region_variant	171482				CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.373+1ATATTGCAG>-	X.37:g.8766191_8766199delCTGCAATAT			8726191	B7ZLH5|Q2M2D1	Frame_Shift_Del	DEL	ENST00000543214.1	37	CCDS14131.1																																																																																				0.321	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951	In_Frame_Del	-	8766199	CTGCAATAT	-	8766191	8	5	9	1	0	1	0	1	0	0	1	0	5678	695	24	0	645	0	FAM9A	23	8766191	Splice_Site	DEL	CTGCAATAT	TCGA-AF-5654-01A-01D-1657-10		8766191	146504369	160	1057	5	2								
FAM9A	171482	hgsc.bcm.edu	37	chrX	8766199	8766199	+	Missense_Mutation	SNP	T	T	C													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cctaaaacatacctgcaataTgttctagcttcatggtatga							TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:8766199T>C	ENST00000543214.1	-	5	500	c.365A>G	c.(364-366)cAt>cGt	p.H122R	FAM9A_ENST00000381003.3_Missense_Mutation_p.H122R	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	122						nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				ACCTGCAATATGTTCTAGCTT	0.318																																																0			X											78	63	68					X																	8766199		2199	4299	6498	8726199	SO:0001583	missense	171482				CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.365A>G	X.37:g.8766199T>C	ENSP00000440163:p.His122Arg		8726199	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	37	CCDS14131.1	.	.	.	.	.	.	.	.	.	.	t	0.360	-0.940099	0.02322	.	.	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.874	-0.771	0.11002	.	.	.	.	.	T	0.12008	0.0292	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29427	-1.0012	7	0.20046	T	0.44	.	.	.	.	.	122	Q8IZU1	FAM9A_HUMAN	R	122	.	ENSP00000370391:H122R	H	-	2	0	FAM9A	8726199	0.074000	0.21230	0.000000	0.03702	0.002000	0.02628	0.305000	0.19254	-0.282000	0.09128	0.433000	0.28618	CAT		0.318	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951		C	8766199	T	C	8766199	3	2	9	1	0	0	0	0	1	0	0	0	5678	1464	51	4	653	4	FAM9A	23	8766199	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	8	8766199	146504361	161	1058	5	2								
POLA1	5422	hgsc.bcm.edu	37	chrX	24766440	24766440	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tttatcaggatggagaacaaGaacagatccctgagttgcca	10	8	1	4			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:24766440G>C	ENST00000379059.3	+	25	2701	c.2686G>C	c.(2686-2688)Gaa>Caa	p.E896Q	POLA1_ENST00000379068.3_Missense_Mutation_p.E902Q	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	896					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TGGAGAACAAGAACAGATCCC	0.388																																																0			X											88	75	79					X																	24766440		2203	4300	6503	24676361	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.2686G>C	X.37:g.24766440G>C	ENSP00000368349:p.Glu896Gln		24676361	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008181	0.75046	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.19105	2.17;2.17	4.96	4.96	0.65561	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.051777	0.85682	D	0.000000	T	0.42449	0.1203	M	0.71296	2.17	0.80722	D	1	D	0.64830	0.994	D	0.67231	0.95	T	0.21861	-1.0233	10	0.12766	T	0.61	-16.6655	17.2332	0.86990	0.0:0.0:1.0:0.0	.	896	P09884	DPOLA_HUMAN	Q	902;896	ENSP00000368358:E902Q;ENSP00000368349:E896Q	ENSP00000368349:E896Q	E	+	1	0	POLA1	24676361	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.081000	0.76844	2.438000	0.82558	0.600000	0.82982	GAA		0.388	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		C	24766440	G	C	24766440	3	2	9	1	0	0	0	0	1	0	0	0	12218	943	33	5	2784	5	POLA1	23	24766440	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	16000241	24766440	130504120	162	1059										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765438	27765438	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gaggaggaggaggaggaggaGgaggaggaagaagaacagcc	22	3	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:27765438G>A	ENST00000451261.2	+	5	825	c.426G>A	c.(424-426)gaG>gaA	p.E142E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	142	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaggaggaggaag	0.592																																																0			X											16	15	15					X																	27765438		692	1590	2282	27675359	SO:0001819	synonymous_variant	0				CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.426G>A	X.37:g.27765438G>A			27675359	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																				0.592	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765438	G	A	27765438	2	1	9	1	0	0	0	0	0	0	0	1	4284	991	35	3		3	DCAF8L2	23	27765438	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	2998998	27765438	127505122	163	1060										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148722	34148722	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tctggagctttgggaggctcCgggtggagactggacacccg	17	10	1	1	rs372486528		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:34148722C>T	ENST00000346193.3	-	1	1725	c.1674G>A	c.(1672-1674)ccG>ccA	p.P558P		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	558										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TGGGAGGCTCCGGGTGGAGAC	0.577																																																0			X						C		2,3785		0,2,1606,571	61	59	60		1674	-0.6	0	X		60	1,6696		0,1,2421,1853	no	coding-synonymous	FAM47A	NM_203408.3		0,3,4027,2424	TT,TC,CC,C		0.0149,0.0528,0.0286		558/792	34148722	3,10481	2179	4275	6454	34058643	SO:0001819	synonymous_variant	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1674G>A	X.37:g.34148722C>T			34058643	A8K8I9|Q8TAA0	Silent	SNP	ENST00000346193.3	37	CCDS43926.1																																																																																				0.577	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148722	C	T	34148722	2	4	9	1	0	0	0	0	0	0	0	1	5588	639	23	1		1	FAM47A	23	34148722	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	6383284	34148722	121121838	164	1061										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35993862	35993862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cagttgtccagccagtaacaCttgagctatcttctaatgag	8	10	2	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:35993862C>T	ENST00000297866.5	+	15	2611	c.2545C>T	c.(2545-2547)Ctt>Ttt	p.L849F		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	849										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						GCCAGTAACACTTGAGCTATC	0.423																																																0			X											141	121	128					X																	35993862		2202	4300	6502	35903783	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2545C>T	X.37:g.35993862C>T	ENSP00000297866:p.Leu849Phe		35903783	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720162	0.48728	.	.	ENSG00000165164	ENST00000297866	T	0.37584	1.19	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000001	T	0.60881	0.2303	M	0.79475	2.455	0.36351	D	0.860078	D	0.89917	1.0	D	0.97110	1.0	T	0.69837	-0.5037	10	0.45353	T	0.12	-26.3368	14.9502	0.71067	0.0:1.0:0.0:0.0	.	849	Q6ZTR5	CX022_HUMAN	F	849	ENSP00000297866:L849F	ENSP00000297866:L849F	L	+	1	0	CXorf22	35903783	0.992000	0.36948	0.402000	0.26371	0.220000	0.24768	3.236000	0.51336	2.117000	0.64856	0.600000	0.82982	CTT		0.423	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		T	35993862	C	T	35993862	3	4	9	1	0	0	0	0	1	0	0	0	4108	565	20	3	2603	3	CXorf22	23	35993862	Missense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	1845140	35993862	119276698	165	1062										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	9	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-AF-5654-01A-01D-1657-10	14356896	50350758	104919802	166	1063										
ASB12	142689	hgsc.bcm.edu	37	chrX	63444779	63444779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	caagggagagagatggaaggTagatattagcaccaaaatcg	13	5	0	3			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:63444779T>C	ENST00000396130.2	-	1	724	c.725A>G	c.(724-726)tAc>tGc	p.Y242C	ASB12_ENST00000362002.2_Missense_Mutation_p.Y251C|MTMR8_ENST00000453546.1_Missense_Mutation_p.Y626C			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	242					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						AGATGGAAGGTAGATATTAGC	0.502																																																2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	X											82	67	72					X																	63444779		2203	4300	6503	63361504	SO:0001583	missense	142689			AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705	ENST00000396130.2:c.725A>G	X.37:g.63444779T>C	ENSP00000379435:p.Tyr242Cys		63361504	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	37		.	.	.	.	.	.	.	.	.	.	T	16.64	3.179658	0.57800	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.53206	0.63;0.63;0.63	4.06	4.06	0.47325	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.55497	0.1924	L	0.32530	0.975	0.31596	N	0.653333	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.62310	-0.6881	10	0.66056	D	0.02	-18.1767	11.3454	0.49556	0.0:0.0:0.0:1.0	.	626;242	B4DQL0;Q8WXK4	.;ASB12_HUMAN	C	251;242;219;626	ENSP00000355195:Y251C;ENSP00000379435:Y242C;ENSP00000394003:Y626C	ENSP00000354626:Y219C	Y	-	2	0	ASB12;MTMR8	63361504	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.526000	0.67116	1.619000	0.50296	0.381000	0.24937	TAC		0.502	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	63444779	T	C	63444779	3	2	9	1	0	0	0	0	1	0	0	0	1017	1638	57	4	212	4	ASB12	23	63444779	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	13094021	63444779	91825781	167	1064										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63569894	63569894	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	aactttgaacttccaaccacCgttcccaaggtaacagattt	5	12	0	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:63569894C>G	ENST00000374852.3	-	5	592	c.525G>C	c.(523-525)acG>acC	p.T175T	MTMR8_ENST00000453546.1_Silent_p.T175T	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	175	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TTCCAACCACCGTTCCCAAGG	0.353																																																1	Whole gene deletion(1)	ovary(1)	X											128	106	114					X																	63569894		2203	4300	6503	63486619	SO:0001819	synonymous_variant	66036			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.525G>C	X.37:g.63569894C>G			63486619	Q5JT99|Q9NXP6	Silent	SNP	ENST00000374852.3	37	CCDS14379.1																																																																																				0.353	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		G	63569894	C	G	63569894	2	3	9	1	0	0	0	0	0	0	0	1	9979	639	23	5		5	MTMR8	23	63569894	Silent	SNP	C	TCGA-AF-5654-01A-01D-1657-10	125115	63569894	91700666	168	1065										
IGBP1	3476	hgsc.bcm.edu	37	chrX	69385814	69385814	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atcctaggggctatgggaacCgacagaacatgggctgatct	13	9	1	2			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:69385814C>T	ENST00000342206.6	+	6	1502	c.1003C>T	c.(1003-1005)Cga>Tga	p.R335*	IGBP1_ENST00000356413.4_Nonsense_Mutation_p.R335*|IGBP1-AS1_ENST00000366397.3_RNA			P78318	IGBP1_HUMAN	immunoglobulin (CD79A) binding protein 1	335					B cell activation (GO:0042113)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dephosphorylation (GO:0035306)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microtubule-based movement (GO:0060632)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	protein phosphatase type 2A regulator activity (GO:0008601)			kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(2)	11						CTATGGGAACCGACAGAACAT	0.552																																					NSCLC(167;1189 1558 6576 8216 30387 37980 41450)											0			X											99	76	84					X																	69385814		2203	4300	6503	69302539	SO:0001587	stop_gained	3476			Y08915	CCDS14396.1	Xq13.1-q13.3	2008-02-05			ENSG00000089289	ENSG00000089289			5461	protein-coding gene	gene with protein product	"alpha 4"	300139		IBP1		9441740	Standard	NM_001551		Approved		uc004dxw.3	P78318	OTTHUMG00000021767	ENST00000342206.6:c.1003C>T	X.37:g.69385814C>T	ENSP00000363661:p.Arg335*		69302539	Q8TAB2	Nonsense_Mutation	SNP	ENST00000342206.6	37	CCDS14396.1	.	.	.	.	.	.	.	.	.	.	.	42	9.254074	0.99115	.	.	ENSG00000089289	ENST00000342206;ENST00000356413	.	.	.	5.5	3.67	0.42095	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.48040	D	0.999576	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.8349	0.40963	0.4146:0.5854:0.0:0.0	.	.	.	.	X	335	.	ENSP00000363661:R335X	R	+	1	2	IGBP1	69302539	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.218000	0.51192	0.617000	0.30160	-0.224000	0.12420	CGA		0.552	IGBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057052.1			T	69385814	C	T	69385814	4	4	9	1	0	0	0	0	0	1	0	0	7588	644	23	1	1025	1	IGBP1	23	69385814	Nonsense_Mutation	SNP	C	TCGA-AF-5654-01A-01D-1657-10	5815920	69385814	85884746	169	1066										
DRP2	1821	hgsc.bcm.edu	37	chrX	100515081	100515081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tggctctgcaggctcgtcccTagcttcctctccacagcagt	9	16	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:100515081T>C	ENST00000395209.3	+	23	3199	c.2672T>C	c.(2671-2673)cTa>cCa	p.L891P	DRP2_ENST00000538510.1_Missense_Mutation_p.L891P|DRP2_ENST00000541709.1_Missense_Mutation_p.L813P|DRP2_ENST00000402866.1_Missense_Mutation_p.L891P	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	891					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GGCTCGTCCCTAGCTTCCTCT	0.567																																																0			X											137	109	119					X																	100515081		2203	4300	6503	100401737	SO:0001583	missense	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2672T>C	X.37:g.100515081T>C	ENSP00000378635:p.Leu891Pro		100401737	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	T	15.39	2.819744	0.50633	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.05513	3.54;3.54;3.43;3.54	5.21	5.21	0.72293	.	0.074145	0.56097	D	0.000031	T	0.03564	0.0102	N	0.12746	0.255	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45571	-0.9252	10	0.12766	T	0.61	-1.4605	8.8963	0.35467	0.0:0.0847:0.0:0.9153	.	891	Q13474	DRP2_HUMAN	P	891;891;813;891	ENSP00000385038:L891P;ENSP00000378635:L891P;ENSP00000444752:L813P;ENSP00000441051:L891P	ENSP00000378635:L891P	L	+	2	0	DRP2	100401737	1.000000	0.71417	0.913000	0.36048	0.996000	0.88848	4.277000	0.58939	1.735000	0.51646	0.430000	0.28490	CTA		0.567	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		C	100515081	T	C	100515081	3	2	9	1	0	0	0	0	1	0	0	0	4775	1522	53	4	2754	4	DRP2	23	100515081	Missense_Mutation	SNP	T	TCGA-AF-5654-01A-01D-1657-10	31129267	100515081	54755479	170	1067										
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395951	101395951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	agtccttgggggaatcgtccGtccccctgtctgtttttctt	10	12	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:101395951G>A	ENST00000372774.3	-	3	602	c.353C>T	c.(352-354)aCg>aTg	p.T118M	TCEAL6_ENST00000372773.1_Missense_Mutation_p.T118M	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						GGAATCGTCCGTCCCCCTGTC	0.582																																																0			X											108	100	103					X																	101395951		2203	4300	6503	101282607	SO:0001583	missense	158931			BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.353C>T	X.37:g.101395951G>A	ENSP00000361860:p.Thr118Met		101282607	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	37	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	8.200	0.797928	0.16327	.	.	ENSG00000204071	ENST00000372774;ENST00000372773;ENST00000536102	T;T	0.10192	2.9;2.9	2.75	0.957	0.19613	.	0.189930	0.26023	N	0.026805	T	0.25901	0.0631	M	0.79258	2.445	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04165	-1.0972	10	0.52906	T	0.07	.	4.6463	0.12574	0.326:0.0:0.674:0.0	.	118	Q6IPX3-2	.	M	118	ENSP00000361860:T118M;ENSP00000361859:T118M	ENSP00000361859:T118M	T	-	2	0	TCEAL6	101282607	0.000000	0.05858	0.002000	0.10522	0.235000	0.25334	-0.086000	0.11233	0.131000	0.18576	0.468000	0.43344	ACG		0.582	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		A	101395951	G	A	101395951	3	1	9	1	0	0	0	0	1	0	0	0	15714	1145	40	1	202	1	TCEAL6	23	101395951	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	880870	101395951	53874609	171	1068										
RNF128	79589	hgsc.bcm.edu	37	chrX	105970343	105970343	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tacggtgtgggagctgagcgAggagggcgtgtacggccagg	21	7	0	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:105970343A>T	ENST00000255499.2	+	1	450	c.200A>T	c.(199-201)gAg>gTg	p.E67V	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	67					negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						GAGCTGAGCGAGGAGGGCGTG	0.701																																																0			X											19	14	15					X																	105970343		2196	4276	6472	105856999	SO:0001583	missense	79589			AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.200A>T	X.37:g.105970343A>T	ENSP00000255499:p.Glu67Val		105856999	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	37	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	a	22.5	4.292017	0.80914	.	.	ENSG00000133135	ENST00000255499	T	0.16073	2.37	4.7	4.7	0.59300	.	0.132798	0.56097	D	0.000040	T	0.20170	0.0485	M	0.65677	2.01	0.49483	D	0.999799	P	0.39480	0.675	B	0.39379	0.298	T	0.02484	-1.1152	10	0.30078	T	0.28	.	10.9672	0.47418	1.0:0.0:0.0:0.0	.	67	Q8TEB7	RN128_HUMAN	V	67	ENSP00000255499:E67V	ENSP00000255499:E67V	E	+	2	0	RNF128	105856999	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.585000	0.53943	1.671000	0.50874	0.414000	0.27820	GAG		0.701	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		T	105970343	A	T	105970343	3	4	9	1	0	0	0	0	1	0	0	0	13473	304	11	5	612	5	RNF128	23	105970343	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	4574392	105970343	49300217	172	1069										
KLHL13	90293	hgsc.bcm.edu	37	chrX	117043745	117043745	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	atgaaatccaccgtttgcacGtaattaatgagctcctgtgg	9	9	0	2	rs150238128		TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:117043745G>A	ENST00000262820.3	-	5	1794	c.885C>T	c.(883-885)taC>taT	p.Y295Y	KLHL13_ENST00000371876.1_Silent_p.Y244Y|KLHL13_ENST00000371882.1_Silent_p.Y244Y|KLHL13_ENST00000545703.1_Silent_p.Y253Y|KLHL13_ENST00000469946.1_Silent_p.Y244Y|KLHL13_ENST00000540167.1_Silent_p.Y279Y|KLHL13_ENST00000371878.1_Silent_p.Y244Y|KLHL13_ENST00000541812.1_Silent_p.Y279Y|KLHL13_ENST00000539496.1_Silent_p.Y298Y	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	295	BACK.				cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						CCGTTTGCACGTAATTAATGA	0.433													G|||	1	0.000264901	8e-04	0	3775	,	,		17857	0		0	False		,,,				2504	0															0			X											117	96	103					X																	117043745		2203	4300	6503	116927773	SO:0001819	synonymous_variant	90293			AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.885C>T	X.37:g.117043745G>A			116927773	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																				0.433	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		A	117043745	G	A	117043745	2	1	9	1	0	0	0	0	0	0	0	1	8390	1140	40	1		1	KLHL13	23	117043745	Silent	SNP	G	TCGA-AF-5654-01A-01D-1657-10	11073402	117043745	38226815	173	1070										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128615123	128615123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	cactgcgtagtttgctttgcGttctcgtttaggaggttcaa	11	8	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:128615123G>A	ENST00000371122.4	-	18	2386	c.2257C>T	c.(2257-2259)Cgc>Tgc	p.R753C	SMARCA1_ENST00000371121.3_Missense_Mutation_p.R741C|SMARCA1_ENST00000371123.1_Missense_Mutation_p.R741C	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	753					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TTTGCTTTGCGTTCTCGTTTA	0.418																																																0			X											184	122	143					X																	128615123		2203	4300	6503	128442804	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.2257C>T	X.37:g.128615123G>A	ENSP00000360163:p.Arg753Cys		128442804	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113797	0.77210	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.94758	-3.51;-3.51;-3.5;-3.46	5.81	5.81	0.92471	.	0.000000	0.64402	D	0.000010	D	0.98267	0.9426	H	0.95402	3.665	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.991;0.991;0.996;0.991	D	0.99289	1.0898	10	0.87932	D	0	-3.9813	18.9713	0.92716	0.0:0.0:1.0:0.0	.	732;753;741;753	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	C	741;741;753;732	ENSP00000360162:R741C;ENSP00000360164:R741C;ENSP00000360163:R753C;ENSP00000404275:R732C	ENSP00000360162:R741C	R	-	1	0	SMARCA1	128442804	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.962000	0.63687	2.428000	0.82296	0.600000	0.82982	CGC		0.418	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		A	128615123	G	A	128615123	3	1	9	1	0	0	0	0	1	0	0	0	14805	1145	40	1	935	1	SMARCA1	23	128615123	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	11571378	128615123	26655437	174	1071										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140995660	140995660	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	tcccctcctccacttcatcgAgtctttcccagagttctcct	4	18	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:140995660A>T	ENST00000285879.4	+	4	2756	c.2470A>T	c.(2470-2472)Agt>Tgt	p.S824C	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	824										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CACTTCATCGAGTCTTTCCCA	0.562										HNSCC(15;0.026)																																						0			X											138	143	141					X																	140995660		2203	4300	6503	140823326	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2470A>T	X.37:g.140995660A>T	ENSP00000285879:p.Ser824Cys		140823326	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	-	13.51	2.259573	0.39995	.	.	ENSG00000155495	ENST00000285879	T	0.02656	4.21	1.81	-3.61	0.04556	.	.	.	.	.	T	0.01661	0.0053	N	0.14661	0.345	0.09310	N	1	B	0.21225	0.053	B	0.17722	0.019	T	0.45644	-0.9247	9	0.72032	D	0.01	.	2.8074	0.05431	0.2269:0.1662:0.0:0.6069	.	824	O60732	MAGC1_HUMAN	C	824	ENSP00000285879:S824C	ENSP00000285879:S824C	S	+	1	0	MAGEC1	140823326	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	0.145000	0.16157	-0.968000	0.03578	0.231000	0.17811	AGT		0.562	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140995660	A	T	140995660	3	4	9	1	0	0	0	0	1	0	0	0	9210	304	11	5	2476	5	MAGEC1	23	140995660	Missense_Mutation	SNP	A	TCGA-AF-5654-01A-01D-1657-10	12380537	140995660	14274900	175	1072										
FLNA	2316	hgsc.bcm.edu	37	chrX	153599408	153599408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	gcagcccgtcgctcaggtccGtctgcaggttggcgatgcgc	15	14	2	0			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:153599408G>A	ENST00000369850.3	-	2	442	c.206C>T	c.(205-207)aCg>aTg	p.T69M	FLNA_ENST00000360319.4_Missense_Mutation_p.T69M|FLNA_ENST00000422373.1_Missense_Mutation_p.T69M|FLNA_ENST00000344736.4_Missense_Mutation_p.T69M	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	69	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTCAGGTCCGTCTGCAGGTT	0.617																																																0			X											56	49	52					X																	153599408		2202	4296	6498	153252602	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.206C>T	X.37:g.153599408G>A	ENSP00000358866:p.Thr69Met		153252602	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.020393	0.35606	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.95307	-3.67;-3.67;-3.67;-3.67	4.88	4.88	0.63580	Calponin homology domain (5);	0.136701	0.47852	D	0.000203	D	0.94039	0.8090	M	0.84948	2.725	0.80722	D	1	P;P	0.50369	0.844;0.934	B;B	0.44315	0.426;0.446	D	0.93527	0.6866	10	0.59425	D	0.04	.	6.9874	0.24735	0.0929:0.0:0.7334:0.1738	.	69;69	P21333-2;P21333	.;FLNA_HUMAN	M	69;42;69;69;69	ENSP00000353467:T69M;ENSP00000416926:T69M;ENSP00000358866:T69M;ENSP00000358863:T69M	ENSP00000358863:T69M	T	-	2	0	FLNA	153252602	0.173000	0.23056	1.000000	0.80357	0.993000	0.82548	0.518000	0.22847	2.014000	0.59158	0.479000	0.44913	ACG		0.617	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			A	153599408	G	A	153599408	3	1	9	1	0	0	0	0	1	0	0	0	5952	1145	40	1	7925	1	FLNA	23	153599408	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	12603748	153599408	1671152	176	1073										
F8	2157	hgsc.bcm.edu	37	chrX	154157962	154157962	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.464538550650019	2.63238512035011	0.254746947130656	1	1	0	ctatctgtgtgagggtgctcGgggtcaaatgtttcatgttt	13	6	3	1			TCGA-AF-5654-01A-01D-1657-10	TCGA-AF-5654-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	be6903cf-cfdc-4923-8991-da2544dce86c	d9a42723-5926-49f6-85ef-c25824c3d39c	g.chrX:154157962G>T	ENST00000360256.4	-	14	4303	c.4103C>A	c.(4102-4104)cCg>cAg	p.P1368Q		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1368	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.P1368Q(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GAGGGTGCTCGGGGTCAAATG	0.438																																																2	Substitution - Missense(2)	lung(2)	X	GRCh37	CD034857	F8	D							235	202	213					X																	154157962		2203	4300	6503	153811156	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4103C>A	X.37:g.154157962G>T	ENSP00000353393:p.Pro1368Gln		153811156	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.155946	0.00028	.	.	ENSG00000185010	ENST00000360256	D	0.98400	-4.91	4.64	0.607	0.17564	.	0.997596	0.08116	N	0.995440	D	0.89294	0.6674	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	D	0.83818	0.0245	10	0.11182	T	0.66	-1.3057	4.214	0.10526	0.3471:0.0:0.1915:0.4614	.	1368	P00451	FA8_HUMAN	Q	1368	ENSP00000353393:P1368Q	ENSP00000353393:P1368Q	P	-	2	0	F8	153811156	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.172000	0.09868	-0.260000	0.09418	-0.321000	0.08615	CCG		0.438	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154157962	G	T	154157962	3	4	9	1	0	0	0	0	1	0	0	0	5363	1116	39	2	3032	2	F8	23	154157962	Missense_Mutation	SNP	G	TCGA-AF-5654-01A-01D-1657-10	558554	154157962	1112598	177	1074										
RERE	473	hgsc.bcm.edu	37	chr1	8421203	8421203	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acaggcgctgtgggagcctgTggctggttaggggcctggga	20	8	0	0	rs13596	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:8421203T>C	ENST00000337907.3	-	19	2998	c.2364A>G	c.(2362-2364)ccA>ccG	p.P788P	RERE_ENST00000476556.1_Silent_p.P234P|RERE_ENST00000377464.1_Silent_p.P520P|RERE_ENST00000400908.2_Silent_p.P788P|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	788	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TGGGAGCCTGTGGCTGGTTAG	0.731													t|||	4006	0.79992	0.8411	0.7925	5008	,	,		12992	0.9206		0.6819	False		,,,				2504	0.7464															0			1						T	,,	3390,752		1409,572,90	6	7	7		2364,702,2364	-10	0	1	dbSNP_52	7	5605,2589		1942,1721,434	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	3351,2293,524	CC,CT,TT		31.5963,18.1555,27.0833	,,	788/1567,234/1013,788/1567	8421203	8995,3341	2071	4097	6168	8343790	SO:0001819	synonymous_variant	473			AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2364A>G	1.37:g.8421203T>C			8343790	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																				0.731	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			C	8421203	T	C	8421203	2	2	10	1	0	0	0	0	0	0	0	1	13268	1683	59	4		4	RERE	1	8421203	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10		8421203	240829418	1	1075										
CDA	978	hgsc.bcm.edu	37	chr1	20931490	20931490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaccgctatccagaaggccgTctcagaagggtacaaggatt	12	10	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:20931490T>C	ENST00000375071.3	+	2	406	c.224T>C	c.(223-225)gTc>gCc	p.V75A	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	75	CMP/dCMP deaminase zinc-binding.				cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	CAGAAGGCCGTCTCAGAAGGG	0.507																																					Pancreas(74;49 1356 2772 27818 40529)											0			1											100	88	92					1																	20931490		2203	4300	6503	20804077	SO:0001583	missense	978			BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.224T>C	1.37:g.20931490T>C	ENSP00000364212:p.Val75Ala		20804077		Missense_Mutation	SNP	ENST00000375071.3	37	CCDS210.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640664	0.87859	.	.	ENSG00000158825	ENST00000375071	T	0.45276	0.9	5.74	5.74	0.90152	APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.235598	0.44097	D	0.000486	T	0.65606	0.2707	M	0.86651	2.83	0.40289	D	0.978481	P	0.51147	0.942	P	0.61070	0.883	T	0.72944	-0.4138	10	0.87932	D	0	.	12.4306	0.55571	0.0:0.0:0.0:1.0	.	75	P32320	CDD_HUMAN	A	75	ENSP00000364212:V75A	ENSP00000364212:V75A	V	+	2	0	CDA	20804077	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	6.790000	0.75115	2.188000	0.69820	0.454000	0.30748	GTC		0.507	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785		C	20931490	T	C	20931490	3	2	10	1	0	0	0	0	1	0	0	0	3058	1667	58	4	230	4	CDA	1	20931490	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	12510287	20931490	228319131	2	1076										
GRHL3	57822	hgsc.bcm.edu	37	chr1	24668617	24668617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtctccaggtgttcatcggcGtaaactgtctgagcacagac	11	11	3	2	rs375437963		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:24668617G>A	ENST00000350501.5	+	9	1187	c.1060G>A	c.(1060-1062)Gta>Ata	p.V354I	GRHL3_ENST00000361548.4_Missense_Mutation_p.V354I|GRHL3_ENST00000342072.4_Missense_Mutation_p.V261I|GRHL3_ENST00000236255.4_Missense_Mutation_p.V359I|GRHL3_ENST00000356046.2_Missense_Mutation_p.V308I	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	354					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GTTCATCGGCGTAAACTGTCT	0.577																																																0			1						G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	108	111	110		1060,1060,1075,922	3.8	0.8	1		110	0,8600		0,0,4300	no	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign	354/627,354/603,359/608,308/557	24668617	1,13005	2203	4300	6503	24541204	SO:0001583	missense	57822			AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"transcription factor CP2-like 4"	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1060G>A	1.37:g.24668617G>A	ENSP00000288955:p.Val354Ile		24541204	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	.	.	.	.	.	.	.	.	.	.	G	12.62	1.993043	0.35131	2.27E-4	0.0	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.65	3.8	0.43715	.	0.198562	0.45126	D	0.000382	T	0.15435	0.0372	L	0.32530	0.975	0.49582	D	0.9998	B;B;B	0.24882	0.113;0.0;0.093	B;B;B	0.13407	0.009;0.001;0.005	T	0.04373	-1.0956	10	0.44086	T	0.13	-29.3575	10.5268	0.44954	0.1693:0.0:0.8307:0.0	.	308;359;354	A2A297;Q8TE85-2;G3XAF0	.;.;.	I	354;261;354;308;359	ENSP00000354943:V354I;ENSP00000340543:V261I;ENSP00000288955:V354I;ENSP00000348333:V308I;ENSP00000236255:V359I	ENSP00000236255:V359I	V	+	1	0	GRHL3	24541204	0.995000	0.38212	0.763000	0.31416	0.397000	0.30659	2.322000	0.43814	0.953000	0.37825	0.655000	0.94253	GTA		0.577	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180		A	24668617	G	A	24668617	3	1	10	1	0	0	0	0	1	0	0	0	6786	1145	40	1	1130	1	GRHL3	1	24668617	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3737127	24668617	224582004	3	1077										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504190	70504190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtccgtttgaagacaggaccGcttttccttccaaattagag	9	10	0	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:70504190G>A	ENST00000035383.5	+	19	2599	c.2569G>A	c.(2569-2571)Gct>Act	p.A857T	LRRC7_ENST00000310961.5_Missense_Mutation_p.A862T|LRRC7_ENST00000415775.2_Missense_Mutation_p.A141T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	857						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.A857T(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						AGACAGGACCGCTTTTCCTTC	0.468																																																1	Substitution - Missense(1)	endometrium(1)	1											80	89	86					1																	70504190		2203	4300	6503	70276778	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2569G>A	1.37:g.70504190G>A	ENSP00000035383:p.Ala857Thr		70276778	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437615	0.83885	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.56275	0.47;0.57;1.68	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.99	T	0.53258	-0.8464	10	0.28530	T	0.3	.	19.3033	0.94151	0.0:0.0:1.0:0.0	.	141;857;857	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	T	862;857;141;680	ENSP00000309245:A862T;ENSP00000035383:A857T;ENSP00000394867:A141T	ENSP00000035383:A857T	A	+	1	0	LRRC7	70276778	1.000000	0.71417	0.998000	0.56505	0.857000	0.48899	9.447000	0.97595	2.809000	0.96659	0.467000	0.42956	GCT		0.468	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70504190	G	A	70504190	3	1	10	1	0	0	0	0	1	0	0	0	9049	1087	38	1	2643	1	LRRC7	1	70504190	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	45835573	70504190	178746431	4	1078										
PIGK	10026	hgsc.bcm.edu	37	chr1	77634963	77634963	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acctcgtaacttctataatcCacttccacatcatctccata	1	15	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:77634963C>T	ENST00000370812.3	-	4	380	c.357G>A	c.(355-357)gtG>gtA	p.V119V	PIGK_ENST00000445065.1_Intron|PIGK_ENST00000478391.1_Intron|PIGK_ENST00000370813.5_Intron|PIGK_ENST00000359130.1_Silent_p.V119V	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	119					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)			endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						TTCTATAATCCACTTCCACAT	0.343																																																0			1											98	86	90					1																	77634963		2203	4299	6502	77407551	SO:0001819	synonymous_variant	10026			AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"Phosphatidylinositol glycan anchor biosynthesis"	8965	protein-coding gene	gene with protein product	"GPI transamidase subunit"	605087	"phosphatidylinositol glycan, class K"			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.357G>A	1.37:g.77634963C>T			77407551	B2R7K3|B4E2M3|O14822|Q5TG77	Silent	SNP	ENST00000370812.3	37	CCDS674.1																																																																																				0.343	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482		T	77634963	C	T	77634963	2	4	10	1	0	0	0	0	0	0	0	1	11921	581	21	3		3	PIGK	1	77634963	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	7130773	77634963	171615658	5	1079										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91404921	91404921	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttgtgaggttgatccaaatgTtcgcttcacatcttgtttta	8	7	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:91404921T>C	ENST00000370440.1	-	3	2207	c.1990A>G	c.(1990-1992)Aca>Gca	p.T664A	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.T664A			Q9H582	ZN644_HUMAN	zinc finger protein 644	664					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GATCCAAATGTTCGCTTCACA	0.373																																																0			1											141	140	140					1																	91404921		2203	4300	6503	91177509	SO:0001583	missense	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.1990A>G	1.37:g.91404921T>C	ENSP00000359469:p.Thr664Ala		91177509	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	9.117	1.007980	0.19199	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.00578	6.44;6.44	6.02	2.52	0.30459	.	0.493565	0.22492	N	0.059345	T	0.00144	0.0004	L	0.36672	1.1	0.28812	N	0.898193	B	0.22480	0.07	B	0.21546	0.035	T	0.41520	-0.9504	10	0.07813	T	0.8	-3.0935	1.2141	0.01910	0.1242:0.2128:0.2174:0.4457	.	664	Q9H582	ZN644_HUMAN	A	664;664;236	ENSP00000359469:T664A;ENSP00000337008:T664A	ENSP00000337008:T664A	T	-	1	0	ZNF644	91177509	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.816000	0.27267	0.186000	0.20125	-0.263000	0.10527	ACA		0.373	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		C	91404921	T	C	91404921	3	2	10	1	0	0	0	0	1	0	0	0	18099	1725	60	4	2009	4	ZNF644	1	91404921	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	13769958	91404921	157845700	6	1080										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94645386	94645386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttcggtttatttctatacacAtatttggccattttttgtct	5	7	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:94645386A>G	ENST00000260526.6	-	20	2557	c.2375T>C	c.(2374-2376)aTg>aCg	p.M792T	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	792	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TTCTATACACATATTTGGCCA	0.308																																																0			1											154	150	152					1																	94645386		2203	4295	6498	94417974	SO:0001583	missense	9411				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.2375T>C	1.37:g.94645386A>G	ENSP00000260526:p.Met792Thr		94417974	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	A	3.019	-0.202144	0.06219	.	.	ENSG00000137962	ENST00000260526	T	0.19669	2.13	5.8	-1.35	0.09114	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.873453	0.09480	N	0.796497	T	0.01320	0.0043	N	0.01168	-0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48281	-0.9049	10	0.07813	T	0.8	0.0157	6.1709	0.20416	0.5417:0.0:0.338:0.1203	.	792;792	F8VWZ8;Q52LW3	.;RHG29_HUMAN	T	792	ENSP00000260526:M792T	ENSP00000260526:M792T	M	-	2	0	ARHGAP29	94417974	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.803000	0.27083	-0.019000	0.14055	0.528000	0.53228	ATG		0.308	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94645386	A	G	94645386	3	3	10	1	0	0	0	0	1	0	0	0	878	217	8	4	1426	4	ARHGAP29	1	94645386	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	3240465	94645386	154605235	7	1081										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcatggcactgtactcttctTgtccagctgtatccagtatg	8	11	3	0	rs11554290	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	1016	Substitution - Missense(1016)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	1											180	156	164					1																	115256529		2203	4300	6503	115058052	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg		115058052	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		C	115256529	T	C	115256529	3	2	10	1	0	0	0	0	1	0	0	0	10671	1812	63	4	399	4	NRAS	1	115256529	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	20611143	115256529	133994092	8	1082										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117131694	117131694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gttttccaccagggtgagggTcctcttcgatttgctcacct	10	12	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:117131694T>C	ENST00000369486.3	-	8	2827	c.2062A>G	c.(2062-2064)Acc>Gcc	p.T688A	IGSF3_ENST00000318837.6_Missense_Mutation_p.T708A|IGSF3_ENST00000369483.1_Missense_Mutation_p.T708A	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	688	Ig-like C2-type 6.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.T688A(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		AGGGTGAGGGTCCTCTTCGAT	0.532																																																1	Substitution - Missense(1)	ovary(1)	1											85	82	83					1																	117131694		2203	4300	6503	116933217	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.2062A>G	1.37:g.117131694T>C	ENSP00000358498:p.Thr688Ala		116933217	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.848969	0.32699	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.64991	-0.13;-0.13;-0.13	4.16	4.16	0.48862	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.472387	0.21950	N	0.066751	T	0.29588	0.0738	N	0.21282	0.65	0.33958	D	0.645311	B;B;B	0.21688	0.012;0.059;0.016	B;B;B	0.22152	0.023;0.038;0.038	T	0.13255	-1.0516	10	0.33141	T	0.24	-34.646	11.1892	0.48675	0.0:0.0:0.0:1.0	.	708;688;708	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	A	688;708;708	ENSP00000358498:T688A;ENSP00000358495:T708A;ENSP00000321184:T708A	ENSP00000321184:T708A	T	-	1	0	IGSF3	116933217	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.606000	0.54095	1.749000	0.51849	0.379000	0.24179	ACC		0.532	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117131694	T	C	117131694	3	2	10	1	0	0	0	0	1	0	0	0	7622	1667	58	4	1538	4	IGSF3	1	117131694	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	1875165	117131694	132118927	9	1083										
NBPF14	25832	hgsc.bcm.edu	37	chr1	148004588	148004588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccatctggaacaccaggtggAgacttgtcaccgtcaaagta	10	11	3	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:148004588A>G	ENST00000369219.1	-	22	2742	c.2726T>C	c.(2725-2727)cTc>cCc	p.L909P				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	909	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CACCAGGTGGAGACTTGTCAC	0.473																																																0			1											59	87	78					1																	148004588		2036	4212	6248	146471212	SO:0001583	missense	25832			AK092351		1q21.1	2013-01-17			ENSG00000122497			"neuroblastoma breakpoint family"	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.2726T>C	1.37:g.148004588A>G	ENSP00000358221:p.Leu909Pro		146471212	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	9.197|9.197	1.027578|1.027578	0.19512|0.19512	.|.	.|.	ENSG00000122497|ENSG00000122497	ENST00000369219;ENST00000369368|ENST00000310701	T|.	0.04758|.	3.56|.	0.512|0.512	0.512|0.512	0.16994|0.16994	DUF1220 (1);|.	.|.	.|.	.|.	.|.	T|T	0.20170|0.20170	0.0485|0.0485	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	P;D;D|.	0.62365|.	0.832;0.991;0.99|.	B;P;P|.	0.54706|.	0.207;0.593;0.759|.	T|T	0.23154|0.23154	-1.0196|-1.0196	7|4	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	257;890;909|.	F8WEX8;B4DH59;Q5TI25|.	.;.;NBPFE_HUMAN|.	P|P	909;257|915	ENSP00000358221:L909P|.	.|.	L|S	-|-	2|1	0|0	NBPF14|NBPF14	146471212|146471212	0.934000|0.934000	0.31675|0.31675	0.003000|0.003000	0.11579|0.11579	0.009000|0.009000	0.06853|0.06853	0.750000|0.750000	0.26334|0.26334	0.492000|0.492000	0.27815|0.27815	0.355000|0.355000	0.21935|0.21935	CTC|TCC		0.473	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		G	148004588	A	G	148004588	3	3	10	1	0	0	0	0	1	0	0	0	10225	304	11	4	43	4	NBPF14	1	148004588	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	30872894	148004588	101246033	10	1084										
FLG	2312	hgsc.bcm.edu	37	chr1	152280074	152280074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tccagtgctggtcccggtccGtccatgggcggactcagact	13	14	1	1	rs140376327		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:152280074G>A	ENST00000368799.1	-	3	7323	c.7288C>T	c.(7288-7290)Cgg>Tgg	p.R2430W	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2430	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R2430W(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCCGGTCCGTCCATGGGCG	0.592									Ichthyosis				G|||	1	0.000199681	0	0	5008	,	,		20890	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	255	238	244		7288	1.6	0	1	dbSNP_134	244	4,8596	4.3+/-15.6	0,4,4296	no	missense	FLG	NM_002016.1	101	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	benign	2430/4062	152280074	5,13001	2203	4300	6503	150546698	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7288C>T	1.37:g.152280074G>A	ENSP00000357789:p.Arg2430Trp		150546698	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	7.286	0.610080	0.14066	2.27E-4	4.65E-4	ENSG00000143631	ENST00000368799	T	0.01745	4.66	4.55	1.57	0.23409	.	.	.	.	.	T	0.00666	0.0022	L	0.41027	1.25	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.45234	-0.9275	9	0.51188	T	0.08	.	7.4395	0.27174	0.0906:0.3128:0.5966:0.0	.	2430	P20930	FILA_HUMAN	W	2430	ENSP00000357789:R2430W	ENSP00000357789:R2430W	R	-	1	2	FLG	150546698	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.114000	0.10757	0.105000	0.17753	-0.347000	0.07816	CGG		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280074	G	A	152280074	3	1	10	1	0	0	0	0	1	0	0	0	5941	1144	40	1	4901	1	FLG	1	152280074	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	4275486	152280074	96970547	11	1085										
NPR1	4881	hgsc.bcm.edu	37	chr1	153657487	153657487	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctcggagctgtggcgggtgcGctgggaggacgttgagccca	19	10	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:153657487G>T	ENST00000368680.3	+	8	2004	c.1532G>T	c.(1531-1533)cGc>cTc	p.R511L		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	511					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TGGCGGGTGCGCTGGGAGGAC	0.642																																					Pancreas(141;1349 1870 15144 15830 40702)											0			1											60	58	58					1																	153657487		2203	4300	6503	151924111	SO:0001583	missense	4881			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1532G>T	1.37:g.153657487G>T	ENSP00000357669:p.Arg511Leu		151924111	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.389815	0.61956	.	.	ENSG00000169418	ENST00000368680;ENST00000428723	T	0.37752	1.18	4.86	3.95	0.45737	.	0.512973	0.19025	N	0.124707	T	0.20047	0.0482	L	0.60067	1.865	0.80722	D	1	P;P	0.43938	0.771;0.822	B;B	0.41510	0.168;0.359	T	0.02654	-1.1128	10	0.24483	T	0.36	.	10.6879	0.45854	0.0925:0.0:0.9075:0.0	.	16;511	B7Z4Y7;P16066	.;ANPRA_HUMAN	L	511;16	ENSP00000357669:R511L	ENSP00000357669:R511L	R	+	2	0	NPR1	151924111	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.252000	0.43196	1.276000	0.44395	0.655000	0.94253	CGC		0.642	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		T	153657487	G	T	153657487	3	4	10	1	0	0	0	0	1	0	0	0	10625	1087	38	2	1562	2	NPR1	1	153657487	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1377413	153657487	95593134	12	1086										
HDGF	3068	hgsc.bcm.edu	37	chr1	156714907	156714907	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cttctccttggattcctcgtAagggaagaggtctttggggc	13	9	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:156714907A>G	ENST00000357325.5	-	3	510	c.196T>C	c.(196-198)Tac>Cac	p.Y66H	HDGF_ENST00000416666.2_Missense_Mutation_p.Y34H|HDGF_ENST00000537739.1_Missense_Mutation_p.Y66H|HDGF_ENST00000465180.1_5'UTR|HDGF_ENST00000368206.5_Missense_Mutation_p.Y82H|HDGF_ENST00000368209.5_Missense_Mutation_p.Y59H	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	66	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)	p.Y66D(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		GATTCCTCGTAAGGGAAGAGG	0.577																																																1	Substitution - Missense(1)	lung(1)	1											90	82	85					1																	156714907		2203	4300	6503	154981531	SO:0001583	missense	3068			D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.196T>C	1.37:g.156714907A>G	ENSP00000349878:p.Tyr66His		154981531	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	37	CCDS1156.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071021	0.76301	.	.	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206	T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78	4.51	4.51	0.55191	PWWP (3);	0.000000	0.64402	U	0.000002	D	0.87549	0.6205	H	0.95745	3.715	0.43902	D	0.996535	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.984	D;D;D;D;D	0.91635	0.999;0.997;0.999;0.999;0.976	D	0.90613	0.4553	10	0.87932	D	0	-9.4067	11.8625	0.52474	1.0:0.0:0.0:0.0	.	34;66;82;59;66	B7Z958;B2RDE8;Q5SZ07;Q5SZ08;P51858	.;.;.;.;HDGF_HUMAN	H	66;59;66;34;82	ENSP00000349878:Y66H;ENSP00000357192:Y59H;ENSP00000443120:Y66H;ENSP00000416752:Y34H;ENSP00000357189:Y82H	ENSP00000349878:Y66H	Y	-	1	0	HDGF	154981531	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.133000	0.94460	1.926000	0.55796	0.254000	0.18369	TAC		0.577	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		G	156714907	A	G	156714907	3	3	10	1	0	0	0	0	1	0	0	0	7039	362	13	4	542	4	HDGF	1	156714907	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	3057420	156714907	92535714	13	1087										
NR1I3	9970	hgsc.bcm.edu	37	chr1	161202999	161202999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	caaacatggtgcccatgtggCgggtgtgggcccccaggagt	16	11	0	0	rs139473535	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:161202999C>T	ENST00000367982.4	-	4	523	c.368G>A	c.(367-369)cGc>cAc	p.R123H	NR1I3_ENST00000505005.1_Missense_Mutation_p.R123H|NR1I3_ENST00000515621.1_Missense_Mutation_p.R48H|NR1I3_ENST00000437437.2_Missense_Mutation_p.R94H|NR1I3_ENST00000428574.2_Missense_Mutation_p.R123H|NR1I3_ENST00000511748.1_Intron|NR1I3_ENST00000506209.1_Missense_Mutation_p.R94H|NR1I3_ENST00000412844.2_Missense_Mutation_p.R94H|NR1I3_ENST00000479324.1_5'Flank|NR1I3_ENST00000367981.3_Missense_Mutation_p.R94H|NR1I3_ENST00000367984.4_Missense_Mutation_p.R123H|NR1I3_ENST00000511944.1_Intron|NR1I3_ENST00000367985.3_Missense_Mutation_p.R123H|NR1I3_ENST00000367983.4_Missense_Mutation_p.R123H|NR1I3_ENST00000512372.1_Missense_Mutation_p.R94H|NR1I3_ENST00000367979.2_Missense_Mutation_p.R123H|NR1I3_ENST00000508387.1_Intron|NR1I3_ENST00000508740.1_Missense_Mutation_p.R94H|NR1I3_ENST00000515452.1_Missense_Mutation_p.R123H|NR1I3_ENST00000502985.1_Intron|NR1I3_ENST00000511676.1_Missense_Mutation_p.R94H|NR1I3_ENST00000367980.2_Missense_Mutation_p.R123H|NR1I3_ENST00000504010.1_Missense_Mutation_p.R94H|NR1I3_ENST00000442691.2_Missense_Mutation_p.R123H			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	123					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCCATGTGGCGGGTGTGGGC	0.562													C|||	5	0.000998403	0.0023	0	5008	,	,		17525	0		0	False		,,,				2504	0.002															0			1											128	133	131					1																	161202999		2203	4300	6503	159469623	SO:0001583	missense	9970			Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"Nuclear hormone receptors"	7969	protein-coding gene	gene with protein product	"constitutive androstane receptor"	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.368G>A	1.37:g.161202999C>T	ENSP00000356961:p.Arg123His		159469623	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	37	CCDS41430.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	17.06	3.291684	0.59976	.	.	ENSG00000143257	ENST00000512372;ENST00000367983;ENST00000367980;ENST00000437437;ENST00000442691;ENST00000412844;ENST00000428574;ENST00000505005;ENST00000508740;ENST00000367982;ENST00000504010;ENST00000511676;ENST00000367981;ENST00000515621;ENST00000367984;ENST00000367985;ENST00000367979;ENST00000506209;ENST00000515452	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66	6.17	5.26	0.73747	Nuclear hormone receptor, ligand-binding (2);	0.265694	0.36972	N	0.002309	D	0.95965	0.8686	M	0.78916	2.43	0.37797	D	0.927558	P;P;D;D;D;D;B;P;D;B;D;D;D;P;B;D;D;D	0.89917	0.905;0.942;0.995;0.978;1.0;0.978;0.017;0.942;0.994;0.017;0.976;1.0;1.0;0.942;0.189;0.999;1.0;0.994	B;B;P;P;D;P;B;B;P;B;P;D;D;B;B;P;P;P	0.65874	0.285;0.285;0.726;0.608;0.939;0.608;0.003;0.391;0.676;0.005;0.497;0.939;0.935;0.391;0.013;0.797;0.873;0.676	D	0.96697	0.9515	9	0.66056	D	0.02	.	13.0116	0.58733	0.1611:0.8389:0.0:0.0	.	123;94;94;123;123;123;123;123;123;123;48;94;94;94;94;94;94;123	B7Z8R7;E9PCF2;E9PHN4;Q6GZ85;E9PHC8;Q0VAC9;F1D8Q1;Q14994;E9PC13;Q4U0F0;D6REZ7;Q6GZ87;E9PDU3;Q6GZ68;E9PH10;Q6GZ84;E9PGH6;E9PB75	.;.;.;.;.;.;.;NR1I3_HUMAN;.;.;.;.;.;.;.;.;.;.	H	94;123;123;94;123;94;123;123;94;123;94;94;94;48;123;123;123;94;123	ENSP00000425417:R94H;ENSP00000356962:R123H;ENSP00000356959:R123H;ENSP00000407446:R94H;ENSP00000406493:R123H;ENSP00000399361:R94H;ENSP00000412672:R123H;ENSP00000424934:R123H;ENSP00000423666:R94H;ENSP00000356961:R123H;ENSP00000424345:R94H;ENSP00000427175:R94H;ENSP00000356960:R94H;ENSP00000421588:R48H;ENSP00000356963:R123H;ENSP00000356965:R123H;ENSP00000356958:R123H;ENSP00000423089:R94H;ENSP00000427034:R123H	ENSP00000356958:R123H	R	-	2	0	NR1I3	159469623	0.195000	0.23338	0.213000	0.23690	0.468000	0.32798	0.830000	0.27462	1.610000	0.50200	0.655000	0.94253	CGC		0.562	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			T	161202999	C	T	161202999	3	4	10	1	0	0	0	0	1	0	0	0	10652	768	27	1	824	1	NR1I3	1	161202999	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	4488092	161202999	88047622	14	1088										
FCRLA	84824	hgsc.bcm.edu	37	chr1	161680613	161680613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgaggagagcagctgccacaCggaggatgacttgactgatg	15	8	0	5	rs149584309		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:161680613C>T	ENST00000236938.6	+	2	436	c.194C>T	c.(193-195)aCg>aTg	p.T65M	FCRLA_ENST00000540521.1_Intron|FCRLA_ENST00000309691.6_Missense_Mutation_p.T48M|FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000294796.4_Intron|FCRLA_ENST00000540926.1_Missense_Mutation_p.T54M|FCRLA_ENST00000349527.4_Missense_Mutation_p.T48M|FCRLA_ENST00000367957.2_Intron|FCRLA_ENST00000546024.1_Missense_Mutation_p.T65M|FCRLA_ENST00000367953.3_Missense_Mutation_p.T54M|FCRLA_ENST00000367949.2_Missense_Mutation_p.T65M|FCRLA_ENST00000367959.2_Missense_Mutation_p.T71M|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367950.1_Missense_Mutation_p.T25M	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	48					cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			AGCTGCCACACGGAGGATGAC	0.552																																																0			1						C	MET/THR,MET/THR,,,,MET/THR,MET/THR	0,4406		0,0,2203	103	78	86		212,194,,,,194,194	-6.6	0	1	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron,intron,missense,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	81,81,,,,81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,,,,benign,benign	71/383,65/288,,,,65/193,65/377	161680613	1,13005	2203	4300	6503	159947237	SO:0001583	missense	84824			AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18504	protein-coding gene	gene with protein product		606891	"Fc receptor-like and mucin-like 1"	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.194C>T	1.37:g.161680613C>T	ENSP00000236938:p.Thr65Met		159947237	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	.	.	.	.	.	.	.	.	.	.	C	6.521	0.464408	0.12402	0.0	1.16E-4	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000367949;ENST00000540926;ENST00000349527;ENST00000309691;ENST00000367953;ENST00000367950	T;T;T;T;T;T;T;T;T	0.47177	5.69;5.69;4.69;0.85;5.71;3.84;4.72;5.71;0.87	4.22	-6.55	0.01854	.	2.079850	0.02016	N	0.047379	T	0.06508	0.0167	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.15473	0.003;0.005;0.002;0.013	B;B;B;B	0.11329	0.003;0.002;0.001;0.006	T	0.06267	-1.0836	10	0.40728	T	0.16	.	0.5896	0.00725	0.224:0.3089:0.2213:0.2458	.	65;65;71;65	A6NL20;G3V1J2;A6NC03;Q7L513-9	.;.;.;.	M	65;71;65;65;54;48;48;54;25	ENSP00000236938:T65M;ENSP00000356936:T71M;ENSP00000439838:T65M;ENSP00000356926:T65M;ENSP00000446380:T54M;ENSP00000294798:T48M;ENSP00000309596:T48M;ENSP00000356930:T54M;ENSP00000356927:T25M	ENSP00000236938:T65M	T	+	2	0	FCRLA	159947237	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.489000	0.00976	-1.106000	0.03008	-1.990000	0.00449	ACG		0.552	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738		T	161680613	C	T	161680613	3	4	10	1	0	0	0	0	1	0	0	0	5819	536	19	1	222	1	FCRLA	1	161680613	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	477614	161680613	87570008	15	1089										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177906532	177906532	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cggctggaggggaaagggctGctgtgggctgggctggagca	22	7	0	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:177906532G>T	ENST00000308284.6	-	19	2409	c.2320C>A	c.(2320-2322)Cag>Aag	p.Q774K	SEC16B_ENST00000495165.1_5'Flank|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	774					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GGAAAGGGCTGCTGTGGGCTG	0.622																																																0			1											20	23	22					1																	177906532		1887	4115	6002	176173155	SO:0001583	missense	89866			AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2320C>A	1.37:g.177906532G>T	ENSP00000308339:p.Gln774Lys		176173155	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927501	0.34002	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.15256	2.44	5.0	5.0	0.66597	.	0.758009	0.12379	N	0.474114	T	0.17874	0.0429	M	0.61703	1.905	0.80722	D	1	B;B;B;B	0.22276	0.067;0.013;0.013;0.013	B;B;B;B	0.12837	0.008;0.003;0.003;0.003	T	0.08330	-1.0727	10	0.06494	T	0.89	-1.6676	13.652	0.62316	0.0:0.0:1.0:0.0	.	329;775;774;471	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	K	774;458;489	ENSP00000308339:Q774K	ENSP00000239472:Q489K	Q	-	1	0	AL359075.1	176173155	0.040000	0.19996	0.097000	0.21041	0.037000	0.13140	1.646000	0.37249	2.589000	0.87451	0.650000	0.86243	CAG		0.622	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		T	177906532	G	T	177906532	3	4	10	1	0	0	0	0	1	0	0	0	14024	1328	46	2	894	2	SEC16B	1	177906532	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	16225919	177906532	71344089	16	1090										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211749326	211749326	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	taaatatagcacccagcaagGaccagcctcataaactgatg	7	11	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:211749326G>A	ENST00000367001.4	-	2	1057	c.928C>T	c.(928-930)Cct>Tct	p.P310S		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	310					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		ACCCAGCAAGGACCAGCCTCA	0.373																																																0			1											142	152	148					1																	211749326		2203	4300	6503	209815949	SO:0001583	missense	7779			AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.928C>T	1.37:g.211749326G>A	ENSP00000355968:p.Pro310Ser		209815949	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	37	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734496	0.69189	.	.	ENSG00000170385	ENST00000367001	T	0.64803	-0.12	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.73984	0.3657	M	0.72118	2.19	0.80722	D	1	D	0.57899	0.981	P	0.56514	0.8	T	0.69903	-0.5019	10	0.22109	T	0.4	-9.6619	19.2601	0.93964	0.0:0.0:1.0:0.0	.	310	Q9Y6M5	ZNT1_HUMAN	S	310	ENSP00000355968:P310S	ENSP00000355968:P310S	P	-	1	0	SLC30A1	209815949	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.711000	0.84669	2.549000	0.85964	0.563000	0.77884	CCT		0.373	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			A	211749326	G	A	211749326	3	1	10	1	0	0	0	0	1	0	0	0	14590	1174	41	3	599	3	SLC30A1	1	211749326	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	33842794	211749326	37501295	17	1091										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213414659	213414659	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atagcgcaagtgaactcctgGgacttgactttggagaaaaa	11	7	0	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:213414659G>T	ENST00000366960.3	+	11	1990	c.1840G>T	c.(1840-1842)Gga>Tga	p.G614*	RPS6KC1_ENST00000366959.3_Nonsense_Mutation_p.G602*|RPS6KC1_ENST00000543354.1_Nonsense_Mutation_p.G317*|RPS6KC1_ENST00000543470.1_Nonsense_Mutation_p.G402*|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	614					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		TGAACTCCTGGGACTTGACTT	0.383																																																0			1											49	53	52					1																	213414659		2203	4300	6503	211481282	SO:0001587	stop_gained	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1840G>T	1.37:g.213414659G>T	ENSP00000355927:p.Gly614*		211481282	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Nonsense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	G	39	7.443776	0.98289	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	.	.	.	5.19	5.19	0.71726	.	0.241459	0.42548	D	0.000696	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-35.4739	16.9253	0.86174	0.0:0.0:1.0:0.0	.	.	.	.	X	402;614;602;317	.	ENSP00000355926:G602X	G	+	1	0	RPS6KC1	211481282	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.249000	0.58766	2.416000	0.81992	0.557000	0.71058	GGA		0.383	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		T	213414659	G	T	213414659	4	4	10	1	0	0	0	0	0	1	0	0	13695	1233	43	2	1882	2	RPS6KC1	1	213414659	Nonsense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1665333	213414659	35835962	18	1092										
PROX1	5629	hgsc.bcm.edu	37	chr1	214178610	214178610	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgaagacctacttctccgacGtaaaggtagggacttttttt	9	8	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:214178610G>A	ENST00000366958.4	+	3	2436	c.1828G>A	c.(1828-1830)Gta>Ata	p.V610I	PROX1_ENST00000261454.4_Missense_Mutation_p.V610I|PROX1_ENST00000498508.2_Missense_Mutation_p.V610I|PROX1_ENST00000435016.1_Missense_Mutation_p.V610I	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	610					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		CTTCTCCGACGTAAAGGTAGG	0.383																																																0			1											85	84	85					1																	214178610		2203	4300	6503	212245233	SO:0001583	missense	5629			U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.1828G>A	1.37:g.214178610G>A	ENSP00000355925:p.Val610Ile		212245233	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	37	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957382	0.73902	.	.	ENSG00000117707	ENST00000541470;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.62	5.62	0.85841	Homeo-prospero domain (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	L	0.49640	1.575	0.80722	D	1	D	0.65815	0.995	D	0.66847	0.947	T	0.61749	-0.6999	10	0.46703	T	0.11	-3.7078	19.6753	0.95930	0.0:0.0:1.0:0.0	.	610	Q92786	PROX1_HUMAN	I	182;610;610;610;610	ENSP00000420283:V610I;ENSP00000355925:V610I;ENSP00000400694:V610I;ENSP00000261454:V610I	ENSP00000261454:V610I	V	+	1	0	PROX1	212245233	1.000000	0.71417	0.981000	0.43875	0.556000	0.35491	9.869000	0.99810	2.648000	0.89879	0.563000	0.77884	GTA		0.383	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		A	214178610	G	A	214178610	3	1	10	1	0	0	0	0	1	0	0	0	12594	1145	40	1	1834	1	PROX1	1	214178610	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	763951	214178610	35072011	19	1093										
CENPF	1063	hgsc.bcm.edu	37	chr1	214815522	214815522	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cagggcctcatgagttgtcaAcaagtcaaaacgacaatgca	9	10	3	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:214815522A>G	ENST00000366955.3	+	12	4009	c.3841A>G	c.(3841-3843)Aca>Gca	p.T1281A		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.T1281A(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TGAGTTGTCAACAAGTCAAAA	0.398																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	ovary(1)	1											65	64	64					1																	214815522		2203	4300	6503	212882145	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3841A>G	1.37:g.214815522A>G	ENSP00000355922:p.Thr1281Ala		212882145	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	8.998	0.979336	0.18812	.	.	ENSG00000117724	ENST00000366955	T	0.22539	1.95	4.96	-2.4	0.06583	.	0.410430	0.18039	N	0.153662	T	0.06280	0.0162	.	.	.	0.23598	N	0.997326	B	0.22683	0.073	B	0.19946	0.027	T	0.31280	-0.9949	9	0.09590	T	0.72	.	1.1552	0.01794	0.337:0.2719:0.2583:0.1327	.	1281	P49454	CENPF_HUMAN	A	1281	ENSP00000355922:T1281A	ENSP00000355922:T1281A	T	+	1	0	CENPF	212882145	0.000000	0.05858	0.988000	0.46212	0.845000	0.48019	-2.184000	0.01254	-0.059000	0.13154	0.418000	0.28097	ACA		0.398	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214815522	A	G	214815522	3	3	10	1	0	0	0	0	1	0	0	0	3237	43	2	4	3883	4	CENPF	1	214815522	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	636912	214815522	34435099	20	1094										
NUP133	55746	hgsc.bcm.edu	37	chr1	229623211	229623211	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctttctaaaactgctactgtAccttgtgcattaaagacaat	5	9	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:229623211A>G	ENST00000261396.3	-	10	1434		c.e10+1		NUP133_ENST00000537506.1_Splice_Site	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CTGCTACTGTACCTTGTGCAT	0.408																																																0			1											102	101	101					1																	229623211		2203	4300	6503	227689834	SO:0001630	splice_region_variant	55746				CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1342+1T>C	1.37:g.229623211A>G			227689834	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Splice_Site	SNP	ENST00000261396.3	37	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854351	0.51270	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6938	0.62564	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NUP133	227689834	1.000000	0.71417	0.990000	0.47175	0.485000	0.33311	7.667000	0.83888	2.042000	0.60477	0.477000	0.44152	.		0.408	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	Intron	G	229623211	A	G	229623211	5	3	10	1	0	0	0	0	0	0	1	0	10785	405	14	4	2194	4	NUP133	1	229623211	Splice_Site	SNP	A	TCGA-AF-6136-01A-11D-1826-10	14807689	229623211	19627410	21	1095										
RYR2	6262	hgsc.bcm.edu	37	chr1	237881796	237881796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgaagtacgagatataatccGcagcaatattcatttacaag	7	7	1	2	rs375947003		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:237881796G>A	ENST00000366574.2	+	73	10846	c.10529G>A	c.(10528-10530)cGc>cAc	p.R3510H	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.R3494H|RYR2_ENST00000360064.6_Missense_Mutation_p.R3508H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3510					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GATATAATCCGCAGCAATATT	0.313																																																0			1						G	HIS/ARG	0,3688		0,0,1844	69	65	66		10529	5.7	1	1		66	1,8165		0,1,4082	no	missense	RYR2	NM_001035.2	29	0,1,5926	AA,AG,GG		0.0122,0.0,0.0084	possibly-damaging	3510/4968	237881796	1,11853	1844	4083	5927	235948419	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10529G>A	1.37:g.237881796G>A	ENSP00000355533:p.Arg3510His		235948419	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.887672	0.72410	0.0	1.22E-4	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96651	-4.08;-4.05;-4.08	5.66	5.66	0.87406	.	0.098059	0.41194	D	0.000935	D	0.89532	0.6742	N	0.04880	-0.145	0.80722	D	1	B	0.26400	0.148	B	0.12837	0.008	D	0.86794	0.1987	10	0.41790	T	0.15	-11.055	13.0125	0.58739	0.0735:0.0:0.9265:0.0	.	3510	Q92736	RYR2_HUMAN	H	3510;3508;3494;465	ENSP00000355533:R3510H;ENSP00000353174:R3508H;ENSP00000443798:R3494H	ENSP00000353174:R3508H	R	+	2	0	RYR2	235948419	0.674000	0.27549	1.000000	0.80357	0.995000	0.86356	1.992000	0.40737	2.662000	0.90505	0.650000	0.86243	CGC		0.313	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237881796	G	A	237881796	3	1	10	1	0	0	0	0	1	0	0	0	13806	1087	38	1	10819	1	RYR2	1	237881796	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	8258585	237881796	11368825	22	1096										
CHML	1122	hgsc.bcm.edu	37	chr1	241797529	241797529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttctcttgctgttttagaagAtgaacatgtcaaatgtacca	7	7	2	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:241797529A>G	ENST00000366553.1	-	1	1703	c.1540T>C	c.(1540-1542)Tct>Cct	p.S514P	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	514					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GTTTTAGAAGATGAACATGTC	0.408																																																0			1											83	79	80					1																	241797529		2203	4299	6502	239864152	SO:0001583	missense	1122			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1540T>C	1.37:g.241797529A>G	ENSP00000355511:p.Ser514Pro		239864152	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.408477	0.62399	.	.	ENSG00000203668	ENST00000366553	D	0.84370	-1.84	5.08	5.08	0.68730	.	0.000000	0.85682	U	0.000000	D	0.91499	0.7316	.	.	.	0.53005	D	0.999965	D	0.89917	1.0	D	0.81914	0.995	D	0.91859	0.5498	9	0.54805	T	0.06	-13.9275	13.1474	0.59470	1.0:0.0:0.0:0.0	.	514	P26374	RAE2_HUMAN	P	514	ENSP00000355511:S514P	ENSP00000355511:S514P	S	-	1	0	CHML	239864152	1.000000	0.71417	0.932000	0.37286	0.971000	0.66376	5.659000	0.68010	2.281000	0.76405	0.533000	0.62120	TCT		0.408	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		G	241797529	A	G	241797529	3	3	10	1	0	0	0	0	1	0	0	0	3357	333	12	4	434	4	CHML	1	241797529	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	3915733	241797529	7453092	23	1097										
CEP170	9859	hgsc.bcm.edu	37	chr1	243385111	243385111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgtgttgcttatccacactaCgagactgaaaggaatgttgt	10	8	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr1:243385111C>T	ENST00000366542.1	-	3	161	c.110G>A	c.(109-111)cGt>cAt	p.R37H	AC092782.1_ENST00000596590.1_5'Flank|CEP170_ENST00000366544.1_Missense_Mutation_p.R37H|CEP170_ENST00000366543.1_Missense_Mutation_p.R37H	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	37	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			ATCCACACTACGAGACTGAAA	0.368																																																0			1											75	66	69					1																	243385111		1878	4106	5984	241451734	SO:0001583	missense	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.110G>A	1.37:g.243385111C>T	ENSP00000355500:p.Arg37His		241451734	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	C	34	5.301248	0.95601	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000522191;ENST00000523424;ENST00000522995	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	5.49	5.49	0.81192	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	D	0.90978	0.7163	L	0.37800	1.135	0.80722	D	1	D;D;D	0.76494	0.978;0.995;0.999	P;D;D	0.87578	0.907;0.913;0.998	D	0.91320	0.5081	10	0.62326	D	0.03	-8.6224	19.7314	0.96182	0.0:1.0:0.0:0.0	.	37;37;37	Q5SW79-3;Q5SW79-2;Q5SW79	.;.;CE170_HUMAN	H	37	ENSP00000355500:R37H;ENSP00000355502:R37H;ENSP00000355501:R37H;ENSP00000427944:R37H;ENSP00000428183:R37H;ENSP00000428400:R37H	ENSP00000355500:R37H	R	-	2	0	CEP170	241451734	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.409000	0.80053	2.727000	0.93392	0.655000	0.94253	CGT		0.368	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		T	243385111	C	T	243385111	3	4	10	1	0	0	0	0	1	0	0	0	3256	536	19	1	4746	1	CEP170	1	243385111	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	1587582	243385111	5865510	24	1098										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1241713	1241713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agtcagctctgggatcctccGgttttacacagcccaggatg	11	12	2	0	rs200548143	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:1241713G>A	ENST00000308624.5	+	10	902	c.773G>A	c.(772-774)cGg>cAg	p.R258Q	SNTG2_ENST00000407292.1_Missense_Mutation_p.R131Q	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	258					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GGGATCCTCCGGTTTTACACA	0.637													g|||	6	0.00119808	0.0045	0	5008	,	,		16958	0		0	False		,,,				2504	0															0			2						A	GLN/ARG	15,4381		0,15,2183	43	47	45		773	-1.1	0	2		45	0,8596		0,0,4298	yes	missense	SNTG2	NM_018968.3	43	0,15,6481	AA,AG,GG		0.0,0.3412,0.1155	benign	258/540	1241713	15,12977	2198	4298	6496	1224264	SO:0001583	missense	54221			AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.773G>A	2.37:g.1241713G>A	ENSP00000311837:p.Arg258Gln		1224264	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	0.017	-1.490283	0.01018	0.003412	0.0	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.63417	-0.04;-0.04	4.68	-1.06	0.10002	.	0.183612	0.48767	N	0.000169	T	0.17408	0.0418	N	0.00109	-2.105	0.18873	N	0.999986	B;B	0.13594	0.008;0.0	B;B	0.04013	0.001;0.0	T	0.44174	-0.9345	10	0.13470	T	0.59	.	9.6423	0.39846	0.7574:0.0:0.2426:0.0	.	131;258	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	Q	258;131	ENSP00000311837:R258Q;ENSP00000385020:R131Q	ENSP00000311837:R258Q	R	+	2	0	SNTG2	1224264	1.000000	0.71417	0.003000	0.11579	0.008000	0.06430	1.987000	0.40687	-0.295000	0.08960	-1.088000	0.02184	CGG		0.637	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		A	1241713	G	A	1241713	3	1	10	1	0	0	0	0	1	0	0	0	14912	1116	39	1	811	1	SNTG2	2	1241713	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10		1241713	241957660	25	1099										
PXDN	7837	hgsc.bcm.edu	37	chr2	1653389	1653389	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgccggtgggcggtacagccCgacaggtttgcgatgaggtt	17	10	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:1653389C>T	ENST00000252804.4	-	17	2213	c.2163G>A	c.(2161-2163)tcG>tcA	p.S721S		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	721					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CGGTACAGCCCGACAGGTTTG	0.582																																																0			2											72	76	75					2																	1653389		2088	4221	6309	1632396	SO:0001819	synonymous_variant	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2163G>A	2.37:g.1653389C>T			1632396	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																				0.582	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1653389	C	T	1653389	2	4	10	1	0	0	0	0	0	0	0	1	12884	639	23	1		1	PXDN	2	1653389	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	411676	1653389	241545984	26	1100										
ALK	238	hgsc.bcm.edu	37	chr2	29443592	29443592	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgggcgagggcgggtctctcGgaggaaggacttgaggtctc	19	9	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:29443592G>A	ENST00000389048.3	-	23	4531	c.3625C>T	c.(3625-3627)Cga>Tga	p.R1209*	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R1209*(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CGGGTCTCTCGGAGGAAGGAC	0.607			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	2											46	45	45					2																	29443592		2203	4300	6503	29297096	SO:0001587	stop_gained	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3625C>T	2.37:g.29443592G>A	ENSP00000373700:p.Arg1209*		29297096	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Nonsense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	g	49	15.862431	0.99847	.	.	ENSG00000171094	ENST00000389048	.	.	.	5.59	4.69	0.59074	.	0.000000	0.43260	U	0.000598	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.97	0.58508	0.0:0.0:0.5426:0.4574	.	.	.	.	X	1209	.	.	R	-	1	2	ALK	29297096	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	3.801000	0.55545	1.439000	0.47511	0.645000	0.84053	CGA		0.607	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29443592	G	A	29443592	4	1	10	1	0	0	0	0	0	1	0	0	525	1124	39	1	1265	1	ALK	2	29443592	Nonsense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	27790203	29443592	213755781	27	1101										
ALK	238	hgsc.bcm.edu	37	chr2	29606622	29606622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	actgcagttcttcagggcaaAgaagtccactgcagacaagc	10	11	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:29606622A>G	ENST00000389048.3	-	5	2164	c.1258T>C	c.(1258-1260)Ttt>Ctt	p.F420L	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	420	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TTCAGGGCAAAGAAGTCCACT	0.507			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	0			2											112	97	102					2																	29606622		2203	4300	6503	29460126	SO:0001583	missense	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1258T>C	2.37:g.29606622A>G	ENSP00000373700:p.Phe420Leu		29460126	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.238236	0.39598	.	.	ENSG00000171094	ENST00000389048	T	0.01647	4.71	5.82	5.82	0.92795	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.222920	0.23035	N	0.052700	T	0.01353	0.0044	N	0.03608	-0.345	0.80722	D	1	P	0.39624	0.681	B	0.40741	0.339	T	0.77517	-0.2558	9	.	.	.	.	13.9215	0.63935	1.0:0.0:0.0:0.0	.	420	Q9UM73	ALK_HUMAN	L	420	ENSP00000373700:F420L	.	F	-	1	0	ALK	29460126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.086000	0.50159	2.221000	0.72209	0.528000	0.53228	TTT		0.507	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29606622	A	G	29606622	3	3	10	1	0	0	0	0	1	0	0	0	525	72	3	4	3704	4	ALK	2	29606622	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	163030	29606622	213592751	28	1102										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86693888	86693888	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agtgatagccctaataactgTtcaggaaaaaaggtagaacc	9	7	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:86693888T>C	ENST00000409556.1	+	11	1766	c.1401T>C	c.(1399-1401)tgT>tgC	p.C467C	KDM3A_ENST00000542128.1_Silent_p.C415C|KDM3A_ENST00000312912.5_Silent_p.C467C|KDM3A_ENST00000409064.1_Silent_p.C467C|KDM3A_ENST00000485171.1_3'UTR			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	467					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CTAATAACTGTTCAGGAAAAA	0.408																																					NSCLC(96;1150 1523 6936 46253 49736)											0			2											70	71	71					2																	86693888		2203	4300	6503	86547399	SO:0001819	synonymous_variant	55818			AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1401T>C	2.37:g.86693888T>C			86547399	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																				0.408	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		C	86693888	T	C	86693888	2	2	10	1	0	0	0	0	0	0	0	1	8147	1731	60	4		4	KDM3A	2	86693888	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	57087266	86693888	156505485	29	1103										
BIN1	274	hgsc.bcm.edu	37	chr2	127809921	127809921	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tccccggaaggcaggctgccGgctggactctctgtgggctg	16	13	1	0	rs373834859		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:127809921G>A	ENST00000316724.5	-	15	1692	c.1281C>T	c.(1279-1281)gcC>gcT	p.A427A	BIN1_ENST00000393040.3_Intron|BIN1_ENST00000393041.3_Silent_p.A309A|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000351659.3_Silent_p.A340A|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000357970.3_Silent_p.A384A|BIN1_ENST00000346226.3_Silent_p.A352A	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	427					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GCAGGCTGCCGGCTGGACTCT	0.682																																																0			2						G	,,,,,,,,,	1,4247		0,1,2123	6	7	6		,1281,1152,1020,,1056,,927,,	-0.8	1	2		6	0,8390		0,0,4195	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,intron,intron	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	0,1,6318	AA,AG,GG		0.0,0.0235,0.0079	,,,,,,,,,	,427/594,384/551,340/507,,352/519,,309/476,,	127809921	1,12637	2124	4195	6319	127526391	SO:0001819	synonymous_variant	274			U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1281C>T	2.37:g.127809921G>A			127526391	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																				0.682	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		A	127809921	G	A	127809921	2	1	10	1	0	0	0	0	0	0	0	1	1433	1103	39	1		1	BIN1	2	127809921	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	41116033	127809921	115389452	30	1104										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141115582	141115582	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgctcatctgaaccatctccGcagtcatcaagtcgatcaca	6	14	6	1	rs35757222	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:141115582G>A	ENST00000389484.3	-	74	12332	c.11361C>T	c.(11359-11361)tgC>tgT	p.C3787C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3787	LDL-receptor class A 32. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AACCATCTCCGCAGTCATCAA	0.418										TSP Lung(27;0.18)			G|||	9	0.00179712	0.0068	0	5008	,	,		17234	0		0	False		,,,				2504	0				Colon(99;50 2074 2507 20106)											0			2						G		47,4359	48.9+/-83.8	0,47,2156	154	143	146		11361	0.9	1	2	dbSNP_126	146	0,8598		0,0,4299	no	coding-synonymous	LRP1B	NM_018557.2		0,47,6455	AA,AG,GG		0.0,1.0667,0.3614		3787/4600	141115582	47,12957	2203	4299	6502	140832052	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.11361C>T	2.37:g.141115582G>A			140832052	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	10.31	1.316147	0.23908	0.010667	0.0	ENSG00000168702	ENST00000437977	.	.	.	5.82	0.945	0.19543	.	.	.	.	.	T	0.49098	0.1537	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45948	-0.9226	4	.	.	.	.	9.1047	0.36689	0.7166:0.0:0.2834:0.0	rs35757222	.	.	.	V	19	.	.	A	-	2	0	LRP1B	140832052	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.323000	0.43823	0.137000	0.18759	-0.312000	0.09012	GCG		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141115582	G	A	141115582	2	1	10	1	0	0	0	0	0	0	0	1	8984	1079	38	1		1	LRP1B	2	141115582	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	13305661	141115582	102083791	31	1105										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160295567	160295567	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	actctctgaatcagaatcatCatcttcactttcttcaatac	2	12	8	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:160295567C>T	ENST00000392783.2	-	7	1348	c.853G>A	c.(853-855)Gat>Aat	p.D285N	BAZ2B_ENST00000392782.1_Missense_Mutation_p.D283N|BAZ2B_ENST00000343439.5_Missense_Mutation_p.D283N|BAZ2B_ENST00000355831.2_Missense_Mutation_p.D285N	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TCAGAATCATCATCTTCACTT	0.328																																																0			2											286	261	269					2																	160295567		1899	4115	6014	160003813	SO:0001583	missense	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.853G>A	2.37:g.160295567C>T	ENSP00000376534:p.Asp285Asn		160003813	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035439	0.75617	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	T;T;T;T	0.09817	2.94;2.94;2.94;2.94	5.25	5.25	0.73442	.	0.000000	0.38111	U	0.001806	T	0.30324	0.0761	L	0.60455	1.87	0.58432	D	0.99999	P;D;D;P;P;P	0.71674	0.925;0.986;0.998;0.827;0.72;0.598	P;P;D;B;B;B	0.66084	0.616;0.797;0.941;0.429;0.429;0.247	T	0.01266	-1.1401	10	0.66056	D	0.02	-9.6363	18.8393	0.92176	0.0:1.0:0.0:0.0	.	283;222;285;283;283;285	Q6MZK7;F5H6H2;Q9UIF8-3;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;.;BAZ2B_HUMAN	N	283;285;285;283;222	ENSP00000376533:D283N;ENSP00000376534:D285N;ENSP00000348087:D285N;ENSP00000339670:D283N	ENSP00000339670:D283N	D	-	1	0	BAZ2B	160003813	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.032000	0.76498	2.408000	0.81797	0.563000	0.77884	GAT		0.328	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160295567	C	T	160295567	3	4	10	1	0	0	0	0	1	0	0	0	1333	826	29	3	5777	3	BAZ2B	2	160295567	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	19179985	160295567	82903806	32	1106										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163228444	163228444	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggatgcctaattggatgaacGtaagtttttctttgccgcag	11	7	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:163228444G>A	ENST00000332142.5	-	16	3585	c.3486C>T	c.(3484-3486)taC>taT	p.Y1162Y		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	1162					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TTGGATGAACGTAAGTTTTTC	0.443																																					GBM(196;1492 2208 17507 24132 45496)											0			2											116	103	108					2																	163228444		2203	4300	6503	162936690	SO:0001819	synonymous_variant	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.3486C>T	2.37:g.163228444G>A			162936690	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	CCDS2219.1																																																																																				0.443	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163228444	G	A	163228444	2	1	10	1	0	0	0	0	0	0	0	1	8058	1140	40	1		1	KCNH7	2	163228444	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	2932877	163228444	79970929	33	1107										
TTN	7273	hgsc.bcm.edu	37	chr2	179552866	179552866	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tctgtaacctctgcttcttcCtcctcctctctttcttcttc	2	17	6	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:179552866C>A	ENST00000591111.1	-	125	31556	c.31332G>T	c.(31330-31332)gaG>gaT	p.E10444D	TTN_ENST00000589042.1_Missense_Mutation_p.E10761D|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E9517D|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTTCTTCCTCCTCCTCTC	0.393																																																0			2											164	166	166					2																	179552866		1876	4096	5972	179261111	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.31332G>T	2.37:g.179552866C>A	ENSP00000465570:p.Glu10444Asp		179261111	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.85	2.061105	0.36373	.	.	ENSG00000155657	ENST00000342992	T	0.65364	-0.15	4.94	1.03	0.20045	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.66127	0.2758	L	0.47190	1.495	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.63998	-0.6510	9	0.87932	D	0	.	7.0274	0.24948	0.0:0.6183:0.0:0.3817	.	10444	Q8WZ42	TITIN_HUMAN	D	9517	ENSP00000343764:E9517D	ENSP00000343764:E9517D	E	-	3	2	TTN	179261111	0.895000	0.30542	1.000000	0.80357	0.942000	0.58702	-0.181000	0.09740	0.222000	0.20900	0.467000	0.42956	GAG		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179552866	C	A	179552866	3	1	10	1	0	0	0	0	1	0	0	0	16775	680	24	2	72190	2	TTN	2	179552866	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	16324422	179552866	63646507	34	1108										
TTN	7273	hgsc.bcm.edu	37	chr2	179611639	179611639	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtgtaccaaatgaatcggaaCgccatatttcataagctgaa	8	8	1	2	rs150492317		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:179611639C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.R5163H|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R5163H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAATCGGAACGCCATATTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2						T	,,HIS/ARG,,	0,4406		0,0,2203	121	119	120		,,15488,,	4.2	0.9	2	dbSNP_134	120	1,8597	1.2+/-3.3	0,1,4298	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,29,,	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	,,,,	,,5163/5605,,	179611639	1,13003	2203	4299	6502	179319884	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-4991G>A	2.37:g.179611639C>T			179319884	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	c	5.845	0.340101	0.11069	0.0	1.16E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.61859	0.07	5.95	4.19	0.49359	.	.	.	.	.	T	0.40297	0.1111	L	0.29908	0.895	0.80722	D	1	B	0.31625	0.332	B	0.19946	0.027	T	0.23368	-1.0190	9	0.42905	T	0.14	.	8.9496	0.35781	0.0:0.7584:0.1194:0.1222	.	5163	Q8WZ42-6	.	H	5163;444	ENSP00000354117:R5163H	ENSP00000304714:R444H	R	-	2	0	TTN	179319884	0.002000	0.14202	0.908000	0.35775	0.481000	0.33189	0.210000	0.17455	0.883000	0.36040	-0.713000	0.03633	CGT		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179611639	C	T	179611639	1	4	10	0	1	0	0	0	0	0	0	0	16775	536	19	1		1	TTN	2	179611639	Intron	SNP	C	TCGA-AF-6136-01A-11D-1826-10	58773	179611639	63587734	35	1109										
FAM126B	285172	hgsc.bcm.edu	37	chr2	201846545	201846545	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cctgatgaaaatccttcatcTgcatcattcaggtttacaga	6	10	4	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:201846545T>C	ENST00000418596.3	-	12	1228	c.1041A>G	c.(1039-1041)gcA>gcG	p.A347A	AC005037.3_ENST00000413848.1_RNA|AC005037.3_ENST00000332935.6_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	347						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						ATCCTTCATCTGCATCATTCA	0.448																																																0			2											78	77	77					2																	201846545		2203	4300	6503	201554790	SO:0001819	synonymous_variant	285172			BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1041A>G	2.37:g.201846545T>C			201554790	B2RCG7|Q4ZG87|Q53TX6	Silent	SNP	ENST00000418596.3	37	CCDS2335.1																																																																																				0.448	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822		C	201846545	T	C	201846545	2	2	10	1	0	0	0	0	0	0	0	1	5446	1567	55	4		4	FAM126B	2	201846545	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	22234906	201846545	41352828	36	1110										
ALS2CR12	130540	hgsc.bcm.edu	37	chr2	202208956	202208956	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	attgctgtcagctctgagatTtgctcttctaggtcagaaat	9	8	5	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:202208956T>C	ENST00000286190.5	-	5	445	c.399A>G	c.(397-399)caA>caG	p.Q133Q	ALS2CR12_ENST00000448967.1_5'UTR|ALS2CR12_ENST00000439709.1_Silent_p.Q133Q|ALS2CR12_ENST00000405148.2_Silent_p.Q133Q|ALS2CR12_ENST00000392257.3_Silent_p.Q133Q			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	133					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)		p.Q133H(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						GCTCTGAGATTTGCTCTTCTA	0.433																																																1	Substitution - Missense(1)	ovary(1)	2											271	255	261					2																	202208956		2203	4300	6503	201917201	SO:0001819	synonymous_variant	130540			AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.399A>G	2.37:g.202208956T>C			201917201	G5E9S3|Q53TT6|Q8N1B6	Silent	SNP	ENST00000286190.5	37	CCDS2346.1																																																																																				0.433	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163		C	202208956	T	C	202208956	2	2	10	1	0	0	0	0	0	0	0	1	553	1838	64	4		4	ALS2CR12	2	202208956	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	362411	202208956	40990417	37	1111										
CHPF	79586	hgsc.bcm.edu	37	chr2	220405095	220405095	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cggtagccattcaccagctgCtgcttctggagccgcaaggc	12	14	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:220405095C>T	ENST00000243776.6	-	4	1586	c.1338G>A	c.(1336-1338)caG>caA	p.Q446Q	CHPF_ENST00000535926.1_Silent_p.Q284Q	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	446					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TCACCAGCTGCTGCTTCTGGA	0.662																																																0			2											35	39	38					2																	220405095		2197	4285	6482	220113339	SO:0001819	synonymous_variant	79586			BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1338G>A	2.37:g.220405095C>T			220113339	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																				0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220405095	C	T	220405095	2	4	10	1	0	0	0	0	0	0	0	1	3374	796	28	3		3	CHPF	2	220405095	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	18196139	220405095	22794278	38	1112										
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228563707	228563707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctggcccttattcagcttccCtgaagtgctgagtatttctg	9	11	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr2:228563707C>T	ENST00000258403.3	-	3	795	c.724G>A	c.(724-726)Ggg>Agg	p.G242R	SLC19A3_ENST00000541617.1_Missense_Mutation_p.G238R|SLC19A3_ENST00000409287.1_Intron	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	242					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TTCAGCTTCCCTGAAGTGCTG	0.478																																																0			2											144	126	132					2																	228563707		2203	4300	6503	228271951	SO:0001583	missense	80704			AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.724G>A	2.37:g.228563707C>T	ENSP00000258403:p.Gly242Arg		228271951		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	C	8.171	0.791588	0.16258	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.85339	-1.97;-1.97	5.73	2.75	0.32379	Major facilitator superfamily domain, general substrate transporter (1);	8.923060	0.00166	N	0.000000	T	0.80944	0.4721	L	0.50333	1.59	0.09310	N	1	B;B	0.16166	0.016;0.006	B;B	0.18561	0.022;0.021	T	0.56541	-0.7962	10	0.12430	T	0.62	-2.2519	5.8112	0.18467	0.0:0.6061:0.1386:0.2553	.	238;242	F5H2M8;Q9BZV2	.;S19A3_HUMAN	R	242;238	ENSP00000258403:G242R;ENSP00000445519:G238R	ENSP00000258403:G242R	G	-	1	0	SLC19A3	228271951	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.075000	0.14686	0.270000	0.21984	0.650000	0.86243	GGG		0.478	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			T	228563707	C	T	228563707	3	4	10	1	0	0	0	0	1	0	0	0	14467	681	24	3	782	3	SLC19A3	2	228563707	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	8158612	228563707	14635666	39	1113										
VHL	7428	hgsc.bcm.edu	37	chr3	10183612	10183612	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaagagtacggccctgaagaAgacggcggggaggagtcggg	20	7	0	4			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:10183612A>G	ENST00000256474.2	+	1	921	c.81A>G	c.(79-81)gaA>gaG	p.E27E	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Silent_p.E27E	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	27	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.E27E(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCCCTGAAGAAGACGGCGGGG	0.731		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	1	Substitution - coding silent(1)	kidney(1)	3											10	13	12					3																	10183612		1939	3854	5793	10158612	SO:0001819	synonymous_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.81A>G	3.37:g.10183612A>G			10158612	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.731	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10183612	A	G	10183612	2	3	10	1	0	0	0	0	0	0	0	1	17202	69	3	4		4	VHL	3	10183612	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10		10183612	187838818	40	1114										
FBLN2	2199	hgsc.bcm.edu	37	chr3	13671426	13671426	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tccgggttcctgctagcagcGgacggcaagcgctgtgaagg	16	11	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:13671426G>A	ENST00000295760.7	+	13	2877	c.2808G>A	c.(2806-2808)gcG>gcA	p.A936A	FBLN2_ENST00000535798.1_Silent_p.A962A|FBLN2_ENST00000492059.1_Silent_p.A983A|FBLN2_ENST00000404922.3_Silent_p.A983A	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	936	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			TGCTAGCAGCGGACGGCAAGC	0.647																																																0			3											22	26	25					3																	13671426		2138	4238	6376	13646427	SO:0001819	synonymous_variant	2199			X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2808G>A	3.37:g.13671426G>A			13646427	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																				0.647	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		A	13671426	G	A	13671426	2	1	10	1	0	0	0	0	0	0	0	1	5718	1103	39	1		1	FBLN2	3	13671426	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3487814	13671426	184351004	41	1115										
KAT2B	8850	hgsc.bcm.edu	37	chr3	20164271	20164271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggttatgtctaccatcacggAccctgcagcaatgcttggac	10	12	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:20164271A>G	ENST00000263754.4	+	9	1843	c.1388A>G	c.(1387-1389)gAc>gGc	p.D463G		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	463					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						ACCATCACGGACCCTGCAGCA	0.522																																																0			3											76	73	74					3																	20164271		2203	4300	6503	20139275	SO:0001583	missense	8850			U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.1388A>G	3.37:g.20164271A>G	ENSP00000263754:p.Asp463Gly		20139275	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	37	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	A	34	5.326534	0.95708	.	.	ENSG00000114166	ENST00000263754	T	0.30714	1.52	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.60064	0.2240	M	0.83223	2.63	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	T	0.64939	-0.6289	10	0.72032	D	0.01	-32.1853	16.8061	0.85666	1.0:0.0:0.0:0.0	.	463	Q92831	KAT2B_HUMAN	G	463	ENSP00000263754:D463G	ENSP00000263754:D463G	D	+	2	0	KAT2B	20139275	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.257000	0.95545	2.367000	0.80283	0.528000	0.53228	GAC		0.522	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		G	20164271	A	G	20164271	3	3	10	1	0	0	0	0	1	0	0	0	8003	275	10	4	1422	4	KAT2B	3	20164271	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	6492845	20164271	177858159	42	1116										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266138	41266138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gccactaccacagctccttcTctgagtggtaaaggcaatcc	8	14	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:41266138T>C	ENST00000349496.5	+	3	415	c.135T>C	c.(133-135)tcT>tcC	p.S45S	CTNNB1_ENST00000396185.3_Silent_p.S45S|CTNNB1_ENST00000405570.1_Silent_p.S45S|CTNNB1_ENST00000453024.1_Silent_p.S38S|CTNNB1_ENST00000396183.3_Silent_p.S45S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45del(53)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.S45S(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CAGCTCCTTCTCTGAGTGGTA	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	181	Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Substitution - Missense(1)|Substitution - coding silent(1)	liver(91)|kidney(35)|large_intestine(28)|stomach(7)|adrenal_gland(5)|skin(4)|soft_tissue(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|bone(1)|pancreas(1)	3											83	73	76					3																	41266138		2203	4300	6503	41241142	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.135T>C	3.37:g.41266138T>C			41241142	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266138	T	C	41266138	2	2	10	1	0	0	0	0	0	0	0	1	4022	1538	54	4		4	CTNNB1	3	41266138	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	21101867	41266138	156756292	43	1117										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47452688	47452688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agcatggcggcactcagtctCctgggggtgggcagcccctg	16	13	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:47452688C>T	ENST00000265562.4	+	20	3477	c.3400C>T	c.(3400-3402)Cct>Tct	p.P1134S	PTPN23_ENST00000431726.1_Missense_Mutation_p.P1008S	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1134					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CACTCAGTCTCCTGGGGGTGG	0.706																																																0			3											7	9	8					3																	47452688		2128	4216	6344	47427692	SO:0001583	missense	25930			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3400C>T	3.37:g.47452688C>T	ENSP00000265562:p.Pro1134Ser		47427692	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.002038	0.54254	.	.	ENSG00000076201	ENST00000265562	T	0.02631	4.22	5.3	4.42	0.53409	.	0.140633	0.48286	D	0.000186	T	0.01976	0.0062	N	0.11560	0.145	0.52099	D	0.999947	P;P	0.47034	0.889;0.798	B;B	0.44224	0.444;0.3	T	0.66360	-0.5943	10	0.24483	T	0.36	-12.644	7.1484	0.25595	0.0:0.8149:0.0:0.1851	.	1008;1134	B4DST5;Q9H3S7	.;PTN23_HUMAN	S	1134	ENSP00000265562:P1134S	ENSP00000265562:P1134S	P	+	1	0	PTPN23	47427692	0.992000	0.36948	1.000000	0.80357	0.820000	0.46376	0.560000	0.23500	2.468000	0.83385	0.563000	0.77884	CCT		0.706	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		T	47452688	C	T	47452688	3	4	10	1	0	0	0	0	1	0	0	0	12825	855	30	3	3478	3	PTPN23	3	47452688	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	6186550	47452688	150569742	44	1118										
SCAP	22937	hgsc.bcm.edu	37	chr3	47458698	47458698	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccttcaatggcgtcccacacCtacgagtccagaggctgtga	10	14	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:47458698C>A	ENST00000265565.5	-	18	3383		c.e18-1		SCAP_ENST00000441517.2_Splice_Site|SCAP_ENST00000545718.1_Splice_Site	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone						aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CGTCCCACACCTACGAGTCCA	0.632																																					Pancreas(149;978 1908 29304 37806 46700)											0			3											72	58	63					3																	47458698		2203	4300	6503	47433702	SO:0001630	splice_region_variant	22937			BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2971-1G>T	3.37:g.47458698C>A			47433702	Q8N2E0|Q8WUA1	Splice_Site	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434137	0.62955	.	.	ENSG00000114650	ENST00000339815;ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	.	.	.	4.74	4.74	0.60224	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5002	0.87728	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCAP	47433702	1.000000	0.71417	1.000000	0.80357	0.491000	0.33493	7.141000	0.77330	2.466000	0.83321	0.561000	0.74099	.		0.632	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	Intron	A	47458698	C	A	47458698	5	1	10	1	0	0	0	0	0	0	1	0	13914	695	24	2	893	2	SCAP	3	47458698	Splice_Site	SNP	C	TCGA-AF-6136-01A-11D-1826-10	6010	47458698	150563732	45	1119										
IFT57	55081	hgsc.bcm.edu	37	chr3	107882575	107882575	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccttttctaattcttccataAcctttcatgaaaacaagttt	2	10	3	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:107882575A>G	ENST00000264538.3	-	10	1293	c.1046T>C	c.(1045-1047)gTt>gCt	p.V349A	IFT57_ENST00000468021.1_5'Flank	NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	349	pDED.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			TTCTTCCATAACCTTTCATGA	0.318																																																0			3											127	115	119					3																	107882575		2203	4300	6503	109365265	SO:0001630	splice_region_variant	55081			AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.1045-1T>C	3.37:g.107882575A>G			109365265	Q96DA9	Missense_Mutation	SNP	ENST00000264538.3	37	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	A	18.82	3.705190	0.68615	.	.	ENSG00000114446	ENST00000264538	.	.	.	6.03	6.03	0.97812	.	0.047324	0.85682	D	0.000000	T	0.56411	0.1983	M	0.61703	1.905	0.46149	D	0.998891	P	0.37122	0.583	B	0.34038	0.174	T	0.61182	-0.7114	9	0.62326	D	0.03	.	16.227	0.82300	1.0:0.0:0.0:0.0	.	349	Q9NWB7	IFT57_HUMAN	A	349	.	ENSP00000264538:V349A	V	-	2	0	IFT57	109365265	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.771000	0.85420	2.302000	0.77476	0.533000	0.62120	GTT		0.318	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010	Missense_Mutation	G	107882575	A	G	107882575	5	3	10	1	0	0	0	0	0	0	1	0	7583	57	2	4	251	4	IFT57	3	107882575	Splice_Site	SNP	A	TCGA-AF-6136-01A-11D-1826-10	60423877	107882575	90139855	46	1120										
C3orf36	80111	hgsc.bcm.edu	37	chr3	133647422	133647422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctgctcctcggggtgtggcgCggcccactcaggagcccctt	14	16	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:133647422C>T	ENST00000408895.2	-	1	1234	c.226G>A	c.(226-228)Gcg>Acg	p.A76T		NM_025041.2	NP_079317.2	Q3SXR2	CC036_HUMAN	chromosome 3 open reading frame 36	76										breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6						GGGTGTGGCGCGGCCCACTCA	0.662																																																0			3											29	33	32					3																	133647422		2203	4300	6503	135130112	SO:0001583	missense	80111			AK025826	CCDS3083.1	3q22.1	2011-09-30			ENSG00000221972	ENSG00000221972			26170	protein-coding gene	gene with protein product						12477932	Standard	NM_025041		Approved	FLJ22173	uc003epz.1	Q3SXR2		ENST00000408895.2:c.226G>A	3.37:g.133647422C>T	ENSP00000386219:p.Ala76Thr		135130112	Q3SXR3|Q9H6K8	Missense_Mutation	SNP	ENST00000408895.2	37	CCDS3083.1	.	.	.	.	.	.	.	.	.	.	C	8.558	0.877092	0.17395	.	.	ENSG00000221972	ENST00000408895	.	.	.	2.06	-4.11	0.03928	.	.	.	.	.	T	0.14960	0.0361	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.12967	-1.0527	8	0.87932	D	0	.	2.5329	0.04707	0.1373:0.2494:0.4418:0.1716	.	76	Q3SXR2	CC036_HUMAN	T	76	.	ENSP00000386219:A76T	A	-	1	0	C3orf36	135130112	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.402000	0.01047	-2.918000	0.00305	-0.657000	0.03884	GCG		0.662	C3orf36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025041		T	133647422	C	T	133647422	3	4	10	1	0	0	0	0	1	0	0	0	2232	768	27	1	275	1	C3orf36	3	133647422	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	25764847	133647422	64375008	47	1121										
PLSCR5	389158	hgsc.bcm.edu	37	chr3	146309556	146309556	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atgtcacacaaggaccaacaAttttcaaaatatcttctttg	4	9	4	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:146309556A>C	ENST00000443512.1	-	5	1569	c.566T>G	c.(565-567)aTt>aGt	p.I189S	PLSCR5_ENST00000482567.1_Missense_Mutation_p.I177S|PLSCR5_ENST00000492200.1_Missense_Mutation_p.I189S|PLSCR5-AS1_ENST00000473817.1_RNA	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	189										endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						AGGACCAACAATTTTCAAAAT	0.383																																																0			3											63	62	63					3																	146309556		1877	4110	5987	147792246	SO:0001583	missense	389158			AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.566T>G	3.37:g.146309556A>C	ENSP00000390111:p.Ile189Ser		147792246	B2RXK5	Missense_Mutation	SNP	ENST00000443512.1	37	CCDS46931.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.320443	0.60634	.	.	ENSG00000231213	ENST00000492200;ENST00000482567;ENST00000443512	T;T;T	0.28454	1.61;1.61;1.61	5.68	4.51	0.55191	Tubby, C-terminal (1);	.	.	.	.	T	0.62901	0.2466	H	0.96943	3.91	0.40646	D	0.98199	P;D	0.53885	0.82;0.963	P;P	0.56916	0.543;0.809	T	0.75136	-0.3424	9	0.87932	D	0	-15.6736	12.0718	0.53620	0.8709:0.0:0.0:0.1291	.	177;189	B2RXK5;A0PG75	.;PLS5_HUMAN	S	189;177;189	ENSP00000417184:I189S;ENSP00000418626:I177S;ENSP00000390111:I189S	ENSP00000390111:I189S	I	-	2	0	PLSCR5	147792246	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	0.965000	0.38133	0.533000	0.62120	ATT		0.383	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670		C	146309556	A	C	146309556	3	2	10	1	0	0	0	0	1	0	0	0	12144	101	4	4	261	4	PLSCR5	3	146309556	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	12662134	146309556	51712874	48	1122										
TRIM59	286827	hgsc.bcm.edu	37	chr3	160156353	160156353	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tagattgccaacatcacagaGagccgttaggaaactttttt	8	8	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:160156353G>C	ENST00000309784.4	-	3	804	c.619C>G	c.(619-621)Ctc>Gtc	p.L207V	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.L207V|TRIM59_ENST00000543469.1_Missense_Mutation_p.L207V	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	207					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACATCACAGAGAGCCGTTAGG	0.353																																																0			3											67	70	69					3																	160156353		2198	4298	6496	161639047	SO:0001583	missense	286827			AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.619C>G	3.37:g.160156353G>C	ENSP00000311219:p.Leu207Val		161639047	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	37	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920812	0.52653	.	.	ENSG00000213186	ENST00000543469;ENST00000309784	T;T	0.32988	1.68;1.43	5.62	4.56	0.56223	.	0.219424	0.39544	N	0.001326	T	0.50599	0.1625	M	0.64404	1.975	0.38815	D	0.955519	D	0.89917	1.0	D	0.83275	0.996	T	0.49615	-0.8921	9	.	.	.	-10.3081	13.1792	0.59645	0.1315:0.0:0.8685:0.0	.	207	Q8IWR1	TRI59_HUMAN	V	207	ENSP00000444313:L207V;ENSP00000311219:L207V	.	L	-	1	0	TRIM59	161639047	0.997000	0.39634	0.998000	0.56505	0.802000	0.45316	1.174000	0.31932	2.648000	0.89879	0.561000	0.74099	CTC		0.353	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		C	160156353	G	C	160156353	3	2	10	1	0	0	0	0	1	0	0	0	16572	942	33	5	596	5	TRIM59	3	160156353	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	13846797	160156353	37866077	49	1123										
WDR49	151790	hgsc.bcm.edu	37	chr3	167248970	167248970	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acagcatttttgccctcagtGtcaatctcaaagttgcggac	8	11	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:167248970G>A	ENST00000308378.3	-	9	1400	c.1095C>T	c.(1093-1095)gaC>gaT	p.D365D	WDR49_ENST00000453925.2_Silent_p.D429D|WDR49_ENST00000476376.1_Silent_p.D190D|WDR49_ENST00000479765.1_Intron	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	365										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TGCCCTCAGTGTCAATCTCAA	0.413																																																0			3											89	92	91					3																	167248970		2203	4300	6503	168731664	SO:0001819	synonymous_variant	151790			AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1095C>T	3.37:g.167248970G>A			168731664	Q8N297	Silent	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	G	4.062	0.009325	0.07912	.	.	ENSG00000174776	ENST00000472600;ENST00000493061	.	.	.	5.68	3.9	0.45041	.	.	.	.	.	T	0.39226	0.1070	.	.	.	0.26631	N	0.972463	.	.	.	.	.	.	T	0.21314	-1.0249	4	.	.	.	.	10.4137	0.44309	0.1587:0.0:0.8413:0.0	.	.	.	.	I	441;3	.	.	T	-	2	0	WDR49	168731664	0.962000	0.33011	0.010000	0.14722	0.063000	0.16089	2.088000	0.41663	0.781000	0.33589	0.650000	0.86243	ACA		0.413	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167248970	G	A	167248970	2	1	10	1	0	0	0	0	0	0	0	1	17342	1368	48	3		3	WDR49	3	167248970	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	7092617	167248970	30773460	50	1124										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178941879	178941879	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttttaatcaggtacagatgaAgtttttagttgagcaaatga	9	3	1	4	rs181194055	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr3:178941879A>G	ENST00000263967.3	+	15	2355	c.2198A>G	c.(2197-2199)aAg>aGg	p.K733R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	733					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.K733R(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTACAGATGAAGTTTTTAGTT	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)			A|||	4	0.000798722	0	0	5008	,	,		17323	0.004		0	False		,,,				2504	0				Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	large_intestine(1)	3											131	117	121					3																	178941879		1817	4083	5900	180424573	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2198A>G	3.37:g.178941879A>G	ENSP00000263967:p.Lys733Arg		180424573	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	17.47	3.397526	0.62177	.	.	ENSG00000121879	ENST00000263967	T	0.81330	-1.48	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.111337	0.64402	D	0.000005	T	0.78091	0.4229	L	0.60455	1.87	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.72239	-0.4351	10	0.27082	T	0.32	-18.203	16.542	0.84395	1.0:0.0:0.0:0.0	.	733	P42336	PK3CA_HUMAN	R	733	ENSP00000263967:K733R	ENSP00000263967:K733R	K	+	2	0	PIK3CA	180424573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.890000	0.63178	2.304000	0.77564	0.528000	0.53228	AAG		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178941879	A	G	178941879	3	3	10	1	0	0	0	0	1	0	0	0	11944	72	3	4	2252	4	PIK3CA	3	178941879	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	11692909	178941879	19080551	51	1125										
RFC1	5981	hgsc.bcm.edu	37	chr4	39302015	39302015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctccagctgcaaacactttcCgggcaacatcaaatgggccc	8	15	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:39302015C>T	ENST00000381897.1	-	20	2691	c.2558G>A	c.(2557-2559)cGg>cAg	p.R853Q	RFC1_ENST00000349703.2_Missense_Mutation_p.R852Q|RNU6-32P_ENST00000383948.1_RNA	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	853					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						AAACACTTTCCGGGCAACATC	0.443																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											0			4											62	64	64					4																	39302015		2203	4300	6503	38978410	SO:0001583	missense	6573			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2558G>A	4.37:g.39302015C>T	ENSP00000371321:p.Arg853Gln		38978410	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	36	5.872871	0.97049	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.44881	0.91;0.91	6.06	6.06	0.98353	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60011	0.2236	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.992;0.997	T	0.46091	-0.9216	10	0.25751	T	0.34	-10.6623	20.6186	0.99473	0.0:1.0:0.0:0.0	.	853;852	P35251;P35251-2	RFC1_HUMAN;.	Q	853;852	ENSP00000371321:R853Q;ENSP00000261424:R852Q	ENSP00000261424:R852Q	R	-	2	0	RFC1	38978410	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.779000	0.85648	2.876000	0.98609	0.643000	0.83706	CGG		0.443	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39302015	C	T	39302015	3	4	10	1	0	0	0	0	1	0	0	0	13281	652	23	1	912	1	RFC1	4	39302015	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10		39302015	151852261	52	1126										
BEND4	389206	hgsc.bcm.edu	37	chr4	42145872	42145872	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgacagtgctcctgtctttcGttgtaacttgagccttcctg	9	11	1	2	rs574971489		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:42145872G>A	ENST00000502486.1	-	3	1206	c.627C>T	c.(625-627)aaC>aaT	p.N209N	BEND4_ENST00000504360.1_Silent_p.N205N	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	209								p.N205N(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						CCTGTCTTTCGTTGTAACTTG	0.443													G|||	1	0.000199681	8e-04	0	5008	,	,		22510	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	4											92	91	91					4																	42145872		1923	4147	6070	41840629	SO:0001819	synonymous_variant	389206			AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.627C>T	4.37:g.42145872G>A			41840629	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Silent	SNP	ENST00000502486.1	37	CCDS47048.1																																																																																				0.443	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		A	42145872	G	A	42145872	2	1	10	1	0	0	0	0	0	0	0	1	1401	1136	40	1		1	BEND4	4	42145872	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	2843857	42145872	149008404	53	1127										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66213862	66213862	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctccagacatcactggcagaAgtaaactttcggaaagctat	8	10	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:66213862A>G	ENST00000273854.3	-	15	3168	c.2568T>C	c.(2566-2568)acT>acC	p.T856T	EPHA5_ENST00000511294.1_Silent_p.T857T|EPHA5_ENST00000354839.4_Silent_p.T834T|EPHA5_ENST00000432638.2_Silent_p.T693T	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	856	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> I (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CACTGGCAGAAGTAAACTTTC	0.398										TSP Lung(17;0.13)																																						0			4											144	139	141					4																	66213862		2203	4300	6503	65896457	SO:0001819	synonymous_variant	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2568T>C	4.37:g.66213862A>G			65896457	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																				0.398	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		G	66213862	A	G	66213862	2	3	10	1	0	0	0	0	0	0	0	1	5183	59	3	4		4	EPHA5	4	66213862	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	24067990	66213862	124940414	54	1128										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489343	76489343	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggacaagaagaggtatttacGcctcctggagattcacaaaa	10	8	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:76489343G>A	ENST00000311623.4	+	2	122	c.87G>A	c.(85-87)acG>acA	p.T29T	C4orf26_ENST00000435974.2_Missense_Mutation_p.R44H	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	29						extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AGGTATTTACGCCTCCTGGAG	0.532																																																0			4											69	72	71					4																	76489343		2203	4300	6503	76708367	SO:0001819	synonymous_variant	152816			AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.87G>A	4.37:g.76489343G>A			76708367	B4DTI3|E7ETQ0|Q8TEC3	Silent	SNP	ENST00000311623.4	37	CCDS3569.1	.	.	.	.	.	.	.	.	.	.	G	8.177	0.793010	0.16327	.	.	ENSG00000174792	ENST00000435974	T	0.50001	0.76	4.6	-5.5	0.02576	.	.	.	.	.	T	0.29256	0.0728	.	.	.	0.09310	N	1	P	0.36712	0.566	B	0.30855	0.121	T	0.14952	-1.0454	8	0.87932	D	0	.	7.0791	0.25221	0.0:0.2007:0.4484:0.3508	.	44	E7ETQ0	.	H	44	ENSP00000406925:R44H	ENSP00000406925:R44H	R	+	2	0	C4orf26	76708367	0.000000	0.05858	0.000000	0.03702	0.196000	0.23810	-1.954000	0.01525	-1.529000	0.01754	-1.040000	0.02373	CGC		0.532	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		A	76489343	G	A	76489343	2	1	10	1	0	0	0	0	0	0	0	1	2263	1074	38	1		1	C4orf26	4	76489343	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	10275481	76489343	114664933	55	1129										
SCD5	79966	hgsc.bcm.edu	37	chr4	83601872	83601872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcacttactttctctggatcCggaccacaggatcagcaagc	8	13	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:83601872C>T	ENST00000319540.4	-	3	876	c.557G>A	c.(556-558)cGg>cAg	p.R186Q	SCD5_ENST00000273908.4_Missense_Mutation_p.R186Q	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	186					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				TCTCTGGATCCGGACCACAGG	0.512																																																0			4											85	80	81					4																	83601872		2203	4300	6503	83820896	SO:0001583	missense	79966			AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.557G>A	4.37:g.83601872C>T	ENSP00000316329:p.Arg186Gln		83820896	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	37	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603393	0.46423	.	.	ENSG00000145284	ENST00000319540;ENST00000273908	T;T	0.13538	2.58;2.58	5.34	-3.29	0.05017	Fatty acid desaturase, type 1 (1);	0.274691	0.36034	N	0.002837	T	0.05135	0.0137	L	0.31664	0.95	0.54753	D	0.99998	P;B	0.41265	0.744;0.104	B;B	0.30401	0.115;0.025	T	0.42965	-0.9420	10	0.39692	T	0.17	-11.999	1.765	0.03000	0.1963:0.3386:0.0973:0.3678	.	186;186	Q86SK9-2;Q86SK9	.;SCD5_HUMAN	Q	186	ENSP00000316329:R186Q;ENSP00000273908:R186Q	ENSP00000273908:R186Q	R	-	2	0	SCD5	83820896	0.809000	0.29036	0.950000	0.38849	0.985000	0.73830	0.050000	0.14120	-0.917000	0.03813	0.591000	0.81541	CGG		0.512	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		T	83601872	C	T	83601872	3	4	10	1	0	0	0	0	1	0	0	0	13924	652	23	1	653	1	SCD5	4	83601872	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	7112529	83601872	107552404	56	1130										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125592694	125592694	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agccgctagagtgagtggtgTatgtccatgagcatcttcta	12	8	2	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:125592694T>G	ENST00000504087.1	-	4	2775	c.1738A>C	c.(1738-1740)Aca>Cca	p.T580P	ANKRD50_ENST00000515641.1_Missense_Mutation_p.T401P	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	580										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GTGAGTGGTGTATGTCCATGA	0.413																																																0			4											101	91	94					4																	125592694		2203	4300	6503	125812144	SO:0001583	missense	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1738A>C	4.37:g.125592694T>G	ENSP00000425658:p.Thr580Pro		125812144	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.338386	0.41398	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	D;T	0.85484	-1.99;1.69	5.12	5.12	0.69794	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.93184	0.7829	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.94449	0.7665	10	0.87932	D	0	.	15.0843	0.72138	0.0:0.0:0.0:1.0	.	580	Q9ULJ7	ANR50_HUMAN	P	580;401	ENSP00000425658:T580P;ENSP00000425355:T401P	ENSP00000425658:T580P	T	-	1	0	ANKRD50	125812144	1.000000	0.71417	0.938000	0.37757	0.103000	0.19146	7.365000	0.79537	2.148000	0.66965	0.528000	0.53228	ACA		0.413	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		G	125592694	T	G	125592694	3	3	10	1	0	0	0	0	1	0	0	0	677	1638	57	4	2555	4	ANKRD50	4	125592694	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	41990822	125592694	65561582	57	1131										
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154507466	154507466	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	taaatctattcaccaatgtaTttttgactacaaacataggt	4	7	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:154507466T>C	ENST00000409663.3	+	14	1466	c.1414T>C	c.(1414-1416)Ttt>Ctt	p.F472L	KIAA0922_ENST00000409959.3_Missense_Mutation_p.F473L|KIAA0922_ENST00000440693.1_Missense_Mutation_p.F473L	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	472						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CACCAATGTATTTTTGACTAC	0.338																																																0			4											103	102	102					4																	154507466		2202	4295	6497	154726916	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1414T>C	4.37:g.154507466T>C	ENSP00000386574:p.Phe472Leu		154726916	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	T	11.20	1.568028	0.28003	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	5.7	5.7	0.88788	.	0.166050	0.53938	D	0.000049	T	0.51432	0.1674	N	0.13043	0.29	0.23162	N	0.998196	B;P;B;B	0.44139	0.029;0.827;0.012;0.007	B;B;B;B	0.41510	0.023;0.359;0.015;0.004	T	0.51317	-0.8721	10	0.02654	T	1	-23.9633	14.5339	0.67947	0.0:0.0:0.0:1.0	.	102;473;473;472	A2VDJ0-2;A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;.;T131L_HUMAN	L	472;473;473;334	ENSP00000386574:F472L;ENSP00000409663:F473L;ENSP00000386787:F473L;ENSP00000240487:F334L	ENSP00000240487:F334L	F	+	1	0	KIAA0922	154726916	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.761000	0.47589	2.178000	0.69098	0.455000	0.32223	TTT		0.338	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		C	154507466	T	C	154507466	3	2	10	1	0	0	0	0	1	0	0	0	8222	1493	52	4	1471	4	KIAA0922	4	154507466	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	28914772	154507466	36646810	58	1132										
FGA	2243	hgsc.bcm.edu	37	chr4	155507482	155507482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccagtgcccagcacttccgcGttcagagctgccaggattcc	10	16	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:155507482G>A	ENST00000302053.3	-	5	1177	c.1099C>T	c.(1099-1101)Cgc>Tgc	p.R367C	FGA_ENST00000403106.3_Missense_Mutation_p.R367C	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	367					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GCACTTCCGCGTTCAGAGCTG	0.547																																					NSCLC(143;340 1922 20892 22370 48145)											0			4											67	70	69					4																	155507482		2203	4300	6503	155726932	SO:0001583	missense	2243				CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1099C>T	4.37:g.155507482G>A	ENSP00000306361:p.Arg367Cys		155726932	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	7.483	0.649142	0.14516	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	D;D	0.83335	-1.71;-1.71	4.43	-1.13	0.09775	.	7.083650	0.00357	N	0.000030	T	0.66665	0.2812	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.56105	-0.8034	10	0.62326	D	0.03	.	3.3206	0.07049	0.3802:0.0:0.3322:0.2876	.	367;367	P02671-2;P02671	.;FIBA_HUMAN	C	367	ENSP00000306361:R367C;ENSP00000385981:R367C	ENSP00000306361:R367C	R	-	1	0	FGA	155726932	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	0.820000	0.27323	-0.357000	0.08175	-1.275000	0.01399	CGC		0.547	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		A	155507482	G	A	155507482	3	1	10	1	0	0	0	0	1	0	0	0	5849	1145	40	1	1553	1	FGA	4	155507482	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1000016	155507482	35646794	59	1133										
FAT1	2195	hgsc.bcm.edu	37	chr4	187629345	187629345	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cttcgacttcccggcggtacGgcaagccccagtctgatgca	11	15	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr4:187629345G>C	ENST00000441802.2	-	2	1846	c.1637C>G	c.(1636-1638)cCg>cGg	p.P546R		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	546	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CCGGCGGTACGGCAAGCCCCA	0.468										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											70	68	68					4																	187629345		1923	4125	6048	187866339	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1637C>G	4.37:g.187629345G>C	ENSP00000406229:p.Pro546Arg		187866339		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758188	0.69763	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.26660	1.72	5.58	5.58	0.84498	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68949	-0.5274	10	0.66056	D	0.02	.	19.769	0.96353	0.0:0.0:1.0:0.0	.	546	Q14517	FAT1_HUMAN	R	546	ENSP00000406229:P546R	ENSP00000260147:P546R	P	-	2	0	FAT1	187866339	1.000000	0.71417	0.967000	0.41034	0.599000	0.36880	9.657000	0.98554	2.906000	0.99361	0.655000	0.94253	CCG		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		C	187629345	G	C	187629345	3	2	10	1	0	0	0	0	1	0	0	0	5708	1116	39	5	12233	5	FAT1	4	187629345	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	32121863	187629345	3524931	60	1134										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31538631	31538631	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acacagagaagtgaccagacTtgcctagaaccatcatgttc	8	11	1	4			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:31538631T>C	ENST00000325366.9	+	4	769	c.642T>C	c.(640-642)acT>acC	p.T214T	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	214										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						GTGACCAGACTTGCCTAGAAC	0.458																																																0			5											68	64	65					5																	31538631		2203	4300	6503	31574388	SO:0001819	synonymous_variant	55322			AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.642T>C	5.37:g.31538631T>C			31574388	Q8ND28|Q8WU61|Q9NUR1	Silent	SNP	ENST00000325366.9	37	CCDS3895.1																																																																																				0.458	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		C	31538631	T	C	31538631	2	2	10	1	0	0	0	0	0	0	0	1	2291	1596	56	4		4	C5orf22	5	31538631	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10		31538631	149376629	61	1135										
LIFR	3977	hgsc.bcm.edu	37	chr5	38485937	38485937	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttacaattttcctttgtcacCacatacatactcttctccgg	3	13	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:38485937C>A	ENST00000263409.4	-	17	2643	c.2481G>T	c.(2479-2481)gtG>gtT	p.V827V	LIFR_ENST00000453190.2_Silent_p.V827V	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	827	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					CCTTTGTCACCACATACATAC	0.458			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	0			5											155	133	140					5																	38485937		2203	4300	6503	38521694	SO:0001819	synonymous_variant	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2481G>T	5.37:g.38485937C>A			38521694	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																				0.458	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38485937	C	A	38485937	2	1	10	1	0	0	0	0	0	0	0	1	8803	581	21	2		2	LIFR	5	38485937	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	6947306	38485937	142429323	62	1136										
LIFR	3977	hgsc.bcm.edu	37	chr5	38510602	38510602	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggttccaaatatgttatcttCggttgtaaaaactacatttg	7	6	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:38510602C>T	ENST00000263409.4	-	7	1117	c.955G>A	c.(955-957)Gaa>Aaa	p.E319K	LIFR_ENST00000453190.2_Missense_Mutation_p.E319K|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	319					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.E319K(2)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ATGTTATCTTCGGTTGTAAAA	0.343			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	2	Substitution - Missense(2)	large_intestine(2)	5											75	73	73					5																	38510602		2203	4300	6503	38546359	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.955G>A	5.37:g.38510602C>T	ENSP00000263409:p.Glu319Lys		38546359	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	2.080	-0.410953	0.04799	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.63913	-0.07;-0.07	5.61	0.974	0.19715	.	1.308700	0.04625	N	0.402531	T	0.54240	0.1846	L	0.60455	1.87	0.09310	N	1	B	0.15719	0.014	B	0.08055	0.003	T	0.19712	-1.0297	10	0.15952	T	0.53	-0.358	5.0558	0.14531	0.0:0.5255:0.1571:0.3173	.	319	P42702	LIFR_HUMAN	K	319	ENSP00000263409:E319K;ENSP00000398368:E319K	ENSP00000263409:E319K	E	-	1	0	LIFR	38546359	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.217000	0.17603	0.246000	0.21394	-0.181000	0.13052	GAA		0.343	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38510602	C	T	38510602	3	4	10	1	0	0	0	0	1	0	0	0	8803	893	31	1	2394	1	LIFR	5	38510602	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	24665	38510602	142404658	63	1137										
DDX4	54514	hgsc.bcm.edu	37	chr5	55056044	55056044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttagaaatggatgatggaccTtctcgaagagatcatttcat	9	6	3	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:55056044T>C	ENST00000505374.1	+	4	236	c.144T>C	c.(142-144)ccT>ccC	p.P48P	DDX4_ENST00000354991.5_Silent_p.P48P|SLC38A9_ENST00000504880.1_Intron|DDX4_ENST00000353507.5_Silent_p.P48P|DDX4_ENST00000508580.1_3'UTR|DDX4_ENST00000514278.2_Silent_p.P48P	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	48					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGATGGACCTTCTCGAAGAG	0.383																																																0			5											186	183	184					5																	55056044		2203	4300	6503	55091801	SO:0001819	synonymous_variant	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.144T>C	5.37:g.55056044T>C			55091801	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Silent	SNP	ENST00000505374.1	37	CCDS3969.1																																																																																				0.383	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		C	55056044	T	C	55056044	2	2	10	1	0	0	0	0	0	0	0	1	4366	1596	56	4		4	DDX4	5	55056044	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	16545442	55056044	125859216	64	1138										
APC	324	hgsc.bcm.edu	37	chr5	112173960	112173960	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgcagcccagattgccaaagTcatggaagaagtgtcagcca	11	10	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:112173960T>C	ENST00000457016.1	+	16	3049	c.2669T>C	c.(2668-2670)gTc>gCc	p.V890A	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.V890A|APC_ENST00000508376.2_Missense_Mutation_p.V890A			P25054	APC_HUMAN	adenomatous polyposis coli	890	Ser-rich.		V -> I (in colorectal carcinoma; from a patient with MMRCS). {ECO:0000269|PubMed:9419979}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATTGCCAAAGTCATGGAAGAA	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											81	79	80					5																	112173960		2202	4300	6502	112201859	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2669T>C	5.37:g.112173960T>C	ENSP00000413133:p.Val890Ala		112201859	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	17.54	3.416097	0.62511	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94793	-2.79;-3.52;-2.79;-2.79;-2.96	5.92	4.73	0.59995	.	0.204155	0.41294	D	0.000918	D	0.95401	0.8507	L	0.57536	1.79	0.48632	D	0.999687	D;D	0.64830	0.994;0.987	P;P	0.58520	0.84;0.772	D	0.94642	0.7831	10	0.51188	T	0.08	-3.2462	13.2206	0.59885	0.0:0.0:0.1328:0.8672	.	892;890	Q4LE70;P25054	.;APC_HUMAN	A	890;872;890;890;890	ENSP00000413133:V890A;ENSP00000423224:V872A;ENSP00000257430:V890A;ENSP00000427089:V890A;ENSP00000423828:V890A	ENSP00000257430:V890A	V	+	2	0	APC	112201859	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.921000	0.70028	1.029000	0.39812	0.455000	0.32223	GTC		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112173960	T	C	112173960	3	2	10	1	0	0	0	0	1	0	0	0	763	1667	58	4	2727	4	APC	5	112173960	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	57117916	112173960	68741300	65	1139										
APC	324	hgsc.bcm.edu	37	chr5	112174744	112174744	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaacgttactctgaagaagaAcagcatgaagaagaagagag	12	5	1	7			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:112174744A>G	ENST00000457016.1	+	16	3833	c.3453A>G	c.(3451-3453)gaA>gaG	p.E1151E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.E1151E|APC_ENST00000508376.2_Silent_p.E1151E			P25054	APC_HUMAN	adenomatous polyposis coli	1151	Asp/Glu-rich (acidic).|Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGAAGAAGAACAGCATGAAG	0.328		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											61	60	60					5																	112174744		2202	4300	6502	112202643	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3453A>G	5.37:g.112174744A>G			112202643	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174744	A	G	112174744	2	3	10	1	0	0	0	0	0	0	0	1	763	40	2	4		4	APC	5	112174744	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	784	112174744	68740516	66	1140										
HK3	3101	hgsc.bcm.edu	37	chr5	176314628	176314628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggcgccggtgggcagccagaCgggcagccacggcagtcacc	17	15	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr5:176314628C>T	ENST00000292432.5	-	11	1515	c.1424G>A	c.(1423-1425)cGt>cAt	p.R475H		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	475	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			GGCAGCCAGACGGGCAGCCAC	0.647																																																0			5											33	33	33					5																	176314628		2203	4300	6503	176247234	SO:0001583	missense	84376				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1424G>A	5.37:g.176314628C>T	ENSP00000292432:p.Arg475His		176247234	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296162	0.60086	.	.	ENSG00000160883	ENST00000292432	D	0.97089	-4.24	4.43	4.43	0.53597	Hexokinase, C-terminal (1);	0.122153	0.37809	N	0.001939	D	0.98160	0.9392	M	0.77103	2.36	0.44976	D	0.997994	D	0.89917	1.0	D	0.79784	0.993	D	0.99094	1.0841	10	0.72032	D	0.01	-16.4523	14.8517	0.70300	0.0:1.0:0.0:0.0	.	475	P52790	HXK3_HUMAN	H	475	ENSP00000292432:R475H	ENSP00000292432:R475H	R	-	2	0	HK3	176247234	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	5.178000	0.65037	2.007000	0.58848	0.561000	0.74099	CGT		0.647	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			T	176314628	C	T	176314628	3	4	10	1	0	0	0	0	1	0	0	0	7213	536	19	1	1383	1	HK3	5	176314628	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	64139884	176314628	4600632	67	1141										
RREB1	6239	hgsc.bcm.edu	37	chr6	7248754	7248754	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	attgttccaggggaaaggccAtacaaatgtcagacctgcga	11	9	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:7248754A>G	ENST00000349384.6	+	12	4931	c.4617A>G	c.(4615-4617)ccA>ccG	p.P1539P	RREB1_ENST00000379938.2_Silent_p.P1594P|RREB1_ENST00000379933.3_Silent_p.P1539P|RREB1_ENST00000334984.6_Silent_p.P1328P	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1539					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGGAAAGGCCATACAAATGTC	0.542																																																0			6											69	66	67					6																	7248754		2203	4300	6503	7193753	SO:0001819	synonymous_variant	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4617A>G	6.37:g.7248754A>G			7193753	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																				0.542	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			G	7248754	A	G	7248754	2	3	10	1	0	0	0	0	0	0	0	1	13716	204	8	4		4	RREB1	6	7248754	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10		7248754	163866313	68	1142										
MAPK14	1432	hgsc.bcm.edu	37	chr6	36070418	36070418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaatgtatttattggtgccaAtcccctgggtaagttgacca	10	8	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:36070418A>G	ENST00000229794.4	+	10	1221	c.833A>G	c.(832-834)aAt>aGt	p.N278S	MAPK14_ENST00000310795.4_Intron|MAPK14_ENST00000229795.3_Missense_Mutation_p.N278S|MAPK14_ENST00000468133.1_Missense_Mutation_p.N201S	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)	p.N278I(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						ATTGGTGCCAATCCCCTGGGT	0.368																																					Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)											1	Substitution - Missense(1)	ovary(1)	6											200	195	197					6																	36070418		2203	4300	6503	36178396	SO:0001583	missense	1432			L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.833A>G	6.37:g.36070418A>G	ENSP00000229794:p.Asn278Ser		36178396	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Missense_Mutation	SNP	ENST00000229794.4	37	CCDS4816.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370732	0.24771	.	.	ENSG00000112062	ENST00000229795;ENST00000229794;ENST00000468133	T;T;T	0.10477	2.87;2.87;2.87	4.82	4.82	0.62117	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.01695	0.0054	N	0.01015	-1.05	0.80722	D	1	B;B;B	0.30211	0.273;0.011;0.045	B;B;B	0.26770	0.073;0.011;0.011	T	0.44528	-0.9322	10	0.66056	D	0.02	.	14.6663	0.68910	1.0:0.0:0.0:0.0	.	278;278;278	Q16539;Q16539-2;Q16539-3	MK14_HUMAN;.;.	S	278;278;201	ENSP00000229795:N278S;ENSP00000229794:N278S;ENSP00000419837:N201S	ENSP00000229794:N278S	N	+	2	0	MAPK14	36178396	1.000000	0.71417	0.998000	0.56505	0.760000	0.43138	9.287000	0.95975	1.932000	0.55993	0.459000	0.35465	AAT		0.368	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		G	36070418	A	G	36070418	3	3	10	1	0	0	0	0	1	0	0	0	9306	101	4	4	955	4	MAPK14	6	36070418	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	28821664	36070418	135044649	69	1143										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46658608	46658609	+	Frame_Shift_Ins	INS	-	-	A													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atttatagataatgcatggcINSaaaaaaatctagaattaaaa							TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:46658608_46658609insA	ENST00000316081.6	+	1	2743_2744	c.2743_2744insA	c.(2743-2745)caafs	p.Q915fs	TDRD6_ENST00000544460.1_Frame_Shift_Ins_p.Q915fs|RP11-446F17.3_ENST00000434329.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	915					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TAATGCATGGCAAAAAAATCTA	0.342																																																0			6																																								46766568	SO:0001589	frameshift_variant	221400			AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2750dupA	6.37:g.46658615_46658615dupA	ENSP00000346065:p.Gln915fs		46766567	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Frame_Shift_Ins	INS	ENST00000316081.6	37	CCDS34470.1																																																																																				0.342	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		A	46658609	-	A	46658608	7	5	10	1	0	1	1	0	0	0	0	0	15773	711	25	0	2745	0	TDRD6	6	46658608	Frame_Shift_Ins	INS	-	TCGA-AF-6136-01A-11D-1826-10	10588190	46658608	124456459	70	1144										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51618063	51618063	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agtctccccctacatgatacGtcaggctgaatttgtatatt	7	10	2	2	rs138464473		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:51618063G>A	ENST00000371117.3	-	57	9161	c.8886C>T	c.(8884-8886)gaC>gaT	p.D2962D	PKHD1_ENST00000340994.4_Silent_p.D2962D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2962			D -> G (in ARPKD). {ECO:0000269|PubMed:15108281}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TACATGATACGTCAGGCTGAA	0.463													g|||	1	0.000199681	0	0	5008	,	,		16593	0		0.001	False		,,,				2504	0															0			6											113	102	106					6																	51618063		2203	4300	6503	51726022	SO:0001819	synonymous_variant	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8886C>T	6.37:g.51618063G>A			51726022	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																				0.463	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51618063	G	A	51618063	2	1	10	1	0	0	0	0	0	0	0	1	12002	1136	40	1		1	PKHD1	6	51618063	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	4959455	51618063	119497004	71	1145										
DST	667	hgsc.bcm.edu	37	chr6	56497759	56497759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agacttgggattcctggctaTcttccagaaaatcttcaaaa	7	9	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:56497759T>C	ENST00000361203.3	-	24	3072	c.3065A>G	c.(3064-3066)gAt>gGt	p.D1022G	DST_ENST00000370754.5_Missense_Mutation_p.D1200G|DST_ENST00000370765.6_Missense_Mutation_p.D696G|DST_ENST00000370788.2_Missense_Mutation_p.D1022G|DST_ENST00000370769.4_Missense_Mutation_p.D1022G|DST_ENST00000312431.6_Missense_Mutation_p.D1022G|DST_ENST00000421834.2_Missense_Mutation_p.D1022G|DST_ENST00000446842.2_Missense_Mutation_p.D696G|DST_ENST00000518935.1_Missense_Mutation_p.D696G|DST_ENST00000244364.6_Missense_Mutation_p.D696G			Q03001	DYST_HUMAN	dystonin	1022					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.D696G(1)|p.D1022G(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCCTGGCTATCTTCCAGAAA	0.368																																																2	Substitution - Missense(2)	ovary(2)	6											114	111	112					6																	56497759		2203	4300	6503	56605718	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3065A>G	6.37:g.56497759T>C	ENSP00000354508:p.Asp1022Gly		56605718	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	T	22.9	4.356114	0.82243	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000028	T	0.58380	0.2118	M	0.84683	2.71	0.34405	D	0.695705	D;D;D;P;D;D;D;B	0.76494	0.966;0.997;0.966;0.901;0.992;0.999;0.966;0.038	P;D;P;P;D;D;P;B	0.78314	0.505;0.989;0.505;0.49;0.953;0.991;0.505;0.054	T	0.66582	-0.5887	9	0.72032	D	0.01	.	16.3123	0.82883	0.0:0.0:0.0:1.0	.	1022;1022;1200;696;696;696;1022;696	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	G	696;1200;1022;1022;696;1022;1022;1022;696;1062;696;696	ENSP00000244364:D696G;ENSP00000359790:D1200G;ENSP00000359805:D1022G;ENSP00000400883:D1022G;ENSP00000393645:D696G;ENSP00000307959:D1022G;ENSP00000359824:D1022G;ENSP00000354508:D1022G;ENSP00000404924:D696G;ENSP00000431030:D1062G;ENSP00000359801:D696G;ENSP00000431003:D696G	ENSP00000244364:D696G	D	-	2	0	DST	56605718	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.880000	0.69698	2.308000	0.77769	0.533000	0.62120	GAT		0.368	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56497759	T	C	56497759	3	2	10	1	0	0	0	0	1	0	0	0	4794	1435	50	4	18352	4	DST	6	56497759	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	4879696	56497759	114617308	72	1146										
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137519296	137519296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggaggtgggggcttttattaCggttatgagctcttgtcctt	14	6	1	1	rs146424575		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:137519296C>T	ENST00000367739.4	-	7	1463	c.1342G>A	c.(1342-1344)Gta>Ata	p.V448I	IFNGR1_ENST00000543628.1_Missense_Mutation_p.V420I	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	448					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	GCTTTTATTACGGTTATGAGC	0.408													C|||	1	0.000199681	0	0.0014	5008	,	,		18768	0		0	False		,,,				2504	0															0			6						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	152	153	153		1342	0.5	0	6	dbSNP_134	153	0,8600		0,0,4300	no	missense	IFNGR1	NM_000416.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	448/490	137519296	1,13005	2203	4300	6503	137560989	SO:0001583	missense	3459				CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1342G>A	6.37:g.137519296C>T	ENSP00000356713:p.Val448Ile		137560989	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	37	CCDS5185.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	9.961	1.222866	0.22457	2.27E-4	0.0	ENSG00000027697	ENST00000367739;ENST00000543628	T;T	0.73047	-0.71;-0.55	6.08	0.475	0.16774	.	1.946140	0.02591	N	0.100007	T	0.32071	0.0817	L	0.27053	0.805	0.09310	N	1	P;P	0.43607	0.812;0.539	B;B	0.30495	0.116;0.016	T	0.26985	-1.0087	10	0.19147	T	0.46	0.1609	11.7671	0.51937	0.0:0.5475:0.3284:0.1241	.	420;448	F5H5M7;P15260	.;INGR1_HUMAN	I	448;420	ENSP00000356713:V448I;ENSP00000443282:V420I	ENSP00000356713:V448I	V	-	1	0	IFNGR1	137560989	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.365000	0.20348	0.395000	0.25257	-0.340000	0.08031	GTA		0.408	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			T	137519296	C	T	137519296	3	4	10	1	0	0	0	0	1	0	0	0	7570	536	19	1	131	1	IFNGR1	6	137519296	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	81021537	137519296	33595771	73	1147										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157511248	157511248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgaaacggaactccatgactCcaaacgccccctaccagcag	7	17	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:157511248C>T	ENST00000350026.5	+	14	3728	c.3727C>T	c.(3727-3729)Cca>Tca	p.P1243S	ARID1B_ENST00000275248.4_Missense_Mutation_p.P1238S|ARID1B_ENST00000346085.5_Missense_Mutation_p.P1256S|ARID1B_ENST00000367148.1_Missense_Mutation_p.P1296S	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1243					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTCCATGACTCCAAACGCCCC	0.522																																																0			6											131	129	130					6																	157511248		2203	4296	6499	157552940	SO:0001583	missense	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3727C>T	6.37:g.157511248C>T	ENSP00000055163:p.Pro1243Ser		157552940	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.123253	0.77436	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02421	4.51;4.44;4.58;4.55;4.3	5.95	5.95	0.96441	.	0.118709	0.56097	D	0.000021	T	0.09291	0.0229	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	T	0.05517	-1.0880	10	0.66056	D	0.02	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	1243;1256;1238	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	S	1256;1243;1296;1238;765	ENSP00000344546:P1256S;ENSP00000055163:P1243S;ENSP00000356116:P1296S;ENSP00000275248:P1238S;ENSP00000412835:P765S	ENSP00000275248:P1238S	P	+	1	0	ARID1B	157552940	1.000000	0.71417	0.770000	0.31555	0.973000	0.67179	7.487000	0.81328	2.824000	0.97209	0.655000	0.94253	CCA		0.522	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157511248	C	T	157511248	3	4	10	1	0	0	0	0	1	0	0	0	914	855	30	3	3824	3	ARID1B	6	157511248	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	19991952	157511248	13603819	74	1148										
LPA	4018	hgsc.bcm.edu	37	chr6	161020555	161020555	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tttgggtagttttctggggtCcgactatgctggtgtggtgt	16	5	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:161020555C>A	ENST00000316300.5	-	20	3308	c.3264G>T	c.(3262-3264)cgG>cgT	p.R1088R	LPA_ENST00000447678.1_Silent_p.R1088R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3596	Kringle 10. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TTTCTGGGGTCCGACTATGCT	0.468																																																0			6											312	338	329					6																	161020555		2201	4300	6501	160940545	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3264G>T	6.37:g.161020555C>A			160940545	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.468	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	161020555	C	A	161020555	2	1	10	1	0	0	0	0	0	0	0	1	8932	842	30	2		2	LPA	6	161020555	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	3509307	161020555	10094512	75	1149										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165756880	165756880	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tataagaatcaaggacatacCtcagcccagaattctgcata	6	10	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr6:165756880C>A	ENST00000366882.1	-	20	2221	c.2067G>T	c.(2065-2067)gaG>gaT	p.E689D	PDE10A_ENST00000354448.4_Splice_Site_p.E689D|PDE10A_ENST00000539869.2_Splice_Site_p.E699D			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	689					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AAGGACATACCTCAGCCCAGA	0.358																																					Esophageal Squamous(22;308 615 5753 12038 40624)											0			6											104	100	102					6																	165756880		2203	4300	6503	165676870	SO:0001630	splice_region_variant	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.2067+1G>T	6.37:g.165756880C>A			165676870	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	C	23.0	4.360100	0.82353	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.76968	-1.06;-1.06	5.67	5.67	0.87782	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	T	0.81898	0.4920	L	0.46157	1.445	0.80722	D	1	D;B	0.58970	0.984;0.416	D;B	0.70487	0.969;0.099	T	0.79045	-0.1964	9	.	.	.	.	19.3597	0.94432	0.0:1.0:0.0:0.0	.	699;689	Q9ULW9;Q9Y233	.;PDE10_HUMAN	D	689;717;699;689;688	ENSP00000355847:E689D;ENSP00000346435:E689D	.	E	-	3	2	PDE10A	165676870	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.105000	0.77031	2.671000	0.90904	0.585000	0.79938	GAG		0.358	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		Missense_Mutation	A	165756880	C	A	165756880	5	1	10	1	0	0	0	0	0	0	1	0	11661	695	24	2	288	2	PDE10A	6	165756880	Splice_Site	SNP	C	TCGA-AF-6136-01A-11D-1826-10	4736325	165756880	5358187	76	1150										
CARD11	84433	hgsc.bcm.edu	37	chr7	2979516	2979516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gagactgatttctctccagcTtacattcctcctccatctta	4	14	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:2979516T>C	ENST00000396946.4	-	6	1134	c.731A>G	c.(730-732)aAg>aGg	p.K244R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	244					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.K237T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TCTCTCCAGCTTACATTCCTC	0.483			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	7											170	155	160					7																	2979516		2203	4300	6503	2946042	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.731A>G	7.37:g.2979516T>C	ENSP00000380150:p.Lys244Arg		2946042	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	28.4	4.921159	0.92249	.	.	ENSG00000198286	ENST00000396946	T	0.34859	1.34	5.67	5.67	0.87782	.	0.151580	0.64402	D	0.000018	T	0.37100	0.0991	L	0.36672	1.1	0.52501	D	0.999959	D	0.57257	0.979	P	0.48488	0.579	T	0.05699	-1.0869	10	0.26408	T	0.33	-32.2671	15.9664	0.79974	0.0:0.0:0.0:1.0	.	244	Q9BXL7	CAR11_HUMAN	R	244	ENSP00000380150:K244R	ENSP00000380150:K244R	K	-	2	0	CARD11	2946042	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.725000	0.68507	2.172000	0.68678	0.472000	0.43445	AAG		0.483	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2979516	T	C	2979516	3	2	10	1	0	0	0	0	1	0	0	0	2651	1609	56	4	2813	4	CARD11	7	2979516	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10		2979516	156159147	77	1151										
PRPS1L1	221823	hgsc.bcm.edu	37	chr7	18066925	18066925	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aataatgcagttcttccactCagggatattctcccttatcc	5	12	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:18066925C>T	ENST00000506618.2	-	1	561	c.481G>A	c.(481-483)Gag>Aag	p.E161K		NM_175886.2	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like 1	161					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|nucleotide biosynthetic process (GO:0009165)|ribonucleoside monophosphate biosynthetic process (GO:0009156)		ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)	18	Lung NSC(10;0.0385)|all_lung(11;0.0736)					TTCTTCCACTCAGGGATATTC	0.443																																																0			7											100	97	98					7																	18066925		2201	4300	6501	18033450	SO:0001583	missense	221823			M57423	CCDS47552.1	7p21.1	2010-12-10			ENSG00000229937	ENSG00000229937			9463	protein-coding gene	gene with protein product		611566		PRPSL		2168892	Standard	NM_175886		Approved	PRPS3	uc003stz.3	P21108	OTTHUMG00000152742	ENST00000506618.2:c.481G>A	7.37:g.18066925C>T	ENSP00000424595:p.Glu161Lys		18033450	Q6P5P6	Missense_Mutation	SNP	ENST00000506618.2	37	CCDS47552.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675206	0.29783	.	.	ENSG00000229937	ENST00000506618	D	0.91124	-2.79	4.62	1.69	0.24217	Phosphoribosyltransferase (1);	.	.	.	.	T	0.79862	0.4519	N	0.12887	0.27	.	.	.	B	0.10296	0.003	B	0.17722	0.019	T	0.72127	-0.4384	8	0.30854	T	0.27	.	8.1643	0.31217	0.0:0.6143:0.2997:0.086	.	161	P21108	PRPS3_HUMAN	K	161	ENSP00000424595:E161K	ENSP00000424595:E161K	E	-	1	0	PRPS1L1	18033450	0.998000	0.40836	0.071000	0.20095	0.960000	0.62799	4.287000	0.59001	0.242000	0.21303	0.650000	0.86243	GAG		0.443	PRPS1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327667.1	NM_175886		T	18066925	C	T	18066925	3	4	10	1	0	0	0	0	1	0	0	0	12613	835	29	3	479	3	PRPS1L1	7	18066925	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	15087409	18066925	141071738	78	1152										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21655915	21655915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cagaaggtttgccaaggcgaGttccataactgtctattaca	9	9	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:21655915G>A	ENST00000328843.6	+	22	4131	c.4100G>A	c.(4099-4101)aGt>aAt	p.S1367N	DNAH11_ENST00000409508.3_Intron			Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1367	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GCCAAGGCGAGTTCCATAACT	0.408									Kartagener syndrome																																							0			7											137	133	134					7																	21655915		1899	4128	6027	21622440	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000328843.6:c.4100G>A	7.37:g.21655915G>A	ENSP00000330671:p.Ser1367Asn		21622440	Q9UJ82	Missense_Mutation	SNP	ENST00000328843.6	37		.	.	.	.	.	.	.	.	.	.	G	11.08	1.532700	0.27387	.	.	ENSG00000105877	ENST00000328843	T	0.23552	1.9	5.79	5.79	0.91817	Dynein heavy chain, domain-2 (1);	0.842937	0.11194	N	0.589535	T	0.44973	0.1319	.	.	.	0.24985	N	0.991572	D	0.53312	0.959	P	0.53313	0.723	T	0.40059	-0.9583	9	0.52906	T	0.07	.	20.0313	0.97540	0.0:0.0:1.0:0.0	.	1367	Q96DT5	DYH11_HUMAN	N	1367	ENSP00000330671:S1367N	ENSP00000330671:S1367N	S	+	2	0	DNAH11	21622440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.009000	0.76347	2.746000	0.94184	0.655000	0.94253	AGT		0.408	DNAH11-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003777		A	21655915	G	A	21655915	3	1	10	1	0	0	0	0	1	0	0	0	4610	1029	36	3	4186	3	DNAH11	7	21655915	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3588990	21655915	137482748	79	1153										
IL6	3569	hgsc.bcm.edu	37	chr7	22767216	22767216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acgaattgacaaacaaattcGgtacatcctcgacggcatct	7	11	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:22767216G>A	ENST00000404625.1	+	3	632	c.173G>A	c.(172-174)cGg>cAg	p.R58Q	IL6_ENST00000401630.3_Missense_Mutation_p.R35Q|IL6_ENST00000420258.2_Missense_Mutation_p.R112Q|IL6_ENST00000258743.5_Missense_Mutation_p.R58Q|IL6_ENST00000407492.1_Intron|IL6_ENST00000401651.1_Intron|AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000406575.1_Missense_Mutation_p.R58Q			P05231	IL6_HUMAN	interleukin 6	58					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	AAACAAATTCGGTACATCCTC	0.587																																					Esophageal Squamous(47;342 1214 13936 33513)											0			7											106	101	103					7																	22767216		2203	4300	6503	22733741	SO:0001583	missense	3569			M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.173G>A	7.37:g.22767216G>A	ENSP00000385675:p.Arg58Gln		22733741	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	37	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.123480	0.77436	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000401630;ENST00000406575	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	5.73	-11.5	0.00074	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.048000	0.07395	N	0.889797	T	0.13157	0.0319	N	0.24115	0.695	0.09310	N	1	D;D;P	0.69078	0.997;0.97;0.815	P;B;B	0.53313	0.723;0.372;0.112	T	0.26883	-1.0090	10	0.49607	T	0.09	1.318	0.9683	0.01410	0.176:0.2687:0.2887:0.2665	.	112;58;58	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	Q	58;58;58;112;35;58	ENSP00000385675:R58Q;ENSP00000405150:R58Q;ENSP00000258743:R58Q;ENSP00000405994:R112Q;ENSP00000384928:R35Q;ENSP00000385227:R58Q	ENSP00000258743:R58Q	R	+	2	0	IL6	22733741	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.856000	0.00729	-2.311000	0.00649	-1.121000	0.02013	CGG		0.587	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		A	22767216	G	A	22767216	3	1	10	1	0	0	0	0	1	0	0	0	7722	1116	39	1	179	1	IL6	7	22767216	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1111301	22767216	136371447	80	1154										
ELMO1	9844	hgsc.bcm.edu	37	chr7	37382250	37382250	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atgagtttggggtaggcgccCggccattctatggccacctt	13	11	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:37382250C>T	ENST00000310758.4	-	2	692	c.45G>A	c.(43-45)ccG>ccA	p.P15P	ELMO1_ENST00000442504.1_Silent_p.P15P|ELMO1_ENST00000448602.1_Silent_p.P15P	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	15					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GGTAGGCGCCCGGCCATTCTA	0.478																																																0			7											150	159	156					7																	37382250		2203	4300	6503	37348775	SO:0001819	synonymous_variant	9844			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.45G>A	7.37:g.37382250C>T			37348775	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Silent	SNP	ENST00000310758.4	37	CCDS5449.1																																																																																				0.478	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		T	37382250	C	T	37382250	2	4	10	1	0	0	0	0	0	0	0	1	5078	639	23	1		1	ELMO1	7	37382250	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	14615034	37382250	121756413	81	1155										
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37901698	37901698	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aataaaaaagttattaatttGatcgatgaggagagaaaaat	8	1	0	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:37901698G>C	ENST00000199447.4	+	7	711	c.339G>C	c.(337-339)ttG>ttC	p.L113F	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.L113F	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	113	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										TTATTAATTTGATCGATGAGG	0.363																																																0			7											55	59	58					7																	37901698		2203	4300	6503	37868223	SO:0001583	missense	51314			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.339G>C	7.37:g.37901698G>C	ENSP00000199447:p.Leu113Phe		37868223	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	G	7.480	0.648536	0.14516	.	.	ENSG00000086288	ENST00000199447;ENST00000455500;ENST00000444718;ENST00000440017	T;T	0.25414	1.8;1.8	5.63	2.82	0.32997	Thioredoxin-like fold (2);	0.000000	0.40385	N	0.001105	T	0.26955	0.0660	M	0.73598	2.24	0.09310	N	1	P	0.36733	0.567	B	0.38500	0.275	T	0.10870	-1.0611	10	0.36615	T	0.2	-3.2266	6.3386	0.21310	0.144:0.3563:0.4996:0.0	.	113	Q8N427	TXND3_HUMAN	F	113;58;58;113	ENSP00000199447:L113F;ENSP00000397063:L113F	ENSP00000199447:L113F	L	+	3	2	TXNDC3	37868223	0.120000	0.22244	0.117000	0.21633	0.005000	0.04900	0.334000	0.19787	1.372000	0.46190	0.561000	0.74099	TTG		0.363	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		C	37901698	G	C	37901698	3	2	10	1	0	0	0	0	1	0	0	0	16838	1281	45	5	357	5	TXNDC3	7	37901698	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	519448	37901698	121236965	82	1156										
GLI3	2737	hgsc.bcm.edu	37	chr7	42004786	42004786	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tttggcgctaccggcaggccGaaattcagctggcccccgct	12	15	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:42004786G>A	ENST00000395925.3	-	15	3969	c.3885C>T	c.(3883-3885)ttC>ttT	p.F1295F	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1295					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CCGGCAGGCCGAAATTCAGCT	0.632									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											37	38	37					7																	42004786		2203	4300	6503	41971311	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3885C>T	7.37:g.42004786G>A			41971311	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.632	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42004786	G	A	42004786	2	1	10	1	0	0	0	0	0	0	0	1	6459	1049	37	1		1	GLI3	7	42004786	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	4103088	42004786	117133877	83	1157										
SLC26A3	1811	hgsc.bcm.edu	37	chr7	107408041	107408041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tacctcatatacccgattacGtaatcctccatttgtattta	3	11	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:107408041G>A	ENST00000340010.5	-	20	2438	c.2254C>T	c.(2254-2256)Cgt>Tgt	p.R752C	SLC26A3_ENST00000422236.2_Missense_Mutation_p.R639C	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	752					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						ACCCGATTACGTAATCCTCCA	0.343																																																0			7																																								107195277	SO:0001583	missense	1811			L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.2254C>T	7.37:g.107408041G>A	ENSP00000345873:p.Arg752Cys		107195277		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.510465	0.44660	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.94650	-3.48;-3.34	4.64	4.64	0.57946	.	0.392271	0.27961	N	0.017141	D	0.96144	0.8743	M	0.71581	2.175	0.38861	D	0.956487	D;B	0.89917	1.0;0.263	P;B	0.61003	0.882;0.031	D	0.96891	0.9653	10	0.62326	D	0.03	.	14.6142	0.68537	0.0:0.0:1.0:0.0	.	639;752	G5E9U3;P40879	.;S26A3_HUMAN	C	639;752	ENSP00000415817:R639C;ENSP00000345873:R752C	ENSP00000345873:R752C	R	-	1	0	SLC26A3	107195277	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.385000	0.52485	2.409000	0.81822	0.644000	0.83932	CGT		0.343	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		A	107408041	G	A	107408041	3	1	10	1	0	0	0	0	1	0	0	0	14555	1145	40	1	48	1	SLC26A3	7	107408041	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	65403255	107408041	51730622	84	1158										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763550	110763550	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	actggaaaacttagaaagcaTctctttttacgataacaggc	7	8	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:110763550T>C	ENST00000422987.3	+	2	1553	c.722T>C	c.(721-723)aTc>aCc	p.I241T	IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.I241T|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.I241T|IMMP2L_ENST00000437687.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	241					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TTAGAAAGCATCTCTTTTTAC	0.343																																																0			7											61	63	62					7																	110763550		2202	4299	6501	110550786	SO:0001583	missense	54674			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.722T>C	7.37:g.110763550T>C	ENSP00000412417:p.Ile241Thr		110550786	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	T	16.13	3.037235	0.54896	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987;ENST00000421101	T;T;T;T	0.60424	0.19;0.19;0.19;0.19	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000011	T	0.71230	0.3315	L	0.58810	1.83	0.58432	D	0.999997	D	0.57571	0.98	P	0.61800	0.894	T	0.73892	-0.3839	10	0.87932	D	0	.	16.4447	0.83919	0.0:0.0:0.0:1.0	.	241	Q9H3W5	LRRN3_HUMAN	T	241	ENSP00000312001:I241T;ENSP00000397312:I241T;ENSP00000412417:I241T;ENSP00000407927:I241T	ENSP00000312001:I241T	I	+	2	0	LRRN3	110550786	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	8.040000	0.89188	2.284000	0.76573	0.528000	0.53228	ATC		0.343	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110763550	T	C	110763550	3	2	10	1	0	0	0	0	1	0	0	0	9065	1435	50	4	724	4	LRRN3	7	110763550	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	3355509	110763550	48375113	85	1159										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127017375	127017375	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	taataaaatatgcttaagttGtttagttcctgagagaaaaa	7	3	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:127017375G>A	ENST00000393313.1	-	4	757	c.166C>T	c.(166-168)Caa>Taa	p.Q56*	ZNF800_ENST00000265827.3_Nonsense_Mutation_p.Q56*|ZNF800_ENST00000393312.1_Nonsense_Mutation_p.Q56*			Q2TB10	ZN800_HUMAN	zinc finger protein 800	56					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TGCTTAAGTTGTTTAGTTCCT	0.313																																																0			7											39	45	43					7																	127017375		2196	4293	6489	126804611	SO:0001587	stop_gained	168850			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.166C>T	7.37:g.127017375G>A	ENSP00000376989:p.Gln56*		126804611	Q9HBN0	Nonsense_Mutation	SNP	ENST00000393313.1	37	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	G	35	5.445189	0.96187	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312;ENST00000434602;ENST00000436992;ENST00000439506	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-0.8968	18.9926	0.92800	0.0:0.0:1.0:0.0	.	.	.	.	X	56	.	ENSP00000265827:Q56X	Q	-	1	0	ZNF800	126804611	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.540000	0.82074	2.714000	0.92807	0.650000	0.86243	CAA		0.313	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		A	127017375	G	A	127017375	4	1	10	1	0	0	0	0	0	1	0	0	18208	1386	48	3	1840	3	ZNF800	7	127017375	Nonsense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	16253825	127017375	32121288	86	1160										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147914416	147914416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgaagaagggatgtggctacGatataactttcaggcaccag	12	7	1	2	rs143879959		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:147914416G>A	ENST00000361727.3	+	19	3563	c.3047G>A	c.(3046-3048)cGa>cAa	p.R1016Q	CNTNAP2_ENST00000538075.1_Missense_Mutation_p.R75Q	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1016					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.R1016Q(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ATGTGGCTACGATATAACTTT	0.488										HNSCC(39;0.1)																																						1	Substitution - Missense(1)	large_intestine(1)	7						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	115	116	115		3047	5.2	1	7	dbSNP_134	115	0,8600		0,0,4300	no	missense	CNTNAP2	NM_014141.5	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1016/1332	147914416	1,13005	2203	4300	6503	147545349	SO:0001583	missense	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3047G>A	7.37:g.147914416G>A	ENSP00000354778:p.Arg1016Gln		147545349	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389917	0.42410	2.27E-4	0.0	ENSG00000174469	ENST00000361727;ENST00000538075	T;T	0.79653	-1.29;-1.29	5.25	5.25	0.73442	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.070850	0.56097	D	0.000027	T	0.72439	0.3460	L	0.41710	1.295	0.30814	N	0.738567	B	0.29212	0.237	B	0.26864	0.074	T	0.66204	-0.5982	10	0.11794	T	0.64	.	17.4392	0.87561	0.0:0.0:1.0:0.0	.	1016	Q9UHC6	CNTP2_HUMAN	Q	1016;75	ENSP00000354778:R1016Q;ENSP00000440732:R75Q	ENSP00000354778:R1016Q	R	+	2	0	CNTNAP2	147545349	0.991000	0.36638	0.984000	0.44739	0.771000	0.43674	5.444000	0.66587	2.438000	0.82558	0.561000	0.74099	CGA		0.488	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	147914416	G	A	147914416	3	1	10	1	0	0	0	0	1	0	0	0	3653	1058	37	1	3121	1	CNTNAP2	7	147914416	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	20897041	147914416	11224247	87	1161										
ZNF775	285971	hgsc.bcm.edu	37	chr7	150093656	150093656	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccggagcggctgctgcagacGctggcgccgcaggccatgct	16	15	0	1	rs375605204		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:150093656G>A	ENST00000329630.5	+	3	194	c.87G>A	c.(85-87)acG>acA	p.T29T		NM_173680.3	NP_775951.2	Q96BV0	ZN775_HUMAN	zinc finger protein 775	29					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(7)|skin(1)	11	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTGCAGACGCTGGCGCCGC	0.657																																																0			7						G		3,3903		0,3,1950	8	12	11		87	-9.2	0	7		11	1,8199		0,1,4099	no	coding-synonymous	ZNF775	NM_173680.3		0,4,6049	AA,AG,GG		0.0122,0.0768,0.033		29/538	150093656	4,12102	1953	4100	6053	149724589	SO:0001819	synonymous_variant	285971			BC038111	CCDS43678.1	7q36.1	2013-01-08			ENSG00000196456	ENSG00000196456		"Zinc fingers, C2H2-type"	28501	protein-coding gene	gene with protein product						12477932	Standard	NM_173680		Approved	MGC33584	uc003whf.1	Q96BV0	OTTHUMG00000158324	ENST00000329630.5:c.87G>A	7.37:g.150093656G>A			149724589	Q8IY24	Silent	SNP	ENST00000329630.5	37	CCDS43678.1																																																																																				0.657	ZNF775-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350679.1	NM_173680		A	150093656	G	A	150093656	2	1	10	1	0	0	0	0	0	0	0	1	18187	1074	38	1		1	ZNF775	7	150093656	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	2179240	150093656	9045007	88	1162										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150768632	150768632	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttgaccctcagtgcctggccGcagtcatcttcatctacttt	7	14	5	1	rs200122092		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr7:150768632G>A	ENST00000485713.1	+	14	3171	c.2131G>A	c.(2131-2133)Gca>Aca	p.A711T	SLC4A2_ENST00000310317.5_Missense_Mutation_p.A629T|SLC4A2_ENST00000392826.2_Missense_Mutation_p.A702T|SLC4A2_ENST00000461735.1_Missense_Mutation_p.A697T|SLC4A2_ENST00000413384.2_Missense_Mutation_p.A711T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	711	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCCTGGCCGCAGTCATCTT	0.652																																																0			7											60	60	60					7																	150768632		2203	4300	6503	150399565	SO:0001583	missense	6522				CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.2131G>A	7.37:g.150768632G>A	ENSP00000419412:p.Ala711Thr		150399565	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553534	0.86127	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	4.45	4.45	0.53987	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87478	0.6187	M	0.64080	1.96	0.80722	D	1	D;D;D	0.56035	0.967;0.967;0.974	P;P;P	0.57720	0.733;0.733;0.826	D	0.88774	0.3266	10	0.66056	D	0.02	.	14.6509	0.68797	0.0:0.0:1.0:0.0	.	702;697;711	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	T	711;711;629;702;697	ENSP00000419412:A711T;ENSP00000405600:A711T;ENSP00000311402:A629T;ENSP00000376571:A702T;ENSP00000419164:A697T	ENSP00000311402:A629T	A	+	1	0	SLC4A2	150399565	1.000000	0.71417	0.646000	0.29493	0.715000	0.41141	9.579000	0.98204	2.318000	0.78349	0.563000	0.77884	GCA		0.652	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150768632	G	A	150768632	3	1	10	1	0	0	0	0	1	0	0	0	14691	1087	38	1	2181	1	SLC4A2	7	150768632	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	674976	150768632	8370031	89	1163										
PI15	51050	hgsc.bcm.edu	37	chr8	75761446	75761446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcttgtactgacaatctgtgTtttccaggagttacgtcaaa	8	8	3	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr8:75761446T>C	ENST00000260113.2	+	6	914	c.735T>C	c.(733-735)tgT>tgC	p.C245C	RP11-758M4.4_ENST00000518128.1_RNA|PI15_ENST00000523773.1_Silent_p.C245C|RP11-758M4.4_ENST00000522914.1_RNA|RP11-758M4.4_ENST00000523860.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	245						extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			ACAATCTGTGTTTTCCAGGAG	0.398																																																0			8											189	163	172					8																	75761446		2203	4300	6503	75924001	SO:0001819	synonymous_variant	51050			D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"protease inhibitor 15"			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.735T>C	8.37:g.75761446T>C			75924001	Q68CY1	Silent	SNP	ENST00000260113.2	37	CCDS6218.1																																																																																				0.398	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		C	75761446	T	C	75761446	2	2	10	1	0	0	0	0	0	0	0	1	11899	1731	60	4		4	PI15	8	75761446	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10		75761446	70602576	90	1164										
JRK	8629	hgsc.bcm.edu	37	chr8	143746191	143746191	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tggcgctggcgaagctggccCgggcaggaggagccttcctt	17	12	0	0	rs369974690	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr8:143746191C>T	ENST00000507178.2	-	0	1619							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				gaagctggcccgggcaggagg	0.657																																																0			8											8	9	9					8																	143746191		1946	4137	6083	143743193			8629			AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746191C>T			143743193	O75565	Silent	SNP	ENST00000507178.2	37																																																																																					0.657	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		T	143746191	C	T	143746191	1	4	10	0	1	0	0	0	0	0	0	0	7985	639	23	1		1	JRK	8	143746191	RNA	SNP	C	TCGA-AF-6136-01A-11D-1826-10	67984745	143746191	2617831	91	1165										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8471014	8471014	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cctcatctaattccatttcaTctggactctcccatggcttg	5	14	5	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:8471014T>C	ENST00000381196.4	-	28	4028	c.3485A>G	c.(3484-3486)gAt>gGt	p.D1162G	PTPRD_ENST00000355233.5_Missense_Mutation_p.D751G|PTPRD_ENST00000486161.1_Missense_Mutation_p.D751G|PTPRD_ENST00000397606.3_Missense_Mutation_p.D741G|PTPRD_ENST00000397611.3_Missense_Mutation_p.D748G|PTPRD_ENST00000358503.5_Missense_Mutation_p.D1140G|PTPRD_ENST00000360074.4_Missense_Mutation_p.D1149G|PTPRD_ENST00000397617.3_Missense_Mutation_p.D741G|PTPRD_ENST00000540109.1_Missense_Mutation_p.D1162G|PTPRD_ENST00000537002.1_Missense_Mutation_p.D748G|PTPRD_ENST00000356435.5_Missense_Mutation_p.D1162G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1162					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		TTCCATTTCATCTGGACTCTC	0.408										TSP Lung(15;0.13)																																						0			9											163	155	158					9																	8471014		2203	4300	6503	8461014	SO:0001583	missense	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3485A>G	9.37:g.8471014T>C	ENSP00000370593:p.Asp1162Gly		8461014	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.435201	0.83885	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.47;0.52;0.66;0.77;0.54;0.43;0.43;0.66;0.77	5.72	5.72	0.89469	.	0.047899	0.85682	D	0.000000	T	0.69726	0.3143	M	0.65498	2.005	0.80722	D	1	B;B;D;B;P;P;B;P;B	0.63880	0.004;0.378;0.993;0.0;0.712;0.763;0.141;0.872;0.0	B;B;D;B;P;B;B;P;B	0.68192	0.004;0.073;0.956;0.001;0.535;0.288;0.173;0.663;0.0	T	0.69950	-0.5006	9	.	.	.	.	15.6732	0.77295	0.0:0.0:0.0:1.0	.	741;746;751;751;748;748;1149;1162;1162	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	G	1162;1162;1149;1140;751;741;748;748;633;1162;751;741	ENSP00000370593:D1162G;ENSP00000348812:D1162G;ENSP00000353187:D1149G;ENSP00000351293:D1140G;ENSP00000347373:D751G;ENSP00000380741:D741G;ENSP00000380735:D748G;ENSP00000440515:D748G;ENSP00000438164:D1162G;ENSP00000417093:D751G;ENSP00000380731:D741G	.	D	-	2	0	PTPRD	8461014	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.351000	0.79395	2.189000	0.69895	0.533000	0.62120	GAT		0.408	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8471014	T	C	8471014	3	2	10	1	0	0	0	0	1	0	0	0	12836	1435	50	4	2382	4	PTPRD	9	8471014	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10		8471014	132742417	92	1166										
PTPLAD2	401494	hgsc.bcm.edu	37	chr9	21029382	21029382	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aagtaatagatgaaaagataCgcattcttcctatacctata	5	7	1	3	rs79392110	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:21029382C>T	ENST00000495827.2	-	2	99	c.54G>A	c.(52-54)gcG>gcA	p.A18A	PTPLAD2_ENST00000513293.2_Silent_p.A18A|PTPLAD2_ENST00000488436.1_5'Flank	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	18					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		TGAAAAGATACGCATTCTTCC	0.338													c|||	5	0.000998403	0	0	5008	,	,		18164	0.005		0	False		,,,				2504	0															0			9											88	88	88					9																	21029382		1856	4077	5933	21019382	SO:0001819	synonymous_variant	401494				CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.54G>A	9.37:g.21029382C>T			21019382	Q7Z385	Silent	SNP	ENST00000495827.2	37	CCDS43791.1																																																																																				0.338	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915		T	21029382	C	T	21029382	2	4	10	1	0	0	0	0	0	0	0	1	12811	523	19	1		1	PTPLAD2	9	21029382	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	12558368	21029382	120184049	93	1167										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21970987	21970987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcaggtaccgtgcgacatcgCgatggcccagctcctcagcc	12	16	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:21970987C>T	ENST00000304494.5	-	2	641	c.371G>A	c.(370-372)cGc>cAc	p.R124H	CDKN2A_ENST00000497750.1_Missense_Mutation_p.R73H|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000579122.1_Missense_Mutation_p.R124H|CDKN2A_ENST00000498628.2_Missense_Mutation_p.R73H|CDKN2A_ENST00000530628.2_3'UTR|CDKN2A_ENST00000479692.2_Missense_Mutation_p.R73H|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000446177.1_Missense_Mutation_p.R124H|CDKN2A_ENST00000578845.2_Missense_Mutation_p.R73H|CDKN2A_ENST00000494262.1_Missense_Mutation_p.R73H|CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000498124.1_Missense_Mutation_p.R124H	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	124			R -> C (in dbSNP:rs34170727).|R -> H (in an esophagus tumor).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(13)|p.R124H(2)|p.0(1)|p.A118fs*10(1)|p.L121fs*21(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TGCGACATCGCGATGGCCCAG	0.706		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1333	Whole gene deletion(1316)|Unknown(13)|Substitution - Missense(2)|Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(278)|skin(168)|central_nervous_system(164)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|oesophagus(50)|upper_aerodigestive_tract(46)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|liver(7)|meninges(7)|large_intestine(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											27	30	29					9																	21970987		2202	4298	6500	21960987	SO:0001583	missense	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.371G>A	9.37:g.21970987C>T	ENSP00000307101:p.Arg124His		21960987	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	C	2.526	-0.309559	0.05458	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	D;D	0.93763	-3.28;-3.28	5.93	0.283	0.15696	Ankyrin repeat-containing domain (4);	.	.	.	.	D	0.84270	0.5435	N	0.20807	0.61	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.70378	-0.4888	9	0.28530	T	0.3	-3.998	4.6273	0.12484	0.1494:0.4595:0.0:0.3911	.	124	P42771	CD2A1_HUMAN	H	124	ENSP00000307101:R124H;ENSP00000394932:R124H	ENSP00000307101:R124H	R	-	2	0	CDKN2A	21960987	0.000000	0.05858	0.005000	0.12908	0.029000	0.11900	-2.792000	0.00766	0.098000	0.17522	0.655000	0.94253	CGC		0.706	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		T	21970987	C	T	21970987	3	4	10	1	0	0	0	0	1	0	0	0	3167	768	27	1	107	1	CDKN2A	9	21970987	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	941605	21970987	119242444	94	1168										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37740470	37740470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acagccaggaggagagaagcGggattgaaaccagtggcttc	15	8	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:37740470G>A	ENST00000539465.1	+	15	2538	c.1945G>A	c.(1945-1947)Ggg>Agg	p.G649R	FRMPD1_ENST00000536622.1_Missense_Mutation_p.G471R|FRMPD1_ENST00000541302.1_Missense_Mutation_p.G518R|FRMPD1_ENST00000377765.3_Missense_Mutation_p.G649R|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	649						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GGAGAGAAGCGGGATTGAAAC	0.577																																																0			9											35	34	35					9																	37740470		2203	4299	6502	37730470	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1945G>A	9.37:g.37740470G>A	ENSP00000444411:p.Gly649Arg		37730470	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.837332	0.00573	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.15834	3.41;3.41;2.39;2.39	5.95	0.338	0.15974	.	1.540640	0.03638	N	0.239045	T	0.03959	0.0111	N	0.00392	-1.555	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39881	-0.9592	10	0.02654	T	1	-3.472	5.8535	0.18707	0.5944:0.2586:0.1469:0.0	.	518;649	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	R	649;649;471;518	ENSP00000366995:G649R;ENSP00000444411:G649R;ENSP00000437762:G471R;ENSP00000444804:G518R	ENSP00000366995:G649R	G	+	1	0	FRMPD1	37730470	0.000000	0.05858	0.011000	0.14972	0.250000	0.25880	-0.006000	0.12833	0.107000	0.17824	-0.290000	0.09829	GGG		0.577	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37740470	G	A	37740470	3	1	10	1	0	0	0	0	1	0	0	0	6076	1116	39	1	1999	1	FRMPD1	9	37740470	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	15769483	37740470	103472961	95	1169										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90254398	90254398	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttgggactccagagtttgtcGgtaagtttctttgctcctgt	11	8	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:90254398G>A	ENST00000408954.3	+	5	888	c.553G>A	c.(553-555)Gct>Act	p.A185T	DAPK1_ENST00000472284.1_Splice_Site_p.A185T|DAPK1_ENST00000469640.2_Splice_Site_p.A185T|DAPK1_ENST00000358077.5_Splice_Site_p.A185T|DAPK1_ENST00000491893.1_Splice_Site_p.A185T	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	185	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						AGAGTTTGTCGGTAAGTTTCT	0.413									Chronic Lymphocytic Leukemia, Familial Clustering of																																							0			9											110	106	107					9																	90254398		1837	4080	5917	89444218	SO:0001630	splice_region_variant	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.553+1G>A	9.37:g.90254398G>A			89444218	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018329	0.93404	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.11	5.11	0.69529	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000087	D	0.87450	0.6180	H	0.98068	4.14	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.48	D;D;B	0.79108	0.992;0.988;0.04	D	0.91759	0.5418	10	0.87932	D	0	.	19.09	0.93223	0.0:0.0:1.0:0.0	.	185;185;185	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	T	185	ENSP00000350785:A185T;ENSP00000417076:A185T;ENSP00000418885:A185T;ENSP00000386135:A185T;ENSP00000419026:A185T	ENSP00000350785:A185T	A	+	1	0	DAPK1	89444218	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	7.712000	0.84684	2.812000	0.96745	0.557000	0.71058	GCT		0.413	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	Missense_Mutation	A	90254398	G	A	90254398	5	1	10	1	0	0	0	0	0	0	1	0	4241	1130	39	1	567	1	DAPK1	9	90254398	Splice_Site	SNP	G	TCGA-AF-6136-01A-11D-1826-10	52513928	90254398	50959033	96	1170										
HDHD3	81932	hgsc.bcm.edu	37	chr9	116136301	116136301	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctcagccccatccaacacctGccaggtgcaggggtggctga	12	15	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:116136301G>A	ENST00000238379.5	-	2	1231	c.334C>T	c.(334-336)Cag>Tag	p.Q112*	HDHD3_ENST00000485934.1_5'UTR|HDHD3_ENST00000374180.3_Nonsense_Mutation_p.Q112*	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	112						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						TCCAACACCTGCCAGGTGCAG	0.607																																																0			9											90	99	96					9																	116136301		2203	4300	6503	115176122	SO:0001587	stop_gained	81932			AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 158"	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.334C>T	9.37:g.116136301G>A	ENSP00000238379:p.Gln112*		115176122	B2RD47	Nonsense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	G	41	8.640443	0.98897	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	.	.	.	5.86	4.91	0.64330	.	0.178215	0.48286	D	0.000184	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-13.074	13.3926	0.60832	0.0:0.2981:0.7019:0.0	.	.	.	.	X	112	.	ENSP00000238379:Q112X	Q	-	1	0	HDHD3	115176122	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.299000	0.43611	2.778000	0.95560	0.655000	0.94253	CAG		0.607	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219		A	116136301	G	A	116136301	4	1	10	1	0	0	0	0	0	1	0	0	7045	1328	46	3	425	3	HDHD3	9	116136301	Nonsense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	25881903	116136301	25077130	97	1171										
OR1L1	26737	hgsc.bcm.edu	37	chr9	125424242	125424242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cattatccctaagatgctggTgaacttcttatcagagacaa	7	9	2	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr9:125424242T>C	ENST00000373686.1	+	1	398	c.398T>C	c.(397-399)gTg>gCg	p.V133A	OR1L1_ENST00000309623.1_Missense_Mutation_p.V83A			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						AAGATGCTGGTGAACTTCTTA	0.438																																																0			9											192	187	188					9																	125424242		2203	4300	6503	124464063	SO:0001583	missense	26737				CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"GPCR / Class A : Olfactory receptors"	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.398T>C	9.37:g.125424242T>C	ENSP00000362790:p.Val133Ala		124464063	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		.	.	.	.	.	.	.	.	.	.	T	0.989	-0.694754	0.03303	.	.	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.01947	4.54;4.54	3.11	-4.62	0.03370	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01156	0.0038	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.48490	-0.9031	9	0.17832	T	0.49	.	5.8432	0.18645	0.2819:0.4891:0.0:0.229	.	133	Q8NH94	OR1L1_HUMAN	A	133;83	ENSP00000362790:V133A;ENSP00000310773:V83A	ENSP00000310773:V83A	V	+	2	0	OR1L1	124464063	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.624000	0.02038	-1.263000	0.02455	-0.736000	0.03550	GTG		0.438	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				C	125424242	T	C	125424242	3	2	10	1	0	0	0	0	1	0	0	0	10994	1696	59	4	250	4	OR1L1	9	125424242	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	9287941	125424242	15789189	98	1172										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7780597	7780597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tacgcaggggccctgtattaCggcagcaaagtggttccaga	13	10	0	1	rs376027605		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:7780597C>T	ENST00000358415.4	+	16	2137	c.1971C>T	c.(1969-1971)taC>taT	p.Y657Y	ITIH2_ENST00000379587.4_Silent_p.Y646Y	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	657					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CCCTGTATTACGGCAGCAAAG	0.502																																																0			10								0,4406		0,0,2203	112	100	104		1971	-5.8	0.2	10		104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITIH2	NM_002216.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		657/947	7780597	1,13005	2203	4300	6503	7820603	SO:0001819	synonymous_variant	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1971C>T	10.37:g.7780597C>T			7820603	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.502	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7780597	C	T	7780597	2	4	10	1	0	0	0	0	0	0	0	1	7925	547	19	1		1	ITIH2	10	7780597	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10		7780597	127754150	99	1173										
CUBN	8029	hgsc.bcm.edu	37	chr10	16962055	16962055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tccaaatgcaatcagcgtgcGggggataattatgagggtgg	15	6	1	1	rs544059289		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:16962055G>A	ENST00000377833.4	-	44	6793	c.6728C>T	c.(6727-6729)cCg>cTg	p.P2243L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2243	CUB 16. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCAGCGTGCGGGGGATAATT	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		19897	0		0	False		,,,				2504	0															0			10											63	56	59					10																	16962055		2203	4300	6503	17002061	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6728C>T	10.37:g.16962055G>A	ENSP00000367064:p.Pro2243Leu		17002061	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	0.301	-0.974031	0.02215	.	.	ENSG00000107611	ENST00000377833	T	0.37235	1.21	4.97	0.749	0.18381	CUB (5);	0.644142	0.12859	N	0.433266	T	0.23410	0.0566	L	0.33710	1.025	0.48511	D	0.999665	B	0.25441	0.126	B	0.14023	0.01	T	0.05869	-1.0859	10	0.25751	T	0.34	.	8.777	0.34767	0.0993:0.0:0.4992:0.4015	.	2243	O60494	CUBN_HUMAN	L	2243	ENSP00000367064:P2243L	ENSP00000367064:P2243L	P	-	2	0	CUBN	17002061	0.962000	0.33011	0.567000	0.28434	0.166000	0.22503	0.806000	0.27126	0.230000	0.21059	-0.553000	0.04205	CCG		0.493	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16962055	G	A	16962055	3	1	10	1	0	0	0	0	1	0	0	0	4057	1116	39	1	4239	1	CUBN	10	16962055	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	9181458	16962055	118572692	100	1174										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363115	17363115	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcatcaagccggtggacaagCggtatgcagtcacaccttta	10	11	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:17363115C>T	ENST00000377602.4	-	8	1033	c.959G>A	c.(958-960)cGc>cAc	p.R320H		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	320					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						GGTGGACAAGCGGTATGCAGT	0.433																																																0			10											176	172	173					10																	17363115		2203	4300	6503	17403121	SO:0001583	missense	338596				CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.959G>A	10.37:g.17363115C>T	ENSP00000366827:p.Arg320His		17403121	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	C	34	5.297270	0.95574	.	.	ENSG00000148488	ENST00000377602	T	0.34072	1.38	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	M	0.84156	2.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68957	-0.5272	10	0.72032	D	0.01	-10.7374	19.5559	0.95347	0.0:1.0:0.0:0.0	.	320	P61647	SIA8F_HUMAN	H	320	ENSP00000366827:R320H	ENSP00000366827:R320H	R	-	2	0	ST8SIA6	17403121	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.651000	0.83577	2.861000	0.98227	0.650000	0.86243	CGC		0.433	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17363115	C	T	17363115	3	4	10	1	0	0	0	0	1	0	0	0	15275	768	27	1	241	1	ST8SIA6	10	17363115	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	401060	17363115	118171632	101	1175										
PTPLA	9200	hgsc.bcm.edu	37	chr10	17636336	17636336	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggcagcgtatattgtaagaaGttcaccagcaactccaacag	9	10	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:17636336G>A	ENST00000361271.3	-	6	689	c.652C>T	c.(652-654)Ctt>Ttt	p.L218F		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	218					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						ATTGTAAGAAGTTCACCAGCA	0.303																																																0			10											60	61	61					10																	17636336		2203	4297	6500	17676342	SO:0001583	missense	9200			AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.652C>T	10.37:g.17636336G>A	ENSP00000355308:p.Leu218Phe		17676342	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170536	0.94807	.	.	ENSG00000165996	ENST00000361271	T	0.33216	1.42	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.86097	2.795	0.80722	D	1	P	0.46859	0.885	P	0.52031	0.688	T	0.59804	-0.7385	10	0.66056	D	0.02	-10.8005	20.2406	0.98372	0.0:0.0:1.0:0.0	.	218	B0YJ81	HACD1_HUMAN	F	218	ENSP00000355308:L218F	ENSP00000355308:L218F	L	-	1	0	PTPLA	17676342	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.848000	0.99507	2.857000	0.98124	0.650000	0.86243	CTT		0.303	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		A	17636336	G	A	17636336	3	1	10	1	0	0	0	0	1	0	0	0	12809	1029	36	3	222	3	PTPLA	10	17636336	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	273221	17636336	117898411	102	1176										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31809187	31809187	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccaagaacaggactcaagacAtctcagtgttcttcaccgtc	7	13	4	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:31809187A>G	ENST00000320985.10	+	7	1034	c.924A>G	c.(922-924)acA>acG	p.T308T	ZEB1_ENST00000361642.5_Silent_p.T309T|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000446923.2_Silent_p.T292T|ZEB1_ENST00000560721.2_Silent_p.T288T|ZEB1_ENST00000542815.3_Silent_p.T241T			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	308					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GACTCAAGACATCTCAGTGTT	0.453																																					Ovarian(40;423 959 14296 36701 49589)											0			10											134	129	131					10																	31809187		2203	4300	6503	31849193	SO:0001819	synonymous_variant	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.924A>G	10.37:g.31809187A>G			31849193	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Silent	SNP	ENST00000320985.10	37	CCDS7169.1																																																																																				0.453	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		G	31809187	A	G	31809187	2	3	10	1	0	0	0	0	0	0	0	1	17662	204	8	4		4	ZEB1	10	31809187	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	14172851	31809187	103725560	103	1177										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72468469	72468469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aggtgctgctggtggtggacGactcggtggttcgcttccat	16	9	0	0	rs147652549		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:72468469G>A	ENST00000373207.1	+	4	805	c.805G>A	c.(805-807)Gac>Aac	p.D269N	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.D269N	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	269	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GGTGGTGGACGACTCGGTGGT	0.612													G|||	1	0.000199681	0	0	5008	,	,		17448	0		0.001	False		,,,				2504	0															0			10						G	ASN/ASP,ASN/ASP	0,4406		0,0,2203	145	115	125		805,805	4.5	1	10	dbSNP_134	125	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	23,23	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	269/1224,269/1227	72468469	2,13004	2203	4300	6503	72138475	SO:0001583	missense	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.805G>A	10.37:g.72468469G>A	ENSP00000362303:p.Asp269Asn		72138475	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.964962	0.92855	0.0	2.33E-4	ENSG00000138316	ENST00000373208;ENST00000373207	D;D	0.85955	-2.05;-2.05	4.48	4.48	0.54585	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.82010	0.4944	N	0.11023	0.085	0.53005	D	0.999964	D;D	0.61080	0.977;0.989	P;P	0.58077	0.701;0.832	T	0.82121	-0.0614	10	0.28530	T	0.3	.	16.9214	0.86165	0.0:0.0:1.0:0.0	.	269;269	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	N	269	ENSP00000362304:D269N;ENSP00000362303:D269N	ENSP00000362303:D269N	D	+	1	0	ADAMTS14	72138475	1.000000	0.71417	0.998000	0.56505	0.820000	0.46376	9.618000	0.98365	2.320000	0.78422	0.491000	0.48974	GAC		0.612	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		A	72468469	G	A	72468469	3	1	10	1	0	0	0	0	1	0	0	0	259	1058	37	1	819	1	ADAMTS14	10	72468469	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	40659282	72468469	63066278	104	1178										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624287	89624287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggagatatcaagaggatggaTtcgacttagacttgacctgt	12	6	1	4			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:89624287T>C	ENST00000371953.3	+	1	1418	c.61T>C	c.(61-63)Ttc>Ctc	p.F21L	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	21	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Y16fs*21(1)|p.R14_D22del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGAGGATGGATTCGACTTAGA	0.463		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Unknown(13)|Deletion - In frame(1)|Deletion - Frameshift(1)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|endometrium(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											180	171	174					10																	89624287		2203	4300	6503	89614267	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.61T>C	10.37:g.89624287T>C	ENSP00000361021:p.Phe21Leu		89614267	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.747744	0.89663	.	.	ENSG00000171862	ENST00000371953	D	0.98455	-4.94	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.115400	0.64402	D	0.000011	D	0.96417	0.8831	L	0.55103	1.725	0.80722	D	1	B	0.23377	0.084	B	0.21708	0.036	D	0.95076	0.8209	9	.	.	.	0.343	14.1807	0.65572	0.0:0.0:0.0:1.0	.	21	P60484	PTEN_HUMAN	L	21	ENSP00000361021:F21L	.	F	+	1	0	PTEN	89614267	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.216000	0.77974	1.996000	0.58369	0.459000	0.35465	TTC		0.463	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89624287	T	C	89624287	3	2	10	1	0	0	0	0	1	0	0	0	12772	1493	52	4	63	4	PTEN	10	89624287	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	17155818	89624287	45910460	105	1179										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717674	89717674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tccaattcaggacccacacgAcgggaagacaagttcatgta	9	11	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:89717674A>G	ENST00000371953.3	+	7	2056	c.699A>G	c.(697-699)cgA>cgG	p.R233R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	233	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.R234fs*11(3)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R233fs*10(1)|p.R233fs*12(1)|p.R233fs*20(1)|p.R234fs*26(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GACCCACACGACGGGAAGACA	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	55	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - frameshift(5)|Deletion - In frame(1)|Insertion - Frameshift(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|haematopoietic_and_lymphoid_tissue(10)|skin(6)|lung(4)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											155	132	140					10																	89717674		2203	4300	6503	89707654	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.699A>G	10.37:g.89717674A>G			89707654	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717674	A	G	89717674	2	3	10	1	0	0	0	0	0	0	0	1	12772	262	10	4		4	PTEN	10	89717674	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	93387	89717674	45817073	106	1180										
TLX1	3195	hgsc.bcm.edu	37	chr10	102896554	102896554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcctggcacagccgctgcccGctgaccctctgtgcgtgcac	12	18	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:102896554G>A	ENST00000370196.6	+	3	2919	c.877G>A	c.(877-879)Gct>Act	p.A293T	RP11-31L23.3_ENST00000411459.1_RNA|TLX1_ENST00000467928.2_3'UTR			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	293					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GCCGCTGCCCGCTGACCCTCT	0.637			T	"TRB@, TRD@"	T-ALL																																		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	0			10											73	67	69					10																	102896554		2203	4300	6503	102886544	SO:0001583	missense	3195			M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"Homeoboxes / ANTP class : NKL subclass"	5056	protein-coding gene	gene with protein product	"Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)", "homeo box 11 (T-cell lymphoma 3-associated breakpoint)"	186770	"homeo box 11 (T-cell lymphoma 3-associated breakpoint)", "T-cell leukemia, homeobox 1"	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.877G>A	10.37:g.102896554G>A	ENSP00000359215:p.Ala293Thr		102886544	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Missense_Mutation	SNP	ENST00000370196.6	37	CCDS7510.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.517611	0.64634	.	.	ENSG00000107807	ENST00000370196	D	0.90133	-2.62	4.39	4.39	0.52855	.	0.054742	0.64402	D	0.000001	D	0.83394	0.5245	N	0.25647	0.755	0.80722	D	1	B	0.26318	0.146	B	0.14578	0.011	T	0.81448	-0.0928	10	0.44086	T	0.13	.	13.1188	0.59314	0.0:0.1612:0.8388:0.0	.	293	P31314	TLX1_HUMAN	T	293	ENSP00000359215:A293T	ENSP00000359215:A293T	A	+	1	0	TLX1	102886544	1.000000	0.71417	0.996000	0.52242	0.810000	0.45777	3.737000	0.55060	2.156000	0.67533	0.462000	0.41574	GCT		0.637	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		A	102896554	G	A	102896554	3	1	10	1	0	0	0	0	1	0	0	0	15998	1087	38	1	887	1	TLX1	10	102896554	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	13178880	102896554	32638193	107	1181										
VWA2	340706	hgsc.bcm.edu	37	chr10	116048996	116048996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tctatgacaaagtgatgaccGtccagaggggtgcccggcct	13	11	1	4	rs376331052		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:116048996G>A	ENST00000392982.3	+	12	2120	c.1870G>A	c.(1870-1872)Gtc>Atc	p.V624I	VWA2_ENST00000603594.1_Missense_Mutation_p.V624I			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	624	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		AGTGATGACCGTCCAGAGGGG	0.662																																																0			10						G	ILE/VAL	0,4406		0,0,2203	46	42	43		1870	0.3	0	10		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	VWA2	NM_198496.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	624/726	116048996	1,13005	2203	4300	6503	116038986	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1870G>A	10.37:g.116048996G>A	ENSP00000376708:p.Val624Ile		116038986	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	G	11.49	1.654536	0.29425	0.0	1.16E-4	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.83163	-1.69	5.29	0.284	0.15701	von Willebrand factor, type A (3);	0.296188	0.31612	N	0.007344	T	0.76828	0.4042	M	0.69358	2.11	0.24060	N	0.996019	B;B;B	0.31769	0.021;0.339;0.29	B;B;B	0.30179	0.012;0.112;0.068	T	0.63825	-0.6549	10	0.34782	T	0.22	.	8.8967	0.35470	0.3576:0.0:0.6424:0.0	.	320;624;624	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	I	624	ENSP00000376708:V624I	ENSP00000298715:V624I	V	+	1	0	VWA2	116038986	0.998000	0.40836	0.034000	0.17996	0.412000	0.31113	2.672000	0.46850	-0.222000	0.09958	-0.136000	0.14681	GTC		0.662	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		A	116048996	G	A	116048996	3	1	10	1	0	0	0	0	1	0	0	0	17279	1145	40	1	1912	1	VWA2	10	116048996	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	13152442	116048996	19485751	108	1182										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117228803	117228803	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cctaacattacattctatgtGtacgtcagcaacttttcctg	5	11	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr10:117228803G>A	ENST00000355044.3	+	24	3744	c.3618G>A	c.(3616-3618)gtG>gtA	p.V1206V	ATRNL1_ENST00000423111.2_Silent_p.V257V|ATRNL1_ENST00000303745.7_Intron	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1206					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CATTCTATGTGTACGTCAGCA	0.294																																																0			10											60	65	63					10																	117228803		2196	4280	6476	117218793	SO:0001819	synonymous_variant	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3618G>A	10.37:g.117228803G>A			117218793	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																				0.294	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		A	117228803	G	A	117228803	2	1	10	1	0	0	0	0	0	0	0	1	1208	1364	48	3		3	ATRNL1	10	117228803	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1179807	117228803	18305944	109	1183										
SIRT3	23410	hgsc.bcm.edu	37	chr11	233380	233380	+	Frame_Shift_Del	DEL	C	C	-													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	actgggtgtgctgatgccggCccccaccatgaccaccaccc					rs147810576	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:233380delC	ENST00000382743.4	-	2	538	c.436delG	c.(436-438)gccfs	p.A146fs	SIRT3_ENST00000532956.1_Frame_Shift_Del_p.A146fs|SIRT3_ENST00000525319.1_Frame_Shift_Del_p.A65fs|SIRT3_ENST00000524564.1_Intron|SIRT3_ENST00000528702.1_5'UTR|SIRT3_ENST00000529382.1_Frame_Shift_Del_p.A4fs	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	146	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		CTGATGCCGGCCCCCACCATG	0.632																																																0			11											83	71	75					11																	233380		2203	4300	6503	223380	SO:0001589	frameshift_variant	23410			AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3", "sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.436delG	11.37:g.233380delC	ENSP00000372191:p.Ala146fs		223380	B7Z5U6|Q9Y6E8	Frame_Shift_Del	DEL	ENST00000382743.4	37	CCDS7691.1																																																																																				0.632	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3			-	233380	C	-	233380	7	5	10	1	0	1	0	1	0	0	0	0	14376	739	26	0	787	0	SIRT3	11	233380	Frame_Shift_Del	DEL	C	TCGA-AF-6136-01A-11D-1826-10		233380	134773136	110	1184										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78775867	78775867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcaggagctgcgccctgaccGtgtgctccggccccacagac	13	17	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:78775867G>A	ENST00000278550.7	-	6	871	c.409C>T	c.(409-411)Cgg>Tgg	p.R137W		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	137	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CGCCCTGACCGTGTGCTCCGG	0.637																																																0			11											34	34	34					11																	78775867		692	1591	2283	78453515	SO:0001583	missense	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.409C>T	11.37:g.78775867G>A	ENSP00000278550:p.Arg137Trp		78453515	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080501	0.76528	.	.	ENSG00000149256	ENST00000278550	T	0.32272	1.46	4.69	2.65	0.31530	Teneurin intracellular, N-terminal (2);	0.078973	0.49305	D	0.000148	T	0.27594	0.0678	N	0.08118	0	0.38923	D	0.957787	D;P	0.76494	0.999;0.913	P;P	0.62298	0.9;0.532	T	0.09729	-1.0661	9	.	.	.	.	11.3404	0.49529	0.0:0.0:0.4413:0.5586	.	137;137	G3CAT1;Q6N022	.;TEN4_HUMAN	W	137	ENSP00000278550:R137W	.	R	-	1	2	ODZ4	78453515	1.000000	0.71417	0.953000	0.39169	0.928000	0.56348	3.763000	0.55257	1.317000	0.45149	-0.311000	0.09066	CGG		0.637	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78775867	G	A	78775867	3	1	10	1	0	0	0	0	1	0	0	0	10868	1144	40	1	8016	1	ODZ4	11	78775867	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	78542487	78775867	56230649	111	1185										
MAML2	84441	hgsc.bcm.edu	37	chr11	95713012	95713012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	actgctgtagataatgatggCattcttgtcccgtgagaagt	11	7	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:95713012C>A	ENST00000524717.1	-	5	3855	c.2571G>T	c.(2569-2571)atG>atT	p.M857I		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	857					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.M857I(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				ATAATGATGGCATTCTTGTCC	0.413			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	1	Substitution - Missense(1)	lung(1)	11											169	157	161					11																	95713012		1913	4119	6032	95352660	SO:0001583	missense	84441			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.2571G>T	11.37:g.95713012C>A	ENSP00000434552:p.Met857Ile		95352660	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	.	.	.	.	.	.	.	.	.	.	C	1.011	-0.687827	0.03328	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.41065	1.01;1.01	5.08	4.17	0.49024	.	0.137304	0.49305	D	0.000146	T	0.36331	0.0963	L	0.53249	1.67	0.35310	D	0.783783	B	0.30824	0.296	B	0.26310	0.068	T	0.45220	-0.9276	10	0.22706	T	0.39	-2.783	13.7438	0.62863	0.0:0.925:0.0:0.075	.	857	Q8IZL2	MAML2_HUMAN	I	857	ENSP00000434552:M857I;ENSP00000412394:M857I	ENSP00000412394:M857I	M	-	3	0	MAML2	95352660	1.000000	0.71417	0.109000	0.21407	0.253000	0.25986	2.904000	0.48719	1.276000	0.44395	0.650000	0.86243	ATG		0.413	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			A	95713012	C	A	95713012	3	1	10	1	0	0	0	0	1	0	0	0	9236	710	25	2	903	2	MAML2	11	95713012	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	16937145	95713012	39293504	112	1186										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101344265	101344265	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaaggcttcattttgttttgCaccaatgtagtaggagtaga	11	5	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:101344265C>A	ENST00000344327.3	-	7	2408	c.1984G>T	c.(1984-1986)Gca>Tca	p.A662S	TRPC6_ENST00000532133.1_Missense_Mutation_p.A584S|TRPC6_ENST00000348423.4_Missense_Mutation_p.A546S|TRPC6_ENST00000360497.4_Missense_Mutation_p.A607S	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	662					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TTTTGTTTTGCACCAATGTAG	0.318																																					Colon(166;1315 1927 11094 12848 34731)											0			11											69	65	67					11																	101344265		2202	4297	6499	100849475	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1984G>T	11.37:g.101344265C>A	ENSP00000340913:p.Ala662Ser		100849475	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687856	0.68271	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	D;D;D;D	0.98493	-4.96;-4.96;-4.34;-4.34	5.72	5.72	0.89469	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97980	0.9335	L	0.41906	1.305	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.71656	0.931;0.974;0.959	D	0.96272	0.9199	10	0.08837	T	0.75	-4.1648	19.8968	0.96969	0.0:1.0:0.0:0.0	.	607;546;662	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	S	662;584;546;607	ENSP00000340913:A662S;ENSP00000435574:A584S;ENSP00000343672:A546S;ENSP00000353687:A607S	ENSP00000340913:A662S	A	-	1	0	TRPC6	100849475	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.807000	0.86032	2.691000	0.91804	0.655000	0.94253	GCA		0.318	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101344265	C	A	101344265	3	1	10	1	0	0	0	0	1	0	0	0	16623	710	25	2	839	2	TRPC6	11	101344265	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	5631253	101344265	33662251	113	1187										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	102985923	102985923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	taggtatccttacaccaagcGatgagttccagttttggata	9	8	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:102985923G>A	ENST00000375735.2	+	4	664	c.520G>A	c.(520-522)Gat>Aat	p.D174N	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.D174N|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.D174N	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	174	Stem. {ECO:0000250}.			D -> G (in Ref. 1; BAE17138). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.D174N(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TACACCAAGCGATGAGTTCCA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	52	55					11																	102985923		1812	4070	5882	102491133	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.520G>A	11.37:g.102985923G>A	ENSP00000364887:p.Asp174Asn		102491133	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410138	0.83340	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.59638	1.18;0.25;1.18	5.28	5.28	0.74379	.	0.279169	0.27478	U	0.019197	T	0.78666	0.4319	M	0.81497	2.545	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.991;0.997	D;P;P	0.87578	0.998;0.754;0.842	T	0.81653	-0.0835	10	0.87932	D	0	.	18.9329	0.92574	0.0:0.0:1.0:0.0	.	174;174;174	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	N	174	ENSP00000364887:D174N;ENSP00000334021:D174N;ENSP00000381167:D174N	ENSP00000334021:D174N	D	+	1	0	DYNC2H1	102491133	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	8.909000	0.92647	2.465000	0.83290	0.655000	0.94253	GAT		0.323	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	102985923	G	A	102985923	3	1	10	1	0	0	0	0	1	0	0	0	4857	1058	37	1	534	1	DYNC2H1	11	102985923	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1641658	102985923	32020593	114	1188										
OR4D5	219875	hgsc.bcm.edu	37	chr11	123811041	123811041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcagcaaggccctgtctaccTgtgcctctcacattgctgtg	10	14	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr11:123811041T>C	ENST00000307033.2	+	1	792	c.718T>C	c.(718-720)Tgt>Cgt	p.C240R		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CCTGTCTACCTGTGCCTCTCA	0.542																																																0			11											237	195	209					11																	123811041		2202	4299	6501	123316251	SO:0001583	missense	219875			BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"GPCR / Class A : Olfactory receptors"	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.718T>C	11.37:g.123811041T>C	ENSP00000305970:p.Cys240Arg		123316251	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	37	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.284937	0.59867	.	.	ENSG00000171014	ENST00000307033	T	0.00372	7.73	5.49	5.49	0.81192	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000063	T	0.01976	0.0062	H	0.97390	3.995	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.10086	-1.0645	10	0.87932	D	0	-10.1946	15.2419	0.73476	0.0:0.0:0.0:1.0	.	240	Q8NGN0	OR4D5_HUMAN	R	240	ENSP00000305970:C240R	ENSP00000305970:C240R	C	+	1	0	OR4D5	123316251	1.000000	0.71417	0.999000	0.59377	0.758000	0.43043	7.739000	0.84976	2.078000	0.62432	0.528000	0.53228	TGT		0.542	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965		C	123811041	T	C	123811041	3	2	10	1	0	0	0	0	1	0	0	0	11088	1580	55	4	720	4	OR4D5	11	123811041	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	20825118	123811041	11195475	115	1189										
WNT5B	81029	hgsc.bcm.edu	37	chr12	1755211	1755211	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cccgactactgcctgcgcaaCgagagcacgggctccctggg	13	16	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:1755211C>T	ENST00000397196.2	+	5	1105	c.873C>T	c.(871-873)aaC>aaT	p.N291N	WNT5B_ENST00000545747.1_3'UTR|WNT5B_ENST00000310594.3_Silent_p.N291N|WNT5B_ENST00000537031.1_Silent_p.N291N	NM_032642.2	NP_116031.1	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	291					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			GCCTGCGCAACGAGAGCACGG	0.682																																																0			12											47	49	48					12																	1755211		2203	4299	6502	1625472	SO:0001819	synonymous_variant	81029			AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186		"Wingless-type MMTV integration sites"	16265	protein-coding gene	gene with protein product		606361				11445850	Standard	NM_030775		Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000397196.2:c.873C>T	12.37:g.1755211C>T			1625472	A8K315|D3DUP9|Q96S49|Q9BV04	Silent	SNP	ENST00000397196.2	37	CCDS8510.1																																																																																				0.682	WNT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206747.2			T	1755211	C	T	1755211	2	4	10	1	0	0	0	0	0	0	0	1	17432	535	19	1		1	WNT5B	12	1755211	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10		1755211	132096684	116	1190										
MLL2	8085	hgsc.bcm.edu	37	chr12	49435156	49435156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgcagaggtagacaagccggCgggggtagtggggctgccaa	19	9	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:49435156C>T	ENST00000301067.7	-	31	6396	c.6397G>A	c.(6397-6399)Gcc>Acc	p.A2133T		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2133	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GACAAGCCGGCGGGGGTAGTG	0.701																																																0			12											7	10	9					12																	49435156		1744	3939	5683	47721423	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.6397G>A	12.37:g.49435156C>T	ENSP00000301067:p.Ala2133Thr		47721423	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	9.348	1.064717	0.20067	.	.	ENSG00000167548	ENST00000301067	T	0.79749	-1.3	3.83	3.83	0.44106	.	0.000000	0.32769	N	0.005666	T	0.60025	0.2237	N	0.08118	0	0.28096	N	0.931616	B	0.30709	0.291	B	0.17979	0.02	T	0.61997	-0.6947	10	0.87932	D	0	.	10.9327	0.47228	0.1881:0.8119:0.0:0.0	.	2133	O14686	MLL2_HUMAN	T	2133	ENSP00000301067:A2133T	ENSP00000301067:A2133T	A	-	1	0	MLL2	47721423	0.976000	0.34144	1.000000	0.80357	0.911000	0.54048	1.924000	0.40065	2.432000	0.82394	0.561000	0.74099	GCC		0.701	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49435156	C	T	49435156	3	4	10	1	0	0	0	0	1	0	0	0	9651	768	27	1	10312	1	MLL2	12	49435156	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	47679945	49435156	84416739	117	1191										
KRT3	3850	hgsc.bcm.edu	37	chr12	53183951	53183951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gccagagatggagccaaagcCgctgccaccgctgaaaccgc	12	15	0	2	rs570613061|rs60125653	byFrequency	TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:53183951C>T	ENST00000417996.2	-	9	1836	c.1762G>A	c.(1762-1764)Ggc>Agc	p.G588S	KRT3_ENST00000309505.3_Missense_Mutation_p.G589S	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	588	Gly-rich.|Tail.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						GAGCCAAAgccgctgccaccg	0.697																																																0			12											14	31	25					12																	53183951		1574	3123	4697	51470218	SO:0001583	missense	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1762G>A	12.37:g.53183951C>T	ENSP00000413479:p.Gly588Ser		51470218	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307617	0.40795	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.91351	-2.83;-2.83	3.4	-1.34	0.09143	.	0.507655	0.14827	N	0.296110	T	0.80149	0.4570	N	0.22421	0.69	0.09310	N	1	B	0.18166	0.026	B	0.08055	0.003	T	0.65302	-0.6201	10	0.34782	T	0.22	.	7.4497	0.27231	0.0:0.4872:0.0:0.5128	.	588	P12035	K2C3_HUMAN	S	588;589	ENSP00000413479:G588S;ENSP00000312206:G589S	ENSP00000312206:G589S	G	-	1	0	KRT3	51470218	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-1.682000	0.01935	-0.284000	0.09102	-0.258000	0.10820	GGC		0.697	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		T	53183951	C	T	53183951	3	4	10	1	0	0	0	0	1	0	0	0	8487	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	3748795	53183951	80667944	118	1192										
CRY1	1407	hgsc.bcm.edu	37	chr12	107386774	107386774	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aggtgagtttgctgactgtcGccatgagcatagtgtaaaat	12	6	0	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:107386774G>A	ENST00000008527.5	-	11	2493	c.1626C>T	c.(1624-1626)ggC>ggT	p.G542G		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	542					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.G542G(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						GCTGACTGTCGCCATGAGCAT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	12											101	87	92					12																	107386774		2203	4300	6503	105910904	SO:0001819	synonymous_variant	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.1626C>T	12.37:g.107386774G>A			105910904		Silent	SNP	ENST00000008527.5	37	CCDS9112.1																																																																																				0.333	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		A	107386774	G	A	107386774	2	1	10	1	0	0	0	0	0	0	0	1	3909	1074	38	1		1	CRY1	12	107386774	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	54202823	107386774	26465121	119	1193										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926901	112926901	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aggtcagggatggtccagacAgaagcacagtaccgatttat	12	8	1	2	rs374285143		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:112926901A>G	ENST00000351677.2	+	13	1719	c.1521A>G	c.(1519-1521)acA>acG	p.T507T		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	511	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		G -> A (in JMML). {ECO:0000269|PubMed:12717436}.|G -> R (in patients with growth retardation, pulmonic stenosis and juvenile myelomonocytic leukemia). {ECO:0000269|PubMed:12717436, ECO:0000269|PubMed:12960218}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TGGTCCAGACAGAAGCACAGT	0.478			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12						A		1,4405	2.1+/-5.4	0,1,2202	180	169	173		1521	-5.9	1	12		173	0,8600		0,0,4300	no	coding-synonymous	PTPN11	NM_002834.3		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		507/594	112926901	1,13005	2203	4300	6503	111411284	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1521A>G	12.37:g.112926901A>G			111411284	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.478	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112926901	A	G	112926901	2	3	10	1	0	0	0	0	0	0	0	1	12815	175	7	4		4	PTPN11	12	112926901	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	5540127	112926901	20924994	120	1194										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124297818	124297818	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aatgatatctctctgaacccTcagataattgaacaagctgt	6	9	3	4			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:124297818T>C	ENST00000409039.3	+	19	2923	c.2898T>C	c.(2896-2898)ccT>ccC	p.P966P		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	966	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P784P(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTCTGAACCCTCAGATAATTG	0.408																																																1	Substitution - coding silent(1)	ovary(1)	12											95	96	95					12																	124297818		2203	4300	6503	122863771	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2898T>C	12.37:g.124297818T>C			122863771	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.408	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124297818	T	C	124297818	2	2	10	1	0	0	0	0	0	0	0	1	4609	1538	54	4		4	DNAH10	12	124297818	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	11370917	124297818	9554077	121	1195										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124821373	124821373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cccggtgcgggtccgaggccGaggcaggtggcgccggcggg	22	13	0	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr12:124821373G>A	ENST00000405201.1	-	38	6041	c.6041C>T	c.(6040-6042)tCg>tTg	p.S2014L	NCOR2_ENST00000404121.2_Missense_Mutation_p.S1575L|NCOR2_ENST00000397355.1_Missense_Mutation_p.S2005L|NCOR2_ENST00000404621.1_Missense_Mutation_p.S2004L|NCOR2_ENST00000429285.2_Missense_Mutation_p.S2004L|NCOR2_ENST00000356219.3_Missense_Mutation_p.S2021L			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	2025					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GTCCGAGGCCGAGGCAGGTGG	0.652																																																0			12											37	44	42					12																	124821373		1976	4140	6116	123387326	SO:0001583	missense	9612			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.6041C>T	12.37:g.124821373G>A	ENSP00000384018:p.Ser2014Leu		123387326	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	g	12.34	1.909207	0.33721	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285	T;T;T;T;T;T	0.19105	2.17;2.44;2.18;2.44;2.18;2.44	4.5	3.54	0.40534	.	0.748718	0.12560	N	0.458298	T	0.20981	0.0505	N	0.24115	0.695	0.27039	N	0.964068	D;D;D	0.63880	0.984;0.993;0.987	P;P;B	0.48840	0.493;0.592;0.388	T	0.07966	-1.0745	10	0.44086	T	0.13	-9.9789	13.848	0.63479	0.0:0.154:0.8459:0.0	.	2005;2014;2025	C9J239;C9JFD3;Q9Y618	.;.;NCOR2_HUMAN	L	2014;2004;2021;2005;2013;1575;106;2004	ENSP00000384018:S2014L;ENSP00000384202:S2004L;ENSP00000348551:S2021L;ENSP00000380513:S2005L;ENSP00000385618:S1575L;ENSP00000400281:S2004L	ENSP00000348551:S2021L	S	-	2	0	NCOR2	123387326	0.997000	0.39634	0.712000	0.30502	0.131000	0.20780	3.242000	0.51384	2.041000	0.60428	0.556000	0.70494	TCG		0.652	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124821373	G	A	124821373	3	1	10	1	0	0	0	0	1	0	0	0	10267	1059	37	1	1543	1	NCOR2	12	124821373	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	523555	124821373	9030522	122	1196										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20638637	20638637	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaatttttattaccacctgtTtttggcgaagaatatgagga	9	5	0	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:20638637T>C	ENST00000382874.2	+	20	3274	c.3084T>C	c.(3082-3084)gtT>gtC	p.V1028V	ZMYM2_ENST00000382869.3_Silent_p.V1028V|ZMYM2_ENST00000382871.2_Silent_p.V1028V	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1028					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		TACCACCTGTTTTTGGCGAAG	0.343																																																0			13											118	108	111					13																	20638637		1819	4087	5906	19536637	SO:0001819	synonymous_variant	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3084T>C	13.37:g.20638637T>C			19536637	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	37	CCDS45016.1																																																																																				0.343	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		C	20638637	T	C	20638637	2	2	10	1	0	0	0	0	0	0	0	1	17739	1828	64	4		4	ZMYM2	13	20638637	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10		20638637	94531241	123	1197										
RNF17	56163	hgsc.bcm.edu	37	chr13	25374502	25374502	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atattacttgaatttctcctAgagttgttgatacccatgtg	7	7	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:25374502A>G	ENST00000255324.5	+	13	1641		c.e13-1		RNF17_ENST00000381921.1_Splice_Site|RNF17_ENST00000255325.6_Splice_Site	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17						multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		AATTTCTCCTAGAGTTGTTGA	0.318																																																0			13											88	93	91					13																	25374502		2203	4300	6503	24272502	SO:0001630	splice_region_variant	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1590-1A>G	13.37:g.25374502A>G			24272502	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Splice_Site	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	A	9.643	1.139523	0.21205	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0965	0.59195	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNF17	24272502	1.000000	0.71417	0.976000	0.42696	0.095000	0.18619	3.327000	0.52045	1.985000	0.57927	0.460000	0.39030	.		0.318	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	Intron	G	25374502	A	G	25374502	5	3	10	1	0	0	0	0	0	0	1	0	13498	434	15	4	1638	4	RNF17	13	25374502	Splice_Site	SNP	A	TCGA-AF-6136-01A-11D-1826-10	4735865	25374502	89795376	124	1198										
FLT1	2321	hgsc.bcm.edu	37	chr13	28964202	28964202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcaggtcctctccttccgtcGgcattttttccaagttaaca	6	13	2	0	rs374335323		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:28964202G>A	ENST00000282397.4	-	13	1951	c.1700C>T	c.(1699-1701)cCg>cTg	p.P567L	FLT1_ENST00000541932.1_Missense_Mutation_p.P567L	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	567	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCCTTCCGTCGGCATTTTTTC	0.353																																																0			13											106	101	103					13																	28964202		2203	4300	6503	27862202	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1700C>T	13.37:g.28964202G>A	ENSP00000282397:p.Pro567Leu		27862202	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.340489	0.81911	.	.	ENSG00000102755	ENST00000282397;ENST00000541932	T;T	0.76316	-1.01;-0.43	6.16	6.16	0.99307	Immunoglobulin-like (1);	0.056194	0.64402	D	0.000001	D	0.87370	0.6160	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.995;0.995;0.996	T	0.82259	-0.0546	10	0.23891	T	0.37	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	567;567;567	P17948-3;P17948-2;P17948	.;.;VGFR1_HUMAN	L	567	ENSP00000282397:P567L;ENSP00000437631:P567L	ENSP00000282397:P567L	P	-	2	0	FLT1	27862202	1.000000	0.71417	0.987000	0.45799	0.979000	0.70002	8.005000	0.88553	2.937000	0.99478	0.650000	0.86243	CCG		0.353	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28964202	G	A	28964202	3	1	10	1	0	0	0	0	1	0	0	0	5960	1116	39	1	2573	1	FLT1	13	28964202	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3589700	28964202	86205676	125	1199										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37678497	37678497	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gctgctttctgctttaacatCgtccaatcaaatgtgtagtc	7	10	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:37678497C>T	ENST00000379800.3	-	1	1306	c.897G>A	c.(895-897)acG>acA	p.T299T		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	299					cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GCTTTAACATCGTCCAATCAA	0.478																																																0			13											174	160	165					13																	37678497		2203	4300	6503	36576497	SO:0001819	synonymous_variant	122011			BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.897G>A	13.37:g.37678497C>T			36576497	Q5T2N2	Silent	SNP	ENST00000379800.3	37	CCDS9363.1																																																																																				0.478	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		T	37678497	C	T	37678497	2	4	10	1	0	0	0	0	0	0	0	1	3957	871	31	1		1	CSNK1A1L	13	37678497	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	8714295	37678497	77491381	126	1200										
CYSLTR2	57105	hgsc.bcm.edu	37	chr13	49281253	49281253	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	agggctgactattatcttagAggctccaattggatatttgg	11	6	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:49281253A>G	ENST00000282018.3	+	1	303	c.300A>G	c.(298-300)agA>agG	p.R100R		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	100					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	ATTATCTTAGAGGCTCCAATT	0.428																																																0			13											96	97	97					13																	49281253		2203	4300	6503	48179254	SO:0001819	synonymous_variant	57105			AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.300A>G	13.37:g.49281253A>G			48179254	Q9HCQ2	Silent	SNP	ENST00000282018.3	37	CCDS9412.1																																																																																				0.428	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			G	49281253	A	G	49281253	2	3	10	1	0	0	0	0	0	0	0	1	4208	301	11	4		4	CYSLTR2	13	49281253	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	11602756	49281253	65888625	127	1201										
SUGT1	10910	hgsc.bcm.edu	37	chr13	53250436	53250436	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gggcaaggagatgtgcctacGccaaaacaattcgtagcagg	13	9	0	1	rs535411991		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:53250436G>A	ENST00000343788.6	+	12	877	c.795G>A	c.(793-795)acG>acA	p.T265T	SUGT1_ENST00000535397.1_Silent_p.T177T|SUGT1_ENST00000310528.8_Silent_p.T233T	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	265					innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		ATGTGCCTACGCCAAAACAAT	0.363													G|||	1	0.000199681	0	0.0014	5008	,	,		15842	0		0	False		,,,				2504	0															0			13											98	101	100					13																	53250436		2203	4300	6503	52148437	SO:0001819	synonymous_variant	10910			AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.795G>A	13.37:g.53250436G>A			52148437	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Silent	SNP	ENST00000343788.6	37	CCDS45050.1																																																																																				0.363	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2			A	53250436	G	A	53250436	2	1	10	1	0	0	0	0	0	0	0	1	15408	1074	38	1		1	SUGT1	13	53250436	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3969183	53250436	61919442	128	1202										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207478	58207478	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acagtggtcatcgatctgaaCgccaccgacgccgatgaagg	12	12	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:58207478C>T	ENST00000377918.3	+	1	824	c.798C>T	c.(796-798)aaC>aaT	p.N266N		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	266	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TCGATCTGAACGCCACCGACG	0.587																																					Melanoma(72;952 1291 1619 12849 33676)											0			13											72	63	66					13																	58207478		2203	4300	6503	57105479	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.798C>T	13.37:g.58207478C>T			57105479	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.587	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58207478	C	T	58207478	2	4	10	1	0	0	0	0	0	0	0	1	11543	535	19	1		1	PCDH17	13	58207478	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	4957042	58207478	56962400	129	1203										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67799644	67799644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcgtttagaaagggtgtcacAacccccaacaaaggtgttgt	11	9	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:67799644A>G	ENST00000377865.2	-	1	3063	c.2929T>C	c.(2929-2931)Tgt>Cgt	p.C977R	PCDH9_ENST00000328454.5_Missense_Mutation_p.C977R|PCDH9_ENST00000377861.3_Missense_Mutation_p.C977R|PCDH9_ENST00000456367.1_Missense_Mutation_p.C977R|PCDH9_ENST00000544246.1_Missense_Mutation_p.C977R			Q9HC56	PCDH9_HUMAN	protocadherin 9	977					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AGGGTGTCACAACCCCCAACA	0.498																																																0			13											137	132	134					13																	67799644		2203	4300	6503	66697645	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.2929T>C	13.37:g.67799644A>G	ENSP00000367096:p.Cys977Arg		66697645	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.495879	0.44352	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	5.63	5.63	0.86233	Protocadherin (1);	0.000000	0.85682	D	0.000000	T	0.57902	0.2085	L	0.61218	1.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.57665	-0.7772	10	0.46703	T	0.11	.	15.8249	0.78690	1.0:0.0:0.0:0.0	.	977;977;977;977	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	R	977	ENSP00000442186:C977R;ENSP00000367096:C977R;ENSP00000401699:C977R;ENSP00000332060:C977R;ENSP00000367092:C977R	ENSP00000332060:C977R	C	-	1	0	PCDH9	66697645	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.962000	0.93254	2.142000	0.66516	0.533000	0.62120	TGT		0.498	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		G	67799644	A	G	67799644	3	3	10	1	0	0	0	0	1	0	0	0	11549	130	5	4	800	4	PCDH9	13	67799644	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	9592166	67799644	47370234	130	1204										
FGF14	2259	hgsc.bcm.edu	37	chr13	103054007	103054007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tttgaaatcagttctcctgaAgaggggcaccggttttacca	10	9	2	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:103054007A>G	ENST00000376131.4	-	1	117	c.22T>C	c.(22-24)Ttc>Ctc	p.F8L	RP11-811P12.3_ENST00000418923.2_RNA	NM_175929.2	NP_787125.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	0					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTTCTCCTGAAGAGGGGCACC	0.413																																																0			13											45	44	44					13																	103054007		2203	4300	6503	101852008	SO:0001583	missense	2259				CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466			3671	protein-coding gene	gene with protein product		601515				8790420, 17236779	Standard	NM_175929		Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376131.4:c.22T>C	13.37:g.103054007A>G	ENSP00000365301:p.Phe8Leu		101852008	Q86YN7|Q96QX6	Missense_Mutation	SNP	ENST00000376131.4	37	CCDS9500.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.048395	0.36181	.	.	ENSG00000102466	ENST00000376131	T	0.79033	-1.23	4.73	4.73	0.59995	.	0.859532	0.10459	N	0.672221	T	0.68485	0.3006	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57341	-0.7828	8	.	.	.	.	14.3812	0.66911	1.0:0.0:0.0:0.0	.	8	Q92915-2	.	L	8	ENSP00000365301:F8L	.	F	-	1	0	FGF14	101852008	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.691000	0.61738	1.984000	0.57885	0.533000	0.62120	TTC		0.413	FGF14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045680.5			G	103054007	A	G	103054007	3	3	10	1	0	0	0	0	1	0	0	0	5862	72	3	4	953	4	FGF14	13	103054007	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	35254363	103054007	12115871	131	1205										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111138051	111138051	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctgtcaggaatccctgggctGcctgggaggcccggccacat	14	14	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr13:111138051G>T	ENST00000360467.5	+	34	3381	c.3075G>T	c.(3073-3075)ctG>ctT	p.L1025L		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1025	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TCCCTGGGCTGCCTGGGAGGC	0.642																																																0			13											41	49	47					13																	111138051		1885	4108	5993	109936052	SO:0001819	synonymous_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3075G>T	13.37:g.111138051G>T			109936052	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																				0.642	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		T	111138051	G	T	111138051	2	4	10	1	0	0	0	0	0	0	0	1	3696	1306	46	2		2	COL4A2	13	111138051	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	8084044	111138051	4031827	132	1206										
G2E3	55632	hgsc.bcm.edu	37	chr14	31081516	31081516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	acttataacgacattaagtgAtaaatatatgttagtaaaag	6	3	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:31081516A>G	ENST00000206595.6	+	13	1758	c.1604A>G	c.(1603-1605)gAt>gGt	p.D535G	G2E3_ENST00000553504.1_Missense_Mutation_p.D565G|G2E3_ENST00000438909.2_Missense_Mutation_p.D489G	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	535	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						ACATTAAGTGATAAATATATG	0.318																																																0			14											91	94	93					14																	31081516		2203	4295	6498	30151267	SO:0001583	missense	55632			AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1604A>G	14.37:g.31081516A>G	ENSP00000206595:p.Asp535Gly		30151267	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	37	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.501429	0.85176	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.58210	0.35;0.35;0.35	5.47	5.47	0.80525	HECT (3);	0.139939	0.64402	D	0.000005	T	0.71913	0.3396	M	0.69823	2.125	0.53005	D	0.999965	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.75280	-0.3373	10	0.72032	D	0.01	-25.9718	15.8434	0.78868	1.0:0.0:0.0:0.0	.	47;535	Q49AD9;Q7L622	.;G2E3_HUMAN	G	535;489;565	ENSP00000206595:D535G;ENSP00000391068:D489G;ENSP00000451653:D565G	ENSP00000206595:D535G	D	+	2	0	G2E3	30151267	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.760000	0.85248	2.194000	0.70268	0.454000	0.30748	GAT		0.318	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		G	31081516	A	G	31081516	3	3	10	1	0	0	0	0	1	0	0	0	6159	333	12	4	1650	4	G2E3	14	31081516	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10		31081516	76268024	133	1207										
FSCB	84075	hgsc.bcm.edu	37	chr14	44974061	44974061	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgtttgtcaacggaggcctcTtctgcagggacatcatcagc	11	11	5	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:44974061T>C	ENST00000340446.4	-	1	2421	c.2130A>G	c.(2128-2130)gaA>gaG	p.E710E	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	710						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CGGAGGCCTCTTCTGCAGGGA	0.532																																																0			14											44	49	47					14																	44974061		2203	4300	6503	44043811	SO:0001819	synonymous_variant	84075			AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2130A>G	14.37:g.44974061T>C			44043811	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																				0.532	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		C	44974061	T	C	44974061	2	2	10	1	0	0	0	0	0	0	0	1	6085	1606	56	4		4	FSCB	14	44974061	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	13892545	44974061	62375479	134	1208										
OTX2	5015	hgsc.bcm.edu	37	chr14	57269021	57269021	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctttgttttgacctccattcTgctgttgttgctgttgttgg	10	8	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:57269021T>C	ENST00000555006.1	-	4	710	c.302A>G	c.(301-303)cAg>cGg	p.Q101R	RP11-1085N6.6_ENST00000602485.1_lincRNA|OTX2_ENST00000554559.1_3'UTR|OTX2_ENST00000408990.3_Missense_Mutation_p.Q101R|OTX2_ENST00000554788.1_3'UTR|OTX2_ENST00000339475.5_Missense_Mutation_p.Q109R			P32243	OTX2_HUMAN	orthodenticle homeobox 2	101	Poly-Gln.				axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.Q109P(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					ACCTCCATTCTGCTGTTGTTG	0.448																																																1	Substitution - Missense(1)	ovary(1)	14											107	110	109					14																	57269021		2203	4300	6503	56338774	SO:0001583	missense	5015			AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.302A>G	14.37:g.57269021T>C	ENSP00000452336:p.Gln101Arg		56338774	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	37	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.183886	0.57800	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006;ENST00000554845;ENST00000555804	D;D;D;D;D	0.91843	-2.74;-2.74;-2.74;-2.79;-2.92	5.78	5.78	0.91487	.	0.000000	0.40554	N	0.001076	D	0.92364	0.7577	M	0.84326	2.69	0.80722	D	1	P;P	0.41313	0.745;0.698	B;B	0.38562	0.276;0.201	D	0.93082	0.6492	10	0.66056	D	0.02	.	14.9485	0.71050	0.0:0.0:0.0:1.0	.	109;101	F1T0D1;P32243	.;OTX2_HUMAN	R	109;101;101;109;101	ENSP00000343819:Q109R;ENSP00000386185:Q101R;ENSP00000452336:Q101R;ENSP00000451357:Q109R;ENSP00000451272:Q101R	ENSP00000343819:Q109R	Q	-	2	0	OTX2	56338774	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	8.040000	0.89188	2.212000	0.71576	0.374000	0.22700	CAG		0.448	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		C	57269021	T	C	57269021	3	2	10	1	0	0	0	0	1	0	0	0	11352	1580	55	4	571	4	OTX2	14	57269021	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	12294960	57269021	50080519	135	1209										
PPM1A	5494	hgsc.bcm.edu	37	chr14	60756550	60756550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	taaagaagcagggggaaggcGtccccgacttagtccatgtg	14	9	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:60756550G>A	ENST00000395076.4	+	4	1409	c.979G>A	c.(979-981)Gtc>Atc	p.V327I	PPM1A_ENST00000325642.3_Missense_Mutation_p.V400I|PPM1A_ENST00000529574.1_Missense_Mutation_p.V327I	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	327					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		GGGGGAAGGCGTCCCCGACTT	0.433																																																0			14											58	58	58					14																	60756550		2203	4300	6503	59826303	SO:0001583	missense	5494			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.979G>A	14.37:g.60756550G>A	ENSP00000378514:p.Val327Ile		59826303	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	G	10.91	1.483731	0.26598	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076	T;T;T	0.30182	1.54;1.56;1.56	5.36	5.36	0.76844	Protein serine/threonine phosphatase 2C, C-terminal (3);	0.050666	0.85682	D	0.000000	T	0.22859	0.0552	N	0.20845	0.615	0.51767	D	0.99993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.05733	-1.0867	10	0.17832	T	0.49	.	19.4366	0.94798	0.0:0.0:1.0:0.0	.	327;327	P35813;B2R8E4	PPM1A_HUMAN;.	I	400;327;327	ENSP00000327255:V400I;ENSP00000432966:V327I;ENSP00000378514:V327I	ENSP00000327255:V400I	V	+	1	0	PPM1A	59826303	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.300000	0.72776	2.669000	0.90835	0.585000	0.79938	GTC		0.433	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003		A	60756550	G	A	60756550	3	1	10	1	0	0	0	0	1	0	0	0	12369	1145	40	1	1235	1	PPM1A	14	60756550	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3487529	60756550	46592990	136	1210										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60923731	60923731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aaaatataggaatttcagacGttcgtggaaaattctcagct	8	6	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:60923731G>A	ENST00000321731.3	-	15	1421	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	421					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		AATTTCAGACGTTCGTGGAAA	0.378																																																0			14											96	111	106					14																	60923731		2203	4297	6500	59993484	SO:0001583	missense	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1262C>T	14.37:g.60923731G>A	ENSP00000324920:p.Thr421Met		59993484	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	6.904	0.536431	0.13188	.	.	ENSG00000179008	ENST00000321731	T	0.27104	1.69	5.32	3.42	0.39159	.	0.196858	0.39274	N	0.001403	T	0.44829	0.1312	M	0.65975	2.015	0.29488	N	0.855838	D	0.89917	1.0	D	0.70487	0.969	T	0.39800	-0.9596	10	0.51188	T	0.08	-4.9895	10.5389	0.45020	0.0:0.0:0.6486:0.3514	.	421	Q8N1H7	S6OS1_HUMAN	M	421	ENSP00000324920:T421M	ENSP00000324920:T421M	T	-	2	0	C14orf39	59993484	0.998000	0.40836	0.989000	0.46669	0.017000	0.09413	1.693000	0.37742	0.750000	0.32877	0.563000	0.77884	ACG		0.378	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		A	60923731	G	A	60923731	3	1	10	1	0	0	0	0	1	0	0	0	1776	1145	40	1	517	1	C14orf39	14	60923731	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	167181	60923731	46425809	137	1211										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86088591	86088591	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tacgtaattcgctgtcccacCctcctcccgatctcccaggt	6	18	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:86088591C>G	ENST00000330753.4	+	2	1500	c.733C>G	c.(733-735)Cct>Gct	p.P245A	FLRT2_ENST00000554746.1_Missense_Mutation_p.P245A	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	245					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GCTGTCCCACCCTCCTCCCGA	0.512																																																0			14											85	84	84					14																	86088591		2203	4300	6503	85158344	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.733C>G	14.37:g.86088591C>G	ENSP00000332879:p.Pro245Ala		85158344	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.634803	0.47049	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.02301	4.35;4.35	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.05686	0.0149	N	0.12569	0.235	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.65965	-0.6040	10	0.21540	T	0.41	-21.0308	20.4043	0.99006	0.0:1.0:0.0:0.0	.	245	O43155	FLRT2_HUMAN	A	245	ENSP00000332879:P245A;ENSP00000451050:P245A	ENSP00000332879:P245A	P	+	1	0	FLRT2	85158344	1.000000	0.71417	0.351000	0.25721	0.866000	0.49608	7.817000	0.86213	2.823000	0.97156	0.650000	0.86243	CCT		0.512	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			G	86088591	C	G	86088591	3	3	10	1	0	0	0	0	1	0	0	0	5958	623	22	5	735	5	FLRT2	14	86088591	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	25164860	86088591	21260949	138	1212										
SERPINA6	866	hgsc.bcm.edu	37	chr14	94780520	94780520	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtcctggaaattcatagccaAgacctctgactcatagtagt	8	10	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr14:94780520A>G	ENST00000341584.3	-	2	612	c.466T>C	c.(466-468)Ttg>Ctg	p.L156L		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	156					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TTCATAGCCAAGACCTCTGAC	0.468																																																0			14											130	127	128					14																	94780520		2203	4300	6503	93850273	SO:0001819	synonymous_variant	866			J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"Serine (or cysteine) peptidase inhibitors"	1540	protein-coding gene	gene with protein product	"corticosteroid binding globulin", "transcortin"	122500	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.466T>C	14.37:g.94780520A>G			93850273	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																				0.468	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756		G	94780520	A	G	94780520	2	3	10	1	0	0	0	0	0	0	0	1	14130	69	3	4		4	SERPINA6	14	94780520	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	8691929	94780520	12569020	139	1213										
C15orf33	196951	hgsc.bcm.edu	37	chr15	49834000	49834000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttgtgccaaacaatcaggatAtatctaccaaaataaaatca	4	8	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr15:49834000A>G	ENST00000299338.6	-	10	1054	c.751T>C	c.(751-753)Tat>Cat	p.Y251H	FAM227B_ENST00000561064.1_Missense_Mutation_p.Y217H	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	251																	CAATCAGGATATATCTACCaa	0.274																																																0			15											54	57	56					15																	49834000		2193	4287	6480	47621292	SO:0001583	missense	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.751T>C	15.37:g.49834000A>G	ENSP00000299338:p.Tyr251His		47621292	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	37	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.007478	0.75046	.	.	ENSG00000166262	ENST00000299338;ENST00000354658	.	.	.	5.7	5.7	0.88788	.	0.000000	0.49305	D	0.000151	T	0.78748	0.4332	M	0.77103	2.36	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.68483	0.958;0.91	T	0.81765	-0.0783	9	0.87932	D	0	-1.2206	14.9375	0.70967	1.0:0.0:0.0:0.0	.	217;251	Q96M60-2;Q96M60	.;CO033_HUMAN	H	251;217	.	ENSP00000299338:Y251H	Y	-	1	0	C15orf33	47621292	1.000000	0.71417	0.860000	0.33809	0.957000	0.61999	5.930000	0.70104	2.165000	0.68154	0.523000	0.50628	TAT		0.274	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		G	49834000	A	G	49834000	3	3	10	1	0	0	0	0	1	0	0	0	1795	449	16	4	803	4	C15orf33	15	49834000	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10		49834000	52697392	140	1214										
HERC1	8925	hgsc.bcm.edu	37	chr15	63940272	63940272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttaaagatgcatttaccttaTgtgcatcaattagaacaatg	6	6	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr15:63940272T>C	ENST00000443617.2	-	55	10961	c.10874A>G	c.(10873-10875)cAt>cGt	p.H3625R		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3625					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ATTTACCTTATGTGCATCAAT	0.338																																																0			15											81	67	71					15																	63940272		1847	4072	5919	61727325	SO:0001583	missense	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.10874A>G	15.37:g.63940272T>C	ENSP00000390158:p.His3625Arg		61727325	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643944	0.67244	.	.	ENSG00000103657	ENST00000443617	T	0.81163	-1.46	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.066712	0.64402	U	0.000019	D	0.87509	0.6195	M	0.93283	3.4	0.80722	D	1	P	0.35208	0.49	B	0.39771	0.309	D	0.89231	0.3577	10	0.66056	D	0.02	.	15.8998	0.79365	0.0:0.0:0.0:1.0	.	3625	Q15751	HERC1_HUMAN	R	3625	ENSP00000390158:H3625R	ENSP00000390158:H3625R	H	-	2	0	HERC1	61727325	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	7.636000	0.83301	2.165000	0.68154	0.260000	0.18958	CAT		0.338	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63940272	T	C	63940272	3	2	10	1	0	0	0	0	1	0	0	0	7078	1464	51	4	3807	4	HERC1	15	63940272	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	14106272	63940272	38591120	141	1215										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75648559	75648559	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggcgctgggggctgctctccGcctgcagaggaacacgtctg	16	13	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr15:75648559G>A	ENST00000267978.5	-	25	2934	c.2888C>T	c.(2887-2889)gCg>gTg	p.A963V	RP11-817O13.6_ENST00000563660.1_lincRNA|MIR631_ENST00000384904.1_RNA|MAN2C1_ENST00000569482.1_Splice_Site_p.A940V|MAN2C1_ENST00000565683.1_Splice_Site_p.A980V|MAN2C1_ENST00000563622.1_Splice_Site_p.A864V	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	963					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						GCTGCTCTCCGCCTGCAGAGG	0.687																																																0			15											20	21	21					15																	75648559		2193	4286	6479	73435612	SO:0001630	splice_region_variant	4123			AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.2887-1C>T	15.37:g.75648559G>A			73435612	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	37	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044969	0.75846	.	.	ENSG00000140400	ENST00000267978	D	0.82619	-1.63	4.54	4.54	0.55810	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.165226	0.52532	N	0.000061	D	0.92163	0.7515	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.987	D	0.93602	0.6931	10	0.72032	D	0.01	-11.3511	16.0095	0.80391	0.0:0.0:1.0:0.0	.	940;963	Q68EM8;Q9NTJ4	.;MA2C1_HUMAN	V	963	ENSP00000267978:A963V	ENSP00000267978:A963V	A	-	2	0	MAN2C1	73435612	1.000000	0.71417	0.927000	0.36925	0.119000	0.20118	6.926000	0.75835	2.376000	0.81061	0.462000	0.41574	GCG		0.687	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		Missense_Mutation	A	75648559	G	A	75648559	5	1	10	1	0	0	0	0	0	0	1	0	9248	1101	38	1	242	1	MAN2C1	15	75648559	Splice_Site	SNP	G	TCGA-AF-6136-01A-11D-1826-10	11708287	75648559	26882833	142	1216										
SCAPER	49855	hgsc.bcm.edu	37	chr15	76995212	76995212	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aggacattgcagagagaacaCtgcttctttctttcataagg	9	8	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr15:76995212C>T	ENST00000563290.1	-	19	2474	c.2379G>A	c.(2377-2379)caG>caA	p.Q793Q	SCAPER_ENST00000538941.2_Silent_p.Q547Q|SCAPER_ENST00000324767.7_Silent_p.Q793Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	793						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						AGAGAGAACACTGCTTCTTTC	0.368																																																0			15											116	116	116					15																	76995212		1870	4099	5969	74782267	SO:0001819	synonymous_variant	49855			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.2379G>A	15.37:g.76995212C>T			74782267	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																				0.368	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	76995212	C	T	76995212	2	4	10	1	0	0	0	0	0	0	0	1	13915	564	20	3		3	SCAPER	15	76995212	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	1346653	76995212	25536180	143	1217										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88678529	88678529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcagaggctgcccattgtgcAgccagtgcagcgttggtggg	17	10	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr15:88678529A>G	ENST00000360948.2	-	9	1168	c.1007T>C	c.(1006-1008)cTg>cCg	p.L336P	NTRK3_ENST00000357724.2_Missense_Mutation_p.L336P|NTRK3_ENST00000558676.1_Missense_Mutation_p.L336P|NTRK3_ENST00000394480.2_Missense_Mutation_p.L336P|NTRK3_ENST00000542733.2_Missense_Mutation_p.L238P|NTRK3_ENST00000355254.2_Missense_Mutation_p.L336P|NTRK3_ENST00000557856.1_Missense_Mutation_p.L336P|NTRK3_ENST00000540489.2_Missense_Mutation_p.L336P|NTRK3_ENST00000317501.3_Missense_Mutation_p.L336P	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	336	Ig-like C2-type 2.		L -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L336Q(2)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCCATTGTGCAGCCAGTGCAG	0.607			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	2	Substitution - Missense(2)	lung(2)	15											82	84	83					15																	88678529		2201	4299	6500	86479533	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1007T>C	15.37:g.88678529A>G	ENSP00000354207:p.Leu336Pro		86479533	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858573	0.71834	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.223524	0.40222	N	0.001151	D	0.89767	0.6810	H	0.95816	3.725	0.80722	D	1	D;D;P;D;D;P	0.89917	0.997;0.966;0.956;1.0;0.967;0.956	D;P;D;D;P;D	0.72338	0.93;0.77;0.936;0.977;0.73;0.936	D	0.92618	0.6105	10	0.72032	D	0.01	.	14.4172	0.67158	1.0:0.0:0.0:0.0	.	238;336;336;336;336;336	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	P	336;336;336;336;238;336;336	ENSP00000377990:L336P;ENSP00000354207:L336P;ENSP00000350356:L336P;ENSP00000347397:L336P;ENSP00000437773:L238P;ENSP00000444673:L336P;ENSP00000318328:L336P	ENSP00000318328:L336P	L	-	2	0	NTRK3	86479533	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.874000	0.75546	1.988000	0.58038	0.460000	0.39030	CTG		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				G	88678529	A	G	88678529	3	3	10	1	0	0	0	0	1	0	0	0	10739	188	7	4	1818	4	NTRK3	15	88678529	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	11683317	88678529	13852863	144	1218										
SRL	6345	hgsc.bcm.edu	37	chr16	4254628	4254628	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcttcttcatttgcatcctcCgtctcttctgtggagagaag	9	11	4	1	rs369887184		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:4254628C>T	ENST00000399609.3	-	2	81	c.69G>A	c.(67-69)acG>acA	p.T23T	SRL_ENST00000537996.1_5'UTR	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	482	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						TTGCATCCTCCGTCTCTTCTG	0.572																																																0			16						C		1,3857		0,1,1928	104	103	103		69	-10.6	0	16		103	0,8280		0,0,4140	no	coding-synonymous	SRL	NM_001098814.1		0,1,6068	TT,TC,CC		0.0,0.0259,0.0082		23/474	4254628	1,12137	1929	4140	6069	4194629	SO:0001819	synonymous_variant	6345			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.69G>A	16.37:g.4254628C>T			4194629		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																				0.572	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		T	4254628	C	T	4254628	2	4	10	1	0	0	0	0	0	0	0	1	15189	639	23	1		1	SRL	16	4254628	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10		4254628	86100125	145	1219										
CIITA	4261	hgsc.bcm.edu	37	chr16	10971207	10971207	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aatgcgttgcctggctccacGccctgctgggtcctacctgt	11	15	0	0	rs374703179		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:10971207G>A	ENST00000324288.8	+	1	153	c.20G>A	c.(19-21)cGc>cAc	p.R7H	CIITA_ENST00000381835.5_Missense_Mutation_p.R7H|RP11-876N24.2_ENST00000572017.1_RNA|RP11-876N24.2_ENST00000573071.1_RNA|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	7					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CTGGCTCCACGCCCTGCTGGG	0.587			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	0			16						G	HIS/ARG	0,4394		0,0,2197	62	57	59		20	-4.7	0	16		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	CIITA	NM_000246.3	29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	7/1131	10971207	1,12993	2197	4300	6497	10878708	SO:0001583	missense	4261			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.20G>A	16.37:g.10971207G>A	ENSP00000316328:p.Arg7His		10878708	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.634063	0.00806	0.0	1.16E-4	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.72725	-0.68;1.63	2.94	-4.73	0.03259	.	.	.	.	.	T	0.49355	0.1552	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.20042	-1.0287	9	0.37606	T	0.19	.	6.3865	0.21563	0.4919:0.1306:0.3775:0.0	.	7;7;7;7;7;7	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	H	7	ENSP00000316328:R7H;ENSP00000371257:R7H	ENSP00000316328:R7H	R	+	2	0	CIITA	10878708	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-0.948000	0.03897	-1.632000	0.01541	-1.786000	0.00637	CGC		0.587	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	10971207	G	A	10971207	3	1	10	1	0	0	0	0	1	0	0	0	3434	1087	38	1	22	1	CIITA	16	10971207	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	6716579	10971207	79383546	146	1220										
BFAR	51283	hgsc.bcm.edu	37	chr16	14743685	14743685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcctgctcgtctatcactggAgcagcagggaatctgaacac	10	12	3	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:14743685A>G	ENST00000261658.2	+	4	770	c.493A>G	c.(493-495)Agc>Ggc	p.S165G	BFAR_ENST00000563971.1_Intron|BFAR_ENST00000426842.2_Missense_Mutation_p.S37G	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	165					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						CTATCACTGGAGCAGCAGGGA	0.572																																																0			16											83	78	80					16																	14743685		2197	4300	6497	14651186	SO:0001583	missense	51283			AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"RING-type (C3HC4) zinc fingers", "Sterile alpha motif (SAM) domain containing"	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.493A>G	16.37:g.14743685A>G	ENSP00000261658:p.Ser165Gly		14651186	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.408562	0.42715	.	.	ENSG00000103429	ENST00000261658;ENST00000426842	T;T	0.48201	3.19;0.82	5.35	3.04	0.35103	.	0.147966	0.64402	N	0.000005	T	0.32436	0.0829	L	0.34521	1.04	0.42239	D	0.991925	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.07385	-1.0775	10	0.33141	T	0.24	-13.5849	7.1432	0.25568	0.775:0.1478:0.0772:0.0	.	37;165	B4DUT0;Q9NZS9	.;BFAR_HUMAN	G	165;37	ENSP00000261658:S165G;ENSP00000400634:S37G	ENSP00000261658:S165G	S	+	1	0	BFAR	14651186	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.749000	0.55150	0.316000	0.23135	0.379000	0.24179	AGC		0.572	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		G	14743685	A	G	14743685	3	3	10	1	0	0	0	0	1	0	0	0	1415	304	11	4	503	4	BFAR	16	14743685	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	3772478	14743685	75611068	147	1221										
SMG1	23049	hgsc.bcm.edu	37	chr16	18841685	18841685	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aattcaccgtactgagcatgTagtagtctacagaaaaacaa	7	8	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:18841685T>C	ENST00000446231.2	-	52	9211	c.8799A>G	c.(8797-8799)ctA>ctG	p.L2933L	SMG1_ENST00000389467.3_Silent_p.L2933L			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2933					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L2929L(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACTGAGCATGTAGTAGTCTAC	0.423																																																1	Substitution - coding silent(1)	lung(1)	16											68	63	65					16																	18841685		1867	4109	5976	18749186	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8799A>G	16.37:g.18841685T>C			18749186	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.423	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18841685	T	C	18841685	2	2	10	1	0	0	0	0	0	0	0	1	14832	1625	57	4		4	SMG1	16	18841685	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	4098000	18841685	71513068	148	1222										
OTOA	146183	hgsc.bcm.edu	37	chr16	21698933	21698933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gccagacatcacagagcggcTccctcgggacctgcgcgagg	14	15	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:21698933T>C	ENST00000286149.4	+	7	600	c.599T>C	c.(598-600)cTc>cCc	p.L200P	OTOA_ENST00000388956.4_Missense_Mutation_p.L121P|OTOA_ENST00000388958.3_Missense_Mutation_p.L200P			Q7RTW8	OTOAN_HUMAN	otoancorin	200					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		ACAGAGCGGCTCCCTCGGGAC	0.532																																																0			16											41	39	39					16																	21698933		2199	4300	6499	21606434	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.599T>C	16.37:g.21698933T>C	ENSP00000286149:p.Leu200Pro		21606434	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	T	13.09	2.132888	0.37630	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.26518	1.73;1.73;1.73	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000005	T	0.47414	0.1444	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.49133	-0.8971	10	0.72032	D	0.01	-9.7355	11.771	0.51958	0.0:0.0:0.0:1.0	.	121;200	B3KWU3;E9PF51	.;.	P	200;200;121	ENSP00000373610:L200P;ENSP00000286149:L200P;ENSP00000373608:L121P	ENSP00000286149:L200P	L	+	2	0	OTOA	21606434	1.000000	0.71417	0.376000	0.26042	0.151000	0.21798	5.478000	0.66806	1.661000	0.50771	0.451000	0.29950	CTC		0.532	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			C	21698933	T	C	21698933	3	2	10	1	0	0	0	0	1	0	0	0	11333	1551	54	4	659	4	OTOA	16	21698933	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	2857248	21698933	68655820	149	1223										
CDH1	999	hgsc.bcm.edu	37	chr16	68845617	68845617	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gatggaggtcacagccacagAcgcggacgatgatgtgaaca	14	9	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:68845617A>G	ENST00000261769.5	+	7	1054	c.863A>G	c.(862-864)gAc>gGc	p.D288G	CDH1_ENST00000422392.2_Missense_Mutation_p.D288G|CDH1_ENST00000562836.1_3'UTR|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	288	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.E283fs*4(1)|p.D288fs*3(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		ACAGCCACAGACGCGGACGAT	0.493			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	3	Unknown(1)|Complex - frameshift(1)|Deletion - Frameshift(1)	breast(3)	16											115	99	105					16																	68845617		2198	4300	6498	67403118	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.863A>G	16.37:g.68845617A>G	ENSP00000261769:p.Asp288Gly		67403118	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.585741	0.86748	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.74737	-0.87;-0.87	5.19	5.19	0.71726	Cadherin (5);Cadherin-like (1);	0.000000	0.52532	D	0.000066	D	0.91540	0.7328	H	0.98682	4.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94689	0.7872	10	0.87932	D	0	.	15.0395	0.71777	1.0:0.0:0.0:0.0	.	288;288	Q9UII8;P12830	.;CADH1_HUMAN	G	288	ENSP00000261769:D288G;ENSP00000414946:D288G	ENSP00000261769:D288G	D	+	2	0	CDH1	67403118	1.000000	0.71417	0.157000	0.22605	0.867000	0.49689	8.962000	0.93254	2.090000	0.63153	0.459000	0.35465	GAC		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68845617	A	G	68845617	3	3	10	1	0	0	0	0	1	0	0	0	3101	275	10	4	889	4	CDH1	16	68845617	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	47146684	68845617	21509136	150	1224										
MAF	4094	hgsc.bcm.edu	37	chr16	79633485	79633485	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcctcggggctgaagcccagCgcctcggggttcagctgctg	15	14	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:79633485C>A	ENST00000393350.1	-	1	1126	c.315G>T	c.(313-315)gcG>gcT	p.A105A	MAF_ENST00000569649.1_Silent_p.A105A|MAF_ENST00000326043.4_Silent_p.A105A	NM_001031804.2	NP_001026974.1	O75444	MAF_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog	105					cell development (GO:0048468)|cytokine production (GO:0001816)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of chondrocyte differentiation (GO:0032330)|transcription from RNA polymerase II promoter (GO:0006366)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)	10		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)		TGAAGCCCAGCGCCTCGGGGT	0.706			T	IGH@	MM																																		Dom	yes		16	16q22-q23	4094	v-maf musculoaponeurotic fibrosarcoma oncogene homolog		L	0			16											7	9	8					16																	79633485		1912	3886	5798	78190986	SO:0001819	synonymous_variant	4094				CCDS10928.1, CCDS42198.1	16q22-q23	2013-07-09	2013-07-09		ENSG00000178573	ENSG00000178573			6776	protein-coding gene	gene with protein product		177075				14998484	Standard	NM_005360		Approved	c-MAF	uc002ffm.3	O75444	OTTHUMG00000137621	ENST00000393350.1:c.315G>T	16.37:g.79633485C>A			78190986	Q66I47|Q9UP93	Silent	SNP	ENST00000393350.1	37	CCDS42198.1																																																																																				0.706	MAF-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317037.1			A	79633485	C	A	79633485	2	1	10	1	0	0	0	0	0	0	0	1	9185	755	27	2		2	MAF	16	79633485	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	10787868	79633485	10721268	151	1225										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81167282	81167282	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atccctgctgctgtttcttcGtgctcggaacaaggcatagg	11	11	1	0	rs547588970		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:81167282G>A	ENST00000534142.1	-	0	131				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000533478.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTGTTTCTTCGTGCTCGGAAC	0.562													G|||	1	0.000199681	8e-04	0	5008	,	,		19033	0		0	False		,,,				2504	0															0			16											97	97	97					16																	81167282		2090	4229	6319	79724783			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81167282G>A			79724783	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000534142.1	37																																																																																					0.562	PKD1L2-009	PUTATIVE	basic|exp_conf	processed_transcript	polymorphic_pseudogene	OTTHUMT00000387969.1			A	81167282	G	A	81167282	1	1	10	0	1	0	0	0	0	0	0	0	11996	1153	40	1		1	PKD1L2	16	81167282	RNA	SNP	G	TCGA-AF-6136-01A-11D-1826-10	1533797	81167282	9187471	152	1226										
CDH13	1012	hgsc.bcm.edu	37	chr16	83817013	83817013	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aattccaaagtggactgcaaCgcggcaggggccctgcgctt	13	12	0	0	rs374049780		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:83817013C>T	ENST00000566620.1	+	13	2360	c.2070C>T	c.(2068-2070)aaC>aaT	p.N690N	CDH13_ENST00000428848.3_Silent_p.N651N|CDH13_ENST00000268613.10_Silent_p.N737N	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	690	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TGGACTGCAACGCGGCAGGGG	0.542																																																0			16						C	,,,	0,4018		0,0,2009	90	89	90		2211,1953,1308,2070	-1.5	0	16		90	1,8347		0,1,4173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,1,6182	TT,TC,CC		0.012,0.0,0.0081	,,,	737/761,651/675,436/460,690/714	83817013	1,12365	2009	4174	6183	82374514	SO:0001819	synonymous_variant	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.2070C>T	16.37:g.83817013C>T			82374514	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																				0.542	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		T	83817013	C	T	83817013	2	4	10	1	0	0	0	0	0	0	0	1	3105	535	19	1		1	CDH13	16	83817013	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	2649731	83817013	6537740	153	1227										
CBFA2T3	863	hgsc.bcm.edu	37	chr16	88951498	88951498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gctcccgggggtctgggtggCggtaggcatctcggaagtgg	20	9	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:88951498C>T	ENST00000268679.4	-	7	1469	c.1073G>A	c.(1072-1074)cGc>cAc	p.R358H	CBFA2T3_ENST00000327483.5_Missense_Mutation_p.R272H|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.R272H|RP11-830F9.5_ENST00000562405.1_RNA|RP11-830F9.5_ENST00000565053.1_RNA|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.R282H|CBFA2T3_ENST00000436887.2_Missense_Mutation_p.R320H|RP11-830F9.5_ENST00000569249.1_RNA|RP11-830F9.5_ENST00000562574.1_RNA	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	358	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		GTCTGGGTGGCGGTAGGCATC	0.701			T	RUNX1	AML																																		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	0			16											71	63	66					16																	88951498		2191	4294	6485	87478999	SO:0001583	missense	863			AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.1073G>A	16.37:g.88951498C>T	ENSP00000268679:p.Arg358His		87478999	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.193536	0.78902	.	.	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.51071	1.34;0.72;0.72;1.33;1.34	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.68805	0.3041	M	0.76574	2.34	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;1.0;0.738	D;D;D;B	0.78314	0.991;0.98;0.985;0.263	T	0.73720	-0.3894	10	0.72032	D	0.01	-8.7407	17.146	0.86767	0.0:1.0:0.0:0.0	.	320;358;358;272	E7EU24;B2RBQ7;O75081;O75081-2	.;.;MTG16_HUMAN;.	H	272;358;320;282;272	ENSP00000332122:R272H;ENSP00000268679:R358H;ENSP00000395739:R320H;ENSP00000401254:R282H;ENSP00000353449:R272H	ENSP00000268679:R358H	R	-	2	0	CBFA2T3	87478999	0.441000	0.25626	0.879000	0.34478	0.385000	0.30292	1.624000	0.37018	2.434000	0.82447	0.561000	0.74099	CGC		0.701	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		T	88951498	C	T	88951498	3	4	10	1	0	0	0	0	1	0	0	0	2704	768	27	1	912	1	CBFA2T3	16	88951498	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	5134485	88951498	1403255	154	1228										
DEF8	54849	hgsc.bcm.edu	37	chr16	90030715	90030715	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aagcacatcaagctggactgCgaggtgggcctctgcccgag	14	12	2	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr16:90030715C>T	ENST00000268676.7	+	11	1412	c.1323C>T	c.(1321-1323)tgC>tgT	p.C441C	DEF8_ENST00000570182.1_Silent_p.C370C|DEF8_ENST00000567874.1_Silent_p.C320C|DEF8_ENST00000563594.1_Silent_p.C380C|DEF8_ENST00000569453.1_Silent_p.C380C|DEF8_ENST00000563795.1_Silent_p.C363C	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	441					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		AGCTGGACTGCGAGGTGGGCC	0.662																																																0			16											28	24	26					16																	90030715		2197	4300	6497	88558216	SO:0001819	synonymous_variant	54849			AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1323C>T	16.37:g.90030715C>T			88558216	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																				0.662	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		T	90030715	C	T	90030715	2	4	10	1	0	0	0	0	0	0	0	1	4393	776	27	1		1	DEF8	16	90030715	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	1079217	90030715	324038	155	1229										
PLD2	5338	hgsc.bcm.edu	37	chr17	4722835	4722835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	catgaatggggcagagtatcAggcgggcaggtttgccttga	16	7	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:4722835A>G	ENST00000263088.6	+	23	2551	c.2420A>G	c.(2419-2421)cAg>cGg	p.Q807R	PLD2_ENST00000572940.1_Missense_Mutation_p.Q807R	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	807			Q -> E (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	GCAGAGTATCAGGCGGGCAGG	0.612																																																0			17											110	80	90					17																	4722835		2203	4300	6503	4669801	SO:0001583	missense	5338			AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.2420A>G	17.37:g.4722835A>G	ENSP00000263088:p.Gln807Arg		4669801	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.095432	0.56075	.	.	ENSG00000129219	ENST00000263088	T	0.07327	3.2	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.09024	0.0223	L	0.47016	1.485	0.58432	D	0.999997	B;B	0.31790	0.34;0.034	B;B	0.33799	0.17;0.032	T	0.24404	-1.0161	10	0.22109	T	0.4	-24.4379	11.6184	0.51102	1.0:0.0:0.0:0.0	.	807;807	O14939-2;O14939	.;PLD2_HUMAN	R	807	ENSP00000263088:Q807R	ENSP00000263088:Q807R	Q	+	2	0	PLD2	4669801	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	6.473000	0.73572	1.859000	0.53934	0.460000	0.39030	CAG		0.612	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		G	4722835	A	G	4722835	3	3	10	1	0	0	0	0	1	0	0	0	12077	188	7	4	2506	4	PLD2	17	4722835	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10		4722835	76472375	156	1230										
TP53	7157	hgsc.bcm.edu	37	chr17	7576915	7576915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctggggagaggagctggtgtTgttgggcagtgctaggaaag	20	4	0	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:7576915T>C	ENST00000269305.4	-	9	1120	c.931A>G	c.(931-933)Aac>Gac	p.N311D	TP53_ENST00000445888.2_Missense_Mutation_p.N311D|TP53_ENST00000359597.4_Missense_Mutation_p.N311D|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.N311D|TP53_ENST00000420246.2_Missense_Mutation_p.N311D	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	311	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		N -> H (in sporadic cancers; somatic mutation).|N -> K (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation; dbSNP:rs56184981).|N -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(2)|p.N311H(1)|p.A307fs*34(1)|p.L308fs*15(1)|p.L308fs*31(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAGCTGGTGTTGTTGGGCAGT	0.483		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	14	Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(2)|Substitution - Missense(1)	bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|lung(1)|breast(1)	17											134	122	126					17																	7576915		2203	4300	6503	7517640	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.931A>G	17.37:g.7576915T>C	ENSP00000269305:p.Asn311Asp		7517640	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	5.436	0.265511	0.10294	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99730	-5.73;-5.45;-5.73;-5.74;-5.45;-6.56	5.16	-0.0565	0.13805	.	3.998070	0.00766	N	0.001171	D	0.98454	0.9485	L	0.39245	1.2	0.09310	N	1	B;B;B;B	0.20988	0.0;0.05;0.0;0.0	B;B;B;B	0.20767	0.003;0.031;0.0;0.001	D	0.99826	1.1050	10	0.33141	T	0.24	-0.4377	3.5917	0.07991	0.166:0.3296:0.0:0.5044	.	311;311;311;311	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	D	311;311;311;311;311;300;179	ENSP00000352610:N311D;ENSP00000269305:N311D;ENSP00000398846:N311D;ENSP00000391127:N311D;ENSP00000391478:N311D;ENSP00000425104:N179D	ENSP00000269305:N311D	N	-	1	0	TP53	7517640	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-0.606000	0.05654	-0.208000	0.10171	0.459000	0.35465	AAC		0.483	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7576915	T	C	7576915	3	2	10	1	0	0	0	0	1	0	0	0	16421	1812	63	4	351	4	TP53	17	7576915	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	2854080	7576915	73618295	157	1231										
TP53	7157	hgsc.bcm.edu	37	chr17	7579406	7579407	+	Frame_Shift_Ins	INS	-	-	AC													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctgggaagggacagaagatgINSacaggggccaggagggggct							TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:7579406_7579407insAC	ENST00000269305.4	-	4	469_470	c.280_281insGT	c.(280-282)tcafs	p.S94fs	TP53_ENST00000445888.2_Frame_Shift_Ins_p.S94fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.S94fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Frame_Shift_Ins_p.S94fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.S94fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.S94fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	94	Interaction with WWOX.		S -> L (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S94*(3)|p.G59fs*23(3)|p.S94T(2)|p.V73fs*9(1)|p.S94fs*29(1)|p.S94fs*54(1)|p.A88fs*52(1)|p.W91fs*13(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GACAGAAGATGACAGGGGCCAG	0.624		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	24	Deletion - Frameshift(11)|Whole gene deletion(8)|Substitution - Nonsense(3)|Substitution - Missense(2)	bone(4)|upper_aerodigestive_tract(3)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|stomach(1)|urinary_tract(1)|liver(1)	17																																								7520132	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.279_280dupGT	17.37:g.7579407_7579408dupAC	ENSP00000269305:p.Ser94fs		7520131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.624	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		AC	7579407	-	AC	7579406	7	5	10	1	0	1	1	0	0	0	0	0	16421	1294	45	0	1021	0	TP53	17	7579406	Frame_Shift_Ins	INS	-	TCGA-AF-6136-01A-11D-1826-10	2491	7579406	73615804	158	1232	6	2								
TP53	7157	hgsc.bcm.edu	37	chr17	7579410	7579410	+	Missense_Mutation	SNP	G	G	C													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggaagggacagaagatgacaGgggccaggagggggctggtg							TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:7579410G>C	ENST00000269305.4	-	4	466	c.277C>G	c.(277-279)Ctg>Gtg	p.L93V	TP53_ENST00000445888.2_Missense_Mutation_p.L93V|TP53_ENST00000359597.4_Missense_Mutation_p.L93V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.L93V|TP53_ENST00000455263.2_Missense_Mutation_p.L93V|TP53_ENST00000420246.2_Missense_Mutation_p.L93V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	93	Interaction with WWOX.		L -> M (in a sporadic cancer; somatic mutation).|L -> P (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L93fs*30(4)|p.G59fs*23(3)|p.V73fs*9(1)|p.A88fs*52(1)|p.L93M(1)|p.W91fs*13(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAAGATGACAGGGGCCAGGAG	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	22	Deletion - Frameshift(13)|Whole gene deletion(8)|Substitution - Missense(1)	breast(6)|lung(4)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)	17											45	50	48					17																	7579410		2203	4300	6503	7520135	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.277C>G	17.37:g.7579410G>C	ENSP00000269305:p.Leu93Val		7520135	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.290267	0.40494	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99388	-5.3;-5.81;-5.53;-5.81;-5.81;-5.53;-4.16;-2.22	4.41	3.36	0.38483	.	0.210998	0.39687	N	0.001299	D	0.98169	0.9395	L	0.27053	0.805	0.31473	N	0.668074	P;D;B;B;B;B;B	0.76494	0.861;0.999;0.072;0.032;0.087;0.161;0.052	B;D;B;B;B;B;B	0.65010	0.277;0.931;0.129;0.014;0.082;0.082;0.013	D	0.95613	0.8674	10	0.28530	T	0.3	-16.6904	9.0956	0.36636	0.0:0.0:0.7815:0.2185	.	54;93;93;93;93;93;93	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	93	ENSP00000410739:L93V;ENSP00000352610:L93V;ENSP00000269305:L93V;ENSP00000398846:L93V;ENSP00000391127:L93V;ENSP00000391478:L93V;ENSP00000424104:L93V;ENSP00000426252:L93V	ENSP00000269305:L93V	L	-	1	2	TP53	7520135	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	1.247000	0.32815	2.450000	0.82876	0.561000	0.74099	CTG		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7579410	G	C	7579410	3	2	10	1	0	0	0	0	1	0	0	0	16421	991	35	5	1025	5	TP53	17	7579410	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	4	7579410	73615800	159	1233	6	2								
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30621389	30621389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcatccacgttacttgaagaActccctggtttaccacccac	5	15	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:30621389A>G	ENST00000269051.4	+	5	610	c.596A>G	c.(595-597)aAc>aGc	p.N199S	RHBDL3_ENST00000536287.1_Missense_Mutation_p.N101S|RHBDL3_ENST00000538145.1_Missense_Mutation_p.N191S	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	199						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				TACTTGAAGAACTCCCTGGTT	0.488																																																0			17											191	155	167					17																	30621389		2203	4300	6503	27645502	SO:0001583	missense	162494			AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.596A>G	17.37:g.30621389A>G	ENSP00000269051:p.Asn199Ser		27645502	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	37	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	A	7.065	0.567181	0.13560	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145;ENST00000536287	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	6.17	6.17	0.99709	.	0.085621	0.85682	D	0.000000	T	0.03348	0.0097	N	0.01493	-0.835	0.46586	D	0.99911	P;B;B	0.38020	0.615;0.002;0.002	B;B;B	0.29267	0.1;0.004;0.004	T	0.43310	-0.9399	10	0.02654	T	1	-40.8496	16.8222	0.85835	1.0:0.0:0.0:0.0	.	199;191;199	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	S	199;199;191;101	ENSP00000394849:N199S;ENSP00000269051:N199S;ENSP00000442092:N191S;ENSP00000466508:N101S	ENSP00000269051:N199S	N	+	2	0	RHBDL3	27645502	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.174000	0.77620	2.371000	0.80710	0.533000	0.62120	AAC		0.488	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		G	30621389	A	G	30621389	3	3	10	1	0	0	0	0	1	0	0	0	13360	43	2	4	614	4	RHBDL3	17	30621389	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	23041979	30621389	50573821	160	1234										
CUEDC1	404093	hgsc.bcm.edu	37	chr17	55945533	55945533	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctgatgcttcaacaagtgttTcctctttgacttcctcattt	5	11	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:55945533T>A	ENST00000577830.1	-	8	1425	c.1012A>T	c.(1012-1014)Aaa>Taa	p.K338*	CUEDC1_ENST00000577840.1_Nonsense_Mutation_p.K201*|CUEDC1_ENST00000578357.1_5'UTR|CUEDC1_ENST00000407144.2_Nonsense_Mutation_p.K338*|CUEDC1_ENST00000360238.2_Nonsense_Mutation_p.K338*	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	338										endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						AACAAGTGTTTCCTCTTTGAC	0.552																																																0			17											218	154	176					17																	55945533		2203	4300	6503	53300532	SO:0001587	stop_gained	404093			AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.1012A>T	17.37:g.55945533T>A	ENSP00000462717:p.Lys338*		53300532	D3DTZ2|Q9NWD0	Nonsense_Mutation	SNP	ENST00000577830.1	37	CCDS11599.1	.	.	.	.	.	.	.	.	.	.	T	42	9.768773	0.99259	.	.	ENSG00000180891	ENST00000407144;ENST00000360238	.	.	.	4.76	4.76	0.60689	.	0.108957	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7125	14.2695	0.66143	0.0:0.0:0.0:1.0	.	.	.	.	X	338	.	ENSP00000353373:K338X	K	-	1	0	CUEDC1	53300532	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.611000	0.67674	1.779000	0.52309	0.379000	0.24179	AAA		0.552	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949		A	55945533	T	A	55945533	4	1	10	1	0	0	0	0	0	1	0	0	4058	1792	62	5	160	5	CUEDC1	17	55945533	Nonsense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	25324144	55945533	25249677	161	1235										
MPO	4353	hgsc.bcm.edu	37	chr17	56349193	56349193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcaggttcctcagcaccgtgCccagctggcccacagtttca	9	16	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:56349193C>T	ENST00000225275.3	-	11	2029	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	MPO_ENST00000340482.3_Missense_Mutation_p.G650D	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	618					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	CAGCACCGTGCCCAGCTGGCC	0.612																																																0			17											111	84	93					17																	56349193		2203	4300	6503	53704192	SO:0001583	missense	4353				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1853G>A	17.37:g.56349193C>T	ENSP00000225275:p.Gly618Asp		53704192	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512711	0.27123	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.68181	-0.31;-0.31	5.16	-2.17	0.07059	.	0.534653	0.20234	N	0.096439	T	0.66528	0.2798	L	0.49778	1.585	0.09310	N	1	P	0.50528	0.936	P	0.52514	0.701	T	0.65500	-0.6153	10	0.42905	T	0.14	-11.8213	14.2148	0.65786	0.0:0.31:0.6191:0.071	.	618	P05164	PERM_HUMAN	D	650;618	ENSP00000344419:G650D;ENSP00000225275:G618D	ENSP00000225275:G618D	G	-	2	0	MPO	53704192	0.000000	0.05858	0.978000	0.43139	0.110000	0.19582	0.422000	0.21296	0.169000	0.19679	0.563000	0.77884	GGC		0.612	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56349193	C	T	56349193	3	4	10	1	0	0	0	0	1	0	0	0	9762	739	26	3	392	3	MPO	17	56349193	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	403660	56349193	24846017	162	1236										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63554408	63554408	+	Frame_Shift_Del	DEL	A	A	-													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaatccattgcaggcaaaccAgaagtctaaggtatccacgc							TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:63554408delA	ENST00000375702.5	-	1	439	c.331delT	c.(331-333)tggfs	p.W111fs	AXIN2_ENST00000307078.5_Frame_Shift_Del_p.W111fs|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	111	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CAGGCAAACCAGAAGTCTAAG	0.463									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																																							0			17											214	196	202					17																	63554408		2203	4300	6503	60984870	SO:0001589	frameshift_variant	8313	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.331delT	17.37:g.63554408delA	ENSP00000364854:p.Trp111fs		60984870	Q3MJ88|Q9H3M6|Q9UH84	Frame_Shift_Del	DEL	ENST00000375702.5	37																																																																																					0.463	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		-	63554408	A	-	63554408	7	5	10	1	0	1	0	1	0	0	0	0	1238	188	7	0	2240	0	AXIN2	17	63554408	Frame_Shift_Del	DEL	A	TCGA-AF-6136-01A-11D-1826-10	7205215	63554408	17640802	163	1237										
GRB2	2885	hgsc.bcm.edu	37	chr17	73389685	73389685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtcgtctgcagtagctttgaAgtcatatttggcgatggctt	12	7	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr17:73389685A>G	ENST00000392562.1	-	2	807	c.25T>C	c.(25-27)Ttc>Ctc	p.F9L	RP11-16C1.1_ENST00000578226.1_RNA|GRB2_ENST00000392564.1_Missense_Mutation_p.F9L|GRB2_ENST00000316615.5_Missense_Mutation_p.F9L|GRB2_ENST00000316804.5_Missense_Mutation_p.F9L|GRB2_ENST00000578961.1_Missense_Mutation_p.F9L|GRB2_ENST00000392563.1_Missense_Mutation_p.F9L			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	9	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	GTAGCTTTGAAGTCATATTTG	0.557																																																0			17											298	237	258					17																	73389685		2203	4300	6503	70901280	SO:0001583	missense	2885				CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885		"SH2 domain containing"	4566	protein-coding gene	gene with protein product		108355					Standard	NM_002086		Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000392562.1:c.25T>C	17.37:g.73389685A>G	ENSP00000376345:p.Phe9Leu		70901280	P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	37	CCDS11721.1	.	.	.	.	.	.	.	.	.	.	A	36	5.756484	0.96898	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564;ENST00000392563;ENST00000316615	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15	5.87	5.87	0.94306	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.80576	0.4649	M	0.91717	3.235	0.80722	D	1	B;P	0.40909	0.321;0.732	B;P	0.59056	0.164;0.851	D	0.83921	0.0301	10	0.87932	D	0	-16.5535	15.942	0.79763	1.0:0.0:0.0:0.0	.	9;9	P62993-2;P62993	.;GRB2_HUMAN	L	9	ENSP00000339007:F9L;ENSP00000376345:F9L;ENSP00000376347:F9L;ENSP00000376346:F9L;ENSP00000317360:F9L	ENSP00000317360:F9L	F	-	1	0	GRB2	70901280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.332000	0.90024	2.248000	0.74166	0.533000	0.62120	TTC		0.557	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1			G	73389685	A	G	73389685	3	3	10	1	0	0	0	0	1	0	0	0	6779	72	3	4	648	4	GRB2	17	73389685	Missense_Mutation	SNP	A	TCGA-AF-6136-01A-11D-1826-10	9835277	73389685	7805525	164	1238										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14273691	14273691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaaggcgttggatgccgagcGcttgtcgtaacccgtctccc	13	13	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:14273691G>A	ENST00000340736.6	-	6	1234	c.937C>T	c.(937-939)Cgc>Tgc	p.R313C	LPHN1_ENST00000591528.1_5'Flank|LPHN1_ENST00000361434.3_Missense_Mutation_p.R308C|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000592086.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	313	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GATGCCGAGCGCTTGTCGTAA	0.622																																																0			19											108	75	86					19																	14273691		2203	4300	6503	14134691	SO:0001583	missense	22859			AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.937C>T	19.37:g.14273691G>A	ENSP00000340688:p.Arg313Cys		14134691	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.041371	0.55003	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89939	-2.59;-2.59	5.14	4.06	0.47325	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.94673	0.8282	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.95175	0.8294	10	0.87932	D	0	.	12.7722	0.57427	0.0:0.0:0.8358:0.1642	.	308;313	O94910-2;O94910	.;LPHN1_HUMAN	C	313;308	ENSP00000340688:R313C;ENSP00000355328:R308C	ENSP00000340688:R313C	R	-	1	0	LPHN1	14134691	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	3.556000	0.53734	2.380000	0.81148	0.561000	0.74099	CGC		0.622	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14273691	G	A	14273691	3	1	10	1	0	0	0	0	1	0	0	0	8944	1087	38	1	3563	1	LPHN1	19	14273691	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10		14273691	44855292	165	1239										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30502057	30502057	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttcagtgaaaagaaagaagaAgccaaacgtaaacgaaagaa	9	5	1	5			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:30502057A>G	ENST00000542441.2	+	9	1389	c.1092A>G	c.(1090-1092)gaA>gaG	p.E364E	URI1_ENST00000312051.6_Silent_p.E324E|URI1_ENST00000360605.4_Silent_p.E346E|URI1_ENST00000392271.1_Silent_p.E288E			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	364					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										AGAAAGAAGAAGCCAAACGTA	0.428																																																0			19											83	88	87					19																	30502057		2203	4300	6503	35193897	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1092A>G	19.37:g.30502057A>G			35193897	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.428	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		G	30502057	A	G	30502057	2	3	10	1	0	0	0	0	0	0	0	1	1917	69	3	4		4	C19orf2	19	30502057	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	16228366	30502057	28626926	166	1240										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934550	30934550	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctgagtggccccgtcctcaaCggccagtatgccatgagtca	11	14	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:30934550C>T	ENST00000355537.3	+	2	228	c.81C>T	c.(79-81)aaC>aaT	p.N27N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	27					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCGTCCTCAACGGCCAGTATG	0.637																																																0			19											99	98	98					19																	30934550		2203	4300	6503	35626390	SO:0001819	synonymous_variant	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.81C>T	19.37:g.30934550C>T			35626390	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																				0.637	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30934550	C	T	30934550	2	4	10	1	0	0	0	0	0	0	0	1	18013	535	19	1		1	ZNF536	19	30934550	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	432493	30934550	28194433	167	1241										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934958	30934958	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cccttcaagtgcccgtactgCgaccacagggcggcgcagaa	12	15	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:30934958C>T	ENST00000355537.3	+	2	636	c.489C>T	c.(487-489)tgC>tgT	p.C163C		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	163					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCCCGTACTGCGACCACAGGG	0.657																																																0			19											41	37	39					19																	30934958		2203	4300	6503	35626798	SO:0001819	synonymous_variant	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.489C>T	19.37:g.30934958C>T			35626798	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																				0.657	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30934958	C	T	30934958	2	4	10	1	0	0	0	0	0	0	0	1	18013	776	27	1		1	ZNF536	19	30934958	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	408	30934958	28194025	168	1242										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32851490	32851490	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	catatgttggtgtcagaaacCacaggcgaatccataactct	8	10	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:32851490C>A	ENST00000311921.4	+	4	2518	c.2326C>A	c.(2326-2328)Cac>Aac	p.H776N	ZNF507_ENST00000355898.5_Missense_Mutation_p.H776N|ZNF507_ENST00000544431.1_Missense_Mutation_p.H776N	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	776					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					TGTCAGAAACCACAGGCGAAT	0.313																																																0			19											147	141	143					19																	32851490		2203	4300	6503	37543330	SO:0001583	missense	22847			AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2326C>A	19.37:g.32851490C>A	ENSP00000312277:p.His776Asn		37543330	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	37	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998052	0.93227	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	D;D;T	0.86865	-2.18;-2.18;0.65	5.57	5.57	0.84162	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97170	0.9075	H	0.99820	4.81	0.52099	D	0.999949	D	0.89917	1.0	D	0.91635	0.999	D	0.99056	1.0829	10	0.87932	D	0	.	19.5547	0.95338	0.0:1.0:0.0:0.0	.	776	Q8TCN5	ZN507_HUMAN	N	776	ENSP00000348162:H776N;ENSP00000312277:H776N;ENSP00000441549:H776N	ENSP00000312277:H776N	H	+	1	0	ZNF507	37543330	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.383000	0.79741	2.606000	0.88127	0.650000	0.86243	CAC		0.313	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		A	32851490	C	A	32851490	3	1	10	1	0	0	0	0	1	0	0	0	17992	594	21	2	2336	2	ZNF507	19	32851490	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	1916532	32851490	26277493	169	1243										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37905300	37905300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgtcctggtttttctgatgcTcatcaactccccatatttct	5	12	4	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:37905300T>C	ENST00000316950.6	-	6	817	c.260A>G	c.(259-261)gAg>gGg	p.E87G	ZNF569_ENST00000392149.2_Missense_Mutation_p.E87G|ZNF569_ENST00000592490.1_Missense_Mutation_p.S13G|ZNF569_ENST00000392150.2_5'UTR	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	87			E -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E87G(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCTGATGCTCATCAACTCC	0.303																																																1	Substitution - Missense(1)	breast(1)	19											45	46	46					19																	37905300		2202	4298	6500	42597140	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.260A>G	19.37:g.37905300T>C	ENSP00000325018:p.Glu87Gly		42597140	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	8.266	0.812358	0.16537	.	.	ENSG00000196437	ENST00000316950	T	0.08102	3.13	3.74	3.74	0.42951	.	0.788279	0.10321	N	0.688728	T	0.05640	0.0148	N	0.21373	0.66	0.80722	D	1	P	0.37781	0.608	B	0.32465	0.146	T	0.45934	-0.9227	10	0.24483	T	0.36	.	8.9857	0.35992	0.0:0.0:0.0:1.0	.	87	Q5MCW4	ZN569_HUMAN	G	87	ENSP00000325018:E87G	ENSP00000325018:E87G	E	-	2	0	ZNF569	42597140	0.105000	0.21958	0.962000	0.40283	0.340000	0.28889	2.999000	0.49473	1.695000	0.51148	0.482000	0.46254	GAG		0.303	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		C	37905300	T	C	37905300	3	2	10	1	0	0	0	0	1	0	0	0	18039	1551	54	4	1804	4	ZNF569	19	37905300	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	5053810	37905300	21223683	170	1244										
KLK14	43847	hgsc.bcm.edu	37	chr19	51582707	51582707	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	aagacgcaggagtcctcaccGatggggctggatatagttcc	13	10	1	1	rs373226064		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:51582707G>A	ENST00000156499.2	-	5	731	c.513C>T	c.(511-513)atC>atT	p.I171I	KLK14_ENST00000391802.1_Splice_Site_p.I171I			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	171	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		AGTCCTCACCGATGGGGCTGG	0.672																																					GBM(117;2161 2172 2448 22911)											0			19								0,3838		0,0,1919	27	29	29		513	-9.8	0	19		29	1,8303		0,1,4151	no	coding-synonymous-near-splice	KLK14	NM_022046.4		0,1,6070	AA,AG,GG		0.012,0.0,0.0082		171/268	51582707	1,12141	1919	4152	6071	56274519	SO:0001630	splice_region_variant	43847			AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"Kallikreins"	6362	protein-coding gene	gene with protein product		606135	"kallikrein 14"			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.514+1C>T	19.37:g.51582707G>A			56274519	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																				0.672	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	Silent	A	51582707	G	A	51582707	5	1	10	1	0	0	0	0	0	0	1	0	8423	1072	37	1	302	1	KLK14	19	51582707	Splice_Site	SNP	G	TCGA-AF-6136-01A-11D-1826-10	13677407	51582707	7546276	171	1245										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51770669	51770669	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	caggcgaagaaagctgcagcGatcagagcaaaaaagagctc	12	9	1	3	rs369648100		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:51770669G>A	ENST00000316401.7	+	5	834	c.453G>A	c.(451-453)gcG>gcA	p.A151A	SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Silent_p.A57A|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	515	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AAGCTGCAGCGATCAGAGCAA	0.468																																																0			19						G		0,4406		0,0,2203	117	118	117		453	-6.6	0	19		117	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C19orf75	NM_173635.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		151/198	51770669	1,13005	2203	4300	6503	56462481	SO:0001819	synonymous_variant	0			AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.453G>A	19.37:g.51770669G>A			56462481	Q8IYH7	Silent	SNP	ENST00000316401.7	37	CCDS12827.1																																																																																				0.468	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		A	51770669	G	A	51770669	2	1	10	1	0	0	0	0	0	0	0	1	1955	1045	37	1		1	C19orf75	19	51770669	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10	187962	51770669	7358314	172	1246										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249305	52249305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ctccagactggcgggaagggCgtggatcagcctctcccgga	15	13	2	1	rs140083445		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:52249305C>T	ENST00000595042.1	-	3	1084	c.943G>A	c.(943-945)Gcc>Acc	p.A315T	FPR1_ENST00000304748.4_Missense_Mutation_p.A315T	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	315					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	GCGGGAAGGGCGTGGATCAGC	0.562													C|||	1	0.000199681	8e-04	0	5008	,	,		14000	0		0	False		,,,				2504	0															0			19						C	THR/ALA,THR/ALA	3,4403		0,3,2200	103	95	98		943,943	2.5	1	19	dbSNP_134	98	0,8600		0,0,4300	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	58,58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign	315/351,315/351	52249305	3,13003	2203	4300	6503	56941117	SO:0001583	missense	2357			M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"GPCR / Class A : Formyl peptide receptors"	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.943G>A	19.37:g.52249305C>T	ENSP00000471493:p.Ala315Thr		56941117	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	10.86	1.470744	0.26423	6.81E-4	0.0	ENSG00000171051	ENST00000304748	T	0.29917	1.55	3.55	2.52	0.30459	.	0.284392	0.28659	N	0.014569	T	0.11623	0.0283	N	0.02539	-0.55	0.25938	N	0.982917	B	0.06786	0.001	B	0.06405	0.002	T	0.21415	-1.0246	10	0.33141	T	0.24	.	8.6857	0.34236	0.8061:0.1939:0.0:0.0	.	315	P21462	FPR1_HUMAN	T	315	ENSP00000302707:A315T	ENSP00000302707:A315T	A	-	1	0	FPR1	56941117	0.875000	0.30112	0.981000	0.43875	0.211000	0.24417	1.867000	0.39499	0.497000	0.27926	-0.272000	0.10252	GCC		0.562	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		T	52249305	C	T	52249305	3	4	10	1	0	0	0	0	1	0	0	0	6057	768	27	1	113	1	FPR1	19	52249305	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	478636	52249305	6879678	173	1247										
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793269	53793269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccttgaaatcaaatcccattCgtatagcttcttgtagcata	5	10	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:53793269C>T	ENST00000426466.1	-	1	1606	c.359G>A	c.(358-360)cGa>cAa	p.R120Q		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	120					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R120Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		AAATCCCATTCGTATAGCTTC	0.383																																																1	Substitution - Missense(1)	NS(1)	19											189	185	187					19																	53793269		2203	4300	6503	58485081	SO:0001583	missense	112401			AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"Baculoviral IAP repeat containing"	14878	protein-coding gene	gene with protein product	"IAP-like protein 2", "inhibitor of apoptosis-like protein 2"		"baculoviral IAP repeat-containing 8"			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.359G>A	19.37:g.53793269C>T	ENSP00000412957:p.Arg120Gln		58485081	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	C	0.204	-1.042575	0.01997	.	.	ENSG00000163098	ENST00000426466	T	0.33654	1.4	0.502	-1.0	0.10196	.	.	.	.	.	T	0.15955	0.0384	L	0.34521	1.04	0.09310	N	1	B	0.30511	0.282	B	0.14578	0.011	T	0.32025	-0.9922	9	0.06625	T	0.88	-16.4135	1.9268	0.03319	0.2682:0.25:0.0:0.4818	.	120	Q96P09	BIRC8_HUMAN	Q	120	ENSP00000412957:R120Q	ENSP00000412957:R120Q	R	-	2	0	BIRC8	58485081	0.639000	0.27234	0.000000	0.03702	0.001000	0.01503	0.452000	0.21795	-1.280000	0.02402	-0.851000	0.03033	CGA		0.383	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793269	C	T	53793269	3	4	10	1	0	0	0	0	1	0	0	0	1441	884	31	1	355	1	BIRC8	19	53793269	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	1543964	53793269	5335714	174	1248										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56303710	56303710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tggaaacagcaagggaaacgTcacatgcaacactccgtaat	9	10	1	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:56303710T>C	ENST00000589093.1	-	7	2563	c.2470A>G	c.(2470-2472)Acg>Gcg	p.T824A	NLRP11_ENST00000592953.1_Missense_Mutation_p.T725A|NLRP11_ENST00000589824.2_Missense_Mutation_p.T770A|NLRP11_ENST00000360133.3_Missense_Mutation_p.T770A|NLRP11_ENST00000443188.1_Missense_Mutation_p.T824A			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	824							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AAGGGAAACGTCACATGCAAC	0.483																																																0			19											201	176	185					19																	56303710		2203	4300	6503	60995522	SO:0001583	missense	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2470A>G	19.37:g.56303710T>C	ENSP00000466285:p.Thr824Ala		60995522	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	T	6.420	0.445561	0.12164	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.48836	0.8;0.8	2.18	-4.36	0.03645	.	.	.	.	.	T	0.26955	0.0660	N	0.14661	0.345	0.09310	N	1	B;P	0.36378	0.09;0.55	B;B	0.41691	0.046;0.364	T	0.22487	-1.0215	9	0.66056	D	0.02	.	1.0411	0.01559	0.4876:0.1279:0.1643:0.2202	.	824;770	P59045;P59045-2	NAL11_HUMAN;.	A	824;770	ENSP00000409898:T824A;ENSP00000353251:T770A	ENSP00000353251:T770A	T	-	1	0	NLRP11	60995522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.012000	0.03649	-2.085000	0.00864	-1.221000	0.01599	ACG		0.483	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56303710	T	C	56303710	3	2	10	1	0	0	0	0	1	0	0	0	10504	1667	58	4	647	4	NLRP11	19	56303710	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	2510441	56303710	2825273	175	1249										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369446	56369446	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccggagagactcttgttcgtCatcgacagcttcgaagagct	11	11	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr19:56369446C>T	ENST00000301295.6	+	3	1109	c.687C>T	c.(685-687)gtC>gtT	p.V229V	NLRP4_ENST00000587891.1_Silent_p.V154V|NLRP4_ENST00000346986.5_Silent_p.V229V	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	229	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCTTGTTCGTCATCGACAGCT	0.557																																																0			19											81	81	81					19																	56369446		2203	4300	6503	61061258	SO:0001819	synonymous_variant	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.687C>T	19.37:g.56369446C>T			61061258	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																				0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369446	C	T	56369446	2	4	10	1	0	0	0	0	0	0	0	1	10510	813	29	3		3	NLRP4	19	56369446	Silent	SNP	C	TCGA-AF-6136-01A-11D-1826-10	65736	56369446	2759537	176	1250										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31024481	31024481	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cgccccaggcctgcggacccGatgcctcttcctgctgagat	11	17	1	1	rs147326327		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr20:31024481G>A	ENST00000375687.4	+	13	4390	c.3966G>A	c.(3964-3966)ccG>ccA	p.P1322P	ASXL1_ENST00000306058.5_Silent_p.P1317P	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1322					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CTGCGGACCCGATGCCTCTTC	0.572			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20						G		1,4405	2.1+/-5.4	0,1,2202	41	44	43		3966	-9.1	0	20	dbSNP_134	43	0,8600		0,0,4300	no	coding-synonymous	ASXL1	NM_015338.5		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1322/1542	31024481	1,13005	2203	4300	6503	30488142	SO:0001819	synonymous_variant	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3966G>A	20.37:g.31024481G>A			30488142	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																				0.572	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31024481	G	A	31024481	2	1	10	1	0	0	0	0	0	0	0	1	1067	1045	37	1		1	ASXL1	20	31024481	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10		31024481	32001039	177	1251										
CHD6	84181	hgsc.bcm.edu	37	chr20	40141530	40141530	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gctgagagtgcagatgttcgAccagctccaagaacagcaat	11	10	0	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr20:40141530A>G	ENST00000373233.3	-	5	984	c.807T>C	c.(805-807)ggT>ggC	p.G269G	CHD6_ENST00000309279.7_Silent_p.G269G|CHD6_ENST00000373222.3_Silent_p.G304G	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	269	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CAGATGTTCGACCAGCTCCAA	0.512																																																0			20											397	328	351					20																	40141530		2203	4300	6503	39574944	SO:0001819	synonymous_variant	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.807T>C	20.37:g.40141530A>G			39574944	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																				0.512	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			G	40141530	A	G	40141530	2	3	10	1	0	0	0	0	0	0	0	1	3335	262	10	4		4	CHD6	20	40141530	Silent	SNP	A	TCGA-AF-6136-01A-11D-1826-10	9117049	40141530	22883990	178	1252										
WISP2	8839	hgsc.bcm.edu	37	chr20	43348542	43348542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtctctgtctcttcaggtgcGtacccagctgtgcccgacac	10	15	3	0			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr20:43348542G>A	ENST00000372868.2	+	3	408	c.65G>A	c.(64-66)cGt>cAt	p.R22H	WISP2_ENST00000190983.4_Missense_Mutation_p.R22H|RP11-445H22.4_ENST00000427598.1_RNA|WISP2_ENST00000372865.4_Missense_Mutation_p.R22H|RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA			O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2	22					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				skin(1)	1		Myeloproliferative disorder(115;0.0122)				CTTCAGGTGCGTACCCAGCTG	0.642																																																0			20											53	39	43					20																	43348542		2202	4300	6502	42781956	SO:0001583	missense	8839			AF100780	CCDS13336.1	20q13.12	2007-05-14			ENSG00000064205	ENSG00000064205			12770	protein-coding gene	gene with protein product		603399				9843955	Standard	NM_003881		Approved	CT58, CTGF-L, CCN5	uc002xmp.3	O76076	OTTHUMG00000033071	ENST00000372868.2:c.65G>A	20.37:g.43348542G>A	ENSP00000361959:p.Arg22His		42781956	B2R9N4|E1P612|Q6PEG3	Missense_Mutation	SNP	ENST00000372868.2	37	CCDS13336.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902414	0.33628	.	.	ENSG00000064205	ENST00000372868;ENST00000372865;ENST00000190983	T;T;T	0.76186	-1.0;-0.12;-1.0	5.56	-0.0714	0.13743	Insulin-like growth factor-binding protein, IGFBP (1);	0.285276	0.39909	N	0.001232	T	0.55433	0.1920	L	0.43152	1.355	0.09310	N	0.999998	B;B	0.30439	0.132;0.279	B;B	0.19666	0.026;0.022	T	0.38178	-0.9673	10	0.15499	T	0.54	-21.5401	6.4051	0.21660	0.2608:0.237:0.5021:0.0	.	22;22	Q6PEG3;O76076	.;WISP2_HUMAN	H	22	ENSP00000361959:R22H;ENSP00000361956:R22H;ENSP00000190983:R22H	ENSP00000190983:R22H	R	+	2	0	WISP2	42781956	0.989000	0.36119	0.986000	0.45419	0.449000	0.32228	1.207000	0.32333	-0.214000	0.10078	0.644000	0.83932	CGT		0.642	WISP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127824.1	NM_003881		A	43348542	G	A	43348542	3	1	10	1	0	0	0	0	1	0	0	0	17413	1145	40	1	71	1	WISP2	20	43348542	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3207012	43348542	19676978	179	1253										
TP53TG5	27296	hgsc.bcm.edu	37	chr20	44002572	44002572	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgtagactcgtgaatttcgcCacccattcctccccttcagc	6	16	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr20:44002572C>T	ENST00000372726.3	-	5	1004	c.848G>A	c.(847-849)tGg>tAg	p.W283*	TP53TG5_ENST00000494455.1_5'Flank|TP53TG5_ENST00000537995.1_Nonsense_Mutation_p.W267*|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000426004.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	283					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TGAATTTCGCCACCCATTCCT	0.532											OREG0025981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			20											174	146	155					20																	44002572		2203	4300	6503	43435986	SO:0001587	stop_gained	27296			AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.848G>A	20.37:g.44002572C>T	ENSP00000361811:p.Trp283*	920	43435986		Nonsense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	C	35	5.440114	0.96168	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	.	.	.	4.39	2.4	0.29515	.	0.437819	0.16771	N	0.200192	.	.	.	.	.	.	0.30253	N	0.793901	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.9174	6.5201	0.22271	0.0:0.7775:0.0:0.2225	.	.	.	.	X	283;267	.	ENSP00000361811:W283X	W	-	2	0	TP53TG5	43435986	0.131000	0.22433	0.378000	0.26068	0.880000	0.50808	0.877000	0.28106	0.747000	0.32809	0.561000	0.74099	TGG		0.532	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		T	44002572	C	T	44002572	4	4	10	1	0	0	0	0	0	1	0	0	16431	595	21	3	28	3	TP53TG5	20	44002572	Nonsense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	654030	44002572	19022948	180	1254										
CDH4	1002	hgsc.bcm.edu	37	chr20	60318802	60318802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gaaatgggacgccgtggtgcGgttgctggtggcccagacct	17	10	0	1	rs373320390		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr20:60318802G>A	ENST00000360469.5	+	3	441	c.353G>A	c.(352-354)cGg>cAg	p.R118Q	RP11-429E11.2_ENST00000447909.1_RNA|CDH4_ENST00000543233.1_Missense_Mutation_p.R44Q|RP11-429E11.2_ENST00000442888.1_RNA	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	118					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GCCGTGGTGCGGTTGCTGGTG	0.637																																																0			20						G	GLN/ARG	2,4402	2.1+/-5.4	0,2,2200	55	45	48		353	5	1	20		48	0,8600		0,0,4300	no	missense	CDH4	NM_001794.2	43	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	benign	118/917	60318802	2,13002	2202	4300	6502	59752197	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.353G>A	20.37:g.60318802G>A	ENSP00000353656:p.Arg118Gln		59752197	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.436840	0.43224	4.54E-4	0.0	ENSG00000179242	ENST00000360469;ENST00000543233	T;T	0.60920	0.15;0.15	5.0	5.0	0.66597	Cadherin-like (1);	0.302326	0.31246	N	0.007999	T	0.44829	0.1312	N	0.21448	0.665	0.47407	D	0.999416	B	0.22346	0.068	B	0.17433	0.018	T	0.31280	-0.9949	9	.	.	.	.	18.2809	0.90097	0.0:0.0:1.0:0.0	.	118	P55283	CADH4_HUMAN	Q	118;44	ENSP00000353656:R118Q;ENSP00000443301:R44Q	.	R	+	2	0	CDH4	59752197	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	4.485000	0.60279	2.304000	0.77564	0.491000	0.48974	CGG		0.637	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60318802	G	A	60318802	3	1	10	1	0	0	0	0	1	0	0	0	3118	1116	39	1	363	1	CDH4	20	60318802	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	16316230	60318802	2706718	181	1255										
KRTAP19-5	337972	hgsc.bcm.edu	37	chr21	31874205	31874205	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggatttcaataaaatccagaGaatccatatcctccatagca	5	10	1	1	rs202202057		TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr21:31874205G>A	ENST00000334151.2	-	1	230	c.204C>T	c.(202-204)ttC>ttT	p.F68F		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	68						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						AAAATCCAGAGAATCCATATC	0.507																																																0			21											89	90	90					21																	31874205		2203	4300	6503	30796076	SO:0001819	synonymous_variant	337972			AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.204C>T	21.37:g.31874205G>A			30796076	A4IF22	Silent	SNP	ENST00000334151.2	37	CCDS13597.1																																																																																				0.507	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			A	31874205	G	A	31874205	2	1	10	1	0	0	0	0	0	0	0	1	8553	933	33	3		3	KRTAP19-5	21	31874205	Silent	SNP	G	TCGA-AF-6136-01A-11D-1826-10		31874205	16255690	182	1256										
KRTAP20-2	337976	hgsc.bcm.edu	37	chr21	32007594	32007594	+	Frame_Shift_Del	DEL	C	C	-													0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cttgaaaccatgtgctactaCagcaactactatggtggtct							TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr21:32007594delC	ENST00000330798.2	+	1	40	c.12delC	c.(10-12)tacfs	p.Y4fs		NM_181616.1	NP_853647.1	Q3LI61	KR202_HUMAN	keratin associated protein 20-2	4						intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|ovary(1)	8						TGTGCTACTACAGCAACTACT	0.498																																																0			21											164	136	146					21																	32007594		2203	4300	6503	30929465	SO:0001589	frameshift_variant	337976			AP001708	CCDS13604.1	21q22.1	2006-03-13			ENSG00000184032	ENSG00000184032		"Keratin associated proteins"	18944	protein-coding gene	gene with protein product						12359730	Standard	NM_181616		Approved	KAP20.2	uc011adg.2	Q3LI61	OTTHUMG00000057786	ENST00000330798.2:c.12delC	21.37:g.32007594delC	ENSP00000330746:p.Tyr4fs		30929465		Frame_Shift_Del	DEL	ENST00000330798.2	37	CCDS13604.1																																																																																				0.498	KRTAP20-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128238.3			-	32007594	C	-	32007594	7	5	10	1	0	1	0	1	0	0	0	0	8558	489	17	0	14	0	KRTAP20-2	21	32007594	Frame_Shift_Del	DEL	C	TCGA-AF-6136-01A-11D-1826-10	133389	32007594	16122301	183	1257										
KCNJ6	3763	hgsc.bcm.edu	37	chr21	39086988	39086988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gcatttatctgtgatgacccGgtagccataaccaatggtgg	11	9	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr21:39086988G>A	ENST00000609713.1	-	3	1061	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	KCNJ6_ENST00000288309.6_Missense_Mutation_p.R158W|KCNJ6-IT1_ENST00000435001.1_RNA	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	158					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	GTGATGACCCGGTAGCCATAA	0.453																																					Pancreas(48;379 1118 2936 19024 28214)											0			21											64	69	68					21																	39086988		1832	4085	5917	38008858	SO:0001583	missense	3763			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.472C>T	21.37:g.39086988G>A	ENSP00000477437:p.Arg158Trp		38008858	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	37	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531774	0.64972	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.97066	-4.23;-4.23	6.03	5.14	0.70334	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98836	0.9607	H	0.94698	3.57	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.99474	1.0946	10	0.87932	D	0	.	14.4932	0.67665	0.0:0.0:0.7337:0.2663	.	158	P48051	IRK6_HUMAN	W	158	ENSP00000383330:R158W;ENSP00000288309:R158W	ENSP00000288309:R158W	R	-	1	2	KCNJ6	38008858	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.054000	0.57434	1.526000	0.49068	0.655000	0.94253	CGG		0.453	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		A	39086988	G	A	39086988	3	1	10	1	0	0	0	0	1	0	0	0	8076	1115	39	1	807	1	KCNJ6	21	39086988	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	7079394	39086988	9042907	184	1258										
ICOSLG	23308	hgsc.bcm.edu	37	chr21	45651316	45651316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tgtgatcttgtctctctctcCgatgtcatttcctacaagaa	6	11	4	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chr21:45651316C>T	ENST00000407780.3	-	5	836	c.709G>A	c.(709-711)Gga>Aga	p.G237R	ICOSLG_ENST00000400379.3_Missense_Mutation_p.G237R|ICOSLG_ENST00000400377.3_Missense_Mutation_p.G120R|ICOSLG_ENST00000344330.4_Missense_Mutation_p.G237R	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	237					B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		TCTCTCTCTCCGATGTCATTT	0.478																																																0			21											127	129	128					21																	45651316		2047	4182	6229	44475744	SO:0001583	missense	23308			AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Endogenous ligands"	17087	protein-coding gene	gene with protein product	"B7-related protein 1", "B7 homologue 2", "B7 homolog 2"	605717		ICOSL		9734811, 11007762	Standard	NM_001283050		Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.709G>A	21.37:g.45651316C>T	ENSP00000384432:p.Gly237Arg		44475744	A8MUZ1|Q9HD18|Q9NRQ1	Missense_Mutation	SNP	ENST00000407780.3	37	CCDS42952.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.293048	0.40594	.	.	ENSG00000160223	ENST00000344330;ENST00000407780;ENST00000400379;ENST00000400377	T;T;T;T	0.23348	5.23;5.24;5.01;1.91	2.28	2.28	0.28536	.	0.272603	0.26297	N	0.025186	T	0.29817	0.0745	L	0.34521	1.04	0.09310	N	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.69142	0.962;0.944;0.962	T	0.10200	-1.0640	10	0.13853	T	0.58	.	8.1675	0.31235	0.0:1.0:0.0:0.0	.	237;120;237	A0N0L8;A8MUZ1;O75144	.;.;ICOSL_HUMAN	R	237;237;237;120	ENSP00000339477:G237R;ENSP00000384432:G237R;ENSP00000383230:G237R;ENSP00000383228:G120R	ENSP00000339477:G237R	G	-	1	0	ICOSLG	44475744	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	0.058000	0.14301	1.599000	0.50093	0.655000	0.94253	GGA		0.478	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259		T	45651316	C	T	45651316	3	4	10	1	0	0	0	0	1	0	0	0	7508	661	23	1	211	1	ICOSLG	21	45651316	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	6564328	45651316	2478579	185	1259										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3235844	3235844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	gtctcccaggtagacagtgaCgtcctggtagtgggaggcta	15	9	1	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:3235844C>T	ENST00000217939.6	-	6	6032	c.5878G>A	c.(5878-5880)Gtc>Atc	p.V1960I		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1960	Ig-like C2-type 4.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TAGACAGTGACGTCCTGGTAG	0.582																																																0			X											114	88	97					X																	3235844		2203	4300	6503	3245844	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5878G>A	X.37:g.3235844C>T	ENSP00000217939:p.Val1960Ile		3245844	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	13.31	2.199540	0.38806	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.69806	-0.43	3.64	3.64	0.41730	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.33382	U	0.004980	T	0.67353	0.2884	L	0.35341	1.055	0.30113	N	0.806406	D	0.60160	0.987	P	0.57009	0.811	T	0.65651	-0.6116	10	0.28530	T	0.3	.	15.1211	0.72443	0.0:1.0:0.0:0.0	.	1960	Q9NR99	MXRA5_HUMAN	I	1960	ENSP00000217939:V1960I	ENSP00000217939:V1960I	V	-	1	0	MXRA5	3245844	0.186000	0.23225	0.962000	0.40283	0.049000	0.14656	0.642000	0.24735	1.443000	0.47586	0.600000	0.82982	GTC		0.582	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3235844	C	T	3235844	3	4	10	1	0	0	0	0	1	0	0	0	10033	536	19	1	2616	1	MXRA5	23	3235844	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10		3235844	152034716	186	1260										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12720004	12720004	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tcttcgcagagttgtaacgaTgtggttcaggagcgatttgg	14	6	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:12720004T>C	ENST00000380682.1	+	10	1451	c.945T>C	c.(943-945)gaT>gaC	p.D315D		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	315	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.D315E(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GTTGTAACGATGTGGTTCAGG	0.527											OREG0019670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	lung(1)	X											138	115	123					X																	12720004		2203	4300	6503	12629925	SO:0001819	synonymous_variant	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.945T>C	X.37:g.12720004T>C		682	12629925	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																				0.527	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		C	12720004	T	C	12720004	2	2	10	1	0	0	0	0	0	0	0	1	6078	1461	51	4		4	FRMPD4	23	12720004	Silent	SNP	T	TCGA-AF-6136-01A-11D-1826-10	9484160	12720004	142550556	187	1261										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820780	35820780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ccacttctctgagatcctccTgagagcttctgagcacctag	8	14	2	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:35820780T>C	ENST00000399989.1	+	2	746	c.467T>C	c.(466-468)cTg>cCg	p.L156P	MAGEB16_ENST00000399988.1_Missense_Mutation_p.L156P|MAGEB16_ENST00000399992.1_Missense_Mutation_p.L188P|MAGEB16_ENST00000399985.1_Missense_Mutation_p.L156P|MAGEB16_ENST00000399987.1_Missense_Mutation_p.L156P	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	156	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.L323R(1)|p.L323Q(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGATCCTCCTGAGAGCTTCT	0.468																																																2	Substitution - Missense(2)	ovary(1)|lung(1)	X											82	80	80					X																	35820780		2040	4177	6217	35730701	SO:0001583	missense	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.467T>C	X.37:g.35820780T>C	ENSP00000382871:p.Leu156Pro		35730701	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.970014	0.34754	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04551	3.6;3.6;3.6;3.6;3.6	2.91	-3.71	0.04424	.	1.151770	0.06335	N	0.706920	T	0.05181	0.0138	L	0.43152	1.355	0.09310	N	0.999999	B	0.26975	0.165	B	0.32624	0.149	T	0.45425	-0.9262	10	0.56958	D	0.05	.	3.7445	0.08542	0.596:0.1302:0.0:0.2738	.	156	A2A368	MAGBG_HUMAN	P	156;188;156;156;156	ENSP00000382870:L156P;ENSP00000382874:L188P;ENSP00000382869:L156P;ENSP00000382871:L156P;ENSP00000382867:L156P	ENSP00000382867:L156P	L	+	2	0	MAGEB16	35730701	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-0.267000	0.08619	-0.885000	0.03971	0.423000	0.28283	CTG		0.468	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			C	35820780	T	C	35820780	3	2	10	1	0	0	0	0	1	0	0	0	9204	1580	55	4	469	4	MAGEB16	23	35820780	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	23100776	35820780	119449780	188	1262										
MAOB	4129	hgsc.bcm.edu	37	chrX	43662574	43662574	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cccatgtcatccattgtcctCcaaaagttgttatgatctaa	5	11	2	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:43662574C>T	ENST00000378069.4	-	4	504	c.357G>A	c.(355-357)tgG>tgA	p.W119*	MAOB_ENST00000536181.1_Nonsense_Mutation_p.W103*|MAOB_ENST00000538942.1_Nonsense_Mutation_p.W103*|MAOB_ENST00000487544.1_5'UTR	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	119					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	CCATTGTCCTCCAAAAGTTGT	0.363																																																0			X											85	80	81					X																	43662574		2203	4300	6503	43547518	SO:0001587	stop_gained	4129				CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.357G>A	X.37:g.43662574C>T	ENSP00000367309:p.Trp119*		43547518	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Nonsense_Mutation	SNP	ENST00000378069.4	37	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.479743	0.63849	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	.	.	.	5.55	5.55	0.83447	.	0.125624	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-9.8881	18.7768	0.91913	0.0:1.0:0.0:0.0	.	.	.	.	X	119;103;103	.	ENSP00000367309:W119X	W	-	3	0	MAOB	43547518	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	4.285000	0.58989	2.467000	0.83353	0.422000	0.28245	TGG		0.363	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43662574	C	T	43662574	4	4	10	1	0	0	0	0	0	1	0	0	9256	856	30	3	1253	3	MAOB	23	43662574	Nonsense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	7841794	43662574	111607986	189	1263										
ZNF630	57232	hgsc.bcm.edu	37	chrX	47918884	47918884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tagtacattcatagggtttcTccccagtatgaatcctctga	7	10	3	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:47918884T>C	ENST00000409324.3	-	5	1173	c.947A>G	c.(946-948)gAg>gGg	p.E316G	ZNF630_ENST00000276054.4_Missense_Mutation_p.E192G|ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Missense_Mutation_p.E302G	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						ATAGGGTTTCTCCCCAGTATG	0.428																																																0			X											62	55	57					X																	47918884		2194	4291	6485	47803828	SO:0001583	missense	57232			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.947A>G	X.37:g.47918884T>C	ENSP00000386393:p.Glu316Gly		47803828	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	14.99	2.700926	0.48307	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324	T;T;T	0.27557	1.66;1.66;1.66	2.31	2.31	0.28768	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41488	0.1161	M	0.77406	2.37	0.29835	N	0.829677	P	0.48503	0.911	P	0.49477	0.612	T	0.42982	-0.9419	9	0.72032	D	0.01	.	7.6956	0.28592	0.0:0.0:0.0:1.0	.	316	Q2M218	ZN630_HUMAN	G	302;192;316	ENSP00000393163:E302G;ENSP00000354683:E192G;ENSP00000386393:E316G	ENSP00000354683:E192G	E	-	2	0	ZNF630	47803828	1.000000	0.71417	0.638000	0.29380	0.600000	0.36913	6.780000	0.75063	0.961000	0.38030	0.441000	0.28932	GAG		0.428	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		C	47918884	T	C	47918884	3	2	10	1	0	0	0	0	1	0	0	0	18093	1551	54	4	1030	4	ZNF630	23	47918884	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	4256310	47918884	107351676	190	1264										
GPR174	84636	hgsc.bcm.edu	37	chrX	78427340	78427340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	atttcattctgtggcattgtGtcttgctagtctgaattcat	8	7	5	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:78427340G>T	ENST00000276077.1	+	1	872	c.836G>T	c.(835-837)tGt>tTt	p.C279F		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						GTGGCATTGTGTCTTGCTAGT	0.388										HNSCC(63;0.18)																																						0			X											176	148	158					X																	78427340		2203	4300	6503	78313996	SO:0001583	missense	84636			AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.836G>T	X.37:g.78427340G>T	ENSP00000276077:p.Cys279Phe		78313996	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	37	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	g	13.13	2.143920	0.37825	.	.	ENSG00000147138	ENST00000276077	T	0.13420	2.59	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.42314	0.1197	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.45775	-0.9238	10	0.72032	D	0.01	.	16.358	0.83243	0.0:0.0:1.0:0.0	.	279	Q9BXC1	GP174_HUMAN	F	279	ENSP00000276077:C279F	ENSP00000276077:C279F	C	+	2	0	GPR174	78313996	1.000000	0.71417	0.995000	0.50966	0.068000	0.16541	9.568000	0.98166	2.172000	0.68678	0.534000	0.68092	TGT		0.388	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		T	78427340	G	T	78427340	3	4	10	1	0	0	0	0	1	0	0	0	6692	1377	48	2	838	2	GPR174	23	78427340	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	30508456	78427340	76843220	191	1265										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83129127	83129127	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ggaagaaagattcaaagaaaGatgacaaaaagaaggatgca	11	3	1	6			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:83129127G>T	ENST00000329312.4	+	4	1448	c.1411G>T	c.(1411-1413)Gat>Tat	p.D471Y		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	471					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TTCAAAGAAAGATGACAAAAA	0.363																																																0			X											44	37	39					X																	83129127		2200	4296	6496	83015783	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1411G>T	X.37:g.83129127G>T	ENSP00000331556:p.Asp471Tyr		83015783	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	10.41	1.341419	0.24339	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.49720	0.77	4.23	3.37	0.38596	.	.	.	.	.	T	0.55242	0.1908	L	0.46157	1.445	0.09310	N	1	D;D	0.64830	0.994;0.987	P;P	0.62740	0.906;0.906	T	0.40327	-0.9569	9	0.72032	D	0.01	0.1997	6.9991	0.24799	0.1244:0.0:0.8756:0.0	.	471;471	P35663;F5H4V5	CYLC1_HUMAN;.	Y	471	ENSP00000331556:D471Y	ENSP00000331556:D471Y	D	+	1	0	CYLC1	83015783	0.998000	0.40836	0.083000	0.20561	0.103000	0.19146	1.516000	0.35856	1.126000	0.42016	0.600000	0.82982	GAT		0.363	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83129127	G	T	83129127	3	4	10	1	0	0	0	0	1	0	0	0	4147	942	33	2	1425	2	CYLC1	23	83129127	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	4701787	83129127	72141433	192	1266										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117815033	117815033	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	tttaatagcttcaaactcgtTtccttacgtgaagaagagga	8	7	1	3			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:117815033T>C	ENST00000276202.7	+	50	5747	c.5684T>C	c.(5683-5685)tTt>tCt	p.F1895S	DOCK11_ENST00000276204.6_Missense_Mutation_p.F1895S	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1895	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TCAAACTCGTTTCCTTACGTG	0.303																																																0			X											68	69	69					X																	117815033		2203	4300	6503	117699061	SO:0001583	missense	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.5684T>C	X.37:g.117815033T>C	ENSP00000276202:p.Phe1895Ser		117699061	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.066347	0.76187	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.26957	1.7;1.7	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.63319	0.2501	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75288	-0.3370	10	0.87932	D	0	-10.8372	13.879	0.63672	0.0:0.0:0.0:1.0	.	1895;1895	A6NIW2;Q5JSL3	.;DOC11_HUMAN	S	1895	ENSP00000276204:F1895S;ENSP00000276202:F1895S	ENSP00000276202:F1895S	F	+	2	0	DOCK11	117699061	1.000000	0.71417	0.968000	0.41197	0.986000	0.74619	7.666000	0.83877	1.874000	0.54306	0.441000	0.28932	TTT		0.303	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		C	117815033	T	C	117815033	3	2	10	1	0	0	0	0	1	0	0	0	4697	1841	64	4	5882	4	DOCK11	23	117815033	Missense_Mutation	SNP	T	TCGA-AF-6136-01A-11D-1826-10	34685906	117815033	37455527	193	1267										
OCRL	4952	hgsc.bcm.edu	37	chrX	128691370	128691370	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttgaaatccctgatgaggaaCactgtttgaagttcctctca	8	9	1	4			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:128691370C>A	ENST00000371113.4	+	5	472	c.307C>A	c.(307-309)Cac>Aac	p.H103N	OCRL_ENST00000486673.1_3'UTR|OCRL_ENST00000357121.5_Missense_Mutation_p.H103N	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	103	PH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						TGATGAGGAACACTGTTTGAA	0.443																																																0			X											94	87	89					X																	128691370		2203	4300	6503	128519051	SO:0001583	missense	4952			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.307C>A	X.37:g.128691370C>A	ENSP00000360154:p.His103Asn		128519051	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.163341	0.38217	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.93811	-3.29;-3.29	5.32	3.54	0.40534	.	1.033840	0.07532	N	0.912389	D	0.86669	0.5988	N	0.14661	0.345	0.22489	N	0.999053	B;B	0.06786	0.001;0.001	B;B	0.13407	0.009;0.006	T	0.75575	-0.3270	10	0.59425	D	0.04	.	6.5008	0.22168	0.3198:0.5937:0.0:0.0865	.	103;103	Q01968-2;Q01968	.;OCRL_HUMAN	N	103	ENSP00000360154:H103N;ENSP00000349635:H103N	ENSP00000349635:H103N	H	+	1	0	OCRL	128519051	0.081000	0.21417	0.985000	0.45067	0.990000	0.78478	1.266000	0.33039	0.438000	0.26450	0.600000	0.82982	CAC		0.443	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		A	128691370	C	A	128691370	3	1	10	1	0	0	0	0	1	0	0	0	10854	478	17	2	325	2	OCRL	23	128691370	Missense_Mutation	SNP	C	TCGA-AF-6136-01A-11D-1826-10	10876337	128691370	26579190	194	1268										
MAMLD1	10046	hgsc.bcm.edu	37	chrX	149639758	149639758	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	ttccatgcctgctctgcccaGacaggtaagacaatctcata	7	13	2	2			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:149639758G>C	ENST00000370401.2	+	4	2223	c.1913G>C	c.(1912-1914)aGa>aCa	p.R638T	MAMLD1_ENST00000426613.2_Missense_Mutation_p.R613T|MAMLD1_ENST00000455522.2_Missense_Mutation_p.R119T|MAMLD1_ENST00000432680.2_Missense_Mutation_p.R613T|MAMLD1_ENST00000262858.5_Missense_Mutation_p.R638T			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	638					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTGCCCAGACAGGTAAGA	0.488																																																0			X											82	73	76					X																	149639758		2203	4300	6503	149390416	SO:0001583	missense	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1913G>C	X.37:g.149639758G>C	ENSP00000359428:p.Arg638Thr		149390416	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	G	6.370	0.436399	0.12104	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000262858;ENST00000426613;ENST00000455522	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.34	4.45	0.53987	.	0.283910	0.35207	N	0.003380	T	0.62258	0.2413	L	0.58101	1.795	0.36279	D	0.855686	B;B;P;B	0.35107	0.033;0.017;0.484;0.041	B;B;B;B	0.33254	0.046;0.007;0.16;0.011	T	0.66031	-0.6024	10	0.31617	T	0.26	0.0074	15.0926	0.72207	0.0:0.1388:0.8612:0.0	.	510;613;613;638	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	T	510;638;613;638;613;119	ENSP00000359428:R638T;ENSP00000414517:R613T;ENSP00000262858:R638T;ENSP00000397438:R613T;ENSP00000389106:R119T	ENSP00000262858:R638T	R	+	2	0	MAMLD1	149390416	1.000000	0.71417	1.000000	0.80357	0.187000	0.23431	4.594000	0.61041	1.001000	0.39076	0.538000	0.68166	AGA		0.488	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		C	149639758	G	C	149639758	3	2	10	1	0	0	0	0	1	0	0	0	9238	942	33	5	1923	5	MAMLD1	23	149639758	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	20948388	149639758	5630802	195	1269										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153039023	153039023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0358974358974359	7	1	0.468656358623996	4.13756613756614	0.281467084188173	1	1	0	cggcctagacgtggtgcagcGgcccctactgtctgtgtggc	15	13	1	1			TCGA-AF-6136-01A-11D-1826-10	TCGA-AF-6136-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	dfc264b8-37fd-4244-aaeb-96a36bb6550e	f1d11847-2db2-429b-aee2-3b6edf9cbd31	g.chrX:153039023G>A	ENST00000361971.5	+	19	3248	c.3134G>A	c.(3133-3135)cGg>cAg	p.R1045Q	SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538776.1_Missense_Mutation_p.R698Q|PLXNB3_ENST00000538966.1_Missense_Mutation_p.R1068Q|PLXNB3_ENST00000538282.1_Missense_Mutation_p.R655Q	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1045	IPT/TIG 3.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	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)					GTGGTGCAGCGGCCCCTACTG	0.687																																																0			X											21	22	22					X																	153039023		2182	4263	6445	152692217	SO:0001583	missense	5365			AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.3134G>A	X.37:g.153039023G>A	ENSP00000355378:p.Arg1045Gln		152692217	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	8.025	0.760377	0.15914	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	4.84	-3.53	0.04667	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912014	0.09484	N	0.795909	T	0.30262	0.0759	N	0.03238	-0.38	0.24401	N	0.99471	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.22068	-1.0227	10	0.19590	T	0.45	.	13.2537	0.60066	0.8068:0.0:0.1932:0.0	.	698;1068;1045	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	Q	1068;1045;698;655	ENSP00000442736:R1068Q;ENSP00000355378:R1045Q;ENSP00000445569:R698Q;ENSP00000441919:R655Q	ENSP00000355378:R1045Q	R	+	2	0	PLXNB3	152692217	0.000000	0.05858	0.357000	0.25798	0.137000	0.21094	-0.209000	0.09358	-0.584000	0.05913	0.436000	0.28706	CGG		0.687	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153039023	G	A	153039023	3	1	10	1	0	0	0	0	1	0	0	0	12156	1116	39	1	3322	1	PLXNB3	23	153039023	Missense_Mutation	SNP	G	TCGA-AF-6136-01A-11D-1826-10	3399265	153039023	2231537	196	1270										
OR4F5	79501	hgsc.bcm.edu	37	chr1	69540	69540	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	attggctttctccattcggtGagccagttggcgtttgccgt	12	10	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:69540G>T	ENST00000335137.3	+	1	450	c.450G>T	c.(448-450)gtG>gtT	p.V150V		NM_001005484.1	NP_001005484.1	Q8NH21	OR4F5_HUMAN	olfactory receptor, family 4, subfamily F, member 5	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(1)|ovary(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;3.48e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.21e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TCCATTCGGTGAGCCAGTTGG	0.473																																																0			1											164	96	121					1																	69540		1766	3010	4776	59403	SO:0001819	synonymous_variant	79501			AB065592	CCDS30547.1	1p36.33	2012-08-09			ENSG00000186092	ENSG00000186092		"GPCR / Class A : Olfactory receptors"	14825	protein-coding gene	gene with protein product							Standard	NM_001005484		Approved		uc001aal.1	Q8NH21	OTTHUMG00000001094	ENST00000335137.3:c.450G>T	1.37:g.69540G>T			59403	Q5VT22	Silent	SNP	ENST00000335137.3	37	CCDS30547.1																																																																																				0.473	OR4F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003223.1	NM_001005484		T	69540	G	T	69540	2	4	11	1	0	0	0	0	0	0	0	1	11096	1277	45	2		2	OR4F5	1	69540	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10		69540	249181081	1	1271										
EXOSC10	5394	hgsc.bcm.edu	37	chr1	11139840	11139840	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	atctgctgccgcacaaggggCggtactgggttgcagcaagc	15	11	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:11139840C>T	ENST00000376936.4	-	14	1726	c.1677G>A	c.(1675-1677)ccG>ccA	p.P559P	EXOSC10_ENST00000485606.1_5'Flank|EXOSC10_ENST00000304457.7_Silent_p.P559P|EXOSC10_ENST00000544779.1_Silent_p.P559P	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	559	HRDC. {ECO:0000255|PROSITE- ProRule:PRU00328}.				CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	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)		GCACAAGGGGCGGTACTGGGT	0.532																																					Colon(179;105 1987 14326 27364 29542)											0			1											88	69	76					1																	11139840		2203	4300	6503	11062427	SO:0001819	synonymous_variant	5394			BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 2 (100kD)"	605960	"polymyositis/scleroderma autoantigen 2, 100kDa"	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.1677G>A	1.37:g.11139840C>T			11062427	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	37	CCDS30584.1																																																																																				0.532	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998		T	11139840	C	T	11139840	2	4	11	1	0	0	0	0	0	0	0	1	5327	755	27	1		1	EXOSC10	1	11139840	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	11070300	11139840	238110781	2	1272										
MACF1	23499	hgsc.bcm.edu	37	chr1	39900294	39900294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcagctcaggcagcaacaagAggaaatgagggtaaggagca	15	7	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:39900294A>G	ENST00000372915.3	+	67	17549	c.17462A>G	c.(17461-17463)gAg>gGg	p.E5821G	MACF1_ENST00000545844.1_Missense_Mutation_p.E3863G|MACF1_ENST00000361689.2_Missense_Mutation_p.E3863G|MACF1_ENST00000564288.1_Missense_Mutation_p.E5925G|MACF1_ENST00000289893.4_Missense_Mutation_p.E4365G|MACF1_ENST00000539005.1_Missense_Mutation_p.E3733G|MACF1_ENST00000567887.1_Missense_Mutation_p.E5962G|MACF1_ENST00000317713.7_Missense_Mutation_p.E3863G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5821					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			CAGCAACAAGAGGAAATGAGG	0.408																																																0			1											61	61	61					1																	39900294		2203	4300	6503	39672881	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.17462A>G	1.37:g.39900294A>G	ENSP00000362006:p.Glu5821Gly		39672881	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	A	28.8	4.953570	0.92660	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000011	T	0.72070	0.3415	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.983	D;D;D	0.76071	0.952;0.987;0.917	T	0.75360	-0.3345	10	0.87932	D	0	.	16.1596	0.81693	1.0:0.0:0.0:0.0	.	5821;3863;3807	Q9UPN3;F8W8Q1;Q9UPN3-3	MACF1_HUMAN;.;.	G	3863;5821;3863;3863;3733;4365	ENSP00000439537:E3863G;ENSP00000362006:E5821G;ENSP00000354573:E3863G;ENSP00000313438:E3863G;ENSP00000444364:E3733G;ENSP00000289893:E4365G	ENSP00000289893:E4365G	E	+	2	0	MACF1	39672881	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.216000	0.71823	0.533000	0.62120	GAG		0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39900294	A	G	39900294	3	3	11	1	0	0	0	0	1	0	0	0	9174	304	11	4	17993	4	MACF1	1	39900294	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	28760454	39900294	209350327	3	1273										
FAM159A	348378	hgsc.bcm.edu	37	chr1	53108595	53108595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cttctcgccttcattgttacCgcctgtgtgctctgctacct	7	15	3	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:53108595C>T	ENST00000517870.1	+	2	393	c.243C>T	c.(241-243)acC>acT	p.T81T	FAM159A_ENST00000401050.3_3'UTR	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN	family with sequence similarity 159, member A	81						integral component of membrane (GO:0016021)				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						TCATTGTTACCGCCTGTGTGC	0.537																																																0			1											211	200	203					1																	53108595		2080	4203	6283	52881183	SO:0001819	synonymous_variant	348378				CCDS41336.1	1p32.3	2008-08-08			ENSG00000182183	ENSG00000182183			28757	protein-coding gene	gene with protein product						12477932	Standard	NM_001042693		Approved	MGC52498	uc001cuf.3	Q6UWV7	OTTHUMG00000008330	ENST00000517870.1:c.243C>T	1.37:g.53108595C>T			52881183	Q6ZRG4	Silent	SNP	ENST00000517870.1	37	CCDS41336.1																																																																																				0.537	FAM159A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022934.2	NM_001042693		T	53108595	C	T	53108595	2	4	11	1	0	0	0	0	0	0	0	1	5484	639	23	1		1	FAM159A	1	53108595	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	13208301	53108595	196142026	4	1274										
LRRC39	127495	hgsc.bcm.edu	37	chr1	100618070	100618070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tttcagtgggttgtctctgaAgttgacaaacctagaagttc	10	7	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:100618070A>G	ENST00000370137.1	-	9	1021	c.823T>C	c.(823-825)Ttc>Ctc	p.F275L	LRRC39_ENST00000342895.3_Missense_Mutation_p.F275L|LRRC39_ENST00000370138.1_Missense_Mutation_p.F275L	NM_001256386.1|NM_144620.3	NP_001243315.1|NP_653221.1	Q96DD0	LRC39_HUMAN	leucine rich repeat containing 39	275										endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	13		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0826)|all cancers(265;0.135)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		TTGTCTCTGAAGTTGACAAAC	0.373																																																0			1											106	100	102					1																	100618070		2203	4300	6503	100390658	SO:0001583	missense	127495			AK096892	CCDS766.1, CCDS58014.1	1p21.3	2008-02-05			ENSG00000122477	ENSG00000122477			28228	protein-coding gene	gene with protein product						12975309	Standard	NM_001256385		Approved	MGC14816	uc001dsx.2	Q96DD0	OTTHUMG00000010839	ENST00000370137.1:c.823T>C	1.37:g.100618070A>G	ENSP00000359156:p.Phe275Leu		100390658	B3KUD2|D3DT56|Q5VVK7	Missense_Mutation	SNP	ENST00000370137.1	37	CCDS766.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.516817	0.44763	.	.	ENSG00000122477	ENST00000370137;ENST00000370138;ENST00000342895;ENST00000370136	T;T;T	0.26518	1.73;1.73;1.73	5.88	5.88	0.94601	.	0.000000	0.64402	D	0.000007	T	0.29190	0.0726	L	0.59436	1.845	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.23476	-1.0187	10	0.02654	T	1	.	16.2997	0.82804	1.0:0.0:0.0:0.0	.	275;275	Q96DD0-2;Q96DD0	.;LRC39_HUMAN	L	275	ENSP00000359156:F275L;ENSP00000359157:F275L;ENSP00000344470:F275L	ENSP00000344470:F275L	F	-	1	0	LRRC39	100390658	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.567000	0.90737	2.250000	0.74265	0.528000	0.53228	TTC		0.373	LRRC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029917.2	NM_144620		G	100618070	A	G	100618070	3	3	11	1	0	0	0	0	1	0	0	0	9024	72	3	4	192	4	LRRC39	1	100618070	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	47509475	100618070	148632551	5	1275										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114249245	114249245	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gatgatgccacttatttccaAcacagacatatccatctttt	4	11	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:114249245A>G	ENST00000369604.1	-	12	1852	c.1369T>C	c.(1369-1371)Ttg>Ctg	p.L457L	PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000357783.2_Silent_p.L457L|PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000369598.1_Silent_p.L412L|PHTF1_ENST00000393357.2_Silent_p.L457L|PHTF1_ENST00000369600.1_Silent_p.L404L|PHTF1_ENST00000369596.2_Silent_p.L404L			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	457					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		CTTATTTCCAACACAGACATA	0.363																																																0			1											159	153	155					1																	114249245		2203	4300	6503	114050768	SO:0001819	synonymous_variant	10745			AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.1369T>C	1.37:g.114249245A>G			114050768	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Silent	SNP	ENST00000369604.1	37	CCDS861.1																																																																																				0.363	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		G	114249245	A	G	114249245	2	3	11	1	0	0	0	0	0	0	0	1	11893	40	2	4		4	PHTF1	1	114249245	Silent	SNP	A	TCGA-AF-6655-01A-11D-1826-10	13631175	114249245	135001376	6	1276										
FLG	2312	hgsc.bcm.edu	37	chr1	152276887	152276887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agccatctcctgattgttcgTcattacgagtttgtctgctg	9	10	3	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:152276887T>C	ENST00000368799.1	-	3	10510	c.10475A>G	c.(10474-10476)gAc>gGc	p.D3492G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3492	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGATTGTTCGTCATTACGAGT	0.572									Ichthyosis																																							0			1											288	282	284					1																	152276887		2203	4297	6500	150543511	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10475A>G	1.37:g.152276887T>C	ENSP00000357789:p.Asp3492Gly		150543511	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	4.501	0.092853	0.08632	.	.	ENSG00000143631	ENST00000368799	T	0.01685	4.69	2.95	0.405	0.16361	.	.	.	.	.	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	P	0.45715	0.865	P	0.45913	0.497	T	0.46735	-0.9170	9	0.24483	T	0.36	.	5.2744	0.15641	0.0:0.304:0.0:0.696	.	3492	P20930	FILA_HUMAN	G	3492	ENSP00000357789:D3492G	ENSP00000357789:D3492G	D	-	2	0	FLG	150543511	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.267000	0.08619	0.191000	0.20236	0.327000	0.21459	GAC		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152276887	T	C	152276887	3	2	11	1	0	0	0	0	1	0	0	0	5941	1667	58	4	1714	4	FLG	1	152276887	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	38027642	152276887	96973734	7	1277										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156933315	156933317	+	In_Frame_Del	DEL	GTT	GTT	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aactaggaaaccgttacctcGttgttgaaataacccgggtc					rs150882302	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	GTT	GTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:156933315_156933317delGTT	ENST00000361409.2	-	11	1655_1657	c.913_915delAAC	c.(913-915)aacdel	p.N305del	ARHGEF11_ENST00000368194.3_In_Frame_Del_p.N345del	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	305					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N345N(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCGTTACCTCGTTGTTGAAATAA	0.433																																																1	Substitution - coding silent(1)	central_nervous_system(1)	1																																								155199941	SO:0001651	inframe_deletion	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.913_915delAAC	1.37:g.156933318_156933320delGTT	ENSP00000354644:p.Asn305del		155199939	D3DVD0|Q5VY40|Q6PFW2	In_Frame_Del	DEL	ENST00000361409.2	37	CCDS1162.1																																																																																				0.433	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		-	156933317	GTT	-	156933315	7	5	11	1	0	1	0	1	0	0	0	0	896	1136	40	0	3773	0	ARHGEF11	1	156933315	In_Frame_Del	DEL	GTT	TCGA-AF-6655-01A-11D-1826-10	4656428	156933315	92317306	8	1278										
USP21	27005	hgsc.bcm.edu	37	chr1	161130911	161130911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcacttctctccgccgcctaGggggctttcctggaccccct	10	18	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:161130911G>A	ENST00000289865.8	+	2	702	c.481G>A	c.(481-483)Ggg>Agg	p.G161R	RP11-297K8.2_ENST00000420498.1_RNA|USP21_ENST00000368001.1_Missense_Mutation_p.G161R|USP21_ENST00000368002.3_Missense_Mutation_p.G161R	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	161					histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G161W(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CCGCCGCCTAGGGGGCTTTCC	0.642																																																1	Substitution - Missense(1)	lung(1)	1											53	54	53					1																	161130911		2203	4300	6503	159397535	SO:0001583	missense	29761			AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.481G>A	1.37:g.161130911G>A	ENSP00000289865:p.Gly161Arg		159397535	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434635	0.43224	.	.	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.43688	0.94;0.94;0.94	4.89	4.89	0.63831	.	0.433672	0.22106	N	0.064552	T	0.07593	0.0191	N	0.08118	0	0.29981	N	0.817726	B	0.33883	0.43	B	0.34093	0.175	T	0.13791	-1.0496	10	0.10636	T	0.68	.	6.8965	0.24259	0.0918:0.1781:0.7301:0.0	.	161	Q9UK80	UBP21_HUMAN	R	161	ENSP00000356981:G161R;ENSP00000289865:G161R;ENSP00000356980:G161R	ENSP00000289865:G161R	G	+	1	0	USP21	159397535	0.996000	0.38824	0.968000	0.41197	0.976000	0.68499	2.831000	0.48144	2.538000	0.85594	0.462000	0.41574	GGG		0.642	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			A	161130911	G	A	161130911	3	1	11	1	0	0	0	0	1	0	0	0	17093	1000	35	3	483	3	USP21	1	161130911	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	4197596	161130911	88119710	9	1279										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181732597	181732597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gaagctcttccgagctgcccGcctcataaagctcctgcgtc	9	16	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:181732597G>A	ENST00000367573.2	+	34	4745	c.4745G>A	c.(4744-4746)cGc>cAc	p.R1582H	CACNA1E_ENST00000357570.5_Missense_Mutation_p.R1533H|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1189H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R1563H|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1514H|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1563H|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R1582H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1582					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGAGCTGCCCGCCTCATAAAG	0.473																																																0			1											81	79	80					1																	181732597		1858	4097	5955	179999220	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4745G>A	1.37:g.181732597G>A	ENSP00000356545:p.Arg1582His		179999220	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907202	0.92107	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.99591	-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24	5.28	4.36	0.52297	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	H	0.99820	4.81	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.97110	1.0;0.996;0.838	D	0.96366	0.9270	10	0.87932	D	0	.	13.9604	0.64175	0.076:0.0:0.924:0.0	.	1563;1582;1582	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	H	1582;1563;1533;1514;1189;1563;1582	ENSP00000356542:R1582H;ENSP00000434814:R1563H;ENSP00000350183:R1533H;ENSP00000351101:R1514H;ENSP00000356539:R1189H;ENSP00000353222:R1563H;ENSP00000356545:R1582H	ENSP00000350183:R1533H	R	+	2	0	CACNA1E	179999220	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.193000	0.94954	2.471000	0.83476	0.467000	0.42956	CGC		0.473	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181732597	G	A	181732597	3	1	11	1	0	0	0	0	1	0	0	0	2548	1087	38	1	4879	1	CACNA1E	1	181732597	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	20601686	181732597	67518024	10	1280										
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203025603	203025603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gctgcggctagagaagcttgGccacccagccctgagccagg	14	14	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:203025603G>A	ENST00000447715.2	+	23	2582	c.2141G>A	c.(2140-2142)gGc>gAc	p.G714D	PPFIA4_ENST00000367240.2_Missense_Mutation_p.G715D|PPFIA4_ENST00000414050.2_Missense_Mutation_p.G443D|PPFIA4_ENST00000599966.1_Missense_Mutation_p.G230D|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G230D|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G230D			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	714					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.G861V(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GAGAAGCTTGGCCACCCAGCC	0.577																																																1	Substitution - Missense(1)	lung(1)	1											32	38	36					1																	203025603		2061	4182	6243	201292226	SO:0001583	missense	8497			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2141G>A	1.37:g.203025603G>A	ENSP00000402576:p.Gly714Asp		201292226	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	g	12.26	1.883894	0.33255	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	4.78	4.78	0.61160	.	0.000000	0.46442	D	0.000298	T	0.29524	0.0736	L	0.40543	1.245	0.47584	D	0.999465	P;B;P;P	0.52842	0.956;0.241;0.846;0.761	P;B;P;B	0.52823	0.71;0.147;0.637;0.434	T	0.01114	-1.1447	10	0.44086	T	0.13	-29.1595	16.1762	0.81855	0.0:0.0:1.0:0.0	.	443;714;230;230	B4DIS5;B1N949;O75335-2;O75335	.;.;.;LIPA4_HUMAN	D	715;714;230;443;230	ENSP00000356209:G715D;ENSP00000402576:G714D;ENSP00000295706:G230D;ENSP00000400379:G443D;ENSP00000272198:G230D	ENSP00000272198:G230D	G	+	2	0	PPFIA4	201292226	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.062000	0.57492	2.489000	0.83994	0.457000	0.33378	GGC		0.577	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203025603	G	A	203025603	3	1	11	1	0	0	0	0	1	0	0	0	12343	1203	42	3	707	3	PPFIA4	1	203025603	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	21293006	203025603	46225018	11	1281										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216850648	216850648	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cagaagggtagagaggtggcGagtcaagtccgttctgatgg	17	6	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:216850648G>A	ENST00000408911.3	-	2	395	c.242C>T	c.(241-243)tCg>tTg	p.S81L	ESRRG_ENST00000391890.3_Missense_Mutation_p.S58L|ESRRG_ENST00000366940.2_Missense_Mutation_p.S58L|ESRRG_ENST00000487276.1_Missense_Mutation_p.S58L|ESRRG_ENST00000360012.3_Missense_Mutation_p.S58L|ESRRG_ENST00000361525.3_Missense_Mutation_p.S58L|ESRRG_ENST00000359162.2_Missense_Mutation_p.S58L|ESRRG_ENST00000493603.1_Missense_Mutation_p.S58L|ESRRG_ENST00000463665.1_Missense_Mutation_p.S58L|ESRRG_ENST00000361395.2_Missense_Mutation_p.S58L|ESRRG_ENST00000366937.1_Missense_Mutation_p.S86L|ESRRG_ENST00000366938.2_Missense_Mutation_p.S58L|ESRRG_ENST00000493748.1_Missense_Mutation_p.S58L	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	81					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S81L(1)		endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	GAGAGGTGGCGAGTCAAGTCC	0.562																																																1	Substitution - Missense(1)	ovary(1)	1											169	147	155					1																	216850648		2203	4300	6503	214917271	SO:0001583	missense	2104			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.242C>T	1.37:g.216850648G>A	ENSP00000386171:p.Ser81Leu		214917271	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	G	36	5.934263	0.97122	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275;ENST00000469486	D;D;D;D;D;D;D;D;D;D;D;D;D;D;T	0.95447	-3.25;-3.25;-3.26;-3.28;-3.25;-3.25;-3.25;-3.25;-3.25;-3.28;-3.71;-3.25;-3.25;-3.08;-0.06	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.97300	0.9117	M	0.62723	1.935	0.80722	D	1	D;D;D	0.69078	0.965;0.997;0.994	P;D;P	0.69479	0.506;0.964;0.885	D	0.96583	0.9432	10	0.51188	T	0.08	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	58;86;81	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	L	58;58;86;81;58;58;58;58;58;58;58;58;58;58;58;58	ENSP00000355225:S58L;ENSP00000355907:S58L;ENSP00000355904:S86L;ENSP00000386171:S81L;ENSP00000352077:S58L;ENSP00000354584:S58L;ENSP00000355905:S58L;ENSP00000353108:S58L;ENSP00000419594:S58L;ENSP00000375761:S58L;ENSP00000418629:S58L;ENSP00000419155:S58L;ENSP00000417374:S58L;ENSP00000419514:S58L;ENSP00000417900:S58L	ENSP00000346386:S58L	S	-	2	0	ESRRG	214917271	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	TCG		0.562	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		A	216850648	G	A	216850648	3	1	11	1	0	0	0	0	1	0	0	0	5275	1059	37	1	1158	1	ESRRG	1	216850648	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	13825045	216850648	32399973	12	1282										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248551325	248551325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcctgtcctcatcagctggcGggtctgctggatgatcctgg	13	12	3	1	rs376407108	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr1:248551325G>A	ENST00000355728.2	+	1	416	c.416G>A	c.(415-417)cGg>cAg	p.R139Q		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATCAGCTGGCGGGTCTGCTGG	0.582													c|||	3	0.000599042	0	0	5008	,	,		18629	0		0	False		,,,				2504	0.0031															0			1						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	80	77	78		416	-2.5	0	1		78	0,8600		0,0,4300	no	missense	OR2T6	NM_001005471.1	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	139/309	248551325	1,13005	2203	4300	6503	246617948	SO:0001583	missense	254879			AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.416G>A	1.37:g.248551325G>A	ENSP00000347965:p.Arg139Gln		246617948	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	.	.	.	.	.	.	.	.	.	.	G	3.197	-0.164473	0.06502	2.27E-4	0.0	ENSG00000198104	ENST00000355728	T	0.41758	0.99	4.19	-2.49	0.06403	GPCR, rhodopsin-like superfamily (1);	0.349689	0.20460	N	0.091918	T	0.28400	0.0702	L	0.45744	1.44	0.09310	N	1	B	0.33512	0.415	B	0.33690	0.168	T	0.15607	-1.0431	10	0.31617	T	0.26	.	6.5184	0.22260	0.5142:0.1284:0.3573:0.0	.	139	Q8NHC8	OR2T6_HUMAN	Q	139	ENSP00000347965:R139Q	ENSP00000347965:R139Q	R	+	2	0	OR2T6	246617948	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.204000	0.09425	-0.353000	0.08224	-0.805000	0.03199	CGG		0.582	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		A	248551325	G	A	248551325	3	1	11	1	0	0	0	0	1	0	0	0	11060	1116	39	1	418	1	OR2T6	1	248551325	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	31700677	248551325	699296	13	1283										
IFT172	26160	hgsc.bcm.edu	37	chr2	27668234	27668234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aggcctcgtaggcgccacgcTcatcccgaggcagaacctgc	12	16	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:27668234T>C	ENST00000260570.3	-	46	5100	c.4997A>G	c.(4996-4998)gAg>gGg	p.E1666G	KRTCAP3_ENST00000543753.1_Intron	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	1666					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GGCGCCACGCTCATCCCGAGG	0.592																																																0			2											28	29	29					2																	27668234		2203	4300	6503	27521738	SO:0001583	missense	26160			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.4997A>G	2.37:g.27668234T>C	ENSP00000260570:p.Glu1666Gly		27521738	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	37	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.996380	0.74818	.	.	ENSG00000138002	ENST00000260570	T	0.46819	0.86	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.44498	0.1296	L	0.55481	1.735	0.80722	D	1	B	0.23990	0.095	B	0.24701	0.055	T	0.40572	-0.9556	10	0.48119	T	0.1	-19.3727	12.429	0.55563	0.0:0.0:0.0:1.0	.	1666	Q9UG01	IF172_HUMAN	G	1666	ENSP00000260570:E1666G	ENSP00000260570:E1666G	E	-	2	0	IFT172	27521738	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	7.506000	0.81665	1.976000	0.57569	0.454000	0.30748	GAG		0.592	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		C	27668234	T	C	27668234	3	2	11	1	0	0	0	0	1	0	0	0	7578	1551	54	4	264	4	IFT172	2	27668234	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10		27668234	215531139	14	1284										
FSHR	2492	hgsc.bcm.edu	37	chr2	49190767	49190767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccaggttgcacataaggaacCtggggactgtgagtttatat	12	7	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:49190767C>A	ENST00000406846.2	-	10	1312	c.1193G>T	c.(1192-1194)aGg>aTg	p.R398M	FSHR_ENST00000346173.3_Missense_Mutation_p.R336M|FSHR_ENST00000541117.1_Missense_Mutation_p.R134M|FSHR_ENST00000304421.4_Missense_Mutation_p.R372M	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	398					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)	p.R398M(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		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)|Suramin(DB04786)|Urofollitropin(DB00094)	CATAAGGAACCTGGGGACTGT	0.458									Gonadal Dysgenesis, 46 XX																																							1	Substitution - Missense(1)	lung(1)	2											129	127	128					2																	49190767		2203	4300	6503	49044271	SO:0001583	missense	2492	Familial Cancer Database			CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1193G>T	2.37:g.49190767C>A	ENSP00000384708:p.Arg398Met		49044271	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802515	0.70682	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117	D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16	5.38	5.38	0.77491	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98654	0.9549	M	0.93678	3.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.99425	1.0934	9	.	.	.	.	18.3052	0.90177	0.0:1.0:0.0:0.0	.	372;336;398	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	M	398;336;372;134	ENSP00000384708:R398M;ENSP00000333908:R336M;ENSP00000306780:R372M;ENSP00000444172:R134M	.	R	-	2	0	FSHR	49044271	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	7.651000	0.83577	2.801000	0.96364	0.655000	0.94253	AGG		0.458	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190767	C	A	49190767	3	1	11	1	0	0	0	0	1	0	0	0	6092	681	24	2	898	2	FSHR	2	49190767	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	21522533	49190767	194008606	15	1285										
USP34	9736	hgsc.bcm.edu	37	chr2	61436103	61436103	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcatcagattctaatagtatTctgaaggcactagaagaaaa	7	6	4	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:61436103T>A	ENST00000398571.2	-	70	8926	c.8850A>T	c.(8848-8850)agA>agT	p.R2950S	USP34_ENST00000472689.1_5'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2950					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CTAATAGTATTCTGAAGGCAC	0.294																																																0			2											75	74	74					2																	61436103		1813	4052	5865	61289607	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.8850A>T	2.37:g.61436103T>A	ENSP00000381577:p.Arg2950Ser		61289607	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.8|25.8	4.673781|4.673781	0.88445|0.88445	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000411912|ENST00000263989;ENST00000398571	.|T	.|0.63913	.|-0.07	6.0|6.0	6.0|6.0	0.97389|0.97389	.|Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61837|0.61837	0.2379|0.2379	L|L	0.58101|0.58101	1.795|1.795	0.53005|0.53005	D|D	0.999967|0.999967	.|B	.|0.15141	.|0.012	.|B	.|0.16289	.|0.015	T|T	0.59736|0.59736	-0.7398|-0.7398	5|10	.|0.87932	.|D	.|0	.|.	16.5044|16.5044	0.84266|0.84266	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2950	.|Q70CQ2	.|UBP34_HUMAN	Y|S	710|2798;2950	.|ENSP00000381577:R2950S	.|ENSP00000263989:R2798S	N|R	-|-	1|3	0|2	USP34|USP34	61289607|61289607	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.140000|2.140000	0.42159|0.42159	2.295000|2.295000	0.77249|0.77249	0.528000|0.528000	0.53228|0.53228	AAT|AGA		0.294	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61436103	T	A	61436103	3	1	11	1	0	0	0	0	1	0	0	0	17105	1780	62	5	1834	5	USP34	2	61436103	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	12245336	61436103	181763270	16	1286										
MERTK	10461	hgsc.bcm.edu	37	chr2	112687111	112687111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agttacagcaataatcgcttCcttcaggtatgtgttctttc	7	9	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:112687111C>A	ENST00000295408.4	+	2	733	c.476C>A	c.(475-477)tCc>tAc	p.S159Y	RN7SL297P_ENST00000483161.2_RNA|MERTK_ENST00000421804.2_Missense_Mutation_p.S159Y|MERTK_ENST00000409780.1_Intron			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	159	Ig-like C2-type 1.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S159F(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						ATAATCGCTTCCTTCAGGTAT	0.338																																																1	Substitution - Missense(1)	lung(1)	2											106	92	97					2																	112687111		2203	4300	6503	112403582	SO:0001583	missense	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.476C>A	2.37:g.112687111C>A	ENSP00000295408:p.Ser159Tyr		112403582	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.436152	0.25813	.	.	ENSG00000153208	ENST00000295408;ENST00000421804	T;T	0.69435	-0.4;-0.4	4.44	2.62	0.31277	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.665962	0.11708	U	0.537240	T	0.63780	0.2540	L	0.52573	1.65	0.28488	N	0.914637	P	0.46142	0.873	P	0.49140	0.601	T	0.52373	-0.8584	10	0.19147	T	0.46	-4.2235	7.3293	0.26573	0.0:0.7867:0.0:0.2133	.	159	Q12866	MERTK_HUMAN	Y	159	ENSP00000295408:S159Y;ENSP00000389152:S159Y	ENSP00000295408:S159Y	S	+	2	0	MERTK	112403582	0.313000	0.24554	0.993000	0.49108	0.960000	0.62799	1.098000	0.31000	0.482000	0.27582	-0.259000	0.10710	TCC		0.338	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			A	112687111	C	A	112687111	3	1	11	1	0	0	0	0	1	0	0	0	9509	855	30	2	482	2	MERTK	2	112687111	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	51251008	112687111	130512262	17	1287										
GLI2	2736	hgsc.bcm.edu	37	chr2	121742291	121742291	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cgtggaggactgcctgcacgTcagagccatcaagaccgaga	13	12	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:121742291T>C	ENST00000452319.1	+	12	1988	c.1928T>C	c.(1927-1929)gTc>gCc	p.V643A	GLI2_ENST00000361492.4_Missense_Mutation_p.V643A|GLI2_ENST00000314490.11_Missense_Mutation_p.V315A|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				TGCCTGCACGTCAGAGCCATC	0.687																																																0			2											24	25	25					2																	121742291		2200	4297	6497	121458761	SO:0001583	missense	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1928T>C	2.37:g.121742291T>C	ENSP00000390436:p.Val643Ala		121458761		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.132223	0.56828	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	T;T;T	0.15718	2.4;2.4;2.45	4.7	4.7	0.59300	.	0.319820	0.32952	N	0.005456	T	0.13841	0.0335	L	0.38838	1.175	0.35128	D	0.767678	B;B;B;B;B	0.27166	0.028;0.0;0.17;0.037;0.003	B;B;B;B;B	0.27170	0.008;0.001;0.046;0.077;0.002	T	0.13229	-1.0517	10	0.48119	T	0.1	.	8.9379	0.35711	0.0:0.0832:0.0:0.9168	.	643;626;298;298;315	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	A	643;643;315	ENSP00000390436:V643A;ENSP00000354586:V643A;ENSP00000312694:V315A	ENSP00000312694:V315A	V	+	2	0	GLI2	121458761	1.000000	0.71417	0.981000	0.43875	0.973000	0.67179	4.985000	0.63845	1.969000	0.57287	0.459000	0.35465	GTC		0.687	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		C	121742291	T	C	121742291	3	2	11	1	0	0	0	0	1	0	0	0	6458	1667	58	4	1970	4	GLI2	2	121742291	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	9055180	121742291	121457082	18	1288										
WDR33	55339	hgsc.bcm.edu	37	chr2	128477435	128477435	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtgaccctgagggccaggcgGgccttgggggcctatgtgac	18	11	0	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:128477435G>A	ENST00000322313.4	-	16	2322	c.2164C>T	c.(2164-2166)Ccg>Tcg	p.P722S		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	722	Collagen-like.				mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GGGCCAGGCGGGCCTTGGGGG	0.637																																																0			2											66	77	73					2																	128477435		2203	4300	6503	128193905	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2164C>T	2.37:g.128477435G>A	ENSP00000325377:p.Pro722Ser		128193905	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069714	0.55539	.	.	ENSG00000136709	ENST00000322313	T	0.15718	2.4	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.18964	0.0455	L	0.48362	1.52	0.80722	D	1	P	0.37914	0.611	B	0.40256	0.324	T	0.01639	-1.1306	10	0.30078	T	0.28	-5.2875	14.0911	0.64990	0.0:0.0:0.8494:0.1506	.	722	Q9C0J8	WDR33_HUMAN	S	722	ENSP00000325377:P722S	ENSP00000325377:P722S	P	-	1	0	WDR33	128193905	1.000000	0.71417	0.953000	0.39169	0.980000	0.70556	6.233000	0.72320	2.616000	0.88540	0.585000	0.79938	CCG		0.637	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128477435	G	A	128477435	3	1	11	1	0	0	0	0	1	0	0	0	17327	1232	43	3	1874	3	WDR33	2	128477435	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	6735144	128477435	114721938	19	1289										
TTN	7273	hgsc.bcm.edu	37	chr2	179414890	179414890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cactccatctttgaaccaagTtactcgaggcactggtcttc	7	13	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:179414890T>C	ENST00000591111.1	-	287	86976	c.86752A>G	c.(86752-86754)Act>Gct	p.T28918A	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T21619A|TTN_ENST00000460472.2_Missense_Mutation_p.T21494A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T21686A|TTN_ENST00000589042.1_Missense_Mutation_p.T30559A|TTN_ENST00000342992.6_Missense_Mutation_p.T27991A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28918	Ig-like 133.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T21494S(1)|p.T27989S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGAACCAAGTTACTCGAGGC	0.428																																																2	Substitution - Missense(2)	ovary(2)	2											204	200	201					2																	179414890		1869	4109	5978	179123136	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.86752A>G	2.37:g.179414890T>C	ENSP00000465570:p.Thr28918Ala		179123136	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	16.03	3.007683	0.54361	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.69967	0.3170	M	0.80982	2.52	0.33697	D	0.614028	P;P;P;P	0.38617	0.454;0.454;0.454;0.64	B;B;B;B	0.40602	0.266;0.266;0.266;0.334	T	0.81846	-0.0745	9	0.87932	D	0	.	10.6581	0.45686	0.0:0.0714:0.0:0.9286	.	21494;21619;21686;28918	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	27991;21494;21686;21619;21491	ENSP00000343764:T27991A;ENSP00000434586:T21494A;ENSP00000340554:T21686A;ENSP00000352154:T21619A	ENSP00000340554:T21686A	T	-	1	0	TTN	179123136	0.921000	0.31238	1.000000	0.80357	0.987000	0.75469	1.254000	0.32897	2.317000	0.78254	0.460000	0.39030	ACT		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179414890	T	C	179414890	3	2	11	1	0	0	0	0	1	0	0	0	16775	1725	60	4	16408	4	TTN	2	179414890	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	50937455	179414890	63784483	20	1290										
TTN	7273	hgsc.bcm.edu	37	chr2	179438359	179438359	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctacatttgtccatgccaatCtgctggtttcacgtttctgt	7	11	3	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:179438359C>A	ENST00000591111.1	-	276	67801	c.67577G>T	c.(67576-67578)aGa>aTa	p.R22526I	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R15227I|TTN_ENST00000460472.2_Missense_Mutation_p.R15102I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R15294I|TTN_ENST00000589042.1_Missense_Mutation_p.R24167I|TTN_ENST00000342992.6_Missense_Mutation_p.R21599I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22526	Fibronectin type-III 63. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R15294T(1)|p.R21597T(1)|p.R21599T(1)|p.R15227T(1)|p.R15102T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATGCCAATCTGCTGGTTTC	0.413																																																5	Substitution - Missense(5)	lung(5)	2											278	274	276					2																	179438359		1935	4140	6075	179146605	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67577G>T	2.37:g.179438359C>A	ENSP00000465570:p.Arg22526Ile		179146605	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.67	2.307771	0.40795	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	6.08	5.19	0.71726	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78515	0.4295	M	0.93197	3.39	0.80722	D	1	D;D;D;D	0.62365	0.991;0.991;0.991;0.983	D;D;D;P	0.64877	0.93;0.93;0.93;0.9	D	0.85046	0.0926	9	0.87932	D	0	.	15.784	0.78289	0.0:0.9343:0.0:0.0657	.	15102;15227;15294;22526	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	21599;15102;15294;15227;15100	ENSP00000343764:R21599I;ENSP00000434586:R15102I;ENSP00000340554:R15294I;ENSP00000352154:R15227I	ENSP00000340554:R15294I	R	-	2	0	TTN	179146605	1.000000	0.71417	0.894000	0.35097	0.991000	0.79684	7.818000	0.86416	1.558000	0.49541	0.655000	0.94253	AGA		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179438359	C	A	179438359	3	1	11	1	0	0	0	0	1	0	0	0	16775	913	32	2	35627	2	TTN	2	179438359	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	23469	179438359	63761014	21	1291										
MYO1B	4430	hgsc.bcm.edu	37	chr2	192256875	192256875	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	taatgaattagaaattcccgTggaagaatactcctttggta	8	6	0	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:192256875T>C	ENST00000392318.3	+	19	2271	c.2024T>C	c.(2023-2025)gTg>gCg	p.V675A	MYO1B_ENST00000392316.1_Missense_Mutation_p.V675A|MYO1B_ENST00000339514.4_Missense_Mutation_p.V675A|MYO1B_ENST00000304164.4_Missense_Mutation_p.V675A|MYO1B_ENST00000439065.2_5'UTR	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	675	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GAAATTCCCGTGGAAGAATAC	0.323																																																0			2											66	73	70					2																	192256875		2203	4299	6502	191965120	SO:0001583	missense	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2024T>C	2.37:g.192256875T>C	ENSP00000376132:p.Val675Ala		191965120	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	T	6.163	0.398266	0.11696	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	5.71	4.57	0.56435	Myosin head, motor domain (2);	0.411684	0.25894	N	0.027618	T	0.38506	0.1043	N	0.02420	-0.555	0.39127	D	0.961786	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.35724	-0.9777	10	0.18276	T	0.48	.	4.8569	0.13564	0.2838:0.0845:0.0:0.6317	.	675;675	O43795;O43795-2	MYO1B_HUMAN;.	A	675	ENSP00000341903:V675A;ENSP00000376132:V675A;ENSP00000306382:V675A;ENSP00000376130:V675A	ENSP00000306382:V675A	V	+	2	0	MYO1B	191965120	0.348000	0.24861	0.994000	0.49952	0.910000	0.53928	1.956000	0.40382	2.180000	0.69256	0.455000	0.32223	GTG		0.323	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		C	192256875	T	C	192256875	3	2	11	1	0	0	0	0	1	0	0	0	10099	1696	59	4	2094	4	MYO1B	2	192256875	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	12818516	192256875	50942498	22	1292										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197639868	197639868	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcacaatttgctgactcttgGtcattgctgtctgatatttt	7	8	4	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:197639868G>A	ENST00000263956.3	-	13	1892	c.1803C>T	c.(1801-1803)gaC>gaT	p.D601D		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	601					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.D601E(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTGACTCTTGGTCATTGCTGT	0.348																																																1	Substitution - Missense(1)	ovary(1)	2											120	111	114					2																	197639868		2203	4300	6503	197348113	SO:0001819	synonymous_variant	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1803C>T	2.37:g.197639868G>A			197348113	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Silent	SNP	ENST00000263956.3	37	CCDS2316.1																																																																																				0.348	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			A	197639868	G	A	197639868	2	1	11	1	0	0	0	0	0	0	0	1	6895	1252	44	3		3	GTF3C3	2	197639868	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	5382993	197639868	45559505	23	1293										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230652244	230652244	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttttctatccaatctaggtgCaactctgctatcttgagaat	6	9	4	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr2:230652244C>A	ENST00000283943.5	-	32	4925	c.4747G>T	c.(4747-4749)Gca>Tca	p.A1583S	TRIP12_ENST00000389044.4_Missense_Mutation_p.A1631S|TRIP12_ENST00000389045.3_Missense_Mutation_p.A1313S	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1583					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.A1583S(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AATCTAGGTGCAACTCTGCTA	0.343																																																1	Substitution - Missense(1)	breast(1)	2											145	143	143					2																	230652244		2203	4300	6503	230360488	SO:0001583	missense	9320			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4747G>T	2.37:g.230652244C>A	ENSP00000283943:p.Ala1583Ser		230360488	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101583	0.76983	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.42513	0.97;0.97;0.97	5.38	4.5	0.54988	HECT (1);	0.000000	0.85682	D	0.000000	T	0.44074	0.1276	N	0.19112	0.55	0.80722	D	1	B;D;B	0.58620	0.243;0.983;0.243	B;P;B	0.59487	0.066;0.858;0.066	T	0.32322	-0.9911	10	0.33940	T	0.23	.	13.9679	0.64221	0.0:0.9269:0.0:0.0731	.	1313;1631;1583	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	S	1583;1313;1631	ENSP00000283943:A1583S;ENSP00000373697:A1313S;ENSP00000373696:A1631S	ENSP00000283943:A1583S	A	-	1	0	TRIP12	230360488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.452000	0.80683	1.257000	0.44085	0.557000	0.71058	GCA		0.343	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230652244	C	A	230652244	3	1	11	1	0	0	0	0	1	0	0	0	16596	710	25	2	1271	2	TRIP12	2	230652244	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	33012376	230652244	12547129	24	1294										
VHL	7428	hgsc.bcm.edu	37	chr3	10191551	10191551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	acaggagactggacatcgtcAggtcgctctacgaagatctg	12	10	3	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:10191551A>G	ENST00000256474.2	+	3	1384	c.544A>G	c.(544-546)Agg>Ggg	p.R182G	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.R141G	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	182					cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.R182fs*32(2)|p.R182fs*1(1)|p.V181fs*20(1)|p.L178_V181del(1)|p.V181fs*19(1)|p.I180fs*21(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GGACATCGTCAGGTCGCTCTA	0.517		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	7	Deletion - Frameshift(4)|Complex - frameshift(1)|Deletion - In frame(1)|Insertion - Frameshift(1)	kidney(7)	3											85	77	80					3																	10191551		2203	4300	6503	10166551	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.544A>G	3.37:g.10191551A>G	ENSP00000256474:p.Arg182Gly		10166551	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.454633	0.43634	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99830	-7.01;-7.01	4.97	0.955	0.19602	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.189261	0.42053	D	0.000772	D	0.99345	0.9770	M	0.63843	1.955	0.09310	N	1	P;P	0.50819	0.939;0.908	P;B	0.50934	0.654;0.433	D	0.99956	1.1625	10	0.72032	D	0.01	-8.6388	6.8061	0.23779	0.4385:0.4772:0.0842:0.0	.	141;182	P40337-2;P40337	.;VHL_HUMAN	G	182;141;100	ENSP00000256474:R182G;ENSP00000344757:R141G	ENSP00000256474:R182G	R	+	1	2	VHL	10166551	0.189000	0.23263	0.134000	0.22075	0.446000	0.32137	0.567000	0.23608	0.071000	0.16664	0.533000	0.62120	AGG		0.517	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191551	A	G	10191551	3	3	11	1	0	0	0	0	1	0	0	0	17202	179	7	4	554	4	VHL	3	10191551	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10		10191551	187830879	25	1295										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37783236	37783236	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cacagtggcaacacggagcgCtctgaatccctgcatgacaa	10	13	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:37783236C>A	ENST00000264741.5	+	21	2506	c.2250C>A	c.(2248-2250)cgC>cgA	p.R750R		NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	750			R -> C (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		ACACGGAGCGCTCTGAATCCC	0.557																																																0			3											107	82	91					3																	37783236		2203	4300	6503	37758240	SO:0001819	synonymous_variant	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2250C>A	3.37:g.37783236C>A			37758240	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																				0.557	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		A	37783236	C	A	37783236	2	1	11	1	0	0	0	0	0	0	0	1	7904	784	28	2		2	ITGA9	3	37783236	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	27591685	37783236	160239194	26	1296										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38802217	38802217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtaaggggtcagaagtgcctCgcttatttatgtagatatct	11	6	2	2	rs201955990	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:38802217C>A	ENST00000449082.2	-	7	904	c.905G>T	c.(904-906)cGa>cTa	p.R302L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	302					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGAAGTGCCTCGCTTATTTAT	0.453																																																0			3											120	107	112					3																	38802217		2203	4300	6503	38777221	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.905G>T	3.37:g.38802217C>A	ENSP00000390600:p.Arg302Leu		38777221	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111985	0.37242	.	.	ENSG00000185313	ENST00000449082	D	0.95588	-3.75	4.36	-2.62	0.06152	Ion transport (1);	3.700920	0.04016	U	0.299077	D	0.89273	0.6668	N	0.08118	0	0.09310	N	1	B	0.22346	0.068	B	0.25987	0.065	T	0.80696	-0.1267	10	0.59425	D	0.04	.	9.8669	0.41150	0.0:0.1199:0.309:0.5711	.	302	Q9Y5Y9	SCNAA_HUMAN	L	302	ENSP00000390600:R302L	ENSP00000390600:R302L	R	-	2	0	SCN10A	38777221	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-2.029000	0.01430	-0.318000	0.08665	-0.929000	0.02709	CGA		0.453	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38802217	C	A	38802217	3	1	11	1	0	0	0	0	1	0	0	0	13949	884	31	2	5049	2	SCN10A	3	38802217	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	1018981	38802217	159220213	27	1297										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266070	41266070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cagacagaaaagcggctgttAgtcactggcagcaacagtct	11	10	2	2	rs121913416		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:41266070A>G	ENST00000349496.5	+	3	347	c.67A>G	c.(67-69)Agt>Ggt	p.S23G	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S23G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S23G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S23G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S16G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	23	Interaction with VCL. {ECO:0000250}.		S -> R (in hepatocellular carcinoma; no effect). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.?(4)|p.V22_G38del(3)|p.T3_A126del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.M5_N141>D(2)|p.S23_S33del(2)|p.L10_N141del(2)|p.S23R(2)|p.A5_Y142>D(2)|p.S23G(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D6_S29del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.S23_I35del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.A5_I35del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		AGCGGCTGTTAGTCACTGGCA	0.453		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	116	Deletion - In frame(88)|Complex - deletion inframe(15)|Unknown(7)|Substitution - Missense(4)|Deletion - Frameshift(2)	liver(87)|large_intestine(18)|haematopoietic_and_lymphoid_tissue(3)|stomach(2)|small_intestine(2)|skin(2)|adrenal_gland(1)|pancreas(1)	3											89	75	80					3																	41266070		2203	4300	6503	41241074	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.67A>G	3.37:g.41266070A>G	ENSP00000344456:p.Ser23Gly		41241074	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.625416	0.46840	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	L	0.29908	0.895	0.80722	D	1	B	0.18968	0.032	B	0.20184	0.028	T	0.08659	-1.0711	10	0.23302	T	0.38	-0.5259	16.0676	0.80897	1.0:0.0:0.0:0.0	.	23	P35222	CTNB1_HUMAN	G	16;23;23;23;23;16;23;23;23	ENSP00000400508:S16G;ENSP00000385604:S23G;ENSP00000412219:S23G;ENSP00000379486:S23G;ENSP00000344456:S23G;ENSP00000411226:S16G;ENSP00000379488:S23G;ENSP00000409302:S23G;ENSP00000401599:S23G	ENSP00000344456:S23G	S	+	1	0	CTNNB1	41241074	1.000000	0.71417	0.971000	0.41717	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	AGT		0.453	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266070	A	G	41266070	3	3	11	1	0	0	0	0	1	0	0	0	4022	420	15	4	73	4	CTNNB1	3	41266070	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	2463853	41266070	156756360	28	1298										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74419063	74419063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccaagggcaaaacattccaaTttcacagtcgaacctttagc	6	12	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:74419063T>C	ENST00000263665.6	-	6	765	c.738A>G	c.(736-738)aaA>aaG	p.K246K		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	246	Ig-like C2-type 3.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		AACATTCCAATTTCACAGTCG	0.348																																																0			3											93	94	94					3																	74419063		2203	4299	6502	74501753	SO:0001819	synonymous_variant	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.738A>G	3.37:g.74419063T>C			74501753	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																				0.348	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		C	74419063	T	C	74419063	2	2	11	1	0	0	0	0	0	0	0	1	3648	1490	52	4		4	CNTN3	3	74419063	Silent	SNP	T	TCGA-AF-6655-01A-11D-1826-10	33152993	74419063	123603367	29	1299										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111988838	111988838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	atcaccaaaaacagttgacaTccaaaattgaatcagttttg	5	8	2	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:111988838T>C	ENST00000305815.5	-	7	952	c.700A>G	c.(700-702)Atg>Gtg	p.M234V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.M234V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	234					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.M234L(1)									ACAGTTGACATCCAAAATTGA	0.338																																																1	Substitution - Missense(1)	ovary(1)	3											68	73	72					3																	111988838		2203	4295	6498	113471528	SO:0001583	missense	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.700A>G	3.37:g.111988838T>C	ENSP00000306627:p.Met234Val		113471528	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.441495	0.25900	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.10668	2.85;2.85	5.9	4.79	0.61399	Cation/H+ exchanger (1);	0.307176	0.30940	N	0.008575	T	0.09335	0.0230	L	0.44542	1.39	0.22737	N	0.998794	P;P	0.40144	0.539;0.704	B;B	0.35470	0.139;0.203	T	0.25047	-1.0143	10	0.52906	T	0.07	-16.2819	9.1526	0.36973	0.0:0.0:0.2365:0.7635	.	234;234	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	234	ENSP00000306627:M234V;ENSP00000420688:M234V	ENSP00000306627:M234V	M	-	1	0	SLC9A10	113471528	0.998000	0.40836	0.961000	0.40146	0.387000	0.30353	0.915000	0.28638	2.258000	0.74832	0.413000	0.27773	ATG		0.338	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111988838	T	C	111988838	3	2	11	1	0	0	0	0	1	0	0	0	14747	1435	50	4	2925	4	SLC9A10	3	111988838	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	37569775	111988838	86033592	30	1300										
FBXO40	51725	hgsc.bcm.edu	37	chr3	121341411	121341411	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	caagtgaacacaaggcagtgGatacttcagatttggggatc	12	7	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:121341411G>T	ENST00000338040.4	+	3	1549	c.1135G>T	c.(1135-1137)Gat>Tat	p.D379Y		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	379					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CAAGGCAGTGGATACTTCAGA	0.488																																																0			3											118	109	112					3																	121341411		2203	4300	6503	122824101	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.1135G>T	3.37:g.121341411G>T	ENSP00000337510:p.Asp379Tyr		122824101	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.166181	0.57476	.	.	ENSG00000163833	ENST00000338040	T	0.50277	0.75	5.73	5.73	0.89815	.	0.045919	0.85682	D	0.000000	T	0.68339	0.2990	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70011	-0.4989	10	0.87932	D	0	-22.3895	17.4071	0.87476	0.0:0.0:1.0:0.0	.	379	Q9UH90	FBX40_HUMAN	Y	379	ENSP00000337510:D379Y	ENSP00000337510:D379Y	D	+	1	0	FBXO40	122824101	1.000000	0.71417	0.408000	0.26446	0.732000	0.41865	9.476000	0.97823	2.721000	0.93114	0.655000	0.94253	GAT		0.488	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121341411	G	T	121341411	3	4	11	1	0	0	0	0	1	0	0	0	5768	1174	41	2	1141	2	FBXO40	3	121341411	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	9352573	121341411	76681019	31	1301										
RAB6B	51560	hgsc.bcm.edu	37	chr3	133583442	133583442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cctcacctggtatgtgttgtCgaagctgtcgtacatgaacc	10	11	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:133583442C>T	ENST00000285208.4	-	2	464	c.115G>A	c.(115-117)Gac>Aac	p.D39N	RAB6B_ENST00000543906.1_Missense_Mutation_p.D39N|RAB6B_ENST00000486858.1_Missense_Mutation_p.D26N|RAB6B_ENST00000469959.1_Intron	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	39					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	11						TATGTGTTGTCGAAGCTGTCG	0.517																																																0			3											239	212	221					3																	133583442		2203	4300	6503	135066132	SO:0001583	missense	51560			AF166492	CCDS3082.1	3q22.1	2008-05-15			ENSG00000154917	ENSG00000154917		"RAB, member RAS oncogene"	14902	protein-coding gene	gene with protein product		615852					Standard	NM_016577		Approved		uc003epy.3	Q9NRW1	OTTHUMG00000159749	ENST00000285208.4:c.115G>A	3.37:g.133583442C>T	ENSP00000285208:p.Asp39Asn		135066132	B2R5Z9|B7Z337|D3DND3|Q92929	Missense_Mutation	SNP	ENST00000285208.4	37	CCDS3082.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944292	0.73672	.	.	ENSG00000154917	ENST00000285208;ENST00000543906;ENST00000486858;ENST00000477759;ENST00000488969	T;T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01;-1.01	5.14	5.14	0.70334	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.61261	0.2333	N	0.11698	0.16	0.80722	D	1	P;P	0.45396	0.857;0.525	B;B	0.37833	0.259;0.083	T	0.70149	-0.4951	10	0.72032	D	0.01	-17.5156	14.121	0.65186	0.0:1.0:0.0:0.0	.	26;39	B7Z337;Q9NRW1	.;RAB6B_HUMAN	N	39;39;26;6;6	ENSP00000285208:D39N;ENSP00000437797:D39N;ENSP00000419381:D26N;ENSP00000419941:D6N;ENSP00000417433:D6N	ENSP00000285208:D39N	D	-	1	0	RAB6B	135066132	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.985000	0.70556	2.393000	0.81446	0.655000	0.94253	GAC		0.517	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1			T	133583442	C	T	133583442	3	4	11	1	0	0	0	0	1	0	0	0	12989	884	31	1	539	1	RAB6B	3	133583442	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	12242031	133583442	64438988	32	1302										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401611	140401611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tgcacgggcgtctcaccaagCgctacatgcaggagcacggc	13	14	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:140401611C>T	ENST00000286349.3	+	2	840	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	217						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TCTCACCAAGCGCTACATGCA	0.617																																																0			3											76	75	75					3																	140401611		2203	4300	6503	141884301	SO:0001583	missense	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.649C>T	3.37:g.140401611C>T	ENSP00000286349:p.Arg217Cys		141884301	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.779527	0.70107	.	.	ENSG00000155890	ENST00000286349	T	0.41758	0.99	5.2	4.26	0.50523	Zinc finger, RING/FYVE/PHD-type (1);	0.121315	0.36591	N	0.002507	T	0.53238	0.1784	L	0.55990	1.75	0.45490	D	0.998452	D	0.89917	1.0	P	0.61874	0.895	T	0.55592	-0.8117	10	0.87932	D	0	-21.371	10.2072	0.43120	0.198:0.802:0.0:0.0	.	217	Q8IWZ5	TRI42_HUMAN	C	217	ENSP00000286349:R217C	ENSP00000286349:R217C	R	+	1	0	TRIM42	141884301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.086000	0.50159	2.435000	0.82474	0.561000	0.74099	CGC		0.617	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140401611	C	T	140401611	3	4	11	1	0	0	0	0	1	0	0	0	16557	768	27	1	655	1	TRIM42	3	140401611	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	6818169	140401611	57620819	33	1303										
C3orf58	205428	hgsc.bcm.edu	37	chr3	143704415	143704415	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctgatgaaggttggccatttGcaaagtatcttggagcttgt	12	6	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:143704415G>T	ENST00000315691.3	+	2	1223	c.688G>T	c.(688-690)Gca>Tca	p.A230S	C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.A21S|C3orf58_ENST00000441925.2_5'UTR	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	230					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)		p.A230P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TTGGCCATTTGCAAAGTATCT	0.383																																																1	Substitution - Missense(1)	ovary(1)	3											148	147	147					3																	143704415		2203	4300	6503	145187105	SO:0001583	missense	205428			AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.688G>T	3.37:g.143704415G>T	ENSP00000320081:p.Ala230Ser		145187105	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410370	0.83340	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000492452	T	0.31247	1.5	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.45397	0.1340	L	0.51422	1.61	0.80722	D	1	P;D	0.61697	0.693;0.99	B;P	0.54664	0.315;0.758	T	0.41980	-0.9478	10	0.66056	D	0.02	.	18.8382	0.92171	0.0:0.0:1.0:0.0	.	21;230	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	S	230;21;36	ENSP00000320081:A230S	ENSP00000320081:A230S	A	+	1	0	C3orf58	145187105	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.461000	0.83175	0.655000	0.94253	GCA		0.383	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		T	143704415	G	T	143704415	3	4	11	1	0	0	0	0	1	0	0	0	2242	1319	46	2	728	2	C3orf58	3	143704415	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	3302804	143704415	54318015	34	1304										
HRG	3273	hgsc.bcm.edu	37	chr3	186392939	186392939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agccttggacttggaaagccCgaaaaaccttgtcataaact	8	10	1	0	rs111439697	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr3:186392939C>T	ENST00000232003.4	+	6	781	c.701C>T	c.(700-702)cCg>cTg	p.P234L		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	234	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TTGGAAAGCCCGAAAAACCTT	0.453													C|||	80	0.0159744	0.0575	0.0058	5008	,	,		20063	0		0	False		,,,				2504	0															0			3						C	LEU/PRO	278,4128	157.0+/-190.0	7,264,1932	237	241	240		701	5.3	0.6	3	dbSNP_132	240	1,8599	1.2+/-3.3	0,1,4299	yes	missense	HRG	NM_000412.2	98	7,265,6231	TT,TC,CC		0.0116,6.3096,2.1452	probably-damaging	234/526	186392939	279,12727	2203	4300	6503	187875633	SO:0001583	missense	3273				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.701C>T	3.37:g.186392939C>T	ENSP00000232003:p.Pro234Leu		187875633	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	C	15.04	2.715998	0.48622	0.063096	1.16E-4	ENSG00000113905	ENST00000232003	T	0.18174	2.23	5.28	5.28	0.74379	Proteinase inhibitor I25, cystatin (1);	0.000000	0.51477	D	0.000083	T	0.05731	0.0150	M	0.62723	1.935	0.44168	D	0.996975	D	0.89917	1.0	D	0.91635	0.999	T	0.00044	-1.2220	10	0.52906	T	0.07	-12.5376	14.794	0.69865	0.0:1.0:0.0:0.0	.	234	P04196	HRG_HUMAN	L	234	ENSP00000232003:P234L	ENSP00000232003:P234L	P	+	2	0	HRG	187875633	0.101000	0.21875	0.565000	0.28409	0.020000	0.10135	2.124000	0.42006	2.646000	0.89796	0.561000	0.74099	CCG		0.453	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		T	186392939	C	T	186392939	3	4	11	1	0	0	0	0	1	0	0	0	7375	652	23	1	723	1	HRG	3	186392939	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	42688524	186392939	11629491	35	1305										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15067925	15067925	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttgggcaaatatccactctcGtgctggacgtgagttccata	10	10	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr4:15067925G>A	ENST00000507071.1	+	11	1778	c.1691G>A	c.(1690-1692)cGt>cAt	p.R564H	CPEB2_ENST00000442003.2_Missense_Mutation_p.R982H|CPEB2_ENST00000259997.5_Missense_Mutation_p.R572H|CPEB2_ENST00000541112.1_Missense_Mutation_p.R1001H|CPEB2_ENST00000538197.1_Missense_Mutation_p.R1009H|CPEB2_ENST00000382395.3_Missense_Mutation_p.R542H|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000345451.3_Missense_Mutation_p.R534H|CPEB2_ENST00000382401.3_Missense_Mutation_p.R537H|RP11-665G4.1_ENST00000502344.1_RNA			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	564					cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						ATCCACTCTCGTGCTGGACGT	0.493																																																0			4											162	145	151					4																	15067925		2203	4300	6503	14677023	SO:0001583	missense	132864			AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.1691G>A	4.37:g.15067925G>A	ENSP00000424084:p.Arg564His		14677023	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	37		.	.	.	.	.	.	.	.	.	.	G	19.33	3.806883	0.70797	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003;ENST00000507071;ENST00000345451;ENST00000382395;ENST00000382401;ENST00000259997;ENST00000382391	T;T;T;T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09;2.09;2.09;2.09	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.44540	0.1298	L	0.47190	1.495	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.971;1.0;1.0	D;D;D;P;D;D	0.87578	0.993;0.998;0.991;0.741;0.998;0.992	T	0.11251	-1.0595	10	0.87932	D	0	-14.8172	20.8598	0.99761	0.0:0.0:1.0:0.0	.	537;542;982;1009;534;564	Q7Z5Q1-4;Q7Z5Q1-6;E7EPM3;F5H160;Q7Z5Q1-5;Q7Z5Q1	.;.;.;.;.;CPEB2_HUMAN	H	1009;1001;982;564;534;542;537;572;551	ENSP00000443985:R1009H;ENSP00000437884:R1001H;ENSP00000414270:R982H;ENSP00000424084:R564H;ENSP00000334058:R534H;ENSP00000371832:R542H;ENSP00000371838:R537H;ENSP00000259997:R572H	ENSP00000259997:R572H	R	+	2	0	CPEB2	14677023	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	CGT		0.493	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		A	15067925	G	A	15067925	3	1	11	1	0	0	0	0	1	0	0	0	3807	1145	40	1	3081	1	CPEB2	4	15067925	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10		15067925	176086351	36	1306										
UBE2K	3093	hgsc.bcm.edu	37	chr4	39757308	39757308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cactaaaatatggcatcctaAtattagttccgtcacagggg	8	9	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr4:39757308A>G	ENST00000261427.5	+	4	532	c.248A>G	c.(247-249)aAt>aGt	p.N83S	UBE2K_ENST00000503368.1_Missense_Mutation_p.N32S|UBE2K_ENST00000295963.6_Intron|UBE2K_ENST00000445950.2_Missense_Mutation_p.N83S|UBE2K_ENST00000438068.2_3'UTR	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	83					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						TGGCATCCTAATATTAGTTCC	0.338																																					NSCLC(101;689 1592 16105 29682 31745)											0			4											161	161	161					4																	39757308		2203	4299	6502	39433703	SO:0001583	missense	3093			U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.248A>G	4.37:g.39757308A>G	ENSP00000261427:p.Asn83Ser		39433703	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	37	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.005931	0.93287	.	.	ENSG00000078140	ENST00000261427;ENST00000503368;ENST00000445950	T;T;T	0.56103	0.48;0.48;0.48	6.08	6.08	0.98989	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	D	0.83031	0.5166	H	0.97940	4.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.985	D	0.89250	0.3590	10	0.87932	D	0	-14.4541	15.6338	0.76933	1.0:0.0:0.0:0.0	.	83;32;83	P61086;P61086-2;C9JGP1	UBE2K_HUMAN;.;.	S	83;32;83	ENSP00000261427:N83S;ENSP00000421203:N32S;ENSP00000390483:N83S	ENSP00000261427:N83S	N	+	2	0	UBE2K	39433703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.872000	0.92352	2.333000	0.79357	0.482000	0.46254	AAT		0.338	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		G	39757308	A	G	39757308	3	3	11	1	0	0	0	0	1	0	0	0	16902	101	4	4	262	4	UBE2K	4	39757308	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	24689383	39757308	151396968	37	1307										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85742596	85742596	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aattggcattgtcagccatgTaaatatttgtgatagcatca	8	6	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr4:85742596T>A	ENST00000295888.4	-	11	1639	c.1232A>T	c.(1231-1233)tAc>tTc	p.Y411F	WDFY3_ENST00000322366.6_Missense_Mutation_p.Y411F	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	411					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.Y411S(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GTCAGCCATGTAAATATTTGT	0.393																																																1	Substitution - Missense(1)	ovary(1)	4											114	115	114					4																	85742596		2203	4300	6503	85961620	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.1232A>T	4.37:g.85742596T>A	ENSP00000295888:p.Tyr411Phe		85961620	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419472	0.83559	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.17370	2.28;2.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	L	0.61387	1.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.05683	-1.0870	10	0.31617	T	0.26	.	16.0204	0.80478	0.0:0.0:0.0:1.0	.	411;411	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	F	411	ENSP00000318466:Y411F;ENSP00000295888:Y411F	ENSP00000295888:Y411F	Y	-	2	0	WDFY3	85961620	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	7.642000	0.83385	2.174000	0.68829	0.533000	0.62120	TAC		0.393	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85742596	T	A	85742596	3	1	11	1	0	0	0	0	1	0	0	0	17310	1638	57	5	9623	5	WDFY3	4	85742596	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	45985288	85742596	105411680	38	1308										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123161215	123161215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctctgccattcaaaactcatCcttctcaggcttcatttgtt	4	13	5	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr4:123161215C>T	ENST00000264501.4	+	29	4751	c.4378C>T	c.(4378-4380)Cct>Tct	p.P1460S	KIAA1109_ENST00000388738.3_Missense_Mutation_p.P1460S|KIAA1109_ENST00000455637.1_Missense_Mutation_p.P1460S			Q2LD37	K1109_HUMAN	KIAA1109	1460					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAAAACTCATCCTTCTCAGGC	0.413																																																0			4											94	89	91					4																	123161215		1863	4098	5961	123380665	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.4378C>T	4.37:g.123161215C>T	ENSP00000264501:p.Pro1460Ser		123380665	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.353048	0.24512	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	T;T;T	0.21932	2.57;2.57;1.98	6.05	6.05	0.98169	.	0.000000	0.44688	U	0.000432	T	0.13372	0.0324	N	0.08118	0	0.37666	D	0.922937	B;B	0.25272	0.122;0.043	B;B	0.28305	0.088;0.04	T	0.23619	-1.0183	10	0.27785	T	0.31	.	16.0133	0.80420	0.0:0.8664:0.1336:0.0	.	1459;1460	Q2LD37-2;Q2LD37	.;K1109_HUMAN	S	1460	ENSP00000264501:P1460S;ENSP00000373390:P1460S;ENSP00000389925:P1460S	ENSP00000264501:P1460S	P	+	1	0	KIAA1109	123380665	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.229000	0.42990	2.878000	0.98634	0.650000	0.86243	CCT		0.413	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123161215	C	T	123161215	3	4	11	1	0	0	0	0	1	0	0	0	8229	855	30	3	4484	3	KIAA1109	4	123161215	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	37418619	123161215	67993061	39	1309										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247208	153247208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctgcaacgtgtgtagacaggTttcagtctctggatcccaca	10	11	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr4:153247208T>C	ENST00000281708.4	-	10	2823	c.1594A>G	c.(1594-1596)Acc>Gcc	p.T532A	FBXW7_ENST00000603841.1_Missense_Mutation_p.T532A|FBXW7_ENST00000296555.5_Missense_Mutation_p.T414A|FBXW7_ENST00000393956.3_Missense_Mutation_p.T356A|FBXW7_ENST00000603548.1_Missense_Mutation_p.T532A|FBXW7_ENST00000263981.5_Missense_Mutation_p.T452A	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	532					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGTAGACAGGTTTCAGTCTCT	0.438			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											197	190	192					4																	153247208		2203	4300	6503	153466658	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1594A>G	4.37:g.153247208T>C	ENSP00000281708:p.Thr532Ala		153466658	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578043	0.45902	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	5.72	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.089480	0.85682	D	0.000000	T	0.37348	0.1000	N	0.05441	-0.05	0.80722	D	1	B;B;B;B	0.11235	0.0;0.004;0.0;0.001	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.11108	-1.0601	10	0.37606	T	0.19	-11.4963	13.2579	0.60089	0.0:0.0:0.1326:0.8674	.	356;532;414;452	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	A	532;414;452;356	ENSP00000281708:T532A;ENSP00000296555:T414A;ENSP00000263981:T452A;ENSP00000377528:T356A	ENSP00000263981:T452A	T	-	1	0	FBXW7	153466658	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.997000	0.88414	1.077000	0.40990	-0.323000	0.08544	ACC		0.438	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153247208	T	C	153247208	3	2	11	1	0	0	0	0	1	0	0	0	5788	1725	60	4	541	4	FBXW7	4	153247208	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	30085993	153247208	37907068	40	1310										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	174192	174192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcatagggaggatcctgtggCggcaggcactaaagagcaga	15	8	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:174192C>T	ENST00000283426.6	+	16	3363	c.3313C>T	c.(3313-3315)Cgg>Tgg	p.R1105W		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1105							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GATCCTGTGGCGGCAGGCACT	0.632																																																0			5											32	24	27					5																	174192		2202	4298	6500	227192	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3313C>T	5.37:g.174192C>T	ENSP00000283426:p.Arg1105Trp		227192		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	C	8.661	0.900514	0.17686	.	.	ENSG00000153404	ENST00000283426	T	0.12465	2.68	3.38	-2.21	0.06973	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	.	.	.	.	T	0.16041	0.0386	L	0.46741	1.465	0.32002	N	0.603189	D	0.59767	0.986	P	0.51701	0.677	T	0.27502	-1.0072	9	0.87932	D	0	.	5.7095	0.17927	0.3002:0.5017:0.0:0.1981	.	1105	Q96PX9	PKH4B_HUMAN	W	1105	ENSP00000283426:R1105W	ENSP00000283426:R1105W	R	+	1	2	PLEKHG4B	227192	0.310000	0.24527	0.763000	0.31416	0.009000	0.06853	0.199000	0.17237	-0.737000	0.04824	-2.051000	0.00406	CGG		0.632	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	174192	C	T	174192	3	4	11	1	0	0	0	0	1	0	0	0	12103	759	27	1	3375	1	PLEKHG4B	5	174192	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10		174192	180741068	41	1311										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13864592	13864592	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccccacatccagactgtgccCggtgagggtggttatccttt	11	13	0	2	rs143567667	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:13864592C>A	ENST00000265104.4	-	28	4614	c.4510G>T	c.(4510-4512)Ggg>Tgg	p.G1504W	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1504	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGACTGTGCCCGGTGAGGGTG	0.458									Kartagener syndrome																																							0			5											65	65	65					5																	13864592		2203	4300	6503	13917592	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4510G>T	5.37:g.13864592C>A	ENSP00000265104:p.Gly1504Trp		13917592	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166362	0.57476	.	.	ENSG00000039139	ENST00000265104	T	0.64618	-0.11	5.32	5.32	0.75619	Dynein heavy chain, domain-2 (1);	0.054301	0.64402	D	0.000001	D	0.86871	0.6037	H	0.96662	3.86	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.91312	0.5075	10	0.87932	D	0	.	19.0581	0.93074	0.0:1.0:0.0:0.0	.	1504	Q8TE73	DYH5_HUMAN	W	1504	ENSP00000265104:G1504W	ENSP00000265104:G1504W	G	-	1	0	DNAH5	13917592	1.000000	0.71417	0.792000	0.32020	0.100000	0.18952	7.365000	0.79537	2.488000	0.83962	0.632000	0.83419	GGG		0.458	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13864592	C	A	13864592	3	1	11	1	0	0	0	0	1	0	0	0	4615	652	23	2	9572	2	DNAH5	5	13864592	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	13690400	13864592	167050668	42	1312										
TRIO	7204	hgsc.bcm.edu	37	chr5	14472720	14472720	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gctacgttttgcaagaactaGtggagacagagcgtgactat	12	7	0	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:14472720G>C	ENST00000344204.4	+	39	5956	c.5932G>C	c.(5932-5934)Gtg>Ctg	p.V1978L	TRIO_ENST00000537187.1_Missense_Mutation_p.V1978L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1978	DH 2. {ECO:0000255|PROSITE- ProRule:PRU00062}.		V -> M (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1978M(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GCAAGAACTAGTGGAGACAGA	0.393																																																1	Substitution - Missense(1)	skin(1)	5											201	175	184					5																	14472720		2203	4300	6503	14525720	SO:0001583	missense	7204			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.5932G>C	5.37:g.14472720G>C	ENSP00000339299:p.Val1978Leu		14525720	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069048	0.55539	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000541447	T;T;T	0.62232	0.04;0.04;0.08	5.38	5.38	0.77491	Dbl homology (DH) domain (5);	0.064020	0.64402	D	0.000007	T	0.44726	0.1307	N	0.20845	0.615	0.51233	D	0.99991	P;B	0.39094	0.659;0.274	B;B	0.32624	0.14;0.149	T	0.43212	-0.9405	10	0.10377	T	0.69	.	19.1549	0.93506	0.0:0.0:1.0:0.0	.	1978;1978	O75962-5;O75962	.;TRIO_HUMAN	L	1978;1978;1665;58	ENSP00000339299:V1978L;ENSP00000446348:V1978L;ENSP00000426342:V1665L	ENSP00000339299:V1978L	V	+	1	0	TRIO	14525720	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.968000	0.87980	2.529000	0.85273	0.655000	0.94253	GTG		0.393	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		C	14472720	G	C	14472720	3	2	11	1	0	0	0	0	1	0	0	0	16592	1029	36	5	6086	5	TRIO	5	14472720	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	608128	14472720	166442540	43	1313										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37169591	37169591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agtggatggtaagttttgagAtgatggaattggtccttttt	13	2	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:37169591A>G	ENST00000508244.1	-	33	6628	c.6535T>C	c.(6535-6537)Tct>Cct	p.S2179P	C5orf42_ENST00000425232.2_Missense_Mutation_p.S2179P|C5orf42_ENST00000274258.7_Missense_Mutation_p.S1059P			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2179						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAGTTTTGAGATGATGGAATT	0.413																																																0			5											75	77	76					5																	37169591		2203	4300	6503	37205348	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6535T>C	5.37:g.37169591A>G	ENSP00000421690:p.Ser2179Pro		37205348	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	A	13.37	2.216443	0.39201	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.25414	1.81;1.81;1.8;1.8	5.53	1.15	0.20763	.	0.528900	0.18498	N	0.139460	T	0.17577	0.0422	L	0.36672	1.1	0.09310	N	1	B;B	0.24186	0.058;0.099	B;B	0.26202	0.013;0.067	T	0.16719	-1.0393	10	0.51188	T	0.08	.	5.6908	0.17829	0.6638:0.1408:0.1954:0.0	.	2179;1059	E9PH94;Q9H799	.;CE042_HUMAN	P	2179;2179;1059;1227;1059	ENSP00000421690:S2179P;ENSP00000389014:S2179P;ENSP00000274258:S1059P;ENSP00000424223:S1227P	ENSP00000274258:S1059P	S	-	1	0	C5orf42	37205348	0.033000	0.19621	0.788000	0.31933	0.184000	0.23303	0.423000	0.21313	0.878000	0.35920	0.533000	0.62120	TCT		0.413	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37169591	A	G	37169591	3	3	11	1	0	0	0	0	1	0	0	0	2307	333	12	4	3134	4	C5orf42	5	37169591	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	22696871	37169591	143745669	44	1314										
OSMR	9180	hgsc.bcm.edu	37	chr5	38932601	38932601	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tatcctgacatccctgacccTtacaagagcagcatcctgtc	6	15	0	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:38932601T>C	ENST00000274276.3	+	17	2733	c.2331T>C	c.(2329-2331)ccT>ccC	p.P777P		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	777					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TCCCTGACCCTTACAAGAGCA	0.403																																																0			5											109	100	103					5																	38932601		2203	4300	6503	38968358	SO:0001819	synonymous_variant	9180			U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.2331T>C	5.37:g.38932601T>C			38968358	Q6P4E8|Q96QJ6	Silent	SNP	ENST00000274276.3	37	CCDS3928.1																																																																																				0.403	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		C	38932601	T	C	38932601	2	2	11	1	0	0	0	0	0	0	0	1	11323	1596	56	4		4	OSMR	5	38932601	Silent	SNP	T	TCGA-AF-6655-01A-11D-1826-10	1763010	38932601	141982659	45	1315										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41008757	41008757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tccctgctgcatcacatgccGcctatggctccagggacaag	10	15	1	0	rs369303264		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:41008757G>A	ENST00000399564.4	-	33	4009	c.3559C>T	c.(3559-3561)Cgg>Tgg	p.R1187W	MROH2B_ENST00000506092.2_Missense_Mutation_p.R742W	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1187																	ATCACATGCCGCCTATGGCTC	0.562																																																0			5						G	TRP/ARG	2,4130		0,2,2064	84	86	85		3559	4	0.1	5		85	0,8414		0,0,4207	no	missense	HEATR7B2	NM_173489.4	101	0,2,6271	AA,AG,GG		0.0,0.0484,0.0159	probably-damaging	1187/1586	41008757	2,12544	2066	4207	6273	41044514	SO:0001583	missense	133558				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.3559C>T	5.37:g.41008757G>A	ENSP00000382476:p.Arg1187Trp		41044514	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963691	0.53507	4.84E-4	0.0	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.01455	4.87;5.11	5.97	4.02	0.46733	Armadillo-type fold (1);	0.104180	0.41605	D	0.000846	T	0.02807	0.0084	N	0.04508	-0.205	0.09310	N	0.999995	D	0.89917	1.0	D	0.77004	0.989	T	0.51826	-0.8656	10	0.49607	T	0.09	.	10.6622	0.45708	0.0:0.0:0.5792:0.4208	.	1187	Q7Z745	HTRB2_HUMAN	W	742;892;1187	ENSP00000441504:R742W;ENSP00000382476:R1187W	ENSP00000296803:R892W	R	-	1	2	HEATR7B2	41044514	0.182000	0.23173	0.106000	0.21319	0.566000	0.35808	1.312000	0.33574	1.512000	0.48834	0.561000	0.74099	CGG		0.562	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		A	41008757	G	A	41008757	3	1	11	1	0	0	0	0	1	0	0	0	7056	1086	38	1	1238	1	HEATR7B2	5	41008757	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	2076156	41008757	139906503	46	1316										
CKMT2	1160	hgsc.bcm.edu	37	chr5	80550909	80550909	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cctgcctccagcctgcacccGggccgagcgaagggaggtag	15	15	0	0	rs368812686		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:80550909G>A	ENST00000424301.2	+	6	783	c.545G>A	c.(544-546)cGg>cAg	p.R182Q	CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2_ENST00000254035.4_Missense_Mutation_p.R182Q|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.R182Q|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2-AS1_ENST00000505295.1_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	182	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	GCCTGCACCCGGGCCGAGCGA	0.652																																																0			5						G	GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	55	52	53		545,545,545	5.8	0.3	5		53	0,8600		0,0,4300	no	missense,missense,missense	CKMT2	NM_001099735.1,NM_001099736.1,NM_001825.2	43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	182/420,182/420,182/420	80550909	1,13005	2203	4300	6503	80586665	SO:0001583	missense	1160				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.545G>A	5.37:g.80550909G>A	ENSP00000404203:p.Arg182Gln		80586665	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	ENST00000424301.2	37	CCDS4053.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.276964	0.80580	2.27E-4	0.0	ENSG00000131730	ENST00000254035;ENST00000437669;ENST00000424301	T;T;T	0.11930	2.73;2.73;2.73	5.8	5.8	0.92144	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51419	-0.8708	10	0.59425	D	0.04	-30.6222	20.0693	0.97712	0.0:0.0:1.0:0.0	.	182	P17540	KCRS_HUMAN	Q	182	ENSP00000254035:R182Q;ENSP00000410289:R182Q;ENSP00000404203:R182Q	ENSP00000254035:R182Q	R	+	2	0	CKMT2	80586665	0.999000	0.42202	0.348000	0.25681	0.015000	0.08874	9.476000	0.97823	2.758000	0.94735	0.563000	0.77884	CGG		0.652	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		A	80550909	G	A	80550909	3	1	11	1	0	0	0	0	1	0	0	0	3457	1116	39	1	559	1	CKMT2	5	80550909	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	39542152	80550909	100364351	47	1317										
APC	324	hgsc.bcm.edu	37	chr5	112155003	112155003	+	Frame_Shift_Del	DEL	A	A	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aacctgttgggagtggcaggAagctcatgaaccaggcatgg					rs77907679		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:112155003delA	ENST00000457016.1	+	10	1654	c.1274delA	c.(1273-1275)gaafs	p.E425fs	APC_ENST00000508376.2_Frame_Shift_Del_p.E425fs|APC_ENST00000257430.4_Frame_Shift_Del_p.E425fs			P25054	APC_HUMAN	adenomatous polyposis coli	425	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAGTGGCAGGAAGCTCATGAA	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	0			5											58	57	57					5																	112155003		2202	4300	6502	112182902	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1274delA	5.37:g.112155003delA	ENSP00000413133:p.Glu425fs		112182902	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112155003	A	-	112155003	7	5	11	1	0	1	0	1	0	0	0	0	763	246	9	0	1308	0	APC	5	112155003	Frame_Shift_Del	DEL	A	TCGA-AF-6655-01A-11D-1826-10	31604094	112155003	68760257	48	1318										
APC	324	hgsc.bcm.edu	37	chr5	112175448	112175448	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gaccccactcatgtttagcaGatgtacttctgtcagttcac	7	12	4	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:112175448G>A	ENST00000457016.1	+	16	4537	c.4157G>A	c.(4156-4158)aGa>aAa	p.R1386K	APC_ENST00000508376.2_Missense_Mutation_p.R1386K|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.R1386K			P25054	APC_HUMAN	adenomatous polyposis coli	1386	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1386>R*(1)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATGTTTAGCAGATGTACTTCT	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											103	97	99					5																	112175448		2202	4300	6502	112203347	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4157G>A	5.37:g.112175448G>A	ENSP00000413133:p.Arg1386Lys		112203347	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837438	0.91117	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.82526	-1.62;-1.62;-1.62	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.90045	0.6891	L	0.58810	1.83	0.53005	D	0.999964	D;D	0.69078	0.997;0.997	D;D	0.79108	0.992;0.992	D	0.87630	0.2515	9	.	.	.	-26.0092	20.4898	0.99202	0.0:0.0:1.0:0.0	.	1388;1386	Q4LE70;P25054	.;APC_HUMAN	K	1386	ENSP00000413133:R1386K;ENSP00000257430:R1386K;ENSP00000427089:R1386K	.	R	+	2	0	APC	112203347	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	AGA		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175448	G	A	112175448	3	1	11	1	0	0	0	0	1	0	0	0	763	942	33	3	4215	3	APC	5	112175448	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	20445	112175448	68739812	49	1319										
APC	324	hgsc.bcm.edu	37	chr5	112175626	112175626	+	Frame_Shift_Del	DEL	A	A	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cctccaccacctcctcaaacAgctcaaaccaagcgagaagt							TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:112175626delA	ENST00000457016.1	+	16	4715	c.4335delA	c.(4333-4335)acafs	p.T1445fs	APC_ENST00000508376.2_Frame_Shift_Del_p.T1445fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.T1445fs			P25054	APC_HUMAN	adenomatous polyposis coli	1445	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1445fs*27(4)|p.A1446fs*27(1)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.S1436fs*22(1)|p.A1446fs*1(1)|p.P1441fs*27(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCCTCAAACAGCTCAAACCA	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	11	Deletion - Frameshift(9)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(9)|soft_tissue(1)|skin(1)	5											109	96	100					5																	112175626		2202	4300	6502	112203525	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4335delA	5.37:g.112175626delA	ENSP00000413133:p.Thr1445fs		112203525	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175626	A	-	112175626	7	5	11	1	0	1	0	1	0	0	0	0	763	175	7	0	4393	0	APC	5	112175626	Frame_Shift_Del	DEL	A	TCGA-AF-6655-01A-11D-1826-10	178	112175626	68739634	50	1320										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129019933	129019933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcttcatgtggacacacacaAgctgggaagattgcgatgcc	11	10	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:129019933A>G	ENST00000274487.4	+	18	2912	c.2767A>G	c.(2767-2769)Agc>Ggc	p.S923G	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	923	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		GACACACACAAGCTGGGAAGA	0.408																																																0			5											86	83	84					5																	129019933		2203	4300	6503	129047832	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2767A>G	5.37:g.129019933A>G	ENSP00000274487:p.Ser923Gly		129047832		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	3.758	-0.050103	0.07407	.	.	ENSG00000145808	ENST00000274487	T	0.61510	0.1	4.56	3.69	0.42338	.	0.220019	0.39020	N	0.001494	T	0.34454	0.0898	N	0.11106	0.095	0.26174	N	0.979826	B	0.06786	0.001	B	0.01281	0.0	T	0.13575	-1.0504	9	.	.	.	.	11.2452	0.48993	0.1604:0.0:0.8396:0.0	.	923	Q8TE59	ATS19_HUMAN	G	923	ENSP00000274487:S923G	.	S	+	1	0	ADAMTS19	129047832	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.732000	0.47352	1.498000	0.48600	-0.248000	0.11899	AGC		0.408	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	129019933	A	G	129019933	3	3	11	1	0	0	0	0	1	0	0	0	264	72	3	4	2837	4	ADAMTS19	5	129019933	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	16844307	129019933	51895327	51	1321										
MYOT	9499	hgsc.bcm.edu	37	chr5	137217668	137217668	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aaatattcttgtagaagtagAtcaacctcaaggggagatgt	10	5	3	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:137217668A>T	ENST00000239926.4	+	6	1064	c.690A>T	c.(688-690)agA>agT	p.R230S	MYOT_ENST00000421631.2_Missense_Mutation_p.R46S|MYOT_ENST00000509812.1_Intron|MYOT_ENST00000515645.1_Missense_Mutation_p.R115S|RP11-381K20.2_ENST00000514616.1_RNA|RP11-381K20.2_ENST00000508281.2_RNA	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	230	Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)			cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GTAGAAGTAGATCAACCTCAA	0.343																																																0			5											96	95	95					5																	137217668		2203	4300	6503	137245567	SO:0001583	missense	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.690A>T	5.37:g.137217668A>T	ENSP00000239926:p.Arg230Ser		137245567	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	A	18.83	3.707835	0.68615	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.69435	-0.35;-0.29;-0.4	5.61	3.24	0.37175	.	0.138225	0.50627	D	0.000114	T	0.48205	0.1487	N	0.24115	0.695	0.40639	D	0.981927	P	0.52842	0.956	B	0.40940	0.344	T	0.47749	-0.9093	10	0.42905	T	0.14	.	8.7386	0.34543	0.7885:0.0:0.2115:0.0	.	230	Q9UBF9	MYOTI_HUMAN	S	230;46;115	ENSP00000239926:R230S;ENSP00000391185:R46S;ENSP00000426281:R115S	ENSP00000239926:R230S	R	+	3	2	MYOT	137245567	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.995000	0.29706	0.954000	0.37851	0.482000	0.46254	AGA		0.343	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		T	137217668	A	T	137217668	3	4	11	1	0	0	0	0	1	0	0	0	10124	330	12	5	708	5	MYOT	5	137217668	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	8197735	137217668	43697592	52	1322										
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148627394	148627394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gaaggaagaaatgaaggcccGgtcgagctcctatgcagatc	13	9	0	3	rs373620710		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:148627394G>A	ENST00000506113.1	+	17	2083	c.1601G>A	c.(1600-1602)cGg>cAg	p.R534Q	ABLIM3_ENST00000356541.3_Missense_Mutation_p.R423Q|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000504238.1_Missense_Mutation_p.R423Q|ABLIM3_ENST00000517451.1_Missense_Mutation_p.R20Q|ABLIM3_ENST00000508983.1_Missense_Mutation_p.R501Q|ABLIM3_ENST00000309868.7_Missense_Mutation_p.R534Q|ABLIM3_ENST00000326685.7_Missense_Mutation_p.R439Q|AC012613.2_ENST00000523176.1_RNA|RP11-331K21.1_ENST00000522685.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	534					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGAAGGCCCGGTCGAGCTCC	0.557																																																0			5											41	45	44					5																	148627394		2203	4300	6503	148607587	SO:0001583	missense	22885			AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1601G>A	5.37:g.148627394G>A	ENSP00000425394:p.Arg534Gln		148607587	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531892	0.85706	.	.	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983;ENST00000517451;ENST00000536903	T;T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33;1.33	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.50446	0.1616	N	0.25485	0.75	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;P	0.83275	0.996;0.984;0.982;0.9	T	0.51419	-0.8708	10	0.59425	D	0.04	.	19.6415	0.95760	0.0:0.0:1.0:0.0	.	20;439;423;534	O94929-4;O94929-3;O94929-2;O94929	.;.;.;ABLM3_HUMAN	Q	439;423;534;534;423;501;20;19	ENSP00000315841:R439Q;ENSP00000348938:R423Q;ENSP00000310309:R534Q;ENSP00000425394:R534Q;ENSP00000421183:R423Q;ENSP00000420855:R501Q;ENSP00000430150:R20Q	ENSP00000310309:R534Q	R	+	2	0	ABLIM3	148607587	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.758000	0.91663	2.651000	0.90000	0.561000	0.74099	CGG		0.557	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		A	148627394	G	A	148627394	3	1	11	1	0	0	0	0	1	0	0	0	96	1116	39	1	1667	1	ABLIM3	5	148627394	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	11409726	148627394	32287866	53	1323										
LARP1	23367	hgsc.bcm.edu	37	chr5	154174737	154174737	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cttcttccctccacttagtgAatactacttcagcgtggaca	6	13	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr5:154174737A>G	ENST00000336314.4	+	8	1028	c.1004A>G	c.(1003-1005)gAa>gGa	p.E335G		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	412					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCACTTAGTGAATACTACTTC	0.463																																																0			5											152	137	142					5																	154174737		2203	4300	6503	154154930	SO:0001583	missense	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1004A>G	5.37:g.154174737A>G	ENSP00000336721:p.Glu335Gly		154154930	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.303886|5.303886	0.95601|0.95601	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000336314;ENST00000518297;ENST00000524248;ENST00000523163;ENST00000518742|ENST00000518194	T;T;T;T;T|.	0.69926|.	-0.44;-0.44;-0.44;-0.44;-0.44|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Winged helix-turn-helix transcription repressor DNA-binding (1);RNA-binding protein Lupus La (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.90998|.	0.7169|.	H|H	0.98738|0.98738	4.315|4.315	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|.	0.94480|.	0.7692|.	10|.	0.87932|.	D|.	0|.	-20.253|-20.253	16.6288|16.6288	0.85011|0.85011	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	412;335|.	Q6PKG0;Q6PKG0-3|.	LARP1_HUMAN;.|.	G|W	335;412;207;120;19|147	ENSP00000336721:E335G;ENSP00000428589:E412G;ENSP00000429904:E207G;ENSP00000430438:E120G;ENSP00000431072:E19G|.	ENSP00000336721:E335G|.	E|X	+|+	2|3	0|0	LARP1|LARP1	154154930|154154930	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.916000|0.916000	0.54674|0.54674	9.262000|9.262000	0.95591|0.95591	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	GAA|TGA		0.463	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		G	154174737	A	G	154174737	3	3	11	1	0	0	0	0	1	0	0	0	8650	246	9	4	1034	4	LARP1	5	154174737	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	5547343	154174737	26740523	54	1324										
GMNN	51053	hgsc.bcm.edu	37	chr6	24784335	24784335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aaaatccatcctctcagtatTggaaggaagtggcagaaaaa	9	7	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:24784335T>C	ENST00000230056.3	+	5	627	c.295T>C	c.(295-297)Tgg>Cgg	p.W99R	GMNN_ENST00000356509.3_Missense_Mutation_p.W99R	NM_015895.4	NP_056979.1	O75496	GEMI_HUMAN	geminin, DNA replication inhibitor	99	Necessary and sufficient for interaction with IDAS and CDT1.				mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	10						CTCTCAGTATTGGAAGGAAGT	0.279																																																0			6											43	44	44					6																	24784335		2203	4300	6503	24892314	SO:0001583	missense	51053			AF067855	CCDS4560.1	6p21.32	2008-10-31			ENSG00000112312	ENSG00000112312			17493	protein-coding gene	gene with protein product		602842				9635433	Standard	NM_001251989		Approved	Gem	uc003nem.3	O75496	OTTHUMG00000014363	ENST00000230056.3:c.295T>C	6.37:g.24784335T>C	ENSP00000230056:p.Trp99Arg		24892314	B3KMM8|Q9H1Z1	Missense_Mutation	SNP	ENST00000230056.3	37	CCDS4560.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.288045	0.80803	.	.	ENSG00000112312	ENST00000356509;ENST00000230056;ENST00000378054;ENST00000378059	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.61223	0.2330	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70004	-0.4991	10	0.87932	D	0	-14.9459	16.3818	0.83467	0.0:0.0:0.0:1.0	.	99	O75496	GEMI_HUMAN	R	99	ENSP00000348902:W99R;ENSP00000230056:W99R;ENSP00000367293:W99R;ENSP00000367298:W99R	ENSP00000230056:W99R	W	+	1	0	GMNN	24892314	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	6.717000	0.74707	2.330000	0.79161	0.528000	0.53228	TGG		0.279	GMNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040021.2	NM_015895		C	24784335	T	C	24784335	3	2	11	1	0	0	0	0	1	0	0	0	6513	1812	63	4	309	4	GMNN	6	24784335	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10		24784335	146330732	55	1325										
STK38	11329	hgsc.bcm.edu	37	chr6	36466155	36466155	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aatacctcaaaattagatccTtggctttctcagagatggga	8	8	2	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:36466155T>C	ENST00000229812.7	-	11	1346	c.1061A>G	c.(1060-1062)aAg>aGg	p.K354R		NM_007271.2	NP_009202.1			serine/threonine kinase 38											NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AATTAGATCCTTGGCTTTCTC	0.368																																					Colon(180;997 3561 16158)											0			6											122	126	124					6																	36466155		2203	4300	6503	36574133	SO:0001583	missense	11329				CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.1061A>G	6.37:g.36466155T>C	ENSP00000229812:p.Lys354Arg		36574133		Missense_Mutation	SNP	ENST00000229812.7	37	CCDS4822.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476938	0.44044	.	.	ENSG00000112079	ENST00000229812	T	0.68025	-0.3	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.35856	0.0946	N	0.17764	0.52	0.80722	D	1	B	0.14805	0.011	B	0.20577	0.03	T	0.33111	-0.9881	10	0.13853	T	0.58	.	16.3469	0.83138	0.0:0.0:0.0:1.0	.	354	Q15208	STK38_HUMAN	R	354	ENSP00000229812:K354R	ENSP00000229812:K354R	K	-	2	0	STK38	36574133	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.286000	0.72665	2.263000	0.75096	0.528000	0.53228	AAG		0.368	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		C	36466155	T	C	36466155	3	2	11	1	0	0	0	0	1	0	0	0	15342	1609	56	4	352	4	STK38	6	36466155	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	11681820	36466155	134648912	56	1326										
OPN5	221391	hgsc.bcm.edu	37	chr6	47763115	47763115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cctggactggtggctggcccAggcctcggtagggggccagg	19	12	0	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:47763115A>G	ENST00000371211.2	+	4	600	c.572A>G	c.(571-573)cAg>cGg	p.Q191R	OPN5_ENST00000393699.2_Missense_Mutation_p.Q191R|OPN5_ENST00000244799.4_3'UTR|OPN5_ENST00000489301.2_Missense_Mutation_p.Q191R	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	191					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						TGGCTGGCCCAGGCCTCGGTA	0.582																																					Melanoma(28;740 973 10870 42660 45347)											0			6											89	80	83					6																	47763115		2203	4300	6503	47871074	SO:0001583	missense	221391			AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"GPCR / Class A : Opsin receptors"	19992	protein-coding gene	gene with protein product	"neuropsin"	609042	"transmembrane protein 13"	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.572A>G	6.37:g.47763115A>G	ENSP00000360255:p.Gln191Arg		47871074	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Missense_Mutation	SNP	ENST00000371211.2	37	CCDS4923.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.778314	0.70107	.	.	ENSG00000124818	ENST00000489301;ENST00000371211;ENST00000393699	T;T;T	0.36699	1.24;1.24;1.24	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.103349	0.64402	D	0.000001	T	0.21387	0.0515	L	0.37466	1.105	0.49915	D	0.999836	P	0.41978	0.767	B	0.42112	0.376	T	0.02037	-1.1225	10	0.30078	T	0.28	.	16.3351	0.83056	1.0:0.0:0.0:0.0	.	191	Q6U736	OPN5_HUMAN	R	191	ENSP00000426991:Q191R;ENSP00000360255:Q191R;ENSP00000377302:Q191R	ENSP00000360255:Q191R	Q	+	2	0	OPN5	47871074	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.262000	0.75019	0.528000	0.53228	CAG		0.582	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744		G	47763115	A	G	47763115	3	3	11	1	0	0	0	0	1	0	0	0	10914	188	7	4	586	4	OPN5	6	47763115	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	11296960	47763115	123351952	57	1327										
BAI3	577	hgsc.bcm.edu	37	chr6	70098768	70098768	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gatgtgcaagagggtgacttTcaaacagaagtttaaaaaaa	10	4	1	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:70098768T>C	ENST00000370598.1	+	32	5375	c.4554T>C	c.(4552-4554)ttT>ttC	p.F1518F	BAI3_ENST00000238918.8_Silent_p.F724F|BAI3_ENST00000546190.1_Silent_p.F482F	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1518					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F1518F(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AGGGTGACTTTCAAACAGAAG	0.418																																																1	Substitution - coding silent(1)	skin(1)	6											65	59	61					6																	70098768		2203	4300	6503	70155489	SO:0001819	synonymous_variant	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4554T>C	6.37:g.70098768T>C			70155489	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																				0.418	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70098768	T	C	70098768	2	2	11	1	0	0	0	0	0	0	0	1	1301	1780	62	4		4	BAI3	6	70098768	Silent	SNP	T	TCGA-AF-6655-01A-11D-1826-10	22335653	70098768	101016299	58	1328										
RRAGD	58528	hgsc.bcm.edu	37	chr6	90097191	90097191	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctctccaagaacagagtttcGttgggagacattttgtgaaa	10	7	1	4	rs145002359		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:90097191G>A	ENST00000369415.4	-	2	543	c.267C>T	c.(265-267)aaC>aaT	p.N89N	RRAGD_ENST00000492783.1_5'UTR|RRAGD_ENST00000359203.3_Intron	NM_021244.4	NP_067067.1			Ras-related GTP binding D											breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(2)	15		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)		ACAGAGTTTCGTTGGGAGACA	0.463																																																0			6						G		0,4406		0,0,2203	207	225	219		267	-0.3	1	6	dbSNP_134	219	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RRAGD	NM_021244.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		89/401	90097191	1,13005	2203	4300	6503	90153910	SO:0001819	synonymous_variant	58528			AF272036	CCDS5022.1	6q15-q16	2008-02-05			ENSG00000025039	ENSG00000025039			19903	protein-coding gene	gene with protein product		608268				11073942	Standard	NM_021244		Approved	DKFZP761H171, bA11D8.2.1	uc003pnd.4	Q9NQL2	OTTHUMG00000015200	ENST00000369415.4:c.267C>T	6.37:g.90097191G>A			90153910		Silent	SNP	ENST00000369415.4	37	CCDS5022.1																																																																																				0.463	RRAGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041484.1	NM_021244		A	90097191	G	A	90097191	2	1	11	1	0	0	0	0	0	0	0	1	13712	1136	40	1		1	RRAGD	6	90097191	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	19998423	90097191	81017876	59	1329										
MAN1A1	4121	hgsc.bcm.edu	37	chr6	119510874	119510874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agtacgggcaatttcagcccCgagttcaaggtagtgttggg	14	8	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:119510874C>T	ENST00000368468.3	-	10	1942	c.1501G>A	c.(1501-1503)Ggg>Agg	p.G501R		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	501					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		ATTTCAGCCCCGAGTTCAAGG	0.498																																					Ovarian(136;8 1825 12608 33541 47587)											0			6											141	138	139					6																	119510874		2203	4300	6503	119552573	SO:0001583	missense	4121			AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.1501G>A	6.37:g.119510874C>T	ENSP00000357453:p.Gly501Arg		119552573	E7EU32|Q6P052|Q9NU44|Q9UJI3	Missense_Mutation	SNP	ENST00000368468.3	37	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.512750	0.85389	.	.	ENSG00000111885	ENST00000368468	T	0.73897	-0.79	5.52	5.52	0.82312	.	0.055863	0.64402	D	0.000001	D	0.90741	0.7094	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93395	0.6755	10	0.87932	D	0	-5.6292	19.4267	0.94743	0.0:1.0:0.0:0.0	.	501	P33908	MA1A1_HUMAN	R	501	ENSP00000357453:G501R	ENSP00000357453:G501R	G	-	1	0	MAN1A1	119552573	1.000000	0.71417	0.928000	0.36995	0.417000	0.31264	7.786000	0.85741	2.596000	0.87737	0.655000	0.94253	GGG		0.498	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		T	119510874	C	T	119510874	3	4	11	1	0	0	0	0	1	0	0	0	9240	652	23	1	476	1	MAN1A1	6	119510874	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	29413683	119510874	51604193	60	1330										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597312	136597312	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tttttcttctctaaatccatCactttctctattgcctttca	1	12	5	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr6:136597312C>A	ENST00000531224.1	-	5	1603	c.1351G>T	c.(1351-1353)Gat>Tat	p.D451Y	BCLAF1_ENST00000527759.1_Missense_Mutation_p.D449Y|BCLAF1_ENST00000353331.4_Missense_Mutation_p.D449Y|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000392348.2_Missense_Mutation_p.D449Y|BCLAF1_ENST00000527536.1_Missense_Mutation_p.D451Y	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	451					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CTAAATCCATCACTTTCTCTA	0.368																																					Colon(142;1534 1789 5427 7063 28491)											0			6											143	145	144					6																	136597312		2203	4300	6503	136639005	SO:0001583	missense	9774			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1351G>T	6.37:g.136597312C>A	ENSP00000435210:p.Asp451Tyr		136639005	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127823	0.56721	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42;2.42	5.21	5.21	0.72293	.	0.087906	0.49305	D	0.000154	T	0.10423	0.0255	N	0.14661	0.345	0.80722	D	1	P;D;P	0.54207	0.471;0.965;0.471	B;P;B	0.47981	0.325;0.563;0.325	T	0.07966	-1.0745	10	0.66056	D	0.02	-11.4404	19.2018	0.93714	0.0:1.0:0.0:0.0	.	449;449;451	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	Y	451;449;451;449;449;451	ENSP00000435210:D451Y;ENSP00000229446:D449Y;ENSP00000435441:D451Y;ENSP00000434826:D449Y;ENSP00000376159:D449Y;ENSP00000431734:D451Y	ENSP00000229446:D449Y	D	-	1	0	BCLAF1	136639005	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.487000	0.53222	2.611000	0.88343	0.644000	0.83932	GAT		0.368	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136597312	C	A	136597312	3	1	11	1	0	0	0	0	1	0	0	0	1384	826	29	2	1447	2	BCLAF1	6	136597312	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	17086438	136597312	34517755	61	1331										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18767220	18767220	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cagcctttcctggaacccacGcacacacgtgcgctctctgt	8	17	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:18767220G>A	ENST00000432645.2	+	12	1740	c.1740G>A	c.(1738-1740)acG>acA	p.T580T	HDAC9_ENST00000401921.1_Silent_p.T539T|HDAC9_ENST00000406451.4_Silent_p.T580T|HDAC9_ENST00000441542.2_Silent_p.T583T	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	580					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	TGGAACCCACGCACACACGTG	0.527																																																0			7											32	36	34					7																	18767220		2021	4169	6190	18733745	SO:0001819	synonymous_variant	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1740G>A	7.37:g.18767220G>A			18733745	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																				0.527	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18767220	G	A	18767220	2	1	11	1	0	0	0	0	0	0	0	1	7035	1074	38	1		1	HDAC9	7	18767220	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10		18767220	140371443	62	1332										
ADCY1	107	hgsc.bcm.edu	37	chr7	45697411	45697411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tctgtggtgtcctgggcttgCgcaagtggcagtacgacgtg	16	9	1	0	rs536487311		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:45697411C>T	ENST00000297323.7	+	6	1256	c.1234C>T	c.(1234-1236)Cgc>Tgc	p.R412C	ADCY1_ENST00000432715.1_Missense_Mutation_p.R187C	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	412					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCTGGGCTTGCGCAAGTGGCA	0.612													C|||	1	0.000199681	0	0	5008	,	,		18206	0		0	False		,,,				2504	0.001															0			7											125	92	103					7																	45697411		2203	4300	6503	45663936	SO:0001583	missense	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1234C>T	7.37:g.45697411C>T	ENSP00000297323:p.Arg412Cys		45663936	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	37	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023242	0.75275	.	.	ENSG00000164742	ENST00000432715;ENST00000297323;ENST00000545300	D;D	0.82433	-1.61;-1.61	4.44	4.44	0.53790	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.87450	0.6180	M	0.79693	2.465	0.80722	D	1	D;D	0.62365	0.991;0.99	P;P	0.51895	0.48;0.683	D	0.88579	0.3135	10	0.49607	T	0.09	.	14.9371	0.70964	0.0:1.0:0.0:0.0	.	412;187	Q08828;C9J1J0	ADCY1_HUMAN;.	C	187;412;412	ENSP00000392721:R187C;ENSP00000297323:R412C	ENSP00000297323:R412C	R	+	1	0	ADCY1	45663936	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.352000	0.59404	2.446000	0.82766	0.655000	0.94253	CGC		0.612	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45697411	C	T	45697411	3	4	11	1	0	0	0	0	1	0	0	0	292	768	27	1	1256	1	ADCY1	7	45697411	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	26930191	45697411	113441252	63	1333										
CROT	54677	hgsc.bcm.edu	37	chr7	86998764	86998764	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttttgtctttgatgtaatacAtgaaggatgtttggtcaccc	9	6	2	2	rs138577783		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:86998764A>G	ENST00000331536.3	+	7	805	c.620A>G	c.(619-621)cAt>cGt	p.H207R	CROT_ENST00000419147.2_Missense_Mutation_p.H235R|CROT_ENST00000442291.1_Missense_Mutation_p.H207R	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	207					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)	p.H207R(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	GATGTAATACATGAAGGATGT	0.423													A|||	1	0.000199681	0	0.0014	5008	,	,		13514	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	7						A	ARG/HIS,ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	210	196	200		704,620	2.7	0.8	7	dbSNP_134	200	13,8587	9.1+/-34.3	0,13,4287	yes	missense,missense	CROT	NM_001143935.1,NM_021151.3	29,29	0,14,6489	GG,GA,AA		0.1512,0.0227,0.1076	benign,benign	235/641,207/613	86998764	14,12992	2203	4300	6503	86836700	SO:0001583	missense	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.620A>G	7.37:g.86998764A>G	ENSP00000331981:p.His207Arg		86836700	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	10.38	1.334571	0.24253	2.27E-4	0.001512	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.89343	-2.5;-2.5;-2.5	5.1	2.7	0.31948	.	0.482216	0.26492	N	0.024063	T	0.77611	0.4156	N	0.24115	0.695	0.37103	D	0.89999	B;B	0.28636	0.195;0.218	B;B	0.34242	0.178;0.04	T	0.65162	-0.6235	10	0.14252	T	0.57	-4.784	3.3824	0.07259	0.6479:0.1427:0.0729:0.1365	.	235;207	E7EQF2;Q9UKG9	.;OCTC_HUMAN	R	235;207;207	ENSP00000413575:H235R;ENSP00000331981:H207R;ENSP00000411983:H207R	ENSP00000331981:H207R	H	+	2	0	CROT	86836700	0.685000	0.27652	0.756000	0.31282	0.973000	0.67179	1.717000	0.37991	0.485000	0.27652	0.477000	0.44152	CAT		0.423	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		G	86998764	A	G	86998764	3	3	11	1	0	0	0	0	1	0	0	0	3900	217	8	4	726	4	CROT	7	86998764	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	41301353	86998764	72139899	64	1334										
GPR37	2861	hgsc.bcm.edu	37	chr7	124387106	124387106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccaccacagtctcgcactgtCgtaggtgagggctagaacat	11	12	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:124387106C>T	ENST00000303921.2	-	2	1965	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	439					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CTCGCACTGTCGTAGGTGAGG	0.493																																																0			7											161	137	145					7																	124387106		2203	4300	6503	124174342	SO:0001583	missense	2861				CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1315G>A	7.37:g.124387106C>T	ENSP00000306449:p.Asp439Asn		124174342	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	37	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870808	0.51695	.	.	ENSG00000170775	ENST00000303921	T	0.34275	1.37	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.23249	0.0562	N	0.08118	0	0.43453	D	0.995647	P	0.36483	0.555	B	0.34452	0.183	T	0.08066	-1.0740	10	0.41790	T	0.15	-31.8891	18.8936	0.92414	0.0:1.0:0.0:0.0	.	439	O15354	GPR37_HUMAN	N	439	ENSP00000306449:D439N	ENSP00000306449:D439N	D	-	1	0	GPR37	124174342	0.998000	0.40836	0.985000	0.45067	0.898000	0.52572	3.808000	0.55598	2.698000	0.92095	0.655000	0.94253	GAC		0.493	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		T	124387106	C	T	124387106	3	4	11	1	0	0	0	0	1	0	0	0	6711	884	31	1	530	1	GPR37	7	124387106	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	37388342	124387106	34751557	65	1335										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128452972	128452972	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agcccatggccccccagaacGacaagaatgaggtaaccact	9	14	0	3	rs540834725		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:128452972G>A	ENST00000297788.4	+	14	3119	c.2752G>A	c.(2752-2754)Gac>Aac	p.D918N	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000464832.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	918						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CCCCCAGAACGACAAGAATGA	0.547																																																0			7											34	36	35					7																	128452972		1924	4141	6065	128240208	SO:0001583	missense	64753				CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.2752G>A	7.37:g.128452972G>A	ENSP00000297788:p.Asp918Asn		128240208	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	37	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343438	0.82022	.	.	ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672	T	0.36520	1.25	5.56	4.46	0.54185	.	0.274240	0.32134	N	0.006536	T	0.45115	0.1326	M	0.66939	2.045	0.25588	N	0.986721	D;P;D	0.67145	0.978;0.939;0.996	P;B;P	0.57911	0.525;0.272;0.829	T	0.34354	-0.9832	10	0.18710	T	0.47	-25.2123	7.2286	0.26030	0.1424:0.0:0.8576:0.0	.	918;918;918	Q96JN2-4;Q96JN2-2;Q96JN2	.;.;CC136_HUMAN	N	918;918;918;509	ENSP00000297788:D918N	ENSP00000297788:D918N	D	+	1	0	CCDC136	128240208	0.998000	0.40836	0.917000	0.36280	0.145000	0.21501	2.716000	0.47219	2.774000	0.95407	0.655000	0.94253	GAC		0.547	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		A	128452972	G	A	128452972	3	1	11	1	0	0	0	0	1	0	0	0	2776	1058	37	1	2806	1	CCDC136	7	128452972	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	4065866	128452972	30685691	66	1336										
PRSS1	5644	hgsc.bcm.edu	37	chr7	142459866	142459866	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tctctggctggggcaacactGcgagctctggcggtgagtgg	17	10	2	1	rs386718744		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr7:142459866G>T	ENST00000311737.7	+	3	448	c.442G>T	c.(442-444)Gcg>Tcg	p.A148S	PRSS1_ENST00000486171.1_Missense_Mutation_p.A162S	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	148	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.A148T(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	GGGCAACACTGCGAGCTCTGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	7											67	69	68					7																	142459866		2203	4300	6503	142139440	SO:0001583	missense	5644			M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"Serine peptidases / Serine peptidases"	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.442G>T	7.37:g.142459866G>T	ENSP00000308720:p.Ala148Ser		142139440	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	G	0.079	-1.187950	0.01607	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243;ENST00000492062	D;D;D	0.88509	-2.39;-2.39;-2.39	3.28	-0.219	0.13135	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.368349	0.27971	N	0.017113	T	0.63943	0.2554	N	0.01705	-0.755	0.20196	N	0.99992	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.56872	-0.7907	10	0.08381	T	0.77	.	5.0834	0.14668	0.0:0.4638:0.3285:0.2077	.	162;148	E7EQ64;P07477	.;TRY1_HUMAN	S	162;148;138;98	ENSP00000417854:A162S;ENSP00000308720:A148S;ENSP00000419912:A98S	ENSP00000308720:A148S	A	+	1	0	PRSS1	142139440	0.002000	0.14202	0.963000	0.40424	0.006000	0.05464	-0.136000	0.10405	0.172000	0.19760	-0.669000	0.03829	GCG		0.577	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2			T	142459866	G	T	142459866	3	4	11	1	0	0	0	0	1	0	0	0	12648	1319	46	2	452	2	PRSS1	7	142459866	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	14006894	142459866	16678797	67	1337										
CYP7A1	1581	hgsc.bcm.edu	37	chr8	59407186	59407186	+	Frame_Shift_Del	DEL	T	T	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcagtagctgctttcattgcTtctgggttcctattaaaagg							TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:59407186delT	ENST00000301645.3	-	4	1055	c.918delA	c.(916-918)gaafs	p.E306fs		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	306					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cholesterol catabolic process (GO:0006707)|cholesterol homeostasis (GO:0042632)|regulation of bile acid biosynthetic process (GO:0070857)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	cholesterol 7-alpha-monooxygenase activity (GO:0008123)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(1)|urinary_tract(1)	34		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				CTTTCATTGCTTCTGGGTTCC	0.373									Neonatal Giant Cell Hepatitis																																							0			8											141	126	131					8																	59407186		2203	4300	6503	59569740	SO:0001589	frameshift_variant	1581	Familial Cancer Database	Neonatal Hemochromatosis	M89803	CCDS6171.1	8q11-q12	2010-05-04	2003-01-14		ENSG00000167910	ENSG00000167910	1.14.13.17	"Cytochrome P450s"	2651	protein-coding gene	gene with protein product	"cholesterol 7 alpha-monooxygenase"	118455	"cytochrome P450, subfamily VIIA (cholesterol 7 alpha-monooxygenase), polypeptide 1"	CYP7		1358792	Standard	NM_000780		Approved		uc003xtm.4	P22680	OTTHUMG00000164301	ENST00000301645.3:c.918delA	8.37:g.59407186delT	ENSP00000301645:p.Glu306fs		59569740	P78454|Q3MIL8|Q7KZ19	Frame_Shift_Del	DEL	ENST00000301645.3	37	CCDS6171.1																																																																																				0.373	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		-	59407186	T	-	59407186	7	5	11	1	0	1	0	1	0	0	0	0	4202	1606	56	0	608	0	CYP7A1	8	59407186	Frame_Shift_Del	DEL	T	TCGA-AF-6655-01A-11D-1826-10		59407186	86956836	68	1338										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766282	77766282	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	caaacggatgcagctaaaaaCgctgctgcccctgcagcaag	10	13	0	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:77766282C>T	ENST00000521891.2	+	10	7573	c.7125C>T	c.(7123-7125)aaC>aaT	p.N2375N	ZFHX4_ENST00000050961.6_Silent_p.N2330N|ZFHX4_ENST00000518282.1_Silent_p.N2349N|ZFHX4_ENST00000455469.2_Silent_p.N2330N	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2330	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.N2359K(1)|p.N2359N(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAGCTAAAAACGCTGCTGCCC	0.507										HNSCC(33;0.089)																																						2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|lung(1)	8											111	110	110					8																	77766282		2001	4168	6169	77928837	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7125C>T	8.37:g.77766282C>T			77928837	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766282	C	T	77766282	2	4	11	1	0	0	0	0	0	0	0	1	17674	535	19	1		1	ZFHX4	8	77766282	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	18359096	77766282	68597740	69	1339										
RSPO2	340419	hgsc.bcm.edu	37	chr8	108970344	108970344	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cattgtcatcttgcatctccTggattcagcaatggttggac	9	10	4	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:108970344T>C	ENST00000276659.5	-	5	1200	c.580A>G	c.(580-582)Agg>Ggg	p.R194G	RSPO2_ENST00000517781.1_Missense_Mutation_p.R130G|RSPO2_ENST00000517939.1_Missense_Mutation_p.R127G|RSPO2_ENST00000378439.2_Missense_Mutation_p.R130G	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	194	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			TTGCATCTCCTGGATTCAGCA	0.453																																																0			8											359	296	317					8																	108970344		2203	4300	6503	109039520	SO:0001583	missense	340419			AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.580A>G	8.37:g.108970344T>C	ENSP00000276659:p.Arg194Gly		109039520	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	T	19.44	3.827365	0.71143	.	.	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502	T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47	5.6	1.65	0.23941	.	0.000000	0.85682	D	0.000000	D	0.87374	0.6161	M	0.71206	2.165	0.52099	D	0.99994	D;D	0.61080	0.989;0.978	D;P	0.75020	0.985;0.806	D	0.86599	0.1865	10	0.62326	D	0.03	0.8103	13.434	0.61073	0.0:0.0:0.3712:0.6288	.	194;130	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	G	127;130;130;194;127	ENSP00000428940:R127G;ENSP00000427937:R130G;ENSP00000367698:R130G;ENSP00000276659:R194G;ENSP00000428614:R127G	ENSP00000276659:R194G	R	-	1	2	RSPO2	109039520	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	3.961000	0.56759	0.094000	0.17404	-0.461000	0.05368	AGG		0.453	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		C	108970344	T	C	108970344	3	2	11	1	0	0	0	0	1	0	0	0	13747	1579	55	4	159	4	RSPO2	8	108970344	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	31204062	108970344	37393678	70	1340										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113316983	113316983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tctttcatttctccaactccAagtaccattaggaagacatt	4	11	3	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:113316983A>G	ENST00000297405.5	-	52	8477	c.8233T>C	c.(8233-8235)Tgg>Cgg	p.W2745R	CSMD3_ENST00000343508.3_Missense_Mutation_p.W2705R|CSMD3_ENST00000352409.3_Missense_Mutation_p.W2675R|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2745	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTCCAACTCCAAGTACCATTA	0.383										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											135	120	125					8																	113316983		2203	4300	6503	113386159	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8233T>C	8.37:g.113316983A>G	ENSP00000297405:p.Trp2745Arg		113386159	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.540442	0.65085	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11	5.04	5.04	0.67666	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000005	D	0.97511	0.9185	H	0.97315	3.98	0.58432	D	0.999997	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.981	D	0.98799	1.0739	10	0.66056	D	0.02	.	15.0749	0.72069	1.0:0.0:0.0:0.0	.	2745;2705	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	R	2705;2745;2015;2675	ENSP00000345799:W2705R;ENSP00000297405:W2745R;ENSP00000341558:W2015R;ENSP00000343124:W2675R	ENSP00000297405:W2745R	W	-	1	0	CSMD3	113386159	1.000000	0.71417	0.992000	0.48379	0.533000	0.34776	9.251000	0.95483	1.988000	0.58038	0.533000	0.62120	TGG		0.383	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113316983	A	G	113316983	3	3	11	1	0	0	0	0	1	0	0	0	3952	130	5	4	2970	4	CSMD3	8	113316983	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	4346639	113316983	33047039	71	1341										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118170071	118170071	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cgtttccagctgcgcagtggCggccaacattgtgtaagtca	12	11	1	0	rs141202988		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:118170071C>A	ENST00000456015.2	+	4	560	c.560C>A	c.(559-561)gCg>gAg	p.A187E	SLC30A8_ENST00000427715.2_Missense_Mutation_p.A138E|SLC30A8_ENST00000519688.1_Missense_Mutation_p.A138E|SLC30A8_ENST00000521243.1_Missense_Mutation_p.A138E	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	187					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.A187V(1)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TGCGCAGTGGCGGCCAACATT	0.517																																					Ovarian(162;1202 1922 6011 16223 52092)											1	Substitution - Missense(1)	ovary(1)	8											179	149	159					8																	118170071		2203	4300	6503	118239252	SO:0001583	missense	169026				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.560C>A	8.37:g.118170071C>A	ENSP00000415011:p.Ala187Glu		118239252	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.732730	0.48939	.	.	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.76	2.11	0.27256	.	0.832250	0.11028	N	0.607612	T	0.73110	0.3545	M	0.86268	2.805	0.26454	N	0.975561	P	0.46656	0.882	P	0.54889	0.763	T	0.61691	-0.7011	10	0.66056	D	0.02	0.941	4.8273	0.13423	0.0:0.2227:0.135:0.6423	.	187	Q8IWU4	ZNT8_HUMAN	E	138;138;138;187	ENSP00000428545:A138E;ENSP00000407505:A138E;ENSP00000431069:A138E;ENSP00000415011:A187E	ENSP00000407505:A138E	A	+	2	0	SLC30A8	118239252	0.389000	0.25205	0.993000	0.49108	0.213000	0.24496	1.004000	0.29822	0.101000	0.17610	0.650000	0.86243	GCG		0.517	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118170071	C	A	118170071	3	1	11	1	0	0	0	0	1	0	0	0	14598	768	27	2	574	2	SLC30A8	8	118170071	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	4853088	118170071	28193951	72	1342										
TIGD5	84948	hgsc.bcm.edu	37	chr8	144681282	144681282	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ggcgctgtgcgggtgctgttCctgtccaaaggcagcagccg	16	12	0	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:144681282C>G	ENST00000504548.2	+	1	1209	c.1209C>G	c.(1207-1209)ttC>ttG	p.F403L	EEF1D_ENST00000532400.1_5'Flank|EEF1D_ENST00000419152.2_5'Flank|EEF1D_ENST00000528610.1_5'Flank|EEF1D_ENST00000531621.1_5'Flank|EEF1D_ENST00000423316.2_5'Flank|RP11-661A12.14_ENST00000606452.1_lincRNA|EEF1D_ENST00000395119.3_5'Flank|EEF1D_ENST00000529272.1_5'Flank|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000524624.1_5'Flank|EEF1D_ENST00000526838.1_5'Flank|EEF1D_ENST00000317198.6_5'Flank|EEF1D_ENST00000442189.2_5'Flank|TIGD5_ENST00000321385.3_Missense_Mutation_p.F354L	NM_032862.4	NP_116251.4	Q53EQ6	TIGD5_HUMAN	tigger transposable element derived 5	403						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	7	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			GGGTGCTGTTCCTGTCCAAAG	0.701																																																0			8											11	12	12					8																	144681282		2162	4279	6441	144752425	SO:0001583	missense	84948			AK027832	CCDS6406.1, CCDS6406.2	8q24.3	2008-02-01				ENSG00000179886			18336	protein-coding gene	gene with protein product							Standard	NM_032862		Approved	FLJ14926	uc003yyx.2	Q53EQ6		ENST00000504548.2:c.1209C>G	8.37:g.144681282C>G	ENSP00000421489:p.Phe403Leu		144752425	E7EWS2|Q6NT83|Q8N5A1|Q96JW8	Missense_Mutation	SNP	ENST00000504548.2	37	CCDS6406.2	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069821	0.55539	.	.	ENSG00000179886	ENST00000504548;ENST00000321385	T;T	0.46819	0.86;0.89	4.75	2.56	0.30785	.	0.000000	0.64402	U	0.000015	T	0.46946	0.1419	M	0.65975	2.015	0.25703	N	0.985564	B	0.27700	0.186	B	0.35470	0.203	T	0.48055	-0.9068	10	0.54805	T	0.06	.	8.8793	0.35365	0.0:0.7232:0.0:0.2768	.	354	Q53EQ6	TIGD5_HUMAN	L	403;354	ENSP00000421489:F403L;ENSP00000315906:F354L	ENSP00000315906:F354L	F	+	3	2	TIGD5	144752425	0.997000	0.39634	0.927000	0.36925	0.590000	0.36582	0.472000	0.22116	0.988000	0.38734	0.655000	0.94253	TTC		0.701	TIGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368269.1	NM_032862		G	144681282	C	G	144681282	3	3	11	1	0	0	0	0	1	0	0	0	15938	854	30	5	1211	5	TIGD5	8	144681282	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	26511211	144681282	1682740	73	1343										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146068363	146068363	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agggtccacctttgtgagccGtaaaaaggttaatactataa	9	7	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr8:146068363G>A	ENST00000528372.1	+	5	2111	c.1871G>A	c.(1870-1872)cGt>cAt	p.R624H	ZNF7_ENST00000325241.6_Missense_Mutation_p.R624H|ZNF7_ENST00000446747.2_Missense_Mutation_p.R635H|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.R528H			P17097	ZNF7_HUMAN	zinc finger protein 7	624					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TTTGTGAGCCGTAAAAAGGTT	0.433																																																0			8											63	67	65					8																	146068363		2203	4300	6503	146039167	SO:0001583	missense	7553			AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1871G>A	8.37:g.146068363G>A	ENSP00000432724:p.Arg624His		146039167	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	37	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	G	5.504	0.277924	0.10403	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.07216	3.33;3.33;3.21;3.33	4.9	1.85	0.25348	.	0.157726	0.30446	N	0.009602	T	0.03305	0.0096	N	0.08118	0	0.80722	D	1	B;B	0.12013	0.005;0.005	B;B	0.04013	0.001;0.001	T	0.45659	-0.9246	9	.	.	.	-19.2372	5.5522	0.17097	0.5113:0.0:0.4887:0.0	.	635;624	B4DT08;P17097	.;ZNF7_HUMAN	H	624;635;528;624	ENSP00000320627:R624H;ENSP00000393260:R635H;ENSP00000439424:R528H;ENSP00000432724:R624H	.	R	+	2	0	ZNF7	146039167	0.573000	0.26676	0.035000	0.18076	0.767000	0.43475	0.000000	0.12993	0.643000	0.30638	0.655000	0.94253	CGT		0.433	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		A	146068363	G	A	146068363	3	1	11	1	0	0	0	0	1	0	0	0	18141	1145	40	1	1885	1	ZNF7	8	146068363	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	1387081	146068363	295659	74	1344										
MLLT3	4300	hgsc.bcm.edu	37	chr9	20620740	20620740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	actgtgctccggaccgcgtaCgaacaccatccagtcgtggg	12	14	0	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:20620740C>T	ENST00000380338.4	-	2	392	c.106G>A	c.(106-108)Gta>Ata	p.V36I	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Missense_Mutation_p.V33I	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	36	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.V36L(2)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		GGACCGCGTACGAACACCATC	0.577			T	MLL	ALL																																		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	2	Substitution - Missense(2)	lung(2)	9											137	130	133					9																	20620740		2203	4300	6503	20610740	SO:0001583	missense	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.106G>A	9.37:g.20620740C>T	ENSP00000369695:p.Val36Ile		20610740	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	37	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.444145	0.83993	.	.	ENSG00000171843	ENST00000380338;ENST00000429426;ENST00000540751	.	.	.	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	T	0.78349	0.4269	M	0.61703	1.905	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.989	D;D;P	0.85130	0.961;0.997;0.891	T	0.79960	-0.1583	9	0.87932	D	0	-5.0283	18.9559	0.92658	0.0:1.0:0.0:0.0	.	36;33;36	B2R7B3;B7Z755;P42568	.;.;AF9_HUMAN	I	36;33;75	.	ENSP00000369695:V36I	V	-	1	0	MLLT3	20610740	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.808000	0.86044	2.551000	0.86045	0.561000	0.74099	GTA		0.577	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		T	20620740	C	T	20620740	3	4	11	1	0	0	0	0	1	0	0	0	9658	536	19	1	1640	1	MLLT3	9	20620740	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10		20620740	120592691	75	1345										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20923750	20923750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aagccagcctctcctcagacTctgacgggctcctggaggtt	11	14	3	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:20923750T>C	ENST00000380249.1	+	27	3308	c.2944T>C	c.(2944-2946)Tct>Cct	p.S982P	FOCAD_ENST00000338382.6_Missense_Mutation_p.S982P|FOCAD_ENST00000605086.1_Missense_Mutation_p.S418P	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	982						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CTCCTCAGACTCTGACGGGCT	0.498																																																0			9											73	60	65					9																	20923750		2203	4300	6503	20913750	SO:0001583	missense	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2944T>C	9.37:g.20923750T>C	ENSP00000369599:p.Ser982Pro		20913750	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	T	12.55	1.970968	0.34754	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.07908	3.15;3.15	5.4	1.49	0.22878	Armadillo-type fold (1);	0.469692	0.23345	N	0.049189	T	0.05686	0.0149	L	0.40543	1.245	0.34950	D	0.751124	P	0.38335	0.627	B	0.32022	0.139	T	0.37056	-0.9722	10	0.48119	T	0.1	-14.6803	5.5734	0.17210	0.5281:0.0:0.1199:0.352	.	982	Q5VW36	K1797_HUMAN	P	982	ENSP00000369599:S982P;ENSP00000344307:S982P	ENSP00000344307:S982P	S	+	1	0	KIAA1797	20913750	0.007000	0.16637	0.297000	0.24988	0.670000	0.39368	0.367000	0.20382	0.356000	0.24157	0.533000	0.62120	TCT		0.498	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		C	20923750	T	C	20923750	3	2	11	1	0	0	0	0	1	0	0	0	8279	1551	54	4	3038	4	KIAA1797	9	20923750	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	303010	20923750	120289681	76	1346										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32542101	32542101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	acgagatggctgagccacttCgttagtaccctccaaatgcc	9	13	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:32542101C>T	ENST00000360538.2	-	3	2538	c.2422G>A	c.(2422-2424)Gaa>Aaa	p.E808K	TOPORS_ENST00000379858.1_Missense_Mutation_p.E743K	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	808	Interaction with TOP1.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E808*(1)|p.E808K(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TGAGCCACTTCGTTAGTACCC	0.423																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	ovary(1)|large_intestine(1)	9	GRCh37	CM081845	TOPORS	M							124	120	121					9																	32542101		2203	4300	6503	32532101	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2422G>A	9.37:g.32542101C>T	ENSP00000353735:p.Glu808Lys		32532101	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.692613	0.30052	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.13778	2.56;2.57	5.91	3.98	0.46160	.	0.123059	0.37348	N	0.002126	T	0.05914	0.0154	N	0.04508	-0.205	0.09310	N	1	B	0.16166	0.016	B	0.11329	0.006	T	0.27806	-1.0063	10	0.35671	T	0.21	-10.6127	8.2296	0.31590	0.1458:0.7289:0.0:0.1252	.	808	Q9NS56	TOPRS_HUMAN	K	808;743	ENSP00000353735:E808K;ENSP00000369187:E743K	ENSP00000353735:E808K	E	-	1	0	TOPORS	32532101	0.009000	0.17119	0.870000	0.34147	0.561000	0.35649	0.740000	0.26188	2.803000	0.96430	0.650000	0.86243	GAA		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32542101	C	T	32542101	3	4	11	1	0	0	0	0	1	0	0	0	16410	893	31	1	719	1	TOPORS	9	32542101	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	11618351	32542101	108671330	77	1347										
TRIM14	9830	hgsc.bcm.edu	37	chr9	100857228	100857228	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cccttaaagaagctcttgacGggctcaaaggagaggggcac	13	10	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:100857228G>A	ENST00000341469.2	-	4	630	c.621C>T	c.(619-621)ccC>ccT	p.P207P	TRIM14_ENST00000342043.3_Silent_p.P207P|TRIM14_ENST00000538344.1_5'Flank|TRIM14_ENST00000375098.3_Silent_p.P207P	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	207					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.P207P(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				AGCTCTTGACGGGCTCAAAGG	0.587																																					Colon(14;460 597 13826 51781)											1	Substitution - coding silent(1)	lung(1)	9											103	94	97					9																	100857228		2203	4300	6503	99897049	SO:0001819	synonymous_variant	9830			AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"Tripartite motif containing / Tripartite motif containing"	16283	protein-coding gene	gene with protein product		606556	"tripartite motif-containing 14"			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.621C>T	9.37:g.100857228G>A			99897049	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																				0.587	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788		A	100857228	G	A	100857228	2	1	11	1	0	0	0	0	0	0	0	1	16529	1103	39	1		1	TRIM14	9	100857228	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	68315127	100857228	40356203	78	1348										
PRPF4	9128	hgsc.bcm.edu	37	chr9	116044949	116044949	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aagaaatatcctctcagttgTcggtactgatgccttgaaaa	8	8	1	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:116044949T>C	ENST00000374198.4	+	4	521	c.419T>C	c.(418-420)gTc>gCc	p.V140A	PRPF4_ENST00000488937.1_3'UTR|PRPF4_ENST00000374199.4_Missense_Mutation_p.V139A	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	140					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						CTCTCAGTTGTCGGTACTGAT	0.308																																																0			9											79	75	76					9																	116044949		2203	4300	6503	115084770	SO:0001583	missense	9128			AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"WD repeat domain containing"	17349	protein-coding gene	gene with protein product	"PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4"	607795	"PRP4 pre-mRNA processing factor 4 homolog (yeast)"			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.419T>C	9.37:g.116044949T>C	ENSP00000363313:p.Val140Ala		115084770	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	37	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.040029	0.55003	.	.	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.61980	0.06;0.11	5.9	5.9	0.94986	Splicing factor motif (1);	0.277862	0.35466	N	0.003181	T	0.60038	0.2238	L	0.56769	1.78	0.58432	D	0.999995	B;B	0.28439	0.212;0.212	B;B	0.27380	0.079;0.079	T	0.58064	-0.7702	10	0.39692	T	0.17	.	15.5056	0.75739	0.0:0.0:0.0:1.0	.	155;140	Q59EL4;O43172	.;PRP4_HUMAN	A	139;140	ENSP00000363315:V139A;ENSP00000363313:V140A	ENSP00000363313:V140A	V	+	2	0	PRPF4	115084770	1.000000	0.71417	0.441000	0.26858	0.964000	0.63967	7.064000	0.76721	2.254000	0.74563	0.460000	0.39030	GTC		0.308	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		C	116044949	T	C	116044949	3	2	11	1	0	0	0	0	1	0	0	0	12604	1667	58	4	433	4	PRPF4	9	116044949	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	15187721	116044949	25168482	79	1349										
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666529	117666529	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gggaattggatcaccagattCccatcctgatatctgactcc	8	12	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr9:117666529C>T	ENST00000223795.2	-	4	500	c.387G>A	c.(385-387)ggG>ggA	p.G129G	TNFSF8_ENST00000474301.1_5'UTR	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	129					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)	p.G129G(1)		endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						TCACCAGATTCCCATCCTGAT	0.403																																																1	Substitution - coding silent(1)	lung(1)	9											150	145	146					9																	117666529		2203	4300	6503	116706350	SO:0001819	synonymous_variant	944			L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.387G>A	9.37:g.117666529C>T			116706350	O43404	Silent	SNP	ENST00000223795.2	37	CCDS6810.1																																																																																				0.403	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			T	117666529	C	T	117666529	2	4	11	1	0	0	0	0	0	0	0	1	16350	842	30	3		3	TNFSF8	9	117666529	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	1621580	117666529	23546902	80	1350										
KIN	22944	hgsc.bcm.edu	37	chr10	7801876	7801877	+	Frame_Shift_Del	DEL	AA	AA	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttcaatgacgatagtagctgAaaaagtcttctcattgatgg							TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr10:7801876_7801877delAA	ENST00000379562.4	-	12	1142_1143	c.1095_1096delTT	c.(1093-1098)ttttcafs	p.S366fs	KIN_ENST00000543003.1_Frame_Shift_Del_p.S260fs|KIN_ENST00000463666.1_5'UTR|KIN_ENST00000535925.1_Frame_Shift_Del_p.S366fs	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						ATAGTAGCTGAAAAAGTCTTCT	0.302																																																0			10																																								7841883	SO:0001589	frameshift_variant	22944			AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.1095_1096delTT	10.37:g.7801878_7801879delAA	ENSP00000368881:p.Ser366fs		7841882		Frame_Shift_Del	DEL	ENST00000379562.4	37	CCDS7080.1																																																																																				0.302	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		-	7801877	AA	-	7801876	7	5	11	1	0	1	0	1	0	0	0	0	8336	246	9	0	93	0	KIN	10	7801876	Frame_Shift_Del	DEL	AA	TCGA-AF-6655-01A-11D-1826-10		7801876	127732871	81	1351										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114710585	114710585	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aactgatttccttcaaagacGagggcgaacaggaggagaag	13	7	1	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr10:114710585G>T	ENST00000355995.4	+	1	577	c.70G>T	c.(70-72)Gag>Tag	p.E24*	TCF7L2_ENST00000536810.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000543371.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000369395.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000349937.2_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000369397.4_Nonsense_Mutation_p.E24*|RP11-57H14.2_ENST00000369391.3_RNA|TCF7L2_ENST00000355717.4_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000538897.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000534894.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000545257.1_Nonsense_Mutation_p.E24*|TCF7L2_ENST00000352065.5_Nonsense_Mutation_p.E24*			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	24	CTNNB1-binding. {ECO:0000250}.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CTTCAAAGACGAGGGCGAACA	0.493			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											41	40	40					10																	114710585		2203	4300	6503	114700575	SO:0001587	stop_gained	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.70G>T	10.37:g.114710585G>T	ENSP00000348274:p.Glu24*		114700575	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Nonsense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	G	41	8.779961	0.98952	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000349937;ENST00000352065;ENST00000369395	.	.	.	3.71	2.79	0.32731	.	0.086790	0.44902	D	0.000410	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-3.6672	10.5252	0.44943	0.0993:0.0:0.9007:0.0	.	.	.	.	X	24	.	ENSP00000298692:E24X	E	+	1	0	TCF7L2	114700575	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.761000	0.91691	0.552000	0.29026	0.460000	0.39030	GAG		0.493	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114710585	G	T	114710585	4	4	11	1	0	0	0	0	0	1	0	0	15737	1059	37	2	72	2	TCF7L2	10	114710585	Nonsense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	106908709	114710585	20824162	82	1352										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123274629	123274629	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tttaaactctttatctacttTctgttacctgtctccgcagg	5	11	4	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr10:123274629T>C	ENST00000358487.5	-	9	1560		c.e9+1		FGFR2_ENST00000369056.1_Splice_Site|FGFR2_ENST00000490349.1_5'Flank|FGFR2_ENST00000457416.2_Splice_Site|FGFR2_ENST00000357555.5_Splice_Site|FGFR2_ENST00000360144.3_Splice_Site|FGFR2_ENST00000369061.4_Splice_Site|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000369059.1_Splice_Site|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000478859.1_Splice_Site|FGFR2_ENST00000351936.6_Intron|FGFR2_ENST00000346997.2_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.?(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TTATCTACTTTCTGTTACCTG	0.507		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	1	Unknown(1)	endometrium(1)	10											84	90	88					10																	123274629		2203	4300	6503	123264619	SO:0001630	splice_region_variant	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1287+1A>G	10.37:g.123274629T>C			123264619	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Splice_Site	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999467	0.74818	.	.	ENSG00000066468	ENST00000357555;ENST00000369061;ENST00000358487;ENST00000369059;ENST00000429361;ENST00000457416;ENST00000360144;ENST00000369056;ENST00000369058	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1095	0.81250	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FGFR2	123264619	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.621000	0.83083	2.205000	0.71048	0.533000	0.62120	.		0.507	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	Intron	C	123274629	T	C	123274629	5	2	11	1	0	0	0	0	0	0	1	0	5885	1797	62	4	1320	4	FGFR2	10	123274629	Splice_Site	SNP	T	TCGA-AF-6655-01A-11D-1826-10	8564044	123274629	12260118	83	1353										
ZDHHC5	25921	hgsc.bcm.edu	37	chr11	57466038	57466038	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctttcttcctcagttgagtcGtggggacagcttgaaggagc	13	9	2	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:57466038G>A	ENST00000287169.3	+	11	2492	c.1130G>A	c.(1129-1131)cGt>cAt	p.R377H	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.R324H	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	377					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						CAGTTGAGTCGTGGGGACAGC	0.517																																																0			11											107	106	107					11																	57466038		2201	4296	6497	57222614	SO:0001583	missense	25921			AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1130G>A	11.37:g.57466038G>A	ENSP00000287169:p.Arg377His		57222614	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	37	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	14.86	2.660875	0.47572	.	.	ENSG00000156599	ENST00000527985;ENST00000287169;ENST00000529447	T;T;D	0.83419	0.28;1.28;-1.72	5.52	5.52	0.82312	.	0.641922	0.16763	N	0.200522	D	0.85243	0.5652	L	0.46157	1.445	0.58432	D	0.999999	D	0.56968	0.978	P	0.52309	0.695	D	0.85797	0.1371	10	0.66056	D	0.02	-7.0692	17.386	0.87416	0.0:0.0:1.0:0.0	.	377	Q9C0B5	ZDHC5_HUMAN	H	324;377;211	ENSP00000432202:R324H;ENSP00000287169:R377H;ENSP00000435722:R211H	ENSP00000287169:R377H	R	+	2	0	ZDHHC5	57222614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.711000	0.91396	2.873000	0.98535	0.563000	0.77884	CGT		0.517	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		A	57466038	G	A	57466038	3	1	11	1	0	0	0	0	1	0	0	0	17657	1145	40	1	1168	1	ZDHHC5	11	57466038	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10		57466038	77540478	84	1354										
RAB3IL1	5866	hgsc.bcm.edu	37	chr11	61673947	61673947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cccaccctcacctccttgccCtctctgtctggggtgagggt	10	17	3	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:61673947C>T	ENST00000394836.2	-	5	805	c.648G>A	c.(646-648)gaG>gaA	p.E216E	RAB3IL1_ENST00000301773.5_Intron	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	216					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CCTCCTTGCCCTCTCTGTCTG	0.706																																																0			11											12	11	11					11																	61673947		2095	4135	6230	61430523	SO:0001819	synonymous_variant	5866			AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.648G>A	11.37:g.61673947C>T			61430523	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																				0.706	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401		T	61673947	C	T	61673947	2	4	11	1	0	0	0	0	0	0	0	1	12974	680	24	3		3	RAB3IL1	11	61673947	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	4207909	61673947	73332569	85	1355										
SCGB1D2	10647	hgsc.bcm.edu	37	chr11	62009833	62009833	+	Splice_Site	DEL	G	G	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctggccctctgctgctaccaGggtgagtacatcagtcatga							TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:62009833delG	ENST00000244926.3	+	1	152	c.54delG	c.(52-54)cag>ca	p.Q18fs	RP11-703H8.9_ENST00000529875.1_RNA	NM_006551.3	NP_006542.1	O95969	SG1D2_HUMAN	secretoglobin, family 1D, member 2	18						extracellular space (GO:0005615)				breast(1)|endometrium(1)|lung(1)	3						GCTGCTACCAGGGTGAGTACA	0.537																																																0			11											158	119	132					11																	62009833		2202	4299	6501	61766409	SO:0001630	splice_region_variant	10647			AJ224172	CCDS8017.1	11q13	2011-12-14			ENSG00000124935	ENSG00000124935		"Secretoglobins"	18396	protein-coding gene	gene with protein product	"prostatein-like lipophilin B", "lipophilin B (uteroglobin family member), prostatein-like"	615061				10066439, 9720917, 22155607	Standard	XM_006718422		Approved	LPHB, LIPB	uc001ntb.3	O95969	OTTHUMG00000167508	ENST00000244926.3:c.55+1G>-	11.37:g.62009833delG			61766409	Q2M3N9	Frame_Shift_Del	DEL	ENST00000244926.3	37	CCDS8017.1																																																																																				0.537	SCGB1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394859.1	NM_006551	Frame_Shift_Del	-	62009833	G	-	62009833	8	5	11	1	0	1	0	1	0	0	1	0	13934	1014	35	0	56	0	SCGB1D2	11	62009833	Splice_Site	DEL	G	TCGA-AF-6655-01A-11D-1826-10	335886	62009833	72996683	86	1356										
FAT3	120114	hgsc.bcm.edu	37	chr11	92570842	92570842	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttggcaggtgtctggatactCtctgcttgtccaggccgtag	13	10	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:92570842C>T	ENST00000298047.6	+	16	10255	c.10238C>T	c.(10237-10239)tCt>tTt	p.S3413F	FAT3_ENST00000525166.1_Missense_Mutation_p.S3263F|FAT3_ENST00000409404.2_Missense_Mutation_p.S3413F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3413	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCTGGATACTCTCTGCTTGTC	0.488										TCGA Ovarian(4;0.039)																																						0			11											113	115	114					11																	92570842		1985	4163	6148	92210490	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10238C>T	11.37:g.92570842C>T	ENSP00000298047:p.Ser3413Phe		92210490	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	24.6	4.549432	0.86127	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01871	4.59;4.59;4.59	4.79	4.79	0.61399	.	.	.	.	.	T	0.11623	0.0283	L	0.61387	1.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00496	-1.1705	9	0.72032	D	0.01	.	18.4248	0.90605	0.0:1.0:0.0:0.0	.	3413	Q8TDW7-3	.	F	3413;3413;3263	ENSP00000298047:S3413F;ENSP00000387040:S3413F;ENSP00000432586:S3263F	ENSP00000298047:S3413F	S	+	2	0	FAT3	92210490	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.546000	0.82137	2.648000	0.89879	0.650000	0.86243	TCT		0.488	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92570842	C	T	92570842	3	4	11	1	0	0	0	0	1	0	0	0	5710	913	32	3	10300	3	FAT3	11	92570842	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	30561009	92570842	42435674	87	1357										
CCDC67	159989	hgsc.bcm.edu	37	chr11	93148220	93148220	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	atgcctcccttgccaccttcGacatttcaagccaaagaaat	5	14	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:93148220G>A	ENST00000298050.3	+	13	1678	c.1578G>A	c.(1576-1578)tcG>tcA	p.S526S	CCDC67_ENST00000525646.1_Silent_p.S268S	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	526					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				TGCCACCTTCGACATTTCAAG	0.413																																																0			11											217	203	207					11																	93148220		1932	4128	6060	92787868	SO:0001819	synonymous_variant	159989			AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1578G>A	11.37:g.93148220G>A			92787868	Q8NEF1|Q96LL7	Silent	SNP	ENST00000298050.3	37	CCDS44707.1																																																																																				0.413	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		A	93148220	G	A	93148220	2	1	11	1	0	0	0	0	0	0	0	1	2845	1045	37	1		1	CCDC67	11	93148220	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	577378	93148220	41858296	88	1358										
ATM	472	hgsc.bcm.edu	37	chr11	108139301	108139301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	taatgttaattgattctagcAcgctagaacctaccaaatcc	5	10	1	2	rs35813135		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:108139301A>G	ENST00000452508.2	+	19	2992	c.2803A>G	c.(2803-2805)Acg>Gcg	p.T935A	ATM_ENST00000278616.4_Missense_Mutation_p.T935A|AP001925.1_ENST00000596081.1_5'Flank			Q13315	ATM_HUMAN	ATM serine/threonine kinase	935			T -> A. {ECO:0000269|PubMed:17344846}.|T -> M (in dbSNP:rs3218708).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGATTCTAGCACGCTAGAACC	0.393			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			A|||	1	0.000199681	0	0	5008	,	,		18115	0.001		0	False		,,,				2504	0					yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											159	146	150					11																	108139301		2201	4298	6499	107644511	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2803A>G	11.37:g.108139301A>G	ENSP00000388058:p.Thr935Ala		107644511	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.655957	0.00779	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70516	-0.49;-0.49;-0.49	5.5	3.14	0.36123	Armadillo-type fold (1);	0.774747	0.12455	N	0.467361	T	0.43010	0.1228	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28933	-1.0028	10	0.08179	T	0.78	.	4.8104	0.13340	0.6646:0.0:0.2072:0.1282	rs35813135	935	Q13315	ATM_HUMAN	A	935	ENSP00000435747:T935A;ENSP00000278616:T935A;ENSP00000388058:T935A	ENSP00000278616:T935A	T	+	1	0	ATM	107644511	0.654000	0.27367	0.559000	0.28332	0.132000	0.20833	1.343000	0.33930	0.375000	0.24679	-0.333000	0.08304	ACG		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108139301	A	G	108139301	3	3	11	1	0	0	0	0	1	0	0	0	1110	159	6	4	2869	4	ATM	11	108139301	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	14991081	108139301	26867215	89	1359										
NLRX1	79671	hgsc.bcm.edu	37	chr11	119045315	119045315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agccgtactgcgggtatgccGttggcggttcaggtgtctct	15	10	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr11:119045315G>A	ENST00000409109.1	+	6	1590	c.1003G>A	c.(1003-1005)Gtt>Att	p.V335I	NLRX1_ENST00000292199.2_Missense_Mutation_p.V335I|NLRX1_ENST00000525863.1_Missense_Mutation_p.V335I|NLRX1_ENST00000409991.1_Missense_Mutation_p.V335I|NLRX1_ENST00000409265.4_Missense_Mutation_p.V335I	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	335	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.|Required for interaction with MAVS.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CGGGTATGCCGTTGGCGGTTC	0.612																																																0			11											108	105	106					11																	119045315		2200	4295	6495	118550525	SO:0001583	missense	79671			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.1003G>A	11.37:g.119045315G>A	ENSP00000387334:p.Val335Ile		118550525	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	G	4.082	0.013095	0.07912	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.70986	-0.42;-0.42;-0.53;-0.42;-0.53	5.57	4.65	0.58169	.	0.817770	0.11194	N	0.589557	T	0.46870	0.1415	N	0.08118	0	0.09310	N	1	B;B	0.27700	0.049;0.186	B;B	0.11329	0.001;0.006	T	0.31724	-0.9933	10	0.44086	T	0.13	.	5.7662	0.18227	0.1601:0.0:0.6834:0.1565	.	335;335	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	I	335	ENSP00000386851:V335I;ENSP00000292199:V335I;ENSP00000386858:V335I;ENSP00000387334:V335I;ENSP00000433442:V335I	ENSP00000292199:V335I	V	+	1	0	NLRX1	118550525	0.280000	0.24249	0.005000	0.12908	0.000000	0.00434	3.019000	0.49635	1.385000	0.46445	-0.164000	0.13417	GTT		0.612	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		A	119045315	G	A	119045315	3	1	11	1	0	0	0	0	1	0	0	0	10516	1145	40	1	1021	1	NLRX1	11	119045315	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	10906014	119045315	15961201	90	1360										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21353504	21353504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	atgttatgtttgtgcttttgAcgttgttacaagtaagcagc	10	5	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:21353504A>G	ENST00000256958.2	+	9	1129	c.1033A>G	c.(1033-1035)Acg>Gcg	p.T345A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	345					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TGTGCTTTTGACGTTGTTACA	0.323																																																0			12											116	105	109					12																	21353504		2203	4299	6502	21244771	SO:0001583	missense	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1033A>G	12.37:g.21353504A>G	ENSP00000256958:p.Thr345Ala		21244771	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	A	8.881	0.951601	0.18431	.	.	ENSG00000134538	ENST00000256958	T	0.57907	0.37	3.34	-1.18	0.09617	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.896444	0.09749	N	0.760806	T	0.36908	0.0984	L	0.42581	1.335	0.09310	N	1	B	0.21071	0.051	B	0.28305	0.088	T	0.33189	-0.9878	10	0.24483	T	0.36	.	0.5125	0.00597	0.3332:0.187:0.1156:0.3643	.	345	Q9Y6L6	SO1B1_HUMAN	A	345	ENSP00000256958:T345A	ENSP00000256958:T345A	T	+	1	0	SLCO1B1	21244771	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.255000	0.08769	0.021000	0.15133	0.402000	0.26972	ACG		0.323	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21353504	A	G	21353504	3	3	11	1	0	0	0	0	1	0	0	0	14760	275	10	4	1063	4	SLCO1B1	12	21353504	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10		21353504	112498391	91	1361										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	11	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	4044777	25398281	108453614	92	1362										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26809461	26809461	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ggcgatccaagcacatccttGcaaagaggtttagctggtac	11	10	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:26809461G>T	ENST00000381340.3	-	19	2629	c.2213C>A	c.(2212-2214)gCa>gAa	p.A738E		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	738					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GCACATCCTTGCAAAGAGGTT	0.423																																																0			12											63	64	64					12																	26809461		1954	4156	6110	26700728	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2213C>A	12.37:g.26809461G>T	ENSP00000370744:p.Ala738Glu		26700728	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892883	0.91889	.	.	ENSG00000123104	ENST00000381340	D	0.93307	-3.2	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.96420	0.8832	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96821	0.9604	10	0.72032	D	0.01	.	18.0329	0.89290	0.0:0.0:1.0:0.0	.	738	Q14571	ITPR2_HUMAN	E	738	ENSP00000370744:A738E	ENSP00000370744:A738E	A	-	2	0	ITPR2	26700728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.584000	0.98220	2.546000	0.85860	0.655000	0.94253	GCA		0.423	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26809461	G	T	26809461	3	4	11	1	0	0	0	0	1	0	0	0	7942	1319	46	2	6048	2	ITPR2	12	26809461	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	1411180	26809461	107042434	93	1363										
BICD1	636	hgsc.bcm.edu	37	chr12	32481359	32481359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcgtcaaagagcagcggctcGggagctagcccccatgattg	13	12	1	2	rs200686810		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:32481359G>A	ENST00000281474.5	+	5	2073	c.1970G>A	c.(1969-1971)cGg>cAg	p.R657Q	BICD1_ENST00000548411.1_Missense_Mutation_p.R657Q	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	657					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.R657Q(2)|p.R657L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GCAGCGGCTCGGGAGCTAGCC	0.502													G|||	1	0.000199681	8e-04	0	5008	,	,		16640	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	central_nervous_system(2)|lung(1)	12											70	75	73					12																	32481359		2203	4300	6503	32372626	SO:0001583	missense	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1970G>A	12.37:g.32481359G>A	ENSP00000281474:p.Arg657Gln		32372626	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	37	CCDS8726.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	16.61	3.171364	0.57584	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.43688	0.94;0.94	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.44603	0.1301	N	0.17594	0.5	0.80722	D	1	D;D	0.76494	0.996;0.999	P;P	0.62089	0.744;0.898	T	0.25813	-1.0121	10	0.13108	T	0.6	.	18.4173	0.90575	0.0:0.0:1.0:0.0	.	657;657	F8W113;Q96G01	.;BICD1_HUMAN	Q	657	ENSP00000446793:R657Q;ENSP00000281474:R657Q	ENSP00000281474:R657Q	R	+	2	0	BICD1	32372626	1.000000	0.71417	0.999000	0.59377	0.924000	0.55760	6.595000	0.74109	2.333000	0.79357	0.655000	0.94253	CGG		0.502	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		A	32481359	G	A	32481359	3	1	11	1	0	0	0	0	1	0	0	0	1429	1116	39	1	1988	1	BICD1	12	32481359	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	5671898	32481359	101370536	94	1364										
FGD4	121512	hgsc.bcm.edu	37	chr12	32751501	32751501	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tgaaagagcttatgtcaaccGacttgacctcttagatcagg	9	9	3	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:32751501G>T	ENST00000427716.2	+	5	1095	c.671G>T	c.(670-672)cGa>cTa	p.R224L	FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000546442.1_Missense_Mutation_p.R131L|FGD4_ENST00000381025.3_5'UTR|FGD4_ENST00000534526.2_Missense_Mutation_p.R361L|FGD4_ENST00000525053.1_Missense_Mutation_p.R336L|FGD4_ENST00000531134.1_Missense_Mutation_p.R309L	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	224	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TATGTCAACCGACTTGACCTC	0.299																																																0			12											84	84	84					12																	32751501		2203	4299	6502	32642768	SO:0001583	missense	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.671G>T	12.37:g.32751501G>T	ENSP00000394487:p.Arg224Leu		32642768	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.460922	0.84317	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	4.91	4.91	0.64330	Dbl homology (DH) domain (5);	0.000000	0.43110	D	0.000613	T	0.78553	0.4301	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	0.99;0.978;1.0	D;D;D	0.97110	0.958;0.93;1.0	T	0.81165	-0.1057	10	0.87932	D	0	-11.1136	18.4768	0.90795	0.0:0.0:1.0:0.0	.	336;309;224	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	L	361;309;224;131;336	ENSP00000449273:R361L;ENSP00000431323:R309L;ENSP00000394487:R224L;ENSP00000446695:R131L;ENSP00000433666:R336L	ENSP00000379089:R224L	R	+	2	0	FGD4	32642768	1.000000	0.71417	0.997000	0.53966	0.761000	0.43186	9.133000	0.94460	2.426000	0.82243	0.655000	0.94253	CGA		0.299	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		T	32751501	G	T	32751501	3	4	11	1	0	0	0	0	1	0	0	0	5854	1058	37	2	681	2	FGD4	12	32751501	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	270142	32751501	101100394	95	1365										
DDX23	9416	hgsc.bcm.edu	37	chr12	49237825	49237825	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctcgttctcgttctttgtgcCgtcgttctctggaagaccgc	10	13	3	1	rs555010780		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:49237825C>A	ENST00000308025.3	-	3	297	c.218G>T	c.(217-219)cGg>cTg	p.R73L	DDX23_ENST00000553182.1_5'UTR	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	73	Arg-rich.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TTCTTTGTGCCGTCGTTCTCT	0.488																																																0			12											314	262	280					12																	49237825		2203	4300	6503	47524092	SO:0001583	missense	9416			AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.218G>T	12.37:g.49237825C>A	ENSP00000310723:p.Arg73Leu		47524092	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.691797	0.68271	.	.	ENSG00000174243	ENST00000308025;ENST00000552512;ENST00000551468	T	0.21932	1.98	5.35	5.35	0.76521	.	0.147458	0.44285	D	0.000468	T	0.35828	0.0945	L	0.36672	1.1	0.58432	D	0.999999	D	0.53745	0.962	D	0.65010	0.931	T	0.03166	-1.1065	10	0.54805	T	0.06	-0.5329	16.0486	0.80740	0.0:1.0:0.0:0.0	.	73	Q9BUQ8	DDX23_HUMAN	L	73	ENSP00000310723:R73L	ENSP00000310723:R73L	R	-	2	0	DDX23	47524092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.486000	0.60286	2.522000	0.85027	0.586000	0.80456	CGG		0.488	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		A	49237825	C	A	49237825	3	1	11	1	0	0	0	0	1	0	0	0	4356	652	23	2	2304	2	DDX23	12	49237825	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	16486324	49237825	84614070	96	1366										
CNPY2	10330	hgsc.bcm.edu	37	chr12	56705176	56705176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccagcagctctgtgaggtggGcctctgagcgggcataaggc	16	11	2	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:56705176G>A	ENST00000273308.4	-	4	767	c.227C>T	c.(226-228)gCc>gTc	p.A76V	CNPY2_ENST00000551720.1_5'UTR|RP11-977G19.10_ENST00000549318.1_Missense_Mutation_p.A76V|RP11-977G19.11_ENST00000549565.1_RNA|RP11-977G19.11_ENST00000549860.1_RNA|RP11-977G19.12_ENST00000546789.1_RNA	NM_014255.5	NP_055070.1	Q9Y2B0	CNPY2_HUMAN	canopy FGF signaling regulator 2	76	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				negative regulation of gene expression (GO:0010629)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of low-density lipoprotein particle clearance (GO:0010988)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(2)	4						TGTGAGGTGGGCCTCTGAGCG	0.478																																																0			12											122	119	120					12																	56705176		2203	4300	6503	54991443	SO:0001583	missense	10330			AB015631	CCDS8914.1	12q15	2013-07-23	2013-07-23	2007-10-22		ENSG00000257727			13529	protein-coding gene	gene with protein product		605861	"transmembrane protein 4", "canopy 2 homolog (zebrafish)"	TMEM4		10072769, 15905959	Standard	NM_001190991		Approved	HP10390, ZSIG9, Cnpy2	uc001sku.2	Q9Y2B0	OTTHUMG00000170330	ENST00000273308.4:c.227C>T	12.37:g.56705176G>A	ENSP00000273308:p.Ala76Val		54991443	B2R7B9|Q9UHE9	Missense_Mutation	SNP	ENST00000273308.4	37	CCDS8914.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.063739	0.55432	.	.	ENSG00000144785;ENSG00000257727;ENSG00000257727;ENSG00000257727	ENST00000549318;ENST00000273308;ENST00000551475;ENST00000551286	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.38	5.38	0.77491	Saposin B (1);	0.055194	0.64402	D	0.000001	T	0.24812	0.0602	N	0.17379	0.485	0.47905	D	0.999548	B	0.26445	0.149	B	0.22386	0.039	T	0.05683	-1.0870	10	0.17369	T	0.5	-8.6163	18.277	0.90087	0.0:0.0:1.0:0.0	.	76	Q9Y2B0	CNPY2_HUMAN	V	76;76;76;24	ENSP00000446743:A76V;ENSP00000273308:A76V;ENSP00000448809:A76V;ENSP00000446784:A24V	ENSP00000273308:A76V	A	-	2	0	RP11-977G19.10;CNPY2	54991443	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.807000	0.69157	2.695000	0.91970	0.561000	0.74099	GCC		0.478	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255		A	56705176	G	A	56705176	3	1	11	1	0	0	0	0	1	0	0	0	3634	1203	42	3	333	3	CNPY2	12	56705176	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	7467351	56705176	77146719	97	1367										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57431361	57431361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcttctaatgaagatctttgTcttgccaaaggccagctccc	8	12	3	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:57431361T>C	ENST00000442789.2	-	20	2313	c.2026A>G	c.(2026-2028)Aca>Gca	p.T676A	MYO1A_ENST00000300119.3_Missense_Mutation_p.T676A|MYO1A_ENST00000476795.1_5'Flank|MYO1A_ENST00000544473.1_Missense_Mutation_p.T514A	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	676	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						AAGATCTTTGTCTTGCCAAAG	0.527																																																0			12											272	283	279					12																	57431361		2203	4300	6503	55717628	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2026A>G	12.37:g.57431361T>C	ENSP00000393392:p.Thr676Ala		55717628	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135035	0.77662	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.90620	-2.7;-2.7;-2.7	4.96	4.96	0.65561	Myosin head, motor domain (2);	0.059684	0.64402	D	0.000003	D	0.95576	0.8562	H	0.96269	3.795	0.53005	D	0.999967	D	0.63046	0.992	P	0.56042	0.79	D	0.96254	0.9185	10	0.87932	D	0	.	11.0233	0.47730	0.0:0.0:0.0:1.0	.	676	Q9UBC5	MYO1A_HUMAN	A	676;676;514	ENSP00000300119:T676A;ENSP00000393392:T676A;ENSP00000440514:T514A	ENSP00000300119:T676A	T	-	1	0	MYO1A	55717628	0.993000	0.37304	1.000000	0.80357	0.965000	0.64279	2.485000	0.45250	1.882000	0.54519	0.482000	0.46254	ACA		0.527	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		C	57431361	T	C	57431361	3	2	11	1	0	0	0	0	1	0	0	0	10098	1667	58	4	1145	4	MYO1A	12	57431361	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	726185	57431361	76420534	98	1368										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66765671	66765671	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcgaggtgttggagcctcatGattcaaactcatcgtgctcc	11	11	3	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:66765671G>C	ENST00000398016.3	-	22	2727	c.2659C>G	c.(2659-2661)Cat>Gat	p.H887D	GRIP1_ENST00000359742.4_Missense_Mutation_p.H939D|GRIP1_ENST00000286445.7_Missense_Mutation_p.H924D	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GGAGCCTCATGATTCAAACTC	0.527																																																0			12											63	68	67					12																	66765671		2055	4198	6253	65051938	SO:0001583	missense	85329			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2659C>G	12.37:g.66765671G>C	ENSP00000381098:p.His887Asp		65051938	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.04|14.04	2.415914|2.415914	0.42817|0.42817	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000538164	T;T;T;T;T;T|.	0.73363|.	-0.74;-0.74;-0.74;-0.74;-0.74;-0.74|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.092455|.	0.64402|.	D|.	0.000001|.	T|T	0.74145|0.74145	0.3678|0.3678	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	B;P;B;P|.	0.40681|.	0.356;0.725;0.356;0.727|.	B;B;B;B|.	0.37267|.	0.138;0.177;0.185;0.245|.	T|T	0.68469|0.68469	-0.5400|-0.5400	9|5	.|.	.|.	.|.	-14.2165|-14.2165	20.6593|20.6593	0.99626|0.99626	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	872;939;887;924|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.	.;GRIP1_HUMAN;.;.|.	D|M	887;939;924;872;831;764|738	ENSP00000381098:H887D;ENSP00000352780:H939D;ENSP00000286445:H924D;ENSP00000446047:H872D;ENSP00000446024:H831D;ENSP00000446011:H764D|.	.|.	H|I	-|-	1|3	0|3	GRIP1|GRIP1	65051938|65051938	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.284000|0.284000	0.27059|0.27059	7.459000|7.459000	0.80802|0.80802	2.885000|2.885000	0.99019|0.99019	0.655000|0.655000	0.94253|0.94253	CAT|ATC		0.527	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			C	66765671	G	C	66765671	3	2	11	1	0	0	0	0	1	0	0	0	6808	1290	45	5	583	5	GRIP1	12	66765671	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	9334310	66765671	67086224	99	1369										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75687098	75687098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtaatgtgttttctttgatgCtttctggaaggctgagatga	12	4	2	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:75687098C>T	ENST00000409445.3	-	13	1347	c.1151G>A	c.(1150-1152)aGc>aAc	p.S384N	RP11-560G2.1_ENST00000534648.2_RNA|CAPS2_ENST00000442339.2_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.S302N|RP11-560G2.1_ENST00000549953.1_RNA|CAPS2_ENST00000393284.3_Missense_Mutation_p.S152N|CAPS2_ENST00000409004.1_5'UTR	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	384							calcium ion binding (GO:0005509)	p.S152I(1)		endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TTCTTTGATGCTTTCTGGAAG	0.323																																																1	Substitution - Missense(1)	ovary(1)	12											123	113	116					12																	75687098		2203	4298	6501	73973365	SO:0001583	missense	84698			AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1151G>A	12.37:g.75687098C>T	ENSP00000386959:p.Ser384Asn		73973365	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	37	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747376	0.49257	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284	T;T;T	0.27104	1.75;1.69;1.86	4.6	1.46	0.22682	.	0.120057	0.53938	D	0.000059	T	0.46092	0.1375	M	0.77103	2.36	0.80722	D	1	D;D;P;D	0.69078	0.997;0.993;0.929;0.989	D;D;P;P	0.67382	0.951;0.932;0.536;0.798	T	0.46148	-0.9212	10	0.66056	D	0.02	-4.1205	10.2991	0.43642	0.0:0.6753:0.251:0.0736	.	152;120;384;302	Q9BXY5-2;Q9BXY5-3;Q9BXY5;B9A061	.;.;CAYP2_HUMAN;.	N	302;384;120;152	ENSP00000386977:S302N;ENSP00000386959:S384N;ENSP00000376963:S152N	ENSP00000367975:S120N	S	-	2	0	CAPS2	73973365	1.000000	0.71417	0.980000	0.43619	0.501000	0.33797	1.667000	0.37471	0.466000	0.27193	0.446000	0.29264	AGC		0.323	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			T	75687098	C	T	75687098	3	4	11	1	0	0	0	0	1	0	0	0	2644	797	28	3	546	3	CAPS2	12	75687098	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	8921427	75687098	58164797	100	1370										
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76791503	76791503	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccaaatagattgctccaaagGatggaaaagtttgaaacaaa	8	6	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:76791503G>T	ENST00000261183.3	-	8	1122	c.643C>A	c.(643-645)Cct>Act	p.P215T	OSBPL8_ENST00000393249.2_Missense_Mutation_p.P173T|OSBPL8_ENST00000393250.4_Missense_Mutation_p.P173T	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	215	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TGCTCCAAAGGATGGAAAAGT	0.378																																																0			12											110	94	100					12																	76791503		2203	4300	6503	75315634	SO:0001583	missense	114882			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.643C>A	12.37:g.76791503G>T	ENSP00000261183:p.Pro215Thr		75315634	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Missense_Mutation	SNP	ENST00000261183.3	37	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111508	0.94339	.	.	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250;ENST00000438913;ENST00000547540;ENST00000546946	T;T;T;T;T	0.74947	-0.89;2.45;-0.89;2.45;-0.89	5.74	5.74	0.90152	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.103332	0.64402	D	0.000002	D	0.86690	0.5993	M	0.75615	2.305	0.80722	D	1	D;P	0.67145	0.996;0.907	D;P	0.74674	0.984;0.821	D	0.87287	0.2296	10	0.87932	D	0	-16.1815	19.9326	0.97124	0.0:0.0:1.0:0.0	.	190;215	F8VUA7;Q9BZF1	.;OSBL8_HUMAN	T	173;215;200;173;215;215;190	ENSP00000376939:P173T;ENSP00000261183:P215T;ENSP00000376940:P173T;ENSP00000450238:P215T;ENSP00000447893:P190T	ENSP00000261183:P215T	P	-	1	0	OSBPL8	75315634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.720000	0.93068	0.650000	0.86243	CCT		0.378	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		T	76791503	G	T	76791503	3	4	11	1	0	0	0	0	1	0	0	0	11314	1174	41	2	2094	2	OSBPL8	12	76791503	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	1104405	76791503	57060392	101	1371										
CEP290	80184	hgsc.bcm.edu	37	chr12	88474161	88474161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttttcacttcatcttcatggTtttcttgaagcctgatgtaa	6	8	5	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:88474161T>C	ENST00000552810.1	-	38	5367	c.5024A>G	c.(5023-5025)aAc>aGc	p.N1675S	CEP290_ENST00000397838.3_Missense_Mutation_p.N735S|CEP290_ENST00000547691.2_Missense_Mutation_p.N735S|CEP290_ENST00000309041.7_Missense_Mutation_p.N1677S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATCTTCATGGTTTTCTTGAAG	0.363																																																0			12											109	97	101					12																	88474161		1818	4077	5895	86998292	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5024A>G	12.37:g.88474161T>C	ENSP00000448012:p.Asn1675Ser		86998292	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	6.030	0.373827	0.11409	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77	4.35	3.17	0.36434	.	0.424145	0.27420	N	0.019448	T	0.81250	0.4783	N	0.24115	0.695	0.26987	N	0.965227	B	0.17852	0.024	B	0.17433	0.018	T	0.62338	-0.6875	10	0.10111	T	0.7	.	10.8553	0.46796	0.0:0.0:0.1651:0.8349	.	1675	O15078	CE290_HUMAN	S	735;1675;1677;735	ENSP00000446905:N735S;ENSP00000448012:N1675S;ENSP00000308021:N1677S;ENSP00000380938:N735S	ENSP00000308021:N1677S	N	-	2	0	CEP290	86998292	1.000000	0.71417	1.000000	0.80357	0.300000	0.27592	3.309000	0.51903	0.614000	0.30107	0.377000	0.23210	AAC		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88474161	T	C	88474161	3	2	11	1	0	0	0	0	1	0	0	0	3259	1725	60	4	2483	4	CEP290	12	88474161	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	11682658	88474161	45377734	102	1372										
ANO4	121601	hgsc.bcm.edu	37	chr12	101490422	101490422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttacatcgcattcttcctcgGaaggtaagaacctgacccct	7	13	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:101490422G>A	ENST00000392977.3	+	19	2057	c.1847G>A	c.(1846-1848)gGa>gAa	p.G616E	ANO4_ENST00000550015.1_Missense_Mutation_p.G136E|ANO4_ENST00000392979.3_Missense_Mutation_p.G581E|ANO4_ENST00000299222.9_Missense_Mutation_p.G136E			Q32M45	ANO4_HUMAN	anoctamin 4	616					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TTCTTCCTCGGAAGGTAAGAA	0.498										HNSCC(74;0.22)																																						0			12											92	83	86					12																	101490422		2203	4300	6503	100014553	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1847G>A	12.37:g.101490422G>A	ENSP00000376703:p.Gly616Glu		100014553	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	G	32	5.140087	0.94560	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000001	T	0.80549	0.4644	M	0.77103	2.36	0.80722	D	1	D;D;D	0.65815	0.957;0.995;0.984	P;D;D	0.70487	0.888;0.969;0.947	T	0.81228	-0.1028	10	0.62326	D	0.03	.	19.6088	0.95594	0.0:0.0:1.0:0.0	.	136;616;581	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	E	581;136;616;136	ENSP00000376705:G581E;ENSP00000299222:G136E;ENSP00000376703:G616E;ENSP00000450192:G136E	ENSP00000299222:G136E	G	+	2	0	ANO4	100014553	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.837000	0.99465	2.734000	0.93682	0.563000	0.77884	GGA		0.498	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101490422	G	A	101490422	3	1	11	1	0	0	0	0	1	0	0	0	699	1174	41	3	1808	3	ANO4	12	101490422	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	13016261	101490422	32361473	103	1373										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017425	109017454	+	In_Frame_Del	DEL	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT	-													0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tggtttgagtggtctgtgccTccatggctgctggtggagtg					rs570639292|rs188941939|rs139943851|rs74792300	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr12:109017425_109017454delTCCATGGCTGCTGGTGGAGTGGTCTGTGCT	ENST00000550948.1	-	2	854_883	c.630_659delAGCACAGACCACTCCACCAGCAGCCATGGA	c.(628-660)gaagcacagaccactccaccagcagccatggag>gag	p.210_220EAQTTPPAAME>E	SELPLG_ENST00000228463.6_In_Frame_Del_p.226_236EAQTTPPAAME>E|SELPLG_ENST00000388962.3_In_Frame_Del_p.200_210EAQTTPPAAME>E			Q14242	SELPL_HUMAN	selectin P ligand	210	12 X 10 AA tandem repeats.			M -> T (in Ref. 3; BAC05283). {ECO:0000305}.	blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GGTCTGTGCCTCCATGGCTGCTGGTGGAGTGGTCTGTGCTTCCATGGCTG	0.622																																																0			12																																								107541583	SO:0001651	inframe_deletion	6404				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.630_659delAGCACAGACCACTCCACCAGCAGCCATGGA	12.37:g.109017425_109017454delTCCATGGCTGCTGGTGGAGTGGTCTGTGCT	ENSP00000447752:p.Glu210_Met219del		107541554	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	In_Frame_Del	DEL	ENST00000550948.1	37	CCDS31895.2																																																																																				0.622	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			-	109017454	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT	-	109017425	7	5	11	1	0	1	0	1	0	0	0	0	14057	1551	54	0	583	0	SELPLG	12	109017425	In_Frame_Del	DEL	TCCATGGCTGCTGGTGGAGTGGTCTGTGCT	TCGA-AF-6655-01A-11D-1826-10	7527003	109017425	24834470	104	1374										
XPO4	64328	hgsc.bcm.edu	37	chr13	21357984	21357984	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcagtgagcttgttgaaggcAtctgctaatctctggtaaat	11	7	2	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr13:21357984A>G	ENST00000255305.6	-	23	3404	c.3333T>C	c.(3331-3333)gaT>gaC	p.D1111D	XPO4_ENST00000400602.2_Silent_p.D1111D			Q9C0E2	XPO4_HUMAN	exportin 4	1111					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		TGTTGAAGGCATCTGCTAATC	0.408																																																0			13											144	138	140					13																	21357984		2036	4189	6225	20255984	SO:0001819	synonymous_variant	64328			AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.3333T>C	13.37:g.21357984A>G			20255984	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	37	CCDS41872.1																																																																																				0.408	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		G	21357984	A	G	21357984	2	3	11	1	0	0	0	0	0	0	0	1	17486	214	8	4		4	XPO4	13	21357984	Silent	SNP	A	TCGA-AF-6655-01A-11D-1826-10		21357984	93811894	105	1375										
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30857794	30857794	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agctggatctctgactgactGgcaatgtctctgaatctgct	10	10	3	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr13:30857794G>A	ENST00000380615.3	-	2	288	c.121C>T	c.(121-123)Cag>Tag	p.Q41*	RNU6-64P_ENST00000517119.1_RNA|KATNAL1_ENST00000380617.3_Nonsense_Mutation_p.Q41*	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		CTGACTGACTGGCAATGTCTC	0.403																																																0			13											248	222	231					13																	30857794		2203	4300	6503	29755794	SO:0001587	stop_gained	84056			AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"ATPases / AAA-type"	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.121C>T	13.37:g.30857794G>A	ENSP00000369989:p.Gln41*		29755794		Nonsense_Mutation	SNP	ENST00000380615.3	37	CCDS31956.1	.	.	.	.	.	.	.	.	.	.	G	37	6.157617	0.97334	.	.	ENSG00000102781	ENST00000380615;ENST00000380617;ENST00000414289;ENST00000441394	.	.	.	5.52	5.52	0.82312	.	0.117718	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-20.3559	19.7975	0.96491	0.0:0.0:1.0:0.0	.	.	.	.	X	41	.	ENSP00000369989:Q41X	Q	-	1	0	KATNAL1	29755794	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.505000	0.81655	2.762000	0.94881	0.591000	0.81541	CAG		0.403	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		A	30857794	G	A	30857794	4	1	11	1	0	0	0	0	0	1	0	0	8006	1357	47	3	1391	3	KATNAL1	13	30857794	Nonsense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	9499810	30857794	84312084	106	1376										
ALG11	440138	hgsc.bcm.edu	37	chr13	52593265	52593265	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gttttatggtgtgctttaagAgccctgcagaaaaagtaggt	12	5	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr13:52593265A>G	ENST00000521508.1	+	2	266	c.261A>G	c.(259-261)agA>agG	p.R87R	ALG11_ENST00000523764.1_Intron	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	87					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		GTGCTTTAAGAGCCCTGCAGA	0.323																																																0			13											58	55	56					13																	52593265		2203	4300	6503	51491266	SO:0001819	synonymous_variant	440138			AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"Glycosyltransferase group 1 domain containing"	32456	protein-coding gene	gene with protein product	"GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"	613666	"asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)", "asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.261A>G	13.37:g.52593265A>G			51491266	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Silent	SNP	ENST00000521508.1	37	CCDS31977.1																																																																																				0.323	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127		G	52593265	A	G	52593265	2	3	11	1	0	0	0	0	0	0	0	1	513	301	11	4		4	ALG11	13	52593265	Silent	SNP	A	TCGA-AF-6655-01A-11D-1826-10	21735471	52593265	62576613	107	1377										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60413500	60413500	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcatgcaagtcctcaggaggGggaaaggtttccaattcctt	11	9	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr13:60413500G>T	ENST00000400324.4	-	23	3040	c.2820C>A	c.(2818-2820)ccC>ccA	p.P940P	DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.P894P|DIAPH3_ENST00000377908.2_Silent_p.P929P|DIAPH3_ENST00000400319.1_Silent_p.P870P|DIAPH3_ENST00000267215.4_Silent_p.P940P|DIAPH3_ENST00000400330.1_Silent_p.P940P	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	940	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CCTCAGGAGGGGGAAAGGTTT	0.383																																																0			13											87	82	84					13																	60413500		1859	4096	5955	59311501	SO:0001819	synonymous_variant	81624			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2820C>A	13.37:g.60413500G>T			59311501	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																				0.383	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		T	60413500	G	T	60413500	2	4	11	1	0	0	0	0	0	0	0	1	4531	1219	43	2		2	DIAPH3	13	60413500	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	7820235	60413500	54756378	108	1378										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70989383	70989383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agcaaccaaaggaagaaggcAcaatagtgacaggtaacgca	11	8	0	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr14:70989383A>G	ENST00000256389.3	-	2	2486	c.2242T>C	c.(2242-2244)Tgc>Cgc	p.C748R	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	698					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		GGAAGAAGGCACAATAGTGAC	0.393																																																0			14											225	188	201					14																	70989383		2203	4300	6503	70059136	SO:0001583	missense	8748			AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2242T>C	14.37:g.70989383A>G	ENSP00000256389:p.Cys748Arg		70059136	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	A	8.748	0.920573	0.17982	.	.	ENSG00000134007	ENST00000256389	T	0.00912	5.55	3.66	3.66	0.41972	.	3.514400	0.01092	U	0.005201	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	0.999994	P	0.36144	0.539	B	0.22880	0.042	T	0.44267	-0.9339	10	0.23891	T	0.37	.	6.584	0.22610	0.7863:0.0:0.0:0.2137	.	698	O43506	ADA20_HUMAN	R	748	ENSP00000256389:C748R	ENSP00000256389:C748R	C	-	1	0	ADAM20	70059136	0.014000	0.17966	0.032000	0.17829	0.066000	0.16364	1.280000	0.33202	1.441000	0.47550	0.477000	0.44152	TGC		0.393	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			G	70989383	A	G	70989383	3	3	11	1	0	0	0	0	1	0	0	0	242	159	6	4	92	4	ADAM20	14	70989383	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10		70989383	36360157	109	1379										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089507	86089507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ggcgggcttgatcgggggcgCggtgatatttgtgctggtgg	21	6	0	2	rs201981148		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr14:86089507C>T	ENST00000330753.4	+	2	2416	c.1649C>T	c.(1648-1650)gCg>gTg	p.A550V	FLRT2_ENST00000554746.1_Missense_Mutation_p.A550V	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	550					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ATCGGGGGCGCGGTGATATTT	0.587													C|||	1	0.000199681	0	0	5008	,	,		15501	0.001		0	False		,,,				2504	0															0			14											76	80	79					14																	86089507		2203	4300	6503	85159260	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1649C>T	14.37:g.86089507C>T	ENSP00000332879:p.Ala550Val		85159260	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	20.5	4.002391	0.74932	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.60040	0.22;0.22	6.17	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.65015	0.2651	M	0.64404	1.975	0.80722	D	1	D	0.67145	0.996	P	0.50352	0.638	T	0.65800	-0.6080	10	0.37606	T	0.19	-16.4932	17.5067	0.87748	0.0:0.8761:0.1239:0.0	.	550	O43155	FLRT2_HUMAN	V	550;550;203	ENSP00000332879:A550V;ENSP00000451050:A550V	ENSP00000332879:A550V	A	+	2	0	FLRT2	85159260	1.000000	0.71417	0.110000	0.21437	0.885000	0.51271	7.817000	0.86213	1.578000	0.49821	0.655000	0.94253	GCG		0.587	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			T	86089507	C	T	86089507	3	4	11	1	0	0	0	0	1	0	0	0	5958	768	27	1	1651	1	FLRT2	14	86089507	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	15100124	86089507	21260033	110	1380										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91947948	91947948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tgccaacaatctctaccttaTtgaaaaagataaaagagtga	6	7	1	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr14:91947948T>C	ENST00000554943.1	-	4	1002	c.887A>G	c.(886-888)aAt>aGt	p.N296S	SMEK1_ENST00000555462.1_Intron|SMEK1_ENST00000337238.4_Missense_Mutation_p.N296S|SMEK1_ENST00000554684.1_Missense_Mutation_p.N296S|SMEK1_ENST00000428424.2_Intron			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	296					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		CTCTACCTTATTGAAAAAGAT	0.338																																																0			14											69	63	65					14																	91947948		2203	4300	6503	91017701	SO:0001583	missense	55671			AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.887A>G	14.37:g.91947948T>C	ENSP00000450883:p.Asn296Ser		91017701	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	37		.	.	.	.	.	.	.	.	.	.	T	22.7	4.323828	0.81580	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000554943;ENST00000554390;ENST00000417249	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.87	5.87	0.94306	Domain of unknown function DUF625 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	M	0.89353	3.025	0.80722	D	1	D;P;P	0.71674	0.998;0.933;0.918	D;P;P	0.80764	0.994;0.812;0.714	T	0.69522	-0.5123	10	0.59425	D	0.04	-22.5612	16.2806	0.82678	0.0:0.0:0.0:1.0	.	296;296;296	G3V5Z3;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	S	296;296;296;296;86	ENSP00000450864:N296S;ENSP00000337125:N296S;ENSP00000450883:N296S;ENSP00000452596:N296S	ENSP00000337125:N296S	N	-	2	0	SMEK1	91017701	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	7.953000	0.87836	2.248000	0.74166	0.533000	0.62120	AAT		0.338	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		C	91947948	T	C	91947948	3	2	11	1	0	0	0	0	1	0	0	0	14830	1493	52	4	1623	4	SMEK1	14	91947948	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	5858441	91947948	15401592	111	1381										
TMEM179	388021	hgsc.bcm.edu	37	chr14	105070791	105070791	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tacccctcgtgtcccttgcaGaggaagaagagcgtgcgcca	12	13	0	3	rs3803313	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr14:105070791G>T	ENST00000556573.1	-	1	529	c.288C>A	c.(286-288)ctC>ctA	p.L96L	TMEM179_ENST00000341595.3_Silent_p.L96L			Q6ZVK1	T179A_HUMAN	transmembrane protein 179	96						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)	4			all cancers(16;0.00276)|OV - Ovarian serous cystadenocarcinoma(23;0.0262)|Epithelial(46;0.058)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.129)		GTCCCTTGCAGAGGAAGAAGA	0.756													G|||	3054	0.609824	0.6884	0.5303	5008	,	,		10526	0.3661		0.7664	False		,,,				2504	0.6503															0			14						G		2828,1184		1007,814,185	4	6	6		288	1.8	1	14	dbSNP_107	6	6311,1779		2483,1345,217	no	coding-synonymous	TMEM179	NM_207379.1		3490,2159,402	TT,TG,GG		21.9901,29.5115,24.4836		96/198	105070791	9139,2963	2006	4045	6051	104141836	SO:0001819	synonymous_variant	388021			AK124477	CCDS66723.1, CCDS73688.1	14q32.33	2012-04-11	2006-10-16	2006-10-16	ENSG00000258986	ENSG00000258986			20137	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 90"	C14orf90			Standard	NM_001286390		Approved	FLJ42486, TMEM179A	uc001yox.1	Q6ZVK1	OTTHUMG00000170829	ENST00000556573.1:c.288C>A	14.37:g.105070791G>T			104141836		Silent	SNP	ENST00000556573.1	37																																																																																					0.756	TMEM179-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410585.1	NM_207379		T	105070791	G	T	105070791	2	4	11	1	0	0	0	0	0	0	0	1	16135	929	33	2		2	TMEM179	14	105070791	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	13122843	105070791	2278749	112	1382										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62167097	62167097	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	actgtgtgtccaaagaggctTctcactccaatcactaaccc	6	14	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr15:62167097T>C	ENST00000261517.5	-	77	10465	c.10392A>G	c.(10390-10392)agA>agG	p.R3464R	VPS13C_ENST00000249837.3_Silent_p.R3421R|VPS13C_ENST00000395898.3_Silent_p.R3421R|VPS13C_ENST00000395896.4_Silent_p.R3464R|VPS13C_ENST00000558919.1_5'Flank	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.R3464S(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CAAAGAGGCTTCTCACTCCAA	0.299																																																1	Substitution - Missense(1)	ovary(1)	15											99	101	100					15																	62167097		2203	4300	6503	59954389	SO:0001819	synonymous_variant	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10392A>G	15.37:g.62167097T>C			59954389		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																				0.299	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62167097	T	C	62167097	2	2	11	1	0	0	0	0	0	0	0	1	17231	1780	62	4		4	VPS13C	15	62167097	Silent	SNP	T	TCGA-AF-6655-01A-11D-1826-10		62167097	40364295	113	1383										
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78893715	78893715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gcatcaacagattcagaactAgagcttctcgtgaggttagc	10	9	3	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr15:78893715A>G	ENST00000326828.5	-	5	1653	c.1269T>C	c.(1267-1269)tcT>tcC	p.S423S	CHRNA3_ENST00000348639.3_Silent_p.S423S	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	423					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	ATTCAGAACTAGAGCTTCTCG	0.473																																																0			15											159	145	150					15																	78893715		2196	4293	6489	76680770	SO:0001819	synonymous_variant	1136				CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1269T>C	15.37:g.78893715A>G			76680770	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																				0.473	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			G	78893715	A	G	78893715	2	3	11	1	0	0	0	0	0	0	0	1	3390	407	15	4		4	CHRNA3	15	78893715	Silent	SNP	A	TCGA-AF-6655-01A-11D-1826-10	16726618	78893715	23637677	114	1384										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687706	61687706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtcatatggcggggccgtggGatcattatctgcctcatgca	13	10	4	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr16:61687706G>A	ENST00000577390.1	-	12	3160	c.2206C>T	c.(2206-2208)Ccc>Tcc	p.P736S	CDH8_ENST00000299345.6_Intron|CDH8_ENST00000577730.1_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	736					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GGGGCCGTGGGATCATTATCT	0.498																																																0			16											72	77	75					16																	61687706		2203	4300	6503	60245207	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2206C>T	16.37:g.61687706G>A	ENSP00000462701:p.Pro736Ser		60245207	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.248324	0.59103	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.79776	0.4504	M	0.75447	2.3	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.79605	-0.1734	9	0.51188	T	0.08	.	18.8311	0.92139	0.0:0.0:1.0:0.0	.	736	P55286	CADH8_HUMAN	S	736	.	ENSP00000299345:P736S	P	-	1	0	CDH8	60245207	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.807000	0.99171	2.679000	0.91253	0.655000	0.94253	CCC		0.498	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		A	61687706	G	A	61687706	3	1	11	1	0	0	0	0	1	0	0	0	3122	1174	41	3	197	3	CDH8	16	61687706	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10		61687706	28667047	115	1385										
SLC16A13	201232	hgsc.bcm.edu	37	chr17	6941499	6941499	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tgggctttgaccttcgctccGaccctggcctgcctgtcctg	11	16	0	1	rs200228263		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:6941499G>A	ENST00000308027.6	+	3	680	c.372G>A	c.(370-372)ccG>ccA	p.P124P		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	124						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CCTTCGCTCCGACCCTGGCCT	0.592																																																0			17											77	77	77					17																	6941499		2203	4300	6503	6882223	SO:0001819	synonymous_variant	201232			BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"Solute carriers"	31037	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 13"		"solute carrier family 16 (monocarboxylic acid transporters), member 13"				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.372G>A	17.37:g.6941499G>A			6882223	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																				0.592	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			A	6941499	G	A	6941499	2	1	11	1	0	0	0	0	0	0	0	1	14443	1045	37	1		1	SLC16A13	17	6941499	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10		6941499	74253711	116	1386										
TP53	7157	hgsc.bcm.edu	37	chr17	7578236	7578236	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agtgtttctgtcatccaaatActccacacgcaaatttcctt	4	12	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:7578236A>C	ENST00000269305.4	-	6	802	c.613T>G	c.(613-615)Tat>Gat	p.Y205D	TP53_ENST00000420246.2_Missense_Mutation_p.Y205D|TP53_ENST00000445888.2_Missense_Mutation_p.Y205D|TP53_ENST00000413465.2_Missense_Mutation_p.Y205D|TP53_ENST00000455263.2_Missense_Mutation_p.Y205D|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.Y205D	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	205	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y205D(13)|p.0?(8)|p.Y205N(8)|p.?(5)|p.Y205H(5)|p.Y112N(2)|p.Y73N(2)|p.Y205fs*43(1)|p.Y205fs*42(1)|p.E204fs*39(1)|p.G199fs*42(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCATCCAAATACTCCACACGC	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	48	Substitution - Missense(30)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(3)|Deletion - In frame(1)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(6)|biliary_tract(5)|large_intestine(5)|endometrium(5)|upper_aerodigestive_tract(4)|central_nervous_system(4)|bone(4)|breast(3)|pancreas(3)|stomach(2)|lung(2)|skin(2)|urinary_tract(1)|oesophagus(1)|ovary(1)	17											136	121	126					17																	7578236		2203	4300	6503	7518961	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.613T>G	17.37:g.7578236A>C	ENSP00000269305:p.Tyr205Asp		7518961	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.153962	0.78114	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99878	0.9942	M	0.92738	3.34	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.997;0.999;0.998;0.999;0.999;0.997;0.999	D;D;D;D;D;D;D	0.79108	0.986;0.991;0.972;0.988;0.992;0.988;0.984	D	0.96347	0.9255	10	0.87932	D	0	-5.8058	13.709	0.62656	1.0:0.0:0.0:0.0	.	166;205;205;112;205;205;205	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	D	205;205;205;205;205;205;194;112;73;112;73	ENSP00000410739:Y205D;ENSP00000352610:Y205D;ENSP00000269305:Y205D;ENSP00000398846:Y205D;ENSP00000391127:Y205D;ENSP00000391478:Y205D;ENSP00000425104:Y73D;ENSP00000423862:Y112D	ENSP00000269305:Y205D	Y	-	1	0	TP53	7518961	1.000000	0.71417	0.163000	0.22734	0.042000	0.13812	7.465000	0.80898	2.183000	0.69458	0.533000	0.62120	TAT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578236	A	C	7578236	3	2	11	1	0	0	0	0	1	0	0	0	16421	391	14	4	681	4	TP53	17	7578236	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	636737	7578236	73616974	117	1387										
PIPOX	51268	hgsc.bcm.edu	37	chr17	27380507	27380507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aaacccagggctactggtcaCggtgaaaaccacctccagga	10	13	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:27380507C>T	ENST00000323372.4	+	4	880	c.554C>T	c.(553-555)aCg>aTg	p.T185M	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	185					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)	p.T185M(1)		endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	CTACTGGTCACGGTGAAAACC	0.562																																																1	Substitution - Missense(1)	prostate(1)	17											137	121	126					17																	27380507		2203	4300	6503	24404633	SO:0001583	missense	51268			AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"L-pipecolic acid oxidase"					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.554C>T	17.37:g.27380507C>T	ENSP00000317721:p.Thr185Met		24404633	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	37	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	C	8.391	0.839660	0.16891	.	.	ENSG00000179761	ENST00000323372;ENST00000419875	D	0.81821	-1.54	6.07	-10.1	0.00402	FAD dependent oxidoreductase (1);	0.650845	0.17280	N	0.180024	T	0.81588	0.4854	M	0.88450	2.955	0.09310	N	0.999999	P	0.35456	0.502	B	0.36244	0.22	T	0.69439	-0.5145	10	0.56958	D	0.05	-6.8642	22.0829	0.99966	0.0806:0.8342:0.0:0.0852	.	185	Q9P0Z9	SOX_HUMAN	M	185;116	ENSP00000317721:T185M	ENSP00000317721:T185M	T	+	2	0	PIPOX	24404633	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.161000	0.01278	-2.573000	0.00466	-2.333000	0.00248	ACG		0.562	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		T	27380507	C	T	27380507	3	4	11	1	0	0	0	0	1	0	0	0	11974	536	19	1	568	1	PIPOX	17	27380507	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	19802271	27380507	53814703	118	1388										
NF1	4763	hgsc.bcm.edu	37	chr17	29677309	29677309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tgttcctatggatacatatcCcattcatcatggtgaccctt	6	11	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:29677309C>A	ENST00000358273.4	+	50	7813	c.7430C>A	c.(7429-7431)cCc>cAc	p.P2477H	NF1_ENST00000444181.2_Missense_Mutation_p.P270H|NF1_ENST00000356175.3_Missense_Mutation_p.P2456H|NF1_ENST00000417592.2_Missense_Mutation_p.P190H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2477					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GATACATATCCCATTCATCAT	0.363			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17	GRCh37	CD000999	NF1	D							121	108	112					17																	29677309		2203	4300	6503	26701435	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7430C>A	17.37:g.29677309C>A	ENSP00000351015:p.Pro2477His		26701435	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275971	0.59649	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181;ENST00000417592	T;T;T;T	0.48836	3.12;3.27;2.96;0.8	5.47	5.47	0.80525	Armadillo-type fold (1);	0.174248	0.52532	D	0.000076	T	0.48768	0.1518	N	0.24115	0.695	0.47737	D	0.999509	P;P	0.48407	0.91;0.511	P;B	0.50617	0.646;0.19	T	0.52830	-0.8523	10	0.72032	D	0.01	.	19.312	0.94192	0.0:1.0:0.0:0.0	.	2456;2477	P21359-2;P21359	.;NF1_HUMAN	H	2477;2456;2122;270;190	ENSP00000351015:P2477H;ENSP00000348498:P2456H;ENSP00000389907:P2122H;ENSP00000396481:P270H	ENSP00000348498:P2456H	P	+	2	0	NF1	26701435	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.381000	0.66208	2.569000	0.86673	0.563000	0.77884	CCC		0.363	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29677309	C	A	29677309	3	1	11	1	0	0	0	0	1	0	0	0	10387	623	22	2	7689	2	NF1	17	29677309	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	2296802	29677309	51517901	119	1389										
ACCN1	40	hgsc.bcm.edu	37	chr17	31350986	31350986	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttgtagcgggttaggttgcaGggtgtcctgcagagacagta	16	6	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:31350986G>T	ENST00000359872.6	-	6	1850	c.1089C>A	c.(1087-1089)ccC>ccA	p.P363P	ASIC2_ENST00000448983.1_5'UTR|ASIC2_ENST00000225823.2_Silent_p.P414P	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	363					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	TTAGGTTGCAGGGTGTCCTGC	0.488																																																0			17											150	133	139					17																	31350986		2203	4300	6503	28375099	SO:0001819	synonymous_variant	40			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.1089C>A	17.37:g.31350986G>T			28375099	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																				0.488	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		T	31350986	G	T	31350986	2	4	11	1	0	0	0	0	0	0	0	1	128	987	35	2		2	ACCN1	17	31350986	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	1673677	31350986	49844224	120	1390										
ACACA	31	hgsc.bcm.edu	37	chr17	35614629	35614629	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	atgctattatactcacgaaaTtgcctcttctctgttttctc	4	11	4	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:35614629T>C	ENST00000394406.2	-	14	1901	c.1711A>G	c.(1711-1713)Att>Gtt	p.I571V	ACACA_ENST00000335166.5_Missense_Mutation_p.I493V|ACACA_ENST00000353139.5_Missense_Mutation_p.I608V|ACACA_ENST00000360679.3_Missense_Mutation_p.I513V	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	571	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	ACTCACGAAATTGCCTCTTCT	0.393																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											0			17											83	77	79					17																	35614629		2203	4300	6503	32688742	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1711A>G	17.37:g.35614629T>C	ENSP00000377928:p.Ile571Val		32688742	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.161993	0.57368	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	5.93	5.93	0.95920	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.74619	0.3740	L	0.41824	1.3	0.80722	D	1	B;B;B	0.24882	0.036;0.113;0.043	B;B;B	0.32677	0.06;0.15;0.132	T	0.68588	-0.5369	10	0.09338	T	0.73	.	15.5755	0.76380	0.0:0.0:0.0:1.0	.	608;571;513	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	V	608;513;571;595;493	ENSP00000344789:I608V;ENSP00000353898:I513V;ENSP00000377928:I571V;ENSP00000335323:I493V	ENSP00000335323:I493V	I	-	1	0	ACACA	32688742	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.281000	0.76405	0.533000	0.62120	ATT		0.393	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35614629	T	C	35614629	3	2	11	1	0	0	0	0	1	0	0	0	106	1493	52	4	5501	4	ACACA	17	35614629	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	4263643	35614629	45580581	121	1391										
KIF19	124602	hgsc.bcm.edu	37	chr17	72342636	72342636	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aacaagtacatcaactatcgCgacagcaagctcacccggct	7	14	2	0	rs189039256	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:72342636C>T	ENST00000389916.4	+	8	1035	c.897C>T	c.(895-897)cgC>cgT	p.R299R		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	299	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						TCAACTATCGCGACAGCAAGC	0.567													C|||	3	0.000599042	0	0.0029	5008	,	,		16018	0		0.001	False		,,,				2504	0															0			17											72	44	53					17																	72342636		2096	4042	6138	69854231	SO:0001819	synonymous_variant	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.897C>T	17.37:g.72342636C>T			69854231	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																				0.567	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72342636	C	T	72342636	2	4	11	1	0	0	0	0	0	0	0	1	8303	755	27	1		1	KIF19	17	72342636	Silent	SNP	C	TCGA-AF-6655-01A-11D-1826-10	36728007	72342636	8852574	122	1392										
RNF213	57674	hgsc.bcm.edu	37	chr17	78320137	78320137	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agctgaatgcctttctctccAagtccagcgtcagcaaaaat	7	12	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr17:78320137A>G	ENST00000582970.1	+	29	8145	c.8002A>G	c.(8002-8004)Aag>Gag	p.K2668E	RNF213_ENST00000508628.2_Missense_Mutation_p.K2717E|RNF213_ENST00000336301.6_Missense_Mutation_p.K741E	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2668					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTTTCTCTCCAAGTCCAGCGT	0.532																																																0			17											67	65	66					17																	78320137		2203	4300	6503	75934732	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.8002A>G	17.37:g.78320137A>G	ENSP00000464087:p.Lys2668Glu		75934732	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	3.647	-0.072354	0.07228	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.23552	1.9	5.37	-10.7	0.00240	.	1.196700	0.05917	N	0.632790	T	0.06690	0.0171	N	0.01219	-0.95	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37776	-0.9691	10	0.12103	T	0.63	.	11.3226	0.49430	0.602:0.2474:0.1506:0.0	.	741	Q63HN8	RN213_HUMAN	E	2668;2717;741	ENSP00000338218:K741E	ENSP00000338218:K741E	K	+	1	0	RNF213	75934732	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.599000	0.02085	-2.090000	0.00859	-0.468000	0.05107	AAG		0.532	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78320137	A	G	78320137	3	3	11	1	0	0	0	0	1	0	0	0	13514	131	5	4	8431	4	RNF213	17	78320137	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	5977501	78320137	2875073	123	1393										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30926183	30926183	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ccctattattacctttctgcAcagccaatgggagttcttga	7	11	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr18:30926183A>G	ENST00000383096.3	-	9	832	c.650T>C	c.(649-651)gTg>gCg	p.V217A	CCDC178_ENST00000579947.1_Missense_Mutation_p.V217A|CCDC178_ENST00000402325.1_Missense_Mutation_p.V217A|CCDC178_ENST00000583930.1_Missense_Mutation_p.V217A|CCDC178_ENST00000300227.8_Missense_Mutation_p.V217A|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000403303.1_Missense_Mutation_p.V217A|CCDC178_ENST00000406524.2_Missense_Mutation_p.V217A			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	217																	ACCTTTCTGCACAGCCAATGG	0.323																																																0			18											99	99	99					18																	30926183		2203	4300	6503	29180181	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.650T>C	18.37:g.30926183A>G	ENSP00000372576:p.Val217Ala		29180181	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	A	10.76	1.442190	0.25987	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.63255	1.36;1.36;1.36;1.37;1.35;-0.03	5.59	5.59	0.84812	.	.	.	.	.	T	0.74030	0.3663	L	0.55990	1.75	0.35289	D	0.782005	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.991;0.991;0.991	T	0.80226	-0.1470	9	0.45353	T	0.12	-16.5976	13.2917	0.60274	1.0:0.0:0.0:0.0	.	217;217;217;217	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	A	217	ENSP00000385591:V217A;ENSP00000372576:V217A;ENSP00000300227:V217A;ENSP00000385867:V217A;ENSP00000385234:V217A;ENSP00000382130:V217A	ENSP00000300227:V217A	V	-	2	0	C18orf34	29180181	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	5.551000	0.67274	2.129000	0.65627	0.455000	0.32223	GTG		0.323	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		G	30926183	A	G	30926183	3	3	11	1	0	0	0	0	1	0	0	0	1908	159	6	4	2013	4	C18orf34	18	30926183	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10		30926183	47151065	124	1394										
DCC	1630	hgsc.bcm.edu	37	chr18	50734111	50734111	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	aaaaaattcaccgaatatagTcttcgattcttagcttataa	4	7	3	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr18:50734111T>C	ENST00000442544.2	+	11	2401	c.1785T>C	c.(1783-1785)agT>agC	p.S595S	DCC_ENST00000412726.1_Silent_p.S443S|DCC_ENST00000581580.1_Silent_p.S250S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	595	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCGAATATAGTCTTCGATTCT	0.383																																																0			18											149	154	152					18																	50734111		2203	4300	6503	48988109	SO:0001819	synonymous_variant	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1785T>C	18.37:g.50734111T>C			48988109		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																				0.383	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50734111	T	C	50734111	2	2	11	1	0	0	0	0	0	0	0	1	4288	1664	58	4		4	DCC	18	50734111	Silent	SNP	T	TCGA-AF-6655-01A-11D-1826-10	19807928	50734111	27343137	125	1395										
C18orf54	162681	hgsc.bcm.edu	37	chr18	51887205	51887205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tatgtcacagttctgcaactAtatttacaaaccaaacaatg	4	9	2	0	rs564302523	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr18:51887205A>G	ENST00000300091.5	+	2	595	c.263A>G	c.(262-264)tAt>tGt	p.Y88C	STARD6_ENST00000577499.1_5'Flank|STARD6_ENST00000581310.1_5'Flank|C18orf54_ENST00000382911.4_Missense_Mutation_p.Y88C|STARD6_ENST00000584040.1_5'Flank|C18orf54_ENST00000578138.1_Intron	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	88						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		TTCTGCAACTATATTTACAAA	0.313													A|||	2	0.000399361	0	0	5008	,	,		20432	0		0	False		,,,				2504	0.002															0			18											68	74	72					18																	51887205		2202	4298	6500	50141203	SO:0001583	missense	162681			AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"lung adenoma susceptibility protein 2"	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.263A>G	18.37:g.51887205A>G	ENSP00000300091:p.Tyr88Cys		50141203	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	37	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	A	9.123	1.009428	0.19277	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	D;D	0.97598	-4.45;-4.45	5.38	-3.95	0.04118	.	0.947638	0.08850	N	0.884566	D	0.91650	0.7361	L	0.38838	1.175	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.81831	-0.0752	10	0.35671	T	0.21	-11.3172	2.7028	0.05154	0.2782:0.1237:0.4202:0.1779	.	88;88	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	C	88	ENSP00000300091:Y88C;ENSP00000372368:Y88C	ENSP00000300091:Y88C	Y	+	2	0	C18orf54	50141203	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.212000	0.09319	-0.185000	0.10550	-0.263000	0.10527	TAT		0.313	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529		G	51887205	A	G	51887205	3	3	11	1	0	0	0	0	1	0	0	0	1910	449	16	4	265	4	C18orf54	18	51887205	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	1153094	51887205	26190043	126	1396										
CCBE1	147372	hgsc.bcm.edu	37	chr18	57363880	57363880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cctgtagcatgtggtgagctCgcctgaagacttcagacacg	12	11	1	4			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr18:57363880C>T	ENST00000439986.4	-	2	230	c.193G>A	c.(193-195)Gag>Aag	p.E65K	RP11-2N1.2_ENST00000588946.1_RNA	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	65					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				GTGGTGAGCTCGCCTGAAGAC	0.567											OREG0025022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)											0			18											106	108	107					18																	57363880		2203	4300	6503	55514860	SO:0001583	missense	147372			AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.193G>A	18.37:g.57363880C>T	ENSP00000404464:p.Glu65Lys	1022	55514860	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	ENST00000439986.4	37	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676186	0.47886	.	.	ENSG00000183287	ENST00000439986	D	0.85339	-1.97	5.95	5.07	0.68467	.	0.000000	0.64402	D	0.000001	T	0.73737	0.3625	L	0.27053	0.805	0.80722	D	1	P	0.42375	0.778	B	0.33690	0.168	T	0.76686	-0.2868	10	0.72032	D	0.01	-25.3637	10.8457	0.46741	0.0:0.914:0.0:0.086	.	65	Q6UXH8	CCBE1_HUMAN	K	65	ENSP00000404464:E65K	ENSP00000404464:E65K	E	-	1	0	CCBE1	55514860	0.999000	0.42202	0.949000	0.38748	0.682000	0.39822	4.408000	0.59761	1.520000	0.48965	0.491000	0.48974	GAG		0.567	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459		T	57363880	C	T	57363880	3	4	11	1	0	0	0	0	1	0	0	0	2737	893	31	1	1067	1	CCBE1	18	57363880	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10	5476675	57363880	20713368	127	1397										
WDR88	126248	hgsc.bcm.edu	37	chr19	33651349	33651349	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	tcatttctggagggtttgatAggactgtggctatttgggat	14	4	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr19:33651349A>T	ENST00000355868.3	+	8	1103	c.1027A>T	c.(1027-1029)Agg>Tgg	p.R343W	WDR88_ENST00000361680.2_Missense_Mutation_p.R343W	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	343										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					AGGGTTTGATAGGACTGTGGC	0.498																																																0			19											215	197	203					19																	33651349		2203	4300	6503	38343189	SO:0001583	missense	126248			BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1027A>T	19.37:g.33651349A>T	ENSP00000348129:p.Arg343Trp		38343189	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700068	0.68501	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.42513	0.97;0.97	5.5	5.5	0.81552	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	1.024610	0.07756	N	0.949352	T	0.68183	0.2973	M	0.85462	2.755	0.30250	N	0.794181	D	0.63880	0.993	P	0.59424	0.857	T	0.63571	-0.6607	10	0.87932	D	0	.	14.7734	0.69696	1.0:0.0:0.0:0.0	.	343	Q6ZMY6	WDR88_HUMAN	W	343	ENSP00000348129:R343W;ENSP00000355148:R343W	ENSP00000348129:R343W	R	+	1	2	WDR88	38343189	1.000000	0.71417	0.815000	0.32552	0.478000	0.33099	5.662000	0.68032	2.232000	0.73038	0.529000	0.55759	AGG		0.498	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		T	33651349	A	T	33651349	3	4	11	1	0	0	0	0	1	0	0	0	17375	411	15	5	1057	5	WDR88	19	33651349	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10		33651349	25477634	128	1398										
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42224098	42224098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gaactcagtgagtgcaaaccGcagtgacccagtcaccctgg	11	13	2	2	rs146319665	byFrequency	TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr19:42224098G>A	ENST00000221992.6	+	7	1856	c.1742G>A	c.(1741-1743)cGc>cAc	p.R581H	CEACAM5_ENST00000398599.4_Missense_Mutation_p.R580H|CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000405816.1_Missense_Mutation_p.R581H	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	581	Ig-like 6.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		AGTGCAAACCGCAGTGACCCA	0.517																																																0			19						A	HIS/ARG	0,4406		0,0,2203	198	181	187		1742	-4.9	0	19	dbSNP_134	187	7,8593	818.9+/-406.8	0,7,4293	yes	missense	CEACAM5	NM_004363.2	29	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	581/703	42224098	7,12999	2203	4300	6503	46915938	SO:0001583	missense	1048			M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1742G>A	19.37:g.42224098G>A	ENSP00000221992:p.Arg581His		46915938	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	A	1.548	-0.539874	0.04053	0.0	8.14E-4	ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181	T;T	0.00760	5.73;5.73	2.46	-4.91	0.03085	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00906	0.0030	L	0.58583	1.82	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.37197	-0.9716	9	0.40728	T	0.16	.	5.2767	0.15653	0.5201:0.0:0.2544:0.2255	.	581;581	P06731;Q53G30	CEAM5_HUMAN;.	H	581;581;299	ENSP00000221992:R581H;ENSP00000385072:R581H	ENSP00000221992:R581H	R	+	2	0	CEACAM5	46915938	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.730000	0.00381	-3.868000	0.00097	-2.407000	0.00222	CGC		0.517	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42224098	G	A	42224098	3	1	11	1	0	0	0	0	1	0	0	0	3201	1087	38	1	1768	1	CEACAM5	19	42224098	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	8572749	42224098	16904885	129	1399										
LIPE	3991	hgsc.bcm.edu	37	chr19	42910417	42910417	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	caggctgcagcattgtggccGggtaggctgccatgatgcca	15	11	0	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr19:42910417G>A	ENST00000244289.4	-	7	2537	c.2261C>T	c.(2260-2262)cCg>cTg	p.P754L	LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000593491.2_RNA|LIPE_ENST00000602000.1_5'Flank	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	754					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CATTGTGGCCGGGTAGGCTGC	0.662																																																0			19											48	46	46					19																	42910417		2203	4300	6503	47602257	SO:0001583	missense	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2261C>T	19.37:g.42910417G>A	ENSP00000244289:p.Pro754Leu		47602257	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.731357	0.89390	.	.	ENSG00000079435	ENST00000244289	T	0.44881	0.91	5.09	5.09	0.68999	Alpha/beta hydrolase fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.79741	0.4498	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86939	0.2078	10	0.42905	T	0.14	-33.719	17.6625	0.88196	0.0:0.0:1.0:0.0	.	754	Q05469	LIPS_HUMAN	L	754	ENSP00000244289:P754L	ENSP00000244289:P754L	P	-	2	0	LIPE	47602257	1.000000	0.71417	0.957000	0.39632	0.838000	0.47535	6.684000	0.74538	2.531000	0.85337	0.645000	0.84053	CCG		0.662	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		A	42910417	G	A	42910417	3	1	11	1	0	0	0	0	1	0	0	0	8845	1116	39	1	985	1	LIPE	19	42910417	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	686319	42910417	16218566	130	1400										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57059202	57059202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtgtttctaagcccgatgtgAtctcctcgttggaacaagga	11	9	2	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr19:57059202A>G	ENST00000301318.3	+	4	525	c.454A>G	c.(454-456)Atc>Gtc	p.I152V	AC007228.11_ENST00000596587.1_RNA|ZFP28_ENST00000591844.1_Missense_Mutation_p.I152V	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	152	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GCCCGATGTGATCTCCTCGTT	0.517																																					Ovarian(124;554 1662 19430 21141 52494)											0			19											208	192	198					19																	57059202		2203	4300	6503	61751014	SO:0001583	missense	140612				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.454A>G	19.37:g.57059202A>G	ENSP00000301318:p.Ile152Val		61751014	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.512421	0.27123	.	.	ENSG00000196867	ENST00000301318	T	0.00848	5.62	4.01	1.91	0.25777	Krueppel-associated box (3);	0.000000	0.40064	N	0.001188	T	0.02929	0.0087	M	0.64567	1.98	0.09310	N	0.999995	B;D	0.67145	0.188;0.996	B;D	0.81914	0.1;0.995	T	0.34700	-0.9818	10	0.51188	T	0.08	.	5.1176	0.14843	0.7575:0.0:0.2425:0.0	.	152;152	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	V	152	ENSP00000301318:I152V	ENSP00000301318:I152V	I	+	1	0	ZFP28	61751014	1.000000	0.71417	0.336000	0.25522	0.886000	0.51366	3.109000	0.50345	0.699000	0.31761	0.460000	0.39030	ATC		0.517	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		G	57059202	A	G	57059202	3	3	11	1	0	0	0	0	1	0	0	0	17681	333	12	4	468	4	ZFP28	19	57059202	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	14148785	57059202	2069781	131	1401										
PDYN	5173	hgsc.bcm.edu	37	chr20	1961195	1961195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agctcctcttggggtatttgCgcaaaaagcccccatagcgt	10	12	1	0	rs377075531		TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:1961195C>T	ENST00000217305.2	-	4	764	c.539G>A	c.(538-540)cGc>cAc	p.R180H	PDYN_ENST00000540134.1_Missense_Mutation_p.R180H|PDYN_ENST00000539905.1_Missense_Mutation_p.R180H|RP4-684O24.5_ENST00000446562.1_RNA	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	180					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GGGGTATTTGCGCAAAAAGCC	0.602																																																0			20											99	103	102					20																	1961195		2203	4300	6503	1909195	SO:0001583	missense	5173				CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.539G>A	20.37:g.1961195C>T	ENSP00000217305:p.Arg180His		1909195	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772531	0.90108	.	.	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	D;D;D	0.86769	-2.17;-2.17;-2.17	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.94162	0.8127	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95090	0.8221	10	0.87932	D	0	-18.2484	15.1657	0.72821	0.0:1.0:0.0:0.0	.	180	P01213	PDYN_HUMAN	H	180	ENSP00000440185:R180H;ENSP00000442259:R180H;ENSP00000217305:R180H	ENSP00000217305:R180H	R	-	2	0	PDYN	1909195	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.652000	0.61454	2.445000	0.82738	0.313000	0.20887	CGC		0.602	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			T	1961195	C	T	1961195	3	4	11	1	0	0	0	0	1	0	0	0	11730	768	27	1	229	1	PDYN	20	1961195	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10		1961195	61064325	132	1402										
LRRN4	164312	hgsc.bcm.edu	37	chr20	6022340	6022340	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	agcagcaagactggaatctcGccctcggaaagactcgggtt	12	11	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:6022340G>A	ENST00000378858.4	-	5	1775	c.1551C>T	c.(1549-1551)ggC>ggT	p.G517G		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	517					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						CTGGAATCTCGCCCTCGGAAA	0.632																																																0			20											104	114	110					20																	6022340		2203	4300	6503	5970340	SO:0001819	synonymous_variant	164312			AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"Fibronectin type III domain containing"	16208	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 75"	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.1551C>T	20.37:g.6022340G>A			5970340	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	37	CCDS13097.1																																																																																				0.632	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		A	6022340	G	A	6022340	2	1	11	1	0	0	0	0	0	0	0	1	9066	1074	38	1		1	LRRN4	20	6022340	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	4061145	6022340	57003180	133	1403										
C20orf132	140699	hgsc.bcm.edu	37	chr20	35743618	35743618	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtcctcatcatggcagccagGgtagtgaaatccattgttct	10	10	3	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:35743618G>A	ENST00000400441.3	-	19	2492	c.2493C>T	c.(2491-2493)acC>acT	p.T831T	MROH8_ENST00000441008.2_Silent_p.T817T|MROH8_ENST00000217333.8_Silent_p.T660T			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	0																	TGGCAGCCAGGGTAGTGAAAT	0.463																																																0			20											145	142	143					20																	35743618		2009	4179	6188	35177032	SO:0001819	synonymous_variant	140699			AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.2493C>T	20.37:g.35743618G>A			35177032	Q5JYQ6	Missense_Mutation	SNP	ENST00000400441.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.444|9.444	1.088836|1.088836	0.20390|0.20390	.|.	.|.	ENSG00000101353|ENSG00000101353	ENST00000343811|ENST00000417458	.|.	.|.	.|.	5.27|5.27	0.0309|0.0309	0.14168|0.14168	.|.	.|.	.|.	.|.	.|.	T|T	0.42854|0.42854	0.1221|0.1221	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25606|0.25606	-1.0127|-1.0127	4|4	.|.	.|.	.|.	-19.0908|-19.0908	2.6134|2.6134	0.04897|0.04897	0.0968:0.2998:0.3788:0.2246|0.0968:0.2998:0.3788:0.2246	.|.	.|.	.|.	.|.	L|S	858|459	.|.	.|.	P|P	-|-	2|1	0|0	C20orf132|C20orf132	35177032|35177032	0.198000|0.198000	0.23374|0.23374	0.992000|0.992000	0.48379|0.48379	0.991000|0.991000	0.79684|0.79684	0.039000|0.039000	0.13884|0.13884	0.250000|0.250000	0.21479|0.21479	0.655000|0.655000	0.94253|0.94253	CCC|CCT		0.463	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		A	35743618	G	A	35743618	2	1	11	1	0	0	0	0	0	0	0	1	2092	1219	43	3		3	C20orf132	20	35743618	Silent	SNP	G	TCGA-AF-6655-01A-11D-1826-10	29721278	35743618	27281902	134	1404										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130350	45130350	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	cacattcattgcattcatatGgtctctcccatatagttctc	4	12	4	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:45130350G>T	ENST00000347606.4	-	5	1810	c.1628C>A	c.(1627-1629)cCa>cAa	p.P543Q	ZNF334_ENST00000457685.2_Missense_Mutation_p.P505Q|ZNF334_ENST00000593880.1_Missense_Mutation_p.P566Q	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	543					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GCATTCATATGGTCTCTCCCA	0.443																																																0			20											185	175	178					20																	45130350		2203	4300	6503	44563757	SO:0001583	missense	55713			AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1628C>A	20.37:g.45130350G>T	ENSP00000255129:p.Pro543Gln		44563757	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	37	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.400385	0.42613	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.51817	0.69;0.69	3.23	2.27	0.28462	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57021	0.2025	M	0.84511	2.7	0.23030	N	0.998402	D;D;D	0.57257	0.979;0.979;0.979	P;P;P	0.48901	0.594;0.594;0.594	T	0.51980	-0.8636	9	0.87932	D	0	.	8.296	0.31986	0.1225:0.0:0.8775:0.0	.	505;543;566	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	Q	505;543	ENSP00000402582:P505Q;ENSP00000255129:P543Q	ENSP00000255129:P543Q	P	-	2	0	ZNF334	44563757	1.000000	0.71417	0.009000	0.14445	0.620000	0.37586	4.862000	0.62976	0.690000	0.31570	-0.229000	0.12294	CCA		0.443	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			T	45130350	G	T	45130350	3	4	11	1	0	0	0	0	1	0	0	0	17890	1348	47	2	418	2	ZNF334	20	45130350	Missense_Mutation	SNP	G	TCGA-AF-6655-01A-11D-1826-10	9386732	45130350	17895170	135	1405										
SULF2	55959	hgsc.bcm.edu	37	chr20	46294671	46294671	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	acaggtccaggtcacactggActgtgtcgttctctaggatg	12	10	2	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:46294671A>G	ENST00000359930.4	-	13	2683	c.1832T>C	c.(1831-1833)gTc>gCc	p.V611A	SULF2_ENST00000467815.1_Missense_Mutation_p.V611A|SULF2_ENST00000484875.1_Missense_Mutation_p.V611A|SULF2_ENST00000361612.4_Missense_Mutation_p.V611A	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	611					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTCACACTGGACTGTGTCGTT	0.602																																																0			20											221	185	197					20																	46294671		2203	4300	6503	45728078	SO:0001583	missense	55959			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1832T>C	20.37:g.46294671A>G	ENSP00000353007:p.Val611Ala		45728078	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.548957	0.65311	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	D;D;D;D	0.99519	-6.07;-6.07;-6.06;-6.07	5.24	5.24	0.73138	Extracellular sulfatase, C-terminal (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99426	0.9797	M	0.74647	2.275	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.996	D	0.98705	1.0702	10	0.87932	D	0	-25.3396	15.1399	0.72601	1.0:0.0:0.0:0.0	.	611;611	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	A	611;611;611;30;611	ENSP00000353007:V611A;ENSP00000418290:V611A;ENSP00000354662:V611A;ENSP00000418442:V611A	ENSP00000353007:V611A	V	-	2	0	SULF2	45728078	1.000000	0.71417	0.994000	0.49952	0.104000	0.19210	9.339000	0.96797	1.979000	0.57680	0.378000	0.23410	GTC		0.602	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		G	46294671	A	G	46294671	3	3	11	1	0	0	0	0	1	0	0	0	15410	275	10	4	816	4	SULF2	20	46294671	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	1164321	46294671	16730849	136	1406										
C20orf177	63939	hgsc.bcm.edu	37	chr20	58519845	58519845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	gtaccaggttttgttctcagAggcaaacccttgaaatgagg	11	8	1	3			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr20:58519845A>G	ENST00000358293.3	+	5	1262	c.847A>G	c.(847-849)Agg>Ggg	p.R283G	FAM217B_ENST00000360816.3_Missense_Mutation_p.R283G|FAM217B_ENST00000469084.1_3'UTR	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	283								p.R283W(1)									TTGTTCTCAGAGGCAAACCCT	0.453																																																1	Substitution - Missense(1)	ovary(1)	20											63	64	63					20																	58519845		2203	4300	6503	57953240	SO:0001583	missense	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.847A>G	20.37:g.58519845A>G	ENSP00000351040:p.Arg283Gly		57953240	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.661572	0.29515	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.26957	1.7;1.7	5.44	2.0	0.26442	.	0.517494	0.17639	N	0.167085	T	0.12987	0.0315	N	0.14661	0.345	0.20196	N	0.999929	B	0.26547	0.152	B	0.21708	0.036	T	0.18524	-1.0334	10	0.72032	D	0.01	-10.4411	5.5494	0.17081	0.648:0.1353:0.2167:0.0	.	283	Q9NTX9	CT177_HUMAN	G	283	ENSP00000351040:R283G;ENSP00000354056:R283G	ENSP00000351040:R283G	R	+	1	2	C20orf177	57953240	0.985000	0.35326	0.194000	0.23346	0.391000	0.30476	1.215000	0.32431	0.368000	0.24481	0.533000	0.62120	AGG		0.453	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		G	58519845	A	G	58519845	3	3	11	1	0	0	0	0	1	0	0	0	2102	295	11	4	849	4	C20orf177	20	58519845	Missense_Mutation	SNP	A	TCGA-AF-6655-01A-11D-1826-10	12225174	58519845	4505675	137	1407										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19725330	19725330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ttagatcctggacccagaaaCaaaagccatcctcaaagtta	6	11	1	2			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chr21:19725330C>A	ENST00000284885.3	-	10	1094	c.1061G>T	c.(1060-1062)tGt>tTt	p.C354F		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	354	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.C354F(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GACCCAGAAACAAAAGCCATC	0.333																																																1	Substitution - Missense(1)	ovary(1)	21											80	84	83					21																	19725330		2203	4300	6503	18647201	SO:0001583	missense	0				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1061G>T	21.37:g.19725330C>A	ENSP00000284885:p.Cys354Phe		18647201	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911554	0.72983	.	.	ENSG00000154646	ENST00000284885	T	0.13538	2.58	5.2	5.2	0.72013	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.85682	D	0.000000	T	0.56140	0.1965	H	0.97874	4.095	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.74432	-0.3667	9	.	.	.	.	18.0723	0.89413	0.0:1.0:0.0:0.0	.	354	P98073	ENTK_HUMAN	F	354	ENSP00000284885:C354F	.	C	-	2	0	TMPRSS15	18647201	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.162000	0.71874	2.572000	0.86782	0.655000	0.94253	TGT		0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19725330	C	A	19725330	3	1	11	1	0	0	0	0	1	0	0	0	16285	478	17	2	2062	2	TMPRSS15	21	19725330	Missense_Mutation	SNP	C	TCGA-AF-6655-01A-11D-1826-10		19725330	28404565	138	1408										
WWC3	55841	hgsc.bcm.edu	37	chrX	10084546	10084546	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	acctccagtcccagttaaaaAggtaggttactttcaaagag	8	9	1	1			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chrX:10084546A>G	ENST00000380861.4	+	10	1454	c.1063A>G	c.(1063-1065)Agc>Ggc	p.S355G	WWC3_ENST00000454666.1_Splice_Site_p.S355G	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	355	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CCAGTTAAAAAGGTAGGTTAC	0.403																																																0			X											114	108	110					X																	10084546		2203	4300	6503	10044546	SO:0001630	splice_region_variant	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1064+1A>G	X.37:g.10084546A>G			10044546	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.787082	0.49997	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.46451	0.87;0.87	4.79	4.79	0.61399	.	0.230668	0.53938	D	0.000041	T	0.54902	0.1887	M	0.79011	2.435	0.58432	D	0.999999	P	0.51449	0.945	P	0.50440	0.641	T	0.62637	-0.6812	10	0.72032	D	0.01	-24.883	13.6327	0.62204	1.0:0.0:0.0:0.0	.	355	Q9ULE0	WWC3_HUMAN	G	355;355;19;355	ENSP00000370242:S355G;ENSP00000399584:S355G	ENSP00000370242:S355G	S	+	1	0	WWC3	10044546	1.000000	0.71417	0.150000	0.22450	0.130000	0.20726	8.499000	0.90494	1.592000	0.50018	0.474000	0.43551	AGC		0.403	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	Missense_Mutation	G	10084546	A	G	10084546	5	3	11	1	0	0	0	0	0	0	1	0	17453	86	3	4	1097	4	WWC3	23	10084546	Splice_Site	SNP	A	TCGA-AF-6655-01A-11D-1826-10		10084546	145186014	139	1409										
NRK	203447	hgsc.bcm.edu	37	chrX	105132356	105132356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214285714285714	3	1	0.358383551931939	2.22994210090984	0.252446275574699	1	1	0	ctttccacaaaaacattgtgTccttctatggagcatttttc	5	10	1	0			TCGA-AF-6655-01A-11D-1826-10	TCGA-AF-6655-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f36bb78a-5fa8-439f-92c9-56ce425206b0	54e3390b-9c67-4934-a891-f259a098de11	g.chrX:105132356T>C	ENST00000243300.9	+	5	625	c.322T>C	c.(322-324)Tcc>Ccc	p.S108P	NRK_ENST00000428173.2_Missense_Mutation_p.S108P|NRK_ENST00000536164.1_Missense_Mutation_p.S108P	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						AAACATTGTGTCCTTCTATGG	0.403										HNSCC(51;0.14)																																						0			X											112	92	98					X																	105132356		1903	4100	6003	105019012	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.322T>C	X.37:g.105132356T>C	ENSP00000434830:p.Ser108Pro		105019012	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	T	18.81	3.703922	0.68501	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000536164	T;T;T	0.51071	1.8;1.8;0.72	4.95	1.98	0.26296	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.172299	0.28332	N	0.015734	T	0.44767	0.1309	L	0.31804	0.96	0.80722	D	1	D	0.53462	0.96	P	0.54815	0.761	T	0.39683	-0.9602	10	0.87932	D	0	.	7.967	0.30104	0.629:0.0:0.0:0.371	.	108	Q7Z2Y5	NRK_HUMAN	P	108	ENSP00000434830:S108P;ENSP00000438378:S108P;ENSP00000438785:S108P	ENSP00000434830:S108P	S	+	1	0	NRK	105019012	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.854000	0.55949	0.611000	0.30052	0.481000	0.45027	TCC		0.403	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		C	105132356	T	C	105132356	3	2	11	1	0	0	0	0	1	0	0	0	10686	1667	58	4	340	4	NRK	23	105132356	Missense_Mutation	SNP	T	TCGA-AF-6655-01A-11D-1826-10	95047810	105132356	50138204	140	1410										
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12837469	12837469	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctcatctccatggccgccctGgagaacctgctgcgccacac	9	18	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:12837469G>T	ENST00000357726.4	+	3	1206	c.1179G>T	c.(1177-1179)ctG>ctT	p.L393L		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	393					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGCCGCCCTGGAGAACCTGC	0.627																																																0			1											101	109	106					1																	12837469		2203	4300	6503	12760056	SO:0001819	synonymous_variant	390999				CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1179G>T	1.37:g.12837469G>T			12760056		Silent	SNP	ENST00000357726.4	37	CCDS41254.1																																																																																				0.627	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12837469	G	T	12837469	2	4	12	1	0	0	0	0	0	0	0	1	12462	1335	47	2		2	PRAMEF12	1	12837469	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10		12837469	236413152	1	1411										
PUM1	9698	hgsc.bcm.edu	37	chr1	31440127	31440127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	caagggcaccagtttggtcaTagtaagcagcaggagccaac	12	10	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:31440127T>C	ENST00000257075.5	-	12	1769	c.1676A>G	c.(1675-1677)tAt>tGt	p.Y559C	SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000373747.3_Missense_Mutation_p.Y560C|PUM1_ENST00000440538.2_Missense_Mutation_p.Y560C|PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Missense_Mutation_p.Y317C|PUM1_ENST00000373741.4_Missense_Mutation_p.Y595C|PUM1_ENST00000373742.2_Missense_Mutation_p.Y500C|PUM1_ENST00000426105.2_Missense_Mutation_p.Y559C	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	559	Ala-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		AGTTTGGTCATAGTAAGCAGC	0.458																																																0			1											117	104	108					1																	31440127		2203	4300	6503	31212714	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1676A>G	1.37:g.31440127T>C	ENSP00000257075:p.Tyr559Cys		31212714	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.972799	0.92919	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000373742	T;T;T;T;T;T;T	0.35236	1.51;1.32;1.57;1.57;1.61;1.54;1.46	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.994;0.963;0.991;0.984;0.991;0.991	P;P;P;P;P;P;P	0.62740	0.906;0.798;0.694;0.798;0.798;0.798;0.798	T	0.62253	-0.6893	10	0.87932	D	0	-7.2849	16.1778	0.81874	0.0:0.0:0.0:1.0	.	500;595;560;559;559;560;559	B4DG92;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;PUM1_HUMAN;.;.;.	C	317;559;560;297;559;560;595;500	ENSP00000400141:Y317C;ENSP00000257075:Y559C;ENSP00000362852:Y560C;ENSP00000391723:Y559C;ENSP00000401777:Y560C;ENSP00000362846:Y595C;ENSP00000362847:Y500C	ENSP00000257075:Y559C	Y	-	2	0	PUM1	31212714	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.279000	0.76181	0.533000	0.62120	TAT		0.458	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			C	31440127	T	C	31440127	3	2	12	1	0	0	0	0	1	0	0	0	12862	1406	49	4	1934	4	PUM1	1	31440127	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	18602658	31440127	217810494	2	1412										
MACF1	23499	hgsc.bcm.edu	37	chr1	39824375	39824375	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tttctctggcacagtgtacaCgattaggatctcacctgaat	8	10	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:39824375C>T	ENST00000372915.3	+	45	12052	c.11965C>T	c.(11965-11967)Cga>Tga	p.R3989*	MACF1_ENST00000545844.1_Nonsense_Mutation_p.R1922*|MACF1_ENST00000289893.4_Nonsense_Mutation_p.R2424*|MACF1_ENST00000564288.1_Nonsense_Mutation_p.R3984*|MACF1_ENST00000539005.1_Nonsense_Mutation_p.R1922*|MACF1_ENST00000317713.7_Nonsense_Mutation_p.R1922*|MACF1_ENST00000567887.1_Nonsense_Mutation_p.R4021*|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000361689.2_Nonsense_Mutation_p.R1922*			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3989					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.R2424*(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACAGTGTACACGATTAGGATC	0.498																																																1	Substitution - Nonsense(1)	central_nervous_system(1)	1											80	78	78					1																	39824375		2203	4300	6503	39596962	SO:0001587	stop_gained	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11965C>T	1.37:g.39824375C>T	ENSP00000362006:p.Arg3989*		39596962	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Nonsense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.912323|6.912323	0.97928|0.97928	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	.|T	.|0.35421	.|1.31	5.47|5.47	3.33|3.33	0.38152|0.38152	.|.	0.556344|.	0.15703|.	N|.	0.248842|.	.|T	.|0.32704	.|0.0838	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.31110	.|-0.9955	.|6	0.09338|0.62326	T|D	0.73|0.03	.|.	3.495|3.495	0.07651|0.07651	0.3168:0.4816:0.1139:0.0877|0.3168:0.4816:0.1139:0.0877	.|.	.|.	.|.	.|.	X|M	1922;3989;1922;1922;1922;2424|1055	.|ENSP00000362016:T1055M	ENSP00000289893:R2424X|ENSP00000362016:T1055M	R|T	+|+	1|2	2|0	MACF1|MACF1	39596962|39596962	0.054000|0.054000	0.20591|0.20591	0.674000|0.674000	0.29902|0.29902	0.938000|0.938000	0.57974|0.57974	1.867000|1.867000	0.39499|0.39499	1.442000|1.442000	0.47568|0.47568	0.655000|0.655000	0.94253|0.94253	CGA|ACG		0.498	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39824375	C	T	39824375	4	4	12	1	0	0	0	0	0	1	0	0	9174	528	19	1	12077	1	MACF1	1	39824375	Nonsense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	8384248	39824375	209426246	3	1413										
HFM1	164045	hgsc.bcm.edu	37	chr1	91781507	91781507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cagtcactaatatttctgccGtcgtatcactatatcttgta	5	10	4	0	rs148381777		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:91781507G>A	ENST00000370425.3	-	28	3103	c.3005C>T	c.(3004-3006)aCg>aTg	p.T1002M	HFM1_ENST00000370424.3_Missense_Mutation_p.T681M|HFM1_ENST00000294696.5_Missense_Mutation_p.T234M|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1002	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TATTTCTGCCGTCGTATCACT	0.313																																																0			1						G	MET/THR	1,4401	2.1+/-5.4	0,1,2200	52	52	52		3005	-10.5	0	1	dbSNP_134	52	1,8595	1.2+/-3.3	0,1,4297	no	missense	HFM1	NM_001017975.3	81	0,2,6497	AA,AG,GG		0.0116,0.0227,0.0154	benign	1002/1436	91781507	2,12996	2201	4298	6499	91554095	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3005C>T	1.37:g.91781507G>A	ENSP00000359454:p.Thr1002Met		91554095	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.729|2.729	-0.264924|-0.264924	0.05754|0.05754	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	.|T;T;T	.|0.61158	.|0.13;0.13;0.13	5.25|5.25	-10.5|-10.5	0.00291|0.00291	.|Sec63 domain (2);	.|0.447307	.|0.25581	.|N	.|0.029700	T|T	0.08935|0.08935	0.0221|0.0221	N|N	0.11201|0.11201	0.11|0.11	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.25743	.|0.02;0.133;0.08	.|B;B;B	.|0.21546	.|0.006;0.035;0.022	T|T	0.08269|0.08269	-1.0730|-1.0730	5|10	.|0.33940	.|T	.|0.23	.|.	4.1282|4.1282	0.10138|0.10138	0.3899:0.0879:0.3937:0.1284|0.3899:0.0879:0.3937:0.1284	.|.	.|681;213;1002	.|A6NGI5;B1B0B5;A2PYH4	.|.;.;HFM1_HUMAN	W|M	214|1002;234;681;686	.|ENSP00000359454:T1002M;ENSP00000294696:T234M;ENSP00000359453:T681M	.|ENSP00000294696:T234M	R|T	-|-	1|2	2|0	HFM1|HFM1	91554095|91554095	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.009000|0.009000	0.06853|0.06853	1.121000|1.121000	0.31283|0.31283	-1.559000|-1.559000	0.01688|0.01688	-0.368000|-0.368000	0.07277|0.07277	CGG|ACG		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91781507	G	A	91781507	3	1	12	1	0	0	0	0	1	0	0	0	7104	1145	40	1	1350	1	HFM1	1	91781507	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	51957132	91781507	157469114	4	1414										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109270590	109270590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actcctgcgtgcaccctttcGgctctagagtgtgacaccaa	9	14	1	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:109270590G>A	ENST00000370017.3	+	7	1549	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	FNDC7_ENST00000271311.2_Silent_p.S425S	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	424	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		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)		GCACCCTTTCGGCTCTAGAGT	0.483																																																0			1											242	208	219					1																	109270590		2203	4300	6503	109072113	SO:0001819	synonymous_variant	163479				CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1272G>A	1.37:g.109270590G>A			109072113	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	6.401	0.442051	0.12164	.	.	ENSG00000143107	ENST00000445274	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	T	0.24661	0.0598	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56745	-0.7928	4	.	.	.	-10.2511	7.5534	0.27810	0.1:0.0588:0.4515:0.3897	.	.	.	.	S	200	.	.	G	+	1	0	FNDC7	109072113	0.000000	0.05858	0.062000	0.19696	0.789000	0.44602	-3.528000	0.00441	-3.670000	0.00123	-1.036000	0.02392	GGC		0.483	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		A	109270590	G	A	109270590	2	1	12	1	0	0	0	0	0	0	0	1	5992	1103	39	1		1	FNDC7	1	109270590	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	17489083	109270590	139980031	5	1415										
GPR61	83873	hgsc.bcm.edu	37	chr1	110086221	110086221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaggagctcccagtgtccccCcaggctgttcactccagtgg	11	15	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:110086221C>T	ENST00000527748.1	+	2	1260	c.577C>T	c.(577-579)Cca>Tca	p.P193S	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.P193S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		CAGTGTCCCCCCAGGCTGTTC	0.582																																																1	Substitution - Missense(1)	central_nervous_system(1)	1											162	153	156					1																	110086221		2203	4300	6503	109887744	SO:0001583	missense	83873			AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"GPCR / Class A : Orphans"	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.577C>T	1.37:g.110086221C>T	ENSP00000432456:p.Pro193Ser		109887744	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	37	CCDS801.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797278	0.31777	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.36157	1.27	5.68	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.190927	0.42548	D	0.000698	T	0.08582	0.0213	N	0.08118	0	0.43574	D	0.995901	B	0.13594	0.008	B	0.14023	0.01	T	0.12167	-1.0558	10	0.10636	T	0.68	-2.3848	14.7202	0.69300	0.0:0.9283:0.0:0.0717	.	193	Q9BZJ8	GPR61_HUMAN	S	193;321	ENSP00000432456:P193S	ENSP00000286603:P321S	P	+	1	0	GPR61	109887744	0.026000	0.19158	1.000000	0.80357	0.980000	0.70556	1.287000	0.33284	2.664000	0.90586	0.655000	0.94253	CCA		0.582	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1			T	110086221	C	T	110086221	3	4	12	1	0	0	0	0	1	0	0	0	6722	623	22	3	579	3	GPR61	1	110086221	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	815631	110086221	139164400	6	1416										
GSTM4	2948	hgsc.bcm.edu	37	chr1	110201532	110201532	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	catggtttgttggagacaagGtaatgggggcatgtgatgag	17	3	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:110201532G>T	ENST00000369836.4	+	6	765		c.e6+1		GSTM4_ENST00000336075.5_Splice_Site|GSTM4_ENST00000369833.1_Splice_Site|GSTM4_ENST00000495742.1_Splice_Site|GSTM4_ENST00000326729.5_Splice_Site	NM_000850.4	NP_000841.1	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4						glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	TGGAGACAAGGTAATGGGGGC	0.478																																																0			1											252	236	241					1																	110201532		2203	4300	6503	110003055	SO:0001630	splice_region_variant	2948			M96234	CCDS806.1, CCDS807.1	1p13.3	2012-06-22	2008-11-26		ENSG00000168765	ENSG00000168765	2.5.1.18	"Glutathione S-transferases / Soluble"	4636	protein-coding gene	gene with protein product		138333	"glutathione S-transferase M4"			8276420	Standard	NM_000850		Approved		uc001dyf.3	Q03013	OTTHUMG00000011642	ENST00000369836.4:c.456+1G>T	1.37:g.110201532G>T			110003055	A8K765|Q05465|Q32NC1|Q4JNT8|Q6FH87	Splice_Site	SNP	ENST00000369836.4	37	CCDS807.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.764174	0.49574	.	.	ENSG00000168765	ENST00000369836;ENST00000336075;ENST00000326729;ENST00000369833	.	.	.	4.0	4.0	0.46444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5221	0.61574	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSTM4	110003055	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	6.215000	0.72206	2.256000	0.74724	0.298000	0.19748	.		0.478	GSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032187.1	NM_000850	Intron	T	110201532	G	T	110201532	5	4	12	1	0	0	0	0	0	0	1	0	6861	1275	44	2	479	2	GSTM4	1	110201532	Splice_Site	SNP	G	TCGA-AF-6672-01A-11D-1826-10	115311	110201532	139049089	7	1417										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114483239	114483239	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cagggcctcctcctcccagcTcctgcagtggagcatattgt	10	15	0	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:114483239T>C	ENST00000369558.1	+	2	466	c.234T>C	c.(232-234)gcT>gcC	p.A78A	HIPK1_ENST00000369561.4_Silent_p.A78A|HIPK1_ENST00000426820.2_Silent_p.A78A|HIPK1_ENST00000369555.2_Silent_p.A78A|HIPK1_ENST00000369559.4_Silent_p.A78A|HIPK1_ENST00000369554.2_Silent_p.A78A			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	78					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-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)		TCCTCCCAGCTCCTGCAGTGG	0.552																																																0			1											100	101	101					1																	114483239		2203	4300	6503	114284762	SO:0001819	synonymous_variant	204851			AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.234T>C	1.37:g.114483239T>C			114284762	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1																																																																																				0.552	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		C	114483239	T	C	114483239	2	2	12	1	0	0	0	0	0	0	0	1	7137	1538	54	4		4	HIPK1	1	114483239	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	4281707	114483239	134767382	8	1418										
AMPD1	270	hgsc.bcm.edu	37	chr1	115229401	115229413	+	Frame_Shift_Del	DEL	GAAAATCAGGCAC	GAAAATCAGGCAC	-													0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	accagtaatctgcactctctGaaaatcaggcacggtctggt					rs61741025	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	GAAAATCAGGCAC	GAAAATCAGGCAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:115229401_115229413delGAAAATCAGGCAC	ENST00000520113.2	-	4	448_460	c.433_445delGTGCCTGATTTTC	c.(433-447)gtgcctgattttcagfs	p.VPDFQ145fs	AMPD1_ENST00000369538.3_Frame_Shift_Del_p.VPDFQ141fs|AMPD1_ENST00000353928.6_Frame_Shift_Del_p.VPDFQ112fs			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	145					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	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)	TGCACTCTCTGAAAATCAGGCACGGTCTGGTAG	0.465																																																0			1																																								115030936	SO:0001589	frameshift_variant	270			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.433_445delGTGCCTGATTTTC	1.37:g.115229401_115229413delGAAAATCAGGCAC	ENSP00000430075:p.Val145fs		115030924	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Frame_Shift_Del	DEL	ENST00000520113.2	37	CCDS876.2																																																																																				0.465	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			-	115229413	GAAAATCAGGCAC	-	115229401	7	5	12	1	0	1	0	1	0	0	0	0	585	1299	45	0	1949	0	AMPD1	1	115229401	Frame_Shift_Del	DEL	GAAAATCAGGCAC	TCGA-AF-6672-01A-11D-1826-10	746162	115229401	134021220	9	1419										
ECM1	1893	hgsc.bcm.edu	37	chr1	150483554	150483554	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tatggtccctggaacctaccAcagtccagctactcccacct	6	17	0	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:150483554A>G	ENST00000369047.4	+	6	713	c.588A>G	c.(586-588)ccA>ccG	p.P196P	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Silent_p.P223P|ECM1_ENST00000346569.6_Silent_p.P196P	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	196	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.P196P(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	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;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGAACCTACCACAGTCCAGCT	0.582																																					Melanoma(156;1696 2560 11093 19685)											1	Substitution - coding silent(1)	ovary(1)	1											144	147	146					1																	150483554		2203	4300	6503	148750178	SO:0001819	synonymous_variant	1893			U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.588A>G	1.37:g.150483554A>G			148750178	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																				0.582	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		G	150483554	A	G	150483554	2	3	12	1	0	0	0	0	0	0	0	1	4908	146	6	4		4	ECM1	1	150483554	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10	35254153	150483554	98767067	10	1420										
TCHHL1	126637	hgsc.bcm.edu	37	chr1	152059508	152059508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tctctgtgggactgctggtcTtttttgatcctgccattggc	11	10	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:152059508T>C	ENST00000368806.1	-	3	714	c.650A>G	c.(649-651)aAg>aGg	p.K217R		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	217							calcium ion binding (GO:0005509)	p.K217M(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			ACTGCTGGTCTTTTTTGATCC	0.448																																																1	Substitution - Missense(1)	ovary(1)	1											137	122	127					1																	152059508		2203	4300	6503	150326132	SO:0001583	missense	126637				CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.650A>G	1.37:g.152059508T>C	ENSP00000357796:p.Lys217Arg		150326132	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	9.743	1.165333	0.21538	.	.	ENSG00000182898	ENST00000368806	T	0.21361	2.01	5.1	5.1	0.69264	.	0.666605	0.12399	N	0.472275	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37957	-0.9683	10	0.15499	T	0.54	0.1954	11.272	0.49144	0.0:0.0:0.0:1.0	.	217	Q5QJ38	TCHL1_HUMAN	R	217	ENSP00000357796:K217R	ENSP00000357796:K217R	K	-	2	0	TCHHL1	150326132	0.173000	0.23056	0.021000	0.16686	0.004000	0.04260	2.330000	0.43885	1.910000	0.55303	0.455000	0.32223	AAG		0.448	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		C	152059508	T	C	152059508	3	2	12	1	0	0	0	0	1	0	0	0	15740	1609	56	4	2068	4	TCHHL1	1	152059508	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	1575954	152059508	97191113	11	1421										
FCRL4	83417	hgsc.bcm.edu	37	chr1	157559005	157559005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctttctcacctgaagaaaagAgcaagcgcacagggttactt	9	10	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:157559005A>G	ENST00000271532.1	-	3	431	c.296T>C	c.(295-297)cTc>cCc	p.L99P	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	99					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L99R(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TGAAGAAAAGAGCAAGCGCAC	0.493																																																1	Substitution - Missense(1)	ovary(1)	1											63	68	66					1																	157559005		2203	4300	6503	155825629	SO:0001583	missense	83417			AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.296T>C	1.37:g.157559005A>G	ENSP00000271532:p.Leu99Pro		155825629	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	A	8.570	0.879827	0.17467	.	.	ENSG00000163518	ENST00000271532	T	0.19394	2.15	4.2	-8.41	0.00961	Immunoglobulin subtype (1);	4.121640	0.01047	N	0.004417	T	0.03305	0.0096	L	0.31664	0.95	0.09310	N	1	B	0.22800	0.075	B	0.25759	0.063	T	0.21415	-1.0246	10	0.30078	T	0.28	.	1.5384	0.02550	0.1751:0.115:0.3146:0.3954	.	99	Q96PJ5	FCRL4_HUMAN	P	99	ENSP00000271532:L99P	ENSP00000271532:L99P	L	-	2	0	FCRL4	155825629	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.190000	0.01247	-1.651000	0.01504	-0.410000	0.06199	CTC		0.493	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		G	157559005	A	G	157559005	3	3	12	1	0	0	0	0	1	0	0	0	5816	304	11	4	1291	4	FCRL4	1	157559005	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	5499497	157559005	91691616	12	1422										
OR10J5	127385	hgsc.bcm.edu	37	chr1	159505349	159505349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgccatagtcagaccaatgCcaaaggacccacacaccagc	7	16	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:159505349C>T	ENST00000334857.2	-	1	493	c.449G>A	c.(448-450)gGc>gAc	p.G150D		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					CAGACCAATGCCAAAGGACCC	0.512																																																0			1											131	101	111					1																	159505349		2203	4300	6503	157771973	SO:0001583	missense	127385				CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"GPCR / Class A : Olfactory receptors"	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.449G>A	1.37:g.159505349C>T	ENSP00000334441:p.Gly150Asp		157771973	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763976	0.31228	.	.	ENSG00000184155	ENST00000334857	T	0.38240	1.15	4.17	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.30696	0.0773	M	0.78637	2.42	0.29532	N	0.852742	P	0.37276	0.589	P	0.48770	0.589	T	0.23368	-1.0190	9	0.41790	T	0.15	.	6.5008	0.22168	0.1801:0.72:0.0:0.0999	.	150	Q8NHC4	O10J5_HUMAN	D	150	ENSP00000334441:G150D	ENSP00000334441:G150D	G	-	2	0	OR10J5	157771973	0.000000	0.05858	0.941000	0.38009	0.150000	0.21749	-0.351000	0.07711	0.448000	0.26722	0.467000	0.42956	GGC		0.512	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		T	159505349	C	T	159505349	3	4	12	1	0	0	0	0	1	0	0	0	10943	739	26	3	482	3	OR10J5	1	159505349	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	1946344	159505349	89745272	13	1423										
PRDX6	9588	hgsc.bcm.edu	37	chr1	173455445	173455445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agctgtctatcctctacccaGctaccactggcaggaacttt	7	14	2	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:173455445G>A	ENST00000340385.5	+	4	583	c.451G>A	c.(451-453)Gct>Act	p.A151T	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	151	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						CCTCTACCCAGCTACCACTGG	0.448																																																0			1											154	162	160					1																	173455445		2203	4300	6503	171722068	SO:0001583	missense	25824			D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.451G>A	1.37:g.173455445G>A	ENSP00000342026:p.Ala151Thr		171722068	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	37	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	G	35	5.429721	0.96131	.	.	ENSG00000117592	ENST00000340385	T	0.14022	2.54	5.63	5.63	0.86233	Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	M	0.91972	3.26	0.80722	D	1	D	0.57899	0.981	P	0.48270	0.572	T	0.36040	-0.9764	10	0.72032	D	0.01	-10.3938	18.8049	0.92032	0.0:0.0:1.0:0.0	.	151	P30041	PRDX6_HUMAN	T	151	ENSP00000342026:A151T	ENSP00000342026:A151T	A	+	1	0	PRDX6	171722068	1.000000	0.71417	0.636000	0.29352	0.994000	0.84299	7.436000	0.80404	2.797000	0.96272	0.655000	0.94253	GCT		0.448	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		A	173455445	G	A	173455445	3	1	12	1	0	0	0	0	1	0	0	0	12503	971	34	3	465	3	PRDX6	1	173455445	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	13950096	173455445	75795176	14	1424										
ASTN1	460	hgsc.bcm.edu	37	chr1	176838003	176838003	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggacctaactcatcctcacaTcgccaggtgaattccccaaa	6	15	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:176838003T>C	ENST00000367654.3	-	22	3859	c.3648A>G	c.(3646-3648)cgA>cgG	p.R1216R	ASTN1_ENST00000367657.3_Silent_p.R1208R|ASTN1_ENST00000424564.2_Silent_p.R1208R|ASTN1_ENST00000361833.2_Silent_p.R1208R	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1216					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CATCCTCACATCGCCAGGTGA	0.468																																																0			1											118	116	117					1																	176838003		2203	4300	6503	175104626	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3648A>G	1.37:g.176838003T>C			175104626	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.468	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		C	176838003	T	C	176838003	2	2	12	1	0	0	0	0	0	0	0	1	1065	1422	50	4		4	ASTN1	1	176838003	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	3382558	176838003	72412618	15	1425										
ZBTB41	360023	hgsc.bcm.edu	37	chr1	197168857	197168857	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttcctttttgatcttcttgcGgagaaacttctctccagcat	6	11	3	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:197168857G>A	ENST00000367405.4	-	1	815	c.747C>T	c.(745-747)tcC>tcT	p.S249S	CRB1_ENST00000535699.1_5'Flank|ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						ATCTTCTTGCGGAGAAACTTC	0.383																																																0			1											43	46	45					1																	197168857		2195	4297	6492	195435480	SO:0001819	synonymous_variant	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.747C>T	1.37:g.197168857G>A			195435480	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Silent	SNP	ENST00000367405.4	37	CCDS30960.1																																																																																				0.383	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		A	197168857	G	A	197168857	2	1	12	1	0	0	0	0	0	0	0	1	17582	1103	39	1		1	ZBTB41	1	197168857	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	20330854	197168857	52081764	16	1426										
KIF14	9928	hgsc.bcm.edu	37	chr1	200524571	200524571	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cccatggcattagttttcatTtctttggtaacctatagaga	7	8	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:200524571T>C	ENST00000367350.4	-	28	4803	c.4365A>G	c.(4363-4365)gaA>gaG	p.E1455E		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1455	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TAGTTTTCATTTCTTTGGTAA	0.259																																																0			1											54	58	57					1																	200524571		2199	4282	6481	198791194	SO:0001819	synonymous_variant	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4365A>G	1.37:g.200524571T>C			198791194	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.259	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200524571	T	C	200524571	2	2	12	1	0	0	0	0	0	0	0	1	8297	1838	64	4		4	KIF14	1	200524571	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	3355714	200524571	48726050	17	1427										
OR2M5	127059	hgsc.bcm.edu	37	chr1	248308552	248308552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tctttctggtcctggccatcTtttcagtggccttcatggga	10	11	5	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:248308552T>C	ENST00000366476.1	+	1	103	c.103T>C	c.(103-105)Ttt>Ctt	p.F35L		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F35I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CCTGGCCATCTTTTCAGTGGC	0.522																																																1	Substitution - Missense(1)	ovary(1)	1											239	237	237					1																	248308552		2203	4296	6499	246375175	SO:0001583	missense	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.103T>C	1.37:g.248308552T>C	ENSP00000355432:p.Phe35Leu		246375175		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	t	10.24	1.295534	0.23564	.	.	ENSG00000162727	ENST00000366476	T	0.00581	6.42	3.28	3.28	0.37604	.	0.250947	0.20653	U	0.088177	T	0.01092	0.0036	M	0.81497	2.545	0.09310	N	1	P	0.41546	0.754	B	0.39119	0.291	T	0.37731	-0.9693	10	0.72032	D	0.01	.	11.5465	0.50696	0.0:0.0:0.0:1.0	.	35	A3KFT3	OR2M5_HUMAN	L	35	ENSP00000355432:F35L	ENSP00000355432:F35L	F	+	1	0	OR2M5	246375175	0.022000	0.18835	0.140000	0.22221	0.115000	0.19883	2.033000	0.41136	1.250000	0.43966	0.403000	0.27427	TTT		0.522	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		C	248308552	T	C	248308552	3	2	12	1	0	0	0	0	1	0	0	0	11044	1609	56	4	105	4	OR2M5	1	248308552	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	47783981	248308552	942069	18	1428										
APOB	338	hgsc.bcm.edu	37	chr2	21233814	21233814	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tttccaggtgcctgtctgctCagctggagtaagcagggcac	13	11	2	0	rs267599184		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:21233814C>T	ENST00000233242.1	-	26	6053	c.5926G>A	c.(5926-5928)Gag>Aag	p.E1976K		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1976					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.E1976*(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTGTCTGCTCAGCTGGAGTA	0.453																																																1	Substitution - Nonsense(1)	skin(1)	2											146	136	140					2																	21233814		2203	4300	6503	21087319	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5926G>A	2.37:g.21233814C>T	ENSP00000233242:p.Glu1976Lys		21087319	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.585906	0.66105	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01240	5.12	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000023	T	0.09335	0.0230	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.00549	-1.1676	10	0.72032	D	0.01	.	19.2954	0.94119	0.0:1.0:0.0:0.0	.	1976	P04114	APOB_HUMAN	K	1976	ENSP00000233242:E1976K	ENSP00000233242:E1976K	E	-	1	0	APOB	21087319	0.938000	0.31826	0.995000	0.50966	0.942000	0.58702	2.074000	0.41529	2.554000	0.86153	0.555000	0.69702	GAG		0.453	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21233814	C	T	21233814	3	4	12	1	0	0	0	0	1	0	0	0	785	835	29	3	7781	3	APOB	2	21233814	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10		21233814	221965559	19	1429										
APOB	338	hgsc.bcm.edu	37	chr2	21238336	21238336	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttggcaggcgaccagtgggcGaggatctcacttctggcttc	14	11	2	0	rs140456702		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:21238336G>A	ENST00000233242.1	-	22	3541	c.3414C>T	c.(3412-3414)ctC>ctT	p.L1138L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1138					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCAGTGGGCGAGGATCTCAC	0.463																																																0			2						G		1,4405	2.1+/-5.4	0,1,2202	144	131	135		3414	-3.4	0	2	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	APOB	NM_000384.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1138/4564	21238336	1,13005	2203	4300	6503	21091841	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3414C>T	2.37:g.21238336G>A			21091841	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21238336	G	A	21238336	2	1	12	1	0	0	0	0	0	0	0	1	785	1045	37	1		1	APOB	2	21238336	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	4522	21238336	221961037	20	1430										
DPP10	57628	hgsc.bcm.edu	37	chr2	116534842	116534842	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aggaaactgggaagtgataaAgatcttggcatacgatgaaa	12	4	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:116534842A>T	ENST00000410059.1	+	14	1760	c.1280A>T	c.(1279-1281)aAg>aTg	p.K427M	DPP10_ENST00000393147.2_Missense_Mutation_p.K431M|DPP10_ENST00000409163.1_Missense_Mutation_p.K377M|DPP10_ENST00000310323.8_Missense_Mutation_p.K420M	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	427						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GAAGTGATAAAGATCTTGGCA	0.363																																																0			2											119	114	116					2																	116534842		2203	4299	6502	116251312	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1280A>T	2.37:g.116534842A>T	ENSP00000386565:p.Lys427Met		116251312	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.862491	0.51482	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	4.97	2.63	0.31362	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.160378	0.53938	D	0.000047	T	0.43722	0.1260	M	0.80746	2.51	0.38323	D	0.943576	B;P;B;B	0.50943	0.165;0.94;0.198;0.198	B;P;B;B	0.52386	0.217;0.697;0.239;0.324	T	0.47824	-0.9087	10	0.72032	D	0.01	-11.4582	7.2268	0.26020	0.8099:0.0:0.1901:0.0	.	420;431;423;427	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	M	427;377;431;420;377	ENSP00000386565:K427M;ENSP00000387038:K377M;ENSP00000376855:K431M;ENSP00000309066:K420M	ENSP00000309066:K420M	K	+	2	0	DPP10	116251312	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.099000	0.50267	0.477000	0.27464	0.533000	0.62120	AAG		0.363	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116534842	A	T	116534842	3	4	12	1	0	0	0	0	1	0	0	0	4738	72	3	5	1505	5	DPP10	2	116534842	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	95296506	116534842	126664531	21	1431										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141643869	141643869	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atcaatccttctgatctcatGacgaatagaaaagatgatga	7	7	3	6			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:141643869G>C	ENST00000389484.3	-	24	4773	c.3802C>G	c.(3802-3804)Cat>Gat	p.H1268D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1268					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CTGATCTCATGACGAATAGAA	0.313										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											71	71	71					2																	141643869		2203	4300	6503	141360339	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3802C>G	2.37:g.141643869G>C	ENSP00000374135:p.His1268Asp		141360339	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841985	0.71488	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90676	-2.71;-2.71	5.78	5.78	0.91487	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95284	0.8470	M	0.75884	2.315	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.978;0.991	D	0.94421	0.7641	10	0.48119	T	0.1	.	20.0175	0.97485	0.0:0.0:1.0:0.0	.	451;1268	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	D	1268;1206;413	ENSP00000374135:H1268D;ENSP00000413239:H413D	ENSP00000374135:H1268D	H	-	1	0	LRP1B	141360339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.805000	0.86005	2.730000	0.93505	0.650000	0.86243	CAT		0.313	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141643869	G	C	141643869	3	2	12	1	0	0	0	0	1	0	0	0	8984	1290	45	5	10269	5	LRP1B	2	141643869	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	25109027	141643869	101555504	22	1432										
NEB	4703	hgsc.bcm.edu	37	chr2	152359931	152359931	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cacagtggttggaatgcctgTtcccaagttttctttgtaca	9	9	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:152359931T>C	ENST00000172853.10	-	138	18811	c.18664A>G	c.(18664-18666)Aca>Gca	p.T6222A	NEB_ENST00000427231.2_Missense_Mutation_p.T7923A|NEB_ENST00000509223.2_Missense_Mutation_p.T53A|NEB_ENST00000603639.1_Missense_Mutation_p.T7923A|NEB_ENST00000498015.2_Intron|NEB_ENST00000397345.3_Missense_Mutation_p.T7923A|NEB_ENST00000409198.1_Missense_Mutation_p.T6222A|NEB_ENST00000397336.2_5'UTR|NEB_ENST00000604864.1_Missense_Mutation_p.T7923A			P20929	NEBU_HUMAN	nebulin	6222					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GGAATGCCTGTTCCCAAGTTT	0.363																																																0			2											90	86	87					2																	152359931		1833	4091	5924	152068177	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18664A>G	2.37:g.152359931T>C	ENSP00000172853:p.Thr6222Ala		152068177	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.26|14.26	2.482567|2.482567	0.44147|0.44147	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000421461|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000509223;ENST00000424585	.|T;T;T;T;T;T;T	.|0.09911	.|3.38;3.37;3.38;3.31;3.38;4.18;2.93	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.667376	.|0.16500	.|N	.|0.211717	T|T	0.19208|0.19208	0.0461|0.0461	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|B;B;B;B;D;B	.|0.58268	.|0.004;0.002;0.015;0.288;0.982;0.039	.|B;B;B;B;D;B	.|0.67548	.|0.017;0.003;0.041;0.137;0.952;0.127	T|T	0.03354|0.03354	-1.1045|-1.1045	5|10	.|0.23891	.|T	.|0.37	.|.	12.2413|12.2413	0.54544|0.54544	0.0:0.0:0.1419:0.8581|0.0:0.0:0.1419:0.8581	.|.	.|53;53;6222;7923;2653;7923	.|B7Z6B9;B7Z6P9;P20929;F8WCP0;Q14215;F8WCL5	.|.;.;NEBU_HUMAN;.;.;.	S|A	99|6222;7923;7923;2271;2653;6222;53;150	.|ENSP00000386259:T6222A;ENSP00000380505:T7923A;ENSP00000416578:T7923A;ENSP00000410961:T2653A;ENSP00000172853:T6222A;ENSP00000427083:T53A;ENSP00000404876:T150A	.|ENSP00000172853:T6222A	N|T	-|-	2|1	0|0	NEB|NEB	152068177|152068177	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.579000|1.579000	0.36536|0.36536	2.169000|2.169000	0.68431|0.68431	0.528000|0.528000	0.53228|0.53228	AAC|ACA		0.363	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152359931	T	C	152359931	3	2	12	1	0	0	0	0	1	0	0	0	10333	1725	60	4	1878	4	NEB	2	152359931	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	10716062	152359931	90839442	23	1433										
NEB	4703	hgsc.bcm.edu	37	chr2	152406166	152406166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcacataactgctcatgtaaCgggtgtccttgatgtgtttg	10	8	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:152406166C>T	ENST00000172853.10	-	102	15077	c.14930G>A	c.(14929-14931)cGt>cAt	p.R4977H	NEB_ENST00000427231.2_Missense_Mutation_p.R6678H|NEB_ENST00000603639.1_Missense_Mutation_p.R6678H|NEB_ENST00000397345.3_Missense_Mutation_p.R6678H|NEB_ENST00000409198.1_Missense_Mutation_p.R4977H|NEB_ENST00000604864.1_Missense_Mutation_p.R6678H			P20929	NEBU_HUMAN	nebulin	4977					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GCTCATGTAACGGGTGTCCTT	0.478																																																0			2											124	121	122					2																	152406166		1954	4168	6122	152114412	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.14930G>A	2.37:g.152406166C>T	ENSP00000172853:p.Arg4977His		152114412	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	16.88	3.243729	0.58995	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	6.16	4.16	0.48862	.	0.358373	0.32687	N	0.005765	T	0.50480	0.1618	L	0.47716	1.5	0.58432	D	0.999999	P;D	0.76494	0.87;0.999	P;D	0.78314	0.667;0.991	T	0.51419	-0.8708	10	0.51188	T	0.08	.	4.9222	0.13876	0.0:0.6757:0.0:0.3243	.	4977;1408	P20929;Q14215	NEBU_HUMAN;.	H	4977;6678;6678;1026;1408;4977	ENSP00000386259:R4977H;ENSP00000380505:R6678H;ENSP00000416578:R6678H;ENSP00000410961:R1408H;ENSP00000172853:R4977H	ENSP00000172853:R4977H	R	-	2	0	NEB	152114412	0.951000	0.32395	0.188000	0.23233	0.384000	0.30261	1.892000	0.39748	1.623000	0.50342	0.650000	0.86243	CGT		0.478	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152406166	C	T	152406166	3	4	12	1	0	0	0	0	1	0	0	0	10333	536	19	1	5865	1	NEB	2	152406166	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	46235	152406166	90793207	24	1434										
ITGB6	3694	hgsc.bcm.edu	37	chr2	161051889	161051889	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	catttacttacctgcaagggTtggcaatttcttctggtgtt	9	8	2	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:161051889T>C	ENST00000283249.2	-	4	821	c.584A>G	c.(583-585)aAc>aGc	p.N195S	ITGB6_ENST00000428609.2_Missense_Mutation_p.N153S|ITGB6_ENST00000409872.1_Missense_Mutation_p.N195S|ITGB6_ENST00000409967.2_Missense_Mutation_p.N195S|ITGB6_ENST00000485635.1_5'UTR	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	195	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CCTGCAAGGGTTGGCAATTTC	0.443																																																0			2											93	99	97					2																	161051889		2203	4300	6503	160760135	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.584A>G	2.37:g.161051889T>C	ENSP00000283249:p.Asn195Ser		160760135	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622898	0.46840	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.97941	-4.62;-4.62;-4.62;-4.62	6.05	6.05	0.98169	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	M	0.70275	2.135	0.51233	D	0.999915	B;B	0.19445	0.036;0.036	B;B	0.16722	0.016;0.016	D	0.94631	0.7822	10	0.39692	T	0.17	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	153;195	E9PEE8;P18564	.;ITB6_HUMAN	S	195;153;195;195	ENSP00000283249:N195S;ENSP00000408024:N153S;ENSP00000386828:N195S;ENSP00000386367:N195S	ENSP00000283249:N195S	N	-	2	0	ITGB6	160760135	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	7.991000	0.88244	2.320000	0.78422	0.528000	0.53228	AAC		0.443	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		C	161051889	T	C	161051889	3	2	12	1	0	0	0	0	1	0	0	0	7920	1725	60	4	1830	4	ITGB6	2	161051889	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	8645723	161051889	82147484	25	1435										
FIGN	55137	hgsc.bcm.edu	37	chr2	164466675	164466675	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cttctcctaaccacttggcgActagtccagaaccggcaatt	7	14	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:164466675A>T	ENST00000333129.3	-	3	1981	c.1667T>A	c.(1666-1668)gTc>gAc	p.V556D	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	556					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						CCACTTGGCGACTAGTCCAGA	0.483																																																0			2											57	56	56					2																	164466675		1925	4125	6050	164174921	SO:0001583	missense	55137			AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1667T>A	2.37:g.164466675A>T	ENSP00000333836:p.Val556Asp		164174921	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760674	0.49468	.	.	ENSG00000182263	ENST00000333129	D	0.95447	-3.71	5.36	5.36	0.76844	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.059606	0.64402	D	0.000003	D	0.96710	0.8926	L	0.50993	1.605	0.80722	D	1	D	0.69078	0.997	D	0.79784	0.993	D	0.97421	1.0009	10	0.87932	D	0	-7.8026	15.6507	0.77091	1.0:0.0:0.0:0.0	.	556	Q5HY92	FIGN_HUMAN	D	556	ENSP00000333836:V556D	ENSP00000333836:V556D	V	-	2	0	FIGN	164174921	1.000000	0.71417	0.098000	0.21074	0.962000	0.63368	7.468000	0.80943	2.163000	0.67991	0.460000	0.39030	GTC		0.483	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164466675	A	T	164466675	3	4	12	1	0	0	0	0	1	0	0	0	5910	275	10	5	616	5	FIGN	2	164466675	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	3414786	164466675	78732698	26	1436										
DUSP19	142679	hgsc.bcm.edu	37	chr2	183960266	183960266	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcatttaccagtgctttttcTttggtgaaaaatgcaagacc	7	8	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:183960266T>C	ENST00000354221.4	+	4	709	c.534T>C	c.(532-534)tcT>tcC	p.S178S	AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_3'UTR|AC064871.3_ENST00000413954.1_RNA|DUSP19_ENST00000342619.6_Silent_p.S127S	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	178	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						GTGCTTTTTCTTTGGTGAAAA	0.408																																																0			2											135	138	137					2																	183960266		2203	4300	6503	183668511	SO:0001819	synonymous_variant	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.534T>C	2.37:g.183960266T>C			183668511	B2RA79|Q547H4|Q8WYN4	Silent	SNP	ENST00000354221.4	37	CCDS2289.1																																																																																				0.408	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			C	183960266	T	C	183960266	2	2	12	1	0	0	0	0	0	0	0	1	4829	1596	56	4		4	DUSP19	2	183960266	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	19493591	183960266	59239107	27	1437										
ALPI	248	hgsc.bcm.edu	37	chr2	233321912	233321912	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gtgcagcacgcctcgccagcCggcacctacgcacacacagt	10	18	0	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:233321912C>T	ENST00000295463.3	+	5	605	c.528C>T	c.(526-528)gcC>gcT	p.A176A		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	176					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		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)		CCTCGCCAGCCGGCACCTACG	0.622																																																0			2											68	68	68					2																	233321912		2203	4300	6503	233030156	SO:0001819	synonymous_variant	248			M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.528C>T	2.37:g.233321912C>T			233030156	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																				0.622	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		T	233321912	C	T	233321912	2	4	12	1	0	0	0	0	0	0	0	1	543	639	23	1		1	ALPI	2	233321912	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	49361646	233321912	9877461	28	1438										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1415428	1415428	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggacaccattttctgtgggtTggcaggctgttgctacaggt	14	8	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:1415428T>A	ENST00000446702.2	+	15	2554	c.1927T>A	c.(1927-1929)Tgg>Agg	p.W643R	CNTN6_ENST00000539053.1_Missense_Mutation_p.W571R|CNTN6_ENST00000350110.2_Missense_Mutation_p.W643R			Q9UQ52	CNTN6_HUMAN	contactin 6	643	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTCTGTGGGTTGGCAGGCTGT	0.348																																																0			3											66	68	67					3																	1415428		2203	4300	6503	1390428	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1927T>A	3.37:g.1415428T>A	ENSP00000407822:p.Trp643Arg		1390428	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955981	0.73902	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.56275	0.47;0.47;0.47	4.77	4.77	0.60923	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000133	T	0.81814	0.4902	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88499	0.3081	10	0.87932	D	0	.	14.5834	0.68308	0.0:0.0:0.0:1.0	.	643	Q9UQ52	CNTN6_HUMAN	R	643;571;643	ENSP00000407822:W643R;ENSP00000442791:W571R;ENSP00000341882:W643R	ENSP00000341882:W643R	W	+	1	0	CNTN6	1390428	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	5.850000	0.69473	1.896000	0.54893	0.482000	0.46254	TGG		0.348	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		A	1415428	T	A	1415428	3	1	12	1	0	0	0	0	1	0	0	0	3651	1812	63	5	1981	5	CNTN6	3	1415428	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10		1415428	196607002	29	1439										
VHL	7428	hgsc.bcm.edu	37	chr3	10188291	10188291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atctctcaatgttgacggacAgcctatttttgccaatatca	6	10	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:10188291A>G	ENST00000256474.2	+	2	1274	c.434A>G	c.(433-435)cAg>cGg	p.Q145R	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	145	Involved in binding to CCT complex.		Q -> H (in VHLD).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.Q145fs*12(1)|p.S139fs*12(1)|p.G144fs*19(1)|p.Q145fs*14(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTTGACGGACAGCCTATTTTT	0.413		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	4	Deletion - Frameshift(4)	kidney(4)	3											216	199	205					3																	10188291		2203	4300	6503	10163291	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.434A>G	3.37:g.10188291A>G	ENSP00000256474:p.Gln145Arg		10163291	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.746540	0.49257	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99800	-6.8	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.262110	0.33591	N	0.004751	D	0.99566	0.9844	L	0.59436	1.845	0.80722	D	1	P	0.50617	0.937	D	0.66847	0.947	D	0.97837	1.0266	10	0.45353	T	0.12	-29.4808	13.0886	0.59154	1.0:0.0:0.0:0.0	.	145	P40337	VHL_HUMAN	R	145;63	ENSP00000256474:Q145R	ENSP00000256474:Q145R	Q	+	2	0	VHL	10163291	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.644000	0.54381	2.047000	0.60756	0.460000	0.39030	CAG		0.413	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10188291	A	G	10188291	3	3	12	1	0	0	0	0	1	0	0	0	17202	188	7	4	440	4	VHL	3	10188291	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	8772863	10188291	187834139	30	1440										
HDAC11	79885	hgsc.bcm.edu	37	chr3	13542268	13542268	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gggggcttctgtgcctatgcGgacatcacgctcgccatcaa	12	13	3	0	rs140627816		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:13542268G>A	ENST00000295757.3	+	6	651	c.468G>A	c.(466-468)gcG>gcA	p.A156A	HDAC11_ENST00000446613.2_Intron|HDAC11_ENST00000433119.1_Missense_Mutation_p.R114Q|HDAC11_ENST00000404548.1_Intron|HDAC11_ENST00000495099.2_Intron|HDAC11_ENST00000405025.1_Intron|HDAC11_ENST00000522202.1_Silent_p.A105A|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000437379.2_Silent_p.A128A|HDAC11_ENST00000402271.1_Intron|HDAC11_ENST00000404040.1_Intron	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	156	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						GTGCCTATGCGGACATCACGC	0.617											OREG0015412	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		16865	0		0.001	False		,,,				2504	0															0			3											32	27	29					3																	13542268		2202	4299	6501	13517268	SO:0001819	synonymous_variant	79885			AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.468G>A	3.37:g.13542268G>A		688	13517268	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Silent	SNP	ENST00000295757.3	37	CCDS2615.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.58	1.679722	0.29783	.	.	ENSG00000163517	ENST00000433119;ENST00000434848	.	.	.	4.52	-7.93	0.01156	.	.	.	.	.	T	0.34600	0.0903	.	.	.	0.80722	D	1	B	0.17465	0.022	B	0.08055	0.003	T	0.13764	-1.0497	7	0.87932	D	0	-15.1823	0.9765	0.01426	0.4251:0.1941:0.1188:0.2621	.	114	Q658J9	.	Q	114;122	.	ENSP00000412514:R114Q	R	+	2	0	HDAC11	13517268	0.178000	0.23122	0.819000	0.32651	0.592000	0.36648	-0.720000	0.04969	-1.460000	0.01911	-0.345000	0.07892	CGG		0.617	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827		A	13542268	G	A	13542268	2	1	12	1	0	0	0	0	0	0	0	1	7027	1103	39	1		1	HDAC11	3	13542268	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	3353977	13542268	184480162	31	1441										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33725898	33725898	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agatccatcctcactttttcTcccacatgtctataaatctc	2	14	4	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:33725898T>C	ENST00000468888.2	-	6	643	c.597A>G	c.(595-597)ggA>ggG	p.G199G	CLASP2_ENST00000399362.4_Silent_p.G199G|CLASP2_ENST00000359576.5_Silent_p.G199G|CLASP2_ENST00000307312.7_5'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1252					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCACTTTTTCTCCCACATGTC	0.318																																																0			3											138	139	139					3																	33725898		1815	4079	5894	33700902	SO:0001819	synonymous_variant	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.597A>G	3.37:g.33725898T>C			33700902	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																					0.318	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		C	33725898	T	C	33725898	2	2	12	1	0	0	0	0	0	0	0	1	3461	1538	54	4		4	CLASP2	3	33725898	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	20183630	33725898	164296532	32	1442										
SCAP	22937	hgsc.bcm.edu	37	chr3	47484371	47484371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	caaaaacataccagcaggctAagatgcagaaccctgtgaag	9	10	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:47484371A>G	ENST00000265565.5	-	2	525	c.113T>C	c.(112-114)tTa>tCa	p.L38S	SCAP_ENST00000545718.1_5'UTR|SCAP_ENST00000441517.2_5'UTR	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	38					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CCAGCAGGCTAAGATGCAGAA	0.517																																					Pancreas(149;978 1908 29304 37806 46700)											0			3											139	120	126					3																	47484371		2203	4300	6503	47459375	SO:0001583	missense	22937			BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.113T>C	3.37:g.47484371A>G	ENSP00000265565:p.Leu38Ser		47459375	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363554	0.82353	.	.	ENSG00000114650	ENST00000339815;ENST00000265565;ENST00000416847;ENST00000495603;ENST00000448217	D	0.87256	-2.23	4.75	4.75	0.60458	.	0.097415	0.39909	N	0.001240	D	0.90933	0.7150	M	0.74881	2.28	0.80722	D	1	P	0.40398	0.716	P	0.51866	0.682	D	0.92014	0.5620	10	0.72032	D	0.01	0.1046	14.0891	0.64977	1.0:0.0:0.0:0.0	.	38	Q12770	SCAP_HUMAN	S	38	ENSP00000265565:L38S	ENSP00000265565:L38S	L	-	2	0	SCAP	47459375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.909000	0.92647	1.997000	0.58415	0.454000	0.30748	TTA		0.517	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		G	47484371	A	G	47484371	3	3	12	1	0	0	0	0	1	0	0	0	13914	372	13	4	3814	4	SCAP	3	47484371	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	13758473	47484371	150538059	33	1443										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64547349	64547349	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggtgtatgggttgcactcggTctctctggctattttgtgtg	14	7	2	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:64547349T>C	ENST00000498707.1	-	30	4945	c.4603A>G	c.(4603-4605)Acc>Gcc	p.T1535A	ADAMTS9-AS1_ENST00000493124.1_RNA|ADAMTS9-AS1_ENST00000492209.1_RNA|ADAMTS9-AS1_ENST00000480831.1_RNA|ADAMTS9-AS1_ENST00000601022.1_RNA|ADAMTS9-AS1_ENST00000470447.1_RNA|ADAMTS9-AS1_ENST00000474313.1_RNA|ADAMTS9_ENST00000295903.4_Missense_Mutation_p.T1507A|ADAMTS9-AS1_ENST00000594810.1_RNA	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1535	TSP type-1 12. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		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)		TTGCACTCGGTCTCTCTGGCT	0.562																																																0			3											173	156	162					3																	64547349		2203	4300	6503	64522389	SO:0001583	missense	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4603A>G	3.37:g.64547349T>C	ENSP00000418735:p.Thr1535Ala		64522389	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.527095	0.27299	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.60171	0.21;0.21	5.7	-1.56	0.08532	.	0.543603	0.18126	N	0.150893	T	0.27278	0.0669	N	0.12443	0.215	0.28668	N	0.905776	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.08166	-1.0735	10	0.19590	T	0.45	.	1.5841	0.02641	0.4191:0.1254:0.108:0.3475	.	1507;1535;1535	B7ZVX9;Q9P2N4-1;Q9P2N4	.;.;ATS9_HUMAN	A	1507;1535	ENSP00000295903:T1507A;ENSP00000418735:T1535A	ENSP00000295903:T1507A	T	-	1	0	ADAMTS9	64522389	0.837000	0.29446	0.101000	0.21167	0.785000	0.44390	0.155000	0.16362	-0.496000	0.06650	-0.480000	0.04831	ACC		0.562	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			C	64547349	T	C	64547349	3	2	12	1	0	0	0	0	1	0	0	0	273	1667	58	4	1244	4	ADAMTS9	3	64547349	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	17062978	64547349	133475081	34	1444										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77651633	77651633	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctctacctgatcagaacaaaGgtaacaatggtgagtcaggt	10	8	3	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:77651633G>C	ENST00000461745.1	+	20	4027	c.3127G>C	c.(3127-3129)Ggt>Cgt	p.G1043R	ROBO2_ENST00000487694.3_Missense_Mutation_p.G1059R|ROBO2_ENST00000332191.8_Missense_Mutation_p.G1043R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1043					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TCAGAACAAAGGTAACAATGG	0.378																																																0			3											100	94	96					3																	77651633		1925	4133	6058	77734323	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3127G>C	3.37:g.77651633G>C	ENSP00000417164:p.Gly1043Arg		77734323	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.35|15.35|15.35	2.806096|2.806096|2.806096	0.50421|0.50421|0.50421	.|.|.	.|.|.	ENSG00000185008|ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000490991|ENST00000471893	T;T;T|T|.	0.62639|0.66280|.	0.01;0.04;0.07|-0.2|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|.|.	0.46758|.|.	D|.|.	0.000263|.|.	T|T|T	0.69387|0.69387|0.69387	0.3105|0.3105|0.3105	L|L|L	0.43923|0.43923|0.43923	1.385|1.385|1.385	.|.|.	.|.|.	.|.|.	P;P;P|.|.	0.46457|.|.	0.766;0.878;0.766|.|.	B;P;B|.|.	0.46825|.|.	0.243;0.528;0.243|.|.	T|T|T	0.63175|0.63175|0.63175	-0.6696|-0.6696|-0.6696	9|6|4	0.25751|0.59425|.	T|D|.	0.34|0.04|.	.|.|.	20.1432|20.1432|20.1432	0.98067|0.98067|0.98067	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	1059;1043;1043|.|.	Q19AB5;F8W703;Q9HCK4|.|.	.;.;ROBO2_HUMAN|.|.	R|N|T	1059;1059;1063;1043;1043|199|117	ENSP00000417335:G1059R;ENSP00000417164:G1043R;ENSP00000327536:G1043R|ENSP00000418344:K199N|.	ENSP00000327536:G1043R|ENSP00000418344:K199N|.	G|K|R	+|+|+	1|3|2	0|2|0	ROBO2|ROBO2|ROBO2	77734323|77734323|77734323	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	6.564000|6.564000|6.564000	0.73969|0.73969|0.73969	2.769000|2.769000|2.769000	0.95229|0.95229|0.95229	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GGT|AAG|AGG		0.378	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77651633	G	C	77651633	3	2	12	1	0	0	0	0	1	0	0	0	13551	1000	35	5	3207	5	ROBO2	3	77651633	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	13104284	77651633	120370797	35	1445										
MYH15	22989	hgsc.bcm.edu	37	chr3	108195349	108195349	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttaatgcccatgaggaaagcAgctttgtcagcatctggtca	10	9	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:108195349A>G	ENST00000273353.3	-	13	1244	c.1188T>C	c.(1186-1188)gcT>gcC	p.A396A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	396	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A396A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TGAGGAAAGCAGCTTTGTCAG	0.403																																																1	Substitution - coding silent(1)	ovary(1)	3											69	63	65					3																	108195349		1908	4127	6035	109678039	SO:0001819	synonymous_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1188T>C	3.37:g.108195349A>G			109678039		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																				0.403	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108195349	A	G	108195349	2	3	12	1	0	0	0	0	0	0	0	1	10064	175	7	4		4	MYH15	3	108195349	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10	30543716	108195349	89827081	36	1446										
PARP14	54625	hgsc.bcm.edu	37	chr3	122437033	122437033	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gttaaagttgttatctttctGcctcaagtactggatgtgtt	9	6	3	0	rs201050912		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:122437033G>T	ENST00000474629.2	+	13	4382	c.4116G>T	c.(4114-4116)ctG>ctT	p.L1372L		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1372	Macro 3. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.L1209L(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTATCTTTCTGCCTCAAGTAC	0.408																																																1	Substitution - coding silent(1)	ovary(1)	3											105	97	99					3																	122437033		1868	4112	5980	123919723	SO:0001819	synonymous_variant	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4116G>T	3.37:g.122437033G>T			123919723	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																				0.408	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122437033	G	T	122437033	2	4	12	1	0	0	0	0	0	0	0	1	11489	1306	46	2		2	PARP14	3	122437033	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	14241684	122437033	75585397	37	1447										
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133327386	133327386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gaatctcacaaacctgcatgAgataatcagcaatgtattct	6	9	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:133327386A>G	ENST00000260810.5	-	27	4549	c.4418T>C	c.(4417-4419)cTc>cCc	p.L1473P		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1473	BRCT 8. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						AACCTGCATGAGATAATCAGC	0.403								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)											0			3											142	134	136					3																	133327386		1909	4125	6034	134810076	SO:0001583	missense	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4418T>C	3.37:g.133327386A>G	ENSP00000260810:p.Leu1473Pro		134810076	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273732	0.80580	.	.	ENSG00000163781	ENST00000260810	T	0.28895	1.59	5.31	5.31	0.75309	.	0.054132	0.85682	D	0.000000	T	0.58566	0.2131	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64964	-0.6283	10	0.87932	D	0	.	15.2583	0.73601	1.0:0.0:0.0:0.0	.	1473	Q92547	TOPB1_HUMAN	P	1473	ENSP00000260810:L1473P	ENSP00000260810:L1473P	L	-	2	0	TOPBP1	134810076	1.000000	0.71417	0.973000	0.42090	0.976000	0.68499	9.289000	0.96061	1.991000	0.58162	0.533000	0.62120	CTC		0.403	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		G	133327386	A	G	133327386	3	3	12	1	0	0	0	0	1	0	0	0	16409	304	11	4	158	4	TOPBP1	3	133327386	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	10890353	133327386	64695044	38	1448										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134911606	134911606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agggtgtggtcaccaagagtCggcctgtcatgatcatcaca	12	10	4	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:134911606C>T	ENST00000398015.3	+	11	2441	c.2071C>T	c.(2071-2073)Cgg>Tgg	p.R691W	EPHB1_ENST00000493838.1_Missense_Mutation_p.R252W	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	691	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CACCAAGAGTCGGCCTGTCAT	0.527																																																0			3											105	104	104					3																	134911606		2198	4298	6496	136394296	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2071C>T	3.37:g.134911606C>T	ENSP00000381097:p.Arg691Trp		136394296	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940438	0.73557	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.62941	-0.01;-0.01	5.44	3.49	0.39957	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76421	0.3985	M	0.73372	2.23	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.79468	-0.1791	10	0.87932	D	0	.	12.9402	0.58337	0.4179:0.5821:0.0:0.0	.	691	P54762	EPHB1_HUMAN	W	691;252	ENSP00000381097:R691W;ENSP00000419574:R252W	ENSP00000381097:R691W	R	+	1	2	EPHB1	136394296	1.000000	0.71417	0.937000	0.37676	0.989000	0.77384	2.392000	0.44433	1.257000	0.44085	0.561000	0.74099	CGG		0.527	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		T	134911606	C	T	134911606	3	4	12	1	0	0	0	0	1	0	0	0	5187	875	31	1	2113	1	EPHB1	3	134911606	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	1584220	134911606	63110824	39	1449										
RSRC1	51319	hgsc.bcm.edu	37	chr3	157839989	157839989	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcgagcagttcttcagatagTagaacatacagccgaaagaa	9	8	2	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:157839989T>A	ENST00000295930.3	+	2	258	c.96T>A	c.(94-96)agT>agA	p.S32R	RSRC1_ENST00000480820.1_Missense_Mutation_p.S32R|RSRC1_ENST00000475278.2_Missense_Mutation_p.S32R|RSRC1_ENST00000464171.1_Missense_Mutation_p.S32R|RSRC1_ENST00000312179.6_Missense_Mutation_p.S32R	NM_001271838.1|NM_016625.2	NP_001258767.1|NP_057709.2	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	32	Arg/Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)|nucleocytoplasmic transport (GO:0006913)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	18			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			CTTCAGATAGTAGAACATACA	0.428																																																0			3											97	93	94					3																	157839989		2203	4300	6503	159322683	SO:0001583	missense	51319			AF208853	CCDS3181.1, CCDS63822.1	3q25.32	2009-09-09			ENSG00000174891	ENSG00000174891			24152	protein-coding gene	gene with protein product	"splicing factor, arginine/serine-rich 21"	613352				15798186, 19065146	Standard	NM_001271838		Approved	MGC12197, BM-011, SRrp53, SFRS21	uc003fbu.2	Q96IZ7	OTTHUMG00000158758	ENST00000295930.3:c.96T>A	3.37:g.157839989T>A	ENSP00000295930:p.Ser32Arg		159322683	A8K2R9|Q96QK2|Q9NZE5	Missense_Mutation	SNP	ENST00000295930.3	37	CCDS3181.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.075802	0.55646	.	.	ENSG00000174891	ENST00000480820;ENST00000494002;ENST00000295930;ENST00000471994;ENST00000464171;ENST00000312179;ENST00000475278;ENST00000476899	.	.	.	5.41	-3.41	0.04839	.	0.432573	0.29616	N	0.011643	T	0.44456	0.1294	L	0.43152	1.355	0.43657	D	0.996071	B;B;B	0.33238	0.275;0.275;0.403	B;B;B	0.30179	0.112;0.112;0.112	T	0.40040	-0.9584	9	0.72032	D	0.01	.	14.1363	0.65289	0.0:0.5696:0.0:0.4304	.	32;32;32	B4DTW0;Q96IZ7-2;Q96IZ7	.;.;RSRC1_HUMAN	R	32	.	ENSP00000295930:S32R	S	+	3	2	RSRC1	159322683	0.926000	0.31397	0.974000	0.42286	0.962000	0.63368	-0.215000	0.09279	-0.491000	0.06697	0.454000	0.30748	AGT		0.428	RSRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352063.2	NM_016625		A	157839989	T	A	157839989	3	1	12	1	0	0	0	0	1	0	0	0	13751	1635	57	5	98	5	RSRC1	3	157839989	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	22928383	157839989	40182441	40	1450										
SKIL	6498	hgsc.bcm.edu	37	chr3	170078891	170078891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cattggcccagttaaaggaaActggcagtgcctttgaagtg	12	8	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:170078891A>G	ENST00000458537.3	+	1	1481	c.772A>G	c.(772-774)Act>Gct	p.T258A	SKIL_ENST00000413427.2_Missense_Mutation_p.T258A|SKIL_ENST00000259119.4_Missense_Mutation_p.T258A|SKIL_ENST00000426052.2_Missense_Mutation_p.T238A	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	258					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			GTTAAAGGAAACTGGCAGTGC	0.438																																																0			3											138	121	127					3																	170078891		2203	4300	6503	171561585	SO:0001583	missense	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.772A>G	3.37:g.170078891A>G	ENSP00000415243:p.Thr258Ala		171561585	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	37	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.862122	0.51482	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.91351	-2.83;-2.82;-2.81;-2.83	5.51	5.51	0.81932	.	0.044394	0.85682	D	0.000000	D	0.85805	0.5782	L	0.34521	1.04	0.38568	D	0.949875	P;P	0.38729	0.644;0.563	B;B	0.38985	0.287;0.214	D	0.87440	0.2394	10	0.56958	D	0.05	-15.4577	11.432	0.50047	0.865:0.0:0.0:0.135	.	258;258	P12757-3;P12757	.;SKIL_HUMAN	A	258;238;258;258	ENSP00000259119:T258A;ENSP00000406520:T238A;ENSP00000400193:T258A;ENSP00000415243:T258A	ENSP00000259119:T258A	T	+	1	0	SKIL	171561585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.902000	0.56310	2.111000	0.64477	0.524000	0.50904	ACT		0.438	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		G	170078891	A	G	170078891	3	3	12	1	0	0	0	0	1	0	0	0	14395	43	2	4	774	4	SKIL	3	170078891	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	12238902	170078891	27943539	41	1451										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952005	178952005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	caatcttttgatgacattgcAtacattcgaaagaccctagc	6	10	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:178952005A>G	ENST00000263967.3	+	21	3217	c.3060A>G	c.(3058-3060)gcA>gcG	p.A1020A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1020	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGACATTGCATACATTCGAA	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											106	94	98					3																	178952005		1877	4119	5996	180434699	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3060A>G	3.37:g.178952005A>G			180434699	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952005	A	G	178952005	2	3	12	1	0	0	0	0	0	0	0	1	11944	204	8	4		4	PIK3CA	3	178952005	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10	8873114	178952005	19070425	42	1452										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952099	178952099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atgcacatcatggtggctggAcaacaaaaatggattggatc	11	7	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:178952099A>G	ENST00000263967.3	+	21	3311	c.3154A>G	c.(3154-3156)Aca>Gca	p.T1052A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1052	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		T -> K (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.T1052A(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGGTGGCTGGACAACAAAAAT	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	breast(1)	3											97	87	90					3																	178952099		1916	4131	6047	180434793	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3154A>G	3.37:g.178952099A>G	ENSP00000263967:p.Thr1052Ala		180434793	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.830182	0.50845	.	.	ENSG00000121879	ENST00000263967	D	0.82803	-1.65	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.78960	0.4366	L	0.47078	1.49	0.80722	D	1	P	0.35433	0.501	B	0.34452	0.183	T	0.76476	-0.2945	10	0.27785	T	0.31	-14.979	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1052	P42336	PK3CA_HUMAN	A	1052	ENSP00000263967:T1052A	ENSP00000263967:T1052A	T	+	1	0	PIK3CA	180434793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	ACA		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952099	A	G	178952099	3	3	12	1	0	0	0	0	1	0	0	0	11944	275	10	4	3232	4	PIK3CA	3	178952099	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	94	178952099	19070331	43	1453										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184298232	184298232	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcatccagctggtgggcatgTtgcggggcattgctgccggc	16	11	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:184298232T>C	ENST00000330394.2	+	12	2667	c.2215T>C	c.(2215-2217)Ttg>Ctg	p.L739L	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	739	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGTGGGCATGTTGCGGGGCAT	0.597																																																0			3											142	129	134					3																	184298232		2203	4300	6503	185780926	SO:0001819	synonymous_variant	2049			X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2215T>C	3.37:g.184298232T>C			185780926	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																				0.597	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		C	184298232	T	C	184298232	2	2	12	1	0	0	0	0	0	0	0	1	5189	1722	60	4		4	EPHB3	3	184298232	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	5346133	184298232	13724198	44	1454										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910747	184910747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gattcaacattcgattccccAcaaatccaaaacagttgcct	4	13	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:184910747A>G	ENST00000231887.3	-	7	1514	c.1439T>C	c.(1438-1440)gTg>gCg	p.V480A	EHHADH_ENST00000456310.1_Missense_Mutation_p.V384A|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	480	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TCGATTCCCCACAAATCCAAA	0.418																																																0			3											108	109	108					3																	184910747		2203	4300	6503	186393441	SO:0001583	missense	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1439T>C	3.37:g.184910747A>G	ENSP00000231887:p.Val480Ala		186393441	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703750	0.68501	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.91124	-2.79;-2.79	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);3-hydroxyacyl-CoA dehydrogenase, conserved site (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.117554	0.56097	D	0.000023	D	0.93897	0.8047	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	D	0.65010	0.931	D	0.93489	0.6834	10	0.44086	T	0.13	-29.7634	16.3483	0.83171	1.0:0.0:0.0:0.0	.	480	Q08426	ECHP_HUMAN	A	480;384	ENSP00000231887:V480A;ENSP00000387746:V384A	ENSP00000231887:V480A	V	-	2	0	EHHADH	186393441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.845000	0.69437	2.254000	0.74563	0.533000	0.62120	GTG		0.418	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			G	184910747	A	G	184910747	3	3	12	1	0	0	0	0	1	0	0	0	4993	159	6	4	736	4	EHHADH	3	184910747	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	612515	184910747	13111683	45	1455										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5827225	5827225	+	Missense_Mutation	SNP	T	T	G													0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	caccactctttcctacctgaTaagctgaagttggactggtg							TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:5827225T>G	ENST00000397890.2	-	13	1837	c.1623A>C	c.(1621-1623)ttA>ttC	p.L541F	CRMP1_ENST00000512574.1_Missense_Mutation_p.L539F|CRMP1_ENST00000324989.7_Missense_Mutation_p.L655F|EVC_ENST00000382674.2_Intron|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	541					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TCCTACCTGATAAGCTGAAGT	0.547																																																0			4											148	146	147					4																	5827225		2203	4300	6503	5878126	SO:0001583	missense	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1623A>C	4.37:g.5827225T>G	ENSP00000380987:p.Leu541Phe		5878126	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447033	0.63178	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.90385	-2.66;-2.48;-2.48	4.13	-3.64	0.04515	.	0.000000	0.64402	D	0.000003	D	0.93572	0.7948	M	0.82193	2.58	0.58432	D	0.99999	D;B;B;D	0.76494	0.999;0.105;0.377;0.992	D;B;B;D	0.76575	0.988;0.068;0.295;0.938	D	0.91387	0.5132	10	0.87932	D	0	-14.4329	10.1534	0.42807	0.0:0.3865:0.0:0.6135	.	655;539;541;478	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	F	655;541;541;539	ENSP00000321606:L655F;ENSP00000380987:L541F;ENSP00000425742:L539F	ENSP00000321606:L655F	L	-	3	2	CRMP1	5878126	0.797000	0.28877	0.938000	0.37757	0.992000	0.81027	-0.172000	0.09868	-0.815000	0.04346	0.459000	0.35465	TTA		0.547	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		G	5827225	T	G	5827225	3	3	12	1	0	0	0	0	1	0	0	0	3896	1403	49	4	103	4	CRMP1	4	5827225	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10		5827225	185327051	46	1456	7	2								
CRMP1	1400	hgsc.bcm.edu	37	chr4	5827227	5827227	+	Missense_Mutation	SNP	A	A	T													0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ccactctttcctacctgataAgctgaagttggactggtgga							TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:5827227A>T	ENST00000397890.2	-	13	1835	c.1621T>A	c.(1621-1623)Tta>Ata	p.L541I	CRMP1_ENST00000512574.1_Missense_Mutation_p.L539I|CRMP1_ENST00000324989.7_Missense_Mutation_p.L655I|EVC_ENST00000382674.2_Intron|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	541					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CTACCTGATAAGCTGAAGTTG	0.547																																																0			4											151	148	149					4																	5827227		2203	4300	6503	5878128	SO:0001583	missense	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1621T>A	4.37:g.5827227A>T	ENSP00000380987:p.Leu541Ile		5878128	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.549020	0.65311	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.89485	-2.52;-2.33;-2.32	4.13	1.69	0.24217	.	0.000000	0.64402	D	0.000003	D	0.89385	0.6700	L	0.58810	1.83	0.58432	D	0.999991	D;B;P;P	0.62365	0.991;0.172;0.517;0.894	P;B;B;P	0.58970	0.849;0.077;0.323;0.573	D	0.85083	0.0947	10	0.35671	T	0.21	-14.4329	6.6721	0.23074	0.7218:0.0:0.2782:0.0	.	655;539;541;478	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	I	655;541;541;539	ENSP00000321606:L655I;ENSP00000380987:L541I;ENSP00000425742:L539I	ENSP00000321606:L655I	L	-	1	2	CRMP1	5878128	1.000000	0.71417	0.953000	0.39169	0.995000	0.86356	3.136000	0.50554	0.270000	0.21984	0.459000	0.35465	TTA		0.547	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		T	5827227	A	T	5827227	3	4	12	1	0	0	0	0	1	0	0	0	3896	69	3	5	105	5	CRMP1	4	5827227	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	2	5827227	185327049	47	1457	7	2								
SORCS2	57537	hgsc.bcm.edu	37	chr4	7715969	7715969	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgatgttcctgctgcagggCgaccgctgtatcatgggcca	13	12	1	1	rs540252369	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:7715969C>T	ENST00000507866.2	+	16	2101	c.1992C>T	c.(1990-1992)ggC>ggT	p.G664G	SORCS2_ENST00000329016.9_Silent_p.G492G	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	664					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGCTGCAGGGCGACCGCTGTA	0.602													C|||	2	0.000399361	0	0.0029	5008	,	,		20055	0		0	False		,,,				2504	0															0			4											34	37	36					4																	7715969		2078	4214	6292	7766869	SO:0001819	synonymous_variant	57537			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.1992C>T	4.37:g.7715969C>T			7766869	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																				0.602	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7715969	C	T	7715969	2	4	12	1	0	0	0	0	0	0	0	1	14968	755	27	1		1	SORCS2	4	7715969	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	1888742	7715969	183438307	48	1458										
BST1	683	hgsc.bcm.edu	37	chr4	15707179	15707179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgggaagcctttaaagtggCgctggacaaggatccctgct	13	10	0	0	rs2302466		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:15707179C>T	ENST00000265016.4	+	2	425	c.230C>T	c.(229-231)gCg>gTg	p.A77V	BST1_ENST00000382346.3_Missense_Mutation_p.A92V	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	77			A -> V (in dbSNP:rs2302466).		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						TTTAAAGTGGCGCTGGACAAG	0.468													C|||	1	0.000199681	0	0	5008	,	,		20677	0.001		0	False		,,,				2504	0															0			4						C	VAL/ALA	0,4406		0,0,2203	139	125	130		230	4.4	1	4	dbSNP_100	130	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BST1	NM_004334.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	77/319	15707179	1,13005	2203	4300	6503	15316277	SO:0001583	missense	683			D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"CD molecules"	1118	protein-coding gene	gene with protein product	"NAD(+) nucleosidase", "ADP-ribosyl cyclase 2"	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.230C>T	4.37:g.15707179C>T	ENSP00000265016:p.Ala77Val		15316277	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.909	0.958139	0.18507	0.0	1.16E-4	ENSG00000109743	ENST00000265016;ENST00000382346	T;T	0.24908	1.83;1.83	5.72	4.45	0.53987	.	0.128393	0.51477	N	0.000090	T	0.05456	0.0144	N	0.00142	-2.005	0.26652	N	0.972072	B	0.14438	0.01	B	0.04013	0.001	T	0.26710	-1.0095	10	0.22706	T	0.39	-15.4407	8.4747	0.33005	0.0:0.0897:0.0:0.9103	rs2302466;rs2302466	77	Q10588	BST1_HUMAN	V	77;92	ENSP00000265016:A77V;ENSP00000371783:A92V	ENSP00000265016:A77V	A	+	2	0	BST1	15316277	0.980000	0.34600	0.994000	0.49952	0.245000	0.25701	1.889000	0.39718	0.995000	0.38917	-0.303000	0.09236	GCG		0.468	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334		T	15707179	C	T	15707179	3	4	12	1	0	0	0	0	1	0	0	0	1536	768	27	1	236	1	BST1	4	15707179	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	7991210	15707179	175447097	49	1459										
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68795672	68795672	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tctgatttaagatgctttggAttttcttctctcttactgcc	6	9	4	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:68795672A>T	ENST00000334830.7	-	5	1162	c.416T>A	c.(415-417)aTc>aAc	p.I139N	TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.I135N|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.I136N|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	139	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						GATGCTTTGGATTTTCTTCTC	0.403																																					NSCLC(26;2 894 10941 14480 22546)											0			4											189	169	176					4																	68795672		2203	4300	6503	68478267	SO:0001583	missense	339967			AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.416T>A	4.37:g.68795672A>T	ENSP00000334611:p.Ile139Asn		68478267	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	A	12.35	1.912354	0.33721	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	6.07	4.87	0.63330	SEA (1);	0.350049	0.24206	N	0.040580	T	0.44664	0.1304	M	0.76002	2.32	0.22620	N	0.99892	P;P	0.50369	0.934;0.934	P;P	0.47528	0.549;0.549	T	0.47045	-0.9147	10	0.87932	D	0	.	9.2693	0.37661	0.8339:0.0:0.0:0.1661	.	136;139	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	N	135;139;136;116	ENSP00000426911:I135N;ENSP00000334611:I139N;ENSP00000379491:I136N;ENSP00000427621:I116N	ENSP00000334611:I139N	I	-	2	0	TMPRSS11A	68478267	0.997000	0.39634	0.066000	0.19879	0.048000	0.14542	1.224000	0.32539	1.073000	0.40885	0.533000	0.62120	ATC		0.403	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		T	68795672	A	T	68795672	3	4	12	1	0	0	0	0	1	0	0	0	16278	333	12	5	873	5	TMPRSS11A	4	68795672	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	53088493	68795672	122358604	50	1460										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79158685	79158685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atgccacaatttggaagcccGattcatgccagagctgccgt	10	12	1	1	rs568676550		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:79158685G>A	ENST00000325942.6	+	3	570	c.130G>A	c.(130-132)Gat>Aat	p.D44N	FRAS1_ENST00000264895.6_Missense_Mutation_p.D44N|FRAS1_ENST00000264899.6_Missense_Mutation_p.D44N	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	44	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.D44N(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTGGAAGCCCGATTCATGCCA	0.448													G|||	1	0.000199681	8e-04	0	5008	,	,		19895	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	4											80	79	79					4																	79158685		1983	4160	6143	79377709	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.130G>A	4.37:g.79158685G>A	ENSP00000326330:p.Asp44Asn		79377709	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772688	0.90108	.	.	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674	T;T;T	0.68903	-0.36;-0.36;-0.36	5.14	5.14	0.70334	.	0.133258	0.49305	D	0.000154	T	0.81456	0.4826	M	0.71920	2.185	0.50632	D	0.999887	D;D	0.89917	1.0;1.0	D;D	0.83275	0.951;0.996	T	0.83078	-0.0139	10	0.66056	D	0.02	.	17.7499	0.88430	0.0:0.0:1.0:0.0	.	44;44	E9PHH6;A2RRR8	.;.	N	44	ENSP00000326330:D44N;ENSP00000264895:D44N;ENSP00000264899:D44N	ENSP00000264895:D44N	D	+	1	0	FRAS1	79377709	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	4.876000	0.63079	2.560000	0.86352	0.467000	0.42956	GAT		0.448	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			A	79158685	G	A	79158685	3	1	12	1	0	0	0	0	1	0	0	0	6061	1058	37	1	140	1	FRAS1	4	79158685	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	10363013	79158685	111995591	51	1461										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87731014	87731014	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gatgatctgcttacttttatCtcctacatgagacacatcca	5	11	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:87731014C>G	ENST00000411767.2	+	46	7239	c.7176C>G	c.(7174-7176)atC>atG	p.I2392M	PTPN13_ENST00000427191.2_Missense_Mutation_p.I2373M|PTPN13_ENST00000316707.6_Missense_Mutation_p.I2201M|PTPN13_ENST00000511467.1_Missense_Mutation_p.I2397M|PTPN13_ENST00000436978.1_Missense_Mutation_p.I2397M			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2392	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTACTTTTATCTCCTACATGA	0.473																																																0			4											168	153	158					4																	87731014		1971	4155	6126	87950038	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.7176C>G	4.37:g.87731014C>G	ENSP00000407249:p.Ile2392Met		87950038	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213074	0.58452	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93	5.38	4.52	0.55395	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.52532	D	0.000070	D	0.89921	0.6855	M	0.64170	1.965	0.46654	D	0.999142	D;D;D;D	0.89917	0.997;0.999;1.0;0.999	D;D;D;D	0.97110	0.988;0.999;1.0;1.0	D	0.89986	0.4104	10	0.87932	D	0	.	10.0341	0.42118	0.1371:0.7905:0.0:0.0724	.	2201;2373;2392;2397	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	M	2373;2397;2201;2392;2397;2341	ENSP00000408368:I2373M;ENSP00000394794:I2397M;ENSP00000322675:I2201M;ENSP00000407249:I2392M;ENSP00000426626:I2397M	ENSP00000322675:I2201M	I	+	3	3	PTPN13	87950038	0.999000	0.42202	0.995000	0.50966	0.933000	0.57130	0.680000	0.25306	1.236000	0.43740	0.655000	0.94253	ATC		0.473	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			G	87731014	C	G	87731014	3	3	12	1	0	0	0	0	1	0	0	0	12817	903	32	5	7369	5	PTPN13	4	87731014	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	8572329	87731014	103423262	52	1462										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122824123	122824123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaatgattttggactaggaaCtagactgaaaggtggaggta	13	3	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:122824123C>T	ENST00000379645.3	-	9	2420	c.2347G>A	c.(2347-2349)Gtt>Att	p.V783I	TRPC3_ENST00000513531.1_Missense_Mutation_p.V655I|TRPC3_ENST00000264811.5_Missense_Mutation_p.V710I	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	698	Binds to IP3R3.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GGACTAGGAACTAGACTGAAA	0.378																																																0			4											113	110	111					4																	122824123		2203	4300	6503	123043573	SO:0001583	missense	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2347G>A	4.37:g.122824123C>T	ENSP00000368966:p.Val783Ile		123043573	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.391188	0.42410	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.83163	-1.69;-1.69;-1.69	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000002	T	0.68833	0.3044	N	0.11364	0.135	0.58432	D	0.999999	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.17979	0.003;0.005;0.02	T	0.65524	-0.6147	10	0.02654	T	1	-11.259	19.9944	0.97379	0.0:1.0:0.0:0.0	.	698;655;783	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	I	710;783;655	ENSP00000264811:V710I;ENSP00000368966:V783I;ENSP00000426899:V655I	ENSP00000264811:V710I	V	-	1	0	TRPC3	123043573	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.855000	0.62925	2.720000	0.93068	0.557000	0.71058	GTT		0.378	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122824123	C	T	122824123	3	4	12	1	0	0	0	0	1	0	0	0	16619	565	20	3	434	3	TRPC3	4	122824123	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	35093109	122824123	68330153	53	1463										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167656168	167656168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcatcattcataatatcgtcTtcatcatcctcatcatcagt	2	12	9	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:167656168T>C	ENST00000357154.3	-	12	1352	c.1215A>G	c.(1213-1215)gaA>gaG	p.E405E	SPOCK3_ENST00000535728.1_Silent_p.E273E|SPOCK3_ENST00000504953.1_Silent_p.E402E|SPOCK3_ENST00000541354.1_Silent_p.E285E|SPOCK3_ENST00000511531.1_Silent_p.E405E|SPOCK3_ENST00000511269.1_Silent_p.E402E|SPOCK3_ENST00000541637.1_Silent_p.E307E|SPOCK3_ENST00000510741.1_Silent_p.E362E|SPOCK3_ENST00000502330.1_Silent_p.E405E|SPOCK3_ENST00000357545.4_Silent_p.E402E|SPOCK3_ENST00000506886.1_Silent_p.E405E|SPOCK3_ENST00000534949.1_Silent_p.E309E|SPOCK3_ENST00000421836.2_Silent_p.E354E|SPOCK3_ENST00000512681.1_Silent_p.E307E|SPOCK3_ENST00000507137.1_5'UTR	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	405	Asp-rich.			E -> G (in Ref. 4; BAG58265). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		taatatcgtcttcatcatcct	0.353																																																0			4											193	179	184					4																	167656168		2203	4299	6502	167892743	SO:0001819	synonymous_variant	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1215A>G	4.37:g.167656168T>C			167892743	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																				0.353	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			C	167656168	T	C	167656168	2	2	12	1	0	0	0	0	0	0	0	1	15120	1606	56	4		4	SPOCK3	4	167656168	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	44832045	167656168	23498108	54	1464										
NEK1	4750	hgsc.bcm.edu	37	chr4	170523707	170523707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ataacatactgtctgccatcTtctgtagatttaacaagaat	5	8	3	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:170523707T>C	ENST00000439128.2	-	2	715	c.75A>G	c.(73-75)gaA>gaG	p.E25E	NEK1_ENST00000512193.1_Silent_p.E25E|NEK1_ENST00000511633.1_Silent_p.E25E|NEK1_ENST00000510533.1_Silent_p.E25E|NEK1_ENST00000507142.1_Silent_p.E25E	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	25	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		GTCTGCCATCTTCTGTAGATT	0.323																																																0			4											148	144	145					4																	170523707		1813	4073	5886	170760282	SO:0001819	synonymous_variant	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.75A>G	4.37:g.170523707T>C			170760282	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																				0.323	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			C	170523707	T	C	170523707	2	2	12	1	0	0	0	0	0	0	0	1	10352	1606	56	4		4	NEK1	4	170523707	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	2867539	170523707	20630569	55	1465										
APC	324	hgsc.bcm.edu	37	chr5	112173958	112173958	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actgcagcccagattgccaaAgtcatggaagaagtgtcagc	11	10	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:112173958A>G	ENST00000457016.1	+	16	3047	c.2667A>G	c.(2665-2667)aaA>aaG	p.K889K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.K889K|APC_ENST00000508376.2_Silent_p.K889K			P25054	APC_HUMAN	adenomatous polyposis coli	889	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGATTGCCAAAGTCATGGAAG	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											80	79	79					5																	112173958		2202	4300	6502	112201857	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2667A>G	5.37:g.112173958A>G			112201857	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173958	A	G	112173958	2	3	12	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112173958	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10		112173958	68741302	56	1466										
APC	324	hgsc.bcm.edu	37	chr5	112175193	112175193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggaagcagattctgctaataCcctgcaaatagcagaaataa	8	8	1	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:112175193C>T	ENST00000457016.1	+	16	4282	c.3902C>T	c.(3901-3903)aCc>aTc	p.T1301I	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.T1301I|APC_ENST00000508376.2_Missense_Mutation_p.T1301I			P25054	APC_HUMAN	adenomatous polyposis coli	1301	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1301fs*10(3)|p.T1301S(2)|p.?(1)|p.T1293fs*2(1)|p.K1192fs*3(1)|p.L1302fs*13(1)|p.L1302fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTGCTAATACCCTGCAAATA	0.403		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	10	Deletion - Frameshift(6)|Substitution - Missense(2)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(6)|stomach(2)|soft_tissue(1)|skin(1)	5											54	56	55					5																	112175193		2202	4300	6502	112203092	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3902C>T	5.37:g.112175193C>T	ENSP00000413133:p.Thr1301Ile		112203092	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	11.81	1.750684	0.31046	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.91180	-2.54;-2.54;-2.54;-2.8	5.73	4.84	0.62591	.	0.183957	0.48286	D	0.000185	D	0.85084	0.5616	L	0.32530	0.975	0.45515	D	0.998472	B;B	0.24132	0.098;0.041	B;B	0.17433	0.018;0.018	T	0.80616	-0.1303	9	.	.	.	-20.5918	15.94	0.79747	0.1362:0.8638:0.0:0.0	.	1303;1301	Q4LE70;P25054	.;APC_HUMAN	I	1301	ENSP00000413133:T1301I;ENSP00000257430:T1301I;ENSP00000427089:T1301I;ENSP00000423828:T1301I	.	T	+	2	0	APC	112203092	1.000000	0.71417	0.993000	0.49108	0.874000	0.50279	4.731000	0.62022	1.515000	0.48885	0.655000	0.94253	ACC		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175193	C	T	112175193	3	4	12	1	0	0	0	0	1	0	0	0	763	507	18	3	3960	3	APC	5	112175193	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	1235	112175193	68740067	57	1467										
HTR4	3360	hgsc.bcm.edu	37	chr5	147889227	147889227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agcagtccacacctgcccagGgacagtgtagtctatgaaag	11	11	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:147889227G>A	ENST00000377888.3	-	6	1006	c.868C>T	c.(868-870)Cct>Tct	p.P290S	HTR4_ENST00000521530.1_Missense_Mutation_p.P290S|HTR4_ENST00000521735.1_Missense_Mutation_p.P290S|HTR4_ENST00000517929.1_Missense_Mutation_p.P290S|HTR4_ENST00000520514.1_Missense_Mutation_p.P290S|HTR4_ENST00000354217.2_Missense_Mutation_p.P290S|HTR4_ENST00000362016.2_Missense_Mutation_p.P304S|HTR4_ENST00000360693.3_Missense_Mutation_p.P290S|HTR4_ENST00000314512.6_Missense_Mutation_p.P290S	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	290					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	ACCTGCCCAGGGACAGTGTAG	0.493																																					GBM(120;370 1604 14007 17804 41573)											0			5											91	90	90					5																	147889227		2203	4300	6503	147869420	SO:0001583	missense	3360			Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5299	protein-coding gene	gene with protein product		602164	"5-hydroxytryptamine (serotonin) receptor 4"			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000377888.3:c.868C>T	5.37:g.147889227G>A	ENSP00000367120:p.Pro290Ser		147869420	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Missense_Mutation	SNP	ENST00000377888.3	37	CCDS4291.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864225	0.32977	.	.	ENSG00000164270	ENST00000521530;ENST00000354217;ENST00000314512;ENST00000521735;ENST00000517929;ENST00000520514;ENST00000377888;ENST00000360693;ENST00000362016	T;T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	6.07	6.07	0.98685	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	L	0.42487	1.325	0.80722	D	1	D;D;P;P;D;D;D	0.76494	0.993;0.973;0.952;0.941;0.995;0.999;0.996	D;P;P;P;D;D;D	0.70227	0.965;0.846;0.81;0.808;0.92;0.968;0.952	T	0.21724	-1.0237	10	0.23891	T	0.37	.	19.2231	0.93806	0.0:0.0:1.0:0.0	.	290;290;290;304;290;290;290	C4WYH4;Q13639;Q712M9;Q13639-6;Q13639-3;Q13639-2;Q684M0	.;5HT4R_HUMAN;.;.;.;.;.	S	290;290;290;290;290;290;290;290;304	ENSP00000428320:P290S;ENSP00000346156:P290S;ENSP00000314906:P290S;ENSP00000430979:P290S;ENSP00000435904:P290S;ENSP00000427913:P290S;ENSP00000367120:P290S;ENSP00000353915:P290S;ENSP00000355037:P304S	ENSP00000314906:P290S	P	-	1	0	HTR4	147869420	1.000000	0.71417	0.639000	0.29394	0.024000	0.10985	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	CCT		0.493	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870		A	147889227	G	A	147889227	3	1	12	1	0	0	0	0	1	0	0	0	7470	1232	43	3	602	3	HTR4	5	147889227	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	35714034	147889227	33026033	58	1468										
CCDC99	54908	hgsc.bcm.edu	37	chr5	169025559	169025559	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cacctattatacagatttacTtcagatgaagctggataact	6	8	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:169025559T>C	ENST00000265295.4	+	9	1391	c.1112T>C	c.(1111-1113)cTt>cCt	p.L371P		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		ACAGATTTACTTCAGATGAAG	0.363																																																0			5											150	156	154					5																	169025559		2203	4300	6503	168958137	SO:0001583	missense	54908			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1112T>C	5.37:g.169025559T>C	ENSP00000265295:p.Leu371Pro		168958137		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384589	0.82792	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.57595	0.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.72317	0.3445	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75249	-0.3384	10	0.72032	D	0.01	-11.0546	16.2332	0.82358	0.0:0.0:0.0:1.0	.	293;272;371	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	P	371;272	ENSP00000265295:L371P	ENSP00000265295:L371P	L	+	2	0	CCDC99	168958137	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.656000	0.74396	2.233000	0.73108	0.523000	0.50628	CTT		0.363	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		C	169025559	T	C	169025559	3	2	12	1	0	0	0	0	1	0	0	0	2882	1609	56	4	1142	4	CCDC99	5	169025559	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	21136332	169025559	11889701	59	1469										
SCGN	10590	hgsc.bcm.edu	37	chr6	25665247	25665247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaacccactggacagcagcgTggagtttatgcaggtgagtg	14	8	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:25665247T>C	ENST00000377961.2	+	4	491	c.323T>C	c.(322-324)gTg>gCg	p.V108A	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	108	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GACAGCAGCGTGGAGTTTATG	0.493																																																0			6											117	107	111					6																	25665247		2203	4300	6503	25773226	SO:0001583	missense	10590			BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.323T>C	6.37:g.25665247T>C	ENSP00000367197:p.Val108Ala		25773226	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	37	CCDS4561.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.080358	0.36662	.	.	ENSG00000079689	ENST00000377961	T	0.08720	3.06	5.09	5.09	0.68999	EF-hand-like domain (1);	0.056322	0.64402	D	0.000001	T	0.06188	0.0160	N	0.21583	0.68	0.80722	D	1	D	0.65815	0.995	P	0.56343	0.796	T	0.50285	-0.8846	10	0.25106	T	0.35	.	13.8698	0.63612	0.0:0.0:0.0:1.0	.	108	O76038	SEGN_HUMAN	A	108	ENSP00000367197:V108A	ENSP00000367197:V108A	V	+	2	0	SCGN	25773226	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	5.889000	0.69766	1.900000	0.55004	0.477000	0.44152	GTG		0.493	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			C	25665247	T	C	25665247	3	2	12	1	0	0	0	0	1	0	0	0	13940	1696	59	4	337	4	SCGN	6	25665247	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10		25665247	145449820	60	1470										
ZNF323	64288	hgsc.bcm.edu	37	chr6	28297345	28297345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaaactgcctaaaaagttgtCgggaggcttcttggccagaa	11	8	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:28297345C>T	ENST00000414429.1	-	6	1019	c.116G>A	c.(115-117)cGa>cAa	p.R39Q	ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.R39Q|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.R39Q|ZSCAN31_ENST00000344279.6_Missense_Mutation_p.R39Q			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	39	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAAAAGTTGTCGGGAGGCTTC	0.502																																																0			6											96	103	101					6																	28297345		2203	4300	6503	28405324	SO:0001583	missense	64288				CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"-", "Zinc fingers, C2H2-type"	14097	protein-coding gene	gene with protein product		610794	"zinc finger protein 310 pseudogene", "zinc finger protein 323"	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.116G>A	6.37:g.28297345C>T	ENSP00000390076:p.Arg39Gln		28405324	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.139596	0.77775	.	.	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021;ENST00000426756;ENST00000446222;ENST00000434036	T;T;T;T;T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15	4.8	0.937	0.19494	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.05593	0.0147	M	0.90369	3.11	0.09310	N	1	P	0.42973	0.796	B	0.35813	0.211	T	0.15607	-1.0431	9	0.49607	T	0.09	.	9.2068	0.37293	0.0:0.6855:0.0:0.3145	.	39	Q96LW9	ZN323_HUMAN	Q	39	ENSP00000380050:R39Q;ENSP00000413705:R39Q;ENSP00000390076:R39Q;ENSP00000345339:R39Q;ENSP00000389479:R39Q;ENSP00000412519:R39Q;ENSP00000416108:R39Q;ENSP00000406376:R39Q;ENSP00000411033:R39Q;ENSP00000416225:R39Q	ENSP00000345339:R39Q	R	-	2	0	ZNF323	28405324	0.000000	0.05858	0.001000	0.08648	0.965000	0.64279	0.654000	0.24918	-0.053000	0.13289	0.563000	0.77884	CGA		0.502	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899		T	28297345	C	T	28297345	3	4	12	1	0	0	0	0	1	0	0	0	17882	884	31	1	1116	1	ZNF323	6	28297345	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	2632098	28297345	142817722	61	1471										
BAI3	577	hgsc.bcm.edu	37	chr6	69723982	69723982	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tgaagaaaacaaggaaaaatGggaagatgcacaacaggtaa	11	4	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:69723982G>T	ENST00000370598.1	+	12	2803	c.1982G>T	c.(1981-1983)tGg>tTg	p.W661L		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	661					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.W661L(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AAGGAAAAATGGGAAGATGCA	0.289																																																1	Substitution - Missense(1)	ovary(1)	6											64	67	66					6																	69723982		2203	4299	6502	69780703	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1982G>T	6.37:g.69723982G>T	ENSP00000359630:p.Trp661Leu		69780703	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725729	0.89298	.	.	ENSG00000135298	ENST00000370598	T	0.81078	-1.45	5.76	5.76	0.90799	Domain of unknown function DUF3497 (1);	0.132166	0.53938	D	0.000042	D	0.88153	0.6360	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88313	0.2957	10	0.87932	D	0	.	19.952	0.97200	0.0:0.0:1.0:0.0	.	661	O60242	BAI3_HUMAN	L	661	ENSP00000359630:W661L	ENSP00000359630:W661L	W	+	2	0	BAI3	69780703	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.781000	0.91805	2.728000	0.93425	0.655000	0.94253	TGG		0.289	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69723982	G	T	69723982	3	4	12	1	0	0	0	0	1	0	0	0	1301	1357	47	2	2020	2	BAI3	6	69723982	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	41426637	69723982	101391085	62	1472										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126236496	126236496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cagggtggatcatttgtacaCattctttgttcagtggtctc	10	8	4	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:126236496C>T	ENST00000368357.3	+	12	2466	c.2114C>T	c.(2113-2115)aCa>aTa	p.T705I	NCOA7_ENST00000392477.2_Missense_Mutation_p.T705I|NCOA7_ENST00000229634.9_Missense_Mutation_p.T590I	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	705					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		CATTTGTACACATTCTTTGTT	0.433																																																0			6											219	184	196					6																	126236496		2203	4300	6503	126278189	SO:0001583	missense	135112			AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2114C>T	6.37:g.126236496C>T	ENSP00000357341:p.Thr705Ile		126278189	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402573	0.83230	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000433571;ENST00000368353	T;T;T;T	0.31510	2.68;2.68;2.69;1.49	5.67	5.67	0.87782	.	0.169666	0.53938	D	0.000058	T	0.25494	0.0620	L	0.43152	1.355	0.42549	D	0.993102	P;P;P	0.50617	0.895;0.937;0.895	B;P;B	0.49252	0.4;0.604;0.4	T	0.00728	-1.1591	10	0.45353	T	0.12	-5.4281	14.9088	0.70740	0.1432:0.8568:0.0:0.0	.	694;694;705	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	I	705;705;590;15;15	ENSP00000357341:T705I;ENSP00000376269:T705I;ENSP00000229634:T590I;ENSP00000411002:T15I	ENSP00000229634:T590I	T	+	2	0	NCOA7	126278189	1.000000	0.71417	0.976000	0.42696	0.992000	0.81027	4.570000	0.60872	2.829000	0.97493	0.655000	0.94253	ACA		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		T	126236496	C	T	126236496	3	4	12	1	0	0	0	0	1	0	0	0	10265	478	17	3	2152	3	NCOA7	6	126236496	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	56512514	126236496	44878571	63	1473										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147631344	147631344	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actattcaattgttgattttCtaacgctgtgtgaaacacca	6	8	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:147631344C>G	ENST00000321680.6	+	10	1042	c.1042C>G	c.(1042-1044)Cta>Gta	p.L348V	STXBP5_ENST00000179882.6_Missense_Mutation_p.L19V|STXBP5_ENST00000367481.3_Missense_Mutation_p.L348V|STXBP5_ENST00000367480.3_Missense_Mutation_p.L348V	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	348					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGTTGATTTTCTAACGCTGTG	0.363																																																0			6											108	109	109					6																	147631344		2203	4300	6503	147673037	SO:0001583	missense	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1042C>G	6.37:g.147631344C>G	ENSP00000321826:p.Leu348Val		147673037	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.584486	0.28268	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.13196	2.62;2.61;2.73;3.31	5.64	4.77	0.60923	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	T	0.10637	0.0260	N	0.11789	0.175	0.80722	D	1	D;D;D	0.76494	0.998;0.997;0.999	D;D;D	0.80764	0.99;0.962;0.994	T	0.35624	-0.9781	10	0.26408	T	0.33	.	14.4505	0.67382	0.0:0.9298:0.0:0.0702	.	348;348;19	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	V	348;348;348;19	ENSP00000356451:L348V;ENSP00000321826:L348V;ENSP00000356450:L348V;ENSP00000179882:L19V	ENSP00000179882:L19V	L	+	1	2	STXBP5	147673037	1.000000	0.71417	0.789000	0.31954	0.784000	0.44337	1.597000	0.36729	1.523000	0.49018	0.650000	0.86243	CTA		0.363	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			G	147631344	C	G	147631344	3	3	12	1	0	0	0	0	1	0	0	0	15395	912	32	5	1080	5	STXBP5	6	147631344	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	21394848	147631344	23483723	64	1474										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152737559	152737559	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gcgggtaggttctttcaatcGctctttgtcagtcctttctt	9	10	5	0	rs200119679		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:152737559G>A	ENST00000367255.5	-	41	6614	c.6013C>T	c.(6013-6015)Cga>Tga	p.R2005*	SYNE1_ENST00000341594.5_Nonsense_Mutation_p.R2042*|SYNE1_ENST00000448038.1_Nonsense_Mutation_p.R2012*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.R2012*|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.R2005*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2005					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTTTCAATCGCTCTTTGTCA	0.428										HNSCC(10;0.0054)			G|||	1	0.000199681	0	0	5008	,	,		17029	0		0.001	False		,,,				2504	0															0			6											216	228	224					6																	152737559		2203	4300	6503	152779252	SO:0001587	stop_gained	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6013C>T	6.37:g.152737559G>A	ENSP00000356224:p.Arg2005*		152779252	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	47	13.363140	0.99737	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.	.	.	5.97	-2.23	0.06930	.	0.555045	0.16100	N	0.229637	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.3578	0.16071	0.0642:0.3916:0.1864:0.3578	.	.	.	.	X	2005;2012;2005;2012;2042	.	ENSP00000265368:R2005X	R	-	1	2	SYNE1	152779252	0.079000	0.21365	0.006000	0.13384	0.030000	0.12068	0.595000	0.24029	-0.130000	0.11599	-0.182000	0.12963	CGA		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152737559	G	A	152737559	4	1	12	1	0	0	0	0	0	1	0	0	15484	1095	38	1	20877	1	SYNE1	6	152737559	Nonsense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	5106215	152737559	18377508	65	1475										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11675820	11675820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctctggtctgatatccaatcTggatgtcccaatatttgttc	7	10	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:11675820T>C	ENST00000423059.4	-	2	1210	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	320					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		ATATCCAATCTGGATGTCCCA	0.413										HNSCC(18;0.044)																																						0			7											160	157	158					7																	11675820		1889	4111	6000	11642345	SO:0001583	missense	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.959A>G	7.37:g.11675820T>C	ENSP00000406482:p.Gln320Arg		11642345		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	T	15.21	2.766098	0.49574	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.58940	0.3	5.62	4.47	0.54385	.	0.050105	0.85682	D	0.000000	T	0.44705	0.1306	L	0.34521	1.04	0.58432	D	0.999999	B	0.12013	0.005	B	0.12837	0.008	T	0.35325	-0.9793	10	0.33141	T	0.24	.	11.283	0.49206	0.0:0.0713:0.0:0.9286	.	320	Q9UPZ6	THS7A_HUMAN	R	320	ENSP00000406482:Q320R	ENSP00000262042:Q320R	Q	-	2	0	THSD7A	11642345	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.247000	0.72411	2.267000	0.75376	0.477000	0.44152	CAG		0.413	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		C	11675820	T	C	11675820	3	2	12	1	0	0	0	0	1	0	0	0	15918	1580	55	4	4118	4	THSD7A	7	11675820	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10		11675820	147462843	66	1476										
BBS9	27241	hgsc.bcm.edu	37	chr7	33380540	33380540	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atgactgagagagaagatgaCttgaacgtttctgtcgtggt	13	5	1	6			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:33380540C>T	ENST00000242067.6	+	11	1751	c.1230C>T	c.(1228-1230)gaC>gaT	p.D410D	BBS9_ENST00000396127.2_Silent_p.D410D|BBS9_ENST00000355070.2_Silent_p.D410D|BBS9_ENST00000350941.3_Silent_p.D410D|BBS9_ENST00000354265.4_Silent_p.D410D	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	410					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			GAGAAGATGACTTGAACGTTT	0.313									Bardet-Biedl syndrome																																							0			7											197	180	186					7																	33380540		2203	4300	6503	33347065	SO:0001819	synonymous_variant	27241	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1230C>T	7.37:g.33380540C>T			33347065	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Silent	SNP	ENST00000242067.6	37	CCDS43566.1																																																																																				0.313	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			T	33380540	C	T	33380540	2	4	12	1	0	0	0	0	0	0	0	1	1343	564	20	3		3	BBS9	7	33380540	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	21704720	33380540	125758123	67	1477										
GLI3	2737	hgsc.bcm.edu	37	chr7	42064965	42064965	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgctcactgcagactcactCgtgggcttgttctgctggtc	11	13	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:42064965C>T	ENST00000395925.3	-	9	1338	c.1254G>A	c.(1252-1254)acG>acA	p.T418T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	418					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CAGACTCACTCGTGGGCTTGT	0.527									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											131	109	116					7																	42064965		2203	4300	6503	42031490	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1254G>A	7.37:g.42064965C>T			42031490	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.527	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42064965	C	T	42064965	2	4	12	1	0	0	0	0	0	0	0	1	6459	871	31	1		1	GLI3	7	42064965	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	8684425	42064965	117073698	68	1478										
STAG3	10734	hgsc.bcm.edu	37	chr7	99801743	99801743	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcctgctgctgagcctcaagCaggtgcgcccttctgccttg	11	15	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:99801743C>G	ENST00000426455.1	+	26	3207	c.2800C>G	c.(2800-2802)Cag>Gag	p.Q934E	STAG3_ENST00000394018.2_Missense_Mutation_p.Q876E|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Missense_Mutation_p.Q934E|STAG3_ENST00000440830.1_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	934					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAGCCTCAAGCAGGTGCGCCC	0.493																																																0			7											122	98	106					7																	99801743		2203	4300	6503	99639679	SO:0001583	missense	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2800C>G	7.37:g.99801743C>G	ENSP00000400359:p.Gln934Glu		99639679	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.955845	0.73902	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.21361	2.01;2.01;2.01	5.65	5.65	0.86999	.	0.000000	0.46442	D	0.000288	T	0.46288	0.1385	M	0.65498	2.005	0.80722	D	1	B;D;P	0.69078	0.427;0.997;0.604	B;D;B	0.75020	0.17;0.985;0.277	T	0.37056	-0.9722	10	0.72032	D	0.01	-16.4344	17.2163	0.86945	0.0:1.0:0.0:0.0	.	876;934;934	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	E	934;876;934	ENSP00000400359:Q934E;ENSP00000377586:Q876E;ENSP00000319318:Q934E	ENSP00000319318:Q934E	Q	+	1	0	STAG3	99639679	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	5.744000	0.68664	2.674000	0.91012	0.655000	0.94253	CAG		0.493	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		G	99801743	C	G	99801743	3	3	12	1	0	0	0	0	1	0	0	0	15283	711	25	5	2898	5	STAG3	7	99801743	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	57736778	99801743	59336920	69	1479										
MLL5	55904	hgsc.bcm.edu	37	chr7	104749520	104749520	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aacaatggtgatggctgtgcCagcagtaatgacaatgggga	14	6	0	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:104749520C>T	ENST00000311117.3	+	23	4145	c.3600C>T	c.(3598-3600)gcC>gcT	p.A1200A	SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000257745.4_Silent_p.A1200A|KMT2E_ENST00000334877.4_Silent_p.A1200A|KMT2E_ENST00000334914.7_Silent_p.A255A	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1200					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ATGGCTGTGCCAGCAGTAATG	0.463																																																0			7											110	94	100					7																	104749520		2203	4300	6503	104536756	SO:0001819	synonymous_variant	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3600C>T	7.37:g.104749520C>T			104536756	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	C	1.750	-0.489433	0.04352	.	.	ENSG00000005483	ENST00000473063	.	.	.	5.65	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.21897	N	0.999485	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1311	0.65255	0.0:0.7144:0.2856:0.0	.	.	.	.	X	12	.	.	Q	+	1	0	MLL5	104536756	0.007000	0.16637	0.033000	0.17914	0.627000	0.37826	0.644000	0.24766	1.348000	0.45733	0.467000	0.42956	CAG		0.463	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104749520	C	T	104749520	2	4	12	1	0	0	0	0	0	0	0	1	9654	581	21	3		3	MLL5	7	104749520	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	4947777	104749520	54389143	70	1480										
COG5	10466	hgsc.bcm.edu	37	chr7	107204319	107204319	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctccgaggccagctacagcgAcgctgccgccgccaccttcc	10	20	0	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:107204319A>G	ENST00000347053.3	-	1	166	c.116T>C	c.(115-117)gTc>gCc	p.V39A	DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000265720.3_5'Flank|COG5_ENST00000297135.3_Missense_Mutation_p.V39A|COG5_ENST00000393603.2_Missense_Mutation_p.V39A|DUS4L_ENST00000402620.1_5'Flank	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	39					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						AGCTACAGCGACGCTGCCGCC	0.672																																																0			7											28	29	29					7																	107204319		2189	4272	6461	106991555	SO:0001583	missense	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.116T>C	7.37:g.107204319A>G	ENSP00000334703:p.Val39Ala		106991555	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	A	9.248	1.040050	0.19669	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.20881	2.06;2.04;2.04	5.83	0.211	0.15236	.	0.555807	0.16328	N	0.219237	T	0.07458	0.0188	N	0.08118	0	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.29941	-0.9995	10	0.21540	T	0.41	0.031	2.3962	0.04390	0.4742:0.2993:0.0821:0.1444	.	39;39	Q9UP83;Q9UP83-2	COG5_HUMAN;.	A	39	ENSP00000334703:V39A;ENSP00000297135:V39A;ENSP00000377228:V39A	ENSP00000297135:V39A	V	-	2	0	COG5	106991555	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.525000	0.06214	0.422000	0.26005	0.482000	0.46254	GTC		0.672	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			G	107204319	A	G	107204319	3	3	12	1	0	0	0	0	1	0	0	0	3667	275	10	4	2558	4	COG5	7	107204319	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	2454799	107204319	51934344	71	1481										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121624099	121624099	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actacttacaaaacaattttCgagagcaacagtacaagttc	5	9	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:121624099C>T	ENST00000393386.2	+	8	1267	c.856C>T	c.(856-858)Cga>Tga	p.R286*	PTPRZ1_ENST00000449182.1_Nonsense_Mutation_p.R286*	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	286	Alpha-carbonic anhydrase.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AAACAATTTTCGAGAGCAACA	0.333																																																0			7											158	153	155					7																	121624099		2203	4299	6502	121411335	SO:0001587	stop_gained	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.856C>T	7.37:g.121624099C>T	ENSP00000377047:p.Arg286*		121411335	A4D0W5|C9JFM0|O76043|Q9UDR6	Nonsense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	38	6.895991	0.97916	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	.	.	.	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8306	0.70146	0.2592:0.7408:0.0:0.0	.	.	.	.	X	286	.	ENSP00000377047:R286X	R	+	1	2	PTPRZ1	121411335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.349000	0.52217	2.894000	0.99253	0.655000	0.94253	CGA		0.333	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121624099	C	T	121624099	4	4	12	1	0	0	0	0	0	1	0	0	12851	876	31	1	886	1	PTPRZ1	7	121624099	Nonsense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	14419780	121624099	37514564	72	1482										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127014460	127014460	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gaatccctccttagtcctctAtgaacttcatcaaaatgcct	4	13	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:127014460A>G	ENST00000393313.1	-	5	1521	c.930T>C	c.(928-930)caT>caC	p.H310H	ZNF800_ENST00000485577.1_5'Flank|ZNF800_ENST00000393312.1_Silent_p.H310H|ZNF800_ENST00000265827.3_Silent_p.H310H			Q2TB10	ZN800_HUMAN	zinc finger protein 800	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TTAGTCCTCTATGAACTTCAT	0.373																																																0			7											95	94	94					7																	127014460		2203	4300	6503	126801696	SO:0001819	synonymous_variant	168850			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.930T>C	7.37:g.127014460A>G			126801696	Q9HBN0	Silent	SNP	ENST00000393313.1	37	CCDS5795.1																																																																																				0.373	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		G	127014460	A	G	127014460	2	3	12	1	0	0	0	0	0	0	0	1	18208	446	16	4		4	ZNF800	7	127014460	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10	5390361	127014460	32124203	73	1483										
EZH2	2146	hgsc.bcm.edu	37	chr7	148525837	148525837	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aataatcaggcataccatctCggtgatcctccagatctttc	6	12	3	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:148525837C>G	ENST00000460911.1	-	6	708	c.620G>C	c.(619-621)cGa>cCa	p.R207P	EZH2_ENST00000536783.1_Missense_Mutation_p.R98P|EZH2_ENST00000350995.2_Missense_Mutation_p.R168P|EZH2_ENST00000320356.2_Missense_Mutation_p.R207P|EZH2_ENST00000478654.1_Missense_Mutation_p.R198P|EZH2_ENST00000483967.1_Missense_Mutation_p.R198P|EZH2_ENST00000541220.1_Missense_Mutation_p.R198P|EZH2_ENST00000476773.1_Missense_Mutation_p.R198P			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	207	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CATACCATCTCGGTGATCCTC	0.388			Mis		DLBCL																																		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	0			7											208	182	191					7																	148525837		2203	4300	6503	148156770	SO:0001583	missense	2146				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.620G>C	7.37:g.148525837C>G	ENSP00000419711:p.Arg207Pro		148156770	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	c	10.44	1.349939	0.24426	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94138	-3.32;-3.35;-3.35;-3.36;-3.32;-3.32;-3.35;0.9	5.54	3.7	0.42460	SANT domain, DNA binding (1);	0.469946	0.22276	N	0.062193	D	0.84202	0.5420	L	0.29908	0.895	0.09310	N	1	P;B;B;B;B;B	0.42757	0.789;0.042;0.185;0.025;0.395;0.002	B;B;B;B;B;B	0.35931	0.214;0.014;0.177;0.058;0.07;0.008	T	0.74945	-0.3491	10	0.28530	T	0.3	.	3.3036	0.06992	0.1434:0.5711:0.1386:0.1469	.	207;198;198;207;168;207	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	P	198;207;207;168;198;198;198;98	ENSP00000417062:R198P;ENSP00000320147:R207P;ENSP00000419711:R207P;ENSP00000223193:R168P;ENSP00000443219:R198P;ENSP00000419050:R198P;ENSP00000419856:R198P;ENSP00000439305:R98P	ENSP00000320147:R207P	R	-	2	0	EZH2	148156770	0.876000	0.30132	0.053000	0.19242	0.818000	0.46254	0.998000	0.29744	0.682000	0.31407	0.585000	0.79938	CGA		0.388	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		G	148525837	C	G	148525837	3	3	12	1	0	0	0	0	1	0	0	0	5347	884	31	5	1695	5	EZH2	7	148525837	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	21511377	148525837	10612826	74	1484										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3015448	3015448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggggagacggatagttccaaCggcgaacggtccctggcata	15	10	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:3015448C>T	ENST00000520002.1	-	40	6443	c.5888G>A	c.(5887-5889)cGt>cAt	p.R1963H	CSMD1_ENST00000539096.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1963H|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1963H|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1963H|CSMD1_ENST00000523387.1_5'UTR			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1963	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				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)		ATAGTTCCAACGGCGAACGGT	0.453																																																0			8											55	53	54					8																	3015448		1959	4100	6059	3002855	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5888G>A	8.37:g.3015448C>T	ENSP00000430733:p.Arg1963His		3002855	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	19.45	3.829321	0.71258	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.45	5.45	0.79879	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.75451	0.3851	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.999;0.998	T	0.77051	-0.2731	10	0.72032	D	0.01	.	18.8862	0.92379	0.0:1.0:0.0:0.0	.	1963;1963;1962;1963	E5RIG2;Q96PZ7;F5H2I8;Q96PZ7-4	.;CSMD1_HUMAN;.;.	H	1963;1963;1824;1962;1962;1962	ENSP00000383047:R1963H;ENSP00000430733:R1963H;ENSP00000441462:R1962H;ENSP00000446243:R1962H;ENSP00000441675:R1962H	ENSP00000320445:R1824H	R	-	2	0	CSMD1	3002855	1.000000	0.71417	0.266000	0.24541	0.030000	0.12068	7.311000	0.78958	2.538000	0.85594	0.655000	0.94253	CGT		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3015448	C	T	3015448	3	4	12	1	0	0	0	0	1	0	0	0	3950	536	19	1	4937	1	CSMD1	8	3015448	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10		3015448	143348574	75	1485										
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87235283	87235283	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actacagtcaccagaggtaaCgcagtaaatatgcatttggg	10	8	1	1	rs55902108	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:87235283C>A	ENST00000297524.3	-	2	838	c.735G>T	c.(733-735)gcG>gcT	p.A245A	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Silent_p.A236A	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	245						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CCAGAGGTAACGCAGTAAATA	0.383																																																0			8											158	161	160					8																	87235283		2203	4300	6503	87304399	SO:0001819	synonymous_variant	157724			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.735G>T	8.37:g.87235283C>A			87304399	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																				0.383	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		A	87235283	C	A	87235283	2	1	12	1	0	0	0	0	0	0	0	1	14732	523	19	2		2	SLC7A13	8	87235283	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	84219835	87235283	59128739	76	1486										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113358402	113358402	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ccaggaaacccaggactgagGatcacaccactgaagtctga	10	12	2	3	rs139487815	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:113358402G>T	ENST00000297405.5	-	41	6610	c.6366C>A	c.(6364-6366)atC>atA	p.I2122I	CSMD3_ENST00000352409.3_Silent_p.I2052I|CSMD3_ENST00000455883.2_Silent_p.I2018I|CSMD3_ENST00000343508.3_Silent_p.I2082I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2122	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I2122M(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAGGACTGAGGATCACACCAC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	ovary(1)	8											111	112	112					8																	113358402		2203	4300	6503	113427578	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6366C>A	8.37:g.113358402G>T			113427578	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113358402	G	T	113358402	2	4	12	1	0	0	0	0	0	0	0	1	3952	1164	41	2		2	CSMD3	8	113358402	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	26123119	113358402	33005620	77	1487										
ADCY8	114	hgsc.bcm.edu	37	chr8	131792656	131792656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttatggcaaatcagatttgtCggtgccttcagcctgggctc	11	10	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:131792656C>T	ENST00000286355.5	-	18	5828	c.3736G>A	c.(3736-3738)Gac>Aac	p.D1246N	ADCY8_ENST00000377928.3_Missense_Mutation_p.D1115N	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1246					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCAGATTTGTCGGTGCCTTCA	0.358										HNSCC(32;0.087)																																						0			8											93	91	92					8																	131792656		2203	4300	6503	131861838	SO:0001583	missense	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3736G>A	8.37:g.131792656C>T	ENSP00000286355:p.Asp1246Asn		131861838		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.027473	0.75390	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.80304	-1.36;-1.34	5.68	5.68	0.88126	.	0.182120	0.44285	D	0.000473	D	0.83714	0.5314	L	0.27053	0.805	0.41093	D	0.985617	D;P	0.76494	0.999;0.649	D;B	0.68621	0.959;0.091	D	0.85809	0.1378	10	0.87932	D	0	.	16.9518	0.86247	0.0:1.0:0.0:0.0	.	1115;1246	E7EVL1;P40145	.;ADCY8_HUMAN	N	1246;1115	ENSP00000286355:D1246N;ENSP00000367161:D1115N	ENSP00000286355:D1246N	D	-	1	0	ADCY8	131861838	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.048000	0.76606	2.689000	0.91719	0.655000	0.94253	GAC		0.358	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131792656	C	T	131792656	3	4	12	1	0	0	0	0	1	0	0	0	300	884	31	1	23	1	ADCY8	8	131792656	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	18434254	131792656	14571366	78	1488										
TG	7038	hgsc.bcm.edu	37	chr8	133899152	133899152	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcttgcaagcttcttgaatgGagggagacaagaagatttgg	13	5	2	4			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:133899152G>C	ENST00000220616.4	+	9	1575	c.1535G>C	c.(1534-1536)gGa>gCa	p.G512A	TG_ENST00000377869.1_Missense_Mutation_p.G512A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	512					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		TTCTTGAATGGAGGGAGACAA	0.443																																																0			8											44	47	46					8																	133899152		2203	4299	6502	133968334	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1535G>C	8.37:g.133899152G>C	ENSP00000220616:p.Gly512Ala		133968334	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	4.351	0.064592	0.08388	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.63255	-0.03;-0.02	5.29	2.46	0.29980	.	1.403590	0.04446	N	0.371705	T	0.53302	0.1788	L	0.47716	1.5	0.09310	N	1	B	0.34372	0.451	B	0.27380	0.079	T	0.40757	-0.9546	10	0.33141	T	0.24	.	8.1981	0.31409	0.1456:0.1294:0.725:0.0	.	512	P01266	THYG_HUMAN	A	512	ENSP00000367100:G512A;ENSP00000220616:G512A	ENSP00000220616:G512A	G	+	2	0	TG	133968334	0.063000	0.20901	0.001000	0.08648	0.028000	0.11728	1.339000	0.33885	0.792000	0.33850	0.557000	0.71058	GGA		0.443	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133899152	G	C	133899152	3	2	12	1	0	0	0	0	1	0	0	0	15852	1174	41	5	1569	5	TG	8	133899152	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	2106496	133899152	12464870	79	1489										
WASH1	0	hgsc.bcm.edu	37	chr9	18075	18075	+	IGR	DEL	G	G	-													0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gtgcttgctctggatcctgtGgcgggggcgtctctgcaggc							TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:18075delG								None (None upstream) : MIR1302-2 (9581 downstream)																							TGGATCCTGTGGCGGGGGCGT	0.662																																																0			9																																								8075	SO:0001628	intergenic_variant	375690																															9.37:g.18075delG			8075		Frame_Shift_Del	DEL		37																																																																																				0	0.662									-	18075	G	-	18075	6	5	12	0	1	1	0	1	0	0	0	0	17295	1348	47	0		0	WASH1	9	18075	IGR	DEL	G	TCGA-AF-6672-01A-11D-1826-10		18075	141195356	80	1490										
JAK2	3717	hgsc.bcm.edu	37	chr9	5070026	5070026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tgaaccaaatggtgtttcacAaaatcagaaatgaagatttg	8	5	2	4	rs121912473		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:5070026A>G	ENST00000381652.3	+	12	2109	c.1615A>G	c.(1615-1617)Aaa>Gaa	p.K539E	JAK2_ENST00000544510.1_Missense_Mutation_p.K390E|JAK2_ENST00000539801.1_Missense_Mutation_p.K539E	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	539			FHK -> L (in myeloproliferative disorder with erythrocytosis). {ECO:0000269|PubMed:17267906}.|HK -> QL (in myeloproliferative disorder with erythrocytosis).|K -> L (in myeloproliferative disorder with erythrocytosis; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:17267906}.		actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.K539L(15)|p.F537_K539>L(13)|p.H538_K539>L(10)|p.H538_K539>QL(4)|p.H538_K539>F(1)|p.H538_K539del(1)|p.H538_K539>I(1)|p.K539E(1)|p.F537_K539>R(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGTGTTTCACAAAATCAGAAA	0.323		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	47	Complex - deletion inframe(26)|Substitution - Missense(16)|Complex - compound substitution(4)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(47)	9											86	81	83					9																	5070026		2202	4300	6502	5060026	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1615A>G	9.37:g.5070026A>G	ENSP00000371067:p.Lys539Glu		5060026	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502094	0.85176	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.23552	1.9;1.9;1.9	5.07	5.07	0.68467	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	M	0.77103	2.36	0.80722	D	1	D	0.58620	0.983	P	0.51101	0.659	T	0.48747	-0.9008	10	0.66056	D	0.02	-24.3061	14.4823	0.67592	1.0:0.0:0.0:0.0	.	539	O60674	JAK2_HUMAN	E	539;539;390	ENSP00000440387:K539E;ENSP00000371067:K539E;ENSP00000443103:K390E	ENSP00000371067:K539E	K	+	1	0	JAK2	5060026	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.912000	0.92726	1.892000	0.54788	0.455000	0.32223	AAA		0.323	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5070026	A	G	5070026	3	3	12	1	0	0	0	0	1	0	0	0	7959	131	5	4	1653	4	JAK2	9	5070026	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	5051951	5070026	136143405	81	1491										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18777556	18777556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gctggcccaggagatcttccGcagccacctggagcaccagg	13	15	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:18777556G>A	ENST00000380548.4	+	19	3668	c.3329G>A	c.(3328-3330)cGc>cAc	p.R1110H		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1110						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GAGATCTTCCGCAGCCACCTG	0.647																																																0			9											19	23	22					9																	18777556		2053	4188	6241	18767556	SO:0001583	missense	92949			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3329G>A	9.37:g.18777556G>A	ENSP00000369921:p.Arg1110His		18767556	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204596	0.58234	.	.	ENSG00000178031	ENST00000380548	T	0.63744	-0.06	5.88	4.99	0.66335	.	0.063246	0.08080	U	1.000000	T	0.47746	0.1462	N	0.14661	0.345	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.31392	-0.9945	10	0.66056	D	0.02	.	9.7332	0.40374	0.1962:0.0:0.8038:0.0	.	1110	Q8N6G6	ATL1_HUMAN	H	1110	ENSP00000369921:R1110H	ENSP00000369921:R1110H	R	+	2	0	ADAMTSL1	18767556	0.999000	0.42202	1.000000	0.80357	0.813000	0.45954	0.469000	0.22067	1.502000	0.48669	0.557000	0.71058	CGC		0.647	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			A	18777556	G	A	18777556	3	1	12	1	0	0	0	0	1	0	0	0	274	1087	38	1	3407	1	ADAMTSL1	9	18777556	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	13707530	18777556	122435875	82	1492										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32630107	32630107	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	catgctttcttcattttccgTgcccatccttgtgttctcct	5	14	3	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:32630107T>C	ENST00000242310.4	-	1	5560	c.5471A>G	c.(5470-5472)cAc>cGc	p.H1824R		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1824			H -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCATTTTCCGTGCCCATCCTT	0.498																																																0			9											191	138	156					9																	32630107		2203	4300	6503	32620107	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5471A>G	9.37:g.32630107T>C	ENSP00000418379:p.His1824Arg		32620107	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	7.702	0.693292	0.15039	.	.	ENSG00000122728	ENST00000242310	T	0.06933	3.24	0.479	0.479	0.16796	.	0.268520	0.39341	N	0.001400	T	0.03178	0.0093	N	0.08118	0	0.20307	N	0.999911	B	0.24186	0.099	B	0.12156	0.007	T	0.41910	-0.9482	10	0.28530	T	0.3	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1824	Q8IZX4	TAF1L_HUMAN	R	1824	ENSP00000418379:H1824R	ENSP00000418379:H1824R	H	-	2	0	TAF1L	32620107	1.000000	0.71417	0.981000	0.43875	0.135000	0.20990	0.972000	0.29409	0.426000	0.26116	0.164000	0.16699	CAC		0.498	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			C	32630107	T	C	32630107	3	2	12	1	0	0	0	0	1	0	0	0	15562	1696	59	4	13	4	TAF1L	9	32630107	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	13852551	32630107	108583324	83	1493										
RNF38	152006	hgsc.bcm.edu	37	chr9	36356448	36356448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	catatggtactggtaagtgcTgaactgaacatgcctgaagc	11	8	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:36356448T>C	ENST00000259605.6	-	6	868	c.761A>G	c.(760-762)cAg>cGg	p.Q254R	RNF38_ENST00000377885.2_Missense_Mutation_p.Q171R|RNF38_ENST00000377877.4_Missense_Mutation_p.Q178R|RNF38_ENST00000491349.1_5'UTR|RNF38_ENST00000357058.3_Missense_Mutation_p.Q171R|RNF38_ENST00000350199.4_Missense_Mutation_p.Q171R|RNF38_ENST00000353739.4_Missense_Mutation_p.Q204R	NM_022781.4	NP_073618.3	Q9H0F5	RNF38_HUMAN	ring finger protein 38	254	Pro-rich.				male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|sperm flagellum (GO:0036126)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q254L(1)		breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(1)|lung(3)|stomach(1)	11			STAD - Stomach adenocarcinoma(86;0.228)			TGGTAAGTGCTGAACTGAACA	0.368																																																1	Substitution - Missense(1)	central_nervous_system(1)	9											176	163	167					9																	36356448		2203	4300	6503	36346448	SO:0001583	missense	152006				CCDS6603.1, CCDS6604.1	9p	2013-01-09			ENSG00000137075	ENSG00000137075		"RING-type (C3HC4) zinc fingers"	18052	protein-coding gene	gene with protein product		612488					Standard	XM_005251364		Approved		uc003zzh.3	Q9H0F5	OTTHUMG00000019905	ENST00000259605.6:c.761A>G	9.37:g.36356448T>C	ENSP00000259605:p.Gln254Arg		36346448	A6PVP9|B1AM81|B1AM82|B3KSG4|E7EVL3|Q7LB33|Q8N0Y0|Q9H748	Missense_Mutation	SNP	ENST00000259605.6	37	CCDS6603.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741990	0.89573	.	.	ENSG00000137075	ENST00000259605;ENST00000353739;ENST00000377885;ENST00000357058;ENST00000350199;ENST00000377876;ENST00000377870;ENST00000377877	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	M	0.68593	2.085	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.85130	0.993;0.997;0.993	T	0.64287	-0.6443	10	0.54805	T	0.06	-4.6694	14.3198	0.66479	0.0:0.0:0.0:1.0	.	178;204;254	B1AM81;Q9H0F5-2;Q9H0F5	.;.;RNF38_HUMAN	R	254;204;171;171;171;71;178;178	ENSP00000259605:Q254R;ENSP00000335239:Q204R;ENSP00000367117:Q171R;ENSP00000349566:Q171R;ENSP00000343947:Q171R;ENSP00000367109:Q178R	ENSP00000259605:Q254R	Q	-	2	0	RNF38	36346448	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.655000	0.83696	2.254000	0.74563	0.528000	0.53228	CAG		0.368	RNF38-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052422.3	NM_022781		C	36356448	T	C	36356448	3	2	12	1	0	0	0	0	1	0	0	0	13527	1580	55	4	814	4	RNF38	9	36356448	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	3726341	36356448	104856983	84	1494										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98229638	98229638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aatgtccgtaaggtccagccCgtctctcactcgggtggtgc	12	13	2	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:98229638C>T	ENST00000331920.6	-	15	2619	c.2320G>A	c.(2320-2322)Ggg>Agg	p.G774R	PTCH1_ENST00000418258.1_Missense_Mutation_p.G623R|PTCH1_ENST00000421141.1_Missense_Mutation_p.G623R|PTCH1_ENST00000430669.2_Missense_Mutation_p.G708R|PTCH1_ENST00000437951.1_Missense_Mutation_p.G708R|PTCH1_ENST00000375274.2_Missense_Mutation_p.G773R|PTCH1_ENST00000429896.2_Missense_Mutation_p.G623R	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	774					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.G774R(2)|p.G773R(2)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGGTCCAGCCCGTCTCTCACT	0.478																																																4	Substitution - Missense(4)	lung(4)	9	GRCh37	CM064176	PTCH1	M							90	90	90					9																	98229638		2203	4300	6503	97269459	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2320G>A	9.37:g.98229638C>T	ENSP00000332353:p.Gly774Arg		97269459	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	33	5.284695	0.95517	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.96587	-4.03;-4.01;-4.02;-4.02;-4.01;-4.02;-4.06	5.82	5.82	0.92795	.	0.047110	0.85682	D	0.000000	D	0.98157	0.9391	M	0.78801	2.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.98630	1.0671	10	0.87932	D	0	-23.8555	20.1013	0.97878	0.0:1.0:0.0:0.0	.	708;773;774	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	R	774;708;623;623;210;708;623;773	ENSP00000332353:G774R;ENSP00000389744:G708R;ENSP00000399981:G623R;ENSP00000396135:G623R;ENSP00000410287:G708R;ENSP00000414823:G623R;ENSP00000364423:G773R	ENSP00000332353:G774R	G	-	1	0	PTCH1	97269459	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.487000	0.81328	2.748000	0.94277	0.655000	0.94253	GGG		0.478	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98229638	C	T	98229638	3	4	12	1	0	0	0	0	1	0	0	0	12764	652	23	1	2059	1	PTCH1	9	98229638	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	61873190	98229638	42983793	85	1495										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21806618	21806618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gatgatccatgcgcttgtgcAcggtcgtcctcgggatgttt	13	10	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:21806618A>G	ENST00000449193.2	-	4	2386	c.134T>C	c.(133-135)gTg>gCg	p.V45A	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Missense_Mutation_p.V45A	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	45						nucleus (GO:0005634)											GCGCTTGTGCACGGTCGTCCT	0.527																																																0			10											87	84	85					10																	21806618		2069	4215	6284	21846624	SO:0001583	missense	387640			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.134T>C	10.37:g.21806618A>G	ENSP00000410041:p.Val45Ala		21846624	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	37	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726890	0.48833	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	D;D	0.86432	-2.12;-2.12	4.96	4.96	0.65561	DNA binding domain, putative (1);Transforming protein Ski (2);	0.000000	0.64402	D	0.000002	D	0.90957	0.7157	L	0.46157	1.445	0.53688	D	0.999979	D;D	0.89917	0.999;1.0	D;D	0.87578	0.997;0.998	D	0.92002	0.5611	10	0.87932	D	0	0.3012	14.6105	0.68512	1.0:0.0:0.0:0.0	.	45;45	Q1XH10;E9PAX1	DLN1_HUMAN;.	A	45	ENSP00000410041:V45A;ENSP00000442432:V45A	ENSP00000442432:V45A	V	-	2	0	C10orf140	21846624	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.249000	0.95470	1.857000	0.53885	0.260000	0.18958	GTG		0.527	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		G	21806618	A	G	21806618	3	3	12	1	0	0	0	0	1	0	0	0	1599	159	6	4	2596	4	C10orf140	10	21806618	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10		21806618	113728129	86	1496										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37454053	37454053	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ccatcagaatccaaacaaaaGgactatgaagaaaattcttg	6	8	2	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:37454053G>T	ENST00000602533.1	+	18	1965	c.1866G>T	c.(1864-1866)aaG>aaT	p.K622N	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.K622N|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.K622N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	678					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CCAAACAAAAGGACTATGAAG	0.294																																																0			10											129	124	126					10																	37454053		1811	4062	5873	37494059	SO:0001583	missense	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1866G>T	10.37:g.37454053G>T	ENSP00000473551:p.Lys622Asn		37494059	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	4.341	0.062630	0.08388	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.08282	3.11;3.11	1.01	-0.0617	0.13784	.	.	.	.	.	T	0.11793	0.0287	L	0.36672	1.1	0.09310	N	1	P	0.45126	0.851	P	0.55391	0.775	T	0.22730	-1.0208	9	0.51188	T	0.08	.	4.0394	0.09745	0.0:0.0:0.5907:0.4093	.	678	Q9BXX3	AN30A_HUMAN	N	622	ENSP00000354432:K622N;ENSP00000363792:K622N	ENSP00000354432:K622N	K	+	3	2	ANKRD30A	37494059	0.070000	0.21116	0.001000	0.08648	0.021000	0.10359	0.834000	0.27518	-0.020000	0.14032	0.391000	0.25812	AAG		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37454053	G	T	37454053	3	4	12	1	0	0	0	0	1	0	0	0	658	991	35	2	1936	2	ANKRD30A	10	37454053	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	15647435	37454053	98080694	87	1497										
MYST4	23522	hgsc.bcm.edu	37	chr10	76789171	76789171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cgatacagagttcaaagaggGaaacccagcaaccatggaaa	10	9	1	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:76789171G>A	ENST00000287239.4	+	18	5078	c.4589G>A	c.(4588-4590)gGa>gAa	p.G1530E	KAT6B_ENST00000372714.1_Missense_Mutation_p.G1238E|KAT6B_ENST00000372724.1_Missense_Mutation_p.G1238E|KAT6B_ENST00000372711.1_Missense_Mutation_p.G1347E|KAT6B_ENST00000372725.1_Missense_Mutation_p.G1238E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1530					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G1530E(1)									TTCAAAGAGGGAAACCCAGCA	0.537																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											114	114	114					10																	76789171		2203	4300	6503	76459177	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4589G>A	10.37:g.76789171G>A	ENSP00000287239:p.Gly1530Glu		76459177	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	3.070	-0.191418	0.06299	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	4.77	-0.229	0.13094	.	0.620256	0.14149	N	0.338149	T	0.30727	0.0774	N	0.00413	-1.525	0.20196	N	0.999928	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.43621	-0.9380	10	0.02654	T	1	1.0449	5.8686	0.18791	0.2365:0.4408:0.3227:0.0	.	1347;1238;1530	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	E	1238;1238;1530;1238;1347	ENSP00000361810:G1238E;ENSP00000361809:G1238E;ENSP00000287239:G1530E;ENSP00000361799:G1238E;ENSP00000361796:G1347E	ENSP00000287239:G1530E	G	+	2	0	KAT6B	76459177	0.983000	0.35010	0.106000	0.21319	0.902000	0.53008	2.263000	0.43293	0.057000	0.16193	0.563000	0.77884	GGA		0.537	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76789171	G	A	76789171	3	1	12	1	0	0	0	0	1	0	0	0	10135	1174	41	3	4651	3	MYST4	10	76789171	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	39335118	76789171	58745576	88	1498										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720709	89720709	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	accaggaccagaggaaacctCagaaaaagtagaaaatggaa	10	7	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:89720709C>T	ENST00000371953.3	+	8	2217	c.860C>T	c.(859-861)tCa>tTa	p.S287L	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	287	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.S287fs*1(1)|p.S287*(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GAGGAAACCTCAGAAAAAGTA	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Deletion - Frameshift(11)|Deletion - In frame(2)|Unknown(2)|Substitution - Nonsense(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											53	57	56					10																	89720709		2201	4295	6496	89710689	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.860C>T	10.37:g.89720709C>T	ENSP00000361021:p.Ser287Leu		89710689	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476338	0.63737	.	.	ENSG00000171862	ENST00000371953	D	0.84944	-1.92	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.313296	0.30602	N	0.009272	T	0.80507	0.4636	L	0.40543	1.245	0.47123	D	0.999321	B	0.06786	0.001	B	0.08055	0.003	T	0.74636	-0.3599	9	.	.	.	-7.973	18.5632	0.91108	0.0:1.0:0.0:0.0	.	287	P60484	PTEN_HUMAN	L	287	ENSP00000361021:S287L	.	S	+	2	0	PTEN	89710689	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.976000	0.49289	2.399000	0.81585	0.591000	0.81541	TCA		0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720709	C	T	89720709	3	4	12	1	0	0	0	0	1	0	0	0	12772	838	29	3	890	3	PTEN	10	89720709	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	12931538	89720709	45814038	89	1499										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720769	89720769	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cgatagcatttgcagtatagAgcgtgcagataatgacaagg	12	6	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:89720769A>G	ENST00000371953.3	+	8	2277	c.920A>G	c.(919-921)gAg>gGg	p.E307G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	307	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TGCAGTATAGAGCGTGCAGAT	0.348		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											104	101	102					10																	89720769		2203	4298	6501	89710749	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.920A>G	10.37:g.89720769A>G	ENSP00000361021:p.Glu307Gly		89710749	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.415677	0.42817	.	.	ENSG00000171862	ENST00000371953	D	0.94758	-3.51	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.181618	0.46758	D	0.000280	D	0.89121	0.6625	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	D	0.84991	0.0894	9	.	.	.	-11.7975	14.9228	0.70854	1.0:0.0:0.0:0.0	.	307	P60484	PTEN_HUMAN	G	307	ENSP00000361021:E307G	.	E	+	2	0	PTEN	89710749	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	8.050000	0.89445	1.942000	0.56320	0.482000	0.46254	GAG		0.348	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720769	A	G	89720769	3	3	12	1	0	0	0	0	1	0	0	0	12772	304	11	4	950	4	PTEN	10	89720769	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	60	89720769	45813978	90	1500										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105990458	105990458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aggggatgttagttgccatgAcgcccacaattccattacta	9	10	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:105990458A>G	ENST00000357060.3	-	2	324	c.209T>C	c.(208-210)gTc>gCc	p.V70A	WDR96_ENST00000428666.1_Missense_Mutation_p.V70A|WDR96_ENST00000369720.1_5'UTR|WDR96_ENST00000369719.1_5'UTR|WDR96_ENST00000278064.2_5'UTR	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGTTGCCATGACGCCCACAAT	0.413																																																0			10											144	132	136					10																	105990458		2203	4300	6503	105980448	SO:0001583	missense	80217																														ENST00000357060.3:c.209T>C	10.37:g.105990458A>G	ENSP00000349568:p.Val70Ala		105980448		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	A	5.632	0.301352	0.10678	.	.	ENSG00000197748	ENST00000357060;ENST00000428666	T;T	0.17528	2.27;2.27	4.83	3.7	0.42460	.	0.291378	0.18676	N	0.134302	T	0.05547	0.0146	N	0.03324	-0.35	0.33001	D	0.526233	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.13407	0.003;0.009;0.007	T	0.23332	-1.0191	10	0.13108	T	0.6	.	3.074	0.06240	0.5736:0.0:0.4264:0.0	.	70;70;70	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	A	70	ENSP00000349568:V70A;ENSP00000400289:V70A	ENSP00000349568:V70A	V	-	2	0	WDR96	105980448	1.000000	0.71417	0.998000	0.56505	0.928000	0.56348	6.531000	0.73820	1.813000	0.52934	0.402000	0.26972	GTC		0.413	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	105990458	A	G	105990458	3	3	12	1	0	0	0	0	1	0	0	0	1622	275	10	4	4936	4	C10orf79	10	105990458	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	16269689	105990458	29544289	91	1501										
PDZD8	118987	hgsc.bcm.edu	37	chr10	119044524	119044524	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttttgacacttgtgctgggtCtgttatctcagaagttttta	9	6	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:119044524C>A	ENST00000334464.5	-	5	1959	c.1720G>T	c.(1720-1722)Gac>Tac	p.D574Y	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	574	Pro-rich.				cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TGTGCTGGGTCTGTTATCTCA	0.468																																																0			10											130	131	131					10																	119044524		2203	4300	6503	119034514	SO:0001583	missense	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1720G>T	10.37:g.119044524C>A	ENSP00000334642:p.Asp574Tyr		119034514	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208659	0.79240	.	.	ENSG00000165650	ENST00000334464	D	0.89485	-2.52	5.93	5.93	0.95920	.	0.154165	0.56097	D	0.000023	D	0.88055	0.6334	L	0.27053	0.805	0.36314	D	0.857848	P	0.47191	0.891	P	0.51918	0.684	D	0.91103	0.4916	10	0.72032	D	0.01	-10.0189	15.789	0.78338	0.0:0.8646:0.1354:0.0	.	574	Q8NEN9	PDZD8_HUMAN	Y	574	ENSP00000334642:D574Y	ENSP00000334642:D574Y	D	-	1	0	PDZD8	119034514	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	3.569000	0.53827	2.814000	0.96858	0.591000	0.81541	GAC		0.468	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119044524	C	A	119044524	3	1	12	1	0	0	0	0	1	0	0	0	11736	913	32	2	1748	2	PDZD8	10	119044524	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	13054066	119044524	16490223	92	1502										
BRSK2	9024	hgsc.bcm.edu	37	chr11	1466584	1466584	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cgcaaggtgcagatccgctcGctgcccagcctggaggacat	13	14	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:1466584G>A	ENST00000528841.1	+	10	1257	c.873G>A	c.(871-873)tcG>tcA	p.S291S	BRSK2_ENST00000308219.9_Silent_p.S291S|BRSK2_ENST00000531197.1_Silent_p.S291S|BRSK2_ENST00000528710.1_Silent_p.S231S|BRSK2_ENST00000308230.5_Silent_p.S291S|BRSK2_ENST00000526678.1_Silent_p.S291S|BRSK2_ENST00000544817.1_De_novo_Start_InFrame|BRSK2_ENST00000382179.1_Silent_p.S337S			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	291					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		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)		AGATCCGCTCGCTGCCCAGCC	0.652																																																0			11											35	45	41					11																	1466584		2155	4255	6410	1423160	SO:0001819	synonymous_variant	9024			AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.873G>A	11.37:g.1466584G>A			1423160	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Silent	SNP	ENST00000528841.1	37	CCDS58107.1																																																																																				0.652	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		A	1466584	G	A	1466584	2	1	12	1	0	0	0	0	0	0	0	1	1527	1074	38	1		1	BRSK2	11	1466584	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10		1466584	133539932	93	1503										
STIM1	6786	hgsc.bcm.edu	37	chr11	4095835	4095835	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ttgctaagcaggaagcccagCggctgaaggagctgcgggag	17	9	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:4095835C>T	ENST00000300737.4	+	7	1464	c.895C>T	c.(895-897)Cgg>Tgg	p.R299W	STIM1_ENST00000533977.1_Missense_Mutation_p.R126W|STIM1_ENST00000527651.1_Missense_Mutation_p.R299W	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	299	Glu-rich.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		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)		GGAAGCCCAGCGGCTGAAGGA	0.572																																																0			11											49	42	45					11																	4095835		2201	4298	6499	4052411	SO:0001583	missense	6786			BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.895C>T	11.37:g.4095835C>T	ENSP00000300737:p.Arg299Trp		4052411	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	37	CCDS7749.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089231	0.76756	.	.	ENSG00000167323	ENST00000300737;ENST00000527651;ENST00000533977	T;D;T	0.81659	-0.51;-1.52;-0.59	5.26	3.36	0.38483	.	0.057916	0.64402	D	0.000001	D	0.88738	0.6518	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.88996	0.3418	10	0.87932	D	0	-21.7865	13.1828	0.59663	0.2906:0.7094:0.0:0.0	.	299;299	E9PQJ4;Q13586	.;STIM1_HUMAN	W	299;299;126	ENSP00000300737:R299W;ENSP00000436208:R299W;ENSP00000434767:R126W	ENSP00000300737:R299W	R	+	1	2	STIM1	4052411	0.770000	0.28543	1.000000	0.80357	0.983000	0.72400	0.960000	0.29253	0.575000	0.29434	0.655000	0.94253	CGG		0.572	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		T	4095835	C	T	4095835	3	4	12	1	0	0	0	0	1	0	0	0	15322	759	27	1	921	1	STIM1	11	4095835	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	2629251	4095835	130910681	94	1504										
OR2AG2	338755	hgsc.bcm.edu	37	chr11	6789691	6789691	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tcccaggacacacagaaaggGaggtgcatagtgtacatggt	13	8	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:6789691G>A	ENST00000338569.2	-	1	595	c.498C>T	c.(496-498)ctC>ctT	p.L166L		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CACAGAAAGGGAGGTGCATAG	0.507																																																0			11											118	96	103					11																	6789691		2201	4296	6497	6746267	SO:0001819	synonymous_variant	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"GPCR / Class A : Olfactory receptors"	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.498C>T	11.37:g.6789691G>A			6746267		Silent	SNP	ENST00000338569.2	37	CCDS31413.1																																																																																				0.507	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		A	6789691	G	A	6789691	2	1	12	1	0	0	0	0	0	0	0	1	11016	1161	41	3		3	OR2AG2	11	6789691	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	2693856	6789691	128216825	95	1505										
WT1	7490	hgsc.bcm.edu	37	chr11	32421544	32421544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tattctgtattgggctccgcAgaggatgggcgttgtgtggt	16	6	1	1	rs142059681	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:32421544A>G	ENST00000379079.2	-	6	685	c.412T>C	c.(412-414)Tgc>Cgc	p.C138R	WT1_ENST00000530998.1_Missense_Mutation_p.C121R|WT1_ENST00000332351.3_Missense_Mutation_p.C350R|WT1_ENST00000448076.3_Missense_Mutation_p.C350R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	282					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C282R(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TGGGCTCCGCAGAGGATGGGC	0.577			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11						A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	1,4403	2.1+/-5.4	0,1,2201	299	249	266		997,412,361,1048,1048	6	1	11	dbSNP_134	266	7,8591	5.0+/-18.6	0,7,4292	yes	missense,missense,missense,missense,missense	WT1	NM_000378.4,NM_001198551.1,NM_001198552.1,NM_024424.3,NM_024426.4	180,180,180,180,180	0,8,6493	GG,GA,AA		0.0814,0.0227,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	333/498,138/303,121/289,350/515,350/518	32421544	8,12994	2202	4299	6501	32378120	SO:0001583	missense	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.412T>C	11.37:g.32421544A>G	ENSP00000368370:p.Cys138Arg		32378120	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	37	CCDS55751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.99|16.99	3.275255|3.275255	0.59649|0.59649	2.27E-4|2.27E-4	8.14E-4|8.14E-4	ENSG00000184937|ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527775|ENST00000527882	D;D;D;D;D;D|D	0.85955|0.87650	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05|-2.28	5.98|5.98	5.98|5.98	0.97165|0.97165	Wilm&apos (1);s tumour protein, N-terminal (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	D|D	0.89801|0.89801	0.6820|0.6820	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.76494|.	0.999;0.998;0.999;0.993;0.984|.	D;D;D;D;D|.	0.74348|.	0.977;0.975;0.983;0.942;0.926|.	D|D	0.88980|0.88980	0.3407|0.3407	10|7	0.87932|0.41790	D|T	0|0.15	.|.	16.4781|16.4781	0.84144|0.84144	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	338;282;355;121;138|.	P19544-8;P19544;P19544-7;B3KSA5;P19544-6|.	.;WT1_HUMAN;.;.;.|.	R|P	138;350;121;333;350;101|40	ENSP00000368370:C138R;ENSP00000331327:C350R;ENSP00000435307:C121R;ENSP00000415516:C333R;ENSP00000413452:C350R;ENSP00000435351:C101R|ENSP00000435624:L40P	ENSP00000331327:C350R|ENSP00000435624:L40P	C|L	-|-	1|2	0|0	WT1|WT1	32378120|32378120	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.165000|0.165000	0.22458|0.22458	3.481000|3.481000	0.53179|0.53179	2.288000|2.288000	0.76882|0.76882	0.528000|0.528000	0.53228|0.53228	TGC|CTG		0.577	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		G	32421544	A	G	32421544	3	3	12	1	0	0	0	0	1	0	0	0	17448	188	7	4	525	4	WT1	11	32421544	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	25631853	32421544	102584972	96	1506										
EIF3M	10480	hgsc.bcm.edu	37	chr11	32610203	32610203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cctggaaccagacaagcaagAagctttgattgaaagcctat	9	9	0	4			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:32610203A>G	ENST00000531120.1	+	3	302	c.239A>G	c.(238-240)gAa>gGa	p.E80G	EIF3M_ENST00000524896.1_Intron|EIF3M_ENST00000532054.1_3'UTR	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M									p.E80G(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					GACAAGCAAGAAGCTTTGATT	0.418																																																1	Substitution - Missense(1)	breast(1)	11											202	182	189					11																	32610203		2202	4299	6501	32566779	SO:0001583	missense	10480			AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"transport and golgi organization 7 homolog (Drosophila)"	609641	"PCI domain containing 1 (herpesvirus entry mediator)"	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.239A>G	11.37:g.32610203A>G	ENSP00000436049:p.Glu80Gly		32566779		Missense_Mutation	SNP	ENST00000531120.1	37	CCDS7880.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935042	0.73442	.	.	ENSG00000149100	ENST00000531120;ENST00000323213;ENST00000533439	T;T	0.39592	1.07;1.07	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.44912	0.1316	M	0.71036	2.16	0.80722	D	1	B	0.14438	0.01	B	0.08055	0.003	T	0.31833	-0.9929	10	0.25751	T	0.34	-4.5193	16.5885	0.84745	1.0:0.0:0.0:0.0	.	80	Q7L2H7	EIF3M_HUMAN	G	80;17;17	ENSP00000436049:E80G;ENSP00000319910:E17G	ENSP00000319910:E17G	E	+	2	0	EIF3M	32566779	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.962000	0.93254	2.317000	0.78254	0.460000	0.39030	GAA		0.418	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360		G	32610203	A	G	32610203	3	3	12	1	0	0	0	0	1	0	0	0	5036	246	9	4	249	4	EIF3M	11	32610203	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	188659	32610203	102396313	97	1507										
OR4S1	256148	hgsc.bcm.edu	37	chr11	48328541	48328541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	catgccccccatgttcatgtAcattcgtccctccaccaccc	4	20	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:48328541A>G	ENST00000319988.1	+	1	767	c.767A>G	c.(766-768)tAc>tGc	p.Y256C		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						ATGTTCATGTACATTCGTCCC	0.488																																																0			11											241	218	226					11																	48328541		2201	4298	6499	48285117	SO:0001583	missense	256148			AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"GPCR / Class A : Olfactory receptors"	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.767A>G	11.37:g.48328541A>G	ENSP00000321447:p.Tyr256Cys		48285117	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.249825	0.59212	.	.	ENSG00000176555	ENST00000319988	T	0.00295	8.25	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01092	0.0036	H	0.95679	3.705	0.24266	N	0.995264	D	0.89917	1.0	D	0.97110	1.0	T	0.24154	-1.0168	9	0.87932	D	0	.	12.9764	0.58540	1.0:0.0:0.0:0.0	.	256	Q8NGB4	OR4S1_HUMAN	C	256	ENSP00000321447:Y256C	ENSP00000321447:Y256C	Y	+	2	0	OR4S1	48285117	1.000000	0.71417	0.543000	0.28128	0.888000	0.51559	6.013000	0.70776	2.020000	0.59435	0.533000	0.62120	TAC		0.488	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		G	48328541	A	G	48328541	3	3	12	1	0	0	0	0	1	0	0	0	11113	391	14	4	769	4	OR4S1	11	48328541	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	15718338	48328541	86677975	98	1508										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58189992	58189992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agattactgtcccatagaagAcggagactgcagtgaagtga	12	7	0	6			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:58189992A>G	ENST00000302581.2	-	1	794	c.743T>C	c.(742-744)gTc>gCc	p.V248A		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CCCATAGAAGACGGAGACTGC	0.468																																																0			11											126	115	119					11																	58189992		2201	4295	6496	57946568	SO:0001583	missense	390190			AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.743T>C	11.37:g.58189992A>G	ENSP00000303076:p.Val248Ala		57946568	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	A	6.289	0.421467	0.11928	.	.	ENSG00000172365	ENST00000302581	T	0.00137	8.68	3.73	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36167	U	0.002757	T	0.00144	0.0004	L	0.46157	1.445	0.09310	N	1	B	0.12013	0.005	B	0.22601	0.04	T	0.33624	-0.9861	10	0.87932	D	0	-5.8228	6.7921	0.23705	0.8895:0.0:0.1105:0.0	.	248	Q96R09	OR5B2_HUMAN	A	248	ENSP00000303076:V248A	ENSP00000303076:V248A	V	-	2	0	OR5B2	57946568	0.058000	0.20735	0.036000	0.18154	0.184000	0.23303	3.499000	0.53310	1.703000	0.51240	0.477000	0.44152	GTC		0.468	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		G	58189992	A	G	58189992	3	3	12	1	0	0	0	0	1	0	0	0	11181	275	10	4	190	4	OR5B2	11	58189992	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	9861451	58189992	76816524	99	1509										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825623	95825623	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tgcatgaggacatctaggtgCccaccctgggctgaggggcc	15	12	1	2	rs373817562		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:95825623C>A	ENST00000524717.1	-	2	2856	c.1572G>T	c.(1570-1572)ggG>ggT	p.G524G		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	524					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CATCTAGGTGCCCACCCTGGG	0.597			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	0			11											37	40	39					11																	95825623		1971	4144	6115	95465271	SO:0001819	synonymous_variant	84441			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1572G>T	11.37:g.95825623C>A			95465271	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																				0.597	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			A	95825623	C	A	95825623	2	1	12	1	0	0	0	0	0	0	0	1	9236	726	26	2		2	MAML2	11	95825623	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	37635631	95825623	39180893	100	1510										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	12	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10		25398284	108453611	101	1511										
ABCD2	225	hgsc.bcm.edu	37	chr12	40013006	40013006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gatgaaagtccgaggcttctTttccacaatgcttttcacga	8	10	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:40013006T>G	ENST00000308666.3	-	1	547	c.412A>C	c.(412-414)Aag>Cag	p.K138Q		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	138	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Interaction with PEX19.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CGAGGCTTCTTTTCCACAATG	0.438																																																0			12											92	91	91					12																	40013006		2203	4300	6503	38299273	SO:0001583	missense	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.412A>C	12.37:g.40013006T>G	ENSP00000310688:p.Lys138Gln		38299273	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.383031	0.61845	.	.	ENSG00000173208	ENST00000308666	D	0.91843	-2.92	4.58	4.58	0.56647	ABC transporter, N-terminal (1);ABC transporter, integral membrane type 1 (1);	0.000000	0.85682	D	0.000000	D	0.94876	0.8344	M	0.67625	2.065	0.58432	D	0.999993	D	0.67145	0.996	D	0.73380	0.98	D	0.94565	0.7766	9	.	.	.	-10.0656	14.1471	0.65357	0.0:0.0:0.0:1.0	.	138	Q9UBJ2	ABCD2_HUMAN	Q	138	ENSP00000310688:K138Q	.	K	-	1	0	ABCD2	38299273	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.384000	0.79751	1.927000	0.55829	0.460000	0.39030	AAG		0.438	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		G	40013006	T	G	40013006	3	3	12	1	0	0	0	0	1	0	0	0	61	1850	64	4	1850	4	ABCD2	12	40013006	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	14614722	40013006	93838889	102	1512										
DDN	23109	hgsc.bcm.edu	37	chr12	49391847	49391847	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agatccgaggatccagcctcTtctttgtgcgccctccgtct	9	15	3	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:49391847T>C	ENST00000421952.2	-	2	833	c.812A>G	c.(811-813)aAg>aGg	p.K271R	RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	271						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						ATCCAGCCTCTTCTTTGTGCG	0.652																																																0			12											50	58	55					12																	49391847		2203	4297	6500	47678114	SO:0001583	missense	23109			AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.812A>G	12.37:g.49391847T>C	ENSP00000390590:p.Lys271Arg		47678114		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	17.46	3.396422	0.62177	.	.	ENSG00000181418	ENST00000421952	T	0.57273	0.41	3.89	3.89	0.44902	.	0.000000	0.48286	D	0.000198	T	0.34164	0.0888	L	0.27053	0.805	0.32752	N	0.506301	P	0.46142	0.873	B	0.40009	0.316	T	0.46789	-0.9166	10	0.38643	T	0.18	-19.3521	6.0274	0.19662	0.0:0.1126:0.0:0.8874	.	271	O94850	DEND_HUMAN	R	271	ENSP00000390590:K271R	ENSP00000390590:K271R	K	-	2	0	DDN	47678114	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.354000	0.44098	2.004000	0.58718	0.459000	0.35465	AAG		0.652	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			C	49391847	T	C	49391847	3	2	12	1	0	0	0	0	1	0	0	0	4339	1609	56	4	1327	4	DDN	12	49391847	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	9378841	49391847	84460048	103	1513										
DCN	1634	hgsc.bcm.edu	37	chr12	91550854	91550854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tggagaatcttctatcacctTgaggaatgctggtgatattg	11	6	3	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:91550854T>C	ENST00000052754.5	-	5	1151	c.650A>G	c.(649-651)cAa>cGa	p.Q217R	DCN_ENST00000547568.2_Intron|DCN_ENST00000303320.3_Intron|DCN_ENST00000420120.2_Missense_Mutation_p.Q108R|DCN_ENST00000456569.2_Intron|DCN_ENST00000228329.5_Missense_Mutation_p.Q108R|DCN_ENST00000393155.1_Missense_Mutation_p.Q217R|DCN_ENST00000441303.2_Intron|DCN_ENST00000552962.1_Missense_Mutation_p.Q217R|DCN_ENST00000425043.1_Intron	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	217					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						TCTATCACCTTGAGGAATGCT	0.368																																																0			12											103	99	100					12																	91550854		2203	4300	6503	90074985	SO:0001583	missense	1634			AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.650A>G	12.37:g.91550854T>C	ENSP00000052754:p.Gln217Arg		90074985	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Missense_Mutation	SNP	ENST00000052754.5	37	CCDS9039.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002247	0.35320	.	.	ENSG00000011465	ENST00000052754;ENST00000228329;ENST00000393155;ENST00000552962;ENST00000420120	T;T;T;T;T	0.04317	3.65;3.65;3.65;3.65;3.65	5.69	0.295	0.15752	.	0.140299	0.64402	D	0.000006	T	0.02848	0.0085	N	0.11698	0.16	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.48175	-0.9058	10	0.56958	D	0.05	.	9.0489	0.36363	0.0:0.0627:0.3505:0.5868	.	217;108	P07585;P07585-2	PGS2_HUMAN;.	R	217;108;217;217;108	ENSP00000052754:Q217R;ENSP00000228329:Q108R;ENSP00000376862:Q217R;ENSP00000447654:Q217R;ENSP00000413723:Q108R	ENSP00000052754:Q217R	Q	-	2	0	DCN	90074985	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	1.519000	0.35888	0.061000	0.16311	0.477000	0.44152	CAA		0.368	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		C	91550854	T	C	91550854	3	2	12	1	0	0	0	0	1	0	0	0	4303	1812	63	4	445	4	DCN	12	91550854	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	42159007	91550854	42301041	104	1514										
CUX2	23316	hgsc.bcm.edu	37	chr12	111729259	111729259	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gaggcggcacgcagcctagaCgacagactgcagccccccag	13	16	0	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:111729259C>T	ENST00000261726.6	+	5	493	c.339C>T	c.(337-339)gaC>gaT	p.D113D		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	113					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						GCAGCCTAGACGACAGACTGC	0.637																																																0			12											56	63	61					12																	111729259		1991	4155	6146	110213642	SO:0001819	synonymous_variant	23316			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.339C>T	12.37:g.111729259C>T			110213642	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																				0.637	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		T	111729259	C	T	111729259	2	4	12	1	0	0	0	0	0	0	0	1	4071	535	19	1		1	CUX2	12	111729259	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	20178405	111729259	22122636	105	1515										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123818625	123818625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgcatatgtaattgcctcaAgctgcaatgctgataaccag	8	10	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:123818625A>G	ENST00000602398.1	-	7	1011	c.884T>C	c.(883-885)cTt>cCt	p.L295P	SBNO1_ENST00000420886.2_Missense_Mutation_p.L295P|SBNO1_ENST00000267176.4_Missense_Mutation_p.L294P|SBNO1_ENST00000602750.1_Missense_Mutation_p.L294P			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	295					regulation of transcription, DNA-templated (GO:0006355)			p.L294H(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		AATTGCCTCAAGCTGCAATGC	0.348																																																1	Substitution - Missense(1)	kidney(1)	12											67	62	64					12																	123818625		2203	4300	6503	122384578	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.884T>C	12.37:g.123818625A>G	ENSP00000473665:p.Leu295Pro		122384578	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533445	0.85812	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.94376	-3.41;-3.41	5.73	5.73	0.89815	Helicase/UvrB domain (1);	0.000000	0.64402	D	0.000001	D	0.97760	0.9265	H	0.95328	3.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.998	D	0.98997	1.0810	10	0.87932	D	0	-20.3217	16.0337	0.80603	1.0:0.0:0.0:0.0	.	295;294;293	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	P	295;294;294	ENSP00000387361:L295P;ENSP00000267176:L294P	ENSP00000267176:L294P	L	-	2	0	SBNO1	122384578	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	9.228000	0.95250	2.189000	0.69895	0.528000	0.53228	CTT		0.348	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		G	123818625	A	G	123818625	3	3	12	1	0	0	0	0	1	0	0	0	13899	72	3	4	3401	4	SBNO1	12	123818625	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	12089366	123818625	10033270	106	1516										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125834830	125834830	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aatctagtccgggaaggggaCacggccacctttttggtctc	12	11	2	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:125834830C>T	ENST00000299308.3	+	2	893	c.885C>T	c.(883-885)gaC>gaT	p.D295D		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	295						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		GGGAAGGGGACACGGCCACCT	0.537																																																0			12											199	190	193					12																	125834830		1970	4138	6108	124400783	SO:0001819	synonymous_variant	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.885C>T	12.37:g.125834830C>T			124400783	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																				0.537	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	125834830	C	T	125834830	2	4	12	1	0	0	0	0	0	0	0	1	16085	477	17	3		3	TMEM132B	12	125834830	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	2016205	125834830	8017065	107	1517										
PGAM5	192111	hgsc.bcm.edu	37	chr12	133294357	133294357	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cccatcgagccagacccgccCgtgtctcattggaagccgga	11	16	1	1	rs371236067		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:133294357C>T	ENST00000498926.2	+	4	616	c.558C>T	c.(556-558)ccC>ccT	p.P186P	PGAM5_ENST00000543955.1_Silent_p.P37P|PGAM5_ENST00000454808.2_Silent_p.P37P|PGAM5_ENST00000317555.2_Silent_p.P186P|PXMP2_ENST00000545677.1_3'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	186					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		CAGACCCGCCCGTGTCTCATT	0.662																																																0			12						C	,,	0,4350		0,0,2175	21	27	25		558,558,558	-7.6	0.2	12		25	1,8559		0,1,4279	no	coding-synonymous,coding-synonymous,coding-synonymous	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	,,	0,1,6454	TT,TC,CC		0.0117,0.0,0.0077	,,	186/290,186/289,186/256	133294357	1,12909	2175	4280	6455	131804430	SO:0001819	synonymous_variant	192111			BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.558C>T	12.37:g.133294357C>T			131804430	A9LN06|C9IZY7|Q96JB0	Silent	SNP	ENST00000498926.2	37	CCDS53845.1																																																																																				0.662	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		T	133294357	C	T	133294357	2	4	12	1	0	0	0	0	0	0	0	1	11807	639	23	1		1	PGAM5	12	133294357	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	7459527	133294357	557538	108	1518										
RB1	5925	hgsc.bcm.edu	37	chr13	48955572	48955572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aatcatggaatcccttgcatGgctctcagtaagtagctaaa	8	9	2	0	rs587778863		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:48955572G>T	ENST00000267163.4	+	17	1826	c.1688G>T	c.(1687-1689)tGg>tTg	p.W563L		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	563	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCCCTTGCATGGCTCTCAGTA	0.343		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13	GRCh37	CM004729|CM040263	RB1	M							67	63	64					13																	48955572		2203	4300	6503	47853573	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1688G>T	13.37:g.48955572G>T	ENSP00000267163:p.Trp563Leu		47853573	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795609	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.96587	-4.06	5.34	5.34	0.76211	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	D	0.98308	0.9439	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99293	1.0899	10	0.87932	D	0	.	19.0281	0.92941	0.0:0.0:1.0:0.0	.	563	P06400	RB_HUMAN	L	542;563	ENSP00000267163:W563L	ENSP00000267163:W563L	W	+	2	0	RB1	47853573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.488000	0.83962	0.650000	0.86243	TGG		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48955572	G	T	48955572	3	4	12	1	0	0	0	0	1	0	0	0	13135	1357	47	2	1754	2	RB1	13	48955572	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10		48955572	66214306	109	1519										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61986435	61986435	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgtacttttctttctcttcTcggtccagctgagtagaaac	7	11	3	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:61986435T>C	ENST00000409186.1	-	5	3902	c.1797A>G	c.(1795-1797)cgA>cgG	p.R599R	PCDH20_ENST00000409204.4_Silent_p.R599R			Q8N6Y1	PCD20_HUMAN	protocadherin 20	599	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		CTTTCTCTTCTCGGTCCAGCT	0.453																																																0			13											115	112	113					13																	61986435		2203	4300	6503	60884436	SO:0001819	synonymous_variant	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1797A>G	13.37:g.61986435T>C			60884436	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	37	CCDS9442.2																																																																																				0.453	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		C	61986435	T	C	61986435	2	2	12	1	0	0	0	0	0	0	0	1	11546	1538	54	4		4	PCDH20	13	61986435	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	13030863	61986435	53183443	110	1520										
FAM155A	728215	hgsc.bcm.edu	37	chr13	107822990	107822990	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tgagtctgctgttgcacagtCttgttgctgatgacactgtg	12	8	2	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:107822990C>G	ENST00000375915.2	-	3	1370	c.1232G>C	c.(1231-1233)aGa>aCa	p.R411T		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	411						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						GTTGCACAGTCTTGTTGCTGA	0.493																																																0			13											272	189	217					13																	107822990		2203	4300	6503	106620991	SO:0001583	missense	728215			L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1232G>C	13.37:g.107822990C>G	ENSP00000365080:p.Arg411Thr		106620991	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	37	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865952	0.91511	.	.	ENSG00000204442	ENST00000375915	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.76364	0.3977	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77305	-0.2637	9	0.87932	D	0	.	19.0063	0.92852	0.0:1.0:0.0:0.0	.	411	B1AL88	F155A_HUMAN	T	411	.	ENSP00000365080:R411T	R	-	2	0	FAM155A	106620991	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	7.135000	0.77276	2.723000	0.93209	0.638000	0.83543	AGA		0.493	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		G	107822990	C	G	107822990	3	3	12	1	0	0	0	0	1	0	0	0	5481	913	32	5	148	5	FAM155A	13	107822990	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	45836555	107822990	7346888	111	1521										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111896589	111896589	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atttaatgggaaatctagaaGaaatatgttctttccagcaa	7	5	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:111896589G>A	ENST00000375741.2	+	9	1211	c.961G>A	c.(961-963)Gaa>Aaa	p.E321K	ARHGEF7_ENST00000375739.2_Missense_Mutation_p.E271K|ARHGEF7_ENST00000375723.1_Missense_Mutation_p.E143K|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.E143K|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.E65K|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.E218K|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.E143K|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.E143K|ARHGEF7_ENST00000317133.5_Missense_Mutation_p.E300K|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.E228K	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	321	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	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)			AAATCTAGAAGAAATATGTTC	0.308																																																0			13											62	66	65					13																	111896589		2202	4294	6496	110694590	SO:0001583	missense	8874			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.961G>A	13.37:g.111896589G>A	ENSP00000364893:p.Glu321Lys		110694590	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	37	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555991	0.86231	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.04	5.04	0.67666	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.66297	2.02	0.80722	D	1	B;P;B;D;D;D	0.69078	0.348;0.904;0.348;0.973;0.994;0.997	P;P;P;P;D;D	0.75484	0.564;0.861;0.564;0.908;0.986;0.968	T	0.43988	-0.9357	10	0.56958	D	0.05	.	18.0048	0.89207	0.0:0.0:1.0:0.0	.	65;218;65;271;321;300	E9PDQ5;B7Z6G2;B7Z344;Q14155-2;Q14155;Q14155-3	.;.;.;.;ARHG7_HUMAN;.	K	300;321;271;228;298;143;143;143;143;218;143;65	ENSP00000325994:E300K;ENSP00000364893:E321K;ENSP00000364891:E271K;ENSP00000359657:E228K;ENSP00000418067:E143K;ENSP00000218789:E143K;ENSP00000364888:E143K;ENSP00000397068:E143K;ENSP00000364889:E218K;ENSP00000364875:E143K;ENSP00000417596:E65K	ENSP00000218789:E143K	E	+	1	0	ARHGEF7	110694590	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.084000	0.89516	2.325000	0.78763	0.563000	0.77884	GAA		0.308	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		A	111896589	G	A	111896589	3	1	12	1	0	0	0	0	1	0	0	0	911	943	33	3	995	3	ARHGEF7	13	111896589	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	4073599	111896589	3273289	112	1522										
EXD2	55218	hgsc.bcm.edu	37	chr14	69704380	69704380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atgtgctgctgctctgcaccTcctgccatgccatttccaac	7	16	1	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr14:69704380T>C	ENST00000409018.3	+	8	1509	c.1381T>C	c.(1381-1383)Tcc>Ccc	p.S461P	EXD2_ENST00000409949.1_Missense_Mutation_p.S336P|EXD2_ENST00000449989.1_Missense_Mutation_p.S336P|EXD2_ENST00000409242.1_Missense_Mutation_p.S336P|EXD2_ENST00000312994.5_Missense_Mutation_p.S461P|RP11-363J20.2_ENST00000556316.1_lincRNA|EXD2_ENST00000409675.1_Missense_Mutation_p.S336P|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409014.1_Missense_Mutation_p.S336P	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	461							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						GCTCTGCACCTCCTGCCATGC	0.567																																																0			14											64	52	56					14																	69704380		2203	4300	6503	68774133	SO:0001583	missense	55218			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.1381T>C	14.37:g.69704380T>C	ENSP00000387331:p.Ser461Pro		68774133	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	37	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.683563	0.47991	.	.	ENSG00000081177	ENST00000409018;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000449989	T;T;T;T;T;T;T	0.64085	0.32;-0.08;-0.08;-0.08;-0.08;0.32;-0.08	5.24	5.24	0.73138	.	0.281373	0.40144	N	0.001161	T	0.48447	0.1500	L	0.27053	0.805	0.53005	D	0.999966	B;B;B	0.20459	0.045;0.004;0.004	B;B;B	0.22386	0.039;0.005;0.005	T	0.42275	-0.9461	10	0.30078	T	0.28	-14.6992	11.9225	0.52799	0.0:0.0:0.1451:0.8549	.	461;336;336	G5E947;B3KP95;Q9NVH0	.;.;EXD2_HUMAN	P	461;336;336;336;336;461;336	ENSP00000387331:S461P;ENSP00000386915:S336P;ENSP00000386762:S336P;ENSP00000386632:S336P;ENSP00000386839:S336P;ENSP00000313140:S461P;ENSP00000392177:S336P	ENSP00000313140:S461P	S	+	1	0	EXD2	68774133	0.985000	0.35326	1.000000	0.80357	0.996000	0.88848	1.557000	0.36299	2.197000	0.70478	0.455000	0.32223	TCC		0.567	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			C	69704380	T	C	69704380	3	2	12	1	0	0	0	0	1	0	0	0	5311	1551	54	4	1028	4	EXD2	14	69704380	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10		69704380	37645160	113	1523										
MEIS2	4212	hgsc.bcm.edu	37	chr15	37329088	37329088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaatgcctcttttcttctggCgttttttgtccttatccgga	7	10	3	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:37329088C>T	ENST00000561208.1	-	8	1245	c.827G>A	c.(826-828)cGc>cAc	p.R276H	MEIS2_ENST00000382766.2_Missense_Mutation_p.R276H|MEIS2_ENST00000397624.3_Missense_Mutation_p.R188H|MEIS2_ENST00000397620.2_Missense_Mutation_p.R188H|MEIS2_ENST00000444725.1_Missense_Mutation_p.R276H|MEIS2_ENST00000340545.5_Missense_Mutation_p.R263H|MEIS2_ENST00000559085.1_Missense_Mutation_p.R263H|MEIS2_ENST00000338564.5_Missense_Mutation_p.R276H|MEIS2_ENST00000557796.2_Missense_Mutation_p.R263H|MEIS2_ENST00000424352.2_Missense_Mutation_p.R276H|MEIS2_ENST00000219869.9_Missense_Mutation_p.R130H|MEIS2_ENST00000559561.1_Missense_Mutation_p.R276H			O14770	MEIS2_HUMAN	Meis homeobox 2	276					eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TTTCTTCTGGCGTTTTTTGTC	0.393																																																0			15											216	185	196					15																	37329088		2201	4297	6498	35116380	SO:0001583	missense	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.827G>A	15.37:g.37329088C>T	ENSP00000453793:p.Arg276His		35116380	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207426	0.39003	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	T;D;D;D;D;D;D;D	0.84442	1.88;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85	5.14	4.2	0.49525	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.85199	0.5642	L	0.35644	1.08	0.80722	D	1	B;B;B;B;D;B;B;B	0.64830	0.016;0.083;0.063;0.006;0.994;0.007;0.002;0.013	B;B;B;B;P;B;B;B	0.57152	0.009;0.046;0.005;0.021;0.814;0.004;0.001;0.009	D	0.84217	0.0459	10	0.39692	T	0.17	-5.1959	13.3746	0.60730	0.0:0.9238:0.0:0.0762	.	263;276;276;276;276;130;188;263	Q96DI2;O14770-4;O14770;O14770-3;O14770-2;B3KP81;B3KPQ6;B3KP98	.;.;MEIS2_HUMAN;.;.;.;.;.	H	276;276;276;276;276;263;263;188;130	ENSP00000326296:R276H;ENSP00000341400:R276H;ENSP00000372216:R276H;ENSP00000404185:R276H;ENSP00000391887:R276H;ENSP00000339549:R263H;ENSP00000380745:R188H;ENSP00000219869:R130H	ENSP00000219869:R130H	R	-	2	0	MEIS2	35116380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.042000	0.70996	2.556000	0.86216	0.650000	0.86243	CGC		0.393	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		T	37329088	C	T	37329088	3	4	12	1	0	0	0	0	1	0	0	0	9498	768	27	1	689	1	MEIS2	15	37329088	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10		37329088	65202304	114	1524										
C15orf56	644809	hgsc.bcm.edu	37	chr15	40544943	40544943	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggcgagaggacgggcctcccAacacgcgcagcccccttcct	12	18	0	1	rs369720850	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:40544943A>G	ENST00000319503.3	-	1	168	c.147T>C	c.(145-147)gtT>gtC	p.V49V	PAK6_ENST00000560346.1_Intron|C15orf56_ENST00000559727.1_Silent_p.V49V|PAK6_ENST00000260404.4_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000453867.1_Intron|PAK6_ENST00000441369.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	49										lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CGGGCCTCCCAACACGCGCAG	0.741													A|||	6	0.00119808	8e-04	0.0014	5008	,	,		11887	0.001		0.002	False		,,,				2504	0.001															0			15						A	,,,	5,3987		0,5,1991	4	5	5		147,,,	0.6	0	15		5	39,7921		0,39,3941	no	coding-synonymous,intron,intron,intron	PAK6,C15orf56	NM_001039905.1,NM_001128628.1,NM_001128629.1,NM_020168.4	,,,	0,44,5932	GG,GA,AA		0.4899,0.1253,0.3681	,,,	49/162,,,	40544943	44,11908	1996	3980	5976	38332235	SO:0001819	synonymous_variant	644809				CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.147T>C	15.37:g.40544943A>G			38332235		Silent	SNP	ENST00000319503.3	37	CCDS32197.1																																																																																				0.741	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905		G	40544943	A	G	40544943	2	3	12	1	0	0	0	0	0	0	0	1	1808	117	5	4		4	C15orf56	15	40544943	Silent	SNP	A	TCGA-AF-6672-01A-11D-1826-10	3215855	40544943	61986449	115	1525										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40751659	40751659	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ccggagcctgggcgcccaggCgaggagtcacctgcccctaa	14	16	1	0	rs534764286		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:40751659C>T	ENST00000416165.1	+	2	1067	c.996C>T	c.(994-996)ggC>ggT	p.G332G	BAHD1_ENST00000561234.1_Silent_p.G332G|BAHD1_ENST00000560846.1_Silent_p.G332G	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	332	Pro-rich.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		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)		GGCGCCCAGGCGAGGAGTCAC	0.672													c|||	1	0.000199681	8e-04	0	5008	,	,		17317	0		0	False		,,,				2504	0															0			15											38	46	43					15																	40751659		2203	4300	6503	38538951	SO:0001819	synonymous_variant	22893			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.996C>T	15.37:g.40751659C>T			38538951	Q8NDF7|Q9Y2F4	Silent	SNP	ENST00000416165.1	37	CCDS10058.1																																																																																				0.672	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		T	40751659	C	T	40751659	2	4	12	1	0	0	0	0	0	0	0	1	1298	755	27	1		1	BAHD1	15	40751659	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	206716	40751659	61779733	116	1526										
TGM7	116179	hgsc.bcm.edu	37	chr15	43572000	43572000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctgcaggtcctggccccactCgggtatcctggccaggtgaa	13	14	0	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:43572000C>T	ENST00000452443.2	-	10	1505	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	501					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TGGCCCCACTCGGGTATCCTG	0.647																																																0			15											36	43	41					15																	43572000		2202	4298	6500	41359292	SO:0001583	missense	116179			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1501G>A	15.37:g.43572000C>T	ENSP00000389466:p.Glu501Lys		41359292		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.500546	0.01001	.	.	ENSG00000159495	ENST00000452443	T	0.28255	1.62	4.55	-0.762	0.11034	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.848314	0.10531	N	0.663871	T	0.12732	0.0309	L	0.27053	0.805	0.09310	N	1	B	0.31837	0.342	B	0.20184	0.028	T	0.26608	-1.0098	10	0.05959	T	0.93	-3.5654	4.0428	0.09760	0.0:0.3907:0.1775:0.4318	.	501	Q96PF1	TGM7_HUMAN	K	501	ENSP00000389466:E501K	ENSP00000389466:E501K	E	-	1	0	TGM7	41359292	0.001000	0.12720	0.003000	0.11579	0.062000	0.15995	-0.386000	0.07370	-0.334000	0.08463	-0.126000	0.14955	GAG		0.647	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43572000	C	T	43572000	3	4	12	1	0	0	0	0	1	0	0	0	15874	893	31	1	647	1	TGM7	15	43572000	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	2820341	43572000	58959392	117	1527										
VPS33B	26276	hgsc.bcm.edu	37	chr15	91542927	91542927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctttctctctgcccaggaacCggagggctgagatctcagag	12	12	3	2	rs147814686		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:91542927C>T	ENST00000333371.3	-	22	2107	c.1754G>A	c.(1753-1755)cGg>cAg	p.R585Q	VPS33B_ENST00000535906.1_Missense_Mutation_p.R558Q|VPS33B_ENST00000535843.1_Missense_Mutation_p.R494Q	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	585					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					GCCCAGGAACCGGAGGGCTGA	0.507																																																0			15						C	GLN/ARG	0,4396		0,0,2198	222	228	226		1754	5.9	1	15	dbSNP_134	226	1,8595	1.2+/-3.3	0,1,4297	no	missense	VPS33B	NM_018668.3	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	585/618	91542927	1,12991	2198	4298	6496	89343931	SO:0001583	missense	26276			AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"vacuolar protein sorting 33B (yeast homolog)"			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.1754G>A	15.37:g.91542927C>T	ENSP00000327650:p.Arg585Gln		89343931	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	37	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	C	36	5.838613	0.97009	0.0	1.16E-4	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.75704	-0.96;-0.96;-0.96	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.87947	0.6306	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.992;0.993	D	0.88511	0.3089	10	0.62326	D	0.03	-32.8143	18.1584	0.89701	0.0:1.0:0.0:0.0	.	558;585	F5H008;Q9H267	.;VP33B_HUMAN	Q	585;558;494;540	ENSP00000327650:R585Q;ENSP00000444053:R558Q;ENSP00000446267:R494Q	ENSP00000327650:R585Q	R	-	2	0	VPS33B	89343931	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	6.396000	0.73234	2.825000	0.97269	0.655000	0.94253	CGG		0.507	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668		T	91542927	C	T	91542927	3	4	12	1	0	0	0	0	1	0	0	0	17242	652	23	1	107	1	VPS33B	15	91542927	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	47970927	91542927	10988465	118	1528										
LINS1	55180	hgsc.bcm.edu	37	chr15	101109902	101109902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atggtgtgagcccccttggaCatcacagctttcagtggttc	11	11	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:101109902C>T	ENST00000314742.8	-	7	2037	c.1815G>A	c.(1813-1815)atG>atA	p.M605I	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	605										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CCCCCTTGGACATCACAGCTT	0.537																																																0			15											69	66	67					15																	101109902		2203	4300	6503	98927425	SO:0001583	missense	0			AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1815G>A	15.37:g.101109902C>T	ENSP00000318423:p.Met605Ile		98927425	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	.	.	.	.	.	.	.	.	.	.	C	8.935	0.964408	0.18583	.	.	ENSG00000140471	ENST00000314742	T	0.09723	2.95	4.85	-2.02	0.07388	.	0.807412	0.11487	N	0.559142	T	0.06050	0.0157	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.37888	-0.9686	10	0.32370	T	0.25	-0.9308	2.4109	0.04424	0.1225:0.3085:0.3576:0.2114	.	605	Q8NG48	LINES_HUMAN	I	605	ENSP00000318423:M605I	ENSP00000318423:M605I	M	-	3	0	LINS	98927425	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.464000	0.06688	-0.801000	0.04427	-1.211000	0.01629	ATG		0.537	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		T	101109902	C	T	101109902	3	4	12	1	0	0	0	0	1	0	0	0	8842	478	17	3	462	3	LINS1	15	101109902	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	9566975	101109902	1421490	119	1529										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3779387	3779387	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gtgggggtcccgggcggtgcTgaggtaggagaaggcagact	21	7	0	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr16:3779387T>C	ENST00000262367.5	-	31	6470	c.5661A>G	c.(5659-5661)tcA>tcG	p.S1887S	CREBBP_ENST00000382070.3_Silent_p.S1849S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1887	Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CGGGCGGTGCTGAGGTAGGAG	0.687			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											39	38	38					16																	3779387		2196	4299	6495	3719388	SO:0001819	synonymous_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.5661A>G	16.37:g.3779387T>C			3719388	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.687	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3779387	T	C	3779387	2	2	12	1	0	0	0	0	0	0	0	1	3867	1567	55	4		4	CREBBP	16	3779387	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10		3779387	86575366	120	1530										
INPP5K	51763	hgsc.bcm.edu	37	chr17	1417206	1417206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	attgaggttccggttgttcaGctgaagcaggtcactgagat	13	7	2	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:1417206G>T	ENST00000421807.2	-	2	500	c.112C>A	c.(112-114)Ctg>Atg	p.L38M	INPP5K_ENST00000406424.4_De_novo_Start_InFrame|INPP5K_ENST00000542125.1_Missense_Mutation_p.L38M|INPP5K_ENST00000320345.6_De_novo_Start_InFrame|INPP5K_ENST00000397335.3_Intron	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	38	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CGGTTGTTCAGCTGAAGCAGG	0.552																																																0			17											140	105	117					17																	1417206		2203	4300	6503	1363956	SO:0001583	missense	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.112C>A	17.37:g.1417206G>T	ENSP00000413937:p.Leu38Met		1363956	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	37	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818146	0.71028	.	.	ENSG00000132376	ENST00000350761;ENST00000542125	T	0.48836	0.8	5.4	4.43	0.53597	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.071765	0.56097	D	0.000022	T	0.67951	0.2948	M	0.83312	2.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.988;0.984	T	0.71337	-0.4623	10	0.66056	D	0.02	-12.1724	9.6004	0.39601	0.159:0.0:0.841:0.0	.	38;38;38	F5GXZ0;B7Z8U3;Q9BT40	.;.;INP5K_HUMAN	M	38	ENSP00000440147:L38M	ENSP00000254712:L38M	L	-	1	2	INPP5K	1363956	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.976000	0.63785	1.413000	0.46997	0.462000	0.41574	CTG		0.552	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			T	1417206	G	T	1417206	3	4	12	1	0	0	0	0	1	0	0	0	7781	962	34	2	1278	2	INPP5K	17	1417206	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10		1417206	79778004	121	1531										
TP53	7157	hgsc.bcm.edu	37	chr17	7578266	7578266	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	caaatttccttccactcggaTaagatgctgaggaggggcca	11	10	0	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:7578266T>A	ENST00000269305.4	-	6	772	c.583A>T	c.(583-585)Atc>Ttc	p.I195F	TP53_ENST00000445888.2_Missense_Mutation_p.I195F|TP53_ENST00000455263.2_Missense_Mutation_p.I195F|TP53_ENST00000413465.2_Missense_Mutation_p.I195F|TP53_ENST00000420246.2_Missense_Mutation_p.I195F|TP53_ENST00000359597.4_Missense_Mutation_p.I195F|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195F(20)|p.0?(8)|p.?(6)|p.I195fs*14(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102F(1)|p.I195fs*52(1)|p.L194fs*52(1)|p.I63fs*14(1)|p.I195fs*50(1)|p.I102fs*14(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.I195L(1)|p.P98_E105>Q(1)|p.I63F(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.H193_I195>AP(1)|p.I195fs*12(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCACTCGGATAAGATGCTGA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	60	Substitution - Missense(23)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - Frameshift(4)|Complex - frameshift(1)	upper_aerodigestive_tract(8)|breast(8)|large_intestine(6)|biliary_tract(5)|skin(5)|lung(5)|oesophagus(4)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|liver(2)|stomach(1)|soft_tissue(1)	17											99	89	92					17																	7578266		2203	4300	6503	7518991	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.583A>T	17.37:g.7578266T>A	ENSP00000269305:p.Ile195Phe		7518991	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493726	0.64186	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99824	-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	D	0.000004	D	0.99802	0.9915	M	0.85099	2.735	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;0.998;0.997;0.998;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.989;0.955;0.972;0.988;0.99;0.992	D	0.96806	0.9593	10	0.87932	D	0	-18.4587	13.709	0.62656	0.0:0.0:0.0:1.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195F;ENSP00000352610:I195F;ENSP00000269305:I195F;ENSP00000398846:I195F;ENSP00000391127:I195F;ENSP00000391478:I195F;ENSP00000425104:I63F;ENSP00000423862:I102F	ENSP00000269305:I195F	I	-	1	0	TP53	7518991	1.000000	0.71417	0.895000	0.35142	0.030000	0.12068	6.159000	0.71856	2.183000	0.69458	0.533000	0.62120	ATC		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578266	T	A	7578266	3	1	12	1	0	0	0	0	1	0	0	0	16421	1406	49	5	711	5	TP53	17	7578266	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	6161060	7578266	73616944	122	1532										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33772552	33772552	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tgagtttaataaagcacacgCggcccgtataactctcgccc	8	13	1	1	rs7216628	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:33772552C>T	ENST00000285013.6	-	3	423	c.148G>A	c.(148-150)Gcg>Acg	p.A50T	SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000542635.1_Missense_Mutation_p.A50T|SLFN13_ENST00000533791.1_Missense_Mutation_p.A50T|SLFN13_ENST00000526861.1_Missense_Mutation_p.A50T|SLFN13_ENST00000360502.2_Intron	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	50			A -> T (in dbSNP:rs7216628).			intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AAAGCACACGCGGCCCGTATA	0.483													C|||	72	0.014377	0.0545	0	5008	,	,		16763	0		0	False		,,,				2504	0															0			17						C	THR/ALA	208,4198	128.6+/-165.4	8,192,2003	114	118	117		148	1.2	0.1	17	dbSNP_116	117	1,8599	2.2+/-6.3	0,1,4299	yes	missense	SLFN13	NM_144682.5	58	8,193,6302	TT,TC,CC		0.0116,4.7208,1.607	benign	50/898	33772552	209,12797	2203	4300	6503	30796665	SO:0001583	missense	146857			AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.148G>A	17.37:g.33772552C>T	ENSP00000285013:p.Ala50Thr		30796665	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	C	3.929	-0.016561	0.07681	0.047208	1.16E-4	ENSG00000154760	ENST00000285013;ENST00000526861;ENST00000542635;ENST00000524511	T;T;T;T	0.23552	4.52;4.52;4.52;1.9	3.28	1.22	0.21188	.	0.225948	0.22432	U	0.060132	T	0.01387	0.0045	L	0.45352	1.415	0.09310	N	1	P	0.50943	0.94	B	0.35182	0.197	T	0.17776	-1.0358	10	0.30078	T	0.28	.	5.3892	0.16234	0.0:0.721:0.0:0.279	rs7216628;rs7216628	50	Q68D06	SLN13_HUMAN	T	50	ENSP00000285013:A50T;ENSP00000434439:A50T;ENSP00000444016:A50T;ENSP00000433181:A50T	ENSP00000285013:A50T	A	-	1	0	SLFN13	30796665	0.000000	0.05858	0.146000	0.22360	0.038000	0.13279	-0.209000	0.09358	0.213000	0.20722	0.205000	0.17691	GCG		0.483	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33772552	C	T	33772552	3	4	12	1	0	0	0	0	1	0	0	0	14773	768	27	1	2561	1	SLFN13	17	33772552	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	26194286	33772552	47422658	123	1533										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3135700	3135700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cagggagctccgtgttcactCgctgccagttttctgttcct	10	13	2	0	rs371246473		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:3135700C>T	ENST00000356443.4	-	15	2387	c.2054G>A	c.(2053-2055)cGa>cAa	p.R685Q	MYOM1_ENST00000400569.3_Missense_Mutation_p.R685Q|MYOM1_ENST00000261606.7_Missense_Mutation_p.R685Q	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	685	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGTTCACTCGCTGCCAGTT	0.527																																																0			18						C	GLN/ARG,GLN/ARG	0,3940		0,0,1970	42	47	45		2054,2054	4.9	1	18		45	1,8317		0,1,4158	no	missense,missense	MYOM1	NM_003803.3,NM_019856.1	43,43	0,1,6128	TT,TC,CC		0.012,0.0,0.0082	probably-damaging,probably-damaging	685/1686,685/1590	3135700	1,12257	1970	4159	6129	3125700	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2054G>A	18.37:g.3135700C>T	ENSP00000348821:p.Arg685Gln		3125700	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177441	0.78564	0.0	1.2E-4	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.56776	0.44;0.44;0.44	5.76	4.9	0.64082	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	L	0.52823	1.66	0.47094	D	0.999314	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.62383	-0.6866	10	0.20519	T	0.43	.	15.4097	0.74908	0.0:0.933:0.0:0.067	.	685;685	P52179-2;P52179	.;MYOM1_HUMAN	Q	685	ENSP00000348821:R685Q;ENSP00000383413:R685Q;ENSP00000261606:R685Q	ENSP00000261606:R685Q	R	-	2	0	MYOM1	3125700	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.934000	0.63491	1.578000	0.49821	0.650000	0.86243	CGA		0.527	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3135700	C	T	3135700	3	4	12	1	0	0	0	0	1	0	0	0	10121	884	31	1	3099	1	MYOM1	18	3135700	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10		3135700	74941548	124	1534										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48593473	48593473	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cttagtgaccacgcggtcttTgtacagagttactacttaga	9	9	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:48593473T>A	ENST00000342988.3	+	10	1762	c.1224T>A	c.(1222-1224)ttT>ttA	p.F408L	SMAD4_ENST00000588745.1_Missense_Mutation_p.F312L|SMAD4_ENST00000398417.2_Missense_Mutation_p.F408L	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	408	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ACGCGGTCTTTGTACAGAGTT	0.433																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											175	144	154					18																	48593473		2203	4300	6503	46847471	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1224T>A	18.37:g.48593473T>A	ENSP00000341551:p.Phe408Leu		46847471	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536060	0.85812	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99194	-5.54;-5.54	5.49	4.3	0.51218	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99266	0.9744	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99529	1.0960	10	0.87932	D	0	.	8.2009	0.31424	0.0:0.1601:0.0:0.8399	.	408	Q13485	SMAD4_HUMAN	L	408	ENSP00000341551:F408L;ENSP00000381452:F408L	ENSP00000341551:F408L	F	+	3	2	SMAD4	46847471	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	0.379000	0.20585	0.870000	0.35726	0.455000	0.32223	TTT		0.433	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48593473	T	A	48593473	3	1	12	1	0	0	0	0	1	0	0	0	14797	1809	63	5	1258	5	SMAD4	18	48593473	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	45457773	48593473	29483775	125	1535										
DCC	1630	hgsc.bcm.edu	37	chr18	50683828	50683828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctggcgcccacctgcagaagCgaaagggaacattcaaactt	10	12	1	1	rs145985306	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:50683828C>T	ENST00000442544.2	+	8	1980	c.1364C>T	c.(1363-1365)gCg>gTg	p.A455V	DCC_ENST00000412726.1_Missense_Mutation_p.A303V|DCC_ENST00000581580.1_Missense_Mutation_p.A110V	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	455	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCTGCAGAAGCGAAAGGGAAC	0.502																																																0			18						C	VAL/ALA	8,4398	12.9+/-30.5	0,8,2195	119	107	111		1364	3.7	1	18	dbSNP_134	111	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DCC	NM_005215.3	64	0,9,6494	TT,TC,CC		0.0116,0.1816,0.0692	benign	455/1448	50683828	9,12997	2203	4300	6503	48937826	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1364C>T	18.37:g.50683828C>T	ENSP00000389140:p.Ala455Val		48937826		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487223	0.44249	0.001816	1.16E-4	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.56941	0.43;0.43	5.44	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.248804	0.33438	N	0.004917	T	0.37210	0.0995	N	0.21324	0.655	0.30963	N	0.723433	B;B;B	0.17852	0.007;0.007;0.024	B;B;B	0.15052	0.004;0.004;0.012	T	0.41716	-0.9493	10	0.51188	T	0.08	.	10.701	0.45926	0.0:0.8431:0.0:0.1569	.	303;303;455	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	V	455;388;303	ENSP00000389140:A455V;ENSP00000397322:A303V	ENSP00000304146:A388V	A	+	2	0	DCC	48937826	0.996000	0.38824	1.000000	0.80357	0.930000	0.56654	3.414000	0.52693	1.326000	0.45319	-0.215000	0.12644	GCG		0.502	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50683828	C	T	50683828	3	4	12	1	0	0	0	0	1	0	0	0	4288	768	27	1	1394	1	DCC	18	50683828	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	2090355	50683828	27393420	126	1536										
ODF3L2	284451	hgsc.bcm.edu	37	chr19	463968	463968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gagccctggctttgttcacgGtgacctgctctgggcagtgg	15	11	2	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:463968G>A	ENST00000315489.4	-	4	981	c.746C>T	c.(745-747)aCc>aTc	p.T249I	SHC2_ENST00000264554.6_5'Flank|ODF3L2_ENST00000382696.3_Missense_Mutation_p.T213I	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	249						cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						TTTGTTCACGGTGACCTGCTC	0.736																																																0			19											24	28	27					19																	463968		2196	4290	6486	414968	SO:0001583	missense	284451			AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 19"	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.746C>T	19.37:g.463968G>A	ENSP00000318029:p.Thr249Ile		414968	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	37	CCDS12027.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.311600	0.40895	.	.	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.47869	1.36;0.83	3.81	3.81	0.43845	.	0.168517	0.51477	D	0.000099	T	0.54663	0.1872	L	0.53671	1.685	0.45261	D	0.998261	D;D	0.67145	0.996;0.991	P;P	0.62184	0.899;0.899	T	0.49835	-0.8897	10	0.23302	T	0.38	-16.8727	9.1293	0.36835	0.0:0.0:0.7816:0.2184	.	213;249	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	I	249;213	ENSP00000318029:T249I;ENSP00000372143:T213I	ENSP00000318029:T249I	T	-	2	0	ODF3L2	414968	1.000000	0.71417	0.873000	0.34254	0.425000	0.31504	6.593000	0.74100	1.850000	0.53721	0.555000	0.69702	ACC		0.736	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577		A	463968	G	A	463968	3	1	12	1	0	0	0	0	1	0	0	0	10863	1261	44	3	127	3	ODF3L2	19	463968	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10		463968	58665015	127	1537										
MLLT1	4298	hgsc.bcm.edu	37	chr19	6218019	6218019	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gtctgagctggagtctgagcTggagctggagttggacgggc	19	7	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:6218019T>C	ENST00000252674.7	-	7	1307	c.1144A>G	c.(1144-1146)Agc>Ggc	p.S382G	MLLT1_ENST00000585588.1_5'Flank	NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	382	Poly-Ser.				negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						gagtctgagctggagCTGGAG	0.612			T	MLL	AL																																		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	0			19											173	137	149					19																	6218019		2199	4298	6497	6169019	SO:0001583	missense	4298				CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.1144A>G	19.37:g.6218019T>C	ENSP00000252674:p.Ser382Gly		6169019	Q14768	Missense_Mutation	SNP	ENST00000252674.7	37	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463410	0.63513	.	.	ENSG00000130382	ENST00000252674	.	.	.	4.59	4.59	0.56863	.	0.084546	0.85682	D	0.000000	T	0.76948	0.4059	M	0.80183	2.485	0.48696	D	0.999698	P	0.52842	0.956	D	0.65010	0.931	T	0.77305	-0.2637	9	0.36615	T	0.2	-6.0912	12.807	0.57619	0.0:0.0:0.0:1.0	.	382	Q03111	ENL_HUMAN	G	382	.	ENSP00000252674:S382G	S	-	1	0	MLLT1	6169019	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.071000	0.57556	1.705000	0.51264	0.379000	0.24179	AGC		0.612	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		C	6218019	T	C	6218019	3	2	12	1	0	0	0	0	1	0	0	0	9655	1580	55	4	559	4	MLLT1	19	6218019	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	5754051	6218019	52910964	128	1538										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10090070	10090070	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aagacaccagctggtccaggCgggcctgtctgaccttggaa	13	12	1	2	rs199880497	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:10090070C>T	ENST00000264828.3	-	38	2821	c.2736G>A	c.(2734-2736)ccG>ccA	p.P912P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	912	Collagen-like 4.|Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTGGTCCAGGCGGGCCTGTCT	0.542													c|||	5	0.000998403	0	0	5008	,	,		17420	0		0	False		,,,				2504	0.0051															0			19											91	97	95					19																	10090070		2203	4300	6503	9951070	SO:0001819	synonymous_variant	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2736G>A	19.37:g.10090070C>T			9951070	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																				0.542	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10090070	C	T	10090070	2	4	12	1	0	0	0	0	0	0	0	1	3704	755	27	1		1	COL5A3	19	10090070	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	3872051	10090070	49038913	129	1539										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17994774	17994774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cctgccatcgtcggctgcccGctgcgtggctctctcagtca	11	17	3	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:17994774G>A	ENST00000222248.3	+	12	1792	c.1445G>A	c.(1444-1446)cGc>cAc	p.R482H		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	482					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TCGGCTGCCCGCTGCGTGGCT	0.682																																					Melanoma(65;1008 1708 7910 46650)											0			19											10	8	9					19																	17994774		2174	4269	6443	17855774	SO:0001583	missense	6528				CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1445G>A	19.37:g.17994774G>A	ENSP00000222248:p.Arg482His		17855774	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	37	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195316	0.38806	.	.	ENSG00000105641	ENST00000222248	D	0.85171	-1.95	4.43	1.86	0.25419	.	0.710769	0.14031	N	0.346148	T	0.61652	0.2364	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55704	-0.8099	10	0.44086	T	0.13	.	6.8823	0.24181	0.2848:0.0:0.7152:0.0	.	482	Q92911	SC5A5_HUMAN	H	482	ENSP00000222248:R482H	ENSP00000222248:R482H	R	+	2	0	SLC5A5	17855774	0.012000	0.17670	0.046000	0.18839	0.147000	0.21601	-0.023000	0.12456	0.991000	0.38814	0.555000	0.69702	CGC		0.682	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			A	17994774	G	A	17994774	3	1	12	1	0	0	0	0	1	0	0	0	14705	1087	38	1	1491	1	SLC5A5	19	17994774	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	7904704	17994774	41134209	130	1540										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32959705	32959705	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gatccagatacagtggagctGatgaactggattaagtaaga	12	5	0	4			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:32959705G>A	ENST00000342179.5	+	16	1898	c.1683G>A	c.(1681-1683)ctG>ctA	p.L561L	DPY19L3_ENST00000586987.1_Silent_p.L561L|DPY19L3_ENST00000392250.2_Silent_p.L561L|DPY19L3_ENST00000590651.1_3'UTR	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	561						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					CAGTGGAGCTGATGAACTGGA	0.333																																																0			19											65	71	69					19																	32959705		2203	4300	6503	37651545	SO:0001819	synonymous_variant	147991				CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1683G>A	19.37:g.32959705G>A			37651545	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																				0.333	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		A	32959705	G	A	32959705	2	1	12	1	0	0	0	0	0	0	0	1	4753	1277	45	3		3	DPY19L3	19	32959705	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	14964931	32959705	26169278	131	1541										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44981815	44981815	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	aaaggtttttcctcctccatGaattttttcatgtatatgta	5	7	1	1			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:44981815G>T	ENST00000221327.4	-	5	1164	c.883C>A	c.(883-885)Cat>Aat	p.H295N	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.H270N|ZNF180_ENST00000592529.1_Missense_Mutation_p.H268N	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CCTCCTCCATGAATTTTTTCA	0.348																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											0			19											70	77	75					19																	44981815		2203	4299	6502	49673655	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.883C>A	19.37:g.44981815G>T	ENSP00000221327:p.His295Asn		49673655	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	6.869	0.529799	0.13127	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.26660	1.72;1.72	5.18	1.78	0.24846	.	1.110340	0.07032	N	0.828678	T	0.16471	0.0396	N	0.08118	0	0.29687	N	0.841251	P;P;P	0.42203	0.773;0.664;0.664	B;B;B	0.43274	0.414;0.235;0.235	T	0.21724	-1.0237	10	0.72032	D	0.01	-0.3399	6.6697	0.23062	0.1492:0.1535:0.6973:0.0	.	270;294;295	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	N	295;270	ENSP00000221327:H295N;ENSP00000375818:H270N	ENSP00000221327:H295N	H	-	1	0	ZNF180	49673655	0.297000	0.24408	0.000000	0.03702	0.340000	0.28889	2.163000	0.42377	0.149000	0.19098	0.655000	0.94253	CAT		0.348	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		T	44981815	G	T	44981815	3	4	12	1	0	0	0	0	1	0	0	0	17787	1290	45	2	1199	2	ZNF180	19	44981815	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	12022110	44981815	14147168	132	1542										
GPR4	2828	hgsc.bcm.edu	37	chr19	46094082	46094082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gctgcacctggtccccctggGagggcggagtggccgcccag	17	15	0	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:46094082G>T	ENST00000323040.4	-	2	1987	c.1043C>A	c.(1042-1044)tCc>tAc	p.S348Y	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	348					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		GTCCCCCTGGGAGGGCGGAGT	0.622																																					Esophageal Squamous(117;181 1612 1673 14956 42937)											0			19											58	59	59					19																	46094082		2203	4300	6503	50785922	SO:0001583	missense	2828			BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"GPCR / Class A : Orphans"	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.1043C>A	19.37:g.46094082G>T	ENSP00000319744:p.Ser348Tyr		50785922	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000323040.4	37	CCDS12669.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383570	0.25031	.	.	ENSG00000177464	ENST00000323040	T	0.62364	0.03	4.53	4.53	0.55603	.	0.918642	0.08962	N	0.868555	T	0.49406	0.1555	N	0.14661	0.345	0.28453	N	0.91624	B	0.26258	0.145	B	0.28011	0.085	T	0.47799	-0.9089	10	0.66056	D	0.02	.	12.6317	0.56661	0.0:0.0:1.0:0.0	.	348	P46093	GPR4_HUMAN	Y	348	ENSP00000319744:S348Y	ENSP00000319744:S348Y	S	-	2	0	GPR4	50785922	0.279000	0.24239	0.924000	0.36721	0.452000	0.32318	0.502000	0.22594	2.356000	0.79943	0.455000	0.32223	TCC		0.622	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282		T	46094082	G	T	46094082	3	4	12	1	0	0	0	0	1	0	0	0	6714	1174	41	2	49	2	GPR4	19	46094082	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	1112267	46094082	13034901	133	1543										
LENG8	114823	hgsc.bcm.edu	37	chr19	54966244	54966244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	cagtggttttggcccccagcCcaaccctgagaaagttcaga	10	13	1	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:54966244C>T	ENST00000326764.5	+	7	1273	c.794C>T	c.(793-795)cCc>cTc	p.P265L	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	228										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GGCCCCCAGCCCAACCCTGAG	0.602																																																0			19											70	68	69					19																	54966244		2203	4300	6503	59658056	SO:0001583	missense	114823			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.794C>T	19.37:g.54966244C>T	ENSP00000318374:p.Pro265Leu		59658056	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310150	0.60414	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376526;ENST00000431846	T;T;T;T	0.44482	1.47;0.92;1.41;1.45	5.38	5.38	0.77491	.	0.247838	0.41605	D	0.000846	T	0.41627	0.1167	L	0.50333	1.59	0.80722	D	1	P;P	0.51933	0.617;0.949	B;P	0.45753	0.173;0.492	T	0.23762	-1.0179	10	0.42905	T	0.14	-33.8854	12.0197	0.53336	0.1726:0.8274:0.0:0.0	.	265;228	Q96PV6-2;F8W9Q9	.;.	L	265;228;265;228;265	ENSP00000318374:P265L;ENSP00000399507:P265L;ENSP00000365709:P228L;ENSP00000388053:P265L	ENSP00000301196:P228L	P	+	2	0	LENG8	59658056	1.000000	0.71417	0.997000	0.53966	0.932000	0.56968	2.432000	0.44784	2.688000	0.91661	0.655000	0.94253	CCC		0.602	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		T	54966244	C	T	54966244	3	4	12	1	0	0	0	0	1	0	0	0	8746	623	22	3	816	3	LENG8	19	54966244	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	8872162	54966244	4162739	134	1544										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3007801	3007801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gtgatcattccagttaagcgGggcgaagagaatacagacta	12	7	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:3007801G>A	ENST00000216877.6	+	18	2116	c.1716G>A	c.(1714-1716)cgG>cgA	p.R572R	PTPRA_ENST00000356147.3_Silent_p.R572R|PTPRA_ENST00000399903.2_Silent_p.R581R|PTPRA_ENST00000318266.5_Silent_p.R572R|PTPRA_ENST00000358719.4_Silent_p.R437R|PTPRA_ENST00000380393.3_Silent_p.R581R|PTPRA_ENST00000425918.2_Silent_p.R592R	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	581	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CAGTTAAGCGGGGCGAAGAGA	0.483																																																0			20											227	201	210					20																	3007801		2203	4300	6503	2955801	SO:0001819	synonymous_variant	5786				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1716G>A	20.37:g.3007801G>A			2955801	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																				0.483	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			A	3007801	G	A	3007801	2	1	12	1	0	0	0	0	0	0	0	1	12832	1219	43	3		3	PTPRA	20	3007801	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10		3007801	60017719	135	1545										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13971154	13971154	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	accccaagaattatcaatatCtctattaacagagacaaggg	6	9	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:13971154C>G	ENST00000284951.5	-	1	101	c.27G>C	c.(25-27)gaG>gaC	p.E9D	SEL1L2_ENST00000378072.5_Missense_Mutation_p.E9D|SEL1L2_ENST00000486903.1_Intron			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	9						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TTATCAATATCTCTATTAACA	0.423																																																0			20											103	96	98					20																	13971154		1840	4098	5938	13919154	SO:0001583	missense	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.27G>C	20.37:g.13971154C>G	ENSP00000284951:p.Glu9Asp		13919154	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	C	13.33	2.205023	0.38905	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23950	1.88;2.22	6.07	4.13	0.48395	.	0.512796	0.17868	N	0.159288	T	0.13927	0.0337	N	0.19112	0.55	0.20074	N	0.999935	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24905	-1.0147	10	0.14252	T	0.57	0.111	7.7472	0.28875	0.0:0.7511:0.1649:0.084	.	9;9	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	D	9	ENSP00000367312:E9D;ENSP00000284951:E9D	ENSP00000284951:E9D	E	-	3	2	SEL1L2	13919154	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	0.809000	0.27168	1.570000	0.49709	0.585000	0.79938	GAG		0.423	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		G	13971154	C	G	13971154	3	3	12	1	0	0	0	0	1	0	0	0	14048	912	32	5	2119	5	SEL1L2	20	13971154	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	10963353	13971154	49054366	136	1546										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16360332	16360332	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ggagctggatcatctcctgcTtctctcggagctgctcttcc	10	14	4	0			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:16360332T>C	ENST00000354981.2	-	19	2472	c.2315A>G	c.(2314-2316)aAg>aGg	p.K772R	KIF16B_ENST00000408042.1_Missense_Mutation_p.K772R|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.K772R	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	772	Glu-rich.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.K772T(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CATCTCCTGCTTCTCTCGGAG	0.567																																																1	Substitution - Missense(1)	breast(1)	20											111	105	107					20																	16360332		2203	4300	6503	16308332	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2315A>G	20.37:g.16360332T>C	ENSP00000347076:p.Lys772Arg		16308332	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.883831	0.33255	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000408042	T;T;T	0.18016	2.24;2.24;2.24	5.31	1.7	0.24286	.	0.275521	0.40064	N	0.001182	T	0.09992	0.0245	L	0.32530	0.975	0.80722	D	1	B;B;B;B	0.15930	0.015;0.011;0.003;0.002	B;B;B;B	0.17722	0.015;0.019;0.01;0.004	T	0.25676	-1.0125	10	0.11485	T	0.65	.	5.9259	0.19112	0.0:0.1431:0.1415:0.7154	.	772;772;772;772	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	R	772	ENSP00000347076:K772R;ENSP00000347995:K772R;ENSP00000384164:K772R	ENSP00000347076:K772R	K	-	2	0	KIF16B	16308332	1.000000	0.71417	0.958000	0.39756	0.915000	0.54546	2.413000	0.44618	0.026000	0.15269	0.477000	0.44152	AAG		0.567	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16360332	T	C	16360332	3	2	12	1	0	0	0	0	1	0	0	0	8299	1609	56	4	1670	4	KIF16B	20	16360332	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	2389178	16360332	46665188	137	1547										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20226845	20226846	+	Frame_Shift_Ins	INS	-	-	T													0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tggacactgaacaaaggaaaINStttttagccagcgagtatga							TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:20226845_20226846insT	ENST00000245957.5	+	19	2221_2222	c.2145_2146insT	c.(2146-2148)tttfs	p.F716fs	C20orf26_ENST00000377309.2_Frame_Shift_Ins_p.F72fs|C20orf26_ENST00000377293.1_Frame_Shift_Ins_p.F72fs|C20orf26_ENST00000389656.3_Frame_Shift_Ins_p.F72fs	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		716										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		AACAAAGGAAATTTTTAGCCAG	0.347																																																0			20																																								20174846	SO:0001589	frameshift_variant	26074																														ENST00000245957.5:c.2150dupT	20.37:g.20226850_20226850dupT	ENSP00000245957:p.Phe716fs		20174845	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Frame_Shift_Ins	INS	ENST00000245957.5	37	CCDS33447.1																																																																																				0.347	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20226846	-	T	20226845	7	5	12	1	0	1	1	0	0	0	0	0	2112	98	4	0	2247	0	C20orf26	20	20226845	Frame_Shift_Ins	INS	-	TCGA-AF-6672-01A-11D-1826-10	3866513	20226845	42798675	138	1548										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31660530	31660530	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	tctcttttcacagtggccctGgatgttggaattcccctgcc	9	13	2	0	rs145354732	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:31660530G>A	ENST00000375494.3	+	14	1332	c.1332G>A	c.(1330-1332)ctG>ctA	p.L444L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	444					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CAGTGGCCCTGGATGTTGGAA	0.493													G|||	5	0.000998403	0.0038	0	5008	,	,		20722	0		0	False		,,,				2504	0															0			20						G		4,4402	8.1+/-20.4	0,4,2199	164	154	157		1332	2.7	0.7	20	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous	BPIFB3	NM_182658.1		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		444/477	31660530	4,13002	2203	4300	6503	31124191	SO:0001819	synonymous_variant	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1332G>A	20.37:g.31660530G>A			31124191	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																				0.493	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		A	31660530	G	A	31660530	2	1	12	1	0	0	0	0	0	0	0	1	2103	1335	47	3		3	C20orf185	20	31660530	Silent	SNP	G	TCGA-AF-6672-01A-11D-1826-10	11433685	31660530	31364990	139	1549										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33330093	33330093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	actgttgcttggacttgcccGttttgttgctccagaattag	10	9	0	1	rs181662709		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:33330093G>A	ENST00000374796.2	-	12	6537	c.3967C>T	c.(3967-3969)Cgg>Tgg	p.R1323W	NCOA6_ENST00000359003.2_Missense_Mutation_p.R1323W			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1323					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.R1323W(2)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GGACTTGCCCGTTTTGTTGCT	0.453																																																2	Substitution - Missense(2)	ovary(2)	20											139	138	138					20																	33330093		2203	4300	6503	32793754	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3967C>T	20.37:g.33330093G>A	ENSP00000363929:p.Arg1323Trp		32793754	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.30	3.084708	0.55861	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.31510	1.49;1.49	5.98	5.02	0.67125	.	0.000000	0.64402	D	0.000007	T	0.45438	0.1342	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.46775	-0.9167	10	0.87932	D	0	-14.3735	14.9392	0.70980	0.0:0.0:0.7266:0.2734	.	1323	Q14686	NCOA6_HUMAN	W	1323	ENSP00000363929:R1323W;ENSP00000351894:R1323W	ENSP00000351894:R1323W	R	-	1	2	NCOA6	32793754	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.918000	0.48829	1.503000	0.48686	0.591000	0.81541	CGG		0.453	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33330093	G	A	33330093	3	1	12	1	0	0	0	0	1	0	0	0	10264	1144	40	1	2244	1	NCOA6	20	33330093	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10	1669563	33330093	29695427	140	1550										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32108222	32108222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agaagaccttgtctgctatgGaggctggagaccgtaaccct	12	10	1	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr22:32108222G>A	ENST00000327423.6	-	4	5792	c.5603C>T	c.(5602-5604)tCc>tTc	p.S1868F	PRR14L_ENST00000434485.1_Missense_Mutation_p.S1868F|PRR14L_ENST00000397493.2_Missense_Mutation_p.S1868F	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1868										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GTCTGCTATGGAGGCTGGAGA	0.527																																																0			22											134	128	130					22																	32108222		2203	4300	6503	30438222	SO:0001583	missense	253143			BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.5603C>T	22.37:g.32108222G>A	ENSP00000331845:p.Ser1868Phe		30438222	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285310	0.59867	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.39997	1.05;1.05;1.05	5.66	5.66	0.87406	.	0.159398	0.44483	D	0.000460	T	0.60983	0.2311	L	0.56769	1.78	0.38691	D	0.952778	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	T	0.64309	-0.6438	10	0.62326	D	0.03	-9.0398	14.7978	0.69891	0.0:0.1449:0.8551:0.0	.	1868;1868;1868	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	F	1868	ENSP00000380630:S1868F;ENSP00000331845:S1868F;ENSP00000388314:S1868F	ENSP00000331845:S1868F	S	-	2	0	PRR14L	30438222	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.597000	0.54031	2.668000	0.90789	0.655000	0.94253	TCC		0.527	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		A	32108222	G	A	32108222	3	1	12	1	0	0	0	0	1	0	0	0	2148	1174	41	3	876	3	C22orf30	22	32108222	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10		32108222	19196344	141	1551										
PARVB	29780	hgsc.bcm.edu	37	chr22	44489860	44489860	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	atcaactcaccgatgtccccCgccctggtggatgttcaccc	8	17	3	0	rs369214399		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr22:44489860C>T	ENST00000338758.7	+	2	228	c.165C>T	c.(163-165)ccC>ccT	p.P55P	PARVB_ENST00000404989.1_Silent_p.P18P|PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000406477.3_Silent_p.P88P	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	55					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				CGATGTCCCCCGCCCTGGTGG	0.547																																																0			22						T	,	0,4406		0,0,2203	99	99	99		264,165	-9.8	0	22		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PARVB	NM_001003828.2,NM_013327.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	88/398,55/365	44489860	1,13005	2203	4300	6503	42821193	SO:0001819	synonymous_variant	29780			AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"Parvins"	14653	protein-coding gene	gene with protein product	"affixin"	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.165C>T	22.37:g.44489860C>T			42821193	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	37	CCDS14056.1																																																																																				0.547	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		T	44489860	C	T	44489860	2	4	12	1	0	0	0	0	0	0	0	1	11500	639	23	1		1	PARVB	22	44489860	Silent	SNP	C	TCGA-AF-6672-01A-11D-1826-10	12381638	44489860	6814706	142	1552										
PRRG1	5638	hgsc.bcm.edu	37	chrX	37312702	37312702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	ctcagattccgtctctactcGcctgtccaattgtgatcccc	6	16	2	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:37312702G>A	ENST00000542554.1	+	5	757	c.485G>A	c.(484-486)cGc>cAc	p.R162H	TM4SF2_ENST00000465127.1_Intron|PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000449135.2_Missense_Mutation_p.R162H|PRRG1_ENST00000543642.1_Missense_Mutation_p.R162H|PRRG1_ENST00000378628.4_Missense_Mutation_p.R162H	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	162						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						GTCTCTACTCGCCTGTCCAAT	0.547																																																0			X											87	73	78					X																	37312702		2202	4300	6502	37197623	SO:0001583	missense	5638			AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.485G>A	X.37:g.37312702G>A	ENSP00000444278:p.Arg162His		37197623	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	37	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450550	0.84101	.	.	ENSG00000130962	ENST00000378628;ENST00000542554;ENST00000543642;ENST00000449135	D;D;D;D	0.99121	-5.45;-5.45;-5.45;-5.45	5.96	5.96	0.96718	.	0.047968	0.85682	D	0.000000	D	0.98043	0.9355	L	0.55481	1.735	0.45403	D	0.99838	D	0.54047	0.964	P	0.44477	0.451	D	0.98691	1.0696	10	0.56958	D	0.05	-12.5273	17.7889	0.88547	0.0:0.0:1.0:0.0	.	162	O14668	TMG1_HUMAN	H	162	ENSP00000367894:R162H;ENSP00000444278:R162H;ENSP00000443271:R162H;ENSP00000390332:R162H	ENSP00000367894:R162H	R	+	2	0	PRRG1	37197623	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.463000	0.60128	2.524000	0.85096	0.600000	0.82982	CGC		0.547	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		A	37312702	G	A	37312702	3	1	12	1	0	0	0	0	1	0	0	0	12639	1087	38	1	577	1	PRRG1	23	37312702	Missense_Mutation	SNP	G	TCGA-AF-6672-01A-11D-1826-10		37312702	117957858	143	1553										
ZNF81	347344	hgsc.bcm.edu	37	chrX	47775003	47775003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agaagccactactcagtataTatctgagagttcatagagat	8	7	3	3			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:47775003T>C	ENST00000376954.1	+	6	1326	c.958T>C	c.(958-960)Tat>Cat	p.Y320H	ZNF81_ENST00000338637.7_Missense_Mutation_p.Y320H			P51508	ZNF81_HUMAN	zinc finger protein 81	320					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				ACTCAGTATATATCTGAGAGT	0.343																																																0			X											30	28	29					X																	47775003		1853	4096	5949	47659947	SO:0001583	missense	347344			AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"Zinc fingers, C2H2-type", "-"	13156	protein-coding gene	gene with protein product		314998	"zinc finger protein 81 (HFZ20)", "mental retardation, X-linked 45"	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.958T>C	X.37:g.47775003T>C	ENSP00000366153:p.Tyr320His		47659947	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	.	.	.	.	.	.	.	.	.	.	T	4.652	0.121137	0.08881	.	.	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.04502	3.61;3.61	4.16	4.16	0.48862	.	0.000000	0.36932	N	0.002325	T	0.00608	0.0020	N	0.00009	-3.09	0.26395	N	0.976514	B	0.13594	0.008	B	0.17433	0.018	T	0.42932	-0.9422	10	0.02654	T	1	.	5.4493	0.16554	0.0:0.1228:0.0:0.8772	.	320	P51508	ZNF81_HUMAN	H	320	ENSP00000366153:Y320H;ENSP00000341151:Y320H	ENSP00000341151:Y320H	Y	+	1	0	ZNF81	47659947	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	2.980000	0.49321	1.853000	0.53794	0.486000	0.48141	TAT		0.343	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137		C	47775003	T	C	47775003	3	2	12	1	0	0	0	0	1	0	0	0	18213	1406	49	4	972	4	ZNF81	23	47775003	Missense_Mutation	SNP	T	TCGA-AF-6672-01A-11D-1826-10	10462301	47775003	107495557	144	1554										
DLG3	1741	hgsc.bcm.edu	37	chrX	69711975	69711975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agggccctgtttgattatgaTcggactcgggacagctgcct	13	10	0	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:69711975T>C	ENST00000374360.3	+	11	1772	c.1539T>C	c.(1537-1539)gaT>gaC	p.D513D	DLG3_ENST00000194900.4_Silent_p.D531D|DLG3_ENST00000542398.1_Silent_p.D30D|DLG3_ENST00000374355.3_Silent_p.D176D	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	513	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)			endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					TTGATTATGATCGGACTCGGG	0.502																																																0			X											56	31	39					X																	69711975		2202	4291	6493	69628700	SO:0001819	synonymous_variant	4356			U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"neuroendocrine-dlg", "protein phosphatase 1, regulatory subunit 82"	300189	"discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.1539T>C	X.37:g.69711975T>C			69628700	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Silent	SNP	ENST00000374360.3	37	CCDS14403.1																																																																																				0.502	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		C	69711975	T	C	69711975	2	2	12	1	0	0	0	0	0	0	0	1	4567	1432	50	4		4	DLG3	23	69711975	Silent	SNP	T	TCGA-AF-6672-01A-11D-1826-10	21936972	69711975	85558585	145	1555										
MED12	9968	hgsc.bcm.edu	37	chrX	70339907	70339907	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	agaggtgtttgggtacttagCcaaatacacagtgcctgtga	12	7	0	2			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:70339907C>G	ENST00000374080.3	+	4	472	c.440C>G	c.(439-441)gCc>gGc	p.A147G	MED12_ENST00000374102.1_Missense_Mutation_p.A147G|MED12_ENST00000333646.6_Missense_Mutation_p.A147G			Q93074	MED12_HUMAN	mediator complex subunit 12	147					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					GGGTACTTAGCCAAATACACA	0.473			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																																Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	0			X											120	113	115					X																	70339907		1974	4152	6126	70256632	SO:0001583	missense	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.440C>G	X.37:g.70339907C>G	ENSP00000363193:p.Ala147Gly		70256632	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.010856	0.75046	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.59638	0.26;0.26;0.26;0.25	5.16	5.16	0.70880	Mediator complex, subunit Med12 (1);	0.000000	0.85682	D	0.000000	T	0.61640	0.2363	L	0.40543	1.245	0.58432	D	0.999998	P;D;P	0.54772	0.486;0.968;0.772	B;P;B	0.54270	0.185;0.747;0.407	T	0.60362	-0.7278	10	0.38643	T	0.18	-13.1395	15.953	0.79859	0.0:1.0:0.0:0.0	.	147;147;147	F5H3Y1;Q93074-3;Q93074	.;.;MED12_HUMAN	G	147;147;147;147;115	ENSP00000333125:A147G;ENSP00000363215:A147G;ENSP00000363193:A147G;ENSP00000414203:A115G	ENSP00000333125:A147G	A	+	2	0	MED12	70256632	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.431000	0.80335	2.391000	0.81399	0.600000	0.82982	GCC		0.473	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		G	70339907	C	G	70339907	3	3	12	1	0	0	0	0	1	0	0	0	9458	739	26	5	454	5	MED12	23	70339907	Missense_Mutation	SNP	C	TCGA-AF-6672-01A-11D-1826-10	627932	70339907	84930653	146	1556										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91133863	91133863	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616438356164384	9	1	0.893228454172367	3.37441860465116	0.465437048917402	1	1	0	gaaaaagaaaaagaagaagaAgcattcccctaagaacttgc	8	7	0	5			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:91133863A>C	ENST00000373094.1	+	2	3469	c.2624A>C	c.(2623-2625)aAg>aCg	p.K875T	PCDH11X_ENST00000373097.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000361724.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000361655.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000504220.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000298274.8_Missense_Mutation_p.K875T|PCDH11X_ENST00000395337.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000406881.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000373088.1_Missense_Mutation_p.K875T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	875	Poly-Lys.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						aagaagaagaagCATTCCCCT	0.398																																					NSCLC(38;925 1092 2571 38200 45895)											0			X											82	75	77					X																	91133863		2203	4300	6503	91020519	SO:0001583	missense	83259			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2624A>C	X.37:g.91133863A>C	ENSP00000362186:p.Lys875Thr		91020519	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.527234	0.27299	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	4.44	4.44	0.53790	Protocadherin (1);	0.090591	0.56097	D	0.000033	T	0.39332	0.1074	M	0.71581	2.175	0.40946	D	0.984508	B;B;B;B;B;B;B;B	0.28026	0.016;0.165;0.165;0.165;0.165;0.198;0.009;0.009	B;B;B;B;B;B;B;B	0.28011	0.03;0.051;0.051;0.051;0.051;0.085;0.012;0.012	T	0.44862	-0.9300	10	0.72032	D	0.01	.	12.5269	0.56091	1.0:0.0:0.0:0.0	.	875;875;875;875;875;875;875;875	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	T	875	ENSP00000378746:K875T;ENSP00000362186:K875T;ENSP00000362189:K875T;ENSP00000355040:K875T;ENSP00000362180:K875T;ENSP00000423762:K875T;ENSP00000355105:K875T;ENSP00000384758:K875T;ENSP00000298274:K875T	ENSP00000298274:K875T	K	+	2	0	PCDH11X	91020519	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	4.566000	0.60843	1.706000	0.51276	0.486000	0.48141	AAG		0.398	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		C	91133863	A	C	91133863	3	2	12	1	0	0	0	0	1	0	0	0	11539	72	3	4	2630	4	PCDH11X	23	91133863	Missense_Mutation	SNP	A	TCGA-AF-6672-01A-11D-1826-10	20793956	91133863	64136697	147	1557										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105570	27105571	+	Frame_Shift_Ins	INS	-	-	T													0	0	1	0	NA	0	1	1	0	gacgatgcctgattgagatcINStttggcattttaaaggagta							TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr1:27105570_27105571insT	ENST00000324856.7	+	20	5552_5553	c.5181_5182insT	c.(5182-5184)tttfs	p.F1728fs	ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.F1345fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.F1511fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.F56fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1728					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.G1729fs*7(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		TGATTGAGATCTTTGGCATTTT	0.475			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Insertion - Frameshift(1)	large_intestine(1)	1																																								26978158	SO:0001589	frameshift_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5184dupT	1.37:g.27105573_27105573dupT	ENSP00000320485:p.Phe1728fs		26978157	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	37	CCDS285.1																																																																																				0.475	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27105571	-	T	27105570	7	5	13	1	0	1	1	0	0	0	0	0	913	903	32	0	5259	0	ARID1A	1	27105570	Frame_Shift_Ins	INS	-	TCGA-AG-3574-01A-01W-0831-10		27105570	222145051	1	1558										
IVL	3713	hgsc.bcm.edu	37	chr1	152882328	152882328	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cccctgccctcagtcaggagCtcctcaagactgttcctcct	7	18	3	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr1:152882328C>A	ENST00000368764.3	+	2	119	c.55C>A	c.(55-57)Ctc>Atc	p.L19I	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	19					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.L19I(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGTCAGGAGCTCCTCAAGAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	77	81					1																	152882328		2203	4300	6503	151148952	SO:0001583	missense	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.55C>A	1.37:g.152882328C>A	ENSP00000357753:p.Leu19Ile		151148952	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	9.769	1.172163	0.21704	.	.	ENSG00000163207	ENST00000368764	T	0.09350	2.99	4.5	-4.9	0.03094	Involucrin, N-terminal (1);	.	.	.	.	T	0.02193	0.0068	L	0.50333	1.59	0.18873	N	0.999986	B	0.23377	0.084	B	0.24006	0.05	T	0.44314	-0.9336	9	0.21540	T	0.41	6.3575	4.2226	0.10565	0.2566:0.2842:0.0:0.4593	.	19	P07476	INVO_HUMAN	I	19	ENSP00000357753:L19I	ENSP00000357753:L19I	L	+	1	0	IVL	151148952	0.000000	0.05858	0.002000	0.10522	0.535000	0.34838	-0.794000	0.04584	-1.234000	0.02548	0.561000	0.74099	CTC		0.552	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152882328	C	A	152882328	3	1	13	1	0	0	0	0	1	0	0	0	7950	797	28	2	57	2	IVL	1	152882328	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	125776758	152882328	96368293	2	1559										
NME7	29922	hgsc.bcm.edu	37	chr1	169279275	169279275	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gtttattatttcaattatttCtccagcctttgatattgcat	4	7	2	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr1:169279275C>A	ENST00000367811.3	-	4	578	c.322G>T	c.(322-324)Gaa>Taa	p.E108*	RP4-800F24.1_ENST00000432081.1_RNA|NME7_ENST00000472647.1_Nonsense_Mutation_p.E72*|NME7_ENST00000469474.1_5'UTR	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	108					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.E108*(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					TCAATTATTTCTCCAGCCTTT	0.264																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											88	92	91					1																	169279275		2200	4289	6489	167545899	SO:0001587	stop_gained	29922			AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.322G>T	1.37:g.169279275C>A	ENSP00000356785:p.Glu108*		167545899	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Nonsense_Mutation	SNP	ENST00000367811.3	37	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	C	40	7.964266	0.98585	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	.	.	.	5.34	5.34	0.76211	.	0.209119	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-33.107	15.77	0.78162	0.0:1.0:0.0:0.0	.	.	.	.	X	72;108	.	ENSP00000356785:E108X	E	-	1	0	NME7	167545899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.664000	0.46783	2.513000	0.84729	0.650000	0.86243	GAA		0.264	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		A	169279275	C	A	169279275	4	1	13	1	0	0	0	0	0	1	0	0	10527	922	32	2	844	2	NME7	1	169279275	Nonsense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	16396947	169279275	79971346	3	1560										
CNRIP1	25927	hgsc.bcm.edu	37	chr2	68546426	68546426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cggtgagcagcttgatggtgCggttctggccgaagcgctgc	17	10	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr2:68546426C>T	ENST00000263655.3	-	1	712	c.107G>A	c.(106-108)cGc>cAc	p.R36H	CNRIP1_ENST00000409559.3_Missense_Mutation_p.R36H|CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Missense_Mutation_p.R36H	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	36								p.R36H(2)		kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CTTGATGGTGCGGTTCTGGCC	0.642																																																2	Substitution - Missense(2)	large_intestine(2)	2											51	40	44					2																	68546426		2154	4235	6389	68399930	SO:0001583	missense	25927			AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 32"	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.107G>A	2.37:g.68546426C>T	ENSP00000263655:p.Arg36His		68399930	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	37	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.841864	0.91197	.	.	ENSG00000119865	ENST00000409559;ENST00000263655;ENST00000409862	.	.	.	4.83	3.94	0.45596	.	0.000000	0.85682	D	0.000000	T	0.68384	0.2995	L	0.58810	1.83	0.54753	D	0.999989	D;D;D	0.76494	0.999;0.997;0.999	P;P;P	0.60886	0.88;0.799;0.855	T	0.72154	-0.4376	9	0.72032	D	0.01	-9.4359	13.6096	0.62068	0.0:0.8447:0.1553:0.0	.	36;36;36	B8ZZB8;Q96F85;Q96F85-2	.;CNRP1_HUMAN;.	H	36	.	ENSP00000263655:R36H	R	-	2	0	CNRIP1	68399930	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.058000	0.76676	1.231000	0.43661	0.491000	0.48974	CGC		0.642	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463		T	68546426	C	T	68546426	3	4	13	1	0	0	0	0	1	0	0	0	3639	768	27	1	460	1	CNRIP1	2	68546426	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10		68546426	174652947	4	1561										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141816607	141816607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aatcttcaaacacagttataCcataaagatgtctaacctat	3	9	3	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr2:141816607C>A	ENST00000389484.3	-	9	2224	c.1253G>T	c.(1252-1254)gGt>gTt	p.G418V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	418					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.G418V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CACAGTTATACCATAAAGATG	0.289										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											80	83	82					2																	141816607		2202	4296	6498	141533077	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1253G>T	2.37:g.141816607C>A	ENSP00000374135:p.Gly418Val		141533077	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830517	0.71258	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94280	-3.39	5.83	4.95	0.65309	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.071450	0.53938	U	0.000044	D	0.96247	0.8776	M	0.89715	3.055	0.80722	D	1	D	0.54047	0.964	P	0.55055	0.767	D	0.96645	0.9477	10	0.87932	D	0	.	14.3481	0.66680	0.0:0.9293:0.0:0.0707	.	418	Q9NZR2	LRP1B_HUMAN	V	418;356	ENSP00000374135:G418V	ENSP00000374135:G418V	G	-	2	0	LRP1B	141533077	0.996000	0.38824	0.998000	0.56505	0.991000	0.79684	2.994000	0.49433	2.757000	0.94681	0.563000	0.77884	GGT		0.289	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141816607	C	A	141816607	3	1	13	1	0	0	0	0	1	0	0	0	8984	507	18	2	12878	2	LRP1B	2	141816607	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	73270181	141816607	101382766	5	1562										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166223786	166223786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aagaaggcaaagggaaactcTggtggaatttgaggaaaaca	13	4	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr2:166223786T>C	ENST00000375437.2	+	19	3870	c.3580T>C	c.(3580-3582)Tgg>Cgg	p.W1194R	SCN2A_ENST00000283256.6_Missense_Mutation_p.W1194R|SCN2A_ENST00000357398.3_Missense_Mutation_p.W1194R|SCN2A_ENST00000375427.2_Missense_Mutation_p.W1194R	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1194					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.W1194R(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGGAAACTCTGGTGGAATTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											167	158	161					2																	166223786		2203	4300	6503	165932032	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3580T>C	2.37:g.166223786T>C	ENSP00000364586:p.Trp1194Arg		165932032	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.703925	0.88924	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09	6.07	6.07	0.98685	Sodium ion transport-associated (1);	0.193849	0.38111	N	0.001818	D	0.97489	0.9178	H	0.96111	3.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.98635	1.0673	10	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	1194;1194	Q99250-2;Q99250	.;SCN2A_HUMAN	R	1194	ENSP00000364586:W1194R;ENSP00000349973:W1194R;ENSP00000283256:W1194R;ENSP00000364576:W1194R	ENSP00000283256:W1194R	W	+	1	0	SCN2A	165932032	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	TGG		0.398	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166223786	T	C	166223786	3	2	13	1	0	0	0	0	1	0	0	0	13953	1580	55	4	3746	4	SCN2A	2	166223786	Missense_Mutation	SNP	T	TCGA-AG-3574-01A-01W-0831-10	24407179	166223786	76975587	6	1563										
NDUFS1	4719	hgsc.bcm.edu	37	chr2	206997720	206997720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cagtaacaccactagtcatcCgaatcttttgtgcaatgcta	6	11	2	0	rs141196622		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr2:206997720C>T	ENST00000233190.6	-	14	1768	c.1502G>A	c.(1501-1503)cGg>cAg	p.R501Q	NDUFS1_ENST00000440274.1_Missense_Mutation_p.R465Q|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R501Q|NDUFS1_ENST00000432169.1_Missense_Mutation_p.R390Q|NDUFS1_ENST00000455934.2_Missense_Mutation_p.R515Q|NDUFS1_ENST00000423725.1_Missense_Mutation_p.R444Q|NDUFS1_ENST00000457011.1_Missense_Mutation_p.R385Q	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	501					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R501Q(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTAGTCATCCGAATCTTTTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	116	107	110		1394,1169,1331,1544,1502	5.9	0.3	2	dbSNP_134	110	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	43,43,43,43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	465/692,390/617,444/671,515/742,501/728	206997720	1,13005	2203	4300	6503	206705965	SO:0001583	missense	4719				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1502G>A	2.37:g.206997720C>T	ENSP00000233190:p.Arg501Gln		206705965	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199892	0.58126	2.27E-4	0.0	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	5.91	5.91	0.95273	Molybdopterin oxidoreductase (1);	0.108901	0.64402	D	0.000016	D	0.86489	0.5945	L	0.45698	1.435	0.80722	D	1	B;B;B;B	0.15930	0.008;0.014;0.015;0.015	B;B;B;B	0.28011	0.085;0.017;0.017;0.017	T	0.80830	-0.1207	10	0.49607	T	0.09	-31.8348	20.2946	0.98546	0.0:1.0:0.0:0.0	.	390;465;515;501	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	Q	501;444;385;465;515;501;390	ENSP00000233190:R501Q;ENSP00000397760:R444Q;ENSP00000400976:R385Q;ENSP00000409766:R465Q;ENSP00000392709:R515Q;ENSP00000399912:R501Q;ENSP00000409689:R390Q	ENSP00000233190:R501Q	R	-	2	0	NDUFS1	206705965	0.998000	0.40836	0.333000	0.25482	0.991000	0.79684	5.493000	0.66899	2.804000	0.96469	0.462000	0.41574	CGG		0.363	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		T	206997720	C	T	206997720	3	4	13	1	0	0	0	0	1	0	0	0	10322	652	23	1	705	1	NDUFS1	2	206997720	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	40773934	206997720	36201653	7	1564										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10370566	10370566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	ggtagctgatttgcttgtgtCggtcgtcaggttgatcccac	13	9	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr3:10370566C>T	ENST00000352432.4	-	22	3733	c.3664G>A	c.(3664-3666)Gac>Aac	p.D1222N	ATP2B2_ENST00000467702.2_5'UTR|MIR378B_ENST00000578876.1_RNA|ATP2B2_ENST00000360273.2_Missense_Mutation_p.D1222N|ATP2B2_ENST00000343816.4_Missense_Mutation_p.D1208N|ATP2B2_ENST00000397077.1_Missense_Mutation_p.D1177N|ATP2B2_ENST00000383800.4_Missense_Mutation_p.D1177N			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1222					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.D1177N(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TTGCTTGTGTCGGTCGTCAGG	0.607																																					Ovarian(125;1619 1709 15675 19819 38835)											1	Substitution - Missense(1)	large_intestine(1)	3											117	102	107					3																	10370566		2203	4300	6503	10345566	SO:0001583	missense	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3664G>A	3.37:g.10370566C>T	ENSP00000324172:p.Asp1222Asn		10345566	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830701	0.50845	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124	D;D;D;D;D;D	0.92299	-3.0;-2.99;-2.99;-3.0;-3.01;-2.99	5.97	5.97	0.96955	.	0.146053	0.64402	D	0.000013	D	0.90397	0.6994	L	0.50333	1.59	0.80722	D	1	B;B;B	0.19331	0.035;0.008;0.004	B;B;B	0.15052	0.012;0.005;0.002	D	0.85029	0.0916	10	0.34782	T	0.22	-28.1009	20.4171	0.99027	0.0:1.0:0.0:0.0	.	1157;1189;1222	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	N	1222;1177;1177;1222;1208;1157;411;1078	ENSP00000324172:D1222N;ENSP00000373311:D1177N;ENSP00000380267:D1177N;ENSP00000353414:D1222N;ENSP00000344677:D1208N;ENSP00000414854:D1078N	ENSP00000344677:D1208N	D	-	1	0	ATP2B2	10345566	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.994000	0.70623	2.832000	0.97577	0.585000	0.79938	GAC		0.607	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		T	10370566	C	T	10370566	3	4	13	1	0	0	0	0	1	0	0	0	1141	884	31	1	71	1	ATP2B2	3	10370566	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10		10370566	187651864	8	1565										
GLT8D1	55830	hgsc.bcm.edu	37	chr3	52728926	52728926	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tttgcctgttgggtctggaaTataccatttttcccaaacat	7	9	1	0			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr3:52728926T>A	ENST00000407584.3	-	11	1901	c.1051A>T	c.(1051-1053)Att>Ttt	p.I351F	GLT8D1_ENST00000463827.1_5'UTR|SNORD69_ENST00000391150.1_RNA|GLT8D1_ENST00000266014.5_Missense_Mutation_p.I351F|GLT8D1_ENST00000478968.2_Missense_Mutation_p.I351F|GLT8D1_ENST00000491606.1_Missense_Mutation_p.I351F|GLT8D1_ENST00000394783.3_Missense_Mutation_p.I351F	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	351						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.I351F(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				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)		GGGTCTGGAATATACCATTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											176	158	164					3																	52728926		2203	4300	6503	52703966	SO:0001583	missense	55830			AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"Glycosyltransferase family 8 domain containing"	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.1051A>T	3.37:g.52728926T>A	ENSP00000385730:p.Ile351Phe		52703966	Q7Z4D1|Q8N2J6|Q9P0I5	Missense_Mutation	SNP	ENST00000407584.3	37	CCDS2862.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.94|17.94	3.511868|3.511868	0.64522|0.64522	.|.	.|.	ENSG00000016864|ENSG00000016864	ENST00000478968;ENST00000394783;ENST00000407584;ENST00000266014;ENST00000491606|ENST00000394786	T;T;T;T;T|.	0.21932|.	1.98;1.98;1.98;1.98;1.98|.	5.63|5.63	4.46|4.46	0.54185|0.54185	.|.	0.149392|.	0.64402|.	D|.	0.000013|.	T|T	0.64616|0.64616	0.2614|0.2614	M|M	0.69823|0.69823	2.125|2.125	0.58432|0.58432	D|D	0.999997|0.999997	P|.	0.43477|.	0.808|.	B|.	0.41860|.	0.368|.	T|T	0.62996|0.62996	-0.6735|-0.6735	10|5	0.46703|.	T|.	0.11|.	-14.4877|-14.4877	8.6744|8.6744	0.34170|0.34170	0.0:0.1773:0.0:0.8227|0.0:0.1773:0.0:0.8227	.|.	351|.	Q68CQ7|.	GL8D1_HUMAN|.	F|F	351|180	ENSP00000419612:I351F;ENSP00000378263:I351F;ENSP00000385730:I351F;ENSP00000266014:I351F;ENSP00000418853:I351F|.	ENSP00000266014:I351F|.	I|Y	-|-	1|2	0|0	GLT8D1|GLT8D1	52703966|52703966	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.382000|1.382000	0.34374|0.34374	1.048000|1.048000	0.40298|0.40298	0.533000|0.533000	0.62120|0.62120	ATT|TAT		0.403	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932		A	52728926	T	A	52728926	3	1	13	1	0	0	0	0	1	0	0	0	6489	1406	49	5	68	5	GLT8D1	3	52728926	Missense_Mutation	SNP	T	TCGA-AG-3574-01A-01W-0831-10	42358360	52728926	145293504	9	1566										
RASA1	5921	hgsc.bcm.edu	37	chr5	86629108	86629108	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tagaagatagaaggcgtgtaCgagctattctaccttacaca	9	8	1	3	rs137853218		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr5:86629108C>T	ENST00000274376.6	+	4	1417	c.853C>T	c.(853-855)Cga>Tga	p.R285*	RASA1_ENST00000512763.1_Nonsense_Mutation_p.R118*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.R119*|RASA1_ENST00000456692.2_Nonsense_Mutation_p.R108*	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	285	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.R285*(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AAGGCGTGTACGAGCTATTCT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	5	GRCh37	CM081410	RASA1	M	rs137853218						67	72	71					5																	86629108		2203	4300	6503	86664864	SO:0001587	stop_gained	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.853C>T	5.37:g.86629108C>T	ENSP00000274376:p.Arg285*		86664864	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	42	9.693761	0.99240	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	15.7476	0.77958	0.1368:0.8631:0.0:0.0	.	.	.	.	X	285;318;108;118;119	.	ENSP00000274376:R285X	R	+	1	2	RASA1	86664864	0.998000	0.40836	0.990000	0.47175	0.957000	0.61999	3.659000	0.54489	2.587000	0.87381	0.650000	0.86243	CGA		0.313	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		T	86629108	C	T	86629108	4	4	13	1	0	0	0	0	0	1	0	0	13097	528	19	1	879	1	RASA1	5	86629108	Nonsense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10		86629108	94286152	10	1567										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140221377	140221377	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cggtttccgctagagggcgcGtccgatgcagatgttggagc	16	10	0	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr5:140221377G>A	ENST00000531613.1	+	1	471	c.471G>A	c.(469-471)gcG>gcA	p.A157A	PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000378123.3_Silent_p.A157A|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	157	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A157A(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGAGGGCGCGTCCGATGCAG	0.458																																																2	Substitution - coding silent(2)	large_intestine(2)	5											80	86	84					5																	140221377		2203	4300	6503	140201561	SO:0001819	synonymous_variant	56140			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.471G>A	5.37:g.140221377G>A			140201561	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																				0.458	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140221377	G	A	140221377	2	1	13	1	0	0	0	0	0	0	0	1	11561	1132	40	1		1	PCDHA8	5	140221377	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10	53592269	140221377	40693883	11	1568										
PPP2R2B	5521	hgsc.bcm.edu	37	chr5	145980011	145980011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	atctgttgcttggatcttccGgctcttcaaaaactgcagaa	8	10	4	1	rs148423117		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr5:145980011G>A	ENST00000394413.3	-	7	1373	c.803C>T	c.(802-804)cCg>cTg	p.P268L	PPP2R2B_ENST00000336640.6_Missense_Mutation_p.P271L|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.P268L|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.P257L|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.P326L|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.P257L|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.P274L|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.P268L|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.P334L|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.P268L			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	268					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.P271L(3)|p.P326L(2)|p.P268L(1)|p.P257L(1)		endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGATCTTCCGGCTCTTCAAA	0.413																																																7	Substitution - Missense(7)	kidney(4)|large_intestine(3)	5						G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	56	56	56		803,803,803,803,812,743,770	5.8	1	5	dbSNP_134	56	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	PPP2R2B	NM_001127381.1,NM_004576.2,NM_181674.2,NM_181675.2,NM_181676.2,NM_181677.2,NM_181678.2	98,98,98,98,98,98,98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	268/444,268/444,268/444,268/444,271/447,248/424,257/433	145980011	1,13005	2203	4300	6503	145960204	SO:0001583	missense	5521			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9305	protein-coding gene	gene with protein product	"PP2A subunit B isoform beta"	604325	"spinocerebellar ataxia 12", "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.803C>T	5.37:g.145980011G>A	ENSP00000377935:p.Pro268Leu		145960204	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928122	0.73327	2.27E-4	0.0	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	M	0.79475	2.455	0.80722	D	1	P;P;P;P;P;P	0.43750	0.816;0.816;0.816;0.664;0.705;0.816	B;B;B;B;B;B	0.34590	0.13;0.186;0.134;0.13;0.035;0.186	T	0.43637	-0.9379	10	0.51188	T	0.08	-22.597	20.0467	0.97609	0.0:0.0:1.0:0.0	.	326;274;257;334;271;268	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	L	268;257;334;268;268;268;257;271;274;326	ENSP00000377935:P268L;ENSP00000431320:P257L;ENSP00000377936:P334L;ENSP00000377933:P268L;ENSP00000349283:P268L;ENSP00000398779:P268L;ENSP00000377932:P257L;ENSP00000336591:P271L;ENSP00000421396:P274L;ENSP00000377931:P326L	ENSP00000336591:P271L	P	-	2	0	AC011357.1	145960204	1.000000	0.71417	0.977000	0.42913	0.992000	0.81027	9.869000	0.99810	2.749000	0.94314	0.655000	0.94253	CCG		0.413	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678		A	145980011	G	A	145980011	3	1	13	1	0	0	0	0	1	0	0	0	12419	1116	39	1	540	1	PPP2R2B	5	145980011	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	5758634	145980011	34935249	12	1569										
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32137800	32137800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ttggtaggaggacatgactaTggggacaatgggaacctggg	17	5	0	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr6:32137800T>C	ENST00000395499.1	-	6	1201	c.622A>G	c.(622-624)Ata>Gta	p.I208V	AGPAT1_ENST00000395497.1_Missense_Mutation_p.I208V|AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000395496.1_Missense_Mutation_p.I208V|AGPAT1_ENST00000375107.3_Missense_Mutation_p.I208V|PPT2-EGFL8_ENST00000422437.1_Intron|AGPAT1_ENST00000375104.2_Missense_Mutation_p.I208V|AGPAT1_ENST00000412465.2_Missense_Mutation_p.I96V|AGPAT1_ENST00000336984.6_Missense_Mutation_p.I208V			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	208					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.I208V(1)		central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						GACATGACTATGGGGACAATG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											84	78	80					6																	32137800		1511	2709	4220	32245778	SO:0001583	missense	10554			U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	324	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, alpha"	603099	"1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.622A>G	6.37:g.32137800T>C	ENSP00000378877:p.Ile208Val		32245778	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	.	.	.	.	.	.	.	.	.	.	T	4.735	0.136739	0.09032	.	.	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984;ENST00000412465	D;D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.99	5.99	0.97316	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.054086	0.85682	D	0.000000	T	0.54382	0.1855	N	0.01086	-1.025	0.40947	D	0.984511	B;B;B	0.24132	0.065;0.098;0.015	B;B;B	0.31101	0.054;0.124;0.011	T	0.61686	-0.7012	10	0.02654	T	1	-16.5371	8.8876	0.35414	0.0:0.0819:0.0:0.9181	.	172;98;208	B4DRH1;B3KPH3;Q99943	.;.;PLCA_HUMAN	V	208;208;208;208;208;208;96	ENSP00000378874:I208V;ENSP00000364248:I208V;ENSP00000378877:I208V;ENSP00000364245:I208V;ENSP00000378875:I208V;ENSP00000337463:I208V;ENSP00000410473:I96V	ENSP00000337463:I208V	I	-	1	0	AGPAT1	32245778	0.973000	0.33851	1.000000	0.80357	0.999000	0.98932	0.468000	0.22051	2.291000	0.77112	0.533000	0.62120	ATA		0.552	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		C	32137800	T	C	32137800	3	2	13	1	0	0	0	0	1	0	0	0	386	1464	51	4	237	4	AGPAT1	6	32137800	Missense_Mutation	SNP	T	TCGA-AG-3574-01A-01W-0831-10		32137800	138977267	13	1570										
MAPK13	5603	hgsc.bcm.edu	37	chr6	36103814	36103814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	agtacatccactctgctgggGtcgtgcacagggtgagtgct	14	10	1	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr6:36103814G>A	ENST00000211287.4	+	5	698	c.436G>A	c.(436-438)Gtc>Atc	p.V146I	MAPK13_ENST00000373761.6_Intron|MAPK13_ENST00000490334.1_3'UTR|MAPK13_ENST00000373759.1_Missense_Mutation_p.V68I|MAPK13_ENST00000373766.5_Missense_Mutation_p.V146I	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.V146I(1)		breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						CTCTGCTGGGGTCGTGCACAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	6											133	117	122					6																	36103814		2203	4300	6503	36211792	SO:0001583	missense	5603			Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.436G>A	6.37:g.36103814G>A	ENSP00000211287:p.Val146Ile		36211792	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Missense_Mutation	SNP	ENST00000211287.4	37	CCDS4818.1	.	.	.	.	.	.	.	.	.	.	G	3.288	-0.145572	0.06627	.	.	ENSG00000156711	ENST00000211287;ENST00000373770;ENST00000373766;ENST00000373759	T;T;T	0.61392	0.11;0.11;0.11	4.88	2.74	0.32292	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.272209	0.26136	N	0.026122	T	0.08626	0.0214	N	0.04132	-0.27	0.23386	N	0.99779	B	0.02656	0.0	B	0.10450	0.005	T	0.40720	-0.9548	10	0.02654	T	1	-22.5091	6.3362	0.21296	0.4583:0.0:0.5417:0.0	.	146	O15264	MK13_HUMAN	I	146;146;146;68	ENSP00000211287:V146I;ENSP00000362871:V146I;ENSP00000362864:V68I	ENSP00000211287:V146I	V	+	1	0	MAPK13	36211792	0.995000	0.38212	0.995000	0.50966	0.857000	0.48899	2.762000	0.47597	0.293000	0.22520	0.555000	0.69702	GTC		0.587	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1			A	36103814	G	A	36103814	3	1	13	1	0	0	0	0	1	0	0	0	9305	1261	44	3	454	3	MAPK13	6	36103814	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	3966014	36103814	135011253	14	1571										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50683108	50683108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	agtactaccagcagatccacCacggggagcccaccgacttt	9	15	0	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr6:50683108C>T	ENST00000008391.3	+	2	547	c.319C>T	c.(319-321)Cac>Tac	p.H107Y		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.H107Y(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GCAGATCCACCACGGGGAGCC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	106	111					6																	50683108		2203	4300	6503	50791067	SO:0001583	missense	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.319C>T	6.37:g.50683108C>T	ENSP00000008391:p.His107Tyr		50791067		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	4.333	0.061241	0.08339	.	.	ENSG00000008197	ENST00000008391	D	0.97114	-4.25	5.21	5.21	0.72293	.	0.100353	0.64402	D	0.000002	D	0.94663	0.8279	N	0.08118	0	0.80722	D	1	P	0.45126	0.851	P	0.55391	0.775	D	0.96344	0.9253	10	0.62326	D	0.03	-16.7743	19.1268	0.93388	0.0:1.0:0.0:0.0	.	107	Q7Z6R9	AP2D_HUMAN	Y	107	ENSP00000008391:H107Y	ENSP00000008391:H107Y	H	+	1	0	TFAP2D	50791067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.604000	0.82830	2.590000	0.87494	0.655000	0.94253	CAC		0.612	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50683108	C	T	50683108	3	4	13	1	0	0	0	0	1	0	0	0	15829	594	21	3	325	3	TFAP2D	6	50683108	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	14579294	50683108	120431959	15	1572										
NR2E1	7101	hgsc.bcm.edu	37	chr6	108502832	108502832	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	caagatgaggctcagctaacGctcaacagctacatccatac	7	13	2	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr6:108502832G>A	ENST00000368986.4	+	8	1680	c.972G>A	c.(970-972)acG>acA	p.T324T	NR2E1_ENST00000368983.3_Silent_p.T361T	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	324	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.T324T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CTCAGCTAACGCTCAACAGCT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	6											136	118	124					6																	108502832		2203	4300	6503	108609525	SO:0001819	synonymous_variant	7101			Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.972G>A	6.37:g.108502832G>A			108609525	Q6ZMP8	Silent	SNP	ENST00000368986.4	37	CCDS5063.1																																																																																				0.478	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108502832	G	A	108502832	2	1	13	1	0	0	0	0	0	0	0	1	10656	1074	38	1		1	NR2E1	6	108502832	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10	57819724	108502832	62612235	16	1573										
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27868361	27868361	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aaggtgtgcccgatgtgcagCgagcagttccctcctgacta	12	12	0	1	rs534866304		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr7:27868361C>T	ENST00000396319.2	+	17	2371	c.2283C>T	c.(2281-2283)agC>agT	p.S761S	TAX1BP1_ENST00000543117.1_Silent_p.S719S|TAX1BP1_ENST00000433216.2_Silent_p.S562S|TAX1BP1_ENST00000265393.6_Silent_p.S719S|TAX1BP1_ENST00000409980.1_Silent_p.S785S	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	761					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.S761S(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CGATGTGCAGCGAGCAGTTCC	0.418													C|||	1	0.000199681	0	0	5008	,	,		17086	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											150	140	143					7																	27868361		2203	4300	6503	27834886	SO:0001819	synonymous_variant	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.2283C>T	7.37:g.27868361C>T			27834886	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	37	CCDS5415.1																																																																																				0.418	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		T	27868361	C	T	27868361	2	4	13	1	0	0	0	0	0	0	0	1	15633	767	27	1		1	TAX1BP1	7	27868361	Silent	SNP	C	TCGA-AG-3574-01A-01W-0831-10		27868361	131270302	17	1574										
IGFBP3	3486	hgsc.bcm.edu	37	chr7	45956967	45956967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gaacttgggatcagacacccGgtgcgtgctggagacggacg	16	10	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr7:45956967G>A	ENST00000275521.6	-	2	608	c.475C>T	c.(475-477)Cgg>Tgg	p.R159W	IGFBP3_ENST00000381083.4_Missense_Mutation_p.R165W|IGFBP3_ENST00000381086.5_Missense_Mutation_p.R62W|IGFBP3_ENST00000465642.1_5'UTR	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	159	Ser/Thr-rich.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)	p.R159W(1)		large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	TCAGACACCCGGTGCGTGCTG	0.532											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	7											85	80	82					7																	45956967		2203	4300	6503	45923492	SO:0001583	missense	3486				CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"growth hormone-dependent binding protein", "acid stable subunit of the 140 K IGF complex", "binding protein 53", "binding protein 29", "IGF-binding protein 3"	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.475C>T	7.37:g.45956967G>A	ENSP00000275521:p.Arg159Trp	935	45923492	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	37	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.28|13.28	2.191392|2.191392	0.38707|0.38707	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000417621|ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047;ENST00000448817	.|T;T;T;T	.|0.27402	.|2.32;1.67;2.33;1.76	5.55|5.55	-2.77|-2.77	0.05877|0.05877	.|.	.|0.888278	.|0.09850	.|N	.|0.747650	T|T	0.28433|0.28433	0.0703|0.0703	M|M	0.80183|0.80183	2.485|2.485	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.42692	.|0.239;0.787;0.646	.|B;B;B	.|0.36464	.|0.035;0.225;0.072	T|T	0.28902|0.28902	-1.0029|-1.0029	5|10	.|0.72032	.|D	.|0.01	-22.1882|-22.1882	4.6062|4.6062	0.12378|0.12378	0.228:0.0:0.3159:0.456|0.228:0.0:0.3159:0.456	.|.	.|62;159;144	.|B3KWK7;P17936;B4DN53	.|.;IBP3_HUMAN;.	L|W	20|136;159;62;145;57;165;131;49	.|ENSP00000275521:R159W;ENSP00000370476:R62W;ENSP00000370473:R165W;ENSP00000389668:R49W	.|ENSP00000275521:R159W	P|R	-|-	2|1	0|2	IGFBP3|IGFBP3	45923492|45923492	0.998000|0.998000	0.40836|0.40836	0.002000|0.002000	0.10522|0.10522	0.048000|0.048000	0.14542|0.14542	0.652000|0.652000	0.24888|0.24888	-0.172000|-0.172000	0.10779|0.10779	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.532	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398		A	45956967	G	A	45956967	3	1	13	1	0	0	0	0	1	0	0	0	7601	1115	39	1	412	1	IGFBP3	7	45956967	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	18088606	45956967	113181696	18	1575										
CSGALNACT1	55790	hgsc.bcm.edu	37	chr8	19363229	19363229	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ggcagtgccagctgctcctcGtcaccttttggggtgcaggc	14	13	1	0			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr8:19363229G>A	ENST00000454498.2	-	4	1130	c.117C>T	c.(115-117)gaC>gaT	p.D39D	CSGALNACT1_ENST00000311540.4_Silent_p.D39D|CSGALNACT1_ENST00000544602.1_Silent_p.D39D|CSGALNACT1_ENST00000332246.6_Silent_p.D39D|CSGALNACT1_ENST00000522854.1_Silent_p.D39D	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	39					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)	p.D39D(1)|p.D39E(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		GCTGCTCCTCGTCACCTTTTG	0.627																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|NS(1)	8											87	85	86					8																	19363229		2203	4300	6503	19407509	SO:0001819	synonymous_variant	55790			AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"Beta 4-glycosyltransferases"	24290	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase"					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.117C>T	8.37:g.19363229G>A			19407509	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Silent	SNP	ENST00000454498.2	37	CCDS6010.1																																																																																				0.627	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371		A	19363229	G	A	19363229	2	1	13	1	0	0	0	0	0	0	0	1	3944	1136	40	1		1	CSGALNACT1	8	19363229	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10		19363229	127000793	19	1576										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113277692	113277692	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ccattaattgtacaagtcctGattctggagccattcaattc	6	10	2	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr8:113277692G>T	ENST00000297405.5	-	60	9880	c.9636C>A	c.(9634-9636)atC>atA	p.I3212I	CSMD3_ENST00000343508.3_Silent_p.I3172I|CSMD3_ENST00000455883.2_Silent_p.I3043I|CSMD3_ENST00000352409.3_Silent_p.I3142I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3212	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I3212I(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TACAAGTCCTGATTCTGGAGC	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											177	154	162					8																	113277692		2203	4300	6503	113346868	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9636C>A	8.37:g.113277692G>T			113346868	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113277692	G	T	113277692	2	4	13	1	0	0	0	0	0	0	0	1	3952	1280	45	2		2	CSMD3	8	113277692	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10	93914463	113277692	33086330	20	1577										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123601446	123601446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tgcctcctggtagcggaagcGtcggaagttctggtgggagg	18	8	1	0			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr11:123601446G>A	ENST00000529691.1	-	2	370	c.151C>T	c.(151-153)Cgc>Tgc	p.R51C	ZNF202_ENST00000530393.1_Missense_Mutation_p.R51C|ZNF202_ENST00000336139.4_Missense_Mutation_p.R51C			O95125	ZN202_HUMAN	zinc finger protein 202	51	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R51C(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		TAGCGGAAGCGTCGGAAGTTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											104	103	103					11																	123601446		2202	4299	6501	123106656	SO:0001583	missense	7753			AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.151C>T	11.37:g.123601446G>A	ENSP00000433881:p.Arg51Cys		123106656	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	37	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	G	5.341	0.248254	0.10130	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691;ENST00000533463	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	4.7	-3.61	0.04556	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.641780	0.12664	N	0.449374	T	0.03827	0.0108	L	0.41961	1.31	0.20074	N	0.999938	B	0.06786	0.001	B	0.06405	0.002	T	0.36553	-0.9743	10	0.46703	T	0.11	-2.5298	4.7731	0.13166	0.3452:0.0:0.4094:0.2454	.	51	O95125	ZN202_HUMAN	C	51	ENSP00000337724:R51C;ENSP00000432504:R51C;ENSP00000433881:R51C;ENSP00000431223:R51C	ENSP00000337724:R51C	R	-	1	0	ZNF202	123106656	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-2.698000	0.00826	-0.454000	0.07066	-1.130000	0.01982	CGC		0.542	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123601446	G	A	123601446	3	1	13	1	0	0	0	0	1	0	0	0	17802	1145	40	1	1819	1	ZNF202	11	123601446	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10		123601446	11405070	21	1578										
OPCML	4978	hgsc.bcm.edu	37	chr11	132306121	132306121	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aatcctcattccatccagacCagtggctaacctgcaagagg	8	13	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr11:132306121C>A	ENST00000331898.7	-	6	1374	c.796G>T	c.(796-798)Ggt>Tgt	p.G266C	OPCML_ENST00000524381.1_Missense_Mutation_p.G259C|OPCML_ENST00000541867.1_Missense_Mutation_p.G266C|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Missense_Mutation_p.G225C	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	266	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.G266C(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CCATCCAGACCAGTGGCTAAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											139	129	132					11																	132306121		2201	4297	6498	131811331	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.796G>T	11.37:g.132306121C>A	ENSP00000330862:p.Gly266Cys		131811331	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.637795	0.67130	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90669	0.7073	M	0.94142	3.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.995;0.992;0.992	D	0.92381	0.5913	10	0.87932	D	0	-22.5285	19.8961	0.96958	0.0:1.0:0.0:0.0	.	266;259;265;266	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	C	266;259;225;233;266	ENSP00000330862:G266C;ENSP00000434750:G259C;ENSP00000363910:G225C;ENSP00000445496:G266C	ENSP00000330862:G266C	G	-	1	0	OPCML	131811331	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	7.480000	0.81109	2.803000	0.96430	0.650000	0.86243	GGT		0.443	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		A	132306121	C	A	132306121	3	1	13	1	0	0	0	0	1	0	0	0	10905	594	21	2	249	2	OPCML	11	132306121	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	8704675	132306121	2700395	22	1579										
WNK1	65125	hgsc.bcm.edu	37	chr12	1017949	1017949	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	cccccaggctccaacctgcgGaccacttagacctagagaca	8	17	0	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr12:1017949G>A	ENST00000315939.6	+	28	7783	c.7140G>A	c.(7138-7140)cgG>cgA	p.R2380R	WNK1_ENST00000340908.4_Silent_p.R1973R|WNK1_ENST00000530271.2_Silent_p.R2878R|WNK1_ENST00000535572.1_Silent_p.R2132R|WNK1_ENST00000537687.1_Silent_p.R2640R	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2380			R -> W (in dbSNP:rs56262445). {ECO:0000269|PubMed:17344846}.		intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.R2380R(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CCAACCTGCGGACCACTTAGA	0.517																																					Colon(19;451 567 6672 12618 28860)											1	Substitution - coding silent(1)	large_intestine(1)	12											41	45	44					12																	1017949		2203	4300	6503	888210	SO:0001819	synonymous_variant	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.7140G>A	12.37:g.1017949G>A			888210	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																				0.517	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	1017949	G	A	1017949	2	1	13	1	0	0	0	0	0	0	0	1	17417	1161	41	3		3	WNK1	12	1017949	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10		1017949	132833946	23	1580										
LIMA1	51474	hgsc.bcm.edu	37	chr12	50594644	50594644	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	attttatgaattttgatttcGccaccactggctttcagctc	6	10	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr12:50594644G>A	ENST00000341247.4	-	7	1037	c.888C>T	c.(886-888)ggC>ggT	p.G296G	LIMA1_ENST00000394943.3_Silent_p.G296G|LIMA1_ENST00000552783.1_Silent_p.G136G|LIMA1_ENST00000552909.1_Silent_p.G136G|LIMA1_ENST00000552008.1_5'UTR|LIMA1_ENST00000547825.1_5'UTR|LIMA1_ENST00000552823.1_Silent_p.G136G|LIMA1_ENST00000552491.1_5'Flank	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	296					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.G296G(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TTTTGATTTCGCCACCACTGG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	12											175	175	175					12																	50594644		2203	4300	6503	48880911	SO:0001819	synonymous_variant	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.888C>T	12.37:g.50594644G>A			48880911	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Silent	SNP	ENST00000341247.4	37	CCDS8802.1																																																																																				0.383	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50594644	G	A	50594644	2	1	13	1	0	0	0	0	0	0	0	1	8819	1074	38	1		1	LIMA1	12	50594644	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10	49576695	50594644	83257251	24	1581										
ZBTB39	9880	hgsc.bcm.edu	37	chr12	57397042	57397042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	gtgctggctgacgtggtagcGataggcagcctctgacttga	15	9	1	3			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr12:57397042G>A	ENST00000300101.2	-	2	1745	c.1660C>T	c.(1660-1662)Cgc>Tgc	p.R554C		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	554					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R554C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						ACGTGGTAGCGATAGGCAGCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	41	42					12																	57397042		2203	4300	6503	55683309	SO:0001583	missense	9880			AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1660C>T	12.37:g.57397042G>A	ENSP00000300101:p.Arg554Cys		55683309	A7MD38|Q9UD98	Missense_Mutation	SNP	ENST00000300101.2	37	CCDS31839.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234742	0.58886	.	.	ENSG00000166860	ENST00000300101	T	0.61510	0.1	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.065623	0.64402	D	0.000010	T	0.76190	0.3953	M	0.87900	2.915	0.52099	D	0.999947	D	0.89917	1.0	D	0.64687	0.928	T	0.78612	-0.2136	10	0.51188	T	0.08	-24.3591	12.2924	0.54825	0.0:0.0:0.8308:0.1692	.	554	O15060	ZBT39_HUMAN	C	554	ENSP00000300101:R554C	ENSP00000300101:R554C	R	-	1	0	ZBTB39	55683309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.889000	0.69766	2.694000	0.91930	0.650000	0.86243	CGC		0.577	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830		A	57397042	G	A	57397042	3	1	13	1	0	0	0	0	1	0	0	0	17579	1058	37	1	482	1	ZBTB39	12	57397042	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	6802398	57397042	76454853	25	1582										
RNF6	6049	hgsc.bcm.edu	37	chr13	26788610	26788610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	atgatggctcaacaagctcaTtctcagaaatcctacgaaga	7	10	3	3			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr13:26788610T>C	ENST00000381588.4	-	5	2161	c.1409A>G	c.(1408-1410)aAt>aGt	p.N470S	RNF6_ENST00000468480.1_Intron|RNF6_ENST00000381570.3_Missense_Mutation_p.N470S|RNF6_ENST00000399762.2_Missense_Mutation_p.N114S|RNF6_ENST00000346166.3_Missense_Mutation_p.N470S	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	470					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N470S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		AACAAGCTCATTCTCAGAAAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	13											92	88	89					13																	26788610		2203	4300	6503	25686610	SO:0001583	missense	6049			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1409A>G	13.37:g.26788610T>C	ENSP00000371000:p.Asn470Ser		25686610	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	37	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.857993	0.32791	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	T;T;T;T	0.13657	3.15;3.15;3.15;2.57	4.5	3.28	0.37604	.	0.268186	0.35739	N	0.003012	T	0.13243	0.0321	L	0.51422	1.61	0.30634	N	0.757192	B;B	0.30406	0.06;0.278	B;B	0.25987	0.065;0.057	T	0.05801	-1.0863	10	0.59425	D	0.04	-5.103	11.0917	0.48119	0.0:0.0:0.5124:0.4876	.	114;470	B4DDP0;Q9Y252	.;RNF6_HUMAN	S	470;470;470;114	ENSP00000342121:N470S;ENSP00000371000:N470S;ENSP00000370982:N470S;ENSP00000382665:N114S	ENSP00000342121:N470S	N	-	2	0	RNF6	25686610	1.000000	0.71417	0.970000	0.41538	0.990000	0.78478	4.291000	0.59025	0.834000	0.34852	0.374000	0.22700	AAT		0.458	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		C	26788610	T	C	26788610	3	2	13	1	0	0	0	0	1	0	0	0	13535	1493	52	4	652	4	RNF6	13	26788610	Missense_Mutation	SNP	T	TCGA-AG-3574-01A-01W-0831-10		26788610	88381268	26	1583										
FREM2	341640	hgsc.bcm.edu	37	chr13	39264109	39264109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	caggcacccaaacatggccaCatgagagtgtctggacagat	11	11	1	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr13:39264109C>T	ENST00000280481.7	+	1	2844	c.2628C>T	c.(2626-2628)caC>caT	p.H876H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	876					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H876H(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACATGGCCACATGAGAGTGT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	13											93	79	84					13																	39264109		2203	4300	6503	38162109	SO:0001819	synonymous_variant	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2628C>T	13.37:g.39264109C>T			38162109	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.507	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39264109	C	T	39264109	2	4	13	1	0	0	0	0	0	0	0	1	6064	477	17	3		3	FREM2	13	39264109	Silent	SNP	C	TCGA-AG-3574-01A-01W-0831-10	12475499	39264109	75905769	27	1584										
MYO16	23026	hgsc.bcm.edu	37	chr13	109445885	109445885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	agtggatttgacctcactgcGccagatgaagcttcagagac	11	10	2	4	rs537057276	byFrequency	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr13:109445885G>A	ENST00000357550.2	+	5	613	c.572G>A	c.(571-573)cGc>cAc	p.R191H	MYO16_ENST00000356711.2_Missense_Mutation_p.R191H|MYO16_ENST00000251041.5_Missense_Mutation_p.R191H	NM_001198950.1	NP_001185879.1			myosin XVI									p.R191H(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ACCTCACTGCGCCAGATGAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	13											129	122	125					13																	109445885		2203	4300	6503	108243886	SO:0001583	missense	23026				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.572G>A	13.37:g.109445885G>A	ENSP00000350160:p.Arg191His		108243886		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.613625	0.28712	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041	T;T;T	0.53206	0.63;0.63;0.63	5.76	3.13	0.36017	Ankyrin repeat-containing domain (3);	0.173228	0.27447	U	0.019329	T	0.29882	0.0747	L	0.28014	0.82	0.80722	D	1	B;B	0.27951	0.08;0.195	B;B	0.21708	0.017;0.036	T	0.04522	-1.0945	9	.	.	.	.	9.1214	0.36788	0.2372:0.0:0.7628:0.0	.	191;191	Q9Y6X6-2;Q9Y6X6	.;MYO16_HUMAN	H	191	ENSP00000349145:R191H;ENSP00000350160:R191H;ENSP00000251041:R191H	.	R	+	2	0	MYO16	108243886	0.996000	0.38824	0.993000	0.49108	0.761000	0.43186	1.317000	0.33631	0.373000	0.24621	-0.218000	0.12543	CGC		0.443	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109445885	G	A	109445885	3	1	13	1	0	0	0	0	1	0	0	0	10094	1087	38	1	590	1	MYO16	13	109445885	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	70181776	109445885	5723993	28	1585										
LACTB	114294	hgsc.bcm.edu	37	chr15	63433510	63433510	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	acaataaaaagaaacgtcttGtcaacacaccttacgtggat	6	9	2	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr15:63433510G>T	ENST00000261893.4	+	6	1222	c.1150G>T	c.(1150-1152)Gtc>Ttc	p.V384F	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	384						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.V384F(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						GAAACGTCTTGTCAACACACC	0.353																																					Melanoma(85;443 1381 6215 27308 35583)											1	Substitution - Missense(1)	large_intestine(1)	15											115	111	112					15																	63433510		2203	4300	6503	61220563	SO:0001583	missense	114294			AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1150G>T	15.37:g.63433510G>T	ENSP00000261893:p.Val384Phe		61220563	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.905164	0.33628	.	.	ENSG00000103642	ENST00000261893	T	0.44083	0.93	5.64	2.78	0.32641	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.166042	0.53938	D	0.000058	T	0.40322	0.1112	M	0.65975	2.015	0.80722	D	1	P	0.37423	0.594	B	0.38921	0.285	T	0.18650	-1.0330	10	0.46703	T	0.11	-4.2337	8.6444	0.33996	0.2867:0.0:0.7133:0.0	.	384	P83111	LACTB_HUMAN	F	384	ENSP00000261893:V384F	ENSP00000261893:V384F	V	+	1	0	LACTB	61220563	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	4.670000	0.61583	0.430000	0.26230	-0.253000	0.11424	GTC		0.353	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		T	63433510	G	T	63433510	3	4	13	1	0	0	0	0	1	0	0	0	8619	1377	48	2	1176	2	LACTB	15	63433510	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10		63433510	39097882	29	1586										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11656242	11656242	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gcgacatagatccaatgtggAttgaatccctgaatactgtc	9	9	0	3			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr17:11656242A>T	ENST00000262442.4	+	33	6771	c.6703A>T	c.(6703-6705)Att>Ttt	p.I2235F	DNAH9_ENST00000454412.2_Missense_Mutation_p.I2235F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2235	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.I2235F(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		TCCAATGTGGATTGAATCCCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17											137	119	125					17																	11656242		2203	4300	6503	11596967	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6703A>T	17.37:g.11656242A>T	ENSP00000262442:p.Ile2235Phe		11596967	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.850476	0.91277	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	D;D	0.92348	-3.02;-3.02	5.56	5.56	0.83823	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	D	0.98046	0.9356	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99780	1.1027	10	0.87932	D	0	.	16.0147	0.80427	1.0:0.0:0.0:0.0	.	2235	Q9NYC9	DYH9_HUMAN	F	2235;2235;817	ENSP00000262442:I2235F;ENSP00000414874:I2235F	ENSP00000262442:I2235F	I	+	1	0	DNAH9	11596967	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	9.287000	0.95975	2.237000	0.73441	0.460000	0.39030	ATT		0.453	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11656242	A	T	11656242	3	4	13	1	0	0	0	0	1	0	0	0	4619	333	12	5	6833	5	DNAH9	17	11656242	Missense_Mutation	SNP	A	TCGA-AG-3574-01A-01W-0831-10		11656242	69538968	30	1587										
TRPV2	51393	hgsc.bcm.edu	37	chr17	16330137	16330137	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ttaaacttcctgtgtaatctGatctacatgttcatcttcac	4	10	5	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr17:16330137G>T	ENST00000338560.7	+	7	1596	c.1197G>T	c.(1195-1197)ctG>ctT	p.L399L	AC093484.4_ENST00000441875.1_RNA|TRPV2_ENST00000577397.1_Intron	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	399					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.L399L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TGTGTAATCTGATCTACATGT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	17											125	94	104					17																	16330137		2203	4300	6503	16270862	SO:0001819	synonymous_variant	51393			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1197G>T	17.37:g.16330137G>T			16270862	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1																																																																																				0.532	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		T	16330137	G	T	16330137	2	4	13	1	0	0	0	0	0	0	0	1	16636	1277	45	2		2	TRPV2	17	16330137	Silent	SNP	G	TCGA-AG-3574-01A-01W-0831-10	4673895	16330137	64865073	31	1588										
ACACA	31	hgsc.bcm.edu	37	chr17	35486332	35486332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gcatccatcgaggatcgtatGgggtctttgtgggaacaaac	13	8	1	0			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr17:35486332G>A	ENST00000394406.2	-	47	5982	c.5792C>T	c.(5791-5793)cCa>cTa	p.P1931L	ACACA_ENST00000353139.5_Missense_Mutation_p.P1968L|ACACA_ENST00000335166.5_Missense_Mutation_p.P1853L|ACACA_ENST00000361253.5_Missense_Mutation_p.P57L|ACACA_ENST00000360679.3_Missense_Mutation_p.P1873L	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1931	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.P1873L(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGGATCGTATGGGGTCTTTGT	0.463																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											1	Substitution - Missense(1)	large_intestine(1)	17											154	127	136					17																	35486332		2203	4300	6503	32560445	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5792C>T	17.37:g.35486332G>A	ENSP00000377928:p.Pro1931Leu		32560445	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178107	0.94846	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330;ENST00000361253	D;D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78;-4.78	5.08	5.08	0.68730	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.99171	0.9713	M	0.91510	3.215	0.80722	D	1	D;D;D;D	0.89917	0.995;1.0;0.998;0.998	D;D;D;D	0.79784	0.931;0.993;0.92;0.95	D	0.99383	1.0923	10	0.87932	D	0	-9.7775	18.46	0.90735	0.0:0.0:1.0:0.0	.	630;1968;1931;1873	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	L	1968;1873;1931;1955;1853;630;57	ENSP00000344789:P1968L;ENSP00000353898:P1873L;ENSP00000377928:P1931L;ENSP00000335323:P1853L;ENSP00000354565:P57L	ENSP00000335323:P1853L	P	-	2	0	ACACA	32560445	1.000000	0.71417	0.400000	0.26346	0.890000	0.51754	9.578000	0.98200	2.345000	0.79718	0.655000	0.94253	CCA		0.463	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35486332	G	A	35486332	3	1	13	1	0	0	0	0	1	0	0	0	106	1348	47	3	1288	3	ACACA	17	35486332	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	19156195	35486332	45708878	32	1589										
AMZ2	51321	hgsc.bcm.edu	37	chr17	66250663	66250663	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tattcaattttcgacaactaTtatattccagaaataactag	3	7	1	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr17:66250663T>C	ENST00000359904.3	+	5	1837	c.705T>C	c.(703-705)taT>taC	p.Y235Y	AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000359783.4_Silent_p.Y177Y|AMZ2_ENST00000577985.1_Silent_p.Y235Y|AMZ2_ENST00000580753.1_Silent_p.Y235Y|AMZ2_ENST00000577273.1_Intron|AMZ2_ENST00000392720.2_Silent_p.Y235Y|AMZ2_ENST00000577866.1_Silent_p.Y235Y	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	235							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y177Y(1)|p.Y235Y(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			TCGACAACTATTATATTCCAG	0.338																																																2	Substitution - coding silent(2)	large_intestine(2)	17											75	73	74					17																	66250663		2203	4300	6503	63762258	SO:0001819	synonymous_variant	51321			CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.705T>C	17.37:g.66250663T>C			63762258	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Silent	SNP	ENST00000359904.3	37	CCDS11674.1																																																																																				0.338	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		C	66250663	T	C	66250663	2	2	13	1	0	0	0	0	0	0	0	1	597	1500	52	4		4	AMZ2	17	66250663	Silent	SNP	T	TCGA-AG-3574-01A-01W-0831-10	30764331	66250663	14944547	33	1590										
BLVRB	645	hgsc.bcm.edu	37	chr19	40957334	40957334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ccgcagcaccttgtgcatccGgatgtggtcatcagtcacag	11	13	3	0	rs200072753		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr19:40957334G>A	ENST00000263368.4	-	4	551	c.400C>T	c.(400-402)Cgg>Tgg	p.R134W	BLVRB_ENST00000595483.1_Intron	NM_000713.2	NP_000704.1	P30043	BLVRB_HUMAN	biliverdin reductase B (flavin reductase (NADPH))	134					heme catabolic process (GO:0042167)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	biliverdin reductase activity (GO:0004074)|riboflavin reductase (NADPH) activity (GO:0042602)	p.R134W(1)		large_intestine(3)|lung(3)	6			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Riboflavin(DB00140)	TTGTGCATCCGGATGTGGTCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											97	64	75					19																	40957334		2203	4300	6503	45649174	SO:0001583	missense	645			D26308	CCDS33029.1	19q13.1-q13.2	2011-09-14				ENSG00000090013	1.3.1.24, 1.5.1.30	"Short chain dehydrogenase/reductase superfamily / Atypical members"	1063	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 43U, member 1"	600941	"Flavin reductase"	FLR		7656592, 19027726	Standard	NM_000713		Approved	SDR43U1	uc002onw.2	P30043		ENST00000263368.4:c.400C>T	19.37:g.40957334G>A	ENSP00000263368:p.Arg134Trp		45649174	A6NKD8|B2R5C6|P32078|P53005|Q32LZ2	Missense_Mutation	SNP	ENST00000263368.4	37	CCDS33029.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181604	0.78677	.	.	ENSG00000090013	ENST00000263368	T	0.31510	1.49	5.37	5.37	0.77165	NAD(P)-binding domain (1);NmrA-like (1);	0.000000	0.85682	D	0.000000	T	0.66597	0.2805	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75199	-0.3402	10	0.87932	D	0	-30.402	18.2503	0.90000	0.0:0.0:1.0:0.0	.	134	P30043	BLVRB_HUMAN	W	134	ENSP00000263368:R134W	ENSP00000263368:R134W	R	-	1	2	BLVRB	45649174	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.757000	0.55212	2.682000	0.91365	0.467000	0.42956	CGG		0.612	BLVRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462563.1			A	40957334	G	A	40957334	3	1	13	1	0	0	0	0	1	0	0	0	1453	1115	39	1	228	1	BLVRB	19	40957334	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10		40957334	18171649	34	1591										
RAE1	8480	hgsc.bcm.edu	37	chr20	55948631	55948631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tattcactatatcaacccccCgaacccgtaagtgtgactct	5	14	3	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr20:55948631C>T	ENST00000395841.2	+	9	1163	c.743C>T	c.(742-744)cCg>cTg	p.P248L	RAE1_ENST00000371242.2_Missense_Mutation_p.P248L|RAE1_ENST00000527947.1_Missense_Mutation_p.P248L|RAE1_ENST00000395840.2_Missense_Mutation_p.P248L	NM_003610.3	NP_003601.1	P78406	RAE1L_HUMAN	ribonucleic acid export 1	248					carbohydrate metabolic process (GO:0005975)|cellular response to organic cyclic compound (GO:0071407)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|nuclear pore (GO:0005643)|nucleolus (GO:0005730)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|RNA binding (GO:0003723)	p.P248L(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(6)|prostate(3)|skin(2)	21	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			ATCAACCCCCCGAACCCGTAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	20											107	109	108					20																	55948631		2203	4300	6503	55382038	SO:0001583	missense	8480			U84720	CCDS13458.1	20q13.31	2013-08-28	2013-08-28		ENSG00000101146	ENSG00000101146		"WD repeat domain containing"	9828	protein-coding gene	gene with protein product		603343	"RAE1 (RNA export 1, S.pombe) homolog", "RAE1 RNA export 1 homolog (S. pombe)"			9370289, 9256445	Standard	XM_005260582		Approved	Mnrp41	uc002xyi.3	P78406	OTTHUMG00000032819	ENST00000395841.2:c.743C>T	20.37:g.55948631C>T	ENSP00000379182:p.Pro248Leu		55382038	A8K882|O15306|Q3SYL7|Q5TCH8|Q6V708|Q9H100|Q9NQM6	Missense_Mutation	SNP	ENST00000395841.2	37	CCDS13458.1	.	.	.	.	.	.	.	.	.	.	c	12.42	1.933081	0.34096	.	.	ENSG00000101146	ENST00000395841;ENST00000371242;ENST00000527947;ENST00000395840	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.66	4.71	0.59529	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.161535	0.56097	D	0.000026	T	0.42268	0.1195	N	0.02539	-0.55	0.80722	D	1	P;B;B	0.46912	0.886;0.003;0.003	B;B;B	0.35510	0.204;0.003;0.003	T	0.51426	-0.8707	10	0.34782	T	0.22	.	14.3391	0.66614	0.1484:0.8516:0.0:0.0	.	248;248;248	E9PQ57;A8K882;P78406	.;.;RAE1L_HUMAN	L	248	ENSP00000379182:P248L;ENSP00000360286:P248L;ENSP00000432609:P248L;ENSP00000379181:P248L	ENSP00000360286:P248L	P	+	2	0	RAE1	55382038	1.000000	0.71417	0.978000	0.43139	0.437000	0.31866	5.486000	0.66856	1.374000	0.46228	-0.182000	0.12963	CCG		0.438	RAE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079842.2			T	55948631	C	T	55948631	3	4	13	1	0	0	0	0	1	0	0	0	13035	652	23	1	773	1	RAE1	20	55948631	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10		55948631	7076889	35	1592										
ETS2	2114	hgsc.bcm.edu	37	chr21	40194713	40194713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ccacaagacgtcggggaagcGctacgtgtaccgcttcgtgt	13	12	0	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr21:40194713G>A	ENST00000360214.3	+	11	1770	c.1310G>A	c.(1309-1311)cGc>cAc	p.R437H	ETS2_ENST00000360938.3_Missense_Mutation_p.R437H	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	437					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R437H(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TCGGGGAAGCGCTACGTGTAC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	21											113	87	96					21																	40194713		2203	4300	6503	39116583	SO:0001583	missense	2114				CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.1310G>A	21.37:g.40194713G>A	ENSP00000353344:p.Arg437His		39116583	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	.	.	.	.	.	.	.	.	.	.	G	36	5.950681	0.97139	.	.	ENSG00000157557	ENST00000360214;ENST00000360938	T;T	0.30448	1.53;1.53	5.62	5.62	0.85841	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.049344	0.85682	D	0.000000	T	0.65439	0.2691	H	0.94925	3.6	0.80722	D	1	D	0.55385	0.971	P	0.58820	0.846	T	0.76022	-0.3111	10	0.87932	D	0	.	19.2718	0.94013	0.0:0.0:1.0:0.0	.	437	P15036	ETS2_HUMAN	H	437	ENSP00000353344:R437H;ENSP00000354194:R437H	ENSP00000353344:R437H	R	+	2	0	ETS2	39116583	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.706000	0.98722	2.634000	0.89283	0.655000	0.94253	CGC		0.567	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1			A	40194713	G	A	40194713	3	1	13	1	0	0	0	0	1	0	0	0	5289	1087	38	1	1344	1	ETS2	21	40194713	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10		40194713	7935182	36	1593										
TCF20	6942	hgsc.bcm.edu	37	chr22	42606146	42606146	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	taatcttggggataaaaaggTccaaagaggtcacccatgtt	10	7	2	1			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chr22:42606146T>G	ENST00000359486.3	-	1	5302	c.5166A>C	c.(5164-5166)ggA>ggC	p.G1722G	TCF20_ENST00000404876.1_Silent_p.G23G|TCF20_ENST00000335626.4_Silent_p.G1722G	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1722					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.G1722G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GATAAAAAGGTCCAAAGAGGT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	22											79	80	80					22																	42606146		2203	4300	6503	40936090	SO:0001819	synonymous_variant	6942			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.5166A>C	22.37:g.42606146T>G			40936090	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																				0.517	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		G	42606146	T	G	42606146	2	3	13	1	0	0	0	0	0	0	0	1	15729	1654	58	4		4	TCF20	22	42606146	Silent	SNP	T	TCGA-AG-3574-01A-01W-0831-10		42606146	8698420	37	1594										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961583	34961583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gactccggtgtccagtcgccGcccagagcctcccaagactc	10	18	0	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chrX:34961583G>A	ENST00000329357.5	+	1	671	c.635G>A	c.(634-636)cGc>cAc	p.R212H		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	212	Pro-rich.							p.R212H(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TCCAGTCGCCGCCCAGAGCCT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	X											36	39	38					X																	34961583		2202	4298	6500	34871504	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.635G>A	X.37:g.34961583G>A	ENSP00000328307:p.Arg212His		34871504	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	G	0.063	-1.218590	0.01542	.	.	ENSG00000189132	ENST00000329357	T	0.21191	2.02	0.217	-0.433	0.12287	.	.	.	.	.	T	0.10294	0.0252	N	0.15975	0.35	0.09310	N	0.999993	B	0.15473	0.013	B	0.06405	0.002	T	0.28933	-1.0028	9	0.38643	T	0.18	.	4.5853	0.12279	0.3225:0.0:0.6775:0.0	.	212	Q8NA70	FA47B_HUMAN	H	212	ENSP00000328307:R212H	ENSP00000328307:R212H	R	+	2	0	FAM47B	34871504	0.086000	0.21541	0.001000	0.08648	0.001000	0.01503	-2.031000	0.01427	-0.777000	0.04572	-0.766000	0.03442	CGC		0.647	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34961583	G	A	34961583	3	1	13	1	0	0	0	0	1	0	0	0	5589	1087	38	1	637	1	FAM47B	23	34961583	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10		34961583	120308977	38	1595										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101138645	101138645	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ttcctgaactgaccttgactCtatcctcctctcttttcctt	3	15	2	3			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chrX:101138645C>A	ENST00000372782.3	-	7	1801	c.1754G>T	c.(1753-1755)aGa>aTa	p.R585I	ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Missense_Mutation_p.R414I|ZMAT1_ENST00000540921.1_Missense_Mutation_p.R585I	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	585						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R414I(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GACCTTGACTCTATCCTCCTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											233	195	208					X																	101138645		2203	4300	6503	101025301	SO:0001583	missense	84460			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1754G>T	X.37:g.101138645C>A	ENSP00000361868:p.Arg585Ile		101025301	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	C	7.412	0.634885	0.14322	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	T;T;T	0.23552	2.48;2.48;1.9	4.27	1.58	0.23477	.	1.576670	0.03473	N	0.213973	T	0.11793	0.0287	N	0.08118	0	0.22803	N	0.998718	P	0.35363	0.497	B	0.23018	0.043	T	0.16719	-1.0393	10	0.52906	T	0.07	-4.693	4.1531	0.10247	0.0:0.1308:0.2007:0.6685	.	585	Q5H9K5	ZMAT1_HUMAN	I	585;585;414	ENSP00000361868:R585I;ENSP00000437529:R585I;ENSP00000413044:R414I	ENSP00000361868:R585I	R	-	2	0	ZMAT1	101025301	0.005000	0.15991	0.553000	0.28255	0.372000	0.29890	-0.006000	0.12833	0.210000	0.20664	-0.380000	0.06706	AGA		0.393	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			A	101138645	C	A	101138645	3	1	13	1	0	0	0	0	1	0	0	0	17730	913	32	2	166	2	ZMAT1	23	101138645	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	66177062	101138645	54131915	39	1596										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122538640	122538640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aaggctattgtgtagacctaGcctatgaaatagccaaacat	8	8	0	2			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chrX:122538640G>T	ENST00000371251.1	+	10	1427	c.1375G>T	c.(1375-1377)Gcc>Tcc	p.A459S	GRIA3_ENST00000542149.1_Missense_Mutation_p.A459S|GRIA3_ENST00000541091.1_Missense_Mutation_p.A443S|GRIA3_ENST00000264357.5_Missense_Mutation_p.A459S|GRIA3_ENST00000371256.5_Missense_Mutation_p.A459S			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	459					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)	p.A459S(2)		breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TGTAGACCTAGCCTATGAAAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	X											178	141	154					X																	122538640		2203	4300	6503	122366321	SO:0001583	missense	2892			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1375G>T	X.37:g.122538640G>T	ENSP00000360297:p.Ala459Ser		122366321	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231590	0.79688	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.7	5.7	0.88788	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.88385	0.6422	M	0.79475	2.455	0.80722	D	1	P;D;D	0.69078	0.875;0.997;0.996	P;D;D	0.79108	0.627;0.992;0.987	D	0.89366	0.3671	10	0.66056	D	0.02	.	17.6357	0.88121	0.0:0.0:1.0:0.0	.	443;459;459	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	S	459;459;459;459;443	ENSP00000264357:A459S;ENSP00000446146:A459S;ENSP00000360302:A459S;ENSP00000360297:A459S;ENSP00000446440:A443S	ENSP00000264357:A459S	A	+	1	0	GRIA3	122366321	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.381000	0.81170	0.506000	0.49869	GCC		0.413	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		T	122538640	G	T	122538640	3	4	13	1	0	0	0	0	1	0	0	0	6790	971	34	2	1413	2	GRIA3	23	122538640	Missense_Mutation	SNP	G	TCGA-AG-3574-01A-01W-0831-10	21399995	122538640	32731920	40	1597										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291466	141291466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tccatgaaaaagaggagcagCaggagctcagaggactctgg	14	8	2	3			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2222043-03f5-4cf4-85a6-1afa7c9d07b4	e24a2ded-ab99-472a-b702-93a3da90e6c3	g.chrX:141291466C>A	ENST00000247452.3	-	3	655	c.308G>T	c.(307-309)tGc>tTc	p.C103F		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	103	Ser-rich.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.C103F(1)		NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGAGCAGCAGGAGCTCAg	0.567										HNSCC(46;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	X											72	68	70					X																	141291466		2203	4300	6503	141119132	SO:0001583	missense	51438			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.308G>T	X.37:g.141291466C>A	ENSP00000354660:p.Cys103Phe		141119132	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	37	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	6.124	0.391135	0.11581	.	.	ENSG00000046774	ENST00000247452	T	0.04194	3.68	1.16	-1.27	0.09347	Melanoma associated antigen, MAGE, N-terminal (1);	1.205610	0.06722	U	0.775049	T	0.03959	0.0111	N	0.24115	0.695	0.09310	N	1	D	0.55385	0.971	B	0.43838	0.433	T	0.43750	-0.9372	10	0.26408	T	0.33	.	6.4755	0.22033	0.0:0.4006:0.5994:0.0	.	103	Q9UBF1	MAGC2_HUMAN	F	103	ENSP00000354660:C103F	ENSP00000354660:C103F	C	-	2	0	MAGEC2	141119132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.915000	0.01578	-0.518000	0.06452	-0.478000	0.04885	TGC		0.567	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		A	141291466	C	A	141291466	3	1	13	1	0	0	0	0	1	0	0	0	9211	710	25	2	817	2	MAGEC2	23	141291466	Missense_Mutation	SNP	C	TCGA-AG-3574-01A-01W-0831-10	18752826	141291466	13979094	41	1598										
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19181156	19181156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgagaacacgaccacgacgcGcgctgtgctctgctgcagct	12	15	1	1	rs138972387		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:19181156G>A	ENST00000375371.3	-	3	829	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	270					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)	p.R270C(2)|p.R270G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ACCACGACGCGCGCTGTGCTC	0.627																																																3	Substitution - Missense(3)	large_intestine(2)|lung(1)	1						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	70	60	64		808	4	0.3	1	dbSNP_134	64	0,8600		0,0,4300	no	missense	TAS1R2	NM_152232.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	270/840	19181156	1,13005	2203	4300	6503	19053743	SO:0001583	missense	80834				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.808C>T	1.37:g.19181156G>A	ENSP00000364520:p.Arg270Cys		19053743	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.725061	0.48833	2.27E-4	0.0	ENSG00000179002	ENST00000375371	D	0.87256	-2.23	4.99	4.01	0.46588	Extracellular ligand-binding receptor (1);	0.613341	0.14245	N	0.331801	D	0.92244	0.7540	M	0.78344	2.41	0.22851	N	0.998653	D	0.89917	1.0	D	0.72982	0.979	D	0.83619	0.0138	10	0.87932	D	0	.	9.9288	0.41510	0.0:0.0:0.7021:0.2979	.	270	Q8TE23	TS1R2_HUMAN	C	270	ENSP00000364520:R270C	ENSP00000364520:R270C	R	-	1	0	TAS1R2	19053743	0.850000	0.29656	0.335000	0.25508	0.266000	0.26442	4.417000	0.59822	2.607000	0.88179	0.561000	0.74099	CGC		0.627	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19181156	G	A	19181156	3	1	14	1	0	0	0	0	1	0	0	0	15602	1087	38	1	1727	1	TAS1R2	1	19181156	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		19181156	230069465	1	1599										
WDR63	126820	hgsc.bcm.edu	37	chr1	85583461	85583461	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaggcagaagaaatgaacccGtatcataatctggaaagtgg	11	6	2	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:85583461G>A	ENST00000294664.6	+	17	2016	c.1836G>A	c.(1834-1836)ccG>ccA	p.P612P	WDR63_ENST00000370596.1_Silent_p.P573P|WDR63_ENST00000326813.8_Silent_p.P573P	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	612								p.P612P(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		AAATGAACCCGTATCATAATC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	1											110	109	109					1																	85583461		2203	4300	6503	85356049	SO:0001819	synonymous_variant	126820				CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.1836G>A	1.37:g.85583461G>A			85356049	A8K988|Q96L72|Q96NU4	Silent	SNP	ENST00000294664.6	37	CCDS702.1																																																																																				0.408	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		A	85583461	G	A	85583461	2	1	14	1	0	0	0	0	0	0	0	1	17354	1132	40	1		1	WDR63	1	85583461	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10	66402305	85583461	163667160	2	1600										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216188	111216188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgcctcggcaaagtagaccGcgctggagaaaaggatgacc	13	11	0	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:111216188G>A	ENST00000369769.2	-	1	1467	c.1244C>T	c.(1243-1245)gCg>gTg	p.A415V		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	415					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)	p.A415V(2)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	AAAGTAGACCGCGCTGGAGAA	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	1											55	52	53					1																	111216188		2203	4300	6503	111017711	SO:0001583	missense	3738			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1244C>T	1.37:g.111216188G>A	ENSP00000358784:p.Ala415Val		111017711	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	37	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613619	0.87359	.	.	ENSG00000177272	ENST00000369769	D	0.98455	-4.94	5.91	5.91	0.95273	Ion transport (1);	0.000000	0.85682	U	0.000000	D	0.98188	0.9401	L	0.38649	1.16	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.99837	1.1058	10	0.87932	D	0	.	20.2896	0.98541	0.0:0.0:1.0:0.0	.	415	P22001	KCNA3_HUMAN	V	415	ENSP00000358784:A415V	ENSP00000358784:A415V	A	-	2	0	KCNA3	111017711	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	9.864000	0.99589	2.794000	0.96219	0.655000	0.94253	GCG		0.572	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		A	111216188	G	A	111216188	3	1	14	1	0	0	0	0	1	0	0	0	8025	1087	38	1	487	1	KCNA3	1	111216188	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	25632727	111216188	138034433	3	1601										
LMX1A	4009	hgsc.bcm.edu	37	chr1	165182967	165182967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggttctcggacgtttggggcGcttatggtccttgccttcct	13	11	1	0	rs149908681		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:165182967G>A	ENST00000342310.3	-	5	962	c.580C>T	c.(580-582)Cgc>Tgc	p.R194C	RP11-38C18.2_ENST00000457106.1_RNA|RP11-38C18.3_ENST00000441773.1_RNA|LMX1A_ENST00000367893.4_Missense_Mutation_p.R194C|LMX1A_ENST00000294816.2_Missense_Mutation_p.R194C|LMX1A_ENST00000489443.2_5'Flank	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	194					axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R194S(1)|p.R194C(1)		NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					CGTTTGGGGCGCTTATGGTCC	0.502																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	241	218	226		580,580	5.6	1	1	dbSNP_134	226	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LMX1A	NM_001174069.1,NM_177398.3	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	194/383,194/383	165182967	1,13005	2203	4300	6503	163449591	SO:0001583	missense	4009			AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"Homeoboxes / LIM class"	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.580C>T	1.37:g.165182967G>A	ENSP00000340226:p.Arg194Cys		163449591	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Missense_Mutation	SNP	ENST00000342310.3	37	CCDS1247.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311206	0.81358	0.0	1.16E-4	ENSG00000162761	ENST00000342310;ENST00000294816;ENST00000367893	D;D;D	0.96073	-3.9;-3.9;-3.9	5.64	5.64	0.86602	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96738	0.8935	L	0.52011	1.625	0.53005	D	0.999965	D	0.89917	1.0	D	0.87578	0.998	D	0.97128	0.9816	9	0.72032	D	0.01	.	19.3003	0.94141	0.0:0.0:1.0:0.0	.	194	Q8TE12	LMX1A_HUMAN	C	194	ENSP00000340226:R194C;ENSP00000294816:R194C;ENSP00000356868:R194C	ENSP00000294816:R194C	R	-	1	0	LMX1A	163449591	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.781000	0.55394	2.637000	0.89404	0.650000	0.86243	CGC		0.502	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398		A	165182967	G	A	165182967	3	1	14	1	0	0	0	0	1	0	0	0	8885	1087	38	1	588	1	LMX1A	1	165182967	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	53966779	165182967	84067654	4	1602										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186060043	186060043	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agctagtggtgaaacagaaaGaatccggtatgtttaaaaat	10	4	0	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:186060043G>T	ENST00000271588.4	+	64	10110	c.9881G>T	c.(9880-9882)aGa>aTa	p.R3294I	HMCN1_ENST00000367492.2_Missense_Mutation_p.R3294I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3294	Ig-like C2-type 31.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R3294I(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAAACAGAAAGAATCCGGTAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	72	72					1																	186060043		2203	4299	6502	184326666	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9881G>T	1.37:g.186060043G>T	ENSP00000271588:p.Arg3294Ile		184326666	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444918	0.63178	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68624	-0.34;-0.34	5.98	4.12	0.48240	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.221097	0.52532	D	0.000062	T	0.77883	0.4197	M	0.80508	2.5	0.45194	D	0.998205	D	0.60575	0.988	P	0.57846	0.828	T	0.78638	-0.2126	10	0.48119	T	0.1	.	12.3322	0.55046	0.1354:0.0:0.8646:0.0	.	3294	Q96RW7	HMCN1_HUMAN	I	3294	ENSP00000271588:R3294I;ENSP00000356462:R3294I	ENSP00000271588:R3294I	R	+	2	0	HMCN1	184326666	1.000000	0.71417	0.985000	0.45067	0.767000	0.43475	1.956000	0.40382	0.867000	0.35654	0.591000	0.81541	AGA		0.353	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186060043	G	T	186060043	3	4	14	1	0	0	0	0	1	0	0	0	7241	942	33	2	10135	2	HMCN1	1	186060043	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	20877076	186060043	63190578	5	1603										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202742358	202742358	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaaccccatcttggtagcaAttttggtccattttctatcc	5	12	2	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr1:202742358A>T	ENST00000367265.3	-	4	1628	c.464T>A	c.(463-465)aTt>aAt	p.I155N	KDM5B_ENST00000367264.2_Missense_Mutation_p.I155N	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	155	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.I155N(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						CTTGGTAGCAATTTTGGTCCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											152	134	140					1																	202742358		2203	4300	6503	201008981	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.464T>A	1.37:g.202742358A>T	ENSP00000356234:p.Ile155Asn		201008981	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	A	32	5.134973	0.94517	.	.	ENSG00000117139	ENST00000367265;ENST00000367264	T;T	0.70516	-0.49;-0.49	5.95	5.95	0.96441	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	D	0.86810	0.6022	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.996	D	0.89198	0.3555	10	0.87932	D	0	-22.6901	16.4069	0.83677	1.0:0.0:0.0:0.0	.	155;155	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	N	155	ENSP00000356234:I155N;ENSP00000356233:I155N	ENSP00000356233:I155N	I	-	2	0	KDM5B	201008981	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.339000	0.96797	2.272000	0.75746	0.460000	0.39030	ATT		0.413	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		T	202742358	A	T	202742358	3	4	14	1	0	0	0	0	1	0	0	0	8155	101	4	5	4266	5	KDM5B	1	202742358	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10	16682315	202742358	46508263	6	1604										
REG1A	5967	hgsc.bcm.edu	37	chr2	79349974	79349974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttccccatctagaaccgccGctggcactggagcagtgggt	12	14	1	1	rs200685695		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr2:79349974G>A	ENST00000233735.1	+	5	432	c.329G>A	c.(328-330)cGc>cAc	p.R110H		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	110	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)	p.R110P(1)|p.R110H(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(26)|prostate(1)|upper_aerodigestive_tract(1)	39						TAGAACCGCCGCTGGCACTGG	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2						G	HIS/ARG	0,4406		0,0,2203	107	107	107		329	2.9	0.9	2		107	2,8598	2.2+/-6.3	0,2,4298	yes	missense	REG1A	NM_002909.4	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	110/167	79349974	2,13004	2203	4300	6503	79203482	SO:0001583	missense	5967				CCDS1964.1	2p12	2008-09-04	2008-06-04		ENSG00000115386	ENSG00000115386			9951	protein-coding gene	gene with protein product	"pancreatic stone protein", "pancreatic thread protein"	167770	"regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein)"	REG		2332435, 8333731	Standard	NM_002909		Approved	PSP, PTP, PSPS, PSPS1	uc002snz.3	P05451	OTTHUMG00000130016	ENST00000233735.1:c.329G>A	2.37:g.79349974G>A	ENSP00000233735:p.Arg110His		79203482	P11379|Q4ZG28	Missense_Mutation	SNP	ENST00000233735.1	37	CCDS1964.1	.	.	.	.	.	.	.	.	.	.	g	11.72	1.723424	0.30503	0.0	2.33E-4	ENSG00000115386	ENST00000233735	T	0.18960	2.18	2.92	2.92	0.33932	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.391148	0.18799	N	0.130853	T	0.17066	0.0410	L	0.43554	1.36	0.26900	N	0.967122	B	0.02656	0.0	B	0.04013	0.001	T	0.10132	-1.0643	10	0.37606	T	0.19	.	9.4067	0.38466	0.0:0.0:1.0:0.0	.	110	P05451	REG1A_HUMAN	H	110	ENSP00000233735:R110H	ENSP00000233735:R110H	R	+	2	0	REG1A	79203482	0.014000	0.17966	0.948000	0.38648	0.801000	0.45260	0.744000	0.26245	1.637000	0.50538	0.557000	0.71058	CGC		0.552	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252289.1	NM_002909		A	79349974	G	A	79349974	3	1	14	1	0	0	0	0	1	0	0	0	13247	1087	38	1	343	1	REG1A	2	79349974	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		79349974	163849399	7	1605										
ACMSD	130013	hgsc.bcm.edu	37	chr2	135621154	135621154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggtccaaattggcacccacGtcaacgagtgggacctgaac	12	12	1	1	rs201644333		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr2:135621154G>A	ENST00000356140.5	+	5	575	c.439G>A	c.(439-441)Gtc>Atc	p.V147I	AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000283054.4_Missense_Mutation_p.V89I|ACMSD_ENST00000392928.1_Missense_Mutation_p.V89I	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	147					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)	p.V147I(1)		endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		TGGCACCCACGTCAACGAGTG	0.652													G|||	1	0.000199681	8e-04	0	5008	,	,		17493	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											66	53	58					2																	135621154		2203	4300	6503	135337624	SO:0001583	missense	130013			AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.439G>A	2.37:g.135621154G>A	ENSP00000348459:p.Val147Ile		135337624	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	37	CCDS2173.2	16	0.007326007326007326	7	0.014227642276422764	1	0.0027624309392265192	2	0.0034965034965034965	6	0.0079155672823219	G	7.444	0.641304	0.14451	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.74	1.71	0.24356	.	0.226724	0.51477	N	0.000099	T	0.19287	0.0463	N	0.10629	0.01	0.37405	D	0.913026	B;B	0.06786	0.001;0.0	B;B	0.16289	0.015;0.011	T	0.10989	-1.0606	9	0.09843	T	0.71	-7.4584	9.4027	0.38442	0.5545:0.0:0.4455:0.0	.	89;147	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	I	147;89;89	.	ENSP00000283054:V89I	V	+	1	0	ACMSD	135337624	0.027000	0.19231	0.996000	0.52242	0.885000	0.51271	0.364000	0.20325	0.146000	0.19002	-0.367000	0.07326	GTC		0.652	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			A	135621154	G	A	135621154	3	1	14	1	0	0	0	0	1	0	0	0	144	1145	40	1	457	1	ACMSD	2	135621154	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	56271180	135621154	107578219	8	1606										
LCT	3938	hgsc.bcm.edu	37	chr2	136562381	136562381	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagtgtatcgatgagcctcaCgtagtagttcaggcccgctt	11	11	2	1	rs371776642		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr2:136562381C>T	ENST00000264162.2	-	10	4430	c.4420G>A	c.(4420-4422)Gtg>Atg	p.V1474M		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1474	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.V1474M(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	ATGAGCCTCACGTAGTAGTTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	MET/VAL	0,4406		0,0,2203	79	81	80		4420	-1	0	2		80	2,8598	2.2+/-6.3	0,2,4298	no	missense	LCT	NM_002299.2	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	1474/1928	136562381	2,13004	2203	4300	6503	136278851	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4420G>A	2.37:g.136562381C>T	ENSP00000264162:p.Val1474Met		136278851	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	5.463	0.270414	0.10349	0.0	2.33E-4	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.54675	0.56	5.34	-1.03	0.10102	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.763143	0.12722	N	0.444660	T	0.45316	0.1336	L	0.52011	1.625	0.09310	N	1	P	0.49696	0.927	P	0.48571	0.582	T	0.32508	-0.9904	10	0.38643	T	0.18	-0.4233	2.7674	0.05324	0.119:0.3411:0.3465:0.1934	.	1474	P09848	LPH_HUMAN	M	1474;906	ENSP00000264162:V1474M	ENSP00000264162:V1474M	V	-	1	0	LCT	136278851	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	-0.158000	0.10070	-0.264000	0.09365	-0.302000	0.09304	GTG		0.587	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136562381	C	T	136562381	3	4	14	1	0	0	0	0	1	0	0	0	8715	536	19	1	1395	1	LCT	2	136562381	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	941227	136562381	106636992	9	1607										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41277892	41277892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agtagctgcaggggtcctctGtgaacttgctcaggacaagg	14	9	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr3:41277892G>A	ENST00000349496.5	+	12	2136	c.1856G>A	c.(1855-1857)tGt>tAt	p.C619Y	CTNNB1_ENST00000453024.1_Missense_Mutation_p.C612Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.C619Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.C619Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.C619Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	619					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.C619Y(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGGGTCCTCTGTGAACTTGCT	0.438		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	3											129	135	133					3																	41277892		2203	4300	6503	41252896	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1856G>A	3.37:g.41277892G>A	ENSP00000344456:p.Cys619Tyr		41252896	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.352586	0.82132	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.6	5.6	0.85130	Armadillo-like helical (1);Armadillo-type fold (1);	0.040249	0.85682	D	0.000000	T	0.82208	0.4987	M	0.80616	2.505	0.80722	D	1	P;D;P	0.63046	0.837;0.992;0.923	B;D;P	0.65573	0.332;0.936;0.455	T	0.80353	-0.1418	10	0.33940	T	0.23	-14.298	19.6229	0.95667	0.0:0.0:1.0:0.0	.	547;54;619	B4DSW9;P35222-2;P35222	.;.;CTNB1_HUMAN	Y	619;619;619;612;619	ENSP00000385604:C619Y;ENSP00000379486:C619Y;ENSP00000344456:C619Y;ENSP00000411226:C612Y;ENSP00000379488:C619Y	ENSP00000344456:C619Y	C	+	2	0	CTNNB1	41252896	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.628000	0.89032	0.655000	0.94253	TGT		0.438	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41277892	G	A	41277892	3	1	14	1	0	0	0	0	1	0	0	0	4022	1377	48	3	1898	3	CTNNB1	3	41277892	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		41277892	156744538	10	1608										
WDR52	55779	hgsc.bcm.edu	37	chr3	113099853	113099853	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcttgctttatggttggaaGtggagcttcaagaatatagc	11	5	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr3:113099853G>C	ENST00000295868.2	-	16	2107	c.1945C>G	c.(1945-1947)Ctt>Gtt	p.L649V	WDR52_ENST00000393845.2_Missense_Mutation_p.L649V|WDR52_ENST00000475568.1_5'Flank	NM_018338.3	NP_060808.2												p.L649V(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						ATGGTTGGAAGTGGAGCTTCA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	92	93					3																	113099853		2201	4298	6499	114582543	SO:0001583	missense	55779																														ENST00000295868.2:c.1945C>G	3.37:g.113099853G>C	ENSP00000295868:p.Leu649Val		114582543		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	G	8.146	0.786260	0.16189	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.19806	2.12;2.12	5.32	-5.52	0.02560	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.12008	0.0292	L	0.35341	1.055	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41698	-0.9494	9	0.14656	T	0.56	.	9.1275	0.36824	0.1655:0.3845:0.45:0.0	.	649	Q96MT7	WDR52_HUMAN	V	649	ENSP00000377428:L649V;ENSP00000295868:L649V	ENSP00000295868:L649V	L	-	1	0	WDR52	114582543	0.000000	0.05858	0.002000	0.10522	0.942000	0.58702	-1.121000	0.03270	-0.521000	0.06426	0.557000	0.71058	CTT		0.299	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			C	113099853	G	C	113099853	3	2	14	1	0	0	0	0	1	0	0	0	17344	1029	36	5	3714	5	WDR52	3	113099853	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	71821961	113099853	84922577	11	1609										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865730	118865730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agattgacagtgggtcatccGtcccatctgaccaaagtcct	9	12	2	3	rs148898242	byFrequency	TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr3:118865730G>A	ENST00000295622.1	+	1	734	c.694G>A	c.(694-696)Gtc>Atc	p.V232I	IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	232								p.V232I(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		TGGGTCATCCGTCCCATCTGA	0.488													G|||	2	0.000399361	0.0015	0	5008	,	,		25566	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	ILE/VAL	24,4382	31.7+/-61.6	0,24,2179	95	97	96		694	-5.5	0	3	dbSNP_134	96	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C3orf30	NM_152539.2	29	0,25,6478	AA,AG,GG		0.0116,0.5447,0.1922	benign	232/537	118865730	25,12981	2203	4300	6503	120348420	SO:0001583	missense	152405			AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.694G>A	3.37:g.118865730G>A	ENSP00000295622:p.Val232Ile		120348420	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	2.851|2.851	-0.238222|-0.238222	0.05944|0.05944	0.005447|0.005447	1.16E-4|1.16E-4	ENSG00000163424|ENSG00000163424	ENST00000460150;ENST00000473121|ENST00000295622;ENST00000470341	.|T	.|0.28454	.|1.61	2.76|2.76	-5.51|-5.51	0.02568|0.02568	.|.	.|2.127150	.|0.02299	.|N	.|0.071028	T|T	0.10895|0.10895	0.0266|0.0266	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B	.|0.25521	.|0.128;0.0	.|B;B	.|0.14578	.|0.011;0.0	T|T	0.11299|0.11299	-1.0593|-1.0593	5|10	.|0.38643	.|T	.|0.18	2.7375|2.7375	5.0795|5.0795	0.14649|0.14649	0.4384:0.0:0.4157:0.1459|0.4384:0.0:0.4157:0.1459	.|.	.|232;232	.|E9PFE5;Q96M34	.|.;CC030_HUMAN	H|I	195;24|232	.|ENSP00000295622:V232I	.|ENSP00000295622:V232I	R|V	+|+	2|1	0|0	C3orf30|C3orf30	120348420|120348420	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.411000|-1.411000	0.02478|0.02478	-1.077000|-1.077000	0.03121|0.03121	-1.429000|-1.429000	0.01096|0.01096	CGT|GTC		0.488	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		A	118865730	G	A	118865730	3	1	14	1	0	0	0	0	1	0	0	0	2226	1145	40	1	696	1	C3orf30	3	118865730	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	5765877	118865730	79156700	12	1610										
CPB1	1360	hgsc.bcm.edu	37	chr3	148563303	148563303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggccctggctgatttcatcCgcaacaaactctcttccatc	6	15	2	1	rs142211299		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr3:148563303C>T	ENST00000491148.1	+	10	1205	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	CPB1_ENST00000282957.4_Missense_Mutation_p.R291C			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	291						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R291C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGATTTCATCCGCAACAAACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	CYS/ARG	0,4406		0,0,2203	135	132	133		871	5.7	1	3	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	missense	CPB1	NM_001871.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	291/418	148563303	1,13005	2203	4300	6503	150045993	SO:0001583	missense	1360			AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.871C>T	3.37:g.148563303C>T	ENSP00000417222:p.Arg291Cys		150045993	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	37	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883883	0.91814	0.0	1.16E-4	ENSG00000153002	ENST00000491148;ENST00000282957	T;T	0.12039	2.72;2.72	5.69	5.69	0.88448	Peptidase M14, carboxypeptidase A (2);	0.048732	0.85682	D	0.000000	T	0.47619	0.1455	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54437	-0.8294	10	0.87932	D	0	.	19.8033	0.96518	0.0:1.0:0.0:0.0	.	291	P15086	CBPB1_HUMAN	C	291	ENSP00000417222:R291C;ENSP00000282957:R291C	ENSP00000282957:R291C	R	+	1	0	CPB1	150045993	1.000000	0.71417	0.988000	0.46212	0.778000	0.44026	7.468000	0.80943	2.677000	0.91161	0.655000	0.94253	CGC		0.463	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		T	148563303	C	T	148563303	3	4	14	1	0	0	0	0	1	0	0	0	3802	652	23	1	905	1	CPB1	3	148563303	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	29697573	148563303	49459127	13	1611										
UNC5C	8633	hgsc.bcm.edu	37	chr4	96140172	96140172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagttgaagctgccaaatgcGgtacaggatggatcagtctg	14	7	2	1	rs544350901		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr4:96140172G>A	ENST00000453304.1	-	9	1941	c.1593C>T	c.(1591-1593)acC>acT	p.T531T	UNC5C_ENST00000506749.1_Silent_p.T550T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	531	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)	p.T531T(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TGCCAAATGCGGTACAGGATG	0.483													G|||	1	0.000199681	8e-04	0	5008	,	,		19990	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4											132	103	113					4																	96140172		2203	4300	6503	96359195	SO:0001819	synonymous_variant	8633			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1593C>T	4.37:g.96140172G>A			96359195	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																				0.483	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		A	96140172	G	A	96140172	2	1	14	1	0	0	0	0	0	0	0	1	17033	1103	39	1		1	UNC5C	4	96140172	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10		96140172	95014104	14	1612										
CDH10	1008	hgsc.bcm.edu	37	chr5	24492994	24492994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaaaaatttctgtccacctAaagggtcatctttgtctact	5	9	4	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr5:24492994A>G	ENST00000264463.4	-	10	2063	c.1556T>C	c.(1555-1557)tTa>tCa	p.L519S	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	519	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L519S(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		CTGTCCACCTAAAGGGTCATC	0.328										HNSCC(23;0.051)																																						1	Substitution - Missense(1)	large_intestine(1)	5											164	177	172					5																	24492994		2203	4298	6501	24528751	SO:0001583	missense	1008			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1556T>C	5.37:g.24492994A>G	ENSP00000264463:p.Leu519Ser		24528751	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	A	9.899	1.206321	0.22205	.	.	ENSG00000040731	ENST00000264463	T	0.51817	0.69	4.94	4.94	0.65067	Cadherin (4);Cadherin-like (1);	0.497760	0.17685	N	0.165493	T	0.24509	0.0594	N	0.04335	-0.225	0.37800	D	0.927671	B	0.19817	0.039	B	0.24155	0.051	T	0.17561	-1.0365	10	0.21540	T	0.41	.	8.7489	0.34602	0.9144:0.0:0.0856:0.0	.	519	Q9Y6N8	CAD10_HUMAN	S	519	ENSP00000264463:L519S	ENSP00000264463:L519S	L	-	2	0	CDH10	24528751	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.269000	0.65542	1.982000	0.57802	0.477000	0.44152	TTA		0.328	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		G	24492994	A	G	24492994	3	3	14	1	0	0	0	0	1	0	0	0	3102	372	13	4	822	4	CDH10	5	24492994	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10		24492994	156422266	15	1613										
CARD6	84674	hgsc.bcm.edu	37	chr5	40853936	40853936	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcctgccctgagagaccacaAatgatgggaactcttgaaag	11	10	1	4			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr5:40853936A>C	ENST00000254691.5	+	3	2701	c.2502A>C	c.(2500-2502)caA>caC	p.Q834H	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	834					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)			p.Q834H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						AGAGACCACAAATGATGGGAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											215	221	219					5																	40853936		2203	4300	6503	40889693	SO:0001583	missense	84674			AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.2502A>C	5.37:g.40853936A>C	ENSP00000254691:p.Gln834His		40889693	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.753474	0.49362	.	.	ENSG00000132357	ENST00000254691	T	0.17854	2.25	4.79	1.4	0.22301	.	0.300334	0.24193	N	0.040685	T	0.18551	0.0445	L	0.32530	0.975	0.09310	N	0.999994	D	0.60160	0.987	P	0.54460	0.753	T	0.04737	-1.0930	10	0.62326	D	0.03	-2.8554	6.6502	0.22957	0.5025:0.0:0.4975:0.0	.	834	Q9BX69	CARD6_HUMAN	H	834	ENSP00000254691:Q834H	ENSP00000254691:Q834H	Q	+	3	2	CARD6	40889693	0.004000	0.15560	0.009000	0.14445	0.037000	0.13140	0.134000	0.15932	0.451000	0.26802	0.260000	0.18958	CAA		0.512	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			C	40853936	A	C	40853936	3	2	14	1	0	0	0	0	1	0	0	0	2656	11	1	4	2512	4	CARD6	5	40853936	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10	16360942	40853936	140061324	16	1614										
IL9	3578	hgsc.bcm.edu	37	chr5	135228122	135228122	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcatcttttctttctggaaAatttccagaagactcttcag	5	10	6	2			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr5:135228122A>G	ENST00000274520.1	-	5	403	c.393T>C	c.(391-393)atT>atC	p.I131I		NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	131					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)		p.I131I(1)		large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTTTCTGGAAAATTTCCAGAA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	5											66	73	70					5																	135228122		2203	4300	6503	135256021	SO:0001819	synonymous_variant	3578			S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"Interleukins and interleukin receptors"	6029	protein-coding gene	gene with protein product	"p40 T-cell and mast cell growth factor", "T-cell growth factor p40", "p40 cytokine", "homolog of mouse T cell and mast cell growth factor 40"	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.393T>C	5.37:g.135228122A>G			135256021		Silent	SNP	ENST00000274520.1	37	CCDS4189.1																																																																																				0.368	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590		G	135228122	A	G	135228122	2	3	14	1	0	0	0	0	0	0	0	1	7728	10	1	4		4	IL9	5	135228122	Silent	SNP	A	TCGA-AG-3575-01A-01W-0831-10	94374186	135228122	45687138	17	1615										
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7904855	7904855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcacacgtcggagtgggccGtgcagtccactttagccaca	12	13	0	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr6:7904855G>A	ENST00000379757.4	-	2	402	c.365C>T	c.(364-366)aCg>aTg	p.T122M	TXNDC5_ENST00000473453.1_Missense_Mutation_p.T14M|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR|TXNDC5_ENST00000539054.1_Missense_Mutation_p.T50M	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	122	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)	p.T122M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					GGAGTGGGCCGTGCAGTCCAC	0.577																																					Ovarian(119;1430 1625 3928 26125 34589)											1	Substitution - Missense(1)	large_intestine(1)	6											179	133	149					6																	7904855		2203	4300	6503	7849854	SO:0001583	missense	81567			AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"Protein disulfide isomerases"	21073	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 15"		"thioredoxin domain containing 5"				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.365C>T	6.37:g.7904855G>A	ENSP00000369081:p.Thr122Met		7849854	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	37	CCDS4505.1	.	.	.	.	.	.	.	.	.	.	.	17.47	3.397491	0.62177	.	.	ENSG00000239264	ENST00000539054;ENST00000379757;ENST00000473453	T;T;T	0.45276	0.9;0.9;0.9	4.99	4.99	0.66335	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.113958	0.64402	D	0.000014	T	0.72104	0.3419	H	0.96015	3.755	0.51482	D	0.999927	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.988	T	0.82651	-0.0352	10	0.87932	D	0	.	17.0573	0.86537	0.0:0.0:1.0:0.0	.	50;122	Q86UY0;Q8NBS9	.;TXND5_HUMAN	M	50;122;14	ENSP00000442453:T50M;ENSP00000369081:T122M;ENSP00000420784:T14M	ENSP00000442453:T50M	T	-	2	0	TXNDC5	7849854	1.000000	0.71417	0.991000	0.47740	0.444000	0.32077	6.685000	0.74543	2.285000	0.76669	0.558000	0.71614	ACG		0.577	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		A	7904855	G	A	7904855	3	1	14	1	0	0	0	0	1	0	0	0	16839	1145	40	1	969	1	TXNDC5	6	7904855	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		7904855	163210212	18	1616										
TMEM63B	55362	hgsc.bcm.edu	37	chr6	44120356	44120356	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcctacgagttccagtttggCgcagcctacgcctggatgat	12	12	0	1	rs145799677		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr6:44120356C>T	ENST00000259746.9	+	20	2046	c.1863C>T	c.(1861-1863)ggC>ggT	p.G621G	TMEM63B_ENST00000323267.6_Silent_p.G621G			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	621					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.G621G(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TCCAGTTTGGCGCAGCCTACG	0.652											OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	6						C		0,4406		0,0,2203	183	136	152		1863	4.6	1	6	dbSNP_134	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM63B	NM_018426.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		621/833	44120356	1,13005	2203	4300	6503	44228334	SO:0001819	synonymous_variant	55362			BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1863C>T	6.37:g.44120356C>T		921	44228334	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	C	9.616	1.132571	0.21041	0.0	1.16E-4	ENSG00000137216	ENST00000371893	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	T	0.46288	0.1385	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46693	-0.9173	4	.	.	.	.	8.043	0.30532	0.1663:0.6483:0.1854:0.0	.	.	.	.	V	550	.	.	A	+	2	0	TMEM63B	44228334	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.365000	0.20348	2.424000	0.82194	0.462000	0.41574	GCG		0.652	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		T	44120356	C	T	44120356	2	4	14	1	0	0	0	0	0	0	0	1	16230	755	27	1		1	TMEM63B	6	44120356	Silent	SNP	C	TCGA-AG-3575-01A-01W-0831-10	36215501	44120356	126994711	19	1617										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102247631	102247631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtaatcgacataaaccctggCgcttcgggacccgctttatg	10	12	0	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr6:102247631C>T	ENST00000421544.1	+	7	1550	c.1060C>T	c.(1060-1062)Cgc>Tgc	p.R354C	GRIK2_ENST00000413795.1_Missense_Mutation_p.R354C|GRIK2_ENST00000369137.3_Missense_Mutation_p.R354C|GRIK2_ENST00000369134.4_Missense_Mutation_p.R305C|GRIK2_ENST00000318991.6_Missense_Mutation_p.R354C|GRIK2_ENST00000369138.1_Missense_Mutation_p.R354C	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	354					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.R354C(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TAAACCCTGGCGCTTCGGGAC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	6											139	126	130					6																	102247631		2203	4300	6503	102354324	SO:0001583	missense	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.1060C>T	6.37:g.102247631C>T	ENSP00000397026:p.Arg354Cys		102354324	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443241	0.83993	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076;ENST00000455610	D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.3	5.3	0.74995	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.86707	0.5997	M	0.69823	2.125	0.58432	D	0.999998	D;D;D	0.67145	0.988;0.996;0.988	P;P;P	0.61328	0.75;0.887;0.67	D	0.88102	0.2820	10	0.66056	D	0.02	.	13.8595	0.63550	0.1528:0.8472:0.0:0.0	.	354;354;354	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	C	354;354;354;354;354;354;305;316;67	ENSP00000397026:R354C;ENSP00000405596:R354C;ENSP00000358134:R354C;ENSP00000358133:R354C;ENSP00000313276:R354C;ENSP00000358130:R305C;ENSP00000391988:R67C	ENSP00000313276:R354C	R	+	1	0	GRIK2	102354324	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.508000	0.60441	2.464000	0.83262	0.655000	0.94253	CGC		0.443	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			T	102247631	C	T	102247631	3	4	14	1	0	0	0	0	1	0	0	0	6795	768	27	1	1086	1	GRIK2	6	102247631	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	58127275	102247631	68867436	20	1618										
HEY2	23493	hgsc.bcm.edu	37	chr6	126073169	126073169	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atagattatagagaaaaggcGtcgggatcggataaataaca	11	4	0	2			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr6:126073169G>A	ENST00000368364.3	+	3	376	c.179G>A	c.(178-180)cGt>cAt	p.R60H	RP11-624M8.1_ENST00000432121.1_RNA|RP11-624M8.1_ENST00000451660.2_RNA|RP11-624M8.1_ENST00000606001.1_RNA|HEY2_ENST00000368365.1_Missense_Mutation_p.R14H	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	60	Transcriptional repression and interaction with NCOR1 and SIN3A. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R60H(1)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		GAGAAAAGGCGTCGGGATCGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	86	82					6																	126073169		2203	4300	6503	126114862	SO:0001583	missense	23493			AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"Basic helix-loop-helix proteins"	4881	protein-coding gene	gene with protein product		604674	"hairy/enhancer-of-split related with YRPW motif 2"			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.179G>A	6.37:g.126073169G>A	ENSP00000357348:p.Arg60His		126114862		Missense_Mutation	SNP	ENST00000368364.3	37	CCDS5131.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032397	0.75504	.	.	ENSG00000135547	ENST00000368365;ENST00000368364	D;D	0.99722	-6.53;-6.53	5.77	4.9	0.64082	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99327	0.9764	H	0.94847	3.59	0.80722	D	1	B	0.22346	0.068	B	0.23852	0.049	D	0.99900	1.1160	10	0.87932	D	0	-7.4102	14.9208	0.70835	0.0687:0.0:0.9313:0.0	.	60	Q9UBP5	HEY2_HUMAN	H	14;60	ENSP00000357349:R14H;ENSP00000357348:R60H	ENSP00000357348:R60H	R	+	2	0	HEY2	126114862	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.476000	0.97823	1.448000	0.47680	0.467000	0.42956	CGT		0.363	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1			A	126073169	G	A	126073169	3	1	14	1	0	0	0	0	1	0	0	0	7100	1145	40	1	189	1	HEY2	6	126073169	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	23825538	126073169	45041898	21	1619										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157528657	157528657	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	atcgcaaaaacccagtctgtCgagaaatgtccatggcgctt	9	11	1	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr6:157528657C>T	ENST00000350026.5	+	19	6344	c.6343C>T	c.(6343-6345)Cga>Tga	p.R2115*	ARID1B_ENST00000367148.1_Nonsense_Mutation_p.R2168*|ARID1B_ENST00000275248.4_Nonsense_Mutation_p.R2110*|ARID1B_ENST00000346085.5_Nonsense_Mutation_p.R2128*	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	2115					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.R2110*(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CCCAGTCTGTCGAGAAATGTC	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											183	190	188					6																	157528657		2203	4296	6499	157570349	SO:0001587	stop_gained	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.6343C>T	6.37:g.157528657C>T	ENSP00000055163:p.Arg2115*		157570349	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Nonsense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	46	12.170940	0.99643	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2386	0.93873	0.0:1.0:0.0:0.0	.	.	.	.	X	2128;2115;2168;2110;1637	.	ENSP00000275248:R2110X	R	+	1	2	ARID1B	157570349	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.809000	0.62591	2.607000	0.88179	0.655000	0.94253	CGA		0.478	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157528657	C	T	157528657	4	4	14	1	0	0	0	0	0	1	0	0	914	876	31	1	6460	1	ARID1B	6	157528657	Nonsense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	31455488	157528657	13586410	22	1620										
PNMA2	10687	hgsc.bcm.edu	37	chr8	26366087	26366087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctctagtaagacagcattgGcattctcctgcttccggaat	9	11	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr8:26366087G>A	ENST00000522362.2	-	3	1079	c.185C>T	c.(184-186)gCc>gTc	p.A62V	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	62					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)		p.A62V(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		gacagcattggcattctcctg	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	8											77	76	76					8																	26366087		2203	4300	6503	26422004	SO:0001583	missense	10687				CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"Paraneoplastic Ma antigens"	9159	protein-coding gene	gene with protein product		603970	"paraneoplastic antigen MA2"			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.185C>T	8.37:g.26366087G>A	ENSP00000429344:p.Ala62Val		26422004	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Missense_Mutation	SNP	ENST00000522362.2	37	CCDS34868.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.555598	0.45487	.	.	ENSG00000240694	ENST00000522362	T	0.10288	2.89	3.77	3.77	0.43336	.	.	.	.	.	T	0.08582	0.0213	L	0.31371	0.925	0.26061	N	0.981346	B	0.33826	0.427	B	0.29176	0.099	T	0.15206	-1.0445	9	0.48119	T	0.1	-21.7407	11.3945	0.49834	0.0:0.0:1.0:0.0	.	62	Q9UL42	PNMA2_HUMAN	V	62	ENSP00000429344:A62V	ENSP00000429344:A62V	A	-	2	0	PNMA2	26422004	0.260000	0.24053	0.984000	0.44739	0.824000	0.46624	1.428000	0.34892	2.389000	0.81357	0.563000	0.77884	GCC		0.502	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375709.2	NM_007257		A	26366087	G	A	26366087	3	1	14	1	0	0	0	0	1	0	0	0	12185	1203	42	3	913	3	PNMA2	8	26366087	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		26366087	119997935	23	1621										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53568950	53568950	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agctttaagtatattagattCttcttcatgtctactaatta	4	6	4	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr8:53568950C>A	ENST00000025008.5	-	15	3962	c.3439G>T	c.(3439-3441)Gaa>Taa	p.E1147*	RB1CC1_ENST00000539297.1_Nonsense_Mutation_p.E1147*|RB1CC1_ENST00000435644.2_Nonsense_Mutation_p.E1147*|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1147					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.E1147*(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				ATATTAGATTCTTCTTCATGT	0.284																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - Nonsense(1)	large_intestine(1)	8											49	50	50					8																	53568950		2197	4293	6490	53731503	SO:0001587	stop_gained	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3439G>T	8.37:g.53568950C>A	ENSP00000025008:p.Glu1147*		53731503	Q86YR4|Q8WVU9|Q92601	Nonsense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	45	11.552433	0.99575	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-21.1131	18.9627	0.92682	0.0:1.0:0.0:0.0	.	.	.	.	X	1147	.	ENSP00000025008:E1147X	E	-	1	0	RB1CC1	53731503	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.432000	0.66514	2.556000	0.86216	0.650000	0.86243	GAA		0.284	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		A	53568950	C	A	53568950	4	1	14	1	0	0	0	0	0	1	0	0	13136	922	32	2	1385	2	RB1CC1	8	53568950	Nonsense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	27202863	53568950	92795072	24	1622										
UBR5	51366	hgsc.bcm.edu	37	chr8	103269876	103269876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttacaagatcttgtcgttctGtcatgctcatcttctctact	5	11	6	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr8:103269876G>A	ENST00000520539.1	-	58	8777	c.8171C>T	c.(8170-8172)aCa>aTa	p.T2724I	UBR5_ENST00000518205.1_Missense_Mutation_p.T452I|UBR5_ENST00000521922.1_Missense_Mutation_p.T2717I|UBR5_ENST00000220959.4_Missense_Mutation_p.T2723I|KB-431C1.5_ENST00000606361.1_RNA	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2724	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.T2724I(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			TTGTCGTTCTGTCATGCTCAT	0.328																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											89	82	84					8																	103269876		2202	4300	6502	103339052	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.8171C>T	8.37:g.103269876G>A	ENSP00000429084:p.Thr2724Ile		103339052	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285195	0.59867	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.47	5.47	0.80525	HECT (4);	0.204743	0.39341	N	0.001387	T	0.37046	0.0989	N	0.04297	-0.235	0.80722	D	1	P;P	0.34800	0.469;0.469	P;P	0.48982	0.597;0.597	T	0.33523	-0.9865	10	0.19147	T	0.46	.	19.3216	0.94243	0.0:0.0:1.0:0.0	.	2717;2724	E7EMW7;O95071	.;UBR5_HUMAN	I	2724;2723;452;2717	ENSP00000429084:T2724I;ENSP00000220959:T2723I;ENSP00000428693:T452I;ENSP00000427819:T2717I	ENSP00000220959:T2723I	T	-	2	0	UBR5	103339052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.578000	0.87016	0.585000	0.79938	ACA		0.328	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103269876	G	A	103269876	3	1	14	1	0	0	0	0	1	0	0	0	16945	1377	48	3	236	3	UBR5	8	103269876	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10	49700926	103269876	43094146	25	1623										
GCNT1	2650	hgsc.bcm.edu	37	chr9	79117338	79117338	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaggagacttttttcttatcCcaccaaatactactttatgg	5	9	1	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr9:79117338C>T	ENST00000376730.4	+	4	524	c.41C>T	c.(40-42)cCc>cTc	p.P14L	GCNT1_ENST00000536223.1_Missense_Mutation_p.P14L|GCNT1_ENST00000444201.2_Missense_Mutation_p.P14L|GCNT1_ENST00000442371.1_Missense_Mutation_p.P14L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	14					cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)	p.P14L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						TTTTCTTATCCCACCAAATAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											103	105	104					9																	79117338		2203	4300	6503	78307158	SO:0001583	missense	2650			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4203	protein-coding gene	gene with protein product	"core 2 beta1,6 N-acetylglucosaminyltransferase-I", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"	600391	"glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.41C>T	9.37:g.79117338C>T	ENSP00000365920:p.Pro14Leu		78307158	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	c	12.90	2.075141	0.36566	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.09073	3.02;3.02;3.02;3.02	5.73	3.72	0.42706	.	0.378660	0.25717	N	0.028764	T	0.06325	0.0163	L	0.41236	1.265	0.45139	D	0.998154	B	0.32245	0.361	B	0.25140	0.058	T	0.38779	-0.9645	9	.	.	.	.	8.0647	0.30654	0.3852:0.5043:0.1105:0.0	.	14	Q02742	GCNT1_HUMAN	L	14	ENSP00000440883:P14L;ENSP00000415454:P14L;ENSP00000390703:P14L;ENSP00000365920:P14L	.	P	+	2	0	GCNT1	78307158	0.979000	0.34478	0.992000	0.48379	0.698000	0.40448	2.481000	0.45215	1.403000	0.46800	0.650000	0.86243	CCC		0.403	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634		T	79117338	C	T	79117338	3	4	14	1	0	0	0	0	1	0	0	0	6320	623	22	3	43	3	GCNT1	9	79117338	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10		79117338	62096093	26	1624										
GOLM1	51280	hgsc.bcm.edu	37	chr9	88694228	88694228	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcgacgcccgtttcccaagCccatcatctcaaaatcagcg	7	16	3	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr9:88694228C>A	ENST00000388712.3	-	2	176	c.8G>T	c.(7-9)gGc>gTc	p.G3V	GOLM1_ENST00000257504.6_5'Flank|GOLM1_ENST00000388711.3_Missense_Mutation_p.G3V	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	3					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)		p.G3V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						GTTTCCCAAGCCCATCATCTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	9											36	38	37					9																	88694228		2203	4300	6503	87884048	SO:0001583	missense	51280			AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"golgi phosphoprotein 2", "chromosome 9 open reading frame 155"	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.8G>T	9.37:g.88694228C>A	ENSP00000373364:p.Gly3Val		87884048	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.097230	0.76870	.	.	ENSG00000135052	ENST00000388712;ENST00000388711;ENST00000486130;ENST00000466178	D;D	0.86297	-2.1;-2.1	5.39	5.39	0.77823	.	0.139249	0.47093	D	0.000246	D	0.92668	0.7670	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93202	0.6592	10	0.87932	D	0	-0.0921	13.4776	0.61318	0.0:0.9227:0.0:0.0773	.	3	Q8NBJ4	GOLM1_HUMAN	V	3	ENSP00000373364:G3V;ENSP00000373363:G3V	ENSP00000373363:G3V	G	-	2	0	GOLM1	87884048	1.000000	0.71417	0.998000	0.56505	0.903000	0.53119	4.658000	0.61497	2.522000	0.85027	0.555000	0.69702	GGC		0.507	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		A	88694228	C	A	88694228	3	1	14	1	0	0	0	0	1	0	0	0	6587	739	26	2	1233	2	GOLM1	9	88694228	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	9576890	88694228	52519203	27	1625										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108431071	108431071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttttccttgcatacacttccGctctgattttcgcttcttat	4	12	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr10:108431071G>A	ENST00000263054.6	-	16	2120	c.2113C>T	c.(2113-2115)Cgg>Tgg	p.R705W	SORCS1_ENST00000344440.6_Missense_Mutation_p.R705W|SORCS1_ENST00000369698.1_Missense_Mutation_p.R240W	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	705					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.R705W(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ATACACTTCCGCTCTGATTTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											254	213	227					10																	108431071		2203	4300	6503	108421061	SO:0001583	missense	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2113C>T	10.37:g.108431071G>A	ENSP00000263054:p.Arg705Trp		108421061	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.314014	0.60414	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.29917	1.55;1.55;1.55	5.45	2.09	0.27110	VPS10 (1);	0.252502	0.35124	N	0.003427	T	0.24314	0.0589	N	0.08118	0	0.32861	D	0.507881	P;P;P;P;P	0.49559	0.877;0.925;0.925;0.877;0.925	B;P;P;P;P	0.52710	0.39;0.707;0.594;0.513;0.594	T	0.30387	-0.9980	9	.	.	.	-20.7334	14.1207	0.65184	0.0:0.0:0.4938:0.5061	.	705;705;705;705;705	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	W	240;705;705	ENSP00000358712:R240W;ENSP00000263054:R705W;ENSP00000345964:R705W	.	R	-	1	2	SORCS1	108421061	0.948000	0.32251	1.000000	0.80357	0.987000	0.75469	0.965000	0.29319	0.774000	0.33427	-0.152000	0.13540	CGG		0.448	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108431071	G	A	108431071	3	1	14	1	0	0	0	0	1	0	0	0	14967	1086	38	1	1671	1	SORCS1	10	108431071	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		108431071	27103676	28	1626										
SAPS3	55291	hgsc.bcm.edu	37	chr11	68343449	68343449	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcccgacgaagtcagggaaCgatgggagacgttctgcaca	13	10	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr11:68343449C>T	ENST00000393800.2	+	14	1737	c.1483C>T	c.(1483-1485)Cga>Tga	p.R495*	PPP6R3_ENST00000534534.1_Nonsense_Mutation_p.R263*|PPP6R3_ENST00000265637.4_Nonsense_Mutation_p.R495*|PPP6R3_ENST00000393799.2_Nonsense_Mutation_p.R495*|PPP6R3_ENST00000265636.5_Nonsense_Mutation_p.R444*|PPP6R3_ENST00000524904.1_Nonsense_Mutation_p.R495*|PPP6R3_ENST00000393801.3_Nonsense_Mutation_p.R495*|PPP6R3_ENST00000529710.1_Nonsense_Mutation_p.R444*|PPP6R3_ENST00000527403.2_Nonsense_Mutation_p.R495*|PPP6R3_ENST00000524845.1_Nonsense_Mutation_p.R495*	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	495					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.R444*(1)|p.R495*(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						AGTCAGGGAACGATGGGAGAC	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											142	135	137					11																	68343449		2200	4294	6494	68100025	SO:0001587	stop_gained	55291			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1483C>T	11.37:g.68343449C>T	ENSP00000377389:p.Arg495*		68100025	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Nonsense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	C	40	8.261745	0.98732	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	.	.	.	5.89	5.89	0.94794	.	0.195950	0.42172	D	0.000742	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1151	0.65149	0.15:0.85:0.0:0.0	.	.	.	.	X	495;495;263;495;495;495;495;444;444;495;231	.	ENSP00000265636:R444X	R	+	1	2	PPP6R3	68100025	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.839000	0.48207	2.763000	0.94921	0.655000	0.94253	CGA		0.413	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		T	68343449	C	T	68343449	4	4	14	1	0	0	0	0	0	1	0	0	13875	528	19	1	1529	1	SAPS3	11	68343449	Nonsense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10		68343449	66663067	29	1627										
C11orf82	220042	hgsc.bcm.edu	37	chr11	82642968	82642969	+	Frame_Shift_Del	DEL	CT	CT	-													0	0	1	0	0	0	1	1	0	ttcaggaaacttcagtgtgaCtctcaggcacctaacaatca							TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr11:82642968_82642969delCT	ENST00000533655.1	+	6	800_801	c.588_589delCT	c.(586-591)gactctfs	p.S197fs	C11orf82_ENST00000525388.1_3'UTR|C11orf82_ENST00000533750.1_3'UTR|C11orf82_ENST00000329143.3_5'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000430323.2_Frame_Shift_Del_p.S197fs	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		197					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.Q198fs*3(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						TTCAGTGTGACTCTCAGGCACC	0.401																																																1	Deletion - Frameshift(1)	large_intestine(1)	11																																								82320617	SO:0001589	frameshift_variant	220042																														ENST00000533655.1:c.588_589delCT	11.37:g.82642970_82642971delCT	ENSP00000435421:p.Ser197fs		82320616	Q96LK6|Q9H856	Frame_Shift_Del	DEL	ENST00000533655.1	37	CCDS8263.1																																																																																				0.401	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			-	82642969	CT	-	82642968	7	5	14	1	0	1	0	1	0	0	0	0	1669	564	20	0	602	0	C11orf82	11	82642968	Frame_Shift_Del	DEL	CT	TCGA-AG-3575-01A-01W-0831-10	14299519	82642968	52363548	30	1628										
ETS1	2113	hgsc.bcm.edu	37	chr11	128350208	128350208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgggcagggcagccggatagTcctctgagtcgaagctgtca	15	10	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr11:128350208T>C	ENST00000319397.6	-	6	1178	c.869A>G	c.(868-870)gAc>gGc	p.D290G	ETS1_ENST00000535549.1_Missense_Mutation_p.D74G|ETS1_ENST00000345075.4_Intron|ETS1_ENST00000392668.4_Missense_Mutation_p.D334G|ETS1_ENST00000531611.1_Intron|ETS1_ENST00000526145.2_Intron	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	290					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.D290G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		AGCCGGATAGTCCTCTGAGTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											130	113	119					11																	128350208		2201	4297	6498	127855418	SO:0001583	missense	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.869A>G	11.37:g.128350208T>C	ENSP00000324578:p.Asp290Gly		127855418	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.386784	0.82902	.	.	ENSG00000134954	ENST00000535549;ENST00000392668;ENST00000319397	T;T;T	0.18016	2.24;2.63;2.65	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.19127	0.0459	M	0.64404	1.975	0.80722	D	1	P;B;P	0.52842	0.849;0.015;0.956	B;B;B	0.38500	0.239;0.023;0.275	T	0.04103	-1.0977	10	0.36615	T	0.2	.	15.2691	0.73686	0.0:0.0:0.0:1.0	.	290;74;334	P14921;F5GYX9;Q6N087	ETS1_HUMAN;.;.	G	74;334;290	ENSP00000441430:D74G;ENSP00000376436:D334G;ENSP00000324578:D290G	ENSP00000324578:D290G	D	-	2	0	ETS1	127855418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.670000	0.83925	1.991000	0.58162	0.528000	0.53228	GAC		0.562	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		C	128350208	T	C	128350208	3	2	14	1	0	0	0	0	1	0	0	0	5288	1667	58	4	468	4	ETS1	11	128350208	Missense_Mutation	SNP	T	TCGA-AG-3575-01A-01W-0831-10	45707240	128350208	6656308	31	1629										
KCNA6	3742	hgsc.bcm.edu	37	chr12	4919742	4919742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cggccaggggcatcgccatcGtctccgtgttggtcattctc	12	14	3	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr12:4919742G>A	ENST00000280684.3	+	1	1401	c.535G>A	c.(535-537)Gtc>Atc	p.V179I	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Missense_Mutation_p.V179I			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	179					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.V179I(1)		NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	CATCGCCATCGTCTCCGTGTT	0.592										HNSCC(72;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											67	59	62					12																	4919742		2203	4300	6503	4790003	SO:0001583	missense	3742			X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.535G>A	12.37:g.4919742G>A	ENSP00000280684:p.Val179Ile		4790003		Missense_Mutation	SNP	ENST00000280684.3	37	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446111	0.43429	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	T;T	0.76060	-0.99;-0.99	4.99	4.99	0.66335	.	0.127069	0.52532	D	0.000077	T	0.60560	0.2278	N	0.25647	0.755	0.58432	D	0.999995	B	0.29188	0.236	B	0.19148	0.024	T	0.57670	-0.7771	10	0.16896	T	0.51	.	17.4425	0.87568	0.0:0.0:1.0:0.0	.	179	P17658	KCNA6_HUMAN	I	179	ENSP00000408321:V179I;ENSP00000280684:V179I	ENSP00000280684:V179I	V	+	1	0	KCNA6	4790003	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.798000	0.85924	2.595000	0.87683	0.563000	0.77884	GTC		0.592	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		A	4919742	G	A	4919742	3	1	14	1	0	0	0	0	1	0	0	0	8028	1145	40	1	537	1	KCNA6	12	4919742	Missense_Mutation	SNP	G	TCGA-AG-3575-01A-01W-0831-10		4919742	128932153	32	1630										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	14	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	20478542	25398284	108453611	33	1631										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816782	75816782	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctatgcagtaagataaagaAaataaacatgaaaaaaatgc	6	4	1	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr12:75816782A>C	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000320460.4_Missense_Mutation_p.K228T	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)		p.K228T(1)		kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						AAGATAAAGAAAATAAACATG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											126	129	128					12																	75816782		2203	4299	6502	74103049	SO:0001627	intron_variant	144321			BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+13A>C	12.37:g.75816782A>C			74103049	Q6MZS1|Q8N6N0|Q8NA43	Missense_Mutation	SNP	ENST00000550916.1	37	CCDS58258.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.800865	0.31869	.	.	ENSG00000180481	ENST00000320460	T	0.06933	3.24	4.46	0.312	0.15837	.	.	.	.	.	T	0.06142	0.0159	.	.	.	0.09310	N	0.999999	P	0.44816	0.844	B	0.41174	0.349	T	0.33675	-0.9859	7	.	.	.	.	4.1383	0.10181	0.6233:0.1748:0.2019:0.0	.	228	Q4G1C9-2	.	T	228	ENSP00000317385:K228T	.	K	+	2	0	GLIPR1L2	74103049	0.974000	0.33945	0.059000	0.19551	0.799000	0.45148	0.476000	0.22180	0.105000	0.17753	0.454000	0.30748	AAA		0.328	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		C	75816782	A	C	75816782	1	2	14	0	1	0	0	0	0	0	0	0	6463	14	1	4		4	GLIPR1L2	12	75816782	Intron	SNP	A	TCGA-AG-3575-01A-01W-0831-10	50418498	75816782	58035113	34	1632										
TMTC4	84899	hgsc.bcm.edu	37	chr13	101287384	101287384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ctgcgaccacgaagcccactCggaagaacaggttactcgcg	11	14	0	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr13:101287384C>T	ENST00000376234.3	-	10	1400	c.1211G>A	c.(1210-1212)cGa>cAa	p.R404Q	TMTC4_ENST00000328767.5_Missense_Mutation_p.R293Q|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000342624.5_Missense_Mutation_p.R423Q	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	404						integral component of membrane (GO:0016021)		p.R423Q(1)		breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GAAGCCCACTCGGAAGAACAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	13											55	50	52					13																	101287384		2203	4300	6503	100085385	SO:0001583	missense	84899				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1211G>A	13.37:g.101287384C>T	ENSP00000365408:p.Arg404Gln		100085385	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	C	34	5.335777	0.95758	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.41400	1.0;1.0;1.0	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.66499	0.2795	M	0.88031	2.925	0.58432	D	0.999997	P;D;P;P	0.56035	0.827;0.974;0.915;0.939	B;P;P;P	0.56514	0.282;0.8;0.556;0.576	T	0.69026	-0.5254	10	0.36615	T	0.2	.	19.425	0.94737	0.0:1.0:0.0:0.0	.	293;404;404;423	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	Q	404;423;293	ENSP00000365408:R404Q;ENSP00000343871:R423Q;ENSP00000365409:R293Q	ENSP00000365409:R293Q	R	-	2	0	TMTC4	100085385	0.998000	0.40836	0.995000	0.50966	0.864000	0.49448	3.982000	0.56909	2.584000	0.87258	0.563000	0.77884	CGA		0.502	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		T	101287384	C	T	101287384	3	4	14	1	0	0	0	0	1	0	0	0	16302	884	31	1	1050	1	TMTC4	13	101287384	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10		101287384	13882494	35	1633										
PYGO1	26108	hgsc.bcm.edu	37	chr15	55839260	55839260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaaatagtattatagttgTcatcaaatggattagcagcc	9	5	2	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr15:55839260T>C	ENST00000302000.6	-	3	315	c.221A>G	c.(220-222)gAc>gGc	p.D74G	PYGO1_ENST00000563719.1_Missense_Mutation_p.D74G	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	74	Pro-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.D74G(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		ATTATAGTTGTCATCAAATGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											67	64	65					15																	55839260		2193	4292	6485	53626552	SO:0001583	missense	26108			AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"Zinc fingers, PHD-type"	30256	protein-coding gene	gene with protein product		606902	"pygopus homolog 1 (Drosophila)"			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.221A>G	15.37:g.55839260T>C	ENSP00000302327:p.Asp74Gly		53626552	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741991	0.69418	.	.	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.68331	-0.32	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.73745	0.3626	L	0.36672	1.1	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.73933	-0.3826	10	0.42905	T	0.14	-16.2368	14.6174	0.68558	0.0:0.0:0.0:1.0	.	74;74	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	G	74	ENSP00000302327:D74G	ENSP00000302327:D74G	D	-	2	0	PYGO1	53626552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.040000	0.76551	2.103000	0.63969	0.477000	0.44152	GAC		0.428	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		C	55839260	T	C	55839260	3	2	14	1	0	0	0	0	1	0	0	0	12900	1667	58	4	1042	4	PYGO1	15	55839260	Missense_Mutation	SNP	T	TCGA-AG-3575-01A-01W-0831-10		55839260	46692132	36	1634										
IDH3A	3419	hgsc.bcm.edu	37	chr15	78453965	78453965	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agccggtcacccatctatgaAtttactgctgcgcaaaacat	7	12	2	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr15:78453965A>G	ENST00000299518.2	+	5	415	c.332A>G	c.(331-333)aAt>aGt	p.N111S	IDH3A_ENST00000441490.2_Missense_Mutation_p.N2S|IDH3A_ENST00000561366.1_5'Flank|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000559205.1_Intron|IDH3A_ENST00000558554.1_Intron	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	111					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.N111S(1)		endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CCATCTATGAATTTACTGCTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	15											136	124	128					15																	78453965		2196	4293	6489	76241020	SO:0001583	missense	3419				CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"H-IDH alpha", "isocitric dehydrogenase", "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "NAD+-specific ICDH", "NAD(H)-specific isocitrate dehydrogenase alpha subunit", "isocitrate dehydrogenase (NAD+) alpha chain"	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.332A>G	15.37:g.78453965A>G	ENSP00000299518:p.Asn111Ser		76241020	D3DW83|Q9H3X0	Missense_Mutation	SNP	ENST00000299518.2	37	CCDS10297.1	.	.	.	.	.	.	.	.	.	.	A	32	5.153617	0.94645	.	.	ENSG00000166411	ENST00000299518;ENST00000441490	T;T	0.58506	0.33;0.33	6.02	6.02	0.97574	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77711	0.4171	M	0.80028	2.48	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.80774	-0.1232	10	0.87932	D	0	-30.3593	15.7232	0.77732	1.0:0.0:0.0:0.0	.	111	P50213	IDH3A_HUMAN	S	111;2	ENSP00000299518:N111S;ENSP00000387506:N2S	ENSP00000299518:N111S	N	+	2	0	IDH3A	76241020	1.000000	0.71417	0.959000	0.39883	0.992000	0.81027	9.081000	0.94049	2.304000	0.77564	0.528000	0.53228	AAT		0.453	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		G	78453965	A	G	78453965	3	3	14	1	0	0	0	0	1	0	0	0	7517	101	4	4	350	4	IDH3A	15	78453965	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10	22614705	78453965	24077427	37	1635										
SLC38A7	55238	hgsc.bcm.edu	37	chr16	58701370	58701370	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agggtgaccaagaggactccGtagctgaccagcacccacca	11	14	0	3	rs374997624		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr16:58701370G>A	ENST00000570101.1	-	11	2191	c.1308C>T	c.(1306-1308)taC>taT	p.Y436Y	SLC38A7_ENST00000219320.4_Silent_p.Y436Y|SLC38A7_ENST00000566953.1_5'UTR|SLC38A7_ENST00000564100.1_Missense_Mutation_p.T302M|SLC38A7_ENST00000564010.1_Silent_p.Y347Y			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	436					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)	p.Y436Y(1)		endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						AGAGGACTCCGTAGCTGACCA	0.522													G|||	1	0.000199681	0	0	5008	,	,		20896	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16						G		0,4396		0,0,2198	112	95	101		1308	-4.6	0.9	16		101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC38A7	NM_018231.1		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		436/463	58701370	1,12995	2198	4300	6498	57258871	SO:0001819	synonymous_variant	55238			BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.1308C>T	16.37:g.58701370G>A			57258871	Q53GJ9|Q9H9I5	Silent	SNP	ENST00000570101.1	37	CCDS10800.1																																																																																				0.522	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		A	58701370	G	A	58701370	2	1	14	1	0	0	0	0	0	0	0	1	14646	1140	40	1		1	SLC38A7	16	58701370	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10		58701370	31653383	38	1636										
CDH8	1006	hgsc.bcm.edu	37	chr16	61689467	61689467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcgacattgcaagactggaCgacaccgtcattgctgcagc	10	12	1	1	rs146415895		TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr16:61689467C>T	ENST00000577390.1	-	11	2767	c.1813G>A	c.(1813-1815)Gtc>Atc	p.V605I	CDH8_ENST00000577730.1_Missense_Mutation_p.V605I|CDH8_ENST00000299345.6_Missense_Mutation_p.V605I	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	605	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.V605I(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CAAGACTGGACGACACCGTCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	153	127	136		1813	5.5	1	16	dbSNP_134	136	0,8600		0,0,4300	no	missense	CDH8	NM_001796.4	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	605/800	61689467	1,13005	2203	4300	6503	60246968	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1813G>A	16.37:g.61689467C>T	ENSP00000462701:p.Val605Ile		60246968	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299669	0.40694	2.27E-4	0.0	ENSG00000150394	ENST00000299345	T	0.54866	0.55	5.52	5.52	0.82312	Cadherin (1);	0.000000	0.85682	D	0.000000	T	0.41190	0.1148	L	0.36672	1.1	0.80722	D	1	P	0.39576	0.679	B	0.34038	0.174	T	0.28299	-1.0048	10	0.12430	T	0.62	.	18.4201	0.90587	0.0:1.0:0.0:0.0	.	605	P55286	CADH8_HUMAN	I	605	ENSP00000299345:V605I	ENSP00000299345:V605I	V	-	1	0	CDH8	60246968	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.934000	0.48956	2.599000	0.87857	0.561000	0.74099	GTC		0.453	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61689467	C	T	61689467	3	4	14	1	0	0	0	0	1	0	0	0	3122	536	19	1	594	1	CDH8	16	61689467	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	2988097	61689467	28665286	39	1637										
TP53	7157	hgsc.bcm.edu	37	chr17	7578268	7578268	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatttccttccactcggataAgatgctgaggaggggccaga	12	9	0	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr17:7578268A>T	ENST00000269305.4	-	6	770	c.581T>A	c.(580-582)cTt>cAt	p.L194H	TP53_ENST00000420246.2_Missense_Mutation_p.L194H|TP53_ENST00000359597.4_Missense_Mutation_p.L194H|TP53_ENST00000445888.2_Missense_Mutation_p.L194H|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.L194H|TP53_ENST00000455263.2_Missense_Mutation_p.L194H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	194	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		L -> F (in sporadic cancers; somatic mutation).|L -> H (in sporadic cancers; somatic mutation).|L -> I (in sporadic cancers; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763}.|L -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.L194R(47)|p.L194P(8)|p.L194H(8)|p.0?(8)|p.?(6)|p.L101R(5)|p.L62R(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.L194fs*15(1)|p.L194fs*14(1)|p.L101H(1)|p.L194fs*52(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.L62H(1)|p.I195fs*52(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACTCGGATAAGATGCTGAGG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	108	Substitution - Missense(75)|Whole gene deletion(8)|Deletion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Insertion - Frameshift(1)|Complex - frameshift(1)	breast(19)|lung(14)|ovary(14)|large_intestine(11)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(6)|oesophagus(6)|biliary_tract(5)|skin(5)|bone(4)|upper_aerodigestive_tract(3)|stomach(3)|central_nervous_system(2)|pancreas(2)|liver(2)|soft_tissue(1)|prostate(1)	17											97	87	90					17																	7578268		2203	4300	6503	7518993	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.581T>A	17.37:g.7578268A>T	ENSP00000269305:p.Leu194His		7518993	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.086635	0.55861	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99857	-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.994;1.0;1.0;1.0;1.0	D	0.96375	0.9277	10	0.87932	D	0	-29.6709	13.709	0.62656	1.0:0.0:0.0:0.0	.	155;194;194;101;194;194;194	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	194;194;194;194;194;194;183;101;62;101;62	ENSP00000410739:L194H;ENSP00000352610:L194H;ENSP00000269305:L194H;ENSP00000398846:L194H;ENSP00000391127:L194H;ENSP00000391478:L194H;ENSP00000425104:L62H;ENSP00000423862:L101H	ENSP00000269305:L194H	L	-	2	0	TP53	7518993	1.000000	0.71417	0.300000	0.25030	0.031000	0.12232	9.287000	0.95975	2.183000	0.69458	0.533000	0.62120	CTT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578268	A	T	7578268	3	4	14	1	0	0	0	0	1	0	0	0	16421	72	3	5	713	5	TP53	17	7578268	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10		7578268	73616942	40	1638										
CD300E	342510	hgsc.bcm.edu	37	chr17	72613483	72613483	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgctctcacatgacgtgtcGtactgtcctcggcaccagta	9	13	1	1	rs111412583	byFrequency	TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr17:72613483G>A	ENST00000328630.3	-	2	202	c.162C>T	c.(160-162)taC>taT	p.Y54Y	CD300E_ENST00000426295.2_Silent_p.Y95Y|CD300E_ENST00000392619.1_Silent_p.Y81Y			Q496F6	CLM2_HUMAN	CD300e molecule	54	Ig-like V-type.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y54Y(1)		breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						ATGACGTGTCGTACTGTCCTC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	17						G		2,4404	4.2+/-10.8	0,2,2201	220	140	167		162	-4.5	0	17	dbSNP_132	167	0,8600		0,0,4300	no	coding-synonymous	CD300E	NM_181449.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		54/206	72613483	2,13004	2203	4300	6503	70125078	SO:0001819	synonymous_variant	342510			BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	28874	protein-coding gene	gene with protein product		609801	"CD300 antigen like family member E", "CD300e antigen"	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.162C>T	17.37:g.72613483G>A			70125078	B4DNS1|Q7Z7I3	Silent	SNP	ENST00000328630.3	37	CCDS11702.1																																																																																				0.562	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449		A	72613483	G	A	72613483	2	1	14	1	0	0	0	0	0	0	0	1	3004	1140	40	1		1	CD300E	17	72613483	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10	65035215	72613483	8581727	41	1639										
CDH2	1000	hgsc.bcm.edu	37	chr18	25572642	25572642	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaccacggtgactaacccgtCgttgctgtttgggtcggtct	13	11	1	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr18:25572642C>A	ENST00000269141.3	-	9	1744	c.1321G>T	c.(1321-1323)Gac>Tac	p.D441Y	CDH2_ENST00000399380.3_Missense_Mutation_p.D410Y	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	441	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.D441Y(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTAACCCGTCGTTGCTGTTT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	18											173	143	153					18																	25572642		2203	4300	6503	23826640	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1321G>T	18.37:g.25572642C>A	ENSP00000269141:p.Asp441Tyr		23826640	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185520	0.78677	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.61627	0.09;0.09	5.39	5.39	0.77823	Cadherin (5);Cadherin-like (1);	0.047096	0.85682	D	0.000000	T	0.74397	0.3711	L	0.60067	1.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.992	T	0.76055	-0.3099	10	0.87932	D	0	.	19.5228	0.95192	0.0:1.0:0.0:0.0	.	410;441	A8MWK3;P19022	.;CADH2_HUMAN	Y	441;410	ENSP00000269141:D441Y;ENSP00000382312:D410Y	ENSP00000269141:D441Y	D	-	1	0	CDH2	23826640	1.000000	0.71417	0.979000	0.43373	0.741000	0.42261	6.046000	0.71029	2.674000	0.91012	0.655000	0.94253	GAC		0.527	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		A	25572642	C	A	25572642	3	1	14	1	0	0	0	0	1	0	0	0	3111	884	31	2	1431	2	CDH2	18	25572642	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10		25572642	52504606	42	1640										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15082669	15082669	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagctgatatgggcgcagggCaaaggccaggctgaccccta	15	11	0	2			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr19:15082669C>A	ENST00000221742.3	-	2	230	c.223G>T	c.(223-225)Gcc>Tcc	p.A75S	SLC1A6_ENST00000598504.1_Missense_Mutation_p.A75S|SLC1A6_ENST00000600144.1_Missense_Mutation_p.A75S|SLC1A6_ENST00000430939.2_Missense_Mutation_p.C79F|SLC1A6_ENST00000544886.2_Missense_Mutation_p.A75S	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	75					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.A75S(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GGGCGCAGGGCAAAGGCCAGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											101	94	97					19																	15082669		2203	4300	6503	14943669	SO:0001583	missense	6511				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.223G>T	19.37:g.15082669C>A	ENSP00000221742:p.Ala75Ser		14943669	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.56|11.56	1.675044|1.675044	0.29783|0.29783	.|.	.|.	ENSG00000105143|ENSG00000105143	ENST00000221742;ENST00000544886;ENST00000542610|ENST00000430939	T;T|T	0.59906|0.74737	0.23;0.23|-0.87	4.26|4.26	2.12|2.12	0.27331|0.27331	.|.	0.331795|.	0.30473|.	N|.	0.009549|.	T|T	0.61515|0.61515	0.2353|0.2353	L|L	0.43757|0.43757	1.38|1.38	0.39567|0.39567	D|D	0.969221|0.969221	B;B;B|B	0.20368|0.02656	0.044;0.01;0.02|0.0	B;B;B|B	0.26864|0.06405	0.074;0.019;0.023|0.002	T|T	0.58075|0.58075	-0.7700|-0.7700	10|9	0.44086|0.87932	T|D	0.13|0	-9.9017|-9.9017	3.6068|3.6068	0.08045|0.08045	0.1964:0.593:0.0:0.2106|0.1964:0.593:0.0:0.2106	.|.	75;76;75|79	Q8N753;Q59GB0;P48664|E7EV13	.;.;EAA4_HUMAN|.	S|F	75;75;76|79	ENSP00000221742:A75S;ENSP00000446175:A75S|ENSP00000409386:C79F	ENSP00000221742:A75S|ENSP00000409386:C79F	A|C	-|-	1|2	0|0	SLC1A6|SLC1A6	14943669|14943669	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.865000|0.865000	0.49528|0.49528	1.442000|1.442000	0.35046|0.35046	0.435000|0.435000	0.26365|0.26365	0.561000|0.561000	0.74099|0.74099	GCC|TGC		0.567	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		A	15082669	C	A	15082669	3	1	14	1	0	0	0	0	1	0	0	0	14473	710	25	2	1503	2	SLC1A6	19	15082669	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10		15082669	44046314	43	1641										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55447774	55447774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagacagaagtcccggtacgCggtgtcaggggtgacgtttt	15	8	1	3			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr19:55447774C>T	ENST00000590030.1	-	5	2195	c.2155G>A	c.(2155-2157)Gcg>Acg	p.A719T	NLRP7_ENST00000588756.1_Missense_Mutation_p.A719T|NLRP7_ENST00000448121.2_Missense_Mutation_p.A691T|NLRP7_ENST00000446217.1_Missense_Mutation_p.A747T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A691T|NLRP7_ENST00000340844.2_Missense_Mutation_p.A719T|NLRP7_ENST00000592784.1_Missense_Mutation_p.A719T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	719							ATP binding (GO:0005524)	p.A691T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TCCCGGTACGCGGTGTCAGGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	78	82					19																	55447774		2203	4300	6503	60139586	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.2155G>A	19.37:g.55447774C>T	ENSP00000465520:p.Ala719Thr		60139586	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791967	0.50102	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T	0.53857	0.6;0.6;0.6	2.21	1.17	0.20885	.	0.566406	0.13372	N	0.392815	T	0.48624	0.1510	L	0.60455	1.87	0.09310	N	1	P;P;P;D	0.55385	0.951;0.951;0.951;0.971	B;B;B;P	0.47299	0.406;0.406;0.406;0.543	T	0.38824	-0.9643	10	0.52906	T	0.07	.	4.619	0.12440	0.0:0.8133:0.0:0.1867	.	747;719;719;691	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	T	719;691;719;747;486	ENSP00000409137:A691T;ENSP00000339491:A719T;ENSP00000414273:A747T	ENSP00000329568:A719T	A	-	1	0	NLRP7	60139586	0.023000	0.18921	0.001000	0.08648	0.338000	0.28826	0.850000	0.27737	0.506000	0.28125	0.561000	0.74099	GCG		0.493	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55447774	C	T	55447774	3	4	14	1	0	0	0	0	1	0	0	0	10513	768	27	1	982	1	NLRP7	19	55447774	Missense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	40365105	55447774	3681209	44	1642										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57066700	57066700	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccctctttaccttccacgtCaaatcctgtggatctgtttc	5	15	3	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr19:57066700C>A	ENST00000301318.3	+	8	2617	c.2546C>A	c.(2545-2547)tCa>tAa	p.S849*	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	849					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S849*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		CCTTCCACGTCAAATCCTGTG	0.458																																					Ovarian(124;554 1662 19430 21141 52494)											1	Substitution - Nonsense(1)	large_intestine(1)	19											326	317	320					19																	57066700		2203	4300	6503	61758512	SO:0001587	stop_gained	140612				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.2546C>A	19.37:g.57066700C>A	ENSP00000301318:p.Ser849*		61758512	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Nonsense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	37	6.053620	0.97241	.	.	ENSG00000196867	ENST00000301318	.	.	.	3.94	3.94	0.45596	.	0.670897	0.12410	N	0.471396	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	14.2775	0.66189	0.0:1.0:0.0:0.0	.	.	.	.	X	849	.	ENSP00000301318:S849X	S	+	2	0	ZFP28	61758512	0.000000	0.05858	0.015000	0.15790	0.647000	0.38526	-0.240000	0.08952	2.492000	0.84095	0.655000	0.94253	TCA		0.458	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		A	57066700	C	A	57066700	4	1	14	1	0	0	0	0	0	1	0	0	17681	838	29	2	2576	2	ZFP28	19	57066700	Nonsense_Mutation	SNP	C	TCGA-AG-3575-01A-01W-0831-10	1618926	57066700	2062283	45	1643										
RPN2	6185	hgsc.bcm.edu	37	chr20	35842165	35842165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cattgtcattcttaacagggAtgtttttgaactaaatttca	6	6	3	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr20:35842165A>G	ENST00000237530.6	+	9	1300	c.989A>G	c.(988-990)gAt>gGt	p.D330G	RPN2_ENST00000373622.5_Missense_Mutation_p.D298G	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	330					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)	p.D330G(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				CTTAACAGGGATGTTTTTGAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	20											141	127	132					20																	35842165		2203	4300	6503	35275579	SO:0001583	missense	6185			Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.989A>G	20.37:g.35842165A>G	ENSP00000237530:p.Asp330Gly		35275579	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	ENST00000237530.6	37	CCDS13291.1	.	.	.	.	.	.	.	.	.	.	A	9.719	1.159077	0.21454	.	.	ENSG00000118705	ENST00000237530;ENST00000373622	T;T	0.43294	0.95;0.95	5.18	5.18	0.71444	.	0.212969	0.48286	D	0.000187	T	0.21674	0.0522	N	0.04203	-0.255	0.38682	D	0.952564	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.12372	-1.0550	10	0.22706	T	0.39	-11.0573	13.0372	0.58879	1.0:0.0:0.0:0.0	.	205;298;330;330	A6NKT1;Q5JYR6;P04844;B2RE46	.;.;RPN2_HUMAN;.	G	330;298	ENSP00000237530:D330G;ENSP00000362724:D298G	ENSP00000237530:D330G	D	+	2	0	RPN2	35275579	1.000000	0.71417	0.998000	0.56505	0.901000	0.52897	5.661000	0.68025	2.180000	0.69256	0.455000	0.32223	GAT		0.393	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		G	35842165	A	G	35842165	3	3	14	1	0	0	0	0	1	0	0	0	13645	333	12	4	1023	4	RPN2	20	35842165	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10		35842165	27183355	46	1644										
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45905279	45905279	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggatgccgtcatgtcaaagTtgagcttgaccttctcctgc	11	11	3	2			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr20:45905279T>A	ENST00000311275.7	-	11	1452	c.1199A>T	c.(1198-1200)aAc>aTc	p.N400I	ZMYND8_ENST00000471951.2_Missense_Mutation_p.N420I|ZMYND8_ENST00000355972.4_Missense_Mutation_p.N400I|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000396281.4_Missense_Mutation_p.N400I|ZMYND8_ENST00000446994.2_Missense_Mutation_p.N337I|ZMYND8_ENST00000262975.4_Missense_Mutation_p.N400I|ZMYND8_ENST00000540497.1_Missense_Mutation_p.N395I|ZMYND8_ENST00000372023.3_Missense_Mutation_p.N395I|ZMYND8_ENST00000360911.3_Missense_Mutation_p.N395I|ZMYND8_ENST00000536340.1_Missense_Mutation_p.N427I|ZMYND8_ENST00000352431.2_Missense_Mutation_p.N420I|ZMYND8_ENST00000458360.2_Missense_Mutation_p.N395I|ZMYND8_ENST00000461685.1_Missense_Mutation_p.N420I	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	400					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.N420I(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			CATGTCAAAGTTGAGCTTGAC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											154	132	140					20																	45905279		2203	4300	6503	45338686	SO:0001583	missense	23613			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1199A>T	20.37:g.45905279T>A	ENSP00000312237:p.Asn400Ile		45338686	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.0|21.0	4.087558|4.087558	0.76642|0.76642	.|.	.|.	ENSG00000101040|ENSG00000101040	ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497|ENST00000467200	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.91686|.	-2.0;-1.88;-1.98;-1.91;-1.9;-1.89;-2.0;-1.9;-1.89;-2.89;-1.91;-1.99;-1.76|.	5.63|5.63	3.39|3.39	0.38822|0.38822	.|.	0.094139|.	0.64402|.	D|.	0.000001|.	T|T	0.57740|0.57740	0.2074|0.2074	L|L	0.51422|0.51422	1.61|1.61	0.41139|0.41139	D|D	0.985946|0.985946	D;P;P;P;D;D;B;P;D;B;P;P;P;P;P;D;P;P|.	0.67145|.	0.983;0.682;0.716;0.716;0.996;0.959;0.214;0.813;0.967;0.127;0.813;0.716;0.716;0.716;0.586;0.963;0.944;0.76|.	P;P;P;P;D;P;B;P;P;B;P;P;P;P;P;P;P;B|.	0.64595|.	0.78;0.625;0.739;0.628;0.927;0.824;0.322;0.795;0.747;0.22;0.795;0.739;0.739;0.628;0.602;0.79;0.563;0.323|.	T|T	0.51537|0.51537	-0.8693|-0.8693	10|5	0.54805|.	T|.	0.06|.	-24.5161|-24.5161	9.7243|9.7243	0.40322|0.40322	0.0:0.1386:0.0:0.8614|0.0:0.1386:0.0:0.8614	.|.	395;427;395;395;375;394;420;400;395;420;420;400;337;395;395;420;395;400|.	B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8|.	.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.|.	I|H	395;400;395;400;420;420;400;427;400;337;420;395;395|326	ENSP00000354166:N395I;ENSP00000312237:N400I;ENSP00000392964:N395I;ENSP00000262975:N400I;ENSP00000420095:N420I;ENSP00000335537:N420I;ENSP00000379577:N400I;ENSP00000439800:N427I;ENSP00000348246:N400I;ENSP00000396725:N337I;ENSP00000418210:N420I;ENSP00000361093:N395I;ENSP00000443086:N395I|.	ENSP00000262975:N400I|.	N|Q	-|-	2|3	0|2	ZMYND8|ZMYND8	45338686|45338686	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.996000|0.996000	0.88848|0.88848	3.324000|3.324000	0.52022|0.52022	0.436000|0.436000	0.26393|0.26393	0.533000|0.533000	0.62120|0.62120	AAC|CAA		0.587	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		A	45905279	T	A	45905279	3	1	14	1	0	0	0	0	1	0	0	0	17750	1725	60	5	2359	5	ZMYND8	20	45905279	Missense_Mutation	SNP	T	TCGA-AG-3575-01A-01W-0831-10	10063114	45905279	17120241	47	1645										
SULF2	55959	hgsc.bcm.edu	37	chr20	46294604	46294604	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcccgctctccactcacctcGtggtcgatgtgcagcttgtg	10	15	2	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr20:46294604G>A	ENST00000359930.4	-	13	2750	c.1899C>T	c.(1897-1899)caC>caT	p.H633H	SULF2_ENST00000361612.4_Silent_p.H633H|SULF2_ENST00000484875.1_Silent_p.H633H|SULF2_ENST00000467815.1_Silent_p.H633H	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	633					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.H633H(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						CACTCACCTCGTGGTCGATGT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	20											183	152	163					20																	46294604		2203	4300	6503	45728011	SO:0001819	synonymous_variant	55959			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1899C>T	20.37:g.46294604G>A			45728011	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Silent	SNP	ENST00000359930.4	37	CCDS13408.1																																																																																				0.622	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		A	46294604	G	A	46294604	2	1	14	1	0	0	0	0	0	0	0	1	15410	1136	40	1		1	SULF2	20	46294604	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10	389325	46294604	16730916	48	1646										
IL17RA	23765	hgsc.bcm.edu	37	chr22	17581356	17581356	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acccaaaccaccagtccaagAatttccttgtgcctggtaag	7	13	0	1			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr22:17581356A>C	ENST00000319363.6	+	5	668	c.535A>C	c.(535-537)Aat>Cat	p.N179H	IL17RA_ENST00000477874.1_3'UTR	NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	179					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)	p.N179H(1)		endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CCAGTCCAAGAATTTCCTTGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											155	126	136					22																	17581356		2203	4300	6503	15961356	SO:0001583	missense	23765			U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.535A>C	22.37:g.17581356A>C	ENSP00000320936:p.Asn179His		15961356	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.610743	0.28712	.	.	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.00522	6.84	4.91	3.83	0.44106	.	0.793754	0.11633	N	0.544656	T	0.00440	0.0014	L	0.40543	1.245	0.09310	N	1	D;D	0.67145	0.978;0.996	P;P	0.46110	0.504;0.504	T	0.50625	-0.8806	10	0.13108	T	0.6	-21.4598	5.2396	0.15464	0.5651:0.2703:0.0:0.1646	.	179;179	D3YTB4;Q96F46	.;I17RA_HUMAN	H	179	ENSP00000320936:N179H	ENSP00000320936:N179H	N	+	1	0	IL17RA	15961356	0.000000	0.05858	0.006000	0.13384	0.465000	0.32709	0.679000	0.25291	2.073000	0.62155	0.454000	0.30748	AAT		0.572	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		C	17581356	A	C	17581356	3	2	14	1	0	0	0	0	1	0	0	0	7660	246	9	4	553	4	IL17RA	22	17581356	Missense_Mutation	SNP	A	TCGA-AG-3575-01A-01W-0831-10		17581356	33723210	49	1647										
THOC5	8563	hgsc.bcm.edu	37	chr22	29908011	29908011	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atccccagctgggtcttaccCgaatgttgtcatcgttgctg	10	12	2	0			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr22:29908011C>T	ENST00000490103.1	-	18	1918	c.1796G>A	c.(1795-1797)cGg>cAg	p.R599Q	THOC5_ENST00000397873.2_Splice_Site_p.R599Q|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397872.1_Splice_Site_p.R599Q|THOC5_ENST00000397871.1_Splice_Site_p.R599Q	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	599					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)	p.R599Q(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGGTCTTACCCGAATGTTGTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	22											119	85	96					22																	29908011		2203	4300	6503	28238011	SO:0001630	splice_region_variant	8563			AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1797+1G>A	22.37:g.29908011C>T			28238011	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086923	0.76642	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.76	3.64	0.41730	.	0.000000	0.85682	D	0.000000	T	0.48714	0.1515	M	0.77820	2.39	0.58432	D	0.999998	D	0.76494	0.999	P	0.59115	0.852	T	0.48779	-0.9005	10	0.48119	T	0.1	-17.9576	10.6258	0.45506	0.1333:0.7978:0.0:0.0689	.	599	Q13769	THOC5_HUMAN	Q	599	ENSP00000420306:R599Q;ENSP00000380970:R599Q;ENSP00000380969:R599Q;ENSP00000380971:R599Q	ENSP00000380969:R599Q	R	-	2	0	THOC5	28238011	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	5.429000	0.66495	0.868000	0.35678	0.650000	0.86243	CGG		0.577	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	Missense_Mutation	T	29908011	C	T	29908011	5	4	14	1	0	0	0	0	0	0	1	0	15907	666	23	1	267	1	THOC5	22	29908011	Splice_Site	SNP	C	TCGA-AG-3575-01A-01W-0831-10	12326655	29908011	21396555	50	1648										
POLR3H	171568	hgsc.bcm.edu	37	chr22	41928717	41928717	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccaatgagaatctcatctaGgaatggatgaaacaccacgc	8	11	2	2			TCGA-AG-3575-01A-01W-0831-10	TCGA-AG-3575-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	630b3742-9f27-422b-b678-30a3d0515814	51d5f06d-766b-47fd-88e6-08220066b246	g.chr22:41928717G>A	ENST00000355209.4	-	3	584	c.241C>T	c.(241-243)Cta>Tta	p.L81L	POLR3H_ENST00000420561.1_5'UTR|POLR3H_ENST00000396504.2_Silent_p.L81L|POLR3H_ENST00000337566.5_Intron|POLR3H_ENST00000407461.1_Silent_p.L81L	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	81					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.L81L(1)		breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						ATCTCATCTAGGAATGGATGA	0.552											OREG0026590	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	22											139	121	127					22																	41928717		2203	4300	6503	40258663	SO:0001819	synonymous_variant	171568			AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"RNA polymerase subunits"	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.241C>T	22.37:g.41928717G>A		904	40258663	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Silent	SNP	ENST00000355209.4	37	CCDS14018.1																																																																																				0.552	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1	NM_138338		A	41928717	G	A	41928717	2	1	14	1	0	0	0	0	0	0	0	1	12267	991	35	3		3	POLR3H	22	41928717	Silent	SNP	G	TCGA-AG-3575-01A-01W-0831-10	12020706	41928717	9375849	51	1649										
SNIP1	79753	hgsc.bcm.edu	37	chr1	38006254	38006254	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctttggtgggaatggccccGgtgtctgtcccggtcactgt	14	12	2	0	rs143428642		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr1:38006254G>A	ENST00000296215.6	-	3	502	c.430C>T	c.(430-432)Cgg>Tgg	p.R144W	SNIP1_ENST00000468040.1_5'UTR	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	144	Arg-rich.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R144W(1)		breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				GAATGGCCCCGGTGTCTGTCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	129	131	130		430	3.3	1	1	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SNIP1	NM_024700.2	101	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	probably-damaging	144/397	38006254	5,13001	2203	4300	6503	37778841	SO:0001583	missense	79753				CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.430C>T	1.37:g.38006254G>A	ENSP00000296215:p.Arg144Trp		37778841	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	37	CCDS419.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000786	0.54254	9.08E-4	1.16E-4	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.15256	2.44	5.25	3.34	0.38264	.	0.401658	0.24638	N	0.036829	T	0.11707	0.0285	L	0.27053	0.805	0.58432	D	0.999992	B	0.22541	0.071	B	0.12156	0.007	T	0.07424	-1.0773	10	0.87932	D	0	-12.1472	8.5955	0.33712	0.0754:0.0:0.6288:0.2958	.	144	Q8TAD8	SNIP1_HUMAN	W	144;128	ENSP00000296215:R144W	ENSP00000296215:R144W	R	-	1	2	SNIP1	37778841	0.895000	0.30542	1.000000	0.80357	0.678000	0.39670	1.070000	0.30653	0.734000	0.32515	-0.150000	0.13652	CGG		0.607	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700		A	38006254	G	A	38006254	3	1	15	1	0	0	0	0	1	0	0	0	14885	1115	39	1	768	1	SNIP1	1	38006254	Missense_Mutation	SNP	G	TCGA-AG-3578-01A-01W-0831-10		38006254	211244367	1	1650										
RNF149	284996	hgsc.bcm.edu	37	chr2	101898446	101898446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catcatctggtaaagctagaCtcaaatttgcagctggatcc	8	10	3	1			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr2:101898446C>T	ENST00000295317.3	-	6	1141	c.1034G>A	c.(1033-1035)aGt>aAt	p.S345N		NM_173647.3	NP_775918.2	Q8NC42	RN149_HUMAN	ring finger protein 149	345					cellular response to drug (GO:0035690)|negative regulation of MAPK cascade (GO:0043409)|regulation of protein stability (GO:0031647)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S345N(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12						TAAAGCTAGACTCAAATTTGC	0.493																																					Colon(25;331 612 6521 7355 31028)											1	Substitution - Missense(1)	large_intestine(1)	2											139	129	132					2																	101898446		2203	4300	6503	101264878	SO:0001583	missense	284996			AK074985	CCDS2051.1	2q12.1	2013-01-09			ENSG00000163162	ENSG00000163162		"RING-type (C3HC4) zinc fingers"	23137	protein-coding gene	gene with protein product							Standard	NM_173647		Approved	FLJ90504	uc002taz.2	Q8NC42	OTTHUMG00000130685	ENST00000295317.3:c.1034G>A	2.37:g.101898446C>T	ENSP00000295317:p.Ser345Asn		101264878	Q53S14|Q8N5I8|Q8NBY5|Q8WUU3	Missense_Mutation	SNP	ENST00000295317.3	37	CCDS2051.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980925	0.53827	.	.	ENSG00000163162	ENST00000295317	T	0.08807	3.05	5.78	4.9	0.64082	.	0.761042	0.12864	N	0.432880	T	0.15609	0.0376	L	0.58101	1.795	0.38517	D	0.948612	P	0.49090	0.919	P	0.47015	0.534	T	0.04128	-1.0975	10	0.42905	T	0.14	.	14.4041	0.67071	0.0:0.9286:0.0:0.0714	.	345	Q8NC42	RN149_HUMAN	N	345	ENSP00000295317:S345N	ENSP00000295317:S345N	S	-	2	0	RNF149	101264878	0.971000	0.33674	0.604000	0.28916	0.052000	0.14988	2.380000	0.44327	1.435000	0.47434	0.563000	0.77884	AGT		0.493	RNF149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253180.2	NM_173647		T	101898446	C	T	101898446	3	4	15	1	0	0	0	0	1	0	0	0	13487	565	20	3	176	3	RNF149	2	101898446	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		101898446	141300927	2	1651										
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228552270	228552270	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttccagcaattactgcaaaaTagctcccataaactaaaaac	3	11	0	0			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr2:228552270T>C	ENST00000258403.3	-	6	1405	c.1334A>G	c.(1333-1335)tAt>tGt	p.Y445C	SLC19A3_ENST00000541617.1_Missense_Mutation_p.Y441C|SLC19A3_ENST00000409287.1_Intron	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	445					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.Y445C(1)		breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TACTGCAAAATAGCTCCCATA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	90	90					2																	228552270		2203	4300	6503	228260514	SO:0001583	missense	80704			AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1334A>G	2.37:g.228552270T>C	ENSP00000258403:p.Tyr445Cys		228260514		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.078409	0.55753	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	T;T	0.80393	-1.37;-1.37	5.65	4.46	0.54185	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.83695	0.5310	M	0.73962	2.25	0.80722	D	1	P;P	0.49696	0.817;0.927	P;P	0.49999	0.518;0.628	D	0.83661	0.0161	10	0.52906	T	0.07	-1.3984	11.881	0.52576	0.1308:0.0:0.0:0.8692	.	441;445	F5H2M8;Q9BZV2	.;S19A3_HUMAN	C	445;441	ENSP00000258403:Y445C;ENSP00000445519:Y441C	ENSP00000258403:Y445C	Y	-	2	0	SLC19A3	228260514	1.000000	0.71417	0.946000	0.38457	0.989000	0.77384	4.132000	0.57977	0.927000	0.37143	0.459000	0.35465	TAT		0.348	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			C	228552270	T	C	228552270	3	2	15	1	0	0	0	0	1	0	0	0	14467	1406	49	4	160	4	SLC19A3	2	228552270	Missense_Mutation	SNP	T	TCGA-AG-3578-01A-01W-0831-10	126653824	228552270	14647103	3	1652										
SENP7	57337	hgsc.bcm.edu	37	chr3	101066780	101066780	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaagataatctgaagagacCcagaagaaaagaatagcatg	10	5	1	7			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr3:101066780C>T	ENST00000394095.2	-	13	1826	c.1773G>A	c.(1771-1773)tgG>tgA	p.W591*	SENP7_ENST00000348610.3_Nonsense_Mutation_p.W558*|SENP7_ENST00000394094.2_Nonsense_Mutation_p.W526*|SENP7_ENST00000314261.7_Nonsense_Mutation_p.W525*|SENP7_ENST00000358203.3_Nonsense_Mutation_p.W427*|SENP7_ENST00000394091.1_Nonsense_Mutation_p.W427*	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	591						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.W525*(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTGAAGAGACCCAGAAGAAAA	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											110	115	114					3																	101066780		2203	4299	6502	102549470	SO:0001587	stop_gained	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1773G>A	3.37:g.101066780C>T	ENSP00000377655:p.Trp591*		102549470	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Nonsense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	C	37	6.581088	0.97680	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	.	.	.	5.69	5.69	0.88448	.	0.162855	0.43260	D	0.000584	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.463	18.593	0.91220	0.0:1.0:0.0:0.0	.	.	.	.	X	591;526;525;427;427;558	.	ENSP00000313624:W525X	W	-	3	0	SENP7	102549470	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	5.208000	0.65203	2.679000	0.91253	0.650000	0.86243	TGG		0.348	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		T	101066780	C	T	101066780	4	4	15	1	0	0	0	0	0	1	0	0	14088	624	22	3	1427	3	SENP7	3	101066780	Nonsense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		101066780	96955650	4	1653										
TRAT1	50852	hgsc.bcm.edu	37	chr3	108572643	108572643	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gacagtttctccccagaaagCcaggcagtagaggaaaacat	10	10	1	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr3:108572643C>A	ENST00000295756.6	+	6	710	c.480C>A	c.(478-480)agC>agA	p.S160R	TRAT1_ENST00000426646.1_Missense_Mutation_p.S123R	NM_016388.2	NP_057472.2	Q6PIZ9	TRAT1_HUMAN	T cell receptor associated transmembrane adaptor 1	160					cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of receptor recycling (GO:0001920)|negative regulation of transport (GO:0051051)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell receptor signaling pathway (GO:0050862)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.S160R(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(3)	28						CCCCAGAAAGCCAGGCAGTAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											88	89	88					3																	108572643		2203	4300	6503	110055333	SO:0001583	missense	50852			AJ240084	CCDS33813.1	3q13	2005-05-04	2005-05-04	2005-05-04	ENSG00000163519	ENSG00000163519			30698	protein-coding gene	gene with protein product		604962	"T cell receptor interacting molecule"	TCRIM		10663578, 9687533	Standard	NM_016388		Approved	HSPC062, TRIM	uc003dxi.1	Q6PIZ9	OTTHUMG00000159198	ENST00000295756.6:c.480C>A	3.37:g.108572643C>A	ENSP00000295756:p.Ser160Arg		110055333	Q9NZX5	Missense_Mutation	SNP	ENST00000295756.6	37	CCDS33813.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.494798	0.26774	.	.	ENSG00000163519	ENST00000295756;ENST00000426646	T;T	0.32988	1.43;1.43	5.85	2.97	0.34412	.	0.794310	0.12132	N	0.496692	T	0.28466	0.0704	L	0.47716	1.5	0.09310	N	1	B;B	0.23806	0.091;0.051	B;B	0.21151	0.018;0.033	T	0.21552	-1.0242	10	0.66056	D	0.02	-3.4942	10.7374	0.46133	0.0:0.683:0.2438:0.0732	.	123;160	C9JF66;Q6PIZ9	.;TRAT1_HUMAN	R	160;123	ENSP00000295756:S160R;ENSP00000410097:S123R	ENSP00000295756:S160R	S	+	3	2	TRAT1	110055333	0.000000	0.05858	0.179000	0.23059	0.006000	0.05464	-0.167000	0.09940	0.385000	0.24970	-0.797000	0.03246	AGC		0.433	TRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353794.1	NM_016388		A	108572643	C	A	108572643	3	1	15	1	0	0	0	0	1	0	0	0	16506	738	26	2	502	2	TRAT1	3	108572643	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10	7505863	108572643	89449787	5	1654										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113303597	113303597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accctgatccaggaggcaaaGgaaatgaagtggcccttcgt	12	10	0	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr4:113303597G>A	ENST00000458497.1	+	4	444	c.165G>A	c.(163-165)aaG>aaA	p.K55K	ALPK1_ENST00000177648.9_Silent_p.K55K|ALPK1_ENST00000504176.2_Intron	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	55							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K55K(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		AGGAGGCAAAGGAAATGAAGT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	4											83	74	77					4																	113303597		2203	4300	6503	113523046	SO:0001819	synonymous_variant	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.165G>A	4.37:g.113303597G>A			113523046	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	37	CCDS3697.1																																																																																				0.507	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113303597	G	A	113303597	2	1	15	1	0	0	0	0	0	0	0	1	544	991	35	3		3	ALPK1	4	113303597	Silent	SNP	G	TCGA-AG-3578-01A-01W-0831-10		113303597	77850679	6	1655										
FLT4	2324	hgsc.bcm.edu	37	chr5	180036939	180036939	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtcgttggggtcatggggAattcctcaaatgtcttcatc	12	8	4	0			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr5:180036939A>T	ENST00000261937.6	-	28	3851	c.3773T>A	c.(3772-3774)tTc>tAc	p.F1258Y	FLT4_ENST00000502649.1_Missense_Mutation_p.F1258Y|FLT4_ENST00000393347.3_Missense_Mutation_p.F1258Y	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1258					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.F1258Y(2)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGTCATGGGGAATTCCTCAAA	0.602																																					Colon(97;1075 1466 27033 27547 35871)											2	Substitution - Missense(2)	large_intestine(2)	5											142	132	135					5																	180036939		2203	4300	6503	179969545	SO:0001583	missense	2324			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3773T>A	5.37:g.180036939A>T	ENSP00000261937:p.Phe1258Tyr		179969545	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.713179	0.48517	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	T;T;T	0.77489	-1.07;-1.1;-1.09	4.79	4.79	0.61399	.	.	.	.	.	T	0.68815	0.3042	L	0.41824	1.3	0.39048	D	0.960269	B;B	0.12630	0.003;0.006	B;B	0.13407	0.009;0.009	T	0.68409	-0.5416	9	0.56958	D	0.05	.	9.9614	0.41699	0.8486:0.0:0.0:0.1514	.	1258;1258	E9PD35;P35916	.;VGFR3_HUMAN	Y	1258	ENSP00000261937:F1258Y;ENSP00000377016:F1258Y;ENSP00000426057:F1258Y	ENSP00000261937:F1258Y	F	-	2	0	FLT4	179969545	1.000000	0.71417	0.998000	0.56505	0.709000	0.40893	5.367000	0.66127	1.938000	0.56188	0.459000	0.35465	TTC		0.602	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			T	180036939	A	T	180036939	3	4	15	1	0	0	0	0	1	0	0	0	5963	246	9	5	338	5	FLT4	5	180036939	Missense_Mutation	SNP	A	TCGA-AG-3578-01A-01W-0831-10		180036939	878321	7	1656										
BRAF	673	hgsc.bcm.edu	37	chr7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acccactccatcgagatttcActgtagctagaccaaaatca	5	13	2	2	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	7											112	104	107					7																	140453136		2203	4300	6503	140099605	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu		140099605	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453136	A	T	140453136	3	4	15	1	0	0	0	0	1	0	0	0	1499	159	6	5	517	5	BRAF	7	140453136	Missense_Mutation	SNP	A	TCGA-AG-3578-01A-01W-0831-10		140453136	18685527	8	1657										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19786158	19786158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acacatctcgaaagagcggcCaccatgtcaggtttaagatt	9	10	2	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr9:19786158C>A	ENST00000341998.2	-	1	768	c.707G>T	c.(706-708)tGg>tTg	p.W236L	SLC24A2_ENST00000286344.3_Missense_Mutation_p.W236L	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	236					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)	p.W236L(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		AAAGAGCGGCCACCATGTCAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											95	89	91					9																	19786158		2203	4300	6503	19776158	SO:0001583	missense	25769			AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.707G>T	9.37:g.19786158C>A	ENSP00000344801:p.Trp236Leu		19776158	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	37	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891147	0.72524	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.62498	0.02;0.02	5.91	5.02	0.67125	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	T	0.81446	0.4824	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.84486	0.0608	9	.	.	.	.	15.0355	0.71744	0.0:0.9321:0.0:0.0679	.	236;236	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	L	236	ENSP00000344801:W236L;ENSP00000286344:W236L	.	W	-	2	0	SLC24A2	19776158	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	1.508000	0.48769	0.655000	0.94253	TGG		0.413	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		A	19786158	C	A	19786158	3	1	15	1	0	0	0	0	1	0	0	0	14503	595	21	2	1318	2	SLC24A2	9	19786158	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		19786158	121427273	9	1658										
LUZP2	338645	hgsc.bcm.edu	37	chr11	24998161	24998161	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcagcttactgatctggaaCaaaaattagctgtagccaaa	8	8	1	1			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr11:24998161C>A	ENST00000336930.6	+	8	613	c.547C>A	c.(547-549)Caa>Aaa	p.Q183K	LUZP2_ENST00000533227.1_Missense_Mutation_p.Q97K			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	183	Leucine-zipper.					extracellular region (GO:0005576)		p.Q183K(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						TGATCTGGAACAAAAATTAGC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	62	60					11																	24998161		2203	4299	6502	24954737	SO:0001583	missense	338645			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.547C>A	11.37:g.24998161C>A	ENSP00000336817:p.Gln183Lys		24954737	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.923206	0.52653	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	T;T;T	0.21191	2.02;2.02;2.02	5.15	5.15	0.70609	.	0.209268	0.40818	N	0.001019	T	0.15349	0.0370	L	0.27053	0.805	0.29049	N	0.884626	P;B	0.36633	0.562;0.122	B;B	0.31337	0.128;0.054	T	0.07271	-1.0781	10	0.33141	T	0.24	-2.3938	16.4555	0.84011	0.0:1.0:0.0:0.0	.	97;183	E9PN53;Q86TE4	.;LUZP2_HUMAN	K	183;141;97	ENSP00000336817:Q183K;ENSP00000437032:Q141K;ENSP00000432952:Q97K	ENSP00000336817:Q183K	Q	+	1	0	LUZP2	24954737	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.138000	0.58017	2.540000	0.85666	0.650000	0.86243	CAA		0.353	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		A	24998161	C	A	24998161	3	1	15	1	0	0	0	0	1	0	0	0	9116	479	17	2	577	2	LUZP2	11	24998161	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		24998161	110008355	10	1659										
SOX5	6660	hgsc.bcm.edu	37	chr12	23998927	23998927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagcctttaccttccggctcGtttttgatgagctcttccat	7	13	1	2	rs149450279		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr12:23998927G>A	ENST00000451604.2	-	3	572	c.471C>T	c.(469-471)aaC>aaT	p.N157N	SOX5_ENST00000546136.1_Silent_p.N144N|SOX5_ENST00000541536.1_Silent_p.N144N|SOX5_ENST00000309359.1_Silent_p.N144N|SOX5_ENST00000381381.2_Silent_p.N144N|SOX5_ENST00000441133.2_Silent_p.N122N|SOX5_ENST00000545921.1_Silent_p.N147N|SOX5_ENST00000541847.1_Silent_p.N147N|SOX5_ENST00000537393.1_Silent_p.N122N			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	157					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.N157N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						CTTCCGGCTCGTTTTTGATGA	0.403													G|||	1	0.000199681	8e-04	0	5008	,	,		17504	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						G	,	0,4406		0,0,2203	105	96	99		471,432	-3	1	12	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous,coding-synonymous	SOX5	NM_006940.4,NM_152989.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	157/764,144/751	23998927	2,13004	2203	4300	6503	23890194	SO:0001819	synonymous_variant	6660			AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.471C>T	12.37:g.23998927G>A			23890194	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Silent	SNP	ENST00000451604.2	37	CCDS8699.1																																																																																				0.403	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		A	23998927	G	A	23998927	2	1	15	1	0	0	0	0	0	0	0	1	14991	1136	40	1		1	SOX5	12	23998927	Silent	SNP	G	TCGA-AG-3578-01A-01W-0831-10		23998927	109852968	11	1660										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40702947	40702947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tactcatccccattttatgaCgcagcgagcattgtaccttg	7	12	1	1	rs72546327	byFrequency	TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr12:40702947C>T	ENST00000298910.7	+	30	4287	c.4229C>T	c.(4228-4230)aCg>aTg	p.T1410M		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1410	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.T1410M(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CATTTTATGACGCAGCGAGCA	0.393													C|||	32	0.00638978	0.0234	0.0014	5008	,	,		15992	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12						C	MET/THR	108,4298	84.8+/-123.5	2,104,2097	96	91	93		4229	5.6	1	12	dbSNP_130	93	0,8600		0,0,4300	yes	missense	LRRK2	NM_198578.3	81	2,104,6397	TT,TC,CC		0.0,2.4512,0.8304	probably-damaging	1410/2528	40702947	108,12898	2203	4300	6503	38989214	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4229C>T	12.37:g.40702947C>T	ENSP00000298910:p.Thr1410Met		38989214	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	C	22.2	4.257757	0.80246	0.024512	0.0	ENSG00000188906	ENST00000298910	T	0.68479	-0.33	5.63	5.63	0.86233	ROC GTPase (1);Small GTP-binding protein domain (1);Mitochondrial Rho-like (1);	0.051061	0.85682	D	0.000000	T	0.76779	0.4035	M	0.88640	2.97	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84414	0.0567	10	0.87932	D	0	.	19.6816	0.95965	0.0:1.0:0.0:0.0	.	1410;1410	Q17RV3;Q5S007	.;LRRK2_HUMAN	M	1410	ENSP00000298910:T1410M	ENSP00000298910:T1410M	T	+	2	0	LRRK2	38989214	1.000000	0.71417	0.986000	0.45419	0.982000	0.71751	5.450000	0.66626	2.654000	0.90174	0.655000	0.94253	ACG		0.393	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40702947	C	T	40702947	3	4	15	1	0	0	0	0	1	0	0	0	9062	536	19	1	4347	1	LRRK2	12	40702947	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10	16704020	40702947	93148948	12	1661										
EEA1	8411	hgsc.bcm.edu	37	chr12	93202867	93202867	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgtgttcagctgtctttgCtgttgtagatcttgcaaagc	10	8	4	1			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr12:93202867C>G	ENST00000322349.8	-	18	2529	c.2265G>C	c.(2263-2265)caG>caC	p.Q755H		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	755	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.Q755H(1)		endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						GCTGTCTTTGCTGTTGTAGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											142	124	130					12																	93202867		2202	4299	6501	91726998	SO:0001583	missense	8411			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2265G>C	12.37:g.93202867C>G	ENSP00000317955:p.Gln755His		91726998	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	C	7.986	0.752248	0.15778	.	.	ENSG00000102189	ENST00000322349	T	0.78707	-1.2	5.84	-0.0883	0.13674	.	0.291553	0.24258	N	0.040114	T	0.64011	0.2560	L	0.27053	0.805	0.33961	D	0.645579	B	0.29805	0.257	B	0.31495	0.131	T	0.62604	-0.6819	10	0.52906	T	0.07	.	11.2228	0.48866	0.0:0.5704:0.0:0.4296	.	755	Q15075	EEA1_HUMAN	H	755	ENSP00000317955:Q755H	ENSP00000317955:Q755H	Q	-	3	2	EEA1	91726998	0.880000	0.30214	0.009000	0.14445	0.021000	0.10359	-0.125000	0.10579	-0.299000	0.08909	-0.137000	0.14449	CAG		0.368	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		G	93202867	C	G	93202867	3	3	15	1	0	0	0	0	1	0	0	0	4932	796	28	5	2018	5	EEA1	12	93202867	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10	52499920	93202867	40649028	13	1662										
DAO	1610	hgsc.bcm.edu	37	chr12	109288126	109288126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accccctgctgcagccaggcCgggggcagatcatgaaggtg	15	13	1	2	rs139166976	byFrequency	TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr12:109288126C>T	ENST00000228476.3	+	7	799	c.595C>T	c.(595-597)Cgg>Tgg	p.R199W	DAO_ENST00000551281.1_Missense_Mutation_p.R133W	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	199					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)	p.R199W(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	GCAGCCAGGCCGGGGGCAGAT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	53	43	46		595	4.6	1	12	dbSNP_134	46	5,8595	5.0+/-18.6	0,5,4295	yes	missense	DAO	NM_001917.4	101	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	199/348	109288126	6,13000	2203	4300	6503	107812255	SO:0001583	missense	1610			D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.595C>T	12.37:g.109288126C>T	ENSP00000228476:p.Arg199Trp		107812255	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.248196	0.80024	2.27E-4	5.81E-4	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	T;T;T	0.62232	0.04;0.04;0.04	5.51	4.6	0.57074	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.84179	0.5415	H	0.94542	3.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.88605	0.3152	10	0.87932	D	0	-9.4689	14.3396	0.66617	0.1497:0.8503:0.0:0.0	.	199;182	P14920;Q7Z312	OXDA_HUMAN;.	W	133;199;76	ENSP00000446853:R133W;ENSP00000228476:R199W;ENSP00000449967:R76W	ENSP00000228476:R199W	R	+	1	2	DAO	107812255	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.640000	0.54350	1.305000	0.44909	0.499000	0.49734	CGG		0.542	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109288126	C	T	109288126	3	4	15	1	0	0	0	0	1	0	0	0	4237	643	23	1	617	1	DAO	12	109288126	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10	16085259	109288126	24563769	14	1663										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211755	38211755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggaaactagaaatgtcttgcTttagttcctacgtagaattt	8	6	1	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr13:38211755T>C	ENST00000379705.3	-	11	3076	c.2219A>G	c.(2218-2220)aAg>aGg	p.K740R	TRPC4_ENST00000379679.1_Missense_Mutation_p.K567R|TRPC4_ENST00000379681.3_Missense_Mutation_p.K745R|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000338947.5_Missense_Mutation_p.K567R|TRPC4_ENST00000447043.1_Intron|TRPC4_ENST00000355779.2_Intron|TRPC4_ENST00000379673.2_Missense_Mutation_p.K675R|TRPC4_ENST00000358477.2_Missense_Mutation_p.K740R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	740	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.K740R(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AATGTCTTGCTTTAGTTCCTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											30	32	31					13																	38211755		2140	4173	6313	37109755	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2219A>G	13.37:g.38211755T>C	ENSP00000369027:p.Lys740Arg		37109755	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885483	0.72410	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000358477;ENST00000379673	D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.91317	0.7262	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.996;0.998;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.987;0.987;0.999;0.999	D	0.90201	0.4257	10	0.34782	T	0.22	-31.2988	16.2479	0.82454	0.0:0.0:0.0:1.0	.	675;745;567;740;740	Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	R	740;745;567;567;740;675	ENSP00000369027:K740R;ENSP00000369003:K745R;ENSP00000342580:K567R;ENSP00000369001:K567R;ENSP00000351264:K740R;ENSP00000368995:K675R	ENSP00000342580:K567R	K	-	2	0	TRPC4	37109755	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.604000	0.82830	2.241000	0.73720	0.533000	0.62120	AAG		0.358	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38211755	T	C	38211755	3	2	15	1	0	0	0	0	1	0	0	0	16620	1609	56	4	718	4	TRPC4	13	38211755	Missense_Mutation	SNP	T	TCGA-AG-3578-01A-01W-0831-10		38211755	76958123	15	1664										
LGMN	5641	hgsc.bcm.edu	37	chr14	93172829	93172829	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagagcctgctggctcaccGtgggggagtgccagttgaag	18	9	1	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr14:93172829G>A	ENST00000393218.2	-	13	1527	c.1190C>T	c.(1189-1191)aCg>aTg	p.T397M	LGMN_ENST00000557434.1_Intron|LGMN_ENST00000555699.1_Intron|LGMN_ENST00000334869.4_Splice_Site_p.T397M	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	397					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.T397M(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		CTGGCTCACCGTGGGGGAGTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	14											52	54	53					14																	93172829		2203	4300	6503	92242582	SO:0001630	splice_region_variant	5641			D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"protease, cysteine, 1 (legumain)"	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1191+1C>T	14.37:g.93172829G>A			92242582	O00123|Q86TV2|Q86TV3|Q9BTY1	Missense_Mutation	SNP	ENST00000393218.2	37	CCDS9904.1	.	.	.	.	.	.	.	.	.	.	G	6.585	0.476210	0.12521	.	.	ENSG00000100600	ENST00000334869;ENST00000393218;ENST00000539531;ENST00000535855	T;T	0.44482	0.92;0.92	5.42	-3.12	0.05282	.	0.735360	0.14128	N	0.339563	T	0.17492	0.0420	N	0.05124	-0.11	0.21782	N	0.999545	B;B	0.15473	0.013;0.013	B;B	0.08055	0.003;0.003	T	0.12630	-1.0540	10	0.46703	T	0.11	-18.6786	6.9579	0.24582	0.6498:0.0:0.2137:0.1365	.	397;397	A8K669;Q99538	.;LGMN_HUMAN	M	397;397;374;362	ENSP00000334052:T397M;ENSP00000376911:T397M	ENSP00000334052:T397M	T	-	2	0	LGMN	92242582	0.001000	0.12720	0.693000	0.30195	0.037000	0.13140	-0.209000	0.09358	-0.415000	0.07484	-0.143000	0.13931	ACG		0.587	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	Missense_Mutation	A	93172829	G	A	93172829	5	1	15	1	0	0	0	0	0	0	1	0	8778	1159	40	1	123	1	LGMN	14	93172829	Splice_Site	SNP	G	TCGA-AG-3578-01A-01W-0831-10		93172829	14176711	16	1665										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000455263.2_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	15	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		7577120	73618090	17	1666										
G6PC	2538	hgsc.bcm.edu	37	chr17	41062997	41062997	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgccagcctcaagaaatatTttctcattaccttcttcctg	4	12	3	1			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr17:41062997T>G	ENST00000253801.2	+	5	707	c.628T>G	c.(628-630)Ttt>Gtt	p.F210V	G6PC_ENST00000585489.1_3'UTR|G6PC_ENST00000592383.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	210					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.F210V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CAAGAAATATTTTCTCATTAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											107	82	91					17																	41062997		2203	4300	6503	38316523	SO:0001583	missense	2538			U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.628T>G	17.37:g.41062997T>G	ENSP00000253801:p.Phe210Val		38316523	A1L4C0|B4E1C3|K7EL82	Missense_Mutation	SNP	ENST00000253801.2	37	CCDS11446.1	.	.	.	.	.	.	.	.	.	.	T	0.442	-0.898213	0.02472	.	.	ENSG00000131482	ENST00000253801	T	0.74526	-0.85	4.86	1.04	0.20106	.	0.312460	0.33772	N	0.004579	T	0.52240	0.1722	L	0.42245	1.32	0.29481	N	0.856338	B	0.02656	0.0	B	0.01281	0.0	T	0.30446	-0.9978	10	0.05525	T	0.97	.	0.6777	0.00869	0.2822:0.1385:0.1453:0.434	.	210	P35575	G6PC_HUMAN	V	210	ENSP00000253801:F210V	ENSP00000253801:F210V	F	+	1	0	G6PC	38316523	0.074000	0.21230	0.011000	0.14972	0.061000	0.15899	-0.064000	0.11636	0.310000	0.22990	-0.472000	0.04984	TTT		0.473	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		G	41062997	T	G	41062997	3	3	15	1	0	0	0	0	1	0	0	0	6162	1841	64	4	646	4	G6PC	17	41062997	Missense_Mutation	SNP	T	TCGA-AG-3578-01A-01W-0831-10	33485877	41062997	40132213	18	1667										
CD22	933	hgsc.bcm.edu	37	chr19	35835756	35835756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	cccggagaccatcggcaggcGagtggctgtgggactcgggt	18	11	0	1	rs371289554		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr19:35835756G>A	ENST00000085219.5	+	10	2126	c.2060G>A	c.(2059-2061)cGa>cAa	p.R687Q	CD22_ENST00000419549.2_Missense_Mutation_p.R515Q|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000594250.1_Missense_Mutation_p.R510Q|CD22_ENST00000536635.2_Missense_Mutation_p.R599Q|CD22_ENST00000341773.6_Missense_Mutation_p.R510Q|CD22_ENST00000544992.2_Missense_Mutation_p.R687Q|CD22_ENST00000270311.6_Missense_Mutation_p.R567Q	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	687					cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.R687Q(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATCGGCAGGCGAGTGGCTGTG	0.627																																					Ovarian(42;1009 1133 23674 26041)											1	Substitution - Missense(1)	large_intestine(1)	19						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	107	112	110		1796,2060,1529,2060	4.2	0.3	19		110	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	43,43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	599/760,687/752,510/671,687/848	35835756	1,13005	2203	4300	6503	40527596	SO:0001583	missense	933			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2060G>A	19.37:g.35835756G>A	ENSP00000085219:p.Arg687Gln		40527596	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361097	0.24684	0.0	1.16E-4	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	T;T;T;T;T;T	0.54279	1.02;0.61;0.58;0.98;0.93;1.1	5.25	4.22	0.49857	.	0.000000	0.38605	N	0.001622	T	0.52661	0.1748	L	0.50333	1.59	0.21579	N	0.999632	P;P;D;P;D	0.69078	0.783;0.931;0.99;0.816;0.997	B;B;P;B;P	0.53722	0.11;0.356;0.596;0.085;0.733	T	0.42732	-0.9434	10	0.13108	T	0.6	.	10.0406	0.42155	0.0942:0.0:0.9058:0.0	.	515;687;599;687;510	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	Q	687;599;510;687;567;515	ENSP00000085219:R687Q;ENSP00000442279:R599Q;ENSP00000339349:R510Q;ENSP00000441237:R687Q;ENSP00000270311:R567Q;ENSP00000403822:R515Q	ENSP00000085219:R687Q	R	+	2	0	CD22	40527596	0.799000	0.28903	0.270000	0.24601	0.003000	0.03518	2.883000	0.48554	1.228000	0.43614	-0.444000	0.05651	CGA		0.627	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		A	35835756	G	A	35835756	3	1	15	1	0	0	0	0	1	0	0	0	2991	1058	37	1	2094	1	CD22	19	35835756	Missense_Mutation	SNP	G	TCGA-AG-3578-01A-01W-0831-10		35835756	23293227	19	1668										
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37643430	37643430	+	Missense_Mutation	SNP	T	T	G													0	0	1	0	0	0	1	1	0	ttttctcctgtgtgaattcgTttatgaacatggagttgcga							TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr19:37643430T>G	ENST00000356958.4	-	5	1629	c.1371A>C	c.(1369-1371)aaA>aaC	p.K457N	ZNF585A_ENST00000292841.5_Missense_Mutation_p.K402N|ZNF585A_ENST00000392157.2_Missense_Mutation_p.K402N|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000355533.2_Intron			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K402N(1)		breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTGAATTCGTTTATGAACAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											123	118	120					19																	37643430		2203	4300	6503	42335270	SO:0001583	missense	199704			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1371A>C	19.37:g.37643430T>G	ENSP00000349440:p.Lys457Asn		42335270	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	37		.	.	.	.	.	.	.	.	.	.	T	14.29	2.492197	0.44352	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157	T;T;T	0.18657	2.2;2.2;2.2	2.72	0.53	0.17102	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39759	N	0.001279	T	0.41971	0.1182	M	0.87269	2.87	0.51233	D	0.999919	D	0.64830	0.994	D	0.70935	0.971	T	0.26780	-1.0093	10	0.87932	D	0	.	4.15	0.10234	0.0:0.3917:0.0:0.6083	.	457	Q6P3V2	Z585A_HUMAN	N	457;402;402	ENSP00000349440:K457N;ENSP00000292841:K402N;ENSP00000375998:K402N	ENSP00000292841:K402N	K	-	3	2	ZNF585A	42335270	0.000000	0.05858	0.572000	0.28498	0.780000	0.44128	-2.616000	0.00881	0.285000	0.22329	0.459000	0.35465	AAA		0.398	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		G	37643430	T	G	37643430	3	3	15	1	0	0	0	0	1	0	0	0	18056	1722	60	4	942	4	ZNF585A	19	37643430	Missense_Mutation	SNP	T	TCGA-AG-3578-01A-01W-0831-10	1807674	37643430	21485553	20	1669	8	2								
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37643432	37643432	+	Nonsense_Mutation	SNP	T	T	A													0	0	1	0	0	0	1	1	0	ttctcctgtgtgaattcgttTatgaacatggagttgcgact							TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr19:37643432T>A	ENST00000356958.4	-	5	1627	c.1369A>T	c.(1369-1371)Aaa>Taa	p.K457*	ZNF585A_ENST00000292841.5_Nonsense_Mutation_p.K402*|ZNF585A_ENST00000392157.2_Nonsense_Mutation_p.K402*|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000355533.2_Intron			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K402*(1)		breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAATTCGTTTATGAACATGG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											123	119	120					19																	37643432		2203	4300	6503	42335272	SO:0001587	stop_gained	199704			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1369A>T	19.37:g.37643432T>A	ENSP00000349440:p.Lys457*		42335272	Q8TE95|Q96MV3	Nonsense_Mutation	SNP	ENST00000356958.4	37		.	.	.	.	.	.	.	.	.	.	T	36	5.967691	0.97156	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157	.	.	.	2.72	-1.47	0.08772	.	0.000000	0.39759	N	0.001279	.	.	.	.	.	.	0.30202	N	0.798566	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	3.8235	0.08845	0.0:0.1498:0.4593:0.3909	.	.	.	.	X	457;402;402	.	ENSP00000292841:K402X	K	-	1	0	ZNF585A	42335272	0.003000	0.15002	0.186000	0.23195	0.654000	0.38779	0.002000	0.13061	-0.118000	0.11851	-0.441000	0.05720	AAA		0.398	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		A	37643432	T	A	37643432	4	1	15	1	0	0	0	0	0	1	0	0	18056	1763	61	5	944	5	ZNF585A	19	37643432	Nonsense_Mutation	SNP	T	TCGA-AG-3578-01A-01W-0831-10	2	37643432	21485551	21	1670	8	2								
SIRPG	55423	hgsc.bcm.edu	37	chr20	1629815	1629815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggggtgatgctactgatgcGgatggaaaagtccatgttgt	15	5	0	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr20:1629815G>A	ENST00000303415.3	-	2	377	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000216927.4_Missense_Mutation_p.R105C|SIRPG_ENST00000381583.2_Missense_Mutation_p.R105C|SIRPG_ENST00000344103.4_Missense_Mutation_p.R105C|SIRPG_ENST00000381580.1_Missense_Mutation_p.R72C	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	105	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R105S(1)|p.R105C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						CTACTGATGCGGATGGAAAAG	0.483																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	20											311	256	275					20																	1629815		2203	4300	6503	1577815	SO:0001583	missense	55423			AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.313C>T	20.37:g.1629815G>A	ENSP00000305529:p.Arg105Cys		1577815	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	8.087	0.773762	0.16051	.	.	ENSG00000089012	ENST00000381580;ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25	1.93	1.93	0.25924	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.198861	0.36167	N	0.002741	T	0.56746	0.2006	M	0.70903	2.155	0.53005	D	0.999969	P;P;P	0.39480	0.565;0.56;0.675	B;B;B	0.31946	0.083;0.083;0.138	T	0.61098	-0.7131	10	0.54805	T	0.06	.	7.3585	0.26733	0.0:0.0:1.0:0.0	.	105;105;105	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	C	72;105;105;105;105	ENSP00000370992:R72C;ENSP00000342759:R105C;ENSP00000305529:R105C;ENSP00000370995:R105C;ENSP00000216927:R105C	ENSP00000216927:R105C	R	-	1	0	SIRPG	1577815	0.625000	0.27111	0.991000	0.47740	0.346000	0.29079	0.286000	0.18902	1.392000	0.46585	0.195000	0.17529	CGC		0.483	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1629815	G	A	1629815	3	1	15	1	0	0	0	0	1	0	0	0	14373	1116	39	1	866	1	SIRPG	20	1629815	Missense_Mutation	SNP	G	TCGA-AG-3578-01A-01W-0831-10		1629815	61395705	22	1671										
KRTAP19-5	337972	hgsc.bcm.edu	37	chr21	31874270	31874270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atagcctccgaagccagagcCgtatccgtagcctccgtagc	10	15	0	1	rs201233367		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chr21:31874270C>T	ENST00000334151.2	-	1	165	c.139G>A	c.(139-141)Ggc>Agc	p.G47S		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	47						intermediate filament (GO:0005882)		p.G47S(1)		endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						AAGCCAGAGCCGTATCCGTAG	0.557													C|||	1	0.000199681	8e-04	0	5008	,	,		17046	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21											124	119	121					21																	31874270		2203	4300	6503	30796141	SO:0001583	missense	337972			AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.139G>A	21.37:g.31874270C>T	ENSP00000334985:p.Gly47Ser		30796141	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	37	CCDS13597.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.75	2.031606	0.35797	.	.	ENSG00000186977	ENST00000334151	T	0.49432	0.78	5.04	5.04	0.67666	.	.	.	.	.	T	0.68805	0.3041	.	.	.	0.40318	D	0.978798	D	0.89917	1.0	D	0.97110	1.0	T	0.73827	-0.3860	8	0.87932	D	0	-0.3985	14.2426	0.65966	0.0:1.0:0.0:0.0	.	47	Q3LI72	KR195_HUMAN	S	47	ENSP00000334985:G47S	ENSP00000334985:G47S	G	-	1	0	KRTAP19-5	30796141	0.110000	0.22057	0.859000	0.33776	0.292000	0.27327	3.188000	0.50958	2.511000	0.84671	0.591000	0.81541	GGC		0.557	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			T	31874270	C	T	31874270	3	4	15	1	0	0	0	0	1	0	0	0	8553	652	23	1	82	1	KRTAP19-5	21	31874270	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10		31874270	16255625	23	1672										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961788	34961788	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagcctcctgatactggagcGtcccatctctgcccggagcc	11	16	1	1	rs372840274		TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chrX:34961788G>A	ENST00000329357.5	+	1	876	c.840G>A	c.(838-840)gcG>gcA	p.A280A		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	280	Pro-rich.							p.A280A(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						ATACTGGAGCGTCCCATCTCT	0.627													G|||	3	0.000794702	0.0023	0	3775	,	,		10399	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X						G		4,3829		0,4,1627,571	58	55	56		840	1	0	X		56	0,6728		0,0,2428,1872	no	coding-synonymous	FAM47B	NM_152631.2		0,4,4055,2443	AA,AG,GG,G		0.0,0.1044,0.0379		280/646	34961788	4,10557	2202	4300	6502	34871709	SO:0001819	synonymous_variant	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.840G>A	X.37:g.34961788G>A			34871709	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																				0.627	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34961788	G	A	34961788	2	1	15	1	0	0	0	0	0	0	0	1	5589	1132	40	1		1	FAM47B	23	34961788	Silent	SNP	G	TCGA-AG-3578-01A-01W-0831-10		34961788	120308772	24	1673										
UPRT	139596	hgsc.bcm.edu	37	chrX	74494247	74494247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggccaaggtgattctcctcaCggggtacgcccattctagcc	11	14	3	1			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chrX:74494247C>T	ENST00000373383.4	+	1	325	c.158C>T	c.(157-159)aCg>aTg	p.T53M	UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000373379.1_Missense_Mutation_p.T53M|UPRT_ENST00000531704.1_3'UTR	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	53					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T53M(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						ATTCTCCTCACGGGGTACGCC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	X											38	33	35					X																	74494247		2203	4300	6503	74410972	SO:0001583	missense	139596			BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.158C>T	X.37:g.74494247C>T	ENSP00000362481:p.Thr53Met		74410972	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Missense_Mutation	SNP	ENST00000373383.4	37	CCDS14429.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170408	0.57584	.	.	ENSG00000094841	ENST00000373383;ENST00000373379	.	.	.	4.88	1.98	0.26296	.	1.213670	0.05820	N	0.615621	T	0.31231	0.0790	N	0.14661	0.345	0.18873	N	0.999989	D;P;P	0.60575	0.988;0.726;0.726	P;B;B	0.50896	0.653;0.276;0.276	T	0.24905	-1.0147	9	0.44086	T	0.13	-5.5346	7.4856	0.27429	0.1737:0.4612:0.365:0.0	.	53;53;53	Q96BW1-2;A8KAF9;Q96BW1	.;.;UPP_HUMAN	M	53	.	ENSP00000362471:T53M	T	+	2	0	UPRT	74410972	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	-0.102000	0.10956	0.157000	0.19338	0.600000	0.82982	ACG		0.642	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052		T	74494247	C	T	74494247	3	4	15	1	0	0	0	0	1	0	0	0	17054	536	19	1	160	1	UPRT	23	74494247	Missense_Mutation	SNP	C	TCGA-AG-3578-01A-01W-0831-10	39532459	74494247	80776313	25	1674										
GPR112	139378	hgsc.bcm.edu	37	chrX	135482100	135482100	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttttgatcaattcttggttGtcatcatttcagaaagtggg	9	5	5	2			TCGA-AG-3578-01A-01W-0831-10	TCGA-AG-3578-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2ea76de8-6361-47f9-bbaa-c9bbdab397d0	a296ea9b-0304-4072-8bb0-efc6fe737e6a	g.chrX:135482100G>T	ENST00000394143.1	+	21	8691	c.8400G>T	c.(8398-8400)ttG>ttT	p.L2800F	GPR112_ENST00000370652.1_Missense_Mutation_p.L2800F|GPR112_ENST00000287534.4_Missense_Mutation_p.L2553F|GPR112_ENST00000394141.1_Missense_Mutation_p.L2595F|GPR112_ENST00000412101.1_Missense_Mutation_p.L2595F	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2800					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L2800F(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ATTCTTGGTTGTCATCATTTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											197	165	176					X																	135482100		2203	4300	6503	135309766	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.8400G>T	X.37:g.135482100G>T	ENSP00000377699:p.Leu2800Phe		135309766	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	G	7.759	0.705049	0.15172	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	5.1	-4.59	0.03400	GPCR, family 2-like (1);	.	.	.	.	T	0.26774	0.0655	L	0.41961	1.31	0.09310	N	1	B;B	0.25955	0.138;0.099	B;B	0.36092	0.066;0.217	T	0.47005	-0.9150	9	0.59425	D	0.04	.	0.6659	0.00850	0.3015:0.1053:0.2675:0.3258	.	2595;2800	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	F	2800;2800;2595;2553;2595	ENSP00000377699:L2800F;ENSP00000359686:L2800F;ENSP00000416526:L2595F;ENSP00000287534:L2553F;ENSP00000377697:L2595F	ENSP00000287534:L2553F	L	+	3	2	GPR112	135309766	0.000000	0.05858	0.070000	0.20053	0.991000	0.79684	-1.044000	0.03532	-0.942000	0.03695	0.544000	0.68410	TTG		0.418	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135482100	G	T	135482100	3	4	15	1	0	0	0	0	1	0	0	0	6649	1368	48	2	8470	2	GPR112	23	135482100	Missense_Mutation	SNP	G	TCGA-AG-3578-01A-01W-0831-10	60987853	135482100	19788460	26	1675										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10720133	10720133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ttctggggccgcagattctcGccggtcttcagtttttggat	12	10	4	1	rs72858531	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:10720133G>A	ENST00000377022.3	-	6	1283	c.966C>T	c.(964-966)ggC>ggT	p.G322G	CASZ1_ENST00000478728.2_5'Flank|CASZ1_ENST00000344008.5_Silent_p.G322G	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	322					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G322G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	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)		GCAGATTCTCGCCGGTCTTCA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	94	92					1																	10720133		2203	4300	6503	10642720	SO:0001819	synonymous_variant	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.966C>T	1.37:g.10720133G>A			10642720	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																				0.582	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10720133	G	A	10720133	2	1	16	1	0	0	0	0	0	0	0	1	2691	1074	38	1		1	CASZ1	1	10720133	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10		10720133	238530488	1	1676										
MAN1C1	57134	hgsc.bcm.edu	37	chr1	26107553	26107553	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	agagctacatgtacctgtggCgacagacccacaaccccatc	8	15	0	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:26107553C>T	ENST00000374332.4	+	10	1930	c.1600C>T	c.(1600-1602)Cga>Tga	p.R534*	MAN1C1_ENST00000263979.3_Nonsense_Mutation_p.R354*|MAN1C1_ENST00000374329.1_Nonsense_Mutation_p.R305*	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	534					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.R534*(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		GTACCTGTGGCGACAGACCCA	0.617																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											76	78	78					1																	26107553		2203	4300	6503	25980140	SO:0001587	stop_gained	57134			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.1600C>T	1.37:g.26107553C>T	ENSP00000363452:p.Arg534*		25980140	A6NNE2|B2RNP2|Q9Y545	Nonsense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	C	43	10.494022	0.99415	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979;ENST00000374329	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0824	0.53677	0.2928:0.7072:0.0:0.0	.	.	.	.	X	534;354;354;305	.	ENSP00000263979:R354X	R	+	1	2	MAN1C1	25980140	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.541000	0.36126	2.459000	0.83118	0.561000	0.74099	CGA		0.617	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		T	26107553	C	T	26107553	4	4	16	1	0	0	0	0	0	1	0	0	9243	760	27	1	1638	1	MAN1C1	1	26107553	Nonsense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	15387420	26107553	223143068	2	1677										
WDTC1	23038	hgsc.bcm.edu	37	chr1	27622879	27622879	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ttcctcttgcctagaaaatgCcactcctcggggggtaagtt	10	11	1	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:27622879C>A	ENST00000319394.3	+	10	1471	c.936C>A	c.(934-936)tgC>tgA	p.C312*	WDTC1_ENST00000361771.3_Nonsense_Mutation_p.C312*	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	312					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.C312*(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CTAGAAAATGCCACTCCTCGG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											172	168	169					1																	27622879		2203	4300	6503	27495466	SO:0001587	stop_gained	23038			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.936C>A	1.37:g.27622879C>A	ENSP00000317971:p.Cys312*		27495466	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Nonsense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	C	40	8.245321	0.98724	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	.	.	.	5.67	1.03	0.20045	.	0.192591	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	7.0046	0.24830	0.0:0.5885:0.1246:0.2869	.	.	.	.	X	312	.	ENSP00000317971:C312X	C	+	3	2	WDTC1	27495466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.356000	0.44116	0.309000	0.22966	0.655000	0.94253	TGC		0.512	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27622879	C	A	27622879	4	1	16	1	0	0	0	0	0	1	0	0	17382	747	26	2	970	2	WDTC1	1	27622879	Nonsense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	1515326	27622879	221627742	3	1678										
DEM1	64789	hgsc.bcm.edu	37	chr1	40981147	40981148	+	Frame_Shift_Del	DEL	AA	AA	-													0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gtactgagattgtagccttcAaagagaaggaggtgagagcc							TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	AA	AA	AA	-	AA	AA	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:40981147_40981148delAA	ENST00000372703.1	+	2	2005_2006	c.931_932delAA	c.(931-933)aaafs	p.K311fs	RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000296380.4_Frame_Shift_Del_p.K311fs|RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000358527.2_Frame_Shift_Del_p.K311fs			Q9H790	EXO5_HUMAN	exonuclease 5	311					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)	p.K311fs*25(1)									TGTAGCCTTCAAAGAGAAGGAG	0.52																																																1	Deletion - Frameshift(1)	large_intestine(1)	1																																								40753735	SO:0001589	frameshift_variant	64789			AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 176", "defects in morphology 1 homolog (S. cerevisiae)"	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	ENST00000372703.1:c.931_932delAA	1.37:g.40981147_40981148delAA	ENSP00000361788:p.Lys311fs		40753734	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Del	DEL	ENST00000372703.1	37	CCDS453.1																																																																																				0.52	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774		-	40981148	AA	-	40981147	7	5	16	1	0	1	0	1	0	0	0	0	4436	131	5	0	933	0	DEM1	1	40981147	Frame_Shift_Del	DEL	AA	TCGA-AG-3580-01A-01W-0831-10	13358268	40981147	208269474	4	1679										
FCRL2	79368	hgsc.bcm.edu	37	chr1	157738276	157738276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	agctctacagtaatatttgcCggcatcactctctttcacag	6	12	4	0			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:157738276C>T	ENST00000361516.3	-	5	859	c.811G>A	c.(811-813)Ggc>Agc	p.G271S	FCRL2_ENST00000469986.1_5'Flank|FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000392274.3_Missense_Mutation_p.G271S	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	271	Ig-like C2-type 3.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.G271S(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TAATATTTGCCGGCATCACTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											181	180	180					1																	157738276		2203	4300	6503	156004900	SO:0001583	missense	79368			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.811G>A	1.37:g.157738276C>T	ENSP00000355157:p.Gly271Ser		156004900	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959991	0.53400	.	.	ENSG00000132704	ENST00000361516;ENST00000392274	T;T	0.25912	1.77;1.77	3.89	2.97	0.34412	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.45606	D	0.000346	T	0.51449	0.1675	H	0.98664	4.295	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.53027	-0.8496	10	0.72032	D	0.01	.	7.6821	0.28520	0.0:0.8815:0.0:0.1185	.	271;271	B4DVJ9;Q96LA5	.;FCRL2_HUMAN	S	271	ENSP00000355157:G271S;ENSP00000376100:G271S	ENSP00000355157:G271S	G	-	1	0	FCRL2	156004900	0.000000	0.05858	0.010000	0.14722	0.005000	0.04900	0.798000	0.27014	0.956000	0.37904	0.655000	0.94253	GGC		0.507	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		T	157738276	C	T	157738276	3	4	16	1	0	0	0	0	1	0	0	0	5814	652	23	1	747	1	FCRL2	1	157738276	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	116757129	157738276	91512345	5	1680										
CRB1	23418	hgsc.bcm.edu	37	chr1	197397039	197397039	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	taagactaaacaaccaaaatCtggaattctttccaaatcca	3	10	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr1:197397039C>A	ENST00000367400.3	+	7	2719	c.2584C>A	c.(2584-2586)Ctg>Atg	p.L862M	CRB1_ENST00000544212.1_Missense_Mutation_p.L343M|CRB1_ENST00000367397.1_Missense_Mutation_p.L243M|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000535699.1_Missense_Mutation_p.L793M|CRB1_ENST00000367399.2_Missense_Mutation_p.L750M	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	862	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L862M(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CAACCAAAATCTGGAATTCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	86	88					1																	197397039		2203	4300	6503	195663662	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2584C>A	1.37:g.197397039C>A	ENSP00000356370:p.Leu862Met		195663662	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.769368	0.31320	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D	0.82081	-1.57;-1.52;-1.52;-1.52;-1.52	4.98	4.04	0.47022	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.88966	0.6581	M	0.69248	2.105	0.58432	D	0.999999	P;P;D;B	0.89917	0.828;0.875;1.0;0.429	B;B;D;B	0.97110	0.328;0.241;1.0;0.133	D	0.87448	0.2399	9	0.34782	T	0.22	.	14.2297	0.65882	0.0:0.9233:0.0:0.0767	.	793;750;511;862	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	M	793;862;750;343;243;511	ENSP00000438786:L793M;ENSP00000356370:L862M;ENSP00000356369:L750M;ENSP00000444556:L343M;ENSP00000356367:L243M	ENSP00000356367:L243M	L	+	1	2	CRB1	195663662	0.961000	0.32948	0.946000	0.38457	0.310000	0.27922	2.220000	0.42908	2.458000	0.83093	0.555000	0.69702	CTG		0.413	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197397039	C	A	197397039	3	1	16	1	0	0	0	0	1	0	0	0	3854	912	32	2	2610	2	CRB1	1	197397039	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	39658763	197397039	51853582	6	1681										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24896255	24896255	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	agaaatcaacaactgatgacGatgtacagaaatcagacatc	7	8	2	5			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr2:24896255G>A	ENST00000406961.1	+	7	929	c.277G>A	c.(277-279)Gat>Aat	p.D93N	NCOA1_ENST00000405141.1_Missense_Mutation_p.D93N|NCOA1_ENST00000348332.3_Missense_Mutation_p.D93N|NCOA1_ENST00000407230.1_De_novo_Start_OutOfFrame|NCOA1_ENST00000288599.5_Missense_Mutation_p.D93N|NCOA1_ENST00000395856.3_Missense_Mutation_p.D93N|NCOA1_ENST00000538539.1_Missense_Mutation_p.D93N|RNU6-936P_ENST00000384005.1_RNA			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	93					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.D93N(2)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACTGATGACGATGTACAGAA	0.348			T	PAX3	alveolar rhadomyosarcoma																																		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	2	Substitution - Missense(2)	large_intestine(2)	2											96	99	98					2																	24896255		2203	4300	6503	24749759	SO:0001583	missense	8648			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.277G>A	2.37:g.24896255G>A	ENSP00000385216:p.Asp93Asn		24749759	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034222	0.93575	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T	0.01947	4.54;4.54;4.54;4.54;4.54;4.54	4.84	4.84	0.62591	Helix-loop-helix DNA-binding (2);	0.214512	0.47852	D	0.000218	T	0.06050	0.0157	L	0.42245	1.32	0.80722	D	1	D;P;B	0.59767	0.986;0.782;0.325	P;B;B	0.52627	0.704;0.261;0.115	T	0.28933	-1.0028	10	0.72032	D	0.01	.	17.7266	0.88367	0.0:0.0:1.0:0.0	.	93;93;93	Q15788-3;Q15788;Q15788-2	.;NCOA1_HUMAN;.	N	93	ENSP00000385216:D93N;ENSP00000385097:D93N;ENSP00000444039:D93N;ENSP00000320940:D93N;ENSP00000288599:D93N;ENSP00000379197:D93N	ENSP00000288599:D93N	D	+	1	0	NCOA1	24749759	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.469000	0.97679	2.498000	0.84270	0.561000	0.74099	GAT		0.348	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		A	24896255	G	A	24896255	3	1	16	1	0	0	0	0	1	0	0	0	10259	1058	37	1	287	1	NCOA1	2	24896255	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		24896255	218303118	7	1682										
TFPI	7035	hgsc.bcm.edu	37	chr2	188348879	188348879	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ctgggaaccttggttgattgCggagtcagggagttattcac	14	7	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr2:188348879C>T	ENST00000233156.3	-	6	894	c.600G>A	c.(598-600)ccG>ccA	p.P200P	TFPI_ENST00000409676.1_Silent_p.P200P|TFPI_ENST00000339091.4_Silent_p.P200P|AC007319.1_ENST00000453517.1_RNA|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000392365.1_Silent_p.P200P	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	200					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.P200P(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	TGGTTGATTGCGGAGTCAGGG	0.378																																																2	Substitution - coding silent(2)	large_intestine(2)	2											100	102	102					2																	188348879		2203	4299	6502	188057124	SO:0001819	synonymous_variant	7035				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.600G>A	2.37:g.188348879C>T			188057124	O95103|Q53TS4	Silent	SNP	ENST00000233156.3	37	CCDS2294.1																																																																																				0.378	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		T	188348879	C	T	188348879	2	4	16	1	0	0	0	0	0	0	0	1	15847	755	27	1		1	TFPI	2	188348879	Silent	SNP	C	TCGA-AG-3580-01A-01W-0831-10	163452624	188348879	54850494	8	1683										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209207315	209207315	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	acttaatgtatgaacatgaaCgagtgcccattgcagtctgc	9	9	1	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr2:209207315C>T	ENST00000264380.4	+	32	5127	c.4969C>T	c.(4969-4971)Cga>Tga	p.R1657*		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1657					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R1657*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TGAACATGAACGAGTGCCCAT	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											174	156	162					2																	209207315		2203	4300	6503	208915560	SO:0001587	stop_gained	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.4969C>T	2.37:g.209207315C>T	ENSP00000264380:p.Arg1657*		208915560	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Nonsense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	46	12.107369	0.99636	.	.	ENSG00000115020	ENST00000264380	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-16.3541	19.5723	0.95425	0.0:1.0:0.0:0.0	.	.	.	.	X	1657	.	ENSP00000264380:R1657X	R	+	1	2	PIKFYVE	208915560	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	4.178000	0.58284	2.695000	0.91970	0.557000	0.71058	CGA		0.338	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209207315	C	T	209207315	4	4	16	1	0	0	0	0	0	1	0	0	11955	528	19	1	5102	1	PIKFYVE	2	209207315	Nonsense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	20858436	209207315	33992058	9	1684										
EEFSEC	60678	hgsc.bcm.edu	37	chr3	127983522	127983522	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ggaccgttcctcatgtctgtGgaccactgtttctccatcaa	8	13	4	0			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr3:127983522G>T	ENST00000254730.6	+	4	738	c.684G>T	c.(682-684)gtG>gtT	p.V228V	EEFSEC_ENST00000483457.1_Intron	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	228					selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)	p.V228V(1)		NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						TCATGTCTGTGGACCACTGTT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	3											202	167	179					3																	127983522		2203	4300	6503	129466212	SO:0001819	synonymous_variant	60678				CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"elongation factor for selenoprotein translation"	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.684G>T	3.37:g.127983522G>T			129466212	Q96HZ6	Silent	SNP	ENST00000254730.6	37	CCDS33849.1																																																																																				0.557	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937		T	127983522	G	T	127983522	2	4	16	1	0	0	0	0	0	0	0	1	4942	1335	47	2		2	EEFSEC	3	127983522	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10		127983522	70038908	10	1685										
ACAD9	28976	hgsc.bcm.edu	37	chr3	128621414	128621414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	aggtggccatgaacatcctcAacagcggccggttcagcatg	12	12	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr3:128621414A>G	ENST00000308982.7	+	9	982	c.901A>G	c.(901-903)Aac>Gac	p.N301D	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	301						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.N301D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						GAACATCCTCAACAGCGGCCG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	98	100					3																	128621414		2203	4300	6503	130104104	SO:0001583	missense	28976			AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.901A>G	3.37:g.128621414A>G	ENSP00000312618:p.Asn301Asp		130104104	D3DNB8|Q8WXX3	Missense_Mutation	SNP	ENST00000308982.7	37	CCDS3053.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894767	0.91962	.	.	ENSG00000177646	ENST00000308982;ENST00000334167	D	0.96136	-3.92	5.19	5.19	0.71726	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.96100	0.8729	L	0.39633	1.23	0.80722	D	1	D;D;D	0.89917	0.991;1.0;1.0	D;D;D	0.97110	0.975;0.998;1.0	D	0.96427	0.9316	10	0.66056	D	0.02	.	12.991	0.58618	1.0:0.0:0.0:0.0	.	178;251;301	Q9H9W4;Q59FN3;Q9H845	.;.;ACAD9_HUMAN	D	301;168	ENSP00000312618:N301D	ENSP00000312618:N301D	N	+	1	0	ACAD9	130104104	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.533000	0.90617	1.953000	0.56701	0.533000	0.62120	AAC		0.622	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		G	128621414	A	G	128621414	3	3	16	1	0	0	0	0	1	0	0	0	111	130	5	4	935	4	ACAD9	3	128621414	Missense_Mutation	SNP	A	TCGA-AG-3580-01A-01W-0831-10	637892	128621414	69401016	11	1686										
IFT122	55764	hgsc.bcm.edu	37	chr3	129183577	129183577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	aaagtaaagatcgagcggccGgggggctccctctcgccaat	13	12	1	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr3:129183577G>A	ENST00000348417.2	+	7	593	c.516G>A	c.(514-516)ccG>ccA	p.P172P	IFT122_ENST00000504021.1_Silent_p.P125P|IFT122_ENST00000347300.2_Silent_p.P172P|IFT122_ENST00000296266.3_Silent_p.P223P|IFT122_ENST00000431818.2_Silent_p.P22P|IFT122_ENST00000349441.2_Silent_p.P120P|IFT122_ENST00000507564.1_Silent_p.P223P|IFT122_ENST00000440957.2_Silent_p.P22P	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	172					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.P223P(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TCGAGCGGCCGGGGGGCTCCC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											99	107	104					3																	129183577		2203	4300	6503	130666267	SO:0001819	synonymous_variant	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.516G>A	3.37:g.129183577G>A			130666267	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																				0.507	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		A	129183577	G	A	129183577	2	1	16	1	0	0	0	0	0	0	0	1	7576	1103	39	1		1	IFT122	3	129183577	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10	562163	129183577	68838853	12	1687										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69968606	69968606	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	caatggtcagtaacatgacaGaagaaagggccaacgtaatt	10	7	1	3			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr4:69968606G>A	ENST00000508661.1	+	3	979	c.952G>A	c.(952-954)Gaa>Aaa	p.E318K	UGT2B7_ENST00000509763.1_3'UTR|UGT2B7_ENST00000305231.7_Missense_Mutation_p.E318K			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	318					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.E318K(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TAACATGACAGAAGAAAGGGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											183	177	179					4																	69968606		2203	4300	6503	70003195	SO:0001583	missense	7364			BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.952G>A	4.37:g.69968606G>A	ENSP00000427659:p.Glu318Lys		70003195	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	G	6.699	0.497663	0.12762	.	.	ENSG00000171234	ENST00000502942;ENST00000305231;ENST00000508661	T;T;T	0.67345	-0.26;-0.26;-0.26	3.0	2.12	0.27331	.	0.964170	0.08529	U	0.932329	T	0.67496	0.2899	L	0.56396	1.775	0.09310	N	1	B;B	0.21905	0.062;0.019	B;B	0.36922	0.236;0.04	T	0.59188	-0.7501	9	.	.	.	.	9.9502	0.41634	0.0:0.2088:0.7912:0.0	.	318;318	E9PBP8;P16662	.;UD2B7_HUMAN	K	69;318;318	ENSP00000426206:E69K;ENSP00000304811:E318K;ENSP00000427659:E318K	.	E	+	1	0	UGT2B7	70003195	0.000000	0.05858	0.139000	0.22197	0.127000	0.20565	0.911000	0.28584	0.551000	0.29008	0.585000	0.79938	GAA		0.448	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		A	69968606	G	A	69968606	3	1	16	1	0	0	0	0	1	0	0	0	17002	943	33	3	962	3	UGT2B7	4	69968606	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		69968606	121185670	13	1688										
FAT4	79633	hgsc.bcm.edu	37	chr4	126370389	126370389	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gggaaaaagtatctcattatGtcctaaccataaaatcatca	5	8	3	0			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr4:126370389G>T	ENST00000394329.3	+	9	8231	c.8218G>T	c.(8218-8220)Gtc>Ttc	p.V2740F	FAT4_ENST00000335110.5_Missense_Mutation_p.V1038F	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2740	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2740F(4)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATCTCATTATGTCCTAACCAT	0.358																																																4	Substitution - Missense(4)	upper_aerodigestive_tract(2)|large_intestine(2)	4											68	69	68					4																	126370389		2203	4299	6502	126589839	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.8218G>T	4.37:g.126370389G>T	ENSP00000377862:p.Val2740Phe		126589839	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	3.613	-0.079218	0.07141	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01821	4.62;4.62	5.6	1.54	0.23209	Cadherin (4);Cadherin-like (1);	0.895446	0.09019	U	0.860422	T	0.01800	0.0057	L	0.28192	0.835	0.09310	N	1	B;B;B	0.27013	0.091;0.166;0.135	B;B;B	0.31337	0.021;0.128;0.06	T	0.49031	-0.8981	10	0.56958	D	0.05	.	4.7413	0.13013	0.5097:0.1648:0.3256:0.0	.	1038;2740;2740	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	F	2740;1038	ENSP00000377862:V2740F;ENSP00000335169:V1038F	ENSP00000335169:V1038F	V	+	1	0	FAT4	126589839	0.000000	0.05858	0.059000	0.19551	0.039000	0.13416	0.140000	0.16056	0.353000	0.24079	-0.145000	0.13849	GTC		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126370389	G	T	126370389	3	4	16	1	0	0	0	0	1	0	0	0	5711	1377	48	2	8252	2	FAT4	4	126370389	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	56401783	126370389	64783887	14	1689										
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561780	147561780	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gagaagaagcgcaagcgcacGtccatcgctgcgccagagaa	13	12	0	3	rs371952832		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr4:147561780G>A	ENST00000281321.3	+	2	1298	c.1050G>A	c.(1048-1050)acG>acA	p.T350T	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	350					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.T350T(1)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					GCAAGCGCACGTCCATCGCTG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	4											83	87	86					4																	147561780		2203	4300	6503	147781230	SO:0001819	synonymous_variant	5458			U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.1050G>A	4.37:g.147561780G>A			147781230	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																				0.622	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147561780	G	A	147561780	2	1	16	1	0	0	0	0	0	0	0	1	12310	1132	40	1		1	POU4F2	4	147561780	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10	21191391	147561780	43592496	15	1690										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162376191	162376191	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	atgagtgttgtggtgggaatGaaaaaatcatccactctgtc	11	6	2	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr4:162376191G>T	ENST00000306100.5	-	15	2242	c.1806C>A	c.(1804-1806)ttC>ttA	p.F602L	FSTL5_ENST00000379164.4_Missense_Mutation_p.F601L|FSTL5_ENST00000427802.2_Missense_Mutation_p.F592L|FSTL5_ENST00000536695.1_Missense_Mutation_p.F601L	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	602						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.F602L(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TGGTGGGAATGAAAAAATCAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											168	126	140					4																	162376191		2203	4300	6503	162595641	SO:0001583	missense	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1806C>A	4.37:g.162376191G>T	ENSP00000305334:p.Phe602Leu		162595641	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435731	0.83885	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.24	3.49	0.39957	WD40/YVTN repeat-like-containing domain (1);	0.096460	0.64402	D	0.000001	T	0.41488	0.1161	M	0.74467	2.265	0.53688	D	0.999978	P;P;P	0.44521	0.518;0.837;0.748	B;P;B	0.47430	0.138;0.547;0.283	T	0.38993	-0.9635	10	0.72032	D	0.01	.	11.3949	0.49836	0.1496:0.0:0.8504:0.0	.	592;601;602	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	L	602;601;592;601	ENSP00000305334:F602L;ENSP00000368462:F601L;ENSP00000389270:F592L;ENSP00000440409:F601L	ENSP00000305334:F602L	F	-	3	2	FSTL5	162595641	1.000000	0.71417	0.977000	0.42913	0.951000	0.60555	3.624000	0.54231	0.688000	0.31529	0.655000	0.94253	TTC		0.413	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162376191	G	T	162376191	3	4	16	1	0	0	0	0	1	0	0	0	6099	1281	45	2	745	2	FSTL5	4	162376191	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	14814411	162376191	28778085	16	1691										
TLL1	7092	hgsc.bcm.edu	37	chr4	166976380	166976380	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tggatgaagtttgtttctgaCggaactgtgaacaaagcagg	13	5	1	3	rs142933283		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr4:166976380C>T	ENST00000061240.2	+	13	2324	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	RNA5SP170_ENST00000517150.1_RNA|TLL1_ENST00000507499.1_Silent_p.D582D	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	559	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D559D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TTGTTTCTGACGGAACTGTGA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	4						T		0,4406		0,0,2203	122	118	120		1677	-4.5	0.8	4	dbSNP_134	120	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous	TLL1	NM_012464.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		559/1014	166976380	2,13004	2203	4300	6503	167195830	SO:0001819	synonymous_variant	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1677C>T	4.37:g.166976380C>T			167195830	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																				0.363	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	166976380	C	T	166976380	2	4	16	1	0	0	0	0	0	0	0	1	15984	535	19	1		1	TLL1	4	166976380	Silent	SNP	C	TCGA-AG-3580-01A-01W-0831-10	4600189	166976380	24177896	17	1692										
HAPLN1	1404	hgsc.bcm.edu	37	chr5	82937441	82937441	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ctagagatggggtagcggacGctgccatccgccaaccagcc	13	14	0	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr5:82937441G>A	ENST00000274341.4	-	5	1789	c.939C>T	c.(937-939)agC>agT	p.S313S		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	313	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.S313S(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	GGTAGCGGACGCTGCCATCCG	0.537																																																2	Substitution - coding silent(2)	large_intestine(2)	5											108	113	111					5																	82937441		2203	4300	6503	82973197	SO:0001819	synonymous_variant	1404				CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"Immunoglobulin superfamily / V-set domain containing"	2380	protein-coding gene	gene with protein product	"Cartilage link protein", "hyaluronan and proteoglycan link protein 1"	115435	"cartilage linking protein 1"	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.939C>T	5.37:g.82937441G>A			82973197	B2R9A9	Silent	SNP	ENST00000274341.4	37	CCDS4061.1																																																																																				0.537	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		A	82937441	G	A	82937441	2	1	16	1	0	0	0	0	0	0	0	1	6975	1078	38	1		1	HAPLN1	5	82937441	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10		82937441	97977819	18	1693										
APC	324	hgsc.bcm.edu	37	chr5	112175060	112175060	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	aagtttcttctattaaccaaGaaacaatacagacttattgt	4	7	2	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr5:112175060G>T	ENST00000457016.1	+	16	4149	c.3769G>T	c.(3769-3771)Gaa>Taa	p.E1257*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1257*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1257*			P25054	APC_HUMAN	adenomatous polyposis coli	1257	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1257*(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATTAACCAAGAAACAATACA	0.378		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											49	51	50					5																	112175060		2202	4300	6502	112202959	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3769G>T	5.37:g.112175060G>T	ENSP00000413133:p.Glu1257*		112202959	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.200291	0.98701	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.9656	20.5568	0.99304	0.0:0.0:1.0:0.0	.	.	.	.	X	1257	.	.	E	+	1	0	APC	112202959	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.861000	0.98227	0.655000	0.94253	GAA		0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175060	G	T	112175060	4	4	16	1	0	0	0	0	0	1	0	0	763	943	33	2	3827	2	APC	5	112175060	Nonsense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	29237619	112175060	68740200	19	1694										
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96997370	96997370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	cttctgggacgggcagaaaaCgcacaatcaaggacttgcaa	11	10	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr6:96997370C>T	ENST00000369278.4	+	14	1669	c.1603C>T	c.(1603-1605)Cgc>Tgc	p.R535C		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	535					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.R535C(1)									GGGCAGAAAACGCACAATCAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	68	69					6																	96997370		2203	4298	6501	97104091	SO:0001583	missense	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1603C>T	6.37:g.96997370C>T	ENSP00000358283:p.Arg535Cys		97104091	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984953	0.74474	.	.	ENSG00000014123	ENST00000369278	T	0.51071	0.72	5.73	5.73	0.89815	.	0.152710	0.64402	D	0.000016	T	0.41880	0.1178	L	0.47716	1.5	0.45837	D	0.998709	D	0.69078	0.997	P	0.47299	0.543	T	0.43426	-0.9392	10	0.72032	D	0.01	-1.9566	18.8905	0.92399	0.0:1.0:0.0:0.0	.	535	O94874	UFL1_HUMAN	C	535	ENSP00000358283:R535C	ENSP00000358283:R535C	R	+	1	0	KIAA0776	97104091	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.345000	0.44018	2.693000	0.91896	0.650000	0.86243	CGC		0.368	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		T	96997370	C	T	96997370	3	4	16	1	0	0	0	0	1	0	0	0	8214	536	19	1	1657	1	KIAA0776	6	96997370	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10		96997370	74117697	20	1695										
SIM1	6492	hgsc.bcm.edu	37	chr6	100838246	100838246	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tcagcaaaacatcagcttccGttggttattataacagatgt	7	8	2	1	rs143803280	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr6:100838246G>A	ENST00000369208.3	-	12	3074	c.2292C>T	c.(2290-2292)aaC>aaT	p.N764N	SIM1_ENST00000262901.4_Silent_p.N764N			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	764	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.N764N(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		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)		ATCAGCTTCCGTTGGTTATTA	0.398													G|||	8	0.00159744	0.003	0	5008	,	,		19807	0.003		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	6						G		18,4388	26.2+/-53.5	0,18,2185	130	130	130		2292	4.9	1	6	dbSNP_134	130	0,8600		0,0,4300	yes	coding-synonymous	SIM1	NM_005068.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		764/767	100838246	18,12988	2203	4300	6503	100944967	SO:0001819	synonymous_variant	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.2292C>T	6.37:g.100838246G>A			100944967	Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.398	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		A	100838246	G	A	100838246	2	1	16	1	0	0	0	0	0	0	0	1	14360	1136	40	1		1	SIM1	6	100838246	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10	3840876	100838246	70276821	21	1696										
MED23	9439	hgsc.bcm.edu	37	chr6	131908863	131908863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gggcacctgattagactgagGtgctggagacccactgttca	13	10	1	4			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr6:131908863G>A	ENST00000368068.3	-	29	4242	c.4063C>T	c.(4063-4065)Cct>Tct	p.P1355S	MED23_ENST00000368060.3_Missense_Mutation_p.P1355S|MED23_ENST00000354577.4_Missense_Mutation_p.P1361S|MED23_ENST00000403834.3_Missense_Mutation_p.P1361S|MED23_ENST00000545957.1_Missense_Mutation_p.P996S|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000368058.1_Missense_Mutation_p.P1361S	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1355					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.P1355S(1)|p.P1361S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TTAGACTGAGGTGCTGGAGAC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	6											125	107	113					6																	131908863		2203	4300	6503	131950556	SO:0001583	missense	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.4063C>T	6.37:g.131908863G>A	ENSP00000357047:p.Pro1355Ser		131950556	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	37	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.942229	0.34283	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957	.	.	.	5.8	4.94	0.65067	.	0.321864	0.37012	N	0.002298	T	0.19327	0.0464	N	0.08118	0	0.80722	D	1	B;B	0.19331	0.02;0.035	B;B	0.18871	0.01;0.023	T	0.07966	-1.0745	9	0.25106	T	0.35	-12.7633	12.0537	0.53522	0.1386:0.0:0.8614:0.0	.	1355;1361	Q9ULK4;Q9ULK4-3	MED23_HUMAN;.	S	1361;1355;1361;1355;1361;996	.	ENSP00000346588:P1361S	P	-	1	0	MED23	131950556	1.000000	0.71417	0.798000	0.32154	0.635000	0.38103	3.796000	0.55507	1.469000	0.48083	-0.150000	0.13652	CCT		0.468	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			A	131908863	G	A	131908863	3	1	16	1	0	0	0	0	1	0	0	0	9471	1261	44	3	54	3	MED23	6	131908863	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	31070617	131908863	39206204	22	1697										
GAL3ST4	79690	hgsc.bcm.edu	37	chr7	99758239	99758239	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tggaaacaggatggatgaggGcattgggattgagggtttgg	19	2	0	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr7:99758239G>A	ENST00000360039.4	-	4	1165	c.773C>T	c.(772-774)gCc>gTc	p.A258V	C7orf43_ENST00000457641.1_5'Flank|GAL3ST4_ENST00000413800.1_Missense_Mutation_p.A258V|C7orf43_ENST00000316937.3_5'Flank|C7orf43_ENST00000419841.1_5'Flank|GAL3ST4_ENST00000411994.1_Missense_Mutation_p.P157S|GAL3ST4_ENST00000426974.2_Missense_Mutation_p.A196V|GAL3ST4_ENST00000423751.1_Missense_Mutation_p.P157S	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	258					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)	p.A258V(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATGGATGAGGGCATTGGGATT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											116	122	120					7																	99758239		2203	4294	6497	99596175	SO:0001583	missense	79690			AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"Sulfotransferases, membrane-bound"	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.773C>T	7.37:g.99758239G>A	ENSP00000353142:p.Ala258Val		99596175	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Missense_Mutation	SNP	ENST00000360039.4	37	CCDS5688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.34|10.34	1.324023|1.324023	0.24080|0.24080	.|.	.|.	ENSG00000197093|ENSG00000197093	ENST00000413800;ENST00000360039;ENST00000426974|ENST00000423751;ENST00000411994	T;T;T|.	0.36157|.	1.39;1.39;1.27|.	4.45|4.45	2.58|2.58	0.30949|0.30949	.|.	3.209450|.	0.01787|.	U|.	0.032105|.	T|T	0.32585|0.32585	0.0834|0.0834	N|N	0.14661|0.14661	0.345|0.345	0.25610|0.25610	N|N	0.986505|0.986505	B;B|.	0.30763|.	0.294;0.22|.	B;B|.	0.24974|.	0.057;0.036|.	T|T	0.30736|0.30736	-0.9968|-0.9968	10|6	0.25106|0.87932	T|D	0.35|0	-0.0676|-0.0676	12.3731|12.3731	0.55265|0.55265	0.0:0.3248:0.6752:0.0|0.0:0.3248:0.6752:0.0	.|.	196;258|.	B4DWL8;Q96RP7|.	.;G3ST4_HUMAN|.	V|S	258;258;196|157	ENSP00000400451:A258V;ENSP00000353142:A258V;ENSP00000398304:A196V|.	ENSP00000353142:A258V|ENSP00000414733:P157S	A|P	-|-	2|1	0|0	GAL3ST4|GAL3ST4	99596175|99596175	0.875000|0.875000	0.30112|0.30112	0.892000|0.892000	0.35008|0.35008	0.266000|0.266000	0.26442|0.26442	1.173000|1.173000	0.31920|0.31920	0.474000|0.474000	0.27392|0.27392	0.511000|0.511000	0.50034|0.50034	GCC|CCC		0.552	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637		A	99758239	G	A	99758239	3	1	16	1	0	0	0	0	1	0	0	0	6220	1203	42	3	691	3	GAL3ST4	7	99758239	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		99758239	59380424	23	1698										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143095154	143095154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ttctagaaccatctggtaccGttcttcatcctgtgggttgg	10	10	4	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr7:143095154G>A	ENST00000275815.3	-	8	1560	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	492	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q (in dbSNP:rs11768549). {ECO:0000269|PubMed:17344846}.		activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.R492W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				ATCTGGTACCGTTCTTCATCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											118	102	108					7																	143095154		2203	4300	6503	142805276	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1474C>T	7.37:g.143095154G>A	ENSP00000275815:p.Arg492Trp		142805276	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	G	4.133	0.022909	0.08006	.	.	ENSG00000146904	ENST00000275815	T	0.58210	0.35	4.52	-5.3	0.02738	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.240490	0.28332	N	0.015722	T	0.17619	0.0423	N	0.02011	-0.69	0.22156	N	0.999323	B	0.09022	0.002	B	0.01281	0.0	T	0.08310	-1.0728	10	0.54805	T	0.06	.	4.7865	0.13227	0.354:0.0:0.2565:0.3895	.	492	P21709	EPHA1_HUMAN	W	492	ENSP00000275815:R492W	ENSP00000275815:R492W	R	-	1	2	EPHA1	142805276	0.212000	0.23540	0.725000	0.30721	0.011000	0.07611	0.100000	0.15231	-0.742000	0.04790	-1.827000	0.00596	CGG		0.572	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143095154	G	A	143095154	3	1	16	1	0	0	0	0	1	0	0	0	5178	1144	40	1	1500	1	EPHA1	7	143095154	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	43336915	143095154	16043509	24	1699										
DLC1	10395	hgsc.bcm.edu	37	chr8	12957275	12957275	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ttcagttccttggggctgtcGctactgttttccctcctgag	10	12	1	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr8:12957275G>A	ENST00000276297.4	-	9	2980	c.2571C>T	c.(2569-2571)agC>agT	p.S857S	DLC1_ENST00000358919.2_Silent_p.S420S|DLC1_ENST00000512044.2_Silent_p.S454S|DLC1_ENST00000520226.1_Silent_p.S346S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	857	Focal adhesion-targeting (FAT).				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.S857S(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGGGGCTGTCGCTACTGTTTT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	8											68	61	63					8																	12957275		2203	4300	6503	13001646	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2571C>T	8.37:g.12957275G>A			13001646	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.582	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	12957275	G	A	12957275	2	1	16	1	0	0	0	0	0	0	0	1	4561	1078	38	1		1	DLC1	8	12957275	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10		12957275	133406747	25	1700										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100050684	100050684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	cattcacttttttaagtggaCatattcatgaattgaggatt	7	5	2	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr8:100050684C>T	ENST00000358544.2	+	3	292	c.181C>T	c.(181-183)Cat>Tat	p.H61Y	VPS13B_ENST00000355155.1_Missense_Mutation_p.H61Y|VPS13B_ENST00000395996.1_Missense_Mutation_p.H61Y|VPS13B_ENST00000441350.2_Missense_Mutation_p.H61Y|VPS13B_ENST00000357162.2_Missense_Mutation_p.H61Y	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	61					protein transport (GO:0015031)			p.H61Y(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTAAGTGGACATATTCATGA	0.284																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											59	58	58					8																	100050684		2203	4296	6499	100119860	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.181C>T	8.37:g.100050684C>T	ENSP00000351346:p.His61Tyr		100119860	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777790	0.70107	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.65	5.65	0.86999	.	0.060483	0.64402	D	0.000005	T	0.82245	0.4995	N	0.20845	0.615	0.80722	D	1	P;P;P;P;B	0.48640	0.808;0.84;0.913;0.839;0.125	P;P;P;P;B	0.52758	0.584;0.708;0.648;0.502;0.064	T	0.82981	-0.0187	10	0.46703	T	0.11	.	19.7238	0.96153	0.0:1.0:0.0:0.0	.	61;61;61;61;61	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	Y	61	ENSP00000347281:H61Y;ENSP00000349685:H61Y;ENSP00000351346:H61Y;ENSP00000379318:H61Y;ENSP00000398472:H61Y	ENSP00000347281:H61Y	H	+	1	0	VPS13B	100119860	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.729000	0.84864	2.649000	0.89929	0.561000	0.74099	CAT		0.284	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100050684	C	T	100050684	3	4	16	1	0	0	0	0	1	0	0	0	17230	478	17	3	187	3	VPS13B	8	100050684	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	87093409	100050684	46313338	26	1701										
KIAA1539	80256	hgsc.bcm.edu	37	chr9	35108115	35108115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ggtaccagccggaggggaaaAgatggatacctggtagaccc	15	9	0	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr9:35108115A>G	ENST00000378561.1	-	2	3212	c.157T>C	c.(157-159)Ttt>Ctt	p.F53L	FAM214B_ENST00000378554.2_Missense_Mutation_p.F53L|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000488109.2_Missense_Mutation_p.F53L|FAM214B_ENST00000603301.1_Missense_Mutation_p.F53L|FAM214B_ENST00000378566.1_Intron|FAM214B_ENST00000605244.1_Missense_Mutation_p.F53L|FAM214B_ENST00000378557.1_Missense_Mutation_p.F53L|FAM214B_ENST00000322813.5_Missense_Mutation_p.F53L			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	53						nucleus (GO:0005634)		p.F53L(1)									GGAGGGGAAAAGATGGATACC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	9											19	20	19					9																	35108115		2159	4229	6388	35098115	SO:0001583	missense	80256			AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"KIAA1539"	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.157T>C	9.37:g.35108115A>G	ENSP00000367823:p.Phe53Leu		35098115	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990536	0.74589	.	.	ENSG00000005238	ENST00000322813;ENST00000378561;ENST00000378557;ENST00000378554	.	.	.	4.72	4.72	0.59763	.	0.087374	0.49305	D	0.000147	T	0.30978	0.0782	L	0.47716	1.5	0.31712	N	0.639336	P	0.38827	0.649	B	0.36186	0.219	T	0.27606	-1.0069	9	0.11485	T	0.65	-2.9156	9.738	0.40399	0.8458:0.0:0.0:0.1542	.	53	Q7L5A3	K1539_HUMAN	L	53	.	ENSP00000319897:F53L	F	-	1	0	KIAA1539	35098115	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.035000	0.49759	1.991000	0.58162	0.459000	0.35465	TTT		0.667	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182		G	35108115	A	G	35108115	3	3	16	1	0	0	0	0	1	0	0	0	8263	72	3	4	1487	4	KIAA1539	9	35108115	Missense_Mutation	SNP	A	TCGA-AG-3580-01A-01W-0831-10		35108115	106105316	27	1702										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72511261	72511261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ccccaactgagggtggccccCgcagcagcctggcctacaag	12	17	0	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr10:72511261C>T	ENST00000373207.1	+	17	2455	c.2455C>T	c.(2455-2457)Cgc>Tgc	p.R819C	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.R822C	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	819	Spacer.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R822C(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GGGTGGCCCCCGCAGCAGCCT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	10											54	56	55					10																	72511261		2203	4300	6503	72181267	SO:0001583	missense	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2455C>T	10.37:g.72511261C>T	ENSP00000362303:p.Arg819Cys		72181267	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420019	0.62622	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.53857	0.6;0.6	4.38	3.4	0.38934	ADAM-TS Spacer 1 (1);	0.074410	0.52532	D	0.000073	T	0.65626	0.2709	M	0.65498	2.005	0.44603	D	0.99757	D;D	0.89917	1.0;1.0	D;D	0.71414	0.959;0.973	T	0.67887	-0.5554	10	0.72032	D	0.01	.	9.1718	0.37086	0.3256:0.6744:0.0:0.0	.	819;822	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	C	822;819	ENSP00000362304:R822C;ENSP00000362303:R819C	ENSP00000362303:R819C	R	+	1	0	ADAMTS14	72181267	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.559000	0.53756	2.280000	0.76307	0.563000	0.77884	CGC		0.632	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72511261	C	T	72511261	3	4	16	1	0	0	0	0	1	0	0	0	259	652	23	1	2530	1	ADAMTS14	10	72511261	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10		72511261	63023486	28	1703										
P2RY6	5031	hgsc.bcm.edu	37	chr11	73007862	73007862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ctttggcgacttcgcctgccGcctggtccgcttcctcttct	9	17	2	0	rs201497467	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr11:73007862G>A	ENST00000393590.2	+	2	598	c.299G>A	c.(298-300)cGc>cAc	p.R100H	P2RY6_ENST00000538328.1_Missense_Mutation_p.R100H|P2RY6_ENST00000393592.2_Missense_Mutation_p.R100H|P2RY6_ENST00000540124.1_Missense_Mutation_p.R100H|P2RY6_ENST00000349767.2_Missense_Mutation_p.R100H|P2RY6_ENST00000542092.1_Missense_Mutation_p.R100H|P2RY6_ENST00000540342.1_Missense_Mutation_p.R100H|P2RY6_ENST00000393591.1_Missense_Mutation_p.R100H	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	100					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)	p.R100H(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						TTCGCCTGCCGCCTGGTCCGC	0.607													G|||	2	0.000399361	0	0.0029	5008	,	,		19382	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	11											137	123	128					11																	73007862		2200	4293	6493	72685510	SO:0001583	missense	5031				CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.299G>A	11.37:g.73007862G>A	ENSP00000377215:p.Arg100His		72685510	Q15754	Missense_Mutation	SNP	ENST00000393590.2	37	CCDS8220.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.27	3.347709	0.61183	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000544437;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000535931;ENST00000538328	T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	4.36	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.138244	0.43919	D	0.000510	T	0.80964	0.4725	M	0.77616	2.38	0.34990	D	0.754975	D	0.89917	1.0	D	0.70935	0.971	D	0.85594	0.1248	10	0.87932	D	0	.	8.377	0.32449	0.2025:0.0:0.7975:0.0	.	100	Q15077	P2RY6_HUMAN	H	100	ENSP00000443427:R100H;ENSP00000445652:R100H;ENSP00000309771:R100H;ENSP00000377217:R100H;ENSP00000441079:R100H;ENSP00000377216:R100H;ENSP00000442551:R100H;ENSP00000377215:R100H;ENSP00000440770:R100H;ENSP00000442990:R100H	ENSP00000309771:R100H	R	+	2	0	P2RY6	72685510	1.000000	0.71417	1.000000	0.80357	0.641000	0.38312	2.687000	0.46976	1.181000	0.42912	0.491000	0.48974	CGC		0.607	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			A	73007862	G	A	73007862	3	1	16	1	0	0	0	0	1	0	0	0	11385	1087	38	1	301	1	P2RY6	11	73007862	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		73007862	61998654	29	1704										
ERP27	121506	hgsc.bcm.edu	37	chr12	15087827	15087827	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tggtgttcccagtgatgttgTagtgtgtcagaacctcagaa	12	7	2	3			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr12:15087827T>C	ENST00000266397.2	-	3	869	c.296A>G	c.(295-297)tAc>tGc	p.Y99C		NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	99	Thioredoxin.					endoplasmic reticulum (GO:0005783)		p.Y99C(1)		breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						AGTGATGTTGTAGTGTGTCAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											129	110	116					12																	15087827		2203	4300	6503	14979094	SO:0001583	missense	121506			AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"Protein disulfide isomerases"	26495	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 8"	610642	"chromosome 12 open reading frame 46", "endoplasmic reticulum protein 27 kDa"	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.296A>G	12.37:g.15087827T>C	ENSP00000266397:p.Tyr99Cys		14979094		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	T	13.00	2.106642	0.37145	.	.	ENSG00000139055	ENST00000266397	T	0.26373	1.74	4.46	3.27	0.37495	Thioredoxin-like fold (2);	0.067697	0.64402	D	0.000009	T	0.44644	0.1303	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.31943	-0.9925	10	0.52906	T	0.07	-10.1405	7.2567	0.26181	0.1962:0.0:0.0:0.8038	.	99	Q96DN0	ERP27_HUMAN	C	99	ENSP00000266397:Y99C	ENSP00000266397:Y99C	Y	-	2	0	ERP27	14979094	1.000000	0.71417	0.994000	0.49952	0.308000	0.27856	2.821000	0.48065	0.980000	0.38523	0.533000	0.62120	TAC		0.473	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321		C	15087827	T	C	15087827	3	2	16	1	0	0	0	0	1	0	0	0	5254	1638	57	4	545	4	ERP27	12	15087827	Missense_Mutation	SNP	T	TCGA-AG-3580-01A-01W-0831-10		15087827	118764068	30	1705										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	16	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10	10310457	25398284	108453611	31	1706										
GEFT	115557	hgsc.bcm.edu	37	chr12	58010124	58010124	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ccagaccaacagcctggggcGgccaagagggcctggagtgg	17	12	0	2	rs116051216		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr12:58010124G>A	ENST00000286494.4	+	14	1938	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q	AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.R532Q	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	493	Sufficient to bind activated GNAQ.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R493Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						AGCCTGGGGCGGCCAAGAGGG	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		17880	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	62	66	65		1595,1478	4.8	1	12	dbSNP_132	65	0,8600		0,0,4300	no	missense,missense	ARHGEF25	NM_001111270.1,NM_182947.2	43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	532/620,493/581	58010124	1,13005	2203	4300	6503	56296391	SO:0001583	missense	115557				CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1478G>A	12.37:g.58010124G>A	ENSP00000286494:p.Arg493Gln		56296391	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	20.3	3.974957	0.74360	2.27E-4	0.0	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.21734	1.99;1.99	4.77	4.77	0.60923	Pleckstrin homology-type (1);	0.000000	0.34067	N	0.004298	T	0.39200	0.1069	L	0.50333	1.59	0.47183	D	0.999344	D;D	0.76494	0.999;0.994	D;D	0.77557	0.99;0.921	T	0.05801	-1.0863	10	0.54805	T	0.06	.	13.5047	0.61477	0.0:0.0:1.0:0.0	.	532;493	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	Q	532;493	ENSP00000335560:R532Q;ENSP00000286494:R493Q	ENSP00000286494:R493Q	R	+	2	0	ARHGEF25	56296391	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.786000	0.62425	2.655000	0.90218	0.650000	0.86243	CGG		0.592	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		A	58010124	G	A	58010124	3	1	16	1	0	0	0	0	1	0	0	0	6348	1116	39	1	1754	1	GEFT	12	58010124	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	32611840	58010124	75841771	32	1707										
E2F7	144455	hgsc.bcm.edu	37	chr12	77449722	77449722	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	cggtcccttatatctgggctGgcagcactaatgagcatctt	10	11	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr12:77449722G>A	ENST00000322886.7	-	3	517	c.282C>T	c.(280-282)gcC>gcT	p.A94A	E2F7_ENST00000416496.2_Silent_p.A94A	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	94					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.A94A(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TATCTGGGCTGGCAGCACTAA	0.458																																																2	Substitution - coding silent(2)	large_intestine(2)	12											155	149	151					12																	77449722		2203	4300	6503	75973853	SO:0001819	synonymous_variant	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.282C>T	12.37:g.77449722G>A			75973853	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																				0.458	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		A	77449722	G	A	77449722	2	1	16	1	0	0	0	0	0	0	0	1	4883	1335	47	3		3	E2F7	12	77449722	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10	19439598	77449722	56402173	33	1708			1	2		2	2	32	G		4.205779e-05
E2F7	144455	hgsc.bcm.edu	37	chr12	77449753	77449753	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tgagcatcttcaggttagctGtgggtgtccatggttccgct	13	9	2	1			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr12:77449753G>T	ENST00000322886.7	-	3	486	c.251C>A	c.(250-252)aCa>aAa	p.T84K	E2F7_ENST00000416496.2_Missense_Mutation_p.T84K	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	84					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.T84K(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CAGGTTAGCTGTGGGTGTCCA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	12											158	153	154					12																	77449753		2203	4300	6503	75973884	SO:0001583	missense	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.251C>A	12.37:g.77449753G>T	ENSP00000323246:p.Thr84Lys		75973884	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	G	34	5.354426	0.95830	.	.	ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669;ENST00000547316	D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.92922	0.7748	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.93350	0.6717	10	0.87932	D	0	-21.1697	18.8265	0.92121	0.0:0.0:1.0:0.0	.	84;84	F8VSE7;Q96AV8	.;E2F7_HUMAN	K	84	ENSP00000323246:T84K;ENSP00000393639:T84K;ENSP00000448245:T84K;ENSP00000449033:T84K	ENSP00000323246:T84K	T	-	2	0	E2F7	75973884	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.683000	0.91414	0.650000	0.86243	ACA		0.438	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		T	77449753	G	T	77449753	3	4	16	1	0	0	0	0	1	0	0	0	4883	1377	48	2	2528	2	E2F7	12	77449753	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	31	77449753	56402142	34	1709			1	2		2	2	32	G		4.205779e-05
DGKH	160851	hgsc.bcm.edu	37	chr13	42795478	42795478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gtacaaagatatcttcatccGtcatgacatcagaggggctg	10	9	4	3			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr13:42795478G>A	ENST00000337343.4	+	29	3542	c.3521G>A	c.(3520-3522)cGt>cAt	p.R1174H	DGKH_ENST00000379274.2_Missense_Mutation_p.R1038H|DGKH_ENST00000261491.5_Intron|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000498255.2_Intron|DGKH_ENST00000536612.1_Missense_Mutation_p.R1038H|DGKH_ENST00000540693.1_Intron	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1174	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R1174H(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		ATCTTCATCCGTCATGACATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											201	182	188					13																	42795478		2203	4300	6503	41693478	SO:0001583	missense	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3521G>A	13.37:g.42795478G>A	ENSP00000337572:p.Arg1174His		41693478	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564522	0.86439	.	.	ENSG00000102780	ENST00000337343;ENST00000379274;ENST00000536612	D;D;D	0.85411	-1.98;-1.98;-1.98	5.58	4.74	0.60224	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.585977	0.18731	N	0.132735	D	0.89979	0.6872	L	0.57130	1.785	0.80722	D	1	D;D	0.71674	0.991;0.998	P;D	0.65323	0.891;0.934	D	0.90224	0.4274	10	0.66056	D	0.02	.	14.4946	0.67678	0.0707:0.0:0.9293:0.0	.	1038;1174	Q86XP1-3;Q86XP1	.;DGKH_HUMAN	H	1174;1038;1038	ENSP00000337572:R1174H;ENSP00000368576:R1038H;ENSP00000445114:R1038H	ENSP00000337572:R1174H	R	+	2	0	DGKH	41693478	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.295000	0.78780	1.371000	0.46172	-0.258000	0.10820	CGT		0.418	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42795478	G	A	42795478	3	1	16	1	0	0	0	0	1	0	0	0	4481	1145	40	1	3635	1	DGKH	13	42795478	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		42795478	72374400	35	1710										
PRMT7	54496	hgsc.bcm.edu	37	chr16	68373360	68373360	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	agcaggtcatcgtccctcccGttgacgtggagagctgccct	12	14	1	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr16:68373360G>A	ENST00000339507.5	+	8	1470	c.640G>A	c.(640-642)Gtt>Att	p.V214I	PRMT7_ENST00000449359.3_Missense_Mutation_p.V164I|PRMT7_ENST00000348497.4_Missense_Mutation_p.V140I|PRMT7_ENST00000564441.1_3'UTR|PRMT7_ENST00000441236.1_Missense_Mutation_p.V164I			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	214	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.V214I(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CGTCCCTCCCGTTGACGTGGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											121	94	103					16																	68373360		2198	4300	6498	66930861	SO:0001583	missense	54496			AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"Protein arginine methyltransferases"	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.640G>A	16.37:g.68373360G>A	ENSP00000343103:p.Val214Ile		66930861	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Missense_Mutation	SNP	ENST00000339507.5	37	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	g	7.369	0.626379	0.14257	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.51	-4.68	0.03309	.	1.330100	0.04538	N	0.387670	T	0.07999	0.0200	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31256	0.09;0.141;0.021;0.316	B;B;B;B	0.23852	0.03;0.012;0.002;0.049	T	0.15378	-1.0439	10	0.34782	T	0.22	1.4427	2.7344	0.05236	0.2074:0.1352:0.4502:0.2072	.	164;140;214;214	Q9NVM4-3;Q9NVM4-2;Q9NVM4;Q9NVM4-4	.;.;ANM7_HUMAN;.	I	164;164;140;214	ENSP00000414716:V164I;ENSP00000409324:V164I;ENSP00000345775:V140I;ENSP00000343103:V214I	ENSP00000343103:V214I	V	+	1	0	PRMT7	66930861	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.065000	0.11617	-1.176000	0.02747	-1.068000	0.02270	GTT		0.592	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023		A	68373360	G	A	68373360	3	1	16	1	0	0	0	0	1	0	0	0	12575	1145	40	1	662	1	PRMT7	16	68373360	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		68373360	21981393	36	1711										
EIF5A	1984	hgsc.bcm.edu	37	chr17	7213108	7213108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	cttcgaagactggcaagcacGgccacgccaaggttagaatt	11	11	0	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr17:7213108G>A	ENST00000336458.8	+	2	555	c.154G>A	c.(154-156)Ggc>Agc	p.G52S	EIF5A_ENST00000416016.2_Missense_Mutation_p.G52S|EIF5A_ENST00000336452.7_Missense_Mutation_p.G82S|EIF5A_ENST00000576930.1_Missense_Mutation_p.G52S|EIF5A_ENST00000571955.1_Missense_Mutation_p.G52S|EIF5A_ENST00000419711.2_Missense_Mutation_p.G52S|EIF5A_ENST00000573542.1_Missense_Mutation_p.G52S|EIF5A_ENST00000572815.1_Missense_Mutation_p.G52S	NM_001970.4	NP_001961.1	P63241	IF5A1_HUMAN	eukaryotic translation initiation factor 5A	52	DOHH-binding.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|mRNA export from nucleus (GO:0006406)|nucleocytoplasmic transport (GO:0006913)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|translational frameshifting (GO:0006452)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation elongation factor activity (GO:0003746)|U6 snRNA binding (GO:0017070)	p.G52S(1)		endometrium(2)|kidney(1)|large_intestine(2)|urinary_tract(1)	6						TGGCAAGCACGGCCACGCCAA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											139	123	128					17																	7213108		2203	4300	6503	7153832	SO:0001583	missense	1984				CCDS11099.1, CCDS45601.1	17p13-p12	2009-05-01			ENSG00000132507	ENSG00000132507			3300	protein-coding gene	gene with protein product		600187				7759117	Standard	NM_001143760		Approved	EIF5A1, EIF-5A, MGC99547, MGC104255	uc002gfr.3	P63241	OTTHUMG00000102197	ENST00000336458.8:c.154G>A	17.37:g.7213108G>A	ENSP00000336776:p.Gly52Ser		7153832	A8K9A0|D3DTP2|P10159|Q16182|Q7L7L3|Q7Z4L1|Q9D0G2	Missense_Mutation	SNP	ENST00000336458.8	37	CCDS11099.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283327	0.95489	.	.	ENSG00000132507	ENST00000336452;ENST00000336458;ENST00000419711;ENST00000416016	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	4.55	4.55	0.56014	KOW (1);Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);	0.000000	0.64402	D	0.000002	T	0.77631	0.4159	H	0.97587	4.035	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.61592	0.891;0.889	D	0.86645	0.1894	10	0.87932	D	0	-4.1262	16.2348	0.82365	0.0:0.0:1.0:0.0	.	52;82	P63241;P63241-2	IF5A1_HUMAN;.	S	82;52;52;52	ENSP00000336702:G82S;ENSP00000336776:G52S;ENSP00000390677:G52S;ENSP00000396073:G52S	ENSP00000336702:G82S	G	+	1	0	EIF5A	7153832	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.972000	0.93424	2.380000	0.81148	0.505000	0.49811	GGC		0.537	EIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220047.3	NM_001970		A	7213108	G	A	7213108	3	1	16	1	0	0	0	0	1	0	0	0	5054	1116	39	1	250	1	EIF5A	17	7213108	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		7213108	73982102	37	1712										
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73489892	73489892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	agctcaatggcaagtgcatcGagctggtacaggtgcccggc	14	11	1	0			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr17:73489892G>A	ENST00000314256.7	+	18	2696	c.2302G>A	c.(2302-2304)Gag>Aag	p.E768K	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000579208.1_Missense_Mutation_p.E419K|KIAA0195_ENST00000375248.5_Missense_Mutation_p.E778K	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	768						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.E768K(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAAGTGCATCGAGCTGGTACA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											129	107	114					17																	73489892		2203	4300	6503	71001487	SO:0001583	missense	9772				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.2302G>A	17.37:g.73489892G>A	ENSP00000313885:p.Glu768Lys		71001487	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826697	0.71143	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.51325	0.72;0.71	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.69753	0.3146	M	0.73598	2.24	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.98;0.991;0.98	T	0.68561	-0.5376	10	0.40728	T	0.16	-30.3485	19.2744	0.94026	0.0:0.0:1.0:0.0	.	778;778;768	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	K	768;778	ENSP00000313885:E768K;ENSP00000364397:E778K	ENSP00000313885:E768K	E	+	1	0	KIAA0195	71001487	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	9.755000	0.98912	2.564000	0.86499	0.561000	0.74099	GAG		0.612	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		A	73489892	G	A	73489892	3	1	16	1	0	0	0	0	1	0	0	0	8181	1059	37	1	2368	1	KIAA0195	17	73489892	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10	66276784	73489892	7705318	38	1713										
APOC2	344	hgsc.bcm.edu	37	chr19	45452096	45452096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	gtacgagaagacatacctgcCcgctgtagatgagaaactca	10	10	1	4			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr19:45452096C>T	ENST00000590360.1	+	3	316	c.194C>T	c.(193-195)cCc>cTc	p.P65L	APOC2_ENST00000591597.1_Intron|APOC4_ENST00000419266.2_3'UTR|APOC2_ENST00000592257.1_Silent_p.A44A|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.P142L|APOC2_ENST00000252490.4_Missense_Mutation_p.P65L|APOC2_ENST00000585786.1_Missense_Mutation_p.P65L			P02655	APOC2_HUMAN	apolipoprotein C-II	65	Lipoprotein lipase cofactor.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)	p.P65L(1)		kidney(1)|large_intestine(1)|liver(1)|lung(3)	6	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		ACATACCTGCCCGCTGTAGAT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	95	93					19																	45452096		2203	4300	6503	50143936	SO:0001583	missense	344			X00568	CCDS12650.1	19q13.2	2013-01-24			ENSG00000234906	ENSG00000234906		"Apolipoproteins"	609	protein-coding gene	gene with protein product		608083					Standard	NM_000483		Approved			P02655	OTTHUMG00000180847	ENST00000590360.1:c.194C>T	19.37:g.45452096C>T	ENSP00000466775:p.Pro65Leu		50143936	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000590360.1	37	CCDS12650.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272478	0.23221	.	.	ENSG00000234906	ENST00000252490	T	0.80909	-1.43	4.29	-2.65	0.06095	ApoC-II domain (1);	1.128180	0.06943	U	0.813166	T	0.68265	0.2982	L	0.60455	1.87	0.09310	N	1	B	0.25441	0.126	B	0.22601	0.04	T	0.48163	-0.9059	10	0.11485	T	0.65	-3.2707	1.2448	0.01970	0.2772:0.3998:0.143:0.1801	.	65	P02655	APOC2_HUMAN	L	65	ENSP00000252490:P65L	ENSP00000252490:P65L	P	+	2	0	APOC2	50143936	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.134000	0.15932	-0.557000	0.06126	-0.781000	0.03364	CCC		0.582	APOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453261.1	NM_000483		T	45452096	C	T	45452096	3	4	16	1	0	0	0	0	1	0	0	0	798	623	22	3	200	3	APOC2	19	45452096	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10		45452096	13676887	39	1714										
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485410	54485410	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	ggcccgaagcgggacgaggaGaagaaaaaccactactcgta	13	10	0	2			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr19:54485410G>A	ENST00000270458.2	+	4	688	c.585G>A	c.(583-585)gaG>gaA	p.E195E	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	195					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.E195E(1)		kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGGACGAGGAGAAGAAAAACC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	19											52	42	46					19																	54485410		2202	4299	6501	59177222	SO:0001819	synonymous_variant	59283			AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.585G>A	19.37:g.54485410G>A			59177222	Q9BXT0|Q9BY23	Silent	SNP	ENST00000270458.2	37	CCDS33104.1																																																																																				0.627	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			A	54485410	G	A	54485410	2	1	16	1	0	0	0	0	0	0	0	1	2569	933	33	3		3	CACNG8	19	54485410	Silent	SNP	G	TCGA-AG-3580-01A-01W-0831-10	9033314	54485410	4643573	40	1715										
NINL	22981	hgsc.bcm.edu	37	chr20	25456725	25456725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tttctccagagcccggacgaCgtcttccagatgtagaagtt	10	11	2	3	rs199894600		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr20:25456725C>T	ENST00000278886.6	-	17	3275	c.3202G>A	c.(3202-3204)Gtc>Atc	p.V1068I	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1068					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.V1068I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GCCCGGACGACGTCTTCCAGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	ILE/VAL	0,4406		0,0,2203	122	105	111		3202	-1.7	0	20		111	1,8599	1.2+/-3.3	0,1,4299	no	missense	NINL	NM_025176.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1068/1383	25456725	1,13005	2203	4300	6503	25404725	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3202G>A	20.37:g.25456725C>T	ENSP00000278886:p.Val1068Ile		25404725	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	C	5.566	0.289211	0.10513	0.0	1.16E-4	ENSG00000101004	ENST00000278886	T	0.05649	3.41	4.85	-1.74	0.08056	.	0.693416	0.13792	N	0.362420	T	0.04272	0.0118	L	0.50333	1.59	0.20975	N	0.999811	P	0.36282	0.546	B	0.26864	0.074	T	0.39840	-0.9594	10	0.23891	T	0.37	-4.8659	5.271	0.15624	0.1429:0.3365:0.0:0.5207	.	1068	Q9Y2I6	NINL_HUMAN	I	1068	ENSP00000278886:V1068I	ENSP00000278886:V1068I	V	-	1	0	NINL	25404725	0.001000	0.12720	0.009000	0.14445	0.008000	0.06430	-0.221000	0.09202	-0.288000	0.09051	-0.258000	0.10820	GTC		0.468	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25456725	C	T	25456725	3	4	16	1	0	0	0	0	1	0	0	0	10451	536	19	1	978	1	NINL	20	25456725	Missense_Mutation	SNP	C	TCGA-AG-3580-01A-01W-0831-10		25456725	37568795	41	1716										
CECR1	51816	hgsc.bcm.edu	37	chr22	17690464	17690464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.408762638420799	NA	0.408762638420799	0.444444444444444	1	0	tttctttcaacaacagatgcGcccgtgtttcatctatggat	7	10	4	1	rs151283756	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	65b602ed-5deb-4ca7-92c9-2022f8c63fec	b8472a0d-a2f7-4974-885c-971c5af10664	g.chr22:17690464G>A	ENST00000399839.1	-	2	374	c.104C>T	c.(103-105)gCg>gTg	p.A35V	CECR1_ENST00000399837.2_Missense_Mutation_p.A35V|CECR1_ENST00000262607.3_Missense_Mutation_p.A35V|CECR1_ENST00000449907.2_5'UTR	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	35	Dimerization.				adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.A35V(2)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CAACAGATGCGCCCGTGTTTC	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	22						G	VAL/ALA	0,4406		0,0,2203	49	49	49		104	-1.8	0	22	dbSNP_134	49	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CECR1	NM_017424.2	64	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	35/512	17690464	4,13002	2203	4300	6503	16070464	SO:0001583	missense	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.104C>T	22.37:g.17690464G>A	ENSP00000382733:p.Ala35Val		16070464	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390416	0.25118	0.0	4.65E-4	ENSG00000093072	ENST00000399839;ENST00000262607;ENST00000399837;ENST00000543038;ENST00000441548	T;T;T	0.47177	0.85;0.85;0.85	4.76	-1.79	0.07932	Adenosine/AMP deaminase N-terminal (1);	0.780754	0.12113	N	0.498308	T	0.26122	0.0637	N	0.19112	0.55	0.09310	N	0.999999	B	0.26445	0.149	B	0.12156	0.007	T	0.07271	-1.0781	10	0.44086	T	0.13	.	6.2898	0.21053	0.0:0.2281:0.2995:0.4724	.	35	Q9NZK5	CECR1_HUMAN	V	35	ENSP00000382733:A35V;ENSP00000262607:A35V;ENSP00000382731:A35V	ENSP00000262607:A35V	A	-	2	0	CECR1	16070464	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.105000	0.15333	-0.861000	0.04094	-0.268000	0.10319	GCG		0.552	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			A	17690464	G	A	17690464	3	1	16	1	0	0	0	0	1	0	0	0	3211	1087	38	1	1501	1	CECR1	22	17690464	Missense_Mutation	SNP	G	TCGA-AG-3580-01A-01W-0831-10		17690464	33614102	42	1717										
KAZ	23254	hgsc.bcm.edu	37	chr1	15392195	15392195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tgggattcggctccatctccCgcgtcttcgccagagggaag	13	13	2	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:15392195C>T	ENST00000376030.2	+	8	1462	c.1168C>T	c.(1168-1170)Cgc>Tgc	p.R390C	KAZN_ENST00000400797.3_Missense_Mutation_p.R296C|KAZN_ENST00000503743.1_Missense_Mutation_p.R390C|KAZN_ENST00000400798.2_Missense_Mutation_p.R296C|KAZN_ENST00000361144.5_Missense_Mutation_p.R384C|KAZN_ENST00000422387.2_Missense_Mutation_p.R390C	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	390					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.R384C(2)|p.R390C(2)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CTCCATCTCCCGCGTCTTCGC	0.542																																																4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	1											75	81	79					1																	15392195		2203	4300	6503	15264782	SO:0001583	missense	23254			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1168C>T	1.37:g.15392195C>T	ENSP00000365198:p.Arg390Cys		15264782	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	.	.	.	.	.	.	.	.	.	.	C	18.19	3.570089	0.65765	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387;ENST00000361144;ENST00000400798;ENST00000400797	T	0.36520	1.25	5.39	3.4	0.38934	.	0.057554	0.64402	D	0.000001	T	0.44435	0.1293	L	0.34521	1.04	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.987	T	0.40059	-0.9583	10	0.87932	D	0	-13.5792	8.006	0.30325	0.2976:0.6227:0.0:0.0797	.	390;384;390	Q674X7-2;Q674X7-3;Q674X7	.;.;KAZRN_HUMAN	C	390;390;390;384;296;296	ENSP00000365198:R390C	ENSP00000354727:R384C	R	+	1	0	KAZN	15264782	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.456000	0.53000	1.264000	0.44198	0.305000	0.20034	CGC		0.542	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15392195	C	T	15392195	3	4	17	1	0	0	0	0	1	0	0	0	8009	652	23	1	1410	1	KAZ	1	15392195	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		15392195	233858426	1	1718										
CDCP2	200008	hgsc.bcm.edu	37	chr1	54610171	54610171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ccgcagaaaagccatggctgGccacatgcttgtccgagtgg	13	12	0	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:54610171G>A	ENST00000371330.1	-	2	1242	c.395C>T	c.(394-396)gCc>gTc	p.A132V	RP11-446E24.4_ENST00000311841.7_3'UTR|RP11-446E24.4_ENST00000525949.1_Intron	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	132	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)		p.A132V(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GCCATGGCTGGCCACATGCTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											48	47	47					1																	54610171		2203	4300	6503	54382759	SO:0001583	missense	200008				CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.395C>T	1.37:g.54610171G>A	ENSP00000360381:p.Ala132Val		54382759	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	37	CCDS588.2	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749386	0.69533	.	.	ENSG00000157211	ENST00000371330	T	0.18502	2.21	5.08	5.08	0.68730	CUB (5);	0.000000	0.85682	D	0.000000	T	0.29716	0.0742	L	0.39245	1.2	0.48901	D	0.99972	D	0.76494	0.999	D	0.70227	0.968	T	0.01516	-1.1335	10	0.20519	T	0.43	-34.0806	14.1564	0.65419	0.0:0.1498:0.8501:0.0	.	132	Q5VXM1	CDCP2_HUMAN	V	132	ENSP00000360381:A132V	ENSP00000360381:A132V	A	-	2	0	CDCP2	54382759	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.796000	0.85898	2.366000	0.80165	0.591000	0.81541	GCC		0.607	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		A	54610171	G	A	54610171	3	1	17	1	0	0	0	0	1	0	0	0	3100	1203	42	3	966	3	CDCP2	1	54610171	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	39217976	54610171	194640450	2	1719										
RPE65	6121	hgsc.bcm.edu	37	chr1	68905269	68905269	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	aacgtaagatggcttgaatcGgtcactgcaggggaattgta	13	6	1	2	rs61752895		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:68905269G>A	ENST00000262340.5	-	7	753	c.700C>T	c.(700-702)Cga>Tga	p.R234*		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	234					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)	p.R234*(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						GGCTTGAATCGGTCACTGCAG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	1	GRCh37	CM971315	RPE65	M	rs61752895						181	173	175					1																	68905269		2203	4300	6503	68677857	SO:0001587	stop_gained	6121			U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.700C>T	1.37:g.68905269G>A	ENSP00000262340:p.Arg234*		68677857	A8K1L0|Q5T9U3	Nonsense_Mutation	SNP	ENST00000262340.5	37	CCDS643.1	.	.	.	.	.	.	.	.	.	.	g	37	6.226034	0.97394	.	.	ENSG00000116745	ENST00000262340	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-12.4526	13.0483	0.58939	0.0:0.0:0.734:0.266	rs61752895	.	.	.	X	234	.	ENSP00000262340:R234X	R	-	1	2	RPE65	68677857	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.324000	0.65863	2.748000	0.94277	0.645000	0.84053	CGA		0.393	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		A	68905269	G	A	68905269	4	1	17	1	0	0	0	0	0	1	0	0	13582	1124	39	1	933	1	RPE65	1	68905269	Nonsense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	14295098	68905269	180345352	3	1720										
CD1A	909	hgsc.bcm.edu	37	chr1	158226760	158226760	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gatgggacatggtatctccgCgcaaccctggaggtggccgc	15	12	1	0	rs376991873		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:158226760C>T	ENST00000289429.5	+	4	1322	c.789C>T	c.(787-789)cgC>cgT	p.R263R		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	263	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.R263R(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	GGTATCTCCGCGCAACCCTGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		2,4404	4.2+/-10.8	0,2,2201	93	86	88		789	-6.3	0	1		88	0,8600		0,0,4300	no	coding-synonymous	CD1A	NM_001763.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		263/328	158226760	2,13004	2203	4300	6503	156493384	SO:0001819	synonymous_variant	909			M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.789C>T	1.37:g.158226760C>T			156493384	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Silent	SNP	ENST00000289429.5	37	CCDS1174.1																																																																																				0.632	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		T	158226760	C	T	158226760	2	4	17	1	0	0	0	0	0	0	0	1	2980	755	27	1		1	CD1A	1	158226760	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	89321491	158226760	91023861	4	1721										
PKP1	5317	hgsc.bcm.edu	37	chr1	201282632	201282632	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	aagcaggaccctgtgtatatCccgcccatctcctgcaacaa	7	15	1	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:201282632C>A	ENST00000352845.3	+	3	645	c.645C>A	c.(643-645)atC>atA	p.I215I	PKP1_ENST00000367324.3_Silent_p.I215I|PKP1_ENST00000263946.3_Silent_p.I215I			Q13835	PKP1_HUMAN	plakophilin 1	215					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)	p.I215I(1)		NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						CTGTGTATATCCCGCCCATCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											52	50	51					1																	201282632		2203	4300	6503	199549255	SO:0001819	synonymous_variant	5317			X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.645C>A	1.37:g.201282632C>A			199549255	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																				0.607	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201282632	C	A	201282632	2	1	17	1	0	0	0	0	0	0	0	1	12015	845	30	2		2	PKP1	1	201282632	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	43055872	201282632	47967989	5	1722										
KCNH1	3756	hgsc.bcm.edu	37	chr1	210948826	210948826	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	aggtcaaggccctaacattgGcacaggactgggcaagggtg	15	9	1	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr1:210948826G>T	ENST00000271751.4	-	10	2003	c.1976C>A	c.(1975-1977)gCc>gAc	p.A659D	KCNH1_ENST00000367007.4_Missense_Mutation_p.A632D			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	659					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.A659D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		CCTAACATTGGCACAGGACTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											150	118	129					1																	210948826		2203	4300	6503	209015449	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1976C>A	1.37:g.210948826G>T	ENSP00000271751:p.Ala659Asp		209015449	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722640	0.89298	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.94793	-3.52;-3.52	5.47	5.47	0.80525	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.98030	0.9351	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.98834	1.0752	10	0.87932	D	0	.	19.3371	0.94324	0.0:0.0:1.0:0.0	.	632;659	Q14CL3;O95259	.;KCNH1_HUMAN	D	659;632	ENSP00000271751:A659D;ENSP00000355974:A632D	ENSP00000271751:A659D	A	-	2	0	KCNH1	209015449	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.507000	0.97996	2.567000	0.86603	0.561000	0.74099	GCC		0.522	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210948826	G	T	210948826	3	4	17	1	0	0	0	0	1	0	0	0	8052	1203	42	2	1001	2	KCNH1	1	210948826	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	9666194	210948826	38301795	6	1723										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212530171	212530171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cacagtttgggccatctttaAaatgagagcactttgtacag	9	8	1	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr2:212530171A>T	ENST00000342788.4	-	15	2058	c.1748T>A	c.(1747-1749)tTt>tAt	p.F583Y	ERBB4_ENST00000402597.1_Missense_Mutation_p.F583Y|ERBB4_ENST00000436443.1_Missense_Mutation_p.F583Y	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	583	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.F583Y(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GCCATCTTTAAAATGAGAGCA	0.408										TSP Lung(8;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	2											108	99	102					2																	212530171		2203	4300	6503	212238416	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1748T>A	2.37:g.212530171A>T	ENSP00000342235:p.Phe583Tyr		212238416	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.456|7.456	0.643640|0.643640	0.14451|0.14451	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.44083|.	0.93;0.93;0.93|.	4.94|4.94	4.94|4.94	0.65067|0.65067	Growth factor, receptor (1);|.	0.047167|.	0.85682|.	D|.	0.000000|.	T|T	0.54663|0.54663	0.1872|0.1872	L|L	0.31157|0.31157	0.91|0.91	0.54753|0.54753	D|D	0.999987|0.999987	P;B;B;P;P|.	0.43826|.	0.818;0.027;0.037;0.818;0.722|.	B;B;B;B;B|.	0.42692|.	0.395;0.038;0.017;0.395;0.274|.	T|T	0.51810|0.51810	-0.8658|-0.8658	10|5	0.07482|.	T|.	0.82|.	.|.	14.9157|14.9157	0.70795|0.70795	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	583;583;442;583;583|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	Y|I	583|583	ENSP00000342235:F583Y;ENSP00000403204:F583Y;ENSP00000385565:F583Y|.	ENSP00000342235:F583Y|.	F|L	-|-	2|1	0|2	ERBB4|ERBB4	212238416|212238416	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.269000|7.269000	0.78482|0.78482	1.992000|1.992000	0.58205|0.58205	0.533000|0.533000	0.62120|0.62120	TTT|TTA		0.408	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212530171	A	T	212530171	3	4	17	1	0	0	0	0	1	0	0	0	5222	14	1	5	2234	5	ERBB4	2	212530171	Missense_Mutation	SNP	A	TCGA-AG-3581-01A-01W-0831-10		212530171	30669202	7	1724										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238277702	238277702	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	actctcactttactggggccGatgttgagtcttcgaacaat	9	10	2	1	rs371075249		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr2:238277702G>A	ENST00000295550.4	-	10	4856	c.4404C>T	c.(4402-4404)atC>atT	p.I1468I	COL6A3_ENST00000472056.1_Silent_p.I861I|COL6A3_ENST00000409809.1_Silent_p.I1262I|COL6A3_ENST00000353578.4_Silent_p.I1262I|COL6A3_ENST00000346358.4_Silent_p.I1268I|COL6A3_ENST00000347401.3_Silent_p.I1267I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1468	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.I1468I(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TACTGGGGCCGATGTTGAGTC	0.493													g|||	1	0.000199681	8e-04	0	5008	,	,		19173	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G	,,	0,4406		0,0,2203	65	62	63		4404,2583,3786	-10.6	0.1	2		63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	1468/3178,861/2571,1262/2972	238277702	1,13005	2203	4300	6503	237942441	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4404C>T	2.37:g.238277702G>A			237942441	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.493	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238277702	G	A	238277702	2	1	17	1	0	0	0	0	0	0	0	1	3707	1048	37	1		1	COL6A3	2	238277702	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	25747531	238277702	4921671	8	1725										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1320107	1320107	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gttttccaagatattgaagaCtttgaaactaaaacaagaag	7	5	0	5			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr3:1320107C>G	ENST00000446702.2	+	5	996	c.369C>G	c.(367-369)gaC>gaG	p.D123E	CNTN6_ENST00000539053.1_Missense_Mutation_p.D51E|CNTN6_ENST00000350110.2_Missense_Mutation_p.D123E			Q9UQ52	CNTN6_HUMAN	contactin 6	123	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.D123E(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		ATATTGAAGACTTTGAAACTA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	84	84					3																	1320107		2203	4300	6503	1295107	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.369C>G	3.37:g.1320107C>G	ENSP00000407822:p.Asp123Glu		1295107	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	C	7.095	0.572980	0.13623	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.76316	-1.01;-1.01;-1.01	5.0	2.13	0.27403	Immunoglobulin-like (1);	0.219047	0.31859	N	0.006943	T	0.50309	0.1608	N	0.12527	0.23	0.30587	N	0.761883	B;B	0.06786	0.001;0.001	B;B	0.13407	0.009;0.004	T	0.43491	-0.9388	10	0.02654	T	1	.	5.0747	0.14625	0.1786:0.6414:0.0:0.1799	.	51;123	B4DGV0;Q9UQ52	.;CNTN6_HUMAN	E	123;51;123	ENSP00000407822:D123E;ENSP00000442791:D51E;ENSP00000341882:D123E	ENSP00000341882:D123E	D	+	3	2	CNTN6	1295107	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.125000	0.31332	0.590000	0.29694	-0.142000	0.14014	GAC		0.348	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1320107	C	G	1320107	3	3	17	1	0	0	0	0	1	0	0	0	3651	564	20	5	383	5	CNTN6	3	1320107	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		1320107	196702323	9	1726										
HGD	3081	hgsc.bcm.edu	37	chr3	120357388	120357388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cagcaatggccactccagggCggacagacttagcagtcaat	11	12	1	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr3:120357388C>T	ENST00000283871.5	-	12	1379	c.920G>A	c.(919-921)cGc>cAc	p.R307H		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	307					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)	p.R307H(1)		cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		CACTCCAGGGCGGACAGACTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	3											111	93	100					3																	120357388		2203	4296	6499	121840078	SO:0001583	missense	3081				CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.920G>A	3.37:g.120357388C>T	ENSP00000283871:p.Arg307His		121840078	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	37	CCDS3000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.96|15.96	2.985881|2.985881	0.53934|0.53934	.|.	.|.	ENSG00000113924|ENSG00000113924	ENST00000494453|ENST00000283871	.|D	.|0.98937	.|-5.25	5.36|5.36	5.36|5.36	0.76844|0.76844	.|Cupin, RmlC-type (1);	.|0.131359	.|0.51477	.|D	.|0.000099	D|D	0.95875|0.95875	0.8657|0.8657	N|N	0.17631|0.17631	0.505|0.505	0.58432|0.58432	D|D	0.999998|0.999998	.|B	.|0.16166	.|0.016	.|B	.|0.11329	.|0.006	D|D	0.92709|0.92709	0.6181|0.6181	5|10	.|0.37606	.|T	.|0.19	-17.1833|-17.1833	16.4102|16.4102	0.83708|0.83708	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|307	.|Q93099	.|HGD_HUMAN	T|H	114|307	.|ENSP00000283871:R307H	.|ENSP00000283871:R307H	A|R	-|-	1|2	0|0	HGD|HGD	121840078|121840078	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.991000|0.991000	0.79684|0.79684	4.267000|4.267000	0.58877|0.58877	2.797000|2.797000	0.96272|0.96272	0.563000|0.563000	0.77884|0.77884	GCC|CGC		0.483	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			T	120357388	C	T	120357388	3	4	17	1	0	0	0	0	1	0	0	0	7105	768	27	1	429	1	HGD	3	120357388	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	119037281	120357388	77665042	10	1727										
CLOCK	9575	hgsc.bcm.edu	37	chr4	56336967	56336967	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gattgctaaaaaaaaaccatCaagagcctgaaattaaacat	5	7	1	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr4:56336967C>T	ENST00000309964.4	-	7	605	c.355G>A	c.(355-357)Gat>Aat	p.D119N	CLOCK_ENST00000381322.1_Missense_Mutation_p.D119N|CLOCK_ENST00000513440.1_Missense_Mutation_p.D119N	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	119	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.D119N(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			AAAAAACCATCAAGAGCCTGA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	88	86					4																	56336967		2201	4298	6499	56031724	SO:0001583	missense	9575			AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.355G>A	4.37:g.56336967C>T	ENSP00000308741:p.Asp119Asn		56031724	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	C	35	5.422042	0.96111	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.19105	2.17;2.17;2.17	5.58	5.58	0.84498	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	L	0.49455	1.56	0.80722	D	1	P	0.40638	0.725	P	0.58620	0.842	T	0.04693	-1.0933	10	0.56958	D	0.05	.	19.9348	0.97133	0.0:1.0:0.0:0.0	.	119	O15516	CLOCK_HUMAN	N	119	ENSP00000308741:D119N;ENSP00000370723:D119N;ENSP00000426983:D119N	ENSP00000308741:D119N	D	-	1	0	CLOCK	56031724	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.228000	0.78079	2.789000	0.95967	0.591000	0.81541	GAT		0.274	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		T	56336967	C	T	56336967	3	4	17	1	0	0	0	0	1	0	0	0	3555	826	29	3	2249	3	CLOCK	4	56336967	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		56336967	134817309	11	1728										
SLC7A11	23657	hgsc.bcm.edu	37	chr4	139093116	139093117	+	Frame_Shift_Ins	INS	-	-	T													0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	caagtccattagttcataacINSttatcttcttctggtacaac							TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr4:139093116_139093117insT	ENST00000280612.5	-	12	1778_1779	c.1499_1500insA	c.(1498-1500)aagfs	p.K500fs	SLC7A11-AS1_ENST00000510767.1_RNA|SLC7A11-AS1_ENST00000512538.1_RNA|SLC7A11-AS1_ENST00000512786.1_RNA	NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	500					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)	p.L501fs*>2(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	TAGTTCATAACTTATCTTCTTC	0.312																																																1	Insertion - Frameshift(1)	large_intestine(1)	4																																								139312567	SO:0001589	frameshift_variant	23657			AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"Solute carriers"	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.1500dupA	4.37:g.139093118_139093118dupT	ENSP00000280612:p.Lys500fs		139312566	A8K2U4	Frame_Shift_Ins	INS	ENST00000280612.5	37	CCDS3742.1																																																																																				0.312	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2			T	139093117	-	T	139093116	7	5	17	1	0	1	1	0	0	0	0	0	14731	564	20	0	9	0	SLC7A11	4	139093116	Frame_Shift_Ins	INS	-	TCGA-AG-3581-01A-01W-0831-10	82756149	139093116	52061160	12	1729										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109049312	109049312	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ctcaaatattagagactcagTcatcaatttgagtgagtctg	8	7	5	3			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr5:109049312T>A	ENST00000261483.4	+	2	1279	c.227T>A	c.(226-228)gTc>gAc	p.V76D		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	76					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.V76D(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AGAGACTCAGTCATCAATTTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											113	105	108					5																	109049312		2202	4300	6502	109077211	SO:0001583	missense	4124				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.227T>A	5.37:g.109049312T>A	ENSP00000261483:p.Val76Asp		109077211	Q16767	Missense_Mutation	SNP	ENST00000261483.4	37	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.672691	0.88445	.	.	ENSG00000112893	ENST00000261483	D	0.81908	-1.55	5.43	5.43	0.79202	.	0.131690	0.50627	D	0.000118	D	0.88768	0.6526	M	0.79693	2.465	0.80722	D	1	P	0.44776	0.843	P	0.51701	0.677	D	0.90369	0.4379	10	0.87932	D	0	-11.4362	15.5213	0.75869	0.0:0.0:0.0:1.0	.	76	Q16706	MA2A1_HUMAN	D	76	ENSP00000261483:V76D	ENSP00000261483:V76D	V	+	2	0	MAN2A1	109077211	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.392000	0.73213	2.081000	0.62600	0.477000	0.44152	GTC		0.423	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			A	109049312	T	A	109049312	3	1	17	1	0	0	0	0	1	0	0	0	9244	1667	58	5	233	5	MAN2A1	5	109049312	Missense_Mutation	SNP	T	TCGA-AG-3581-01A-01W-0831-10		109049312	71865948	13	1730										
APC	324	hgsc.bcm.edu	37	chr5	112164616	112164616	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	taaatagtaaaaagacgttgCgagaagttggaagtgtgaaa	12	2	0	3	rs137854574		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr5:112164616C>T	ENST00000457016.1	+	14	2070	c.1690C>T	c.(1690-1692)Cga>Tga	p.R564*	APC_ENST00000508376.2_Nonsense_Mutation_p.R564*|CTC-554D6.1_ENST00000520401.1_Silent_p.C59C|APC_ENST00000257430.4_Nonsense_Mutation_p.R564*			P25054	APC_HUMAN	adenomatous polyposis coli	564	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R564*(14)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGACGTTGCGAGAAGTTGG	0.313		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(14)|Unknown(1)	large_intestine(14)|skin(1)	5	GRCh37	CM920035	APC	M	rs137854574						126	137	134					5																	112164616		2202	4300	6502	112192515	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1690C>T	5.37:g.112164616C>T	ENSP00000413133:p.Arg564*		112192515	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	7.921767	0.98563	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.62	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3959	14.5777	0.68262	0.2726:0.7274:0.0:0.0	.	.	.	.	X	564;546;564;564;564	.	ENSP00000257430:R564X	R	+	1	2	APC	112192515	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.526000	0.45607	1.313000	0.45069	0.655000	0.94253	CGA		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112164616	C	T	112164616	4	4	17	1	0	0	0	0	0	1	0	0	763	760	27	1	1740	1	APC	5	112164616	Nonsense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	3115304	112164616	68750644	14	1731										
PAIP2	51247	hgsc.bcm.edu	37	chr5	138699557	138699557	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ggtcattctcatgaagatgaCaatccatttgcagagtacat	8	8	2	4			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr5:138699557C>G	ENST00000394795.2	+	2	1075	c.84C>G	c.(82-84)gaC>gaG	p.D28E	PAIP2_ENST00000511706.1_Missense_Mutation_p.D28E|PAIP2_ENST00000511381.1_Intron|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000510080.1_Missense_Mutation_p.D28E|PAIP2_ENST00000265192.4_Missense_Mutation_p.D28E			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	28	PABPC1-interacting motif-1 (PAM1).				memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)	p.D28E(1)		kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATGAAGATGACAATCCATTTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											139	122	128					5																	138699557		2203	4300	6503	138727456	SO:0001583	missense	51247			AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.84C>G	5.37:g.138699557C>G	ENSP00000378275:p.Asp28Glu		138727456	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.778300	0.31502	.	.	ENSG00000120727	ENST00000507755;ENST00000265192;ENST00000511706;ENST00000394795;ENST00000510080	.	.	.	5.87	3.07	0.35406	.	0.057693	0.64402	D	0.000002	T	0.38852	0.1056	L	0.42245	1.32	0.35773	D	0.821064	B	0.32753	0.383	B	0.33339	0.162	T	0.35748	-0.9776	9	0.10902	T	0.67	-18.6493	9.0698	0.36486	0.0:0.6358:0.0:0.3642	.	28	Q9BPZ3	PAIP2_HUMAN	E	28	.	ENSP00000265192:D28E	D	+	3	2	PAIP2	138727456	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.937000	0.28951	0.915000	0.36847	0.655000	0.94253	GAC		0.388	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480		G	138699557	C	G	138699557	3	3	17	1	0	0	0	0	1	0	0	0	11428	477	17	5	86	5	PAIP2	5	138699557	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	26534941	138699557	42215703	15	1732										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140855826	140855826	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	agagaagggtttcgctgtggGcaacgtggtcgcgaaccttg	16	8	0	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr5:140855826G>C	ENST00000308177.3	+	1	247	c.143G>C	c.(142-144)gGc>gCc	p.G48A	PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	48	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G48A(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCGCTGTGGGCAACGTGGTC	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	5											146	150	149					5																	140855826		2203	4300	6503	140836010	SO:0001583	missense	5098			AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.143G>C	5.37:g.140855826G>C	ENSP00000312070:p.Gly48Ala		140836010	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	37	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723382	0.68959	.	.	ENSG00000240184	ENST00000308177	T	0.36878	1.23	5.65	4.78	0.61160	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.55465	0.1922	L	0.59436	1.845	0.40497	D	0.980606	D;D	0.69078	0.997;0.994	D;D	0.69824	0.966;0.91	T	0.61367	-0.7077	9	0.87932	D	0	.	14.6984	0.69139	0.0687:0.0:0.9313:0.0	.	48;48	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	A	48	ENSP00000312070:G48A	ENSP00000312070:G48A	G	+	2	0	PCDHGC3	140836010	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.816000	0.86201	1.636000	0.50526	-0.136000	0.14681	GGC		0.557	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140855826	G	C	140855826	3	2	17	1	0	0	0	0	1	0	0	0	11600	1203	42	5	145	5	PCDHGC3	5	140855826	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	2156269	140855826	40059434	16	1733										
STK10	6793	hgsc.bcm.edu	37	chr5	171544539	171544539	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gttgccagctttcagatctcGgtggatgatcctcttgctgt	11	10	3	2	rs199657750		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr5:171544539G>A	ENST00000176763.5	-	4	809	c.466C>T	c.(466-468)Cga>Tga	p.R156*		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.R156*(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTCAGATCTCGGTGGATGATC	0.592													G|||	1	0.000199681	0	0	5008	,	,		13892	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	5											109	92	98					5																	171544539		2203	4300	6503	171477144	SO:0001587	stop_gained	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.466C>T	5.37:g.171544539G>A	ENSP00000176763:p.Arg156*		171477144	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Nonsense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	40	8.467876	0.98825	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0851	0.53691	0.0:0.0:0.8282:0.1718	.	.	.	.	X	156	.	ENSP00000176763:R156X	R	-	1	2	STK10	171477144	1.000000	0.71417	0.995000	0.50966	0.972000	0.66771	2.918000	0.48829	2.619000	0.88677	0.563000	0.77884	CGA		0.592	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171544539	G	A	171544539	4	1	17	1	0	0	0	0	0	1	0	0	15325	1124	39	1	2504	1	STK10	5	171544539	Nonsense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	30688713	171544539	9370721	17	1734										
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37429332	37429332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gctctcatttcagggtttctCggtggaggggcaggagaacc	15	9	3	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr6:37429332C>T	ENST00000373451.4	+	11	1267	c.1103C>T	c.(1102-1104)tCg>tTg	p.S368L	CMTR1_ENST00000493656.1_3'UTR	NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	368	RrmJ-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00945}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.S368L(1)									CAGGGTTTCTCGGTGGAGGGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	6											102	99	100					6																	37429332		2203	4300	6503	37537310	SO:0001583	missense	23070			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1103C>T	6.37:g.37429332C>T	ENSP00000362550:p.Ser368Leu		37537310	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	37	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522778	0.96431	.	.	ENSG00000137200	ENST00000373451;ENST00000455891;ENST00000373427	T;T	0.30981	1.51;1.51	5.64	5.64	0.86602	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;0.989	D;P	0.75020	0.985;0.875	T	0.48115	-0.9063	10	0.51188	T	0.08	-8.5268	18.6931	0.91590	0.0:1.0:0.0:0.0	.	312;368	Q5T7F5;Q8N1G2	.;MTR1_HUMAN	L	368;312;312	ENSP00000362550:S368L;ENSP00000414233:S312L	ENSP00000362526:S312L	S	+	2	0	FTSJD2	37537310	1.000000	0.71417	0.975000	0.42487	0.992000	0.81027	7.626000	0.83164	2.655000	0.90218	0.591000	0.81541	TCG		0.507	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		T	37429332	C	T	37429332	3	4	17	1	0	0	0	0	1	0	0	0	6110	893	31	1	1141	1	FTSJD2	6	37429332	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		37429332	133685735	18	1735										
HTR1E	3354	hgsc.bcm.edu	37	chr6	87725676	87725676	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tattaccggatttaccacgcGgccaagagcctttaccagaa	8	12	0	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr6:87725676G>A	ENST00000305344.5	+	2	1327	c.624G>A	c.(622-624)gcG>gcA	p.A208A		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	208			A -> T (in dbSNP:rs3828741).		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.A208A(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	TTTACCACGCGGCCAAGAGCC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6											89	88	89					6																	87725676		2203	4300	6503	87782395	SO:0001819	synonymous_variant	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.624G>A	6.37:g.87725676G>A			87782395	E1P503|Q9P1Y1	Silent	SNP	ENST00000305344.5	37	CCDS5006.1																																																																																				0.443	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		A	87725676	G	A	87725676	2	1	17	1	0	0	0	0	0	0	0	1	7460	1103	39	1		1	HTR1E	6	87725676	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	50296344	87725676	83389391	19	1736										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152786552	152786552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gagagattcctccactgagcGgtggtttcattcatgaattt	10	8	2	3	rs577191787		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr6:152786552G>A	ENST00000367255.5	-	18	2374	c.1773C>T	c.(1771-1773)acC>acT	p.T591T	SYNE1_ENST00000423061.1_Silent_p.T598T|SYNE1_ENST00000495090.2_Silent_p.T158T|SYNE1_ENST00000413186.2_Silent_p.T591T|SYNE1_ENST00000367248.3_Silent_p.T581T|SYNE1_ENST00000341594.5_Silent_p.T598T|SYNE1_ENST00000466159.2_Silent_p.T591T|SYNE1_ENST00000367253.4_Silent_p.T591T|SYNE1_ENST00000265368.4_Silent_p.T591T|SYNE1_ENST00000448038.1_Silent_p.T598T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	591					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.T591T(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCCACTGAGCGGTGGTTTCAT	0.418										HNSCC(10;0.0054)			G|||	0	0	0	0	5008	,	,		17904	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	6											110	94	100					6																	152786552		2203	4300	6503	152828245	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.1773C>T	6.37:g.152786552G>A			152828245	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.418	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152786552	G	A	152786552	2	1	17	1	0	0	0	0	0	0	0	1	15484	1103	39	1		1	SYNE1	6	152786552	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	65060876	152786552	18328515	20	1737										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133933772	133933772	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ttagaagaactctggaaaagTtttgatctttgtgaagacta	9	4	2	5			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr7:133933772T>G	ENST00000285928.2	+	18	2211	c.2142T>G	c.(2140-2142)agT>agG	p.S714R		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	714						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)	p.S714R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						TCTGGAAAAGTTTTGATCTTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	92	91					7																	133933772		2203	4300	6503	133584312	SO:0001583	missense	136332			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.2142T>G	7.37:g.133933772T>G	ENSP00000285928:p.Ser714Arg		133584312	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	T	9.186	1.024881	0.19433	.	.	ENSG00000155530	ENST00000285928	T	0.36157	1.27	4.52	-2.23	0.06930	.	0.907551	0.09586	N	0.782176	T	0.19327	0.0464	L	0.27053	0.805	0.09310	N	1	B	0.26002	0.139	B	0.22386	0.039	T	0.26985	-1.0087	10	0.72032	D	0.01	0.052	0.9252	0.01323	0.1541:0.1819:0.3185:0.3455	.	714	Q96M69	LRGUK_HUMAN	R	714	ENSP00000285928:S714R	ENSP00000285928:S714R	S	+	3	2	LRGUK	133584312	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.124000	0.10595	-0.359000	0.08150	-0.341000	0.08007	AGT		0.368	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		G	133933772	T	G	133933772	3	3	17	1	0	0	0	0	1	0	0	0	8972	1722	60	4	2212	4	LRGUK	7	133933772	Missense_Mutation	SNP	T	TCGA-AG-3581-01A-01W-0831-10		133933772	25204891	21	1738										
FAM180A	389558	hgsc.bcm.edu	37	chr7	135433277	135433277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gctccacctgtggcacatagAagcctcagcattgtaataca	8	12	1	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr7:135433277A>G	ENST00000338588.3	-	1	317	c.52T>C	c.(52-54)Tct>Cct	p.S18P	FAM180A_ENST00000415751.1_Missense_Mutation_p.S18P|FAM180A_ENST00000435869.1_5'UTR	NM_205855.3	NP_995327.1	Q6UWF9	F180A_HUMAN	family with sequence similarity 180, member A	18						extracellular region (GO:0005576)		p.S18P(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)	14						TGGCACATAGAAGCCTCAGCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	7											211	214	213					7																	135433277		2203	4300	6503	135083817	SO:0001583	missense	389558			AC091736, AK290250, AK310180, AY358803	CCDS5841.1	7q33	2008-07-25			ENSG00000189320	ENSG00000189320			33773	protein-coding gene	gene with protein product						12975309, 12690205	Standard	NM_205855		Approved	HWKM1940, UNQ1940	uc003vtd.3	Q6UWF9	OTTHUMG00000155537	ENST00000338588.3:c.52T>C	7.37:g.135433277A>G	ENSP00000342336:p.Ser18Pro		135083817	B2RP85	Missense_Mutation	SNP	ENST00000338588.3	37	CCDS5841.1	.	.	.	.	.	.	.	.	.	.	A	2.808	-0.247625	0.05867	.	.	ENSG00000189320	ENST00000338588;ENST00000415751	T;T	0.31247	1.5;1.5	5.19	2.77	0.32553	.	0.566902	0.18713	N	0.133256	T	0.12689	0.0308	N	0.08118	0	0.09310	N	1	B	0.29716	0.255	B	0.26416	0.069	T	0.17961	-1.0352	10	0.30078	T	0.28	-26.2472	4.7154	0.12893	0.1732:0.0919:0.0:0.7349	.	18	Q6UWF9	F180A_HUMAN	P	18	ENSP00000342336:S18P;ENSP00000395467:S18P	ENSP00000342336:S18P	S	-	1	0	FAM180A	135083817	0.436000	0.25586	0.013000	0.15412	0.014000	0.08584	0.575000	0.23729	0.366000	0.24427	-0.357000	0.07601	TCT		0.423	FAM180A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340554.2	NM_205855		G	135433277	A	G	135433277	3	3	17	1	0	0	0	0	1	0	0	0	5523	246	9	4	481	4	FAM180A	7	135433277	Missense_Mutation	SNP	A	TCGA-AG-3581-01A-01W-0831-10	1499505	135433277	23705386	22	1739										
CTSB	1508	hgsc.bcm.edu	37	chr8	11703285	11703285	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cccatcatctctccggtgacGtgttggtacactcctgaaaa	8	13	2	2	rs202010757	byFrequency	TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr8:11703285G>C	ENST00000353047.6	-	9	1060	c.807C>G	c.(805-807)caC>caG	p.H269Q	CTSB_ENST00000533455.1_Missense_Mutation_p.H269Q|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000345125.3_Missense_Mutation_p.H269Q|CTSB_ENST00000434271.1_Missense_Mutation_p.H269Q|CTSB_ENST00000531089.1_Missense_Mutation_p.H269Q|CTSB_ENST00000415599.2_3'UTR|CTSB_ENST00000453527.2_Missense_Mutation_p.H269Q|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000534510.1_Missense_Mutation_p.H269Q|CTSB_ENST00000530640.2_Missense_Mutation_p.H269Q	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	269					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.H269Q(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		CTCCGGTGACGTGTTGGTACA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	8											99	72	81					8																	11703285		2203	4300	6503	11740694	SO:0001583	missense	1508			M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.807C>G	8.37:g.11703285G>C	ENSP00000345672:p.His269Gln		11740694	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.679334	0.29783	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	D;D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	5.19	-4.69	0.03299	Peptidase C1A, papain C-terminal (2);	0.087198	0.85682	D	0.000000	D	0.92616	0.7654	M	0.87328	2.875	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;P;D;D	0.97110	1.0;0.834;0.993;0.999	D	0.91982	0.5595	10	0.72032	D	0.01	.	15.7027	0.77555	0.7645:0.0:0.2355:0.0	.	206;269;269;206	B3KUJ8;A8K2H4;P07858;F5H2P9	.;.;CATB_HUMAN;.	Q	269;206;269;269;269;269;269;269;269;175	ENSP00000415889:H269Q;ENSP00000345672:H269Q;ENSP00000435105:H269Q;ENSP00000433215:H269Q;ENSP00000409917:H269Q;ENSP00000342070:H269Q;ENSP00000432244:H269Q;ENSP00000434217:H269Q	ENSP00000342070:H269Q	H	-	3	2	CTSB	11740694	0.000000	0.05858	0.010000	0.14722	0.071000	0.16799	-0.860000	0.04272	-0.756000	0.04703	-0.137000	0.14449	CAC		0.617	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		C	11703285	G	C	11703285	3	2	17	1	0	0	0	0	1	0	0	0	4036	1136	40	5	220	5	CTSB	8	11703285	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10		11703285	134660737	23	1740										
ELP3	55140	hgsc.bcm.edu	37	chr8	28047218	28047218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ggctacagattacaaggcccGtacatggtgaagatgctgaa	12	8	0	4	rs149193033	byFrequency	TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr8:28047218G>A	ENST00000256398.8	+	15	1997	c.1620G>A	c.(1618-1620)ccG>ccA	p.P540P	ELP3_ENST00000524103.1_Silent_p.P468P|ELP3_ENST00000537665.1_Silent_p.P421P|ELP3_ENST00000521015.1_Silent_p.P526P|ELP3_ENST00000542181.1_Silent_p.P411P|ELP3_ENST00000380353.4_Silent_p.P448P	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	540	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)	p.P540P(1)		kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		TACAAGGCCCGTACATGGTGA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	8						G		0,4406		0,0,2203	135	136	136		1620	-9.9	0.9	8	dbSNP_134	136	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ELP3	NM_018091.5		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		540/548	28047218	2,13004	2203	4300	6503	28103137	SO:0001819	synonymous_variant	55140				CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.1620G>A	8.37:g.28047218G>A			28103137	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Silent	SNP	ENST00000256398.8	37	CCDS6065.1																																																																																				0.433	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		A	28047218	G	A	28047218	2	1	17	1	0	0	0	0	0	0	0	1	5094	1132	40	1		1	ELP3	8	28047218	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	16343933	28047218	118316804	24	1741										
APBA1	320	hgsc.bcm.edu	37	chr9	72130950	72130950	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tccgtccatcggcctctggtCgtcacagtccctggtggggc	13	15	2	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr9:72130950C>T	ENST00000265381.4	-	2	1399	c.1177G>A	c.(1177-1179)Gac>Aac	p.D393N		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	393	LIN-2/CASK binding.|Pro-rich.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.D393N(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						GGCCTCTGGTCGTCACAGTCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	105	111					9																	72130950		2203	4300	6503	71320770	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1177G>A	9.37:g.72130950C>T	ENSP00000265381:p.Asp393Asn		71320770	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.916208	0.73098	.	.	ENSG00000107282	ENST00000265381	T	0.04317	3.65	5.95	5.95	0.96441	.	0.133496	0.52532	D	0.000071	T	0.07143	0.0181	N	0.24115	0.695	0.52099	D	0.999947	D	0.63046	0.992	P	0.48334	0.574	T	0.51841	-0.8654	10	0.21014	T	0.42	-26.3813	20.3932	0.98965	0.0:1.0:0.0:0.0	.	393	Q02410	APBA1_HUMAN	N	393	ENSP00000265381:D393N	ENSP00000265381:D393N	D	-	1	0	APBA1	71320770	1.000000	0.71417	0.959000	0.39883	0.980000	0.70556	3.990000	0.56965	2.824000	0.97209	0.655000	0.94253	GAC		0.637	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72130950	C	T	72130950	3	4	17	1	0	0	0	0	1	0	0	0	756	884	31	1	1384	1	APBA1	9	72130950	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		72130950	69082481	25	1742										
S1PR3	1903	hgsc.bcm.edu	37	chr9	91616761	91616761	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tgaccatcgtgatcctctacGcacgcatctacttcctggtg	8	14	2	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr9:91616761G>A	ENST00000375846.3	+	1	5341	c.646G>A	c.(646-648)Gca>Aca	p.A216T	S1PR3_ENST00000358157.2_Missense_Mutation_p.A216T			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	216					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.A216T(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GATCCTCTACGCACGCATCTA	0.567											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	9											153	122	133					9																	91616761		2203	4300	6503	90806581	SO:0001583	missense	1903			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.646G>A	9.37:g.91616761G>A	ENSP00000365006:p.Ala216Thr	1283	90806581	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	37	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591697	0.46214	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.71341	-0.56;-0.56	5.11	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.121890	0.56097	D	0.000038	T	0.67088	0.2856	L	0.42581	1.335	0.53688	D	0.999979	D	0.53885	0.963	P	0.48795	0.59	T	0.64141	-0.6477	10	0.33141	T	0.24	.	12.1727	0.54167	0.1397:0.0:0.8603:0.0	.	216	Q99500	S1PR3_HUMAN	T	216	ENSP00000350878:A216T;ENSP00000365006:A216T	ENSP00000350878:A216T	A	+	1	0	S1PR3	90806581	1.000000	0.71417	0.040000	0.18447	0.653000	0.38743	6.379000	0.73154	0.844000	0.35094	0.561000	0.74099	GCA		0.567	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		A	91616761	G	A	91616761	3	1	17	1	0	0	0	0	1	0	0	0	13832	1087	38	1	648	1	S1PR3	9	91616761	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	19485811	91616761	49596670	26	1743										
THNSL1	79896	hgsc.bcm.edu	37	chr10	25313675	25313675	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	agtcgatgtctgtattcccaCaggaaactttggtaacattt	8	8	1	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr10:25313675C>T	ENST00000524413.1	+	3	1870	c.1523C>T	c.(1522-1524)aCa>aTa	p.T508I	THNSL1_ENST00000376356.4_Missense_Mutation_p.T508I			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	508						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.T508I(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TGTATTCCCACAGGAAACTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											78	80	80					10																	25313675		2203	4300	6503	25353681	SO:0001583	missense	79896			AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1523C>T	10.37:g.25313675C>T	ENSP00000434887:p.Thr508Ile		25353681	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860685	0.71834	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	D;D	0.96365	-3.99;-3.99	5.94	5.94	0.96194	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.98966	0.9648	H	0.97340	3.985	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.99056	1.0829	10	0.87932	D	0	-27.8639	20.3633	0.98874	0.0:1.0:0.0:0.0	.	508	Q8IYQ7	THNS1_HUMAN	I	508	ENSP00000434887:T508I;ENSP00000365534:T508I	ENSP00000365534:T508I	T	+	2	0	THNSL1	25353681	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.075000	0.76798	2.826000	0.97356	0.561000	0.74099	ACA		0.403	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		T	25313675	C	T	25313675	3	4	17	1	0	0	0	0	1	0	0	0	15901	478	17	3	1525	3	THNSL1	10	25313675	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		25313675	110221072	27	1744										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26455008	26455008	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	attccaaggtactaccttctCtgctacaagtcgagcgagga	9	11	1	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr10:26455008C>T	ENST00000265944.5	+	27	3178	c.3012C>T	c.(3010-3012)ctC>ctT	p.L1004L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1004	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1004L(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ACTACCTTCTCTGCTACAAGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	10											167	178	175					10																	26455008		2203	4300	6503	26495014	SO:0001819	synonymous_variant	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3012C>T	10.37:g.26455008C>T			26495014	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																				0.493	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26455008	C	T	26455008	2	4	17	1	0	0	0	0	0	0	0	1	10106	900	32	3		3	MYO3A	10	26455008	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	1141333	26455008	109079739	28	1745										
MARCH8	220972	hgsc.bcm.edu	37	chr10	46028575	46028575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tacctgttcttccctctcctTttctttggtcttacttctgt	4	13	5	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr10:46028575T>C	ENST00000319836.3	-	2	834	c.85A>G	c.(85-87)Aag>Gag	p.K29E	MARCH8_ENST00000395771.3_Missense_Mutation_p.K29E|MARCH8_ENST00000453424.2_Missense_Mutation_p.K29E|MARCH8_ENST00000395769.2_Missense_Mutation_p.K29E	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	29					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K29E(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						TCCCTCTCCTTTTCTTTGGTC	0.388																																					NSCLC(102;658 1594 2173 16344 34808)											1	Substitution - Missense(1)	large_intestine(1)	10											117	108	111					10																	46028575		2203	4300	6503	45348581	SO:0001583	missense	220972			AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	23356	protein-coding gene	gene with protein product		613335	"c-mir, cellular modulator of immune recognition", "membrane-associated ring finger (C3HC4) 8"	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.85A>G	10.37:g.46028575T>C	ENSP00000317087:p.Lys29Glu		45348581	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463202	0.63513	.	.	ENSG00000165406	ENST00000395771;ENST00000319836;ENST00000395769;ENST00000453980	T;T;T	0.12774	2.65;2.65;2.65	5.04	5.04	0.67666	.	.	.	.	.	T	0.17577	0.0422	L	0.47716	1.5	0.31473	N	0.668162	D	0.57257	0.979	P	0.51777	0.679	T	0.01195	-1.1422	9	0.08599	T	0.76	.	11.1647	0.48537	0.0:0.0:0.0:1.0	.	29	Q5T0T0	MARH8_HUMAN	E	29	ENSP00000379118:K29E;ENSP00000317087:K29E;ENSP00000379116:K29E	ENSP00000317087:K29E	K	-	1	0	MARCH8	45348581	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.393000	0.66279	1.884000	0.54569	0.460000	0.39030	AAG		0.388	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021		C	46028575	T	C	46028575	3	2	17	1	0	0	0	0	1	0	0	0	9337	1850	64	4	814	4	MARCH8	10	46028575	Missense_Mutation	SNP	T	TCGA-AG-3581-01A-01W-0831-10	19573567	46028575	89506172	29	1746										
PTPRE	5791	hgsc.bcm.edu	37	chr10	129861358	129861358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tacacacaggtcccaaacagGaaacggttaacgacttctgg	9	11	1	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr10:129861358G>A	ENST00000254667.3	+	10	916	c.637G>A	c.(637-639)Gaa>Aaa	p.E213K	PTPRE_ENST00000430713.2_3'UTR|PTPRE_ENST00000419012.2_Missense_Mutation_p.E213K|PTPRE_ENST00000306042.5_Missense_Mutation_p.E155K	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	213	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E213K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	TCCCAAACAGGAAACGGTTAA	0.522																																					Colon(52;977 1184 20575 41685)											1	Substitution - Missense(1)	large_intestine(1)	10											96	87	90					10																	129861358		2203	4300	6503	129751348	SO:0001583	missense	5791			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.637G>A	10.37:g.129861358G>A	ENSP00000254667:p.Glu213Lys		129751348	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Missense_Mutation	SNP	ENST00000254667.3	37	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835253	0.91117	.	.	ENSG00000132334	ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042	T;T;T	0.12147	2.71;2.71;2.71	4.38	4.38	0.52667	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.062472	0.64402	U	0.000008	T	0.20210	0.0486	L	0.49640	1.575	0.80722	D	1	P;P;P;P	0.40909	0.732;0.615;0.561;0.615	B;B;B;B	0.44315	0.446;0.211;0.095;0.211	T	0.02064	-1.1220	10	0.87932	D	0	.	16.4948	0.84237	0.0:0.0:1.0:0.0	.	191;213;155;213	F5H0X4;Q5VWH4;P23469-2;P23469	.;.;.;PTPRE_HUMAN	K	213;191;213;155	ENSP00000254667:E213K;ENSP00000402337:E213K;ENSP00000303350:E155K	ENSP00000254667:E213K	E	+	1	0	PTPRE	129751348	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.378000	0.97191	2.433000	0.82419	0.563000	0.77884	GAA		0.522	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			A	129861358	G	A	129861358	3	1	17	1	0	0	0	0	1	0	0	0	12837	1175	41	3	706	3	PTPRE	10	129861358	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	83832783	129861358	5673389	30	1747										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5537034	5537034	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cagaattatcaagaagaaggCgggaaacttctgggttctgc	12	7	3	3	rs147885423	byFrequency	TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr11:5537034C>T	ENST00000380184.1	-	1	901	c.638G>A	c.(637-639)cGc>cAc	p.R213H	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	213								p.R213H(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		AAGAAGAAGGCGGGAAACTTC	0.463													c|||	7	0.00139776	0	0	5008	,	,		21105	0.001		0	False		,,,				2504	0.0061															1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	124	128	127		638	2.7	0	11	dbSNP_134	127	4,8590	3.7+/-12.6	0,4,4293	yes	missense	UBQLNL	NM_145053.4	29	0,5,6493	TT,TC,CC		0.0465,0.0227,0.0385	benign	213/476	5537034	5,12991	2201	4297	6498	5493610	SO:0001583	missense	143630			AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.638G>A	11.37:g.5537034C>T	ENSP00000369531:p.Arg213His		5493610	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.004	-2.342822	0.00222	2.27E-4	4.65E-4	ENSG00000175518	ENST00000380184	T	0.35605	1.3	5.05	2.71	0.32032	.	0.243046	0.29192	N	0.012869	T	0.06735	0.0172	N	0.00179	-1.91	0.20638	N	0.999877	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	10	0.02654	T	1	-12.1084	6.8781	0.24158	0.0:0.1839:0.0:0.8161	.	213	Q8IYU4	UBQLN_HUMAN	H	213	ENSP00000369531:R213H	ENSP00000369531:R213H	R	-	2	0	UBQLNL	5493610	1.000000	0.71417	0.041000	0.18516	0.010000	0.07245	1.810000	0.38932	0.383000	0.24910	-0.301000	0.09380	CGC		0.463	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		T	5537034	C	T	5537034	3	4	17	1	0	0	0	0	1	0	0	0	16940	768	27	1	793	1	UBQLNL	11	5537034	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		5537034	129469482	31	1748										
EIF3F	8665	hgsc.bcm.edu	37	chr11	8013380	8013380	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	aattgcttttcagtgccgcaCaatgagtcagaagatgaagt	10	7	2	4			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr11:8013380C>T	ENST00000533626.1	+	4	1043	c.417C>T	c.(415-417)caC>caT	p.H139H	EIF3F_ENST00000537635.1_Silent_p.H154H|EIF3F_ENST00000449102.2_Intron|EIF3F_ENST00000309828.4_Silent_p.H139H					eukaryotic translation initiation factor 3, subunit F									p.H139H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTGCCGCACAATGAGTCAG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	11											168	156	160					11																	8013380		2201	4296	6497	7969956	SO:0001819	synonymous_variant	8665			U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.417C>T	11.37:g.8013380C>T			7969956		Silent	SNP	ENST00000533626.1	37	CCDS7785.1																																																																																				0.493	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754		T	8013380	C	T	8013380	2	4	17	1	0	0	0	0	0	0	0	1	5029	477	17	3		3	EIF3F	11	8013380	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	2476346	8013380	126993136	32	1749										
NELL1	4745	hgsc.bcm.edu	37	chr11	20869170	20869170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tggcctgagggatgagattcGgtatcactacatacacaatg	11	8	1	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr11:20869170G>A	ENST00000357134.5	+	4	529	c.377G>A	c.(376-378)cGg>cAg	p.R126Q	NELL1_ENST00000325319.5_Intron|NELL1_ENST00000532434.1_Missense_Mutation_p.R126Q|NELL1_ENST00000298925.5_Missense_Mutation_p.R154Q	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	126	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)	p.R126Q(1)		NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						GATGAGATTCGGTATCACTAC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											209	154	173					11																	20869170		2203	4300	6503	20825746	SO:0001583	missense	4745			AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.377G>A	11.37:g.20869170G>A	ENSP00000349654:p.Arg126Gln		20825746	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	G	36	5.608771	0.96626	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000532434	T;T;T	0.78246	-1.16;-1.16;-1.16	5.62	5.62	0.85841	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.89227	0.6655	M	0.81942	2.565	0.80722	D	1	D;D;D	0.89917	1.0;0.957;1.0	D;P;D	0.87578	0.998;0.63;0.998	D	0.89140	0.3516	10	0.59425	D	0.04	-15.8207	20.0377	0.97569	0.0:0.0:1.0:0.0	.	154;126;126	B3KXR2;Q92832-2;Q92832	.;.;NELL1_HUMAN	Q	154;126;126	ENSP00000298925:R154Q;ENSP00000349654:R126Q;ENSP00000437170:R126Q	ENSP00000298925:R154Q	R	+	2	0	NELL1	20825746	1.000000	0.71417	0.958000	0.39756	0.912000	0.54170	9.813000	0.99286	2.822000	0.97130	0.650000	0.86243	CGG		0.453	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		A	20869170	G	A	20869170	3	1	17	1	0	0	0	0	1	0	0	0	10364	1116	39	1	391	1	NELL1	11	20869170	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	12855790	20869170	114137346	33	1750										
PC	5091	hgsc.bcm.edu	37	chr11	66616434	66616434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ccttggtcacatgaaccttgCggacagtaccctccatgggt	10	13	1	1	rs149054698		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr11:66616434C>T	ENST00000393958.2	-	22	3566	c.3473G>A	c.(3472-3474)cGc>cAc	p.R1158H	PC_ENST00000529047.1_Missense_Mutation_p.R278H|PC_ENST00000393955.2_Missense_Mutation_p.R1158H|PC_ENST00000393960.1_Missense_Mutation_p.R1158H|PC_ENST00000528224.1_5'UTR	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1158	Biotinyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.R1158H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	ATGAACCTTGCGGACAGTACC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4400		0,0,2200	136	106	116		3473,3473,3473	1.8	1	11	dbSNP_134	116	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,missense	PC	NM_000920.3,NM_001040716.1,NM_022172.2	29,29,29	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	1158/1179,1158/1179,1158/1179	66616434	1,12989	2200	4295	6495	66373010	SO:0001583	missense	5091			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.3473G>A	11.37:g.66616434C>T	ENSP00000377530:p.Arg1158His		66373010	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457374	0.43634	0.0	1.16E-4	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	4.79	1.75	0.24633	Single hybrid motif (1);Biotin/lipoyl attachment (2);	0.906024	0.09618	N	0.777938	T	0.39708	0.1088	L	0.42245	1.32	0.80722	D	1	P	0.39920	0.695	B	0.35182	0.197	T	0.38824	-0.9643	10	0.87932	D	0	-13.0091	4.2498	0.10689	0.0:0.5499:0.1698:0.2803	.	1158	P11498	PYC_HUMAN	H	278;1158;1158;1158	ENSP00000435905:R278H;ENSP00000377527:R1158H;ENSP00000377530:R1158H;ENSP00000377532:R1158H	ENSP00000377527:R1158H	R	-	2	0	PC	66373010	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.063000	0.30567	0.630000	0.30394	0.561000	0.74099	CGC		0.607	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66616434	C	T	66616434	3	4	17	1	0	0	0	0	1	0	0	0	11528	768	27	1	67	1	PC	11	66616434	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	45747264	66616434	68390082	34	1751										
OR10S1	219873	hgsc.bcm.edu	37	chr11	123847892	123847892	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	agggaggtgtggattgcagcGtgcgtggcacctatggccca	17	9	0	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr11:123847892G>A	ENST00000531945.1	-	1	596	c.507C>T	c.(505-507)caC>caT	p.H169H		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H169H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GGATTGCAGCGTGCGTGGCAC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	11											112	98	103					11																	123847892		2202	4299	6501	123353102	SO:0001819	synonymous_variant	219873			BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.507C>T	11.37:g.123847892G>A			123353102	B9EH43|Q6IEV3|Q96R78	Silent	SNP	ENST00000531945.1	37	CCDS31701.1																																																																																				0.567	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		A	123847892	G	A	123847892	2	1	17	1	0	0	0	0	0	0	0	1	10949	1136	40	1		1	OR10S1	11	123847892	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	57231458	123847892	11158624	35	1752										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	17	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		25398281	108453614	36	1753										
MCRS1	10445	hgsc.bcm.edu	37	chr12	49960215	49960215	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gggcagttcccccggtgccaCgtgtcatgtcgtgcagcaca	13	14	1	0	rs148437866	byFrequency	TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr12:49960215C>T	ENST00000550165.1	-	4	277				MCRS1_ENST00000343810.4_Intron|MCRS1_ENST00000357123.4_Missense_Mutation_p.R3H|MCRS1_ENST00000546244.1_Intron			Q96EZ8	MCRS1_HUMAN	microspherule protein 1						cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R3H(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						CCCGGTGCCACGTGTCATGTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	HIS/ARG,	0,4402		0,0,2201	33	30	31		8,	-0.4	0.3	12	dbSNP_134	31	10,8580		0,10,4285	yes	missense,intron	MCRS1	NM_001012300.1,NM_006337.3	29,	0,10,6486	TT,TC,CC		0.1164,0.0,0.077	possibly-damaging,	3/476,	49960215	10,12982	2201	4295	6496	48246482	SO:0001627	intron_variant	10445			BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"INO80 complex subunits"	6960	protein-coding gene	gene with protein product	"INO80 complex subunit Q"	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.11-217G>A	12.37:g.49960215C>T			48246482	O14742|O75497|Q6VN53|Q7Z372	Missense_Mutation	SNP	ENST00000550165.1	37	CCDS8787.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322829	0.23994	0.0	0.001164	ENSG00000187778	ENST00000357123	.	.	.	2.86	-0.365	0.12549	.	2.437060	0.01898	N	0.039017	T	0.17534	0.0421	.	.	.	0.09310	N	1	P	0.46277	0.875	B	0.29862	0.108	T	0.27806	-1.0063	8	0.87932	D	0	4.4626	3.3578	0.07176	0.4516:0.4104:0.0:0.138	.	3	Q96EZ8-2	.	H	3	.	ENSP00000349640:R3H	R	-	2	0	MCRS1	48246482	0.018000	0.18449	0.280000	0.24747	0.985000	0.73830	0.160000	0.16462	-0.075000	0.12798	-0.253000	0.11424	CGT		0.587	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337		T	49960215	C	T	49960215	1	4	17	0	1	0	0	0	0	0	0	0	9429	536	19	1		1	MCRS1	12	49960215	Intron	SNP	C	TCGA-AG-3581-01A-01W-0831-10	24561934	49960215	83891680	37	1754										
STARD13	90627	hgsc.bcm.edu	37	chr13	33703505	33703505	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ctccctggcaccagggacctGctctctgcccagggagatgc	12	16	1	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr13:33703505G>A	ENST00000336934.5	-	5	1425	c.1309C>T	c.(1309-1311)Cag>Tag	p.Q437*	STARD13_ENST00000399365.3_Nonsense_Mutation_p.Q319*|STARD13_ENST00000255486.4_Nonsense_Mutation_p.Q429*	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	437					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.Q437*(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		CCAGGGACCTGCTCTCTGCCC	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											43	45	45					13																	33703505		2203	4300	6503	32601505	SO:0001587	stop_gained	90627			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1309C>T	13.37:g.33703505G>A	ENSP00000338785:p.Gln437*		32601505	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Nonsense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746309	0.69418	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	.	.	.	5.73	4.88	0.63580	.	0.556583	0.20585	N	0.089451	.	.	.	.	.	.	0.51767	D	0.999939	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	13.1661	0.59571	0.0:0.0:0.5653:0.4347	.	.	.	.	X	319;429;437;429	.	ENSP00000255486:Q429X	Q	-	1	0	STARD13	32601505	0.067000	0.21026	0.586000	0.28679	0.032000	0.12392	1.083000	0.30815	1.411000	0.46957	0.655000	0.94253	CAG		0.567	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		A	33703505	G	A	33703505	4	1	17	1	0	0	0	0	0	1	0	0	15295	1328	46	3	2072	3	STARD13	13	33703505	Nonsense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10		33703505	81466373	38	1755										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208018	58208018	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gtgaccatcgtggcgcgggaCgggggctctcctcccctcaa	14	15	2	1	rs368374245		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr13:58208018C>T	ENST00000377918.3	+	1	1364	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	446	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D446D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TGGCGCGGGACGGGGGCTCTC	0.587																																					Melanoma(72;952 1291 1619 12849 33676)											1	Substitution - coding silent(1)	large_intestine(1)	13											53	40	45					13																	58208018		2202	4299	6501	57106019	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1338C>T	13.37:g.58208018C>T			57106019	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.587	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58208018	C	T	58208018	2	4	17	1	0	0	0	0	0	0	0	1	11543	535	19	1		1	PCDH17	13	58208018	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	24504513	58208018	56961860	39	1756										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30047487	30047487	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tgattattgtttacctgtagCcaagggtggctcaaggtctt	11	7	2	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr14:30047487C>G	ENST00000331968.5	-	17	2743	c.2514G>C	c.(2512-2514)tgG>tgC	p.W838C	PRKD1_ENST00000415220.2_Missense_Mutation_p.W846C	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	838	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.W838C(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TTACCTGTAGCCAAGGGTGGC	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	14											86	84	85					14																	30047487		2203	4300	6503	29117238	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2514G>C	14.37:g.30047487C>G	ENSP00000333568:p.Trp838Cys		29117238	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.774259	0.69992	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.69561	-0.41;-0.41	5.7	5.7	0.88788	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90126	0.6915	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93692	0.7008	10	0.87932	D	0	-20.5906	19.8276	0.96624	0.0:1.0:0.0:0.0	.	838	Q15139	KPCD1_HUMAN	C	838;846	ENSP00000333568:W838C;ENSP00000390535:W846C	ENSP00000333568:W838C	W	-	3	0	PRKD1	29117238	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.056000	0.71111	2.697000	0.92050	0.585000	0.79938	TGG		0.313	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		G	30047487	C	G	30047487	3	3	17	1	0	0	0	0	1	0	0	0	12552	740	26	5	232	5	PRKD1	14	30047487	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		30047487	77302053	40	1757										
HHIPL1	84439	hgsc.bcm.edu	37	chr14	100135193	100135193	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	aaggccagaagcgccatgccCggctatgtcccagctccttc	10	16	0	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr14:100135193C>T	ENST00000330710.5	+	7	1828				HHIPL1_ENST00000357223.2_Silent_p.P585P	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1						carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)	p.P585P(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				GCGCCATGCCCGGCTATGTCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	14											91	89	90					14																	100135193		2203	4300	6503	99204946	SO:0001627	intron_variant	84439			AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"KIAA1822"	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.1730+553C>T	14.37:g.100135193C>T			99204946	A2RUF8|B2RN09|Q6UXX2	Silent	SNP	ENST00000330710.5	37	CCDS45162.1																																																																																				0.572	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566		T	100135193	C	T	100135193	1	4	17	0	1	0	0	0	0	0	0	0	7114	639	23	1		1	HHIPL1	14	100135193	Intron	SNP	C	TCGA-AG-3581-01A-01W-0831-10	70087706	100135193	7214347	41	1758										
GLDN	342035	hgsc.bcm.edu	37	chr15	51696614	51696614	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cctttggattatctatgcgtCaagtgtggacggctcgagca	12	9	2	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr15:51696614C>T	ENST00000335449.6	+	10	1375	c.1319C>T	c.(1318-1320)tCa>tTa	p.S440L	GLDN_ENST00000396399.2_Missense_Mutation_p.S316L	NM_181789.2	NP_861454.2	Q6ZMI3	GLDN_HUMAN	gliomedin	440	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|microvillus organization (GO:0032528)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S440L(1)		central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		ATCTATGCGTCAAGTGTGGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											151	146	148					15																	51696614		2196	4293	6489	49483906	SO:0001583	missense	342035			AY358144	CCDS10140.2	15q15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000186417	ENSG00000186417			29514	protein-coding gene	gene with protein product		608603	"collomin"	COLM		16039564, 12642876	Standard	XM_005254338		Approved	CRG-L2, CLOM, colmedin, UNC-112	uc002aba.3	Q6ZMI3	OTTHUMG00000131746	ENST00000335449.6:c.1319C>T	15.37:g.51696614C>T	ENSP00000335196:p.Ser440Leu		49483906	Q6UXZ7|Q7Z359	Missense_Mutation	SNP	ENST00000335449.6	37	CCDS10140.2	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632893	0.67015	.	.	ENSG00000186417	ENST00000335449;ENST00000396399;ENST00000537339	D;D	0.90900	-2.75;-2.75	5.71	5.71	0.89125	Olfactomedin-like (3);	0.000000	0.37669	N	0.001981	D	0.94608	0.8262	L	0.58428	1.81	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94548	0.7751	10	0.72032	D	0.01	.	19.8534	0.96748	0.0:1.0:0.0:0.0	.	440	Q6ZMI3	GLDN_HUMAN	L	440;316;316	ENSP00000335196:S440L;ENSP00000379681:S316L	ENSP00000335196:S440L	S	+	2	0	GLDN	49483906	1.000000	0.71417	0.133000	0.22050	0.111000	0.19643	7.487000	0.81328	2.711000	0.92665	0.563000	0.77884	TCA		0.428	GLDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254667.2	NM_181789		T	51696614	C	T	51696614	3	4	17	1	0	0	0	0	1	0	0	0	6454	838	29	3	1357	3	GLDN	15	51696614	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10		51696614	50834778	42	1759										
SNX22	79856	hgsc.bcm.edu	37	chr15	64446163	64446163	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gcaccagcggcctgtcctgaGcttccatgtggatccctatg	11	14	0	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr15:64446163G>C	ENST00000325881.4	+	6	481	c.422G>C	c.(421-423)aGc>aCc	p.S141T	PPIB_ENST00000558492.1_5'Flank	NM_024798.2	NP_079074.2	Q96L94	SNX22_HUMAN	sorting nexin 22	141					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.S141T(1)		large_intestine(3)|lung(1)|urinary_tract(2)	6						CCTGTCCTGAGCTTCCATGTG	0.612											OREG0023180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											130	130	130					15																	64446163		2203	4300	6503	62233216	SO:0001583	missense	79856			AK024014	CCDS10190.1	15q22.1	2010-01-15			ENSG00000157734	ENSG00000157734		"Sorting nexins"	16315	protein-coding gene	gene with protein product						12461558, 17400918	Standard	NR_073534		Approved	FLJ13952	uc002anc.1	Q96L94	OTTHUMG00000132965	ENST00000325881.4:c.422G>C	15.37:g.64446163G>C	ENSP00000323435:p.Ser141Thr	1076	62233216	Q8WUS9|Q9H844	Missense_Mutation	SNP	ENST00000325881.4	37	CCDS10190.1	.	.	.	.	.	.	.	.	.	.	G	4.090	0.014689	0.07959	.	.	ENSG00000157734	ENST00000380278;ENST00000325881	T	0.76186	-1.0	5.41	3.24	0.37175	.	0.419599	0.29355	N	0.012388	T	0.54240	0.1846	L	0.34521	1.04	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.06405	0.001;0.002	T	0.34976	-0.9807	10	0.05833	T	0.94	-14.0235	6.3677	0.21463	0.1298:0.1916:0.6786:0.0	.	141;113	Q96L94;Q6ZTF9	SNX22_HUMAN;.	T	113;141	ENSP00000323435:S141T	ENSP00000323435:S141T	S	+	2	0	SNX22	62233216	0.997000	0.39634	0.228000	0.23943	0.325000	0.28411	0.704000	0.25661	1.244000	0.43870	0.491000	0.48974	AGC		0.612	SNX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256524.2	NM_024798		C	64446163	G	C	64446163	3	2	17	1	0	0	0	0	1	0	0	0	14931	971	34	5	444	5	SNX22	15	64446163	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10	12749549	64446163	38085229	43	1760										
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3569975	3569975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ctaatttagaagccaaaatcGaaaagagaaaattagaactg	7	5	0	3			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr16:3569975G>A	ENST00000576634.1	+	7	796	c.652G>A	c.(652-654)Gaa>Aaa	p.E218K	CLUAP1_ENST00000571025.1_Missense_Mutation_p.E218K|CLUAP1_ENST00000572600.1_Missense_Mutation_p.E52K|CLUAP1_ENST00000341633.5_Missense_Mutation_p.E218K|CLUAP1_ENST00000445795.2_5'UTR|CLUAP1_ENST00000417763.2_Missense_Mutation_p.E52K	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	218					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)		p.E218K(2)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						AGCCAAAATCGAAAAGAGAAA	0.383																																																2	Substitution - Missense(2)	urinary_tract(1)|large_intestine(1)	16											100	103	102					16																	3569975		2197	4300	6497	3509976	SO:0001583	missense	23059			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.652G>A	16.37:g.3569975G>A	ENSP00000460850:p.Glu218Lys		3509976	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457052	0.63401	.	.	ENSG00000103351	ENST00000341633;ENST00000417763	T;T	0.43294	0.95;0.95	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.56587	0.1995	L	0.48986	1.54	0.80722	D	1	D;D	0.65815	0.983;0.995	P;D	0.62955	0.714;0.909	T	0.54820	-0.8236	10	0.45353	T	0.12	-9.3317	16.3104	0.82865	0.0:0.0:1.0:0.0	.	52;218	Q96AJ1-2;Q96AJ1	.;CLUA1_HUMAN	K	218;52	ENSP00000344392:E218K;ENSP00000388642:E52K	ENSP00000344392:E218K	E	+	1	0	CLUAP1	3509976	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.195000	0.94971	2.444000	0.82710	0.650000	0.86243	GAA		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		A	3569975	G	A	3569975	3	1	17	1	0	0	0	0	1	0	0	0	3575	1059	37	1	678	1	CLUAP1	16	3569975	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10		3569975	86784778	44	1761										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30745834	30745834	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tagcagaccatccgagagctGtttgatatgcccctggagga	12	10	0	3			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr16:30745834G>C	ENST00000262518.4	+	31	7012	c.6627G>C	c.(6625-6627)ctG>ctC	p.L2209L	SRCAP_ENST00000395059.2_Silent_p.L2147L|SRCAP_ENST00000344771.4_Silent_p.L2051L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2209					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.L2209L(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCCGAGAGCTGTTTGATATGC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	16											170	157	161					16																	30745834		2197	4300	6497	30653335	SO:0001819	synonymous_variant	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6627G>C	16.37:g.30745834G>C			30653335	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																				0.512	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30745834	G	C	30745834	2	2	17	1	0	0	0	0	0	0	0	1	15174	1364	48	5		5	SRCAP	16	30745834	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	27175859	30745834	59608919	45	1762										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67578314	67578314	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ccttggtccggcacctgtacCactgcagtcgcctcctgctg	10	17	0	0			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr16:67578314C>T	ENST00000379312.3	+	15	2846	c.2725C>T	c.(2725-2727)Cac>Tac	p.H909Y	CTD-2012K14.3_ENST00000563083.1_RNA|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.H919Y|FAM65A_ENST00000042381.4_Missense_Mutation_p.H905Y|FAM65A_ENST00000422602.2_Missense_Mutation_p.H925Y|FAM65A_ENST00000540839.3_Missense_Mutation_p.H924Y	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	909						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.H905Y(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		GCACCTGTACCACTGCAGTCG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	16											96	87	90					16																	67578314		2198	4300	6498	66135815	SO:0001583	missense	79567			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2725C>T	16.37:g.67578314C>T	ENSP00000368614:p.His909Tyr		66135815	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.444|7.444	0.641202|0.641202	0.14451|0.14451	.|.	.|.	ENSG00000039523|ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839|ENST00000428437	T;T;T|.	0.76060|.	-0.99;-0.99;-0.99|.	5.55|5.55	4.6|4.6	0.57074|0.57074	.|.	0.213898|.	0.45606|.	N|.	0.000343|.	T|T	0.23289|0.23289	0.0563|0.0563	N|N	0.08118|0.08118	0|0	0.30076|0.30076	N|N	0.809571|0.809571	B;B;B|.	0.22346|.	0.068;0.068;0.068|.	B;B;B|.	0.14578|.	0.011;0.011;0.011|.	T|T	0.19160|0.19160	-1.0314|-1.0314	10|5	0.02654|.	T|.	1|.	-9.8436|-9.8436	8.5739|8.5739	0.33587|0.33587	0.2502:0.6751:0.0:0.0747|0.2502:0.6751:0.0:0.0747	.|.	919;925;909|.	B4DIM2;E9PBS3;Q6ZS17|.	.;.;FA65A_HUMAN|.	Y|L	909;905;925;919|898	ENSP00000368614:H909Y;ENSP00000042381:H905Y;ENSP00000400099:H925Y|.	ENSP00000042381:H905Y|.	H|P	+|+	1|2	0|0	FAM65A|FAM65A	66135815|66135815	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.027000|2.027000	0.41078|0.41078	1.353000|1.353000	0.45828|0.45828	0.655000|0.655000	0.94253|0.94253	CAC|CCA		0.642	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		T	67578314	C	T	67578314	3	4	17	1	0	0	0	0	1	0	0	0	5618	594	21	3	2767	3	FAM65A	16	67578314	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	36832480	67578314	22776439	46	1763										
WWP2	11060	hgsc.bcm.edu	37	chr16	69905710	69905710	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	ctactttgaacccccaggacGcacagacattcgggtgcttc	9	14	0	2	rs369827464		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr16:69905710G>A	ENST00000359154.2	+	7	680	c.579G>A	c.(577-579)acG>acA	p.T193T	WWP2_ENST00000542271.1_Silent_p.T77T|WWP2_ENST00000356003.2_Silent_p.T193T|WWP2_ENST00000569174.1_Silent_p.T193T|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.T193T	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	193					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.T193T(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCCCCAGGACGCACAGACATT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G	,	0,4396		0,0,2198	57	60	59		579,579	-5.8	1	16		59	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199423.1	,	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	,	193/871,193/336	69905710	1,12991	2198	4298	6496	68463211	SO:0001819	synonymous_variant	11060			BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.579G>A	16.37:g.69905710G>A			68463211	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																				0.552	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		A	69905710	G	A	69905710	2	1	17	1	0	0	0	0	0	0	0	1	17456	1074	38	1		1	WWP2	16	69905710	Silent	SNP	G	TCGA-AG-3581-01A-01W-0831-10	2327396	69905710	20449043	47	1764										
ASPA	443	hgsc.bcm.edu	37	chr17	3402307	3402307	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gtgaatgaggccgcatattaCgaaaagaaagaagcttttgc	11	6	0	4	rs375736464		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr17:3402307C>T	ENST00000263080.2	+	6	1025	c.867C>T	c.(865-867)taC>taT	p.Y289Y	ASPA_ENST00000456349.2_Silent_p.Y289Y|SPATA22_ENST00000541913.1_Intron	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	289					aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)	p.Y289Y(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	CCGCATATTACGAAAAGAAAG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C	,	0,4406		0,0,2203	97	82	87		867,867	-1.8	1	17		87	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ASPA	NM_000049.2,NM_001128085.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	289/314,289/314	3402307	1,13005	2203	4300	6503	3349057	SO:0001819	synonymous_variant	443			S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"aminoacylase 2", "Canavan disease"	608034	"aspartoacylase (aminoacylase 2, Canavan disease)"			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.867C>T	17.37:g.3402307C>T			3349057		Silent	SNP	ENST00000263080.2	37	CCDS11028.1																																																																																				0.433	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049		T	3402307	C	T	3402307	2	4	17	1	0	0	0	0	0	0	0	1	1051	547	19	1		1	ASPA	17	3402307	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10		3402307	77792903	48	1765										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	17	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	4174813	7577120	73618090	49	1766										
CPD	1362	hgsc.bcm.edu	37	chr17	28791618	28791618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tttgtcaggtgctactatgtCggcattgatcctaacagctt	9	9	1	1			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr17:28791618C>T	ENST00000225719.4	+	21	4005	c.3929C>T	c.(3928-3930)tCg>tTg	p.S1310L	CPD_ENST00000543464.2_Missense_Mutation_p.S1063L	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	1310						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)	p.S1310L(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						GCTACTATGTCGGCATTGATC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											168	148	155					17																	28791618		2203	4300	6503	25815744	SO:0001583	missense	1362			U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.3929C>T	17.37:g.28791618C>T	ENSP00000225719:p.Ser1310Leu		25815744	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Missense_Mutation	SNP	ENST00000225719.4	37	CCDS11257.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.122162	0.56613	.	.	ENSG00000108582	ENST00000225719;ENST00000543464	T;T	0.14640	2.49;2.49	5.42	5.42	0.78866	Carboxypeptidase-like, regulatory domain (1);	0.074779	0.56097	D	0.000029	T	0.10637	0.0260	N	0.14661	0.345	0.54753	D	0.99998	P;D	0.59357	0.675;0.985	B;B	0.40702	0.094;0.338	T	0.06516	-1.0822	10	0.87932	D	0	-2.7302	18.1989	0.89831	0.0:1.0:0.0:0.0	.	1063;1310	F5GZH6;O75976	.;CBPD_HUMAN	L	1310;1063	ENSP00000225719:S1310L;ENSP00000444443:S1063L	ENSP00000225719:S1310L	S	+	2	0	CPD	25815744	1.000000	0.71417	0.996000	0.52242	0.924000	0.55760	7.084000	0.76866	2.509000	0.84616	0.655000	0.94253	TCG		0.388	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		T	28791618	C	T	28791618	3	4	17	1	0	0	0	0	1	0	0	0	3804	893	31	1	4011	1	CPD	17	28791618	Missense_Mutation	SNP	C	TCGA-AG-3581-01A-01W-0831-10	21214498	28791618	52403592	50	1767										
PDCD2L	84306	hgsc.bcm.edu	37	chr19	34900368	34900368	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gcccacagccttctgagggaCtatcagcagagagaaggcat	12	11	2	3			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr19:34900368C>T	ENST00000246535.3	+	4	686	c.639C>T	c.(637-639)gaC>gaT	p.D213D	PDCD2L_ENST00000587065.2_Intron	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	213					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.D213D(1)		breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TTCTGAGGGACTATCAGCAGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	19											122	112	115					19																	34900368		2203	4300	6503	39592208	SO:0001819	synonymous_variant	84306			BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.639C>T	19.37:g.34900368C>T			39592208		Silent	SNP	ENST00000246535.3	37	CCDS12438.1																																																																																				0.532	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		T	34900368	C	T	34900368	2	4	17	1	0	0	0	0	0	0	0	1	11651	564	20	3		3	PDCD2L	19	34900368	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10		34900368	24228615	51	1768										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50278821	50278821	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	gatgagacatctctaccggcGccatccagaagttgtcggga	12	11	1	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chr22:50278821G>T	ENST00000216268.5	+	2	1988	c.1511G>T	c.(1510-1512)cGc>cTc	p.R504L		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	504						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R504L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		CTCTACCGGCGCCATCCAGAA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	22											92	98	96					22																	50278821		2203	4300	6503	48664825	SO:0001583	missense	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1511G>T	22.37:g.50278821G>T	ENSP00000216268:p.Arg504Leu		48664825	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.554526	0.65425	.	.	ENSG00000100426	ENST00000216268	T	0.52983	0.64	5.23	5.23	0.72850	Zinc finger, BED-type predicted (3);	0.000000	0.85682	D	0.000000	T	0.61590	0.2359	L	0.50333	1.59	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.63431	-0.6639	10	0.72032	D	0.01	-22.4347	18.5754	0.91153	0.0:0.0:1.0:0.0	.	504	O75132	ZBED4_HUMAN	L	504	ENSP00000216268:R504L	ENSP00000216268:R504L	R	+	2	0	ZBED4	48664825	1.000000	0.71417	0.996000	0.52242	0.039000	0.13416	9.003000	0.93577	2.728000	0.93425	0.591000	0.81541	CGC		0.587	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50278821	G	T	50278821	3	4	17	1	0	0	0	0	1	0	0	0	17559	1087	38	2	1513	2	ZBED4	22	50278821	Missense_Mutation	SNP	G	TCGA-AG-3581-01A-01W-0831-10		50278821	1025745	52	1769										
WWC3	55841	hgsc.bcm.edu	37	chrX	10098062	10098062	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	cagaccagccctccgtacccAgagccctgttgcatgggtat	10	15	0	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chrX:10098062A>G	ENST00000380861.4	+	18	2890	c.2499A>G	c.(2497-2499)ccA>ccG	p.P833P	WWC3_ENST00000454666.1_Silent_p.P833P	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	833					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.P833P(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CTCCGTACCCAGAGCCCTGTT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	X											101	79	86					X																	10098062		2203	4300	6503	10058062	SO:0001819	synonymous_variant	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2499A>G	X.37:g.10098062A>G			10058062	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																				0.592	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		G	10098062	A	G	10098062	2	3	17	1	0	0	0	0	0	0	0	1	17453	175	7	4		4	WWC3	23	10098062	Silent	SNP	A	TCGA-AG-3581-01A-01W-0831-10		10098062	145172498	53	1770										
KIF4A	24137	hgsc.bcm.edu	37	chrX	69573483	69573483	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.507474069554606	0	0.603482677308181	0.1	0.466258722490609	0	tttttccagcaagtagaaacCagtccagagacgagcaggtc	10	10	0	2			TCGA-AG-3581-01A-01W-0831-10	TCGA-AG-3581-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	940c33a1-8598-42c3-b299-023d9532d86d	933eaf29-6dc5-4648-b2f2-4be136668997	g.chrX:69573483C>T	ENST00000374403.3	+	15	1582	c.1500C>T	c.(1498-1500)acC>acT	p.T500T	KIF4A_ENST00000374388.3_Silent_p.T500T	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	500					anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.T500T(1)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AAGTAGAAACCAGTCCAGAGA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	X											40	38	38					X																	69573483		2203	4300	6503	69490208	SO:0001819	synonymous_variant	24137			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1500C>T	X.37:g.69573483C>T			69490208	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																				0.438	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		T	69573483	C	T	69573483	2	4	17	1	0	0	0	0	0	0	0	1	8324	581	21	3		3	KIF4A	23	69573483	Silent	SNP	C	TCGA-AG-3581-01A-01W-0831-10	59475421	69573483	85697077	54	1771										
PINK1	65018	hgsc.bcm.edu	37	chr1	20977046	20977046	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggctcctccaacaatcggcCgccactttgttggccaacag	9	15	0	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr1:20977046C>T	ENST00000321556.4	+	8	1702	c.1608C>T	c.(1606-1608)gcC>gcT	p.A536A	PINK1_ENST00000492302.1_3'UTR|PINK1-AS_ENST00000451424.1_RNA	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	536					activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.A536A(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AACAATCGGCCGCCACTTTGT	0.493																																					Esophageal Squamous(145;853 1803 8146 34412 35011)											1	Substitution - coding silent(1)	large_intestine(1)	1											70	64	66					1																	20977046		2203	4300	6503	20849633	SO:0001819	synonymous_variant	65018			AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"Parkinson disease"	14581	protein-coding gene	gene with protein product		608309	"Parkinson disease (autosomal recessive) 6"	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1608C>T	1.37:g.20977046C>T			20849633	Q8N6T9|Q8NBU3|Q96DE4	Silent	SNP	ENST00000321556.4	37	CCDS211.1																																																																																				0.493	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409		T	20977046	C	T	20977046	2	4	18	1	0	0	0	0	0	0	0	1	11963	639	23	1		1	PINK1	1	20977046	Silent	SNP	C	TCGA-AG-3582-01A-01W-0831-10		20977046	228273575	1	1772										
FLG	2312	hgsc.bcm.edu	37	chr1	152282747	152282747	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcttgtttgcctgcttgcacTtctgggtcctgactgcccat	9	13	2	1	rs536230632		TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr1:152282747T>G	ENST00000368799.1	-	3	4650	c.4615A>C	c.(4615-4617)Agt>Cgt	p.S1539R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1539	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1539R(2)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTTGCACTTCTGGGTCCT	0.572									Ichthyosis				T|||	1	0.000199681	0	0	5008	,	,		20676	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											303	293	296					1																	152282747		2203	4300	6503	150549371	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4615A>C	1.37:g.152282747T>G	ENSP00000357789:p.Ser1539Arg		150549371	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	9.888	1.203497	0.22121	.	.	ENSG00000143631	ENST00000368799	T	0.01821	4.62	2.67	-0.792	0.10925	.	.	.	.	.	T	0.00784	0.0026	M	0.75447	2.3	0.09310	N	1	B	0.17852	0.024	B	0.15870	0.014	T	0.42050	-0.9474	9	0.25106	T	0.35	.	5.1967	0.15243	0.0:0.4182:0.0:0.5818	.	1539	P20930	FILA_HUMAN	R	1539	ENSP00000357789:S1539R	ENSP00000357789:S1539R	S	-	1	0	FLG	150549371	0.003000	0.15002	0.000000	0.03702	0.169000	0.22640	0.226000	0.17776	-0.281000	0.09141	0.397000	0.26171	AGT		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152282747	T	G	152282747	3	3	18	1	0	0	0	0	1	0	0	0	5941	1609	56	4	7574	4	FLG	1	152282747	Missense_Mutation	SNP	T	TCGA-AG-3582-01A-01W-0831-10	131305701	152282747	96967874	2	1773										
TADA1	117143	hgsc.bcm.edu	37	chr1	166833127	166833127	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttccaggttttgctgcggaAccccctggccaaggcaaaga	11	12	0	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr1:166833127A>G	ENST00000367874.4	-	4	357	c.264T>C	c.(262-264)ggT>ggC	p.G88G	TADA1_ENST00000467021.1_5'Flank	NM_053053.3	NP_444281.1	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1	88					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.G88G(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	11						TTGCTGCGGAACCCCCTGGCC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	1											76	81	79					1																	166833127		2203	4300	6503	165099751	SO:0001819	synonymous_variant	117143			BC015401	CCDS1255.1	1q24.1	2009-10-02	2009-10-02	2009-10-02	ENSG00000152382	ENSG00000152382			30631	protein-coding gene	gene with protein product		612763	"transcriptional adaptor 1 (HFI1 homolog, yeast)-like", "transcriptional adaptor 1 (HFI1 homolog, yeast)"	TADA1L		11564863	Standard	NM_053053		Approved	STAF42, ADA1, hADA1, HFI1	uc001gdw.3	Q96BN2	OTTHUMG00000034321	ENST00000367874.4:c.264T>C	1.37:g.166833127A>G			165099751	A8K4J9	Silent	SNP	ENST00000367874.4	37	CCDS1255.1																																																																																				0.378	TADA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082881.1	NM_053053		G	166833127	A	G	166833127	2	3	18	1	0	0	0	0	0	0	0	1	15548	30	2	4		4	TADA1	1	166833127	Silent	SNP	A	TCGA-AG-3582-01A-01W-0831-10	14550380	166833127	82417494	3	1774										
CRB1	23418	hgsc.bcm.edu	37	chr1	197446800	197446800	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcaatctttccagttggcaGatgacttgatctccgacatt	7	10	3	3			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr1:197446800G>T	ENST00000367400.3	+	12	4147	c.4012G>T	c.(4012-4014)Gat>Tat	p.D1338Y	CRB1_ENST00000367399.2_Missense_Mutation_p.D1226Y|CRB1_ENST00000535699.1_Missense_Mutation_p.D1314Y|CRB1_ENST00000538660.1_Missense_Mutation_p.D802Y|CRB1_ENST00000544212.1_Missense_Mutation_p.D819Y	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1338					cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1338Y(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CCAGTTGGCAGATGACTTGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	71	75					1																	197446800		2203	4300	6503	195713423	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.4012G>T	1.37:g.197446800G>T	ENSP00000356370:p.Asp1338Tyr		195713423	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145939	0.37923	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212	D;D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77;-3.77	5.92	5.0	0.66597	.	.	.	.	.	D	0.94414	0.8203	L	0.56124	1.755	0.50313	D	0.999866	P;P;P;P	0.47253	0.57;0.892;0.892;0.828	B;P;B;B	0.47251	0.235;0.542;0.413;0.293	D	0.94109	0.7369	9	0.72032	D	0.01	.	11.2422	0.48977	0.1903:0.0:0.8097:0.0	.	802;1314;1226;1338	B7Z5T2;F5H0L2;P82279-3;P82279	.;.;.;CRUM1_HUMAN	Y	1314;802;1338;1226;819	ENSP00000438786:D1314Y;ENSP00000438091:D802Y;ENSP00000356370:D1338Y;ENSP00000356369:D1226Y;ENSP00000444556:D819Y	ENSP00000356369:D1226Y	D	+	1	0	CRB1	195713423	1.000000	0.71417	0.317000	0.25265	0.018000	0.09664	3.469000	0.53093	1.492000	0.48499	0.650000	0.86243	GAT		0.433	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197446800	G	T	197446800	3	4	18	1	0	0	0	0	1	0	0	0	3854	942	33	2	4058	2	CRB1	1	197446800	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	30613673	197446800	51803821	4	1775										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233482260	233482260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gattacagattttgggttggCgagggaatggcacaggacca	15	6	0	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr1:233482260C>T	ENST00000366624.3	+	2	1139	c.878C>T	c.(877-879)gCg>gTg	p.A293V	MLK4_ENST00000366623.3_Missense_Mutation_p.A293V	NM_032435.2	NP_115811.2												p.A293V(1)									TTTGGGTTGGCGAGGGAATGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	88	90					1																	233482260		2203	4300	6503	231548883	SO:0001583	missense	84451																														ENST00000366624.3:c.878C>T	1.37:g.233482260C>T	ENSP00000355583:p.Ala293Val		231548883		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973935	0.92919	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.91740	-2.9;-2.9	4.49	4.49	0.54785	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.96575	0.9426	10	0.87932	D	0	.	17.3739	0.87386	0.0:1.0:0.0:0.0	.	293;293	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	V	293	ENSP00000355582:A293V;ENSP00000355583:A293V	ENSP00000355582:A293V	A	+	2	0	RP5-862P8.2	231548883	1.000000	0.71417	0.102000	0.21198	0.965000	0.64279	7.645000	0.83430	2.319000	0.78375	0.563000	0.77884	GCG		0.428	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233482260	C	T	233482260	3	4	18	1	0	0	0	0	1	0	0	0	8280	768	27	1	884	1	KIAA1804	1	233482260	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10	36035460	233482260	15768361	5	1776										
BSN	8927	hgsc.bcm.edu	37	chr3	49662512	49662512	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tcctggccatgagagcccccGagagacaagggcacagggac	14	13	0	2			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr3:49662512G>A	ENST00000296452.4	+	2	443	c.329G>A	c.(328-330)cGa>cAa	p.R110Q		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	110					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.R110Q(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GAGAGCCCCCGAGAGACAAGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	3											46	48	48					3																	49662512		2203	4300	6503	49637516	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.329G>A	3.37:g.49662512G>A	ENSP00000296452:p.Arg110Gln		49637516	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	2.316	-0.356775	0.05138	.	.	ENSG00000164061	ENST00000296452	T	0.17370	2.28	5.48	0.701	0.18104	.	0.736785	0.12006	N	0.508282	T	0.11196	0.0273	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.40440	-0.9563	10	0.10377	T	0.69	-10.161	11.2435	0.48982	0.2965:0.0:0.7035:0.0	.	110	Q9UPA5	BSN_HUMAN	Q	110	ENSP00000296452:R110Q	ENSP00000296452:R110Q	R	+	2	0	BSN	49637516	0.005000	0.15991	0.888000	0.34837	0.010000	0.07245	0.148000	0.16224	-0.152000	0.11156	-2.311000	0.00256	CGA		0.642	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49662512	G	A	49662512	3	1	18	1	0	0	0	0	1	0	0	0	1533	1058	37	1	335	1	BSN	3	49662512	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		49662512	148359918	6	1777										
TIPARP	25976	hgsc.bcm.edu	37	chr3	156413774	156413774	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagagagataaaaaggagaCccctcttccgctcctgtttt	10	10	1	3			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr3:156413774C>A	ENST00000461166.1	+	4	1795	c.1207C>A	c.(1207-1209)Ccc>Acc	p.P403T	TIPARP_ENST00000486483.1_Missense_Mutation_p.P403T|TIPARP_ENST00000542783.1_Missense_Mutation_p.P403T|TIPARP_ENST00000295924.7_Missense_Mutation_p.P403T	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	403	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.P403T(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AAAAAGGAGACCCCTCTTCCG	0.393																																					Ovarian(171;276 1987 3319 6837 11197)											1	Substitution - Missense(1)	large_intestine(1)	3											110	114	113					3																	156413774		2203	4300	6503	157896468	SO:0001583	missense	25976			BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.1207C>A	3.37:g.156413774C>A	ENSP00000420612:p.Pro403Thr		157896468	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	Missense_Mutation	SNP	ENST00000461166.1	37	CCDS3177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.9|24.9	4.578356|4.578356	0.86645|0.86645	.|.	.|.	ENSG00000163659|ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783|ENST00000495891	T;T;T;T;T;T|.	0.24908|.	2.86;2.86;2.86;1.83;2.86;2.86|.	5.47|5.47	5.47|5.47	0.80525|0.80525	WWE domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79191|0.79191	0.4404|0.4404	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	P|.	0.62435|.	0.902|.	T|T	0.79729|0.79729	-0.1681|-0.1681	10|5	0.87932|.	D|.	0|.	.|.	18.9343|18.9343	0.92579|0.92579	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	403|.	Q7Z3E1|.	PARPT_HUMAN|.	T|N	403|105	ENSP00000418757:P403T;ENSP00000295924:P403T;ENSP00000420612:P403T;ENSP00000419982:P403T;ENSP00000418829:P403T;ENSP00000438345:P403T|.	ENSP00000295924:P403T|.	P|T	+|+	1|2	0|0	TIPARP|TIPARP	157896468|157896468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.375000|7.375000	0.79646|0.79646	2.579000|2.579000	0.87056|0.87056	0.460000|0.460000	0.39030|0.39030	CCC|ACC		0.393	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		A	156413774	C	A	156413774	3	1	18	1	0	0	0	0	1	0	0	0	15963	507	18	2	1217	2	TIPARP	3	156413774	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10	106751262	156413774	41608656	7	1778										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907802	164907802	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttctgtcttcctgatttctcGtaggtcctttccatggaagt	8	10	3	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr3:164907802G>A	ENST00000475390.1	-	2	1260	c.817C>T	c.(817-819)Cga>Tga	p.R273*	SLITRK3_ENST00000241274.3_Nonsense_Mutation_p.R273*			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	273	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.R273*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						CTGATTTCTCGTAGGTCCTTT	0.468										HNSCC(40;0.11)																																						1	Substitution - Nonsense(1)	large_intestine(1)	3											121	125	124					3																	164907802		2203	4300	6503	166390496	SO:0001587	stop_gained	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.817C>T	3.37:g.164907802G>A	ENSP00000420091:p.Arg273*		166390496	Q1RMY6	Nonsense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	38	6.837759	0.97877	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	.	.	.	5.85	3.98	0.46160	.	0.000000	0.30969	N	0.008502	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-10.7448	14.3566	0.66742	0.0:0.0:0.5045:0.4955	.	.	.	.	X	273	.	ENSP00000241274:R273X	R	-	1	2	SLITRK3	166390496	0.994000	0.37717	0.987000	0.45799	0.941000	0.58515	1.654000	0.37334	1.453000	0.47775	0.655000	0.94253	CGA		0.468	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		A	164907802	G	A	164907802	4	1	18	1	0	0	0	0	0	1	0	0	14781	1153	40	1	2120	1	SLITRK3	3	164907802	Nonsense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	8494028	164907802	33114628	8	1779										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193081069	193081069	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttggtttatgacagagtggcGgtcagccaccagggattctt	13	8	2	2			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr3:193081069G>A	ENST00000342358.4	-	3	457	c.340C>T	c.(340-342)Cgc>Tgc	p.R114C		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	114						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.R114C(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		ACAGAGTGGCGGTCAGCCACC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	94	94					3																	193081069		2203	4300	6503	194563763	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.340C>T	3.37:g.193081069G>A	ENSP00000341942:p.Arg114Cys		194563763	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	4.150	0.026205	0.08054	.	.	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.30448	1.53;1.53	5.02	-1.63	0.08345	.	1.281950	0.04988	N	0.466804	T	0.15825	0.0381	N	0.08118	0	0.09310	N	1	B	0.18863	0.031	B	0.15484	0.013	T	0.28650	-1.0037	10	0.56958	D	0.05	3.2484	5.8292	0.18570	0.3486:0.0:0.5274:0.1239	.	114	Q4VNC0	AT135_HUMAN	C	114;136	ENSP00000341942:R114C;ENSP00000389416:R136C	ENSP00000341942:R114C	R	-	1	0	ATP13A5	194563763	0.000000	0.05858	0.014000	0.15608	0.010000	0.07245	-1.510000	0.02262	-0.447000	0.07138	-0.850000	0.03035	CGC		0.388	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193081069	G	A	193081069	3	1	18	1	0	0	0	0	1	0	0	0	1128	1116	39	1	3426	1	ATP13A5	3	193081069	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	28173267	193081069	4941361	9	1780										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10447328	10447328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctttcatgtactctcttcgTgtgtttgacaatataatcat	5	9	3	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr4:10447328T>C	ENST00000326756.3	-	3	1063	c.625A>G	c.(625-627)Acg>Gcg	p.T209A		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	209					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.T209A(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						ACTCTCTTCGTGTGTTTGACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											172	177	175					4																	10447328		2203	4300	6503	10056426	SO:0001583	missense	85460			AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.625A>G	4.37:g.10447328T>C	ENSP00000317614:p.Thr209Ala		10056426	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458789	0.43634	.	.	ENSG00000178163	ENST00000326756	T	0.27720	1.65	6.16	0.538	0.17150	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.279835	0.28354	N	0.015648	T	0.20373	0.0490	L	0.27053	0.805	0.09310	N	0.999999	B	0.27791	0.189	B	0.22386	0.039	T	0.09751	-1.0660	10	0.30854	T	0.27	-16.6232	15.1324	0.72536	0.0:0.0:0.5332:0.4668	.	209	Q9C0D4	Z518B_HUMAN	A	209	ENSP00000317614:T209A	ENSP00000317614:T209A	T	-	1	0	ZNF518B	10056426	1.000000	0.71417	0.818000	0.32626	0.955000	0.61496	1.899000	0.39818	-0.117000	0.11872	0.528000	0.53228	ACG		0.428	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		C	10447328	T	C	10447328	3	2	18	1	0	0	0	0	1	0	0	0	18002	1696	59	4	2603	4	ZNF518B	4	10447328	Missense_Mutation	SNP	T	TCGA-AG-3582-01A-01W-0831-10		10447328	180706948	10	1781										
DKK2	27123	hgsc.bcm.edu	37	chr4	107845202	107845202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcccttcgcacagtcgcaaCgctggaaaatttccagccca	9	15	0	0	rs539488952		TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr4:107845202C>T	ENST00000285311.3	-	4	1394	c.689G>A	c.(688-690)cGt>cAt	p.R230H	DKK2_ENST00000510463.1_Missense_Mutation_p.R184H|DKK2_ENST00000513208.1_Missense_Mutation_p.R130H	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	230	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R230H(3)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ACAGTCGCAACGCTGGAAAAT	0.488													C|||	1	0.000199681	0	0	5008	,	,		18840	0.001		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(2)|prostate(1)	4											161	147	152					4																	107845202		2203	4300	6503	108064651	SO:0001583	missense	27123			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.689G>A	4.37:g.107845202C>T	ENSP00000285311:p.Arg230His		108064651	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897895	0.91962	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.57595	0.39;0.52;0.54	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.75361	0.3839	M	0.81341	2.54	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.77051	-0.2731	10	0.59425	D	0.04	-11.8314	19.6876	0.95986	0.0:1.0:0.0:0.0	.	230	Q9UBU2	DKK2_HUMAN	H	230;130;184	ENSP00000285311:R230H;ENSP00000421255:R130H;ENSP00000423797:R184H	ENSP00000285311:R230H	R	-	2	0	DKK2	108064651	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	7.487000	0.81328	2.657000	0.90304	0.585000	0.79938	CGT		0.488	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			T	107845202	C	T	107845202	3	4	18	1	0	0	0	0	1	0	0	0	4556	536	19	1	94	1	DKK2	4	107845202	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10	97397874	107845202	83309074	11	1782										
HTR1A	3350	hgsc.bcm.edu	37	chr5	63257014	63257014	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cggggtccgagcggtcttccGgggtgcgccagcccagcatg	17	14	1	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr5:63257014G>T	ENST00000323865.3	-	1	766	c.533C>A	c.(532-534)cCg>cAg	p.P178Q	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	178					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.P178Q(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GCGGTCTTCCGGGGTGCGCCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	126	120					5																	63257014		2203	4300	6503	63292770	SO:0001583	missense	3350			AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.533C>A	5.37:g.63257014G>T	ENSP00000316244:p.Pro178Gln		63292770	Q6LAE7	Missense_Mutation	SNP	ENST00000323865.3	37	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841366	0.71488	.	.	ENSG00000178394	ENST00000323865	T	0.36520	1.25	5.7	4.83	0.62350	GPCR, rhodopsin-like superfamily (1);	0.174290	0.50627	D	0.000118	T	0.44201	0.1282	N	0.20766	0.605	0.80722	D	1	D	0.69078	0.997	D	0.69654	0.965	T	0.41215	-0.9521	10	0.40728	T	0.16	.	15.8421	0.78857	0.0:0.136:0.864:0.0	.	178	P08908	5HT1A_HUMAN	Q	178	ENSP00000316244:P178Q	ENSP00000316244:P178Q	P	-	2	0	HTR1A	63292770	1.000000	0.71417	0.901000	0.35422	0.997000	0.91878	5.748000	0.68697	1.402000	0.46780	0.655000	0.94253	CCG		0.597	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		T	63257014	G	T	63257014	3	4	18	1	0	0	0	0	1	0	0	0	7457	1116	39	2	738	2	HTR1A	5	63257014	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		63257014	117658246	12	1783										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140517265	140517265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctatcccagagctaccactAcgaggtgtgtttgaccggag	11	12	0	2			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr5:140517265A>G	ENST00000231134.5	+	1	2466	c.2249A>G	c.(2248-2250)tAc>tGc	p.Y750C		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	750					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y750C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCTACCACTACGAGGTGTGT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											107	126	120					5																	140517265		2203	4300	6503	140497449	SO:0001583	missense	26167			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2249A>G	5.37:g.140517265A>G	ENSP00000231134:p.Tyr750Cys		140497449	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712323	0.48517	.	.	ENSG00000113209	ENST00000231134	T	0.55413	0.52	4.38	4.38	0.52667	.	.	.	.	.	T	0.61788	0.2375	M	0.93016	3.37	0.41808	D	0.989951	P	0.36577	0.558	B	0.33620	0.167	T	0.72852	-0.4167	9	0.72032	D	0.01	.	13.9261	0.63964	1.0:0.0:0.0:0.0	.	750	Q9Y5E4	PCDB5_HUMAN	C	750	ENSP00000231134:Y750C	ENSP00000231134:Y750C	Y	+	2	0	PCDHB5	140497449	1.000000	0.71417	0.837000	0.33122	0.083000	0.17756	6.884000	0.75600	1.756000	0.51951	0.414000	0.27820	TAC		0.627	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		G	140517265	A	G	140517265	3	3	18	1	0	0	0	0	1	0	0	0	11576	391	14	4	2251	4	PCDHB5	5	140517265	Missense_Mutation	SNP	A	TCGA-AG-3582-01A-01W-0831-10	77260251	140517265	40397995	13	1784										
VARS2	57176	hgsc.bcm.edu	37	chr6	30886629	30886629	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggttgtggtaggaaccacAaggccagagacgctgcctgg	16	9	0	1	rs190268810		TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr6:30886629A>C	ENST00000321897.5	+	10	1643	c.1011A>C	c.(1009-1011)acA>acC	p.T337T	VARS2_ENST00000542001.1_Silent_p.T197T|VARS2_ENST00000541562.1_Silent_p.T367T|VARS2_ENST00000416670.2_Silent_p.T337T			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	337			T -> I (in COXPD20; decreased levels of the protein). {ECO:0000269|PubMed:24827421}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)	p.T337T(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TAGGAACCACAAGGCCAGAGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	6											100	83	89					6																	30886629		1510	2708	4218	30994608	SO:0001819	synonymous_variant	57176			AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1011A>C	6.37:g.30886629A>C			30994608	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																				0.532	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30886629	A	C	30886629	2	2	18	1	0	0	0	0	0	0	0	1	17164	117	5	4		4	VARS2	6	30886629	Silent	SNP	A	TCGA-AG-3582-01A-01W-0831-10		30886629	140228438	14	1785										
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110746109	110746109	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ccagaatccctgggggtaatCgcttccgttttttccagccc	9	14	0	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr6:110746109C>T	ENST00000368919.3	-	8	1767	c.1701G>A	c.(1699-1701)gcG>gcA	p.A567A	SLC22A16_ENST00000330550.4_Silent_p.A533A	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	567					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)	p.A567A(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	TGGGGGTAATCGCTTCCGTTT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	6											147	138	141					6																	110746109		2203	4300	6503	110852802	SO:0001819	synonymous_variant	85413				CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1701G>A	6.37:g.110746109C>T			110852802	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Silent	SNP	ENST00000368919.3	37	CCDS5084.1																																																																																				0.428	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		T	110746109	C	T	110746109	2	4	18	1	0	0	0	0	0	0	0	1	14484	871	31	1		1	SLC22A16	6	110746109	Silent	SNP	C	TCGA-AG-3582-01A-01W-0831-10	79859480	110746109	60368958	15	1786										
MOGAT3	346606	hgsc.bcm.edu	37	chr7	100839608	100839608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatgctgccaggagcctgtgGcaaaagccttaagtctaaag	11	9	1	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr7:100839608G>T	ENST00000223114.4	-	6	897	c.731C>A	c.(730-732)gCc>gAc	p.A244D	MOGAT3_ENST00000379423.3_Intron|MOGAT3_ENST00000440203.2_Missense_Mutation_p.A244D	NM_178176.2	NP_835470.1	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	244					glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)	p.A244D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3)	22	Lung NSC(181;0.168)|all_lung(186;0.215)					GGAGCCTGTGGCAAAAGCCTT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	7											42	46	45					7																	100839608		2203	4300	6503	100626328	SO:0001583	missense	346606			AY229854	CCDS5714.1, CCDS75643.1	7q22	2012-09-06			ENSG00000106384	ENSG00000106384	2.3.1.20, 2.3.1.22		23249	protein-coding gene	gene with protein product		610184				12618427, 14970677	Standard	XM_005250309		Approved	DC7, MGAT3	uc003uyc.3	Q86VF5	OTTHUMG00000023328	ENST00000223114.4:c.731C>A	7.37:g.100839608G>T	ENSP00000223114:p.Ala244Asp		100626328	Q496A6|Q496A7|Q496A8|Q9UDW7	Missense_Mutation	SNP	ENST00000223114.4	37	CCDS5714.1	.	.	.	.	.	.	.	.	.	.	G	7.391	0.630703	0.14322	.	.	ENSG00000106384	ENST00000223114;ENST00000440203	T;T	0.12039	2.72;2.72	4.83	2.92	0.33932	.	0.802766	0.11371	N	0.570828	T	0.07143	0.0181	N	0.05608	-0.01	0.09310	N	1	B	0.12630	0.006	B	0.14578	0.011	T	0.22277	-1.0221	10	0.33141	T	0.24	-3.4709	8.8231	0.35039	0.0:0.1693:0.677:0.1537	.	244	Q86VF5	MOGT3_HUMAN	D	244	ENSP00000223114:A244D;ENSP00000403756:A244D	ENSP00000223114:A244D	A	-	2	0	MOGAT3	100626328	0.000000	0.05858	0.003000	0.11579	0.045000	0.14185	0.050000	0.14120	2.216000	0.71823	0.650000	0.86243	GCC		0.577	MOGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059649.3	NM_178176		T	100839608	G	T	100839608	3	4	18	1	0	0	0	0	1	0	0	0	9726	1203	42	2	302	2	MOGAT3	7	100839608	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		100839608	58299055	16	1787										
DKK4	27121	hgsc.bcm.edu	37	chr8	42233224	42233224	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cacagagtgtcccagggcagCacatggcatctcgctggcac	12	14	1	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr8:42233224C>G	ENST00000220812.2	-	2	422	c.236G>C	c.(235-237)tGc>tCc	p.C79S		NM_014420.2	NP_055235.1	Q9UBT3	DKK4_HUMAN	dickkopf WNT signaling pathway inhibitor 4	79	DKK-type Cys-1.				multicellular organismal development (GO:0007275)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)		p.C79S(1)		NS(1)|endometrium(1)|large_intestine(7)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|Lung(22;0.00597)|LUSC - Lung squamous cell carcinoma(45;0.024)			CCCAGGGCAGCACATGGCATC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	8											113	93	100					8																	42233224		2203	4300	6503	42352381	SO:0001583	missense	27121			AF177397	CCDS6130.1	8p11.2-p11.1	2013-05-15	2013-05-15		ENSG00000104371	ENSG00000104371			2894	protein-coding gene	gene with protein product		605417	"dickkopf (Xenopus laevis) homolog 4", "dickkopf homolog 4 (Xenopus laevis)"			10570958, 11701963	Standard	NM_014420		Approved		uc003xpb.3	Q9UBT3	OTTHUMG00000164167	ENST00000220812.2:c.236G>C	8.37:g.42233224C>G	ENSP00000220812:p.Cys79Ser		42352381	Q3KNX0|Q9Y4C3	Missense_Mutation	SNP	ENST00000220812.2	37	CCDS6130.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595072	0.86953	.	.	ENSG00000104371	ENST00000543914;ENST00000220812	T	0.64991	-0.13	5.2	5.2	0.72013	Dickkopf, N-terminal cysteine-rich (1);	0.184843	0.39146	N	0.001460	T	0.80919	0.4716	M	0.84326	2.69	0.46564	D	0.999101	D	0.89917	1.0	D	0.91635	0.999	D	0.83760	0.0214	10	0.87932	D	0	-7.3548	16.5637	0.84573	0.0:1.0:0.0:0.0	.	79	Q9UBT3	DKK4_HUMAN	S	79	ENSP00000220812:C79S	ENSP00000220812:C79S	C	-	2	0	DKK4	42352381	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	6.738000	0.74822	2.567000	0.86603	0.491000	0.48974	TGC		0.537	DKK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377563.1			G	42233224	C	G	42233224	3	3	18	1	0	0	0	0	1	0	0	0	4558	710	25	5	450	5	DKK4	8	42233224	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10		42233224	104130798	17	1788										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19358055	19358055	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcgaaatgtgtctttgactcGaagtcacagtgttggaggcc	13	8	2	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr9:19358055G>T	ENST00000380432.2	+	23	4235	c.4202G>T	c.(4201-4203)cGa>cTa	p.R1401L	DENND4C_ENST00000434457.2_Missense_Mutation_p.R1686L|DENND4C_ENST00000602925.1_Missense_Mutation_p.R1637L			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1401					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1401L(1)		breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TCTTTGACTCGAAGTCACAGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	91	95					9																	19358055		2203	4300	6503	19348055	SO:0001583	missense	55667			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4202G>T	9.37:g.19358055G>T	ENSP00000369797:p.Arg1401Leu		19348055	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	34	5.370031	0.95900	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.36340	1.27;1.26	5.67	5.67	0.87782	.	1.146860	0.06258	N	0.693460	T	0.68375	0.2994	M	0.78049	2.395	0.54753	D	0.999985	D;D;D	0.71674	0.998;0.998;0.992	D;D;P	0.72982	0.972;0.979;0.702	T	0.59984	-0.7351	10	0.72032	D	0.01	-10.0663	20.1358	0.98028	0.0:0.0:1.0:0.0	.	731;583;1401	B7Z660;Q5VZ89-3;Q5VZ89	.;.;DEN4C_HUMAN	L	1401;874;583;731;874;583;398	ENSP00000305795:R874L;ENSP00000443804:R731L	ENSP00000305795:R874L	R	+	2	0	DENND4C	19348055	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.765000	0.74965	2.833000	0.97629	0.585000	0.79938	CGA		0.398	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19358055	G	T	19358055	3	4	18	1	0	0	0	0	1	0	0	0	4446	1058	37	2	4292	2	DENND4C	9	19358055	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		19358055	121855376	18	1789										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90252859	90252859	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgcttccgggttctcagcGttgcaggtggcgagctgttt	14	10	2	0	rs200255856		TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr9:90252859G>A	ENST00000408954.3	+	4	621	c.286G>A	c.(286-288)Gtt>Att	p.V96I	DAPK1_ENST00000469640.2_Splice_Site_p.V96I|DAPK1_ENST00000358077.5_Splice_Site_p.V96I|DAPK1_ENST00000491893.1_Splice_Site_p.V96I|DAPK1_ENST00000472284.1_Splice_Site_p.V96I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V96I(2)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GGTTCTCAGCGTTGCAGGTGG	0.398									Chronic Lymphocytic Leukemia, Familial Clustering of																																							2	Substitution - Missense(2)	large_intestine(2)	9											103	103	103					9																	90252859		2074	4243	6317	89442679	SO:0001630	splice_region_variant	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.285-1G>A	9.37:g.90252859G>A			89442679	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474124	0.84640	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43579	D	0.000544	T	0.53658	0.1810	N	0.25825	0.765	0.80722	D	1	P;P;D	0.64830	0.792;0.802;0.994	P;B;D	0.71414	0.502;0.218;0.973	T	0.57271	-0.7840	10	0.87932	D	0	.	19.0661	0.93110	0.0:0.0:1.0:0.0	.	96;96;96	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	I	96	ENSP00000350785:V96I;ENSP00000417076:V96I;ENSP00000418885:V96I;ENSP00000386135:V96I;ENSP00000419026:V96I	ENSP00000350785:V96I	V	+	1	0	DAPK1	89442679	1.000000	0.71417	0.973000	0.42090	0.688000	0.40055	9.657000	0.98554	2.746000	0.94184	0.655000	0.94253	GTT		0.398	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	Missense_Mutation	A	90252859	G	A	90252859	5	1	18	1	0	0	0	0	0	0	1	0	4241	1159	40	1	296	1	DAPK1	9	90252859	Splice_Site	SNP	G	TCGA-AG-3582-01A-01W-0831-10	70894804	90252859	50960572	19	1790										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114912186	114912186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	actgtaccccggctggtccgCgcgggataactatgtaggtg	14	11	0	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr10:114912186C>T	ENST00000355995.4	+	11	1763	c.1256C>T	c.(1255-1257)gCg>gTg	p.A419V	TCF7L2_ENST00000352065.5_Missense_Mutation_p.A396V|TCF7L2_ENST00000369389.1_Missense_Mutation_p.A130V|TCF7L2_ENST00000369386.1_Missense_Mutation_p.A62V|TCF7L2_ENST00000545257.1_Missense_Mutation_p.A419V|TCF7L2_ENST00000536810.1_Missense_Mutation_p.A419V|TCF7L2_ENST00000542695.1_Missense_Mutation_p.A135V|TCF7L2_ENST00000538897.1_Missense_Mutation_p.A419V|TCF7L2_ENST00000355717.4_Missense_Mutation_p.A443V|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000534894.1_Missense_Mutation_p.A419V|TCF7L2_ENST00000369397.4_Missense_Mutation_p.A396V|TCF7L2_ENST00000543371.1_Missense_Mutation_p.A419V			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	419					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A396V(1)|p.A419V(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GGCTGGTCCGCGCGGGATAAC	0.527			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	2	Substitution - Missense(2)	large_intestine(2)	10											109	115	113					10																	114912186		2203	4300	6503	114902176	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1256C>T	10.37:g.114912186C>T	ENSP00000348274:p.Ala419Val		114902176	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	c	36	5.635243	0.96682	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945;ENST00000369386	D;D;D;D;D;D;D;D;D;D;D;D	0.99376	-5.27;-5.28;-5.26;-5.27;-5.75;-5.79;-5.79;-5.28;-5.78;-5.22;-5.68;-5.71	5.66	5.66	0.87406	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (2);	0.105150	0.64402	D	0.000005	D	0.99453	0.9806	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.997;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0	P;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.846;0.957;0.987;0.842;0.98;0.956;0.997;0.976;0.987;0.956;0.98;0.97;0.97;0.973;0.996;0.967;0.987;0.992;0.999	D	0.99129	1.0852	10	0.54805	T	0.06	-5.0689	19.7439	0.96243	0.0:1.0:0.0:0.0	.	276;236;318;419;290;334;392;396;396;362;419;396;396;401;443;396;419;392;396	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	V	419;419;419;419;443;419;419;396;396;135;130;136;62	ENSP00000348274:A419V;ENSP00000440547:A419V;ENSP00000444972:A419V;ENSP00000446238:A419V;ENSP00000347949:A443V;ENSP00000446172:A419V;ENSP00000443626:A419V;ENSP00000358404:A396V;ENSP00000344823:A396V;ENSP00000443883:A135V;ENSP00000358396:A130V;ENSP00000277945:A136V	ENSP00000277945:A136V	A	+	2	0	TCF7L2	114902176	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.814000	0.86154	2.669000	0.90835	0.655000	0.94253	GCG		0.527	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114912186	C	T	114912186	3	4	18	1	0	0	0	0	1	0	0	0	15737	768	27	1	1443	1	TCF7L2	10	114912186	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10		114912186	20622561	20	1791										
MRE11A	4361	hgsc.bcm.edu	37	chr11	94180584	94180584	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcctctgactgagatctgagTgctctggccctggtcatagc	11	12	4	3			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr11:94180584T>C	ENST00000323929.3	-	15	1806	c.1584A>G	c.(1582-1584)gcA>gcG	p.A528A	MRE11A_ENST00000393241.4_Silent_p.A528A|MRE11A_ENST00000407439.3_Silent_p.A531A|MRE11A_ENST00000323977.3_Silent_p.A528A	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	528					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.A528A(2)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				GAGATCTGAGTGCTCTGGCCC	0.423								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																																							2	Substitution - coding silent(2)	large_intestine(2)	11											84	77	79					11																	94180584		2201	4298	6499	93820232	SO:0001819	synonymous_variant	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.1584A>G	11.37:g.94180584T>C			93820232	O43475	Silent	SNP	ENST00000323929.3	37	CCDS8299.1																																																																																				0.423	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		C	94180584	T	C	94180584	2	2	18	1	0	0	0	0	0	0	0	1	9789	1683	59	4		4	MRE11A	11	94180584	Silent	SNP	T	TCGA-AG-3582-01A-01W-0831-10		94180584	40825932	21	1792										
GMFB	2764	hgsc.bcm.edu	37	chr14	54950418	54950418	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagcgttgttcgtttctttgCgaaaacgaaactttctcagc	8	10	2	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr14:54950418C>A	ENST00000358056.3	-	2	339	c.71G>T	c.(70-72)cGc>cTc	p.R24L	GMFB_ENST00000554908.1_Missense_Mutation_p.R24L|GMFB_ENST00000553566.1_5'UTR	NM_004124.2	NP_004115.1	P60983	GMFB_HUMAN	glia maturation factor, beta	24	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of protein kinase activity (GO:0006469)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)|signal transducer activity (GO:0004871)	p.R24L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)	8						CGTTTCTTTGCGAAAACGAAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	14											83	72	76					14																	54950418		2202	4300	6502	54020168	SO:0001583	missense	2764			M86492	CCDS9718.1	14q22.2	2010-07-06			ENSG00000197045	ENSG00000197045			4373	protein-coding gene	gene with protein product		601713				1712830	Standard	NM_004124		Approved	GMF	uc021rtf.1	P60983	OTTHUMG00000140307	ENST00000358056.3:c.71G>T	14.37:g.54950418C>A	ENSP00000350757:p.Arg24Leu		54020168	B2R499|P17774|Q9BS35	Missense_Mutation	SNP	ENST00000358056.3	37	CCDS9718.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046402	0.93740	.	.	ENSG00000197045	ENST00000554908;ENST00000358056;ENST00000354747;ENST00000553333	T;T	0.32753	1.44;1.44	5.44	5.44	0.79542	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	T	0.57315	0.2045	M	0.77616	2.38	0.80722	D	1	P	0.41569	0.755	P	0.59288	0.855	T	0.55872	-0.8072	10	0.54805	T	0.06	-15.3782	18.5988	0.91240	0.0:1.0:0.0:0.0	.	24	P60983	GMFB_HUMAN	L	24;24;24;36	ENSP00000350757:R24L;ENSP00000451920:R36L	ENSP00000346789:R24L	R	-	2	0	GMFB	54020168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.265000	0.78442	2.714000	0.92807	0.585000	0.79938	CGC		0.333	GMFB-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276903.2	NM_004124		A	54950418	C	A	54950418	3	1	18	1	0	0	0	0	1	0	0	0	6509	768	27	2	381	2	GMFB	14	54950418	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10		54950418	52399122	22	1793										
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71199547	71199547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcggagcgcagcagggagcGtgtggagttgcactcggaga	19	8	0	1	rs140360648		TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr14:71199547G>A	ENST00000554752.2	-	11	2538	c.2539C>T	c.(2539-2541)Cgc>Tgc	p.R847C	MAP3K9_ENST00000555993.2_Missense_Mutation_p.R861C|MAP3K9_ENST00000553414.1_Missense_Mutation_p.R580C|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R575C|MAP3K9_ENST00000381250.4_Missense_Mutation_p.R824C	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	847					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R861C(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		AGCAGGGAGCGTGTGGAGTTG	0.592																																					GBM(114;411 1587 13539 28235 50070)											1	Substitution - Missense(1)	large_intestine(1)	14						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	64	58	60		2581	4.6	1	14	dbSNP_134	60	0,8600		0,0,4300	no	missense	MAP3K9	NM_033141.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	861/1119	71199547	1,13005	2203	4300	6503	70269300	SO:0001583	missense	4293			AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2539C>T	14.37:g.71199547G>A	ENSP00000451612:p.Arg847Cys		70269300	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	37		.	.	.	.	.	.	.	.	.	.	G	19.48	3.835040	0.71373	2.27E-4	0.0	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.79940	-1.28;-1.32;-1.25;-1.29	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.87026	0.6075	L	0.54323	1.7	0.58432	D	0.999993	D;D;D;D	0.89917	0.999;0.998;0.999;1.0	P;P;P;D	0.67103	0.862;0.623;0.897;0.949	D	0.88471	0.3062	10	0.72032	D	0.01	.	17.6702	0.88214	0.0:0.0:1.0:0.0	.	575;847;861;580	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	C	847;861;580;824;575;563	ENSP00000451612:R847C;ENSP00000451038:R580C;ENSP00000370649:R824C;ENSP00000451921:R575C	ENSP00000005198:R861C	R	-	1	0	MAP3K9	70269300	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	4.332000	0.59279	2.397000	0.81536	0.561000	0.74099	CGC		0.592	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			A	71199547	G	A	71199547	3	1	18	1	0	0	0	0	1	0	0	0	9287	1145	40	1	783	1	MAP3K9	14	71199547	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	16249129	71199547	36149993	23	1794										
HYDIN	54768	hgsc.bcm.edu	37	chr16	71065798	71065798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgccttcattgggttcaatcGtccaaagggattttttgtgt	10	7	2	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr16:71065798G>A	ENST00000393567.2	-	19	2702	c.2552C>T	c.(2551-2553)aCg>aTg	p.T851M	HYDIN_ENST00000321489.5_Missense_Mutation_p.T851M|HYDIN_ENST00000448089.2_Missense_Mutation_p.T851M|HYDIN_ENST00000538248.1_Missense_Mutation_p.T878M|HYDIN_ENST00000541601.1_Missense_Mutation_p.T868M|HYDIN_ENST00000448691.1_Missense_Mutation_p.T851M	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	851					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.T851M(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGGTTCAATCGTCCAAAGGGA	0.428																																																3	Substitution - Missense(3)	large_intestine(3)	16																																								69623299	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2552C>T	16.37:g.71065798G>A	ENSP00000377197:p.Thr851Met		69623299	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.129842	0.37630	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601	T;T;T;T;T;T	0.04156	5.55;3.7;3.7;3.7;3.69;3.7	4.78	1.47	0.22746	.	0.558512	0.13102	N	0.413710	T	0.04952	0.0133	L	0.52364	1.645	0.58432	D	0.999995	B;B;B;B	0.29716	0.129;0.129;0.129;0.255	B;B;B;B	0.32289	0.143;0.143;0.112;0.024	T	0.38542	-0.9656	10	0.31617	T	0.26	.	3.344	0.07128	0.1019:0.3663:0.3908:0.141	.	878;868;851;851	B4DRN4;F5H6V3;Q4G0P3-5;F8WD23	.;.;.;.	M	851;851;851;851;851;878;868	ENSP00000377197:T851M;ENSP00000398544:T851M;ENSP00000394826:T851M;ENSP00000314736:T851M;ENSP00000444970:T878M;ENSP00000437341:T868M	ENSP00000313052:T851M	T	-	2	0	HYDIN	69623299	0.988000	0.35896	0.780000	0.31762	0.958000	0.62258	2.377000	0.44300	1.039000	0.40074	0.499000	0.49734	ACG		0.428	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71065798	G	A	71065798	3	1	18	1	0	0	0	0	1	0	0	0	7488	1145	40	1	13094	1	HYDIN	16	71065798	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		71065798	19288955	24	1795										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42942346	42942346	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaccagcctgagcaaggggcGgatgttcagcttcagctcct	13	12	2	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr17:42942346G>A	ENST00000426333.2	-	14	1534	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	EFTUD2_ENST00000402521.3_Missense_Mutation_p.R378C|EFTUD2_ENST00000591382.1_Missense_Mutation_p.R413C|EFTUD2_ENST00000592576.1_Missense_Mutation_p.R403C	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	413					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.R413C(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				AGCAAGGGGCGGATGTTCAGC	0.562											OREG0024466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Ovarian(10;65 485 10258 29980 30707)											1	Substitution - Missense(1)	large_intestine(1)	17											168	145	153					17																	42942346		2203	4300	6503	40297872	SO:0001583	missense	9343			D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1237C>T	17.37:g.42942346G>A	ENSP00000392094:p.Arg413Cys	912	40297872	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	37	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858946	0.71834	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.78246	-1.16;-1.16	5.95	5.95	0.96441	.	0.106362	0.64402	D	0.000006	D	0.90359	0.6983	M	0.90019	3.08	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.64776	0.929;0.929	D	0.91326	0.5086	10	0.87932	D	0	-5.2287	20.3931	0.98965	0.0:0.0:1.0:0.0	.	403;413	B4DMC0;Q15029	.;U5S1_HUMAN	C	413;403;378	ENSP00000392094:R413C;ENSP00000385873:R378C	ENSP00000262414:R403C	R	-	1	0	EFTUD2	40297872	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.687000	0.68219	2.824000	0.97209	0.655000	0.94253	CGC		0.562	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		A	42942346	G	A	42942346	3	1	18	1	0	0	0	0	1	0	0	0	4972	1116	39	1	1741	1	EFTUD2	17	42942346	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		42942346	38252864	25	1796										
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55027480	55027480	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatgcatggggaagggctcaCcaagctgactctgtcacact	11	11	3	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr18:55027480C>A	ENST00000324000.3	+	4	3149	c.1115C>A	c.(1114-1116)aCc>aAc	p.T372N		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	372					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.T372N(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GAAGGGCTCACCAAGCTGACT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											52	45	47					18																	55027480		2203	4300	6503	53178478	SO:0001583	missense	51046			AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.1115C>A	18.37:g.55027480C>A	ENSP00000320431:p.Thr372Asn		53178478	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.226499	0.58668	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.29917	1.55	6.11	5.23	0.72850	.	0.313497	0.38436	N	0.001686	T	0.20861	0.0502	N	0.08118	0	0.37651	D	0.92242	B	0.30937	0.301	B	0.35770	0.21	T	0.22034	-1.0228	10	0.87932	D	0	-11.0866	14.5541	0.68089	0.0:0.9299:0.0:0.0701	.	372	O43173	SIA8C_HUMAN	N	479;372	ENSP00000320431:T372N	ENSP00000320431:T372N	T	+	2	0	ST8SIA3	53178478	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.505000	0.60421	2.906000	0.99361	0.655000	0.94253	ACC		0.473	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		A	55027480	C	A	55027480	3	1	18	1	0	0	0	0	1	0	0	0	15272	507	18	2	1129	2	ST8SIA3	18	55027480	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10		55027480	23049768	26	1797										
SERPINB13	5275	hgsc.bcm.edu	37	chr18	61264545	61264545	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcccttcctgttcttcatcaGgcacaatgaatccaacagca	5	14	3	1			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr18:61264545G>T	ENST00000344731.5	+	8	1226	c.1124G>T	c.(1123-1125)aGg>aTg	p.R375M	SERPINB13_ENST00000269489.5_Missense_Mutation_p.R323M	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	375					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R375M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						TTCTTCATCAGGCACAATGAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	18											108	89	95					18																	61264545		2203	4300	6503	59415525	SO:0001583	missense	5275			AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.1124G>T	18.37:g.61264545G>T	ENSP00000341584:p.Arg375Met		59415525	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	37	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.479228	0.63849	.	.	ENSG00000197641	ENST00000269489;ENST00000539341;ENST00000344731	D;D	0.86432	-2.12;-2.12	5.4	2.65	0.31530	Serpin domain (3);	0.210090	0.33180	N	0.005200	D	0.90696	0.7081	M	0.78223	2.4	0.40421	D	0.979842	D;P;D	0.76494	0.997;0.794;0.999	D;B;D	0.69479	0.964;0.268;0.923	D	0.87928	0.2708	10	0.66056	D	0.02	.	4.3779	0.11279	0.3277:0.0:0.5258:0.1464	.	384;293;375	B7ZKV6;F5GZ40;Q9UIV8	.;.;SPB13_HUMAN	M	323;293;375	ENSP00000269489:R323M;ENSP00000341584:R375M	ENSP00000269489:R323M	R	+	2	0	SERPINB13	59415525	0.016000	0.18221	0.996000	0.52242	0.979000	0.70002	1.188000	0.32102	0.272000	0.22027	-0.262000	0.10625	AGG		0.483	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		T	61264545	G	T	61264545	3	4	18	1	0	0	0	0	1	0	0	0	14137	1000	35	2	1150	2	SERPINB13	18	61264545	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	6237065	61264545	16812703	27	1798										
C3	718	hgsc.bcm.edu	37	chr19	6678219	6678221	+	In_Frame_Del	DEL	CTC	CTC	-													0	0	1	0	0	0	1	1	0	cacatgaggtagtgtttcttCtcctccagcttcagggcttc							TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	CTC	CTC	CTC	-	CTC	CTC	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr19:6678219_6678221delCTC	ENST00000245907.6	-	40	4884_4886	c.4792_4794delGAG	c.(4792-4794)gagdel	p.E1598del	C3_ENST00000599668.1_5'UTR	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1598	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.E1598delE(1)		breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	AGTGTTTCTTCTCCTCCAGCTTC	0.616																																																1	Deletion - In frame(1)	large_intestine(1)	19																																								6629221	SO:0001651	inframe_deletion	718			J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4792_4794delGAG	19.37:g.6678222_6678224delCTC	ENSP00000245907:p.Glu1598del		6629219	A7E236	In_Frame_Del	DEL	ENST00000245907.6	37	CCDS32883.1																																																																																				0.616	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		-	6678221	CTC	-	6678219	7	5	18	1	0	1	0	1	0	0	0	0	2210	912	32	0	205	0	C3	19	6678219	In_Frame_Del	DEL	CTC	TCGA-AG-3582-01A-01W-0831-10		6678219	52450764	28	1799										
ZNF420	147923	hgsc.bcm.edu	37	chr19	37618514	37618514	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggaaggcctttactcaaagCtcacaacttattttacatca	6	10	3	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr19:37618514C>A	ENST00000337995.3	+	5	836	c.621C>A	c.(619-621)agC>agA	p.S207R	ZNF420_ENST00000304239.7_Missense_Mutation_p.S207R|CTC-454I21.4_ENST00000587645.1_RNA|ZNF585A_ENST00000588723.1_Intron	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S207R(1)		breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTACTCAAAGCTCACAACTTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	55	55					19																	37618514		2203	4300	6503	42310354	SO:0001583	missense	147923			AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.621C>A	19.37:g.37618514C>A	ENSP00000338770:p.Ser207Arg		42310354	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	37	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	C	3.655	-0.070696	0.07228	.	.	ENSG00000197050	ENST00000304239;ENST00000337995	T;T	0.06768	3.26;3.26	3.65	-0.0537	0.13816	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02929	0.0087	N	0.05574	-0.02	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.46871	-0.9160	9	0.12103	T	0.63	.	1.1725	0.01829	0.1737:0.4394:0.1702:0.2167	.	207	Q8TAQ5	ZN420_HUMAN	R	207	ENSP00000306102:S207R;ENSP00000338770:S207R	ENSP00000306102:S207R	S	+	3	2	ZNF420	42310354	0.000000	0.05858	0.987000	0.45799	0.985000	0.73830	-3.132000	0.00590	0.238000	0.21222	-0.150000	0.13652	AGC		0.398	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		A	37618514	C	A	37618514	3	1	18	1	0	0	0	0	1	0	0	0	17936	796	28	2	631	2	ZNF420	19	37618514	Missense_Mutation	SNP	C	TCGA-AG-3582-01A-01W-0831-10	30940295	37618514	21510469	29	1800										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47969377	47969377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgtgatgacctcgatggccGccatgaaacggtcggcgatg	14	11	0	3			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr19:47969377G>A	ENST00000236877.6	-	2	679	c.284C>T	c.(283-285)gCg>gTg	p.A95V	SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	95					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)	p.A95V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		CTCGATGGCCGCCATGAAACG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											125	84	98					19																	47969377		2203	4300	6503	52661189	SO:0001583	missense	6543			AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.284C>T	19.37:g.47969377G>A	ENSP00000236877:p.Ala95Val		52661189	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	37	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944860	0.92593	.	.	ENSG00000118160	ENST00000236877	T	0.63744	-0.06	4.25	4.25	0.50352	Sodium/calcium exchanger membrane region (1);	0.062961	0.64402	D	0.000007	T	0.79730	0.4496	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.70016	0.967	D	0.83859	0.0267	10	0.87932	D	0	.	15.6004	0.76620	0.0:0.0:1.0:0.0	.	95	Q9UPR5	NAC2_HUMAN	V	95	ENSP00000236877:A95V	ENSP00000236877:A95V	A	-	2	0	SLC8A2	52661189	1.000000	0.71417	0.935000	0.37517	0.950000	0.60333	9.587000	0.98229	2.210000	0.71456	0.462000	0.41574	GCG		0.582	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			A	47969377	G	A	47969377	3	1	18	1	0	0	0	0	1	0	0	0	14744	1087	38	1	2517	1	SLC8A2	19	47969377	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	10350863	47969377	11159606	30	1801										
LILRB2	10288	hgsc.bcm.edu	37	chr19	54783718	54783718	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtaatactgacagccatatcGccctgtgtgttcccaggtga	10	11	0	2			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr19:54783718G>A	ENST00000391749.4	-	4	554	c.283C>T	c.(283-285)Cga>Tga	p.R95*	LILRB2_ENST00000471216.1_5'UTR|LILRB2_ENST00000434421.1_5'UTR|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000391746.1_Nonsense_Mutation_p.R95*|LILRB2_ENST00000314446.5_Nonsense_Mutation_p.R95*|LILRB2_ENST00000391748.1_Nonsense_Mutation_p.R95*	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	95	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)	p.R95*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CAGCCATATCGCCCTGTGTGT	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											177	168	171					19																	54783718		2203	4300	6503	59475530	SO:0001587	stop_gained	10288			AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.283C>T	19.37:g.54783718G>A	ENSP00000375629:p.Arg95*		59475530	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Nonsense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093368	0.56075	.	.	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746	.	.	.	1.76	-0.909	0.10514	.	1.592300	0.04262	N	0.340541	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.8451	0.08931	0.0:0.273:0.4491:0.2779	.	.	.	.	X	95	.	ENSP00000319960:R95X	R	-	1	2	LILRB2	59475530	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.741000	0.01837	-0.094000	0.12374	0.289000	0.19496	CGA		0.552	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			A	54783718	G	A	54783718	4	1	18	1	0	0	0	0	0	1	0	0	8814	1095	38	1	1557	1	LILRB2	19	54783718	Nonsense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10	6814341	54783718	4345265	31	1802										
LARGE	9215	hgsc.bcm.edu	37	chr22	34000485	34000485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccatccaggtctggaagagcGtggccaggatctgctccgca	13	13	2	1	rs138676820	byFrequency	TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chr22:34000485G>A	ENST00000354992.2	-	6	1122	c.551C>T	c.(550-552)aCg>aTg	p.T184M	LARGE_ENST00000397394.2_Missense_Mutation_p.T184M|LARGE_ENST00000437602.2_Missense_Mutation_p.T184M|LARGE_ENST00000337431.2_Missense_Mutation_p.T184M|LARGE_ENST00000402320.1_Missense_Mutation_p.T184M	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	184					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.T184M(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CTGGAAGAGCGTGGCCAGGAT	0.582													G|||	2	0.000399361	0	0	5008	,	,		19556	0.002		0	False		,,,				2504	0				Colon(70;397 1175 4573 19089 45288)											1	Substitution - Missense(1)	large_intestine(1)	22						G	MET/THR,MET/THR	0,4406		0,0,2203	152	125	134		551,551	5.8	1	22	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LARGE	NM_004737.4,NM_133642.3	81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	184/757,184/757	34000485	1,13005	2203	4300	6503	32330485	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.551C>T	22.37:g.34000485G>A	ENSP00000347088:p.Thr184Met		32330485	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	37	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.125012	0.56721	0.0	1.16E-4	ENSG00000133424	ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000437602	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.79	5.79	0.91817	.	0.209207	0.50627	D	0.000109	T	0.44829	0.1312	M	0.69358	2.11	0.80722	D	1	P;P;P	0.44946	0.694;0.794;0.846	B;B;B	0.37888	0.223;0.26;0.149	T	0.50550	-0.8815	10	0.54805	T	0.06	-2.9973	18.7926	0.91980	0.0:0.0:1.0:0.0	.	184;184;184	B7Z2I9;O95461-2;O95461	.;.;LARGE_HUMAN	M	184	ENSP00000347088:T184M;ENSP00000336636:T184M;ENSP00000380549:T184M;ENSP00000385223:T184M;ENSP00000388544:T184M	ENSP00000336636:T184M	T	-	2	0	LARGE	32330485	0.991000	0.36638	0.959000	0.39883	0.998000	0.95712	3.390000	0.52523	2.735000	0.93741	0.561000	0.74099	ACG		0.582	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	34000485	G	A	34000485	3	1	18	1	0	0	0	0	1	0	0	0	8649	1145	40	1	1763	1	LARGE	22	34000485	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		34000485	17304081	32	1803										
ITGB1BP2	26548	hgsc.bcm.edu	37	chrX	70522363	70522363	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggagcaaaaacctctgaatGtgattccaaagtcagcagag	10	8	2	3			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chrX:70522363G>C	ENST00000373829.3	+	4	347	c.274G>C	c.(274-276)Gtg>Ctg	p.V92L	ITGB1BP2_ENST00000538820.1_Missense_Mutation_p.V74L	NM_012278.1	NP_036410.1	Q9UKP3	ITBP2_HUMAN	integrin beta 1 binding protein (melusin) 2	92					muscle organ development (GO:0007517)|signal transduction (GO:0007165)	Z disc (GO:0030018)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.V92L(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)	14	Renal(35;0.156)					ACCTCTGAATGTGATTCCAAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											40	39	39					X																	70522363		2203	4300	6503	70439088	SO:0001583	missense	26548			AF140690	CCDS14411.1	Xq12.1-q13	2008-02-05			ENSG00000147166	ENSG00000147166			6154	protein-coding gene	gene with protein product		300332				10506186	Standard	XM_005262255		Approved	CHORDC3	uc004dzr.1	Q9UKP3	OTTHUMG00000021793	ENST00000373829.3:c.274G>C	X.37:g.70522363G>C	ENSP00000362935:p.Val92Leu		70439088	Q32N04|Q549J7	Missense_Mutation	SNP	ENST00000373829.3	37	CCDS14411.1	.	.	.	.	.	.	.	.	.	.	g	0.195	-1.049826	0.01981	.	.	ENSG00000147166	ENST00000373829;ENST00000538820	.	.	.	4.84	-2.27	0.06846	.	1.038600	0.07547	N	0.914778	T	0.12092	0.0294	N	0.02539	-0.55	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.08055	0.0;0.003	T	0.20174	-1.0283	9	0.24483	T	0.36	4.818	3.1423	0.06460	0.322:0.0:0.344:0.3339	.	74;92	Q32N04;Q9UKP3	.;ITBP2_HUMAN	L	92;74	.	ENSP00000362935:V92L	V	+	1	0	ITGB1BP2	70439088	0.763000	0.28462	0.006000	0.13384	0.888000	0.51559	0.466000	0.22019	-0.646000	0.05452	-0.229000	0.12294	GTG		0.517	ITGB1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057126.1	NM_012278		C	70522363	G	C	70522363	3	2	18	1	0	0	0	0	1	0	0	0	7913	1377	48	5	288	5	ITGB1BP2	23	70522363	Missense_Mutation	SNP	G	TCGA-AG-3582-01A-01W-0831-10		70522363	84748197	33	1804										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123780572	123780572	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acattacctctagcacagtcAggtccaaggaatcctgggaa	9	11	2	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chrX:123780572A>G	ENST00000371130.3	-	9	1731	c.1668T>C	c.(1666-1668)ccT>ccC	p.P556P	TENM1_ENST00000422452.2_Silent_p.P556P	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	556	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.P558P(1)									TAGCACAGTCAGGTCCAAGGA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	X											126	97	107					X																	123780572		2203	4300	6503	123608253	SO:0001819	synonymous_variant	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.1668T>C	X.37:g.123780572A>G			123608253	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.368	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	123780572	A	G	123780572	2	3	18	1	0	0	0	0	0	0	0	1	10865	175	7	4		4	ODZ1	23	123780572	Silent	SNP	A	TCGA-AG-3582-01A-01W-0831-10	53258209	123780572	31489988	34	1805										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718116	142718116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggcaggatgcgcacgtcaAaatcactgccggtgcccatg	13	12	2	0			TCGA-AG-3582-01A-01W-0831-10	TCGA-AG-3582-10A-01W-0831-10	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	184cc2b0-cce0-4731-a276-7174e9efe1bd	2aba7833-f326-43fe-a7e7-0f3c23aec2b1	g.chrX:142718116A>G	ENST00000381779.4	-	2	1034	c.809T>C	c.(808-810)tTt>tCt	p.F270S	SLITRK4_ENST00000338017.4_Missense_Mutation_p.F270S|SLITRK4_ENST00000356928.1_Missense_Mutation_p.F270S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	270						integral component of membrane (GO:0016021)		p.F270S(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					GCGCACGTCAAAATCACTGCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											102	89	94					X																	142718116		2203	4300	6503	142545782	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.809T>C	X.37:g.142718116A>G	ENSP00000371198:p.Phe270Ser		142545782	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	A	11.32	1.605153	0.28623	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.41758	0.99;0.99;0.99	5.88	5.88	0.94601	.	0.000000	0.85682	U	0.000000	T	0.26629	0.0651	N	0.12569	0.235	0.80722	D	1	B	0.15141	0.012	B	0.19148	0.024	T	0.09530	-1.0670	10	0.21540	T	0.41	-11.152	13.9232	0.63945	1.0:0.0:0.0:0.0	.	270	Q8IW52	SLIK4_HUMAN	S	270	ENSP00000371198:F270S;ENSP00000349400:F270S;ENSP00000336627:F270S	ENSP00000336627:F270S	F	-	2	0	SLITRK4	142545782	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.522000	0.81844	1.973000	0.57446	0.486000	0.48141	TTT		0.448	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		G	142718116	A	G	142718116	3	3	18	1	0	0	0	0	1	0	0	0	14782	14	1	4	1708	4	SLITRK4	23	142718116	Missense_Mutation	SNP	A	TCGA-AG-3582-01A-01W-0831-10	18937544	142718116	12552444	35	1806										
C8A	731	hgsc.bcm.edu	37	chr1	57347272	57347272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gagatgatgagaaatactttCggaaaccctacaactttctg	8	8	1	3	rs142382705		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr1:57347272C>T	ENST00000361249.3	+	5	715	c.619C>T	c.(619-621)Cgg>Tgg	p.R207W		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	207	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)		p.R207W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GAAATACTTTCGGAAACCCTA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG	0,4406		0,0,2203	112	114	113		619	5.4	1	1	dbSNP_134	113	1,8599	1.2+/-3.3	0,1,4299	no	missense	C8A	NM_000562.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	207/585	57347272	1,13005	2203	4300	6503	57119860	SO:0001583	missense	731			M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.619C>T	1.37:g.57347272C>T	ENSP00000354458:p.Arg207Trp		57119860	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506679	0.85282	0.0	1.16E-4	ENSG00000157131	ENST00000361249	D	0.84298	-1.83	5.45	5.45	0.79879	Membrane attack complex component/perforin (MACPF) domain (1);	0.048911	0.85682	D	0.000000	D	0.94082	0.8103	M	0.89715	3.055	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.94904	0.8059	10	0.87932	D	0	-25.4107	19.2776	0.94038	0.0:1.0:0.0:0.0	.	207	P07357	CO8A_HUMAN	W	207	ENSP00000354458:R207W	ENSP00000354458:R207W	R	+	1	2	C8A	57119860	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	3.560000	0.53763	2.556000	0.86216	0.655000	0.94253	CGG		0.498	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		T	57347272	C	T	57347272	3	4	19	1	0	0	0	0	1	0	0	0	2422	875	31	1	637	1	C8A	1	57347272	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		57347272	191903349	1	1807										
BCL9	607	hgsc.bcm.edu	37	chr1	147091810	147091810	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gcattttcagcggtcctggcCgaggggaacgcttcccaaac	12	13	1	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr1:147091810C>T	ENST00000234739.3	+	8	2589	c.1849C>T	c.(1849-1851)Cga>Tga	p.R617*		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	617	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.R617*(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CGGTCCTGGCCGAGGGGAACG	0.552			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	1	Substitution - Nonsense(1)	large_intestine(1)	1											65	72	69					1																	147091810		2203	4300	6503	145558434	SO:0001587	stop_gained	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1849C>T	1.37:g.147091810C>T	ENSP00000234739:p.Arg617*		145558434	Q5T489	Nonsense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	44	10.830589	0.99474	.	.	ENSG00000116128	ENST00000234739	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-7.5026	18.7977	0.92001	0.0:1.0:0.0:0.0	.	.	.	.	X	617	.	ENSP00000234739:R617X	R	+	1	2	BCL9	145558434	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.125000	0.57931	2.666000	0.90696	0.561000	0.74099	CGA		0.552	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		T	147091810	C	T	147091810	4	4	19	1	0	0	0	0	0	1	0	0	1382	644	23	1	1867	1	BCL9	1	147091810	Nonsense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	89744538	147091810	102158811	2	1808										
C1orf77	26097	hgsc.bcm.edu	37	chr1	153617611	153617611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gccgtggacgagggagaggtGcccttgctcgccctgtattg	16	11	0	1	rs535145459		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr1:153617611G>A	ENST00000368694.3	+	6	925	c.613G>A	c.(613-615)Gcc>Acc	p.A205T	CHTOP_ENST00000403433.1_Missense_Mutation_p.A159T|CHTOP_ENST00000495554.1_3'UTR|CHTOP_ENST00000368690.3_Missense_Mutation_p.A159T|CHTOP_ENST00000368687.1_Missense_Mutation_p.A180T	NM_001206612.1|NM_015607.3	NP_001193541.1|NP_056422.2	Q9Y3Y2	CHTOP_HUMAN	chromatin target of PRMT1	205	Arg/Gly-rich.|Interaction with PRMT1. {ECO:0000250}.				mRNA export from nucleus (GO:0006406)|positive regulation of ATPase activity (GO:0032781)|positive regulation of helicase activity (GO:0051096)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|transcription export complex (GO:0000346)	poly(A) RNA binding (GO:0044822)	p.A205T(1)		endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(6)	13						AGGGAGAGGTGCCCTTGCTCG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	106	106					1																	153617611		2203	4300	6503	151884235	SO:0001583	missense	26097				CCDS1048.1, CCDS72917.1, CCDS72918.1	1q21.3	2011-03-24	2011-03-24	2011-03-24	ENSG00000160679	ENSG00000160679			24511	protein-coding gene	gene with protein product	"small protein rich in arginine and glycine", "Friend of Prmt1"	614206	"chromosome 1 open reading frame 77"	C1orf77		19254951	Standard	NM_015607		Approved	DKFZP547E1010, SRAG, FOP	uc001fcn.2	Q9Y3Y2	OTTHUMG00000037052	ENST00000368694.3:c.613G>A	1.37:g.153617611G>A	ENSP00000357683:p.Ala205Thr		151884235	D3DV55|Q0VAQ8|Q2VPI9|Q5T7Y8|Q5T7Y9|Q5T7Z0|Q6NSM4|Q6PB28|Q8WYT9|Q9BUC5|Q9H034|Q9H2L0	Missense_Mutation	SNP	ENST00000368694.3	37	CCDS1048.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.074826	0.55646	.	.	ENSG00000160679	ENST00000368694;ENST00000403433;ENST00000368690;ENST00000368687	.	.	.	5.85	4.84	0.62591	.	0.209002	0.41001	D	0.000967	T	0.53981	0.1830	L	0.27053	0.805	0.40901	D	0.984157	D;D	0.62365	0.988;0.991	P;D	0.66602	0.908;0.945	T	0.56577	-0.7956	9	0.56958	D	0.05	-28.2603	13.46	0.61221	0.0:0.0:0.8114:0.1886	.	206;205	Q9Y3Y2-3;Q9Y3Y2	.;CHTOP_HUMAN	T	205;159;159;180	.	ENSP00000357676:A180T	A	+	1	0	CHTOP	151884235	0.997000	0.39634	1.000000	0.80357	0.968000	0.65278	1.585000	0.36600	2.932000	0.99384	0.643000	0.83706	GCC		0.537	CHTOP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089967.1	NM_015607		A	153617611	G	A	153617611	3	1	19	1	0	0	0	0	1	0	0	0	2065	1319	46	3	631	3	C1orf77	1	153617611	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	6525801	153617611	95633010	3	1809										
TNN	63923	hgsc.bcm.edu	37	chr1	175116180	175116180	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ctgggcagaaagaagcggacGctgagaggaaggctgcgaac	17	8	0	3			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr1:175116180G>A	ENST00000239462.4	+	19	3986	c.3873G>A	c.(3871-3873)acG>acA	p.T1291T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1291					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.T1291T(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		AGAAGCGGACGCTGAGAGGAA	0.587											OREG0013992	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	1											58	55	56					1																	175116180		2203	4300	6503	173382803	SO:0001819	synonymous_variant	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3873G>A	1.37:g.175116180G>A		1921	173382803	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																				0.587	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175116180	G	A	175116180	2	1	19	1	0	0	0	0	0	0	0	1	16362	1074	38	1		1	TNN	1	175116180	Silent	SNP	G	TCGA-AG-3583-01A-01W-0831-10	21498569	175116180	74134441	4	1810										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186056372	186056372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gtcgaactctacagattattCgggccaaggtatcagatggt	11	8	2	2	rs138982761		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr1:186056372C>T	ENST00000271588.4	+	59	9299	c.9070C>T	c.(9070-9072)Cgg>Tgg	p.R3024W	HMCN1_ENST00000367492.2_Missense_Mutation_p.R3024W	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3024	Ig-like C2-type 28.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R3024W(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACAGATTATTCGGGCCAAGGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG	0,4406		0,0,2203	136	130	132		9070	4.7	1	1	dbSNP_134	132	1,8599	1.2+/-3.3	0,1,4299	no	missense	HMCN1	NM_031935.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	3024/5636	186056372	1,13005	2203	4300	6503	184322995	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9070C>T	1.37:g.186056372C>T	ENSP00000271588:p.Arg3024Trp		184322995	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457369	0.63401	0.0	1.16E-4	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31769	1.48;1.48	5.63	4.7	0.59300	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.161654	0.56097	D	0.000035	T	0.61286	0.2335	M	0.89353	3.025	0.36029	D	0.839268	D	0.89917	1.0	D	0.91635	0.999	T	0.75402	-0.3330	10	0.59425	D	0.04	.	14.0744	0.64880	0.2742:0.7258:0.0:0.0	.	3024	Q96RW7	HMCN1_HUMAN	W	3024	ENSP00000271588:R3024W;ENSP00000356462:R3024W	ENSP00000271588:R3024W	R	+	1	2	HMCN1	184322995	0.938000	0.31826	0.952000	0.39060	0.826000	0.46750	3.244000	0.51399	1.320000	0.45209	0.655000	0.94253	CGG		0.373	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186056372	C	T	186056372	3	4	19	1	0	0	0	0	1	0	0	0	7241	875	31	1	9304	1	HMCN1	1	186056372	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	10940192	186056372	63194249	5	1811										
GCKR	2646	hgsc.bcm.edu	37	chr2	27730606	27730606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ttccatccttccctctctcaCggaaatcgatactgtggtct	6	14	3	0	rs544395651		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:27730606C>T	ENST00000264717.2	+	14	1265	c.1202C>T	c.(1201-1203)aCg>aTg	p.T401M	GCKR_ENST00000424318.2_Missense_Mutation_p.T211M	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	401	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)	p.T401M(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					CCCTCTCTCACGGAAATCGAT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	2											97	90	92					2																	27730606		2203	4300	6503	27584110	SO:0001583	missense	2646			Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"glucokinase (hexokinase 4) regulatory protein"			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1202C>T	2.37:g.27730606C>T	ENSP00000264717:p.Thr401Met		27584110	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	2.446|2.446	-0.327535|-0.327535	0.05314|0.05314	.|.	.|.	ENSG00000084734|ENSG00000084734	ENST00000411584|ENST00000264717;ENST00000424318	.|D;D	.|0.83250	.|-1.7;-1.7	4.52|4.52	-1.74|-1.74	0.08056|0.08056	.|Sugar isomerase (SIS) (1);	.|0.445818	.|0.22925	.|N	.|0.053975	T|T	0.74168|0.74168	0.3681|0.3681	L|L	0.55481|0.55481	1.735|1.735	0.09310|0.09310	N|N	1|1	.|D;P;P	.|0.54397	.|0.966;0.579;0.579	.|P;B;B	.|0.44561	.|0.453;0.07;0.103	T|T	0.67684|0.67684	-0.5607|-0.5607	5|10	.|0.59425	.|D	.|0.04	0.1301|0.1301	3.1313|3.1313	0.06424|0.06424	0.302:0.341:0.0:0.357|0.302:0.341:0.0:0.357	.|.	.|211;399;401	.|F5H1P6;A8K731;Q14397	.|.;.;GCKR_HUMAN	W|M	102|401;211	.|ENSP00000264717:T401M;ENSP00000409109:T211M	.|ENSP00000264717:T401M	R|T	+|+	1|2	2|0	GCKR|GCKR	27584110|27584110	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.674000|-0.674000	0.05233|0.05233	-0.676000|-0.676000	0.05238|0.05238	-0.735000|-0.735000	0.03563|0.03563	CGG|ACG		0.552	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486		T	27730606	C	T	27730606	3	4	19	1	0	0	0	0	1	0	0	0	6314	536	19	1	1256	1	GCKR	2	27730606	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		27730606	215468767	6	1812										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39570593	39570593	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	caaatccaaagcttatctcgCctataaagagaaaagaagca	6	9	1	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:39570593C>T	ENST00000263881.3	-	4	570	c.246G>A	c.(244-246)agG>agA	p.R82R	MAP4K3_ENST00000437545.1_Splice_Site_p.R19R|MAP4K3_ENST00000341681.5_Splice_Site_p.R82R	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	82	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R82R(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				GCTTATCTCGCCTATAAAGAG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	2											78	80	80					2																	39570593		2203	4297	6500	39424097	SO:0001630	splice_region_variant	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.246-1G>A	2.37:g.39570593C>T			39424097	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	37	CCDS1803.1																																																																																				0.343	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	Silent	T	39570593	C	T	39570593	5	4	19	1	0	0	0	0	0	0	1	0	9291	753	26	3	2562	3	MAP4K3	2	39570593	Splice_Site	SNP	C	TCGA-AG-3583-01A-01W-0831-10	11839987	39570593	203628780	7	1813										
EPAS1	2034	hgsc.bcm.edu	37	chr2	46603773	46603773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gaacagcatctttgatagcaGtggcaagggggctgtgtctg	15	7	2	1	rs144038192	byFrequency	TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:46603773G>A	ENST00000263734.3	+	9	1640	c.1130G>A	c.(1129-1131)aGt>aAt	p.S377N		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	377					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)	p.S377N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			TTTGATAGCAGTGGCAAGGGG	0.542													G|||	6	0.00119808	0.0045	0	5008	,	,		18194	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	ASN/SER	1,4405	2.1+/-5.4	0,1,2202	129	127	128		1130	2.4	0	2	dbSNP_134	128	0,8600		0,0,4300	yes	missense	EPAS1	NM_001430.4	46	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	377/871	46603773	1,13005	2203	4300	6503	46457277	SO:0001583	missense	2034			U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1130G>A	2.37:g.46603773G>A	ENSP00000263734:p.Ser377Asn		46457277	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	37	CCDS1825.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	7.133	0.580194	0.13686	2.27E-4	0.0	ENSG00000116016	ENST00000263734	T	0.47528	0.84	4.27	2.4	0.29515	.	1.058270	0.07275	N	0.869793	T	0.24005	0.0581	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.17098	0.017	T	0.21827	-1.0234	10	0.18276	T	0.48	.	7.8779	0.29605	0.0839:0.0:0.7566:0.1595	.	377	Q99814	EPAS1_HUMAN	N	377	ENSP00000263734:S377N	ENSP00000263734:S377N	S	+	2	0	EPAS1	46457277	0.008000	0.16893	0.001000	0.08648	0.746000	0.42486	1.722000	0.38042	0.698000	0.31739	0.462000	0.41574	AGT		0.542	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		A	46603773	G	A	46603773	3	1	19	1	0	0	0	0	1	0	0	0	5163	1029	36	3	1164	3	EPAS1	2	46603773	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	7033180	46603773	196595600	8	1814										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69049780	69049780	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tcccaacggacttccacctaCgataacgtcccttccctgcc	5	19	0	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:69049780C>T	ENST00000295381.3	+	10	1925	c.1506C>T	c.(1504-1506)taC>taT	p.Y502Y	ARHGAP25_ENST00000409202.3_Silent_p.Y503Y|ARHGAP25_ENST00000409030.3_Silent_p.Y495Y|ARHGAP25_ENST00000479844.1_Silent_p.Y196Y|ARHGAP25_ENST00000409220.1_Silent_p.Y496Y|ARHGAP25_ENST00000467265.1_Silent_p.Y463Y	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	502					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.Y496Y(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTTCCACCTACGATAACGTCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	2											109	105	107					2																	69049780		2203	4300	6503	68903284	SO:0001819	synonymous_variant	9938			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1506C>T	2.37:g.69049780C>T			68903284	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	C	0.731	-0.780021	0.02929	.	.	ENSG00000163219	ENST00000497259	.	.	.	5.16	-10.3	0.00346	.	.	.	.	.	T	0.64000	0.2559	.	.	.	0.46823	D	0.999215	.	.	.	.	.	.	T	0.79829	-0.1638	4	.	.	.	.	18.5551	0.91081	0.0727:0.7054:0.0:0.2218	.	.	.	.	M	362	.	.	T	+	2	0	ARHGAP25	68903284	0.000000	0.05858	0.039000	0.18376	0.349000	0.29174	-5.130000	0.00148	-3.738000	0.00113	-1.028000	0.02416	ACG		0.572	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		T	69049780	C	T	69049780	2	4	19	1	0	0	0	0	0	0	0	1	874	547	19	1		1	ARHGAP25	2	69049780	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	22446007	69049780	174149593	9	1815										
ATP6V1B1	525	hgsc.bcm.edu	37	chr2	71185268	71185268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gtggctggcaccaaggcgatTgttcaggtgagtggggtcaa	17	7	2	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:71185268T>G	ENST00000234396.4	+	3	340	c.267T>G	c.(265-267)atT>atG	p.I89M	AC007040.11_ENST00000606025.1_Intron|ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.I89M	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	89					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)	p.I89M(1)		endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						CCAAGGCGATTGTTCAGGTGA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											77	78	77					2																	71185268		2203	4300	6503	71038776	SO:0001583	missense	525			AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"ATPases / V-type"	853	protein-coding gene	gene with protein product	"Renal tubular acidosis with deafness"	192132	"vacuolar proton pump 3"	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.267T>G	2.37:g.71185268T>G	ENSP00000234396:p.Ile89Met		71038776	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.034535	0.35893	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314;ENST00000454446	D;D;D	0.86164	-2.08;-2.08;-2.08	4.79	2.32	0.28847	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal (1);	0.170119	0.40728	N	0.001030	D	0.88855	0.6550	M	0.69248	2.105	0.38684	D	0.952607	P;P;P	0.46064	0.872;0.766;0.766	P;P;P	0.58454	0.595;0.774;0.839	D	0.85189	0.1008	10	0.36615	T	0.2	-5.5439	5.478	0.16706	0.1533:0.0869:0.0:0.7598	.	64;89;89	B4DWH7;C9JL73;P15313	.;.;VATB1_HUMAN	M	89;64;89;106	ENSP00000234396:I89M;ENSP00000388353:I89M;ENSP00000408361:I106M	ENSP00000234396:I89M	I	+	3	3	ATP6V1B1	71038776	0.060000	0.20803	1.000000	0.80357	0.961000	0.63080	-0.827000	0.04424	0.307000	0.22880	0.533000	0.62120	ATT		0.517	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692		G	71185268	T	G	71185268	3	3	19	1	0	0	0	0	1	0	0	0	1179	1800	63	4	277	4	ATP6V1B1	2	71185268	Missense_Mutation	SNP	T	TCGA-AG-3583-01A-01W-0831-10	2135488	71185268	172014105	10	1816										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109463198	109463198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tacatatttttaacagcactCgactatgacatcaacattga	4	9	1	2	rs367747465		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:109463198C>T	ENST00000295124.4	+	12	1388	c.1328C>T	c.(1327-1329)tCg>tTg	p.S443L	CCDC138_ENST00000412964.2_Missense_Mutation_p.S443L	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	443								p.S443L(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TAACAGCACTCGACTATGACA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											79	82	81					2																	109463198		2203	4300	6503	108829630	SO:0001583	missense	165055			AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.1328C>T	2.37:g.109463198C>T	ENSP00000295124:p.Ser443Leu		108829630	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.35|15.35	2.808471|2.808471	0.50421|0.50421	.|.	.|.	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|T;T	.|0.34072	.|1.38;1.39	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	.|0.434355	.|0.23549	.|N	.|0.046989	.|T	.|0.38295	.|0.1035	L|L	0.48362|0.48362	1.52|1.52	0.43287|0.43287	D|D	0.995261|0.995261	.|P;B	.|0.45240	.|0.854;0.007	.|B;B	.|0.41466	.|0.358;0.004	.|T	.|0.05053	.|-1.0909	.|10	.|0.33141	.|T	.|0.24	-2.6465|-2.6465	20.1575|20.1575	0.98120|0.98120	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|443;443	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	X|L	340|443	.|ENSP00000411800:S443L;ENSP00000295124:S443L	.|ENSP00000295124:S443L	R|S	+|+	1|2	2|0	CCDC138|CCDC138	108829630|108829630	0.777000|0.777000	0.28628|0.28628	0.997000|0.997000	0.53966|0.53966	0.989000|0.989000	0.77384|0.77384	3.852000|3.852000	0.55934|0.55934	2.850000|2.850000	0.98022|0.98022	0.650000|0.650000	0.86243|0.86243	CGA|TCG		0.348	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		T	109463198	C	T	109463198	3	4	19	1	0	0	0	0	1	0	0	0	2778	893	31	1	1374	1	CCDC138	2	109463198	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	38277930	109463198	133736175	11	1817										
DNER	92737	hgsc.bcm.edu	37	chr2	230456366	230456366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gccaggtaggcagtgtcaccGttgcctgagagcgaggcagg	17	10	1	1	rs143332732	byFrequency	TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr2:230456366G>A	ENST00000341772.4	-	2	649	c.515C>T	c.(514-516)aCg>aTg	p.T172M		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	172					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.T172M(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CAGTGTCACCGTTGCCTGAGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	MET/THR	0,4406		0,0,2203	88	79	82		515	5.8	0.1	2	dbSNP_134	82	2,8598	2.2+/-6.3	0,2,4298	no	missense	DNER	NM_139072.3	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	172/738	230456366	2,13004	2203	4300	6503	230164610	SO:0001583	missense	92737			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.515C>T	2.37:g.230456366G>A	ENSP00000345229:p.Thr172Met		230164610	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.947916	0.53186	0.0	2.33E-4	ENSG00000187957	ENST00000341772	D	0.85258	-1.96	5.75	5.75	0.90469	.	0.266104	0.43110	D	0.000607	D	0.82944	0.5147	N	0.19112	0.55	0.46749	D	0.999183	D	0.67145	0.996	P	0.50791	0.65	T	0.83019	-0.0168	10	0.39692	T	0.17	.	19.9405	0.97159	0.0:0.0:1.0:0.0	.	172	Q8NFT8	DNER_HUMAN	M	172	ENSP00000345229:T172M	ENSP00000345229:T172M	T	-	2	0	DNER	230164610	1.000000	0.71417	0.112000	0.21494	0.037000	0.13140	4.399000	0.59703	2.708000	0.92522	0.655000	0.94253	ACG		0.527	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		A	230456366	G	A	230456366	3	1	19	1	0	0	0	0	1	0	0	0	4678	1145	40	1	1746	1	DNER	2	230456366	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	120993168	230456366	12743007	12	1818										
AGA	175	hgsc.bcm.edu	37	chr4	178352946	178352947	+	Frame_Shift_Del	DEL	TT	TT	-													0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	aactgagtaaatgttgaaagTttattgcaagcagcacctgg							TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	TT	TT	TT	-	TT	TT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr4:178352946_178352947delTT	ENST00000264595.2	-	9	1083_1084	c.956_957delAA	c.(955-957)aaafs	p.K319fs	AGA_ENST00000506853.1_5'Flank	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	319					protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)	p.K319fs*8(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		ATGTTGAAAGTTTATTGCAAGC	0.351																																																1	Deletion - Frameshift(1)	large_intestine(1)	4																																								178589941	SO:0001589	frameshift_variant	175			X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"glycosylasparaginase", "N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.956_957delAA	4.37:g.178352946_178352947delTT	ENSP00000264595:p.Lys319fs		178589940	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Frame_Shift_Del	DEL	ENST00000264595.2	37	CCDS3829.1																																																																																				0.351	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		-	178352947	TT	-	178352946	7	5	19	1	0	1	0	1	0	0	0	0	365	1722	60	0	87	0	AGA	4	178352946	Frame_Shift_Del	DEL	TT	TCGA-AG-3583-01A-01W-0831-10		178352946	12801330	13	1819										
OSMR	9180	hgsc.bcm.edu	37	chr5	38904527	38904527	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ctgccacagagtacatggcgCgagtacggtgtgctgatgcc	14	11	0	2	rs147586955		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr5:38904527C>T	ENST00000274276.3	+	9	1609	c.1207C>T	c.(1207-1209)Cga>Tga	p.R403*		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	403	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)	p.R403*(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					GTACATGGCGCGAGTACGGTG	0.468													C|||	1	0.000199681	0	0.0014	5008	,	,		17816	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	5											109	97	101					5																	38904527		2203	4300	6503	38940284	SO:0001587	stop_gained	9180			U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1207C>T	5.37:g.38904527C>T	ENSP00000274276:p.Arg403*		38940284	Q6P4E8|Q96QJ6	Nonsense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	41	8.829233	0.98970	.	.	ENSG00000145623	ENST00000274276;ENST00000513831	.	.	.	5.7	4.61	0.57282	.	0.976288	0.08391	N	0.952939	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2671	0.31821	0.0:0.8574:0.0:0.1426	.	.	.	.	X	403;10	.	ENSP00000274276:R403X	R	+	1	2	OSMR	38940284	0.000000	0.05858	0.005000	0.12908	0.021000	0.10359	0.394000	0.20834	1.081000	0.41110	0.650000	0.86243	CGA		0.468	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		T	38904527	C	T	38904527	4	4	19	1	0	0	0	0	0	1	0	0	11323	760	27	1	1275	1	OSMR	5	38904527	Nonsense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		38904527	142010733	14	1820										
APC	324	hgsc.bcm.edu	37	chr5	112136975	112136975	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atgttaactccatcttaacaGaggtcatctcagaacaagca	6	10	3	2	rs387906228		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr5:112136975G>A	ENST00000457016.1	+	8	1109		c.e8-1		APC_ENST00000508376.2_Splice_Site|APC_ENST00000257430.4_Splice_Site			P25054	APC_HUMAN	adenomatous polyposis coli						anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CATCTTAACAGAGGTCATCTC	0.418		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	large_intestine(1)	5	GRCh37	CS941417	APC	S							78	72	74					5																	112136975		2202	4300	6502	112164874	SO:0001630	splice_region_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.730-1G>A	5.37:g.112136975G>A			112164874	D3DT03|Q15162|Q15163|Q93042	Splice_Site	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.142368	0.77888	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1327	0.93414	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APC	112164874	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.060000	0.76692	2.516000	0.84829	0.585000	0.79938	.		0.418	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Intron	A	112136975	G	A	112136975	5	1	19	1	0	0	0	0	0	0	1	0	763	956	33	3	755	3	APC	5	112136975	Splice_Site	SNP	G	TCGA-AG-3583-01A-01W-0831-10	73232448	112136975	68778285	15	1821										
APC	324	hgsc.bcm.edu	37	chr5	112174862	112174862	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ccacagatattccttcatcaCagaaacagtcattttcattc	3	12	4	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr5:112174862C>T	ENST00000457016.1	+	16	3951	c.3571C>T	c.(3571-3573)Cag>Tag	p.Q1191*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1191*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1191*			P25054	APC_HUMAN	adenomatous polyposis coli	1191	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1191*(3)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCCTTCATCACAGAAACAGTC	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Substitution - Nonsense(3)|Unknown(1)	large_intestine(2)|breast(1)|skin(1)	5											83	88	86					5																	112174862		2200	4299	6499	112202761	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3571C>T	5.37:g.112174862C>T	ENSP00000413133:p.Gln1191*		112202761	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.712523	0.96830	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	5.76	0.90799	.	0.114673	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.8565	16.9524	0.86249	0.0:0.8727:0.1273:0.0	.	.	.	.	X	1191	.	.	Q	+	1	0	APC	112202761	1.000000	0.71417	0.998000	0.56505	0.604000	0.37047	4.187000	0.58344	2.732000	0.93576	0.655000	0.94253	CAG		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174862	C	T	112174862	4	4	19	1	0	0	0	0	0	1	0	0	763	479	17	3	3629	3	APC	5	112174862	Nonsense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	37887	112174862	68740398	16	1822										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262952	140262952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gagaagacactcagcctagcGccattattgccctaatcagt	8	12	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr5:140262952G>A	ENST00000289272.2	+	1	1099	c.1099G>A	c.(1099-1101)Gcc>Acc	p.A367T	PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.A367T|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	367	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A367T(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGCCTAGCGCCATTATTGC	0.507																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											119	119	119					5																	140262952		2203	4300	6503	140243136	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1099G>A	5.37:g.140262952G>A	ENSP00000289272:p.Ala367Thr		140243136	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.646199	0.00111	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.41065	1.01;1.01	5.33	-2.13	0.07144	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.08223	0.0205	N	0.00197	-1.87	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.04013	0.0;0.001;0.0	T	0.34950	-0.9808	9	0.02654	T	1	.	7.8728	0.29576	0.7682:0.0:0.1285:0.1033	.	367;367;367	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	T	367	ENSP00000386821:A367T;ENSP00000289272:A367T	ENSP00000289272:A367T	A	+	1	0	PCDHA13	140243136	0.802000	0.28943	0.000000	0.03702	0.005000	0.04900	2.460000	0.45031	-0.673000	0.05259	-2.118000	0.00350	GCC		0.507	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140262952	G	A	140262952	3	1	19	1	0	0	0	0	1	0	0	0	11554	1087	38	1	1101	1	PCDHA13	5	140262952	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	28088090	140262952	40652308	17	1823										
IRF4	3662	hgsc.bcm.edu	37	chr6	401501	401501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	cgtccagccccgagggctgcCggatctcccatggacatacg	12	16	1	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr6:401501C>T	ENST00000380956.4	+	7	949	c.823C>T	c.(823-825)Cgg>Tgg	p.R275W		NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	275					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R275W(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CGAGGGCTGCCGGATCTCCCA	0.582			T	IGH@	MM																																		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	1	Substitution - Missense(1)	large_intestine(1)	6											66	52	57					6																	401501		2203	4300	6503	346501	SO:0001583	missense	3662			U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.823C>T	6.37:g.401501C>T	ENSP00000370343:p.Arg275Trp		346501	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955369	0.73902	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97114	-4.25	5.76	1.35	0.21983	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.097281	0.64402	D	0.000003	D	0.98012	0.9345	M	0.84683	2.71	0.50313	D	0.999869	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.973;0.993;0.982;0.994	D	0.98446	1.0589	10	0.72032	D	0.01	-32.1881	15.7271	0.77770	0.7875:0.2125:0.0:0.0	.	275;305;274;275	F2Z3D5;Q99419;Q15306-2;Q15306	.;.;.;IRF4_HUMAN	W	275;304	ENSP00000370343:R275W	ENSP00000370343:R275W	R	+	1	2	IRF4	346501	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	2.128000	0.42045	0.290000	0.22444	-0.182000	0.12963	CGG		0.582	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	401501	C	T	401501	3	4	19	1	0	0	0	0	1	0	0	0	7853	643	23	1	845	1	IRF4	6	401501	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		401501	170713566	18	1824										
CUL7	9820	hgsc.bcm.edu	37	chr6	43010598	43010598	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ccgcacagccattttgcagcGccagcaagaaggctgcccga	11	15	0	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr6:43010598G>A	ENST00000265348.3	-	19	3672	c.3587C>T	c.(3586-3588)gCg>gTg	p.A1196V	CUL7_ENST00000535468.1_Missense_Mutation_p.A1280V|CUL7_ENST00000478630.1_5'Flank			Q14999	CUL7_HUMAN	cullin 7	1196					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.A1196V(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			ATTTTGCAGCGCCAGCAAGAA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											43	40	41					6																	43010598		2203	4300	6503	43118576	SO:0001583	missense	9820			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3587C>T	6.37:g.43010598G>A	ENSP00000265348:p.Ala1196Val		43118576	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	G	35	5.541788	0.96474	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.76060	-0.99;-0.99	5.59	5.59	0.84812	Cullin, N-terminal (1);	0.221347	0.46758	D	0.000280	D	0.83760	0.5324	M	0.68593	2.085	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.985;0.994;0.998;0.998	D	0.84407	0.0563	10	0.66056	D	0.02	-9.0074	19.5991	0.95552	0.0:0.0:1.0:0.0	.	1280;1196;1280;1196	F5H0L1;A8K9U1;B4DYZ0;Q14999	.;.;.;CUL7_HUMAN	V	1196;1280	ENSP00000265348:A1196V;ENSP00000438788:A1280V	ENSP00000265348:A1196V	A	-	2	0	CUL7	43118576	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.277000	0.95755	2.632000	0.89209	0.579000	0.79373	GCG		0.542	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		A	43010598	G	A	43010598	3	1	19	1	0	0	0	0	1	0	0	0	4066	1087	38	1	1541	1	CUL7	6	43010598	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	42609097	43010598	128104469	19	1825										
CD2AP	23607	hgsc.bcm.edu	37	chr6	47522495	47522495	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gaaactcatgaagcccaggaCgattcaggtagactattttt	9	8	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr6:47522495C>T	ENST00000359314.5	+	5	990	c.534C>T	c.(532-534)gaC>gaT	p.D178D		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	178					mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.D178D(1)		kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			AAGCCCAGGACGATTCAGGTA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	6											65	60	62					6																	47522495		2203	4300	6503	47630454	SO:0001819	synonymous_variant	23607			AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.534C>T	6.37:g.47522495C>T			47630454	A6NL34|Q5VYA3|Q9UG97	Silent	SNP	ENST00000359314.5	37	CCDS34472.1																																																																																				0.318	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			T	47522495	C	T	47522495	2	4	19	1	0	0	0	0	0	0	0	1	3000	535	19	1		1	CD2AP	6	47522495	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	4511897	47522495	123592572	20	1826										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134475	128134475	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tactgtttcttatcatgaatCacctctacaaaacctccttc	2	13	4	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr6:128134475C>A	ENST00000368248.2	-	4	1459	c.1311G>T	c.(1309-1311)gtG>gtT	p.V437V	THEMIS_ENST00000543064.1_Silent_p.V437V|THEMIS_ENST00000368250.1_Silent_p.V358V|THEMIS_ENST00000537166.1_Silent_p.V402V	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	437	CABIT 2.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V437V(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TATCATGAATCACCTCTACAA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	6											92	98	96					6																	128134475		2203	4300	6503	128176168	SO:0001819	synonymous_variant	387357			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1311G>T	6.37:g.128134475C>A			128176168	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Silent	SNP	ENST00000368248.2	37	CCDS34534.1																																																																																				0.433	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		A	128134475	C	A	128134475	2	1	19	1	0	0	0	0	0	0	0	1	15899	813	29	2		2	THEMIS	6	128134475	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	80611980	128134475	42980592	21	1827										
DDX56	54606	hgsc.bcm.edu	37	chr7	44611173	44611173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	caggcgtagccggtaactccGttctagagtgttgacaaaga	12	9	1	3	rs200686546		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr7:44611173G>A	ENST00000258772.5	-	6	914	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W	DDX56_ENST00000485367.1_5'UTR|DDX56_ENST00000431640.1_Missense_Mutation_p.R270W	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	270	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.R270W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CGGTAACTCCGTTCTAGAGTG	0.532													G|||	1	0.000199681	0	0	5008	,	,		19857	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7											91	82	85					7																	44611173		2203	4300	6503	44577698	SO:0001583	missense	54606			AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.808C>T	7.37:g.44611173G>A	ENSP00000258772:p.Arg270Trp		44577698	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	37	CCDS5492.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	18.44	3.625340	0.66901	.	.	ENSG00000136271	ENST00000258772;ENST00000431640	T;T	0.04156	3.69;3.75	5.82	0.162	0.14981	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.21674	0.0522	M	0.82056	2.57	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.01829	-1.1265	10	0.87932	D	0	-26.1822	16.9155	0.86150	0.0:0.0:0.2375:0.7625	.	270;270	C9JV95;Q9NY93	.;DDX56_HUMAN	W	270	ENSP00000258772:R270W;ENSP00000393488:R270W	ENSP00000258772:R270W	R	-	1	2	DDX56	44577698	0.997000	0.39634	0.988000	0.46212	0.767000	0.43475	1.053000	0.30442	-0.288000	0.09051	-0.261000	0.10672	CGG		0.532	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		A	44611173	G	A	44611173	3	1	19	1	0	0	0	0	1	0	0	0	4380	1144	40	1	871	1	DDX56	7	44611173	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10		44611173	114527490	22	1828										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133164872	133164872	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	acagagaagggagctctataGtcggagtggagaactgcaag	15	6	1	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr7:133164872G>C	ENST00000253861.4	+	9	1426	c.1397G>C	c.(1396-1398)aGt>aCt	p.S466T	EXOC4_ENST00000393161.2_Missense_Mutation_p.S466T|EXOC4_ENST00000539845.1_Missense_Mutation_p.S365T	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	466					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)	p.S466T(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GAGCTCTATAGTCGGAGTGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7											118	114	115					7																	133164872		2203	4300	6503	132815412	SO:0001583	missense	60412			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1397G>C	7.37:g.133164872G>C	ENSP00000253861:p.Ser466Thr		132815412	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.950355	0.53186	.	.	ENSG00000131558	ENST00000253861;ENST00000393161;ENST00000546185;ENST00000539845	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54481	0.1861	L	0.42245	1.32	0.80722	D	1	P;P	0.48764	0.915;0.779	B;B	0.44224	0.444;0.351	T	0.46762	-0.9168	9	0.15066	T	0.55	.	19.8933	0.96939	0.0:0.0:1.0:0.0	.	466;466	Q96A65;Q8TAR2	EXOC4_HUMAN;.	T	466;466;85;365	.	ENSP00000253861:S466T	S	+	2	0	EXOC4	132815412	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	7.419000	0.80179	2.802000	0.96397	0.655000	0.94253	AGT		0.458	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		C	133164872	G	C	133164872	3	2	19	1	0	0	0	0	1	0	0	0	5319	1029	36	5	1431	5	EXOC4	7	133164872	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	88553699	133164872	25973791	23	1829										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154863063	154863063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gccacatggaatacacgctcCgcacccgcaagtgcgtctcc	9	17	1	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr7:154863063C>T	ENST00000287907.2	+	1	1030	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	HTR5A-AS1_ENST00000493904.1_5'UTR|HTR5A-AS1_ENST00000395731.2_5'UTR|HTR5A-AS1_ENST00000543018.1_5'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	152					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)	p.R152C(2)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	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)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	ATACACGCTCCGCACCCGCAA	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	7											97	71	80					7																	154863063		2203	4300	6503	154493996	SO:0001583	missense	3361				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.454C>T	7.37:g.154863063C>T	ENSP00000287907:p.Arg152Cys		154493996	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.183618	0.78677	.	.	ENSG00000157219	ENST00000287907	T	0.73469	-0.75	4.75	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.124687	0.56097	D	0.000034	D	0.86969	0.6061	M	0.94142	3.5	0.53688	D	0.99997	D	0.62365	0.991	P	0.60012	0.867	D	0.88615	0.3159	10	0.66056	D	0.02	.	10.0952	0.42471	0.1551:0.6954:0.1494:0.0	.	152	P47898	5HT5A_HUMAN	C	152	ENSP00000287907:R152C	ENSP00000287907:R152C	R	+	1	0	HTR5A	154493996	1.000000	0.71417	0.800000	0.32199	0.948000	0.59901	3.890000	0.56220	1.187000	0.43000	0.655000	0.94253	CGC		0.627	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154863063	C	T	154863063	3	4	19	1	0	0	0	0	1	0	0	0	7471	652	23	1	456	1	HTR5A	7	154863063	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	21698191	154863063	4275600	24	1830										
DLC1	10395	hgsc.bcm.edu	37	chr8	12948826	12948826	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ccaaacttctcaattccttaCctggaaaagcttcttgcact	4	13	2	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr8:12948826C>T	ENST00000276297.4	-	14	4265		c.e14+1		DLC1_ENST00000520226.1_Splice_Site|DLC1_ENST00000510318.1_Splice_Site|DLC1_ENST00000512044.2_Splice_Site|DLC1_ENST00000358919.2_Splice_Site	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein						actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.?(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CAATTCCTTACCTGGAAAAGC	0.423																																																1	Unknown(1)	large_intestine(1)	8											106	105	105					8																	12948826		2203	4300	6503	12993197	SO:0001630	splice_region_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.3855+1G>A	8.37:g.12948826C>T			12993197	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Splice_Site	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379406	0.82682	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000510318;ENST00000512044;ENST00000520226	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1942	0.89815	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLC1	12993197	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.648000	0.83479	2.614000	0.88457	0.650000	0.86243	.		0.423	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	Intron	T	12948826	C	T	12948826	5	4	19	1	0	0	0	0	0	0	1	0	4561	521	18	3	750	3	DLC1	8	12948826	Splice_Site	SNP	C	TCGA-AG-3583-01A-01W-0831-10		12948826	133415196	25	1831										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53568975	53568975	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tcatgtctactaattaactcGgaaatacactgatctttttc	4	9	3	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr8:53568975G>A	ENST00000025008.5	-	15	3937	c.3414C>T	c.(3412-3414)tcC>tcT	p.S1138S	RB1CC1_ENST00000435644.2_Silent_p.S1138S|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Silent_p.S1138S	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1138					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.S1138S(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TAATTAACTCGGAAATACACT	0.299																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - coding silent(1)	large_intestine(1)	8											45	47	46					8																	53568975		2199	4297	6496	53731528	SO:0001819	synonymous_variant	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3414C>T	8.37:g.53568975G>A			53731528	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																				0.299	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		A	53568975	G	A	53568975	2	1	19	1	0	0	0	0	0	0	0	1	13136	1103	39	1		1	RB1CC1	8	53568975	Silent	SNP	G	TCGA-AG-3583-01A-01W-0831-10	40620149	53568975	92795047	26	1832										
ATP6V1H	51606	hgsc.bcm.edu	37	chr8	54708292	54708292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gaactggaatgatattatagCgccgcaggtgttcacacatt	10	8	1	1	rs200328593		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr8:54708292C>T	ENST00000359530.2	-	9	1048	c.785G>A	c.(784-786)cGc>cAc	p.R262H	ATP6V1H_ENST00000520188.1_Missense_Mutation_p.R222H|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.R262H|ATP6V1H_ENST00000355221.3_Missense_Mutation_p.R244H	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	262					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.R244H(1)		endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			GATATTATAGCGCCGCAGGTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	103	108	106		785,731,785	5.8	1	8		106	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ATP6V1H	NM_015941.2,NM_213619.1,NM_213620.1	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	262/484,244/466,262/484	54708292	1,13005	2203	4300	6503	54870845	SO:0001583	missense	51606			AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"ATPases / V-type"	18303	protein-coding gene	gene with protein product	"vacuolar ATP synthase subunit H"	608861	"ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.785G>A	8.37:g.54708292C>T	ENSP00000352522:p.Arg262His		54870845	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	37	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168523	0.78339	0.0	1.16E-4	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.8	5.8	0.92144	Armadillo-like helical (1);Armadillo-type fold (1);	0.095397	0.85682	D	0.000000	T	0.53818	0.1820	L	0.29908	0.895	0.80722	D	1	B;B	0.19445	0.036;0.018	B;B	0.15870	0.009;0.014	T	0.43278	-0.9401	9	0.31617	T	0.26	-10.9483	20.0693	0.97712	0.0:1.0:0.0:0.0	.	244;262	Q9UI12-2;Q9UI12	.;VATH_HUMAN	H	244;222;262;262	.	ENSP00000347359:R244H	R	-	2	0	ATP6V1H	54870845	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.758000	0.94735	0.563000	0.77884	CGC		0.403	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941		T	54708292	C	T	54708292	3	4	19	1	0	0	0	0	1	0	0	0	1190	768	27	1	690	1	ATP6V1H	8	54708292	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	1139317	54708292	91655730	27	1833										
TRIM55	84675	hgsc.bcm.edu	37	chr8	67066360	67066360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	cagcagcagaaactgcggatCccttgttttaccctagttgg	10	11	0	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr8:67066360C>T	ENST00000315962.4	+	9	1688	c.1315C>T	c.(1315-1317)Ccc>Tcc	p.P439S	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.P439S|TRIM55_ENST00000353317.5_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	439					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.P439S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			AACTGCGGATCCCTTGTTTTA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	8											66	61	63					8																	67066360		2203	4300	6503	67228914	SO:0001583	missense	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1315C>T	8.37:g.67066360C>T	ENSP00000323913:p.Pro439Ser		67228914	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.882914	0.91740	.	.	ENSG00000147573	ENST00000315962;ENST00000276573	T;T	0.57107	0.42;0.43	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000005	T	0.66934	0.2840	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.66472	-0.5915	10	0.62326	D	0.03	.	20.4237	0.99064	0.0:1.0:0.0:0.0	.	439;439	Q9BYV6;Q9BYV6-3	TRI55_HUMAN;.	S	439	ENSP00000323913:P439S;ENSP00000276573:P439S	ENSP00000276573:P439S	P	+	1	0	TRIM55	67228914	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.348000	0.66004	2.834000	0.97654	0.650000	0.86243	CCC		0.547	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		T	67066360	C	T	67066360	3	4	19	1	0	0	0	0	1	0	0	0	16569	855	30	3	1349	3	TRIM55	8	67066360	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	12358068	67066360	79297662	28	1834										
PYROXD2	84795	hgsc.bcm.edu	37	chr10	100144773	100144773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gtagccagaatgcaggggcaCggggcgggcgaagtagagct	19	8	0	2	rs141962703		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr10:100144773C>T	ENST00000370575.4	-	15	1654	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	536							oxidoreductase activity (GO:0016491)	p.V536M(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						TGCAGGGGCACGGGGCGGGCG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	MET/VAL	0,4406		0,0,2203	75	73	74		1606	-4.3	0	10	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	no	missense	PYROXD2	NM_032709.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	536/582	100144773	1,13005	2203	4300	6503	100134763	SO:0001583	missense	84795			AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1606G>A	10.37:g.100144773C>T	ENSP00000359607:p.Val536Met		100134763	D3DR61|Q5TAA9|Q9BRQ1	Missense_Mutation	SNP	ENST00000370575.4	37	CCDS7474.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040632	0.35989	0.0	1.16E-4	ENSG00000119943	ENST00000370575	T	0.46451	0.87	5.16	-4.3	0.03710	.	0.739377	0.13556	N	0.379121	T	0.31979	0.0814	M	0.67397	2.05	0.18873	N	0.999987	B	0.26547	0.152	B	0.23574	0.047	T	0.27673	-1.0067	10	0.49607	T	0.09	-1.2767	4.2959	0.10901	0.0917:0.4268:0.2933:0.1882	.	536	Q8N2H3	PYRD2_HUMAN	M	536	ENSP00000359607:V536M	ENSP00000359607:V536M	V	-	1	0	PYROXD2	100134763	0.103000	0.21917	0.016000	0.15963	0.948000	0.59901	0.637000	0.24659	-0.631000	0.05560	0.557000	0.71058	GTG		0.607	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		T	100144773	C	T	100144773	3	4	19	1	0	0	0	0	1	0	0	0	12904	536	19	1	147	1	PYROXD2	10	100144773	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		100144773	35389974	29	1835										
BTRC	8945	hgsc.bcm.edu	37	chr10	103294568	103294568	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atggcctccccaactgacatTaccctccggagggtgctggt	11	14	0	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr10:103294568T>G	ENST00000370187.3	+	10	1366	c.1248T>G	c.(1246-1248)atT>atG	p.I416M	BTRC_ENST00000393441.4_Missense_Mutation_p.I375M|BTRC_ENST00000408038.2_Missense_Mutation_p.I380M	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	416					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I416M(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		CAACTGACATTACCCTCCGGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10											254	218	230					10																	103294568		2203	4300	6503	103284558	SO:0001583	missense	8945			Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1248T>G	10.37:g.103294568T>G	ENSP00000359206:p.Ile416Met		103284558	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089199	0.76756	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.61510	1.15;1.15;0.1	5.69	-7.31	0.01441	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.46678	0.1405	N	0.04880	-0.145	0.58432	D	0.999995	P;P;D	0.69078	0.577;0.699;0.997	P;P;D	0.76071	0.553;0.554;0.987	T	0.63924	-0.6527	10	0.51188	T	0.08	-12.033	11.9141	0.52755	0.0786:0.7796:0.0:0.1418	.	390;380;416	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	M	416;375;380	ENSP00000359206:I416M;ENSP00000377088:I375M;ENSP00000385339:I380M	ENSP00000359206:I416M	I	+	3	3	BTRC	103284558	0.003000	0.15002	0.758000	0.31321	0.991000	0.79684	-1.137000	0.03219	-1.481000	0.01863	-0.250000	0.11733	ATT		0.483	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		G	103294568	T	G	103294568	3	3	19	1	0	0	0	0	1	0	0	0	1572	1742	61	4	1286	4	BTRC	10	103294568	Missense_Mutation	SNP	T	TCGA-AG-3583-01A-01W-0831-10	3149795	103294568	32240179	30	1836										
ADD3	120	hgsc.bcm.edu	37	chr10	111876094	111876094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tgaagggagaaaaacttactCgctgtaaacttgccagcctg	10	9	0	2	rs559836081		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr10:111876094C>T	ENST00000356080.4	+	4	779	c.412C>T	c.(412-414)Cgc>Tgc	p.R138C	ADD3_ENST00000277900.8_Missense_Mutation_p.R138C|ADD3_ENST00000497125.1_3'UTR|ADD3_ENST00000360162.3_Missense_Mutation_p.R138C	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	138						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.R138C(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		AAAACTTACTCGCTGTAAACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											170	148	155					10																	111876094		2203	4300	6503	111866084	SO:0001583	missense	120			U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.412C>T	10.37:g.111876094C>T	ENSP00000348381:p.Arg138Cys		111866084	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	37	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182171	0.78677	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.28454	1.61;1.61;1.61	5.6	4.7	0.59300	Class II aldolase/adducin, N-terminal (2);	0.048695	0.85682	D	0.000000	T	0.62233	0.2411	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.71178	-0.4669	10	0.87932	D	0	-5.3828	13.6678	0.62407	0.2811:0.7189:0.0:0.0	.	138;138	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	C	138	ENSP00000353286:R138C;ENSP00000348381:R138C;ENSP00000277900:R138C	ENSP00000277900:R138C	R	+	1	0	ADD3	111866084	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	5.930000	0.70104	1.362000	0.46000	-0.169000	0.13324	CGC		0.433	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		T	111876094	C	T	111876094	3	4	19	1	0	0	0	0	1	0	0	0	306	884	31	1	422	1	ADD3	10	111876094	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	8581526	111876094	23658653	31	1837										
EBF3	253738	hgsc.bcm.edu	37	chr10	131646712	131646712	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gatcactttctgcaacctctGaaagccgtaatctatggttg	8	10	4	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr10:131646712G>A	ENST00000355311.5	-	11	1144	c.1072C>T	c.(1072-1074)Cag>Tag	p.Q358*	EBF3_ENST00000368648.3_Nonsense_Mutation_p.Q349*			Q9H4W6	COE3_HUMAN	early B-cell factor 3	358					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q349*(3)|p.Q358*(3)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		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)		TGCAACCTCTGAAAGCCGTAA	0.468																																																6	Substitution - Nonsense(6)	lung(4)|large_intestine(2)	10											166	154	158					10																	131646712		2203	4300	6503	131536702	SO:0001587	stop_gained	253738				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.1072C>T	10.37:g.131646712G>A	ENSP00000347463:p.Gln358*		131536702	A0AUY1|Q5T6H9|Q9H4W5	Nonsense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	G	37	6.270420	0.97431	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.9271	20.0887	0.97806	0.0:0.0:1.0:0.0	.	.	.	.	X	358;349	.	ENSP00000347463:Q358X	Q	-	1	0	EBF3	131536702	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.809000	0.99208	2.825000	0.97269	0.655000	0.94253	CAG		0.468	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		A	131646712	G	A	131646712	4	1	19	1	0	0	0	0	0	1	0	0	4893	1299	45	3	634	3	EBF3	10	131646712	Nonsense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	19770618	131646712	3888035	32	1838										
RAG1	5896	hgsc.bcm.edu	37	chr11	36596949	36596949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ttgagctgggaggcattctcCggactttcaagttcatcttc	10	10	4	1	rs199474676		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr11:36596949C>T	ENST00000299440.5	+	2	2207	c.2095C>T	c.(2095-2097)Cgg>Tgg	p.R699W		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	699			R -> W (in OS; also in a patient with multiple autoimmune disorders; dbSNP:rs199474676). {ECO:0000269|PubMed:21771083}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R699W(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				AGGCATTCTCCGGACTTTCAA	0.522									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - Missense(1)	large_intestine(1)	11											57	56	57					11																	36596949		2202	4298	6500	36553525	SO:0001583	missense	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2095C>T	11.37:g.36596949C>T	ENSP00000299440:p.Arg699Trp		36553525	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.948423	0.34377	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	D;D	0.91740	-2.9;-2.9	6.13	1.42	0.22433	.	0.000000	0.85682	D	0.000000	D	0.97179	0.9078	H	0.96460	3.825	0.54753	D	0.999987	D	0.89917	1.0	D	0.87578	0.998	D	0.97710	1.0190	10	0.87932	D	0	.	16.2267	0.82300	0.3939:0.6061:0.0:0.0	.	699	P15918	RAG1_HUMAN	W	699	ENSP00000434610:R699W;ENSP00000299440:R699W	ENSP00000299440:R699W	R	+	1	2	RAG1	36553525	0.999000	0.42202	0.567000	0.28434	0.476000	0.33039	4.226000	0.58606	0.025000	0.15241	-1.075000	0.02238	CGG		0.522	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36596949	C	T	36596949	3	4	19	1	0	0	0	0	1	0	0	0	13040	643	23	1	2097	1	RAG1	11	36596949	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		36596949	98409567	33	1839										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118920536	118920536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tgtcctctaccagtgtctcaAatacagactccacctgaaaa	5	13	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr11:118920536A>G	ENST00000404233.3	-	15	1803	c.1679T>C	c.(1678-1680)tTt>tCt	p.F560S	HYOU1_ENST00000525859.1_Missense_Mutation_p.F560S|HYOU1_ENST00000529972.1_Missense_Mutation_p.F560S|HYOU1_ENST00000543287.1_Missense_Mutation_p.F473S	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	560					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.F560S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CAGTGTCTCAAATACAGACTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											264	242	250					11																	118920536		2200	4295	6495	118425746	SO:0001583	missense	10525			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.1679T>C	11.37:g.118920536A>G	ENSP00000384144:p.Phe560Ser		118425746	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.025777	0.75390	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.02258	5.6;5.6;5.6;4.37;5.6	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.08358	0.0208	L	0.52573	1.65	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.972;0.997;0.997	T	0.49862	-0.8894	10	0.20046	T	0.44	-11.3965	14.4125	0.67124	1.0:0.0:0.0:0.0	.	551;604;560;560	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	S	560;551;560;560;409;560;603;473;560	ENSP00000384144:F560S;ENSP00000437313:F560S;ENSP00000433397:F560S;ENSP00000442727:F473S;ENSP00000431874:F560S	ENSP00000278752:F551S	F	-	2	0	HYOU1	118425746	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.780000	0.85658	2.175000	0.68902	0.533000	0.62120	TTT		0.428	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		G	118920536	A	G	118920536	3	3	19	1	0	0	0	0	1	0	0	0	7491	14	1	4	1368	4	HYOU1	11	118920536	Missense_Mutation	SNP	A	TCGA-AG-3583-01A-01W-0831-10	82323587	118920536	16085980	34	1840										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	19	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		25398284	108453611	35	1841										
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30888072	30888072	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	acttgaagtatagttcgaagCtttttcttctcagcctcaag	7	9	3	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:30888072C>A	ENST00000395805.2	-	4	1186	c.639G>T	c.(637-639)aaG>aaT	p.K213N	CAPRIN2_ENST00000251071.5_Missense_Mutation_p.K213N|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.K213N|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.K213N|CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000538387.1_5'UTR	NM_001206856.1	NP_001193785.1			caprin family member 2									p.K213N(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TAGTTCGAAGCTTTTTCTTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											180	170	173					12																	30888072		2203	4300	6503	30779339	SO:0001583	missense	65981			AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.639G>T	12.37:g.30888072C>A	ENSP00000379150:p.Lys213Asn		30779339		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.245137	0.59103	.	.	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000537108;ENST00000541765;ENST00000543380;ENST00000542550	T;T;T;T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69	4.61	-0.684	0.11331	.	0.201608	0.43579	D	0.000557	T	0.39064	0.1064	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.76494	0.995;0.997;0.999;0.996;0.983	P;D;D;D;P	0.64321	0.878;0.924;0.922;0.922;0.782	T	0.14227	-1.0480	10	0.87932	D	0	-16.9831	10.6726	0.45768	0.0:0.4965:0.0:0.5035	.	213;213;213;213;213	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;CAPR2_HUMAN;.;.	N	213;213;213;213;132;10;10;132	ENSP00000298892:K213N;ENSP00000379150:K213N;ENSP00000251071:K213N;ENSP00000391479:K213N;ENSP00000438010:K132N;ENSP00000444137:K10N;ENSP00000440785:K10N;ENSP00000443353:K132N	ENSP00000251071:K213N	K	-	3	2	CAPRIN2	30779339	0.920000	0.31207	0.988000	0.46212	0.982000	0.71751	-0.116000	0.10724	-0.341000	0.08376	-0.229000	0.12294	AAG		0.408	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		A	30888072	C	A	30888072	3	1	19	1	0	0	0	0	1	0	0	0	2642	796	28	2	2804	2	CAPRIN2	12	30888072	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	5489788	30888072	102963823	36	1842										
NUP107	57122	hgsc.bcm.edu	37	chr12	69135645	69135646	+	Frame_Shift_Del	DEL	TT	TT	-													0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	aatggtcttactgagaaagcTttgtctgccaatgttgtgtt							TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	TT	TT	TT	-	TT	TT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:69135645_69135646delTT	ENST00000229179.4	+	27	2887_2888	c.2555_2556delTT	c.(2554-2556)cttfs	p.L852fs	NUP107_ENST00000539906.1_Frame_Shift_Del_p.L823fs|NUP107_ENST00000378905.2_Frame_Shift_Del_p.L613fs	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	852					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)	p.C853fs*31(1)	NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			CTGAGAAAGCTTTGTCTGCCAA	0.386																																																1	Deletion - Frameshift(1)	large_intestine(1)	12																																								67421913	SO:0001589	frameshift_variant	57122			AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.2555_2556delTT	12.37:g.69135645_69135646delTT	ENSP00000229179:p.Leu852fs		67421912	B4DZ67|Q6PJE1	Frame_Shift_Del	DEL	ENST00000229179.4	37	CCDS8985.1																																																																																				0.386	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		-	69135646	TT	-	69135645	7	5	19	1	0	1	0	1	0	0	0	0	10784	1609	56	0	2661	0	NUP107	12	69135645	Frame_Shift_Del	DEL	TT	TCGA-AG-3583-01A-01W-0831-10	38247573	69135645	64716250	37	1843										
ANO4	121601	hgsc.bcm.edu	37	chr12	101520844	101520844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	agcacaccacaacgagtggcCgtgaccatgtaggtgagagg	14	10	0	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:101520844C>T	ENST00000392977.3	+	27	3074	c.2864C>T	c.(2863-2865)cCg>cTg	p.P955L	ANO4_ENST00000392979.3_Missense_Mutation_p.P920L|ANO4_ENST00000550015.1_Missense_Mutation_p.P475L|ANO4_ENST00000299222.9_Missense_Mutation_p.P475L			Q32M45	ANO4_HUMAN	anoctamin 4	955					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.P920L(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AACGAGTGGCCGTGACCATGT	0.483										HNSCC(74;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											97	66	76					12																	101520844		2203	4300	6503	100044975	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2864C>T	12.37:g.101520844C>T	ENSP00000376703:p.Pro955Leu		100044975	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	C	27.4	4.824592	0.90955	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.72167	-0.57;-0.3;-0.63;-0.3	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.78039	0.4221	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.80165	-0.1496	10	0.87932	D	0	.	19.9299	0.97115	0.0:1.0:0.0:0.0	.	475;955;920	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	L	920;475;955;475	ENSP00000376705:P920L;ENSP00000299222:P475L;ENSP00000376703:P955L;ENSP00000450192:P475L	ENSP00000299222:P475L	P	+	2	0	ANO4	100044975	1.000000	0.71417	0.972000	0.41901	0.680000	0.39746	7.772000	0.85439	2.769000	0.95229	0.655000	0.94253	CCG		0.483	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		T	101520844	C	T	101520844	3	4	19	1	0	0	0	0	1	0	0	0	699	652	23	1	2857	1	ANO4	12	101520844	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	32385199	101520844	32331051	38	1844										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109924290	109924290	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ctataggtgtggtatgtgtcCctggcttgttctaaggacct	12	8	1	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:109924290C>T	ENST00000342494.3	+	6	952	c.357C>T	c.(355-357)tcC>tcT	p.S119S	UBE3B_ENST00000340074.5_Silent_p.S119S|UBE3B_ENST00000434735.2_Silent_p.S119S|UBE3B_ENST00000280774.5_Silent_p.S119S|UBE3B_ENST00000537063.1_Silent_p.S119S|UBE3B_ENST00000540230.1_Silent_p.S119S|UBE3B_ENST00000536398.1_Silent_p.S119S	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	119					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S119S(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GGTATGTGTCCCTGGCTTGTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	12											171	148	156					12																	109924290		2203	4300	6503	108408673	SO:0001819	synonymous_variant	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.357C>T	12.37:g.109924290C>T			108408673	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Silent	SNP	ENST00000342494.3	37	CCDS9129.1																																																																																				0.423	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109924290	C	T	109924290	2	4	19	1	0	0	0	0	0	0	0	1	16920	610	22	3		3	UBE3B	12	109924290	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	8403446	109924290	23927605	39	1845										
FBXO21	23014	hgsc.bcm.edu	37	chr12	117595862	117595862	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ttggatgtgctggaggatgtCaagcaccttcaaaacaagac	11	8	2	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr12:117595862C>T	ENST00000330622.5	-	10	1353	c.1354G>A	c.(1354-1356)Gac>Aac	p.D452N	FBXO21_ENST00000427718.2_Missense_Mutation_p.D445N			O94952	FBX21_HUMAN	F-box protein 21	452					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)	p.D452N(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|pancreas(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	29	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		TGGAGGATGTCAAGCACCTTC	0.493																																					GBM(168;452 2038 13535 17701 43680)											1	Substitution - Missense(1)	large_intestine(1)	12											145	147	146					12																	117595862		2203	4300	6503	116080245	SO:0001583	missense	23014			AB020682	CCDS9184.1, CCDS44989.1	12q24.23	2004-06-15	2004-06-15					"F-boxes /  "other""	13592	protein-coding gene	gene with protein product		609095	"F-box only protein 21"			10048485, 10531035	Standard	NM_033624		Approved	FBX21, KIAA0875	uc001twk.3	O94952	OTTHUMG00000169495	ENST00000330622.5:c.1354G>A	12.37:g.117595862C>T	ENSP00000328187:p.Asp452Asn		116080245	B3KMF0|Q5BJG0|Q9H087	Missense_Mutation	SNP	ENST00000330622.5	37	CCDS9184.1	.	.	.	.	.	.	.	.	.	.	C	33	5.193492	0.94960	.	.	ENSG00000135108	ENST00000427718;ENST00000257563;ENST00000535590;ENST00000330622;ENST00000548840	T;T	0.50813	0.73;0.8	5.02	5.02	0.67125	F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.55893	0.1949	N	0.24115	0.695	0.80722	D	1	D;P;D;D	0.65815	0.995;0.907;0.993;0.978	P;B;D;P	0.74674	0.858;0.444;0.984;0.736	T	0.54984	-0.8211	10	0.37606	T	0.19	-2.1842	18.5372	0.91014	0.0:1.0:0.0:0.0	.	301;195;452;445	Q8IUQ5;B3KQC8;O94952;O94952-1	.;.;FBX21_HUMAN;.	N	445;361;301;452;104	ENSP00000414468:D445N;ENSP00000328187:D452N	ENSP00000257563:D361N	D	-	1	0	FBXO21	116080245	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.320000	0.79064	2.607000	0.88179	0.655000	0.94253	GAC		0.493	FBXO21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404409.1	NM_033624		T	117595862	C	T	117595862	3	4	19	1	0	0	0	0	1	0	0	0	5752	826	29	3	544	3	FBXO21	12	117595862	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	7671572	117595862	16256033	40	1846										
SPG20	23111	hgsc.bcm.edu	37	chr13	36878766	36878766	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gcttctcctgcattatatccGtatctttaaaagaaagatta	5	8	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr13:36878766G>A	ENST00000451493.1	-	9	1954	c.1737C>T	c.(1735-1737)taC>taT	p.Y579Y	SPG20_ENST00000494062.2_Silent_p.Y579Y|SPG20_ENST00000438666.2_Silent_p.Y579Y|SPG20_ENST00000355182.4_Silent_p.Y579Y	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	579					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)	p.Y579Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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)		CATTATATCCGTATCTTTAAA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	13											70	62	65					13																	36878766		2203	4300	6503	35776766	SO:0001819	synonymous_variant	23111			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1737C>T	13.37:g.36878766G>A			35776766	O60349|Q86Y67|Q9H1T2|Q9H1T3	Silent	SNP	ENST00000451493.1	37	CCDS9356.1																																																																																				0.343	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			A	36878766	G	A	36878766	2	1	19	1	0	0	0	0	0	0	0	1	15081	1140	40	1		1	SPG20	13	36878766	Silent	SNP	G	TCGA-AG-3583-01A-01W-0831-10		36878766	78291112	41	1847										
PCNX	22990	hgsc.bcm.edu	37	chr14	71445269	71445269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atgagctatctttattaggaCgggcttcccagttagagaca	10	8	1	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr14:71445269C>T	ENST00000304743.2	+	6	2661	c.2215C>T	c.(2215-2217)Cgg>Tgg	p.R739W	PCNX_ENST00000238570.5_Missense_Mutation_p.R739W|PCNX_ENST00000439984.3_Missense_Mutation_p.R739W	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	739						integral component of membrane (GO:0016021)		p.R739W(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTTATTAGGACGGGCTTCCCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											78	76	77					14																	71445269		2203	4300	6503	70515022	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.2215C>T	14.37:g.71445269C>T	ENSP00000304192:p.Arg739Trp		70515022	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.424458	0.25639	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.12361	5.27;5.27;2.69	5.56	3.48	0.39840	.	0.000000	0.85682	D	0.000000	T	0.31888	0.0811	L	0.54323	1.7	0.50039	D	0.999842	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.993;0.993;0.997	T	0.07654	-1.0761	10	0.66056	D	0.02	.	14.5084	0.67767	0.2578:0.7422:0.0:0.0	.	739;739;739	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	W	739	ENSP00000304192:R739W;ENSP00000238570:R739W;ENSP00000396617:R739W	ENSP00000238570:R739W	R	+	1	2	PCNX	70515022	0.998000	0.40836	0.998000	0.56505	0.961000	0.63080	1.761000	0.38440	1.269000	0.44280	0.655000	0.94253	CGG		0.463	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71445269	C	T	71445269	3	4	19	1	0	0	0	0	1	0	0	0	11622	527	19	1	2237	1	PCNX	14	71445269	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		71445269	35904271	42	1848										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62327204	62327204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tccttccagggtcgcaacaaCtgcttctccataaaggttct	7	13	2	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr15:62327204C>T	ENST00000261517.5	-	4	308	c.235G>A	c.(235-237)Gtt>Att	p.V79I	VPS13C_ENST00000249837.3_Missense_Mutation_p.V79I|VPS13C_ENST00000395896.4_Missense_Mutation_p.V79I|VPS13C_ENST00000395898.3_Missense_Mutation_p.V79I	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.V79I(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GTCGCAACAACTGCTTCTCCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	15											92	92	92					15																	62327204		2203	4300	6503	60114496	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.235G>A	15.37:g.62327204C>T	ENSP00000261517:p.Val79Ile		60114496		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120493	0.94385	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	D	0.91865	0.7425	M	0.68952	2.095	0.58432	D	0.999999	D;D;P;D	0.89917	0.983;1.0;0.898;1.0	P;D;P;D	0.91635	0.866;0.999;0.779;0.999	D	0.92150	0.5727	10	0.87932	D	0	.	18.7178	0.91682	0.0:1.0:0.0:0.0	.	79;79;79;79	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	I	79	ENSP00000249837:V79I;ENSP00000261517:V79I;ENSP00000379233:V79I;ENSP00000379235:V79I	ENSP00000249837:V79I	V	-	1	0	VPS13C	60114496	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.776000	0.75023	2.774000	0.95407	0.655000	0.94253	GTT		0.328	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62327204	C	T	62327204	3	4	19	1	0	0	0	0	1	0	0	0	17231	565	20	3	11382	3	VPS13C	15	62327204	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		62327204	40204188	43	1849										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72190711	72190711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gctctgcactgctagtctcaTttgaggcactgagggcattg	12	10	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr15:72190711T>C	ENST00000356056.5	-	25	4605	c.4133A>G	c.(4132-4134)aAt>aGt	p.N1378S	MYO9A_ENST00000444904.1_Missense_Mutation_p.N1359S|MYO9A_ENST00000564571.1_Missense_Mutation_p.N1378S|MYO9A_ENST00000424560.1_Missense_Mutation_p.N1378S|MYO9A_ENST00000566885.1_Missense_Mutation_p.N998S|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1378	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.N1378S(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GCTAGTCTCATTTGAGGCACT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	100	100					15																	72190711		2199	4297	6496	69977765	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.4133A>G	15.37:g.72190711T>C	ENSP00000348349:p.Asn1378Ser		69977765	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.830407	0.00070	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83419	-1.72;-1.72;-1.72	5.51	-1.77	0.07982	.	.	.	.	.	T	0.44138	0.1279	N	0.00347	-1.61	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.49818	-0.8899	9	0.08179	T	0.78	.	4.5861	0.12282	0.0:0.2474:0.2649:0.4878	.	1359;1378;1378	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	S	1378;1378;1359	ENSP00000348349:N1378S;ENSP00000399162:N1378S;ENSP00000398250:N1359S	ENSP00000348349:N1378S	N	-	2	0	MYO9A	69977765	0.774000	0.28592	0.191000	0.23289	0.014000	0.08584	1.121000	0.31283	-0.087000	0.12528	-1.724000	0.00704	AAT		0.448	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72190711	T	C	72190711	3	2	19	1	0	0	0	0	1	0	0	0	10114	1493	52	4	3585	4	MYO9A	15	72190711	Missense_Mutation	SNP	T	TCGA-AG-3583-01A-01W-0831-10	9863507	72190711	30340681	44	1850										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30507468	30507468	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ggggaccccggctacccactCgggcggtttggagaagccat	15	13	0	1	rs185420636		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr16:30507468C>T	ENST00000356798.6	+	14	1734	c.1554C>T	c.(1552-1554)ctC>ctT	p.L518L	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000568012.1_3'UTR|ITGAL_ENST00000358164.5_Silent_p.L435L|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	518					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.L518L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GCTACCCACTCGGGCGGTTTG	0.602													C|||	1	0.000199681	8e-04	0	5008	,	,		15173	0		0	False		,,,				2504	0				NSCLC(110;1462 1641 3311 33990 49495)											1	Substitution - coding silent(1)	large_intestine(1)	16											75	82	79					16																	30507468		2197	4300	6497	30414969	SO:0001819	synonymous_variant	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1554C>T	16.37:g.30507468C>T			30414969	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.602	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30507468	C	T	30507468	2	4	19	1	0	0	0	0	0	0	0	1	7907	871	31	1		1	ITGAL	16	30507468	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10		30507468	59847285	45	1851										
SMPD3	55512	hgsc.bcm.edu	37	chr16	68404972	68404972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	agctgctctttcaatttggtGgctgctcgcttgtcaaacac	9	11	3	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr16:68404972G>A	ENST00000219334.5	-	3	1716	c.1113C>T	c.(1111-1113)gcC>gcT	p.A371A	SMPD3_ENST00000563226.1_Silent_p.A371A|SMPD3_ENST00000568373.1_Silent_p.A371A|SMPD3_ENST00000566009.1_5'Flank	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	371					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)	p.A371A(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	TCAATTTGGTGGCTGCTCGCT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	16											73	60	64					16																	68404972		2198	4300	6498	66962473	SO:0001819	synonymous_variant	55512			AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.1113C>T	16.37:g.68404972G>A			66962473	B7ZL82|Q2M1S8	Silent	SNP	ENST00000219334.5	37	CCDS10867.1																																																																																				0.602	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667		A	68404972	G	A	68404972	2	1	19	1	0	0	0	0	0	0	0	1	14843	1335	47	3		3	SMPD3	16	68404972	Silent	SNP	G	TCGA-AG-3583-01A-01W-0831-10	37897504	68404972	21949781	46	1852										
USP6	9098	hgsc.bcm.edu	37	chr17	5058851	5058851	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gtttggattcaagtatcctgGttagcaagaccactcccacc	8	12	1	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr17:5058851G>A	ENST00000574788.1	+	31	5008	c.2778G>A	c.(2776-2778)tgG>tgA	p.W926*	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Nonsense_Mutation_p.W609*|USP6_ENST00000250066.6_Nonsense_Mutation_p.W926*			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	926	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.W926*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AAGTATCCTGGTTAGCAAGAC	0.473			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	1	Substitution - Nonsense(1)	large_intestine(1)	17											154	132	140					17																	5058851		2203	4300	6503	4999575	SO:0001587	stop_gained	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.2778G>A	17.37:g.5058851G>A	ENSP00000460380:p.Trp926*		4999575	Q15634|Q86WP6|Q8IWT4	Nonsense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	G	50	16.419912	0.99863	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	.	.	.	2.91	0.376	0.16193	.	0.060911	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	6.1526	0.20320	0.5114:0.0:0.4886:0.0	.	.	.	.	X	926;609	.	ENSP00000250066:W926X	W	+	3	0	USP6	4999575	0.988000	0.35896	0.982000	0.44146	0.050000	0.14768	0.249000	0.18216	-0.090000	0.12462	0.398000	0.26397	TGG		0.473	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		A	5058851	G	A	5058851	4	1	19	1	0	0	0	0	0	1	0	0	17126	1270	44	3	2864	3	USP6	17	5058851	Nonsense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10		5058851	76136359	47	1853										
GAST	2520	hgsc.bcm.edu	37	chr17	39872102	39872102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atggatggacttcggccgccGcagtgctgaggatgagaact	15	9	0	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr17:39872102G>A	ENST00000329402.3	+	3	351	c.284G>A	c.(283-285)cGc>cAc	p.R95H	RNA5SP442_ENST00000365050.1_RNA|JUP_ENST00000540235.1_Intron	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	95		Cleavage.			G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.R95H(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TTCGGCCGCCGCAGTGCTGAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											63	64	64					17																	39872102		2203	4300	6503	37125628	SO:0001583	missense	2520				CCDS11404.1	17q21.2	2013-02-26	2005-06-14	2005-06-14	ENSG00000184502	ENSG00000184502		"Endogenous ligands"	4164	protein-coding gene	gene with protein product	"preprogastrin"	137250		GAS			Standard	NM_000805		Approved		uc002hxl.3	P01350	OTTHUMG00000133496	ENST00000329402.3:c.284G>A	17.37:g.39872102G>A	ENSP00000331358:p.Arg95His		37125628	P78463|P78464	Missense_Mutation	SNP	ENST00000329402.3	37	CCDS11404.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.281138	0.40394	.	.	ENSG00000184502	ENST00000329402	T	0.68624	-0.34	4.74	3.78	0.43462	Gastrin/cholecystokinin peptide hormone (2);	0.000000	0.51477	D	0.000084	T	0.62466	0.2430	M	0.75447	2.3	0.49582	D	0.999801	P	0.43701	0.815	B	0.37943	0.261	T	0.66945	-0.5795	10	0.87932	D	0	-18.3216	8.7031	0.34338	0.1021:0.0:0.8979:0.0	.	95	P01350	GAST_HUMAN	H	95	ENSP00000331358:R95H	ENSP00000331358:R95H	R	+	2	0	GAST	37125628	1.000000	0.71417	0.995000	0.50966	0.002000	0.02628	4.178000	0.58284	1.224000	0.43551	-0.136000	0.14681	CGC		0.552	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1			A	39872102	G	A	39872102	3	1	19	1	0	0	0	0	1	0	0	0	6272	1087	38	1	290	1	GAST	17	39872102	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	34813251	39872102	41323108	48	1854										
OR7C1	26664	hgsc.bcm.edu	37	chr19	14910361	14910361	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gttgcaaagtatatcaccacGttattaatgaaggtgtcaga	9	6	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr19:14910361G>A	ENST00000248073.2	-	1	662	c.588C>T	c.(586-588)aaC>aaT	p.N196N	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	196					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N196N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						ATATCACCACGTTATTAATGA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	19											84	84	84					19																	14910361		2203	4300	6503	14771361	SO:0001819	synonymous_variant	26664			X89676	CCDS12317.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.588C>T	19.37:g.14910361G>A			14771361	Q15621|Q6IFP2|Q96R94	Silent	SNP	ENST00000248073.2	37	CCDS12317.1																																																																																				0.393	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			A	14910361	G	A	14910361	2	1	19	1	0	0	0	0	0	0	0	1	11248	1136	40	1		1	OR7C1	19	14910361	Silent	SNP	G	TCGA-AG-3583-01A-01W-0831-10		14910361	44218622	49	1855										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53651985	53651985	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atctgggtttcctgctatttGtacttggctctccaaagtga	9	9	2	1	rs543465832		TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr19:53651985G>T	ENST00000334197.7	-	4	288	c.220C>A	c.(220-222)Caa>Aaa	p.Q74K	ZNF347_ENST00000601804.1_Missense_Mutation_p.Q16K|ZNF347_ENST00000452676.2_Missense_Mutation_p.Q75K|ZNF347_ENST00000601469.2_Missense_Mutation_p.Q75K	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q74K(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CCTGCTATTTGTACTTGGCTC	0.403																																					Melanoma(64;205 1597 17324 45721)											1	Substitution - Missense(1)	large_intestine(1)	19											291	265	274					19																	53651985		2203	4300	6503	58343797	SO:0001583	missense	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.220C>A	19.37:g.53651985G>T	ENSP00000334146:p.Gln74Lys		58343797	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.477228	0.00165	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.06068	3.35;3.35	1.82	-3.63	0.04529	Krueppel-associated box (1);	.	.	.	.	T	0.01320	0.0043	N	0.00633	-1.31	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.37842	-0.9688	9	0.02654	T	1	.	5.5139	0.16896	0.1769:0.0:0.5878:0.2353	.	75;74	G5E9N4;Q96SE7	.;ZN347_HUMAN	K	74;75	ENSP00000334146:Q74K;ENSP00000405218:Q75K	ENSP00000334146:Q74K	Q	-	1	0	ZNF347	58343797	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.514000	0.02254	-1.526000	0.01760	-0.485000	0.04761	CAA		0.403	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53651985	G	T	53651985	3	4	19	1	0	0	0	0	1	0	0	0	17900	1386	48	2	2307	2	ZNF347	19	53651985	Missense_Mutation	SNP	G	TCGA-AG-3583-01A-01W-0831-10	38741624	53651985	5476998	50	1856										
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31372633	31372633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	cagtcatgccaaagctcttcCgggaaaccaggactcgttca	9	13	3	0	rs149520896	byFrequency	TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr20:31372633C>T	ENST00000328111.2	+	4	595	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	DNMT3B_ENST00000375623.4_Missense_Mutation_p.R92W|DNMT3B_ENST00000443239.3_Missense_Mutation_p.R92W|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000344505.4_Missense_Mutation_p.R92W|DNMT3B_ENST00000348286.2_Missense_Mutation_p.R92W|DNMT3B_ENST00000353855.2_Missense_Mutation_p.R92W|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R104W	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	92	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.R92W(2)|p.R104W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AAAGCTCTTCCGGGAAACCAG	0.507													C|||	2	0.000399361	8e-04	0	5008	,	,		17093	0		0.001	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	20						C	TRP/ARG,,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	80	67	72		274,,274,274,274,310	5	1	20	dbSNP_134	72	0,8600		0,0,4300	no	missense,intron,missense,missense,missense,missense	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	101,,101,101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging	92/729,,92/854,92/834,92/771,104/846	31372633	1,13005	2203	4300	6503	30836294	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.274C>T	20.37:g.31372633C>T	ENSP00000328547:p.Arg92Trp		30836294	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409996	0.83340	2.27E-4	0.0	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000344505;ENST00000375623;ENST00000201963	D;D;D;D;D;T;D	0.97772	-4.39;-4.52;-4.45;-4.48;-4.36;-0.38;-4.53	4.98	4.98	0.66077	.	0.415723	0.25222	N	0.032240	D	0.97142	0.9066	L	0.27053	0.805	0.43000	D	0.994512	P;D;D;D;D	0.89917	0.765;1.0;1.0;1.0;1.0	B;D;D;D;D	0.67231	0.09;0.95;0.939;0.95;0.947	D	0.97331	0.9950	10	0.72032	D	0.01	-14.4438	13.9551	0.64142	0.0:1.0:0.0:0.0	.	92;104;92;92;92	E7EN63;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;DNM3B_HUMAN	W	92;178;92;92;92;92;92;104	ENSP00000328547:R92W;ENSP00000313397:R92W;ENSP00000337764:R92W;ENSP00000403169:R92W;ENSP00000345105:R92W;ENSP00000364774:R92W;ENSP00000201963:R104W	ENSP00000201963:R104W	R	+	1	2	DNMT3B	30836294	0.370000	0.25047	1.000000	0.80357	0.989000	0.77384	1.823000	0.39062	2.742000	0.94016	0.655000	0.94253	CGG		0.507	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		T	31372633	C	T	31372633	3	4	19	1	0	0	0	0	1	0	0	0	4688	643	23	1	324	1	DNMT3B	20	31372633	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10		31372633	31652887	51	1857										
DOK5	55816	hgsc.bcm.edu	37	chr20	53260081	53260081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	cctactggcagcacatcacaCggcagcacagcacgggacag	11	15	1	0			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chr20:53260081C>T	ENST00000262593.5	+	7	1170	c.820C>T	c.(820-822)Cgg>Tgg	p.R274W	DOK5_ENST00000395939.1_Missense_Mutation_p.R166W	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	274					MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)	p.R274W(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			GCACATCACACGGCAGCACAG	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	20											54	48	50					20																	53260081		2203	4300	6503	52693488	SO:0001583	missense	55816			AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"Pleckstrin homology (PH) domain containing"	16173	protein-coding gene	gene with protein product		608334	"chromosome 20 open reading frame 180"	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.820C>T	20.37:g.53260081C>T	ENSP00000262593:p.Arg274Trp		52693488	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Missense_Mutation	SNP	ENST00000262593.5	37	CCDS13446.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.465314	0.63513	.	.	ENSG00000101134	ENST00000262593;ENST00000395939	D;D	0.93659	-2.27;-3.26	5.42	-1.32	0.09201	.	0.000000	0.85682	D	0.000000	D	0.93200	0.7834	L	0.27053	0.805	0.32349	N	0.558736	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.973	D	0.92644	0.6127	10	0.66056	D	0.02	-7.4003	16.721	0.85410	0.7627:0.2373:0.0:0.0	.	166;274	Q9P104-2;Q9P104	.;DOK5_HUMAN	W	274;166	ENSP00000262593:R274W;ENSP00000379270:R166W	ENSP00000262593:R274W	R	+	1	2	DOK5	52693488	0.123000	0.22298	0.098000	0.21074	0.980000	0.70556	0.291000	0.18994	-0.142000	0.11354	-0.122000	0.15005	CGG		0.652	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079777.2			T	53260081	C	T	53260081	3	4	19	1	0	0	0	0	1	0	0	0	4711	527	19	1	846	1	DOK5	20	53260081	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	21887448	53260081	9765439	52	1858										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411333	23411333	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	atatatgagtctatagaataCtggaacactagtgtccaaga	8	6	1	3			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:23411333C>T	ENST00000379361.4	+	3	2558	c.1698C>T	c.(1696-1698)taC>taT	p.Y566Y		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	566					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)	p.Y461Y(1)		NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						CTATAGAATACTGGAACACTA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	X											96	92	93					X																	23411333		2203	4300	6503	23321254	SO:0001819	synonymous_variant	139411			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1698C>T	X.37:g.23411333C>T			23321254	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	37	CCDS35215.2																																																																																				0.413	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		T	23411333	C	T	23411333	2	4	19	1	0	0	0	0	0	0	0	1	12766	576	20	3		3	PTCHD1	23	23411333	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10		23411333	131859227	53	1859										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34962542	34962542	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	taaaatactgggacaggagaCgccgggcggcaccgcattct	13	11	1	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:34962542C>T	ENST00000329357.5	+	1	1630	c.1594C>T	c.(1594-1596)Cgc>Tgc	p.R532C		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	532								p.R532C(2)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						GGACAGGAGACGCCGGGCGGC	0.498																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	X											94	84	87					X																	34962542		2202	4300	6502	34872463	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1594C>T	X.37:g.34962542C>T	ENSP00000328307:p.Arg532Cys		34872463	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	5.656	0.305749	0.10733	.	.	ENSG00000189132	ENST00000329357	T	0.41758	0.99	0.602	0.602	0.17535	.	.	.	.	.	T	0.18718	0.0449	N	0.14661	0.345	0.09310	N	1	P	0.36768	0.569	B	0.14023	0.01	T	0.11179	-1.0598	8	0.72032	D	0.01	.	.	.	.	.	532	Q8NA70	FA47B_HUMAN	C	532	ENSP00000328307:R532C	ENSP00000328307:R532C	R	+	1	0	FAM47B	34872463	0.002000	0.14202	0.003000	0.11579	0.002000	0.02628	0.279000	0.18771	0.543000	0.28864	0.292000	0.19580	CGC		0.498	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34962542	C	T	34962542	3	4	19	1	0	0	0	0	1	0	0	0	5589	536	19	1	1596	1	FAM47B	23	34962542	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	11551209	34962542	120308018	54	1860										
RBM10	8241	hgsc.bcm.edu	37	chrX	47032536	47032536	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tccccgtatagatccgtggcCagctgcagtcgcacggcgtg	13	14	0	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:47032536C>T	ENST00000377604.3	+	5	1184	c.442C>T	c.(442-444)Cag>Tag	p.Q148*	RBM10_ENST00000329236.7_Nonsense_Mutation_p.Q71*|RBM10_ENST00000345781.6_Nonsense_Mutation_p.Q71*	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	148	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.Q148*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						GATCCGTGGCCAGCTGCAGTC	0.612																																					Melanoma(171;120 2705 19495 39241)											1	Substitution - Nonsense(1)	large_intestine(1)	X											86	70	75					X																	47032536		2203	4300	6503	46917480	SO:0001587	stop_gained	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.442C>T	X.37:g.47032536C>T	ENSP00000366829:p.Gln148*		46917480	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Nonsense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	39	7.378596	0.98248	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	.	.	.	3.81	3.81	0.43845	.	0.158984	0.42172	D	0.000750	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-5.9209	10.7407	0.46152	0.0:1.0:0.0:0.0	.	.	.	.	X	148;71;71	.	ENSP00000328848:Q71X	Q	+	1	0	RBM10	46917480	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.328000	0.72915	1.641000	0.50575	0.436000	0.28706	CAG		0.612	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47032536	C	T	47032536	4	4	19	1	0	0	0	0	0	1	0	0	13148	595	21	3	456	3	RBM10	23	47032536	Nonsense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	12069994	47032536	108238024	55	1861										
SSX5	6758	hgsc.bcm.edu	37	chrX	48049588	48049588	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	ccagatgtcttgttaaccttCtcagaggtatttagttttcc	7	9	2	2			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:48049588C>G	ENST00000376923.1	-	5	446	c.447G>C	c.(445-447)gaG>gaC	p.E149D	SSX5_ENST00000347757.1_Missense_Mutation_p.E149D|SSX5_ENST00000311798.1_Missense_Mutation_p.E190D			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.E190D(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						TGTTAACCTTCTCAGAGGTAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											129	112	118					X																	48049588		2203	4299	6502	47934532	SO:0001583	missense	6758			BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.447G>C	X.37:g.48049588C>G	ENSP00000366122:p.Glu149Asp		47934532	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	37	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	8.617	0.890538	0.17613	.	.	ENSG00000165583	ENST00000311798;ENST00000376923;ENST00000347757;ENST00000403001	T;T;T;T	0.35048	3.02;3.05;3.05;1.33	1.66	-3.17	0.05202	.	1.504810	0.04642	N	0.405509	T	0.40119	0.1104	M	0.62723	1.935	0.09310	N	1	B;P	0.34462	0.325;0.454	B;P	0.44946	0.275;0.465	T	0.40961	-0.9535	10	0.36615	T	0.2	.	2.8846	0.05657	0.0:0.3619:0.2425:0.3955	.	149;190	O60225;O60225-2	SSX5_HUMAN;.	D	190;149;149;89	ENSP00000312415:E190D;ENSP00000366122:E149D;ENSP00000290558:E149D;ENSP00000385051:E89D	ENSP00000312415:E190D	E	-	3	2	SSX5	47934532	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	0.067000	0.14510	-0.931000	0.03746	0.171000	0.16805	GAG		0.488	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		G	48049588	C	G	48049588	3	3	19	1	0	0	0	0	1	0	0	0	15247	912	32	5	127	5	SSX5	23	48049588	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	1017052	48049588	107220972	56	1862										
APEX2	27301	hgsc.bcm.edu	37	chrX	55033487	55033487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	tctagcagaggccagaaaaaCctgaagagctactttcagcc	9	11	2	4			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:55033487C>T	ENST00000374987.3	+	6	1242	c.1176C>T	c.(1174-1176)aaC>aaT	p.N392N	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	392	Required for the colocalization with PCNA in nuclear foci in presence of oxidative- induced DNA damaging agents.		N -> H (identified in a patient with mtDNA maintenance disorders). {ECO:0000269|PubMed:20843780}.		base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)	p.N392N(1)		breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						GCCAGAAAAACCTGAAGAGCT	0.557								Other BER factors																																								1	Substitution - coding silent(1)	large_intestine(1)	X											56	54	55					X																	55033487		2203	4300	6503	55050212	SO:0001819	synonymous_variant	27301			AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.1176C>T	X.37:g.55033487C>T			55050212	Q9Y5X7	Silent	SNP	ENST00000374987.3	37	CCDS14365.1																																																																																				0.557	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			T	55033487	C	T	55033487	2	4	19	1	0	0	0	0	0	0	0	1	770	506	18	3		3	APEX2	23	55033487	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	6983899	55033487	100237073	57	1863										
FAM133A	286499	hgsc.bcm.edu	37	chrX	92964843	92964843	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	gaaccgttcatacaaatcatCccaaagctctacgcatgaat	5	12	3	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:92964843C>T	ENST00000355813.5	+	4	951	c.425C>T	c.(424-426)tCc>tTc	p.S142F	FAM133A_ENST00000332647.4_Missense_Mutation_p.S142F|FAM133A_ENST00000538690.1_Missense_Mutation_p.S142F|FAM133A_ENST00000322139.4_Missense_Mutation_p.S142F	NM_001171109.1|NM_173698.2	NP_001164580.1|NP_775969.1	Q8N9E0	F133A_HUMAN	family with sequence similarity 133, member A	142	Lys-rich.|Ser-rich.							p.S142F(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(7)|upper_aerodigestive_tract(1)	20						TACAAATCATCCCAAAGCTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											32	27	28					X																	92964843		2201	4295	6496	92851499	SO:0001583	missense	286499			AK094978	CCDS14466.1	Xq21.32	2010-05-04			ENSG00000179083	ENSG00000179083			26748	protein-coding gene	gene with protein product	"cancer/testis antigen 115"						Standard	NM_173698		Approved	RP1-32F7.2, FLJ37659, CT115	uc022bzv.1	Q8N9E0	OTTHUMG00000021975	ENST00000355813.5:c.425C>T	X.37:g.92964843C>T	ENSP00000348067:p.Ser142Phe		92851499		Missense_Mutation	SNP	ENST00000355813.5	37	CCDS14466.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.737830	0.30774	.	.	ENSG00000179083	ENST00000538690;ENST00000355813;ENST00000322139;ENST00000332647	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	3.0	3.0	0.34707	.	0.074149	0.56097	U	0.000027	T	0.60919	0.2306	M	0.76002	2.32	0.25184	N	0.990181	D	0.69078	0.997	P	0.62184	0.899	T	0.51919	-0.8644	10	0.72032	D	0.01	-2.6891	8.661	0.34093	0.0:1.0:0.0:0.0	.	142	Q8N9E0	F133A_HUMAN	F	142	ENSP00000441389:S142F;ENSP00000348067:S142F;ENSP00000318974:S142F;ENSP00000362169:S142F	ENSP00000318974:S142F	S	+	2	0	FAM133A	92851499	0.998000	0.40836	0.868000	0.34077	0.829000	0.46940	1.658000	0.37376	1.768000	0.52137	0.597000	0.82753	TCC		0.373	FAM133A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057452.1	NM_173698		T	92964843	C	T	92964843	3	4	19	1	0	0	0	0	1	0	0	0	5459	855	30	3	427	3	FAM133A	23	92964843	Missense_Mutation	SNP	C	TCGA-AG-3583-01A-01W-0831-10	37931356	92964843	62305717	58	1864										
FMR1	2332	hgsc.bcm.edu	37	chrX	147024827	147024827	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0677966101694915	4	1	0.5865	3.665625	0.458203125	0.523809523809524	1	0	aatagggggcacggcagacgCggtcctggatatacttcagg	15	9	1	1			TCGA-AG-3583-01A-01W-0831-10	TCGA-AG-3583-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	ce45b9fe-f42b-4933-8d06-31cb8a528f9d	ba86e5b4-dd24-4497-8df7-aab5cb75c5db	g.chrX:147024827C>T	ENST00000370475.4	+	14	1580	c.1452C>T	c.(1450-1452)cgC>cgT	p.R484R	FMR1_ENST00000439526.2_Silent_p.R461R|FMR1_ENST00000370470.1_Silent_p.R484R|FMR1_ENST00000370477.1_Silent_p.R463R|FMR1_ENST00000492846.1_3'UTR|FMR1_ENST00000218200.8_Silent_p.R463R|FMR1_ENST00000370471.3_Intron|FMR1_ENST00000440235.2_Silent_p.R131R	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	484	Interaction with RANBP9.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R484R(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					ACGGCAGACGCGGTCCTGGAT	0.418									Fragile X syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	X											127	118	121					X																	147024827		2203	4300	6503	146832519	SO:0001819	synonymous_variant	2332	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.1452C>T	X.37:g.147024827C>T			146832519	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																				0.418	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		T	147024827	C	T	147024827	2	4	19	1	0	0	0	0	0	0	0	1	5979	755	27	1		1	FMR1	23	147024827	Silent	SNP	C	TCGA-AG-3583-01A-01W-0831-10	54059984	147024827	8245733	59	1865										
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3750457	3750457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgcagctgtgacgcggaggCgggcagaagaatctccagtt	15	9	1	3	rs200715031		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr1:3750457C>T	ENST00000378230.3	-	12	1952	c.1628G>A	c.(1627-1629)cGc>cAc	p.R543H	CEP104_ENST00000460038.1_5'UTR	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	543						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.R543H(1)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						GACGCGGAGGCGGGCAGAAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	110	111					1																	3750457		2203	4300	6503	3740317	SO:0001583	missense	9731			AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1628G>A	1.37:g.3750457C>T	ENSP00000367476:p.Arg543His		3740317	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.009810	0.75046	.	.	ENSG00000116198	ENST00000378230	T	0.68331	-0.32	5.03	5.03	0.67393	Armadillo-like helical (1);Armadillo-type fold (1);	0.065109	0.64402	D	0.000013	T	0.81273	0.4788	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	0.995;1.0	P;D	0.87578	0.742;0.998	T	0.83003	-0.0176	10	0.59425	D	0.04	.	17.3632	0.87357	0.0:1.0:0.0:0.0	.	543;543	O60308-3;O60308	.;CE104_HUMAN	H	543	ENSP00000367476:R543H	ENSP00000367476:R543H	R	-	2	0	CEP104	3740317	1.000000	0.71417	0.326000	0.25389	0.466000	0.32739	6.734000	0.74801	2.329000	0.79093	0.467000	0.42956	CGC		0.438	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		T	3750457	C	T	3750457	3	4	20	1	0	0	0	0	1	0	0	0	8205	768	27	1	1193	1	KIAA0562	1	3750457	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		3750457	245500164	1	1866										
LEPR	3953	hgsc.bcm.edu	37	chr1	66102556	66102556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catcagagttctccaggacaGttgctcacactttgtagaaa	8	10	3	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr1:66102556G>T	ENST00000349533.6	+	20	3541	c.3356G>T	c.(3355-3357)aGt>aTt	p.S1119I	LEPR_ENST00000406510.3_Missense_Mutation_p.S186I	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.S1119I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTCCAGGACAGTTGCTCACAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	68	69					1																	66102556		2203	4300	6503	65875144	SO:0001583	missense	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3356G>T	1.37:g.66102556G>T	ENSP00000330393:p.Ser1119Ile		65875144	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	G	6.194	0.403880	0.11754	.	.	ENSG00000116678	ENST00000349533;ENST00000406510	T	0.55413	0.52	5.37	0.96	0.19631	.	0.793988	0.12269	N	0.483994	T	0.28433	0.0703	M	0.65975	2.015	0.21499	N	0.999663	B	0.20671	0.047	B	0.12837	0.008	T	0.33471	-0.9867	10	0.38643	T	0.18	-5.7727	10.0644	0.42295	0.0817:0.5762:0.3421:0.0	.	1119	P48357	LEPR_HUMAN	I	1119;186	ENSP00000330393:S1119I	ENSP00000330393:S1119I	S	+	2	0	LEPR	65875144	0.743000	0.28239	0.921000	0.36526	0.014000	0.08584	1.689000	0.37700	0.205000	0.20568	0.585000	0.79938	AGT		0.418	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		T	66102556	G	T	66102556	3	4	20	1	0	0	0	0	1	0	0	0	8750	1029	36	2	3656	2	LEPR	1	66102556	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	62352099	66102556	183148065	2	1867										
ZNF326	284695	hgsc.bcm.edu	37	chr1	90486384	90486384	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgatcacatgatgaaggtagAgacagttcattgcagcgctt	11	7	2	4			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr1:90486384A>G	ENST00000340281.4	+	10	1351	c.1208A>G	c.(1207-1209)gAg>gGg	p.E403G	ZNF326_ENST00000370447.3_Missense_Mutation_p.E314G|ZNF326_ENST00000455342.2_Missense_Mutation_p.E197G	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	403					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.E403G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ATGAAGGTAGAGACAGTTCAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											154	153	153					1																	90486384		2203	4300	6503	90258972	SO:0001583	missense	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1208A>G	1.37:g.90486384A>G	ENSP00000340796:p.Glu403Gly		90258972	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.839269	0.91117	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.54479	0.57;0.57;0.57	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.66458	0.2791	M	0.72894	2.215	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.71540	-0.4562	10	0.87932	D	0	-11.8054	15.9813	0.80111	1.0:0.0:0.0:0.0	.	403;403	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	G	403;403;314;197	ENSP00000340796:E403G;ENSP00000359476:E314G;ENSP00000403470:E197G	ENSP00000340796:E403G	E	+	2	0	ZNF326	90258972	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.387000	0.79785	2.185000	0.69588	0.460000	0.39030	GAG		0.353	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		G	90486384	A	G	90486384	3	3	20	1	0	0	0	0	1	0	0	0	17885	304	11	4	1250	4	ZNF326	1	90486384	Missense_Mutation	SNP	A	TCGA-AG-3584-01A-01W-0831-10	24383828	90486384	158764237	3	1868										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186646812	186646812	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcccgttggtgaaagctggcCctcgcttatgatctgtcttg	12	11	2	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr1:186646812C>A	ENST00000367468.5	-	5	744	c.608G>T	c.(607-609)gGg>gTg	p.G203V	RP5-973M2.2_ENST00000608917.1_lincRNA|PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	203					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.G203V(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GAAAGCTGGCCCTCGCTTATG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	1											107	112	110					1																	186646812		2203	4300	6503	184913435	SO:0001583	missense	5743			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.608G>T	1.37:g.186646812C>A	ENSP00000356438:p.Gly203Val		184913435	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	37	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	C	32	5.187310	0.94923	.	.	ENSG00000073756	ENST00000367468	T	0.68765	-0.35	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	D	0.89270	0.3604	10	0.87932	D	0	-20.0984	20.0465	0.97608	0.0:1.0:0.0:0.0	.	203;203	Q8IZA9;P35354	.;PGH2_HUMAN	V	203	ENSP00000356438:G203V	ENSP00000356438:G203V	G	-	2	0	PTGS2	184913435	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.627000	0.83176	2.735000	0.93741	0.557000	0.71058	GGG		0.428	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		A	186646812	C	A	186646812	3	1	20	1	0	0	0	0	1	0	0	0	12791	623	22	2	1230	2	PTGS2	1	186646812	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	96160428	186646812	62603809	4	1869										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145157772	145157772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acatttcttgctgctgatgtGcgaactgtaggaaccagaat	10	8	1	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr2:145157772G>A	ENST00000558170.2	-	8	2166	c.982C>T	c.(982-984)Cac>Tac	p.H328Y	ZEB2_ENST00000539609.3_Missense_Mutation_p.H304Y|ZEB2_ENST00000409487.3_Missense_Mutation_p.H328Y|ZEB2_ENST00000303660.4_Missense_Mutation_p.H328Y	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	328					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.H328Y(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CTGCTGATGTGCGAACTGTAG	0.388																																					Melanoma(33;1235 1264 5755 16332)											1	Substitution - Missense(1)	large_intestine(1)	2											48	51	50					2																	145157772		2202	4300	6502	144874242	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.982C>T	2.37:g.145157772G>A	ENSP00000454157:p.His328Tyr		144874242	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.667655	0.67814	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93	5.64	5.64	0.86602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97374	0.9141	M	0.62209	1.925	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.981;0.981	D;D;D;D	0.91635	0.999;0.978;0.954;0.954	D	0.97793	1.0239	10	0.87932	D	0	-11.5597	19.7156	0.96119	0.0:0.0:1.0:0.0	.	304;193;327;328	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	Y	323;304;328;328;328;328	ENSP00000443792:H304Y;ENSP00000302501:H328Y;ENSP00000386854:H328Y;ENSP00000395496:H328Y;ENSP00000376601:H328Y	ENSP00000302501:H328Y	H	-	1	0	ZEB2	144874242	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.658000	0.90341	0.655000	0.94253	CAC		0.388	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145157772	G	A	145157772	3	1	20	1	0	0	0	0	1	0	0	0	17663	1319	46	3	2674	3	ZEB2	2	145157772	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10		145157772	98041601	5	1870										
PRKAG3	53632	hgsc.bcm.edu	37	chr2	219695534	219695534	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgtccatctcaaggctttgGccctccgtttcccacggatt	8	14	1	0			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr2:219695534G>T	ENST00000529249.1	-	3	479	c.164C>A	c.(163-165)gCc>gAc	p.A55D	PRKAG3_ENST00000545803.1_5'UTR|PRKAG3_ENST00000439262.2_Missense_Mutation_p.A30D|PRKAG3_ENST00000392098.3_Missense_Mutation_p.A55D			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	55					cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)	p.A55D(1)		large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	CAAGGCTTTGGCCCTCCGTTT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	2											180	148	159					2																	219695534		2203	4300	6503	219403778	SO:0001583	missense	53632			AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.164C>A	2.37:g.219695534G>T	ENSP00000436068:p.Ala55Asp		219403778	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065659	0.36470	.	.	ENSG00000115592	ENST00000439262;ENST00000529249;ENST00000392098;ENST00000430489	D;D;T;T	0.82433	-1.6;-1.61;0.24;0.91	4.78	-0.797	0.10909	.	1.075700	0.07193	N	0.856176	T	0.64316	0.2587	N	0.24115	0.695	0.09310	N	1	P;B;B	0.47910	0.902;0.178;0.112	B;B;B	0.40741	0.339;0.054;0.024	T	0.56372	-0.7990	10	0.10902	T	0.67	-1.0118	0.6674	0.00853	0.1974:0.1588:0.3194:0.3243	.	55;30;55	B4DUK8;Q9UGI9-2;Q9UGI9	.;.;AAKG3_HUMAN	D	30;55;55;55	ENSP00000397133:A30D;ENSP00000436068:A55D;ENSP00000375947:A55D;ENSP00000416100:A55D	ENSP00000233944:A55D	A	-	2	0	PRKAG3	219403778	0.440000	0.25618	0.002000	0.10522	0.406000	0.30931	0.506000	0.22658	-0.159000	0.11021	0.655000	0.94253	GCC		0.592	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1			T	219695534	G	T	219695534	3	4	20	1	0	0	0	0	1	0	0	0	12536	1203	42	2	1349	2	PRKAG3	2	219695534	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	74537762	219695534	23503839	6	1871										
LPP	4026	hgsc.bcm.edu	37	chr3	188327306	188327306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ttcctgtctctgggcagtgtCcacctccttcaacacgggga	10	14	2	0			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr3:188327306C>T	ENST00000312675.4	+	6	1033	c.787C>T	c.(787-789)Cca>Tca	p.P263S	LPP_ENST00000448637.1_Missense_Mutation_p.P263S|LPP_ENST00000471917.1_3'UTR|LPP_ENST00000543006.1_Missense_Mutation_p.P263S	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	263	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.P263S(1)	HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TGGGCAGTGTCCACCTCCTTC	0.572			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"																																		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	1	Substitution - Missense(1)	large_intestine(1)	3											74	66	68					3																	188327306		2203	4300	6503	189810000	SO:0001583	missense	4026			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.787C>T	3.37:g.188327306C>T	ENSP00000318089:p.Pro263Ser		189810000	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.775629	0.31411	.	.	ENSG00000145012	ENST00000448637;ENST00000312675;ENST00000543006;ENST00000415906	T;T;T;T	0.56275	1.94;0.47;0.47;1.53	5.54	3.58	0.41010	.	1.331800	0.04465	N	0.375095	T	0.47488	0.1448	L	0.54323	1.7	0.24338	N	0.994971	B;B	0.30236	0.274;0.204	B;B	0.30943	0.122;0.035	T	0.37753	-0.9692	10	0.07175	T	0.84	.	9.2715	0.37675	0.1278:0.5661:0.3061:0.0	.	263;263	C9JUT4;Q93052	.;LPP_HUMAN	S	263;263;263;100	ENSP00000393602:P263S;ENSP00000318089:P263S;ENSP00000438891:P263S;ENSP00000393008:P100S	ENSP00000318089:P263S	P	+	1	0	LPP	189810000	1.000000	0.71417	0.611000	0.29010	0.770000	0.43624	3.651000	0.54431	1.436000	0.47453	0.655000	0.94253	CCA		0.572	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		T	188327306	C	T	188327306	3	4	20	1	0	0	0	0	1	0	0	0	8952	855	30	3	801	3	LPP	3	188327306	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		188327306	9695124	7	1872										
CLDN16	10686	hgsc.bcm.edu	37	chr3	190106053	190106053	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaacacagaagactgacaccCgccacttaagtggggccagg	11	12	0	3	rs200400125		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr3:190106053C>T	ENST00000264734.2	+	1	393	c.145C>T	c.(145-147)Cgc>Tgc	p.R49C	CLDN16_ENST00000456423.1_Missense_Mutation_p.R49C|CLDN16_ENST00000468220.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	49					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)	p.R49C(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GACTGACACCCGCCACTTAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											129	114	119					3																	190106053		2203	4300	6503	191588747	SO:0001583	missense	10686			AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.145C>T	3.37:g.190106053C>T	ENSP00000264734:p.Arg49Cys		191588747		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	C	2.577	-0.298336	0.05532	.	.	ENSG00000113946	ENST00000264734;ENST00000456423	D;D	0.93811	-2.93;-3.29	5.21	-3.34	0.04943	.	1.406730	0.04561	N	0.391642	T	0.80491	0.4633	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.68409	-0.5416	10	0.46703	T	0.11	-14.2408	1.1877	0.01859	0.3037:0.2917:0.2675:0.1371	.	49;49	A0SDD8;Q9Y5I7	.;CLD16_HUMAN	C	49	ENSP00000264734:R49C;ENSP00000414136:R49C	ENSP00000264734:R49C	R	+	1	0	CLDN16	191588747	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	0.437000	0.21543	-0.492000	0.06687	-1.546000	0.00904	CGC		0.498	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		T	190106053	C	T	190106053	3	4	20	1	0	0	0	0	1	0	0	0	3483	652	23	1	147	1	CLDN16	3	190106053	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	1778747	190106053	7916377	8	1873										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197556461	197556461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ataaaaggcaaagtccacatAtttaaatacctgaacataca	4	8	0	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr3:197556461A>G	ENST00000425562.2	+	6	804	c.804A>G	c.(802-804)atA>atG	p.I268M	LRCH3_ENST00000536618.1_5'Flank|LRCH3_ENST00000438796.2_Missense_Mutation_p.I268M|LRCH3_ENST00000334859.4_Missense_Mutation_p.I268M|LRCH3_ENST00000414675.2_Missense_Mutation_p.I268M|AC055764.1_ENST00000454526.1_RNA|LRCH3_ENST00000441090.2_Missense_Mutation_p.I142M			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	268						cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.F269fs*7(1)|p.I268M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AAGTCCACATATTTAAATACC	0.358																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|breast(1)	3											136	139	138					3																	197556461		2203	4300	6503	199040858	SO:0001583	missense	84859			AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.804A>G	3.37:g.197556461A>G	ENSP00000393579:p.Ile268Met		199040858	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	A	18.54	3.645911	0.67358	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562	T;T;T;T;T	0.51817	2.23;0.69;2.23;2.23;2.23	5.44	1.59	0.23543	.	0.000000	0.85682	D	0.000000	T	0.63663	0.2530	M	0.79011	2.435	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.998;0.99;1.0;0.997	T	0.61197	-0.7111	10	0.87932	D	0	-18.4273	7.2713	0.26258	0.6165:0.1429:0.0:0.2406	.	142;268;268;268	E9PD99;B4E0T7;Q96II8-2;Q96II8-3	.;.;.;.	M	268;142;268;268;268	ENSP00000399751:I268M;ENSP00000394609:I142M;ENSP00000394965:I268M;ENSP00000334375:I268M;ENSP00000393579:I268M	ENSP00000334375:I268M	I	+	3	3	LRCH3	199040858	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.506000	0.45433	0.027000	0.15297	0.529000	0.55759	ATA		0.358	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		G	197556461	A	G	197556461	3	3	20	1	0	0	0	0	1	0	0	0	8963	439	16	4	826	4	LRCH3	3	197556461	Missense_Mutation	SNP	A	TCGA-AG-3584-01A-01W-0831-10	7450408	197556461	465969	9	1874										
MAPK10	5602	hgsc.bcm.edu	37	chr4	87028454	87028454	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtttggttctgaaagggtctGctgagcttcttaatggccac	12	8	3	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr4:87028454G>T	ENST00000359221.3	-	5	814	c.288C>A	c.(286-288)agC>agA	p.S96R	MAPK10_ENST00000395166.1_Missense_Mutation_p.S58R|MAPK10_ENST00000513839.1_5'UTR|MAPK10_ENST00000449047.2_5'UTR|MAPK10_ENST00000395169.3_Missense_Mutation_p.S58R|MAPK10_ENST00000361569.2_Missense_Mutation_p.S96R|MAPK10_ENST00000395160.3_5'UTR|MAPK10_ENST00000395157.3_5'UTR|MAPK10_ENST00000395161.2_Missense_Mutation_p.S96R			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)	p.S96R(1)		breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		GAAAGGGTCTGCTGAGCTTCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											135	125	129					4																	87028454		2203	4300	6503	87247478	SO:0001583	missense	5602			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.288C>A	4.37:g.87028454G>T	ENSP00000352157:p.Ser96Arg		87247478	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	37	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.3|27.3	4.822838|4.822838	0.90873|0.90873	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000515400|ENST00000395169;ENST00000359221;ENST00000361569;ENST00000395166;ENST00000395161;ENST00000512017;ENST00000512564;ENST00000511167;ENST00000511328;ENST00000509464	.|T;T;T;T;T;T;T;T;T;T	.|0.65364	.|-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	5.9|5.9	5.9|5.9	0.94986|0.94986	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62060|0.62060	0.2397|0.2397	N|N	0.10809|0.10809	0.05|0.05	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.998;0.998;0.996	.|D;D;D	.|0.69307	.|0.938;0.961;0.963	T|T	0.68250|0.68250	-0.5458|-0.5458	5|10	.|0.87932	.|D	.|0	-16.9761|-16.9761	13.4734|13.4734	0.61295|0.61295	0.0712:0.0:0.9288:0.0|0.0712:0.0:0.9288:0.0	.|.	.|58;96;96	.|P53779-3;P53779-2;P53779	.|.;.;MK10_HUMAN	K|R	9|58;96;96;58;96;96;58;96;96;58	.|ENSP00000378598:S58R;ENSP00000352157:S96R;ENSP00000355297:S96R;ENSP00000378595:S58R;ENSP00000378590:S96R;ENSP00000424755:S96R;ENSP00000422985:S58R;ENSP00000422277:S96R;ENSP00000421762:S96R;ENSP00000424128:S58R	.|ENSP00000309857:S96R	Q|S	-|-	1|3	0|2	MAPK10|MAPK10	87247478|87247478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.838000|6.838000	0.75359|0.75359	2.798000|2.798000	0.96311|0.96311	0.650000|0.650000	0.86243|0.86243	CAG|AGC		0.433	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			T	87028454	G	T	87028454	3	4	20	1	0	0	0	0	1	0	0	0	9302	1310	46	2	1151	2	MAPK10	4	87028454	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10		87028454	104125822	10	1875										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13922244	13922244	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tcagactctcctgtgcacccGacaggacgttcacaaagcct	8	15	3	1	rs139857637		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr5:13922244G>A	ENST00000265104.4	-	5	736	c.632C>T	c.(631-633)tCg>tTg	p.S211L		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	211	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S211L(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTGTGCACCCGACAGGACGTT	0.532									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5						G	LEU/SER	0,4406		0,0,2203	83	76	78		632	1.4	0	5	dbSNP_134	78	1,8599		0,1,4299	no	missense	DNAH5	NM_001369.2	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	211/4625	13922244	1,13005	2203	4300	6503	13975244	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.632C>T	5.37:g.13922244G>A	ENSP00000265104:p.Ser211Leu		13975244	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	.	5.858	0.342421	0.11069	0.0	1.16E-4	ENSG00000039139	ENST00000265104	T	0.24908	1.83	5.44	1.44	0.22558	.	0.973885	0.08457	N	0.943006	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35847	-0.9772	10	0.22109	T	0.4	.	6.6197	0.22796	0.2035:0.239:0.5575:0.0	.	211	Q8TE73	DYH5_HUMAN	L	211	ENSP00000265104:S211L	ENSP00000265104:S211L	S	-	2	0	DNAH5	13975244	0.001000	0.12720	0.002000	0.10522	0.097000	0.18754	0.955000	0.29188	0.276000	0.22118	-0.304000	0.09214	TCG		0.532	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13922244	G	A	13922244	3	1	20	1	0	0	0	0	1	0	0	0	4615	1059	37	1	13542	1	DNAH5	5	13922244	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10		13922244	166993016	11	1876										
SLC45A2	51151	hgsc.bcm.edu	37	chr5	33951728	33951729	+	In_Frame_Ins	INS	-	-	GAT													0	0	1	0	0	0	1	1	0	acctcgactcctctttcgtaINSgatgagaaactctgtggagt							TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	-	-	-	GAT	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr5:33951728_33951729insGAT	ENST00000296589.4	-	5	1232_1233	c.1086_1087insATC	c.(1084-1089)atctac>atcATCtac	p.362_363insI	SLC45A2_ENST00000342059.3_In_Frame_Ins_p.303_304insI|SLC45A2_ENST00000345083.5_In_Frame_Ins_p.254_255insI|SLC45A2_ENST00000382102.3_In_Frame_Ins_p.362_363insI|SLC45A2_ENST00000509381.1_3'UTR	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	362					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.I362_Y363insI(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						CCTCTTTCGTAGATGAGAAACT	0.45																																					Ovarian(31;380 859 8490 22203 49048)											1	Insertion - In frame(1)	large_intestine(1)	5																																								33987486	SO:0001652	inframe_insertion	51151			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.1084_1086dupATC	5.37:g.33951729_33951731dupGAT	ENSP00000296589:p.Ile362_Ile362dup		33987485	Q6P2P0|Q9BTM3	In_Frame_Ins	INS	ENST00000296589.4	37	CCDS3901.1																																																																																				0.45	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		GAT	33951729	-	GAT	33951728	7	5	20	1	0	1	1	0	0	0	0	0	14678	420	15	0	532	0	SLC45A2	5	33951728	In_Frame_Ins	INS	-	TCGA-AG-3584-01A-01W-0831-10	20029484	33951728	146963532	12	1877										
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	20	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	78223911	112175639	68739621	13	1878										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126734452	126734452	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatggaggagtgtgtcatcaCgtcactggagaatgctcttg	13	7	4	1	rs190469012		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr5:126734452C>T	ENST00000274473.6	+	8	1011	c.744C>T	c.(742-744)caC>caT	p.H248H	MEGF10_ENST00000503335.2_Silent_p.H248H|MEGF10_ENST00000418761.2_Silent_p.H248H|MEGF10_ENST00000508365.1_Silent_p.H248H	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	248	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.H248H(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		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)		TGTGTCATCACGTCACTGGAG	0.527													C|||	1	0.000199681	8e-04	0	5008	,	,		20616	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											265	198	220					5																	126734452		2203	4300	6503	126762351	SO:0001819	synonymous_variant	84466			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.744C>T	5.37:g.126734452C>T			126762351	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																				0.527	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126734452	C	T	126734452	2	4	20	1	0	0	0	0	0	0	0	1	9490	535	19	1		1	MEGF10	5	126734452	Silent	SNP	C	TCGA-AG-3584-01A-01W-0831-10	14558813	126734452	54180808	14	1879										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132006580	132006580	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ataaacttcttctacatgtaCgaagggcctgccccccgcat	7	14	2	0	rs148138275		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr6:132006580C>T	ENST00000414305.1	+	14	1525	c.1197C>T	c.(1195-1197)taC>taT	p.Y399Y	ENPP3_ENST00000358229.5_Silent_p.Y399Y|ENPP3_ENST00000357639.3_Silent_p.Y399Y			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	399	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.Y399Y(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TCTACATGTACGAAGGGCCTG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		1,4405	2.1+/-5.4	0,1,2202	135	152	146		1197	0.6	0.9	6	dbSNP_134	146	0,8600		0,0,4300	no	coding-synonymous	ENPP3	NM_005021.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		399/876	132006580	1,13005	2203	4300	6503	132048273	SO:0001819	synonymous_variant	5169			AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.1197C>T	6.37:g.132006580C>T			132048273	Q5JTL3	Silent	SNP	ENST00000414305.1	37	CCDS5148.1																																																																																				0.353	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			T	132006580	C	T	132006580	2	4	20	1	0	0	0	0	0	0	0	1	5144	547	19	1		1	ENPP3	6	132006580	Silent	SNP	C	TCGA-AG-3584-01A-01W-0831-10		132006580	39108487	15	1880										
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92762589	92762589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgactacattttctatatatGtttcatcaaaattgcttttc	3	7	3	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr7:92762589G>A	ENST00000318238.4	-	5	3912	c.2696C>T	c.(2695-2697)aCa>aTa	p.T899I	SAMD9L_ENST00000411955.1_Missense_Mutation_p.T899I|SAMD9L_ENST00000437805.1_Missense_Mutation_p.T899I	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	899					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.T899I(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTCTATATATGTTTCATCAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											69	72	71					7																	92762589		2203	4300	6503	92600525	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.2696C>T	7.37:g.92762589G>A	ENSP00000326247:p.Thr899Ile		92600525	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	5.445	0.267210	0.10294	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.23552	1.9;1.9;1.9	5.22	-6.98	0.01611	.	1.034640	0.07659	N	0.933222	T	0.10423	0.0255	N	0.11560	0.145	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.32481	-0.9905	10	0.36615	T	0.2	2.8241	5.8357	0.18605	0.2653:0.0:0.2998:0.4349	.	899	Q8IVG5	SAM9L_HUMAN	I	899	ENSP00000326247:T899I;ENSP00000405760:T899I;ENSP00000408796:T899I	ENSP00000326247:T899I	T	-	2	0	SAMD9L	92600525	0.000000	0.05858	0.000000	0.03702	0.992000	0.81027	-1.249000	0.02888	-1.064000	0.03172	0.467000	0.42956	ACA		0.363	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92762589	G	A	92762589	3	1	20	1	0	0	0	0	1	0	0	0	13864	1377	48	3	2062	3	SAMD9L	7	92762589	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10		92762589	66376074	16	1881										
UBR5	51366	hgsc.bcm.edu	37	chr8	103317375	103317375	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgatacacaagcatgcaaaAtatttcgatttccatcacat	4	10	1	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr8:103317375A>C	ENST00000520539.1	-	21	3371	c.2765T>G	c.(2764-2766)aTt>aGt	p.I922S	UBR5_ENST00000521922.1_Missense_Mutation_p.I916S|UBR5_ENST00000220959.4_Missense_Mutation_p.I922S	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	922					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.I922S(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			AGCATGCAAAATATTTCGATT	0.383																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											171	165	167					8																	103317375		2203	4300	6503	103386551	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.2765T>G	8.37:g.103317375A>C	ENSP00000429084:p.Ile922Ser		103386551	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.95|17.95	3.513892|3.513892	0.64522|0.64522	.|.	.|.	ENSG00000104517|ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922|ENST00000520898;ENST00000519365	T;T;T|.	0.53857|.	0.6;0.6;0.6|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.057613|.	0.64402|.	D|.	0.000002|.	T|.	0.68595|.	0.3018|.	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999999|0.999999	B;B|.	0.27498|.	0.18;0.18|.	B;B|.	0.20955|.	0.032;0.032|.	T|.	0.67221|.	-0.5725|.	10|.	0.87932|.	D|.	0|.	.|.	15.0704|15.0704	0.72030|0.72030	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	916;922|.	E7EMW7;O95071|.	.;UBR5_HUMAN|.	S|X	922;922;916|12;37	ENSP00000429084:I922S;ENSP00000220959:I922S;ENSP00000427819:I916S|.	ENSP00000220959:I922S|.	I|Y	-|-	2|3	0|2	UBR5|UBR5	103386551|103386551	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	9.339000|9.339000	0.96797|0.96797	1.967000|1.967000	0.57214|0.57214	0.254000|0.254000	0.18369|0.18369	ATT|TAT		0.383	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		C	103317375	A	C	103317375	3	2	20	1	0	0	0	0	1	0	0	0	16945	101	4	4	5790	4	UBR5	8	103317375	Missense_Mutation	SNP	A	TCGA-AG-3584-01A-01W-0831-10		103317375	43046647	17	1882										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142228979	142228979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	cgggctgtactgctcctcgtCgatgctgaacaggtgcaggg	15	11	0	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr8:142228979C>T	ENST00000024061.3	-	4	914	c.607G>A	c.(607-609)Gac>Aac	p.D203N	SLC45A4_ENST00000519067.1_Missense_Mutation_p.D203N|SLC45A4_ENST00000517878.1_Missense_Mutation_p.D254N|SLC45A4_ENST00000433583.2_Missense_Mutation_p.D196N	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)		p.D203N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|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;0.0493)			TGCTCCTCGTCGATGCTGAAC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	8											79	83	81					8																	142228979		2203	4300	6503	142298161	SO:0001583	missense	57210			AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.607G>A	8.37:g.142228979C>T	ENSP00000024061:p.Asp203Asn		142298161	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.809098	0.50421	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000520137	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	5.57	3.77	0.43336	.	0.565347	0.20662	N	0.088008	D	0.82318	0.5011	N	0.12182	0.205	0.25639	N	0.986229	P;P;B	0.38300	0.535;0.626;0.084	B;B;B	0.32090	0.115;0.14;0.057	T	0.74016	-0.3800	10	0.52906	T	0.07	-17.0506	11.9038	0.52699	0.0:0.8603:0.0:0.1397	.	254;203;203	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	N	203;254;196;203;61	ENSP00000429059:D203N;ENSP00000428137:D254N;ENSP00000400799:D196N;ENSP00000024061:D203N;ENSP00000429033:D61N	ENSP00000024061:D203N	D	-	1	0	SLC45A4	142298161	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	1.771000	0.38542	0.722000	0.32252	0.555000	0.69702	GAC		0.667	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		T	142228979	C	T	142228979	3	4	20	1	0	0	0	0	1	0	0	0	14680	884	31	1	1809	1	SLC45A4	8	142228979	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	38911604	142228979	4135043	18	1883										
SFXN2	118980	hgsc.bcm.edu	37	chr10	104486809	104486809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgccaagaagctgtatgactCggccttccaccccgacactg	9	15	0	2	rs200250986		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr10:104486809C>T	ENST00000369893.5	+	3	394	c.227C>T	c.(226-228)tCg>tTg	p.S76L	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	76					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)	p.S76L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CTGTATGACTCGGCCTTCCAC	0.592													C|||	1	0.000199681	0	0	5008	,	,		18461	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											81	71	74					10																	104486809		2203	4300	6503	104476799	SO:0001583	missense	118980			AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.227C>T	10.37:g.104486809C>T	ENSP00000358909:p.Ser76Leu		104476799	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	37	CCDS7539.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.600879	0.96614	.	.	ENSG00000156398	ENST00000369893	T	0.54071	0.59	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.81470	0.4829	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86285	0.1670	10	0.72032	D	0.01	-41.2812	19.4753	0.94985	0.0:1.0:0.0:0.0	.	76	Q96NB2	SFXN2_HUMAN	L	76	ENSP00000358909:S76L	ENSP00000358909:S76L	S	+	2	0	SFXN2	104476799	1.000000	0.71417	0.959000	0.39883	0.980000	0.70556	7.818000	0.86416	2.607000	0.88179	0.561000	0.74099	TCG		0.592	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		T	104486809	C	T	104486809	3	4	20	1	0	0	0	0	1	0	0	0	14232	893	31	1	233	1	SFXN2	10	104486809	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		104486809	31047938	19	1884										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6261565	6261565	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttacatttttgtcgtcatcCattggaacagctgcctatac	6	10	1	0			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr11:6261565C>A	ENST00000379936.2	+	4	656	c.541C>A	c.(541-543)Cat>Aat	p.H181N	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	181					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.H181N(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCGTCATCCATTGGAACAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11											67	66	66					11																	6261565		2201	4295	6496	6218141	SO:0001583	missense	1262			AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.541C>A	11.37:g.6261565C>A	ENSP00000369268:p.His181Asn		6218141		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732006	0.89390	.	.	ENSG00000132259	ENST00000379936	D	0.99545	-6.13	5.25	5.25	0.73442	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	H	0.96833	3.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.97027	0.9747	10	0.87932	D	0	.	17.7596	0.88461	0.0:1.0:0.0:0.0	.	181;141	Q8IV77;Q8IV77-2	CNGA4_HUMAN;.	N	181	ENSP00000369268:H181N	ENSP00000369268:H181N	H	+	1	0	CNGA4	6218141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.602000	0.87976	0.650000	0.86243	CAT		0.592	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		A	6261565	C	A	6261565	3	1	20	1	0	0	0	0	1	0	0	0	3605	594	21	2	555	2	CNGA4	11	6261565	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		6261565	128744951	20	1885										
KCNJ5	3762	hgsc.bcm.edu	37	chr11	128781290	128781290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cattgccacagaccgtacgcGcctgctggccgagggcaaga	13	14	0	2	rs139073333	byFrequency	TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr11:128781290G>A	ENST00000338350.4	+	3	474	c.122G>A	c.(121-123)cGc>cAc	p.R41H	KCNJ5_ENST00000529694.1_Missense_Mutation_p.R41H|KCNJ5_ENST00000533599.1_Missense_Mutation_p.R41H			P48544	KCNJ5_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 5	41					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)	p.R41H(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(4)|liver(2)|lung(9)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glyburide(DB01016)	GACCGTACGCGCCTGCTGGCC	0.597													G|||	2	0.000399361	0.0015	0	5008	,	,		19335	0		0	False		,,,				2504	0				Pancreas(108;2548 5082)|Esophageal Squamous(165;4544 6231)											1	Substitution - Missense(1)	large_intestine(1)	11						G	HIS/ARG	2,4400	4.2+/-10.8	0,2,2199	84	78	80		122	5.8	1	11	dbSNP_134	80	0,8594		0,0,4297	yes	missense	KCNJ5	NM_000890.3	29	0,2,6496	AA,AG,GG		0.0,0.0454,0.0154	benign	41/420	128781290	2,12994	2201	4297	6498	128286500	SO:0001583	missense	3762			D50134	CCDS8479.1	11q24	2014-09-17				ENSG00000120457		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6266	protein-coding gene	gene with protein product		600734				16382105	Standard	NM_000890		Approved	Kir3.4, CIR, KATP1, GIRK4, LQT13	uc001qet.3	P48544		ENST00000338350.4:c.122G>A	11.37:g.128781290G>A	ENSP00000339960:p.Arg41His		128286500	B2R744|Q6DK13|Q6DK14|Q92807	Missense_Mutation	SNP	ENST00000338350.4	37	CCDS8479.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.58	2.875522	0.51695	4.54E-4	0.0	ENSG00000120457	ENST00000533356;ENST00000529694;ENST00000338350;ENST00000533599	D;D;D	0.89270	-2.49;-2.49;-2.49	5.79	5.79	0.91817	.	1.137250	0.06446	N	0.726958	T	0.81197	0.4772	N	0.05510	-0.035	0.45464	D	0.998439	B	0.12013	0.005	B	0.04013	0.001	T	0.60510	-0.7249	10	0.39692	T	0.17	.	13.2623	0.60113	0.072:0.0:0.9279:0.0	.	41	P48544	IRK5_HUMAN	H	41	ENSP00000433295:R41H;ENSP00000339960:R41H;ENSP00000434266:R41H	ENSP00000339960:R41H	R	+	2	0	KCNJ5	128286500	1.000000	0.71417	0.965000	0.40720	0.939000	0.58152	6.270000	0.72563	2.731000	0.93534	0.650000	0.86243	CGC		0.597	KCNJ5-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386239.1	NM_000890		A	128781290	G	A	128781290	3	1	20	1	0	0	0	0	1	0	0	0	8075	1087	38	1	124	1	KCNJ5	11	128781290	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	122519725	128781290	6225226	21	1886										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5021872	5021872	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctctgacagtgacctcagtcGccgcagttcctctactatga	8	14	3	3	rs139383685		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr12:5021872G>A	ENST00000382545.3	+	2	2435	c.1328G>A	c.(1327-1329)cGc>cAc	p.R443H	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	443					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)	p.R443H(1)		NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	GACCTCAGTCGCCGCAGTTCC	0.468													G|||	1	0.000199681	8e-04	0	5008	,	,		19396	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											199	197	198					12																	5021872		2203	4300	6503	4892133	SO:0001583	missense	3736			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.1328G>A	12.37:g.5021872G>A	ENSP00000371985:p.Arg443His		4892133	A6NM83|Q3MIQ9	Missense_Mutation	SNP	ENST00000382545.3	37	CCDS8535.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.85	2.953515	0.53293	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	D	0.96396	-4.0	5.35	4.45	0.53987	.	0.000000	0.64402	D	0.000001	D	0.94699	0.8290	M	0.63843	1.955	0.80722	D	1	P	0.50943	0.94	B	0.41202	0.35	D	0.94002	0.7276	10	0.40728	T	0.16	.	15.5422	0.76062	0.0:0.1384:0.8616:0.0	.	443	Q09470	KCNA1_HUMAN	H	443	ENSP00000371985:R443H	ENSP00000228858:R443H	R	+	2	0	KCNA1	4892133	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.620000	0.74224	1.603000	0.50134	0.655000	0.94253	CGC		0.468	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		A	5021872	G	A	5021872	3	1	20	1	0	0	0	0	1	0	0	0	8022	1087	38	1	1330	1	KCNA1	12	5021872	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10		5021872	128830023	22	1887										
DUSP16	80824	hgsc.bcm.edu	37	chr12	12630318	12630318	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggttctgaccgaatgcaatcGcttgctctggctgtctgaag	12	10	3	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr12:12630318G>A	ENST00000228862.2	-	7	2078	c.1447C>T	c.(1447-1449)Cga>Tga	p.R483*	DUSP16_ENST00000545864.1_5'Flank|DUSP16_ENST00000298573.4_3'UTR	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	483					dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R483*(2)		endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GAATGCAATCGCTTGCTCTGG	0.572																																					Ovarian(158;443 1896 15437 36069 46477)											2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	12											105	102	103					12																	12630318		2203	4300	6503	12521585	SO:0001587	stop_gained	80824			AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	17909	protein-coding gene	gene with protein product	"MAPK phosphatase-7"	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.1447C>T	12.37:g.12630318G>A	ENSP00000228862:p.Arg483*		12521585	Q547C7|Q96QS2|Q9C0G3	Nonsense_Mutation	SNP	ENST00000228862.2	37	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	G	38	6.899472	0.97920	.	.	ENSG00000111266	ENST00000228862	.	.	.	5.27	2.23	0.28157	.	0.314503	0.22770	N	0.055846	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.796	0.29148	0.1387:0.0:0.6144:0.2469	.	.	.	.	X	483	.	ENSP00000228862:R483X	R	-	1	2	DUSP16	12521585	0.540000	0.26410	0.012000	0.15200	0.306000	0.27790	1.234000	0.32660	0.792000	0.33850	0.655000	0.94253	CGA		0.572	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640		A	12630318	G	A	12630318	4	1	20	1	0	0	0	0	0	1	0	0	4827	1095	38	1	554	1	DUSP16	12	12630318	Nonsense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	7608446	12630318	121221577	23	1888										
DDIT3	1649	hgsc.bcm.edu	37	chr12	57910760	57910760	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcatgcgctgctttccagcCcgggctggggaatgaccact	12	13	1	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr12:57910760C>T	ENST00000346473.3	-	4	521	c.342G>A	c.(340-342)cgG>cgA	p.R114R	MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000551116.1_Silent_p.R137R|DDIT3_ENST00000552740.1_Silent_p.R137R|RN7SL312P_ENST00000582079.1_RNA|DDIT3_ENST00000547303.1_Silent_p.R114R	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	114	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R114R(1)	EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						GCTTTCCAGCCCGGGCTGGGG	0.542			T	FUS	liposarcoma																																GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	1	Substitution - coding silent(1)	large_intestine(1)	12											138	147	144					12																	57910760		2203	4300	6503	56197027	SO:0001819	synonymous_variant	1649			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"C/EBP zeta"	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.342G>A	12.37:g.57910760C>T			56197027	F8VS99	Silent	SNP	ENST00000346473.3	37	CCDS8943.1																																																																																				0.542	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083		T	57910760	C	T	57910760	2	4	20	1	0	0	0	0	0	0	0	1	4336	610	22	3		3	DDIT3	12	57910760	Silent	SNP	C	TCGA-AG-3584-01A-01W-0831-10	45280442	57910760	75941135	24	1889										
ANO4	121601	hgsc.bcm.edu	37	chr12	101493387	101493387	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attggtggactagaagaaaaGtacgacaagaacatggacct	11	6	0	3			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr12:101493387G>C	ENST00000392977.3	+	22	2248	c.2038G>C	c.(2038-2040)Gta>Cta	p.V680L	ANO4_ENST00000550015.1_Missense_Mutation_p.V200L|ANO4_ENST00000392979.3_Missense_Mutation_p.V645L|ANO4_ENST00000299222.9_Missense_Mutation_p.V200L			Q32M45	ANO4_HUMAN	anoctamin 4	680					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.V645L(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TAGAAGAAAAGTACGACAAGA	0.358										HNSCC(74;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											111	112	112					12																	101493387		2203	4300	6503	100017518	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2038G>C	12.37:g.101493387G>C	ENSP00000376703:p.Val680Leu		100017518	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	G	6.553	0.470348	0.12461	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.73	2.67	0.31697	.	0.184715	0.34725	N	0.003737	T	0.29716	0.0742	N	0.02765	-0.5	0.39377	D	0.966186	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.15009	-1.0452	10	0.06891	T	0.86	.	8.6216	0.33864	0.0:0.2481:0.3197:0.4322	.	200;680;645	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	L	645;200;680;200	ENSP00000376705:V645L;ENSP00000299222:V200L;ENSP00000376703:V680L;ENSP00000450192:V200L	ENSP00000299222:V200L	V	+	1	0	ANO4	100017518	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.116000	0.31221	0.729000	0.32403	0.650000	0.86243	GTA		0.358	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		C	101493387	G	C	101493387	3	2	20	1	0	0	0	0	1	0	0	0	699	1029	36	5	2011	5	ANO4	12	101493387	Missense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	43582627	101493387	32358508	25	1890										
SCFD1	23256	hgsc.bcm.edu	37	chr14	31119838	31119838	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctttttacaggtgatacacTtggagctggccaattcaggt	10	8	2	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr14:31119838T>G	ENST00000458591.2	+	9	964	c.737T>G	c.(736-738)cTt>cGt	p.L246R	SCFD1_ENST00000396629.2_Missense_Mutation_p.L154R|SCFD1_ENST00000541123.1_Missense_Mutation_p.L61R|SCFD1_ENST00000544052.2_Missense_Mutation_p.L179R|SCFD1_ENST00000421551.3_Missense_Mutation_p.L187R	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	246					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)	p.L246R(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		GGTGATACACTTGGAGCTGGC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	63	61					14																	31119838		2203	4294	6497	30189589	SO:0001583	missense	23256			AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.737T>G	14.37:g.31119838T>G	ENSP00000390783:p.Leu246Arg		30189589	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.951585	0.34471	.	.	ENSG00000092108	ENST00000458591;ENST00000544052;ENST00000421551;ENST00000541123;ENST00000396629;ENST00000469043	T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.71	5.71	0.89125	.	0.054730	0.64402	D	0.000001	T	0.58177	0.2104	N	0.12182	0.205	0.58432	D	0.999992	B;P;B;P	0.41393	0.044;0.539;0.336;0.748	B;B;B;B	0.40410	0.063;0.328;0.319;0.328	T	0.58607	-0.7607	10	0.15066	T	0.55	-17.3627	15.1704	0.72869	0.0:0.0:0.0:1.0	.	187;179;154;246	B7Z738;B7Z4U7;B7Z594;Q8WVM8	.;.;.;SCFD1_HUMAN	R	246;179;187;61;154;101	ENSP00000390783:L246R;ENSP00000443010:L179R;ENSP00000388078:L187R;ENSP00000443537:L61R;ENSP00000379870:L154R;ENSP00000452448:L101R	ENSP00000309417:L254R	L	+	2	0	SCFD1	30189589	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.393000	0.79851	2.180000	0.69256	0.533000	0.62120	CTT		0.289	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		G	31119838	T	G	31119838	3	3	20	1	0	0	0	0	1	0	0	0	13926	1609	56	4	771	4	SCFD1	14	31119838	Missense_Mutation	SNP	T	TCGA-AG-3584-01A-01W-0831-10		31119838	76229702	26	1891										
AHSA1	10598	hgsc.bcm.edu	37	chr14	77925961	77925961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgtttctgctttgcaggaCggagagagatgcttcaaatt	11	7	3	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr14:77925961C>T	ENST00000216479.3	+	2	243	c.83C>T	c.(82-84)aCg>aTg	p.T28M	VIPAS39_ENST00000343765.2_5'Flank|VIPAS39_ENST00000556909.1_5'Flank|VIPAS39_ENST00000448935.2_5'Flank|VIPAS39_ENST00000556412.1_5'Flank|VIPAS39_ENST00000327028.4_5'Flank|VIPAS39_ENST00000553888.1_5'Flank|VIPAS39_ENST00000557658.1_5'Flank|AHSA1_ENST00000535854.2_Missense_Mutation_p.T28M|AHSA1_ENST00000555517.1_Missense_Mutation_p.T28M	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	28					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)	p.T28M(1)		endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		CTTTGCAGGACGGAGAGAGAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											124	114	118					14																	77925961		2203	4300	6503	76995714	SO:0001583	missense	10598			AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"chromosome 14 open reading frame 3"	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.83C>T	14.37:g.77925961C>T	ENSP00000216479:p.Thr28Met		76995714	B2R9L2|B4DUR9|Q96IL6|Q9P060	Missense_Mutation	SNP	ENST00000216479.3	37	CCDS9863.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090322	0.94149	.	.	ENSG00000100591	ENST00000216479;ENST00000535854;ENST00000555517	.	.	.	5.58	5.58	0.84498	Activator of Hsp90 ATPase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85444	0.5698	M	0.91090	3.175	0.80722	D	1	D;D	0.76494	0.999;0.996	D;P	0.64877	0.93;0.664	D	0.88094	0.2815	9	0.66056	D	0.02	-12.8383	19.5483	0.95308	0.0:1.0:0.0:0.0	.	28;28	B4DUR9;O95433	.;AHSA1_HUMAN	M	28	.	ENSP00000216479:T28M	T	+	2	0	AHSA1	76995714	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.875000	0.69660	2.624000	0.88883	0.650000	0.86243	ACG		0.473	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111		T	77925961	C	T	77925961	3	4	20	1	0	0	0	0	1	0	0	0	418	536	19	1	89	1	AHSA1	14	77925961	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	46806123	77925961	29423579	27	1892										
CXXC1	30827	hgsc.bcm.edu	37	chr18	47810355	47810355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccatttcctgaaggcgagtgCgggcactctgctgctctcgg	13	13	2	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr18:47810355C>T	ENST00000285106.6	-	10	2036	c.1322G>A	c.(1321-1323)cGc>cAc	p.R441H	MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000590208.1_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000424334.2_5'Flank|MBD1_ENST00000339998.6_5'Flank|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000587396.1_5'Flank|MBD1_ENST00000585595.1_5'Flank|CXXC1_ENST00000589940.1_Missense_Mutation_p.R441H|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000269468.5_5'Flank|CXXC1_ENST00000412036.2_Missense_Mutation_p.R445H|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000457839.2_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	441					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R441H(1)		autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						AAGGCGAGTGCGGGCACTCTG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	18											102	92	96					18																	47810355		2203	4300	6503	46064353	SO:0001583	missense	30827			BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"Zinc fingers, PHD-type"	24343	protein-coding gene	gene with protein product	"CpG binding protein", "DNA-binding protein with PHD finger and CXXC domain", "zinc finger, CpG binding-type containing 1"	609150	"CXXC finger 1 (PHD domain)"			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.1322G>A	18.37:g.47810355C>T	ENSP00000285106:p.Arg441His		46064353	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Missense_Mutation	SNP	ENST00000285106.6	37	CCDS11945.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.967806	0.92855	.	.	ENSG00000154832	ENST00000285106;ENST00000412036	T;T	0.25749	1.78;1.78	4.63	4.63	0.57726	CpG binding protein, C-terminal (1);	0.132049	0.50627	D	0.000106	T	0.22781	0.0550	L	0.45137	1.4	0.80722	D	1	P;P;P;B	0.36599	0.499;0.504;0.56;0.279	B;B;B;B	0.32928	0.155;0.057;0.053;0.037	T	0.04855	-1.0922	10	0.45353	T	0.12	-14.6537	15.3385	0.74277	0.0:1.0:0.0:0.0	.	441;445;441;308	B2RC03;Q9P0U4-2;Q9P0U4;Q59EC8	.;.;CXXC1_HUMAN;.	H	441;445	ENSP00000285106:R441H;ENSP00000390475:R445H	ENSP00000285106:R441H	R	-	2	0	CXXC1	46064353	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.389000	0.66255	2.281000	0.76405	0.453000	0.30009	CGC		0.602	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		T	47810355	C	T	47810355	3	4	20	1	0	0	0	0	1	0	0	0	4103	768	27	1	672	1	CXXC1	18	47810355	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		47810355	30266893	28	1893										
CNN1	1264	hgsc.bcm.edu	37	chr19	11660520	11660520	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggctgccacgccaggtctaCgaccccaagtactgtctgac	11	15	2	1	rs376859144		TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr19:11660520C>T	ENST00000252456.2	+	7	1015	c.804C>T	c.(802-804)taC>taT	p.Y268Y	CNN1_ENST00000592923.1_Silent_p.Y218Y|CNN1_ENST00000535659.2_Silent_p.Y218Y|CNN1_ENST00000544952.1_Silent_p.Y248Y	NM_001299.4	NP_001290.2	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle	268					actomyosin structure organization (GO:0031032)|regulation of smooth muscle contraction (GO:0006940)	cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)		p.Y268Y(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9						GCCAGGTCTACGACCCCAAGT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	19											79	70	73					19																	11660520		2203	4300	6503	11521520	SO:0001819	synonymous_variant	1264			U37019	CCDS12263.1	19p13.2-p13.1	2008-07-16				ENSG00000130176			2155	protein-coding gene	gene with protein product		600806				8526917, 9332369	Standard	XM_005259741		Approved	SMCC, Sm-Calp	uc002msc.1	P51911		ENST00000252456.2:c.804C>T	19.37:g.11660520C>T			11521520	B2R868|B4DUX6|O00638|Q15416|Q8IY93|Q99438	Silent	SNP	ENST00000252456.2	37	CCDS12263.1																																																																																				0.622	CNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458854.1	NM_001299		T	11660520	C	T	11660520	2	4	20	1	0	0	0	0	0	0	0	1	3615	547	19	1		1	CNN1	19	11660520	Silent	SNP	C	TCGA-AG-3584-01A-01W-0831-10		11660520	47468463	29	1894										
LSM14A	26065	hgsc.bcm.edu	37	chr19	34687545	34687545	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgattttccttcagtcctcaCtaggctcatcgacttcttca	5	13	5	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr19:34687545C>T	ENST00000433627.5	+	3	367	c.292C>T	c.(292-294)Cta>Tta	p.L98L	LSM14A_ENST00000540746.2_Silent_p.L98L|LSM14A_ENST00000544216.3_Silent_p.L98L	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	98					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.L98L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					TCAGTCCTCACTAGGCTCATC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	19											172	153	160					19																	34687545		2203	4300	6503	39379385	SO:0001819	synonymous_variant	26065			AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.292C>T	19.37:g.34687545C>T			39379385	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Silent	SNP	ENST00000433627.5	37	CCDS46040.1																																																																																				0.393	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		T	34687545	C	T	34687545	2	4	20	1	0	0	0	0	0	0	0	1	9083	564	20	3		3	LSM14A	19	34687545	Silent	SNP	C	TCGA-AG-3584-01A-01W-0831-10	23027025	34687545	24441438	30	1895										
ZNF567	163081	hgsc.bcm.edu	37	chr19	37211317	37211317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccagaaatcctatgaatgtcCtcagtgtgggaaagccttta	9	9	1	2			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chr19:37211317C>T	ENST00000536254.2	+	6	1913	c.1691C>T	c.(1690-1692)cCt>cTt	p.P564L	ZNF567_ENST00000360729.4_Missense_Mutation_p.P533L|ZNF567_ENST00000585696.1_Missense_Mutation_p.P533L|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.P533L|ZNF567_ENST00000392163.2_Missense_Mutation_p.P533L			Q8N184	ZN567_HUMAN	zinc finger protein 567	564					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P533L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TATGAATGTCCTCAGTGTGGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	68	67					19																	37211317		2203	4300	6503	41903157	SO:0001583	missense	163081			AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.1691C>T	19.37:g.37211317C>T	ENSP00000441838:p.Pro564Leu		41903157	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	37		.	.	.	.	.	.	.	.	.	.	C	10.79	1.449007	0.26074	.	.	ENSG00000189042	ENST00000536254;ENST00000378686;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.27256	3.23;1.68;1.68	4.92	-0.0607	0.13788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.885835	0.09533	N	0.789250	T	0.23054	0.0557	L	0.48877	1.53	0.09310	N	0.999999	B;P	0.38922	0.002;0.651	B;B	0.42030	0.002;0.373	T	0.25779	-1.0122	10	0.59425	D	0.04	.	4.3613	0.11203	0.2715:0.5148:0.1326:0.0811	.	564;533	Q8N184;F8WEL6	ZN567_HUMAN;.	L	564;508;533;563;533	ENSP00000441838:P564L;ENSP00000353957:P533L;ENSP00000376003:P533L	ENSP00000353957:P533L	P	+	2	0	ZNF567	41903157	0.000000	0.05858	0.982000	0.44146	0.998000	0.95712	-2.077000	0.01371	0.335000	0.23614	0.561000	0.74099	CCT		0.413	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		T	37211317	C	T	37211317	3	4	20	1	0	0	0	0	1	0	0	0	18037	681	24	3	1608	3	ZNF567	19	37211317	Missense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10	2523772	37211317	21917666	31	1896										
TBL1X	6907	hgsc.bcm.edu	37	chrX	9661421	9661421	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctttgccttgaaatggaacCgaaaggggaattacattttg	10	6	1	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chrX:9661421C>T	ENST00000217964.7	+	11	1655	c.1015C>T	c.(1015-1017)Cga>Tga	p.R339*	TBL1X_ENST00000424279.1_Nonsense_Mutation_p.R288*|TBL1X_ENST00000380961.1_Nonsense_Mutation_p.R288*|TBL1X_ENST00000536365.1_Nonsense_Mutation_p.R288*|TBL1X_ENST00000407597.2_Nonsense_Mutation_p.R339*	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	339					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R339*(1)		breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				GAAATGGAACCGAAAGGGGAA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											103	79	87					X																	9661421		2203	4300	6503	9621421	SO:0001587	stop_gained	6907			Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1015C>T	X.37:g.9661421C>T	ENSP00000217964:p.Arg339*		9621421	A8K044|A8K4J7|Q86UY2	Nonsense_Mutation	SNP	ENST00000217964.7	37	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	C	40	8.056139	0.98632	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	.	.	.	4.56	3.38	0.38709	.	0.057091	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	10.8589	0.46815	0.8422:0.1578:0.0:0.0	.	.	.	.	X	339;288;288;288;339	.	ENSP00000217964:R339X	R	+	1	2	TBL1X	9621421	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.904000	0.75708	0.552000	0.29026	-0.316000	0.08728	CGA		0.393	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		T	9661421	C	T	9661421	4	4	20	1	0	0	0	0	0	1	0	0	15678	644	23	1	1045	1	TBL1X	23	9661421	Nonsense_Mutation	SNP	C	TCGA-AG-3584-01A-01W-0831-10		9661421	145609139	32	1897										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63411246	63411246	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgccgggcctgggtctctcGgacttgagtctctctacaac	11	14	3	1			TCGA-AG-3584-01A-01W-0831-10	TCGA-AG-3584-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	9b11bde3-b798-4ff6-8b7f-61b8bb40fd31	338311a8-6c7c-4c60-b6bb-8aad73f76db3	g.chrX:63411246G>A	ENST00000330258.3	-	2	2193	c.1921C>T	c.(1921-1923)Cga>Tga	p.R641*	AMER1_ENST00000374869.3_Nonsense_Mutation_p.R641*|AMER1_ENST00000403336.1_Nonsense_Mutation_p.R641*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	641					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R641*(2)									TGGGTCTCTCGGACTTGAGTC	0.617																																																69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											26	25	25					X																	63411246		2203	4299	6502	63327971	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1921C>T	X.37:g.63411246G>A	ENSP00000329117:p.Arg641*		63327971	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	31	5.075055	0.94000	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.21	4.34	0.51931	.	1.243660	0.05695	N	0.592862	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	0.5658	11.2447	0.48990	0.0:0.0:0.6691:0.3309	.	.	.	.	X	641	.	ENSP00000329117:R641X	R	-	1	2	FAM123B	63327971	0.870000	0.30015	0.001000	0.08648	0.015000	0.08874	4.385000	0.59613	1.297000	0.44761	0.600000	0.82982	CGA		0.617	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411246	G	A	63411246	4	1	20	1	0	0	0	0	0	1	0	0	5439	1124	39	1	1490	1	FAM123B	23	63411246	Nonsense_Mutation	SNP	G	TCGA-AG-3584-01A-01W-0831-10	53749825	63411246	91859314	33	1898										
DDOST	1650	hgsc.bcm.edu	37	chr1	20980730	20980730	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	agctacctctgggagccgggCgccgccttctgcactgctga	13	15	2	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:20980730C>T	ENST00000375048.3	-	7	936	c.831G>A	c.(829-831)gcG>gcA	p.A277A	DDOST_ENST00000415136.2_Silent_p.A240A|DDOST_ENST00000602624.2_Silent_p.A260A|PINK1-AS_ENST00000451424.1_RNA	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	277					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.A277A(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGAGCCGGGCGCCGCCTTCT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	1											16	17	17					1																	20980730		2052	4023	6075	20853317	SO:0001819	synonymous_variant	1650			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"oligosaccharyltransferase subunit 48"	602202	"dolichyl-diphosphooligosaccharide-protein glycosyltransferase", "dolichyl-diphosphooligosaccharide--protein glycosyltransferase"			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.831G>A	1.37:g.20980730C>T			20853317	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.622	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216		T	20980730	C	T	20980730	2	4	21	1	0	0	0	0	0	0	0	1	4341	755	27	1		1	DDOST	1	20980730	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10		20980730	228269891	1	1899										
RPL11	6135	hgsc.bcm.edu	37	chr1	24022845	24022845	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ctctttcagtatgatgggatCatccttcctggcaaataaat	7	9	3	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:24022845C>T	ENST00000374550.3	+	6	564	c.519C>T	c.(517-519)atC>atT	p.I173I	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	173					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.I173I(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		ATGATGGGATCATCCTTCCTG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											91	89	90					1																	24022845		2203	4300	6503	23895432	SO:0001819	synonymous_variant	6135			L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.519C>T	1.37:g.24022845C>T			23895432	P25121|P39026|Q8TDH2|Q9Y674	Silent	SNP	ENST00000374550.3	37	CCDS238.1																																																																																				0.373	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		T	24022845	C	T	24022845	2	4	21	1	0	0	0	0	0	0	0	1	13594	816	29	3		3	RPL11	1	24022845	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10	3042115	24022845	225227776	2	1900										
CNKSR1	10256	hgsc.bcm.edu	37	chr1	26507258	26507258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cctgacagagggacttctggGggcaacccatgacttccaga	12	12	1	4			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:26507258G>A	ENST00000374253.5	+	3	302	c.263G>A	c.(262-264)gGg>gAg	p.G88E	CNKSR1_ENST00000531191.1_5'UTR|CNKSR1_ENST00000480348.2_3'UTR|CNKSR1_ENST00000361530.6_Missense_Mutation_p.G88E	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	88	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.G88E(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		GGACTTCTGGGGGCAACCCAT	0.587																																					NSCLC(180;1396 2109 28270 30756 34275)											1	Substitution - Missense(1)	large_intestine(1)	1											52	53	53					1																	26507258		2203	4300	6503	26379845	SO:0001583	missense	10256			AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.263G>A	1.37:g.26507258G>A	ENSP00000363371:p.Gly88Glu		26379845	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37		.	.	.	.	.	.	.	.	.	.	G	1.025	-0.683563	0.03353	.	.	ENSG00000142675	ENST00000361530;ENST00000422547;ENST00000374253	T;T	0.12774	2.65;2.65	4.93	-1.8	0.07907	CRIC domain (1);CRIC domain, Chordata (1);	0.710106	0.13550	N	0.379532	T	0.03434	0.0099	N	0.01800	-0.715	0.28868	N	0.895134	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.34925	-0.9809	10	0.30078	T	0.28	-1.8163	1.2498	0.01980	0.2629:0.3008:0.2902:0.1461	.	88;88	Q969H4;Q53GM7	CNKR1_HUMAN;.	E	88	ENSP00000354609:G88E;ENSP00000363371:G88E	ENSP00000354609:G88E	G	+	2	0	CNKSR1	26379845	0.002000	0.14202	0.065000	0.19835	0.012000	0.07955	-0.241000	0.08940	-0.191000	0.10448	-0.302000	0.09304	GGG		0.587	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314		A	26507258	G	A	26507258	3	1	21	1	0	0	0	0	1	0	0	0	3612	1232	43	3	273	3	CNKSR1	1	26507258	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	2484413	26507258	222743363	3	1901										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29641954	29641954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	acatggcagagtgtgagggcGtcgtggacatttacaactgt	14	7	0	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:29641954G>A	ENST00000345512.3	+	24	3457	c.3328G>A	c.(3328-3330)Gtc>Atc	p.V1110I	PTPRU_ENST00000460170.2_Missense_Mutation_p.V1106I|PTPRU_ENST00000323874.8_Missense_Mutation_p.V1106I|PTPRU_ENST00000373779.3_Missense_Mutation_p.V1100I|PTPRU_ENST00000356870.3_Missense_Mutation_p.V1106I|PTPRU_ENST00000428026.2_Missense_Mutation_p.V1097I	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1110	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V1110I(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GTGTGAGGGCGTCGTGGACAT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	120	124					1																	29641954		2203	4300	6503	29514541	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3328G>A	1.37:g.29641954G>A	ENSP00000334941:p.Val1110Ile		29514541	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142054	0.94560	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	4.66	4.66	0.58398	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000001	D	0.85703	0.5758	L	0.31371	0.925	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.80764	0.989;0.989;0.989;0.994;0.994	D	0.84377	0.0547	9	.	.	.	.	17.0877	0.86615	0.0:0.0:1.0:0.0	.	1097;1106;1100;1106;1110	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	I	1110;1100;1106;1106;1097;1106	ENSP00000334941:V1110I;ENSP00000362884:V1100I;ENSP00000349333:V1106I;ENSP00000314987:V1106I;ENSP00000392332:V1097I;ENSP00000432906:V1106I	.	V	+	1	0	PTPRU	29514541	1.000000	0.71417	0.927000	0.36925	0.996000	0.88848	9.657000	0.98554	2.579000	0.87056	0.561000	0.74099	GTC		0.592	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29641954	G	A	29641954	3	1	21	1	0	0	0	0	1	0	0	0	12850	1145	40	1	3444	1	PTPRU	1	29641954	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	3134696	29641954	219608667	4	1902										
IQCC	55721	hgsc.bcm.edu	37	chr1	32673149	32673149	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ccaccgtcgtctataccatcAaacagccaggccttggggga	10	14	2	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:32673149A>G	ENST00000291358.6	+	5	888	c.867A>G	c.(865-867)tcA>tcG	p.S289S	RP4-622L5.7_ENST00000421616.1_RNA|RP4-622L5.7_ENST00000373604.4_RNA|DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Silent_p.S369S	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	289								p.S289S(1)		endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTATACCATCAAACAGCCAGG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	1											57	57	57					1																	32673149		2203	4300	6503	32445736	SO:0001819	synonymous_variant	55721			AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.867A>G	1.37:g.32673149A>G			32445736	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Silent	SNP	ENST00000291358.6	37	CCDS355.1																																																																																				0.542	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		G	32673149	A	G	32673149	2	3	21	1	0	0	0	0	0	0	0	1	7825	117	5	4		4	IQCC	1	32673149	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	3031195	32673149	216577472	5	1903										
LRRC40	55631	hgsc.bcm.edu	37	chr1	70614267	70614267	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttccatcatcttcattttctGagggtccacagatccaacct	5	13	4	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:70614267G>A	ENST00000370952.3	-	14	1685	c.1606C>T	c.(1606-1608)Cag>Tag	p.Q536*		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	536						membrane (GO:0016020)		p.Q536*(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TTCATTTTCTGAGGGTCCACA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											155	155	155					1																	70614267		2203	4300	6503	70386855	SO:0001587	stop_gained	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1606C>T	1.37:g.70614267G>A	ENSP00000359990:p.Gln536*		70386855	Q9BTR7|Q9NSK1|Q9NXC1	Nonsense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	G	37	6.318975	0.97471	.	.	ENSG00000066557	ENST00000370952	.	.	.	5.46	3.52	0.40303	.	0.972957	0.08504	N	0.935927	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	16.4263	0.83815	0.0:0.3693:0.6307:0.0	.	.	.	.	X	536	.	ENSP00000359990:Q536X	Q	-	1	0	LRRC40	70386855	0.980000	0.34600	0.998000	0.56505	0.998000	0.95712	1.146000	0.31589	0.615000	0.30124	0.650000	0.86243	CAG		0.353	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		A	70614267	G	A	70614267	4	1	21	1	0	0	0	0	0	1	0	0	9027	1299	45	3	210	3	LRRC40	1	70614267	Nonsense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	37941118	70614267	178636354	6	1904										
ABCA4	24	hgsc.bcm.edu	37	chr1	94476936	94476936	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	agcacggcgttgaacctgagCagcgtctgaaacagagaagt	13	9	1	4			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:94476936C>T	ENST00000370225.3	-	39	5552	c.5466G>A	c.(5464-5466)ctG>ctA	p.L1822L	ABCA4_ENST00000535881.1_5'UTR|ABCA4_ENST00000536513.1_Silent_p.L92L|ABCA4_ENST00000465352.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1822					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.L1822L(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGAACCTGAGCAGCGTCTGAA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	1											80	80	80					1																	94476936		2203	4300	6503	94249524	SO:0001819	synonymous_variant	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5466G>A	1.37:g.94476936C>T			94249524	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.602	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94476936	C	T	94476936	2	4	21	1	0	0	0	0	0	0	0	1	34	697	25	3		3	ABCA4	1	94476936	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10	23862669	94476936	154773685	7	1905										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103488320	103488320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttgtttctgtaatatcagttTctgctggtacacctggacca	8	9	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:103488320T>G	ENST00000370096.3	-	8	1535	c.1223A>C	c.(1222-1224)gAa>gCa	p.E408A	COL11A1_ENST00000353414.4_Missense_Mutation_p.E369A|COL11A1_ENST00000358392.2_Missense_Mutation_p.E420A|COL11A1_ENST00000512756.1_Intron	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	408	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E420A(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		AATATCAGTTTCTGCTGGTAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	100	100					1																	103488320		2203	4300	6503	103260908	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1223A>C	1.37:g.103488320T>G	ENSP00000359114:p.Glu408Ala		103260908	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.231650	0.39399	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000427239	D;T;D;T	0.88124	-2.34;-0.5;-2.34;-0.61	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.90126	0.6915	M	0.82517	2.595	0.51482	D	0.999921	D;D;P	0.67145	0.974;0.996;0.956	D;D;D	0.76071	0.969;0.987;0.931	D	0.89545	0.3795	10	0.09590	T	0.72	.	14.0148	0.64517	0.0:0.0:0.0:1.0	.	369;420;408	P12107-3;P12107-2;P12107	.;.;COBA1_HUMAN	A	408;420;369;420	ENSP00000359114:E408A;ENSP00000351163:E420A;ENSP00000302551:E369A;ENSP00000408640:E420A	ENSP00000302551:E369A	E	-	2	0	COL11A1	103260908	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.998000	0.76277	2.038000	0.60285	0.523000	0.50628	GAA		0.343	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103488320	T	G	103488320	3	3	21	1	0	0	0	0	1	0	0	0	3673	1783	62	4	4437	4	COL11A1	1	103488320	Missense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10	9011384	103488320	145762301	8	1906										
EFCAB2	84288	hgsc.bcm.edu	37	chr1	245222746	245222746	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ctacggaaggagagctgcatGatctgattgcagaggtgagt	15	6	1	5			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr1:245222746G>T	ENST00000366522.2	+	4	718	c.577G>T	c.(577-579)Gat>Tat	p.D193Y	EFCAB2_ENST00000447569.2_Missense_Mutation_p.D57Y|EFCAB2_ENST00000487845.1_3'UTR|EFCAB2_ENST00000366523.1_Missense_Mutation_p.D57Y			Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	193							calcium ion binding (GO:0005509)	p.D57Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			AGAGCTGCATGATCTGATTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	83	85					1																	245222746		2203	4300	6503	243289369	SO:0001583	missense	84288			AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666		"EF-hand domain containing"	28166	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 8"					23427265	Standard	NM_032328		Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366522.2:c.577G>T	1.37:g.245222746G>T	ENSP00000355479:p.Asp193Tyr		243289369	B4DZE9|Q59G23|Q9BS36	Missense_Mutation	SNP	ENST00000366522.2	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.99|19.99|19.99	3.929011|3.929011|3.929011	0.73327|0.73327|0.73327	.|.|.	.|.|.	ENSG00000203666|ENSG00000203666|ENSG00000203666	ENST00000366523;ENST00000366522;ENST00000447569|ENST00000551317;ENST00000425550|ENST00000366521	T;T;D|.|.	0.82526|.|.	-1.22;-1.21;-1.62|.|.	5.79|5.79|5.79	5.79|5.79|5.79	0.91817|0.91817|0.91817	EF-hand-like domain (1);|.|.	0.229068|.|.	0.33217|.|.	N|.|.	0.005147|.|.	D|D|.	0.86781|0.86781|.	0.6015|0.6015|.	M|M|M	0.93939|0.93939|0.93939	3.475|3.475|3.475	0.49213|0.49213|0.49213	D|D|D	0.999768|0.999768|0.999768	D;D;D;D|.|.	0.71674|.|.	0.996;0.998;0.998;0.996|.|.	P;D;D;D|.|.	0.68353|.|.	0.868;0.926;0.952;0.957|.|.	D|D|.	0.89593|0.89593|.	0.3829|0.3829|.	10|5|.	0.87932|.|.	D|.|.	0|.|.	.|.|.	17.5436|17.5436|17.5436	0.87855|0.87855|0.87855	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	57;115;193;57|.|.	B4DZE9;B1AN33;Q5VUJ9;Q5VUJ9-2|.|.	.;.;EFCB2_HUMAN;.|.|.	Y|I|L	57;193;57|48|115	ENSP00000355480:D57Y;ENSP00000355479:D193Y;ENSP00000408661:D57Y|.|.	ENSP00000355479:D193Y|.|.	D|M|X	+|+|+	1|3|2	0|0|2	EFCAB2|EFCAB2|EFCAB2	243289369|243289369|243289369	0.995000|0.995000|0.995000	0.38212|0.38212|0.38212	0.681000|0.681000|0.681000	0.30009|0.30009|0.30009	0.984000|0.984000|0.984000	0.73092|0.73092|0.73092	4.281000|4.281000|4.281000	0.58965|0.58965|0.58965	2.753000|2.753000|2.753000	0.94483|0.94483|0.94483	0.557000|0.557000|0.557000	0.71058|0.71058|0.71058	GAT|ATG|TGA		0.398	EFCAB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000097407.2			T	245222746	G	T	245222746	3	4	21	1	0	0	0	0	1	0	0	0	4945	1290	45	2	179	2	EFCAB2	1	245222746	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	141734426	245222746	4027875	9	1907										
SLC5A6	8884	hgsc.bcm.edu	37	chr2	27423971	27423971	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gcagggttcagggaccggccTcgcattctccctgaatggaa	13	12	2	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr2:27423971T>C	ENST00000310574.3	-	16	2132	c.1659A>G	c.(1657-1659)cgA>cgG	p.R553R	SLC5A6_ENST00000408041.1_Silent_p.R553R|SLC5A6_ENST00000461319.1_5'UTR	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	553					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.R553R(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GGGACCGGCCTCGCATTCTCC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	2											92	90	91					2																	27423971		2203	4300	6503	27277475	SO:0001819	synonymous_variant	8884			AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.1659A>G	2.37:g.27423971T>C			27277475	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	37	CCDS1740.1																																																																																				0.607	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		C	27423971	T	C	27423971	2	2	21	1	0	0	0	0	0	0	0	1	14706	1538	54	4		4	SLC5A6	2	27423971	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		27423971	215775402	10	1908										
B3GNT2	10678	hgsc.bcm.edu	37	chr2	62449423	62449423	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ggcaaatgtcttcatttattTtattatggaagtctccaaaa	6	6	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr2:62449423T>A	ENST00000301998.4	+	2	320	c.68T>A	c.(67-69)tTt>tAt	p.F23Y	B3GNT2_ENST00000405767.1_Missense_Mutation_p.F23Y	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	23					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.F23Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			TTCATTTATTTTATTATGGAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	72	70					2																	62449423		2203	4300	6503	62302927	SO:0001583	missense	10678			AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"Beta 3-glycosyltransferases"	15629	protein-coding gene	gene with protein product		605581	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.68T>A	2.37:g.62449423T>A	ENSP00000305595:p.Phe23Tyr		62302927	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Missense_Mutation	SNP	ENST00000301998.4	37	CCDS1870.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017327	0.54576	.	.	ENSG00000170340	ENST00000301998;ENST00000405767	T;T	0.27402	1.67;1.67	6.02	6.02	0.97574	.	0.559141	0.18375	N	0.143144	T	0.20901	0.0503	N	0.08118	0	0.21325	N	0.999722	B	0.15473	0.013	B	0.16722	0.016	T	0.26916	-1.0089	10	0.72032	D	0.01	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	23	Q9NY97	B3GN2_HUMAN	Y	23	ENSP00000305595:F23Y;ENSP00000384692:F23Y	ENSP00000305595:F23Y	F	+	2	0	B3GNT2	62302927	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.698000	0.84413	2.311000	0.77944	0.533000	0.62120	TTT		0.388	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577		A	62449423	T	A	62449423	3	1	21	1	0	0	0	0	1	0	0	0	1258	1841	64	5	70	5	B3GNT2	2	62449423	Missense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10	35025452	62449423	180749950	11	1909										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118704387	118704387	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gactaattcagagcctttacCttttcatctccacgtggtgc	7	12	3	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr2:118704387C>G	ENST00000376300.2	-	16	1433	c.1296G>C	c.(1294-1296)aaG>aaC	p.K432N	CCDC93_ENST00000319432.5_Splice_Site_p.K431N	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	432								p.K432N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						GAGCCTTTACCTTTTCATCTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											164	139	147					2																	118704387		2203	4300	6503	118420857	SO:0001630	splice_region_variant	54520			BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.1296+1G>C	2.37:g.118704387C>G			118420857	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	37	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450299	0.43531	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.18174	2.23;2.23	5.39	5.39	0.77823	.	0.245137	0.42294	D	0.000731	T	0.13372	0.0324	L	0.44542	1.39	0.50632	D	0.999884	P	0.40000	0.698	B	0.21546	0.035	T	0.07102	-1.0790	9	.	.	.	-24.1956	17.5251	0.87798	0.0:1.0:0.0:0.0	.	432	Q567U6	CCD93_HUMAN	N	432;431	ENSP00000365477:K432N;ENSP00000324135:K431N	.	K	-	3	2	CCDC93	118420857	1.000000	0.71417	0.998000	0.56505	0.564000	0.35744	5.024000	0.64090	2.804000	0.96469	0.655000	0.94253	AAG		0.418	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	Missense_Mutation	G	118704387	C	G	118704387	5	3	21	1	0	0	0	0	0	0	1	0	2878	695	24	5	635	5	CCDC93	2	118704387	Splice_Site	SNP	C	TCGA-AG-3586-01A-02W-0831-10	56254964	118704387	124494986	12	1910										
MARCH7	64844	hgsc.bcm.edu	37	chr2	160599695	160599695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	atcatgattcaaaaagacctAaactttcctgtacaaactgt	4	9	2	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr2:160599695A>G	ENST00000259050.4	+	3	399	c.277A>G	c.(277-279)Aaa>Gaa	p.K93E	MARCH7_ENST00000409175.1_Missense_Mutation_p.K93E|MARCH7_ENST00000539065.1_Missense_Mutation_p.K93E|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000409591.1_Missense_Mutation_p.K55E	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	93	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.K93E(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						AAAAAGACCTAAACTTTCCTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											135	130	132					2																	160599695		2203	4300	6503	160307941	SO:0001583	missense	64844			AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	17393	protein-coding gene	gene with protein product		613334	"axotrophin", "membrane-associated ring finger (C3HC4) 7"	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.277A>G	2.37:g.160599695A>G	ENSP00000259050:p.Lys93Glu		160307941	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	A	18.51	3.639934	0.67244	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000421037;ENST00000409591	T;T;T;T;T	0.59638	2.13;2.42;2.13;0.25;2.13	5.54	5.54	0.83059	.	0.046653	0.85682	D	0.000000	T	0.72653	0.3487	M	0.62723	1.935	0.45307	D	0.998305	D;D;D	0.69078	0.974;0.997;0.997	P;D;D	0.73380	0.655;0.98;0.98	T	0.75548	-0.3279	10	0.72032	D	0.01	-5.003	14.2554	0.66048	1.0:0.0:0.0:0.0	.	93;55;93	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	E	93;93;93;93;55	ENSP00000386830:K93E;ENSP00000442992:K93E;ENSP00000259050:K93E;ENSP00000392862:K93E;ENSP00000387238:K55E	ENSP00000259050:K93E	K	+	1	0	MARCH7	160307941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.766000	0.74970	2.107000	0.64212	0.528000	0.53228	AAA		0.403	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		G	160599695	A	G	160599695	3	3	21	1	0	0	0	0	1	0	0	0	9336	363	13	4	283	4	MARCH7	2	160599695	Missense_Mutation	SNP	A	TCGA-AG-3586-01A-02W-0831-10	41895308	160599695	82599678	13	1911										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233347830	233347830	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cccacctcatactccttgtcCacagcatcgggtttcagcag	7	16	2	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr2:233347830C>T	ENST00000304546.1	-	9	1776	c.1566G>A	c.(1564-1566)gtG>gtA	p.V522V	ECEL1_ENST00000409941.1_Silent_p.V522V	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	522					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)	p.V522V(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		ACTCCTTGTCCACAGCATCGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	2											55	35	42					2																	233347830		2203	4300	6503	233056074	SO:0001819	synonymous_variant	9427			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1566G>A	2.37:g.233347830C>T			233056074	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.652	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		T	233347830	C	T	233347830	2	4	21	1	0	0	0	0	0	0	0	1	4902	581	21	3		3	ECEL1	2	233347830	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10	72748135	233347830	9851543	14	1912										
MST1R	4486	hgsc.bcm.edu	37	chr3	49933985	49933985	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tcactcaccctgctttccacTgccctaagcccgtcatggaa	6	17	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr3:49933985T>A	ENST00000296474.3	-	9	2454	c.2427A>T	c.(2425-2427)gcA>gcT	p.A809A	MST1R_ENST00000344206.4_Silent_p.A809A|CTD-2330K9.2_ENST00000435478.1_RNA	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	809	IPT/TIG 3.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)	p.A809A(2)		cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		TGCTTTCCACTGCCCTAAGCC	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	3											120	103	108					3																	49933985		2203	4300	6503	49908989	SO:0001819	synonymous_variant	4486			X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.2427A>T	3.37:g.49933985T>A			49908989	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	37	CCDS2807.1																																																																																				0.582	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49933985	T	A	49933985	2	1	21	1	0	0	0	0	0	0	0	1	9921	1567	55	5		5	MST1R	3	49933985	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		49933985	148088445	15	1913										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170723098	170723098	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttgattccggaaaattgctgAgccacatgcagcatcagtgc	10	10	1	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr3:170723098A>C	ENST00000314251.3	-	7	1018	c.939T>G	c.(937-939)gcT>gcG	p.A313A	SLC2A2_ENST00000382808.4_Silent_p.A194A	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	313					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.A313A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	AAAATTGCTGAGCCACATGCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	3											183	169	174					3																	170723098		2203	4300	6503	172205792	SO:0001819	synonymous_variant	6514			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.939T>G	3.37:g.170723098A>C			172205792	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																				0.433	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		C	170723098	A	C	170723098	2	2	21	1	0	0	0	0	0	0	0	1	14581	291	11	4		4	SLC2A2	3	170723098	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	120789113	170723098	27299332	16	1914										
HTR3C	170572	hgsc.bcm.edu	37	chr3	183772635	183772635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	caactacagcatccctacccGtgtcaacatctccttcaccc	3	19	3	0	rs183919204		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr3:183772635G>A	ENST00000318351.1	+	2	228	c.194G>A	c.(193-195)cGt>cAt	p.R65H		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	65					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.R65H(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	ATCCCTACCCGTGTCAACATC	0.532													G|||	1	0.000199681	0	0	5008	,	,		20689	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	3											137	111	120					3																	183772635		2203	4300	6503	185255329	SO:0001583	missense	170572			AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24003	protein-coding gene	gene with protein product		610121	"5-hydroxytryptamine (serotonin) receptor 3, family member C"			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.194G>A	3.37:g.183772635G>A	ENSP00000322617:p.Arg65His		185255329	A2RRR5	Missense_Mutation	SNP	ENST00000318351.1	37	CCDS3250.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	.	1.781	-0.481841	0.04383	.	.	ENSG00000178084	ENST00000318351	T	0.79454	-1.27	4.43	-6.54	0.01860	Neurotransmitter-gated ion-channel ligand-binding (3);	2.322460	0.01299	N	0.010255	T	0.49304	0.1549	N	0.04686	-0.185	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.45716	-0.9242	10	0.13470	T	0.59	5.3539	2.3097	0.04183	0.255:0.1178:0.3962:0.231	.	65	Q8WXA8	5HT3C_HUMAN	H	65	ENSP00000322617:R65H	ENSP00000322617:R65H	R	+	2	0	HTR3C	185255329	0.000000	0.05858	0.000000	0.03702	0.451000	0.32288	-1.183000	0.03079	-1.188000	0.02705	-1.267000	0.01435	CGT		0.532	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		A	183772635	G	A	183772635	3	1	21	1	0	0	0	0	1	0	0	0	7467	1145	40	1	200	1	HTR3C	3	183772635	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	13049537	183772635	14249795	17	1915										
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48486118	48486119	+	Frame_Shift_Ins	INS	-	-	A													0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gtggctgctgtcccggcggcINSaatctctccaatcttatgtc							TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr4:48486118_48486119insA	ENST00000273861.4	+	1	759_760	c.540_541insA	c.(541-543)aatfs	p.N181fs		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)	p.N181fs*11(1)		central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						GTCCCGGCGGCAATCTCTCCAA	0.624																																																1	Insertion - Frameshift(1)	large_intestine(1)	4																																								48180876	SO:0001589	frameshift_variant	201780			BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.542dupA	4.37:g.48486120_48486120dupA	ENSP00000273861:p.Asn181fs		48180875	Q8WUZ2	Frame_Shift_Ins	INS	ENST00000273861.4	37	CCDS3482.1																																																																																				0.624	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		A	48486119	-	A	48486118	7	5	21	1	0	1	1	0	0	0	0	0	14413	697	25	0	542	0	SLC10A4	4	48486118	Frame_Shift_Ins	INS	-	TCGA-AG-3586-01A-02W-0831-10		48486118	142668158	18	1916										
CENPE	1062	hgsc.bcm.edu	37	chr4	104044047	104044047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cctctgtggttaactgtgtaGctcttgatgtaacatgagga	11	7	2	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr4:104044047G>A	ENST00000265148.3	-	43	7213	c.7124C>T	c.(7123-7125)gCt>gTt	p.A2375V	CENPE_ENST00000380026.3_Missense_Mutation_p.A2254V	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2375	Kinetochore-binding domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.A2338V(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TAACTGTGTAGCTCTTGATGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											174	179	177					4																	104044047		2203	4300	6503	104263496	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.7124C>T	4.37:g.104044047G>A	ENSP00000265148:p.Ala2375Val		104263496	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.453218	0.43531	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.68903	-0.36;-0.35	4.57	2.59	0.31030	.	.	.	.	.	T	0.54565	0.1866	L	0.51422	1.61	0.09310	N	1	B;B	0.33073	0.102;0.396	B;B	0.29785	0.022;0.107	T	0.53236	-0.8467	9	0.66056	D	0.02	.	4.2443	0.10663	0.1212:0.0:0.6328:0.246	.	2254;2375	Q02224-3;Q02224	.;CENPE_HUMAN	V	2375;2339;2254	ENSP00000265148:A2375V;ENSP00000369365:A2254V	ENSP00000265148:A2375V	A	-	2	0	CENPE	104263496	0.000000	0.05858	0.075000	0.20258	0.367000	0.29736	0.544000	0.23253	2.070000	0.61991	0.467000	0.42956	GCT		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104044047	G	A	104044047	3	1	21	1	0	0	0	0	1	0	0	0	3236	971	34	3	1009	3	CENPE	4	104044047	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	55557929	104044047	87110229	19	1917										
ANXA10	11199	hgsc.bcm.edu	37	chr4	169060676	169060676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gatcaacattctgactcagcGctgcaatgcacaaaggatga	9	10	3	2	rs202148101		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr4:169060676G>A	ENST00000359299.3	+	3	326	c.140G>A	c.(139-141)cGc>cAc	p.R47H		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	47						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)	p.R47H(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		CTGACTCAGCGCTGCAATGCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	HIS/ARG	0,4406		0,0,2203	107	101	103		140	3.2	0.7	4		103	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ANXA10	NM_007193.4	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	47/325	169060676	2,13004	2203	4300	6503	169297251	SO:0001583	missense	11199			AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"Annexins"	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.140G>A	4.37:g.169060676G>A	ENSP00000352248:p.Arg47His		169297251	Q96IQ5|Q9UJV4	Missense_Mutation	SNP	ENST00000359299.3	37	CCDS34096.1	.	.	.	.	.	.	.	.	.	.	G	9.801	1.180530	0.21787	0.0	2.33E-4	ENSG00000109511	ENST00000359299;ENST00000393751	T	0.12774	2.65	5.82	3.19	0.36642	.	0.211827	0.40385	N	0.001107	T	0.18841	0.0452	M	0.81179	2.53	0.43149	D	0.994913	B	0.25719	0.132	B	0.22386	0.039	T	0.03863	-1.0997	10	0.72032	D	0.01	.	10.1456	0.42762	0.2196:0.0:0.7804:0.0	.	47	Q9UJ72	ANX10_HUMAN	H	47	ENSP00000352248:R47H	ENSP00000352248:R47H	R	+	2	0	ANXA10	169297251	1.000000	0.71417	0.701000	0.30321	0.008000	0.06430	3.810000	0.55613	0.833000	0.34828	-0.742000	0.03525	CGC		0.418	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193		A	169060676	G	A	169060676	3	1	21	1	0	0	0	0	1	0	0	0	715	1087	38	1	150	1	ANXA10	4	169060676	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	65016629	169060676	22093600	20	1918										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71495396	71495396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gctacactgcagaaaagaagTccccctcagaagcccgtcag	9	14	2	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:71495396T>C	ENST00000296755.7	+	5	6512	c.6214T>C	c.(6214-6216)Tcc>Ccc	p.S2072P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2072					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.S2072P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AGAAAAGAAGTCCCCCTCAGA	0.473																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											125	134	131					5																	71495396		2203	4300	6503	71531152	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6214T>C	5.37:g.71495396T>C	ENSP00000296755:p.Ser2072Pro		71531152	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803411	0.31869	.	.	ENSG00000131711	ENST00000296755	T	0.03496	3.91	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000007	T	0.02807	0.0084	N	0.08118	0	0.42349	D	0.992366	B;B	0.23442	0.085;0.029	B;B	0.19391	0.025;0.018	T	0.56848	-0.7911	10	0.41790	T	0.15	-16.9263	14.8253	0.70107	0.0:0.0:0.0:1.0	.	1946;2072	A2BDK6;P46821	.;MAP1B_HUMAN	P	2072	ENSP00000296755:S2072P	ENSP00000296755:S2072P	S	+	1	0	MAP1B	71531152	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	1.685000	0.37659	2.104000	0.64026	0.533000	0.62120	TCC		0.473	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71495396	T	C	71495396	3	2	21	1	0	0	0	0	1	0	0	0	9258	1667	58	4	6232	4	MAP1B	5	71495396	Missense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10		71495396	109419864	21	1919										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72157665	72157665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cacaactatagcctccaaggGagaattgcagaattggcctg	10	10	0	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:72157665G>A	ENST00000337273.5	+	5	812	c.386G>A	c.(385-387)gGa>gAa	p.G129E	TNPO1_ENST00000523768.1_Missense_Mutation_p.G79E|TNPO1_ENST00000447967.2_Intron|TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000506351.2_Missense_Mutation_p.G121E|TNPO1_ENST00000454282.1_Missense_Mutation_p.G79E	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	129					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)	p.G121E(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		GCCTCCAAGGGAGAATTGCAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											132	123	126					5																	72157665		2203	4300	6503	72193421	SO:0001583	missense	3842			U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.386G>A	5.37:g.72157665G>A	ENSP00000336712:p.Gly129Glu		72193421	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.411142	0.25465	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.79	5.79	0.91817	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	M	0.64676	1.99	0.80722	D	1	B;B	0.17038	0.014;0.02	B;B	0.17979	0.02;0.012	T	0.56685	-0.7938	10	0.23302	T	0.38	-14.2435	20.0349	0.97554	0.0:0.0:1.0:0.0	.	79;129	Q92973-3;Q92973	.;TNPO1_HUMAN	E	129;79;79;121	ENSP00000336712:G129E;ENSP00000398524:G79E;ENSP00000428899:G79E;ENSP00000425118:G121E	ENSP00000336712:G129E	G	+	2	0	TNPO1	72193421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.452000	0.97615	2.741000	0.93983	0.585000	0.79938	GGA		0.388	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		A	72157665	G	A	72157665	3	1	21	1	0	0	0	0	1	0	0	0	16374	1174	41	3	404	3	TNPO1	5	72157665	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	662269	72157665	108757595	22	1920										
APC	324	hgsc.bcm.edu	37	chr5	112173600	112173600	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	attagatgctcagcacttatCagaaacttttgacaatatag	6	7	2	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:112173600C>A	ENST00000457016.1	+	16	2689	c.2309C>A	c.(2308-2310)tCa>tAa	p.S770*	APC_ENST00000508376.2_Nonsense_Mutation_p.S770*|APC_ENST00000257430.4_Nonsense_Mutation_p.S770*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	770	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S770*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCACTTATCAGAAACTTTT	0.393		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5	GRCh37	CD941579|CM035803	APC	D|M							56	57	57					5																	112173600		2202	4300	6502	112201499	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2309C>A	5.37:g.112173600C>A	ENSP00000413133:p.Ser770*		112201499	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.220596	0.97390	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3781	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	770;752;770;770;770	.	ENSP00000257430:S770X	S	+	2	0	APC	112201499	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	TCA		0.393	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112173600	C	A	112173600	4	1	21	1	0	0	0	0	0	1	0	0	763	838	29	2	2367	2	APC	5	112173600	Nonsense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10	40015935	112173600	68741660	23	1921										
APC	324	hgsc.bcm.edu	37	chr5	112174158	112174158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gccttatgccaaattagaatAcaagagatcttcaaatgata	6	7	2	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:112174158A>G	ENST00000457016.1	+	16	3247	c.2867A>G	c.(2866-2868)tAc>tGc	p.Y956C	APC_ENST00000508376.2_Missense_Mutation_p.Y956C|APC_ENST00000257430.4_Missense_Mutation_p.Y956C|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	956	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.Y956C(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAATTAGAATACAAGAGATCT	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											68	68	68					5																	112174158		2202	4300	6502	112202057	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2867A>G	5.37:g.112174158A>G	ENSP00000413133:p.Tyr956Cys		112202057	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.455127	0.43634	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.93906	-2.59;-3.31;-2.59;-2.59;-2.77	5.77	4.61	0.57282	.	0.200690	0.44688	N	0.000428	D	0.95017	0.8387	L	0.55481	1.735	0.49687	D	0.999818	P;D	0.89917	0.66;1.0	B;D	0.75484	0.154;0.986	D	0.94156	0.7410	10	0.49607	T	0.09	-5.9424	11.6284	0.51160	0.9305:0.0:0.0695:0.0	.	958;956	Q4LE70;P25054	.;APC_HUMAN	C	956;938;956;956;956	ENSP00000413133:Y956C;ENSP00000423224:Y938C;ENSP00000257430:Y956C;ENSP00000427089:Y956C;ENSP00000423828:Y956C	ENSP00000257430:Y956C	Y	+	2	0	APC	112202057	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	4.760000	0.62235	1.012000	0.39366	0.455000	0.32223	TAC		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174158	A	G	112174158	3	3	21	1	0	0	0	0	1	0	0	0	763	391	14	4	2925	4	APC	5	112174158	Missense_Mutation	SNP	A	TCGA-AG-3586-01A-02W-0831-10	558	112174158	68741102	24	1922										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123984478	123984478	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gtctctggtttcccttgaggGgtagtgggagtgcttctgga	16	7	2	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:123984478G>T	ENST00000306315.5	-	4	2034	c.1599C>A	c.(1597-1599)acC>acA	p.T533T	ZNF608_ENST00000504926.1_Silent_p.T106T	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	533							metal ion binding (GO:0046872)	p.T533T(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		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)		TCCCTTGAGGGGTAGTGGGAG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											140	134	136					5																	123984478		2203	4300	6503	124012377	SO:0001819	synonymous_variant	57507			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1599C>A	5.37:g.123984478G>T			124012377	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	37	CCDS34219.1																																																																																				0.498	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		T	123984478	G	T	123984478	2	4	21	1	0	0	0	0	0	0	0	1	18073	1219	43	2		2	ZNF608	5	123984478	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	11810320	123984478	56930782	25	1923										
LARP1	23367	hgsc.bcm.edu	37	chr5	154181722	154181722	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gggcggaagaacaccttcacTgcctggtctgatgaggaatc	13	10	2	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:154181722T>G	ENST00000336314.4	+	11	1665	c.1641T>G	c.(1639-1641)acT>acG	p.T547T		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	624					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.T624T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACACCTTCACTGCCTGGTCTG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	5											162	143	150					5																	154181722		2203	4300	6503	154161915	SO:0001819	synonymous_variant	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1641T>G	5.37:g.154181722T>G			154161915	O94836|Q8N4M2|Q8NB73|Q9UFD7	Silent	SNP	ENST00000336314.4	37	CCDS4328.1																																																																																				0.512	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		G	154181722	T	G	154181722	2	3	21	1	0	0	0	0	0	0	0	1	8650	1567	55	4		4	LARP1	5	154181722	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10	30197244	154181722	26733538	26	1924										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169145673	169145673	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttattcaggaaattgatgacAgtgctgaagacttacttgga	10	5	1	4			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr5:169145673A>G	ENST00000256935.8	+	22	2225	c.2145A>G	c.(2143-2145)acA>acG	p.T715T	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Silent_p.T207T	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	715					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.T715T(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATTGATGACAGTGCTGAAGA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	5											111	98	102					5																	169145673		2203	4300	6503	169078251	SO:0001819	synonymous_variant	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2145A>G	5.37:g.169145673A>G			169078251	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.373	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169145673	A	G	169145673	2	3	21	1	0	0	0	0	0	0	0	1	4698	175	7	4		4	DOCK2	5	169145673	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	14963951	169145673	11769587	27	1925										
PURG	29942	hgsc.bcm.edu	37	chr8	30889624	30889624	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	aactcaatcattccttgtgcTgggaggacaatagtctgttc	9	9	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr8:30889624T>C	ENST00000475541.1	-	1	1607	c.675A>G	c.(673-675)ccA>ccG	p.P225P	PURG_ENST00000339382.2_Silent_p.P225P|WRN_ENST00000298139.5_5'Flank	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	225						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.P225P(2)		endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		TTCCTTGTGCTGGGAGGACAA	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	8											128	108	115					8																	30889624		2203	4300	6503	31009166	SO:0001819	synonymous_variant	29942			AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.675A>G	8.37:g.30889624T>C			31009166	Q8TE64	Silent	SNP	ENST00000475541.1	37	CCDS6081.1																																																																																				0.502	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1	NM_013357		C	30889624	T	C	30889624	2	2	21	1	0	0	0	0	0	0	0	1	12866	1567	55	4		4	PURG	8	30889624	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		30889624	115474398	28	1926										
TPM2	7169	hgsc.bcm.edu	37	chr9	35689790	35689790	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cttgtccagcttcagcatctGcatcttcttcttgatggcgt	8	12	5	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr9:35689790G>C	ENST00000360958.2	-	1	129	c.25C>G	c.(25-27)Cag>Gag	p.Q9E	TPM2_ENST00000378300.5_Missense_Mutation_p.Q9E|TPM2_ENST00000329305.2_Missense_Mutation_p.Q9E|TPM2_ENST00000378292.3_Missense_Mutation_p.Q9E	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)	9					muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.Q9E(2)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTCAGCATCTGCATCTTCTTC	0.667																																																2	Substitution - Missense(2)	large_intestine(2)	9											204	195	198					9																	35689790		2203	4300	6503	35679790	SO:0001583	missense	7169				CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"Tropomyosins"	12011	protein-coding gene	gene with protein product	"nemaline myopathy type 4"	190990	"arthrogryposis multiplex congenital, distal, type 1"	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.25C>G	9.37:g.35689790G>C	ENSP00000354219:p.Gln9Glu		35679790	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Missense_Mutation	SNP	ENST00000360958.2	37	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.355778	0.82243	.	.	ENSG00000198467	ENST00000378300;ENST00000378292;ENST00000329305;ENST00000360958	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	4.62	4.62	0.57501	.	.	.	.	.	D	0.94427	0.8207	M	0.90252	3.1	0.52501	D	0.99995	P;P;P;B;B	0.51653	0.526;0.72;0.947;0.202;0.023	P;P;D;B;B	0.71656	0.539;0.528;0.974;0.105;0.442	D	0.95490	0.8568	9	0.87932	D	0	-8.3255	16.185	0.81946	0.0:0.0:1.0:0.0	.	9;9;9;9;9	B4DGC2;A7XZE4;P07951;Q5TCU8;P07951-2	.;.;TPM2_HUMAN;.;.	E	9	ENSP00000367550:Q9E;ENSP00000367542:Q9E;ENSP00000367541:Q9E;ENSP00000354219:Q9E	ENSP00000367541:Q9E	Q	-	1	0	TPM2	35679790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.546000	0.98097	2.384000	0.81235	0.561000	0.74099	CAG		0.667	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289		C	35689790	G	C	35689790	3	2	21	1	0	0	0	0	1	0	0	0	16446	1328	46	5	1032	5	TPM2	9	35689790	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10		35689790	105523641	29	1927										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88247631	88247631	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ctttgaatggaggcggaatgTgaccaaaataatcgggataa	12	5	0	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr9:88247631T>A	ENST00000357081.3	-	14	2105	c.1961A>T	c.(1960-1962)cAc>cTc	p.H654L	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.H492L|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.H666L|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.H614L			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	654					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.H614L(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGGCGGAATGTGACCAAAATA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											82	80	80					9																	88247631		2203	4300	6503	87437451	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1961A>T	9.37:g.88247631T>A	ENSP00000349592:p.His654Leu		87437451	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	T	22.5	4.298759	0.81025	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.54479	2.05;2.06;2.03;0.57	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.72993	0.3530	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	0.97;1.0;1.0;0.995	P;D;D;D	0.83275	0.885;0.988;0.996;0.964	T	0.75425	-0.3322	10	0.59425	D	0.04	-17.5333	16.3015	0.82820	0.0:0.0:0.0:1.0	.	666;654;492;614	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	L	654;614;666;492	ENSP00000349592:H654L;ENSP00000365251:H614L;ENSP00000365277:H666L;ENSP00000402804:H492L	ENSP00000349592:H654L	H	-	2	0	AGTPBP1	87437451	1.000000	0.71417	0.988000	0.46212	0.803000	0.45373	7.374000	0.79633	2.239000	0.73571	0.533000	0.62120	CAC		0.413	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88247631	T	A	88247631	3	1	21	1	0	0	0	0	1	0	0	0	400	1696	59	5	1771	5	AGTPBP1	9	88247631	Missense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10	52557841	88247631	52965800	30	1928										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767934	105767934	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	atgcaaagaaggatgaaaagAaggatgcaaagaagaagggc	14	3	0	5			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr9:105767934A>C	ENST00000374798.3	+	5	1091	c.1021A>C	c.(1021-1023)Aag>Cag	p.K341Q	CYLC2_ENST00000487798.1_Missense_Mutation_p.K341Q	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	341	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.K341Q(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				ggatgaaaagaaggatgcaaa	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	9											51	54	53					9																	105767934		2202	4299	6501	104807755	SO:0001583	missense	1539			Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.1021A>C	9.37:g.105767934A>C	ENSP00000420256:p.Lys341Gln		104807755	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	37	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	a	4.983	0.182600	0.09495	.	.	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.23754	1.89;1.89	2.26	1.12	0.20585	.	.	.	.	.	T	0.16811	0.0404	N	0.14661	0.345	0.26485	N	0.975049	D	0.65815	0.995	P	0.52598	0.703	T	0.12553	-1.0543	9	0.14252	T	0.57	.	3.4745	0.07579	0.7886:0.0:0.2114:0.0	.	341	Q14093	CYLC2_HUMAN	Q	341	ENSP00000420256:K341Q;ENSP00000417674:K341Q	ENSP00000420256:K341Q	K	+	1	0	CYLC2	104807755	0.535000	0.26370	0.993000	0.49108	0.203000	0.24098	0.708000	0.25719	1.039000	0.40074	0.392000	0.25879	AAG		0.368	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		C	105767934	A	C	105767934	3	2	21	1	0	0	0	0	1	0	0	0	4148	247	9	4	1039	4	CYLC2	9	105767934	Missense_Mutation	SNP	A	TCGA-AG-3586-01A-02W-0831-10	17520303	105767934	35445497	31	1929										
RBM18	92400	hgsc.bcm.edu	37	chr9	125014165	125014165	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	acaaaacagtagcctcgaggCtgtccctccaaagcacctga	8	14	0	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr9:125014165C>T	ENST00000417201.3	-	3	341	c.201G>A	c.(199-201)caG>caA	p.Q67Q	RBM18_ENST00000483428.1_5'UTR	NM_033117.3	NP_149108.1	Q96H35	RBM18_HUMAN	RNA binding motif protein 18	67	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.Q67Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7						AGCCTCGAGGCTGTCCCTCCA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	86	85					9																	125014165		2203	4300	6503	124053986	SO:0001819	synonymous_variant	92400			AK057676	CCDS6839.1	9q34.11	2013-02-12			ENSG00000119446	ENSG00000119446		"RNA binding motif (RRM) containing"	28413	protein-coding gene	gene with protein product						12477932	Standard	NM_033117		Approved	MGC2734	uc004bma.2	Q96H35	OTTHUMG00000020602	ENST00000417201.3:c.201G>A	9.37:g.125014165C>T			124053986	B3KQ89	Silent	SNP	ENST00000417201.3	37	CCDS6839.1																																																																																				0.413	RBM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053928.2	NM_033117		T	125014165	C	T	125014165	2	4	21	1	0	0	0	0	0	0	0	1	13157	796	28	3		3	RBM18	9	125014165	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10	19246231	125014165	16199266	32	1930										
PRKG1	5592	hgsc.bcm.edu	37	chr10	54042069	54042069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tcctaatgtatgaactcctgActggcaggtatggatattga	10	7	0	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr10:54042069A>G	ENST00000401604.2	+	14	1851	c.1657A>G	c.(1657-1659)Act>Gct	p.T553A	PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.T568A|PRKG1_ENST00000373985.1_Missense_Mutation_p.T541A|PRKG1-AS1_ENST00000426785.2_RNA|PRKG1_ENST00000373975.2_Missense_Mutation_p.T271A			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	553	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.T568A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TGAACTCCTGACTGGCAGGTA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											89	77	81					10																	54042069		2203	4300	6503	53712075	SO:0001583	missense	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1657A>G	10.37:g.54042069A>G	ENSP00000384200:p.Thr553Ala		53712075	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.274858	0.80580	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.10192	2.9;2.9;2.9	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.15869	0.0382	L	0.31207	0.915	0.80722	D	1	B;P;P	0.44344	0.044;0.582;0.833	B;P;P	0.53760	0.034;0.477;0.734	T	0.12319	-1.0552	10	0.13853	T	0.58	-16.7666	15.791	0.78364	1.0:0.0:0.0:0.0	.	271;568;553	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	A	553;541;568;271;165	ENSP00000384200:T553A;ENSP00000363097:T541A;ENSP00000363092:T568A	ENSP00000327642:T271A	T	+	1	0	PRKG1	53712075	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.518000	0.81795	2.270000	0.75569	0.460000	0.39030	ACT		0.453	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	54042069	A	G	54042069	3	3	21	1	0	0	0	0	1	0	0	0	12556	275	10	4	2026	4	PRKG1	10	54042069	Missense_Mutation	SNP	A	TCGA-AG-3586-01A-02W-0831-10		54042069	81492678	33	1931										
BICC1	80114	hgsc.bcm.edu	37	chr10	60588615	60588615	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ggaaggctaccccgtcagtaTcactcagacattgctagtgt	10	11	3	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr10:60588615T>A	ENST00000373886.3	+	21	2893	c.2889T>A	c.(2887-2889)taT>taA	p.Y963*		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	963					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.Y963*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CCCGTCAGTATCACTCAGACA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											113	101	105					10																	60588615		2203	4300	6503	60258621	SO:0001587	stop_gained	80114			AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.2889T>A	10.37:g.60588615T>A	ENSP00000362993:p.Tyr963*		60258621		Nonsense_Mutation	SNP	ENST00000373886.3	37	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	T	37	6.378379	0.97520	.	.	ENSG00000122870	ENST00000373886	.	.	.	5.87	-0.463	0.12164	.	0.290182	0.39759	N	0.001270	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5457	10.2871	0.43573	0.0:0.3085:0.0:0.6915	.	.	.	.	X	963	.	ENSP00000362993:Y963X	Y	+	3	2	BICC1	60258621	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	0.829000	0.27449	-0.235000	0.09767	0.533000	0.62120	TAT		0.498	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		A	60588615	T	A	60588615	4	1	21	1	0	0	0	0	0	1	0	0	1428	1442	50	5	2971	5	BICC1	10	60588615	Nonsense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10	6546546	60588615	74946132	34	1932										
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7662817	7662817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ctctgacaccagatggtaaaCggaatcccaaaggcattaag	9	10	1	2	rs150660067		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr11:7662817C>T	ENST00000299492.4	+	16	1871	c.1483C>T	c.(1483-1485)Cgg>Tgg	p.R495W	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.R352W|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.R337W|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.R383W	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	495					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.R495W(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGATGGTAAACGGAATCCCAA	0.453													C|||	1	0.000199681	8e-04	0	5008	,	,		21042	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						C	TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	146	129	135		1483	4.1	1	11	dbSNP_134	135	1,8591	1.2+/-3.3	0,1,4295	no	missense	PPFIBP2	NM_003621.2	101	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	495/877	7662817	2,12992	2201	4296	6497	7619393	SO:0001583	missense	8495			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1483C>T	11.37:g.7662817C>T	ENSP00000299492:p.Arg495Trp		7619393	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.9|20.9	4.071203|4.071203	0.76301|0.76301	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000166387|ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000530081|ENST00000534409	T;T;T;T|.	0.36878|.	1.66;1.24;1.66;1.23|.	6.03|6.03	4.05|4.05	0.47172|0.47172	.|.	0.084158|.	0.49916|.	D|.	0.000133|.	T|T	0.58836|0.58836	0.2150|0.2150	L|L	0.47716|0.47716	1.5|1.5	0.50467|0.50467	D|D	0.999878|0.999878	D;D;D;D;D;D|.	0.89917|.	0.999;0.997;1.0;1.0;1.0;0.999|.	P;P;D;D;D;P|.	0.67382|.	0.895;0.821;0.951;0.92;0.92;0.895|.	T|T	0.56360|0.56360	-0.7992|-0.7992	10|5	0.72032|.	D|.	0.01|.	-23.3711|-23.3711	11.8116|11.8116	0.52185|0.52185	0.4353:0.5647:0.0:0.0|0.4353:0.5647:0.0:0.0	.|.	383;383;418;337;352;495|.	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30|.	.;.;.;.;.;LIPB2_HUMAN|.	W|M	495;337;337;418;383;352;156|185	ENSP00000299492:R495W;ENSP00000436498:R337W;ENSP00000435469:R383W;ENSP00000437321:R352W|.	ENSP00000299492:R495W|.	R|T	+|+	1|2	2|0	PPFIBP2|PPFIBP2	7619393|7619393	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.870000|4.870000	0.63035|0.63035	1.531000|1.531000	0.49152|0.49152	-0.182000|-0.182000	0.12963|0.12963	CGG|ACG		0.453	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		T	7662817	C	T	7662817	3	4	21	1	0	0	0	0	1	0	0	0	12345	527	19	1	1541	1	PPFIBP2	11	7662817	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10		7662817	127343699	35	1933										
FCHSD2	9873	hgsc.bcm.edu	37	chr11	72553764	72553764	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	aatacgcccattgaattcccCttcccagaagccatcatcat	4	15	2	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr11:72553764C>G	ENST00000409418.4	-	17	2211	c.1828G>C	c.(1828-1830)Ggg>Cgg	p.G610R	ATG16L2_ENST00000534905.1_3'UTR|FCHSD2_ENST00000311172.7_Missense_Mutation_p.G554R|FCHSD2_ENST00000458644.2_Missense_Mutation_p.G474R|FCHSD2_ENST00000409263.1_Intron|FCHSD2_ENST00000409314.1_Missense_Mutation_p.G634R	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	610	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.							p.G554R(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TTGAATTCCCCTTCCCAGAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											152	144	146					11																	72553764		2200	4293	6493	72231412	SO:0001583	missense	9873			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.1828G>C	11.37:g.72553764C>G	ENSP00000386722:p.Gly610Arg		72231412	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636300	0.87760	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	6.03	6.03	0.97812	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.86331	0.5907	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.995;1.0	D	0.89344	0.3656	10	0.87932	D	0	-20.5438	19.5548	0.95338	0.0:1.0:0.0:0.0	.	474;610	E7ENZ2;O94868	.;FCSD2_HUMAN	R	554;634;610;474	ENSP00000308978:G554R;ENSP00000386987:G634R;ENSP00000386722:G610R;ENSP00000402972:G474R	ENSP00000308978:G554R	G	-	1	0	FCHSD2	72231412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	GGG		0.443	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		G	72553764	C	G	72553764	3	3	21	1	0	0	0	0	1	0	0	0	5809	681	24	5	410	5	FCHSD2	11	72553764	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10	64890947	72553764	62452752	36	1934										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20890176	20890176	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tcagcttgtcttgctggttgTcaaacctccaacaggagtgg	11	10	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr12:20890176T>C	ENST00000266509.2	+	11	1886	c.1518T>C	c.(1516-1518)tgT>tgC	p.C506C	SLCO1C1_ENST00000381552.1_Silent_p.C506C|SLCO1C1_ENST00000545102.1_Silent_p.C388C|SLCO1C1_ENST00000545604.1_Silent_p.C506C|SLCO1C1_ENST00000540354.1_Silent_p.C457C	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	506	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.C506C(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TTGCTGGTTGTCAAACCTCCA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	12											101	94	96					12																	20890176		2203	4300	6503	20781443	SO:0001819	synonymous_variant	53919			AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1518T>C	12.37:g.20890176T>C			20781443	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																				0.398	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		C	20890176	T	C	20890176	2	2	21	1	0	0	0	0	0	0	0	1	14762	1673	58	4		4	SLCO1C1	12	20890176	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		20890176	112961719	37	1935										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	21	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10	4508108	25398284	108453611	38	1936										
ESPL1	9700	hgsc.bcm.edu	37	chr12	53683296	53683296	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gcccgcatccagcgcctcttTtccttcagggctttggaatc	9	15	2	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr12:53683296T>C	ENST00000257934.4	+	22	5122	c.5031T>C	c.(5029-5031)ttT>ttC	p.F1677F	ESPL1_ENST00000552462.1_Silent_p.F1677F	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1677					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)	p.F1677F(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						AGCGCCTCTTTTCCTTCAGGG	0.592																																					Colon(53;1069 1201 2587 5382)											1	Substitution - coding silent(1)	large_intestine(1)	12											49	52	51					12																	53683296		2203	4300	6503	51969563	SO:0001819	synonymous_variant	9700			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5031T>C	12.37:g.53683296T>C			51969563		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																				0.592	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		C	53683296	T	C	53683296	2	2	21	1	0	0	0	0	0	0	0	1	5266	1838	64	4		4	ESPL1	12	53683296	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10	28285012	53683296	80168599	39	1937										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130941072	130941072	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gaggtggctaggccattcatGaactgtgggaaaggcttgct	15	7	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr12:130941072G>T	ENST00000261655.4	-	4	439	c.276C>A	c.(274-276)ttC>ttA	p.F92L	RIMBP2_ENST00000536002.1_5'UTR|RIMBP2_ENST00000535703.1_5'UTR	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	92					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.F92L(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GGCCATTCATGAACTGTGGGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	12											58	47	51					12																	130941072		2203	4300	6503	129507025	SO:0001583	missense	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.276C>A	12.37:g.130941072G>T	ENSP00000261655:p.Phe92Leu		129507025	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.439898	0.01098	.	.	ENSG00000060709	ENST00000261655	T	0.16073	2.37	4.06	0.628	0.17681	.	0.485666	0.20418	N	0.092726	T	0.06005	0.0156	N	0.13327	0.33	0.25634	N	0.986276	B	0.02656	0.0	B	0.01281	0.0	T	0.29792	-1.0000	10	0.11485	T	0.65	-2.6383	0.2462	0.00199	0.3056:0.1344:0.2423:0.3177	.	92	O15034	RIMB2_HUMAN	L	92	ENSP00000261655:F92L	ENSP00000261655:F92L	F	-	3	2	RIMBP2	129507025	1.000000	0.71417	0.040000	0.18447	0.013000	0.08279	1.249000	0.32839	0.711000	0.32018	-0.123000	0.14984	TTC		0.642	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130941072	G	T	130941072	3	4	21	1	0	0	0	0	1	0	0	0	13400	1281	45	2	2946	2	RIMBP2	12	130941072	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	77257776	130941072	2910823	40	1938										
FREM2	341640	hgsc.bcm.edu	37	chr13	39266024	39266024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	agtttcaagtcaccgatggaCgtaaccctgtctttcggaca	9	11	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr13:39266024C>T	ENST00000280481.7	+	1	4759	c.4543C>T	c.(4543-4545)Cgt>Tgt	p.R1515C		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1515					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1515C(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CACCGATGGACGTAACCCTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											141	127	132					13																	39266024		2203	4300	6503	38164024	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4543C>T	13.37:g.39266024C>T	ENSP00000280481:p.Arg1515Cys		38164024	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025214	0.35701	.	.	ENSG00000150893	ENST00000280481	T	0.26518	1.73	6.07	6.07	0.98685	.	0.471167	0.26237	N	0.025532	T	0.19327	0.0464	L	0.40543	1.245	0.41873	D	0.990288	P	0.44659	0.84	B	0.38562	0.276	T	0.01630	-1.1308	10	0.38643	T	0.18	.	7.9903	0.30237	0.0:0.816:0.0:0.184	.	1515	Q5SZK8	FREM2_HUMAN	C	1515	ENSP00000280481:R1515C	ENSP00000280481:R1515C	R	+	1	0	FREM2	38164024	0.947000	0.32204	0.176000	0.23000	0.988000	0.76386	6.120000	0.71596	2.890000	0.99128	0.650000	0.86243	CGT		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39266024	C	T	39266024	3	4	21	1	0	0	0	0	1	0	0	0	6064	536	19	1	4545	1	FREM2	13	39266024	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10		39266024	75903854	41	1939										
SEPT12	124404	hgsc.bcm.edu	37	chr16	4836036	4836036	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gtgggcacccccaagcccggTgggtttgacttccacacttt	11	14	0	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr16:4836036T>A	ENST00000268231.8	-	3	500	c.237A>T	c.(235-237)ccA>ccT	p.P79P	SMIM22_ENST00000589721.1_5'Flank|SEPT12_ENST00000591861.1_5'UTR|SMIM22_ENST00000589327.1_5'Flank|SEPT12_ENST00000396693.5_Silent_p.P79P	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	79	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.P79P(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CCAAGCCCGGTGGGTTTGACT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	16											54	47	49					16																	4836036		2197	4300	6497	4776037	SO:0001819	synonymous_variant	124404			AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"Septins"	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.237A>T	16.37:g.4836036T>A			4776037	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																				0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605		A	4836036	T	A	4836036	2	1	21	1	0	0	0	0	0	0	0	1	14099	1683	59	5		5	SEPT12	16	4836036	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		4836036	85518717	42	1940										
MYST1	84148	hgsc.bcm.edu	37	chr16	31131563	31131563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	aggagggccgagaggaattcTatgtacactacgtgggctgt	15	7	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr16:31131563T>C	ENST00000543774.2	+	3	603	c.268T>C	c.(268-270)Tat>Cat	p.Y90H	KAT8_ENST00000219797.4_Missense_Mutation_p.Y90H|KAT8_ENST00000448516.2_Missense_Mutation_p.Y90H|RP11-196G11.4_ENST00000576336.1_RNA			Q9H7Z6	KAT8_HUMAN	K(lysine) acetyltransferase 8	90	Chromo.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|myeloid cell differentiation (GO:0030099)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	histone acetyltransferase complex (GO:0000123)|kinetochore (GO:0000776)|MLL1 complex (GO:0071339)|MSL complex (GO:0072487)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|transcription factor binding (GO:0008134)	p.Y90H(1)									AGAGGAATTCTATGTACACTA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	16											152	137	142					16																	31131563		2197	4300	6497	31039064	SO:0001583	missense	84148			AF217501	CCDS10706.1, CCDS45468.1	16p11.1	2013-01-10	2011-07-21	2011-07-21	ENSG00000103510	ENSG00000103510	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17933	protein-coding gene	gene with protein product		609912	"MYST histone acetyltransferase 1"	MYST1		10786633	Standard	NM_032188		Approved	MOF, FLJ14040, hMOF, ZC2HC8	uc002eax.3	Q9H7Z6	OTTHUMG00000132410	ENST00000543774.2:c.268T>C	16.37:g.31131563T>C	ENSP00000456933:p.Tyr90His		31039064	A8K4Z1|G5E9P2|Q659G0|Q7LC17|Q8IY59|Q8WYB4|Q8WZ14|Q9HAC5|Q9NR35	Missense_Mutation	SNP	ENST00000543774.2	37	CCDS10706.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601576	0.87055	.	.	ENSG00000103510	ENST00000219797;ENST00000448516	T;T	0.55930	0.49;0.49	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.77598	0.4154	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.81976	-0.0686	10	0.59425	D	0.04	-14.9295	15.1835	0.72978	0.0:0.0:0.0:1.0	.	90;90	Q9H7Z6;G5E9P2	KAT8_HUMAN;.	H	90	ENSP00000219797:Y90H;ENSP00000406037:Y90H	ENSP00000219797:Y90H	Y	+	1	0	KAT8	31039064	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.131000	0.77243	2.235000	0.73313	0.533000	0.62120	TAT		0.537	KAT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000255546.3	NM_032188		C	31131563	T	C	31131563	3	2	21	1	0	0	0	0	1	0	0	0	10132	1522	53	4	274	4	MYST1	16	31131563	Missense_Mutation	SNP	T	TCGA-AG-3586-01A-02W-0831-10	26295527	31131563	59223190	43	1941										
AMFR	267	hgsc.bcm.edu	37	chr16	56397907	56397907	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tcatcagcagacttggagaaGcggctcccacgagcctcgaa	11	13	2	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr16:56397907G>A	ENST00000290649.5	-	13	1920	c.1710C>T	c.(1708-1710)cgC>cgT	p.R570R		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	570					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R570R(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						ACTTGGAGAAGCGGCTCCCAC	0.612																																					Pancreas(2;144 323 39528)											1	Substitution - coding silent(1)	large_intestine(1)	16											59	50	53					16																	56397907		2198	4300	6498	54955408	SO:0001819	synonymous_variant	267			L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1710C>T	16.37:g.56397907G>A			54955408	P26442|Q8IZ70	Silent	SNP	ENST00000290649.5	37	CCDS10758.1																																																																																				0.612	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			A	56397907	G	A	56397907	2	1	21	1	0	0	0	0	0	0	0	1	571	958	34	3		3	AMFR	16	56397907	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	25266344	56397907	33956846	44	1942										
GGT6	124975	hgsc.bcm.edu	37	chr17	4461463	4461463	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tgctggtgctgggcctgggtAgggggccttgctgccagatg	19	9	0	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:4461463A>T	ENST00000574154.1	-	4	1625	c.1329T>A	c.(1327-1329)ccT>ccA	p.P443P	GGT6_ENST00000381550.3_Silent_p.P449P|MYBBP1A_ENST00000381556.2_5'Flank|MYBBP1A_ENST00000254718.4_5'Flank|GGT6_ENST00000573591.1_Silent_p.P295P|GGT6_ENST00000301395.3_Silent_p.P411P			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	443					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.P411P(1)		endometrium(2)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GGGCCTGGGTAGGGGGCCTTG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	17											91	80	84					17																	4461463		2203	4300	6503	4408212	SO:0001819	synonymous_variant	124975			AK074646	CCDS11047.1, CCDS45582.1, CCDS73942.1	17p13.2	2014-08-12	2008-03-10		ENSG00000167741	ENSG00000167741		"Gamma-glutamyltransferases"	26891	protein-coding gene	gene with protein product		612341	"gamma-glutamyltransferase 6 homolog (rat)"			18357469	Standard	NM_001122890		Approved	FLJ90165	uc002fyd.4	Q6P531	OTTHUMG00000177827	ENST00000574154.1:c.1329T>A	17.37:g.4461463A>T			4408212	B4DUH4|Q8NCM0	Silent	SNP	ENST00000574154.1	37	CCDS45582.1																																																																																				0.622	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338		T	4461463	A	T	4461463	2	4	21	1	0	0	0	0	0	0	0	1	6383	407	15	5		5	GGT6	17	4461463	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10		4461463	76733747	45	1943										
ODF4	146852	hgsc.bcm.edu	37	chr17	8249110	8249110	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ccaagggcacagacgatcacAgacacccccatcacccagga	8	17	2	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:8249110A>C	ENST00000328248.2	+	3	902	c.714A>C	c.(712-714)acA>acC	p.T238T	ODF4_ENST00000584943.1_Silent_p.T123T	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	238					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)		p.T238T(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						AGACGATCACAGACACCCCCA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	17											93	92	93					17																	8249110		2203	4300	6503	8189835	SO:0001819	synonymous_variant	146852			AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"cancer/testis antigen 136"	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.714A>C	17.37:g.8249110A>C			8189835	Q8J021	Silent	SNP	ENST00000328248.2	37	CCDS11140.1																																																																																				0.522	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1			C	8249110	A	C	8249110	2	2	21	1	0	0	0	0	0	0	0	1	10864	175	7	4		4	ODF4	17	8249110	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	3787647	8249110	72946100	46	1944										
NOS2	4843	hgsc.bcm.edu	37	chr17	26101433	26101433	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttctgcatgtacttcatgaaGgattctgcagccgagtggtg	12	8	3	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:26101433G>T	ENST00000313735.6	-	12	1559	c.1326C>A	c.(1324-1326)tcC>tcA	p.S442S		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	442					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.S442S(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	ACTTCATGAAGGATTCTGCAG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	17											101	95	97					17																	26101433		2203	4300	6503	23125560	SO:0001819	synonymous_variant	4843			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1326C>A	17.37:g.26101433G>T			23125560	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																				0.562	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		T	26101433	G	T	26101433	2	4	21	1	0	0	0	0	0	0	0	1	10574	987	35	2		2	NOS2	17	26101433	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	17852323	26101433	55093777	47	1945										
CDC27	996	hgsc.bcm.edu	37	chr17	45216210	45216210	+	Silent	SNP	A	A	G													0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gagtagatctccatgccttcAactctataattctcaatcct					rs62075659		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:45216210A>G	ENST00000066544.3	-	13	1692	c.1599T>C	c.(1597-1599)gtT>gtC	p.V533V	CDC27_ENST00000531206.1_Silent_p.V539V|CDC27_ENST00000446365.2_Silent_p.V472V|CDC27_ENST00000527547.1_Silent_p.V532V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	533					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.V533V(1)|p.V539V(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CCATGCCTTCAACTCTATAAT	0.318																																																2	Substitution - coding silent(2)	large_intestine(2)	17											36	40	39					17																	45216210		2200	4297	6497	42571209	SO:0001819	synonymous_variant	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1599T>C	17.37:g.45216210A>G			42571209	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																				0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			G	45216210	A	G	45216210	2	3	21	1	0	0	0	0	0	0	0	1	3072	117	5	4		4	CDC27	17	45216210	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	19114777	45216210	35979000	48	1946	9	2								
CDC27	996	hgsc.bcm.edu	37	chr17	45216216	45216216	+	Silent	SNP	A	A	G													0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	atctccatgccttcaactctAtaattctcaatccttctaac					rs62077260		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:45216216A>G	ENST00000066544.3	-	13	1686	c.1593T>C	c.(1591-1593)taT>taC	p.Y531Y	CDC27_ENST00000531206.1_Silent_p.Y537Y|CDC27_ENST00000446365.2_Silent_p.Y470Y|CDC27_ENST00000527547.1_Silent_p.Y530Y	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	531					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.Y537Y(1)|p.Y531Y(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTTCAACTCTATAATTCTCAA	0.318																																																2	Substitution - coding silent(2)	large_intestine(2)	17											34	39	37					17																	45216216		2200	4297	6497	42571215	SO:0001819	synonymous_variant	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1593T>C	17.37:g.45216216A>G			42571215	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																				0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			G	45216216	A	G	45216216	2	3	21	1	0	0	0	0	0	0	0	1	3072	456	16	4		4	CDC27	17	45216216	Silent	SNP	A	TCGA-AG-3586-01A-02W-0831-10	6	45216216	35978994	49	1947	9	2								
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68129146	68129146	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gttccccgagaaattctctgGggccataggtttaatgatgt	11	8	1	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:68129146G>A	ENST00000589377.1	+	2	1081	c.918G>A	c.(916-918)tgG>tgA	p.W306*	KCNJ16_ENST00000392671.1_Nonsense_Mutation_p.W306*|KCNJ16_ENST00000586462.1_Nonsense_Mutation_p.W345*|KCNJ16_ENST00000392670.1_Nonsense_Mutation_p.W306*|KCNJ16_ENST00000283936.1_Nonsense_Mutation_p.W306*|KCNJ16_ENST00000585558.1_Nonsense_Mutation_p.W341*	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	306					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.W306*(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					AAATTCTCTGGGGCCATAGGT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											72	77	75					17																	68129146		2203	4300	6503	65640741	SO:0001587	stop_gained	3773			AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.918G>A	17.37:g.68129146G>A	ENSP00000465967:p.Trp306*		65640741		Nonsense_Mutation	SNP	ENST00000589377.1	37	CCDS11687.1	.	.	.	.	.	.	.	.	.	.	G	38	6.869311	0.97897	.	.	ENSG00000153822	ENST00000283936;ENST00000392671;ENST00000392670	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5977	0.95547	0.0:0.0:1.0:0.0	.	.	.	.	X	306	.	.	W	+	3	0	KCNJ16	65640741	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	9.771000	0.98977	2.722000	0.93159	0.650000	0.86243	TGG		0.398	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68129146	G	A	68129146	4	1	21	1	0	0	0	0	0	1	0	0	8071	1241	43	3	920	3	KCNJ16	17	68129146	Nonsense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	22912930	68129146	13066064	50	1948										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288615	74288615	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cgctgatctactccaggttgGaccaaaccatgctgaactgc	9	13	1	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:74288615G>T	ENST00000262765.5	-	4	1874	c.1695C>A	c.(1693-1695)gtC>gtA	p.V565V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	565	Gln-rich.							p.V565V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTCCAGGTTGGACCAAACCAT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	17											198	158	171					17																	74288615		2203	4300	6503	71800210	SO:0001819	synonymous_variant	84074			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1695C>A	17.37:g.74288615G>T			71800210	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																				0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		T	74288615	G	T	74288615	2	4	21	1	0	0	0	0	0	0	0	1	12917	1161	41	2		2	QRICH2	17	74288615	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	6159469	74288615	6906595	51	1949										
BAIAP2	10458	hgsc.bcm.edu	37	chr17	79027481	79027481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cttccagaccatcatggagcAgttcaaccctagcctccgga	8	15	2	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr17:79027481A>G	ENST00000321300.6	+	2	161	c.68A>G	c.(67-69)cAg>cGg	p.Q23R	BAIAP2_ENST00000321280.7_Missense_Mutation_p.Q23R|BAIAP2_ENST00000435091.3_Missense_Mutation_p.Q23R|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000575712.1_Missense_Mutation_p.Q23R|BAIAP2_ENST00000392411.3_Intron|BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q23R|BAIAP2_ENST00000575245.1_Missense_Mutation_p.Q56R	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	23	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)	p.Q23R(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ATCATGGAGCAGTTCAACCCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											172	147	155					17																	79027481		2203	4300	6503	76642076	SO:0001583	missense	10458			AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.68A>G	17.37:g.79027481A>G	ENSP00000316338:p.Gln23Arg		76642076	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	37	CCDS11775.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505427	0.85282	.	.	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000435091;ENST00000321280	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	5.34	5.34	0.76211	IRSp53/MIM homology domain (IMD) (3);	0.000000	0.85682	D	0.000000	T	0.57504	0.2058	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.997;0.994;0.999;0.999;0.997	D;P;P;D;D;P	0.75020	0.985;0.825;0.873;0.946;0.946;0.872	T	0.56535	-0.7963	10	0.34782	T	0.22	-2.4451	14.3024	0.66362	1.0:0.0:0.0:0.0	.	23;23;23;23;23;23	Q9UQB8;Q9UQB8-2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-6;Q9UQB8-4	BAIP2_HUMAN;.;.;.;.;.	R	23	ENSP00000316338:Q23R;ENSP00000401022:Q23R;ENSP00000413069:Q23R;ENSP00000315685:Q23R	ENSP00000315685:Q23R	Q	+	2	0	BAIAP2	76642076	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.341000	0.90046	2.019000	0.59389	0.533000	0.62120	CAG		0.582	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1			G	79027481	A	G	79027481	3	3	21	1	0	0	0	0	1	0	0	0	1302	188	7	4	74	4	BAIAP2	17	79027481	Missense_Mutation	SNP	A	TCGA-AG-3586-01A-02W-0831-10	4738866	79027481	2167729	52	1950										
CASP14	23581	hgsc.bcm.edu	37	chr19	15163075	15163075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	aaggagaaatgagcaatccgCggtctttggaagaggtaggc	15	6	1	3	rs77227419	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr19:15163075C>T	ENST00000427043.3	+	2	321	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	CASP14_ENST00000221740.1_Missense_Mutation_p.R5W|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	5					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.R5W(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						GAGCAATCCGCGGTCTTTGGA	0.502													C|||	9	0.00179712	0.0068	0	5008	,	,		16614	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	19						C	TRP/ARG	17,4389		0,17,2186	89	74	79		13	-0.8	0	19	dbSNP_131	79	0,8600		0,0,4300	yes	missense	CASP14	NM_012114.2	101	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	probably-damaging	5/243	15163075	17,12989	2203	4300	6503	15024075	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.13C>T	19.37:g.15163075C>T	ENSP00000393417:p.Arg5Trp		15024075	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	.	11.21	1.572012	0.28092	0.003858	0.0	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.02944	4.1;4.1	4.2	-0.76	0.11041	.	4.671220	0.00166	N	0.000014	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	D	0.56968	0.978	B	0.38106	0.265	T	0.29212	-1.0019	10	0.59425	D	0.04	.	1.9888	0.03442	0.3634:0.3547:0.1773:0.1047	.	5	P31944	CASPE_HUMAN	W	5	ENSP00000393417:R5W;ENSP00000221740:R5W	ENSP00000221740:R5W	R	+	1	2	CASP14	15024075	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.245000	0.18142	0.082000	0.17018	0.491000	0.48974	CGG		0.502	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15163075	C	T	15163075	3	4	21	1	0	0	0	0	1	0	0	0	2676	759	27	1	15	1	CASP14	19	15163075	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10		15163075	43965908	53	1951										
FAM129C	199786	hgsc.bcm.edu	37	chr19	17654358	17654358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	caaatcggacagcgggttggCgcagaggaggttcatccgag	16	9	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr19:17654358C>T	ENST00000335393.4	+	13	1703	c.1565C>T	c.(1564-1566)gCg>gTg	p.A522V	FAM129C_ENST00000595684.1_Missense_Mutation_p.A522V|FAM129C_ENST00000599124.1_Intron|FAM129C_ENST00000599164.1_Missense_Mutation_p.A491V|FAM129C_ENST00000449408.2_Missense_Mutation_p.A248V|FAM129C_ENST00000352727.3_Intron|FAM129C_ENST00000601861.1_Missense_Mutation_p.A491V|FAM129C_ENST00000600871.1_Missense_Mutation_p.A468V|FAM129C_ENST00000332386.5_Missense_Mutation_p.A522V|FAM129C_ENST00000300971.2_Missense_Mutation_p.A522V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	522								p.A522V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						AGCGGGTTGGCGCAGAGGAGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											104	91	95					19																	17654358		2203	4300	6503	17515358	SO:0001583	missense	199786			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1565C>T	19.37:g.17654358C>T	ENSP00000335040:p.Ala522Val		17515358	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	.	.	.	.	.	.	.	.	.	.	c	4.310	0.056751	0.08339	.	.	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000300971;ENST00000449408;ENST00000435646	T;T;T;T	0.19394	2.5;2.53;2.26;2.15	5.01	3.94	0.45596	.	0.346122	0.24742	N	0.035962	T	0.14227	0.0344	L	0.43923	1.385	0.09310	N	1	P;P;P;P;P	0.52170	0.695;0.951;0.951;0.918;0.883	B;B;B;B;B	0.40134	0.177;0.242;0.32;0.185;0.241	T	0.12344	-1.0551	10	0.02654	T	1	-13.7759	11.2789	0.49181	0.0:0.8152:0.1848:0.0	.	468;522;522;248;522	E7ENP6;Q86XR2;Q86XR2-3;B4DNU3;Q86XR2-2	.;NIBL2_HUMAN;.;.;.	V	522;522;522;248;468	ENSP00000335040:A522V;ENSP00000333447:A522V;ENSP00000300971:A522V;ENSP00000394929:A248V	ENSP00000300971:A522V	A	+	2	0	FAM129C	17515358	0.000000	0.05858	0.001000	0.08648	0.131000	0.20780	-0.235000	0.09016	1.065000	0.40693	0.306000	0.20318	GCG		0.572	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		T	17654358	C	T	17654358	3	4	21	1	0	0	0	0	1	0	0	0	5454	768	27	1	1615	1	FAM129C	19	17654358	Missense_Mutation	SNP	C	TCGA-AG-3586-01A-02W-0831-10	2491283	17654358	41474625	54	1952										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38590710	38590710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ccctggagtatgtcatccccGagctcaacatccactgcctg	8	16	2	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr19:38590710G>A	ENST00000222345.6	+	5	2283	c.1774G>A	c.(1774-1776)Gag>Aag	p.E592K		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	592					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)	p.E592K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGTCATCCCCGAGCTCAACAT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	61	64					19																	38590710		2203	4300	6503	43282550	SO:0001583	missense	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1774G>A	19.37:g.38590710G>A	ENSP00000222345:p.Glu592Lys		43282550	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	G	36	5.895053	0.97074	.	.	ENSG00000105738	ENST00000222345	D	0.94417	-3.42	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.93275	0.7857	M	0.73372	2.23	0.80722	D	1	P	0.38078	0.617	B	0.31101	0.124	D	0.93298	0.6674	10	0.62326	D	0.03	-41.2177	19.012	0.92877	0.0:0.0:1.0:0.0	.	592	O60292	SI1L3_HUMAN	K	592	ENSP00000222345:E592K	ENSP00000222345:E592K	E	+	1	0	SIPA1L3	43282550	1.000000	0.71417	0.968000	0.41197	0.918000	0.54935	9.692000	0.98682	2.797000	0.96272	0.561000	0.74099	GAG		0.642	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		A	38590710	G	A	38590710	3	1	21	1	0	0	0	0	1	0	0	0	14368	1059	37	1	1784	1	SIPA1L3	19	38590710	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	20936352	38590710	20538273	55	1953										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45490670	45490670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	agcagtcagatgaggagcagGactcggtgaaggtgagtgcg	18	6	1	4			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr19:45490670G>T	ENST00000337392.5	+	8	1177	c.1027G>T	c.(1027-1029)Gac>Tac	p.D343Y	CLPTM1_ENST00000546079.1_Missense_Mutation_p.D241Y|CLPTM1_ENST00000541297.2_Missense_Mutation_p.D329Y	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	343					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.D343Y(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		TGAGGAGCAGGACTCGGTGAA	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	19											49	45	47					19																	45490670		2203	4300	6503	50182510	SO:0001583	missense	1209			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1027G>T	19.37:g.45490670G>T	ENSP00000336994:p.Asp343Tyr		50182510	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013476	0.75161	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	4.51	4.51	0.55191	.	0.109050	0.64402	D	0.000012	D	0.85703	0.5758	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.89525	0.3781	9	0.87932	D	0	-30.5248	14.8528	0.70309	0.0:0.0:1.0:0.0	.	329;343;343	F5H8J3;B3KQH2;O96005	.;.;CLPT1_HUMAN	Y	241;329;343;343	.	ENSP00000336994:D343Y	D	+	1	0	CLPTM1	50182510	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	8.953000	0.93041	2.357000	0.79964	0.650000	0.86243	GAC		0.632	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		T	45490670	G	T	45490670	3	4	21	1	0	0	0	0	1	0	0	0	3560	1174	41	2	1057	2	CLPTM1	19	45490670	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	6899960	45490670	13638313	56	1954										
ZNF133	7692	hgsc.bcm.edu	37	chr20	18296626	18296626	+	Silent	SNP	T	T	A													0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tcccaccagaggacgcactcTggggagaagccctacgcctg							TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr20:18296626T>A	ENST00000316358.4	+	4	1228	c.1131T>A	c.(1129-1131)tcT>tcA	p.S377S	RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000377671.3_Silent_p.S376S|ZNF133_ENST00000538547.1_Silent_p.S282S|ZNF133_ENST00000402618.2_Silent_p.S314S|ZNF133_ENST00000396026.3_Silent_p.S380S|ZNF133_ENST00000535822.1_Silent_p.S282S|ZNF133_ENST00000401790.1_Silent_p.S377S	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	377					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S376S(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GGACGCACTCTGGGGAGAAGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	20											65	62	63					20																	18296626		2203	4300	6503	18244626	SO:0001819	synonymous_variant	7692			AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"Zinc fingers, C2H2-type", "-"	12917	protein-coding gene	gene with protein product		604075	"zinc finger protein 150 (pHZ-66)", "zinc finger protein 133 (clone pHZ-13)"	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1131T>A	20.37:g.18296626T>A			18244626	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																					0.582	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434		A	18296626	T	A	18296626	2	1	21	1	0	0	0	0	0	0	0	1	17762	1567	55	5		5	ZNF133	20	18296626	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10		18296626	44728894	57	1955	10	2								
ZNF133	7692	hgsc.bcm.edu	37	chr20	18296629	18296629	+	Silent	SNP	G	G	C													0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	caccagaggacgcactctggGgagaagccctacgcctgcaa							TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr20:18296629G>C	ENST00000316358.4	+	4	1231	c.1134G>C	c.(1132-1134)ggG>ggC	p.G378G	RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000377671.3_Silent_p.G377G|ZNF133_ENST00000538547.1_Silent_p.G283G|ZNF133_ENST00000402618.2_Silent_p.G315G|ZNF133_ENST00000396026.3_Silent_p.G381G|ZNF133_ENST00000535822.1_Silent_p.G283G|ZNF133_ENST00000401790.1_Silent_p.G378G	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	378					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G377G(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						CGCACTCTGGGGAGAAGCCCT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	20											66	63	64					20																	18296629		2203	4300	6503	18244629	SO:0001819	synonymous_variant	7692			AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"Zinc fingers, C2H2-type", "-"	12917	protein-coding gene	gene with protein product		604075	"zinc finger protein 150 (pHZ-66)", "zinc finger protein 133 (clone pHZ-13)"	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1134G>C	20.37:g.18296629G>C			18244629	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																					0.577	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434		C	18296629	G	C	18296629	2	2	21	1	0	0	0	0	0	0	0	1	17762	1219	43	5		5	ZNF133	20	18296629	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	3	18296629	44728891	58	1956	10	2								
SALL4	57167	hgsc.bcm.edu	37	chr20	50407573	50407573	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gaaagattctgaggtagcccTacagaggtggttacaaggac	13	7	1	3			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr20:50407573T>C	ENST00000217086.4	-	2	1560	c.1449A>G	c.(1447-1449)gtA>gtG	p.V483V	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	483					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V483V(1)		endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GAGGTAGCCCTACAGAGGTGG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	20											97	103	101					20																	50407573		2203	4299	6502	49840980	SO:0001819	synonymous_variant	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1449A>G	20.37:g.50407573T>C			49840980	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.557	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			C	50407573	T	C	50407573	2	2	21	1	0	0	0	0	0	0	0	1	13850	1509	53	4		4	SALL4	20	50407573	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10	32110944	50407573	12617947	59	1957										
SIM2	6493	hgsc.bcm.edu	37	chr21	38092190	38092190	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cacgatgagatgaccgctgtCctcacggcccaccagccgct	10	17	1	2			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr21:38092190C>T	ENST00000290399.6	+	4	1030	c.417C>T	c.(415-417)gtC>gtT	p.V139V	SIM2_ENST00000430056.3_Silent_p.V139V	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	139	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.V139V(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						TGACCGCTGTCCTCACGGCCC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	21											81	81	81					21																	38092190		2203	4300	6503	37014060	SO:0001819	synonymous_variant	6493				CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"Basic helix-loop-helix proteins"	10883	protein-coding gene	gene with protein product	"transcription factor SIM2"	600892	"single-minded (Drosophila) homolog 2", "single-minded homolog 2 (Drosophila)"	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.417C>T	21.37:g.38092190C>T			37014060	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.424142	0.25639	.	.	ENSG00000159263	ENST00000431229	.	.	.	4.93	-1.31	0.09230	.	.	.	.	.	T	0.42854	0.1221	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31194	-0.9952	4	.	.	.	.	3.4661	0.07550	0.2175:0.2659:0.4057:0.1109	.	.	.	.	S	77	.	.	P	+	1	0	SIM2	37014060	0.001000	0.12720	0.837000	0.33122	0.994000	0.84299	-2.206000	0.01231	0.082000	0.17018	0.655000	0.94253	CCT		0.512	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		T	38092190	C	T	38092190	2	4	21	1	0	0	0	0	0	0	0	1	14361	842	30	3		3	SIM2	21	38092190	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10		38092190	10037705	60	1958										
LARGE	9215	hgsc.bcm.edu	37	chr22	34022287	34022287	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cggctggcattgtatccggcGcagacaatagcaacgtggat	13	10	0	1	rs201977889		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr22:34022287G>A	ENST00000354992.2	-	5	1003	c.432C>T	c.(430-432)tgC>tgT	p.C144C	LARGE_ENST00000337431.2_Silent_p.C144C|LARGE_ENST00000397394.2_Silent_p.C144C|LARGE_ENST00000437602.2_Silent_p.C144C|LARGE_ENST00000402320.1_Silent_p.C144C	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	144					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.C144C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TGTATCCGGCGCAGACAATAG	0.532																																					Colon(70;397 1175 4573 19089 45288)											1	Substitution - coding silent(1)	large_intestine(1)	22						G	,	0,4406		0,0,2203	100	80	87		432,432	-0.6	1	22		87	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,	144/757,144/757	34022287	3,13003	2203	4300	6503	32352287	SO:0001819	synonymous_variant	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.432C>T	22.37:g.34022287G>A			32352287	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																				0.532	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	34022287	G	A	34022287	2	1	21	1	0	0	0	0	0	0	0	1	8649	1079	38	1		1	LARGE	22	34022287	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10		34022287	17282279	61	1959										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40415324	40415324	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tgtcaggacctgcagctcacTgacttccggattcgggtaag	12	11	2	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr22:40415324T>G	ENST00000333407.6	+	2	736	c.642T>G	c.(640-642)acT>acG	p.T214T	FAM83F_ENST00000473717.1_Silent_p.T46T	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	214								p.T214T(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						TGCAGCTCACTGACTTCCGGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	22											131	101	111					22																	40415324		2203	4300	6503	38745270	SO:0001819	synonymous_variant	113828				CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.642T>G	22.37:g.40415324T>G			38745270	Q96FD6	Silent	SNP	ENST00000333407.6	37	CCDS14000.2																																																																																				0.577	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		G	40415324	T	G	40415324	2	3	21	1	0	0	0	0	0	0	0	1	5657	1567	55	4		4	FAM83F	22	40415324	Silent	SNP	T	TCGA-AG-3586-01A-02W-0831-10	6393037	40415324	10889242	62	1960										
NAGA	4668	hgsc.bcm.edu	37	chr22	42466293	42466293	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ccggtgtaggtacctgtcttCagcagcatcgctctggactc	11	13	3	0			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chr22:42466293C>A	ENST00000396398.3	-	1	541	c.9G>T	c.(7-9)ctG>ctT	p.L3L	NAGA_ENST00000402937.1_Silent_p.L3L|NAGA_ENST00000403363.1_Silent_p.L3L	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	3					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)	p.L3L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						TACCTGTCTTCAGCAGCATCG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	22											239	203	216					22																	42466293		2203	4300	6503	40796239	SO:0001819	synonymous_variant	4668				CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.9G>T	22.37:g.42466293C>A			40796239		Silent	SNP	ENST00000396398.3	37	CCDS14030.1																																																																																				0.547	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1			A	42466293	C	A	42466293	2	1	21	1	0	0	0	0	0	0	0	1	10171	813	29	2		2	NAGA	22	42466293	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10	2050969	42466293	8838273	63	1961										
XAGE3	170626	hgsc.bcm.edu	37	chrX	52891653	52891653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	cagcttgtcttcatttaaacCtgtggttgcctgtcacctat	7	11	3	0	rs73206488		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chrX:52891653C>T	ENST00000346279.3	-	5	400	c.330G>A	c.(328-330)caG>caA	p.Q110Q	XAGE3_ENST00000375491.3_Silent_p.Q110Q	NM_133179.2	NP_573440.1	Q8WTP9	XAGE3_HUMAN	X antigen family, member 3	110								p.Q110Q(1)		kidney(1)|large_intestine(1)|lung(2)	4						TCATTTAAACCTGTGGTTGCC	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	X																																								52908378	SO:0001819	synonymous_variant	170626			BG354572	CCDS14347.1	Xp11.22	2010-09-27	2004-06-07	2005-01-27	ENSG00000171402	ENSG00000171402			14618	protein-coding gene	gene with protein product	"cancer/testis antigen family 12, member 3a", "cancer/testis antigen family 12, member 3b"	300740	"placenta-specific 6; G antigen, family D, 4"	PLAC6, GAGED4			Standard	NM_133179		Approved	XAGE-3, pp9012, CT12.3a, CT12.3b	uc004dre.3	Q8WTP9	OTTHUMG00000021587	ENST00000346279.3:c.330G>A	X.37:g.52891653C>T			52908378	Q5JS82|Q8WYS9	Silent	SNP	ENST00000346279.3	37	CCDS14347.1																																																																																				0.338	XAGE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056686.1	NM_133179		T	52891653	C	T	52891653	2	4	21	1	0	0	0	0	0	0	0	1	17460	680	24	3		3	XAGE3	23	52891653	Silent	SNP	C	TCGA-AG-3586-01A-02W-0831-10		52891653	102378907	64	1962										
ATP7A	538	hgsc.bcm.edu	37	chrX	77284880	77284880	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	tgctgtgatggtgggtacagGagtaggtgctcaaaatggca	16	5	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chrX:77284880G>C	ENST00000341514.6	+	15	3205	c.3050G>C	c.(3049-3051)gGa>gCa	p.G1017A	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.G939A	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	1017					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)	p.G1017A(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	GTGGGTACAGGAGTAGGTGCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	X											139	121	127					X																	77284880		2203	4296	6499	77171536	SO:0001583	missense	538			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.3050G>C	X.37:g.77284880G>C	ENSP00000345728:p.Gly1017Ala		77171536	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926982	0.92319	.	.	ENSG00000165240	ENST00000343533;ENST00000341514	D;D	0.90133	-2.62;-2.62	5.94	5.94	0.96194	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95382	0.8501	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95406	0.8494	10	0.72032	D	0.01	1.3434	19.2446	0.93896	0.0:0.0:1.0:0.0	.	1017	Q04656	ATP7A_HUMAN	A	939;1017	ENSP00000343026:G939A;ENSP00000345728:G1017A	ENSP00000345728:G1017A	G	+	2	0	ATP7A	77171536	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.497000	0.84241	0.506000	0.49869	GGA		0.463	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		C	77284880	G	C	77284880	3	2	21	1	0	0	0	0	1	0	0	0	1191	1174	41	5	3104	5	ATP7A	23	77284880	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	24393227	77284880	77985680	65	1963										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86772949	86772949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	gaaacagatcctaaggctacGctggaggtggtttagtcatc	12	8	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chrX:86772949G>A	ENST00000373119.4	+	1	198	c.53G>A	c.(52-54)cGc>cAc	p.R18H	KLHL4_ENST00000373114.4_Missense_Mutation_p.R18H	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	18						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R18H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						CTAAGGCTACGCTGGAGGTGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X											116	106	110					X																	86772949		2203	4300	6503	86659605	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.53G>A	X.37:g.86772949G>A	ENSP00000362211:p.Arg18His		86659605	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902316	0.52227	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.86769	-2.17;-2.15	5.05	4.16	0.48862	.	0.000000	0.64402	D	0.000003	D	0.83613	0.5292	L	0.47016	1.485	0.58432	D	0.999996	B;B	0.28933	0.157;0.228	B;B	0.33846	0.081;0.171	T	0.81346	-0.0974	10	0.59425	D	0.04	.	10.9597	0.47379	0.0963:0.0:0.9037:0.0	.	18;18	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	H	18	ENSP00000362211:R18H;ENSP00000362206:R18H	ENSP00000362206:R18H	R	+	2	0	KLHL4	86659605	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.672000	0.68102	1.047000	0.40274	0.513000	0.50165	CGC		0.493	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			A	86772949	G	A	86772949	3	1	21	1	0	0	0	0	1	0	0	0	8412	1087	38	1	55	1	KLHL4	23	86772949	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	9488069	86772949	68497611	66	1964										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117739300	117739300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	atatgacccatgaagatgacGttcctatcaactgcaccatg	7	11	1	4			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chrX:117739300G>A	ENST00000276202.7	+	24	2725	c.2662G>A	c.(2662-2664)Gtt>Att	p.V888I	DOCK11_ENST00000276204.6_Missense_Mutation_p.V888I	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	888					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V888I(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGAAGATGACGTTCCTATCAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											139	121	127					X																	117739300		2203	4300	6503	117623328	SO:0001583	missense	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.2662G>A	X.37:g.117739300G>A	ENSP00000276202:p.Val888Ile		117623328	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.535761	0.27475	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.69806	-0.43;-0.43	5.43	5.43	0.79202	.	0.119735	0.56097	D	0.000022	T	0.47358	0.1441	N	0.25060	0.705	0.47374	D	0.999409	P;P	0.40266	0.71;0.71	B;B	0.28385	0.089;0.089	T	0.49643	-0.8918	10	0.13470	T	0.59	-7.932	17.4229	0.87519	0.0:0.0:1.0:0.0	.	888;888	A6NIW2;Q5JSL3	.;DOC11_HUMAN	I	888	ENSP00000276204:V888I;ENSP00000276202:V888I	ENSP00000276202:V888I	V	+	1	0	DOCK11	117623328	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	4.283000	0.58977	2.415000	0.81967	0.600000	0.82982	GTT		0.348	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117739300	G	A	117739300	3	1	21	1	0	0	0	0	1	0	0	0	4697	1145	40	1	2756	1	DOCK11	23	117739300	Missense_Mutation	SNP	G	TCGA-AG-3586-01A-02W-0831-10	30966351	117739300	37531260	67	1965										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904519	144904519	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.434018567639257	0	0.503461538461539	0.454545454545454	1	0	ttagacctcagggggaatagGctaaaagtaatgccttttgc	11	7	1	1			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	3762ec80-63f9-4e74-8691-7a9d94888b4b	2bc5cda0-9b7d-4e3f-be66-a6711ac6aa51	g.chrX:144904519G>A	ENST00000370490.1	+	1	4831	c.576G>A	c.(574-576)agG>agA	p.R192R	SLITRK2_ENST00000447897.2_Silent_p.R192R|SLITRK2_ENST00000434188.2_Silent_p.R192R|SLITRK2_ENST00000413937.2_Silent_p.R192R|SLITRK2_ENST00000428560.2_Silent_p.R192R			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	192					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.R192S(1)|p.R192R(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGGAATAGGCTAAAAGTAA	0.473																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	X											146	125	132					X																	144904519		2203	4300	6503	144712211	SO:0001819	synonymous_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.576G>A	X.37:g.144904519G>A			144712211	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																				0.473	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144904519	G	A	144904519	2	1	21	1	0	0	0	0	0	0	0	1	14780	1194	42	3		3	SLITRK2	23	144904519	Silent	SNP	G	TCGA-AG-3586-01A-02W-0831-10	27165219	144904519	10366041	68	1966										
DIRAS3	9077	hgsc.bcm.edu	37	chr1	68512353	68512353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gggcatctgggatttcttctCgggctcctggaggccggtgg	17	10	3	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:68512353C>T	ENST00000370981.1	-	4	1264	c.628G>A	c.(628-630)Gag>Aag	p.E210K	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Missense_Mutation_p.E210K			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	210					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E210K(1)|p.E210Q(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCTTCTCGGGCTCCTGG	0.517																																																2	Substitution - Missense(2)	cervix(1)|large_intestine(1)	1											118	120	119					1																	68512353		2203	4300	6503	68284941	SO:0001583	missense	9077			U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"ras homolog gene family, member I"	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.628G>A	1.37:g.68512353C>T	ENSP00000360020:p.Glu210Lys		68284941	B3KMP3	Missense_Mutation	SNP	ENST00000370981.1	37	CCDS641.1	.	.	.	.	.	.	.	.	.	.	C	7.214	0.596096	0.13875	.	.	ENSG00000162595	ENST00000370981;ENST00000395201	T;T	0.72725	-0.68;-0.68	4.66	-6.76	0.01732	.	.	.	.	.	T	0.15349	0.0370	N	0.02539	-0.55	0.09310	N	1	B	0.21753	0.06	B	0.15870	0.014	T	0.35325	-0.9793	9	0.08599	T	0.76	.	11.8348	0.52316	0.0:0.6059:0.141:0.2531	.	210	O95661	DIRA3_HUMAN	K	210	ENSP00000360020:E210K;ENSP00000378627:E210K	ENSP00000360020:E210K	E	-	1	0	DIRAS3	68284941	0.926000	0.31397	0.000000	0.03702	0.002000	0.02628	0.746000	0.26275	-0.807000	0.04393	-0.171000	0.13296	GAG		0.517	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675		T	68512353	C	T	68512353	3	4	22	1	0	0	0	0	1	0	0	0	4543	893	31	1	65	1	DIRAS3	1	68512353	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		68512353	180738268	1	1967										
TTLL7	79739	hgsc.bcm.edu	37	chr1	84394906	84394906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cagttccaaagcttggggctCggttaatctgaaatttacaa	9	8	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:84394906C>T	ENST00000260505.8	-	10	1432	c.1055G>A	c.(1054-1056)cGa>cAa	p.R352Q	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	352	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)	p.R352Q(1)		kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		GCTTGGGGCTCGGTTAATCTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											104	97	99					1																	84394906		2202	4298	6500	84167494	SO:0001583	missense	79739			AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1055G>A	1.37:g.84394906C>T	ENSP00000260505:p.Arg352Gln		84167494	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	37	CCDS690.2	.	.	.	.	.	.	.	.	.	.	C	35	5.433541	0.96150	.	.	ENSG00000137941	ENST00000260505;ENST00000370704;ENST00000370703	T	0.07800	3.16	5.11	5.11	0.69529	.	0.068061	0.64402	D	0.000008	T	0.15349	0.0370	M	0.63428	1.95	0.58432	D	0.999998	D	0.76494	0.999	P	0.60173	0.87	T	0.00738	-1.1587	10	0.41790	T	0.15	.	17.1161	0.86689	0.0:1.0:0.0:0.0	.	352	Q6ZT98	TTLL7_HUMAN	Q	352;129;352	ENSP00000260505:R352Q	ENSP00000260505:R352Q	R	-	2	0	TTLL7	84167494	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.330000	0.79181	2.538000	0.85594	0.650000	0.86243	CGA		0.348	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		T	84394906	C	T	84394906	3	4	22	1	0	0	0	0	1	0	0	0	16772	884	31	1	1656	1	TTLL7	1	84394906	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	15882553	84394906	164855715	2	1968										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060545	111060545	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gctggggcagaccacgaaccGgagcaccagctcgaaggtga	15	12	0	2	rs371836114		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:111060545G>T	ENST00000369771.2	-	1	1252	c.865C>A	c.(865-867)Cgg>Agg	p.R289R		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	289					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.R289R(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	ACCACGAACCGGAGCACCAGC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											147	123	131					1																	111060545		2203	4300	6503	110862068	SO:0001819	synonymous_variant	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.865C>A	1.37:g.111060545G>T			110862068		Silent	SNP	ENST00000369771.2	37	CCDS826.1																																																																																				0.502	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060545	G	T	111060545	2	4	22	1	0	0	0	0	0	0	0	1	8023	1115	39	2		2	KCNA10	1	111060545	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10	26665639	111060545	138190076	3	1969										
DCST2	127579	hgsc.bcm.edu	37	chr1	155002999	155002999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cagcttcatgctgacagcctCgtggaggtccatggctacct	11	13	1	1	rs149729324		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:155002999C>T	ENST00000368424.3	-	6	986	c.928G>A	c.(928-930)Gag>Aag	p.E310K	DCST2_ENST00000295536.5_Missense_Mutation_p.E310K	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	310						integral component of membrane (GO:0016021)		p.E310K(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	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)			CTGACAGCCTCGTGGAGGTCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	LYS/GLU	1,4405		0,1,2202	71	55	61		928	5.4	0.9	1	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DCST2	NM_144622.2	56	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	310/774	155002999	2,13004	2203	4300	6503	153269623	SO:0001583	missense	127579			AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.928G>A	1.37:g.155002999C>T	ENSP00000357409:p.Glu310Lys		153269623	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	C	12.71	2.019604	0.35606	2.27E-4	1.16E-4	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.24151	1.87;1.92	5.38	5.38	0.77491	.	0.268647	0.33875	N	0.004467	T	0.09024	0.0223	L	0.34521	1.04	0.42341	D	0.992333	B	0.29671	0.254	B	0.19946	0.027	T	0.08126	-1.0737	10	0.14252	T	0.57	-16.5965	16.0404	0.80679	0.0:1.0:0.0:0.0	.	310	Q5T1A1	DCST2_HUMAN	K	310	ENSP00000357409:E310K;ENSP00000295536:E310K	ENSP00000295536:E310K	E	-	1	0	DCST2	153269623	0.997000	0.39634	0.929000	0.37066	0.401000	0.30781	5.077000	0.64419	2.531000	0.85337	0.655000	0.94253	GAG		0.597	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		T	155002999	C	T	155002999	3	4	22	1	0	0	0	0	1	0	0	0	4309	893	31	1	1433	1	DCST2	1	155002999	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	43942454	155002999	94247622	4	1970										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155920267	155920267	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	atccaggcggtcagtgcctcGgctgggctgtggacagtggg	18	10	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:155920267G>A	ENST00000361247.4	-	21	2809	c.2710C>T	c.(2710-2712)Cga>Tga	p.R904*	ARHGEF2_ENST00000313667.4_Nonsense_Mutation_p.R903*|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000462460.2_Nonsense_Mutation_p.R949*|ARHGEF2_ENST00000368315.4_Nonsense_Mutation_p.R905*|ARHGEF2_ENST00000368316.1_Nonsense_Mutation_p.R876*|ARHGEF2_ENST00000313695.7_Nonsense_Mutation_p.R876*	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	904					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R876*(1)		breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCAGTGCCTCGGCTGGGCTGT	0.597																																					Melanoma(178;35 2768 6610 28839)											1	Substitution - Nonsense(1)	large_intestine(1)	1											62	56	58					1																	155920267		2203	4300	6503	154186891	SO:0001587	stop_gained	9181			AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.2710C>T	1.37:g.155920267G>A	ENSP00000354837:p.Arg904*		154186891	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Nonsense_Mutation	SNP	ENST00000361247.4	37	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	40	8.396271	0.98794	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	.	.	.	5.45	5.45	0.79879	.	0.000000	0.36519	N	0.002552	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3685	14.657	0.68841	0.0:0.0:1.0:0.0	.	.	.	.	X	876;904;905;876;903	.	ENSP00000314787:R903X	R	-	1	2	ARHGEF2	154186891	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.479000	0.35453	2.838000	0.97847	0.655000	0.94253	CGA		0.597	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		A	155920267	G	A	155920267	4	1	22	1	0	0	0	0	0	1	0	0	903	1124	39	1	258	1	ARHGEF2	1	155920267	Nonsense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	917268	155920267	93330354	5	1971										
ACTN2	88	hgsc.bcm.edu	37	chr1	236902652	236902652	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tggctggagaaccggactccCgagaagaccatgcaagccat	12	12	0	3	rs145411160		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr1:236902652C>T	ENST00000366578.4	+	10	1093	c.927C>T	c.(925-927)ccC>ccT	p.P309P	ACTN2_ENST00000546208.1_Intron|ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Silent_p.P309P	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	309					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)	p.P309P(1)		endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	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)			ACCGGACTCCCGAGAAGACCA	0.567													C|||	1	0.000199681	8e-04	0	5008	,	,		17396	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						C		7,4399	12.9+/-30.5	0,7,2196	111	112	112		927	-8.2	1	1	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous	ACTN2	NM_001103.2		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		309/895	236902652	7,12999	2203	4300	6503	234969275	SO:0001819	synonymous_variant	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.927C>T	1.37:g.236902652C>T			234969275	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																				0.567	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		T	236902652	C	T	236902652	2	4	22	1	0	0	0	0	0	0	0	1	205	639	23	1		1	ACTN2	1	236902652	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10	80982385	236902652	12347969	6	1972										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24535212	24535212	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tggagaactcttgctgatccAtcttcccatccttgtttagg	8	11	2	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr2:24535212A>T	ENST00000355123.4	-	5	664	c.221T>A	c.(220-222)aTg>aAg	p.M74K	ITSN2_ENST00000361999.3_Missense_Mutation_p.M74K|ITSN2_ENST00000406921.3_Missense_Mutation_p.M74K|ITSN2_ENST00000407704.1_5'UTR	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	74	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.M73K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCTGATCCATCTTCCCATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											203	167	179					2																	24535212		2203	4300	6503	24388716	SO:0001583	missense	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.221T>A	2.37:g.24535212A>T	ENSP00000347244:p.Met74Lys		24388716	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.508898	0.85282	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011;ENST00000443927	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.07	5.07	0.68467	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.44902	U	0.000410	T	0.56775	0.2008	M	0.79614	2.46	0.80722	D	1	D;D;D;P	0.76494	0.999;0.999;0.999;0.915	D;D;D;D	0.79108	0.984;0.992;0.992;0.937	T	0.62397	-0.6863	10	0.87932	D	0	.	14.9724	0.71243	1.0:0.0:0.0:0.0	.	74;74;74;74	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	K	74;74;74;73;74;74;60	ENSP00000354561:M74K;ENSP00000347244:M74K;ENSP00000370250:M74K;ENSP00000384499:M74K;ENSP00000391224:M74K;ENSP00000391715:M60K	ENSP00000347244:M74K	M	-	2	0	ITSN2	24388716	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.737000	0.91562	2.266000	0.75297	0.533000	0.62120	ATG		0.453	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		T	24535212	A	T	24535212	3	4	22	1	0	0	0	0	1	0	0	0	7948	217	8	5	5067	5	ITSN2	2	24535212	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10		24535212	218664161	7	1973										
CAPG	822	hgsc.bcm.edu	37	chr2	85622746	85622746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gctccttctcattcgcttttCgccctagatcataggaagga	8	12	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr2:85622746C>T	ENST00000409921.1	-	9	917	c.851G>A	c.(850-852)cGa>cAa	p.R284Q	CAPG_ENST00000483659.1_5'UTR|CAPG_ENST00000263867.4_Missense_Mutation_p.R299Q|CAPG_ENST00000409724.1_Missense_Mutation_p.R299Q|CAPG_ENST00000409670.1_Missense_Mutation_p.R299Q			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R299Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						ATTCGCTTTTCGCCCTAGATC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											35	33	34					2																	85622746		2203	4300	6503	85476257	SO:0001583	missense	822			M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"macrophage capping protein"	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.851G>A	2.37:g.85622746C>T	ENSP00000387063:p.Arg284Gln		85476257	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	37	CCDS58715.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.055063	0.36277	.	.	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000453973;ENST00000409921;ENST00000409670;ENST00000409724	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.68	3.87	0.44632	Gelsolin domain (1);	0.284093	0.32736	N	0.005719	T	0.31295	0.0792	L	0.35288	1.05	0.09310	N	1	B;B;P	0.49185	0.019;0.018;0.92	B;B;B	0.29267	0.013;0.003;0.1	T	0.39292	-0.9621	10	0.87932	D	0	.	7.6992	0.28613	0.0:0.8143:0.0:0.1857	.	278;284;299	B4DU58;B8ZZS7;P40121	.;.;CAPG_HUMAN	Q	278;299;54;284;299;299	ENSP00000263867:R299Q;ENSP00000397381:R54Q;ENSP00000387063:R284Q;ENSP00000386315:R299Q;ENSP00000386965:R299Q	ENSP00000263867:R299Q	R	-	2	0	CAPG	85476257	0.001000	0.12720	0.988000	0.46212	0.141000	0.21300	1.223000	0.32527	1.406000	0.46857	0.491000	0.48974	CGA		0.532	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747		T	85622746	C	T	85622746	3	4	22	1	0	0	0	0	1	0	0	0	2627	884	31	1	158	1	CAPG	2	85622746	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	61087534	85622746	157576627	8	1974										
RIF1	55183	hgsc.bcm.edu	37	chr2	152322564	152322564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctggtctcctttggcttctcCgtctacgagcattttaaaga	8	11	3	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr2:152322564C>T	ENST00000243326.5	+	29	7013	c.6530C>T	c.(6529-6531)cCg>cTg	p.P2177L	RIF1_ENST00000453091.2_Missense_Mutation_p.P2177L|RIF1_ENST00000430328.2_Missense_Mutation_p.P2177L|RIF1_ENST00000428287.2_Missense_Mutation_p.P2177L|RIF1_ENST00000444746.2_Missense_Mutation_p.P2177L			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.P2177L(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTGGCTTCTCCGTCTACGAGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											79	77	78					2																	152322564		2203	4300	6503	152030810	SO:0001583	missense	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.6530C>T	2.37:g.152322564C>T	ENSP00000243326:p.Pro2177Leu		152030810	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222962	0.95139	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.69926	-0.23;-0.44;-0.44;-0.23;-0.44	5.9	5.9	0.94986	.	0.096271	0.64402	D	0.000001	T	0.80909	0.4714	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.81138	-0.1069	10	0.87932	D	0	-14.5893	19.874	0.96863	0.0:1.0:0.0:0.0	.	2177;2177	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	L	2177	ENSP00000390181:P2177L;ENSP00000414615:P2177L;ENSP00000415691:P2177L;ENSP00000243326:P2177L;ENSP00000416123:P2177L	ENSP00000243326:P2177L	P	+	2	0	RIF1	152030810	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.151000	0.77411	2.788000	0.95919	0.650000	0.86243	CCG		0.423	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152322564	C	T	152322564	3	4	22	1	0	0	0	0	1	0	0	0	13396	652	23	1	6644	1	RIF1	2	152322564	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	66699818	152322564	90876809	9	1975										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166859191	166859191	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gcccatgatgctgaaaattaGccagaatataagacaaacca	7	9	0	4			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr2:166859191G>T	ENST00000303395.4	-	21	4074	c.4075C>A	c.(4075-4077)Cta>Ata	p.L1359I	AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.L1348I|SCN1A_ENST00000409050.1_Missense_Mutation_p.L1331I|SCN1A_ENST00000423058.2_Missense_Mutation_p.L1359I|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1359					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.L1348I(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAAATTAGCCAGAATATA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	81	81					2																	166859191		2203	4299	6502	166567437	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4075C>A	2.37:g.166859191G>T	ENSP00000303540:p.Leu1359Ile		166567437	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176811	0.78564	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.98550	-4.99;-4.99;-4.99;-4.99	5.54	4.66	0.58398	Ion transport (1);	0.000000	0.52532	D	0.000068	D	0.98760	0.9583	M	0.77103	2.36	0.58432	D	0.999996	P;D;D	0.76494	0.955;0.997;0.999	P;D;D	0.85130	0.665;0.997;0.99	D	0.99793	1.1032	10	0.87932	D	0	.	14.4334	0.67266	0.0709:0.0:0.9291:0.0	.	1348;1331;1359	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	I	1359;1359;1348;1331	ENSP00000407030:L1359I;ENSP00000303540:L1359I;ENSP00000364554:L1348I;ENSP00000386312:L1331I	ENSP00000303540:L1359I	L	-	1	2	SCN1A	166567437	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.967000	0.87967	1.473000	0.48159	0.591000	0.81541	CTA		0.383	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166859191	G	T	166859191	3	4	22	1	0	0	0	0	1	0	0	0	13951	962	34	2	1978	2	SCN1A	2	166859191	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	14536627	166859191	76340182	10	1976										
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28476708	28476708	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	attcctgggcgatccccattCaagatcatggataaaggcaa	9	10	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr3:28476708C>G	ENST00000383768.2	+	4	628	c.440C>G	c.(439-441)tCa>tGa	p.S147*	ZCWPW2_ENST00000421010.1_Nonsense_Mutation_p.S147*			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	147	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.						zinc ion binding (GO:0008270)	p.S147*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						GATCCCCATTCAAGATCATGG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											110	113	112					3																	28476708		2203	4300	6503	28451712	SO:0001587	stop_gained	152098			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.440C>G	3.37:g.28476708C>G	ENSP00000373278:p.Ser147*		28451712		Nonsense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.044880|7.044880	0.98025|0.98025	.|.	.|.	ENSG00000206559|ENSG00000206559	ENST00000428875|ENST00000383768;ENST00000421010	.|.	.|.	.|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|0.119564	.|0.38548	.|N	.|0.001654	T|.	0.72137|.	0.3423|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71902|.	-0.4452|.	3|.	.|.	.|.	.|.	-9.5709|-9.5709	16.1245|16.1245	0.81382|0.81382	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	130|147	.|.	.|.	F|S	+|+	3|2	2|0	ZCWPW2|ZCWPW2	28451712|28451712	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.954000|0.954000	0.61252|0.61252	4.220000|4.220000	0.58567|0.58567	2.879000|2.879000	0.98667|0.98667	0.650000|0.650000	0.86243|0.86243	TTC|TCA		0.363	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		G	28476708	C	G	28476708	4	3	22	1	0	0	0	0	0	1	0	0	17637	838	29	5	446	5	ZCWPW2	3	28476708	Nonsense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		28476708	169545722	11	1977										
DUSP7	1849	hgsc.bcm.edu	37	chr3	52084880	52084880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	acaggttgtggttggtgggcGtggaaaagtagagctgctca	17	5	1	1	rs201355085		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr3:52084880G>A	ENST00000495880.1	-	3	1394	c.1211C>T	c.(1210-1212)aCg>aTg	p.T404M	DUSP7_ENST00000296483.6_Missense_Mutation_p.T353M			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	404					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.T353M(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTTGGTGGGCGTGGAAAAGTA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3											152	119	130					3																	52084880		2203	4300	6503	52059920	SO:0001583	missense	1849			X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.1211C>T	3.37:g.52084880G>A	ENSP00000417183:p.Thr404Met		52059920	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	37	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	g	22.9	4.356160	0.82243	.	.	ENSG00000164086	ENST00000495880;ENST00000296483	T;T	0.02863	4.13;4.17	5.75	4.88	0.63580	.	0.048847	0.85682	N	0.000000	T	0.12178	0.0296	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.00460	-1.1726	10	0.87932	D	0	.	14.4233	0.67198	0.0715:0.0:0.9285:0.0	.	404	Q16829	DUS7_HUMAN	M	404;353	ENSP00000417183:T404M;ENSP00000296483:T353M	ENSP00000296483:T353M	T	-	2	0	DUSP7	52059920	1.000000	0.71417	0.937000	0.37676	0.813000	0.45954	9.859000	0.99545	1.448000	0.47680	-0.148000	0.13756	ACG		0.622	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947		A	52084880	G	A	52084880	3	1	22	1	0	0	0	0	1	0	0	0	4841	1145	40	1	52	1	DUSP7	3	52084880	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	23608172	52084880	145937550	12	1978										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	192994585	192994586	+	Frame_Shift_Ins	INS	-	-	C													0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ggtgagggctaccaccaaaaINSttaaaaccctccacgatgtt							TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr3:192994585_192994586insC	ENST00000342358.4	-	29	3466_3467	c.3349_3350insG	c.(3349-3351)attfs	p.I1117fs	ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	1117						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.I1117fs*24(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TACCACCAAAATTAAAACCCTC	0.327																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								194477280	SO:0001589	frameshift_variant	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.3349_3350insG	3.37:g.192994585_192994586insC	ENSP00000341942:p.Ile1117fs		194477279	Q6UWS4|Q6ZWL0	Frame_Shift_Ins	INS	ENST00000342358.4	37	CCDS33914.1																																																																																				0.327	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		C	192994586	-	C	192994585	7	5	22	1	0	1	1	0	0	0	0	0	1128	101	4	0	312	0	ATP13A5	3	192994585	Frame_Shift_Ins	INS	-	TCGA-AG-3587-01A-01W-0831-10	140909705	192994585	5027845	13	1979										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37014821	37014821	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tcattactaactcttatgaaAcagctatgcgaacagcccaa	5	11	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:37014821A>C	ENST00000282516.8	+	22	5096	c.4597A>C	c.(4597-4599)Aca>Cca	p.T1533P	NIPBL_ENST00000448238.2_Missense_Mutation_p.T1533P	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1533					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.T1533P(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			CTCTTATGAAACAGCTATGCG	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	5											143	153	150					5																	37014821		2202	4297	6499	37050578	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4597A>C	5.37:g.37014821A>C	ENSP00000282516:p.Thr1533Pro		37050578	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844797	0.71603	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.93811	-3.28;-3.29	4.83	3.65	0.41850	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	D	0.94703	0.8291	L	0.55834	1.745	0.53688	D	0.999974	D;D	0.71674	0.997;0.998	P;D	0.67548	0.897;0.952	D	0.93690	0.7006	10	0.51188	T	0.08	.	11.8808	0.52574	0.8535:0.1465:0.0:0.0	.	1533;1533	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	P	1533	ENSP00000282516:T1533P;ENSP00000406266:T1533P	ENSP00000282516:T1533P	T	+	1	0	NIPBL	37050578	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.821000	0.75272	0.782000	0.33613	0.482000	0.46254	ACA		0.318	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	37014821	A	C	37014821	3	2	22	1	0	0	0	0	1	0	0	0	10459	43	2	4	4679	4	NIPBL	5	37014821	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10		37014821	143900439	14	1980										
NNT	23530	hgsc.bcm.edu	37	chr5	43656777	43656777	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctcctgaaatctgcccctctCctactgcctggaaggcactt	7	16	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:43656777C>A	ENST00000264663.5	+	16	2537	c.2316C>A	c.(2314-2316)ctC>ctA	p.L772L	NNT_ENST00000344920.4_Silent_p.L772L|NNT_ENST00000512996.2_Silent_p.L641L	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	772					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.L772L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CTGCCCCTCTCCTACTGCCTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											164	149	154					5																	43656777		2203	4300	6503	43692534	SO:0001819	synonymous_variant	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2316C>A	5.37:g.43656777C>A			43692534	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																				0.448	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43656777	C	A	43656777	2	1	22	1	0	0	0	0	0	0	0	1	10541	842	30	2		2	NNT	5	43656777	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10	6641956	43656777	137258483	15	1981										
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	22	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	68517854	112174631	68740629	16	1982										
APC	324	hgsc.bcm.edu	37	chr5	112175207	112175207	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctaataccctgcaaatagcaGaaataaaagaaaagattgga	7	6	0	3	rs121913462		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:112175207G>T	ENST00000457016.1	+	16	4296	c.3916G>T	c.(3916-3918)Gaa>Taa	p.E1306*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1306*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1306*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1306	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1306*(25)|p.E1306K(2)|p.K1192fs*3(1)|p.?(1)|p.E1306fs*8(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCAAATAGCAGAAATAAAAGA	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Substitution - Nonsense(25)|Substitution - Missense(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(26)|pancreas(1)|soft_tissue(1)|liver(1)|skin(1)	5	GRCh37	CM077502	APC	M	rs121913462						53	55	54					5																	112175207		2202	4300	6502	112203106	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3916G>T	5.37:g.112175207G>T	ENSP00000413133:p.Glu1306*		112203106	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	37	6.245438	0.97408	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	5.73	5.73	0.89815	.	0.179091	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.6779	14.1203	0.65182	0.0727:0.0:0.9273:0.0	.	.	.	.	X	1306	.	.	E	+	1	0	APC	112203106	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.734000	0.62043	2.861000	0.98227	0.655000	0.94253	GAA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175207	G	T	112175207	4	4	22	1	0	0	0	0	0	1	0	0	763	943	33	2	3974	2	APC	5	112175207	Nonsense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	576	112175207	68740053	17	1983										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147806906	147806906	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	accagtgagcagatcaaagcCgatatgaaagcagctaggga	12	8	1	3			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:147806906C>T	ENST00000340253.5	+	15	2217	c.2049C>T	c.(2047-2049)gcC>gcT	p.A683A	CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000513826.1_Intron|FBXO38_ENST00000296701.6_Intron|FBXO38_ENST00000394370.3_Silent_p.A683A			Q6PIJ6	FBX38_HUMAN	F-box protein 38	683					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A683A(1)	ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGATCAAAGCCGATATGAAAG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	5											61	57	58					5																	147806906		2203	4300	6503	147787099	SO:0001819	synonymous_variant	81545			BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.2049C>T	5.37:g.147806906C>T			147787099	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Silent	SNP	ENST00000340253.5	37																																																																																					0.507	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		T	147806906	C	T	147806906	2	4	22	1	0	0	0	0	0	0	0	1	5765	639	23	1		1	FBXO38	5	147806906	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10	35631699	147806906	33108354	18	1984										
FAT2	2196	hgsc.bcm.edu	37	chr5	150946260	150946260	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gaccagtttgccattaaaacCagcatcagggtcagtggctg	11	10	2	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:150946260C>A	ENST00000261800.5	-	1	2245	c.2233G>T	c.(2233-2235)Ggt>Tgt	p.G745C		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	745	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G745C(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCATTAAAACCAGCATCAGGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	5											69	73	72					5																	150946260		2203	4300	6503	150926453	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2233G>T	5.37:g.150946260C>A	ENSP00000261800:p.Gly745Cys		150926453	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.535822	0.64972	.	.	ENSG00000086570	ENST00000261800	T	0.56776	0.44	5.78	4.91	0.64330	Cadherin (4);Cadherin-like (1);	0.169327	0.42053	D	0.000776	D	0.82986	0.5156	H	0.98388	4.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89649	0.3868	10	0.66056	D	0.02	.	15.0656	0.71992	0.0:0.9319:0.0:0.0681	.	745	Q9NYQ8	FAT2_HUMAN	C	745	ENSP00000261800:G745C	ENSP00000261800:G745C	G	-	1	0	FAT2	150926453	1.000000	0.71417	0.930000	0.37139	0.936000	0.57629	4.888000	0.63164	1.593000	0.50029	0.655000	0.94253	GGT		0.537	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150946260	C	A	150946260	3	1	22	1	0	0	0	0	1	0	0	0	5709	594	21	2	10908	2	FAT2	5	150946260	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	3139354	150946260	29969000	19	1985										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168620552	168620552	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gcagcttattcttgttcaggCgcctaaagaggaaagagaat	11	7	2	2	rs150636880		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:168620552C>T	ENST00000519560.1	-	4	763	c.344G>A	c.(343-345)cGc>cAc	p.R115H	SLIT3_ENST00000404867.3_Missense_Mutation_p.R115H|SLIT3_ENST00000521130.1_5'UTR|SLIT3_ENST00000332966.8_Missense_Mutation_p.R115H	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	115					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.R115H(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTGTTCAGGCGCCTAAAGAG	0.433																																					Ovarian(29;311 847 10864 17279 24903)											1	Substitution - Missense(1)	large_intestine(1)	5						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	120	113	115		344	5.5	1	5	dbSNP_134	115	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLIT3	NM_003062.2	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	115/1524	168620552	2,13004	2203	4300	6503	168553130	SO:0001583	missense	6586			AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.344G>A	5.37:g.168620552C>T	ENSP00000430333:p.Arg115His		168553130	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731929	0.89390	2.27E-4	1.16E-4	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.24538	1.85;1.85;1.85	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000002	T	0.37865	0.1019	N	0.17922	0.545	0.53688	D	0.99997	D;D	0.89917	0.999;1.0	D;D	0.80764	0.984;0.994	T	0.26780	-1.0093	10	0.87932	D	0	.	17.2915	0.87158	0.0:1.0:0.0:0.0	.	115;115	O75094-2;O75094	.;SLIT3_HUMAN	H	115	ENSP00000430333:R115H;ENSP00000332164:R115H;ENSP00000384890:R115H	ENSP00000332164:R115H	R	-	2	0	SLIT3	168553130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.033000	0.64146	2.752000	0.94435	0.655000	0.94253	CGC		0.433	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		T	168620552	C	T	168620552	3	4	22	1	0	0	0	0	1	0	0	0	14778	768	27	1	4359	1	SLIT3	5	168620552	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	17674292	168620552	12294708	20	1986										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169461457	169461457	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gccaagtcggtggagaacttCgtgaacctggtcaaaggcct	13	10	1	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:169461457C>T	ENST00000256935.8	+	35	3602	c.3522C>T	c.(3520-3522)ttC>ttT	p.F1174F	DOCK2_ENST00000540750.1_Silent_p.F235F|DOCK2_ENST00000520908.1_Silent_p.F666F|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1174	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.F1174F(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGAGAACTTCGTGAACCTGG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											110	104	106					5																	169461457		2203	4300	6503	169394035	SO:0001819	synonymous_variant	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3522C>T	5.37:g.169461457C>T			169394035	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.572	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169461457	C	T	169461457	2	4	22	1	0	0	0	0	0	0	0	1	4698	883	31	1		1	DOCK2	5	169461457	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10	840905	169461457	11453803	21	1987										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172324072	172324072	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctcaccggatttataacgacAgaagtgtaagtcatactttc	7	9	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr5:172324072A>C	ENST00000393784.3	+	3	289	c.150A>C	c.(148-150)acA>acC	p.T50T	ERGIC1_ENST00000523291.1_Silent_p.T50T|ERGIC1_ENST00000519860.1_3'UTR	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	50					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.T50T(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTATAACGACAGAAGTGTAAG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5											197	159	172					5																	172324072		2203	4300	6503	172256678	SO:0001819	synonymous_variant	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.150A>C	5.37:g.172324072A>C			172256678	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	37	CCDS34292.1																																																																																				0.502	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		C	172324072	A	C	172324072	2	2	22	1	0	0	0	0	0	0	0	1	5236	175	7	4		4	ERGIC1	5	172324072	Silent	SNP	A	TCGA-AG-3587-01A-01W-0831-10	2862615	172324072	8591188	22	1988										
CD83	9308	hgsc.bcm.edu	37	chr6	14133926	14133926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	acttttaagaaatacagagcGgagattgtcctgctgctggc	11	8	0	3			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr6:14133926G>A	ENST00000379153.3	+	4	600	c.429G>A	c.(427-429)gcG>gcA	p.A143A		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	143					defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.A143A(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				AATACAGAGCGGAGATTGTCC	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	6											135	137	137					6																	14133926		2203	4300	6503	14241905	SO:0001819	synonymous_variant	9308			Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.429G>A	6.37:g.14133926G>A			14241905	Q5THX9	Silent	SNP	ENST00000379153.3	37	CCDS4532.1																																																																																				0.358	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			A	14133926	G	A	14133926	2	1	22	1	0	0	0	0	0	0	0	1	3047	1103	39	1		1	CD83	6	14133926	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10		14133926	156981141	23	1989										
GPR115	221393	hgsc.bcm.edu	37	chr6	47680271	47680271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	agaaacaacatctggaaataTtgcatttatagtggagttat	8	4	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr6:47680271T>C	ENST00000283303.2	+	5	737	c.479T>C	c.(478-480)aTt>aCt	p.I160T	RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Missense_Mutation_p.I217T|GPR115_ENST00000327753.3_Missense_Mutation_p.I160T	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	160					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I160T(1)		NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TCTGGAAATATTGCATTTATA	0.338																																					GBM(22;431 510 9010 26644 32828)											1	Substitution - Missense(1)	large_intestine(1)	6											93	95	94					6																	47680271		2203	4300	6503	47788230	SO:0001583	missense	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.479T>C	6.37:g.47680271T>C	ENSP00000283303:p.Ile160Thr		47788230	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Missense_Mutation	SNP	ENST00000283303.2	37	CCDS4922.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192629	0.78902	.	.	ENSG00000153294	ENST00000371220;ENST00000327753;ENST00000283303	T;T;T	0.43688	1.15;0.94;0.94	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000001	T	0.57946	0.2088	M	0.79258	2.445	0.36953	D	0.892947	D	0.89917	1.0	D	0.91635	0.999	T	0.66677	-0.5863	10	0.87932	D	0	-21.214	13.8563	0.63529	0.0:0.0:0.0:1.0	.	160	Q8IZF3	GP115_HUMAN	T	217;160;160	ENSP00000360264:I217T;ENSP00000328319:I160T;ENSP00000283303:I160T	ENSP00000283303:I160T	I	+	2	0	GPR115	47788230	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.845000	0.62853	2.210000	0.71456	0.533000	0.62120	ATT		0.338	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		C	47680271	T	C	47680271	3	2	22	1	0	0	0	0	1	0	0	0	6652	1493	52	4	493	4	GPR115	6	47680271	Missense_Mutation	SNP	T	TCGA-AG-3587-01A-01W-0831-10	33546345	47680271	123434796	24	1990										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70239028	70239028	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ttgtagacatccaaccctatCgatgtcgctgctcggcctgg	10	13	0	1	rs200480602		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr7:70239028C>T	ENST00000342771.4	+	12	2166	c.1845C>T	c.(1843-1845)atC>atT	p.I615I	AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	615								p.I615I(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCAACCCTATCGATGTCGCTG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	7											123	98	106					7																	70239028		2203	4300	6503	69876964	SO:0001819	synonymous_variant	26053			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1845C>T	7.37:g.70239028C>T			69876964	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.277072	0.23307	.	.	ENSG00000158321	ENST00000443672	.	.	.	6.06	-1.91	0.07641	.	.	.	.	.	T	0.63593	0.2524	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62058	-0.6934	4	.	.	.	-25.5569	13.1112	0.59275	0.0:0.3717:0.0:0.6283	.	.	.	.	L	142	.	.	S	+	2	0	AUTS2	69876964	0.542000	0.26426	0.992000	0.48379	0.990000	0.78478	-0.400000	0.07241	-0.150000	0.11195	-0.136000	0.14681	TCG		0.488	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70239028	C	T	70239028	2	4	22	1	0	0	0	0	0	0	0	1	1226	874	31	1		1	AUTS2	7	70239028	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10		70239028	88899635	25	1991										
DBF4	10926	hgsc.bcm.edu	37	chr7	87536887	87536887	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aatgacttagaagaactaagGgtagatcactataaatgtaa	8	4	1	4			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr7:87536887G>A	ENST00000265728.1	+	12	1938	c.1434G>A	c.(1432-1434)agG>agA	p.R478R		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	478					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R478R(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				AAGAACTAAGGGTAGATCACT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	7											79	76	77					7																	87536887		2203	4300	6503	87374823	SO:0001819	synonymous_variant	10926			AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1434G>A	7.37:g.87536887G>A			87374823	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Silent	SNP	ENST00000265728.1	37	CCDS5611.1																																																																																				0.353	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		A	87536887	G	A	87536887	2	1	22	1	0	0	0	0	0	0	0	1	4254	1223	43	3		3	DBF4	7	87536887	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10	17297859	87536887	71601776	26	1992										
SLC26A3	1811	hgsc.bcm.edu	37	chr7	107414556	107414556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctgattgttgtccagctcttCgtcagaatcttttatggtgt	9	8	3	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr7:107414556C>T	ENST00000340010.5	-	17	2000	c.1816G>A	c.(1816-1818)Gaa>Aaa	p.E606K	SLC26A3_ENST00000422236.2_Intron	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	606	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)	p.E606K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TCCAGCTCTTCGTCAGAATCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											296	263	274					7																	107414556		2203	4300	6503	107201792	SO:0001583	missense	1811			L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1816G>A	7.37:g.107414556C>T	ENSP00000345873:p.Glu606Lys		107201792		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991506	0.54041	.	.	ENSG00000091138	ENST00000340010	D	0.93133	-3.17	6.16	6.16	0.99307	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.389798	0.33092	N	0.005298	D	0.92586	0.7645	M	0.78637	2.42	0.80722	D	1	P	0.43633	0.813	B	0.37239	0.244	D	0.90487	0.4464	10	0.14656	T	0.56	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	606	P40879	S26A3_HUMAN	K	606	ENSP00000345873:E606K	ENSP00000345873:E606K	E	-	1	0	SLC26A3	107201792	1.000000	0.71417	0.987000	0.45799	0.542000	0.35054	5.338000	0.65947	2.937000	0.99478	0.650000	0.86243	GAA		0.398	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		T	107414556	C	T	107414556	3	4	22	1	0	0	0	0	1	0	0	0	14555	893	31	1	498	1	SLC26A3	7	107414556	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	19877669	107414556	51724107	27	1993										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	148112614	148112614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	taccaacgaagcaaagggggCggagtcggcagagagcgcgg	18	9	0	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr7:148112614C>T	ENST00000361727.3	+	24	4418	c.3902C>T	c.(3901-3903)gCg>gTg	p.A1301V	CNTNAP2_ENST00000538075.1_Missense_Mutation_p.A360V|CNTNAP2_ENST00000463592.2_3'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1301					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.A1301V(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GCAAAGGGGGCGGAGTCGGCA	0.542										HNSCC(39;0.1)																																						1	Substitution - Missense(1)	large_intestine(1)	7											94	83	87					7																	148112614		2203	4300	6503	147743547	SO:0001583	missense	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3902C>T	7.37:g.148112614C>T	ENSP00000354778:p.Ala1301Val		147743547	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.259586	0.59321	.	.	ENSG00000174469	ENST00000361727;ENST00000538075	D;T	0.89196	-2.48;2.74	5.42	5.42	0.78866	.	0.158047	0.45361	D	0.000376	D	0.89015	0.6595	L	0.52573	1.65	0.34628	D	0.719271	P	0.51240	0.943	P	0.47346	0.544	D	0.92495	0.6003	10	0.51188	T	0.08	.	17.8137	0.88624	0.0:1.0:0.0:0.0	.	1301	Q9UHC6	CNTP2_HUMAN	V	1301;360	ENSP00000354778:A1301V;ENSP00000440732:A360V	ENSP00000354778:A1301V	A	+	2	0	CNTNAP2	147743547	0.997000	0.39634	0.888000	0.34837	0.428000	0.31595	3.310000	0.51911	2.534000	0.85438	0.655000	0.94253	GCG		0.542	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	148112614	C	T	148112614	3	4	22	1	0	0	0	0	1	0	0	0	3653	768	27	1	3996	1	CNTNAP2	7	148112614	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	40698058	148112614	11026049	28	1994										
ANK1	286	hgsc.bcm.edu	37	chr8	41521208	41521208	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	caatgttgccctgctcatccGtgaattgctcctctgtcacc	7	15	3	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr8:41521208G>A	ENST00000347528.4	-	40	5530	c.5447C>T	c.(5446-5448)aCg>aTg	p.T1816M	ANK1_ENST00000352337.4_Missense_Mutation_p.T1816M|ANK1_ENST00000265709.8_Missense_Mutation_p.T1857M|ANK1_ENST00000396942.1_Missense_Mutation_p.T1816M|ANK1_ENST00000457297.1_Missense_Mutation_p.T91M|RP11-930P14.1_ENST00000520418.1_RNA|RP11-930P14.1_ENST00000585088.1_RNA|ANK1_ENST00000396945.1_Intron|ANK1_ENST00000379758.2_Missense_Mutation_p.T1816M|ANK1_ENST00000522543.1_Missense_Mutation_p.T91M|RP11-930P14.1_ENST00000522388.1_RNA|ANK1_ENST00000522231.1_Missense_Mutation_p.T91M|ANK1_ENST00000314214.8_Missense_Mutation_p.T91M|ANK1_ENST00000289734.7_Missense_Mutation_p.T1816M	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1816	55 kDa regulatory domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.T1816M(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	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)			CTGCTCATCCGTGAATTGCTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	8											216	154	175					8																	41521208		2203	4300	6503	41640365	SO:0001583	missense	286			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.5447C>T	8.37:g.41521208G>A	ENSP00000339620:p.Thr1816Met		41640365	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174116	0.78452	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000457297;ENST00000396942;ENST00000352337;ENST00000522231;ENST00000522543;ENST00000314214;ENST00000265709;ENST00000348036;ENST00000335651	T;T;T;T;T;D;D;D;T	0.88277	-0.38;-0.4;-0.74;-0.36;-0.64;-1.95;-2.36;-2.33;-0.46	6.04	6.04	0.98038	.	0.116472	0.56097	D	0.000040	D	0.93220	0.7840	L	0.49513	1.565	0.53005	D	0.999967	D;P;P;D;P;P;D;D;D;D	0.89917	0.995;0.888;0.861;1.0;0.916;0.888;0.985;0.978;1.0;0.987	P;B;B;D;P;B;B;B;D;P	0.97110	0.897;0.242;0.173;0.915;0.505;0.242;0.297;0.395;1.0;0.782	D	0.93089	0.6498	10	0.72032	D	0.01	.	19.1573	0.93516	0.0:0.0:1.0:0.0	.	91;1857;1654;1816;1816;1816;970;91;91;91	Q6PK32;P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39;A0PJN8;Q53ER1;E5RFL7	.;.;.;ANK1_HUMAN;.;.;.;.;.;.	M	1816;1816;1816;91;1816;1816;91;91;91;1857;91;91	ENSP00000339620:T1816M;ENSP00000289734:T1816M;ENSP00000369082:T1816M;ENSP00000380147:T1816M;ENSP00000309131:T1816M;ENSP00000428750:T91M;ENSP00000430368:T91M;ENSP00000319123:T91M;ENSP00000265709:T1857M	ENSP00000265709:T1857M	T	-	2	0	ANK1	41640365	1.000000	0.71417	0.993000	0.49108	0.982000	0.71751	7.161000	0.77505	2.873000	0.98535	0.561000	0.74099	ACG		0.512	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41521208	G	A	41521208	3	1	22	1	0	0	0	0	1	0	0	0	620	1145	40	1	313	1	ANK1	8	41521208	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10		41521208	104842814	29	1995										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73849449	73849449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cacagagacagagagatcgcCgctgccgccgccctccgcct	11	18	0	3			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr8:73849449C>T	ENST00000523207.1	+	3	2447	c.1859C>T	c.(1858-1860)cCg>cTg	p.P620L		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	620					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.P620L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAGAGATCGCCGCTGCCGCCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	8											71	77	75					8																	73849449		2203	4300	6503	74012003	SO:0001583	missense	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1859C>T	8.37:g.73849449C>T	ENSP00000430846:p.Pro620Leu		74012003	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	6.680	0.494028	0.12702	.	.	ENSG00000182674	ENST00000523207	T	0.26067	1.76	5.04	5.04	0.67666	.	0.822792	0.09883	N	0.743415	T	0.29620	0.0739	L	0.48642	1.525	0.39033	D	0.959976	P	0.40834	0.73	B	0.38803	0.282	T	0.25433	-1.0132	10	0.35671	T	0.21	.	18.5564	0.91086	0.0:1.0:0.0:0.0	.	620	Q92953	KCNB2_HUMAN	L	620	ENSP00000430846:P620L	ENSP00000430846:P620L	P	+	2	0	KCNB2	74012003	0.162000	0.22906	0.887000	0.34795	0.068000	0.16541	2.678000	0.46900	2.602000	0.87976	0.591000	0.81541	CCG		0.602	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73849449	C	T	73849449	3	4	22	1	0	0	0	0	1	0	0	0	8034	652	23	1	1865	1	KCNB2	8	73849449	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	32328241	73849449	72514573	30	1996										
ERP44	23071	hgsc.bcm.edu	37	chr9	102784447	102784447	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tattctctcttcatcatcatCccattacgaaacaatttgag	3	11	5	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr9:102784447C>T	ENST00000262455.6	-	5	547	c.348G>A	c.(346-348)ggG>ggA	p.G116G		NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	116	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|glycoprotein metabolic process (GO:0009100)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	protein disulfide isomerase activity (GO:0003756)	p.G116G(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)	19						TCATCATCATCCCATTACGAA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	9											161	150	154					9																	102784447		2203	4300	6503	101824268	SO:0001819	synonymous_variant	23071			AB011145	CCDS35082.1	9q22.33	2011-10-19	2009-02-23	2009-02-23	ENSG00000023318	ENSG00000023318		"Protein disulfide isomerases"	18311	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 10"	609170	"thioredoxin domain containing 4 (endoplasmic reticulum)"	TXNDC4		11847130	Standard	NM_015051		Approved	KIAA0573, PDIA10	uc004bam.3	Q9BS26	OTTHUMG00000020363	ENST00000262455.6:c.348G>A	9.37:g.102784447C>T			101824268	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Silent	SNP	ENST00000262455.6	37	CCDS35082.1																																																																																				0.393	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1	XM_088476		T	102784447	C	T	102784447	2	4	22	1	0	0	0	0	0	0	0	1	5256	842	30	3		3	ERP44	9	102784447	Silent	SNP	C	TCGA-AG-3587-01A-01W-0831-10		102784447	38428984	31	1997										
FAM102A	399665	hgsc.bcm.edu	37	chr9	130716198	130716198	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cgcacacagttctcctgtacCtcctccctgtgggccagagg	10	16	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr9:130716198C>A	ENST00000373095.1	-	2	528	c.153G>T	c.(151-153)gaG>gaT	p.E51D		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	51								p.E51D(1)		breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						TCTCCTGTACCTCCTCCCTGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	9											78	69	72					9																	130716198		2203	4300	6503	129756019	SO:0001583	missense	399665				CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.153G>T	9.37:g.130716198C>A	ENSP00000362187:p.Glu51Asp		129756019	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.730204	0.69074	.	.	ENSG00000167106	ENST00000373095	T	0.40756	1.02	5.9	1.1	0.20463	.	0.099394	0.64402	D	0.000002	T	0.47967	0.1474	M	0.85542	2.76	0.80722	D	1	P	0.47484	0.896	P	0.50754	0.649	T	0.43845	-0.9366	10	0.22109	T	0.4	-32.9067	3.8517	0.08957	0.1671:0.3627:0.0:0.4702	.	51	Q5T9C2	F102A_HUMAN	D	51	ENSP00000362187:E51D	ENSP00000362187:E51D	E	-	3	2	FAM102A	129756019	0.998000	0.40836	1.000000	0.80357	0.952000	0.60782	0.684000	0.25364	0.310000	0.22990	-0.140000	0.14226	GAG		0.617	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			A	130716198	C	A	130716198	3	1	22	1	0	0	0	0	1	0	0	0	5398	680	24	2	1041	2	FAM102A	9	130716198	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	27931751	130716198	10497233	32	1998										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131346721	131346721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gaagctggccgattctctgcGgttgcagcagctcttccggg	14	12	2	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr9:131346721G>A	ENST00000372731.4	+	17	2464	c.2354G>A	c.(2353-2355)cGg>cAg	p.R785Q	SPTAN1_ENST00000358161.5_Missense_Mutation_p.R785Q|SPTAN1_ENST00000372739.3_Missense_Mutation_p.R785Q	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	785					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R785Q(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GATTCTCTGCGGTTGCAGCAG	0.557																																					NSCLC(120;833 1744 2558 35612 37579)											1	Substitution - Missense(1)	large_intestine(1)	9											49	51	50					9																	131346721		2203	4300	6503	130386542	SO:0001583	missense	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.2354G>A	9.37:g.131346721G>A	ENSP00000361816:p.Arg785Gln		130386542	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883626	0.33255	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.32272	1.46;1.46;1.46	5.63	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.17450	0.0419	N	0.16862	0.45	0.50813	D	0.999894	B;P;B;B;B	0.46142	0.114;0.873;0.008;0.007;0.077	B;B;B;B;B	0.38880	0.057;0.284;0.005;0.001;0.046	T	0.03773	-1.1005	10	0.12766	T	0.61	.	13.6241	0.62155	0.0741:0.0:0.9259:0.0	.	785;785;785;785;785	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	Q	785	ENSP00000350882:R785Q;ENSP00000361816:R785Q;ENSP00000361824:R785Q	ENSP00000350882:R785Q	R	+	2	0	SPTAN1	130386542	1.000000	0.71417	0.706000	0.30403	0.597000	0.36814	9.400000	0.97290	1.386000	0.46466	0.561000	0.74099	CGG		0.557	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131346721	G	A	131346721	3	1	22	1	0	0	0	0	1	0	0	0	15156	1116	39	1	2416	1	SPTAN1	9	131346721	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	630523	131346721	9866710	33	1999										
PHYHD1	254295	hgsc.bcm.edu	37	chr9	131702678	131702678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tcaggacgcctccttcctgtAcacggagcccctgggccggg	13	16	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr9:131702678A>G	ENST00000372592.3	+	10	1421	c.488A>G	c.(487-489)tAc>tGc	p.Y163C	RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000421063.2_Missense_Mutation_p.Y142C|PHYHD1_ENST00000308941.5_Missense_Mutation_p.T156A|PHYHD1_ENST00000353176.5_Missense_Mutation_p.Y142C	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	163							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.T156A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TCCTTCCTGTACACGGAGCCC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	9											72	76	75					9																	131702678		2203	4300	6503	130742499	SO:0001583	missense	254295			BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.488A>G	9.37:g.131702678A>G	ENSP00000361673:p.Tyr163Cys		130742499	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	37	CCDS43885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.0|25.0	4.597116|4.597116	0.87055|0.87055	.|.	.|.	ENSG00000175287|ENSG00000175287	ENST00000308941;ENST00000419872|ENST00000372592;ENST00000353176;ENST00000426694;ENST00000421063	.|D;D;D;D	.|0.90444	.|-2.67;-2.67;-2.67;-2.67	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	1.045490|.	0.07474|.	N|.	0.902729|.	D|D	0.94627|0.94627	0.8268|0.8268	.|.	.|.	.|.	0.43761|0.43761	D|D	0.996272|0.996272	P|D;D	0.51791|0.76494	0.948|0.998;0.999	P|D;D	0.47645|0.68943	0.553|0.952;0.961	D|D	0.94614|0.94614	0.7807|0.7807	8|8	0.10377|0.49607	T|T	0.69|0.09	-0.4037|-0.4037	14.3375|14.3375	0.66600|0.66600	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	156|142;163	Q5SRE7-3|Q5SRE7-2;Q5SRE7	.|.;PHYD1_HUMAN	A|C	156;21|163;142;163;142	.|ENSP00000361673:Y163C;ENSP00000340945:Y142C;ENSP00000412377:Y163C;ENSP00000409928:Y142C	ENSP00000309515:T156A|ENSP00000340945:Y142C	T|Y	+|+	1|2	0|0	PHYHD1|PHYHD1	130742499|130742499	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	7.356000|7.356000	0.79445|0.79445	1.998000|1.998000	0.58463|0.58463	0.454000|0.454000	0.30748|0.30748	ACA|TAC		0.627	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933		G	131702678	A	G	131702678	3	3	22	1	0	0	0	0	1	0	0	0	11896	391	14	4	518	4	PHYHD1	9	131702678	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10	355957	131702678	9510753	34	2000										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7773807	7773807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aggtctccactccattgctcCggaatgttcagttcaactat	7	12	3	0	rs202086391		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr10:7773807C>T	ENST00000358415.4	+	13	1661	c.1495C>T	c.(1495-1497)Cgg>Tgg	p.R499W	ITIH2_ENST00000379587.4_Missense_Mutation_p.R488W	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	499					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R499W(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TCCATTGCTCCGGAATGTTCA	0.408													C|||	1	0.000199681	8e-04	0	5008	,	,		18351	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											142	140	141					10																	7773807		2203	4300	6503	7813813	SO:0001583	missense	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1495C>T	10.37:g.7773807C>T	ENSP00000351190:p.Arg499Trp		7813813	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	17.70	3.454874	0.63290	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.11821	2.74;2.74	5.44	4.51	0.55191	.	0.100909	0.64402	D	0.000005	T	0.33789	0.0875	M	0.78049	2.395	0.38545	D	0.94931	D	0.89917	1.0	P	0.61592	0.891	T	0.28332	-1.0047	10	0.54805	T	0.06	-11.6559	12.46	0.55727	0.4824:0.5176:0.0:0.0	.	499	P19823	ITIH2_HUMAN	W	499;488	ENSP00000351190:R499W;ENSP00000368906:R488W	ENSP00000351190:R499W	R	+	1	2	ITIH2	7813813	1.000000	0.71417	0.992000	0.48379	0.934000	0.57294	3.104000	0.50306	1.235000	0.43724	0.643000	0.83706	CGG		0.408	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7773807	C	T	7773807	3	4	22	1	0	0	0	0	1	0	0	0	7925	643	23	1	1545	1	ITIH2	10	7773807	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		7773807	127760940	35	2001										
MYST4	23522	hgsc.bcm.edu	37	chr10	76735323	76735323	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	accccactcggcctggtgccAccaccaaaatcaccaccacc	5	21	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr10:76735323A>G	ENST00000287239.4	+	8	1717	c.1228A>G	c.(1228-1230)Acc>Gcc	p.T410A	KAT6B_ENST00000372714.1_Intron|KAT6B_ENST00000372725.1_Intron|KAT6B_ENST00000372724.1_Intron|KAT6B_ENST00000372711.1_Missense_Mutation_p.T410A	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	410	Negatively regulates HAT activity.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.T410A(1)									GCCTGGTGCCACCACCAAAAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	10											130	107	115					10																	76735323		2203	4300	6503	76405329	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.1228A>G	10.37:g.76735323A>G	ENSP00000287239:p.Thr410Ala		76405329	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	7.746	0.702395	0.15172	.	.	ENSG00000156650	ENST00000287239;ENST00000372711	T;T	0.76316	-1.01;-1.0	5.97	4.83	0.62350	.	0.000000	0.51477	D	0.000089	T	0.62134	0.2403	N	0.19112	0.55	0.31529	N	0.661386	B;B	0.14805	0.011;0.007	B;B	0.14023	0.01;0.004	T	0.58825	-0.7568	9	.	.	.	-2.4079	10.9408	0.47273	0.9288:0.0:0.0712:0.0	.	410;410	Q8WYB5-2;Q8WYB5	.;KAT6B_HUMAN	A	410	ENSP00000287239:T410A;ENSP00000361796:T410A	.	T	+	1	0	KAT6B	76405329	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.179000	0.58290	1.068000	0.40764	0.533000	0.62120	ACC		0.468	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76735323	A	G	76735323	3	3	22	1	0	0	0	0	1	0	0	0	10135	159	6	4	1250	4	MYST4	10	76735323	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10	68961516	76735323	58799424	36	2002										
NOC3L	64318	hgsc.bcm.edu	37	chr10	96106249	96106249	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	taaatttttttggtttattaAtgtcttctgtatcttttttc	4	4	3	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr10:96106249A>C	ENST00000371361.3	-	11	1422	c.1322T>G	c.(1321-1323)aTt>aGt	p.I441S	NOC3L_ENST00000543788.1_Missense_Mutation_p.I179S|NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.I441S	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	441					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.I441S(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				TGGTTTATTAATGTCTTCTGT	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	10											65	64	64					10																	96106249		2188	4271	6459	96096239	SO:0001583	missense	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1322T>G	10.37:g.96106249A>C	ENSP00000360412:p.Ile441Ser		96096239	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.840600	0.32513	.	.	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.13307	2.6;2.81;2.81	5.83	5.83	0.93111	.	0.164239	0.52532	D	0.000066	T	0.08802	0.0218	N	0.14661	0.345	0.38834	D	0.955914	B	0.16396	0.017	B	0.10450	0.005	T	0.21381	-1.0247	10	0.09590	T	0.72	-18.6994	15.8742	0.79148	1.0:0.0:0.0:0.0	.	441	Q8WTT2	NOC3L_HUMAN	S	179;441;441	ENSP00000437838:I179S;ENSP00000360412:I441S;ENSP00000360401:I441S	ENSP00000360401:I441S	I	-	2	0	NOC3L	96096239	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.254000	0.58798	2.236000	0.73375	0.533000	0.62120	ATT		0.259	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		C	96106249	A	C	96106249	3	2	22	1	0	0	0	0	1	0	0	0	10545	101	4	4	1124	4	NOC3L	10	96106249	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10	19370926	96106249	39428498	37	2003										
E2F8	79733	hgsc.bcm.edu	37	chr11	19252185	19252185	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cctgaaaacatacctttgttGgtcttgatagggctactggg	11	8	1	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr11:19252185G>A	ENST00000527884.1	-	8	1495	c.1263C>T	c.(1261-1263)acC>acT	p.T421T	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Silent_p.T421T	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	421					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.T421T(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TACCTTTGTTGGTCTTGATAG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	11											93	90	91					11																	19252185		2199	4293	6492	19208761	SO:0001819	synonymous_variant	79733				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1263C>T	11.37:g.19252185G>A			19208761	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Silent	SNP	ENST00000527884.1	37	CCDS7849.1																																																																																				0.388	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		A	19252185	G	A	19252185	2	1	22	1	0	0	0	0	0	0	0	1	4884	1335	47	3		3	E2F8	11	19252185	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10		19252185	115754331	38	2004										
CST6	1474	hgsc.bcm.edu	37	chr11	65780352	65780352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gatggggagcacagactgccGcaagaccagggtcactggag	16	10	1	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr11:65780352G>A	ENST00000312134.2	+	2	500	c.296G>A	c.(295-297)cGc>cAc	p.R99H		NM_001323.3	NP_001314.1	Q15828	CYTM_HUMAN	cystatin E/M	99					anatomical structure morphogenesis (GO:0009653)|epidermis development (GO:0008544)|negative regulation of endopeptidase activity (GO:0010951)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.R99H(1)		large_intestine(1)|lung(1)|ovary(1)	3						ACAGACTGCCGCAAGACCAGG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	70	76					11																	65780352		2201	4296	6497	65536928	SO:0001583	missense	1474			U62800	CCDS8126.1	11q13	2005-09-29			ENSG00000175315	ENSG00000175315			2478	protein-coding gene	gene with protein product		601891				9154125, 9099741	Standard	NM_001323		Approved		uc001ogr.3	Q15828	OTTHUMG00000166750	ENST00000312134.2:c.296G>A	11.37:g.65780352G>A	ENSP00000311313:p.Arg99His		65536928	Q540N7	Missense_Mutation	SNP	ENST00000312134.2	37	CCDS8126.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073218	0.36566	.	.	ENSG00000175315	ENST00000312134	T	0.26373	1.74	5.66	1.5	0.22942	Proteinase inhibitor I25, cystatin (2);	0.063724	0.64402	N	0.000013	T	0.22244	0.0536	M	0.62266	1.93	0.09310	N	1	P;B	0.38729	0.644;0.238	B;B	0.40165	0.321;0.062	T	0.13495	-1.0507	10	0.48119	T	0.1	-0.1923	2.0922	0.03660	0.1703:0.1558:0.513:0.161	.	99;99	Q6IBD2;Q15828	.;CYTM_HUMAN	H	99	ENSP00000311313:R99H	ENSP00000311313:R99H	R	+	2	0	CST6	65536928	0.004000	0.15560	0.023000	0.16930	0.004000	0.04260	1.098000	0.31000	0.339000	0.23719	-0.253000	0.11424	CGC		0.647	CST6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391348.1	NM_001323		A	65780352	G	A	65780352	3	1	22	1	0	0	0	0	1	0	0	0	3982	1087	38	1	302	1	CST6	11	65780352	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	46528167	65780352	69226164	39	2005										
WNK1	65125	hgsc.bcm.edu	37	chr12	936259	936259	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aaagttctaagaagctggtgCcgtcagatccttaaaggtct	10	8	3	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr12:936259C>G	ENST00000315939.6	+	3	1627	c.984C>G	c.(982-984)tgC>tgG	p.C328W	WNK1_ENST00000535572.1_Missense_Mutation_p.C328W|WNK1_ENST00000447667.2_Missense_Mutation_p.C328W|WNK1_ENST00000537687.1_Missense_Mutation_p.C328W|WNK1_ENST00000530271.2_Missense_Mutation_p.C328W	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	328	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.C328W(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GAAGCTGGTGCCGTCAGATCC	0.388																																					Colon(19;451 567 6672 12618 28860)											1	Substitution - Missense(1)	large_intestine(1)	12											137	131	133					12																	936259		2203	4300	6503	806520	SO:0001583	missense	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.984C>G	12.37:g.936259C>G	ENSP00000313059:p.Cys328Trp		806520	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.299408	0.60195	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.54	4.42	0.53409	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.73999	0.3659	M	0.62088	1.915	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.995	T	0.75007	-0.3469	10	0.87932	D	0	-7.7639	9.5683	0.39411	0.0:0.7381:0.0:0.2619	.	328;328;328	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	W	328	ENSP00000441972:C328W;ENSP00000313059:C328W;ENSP00000444465:C328W;ENSP00000392542:C328W;ENSP00000433548:C328W	ENSP00000313059:C328W	C	+	3	2	WNK1	806520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.322000	0.33689	1.008000	0.39264	0.591000	0.81541	TGC		0.388	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		G	936259	C	G	936259	3	3	22	1	0	0	0	0	1	0	0	0	17417	747	26	5	994	5	WNK1	12	936259	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		936259	132915636	40	2006										
PZP	5858	hgsc.bcm.edu	37	chr12	9310407	9310407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aagggcaatagtaacataggCggagagggtcgcttcatctt	13	7	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr12:9310407C>T	ENST00000261336.2	-	27	3353	c.3325G>A	c.(3325-3327)Gcc>Acc	p.A1109T	PZP_ENST00000539983.1_5'Flank|PZP_ENST00000381997.2_Missense_Mutation_p.A895T	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1109					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A895T(1)|p.A1109T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GTAACATAGGCGGAGAGGGTC	0.433																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											139	115	123					12																	9310407		2203	4300	6503	9201674	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3325G>A	12.37:g.9310407C>T	ENSP00000261336:p.Ala1109Thr		9201674	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831214	0.50845	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.57273	0.41;0.41	3.95	1.03	0.20045	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.176745	0.33572	N	0.004771	T	0.68824	0.3043	M	0.92507	3.315	0.27261	N	0.958621	B;D	0.69078	0.039;0.997	B;P	0.55391	0.028;0.775	T	0.64613	-0.6366	10	0.72032	D	0.01	.	8.6886	0.34254	0.0:0.7292:0.0:0.2708	.	895;1109	P20742-2;P20742	.;PZP_HUMAN	T	1109;895	ENSP00000261336:A1109T;ENSP00000371427:A895T	ENSP00000261336:A1109T	A	-	1	0	PZP	9201674	0.997000	0.39634	0.318000	0.25279	0.300000	0.27592	3.106000	0.50322	0.078000	0.16900	-0.219000	0.12488	GCC		0.433	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9310407	C	T	9310407	3	4	22	1	0	0	0	0	1	0	0	0	12906	768	27	1	1163	1	PZP	12	9310407	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	8374148	9310407	124541488	41	2007										
ENDOU	8909	hgsc.bcm.edu	37	chr12	48111365	48111365	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aactcttggcagcgggcattGcagtgacattggtggtgctt	14	8	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr12:48111365G>T	ENST00000422538.3	-	4	440	c.318C>A	c.(316-318)tgC>tgA	p.C106*	RP1-197B17.3_ENST00000547799.1_lincRNA|ENDOU_ENST00000545824.2_Nonsense_Mutation_p.C43*|ENDOU_ENST00000542202.1_5'UTR|ENDOU_ENST00000229003.3_Nonsense_Mutation_p.C65*	NM_001172439.1	NP_001165910.1	P21128	ENDOU_HUMAN	endonuclease, polyU-specific	106	SMB 2. {ECO:0000255|PROSITE- ProRule:PRU00350}.				female pregnancy (GO:0007565)|immune response (GO:0006955)|proteolysis (GO:0006508)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endoribonuclease activity (GO:0004521)|growth factor activity (GO:0008083)|manganese ion binding (GO:0030145)|polysaccharide binding (GO:0030247)|RNA binding (GO:0003723)|scavenger receptor activity (GO:0005044)|serine-type peptidase activity (GO:0008236)	p.C65*(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(3)|pancreas(1)|stomach(1)	14						AGCGGGCATTGCAGTGACATT	0.562											OREG0021752	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	12											150	144	146					12																	48111365		2203	4300	6503	46397632	SO:0001587	stop_gained	8909			M32402	CCDS8754.1, CCDS53784.1, CCDS53785.1	12q13.1	2011-08-31			ENSG00000111405	ENSG00000111405		"Serine peptidases / Serine peptidases"	14369	protein-coding gene	gene with protein product		606720				2350438, 1710108, 15755742, 18936097	Standard	NM_006025		Approved	PP11, P11, PRSS26	uc001rpu.2	P21128	OTTHUMG00000169670	ENST00000422538.3:c.318C>A	12.37:g.48111365G>T	ENSP00000397679:p.Cys106*	952	46397632	B2RBJ3|B3KQS7|B7Z6E1|Q2NKJ4	Nonsense_Mutation	SNP	ENST00000422538.3	37	CCDS53785.1	.	.	.	.	.	.	.	.	.	.	G	36	5.907925	0.97093	.	.	ENSG00000111405	ENST00000229003;ENST00000422538;ENST00000545824	.	.	.	5.26	-2.02	0.07388	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.2376	5.7931	0.18371	0.3821:0.0:0.5006:0.1173	.	.	.	.	X	65;106;43	.	ENSP00000229003:C65X	C	-	3	2	ENDOU	46397632	0.937000	0.31787	0.849000	0.33467	0.956000	0.61745	0.140000	0.16056	-0.362000	0.08113	0.563000	0.77884	TGC		0.562	ENDOU-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405352.1	NM_006025.2		T	48111365	G	T	48111365	4	4	22	1	0	0	0	0	0	1	0	0	5129	1311	46	2	942	2	ENDOU	12	48111365	Nonsense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	38800958	48111365	85740530	42	2008										
POLR3B	55703	hgsc.bcm.edu	37	chr12	106824219	106824219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tccagccatctcagtggggaAtgctgtgtccttcggacact	11	12	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr12:106824219A>G	ENST00000228347.4	+	14	1654	c.1432A>G	c.(1432-1434)Atg>Gtg	p.M478V	POLR3B_ENST00000539066.1_Missense_Mutation_p.M420V	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	478					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.M478V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						TCAGTGGGGAATGCTGTGTCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	91	94					12																	106824219		2203	4300	6503	105348349	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1432A>G	12.37:g.106824219A>G	ENSP00000228347:p.Met478Val		105348349	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230505	0.79688	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.75938	-0.98;-0.98	5.56	5.56	0.83823	RNA polymerase Rpb2, domain 3 (1);	0.000000	0.85682	D	0.000000	T	0.81973	0.4936	M	0.80508	2.5	0.80722	D	1	P	0.35575	0.51	P	0.45406	0.479	D	0.83753	0.0210	10	0.66056	D	0.02	-32.6932	15.7123	0.77641	1.0:0.0:0.0:0.0	.	478	Q9NW08	RPC2_HUMAN	V	478;478;420	ENSP00000228347:M478V;ENSP00000445721:M420V	ENSP00000228347:M478V	M	+	1	0	POLR3B	105348349	1.000000	0.71417	0.996000	0.52242	0.980000	0.70556	8.918000	0.92759	2.093000	0.63338	0.533000	0.62120	ATG		0.502	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		G	106824219	A	G	106824219	3	3	22	1	0	0	0	0	1	0	0	0	12260	101	4	4	1486	4	POLR3B	12	106824219	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10	58712854	106824219	27027676	43	2009										
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30805468	30805468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	caccatctcaaacaacagacGaactaacttctcagattcac	3	14	3	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr13:30805468G>A	ENST00000380615.3	-	7	1035	c.868C>T	c.(868-870)Cgt>Tgt	p.R290C	KATNAL1_ENST00000380617.3_Missense_Mutation_p.R290C	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1									p.R290C(2)		autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		AACAACAGACGAACTAACTTC	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	13											126	120	122					13																	30805468		2203	4300	6503	29703468	SO:0001583	missense	84056			AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"ATPases / AAA-type"	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.868C>T	13.37:g.30805468G>A	ENSP00000369989:p.Arg290Cys		29703468		Missense_Mutation	SNP	ENST00000380615.3	37	CCDS31956.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452952	0.84209	.	.	ENSG00000102781	ENST00000380615;ENST00000380617	D;D	0.94417	-3.42;-3.42	5.86	5.02	0.67125	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.98495	0.9498	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99466	1.0944	10	0.87932	D	0	-9.7106	15.1804	0.72952	0.0677:0.0:0.9323:0.0	.	290	Q9BW62	KATL1_HUMAN	C	290	ENSP00000369989:R290C;ENSP00000369991:R290C	ENSP00000369989:R290C	R	-	1	0	KATNAL1	29703468	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	9.755000	0.98912	1.486000	0.48398	0.591000	0.81541	CGT		0.418	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		A	30805468	G	A	30805468	3	1	22	1	0	0	0	0	1	0	0	0	8006	1058	37	1	624	1	KATNAL1	13	30805468	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10		30805468	84364410	44	2010										
RHOJ	57381	hgsc.bcm.edu	37	chr14	63671738	63671738	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	acgccttcccagaggaatacGtgcccactgtgtttgaccac	9	14	0	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr14:63671738G>A	ENST00000316754.3	+	1	613	c.151G>A	c.(151-153)Gtg>Atg	p.V51M	RHOJ_ENST00000555125.1_Missense_Mutation_p.V51M|RHOJ_ENST00000557133.1_3'UTR	NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	51					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.V51M(3)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		AGAGGAATACGTGCCCACTGT	0.557																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	14											110	89	96					14																	63671738		2203	4300	6503	62741491	SO:0001583	missense	57381			AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"RAS-like, family 7, member B", "ras homolog gene family, member J"	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.151G>A	14.37:g.63671738G>A	ENSP00000316729:p.Val51Met		62741491	Q96KC1	Missense_Mutation	SNP	ENST00000316754.3	37	CCDS9757.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.672079	0.67928	.	.	ENSG00000126785	ENST00000316754;ENST00000555125	T;T	0.77229	-1.08;-1.08	4.41	4.41	0.53225	Small GTP-binding protein domain (1);	0.082559	0.49916	D	0.000134	T	0.80476	0.4630	M	0.84585	2.705	0.80722	D	1	D	0.55385	0.971	B	0.40741	0.339	D	0.86285	0.1670	10	0.72032	D	0.01	.	17.5398	0.87844	0.0:0.0:1.0:0.0	.	51	Q9H4E5	RHOJ_HUMAN	M	51	ENSP00000316729:V51M;ENSP00000451643:V51M	ENSP00000316729:V51M	V	+	1	0	RHOJ	62741491	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.371000	0.66150	2.445000	0.82738	0.563000	0.77884	GTG		0.557	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3			A	63671738	G	A	63671738	3	1	22	1	0	0	0	0	1	0	0	0	13378	1145	40	1	153	1	RHOJ	14	63671738	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10		63671738	43677802	45	2011										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76957940	76957940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	catggatgaggagcactcccGcctcgcggggctgctggagc	16	13	0	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr14:76957940G>A	ENST00000509242.1	+	7	1036	c.938G>A	c.(937-939)cGc>cAc	p.R313H	ESRRB_ENST00000261532.7_Missense_Mutation_p.R313H|ESRRB_ENST00000380887.2_Missense_Mutation_p.R313H|ESRRB_ENST00000556177.1_Missense_Mutation_p.R313H	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	313					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R313H(1)		endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		GAGCACTCCCGCCTCGCGGGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	14											49	41	44					14																	76957940		2201	4298	6499	76027693	SO:0001583	missense	2103			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.938G>A	14.37:g.76957940G>A	ENSP00000422488:p.Arg313His		76027693	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289576	0.80914	.	.	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000556177;ENST00000380887;ENST00000261532	D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.96824	0.8963	L	0.46741	1.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70487	0.969;0.969	D	0.95684	0.8734	10	0.39692	T	0.17	.	13.7717	0.63029	0.0697:0.0:0.9303:0.0	.	313;318	Q5F0P7;E7EWD9	.;.	H	318;313;313;313;313	ENSP00000424992:R318H;ENSP00000422488:R313H;ENSP00000451658:R313H;ENSP00000370270:R313H;ENSP00000261532:R313H	ENSP00000261532:R313H	R	+	2	0	ESRRB	76027693	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	CGC		0.592	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			A	76957940	G	A	76957940	3	1	22	1	0	0	0	0	1	0	0	0	5274	1087	38	1	956	1	ESRRB	14	76957940	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	13286202	76957940	30391600	46	2012										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88904598	88904598	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gtgaatgtcattgaaggtgaTagtgaccctgaaaaggttga	13	4	1	6			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr14:88904598T>C	ENST00000393545.4	+	12	1921	c.1632T>C	c.(1630-1632)gaT>gaC	p.D544D	SPATA7_ENST00000356583.5_Silent_p.D512D|SPATA7_ENST00000556553.1_Silent_p.D512D|SPATA7_ENST00000045347.7_Intron	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	544					response to stimulus (GO:0050896)|visual perception (GO:0007601)			p.D544D(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TTGAAGGTGATAGTGACCCTG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	14											102	89	93					14																	88904598		2203	4300	6503	87974351	SO:0001819	synonymous_variant	55812			AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.1632T>C	14.37:g.88904598T>C			87974351	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Silent	SNP	ENST00000393545.4	37	CCDS9883.1																																																																																				0.378	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			C	88904598	T	C	88904598	2	2	22	1	0	0	0	0	0	0	0	1	15053	1403	49	4		4	SPATA7	14	88904598	Silent	SNP	T	TCGA-AG-3587-01A-01W-0831-10	11946658	88904598	18444942	47	2013										
SPRED1	161742	hgsc.bcm.edu	37	chr15	38641631	38641631	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tttgtattttagataacattTggtcagccaggcttggacat	9	6	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr15:38641631T>C	ENST00000299084.4	+	6	1451	c.591T>C	c.(589-591)ttT>ttC	p.F197F		NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	197					inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.F197F(1)		kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		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)		AGATAACATTTGGTCAGCCAG	0.343									Legius syndrome																												Melanoma(196;2146 2959 7698 16532)											1	Substitution - coding silent(1)	large_intestine(1)	15											86	83	84					15																	38641631		2200	4297	6497	36428923	SO:0001819	synonymous_variant	161742	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 147"	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.591T>C	15.37:g.38641631T>C			36428923	B2RPJ8|Q05D53|Q8N256	Silent	SNP	ENST00000299084.4	37	CCDS32193.1																																																																																				0.343	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1			C	38641631	T	C	38641631	2	2	22	1	0	0	0	0	0	0	0	1	15131	1809	63	4		4	SPRED1	15	38641631	Silent	SNP	T	TCGA-AG-3587-01A-01W-0831-10		38641631	63889761	48	2014										
FBN1	2200	hgsc.bcm.edu	37	chr15	48782244	48782244	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	agggtgcactcctcgtcctcGtacctcaggaagcaggtttc	11	13	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr15:48782244G>A	ENST00000316623.5	-	25	3341	c.2886C>T	c.(2884-2886)taC>taT	p.Y962Y		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	962	TB 5.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.Y962Y(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CCTCGTCCTCGTACCTCAGGA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	15											50	45	47					15																	48782244		2198	4296	6494	46569536	SO:0001819	synonymous_variant	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.2886C>T	15.37:g.48782244G>A			46569536	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																				0.602	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48782244	G	A	48782244	2	1	22	1	0	0	0	0	0	0	0	1	5721	1140	40	1		1	FBN1	15	48782244	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10	10140613	48782244	53749148	49	2015										
C15orf33	196951	hgsc.bcm.edu	37	chr15	49663509	49663509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tactccaaacctttgttgctAgtcttgataatcttgattct	5	9	3	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr15:49663509A>G	ENST00000299338.6	-	12	1403	c.1100T>C	c.(1099-1101)cTa>cCa	p.L367P		NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	367								p.L367P(1)									CTTTGTTGCTAGTCTTGATAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	15											101	107	105					15																	49663509		2196	4289	6485	47450801	SO:0001583	missense	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.1100T>C	15.37:g.49663509A>G	ENSP00000299338:p.Leu367Pro		47450801	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	37	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	A	7.751	0.703363	0.15172	.	.	ENSG00000166262	ENST00000299338	.	.	.	3.9	-4.78	0.03209	.	4.691850	0.00357	N	0.000039	T	0.40595	0.1123	M	0.63843	1.955	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.12915	-1.0529	9	0.35671	T	0.21	-0.0521	3.4719	0.07570	0.4158:0.0:0.3014:0.2828	.	367	Q96M60	CO033_HUMAN	P	367	.	ENSP00000299338:L367P	L	-	2	0	C15orf33	47450801	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.229000	0.09098	-0.954000	0.03640	-0.297000	0.09499	CTA		0.318	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		G	49663509	A	G	49663509	3	3	22	1	0	0	0	0	1	0	0	0	1795	420	15	4	446	4	C15orf33	15	49663509	Missense_Mutation	SNP	A	TCGA-AG-3587-01A-01W-0831-10	881265	49663509	52867883	50	2016										
CDH3	1001	hgsc.bcm.edu	37	chr16	68718642	68718642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ttgtcccaccctccaaagtcGttgaggtccaggagggcatc	11	13	0	1	rs145160881		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr16:68718642G>A	ENST00000264012.4	+	10	1883	c.1339G>A	c.(1339-1341)Gtt>Att	p.V447I	CDH3_ENST00000581171.1_Missense_Mutation_p.V392I|CDH3_ENST00000429102.2_Missense_Mutation_p.V447I	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	447	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)|p.V447I(1)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		CTCCAAAGTCGTTGAGGTCCA	0.562																																																3	Unknown(2)|Substitution - Missense(1)	breast(2)|large_intestine(1)	16						G	ILE/VAL	0,4396		0,0,2198	152	151	151		1339	-2.7	0	16	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDH3	NM_001793.4	29	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	benign	447/830	68718642	1,12995	2198	4300	6498	67276143	SO:0001583	missense	1001			X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"Cadherins / Major cadherins"	1762	protein-coding gene	gene with protein product		114021	"cadherin 3, P-cadherin (placental)"			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1339G>A	16.37:g.68718642G>A	ENSP00000264012:p.Val447Ile		67276143	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	.	.	.	.	.	.	.	.	.	.	G	0.416	-0.910867	0.02434	0.0	1.16E-4	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.50813	0.73;0.73	5.46	-2.65	0.06095	Cadherin (3);Cadherin-like (1);	1.034090	0.07730	N	0.945054	T	0.28830	0.0715	N	0.17723	0.515	0.09310	N	1	B	0.16166	0.016	B	0.12156	0.007	T	0.37596	-0.9699	10	0.02654	T	1	.	14.6385	0.68706	0.2982:0.0:0.7018:0.0	.	447	P22223	CADH3_HUMAN	I	447;447;392	ENSP00000398485:V447I;ENSP00000264012:V447I	ENSP00000264012:V447I	V	+	1	0	CDH3	67276143	0.000000	0.05858	0.034000	0.17996	0.635000	0.38103	0.061000	0.14366	-0.752000	0.04728	-0.367000	0.07326	GTT		0.562	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		A	68718642	G	A	68718642	3	1	22	1	0	0	0	0	1	0	0	0	3117	1145	40	1	1377	1	CDH3	16	68718642	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10		68718642	21636111	51	2017										
FAM57A	79850	hgsc.bcm.edu	37	chr17	641189	641189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gccgaaccagagaccagaacCgtgcgccctccctcactctt	8	18	2	2	rs371723776		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr17:641189C>T	ENST00000308278.8	+	3	546	c.310C>T	c.(310-312)Cgt>Tgt	p.R104C	FAM57A_ENST00000572018.1_Intron|FAM57A_ENST00000301324.8_Missense_Mutation_p.R104C	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	104	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R104C(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		AGACCAGAACCGTGCGCCCTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	213	185	194		310	2.5	0	17		194	0,8600		0,0,4300	no	missense	FAM57A	NM_024792.1	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	104/258	641189	1,13005	2203	4300	6503	587939	SO:0001583	missense	79850			AK025935	CCDS10996.1	17p13.3	2014-08-14				ENSG00000167695			29646	protein-coding gene	gene with protein product		611627				12270127	Standard	NM_024792		Approved	FLJ22282, CT120	uc002frp.3	Q8TBR7		ENST00000308278.8:c.310C>T	17.37:g.641189C>T	ENSP00000312017:p.Arg104Cys		587939	A8K7Q0|Q7Z464|Q96D97|Q9H6H3	Missense_Mutation	SNP	ENST00000308278.8	37	CCDS10996.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726624	0.30593	2.27E-4	0.0	ENSG00000167695	ENST00000308278;ENST00000301324;ENST00000451373	.	.	.	5.89	2.52	0.30459	TRAM/LAG1/CLN8 homology domain (3);	3.888680	0.03023	U	0.151098	T	0.41511	0.1162	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.01;0.005	B;B	0.08055	0.002;0.003	T	0.37979	-0.9682	9	0.59425	D	0.04	0.666	10.9356	0.47243	0.3059:0.6241:0.0:0.07	.	104;104	Q8TBR7-1;Q8TBR7	.;FA57A_HUMAN	C	104;104;177	.	ENSP00000301324:R104C	R	+	1	0	FAM57A	587939	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	0.600000	0.24104	0.824000	0.34613	0.638000	0.83543	CGT		0.517	FAM57A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437155.2	NM_024792		T	641189	C	T	641189	3	4	22	1	0	0	0	0	1	0	0	0	5607	652	23	1	320	1	FAM57A	17	641189	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		641189	80554021	52	2018										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	22	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	6935931	7577120	73618090	53	2019										
TBX21	30009	hgsc.bcm.edu	37	chr17	45822604	45822604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ccagtgattcaggactgggcGaaggagactctaagaggagg	16	7	2	3			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr17:45822604G>A	ENST00000177694.1	+	6	1691	c.1480G>A	c.(1480-1482)Gaa>Aaa	p.E494K		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	494					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E494K(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						AGGACTGGGCGAAGGAGACTC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											44	45	45					17																	45822604		2203	4300	6503	43177603	SO:0001583	missense	30009			AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1480G>A	17.37:g.45822604G>A	ENSP00000177694:p.Glu494Lys		43177603		Missense_Mutation	SNP	ENST00000177694.1	37	CCDS11514.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447346	0.63178	.	.	ENSG00000073861	ENST00000177694	D	0.86230	-2.09	5.38	5.38	0.77491	.	0.206123	0.31601	N	0.007363	D	0.88336	0.6409	M	0.73598	2.24	0.36175	D	0.849049	D	0.61697	0.99	P	0.45998	0.5	D	0.92221	0.5784	10	0.62326	D	0.03	.	14.6327	0.68668	0.0:0.0:1.0:0.0	.	494	Q9UL17	TBX21_HUMAN	K	494	ENSP00000177694:E494K	ENSP00000177694:E494K	E	+	1	0	TBX21	43177603	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	3.340000	0.52143	2.499000	0.84300	0.655000	0.94253	GAA		0.617	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		A	45822604	G	A	45822604	3	1	22	1	0	0	0	0	1	0	0	0	15696	1059	37	1	1502	1	TBX21	17	45822604	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	38245484	45822604	35372606	54	2020										
MAP3K3	4215	hgsc.bcm.edu	37	chr17	61771046	61771046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ccacatctctgaacatggccGggacttcctgaggcgcattt	10	13	1	2			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr17:61771046G>A	ENST00000361733.3	+	16	2110	c.1790G>A	c.(1789-1791)cGg>cAg	p.R597Q	MAP3K3_ENST00000579585.1_Missense_Mutation_p.R628Q|MAP3K3_ENST00000577395.1_Missense_Mutation_p.R593Q|MAP3K3_ENST00000361357.3_Missense_Mutation_p.R628Q|MAP3K3_ENST00000584573.1_Missense_Mutation_p.R624Q	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)	p.R597Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						GAACATGGCCGGGACTTCCTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											107	96	100					17																	61771046		2203	4300	6503	59124778	SO:0001583	missense	4215			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6855	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 3", "MAPK/ERK kinase kinase 3"	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1790G>A	17.37:g.61771046G>A	ENSP00000354485:p.Arg597Gln		59124778	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Missense_Mutation	SNP	ENST00000361733.3	37	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592291	0.86953	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	T;T	0.64618	-0.11;-0.11	4.95	3.98	0.46160	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68476	0.3005	L	0.31926	0.97	0.80722	D	1	D;D;D;P	0.76494	0.999;0.999;0.975;0.936	D;D;P;P	0.70935	0.971;0.929;0.608;0.56	T	0.71148	-0.4677	10	0.66056	D	0.02	.	13.4432	0.61125	0.0765:0.0:0.9235:0.0	.	593;565;597;628	Q1PBM3;Q96HN9;Q99759;Q99759-2	.;.;M3K3_HUMAN;.	Q	628;597	ENSP00000354927:R628Q;ENSP00000354485:R597Q	ENSP00000354927:R628Q	R	+	2	0	MAP3K3	59124778	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	1.085000	0.41206	0.561000	0.74099	CGG		0.567	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401		A	61771046	G	A	61771046	3	1	22	1	0	0	0	0	1	0	0	0	9281	1116	39	1	1949	1	MAP3K3	17	61771046	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	15948442	61771046	19424164	55	2021										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42532218	42532218	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	caagtgttcagaatctcccaCcggagttacaccttctacca	6	14	3	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr18:42532218C>A	ENST00000282030.5	+	4	3209	c.2913C>A	c.(2911-2913)caC>caA	p.H971Q		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	971						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.H917Q(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GAATCTCCCACCGGAGTTACA	0.473									Schinzel-Giedion syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	18											94	91	92					18																	42532218		2203	4300	6503	40786216	SO:0001583	missense	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.2913C>A	18.37:g.42532218C>A	ENSP00000282030:p.His971Gln		40786216	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898324	0.52227	.	.	ENSG00000152217	ENST00000282030	D	0.92397	-3.03	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.93367	0.7885	L	0.32530	0.975	0.41902	D	0.990422	D	0.89917	1.0	D	0.87578	0.998	D	0.93721	0.7033	10	0.87932	D	0	.	13.9146	0.63890	0.0:0.9221:0.0:0.0779	.	971	Q9Y6X0	SETBP_HUMAN	Q	971	ENSP00000282030:H971Q	ENSP00000282030:H971Q	H	+	3	2	SETBP1	40786216	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.951000	0.40333	2.808000	0.96608	0.655000	0.94253	CAC		0.473	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42532218	C	A	42532218	3	1	22	1	0	0	0	0	1	0	0	0	14166	506	18	2	3116	2	SETBP1	18	42532218	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		42532218	35545030	56	2022										
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6183157	6183157	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctcttttatcagtgggactgCgcccctcaaccaagagactg	9	13	3	1	rs139677949	byFrequency	TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr19:6183157C>T	ENST00000586696.1	+	10	1472	c.1196C>T	c.(1195-1197)gCg>gTg	p.A399V	ACSBG2_ENST00000588485.1_Missense_Mutation_p.A212V|ACSBG2_ENST00000588304.1_Missense_Mutation_p.A349V|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000591403.1_Missense_Mutation_p.A399V|ACSBG2_ENST00000252669.5_Missense_Mutation_p.A399V			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	399					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.A399V(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTGGGACTGCGCCCCTCAAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	102	95	97		1196	1.8	0	19	dbSNP_134	97	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ACSBG2	NM_030924.3	64	0,7,6496	TT,TC,CC		0.0233,0.1135,0.0538	possibly-damaging	399/667	6183157	7,12999	2203	4300	6503	6134157	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1196C>T	19.37:g.6183157C>T	ENSP00000465589:p.Ala399Val		6134157	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347586	0.61183	0.001135	2.33E-4	ENSG00000130377	ENST00000252669	T	0.13778	2.56	5.16	1.83	0.25207	AMP-dependent synthetase/ligase (1);	0.635484	0.13108	N	0.413193	T	0.45816	0.1361	H	0.95402	3.665	0.38212	D	0.940503	D;D	0.71674	0.998;0.987	D;P	0.68621	0.959;0.694	T	0.51593	-0.8686	10	0.72032	D	0.01	-14.5884	9.7467	0.40451	0.0:0.7366:0.1192:0.1442	.	399;399	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	V	399	ENSP00000252669:A399V	ENSP00000252669:A399V	A	+	2	0	ACSBG2	6134157	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	4.649000	0.61433	-0.037000	0.13646	-0.813000	0.03139	GCG		0.512	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		T	6183157	C	T	6183157	3	4	22	1	0	0	0	0	1	0	0	0	174	768	27	1	1230	1	ACSBG2	19	6183157	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		6183157	52945826	57	2023										
TIMM44	10469	hgsc.bcm.edu	37	chr19	7998369	7998369	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ctccaagacaccttcactcaCggttaaacaccacgttgttc	5	15	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr19:7998369C>T	ENST00000270538.3	-	7	1038		c.e7+1		TIMM44_ENST00000598968.1_5'Flank	NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)						cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)	p.?(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						CCTTCACTCACGGTTAAACAC	0.592																																																1	Unknown(1)	large_intestine(1)	19											304	258	274					19																	7998369		2203	4300	6503	7904369	SO:0001630	splice_region_variant	10469			AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.769+1G>A	19.37:g.7998369C>T			7904369	A8K0R9|D6W664|Q8N193	Splice_Site	SNP	ENST00000270538.3	37	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.016199	0.75161	.	.	ENSG00000104980	ENST00000270538	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7709	0.78167	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TIMM44	7904369	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	4.353000	0.59411	2.335000	0.79485	0.561000	0.74099	.		0.592	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3		Intron	T	7998369	C	T	7998369	5	4	22	1	0	0	0	0	0	0	1	0	15951	550	19	1	616	1	TIMM44	19	7998369	Splice_Site	SNP	C	TCGA-AG-3587-01A-01W-0831-10	1815212	7998369	51130614	58	2024										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953003	56953003	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gttcaataagaaatgattggCggccgaaaactttactacat	8	7	1	2	rs376504755		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr19:56953003C>T	ENST00000504904.3	-	7	2080	c.1361G>A	c.(1360-1362)cGc>cAc	p.R454H	ZNF667_ENST00000292069.6_Missense_Mutation_p.R454H|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.R582H			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R454H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AAATGATTGGCGGCCGAAAAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	HIS/ARG	0,4406		0,0,2203	51	52	51		1361	3.9	0.9	19		51	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF667	NM_022103.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	454/611	56953003	1,13005	2203	4300	6503	61644815	SO:0001583	missense	63934				CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1361G>A	19.37:g.56953003C>T	ENSP00000439402:p.Arg454His		61644815	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	C	8.627	0.892747	0.17613	0.0	1.16E-4	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518;ENST00000360227	T;T;T	0.07327	3.2;3.2;3.2	5.03	3.94	0.45596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45126	D	0.000397	T	0.03390	0.0098	N	0.13299	0.325	0.09310	N	1	P;P	0.49447	0.924;0.924	B;B	0.31337	0.128;0.128	T	0.48502	-0.9030	10	0.19147	T	0.46	-12.2436	10.2221	0.43203	0.0:0.8955:0.0:0.1045	.	582;454	E7EPS0;Q5HYK9	.;ZN667_HUMAN	H	582;454;454;236;169	ENSP00000344699:R582H;ENSP00000439402:R454H;ENSP00000292069:R454H	ENSP00000292069:R454H	R	-	2	0	ZNF667	61644815	0.000000	0.05858	0.947000	0.38551	0.003000	0.03518	-0.443000	0.06862	2.599000	0.87857	0.655000	0.94253	CGC		0.373	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		T	56953003	C	T	56953003	3	4	22	1	0	0	0	0	1	0	0	0	18113	768	27	1	475	1	ZNF667	19	56953003	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	48954634	56953003	2175980	59	2025										
PHF20	51230	hgsc.bcm.edu	37	chr20	34451072	34451072	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	aaagaagataaacccttaaaGacagaaaagcgacccaagca	7	9	0	4			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr20:34451072G>T	ENST00000374012.3	+	6	687	c.558G>T	c.(556-558)aaG>aaT	p.K186N	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_Missense_Mutation_p.K186N			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	186	Lys-rich.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K186N(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AACCCTTAAAGACAGAAAAGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	20											107	103	104					20																	34451072		2203	4300	6503	33914486	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.558G>T	20.37:g.34451072G>T	ENSP00000363124:p.Lys186Asn		33914486	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.476161	0.63737	.	.	ENSG00000025293	ENST00000374012;ENST00000439301;ENST00000339089;ENST00000374000;ENST00000449988	T;T;T;T	0.50813	1.35;0.75;0.73;0.73	5.5	2.42	0.29668	.	0.086755	0.49916	D	0.000138	T	0.42359	0.1199	N	0.14661	0.345	0.31931	N	0.612182	D;D;D	0.76494	0.998;0.997;0.999	D;D;D	0.69824	0.966;0.939;0.966	T	0.45396	-0.9264	10	0.25751	T	0.34	.	5.4787	0.16710	0.2454:0.1421:0.6125:0.0	.	186;186;186	Q566Q2;Q9BVI0;Q66K49	.;PHF20_HUMAN;.	N	186;186;186;186;79	ENSP00000363124:K186N;ENSP00000410373:K186N;ENSP00000341900:K186N;ENSP00000363112:K186N	ENSP00000341900:K186N	K	+	3	2	PHF20	33914486	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	1.382000	0.34374	0.333000	0.23563	0.561000	0.74099	AAG		0.383	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		T	34451072	G	T	34451072	3	4	22	1	0	0	0	0	1	0	0	0	11862	933	33	2	576	2	PHF20	20	34451072	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10		34451072	28574448	60	2026										
PHF20	51230	hgsc.bcm.edu	37	chr20	34451231	34451231	+	Missense_Mutation	SNP	G	G	T													0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ggagatgcccaagtggataaGaaacctgaaaatgacattgt							TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr20:34451231G>T	ENST00000374012.3	+	6	846	c.717G>T	c.(715-717)aaG>aaT	p.K239N	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_Intron			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	239					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K239N(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AAGTGGATAAGAAACCTGAAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	20											118	127	124					20																	34451231		2203	4300	6503	33914645	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.717G>T	20.37:g.34451231G>T	ENSP00000363124:p.Lys239Asn		33914645	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960263	0.74016	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000;ENST00000449988	T;T;T	0.55760	1.15;0.5;0.5	5.83	1.71	0.24356	.	0.048452	0.85682	D	0.000000	T	0.54791	0.1880	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.997	D;D;D	0.87578	0.966;0.998;0.951	T	0.50355	-0.8838	10	0.46703	T	0.11	.	10.6635	0.45717	0.2576:0.0:0.7424:0.0	.	239;239;239	Q566Q2;Q9BVI0;Q66K49	.;PHF20_HUMAN;.	N	239;239;239;132	ENSP00000363124:K239N;ENSP00000341900:K239N;ENSP00000363112:K239N	ENSP00000341900:K239N	K	+	3	2	PHF20	33914645	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	1.009000	0.29886	0.099000	0.17552	0.561000	0.74099	AAG		0.433	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		T	34451231	G	T	34451231	3	4	22	1	0	0	0	0	1	0	0	0	11862	933	33	2	735	2	PHF20	20	34451231	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	159	34451231	28574289	61	2027	11	2								
PHF20	51230	hgsc.bcm.edu	37	chr20	34451238	34451238	+	Missense_Mutation	SNP	G	G	A													0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cccaagtggataagaaacctGaaaatgacattgtgaagagt							TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr20:34451238G>A	ENST00000374012.3	+	6	853	c.724G>A	c.(724-726)Gaa>Aaa	p.E242K	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_Intron			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	242					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E242K(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					TAAGAAACCTGAAAATGACAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	20											119	128	125					20																	34451238		2203	4300	6503	33914652	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.724G>A	20.37:g.34451238G>A	ENSP00000363124:p.Glu242Lys		33914652	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614276	0.66672	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000;ENST00000449988	T;T;T	0.55760	1.2;0.5;0.5	5.83	5.83	0.93111	.	0.507538	0.21818	N	0.068668	T	0.41673	0.1169	N	0.19112	0.55	0.80722	D	1	P;B;P	0.36354	0.549;0.324;0.549	B;B;B	0.39617	0.305;0.207;0.305	T	0.21895	-1.0232	10	0.22706	T	0.39	.	15.5855	0.76479	0.0:0.137:0.863:0.0	.	242;242;242	Q566Q2;Q9BVI0;Q66K49	.;PHF20_HUMAN;.	K	242;242;242;135	ENSP00000363124:E242K;ENSP00000341900:E242K;ENSP00000363112:E242K	ENSP00000341900:E242K	E	+	1	0	PHF20	33914652	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	4.956000	0.63645	2.763000	0.94921	0.561000	0.74099	GAA		0.428	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		A	34451238	G	A	34451238	3	1	22	1	0	0	0	0	1	0	0	0	11862	1291	45	3	742	3	PHF20	20	34451238	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	7	34451238	28574282	62	2028	11	2								
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32625329	32625329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	cgaaagcatcaggcctcgcaGtcctggagccgggaaagggt	15	11	1	0			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr22:32625329G>A	ENST00000266086.4	-	11	1143	c.1132C>T	c.(1132-1134)Ctg>Ttg	p.L378L	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	378					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.L378L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AGGCCTCGCAGTCCTGGAGCC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	22											64	62	63					22																	32625329		2203	4300	6503	30955329	SO:0001819	synonymous_variant	6527			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1132C>T	22.37:g.32625329G>A			30955329	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																				0.532	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		A	32625329	G	A	32625329	2	1	22	1	0	0	0	0	0	0	0	1	14704	1020	36	3		3	SLC5A4	22	32625329	Silent	SNP	G	TCGA-AG-3587-01A-01W-0831-10		32625329	18679237	63	2029										
RANGAP1	5905	hgsc.bcm.edu	37	chr22	41647072	41647072	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	ttgaacacagatgacaccttTaggaaggcagagaccacctt	9	10	0	4			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chr22:41647072T>C	ENST00000455915.2	-	12	2891	c.1422A>G	c.(1420-1422)ctA>ctG	p.L474L	RANGAP1_ENST00000405486.1_Silent_p.L474L|RANGAP1_ENST00000407260.4_Silent_p.L419L|RANGAP1_ENST00000356244.3_Silent_p.L474L			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	474					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)	p.L474L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATGACACCTTTAGGAAGGCAG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	22											199	136	158					22																	41647072		2203	4300	6503	39977018	SO:0001819	synonymous_variant	5905			X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"segregation distorter homolog (Drosophila)"	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1422A>G	22.37:g.41647072T>C			39977018	Q96JJ2	Silent	SNP	ENST00000455915.2	37	CCDS14012.1																																																																																				0.567	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883		C	41647072	T	C	41647072	2	2	22	1	0	0	0	0	0	0	0	1	13070	1741	61	4		4	RANGAP1	22	41647072	Silent	SNP	T	TCGA-AG-3587-01A-01W-0831-10	9021743	41647072	9657494	64	2030										
PRPS1	5631	hgsc.bcm.edu	37	chrX	106882652	106882652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gcaagattgcttcagccagcCgggttactgcagtcatccca	10	13	2	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chrX:106882652C>T	ENST00000372435.4	+	2	372	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	PRPS1_ENST00000543248.1_Missense_Mutation_p.R84W|PRPS1_ENST00000372418.1_Missense_Mutation_p.R17W|PRPS1_ENST00000372419.3_Missense_Mutation_p.R84W|PRPS1_ENST00000372428.4_Missense_Mutation_p.R17W	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	84					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)	p.R84W(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						TTCAGCCAGCCGGGTTACTGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											159	150	153					X																	106882652		2203	4300	6503	106769308	SO:0001583	missense	5631			X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"PRS I", "ribose-phosphate diphosphokinase 1"	311850	"deafness, X-linked 2, perceptive, congenital"	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.250C>T	X.37:g.106882652C>T	ENSP00000361512:p.Arg84Trp		106769308	B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	37	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.524202	0.64747	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000372419;ENST00000543248;ENST00000372418	D;D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32;-3.32	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.95793	0.8631	H	0.99197	4.465	0.54753	D	0.999989	P;P	0.49559	0.925;0.925	B;B	0.39971	0.315;0.315	D	0.96508	0.9376	10	0.87932	D	0	.	11.7434	0.51807	0.1887:0.8113:0.0:0.0	.	84;84	Q53FW2;P60891	.;PRPS1_HUMAN	W	84;17;84;84;17	ENSP00000361512:R84W;ENSP00000361505:R17W;ENSP00000361496:R84W;ENSP00000443185:R84W;ENSP00000361495:R17W	ENSP00000361495:R17W	R	+	1	2	PRPS1	106769308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.825000	0.39081	2.169000	0.68431	0.600000	0.82982	CGG		0.443	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1			T	106882652	C	T	106882652	3	4	22	1	0	0	0	0	1	0	0	0	12612	643	23	1	256	1	PRPS1	23	106882652	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10		106882652	48387908	65	2031										
SEPT6	23157	hgsc.bcm.edu	37	chrX	118771001	118771001	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	gagcggtacctgaagggtttGctgtcagggtcggtgtcctt	16	8	1	1			TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chrX:118771001G>T	ENST00000343984.5	-	7	1209	c.945C>A	c.(943-945)agC>agA	p.S315R	SEPT6_ENST00000394610.1_Missense_Mutation_p.S315R|SEPT6_ENST00000354228.4_Missense_Mutation_p.S315R|SEPT6_ENST00000394617.2_Missense_Mutation_p.S345R|SEPT6_ENST00000489216.1_Missense_Mutation_p.S315R|SEPT6_ENST00000360156.7_Missense_Mutation_p.S315R|SEPT6_ENST00000354416.3_Missense_Mutation_p.S315R|SEPT6_ENST00000394616.4_Missense_Mutation_p.S257R	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	315					cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)	p.S315R(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						TGAAGGGTTTGCTGTCAGGGT	0.617			T	MLL	AML																																		Dom	yes		X	Xq24	23157	septin 6		L	1	Substitution - Missense(1)	large_intestine(1)	X											100	70	80					X																	118771001		2203	4300	6503	118655029	SO:0001583	missense	23157			D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354		"Septins"	15848	protein-coding gene	gene with protein product		300683				8590280, 10744683	Standard	NM_015129		Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000343984.5:c.945C>A	X.37:g.118771001G>T	ENSP00000341524:p.Ser315Arg		118655029	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	37	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243490	0.58995	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394616;ENST00000394617	D;D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.29	4.41	0.53225	.	0.076593	0.85682	D	0.000000	D	0.83672	0.5305	L	0.56769	1.78	0.80722	D	1	P;B;B;B	0.37824	0.609;0.001;0.159;0.031	P;B;B;B	0.47528	0.549;0.005;0.185;0.027	T	0.80783	-0.1228	10	0.25751	T	0.34	.	12.5008	0.55953	0.0843:0.0:0.9157:0.0	.	345;257;315;315	F5H1J5;B4E049;Q14141;Q548C9	.;.;SEPT6_HUMAN;.	R	315;315;315;315;315;315;257;345	ENSP00000353278:S315R;ENSP00000346169:S315R;ENSP00000418715:S315R;ENSP00000346397:S315R;ENSP00000378108:S315R;ENSP00000341524:S315R;ENSP00000378114:S257R;ENSP00000378115:S345R	ENSP00000341524:S315R	S	-	3	2	SEPT6	118655029	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.642000	0.83385	2.200000	0.70718	0.594000	0.82650	AGC		0.617	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		T	118771001	G	T	118771001	3	4	22	1	0	0	0	0	1	0	0	0	14105	1310	46	2	397	2	SEPT6	23	118771001	Missense_Mutation	SNP	G	TCGA-AG-3587-01A-01W-0831-10	11888349	118771001	36499559	66	2032										
CDR1	1038	hgsc.bcm.edu	37	chrX	139865904	139865904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167296548248929	3.51322751322751	0	1	1	0	tccagtcaatccacatcttcCggaaaaaatccaggtcttcc	5	14	3	0	rs143948461		TCGA-AG-3587-01A-01W-0831-10	TCGA-AG-3587-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	5b31ee61-d86c-401f-849b-3326498134f5	9cf1398c-86c0-4fd8-823d-7ae1d01ba017	g.chrX:139865904C>T	ENST00000370532.2	-	1	819	c.628G>A	c.(628-630)Gga>Aga	p.G210R		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	210								p.G210R(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CCACATCTTCCGGAAAAAATC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	ARG/GLY	2,3833		0,2,1630,571	112	108	109		628	3.7	1	X	dbSNP_134	109	0,6728		0,0,2428,1872	no	missense	CDR1	NM_004065.2	125	0,2,4058,2443	TT,TC,CC,C		0.0,0.0522,0.0189	possibly-damaging	210/263	139865904	2,10561	2203	4300	6503	139693570	SO:0001583	missense	1038				CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.628G>A	X.37:g.139865904C>T	ENSP00000359563:p.Gly210Arg		139693570	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.250435	0.39797	5.22E-4	0.0	ENSG00000184258	ENST00000370532	.	.	.	4.58	3.7	0.42460	.	.	.	.	.	T	0.32704	0.0838	N	0.08118	0	0.24558	N	0.993987	D	0.76494	0.999	D	0.63381	0.914	T	0.09509	-1.0671	7	.	.	.	.	8.8416	0.35146	0.0:0.8854:0.0:0.1146	.	210	P51861	CDR1_HUMAN	R	210	.	.	G	-	1	0	CDR1	139693570	0.061000	0.20836	0.970000	0.41538	0.193000	0.23685	0.177000	0.16801	2.181000	0.69327	0.422000	0.28245	GGA		0.438	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		T	139865904	C	T	139865904	3	4	22	1	0	0	0	0	1	0	0	0	3177	661	23	1	164	1	CDR1	23	139865904	Missense_Mutation	SNP	C	TCGA-AG-3587-01A-01W-0831-10	21094903	139865904	15404656	67	2033										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178426964	178426964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aagtagccttcctaatggtcGgagcgtctccctcatggacc	10	13	2	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr1:178426964G>A	ENST00000462775.1	+	12	2239	c.2114G>A	c.(2113-2115)cGg>cAg	p.R705Q	RASAL2_ENST00000367649.3_Missense_Mutation_p.R846Q|RASAL2_ENST00000448150.3_Missense_Mutation_p.R835Q	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	705					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)	p.R846Q(1)|p.R835Q(1)		biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CCTAATGGTCGGAGCGTCTCC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	1											95	92	93					1																	178426964		2203	4300	6503	176693587	SO:0001583	missense	9462			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2114G>A	1.37:g.178426964G>A	ENSP00000420558:p.Arg705Gln		176693587	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965816	0.92855	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	T;T;T	0.13778	2.56;2.56;2.56	5.42	5.42	0.78866	.	0.061537	0.64402	D	0.000012	T	0.34366	0.0895	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.999;0.982;0.976	D;P;P	0.63703	0.917;0.791;0.601	T	0.02320	-1.1177	10	0.66056	D	0.02	.	19.2521	0.93929	0.0:0.0:1.0:0.0	.	835;705;846	B1AKC7;Q9UJF2;F8W755	.;NGAP_HUMAN;.	Q	835;846;705	ENSP00000407768:R835Q;ENSP00000356621:R846Q;ENSP00000420558:R705Q	ENSP00000356621:R846Q	R	+	2	0	RASAL2	176693587	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.433000	0.97501	2.542000	0.85734	0.655000	0.94253	CGG		0.493	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		A	178426964	G	A	178426964	3	1	23	1	0	0	0	0	1	0	0	0	13101	1116	39	1	2629	1	RASAL2	1	178426964	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		178426964	70823657	1	2034										
SMG7	9887	hgsc.bcm.edu	37	chr1	183520213	183520213	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tggcattgattatctctcagCaacgtcatcctctgagagca	8	11	4	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr1:183520213C>A	ENST00000347615.2	+	21	3307	c.3188C>A	c.(3187-3189)gCa>gAa	p.A1063E	SMG7_ENST00000367537.3_Missense_Mutation_p.A1096E|SMG7_ENST00000456731.2_Missense_Mutation_p.A975E|SMG7_ENST00000515829.2_Missense_Mutation_p.A1017E|SMG7_ENST00000508461.1_Missense_Mutation_p.A1071E|SMG7_ENST00000507469.1_Missense_Mutation_p.A1067E	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	1063					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.A1063E(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						TATCTCTCAGCAACGTCATCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	75	77					1																	183520213		2203	4300	6503	181786836	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.3188C>A	1.37:g.183520213C>A	ENSP00000340766:p.Ala1063Glu		181786836	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.481611	0.44147	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.23552	1.96;1.94;1.9;1.93;1.93;1.95	5.34	4.41	0.53225	.	0.335281	0.31734	N	0.007146	T	0.16557	0.0398	N	0.24115	0.695	0.09310	N	0.999995	B;B;B;B;B	0.31125	0.09;0.037;0.062;0.09;0.309	B;B;B;B;B	0.27608	0.031;0.035;0.076;0.051;0.081	T	0.17018	-1.0383	10	0.66056	D	0.02	-0.6955	9.7281	0.40344	0.0:0.7845:0.1419:0.0736	.	1071;975;1017;1063;1067	E9PCI0;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;SMG7_HUMAN;.	E	975;1096;1071;1063;1067;1017	ENSP00000407629:A975E;ENSP00000356507:A1096E;ENSP00000426915:A1071E;ENSP00000340766:A1063E;ENSP00000425133:A1067E;ENSP00000421358:A1017E	ENSP00000340766:A1063E	A	+	2	0	SMG7	181786836	0.968000	0.33430	0.388000	0.26195	0.783000	0.44284	4.301000	0.59086	1.327000	0.45338	0.650000	0.86243	GCA		0.507	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		A	183520213	C	A	183520213	3	1	23	1	0	0	0	0	1	0	0	0	14835	710	25	2	3424	2	SMG7	1	183520213	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	5093249	183520213	65730408	2	2035										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201046094	201046094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gaaagttgtcaaagttgctgCgccgtacttctgtgtcttca	10	9	4	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr1:201046094C>T	ENST00000362061.3	-	12	2007	c.1781G>A	c.(1780-1782)cGc>cAc	p.R594H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R594H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	594					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R594H(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AAAGTTGCTGCGCCGTACTTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											194	166	175					1																	201046094		2203	4300	6503	199312717	SO:0001583	missense	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1781G>A	1.37:g.201046094C>T	ENSP00000355192:p.Arg594His		199312717	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922940	0.92319	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98474	-4.95;-4.95	4.55	4.55	0.56014	Ion transport (1);	.	.	.	.	D	0.98893	0.9625	M	0.80982	2.52	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.99857	1.1078	9	0.87932	D	0	.	17.6809	0.88242	0.0:1.0:0.0:0.0	.	594	Q13698	CAC1S_HUMAN	H	594	ENSP00000355192:R594H;ENSP00000356307:R594H	ENSP00000355192:R594H	R	-	2	0	CACNA1S	199312717	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.795000	0.85887	2.249000	0.74217	0.549000	0.68633	CGC		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201046094	C	T	201046094	3	4	23	1	0	0	0	0	1	0	0	0	2553	768	27	1	3972	1	CACNA1S	1	201046094	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	17525881	201046094	48204527	3	2036										
TPO	7173	hgsc.bcm.edu	37	chr2	1497771	1497771	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cagggcccctgtttgcctgtCtcattgggaagcagatgaag	13	10	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:1497771C>G	ENST00000345913.4	+	11	2057	c.1966C>G	c.(1966-1968)Ctc>Gtc	p.L656V	TPO_ENST00000329066.4_Missense_Mutation_p.L656V|TPO_ENST00000382201.3_Missense_Mutation_p.L599V|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382198.1_Missense_Mutation_p.L483V|TPO_ENST00000337415.3_Missense_Mutation_p.L656V|TPO_ENST00000349624.3_Missense_Mutation_p.L483V|TPO_ENST00000346956.3_Missense_Mutation_p.L656V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	656					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.L656V(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GTTTGCCTGTCTCATTGGGAA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											83	81	82					2																	1497771		2203	4300	6503	1476778	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1966C>G	2.37:g.1497771C>G	ENSP00000318820:p.Leu656Val		1476778	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.407133	0.42715	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	T;T;T;T;T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76	4.84	-2.62	0.06152	.	0.402568	0.27622	N	0.018553	T	0.71626	0.3362	L	0.55213	1.73	0.80722	D	1	D;P;P;D	0.55385	0.964;0.543;0.633;0.971	P;B;B;P	0.51079	0.527;0.215;0.221;0.658	T	0.70753	-0.4786	10	0.72032	D	0.01	-23.9214	10.0126	0.41995	0.2684:0.5388:0.0:0.1928	.	656;483;599;656	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	V	656;656;656;483;656;599;483;585;130	ENSP00000337263:L656V;ENSP00000318820:L656V;ENSP00000263886:L656V;ENSP00000332044:L483V;ENSP00000329869:L656V;ENSP00000371636:L599V;ENSP00000371633:L483V;ENSP00000405788:L585V;ENSP00000419461:L130V	ENSP00000329869:L656V	L	+	1	0	TPO	1476778	0.193000	0.23313	0.245000	0.24217	0.509000	0.34042	0.273000	0.18662	-0.654000	0.05394	-0.314000	0.08810	CTC		0.567	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		G	1497771	C	G	1497771	3	3	23	1	0	0	0	0	1	0	0	0	16450	913	32	5	2004	5	TPO	2	1497771	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		1497771	241701602	4	2037										
LPIN1	23175	hgsc.bcm.edu	37	chr2	11960606	11960606	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ccgtcaaccctaaaggagagCtggtacaggaacatgcaaag	11	10	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:11960606C>T	ENST00000256720.2	+	19	2572	c.2479C>T	c.(2479-2481)Ctg>Ttg	p.L827L	LPIN1_ENST00000396099.1_Silent_p.L869L|LPIN1_ENST00000396097.1_Silent_p.L557L|LPIN1_ENST00000404113.2_Silent_p.L328L|LPIN1_ENST00000425416.2_Silent_p.L833L|LPIN1_ENST00000449576.2_Silent_p.L912L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	827	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.L827L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TAAAGGAGAGCTGGTACAGGA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											126	115	118					2																	11960606		2203	4300	6503	11878057	SO:0001819	synonymous_variant	23175			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2479C>T	2.37:g.11960606C>T			11878057	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																				0.358	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		T	11960606	C	T	11960606	2	4	23	1	0	0	0	0	0	0	0	1	8947	796	28	3		3	LPIN1	2	11960606	Silent	SNP	C	TCGA-AG-3593-01A-01W-0831-10	10462835	11960606	231238767	5	2038										
C2orf44	80304	hgsc.bcm.edu	37	chr2	24261324	24261324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	actacgtgggctttaagattAaatgctatcagatcaggaac	9	7	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:24261324A>T	ENST00000295148.4	-	2	1098	c.1041T>A	c.(1039-1041)ttT>ttA	p.F347L	C2orf44_ENST00000406895.3_Missense_Mutation_p.F347L	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	347								p.F347L(1)	C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTAAGATTAAATGCTATCA	0.403			T	ALK	NSCLC																																		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	1	Substitution - Missense(1)	large_intestine(1)	2											56	55	55					2																	24261324		2201	4296	6497	24114828	SO:0001583	missense	80304			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.1041T>A	2.37:g.24261324A>T	ENSP00000295148:p.Phe347Leu		24114828	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951580	0.53186	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.49139	0.79;0.79	5.38	0.371	0.16168	WD40/YVTN repeat-like-containing domain (1);	0.046236	0.85682	D	0.000000	T	0.54303	0.1850	M	0.76328	2.33	0.44036	D	0.99676	P;D	0.55385	0.944;0.971	P;P	0.53146	0.719;0.719	T	0.54768	-0.8244	10	0.51188	T	0.08	-17.5121	9.0493	0.36367	0.715:0.0:0.285:0.0	.	347;347	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	L	347	ENSP00000295148:F347L;ENSP00000385816:F347L	ENSP00000295148:F347L	F	-	3	2	C2orf44	24114828	0.999000	0.42202	0.004000	0.12327	0.783000	0.44284	0.924000	0.28777	0.113000	0.18004	0.533000	0.62120	TTT		0.403	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		T	24261324	A	T	24261324	3	4	23	1	0	0	0	0	1	0	0	0	2174	359	13	5	1136	5	C2orf44	2	24261324	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10	12300718	24261324	218938049	6	2039										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48873903	48873903	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tcgtgcctgaagctttgttgTgtcatcaggaaagttctcac	10	9	3	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:48873903T>C	ENST00000403751.3	+	6	737	c.700T>C	c.(700-702)Tgt>Cgt	p.C234R	GTF2A1L_ENST00000430487.2_Missense_Mutation_p.C200R|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.C891R|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.C938R|LHCGR_ENST00000420913.3_Intron	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	234					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.C938R(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCTTTGTTGTGTCATCAGGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	117	122					2																	48873903		2203	4300	6503	48727407	SO:0001583	missense	286749			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.700T>C	2.37:g.48873903T>C	ENSP00000384597:p.Cys234Arg		48727407	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	T	0.406	-0.915918	0.02415	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T	0.43688	3.02;3.0;3.02;3.02;3.2;0.94	4.88	1.03	0.20045	.	0.441341	0.22106	N	0.064546	T	0.15478	0.0373	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.14012	0.0;0.0;0.009;0.0;0.0	B;B;B;B;B	0.18871	0.0;0.0;0.023;0.0;0.0	T	0.20672	-1.0268	10	0.27082	T	0.32	.	6.5697	0.22531	0.5515:0.3021:0.0:0.1464	.	200;891;938;234;938	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	R	938;938;938;938;891;233;243;200;234	ENSP00000385499:C938R;ENSP00000385701:C938R;ENSP00000378236:C938R;ENSP00000311493:C938R;ENSP00000378234:C891R;ENSP00000396702:C243R	ENSP00000384597:C234R	C	+	1	0	STON1-GTF2A1L;GTF2A1L	48727407	0.261000	0.24063	0.006000	0.13384	0.004000	0.04260	0.633000	0.24598	0.023000	0.15187	-1.616000	0.00795	TGT		0.418	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		C	48873903	T	C	48873903	3	2	23	1	0	0	0	0	1	0	0	0	6874	1696	59	4	722	4	GTF2A1L	2	48873903	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	24612579	48873903	194325470	7	2040										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55561549	55561549	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gtcttttgctagatatttttAgttcttctaggtttttctgc	7	6	4	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:55561549A>T	ENST00000436346.1	-	15	3249	c.2408T>A	c.(2407-2409)cTa>cAa	p.L803Q	AC012358.8_ENST00000599475.1_RNA|CCDC88A_ENST00000336838.6_Missense_Mutation_p.L803Q|AC012358.8_ENST00000608103.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.L803Q|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000594078.1_RNA|AC012358.8_ENST00000599352.1_RNA|CCDC88A_ENST00000413716.2_Missense_Mutation_p.L803Q	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	803					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.L803Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						AGATATTTTTAGTTCTTCTAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	89	89					2																	55561549		2202	4298	6500	55415053	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.2408T>A	2.37:g.55561549A>T	ENSP00000410608:p.Leu803Gln		55415053	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	A	17.39	3.377157	0.61735	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.19806	2.12;2.38;2.33;2.15	5.03	5.03	0.67393	.	0.000000	0.37577	U	0.002040	T	0.47358	0.1441	M	0.76838	2.35	0.80722	D	1	D;D;D;D;D	0.89917	0.98;1.0;0.996;1.0;1.0	P;D;P;D;D	0.91635	0.814;0.999;0.882;0.997;0.999	T	0.45249	-0.9274	10	0.39692	T	0.17	-5.2718	15.1059	0.72322	1.0:0.0:0.0:0.0	.	803;803;803;803;803	B7ZM78;Q3V6T2-2;Q3V6T2;Q3V6T2-3;Q3V6T2-4	.;.;GRDN_HUMAN;.;.	Q	803	ENSP00000338728:L803Q;ENSP00000263630:L803Q;ENSP00000410608:L803Q;ENSP00000404431:L803Q	ENSP00000263630:L803Q	L	-	2	0	CCDC88A	55415053	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.300000	0.78841	2.034000	0.60081	0.369000	0.22263	CTA		0.318	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		T	55561549	A	T	55561549	3	4	23	1	0	0	0	0	1	0	0	0	2869	420	15	5	3279	5	CCDC88A	2	55561549	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10	6687646	55561549	187637824	8	2041										
RNF103	7844	hgsc.bcm.edu	37	chr2	86847522	86847522	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgcatttcaccactgaaattGgtactagaaaccgattcgga	8	9	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:86847522G>A	ENST00000237455.4	-	2	1265	c.297C>T	c.(295-297)acC>acT	p.T99T	AC015971.2_ENST00000424788.1_RNA|CHMP3_ENST00000439940.2_Silent_p.T21T|RNF103_ENST00000477307.1_5'UTR|RNF103-CHMP3_ENST00000604011.1_Silent_p.T21T|AC015971.2_ENST00000426549.1_RNA|AC015971.2_ENST00000439077.1_RNA	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	99					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T99T(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						CACTGAAATTGGTACTAGAAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	2											99	96	97					2																	86847522		2203	4300	6503	86701033	SO:0001819	synonymous_variant	7844			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.297C>T	2.37:g.86847522G>A			86701033	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Silent	SNP	ENST00000237455.4	37	CCDS33237.1																																																																																				0.398	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		A	86847522	G	A	86847522	2	1	23	1	0	0	0	0	0	0	0	1	13460	1335	47	3		3	RNF103	2	86847522	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	31285973	86847522	156351851	9	2042										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96944361	96944361	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gccacgtccatctcgtcctcGatgctgatgcacttggactg	10	14	1	1	rs142524062		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:96944361G>A	ENST00000323853.5	-	38	5489	c.5412C>T	c.(5410-5412)atC>atT	p.I1804I	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1804					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.I1804I(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCTCGTCCTCGATGCTGATGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		0,4406		0,0,2203	105	96	99		5412	-8.4	0.7	2	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SNRNP200	NM_014014.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1804/2137	96944361	1,13005	2203	4300	6503	96308088	SO:0001819	synonymous_variant	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5412C>T	2.37:g.96944361G>A			96308088	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																				0.582	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		A	96944361	G	A	96944361	2	1	23	1	0	0	0	0	0	0	0	1	14889	1048	37	1		1	SNRNP200	2	96944361	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	10096839	96944361	146255012	10	2043										
DPP10	57628	hgsc.bcm.edu	37	chr2	116548684	116548684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tatattggaaagcaattctaTgctgaaggaagctatcctga	9	6	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:116548684T>C	ENST00000410059.1	+	18	2039	c.1559T>C	c.(1558-1560)aTg>aCg	p.M520T	DPP10_ENST00000393147.2_Missense_Mutation_p.M524T|DPP10_ENST00000310323.8_Missense_Mutation_p.M513T|DPP10_ENST00000409163.1_Missense_Mutation_p.M470T	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	520						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.M513T(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGCAATTCTATGCTGAAGGAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	64	63					2																	116548684		2202	4297	6499	116265154	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1559T>C	2.37:g.116548684T>C	ENSP00000386565:p.Met520Thr		116265154	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	T	6.504	0.461244	0.12342	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.54	3.1	0.35709	.	0.638830	0.17490	N	0.172389	T	0.19927	0.0479	L	0.36672	1.1	0.21652	N	0.999601	B;B;B;B	0.12630	0.006;0.005;0.003;0.003	B;B;B;B	0.09377	0.003;0.004;0.001;0.001	T	0.28618	-1.0038	10	0.13853	T	0.58	-1.6166	7.2627	0.26212	0.1447:0.0:0.1519:0.7035	.	513;524;516;520	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	T	520;470;524;513;470	ENSP00000386565:M520T;ENSP00000387038:M470T;ENSP00000376855:M524T;ENSP00000309066:M513T	ENSP00000309066:M513T	M	+	2	0	DPP10	116265154	0.995000	0.38212	0.925000	0.36789	0.956000	0.61745	2.876000	0.48498	0.489000	0.27749	0.528000	0.53228	ATG		0.328	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116548684	T	C	116548684	3	2	23	1	0	0	0	0	1	0	0	0	4738	1464	51	4	1800	4	DPP10	2	116548684	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	19604323	116548684	126650689	11	2044										
MARCH7	64844	hgsc.bcm.edu	37	chr2	160619487	160619487	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgatgggaaatacaaatgaaCcaagcacacgtgtccgagta	10	8	0	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:160619487C>G	ENST00000259050.4	+	8	2112	c.1990C>G	c.(1990-1992)Cca>Gca	p.P664A	MARCH7_ENST00000409591.1_Missense_Mutation_p.P626A|MARCH7_ENST00000409175.1_Missense_Mutation_p.P664A|MARCH7_ENST00000539065.1_Missense_Mutation_p.P608A	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	664					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P664A(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						TACAAATGAACCAAGCACACG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	104	108					2																	160619487		2203	4300	6503	160327733	SO:0001583	missense	64844			AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	17393	protein-coding gene	gene with protein product		613334	"axotrophin", "membrane-associated ring finger (C3HC4) 7"	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1990C>G	2.37:g.160619487C>G	ENSP00000259050:p.Pro664Ala		160327733	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	C	3.163	-0.171718	0.06421	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591;ENST00000420397	T;T;T;T;T	0.39406	3.09;2.99;3.09;3.07;1.08	5.11	4.16	0.48862	.	0.054440	0.64402	D	0.000001	T	0.11665	0.0284	N	0.00538	-1.39	0.33402	D	0.57746	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.09377	0.004;0.003;0.002	T	0.21999	-1.0229	10	0.02654	T	1	-13.7879	12.4292	0.55565	0.0:0.5886:0.4114:0.0	.	608;626;664	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	A	664;608;664;626;97	ENSP00000386830:P664A;ENSP00000442992:P608A;ENSP00000259050:P664A;ENSP00000387238:P626A;ENSP00000391493:P97A	ENSP00000259050:P664A	P	+	1	0	MARCH7	160327733	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.995000	0.63908	2.527000	0.85204	0.650000	0.86243	CCA		0.428	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		G	160619487	C	G	160619487	3	3	23	1	0	0	0	0	1	0	0	0	9336	507	18	5	2016	5	MARCH7	2	160619487	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	44070803	160619487	82579886	12	2045										
SDPR	8436	hgsc.bcm.edu	37	chr2	192701302	192701302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cagggcctcctcatcgtgggGcaaatcatcatctgaggaga	12	11	4	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:192701302G>A	ENST00000304141.4	-	2	954	c.625C>T	c.(625-627)Ccc>Tcc	p.P209S		NM_004657.5	NP_004648.1			serum deprivation response									p.P209S(1)		NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			TCATCGTGGGGCAAATCATCA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	95	93					2																	192701302		2203	4300	6503	192409547	SO:0001583	missense	8436			AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.625C>T	2.37:g.192701302G>A	ENSP00000305675:p.Pro209Ser		192409547		Missense_Mutation	SNP	ENST00000304141.4	37	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	G	1.432	-0.570067	0.03910	.	.	ENSG00000168497	ENST00000304141	T	0.58358	0.34	5.16	-0.0679	0.13758	.	0.464038	0.23069	N	0.052299	T	0.39226	0.1070	L	0.54323	1.7	0.09310	N	1	B	0.28933	0.228	B	0.27796	0.083	T	0.32561	-0.9902	10	0.09843	T	0.71	-15.744	9.289	0.37775	0.063:0.5258:0.303:0.1083	.	209	O95810	SDPR_HUMAN	S	209	ENSP00000305675:P209S	ENSP00000305675:P209S	P	-	1	0	SDPR	192409547	0.433000	0.25562	0.019000	0.16419	0.009000	0.06853	1.035000	0.30216	-0.185000	0.10550	-0.344000	0.07964	CCC		0.527	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		A	192701302	G	A	192701302	3	1	23	1	0	0	0	0	1	0	0	0	14007	1203	42	3	656	3	SDPR	2	192701302	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	32081815	192701302	50498071	13	2046										
FN1	2335	hgsc.bcm.edu	37	chr2	216274441	216274441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	caagaggagaaaagggagtcGtctctcctgtcacggtgttg	14	8	2	2	rs144664306	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr2:216274441G>A	ENST00000359671.1	-	15	2409	c.2144C>T	c.(2143-2145)aCg>aTg	p.T715M	FN1_ENST00000323926.6_Missense_Mutation_p.T715M|FN1_ENST00000432072.2_Missense_Mutation_p.T715M|FN1_ENST00000336916.4_Missense_Mutation_p.T715M|FN1_ENST00000346544.3_Missense_Mutation_p.T715M|FN1_ENST00000357009.2_Missense_Mutation_p.T715M|FN1_ENST00000421182.1_Missense_Mutation_p.T715M|FN1_ENST00000345488.5_Missense_Mutation_p.T715M|FN1_ENST00000357867.4_Missense_Mutation_p.T715M|FN1_ENST00000446046.1_Missense_Mutation_p.T715M|FN1_ENST00000443816.1_Missense_Mutation_p.T715M|FN1_ENST00000356005.4_Missense_Mutation_p.T715M|FN1_ENST00000354785.4_Missense_Mutation_p.T715M			P02751	FINC_HUMAN	fibronectin 1	715					acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.T715M(3)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	AAAGGGAGTCGTCTCTCCTGT	0.502													G|||	6	0.00119808	8e-04	0	5008	,	,		19769	0.001		0	False		,,,				2504	0.0041															3	Substitution - Missense(3)	lung(2)|large_intestine(1)	2						G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	49	43	45		2144,2144,2144,2144,2144	3.9	0.7	2	dbSNP_134	45	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense,missense,missense	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	81,81,81,81,81	0,9,6494	AA,AG,GG		0.1047,0.0,0.0692	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/2356,715/2177,715/2297,715/2331,715/2478	216274441	9,12997	2203	4300	6503	215982686	SO:0001583	missense	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2144C>T	2.37:g.216274441G>A	ENSP00000352696:p.Thr715Met		215982686	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	18.71	3.683226	0.68157	0.0	0.001047	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.52295	0.67;2.03;2.21;0.74;2.26;1.89;2.25;1.91;2.2;1.92;1.41;0.75;1.32	5.81	3.94	0.45596	.	0.166645	0.41823	D	0.000804	T	0.63780	0.2540	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.996;0.992;0.998;0.997;1.0;0.999;0.998;0.998;0.995	D;D;P;P;B;D;P;P;P;P	0.71656	0.911;0.913;0.72;0.633;0.43;0.974;0.869;0.633;0.633;0.892	T	0.66069	-0.6015	10	0.72032	D	0.01	.	13.0344	0.58862	0.0:0.124:0.7468:0.1292	.	715;715;715;715;715;715;715;715;715;715	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	M	715	ENSP00000394423:T715M;ENSP00000323534:T715M;ENSP00000338200:T715M;ENSP00000350534:T715M;ENSP00000346839:T715M;ENSP00000352696:T715M;ENSP00000265312:T715M;ENSP00000273049:T715M;ENSP00000349509:T715M;ENSP00000410422:T715M;ENSP00000415018:T715M;ENSP00000399538:T715M;ENSP00000348285:T715M	ENSP00000265313:T715M	T	-	2	0	FN1	215982686	1.000000	0.71417	0.667000	0.29798	0.619000	0.37552	7.539000	0.82063	0.836000	0.34901	0.655000	0.94253	ACG		0.502	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216274441	G	A	216274441	3	1	23	1	0	0	0	0	1	0	0	0	5981	1145	40	1	5417	1	FN1	2	216274441	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	23573139	216274441	26924932	14	2047										
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10979978	10979978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ccagcacagatctgaaaatgCggggcaagcttggggtgagc	15	9	1	3	rs142712079	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr3:10979978C>T	ENST00000254488.2	+	14	1855	c.1789C>T	c.(1789-1791)Cgg>Tgg	p.R597W		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	597					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R597W(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	TCTGAAAATGCGGGGCAAGCT	0.547													C|||	7	0.00139776	0	0	5008	,	,		18261	0.0069		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	117	108	111		1789	1.5	1	3	dbSNP_134	111	0,8600		0,0,4300	yes	missense	SLC6A11	NM_014229.1	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	597/633	10979978	2,13004	2203	4300	6503	10954978	SO:0001583	missense	6538			S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"Solute carriers"	11044	protein-coding gene	gene with protein product	"GABA transporter 3"	607952	"solute carrier family 6 (neurotransmitter transporter, GABA), member 11"			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1789C>T	3.37:g.10979978C>T	ENSP00000254488:p.Arg597Trp		10954978	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	37	CCDS2602.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	14.81	2.647594	0.47258	4.54E-4	0.0	ENSG00000132164	ENST00000254488	T	0.74842	-0.88	4.81	1.53	0.23141	.	0.361639	0.26542	N	0.023798	T	0.53997	0.1831	L	0.29908	0.895	0.80722	D	1	B	0.18863	0.031	B	0.12837	0.008	T	0.56189	-0.8020	10	0.51188	T	0.08	.	13.7065	0.62644	0.5834:0.4166:0.0:0.0	.	597	P48066	S6A11_HUMAN	W	597	ENSP00000254488:R597W	ENSP00000254488:R597W	R	+	1	2	SLC6A11	10954978	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.124000	0.42006	0.418000	0.25898	0.655000	0.94253	CGG		0.547	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		T	10979978	C	T	10979978	3	4	23	1	0	0	0	0	1	0	0	0	14711	759	27	1	1843	1	SLC6A11	3	10979978	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		10979978	187042452	15	2048										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401925	140401925	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ttctctttccacaatggccaCgacaccattagcctcatcga	5	15	2	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr3:140401925C>T	ENST00000286349.3	+	2	1154	c.963C>T	c.(961-963)caC>caT	p.H321H		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	321						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.H321H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ACAATGGCCACGACACCATTA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	3											224	194	204					3																	140401925		2203	4300	6503	141884615	SO:0001819	synonymous_variant	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.963C>T	3.37:g.140401925C>T			141884615	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																				0.552	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140401925	C	T	140401925	2	4	23	1	0	0	0	0	0	0	0	1	16557	535	19	1		1	TRIM42	3	140401925	Silent	SNP	C	TCGA-AG-3593-01A-01W-0831-10	129421947	140401925	57620505	16	2049										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172052861	172052861	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	agttacatctcatggctttaGtgtcaaatggggtatgtttt	10	5	2	0	rs148414755		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr3:172052861G>C	ENST00000336824.4	+	15	1868	c.1769G>C	c.(1768-1770)aGt>aCt	p.S590T	FNDC3B_ENST00000415807.2_Missense_Mutation_p.S590T|FNDC3B_ENST00000416957.1_Missense_Mutation_p.S590T	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	590	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S590T(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CATGGCTTTAGTGTCAAATGG	0.408													G|||	1	0.000199681	0	0	5008	,	,		14203	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	THR/SER,THR/SER	0,4406		0,0,2203	223	213	216		1769,1769	6.2	1	3	dbSNP_134	216	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FNDC3B	NM_001135095.1,NM_022763.3	58,58	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	benign,benign	590/1205,590/1205	172052861	1,13005	2203	4300	6503	173535555	SO:0001583	missense	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1769G>C	3.37:g.172052861G>C	ENSP00000338523:p.Ser590Thr		173535555	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.530713	0.27387	0.0	1.16E-4	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.55930	0.49;0.49;0.49	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.167364	0.64402	D	0.000004	T	0.31295	0.0792	N	0.03268	-0.37	0.80722	D	1	B;B	0.20780	0.048;0.002	B;B	0.21360	0.034;0.01	T	0.18398	-1.0338	10	0.21014	T	0.42	-14.8476	16.2608	0.82541	0.0:0.1316:0.8683:0.0	.	590;590	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	T	590	ENSP00000411242:S590T;ENSP00000338523:S590T;ENSP00000389094:S590T	ENSP00000338523:S590T	S	+	2	0	FNDC3B	173535555	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.042000	0.49815	2.941000	0.99782	0.655000	0.94253	AGT		0.408	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		C	172052861	G	C	172052861	3	2	23	1	0	0	0	0	1	0	0	0	5989	1029	36	5	1823	5	FNDC3B	3	172052861	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	31650936	172052861	25969569	17	2050										
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183859765	183859765	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tggcagggtgttcgagtggcGgctggagcacagatccatca	16	9	1	1	rs143448763		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr3:183859765G>A	ENST00000273783.3	+	8	1331	c.1209G>A	c.(1207-1209)gcG>gcA	p.A403A	EIF2B5_ENST00000444495.1_Silent_p.A403A	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	403					astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)	p.A403A(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			TTCGAGTGGCGGCTGGAGCAC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		1,4405	2.1+/-5.4	0,1,2202	127	113	118		1209	-3.2	0.8	3	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	EIF2B5	NM_003907.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		403/722	183859765	1,13005	2203	4300	6503	185342459	SO:0001819	synonymous_variant	8893			U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.1209G>A	3.37:g.183859765G>A			185342459	Q541Z1|Q96D04	Silent	SNP	ENST00000273783.3	37	CCDS3252.1																																																																																				0.562	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1			A	183859765	G	A	183859765	2	1	23	1	0	0	0	0	0	0	0	1	5015	1103	39	1		1	EIF2B5	3	183859765	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	11806904	183859765	14162665	18	2051										
RFC4	5984	hgsc.bcm.edu	37	chr3	186508157	186508157	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tcaaaagagccactctgacaGgcagcaaatactccatcaat	6	12	3	2	rs201614562		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr3:186508157G>C	ENST00000392481.2	-	9	1121	c.840C>G	c.(838-840)gcC>gcG	p.A280A	RFC4_ENST00000296273.2_Silent_p.A280A|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000433496.1_Intron	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	280					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.A280A(1)		breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		CACTCTGACAGGCAGCAAATA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3											110	111	111					3																	186508157		2203	4300	6503	187990851	SO:0001819	synonymous_variant	5984				CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"ATPases / AAA-type"	9972	protein-coding gene	gene with protein product	"A1 37 kDa subunit", "activator 1 37 kDa subunit", "RFC 37 kDa subunit"	102577	"replication factor C (activator 1) 4 (37kD)"			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.840C>G	3.37:g.186508157G>C			187990851	B4DM41|D3DNV2|Q6FHX7	Silent	SNP	ENST00000392481.2	37	CCDS3283.1																																																																																				0.388	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		C	186508157	G	C	186508157	2	2	23	1	0	0	0	0	0	0	0	1	13284	987	35	5		5	RFC4	3	186508157	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	2648392	186508157	11514273	19	2052										
EVC2	132884	hgsc.bcm.edu	37	chr4	5690922	5690922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	taaaagcctggaatccttccGaggtcctgtttcccacagag	9	12	0	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:5690922G>A	ENST00000344408.5	-	5	721	c.668C>T	c.(667-669)tCg>tTg	p.S223L	EVC2_ENST00000344938.1_Missense_Mutation_p.S223L|EVC2_ENST00000310917.2_Missense_Mutation_p.S143L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	223					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S223L(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						GAATCCTTCCGAGGTCCTGTT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4											100	92	94					4																	5690922		2203	4300	6503	5741823	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.668C>T	4.37:g.5690922G>A	ENSP00000342144:p.Ser223Leu		5741823	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	5.073	0.199175	0.09652	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.75050	-0.9;-0.89;-0.89	4.54	2.7	0.31948	.	0.000000	0.85682	D	0.000000	T	0.56949	0.2020	L	0.42245	1.32	0.09310	N	1	P	0.43633	0.813	B	0.25405	0.06	T	0.50558	-0.8814	10	0.48119	T	0.1	-1.4813	9.8406	0.40996	0.0:0.0:0.6552:0.3448	.	223	Q86UK5	LBN_HUMAN	L	223;143;223	ENSP00000339954:S223L;ENSP00000311683:S143L;ENSP00000342144:S223L	ENSP00000311683:S143L	S	-	2	0	EVC2	5741823	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.417000	0.21214	0.403000	0.25479	0.561000	0.74099	TCG		0.488	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5690922	G	A	5690922	3	1	23	1	0	0	0	0	1	0	0	0	5299	1059	37	1	3330	1	EVC2	4	5690922	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		5690922	185463354	20	2053										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47907326	47907326	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gcttgaaaagcttcatttacAtattgttttgttcgctctaa	6	7	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:47907326A>G	ENST00000507489.1	-	4	620	c.444T>C	c.(442-444)taT>taC	p.Y148Y	NFXL1_ENST00000381538.3_Silent_p.Y148Y|NFXL1_ENST00000329043.3_Silent_p.Y148Y	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	148						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Y148Y(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CTTCATTTACATATTGTTTTG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	4											156	163	160					4																	47907326		2203	4300	6503	47602083	SO:0001819	synonymous_variant	152518			AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.444T>C	4.37:g.47907326A>G			47602083	B1Q2K1|Q86VG1|Q8WVH1	Silent	SNP	ENST00000507489.1	37	CCDS3478.2																																																																																				0.333	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		G	47907326	A	G	47907326	2	3	23	1	0	0	0	0	0	0	0	1	10419	224	8	4		4	NFXL1	4	47907326	Silent	SNP	A	TCGA-AG-3593-01A-01W-0831-10	42216404	47907326	143246950	21	2054										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77231020	77231020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tcattccattttcctgcctgCagatacagtggtggagtgga	11	9	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:77231020C>T	ENST00000237642.6	+	2	1688	c.944C>T	c.(943-945)gCa>gTa	p.A315V	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Missense_Mutation_p.A166V	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough									p.A315V(1)									TTCCTGCCTGCAGATACAGTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											187	178	181					4																	77231020		2203	4300	6503	77450044	SO:0001583	missense	8987				CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.944C>T	4.37:g.77231020C>T	ENSP00000237642:p.Ala315Val		77450044		Missense_Mutation	SNP	ENST00000237642.6	37	CCDS3578.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.534899	0.27475	.	.	ENSG00000118804	ENST00000539752;ENST00000237642	D;D	0.94497	-3.44;-3.44	5.4	4.48	0.54585	Carbohydrate-binding-like fold (1);Glycoside hydrolase, carbohydrate-binding (2);Immunoglobulin-like fold (1);	0.218818	0.29438	N	0.012146	D	0.92244	0.7540	L	0.52759	1.655	0.19775	N	0.999957	P	0.39094	0.659	P	0.44673	0.457	D	0.85032	0.0918	10	0.34782	T	0.22	-14.9282	7.997	0.30273	0.0:0.8423:0.0:0.1577	.	315	O95210	STBD1_HUMAN	V	166;315	ENSP00000442265:A166V;ENSP00000237642:A315V	ENSP00000237642:A315V	A	+	2	0	STBD1	77450044	0.013000	0.17824	0.770000	0.31555	0.105000	0.19272	0.168000	0.16622	2.805000	0.96524	0.655000	0.94253	GCA		0.483	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			T	77231020	C	T	77231020	3	4	23	1	0	0	0	0	1	0	0	0	15313	710	25	3	950	3	STBD1	4	77231020	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	29323694	77231020	113923256	22	2055										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122254012	122254012	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tttcttttccatgaatagttCgaagcactgaaccatcccca	5	12	1	2	rs543792498	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:122254012C>T	ENST00000394427.2	-	4	1172	c.761G>A	c.(760-762)cGa>cAa	p.R254Q	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	254				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.R254Q(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						ATGAATAGTTCGAAGCACTGA	0.353													C|||	2	0.000399361	0	0.0014	5008	,	,		14668	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											84	81	82					4																	122254012		2203	4300	6503	122473462	SO:0001583	missense	84109			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.761G>A	4.37:g.122254012C>T	ENSP00000377948:p.Arg254Gln		122473462		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	C	0.817	-0.750009	0.03041	.	.	ENSG00000186867	ENST00000394427	T	0.74315	-0.83	6.17	0.811	0.18739	GPCR, rhodopsin-like superfamily (1);	0.459160	0.25857	N	0.027850	T	0.49236	0.1545	N	0.12961	0.28	0.29769	N	0.834915	B	0.14012	0.009	B	0.08055	0.003	T	0.38845	-0.9642	10	0.06625	T	0.88	.	9.4707	0.38839	0.0:0.3941:0.0:0.6058	.	254	Q96P65	QRFPR_HUMAN	Q	254	ENSP00000377948:R254Q	ENSP00000377948:R254Q	R	-	2	0	QRFPR	122473462	0.996000	0.38824	0.819000	0.32651	0.170000	0.22686	0.324000	0.19610	-0.020000	0.14032	-0.797000	0.03246	CGA		0.353	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		T	122254012	C	T	122254012	3	4	23	1	0	0	0	0	1	0	0	0	12915	884	31	1	546	1	QRFPR	4	122254012	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	45022992	122254012	68900264	23	2056										
FAT4	79633	hgsc.bcm.edu	37	chr4	126371394	126371394	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cactttcttcccaagcaactGttcacataactgtcactgag	5	13	3	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:126371394G>C	ENST00000394329.3	+	9	9236	c.9223G>C	c.(9223-9225)Gtt>Ctt	p.V3075L	FAT4_ENST00000335110.5_Missense_Mutation_p.V1373L	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3075	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V3075L(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCAAGCAACTGTTCACATAAC	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	4											98	93	94					4																	126371394		2203	4300	6503	126590844	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9223G>C	4.37:g.126371394G>C	ENSP00000377862:p.Val3075Leu		126590844	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	10.66	1.411790	0.25465	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.57107	0.42;1.81	5.63	4.78	0.61160	Cadherin (4);Cadherin-like (1);	0.275170	0.18282	U	0.145996	T	0.44726	0.1307	L	0.38692	1.165	0.58432	D	0.999999	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.15052	0.005;0.012;0.007	T	0.24941	-1.0146	10	0.32370	T	0.25	.	14.9304	0.70911	0.0691:0.0:0.9309:0.0	.	1373;3075;3075	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	L	3075;1373	ENSP00000377862:V3075L;ENSP00000335169:V1373L	ENSP00000335169:V1373L	V	+	1	0	FAT4	126590844	1.000000	0.71417	0.894000	0.35097	0.463000	0.32649	3.729000	0.54999	1.353000	0.45828	0.655000	0.94253	GTT		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126371394	G	C	126371394	3	2	23	1	0	0	0	0	1	0	0	0	5711	1377	48	5	9257	5	FAT4	4	126371394	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	4117382	126371394	64782882	24	2057										
FGA	2243	hgsc.bcm.edu	37	chr4	155507733	155507733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tagggttcctggggctttccGtctctgatccggttccataa	11	11	1	1	rs555704618		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:155507733G>A	ENST00000302053.3	-	5	926	c.848C>T	c.(847-849)aCg>aTg	p.T283M	FGA_ENST00000403106.3_Missense_Mutation_p.T283M	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	283					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.T283M(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GGGGCTTTCCGTCTCTGATCC	0.542													G|||	1	0.000199681	8e-04	0	5008	,	,		18029	0		0	False		,,,				2504	0				NSCLC(143;340 1922 20892 22370 48145)											1	Substitution - Missense(1)	large_intestine(1)	4											99	107	104					4																	155507733		2203	4300	6503	155727183	SO:0001583	missense	2243				CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.848C>T	4.37:g.155507733G>A	ENSP00000306361:p.Thr283Met		155727183	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630623	0.46944	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	D;D	0.82619	-1.63;-1.63	4.91	-2.44	0.06502	.	32.388400	0.00166	N	0.000000	T	0.72566	0.3476	L	0.38175	1.15	0.09310	N	1	P;P	0.49862	0.929;0.928	B;B	0.38712	0.28;0.109	T	0.65413	-0.6174	10	0.59425	D	0.04	.	4.3068	0.10951	0.0741:0.3172:0.3568:0.2519	.	283;283	P02671-2;P02671	.;FIBA_HUMAN	M	283	ENSP00000306361:T283M;ENSP00000385981:T283M	ENSP00000306361:T283M	T	-	2	0	FGA	155727183	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.274000	0.18680	-0.382000	0.07870	-0.344000	0.07964	ACG		0.542	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		A	155507733	G	A	155507733	3	1	23	1	0	0	0	0	1	0	0	0	5849	1145	40	1	1804	1	FGA	4	155507733	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	29136339	155507733	35646543	25	2058										
CCDC111	201973	hgsc.bcm.edu	37	chr4	185612854	185612854	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gctgaagtatgtctcctgttTcttttcaaagaggtaagtac	9	7	3	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr4:185612854T>A	ENST00000314970.6	+	13	1846	c.1413T>A	c.(1411-1413)ttT>ttA	p.F471L	PRIMPOL_ENST00000515774.1_Missense_Mutation_p.F342L|PRIMPOL_ENST00000512834.1_Missense_Mutation_p.F470L|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.F471L	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	471					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)	p.F471L(1)									GTCTCCTGTTTCTTTTCAAAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											158	156	156					4																	185612854		2202	4300	6502	185849848	SO:0001583	missense	201973			AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1413T>A	4.37:g.185612854T>A	ENSP00000313816:p.Phe471Leu		185849848	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.741093	0.30865	.	.	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834;ENST00000508001	T;T;T;T	0.30448	1.54;1.53;1.54;1.54	4.84	1.15	0.20763	.	0.596983	0.19257	N	0.118768	T	0.25121	0.0610	L	0.59436	1.845	0.80722	D	1	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.05084	-1.0907	10	0.41790	T	0.15	-9.7233	5.6268	0.17487	0.0:0.2281:0.1515:0.6204	.	342;471;470	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	L	471;342;471;470;145	ENSP00000313816:F471L;ENSP00000421913:F342L;ENSP00000420860:F471L;ENSP00000425316:F470L	ENSP00000313816:F471L	F	+	3	2	CCDC111	185849848	0.315000	0.24571	0.045000	0.18777	0.800000	0.45204	0.511000	0.22739	0.115000	0.18071	0.260000	0.18958	TTT		0.353	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		A	185612854	T	A	185612854	3	1	23	1	0	0	0	0	1	0	0	0	2754	1780	62	5	1455	5	CCDC111	4	185612854	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	30105121	185612854	5541422	26	2059										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75973062	75973062	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ggaaatatttcaaagaagcaTgtaatgtccctgagccagaa	9	7	1	3			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:75973062T>G	ENST00000274364.6	+	28	3844	c.3547T>G	c.(3547-3549)Tgt>Ggt	p.C1183G	IQGAP2_ENST00000379730.3_Missense_Mutation_p.C685G|IQGAP2_ENST00000502745.1_Missense_Mutation_p.C679G|IQGAP2_ENST00000396234.3_Missense_Mutation_p.C679G	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1183					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.C1183G(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CAAAGAAGCATGTAATGTCCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	73	73					5																	75973062		2203	4300	6503	76008818	SO:0001583	missense	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3547T>G	5.37:g.75973062T>G	ENSP00000274364:p.Cys1183Gly		76008818	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.088412	0.76756	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.15	5.15	0.70609	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.000000	0.85682	D	0.000000	T	0.81446	0.4824	M	0.86953	2.85	0.80722	D	1	D;D;D	0.60575	0.988;0.988;0.965	D;D;D	0.75484	0.986;0.986;0.917	D	0.85149	0.0985	10	0.87932	D	0	-14.4369	15.1126	0.72372	0.0:0.0:0.0:1.0	.	685;679;1183	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	G	1183;685;1133;679;679	ENSP00000274364:C1183G;ENSP00000442313:C685G;ENSP00000421097:C1133G;ENSP00000379535:C679G;ENSP00000426027:C679G	ENSP00000274364:C1183G	C	+	1	0	IQGAP2	76008818	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.771000	0.85420	2.162000	0.67917	0.482000	0.46254	TGT		0.343	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		G	75973062	T	G	75973062	3	3	23	1	0	0	0	0	1	0	0	0	7836	1464	51	4	3657	4	IQGAP2	5	75973062	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10		75973062	104942198	27	2060										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101816000	101816000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	atattactttttttctgtctCcatagaatgctataaatatt	3	6	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:101816000C>T	ENST00000506729.1	-	2	668	c.497G>A	c.(496-498)gGa>gAa	p.G166E	SLCO6A1_ENST00000513675.1_Missense_Mutation_p.G166E|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.G166E|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.G166E|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.G166E|SLCO6A1_ENST00000514551.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.G166E(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TTTTCTGTCTCCATAGAATGC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											117	120	119					5																	101816000		2203	4300	6503	101843899	SO:0001583	missense	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.497G>A	5.37:g.101816000C>T	ENSP00000421339:p.Gly166Glu		101843899	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.784825	0.31593	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	4.56	2.67	0.31697	Major facilitator superfamily domain, general substrate transporter (1);	0.257140	0.32640	N	0.005823	T	0.72859	0.3513	M	0.90542	3.125	0.22127	N	0.99935	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.993;1.0	T	0.63391	-0.6648	10	0.87932	D	0	.	7.4958	0.27487	0.1902:0.6261:0.1837:0.0	.	166;166;166	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	E	166	ENSP00000421339:G166E;ENSP00000369135:G166E;ENSP00000373671:G166E;ENSP00000421990:G166E;ENSP00000369138:G166E	ENSP00000369135:G166E	G	-	2	0	SLCO6A1	101843899	0.993000	0.37304	0.503000	0.27626	0.096000	0.18686	1.244000	0.32778	0.583000	0.29574	0.655000	0.94253	GGA		0.328	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		T	101816000	C	T	101816000	3	4	23	1	0	0	0	0	1	0	0	0	14769	855	30	3	1710	3	SLCO6A1	5	101816000	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	25842938	101816000	79099260	28	2061										
APC	324	hgsc.bcm.edu	37	chr5	112175348	112175348	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cagccaggcacaaagctgttGaattttcttcaggagcgaaa	10	9	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:112175348G>T	ENST00000457016.1	+	16	4437	c.4057G>T	c.(4057-4059)Gaa>Taa	p.E1353*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1353*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1353*			P25054	APC_HUMAN	adenomatous polyposis coli	1353	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1353*(12)|p.E1353fs*19(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAAAGCTGTTGAATTTTCTTC	0.483		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(12)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5	GRCh37	CD972008	APC	D							62	65	64					5																	112175348		2202	4300	6502	112203247	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4057G>T	5.37:g.112175348G>T	ENSP00000413133:p.Glu1353*		112203247	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.431314	0.98808	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.111916	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8759	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1353	.	.	E	+	1	0	APC	112203247	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	5.308000	0.65768	2.861000	0.98227	0.655000	0.94253	GAA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175348	G	T	112175348	4	4	23	1	0	0	0	0	0	1	0	0	763	1291	45	2	4115	2	APC	5	112175348	Nonsense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	10359348	112175348	68739912	29	2062										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118483022	118483022	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ttcttctccagagaagatccTatctcctttttcacaaaagt	4	11	4	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:118483022T>A	ENST00000311085.8	+	17	2848	c.2768T>A	c.(2767-2769)cTa>cAa	p.L923Q	DMXL1_ENST00000539542.1_Missense_Mutation_p.L923Q	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	923								p.L923Q(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GAGAAGATCCTATCTCCTTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											62	66	65					5																	118483022		2202	4300	6502	118510921	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2768T>A	5.37:g.118483022T>A	ENSP00000309690:p.Leu923Gln		118510921		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	0.897	-0.723556	0.03158	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.29397	1.57;1.57	5.82	-1.89	0.07689	.	0.855312	0.10769	N	0.636297	T	0.08714	0.0216	N	0.01800	-0.715	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37079	-0.9721	10	0.12430	T	0.62	1.5231	4.7123	0.12879	0.4428:0.2477:0.0:0.3096	.	923;923	F5H269;Q9Y485	.;DMXL1_HUMAN	Q	923	ENSP00000309690:L923Q;ENSP00000439479:L923Q	ENSP00000309690:L923Q	L	+	2	0	DMXL1	118510921	0.000000	0.05858	0.000000	0.03702	0.359000	0.29487	-0.029000	0.12329	-0.143000	0.11334	-0.376000	0.06991	CTA		0.378	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118483022	T	A	118483022	3	1	23	1	0	0	0	0	1	0	0	0	4605	1522	53	5	2834	5	DMXL1	5	118483022	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	6307674	118483022	62432238	30	2063										
SNX2	6643	hgsc.bcm.edu	37	chr5	122165298	122165298	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aattatcattcacagctgatAaaatactgggaagcattcct	6	8	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:122165298A>T	ENST00000379516.2	+	15	1623	c.1515A>T	c.(1513-1515)atA>atT	p.I505I	SNX2_ENST00000510372.1_3'UTR|CTB-36H16.2_ENST00000565823.1_RNA|SNX2_ENST00000514949.1_Silent_p.I388I	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	505					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.I505I(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		CACAGCTGATAAAATACTGGG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	5											93	95	95					5																	122165298		2203	4300	6503	122193197	SO:0001819	synonymous_variant	6643			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1515A>T	5.37:g.122165298A>T			122193197	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Silent	SNP	ENST00000379516.2	37	CCDS34217.1																																																																																				0.333	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		T	122165298	A	T	122165298	2	4	23	1	0	0	0	0	0	0	0	1	14928	352	13	5		5	SNX2	5	122165298	Silent	SNP	A	TCGA-AG-3593-01A-01W-0831-10	3682276	122165298	58749962	31	2064										
SLC22A5	6584	hgsc.bcm.edu	37	chr5	131722803	131722803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ccgcaaggctgccaaagccaAtgggattgttgtgccttcca	11	12	0	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:131722803A>G	ENST00000245407.3	+	5	1132	c.911A>G	c.(910-912)aAt>aGt	p.N304S	SLC22A5_ENST00000435065.2_Missense_Mutation_p.N328S	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	304					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)	p.N304S(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	GCCAAAGCCAATGGGATTGTT	0.552											OREG0016767	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	5											307	261	276					5																	131722803		2203	4300	6503	131750702	SO:0001583	missense	6584			AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"Solute carriers"	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.911A>G	5.37:g.131722803A>G	ENSP00000245407:p.Asn304Ser	1589	131750702	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	37	CCDS4154.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342404	0.61073	.	.	ENSG00000197375	ENST00000245407;ENST00000435065;ENST00000415928	T;T;T	0.57752	0.38;0.38;0.38	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.042955	0.85682	D	0.000000	T	0.81791	0.4897	H	0.96576	3.845	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.992;0.999	D	0.88218	0.2895	10	0.87932	D	0	.	15.4222	0.75022	1.0:0.0:0.0:0.0	.	328;304	A2Q0V1;O76082	.;S22A5_HUMAN	S	304;328;227	ENSP00000245407:N304S;ENSP00000402760:N328S;ENSP00000388838:N227S	ENSP00000245407:N304S	N	+	2	0	SLC22A5	131750702	1.000000	0.71417	0.912000	0.35992	0.029000	0.11900	8.842000	0.92136	2.048000	0.60808	0.460000	0.39030	AAT		0.552	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060		G	131722803	A	G	131722803	3	3	23	1	0	0	0	0	1	0	0	0	14494	101	4	4	929	4	SLC22A5	5	131722803	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10	9557505	131722803	49192457	32	2065										
ZNF454	285676	hgsc.bcm.edu	37	chr5	178392836	178392836	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aaaatctgtgagaaagccttTatccgaagcactcacctgac	7	11	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr5:178392836T>A	ENST00000320129.3	+	5	1734	c.1431T>A	c.(1429-1431)ttT>ttA	p.F477L	ZNF454_ENST00000519564.1_Missense_Mutation_p.F477L	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	477					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F477L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		AGAAAGCCTTTATCCGAAGCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	78	77					5																	178392836		2203	4300	6503	178325442	SO:0001583	missense	285676			AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.1431T>A	5.37:g.178392836T>A	ENSP00000326249:p.Phe477Leu		178325442	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.271478	0.40194	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.46063	0.88;0.88	4.46	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40469	N	0.001081	T	0.60235	0.2253	M	0.83483	2.645	0.33249	D	0.558288	D	0.89917	1.0	D	0.91635	0.999	T	0.67837	-0.5567	10	0.87932	D	0	-13.3973	5.3466	0.16012	0.0:0.3117:0.0:0.6883	.	477	Q8N9F8	ZN454_HUMAN	L	477	ENSP00000326249:F477L;ENSP00000430354:F477L	ENSP00000326249:F477L	F	+	3	2	ZNF454	178325442	0.000000	0.05858	1.000000	0.80357	0.019000	0.09904	-0.770000	0.04705	0.853000	0.35312	0.528000	0.53228	TTT		0.393	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		A	178392836	T	A	178392836	3	1	23	1	0	0	0	0	1	0	0	0	17962	1751	61	5	1445	5	ZNF454	5	178392836	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	46670033	178392836	2522424	33	2066										
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429905	29429905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gacagtgatggcctttgaccGatacgtggctgtctgccagc	13	11	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:29429905G>A	ENST00000377136.1	+	4	824	c.359G>A	c.(358-360)cGa>cAa	p.R120Q	OR2H1_ENST00000377132.1_Missense_Mutation_p.R120Q|OR2H1_ENST00000377133.1_Missense_Mutation_p.R120Q|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000396792.2_Missense_Mutation_p.R120Q|OR2H1_ENST00000442615.1_Missense_Mutation_p.R120Q			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R120Q(1)		large_intestine(5)|lung(12)	17						GCCTTTGACCGATACGTGGCT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	6											166	169	168					6																	29429905		1509	2709	4218	29537884	SO:0001583	missense	26716			AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.359G>A	6.37:g.29429905G>A	ENSP00000366340:p.Arg120Gln		29537884	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475107	0.43942	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	2.92	-1.05	0.10036	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000946	T	0.70928	0.3280	M	0.91612	3.225	0.23126	N	0.998253	D	0.59357	0.985	P	0.48270	0.572	T	0.68318	-0.5440	10	0.87932	D	0	.	4.9109	0.13821	0.2665:0.0:0.5872:0.1463	.	120	Q9GZK4	OR2H1_HUMAN	Q	120	ENSP00000366340:R120Q;ENSP00000366337:R120Q;ENSP00000393254:R120Q;ENSP00000366336:R120Q;ENSP00000380010:R120Q	ENSP00000366336:R120Q	R	+	2	0	OR2H1	29537884	0.963000	0.33076	0.567000	0.28434	0.044000	0.14063	4.391000	0.59652	-0.274000	0.09232	-0.895000	0.02911	CGA		0.577	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			A	29429905	G	A	29429905	3	1	23	1	0	0	0	0	1	0	0	0	11032	1058	37	1	361	1	OR2H1	6	29429905	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		29429905	141685162	34	2067										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32163252	32163252	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tccttggtttatgggcatttCttggagggctgggggaccac	15	8	1	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:32163252C>A	ENST00000375023.3	-	30	6112	c.5974G>T	c.(5974-5976)Gaa>Taa	p.E1992*	GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000375043.3_5'UTR|GPSM3_ENST00000487761.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1992					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.E1992*(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						ATGGGCATTTCTTGGAGGGCT	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											90	112	104					6																	32163252		1507	2707	4214	32271230	SO:0001587	stop_gained	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5974G>T	6.37:g.32163252C>A	ENSP00000364163:p.Glu1992*		32271230	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Nonsense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	46	12.153790	0.99641	.	.	ENSG00000204301	ENST00000375023	.	.	.	4.0	4.0	0.46444	.	1.335850	0.05821	N	0.615832	.	.	.	.	.	.	0.58432	D	0.999992	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	11.7766	0.51989	0.0:1.0:0.0:0.0	.	.	.	.	X	1992	.	ENSP00000364163:E1992X	E	-	1	0	NOTCH4	32271230	0.015000	0.18098	0.005000	0.12908	0.032000	0.12392	2.997000	0.49457	2.246000	0.74042	0.655000	0.94253	GAA		0.517	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32163252	C	A	32163252	4	1	23	1	0	0	0	0	0	1	0	0	10582	922	32	2	41	2	NOTCH4	6	32163252	Nonsense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	2733347	32163252	138951815	35	2068										
TAPBP	6892	hgsc.bcm.edu	37	chr6	33271752	33271752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cttctttgaatccttgcaggTggacaggtagacagctgtgg	13	8	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:33271752T>C	ENST00000489157.1	-	6	1266	c.1054A>G	c.(1054-1056)Acc>Gcc	p.T352A	TAPBP_ENST00000475304.1_Missense_Mutation_p.T457A|TAPBP_ENST00000426633.2_Missense_Mutation_p.T439A|TAPBP_ENST00000434618.2_Missense_Mutation_p.T439A|TAPBP_ENST00000456592.2_Missense_Mutation_p.T439A			O15533	TPSN_HUMAN	TAP binding protein (tapasin)	439	Ig-like C1-type.				amide transport (GO:0042886)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|peptide antigen stabilization (GO:0050823)|peptide transport (GO:0015833)|protein complex assembly (GO:0006461)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|MHC class I peptide loading complex (GO:0042824)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)|peptide antigen-transporting ATPase activity (GO:0015433)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)|unfolded protein binding (GO:0051082)	p.T439A(1)		endometrium(2)|large_intestine(5)|lung(8)|ovary(3)	18						TCCTTGCAGGTGGACAGGTAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											126	109	115					6																	33271752		2203	4300	6503	33379730	SO:0001583	missense	6892			Y13582	CCDS34426.1, CCDS34427.1, CCDS34428.1, CCDS34427.2, CCDS34428.2	6p21.3	2014-09-17			ENSG00000231925	ENSG00000231925		"Immunoglobulin superfamily / C1-set domain containing"	11566	protein-coding gene	gene with protein product		601962				9238042	Standard	NM_003190		Approved	TAPA	uc003odz.3	O15533	OTTHUMG00000031090	ENST00000489157.1:c.1054A>G	6.37:g.33271752T>C	ENSP00000419659:p.Thr352Ala		33379730	A2AB91|A2ABC0|B0V003|B0V0A6|B2ZUA4|E9PGM2|O15210|O15272|Q5STJ8|Q5STK6|Q5STQ5|Q5STQ6|Q66K65|Q96KK7|Q9HAN8|Q9UEE0|Q9UEE4|Q9UIZ6|Q9Y6K2	Missense_Mutation	SNP	ENST00000489157.1	37	CCDS34427.2	.	.	.	.	.	.	.	.	.	.	T	13.40	2.224544	0.39300	.	.	ENSG00000231925	ENST00000434618;ENST00000475304;ENST00000489157;ENST00000426633;ENST00000456592	T;T;T;T;T	0.30448	1.57;1.57;1.57;1.53;1.57	4.0	1.38	0.22167	.	0.554122	0.18317	N	0.144933	T	0.05777	0.0151	N	0.17674	0.51	0.09310	N	1	B;B;B;B	0.11235	0.001;0.001;0.003;0.004	B;B;B;B	0.10450	0.001;0.002;0.005;0.001	T	0.35674	-0.9779	10	0.35671	T	0.21	-0.1021	5.0817	0.14661	0.0:0.3167:0.0:0.6833	.	352;457;439;439	E9PGM2;A2AB90;O15533-3;O15533	.;.;.;TPSN_HUMAN	A	439;457;352;439;439	ENSP00000395701:T439A;ENSP00000417949:T457A;ENSP00000419659:T352A;ENSP00000404833:T439A;ENSP00000387803:T439A	ENSP00000404833:T439A	T	-	1	0	TAPBP	33379730	0.000000	0.05858	0.000000	0.03702	0.898000	0.52572	0.016000	0.13377	0.276000	0.22118	0.448000	0.29417	ACC		0.527	TAPBP-006	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276425.2			C	33271752	T	C	33271752	3	2	23	1	0	0	0	0	1	0	0	0	15591	1696	59	4	219	4	TAPBP	6	33271752	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	1108500	33271752	137843315	36	2069										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42200566	42200566	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ggatggcacctcgggccttgGtcacctggttggtgcccccg	15	14	1	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:42200566G>T	ENST00000372922.4	-	17	3693	c.3131C>A	c.(3130-3132)aCc>aAc	p.T1044N	TRERF1_ENST00000340840.2_Missense_Mutation_p.T973N|TRERF1_ENST00000354325.2_Missense_Mutation_p.T961N|TRERF1_ENST00000372917.4_Missense_Mutation_p.T973N|TRERF1_ENST00000541110.1_Missense_Mutation_p.T1064N	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1044	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.T1044N(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCGGGCCTTGGTCACCTGGTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											43	37	39					6																	42200566		2203	4300	6503	42308544	SO:0001583	missense	55809			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3131C>A	6.37:g.42200566G>T	ENSP00000362013:p.Thr1044Asn		42308544	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.540630	0.65085	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.54	5.54	0.83059	.	0.473238	0.19242	N	0.119150	T	0.14442	0.0349	N	0.19112	0.55	0.42849	D	0.994072	B;B;B;B;P	0.42692	0.161;0.1;0.1;0.161;0.787	B;B;B;B;B	0.44108	0.067;0.03;0.03;0.067;0.441	T	0.02983	-1.1086	10	0.31617	T	0.26	-5.9318	13.7851	0.63105	0.073:0.0:0.927:0.0	.	961;1064;1044;800;812	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	N	1064;973;1044;973;961	ENSP00000439689:T1064N;ENSP00000362008:T973N;ENSP00000362013:T1044N;ENSP00000339438:T973N;ENSP00000346285:T961N	ENSP00000339438:T973N	T	-	2	0	TRERF1	42308544	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.108000	0.64609	2.626000	0.88956	0.585000	0.79938	ACC		0.607	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		T	42200566	G	T	42200566	3	4	23	1	0	0	0	0	1	0	0	0	16515	1261	44	2	479	2	TRERF1	6	42200566	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	8928814	42200566	128914501	37	2070										
MDN1	23195	hgsc.bcm.edu	37	chr6	90377798	90377798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gccttctccaattccacctcCctcatagtcatggaactcag	5	16	4	0	rs370775568		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:90377798C>T	ENST00000369393.3	-	84	14144	c.14029G>A	c.(14029-14031)Gga>Aga	p.G4677R	MDN1_ENST00000428876.1_Missense_Mutation_p.G4677R|MDN1_ENST00000468568.1_5'Flank			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4677					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.G4677R(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATTCCACCTCCCTCATAGTCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											225	172	190					6																	90377798		2203	4300	6503	90434519	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14029G>A	6.37:g.90377798C>T	ENSP00000358400:p.Gly4677Arg		90434519	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520014	0.85495	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.13196	2.61;2.61	5.86	5.86	0.93980	.	0.063063	0.64402	D	0.000008	T	0.30916	0.0780	M	0.80746	2.51	0.58432	D	0.999999	D	0.59767	0.986	P	0.58577	0.841	T	0.05099	-1.0906	10	0.72032	D	0.01	.	20.1823	0.98208	0.0:1.0:0.0:0.0	.	4677	Q9NU22	MDN1_HUMAN	R	4677	ENSP00000358400:G4677R;ENSP00000413970:G4677R	ENSP00000358400:G4677R	G	-	1	0	MDN1	90434519	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.771000	0.95319	0.650000	0.86243	GGA		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90377798	C	T	90377798	3	4	23	1	0	0	0	0	1	0	0	0	9445	632	22	3	2837	3	MDN1	6	90377798	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	48177232	90377798	80737269	38	2071										
GRM1	2911	hgsc.bcm.edu	37	chr6	146720520	146720520	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	caacgtgcccgccaacttcaAcgaggccaaatatatcgcgt	8	14	1	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:146720520A>T	ENST00000282753.1	+	7	2580	c.2345A>T	c.(2344-2346)aAc>aTc	p.N782I	GRM1_ENST00000392299.2_Missense_Mutation_p.N782I|GRM1_ENST00000361719.2_Missense_Mutation_p.N782I|GRM1_ENST00000507907.1_Missense_Mutation_p.N782I|GRM1_ENST00000492807.2_Missense_Mutation_p.N782I|GRM1_ENST00000355289.4_Missense_Mutation_p.N782I			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	782					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.N782I(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCCAACTTCAACGAGGCCAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											170	146	154					6																	146720520		2203	4300	6503	146762213	SO:0001583	missense	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2345A>T	6.37:g.146720520A>T	ENSP00000282753:p.Asn782Ile		146762213	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301296	0.81136	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.91237	-2.81;-2.81;-2.81;-2.81;-2.81;-2.81	5.68	5.68	0.88126	GPCR, family 3, conserved site (1);GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96812	0.8959	H	0.96691	3.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98206	1.0470	10	0.87932	D	0	.	15.9149	0.79503	1.0:0.0:0.0:0.0	.	782;782;782	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	I	782	ENSP00000354896:N782I;ENSP00000376119:N782I;ENSP00000424095:N782I;ENSP00000282753:N782I;ENSP00000347437:N782I;ENSP00000425599:N782I	ENSP00000282753:N782I	N	+	2	0	GRM1	146762213	1.000000	0.71417	0.970000	0.41538	0.985000	0.73830	9.339000	0.96797	2.169000	0.68431	0.477000	0.44152	AAC		0.502	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146720520	A	T	146720520	3	4	23	1	0	0	0	0	1	0	0	0	6817	43	2	5	2371	5	GRM1	6	146720520	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10	56342722	146720520	24394547	39	2072										
SMOC2	64094	hgsc.bcm.edu	37	chr6	168999543	168999543	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gtctgccctggaggaagccaAgcagcccaagaacgacaatg	12	12	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr6:168999543A>T	ENST00000356284.2	+	8	903	c.683A>T	c.(682-684)aAg>aTg	p.K228M	SMOC2_ENST00000354536.5_Missense_Mutation_p.K239M	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	228	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.K239M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GAGGAAGCCAAGCAGCCCAAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											195	144	161					6																	168999543		2203	4300	6503	168741468	SO:0001583	missense	64094			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"EF-hand domain containing"	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.683A>T	6.37:g.168999543A>T	ENSP00000348630:p.Lys228Met		168741468	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799490	0.70567	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.65178	-0.14;-0.14	5.21	1.7	0.24286	Thyroglobulin type-1 (3);	0.324845	0.28398	N	0.015483	T	0.41166	0.1147	L	0.48877	1.53	0.28568	N	0.910753	P;P	0.42337	0.708;0.776	P;B	0.47102	0.537;0.445	T	0.32877	-0.9890	10	0.59425	D	0.04	-14.7243	6.8649	0.24088	0.665:0.0:0.335:0.0	.	228;239	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	M	228;239;228	ENSP00000348630:K228M;ENSP00000346537:K239M	ENSP00000346537:K239M	K	+	2	0	SMOC2	168741468	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	3.191000	0.50981	0.073000	0.16731	0.317000	0.21355	AAG		0.607	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1			T	168999543	A	T	168999543	3	4	23	1	0	0	0	0	1	0	0	0	14839	72	3	5	746	5	SMOC2	6	168999543	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10	22279023	168999543	2115524	40	2073										
ZNF498	221785	hgsc.bcm.edu	37	chr7	99227087	99227087	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgggaaaggattcagtcggaGctccaatctcgtcaggcacc	12	11	3	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr7:99227087G>C	ENST00000394152.2	+	8	1406	c.1079G>C	c.(1078-1080)aGc>aCc	p.S360T	ZSCAN25_ENST00000262941.6_Missense_Mutation_p.S288T|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.S360T|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	360					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S360T(1)									TTCAGTCGGAGCTCCAATCTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	69	71					7																	99227087		2203	4300	6503	99065023	SO:0001583	missense	221785			AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1079G>C	7.37:g.99227087G>C	ENSP00000377708:p.Ser360Thr		99065023	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	G	13.55	2.270188	0.40194	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.52983	0.64;0.64;0.64	3.89	3.89	0.44902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000044	T	0.34803	0.0910	L	0.37750	1.13	0.28610	N	0.908737	B;B	0.14012	0.007;0.009	B;B	0.15484	0.008;0.013	T	0.24297	-1.0164	10	0.59425	D	0.04	-20.7176	7.5921	0.28027	0.1122:0.0:0.8878:0.0	.	288;360	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	T	360;360;288	ENSP00000377708:S360T;ENSP00000334800:S360T;ENSP00000262941:S288T	ENSP00000262941:S288T	S	+	2	0	ZNF498	99065023	0.000000	0.05858	1.000000	0.80357	0.937000	0.57800	0.012000	0.13287	2.454000	0.82982	0.561000	0.74099	AGC		0.562	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		C	99227087	G	C	99227087	3	2	23	1	0	0	0	0	1	0	0	0	17986	971	34	5	1097	5	ZNF498	7	99227087	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		99227087	59911576	41	2074										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700131	136700131	+	Missense_Mutation	SNP	T	T	A													0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ggggtgagaactgtggaggaTggggagtgctacattcagtt							TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr7:136700131T>A	ENST00000445907.2	+	3	1047	c.519T>A	c.(517-519)gaT>gaA	p.D173E	hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.D173E|CHRM2_ENST00000401861.1_Missense_Mutation_p.D173E|CHRM2_ENST00000397608.3_Missense_Mutation_p.D173E	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	173					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.D173E(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CTGTGGAGGATGGGGAGTGCT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											114	106	109					7																	136700131		2203	4300	6503	136350671	SO:0001583	missense	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.519T>A	7.37:g.136700131T>A	ENSP00000399745:p.Asp173Glu		136350671	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	T	2.030	-0.422677	0.04734	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24	5.75	-3.77	0.04346	GPCR, rhodopsin-like superfamily (1);	0.236240	0.42821	D	0.000641	T	0.06416	0.0165	N	0.01048	-1.04	0.30656	N	0.754957	B	0.02656	0.0	B	0.06405	0.002	T	0.33137	-0.9880	10	0.02654	T	1	-17.3461	1.9467	0.03358	0.1821:0.306:0.0968:0.4151	.	173	P08172	ACM2_HUMAN	E	173	ENSP00000399745:D173E;ENSP00000415386:D173E;ENSP00000319984:D173E;ENSP00000380733:D173E;ENSP00000384937:D173E;ENSP00000384401:D173E	ENSP00000319984:D173E	D	+	3	2	CHRM2	136350671	0.195000	0.23338	0.997000	0.53966	0.980000	0.70556	-0.659000	0.05323	-0.146000	0.11274	0.533000	0.62120	GAT		0.483	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			A	136700131	T	A	136700131	3	1	23	1	0	0	0	0	1	0	0	0	3383	1461	51	5	521	5	CHRM2	7	136700131	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	37473044	136700131	22438532	42	2075	12	2								
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700137	136700137	+	Silent	SNP	G	G	A													0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	agaactgtggaggatggggaGtgctacattcagtttttttc					rs576281726	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr7:136700137G>A	ENST00000445907.2	+	3	1053	c.525G>A	c.(523-525)gaG>gaA	p.E175E	hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000453373.1_Silent_p.E175E|hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000320658.5_Silent_p.E175E|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000402486.3_Silent_p.E175E|CHRM2_ENST00000401861.1_Silent_p.E175E|CHRM2_ENST00000397608.3_Silent_p.E175E	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	175					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.E175E(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGGATGGGGAGTGCTACATTC	0.488													G|||	2	0.000399361	0	0	5008	,	,		19822	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	7											113	105	108					7																	136700137		2203	4300	6503	136350677	SO:0001819	synonymous_variant	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.525G>A	7.37:g.136700137G>A			136350677	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	37	CCDS5843.1																																																																																				0.488	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			A	136700137	G	A	136700137	2	1	23	1	0	0	0	0	0	0	0	1	3383	1020	36	3		3	CHRM2	7	136700137	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	6	136700137	22438526	43	2076	12	2								
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138424341	138424341	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cactcctggtatggctgggtCcagctgcagatatagacttt	11	10	0	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr7:138424341C>A	ENST00000310018.2	-	15	1798	c.1516G>T	c.(1516-1518)Gac>Tac	p.D506Y	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.D506Y|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.D506Y	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	506					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.D506Y(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ATGGCTGGGTCCAGCTGCAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											72	66	68					7																	138424341		2203	4300	6503	138074881	SO:0001583	missense	50617			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1516G>T	7.37:g.138424341C>A	ENSP00000308122:p.Asp506Tyr		138074881	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600363	0.66332	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.86097	-2.07;-2.07;-2.07	5.23	4.35	0.52113	.	0.000000	0.64402	D	0.000001	D	0.91717	0.7381	M	0.83483	2.645	0.53688	D	0.999976	D	0.89917	1.0	D	0.77004	0.989	D	0.92051	0.5648	10	0.87932	D	0	-32.9134	10.8407	0.46712	0.0:0.8478:0.0:0.1522	.	506	Q9HBG4	VPP4_HUMAN	Y	506	ENSP00000308122:D506Y;ENSP00000376774:D506Y;ENSP00000253856:D506Y	ENSP00000308122:D506Y	D	-	1	0	ATP6V0A4	138074881	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	2.217000	0.42880	1.183000	0.42943	0.643000	0.83706	GAC		0.388	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		A	138424341	C	A	138424341	3	1	23	1	0	0	0	0	1	0	0	0	1171	855	30	2	1038	2	ATP6V0A4	7	138424341	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	1724204	138424341	20714322	44	2077										
TOX	9760	hgsc.bcm.edu	37	chr8	59720810	59720810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	attgataatagtctgatagtCgggttgaagagtaaatccct	10	5	1	4	rs372921240		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr8:59720810C>T	ENST00000361421.1	-	8	1631	c.1411G>A	c.(1411-1413)Gac>Aac	p.D471N		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	471						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D471N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GTCTGATAGTCGGGTTGAAGA	0.423											OREG0018787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(161;610 1969 17913 21374 22725)											1	Substitution - Missense(1)	large_intestine(1)	8						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	101	98	99		1411	6.2	1	8		99	0,8600		0,0,4300	no	missense	TOX	NM_014729.2	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	471/527	59720810	1,13005	2203	4300	6503	59883364	SO:0001583	missense	9760				CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.1411G>A	8.37:g.59720810C>T	ENSP00000354842:p.Asp471Asn	1040	59883364	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698442	0.68386	2.27E-4	0.0	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.12569	2.67	6.17	6.17	0.99709	.	0.102660	0.64402	D	0.000005	T	0.09686	0.0238	N	0.17082	0.46	0.54753	D	0.999982	P	0.35551	0.509	B	0.26969	0.075	T	0.29882	-0.9997	9	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	471	O94900	TOX_HUMAN	N	471;221	ENSP00000354842:D471N	.	D	-	1	0	TOX	59883364	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.013000	0.70776	2.941000	0.99782	0.655000	0.94253	GAC		0.423	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59720810	C	T	59720810	3	4	23	1	0	0	0	0	1	0	0	0	16417	884	31	1	177	1	TOX	8	59720810	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		59720810	86643212	45	2078										
TMEM71	137835	hgsc.bcm.edu	37	chr8	133726435	133726435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tcaatgagcatgtgaagacaCtggctaatatttctcccata	7	9	2	3			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr8:133726435C>T	ENST00000356838.3	-	8	864	c.722G>A	c.(721-723)aGt>aAt	p.S241N	TMEM71_ENST00000377901.4_Missense_Mutation_p.S197N|TMEM71_ENST00000523829.1_Missense_Mutation_p.S260N	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	260						integral component of membrane (GO:0016021)		p.S241N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGTGAAGACACTGGCTAATAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											141	137	139					8																	133726435		2203	4300	6503	133795617	SO:0001583	missense	137835			AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.722G>A	8.37:g.133726435C>T	ENSP00000349296:p.Ser241Asn		133795617	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624509	0.28889	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901	.	.	.	5.59	1.36	0.22044	.	0.712158	0.14341	N	0.325698	T	0.34861	0.0912	M	0.68317	2.08	0.09310	N	1	B;B;B	0.32653	0.208;0.021;0.379	B;B;B	0.28553	0.077;0.027;0.091	T	0.33420	-0.9869	9	0.72032	D	0.01	-1.9095	4.565	0.12180	0.0:0.5207:0.2096:0.2697	.	260;197;241	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	N	260;241;197	.	ENSP00000349296:S241N	S	-	2	0	TMEM71	133795617	0.000000	0.05858	0.064000	0.19789	0.125000	0.20455	-0.264000	0.08658	0.405000	0.25532	0.561000	0.74099	AGT		0.353	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649		T	133726435	C	T	133726435	3	4	23	1	0	0	0	0	1	0	0	0	16239	565	20	3	120	3	TMEM71	8	133726435	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	74005625	133726435	12637587	46	2079										
COMMD5	28991	hgsc.bcm.edu	37	chr8	146076065	146076065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ggggtcagtcctgcagtctgCgctcacacctcttctccaga	10	15	5	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr8:146076065C>T	ENST00000305103.3	-	2	911	c.659G>A	c.(658-660)cGc>cAc	p.R220H	AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000402718.3_Missense_Mutation_p.R220H|COMMD5_ENST00000450361.2_Missense_Mutation_p.R220H	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	220						nucleus (GO:0005634)		p.R220H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CTGCAGTCTGCGCTCACACCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	8											94	62	73					8																	146076065		2203	4300	6503	146046869	SO:0001583	missense	28991			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.659G>A	8.37:g.146076065C>T	ENSP00000304544:p.Arg220His		146046869	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	37	CCDS6436.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.840990	0.32513	.	.	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103	T;T;T	0.32272	1.46;1.46;1.46	4.31	-1.44	0.08856	.	0.221722	0.36703	N	0.002445	T	0.18551	0.0445	L	0.36672	1.1	0.09310	N	0.999992	B	0.17268	0.021	B	0.10450	0.005	T	0.13308	-1.0514	10	0.36615	T	0.2	-23.815	6.7576	0.23523	0.6368:0.2681:0.0:0.0951	.	220	Q9GZQ3	COMD5_HUMAN	H	220	ENSP00000385793:R220H;ENSP00000394331:R220H;ENSP00000304544:R220H	ENSP00000304544:R220H	R	-	2	0	COMMD5	146046869	0.080000	0.21391	0.983000	0.44433	0.932000	0.56968	0.606000	0.24194	-0.089000	0.12484	0.557000	0.71058	CGC		0.587	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066		T	146076065	C	T	146076065	3	4	23	1	0	0	0	0	1	0	0	0	3725	768	27	1	19	1	COMMD5	8	146076065	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	12349630	146076065	287957	47	2080										
DDX58	23586	hgsc.bcm.edu	37	chr9	32457312	32457312	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cagttctgtcgggcacagaaTatctttgctcttttttcaaa	7	9	4	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr9:32457312T>C	ENST00000379883.2	-	18	2743	c.2586A>G	c.(2584-2586)atA>atG	p.I862M	DDX58_ENST00000542096.1_Missense_Mutation_p.I791M|DDX58_ENST00000379868.1_Missense_Mutation_p.I659M|DDX58_ENST00000379882.1_Missense_Mutation_p.I817M	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	862	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.I862M(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GGGCACAGAATATCTTTGCTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											115	108	111					9																	32457312		2203	4300	6503	32447312	SO:0001583	missense	23586			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2586A>G	9.37:g.32457312T>C	ENSP00000369213:p.Ile862Met		32447312	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533196	0.27387	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.83	2.06	0.26882	C-terminal domain of RIG-I (1);	0.062472	0.64402	D	0.000006	T	0.40743	0.1129	L	0.38838	1.175	0.80722	D	1	B;B	0.33266	0.404;0.059	B;B	0.40165	0.321;0.059	T	0.13737	-1.0498	10	0.39692	T	0.17	-14.8116	3.5993	0.08019	0.1196:0.0709:0.293:0.5165	.	791;862	B3KWW1;O95786	.;DDX58_HUMAN	M	817;862;659;791	ENSP00000369212:I817M;ENSP00000369213:I862M;ENSP00000369197:I659M;ENSP00000442160:I791M	ENSP00000369197:I659M	I	-	3	3	DDX58	32447312	1.000000	0.71417	0.998000	0.56505	0.831000	0.47069	1.089000	0.30890	0.086000	0.17137	0.528000	0.53228	ATA		0.413	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		C	32457312	T	C	32457312	3	2	23	1	0	0	0	0	1	0	0	0	4381	1396	49	4	195	4	DDX58	9	32457312	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10		32457312	108756119	48	2081										
CCL21	6366	hgsc.bcm.edu	37	chr9	34709648	34709648	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ctcctttgggtctgcacataGctctgcctgagagcgcttgc	11	13	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr9:34709648G>A	ENST00000259607.2	-	3	277	c.220C>T	c.(220-222)Cta>Tta	p.L74L	CCL21_ENST00000378792.1_Silent_p.L74L	NM_002989.2	NP_002980.1	O00585	CCL21_HUMAN	chemokine (C-C motif) ligand 21	74					activation of Rho GTPase activity (GO:0032862)|cell chemotaxis (GO:0060326)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|dendritic cell chemotaxis (GO:0002407)|dendritic cell dendrite assembly (GO:0097026)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|immunological synapse formation (GO:0001771)|inflammatory response (GO:0006954)|mesangial cell-matrix adhesion (GO:0035759)|negative regulation of dendritic cell dendrite assembly (GO:2000548)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process (GO:0010560)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myeloid dendritic cell chemotaxis (GO:2000529)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of T cell migration (GO:2000406)|release of sequestered calcium ion into cytosol (GO:0051209)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)|T cell costimulation (GO:0031295)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR7 chemokine receptor binding (GO:0031732)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)	p.L74L(1)		large_intestine(4)	4	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		TCTGCACATAGCTCTGCCTGA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	9											43	43	43					9																	34709648		2203	4300	6503	34699648	SO:0001819	synonymous_variant	6366			AB002409	CCDS6571.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000137077	ENSG00000137077		"Chemokine ligands", "Endogenous ligands"	10620	protein-coding gene	gene with protein product	"beta chemokine exodus-2", "secondary lymphoid tissue chemokine", "Efficient Chemoattractant for Lymphocytes"	602737	"small inducible cytokine subfamily A (Cys-Cys), member 21"	SCYA21		9235955	Standard	NM_002989		Approved	SLC, exodus-2, TCA4, CKb9, 6Ckine, ECL	uc003zvo.4	O00585	OTTHUMG00000019838	ENST00000259607.2:c.220C>T	9.37:g.34709648G>A			34699648		Silent	SNP	ENST00000259607.2	37	CCDS6571.1																																																																																				0.617	CCL21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052245.1	NM_002989		A	34709648	G	A	34709648	2	1	23	1	0	0	0	0	0	0	0	1	2899	962	34	3		3	CCL21	9	34709648	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	2252336	34709648	106503783	49	2082										
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82273790	82273790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgcagcaaaaagttgtgaacAcacagtgtggatatgatgtc	11	6	0	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr10:82273790A>G	ENST00000429989.3	+	7	815	c.592A>G	c.(592-594)Aca>Gca	p.T198A	TSPAN14_ENST00000372158.1_Missense_Mutation_p.T198A|TSPAN14_ENST00000372156.1_Missense_Mutation_p.T198A|TSPAN14_ENST00000341863.6_Missense_Mutation_p.T141A|TSPAN14_ENST00000372164.3_Missense_Mutation_p.T181A|TSPAN14_ENST00000481124.1_Missense_Mutation_p.T75A	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	198					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)	p.T198A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			AGTTGTGAACACACAGTGTGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											122	111	115					10																	82273790		2203	4300	6503	82263770	SO:0001583	missense	81619			AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"Tetraspanins"	23303	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 14"	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.592A>G	10.37:g.82273790A>G	ENSP00000396270:p.Thr198Ala		82263770	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	37	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.161814	0.78226	.	.	ENSG00000108219	ENST00000429989;ENST00000481124;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000341863;ENST00000372156	T;T;T;T;T;T;T	0.46819	1.92;0.86;2.98;2.99;1.92;2.22;1.92	4.87	4.87	0.63330	Tetraspanin, EC2 domain (1);	0.093442	0.64402	D	0.000001	T	0.61726	0.2370	L	0.57536	1.79	0.58432	D	0.999993	D;P;P	0.76494	0.999;0.767;0.918	D;P;P	0.73380	0.98;0.685;0.604	T	0.59177	-0.7503	10	0.30854	T	0.27	-17.4747	12.7185	0.57129	1.0:0.0:0.0:0.0	.	75;198;181	B4DHY6;Q8NG11;Q8NG11-2	.;TSN14_HUMAN;.	A	198;75;168;181;198;141;198	ENSP00000396270:T198A;ENSP00000418195:T75A;ENSP00000361230:T168A;ENSP00000361237:T181A;ENSP00000361231:T198A;ENSP00000344076:T141A;ENSP00000361229:T198A	ENSP00000344076:T141A	T	+	1	0	TSPAN14	82263770	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.952000	0.93031	1.956000	0.56807	0.459000	0.35465	ACA		0.403	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		G	82273790	A	G	82273790	3	3	23	1	0	0	0	0	1	0	0	0	16678	159	6	4	614	4	TSPAN14	10	82273790	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10		82273790	53260957	50	2083										
PDZD8	118987	hgsc.bcm.edu	37	chr10	119042953	119042953	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aaagtttctatatcttcaatGcctgctctgtagtgaatcat	6	8	5	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr10:119042953G>A	ENST00000334464.5	-	5	3530	c.3291C>T	c.(3289-3291)ggC>ggT	p.G1097G	PDZD8_ENST00000482496.1_5'Flank	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	1097					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.G1097G(1)		kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TATCTTCAATGCCTGCTCTGT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	10											133	126	128					10																	119042953		2203	4300	6503	119032943	SO:0001819	synonymous_variant	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.3291C>T	10.37:g.119042953G>A			119032943	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																				0.363	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119042953	G	A	119042953	2	1	23	1	0	0	0	0	0	0	0	1	11736	1306	46	3		3	PDZD8	10	119042953	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	36769163	119042953	16491794	51	2084										
MKI67	4288	hgsc.bcm.edu	37	chr10	129910475	129910475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	atcatgttgacttcggctgaTagacactctctttgaaggca	9	9	2	4	rs997983	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr10:129910475T>C	ENST00000368654.3	-	9	2266	c.1891A>G	c.(1891-1893)Atc>Gtc	p.I631V	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.I271V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	631			I -> L (in dbSNP:rs997983).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I631V(1)|p.I631L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCGGCTGATAGACACTCTC	0.443																																																2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	10											112	100	104					10																	129910475		2203	4300	6503	129800465	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1891A>G	10.37:g.129910475T>C	ENSP00000357643:p.Ile631Val		129800465	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	2.392	-0.339566	0.05243	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01295	5.07;5.04	4.03	-8.06	0.01102	.	0.788319	0.11269	N	0.581682	T	0.00998	0.0033	L	0.44542	1.39	0.80722	P	0.0	B;B;B	0.21225	0.053;0.011;0.006	B;B;B	0.20767	0.031;0.023;0.01	T	0.46359	-0.9197	9	0.17832	T	0.49	.	1.3818	0.02232	0.1695:0.3373:0.2008:0.2923	.	630;271;631	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	631;271;630;206	ENSP00000357643:I631V;ENSP00000357642:I271V	ENSP00000357641:I206V	I	-	1	0	MKI67	129800465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.743000	0.04845	-2.155000	0.00791	-0.291000	0.09656	ATC		0.443	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129910475	T	C	129910475	3	2	23	1	0	0	0	0	1	0	0	0	9628	1406	49	4	7907	4	MKI67	10	129910475	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10	10867522	129910475	5624272	52	2085										
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62996023	62996023	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aattcagtggttgagattcgCataccagatcccactggaag	10	9	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr11:62996023C>A	ENST00000306494.6	-	2	415	c.416G>T	c.(415-417)tGc>tTc	p.C139F	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25									p.C139F(1)		NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TTGAGATTCGCATACCAGATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											107	96	100					11																	62996023		2201	4298	6499	62752599	SO:0001583	missense	387601			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.416G>T	11.37:g.62996023C>A	ENSP00000307443:p.Cys139Phe		62752599		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.909086	0.33721	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.81163	-1.46	3.47	3.47	0.39725	Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	D	0.92941	0.7754	H	0.98238	4.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94893	0.8049	10	0.87932	D	0	.	12.9802	0.58559	0.0:1.0:0.0:0.0	.	137;139	A4IF29;Q6T423	.;S22AP_HUMAN	F	139	ENSP00000307443:C139F	ENSP00000307443:C139F	C	-	2	0	SLC22A25	62752599	1.000000	0.71417	0.900000	0.35374	0.183000	0.23260	4.531000	0.60602	1.698000	0.51180	0.478000	0.44815	TGC		0.418	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		A	62996023	C	A	62996023	3	1	23	1	0	0	0	0	1	0	0	0	14491	710	25	2	1259	2	SLC22A25	11	62996023	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		62996023	72010493	53	2086										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101832753	101832753	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	aatgtcacagctttctcagaTattttaagtaaatctaatgt	5	6	3	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr11:101832753T>C	ENST00000263468.8	+	6	1257	c.987T>C	c.(985-987)gaT>gaC	p.D329D	KIAA1377_ENST00000537689.1_Silent_p.D130D	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	329								p.D329D(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		CTTTCTCAGATATTTTAAGTA	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	11											41	43	43					11																	101832753		2203	4297	6500	101337963	SO:0001819	synonymous_variant	57562			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.987T>C	11.37:g.101832753T>C			101337963	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																				0.308	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		C	101832753	T	C	101832753	2	2	23	1	0	0	0	0	0	0	0	1	8248	1403	49	4		4	KIAA1377	11	101832753	Silent	SNP	T	TCGA-AG-3593-01A-01W-0831-10	38836730	101832753	33173763	54	2087										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110477339	110477339	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cttcaggatgaactggcactGcatctctcgggggagctgtt	13	10	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr11:110477339G>A	ENST00000260283.4	-	10	1194	c.910C>T	c.(910-912)Cag>Tag	p.Q304*	ARHGAP20_ENST00000528829.1_Nonsense_Mutation_p.Q268*|ARHGAP20_ENST00000527598.1_Nonsense_Mutation_p.Q268*|ARHGAP20_ENST00000524756.1_Nonsense_Mutation_p.Q281*|ARHGAP20_ENST00000357139.3_Nonsense_Mutation_p.Q278*|ARHGAP20_ENST00000533353.1_Nonsense_Mutation_p.Q278*	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	304					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.Q304*(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AACTGGCACTGCATCTCTCGG	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											153	161	158					11																	110477339		2201	4298	6499	109982549	SO:0001587	stop_gained	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.910C>T	11.37:g.110477339G>A	ENSP00000260283:p.Gln304*		109982549	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Nonsense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	38	7.184560	0.98121	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	.	.	.	5.91	3.96	0.45880	.	0.111387	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.8896	0.58064	0.0:0.125:0.7449:0.1301	.	.	.	.	X	304;278;281;268;278;268	.	ENSP00000260283:Q304X	Q	-	1	0	ARHGAP20	109982549	1.000000	0.71417	0.424000	0.26647	0.755000	0.42902	6.422000	0.73357	0.750000	0.32877	0.650000	0.86243	CAG		0.527	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		A	110477339	G	A	110477339	4	1	23	1	0	0	0	0	0	1	0	0	870	1328	46	3	2693	3	ARHGAP20	11	110477339	Nonsense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	8644586	110477339	24529177	55	2088										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14633967	14633967	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cgtgaatgtaacacatcgtcCagtaactcaggtgaccacaa	8	11	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr12:14633967C>T	ENST00000540793.1	+	12	3283	c.3128C>T	c.(3127-3129)cCa>cTa	p.P1043L	ATF7IP_ENST00000536444.1_Missense_Mutation_p.P1042L|ATF7IP_ENST00000544627.1_Missense_Mutation_p.P1051L|ATF7IP_ENST00000261168.4_Missense_Mutation_p.P1043L|ATF7IP_ENST00000543189.1_Missense_Mutation_p.P1042L			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1043					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.P1043L(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						ACACATCGTCCAGTAACTCAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											112	112	112					12																	14633967		2203	4300	6503	14525234	SO:0001583	missense	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3128C>T	12.37:g.14633967C>T	ENSP00000444589:p.Pro1043Leu		14525234	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.597010	0.87055	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T;T	0.57907	1.62;0.37;1.6;1.62;1.62	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000007	T	0.72053	0.3413	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.73792	-0.3871	10	0.87932	D	0	-13.311	19.6057	0.95580	0.0:1.0:0.0:0.0	.	1042;1043;1042	G3V1U0;Q6VMQ6;Q6VMQ6-2	.;MCAF1_HUMAN;.	L	1043;1042;1042;1051;1043	ENSP00000261168:P1043L;ENSP00000443179:P1042L;ENSP00000445955:P1042L;ENSP00000440440:P1051L;ENSP00000444589:P1043L	ENSP00000261168:P1043L	P	+	2	0	ATF7IP	14525234	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.042000	0.64202	2.693000	0.91896	0.650000	0.86243	CCA		0.443	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		T	14633967	C	T	14633967	3	4	23	1	0	0	0	0	1	0	0	0	1088	594	21	3	3174	3	ATF7IP	12	14633967	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		14633967	119217928	56	2089										
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76780014	76780014	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cataaacaacggaaagtctcGccaagtataggattataagg	9	7	1	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr12:76780014G>A	ENST00000261183.3	-	14	1946	c.1467C>T	c.(1465-1467)ggC>ggT	p.G489G	OSBPL8_ENST00000393250.4_Silent_p.G447G|OSBPL8_ENST00000393249.2_Silent_p.G447G	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	489					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)	p.G489G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						GGAAAGTCTCGCCAAGTATAG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	12											50	50	50					12																	76780014		2203	4298	6501	75304145	SO:0001819	synonymous_variant	114882			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.1467C>T	12.37:g.76780014G>A			75304145	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Silent	SNP	ENST00000261183.3	37	CCDS31862.1																																																																																				0.308	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		A	76780014	G	A	76780014	2	1	23	1	0	0	0	0	0	0	0	1	11314	1074	38	1		1	OSBPL8	12	76780014	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	62146047	76780014	57071881	57	2090										
FREM2	341640	hgsc.bcm.edu	37	chr13	39343884	39343884	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	caggtggtactctcagagccCgtgctggctgccttggaatt	13	11	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr13:39343884C>T	ENST00000280481.7	+	4	5796	c.5580C>T	c.(5578-5580)ccC>ccT	p.P1860P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1860					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1860P(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TCTCAGAGCCCGTGCTGGCTG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	13											121	100	107					13																	39343884		2203	4300	6503	38241884	SO:0001819	synonymous_variant	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5580C>T	13.37:g.39343884C>T			38241884	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.547	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39343884	C	T	39343884	2	4	23	1	0	0	0	0	0	0	0	1	6064	639	23	1		1	FREM2	13	39343884	Silent	SNP	C	TCGA-AG-3593-01A-01W-0831-10		39343884	75825994	58	2091										
GPC6	10082	hgsc.bcm.edu	37	chr13	94482694	94482694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	agctcaagccatttggagacGtgccccggaaactgaagatt	11	10	1	3	rs376951709		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr13:94482694G>A	ENST00000377047.4	+	3	1222	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	203					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.V203L(1)|p.V203M(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATTTGGAGACGTGCCCCGGAA	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	13						G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	76	71	73		607	5.5	1	13		73	0,8600		0,0,4300	no	missense	GPC6	NM_005708.3	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	203/556	94482694	1,13005	2203	4300	6503	93280695	SO:0001583	missense	10082			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.607G>A	13.37:g.94482694G>A	ENSP00000366246:p.Val203Met		93280695	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.330632	0.81690	2.27E-4	0.0	ENSG00000183098	ENST00000377047	T	0.54071	0.59	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000001	T	0.74566	0.3733	M	0.89414	3.03	0.44234	D	0.997074	D;D	0.71674	0.998;0.998	D;D	0.67900	0.954;0.954	T	0.78625	-0.2131	10	0.66056	D	0.02	.	13.0682	0.59046	0.0736:0.0:0.9264:0.0	.	203;203	B4E2M1;Q9Y625	.;GPC6_HUMAN	M	203	ENSP00000366246:V203M	ENSP00000366246:V203M	V	+	1	0	GPC6	93280695	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.536000	0.60636	2.771000	0.95319	0.644000	0.83932	GTG		0.512	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		A	94482694	G	A	94482694	3	1	23	1	0	0	0	0	1	0	0	0	6622	1145	40	1	617	1	GPC6	13	94482694	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	55138810	94482694	20687184	59	2092										
MAP2K5	5607	hgsc.bcm.edu	37	chr15	67995740	67995740	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tggagcttaggaatctctttTatggaggtacgttgtttgca	12	5	1	0			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr15:67995740T>A	ENST00000178640.5	+	16	1665	c.1038T>A	c.(1036-1038)ttT>ttA	p.F346L	MAP2K5_ENST00000340972.4_Missense_Mutation_p.F156L|MAP2K5_ENST00000395476.2_Missense_Mutation_p.F346L|MAP2K5_ENST00000354498.5_Missense_Mutation_p.F310L	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	346	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.F346L(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						GAATCTCTTTTATGGAGGTAC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	15											147	139	142					15																	67995740		2200	4298	6498	65782794	SO:0001583	missense	5607			U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.1038T>A	15.37:g.67995740T>A	ENSP00000178640:p.Phe346Leu		65782794	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	37	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	T	5.103	0.204602	0.09704	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.96	3.91	0.45181	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.088940	0.85682	N	0.000000	T	0.14787	0.0357	N	0.00124	-2.055	0.54753	D	0.999984	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.32666	-0.9898	10	0.02654	T	1	-14.3721	8.5833	0.33642	0.0:0.6811:0.0:0.3189	.	156;346;346	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	L	346;346;346;310;156	ENSP00000378859:F346L;ENSP00000178640:F346L;ENSP00000346493:F310L;ENSP00000342101:F156L	ENSP00000178640:F346L	F	+	3	2	MAP2K5	65782794	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	0.714000	0.25808	0.703000	0.31848	-0.417000	0.06048	TTT		0.393	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		A	67995740	T	A	67995740	3	1	23	1	0	0	0	0	1	0	0	0	9270	1751	61	5	1100	5	MAP2K5	15	67995740	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10		67995740	34535652	60	2093										
ZP2	7783	hgsc.bcm.edu	37	chr16	21212710	21212710	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ccatccacgacaacgttccaCtgggggaaagagtctggatc	11	12	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr16:21212710C>G	ENST00000574002.1	-	15	2156	c.1674G>C	c.(1672-1674)caG>caC	p.Q558H	ZP2_ENST00000219593.4_Missense_Mutation_p.Q558H|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000574091.1_Missense_Mutation_p.Q549H			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	558	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)	p.Q558H(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		CAACGTTCCACTGGGGGAAAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	16											146	131	136					16																	21212710		2200	4300	6500	21120211	SO:0001583	missense	7783			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1674G>C	16.37:g.21212710C>G	ENSP00000460971:p.Gln558His		21120211	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109892	0.56398	.	.	ENSG00000103310	ENST00000219593	D	0.83163	-1.69	5.31	2.2	0.27929	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.284895	0.29814	N	0.011126	D	0.91379	0.7280	M	0.93638	3.44	0.48696	D	0.999694	P;P	0.50272	0.881;0.933	D;D	0.64877	0.93;0.93	D	0.90827	0.4713	10	0.87932	D	0	-1.1199	8.7021	0.34332	0.0:0.7269:0.1273:0.1458	.	549;558	Q4VAP1;Q05996	.;ZP2_HUMAN	H	558	ENSP00000219593:Q558H	ENSP00000219593:Q558H	Q	-	3	2	ZP2	21120211	1.000000	0.71417	0.810000	0.32431	0.638000	0.38207	1.199000	0.32235	0.708000	0.31955	0.591000	0.81541	CAG		0.502	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			G	21212710	C	G	21212710	3	3	23	1	0	0	0	0	1	0	0	0	18255	564	20	5	587	5	ZP2	16	21212710	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10		21212710	69142043	61	2094										
TP53	7157	hgsc.bcm.edu	37	chr17	7577588	7577588	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cacatgtagttgtagtggatGgtggtacagtcagagccaac	13	7	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr17:7577588G>A	ENST00000269305.4	-	7	882	c.693C>T	c.(691-693)acC>acT	p.T231T	TP53_ENST00000359597.4_Silent_p.T231T|TP53_ENST00000413465.2_Silent_p.T231T|TP53_ENST00000445888.2_Silent_p.T231T|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Silent_p.T231T|TP53_ENST00000420246.2_Silent_p.T231T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	231	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> N (in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.T231T(7)|p.?(5)|p.T230fs*6(2)|p.C229_H233delCTTIH(2)|p.T230_Y234delTTIHY(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.T138T(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.T231del(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGTAGTGGATGGTGGTACAGT	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	31	Whole gene deletion(8)|Substitution - coding silent(8)|Deletion - In frame(6)|Unknown(5)|Deletion - Frameshift(4)	biliary_tract(5)|large_intestine(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|urinary_tract(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|oesophagus(2)|breast(2)|stomach(1)|lung(1)|ovary(1)|liver(1)	17											111	89	96					17																	7577588		2203	4300	6503	7518313	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.693C>T	17.37:g.7577588G>A			7518313	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577588	G	A	7577588	2	1	23	1	0	0	0	0	0	0	0	1	16421	1335	47	3		3	TP53	17	7577588	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10		7577588	73617622	62	2095										
ACACA	31	hgsc.bcm.edu	37	chr17	35564696	35564696	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gtcatgccatagtggttgagGttggaggagaaggacattct	15	5	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr17:35564696G>A	ENST00000394406.2	-	31	3805	c.3615C>T	c.(3613-3615)aaC>aaT	p.N1205N	ACACA_ENST00000360679.3_Silent_p.N1147N|ACACA_ENST00000353139.5_Silent_p.N1242N|ACACA_ENST00000335166.5_Silent_p.N1127N	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1205					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.N1147N(1)|p.N1242N(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGTGGTTGAGGTTGGAGGAGA	0.468																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											2	Substitution - coding silent(2)	large_intestine(2)	17											153	124	134					17																	35564696		2203	4300	6503	32638809	SO:0001819	synonymous_variant	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3615C>T	17.37:g.35564696G>A			32638809	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.468	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35564696	G	A	35564696	2	1	23	1	0	0	0	0	0	0	0	1	106	1252	44	3		3	ACACA	17	35564696	Silent	SNP	G	TCGA-AG-3593-01A-01W-0831-10	27987108	35564696	45630514	63	2096										
MC2R	4158	hgsc.bcm.edu	37	chr18	13885364	13885364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gggtgcctggagattcttatTcttgaacacagccagcagga	12	9	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr18:13885364T>C	ENST00000327606.3	-	2	334	c.154A>G	c.(154-156)Aat>Gat	p.N52D		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	52					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.N52D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	AGATTCTTATTCTTGAACACA	0.428																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - Missense(1)	large_intestine(1)	18											84	79	81					18																	13885364		2203	4300	6503	13875364	SO:0001583	missense	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.154A>G	18.37:g.13885364T>C	ENSP00000333821:p.Asn52Asp		13875364	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	37	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.233183	0.79688	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T;T	0.72835	2.84;-0.69	4.13	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83124	0.5186	M	0.78344	2.41	0.50171	D	0.999857	D	0.89917	1.0	D	0.91635	0.999	D	0.85567	0.1231	10	0.72032	D	0.01	.	13.4468	0.61146	0.0:0.0:0.0:1.0	.	52	Q01718	ACTHR_HUMAN	D	52	ENSP00000333821:N52D;ENSP00000382718:N52D	ENSP00000333821:N52D	N	-	1	0	MC2R	13875364	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.355000	0.79434	1.643000	0.50594	0.528000	0.53228	AAT		0.428	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			C	13885364	T	C	13885364	3	2	23	1	0	0	0	0	1	0	0	0	9394	1783	62	4	743	4	MC2R	18	13885364	Missense_Mutation	SNP	T	TCGA-AG-3593-01A-01W-0831-10		13885364	64191884	64	2097										
ZNF121	7675	hgsc.bcm.edu	37	chr19	9677373	9677373	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	attcgtagggtttttctacaGtatgcattttaacagacaca	7	7	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr19:9677373G>C	ENST00000586602.1	-	6	832	c.416C>G	c.(415-417)aCt>aGt	p.T139S	ZNF121_ENST00000320451.6_Missense_Mutation_p.T139S			P58317	ZN121_HUMAN	zinc finger protein 121	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T139S(1)		breast(3)|kidney(4)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	24						TTTTTCTACAGTATGCATTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	76	79					19																	9677373		2203	4300	6503	9538373	SO:0001583	missense	7675			M99593	CCDS32902.1	19p13.2	2013-01-08	2006-08-22			ENSG00000197961		"Zinc fingers, C2H2-type"	12904	protein-coding gene	gene with protein product		194628	"zinc finger protein 121 (clone ZHC32)"	D19S204		8468057	Standard	NM_001008727		Approved	ZHC32, ZNF20	uc010xkp.1	P58317		ENST00000586602.1:c.416C>G	19.37:g.9677373G>C	ENSP00000468643:p.Thr139Ser		9538373		Missense_Mutation	SNP	ENST00000586602.1	37		.	.	.	.	.	.	.	.	.	.	G	5.726	0.318503	0.10845	.	.	ENSG00000197961	ENST00000538300;ENST00000320451	T	0.24151	1.87	1.3	-1.41	0.08941	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16896	0.0406	L	0.39085	1.19	0.09310	N	1	B	0.12630	0.006	B	0.20955	0.032	T	0.30446	-0.9978	9	0.56958	D	0.05	.	3.3749	0.07234	0.1769:0.0:0.5768:0.2463	.	139	P58317	ZN121_HUMAN	S	139	ENSP00000326967:T139S	ENSP00000326967:T139S	T	-	2	0	ZNF121	9538373	0.966000	0.33281	0.001000	0.08648	0.005000	0.04900	1.490000	0.35573	-0.307000	0.08804	-0.327000	0.08410	ACT		0.378	ZNF121-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000449910.1	NM_001008727		C	9677373	G	C	9677373	3	2	23	1	0	0	0	0	1	0	0	0	17758	1029	36	5	760	5	ZNF121	19	9677373	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		9677373	49451610	65	2098										
KIR3DL3	115653	hgsc.bcm.edu	37	chr19	55237553	55237553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	cccttcctctctgcctggccCggcactgtggtgtctgaagg	12	15	2	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr19:55237553C>T	ENST00000291860.1	+	3	123	c.105C>T	c.(103-105)ccC>ccT	p.P35P	KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P35P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CTGCCTGGCCCGGCACTGTGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	19											1	1	1					19																	55237553		156	336	492	59929365	SO:0001819	synonymous_variant	115653			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.105C>T	19.37:g.55237553C>T			59929365	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Silent	SNP	ENST00000291860.1	37	CCDS12903.1																																																																																				0.577	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443		T	55237553	C	T	55237553	2	4	23	1	0	0	0	0	0	0	0	1	8343	639	23	1		1	KIR3DL3	19	55237553	Silent	SNP	C	TCGA-AG-3593-01A-01W-0831-10	45560180	55237553	3891430	66	2099										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56392880	56392880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	ggaaacccaggcacttctgaCggctgaggaagagagaaatc	13	9	1	4	rs374023533		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr19:56392880C>T	ENST00000301295.6	+	10	3334	c.2912C>T	c.(2911-2913)aCg>aTg	p.T971M	NLRP4_ENST00000587891.1_Missense_Mutation_p.T896M|NLRP4_ENST00000346986.5_Missense_Mutation_p.T915M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	971					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.T971M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GCACTTCTGACGGCTGAGGAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	75	62	66		2912	-6.7	0	19		66	2,8598	2.2+/-6.3	0,2,4298	no	missense	NLRP4	NM_134444.4	81	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	971/995	56392880	3,13003	2203	4300	6503	61084692	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2912C>T	19.37:g.56392880C>T	ENSP00000301295:p.Thr971Met		61084692	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	2.304	-0.359501	0.05138	2.27E-4	2.33E-4	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.53640	0.61;0.64	3.34	-6.67	0.01783	.	.	.	.	.	T	0.19565	0.0470	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.13594	0.008;0.005;0.003	B;B;B	0.11329	0.003;0.006;0.001	T	0.18745	-1.0327	9	0.38643	T	0.18	.	5.7472	0.18126	0.1235:0.5455:0.1253:0.2057	.	915;896;971	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	M	971;915	ENSP00000301295:T971M;ENSP00000344787:T915M	ENSP00000301295:T971M	T	+	2	0	NLRP4	61084692	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.944000	0.00681	-2.776000	0.00362	-0.966000	0.02617	ACG		0.423	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56392880	C	T	56392880	3	4	23	1	0	0	0	0	1	0	0	0	10510	536	19	1	2946	1	NLRP4	19	56392880	Missense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	1155327	56392880	2736103	67	2100										
ZNF552	79818	hgsc.bcm.edu	37	chr19	58319947	58319947	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	agggagcagtctctcgtgctGactgagtatatctttggtgc	13	8	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr19:58319947G>A	ENST00000391701.1	-	3	854	c.685C>T	c.(685-687)Cag>Tag	p.Q229*	ZNF586_ENST00000599802.1_Intron|ZNF586_ENST00000598885.1_Intron	NM_024762.3	NP_079038.2	Q9H707	ZN552_HUMAN	zinc finger protein 552	229					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q229*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11		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)		CTCTCGTGCTGACTGAGTATA	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											83	71	75					19																	58319947		2203	4300	6503	63011759	SO:0001587	stop_gained	79818			AK097041	CCDS12963.1	19q13.43	2013-09-20			ENSG00000178935	ENSG00000178935		"Zinc fingers, C2H2-type", "-"	26135	protein-coding gene	gene with protein product							Standard	XM_005259267		Approved	FLJ21603	uc002qqg.3	Q9H707	OTTHUMG00000183478	ENST00000391701.1:c.685C>T	19.37:g.58319947G>A	ENSP00000375582:p.Gln229*		63011759	B3KUE9|Q6P5A6	Nonsense_Mutation	SNP	ENST00000391701.1	37	CCDS12963.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.982381	0.53827	.	.	ENSG00000178935	ENST00000391701	.	.	.	1.96	-2.23	0.06930	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	0.3012	0.00273	0.2674:0.2101:0.3107:0.2118	.	.	.	.	X	229	.	ENSP00000375582:Q229X	Q	-	1	0	ZNF552	63011759	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-1.278000	0.02809	-0.681000	0.05204	0.205000	0.17691	CAG		0.433	ZNF552-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466829.1	NM_024762		A	58319947	G	A	58319947	4	1	23	1	0	0	0	0	0	1	0	0	18023	1299	45	3	542	3	ZNF552	19	58319947	Nonsense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	1927067	58319947	809036	68	2101										
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36892062	36892062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gacaggatgaagaaagttagActgccaggcatcttctgtgt	12	7	2	3			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chr22:36892062A>G	ENST00000397224.4	-	7	1669	c.1576T>C	c.(1576-1578)Tct>Cct	p.S526P	FOXRED2_ENST00000366463.3_Missense_Mutation_p.S78P|FOXRED2_ENST00000216187.6_Missense_Mutation_p.S526P|FOXRED2_ENST00000397223.4_Missense_Mutation_p.S526P	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	526					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)	p.S526P(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AGAAAGTTAGACTGCCAGGCA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	22											108	100	102					22																	36892062		2203	4300	6503	35222008	SO:0001583	missense	80020			BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1576T>C	22.37:g.36892062A>G	ENSP00000380401:p.Ser526Pro		35222008	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.909693	0.72983	.	.	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000366463;ENST00000397223	T;T;T;T	0.57752	1.91;1.91;0.38;1.91	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.75398	0.3844	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79838	-0.1634	10	0.66056	D	0.02	-23.3329	15.6826	0.77385	1.0:0.0:0.0:0.0	.	526	Q8IWF2	FXRD2_HUMAN	P	526;526;78;526	ENSP00000380401:S526P;ENSP00000216187:S526P;ENSP00000382543:S78P;ENSP00000380400:S526P	ENSP00000216187:S526P	S	-	1	0	FOXRED2	35222008	1.000000	0.71417	0.998000	0.56505	0.429000	0.31625	8.381000	0.90152	2.108000	0.64289	0.529000	0.55759	TCT		0.527	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		G	36892062	A	G	36892062	3	3	23	1	0	0	0	0	1	0	0	0	6053	275	10	4	490	4	FOXRED2	22	36892062	Missense_Mutation	SNP	A	TCGA-AG-3593-01A-01W-0831-10		36892062	14412504	69	2102										
MSN	4478	hgsc.bcm.edu	37	chrX	64951047	64951047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	catgaggaacaccgtggcatGctcaggtaagcttgcccaag	12	11	1	1			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:64951047G>A	ENST00000360270.5	+	5	718	c.546G>A	c.(544-546)atG>atA	p.M182I		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	182	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.M182I(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						ACCGTGGCATGCTCAGGTAAG	0.537			T	ALK	ALCL																																		Dom	yes		X	Xq11.2-q12	4478	moesin		L	1	Substitution - Missense(1)	large_intestine(1)	X											104	66	79					X																	64951047		2203	4300	6503	64867772	SO:0001583	missense	4478			M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.546G>A	X.37:g.64951047G>A	ENSP00000353408:p.Met182Ile		64867772		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017043	0.75161	.	.	ENSG00000147065	ENST00000360270	T	0.78595	-1.19	5.8	5.8	0.92144	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	T	0.81211	0.4775	M	0.78344	2.41	0.80722	D	1	B	0.21606	0.058	B	0.30855	0.121	T	0.78453	-0.2198	10	0.51188	T	0.08	.	17.4025	0.87464	0.0:0.0:1.0:0.0	.	182	P26038	MOES_HUMAN	I	182	ENSP00000353408:M182I	ENSP00000353408:M182I	M	+	3	0	MSN	64867772	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.732000	0.98816	2.434000	0.82447	0.600000	0.82982	ATG		0.537	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		A	64951047	G	A	64951047	3	1	23	1	0	0	0	0	1	0	0	0	9915	1319	46	3	564	3	MSN	23	64951047	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10		64951047	90319513	70	2103										
NONO	4841	hgsc.bcm.edu	37	chrX	70517755	70517755	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gaagaaatgatgcggcgacaGcaggaaggattcaagggaac	15	6	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:70517755G>C	ENST00000276079.8	+	9	1303	c.1098G>C	c.(1096-1098)caG>caC	p.Q366H	NONO_ENST00000373841.1_Missense_Mutation_p.Q366H|NONO_ENST00000373856.3_Missense_Mutation_p.Q366H|NONO_ENST00000490044.1_3'UTR|NONO_ENST00000535149.1_Missense_Mutation_p.Q277H	NM_007363.4	NP_031389.3	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	366	DBHS.			QQ -> HE (in Ref. 3; CAA72157 and 4; AAA03427). {ECO:0000305}.	circadian rhythm (GO:0007623)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mRNA processing (GO:0006397)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Q366H(1)	NONO/TFE3(2)	endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	19	Renal(35;0.156)					TGCGGCGACAGCAGGAAGGAT	0.517			T	TFE3	papillary renal cancer																																		Dom	yes		X	Xq13.1	4841	"non-POU domain containing, octamer-binding"		E	1	Substitution - Missense(1)	large_intestine(1)	X											91	68	76					X																	70517755		2203	4300	6503	70434480	SO:0001583	missense	4841			L14599	CCDS14410.1, CCDS55445.1	Xq13.1	2014-06-13	2002-01-14		ENSG00000147140	ENSG00000147140		"RNA binding motif (RRM) containing"	7871	protein-coding gene	gene with protein product	"Nuclear RNA-binding protein, 54-kD", "non-Pou domain-containing octamer (ATGCAAAT) binding protein", "protein phosphatase 1, regulatory subunit 114"	300084	"non-POU-domain-containing, octamer-binding"			8371983, 9360842	Standard	NM_007363		Approved	NRB54, NMT55, P54NRB, P54, PPP1R114	uc004dzp.3	Q15233	OTTHUMG00000021798	ENST00000276079.8:c.1098G>C	X.37:g.70517755G>C	ENSP00000276079:p.Gln366His		70434480	B7Z4C2|D3DVV4|F5GYZ3|O00201|P30807|Q12786|Q9BQC5	Missense_Mutation	SNP	ENST00000276079.8	37	CCDS14410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.57|15.57	2.872809|2.872809	0.51695|0.51695	.|.	.|.	ENSG00000147140|ENSG00000147140	ENST00000535149;ENST00000276079;ENST00000373856;ENST00000373841|ENST00000418921	T;T;T;T|.	0.23552|.	1.95;1.9;1.9;1.9|.	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70482|0.70482	0.3229|0.3229	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	D|.	0.61080|.	0.989|.	P|.	0.50708|.	0.648|.	T|T	0.69993|0.69993	-0.4994|-0.4994	10|5	0.54805|.	T|.	0.06|.	-9.9515|-9.9515	12.2602|12.2602	0.54647|0.54647	0.0825:0.0:0.9175:0.0|0.0825:0.0:0.9175:0.0	.|.	366|.	Q15233|.	NONO_HUMAN|.	H|T	277;366;366;366|228	ENSP00000441364:Q277H;ENSP00000276079:Q366H;ENSP00000362963:Q366H;ENSP00000362947:Q366H|.	ENSP00000276079:Q366H|.	Q|S	+|+	3|2	2|0	NONO|NONO	70434480|70434480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.257000|5.257000	0.65473|0.65473	2.427000|2.427000	0.82271|0.82271	0.529000|0.529000	0.55759|0.55759	CAG|AGC		0.517	NONO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057138.1	NM_007363		C	70517755	G	C	70517755	3	2	23	1	0	0	0	0	1	0	0	0	10565	962	34	5	1124	5	NONO	23	70517755	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	5566708	70517755	84752805	71	2104										
ITM2A	9452	hgsc.bcm.edu	37	chrX	78618104	78618104	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tttgccaaagagctctaccaGattttttggaggcataacaa	8	8	1	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:78618104G>C	ENST00000373298.2	-	4	669	c.526C>G	c.(526-528)Ctg>Gtg	p.L176V	ITM2A_ENST00000469541.1_5'UTR|ITM2A_ENST00000434584.2_Missense_Mutation_p.L132V	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	176	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)		p.L176V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						AGCTCTACCAGATTTTTTGGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											66	61	63					X																	78618104		2203	4299	6502	78504760	SO:0001583	missense	9452			BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"BRICHOS domain containing"	6173	protein-coding gene	gene with protein product	"BRICHOS domain containing 2A"	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.526C>G	X.37:g.78618104G>C	ENSP00000362395:p.Leu176Val		78504760	B2R7X5|B4E062|Q6IBC9	Missense_Mutation	SNP	ENST00000373298.2	37	CCDS14444.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.472995	0.26423	.	.	ENSG00000078596	ENST00000373298;ENST00000434584	D;D	0.83992	-1.79;-1.79	4.95	3.16	0.36331	BRICHOS (2);	0.000000	0.64402	D	0.000002	D	0.87597	0.6217	M	0.76170	2.325	0.45239	D	0.998247	D;D	0.56746	0.961;0.977	P;P	0.61328	0.887;0.735	D	0.85693	0.1308	10	0.72032	D	0.01	-12.0285	7.8383	0.29382	0.0883:0.0:0.7508:0.1609	.	132;176	B4E062;O43736	.;ITM2A_HUMAN	V	176;132	ENSP00000362395:L176V;ENSP00000415533:L132V	ENSP00000362395:L176V	L	-	1	2	ITM2A	78504760	1.000000	0.71417	0.996000	0.52242	0.053000	0.15095	1.011000	0.29911	0.328000	0.23435	-0.245000	0.11935	CTG		0.373	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057329.1	NM_004867		C	78618104	G	C	78618104	3	2	23	1	0	0	0	0	1	0	0	0	7933	933	33	5	277	5	ITM2A	23	78618104	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	8100349	78618104	76652456	72	2105										
TBX22	50945	hgsc.bcm.edu	37	chrX	79281207	79281207	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tcaccctgctcgggagagacCtggatgcggcagatcatcag	13	12	3	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:79281207C>A	ENST00000373294.5	+	4	592	c.564C>A	c.(562-564)acC>acA	p.T188T	TBX22_ENST00000373291.1_Silent_p.T68T|TBX22_ENST00000373296.3_Silent_p.T188T|TBX22_ENST00000442340.1_Silent_p.T68T	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	188					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T188T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CGGGAGAGACCTGGATGCGGC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	X											107	72	84					X																	79281207		2203	4300	6503	79167863	SO:0001819	synonymous_variant	50945			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.564C>A	X.37:g.79281207C>A			79167863	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	37	CCDS14445.1																																																																																				0.502	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		A	79281207	C	A	79281207	2	1	23	1	0	0	0	0	0	0	0	1	15697	668	24	2		2	TBX22	23	79281207	Silent	SNP	C	TCGA-AG-3593-01A-01W-0831-10	663103	79281207	75989353	73	2106										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109696873	109696873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgtcacaaacaacatataccGtgtctggaaggatggccaca	9	10	2	0	rs148401387	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:109696873G>A	ENST00000465301.2	+	3	3274	c.3028G>A	c.(3028-3030)Gtg>Atg	p.V1010M	RGAG1_ENST00000540313.1_Missense_Mutation_p.V1010M	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1010								p.V1010M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						AACATATACCGTGTCTGGAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	MET/VAL	5,3830		1,3,1628,571	230	200	210		3028	0.1	0	X	dbSNP_134	210	0,6728		0,0,2428,1872	yes	missense	RGAG1	NM_020769.2	21	1,3,4056,2443	AA,AG,GG,G		0.0,0.1304,0.0473	possibly-damaging	1010/1389	109696873	5,10558	2203	4300	6503	109583529	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3028G>A	X.37:g.109696873G>A	ENSP00000419786:p.Val1010Met		109583529	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	6.766	0.510246	0.12883	0.001304	0.0	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.46451	0.87;0.87	4.24	0.0714	0.14382	.	1.266790	0.06086	N	0.662793	T	0.34106	0.0886	L	0.40543	1.245	0.09310	N	1	D	0.64830	0.994	P	0.44597	0.454	T	0.23190	-1.0195	9	.	.	.	0.9452	4.6263	0.12479	0.2612:0.3264:0.4124:0.0	.	1010	Q8NET4	RGAG1_HUMAN	M	1010;1010;571	ENSP00000419786:V1010M;ENSP00000441452:V1010M	.	V	+	1	0	RGAG1	109583529	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.403000	0.20982	-0.123000	0.11745	-0.192000	0.12808	GTG		0.498	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109696873	G	A	109696873	3	1	23	1	0	0	0	0	1	0	0	0	13311	1145	40	1	3030	1	RGAG1	23	109696873	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	30415666	109696873	45573687	74	2107										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117695437	117695437	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	tgagaaaaattcaaaagaatCgaaaggttgcatctacttgg	9	5	2	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:117695437C>A	ENST00000276202.7	+	7	713	c.650C>A	c.(649-651)tCg>tAg	p.S217*	DOCK11_ENST00000276204.6_Nonsense_Mutation_p.S217*	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	217	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S217W(1)|p.S217*(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TCAAAAGAATCGAAAGGTTGC	0.363																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	X											108	98	102					X																	117695437		2203	4300	6503	117579465	SO:0001587	stop_gained	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.650C>A	X.37:g.117695437C>A	ENSP00000276202:p.Ser217*		117579465	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Nonsense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	c	38	6.854179	0.97889	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	.	.	.	5.41	5.41	0.78517	.	0.185584	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-4.9426	18.1276	0.89591	0.0:1.0:0.0:0.0	.	.	.	.	X	217	.	ENSP00000276202:S217X	S	+	2	0	DOCK11	117579465	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.373000	0.79623	2.405000	0.81733	0.417000	0.27973	TCG		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117695437	C	A	117695437	4	1	23	1	0	0	0	0	0	1	0	0	4697	893	31	2	676	2	DOCK11	23	117695437	Nonsense_Mutation	SNP	C	TCGA-AG-3593-01A-01W-0831-10	7998564	117695437	37575123	75	2108										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153134140	153134140	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	3	1	0.412514263978699	1.21004184100418	0.177947329559439	1	1	0	gtcccattggcataggggaaGaagcgttcgtcctgaagcac	13	10	0	2			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	027b7b82-7529-46fb-bb00-85671db59968	d65bd3d4-a33f-4b54-b8c2-25e1990e9c9c	g.chrX:153134140G>T	ENST00000370060.1	-	13	1611	c.1422C>A	c.(1420-1422)ttC>ttA	p.F474L	L1CAM_ENST00000370057.3_Missense_Mutation_p.F474L|L1CAM_ENST00000361699.4_Missense_Mutation_p.F474L|L1CAM_ENST00000370055.1_Missense_Mutation_p.F469L|L1CAM_ENST00000543994.1_Missense_Mutation_p.F476L|L1CAM_ENST00000361981.3_Missense_Mutation_p.F469L|L1CAM_ENST00000538883.1_Missense_Mutation_p.F476L	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	474	Ig-like C2-type 5.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.F474L(1)|p.F474F(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CATAGGGGAAGAAGCGTTCGT	0.617																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|breast(1)	X											144	104	118					X																	153134140		2203	4300	6503	152787334	SO:0001583	missense	3897			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1422C>A	X.37:g.153134140G>T	ENSP00000359077:p.Phe474Leu		152787334	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216898	0.58452	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.62	3.49	0.39957	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000004	T	0.60728	0.2291	N	0.20304	0.555	0.39560	D	0.969112	D;B;P	0.55800	0.973;0.257;0.948	P;B;P	0.57152	0.718;0.202;0.814	T	0.63782	-0.6559	10	0.66056	D	0.02	.	6.5262	0.22303	0.3927:0.0:0.6073:0.0	.	469;474;474	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	L	474;476;474;476;469;469;474	ENSP00000359077:F474L;ENSP00000438430:F476L;ENSP00000359074:F474L;ENSP00000439645:F476L;ENSP00000354712:F469L;ENSP00000359072:F469L;ENSP00000355380:F474L	ENSP00000355380:F474L	F	-	3	2	L1CAM	152787334	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	1.559000	0.36320	1.128000	0.42052	0.529000	0.55759	TTC		0.617	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		T	153134140	G	T	153134140	3	4	23	1	0	0	0	0	1	0	0	0	8610	933	33	2	2419	2	L1CAM	23	153134140	Missense_Mutation	SNP	G	TCGA-AG-3593-01A-01W-0831-10	35438703	153134140	2136420	76	2109										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9777133	9777133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gccccccaggtccagaaaccGcgtgccaaaccacctcccat	7	20	0	1	rs149279787		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr1:9777133G>A	ENST00000377346.4	+	7	1092	c.897G>A	c.(895-897)ccG>ccA	p.P299P	PIK3CD_ENST00000361110.2_Silent_p.P264P|PIK3CD_ENST00000536656.1_Silent_p.P264P|PIK3CD_ENST00000543390.1_5'Flank	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	299					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.P299P(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	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)	Caffeine(DB00201)	TCCAGAAACCGCGTGCCAAAC	0.617													G|||	1	0.000199681	8e-04	0	5008	,	,		18491	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		2,4404	4.2+/-10.8	0,2,2201	128	116	120		897	-9.9	0	1	dbSNP_134	120	0,8600		0,0,4300	no	coding-synonymous	PIK3CD	NM_005026.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		299/1045	9777133	2,13004	2203	4300	6503	9699720	SO:0001819	synonymous_variant	5293				CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.897G>A	1.37:g.9777133G>A			9699720	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	37	CCDS104.1																																																																																				0.617	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		A	9777133	G	A	9777133	2	1	24	1	0	0	0	0	0	0	0	1	11946	1074	38	1		1	PIK3CD	1	9777133	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10		9777133	239473488	1	2110										
DDOST	1650	hgsc.bcm.edu	37	chr1	20978950	20978950	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cccagcatcatggagaaggcGctggcgtagtaggggtaggc	17	9	1	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr1:20978950G>A	ENST00000375048.3	-	11	1398	c.1293C>T	c.(1291-1293)agC>agT	p.S431S	DDOST_ENST00000602624.2_Silent_p.S414S|DDOST_ENST00000415136.2_Silent_p.S394S|PINK1-AS_ENST00000451424.1_RNA	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	431					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.S431S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TGGAGAAGGCGCTGGCGTAGT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	1											59	58	59					1																	20978950		2203	4300	6503	20851537	SO:0001819	synonymous_variant	1650			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"oligosaccharyltransferase subunit 48"	602202	"dolichyl-diphosphooligosaccharide-protein glycosyltransferase", "dolichyl-diphosphooligosaccharide--protein glycosyltransferase"			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.1293C>T	1.37:g.20978950G>A			20851537	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.602	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216		A	20978950	G	A	20978950	2	1	24	1	0	0	0	0	0	0	0	1	4341	1078	38	1		1	DDOST	1	20978950	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10	11201817	20978950	228271671	2	2111										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204419032	204419032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ccagggcttcaggcacccgcCgctgcttattggcctctgag	12	15	2	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr1:204419032C>T	ENST00000367187.3	-	14	2736	c.2180G>A	c.(2179-2181)cGg>cAg	p.R727Q	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R727Q	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	727	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R727Q(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			AGGCACCCGCCGCTGCTTATT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											23	27	26					1																	204419032		2203	4300	6503	202685655	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2180G>A	1.37:g.204419032C>T	ENSP00000356155:p.Arg727Gln		202685655	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848435	0.91277	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.77358	-1.09;-1.09	4.88	3.96	0.45880	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.223973	0.35378	N	0.003248	T	0.73094	0.3543	L	0.49778	1.585	0.32741	N	0.507687	B;P	0.35780	0.426;0.52	B;B	0.38056	0.264;0.237	T	0.79569	-0.1749	10	0.62326	D	0.03	.	11.9068	0.52717	0.0:0.9122:0.0:0.0878	.	727;727	F5GWN5;O00750	.;P3C2B_HUMAN	Q	727	ENSP00000356155:R727Q;ENSP00000400561:R727Q	ENSP00000356155:R727Q	R	-	2	0	PIK3C2B	202685655	1.000000	0.71417	0.997000	0.53966	0.836000	0.47400	4.506000	0.60428	1.033000	0.39918	0.305000	0.20034	CGG		0.627	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		T	204419032	C	T	204419032	3	4	24	1	0	0	0	0	1	0	0	0	11941	652	23	1	2808	1	PIK3C2B	1	204419032	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	183440082	204419032	44831589	3	2112										
GLI2	2736	hgsc.bcm.edu	37	chr2	121726311	121726311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gtcccgtttctccagcccgcGggtgacgccccgcctgagcc	12	19	1	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr2:121726311G>A	ENST00000452319.1	+	6	725	c.665G>A	c.(664-666)cGg>cAg	p.R222Q	GLI2_ENST00000361492.4_Missense_Mutation_p.R222Q|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2									p.R222Q(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				TCCAGCCCGCGGGTGACGCCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	63	63					2																	121726311		2203	4300	6503	121442781	SO:0001583	missense	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.665G>A	2.37:g.121726311G>A	ENSP00000390436:p.Arg222Gln		121442781		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207762	0.95033	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.70282	-0.47;-0.47	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.84579	0.5503	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.992	D	0.86643	0.1893	10	0.87932	D	0	.	18.2868	0.90117	0.0:0.0:1.0:0.0	.	222;222	P10070;Q0VGA0	GLI2_HUMAN;.	Q	222	ENSP00000390436:R222Q;ENSP00000354586:R222Q	ENSP00000354586:R222Q	R	+	2	0	GLI2	121442781	1.000000	0.71417	0.816000	0.32577	0.596000	0.36781	9.601000	0.98297	2.557000	0.86248	0.655000	0.94253	CGG		0.647	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121726311	G	A	121726311	3	1	24	1	0	0	0	0	1	0	0	0	6458	1116	39	1	683	1	GLI2	2	121726311	Missense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10		121726311	121473062	4	2113										
HOXD4	3233	hgsc.bcm.edu	37	chr2	177017660	177017660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	agaccaccacacggacctgaCgaccttatagaagtggggac	11	12	0	3			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr2:177017660C>T	ENST00000306324.3	+	2	1170	c.758C>T	c.(757-759)aCg>aTg	p.T253M	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	253					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T253M(1)		kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ACGGACCTGACGACCTTATAG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	72	70					2																	177017660		2203	4300	6503	176725906	SO:0001583	missense	3233				CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"Homeoboxes / ANTP class : HOXL subclass"	5138	protein-coding gene	gene with protein product		142981	"homeo box D4"	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.758C>T	2.37:g.177017660C>T	ENSP00000302548:p.Thr253Met		176725906	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	37	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061367	0.76187	.	.	ENSG00000170166	ENST00000306324	D	0.90732	-2.72	5.67	5.67	0.87782	.	7.610600	0.00397	N	0.000055	D	0.96284	0.8788	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85608	0.1256	10	0.87932	D	0	.	19.7626	0.96329	0.0:1.0:0.0:0.0	.	253	P09016	HXD4_HUMAN	M	253	ENSP00000302548:T253M	ENSP00000302548:T253M	T	+	2	0	HOXD4	176725906	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.055000	0.71103	2.676000	0.91093	0.561000	0.74099	ACG		0.642	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			T	177017660	C	T	177017660	3	4	24	1	0	0	0	0	1	0	0	0	7345	536	19	1	764	1	HOXD4	2	177017660	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	55291349	177017660	66181713	5	2114										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253585	238253585	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gtcaccaaaatcaacttaccGtaacagcaagctagaaaaga	6	10	2	2	rs114248590	byFrequency	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr2:238253585G>A	ENST00000295550.4	-	35	7625	c.7173C>T	c.(7171-7173)taC>taT	p.Y2391Y	COL6A3_ENST00000472056.1_Splice_Site_p.Y1784Y|COL6A3_ENST00000347401.3_Splice_Site_p.Y2190Y|COL6A3_ENST00000346358.4_Splice_Site_p.Y2191Y|COL6A3_ENST00000409809.1_Splice_Site_p.Y2185Y|COL6A3_ENST00000353578.4_Splice_Site_p.Y2185Y	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2391	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y2391Y(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TCAACTTACCGTAACAGCAAG	0.408													A|||	3	0.000599042	8e-04	0	5008	,	,		20521	0.001		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	2											111	109	110					2																	238253585		2203	4300	6503	237918324	SO:0001630	splice_region_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7174+1C>T	2.37:g.238253585G>A			237918324	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.408	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	Silent	A	238253585	G	A	238253585	5	1	24	1	0	0	0	0	0	0	1	0	3707	1159	40	1	2400	1	COL6A3	2	238253585	Splice_Site	SNP	G	TCGA-AG-3594-01A-02W-0831-10	61235925	238253585	4945788	6	2115										
TMPPE	643853	hgsc.bcm.edu	37	chr3	33135619	33135619	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tacgagcgggaggcgatcatGgacacgaagacagtgacagc	15	9	1	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr3:33135619G>A	ENST00000342462.4	-	2	259	c.69C>T	c.(67-69)tcC>tcT	p.S23S	GLB1_ENST00000307363.5_Intron|GLB1_ENST00000399402.3_Intron|GLB1_ENST00000445488.2_Intron|TMPPE_ENST00000416695.2_Intron|GLB1_ENST00000307377.8_Intron	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	23						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.S23S(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						AGGCGATCATGGACACGAAGA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											66	63	64					3																	33135619		2203	4300	6503	33110623	SO:0001819	synonymous_variant	643853			AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.69C>T	3.37:g.33135619G>A			33110623	B2RNG5|Q6ZRG1	Silent	SNP	ENST00000342462.4	37	CCDS33732.1																																																																																				0.602	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770		A	33135619	G	A	33135619	2	1	24	1	0	0	0	0	0	0	0	1	16277	1335	47	3		3	TMPPE	3	33135619	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10		33135619	164886811	7	2116										
TRA2B	6434	hgsc.bcm.edu	37	chr3	185635510	185635510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aagtcttcatgctttaatagCgacctgggaagaaaagaatg	10	6	2	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr3:185635510C>T	ENST00000453386.2	-	9	1135	c.860G>A	c.(859-861)cGc>cAc	p.R287H	TRA2B_ENST00000382191.4_Missense_Mutation_p.R187H	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	287	Arg/Ser-rich (RS2 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R287H(1)		breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						GCTTTAATAGCGACCTGGGAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											86	91	89					3																	185635510		2203	4300	6503	187118204	SO:0001583	missense	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"RNA binding motif (RRM) containing"	10781	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 156"	602719	"splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.860G>A	3.37:g.185635510C>T	ENSP00000416959:p.Arg287His		187118204	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Missense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.57|15.57	2.871579|2.871579	0.51695|0.51695	.|.	.|.	ENSG00000136527|ENSG00000136527	ENST00000259043;ENST00000414862|ENST00000453386;ENST00000382191	.|T;T	.|0.27402	.|1.83;1.67	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|1.623140	.|0.02892	.|N	.|0.134297	T|T	0.29588|0.29588	0.0738|0.0738	N|N	0.16656|0.16656	0.425|0.425	0.80722|0.80722	D|D	1|1	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.05194|0.05194	-1.0900|-1.0900	5|10	.|0.28530	.|T	.|0.3	-2.1221|-2.1221	18.9107|18.9107	0.92483|0.92483	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|287;287	.|B2RDQ3;P62995	.|.;TRA2B_HUMAN	T|H	126;106|287;187	.|ENSP00000416959:R287H;ENSP00000371626:R187H	.|ENSP00000371626:R187H	A|R	-|-	1|2	0|0	TRA2B|TRA2B	187118204|187118204	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.863000|0.863000	0.49368|0.49368	4.054000|4.054000	0.57434|0.57434	2.751000|2.751000	0.94390|0.94390	0.591000|0.591000	0.81541|0.81541	GCT|CGC		0.338	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		T	185635510	C	T	185635510	3	4	24	1	0	0	0	0	1	0	0	0	16474	768	27	1	10	1	TRA2B	3	185635510	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	152499891	185635510	12386920	8	2117										
EVC2	132884	hgsc.bcm.edu	37	chr4	5624468	5624468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ggaagagccagggcaccccaCgcttgagcagctcctgggtc	14	14	0	2	rs149854557		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr4:5624468C>T	ENST00000344408.5	-	14	2350	c.2297G>A	c.(2296-2298)cGt>cAt	p.R766H	EVC2_ENST00000344938.1_Missense_Mutation_p.R766H|EVC2_ENST00000310917.2_Missense_Mutation_p.R686H	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	766					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R766H(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						GGGCACCCCACGCTTGAGCAG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	49	47	48		2057,2297	2	0.4	4	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	686/1229,766/1309	5624468	1,13005	2203	4300	6503	5675369	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2297G>A	4.37:g.5624468C>T	ENSP00000342144:p.Arg766His		5675369	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	9.512	1.105964	0.20632	0.0	1.16E-4	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74632	-0.86;-0.85;-0.86	5.32	1.95	0.26073	.	0.435130	0.24698	N	0.036337	T	0.59851	0.2224	L	0.51422	1.61	0.23568	N	0.997395	B	0.15719	0.014	B	0.08055	0.003	T	0.36504	-0.9745	10	0.15066	T	0.55	-9.7772	4.5016	0.11867	0.3113:0.4754:0.0:0.2133	.	766	Q86UK5	LBN_HUMAN	H	766;686;766	ENSP00000339954:R766H;ENSP00000311683:R686H;ENSP00000342144:R766H	ENSP00000311683:R686H	R	-	2	0	EVC2	5675369	0.676000	0.27567	0.383000	0.26132	0.377000	0.30045	1.072000	0.30678	0.504000	0.28082	0.462000	0.41574	CGT		0.647	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		T	5624468	C	T	5624468	3	4	24	1	0	0	0	0	1	0	0	0	5299	536	19	1	1665	1	EVC2	4	5624468	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10		5624468	185529808	9	2118										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153250856	153250858	+	In_Frame_Del	DEL	TGT	TGT	-													0	0	1	0	NA	0	1	1	0	tgctgaccaaacttttaaagTgttgtcatcagaaccactaa							TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	TGT	TGT	TGT	-	TGT	TGT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr4:153250856_153250858delTGT	ENST00000281708.4	-	8	2431_2433	c.1202_1204delACA	c.(1201-1206)aacact>act	p.N401del	FBXW7_ENST00000296555.5_In_Frame_Del_p.N283del|FBXW7_ENST00000603548.1_In_Frame_Del_p.N401del|FBXW7_ENST00000263981.5_In_Frame_Del_p.N321del|FBXW7_ENST00000393956.3_In_Frame_Del_p.N225del|FBXW7_ENST00000603841.1_In_Frame_Del_p.N401del	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	401					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.N401delN(2)|p.N162delN(1)|p.N321delN(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTTTTAAAGTGTTGTCATCAGA	0.374			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	5	Deletion - In frame(4)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)	4																																								153470308	SO:0001651	inframe_deletion	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1202_1204delACA	4.37:g.153250859_153250861delTGT	ENSP00000281708:p.Asn401del		153470306	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	In_Frame_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				0.374	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			-	153250858	TGT	-	153250856	7	5	24	1	0	1	0	1	0	0	0	0	5788	1696	59	0	939	0	FBXW7	4	153250856	In_Frame_Del	DEL	TGT	TCGA-AG-3594-01A-02W-0831-10	147626388	153250856	37903420	10	2119										
TLL1	7092	hgsc.bcm.edu	37	chr4	166996031	166996031	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ggattgatctctttgctagaCaaagatgaatgctctaagga	10	6	2	4			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr4:166996031C>A	ENST00000061240.2	+	17	2837	c.2190C>A	c.(2188-2190)gaC>gaA	p.D730E	TLL1_ENST00000507499.1_Splice_Site_p.D753E	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	730	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.|EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D730E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTTTGCTAGACAAAGATGAAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											153	129	137					4																	166996031		2203	4300	6503	167215481	SO:0001630	splice_region_variant	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2189-1C>A	4.37:g.166996031C>A			167215481	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	37	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676725	0.47886	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	D;D	0.96427	-4.01;-1.85	5.59	1.92	0.25849	EGF-like calcium-binding, conserved site (1);CUB (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.96691	0.8920	L	0.59967	1.855	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.83275	0.996;0.984	D	0.94456	0.7672	10	0.45353	T	0.12	.	8.7137	0.34399	0.0:0.5518:0.0:0.4482	.	753;730	E9PD25;O43897	.;TLL1_HUMAN	E	730;753	ENSP00000061240:D730E;ENSP00000426082:D753E	ENSP00000061240:D730E	D	+	3	2	TLL1	167215481	1.000000	0.71417	0.998000	0.56505	0.251000	0.25915	1.216000	0.32443	0.106000	0.17784	0.557000	0.71058	GAC		0.403	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		Missense_Mutation	A	166996031	C	A	166996031	5	1	24	1	0	0	0	0	0	0	1	0	15984	492	17	2	2256	2	TLL1	4	166996031	Splice_Site	SNP	C	TCGA-AG-3594-01A-02W-0831-10	13745175	166996031	24158245	11	2120										
APC	324	hgsc.bcm.edu	37	chr5	112175001	112175002	+	Frame_Shift_Del	DEL	AG	AG	-													0	0	1	0	NA	0	1	1	0	gctccatccaagttctgcacAgagtagaagtggtcagcctc							TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr5:112175001_112175002delAG	ENST00000457016.1	+	16	4090_4091	c.3710_3711delAG	c.(3709-3711)cagfs	p.Q1237fs	APC_ENST00000508376.2_Frame_Shift_Del_p.Q1237fs|APC_ENST00000257430.4_Frame_Shift_Del_p.Q1237fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1237	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1237fs*2(1)|p.S1238fs*1(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGTTCTGCACAGAGTAGAAGTG	0.411		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5																																								112202901	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3710_3711delAG	5.37:g.112175003_112175004delAG	ENSP00000413133:p.Gln1237fs		112202900	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.411	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175002	AG	-	112175001	7	5	24	1	0	1	0	1	0	0	0	0	763	188	7	0	3768	0	APC	5	112175001	Frame_Shift_Del	DEL	AG	TCGA-AG-3594-01A-02W-0831-10		112175001	68740259	12	2121										
MYOT	9499	hgsc.bcm.edu	37	chr5	137213210	137213210	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ctcaataaattctctaaagcGtctaacatatgaagagaaga	6	7	3	3	rs150293853		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr5:137213210G>A	ENST00000239926.4	+	4	907	c.533G>A	c.(532-534)cGt>cAt	p.R178H	RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000421631.2_5'UTR|MYOT_ENST00000515645.1_Splice_Site_p.R63H|MYOT_ENST00000509812.1_3'UTR	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	178					muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.R178H(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCTCTAAAGCGTCTAACATAT	0.398													G|||	1	0.000199681	0	0	5008	,	,		14939	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						G	,HIS/ARG	0,4406		0,0,2203	77	77	77		,533	5.7	1	5	dbSNP_134	77	4,8596	3.7+/-12.6	0,4,4296	yes	utr-5,missense-near-splice	MYOT	NM_001135940.1,NM_006790.2	,29	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,probably-damaging	,178/499	137213210	4,13002	2203	4300	6503	137241109	SO:0001630	splice_region_variant	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.532-1G>A	5.37:g.137213210G>A			137241109	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.39	3.614239	0.66672	0.0	4.65E-4	ENSG00000120729	ENST00000239926;ENST00000515645	T;T	0.72942	-0.7;-0.68	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000004	T	0.76212	0.3956	L	0.27053	0.805	0.40095	D	0.976309	D	0.89917	1.0	D	0.65874	0.939	T	0.76296	-0.3011	10	0.42905	T	0.14	.	19.8298	0.96631	0.0:0.0:1.0:0.0	.	178	Q9UBF9	MYOTI_HUMAN	H	178;63	ENSP00000239926:R178H;ENSP00000426281:R63H	ENSP00000239926:R178H	R	+	2	0	MYOT	137241109	1.000000	0.71417	0.999000	0.59377	0.327000	0.28475	6.020000	0.70826	2.687000	0.91594	0.591000	0.81541	CGT		0.398	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790	Missense_Mutation	A	137213210	G	A	137213210	5	1	24	1	0	0	0	0	0	0	1	0	10124	1159	40	1	543	1	MYOT	5	137213210	Splice_Site	SNP	G	TCGA-AG-3594-01A-02W-0831-10	25038209	137213210	43702050	13	2122										
MAK	4117	hgsc.bcm.edu	37	chr6	10791978	10791978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cttcttggaatgggaggctcCgaaatcatagtcctccaact	9	11	2	0			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr6:10791978C>T	ENST00000313243.2	-	10	1628	c.1246G>A	c.(1246-1248)Gga>Aga	p.G416R	MAK_ENST00000538030.1_Missense_Mutation_p.G416R|RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000474039.1_Missense_Mutation_p.G416R|MAK_ENST00000354489.2_Missense_Mutation_p.G416R|MAK_ENST00000536370.1_3'UTR			P20794	MAK_HUMAN	male germ cell-associated kinase	416					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)	p.G416R(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				TGGGAGGCTCCGAAATCATAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	6											92	90	91					6																	10791978		2203	4300	6503	10899964	SO:0001583	missense	4117				CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1246G>A	6.37:g.10791978C>T	ENSP00000313021:p.Gly416Arg		10899964	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960823	0.74016	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.72505	-0.66;-0.66;-0.63	5.25	5.25	0.73442	.	0.197055	0.45126	D	0.000381	T	0.76884	0.4050	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	P	0.60345	0.873	T	0.77011	-0.2746	10	0.48119	T	0.1	.	17.4017	0.87461	0.0:1.0:0.0:0.0	.	416	P20794	MAK_HUMAN	R	416	ENSP00000313021:G416R;ENSP00000346484:G416R;ENSP00000442250:G416R	ENSP00000313021:G416R	G	-	1	0	MAK	10899964	0.999000	0.42202	0.955000	0.39395	0.594000	0.36715	2.814000	0.48010	2.603000	0.88011	0.655000	0.94253	GGA		0.418	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		T	10791978	C	T	10791978	3	4	24	1	0	0	0	0	1	0	0	0	9227	661	23	1	645	1	MAK	6	10791978	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10		10791978	160323089	14	2123										
NRM	11270	hgsc.bcm.edu	37	chr6	30657088	30657088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gagctcagcatagtcaaagaCgagaaggatgctaaagatga	12	6	2	4	rs573111369		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr6:30657088C>T	ENST00000259953.4	-	4	823	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	PPP1R18_ENST00000274853.3_5'Flank|NRM_ENST00000470733.1_5'UTR|NRM_ENST00000376421.5_Missense_Mutation_p.V158I|NRM_ENST00000376420.5_Intron|PPP1R18_ENST00000488324.1_5'Flank|PPP1R18_ENST00000399199.3_5'Flank	NM_007243.2	NP_009174.1	Q8IXM6	NRM_HUMAN	nurim (nuclear envelope membrane protein)	158	Leu-rich.					integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.V158I(1)		large_intestine(1)|lung(2)	3						TAGTCAAAGACGAGAAGGATG	0.552													C|||	1	0.000199681	0	0.0014	5008	,	,		20816	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											57	46	50					6																	30657088		2186	4266	6452	30765067	SO:0001583	missense	11270			AF143676	CCDS4686.1, CCDS59498.1	6p21.3	2010-02-17			ENSG00000137404	ENSG00000137404			8003	protein-coding gene	gene with protein product						10402458, 17517639	Standard	NM_007243		Approved	NRM29	uc031sng.1	Q8IXM6	OTTHUMG00000031223	ENST00000259953.4:c.472G>A	6.37:g.30657088C>T	ENSP00000259953:p.Val158Ile		30765067	B0S7R0|B0S7R1|I3XIE2|I3XIE3|Q5JP57|Q5JP58|Q5JP59|Q5JP60|Q8WU45|Q9BSX3|Q9UN92	Missense_Mutation	SNP	ENST00000259953.4	37	CCDS4686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.581|6.581	0.475489|0.475489	0.12521|0.12521	.|.	.|.	ENSG00000137404|ENSG00000137404	ENST00000444096|ENST00000259953;ENST00000376421	.|T;T	.|0.26223	.|1.75;1.75	4.72|4.72	3.85|3.85	0.44370|0.44370	.|.	.|0.123897	.|0.52532	.|N	.|0.000066	T|T	0.01870|0.01870	0.0059|0.0059	N|N	0.00621|0.00621	-1.32|-1.32	0.34152|0.34152	D|D	0.667684|0.667684	.|B	.|0.13594	.|0.008	.|B	.|0.12156	.|0.007	T|T	0.42344|0.42344	-0.9457|-0.9457	5|10	.|0.10377	.|T	.|0.69	-3.6216|-3.6216	7.3878|7.3878	0.26893|0.26893	0.0:0.803:0.0:0.197|0.0:0.803:0.0:0.197	.|.	.|158	.|Q8IXM6	.|NRM_HUMAN	H|I	157|158	.|ENSP00000259953:V158I;ENSP00000365603:V158I	.|ENSP00000259953:V158I	R|V	-|-	2|1	0|0	NRM|NRM	30765067|30765067	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.705000|3.705000	0.54823|0.54823	1.128000|1.128000	0.42052|0.42052	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.552	NRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076466.2			T	30657088	C	T	30657088	3	4	24	1	0	0	0	0	1	0	0	0	10688	536	19	1	324	1	NRM	6	30657088	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	19865110	30657088	140457979	15	2124										
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72006228	72006228	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ctgagagaacaaggcttgaaCttctatgccaaagaactaac	8	9	1	4			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr6:72006228C>T	ENST00000370435.4	+	5	644	c.510C>T	c.(508-510)aaC>aaT	p.N170N	RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	170						membrane (GO:0016020)	receptor activity (GO:0004872)	p.N170N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						AAGGCTTGAACTTCTATGCCA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	6											45	43	44					6																	72006228		2184	4268	6452	72062949	SO:0001819	synonymous_variant	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.510C>T	6.37:g.72006228C>T			72062949	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	37	CCDS34482.1																																																																																				0.318	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		T	72006228	C	T	72006228	2	4	24	1	0	0	0	0	0	0	0	1	10875	564	20	3		3	OGFRL1	6	72006228	Silent	SNP	C	TCGA-AG-3594-01A-02W-0831-10	41349140	72006228	99108839	16	2125										
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134350498	134350498	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	tgttgaggagcaatctctgcGatgtaaacacaagtggcaat	11	7	1	1	rs377021554		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr6:134350498G>A	ENST00000275230.5	-	2	620	c.465C>T	c.(463-465)atC>atT	p.I155I		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	155					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.I155I(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		CAATCTCTGCGATGTAAACAC	0.448													G|||	1	0.000199681	8e-04	0	5008	,	,		23105	0		0	False		,,,				2504	0				Melanoma(122;1663 1672 14489 35294 41228)											1	Substitution - coding silent(1)	large_intestine(1)	6						G		1,4405	2.1+/-5.4	0,1,2202	110	110	110		465	-3.2	0.9	6		110	0,8600		0,0,4300	no	coding-synonymous	SLC2A12	NM_145176.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		155/618	134350498	1,13005	2203	4300	6503	134392191	SO:0001819	synonymous_variant	154091			AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.465C>T	6.37:g.134350498G>A			134392191	B3KV17|Q7Z6U3|Q96MR8	Silent	SNP	ENST00000275230.5	37	CCDS5169.1																																																																																				0.448	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			A	134350498	G	A	134350498	2	1	24	1	0	0	0	0	0	0	0	1	14578	1048	37	1		1	SLC2A12	6	134350498	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10	62344270	134350498	36764569	17	2126										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152485429	152485429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gttcttatcaagctgctgcaCggctaccagggtctccttca	9	13	4	0	rs143842011		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr6:152485429C>T	ENST00000367255.5	-	131	24260	c.23659G>A	c.(23659-23661)Gtg>Atg	p.V7887M	SYNE1_ENST00000539504.1_Missense_Mutation_p.V42M|SYNE1_ENST00000356820.4_Missense_Mutation_p.V2411M|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.V7816M|SYNE1_ENST00000265368.4_Missense_Mutation_p.V7887M|SYNE1_ENST00000354674.4_Missense_Mutation_p.V42M|SYNE1_ENST00000423061.1_Missense_Mutation_p.V7816M|SYNE1_ENST00000341594.5_Missense_Mutation_p.V7499M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7887					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V7887M(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCTGCTGCACGGCTACCAGG	0.557										HNSCC(10;0.0054)			C|||	1	0.000199681	0	0	5008	,	,		18263	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	6						C	MET/VAL,MET/VAL	4,4402	8.1+/-20.4	0,4,2199	79	72	75		23446,23659	5.3	0.9	6	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	21,21	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging	7816/8750,7887/8798	152485429	4,13002	2203	4300	6503	152527122	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23659G>A	6.37:g.152485429C>T	ENSP00000356224:p.Val7887Met		152527122	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	29.8	5.038313	0.93630	9.08E-4	0.0	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.52983	1.33;0.64;1.33;1.33;1.33;1.33;1.33;1.33;1.33;0.64	5.34	5.34	0.76211	.	0.000000	0.49305	D	0.000154	T	0.60248	0.2254	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;0.832	T	0.63175	-0.6696	10	0.72032	D	0.01	.	19.033	0.92965	0.0:1.0:0.0:0.0	.	7887;7887;7816;7816;89	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	M	7887;42;533;7816;7887;7816;7499;2411;49;44;809;42	ENSP00000356224:V7887M;ENSP00000441052:V42M;ENSP00000356226:V533M;ENSP00000396024:V7816M;ENSP00000265368:V7887M;ENSP00000390975:V7816M;ENSP00000341887:V7499M;ENSP00000349276:V2411M;ENSP00000356220:V809M;ENSP00000346701:V42M	ENSP00000265368:V7887M	V	-	1	0	SYNE1	152527122	1.000000	0.71417	0.857000	0.33713	0.967000	0.64934	7.757000	0.85209	2.497000	0.84241	0.585000	0.79938	GTG		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152485429	C	T	152485429	3	4	24	1	0	0	0	0	1	0	0	0	15484	536	19	1	2871	1	SYNE1	6	152485429	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	18134931	152485429	18629638	18	2127										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47860768	47860768	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aagcagaagcagcatgaggaTgtccatggaaatgtctctgt	12	7	1	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr7:47860768T>C	ENST00000289672.2	-	46	6921	c.6871A>G	c.(6871-6873)Atc>Gtc	p.I2291V		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2291					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.I2291V(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGCATGAGGATGTCCATGGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											83	77	79					7																	47860768		2203	4300	6503	47827293	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6871A>G	7.37:g.47860768T>C	ENSP00000289672:p.Ile2291Val		47827293	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.674357	0.29693	.	.	ENSG00000158683	ENST00000289672	T	0.18657	2.2	5.27	-1.83	0.07833	.	1.592510	0.03401	N	0.203333	T	0.12390	0.0301	N	0.25647	0.755	0.09310	N	1	B	0.18166	0.026	B	0.10450	0.005	T	0.24941	-1.0146	10	0.05525	T	0.97	-7.6636	7.0451	0.25040	0.0:0.4951:0.1533:0.3516	.	2291	Q8TDX9	PK1L1_HUMAN	V	2291	ENSP00000289672:I2291V	ENSP00000289672:I2291V	I	-	1	0	PKD1L1	47827293	0.000000	0.05858	0.000000	0.03702	0.821000	0.46438	-0.577000	0.05847	-0.471000	0.06891	0.528000	0.53228	ATC		0.378	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47860768	T	C	47860768	3	2	24	1	0	0	0	0	1	0	0	0	11995	1464	51	4	1726	4	PKD1L1	7	47860768	Missense_Mutation	SNP	T	TCGA-AG-3594-01A-02W-0831-10		47860768	111277895	19	2128										
DLX5	1749	hgsc.bcm.edu	37	chr7	96653612	96653612	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gtggcgcttgggacgcggttGtaggcgccgccgtactggtg	19	10	0	0			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr7:96653612G>A	ENST00000222598.4	-	1	797	c.324C>T	c.(322-324)taC>taT	p.Y108Y	DLX5_ENST00000486603.2_Silent_p.Y108Y|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	108					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.Y108Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGACGCGGTTGTAGGCGCCGC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	7											45	43	44					7																	96653612		2203	4300	6503	96491548	SO:0001819	synonymous_variant	1749				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.324C>T	7.37:g.96653612G>A			96491548	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																				0.637	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			A	96653612	G	A	96653612	2	1	24	1	0	0	0	0	0	0	0	1	4585	1372	48	3		3	DLX5	7	96653612	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10	48792844	96653612	62485051	20	2129										
TNC	3371	hgsc.bcm.edu	37	chr9	117849482	117849482	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gggcctttccagccaggttcGcagacacagccacatccttc	9	16	0	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr9:117849482G>A	ENST00000350763.4	-	3	939	c.528C>T	c.(526-528)tgC>tgT	p.C176C	TNC_ENST00000340094.3_Silent_p.C176C|TNC_ENST00000346706.3_Silent_p.C176C|TNC_ENST00000345230.3_Silent_p.C176C|TNC_ENST00000542877.1_Silent_p.C176C|TNC_ENST00000423613.2_Silent_p.C176C|TNC_ENST00000341037.4_Silent_p.C176C|TNC_ENST00000535648.1_Silent_p.C176C|TNC_ENST00000537320.1_Silent_p.C176C	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	176	EGF-like 1; incomplete. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.C176C(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGCCAGGTTCGCAGACACAGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	76	78					9																	117849482		2203	4300	6503	116889303	SO:0001819	synonymous_variant	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.528C>T	9.37:g.117849482G>A			116889303	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.582	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		A	117849482	G	A	117849482	2	1	24	1	0	0	0	0	0	0	0	1	16309	1079	38	1		1	TNC	9	117849482	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10		117849482	23363949	21	2130										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7627983	7627983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aaaatccaatgatactgaaaCggtcctggggtcggaggtca	12	8	1	2	rs529878669		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr10:7627983C>T	ENST00000256861.6	-	8	1067	c.989G>A	c.(988-990)cGt>cAt	p.R330H	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_Missense_Mutation_p.R112H|ITIH5_ENST00000397146.2_Missense_Mutation_p.R330H|ITIH5_ENST00000298441.6_Missense_Mutation_p.R116H|ITIH5_ENST00000397145.2_Missense_Mutation_p.R330H	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	330	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R330H(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GATACTGAAACGGTCCTGGGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											148	127	134					10																	7627983		2203	4300	6503	7667989	SO:0001583	missense	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.989G>A	10.37:g.7627983C>T	ENSP00000256861:p.Arg330His		7667989	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	0.568	-0.842188	0.02671	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08	5.3	-4.52	0.03472	von Willebrand factor, type A (3);	0.446927	0.26623	N	0.023357	T	0.72112	0.3420	.	.	.	0.20403	N	0.999908	B;B;B	0.12013	0.005;0.004;0.003	B;B;B	0.15052	0.012;0.003;0.002	T	0.55970	-0.8056	9	0.12103	T	0.63	-5.4197	13.2689	0.60150	0.0:0.2223:0.0:0.7777	.	330;330;116	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	H	330;330;116;112;330	ENSP00000256861:R330H;ENSP00000380333:R330H;ENSP00000298441:R116H;ENSP00000387969:R112H;ENSP00000380332:R330H	ENSP00000256861:R330H	R	-	2	0	ITIH5	7667989	0.017000	0.18338	0.009000	0.14445	0.699000	0.40488	-0.105000	0.10907	-1.191000	0.02695	-0.997000	0.02515	CGT		0.473	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7627983	C	T	7627983	3	4	24	1	0	0	0	0	1	0	0	0	7928	536	19	1	1990	1	ITIH5	10	7627983	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10		7627983	127906764	22	2131										
SGMS1	259230	hgsc.bcm.edu	37	chr10	52103403	52103403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	ctccttaggaggtactcgttCgtggacgaccgagatcatca	11	11	2	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr10:52103403C>T	ENST00000361781.2	-	7	1431	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	SGMS1_ENST00000361543.2_Missense_Mutation_p.E158K|SGMS1_ENST00000492601.2_5'Flank|SGMS1_ENST00000429490.1_Intron	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	164					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.E158K(1)		endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGTACTCGTTCGTGGACGACC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10											59	53	55					10																	52103403		2203	4300	6503	51773409	SO:0001583	missense	259230			AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.472G>A	10.37:g.52103403C>T	ENSP00000354829:p.Glu158Lys		51773409	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	37	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165193	0.94768	.	.	ENSG00000198964	ENST00000361781;ENST00000361543	T;T	0.60424	0.71;0.19	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.75686	0.3883	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.77768	-0.2464	10	0.87932	D	0	-14.4732	17.1838	0.86861	0.0:1.0:0.0:0.0	.	164	Q86VZ5	SMS1_HUMAN	K	158	ENSP00000354829:E158K;ENSP00000355235:E158K	ENSP00000355235:E158K	E	-	1	0	SGMS1	51773409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.403000	0.79983	2.648000	0.89879	0.650000	0.86243	GAA		0.493	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		T	52103403	C	T	52103403	3	4	24	1	0	0	0	0	1	0	0	0	14251	893	31	1	789	1	SGMS1	10	52103403	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	44475420	52103403	83431344	23	2132										
KIF18A	81930	hgsc.bcm.edu	37	chr11	28057931	28057931	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tcacacaacattttcagacaAttatcactgtttatgtttga	4	8	3	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr11:28057931A>C	ENST00000263181.6	-	14	2519	c.2229T>G	c.(2227-2229)aaT>aaG	p.N743K		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	743					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.N743K(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TTTTCAGACAATTATCACTGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	11											150	145	147					11																	28057931		2202	4298	6500	28014507	SO:0001583	missense	81930			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2229T>G	11.37:g.28057931A>C	ENSP00000263181:p.Asn743Lys		28014507	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.718996	0.30503	.	.	ENSG00000121621	ENST00000263181	T	0.71934	-0.61	5.67	1.87	0.25490	.	0.665589	0.15988	N	0.234993	T	0.54191	0.1843	L	0.57536	1.79	0.09310	N	1	P	0.35433	0.501	B	0.25140	0.058	T	0.44847	-0.9301	10	0.05959	T	0.93	.	8.0859	0.30771	0.6799:0.0:0.3201:0.0	.	743	Q8NI77	KI18A_HUMAN	K	743	ENSP00000263181:N743K	ENSP00000263181:N743K	N	-	3	2	KIF18A	28014507	0.010000	0.17322	0.005000	0.12908	0.007000	0.05969	0.245000	0.18142	0.400000	0.25396	0.533000	0.62120	AAT		0.348	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		C	28057931	A	C	28057931	3	2	24	1	0	0	0	0	1	0	0	0	8301	98	4	4	483	4	KIF18A	11	28057931	Missense_Mutation	SNP	A	TCGA-AG-3594-01A-02W-0831-10		28057931	106948585	24	2133										
WNT11	7481	hgsc.bcm.edu	37	chr11	75898130	75898130	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cacttgcagacatagcgctcCacggtacgctcacacctgcg	9	16	1	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr11:75898130C>T	ENST00000322563.3	-	5	1168	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V		NM_004626.2	NP_004617.2	O96014	WNT11_HUMAN	wingless-type MMTV integration site family, member 11	348					adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|bone mineralization (GO:0030282)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cloacal septation (GO:0060197)|embryonic skeletal system development (GO:0048706)|lung-associated mesenchyme development (GO:0060484)|mesonephric duct development (GO:0072177)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroendocrine cell differentiation (GO:0061101)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway (GO:0035567)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta2 production (GO:0032915)|protein localization to cell surface (GO:0034394)|protein phosphorylation (GO:0006468)|response to nutrient levels (GO:0031667)|tight junction assembly (GO:0070830)|ureteric bud morphogenesis (GO:0060675)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|protein kinase activator activity (GO:0030295)|Ras GTPase activator activity (GO:0005099)|transcription regulatory region DNA binding (GO:0044212)	p.V348V(1)		breast(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20						CATAGCGCTCCACGGTACGCT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	11											109	81	91					11																	75898130		2200	4292	6492	75575778	SO:0001819	synonymous_variant	7481			Y12692	CCDS8242.1	11q13.5	2008-02-05			ENSG00000085741	ENSG00000085741		"Wingless-type MMTV integration sites"	12776	protein-coding gene	gene with protein product		603699				9757009	Standard	NM_004626		Approved		uc001oxe.3	O96014	OTTHUMG00000165264	ENST00000322563.3:c.1044G>A	11.37:g.75898130C>T			75575778	B2R8Z6|Q14DE8|Q8WZ98	Silent	SNP	ENST00000322563.3	37	CCDS8242.1																																																																																				0.652	WNT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383083.1	NM_004626		T	75898130	C	T	75898130	2	4	24	1	0	0	0	0	0	0	0	1	17424	581	21	3		3	WNT11	11	75898130	Silent	SNP	C	TCGA-AG-3594-01A-02W-0831-10	47840199	75898130	59108386	25	2134										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101353851	101353851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aaaaatggtgaaggaggctgCgtgtgctacaaacttcatga	12	6	1	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr11:101353851C>T	ENST00000344327.3	-	5	1763	c.1339G>A	c.(1339-1341)Gca>Aca	p.A447T	TRPC6_ENST00000348423.4_Missense_Mutation_p.A331T|TRPC6_ENST00000360497.4_Missense_Mutation_p.A392T|TRPC6_ENST00000532133.1_Missense_Mutation_p.A447T	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	447					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.A447T(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		AAGGAGGCTGCGTGTGCTACA	0.418																																					Colon(166;1315 1927 11094 12848 34731)											1	Substitution - Missense(1)	large_intestine(1)	11											105	95	98					11																	101353851		2203	4299	6502	100859061	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1339G>A	11.37:g.101353851C>T	ENSP00000340913:p.Ala447Thr		100859061	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319186	0.60524	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.59169	0.2174	L	0.48218	1.51	0.80722	D	1	D;P;D	0.89917	1.0;0.905;1.0	D;B;D	0.91635	0.999;0.346;0.998	T	0.50931	-0.8769	10	0.27785	T	0.31	-0.7414	19.431	0.94765	0.0:1.0:0.0:0.0	.	392;331;447	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	T	447;447;331;392	ENSP00000340913:A447T;ENSP00000435574:A447T;ENSP00000343672:A331T;ENSP00000353687:A392T	ENSP00000340913:A447T	A	-	1	0	TRPC6	100859061	1.000000	0.71417	0.850000	0.33497	0.989000	0.77384	7.818000	0.86416	2.584000	0.87258	0.591000	0.81541	GCA		0.418	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		T	101353851	C	T	101353851	3	4	24	1	0	0	0	0	1	0	0	0	16623	768	27	1	1492	1	TRPC6	11	101353851	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	25455721	101353851	33652665	26	2135										
WNK1	65125	hgsc.bcm.edu	37	chr12	970298	970298	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ttggtacgggaggagcaagaAaaaaaaaagcaggaagagag	15	3	0	2	rs112022175		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:970298A>G	ENST00000315939.6	+	7	2383	c.1740A>G	c.(1738-1740)gaA>gaG	p.E580E	WNK1_ENST00000535572.1_Silent_p.E580E|WNK1_ENST00000537687.1_Silent_p.E580E|WNK1_ENST00000340908.4_Silent_p.E173E|WNK1_ENST00000530271.2_Silent_p.E580E|WNK1_ENST00000540360.1_3'UTR	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	580					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.E580E(2)|p.?(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AGGAGCAAGAAAAAAAAAAGC	0.473																																					Colon(19;451 567 6672 12618 28860)											3	Substitution - coding silent(2)|Unknown(1)	large_intestine(2)|skin(1)	12											101	99	100					12																	970298		2203	4300	6503	840559	SO:0001819	synonymous_variant	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1740A>G	12.37:g.970298A>G			840559	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																				0.473	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		G	970298	A	G	970298	2	3	24	1	0	0	0	0	0	0	0	1	17417	11	1	4		4	WNK1	12	970298	Silent	SNP	A	TCGA-AG-3594-01A-02W-0831-10		970298	132881597	27	2136										
CHD4	1108	hgsc.bcm.edu	37	chr12	6704571	6704571	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cttgagcttcttgcctggtcGgccttcctcacccctcatta	7	16	3	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:6704571G>A	ENST00000357008.2	-	14	2213	c.2050C>T	c.(2050-2052)Cga>Tga	p.R684*	CHD4_ENST00000544484.1_Nonsense_Mutation_p.R681*|CHD4_ENST00000309577.6_Nonsense_Mutation_p.R684*|CHD4_ENST00000544040.1_Nonsense_Mutation_p.R677*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	684	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R684*(1)		central_nervous_system(2)	2						TTGCCTGGTCGGCCTTCCTCA	0.502																																					Colon(32;586 792 4568 16848 45314)											1	Substitution - Nonsense(1)	large_intestine(1)	12											142	119	126					12																	6704571		2203	4300	6503	6574832	SO:0001587	stop_gained	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2050C>T	12.37:g.6704571G>A	ENSP00000349508:p.Arg684*		6574832	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	40	8.467431	0.98825	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	5.59	5.59	0.84812	.	0.138691	0.46758	D	0.000261	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0115	12.4852	0.55868	0.0:0.0:0.7234:0.2766	.	.	.	.	X	681;677;684;684;658	.	ENSP00000312419:R684X	R	-	1	2	CHD4	6574832	0.999000	0.42202	0.995000	0.50966	0.991000	0.79684	2.543000	0.45752	2.643000	0.89663	0.655000	0.94253	CGA		0.502	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6704571	G	A	6704571	4	1	24	1	0	0	0	0	0	1	0	0	3333	1124	39	1	3796	1	CHD4	12	6704571	Nonsense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10	5734273	6704571	127147324	28	2137										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	24	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	18693713	25398284	108453611	29	2138										
IRAK4	51135	hgsc.bcm.edu	37	chr12	44176264	44176264	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ctttgcgtggagaaataacaCccaaatctgatatttacagc	7	9	1	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:44176264C>A	ENST00000448290.2	+	9	1167	c.1096C>A	c.(1096-1098)Ccc>Acc	p.P366T	IRAK4_ENST00000551736.1_Missense_Mutation_p.P366T|IRAK4_ENST00000440781.2_Missense_Mutation_p.P242T|IRAK4_ENST00000431837.1_Missense_Mutation_p.P242T	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P366T(1)				all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		AGAAATAACACCCAAATCTGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											72	71	72					12																	44176264		2203	4300	6503	42462531	SO:0001583	missense	51135			AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1096C>A	12.37:g.44176264C>A	ENSP00000390651:p.Pro366Thr		42462531	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251888	0.59212	.	.	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.62	2.82	0.32997	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113654	0.64402	D	0.000010	T	0.39118	0.1066	N	0.11560	0.145	0.36543	D	0.871396	B	0.33135	0.399	B	0.40659	0.336	T	0.25012	-1.0144	10	0.11485	T	0.65	-0.0011	4.1529	0.10247	0.1315:0.605:0.1269:0.1365	.	366	Q9NWZ3	IRAK4_HUMAN	T	242;242;366;366	ENSP00000408734:P242T;ENSP00000390327:P242T;ENSP00000390651:P366T;ENSP00000446490:P366T	ENSP00000390327:P242T	P	+	1	0	IRAK4	42462531	0.969000	0.33509	0.998000	0.56505	0.993000	0.82548	2.356000	0.44116	0.321000	0.23259	-0.237000	0.12165	CCC		0.368	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			A	44176264	C	A	44176264	3	1	24	1	0	0	0	0	1	0	0	0	7846	507	18	2	1126	2	IRAK4	12	44176264	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	18777980	44176264	89675631	30	2139										
TMEM117	84216	hgsc.bcm.edu	37	chr12	44782383	44782383	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tcggaaaacttgagctcacaGttgaacgaatctactagtgc	9	9	2	2			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:44782383G>T	ENST00000266534.3	+	8	1600	c.1473G>T	c.(1471-1473)caG>caT	p.Q491H	TMEM117_ENST00000551577.1_3'UTR|TMEM117_ENST00000546978.1_3'UTR|TMEM117_ENST00000536799.1_Missense_Mutation_p.Q387H	NM_032256.1	NP_115632.1	Q9H0C3	TM117_HUMAN	transmembrane protein 117	491						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.Q491H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|urinary_tract(1)	23	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		TGAGCTCACAGTTGAACGAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											166	158	161					12																	44782383		2203	4300	6503	43068650	SO:0001583	missense	84216			BC060798	CCDS8745.1, CCDS73462.1	12q12	2006-02-03				ENSG00000139173			25308	protein-coding gene	gene with protein product						11230166	Standard	NM_001286211		Approved	DKFZp434K2435	uc001rod.3	Q9H0C3	OTTHUMG00000169427	ENST00000266534.3:c.1473G>T	12.37:g.44782383G>T	ENSP00000266534:p.Gln491His		43068650		Missense_Mutation	SNP	ENST00000266534.3	37	CCDS8745.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.839373	0.00573	.	.	ENSG00000139173	ENST00000266534;ENST00000536799;ENST00000417623	T	0.42513	0.97	5.73	2.91	0.33838	.	0.144170	0.49305	N	0.000158	T	0.12774	0.0310	N	0.03115	-0.41	0.29072	N	0.883207	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26573	-1.0099	10	0.02654	T	1	-15.0365	1.6226	0.02716	0.1525:0.4734:0.1351:0.239	.	387;491	F5H3Q2;Q9H0C3	.;TM117_HUMAN	H	491;387;239	ENSP00000266534:Q491H	ENSP00000266534:Q491H	Q	+	3	2	TMEM117	43068650	0.798000	0.28890	0.935000	0.37517	0.695000	0.40330	-0.103000	0.10940	0.337000	0.23665	-0.153000	0.13522	CAG		0.443	TMEM117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403969.1	NM_032256		T	44782383	G	T	44782383	3	4	24	1	0	0	0	0	1	0	0	0	16070	1020	36	2	1499	2	TMEM117	12	44782383	Missense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10	606119	44782383	89069512	31	2140										
DDIT3	1649	hgsc.bcm.edu	37	chr12	57910757	57910757	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tccttcatgcgctgctttccAgcccgggctggggaatgacc	12	14	1	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:57910757A>G	ENST00000346473.3	-	4	524	c.345T>C	c.(343-345)gcT>gcC	p.A115A	DDIT3_ENST00000551116.1_Silent_p.A138A|DDIT3_ENST00000552740.1_Silent_p.A138A|MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000547303.1_Silent_p.A115A|RN7SL312P_ENST00000582079.1_RNA	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	115	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A115A(1)	EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						GCTGCTTTCCAGCCCGGGCTG	0.542			T	FUS	liposarcoma																																GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	1	Substitution - coding silent(1)	large_intestine(1)	12											142	151	148					12																	57910757		2203	4300	6503	56197024	SO:0001819	synonymous_variant	1649			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"C/EBP zeta"	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.345T>C	12.37:g.57910757A>G			56197024	F8VS99	Silent	SNP	ENST00000346473.3	37	CCDS8943.1																																																																																				0.542	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083		G	57910757	A	G	57910757	2	3	24	1	0	0	0	0	0	0	0	1	4336	175	7	4		4	DDIT3	12	57910757	Silent	SNP	A	TCGA-AG-3594-01A-02W-0831-10	13128374	57910757	75941138	32	2141										
SFRS8	6433	hgsc.bcm.edu	37	chr12	132198667	132198667	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tctgagtacgatgctgagtaTtccacgtggaacagagatta	11	7	1	3			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr12:132198667T>C	ENST00000261674.4	+	2	411	c.270T>C	c.(268-270)taT>taC	p.Y90Y	SFSWAP_ENST00000541286.1_Silent_p.Y90Y	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	90					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.Y90Y(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						ATGCTGAGTATTCCACGTGGA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	12											137	117	124					12																	132198667		2203	4300	6503	130764620	SO:0001819	synonymous_variant	6433			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)"	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.270T>C	12.37:g.132198667T>C			130764620	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1																																																																																				0.458	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		C	132198667	T	C	132198667	2	2	24	1	0	0	0	0	0	0	0	1	14220	1500	52	4		4	SFRS8	12	132198667	Silent	SNP	T	TCGA-AG-3594-01A-02W-0831-10	74287910	132198667	1653228	33	2142										
IMP3	55272	hgsc.bcm.edu	37	chr15	75931989	75931989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cgaagtcatcgcgctcctcaTtgtactctagcacgtgccgc	9	15	3	0	rs200453864		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr15:75931989T>C	ENST00000314852.2	-	2	1464	c.521A>G	c.(520-522)aAt>aGt	p.N174S	IMP3_ENST00000565349.1_5'Flank|CTD-2026K11.2_ENST00000564683.1_RNA|IMP3_ENST00000403490.1_Missense_Mutation_p.N174S			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	0					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.N174S(1)		large_intestine(1)	1						GCGCTCCTCATTGTACTCTAG	0.547													T|||	1	0.000199681	0	0	5008	,	,		20050	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											99	85	90					15																	75931989		2197	4294	6491	73719044	SO:0001583	missense	55272			AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"mitochondrial ribosomal protein S4", "chromosome 15 open reading frame 12", "IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.521A>G	15.37:g.75931989T>C	ENSP00000326981:p.Asn174Ser		73719044	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000314852.2	37	CCDS10282.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	16.22	3.060326	0.55432	.	.	ENSG00000177971	ENST00000314852;ENST00000403490;ENST00000542473	T;T	0.40476	1.03;1.03	6.17	4.87	0.63330	RNA-binding S4 (2);	0.051204	0.85682	D	0.000000	T	0.49729	0.1574	M	0.90542	3.125	0.58432	D	0.999999	B	0.23937	0.094	B	0.25884	0.064	T	0.57254	-0.7843	10	0.59425	D	0.04	-15.2102	8.8492	0.35190	0.0:0.0932:0.0:0.9068	.	174	Q9NV31	IMP3_HUMAN	S	174;174;21	ENSP00000326981:N174S;ENSP00000385217:N174S	ENSP00000326981:N174S	N	-	2	0	IMP3	73719044	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	4.724000	0.61972	2.371000	0.80710	0.533000	0.62120	AAT		0.547	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285		C	75931989	T	C	75931989	3	2	24	1	0	0	0	0	1	0	0	0	7740	1493	52	4	37	4	IMP3	15	75931989	Missense_Mutation	SNP	T	TCGA-AG-3594-01A-02W-0831-10		75931989	26599403	34	2143										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49670253	49670253	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cgttctccgagaagaaagtcCgtgaacaaacgttgcacttg	10	10	1	3			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr16:49670253C>T	ENST00000561648.1	-	4	2863	c.2810G>A	c.(2809-2811)cGg>cAg	p.R937Q	ZNF423_ENST00000262383.2_Missense_Mutation_p.R937Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.R820Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.R877Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.R877Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.R877Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.R820Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	937					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R937Q(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GAAGAAAGTCCGTGAACAAAC	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	16											76	63	67					16																	49670253		2198	4300	6498	48227754	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2810G>A	16.37:g.49670253C>T	ENSP00000455426:p.Arg937Gln		48227754	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640974	0.87859	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.29142	1.58;1.58	4.81	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.72894	2.215	0.47407	D	0.999415	D	0.89917	1.0	D	0.73380	0.98	T	0.56962	-0.7892	9	.	.	.	-26.5821	17.8857	0.88854	0.0:1.0:0.0:0.0	.	937	Q2M1K9	ZN423_HUMAN	Q	937;820	ENSP00000262383:R937Q;ENSP00000442321:R820Q	.	R	-	2	0	ZNF423	48227754	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.487000	0.81328	2.234000	0.73211	0.561000	0.74099	CGG		0.597	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49670253	C	T	49670253	3	4	24	1	0	0	0	0	1	0	0	0	17937	652	23	1	1064	1	ZNF423	16	49670253	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10		49670253	40684500	35	2144										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1579255	1579255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ctctgtgtgaggaggtgacgCttgatgcgggacagcgcctc	16	10	1	3			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr17:1579255C>T	ENST00000572621.1	-	17	2911	c.2646G>A	c.(2644-2646)aaG>aaA	p.K882K	PRPF8_ENST00000304992.6_Silent_p.K882K			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	882	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.K882K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGAGGTGACGCTTGATGCGGG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	17											72	68	70					17																	1579255		2203	4300	6503	1526005	SO:0001819	synonymous_variant	10594			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2646G>A	17.37:g.1579255C>T			1526005	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																				0.532	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1579255	C	T	1579255	2	4	24	1	0	0	0	0	0	0	0	1	12609	796	28	3		3	PRPF8	17	1579255	Silent	SNP	C	TCGA-AG-3594-01A-02W-0831-10		1579255	79615955	36	2145										
TP53	7157	hgsc.bcm.edu	37	chr17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	gggcaccaccacactatgtcGaaaagtgtttctgtcatcca	8	12	2	0	rs397516436		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	large_intestine(89)|breast(45)|lung(37)|upper_aerodigestive_tract(30)|central_nervous_system(18)|skin(16)|oesophagus(15)|stomach(14)|ovary(14)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(9)|biliary_tract(8)|liver(8)|soft_tissue(5)|endometrium(5)|bone(4)|prostate(3)|thyroid(1)|pancreas(1)|autonomic_ganglia(1)	17	GRCh37	CM951226	TP53	M							132	118	123					17																	7578212		2203	4300	6503	7518937	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.637C>T	17.37:g.7578212G>A	ENSP00000269305:p.Arg213*		7518937	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578212	G	A	7578212	4	1	24	1	0	0	0	0	0	1	0	0	16421	1066	37	1	657	1	TP53	17	7578212	Nonsense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10	5998957	7578212	73616998	37	2146										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57109344	57109344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gtccttaaggtccaacaaatGtattaaaattaatggatcaa	6	6	1	0			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr17:57109344G>A	ENST00000262294.7	-	18	2120	c.1861C>T	c.(1861-1863)Cat>Tat	p.H621Y	TRIM37_ENST00000393066.3_Missense_Mutation_p.H621Y|TRIM37_ENST00000393065.2_Missense_Mutation_p.H587Y|TRIM37_ENST00000376149.3_Missense_Mutation_p.H499Y	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	621					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H621Y(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TCCAACAAATGTATTAAAATT	0.418									Mulibrey Nanism																																							1	Substitution - Missense(1)	large_intestine(1)	17											123	132	129					17																	57109344		2203	4300	6503	54464126	SO:0001583	missense	4591	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1861C>T	17.37:g.57109344G>A	ENSP00000262294:p.His621Tyr		54464126	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815843	0.90790	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.68025	1.46;1.46;-0.3;1.07	5.75	5.75	0.90469	.	0.051124	0.85682	D	0.000000	T	0.72366	0.3451	L	0.29908	0.895	0.51012	D	0.999904	D;D;D	0.62365	0.991;0.991;0.971	P;P;P	0.59056	0.851;0.851;0.572	T	0.74867	-0.3518	10	0.87932	D	0	-17.3392	19.938	0.97149	0.0:0.0:1.0:0.0	.	587;499;621	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	Y	621;621;499;587	ENSP00000376785:H621Y;ENSP00000262294:H621Y;ENSP00000365319:H499Y;ENSP00000376784:H587Y	ENSP00000262294:H621Y	H	-	1	0	TRIM37	54464126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.432000	0.90288	2.732000	0.93576	0.650000	0.86243	CAT		0.418	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		A	57109344	G	A	57109344	3	1	24	1	0	0	0	0	1	0	0	0	16551	1377	48	3	1069	3	TRIM37	17	57109344	Missense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10	49531132	57109344	24085866	38	2147										
C17orf28	283987	hgsc.bcm.edu	37	chr17	72950430	72950430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ggtggaagatgctgcgcttgCggatgatggcgtagaccagg	18	7	0	3			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr17:72950430C>T	ENST00000425042.2	-	14	1744	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	556					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)		p.R556H(1)									GCTGCGCTTGCGGATGATGGC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	17											49	35	40					17																	72950430		2195	4288	6483	70462025	SO:0001583	missense	283987				CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1667G>A	17.37:g.72950430C>T	ENSP00000413520:p.Arg556His		70462025	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	37	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	34	5.294198	0.95546	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	D	0.85927	0.5811	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90168	0.4233	9	0.87932	D	0	-21.4586	17.1283	0.86720	0.0:1.0:0.0:0.0	.	556	Q8IV36	CQ028_HUMAN	H	328;556;328	.	ENSP00000317795:R328H	R	-	2	0	C17orf28	70462025	1.000000	0.71417	0.954000	0.39281	0.988000	0.76386	7.584000	0.82572	2.026000	0.59711	0.561000	0.74099	CGC		0.677	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		T	72950430	C	T	72950430	3	4	24	1	0	0	0	0	1	0	0	0	1858	768	27	1	723	1	C17orf28	17	72950430	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10	15841086	72950430	8244780	39	2148										
KRTAP15-1	254950	hgsc.bcm.edu	37	chr21	31812774	31812774	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	tctccaaatacctgccaactGggctcctctctctacaatgg	6	15	3	0			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr21:31812774G>T	ENST00000334067.3	+	1	178	c.129G>T	c.(127-129)ctG>ctT	p.L43L		NM_181623.1	NP_853654.1	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	43			L -> M (in dbSNP:rs2832873). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			intermediate filament (GO:0005882)		p.L43L(1)		kidney(1)|large_intestine(3)|lung(6)|skin(1)	11						CCTGCCAACTGGGCTCCTCTC	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	21											86	86	86					21																	31812774		2203	4300	6503	30734645	SO:0001819	synonymous_variant	254950			AP001708	CCDS13593.1	21q22.1	2008-05-21			ENSG00000186970	ENSG00000186970		"Keratin associated proteins"	18927	protein-coding gene	gene with protein product						12359730	Standard	NM_181623		Approved	KAP15.1	uc002yod.3	Q3LI76	OTTHUMG00000057784	ENST00000334067.3:c.129G>T	21.37:g.31812774G>T			30734645	Q2M3F4	Silent	SNP	ENST00000334067.3	37	CCDS13593.1																																																																																				0.488	KRTAP15-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128236.1			T	31812774	G	T	31812774	2	4	24	1	0	0	0	0	0	0	0	1	8547	1335	47	2		2	KRTAP15-1	21	31812774	Silent	SNP	G	TCGA-AG-3594-01A-02W-0831-10		31812774	16317121	40	2149										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26688743	26688743	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	cagcgtcccagggcctagatCtcctctcctcctccacggag	9	18	2	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chr22:26688743C>A	ENST00000248933.6	+	2	561	c.466C>A	c.(466-468)Ctc>Atc	p.L156I	SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000404234.3_Missense_Mutation_p.L156I|SEZ6L_ENST00000343706.4_Missense_Mutation_p.L156I|SEZ6L_ENST00000529632.2_Missense_Mutation_p.L156I|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000360929.3_Missense_Mutation_p.L156I			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	156	O-glycosylated at one site.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.L156I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGGCCTAGATCTCCTCTCCTC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	22											44	41	42					22																	26688743		2203	4300	6503	25018743	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.466C>A	22.37:g.26688743C>A	ENSP00000248933:p.Leu156Ile		25018743	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	6.953	0.545655	0.13312	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.27720	1.9;2.02;2.08;1.9;1.65	2.02	0.956	0.19608	.	0.447569	0.13544	U	0.379972	T	0.13457	0.0326	N	0.08118	0	0.20074	N	0.999937	B;B;B;B;B;B	0.28291	0.015;0.015;0.103;0.206;0.007;0.007	B;B;B;B;B;B	0.24269	0.01;0.01;0.024;0.052;0.006;0.006	T	0.25779	-1.0122	10	0.25106	T	0.35	.	8.4456	0.32841	0.0:0.7567:0.2433:0.0	.	156;156;156;156;156;156	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	I	156	ENSP00000384772:L156I;ENSP00000437037:L156I;ENSP00000354185:L156I;ENSP00000248933:L156I;ENSP00000342661:L156I	ENSP00000248933:L156I	L	+	1	0	SEZ6L	25018743	0.000000	0.05858	0.007000	0.13788	0.050000	0.14768	-0.224000	0.09164	0.434000	0.26340	0.508000	0.49915	CTC		0.662	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26688743	C	A	26688743	3	1	24	1	0	0	0	0	1	0	0	0	14180	913	32	2	472	2	SEZ6L	22	26688743	Missense_Mutation	SNP	C	TCGA-AG-3594-01A-02W-0831-10		26688743	24615823	41	2150										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86887365	86887365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	NA	0	1	1	0	taaaaactttgaatacagtgGaatgttttaatccagttggc	8	5	0	1			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	a2974b0a-076a-4610-bd2f-7d2b7d018e1f	1e0918f2-8b94-404d-91db-dcd6b9bc0217	g.chrX:86887365G>A	ENST00000373119.4	+	7	1625	c.1480G>A	c.(1480-1482)Gaa>Aaa	p.E494K	KLHL4_ENST00000373114.4_Missense_Mutation_p.E494K	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	494						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E494K(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GAATACAGTGGAATGTTTTAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	96	100					X																	86887365		2203	4300	6503	86774021	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1480G>A	X.37:g.86887365G>A	ENSP00000362211:p.Glu494Lys		86774021	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	33	5.286038	0.95517	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.84516	-1.86;-1.86	5.32	5.32	0.75619	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.95360	0.8494	H	0.97732	4.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.97172	0.9845	10	0.87932	D	0	.	16.9539	0.86253	0.0:0.0:1.0:0.0	.	494;494	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	K	494	ENSP00000362211:E494K;ENSP00000362206:E494K	ENSP00000362206:E494K	E	+	1	0	KLHL4	86774021	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.225000	0.95219	2.211000	0.71520	0.506000	0.49869	GAA		0.418	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			A	86887365	G	A	86887365	3	1	24	1	0	0	0	0	1	0	0	0	8412	1175	41	3	1506	3	KLHL4	23	86887365	Missense_Mutation	SNP	G	TCGA-AG-3594-01A-02W-0831-10		86887365	68383195	42	2151										
UBR4	23352	hgsc.bcm.edu	37	chr1	19510612	19510612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gtttcggataaaattgttccGagagttcagcatggaagagg	13	5	1	2	rs545822812		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:19510612G>A	ENST00000375254.3	-	16	2023	c.1996C>T	c.(1996-1998)Cgg>Tgg	p.R666W	UBR4_ENST00000375217.2_Missense_Mutation_p.R666W|UBR4_ENST00000375226.2_Missense_Mutation_p.R666W|UBR4_ENST00000375267.2_Missense_Mutation_p.R666W	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	666					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R666W(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAATTGTTCCGAGAGTTCAGC	0.423													G|||	1	0.000199681	0	0.0014	5008	,	,		19312	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											108	105	106					1																	19510612		2203	4300	6503	19383199	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.1996C>T	1.37:g.19510612G>A	ENSP00000364403:p.Arg666Trp		19383199	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.030841	0.75504	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.85	4.93	0.64822	.	0.058027	0.64402	D	0.000002	T	0.72977	0.3528	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.76184	-0.3052	10	0.87932	D	0	.	13.7133	0.62680	0.0:0.0:0.7217:0.2783	.	666	Q5T4S7	UBR4_HUMAN	W	666	ENSP00000364403:R666W;ENSP00000364416:R666W;ENSP00000364365:R666W;ENSP00000364374:R666W	ENSP00000364365:R666W	R	-	1	2	UBR4	19383199	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	3.496000	0.53288	1.451000	0.47736	0.655000	0.94253	CGG		0.423	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19510612	G	A	19510612	3	1	25	1	0	0	0	0	1	0	0	0	16944	1057	37	1	13919	1	UBR4	1	19510612	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10		19510612	229740009	1	2152										
SLC2A1	6513	hgsc.bcm.edu	37	chr1	43396494	43396494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cgagaagcccatgagcacggCggacacgaaggccagcaggt	15	12	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:43396494C>T	ENST00000426263.3	-	4	497	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	SLC2A1_ENST00000372500.3_Missense_Mutation_p.A107T|SLC2A1_ENST00000475162.1_5'UTR|SLC2A1_ENST00000415851.2_Missense_Mutation_p.A107T	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	107					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)	p.A107T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	ATGAGCACGGCGGACACGAAG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	65	68					1																	43396494		2203	4300	6503	43169081	SO:0001583	missense	6513			K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.319G>A	1.37:g.43396494C>T	ENSP00000416293:p.Ala107Thr		43169081	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Missense_Mutation	SNP	ENST00000426263.3	37	CCDS477.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261683	0.80358	.	.	ENSG00000117394	ENST00000426263;ENST00000372501;ENST00000439722;ENST00000415851;ENST00000372500	T;T;T	0.79940	-1.32;-1.32;-1.32	5.51	2.38	0.29361	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.198170	0.52532	D	0.000062	T	0.80199	0.4579	M	0.78285	2.405	0.80722	D	1	B	0.30326	0.276	B	0.32090	0.14	T	0.79759	-0.1668	10	0.72032	D	0.01	.	12.7798	0.57471	0.448:0.552:0.0:0.0	.	107	P11166	GTR1_HUMAN	T	107;107;12;107;107	ENSP00000416293:A107T;ENSP00000395521:A12T;ENSP00000361578:A107T	ENSP00000361578:A107T	A	-	1	0	SLC2A1	43169081	0.947000	0.32204	0.091000	0.20842	0.954000	0.61252	2.536000	0.45693	0.621000	0.30232	0.555000	0.69702	GCC		0.602	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		T	43396494	C	T	43396494	3	4	25	1	0	0	0	0	1	0	0	0	14575	768	27	1	1187	1	SLC2A1	1	43396494	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	23885882	43396494	205854127	2	2153										
BEND5	79656	hgsc.bcm.edu	37	chr1	49201937	49201937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cgatgcttagtttgtgaggcGagaggggtggtttagggact	18	4	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:49201937G>A	ENST00000371833.3	-	5	1168	c.1082C>T	c.(1081-1083)tCg>tTg	p.S361L	AGBL4_ENST00000371838.1_Intron|BEND5_ENST00000476096.1_Intron|AGBL4_ENST00000371839.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	361	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					Golgi apparatus (GO:0005794)		p.S192L(1)		large_intestine(5)|lung(2)|skin(1)	8						TTTGTGAGGCGAGAGGGGTGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	136	142					1																	49201937		2203	4300	6503	48974524	SO:0001583	missense	79656			BC007932	CCDS552.2	1p33	2012-11-22	2008-10-03	2008-10-03	ENSG00000162373	ENSG00000162373		"BEN domain containing"	25668	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 165"	C1orf165		12477932	Standard	NM_024603		Approved	FLJ11588	uc001crx.4	Q7L4P6	OTTHUMG00000008153	ENST00000371833.3:c.1082C>T	1.37:g.49201937G>A	ENSP00000360899:p.Ser361Leu		48974524	D3DQ27|Q96A62|Q9HAI3	Missense_Mutation	SNP	ENST00000371833.3	37	CCDS552.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.229041	0.79688	.	.	ENSG00000162373	ENST00000371833;ENST00000294347	T	0.47177	0.85	5.35	5.35	0.76521	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.54464	0.1860	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.52253	-0.8600	9	.	.	.	-22.0799	18.0379	0.89309	0.0:0.0:1.0:0.0	.	361	Q7L4P6	BEND5_HUMAN	L	361;73	ENSP00000360899:S361L	.	S	-	2	0	BEND5	48974524	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.414000	0.97362	2.516000	0.84829	0.555000	0.69702	TCG		0.453	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603		A	49201937	G	A	49201937	3	1	25	1	0	0	0	0	1	0	0	0	1402	1059	37	1	191	1	BEND5	1	49201937	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	5805443	49201937	200048684	3	2154										
TSPAN2	10100	hgsc.bcm.edu	37	chr1	115596024	115596024	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agacctgcaattccaataccGacaattccaatgagctggag	8	11	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:115596024G>A	ENST00000369516.2	-	7	607	c.576C>T	c.(574-576)gtC>gtT	p.V192V	TSPAN2_ENST00000369514.2_Intron|TSPAN2_ENST00000491992.1_5'UTR|TSPAN2_ENST00000369515.2_Silent_p.V167V	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	192					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)		p.V192V(1)		central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TTCCAATACCGACAATTCCAA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											114	109	111					1																	115596024		2203	4300	6503	115397547	SO:0001819	synonymous_variant	10100			AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"Tetraspanins"	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.576C>T	1.37:g.115596024G>A			115397547	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	37	CCDS881.1																																																																																				0.373	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725		A	115596024	G	A	115596024	2	1	25	1	0	0	0	0	0	0	0	1	16684	1045	37	1		1	TSPAN2	1	115596024	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10	66394087	115596024	133654597	4	2155										
KLHL20	27252	hgsc.bcm.edu	37	chr1	173743565	173743565	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gtggctctgacgggacatctCctctcaacacaggttagtcc	10	13	3	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:173743565C>G	ENST00000209884.4	+	9	1553	c.1417C>G	c.(1417-1419)Cct>Gct	p.P473A	KLHL20_ENST00000546011.1_Missense_Mutation_p.P284A	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	473					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)	p.P473A(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						CGGGACATCTCCTCTCAACAC	0.502																																					GBM(159;862 2695 6559 23041)											1	Substitution - Missense(1)	large_intestine(1)	1											205	182	190					1																	173743565		2203	4300	6503	172010188	SO:0001583	missense	27252			AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"Kelch-like", "BTB/POZ domain containing"	25056	protein-coding gene	gene with protein product			"kelch-like 20 (Drosophila)"			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1417C>G	1.37:g.173743565C>G	ENSP00000209884:p.Pro473Ala		172010188	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	37	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170770	0.57584	.	.	ENSG00000076321	ENST00000546011;ENST00000209884	T;T	0.77098	-1.07;-1.07	5.27	5.27	0.74061	Galactose oxidase, beta-propeller (1);	0.202935	0.53938	D	0.000059	T	0.72930	0.3522	N	0.24115	0.695	0.80722	D	1	P;D	0.61080	0.891;0.989	P;D	0.67231	0.852;0.95	T	0.69953	-0.5005	10	0.17832	T	0.49	.	17.6701	0.88214	0.0:1.0:0.0:0.0	.	284;473	B4DUR0;Q9Y2M5	.;KLH20_HUMAN	A	284;473	ENSP00000443121:P284A;ENSP00000209884:P473A	ENSP00000209884:P473A	P	+	1	0	KLHL20	172010188	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.592000	0.82676	2.456000	0.83038	0.655000	0.94253	CCT		0.502	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		G	173743565	C	G	173743565	3	3	25	1	0	0	0	0	1	0	0	0	8396	855	30	5	1447	5	KLHL20	1	173743565	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	58147541	173743565	75507056	5	2156										
PRG4	10216	hgsc.bcm.edu	37	chr1	186275555	186275555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tggtgacttcaaggtcacaaCtcctgacacgtctaccaccc	7	15	3	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:186275555C>T	ENST00000445192.2	+	7	749	c.704C>T	c.(703-705)aCt>aTt	p.T235I	PRG4_ENST00000367483.4_Missense_Mutation_p.T194I|PRG4_ENST00000367486.3_Missense_Mutation_p.T192I|PRG4_ENST00000367485.4_Missense_Mutation_p.T142I|PRG4_ENST00000367484.3_Missense_Mutation_p.T194I	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	235					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.T235I(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AAGGTCACAACTCCTGACACG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											245	229	234					1																	186275555		2203	4300	6503	184542178	SO:0001583	missense	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.704C>T	1.37:g.186275555C>T	ENSP00000399679:p.Thr235Ile		184542178	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	C	5.997	0.367779	0.11352	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000533951;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T;T	0.48522	3.12;3.45;0.81;3.44;3.49;3.39	3.97	3.03	0.35002	.	0.957255	0.08565	U	0.926928	T	0.31918	0.0812	N	0.22421	0.69	0.23056	N	0.998361	P;P;B;B	0.42518	0.782;0.557;0.267;0.386	B;B;B;B	0.36766	0.232;0.232;0.116;0.232	T	0.09400	-1.0676	10	0.41790	T	0.15	-1.3861	8.8966	0.35467	0.0:0.8863:0.0:0.1137	.	101;142;235;194	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	I	192;194;144;101;194;142;235	ENSP00000356456:T192I;ENSP00000356454:T194I;ENSP00000431330:T144I;ENSP00000356453:T194I;ENSP00000356455:T142I;ENSP00000399679:T235I	ENSP00000356452:T101I	T	+	2	0	PRG4	184542178	0.480000	0.25933	0.890000	0.34922	0.066000	0.16364	0.786000	0.26844	1.931000	0.55961	0.467000	0.42956	ACT		0.438	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		T	186275555	C	T	186275555	3	4	25	1	0	0	0	0	1	0	0	0	12515	565	20	3	726	3	PRG4	1	186275555	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	12531990	186275555	62975066	6	2157										
C4BPA	722	hgsc.bcm.edu	37	chr1	207305032	207305032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	acccactacagatgagcctaCgactgtgatttgtcagaaaa	8	10	1	4			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:207305032C>T	ENST00000367070.3	+	8	1225	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	344	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.T344M(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GATGAGCCTACGACTGTGATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											155	121	132					1																	207305032		2203	4300	6503	205371655	SO:0001583	missense	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1031C>T	1.37:g.207305032C>T	ENSP00000356037:p.Thr344Met		205371655	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	c	5.931	0.355889	0.11239	.	.	ENSG00000123838	ENST00000367070	T	0.64438	-0.1	4.66	-9.31	0.00646	Complement control module (2);Sushi/SCR/CCP (3);	1.519990	0.03884	N	0.277602	T	0.46229	0.1382	L	0.31578	0.945	0.09310	N	1	B	0.17852	0.024	B	0.18263	0.021	T	0.40175	-0.9577	10	0.42905	T	0.14	.	10.4152	0.44318	0.1829:0.1261:0.0:0.691	.	344	P04003	C4BPA_HUMAN	M	344	ENSP00000356037:T344M	ENSP00000356037:T344M	T	+	2	0	C4BPA	205371655	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.198000	0.00142	-2.705000	0.00396	-1.674000	0.00743	ACG		0.403	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207305032	C	T	207305032	3	4	25	1	0	0	0	0	1	0	0	0	2255	536	19	1	1057	1	C4BPA	1	207305032	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	21029477	207305032	41945589	7	2158										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211452612	211452612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agaagaaacacatccaatggAtgggaatgatagtgattatg	11	4	0	4			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:211452612A>G	ENST00000367005.4	+	6	641	c.500A>G	c.(499-501)gAt>gGt	p.D167G	RCOR3_ENST00000452621.2_Missense_Mutation_p.D225G|RCOR3_ENST00000419091.2_Missense_Mutation_p.D225G|RCOR3_ENST00000367006.4_Missense_Mutation_p.D225G	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D167G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CATCCAATGGATGGGAATGAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	115	119					1																	211452612		2203	4300	6503	209519235	SO:0001583	missense	55758			AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.500A>G	1.37:g.211452612A>G	ENSP00000355972:p.Asp167Gly		209519235	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	37	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.264727	0.40095	.	.	ENSG00000117625	ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.69	4.54	0.55810	.	0.044536	0.85682	D	0.000000	T	0.35364	0.0929	L	0.43152	1.355	0.54753	D	0.999983	P;B;P;B	0.39216	0.664;0.037;0.613;0.356	B;B;B;B	0.39258	0.295;0.039;0.249;0.185	T	0.05037	-1.0910	10	0.23891	T	0.37	-19.1116	12.1109	0.53838	0.8712:0.0:0.0:0.1288	.	225;167;225;225	Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.;RCOR3_HUMAN;.;.	G	225;225;225;167	ENSP00000355973:D225G;ENSP00000398558:D225G;ENSP00000413929:D225G;ENSP00000355972:D167G	ENSP00000355972:D167G	D	+	2	0	RCOR3	209519235	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	9.061000	0.93913	0.959000	0.37980	-0.509000	0.04479	GAT		0.323	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		G	211452612	A	G	211452612	3	3	25	1	0	0	0	0	1	0	0	0	13221	333	12	4	700	4	RCOR3	1	211452612	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	4147580	211452612	37798009	8	2159										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223976784	223976784	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ctgcagcagtctgcatgtcaCtgtaggtcatggcaaacaca	10	11	3	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:223976784C>A	ENST00000343537.7	-	16	3380	c.3089G>T	c.(3088-3090)aGt>aTt	p.S1030I	TP53BP2_ENST00000391879.2_Missense_Mutation_p.S263I|TP53BP2_ENST00000391878.2_Missense_Mutation_p.S901I|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	1024	Mediates interaction with APC2.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.S901I(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		CTGCATGTCACTGTAGGTCAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											205	176	186					1																	223976784		2203	4300	6503	222043407	SO:0001583	missense	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.3089G>T	1.37:g.223976784C>A	ENSP00000341957:p.Ser1030Ile		222043407	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	C	34	5.350377	0.95830	.	.	ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879	T;T;T	0.56103	0.53;0.69;0.48	5.74	5.74	0.90152	Src homology-3 domain (1);Ankyrin repeat-containing domain (2);	0.073769	0.85682	D	0.000000	T	0.74650	0.3744	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.76291	-0.3013	10	0.87932	D	0	.	19.9151	0.97057	0.0:1.0:0.0:0.0	.	1030;1024	B4DG66;Q13625	.;ASPP2_HUMAN	I	901;1030;263	ENSP00000375750:S901I;ENSP00000341957:S1030I;ENSP00000375751:S263I	ENSP00000341957:S1030I	S	-	2	0	TP53BP2	222043407	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.792000	0.85828	2.716000	0.92895	0.591000	0.81541	AGT		0.458	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223976784	C	A	223976784	3	1	25	1	0	0	0	0	1	0	0	0	16424	565	20	2	327	2	TP53BP2	1	223976784	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	12524172	223976784	25273837	9	2160										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233489656	233489656	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cagtcaataaactcactttgCccattccatccacctgccct	3	17	2	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr1:233489656C>G	ENST00000366624.3	+	3	1351	c.1090C>G	c.(1090-1092)Ccc>Gcc	p.P364A	MLK4_ENST00000366623.3_Missense_Mutation_p.P364A	NM_032435.2	NP_115811.2												p.P364A(1)									ACTCACTTTGCCCATTCCATC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											143	124	130					1																	233489656		2203	4300	6503	231556279	SO:0001583	missense	84451																														ENST00000366624.3:c.1090C>G	1.37:g.233489656C>G	ENSP00000355583:p.Pro364Ala		231556279		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708354	0.89018	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.82344	-1.6;-1.6	4.91	4.91	0.64330	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88768	0.6526	L	0.45470	1.425	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.987	D	0.89845	0.4005	10	0.87932	D	0	.	18.301	0.90163	0.0:1.0:0.0:0.0	.	364;364	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	A	364	ENSP00000355582:P364A;ENSP00000355583:P364A	ENSP00000355582:P364A	P	+	1	0	RP5-862P8.2	231556279	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.645000	0.83430	2.538000	0.85594	0.563000	0.77884	CCC		0.517	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			G	233489656	C	G	233489656	3	3	25	1	0	0	0	0	1	0	0	0	8280	739	26	5	1100	5	KIAA1804	1	233489656	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	9512872	233489656	15760965	10	2161										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40366774	40366774	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tcacgtaatcgaaacaggagGgcagcttctcttccccacat	8	13	2	0	rs373510583		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:40366774G>C	ENST00000403092.1	-	10	2345	c.2312C>G	c.(2311-2313)cCc>cGc	p.P771R	SLC8A1_ENST00000405269.1_Missense_Mutation_p.P735R|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000332839.4_Missense_Mutation_p.P771R|SLC8A1_ENST00000406391.2_Missense_Mutation_p.P735R|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.P766R|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1_ENST00000402441.1_Missense_Mutation_p.P735R|SLC8A1_ENST00000542024.1_Missense_Mutation_p.P735R|SLC8A1_ENST00000406785.2_Missense_Mutation_p.P735R|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000408028.2_Missense_Mutation_p.P763R|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1_ENST00000405901.3_Missense_Mutation_p.P766R|SLC8A1-AS1_ENST00000435515.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	771					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.P771R(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	GAAACAGGAGGGCAGCTTCTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											195	169	178					2																	40366774		2203	4300	6503	40220278	SO:0001583	missense	6546				CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.2312C>G	2.37:g.40366774G>C	ENSP00000384763:p.Pro771Arg		40220278	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.368914	0.82463	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.34275	1.4;1.41;1.42;1.41;1.4;1.4;1.42;1.37;1.4;1.41	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.64091	0.2567	M	0.83953	2.67	0.80722	D	1	D;D;D;D	0.89917	0.994;1.0;1.0;1.0	D;D;D;D	0.97110	0.98;1.0;1.0;1.0	T	0.70004	-0.4991	10	0.87932	D	0	.	16.17	0.81801	0.0:0.0:1.0:0.0	.	735;758;766;771	P32418-2;P32418-3;F6VPY9;P32418	.;.;.;NAC1_HUMAN	R	735;771;766;771;766;735;735;771;763;758;735;735	ENSP00000383886:P735R;ENSP00000440727:P766R;ENSP00000384763:P771R;ENSP00000385678:P766R;ENSP00000385188:P735R;ENSP00000385535:P735R;ENSP00000332931:P771R;ENSP00000384908:P763R;ENSP00000385811:P735R;ENSP00000443515:P735R	ENSP00000332931:P771R	P	-	2	0	SLC8A1	40220278	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.731000	0.98807	2.391000	0.81399	0.563000	0.77884	CCC		0.507	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		C	40366774	G	C	40366774	3	2	25	1	0	0	0	0	1	0	0	0	14743	1232	43	5	617	5	SLC8A1	2	40366774	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10		40366774	202832599	11	2162										
EGR4	1961	hgsc.bcm.edu	37	chr2	73518870	73518870	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cgattgagctcgtcggagcgCgcaaagctccgcacacaact	11	14	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:73518870C>T	ENST00000545030.1	-	2	1559	c.1485G>A	c.(1483-1485)gcG>gcA	p.A495A	EGR4_ENST00000436467.2_Silent_p.A392A	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	495					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A392A(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CGTCGGAGCGCGCAAAGCTCC	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	2											42	38	39					2																	73518870		2203	4300	6503	73372378	SO:0001819	synonymous_variant	1961				CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"Zinc fingers, C2H2-type"	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1485G>A	2.37:g.73518870C>T			73372378	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	37	CCDS1925.2																																																																																				0.682	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		T	73518870	C	T	73518870	2	4	25	1	0	0	0	0	0	0	0	1	4985	755	27	1		1	EGR4	2	73518870	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	33152096	73518870	169680503	12	2163										
CNGA3	1261	hgsc.bcm.edu	37	chr2	98996644	98996644	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gtgtcaccttccaggctgtcGcgcctcatcttcttgctgcg	10	15	4	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:98996644G>A	ENST00000272602.2	+	3	261	c.222G>A	c.(220-222)tcG>tcA	p.S74S	CNGA3_ENST00000393504.1_Silent_p.S74S|CNGA3_ENST00000436404.2_Silent_p.S74S|CNGA3_ENST00000409937.1_Silent_p.S78S			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	74					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.S74S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						CCAGGCTGTCGCGCCTCATCT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	2											51	51	51					2																	98996644		2203	4300	6503	98363076	SO:0001819	synonymous_variant	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.222G>A	2.37:g.98996644G>A			98363076	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																				0.602	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	98996644	G	A	98996644	2	1	25	1	0	0	0	0	0	0	0	1	3604	1074	38	1		1	CNGA3	2	98996644	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10	25477774	98996644	144202729	13	2164										
TTL	150465	hgsc.bcm.edu	37	chr2	113286271	113286271	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atttcaggaagctctatgcaGaactgtgccaaggcatcgtg	11	9	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:113286271G>T	ENST00000233336.6	+	7	1224	c.1033G>T	c.(1033-1035)Gaa>Taa	p.E345*	TTL_ENST00000460450.1_3'UTR	NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	345	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)	p.E345*(1)		breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		GCTCTATGCAGAACTGTGCCA	0.433			T	ETV6	ALL																																		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	1	Substitution - Nonsense(1)	large_intestine(1)	2											96	90	92					2																	113286271		2203	4300	6503	113002742	SO:0001587	stop_gained	150465				CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.1033G>T	2.37:g.113286271G>T	ENSP00000233336:p.Glu345*		113002742	Q585T3|Q7Z302|Q8N426	Nonsense_Mutation	SNP	ENST00000233336.6	37	CCDS2096.1	.	.	.	.	.	.	.	.	.	.	G	38	7.120203	0.98077	.	.	ENSG00000114999	ENST00000233336	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	16.5285	0.84344	0.0:0.0:1.0:0.0	.	.	.	.	X	345	.	ENSP00000233336:E345X	E	+	1	0	TTL	113002742	1.000000	0.71417	0.981000	0.43875	0.999000	0.98932	8.536000	0.90627	2.409000	0.81822	0.650000	0.86243	GAA		0.433	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		T	113286271	G	T	113286271	4	4	25	1	0	0	0	0	0	1	0	0	16761	943	33	2	1059	2	TTL	2	113286271	Nonsense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	14289627	113286271	129913102	14	2165										
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113416569	113416569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aggctgtggtggaggagagaAcagtctcattcaaacttgga	14	6	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:113416569A>G	ENST00000272542.3	+	7	1485	c.946A>G	c.(946-948)Aca>Gca	p.T316A	SLC20A1_ENST00000480984.1_3'UTR	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	316					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)	p.T316A(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GGAGGAGAGAACAGTCTCATT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											98	96	97					2																	113416569		2203	4300	6503	113133040	SO:0001583	missense	6574				CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.946A>G	2.37:g.113416569A>G	ENSP00000272542:p.Thr316Ala		113133040	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	37	CCDS2099.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.070|9.070	0.996711|0.996711	0.19043|0.19043	.|.	.|.	ENSG00000144136|ENSG00000144136	ENST00000433924|ENST00000272542;ENST00000409095	.|D	.|0.90069	.|-2.61	5.9|5.9	4.76|4.76	0.60689|0.60689	.|.	.|0.177605	.|0.64402	.|N	.|0.000015	T|T	0.78027|0.78027	0.4219|0.4219	N|N	0.17872|0.17872	0.535|0.535	0.20873|0.20873	N|N	0.999837|0.999837	.|B;B	.|0.16166	.|0.016;0.016	.|B;B	.|0.15484	.|0.013;0.013	T|T	0.58978|0.58978	-0.7540|-0.7540	6|10	0.07325|0.09843	T|T	0.83|0.71	-23.0946|-23.0946	9.9561|9.9561	0.41668|0.41668	0.9204:0.0:0.0796:0.0|0.9204:0.0:0.0796:0.0	.|.	.|316;316	.|A7LNJ1;Q8WUM9	.|.;S20A1_HUMAN	S|A	99|316;128	.|ENSP00000272542:T316A	ENSP00000413393:N86S|ENSP00000272542:T316A	N|T	+|+	2|1	0|0	SLC20A1|SLC20A1	113133040|113133040	0.883000|0.883000	0.30277|0.30277	0.387000|0.387000	0.26183|0.26183	0.990000|0.990000	0.78478|0.78478	2.347000|2.347000	0.44036|0.44036	1.073000|1.073000	0.40885|0.40885	0.533000|0.533000	0.62120|0.62120	AAC|ACA		0.493	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		G	113416569	A	G	113416569	3	3	25	1	0	0	0	0	1	0	0	0	14475	43	2	4	968	4	SLC20A1	2	113416569	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	130298	113416569	129782804	15	2166										
GPR39	2863	hgsc.bcm.edu	37	chr2	133174726	133174726	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atcacccttattctggtgtaCctgatcatcttcgtgatggg	9	10	4	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:133174726C>T	ENST00000329321.3	+	1	580	c.111C>T	c.(109-111)taC>taT	p.Y37Y		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	37					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)	p.Y37Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTCTGGTGTACCTGATCATCT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	2											115	109	111					2																	133174726		2203	4300	6503	132891196	SO:0001819	synonymous_variant	2863			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"GPCR / Class A : Orphans"	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.111C>T	2.37:g.133174726C>T			132891196	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																				0.547	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			T	133174726	C	T	133174726	2	4	25	1	0	0	0	0	0	0	0	1	6713	518	18	3		3	GPR39	2	133174726	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	19758157	133174726	110024647	16	2167										
NDUFS1	4719	hgsc.bcm.edu	37	chr2	207009666	207009666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atgtcctcatgcatacgtggCaaaatcctcatcacttctcc	5	14	4	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:207009666C>A	ENST00000233190.6	-	9	1088	c.822G>T	c.(820-822)ttG>ttT	p.L274F	NDUFS1_ENST00000457011.1_Missense_Mutation_p.L158F|NDUFS1_ENST00000423725.1_Missense_Mutation_p.L217F|NDUFS1_ENST00000449699.1_Missense_Mutation_p.L274F|NDUFS1_ENST00000440274.1_Missense_Mutation_p.L238F|NDUFS1_ENST00000432169.1_Missense_Mutation_p.L163F|NDUFS1_ENST00000455934.2_Missense_Mutation_p.L288F	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	274	4Fe-4S Mo/W bis-MGD-type. {ECO:0000255|PROSITE-ProRule:PRU01004}.				apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.L274F(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCATACGTGGCAAAATCCTCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											189	156	167					2																	207009666		2203	4300	6503	206717911	SO:0001583	missense	4719				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.822G>T	2.37:g.207009666C>A	ENSP00000233190:p.Leu274Phe		206717911	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457320	0.84317	.	.	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.47	5.47	0.80525	.	0.067775	0.64402	D	0.000010	D	0.94545	0.8243	H	0.94698	3.57	0.80722	D	1	D;D;D;D	0.76494	0.999;0.991;0.975;0.975	D;P;P;P	0.65684	0.937;0.846;0.835;0.707	D	0.95722	0.8767	10	0.87932	D	0	-31.7273	19.3299	0.94281	0.0:1.0:0.0:0.0	.	163;238;288;274	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	F	274;217;158;238;288;274;163	ENSP00000233190:L274F;ENSP00000397760:L217F;ENSP00000400976:L158F;ENSP00000409766:L238F;ENSP00000392709:L288F;ENSP00000399912:L274F;ENSP00000409689:L163F	ENSP00000233190:L274F	L	-	3	2	NDUFS1	206717911	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.209000	0.32357	2.563000	0.86464	0.655000	0.94253	TTG		0.363	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		A	207009666	C	A	207009666	3	1	25	1	0	0	0	0	1	0	0	0	10322	709	25	2	1405	2	NDUFS1	2	207009666	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	73834940	207009666	36189707	17	2168										
SPAG16	79582	hgsc.bcm.edu	37	chr2	215274985	215274985	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	acggttgtgttttctcacgaCggggagattctcttttctgg	12	8	3	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:215274985C>T	ENST00000331683.5	+	16	1937	c.1842C>T	c.(1840-1842)gaC>gaT	p.D614D	AC107218.3_ENST00000412896.1_RNA|AC107218.3_ENST00000437883.1_RNA|VWC2L_ENST00000312504.5_5'Flank|VWC2L_ENST00000427124.1_5'Flank|SPAG16_ENST00000374309.3_Silent_p.D520D	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	614					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.D614D(2)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		TTTCTCACGACGGGGAGATTC	0.502																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	2											132	126	128					2																	215274985		2203	4300	6503	214983230	SO:0001819	synonymous_variant	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1842C>T	2.37:g.215274985C>T			214983230	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Silent	SNP	ENST00000331683.5	37	CCDS2396.1																																																																																				0.502	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		T	215274985	C	T	215274985	2	4	25	1	0	0	0	0	0	0	0	1	15017	535	19	1		1	SPAG16	2	215274985	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	8265319	215274985	27924388	18	2169										
GAL3ST2	64090	hgsc.bcm.edu	37	chr2	242741273	242741273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gcacaagacggccagcagcaCggtgctcaacatcctctacc	9	16	2	1	rs372108744		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr2:242741273C>T	ENST00000192314.6	+	3	328	c.197C>T	c.(196-198)aCg>aTg	p.T66M	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	66					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)	p.T66M(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		GCCAGCAGCACGGTGCTCAAC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2							MET/THR	0,4406		0,0,2203	63	55	57		197	3.8	0.9	2		57	1,8597	1.2+/-3.3	0,1,4298	no	missense	GAL3ST2	NM_022134.2	81	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	66/399	242741273	1,13003	2203	4299	6502	242389946	SO:0001583	missense	64090			AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"Sulfotransferases, membrane-bound"	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.197C>T	2.37:g.242741273C>T	ENSP00000192314:p.Thr66Met		242389946	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.771599	0.49680	0.0	1.16E-4	ENSG00000154252	ENST00000192314	T	0.23348	1.91	3.8	3.8	0.43715	.	0.181747	0.38663	N	0.001614	T	0.59542	0.2201	H	0.95187	3.635	0.39602	D	0.96974	D	0.89917	1.0	D	0.97110	1.0	T	0.70662	-0.4810	10	0.72032	D	0.01	-19.5362	9.9902	0.41865	0.0:0.9045:0.0:0.0954	.	66	Q9H3Q3	G3ST2_HUMAN	M	66	ENSP00000192314:T66M	ENSP00000192314:T66M	T	+	2	0	GAL3ST2	242389946	1.000000	0.71417	0.909000	0.35828	0.142000	0.21351	4.993000	0.63895	2.118000	0.64928	0.306000	0.20318	ACG		0.667	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134		T	242741273	C	T	242741273	3	4	25	1	0	0	0	0	1	0	0	0	6218	536	19	1	207	1	GAL3ST2	2	242741273	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	27466288	242741273	458100	19	2170										
C3orf67	200844	hgsc.bcm.edu	37	chr3	58853603	58853603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ccgtaatcttcttctgttatTattcttatctgctgatggtt	6	8	5	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:58853603T>C	ENST00000482387.1	-	6	796	c.700A>G	c.(700-702)Aat>Gat	p.N234D	C3orf67_ENST00000295966.7_Missense_Mutation_p.N234D|C3orf67_ENST00000472469.1_Missense_Mutation_p.N141D|RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	234								p.N234D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		CTTCTGTTATTATTCTTATCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											207	201	203					3																	58853603		2203	4300	6503	58828643	SO:0001583	missense	200844			AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.700A>G	3.37:g.58853603T>C	ENSP00000417122:p.Asn234Asp		58828643	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		.	.	.	.	.	.	.	.	.	.	T	17.89	3.500296	0.64298	.	.	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000472469	T;T;T	0.48836	0.8;0.8;0.8	5.57	4.34	0.51931	.	0.315119	0.33180	N	0.005190	T	0.50171	0.1600	L	0.56769	1.78	0.80722	D	1	P;P;P	0.52316	0.952;0.728;0.787	P;B;B	0.50860	0.652;0.297;0.23	T	0.44345	-0.9334	10	0.28530	T	0.3	-18.592	10.2757	0.43507	0.147:0.0:0.0:0.853	.	141;234;234	C9J3M8;Q6ZVT6-2;Q6ZVT6	.;.;CC067_HUMAN	D	234;234;141	ENSP00000295966:N234D;ENSP00000417122:N234D;ENSP00000417271:N141D	ENSP00000295966:N234D	N	-	1	0	C3orf67	58828643	0.953000	0.32496	1.000000	0.80357	0.998000	0.95712	1.864000	0.39469	2.111000	0.64477	0.533000	0.62120	AAT		0.383	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		C	58853603	T	C	58853603	3	2	25	1	0	0	0	0	1	0	0	0	2247	1754	61	4	1019	4	C3orf67	3	58853603	Missense_Mutation	SNP	T	TCGA-AG-3598-01A-01W-0833-10		58853603	139168827	20	2171										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64589754	64589754	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atccgggtacctttcccacaAgtggctgagcactgggtgtt	12	11	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:64589754A>T	ENST00000498707.1	-	25	3933	c.3591T>A	c.(3589-3591)acT>acA	p.T1197T	ADAMTS9_ENST00000295903.4_Silent_p.T1169T	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1197	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T1197T(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		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)		CTTTCCCACAAGTGGCTGAGC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	3											101	94	96					3																	64589754		2203	4300	6503	64564794	SO:0001819	synonymous_variant	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.3591T>A	3.37:g.64589754A>T			64564794	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	A	7.903	0.734732	0.15574	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.22	-6.47	0.01902	.	.	.	.	.	T	0.34250	0.0891	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43360	-0.9396	4	.	.	.	.	0.54	0.00644	0.2907:0.1685:0.2891:0.2518	.	.	.	.	H	253	.	.	L	-	2	0	ADAMTS9	64564794	0.289000	0.24334	0.968000	0.41197	0.639000	0.38242	-0.357000	0.07651	-0.801000	0.04427	-1.237000	0.01550	CTT		0.512	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64589754	A	T	64589754	2	4	25	1	0	0	0	0	0	0	0	1	273	59	3	5		5	ADAMTS9	3	64589754	Silent	SNP	A	TCGA-AG-3598-01A-01W-0833-10	5736151	64589754	133432676	21	2172										
CPOX	1371	hgsc.bcm.edu	37	chr3	98307680	98307680	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tgaggtcacatccaccaccaAaccaccactgcttgttgcct	6	16	1	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:98307680A>T	ENST00000264193.2	-	4	1048	c.830T>A	c.(829-831)tTt>tAt	p.F277Y		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	277					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)	p.F277Y(1)		endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						TCCACCACCAAACCACCACTG	0.438																																					Esophageal Squamous(75;7 1223 22300 43648 48951)											1	Substitution - Missense(1)	large_intestine(1)	3											94	82	86					3																	98307680		2203	4300	6503	99790370	SO:0001583	missense	1371			BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"coproporphyria"	612732	"coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.830T>A	3.37:g.98307680A>T	ENSP00000264193:p.Phe277Tyr		99790370	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Missense_Mutation	SNP	ENST00000264193.2	37	CCDS2932.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.598533	0.87055	.	.	ENSG00000080819	ENST00000264193	D	0.96104	-3.91	5.93	4.76	0.60689	.	0.047462	0.85682	D	0.000000	D	0.97876	0.9302	H	0.94771	3.58	0.80722	D	1	D	0.54207	0.965	P	0.60886	0.88	D	0.97670	1.0166	10	0.54805	T	0.06	-14.4467	11.6141	0.51078	0.8509:0.1491:0.0:0.0	.	277	P36551	HEM6_HUMAN	Y	277	ENSP00000264193:F277Y	ENSP00000264193:F277Y	F	-	2	0	CPOX	99790370	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.932000	0.92897	1.048000	0.40298	0.460000	0.39030	TTT		0.438	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097		T	98307680	A	T	98307680	3	4	25	1	0	0	0	0	1	0	0	0	3827	14	1	5	550	5	CPOX	3	98307680	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	33717926	98307680	99714750	22	2173										
RUVBL1	8607	hgsc.bcm.edu	37	chr3	127819445	127819445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atcgaggcagtacctggggcCgcgcattagccacatccaag	12	13	0	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:127819445C>T	ENST00000322623.5	-	6	845	c.746G>A	c.(745-747)cGg>cAg	p.R249Q	RUVBL1_ENST00000417360.1_Missense_Mutation_p.R249Q|RUVBL1_ENST00000464873.1_Missense_Mutation_p.R189Q	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	249					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)	p.R249Q(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		TACCTGGGGCCGCGCATTAGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											135	96	109					3																	127819445		2203	4300	6503	129302135	SO:0001583	missense	8607			AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"INO80 complex subunits", "ATPases / AAA-type"	10474	protein-coding gene	gene with protein product	"pontin", "INO80 complex subunit H"	603449	"RuvB (E coli homolog)-like 1", "RuvB-like 1 (E. coli)", "RuvB-like AAA ATPase"			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.746G>A	3.37:g.127819445C>T	ENSP00000318297:p.Arg249Gln		129302135	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Missense_Mutation	SNP	ENST00000322623.5	37	CCDS3047.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881742	0.72294	.	.	ENSG00000175792	ENST00000464873;ENST00000322623;ENST00000417360;ENST00000478892	T;T;T	0.69175	-0.38;-0.38;0.07	5.65	5.65	0.86999	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.67002	0.2847	M	0.64260	1.97	0.80722	D	1	B;B;B	0.27679	0.079;0.185;0.04	B;B;B	0.21546	0.009;0.035;0.024	T	0.65809	-0.6078	10	0.59425	D	0.04	-10.7574	19.7222	0.96147	0.0:1.0:0.0:0.0	.	249;249;189	Q9Y265-2;Q9Y265;E7ETR0	.;RUVB1_HUMAN;.	Q	189;249;249;48	ENSP00000420738:R189Q;ENSP00000318297:R249Q;ENSP00000393755:R249Q	ENSP00000318297:R249Q	R	-	2	0	RUVBL1	129302135	0.964000	0.33143	0.979000	0.43373	0.942000	0.58702	5.849000	0.69465	2.648000	0.89879	0.591000	0.81541	CGG		0.493	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			T	127819445	C	T	127819445	3	4	25	1	0	0	0	0	1	0	0	0	13789	652	23	1	648	1	RUVBL1	3	127819445	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	29511765	127819445	70202985	23	2174										
ATP2C1	27032	hgsc.bcm.edu	37	chr3	130715625	130715625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gatcaatattattatggatgGacccccagctcagaggtacg	10	9	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:130715625G>A	ENST00000510168.1	+	24	2778	c.2228G>A	c.(2227-2229)gGa>gAa	p.G743E	ATP2C1_ENST00000393221.4_Missense_Mutation_p.G777E|ATP2C1_ENST00000533801.2_Missense_Mutation_p.G738E|ATP2C1_ENST00000504381.1_Missense_Mutation_p.G688E|ATP2C1_ENST00000508532.1_Missense_Mutation_p.G743E|ATP2C1_ENST00000513801.1_Missense_Mutation_p.G727E|ATP2C1_ENST00000428331.2_Missense_Mutation_p.G743E|ATP2C1_ENST00000328560.8_Missense_Mutation_p.G743E|ATP2C1_ENST00000504948.1_Missense_Mutation_p.G727E|ATP2C1_ENST00000505330.1_Missense_Mutation_p.G727E|ATP2C1_ENST00000507488.2_Missense_Mutation_p.G727E|ATP2C1_ENST00000422190.2_Missense_Mutation_p.G743E|ATP2C1_ENST00000359644.3_Missense_Mutation_p.G743E			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	743					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.G743E(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	ATTATGGATGGACCCCCAGCT	0.358									Hailey-Hailey disease																												Esophageal Squamous(99;456 1443 27647 34099 42636)											1	Substitution - Missense(1)	large_intestine(1)	3	GRCh37	CD003708	ATP2C1	D							130	128	129					3																	130715625		2203	4300	6503	132198315	SO:0001583	missense	27032	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2228G>A	3.37:g.130715625G>A	ENSP00000427461:p.Gly743Glu		132198315	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Missense_Mutation	SNP	ENST00000510168.1	37	CCDS46914.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	30|30	5.056841|5.056841	0.93793|0.93793	.|.	.|.	ENSG00000017260|ENSG00000017260	ENST00000504612;ENST00000508660|ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.99113	.|-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44;-5.44	5.73|5.73	5.73|5.73	0.89815|0.89815	.|ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99560|0.99560	0.9842|0.9842	H|H	0.95187|0.95187	3.635|3.635	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	D|D	0.98162|0.98162	1.0447|1.0447	5|10	.|0.87932	.|D	.|0	.|.	19.8961|19.8961	0.96958|0.96958	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|777;738;777;743;777;743;743	.|G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194	.|.;.;.;.;.;.;AT2C1_HUMAN	N|E	697;261|727;688;727;777;738;743;743;727;727;743;743;743;743;742	.|ENSP00000423774:G727E;ENSP00000425320:G688E;ENSP00000421326:G727E;ENSP00000376914:G777E;ENSP00000432956:G738E;ENSP00000427461:G743E;ENSP00000424783:G743E;ENSP00000423330:G727E;ENSP00000422872:G727E;ENSP00000329664:G743E;ENSP00000395809:G743E;ENSP00000352665:G743E;ENSP00000402677:G743E	.|ENSP00000329664:G743E	D|G	+|+	1|2	0|0	ATP2C1|ATP2C1	132198315|132198315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	9.869000|9.869000	0.99810|0.99810	2.699000|2.699000	0.92147|0.92147	0.655000|0.655000	0.94253|0.94253	GAC|GGA		0.358	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		A	130715625	G	A	130715625	3	1	25	1	0	0	0	0	1	0	0	0	1144	1174	41	3	2318	3	ATP2C1	3	130715625	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	2896180	130715625	67306805	24	2175										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098901	133098901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ctgaaagctccctgtccacaGggcccgctccagcagccatg	10	17	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:133098901G>T	ENST00000321871.6	+	4	556	c.346G>T	c.(346-348)Ggg>Tgg	p.G116W	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Missense_Mutation_p.G116W|TMEM108_ENST00000393130.3_Missense_Mutation_p.G116W	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	116	Pro-rich.					integral component of membrane (GO:0016021)		p.G116W(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CCTGTCCACAGGGCCCGCTCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	3											48	42	44					3																	133098901		2201	4298	6499	134581591	SO:0001583	missense	66000			AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.346G>T	3.37:g.133098901G>T	ENSP00000324651:p.Gly116Trp		134581591	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	G	0.119	-1.127996	0.01770	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000514894;ENST00000512662;ENST00000512137;ENST00000515826;ENST00000510183	T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8	3.81	-0.254	0.12992	.	0.985693	0.08228	N	0.978048	T	0.35508	0.0934	L	0.44542	1.39	0.09310	N	1	B;B	0.14805	0.0;0.011	B;B	0.12156	0.004;0.007	T	0.38373	-0.9664	10	0.87932	D	0	0.1332	2.5347	0.04711	0.1921:0.1447:0.5156:0.1476	.	116;116	E9PB58;Q6UXF1	.;TM108_HUMAN	W	116;116;67;67;116;116;116	ENSP00000324651:G116W;ENSP00000376838:G116W;ENSP00000422072:G67W;ENSP00000427447:G67W;ENSP00000426301:G116W;ENSP00000423338:G116W;ENSP00000421486:G116W	ENSP00000324651:G116W	G	+	1	0	TMEM108	134581591	0.013000	0.17824	0.000000	0.03702	0.002000	0.02628	0.458000	0.21892	-0.171000	0.10797	-1.134000	0.01955	GGG		0.667	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133098901	G	T	133098901	3	4	25	1	0	0	0	0	1	0	0	0	16063	1000	35	2	352	2	TMEM108	3	133098901	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	2383276	133098901	64923529	25	2176										
P2RY14	9934	hgsc.bcm.edu	37	chr3	150931440	150931440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ttttgaccgaagtggaattcCgacttgacttaaggtgggac	12	7	0	2	rs150238875		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:150931440C>T	ENST00000309170.3	-	3	977	c.665G>A	c.(664-666)cGg>cAg	p.R222Q	MED12L_ENST00000474524.1_Intron|P2RY14_ENST00000424796.2_Missense_Mutation_p.R222Q|MED12L_ENST00000273432.4_Intron	NM_001081455.1|NM_014879.3	NP_001074924.1|NP_055694.3	Q15391	P2Y14_HUMAN	purinergic receptor P2Y, G-protein coupled, 14	222					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|UDP-activated nucleotide receptor activity (GO:0045029)	p.R222L(1)|p.R222Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)	20			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGTGGAATTCCGACTTGACTT	0.383																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3						C	GLN/ARG,GLN/ARG,	2,4404	4.2+/-10.8	0,2,2201	97	97	97		665,665,	-6.9	0	3	dbSNP_134	97	0,8600		0,0,4300	no	missense,missense,intron	P2RY14,MED12L	NM_001081455.1,NM_014879.3,NM_053002.4	43,43,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign,	222/339,222/339,	150931440	2,13004	2203	4300	6503	152414130	SO:0001583	missense	9934			D13626	CCDS3156.1	3q21-q25	2012-08-08	2004-07-12	2004-07-14	ENSG00000174944	ENSG00000174944		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	16442	protein-coding gene	gene with protein product		610116	"G protein-coupled receptor 105"	GPR105			Standard	NM_014879		Approved	KIAA0001	uc003eys.1	Q15391	OTTHUMG00000159859	ENST00000309170.3:c.665G>A	3.37:g.150931440C>T	ENSP00000308361:p.Arg222Gln		152414130	Q8IYT7	Missense_Mutation	SNP	ENST00000309170.3	37	CCDS3156.1	.	.	.	.	.	.	.	.	.	.	C	3.226	-0.158543	0.06544	4.54E-4	0.0	ENSG00000174944	ENST00000309170;ENST00000424796	T;T	0.37235	1.21;1.21	5.9	-6.89	0.01660	GPCR, rhodopsin-like superfamily (1);	0.590962	0.17921	N	0.157489	T	0.11580	0.0282	N	0.03050	-0.425	0.09310	N	1	B	0.26708	0.157	B	0.24848	0.056	T	0.19321	-1.0309	10	0.19590	T	0.45	-3.1123	11.2014	0.48743	0.0:0.2983:0.0867:0.615	.	222	Q15391	P2Y14_HUMAN	Q	222	ENSP00000308361:R222Q;ENSP00000408733:R222Q	ENSP00000308361:R222Q	R	-	2	0	P2RY14	152414130	0.000000	0.05858	0.002000	0.10522	0.074000	0.17049	0.121000	0.15667	-1.897000	0.01101	-0.781000	0.03364	CGG		0.383	P2RY14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357789.1	NM_014879		T	150931440	C	T	150931440	3	4	25	1	0	0	0	0	1	0	0	0	11382	652	23	1	355	1	P2RY14	3	150931440	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	17832539	150931440	47090990	26	2177										
ZMAT3	64393	hgsc.bcm.edu	37	chr3	178742841	178742841	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ttctccatctcattcctgtaCcgctgttcagacaccttgct	5	15	3	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:178742841C>T	ENST00000311417.2	-	6	1575	c.834G>A	c.(832-834)cgG>cgA	p.R278R	ZMAT3_ENST00000432729.1_Silent_p.R277R	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3									p.R278R(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			CATTCCTGTACCGCTGTTCAG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	3											241	215	224					3																	178742841		2203	4300	6503	180225535	SO:0001819	synonymous_variant	64393			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.834G>A	3.37:g.178742841C>T			180225535		Silent	SNP	ENST00000311417.2	37	CCDS3224.1																																																																																				0.428	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		T	178742841	C	T	178742841	2	4	25	1	0	0	0	0	0	0	0	1	17732	494	18	3		3	ZMAT3	3	178742841	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	27811401	178742841	19279589	27	2178										
ZMAT3	64393	hgsc.bcm.edu	37	chr3	178745465	178745465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	actctgagcttccgccagccGcagcctcttggcatgattct	9	15	3	2	rs139328684		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr3:178745465G>A	ENST00000311417.2	-	4	1267	c.526C>T	c.(526-528)Cgg>Tgg	p.R176W	ZMAT3_ENST00000432729.1_Missense_Mutation_p.R176W	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3									p.R176W(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			TCCGCCAGCCGCAGCCTCTTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											63	66	65					3																	178745465		2203	4300	6503	180228159	SO:0001583	missense	64393			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.526C>T	3.37:g.178745465G>A	ENSP00000311221:p.Arg176Trp		180228159		Missense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.897582	0.91962	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	T;T	0.49720	0.77;0.77	5.61	4.72	0.59763	Zinc finger, U1-type (1);	0.000000	0.85682	D	0.000000	T	0.59004	0.2162	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.992;0.998	T	0.63292	-0.6670	10	0.72032	D	0.01	-12.2286	15.7294	0.77790	0.0:0.0:0.8623:0.1377	.	176;176	Q9HA38-2;Q9HA38	.;ZMAT3_HUMAN	W	176	ENSP00000311221:R176W;ENSP00000396506:R176W	ENSP00000311221:R176W	R	-	1	2	ZMAT3	180228159	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.631000	0.83237	1.326000	0.45319	0.655000	0.94253	CGG		0.478	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		A	178745465	G	A	178745465	3	1	25	1	0	0	0	0	1	0	0	0	17732	1086	38	1	355	1	ZMAT3	3	178745465	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	2624	178745465	19276965	28	2179										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156488	155156488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ctcatttatcctctggatttCcttatcttctgcagtttctc	4	12	5	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr4:155156488C>T	ENST00000357232.4	-	25	7950	c.7951G>A	c.(7951-7953)Gaa>Aaa	p.E2651K		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2651					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E2651K(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTCTGGATTTCCTTATCTTCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	100	102					4																	155156488		2203	4300	6503	155375938	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7951G>A	4.37:g.155156488C>T	ENSP00000349768:p.Glu2651Lys		155375938	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982350	0.93044	.	.	ENSG00000197410	ENST00000357232	T	0.71222	-0.55	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	D	0.85703	0.5758	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86949	0.2084	10	0.72032	D	0.01	.	19.4946	0.95067	0.0:1.0:0.0:0.0	.	2651	Q6V1P9	PCD23_HUMAN	K	2651	ENSP00000349768:E2651K	ENSP00000349768:E2651K	E	-	1	0	DCHS2	155375938	1.000000	0.71417	0.974000	0.42286	0.903000	0.53119	7.818000	0.86416	2.599000	0.87857	0.460000	0.39030	GAA		0.478	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155156488	C	T	155156488	3	4	25	1	0	0	0	0	1	0	0	0	4294	864	30	3	803	3	DCHS2	4	155156488	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		155156488	35997788	29	2180										
IRX1	79192	hgsc.bcm.edu	37	chr5	3600194	3600194	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tctccaactggaccaacagcGcattcctcgcacagggctcc	8	17	1	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:3600194G>A	ENST00000302006.3	+	2	1184	c.1132G>A	c.(1132-1134)Gca>Aca	p.A378T	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	378					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.A378T(1)		biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GACCAACAGCGCATTCCTCGC	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	5											49	41	43					5																	3600194		2201	4300	6501	3653194	SO:0001583	missense	79192			U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.1132G>A	5.37:g.3600194G>A	ENSP00000305244:p.Ala378Thr		3653194	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	37	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895790	0.52121	.	.	ENSG00000170549	ENST00000302006	T	0.64438	-0.1	4.3	4.3	0.51218	.	0.055128	0.64402	D	0.000001	T	0.77691	0.4168	M	0.70275	2.135	0.53688	D	0.999973	D	0.89917	1.0	D	0.83275	0.996	T	0.78568	-0.2154	10	0.40728	T	0.16	.	16.7647	0.85521	0.0:0.0:1.0:0.0	.	378	P78414	IRX1_HUMAN	T	378	ENSP00000305244:A378T	ENSP00000305244:A378T	A	+	1	0	IRX1	3653194	1.000000	0.71417	0.995000	0.50966	0.113000	0.19764	6.847000	0.75404	1.900000	0.55004	0.563000	0.77884	GCA		0.687	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3600194	G	A	3600194	3	1	25	1	0	0	0	0	1	0	0	0	7864	1087	38	1	1138	1	IRX1	5	3600194	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10		3600194	177315066	30	2181										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13922251	13922251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ctcctgtgcacccgacaggaCgttcacaaagccttccaggg	10	15	1	0	rs149833711		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:13922251C>T	ENST00000265104.4	-	5	729	c.625G>A	c.(625-627)Gtc>Atc	p.V209I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	209	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V209I(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCCGACAGGACGTTCACAAAG	0.532									Kartagener syndrome				C|||	1	0.000199681	0	0.0014	5008	,	,		18602	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	ILE/VAL	1,4405		0,1,2202	85	78	81		625	2.2	0.1	5	dbSNP_134	81	1,8599		0,1,4299	no	missense	DNAH5	NM_001369.2	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	209/4625	13922251	2,13004	2203	4300	6503	13975251	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.625G>A	5.37:g.13922251C>T	ENSP00000265104:p.Val209Ile		13975251	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	.	7.684	0.689640	0.14973	2.27E-4	1.16E-4	ENSG00000039139	ENST00000265104	T	0.22539	1.95	5.44	2.15	0.27550	.	0.207319	0.40385	N	0.001101	T	0.09468	0.0233	N	0.08118	0	0.40213	D	0.977653	B	0.06786	0.001	B	0.04013	0.001	T	0.24261	-1.0165	10	0.21014	T	0.42	.	9.4147	0.38514	0.0:0.7346:0.0:0.2654	.	209	Q8TE73	DYH5_HUMAN	I	209	ENSP00000265104:V209I	ENSP00000265104:V209I	V	-	1	0	DNAH5	13975251	0.205000	0.23458	0.051000	0.19133	0.251000	0.25915	0.807000	0.27140	0.107000	0.17824	0.561000	0.74099	GTC		0.532	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13922251	C	T	13922251	3	4	25	1	0	0	0	0	1	0	0	0	4615	536	19	1	13549	1	DNAH5	5	13922251	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	10322057	13922251	166993009	31	2182										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32074051	32074051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ccagacaagccagtctccccGgaagcccacaggccctccga	9	19	1	1	rs384728	byFrequency	TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:32074051G>A	ENST00000438447.1	+	18	3227	c.2839G>A	c.(2839-2841)Gga>Aga	p.G947R	PDZD2_ENST00000282493.3_Missense_Mutation_p.G947R			O15018	PDZD2_HUMAN	PDZ domain containing 2	947					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.G947R(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CAGTCTCCCCGGAAGCCCACA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											54	60	58					5																	32074051		2203	4300	6503	32109808	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2839G>A	5.37:g.32074051G>A	ENSP00000402033:p.Gly947Arg		32109808	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.266746	0.80358	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.09817	2.94;2.94	5.78	5.78	0.91487	.	0.000000	0.50627	D	0.000118	T	0.20373	0.0490	L	0.29908	0.895	0.39286	D	0.964657	D;D	0.89917	1.0;1.0	D;D	0.85130	0.95;0.997	T	0.01140	-1.1439	10	0.54805	T	0.06	.	10.8624	0.46833	0.0847:0.0:0.9153:0.0	.	773;947	B4E3P2;O15018	.;PDZD2_HUMAN	R	947;749;947	ENSP00000402033:G947R;ENSP00000282493:G947R	ENSP00000282493:G947R	G	+	1	0	PDZD2	32109808	1.000000	0.71417	0.994000	0.49952	0.867000	0.49689	3.961000	0.56759	2.724000	0.93272	0.563000	0.77884	GGA		0.587	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32074051	G	A	32074051	3	1	25	1	0	0	0	0	1	0	0	0	11732	1117	39	1	2905	1	PDZD2	5	32074051	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	18151800	32074051	148841209	32	2183										
APC	324	hgsc.bcm.edu	37	chr5	112128143	112128143	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ggtttcttgttttattttagCgaagaatagccagaattcag	9	5	2	2	rs62619935		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:112128143C>T	ENST00000457016.1	+	7	1026	c.646C>T	c.(646-648)Cga>Tga	p.R216*	APC_ENST00000508376.2_Splice_Site_p.R216*|APC_ENST00000257430.4_Splice_Site_p.R216*			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R216*(12)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATTTTAGCGAAGAATAGC	0.323		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	12	Substitution - Nonsense(12)	large_intestine(12)	5	GRCh37	CM992133	APC	M	rs62619935						52	51	51					5																	112128143		2202	4300	6502	112156042	SO:0001630	splice_region_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.646-1C>T	5.37:g.112128143C>T			112156042	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.466758	0.98302	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	2.99	0.34606	.	0.630262	0.16042	N	0.232387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2274	1.7088	0.02888	0.2899:0.3634:0.2259:0.1208	rs62619935	.	.	.	X	216	.	.	R	+	1	2	APC	112156042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.662000	0.25038	1.304000	0.44892	-0.158000	0.13435	CGA		0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation	T	112128143	C	T	112128143	5	4	25	1	0	0	0	0	0	0	1	0	763	782	27	1	668	1	APC	5	112128143	Splice_Site	SNP	C	TCGA-AG-3598-01A-01W-0833-10	80054092	112128143	68787117	33	2184										
APC	324	hgsc.bcm.edu	37	chr5	112128191	112128191	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aaaaggacatacttcgtataCgacagcttttacagtcccaa	6	10	0	0	rs397515734		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:112128191C>T	ENST00000457016.1	+	7	1074	c.694C>T	c.(694-696)Cga>Tga	p.R232*	APC_ENST00000508376.2_Nonsense_Mutation_p.R232*|APC_ENST00000257430.4_Nonsense_Mutation_p.R232*			P25054	APC_HUMAN	adenomatous polyposis coli	232	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R232*(13)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACTTCGTATACGACAGCTTTT	0.308		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	13	Substitution - Nonsense(13)	large_intestine(13)	5	GRCh37	CM920029	APC	M							82	79	80					5																	112128191		2202	4300	6502	112156090	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.694C>T	5.37:g.112128191C>T	ENSP00000413133:p.Arg232*		112156090	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.033640	0.98621	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	4.32	0.51571	.	0.206644	0.42682	D	0.000664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.475	13.9715	0.64242	0.2757:0.7243:0.0:0.0	.	.	.	.	X	232	.	ENSP00000257430:R232X	R	+	1	2	APC	112156090	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.535000	0.36061	1.304000	0.44892	-0.158000	0.13435	CGA		0.308	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112128191	C	T	112128191	4	4	25	1	0	0	0	0	0	1	0	0	763	528	19	1	716	1	APC	5	112128191	Nonsense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	48	112128191	68787069	34	2185										
TCF7	6932	hgsc.bcm.edu	37	chr5	133478730	133478730	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ggccaagtactatgagctggCccgcaaggagaggcagctgc	15	11	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:133478730C>T	ENST00000321584.4	+	8	1161	c.965C>T	c.(964-966)gCc>gTc	p.A322V	TCF7_ENST00000395029.1_Missense_Mutation_p.A322V|TCF7_ENST00000321603.6_Missense_Mutation_p.A322V|TCF7_ENST00000378564.1_Missense_Mutation_p.A322V|TCF7_ENST00000518915.1_Missense_Mutation_p.A207V|TCF7_ENST00000432532.2_Missense_Mutation_p.A207V|TCF7_ENST00000520958.1_Missense_Mutation_p.A207V|TCF7_ENST00000378560.4_Missense_Mutation_p.A207V|TCF7_ENST00000342854.5_Missense_Mutation_p.A322V|TCF7_ENST00000395023.1_Missense_Mutation_p.A207V			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	322					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.A322V(2)		kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATGAGCTGGCCCGCAAGGAG	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	5											33	31	32					5																	133478730		2203	4300	6503	133506629	SO:0001583	missense	6932			Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.965C>T	5.37:g.133478730C>T	ENSP00000326540:p.Ala322Val		133506629	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.741071|5.741071	0.96873|0.96873	.|.	.|.	ENSG00000081059|ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023;ENST00000517799|ENST00000520699	D;D;D;D;D;D;D;D;D;D;D|.	0.98732|.	-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1|.	5.69|5.69	5.69|5.69	0.88448|0.88448	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.90865|0.90865	0.7130|0.7130	H|H	0.98155|0.98155	4.16|4.16	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;0.996;1.0;0.997;1.0;0.998|.	D;D;D;D;D;D|.	0.91635|.	0.999;0.99;0.999;0.948;0.998;0.994|.	D|D	0.93759|0.93759	0.7065|0.7065	10|5	0.87932|.	D|.	0|.	.|.	19.8047|19.8047	0.96525|0.96525	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	136;322;322;120;322;322|.	B3KSI6;P36402-9;B7WNT5;B3KQ75;P36402;P36402-5|.	.;.;.;.;TCF7_HUMAN;.|.	V|S	322;322;322;322;322;322;207;207;207;207;207;100|47	ENSP00000340347:A322V;ENSP00000326654:A322V;ENSP00000326540:A322V;ENSP00000367827:A322V;ENSP00000378472:A322V;ENSP00000367822:A207V;ENSP00000397946:A207V;ENSP00000429547:A207V;ENSP00000430179:A207V;ENSP00000378469:A207V;ENSP00000427968:A100V|.	ENSP00000326540:A322V|.	A|P	+|+	2|1	0|0	TCF7|TCF7	133506629|133506629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.818000|7.818000	0.86416|0.86416	2.692000|2.692000	0.91855|0.91855	0.563000|0.563000	0.77884|0.77884	GCC|CCC		0.632	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		T	133478730	C	T	133478730	3	4	25	1	0	0	0	0	1	0	0	0	15735	739	26	3	995	3	TCF7	5	133478730	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	21350539	133478730	47436530	35	2186										
POU4F3	5459	hgsc.bcm.edu	37	chr5	145719605	145719605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	atcaagctgggggtgacccaGgcggacgtgggcgcggctct	18	11	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:145719605G>T	ENST00000230732.4	+	2	704	c.615G>T	c.(613-615)caG>caT	p.Q205H	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	205	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q205H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGTGACCCAGGCGGACGTGG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	5											39	43	42					5																	145719605		2203	4300	6503	145699798	SO:0001583	missense	5459			U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.615G>T	5.37:g.145719605G>T	ENSP00000230732:p.Gln205His		145699798	O60557|Q2M3F8	Missense_Mutation	SNP	ENST00000230732.4	37	CCDS4281.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.884052	0.51908	.	.	ENSG00000091010	ENST00000230732	D	0.88201	-2.35	4.51	2.58	0.30949	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.93510	0.7929	M	0.89214	3.015	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91065	0.4888	10	0.87932	D	0	.	4.6223	0.12461	0.2184:0.183:0.5987:0.0	.	205	Q15319	PO4F3_HUMAN	H	205	ENSP00000230732:Q205H	ENSP00000230732:Q205H	Q	+	3	2	POU4F3	145699798	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.524000	0.73791	0.442000	0.26555	0.462000	0.41574	CAG		0.652	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		T	145719605	G	T	145719605	3	4	25	1	0	0	0	0	1	0	0	0	12311	991	35	2	621	2	POU4F3	5	145719605	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	12240875	145719605	35195655	36	2187										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151784215	151784215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ccgggtgctctgcagtttggCgcggaacgggtgtaggatgg	19	8	1	0	rs377153615		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:151784215C>T	ENST00000255262.3	-	1	625	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	154					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.A154T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			TGCAGTTTGGCGCGGAACGGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	THR/ALA	0,4406		0,0,2203	46	52	50		460	5.3	0.9	5		50	1,8599	1.2+/-3.3	0,1,4299	no	missense	NMUR2	NM_020167.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	154/416	151784215	1,13005	2203	4300	6503	151764408	SO:0001583	missense	56923			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.460G>A	5.37:g.151784215C>T	ENSP00000255262:p.Ala154Thr		151764408	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.365243	0.82463	0.0	1.16E-4	ENSG00000132911	ENST00000255262	T	0.38077	1.16	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.074714	0.56097	D	0.000035	T	0.57154	0.2034	L	0.59912	1.85	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	T	0.52616	-0.8552	10	0.37606	T	0.19	-27.6655	18.0632	0.89383	0.0:1.0:0.0:0.0	.	154	Q9GZQ4	NMUR2_HUMAN	T	154	ENSP00000255262:A154T	ENSP00000255262:A154T	A	-	1	0	NMUR2	151764408	1.000000	0.71417	0.950000	0.38849	0.287000	0.27160	4.679000	0.61649	2.502000	0.84385	0.591000	0.81541	GCC		0.637	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151784215	C	T	151784215	3	4	25	1	0	0	0	0	1	0	0	0	10538	768	27	1	803	1	NMUR2	5	151784215	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	6064610	151784215	29131045	37	2188										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172341769	172341769	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aggcacgaagtgggccacatCgacaactccatgaagatccc	10	13	0	2	rs368325900		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:172341769C>T	ENST00000393784.3	+	5	442	c.303C>T	c.(301-303)atC>atT	p.I101I	ERGIC1_ENST00000326654.2_Silent_p.I56I|ERGIC1_ENST00000523291.1_Silent_p.I101I	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	101					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.I101I(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGGCCACATCGACAACTCCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	66	64	64		303	-3.2	0.9	5		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ERGIC1	NM_001031711.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		101/291	172341769	1,13005	2203	4300	6503	172274375	SO:0001819	synonymous_variant	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.303C>T	5.37:g.172341769C>T			172274375	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	37	CCDS34292.1	.	.	.	.	.	.	.	.	.	.	C	9.666	1.145508	0.21288	0.0	1.16E-4	ENSG00000113719	ENST00000519567	.	.	.	5.37	-3.15	0.05233	.	.	.	.	.	T	0.62816	0.2459	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60000	-0.7348	4	.	.	.	-27.766	13.3474	0.60582	0.0:0.4133:0.0:0.5867	.	.	.	.	L	90	.	.	S	+	2	0	ERGIC1	172274375	0.001000	0.12720	0.933000	0.37362	0.921000	0.55340	-1.868000	0.01644	-0.844000	0.04184	-1.736000	0.00690	TCG		0.572	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		T	172341769	C	T	172341769	2	4	25	1	0	0	0	0	0	0	0	1	5236	874	31	1		1	ERGIC1	5	172341769	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	20557554	172341769	8573491	38	2189										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178579248	178579248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agctgcttgcaggggtcaaaGgtccggaactggaagacagc	15	9	1	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:178579248G>A	ENST00000251582.7	-	10	1625	c.1524C>T	c.(1522-1524)acC>acT	p.T508T	ADAMTS2_ENST00000274609.5_Silent_p.T508T	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	508	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T508T(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGGGGTCAAAGGTCCGGAACT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	5											71	61	64					5																	178579248		2203	4300	6503	178511854	SO:0001819	synonymous_variant	9509			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1524C>T	5.37:g.178579248G>A			178511854		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																				0.612	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178579248	G	A	178579248	2	1	25	1	0	0	0	0	0	0	0	1	265	987	35	3		3	ADAMTS2	5	178579248	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10	6237479	178579248	2336012	39	2190										
RASGEF1C	255426	hgsc.bcm.edu	37	chr5	179545655	179545655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gggagcggtgggccgccccgCgcagggctgtcctgtagttg	19	12	0	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr5:179545655C>T	ENST00000393371.2	-	9	1333	c.1037G>A	c.(1036-1038)cGc>cAc	p.R346H	RASGEF1C_ENST00000519883.1_5'Flank|RASGEF1C_ENST00000522500.1_Missense_Mutation_p.R195H|RASGEF1C_ENST00000361132.4_Missense_Mutation_p.R346H			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	346	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R346H(1)		breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCCGCCCCGCGCAGGGCTGT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	5											58	67	64					5																	179545655		2203	4300	6503	179478261	SO:0001583	missense	255426			AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090			27400	protein-coding gene	gene with protein product						12477932	Standard	XM_006714839		Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.1037G>A	5.37:g.179545655C>T	ENSP00000377037:p.Arg346His		179478261	D3DWQ7|Q7Z4T0|Q8NA49	Missense_Mutation	SNP	ENST00000393371.2	37	CCDS4452.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417212	0.62622	.	.	ENSG00000146090	ENST00000361132;ENST00000393371;ENST00000522500	T;T;T	0.32272	1.46;1.46;1.46	4.18	4.18	0.49190	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.23688	0.0573	N	0.17082	0.46	0.58432	D	0.999997	P	0.47910	0.902	P	0.45406	0.479	T	0.03034	-1.1080	10	0.23302	T	0.38	.	15.9577	0.79898	0.0:1.0:0.0:0.0	.	346	Q8N431	RGF1C_HUMAN	H	346;346;195	ENSP00000354963:R346H;ENSP00000377037:R346H;ENSP00000429114:R195H	ENSP00000354963:R346H	R	-	2	0	RASGEF1C	179478261	1.000000	0.71417	0.889000	0.34880	0.149000	0.21700	6.952000	0.75989	2.268000	0.75426	0.313000	0.20887	CGC		0.677	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062		T	179545655	C	T	179545655	3	4	25	1	0	0	0	0	1	0	0	0	13108	768	27	1	383	1	RASGEF1C	5	179545655	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	966407	179545655	1369605	40	2191										
PSMB8	5696	hgsc.bcm.edu	37	chr6	32811701	32811701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tcctgggtccgagcgacgccCgcttcccgcaaccgggagag	14	16	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr6:32811701C>A	ENST00000374882.3	-	1	123	c.73G>T	c.(73-75)Ggg>Tgg	p.G25W	PSMB9_ENST00000395330.1_5'Flank|PSMB8_ENST00000395339.3_Missense_Mutation_p.G25W|PSMB8_ENST00000374881.2_Intron|TAPSAR1_ENST00000453426.1_lincRNA	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	25					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.G25W(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	GAGCGACGCCCGCTTCCCGCA	0.652																																					NSCLC(48;53 1172 10859 13624 22883)											1	Substitution - Missense(1)	large_intestine(1)	6											77	101	92					6																	32811701		1509	2709	4218	32919679	SO:0001583	missense	5696				CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"Proteasome (prosome, macropain) subunits"	9545	protein-coding gene	gene with protein product		177046	"proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)", "large multifunctional peptidase 7"	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.73G>T	6.37:g.32811701C>A	ENSP00000364016:p.Gly25Trp		32919679	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Missense_Mutation	SNP	ENST00000374882.3	37	CCDS4757.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505307	0.26949	.	.	ENSG00000204264	ENST00000395339;ENST00000374882	T;T	0.38560	1.13;1.81	5.11	-8.9	0.00782	.	2.336620	0.01080	N	0.004965	T	0.23766	0.0575	L	0.29908	0.895	0.18873	N	0.999986	D;B	0.71674	0.998;0.004	P;B	0.61477	0.889;0.01	T	0.45366	-0.9266	10	0.33940	T	0.23	-0.0286	8.3141	0.32088	0.0905:0.5733:0.22:0.1163	.	25;25	B7Z6U7;P28062	.;PSB8_HUMAN	W	25	ENSP00000378748:G25W;ENSP00000364016:G25W	ENSP00000364016:G25W	G	-	1	0	PSMB8	32919679	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.183000	0.03079	-1.740000	0.01345	-1.292000	0.01352	GGG		0.652	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919		A	32811701	C	A	32811701	3	1	25	1	0	0	0	0	1	0	0	0	12717	652	23	2	781	2	PSMB8	6	32811701	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		32811701	138303366	41	2192										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39034027	39034027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tcatctacacggtgggctacGcactctccttctctgctctg	8	15	5	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr6:39034027G>A	ENST00000373256.4	+	5	500	c.457G>A	c.(457-459)Gca>Aca	p.A153T		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	153					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.A153T(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	GGTGGGCTACGCACTCTCCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											178	131	147					6																	39034027		2203	4300	6503	39142005	SO:0001583	missense	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.457G>A	6.37:g.39034027G>A	ENSP00000362353:p.Ala153Thr		39142005	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845353	0.51164	.	.	ENSG00000112164	ENST00000373256	T	0.37235	1.21	4.77	3.87	0.44632	GPCR, family 2-like (1);	0.335596	0.25377	N	0.031101	T	0.13670	0.0331	L	0.37850	1.14	0.35020	D	0.75779	B	0.13145	0.007	B	0.15870	0.014	T	0.03969	-1.0988	10	0.41790	T	0.15	.	10.5213	0.44920	0.0941:0.0:0.9059:0.0	.	153	P43220	GLP1R_HUMAN	T	153	ENSP00000362353:A153T	ENSP00000362353:A153T	A	+	1	0	GLP1R	39142005	0.972000	0.33761	0.817000	0.32601	0.746000	0.42486	2.825000	0.48096	0.944000	0.37579	0.650000	0.86243	GCA		0.622	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			A	39034027	G	A	39034027	3	1	25	1	0	0	0	0	1	0	0	0	6472	1087	38	1	475	1	GLP1R	6	39034027	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	6222326	39034027	132081040	42	2193										
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72006484	72006484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aactggaaatgttgctcgggCtgttaactggcaggaaagat	13	6	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr6:72006484C>T	ENST00000370435.4	+	6	790	c.656C>T	c.(655-657)gCt>gTt	p.A219V	RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	219						membrane (GO:0016020)	receptor activity (GO:0004872)	p.A219V(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GTTGCTCGGGCTGTTAACTGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	67	64					6																	72006484		2201	4296	6497	72063205	SO:0001583	missense	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.656C>T	6.37:g.72006484C>T	ENSP00000359464:p.Ala219Val		72063205	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	C	34	5.364874	0.95877	.	.	ENSG00000119900	ENST00000370435	T	0.52983	0.64	5.63	5.63	0.86233	Opioid growth factor receptor (OGFr) conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	M	0.75615	2.305	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	T	0.65598	-0.6129	10	0.56958	D	0.05	-15.7834	20.0429	0.97598	0.0:1.0:0.0:0.0	.	219	Q5TC84	OGRL1_HUMAN	V	219	ENSP00000359464:A219V	ENSP00000359464:A219V	A	+	2	0	OGFRL1	72063205	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	5.986000	0.70563	2.812000	0.96745	0.555000	0.69702	GCT		0.388	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		T	72006484	C	T	72006484	3	4	25	1	0	0	0	0	1	0	0	0	10875	797	28	3	678	3	OGFRL1	6	72006484	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	32972457	72006484	99108583	43	2194										
HTR1B	3351	hgsc.bcm.edu	37	chr6	78173018	78173018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ctggtaaatgtagtccttggCgctgcagttttgggagggag	16	6	0	0	rs200659363		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr6:78173018C>T	ENST00000369947.2	-	1	472	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	35					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.A35T(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	TAGTCCTTGGCGCTGCAGTTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											152	136	141					6																	78173018		2203	4300	6503	78229737	SO:0001583	missense	3351			BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5287	protein-coding gene	gene with protein product		182131	"5-hydroxytryptamine (serotonin) receptor 1B"			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.103G>A	6.37:g.78173018C>T	ENSP00000358963:p.Ala35Thr		78229737	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	C	0.322	-0.961104	0.02249	.	.	ENSG00000135312	ENST00000369947	T	0.34859	1.34	4.6	-1.32	0.09201	.	1.768550	0.03522	N	0.221110	T	0.06050	0.0157	N	0.12182	0.205	0.09310	N	0.999993	B	0.10296	0.003	B	0.04013	0.001	T	0.18650	-1.0330	9	.	.	.	.	5.1226	0.14867	0.2111:0.5528:0.096:0.1401	.	35	P28222	5HT1B_HUMAN	T	35	ENSP00000358963:A35T	.	A	-	1	0	HTR1B	78229737	0.314000	0.24563	0.079000	0.20413	0.098000	0.18820	0.201000	0.17276	-0.338000	0.08413	-1.134000	0.01955	GCC		0.597	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		T	78173018	C	T	78173018	3	4	25	1	0	0	0	0	1	0	0	0	7458	768	27	1	1073	1	HTR1B	6	78173018	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	6166534	78173018	92942049	44	2195										
BACH2	60468	hgsc.bcm.edu	37	chr6	90660822	90660822	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	taagcaggagggcgaggccaCgctcctggatctctccaggc	14	13	1	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr6:90660822C>T	ENST00000257749.4	-	7	1710	c.1003G>A	c.(1003-1005)Gtg>Atg	p.V335M	BACH2_ENST00000537989.1_Missense_Mutation_p.V335M|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000343122.3_Missense_Mutation_p.V335M|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	335						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.V335M(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		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)		GGCGAGGCCACGCTCCTGGAT	0.637																																																2	Substitution - Missense(2)	large_intestine(2)	6											38	42	41					6																	90660822		2203	4299	6502	90717543	SO:0001583	missense	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1003G>A	6.37:g.90660822C>T	ENSP00000257749:p.Val335Met		90717543	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	37	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	C	1.353	-0.590892	0.03799	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.37752	1.18;1.18;1.18	5.03	1.14	0.20703	.	1.015500	0.07846	N	0.963896	T	0.06050	0.0157	N	0.14661	0.345	0.09310	N	1	P	0.41265	0.744	B	0.25140	0.058	T	0.18840	-1.0324	10	0.48119	T	0.1	-28.1707	7.0582	0.25111	0.0:0.5915:0.2622:0.1463	.	335	Q9BYV9	BACH2_HUMAN	M	335	ENSP00000257749:V335M;ENSP00000437473:V335M;ENSP00000345642:V335M	ENSP00000257749:V335M	V	-	1	0	BACH2	90717543	0.000000	0.05858	0.167000	0.22817	0.160000	0.22226	-0.424000	0.07025	0.292000	0.22492	-0.878000	0.02970	GTG		0.637	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		T	90660822	C	T	90660822	3	4	25	1	0	0	0	0	1	0	0	0	1285	536	19	1	1534	1	BACH2	6	90660822	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	12487804	90660822	80454245	45	2196										
ZNF703	80139	hgsc.bcm.edu	37	chr8	37556142	37556142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gaccctactattcgccatacGcgctgtatggacagagacta	9	12	0	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr8:37556142G>A	ENST00000331569.4	+	2	1952	c.1723G>A	c.(1723-1725)Gcg>Acg	p.A575T		NM_025069.1	NP_079345.1	Q9H7S9	ZN703_HUMAN	zinc finger protein 703	575					adherens junction assembly (GO:0034333)|cellular response to estradiol stimulus (GO:0071392)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A575T(1)	FGFR1/ZNF703(2)	breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)	7			BRCA - Breast invasive adenocarcinoma(5;7.93e-25)|LUSC - Lung squamous cell carcinoma(8;1.05e-09)			TTCGCCATACGCGCTGTATGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	8											36	32	33					8																	37556142		2203	4300	6503	37675300	SO:0001583	missense	80139			AK024361	CCDS6094.1	8p12	2008-05-02				ENSG00000183779			25883	protein-coding gene	gene with protein product						15897872	Standard	NM_025069		Approved	FLJ14299, ZNF503L	uc003xjy.1	Q9H7S9		ENST00000331569.4:c.1723G>A	8.37:g.37556142G>A	ENSP00000332325:p.Ala575Thr		37675300	Q5XG76	Missense_Mutation	SNP	ENST00000331569.4	37	CCDS6094.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.119142	0.77323	.	.	ENSG00000183779	ENST00000331569;ENST00000397235	T	0.61859	0.07	3.22	3.22	0.36961	.	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.78720	-0.2094	10	0.87932	D	0	-8.9695	15.0086	0.71533	0.0:0.0:1.0:0.0	.	575	Q9H7S9	ZN703_HUMAN	T	575;148	ENSP00000332325:A575T	ENSP00000332325:A575T	A	+	1	0	ZNF703	37675300	1.000000	0.71417	0.993000	0.49108	0.814000	0.46013	9.057000	0.93889	1.801000	0.52704	0.306000	0.20318	GCG		0.637	ZNF703-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376683.2	NM_025069		A	37556142	G	A	37556142	3	1	25	1	0	0	0	0	1	0	0	0	18145	1087	38	1	1729	1	ZNF703	8	37556142	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10		37556142	108807880	46	2197										
SFRP1	6422	hgsc.bcm.edu	37	chr8	41122692	41122692	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tgcccccgggagaatcacttAaacacggactgaaaggtggg	13	10	1	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr8:41122692A>C	ENST00000220772.3	-	3	1276	c.939T>G	c.(937-939)ttT>ttG	p.F313L	SFRP1_ENST00000379845.3_Missense_Mutation_p.F177L	NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	313					bone trabecula formation (GO:0060346)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to BMP stimulus (GO:0071773)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to prostaglandin E stimulus (GO:0071380)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vitamin D (GO:0071305)|cellular response to X-ray (GO:0071481)|convergent extension involved in somitogenesis (GO:0090246)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral axis specification (GO:0009950)|female gonad development (GO:0008585)|gonad development (GO:0008406)|hematopoietic progenitor cell differentiation (GO:0002244)|hematopoietic stem cell differentiation (GO:0060218)|male gonad development (GO:0008584)|menstrual cycle phase (GO:0022601)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone remodeling (GO:0046851)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000080)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|neural crest cell fate commitment (GO:0014034)|neural tube closure (GO:0001843)|osteoblast differentiation (GO:0001649)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|proteolysis (GO:0006508)|regulation of angiogenesis (GO:0045765)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell cycle process (GO:0010564)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|somatic stem cell maintenance (GO:0035019)|stromal-epithelial cell signaling involved in prostate gland development (GO:0044345)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cysteine-type endopeptidase activity (GO:0004197)|drug binding (GO:0008144)|frizzled binding (GO:0005109)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.F313L(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			AGAATCACTTAAACACGGACT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8											29	24	26					8																	41122692		2202	4300	6502	41241849	SO:0001583	missense	6422			AF017987	CCDS34886.1	8p11.21	2006-12-15			ENSG00000104332	ENSG00000104332		"Secreted frizzled-related proteins"	10776	protein-coding gene	gene with protein product		604156				9391078, 9192640	Standard	NM_003012		Approved	SARP2, FRP, FRP-1	uc003xnt.3	Q8N474	OTTHUMG00000164074	ENST00000220772.3:c.939T>G	8.37:g.41122692A>C	ENSP00000220772:p.Phe313Leu		41241849	O00546|O14779	Missense_Mutation	SNP	ENST00000220772.3	37	CCDS34886.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.565993	0.45694	.	.	ENSG00000104332	ENST00000220772;ENST00000379845;ENST00000535263	T	0.68624	-0.34	4.89	-3.21	0.05140	.	0.188416	0.47455	D	0.000238	T	0.53045	0.1772	L	0.39898	1.24	0.48632	D	0.999685	B	0.24920	0.114	B	0.24974	0.057	T	0.40997	-0.9533	10	0.52906	T	0.07	.	13.0845	0.59132	0.3385:0.0:0.6615:0.0	.	313	Q8N474	SFRP1_HUMAN	L	313;177;313	ENSP00000220772:F313L	ENSP00000220772:F313L	F	-	3	2	SFRP1	41241849	1.000000	0.71417	0.975000	0.42487	0.038000	0.13279	1.065000	0.30592	-0.452000	0.07087	-0.371000	0.07208	TTT		0.577	SFRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377132.1	NM_003012		C	41122692	A	C	41122692	3	2	25	1	0	0	0	0	1	0	0	0	14198	359	13	4	9	4	SFRP1	8	41122692	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	3566550	41122692	105241330	47	2198										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101252701	101252701	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gggatgccttgcttctgagaAgggaggcaaaagcagcaggt	16	7	1	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr8:101252701A>C	ENST00000388798.2	+	18	2542	c.2351A>C	c.(2350-2352)aAg>aCg	p.K784T	SPAG1_ENST00000251809.3_Missense_Mutation_p.K784T	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	784					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.K784T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GCTTCTGAGAAGGGAGGCAAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											76	83	80					8																	101252701		2203	4300	6503	101321877	SO:0001583	missense	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2351A>C	8.37:g.101252701A>C	ENSP00000373450:p.Lys784Thr		101321877	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.421095	0.42918	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.61859	0.07;0.07	5.79	3.34	0.38264	.	2.721960	0.00567	N	0.000284	T	0.57725	0.2073	L	0.56769	1.78	0.09310	N	1	B	0.18863	0.031	B	0.14023	0.01	T	0.38045	-0.9679	10	0.52906	T	0.07	-1.2471	7.8503	0.29451	0.6699:0.2618:0.0683:0.0	.	784	Q07617	SPAG1_HUMAN	T	784	ENSP00000251809:K784T;ENSP00000373450:K784T	ENSP00000251809:K784T	K	+	2	0	SPAG1	101321877	0.001000	0.12720	0.001000	0.08648	0.180000	0.23129	0.749000	0.26320	0.424000	0.26061	0.459000	0.35465	AAG		0.468	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101252701	A	C	101252701	3	2	25	1	0	0	0	0	1	0	0	0	15014	72	3	4	2417	4	SPAG1	8	101252701	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	60130009	101252701	45111321	48	2199										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73399089	73399089	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cgtccactcccatcacagacAaccactggcacgggaggggt	11	15	1	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr9:73399089A>G	ENST00000377111.2	-	7	1323	c.1080T>C	c.(1078-1080)gtT>gtC	p.V360V	TRPM3_ENST00000358082.3_Silent_p.V232V|TRPM3_ENST00000357533.2_Silent_p.V362V|TRPM3_ENST00000396280.5_Silent_p.V207V|TRPM3_ENST00000396285.1_Silent_p.V207V|TRPM3_ENST00000423814.3_Silent_p.V387V|TRPM3_ENST00000360823.2_Silent_p.V232V|TRPM3_ENST00000396292.4_Silent_p.V232V|TRPM3_ENST00000361823.5_Silent_p.V207V|TRPM3_ENST00000377105.1_Silent_p.V207V|TRPM3_ENST00000377110.3_Silent_p.V360V|TRPM3_ENST00000396283.1_Silent_p.V232V|TRPM3_ENST00000377101.1_Silent_p.V207V|TRPM3_ENST00000408909.2_Silent_p.V207V|TRPM3_ENST00000377106.1_Silent_p.V232V	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	385					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.V232V(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CATCACAGACAACCACTGGCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	9											116	99	105					9																	73399089		2203	4300	6503	72588909	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.1080T>C	9.37:g.73399089A>G			72588909	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	A	11.34	1.608701	0.28623	.	.	ENSG00000083067	ENST00000396280	.	.	.	6.17	-2.39	0.06602	.	.	.	.	.	T	0.50701	0.1631	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44847	-0.9301	4	.	.	.	-14.888	6.9792	0.24694	0.1931:0.5885:0.1311:0.0872	.	.	.	.	R	207	.	.	C	-	1	0	TRPM3	72588909	0.999000	0.42202	0.963000	0.40424	0.982000	0.71751	0.819000	0.27308	-0.291000	0.09012	0.533000	0.62120	TGT		0.542	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		G	73399089	A	G	73399089	2	3	25	1	0	0	0	0	0	0	0	1	16627	117	5	4		4	TRPM3	9	73399089	Silent	SNP	A	TCGA-AG-3598-01A-01W-0833-10		73399089	67814342	49	2200										
TGFBR1	7046	hgsc.bcm.edu	37	chr9	101891312	101891312	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gtatgtgcaccctcttcaaaAactgggtctgtgactacaac	8	11	3	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr9:101891312A>C	ENST00000374994.4	+	2	390	c.273A>C	c.(271-273)aaA>aaC	p.K91N	TGFBR1_ENST00000550253.1_Missense_Mutation_p.K22N|TGFBR1_ENST00000374990.2_Missense_Mutation_p.K91N|TGFBR1_ENST00000552516.1_Missense_Mutation_p.K91N	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	91					activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.K91N(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				CCTCTTCAAAAACTGGGTCTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	87	92					9																	101891312		2203	4300	6503	100931133	SO:0001583	missense	7046				CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.273A>C	9.37:g.101891312A>C	ENSP00000364133:p.Lys91Asn		100931133	Q6IR47|Q706C0|Q706C1	Missense_Mutation	SNP	ENST00000374994.4	37	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	A	8.848	0.943914	0.18281	.	.	ENSG00000106799	ENST00000547314;ENST00000552573;ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000549021;ENST00000548365;ENST00000550253;ENST00000546584	T;T;T;T;T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6	6.08	3.77	0.43336	TGF-beta receptor/activin receptor, type I/II (1);	0.259853	0.43919	D	0.000508	T	0.42787	0.1218	N	0.05078	-0.115	0.33289	D	0.563314	B;B;B	0.18968	0.006;0.032;0.0	B;B;B	0.19391	0.009;0.025;0.009	T	0.40924	-0.9537	10	0.16896	T	0.51	.	4.9788	0.14155	0.7121:0.0:0.15:0.1379	.	22;91;91	F8VRH6;P36897-3;P36897	.;.;TGFR1_HUMAN	N	22;22;91;91;91;91;22;22;22;88	ENSP00000449934:K22N;ENSP00000447182:K22N;ENSP00000364133:K91N;ENSP00000364129:K91N;ENSP00000447297:K91N;ENSP00000449028:K22N;ENSP00000448518:K22N;ENSP00000450052:K22N;ENSP00000447707:K88N	ENSP00000364129:K91N	K	+	3	2	TGFBR1	100931133	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.595000	0.36708	1.117000	0.41842	0.482000	0.46254	AAA		0.373	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			C	101891312	A	C	101891312	3	2	25	1	0	0	0	0	1	0	0	0	15860	11	1	4	279	4	TGFBR1	9	101891312	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	28492223	101891312	39322119	50	2201										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109689973	109689973	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aatctggagcgggacaaaacGaaactccgagcactcaaatg	10	10	2	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr9:109689973G>A	ENST00000277225.5	+	3	4069	c.3780G>A	c.(3778-3780)acG>acA	p.T1260T	ZNF462_ENST00000457913.1_Silent_p.T1260T|ZNF462_ENST00000441147.2_Silent_p.T105T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1260					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T1260T(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GGGACAAAACGAAACTCCGAG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	9											154	162	159					9																	109689973		2203	4300	6503	108729794	SO:0001819	synonymous_variant	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3780G>A	9.37:g.109689973G>A			108729794	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																				0.542	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109689973	G	A	109689973	2	1	25	1	0	0	0	0	0	0	0	1	17965	1045	37	1		1	ZNF462	9	109689973	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10	7798661	109689973	31523458	51	2202										
STXBP1	6812	hgsc.bcm.edu	37	chr9	130446647	130446647	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tggcctctgttctcccacagGttctactcacattcttactc	5	15	5	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr9:130446647G>T	ENST00000373299.1	+	18	1817				STXBP1_ENST00000481942.1_Intron|STXBP1_ENST00000373302.3_Splice_Site_p.G568V	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1						axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)	p.G568V(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						TCTCCCACAGGTTCTACTCAC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	9											111	97	101					9																	130446647		2203	4300	6503	129486468	SO:0001627	intron_variant	6812			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.1702+1808G>T	9.37:g.130446647G>T			129486468	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	37	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477151	0.84640	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198	D	0.83506	-1.73	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.92838	0.7722	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94089	0.7351	9	.	.	.	.	16.3897	0.83531	0.0:0.0:1.0:0.0	.	568	P61764-2	.	V	522;568;400	ENSP00000362399:G568V	.	G	+	2	0	STXBP1	129486468	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.439000	0.97543	2.473000	0.83533	0.561000	0.74099	GGT		0.483	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		T	130446647	G	T	130446647	1	4	25	0	1	0	0	0	0	0	0	0	15391	1275	44	2		2	STXBP1	9	130446647	Intron	SNP	G	TCGA-AG-3598-01A-01W-0833-10	20756674	130446647	10766784	52	2203										
APBB1IP	54518	hgsc.bcm.edu	37	chr10	26789858	26789858	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aggcacagaaagagtccttgCagaatcaacatcattcagca	8	10	3	3			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr10:26789858C>A	ENST00000376236.4	+	5	726	c.271C>A	c.(271-273)Cag>Aag	p.Q91K	APBB1IP_ENST00000356785.4_Missense_Mutation_p.Q91K	NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	91					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.Q91K(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						AGAGTCCTTGCAGAATCAACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											164	143	150					10																	26789858		2203	4300	6503	26829864	SO:0001583	missense	54518			AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"Pleckstrin homology (PH) domain containing"	17379	protein-coding gene	gene with protein product	"Rap1-GTP-interacting adaptor molecule"	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.271C>A	10.37:g.26789858C>A	ENSP00000365411:p.Gln91Lys		26829864	Q8IWS8|Q8IYL7|Q8IZZ7	Missense_Mutation	SNP	ENST00000376236.4	37	CCDS31167.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.241766	0.22711	.	.	ENSG00000077420	ENST00000445780;ENST00000376236;ENST00000356785	T	0.28666	1.6	5.84	5.84	0.93424	.	0.570980	0.19712	N	0.107783	T	0.37972	0.1023	M	0.63843	1.955	0.09310	N	1	P;P;D	0.56035	0.924;0.915;0.974	P;B;P	0.53861	0.603;0.169;0.736	T	0.41431	-0.9509	10	0.23302	T	0.38	.	5.4204	0.16398	0.1469:0.6359:0.1413:0.0759	.	91;91;91	B4E100;Q7Z5R6;Q8IYL7	.;AB1IP_HUMAN;.	K	91	ENSP00000365411:Q91K	ENSP00000349237:Q91K	Q	+	1	0	APBB1IP	26829864	0.012000	0.17670	0.138000	0.22173	0.094000	0.18550	0.661000	0.25023	2.759000	0.94783	0.563000	0.77884	CAG		0.458	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043		A	26789858	C	A	26789858	3	1	25	1	0	0	0	0	1	0	0	0	760	711	25	2	281	2	APBB1IP	10	26789858	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		26789858	108744889	53	2204										
FAS	355	hgsc.bcm.edu	37	chr10	90770540	90770540	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	taacttggggtggctttgtcTtcttcttttgccaattccac	8	10	3	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr10:90770540T>A	ENST00000355279.2	+	6	536	c.536T>A	c.(535-537)cTt>cAt	p.L179H	FAS_ENST00000313771.5_3'UTR|FAS_ENST00000355740.2_Missense_Mutation_p.L179H|FAS_ENST00000352159.4_Missense_Mutation_p.L179H|FAS_ENST00000357339.2_Intron			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L179H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	TGGCTTTGTCTTCTTCTTTTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											299	270	280					10																	90770540		2203	4300	6503	90760520	SO:0001583	missense	355			M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.536T>A	10.37:g.90770540T>A	ENSP00000347426:p.Leu179His		90760520	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	T	7.138	0.581307	0.13686	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000355279;ENST00000371875	D;T;T	0.94232	-3.38;-0.94;-0.84	0.591	0.591	0.17465	.	2.604410	0.01260	N	0.009148	D	0.94945	0.8365	L	0.59436	1.845	0.09310	N	1	D;D	0.76494	0.999;0.995	D;P	0.65443	0.935;0.706	D	0.83784	0.0227	9	0.19147	T	0.46	11.9558	.	.	.	.	179;179	Q5T9P3;P25445	.;TNR6_HUMAN	H	206;179;179;179;179	ENSP00000347979:L179H;ENSP00000345601:L179H;ENSP00000347426:L179H	ENSP00000345601:L179H	L	+	2	0	FAS	90760520	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.268000	0.08607	0.492000	0.27815	0.352000	0.21897	CTT		0.353	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			A	90770540	T	A	90770540	3	1	25	1	0	0	0	0	1	0	0	0	5700	1609	56	5	558	5	FAS	10	90770540	Missense_Mutation	SNP	T	TCGA-AG-3598-01A-01W-0833-10	63980682	90770540	44764207	54	2205										
SMPD1	322	hgsc.bcm.edu	37	chr11	6413381	6413381	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cctgccgaagccctgcgcacCctcaggtacttatcgtccgt	9	17	1	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr11:6413381C>T	ENST00000609360.1	-	0	2642				SMPD1_ENST00000527275.1_Silent_p.T361T|SMPD1_ENST00000299397.3_Silent_p.T362T|SMPD1_ENST00000342245.4_Silent_p.T362T|SMPD1_ENST00000356761.2_Silent_p.T362T|APBB1_ENST00000526240.1_5'Flank	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.T362T(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		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)		CCCTGCGCACCCTCAGGTACT	0.577																																					GBM(147;1810 2556 5672 39622)											1	Substitution - coding silent(1)	large_intestine(1)	11											47	45	46					11																	6413381		2201	4296	6497	6369957	SO:0001628	intergenic_variant	6609			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			11.37:g.6413381C>T			6369957	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Silent	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	C	8.776	0.927139	0.18056	.	.	ENSG00000166311	ENST00000526280	.	.	.	4.87	0.572	0.17357	.	.	.	.	.	T	0.42268	0.1195	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21449	-1.0245	4	.	.	.	-43.7837	1.925	0.03315	0.1399:0.4915:0.1363:0.2323	.	.	.	.	L	92	.	.	P	+	2	0	SMPD1	6369957	0.487000	0.25988	0.986000	0.45419	0.963000	0.63663	-0.347000	0.07750	0.100000	0.17581	0.561000	0.74099	CCC		0.577	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		T	6413381	C	T	6413381	1	4	25	0	1	0	0	0	0	0	0	0	14841	610	22	3		3	SMPD1	11	6413381	IGR	SNP	C	TCGA-AG-3598-01A-01W-0833-10		6413381	128593135	55	2206										
NUDT22	84304	hgsc.bcm.edu	37	chr11	63995078	63995078	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agcccccagcaccaggacctCgctgggcagctggtggtaca	13	15	0	0	rs151057740	byFrequency	TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr11:63995078C>G	ENST00000279206.3	+	3	675	c.519C>G	c.(517-519)ctC>ctG	p.L173L	TRPT1_ENST00000546133.1_5'Flank|TRPT1_ENST00000394547.3_5'Flank|DNAJC4_ENST00000355040.4_5'Flank|TRPT1_ENST00000546089.1_5'Flank|NUDT22_ENST00000441250.2_Intron|DNAJC4_ENST00000321685.3_5'Flank|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000394546.2_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|TRPT1_ENST00000317459.6_5'Flank|TRPT1_ENST00000540472.1_5'Flank	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	173	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.						hydrolase activity (GO:0016787)	p.L173L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						ACCAGGACCTCGCTGGGCAGC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C	,,	0,4402		0,0,2201	87	82	83		519,,519	-1.8	0.9	11	dbSNP_134	83	3,8591	3.0+/-9.4	0,3,4294	no	coding-synonymous,intron,coding-synonymous	NUDT22	NM_001128612.1,NM_001128613.1,NM_032344.2	,,	0,3,6495	GG,GC,CC		0.0349,0.0,0.0231	,,	173/304,,173/304	63995078	3,12993	2201	4297	6498	63751654	SO:0001819	synonymous_variant	84304			BC006129	CCDS8061.1, CCDS44640.1	11q13.1	2008-02-05			ENSG00000149761	ENSG00000149761		"Nudix motif containing"	28189	protein-coding gene	gene with protein product						12477932	Standard	NM_032344		Approved	MGC13045	uc009ype.4	Q9BRQ3	OTTHUMG00000167791	ENST00000279206.3:c.519C>G	11.37:g.63995078C>G			63751654	C9JY06|Q71RD5	Silent	SNP	ENST00000279206.3	37	CCDS8061.1																																																																																				0.612	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344		G	63995078	C	G	63995078	2	3	25	1	0	0	0	0	0	0	0	1	10770	871	31	5		5	NUDT22	11	63995078	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10	57581697	63995078	71011438	56	2207										
RNF41	10193	hgsc.bcm.edu	37	chr12	56604131	56604131	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ttcgggttgtgctcacagtcGctgaggtgagacatgaggtt	15	7	1	3			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr12:56604131G>A	ENST00000345093.4	-	4	681	c.312C>T	c.(310-312)agC>agT	p.S104S	RNF41_ENST00000552656.1_Silent_p.S104S|RNF41_ENST00000394013.2_Silent_p.S33S|RNF41_ENST00000552244.1_Silent_p.S104S	NM_005785.3|NM_194359.2	NP_005776.1|NP_919340.1	Q9H4P4	RNF41_HUMAN	ring finger protein 41, E3 ubiquitin protein ligase	104					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|proteasomal protein catabolic process (GO:0010498)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|regulation of establishment of cell polarity (GO:2000114)|regulation of lymphocyte differentiation (GO:0045619)|regulation of MAPK cascade (GO:0043408)|regulation of myeloid cell differentiation (GO:0045637)|regulation of protein kinase B signaling (GO:0051896)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytosol (GO:0005829)	acid-amino acid ligase activity (GO:0016881)|protein tag (GO:0031386)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S104S(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	11						GCTCACAGTCGCTGAGGTGAG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	12											113	92	99					12																	56604131		2203	4300	6503	54890398	SO:0001819	synonymous_variant	10193			AF077599	CCDS8909.1, CCDS8910.1	12q13.13	2014-03-24	2014-03-24		ENSG00000181852	ENSG00000181852		"RING-type (C3HC4) zinc fingers"	18401	protein-coding gene	gene with protein product			"ring finger protein 41"				Standard	NM_005785		Approved	SBBI03, NRDP1	uc001skg.2	Q9H4P4	OTTHUMG00000170328	ENST00000345093.4:c.312C>T	12.37:g.56604131G>A			54890398	A6NFW0|B2RBT8|O75598	Silent	SNP	ENST00000345093.4	37	CCDS8909.1																																																																																				0.537	RNF41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408525.1	NM_005785		A	56604131	G	A	56604131	2	1	25	1	0	0	0	0	0	0	0	1	13531	1078	38	1		1	RNF41	12	56604131	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10		56604131	77247764	57	2208										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49742763	49742763	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ccatagagtccaggcagaatAtaattctataaagggaactc	8	8	1	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr13:49742763A>T	ENST00000492622.2	+	10	1357	c.1052A>T	c.(1051-1053)tAt>tTt	p.Y351F	FNDC3A_ENST00000541916.1_Missense_Mutation_p.Y351F|FNDC3A_ENST00000398316.3_Missense_Mutation_p.Y295F	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	351	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)	p.Y351F(1)		endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CAGGCAGAATATAATTCTATA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											100	104	103					13																	49742763		2203	4300	6503	48640764	SO:0001583	missense	22862			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.1052A>T	13.37:g.49742763A>T	ENSP00000417257:p.Tyr351Phe		48640764	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.446293	0.43429	.	.	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.57273	0.41;0.41;0.41	5.54	0.0851	0.14440	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.567589	0.16800	N	0.199006	T	0.45256	0.1333	L	0.55213	1.73	0.29735	N	0.837576	B;B;B	0.15930	0.012;0.001;0.015	B;B;B	0.33690	0.164;0.027;0.168	T	0.43909	-0.9362	10	0.20046	T	0.44	-5.8623	6.837	0.23941	0.2104:0.5612:0.2284:0.0	.	295;351;351	Q9Y2H6-2;G5E9X3;Q9Y2H6	.;.;FND3A_HUMAN	F	351;287;351;295	ENSP00000417257:Y351F;ENSP00000441831:Y351F;ENSP00000381362:Y295F	ENSP00000338579:Y287F	Y	+	2	0	FNDC3A	48640764	0.997000	0.39634	0.991000	0.47740	0.984000	0.73092	1.316000	0.33620	0.144000	0.18951	-0.332000	0.08345	TAT		0.373	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		T	49742763	A	T	49742763	3	4	25	1	0	0	0	0	1	0	0	0	5988	449	16	5	1097	5	FNDC3A	13	49742763	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10		49742763	65427115	58	2209										
KLF5	688	hgsc.bcm.edu	37	chr13	73636462	73636462	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ggatctagatatgcccagttCtacaaatcagacagcagcaa	8	10	3	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr13:73636462C>G	ENST00000377687.4	+	2	1261	c.725C>G	c.(724-726)tCt>tGt	p.S242C	KLF5_ENST00000477333.1_3'UTR|KLF5_ENST00000539231.1_Missense_Mutation_p.S151C	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	242					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.S242C(1)|p.S242Y(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ATGCCCAGTTCTACAAATCAG	0.488																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	13											107	105	106					13																	73636462		2203	4300	6503	72534463	SO:0001583	missense	688			D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.725C>G	13.37:g.73636462C>G	ENSP00000366915:p.Ser242Cys		72534463	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	37	CCDS9448.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770709	0.69992	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	T;T	0.08807	3.25;3.05	5.94	5.94	0.96194	.	0.398451	0.31415	N	0.007692	T	0.15825	0.0381	M	0.61703	1.905	0.53005	D	0.999967	D	0.55172	0.97	B	0.43916	0.436	T	0.00317	-1.1822	10	0.49607	T	0.09	.	20.3591	0.98849	0.0:1.0:0.0:0.0	.	242	Q13887	KLF5_HUMAN	C	151;242;222	ENSP00000440407:S151C;ENSP00000366915:S242C	ENSP00000366915:S242C	S	+	2	0	KLF5	72534463	0.677000	0.27577	1.000000	0.80357	0.998000	0.95712	3.652000	0.54439	2.816000	0.96949	0.561000	0.74099	TCT		0.488	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1			G	73636462	C	G	73636462	3	3	25	1	0	0	0	0	1	0	0	0	8370	913	32	5	731	5	KLF5	13	73636462	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	23893699	73636462	41533416	59	2210										
CLDN10	9071	hgsc.bcm.edu	37	chr13	96086260	96086260	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	cgcaggtaacgcgttgggttCtttccattgccgaccgcatt	11	12	1	0			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr13:96086260C>A	ENST00000376873.3	+	1	403	c.173C>A	c.(172-174)tCt>tAt	p.S58Y		NM_001160100.1|NM_182848.3	NP_001153572.1|NP_878268.1	P78369	CLD10_HUMAN	claudin 10	60					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|ion transport (GO:0006811)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.S58Y(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	15	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			GCGTTGGGTTCTTTCCATTGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	13											126	120	122					13																	96086260		2203	4300	6503	94884261	SO:0001583	missense	9071			U89916	CCDS9475.1, CCDS9476.1	13q31-q34	2008-07-18			ENSG00000134873	ENSG00000134873		"Claudins"	2033	protein-coding gene	gene with protein product						18025272	Standard	NM_182848		Approved	OSP-L, CPETRL3	uc001vmh.2	P78369	OTTHUMG00000017217	ENST00000376873.3:c.173C>A	13.37:g.96086260C>A	ENSP00000366069:p.Ser58Tyr		94884261	Q6IBF9|Q96N78	Missense_Mutation	SNP	ENST00000376873.3	37	CCDS9475.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.538808	0.85917	.	.	ENSG00000134873	ENST00000376873	D	0.89343	-2.5	5.24	5.24	0.73138	.	.	.	.	.	D	0.91392	0.7284	.	.	.	0.80722	D	1	P	0.42203	0.773	P	0.49451	0.611	D	0.91549	0.5255	8	0.52906	T	0.07	.	17.3607	0.87349	0.0:1.0:0.0:0.0	.	58	Q96N78	.	Y	58	ENSP00000366069:S58Y	ENSP00000366069:S58Y	S	+	2	0	CLDN10	94884261	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.361000	0.79497	2.602000	0.87976	0.563000	0.77884	TCT		0.493	CLDN10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045483.3	NM_006984		A	96086260	C	A	96086260	3	1	25	1	0	0	0	0	1	0	0	0	3478	913	32	2	175	2	CLDN10	13	96086260	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10	22449798	96086260	19083618	60	2211										
CTSG	1511	hgsc.bcm.edu	37	chr14	25044607	25044607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gggcctgctctcccggcctcCgatgatctcccctggaagga	12	16	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr14:25044607C>T	ENST00000216336.2	-	2	103	c.67G>A	c.(67-69)Gga>Aga	p.G23R		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	23	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.G23R(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TCCCGGCCTCCGATGATCTCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	14											97	101	100					14																	25044607		2203	4300	6503	24114447	SO:0001583	missense	1511			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"Cathepsins", "Endogenous ligands"	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.67G>A	14.37:g.25044607C>T	ENSP00000216336:p.Gly23Arg		24114447	Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.356037	0.61293	.	.	ENSG00000100448	ENST00000216336	D	0.95554	-3.74	5.38	4.5	0.54988	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.37095	N	0.002246	D	0.98108	0.9376	H	0.95260	3.645	0.42745	D	0.993751	D	0.89917	1.0	D	0.73708	0.981	D	0.98643	1.0676	10	0.87932	D	0	.	10.4166	0.44325	0.0:0.9099:0.0:0.0901	.	23	P08311	CATG_HUMAN	R	23	ENSP00000216336:G23R	ENSP00000216336:G23R	G	-	1	0	CTSG	24114447	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	2.315000	0.43752	1.420000	0.47138	0.655000	0.94253	GGA		0.572	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		T	25044607	C	T	25044607	3	4	25	1	0	0	0	0	1	0	0	0	4041	661	23	1	716	1	CTSG	14	25044607	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		25044607	82304933	61	2212										
G2E3	55632	hgsc.bcm.edu	37	chr14	31081500	31081500	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	taattggatgtctcagacttAtaacgacattaagtgataaa	7	5	1	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr14:31081500A>C	ENST00000206595.6	+	13	1742	c.1588A>C	c.(1588-1590)Ata>Cta	p.I530L	G2E3_ENST00000438909.2_Missense_Mutation_p.I484L|G2E3_ENST00000553504.1_Missense_Mutation_p.I560L	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	530	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I530L(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						TCTCAGACTTATAACGACATT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											102	106	105					14																	31081500		2203	4294	6497	30151251	SO:0001583	missense	55632			AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1588A>C	14.37:g.31081500A>C	ENSP00000206595:p.Ile530Leu		30151251	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	37	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.704822	0.48412	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.56611	0.45;0.45;0.45	5.47	-0.099	0.13626	HECT (3);	0.681685	0.15924	N	0.237995	T	0.45196	0.1330	L	0.53249	1.67	0.27300	N	0.957599	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.002	T	0.47355	-0.9124	10	0.66056	D	0.02	-0.0254	10.7542	0.46225	0.5411:0.0:0.4589:0.0	.	42;530	Q49AD9;Q7L622	.;G2E3_HUMAN	L	530;484;560	ENSP00000206595:I530L;ENSP00000391068:I484L;ENSP00000451653:I560L	ENSP00000206595:I530L	I	+	1	0	G2E3	30151251	0.774000	0.28592	0.879000	0.34478	0.849000	0.48306	-0.002000	0.12924	0.100000	0.17581	0.454000	0.30748	ATA		0.323	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		C	31081500	A	C	31081500	3	2	25	1	0	0	0	0	1	0	0	0	6159	449	16	4	1634	4	G2E3	14	31081500	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10	6036893	31081500	76268040	62	2213										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9858336	9858336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	tctgggatagtgaatcctggCgtatggaatccacggatttc	12	8	1	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr16:9858336C>T	ENST00000396573.2	-	14	3374	c.3065G>A	c.(3064-3066)cGc>cAc	p.R1022H	GRIN2A_ENST00000535259.1_Missense_Mutation_p.R865H|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R1022H|GRIN2A_ENST00000396575.2_Missense_Mutation_p.R1022H|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R1022H|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R1022H	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1022					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.R1022H(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGAATCCTGGCGTATGGAATC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	114	111					16																	9858336		2197	4300	6497	9765837	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3065G>A	16.37:g.9858336C>T	ENSP00000379818:p.Arg1022His		9765837	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	19.79	3.893778	0.72639	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.12879	2.64;2.64;2.65;2.64;2.64	5.33	5.33	0.75918	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.050105	0.85682	D	0.000000	T	0.37404	0.1002	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.994;0.964;0.997	T	0.03139	-1.1068	9	.	.	.	.	18.0263	0.89270	0.0:1.0:0.0:0.0	.	865;1022;1022	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	H	1022;1022;865;1022;1022	ENSP00000379818:R1022H;ENSP00000385872:R1022H;ENSP00000441572:R865H;ENSP00000332549:R1022H;ENSP00000379820:R1022H	.	R	-	2	0	GRIN2A	9765837	1.000000	0.71417	0.991000	0.47740	0.817000	0.46193	7.376000	0.79658	2.491000	0.84063	0.655000	0.94253	CGC		0.532	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9858336	C	T	9858336	3	4	25	1	0	0	0	0	1	0	0	0	6800	768	27	1	1333	1	GRIN2A	16	9858336	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		9858336	80496417	63	2214										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	25	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		7578406	73616804	64	2215										
MYH1	4619	hgsc.bcm.edu	37	chr17	10409146	10409146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gacctctgtttgaagtctgcAtaaaggattctgcttgggaa	11	7	3	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr17:10409146A>G	ENST00000226207.5	-	19	2251	c.2157T>C	c.(2155-2157)taT>taC	p.Y719Y	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	719	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Y719Y(2)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TGAAGTCTGCATAAAGGATTC	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	17											53	50	51					17																	10409146		2203	4300	6503	10349871	SO:0001819	synonymous_variant	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2157T>C	17.37:g.10409146A>G			10349871	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																				0.408	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10409146	A	G	10409146	2	3	25	1	0	0	0	0	0	0	0	1	10059	224	8	4		4	MYH1	17	10409146	Silent	SNP	A	TCGA-AG-3598-01A-01W-0833-10	2830740	10409146	70786064	65	2216										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56585939	56585939	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agtgctgaagagtttgatgaCgacgagaagattgaggtgga	16	3	0	7			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr18:56585939C>T	ENST00000336078.4	+	4	1196	c.420C>T	c.(418-420)gaC>gaT	p.D140D	ZNF532_ENST00000589288.1_Silent_p.D140D|ZNF532_ENST00000591230.1_Silent_p.D140D|ZNF532_ENST00000591808.1_Silent_p.D140D|ZNF532_ENST00000591083.1_Silent_p.D140D	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D140D(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						AGTTTGATGACGACGAGAAGA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	18											121	108	112					18																	56585939		2203	4300	6503	54736919	SO:0001819	synonymous_variant	55205			AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.420C>T	18.37:g.56585939C>T			54736919	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	37	CCDS11969.1																																																																																				0.537	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56585939	C	T	56585939	2	4	25	1	0	0	0	0	0	0	0	1	18011	535	19	1		1	ZNF532	18	56585939	Silent	SNP	C	TCGA-AG-3598-01A-01W-0833-10		56585939	21491309	66	2217										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39329199	39329199	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	caagacccgtcttccaacccGtatgactgaccaggcatgat	8	14	1	4			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr19:39329199G>A	ENST00000221419.5	-	10	1761	c.1395C>T	c.(1393-1395)taC>taT	p.Y465Y	AC104534.3_ENST00000594769.1_Missense_Mutation_p.T82M|HNRNPL_ENST00000600873.1_Silent_p.Y332Y	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	465	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)	p.Y332Y(1)|p.Y465Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CTTCCAACCCGTATGACTGAC	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	19											68	56	60					19																	39329199		2203	4300	6503	44021039	SO:0001819	synonymous_variant	3191			X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1395C>T	19.37:g.39329199G>A			44021039	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																				0.547	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			A	39329199	G	A	39329199	2	1	25	1	0	0	0	0	0	0	0	1	7291	1140	40	1		1	HNRNPL	19	39329199	Silent	SNP	G	TCGA-AG-3598-01A-01W-0833-10		39329199	19799784	67	2218										
CASS4	57091	hgsc.bcm.edu	37	chr20	55012440	55012440	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	gtgccccccattcctgagagGcctggaagaagctcctgcca	11	15	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr20:55012440G>T	ENST00000360314.3	+	3	482	c.257G>T	c.(256-258)gGc>gTc	p.G86V	CASS4_ENST00000371336.3_Missense_Mutation_p.G86V|CASS4_ENST00000434344.1_Missense_Mutation_p.G86V	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	86					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)	p.G86V(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						TTCCTGAGAGGCCTGGAAGAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	20											30	33	32					20																	55012440		2203	4300	6503	54445847	SO:0001583	missense	57091			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.257G>T	20.37:g.55012440G>T	ENSP00000353462:p.Gly86Val		54445847	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999998	0.74818	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.24151	2.36;2.36;1.87	5.57	1.13	0.20643	.	0.666605	0.15562	N	0.255879	T	0.21631	0.0521	M	0.65975	2.015	0.21020	N	0.999803	D;B;B;B	0.53462	0.96;0.091;0.186;0.117	B;B;B;B	0.42422	0.387;0.026;0.063;0.028	T	0.19257	-1.0311	10	0.44086	T	0.13	-16.946	1.0146	0.01505	0.2423:0.3115:0.2869:0.1592	.	86;86;86;86	B4DII4;Q9NQ75-3;Q9NQ75-2;Q9NQ75	.;.;.;CASS4_HUMAN	V	86	ENSP00000353462:G86V;ENSP00000360387:G86V;ENSP00000410027:G86V	ENSP00000353462:G86V	G	+	2	0	CASS4	54445847	0.000000	0.05858	0.057000	0.19452	0.690000	0.40134	0.188000	0.17018	0.274000	0.22072	0.655000	0.94253	GGC		0.627	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		T	55012440	G	T	55012440	3	4	25	1	0	0	0	0	1	0	0	0	2689	1203	42	2	263	2	CASS4	20	55012440	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10		55012440	8013080	68	2219										
TUBA8	51807	hgsc.bcm.edu	37	chr22	18609377	18609377	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	ggacaacgaagccatctatgAcatctgccgcaggaaccttg	10	12	2	1			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr22:18609377A>C	ENST00000330423.3	+	4	705	c.632A>C	c.(631-633)gAc>gCc	p.D211A	TUBA8_ENST00000316027.6_Missense_Mutation_p.D145A	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	211					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.D211A(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						GCCATCTATGACATCTGCCGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	22											178	154	162					22																	18609377		2203	4300	6503	16989377	SO:0001583	missense	51807			AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"Tubulins"	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.632A>C	22.37:g.18609377A>C	ENSP00000333326:p.Asp211Ala		16989377	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	.	17.11	3.306233	0.60305	.	.	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	T;T;T	0.70749	-0.51;-0.51;-0.51	5.67	5.67	0.87782	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.89570	0.6753	H	0.97465	4.01	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.987	D;D;D	0.74023	0.971;0.982;0.942	D	0.93081	0.6491	10	0.87932	D	0	.	15.3851	0.74691	1.0:0.0:0.0:0.0	.	145;235;211	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	A	145;211;235	ENSP00000318575:D145A;ENSP00000333326:D211A;ENSP00000412646:D235A	ENSP00000318575:D145A	D	+	2	0	TUBA8	16989377	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.288000	0.76882	0.533000	0.62120	GAC		0.512	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		C	18609377	A	C	18609377	3	2	25	1	0	0	0	0	1	0	0	0	16790	275	10	4	646	4	TUBA8	22	18609377	Missense_Mutation	SNP	A	TCGA-AG-3598-01A-01W-0833-10		18609377	32695189	69	2220										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44285724	44285724	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agcccgcagtagaaaggaaaGtataaggtgcagaccaaggc	13	8	0	2			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chr22:44285724G>T	ENST00000597664.1	-	3	576	c.447C>A	c.(445-447)taC>taA	p.Y149*	PNPLA5_ENST00000593866.1_Intron|PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000216177.4_Nonsense_Mutation_p.Y149*			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	149	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)	p.Y149*(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AGAAAGGAAAGTATAAGGTGC	0.557																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											63	62	62					22																	44285724		2203	4300	6503	42617057	SO:0001587	stop_gained	150379			Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.447C>A	22.37:g.44285724G>T	ENSP00000471069:p.Tyr149*		42617057	B1AHL8|B3KPR1|Q6ZST0	Nonsense_Mutation	SNP	ENST00000597664.1	37		.	.	.	.	.	.	.	.	.	.	G	18.54	3.645968	0.67358	.	.	ENSG00000100341	ENST00000216177	.	.	.	4.36	0.827	0.18835	.	0.096386	0.43747	D	0.000537	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-12.1507	6.1496	0.20304	0.621:0.0:0.379:0.0	.	.	.	.	X	149	.	ENSP00000216177:Y149X	Y	-	3	2	PNPLA5	42617057	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.082000	0.14847	0.127000	0.18452	-0.339000	0.08088	TAC		0.557	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		T	44285724	G	T	44285724	4	4	25	1	0	0	0	0	0	1	0	0	12199	1024	36	2	870	2	PNPLA5	22	44285724	Nonsense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	25676347	44285724	7018842	70	2221										
PPEF1	5475	hgsc.bcm.edu	37	chrX	18767935	18767935	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	agaaatcagtctcttgaaagCgaacaggacatgagggatag	12	6	2	3			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chrX:18767935C>A	ENST00000361511.4	+	7	755	c.261C>A	c.(259-261)agC>agA	p.S87R	PPEF1_ENST00000543630.1_Missense_Mutation_p.S87R|PPEF1_ENST00000349874.5_Missense_Mutation_p.S87R|PPEF1_ENST00000471570.1_3'UTR|PPEF1_ENST00000544635.1_Missense_Mutation_p.S22R|PPEF1_ENST00000359763.6_Intron	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	87					detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.S87R(1)		breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					CTCTTGAAAGCGAACAGGACA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											121	101	107					X																	18767935		2203	4300	6503	18677856	SO:0001583	missense	5475			BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9243	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, alpha isozyme"	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.261C>A	X.37:g.18767935C>A	ENSP00000354871:p.Ser87Arg		18677856	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	37	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	C	8.429	0.848199	0.17034	.	.	ENSG00000086717	ENST00000361511;ENST00000349874;ENST00000543630;ENST00000544635	T;T;T;T	0.23147	3.24;3.1;1.92;3.26	3.72	0.984	0.19773	.	1.520740	0.03926	N	0.284486	T	0.34542	0.0901	L	0.41824	1.3	0.09310	N	1	D;D;D	0.69078	0.997;0.978;0.966	P;P;P	0.61328	0.887;0.825;0.559	T	0.25710	-1.0124	10	0.18710	T	0.47	0.1075	5.3118	0.15835	0.0:0.5993:0.0:0.4006	.	87;87;87	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	R	87;87;87;22	ENSP00000354871:S87R;ENSP00000341892:S87R;ENSP00000437785:S87R;ENSP00000441289:S22R	ENSP00000341892:S87R	S	+	3	2	PPEF1	18677856	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.797000	0.04570	0.079000	0.16929	-0.312000	0.09012	AGC		0.438	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240		A	18767935	C	A	18767935	3	1	25	1	0	0	0	0	1	0	0	0	12338	767	27	2	275	2	PPEF1	23	18767935	Missense_Mutation	SNP	C	TCGA-AG-3598-01A-01W-0833-10		18767935	136502625	71	2222										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35984744	35984744	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0277777777777778	2	1	0.335403726708075	2.57142857142857	0	0.428571428571429	1	0	aaagtgaagcagatgatagaGattattggtttagtggcaga	13	2	0	5			TCGA-AG-3598-01A-01W-0833-10	TCGA-AG-3598-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	7f987d01-01ba-4ec9-a775-bef2f1aaddfd	726a5de6-6979-4171-88dd-83f4bdf7fc3c	g.chrX:35984744G>C	ENST00000297866.5	+	9	1539	c.1473G>C	c.(1471-1473)gaG>gaC	p.E491D		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	491								p.E491D(2)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AGATGATAGAGATTATTGGTT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	X											112	105	108					X																	35984744		2202	4300	6502	35894665	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1473G>C	X.37:g.35984744G>C	ENSP00000297866:p.Glu491Asp		35894665	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.347324	0.00219	.	.	ENSG00000165164	ENST00000297866	T	0.13196	2.61	5.55	-5.01	0.02991	.	0.159507	0.53938	N	0.000054	T	0.04998	0.0134	L	0.34521	1.04	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.44559	-0.9320	10	0.02654	T	1	-11.994	1.3189	0.02112	0.4105:0.0953:0.1727:0.3215	.	491	Q6ZTR5	CX022_HUMAN	D	491	ENSP00000297866:E491D	ENSP00000297866:E491D	E	+	3	2	CXorf22	35894665	0.517000	0.26226	0.001000	0.08648	0.001000	0.01503	-0.169000	0.09911	-1.054000	0.03214	-0.928000	0.02712	GAG		0.338	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35984744	G	C	35984744	3	2	25	1	0	0	0	0	1	0	0	0	4108	933	33	5	1507	5	CXorf22	23	35984744	Missense_Mutation	SNP	G	TCGA-AG-3598-01A-01W-0833-10	17216809	35984744	119285816	72	2223										
PLOD1	5351	hgsc.bcm.edu	37	chr1	12017947	12017947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tcccgcgcttctggaccttcGaaacaggctgcaccgtgtgt	11	14	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:12017947G>A	ENST00000196061.4	+	8	817	c.790G>A	c.(790-792)Gaa>Aaa	p.E264K	PLOD1_ENST00000485046.1_3'UTR|PLOD1_ENST00000376369.3_Missense_Mutation_p.E311K	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	264					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)	p.E264K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CTGGACCTTCGAAACAGGCTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											113	105	108					1																	12017947		2203	4300	6503	11940534	SO:0001583	missense	5351			BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"lysyl hydroxlase 1"	153454	"procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.790G>A	1.37:g.12017947G>A	ENSP00000196061:p.Glu264Lys		11940534	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.803924	0.90623	.	.	ENSG00000083444	ENST00000376369;ENST00000429000;ENST00000196061	T;T;T	0.65732	-0.17;1.61;-0.17	4.69	3.75	0.43078	.	0.053206	0.64402	D	0.000001	T	0.67458	0.2895	M	0.84948	2.725	0.58432	D	0.999999	D;P	0.61080	0.989;0.939	B;B	0.43867	0.434;0.284	T	0.75614	-0.3257	10	0.66056	D	0.02	.	13.7833	0.63094	0.0:0.1548:0.8452:0.0	.	311;264	B4DR87;Q02809	.;PLOD1_HUMAN	K	311;266;264	ENSP00000365548:E311K;ENSP00000405372:E266K;ENSP00000196061:E264K	ENSP00000196061:E264K	E	+	1	0	PLOD1	11940534	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.579000	0.82511	1.156000	0.42514	0.561000	0.74099	GAA		0.637	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302		A	12017947	G	A	12017947	3	1	26	1	0	0	0	0	1	0	0	0	12132	1059	37	1	820	1	PLOD1	1	12017947	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		12017947	237232674	1	2224										
LUZP1	7798	hgsc.bcm.edu	37	chr1	23417961	23417961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agttggggggtcttctaaagAtttcaagtctcgcctactct	10	9	5	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:23417961A>G	ENST00000302291.4	-	4	3595	c.2794T>C	c.(2794-2796)Tct>Cct	p.S932P	LUZP1_ENST00000314174.5_Missense_Mutation_p.S932P|LUZP1_ENST00000374623.3_Missense_Mutation_p.S932P|LUZP1_ENST00000418342.1_Missense_Mutation_p.S932P			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	932					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)		p.S932P(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TCTTCTAAAGATTTCAAGTCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	110	109					1																	23417961		2203	4300	6503	23290548	SO:0001583	missense	7798			BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.2794T>C	1.37:g.23417961A>G	ENSP00000303758:p.Ser932Pro		23290548	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266598	0.59540	.	.	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.20881	2.24;2.24;2.24;2.04	5.08	5.08	0.68730	.	0.141869	0.32987	N	0.005402	T	0.33030	0.0849	L	0.44542	1.39	0.26583	N	0.973338	D;D	0.64830	0.994;0.994	P;P	0.61800	0.894;0.894	T	0.09552	-1.0669	10	0.33940	T	0.23	.	12.6249	0.56623	1.0:0.0:0.0:0.0	.	932;932	Q86V48-2;Q86V48	.;LUZP1_HUMAN	P	932	ENSP00000393460:S932P;ENSP00000363752:S932P;ENSP00000303758:S932P;ENSP00000313705:S932P	ENSP00000303758:S932P	S	-	1	0	LUZP1	23290548	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	3.891000	0.56227	1.933000	0.56026	0.397000	0.26171	TCT		0.478	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		G	23417961	A	G	23417961	3	3	26	1	0	0	0	0	1	0	0	0	9115	333	12	4	444	4	LUZP1	1	23417961	Missense_Mutation	SNP	A	TCGA-AG-3599-01A-02W-0833-10	11400014	23417961	225832660	2	2225										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35855606	35855606	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcagtgagtccttgaaatggCgaggggaaatgaaacatttc	12	6	1	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:35855606C>T	ENST00000314607.6	+	15	2574	c.2494C>T	c.(2494-2496)Cga>Tga	p.R832*	ZMYM4_ENST00000373297.2_Nonsense_Mutation_p.R743*	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	832					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R832*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTTGAAATGGCGAGGGGAAAT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											148	139	142					1																	35855606		2203	4300	6503	35628193	SO:0001587	stop_gained	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2494C>T	1.37:g.35855606C>T	ENSP00000322915:p.Arg832*		35628193	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Nonsense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.153936|6.153936	0.97329|0.97329	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000457946|ENST00000314607;ENST00000373297	.|.	.|.	.|.	5.39|5.39	4.46|4.46	0.54185|0.54185	.|.	.|0.372428	.|0.24206	.|N	.|0.040572	T|.	0.33527|.	0.0866|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34204|.	-0.9838|.	3|.	.|0.02654	.|T	.|1	-6.6399|-6.6399	13.0919|13.0919	0.59171|0.59171	0.2923:0.7077:0.0:0.0|0.2923:0.7077:0.0:0.0	.|.	.|.	.|.	.|.	V|X	491|832;743	.|.	.|ENSP00000322915:R832X	A|R	+|+	2|1	0|2	ZMYM4|ZMYM4	35628193|35628193	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	0.759000|0.759000	0.26461|0.26461	1.237000|1.237000	0.43756|0.43756	0.591000|0.591000	0.81541|0.81541	GCG|CGA		0.388	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		T	35855606	C	T	35855606	4	4	26	1	0	0	0	0	0	1	0	0	17741	760	27	1	2552	1	ZMYM4	1	35855606	Nonsense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	12437645	35855606	213395015	3	2226										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99772387	99772387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acggaattaccaccatccgcGtcaccccagtagagggcagc	10	15	1	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:99772387G>A	ENST00000370185.3	+	7	2610	c.2113G>A	c.(2113-2115)Gtc>Atc	p.V705I	LPPR4_ENST00000457765.1_Missense_Mutation_p.V647I|LPPR4_ENST00000370184.1_Missense_Mutation_p.V547I	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		705					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.V705I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		CACCATCCGCGTCACCCCAGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	57	60					1																	99772387		2203	4300	6503	99544975	SO:0001583	missense	9890																														ENST00000370185.3:c.2113G>A	1.37:g.99772387G>A	ENSP00000359204:p.Val705Ile		99544975	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603781	0.87157	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000370184	T;T;T	0.27104	2.25;2.2;1.69	6.02	6.02	0.97574	.	0.416961	0.26761	N	0.022631	T	0.38401	0.1039	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.998;0.994	D;P	0.73708	0.981;0.543	T	0.01033	-1.1474	9	.	.	.	-36.1055	20.5407	0.99260	0.0:0.0:1.0:0.0	.	647;705	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	I	705;647;547	ENSP00000359204:V705I;ENSP00000394913:V647I;ENSP00000359203:V547I	.	V	+	1	0	RP4-788L13.1	99544975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.438000	0.97539	2.865000	0.98341	0.655000	0.94253	GTC		0.512	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			A	99772387	G	A	99772387	3	1	26	1	0	0	0	0	1	0	0	0	8956	1145	40	1	2139	1	LPPR4	1	99772387	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	63916781	99772387	149478234	4	2227										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103467497	103467497	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttactttttcaccaggaggaCcaattggaccttgtggacca	9	10	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:103467497C>A	ENST00000370096.3	-	24	2438	c.2126G>T	c.(2125-2127)gGt>gTt	p.G709V	COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000358392.2_Missense_Mutation_p.G721V|COL11A1_ENST00000512756.1_Missense_Mutation_p.G593V|COL11A1_ENST00000353414.4_Missense_Mutation_p.G670V	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	709	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.G721V(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		ACCAGGAGGACCAATTGGACC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											101	101	101					1																	103467497		2203	4299	6502	103240085	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2126G>T	1.37:g.103467497C>A	ENSP00000359114:p.Gly709Val		103240085	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.734046	0.89482	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.99802	0.9915	H	0.94698	3.57	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;1.0;0.999	D	0.97332	0.9951	10	0.87932	D	0	.	19.949	0.97192	0.0:1.0:0.0:0.0	.	593;670;721;709	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	V	709;721;670;593	ENSP00000359114:G709V;ENSP00000351163:G721V;ENSP00000302551:G670V;ENSP00000426533:G593V	ENSP00000302551:G670V	G	-	2	0	COL11A1	103240085	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.990000	0.76225	2.706000	0.92434	0.655000	0.94253	GGT		0.353	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103467497	C	A	103467497	3	1	26	1	0	0	0	0	1	0	0	0	3673	507	18	2	3470	2	COL11A1	1	103467497	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	3695110	103467497	145783124	5	2228										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120437809	120437809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tatttagacatgttgctcccGaagagatatgtttaaaaaaa	7	5	0	2	rs141186333		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:120437809G>A	ENST00000369400.1	-	1	1309	c.1151C>T	c.(1150-1152)tCg>tTg	p.S384L		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	384	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S384L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		TGTTGCTCCCGAAGAGATATG	0.413													G|||	1	0.000199681	0	0.0014	5008	,	,		22065	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	LEU/SER	0,4406		0,0,2203	116	121	119		1151	-9.1	0	1	dbSNP_134	119	8,8592	5.7+/-21.5	0,8,4292	yes	missense	ADAM30	NM_021794.3	145	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	benign	384/791	120437809	8,12998	2203	4300	6503	120239332	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.1151C>T	1.37:g.120437809G>A	ENSP00000358407:p.Ser384Leu		120239332	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.03	1.519198	0.27211	0.0	9.3E-4	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.64438	-0.1	4.88	-9.07	0.00724	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	3.053280	0.01374	N	0.012689	T	0.23014	0.0556	L	0.51422	1.61	0.09310	N	1	B	0.19817	0.039	B	0.22152	0.038	T	0.16276	-1.0408	10	0.23891	T	0.37	.	1.4456	0.02364	0.3134:0.096:0.1515:0.4391	.	384	Q9UKF2	ADA30_HUMAN	L	384	ENSP00000358407:S384L	ENSP00000358407:S384L	S	-	2	0	ADAM30	120239332	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-2.033000	0.01425	-1.650000	0.01506	0.563000	0.77884	TCG		0.413	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		A	120437809	G	A	120437809	3	1	26	1	0	0	0	0	1	0	0	0	248	1059	37	1	1225	1	ADAM30	1	120437809	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	16970312	120437809	128812812	6	2229										
HRNR	388697	hgsc.bcm.edu	37	chr1	152191466	152191466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atccagagccatgtcggccgCggcccgaagcgtgatgggag	16	12	0	2	rs376040395	byFrequency	TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:152191466C>T	ENST00000368801.2	-	3	2714	c.2639G>A	c.(2638-2640)cGc>cAc	p.R880H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	880					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R880H(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTCGGCCGCGGCCCGAAGC	0.627													C|||	2	0.000399361	0	0	5008	,	,		20954	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						C	HIS/ARG	0,4406		0,0,2203	87	95	93		2639	-4.1	0	1		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	HRNR	NM_001009931.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	880/2851	152191466	1,13005	2203	4300	6503	150458090	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2639G>A	1.37:g.152191466C>T	ENSP00000357791:p.Arg880His		150458090	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	3.616	-0.078540	0.07184	0.0	1.16E-4	ENSG00000197915	ENST00000368801	T	0.01871	4.59	2.07	-4.14	0.03892	.	.	.	.	.	T	0.00271	0.0008	N	0.19112	0.55	0.09310	N	1	P	0.46578	0.88	B	0.19946	0.027	T	0.49214	-0.8963	9	0.15499	T	0.54	.	4.0907	0.09968	0.0:0.2699:0.3225:0.4077	.	880	Q86YZ3	HORN_HUMAN	H	880	ENSP00000357791:R880H	ENSP00000357791:R880H	R	-	2	0	HRNR	150458090	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.906000	0.00171	-2.279000	0.00676	-0.362000	0.07510	CGC		0.627	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152191466	C	T	152191466	3	4	26	1	0	0	0	0	1	0	0	0	7380	768	27	1	5917	1	HRNR	1	152191466	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	31753657	152191466	97059155	7	2230										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155883954	155883954	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atctgttgtttagctcgtggTtgtgatgaaggatattggta	13	3	1	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:155883954T>C	ENST00000368321.3	-	14	1826	c.1803A>G	c.(1801-1803)caA>caG	p.Q601Q	RIT1_ENST00000539040.1_5'Flank|KIAA0907_ENST00000368320.3_3'UTR|RIT1_ENST00000368323.3_5'Flank	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	601							RNA binding (GO:0003723)	p.Q601Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			TAGCTCGTGGTTGTGATGAAG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											162	142	149					1																	155883954		2203	4300	6503	154150578	SO:0001819	synonymous_variant	22889			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1803A>G	1.37:g.155883954T>C			154150578	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Silent	SNP	ENST00000368321.3	37	CCDS30885.1																																																																																				0.443	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		C	155883954	T	C	155883954	2	2	26	1	0	0	0	0	0	0	0	1	8220	1722	60	4		4	KIAA0907	1	155883954	Silent	SNP	T	TCGA-AG-3599-01A-02W-0833-10	3692488	155883954	93366667	8	2231										
OR10X1	128367	hgsc.bcm.edu	37	chr1	158549277	158549277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggttacagatggccaggaagCggtcatatcccatcaaagtg	12	9	2	1	rs41273507	byFrequency	TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:158549277C>T	ENST00000368150.1	-	1	412	c.413G>A	c.(412-414)cGc>cAc	p.R138H		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R138H(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GGCCAGGAAGCGGTCATATCC	0.458													C|||	5	0.000998403	0	0	5008	,	,		22562	0		0.004	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						C	HIS/ARG	3,4403	8.1+/-20.4	0,3,2200	82	83	83		413	5	0.6	1	dbSNP_127	83	18,8582	12.6+/-44.7	0,18,4282	yes	missense	OR10X1	NM_001004477.1	29	0,21,6482	TT,TC,CC		0.2093,0.0681,0.1615	probably-damaging	138/327	158549277	21,12985	2203	4300	6503	156815901	SO:0001583	missense	128367			BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"GPCR / Class A : Olfactory receptors"	14995	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily X, member 1"	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.413G>A	1.37:g.158549277C>T	ENSP00000357132:p.Arg138His		156815901	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	17.83	3.484824	0.63962	6.81E-4	0.002093	ENSG00000186400	ENST00000368150	T	0.77489	-1.1	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000172	D	0.87489	0.6190	M	0.85373	2.75	0.43564	D	0.995882	D	0.89917	1.0	D	0.71414	0.973	D	0.89221	0.3571	10	0.87932	D	0	.	17.2345	0.86995	0.0:1.0:0.0:0.0	rs41273507	138	Q8NGY0	O10X1_HUMAN	H	138	ENSP00000357132:R138H	ENSP00000357132:R138H	R	-	2	0	OR10X1	156815901	1.000000	0.71417	0.618000	0.29105	0.173000	0.22820	5.560000	0.67332	2.579000	0.87056	0.557000	0.71058	CGC		0.458	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		T	158549277	C	T	158549277	3	4	26	1	0	0	0	0	1	0	0	0	10953	768	27	1	562	1	OR10X1	1	158549277	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	2665323	158549277	90701344	9	2232										
OR6K3	391114	hgsc.bcm.edu	37	chr1	158687151	158687151	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agtacatgagtgatacactgCcaaagaatatcgggaagacc	10	8	0	4			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:158687151C>A	ENST00000368146.1	-	1	802	c.803G>T	c.(802-804)gGc>gTc	p.G268V	OR6K3_ENST00000368145.1_Missense_Mutation_p.G252V			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G268V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					TGATACACTGCCAAAGAATAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											136	117	124					1																	158687151		2203	4300	6503	156953775	SO:0001583	missense	391114			AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"GPCR / Class A : Olfactory receptors"	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.803G>T	1.37:g.158687151C>A	ENSP00000357128:p.Gly268Val		156953775	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		.	.	.	.	.	.	.	.	.	.	C	14.50	2.552492	0.45487	.	.	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.35605	1.3;1.3	3.77	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.40171	0.1106	M	0.72479	2.2	0.41461	D	0.988045	D	0.64830	0.994	P	0.59012	0.85	T	0.40905	-0.9538	9	0.66056	D	0.02	.	10.3267	0.43798	0.0:0.8989:0.0:0.1011	.	268	Q8NGY3	OR6K3_HUMAN	V	252;268	ENSP00000357127:G252V;ENSP00000357128:G268V	ENSP00000357127:G252V	G	-	2	0	OR6K3	156953775	0.000000	0.05858	0.183000	0.23137	0.118000	0.20060	-0.281000	0.08456	0.907000	0.36646	0.467000	0.42956	GGC		0.448	OR6K3-201	KNOWN	basic	protein_coding	protein_coding				A	158687151	C	A	158687151	3	1	26	1	0	0	0	0	1	0	0	0	11234	739	26	2	194	2	OR6K3	1	158687151	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	137874	158687151	90563470	10	2233										
ELF3	1999	hgsc.bcm.edu	37	chr1	201983015	201983016	+	Frame_Shift_Ins	INS	-	-	AACG													0	0	1	0	0	0	1	1	0	tcctcatccacccggagctcINSaacgagggcctcatgaagtg					rs569552742		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	-	-	-	AACG	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:201983015_201983016insAACG	ENST00000359651.3	+	7	4056_4057	c.864_865insAACG	c.(865-867)aacfs	p.-290fs	ELF3_ENST00000367283.3_Frame_Shift_Ins_p.-290fs|ELF3_ENST00000367284.5_Frame_Shift_Ins_p.-290fs|RP11-510N19.5_ENST00000504773.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.G291fs*11(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						ACCCGGAGCTCAACGAGGGCCT	0.594																																																1	Insertion - Frameshift(1)	large_intestine(1)	1																																								200249639	SO:0001589	frameshift_variant	1999			AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.865_868dupAACG	1.37:g.201983016_201983019dupAACG	ENSP00000352673:p.Glu290fs		200249638		Frame_Shift_Ins	INS	ENST00000359651.3	37	CCDS1419.1																																																																																				0.594	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		AACG	201983016	-	AACG	201983015	7	5	26	1	0	1	1	0	0	0	0	0	5068	813	29	0	890	0	ELF3	1	201983015	Frame_Shift_Ins	INS	-	TCGA-AG-3599-01A-02W-0833-10	43295864	201983015	47267606	11	2234										
ADORA1	134	hgsc.bcm.edu	37	chr1	203098226	203098226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgcctcatggttgcctgtcCggtcctcatcctcacccaga	8	17	3	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr1:203098226C>T	ENST00000367236.4	+	2	1178	c.257C>T	c.(256-258)cCg>cTg	p.P86L	ADORA1_ENST00000337894.4_Missense_Mutation_p.P86L|ADORA1_ENST00000367235.1_Missense_Mutation_p.P86L|RP11-335O13.7_ENST00000421055.1_RNA|ADORA1_ENST00000309502.3_Missense_Mutation_p.P86L	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	86					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)	p.P86L(2)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	GTTGCCTGTCCGGTCCTCATC	0.627																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	1											194	177	182					1																	203098226		2203	4300	6503	201364849	SO:0001583	missense	134			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.257C>T	1.37:g.203098226C>T	ENSP00000356205:p.Pro86Leu		201364849	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1	.	.	.	.	.	.	.	.	.	.	C	9.697	1.153357	0.21371	.	.	ENSG00000163485	ENST00000309502;ENST00000367236;ENST00000337894;ENST00000367235	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.157286	0.56097	D	0.000027	T	0.12008	0.0292	N	0.04508	-0.205	0.58432	D	0.999999	P;B	0.35481	0.504;0.004	B;B	0.29440	0.102;0.002	T	0.18967	-1.0320	10	0.09338	T	0.73	-9.5203	12.0785	0.53657	0.0:0.9208:0.0:0.0792	.	119;86	B7Z379;P30542	.;AA1R_HUMAN	L	86	ENSP00000308549:P86L;ENSP00000356205:P86L;ENSP00000338435:P86L;ENSP00000356204:P86L	ENSP00000308549:P86L	P	+	2	0	ADORA1	201364849	0.999000	0.42202	0.997000	0.53966	0.987000	0.75469	4.088000	0.57678	2.389000	0.81357	0.655000	0.94253	CCG		0.627	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		T	203098226	C	T	203098226	3	4	26	1	0	0	0	0	1	0	0	0	326	652	23	1	259	1	ADORA1	1	203098226	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	1115211	203098226	46152395	12	2235										
NBAS	51594	hgsc.bcm.edu	37	chr2	15415752	15415752	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggacttgtttaatgagatgAgggtctccagtccagaacaa	12	7	1	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:15415752A>T	ENST00000281513.5	-	44	5605	c.5580T>A	c.(5578-5580)ccT>ccA	p.P1860P	NBAS_ENST00000441750.1_Silent_p.P1740P	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1860					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.P1860P(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TAATGAGATGAGGGTCTCCAG	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	2											109	107	108					2																	15415752		2203	4300	6503	15333203	SO:0001819	synonymous_variant	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.5580T>A	2.37:g.15415752A>T			15333203	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.327219	0.24080	.	.	ENSG00000151779	ENST00000442506	.	.	.	5.57	1.78	0.24846	.	.	.	.	.	T	0.53867	0.1823	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44050	-0.9353	4	.	.	.	.	6.1768	0.20449	0.574:0.3101:0.1159:0.0	.	.	.	.	H	908	.	.	L	-	2	0	NBAS	15333203	0.802000	0.28943	1.000000	0.80357	0.972000	0.66771	-0.088000	0.11198	0.457000	0.26962	0.482000	0.46254	CTC		0.483	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15415752	A	T	15415752	2	4	26	1	0	0	0	0	0	0	0	1	10216	291	11	5		5	NBAS	2	15415752	Silent	SNP	A	TCGA-AG-3599-01A-02W-0833-10		15415752	227783621	13	2236										
SPRED2	200734	hgsc.bcm.edu	37	chr2	65541139	65541139	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcgcccttggcgaagcgcacGtaggaggagtccgcgtcctc	14	14	0	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:65541139G>A	ENST00000356388.4	-	6	942	c.753C>T	c.(751-753)taC>taT	p.Y251Y	SPRED2_ENST00000443619.2_Silent_p.Y248Y|SPRED2_ENST00000474228.1_5'Flank	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	251	KBD. {ECO:0000255|PROSITE- ProRule:PRU00821}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.Y251Y(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						CGAAGCGCACGTAGGAGGAGT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	2											66	64	65					2																	65541139		2203	4300	6503	65394643	SO:0001819	synonymous_variant	200734			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.753C>T	2.37:g.65541139G>A			65394643	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Silent	SNP	ENST00000356388.4	37	CCDS33211.1																																																																																				0.652	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			A	65541139	G	A	65541139	2	1	26	1	0	0	0	0	0	0	0	1	15132	1140	40	1		1	SPRED2	2	65541139	Silent	SNP	G	TCGA-AG-3599-01A-02W-0833-10	50125387	65541139	177658234	14	2237										
IL1R2	7850	hgsc.bcm.edu	37	chr2	102641110	102641110	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcgcctacccgggaggccgCgtgaccgaggggccacgcca	16	16	0	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:102641110C>T	ENST00000332549.3	+	7	1096	c.867C>T	c.(865-867)cgC>cgT	p.R289R	IL1R2_ENST00000393414.2_Silent_p.R289R|IL1R2_ENST00000485335.1_3'UTR|IL1R2_ENST00000441002.1_Silent_p.R289R	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	289	Ig-like C2-type 3.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R289R(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						CGGGAGGCCGCGTGACCGAGG	0.577																																					Pancreas(106;189 1628 2302 5133 12295)											1	Substitution - coding silent(1)	large_intestine(1)	2											51	48	49					2																	102641110		2203	4300	6503	102007542	SO:0001819	synonymous_variant	7850			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.867C>T	2.37:g.102641110C>T			102007542	D3DVJ5|Q6LCE6|Q9UE68	Silent	SNP	ENST00000332549.3	37	CCDS2054.1																																																																																				0.577	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		T	102641110	C	T	102641110	2	4	26	1	0	0	0	0	0	0	0	1	7680	755	27	1		1	IL1R2	2	102641110	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10	37099971	102641110	140558263	15	2238										
BUB1	699	hgsc.bcm.edu	37	chr2	111425403	111425403	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctttatcacaagctgaagaTatcactccagaaagctctga	6	10	4	4			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:111425403T>C	ENST00000302759.6	-	7	709	c.591A>G	c.(589-591)atA>atG	p.I197M	BUB1_ENST00000409311.1_Missense_Mutation_p.I197M|BUB1_ENST00000535254.1_Missense_Mutation_p.I177M	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	197					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I197M(1)		breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		AAGCTGAAGATATCACTCCAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											151	163	159					2																	111425403		2203	4300	6503	111141874	SO:0001583	missense	699			AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.591A>G	2.37:g.111425403T>C	ENSP00000302530:p.Ile197Met		111141874	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.961068	0.34565	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.30182	2.27;1.54;2.54	5.73	-9.39	0.00619	.	2.908700	0.00649	N	0.000541	T	0.10680	0.0261	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.10450	0.005;0.004;0.004	T	0.21042	-1.0257	10	0.34782	T	0.22	7.9325	7.6836	0.28528	0.3397:0.4916:0.0:0.1687	.	177;197;197	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	M	177;197;197;197	ENSP00000441013:I177M;ENSP00000386701:I197M;ENSP00000302530:I197M	ENSP00000302530:I197M	I	-	3	3	BUB1	111141874	0.000000	0.05858	0.000000	0.03702	0.968000	0.65278	-1.662000	0.01970	-1.702000	0.01411	-0.250000	0.11733	ATA		0.318	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		C	111425403	T	C	111425403	3	2	26	1	0	0	0	0	1	0	0	0	1573	1396	49	4	2742	4	BUB1	2	111425403	Missense_Mutation	SNP	T	TCGA-AG-3599-01A-02W-0833-10	8784293	111425403	131773970	16	2239										
CSRNP3	80034	hgsc.bcm.edu	37	chr2	166536038	166536038	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcctcttccgaaaatgatagCggtgtgccctgcaatagttt	9	10	1	1	rs144711438		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:166536038C>T	ENST00000342316.4	+	5	1805	c.1533C>T	c.(1531-1533)agC>agT	p.S511S	CSRNP3_ENST00000409420.1_Silent_p.S543S|CSRNP3_ENST00000314499.7_Silent_p.S511S	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	511					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S511S(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						AAAATGATAGCGGTGTGCCCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	0,4406		0,0,2203	93	78	83		1533,1533	-0.1	0	2	dbSNP_134	83	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CSRNP3	NM_001172173.1,NM_024969.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	511/586,511/586	166536038	1,13005	2203	4300	6503	166244284	SO:0001819	synonymous_variant	80034			AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1533C>T	2.37:g.166536038C>T			166244284	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Silent	SNP	ENST00000342316.4	37	CCDS2225.1																																																																																				0.502	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		T	166536038	C	T	166536038	2	4	26	1	0	0	0	0	0	0	0	1	3971	767	27	1		1	CSRNP3	2	166536038	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10	55110635	166536038	76663335	17	2240										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212295748	212295748	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaatctgtgattttcacatgGtttggagatttcactaagac	8	6	3	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:212295748G>T	ENST00000342788.4	-	21	2875	c.2565C>A	c.(2563-2565)aaC>aaA	p.N855K	ERBB4_ENST00000436443.1_Missense_Mutation_p.N855K|ERBB4_ENST00000402597.1_Missense_Mutation_p.N845K	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	855	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N855K(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TTTTCACATGGTTTGGAGATT	0.418										TSP Lung(8;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	2											146	140	142					2																	212295748		2203	4300	6503	212003993	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2565C>A	2.37:g.212295748G>T	ENSP00000342235:p.Asn855Lys		212003993	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.516741	0.64634	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.62105	0.05;0.05;0.05	5.04	3.12	0.35913	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	N	0.25094	0.71	0.80722	D	1	D;P;D;D	0.58970	0.965;0.908;0.98;0.984	P;P;P;P	0.53518	0.452;0.523;0.607;0.728	T	0.55692	-0.8101	10	0.72032	D	0.01	.	7.3936	0.26923	0.2925:0.0:0.7075:0.0	.	845;845;855;855	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	K	855;855;845	ENSP00000342235:N855K;ENSP00000403204:N855K;ENSP00000385565:N845K	ENSP00000342235:N855K	N	-	3	2	ERBB4	212003993	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.334000	0.33827	0.514000	0.28300	0.563000	0.77884	AAC		0.418	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212295748	G	T	212295748	3	4	26	1	0	0	0	0	1	0	0	0	5222	1252	44	2	1393	2	ERBB4	2	212295748	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	45759710	212295748	30903625	18	2241										
GBX2	2637	hgsc.bcm.edu	37	chr2	237074648	237074648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggacgacgatcttagggttcCgggagggctcccctgtcttg	15	11	2	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr2:237074648C>T	ENST00000306318.4	-	2	1353	c.956G>A	c.(955-957)cGg>cAg	p.R319Q	GBX2_ENST00000465889.1_5'UTR|AC079135.1_ENST00000483218.1_RNA|GBX2_ENST00000551105.1_3'UTR|AC079135.1_ENST00000415226.1_RNA	NM_001485.2	NP_001476.2	P52951	GBX2_HUMAN	gastrulation brain homeobox 2	319					autonomic nervous system development (GO:0048483)|axon guidance (GO:0007411)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellum development (GO:0021549)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|patterning of blood vessels (GO:0001569)|rhombomere 2 development (GO:0021568)|thalamus development (GO:0021794)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R319Q(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)		CTTAGGGTTCCGGGAGGGCTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	2											122	112	115					2																	237074648		2203	4300	6503	236739387	SO:0001583	missense	2637			AF118452	CCDS2515.1	2q37.2	2012-03-09	2005-12-22		ENSG00000168505	ENSG00000168505		"Homeoboxes / ANTP class : HOXL subclass"	4186	protein-coding gene	gene with protein product		601135	"gastrulation brain homeo box 2"			9346236, 8838315	Standard	XM_005246071		Approved		uc002vvw.1	P52951	OTTHUMG00000133294	ENST00000306318.4:c.956G>A	2.37:g.237074648C>T	ENSP00000302251:p.Arg319Gln		236739387	B2RPH7|O43833|Q53RX5|Q9Y5Y1	Missense_Mutation	SNP	ENST00000306318.4	37	CCDS2515.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334566	0.81801	.	.	ENSG00000168505	ENST00000306318	D	0.91894	-2.93	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.88470	0.6445	L	0.41236	1.265	0.80722	D	1	P	0.42973	0.796	B	0.38156	0.266	D	0.88924	0.3368	10	0.42905	T	0.14	-18.1377	17.5569	0.87894	0.0:1.0:0.0:0.0	.	319	P52951	GBX2_HUMAN	Q	319	ENSP00000302251:R319Q	ENSP00000302251:R319Q	R	-	2	0	GBX2	236739387	0.999000	0.42202	0.984000	0.44739	0.996000	0.88848	7.692000	0.84203	2.133000	0.65898	0.561000	0.74099	CGG		0.592	GBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257078.3	NM_001485		T	237074648	C	T	237074648	3	4	26	1	0	0	0	0	1	0	0	0	6301	652	23	1	94	1	GBX2	2	237074648	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	24778900	237074648	6124725	19	2242										
UROC1	131669	hgsc.bcm.edu	37	chr3	126207087	126207087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ggcgacccaggtggctccgcGacaggcatctcccacgaagt	13	15	1	0	rs199874583		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr3:126207087G>A	ENST00000290868.2	-	18	1797	c.1744C>T	c.(1744-1746)Cgc>Tgc	p.R582C	UROC1_ENST00000383579.3_Missense_Mutation_p.R642C	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	582					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)	p.R582C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		GTGGCTCCGCGACAGGCATCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											130	128	129					3																	126207087		2203	4300	6503	127689777	SO:0001583	missense	131669			AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1744C>T	3.37:g.126207087G>A	ENSP00000290868:p.Arg582Cys		127689777	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	37	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.037335	0.54896	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.46819	0.86;0.86	5.46	3.56	0.40772	Urocanase domain (2);	0.000000	0.85682	D	0.000000	T	0.68403	0.2997	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.71520	-0.4568	10	0.87932	D	0	-13.3842	8.09	0.30795	0.0846:0.0:0.7579:0.1575	.	642;582	E9PE13;Q96N76	.;HUTU_HUMAN	C	582;642	ENSP00000290868:R582C;ENSP00000373073:R642C	ENSP00000290868:R582C	R	-	1	0	UROC1	127689777	1.000000	0.71417	0.770000	0.31555	0.413000	0.31143	2.962000	0.49176	1.295000	0.44724	0.591000	0.81541	CGC		0.612	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		A	126207087	G	A	126207087	3	1	26	1	0	0	0	0	1	0	0	0	17068	1058	37	1	298	1	UROC1	3	126207087	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		126207087	71815343	20	2243										
FAT4	79633	hgsc.bcm.edu	37	chr4	126355455	126355455	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcatagtagatgatgtcaaTgacaatgtccccacatttgc	8	9	2	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr4:126355455T>C	ENST00000394329.3	+	7	7087	c.7074T>C	c.(7072-7074)aaT>aaC	p.N2358N	FAT4_ENST00000335110.5_Silent_p.N656N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2358	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N2358N(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATGATGTCAATGACAATGTCC	0.383																																																2	Substitution - coding silent(2)	large_intestine(2)	4											187	158	168					4																	126355455		2203	4300	6503	126574905	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7074T>C	4.37:g.126355455T>C			126574905	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.383	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126355455	T	C	126355455	2	2	26	1	0	0	0	0	0	0	0	1	5711	1461	51	4		4	FAT4	4	126355455	Silent	SNP	T	TCGA-AG-3599-01A-02W-0833-10		126355455	64798821	21	2244										
GLRB	2743	hgsc.bcm.edu	37	chr4	158065029	158065029	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttttacatgatgggggtctaCgccccaactctgctcattgt	9	11	3	1	rs147320218		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr4:158065029C>T	ENST00000264428.4	+	8	1092	c.822C>T	c.(820-822)taC>taT	p.Y274Y	GLRB_ENST00000512619.1_Intron|GLRB_ENST00000541722.1_Silent_p.Y274Y|GLRB_ENST00000509282.1_Silent_p.Y274Y	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	274					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)	p.Y274Y(1)		central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	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)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	TGGGGGTCTACGCCCCAACTC	0.532													C|||	1	0.000199681	0	0	5008	,	,		17032	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						C	,,	1,4405	2.1+/-5.4	0,1,2202	182	139	153		822,822,822	-11.9	0.1	4	dbSNP_134	153	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	GLRB	NM_000824.4,NM_001166060.1,NM_001166061.1	,,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,,	274/498,274/498,274/304	158065029	4,13002	2203	4300	6503	158284479	SO:0001819	synonymous_variant	2743			U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.822C>T	4.37:g.158065029C>T			158284479	A8K3K2|D3DP23|F5GWE1	Silent	SNP	ENST00000264428.4	37	CCDS3796.1																																																																																				0.532	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		T	158065029	C	T	158065029	2	4	26	1	0	0	0	0	0	0	0	1	6478	547	19	1		1	GLRB	4	158065029	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10	31709574	158065029	33089247	22	2245										
APC	324	hgsc.bcm.edu	37	chr5	112163652	112163652	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctatgctctatgaaaggctgCatgagagcacttgtggccca	11	10	1	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr5:112163652C>A	ENST00000457016.1	+	13	1955	c.1575C>A	c.(1573-1575)tgC>tgA	p.C525*	APC_ENST00000257430.4_Nonsense_Mutation_p.C525*|APC_ENST00000508376.2_Nonsense_Mutation_p.C525*|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.A21E			P25054	APC_HUMAN	adenomatous polyposis coli	525	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.C525*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGAAAGGCTGCATGAGAGCAC	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											90	88	88					5																	112163652		2202	4300	6502	112191551	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1575C>A	5.37:g.112163652C>A	ENSP00000413133:p.Cys525*		112191551	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	7.036883	0.98017	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.43	4.33	0.51752	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1749	12.8833	0.58030	0.0:0.8886:0.0:0.1114	.	.	.	.	X	525;507;525;525;525	.	ENSP00000257430:C525X	C	+	3	2	APC	112191551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.379000	0.44318	2.703000	0.92315	0.650000	0.86243	TGC		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112163652	C	A	112163652	4	1	26	1	0	0	0	0	0	1	0	0	763	718	25	2	1621	2	APC	5	112163652	Nonsense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10		112163652	68751608	23	2246										
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	26	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	11987	112175639	68739621	24	2247										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129019948	129019948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	acacaagctgggaagattgcGatgccacttgtggaggaggt	15	7	0	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr5:129019948G>A	ENST00000274487.4	+	18	2927	c.2782G>A	c.(2782-2784)Gat>Aat	p.D928N	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	928	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D928N(1)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		GGAAGATTGCGATGCCACTTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	74	75					5																	129019948		2203	4300	6503	129047847	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2782G>A	5.37:g.129019948G>A	ENSP00000274487:p.Asp928Asn		129047847		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028928	0.35797	.	.	ENSG00000145808	ENST00000274487	T	0.60920	0.15	4.56	2.77	0.32553	.	0.227351	0.37393	N	0.002109	T	0.36853	0.0982	N	0.17082	0.46	0.34979	D	0.753911	B	0.14438	0.01	B	0.06405	0.002	T	0.36040	-0.9764	9	.	.	.	.	10.9237	0.47180	0.1578:0.0:0.8422:0.0	.	928	Q8TE59	ATS19_HUMAN	N	928	ENSP00000274487:D928N	.	D	+	1	0	ADAMTS19	129047847	0.960000	0.32886	0.934000	0.37439	0.982000	0.71751	1.628000	0.37060	0.839000	0.34971	-0.143000	0.13931	GAT		0.403	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		A	129019948	G	A	129019948	3	1	26	1	0	0	0	0	1	0	0	0	264	1058	37	1	2852	1	ADAMTS19	5	129019948	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	16844309	129019948	51895312	25	2248										
JARID2	3720	hgsc.bcm.edu	37	chr6	15487765	15487765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atcggtcggctcaggacttaCggaaacaggtaaagtccagc	12	10	1	0	rs375479047		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr6:15487765C>T	ENST00000341776.2	+	6	1142	c.898C>T	c.(898-900)Cgg>Tgg	p.R300W	JARID2_ENST00000397311.3_Missense_Mutation_p.R128W|JARID2_ENST00000541660.1_Missense_Mutation_p.R262W	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	300					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R300W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TCAGGACTTACGGAAACAGGT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											22	24	23					6																	15487765		2203	4300	6503	15595744	SO:0001583	missense	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.898C>T	6.37:g.15487765C>T	ENSP00000341280:p.Arg300Trp		15595744	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.914234	0.72983	.	.	ENSG00000008083	ENST00000538175;ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.36520	1.25;1.25;1.25	5.17	3.25	0.37280	.	0.053996	0.64402	D	0.000001	T	0.34948	0.0915	L	0.29908	0.895	0.47476	D	0.999434	D;D;D	0.89917	1.0;1.0;0.998	D;D;P	0.74674	0.973;0.984;0.803	T	0.34378	-0.9831	10	0.87932	D	0	-11.8615	13.0654	0.59030	0.4525:0.5475:0.0:0.0	.	262;164;300	F5H590;B7Z7X9;Q92833	.;.;JARD2_HUMAN	W	164;300;128;262	ENSP00000341280:R300W;ENSP00000380478:R128W;ENSP00000444623:R262W	ENSP00000341280:R300W	R	+	1	2	JARID2	15595744	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	0.909000	0.28558	1.284000	0.44531	0.561000	0.74099	CGG		0.592	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15487765	C	T	15487765	3	4	26	1	0	0	0	0	1	0	0	0	7966	527	19	1	920	1	JARID2	6	15487765	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10		15487765	155627302	26	2249										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39033490	39033490	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtctccccaccccagtgcCgcagggccacgtgtaccggt	12	17	1	0	rs201355669		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr6:39033490C>T	ENST00000373256.4	+	4	330	c.287C>T	c.(286-288)cCg>cTg	p.P96L		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	96					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.P96L(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	ACCCCAGTGCCGCAGGGCCAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											27	22	24					6																	39033490		2195	4289	6484	39141468	SO:0001583	missense	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.287C>T	6.37:g.39033490C>T	ENSP00000362353:p.Pro96Leu		39141468	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	C	9.366	1.069280	0.20147	.	.	ENSG00000112164	ENST00000373256	T	0.63417	-0.04	4.97	0.234	0.15390	GPCR, family 2, extracellular hormone receptor domain (3);	0.599918	0.14760	N	0.300046	T	0.17789	0.0427	N	0.20685	0.6	0.25144	N	0.990475	B	0.02656	0.0	B	0.01281	0.0	T	0.13710	-1.0499	10	0.22109	T	0.4	.	3.7531	0.08575	0.1598:0.2357:0.0:0.6045	.	96	P43220	GLP1R_HUMAN	L	96	ENSP00000362353:P96L	ENSP00000362353:P96L	P	+	2	0	GLP1R	39141468	0.190000	0.23276	0.998000	0.56505	0.921000	0.55340	0.236000	0.17967	0.747000	0.32809	-0.696000	0.03686	CCG		0.647	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			T	39033490	C	T	39033490	3	4	26	1	0	0	0	0	1	0	0	0	6472	652	23	1	301	1	GLP1R	6	39033490	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	23545725	39033490	132081577	27	2250										
NDUFAF4	29078	hgsc.bcm.edu	37	chr6	97344645	97344645	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaagacacaggatctttgGaatcaacatacacatctttt	7	8	3	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr6:97344645G>C	ENST00000316149.7	-	2	294	c.215C>G	c.(214-216)tCc>tGc	p.S72C	NDUFAF4_ENST00000489477.1_5'UTR	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	72					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)		p.S72C(1)		large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						AGGATCTTTGGAATCAACATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											146	147	147					6																	97344645		2203	4300	6503	97451366	SO:0001583	missense	29078			AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.215C>G	6.37:g.97344645G>C	ENSP00000358272:p.Ser72Cys		97451366	B2R4J5	Missense_Mutation	SNP	ENST00000316149.7	37	CCDS5037.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852547	0.71719	.	.	ENSG00000123545	ENST00000316149	D	0.90324	-2.65	3.93	3.93	0.45458	.	0.000000	0.85682	D	0.000000	D	0.95595	0.8568	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.96523	0.9387	10	0.87932	D	0	.	16.5355	0.84372	0.0:0.0:1.0:0.0	.	72	Q9P032	NDUF4_HUMAN	C	72	ENSP00000358272:S72C	ENSP00000358272:S72C	S	-	2	0	NDUFAF4	97451366	1.000000	0.71417	0.998000	0.56505	0.861000	0.49209	6.374000	0.73132	2.191000	0.70037	0.557000	0.71058	TCC		0.358	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		C	97344645	G	C	97344645	3	2	26	1	0	0	0	0	1	0	0	0	10308	1174	41	5	320	5	NDUFAF4	6	97344645	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	58311155	97344645	73770422	28	2251										
SASH1	23328	hgsc.bcm.edu	37	chr6	148846474	148846474	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgacgaatcgctctctgcaCgttggcagtaataattctga	9	9	2	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr6:148846474C>T	ENST00000367467.3	+	11	1732	c.1257C>T	c.(1255-1257)caC>caT	p.H419H	AL033378.1_ENST00000411390.2_RNA	NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	419					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.H419H(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCTCTCTGCACGTTGGCAGTA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	6											198	183	188					6																	148846474		2203	4300	6503	148888167	SO:0001819	synonymous_variant	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1257C>T	6.37:g.148846474C>T			148888167	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																				0.438	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		T	148846474	C	T	148846474	2	4	26	1	0	0	0	0	0	0	0	1	13885	535	19	1		1	SASH1	6	148846474	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10	51501829	148846474	22268593	29	2252										
NOX3	50508	hgsc.bcm.edu	37	chr6	155750013	155750013	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtccagtctcctgctgcccGgatgtgcacgctgaaaaagt	11	12	1	1	rs563228632		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr6:155750013G>A	ENST00000159060.2	-	9	1162	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	354	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.R354W(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		CCTGCTGCCCGGATGTGCACG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											55	58	57					6																	155750013		2203	4300	6503	155791705	SO:0001583	missense	50508			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.1060C>T	6.37:g.155750013G>A	ENSP00000159060:p.Arg354Trp		155791705	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962220	0.74016	.	.	ENSG00000074771	ENST00000159060	D	0.93712	-3.27	5.78	3.89	0.44902	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.101925	0.41500	D	0.000866	D	0.97742	0.9259	H	0.98048	4.135	0.44780	D	0.997787	D	0.89917	1.0	D	0.87578	0.998	D	0.99204	1.0874	10	0.87932	D	0	-21.0121	14.5669	0.68182	0.0:0.0:0.5795:0.4205	.	354	Q9HBY0	NOX3_HUMAN	W	354	ENSP00000159060:R354W	ENSP00000159060:R354W	R	-	1	2	NOX3	155791705	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.258000	0.51507	1.420000	0.47138	0.557000	0.71058	CGG		0.622	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			A	155750013	G	A	155750013	3	1	26	1	0	0	0	0	1	0	0	0	10588	1115	39	1	666	1	NOX3	6	155750013	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	6903539	155750013	15365054	30	2253										
AASS	10157	hgsc.bcm.edu	37	chr7	121769447	121769447	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcatccaacaagcccatatTggcctcctgagcttttattg	6	13	1	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr7:121769447T>C	ENST00000393376.1	-	2	450	c.355A>G	c.(355-357)Aat>Gat	p.N119D	AASS_ENST00000417368.2_Missense_Mutation_p.N119D|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	119	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.N119D(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						AAGCCCATATTGGCCTCCTGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	7											60	59	59					7																	121769447		2203	4300	6503	121556683	SO:0001583	missense	10157			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.355A>G	7.37:g.121769447T>C	ENSP00000377040:p.Asn119Asp		121556683	O95462	Missense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	26.6	4.754380	0.89843	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.77489	-1.1;-1.1	5.3	5.3	0.74995	Alanine dehydrogenase/PNT, N-terminal (1);	0.134054	0.64402	D	0.000003	D	0.89959	0.6866	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.90965	0.4815	10	0.42905	T	0.14	-18.6832	15.5046	0.75728	0.0:0.0:0.0:1.0	.	119	Q9UDR5	AASS_HUMAN	D	119	ENSP00000377040:N119D;ENSP00000403768:N119D	ENSP00000351834:N119D	N	-	1	0	AASS	121556683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.986000	0.88173	2.126000	0.65437	0.482000	0.46254	AAT		0.308	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		C	121769447	T	C	121769447	3	2	26	1	0	0	0	0	1	0	0	0	24	1812	63	4	2513	4	AASS	7	121769447	Missense_Mutation	SNP	T	TCGA-AG-3599-01A-02W-0833-10		121769447	37369216	31	2254										
WDR91	29062	hgsc.bcm.edu	37	chr7	134881005	134881005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	agggcctgccgaggatgcccGagtcagtggctccactggct	15	13	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr7:134881005G>A	ENST00000354475.4	-	8	1166	c.1135C>T	c.(1135-1137)Cgg>Tgg	p.R379W	WDR91_ENST00000485942.1_5'Flank|AC009542.2_ENST00000412549.2_RNA|WDR91_ENST00000344400.5_Missense_Mutation_p.R379W|WDR91_ENST00000423565.1_Missense_Mutation_p.R344W	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	379								p.R379W(1)|p.R379R(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GAGGATGCCCGAGTCAGTGGC	0.622																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	7											47	48	47					7																	134881005		2203	4300	6503	134531545	SO:0001583	missense	29062			AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1135C>T	7.37:g.134881005G>A	ENSP00000346466:p.Arg379Trp		134531545	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.574753	0.65878	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.66638	1.26;-0.22;0.36	5.76	2.54	0.30619	.	0.466175	0.21671	N	0.070875	T	0.65123	0.2661	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	P	0.53490	0.727	T	0.61501	-0.7050	10	0.87932	D	0	-21.1383	14.1144	0.65144	0.0:0.0:0.4626:0.5374	.	379	A4D1P6	WDR91_HUMAN	W	379;379;344	ENSP00000340877:R379W;ENSP00000346466:R379W;ENSP00000392555:R344W	ENSP00000340877:R379W	R	-	1	2	WDR91	134531545	0.027000	0.19231	0.246000	0.24233	0.022000	0.10575	1.186000	0.32078	0.721000	0.32231	0.650000	0.86243	CGG		0.622	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134881005	G	A	134881005	3	1	26	1	0	0	0	0	1	0	0	0	17378	1057	37	1	1140	1	WDR91	7	134881005	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	13111558	134881005	24257658	32	2255										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72964994	72964994	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccttgcagcaaagtgaagtgCagtgttcttttgaagaaaaa	10	6	1	3	rs373925434		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr8:72964994C>A	ENST00000262209.4	-	14	1858	c.1651G>T	c.(1651-1653)Gca>Tca	p.A551S	RP11-383H13.1_ENST00000457356.4_3'UTR|RP11-383H13.1_ENST00000537896.1_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	551					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.A551S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	AAGTGAAGTGCAGTGTTCTTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											111	95	101					8																	72964994		2203	4300	6503	73127548	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1651G>T	8.37:g.72964994C>A	ENSP00000262209:p.Ala551Ser		73127548	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452975	0.63290	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.75367	-0.93;-0.93	4.98	4.98	0.66077	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.85186	0.5639	M	0.70787	2.145	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	D	0.84923	0.0855	10	0.42905	T	0.14	-4.5381	18.6199	0.91317	0.0:1.0:0.0:0.0	.	551	O75762	TRPA1_HUMAN	S	403;551	ENSP00000428151:A403S;ENSP00000262209:A551S	ENSP00000262209:A551S	A	-	1	0	TRPA1	73127548	1.000000	0.71417	0.143000	0.22291	0.154000	0.21943	6.881000	0.75584	2.466000	0.83321	0.585000	0.79938	GCA		0.448	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72964994	C	A	72964994	3	1	26	1	0	0	0	0	1	0	0	0	16617	710	25	2	1764	2	TRPA1	8	72964994	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10		72964994	73399028	33	2256										
ERMP1	79956	hgsc.bcm.edu	37	chr9	5787593	5787593	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agaaggacatatggcttggtCctgtaaggtaaaaggaagaa	13	4	0	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr9:5787593C>A	ENST00000339450.5	-	14	2476	c.2387G>T	c.(2386-2388)gGa>gTa	p.G796V	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_3'UTR|ERMP1_ENST00000543230.1_Splice_Site_p.M390I	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	796						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.G796V(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		ATGGCTTGGTCCTGTAAGGTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											122	118	119					9																	5787593		2203	4300	6503	5777593	SO:0001630	splice_region_variant	79956			AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.2387-1G>T	9.37:g.5787593C>A			5777593	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.31|10.31	1.315241|1.315241	0.23908|0.23908	.|.	.|.	ENSG00000099219|ENSG00000099219	ENST00000339450|ENST00000543230	T|.	0.57273|.	0.41|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72669|0.72669	0.3489|0.3489	M|M	0.67397|0.67397	2.05|2.05	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.77004|.	0.989|.	T|T	0.65134|0.65134	-0.6242|-0.6242	10|6	0.42905|0.17832	T|T	0.14|0.49	.|.	19.577|19.577	0.95449|0.95449	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	796|.	Q7Z2K6|.	ERMP1_HUMAN|.	V|I	796|390	ENSP00000340427:G796V|.	ENSP00000340427:G796V|ENSP00000417474:M812I	G|M	-|-	2|3	0|0	ERMP1|ERMP1	5777593|5777593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.230000|0.230000	0.25150|0.25150	6.848000|6.848000	0.75409|0.75409	2.798000|2.798000	0.96311|0.96311	0.650000|0.650000	0.86243|0.86243	GGA|ATG		0.423	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	Missense_Mutation	A	5787593	C	A	5787593	5	1	26	1	0	0	0	0	0	0	1	0	5249	869	30	2	335	2	ERMP1	9	5787593	Splice_Site	SNP	C	TCGA-AG-3599-01A-02W-0833-10		5787593	135425838	34	2257										
ABCA1	19	hgsc.bcm.edu	37	chr9	107556758	107556758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgtgggaagatcaagaacaCggacttcaggatatcattga	11	6	3	3	rs372779604		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr9:107556758C>T	ENST00000374736.3	-	40	5810	c.5416G>A	c.(5416-5418)Gtg>Atg	p.V1806M		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1806					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.V1806M(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	ATCAAGAACACGGACTTCAGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	MET/VAL	0,4406		0,0,2203	88	80	83		5416	5.5	1	9		83	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCA1	NM_005502.3	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1806/2262	107556758	1,13005	2203	4300	6503	106596579	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.5416G>A	9.37:g.107556758C>T	ENSP00000363868:p.Val1806Met		106596579	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.163143	0.78226	0.0	1.16E-4	ENSG00000165029	ENST00000374736	D	0.89343	-2.5	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.94991	0.8379	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.95062	0.8196	10	0.72032	D	0.01	.	19.7532	0.96277	0.0:1.0:0.0:0.0	.	1806	O95477	ABCA1_HUMAN	M	1806	ENSP00000363868:V1806M	ENSP00000363868:V1806M	V	-	1	0	ABCA1	106596579	1.000000	0.71417	0.995000	0.50966	0.365000	0.29674	7.772000	0.85439	2.734000	0.93682	0.650000	0.86243	GTG		0.448	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107556758	C	T	107556758	3	4	26	1	0	0	0	0	1	0	0	0	28	536	19	1	1413	1	ABCA1	9	107556758	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	101769165	107556758	33656673	35	2258										
DNM1	1759	hgsc.bcm.edu	37	chr9	130981460	130981460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagaactgcctcatcctggCcgtgtcccccgccaactctg	10	17	2	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr9:130981460C>T	ENST00000372923.3	+	4	610	c.518C>T	c.(517-519)gCc>gTc	p.A173V	DNM1_ENST00000393594.3_Missense_Mutation_p.A173V|DNM1_ENST00000475805.1_Missense_Mutation_p.A173V|DNM1_ENST00000341179.7_Missense_Mutation_p.A173V|DNM1_ENST00000486160.1_Missense_Mutation_p.A173V	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	173	Dynamin-type G.				endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.A173V(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						CTCATCCTGGCCGTGTCCCCC	0.607																																					GBM(113;146 1575 2722 28670 29921)											2	Substitution - Missense(2)	large_intestine(2)	9											117	108	111					9																	130981460		2203	4300	6503	130021281	SO:0001583	missense	1759			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.518C>T	9.37:g.130981460C>T	ENSP00000362014:p.Ala173Val		130021281	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	C	36	5.681647	0.96774	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160	D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64	5.42	5.42	0.78866	Dynamin, GTPase domain (2);	0.000000	0.85682	D	0.000000	D	0.97483	0.9176	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.997	D	0.98030	1.0376	10	0.87932	D	0	-13.2304	19.2078	0.93739	0.0:1.0:0.0:0.0	.	173;173;173	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	V	173;173;173;168;173;173	ENSP00000419225:A173V;ENSP00000345680:A173V;ENSP00000362014:A173V;ENSP00000377219:A173V;ENSP00000420045:A173V	ENSP00000345680:A173V	A	+	2	0	DNM1	130021281	1.000000	0.71417	0.984000	0.44739	0.920000	0.55202	7.818000	0.86416	2.532000	0.85374	0.462000	0.41574	GCC		0.607	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		T	130981460	C	T	130981460	3	4	26	1	0	0	0	0	1	0	0	0	4681	739	26	3	532	3	DNM1	9	130981460	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	23424702	130981460	10231971	36	2259										
C9orf171	389799	hgsc.bcm.edu	37	chr9	135374838	135374838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aattatatcgcaatgaaccgCggggcggtgaaagccggcct	13	10	0	2	rs199521952	byFrequency	TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr9:135374838C>T	ENST00000343036.2	+	4	531	c.483C>T	c.(481-483)cgC>cgT	p.R161R	C9orf171_ENST00000393216.2_Silent_p.R125R|C9orf171_ENST00000393215.3_Silent_p.R125R	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	161								p.R161R(1)		large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						CAATGAACCGCGGGGCGGTGA	0.612													C|||	2	0.000399361	8e-04	0	5008	,	,		17294	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	9						C		0,4406		0,0,2203	72	73	73		483	-10.5	0	9		73	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	C9orf171	NM_207417.1		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		161/321	135374838	3,13003	2203	4300	6503	134364659	SO:0001819	synonymous_variant	389799			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.483C>T	9.37:g.135374838C>T			134364659	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																				0.612	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		T	135374838	C	T	135374838	2	4	26	1	0	0	0	0	0	0	0	1	2476	755	27	1		1	C9orf171	9	135374838	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10	4393378	135374838	5838593	37	2260										
DKK1	22943	hgsc.bcm.edu	37	chr10	54076332	54076332	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggacaagaaggttctgtttGtctccggtcatcagactgtg	12	8	4	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr10:54076332G>C	ENST00000373970.3	+	4	705	c.566G>C	c.(565-567)tGt>tCt	p.C189S	PRKG1-AS1_ENST00000420193.1_RNA	NM_012242.2	NP_036374.1	O94907	DKK1_HUMAN	dickkopf WNT signaling pathway inhibitor 1	189	DKK-type Cys-2.				cell morphogenesis involved in differentiation (GO:0000904)|embryonic limb morphogenesis (GO:0030326)|endoderm formation (GO:0001706)|extracellular negative regulation of signal transduction (GO:1900116)|face morphogenesis (GO:0060325)|forebrain development (GO:0030900)|hair follicle development (GO:0001942)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901296)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway (GO:0090082)|regulation of endodermal cell fate specification (GO:0042663)|regulation of receptor internalization (GO:0002090)|response to retinoic acid (GO:0032526)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|signal transducer activity (GO:0004871)	p.C189S(1)		kidney(2)|large_intestine(4)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	16						GGTTCTGTTTGTCTCCGGTCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											129	119	122					10																	54076332		2203	4300	6503	53746338	SO:0001583	missense	22943				CCDS7246.1	10q11.2	2013-05-15	2013-05-15		ENSG00000107984	ENSG00000107984			2891	protein-coding gene	gene with protein product		605189	"dickkopf (Xenopus laevis) homolog 1", "dickkopf 1 homolog (Xenopus laevis)"				Standard	NM_012242		Approved	SK, DKK-1	uc001jjr.3	O94907	OTTHUMG00000018247	ENST00000373970.3:c.566G>C	10.37:g.54076332G>C	ENSP00000363081:p.Cys189Ser		53746338	B2RC19	Missense_Mutation	SNP	ENST00000373970.3	37	CCDS7246.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.424716	0.62733	.	.	ENSG00000107984	ENST00000373970	T	0.80824	-1.42	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.90594	0.7051	M	0.80183	2.485	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.91013	0.4851	10	0.87932	D	0	-1.9238	19.688	0.95987	0.0:0.0:1.0:0.0	.	189	O94907	DKK1_HUMAN	S	189	ENSP00000363081:C189S	ENSP00000363081:C189S	C	+	2	0	DKK1	53746338	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	9.476000	0.97823	2.756000	0.94617	0.561000	0.74099	TGT		0.418	DKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048100.1			C	54076332	G	C	54076332	3	2	26	1	0	0	0	0	1	0	0	0	4555	1377	48	5	580	5	DKK1	10	54076332	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		54076332	81458415	38	2261										
UNC5B	219699	hgsc.bcm.edu	37	chr10	73057801	73057801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcctagatgcccccaactcaCggggcaatgactggcggatg	13	13	1	2	rs533188246		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr10:73057801C>T	ENST00000335350.6	+	16	3042	c.2626C>T	c.(2626-2628)Cgg>Tgg	p.R876W	UNC5B_ENST00000373192.4_Missense_Mutation_p.R865W	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	876	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)		p.R876W(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						CCCCAACTCACGGGGCAATGA	0.567													C|||	1	0.000199681	0	0	5008	,	,		23320	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	10											117	87	97					10																	73057801		2203	4300	6503	72727807	SO:0001583	missense	219699			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.2626C>T	10.37:g.73057801C>T	ENSP00000334329:p.Arg876Trp		72727807	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301950	0.81136	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	D;D	0.85629	-2.01;-2.01	5.73	4.82	0.62117	Death (2);DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.91693	0.7374	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92455	0.5973	10	0.87932	D	0	-40.9533	12.9927	0.58630	0.4432:0.5568:0.0:0.0	.	865;876	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	W	876;865	ENSP00000334329:R876W;ENSP00000362288:R865W	ENSP00000334329:R876W	R	+	1	2	UNC5B	72727807	0.994000	0.37717	0.893000	0.35052	0.994000	0.84299	3.226000	0.51254	1.402000	0.46780	0.655000	0.94253	CGG		0.567	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73057801	C	T	73057801	3	4	26	1	0	0	0	0	1	0	0	0	17032	527	19	1	2688	1	UNC5B	10	73057801	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	18981469	73057801	62476946	39	2262										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108459130	108459130	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcgaacacctgattctcatCggtgctgataacatgcatgt	9	10	1	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr10:108459130C>A	ENST00000263054.6	-	9	1262	c.1255G>T	c.(1255-1257)Gat>Tat	p.D419Y	SORCS1_ENST00000369698.1_5'Flank|SORCS1_ENST00000344440.6_Missense_Mutation_p.D419Y	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	419					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.D419Y(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TGATTCTCATCGGTGCTGATA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	10											183	146	158					10																	108459130		2203	4300	6503	108449120	SO:0001583	missense	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.1255G>T	10.37:g.108459130C>A	ENSP00000263054:p.Asp419Tyr		108449120	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559410	0.86335	.	.	ENSG00000108018	ENST00000263054;ENST00000344440	T;T	0.25579	1.79;1.79	6.06	6.06	0.98353	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.56775	0.2008	M	0.80847	2.515	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.998;1.0	D;D;D;D;D	0.79784	0.971;0.993;0.993;0.971;0.993	T	0.53272	-0.8462	9	.	.	.	-21.8491	20.6397	0.99537	0.0:1.0:0.0:0.0	.	419;419;419;419;419	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	Y	419	ENSP00000263054:D419Y;ENSP00000345964:D419Y	.	D	-	1	0	SORCS1	108449120	1.000000	0.71417	0.998000	0.56505	0.817000	0.46193	7.433000	0.80362	2.880000	0.98712	0.650000	0.86243	GAT		0.468	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108459130	C	A	108459130	3	1	26	1	0	0	0	0	1	0	0	0	14967	884	31	2	2557	2	SORCS1	10	108459130	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	35401329	108459130	27075617	40	2263										
C11orf66	220004	hgsc.bcm.edu	37	chr11	61252816	61252816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctctctgttccagggcccaCgcttcatgacgtcggagtac	10	15	2	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr11:61252816C>T	ENST00000338608.2	+	6	642	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	RP11-286N22.8_ENST00000544880.1_3'UTR|PPP1R32_ENST00000432063.2_Missense_Mutation_p.R173C	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	173							phosphatase binding (GO:0019902)	p.R173C(1)									CCAGGGCCCACGCTTCATGAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											101	89	93					11																	61252816		2202	4299	6501	61009392	SO:0001583	missense	220004			AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.517C>T	11.37:g.61252816C>T	ENSP00000344140:p.Arg173Cys		61009392	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202113	0.58234	.	.	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.48522	0.81;1.39	4.92	3.97	0.46021	.	0.334264	0.26262	N	0.025382	T	0.63686	0.2532	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.969;0.979	T	0.65809	-0.6078	10	0.56958	D	0.05	-29.3353	11.8968	0.52661	0.1734:0.8266:0.0:0.0	.	173;173	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	C	173	ENSP00000391560:R173C;ENSP00000344140:R173C	ENSP00000344140:R173C	R	+	1	0	C11orf66	61009392	0.126000	0.22350	0.995000	0.50966	0.637000	0.38172	0.764000	0.26532	2.268000	0.75426	0.462000	0.41574	CGC		0.612	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		T	61252816	C	T	61252816	3	4	26	1	0	0	0	0	1	0	0	0	1660	536	19	1	535	1	C11orf66	11	61252816	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10		61252816	73753700	41	2264										
FXYD6	53826	hgsc.bcm.edu	37	chr11	117711884	117711884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggggcttctgattgaaactgCacttgcacctgcgacctgaa	11	11	1	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr11:117711884C>T	ENST00000526014.1	-	5	783	c.188G>A	c.(187-189)tGc>tAc	p.C63Y	FXYD6_ENST00000260282.4_Missense_Mutation_p.C63Y|FXYD6_ENST00000527429.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000584394.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000529335.2_Missense_Mutation_p.C62Y|FXYD6_ENST00000583233.1_5'UTR|FXYD6_ENST00000539526.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000584230.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000530956.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000527717.1_Missense_Mutation_p.C63Y|FXYD6_ENST00000524656.1_Missense_Mutation_p.C63Y|FXYD6-FXYD2_ENST00000532984.1_Intron|FXYD6_ENST00000540359.1_Missense_Mutation_p.C63Y|RP11-728F11.4_ENST00000581173.2_RNA	NM_022003.3	NP_071286.1	Q9H0Q3	FXYD6_HUMAN	FXYD domain containing ion transport regulator 6	63					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)	p.C63Y(1)		central_nervous_system(1)|large_intestine(5)|lung(1)|skin(1)	8	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)		ATTGAAACTGCACTTGCACCT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	11											97	82	87					11																	117711884		2201	4296	6497	117217094	SO:0001583	missense	53826			BC093040	CCDS8387.1	11q23.3	2010-04-14	2002-01-14		ENSG00000137726	ENSG00000137726			4030	protein-coding gene	gene with protein product	"phosphohippolin"	606683	"FXYD domain-containing ion transport regulator 6"			10950925	Standard	NM_022003		Approved			Q9H0Q3		ENST00000526014.1:c.188G>A	11.37:g.117711884C>T	ENSP00000433312:p.Cys63Tyr		117217094	A8K0R4|J3QLD2|Q6FIG9|Q6UW52	Missense_Mutation	SNP	ENST00000526014.1	37	CCDS8387.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041325	0.75732	.	.	ENSG00000137726	ENST00000540359;ENST00000539526;ENST00000260282;ENST00000527717;ENST00000526014;ENST00000524656;ENST00000529335	T;T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22	5.56	5.56	0.83823	.	.	.	.	.	D	0.87680	0.6238	.	.	.	0.58432	D	0.999991	D;D	0.89917	1.0;0.997	D;D	0.77004	0.989;0.964	D	0.88473	0.3063	8	0.62326	D	0.03	.	15.0344	0.71734	0.0:1.0:0.0:0.0	.	63;63	E9PJ02;Q9H0Q3	.;FXYD6_HUMAN	Y	63;63;63;63;63;63;62	ENSP00000444243:C63Y;ENSP00000442756:C63Y;ENSP00000260282:C63Y;ENSP00000431446:C63Y;ENSP00000433312:C63Y;ENSP00000431427:C63Y;ENSP00000436629:C62Y	ENSP00000260282:C63Y	C	-	2	0	FXYD6	117217094	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.008000	0.63991	2.601000	0.87937	0.655000	0.94253	TGC		0.577	FXYD6-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392307.1	NM_022003		T	117711884	C	T	117711884	3	4	26	1	0	0	0	0	1	0	0	0	6141	710	25	3	111	3	FXYD6	11	117711884	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	56459068	117711884	17294632	42	2265										
CHD4	1108	hgsc.bcm.edu	37	chr12	6697516	6697516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catagataataactgtgtcaGcagtggccagattgattcca	9	8	1	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr12:6697516G>A	ENST00000357008.2	-	23	3576	c.3413C>T	c.(3412-3414)gCt>gTt	p.A1138V	CHD4_ENST00000544040.1_Missense_Mutation_p.A1131V|CHD4_ENST00000544484.1_Missense_Mutation_p.A1135V|CHD4_ENST00000309577.6_Missense_Mutation_p.A1138V|CHD4_ENST00000540960.1_5'Flank	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1138	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.A1138V(1)		central_nervous_system(2)	2						AACTGTGTCAGCAGTGGCCAG	0.468																																					Colon(32;586 792 4568 16848 45314)											1	Substitution - Missense(1)	large_intestine(1)	12											85	83	84					12																	6697516		2203	4300	6503	6567777	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.3413C>T	12.37:g.6697516G>A	ENSP00000349508:p.Ala1138Val		6567777	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595032	0.86953	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.77	5.77	0.91146	Helicase, C-terminal (3);	0.127057	0.52532	D	0.000068	D	0.92805	0.7712	H	0.97758	4.07	0.80722	D	1	P;B;D	0.67145	0.51;0.29;0.996	B;B;D	0.73380	0.407;0.353;0.98	D	0.94771	0.7945	10	0.87932	D	0	.	19.598	0.95548	0.0:0.0:1.0:0.0	.	1138;1138;1131	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	V	1135;1131;1138;1138;1112	ENSP00000440392:A1135V;ENSP00000440542:A1131V;ENSP00000312419:A1138V;ENSP00000349508:A1138V	ENSP00000312419:A1138V	A	-	2	0	CHD4	6567777	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.817000	0.99352	2.734000	0.93682	0.436000	0.28706	GCT		0.468	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6697516	G	A	6697516	3	1	26	1	0	0	0	0	1	0	0	0	3333	971	34	3	2397	3	CHD4	12	6697516	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		6697516	127154379	43	2266										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	26	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	18700768	25398284	108453611	44	2267										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41327650	41327650	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgagaacattagaggaaagGataaacatcaagcaagaatt	9	5	1	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr12:41327650G>T	ENST00000551295.2	+	9	1072	c.955G>T	c.(955-957)Gat>Tat	p.D319Y	CNTN1_ENST00000547849.1_Missense_Mutation_p.D319Y|CNTN1_ENST00000347616.1_Missense_Mutation_p.D319Y|CNTN1_ENST00000360099.3_Missense_Mutation_p.D319Y|CNTN1_ENST00000348761.2_Missense_Mutation_p.D308Y|CNTN1_ENST00000547702.1_Missense_Mutation_p.D319Y	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	319	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.D319Y(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TAGAGGAAAGGATAAACATCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											81	82	82					12																	41327650		2203	4299	6502	39613917	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.955G>T	12.37:g.41327650G>T	ENSP00000447006:p.Asp319Tyr		39613917	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709798	0.68730	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	5.11	4.21	0.49690	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.158424	0.53938	D	0.000047	T	0.81049	0.4742	M	0.75447	2.3	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.83588	0.0121	10	0.66056	D	0.02	.	15.219	0.73296	0.0:0.0:0.8581:0.1419	.	319;308;319	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	Y	319;319;319;319;319;308	ENSP00000448004:D319Y;ENSP00000447006:D319Y;ENSP00000448653:D319Y;ENSP00000325660:D319Y;ENSP00000353213:D319Y;ENSP00000261160:D308Y	ENSP00000325660:D319Y	D	+	1	0	CNTN1	39613917	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	9.230000	0.95299	1.280000	0.44463	0.561000	0.74099	GAT		0.333	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41327650	G	T	41327650	3	4	26	1	0	0	0	0	1	0	0	0	3646	1174	41	2	985	2	CNTN1	12	41327650	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	15929366	41327650	92524245	45	2268										
EP400	57634	hgsc.bcm.edu	37	chr12	132530375	132530375	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	cgttgttaactcctgtagccGaatctaccgctcttccaaac	6	14	2	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr12:132530375G>A	ENST00000333577.4	+	40	7347	c.7238G>A	c.(7237-7239)cGa>cAa	p.R2413Q	EP400_ENST00000389561.2_Missense_Mutation_p.R2377Q|EP400_ENST00000332482.4_Missense_Mutation_p.R2340Q|EP400_ENST00000330386.6_Missense_Mutation_p.R2296Q|EP400_ENST00000389562.2_Missense_Mutation_p.R2376Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2413	Myb-like. {ECO:0000255|PROSITE- ProRule:PRU00133}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R2376Q(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		TCCTGTAGCCGAATCTACCGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12											140	104	116					12																	132530375		2203	4300	6503	131096328	SO:0001583	missense	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.7238G>A	12.37:g.132530375G>A	ENSP00000333602:p.Arg2413Gln		131096328	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	17.81	3.480416	0.63849	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.92348	-3.01;-3.0;-3.02;-3.02;-3.0	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.95962	0.8685	M	0.75447	2.3	0.44345	D	0.997238	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.997	D	0.96288	0.9211	10	0.72032	D	0.01	.	18.7731	0.91900	0.0:0.0:1.0:0.0	.	2377;2296;2376	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	Q	2413;2377;2376;2340;2296;2377	ENSP00000333602:R2413Q;ENSP00000374212:R2377Q;ENSP00000374213:R2376Q;ENSP00000331737:R2340Q;ENSP00000330620:R2296Q	ENSP00000330620:R2296Q	R	+	2	0	EP400	131096328	1.000000	0.71417	0.956000	0.39512	0.816000	0.46133	9.476000	0.97823	2.439000	0.82584	0.655000	0.94253	CGA		0.502	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132530375	G	A	132530375	3	1	26	1	0	0	0	0	1	0	0	0	5162	1058	37	1	7277	1	EP400	12	132530375	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	91202725	132530375	1321520	46	2269										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36445396	36445396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	caggggacttgctacgcctgGacggtcctgggctcttggtg	16	11	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr13:36445396G>A	ENST00000360631.3	-	5	1116	c.905C>T	c.(904-906)tCc>tTc	p.S302F	DCLK1_ENST00000379892.4_Missense_Mutation_p.S302F|DCLK1_ENST00000255448.4_Missense_Mutation_p.S302F			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	302	Pro/Ser-rich.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.S302F(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GCTACGCCTGGACGGTCCTGG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	13											216	205	209					13																	36445396		2203	4300	6503	35343396	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.905C>T	13.37:g.36445396G>A	ENSP00000353846:p.Ser302Phe		35343396	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	21.5	4.158220	0.78114	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.69685	-0.42;-0.41;1.73	5.28	5.28	0.74379	.	0.068772	0.64402	D	0.000011	T	0.69133	0.3077	L	0.61218	1.895	0.58432	D	0.999999	P	0.43607	0.812	B	0.42245	0.381	T	0.74009	-0.3802	10	0.66056	D	0.02	.	19.2736	0.94021	0.0:0.0:1.0:0.0	.	302	O15075-2	.	F	302	ENSP00000255448:S302F;ENSP00000353846:S302F;ENSP00000369222:S302F	ENSP00000255448:S302F	S	-	2	0	DCLK1	35343396	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.879000	0.75572	2.617000	0.88574	0.655000	0.94253	TCC		0.517	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36445396	G	A	36445396	3	1	26	1	0	0	0	0	1	0	0	0	4297	1174	41	3	1340	3	DCLK1	13	36445396	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		36445396	78724482	47	2270										
RNF219	79596	hgsc.bcm.edu	37	chr13	79213164	79213164	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctccaagctgagatttttacTcttaagctcttctacttctt	4	11	4	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr13:79213164T>A	ENST00000282003.6	-	4	401	c.343A>T	c.(343-345)Agt>Tgt	p.S115C		NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	115							zinc ion binding (GO:0008270)	p.S115C(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		AGATTTTTACTCTTAAGCTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											99	97	98					13																	79213164		2202	4300	6502	78111165	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.343A>T	13.37:g.79213164T>A	ENSP00000282003:p.Ser115Cys		78111165	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.053641	0.55218	.	.	ENSG00000152193	ENST00000282003	.	.	.	5.38	4.25	0.50352	.	0.694043	0.14953	N	0.288782	T	0.19967	0.0480	N	0.19112	0.55	0.31478	N	0.667574	P	0.47106	0.89	B	0.39971	0.315	T	0.23762	-1.0179	9	0.66056	D	0.02	-0.7802	2.3594	0.04303	0.0:0.1954:0.3168:0.4878	.	115	Q5W0B1	RN219_HUMAN	C	115	.	ENSP00000282003:S115C	S	-	1	0	RNF219	78111165	0.918000	0.31147	1.000000	0.80357	0.998000	0.95712	1.082000	0.30803	2.036000	0.60181	0.533000	0.62120	AGT		0.373	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79213164	T	A	79213164	3	1	26	1	0	0	0	0	1	0	0	0	13519	1551	54	5	1849	5	RNF219	13	79213164	Missense_Mutation	SNP	T	TCGA-AG-3599-01A-02W-0833-10	42767768	79213164	35956714	48	2271										
GPC6	10082	hgsc.bcm.edu	37	chr13	94482727	94482727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaagattcaggttacccgcGccttcattgctgccaggacc	10	13	2	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr13:94482727G>A	ENST00000377047.4	+	3	1255	c.640G>A	c.(640-642)Gcc>Acc	p.A214T	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	214					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.A214T(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GGTTACCCGCGCCTTCATTGC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	13											56	54	55					13																	94482727		2203	4300	6503	93280728	SO:0001583	missense	10082			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.640G>A	13.37:g.94482727G>A	ENSP00000366246:p.Ala214Thr		93280728	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566736	0.86439	.	.	ENSG00000183098	ENST00000377047	T	0.59083	0.29	5.49	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.72526	0.3471	M	0.79258	2.445	0.46298	D	0.998978	D;P	0.60575	0.988;0.943	P;P	0.58130	0.833;0.694	T	0.76187	-0.3051	10	0.49607	T	0.09	.	16.1766	0.81857	0.0:0.0:0.8657:0.1343	.	214;214	B4E2M1;Q9Y625	.;GPC6_HUMAN	T	214	ENSP00000366246:A214T	ENSP00000366246:A214T	A	+	1	0	GPC6	93280728	1.000000	0.71417	0.976000	0.42696	0.867000	0.49689	7.583000	0.82559	1.477000	0.48234	-0.164000	0.13417	GCC		0.493	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		A	94482727	G	A	94482727	3	1	26	1	0	0	0	0	1	0	0	0	6622	1087	38	1	650	1	GPC6	13	94482727	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	15269563	94482727	20687151	49	2272										
CTSG	1511	hgsc.bcm.edu	37	chr14	25043995	25043995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgtctctggatattgtgggcGcccagggtgacatttatatt	12	8	1	1	rs143803246		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:25043995G>A	ENST00000216336.2	-	3	261	c.225C>T	c.(223-225)ggC>ggT	p.G75G		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	75	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.G75G(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TATTGTGGGCGCCCAGGGTGA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	14											139	122	128					14																	25043995		2203	4300	6503	24113835	SO:0001819	synonymous_variant	1511			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"Cathepsins", "Endogenous ligands"	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.225C>T	14.37:g.25043995G>A			24113835	Q6IBJ6|Q9UCA5|Q9UCU6	Silent	SNP	ENST00000216336.2	37	CCDS9631.1																																																																																				0.557	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		A	25043995	G	A	25043995	2	1	26	1	0	0	0	0	0	0	0	1	4041	1074	38	1		1	CTSG	14	25043995	Silent	SNP	G	TCGA-AG-3599-01A-02W-0833-10		25043995	82305545	50	2273										
KTN1	3895	hgsc.bcm.edu	37	chr14	56096735	56096735	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaggatgaaagatcgaattGgaacattagaaaaggaacat	10	4	0	3			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:56096735G>A	ENST00000395314.3	+	7	1209	c.1141G>A	c.(1141-1143)Gga>Aga	p.G381R	KTN1_ENST00000395309.3_Missense_Mutation_p.G381R|KTN1_ENST00000413890.2_Missense_Mutation_p.G381R|KTN1_ENST00000395308.1_Missense_Mutation_p.G381R|KTN1_ENST00000395311.1_Missense_Mutation_p.G381R|KTN1_ENST00000416613.1_Missense_Mutation_p.G381R|KTN1_ENST00000438792.2_Missense_Mutation_p.G381R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	381					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.G381R(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AGATCGAATTGGAACATTAGA	0.294			T	RET	papillary thryoid																																		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	2	Substitution - Missense(2)	large_intestine(2)	14											123	123	123					14																	56096735		2203	4300	6503	55166488	SO:0001583	missense	3895				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1141G>A	14.37:g.56096735G>A	ENSP00000378725:p.Gly381Arg		55166488	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952734	0.73787	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18	5.97	5.97	0.96955	.	0.276236	0.26828	N	0.022289	T	0.46425	0.1392	L	0.36672	1.1	0.30540	N	0.766517	D;D;P;D	0.76494	0.974;0.999;0.906;0.985	P;D;P;D	0.71414	0.889;0.973;0.802;0.923	T	0.37888	-0.9686	10	0.21540	T	0.41	-16.9036	12.8183	0.57677	0.0768:0.0:0.9232:0.0	.	381;381;381;381	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	R	381	ENSP00000394992:G381R;ENSP00000378720:G381R;ENSP00000391964:G381R;ENSP00000378725:G381R;ENSP00000378719:G381R;ENSP00000378722:G381R;ENSP00000388807:G381R	ENSP00000378719:G381R	G	+	1	0	KTN1	55166488	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.552000	0.60747	2.835000	0.97688	0.591000	0.81541	GGA		0.294	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			A	56096735	G	A	56096735	3	1	26	1	0	0	0	0	1	0	0	0	8607	1349	47	3	1163	3	KTN1	14	56096735	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	31052740	56096735	51252805	51	2274										
SPTB	6710	hgsc.bcm.edu	37	chr14	65240071	65240071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgttctccagcttgcgcttgCgctcttccgccacgtccttc	8	17	2	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:65240071C>T	ENST00000389721.5	-	24	5077	c.5045G>A	c.(5044-5046)cGc>cAc	p.R1682H	SPTB_ENST00000556626.1_Missense_Mutation_p.R1682H|SPTB_ENST00000542895.1_Missense_Mutation_p.R1682H|SPTB_ENST00000389720.3_Missense_Mutation_p.R1682H|SPTB_ENST00000389722.3_Missense_Mutation_p.R1682H	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1682					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.R1682H(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTTGCGCTTGCGCTCTTCCGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	14											131	113	119					14																	65240071		2203	4300	6503	64309824	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.5045G>A	14.37:g.65240071C>T	ENSP00000374371:p.Arg1682His		64309824	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.912487	0.72983	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.80999	0.4732	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.85189	0.1008	10	0.87932	D	0	.	17.6535	0.88171	0.0:1.0:0.0:0.0	.	466;1682;1686	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	H	1686;1682;466;347;1682;1682;1682;1682	ENSP00000374372:R1682H;ENSP00000451324:R347H;ENSP00000451752:R1682H;ENSP00000374371:R1682H;ENSP00000443882:R1682H;ENSP00000374370:R1682H	ENSP00000334218:R466H	R	-	2	0	SPTB	64309824	1.000000	0.71417	0.353000	0.25747	0.147000	0.21601	7.792000	0.85828	2.537000	0.85549	0.561000	0.74099	CGC		0.552	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65240071	C	T	65240071	3	4	26	1	0	0	0	0	1	0	0	0	15157	768	27	1	2058	1	SPTB	14	65240071	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	9143336	65240071	42109469	52	2275										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79175869	79175869	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	aagtagacttctttgccgtgGaactcctcgatggcaacctg	10	11	1	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:79175869G>C	ENST00000554719.1	+	4	903	c.412G>C	c.(412-414)Gaa>Caa	p.E138Q	RP11-232C2.2_ENST00000555680.1_RNA|NRXN3_ENST00000335750.5_Missense_Mutation_p.E138Q	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	142	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.E138Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CTTTGCCGTGGAACTCCTCGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	14											141	143	142					14																	79175869		2203	4300	6503	78245622	SO:0001583	missense	9369			AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.412G>C	14.37:g.79175869G>C	ENSP00000451648:p.Glu138Gln		78245622	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.508784	0.85282	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557081	T;T;T	0.80123	-1.34;-1.34;-1.34	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.90570	0.7044	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76071	0.981;0.987	D	0.90781	0.4679	9	.	.	.	.	19.1251	0.93380	0.0:0.0:1.0:0.0	.	511;138	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	Q	511;509;138;138;82	ENSP00000451648:E138Q;ENSP00000338349:E138Q;ENSP00000450462:E82Q	.	E	+	1	0	NRXN3	78245622	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.869000	0.99810	2.518000	0.84900	0.563000	0.77884	GAA		0.507	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		C	79175869	G	C	79175869	3	2	26	1	0	0	0	0	1	0	0	0	10698	1175	41	5	418	5	NRXN3	14	79175869	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	13935798	79175869	28173671	53	2276										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90651117	90651117	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccatagagacagacggggtgGcagagagtgacacggacggg	18	8	0	4			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:90651117G>A	ENST00000282146.4	+	2	1438	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	333					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A333T(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				AGACGGGGTGGCAGAGAGTGA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14											61	62	62					14																	90651117		2203	4300	6503	89720870	SO:0001583	missense	56659			AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.997G>A	14.37:g.90651117G>A	ENSP00000282146:p.Ala333Thr		89720870	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	7.001	0.554858	0.13436	.	.	ENSG00000152315	ENST00000282146	T	0.11604	2.76	5.3	1.2	0.21068	.	1.551420	0.04012	N	0.298327	T	0.05686	0.0149	N	0.14661	0.345	0.22156	N	0.999325	B	0.06786	0.001	B	0.04013	0.001	T	0.36114	-0.9761	10	0.10636	T	0.68	.	1.8219	0.03112	0.4407:0.3101:0.0989:0.1503	.	333	Q9HB14	KCNKD_HUMAN	T	333	ENSP00000282146:A333T	ENSP00000282146:A333T	A	+	1	0	KCNK13	89720870	1.000000	0.71417	0.899000	0.35326	0.015000	0.08874	2.254000	0.43214	-0.035000	0.13691	0.655000	0.94253	GCA		0.612	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		A	90651117	G	A	90651117	3	1	26	1	0	0	0	0	1	0	0	0	8082	1203	42	3	1003	3	KCNK13	14	90651117	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	11475248	90651117	16698423	54	2277										
DICER1	23405	hgsc.bcm.edu	37	chr14	95566250	95566250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcccttcttttttccaaggCgatacagattacagttgctg	8	10	1	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr14:95566250C>T	ENST00000526495.1	-	24	4364	c.4073G>A	c.(4072-4074)cGc>cAc	p.R1358H	DICER1_ENST00000541352.1_Missense_Mutation_p.R1358H|DICER1_ENST00000556045.1_Missense_Mutation_p.R256H|DICER1_ENST00000527414.1_Missense_Mutation_p.R1358H|DICER1_ENST00000343455.3_Missense_Mutation_p.R1358H|DICER1_ENST00000393063.1_Missense_Mutation_p.R1358H			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1358	RNase III 1. {ECO:0000255|PROSITE- ProRule:PRU00177}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)	p.R1358H(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TTTTCCAAGGCGATACAGATT	0.398			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																													yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	14											115	109	111					14																	95566250		2203	4300	6503	94636003	SO:0001583	missense	23405	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4073G>A	14.37:g.95566250C>T	ENSP00000437256:p.Arg1358His		94636003	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	37	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.666351	0.88251	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045;ENST00000541352	T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	5.91	5.91	0.95273	Ribonuclease III (5);	0.000000	0.85682	D	0.000000	D	0.86830	0.6027	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.87578	0.998;0.992;0.975	T	0.81479	-0.0914	10	0.16896	T	0.51	-19.1274	20.2985	0.98592	0.0:1.0:0.0:0.0	.	256;1358;1358	B3KRG4;E0AD28;Q9UPY3	.;.;DICER_HUMAN	H	1358;1358;1358;1358;256;1358	ENSP00000343745:R1358H;ENSP00000437256:R1358H;ENSP00000376783:R1358H;ENSP00000435681:R1358H;ENSP00000451041:R256H;ENSP00000444719:R1358H	ENSP00000343745:R1358H	R	-	2	0	DICER1	94636003	1.000000	0.71417	1.000000	0.80357	0.429000	0.31625	7.456000	0.80751	2.793000	0.96121	0.655000	0.94253	CGC		0.398	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			T	95566250	C	T	95566250	3	4	26	1	0	0	0	0	1	0	0	0	4532	768	27	1	1719	1	DICER1	14	95566250	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	4915133	95566250	11783290	55	2278										
RILP	8578	hgsc.bcm.edu	37	chr17	1551177	1551177	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acatcttggccttgatcttcTtccgctgcttccggacagcc	8	15	3	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr17:1551177T>C	ENST00000263071.4	-	0	0				RILP_ENST00000301336.6_Missense_Mutation_p.K299R|SCARF1_ENST00000571272.1_5'Flank|SCARF1_ENST00000348987.3_5'Flank	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1						cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.K299R(1)		cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CTTGATCTTCTTCCGCTGCTT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											198	136	157					17																	1551177		2203	4300	6503	1497927	SO:0001631	upstream_gene_variant	83547			D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555		17.37:g.1551177T>C	Exception_encountered		1497927	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.693626	0.30052	.	.	ENSG00000167705	ENST00000301336	T	0.43294	0.95	5.6	2.02	0.26589	.	0.216972	0.37219	N	0.002196	T	0.14056	0.0340	N	0.01352	-0.895	0.29109	N	0.881013	B	0.25048	0.117	B	0.25884	0.064	T	0.20207	-1.0282	10	0.22109	T	0.4	-9.8949	7.9966	0.30271	0.0:0.3233:0.0:0.6767	.	299	Q96NA2	RILP_HUMAN	R	299	ENSP00000301336:K299R	ENSP00000301336:K299R	K	-	2	0	RILP	1497927	0.106000	0.21978	0.998000	0.56505	0.477000	0.33069	-0.029000	0.12329	0.422000	0.26005	0.533000	0.62120	AAG		0.612	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		C	1551177	T	C	1551177	1	2	26	0	1	0	0	0	0	0	0	0	13397	1609	56	4		4	RILP	17	1551177	5'Flank	SNP	T	TCGA-AG-3599-01A-02W-0833-10		1551177	79644033	56	2279										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37881332	37881332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acctggaggatgtgcggctcGtacacagggacttggccgct	15	11	0	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr17:37881332G>A	ENST00000269571.5	+	21	2683	c.2524G>A	c.(2524-2526)Gta>Ata	p.V842I	ERBB2_ENST00000445658.2_Missense_Mutation_p.V566I|ERBB2_ENST00000584601.1_Missense_Mutation_p.V812I|ERBB2_ENST00000406381.2_Missense_Mutation_p.V812I|ERBB2_ENST00000540147.1_Missense_Mutation_p.V812I|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584450.1_Missense_Mutation_p.V842I|ERBB2_ENST00000541774.1_Missense_Mutation_p.V827I			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	842	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.V842I(6)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGTGCGGCTCGTACACAGGGA	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	6	Substitution - Missense(6)	large_intestine(5)|stomach(1)	17											70	61	64					17																	37881332		2203	4300	6503	35134858	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2524G>A	17.37:g.37881332G>A	ENSP00000269571:p.Val842Ile		35134858	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.241303	0.58995	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	5.09	5.09	0.68999	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.85106	0.5621	N	0.21142	0.635	0.80722	D	1	D;D;D	0.76494	0.997;0.979;0.999	D;P;D	0.64506	0.92;0.559;0.926	D	0.87344	0.2333	9	0.87932	D	0	.	18.2846	0.90110	0.0:0.0:1.0:0.0	.	566;827;842	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	I	812;827;566;842;812	ENSP00000385185:V812I;ENSP00000446466:V827I;ENSP00000404047:V566I;ENSP00000269571:V842I;ENSP00000443562:V812I	ENSP00000269571:V842I	V	+	1	0	ERBB2	35134858	1.000000	0.71417	0.919000	0.36401	0.900000	0.52787	9.657000	0.98554	2.651000	0.90000	0.563000	0.77884	GTA		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37881332	G	A	37881332	3	1	26	1	0	0	0	0	1	0	0	0	5219	1145	40	1	2606	1	ERBB2	17	37881332	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	36330155	37881332	43313878	57	2280										
CA10	56934	hgsc.bcm.edu	37	chr17	49710917	49710917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgatattggtgcggatgcagCggttgttgagtggctggaca	17	5	0	2	rs201368392		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr17:49710917C>T	ENST00000285273.4	-	9	1995	c.884G>A	c.(883-885)cGc>cAc	p.R295H	CA10_ENST00000442502.2_Missense_Mutation_p.R295H|CA10_ENST00000571918.1_5'Flank|CA10_ENST00000451037.2_Missense_Mutation_p.R295H|CA10_ENST00000570565.1_Missense_Mutation_p.R220H|CA10_ENST00000340813.6_Missense_Mutation_p.R301H	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	295					brain development (GO:0007420)			p.R295H(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	GCGGATGCAGCGGTTGTTGAG	0.527													C|||	1	0.000199681	0	0	5008	,	,		20658	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											128	111	117					17																	49710917		2203	4300	6503	47065916	SO:0001583	missense	56934			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.884G>A	17.37:g.49710917C>T	ENSP00000285273:p.Arg295His		47065916	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	35	5.491476	0.96339	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.44	5.44	0.79542	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.051150	0.85682	D	0.000000	D	0.93517	0.7931	H	0.96996	3.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95447	0.8531	10	0.87932	D	0	.	18.2623	0.90039	0.0:1.0:0.0:0.0	.	295;301;220	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	H	295;295;295;301	ENSP00000390666:R295H;ENSP00000285273:R295H;ENSP00000405388:R295H;ENSP00000340363:R301H	ENSP00000285273:R295H	R	-	2	0	CA10	47065916	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.666000	0.83877	2.558000	0.86282	0.655000	0.94253	CGC		0.527	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		T	49710917	C	T	49710917	3	4	26	1	0	0	0	0	1	0	0	0	2517	768	27	1	110	1	CA10	17	49710917	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	11829585	49710917	31484293	58	2281										
CPLX4	339302	hgsc.bcm.edu	37	chr18	56963955	56963955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcacggaacacttctgctccGctgtctgcttgatttcagtg	9	12	4	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr18:56963955G>A	ENST00000299721.3	-	3	644	c.458C>T	c.(457-459)gCg>gTg	p.A153V	CPLX4_ENST00000587244.1_Intron	NM_181654.3	NP_857637.1	Q7Z7G2	CPLX4_HUMAN	complexin 4	153					exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter secretion (GO:0046928)	cell junction (GO:0030054)|membrane (GO:0016020)|synapse (GO:0045202)		p.A153V(1)		autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	16		Colorectal(73;0.175)				CTTCTGCTCCGCTGTCTGCTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	18											91	84	87					18																	56963955		2203	4300	6503	55114935	SO:0001583	missense	339302			AY286502	CCDS11973.1	18q21.32	2005-08-02			ENSG00000166569	ENSG00000166569			24330	protein-coding gene	gene with protein product		609586				15911881	Standard	NM_181654		Approved	CPX-IV	uc002lhy.3	Q7Z7G2	OTTHUMG00000132756	ENST00000299721.3:c.458C>T	18.37:g.56963955G>A	ENSP00000299721:p.Ala153Val		55114935	F1T0L6	Missense_Mutation	SNP	ENST00000299721.3	37	CCDS11973.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349439	0.95830	.	.	ENSG00000166569	ENST00000299721	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.80019	0.4547	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.81331	-0.0981	9	0.72032	D	0.01	-9.7614	19.3422	0.94347	0.0:0.0:1.0:0.0	.	153	Q7Z7G2	CPLX4_HUMAN	V	153	.	ENSP00000299721:A153V	A	-	2	0	CPLX4	55114935	1.000000	0.71417	0.205000	0.23548	0.994000	0.84299	9.393000	0.97256	2.653000	0.90120	0.561000	0.74099	GCG		0.498	CPLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256127.1	NM_181654		A	56963955	G	A	56963955	3	1	26	1	0	0	0	0	1	0	0	0	3813	1087	38	1	28	1	CPLX4	18	56963955	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10		56963955	21113293	59	2282										
NETO1	81832	hgsc.bcm.edu	37	chr18	70532111	70532111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agttgggagaggtaaagataCctccctctgcatgttttgtc	11	8	1	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr18:70532111C>A	ENST00000327305.6	-	3	809	c.152G>T	c.(151-153)gGt>gTt	p.G51V	NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Missense_Mutation_p.G50V|NETO1_ENST00000397929.1_Missense_Mutation_p.G50V|NETO1_ENST00000583169.1_Missense_Mutation_p.G51V	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	51	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.G51V(1)		NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GGTAAAGATACCTCCCTCTGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											122	111	115					18																	70532111		2203	4300	6503	68683091	SO:0001583	missense	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.152G>T	18.37:g.70532111C>A	ENSP00000313088:p.Gly51Val		68683091	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834090	0.91036	.	.	ENSG00000166342	ENST00000327305;ENST00000299430;ENST00000397929	T;T;T	0.58060	0.36;0.36;0.7	5.7	5.7	0.88788	CUB (5);	0.000000	0.64402	D	0.000009	D	0.82715	0.5097	H	0.96080	3.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.87335	0.2327	10	0.87932	D	0	-14.9843	20.202	0.98263	0.0:1.0:0.0:0.0	.	50;50;51	Q8TDF5-1;Q8TDF5-2;Q8TDF5	.;.;NETO1_HUMAN	V	51;50;50	ENSP00000313088:G51V;ENSP00000299430:G50V;ENSP00000381024:G50V	ENSP00000299430:G50V	G	-	2	0	NETO1	68683091	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.855000	0.98099	0.650000	0.86243	GGT		0.423	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		A	70532111	C	A	70532111	3	1	26	1	0	0	0	0	1	0	0	0	10370	507	18	2	1490	2	NETO1	18	70532111	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10	13568156	70532111	7545137	60	2283										
ZNF540	163255	hgsc.bcm.edu	37	chr19	38103868	38103868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgggaagtcctttagtcggCgtgggcagttcactgaacat	14	8	1	1	rs201168289	byFrequency	TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr19:38103868C>T	ENST00000592533.1	+	5	2019	c.1687C>T	c.(1687-1689)Cgt>Tgt	p.R563C	ZNF540_ENST00000343599.5_Missense_Mutation_p.R563C|ZNF540_ENST00000316433.4_Missense_Mutation_p.R563C|ZNF540_ENST00000589117.1_Missense_Mutation_p.R531C	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	563					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.R563C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTTAGTCGGCGTGGGCAGTT	0.388													C|||	2	0.000399361	0	0.0014	5008	,	,		19439	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19						C	CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	93	102	99		1687,1591,1687	-4.1	0	19		99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ZNF540	NM_152606.3,NM_001172226.1,NM_001172225.1	180,180,180	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign,benign	563/661,531/629,563/661	38103868	2,13004	2203	4300	6503	42795708	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.1687C>T	19.37:g.38103868C>T	ENSP00000466274:p.Arg563Cys		42795708	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	13.88	2.368408	0.42003	2.27E-4	1.16E-4	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.08634	3.07	2.05	-4.09	0.03951	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04003	0.0112	N	0.21373	0.66	0.09310	N	1	B;B	0.14438	0.01;0.006	B;B	0.06405	0.002;0.001	T	0.43988	-0.9357	9	0.33940	T	0.23	.	0.7183	0.00936	0.2719:0.2271:0.3249:0.1762	.	531;563	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	C	563;531	ENSP00000324598:R563C	ENSP00000324598:R563C	R	+	1	0	ZNF540	42795708	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-2.507000	0.00961	-0.345000	0.08325	0.305000	0.20034	CGT		0.388	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		T	38103868	C	T	38103868	3	4	26	1	0	0	0	0	1	0	0	0	18014	768	27	1	1701	1	ZNF540	19	38103868	Missense_Mutation	SNP	C	TCGA-AG-3599-01A-02W-0833-10		38103868	21025115	61	2284										
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40711125	40711125	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gccctgttccagatgccactGgagtccttccactcgctgca	9	16	0	1			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr19:40711125G>A	ENST00000253055.3	+	4	1398	c.1110G>A	c.(1108-1110)ctG>ctA	p.L370L	AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	370					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)	p.L370L(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						AGATGCCACTGGAGTCCTTCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	19											80	77	78					19																	40711125		2203	4300	6503	45402965	SO:0001819	synonymous_variant	4294			X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1110G>A	19.37:g.40711125G>A			45402965	Q12761|Q14871	Silent	SNP	ENST00000253055.3	37	CCDS12549.1																																																																																				0.572	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40711125	G	A	40711125	2	1	26	1	0	0	0	0	0	0	0	1	9274	1335	47	3		3	MAP3K10	19	40711125	Silent	SNP	G	TCGA-AG-3599-01A-02W-0833-10	2607257	40711125	18417858	62	2285										
FUT1	2523	hgsc.bcm.edu	37	chr19	49253517	49253517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgggcaggaaggccgcctccGgcttaaagatcttcaggaac	13	12	2	1	rs146216905		TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr19:49253517G>A	ENST00000310160.3	-	4	1996	c.1022C>T	c.(1021-1023)cCg>cTg	p.P341L	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	341					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)	p.P341L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		GGCCGCCTCCGGCTTAAAGAT	0.572													G|||	1	0.000199681	0	0	5008	,	,		19326	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						G	LEU/PRO	0,4406		0,0,2203	44	41	42		1022	4.7	0.6	19	dbSNP_134	42	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FUT1	NM_000148.3	98	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	341/366	49253517	4,13002	2203	4300	6503	53945329	SO:0001583	missense	2523				CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.1022C>T	19.37:g.49253517G>A	ENSP00000312021:p.Pro341Leu		53945329	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	37	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014220	0.35511	0.0	4.65E-4	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.94793	-3.52	4.69	4.69	0.59074	.	0.103160	0.43747	D	0.000526	D	0.96920	0.8994	M	0.85373	2.75	0.23754	N	0.996939	D	0.89917	1.0	D	0.97110	1.0	D	0.91483	0.5206	10	0.66056	D	0.02	-2.8763	10.5302	0.44973	0.0:0.0:0.8069:0.193	.	341	P19526	FUT1_HUMAN	L	341;331	ENSP00000312021:P341L	ENSP00000312021:P341L	P	-	2	0	FUT1	53945329	0.998000	0.40836	0.557000	0.28306	0.070000	0.16714	3.552000	0.53705	2.619000	0.88677	0.561000	0.74099	CCG		0.572	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		A	49253517	G	A	49253517	3	1	26	1	0	0	0	0	1	0	0	0	6120	1116	39	1	79	1	FUT1	19	49253517	Missense_Mutation	SNP	G	TCGA-AG-3599-01A-02W-0833-10	8542392	49253517	9875466	63	2286										
SYS1	90196	hgsc.bcm.edu	37	chr20	43994315	43994315	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgatgtccttcatcctcaaCgccctcacctggtgagtatc	7	14	3	2			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr20:43994315C>T	ENST00000243918.5	+	3	510	c.219C>T	c.(217-219)aaC>aaT	p.N73N	SYS1_ENST00000479779.1_3'UTR|SYS1_ENST00000426004.1_Silent_p.N73N|SYS1_ENST00000372727.1_Silent_p.N73N|SYS1_ENST00000414310.1_Silent_p.N52N|SYS1-DBNDD2_ENST00000475242.1_3'UTR|SYS1-DBNDD2_ENST00000452133.1_Silent_p.N73N	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	73					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)		p.N73N(1)		cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TCATCCTCAACGCCCTCACCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	20											233	231	232					20																	43994315		2203	4300	6503	43427729	SO:0001819	synonymous_variant	90196			AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"chromosome 20 open reading frame 169", "SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.219C>T	20.37:g.43994315C>T			43427729	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Silent	SNP	ENST00000243918.5	37	CCDS13351.1																																																																																				0.502	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542		T	43994315	C	T	43994315	2	4	26	1	0	0	0	0	0	0	0	1	15503	535	19	1		1	SYS1	20	43994315	Silent	SNP	C	TCGA-AG-3599-01A-02W-0833-10		43994315	19031205	64	2287										
GMEB2	26205	hgsc.bcm.edu	37	chr20	62224377	62224377	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcgtacctccaatggccgcGgtccagtcgccagggtcttc	11	16	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr20:62224377G>A	ENST00000266068.1	-	6	1156	c.678C>T	c.(676-678)acC>acT	p.T226T	GMEB2_ENST00000370069.1_Silent_p.T175T|GMEB2_ENST00000370077.1_Silent_p.T226T			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	226					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.T226T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CAATGGCCGCGGTCCAGTCGC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	20											60	52	55					20																	62224377		2203	4300	6503	61694821	SO:0001819	synonymous_variant	26205			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.678C>T	20.37:g.62224377G>A			61694821	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Silent	SNP	ENST00000266068.1	37	CCDS13528.1																																																																																				0.627	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384		A	62224377	G	A	62224377	2	1	26	1	0	0	0	0	0	0	0	1	6508	1103	39	1		1	GMEB2	20	62224377	Silent	SNP	G	TCGA-AG-3599-01A-02W-0833-10	18230062	62224377	801143	65	2288										
ACR	49	hgsc.bcm.edu	37	chr22	51177898	51177898	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgctcactgcttcgtcggcAaaaagtacgtgtagggatgc	12	10	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chr22:51177898A>G	ENST00000216139.5	+	2	317	c.277A>G	c.(277-279)Aaa>Gaa	p.K93E	AC002056.5_ENST00000532913.1_RNA|ACR_ENST00000529621.1_Missense_Mutation_p.K93E|AC000036.4_ENST00000449652.1_RNA	NM_001097.2	NP_001088.2	P10323	ACRO_HUMAN	acrosin	93	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acrosome matrix dispersal (GO:0002077)|acrosome reaction (GO:0007340)|activation of adenylate cyclase activity (GO:0007190)|binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|response to steroid hormone (GO:0048545)|single fertilization (GO:0007338)	acrosomal matrix (GO:0043159)|extracellular region (GO:0005576)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|protein complex (GO:0043234)	amidase activity (GO:0004040)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|drug binding (GO:0008144)|fucose binding (GO:0042806)|mannose binding (GO:0005537)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.K93E(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	7		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		CTTCGTCGGCAAAAAGTACGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	22											82	60	67					22																	51177898		2203	4300	6503	49524764	SO:0001583	missense	49			CR456366	CCDS14101.1	22q13.33	2012-10-23	2012-10-23		ENSG00000100312	ENSG00000100312	3.4.21.10		126	protein-coding gene	gene with protein product	"preproacrosin", "acrosin light and heavy chain prepropeptide"	102480				2298447, 12398221	Standard	NM_001097		Approved		uc003bnh.4	P10323	OTTHUMG00000150155	ENST00000216139.5:c.277A>G	22.37:g.51177898A>G	ENSP00000216139:p.Lys93Glu		49524764	Q6ICK2	Missense_Mutation	SNP	ENST00000216139.5	37	CCDS14101.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710645	0.30322	.	.	ENSG00000100312	ENST00000216139;ENST00000529621	T;D	0.92858	0.27;-3.12	4.43	4.43	0.53597	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.665977	0.12425	N	0.470076	D	0.82967	0.5152	N	0.20807	0.61	0.09310	N	1	P;P	0.38440	0.631;0.631	B;B	0.30105	0.111;0.111	T	0.71682	-0.4519	10	0.19147	T	0.46	-6.7718	11.9647	0.53027	1.0:0.0:0.0:0.0	.	93;93	E9PLV5;P10323	.;ACRO_HUMAN	E	93	ENSP00000216139:K93E;ENSP00000435120:K93E	ENSP00000216139:K93E	K	+	1	0	ACR	49524764	0.000000	0.05858	0.270000	0.24601	0.061000	0.15899	-0.471000	0.06631	2.001000	0.58596	0.379000	0.24179	AAA		0.577	ACR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000316605.2	NM_001097		G	51177898	A	G	51177898	3	3	26	1	0	0	0	0	1	0	0	0	169	131	5	4	283	4	ACR	22	51177898	Missense_Mutation	SNP	A	TCGA-AG-3599-01A-02W-0833-10		51177898	126668	66	2289										
SLC25A14	9016	hgsc.bcm.edu	37	chrX	129498622	129498622	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtgtggttccaactgctcaGcgtgctgccatcgttgtagg	14	10	1	0			TCGA-AG-3599-01A-02W-0833-10	TCGA-AG-3599-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	285b8163-5c9f-4376-a108-006f70d22299	2dc2ec42-f7b6-4030-b2d3-ca56cca9ea29	g.chrX:129498622G>A	ENST00000218197.5	+	7	842	c.615G>A	c.(613-615)caG>caA	p.Q205Q	SLC25A14_ENST00000467496.1_3'UTR|SLC25A14_ENST00000339231.3_Silent_p.Q233Q|SLC25A14_ENST00000543953.1_Silent_p.Q170Q|SLC25A14_ENST00000545805.1_Silent_p.Q205Q|SLC25A14_ENST00000361980.5_Silent_p.Q202Q	NM_001282195.1|NM_001282196.1|NM_001282198.1	NP_001269124.1|NP_001269125.1|NP_001269127.1	O95258	UCP5_HUMAN	solute carrier family 25 (mitochondrial carrier, brain), member 14	205					aerobic respiration (GO:0009060)|mitochondrial transport (GO:0006839)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.Q205Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)	22						CAACTGCTCAGCGTGCTGCCA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	X											217	163	181					X																	129498622		2203	4300	6503	129326303	SO:0001819	synonymous_variant	9016			AF078544	CCDS14623.1, CCDS14624.1, CCDS76020.1, CCDS76021.1	Xq24	2013-05-22			ENSG00000102078	ENSG00000102078		"Solute carriers"	10984	protein-coding gene	gene with protein product		300242				9852133	Standard	XM_005262485		Approved	BMCP1, UCP5	uc004evp.1	O95258	OTTHUMG00000022394	ENST00000218197.5:c.615G>A	X.37:g.129498622G>A			129326303	D3DTG2|Q0VDH7|Q9HC60|Q9HC61	Silent	SNP	ENST00000218197.5	37	CCDS14623.1																																																																																				0.418	SLC25A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058253.1	NM_022810, NM_003951		A	129498622	G	A	129498622	2	1	26	1	0	0	0	0	0	0	0	1	14513	962	34	3		3	SLC25A14	23	129498622	Silent	SNP	G	TCGA-AG-3599-01A-02W-0833-10		129498622	25771938	67	2290										
DNAJC11	55735	hgsc.bcm.edu	37	chr1	6712917	6712917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atccctttgccgaagttactCgtctgagcgcaaagttaatg	9	10	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:6712917C>T	ENST00000377577.5	-	6	725	c.602G>A	c.(601-603)cGa>cAa	p.R201Q	DNAJC11_ENST00000542246.1_Missense_Mutation_p.R163Q|DNAJC11_ENST00000349363.6_Missense_Mutation_p.R163Q|DNAJC11_ENST00000294401.7_Missense_Mutation_p.R201Q|DNAJC11_ENST00000377573.5_Missense_Mutation_p.R111Q	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	201						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.R201Q(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		CGAAGTTACTCGTCTGAGCGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											146	138	140					1																	6712917		2203	4300	6503	6635504	SO:0001583	missense	55735			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.602G>A	1.37:g.6712917C>T	ENSP00000366800:p.Arg201Gln		6635504	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	.	.	.	.	.	.	.	.	.	.	C	36	5.732264	0.96856	.	.	ENSG00000007923	ENST00000377577;ENST00000451196;ENST00000349363;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T;T;T	0.36699	2.39;1.68;1.24;2.37;2.13;1.75;2.4	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.63792	0.2541	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	1.0;0.977;1.0;1.0	D;P;D;D	0.74023	0.915;0.487;0.982;0.967	T	0.66988	-0.5784	10	0.62326	D	0.03	-4.9626	18.4511	0.90704	0.0:1.0:0.0:0.0	.	111;177;201;201	B4DGD5;Q5TH61;Q9NVH1-3;Q9NVH1	.;.;.;DJC11_HUMAN	Q	201;177;163;201;163;111;201	ENSP00000366800:R201Q;ENSP00000415871:R177Q;ENSP00000326304:R163Q;ENSP00000294401:R201Q;ENSP00000444020:R163Q;ENSP00000366796:R111Q;ENSP00000410194:R201Q	ENSP00000294401:R201Q	R	-	2	0	DNAJC11	6635504	0.969000	0.33509	0.995000	0.50966	0.995000	0.86356	7.374000	0.79633	2.666000	0.90696	0.655000	0.94253	CGA		0.473	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		T	6712917	C	T	6712917	3	4	27	1	0	0	0	0	1	0	0	0	4641	884	31	1	1121	1	DNAJC11	1	6712917	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		6712917	242537704	1	2291										
TRIM62	55223	hgsc.bcm.edu	37	chr1	33612944	33612944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgagcaagccttggtcatagTccaggaagacacccaccttg	10	12	1	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:33612944T>C	ENST00000291416.5	-	5	1495	c.1262A>G	c.(1261-1263)gAc>gGc	p.D421G	TRIM62_ENST00000543586.1_Missense_Mutation_p.D300G	NM_018207.2	NP_060677.2	Q9BVG3	TRI62_HUMAN	tripartite motif containing 62	421	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D421G(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)				TTGGTCATAGTCCAGGAAGAC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	110	114					1																	33612944		2203	4300	6503	33385531	SO:0001583	missense	55223			BC007999	CCDS376.1	1p35.1	2013-10-11	2011-01-25		ENSG00000116525	ENSG00000116525		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	25574	protein-coding gene	gene with protein product	"ductal epithelium-associated RING Chromosome 1"		"tripartite motif-containing 62"			19536326	Standard	NM_018207		Approved	FLJ10759, DEAR1	uc001bxb.3	Q9BVG3	OTTHUMG00000004132	ENST00000291416.5:c.1262A>G	1.37:g.33612944T>C	ENSP00000291416:p.Asp421Gly		33385531	B3KVH5|B4DTE4|D3DPR1|Q9NVG0	Missense_Mutation	SNP	ENST00000291416.5	37	CCDS376.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535596	0.85812	.	.	ENSG00000116525	ENST00000291416;ENST00000543586	T;T	0.81247	-1.47;-1.47	5.6	5.6	0.85130	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.92928	0.7750	H	0.97158	3.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94909	0.8063	10	0.87932	D	0	.	13.7214	0.62730	0.0:0.0:0.0:1.0	.	421	Q9BVG3	TRI62_HUMAN	G	421;300	ENSP00000291416:D421G;ENSP00000441173:D300G	ENSP00000291416:D421G	D	-	2	0	TRIM62	33385531	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.040000	0.89188	2.133000	0.65898	0.402000	0.26972	GAC		0.557	TRIM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011890.1	NM_018207		C	33612944	T	C	33612944	3	2	27	1	0	0	0	0	1	0	0	0	16577	1667	58	4	169	4	TRIM62	1	33612944	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	26900027	33612944	215637677	2	2292										
WDR78	79819	hgsc.bcm.edu	37	chr1	67306347	67306347	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	acatcttcaggctcttcaggTtcaggttctaaagtttaaac	7	9	6	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:67306347T>G	ENST00000371026.3	-	9	1354	c.1299A>C	c.(1297-1299)gaA>gaC	p.E433D	WDR78_ENST00000371023.3_Missense_Mutation_p.E433D|WDR78_ENST00000431318.1_Missense_Mutation_p.E179D	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	433	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)			p.E433D(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GCTCTTCAGGTTCAGGTTCTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	95	93					1																	67306347		2203	4300	6503	67078935	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.1299A>C	1.37:g.67306347T>G	ENSP00000360065:p.Glu433Asp		67078935	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	T	7.269	0.606760	0.14002	.	.	ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352;ENST00000371023;ENST00000531552	T;T;T;T;T	0.68181	0.33;-0.27;-0.31;2.09;1.4	5.62	2.09	0.27110	.	0.725056	0.13701	N	0.368817	T	0.27697	0.0681	L	0.36672	1.1	0.24950	N	0.991795	B;B;B	0.11235	0.002;0.002;0.004	B;B;B	0.09377	0.004;0.003;0.004	T	0.22871	-1.0204	10	0.14656	T	0.56	-15.4052	7.1892	0.25816	0.0:0.251:0.0:0.749	.	179;433;433	Q5VTH9-3;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	D	433;179;199;433;55	ENSP00000360065:E433D;ENSP00000393182:E179D;ENSP00000433682:E199D;ENSP00000360062:E433D;ENSP00000433037:E55D	ENSP00000360062:E433D	E	-	3	2	WDR78	67078935	0.094000	0.21725	0.835000	0.33067	0.090000	0.18270	0.029000	0.13666	0.165000	0.19558	0.528000	0.53228	GAA		0.393	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		G	67306347	T	G	67306347	3	3	27	1	0	0	0	0	1	0	0	0	17368	1722	60	4	1340	4	WDR78	1	67306347	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	33693403	67306347	181944274	3	2293										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111061227	111061227	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cccggaagcttggagaaggcCgtctcatggttggtgctttc	14	10	1	1	rs543046084		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:111061227C>T	ENST00000369771.2	-	1	570	c.183G>A	c.(181-183)acG>acA	p.T61T		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	61					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.T61T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TGGAGAAGGCCGTCTCATGGT	0.582													C|||	1	0.000199681	0	0.0014	5008	,	,		17159	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											84	92	89					1																	111061227		2203	4300	6503	110862750	SO:0001819	synonymous_variant	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.183G>A	1.37:g.111061227C>T			110862750		Silent	SNP	ENST00000369771.2	37	CCDS826.1																																																																																				0.582	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111061227	C	T	111061227	2	4	27	1	0	0	0	0	0	0	0	1	8023	639	23	1		1	KCNA10	1	111061227	Silent	SNP	C	TCGA-AG-3600-01A-01W-0833-10	43754880	111061227	138189394	4	2294										
ASTN1	460	hgsc.bcm.edu	37	chr1	176934332	176934332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cagagggctgctctcccaaaAccaggtcaaagcctcgctga	10	14	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:176934332A>G	ENST00000367654.3	-	9	1800	c.1589T>C	c.(1588-1590)gTt>gCt	p.V530A	ASTN1_ENST00000361833.2_Missense_Mutation_p.V522A|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.V522A|ASTN1_ENST00000367657.3_Missense_Mutation_p.V522A	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	530					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.V522A(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CTCTCCCAAAACCAGGTCAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	134	132					1																	176934332		2203	4300	6503	175200955	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1589T>C	1.37:g.176934332A>G	ENSP00000356626:p.Val530Ala		175200955	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	A	19.01	3.744603	0.69418	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.23950	1.88;2.29;2.29;1.89	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.38453	0.1041	L	0.29908	0.895	0.80722	D	1	P;P;P	0.52577	0.954;0.954;0.954	D;D;D	0.67900	0.954;0.954;0.932	T	0.20306	-1.0279	10	0.59425	D	0.04	-9.9244	14.8608	0.70379	1.0:0.0:0.0:0.0	.	530;522;522	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	A	522;522;530;522;522	ENSP00000356629:V522A;ENSP00000354536:V522A;ENSP00000356626:V530A;ENSP00000395041:V522A	ENSP00000354536:V522A	V	-	2	0	ASTN1	175200955	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.400000	0.90200	2.036000	0.60181	0.454000	0.30748	GTT		0.428	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		G	176934332	A	G	176934332	3	3	27	1	0	0	0	0	1	0	0	0	1065	43	2	4	2383	4	ASTN1	1	176934332	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10	65873105	176934332	72316289	5	2295										
CENPF	1063	hgsc.bcm.edu	37	chr1	214825154	214825154	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaagggaaagtgagagaggaAatagctgaatatcagctacg	14	4	1	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:214825154A>G	ENST00000366955.3	+	15	8253	c.8085A>G	c.(8083-8085)gaA>gaG	p.E2695E	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2791	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E2695E(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TGAGAGAGGAAATAGCTGAAT	0.423																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - coding silent(1)	large_intestine(1)	1											106	109	108					1																	214825154		2203	4300	6503	212891777	SO:0001819	synonymous_variant	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8085A>G	1.37:g.214825154A>G			212891777	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.423	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214825154	A	G	214825154	2	3	27	1	0	0	0	0	0	0	0	1	3237	11	1	4		4	CENPF	1	214825154	Silent	SNP	A	TCGA-AG-3600-01A-01W-0833-10	37890822	214825154	34425467	6	2296										
LIN9	286826	hgsc.bcm.edu	37	chr1	226474076	226474076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gccgaatttttccccattctActcttgttaactttcttgtt	4	11	3	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:226474076A>G	ENST00000328205.5	-	6	1075	c.530T>C	c.(529-531)gTa>gCa	p.V177A	LIN9_ENST00000366801.1_Missense_Mutation_p.V126A|LIN9_ENST00000481685.1_Missense_Mutation_p.V142A	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	161	Sufficient for interaction with RB1.				DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)		p.V177A(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		TCCCCATTCTACTCTTGTTAA	0.333																																					Ovarian(197;1696 2974 11248 14117)											1	Substitution - Missense(1)	large_intestine(1)	1											68	75	72					1																	226474076		2201	4298	6499	224540699	SO:0001583	missense	286826			AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"TUDOR gene similar", "rb related pathway actor"	609375	"lin-9 homolog (C. elegans)"			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.530T>C	1.37:g.226474076A>G	ENSP00000329102:p.Val177Ala		224540699	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.623090	0.28889	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.62780	0.2456	N	0.21282	0.65	0.80722	D	1	B;B;D	0.69078	0.001;0.001;0.997	B;B;D	0.79108	0.002;0.003;0.992	T	0.59107	-0.7516	9	0.20519	T	0.43	.	16.2265	0.82298	1.0:0.0:0.0:0.0	.	142;161;311	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	A	137;177;232;126;142;311	.	ENSP00000329102:V177A	V	-	2	0	LIN9	224540699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.794000	0.91867	2.233000	0.73108	0.533000	0.62120	GTA		0.333	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083		G	226474076	A	G	226474076	3	3	27	1	0	0	0	0	1	0	0	0	8837	391	14	4	1186	4	LIN9	1	226474076	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10	11648922	226474076	22776545	7	2297										
OR11L1	391189	hgsc.bcm.edu	37	chr1	248004646	248004646	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tctggaacaggagagctgcaTgagtggcgggaggtcgcaga	18	7	1	3	rs375462936		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr1:248004646T>A	ENST00000355784.2	-	1	608	c.553A>T	c.(553-555)Atg>Ttg	p.M185L		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	185						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M185L(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGAGCTGCATGAGTGGCGGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	100	99					1																	248004646		2203	4300	6503	246071269	SO:0001583	missense	391189			AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"GPCR / Class A : Olfactory receptors"	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.553A>T	1.37:g.248004646T>A	ENSP00000348033:p.Met185Leu		246071269		Missense_Mutation	SNP	ENST00000355784.2	37	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.673889	0.00758	.	.	ENSG00000197591	ENST00000355784	T	0.00010	9.41	4.27	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.333979	0.21349	U	0.075982	T	0.00039	0.0001	N	0.00424	-1.51	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27400	-1.0075	10	0.02654	T	1	.	5.6055	0.17377	0.1524:0.0:0.2889:0.5587	.	185	Q8NGX0	O11L1_HUMAN	L	185	ENSP00000348033:M185L	ENSP00000348033:M185L	M	-	1	0	OR11L1	246071269	0.000000	0.05858	0.940000	0.37924	0.569000	0.35902	-0.184000	0.09698	1.922000	0.55676	0.443000	0.29094	ATG		0.507	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959		A	248004646	T	A	248004646	3	1	27	1	0	0	0	0	1	0	0	0	10961	1464	51	5	419	5	OR11L1	1	248004646	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	21530570	248004646	1245975	8	2298										
XDH	7498	hgsc.bcm.edu	37	chr2	31588407	31588407	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atgcatcgcacagggcggccGgtcctgggggttaccgacag	16	12	0	0	rs143539472	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:31588407G>A	ENST00000379416.3	-	23	2508	c.2460C>T	c.(2458-2460)acC>acT	p.T820T		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	820					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)	p.T820T(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CAGGGCGGCCGGTCCTGGGGG	0.552																																					Colon(66;682 1445 30109 40147)											1	Substitution - coding silent(1)	large_intestine(1)	2						G		4,4402	8.1+/-20.4	0,4,2199	89	81	84		2460	-12.3	0	2	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	XDH	NM_000379.3		0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384		820/1334	31588407	5,13001	2203	4300	6503	31441911	SO:0001819	synonymous_variant	7498			D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2460C>T	2.37:g.31588407G>A			31441911	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																				0.552	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		A	31588407	G	A	31588407	2	1	27	1	0	0	0	0	0	0	0	1	17466	1103	39	1		1	XDH	2	31588407	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10		31588407	211610966	9	2299										
ARHGAP15	55843	hgsc.bcm.edu	37	chr2	143986188	143986188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctggattgttctttctagtcGaagaattgaattttacaaag	8	5	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:143986188G>A	ENST00000295095.6	+	5	502	c.335G>A	c.(334-336)cGa>cAa	p.R112Q	ARHGAP15_ENST00000409869.1_Missense_Mutation_p.R112Q	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	112	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)	p.R112Q(1)		endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		CTTTCTAGTCGAAGAATTGAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	93	91					2																	143986188		2203	4298	6501	143702658	SO:0001583	missense	55843			AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.335G>A	2.37:g.143986188G>A	ENSP00000295095:p.Arg112Gln		143702658	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	37	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.501846	0.44455	.	.	ENSG00000075884	ENST00000409869;ENST00000295095	T;T	0.75367	-0.93;-0.93	5.6	-0.35	0.12606	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.778678	0.12196	N	0.490747	T	0.57607	0.2065	N	0.24115	0.695	0.23174	N	0.998173	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.002	T	0.40496	-0.9560	10	0.34782	T	0.22	.	9.3426	0.38089	0.411:0.0:0.589:0.0	.	112;112	B4E0R3;Q53QZ3	.;RHG15_HUMAN	Q	112	ENSP00000386560:R112Q;ENSP00000295095:R112Q	ENSP00000295095:R112Q	R	+	2	0	ARHGAP15	143702658	0.026000	0.19158	0.603000	0.28903	0.993000	0.82548	-0.207000	0.09384	-0.392000	0.07751	-0.157000	0.13467	CGA		0.303	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		A	143986188	G	A	143986188	3	1	27	1	0	0	0	0	1	0	0	0	866	1058	37	1	349	1	ARHGAP15	2	143986188	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	112397781	143986188	99213185	10	2300										
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155555806	155555806	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atcctgggctccatcgtggaCgccttcctcatcggctgcat	10	15	1	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:155555806C>T	ENST00000295101.2	+	1	996	c.519C>T	c.(517-519)gaC>gaT	p.D173D	KCNJ3_ENST00000544049.1_Silent_p.D173D|AC061961.2_ENST00000443901.1_RNA	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	173		Role in the control of polyamine-mediated channel gating and in the blocking by intracellular magnesium. {ECO:0000250}.			potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)	p.D173D(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	CCATCGTGGACGCCTTCCTCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	2											92	77	82					2																	155555806		2203	4300	6503	155264052	SO:0001819	synonymous_variant	3760			U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.519C>T	2.37:g.155555806C>T			155264052	B4DEW7|Q8TBI0	Silent	SNP	ENST00000295101.2	37	CCDS2200.1																																																																																				0.597	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		T	155555806	C	T	155555806	2	4	27	1	0	0	0	0	0	0	0	1	8073	535	19	1		1	KCNJ3	2	155555806	Silent	SNP	C	TCGA-AG-3600-01A-01W-0833-10	11569618	155555806	87643567	11	2301										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180383311	180383311	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aataacttgtttcttctttgGgggaatggatactccaaatg	9	6	2	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:180383311G>C	ENST00000410066.1	-	5	1054	c.451C>G	c.(451-453)Cca>Gca	p.P151A	ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.P75A|ZNF385B_ENST00000336917.5_Missense_Mutation_p.P49A|ZNF385B_ENST00000409692.1_Missense_Mutation_p.P49A	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	151	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)	p.P151A(1)		breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TTCTTCTTTGGGGGAATGGAT	0.343																																					Colon(155;204 2491 32774 51842)											1	Substitution - Missense(1)	large_intestine(1)	2											117	121	120					2																	180383311		2203	4300	6503	180091556	SO:0001583	missense	151126			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.451C>G	2.37:g.180383311G>C	ENSP00000386845:p.Pro151Ala		180091556	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363625	0.41902	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692;ENST00000457304;ENST00000439340	T;T;T;T;T;T	0.43294	1.54;1.54;1.53;1.54;1.51;0.95	5.87	5.87	0.94306	.	0.047288	0.85682	D	0.000000	T	0.60650	0.2285	L	0.53249	1.67	0.51767	D	0.999938	D;D	0.69078	0.996;0.997	P;D	0.66716	0.883;0.946	T	0.51608	-0.8684	10	0.32370	T	0.25	2.3982	20.2119	0.98289	0.0:0.0:1.0:0.0	.	151;75	Q569K4;Q569K4-2	Z385B_HUMAN;.	A	151;49;75;49;49;82	ENSP00000386845:P151A;ENSP00000338225:P49A;ENSP00000386379:P75A;ENSP00000386507:P49A;ENSP00000394038:P49A;ENSP00000399198:P82A	ENSP00000338225:P49A	P	-	1	0	ZNF385B	180091556	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.377000	0.66184	2.784000	0.95788	0.585000	0.79938	CCA		0.343	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		C	180383311	G	C	180383311	3	2	27	1	0	0	0	0	1	0	0	0	17916	1232	43	5	988	5	ZNF385B	2	180383311	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	24827505	180383311	62816062	12	2302										
NUP35	129401	hgsc.bcm.edu	37	chr2	183993068	183993069	+	Frame_Shift_Ins	INS	-	-	C													0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tccaaagccaggagttaatgINScccagttcttacctggattt					rs146685934		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:183993068_183993069insC	ENST00000295119.4	+	2	197_198	c.94_95insC	c.(94-96)gccfs	p.A32fs	NUP35_ENST00000541912.1_5'UTR|NUP35_ENST00000409798.1_Frame_Shift_Ins_p.A15fs|NUP35_ENST00000497330.1_3'UTR	NM_138285.3	NP_612142.2	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	32					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Q33fs*23(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						AGGAGTTAATGCCCAGTTCTTA	0.426																																																1	Insertion - Frameshift(1)	large_intestine(1)	2																																								183701314	SO:0001589	frameshift_variant	129401			AF514993	CCDS2290.1, CCDS74614.1	2q32	2008-02-05			ENSG00000163002	ENSG00000163002			29797	protein-coding gene	gene with protein product		608140					Standard	XM_005246284		Approved	MP44	uc002upf.3	Q8NFH5	OTTHUMG00000132621	ENST00000295119.4:c.97dupC	2.37:g.183993071_183993071dupC	ENSP00000295119:p.Ala32fs		183701313	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	Frame_Shift_Ins	INS	ENST00000295119.4	37	CCDS2290.1																																																																																				0.426	NUP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255865.1	NM_138285		C	183993069	-	C	183993068	7	5	27	1	0	1	1	0	0	0	0	0	10794	1319	46	0	100	0	NUP35	2	183993068	Frame_Shift_Ins	INS	-	TCGA-AG-3600-01A-01W-0833-10	3609757	183993068	59206305	13	2303										
PID1	55022	hgsc.bcm.edu	37	chr2	229890815	229890815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	agtggtggagactttgcccaGgtaggtaacctgcagatgca	14	8	0	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr2:229890815G>A	ENST00000354069.6	-	3	316	c.286C>T	c.(286-288)Ctg>Ttg	p.L96L	PID1_ENST00000482518.2_Intron|PID1_ENST00000409462.1_Silent_p.L14L|PID1_ENST00000392055.3_Silent_p.L63L|PID1_ENST00000392054.3_Silent_p.L94L			Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	96	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to cytokine stimulus (GO:0071345)|cellular response to fatty acid (GO:0071398)|cellular response to interleukin-6 (GO:0071354)|cellular response to leptin stimulus (GO:0044320)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|mitochondrion morphogenesis (GO:0070584)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of mitochondrial DNA replication (GO:0090298)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of fat cell proliferation (GO:0070346)|positive regulation of gene expression (GO:0010628)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial fusion (GO:0010635)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L94L(1)		breast(4)|endometrium(3)|large_intestine(5)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		ACTTTGCCCAGGTAGGTAACC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	2											61	60	60					2																	229890815		2203	4300	6503	229599059	SO:0001819	synonymous_variant	55022			AK096636	CCDS2471.1, CCDS42830.1	2q36.3	2007-02-02			ENSG00000153823	ENSG00000153823			26084	protein-coding gene	gene with protein product		612930				17124247, 16815647, 15221005	Standard	NM_001100818		Approved	NYGGF4, FLJ20701	uc002vps.4	Q7Z2X4	OTTHUMG00000133191	ENST00000354069.6:c.286C>T	2.37:g.229890815G>A			229599059	B3KU82|Q68CJ2|Q6ZUS3|Q8IXL0|Q9NWP6	Silent	SNP	ENST00000354069.6	37																																																																																					0.502	PID1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000331810.2	NM_017933		A	229890815	G	A	229890815	2	1	27	1	0	0	0	0	0	0	0	1	11913	991	35	3		3	PID1	2	229890815	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	45897747	229890815	13308558	14	2304										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29910415	29910415	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaagcgacagaatcaaagcaAatatacccagaatgggaggc	11	8	1	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:29910415A>C	ENST00000383767.2	+	7	1040	c.704A>C	c.(703-705)aAa>aCa	p.K235T	RBMS3_ENST00000273139.9_Missense_Mutation_p.K235T|RBMS3_ENST00000445033.1_Missense_Mutation_p.K235T|RBMS3_ENST00000452462.1_Missense_Mutation_p.K235T|RBMS3_ENST00000396583.3_Missense_Mutation_p.K235T|RBMS3_ENST00000456853.1_Missense_Mutation_p.K235T|RBMS3_ENST00000434693.2_Missense_Mutation_p.K234T|RBMS3_ENST00000383766.2_Missense_Mutation_p.K234T			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	235					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)	p.K235T(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				AATCAAAGCAAATATACCCAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	58	60					3																	29910415		2203	4300	6503	29885419	SO:0001583	missense	27303			AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.704A>C	3.37:g.29910415A>C	ENSP00000373277:p.Lys235Thr		29885419	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	37	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.339000	0.81911	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000445033;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T;T	0.74002	-0.8;1.68;-0.8;-0.8;-0.8;1.79;-0.8;1.68	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.85869	0.5797	M	0.79805	2.47	0.80722	D	1	D;P;P;D	0.63046	0.991;0.935;0.575;0.992	D;P;B;D	0.65010	0.931;0.856;0.372;0.917	D	0.86635	0.1888	9	.	.	.	.	16.2762	0.82644	1.0:0.0:0.0:0.0	.	235;235;234;235	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	T	234;235;235;235;235;234;235;235	ENSP00000395592:K234T;ENSP00000379828:K235T;ENSP00000373277:K235T;ENSP00000391934:K235T;ENSP00000273139:K235T;ENSP00000373276:K234T;ENSP00000397926:K235T;ENSP00000400519:K235T	.	K	+	2	0	RBMS3	29885419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.243000	0.73865	0.482000	0.46254	AAA		0.463	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		C	29910415	A	C	29910415	3	2	27	1	0	0	0	0	1	0	0	0	13187	14	1	4	730	4	RBMS3	3	29910415	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10		29910415	168112015	15	2305										
UBP1	7342	hgsc.bcm.edu	37	chr3	33450220	33450220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	agaatcaccgtagtctgctgGcaaagtccgcttgctggact	11	11	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:33450220G>A	ENST00000283629.3	-	8	1418	c.889C>T	c.(889-891)Cca>Tca	p.P297S	UBP1_ENST00000283628.5_Missense_Mutation_p.P297S|UBP1_ENST00000486388.1_5'Flank|UBP1_ENST00000447368.2_Intron	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	297				SSKRTLP -> VQQADFA (in Ref. 1). {ECO:0000305}.	angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P297S(2)		breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TAGTCTGCTGGCAAAGTCCGC	0.448																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	3											121	115	117					3																	33450220		2203	4300	6503	33425224	SO:0001583	missense	7342			AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.889C>T	3.37:g.33450220G>A	ENSP00000283629:p.Pro297Ser		33425224	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011871	0.75046	.	.	ENSG00000153560	ENST00000283629;ENST00000283628	T;T	0.16897	2.31;2.31	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00376	-1.1779	10	0.31617	T	0.26	-11.0023	18.833	0.92148	0.0:0.0:1.0:0.0	.	297	Q9NZI7	UBIP1_HUMAN	S	297	ENSP00000283629:P297S;ENSP00000283628:P297S	ENSP00000283628:P297S	P	-	1	0	UBP1	33425224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	2.890000	0.99128	0.585000	0.79938	CCA		0.448	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		A	33450220	G	A	33450220	3	1	27	1	0	0	0	0	1	0	0	0	16935	1203	42	3	769	3	UBP1	3	33450220	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	3539805	33450220	164572210	16	2306										
ZNF502	91392	hgsc.bcm.edu	37	chr3	44763242	44763242	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cgaaaacactcaaatcttacGcaacatcagagaattcacac	4	12	4	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:44763242G>A	ENST00000296091.4	+	4	1189	c.933G>A	c.(931-933)acG>acA	p.T311T	ZNF502_ENST00000436624.2_Silent_p.T311T|ZNF502_ENST00000449836.1_Silent_p.T311T	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T311T(1)		NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		CAAATCTTACGCAACATCAGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	3											131	138	136					3																	44763242		2202	4300	6502	44738246	SO:0001819	synonymous_variant	91392			AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.933G>A	3.37:g.44763242G>A			44738246		Silent	SNP	ENST00000296091.4	37	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	A	4.482	0.089388	0.08632	.	.	ENSG00000196653	ENST00000427783	.	.	.	4.27	-4.48	0.03515	.	.	.	.	.	T	0.38799	0.1054	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.50004	-0.8878	5	0.56958	D	0.05	-0.2728	9.2112	0.37320	0.1566:0.6668:0.0777:0.0989	.	.	.	.	H	311	.	ENSP00000397812:R311H	R	+	2	0	ZNF502	44738246	0.000000	0.05858	0.004000	0.12327	0.931000	0.56810	-5.056000	0.00155	-0.801000	0.04427	-0.254000	0.11334	CGC		0.403	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		A	44763242	G	A	44763242	2	1	27	1	0	0	0	0	0	0	0	1	17989	1074	38	1		1	ZNF502	3	44763242	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	11313022	44763242	153259188	17	2307										
IQCF2	389123	hgsc.bcm.edu	37	chr3	51897156	51897156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cgagggtgctggagaagaaaCggcaggcagctctgatcgcc	16	10	1	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:51897156C>T	ENST00000333127.3	+	3	294	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	89								p.R89W(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGAGAAGAAACGGCAGGCAGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	95	97					3																	51897156		2203	4300	6503	51872196	SO:0001583	missense	389123			AK128883	CCDS2835.1	3p21.31	2008-02-05			ENSG00000184345	ENSG00000184345			31815	protein-coding gene	gene with protein product							Standard	NM_203424		Approved		uc003dbt.1	Q8IXL9	OTTHUMG00000156914	ENST00000333127.3:c.265C>T	3.37:g.51897156C>T	ENSP00000329904:p.Arg89Trp		51872196		Missense_Mutation	SNP	ENST00000333127.3	37	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160000	0.78226	.	.	ENSG00000184345	ENST00000333127	T	0.71461	-0.57	4.95	3.06	0.35304	.	0.148704	0.31392	N	0.007731	D	0.83238	0.5211	M	0.86502	2.82	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.74856	-0.3522	10	0.87932	D	0	-25.0702	10.1516	0.42796	0.3886:0.6114:0.0:0.0	.	89	Q8IXL9	IQCF2_HUMAN	W	89	ENSP00000329904:R89W	ENSP00000329904:R89W	R	+	1	2	IQCF2	51872196	0.284000	0.24287	0.286000	0.24833	0.636000	0.38137	2.134000	0.42102	0.702000	0.31825	0.561000	0.74099	CGG		0.612	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		T	51897156	C	T	51897156	3	4	27	1	0	0	0	0	1	0	0	0	7829	527	19	1	275	1	IQCF2	3	51897156	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	7133914	51897156	146125274	18	2308										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73433742	73433742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gtacaggccgtaaggggtggCgctcttcacctggcacttga	14	11	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:73433742C>T	ENST00000263666.4	-	10	2089	c.1975G>A	c.(1975-1977)Gcc>Acc	p.A659T	PDZRN3_ENST00000466780.1_Missense_Mutation_p.A316T|PDZRN3_ENST00000462146.2_Missense_Mutation_p.A316T|PDZRN3_ENST00000535920.1_Missense_Mutation_p.A381T|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Missense_Mutation_p.A376T	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	659					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A659T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TAAGGGGTGGCGCTCTTCACC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	3											46	50	49					3																	73433742		2203	4300	6503	73516432	SO:0001583	missense	23024			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1975G>A	3.37:g.73433742C>T	ENSP00000263666:p.Ala659Thr		73516432	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	C	2.462	-0.323797	0.05350	.	.	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000492909	T;T;T;T;T;T	0.09817	2.94;3.63;3.52;3.52;3.64;3.63	4.84	-0.324	0.12706	.	0.793883	0.11793	N	0.529012	T	0.08714	0.0216	L	0.51422	1.61	0.09310	N	1	B;B;B;B	0.12013	0.001;0.005;0.003;0.001	B;B;B;B	0.08055	0.003;0.002;0.001;0.001	T	0.38436	-0.9661	10	0.24483	T	0.36	.	4.8184	0.13378	0.1367:0.4536:0.0:0.4098	.	381;376;376;659	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	T	659;381;316;316;376;357	ENSP00000263666:A659T;ENSP00000442026:A381T;ENSP00000418168:A316T;ENSP00000418484:A316T;ENSP00000418624:A376T;ENSP00000419250:A357T	ENSP00000263666:A659T	A	-	1	0	PDZRN3	73516432	0.554000	0.26522	0.000000	0.03702	0.027000	0.11550	-0.071000	0.11505	-0.163000	0.10946	0.655000	0.94253	GCC		0.652	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73433742	C	T	73433742	3	4	27	1	0	0	0	0	1	0	0	0	11740	768	27	1	1229	1	PDZRN3	3	73433742	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	21536586	73433742	124588688	19	2309										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74411158	74411158	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cctgcacctgaaccaacttcTtcattggattctttgaaaaa	5	11	3	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:74411158T>A	ENST00000263665.6	-	10	1274	c.1247A>T	c.(1246-1248)aAg>aTg	p.K416M		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	416	Ig-like C2-type 5.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.K416M(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		AACCAACTTCTTCATTGGATT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	66	65					3																	74411158		2203	4300	6503	74493848	SO:0001583	missense	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1247A>T	3.37:g.74411158T>A	ENSP00000263665:p.Lys416Met		74493848	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022176	0.75275	.	.	ENSG00000113805	ENST00000263665	T	0.61040	0.14	5.71	3.33	0.38152	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.104953	0.64402	D	0.000004	T	0.67711	0.2922	M	0.72118	2.19	0.53005	D	0.999969	D	0.54207	0.965	P	0.57548	0.823	T	0.68104	-0.5497	10	0.87932	D	0	.	9.797	0.40742	0.0:0.141:0.0:0.859	.	416	Q9P232	CNTN3_HUMAN	M	416	ENSP00000263665:K416M	ENSP00000263665:K416M	K	-	2	0	CNTN3	74493848	1.000000	0.71417	0.917000	0.36280	0.987000	0.75469	1.784000	0.38674	0.442000	0.26555	0.482000	0.46254	AAG		0.473	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		A	74411158	T	A	74411158	3	1	27	1	0	0	0	0	1	0	0	0	3648	1609	56	5	1891	5	CNTN3	3	74411158	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	977416	74411158	123611272	20	2310										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89468517	89468517	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgaccaccccaatatcattcGactggaaggagttgttacca	8	11	1	1	rs372257039		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:89468517G>C	ENST00000336596.2	+	11	2276	c.2051G>C	c.(2050-2052)cGa>cCa	p.R684P	EPHA3_ENST00000494014.1_Missense_Mutation_p.R684P	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	684	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.R684Q(1)|p.R684P(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AATATCATTCGACTGGAAGGA	0.433										TSP Lung(6;0.00050)																																						2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	3											104	98	100					3																	89468517		2203	4299	6502	89551207	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2051G>C	3.37:g.89468517G>C	ENSP00000337451:p.Arg684Pro		89551207	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289774	0.80914	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.64438	-0.1;-0.1	5.71	5.71	0.89125	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75199	0.3817	L	0.47016	1.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71692	-0.4516	9	.	.	.	.	19.8493	0.96733	0.0:0.0:1.0:0.0	.	684	P29320	EPHA3_HUMAN	P	684	ENSP00000337451:R684P;ENSP00000419190:R684P	.	R	+	2	0	EPHA3	89551207	1.000000	0.71417	0.766000	0.31476	0.590000	0.36582	9.869000	0.99810	2.701000	0.92244	0.563000	0.77884	CGA		0.433	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89468517	G	C	89468517	3	2	27	1	0	0	0	0	1	0	0	0	5181	1058	37	5	2119	5	EPHA3	3	89468517	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	15057359	89468517	108553913	21	2311										
STAG1	10274	hgsc.bcm.edu	37	chr3	136141796	136141796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctgtaaatgaaactgtacctTtgacagtaacataggaagtg	9	6	0	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:136141796T>C	ENST00000383202.2	-	17	1997	c.1741A>G	c.(1741-1743)Aag>Gag	p.K581E	STAG1_ENST00000536929.1_Missense_Mutation_p.K165E|STAG1_ENST00000434713.2_Missense_Mutation_p.K355E|STAG1_ENST00000236698.5_Missense_Mutation_p.K581E	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	581					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.K581E(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AACTGTACCTTTGACAGTAAC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	100	101					3																	136141796		2202	4299	6501	137624486	SO:0001583	missense	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1741A>G	3.37:g.136141796T>C	ENSP00000372689:p.Lys581Glu		137624486	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.047868	0.75846	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.15017	2.46;2.46;2.46;2.46	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.045892	0.85682	N	0.000000	T	0.27629	0.0679	M	0.67569	2.06	0.80722	D	1	P;B;P	0.41450	0.75;0.09;0.75	B;B;B	0.43360	0.417;0.076;0.417	T	0.02196	-1.1197	10	0.87932	D	0	.	16.2913	0.82755	0.0:0.0:0.0:1.0	.	598;581;581	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	E	581;581;355;165	ENSP00000372689:K581E;ENSP00000236698:K581E;ENSP00000404396:K355E;ENSP00000445787:K165E	ENSP00000236698:K581E	K	-	1	0	STAG1	137624486	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.040000	0.89188	2.248000	0.74166	0.529000	0.55759	AAG		0.308	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		C	136141796	T	C	136141796	3	2	27	1	0	0	0	0	1	0	0	0	15281	1850	64	4	2107	4	STAG1	3	136141796	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	46673279	136141796	61880634	22	2312										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157081404	157081404	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gtgatctctcagtgtctgtcTtaaacggcagcttgtcattt	9	9	5	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr3:157081404T>G	ENST00000362010.2	-	9	1791	c.1484A>C	c.(1483-1485)aAg>aCg	p.K495T	VEPH1_ENST00000392833.2_Missense_Mutation_p.K495T|VEPH1_ENST00000543418.1_Missense_Mutation_p.K495T|VEPH1_ENST00000392832.2_Missense_Mutation_p.K495T|RP11-550I24.2_ENST00000487238.1_RNA	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	495						plasma membrane (GO:0005886)		p.K495T(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			AGTGTCTGTCTTAAACGGCAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											102	108	106					3																	157081404		2203	4300	6503	158564098	SO:0001583	missense	79674			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1484A>C	3.37:g.157081404T>G	ENSP00000354919:p.Lys495Thr		158564098	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	T	9.758	1.169232	0.21621	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.37	4.22	0.49857	.	0.604741	0.18000	N	0.154931	T	0.08537	0.0212	L	0.32530	0.975	0.09310	N	0.999995	B;B	0.22983	0.078;0.002	B;B	0.21708	0.036;0.006	T	0.29971	-0.9994	10	0.34782	T	0.22	-2.2986	7.406	0.26991	0.0:0.2168:0.0:0.7832	.	495;495	Q14D04-2;Q14D04	.;MELT_HUMAN	T	495	ENSP00000376578:K495T;ENSP00000354919:K495T;ENSP00000446258:K495T;ENSP00000376577:K495T	ENSP00000354919:K495T	K	-	2	0	VEPH1	158564098	0.003000	0.15002	0.017000	0.16124	0.724000	0.41520	1.138000	0.31491	0.887000	0.36136	0.528000	0.53228	AAG		0.428	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		G	157081404	T	G	157081404	3	3	27	1	0	0	0	0	1	0	0	0	17194	1609	56	4	1041	4	VEPH1	3	157081404	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	20939608	157081404	40941026	23	2313										
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2341226	2341226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gtcgaagtgcctcagcgcttCcctcatcttctctgtgtagg	10	13	4	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:2341226C>T	ENST00000290974.2	-	4	814	c.475G>A	c.(475-477)Gaa>Aaa	p.E159K	ZFYVE28_ENST00000503000.1_Missense_Mutation_p.E159K|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.E89K|ZFYVE28_ENST00000515169.1_Missense_Mutation_p.E89K|ZFYVE28_ENST00000509171.1_Missense_Mutation_p.E112K|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.E159K	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	159					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.E159K(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						CTCAGCGCTTCCCTCATCTTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	80	87					4																	2341226		2203	4300	6503	2311024	SO:0001583	missense	57732			AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.475G>A	4.37:g.2341226C>T	ENSP00000290974:p.Glu159Lys		2311024	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	37	CCDS33942.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.969920	0.92855	.	.	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312;ENST00000515169;ENST00000509171;ENST00000503000	T;T;T;T;T;T	0.36878	1.59;1.59;1.59;1.23;1.23;1.59	4.5	4.5	0.54988	.	0.177355	0.49305	D	0.000158	T	0.34513	0.0900	L	0.38175	1.15	0.80722	D	1	P;P;P	0.47762	0.827;0.787;0.9	B;B;B	0.44133	0.442;0.218;0.438	T	0.20739	-1.0266	10	0.51188	T	0.08	.	16.255	0.82510	0.0:1.0:0.0:0.0	.	159;112;159	Q9HCC9-2;E9PB54;Q9HCC9	.;.;LST2_HUMAN	K	159;159;89;89;112;159	ENSP00000290974:E159K;ENSP00000425706:E159K;ENSP00000426299:E89K;ENSP00000425766:E89K;ENSP00000422638:E112K;ENSP00000423694:E159K	ENSP00000290974:E159K	E	-	1	0	ZFYVE28	2311024	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.340000	0.65958	2.056000	0.61249	0.585000	0.79938	GAA		0.647	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		T	2341226	C	T	2341226	3	4	27	1	0	0	0	0	1	0	0	0	17709	864	30	3	2448	3	ZFYVE28	4	2341226	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		2341226	188813050	24	2314										
EVC2	132884	hgsc.bcm.edu	37	chr4	5627563	5627563	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aagtcattgtccaacttctgCttgattgaaaagacttctgt	7	8	3	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:5627563C>A	ENST00000344408.5	-	13	2012	c.1959G>T	c.(1957-1959)aaG>aaT	p.K653N	EVC2_ENST00000344938.1_Missense_Mutation_p.K653N|EVC2_ENST00000310917.2_Missense_Mutation_p.K573N	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	653					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K653N(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CCAACTTCTGCTTGATTGAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											177	165	169					4																	5627563		2203	4300	6503	5678464	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1959G>T	4.37:g.5627563C>A	ENSP00000342144:p.Lys653Asn		5678464	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048302	0.55110	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.81078	-1.45;-1.45;-1.45	5.54	-1.13	0.09775	.	0.161694	0.56097	D	0.000040	D	0.84320	0.5446	M	0.67953	2.075	0.25771	N	0.984834	D	0.71674	0.998	D	0.66847	0.947	T	0.77094	-0.2715	10	0.36615	T	0.2	-13.4318	10.4079	0.44274	0.0:0.4326:0.0:0.5674	.	653	Q86UK5	LBN_HUMAN	N	653;573;653	ENSP00000339954:K653N;ENSP00000311683:K573N;ENSP00000342144:K653N	ENSP00000311683:K573N	K	-	3	2	EVC2	5678464	0.937000	0.31787	0.050000	0.19076	0.963000	0.63663	0.150000	0.16263	-0.435000	0.07264	-0.157000	0.13467	AAG		0.393	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5627563	C	A	5627563	3	1	27	1	0	0	0	0	1	0	0	0	5299	796	28	2	2007	2	EVC2	4	5627563	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	3286337	5627563	185526713	25	2315										
PPAT	5471	hgsc.bcm.edu	37	chr4	57272716	57272716	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cattatgtgccacagctatcTtcccatgaagtgtttcaaca	6	11	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:57272716T>G	ENST00000264220.2	-	3	484	c.347A>C	c.(346-348)aAg>aCg	p.K116T	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	116	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.K116T(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	CACAGCTATCTTCCCATGAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											165	138	147					4																	57272716		2203	4300	6503	56967473	SO:0001583	missense	5471				CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.347A>C	4.37:g.57272716T>G	ENSP00000264220:p.Lys116Thr		56967473		Missense_Mutation	SNP	ENST00000264220.2	37	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289934	0.40494	.	.	ENSG00000128059	ENST00000264220	T	0.76578	-1.03	5.62	5.62	0.85841	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.042317	0.85682	D	0.000000	T	0.58293	0.2112	N	0.03154	-0.405	0.80722	D	1	B	0.18166	0.026	B	0.25987	0.065	T	0.56523	-0.7965	10	0.14252	T	0.57	-33.0574	15.8261	0.78709	0.0:0.0:0.0:1.0	.	116	Q06203	PUR1_HUMAN	T	116	ENSP00000264220:K116T	ENSP00000264220:K116T	K	-	2	0	PPAT	56967473	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.639000	0.67868	2.138000	0.66242	0.477000	0.44152	AAG		0.393	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		G	57272716	T	G	57272716	3	3	27	1	0	0	0	0	1	0	0	0	12333	1609	56	4	1242	4	PPAT	4	57272716	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	51645153	57272716	133881560	26	2316										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346670	71346670	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	taaatgtctgcacaaacgctGtaggcctaagcttccacctt	7	12	1	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:71346670G>C	ENST00000304887.5	+	3	399	c.209G>C	c.(208-210)tGt>tCt	p.C70S	MUC7_ENST00000456088.1_Missense_Mutation_p.C70S|MUC7_ENST00000413702.1_Missense_Mutation_p.C70S|MUC7_ENST00000514512.1_3'UTR	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	70				C -> S (in Ref. 4; AA sequence). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.C70S(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			CACAAACGCTGTAGGCCTAAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											158	153	155					4																	71346670		2203	4300	6503	71381259	SO:0001583	missense	4589			BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.209G>C	4.37:g.71346670G>C	ENSP00000302021:p.Cys70Ser		71381259	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	G	5.451	0.268263	0.10349	.	.	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.54866	0.57;0.55;0.57;0.57	3.06	-3.31	0.04988	.	.	.	.	.	T	0.29749	0.0743	N	0.19112	0.55	0.09310	N	1	B	0.24823	0.112	B	0.23574	0.047	T	0.20907	-1.0261	9	0.19590	T	0.45	3.3226	6.1604	0.20360	0.4666:0.3683:0.1651:0.0	.	70	Q8TAX7	MUC7_HUMAN	S	70	ENSP00000407422:C70S;ENSP00000427594:C70S;ENSP00000400585:C70S;ENSP00000302021:C70S	ENSP00000302021:C70S	C	+	2	0	MUC7	71381259	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.136000	0.01305	-0.877000	0.04012	-0.345000	0.07892	TGT		0.448	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		C	71346670	G	C	71346670	3	2	27	1	0	0	0	0	1	0	0	0	10011	1377	48	5	215	5	MUC7	4	71346670	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	14073954	71346670	119807606	27	2317										
PLAC8	51316	hgsc.bcm.edu	37	chr4	84029023	84029023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggagttctggggggccggacCgggaccgactccaggttggg	20	10	1	0	rs374282306		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:84029023C>T	ENST00000426923.2	-	2	130	c.52G>A	c.(52-54)Ggt>Agt	p.G18S	PLAC8_ENST00000411416.2_Missense_Mutation_p.G18S|PLAC8_ENST00000515389.1_Intron|PLAC8_ENST00000311507.4_Missense_Mutation_p.G18S|PLAC8_ENST00000509973.1_Intron|PLAC8_ENST00000505406.1_Missense_Mutation_p.G18S	NM_001130715.1	NP_001124187.1	Q9UHV8	PP13_HUMAN	placenta-specific 8	6	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)	p.G18S(1)		large_intestine(2)|lung(3)|ovary(1)	6		Hepatocellular(203;0.114)				GGGGCCGGACCGGGACCGACT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	4											35	33	34					4																	84029023		2203	4300	6503	84248047	SO:0001583	missense	51316			AF208846	CCDS3601.1	4q21.22	2006-05-20			ENSG00000145287	ENSG00000145287			19254	protein-coding gene	gene with protein product		607515				12758124, 12384430	Standard	NM_016619		Approved	onzin, C15	uc003hoe.3	Q9NZF1	OTTHUMG00000130294	ENST00000426923.2:c.52G>A	4.37:g.84029023C>T	ENSP00000399700:p.Gly18Ser		84248047	C5HZ15	Missense_Mutation	SNP	ENST00000426923.2	37	CCDS3601.1	.	.	.	.	.	.	.	.	.	.	C	8.381	0.837626	0.16891	.	.	ENSG00000145287	ENST00000311507;ENST00000411416;ENST00000505406;ENST00000426923	.	.	.	0.0465	0.0465	0.14256	.	7739.210000	0.00166	N	0.000000	T	0.17746	0.0426	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.11036	-1.0604	6	0.17369	T	0.5	-6.066	.	.	.	.	18	Q9NZF1	PLAC8_HUMAN	S	18	.	ENSP00000309509:G18S	G	-	1	0	PLAC8	84248047	0.003000	0.15002	0.003000	0.11579	0.008000	0.06430	0.145000	0.16157	0.132000	0.18615	0.134000	0.15878	GGT		0.562	PLAC8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363079.1	NM_016619		T	84029023	C	T	84029023	3	4	27	1	0	0	0	0	1	0	0	0	12046	652	23	1	307	1	PLAC8	4	84029023	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	12682353	84029023	107125253	28	2318										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85708719	85708719	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atttgaagaaggtaaaacttCttctagaaaatgtgtgggtc	10	4	2	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:85708719C>G	ENST00000295888.4	-	23	4224	c.3817G>C	c.(3817-3819)Gaa>Caa	p.E1273Q	WDFY3_ENST00000322366.6_Missense_Mutation_p.E1273Q	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1273					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.E1273Q(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GGTAAAACTTCTTCTAGAAAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											73	71	72					4																	85708719		2203	4300	6503	85927743	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3817G>C	4.37:g.85708719C>G	ENSP00000295888:p.Glu1273Gln		85927743	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441767	0.63067	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.74002	-0.8;-0.8	5.94	5.09	0.68999	Concanavalin A-like lectin/glucanase (1);	0.110926	0.64402	D	0.000003	T	0.75642	0.3877	M	0.80982	2.52	0.80722	D	1	B	0.31968	0.349	B	0.30179	0.112	T	0.76435	-0.2960	10	0.52906	T	0.07	.	15.0493	0.71854	0.0:0.932:0.0:0.068	.	1273	Q8IZQ1	WDFY3_HUMAN	Q	1273	ENSP00000318466:E1273Q;ENSP00000295888:E1273Q	ENSP00000295888:E1273Q	E	-	1	0	WDFY3	85927743	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.478000	0.81082	1.517000	0.48917	0.484000	0.47621	GAA		0.433	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		G	85708719	C	G	85708719	3	3	27	1	0	0	0	0	1	0	0	0	17310	922	32	5	6947	5	WDFY3	4	85708719	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	1679696	85708719	105445557	29	2319										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113360884	113360884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	agggatgtatcagtgtggagCcttacatactgggagaattt	13	5	1	1	rs188598288	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:113360884C>T	ENST00000458497.1	+	14	3673	c.3394C>T	c.(3394-3396)Cct>Tct	p.P1132S	ALPK1_ENST00000504176.2_Missense_Mutation_p.P1054S|ALPK1_ENST00000177648.9_Missense_Mutation_p.P1132S	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1132	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P1132S(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CAGTGTGGAGCCTTACATACT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	101	103					4																	113360884		2203	4300	6503	113580333	SO:0001583	missense	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.3394C>T	4.37:g.113360884C>T	ENSP00000398048:p.Pro1132Ser		113580333	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.666898	0.88251	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.14640	2.49;2.49;2.49	5.2	5.2	0.72013	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.38453	0.1041	M	0.66506	2.035	0.54753	D	0.999988	D;D;D	0.89917	0.998;1.0;0.998	D;D;D	0.97110	0.979;1.0;0.988	T	0.14476	-1.0471	10	0.66056	D	0.02	-20.2205	18.7346	0.91749	0.0:1.0:0.0:0.0	.	1054;1054;1132	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	S	1132;1132;1054	ENSP00000398048:P1132S;ENSP00000177648:P1132S;ENSP00000426044:P1054S	ENSP00000177648:P1132S	P	+	1	0	ALPK1	113580333	1.000000	0.71417	0.896000	0.35187	0.959000	0.62525	7.186000	0.77722	2.415000	0.81967	0.544000	0.68410	CCT		0.373	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		T	113360884	C	T	113360884	3	4	27	1	0	0	0	0	1	0	0	0	544	739	26	3	3440	3	ALPK1	4	113360884	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	27652165	113360884	77793392	30	2320										
USP38	84640	hgsc.bcm.edu	37	chr4	144119068	144119068	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tttcagcattctccagaggcGttccatttggtaagttatga	9	8	2	2	rs141985651		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:144119068G>A	ENST00000307017.4	+	4	1547	c.1041G>A	c.(1039-1041)gcG>gcA	p.A347A	USP38_ENST00000510377.1_Silent_p.A347A	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	347					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.A347A(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CTCCAGAGGCGTTCCATTTGG	0.348													G|||	1	0.000199681	8e-04	0	5008	,	,		17995	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4											150	136	140					4																	144119068		2203	4300	6503	144338518	SO:0001819	synonymous_variant	84640			AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1041G>A	4.37:g.144119068G>A			144338518	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	37	CCDS3758.1																																																																																				0.348	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		A	144119068	G	A	144119068	2	1	27	1	0	0	0	0	0	0	0	1	17109	1132	40	1		1	USP38	4	144119068	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	30758184	144119068	47035208	31	2321										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247318	153247318	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	caacatgacccatcaaaacaTgtaaacactggcctgtctca	5	13	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr4:153247318T>G	ENST00000281708.4	-	10	2713	c.1484A>C	c.(1483-1485)cAt>cCt	p.H495P	FBXW7_ENST00000393956.3_Missense_Mutation_p.H319P|FBXW7_ENST00000603841.1_Missense_Mutation_p.H495P|FBXW7_ENST00000296555.5_Missense_Mutation_p.H377P|FBXW7_ENST00000603548.1_Missense_Mutation_p.H495P|FBXW7_ENST00000263981.5_Missense_Mutation_p.H415P	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	495					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.H495P(2)|p.H256P(1)|p.H415P(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CATCAAAACATGTAAACACTG	0.443			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	5	Substitution - Missense(4)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)	4											144	135	138					4																	153247318		2203	4300	6503	153466768	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1484A>C	4.37:g.153247318T>G	ENSP00000281708:p.His495Pro		153466768	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.835418	0.50951	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.72	4.54	0.55810	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.043646	0.85682	D	0.000000	T	0.71204	0.3312	M	0.63428	1.95	0.80722	D	1	P;D;D;D	0.71674	0.89;0.998;0.985;0.991	P;D;P;D	0.75484	0.844;0.986;0.893;0.936	T	0.72083	-0.4397	10	0.54805	T	0.06	-19.3096	11.9002	0.52680	0.0:0.0681:0.0:0.9319	.	319;495;377;415	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	P	495;377;415;319	ENSP00000281708:H495P;ENSP00000296555:H377P;ENSP00000263981:H415P;ENSP00000377528:H319P	ENSP00000263981:H415P	H	-	2	0	FBXW7	153466768	1.000000	0.71417	0.977000	0.42913	0.162000	0.22319	7.965000	0.87945	1.101000	0.41535	-0.263000	0.10527	CAT		0.443	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153247318	T	G	153247318	3	3	27	1	0	0	0	0	1	0	0	0	5788	1464	51	4	651	4	FBXW7	4	153247318	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	9128250	153247318	37906958	32	2322										
LIFR	3977	hgsc.bcm.edu	37	chr5	38504163	38504163	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgcctggtaaatgccaagaaAgtttaacagctgttgaatta	9	6	0	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr5:38504163A>G	ENST00000263409.4	-	10	1514	c.1352T>C	c.(1351-1353)cTt>cCt	p.L451P	LIFR_ENST00000503088.1_5'UTR|LIFR_ENST00000453190.2_Missense_Mutation_p.L451P	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	451	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.L451P(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ATGCCAAGAAAGTTTAACAGC	0.279			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	1	Substitution - Missense(1)	large_intestine(1)	5											55	61	59					5																	38504163		2202	4292	6494	38539920	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1352T>C	5.37:g.38504163A>G	ENSP00000263409:p.Leu451Pro		38539920	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.958729	0.74016	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.66995	-0.24;-0.24	5.65	5.65	0.86999	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.637724	0.17132	N	0.185789	T	0.82181	0.4981	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.83781	0.0225	10	0.87932	D	0	-22.4314	14.7008	0.69154	1.0:0.0:0.0:0.0	.	451	P42702	LIFR_HUMAN	P	451	ENSP00000263409:L451P;ENSP00000398368:L451P	ENSP00000263409:L451P	L	-	2	0	LIFR	38539920	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	5.634000	0.67833	2.139000	0.66308	0.528000	0.53228	CTT		0.279	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		G	38504163	A	G	38504163	3	3	27	1	0	0	0	0	1	0	0	0	8803	72	3	4	1985	4	LIFR	5	38504163	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10		38504163	142411097	33	2323										
FAT2	2196	hgsc.bcm.edu	37	chr5	150947634	150947634	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	accaacaacttccactgactCcacttcagctcctgagctat	4	16	1	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr5:150947634C>G	ENST00000261800.5	-	1	871	c.859G>C	c.(859-861)Gag>Cag	p.E287Q		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	287					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E287Q(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCACTGACTCCACTTCAGCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											79	80	80					5																	150947634		2203	4300	6503	150927827	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.859G>C	5.37:g.150947634C>G	ENSP00000261800:p.Glu287Gln		150927827	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	5.004	0.186486	0.09495	.	.	ENSG00000086570	ENST00000261800	T	0.71103	-0.54	4.99	4.11	0.48088	.	0.701517	0.13727	N	0.366993	T	0.61135	0.2323	L	0.38175	1.15	0.28370	N	0.920024	B	0.27559	0.181	B	0.28638	0.092	T	0.48490	-0.9031	10	0.12766	T	0.61	.	15.3962	0.74794	0.0:0.8601:0.1399:0.0	.	287	Q9NYQ8	FAT2_HUMAN	Q	287	ENSP00000261800:E287Q	ENSP00000261800:E287Q	E	-	1	0	FAT2	150927827	0.997000	0.39634	0.230000	0.23976	0.174000	0.22865	4.904000	0.63279	1.305000	0.44909	-0.494000	0.04653	GAG		0.507	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150947634	C	G	150947634	3	3	27	1	0	0	0	0	1	0	0	0	5709	864	30	5	12282	5	FAT2	5	150947634	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	112443471	150947634	29967626	34	2324										
MRPL22	29093	hgsc.bcm.edu	37	chr5	154320684	154320684	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gcgaaagatggcggcggcagTactgggacagttgggtaagg	19	6	0	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr5:154320684T>G	ENST00000523037.1	+	1	55	c.14T>G	c.(13-15)gTa>gGa	p.V5G	GEMIN5_ENST00000285873.7_5'Flank|MRPL22_ENST00000265229.8_5'UTR|MRPL22_ENST00000522038.1_Missense_Mutation_p.V5G|MRPL22_ENST00000439747.3_Missense_Mutation_p.V5G	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	5					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.V5G(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GCGGCGGCAGTACTGGGACAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											145	147	146					5																	154320684		2203	4300	6503	154300877	SO:0001583	missense	29093			AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.14T>G	5.37:g.154320684T>G	ENSP00000431040:p.Val5Gly		154300877	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Missense_Mutation	SNP	ENST00000523037.1	37	CCDS4331.1	.	.	.	.	.	.	.	.	.	.	T	12.50	1.957767	0.34565	.	.	ENSG00000082515	ENST00000523037;ENST00000439747;ENST00000522038	T;T;T	0.53206	0.78;0.63;0.79	4.79	3.62	0.41486	.	1.561580	0.03406	N	0.203983	T	0.39835	0.1093	L	0.29908	0.895	0.09310	N	1	B	0.23058	0.079	B	0.19391	0.025	T	0.33007	-0.9885	10	0.87932	D	0	-7.0518	6.6955	0.23197	0.0:0.1116:0.0:0.8884	.	5	Q9NWU5	RM22_HUMAN	G	5	ENSP00000431040:V5G;ENSP00000411177:V5G;ENSP00000429039:V5G	ENSP00000411177:V5G	V	+	2	0	MRPL22	154300877	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.072000	0.14617	0.948000	0.37687	0.528000	0.53228	GTA		0.552	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			G	154320684	T	G	154320684	3	3	27	1	0	0	0	0	1	0	0	0	9818	1638	57	4	16	4	MRPL22	5	154320684	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	3373050	154320684	26594576	35	2325										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169423160	169423160	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tcctagaacacacgaactttGagttccaggtgagtataagc	9	9	0	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr5:169423160G>T	ENST00000256935.8	+	30	3144	c.3064G>T	c.(3064-3066)Gag>Tag	p.E1022*	DOCK2_ENST00000540750.1_Nonsense_Mutation_p.E83*|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Nonsense_Mutation_p.E514*	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1022	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.E1022*(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACGAACTTTGAGTTCCAGGT	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											85	78	80					5																	169423160		2203	4300	6503	169355738	SO:0001587	stop_gained	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3064G>T	5.37:g.169423160G>T	ENSP00000256935:p.Glu1022*		169355738	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	48	14.694421	0.99806	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	.	.	.	5.5	5.5	0.81552	.	0.170777	0.51477	D	0.000090	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.9036	0.86119	0.0:0.0:1.0:0.0	.	.	.	.	X	1022;514;83	.	ENSP00000256935:E1022X	E	+	1	0	DOCK2	169355738	1.000000	0.71417	1.000000	0.80357	0.439000	0.31926	7.136000	0.77285	2.588000	0.87417	0.643000	0.83706	GAG		0.502	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169423160	G	T	169423160	4	4	27	1	0	0	0	0	0	1	0	0	4698	1291	45	2	3182	2	DOCK2	5	169423160	Nonsense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	15102476	169423160	11492100	36	2326										
RREB1	6239	hgsc.bcm.edu	37	chr6	7248771	7248771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gccatacaaatgtcagacctGcgagcgaaccttcaccttga	8	13	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr6:7248771G>A	ENST00000349384.6	+	12	4948	c.4634G>A	c.(4633-4635)tGc>tAc	p.C1545Y	RREB1_ENST00000334984.6_Missense_Mutation_p.C1334Y|RREB1_ENST00000379938.2_Missense_Mutation_p.C1600Y|RREB1_ENST00000379933.3_Missense_Mutation_p.C1545Y	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1545					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C1545Y(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TGTCAGACCTGCGAGCGAACC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											81	75	77					6																	7248771		2203	4300	6503	7193770	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4634G>A	6.37:g.7248771G>A	ENSP00000305560:p.Cys1545Tyr		7193770	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.490235	0.84962	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	D;D;D;D	0.99974	-2.04;-2.04;-2.04;-10.2	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000002	D	0.99985	0.9996	H	0.95260	3.645	0.39188	D	0.962905	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	0.999;1.0;0.997	D	0.98308	1.0522	10	0.87932	D	0	-31.3866	19.8411	0.96685	0.0:0.0:1.0:0.0	.	1334;1545;1600	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	Y	1545;1600;1545;1334	ENSP00000369265:C1545Y;ENSP00000369270:C1600Y;ENSP00000305560:C1545Y;ENSP00000335574:C1334Y	ENSP00000335574:C1334Y	C	+	2	0	RREB1	7193770	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.199000	0.95003	2.683000	0.91414	0.655000	0.94253	TGC		0.537	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			A	7248771	G	A	7248771	3	1	27	1	0	0	0	0	1	0	0	0	13716	1319	46	3	4837	3	RREB1	6	7248771	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		7248771	163866296	37	2327										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40400699	40400699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gcgcagctccactgtccgccGgtcaatatcagggggtacaa	12	13	2	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr6:40400699G>A	ENST00000338305.6	-	2	696	c.154C>T	c.(154-156)Cgg>Tgg	p.R52W		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	52	LRRNT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.R52W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACTGTCCGCCGGTCAATATCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6											46	51	50					6																	40400699		2203	4300	6503	40508677	SO:0001583	missense	57497			AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.154C>T	6.37:g.40400699G>A	ENSP00000345985:p.Arg52Trp		40508677	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	37	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.301056	0.60195	.	.	ENSG00000156564	ENST00000338305	T	0.02631	4.22	5.76	5.76	0.90799	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.05868	0.0153	M	0.68317	2.08	0.80722	D	1	D	0.64830	0.994	P	0.55667	0.781	T	0.03193	-1.1062	10	0.87932	D	0	.	13.4862	0.61366	0.0:0.0:0.8436:0.1564	.	52	Q9ULH4	LRFN2_HUMAN	W	52	ENSP00000345985:R52W	ENSP00000345985:R52W	R	-	1	2	LRFN2	40508677	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.141000	0.50593	2.736000	0.93811	0.655000	0.94253	CGG		0.617	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		A	40400699	G	A	40400699	3	1	27	1	0	0	0	0	1	0	0	0	8967	1115	39	1	2223	1	LRFN2	6	40400699	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	33151928	40400699	130714368	38	2328										
MDN1	23195	hgsc.bcm.edu	37	chr6	90421780	90421786	+	Frame_Shift_Del	DEL	TAAATGA	TAAATGA	-													0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ccctgcggtatattcttggcTaaatgataaagccatttaac							TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	TAAATGA	TAAATGA	TAAATGA	-	TAAATGA	TAAATGA	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr6:90421780_90421786delTAAATGA	ENST00000369393.3	-	49	7735_7741	c.7620_7626delTCATTTA	c.(7618-7626)tatcatttafs	p.YHL2540fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.YHL2540fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2540					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.Y2540fs*1(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TATTCTTGGCTAAATGATAAAGCCATT	0.401																																																1	Deletion - Frameshift(1)	large_intestine(1)	6																																								90478507	SO:0001589	frameshift_variant	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.7620_7626delTCATTTA	6.37:g.90421780_90421786delTAAATGA	ENSP00000358400:p.Tyr2540fs		90478501	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	37	CCDS5024.1																																																																																				0.401	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90421786	TAAATGA	-	90421780	7	5	27	1	0	1	0	1	0	0	0	0	9445	1519	53	0	9380	0	MDN1	6	90421780	Frame_Shift_Del	DEL	TAAATGA	TCGA-AG-3600-01A-01W-0833-10	50021081	90421780	80693287	39	2329										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15508246	15508246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aaatactggcgaactcctggCgctattcatctgctttttgt	8	10	2	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr8:15508246C>T	ENST00000503731.1	+	3	497	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	TUSC3_ENST00000509380.1_Missense_Mutation_p.R117C|TUSC3_ENST00000506802.1_Missense_Mutation_p.R117C|TUSC3_ENST00000382020.4_Missense_Mutation_p.R117C|TUSC3_ENST00000503191.1_Intron	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	117	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)	p.R117C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GAACTCCTGGCGCTATTCATC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	8											232	225	228					8																	15508246		2203	4300	6503	15552617	SO:0001583	missense	7991			AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.349C>T	8.37:g.15508246C>T	ENSP00000424544:p.Arg117Cys		15552617	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	37	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	C	33	5.219528	0.95139	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.6	5.6	0.85130	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.69646	0.3134	M	0.85373	2.75	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.99;0.985;0.992;0.993;0.993;0.997	T	0.70033	-0.4983	10	0.44086	T	0.13	-12.7594	18.9923	0.92798	0.0:1.0:0.0:0.0	.	117;117;117;117;117;117	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	C	117	ENSP00000371450:R117C;ENSP00000425777:R117C;ENSP00000423426:R117C;ENSP00000424544:R117C	ENSP00000221167:R117C	R	+	1	0	TUSC3	15552617	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.644000	0.67902	2.805000	0.96524	0.655000	0.94253	CGC		0.398	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		T	15508246	C	T	15508246	3	4	27	1	0	0	0	0	1	0	0	0	16818	768	27	1	359	1	TUSC3	8	15508246	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		15508246	130855776	40	2330										
NRG1	3084	hgsc.bcm.edu	37	chr8	32616869	32616869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ccagtgagcatattgttgagAgagaagcagagacatccttt	11	7	0	4			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr8:32616869A>G	ENST00000405005.3	+	10	976	c.976A>G	c.(976-978)Aga>Gga	p.R326G	NRG1_ENST00000519301.1_Missense_Mutation_p.R276G|NRG1_ENST00000523079.1_Missense_Mutation_p.R323G|NRG1_ENST00000287845.5_Missense_Mutation_p.R297G|NRG1_ENST00000287842.3_Missense_Mutation_p.R323G|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Missense_Mutation_p.R331G|NRG1_ENST00000338921.4_Missense_Mutation_p.R334G|NRG1_ENST00000521670.1_Missense_Mutation_p.R326G|NRG1_ENST00000539990.1_Missense_Mutation_p.R169G			Q02297	NRG1_HUMAN	neuregulin 1	326					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.R331G(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TATTGTTGAGAGAGAAGCAGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											198	167	177					8																	32616869		2203	4300	6503	32736411	SO:0001583	missense	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.976A>G	8.37:g.32616869A>G	ENSP00000384620:p.Arg326Gly		32736411	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.977529	0.74360	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	6.16	4.97	0.65823	Neuregulin 1-related, C-terminal (1);	0.101521	0.64402	D	0.000004	T	0.74481	0.3722	M	0.62723	1.935	0.44055	D	0.99679	D;D;D;D;D;D;P;P;P;D;D	0.63046	0.992;0.987;0.976;0.968;0.974;0.976;0.774;0.941;0.952;0.968;0.984	D;P;D;P;P;D;B;P;P;P;P	0.65684	0.937;0.855;0.932;0.669;0.777;0.932;0.236;0.669;0.842;0.669;0.888	T	0.77316	-0.2633	10	0.87932	D	0	2.7449	13.5076	0.61493	0.6912:0.3088:0.0:0.0	.	169;172;323;297;331;322;334;323;326;331;326	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	G	293;276;399;323;334;331;326;297;323;326;326;169	ENSP00000430053:R293G;ENSP00000429582:R276G;ENSP00000429067:R399G;ENSP00000430120:R323G;ENSP00000343395:R334G;ENSP00000349275:R331G;ENSP00000287840:R326G;ENSP00000287845:R297G;ENSP00000287842:R323G;ENSP00000384620:R326G;ENSP00000428828:R326G;ENSP00000439276:R169G	ENSP00000287840:R326G	R	+	1	2	NRG1	32736411	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.107000	0.41844	2.367000	0.80283	0.528000	0.53228	AGA		0.413	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			G	32616869	A	G	32616869	3	3	27	1	0	0	0	0	1	0	0	0	10678	296	11	4	2610	4	NRG1	8	32616869	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10	17108623	32616869	113747153	41	2331										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72964964	72964964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aagaagcgcaacggctttggCgtggccttcccttgcagcaa	12	12	0	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr8:72964964C>T	ENST00000262209.4	-	14	1888	c.1681G>A	c.(1681-1683)Gcc>Acc	p.A561T	RP11-383H13.1_ENST00000537896.1_3'UTR|RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	561					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.A561T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ACGGCTTTGGCGTGGCCTTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											144	122	129					8																	72964964		2203	4300	6503	73127518	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1681G>A	8.37:g.72964964C>T	ENSP00000262209:p.Ala561Thr		73127518	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799815	0.70567	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.63913	-0.07;-0.07	4.98	4.98	0.66077	Ankyrin repeat-containing domain (4);	0.047663	0.85682	D	0.000000	T	0.64571	0.2610	N	0.21324	0.655	0.44890	D	0.997905	D	0.89917	1.0	D	0.76071	0.987	T	0.57854	-0.7739	10	0.13108	T	0.6	-4.8061	15.0441	0.71813	0.0:0.8574:0.1426:0.0	.	561	O75762	TRPA1_HUMAN	T	413;561	ENSP00000428151:A413T;ENSP00000262209:A561T	ENSP00000262209:A561T	A	-	1	0	TRPA1	73127518	0.985000	0.35326	0.992000	0.48379	0.439000	0.31926	2.548000	0.45794	2.466000	0.83321	0.585000	0.79938	GCC		0.468	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72964964	C	T	72964964	3	4	27	1	0	0	0	0	1	0	0	0	16617	768	27	1	1734	1	TRPA1	8	72964964	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	40348095	72964964	73399058	42	2332										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98232133	98232133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atatccagtctcctgtcctcGcgtcgatataaatccatgct	6	13	1	0	rs145690756	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr9:98232133G>A	ENST00000331920.6	-	13	2108	c.1809C>T	c.(1807-1809)cgC>cgT	p.R603R	PTCH1_ENST00000430669.2_Silent_p.R537R|PTCH1_ENST00000429896.2_Silent_p.R452R|PTCH1_ENST00000418258.1_Silent_p.R452R|PTCH1_ENST00000437951.1_Silent_p.R537R|PTCH1_ENST00000421141.1_Silent_p.R452R|PTCH1_ENST00000375274.2_Silent_p.R602R	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	603					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.R602R(2)|p.R603R(2)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TCCTGTCCTCGCGTCGATATA	0.438													G|||	3	0.000599042	0	0	5008	,	,		20000	0.003		0	False		,,,				2504	0															4	Substitution - coding silent(4)	large_intestine(4)	9						G	,,,,,,	2,4404	4.2+/-10.8	0,2,2201	148	143	145		1809,1611,1806,1356,1356,1356,1356	-10.4	0.9	9	dbSNP_134	145	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	,,,,,,	603/1448,537/1382,602/1447,452/1297,452/1297,452/1297,452/1297	98232133	3,13003	2203	4300	6503	97271954	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1809C>T	9.37:g.98232133G>A			97271954	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.438	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98232133	G	A	98232133	2	1	27	1	0	0	0	0	0	0	0	1	12764	1074	38	1		1	PTCH1	9	98232133	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10		98232133	42981298	43	2333										
PAPPA	5069	hgsc.bcm.edu	37	chr9	118989765	118989765	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggagaatcctggtgcagtatGcttccaacgcttcctcccca	9	14	0	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr9:118989765G>T	ENST00000328252.3	+	6	2536	c.2167G>T	c.(2167-2169)Gct>Tct	p.A723S	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	723					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A723S(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						GGTGCAGTATGCTTCCAACGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	9											172	150	158					9																	118989765		2203	4300	6503	118029586	SO:0001583	missense	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2167G>T	9.37:g.118989765G>T	ENSP00000330658:p.Ala723Ser		118029586	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323596	0.95708	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.02763	4.17	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	M	0.79475	2.455	0.80722	D	1	D;D	0.65815	0.995;0.994	P;P	0.56700	0.793;0.804	T	0.00035	-1.2260	10	0.59425	D	0.04	-11.9823	20.1624	0.98139	0.0:0.0:1.0:0.0	.	167;723	E7EMD3;Q13219	.;PAPP1_HUMAN	S	723;167	ENSP00000330658:A723S	ENSP00000330658:A723S	A	+	1	0	PAPPA	118029586	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.701000	0.98710	2.764000	0.94973	0.591000	0.81541	GCT		0.537	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118989765	G	T	118989765	3	4	27	1	0	0	0	0	1	0	0	0	11463	1319	46	2	2189	2	PAPPA	9	118989765	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	20757632	118989765	22223666	44	2334										
C5	727	hgsc.bcm.edu	37	chr9	123719634	123719634	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctacagtgatggatgtgatgCtaactttataagctggcaaa	10	6	0	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr9:123719634C>G	ENST00000223642.1	-	39	4720	c.4691G>C	c.(4690-4692)aGc>aCc	p.S1564T		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1564	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.S1564T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	GGATGTGATGCTAACTTTATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											171	165	167					9																	123719634		2203	4300	6503	122759455	SO:0001583	missense	727			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4691G>C	9.37:g.123719634C>G	ENSP00000223642:p.Ser1564Thr		122759455	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	0.181	-1.062212	0.01950	.	.	ENSG00000106804	ENST00000223642	T	0.20738	2.05	5.86	-1.92	0.07618	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	1.682700	0.02491	N	0.089439	T	0.10465	0.0256	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.21151	0.033	T	0.22138	-1.0225	10	0.19590	T	0.45	.	5.2408	0.15471	0.1575:0.2482:0.0:0.5943	.	1564	P01031	CO5_HUMAN	T	1564	ENSP00000223642:S1564T	ENSP00000223642:S1564T	S	-	2	0	C5	122759455	0.005000	0.15991	0.001000	0.08648	0.200000	0.23975	0.217000	0.17603	-0.205000	0.10219	-0.122000	0.15005	AGC		0.358	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		G	123719634	C	G	123719634	3	3	27	1	0	0	0	0	1	0	0	0	2286	797	28	5	351	5	C5	9	123719634	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	4729869	123719634	17493797	45	2335										
SETX	23064	hgsc.bcm.edu	37	chr9	135140105	135140106	+	Frame_Shift_Ins	INS	-	-	A													0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tttgaagtaacagtaagagtINSaatttccttggagtcagagg							TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr9:135140105_135140106insA	ENST00000224140.5	-	26	7736_7737	c.7554_7555insT	c.(7552-7557)attactfs	p.T2519fs	SETX_ENST00000477049.1_5'UTR|SETX_ENST00000372169.2_Frame_Shift_Ins_p.T2548fs|SETX_ENST00000393220.1_Frame_Shift_Ins_p.T2486fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2519					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.T2519fs*10(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ACAGTAAGAGTAATTTCCTTGG	0.505																																																1	Insertion - Frameshift(1)	large_intestine(1)	9																																								134129927	SO:0001589	frameshift_variant	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.7555dupT	9.37:g.135140107_135140107dupA	ENSP00000224140:p.Thr2519fs		134129926	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Ins	INS	ENST00000224140.5	37	CCDS6947.1																																																																																				0.505	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		A	135140106	-	A	135140105	7	5	27	1	0	1	1	0	0	0	0	0	14178	1638	57	0	482	0	SETX	9	135140105	Frame_Shift_Ins	INS	-	TCGA-AG-3600-01A-01W-0833-10	11420471	135140105	6073326	46	2336										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15617579	15617579	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaatgggcagaacaatctgcGgagggtgtgacactctgaaa	14	7	2	3	rs147383371		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr10:15617579G>C	ENST00000378076.3	-	24	2740	c.2387C>G	c.(2386-2388)cCg>cGg	p.P796R		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	796					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.P796R(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						AACAATCTGCGGAGGGTGTGA	0.443													G|||	1	0.000199681	0	0	5008	,	,		17937	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											121	107	112					10																	15617579		2203	4300	6503	15657585	SO:0001583	missense	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.2387C>G	10.37:g.15617579G>C	ENSP00000367316:p.Pro796Arg		15657585	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.36	1.915891	0.33815	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.43294	0.95	5.5	2.58	0.30949	Integrin alpha-2 (1);	0.153629	0.64402	D	0.000011	T	0.43722	0.1260	M	0.64997	1.995	0.37815	D	0.928187	B;B	0.33857	0.376;0.429	B;P	0.44597	0.325;0.454	T	0.31336	-0.9947	10	0.22109	T	0.4	.	7.4146	0.27036	0.1475:0.0:0.7161:0.1364	.	781;796	F5H818;P53708	.;ITA8_HUMAN	R	796;781	ENSP00000367316:P796R	ENSP00000367316:P796R	P	-	2	0	ITGA8	15657585	1.000000	0.71417	0.520000	0.27837	0.372000	0.29890	3.000000	0.49481	0.346000	0.23899	0.650000	0.86243	CCG		0.443	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		C	15617579	G	C	15617579	3	2	27	1	0	0	0	0	1	0	0	0	7903	1116	39	5	832	5	ITGA8	10	15617579	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		15617579	119917168	47	2337										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26355942	26355942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaagaaagggaacttcaaccGacctctaatatccaatctga	7	10	3	2	rs564946468		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr10:26355942G>A	ENST00000265944.5	+	11	1158	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	MYO3A_ENST00000543632.1_Missense_Mutation_p.R331Q	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	331					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R331Q(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AACTTCAACCGACCTCTAATA	0.348													G|||	1	0.000199681	0	0	5008	,	,		17660	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											99	92	94					10																	26355942		2203	4300	6503	26395948	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.992G>A	10.37:g.26355942G>A	ENSP00000265944:p.Arg331Gln		26395948	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	8.015	0.758356	0.15846	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;T	0.77229	-1.08;-0.84	5.56	1.15	0.20763	Protein kinase-like domain (1);	0.294555	0.41396	N	0.000894	T	0.63462	0.2513	L	0.51422	1.61	0.09310	N	1	P;B;B	0.36027	0.533;0.398;0.169	B;B;B	0.28553	0.091;0.038;0.019	T	0.50583	-0.8811	10	0.23891	T	0.37	.	8.0642	0.30651	0.5156:0.0:0.4844:0.0	.	331;331;331	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	Q	331	ENSP00000265944:R331Q;ENSP00000445909:R331Q	ENSP00000265944:R331Q	R	+	2	0	MYO3A	26395948	0.019000	0.18553	0.002000	0.10522	0.028000	0.11728	1.050000	0.30404	0.330000	0.23485	0.650000	0.86243	CGA		0.348	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26355942	G	A	26355942	3	1	27	1	0	0	0	0	1	0	0	0	10106	1058	37	1	1026	1	MYO3A	10	26355942	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	10738363	26355942	109178805	48	2338										
C10orf96	374355	hgsc.bcm.edu	37	chr10	118101627	118101627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctttaataatgattatgaaaTaacaaagaaaagagagcttt	6	3	0	4			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr10:118101627T>C	ENST00000333254.3	+	5	613	c.362T>C	c.(361-363)aTa>aCa	p.I121T	CCDC172_ENST00000497093.1_3'UTR	NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	121								p.I121T(1)									GATTATGAAATAACAAAGAAA	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	10											35	40	38					10																	118101627		2186	4250	6436	118091617	SO:0001583	missense	374355			BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.362T>C	10.37:g.118101627T>C	ENSP00000329860:p.Ile121Thr		118091617		Missense_Mutation	SNP	ENST00000333254.3	37	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471523	0.43942	.	.	ENSG00000182645	ENST00000333254;ENST00000423072	.	.	.	5.41	4.28	0.50868	.	0.420430	0.25227	N	0.032196	T	0.42381	0.1200	L	0.51422	1.61	0.24154	N	0.995688	B	0.17667	0.023	B	0.15052	0.012	T	0.41875	-0.9484	9	0.72032	D	0.01	-17.191	11.1923	0.48691	0.0:0.0722:0.0:0.9277	.	121	P0C7W6	CJ096_HUMAN	T	121	.	ENSP00000329860:I121T	I	+	2	0	C10orf96	118091617	1.000000	0.71417	0.967000	0.41034	0.960000	0.62799	3.982000	0.56909	1.005000	0.39183	0.533000	0.62120	ATA		0.264	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		C	118101627	T	C	118101627	3	2	27	1	0	0	0	0	1	0	0	0	1631	1406	49	4	376	4	C10orf96	10	118101627	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	91745685	118101627	17433120	49	2339										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5536943	5536943	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tactcaaggttttgtgaaggTtgttggatctgcattatctc	10	6	3	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:5536943T>G	ENST00000380184.1	-	1	992	c.729A>C	c.(727-729)caA>caC	p.Q243H	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	243								p.Q243H(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TTTGTGAAGGTTGTTGGATCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	92	91					11																	5536943		2201	4297	6498	5493519	SO:0001583	missense	143630			AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.729A>C	11.37:g.5536943T>G	ENSP00000369531:p.Gln243His		5493519	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	.	.	.	.	.	.	.	.	.	.	T	8.063	0.768656	0.15983	.	.	ENSG00000175518	ENST00000380184	T	0.50813	0.73	4.19	-0.611	0.11601	.	0.164374	0.29046	N	0.013318	T	0.54581	0.1867	M	0.72894	2.215	0.22171	N	0.999318	D	0.67145	0.996	P	0.57371	0.819	T	0.49735	-0.8908	10	0.87932	D	0	.	7.1044	0.25356	0.0:0.4325:0.0:0.5675	.	243	Q8IYU4	UBQLN_HUMAN	H	243	ENSP00000369531:Q243H	ENSP00000369531:Q243H	Q	-	3	2	UBQLNL	5493519	0.221000	0.23642	0.171000	0.22900	0.012000	0.07955	-0.229000	0.09098	-0.115000	0.11915	-0.262000	0.10625	CAA		0.463	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		G	5536943	T	G	5536943	3	3	27	1	0	0	0	0	1	0	0	0	16940	1722	60	4	702	4	UBQLNL	11	5536943	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10		5536943	129469573	50	2340										
ST5	6764	hgsc.bcm.edu	37	chr11	8739381	8739381	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gacagttgctgggattttcgTcctgctcttcggctctttaa	10	10	2	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:8739381T>C	ENST00000534127.1	-	8	1921	c.1536A>G	c.(1534-1536)ggA>ggG	p.G512G	ST5_ENST00000526099.1_Silent_p.G25G|ST5_ENST00000357665.1_Silent_p.G512G|ST5_ENST00000530438.1_Silent_p.G92G|ST5_ENST00000313726.6_Silent_p.G512G|ST5_ENST00000526757.1_Silent_p.G92G|ST5_ENST00000530991.1_5'UTR	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	512					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.G512G(1)		NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GGGATTTTCGTCCTGCTCTTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	11											193	144	161					11																	8739381		2201	4296	6497	8695957	SO:0001819	synonymous_variant	6764			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1536A>G	11.37:g.8739381T>C			8695957	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Silent	SNP	ENST00000534127.1	37	CCDS7791.1																																																																																				0.517	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		C	8739381	T	C	8739381	2	2	27	1	0	0	0	0	0	0	0	1	15259	1654	58	4		4	ST5	11	8739381	Silent	SNP	T	TCGA-AG-3600-01A-01W-0833-10	3202438	8739381	126267135	51	2341										
ACCS	84680	hgsc.bcm.edu	37	chr11	44098876	44098876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	atggcgctatcacacagcacGtgtgtctctatggcaacatc	9	12	2	0	rs375075014		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:44098876G>A	ENST00000263776.8	+	7	1038	c.604G>A	c.(604-606)Gtg>Atg	p.V202M	ACCS_ENST00000533208.1_3'UTR|ACCS_ENST00000432284.2_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	202					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.V202M(2)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CACACAGCACGTGTGTCTCTA	0.577																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	11						G	MET/VAL,MET/VAL	0,4406		0,0,2203	190	171	178		604,604	-1	0.9	11		178	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ACCS	NM_001127219.1,NM_032592.3	21,21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	202/502,202/502	44098876	1,13005	2203	4300	6503	44055452	SO:0001583	missense	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.604G>A	11.37:g.44098876G>A	ENSP00000263776:p.Val202Met		44055452	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.237682	0.22711	0.0	1.16E-4	ENSG00000110455	ENST00000263776	D	0.91351	-2.83	4.58	-0.992	0.10232	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.314579	0.29638	N	0.011592	T	0.78723	0.4328	N	0.20483	0.58	0.80722	D	1	P	0.44627	0.839	B	0.40375	0.327	T	0.70371	-0.4890	10	0.45353	T	0.12	-17.2656	4.6764	0.12713	0.352:0.0:0.505:0.143	.	202	Q96QU6	1A1L1_HUMAN	M	202	ENSP00000263776:V202M	ENSP00000263776:V202M	V	+	1	0	ACCS	44055452	0.273000	0.24181	0.859000	0.33776	0.171000	0.22731	0.282000	0.18829	0.125000	0.18397	-0.232000	0.12228	GTG		0.577	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		A	44098876	G	A	44098876	3	1	27	1	0	0	0	0	1	0	0	0	133	1145	40	1	626	1	ACCS	11	44098876	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	35359495	44098876	90907640	52	2342										
LRP4	4038	hgsc.bcm.edu	37	chr11	46880824	46880824	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	caggaggcagattccctctaCgatcttgatcttctccttgg	9	12	4	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:46880824C>T	ENST00000378623.1	-	38	5670	c.5428G>A	c.(5428-5430)Gta>Ata	p.V1810I	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1810					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.V1810I(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		ATTCCCTCTACGATCTTGATC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											151	141	144					11																	46880824		2201	4299	6500	46837400	SO:0001583	missense	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.5428G>A	11.37:g.46880824C>T	ENSP00000367888:p.Val1810Ile		46837400	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.693605	0.68386	.	.	ENSG00000134569	ENST00000378623	D	0.90261	-2.64	6.06	6.06	0.98353	.	0.069463	0.56097	N	0.000021	D	0.83027	0.5165	N	0.19112	0.55	0.51012	D	0.9999	B	0.34181	0.44	B	0.24394	0.053	T	0.83227	-0.0065	10	0.59425	D	0.04	.	16.0307	0.80574	0.0:0.8665:0.1335:0.0	.	1810	O75096	LRP4_HUMAN	I	1810	ENSP00000367888:V1810I	ENSP00000367888:V1810I	V	-	1	0	LRP4	46837400	1.000000	0.71417	0.979000	0.43373	0.872000	0.50106	5.672000	0.68102	2.882000	0.98803	0.655000	0.94253	GTA		0.547	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46880824	C	T	46880824	3	4	27	1	0	0	0	0	1	0	0	0	8988	536	19	1	293	1	LRP4	11	46880824	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	2781948	46880824	88125692	53	2343										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55904460	55904460	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tagaaaaccgtgactgctatCatatgcgaagcgcaggtgga	12	8	1	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:55904460C>G	ENST00000301529.1	-	1	734	c.735G>C	c.(733-735)atG>atC	p.M245I		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M245I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					TGACTGCTATCATATGCGAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											126	118	120					11																	55904460		2201	4296	6497	55661036	SO:0001583	missense	81168				CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.735G>C	11.37:g.55904460C>G	ENSP00000301529:p.Met245Ile		55661036	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	C	2.478	-0.320387	0.05386	.	.	ENSG00000167822	ENST00000301529	T	0.32988	1.43	2.75	0.634	0.17718	GPCR, rhodopsin-like superfamily (1);	0.378221	0.28730	N	0.014336	T	0.14485	0.0350	N	0.16307	0.4	0.09310	N	1	B	0.10296	0.003	B	0.17979	0.02	T	0.25745	-1.0123	10	0.17832	T	0.49	.	6.1247	0.20172	0.184:0.7088:0.0:0.1072	.	245	Q8NGG0	OR8J3_HUMAN	I	245	ENSP00000301529:M245I	ENSP00000301529:M245I	M	-	3	0	OR8J3	55661036	0.000000	0.05858	0.006000	0.13384	0.128000	0.20619	-1.102000	0.03332	0.032000	0.15435	0.297000	0.19635	ATG		0.393	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		G	55904460	C	G	55904460	3	3	27	1	0	0	0	0	1	0	0	0	11273	826	29	5	214	5	OR8J3	11	55904460	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	9023636	55904460	79102056	54	2344										
ATM	472	hgsc.bcm.edu	37	chr11	108218092	108218092	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aacttgtacatatagatctaGgtaagtaataaaatctatgt	6	4	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:108218092G>C	ENST00000452508.2	+	60	8860	c.8671G>C	c.(8671-8673)Ggt>Cgt	p.G2891R	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Splice_Site_p.G2891R|ATM_ENST00000525178.1_3'UTR			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2891	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.G2891R(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TATAGATCTAGGTAAGTAATA	0.308			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											74	79	77					11																	108218092		2201	4297	6498	107723302	SO:0001630	splice_region_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8671+1G>C	11.37:g.108218092G>C			107723302	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.865212	0.71949	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.85702	-2.02;-2.02	5.52	5.52	0.82312	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.95781	0.8627	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97255	0.9900	10	0.87932	D	0	.	19.45	0.94862	0.0:0.0:1.0:0.0	.	2891	Q13315	ATM_HUMAN	R	2891	ENSP00000278616:G2891R;ENSP00000388058:G2891R	ENSP00000278616:G2891R	G	+	1	0	ATM	107723302	1.000000	0.71417	0.998000	0.56505	0.273000	0.26683	9.175000	0.94831	2.585000	0.87301	0.555000	0.69702	GGT		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Missense_Mutation	C	108218092	G	C	108218092	5	2	27	1	0	0	0	0	0	0	1	0	1110	1014	35	5	8901	5	ATM	11	108218092	Splice_Site	SNP	G	TCGA-AG-3600-01A-01W-0833-10	52313632	108218092	26788424	55	2345										
ACRV1	56	hgsc.bcm.edu	37	chr11	125547721	125547721	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgcttgaaattggtgcacctGaagcctgttcccctgaagcg	11	11	0	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr11:125547721G>A	ENST00000533904.1	-	2	866	c.524C>T	c.(523-525)tCa>tTa	p.S175L	ACRV1_ENST00000315608.3_Intron|ACRV1_ENST00000527795.1_Missense_Mutation_p.S105L|ACRV1_ENST00000445562.1_Missense_Mutation_p.S80L|ACRV1_ENST00000425431.1_Intron|ACRV1_ENST00000345274.1_Missense_Mutation_p.S105L|ACRV1_ENST00000453509.1_Intron|ACRV1_ENST00000348856.3_Missense_Mutation_p.S75L|ACRV1_ENST00000530048.1_Missense_Mutation_p.S120L|ACRV1_ENST00000353070.1_Intron			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	175					multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)		p.S175L(1)		kidney(1)|large_intestine(3)|lung(2)	6	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		TGGTGCACCTGAAGCCTGTTC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											126	108	114					11																	125547721		2201	4299	6500	125052931	SO:0001583	missense	56			AK223335	CCDS8460.1, CCDS8461.1, CCDS44759.1, CCDS44761.1	11q24.2	2012-05-16			ENSG00000134940	ENSG00000134940			127	protein-coding gene	gene with protein product	"sperm protein 10"	102525				1693291, 8288254	Standard	NM_001612		Approved	SPACA2, SP-10, D11S4365	uc001qcs.3	P26436	OTTHUMG00000165854	ENST00000533904.1:c.524C>T	11.37:g.125547721G>A	ENSP00000432816:p.Ser175Leu		125052931	Q53FF4	Missense_Mutation	SNP	ENST00000533904.1	37	CCDS8460.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.701492	0.48307	.	.	ENSG00000134940	ENST00000533904;ENST00000257382;ENST00000426183;ENST00000445562;ENST00000348856;ENST00000345274;ENST00000530048;ENST00000527795	T;T;T;T;T;T;T;T	0.24538	1.99;1.95;1.96;1.85;2.02;2.37;1.95;1.96	4.83	2.76	0.32466	.	1.086300	0.07215	N	0.859924	T	0.48429	0.1499	M	0.66939	2.045	0.25785	N	0.984684	P;B;B;P;D	0.89917	0.655;0.022;0.027;0.749;1.0	B;B;B;B;D	0.83275	0.231;0.054;0.019;0.393;0.996	T	0.16748	-1.0392	10	0.62326	D	0.03	0.851	8.1389	0.31071	0.2317:0.0:0.7683:0.0	.	175;105;80;120;105	P26436;P26436-8;P26436-6;P26436-3;P26436-4	ASPX_HUMAN;.;.;.;.	L	175;120;105;80;75;105;120;105	ENSP00000432816:S175L;ENSP00000257382:S120L;ENSP00000411583:S105L;ENSP00000412653:S80L;ENSP00000257385:S75L;ENSP00000257383:S105L;ENSP00000433720:S120L;ENSP00000436819:S105L	ENSP00000257382:S120L	S	-	2	0	ACRV1	125052931	0.015000	0.18098	0.003000	0.11579	0.030000	0.12068	1.847000	0.39299	0.577000	0.29470	0.650000	0.86243	TCA		0.537	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612		A	125547721	G	A	125547721	3	1	27	1	0	0	0	0	1	0	0	0	172	1294	45	3	285	3	ACRV1	11	125547721	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	17329629	125547721	9458795	56	2346										
PZP	5858	hgsc.bcm.edu	37	chr12	9307432	9307432	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggcgctcccaatggacgaggTtgtcttaagggtgagaaaaa	14	7	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:9307432T>G	ENST00000261336.2	-	29	3582	c.3554A>C	c.(3553-3555)aAc>aCc	p.N1185T	PZP_ENST00000381997.2_Missense_Mutation_p.N971T	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1185					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.N971T(1)|p.N1185T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						ATGGACGAGGTTGTCTTAAGG	0.448																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											48	49	48					12																	9307432		2203	4300	6503	9198699	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3554A>C	12.37:g.9307432T>G	ENSP00000261336:p.Asn1185Thr		9198699	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.326510	0.24080	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.38401	1.14;1.14	4.03	1.6	0.23607	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.30634	0.0771	M	0.66506	2.035	0.09310	N	1	P;B	0.38020	0.615;0.167	B;B	0.35278	0.199;0.196	T	0.30995	-0.9959	9	0.54805	T	0.06	.	2.7001	0.05146	0.2172:0.194:0.0:0.5888	.	971;1185	P20742-2;P20742	.;PZP_HUMAN	T	1185;971	ENSP00000261336:N1185T;ENSP00000371427:N971T	ENSP00000261336:N1185T	N	-	2	0	PZP	9198699	0.004000	0.15560	0.002000	0.10522	0.076000	0.17211	1.743000	0.38258	0.622000	0.30249	0.460000	0.39030	AAC		0.448	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		G	9307432	T	G	9307432	3	3	27	1	0	0	0	0	1	0	0	0	12906	1725	60	4	926	4	PZP	12	9307432	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10		9307432	124544463	57	2347										
PZP	5858	hgsc.bcm.edu	37	chr12	9312956	9312956	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gccttgatctcctgcgtcagCtgctgggtttcattcagata	10	11	4	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:9312956C>A	ENST00000261336.2	-	24	3031	c.3003G>T	c.(3001-3003)caG>caT	p.Q1001H	PZP_ENST00000539983.1_5'Flank|PZP_ENST00000381997.2_Missense_Mutation_p.Q787H	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1001					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q1001H(1)|p.Q787H(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CCTGCGTCAGCTGCTGGGTTT	0.423																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											130	119	123					12																	9312956		2203	4300	6503	9204223	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3003G>T	12.37:g.9312956C>A	ENSP00000261336:p.Gln1001His		9204223	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689487	0.29962	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.40756	1.02;1.02	4.56	0.539	0.17156	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.083862	0.47455	N	0.000231	T	0.69115	0.3075	H	0.97077	3.935	0.27109	N	0.962419	P;D	0.89917	0.933;1.0	P;D	0.91635	0.479;0.999	T	0.61013	-0.7148	10	0.87932	D	0	.	5.247	0.15502	0.0:0.5494:0.1372:0.3134	.	787;1001	P20742-2;P20742	.;PZP_HUMAN	H	1001;787	ENSP00000261336:Q1001H;ENSP00000371427:Q787H	ENSP00000261336:Q1001H	Q	-	3	2	PZP	9204223	0.979000	0.34478	0.022000	0.16811	0.013000	0.08279	0.265000	0.18515	-0.110000	0.12022	-0.244000	0.11960	CAG		0.423	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9312956	C	A	9312956	3	1	27	1	0	0	0	0	1	0	0	0	12906	796	28	2	1497	2	PZP	12	9312956	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	5524	9312956	124538939	58	2348										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40753134	40753134	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cattgatgtgtttgagtgaaTccacaaattcaacggaaaga	9	6	1	4			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:40753134T>C	ENST00000298910.7	+	47	6974	c.6916T>C	c.(6916-6918)Tcc>Ccc	p.S2306P		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2306					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.S2313P(1)|p.S2306P(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTTGAGTGAATCCACAAATTC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	12											104	100	102					12																	40753134		2203	4300	6503	39039401	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6916T>C	12.37:g.40753134T>C	ENSP00000298910:p.Ser2306Pro		39039401	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433254	0.83776	.	.	ENSG00000188906	ENST00000298910	T	0.35973	1.28	5.92	5.92	0.95590	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	M	0.64997	1.995	0.50813	D	0.999892	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.58934	-0.7548	10	0.54805	T	0.06	.	16.371	0.83361	0.0:0.0:0.0:1.0	.	2306;2306	Q17RV3;Q5S007	.;LRRK2_HUMAN	P	2306	ENSP00000298910:S2306P	ENSP00000298910:S2306P	S	+	1	0	LRRK2	39039401	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	6.364000	0.73086	2.267000	0.75376	0.477000	0.44152	TCC		0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		C	40753134	T	C	40753134	3	2	27	1	0	0	0	0	1	0	0	0	9062	1435	50	4	7102	4	LRRK2	12	40753134	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	31440178	40753134	93098761	59	2349										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56491645	56491645	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cgtgctactcaagtcacccaGtcaggttcaggtggcagatt	11	11	4	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:56491645G>T	ENST00000267101.3	+	21	2977	c.2537G>T	c.(2536-2538)aGt>aTt	p.S846I	ERBB3_ENST00000549832.1_5'Flank|ERBB3_ENST00000553131.1_Missense_Mutation_p.S87I|ERBB3_ENST00000415288.2_Missense_Mutation_p.S787I|ERBB3_ENST00000450146.2_Missense_Mutation_p.S203I	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	846	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)	p.S846I(1)		central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			AAGTCACCCAGTCAGGTTCAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12											185	151	163					12																	56491645		2203	4300	6503	54777912	SO:0001583	missense	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.2537G>T	12.37:g.56491645G>T	ENSP00000267101:p.Ser846Ile		54777912	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174093	0.78452	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000553131	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.87	5.87	0.94306	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.064574	0.64402	D	0.000005	T	0.47619	0.1455	N	0.16833	0.445	0.40655	D	0.982077	D	0.54397	0.966	P	0.47346	0.544	T	0.52571	-0.8558	10	0.62326	D	0.03	.	12.6639	0.56830	0.0764:0.0:0.9236:0.0	.	846	P21860	ERBB3_HUMAN	I	846;203;787;87	ENSP00000267101:S846I;ENSP00000399178:S203I;ENSP00000408340:S787I;ENSP00000449129:S87I	ENSP00000267101:S846I	S	+	2	0	ERBB3	54777912	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.509000	0.53386	2.941000	0.99782	0.655000	0.94253	AGT		0.502	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56491645	G	T	56491645	3	4	27	1	0	0	0	0	1	0	0	0	5221	1029	36	2	2750	2	ERBB3	12	56491645	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	15738511	56491645	77360250	60	2350										
UTP20	27340	hgsc.bcm.edu	37	chr12	101736764	101736764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ttgatgatatcaacttcgacGttcgctttgagactttccag	8	9	1	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:101736764G>A	ENST00000261637.4	+	35	4516	c.4342G>A	c.(4342-4344)Gtt>Att	p.V1448I		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1448					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.V1448I(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAACTTCGACGTTCGCTTTGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											121	114	117					12																	101736764		2203	4300	6503	100260895	SO:0001583	missense	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4342G>A	12.37:g.101736764G>A	ENSP00000261637:p.Val1448Ile		100260895	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702863	0.30232	.	.	ENSG00000120800	ENST00000261637	T	0.69435	-0.4	5.56	3.76	0.43208	Armadillo-type fold (1);	0.121365	0.56097	D	0.000033	T	0.58906	0.2155	L	0.53249	1.67	0.39380	D	0.966236	B	0.29232	0.238	B	0.21360	0.034	T	0.52320	-0.8591	10	0.26408	T	0.33	-7.6438	14.106	0.65091	0.0635:0.1115:0.825:0.0	.	1448	O75691	UTP20_HUMAN	I	1448	ENSP00000261637:V1448I	ENSP00000261637:V1448I	V	+	1	0	UTP20	100260895	1.000000	0.71417	0.597000	0.28824	0.662000	0.39071	3.941000	0.56607	0.328000	0.23435	-1.872000	0.00552	GTT		0.328	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101736764	G	A	101736764	3	1	27	1	0	0	0	0	1	0	0	0	17139	1145	40	1	4480	1	UTP20	12	101736764	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	45245119	101736764	32115131	61	2351										
UTP20	27340	hgsc.bcm.edu	37	chr12	101760432	101760432	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggtggacagaaagctgttgtGagcaggaaaaccaacatgca	13	7	0	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:101760432G>A	ENST00000261637.4	+	47	6396	c.6222G>A	c.(6220-6222)gtG>gtA	p.V2074V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2074					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.V2074V(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AAGCTGTTGTGAGCAGGAAAA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	12											165	152	157					12																	101760432		2203	4300	6503	100284563	SO:0001819	synonymous_variant	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6222G>A	12.37:g.101760432G>A			100284563	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																				0.488	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101760432	G	A	101760432	2	1	27	1	0	0	0	0	0	0	0	1	17139	1277	45	3		3	UTP20	12	101760432	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	23668	101760432	32091463	62	2352										
CLIP1	6249	hgsc.bcm.edu	37	chr12	122825559	122825559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cttcctgtaatttgtttaacGtgtcttccatttctacgaga	6	9	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr12:122825559G>A	ENST00000540338.1	-	10	2233	c.2192C>T	c.(2191-2193)aCg>aTg	p.T731M	CLIP1_ENST00000358808.2_Missense_Mutation_p.T720M|CLIP1_ENST00000361654.4_Missense_Mutation_p.T685M|CLIP1_ENST00000537178.1_Missense_Mutation_p.T685M|CLIP1_ENST00000302528.7_Missense_Mutation_p.T720M|CLIP1_ENST00000545889.1_Missense_Mutation_p.T421M			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	731					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.T720M(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TTTGTTTAACGTGTCTTCCAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											272	266	268					12																	122825559		2203	4300	6503	121391512	SO:0001583	missense	6249				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.2192C>T	12.37:g.122825559G>A	ENSP00000439093:p.Thr731Met		121391512	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.269708	0.23221	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.61627	2.6;0.64;0.64;0.68;0.69;0.09	5.87	3.06	0.35304	.	0.390391	0.31760	N	0.007105	T	0.49508	0.1561	L	0.54323	1.7	0.35316	D	0.784346	B;B;B;B	0.25743	0.133;0.116;0.116;0.07	B;B;B;B	0.28638	0.034;0.092;0.092;0.042	T	0.53450	-0.8437	10	0.44086	T	0.13	-2.3394	7.4886	0.27447	0.1898:0.0:0.6927:0.1175	.	421;685;720;731	F5H0N7;P30622-2;P30622-1;P30622	.;.;.;CLIP1_HUMAN	M	421;720;720;565;685;731;654	ENSP00000438743:T421M;ENSP00000303585:T720M;ENSP00000351665:T720M;ENSP00000445531:T685M;ENSP00000439093:T731M;ENSP00000437786:T654M	ENSP00000303585:T720M	T	-	2	0	CLIP1	121391512	0.612000	0.27000	0.023000	0.16930	0.599000	0.36880	3.518000	0.53451	0.480000	0.27534	0.655000	0.94253	ACG		0.373	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		A	122825559	G	A	122825559	3	1	27	1	0	0	0	0	1	0	0	0	3538	1145	40	1	2188	1	CLIP1	12	122825559	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	21065127	122825559	11026336	63	2353										
PCDH9	5101	hgsc.bcm.edu	37	chr13	66878829	66878829	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctctcagtagcacctcctgcTtgcttataagacttcagatt	6	12	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr13:66878829T>G	ENST00000377865.2	-	4	3806	c.3672A>C	c.(3670-3672)caA>caC	p.Q1224H	PCDH9_ENST00000544246.1_Missense_Mutation_p.Q1224H|PCDH9_ENST00000456367.1_Missense_Mutation_p.Q1190H|PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000328454.5_Missense_Mutation_p.Q1190H			Q9HC56	PCDH9_HUMAN	protocadherin 9	1224					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q1224H(1)|p.Q1224Q(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CACCTCCTGCTTGCTTATAAG	0.438																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|stomach(1)	13											120	112	114					13																	66878829		2203	4300	6503	65776830	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3672A>C	13.37:g.66878829T>G	ENSP00000367096:p.Gln1224His		65776830	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.054451	0.36277	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.55930	0.57;0.57;0.49;0.49	6.05	4.91	0.64330	.	0.000000	0.45606	D	0.000344	T	0.31857	0.0810	N	0.19112	0.55	0.29867	N	0.827155	P;B;P	0.36616	0.561;0.289;0.561	B;B;B	0.31946	0.066;0.138;0.066	T	0.38802	-0.9644	10	0.87932	D	0	.	5.6712	0.17723	0.0:0.1792:0.0:0.8208	.	1182;1190;1224	B7ZM79;Q9HC56-2;Q9HC56	.;.;PCDH9_HUMAN	H	1224;1224;1190;1190	ENSP00000442186:Q1224H;ENSP00000367096:Q1224H;ENSP00000401699:Q1190H;ENSP00000332060:Q1190H	ENSP00000332060:Q1190H	Q	-	3	2	PCDH9	65776830	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.115000	0.31209	2.320000	0.78422	0.528000	0.53228	CAA		0.438	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		G	66878829	T	G	66878829	3	3	27	1	0	0	0	0	1	0	0	0	11549	1606	56	4	45	4	PCDH9	13	66878829	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10		66878829	48291049	64	2354										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63473136	63473136	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tttgattcgtagttgtcaaaAgtttgcctgactttctcaat	7	7	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr14:63473136A>G	ENST00000322893.7	-	3	520	c.252T>C	c.(250-252)acT>acC	p.T84T	KCNH5_ENST00000394968.1_Silent_p.T26T|KCNH5_ENST00000420622.2_Silent_p.T84T|KCNH5_ENST00000394964.2_Silent_p.T26T	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	84	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.T84T(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		AGTTGTCAAAAGTTTGCCTGA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	14											106	103	104					14																	63473136		2202	4299	6501	62542889	SO:0001819	synonymous_variant	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.252T>C	14.37:g.63473136A>G			62542889	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																				0.343	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		G	63473136	A	G	63473136	2	3	27	1	0	0	0	0	0	0	0	1	8056	59	3	4		4	KCNH5	14	63473136	Silent	SNP	A	TCGA-AG-3600-01A-01W-0833-10		63473136	43876404	65	2355										
C14orf50	145376	hgsc.bcm.edu	37	chr14	65035069	65035069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tttcaaatctccccataggaAtaagaatcttgataatttcc	4	9	3	2	rs149616368	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr14:65035069A>G	ENST00000298705.1	+	7	533	c.437A>G	c.(436-438)aAt>aGt	p.N146S	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	146					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.N146S(1)									CCCCATAGGAATAAGAATCTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	14											50	49	50					14																	65035069		2202	4293	6495	64104822	SO:0001583	missense	145376				CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.437A>G	14.37:g.65035069A>G	ENSP00000298705:p.Asn146Ser		64104822	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015687	0.35606	.	.	ENSG00000165807	ENST00000298705;ENST00000557202	T;T	0.29142	1.58;1.58	5.87	4.73	0.59995	.	0.147056	0.48286	N	0.000191	T	0.25044	0.0608	L	0.56769	1.78	0.33349	D	0.570835	B	0.25667	0.131	B	0.20955	0.032	T	0.29027	-1.0025	10	0.09590	T	0.72	-21.2003	8.6299	0.33913	0.9136:0.0:0.0864:0.0	.	146	Q96LQ0	PPR36_HUMAN	S	146;13	ENSP00000298705:N146S;ENSP00000452491:N13S	ENSP00000298705:N146S	N	+	2	0	C14orf50	64104822	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.801000	0.38843	1.045000	0.40225	0.533000	0.62120	AAT		0.308	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		G	65035069	A	G	65035069	3	3	27	1	0	0	0	0	1	0	0	0	1781	101	4	4	463	4	C14orf50	14	65035069	Missense_Mutation	SNP	A	TCGA-AG-3600-01A-01W-0833-10	1561933	65035069	42314471	66	2356										
GOLGA5	9950	hgsc.bcm.edu	37	chr14	93290963	93290963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gcagaattaaagatcgagacGaagaaattcaaaaactcagg	9	6	2	4			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr14:93290963G>A	ENST00000163416.2	+	9	1949	c.1693G>A	c.(1693-1695)Gaa>Aaa	p.E565K	GOLGA5_ENST00000355976.2_Missense_Mutation_p.E565K	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	565					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.E565K(2)		large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		AGATCGAGACGAAGAAATTCA	0.343			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	2	Substitution - Missense(2)	large_intestine(2)	14											80	78	79					14																	93290963		2203	4300	6503	92360716	SO:0001583	missense	9950			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.1693G>A	14.37:g.93290963G>A	ENSP00000163416:p.Glu565Lys		92360716	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.317533	0.81469	.	.	ENSG00000066455	ENST00000163416;ENST00000355976;ENST00000439315	T;T	0.44083	0.93;0.93	5.66	5.66	0.87406	.	0.307474	0.22867	N	0.054669	T	0.37320	0.0999	L	0.36672	1.1	0.58432	D	0.999997	B	0.21452	0.056	B	0.19391	0.025	T	0.11036	-1.0604	10	0.19590	T	0.45	-15.0819	20.1253	0.97977	0.0:0.0:1.0:0.0	.	565	Q8TBA6	GOGA5_HUMAN	K	565;565;474	ENSP00000163416:E565K;ENSP00000348252:E565K	ENSP00000163416:E565K	E	+	1	0	GOLGA5	92360716	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.527000	0.90594	2.832000	0.97577	0.655000	0.94253	GAA		0.343	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			A	93290963	G	A	93290963	3	1	27	1	0	0	0	0	1	0	0	0	6576	1059	37	1	1723	1	GOLGA5	14	93290963	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	28255894	93290963	14058577	67	2357										
UACA	55075	hgsc.bcm.edu	37	chr15	70961054	70961054	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ttcactaagtgatttttcatGttctctttccatttctacta	3	9	4	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr15:70961054G>T	ENST00000322954.6	-	16	2154	c.1969C>A	c.(1969-1971)Cat>Aat	p.H657N	UACA_ENST00000539319.1_Missense_Mutation_p.H548N|UACA_ENST00000560441.1_Missense_Mutation_p.H642N|UACA_ENST00000379983.2_Missense_Mutation_p.H644N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	657					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.H644N(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GATTTTTCATGTTCTCTTTCC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											92	90	91					15																	70961054		2199	4297	6496	68748108	SO:0001583	missense	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1969C>A	15.37:g.70961054G>T	ENSP00000314556:p.His657Asn		68748108	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	8.748	0.920649	0.17982	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.31769	1.48;1.5;1.97	5.4	1.84	0.25277	.	0.477477	0.19675	N	0.108646	T	0.17450	0.0419	N	0.14661	0.345	0.21105	N	0.99978	B;B;B;B	0.21452	0.056;0.013;0.013;0.023	B;B;B;B	0.22753	0.041;0.019;0.019;0.041	T	0.18178	-1.0345	10	0.38643	T	0.18	-1.7893	10.0172	0.42022	0.5609:0.0:0.4391:0.0	.	548;657;657;644	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	N	657;644;548	ENSP00000314556:H657N;ENSP00000369319:H644N;ENSP00000438667:H548N	ENSP00000314556:H657N	H	-	1	0	UACA	68748108	0.202000	0.23423	0.604000	0.28916	0.973000	0.67179	0.534000	0.23098	0.064000	0.16427	-0.339000	0.08088	CAT		0.363	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70961054	G	T	70961054	3	4	27	1	0	0	0	0	1	0	0	0	16864	1377	48	2	2297	2	UACA	15	70961054	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		70961054	31570338	68	2358										
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78322443	78322443	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tctaaaagttcccactcttcAttggtataaaacacagtcct	4	11	3	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr15:78322443A>G	ENST00000300584.3	-	4	752	c.753T>C	c.(751-753)aaT>aaC	p.N251N	TBC1D2B_ENST00000409931.3_Silent_p.N251N	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	251							Rab GTPase activator activity (GO:0005097)	p.N251N(2)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						CCCACTCTTCATTGGTATAAA	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	15											96	79	85					15																	78322443		2196	4293	6489	76109498	SO:0001819	synonymous_variant	23102			AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.753T>C	15.37:g.78322443A>G			76109498	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	A	5.890	0.348256	0.11126	.	.	ENSG00000167202	ENST00000418039	.	.	.	5.03	0.0265	0.14150	.	.	.	.	.	T	0.54854	0.1884	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44832	-0.9302	4	.	.	.	.	8.6127	0.33813	0.6896:0.0:0.3104:0.0	.	.	.	.	T	133	.	.	M	-	2	0	TBC1D2B	76109498	0.006000	0.16342	0.089000	0.20774	0.747000	0.42532	0.505000	0.22642	-0.252000	0.09528	0.378000	0.23410	ATG		0.423	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		G	78322443	A	G	78322443	2	3	27	1	0	0	0	0	0	0	0	1	15658	214	8	4		4	TBC1D2B	15	78322443	Silent	SNP	A	TCGA-AG-3600-01A-01W-0833-10	7361389	78322443	24208949	69	2359										
PDILT	204474	hgsc.bcm.edu	37	chr16	20410496	20410496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cgttagcactaggagactgcGttcctccaggatgtgcacag	12	11	0	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr16:20410496G>A	ENST00000302451.4	-	2	375	c.127C>T	c.(127-129)Cgc>Tgc	p.R43C		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	43					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.R43C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						AGGAGACTGCGTTCCTCCAGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											159	144	149					16																	20410496		2203	4300	6503	20317997	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.127C>T	16.37:g.20410496G>A	ENSP00000305465:p.Arg43Cys		20317997	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.312419	0.60414	.	.	ENSG00000169340	ENST00000302451	T	0.03272	3.99	4.21	-8.41	0.00961	Thioredoxin-like fold (2);	2.670990	0.00877	N	0.002086	T	0.03053	0.0090	N	0.14661	0.345	0.09310	N	1	D	0.67145	0.996	B	0.43575	0.424	T	0.42241	-0.9463	10	0.72032	D	0.01	.	12.0005	0.53228	0.0:0.179:0.6609:0.1601	.	43	Q8N807	PDILT_HUMAN	C	43	ENSP00000305465:R43C	ENSP00000305465:R43C	R	-	1	0	PDILT	20317997	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	-1.517000	0.02248	-1.529000	0.01754	0.591000	0.81541	CGC		0.592	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		A	20410496	G	A	20410496	3	1	27	1	0	0	0	0	1	0	0	0	11705	1145	40	1	1671	1	PDILT	16	20410496	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		20410496	69944257	70	2360										
CHP2	63928	hgsc.bcm.edu	37	chr16	23767170	23767170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgaaatttggctttgcagccGcatggatctccagcagatag	11	9	1	2	rs147617371	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr16:23767170G>A	ENST00000300113.2	+	3	566	c.143G>A	c.(142-144)cGc>cAc	p.R48H		NM_022097.2	NP_071380.1	O43745	CHP2_HUMAN	calcineurin-like EF-hand protein 2	48	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to calcium ion (GO:0071277)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R48H(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|stomach(1)	9				GBM - Glioblastoma multiforme(48;0.0144)		CTTTGCAGCCGCATGGATCTC	0.567													G|||	14	0.00279553	0.0106	0	5008	,	,		16873	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16						G	HIS/ARG	18,4376	25.3+/-52.1	0,18,2179	41	47	45		143	3.7	1	16	dbSNP_134	45	0,8600		0,0,4300	yes	missense	CHP2	NM_022097.2	29	0,18,6479	AA,AG,GG		0.0,0.4096,0.1385	probably-damaging	48/197	23767170	18,12976	2197	4300	6497	23674671	SO:0001583	missense	63928				CCDS10617.1	16p12.2	2013-01-11	2013-01-11		ENSG00000166869	ENSG00000166869		"EF-hand domain containing"	24927	protein-coding gene	gene with protein product						12226101	Standard	NM_022097		Approved		uc002dmb.1	O43745	OTTHUMG00000131611	ENST00000300113.2:c.143G>A	16.37:g.23767170G>A	ENSP00000300113:p.Arg48His		23674671	A8K2I8	Missense_Mutation	SNP	ENST00000300113.2	37	CCDS10617.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	16.23	3.065810	0.55539	0.004096	0.0	ENSG00000166869	ENST00000300113	T	0.69561	-0.41	4.65	3.69	0.42338	EF-hand-like domain (1);	0.071753	0.56097	D	0.000035	T	0.60011	0.2236	M	0.77616	2.38	0.52501	D	0.999954	P	0.35774	0.519	B	0.40066	0.318	T	0.63014	-0.6731	10	0.30078	T	0.28	-13.3438	10.6331	0.45549	0.0946:0.0:0.9054:0.0	.	48	O43745	CHP2_HUMAN	H	48	ENSP00000300113:R48H	ENSP00000300113:R48H	R	+	2	0	AC130454.2	23674671	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	3.574000	0.53863	1.311000	0.45024	0.591000	0.81541	CGC		0.567	CHP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254498.1	NM_022097		A	23767170	G	A	23767170	3	1	27	1	0	0	0	0	1	0	0	0	3373	1087	38	1	153	1	CHP2	16	23767170	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	3356674	23767170	66587583	71	2361										
PRSS54	221191	hgsc.bcm.edu	37	chr16	58325009	58325009	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ccctccttggggtcaggaccGtagaaaacggaagctttctg	12	11	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr16:58325009G>A	ENST00000219301.4	-	4	511	c.117C>T	c.(115-117)taC>taT	p.Y39Y	PRSS54_ENST00000543437.1_Intron|PRSS54_ENST00000567164.1_Silent_p.Y39Y	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	39	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.Y39Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGTCAGGACCGTAGAAAACGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	16											69	58	61					16																	58325009		2198	4300	6498	56882510	SO:0001819	synonymous_variant	221191			AK058068	CCDS32463.1	16q21	2010-05-07			ENSG00000103023	ENSG00000103023		"Serine peptidases / Serine peptidases"	26336	protein-coding gene	gene with protein product	"cancer/testis antigen 67"					17521433	Standard	NM_001080492		Approved	FLJ25339, KLKBL4, CT67	uc002enf.3	Q6PEW0		ENST00000219301.4:c.117C>T	16.37:g.58325009G>A			56882510	Q96LN9|Q9NT77	Silent	SNP	ENST00000219301.4	37	CCDS32463.1																																																																																				0.632	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492		A	58325009	G	A	58325009	2	1	27	1	0	0	0	0	0	0	0	1	12667	1140	40	1		1	PRSS54	16	58325009	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	34557839	58325009	32029744	72	2362										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58581144	58581144	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	acaaagggcactacatagagCaattcttgttgtcctttaac	7	9	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr16:58581144C>A	ENST00000317147.5	-	27	4028	c.3696G>T	c.(3694-3696)ttG>ttT	p.L1232F	CNOT1_ENST00000245138.4_Missense_Mutation_p.L83F|CNOT1_ENST00000569240.1_Missense_Mutation_p.L1227F|SNORA46_ENST00000384762.1_RNA|CNOT1_ENST00000441024.2_Missense_Mutation_p.L1232F	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1232	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.L1232F(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTACATAGAGCAATTCTTGTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	16											115	119	117					16																	58581144		2198	4300	6498	57138645	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3696G>T	16.37:g.58581144C>A	ENSP00000320949:p.Leu1232Phe		57138645	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742300	0.69418	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.20598	2.06;2.06	5.65	5.65	0.86999	.	0.063154	0.64402	D	0.000007	T	0.50531	0.1621	M	0.85542	2.76	0.80722	D	1	D;P;D;D	0.71674	0.998;0.944;0.986;0.995	D;P;P;D	0.74348	0.983;0.646;0.87;0.971	T	0.55642	-0.8109	10	0.87932	D	0	.	14.5474	0.68041	0.1464:0.8536:0.0:0.0	.	83;1232;1232;1227	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	F	1232;83;1227;1232	ENSP00000320949:L1232F;ENSP00000413113:L1232F	ENSP00000245138:L83F	L	-	3	2	CNOT1	57138645	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.561000	0.23515	2.675000	0.91044	0.650000	0.86243	TTG		0.358	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58581144	C	A	58581144	3	1	27	1	0	0	0	0	1	0	0	0	3623	709	25	2	3748	2	CNOT1	16	58581144	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	256135	58581144	31773609	73	2363										
C17orf66	256957	hgsc.bcm.edu	37	chr17	34191815	34191815	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aggctctaagggcctggatcGcatctcagattttatagtca	10	9	3	1	rs116191233		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:34191815G>A	ENST00000311880.2	-	4	548	c.400C>T	c.(400-402)Cga>Tga	p.R134*	C17orf66_ENST00000592980.1_Intron|C17orf66_ENST00000587585.1_5'UTR	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		134					hematopoietic progenitor cell differentiation (GO:0002244)			p.R134*(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		GGCCTGGATCGCATCTCAGAT	0.507													G|||	1	0.000199681	0	0	5008	,	,		20473	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	17						G	stop/ARG	0,4406		0,0,2203	220	199	206		400	-3.3	0	17	dbSNP_132	206	7,8593	6.4+/-24.3	0,7,4293	yes	stop-gained	C17orf66	NM_152781.2		0,7,6496	AA,AG,GG		0.0814,0.0,0.0538		134/571	34191815	7,12999	2203	4300	6503	31215928	SO:0001587	stop_gained	256957																														ENST00000311880.2:c.400C>T	17.37:g.34191815G>A	ENSP00000309560:p.Arg134*		31215928	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Nonsense_Mutation	SNP	ENST00000311880.2	37	CCDS11299.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.20	3.328541	0.60743	0.0	8.14E-4	ENSG00000172653	ENST00000311880	.	.	.	4.53	-3.27	0.05048	.	2.187690	0.01755	N	0.030215	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	4.9785	0.14153	0.0:0.2957:0.2948:0.4096	.	.	.	.	X	134	.	ENSP00000309560:R134X	R	-	1	2	C17orf66	31215928	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.361000	0.07612	-0.492000	0.06687	-0.171000	0.13296	CGA		0.507	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			A	34191815	G	A	34191815	4	1	27	1	0	0	0	0	0	1	0	0	1879	1095	38	1	1360	1	C17orf66	17	34191815	Nonsense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		34191815	47003395	74	2364										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42338114	42338114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctcctccagttgcacccagcGcgccgcctccatccatctca	6	21	1	0	rs199535281		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:42338114G>A	ENST00000262418.6	-	5	393	c.238C>T	c.(238-240)Cgc>Tgc	p.R80C	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'UTR	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	80	Globular.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.R80C(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TGCACCCAGCGCGCCGCCTCC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											68	63	64					17																	42338114		2203	4300	6503	39693640	SO:0001583	missense	6521				CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.238C>T	17.37:g.42338114G>A	ENSP00000262418:p.Arg80Cys		39693640	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	g	20.7	4.031257	0.75504	.	.	ENSG00000004939	ENST00000262418	D	0.86030	-2.06	5.51	5.51	0.81932	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.327353	0.32314	N	0.006266	D	0.93038	0.7784	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.98;1.0	D	0.93728	0.7039	10	0.87932	D	0	.	18.1867	0.89795	0.0:0.0:1.0:0.0	.	80;80	E2RVJ0;P02730	.;B3AT_HUMAN	C	80	ENSP00000262418:R80C	ENSP00000262418:R80C	R	-	1	0	SLC4A1	39693640	1.000000	0.71417	0.031000	0.17742	0.182000	0.23217	9.824000	0.99380	2.595000	0.87683	0.561000	0.74099	CGC		0.617	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42338114	G	A	42338114	3	1	27	1	0	0	0	0	1	0	0	0	14687	1087	38	1	2561	1	SLC4A1	17	42338114	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	8146299	42338114	38857096	75	2365										
MYL4	4635	hgsc.bcm.edu	37	chr17	45286835	45286835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaaggaggcagccaagccagCtccagctccagctccagccc	11	17	0	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:45286835C>A	ENST00000354968.1	+	2	175	c.47C>A	c.(46-48)gCt>gAt	p.A16D	MYL4_ENST00000572316.1_Missense_Mutation_p.A16D|MYL4_ENST00000393450.1_Missense_Mutation_p.A16D	NM_001002841.1	NP_001002841.1	P12829	MYL4_HUMAN	myosin, light chain 4, alkali; atrial, embryonic	16					cardiac muscle contraction (GO:0060048)|muscle filament sliding (GO:0030049)|positive regulation of ATPase activity (GO:0032781)|regulation of the force of heart contraction (GO:0002026)	A band (GO:0031672)|cytosol (GO:0005829)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin II heavy chain binding (GO:0032038)	p.A16D(1)		endometrium(2)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)	11						GCCAAGccagctccagctcca	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	17											65	65	65					17																	45286835		2203	4300	6503	42641834	SO:0001583	missense	4635				CCDS11510.1	17q21.32	2013-09-19	2006-09-29		ENSG00000198336	ENSG00000198336		"Myosins / Light chain", "EF-hand domain containing"	7585	protein-coding gene	gene with protein product	"myosin, atrial/fetal muscle, light chain"	160770	"myosin, light polypeptide 4, alkali; atrial, embryonic"			3417683	Standard	NM_002476		Approved	ALC1, AMLC, GT1, PRO1957	uc002ilg.3	P12829	OTTHUMG00000178232	ENST00000354968.1:c.47C>A	17.37:g.45286835C>A	ENSP00000347055:p.Ala16Asp		42641834	D3DXJ7|P11783	Missense_Mutation	SNP	ENST00000354968.1	37	CCDS11510.1	.	.	.	.	.	.	.	.	.	.	C	1.073	-0.669416	0.03403	.	.	ENSG00000198336	ENST00000354968;ENST00000393450	T;T	0.15017	2.46;2.46	5.09	3.07	0.35406	.	0.515048	0.18750	N	0.132213	T	0.11153	0.0272	L	0.34521	1.04	0.39901	D	0.97389	B	0.23058	0.079	B	0.17979	0.02	T	0.15867	-1.0422	10	0.20519	T	0.43	-8.6985	7.068	0.25164	0.0:0.7318:0.1737:0.0945	.	16	P12829	MYL4_HUMAN	D	16	ENSP00000347055:A16D;ENSP00000377096:A16D	ENSP00000347055:A16D	A	+	2	0	MYL4	42641834	0.446000	0.25665	0.467000	0.27180	0.020000	0.10135	0.776000	0.26704	0.543000	0.28864	-0.175000	0.13238	GCT		0.572	MYL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441059.1	NM_001002841		A	45286835	C	A	45286835	3	1	27	1	0	0	0	0	1	0	0	0	10079	797	28	2	49	2	MYL4	17	45286835	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	2948721	45286835	35908375	76	2366										
NXPH3	11248	hgsc.bcm.edu	37	chr17	47656407	47656407	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cagatcttcatcgaagccaaGgcctccaaaatcttcaactg	6	13	4	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:47656407G>T	ENST00000328741.5	+	2	866	c.504G>T	c.(502-504)aaG>aaT	p.K168N	RP5-1029K10.4_ENST00000503624.1_RNA|NXPH3_ENST00000513748.1_Missense_Mutation_p.K168N	NM_007225.2	NP_009156.2	O95157	NXPH3_HUMAN	neurexophilin 3	168	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.K168N(1)		endometrium(2)|large_intestine(3)|lung(4)|pancreas(1)|skin(2)	12	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)					TCGAAGCCAAGGCCTCCAAAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											109	99	102					17																	47656407		2203	4300	6503	45011406	SO:0001583	missense	11248			AF043468	CCDS11550.1	17q	2008-07-03				ENSG00000182575			8077	protein-coding gene	gene with protein product		604636				9570794	Standard	NM_007225		Approved	NPH3	uc002ipa.3	O95157		ENST00000328741.5:c.504G>T	17.37:g.47656407G>T	ENSP00000329295:p.Lys168Asn		45011406	Q8NDC3|Q8TBF6|Q9ULR1	Missense_Mutation	SNP	ENST00000328741.5	37	CCDS11550.1	.	.	.	.	.	.	.	.	.	.	g	17.11	3.305766	0.60305	.	.	ENSG00000182575	ENST00000328741;ENST00000513748	.	.	.	4.44	2.28	0.28536	.	0.000000	0.85682	D	0.000000	T	0.75874	0.3909	M	0.82517	2.595	0.50313	D	0.999862	D;D	0.89917	1.0;0.993	D;D	0.91635	0.999;0.909	T	0.75955	-0.3135	9	0.72032	D	0.01	-17.1607	6.7992	0.23742	0.3078:0.0:0.6922:0.0	.	168;168	D6RGW2;O95157	.;NXPH3_HUMAN	N	168	.	ENSP00000329295:K168N	K	+	3	2	NXPH3	45011406	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.518000	0.35877	1.093000	0.41377	0.556000	0.70494	AAG		0.577	NXPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365143.1			T	47656407	G	T	47656407	3	4	27	1	0	0	0	0	1	0	0	0	10823	991	35	2	510	2	NXPH3	17	47656407	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	2369572	47656407	33538803	77	2367										
RNF43	54894	hgsc.bcm.edu	37	chr17	56435547	56435547	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	accaccgagtccaaggaacgAggccgagaggtcacactagg	13	12	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:56435547A>G	ENST00000584437.1	-	8	3545	c.1590T>C	c.(1588-1590)ccT>ccC	p.P530P	RNF43_ENST00000500597.2_Silent_p.P489P|RNF43_ENST00000577625.1_Silent_p.P403P|RNF43_ENST00000583753.1_Silent_p.P489P|RNF43_ENST00000577716.1_Silent_p.P530P|RNF43_ENST00000407977.2_Silent_p.P530P|RNF43_ENST00000581868.1_Silent_p.P403P|BZRAP1-AS1_ENST00000583841.1_RNA			Q68DV7	RNF43_HUMAN	ring finger protein 43	530					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P530P(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCAAGGAACGAGGCCGAGAGG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											77	75	76					17																	56435547		2203	4300	6503	53790546	SO:0001819	synonymous_variant	54894				CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1590T>C	17.37:g.56435547A>G			53790546	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Silent	SNP	ENST00000584437.1	37	CCDS11607.1																																																																																				0.592	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		G	56435547	A	G	56435547	2	3	27	1	0	0	0	0	0	0	0	1	13532	291	11	4		4	RNF43	17	56435547	Silent	SNP	A	TCGA-AG-3600-01A-01W-0833-10	8779140	56435547	24759663	78	2368										
TTYH2	94015	hgsc.bcm.edu	37	chr17	72245194	72245194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cctgacaccttcatcctgaaCgtcacggagggccagatcag	10	14	3	3	rs371708540		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr17:72245194C>T	ENST00000269346.4	+	7	923	c.849C>T	c.(847-849)aaC>aaT	p.N283N	TTYH2_ENST00000529107.1_Silent_p.N262N|TTYH2_ENST00000534346.1_3'UTR|TTYH2_ENST00000441391.2_5'UTR	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	283						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.N283N(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						TCATCCTGAACGTCACGGAGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C	,	0,4406		0,0,2203	147	116	126		849,	0.8	0.7	17		126	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-5	TTYH2	NM_032646.5,NM_052869.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	283/535,	72245194	1,13005	2203	4300	6503	69756789	SO:0001819	synonymous_variant	94015				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.849C>T	17.37:g.72245194C>T			69756789	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Silent	SNP	ENST00000269346.4	37	CCDS32717.1																																																																																				0.577	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			T	72245194	C	T	72245194	2	4	27	1	0	0	0	0	0	0	0	1	16780	535	19	1		1	TTYH2	17	72245194	Silent	SNP	C	TCGA-AG-3600-01A-01W-0833-10	15809647	72245194	8950016	79	2369										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46197071	46197071	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggaagctggaagatggggatGgcatcaacctgaatgacatc	14	7	1	3			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr18:46197071G>C	ENST00000256413.3	+	6	758	c.463G>C	c.(463-465)Ggc>Cgc	p.G155R	RP11-426J5.2_ENST00000589818.1_RNA|CTIF_ENST00000382998.4_Missense_Mutation_p.G155R|MIR4743_ENST00000584576.1_RNA	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	155	Interaction with NCBP1/CBP80.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)	p.G155R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						AGATGGGGATGGCATCAACCT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	18											213	165	181					18																	46197071		2203	4300	6503	44451069	SO:0001583	missense	9811			AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.463G>C	18.37:g.46197071G>C	ENSP00000256413:p.Gly155Arg		44451069	B3KTR8|Q8IVD5	Missense_Mutation	SNP	ENST00000256413.3	37	CCDS11935.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.096293	0.76870	.	.	ENSG00000134030	ENST00000256413;ENST00000382998;ENST00000420275	T;T	0.52754	0.65;0.65	5.11	4.19	0.49359	.	0.355965	0.27035	N	0.021255	T	0.50034	0.1592	L	0.43152	1.355	0.45995	D	0.9988	P;P	0.49783	0.928;0.883	P;B	0.51385	0.668;0.391	T	0.52373	-0.8584	10	0.87932	D	0	-14.7168	11.6303	0.51171	0.0939:0.0:0.9061:0.0	.	155;155	O43310-2;O43310	.;CTIF_HUMAN	R	155;155;107	ENSP00000256413:G155R;ENSP00000372459:G155R	ENSP00000256413:G155R	G	+	1	0	CTIF	44451069	1.000000	0.71417	0.983000	0.44433	0.950000	0.60333	2.489000	0.45285	1.068000	0.40764	-0.378000	0.06908	GGC		0.577	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		C	46197071	G	C	46197071	3	2	27	1	0	0	0	0	1	0	0	0	8197	1348	47	5	481	5	KIAA0427	18	46197071	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10		46197071	31880177	80	2370										
ILVBL	10994	hgsc.bcm.edu	37	chr19	15226087	15226087	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	acagcaatggagccatcgcgGaagtccgtcctcccaatgag	11	13	0	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr19:15226087G>A	ENST00000263383.3	-	16	2014	c.1875C>T	c.(1873-1875)ttC>ttT	p.F625F	ILVBL_ENST00000534378.1_Silent_p.F518F	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	625						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)	p.F625F(1)		NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						AGCCATCGCGGAAGTCCGTCC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	19											140	106	117					19																	15226087		2203	4300	6503	15087087	SO:0001819	synonymous_variant	10994			U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1875C>T	19.37:g.15226087G>A			15087087	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	37	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	G	9.240	1.037937	0.19669	.	.	ENSG00000105135	ENST00000269733	.	.	.	5.37	4.34	0.51931	.	.	.	.	.	T	0.65260	0.2674	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66264	-0.5967	5	0.52906	T	0.07	-18.5732	10.1473	0.42771	0.0927:0.0:0.9073:0.0	.	.	.	.	S	186	.	ENSP00000269733:P186S	P	-	1	0	ILVBL	15087087	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	2.474000	0.45154	1.272000	0.44329	0.655000	0.94253	CCG		0.597	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		A	15226087	G	A	15226087	2	1	27	1	0	0	0	0	0	0	0	1	7736	1165	41	3		3	ILVBL	19	15226087	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10		15226087	43902896	81	2371										
PSG2	5670	hgsc.bcm.edu	37	chr19	43576062	43576062	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gtagaggttatctcctgaacGgtaattggtgtatgaagggt	14	4	1	3	rs3207962		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr19:43576062G>C	ENST00000406487.1	-	4	852	c.754C>G	c.(754-756)Cgt>Ggt	p.R252G		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	252	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R252G(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TCTCCTGAACGGTAATTGGTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											166	177	173					19																	43576062		2203	4299	6502	48267902	SO:0001583	missense	5670				CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9519	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta-1-glycoprotein 7", "carcinoembryonic antigen SG8"	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.754C>G	19.37:g.43576062G>C	ENSP00000385706:p.Arg252Gly		48267902	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	.	.	.	.	.	.	.	.	.	.	g	0.504	-0.869597	0.02570	.	.	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.13778	2.56	1.26	-2.53	0.06326	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19927	0.0479	M	0.89163	3.01	0.09310	N	1	B;B	0.23591	0.088;0.0	B;B	0.32342	0.144;0.012	T	0.39313	-0.9620	9	0.56958	D	0.05	.	2.7042	0.05157	0.2045:0.0:0.5379:0.2577	.	252;252	B5MCM8;P11465	.;PSG2_HUMAN	G	252	ENSP00000385706:R252G	ENSP00000332984:R252G	R	-	1	0	PSG2	48267902	0.021000	0.18746	0.000000	0.03702	0.001000	0.01503	1.186000	0.32078	-1.642000	0.01521	-2.089000	0.00373	CGT		0.478	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		C	43576062	G	C	43576062	3	2	27	1	0	0	0	0	1	0	0	0	12689	1116	39	5	261	5	PSG2	19	43576062	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	28349975	43576062	15552921	82	2372										
NUCB1	4924	hgsc.bcm.edu	37	chr19	49407641	49407641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ccaccggtacctccaggaggTcatcgatgtactggagacgg	13	12	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr19:49407641T>C	ENST00000405315.4	+	3	507	c.173T>C	c.(172-174)gTc>gCc	p.V58A	NUCB1_ENST00000263273.5_Missense_Mutation_p.V58A|NUCB1_ENST00000407032.1_Missense_Mutation_p.V58A|NUCB1_ENST00000485798.1_Intron	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	58						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)	p.V58A(1)		cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		CTCCAGGAGGTCATCGATGTA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											97	70	79					19																	49407641		2203	4300	6503	54099453	SO:0001583	missense	4924			BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.173T>C	19.37:g.49407641T>C	ENSP00000385923:p.Val58Ala		54099453	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Missense_Mutation	SNP	ENST00000405315.4	37	CCDS12740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	18.25|18.25	3.583529|3.583529	0.65992|0.65992	.|.	.|.	ENSG00000104805|ENSG00000104805	ENST00000424608|ENST00000405315;ENST00000407032;ENST00000452087;ENST00000411700;ENST00000451312;ENST00000263273	.|T;T;T	.|0.36699	.|1.24;1.24;1.24	4.27|4.27	4.27|4.27	0.50696|0.50696	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64438|0.64438	0.2598|0.2598	M|M	0.90542|0.90542	3.125|3.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.77557	.|0.99;0.99	T|T	0.71899|0.71899	-0.4453|-0.4453	5|10	.|0.72032	.|D	.|0.01	.|.	11.6478|11.6478	0.51271|0.51271	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|58;58	.|Q02818;Q53GX6	.|NUCB1_HUMAN;.	P|A	58|58	.|ENSP00000385923:V58A;ENSP00000385211:V58A;ENSP00000263273:V58A	.|ENSP00000263273:V58A	S|V	+|+	1|2	0|0	NUCB1|NUCB1	54099453|54099453	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.383000|0.383000	0.30230|0.30230	7.626000|7.626000	0.83164|0.83164	1.722000|1.722000	0.51474|0.51474	0.241000|0.241000	0.17934|0.17934	TCA|GTC		0.617	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		C	49407641	T	C	49407641	3	2	27	1	0	0	0	0	1	0	0	0	10749	1667	58	4	179	4	NUCB1	19	49407641	Missense_Mutation	SNP	T	TCGA-AG-3600-01A-01W-0833-10	5831579	49407641	9721342	83	2373										
KIR3DL1	3811	hgsc.bcm.edu	37	chr19	55333226	55333226	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ctctgggccctgccacccacGgagggacctacagatgcttc	11	16	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr19:55333226G>T	ENST00000391728.4	+	5	895	c.862G>T	c.(862-864)Gga>Tga	p.G288*	KIR3DL1_ENST00000358178.4_Nonsense_Mutation_p.G193*|KIR3DL1_ENST00000541392.1_Nonsense_Mutation_p.G288*|KIR3DL1_ENST00000402254.2_Nonsense_Mutation_p.G288*|KIR3DL1_ENST00000538269.1_Nonsense_Mutation_p.G288*|KIR3DL1_ENST00000326542.7_Nonsense_Mutation_p.G288*	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	288	Ig-like C2-type 3.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.G288*(2)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGCCACCCACGGAGGGACCTA	0.587																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											4	4	4					19																	55333226		1614	3307	4921	60025038	SO:0001587	stop_gained	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.862G>T	19.37:g.55333226G>T	ENSP00000375608:p.Gly288*		60025038	O43473|Q14946|Q16541	Nonsense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	-	13.83	2.352992	0.41700	.	.	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	.	.	.	1.33	-2.35	0.06684	.	3.077760	0.01985	U	0.045087	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	4.7833	0.13213	0.577:0.0:0.423:0.0	.	.	.	.	X	288;288;288;266;288;288;193	.	ENSP00000326868:G288X	G	+	1	0	KIR3DL1	60025038	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.599000	0.05700	-0.638000	0.05509	0.184000	0.17185	GGA		0.587	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		T	55333226	G	T	55333226	4	4	27	1	0	0	0	0	0	1	0	0	8341	1117	39	2	880	2	KIR3DL1	19	55333226	Nonsense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	5925585	55333226	3795757	84	2374										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10023852	10023852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaacatggtgcagatgtcaaCaattctacctatgaaggaaa	9	7	2	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr20:10023852C>A	ENST00000378380.3	+	3	758	c.429C>A	c.(427-429)aaC>aaA	p.N143K	ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.N143K	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	143							calcium ion binding (GO:0005509)	p.N143K(1)									CAGATGTCAACAATTCTACCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	20											190	169	176					20																	10023852		2203	4300	6503	9971852	SO:0001583	missense	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.429C>A	20.37:g.10023852C>A	ENSP00000367631:p.Asn143Lys		9971852	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.053028	0.75960	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.58797	0.31;0.31	5.63	2.5	0.30297	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.73265	0.3565	M	0.84082	2.675	0.53688	D	0.999977	D	0.89917	1.0	D	0.91635	0.999	T	0.70992	-0.4721	9	.	.	.	-0.0278	8.0573	0.30612	0.0:0.6665:0.0:0.3335	.	143	Q9NU02	ANKR5_HUMAN	K	143	ENSP00000367644:N143K;ENSP00000367631:N143K	.	N	+	3	2	ANKRD5	9971852	1.000000	0.71417	0.989000	0.46669	0.942000	0.58702	2.287000	0.43505	0.251000	0.21505	0.655000	0.94253	AAC		0.408	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		A	10023852	C	A	10023852	3	1	27	1	0	0	0	0	1	0	0	0	676	477	17	2	435	2	ANKRD5	20	10023852	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		10023852	53001668	85	2375										
TGM2	7052	hgsc.bcm.edu	37	chr20	36776426	36776426	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cgggagcagtcacggccggcGttcttcaggaacttggggtt	16	10	3	0	rs369157574		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr20:36776426G>A	ENST00000361475.2	-	5	791	c.618C>T	c.(616-618)aaC>aaT	p.N206N	TGM2_ENST00000536724.1_Silent_p.N146N|TGM2_ENST00000536701.1_Silent_p.N125N	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	206					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.N206N(1)		endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	CACGGCCGGCGTTCTTCAGGA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G	,	1,4405	2.1+/-5.4	0,1,2202	43	40	41		618,618	-3.4	0	20		41	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	206/688,206/549	36776426	1,13005	2203	4300	6503	36209840	SO:0001819	synonymous_variant	7052			M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"Transglutaminases"	11778	protein-coding gene	gene with protein product	"C polypeptide, protein-glutamine-gamma-glutamyltransferase"	190196	"transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.618C>T	20.37:g.36776426G>A			36209840	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																				0.602	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951		A	36776426	G	A	36776426	2	1	27	1	0	0	0	0	0	0	0	1	15869	1136	40	1		1	TGM2	20	36776426	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	26752574	36776426	26249094	86	2376										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46255826	46255826	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	aatgtcacacaatacctgcaAtataagcaagaggacctggt	8	9	1	1	rs141875108		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr20:46255826A>G	ENST00000371998.3	+	6	629	c.438A>G	c.(436-438)caA>caG	p.Q146Q	NCOA3_ENST00000497292.1_3'UTR|NCOA3_ENST00000341724.6_Silent_p.Q146Q|NCOA3_ENST00000372004.3_Silent_p.Q146Q|NCOA3_ENST00000371997.3_Silent_p.Q146Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	146	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q146Q(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						AATACCTGCAATATAAGCAAG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	20						A	,,,	0,4406		0,0,2203	135	126	129		438,438,438,438	-5	0.8	20	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,,,	146/1424,146/1416,146/1421,146/1425	46255826	1,13005	2203	4300	6503	45689233	SO:0001819	synonymous_variant	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.438A>G	20.37:g.46255826A>G			45689233	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																				0.343	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46255826	A	G	46255826	2	3	27	1	0	0	0	0	0	0	0	1	10261	98	4	4		4	NCOA3	20	46255826	Silent	SNP	A	TCGA-AG-3600-01A-01W-0833-10	9479400	46255826	16769694	87	2377										
KRTAP19-6	337973	hgsc.bcm.edu	37	chr21	31914112	31914112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gaccaccaaagcctccacagCcatatcccaggcctctgtag	7	17	1	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr21:31914112C>T	ENST00000334046.5	-	1	71	c.41G>A	c.(40-42)gGc>gAc	p.G14D		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	14						intermediate filament (GO:0005882)		p.G14D(1)		breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCCTCCACAGCCATATCCCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	21											101	105	104					21																	31914112		2203	4300	6503	30835983	SO:0001583	missense	337973			AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"Keratin associated proteins"	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.41G>A	21.37:g.31914112C>T	ENSP00000375107:p.Gly14Asp		30835983	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	.	.	.	.	.	.	.	.	.	.	c	3.197	-0.164647	0.06502	.	.	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.27557	1.66	4.33	3.45	0.39498	.	0.451539	0.16460	U	0.213473	T	0.40322	0.1112	.	.	.	0.20764	N	0.999857	P	0.46952	0.887	P	0.52454	0.699	T	0.18398	-1.0338	9	0.87932	D	0	-1.3093	8.5138	0.33233	0.0:0.8884:0.0:0.1116	.	14	Q3LI70	KR196_HUMAN	D	14	ENSP00000375107:G14D	ENSP00000375107:G14D	G	-	2	0	KRTAP19-6	30835983	0.055000	0.20627	0.188000	0.23233	0.069000	0.16628	1.709000	0.37909	0.975000	0.38392	0.597000	0.82753	GGC		0.517	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4			T	31914112	C	T	31914112	3	4	27	1	0	0	0	0	1	0	0	0	8554	739	26	3	139	3	KRTAP19-6	21	31914112	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		31914112	16215783	88	2378										
RTDR1	27156	hgsc.bcm.edu	37	chr22	23404020	23404020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	tgtggcgaacatcagggcacCggcagcgttagacttcacat	12	11	2	1	rs199729382	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr22:23404020C>T	ENST00000216036.4	-	6	953	c.757G>A	c.(757-759)Ggt>Agt	p.G253S		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		253								p.G253S(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		ATCAGGGCACCGGCAGCGTTA	0.577													C|||	2	0.000399361	0.0015	0	5008	,	,		18175	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						C	SER/GLY	2,4404	4.2+/-10.8	0,2,2201	99	73	82		757	4.8	0.8	22		82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RTDR1	NM_014433.2	56	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging	253/349	23404020	3,13003	2203	4300	6503	21734020	SO:0001583	missense	27156																														ENST00000216036.4:c.757G>A	22.37:g.23404020C>T	ENSP00000216036:p.Gly253Ser		21734020		Missense_Mutation	SNP	ENST00000216036.4	37	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278417	0.59758	4.54E-4	1.16E-4	ENSG00000100218	ENST00000216036	T	0.15718	2.4	4.77	4.77	0.60923	Armadillo-like helical (1);Armadillo-type fold (1);	0.116572	0.56097	D	0.000027	T	0.36082	0.0954	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03121	-1.1070	10	0.22109	T	0.4	-43.5576	13.6483	0.62294	0.0:1.0:0.0:0.0	.	253	Q9UHP6	RTDR1_HUMAN	S	253	ENSP00000216036:G253S	ENSP00000216036:G253S	G	-	1	0	RTDR1	21734020	0.970000	0.33590	0.845000	0.33349	0.005000	0.04900	5.136000	0.64783	2.389000	0.81357	0.462000	0.41574	GGT		0.577	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			T	23404020	C	T	23404020	3	4	27	1	0	0	0	0	1	0	0	0	13756	652	23	1	297	1	RTDR1	22	23404020	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10		23404020	27900546	89	2379										
DRG1	4733	hgsc.bcm.edu	37	chr22	31799071	31799071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gatttgttggttttccatctGtggggaagtcaacactgctt	11	7	2	0			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr22:31799071G>A	ENST00000331457.4	+	3	384	c.223G>A	c.(223-225)Gtg>Atg	p.V75M	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	75	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)	p.V75M(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						TTTTCCATCTGTGGGGAAGTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	22											233	207	216					22																	31799071		2203	4300	6503	30129071	SO:0001583	missense	4733			AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"developmentally regulated GTP-binding protein 1"	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.223G>A	22.37:g.31799071G>A	ENSP00000329715:p.Val75Met		30129071	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Missense_Mutation	SNP	ENST00000331457.4	37	CCDS13897.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605132	0.87157	.	.	ENSG00000185721	ENST00000331457	T	0.30714	1.52	5.06	5.06	0.68205	Small GTP-binding protein domain (1);GTP1/OBG (1);	0.057868	0.64402	D	0.000002	T	0.66066	0.2752	M	0.93898	3.47	0.80722	D	1	D	0.64830	0.994	D	0.67900	0.954	T	0.75855	-0.3170	10	0.87932	D	0	-17.1015	18.314	0.90213	0.0:0.0:1.0:0.0	.	75	Q9Y295	DRG1_HUMAN	M	75	ENSP00000329715:V75M	ENSP00000329715:V75M	V	+	1	0	DRG1	30129071	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.856000	0.92245	2.734000	0.93682	0.655000	0.94253	GTG		0.453	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147		A	31799071	G	A	31799071	3	1	27	1	0	0	0	0	1	0	0	0	4772	1377	48	3	233	3	DRG1	22	31799071	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	8395051	31799071	19505495	90	2380										
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38541454	38541454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	cccttgctcacctgatgataCggctgtgatggaagcactcg	11	12	1	3	rs141825182	byFrequency	TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chr22:38541454C>T	ENST00000332509.3	-	3	599	c.416G>A	c.(415-417)cGt>cAt	p.R139H	PLA2G6_ENST00000402064.1_Missense_Mutation_p.R139H|PLA2G6_ENST00000436218.1_Missense_Mutation_p.R139H|PLA2G6_ENST00000335539.3_Missense_Mutation_p.R139H	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	139					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)	p.R139H(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CCTGATGATACGGCTGTGATG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	22						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	68	44	52		416,416,416	2.1	0.6	22	dbSNP_134	52	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,missense	PLA2G6	NM_001004426.1,NM_001199562.1,NM_003560.2	29,29,29	0,8,6495	TT,TC,CC		0.093,0.0,0.0615	benign,benign,benign	139/753,139/753,139/807	38541454	8,12998	2203	4300	6503	36871400	SO:0001583	missense	8398			AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.416G>A	22.37:g.38541454C>T	ENSP00000333142:p.Arg139His		36871400	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	37	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169377	0.38315	0.0	9.3E-4	ENSG00000184381	ENST00000332509;ENST00000335539;ENST00000402064;ENST00000396860;ENST00000451461	T;T;T	0.63580	-0.05;0.0;0.0	5.3	2.09	0.27110	Ankyrin repeat-containing domain (1);	0.411187	0.29948	N	0.010797	T	0.31670	0.0804	N	0.03608	-0.345	0.09310	N	0.999993	B;B;B	0.15719	0.014;0.003;0.0	B;B;B	0.08055	0.003;0.003;0.001	T	0.17349	-1.0372	10	0.15499	T	0.54	-19.2822	8.1041	0.30874	0.0:0.676:0.0:0.324	.	139;139;139	B7Z6K3;O60733-2;O60733	.;.;PA2G6_HUMAN	H	139	ENSP00000333142:R139H;ENSP00000335149:R139H;ENSP00000386100:R139H	ENSP00000333142:R139H	R	-	2	0	PLA2G6	36871400	0.547000	0.26465	0.633000	0.29310	0.911000	0.54048	0.835000	0.27531	0.620000	0.30215	0.655000	0.94253	CGT		0.602	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		T	38541454	C	T	38541454	3	4	27	1	0	0	0	0	1	0	0	0	12039	536	19	1	2064	1	PLA2G6	22	38541454	Missense_Mutation	SNP	C	TCGA-AG-3600-01A-01W-0833-10	6742383	38541454	12763112	91	2381										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71358766	71358766	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggatgcagtgggtcagctggCtaccctgagcgccttattca	13	11	2	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chrX:71358766C>A	ENST00000373677.1	+	2	1532	c.270C>A	c.(268-270)ggC>ggA	p.G90G	NHSL2_ENST00000535692.1_Silent_p.G90G|NHSL2_ENST00000540800.1_Silent_p.G456G|NHSL2_ENST00000510661.1_Silent_p.G225G			Q5HYW2	NHSL2_HUMAN	NHS-like 2	90								p.G456G(1)|p.G87G(1)		NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					GGTCAGCTGGCTACCCTGAGC	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	X											37	30	32					X																	71358766		2203	4300	6503	71275491	SO:0001819	synonymous_variant	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.270C>A	X.37:g.71358766C>A			71275491	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																					0.582	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71358766	C	A	71358766	2	1	27	1	0	0	0	0	0	0	0	1	10443	784	28	2		2	NHSL2	23	71358766	Silent	SNP	C	TCGA-AG-3600-01A-01W-0833-10		71358766	83911794	92	2382										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73960927	73960927	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	ggatcattaaatgttgacagGcaagggtttttttggagcag	13	4	1	1			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chrX:73960927G>C	ENST00000055682.6	-	3	4076	c.3465C>G	c.(3463-3465)tgC>tgG	p.C1155W		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1155					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.C1155W(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						ATGTTGACAGGCAAGGGTTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											98	94	96					X																	73960927		2203	4300	6503	73877652	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3465C>G	X.37:g.73960927G>C	ENSP00000055682:p.Cys1155Trp		73877652	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	g	13.18	2.159279	0.38119	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.29655	1.56;1.56	4.74	3.88	0.44766	.	0.320987	0.38058	N	0.001838	T	0.40570	0.1122	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	T	0.31392	-0.9945	10	0.87932	D	0	-1.0573	12.3102	0.54924	0.0839:0.0:0.9161:0.0	.	1155	Q5QGS0	K2022_HUMAN	W	1155	ENSP00000362567:C1155W;ENSP00000055682:C1155W	ENSP00000055682:C1155W	C	-	3	2	KIAA2022	73877652	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.801000	0.47908	1.006000	0.39211	0.597000	0.82753	TGC		0.393	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		C	73960927	G	C	73960927	3	2	27	1	0	0	0	0	1	0	0	0	8290	1195	42	5	1093	5	KIAA2022	23	73960927	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	2602161	73960927	81309633	93	2383										
ELF4	2000	hgsc.bcm.edu	37	chrX	129205113	129205113	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	gagtccaccagtttgaagatGcctttctctcgctgggtcca	10	12	1	2			TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chrX:129205113G>A	ENST00000308167.5	-	7	1090	c.711C>T	c.(709-711)ggC>ggT	p.G237G	ELF4_ENST00000335997.7_Silent_p.G237G	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)									p.G237G(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GTTTGAAGATGCCTTTCTCTC	0.522			T	ERG	AML																																		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	1	Substitution - coding silent(1)	large_intestine(1)	X											177	145	156					X																	129205113		2203	4300	6503	129032794	SO:0001819	synonymous_variant	2000			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.711C>T	X.37:g.129205113G>A			129032794		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																				0.522	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		A	129205113	G	A	129205113	2	1	27	1	0	0	0	0	0	0	0	1	5069	1306	46	3		3	ELF4	23	129205113	Silent	SNP	G	TCGA-AG-3600-01A-01W-0833-10	55244186	129205113	26065447	94	2384										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144906081	144906081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.480010555482254	1.06002331002331	0.310250724884871	1	1	0	agacccagtagcctattaccGaaacctgcaagagttcagct	8	12	1	2	rs192056413		TCGA-AG-3600-01A-01W-0833-10	TCGA-AG-3600-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	4cac9922-7864-46b0-a273-f9d2f12f4813	d96bc1c5-d969-482c-809c-6cb2524d91e5	g.chrX:144906081G>A	ENST00000370490.1	+	1	6393	c.2138G>A	c.(2137-2139)cGa>cAa	p.R713Q	SLITRK2_ENST00000428560.2_Missense_Mutation_p.R713Q|SLITRK2_ENST00000434188.2_Missense_Mutation_p.R713Q|SLITRK2_ENST00000447897.2_Missense_Mutation_p.R713Q|SLITRK2_ENST00000413937.2_Missense_Mutation_p.R713Q|TMEM257_ENST00000408967.2_5'Flank			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	713					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.R713Q(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GCCTATTACCGAAACCTGCAA	0.498													G|||	1	0.000264901	0	0.0014	3775	,	,		12788	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											78	80	80					X																	144906081		2203	4300	6503	144713773	SO:0001583	missense	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2138G>A	X.37:g.144906081G>A	ENSP00000359521:p.Arg713Gln		144713773	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	1	6.027727546714888E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.05	3.291022	0.59976	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.54479	0.57;0.7;0.7;0.7;0.7;0.7	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.45538	0.1347	L	0.54323	1.7	0.54753	D	0.99998	P	0.47409	0.895	B	0.35240	0.198	T	0.51012	-0.8759	10	0.41790	T	0.15	-4.5445	15.3882	0.74718	0.0:0.0:1.0:0.0	.	713	Q9H156	SLIK2_HUMAN	Q	713	ENSP00000334374:R713Q;ENSP00000411681:R713Q;ENSP00000359521:R713Q;ENSP00000397015:R713Q;ENSP00000407347:R713Q;ENSP00000412010:R713Q	ENSP00000334374:R713Q	R	+	2	0	SLITRK2	144713773	1.000000	0.71417	0.988000	0.46212	0.950000	0.60333	6.457000	0.73505	2.224000	0.72417	0.513000	0.50165	CGA		0.498	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144906081	G	A	144906081	3	1	27	1	0	0	0	0	1	0	0	0	14780	1058	37	1	2140	1	SLITRK2	23	144906081	Missense_Mutation	SNP	G	TCGA-AG-3600-01A-01W-0833-10	15700968	144906081	10364479	95	2385										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23236992	23236992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gcaaccaccggcccaagttcGgccaaattgtcaacacgcta	8	15	1	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:23236992G>A	ENST00000400191.3	+	14	2638	c.2620G>A	c.(2620-2622)Ggc>Agc	p.G874S	EPHB2_ENST00000374630.3_Missense_Mutation_p.G874S|EPHB2_ENST00000374627.1_Missense_Mutation_p.G869S|EPHB2_ENST00000374632.3_Missense_Mutation_p.G875S	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	874	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)	p.G874S(2)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GCCCAAGTTCGGCCAAATTGT	0.627																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											109	81	90					1																	23236992		2203	4300	6503	23109579	SO:0001583	missense	2048			AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.2620G>A	1.37:g.23236992G>A	ENSP00000383053:p.Gly874Ser		23109579	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	37		.	.	.	.	.	.	.	.	.	.	G	6.868	0.529507	0.13127	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48	4.55	3.62	0.41486	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.110120	0.64402	N	0.000007	T	0.48786	0.1519	N	0.01081	-1.03	0.80722	D	1	B;B;B;B	0.13594	0.006;0.008;0.001;0.0	B;B;B;B	0.14578	0.007;0.011;0.007;0.002	T	0.53899	-0.8373	10	0.02654	T	1	.	11.6165	0.51092	0.0886:0.0:0.9114:0.0	.	816;874;892;875	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	S	816;874;874;875;869	ENSP00000363761:G874S;ENSP00000383053:G874S;ENSP00000363763:G875S;ENSP00000363758:G869S	ENSP00000363755:G816S	G	+	1	0	EPHB2	23109579	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.204000	0.72143	1.272000	0.44329	0.485000	0.47835	GGC		0.627	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		A	23236992	G	A	23236992	3	1	28	1	0	0	0	0	1	0	0	0	5188	1116	39	1	2677	1	EPHB2	1	23236992	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10		23236992	226013629	1	2386										
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36372648	36372648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acagcgtggagcctatgttcCggcatctcaagaacacctac	9	13	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:36372648C>T	ENST00000373204.4	+	12	1723	c.1510C>T	c.(1510-1512)Cgg>Tgg	p.R504W	AGO1_ENST00000373206.1_Missense_Mutation_p.R429W	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	504					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R504W(1)									GCCTATGTTCCGGCATCTCAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	107	115					1																	36372648		2203	4300	6503	36145235	SO:0001583	missense	26523			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.1510C>T	1.37:g.36372648C>T	ENSP00000362300:p.Arg504Trp		36145235	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	37	CCDS398.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689184	0.88735	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.11385	2.79;2.78	5.58	5.58	0.84498	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.34395	0.0896	M	0.86573	2.825	0.80722	D	1	D	0.58970	0.984	P	0.54401	0.751	T	0.29397	-1.0013	10	0.87932	D	0	-14.0389	19.5797	0.95461	0.0:1.0:0.0:0.0	.	504	Q9UL18	AGO1_HUMAN	W	429;504	ENSP00000362302:R429W;ENSP00000362300:R504W	ENSP00000362300:R504W	R	+	1	2	EIF2C1	36145235	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.357000	0.52277	2.623000	0.88846	0.650000	0.86243	CGG		0.532	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36372648	C	T	36372648	3	4	28	1	0	0	0	0	1	0	0	0	5016	643	23	1	1556	1	EIF2C1	1	36372648	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	13135656	36372648	212877973	2	2387										
SMAP2	64744	hgsc.bcm.edu	37	chr1	40872452	40872452	+	5'UTR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttggtgtgttcatctgcattCgatgtgctggaatccacagg	12	8	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:40872452C>T	ENST00000539317.1	+	0	101					NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2						regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R50*(1)		central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			CATCTGCATTCGATGTGCTGG	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											109	105	106					1																	40872452		2203	4300	6503	40645039	SO:0001623	5_prime_UTR_variant	64744			AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"ADP-ribosylation factor GTPase activating proteins"	25082	protein-coding gene	gene with protein product			"stromal membrane-associated protein 1-like", "stromal membrane-associated GTPase-activating protein 2"	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.-93C>T	1.37:g.40872452C>T			40645039	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Nonsense_Mutation	SNP	ENST00000539317.1	37	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	C	41	8.859304	0.98980	.	.	ENSG00000084070	ENST00000435168;ENST00000372718;ENST00000372708	.	.	.	6.06	6.06	0.98353	.	0.048984	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.999	18.1147	0.89549	0.0:1.0:0.0:0.0	.	.	.	.	X	50;50;20	.	ENSP00000361793:R20X	R	+	1	2	SMAP2	40645039	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.926000	0.63433	2.882000	0.98803	0.655000	0.94253	CGA		0.478	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733		T	40872452	C	T	40872452	1	4	28	0	1	0	0	0	0	0	0	0	14804	876	31	1		1	SMAP2	1	40872452	5'UTR	SNP	C	TCGA-AG-3601-01A-01W-0833-10	4499804	40872452	208378169	3	2388										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65145385	65145385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tcctggcggtgtatgcctacCgccaccagattcatcgccgg	11	15	1	1	rs369700188		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:65145385C>T	ENST00000371073.2	+	24	3352	c.3352C>T	c.(3352-3354)Cgc>Tgc	p.R1118C	CACHD1_ENST00000290039.5_Missense_Mutation_p.R1067C|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1118					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.R1067C(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTATGCCTACCGCCACCAGAT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	CYS/ARG	0,4406		0,0,2203	88	84	85		3199	6.1	1	1		85	1,8599	1.2+/-3.3	0,1,4299	no	missense	CACHD1	NM_020925.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1067/1224	65145385	1,13005	2203	4300	6503	64917973	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3352C>T	1.37:g.65145385C>T	ENSP00000360113:p.Arg1118Cys		64917973	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	C	26.0	4.698549	0.88830	0.0	1.16E-4	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.50001	0.76;0.79	6.06	6.06	0.98353	.	0.044336	0.85682	D	0.000000	T	0.61640	0.2363	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.61347	-0.7081	10	0.87932	D	0	-32.4367	20.6244	0.99512	0.0:1.0:0.0:0.0	.	1118	Q5VU97	CAHD1_HUMAN	C	1118;1067	ENSP00000360113:R1118C;ENSP00000290039:R1067C	ENSP00000290039:R1067C	R	+	1	0	CACHD1	64917973	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.439000	0.59968	2.879000	0.98667	0.650000	0.86243	CGC		0.557	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		T	65145385	C	T	65145385	3	4	28	1	0	0	0	0	1	0	0	0	2543	652	23	1	3293	1	CACHD1	1	65145385	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	24272933	65145385	184105236	4	2389										
OR6N1	128372	hgsc.bcm.edu	37	chr1	158735956	158735956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acaaaagacgtgctgaatgcGattggggccacagaatggga	14	7	0	3	rs150316932	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:158735956G>A	ENST00000335094.2	-	1	536	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	173						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R173C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					TGCTGAATGCGATTGGGGCCA	0.463													G|||	2	0.000399361	0	0	5008	,	,		20633	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	89	92	91		517	4.8	1	1	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR6N1	NM_001005185.1	180	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging	173/313	158735956	3,13003	2203	4300	6503	157002580	SO:0001583	missense	128372			BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"GPCR / Class A : Olfactory receptors"	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.517C>T	1.37:g.158735956G>A	ENSP00000335535:p.Arg173Cys		157002580	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.777959	0.49786	2.27E-4	2.33E-4	ENSG00000197403	ENST00000335094	T	0.00058	8.79	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.700637	0.11921	N	0.516653	T	0.00109	0.0003	L	0.46670	1.46	0.29016	N	0.886589	D	0.63046	0.992	P	0.53549	0.729	T	0.53982	-0.8361	10	0.56958	D	0.05	-4.115	13.1198	0.59318	0.0:0.1623:0.8377:0.0	.	173	Q8NGY5	OR6N1_HUMAN	C	173	ENSP00000335535:R173C	ENSP00000335535:R173C	R	-	1	0	OR6N1	157002580	0.000000	0.05858	0.977000	0.42913	0.951000	0.60555	-0.293000	0.08320	2.454000	0.82982	0.655000	0.94253	CGC		0.463	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		A	158735956	G	A	158735956	3	1	28	1	0	0	0	0	1	0	0	0	11237	1058	37	1	424	1	OR6N1	1	158735956	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	93590571	158735956	90514665	5	2390										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177249985	177249985	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gctcaccctgaagagcaacaAgtacaagcctgggctggtgc	12	12	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:177249985A>G	ENST00000361539.4	+	8	1985	c.1673A>G	c.(1672-1674)aAg>aGg	p.K558R	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	558					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.K558R(1)									AAGAGCAACAAGTACAAGCCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	47	50					1																	177249985		2203	4300	6503	175516608	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1673A>G	1.37:g.177249985A>G	ENSP00000354481:p.Lys558Arg		175516608	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777938	0.70107	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.17370	2.28	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.41073	0.1143	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.993	D;D	0.85130	0.997;0.978	T	0.29427	-1.0012	10	0.72032	D	0.01	-27.5365	15.0226	0.71643	1.0:0.0:0.0:0.0	.	453;558	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	R	311;558	ENSP00000354481:K558R	ENSP00000354481:K558R	K	+	2	0	FAM5B	175516608	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.452000	0.80683	2.034000	0.60081	0.260000	0.18958	AAG		0.547	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		G	177249985	A	G	177249985	3	3	28	1	0	0	0	0	1	0	0	0	5612	72	3	4	1699	4	FAM5B	1	177249985	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	18514029	177249985	72000636	6	2391										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186113778	186113778	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctgtgccccagtatggaggaAggaaatgcgaagggagtgat	16	6	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:186113778A>C	ENST00000271588.4	+	91	14438	c.14209A>C	c.(14209-14211)Agg>Cgg	p.R4737R	HMCN1_ENST00000367492.2_Silent_p.R4737R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4737	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R4737R(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTATGGAGGAAGGAAATGCGA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	1											127	118	121					1																	186113778		2203	4300	6503	184380401	SO:0001819	synonymous_variant	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14209A>C	1.37:g.186113778A>C			184380401	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.512	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186113778	A	C	186113778	2	2	28	1	0	0	0	0	0	0	0	1	7241	63	3	4		4	HMCN1	1	186113778	Silent	SNP	A	TCGA-AG-3601-01A-01W-0833-10	8863793	186113778	63136843	7	2392										
NEK7	140609	hgsc.bcm.edu	37	chr1	198233321	198233321	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aagataatgaactaaacataGttttggaactagcagatgct	8	5	0	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:198233321G>C	ENST00000367385.4	+	5	670	c.328G>C	c.(328-330)Gtt>Ctt	p.V110L	NEK7_ENST00000538004.1_Missense_Mutation_p.V110L	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.V110L(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						ACTAAACATAGTTTTGGAACT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	101	98					1																	198233321		2203	4298	6501	196499944	SO:0001583	missense	140609			AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.328G>C	1.37:g.198233321G>C	ENSP00000356355:p.Val110Leu		196499944	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	37	CCDS1394.1	.	.	.	.	.	.	.	.	.	.	G	35	5.478572	0.96291	.	.	ENSG00000151414	ENST00000367385;ENST00000538004	T;T	0.54479	0.57;0.57	5.79	5.79	0.91817	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	L	0.33668	1.02	0.80722	D	1	D	0.59767	0.986	P	0.61328	0.887	T	0.63989	-0.6512	10	0.66056	D	0.02	.	20.0349	0.97554	0.0:0.0:1.0:0.0	.	110	Q8TDX7	NEK7_HUMAN	L	110	ENSP00000356355:V110L;ENSP00000444621:V110L	ENSP00000356355:V110L	V	+	1	0	NEK7	196499944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.048000	0.93830	2.744000	0.94065	0.650000	0.86243	GTT		0.294	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		C	198233321	G	C	198233321	3	2	28	1	0	0	0	0	1	0	0	0	10360	1029	36	5	342	5	NEK7	1	198233321	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	12119543	198233321	51017300	8	2393										
IL20	50604	hgsc.bcm.edu	37	chr1	207039839	207039839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttttttgcagcctgcgaatcGatgctgcctcctgcgccatt	9	13	0	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:207039839G>A	ENST00000367098.1	+	4	599	c.236G>A	c.(235-237)cGa>cAa	p.R79Q	IL20_ENST00000391930.2_Missense_Mutation_p.R79Q|IL20_ENST00000367096.3_Missense_Mutation_p.R79Q			Q9UHF5	IL17B_HUMAN	interleukin 20	0					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)	p.R79Q(1)		endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)|urinary_tract(1)	9	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)		CCTGCGAATCGATGCTGCCTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											287	299	295					1																	207039839		2203	4300	6503	205106462	SO:0001583	missense	50604			AF224266	CCDS1470.1	1q32	2008-02-05			ENSG00000162891	ENSG00000162891		"Interleukins and interleukin receptors"	6002	protein-coding gene	gene with protein product		605619				11163236	Standard	NM_018724		Approved	ZCYTO10, IL10D, IL-20	uc001her.3	Q9NYY1	OTTHUMG00000036456	ENST00000367098.1:c.236G>A	1.37:g.207039839G>A	ENSP00000356065:p.Arg79Gln		205106462	Q14CE5	Missense_Mutation	SNP	ENST00000367098.1	37	CCDS1470.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.254367	0.22965	.	.	ENSG00000162891	ENST00000367098;ENST00000367096;ENST00000391930	T;T;T	0.62788	-0.0;-0.0;2.23	5.18	-2.19	0.07015	Interleukin-10, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.338840	0.28883	N	0.013829	T	0.32852	0.0843	N	0.11756	0.17	0.09310	N	1	B;B	0.33000	0.341;0.393	B;B	0.21360	0.029;0.034	T	0.22347	-1.0219	10	0.25106	T	0.35	-1.7943	10.5247	0.44941	0.3875:0.0:0.6125:0.0	.	79;79	Q2THG6;Q9NYY1	.;IL20_HUMAN	Q	79	ENSP00000356065:R79Q;ENSP00000356063:R79Q;ENSP00000375796:R79Q	ENSP00000356063:R79Q	R	+	2	0	IL20	205106462	0.001000	0.12720	0.008000	0.14137	0.003000	0.03518	0.340000	0.19892	-0.303000	0.08856	-0.122000	0.15005	CGA		0.517	IL20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088676.1	NM_018724		A	207039839	G	A	207039839	3	1	28	1	0	0	0	0	1	0	0	0	7688	1058	37	1	246	1	IL20	1	207039839	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	8806518	207039839	42210782	9	2394										
USH2A	7399	hgsc.bcm.edu	37	chr1	216138718	216138718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtgttaagagtccattagggCgaaaaggtgcttcccacctc	11	10	0	1	rs201386640		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr1:216138718C>T	ENST00000307340.3	-	37	7447	c.7061G>A	c.(7060-7062)cGc>cAc	p.R2354H	USH2A_ENST00000366943.2_Missense_Mutation_p.R2354H	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2354	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in USH2A). {ECO:0000269|PubMed:17085681}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.R2354H(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCCATTAGGGCGAAAAGGTGC	0.403										HNSCC(13;0.011)			C|||	1	0.000199681	0	0	5008	,	,		16044	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM065510	USH2A	M							151	149	150					1																	216138718		2203	4300	6503	214205341	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7061G>A	1.37:g.216138718C>T	ENSP00000305941:p.Arg2354His		214205341	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.917	1.211142	0.22289	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53640	0.61;0.61	5.56	-5.71	0.02413	Fibronectin, type III (3);Immunoglobulin-like fold (1);	1.141870	0.06669	N	0.765866	T	0.13072	0.0317	N	0.00621	-1.32	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21655	-1.0239	10	0.18276	T	0.48	.	5.5397	0.17031	0.0751:0.2583:0.1031:0.5634	.	2354	O75445	USH2A_HUMAN	H	2354	ENSP00000305941:R2354H;ENSP00000355910:R2354H	ENSP00000305941:R2354H	R	-	2	0	USH2A	214205341	0.095000	0.21747	0.000000	0.03702	0.490000	0.33462	0.145000	0.16157	-0.801000	0.04427	-0.136000	0.14681	CGC		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216138718	C	T	216138718	3	4	28	1	0	0	0	0	1	0	0	0	17076	768	27	1	8691	1	USH2A	1	216138718	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	9098879	216138718	33111903	10	2395										
SOS1	6654	hgsc.bcm.edu	37	chr2	39278370	39278370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctgtatcttctatatggcccAgtaactttacactaagttca	5	10	3	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:39278370A>G	ENST00000426016.1	-	7	865	c.779T>C	c.(778-780)cTg>cCg	p.L260P	SOS1_ENST00000428721.2_Missense_Mutation_p.L203P|SOS1_ENST00000402219.2_Missense_Mutation_p.L260P|SOS1_ENST00000395038.2_Missense_Mutation_p.L260P			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	260	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L260P(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TATATGGCCCAGTAACTTTAC	0.373									Noonan syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	2											133	131	131					2																	39278370		2203	4300	6503	39131874	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.779T>C	2.37:g.39278370A>G	ENSP00000387784:p.Leu260Pro		39131874	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472206	0.84533	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	T;T;T;T	0.72282	-0.64;-0.64;-0.64;0.7	5.65	5.65	0.86999	Dbl homology (DH) domain (5);	0.077573	0.53938	D	0.000060	D	0.85164	0.5634	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87350	0.2337	10	0.72032	D	0.01	.	15.541	0.76048	1.0:0.0:0.0:0.0	.	260	Q07889	SOS1_HUMAN	P	260;260;260;260;203	ENSP00000387784:L260P;ENSP00000384675:L260P;ENSP00000378479:L260P;ENSP00000399992:L203P	ENSP00000263879:L260P	L	-	2	0	SOS1	39131874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.210000	0.95106	2.152000	0.67230	0.460000	0.39030	CTG		0.373	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		G	39278370	A	G	39278370	3	3	28	1	0	0	0	0	1	0	0	0	14973	188	7	4	3294	4	SOS1	2	39278370	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10		39278370	203921003	11	2396										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54856136	54856136	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	catggagttctgttatcaagAgctttgccagctggcggctg	13	9	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:54856136A>C	ENST00000356805.4	+	14	2146	c.1865A>C	c.(1864-1866)gAg>gCg	p.E622A	SPTBN1_ENST00000333896.5_Missense_Mutation_p.E609A	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	622					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.E622A(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TGTTATCAAGAGCTTTGCCAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	79	76					2																	54856136		2203	4300	6503	54709640	SO:0001583	missense	6711				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1865A>C	2.37:g.54856136A>C	ENSP00000349259:p.Glu622Ala		54709640	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451876	0.63290	.	.	ENSG00000115306	ENST00000356805;ENST00000389980;ENST00000333896	T;T;T	0.50548	0.74;0.74;0.74	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.53498	0.1800	L	0.52126	1.63	0.80722	D	1	P;P	0.44260	0.686;0.83	B;P	0.49085	0.367;0.6	T	0.52997	-0.8500	10	0.45353	T	0.12	.	15.8024	0.78463	1.0:0.0:0.0:0.0	.	609;622	Q01082-3;Q01082	.;SPTB2_HUMAN	A	622;622;609	ENSP00000349259:E622A;ENSP00000374630:E622A;ENSP00000334156:E609A	ENSP00000334156:E609A	E	+	2	0	SPTBN1	54709640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.271000	0.95698	2.143000	0.66587	0.533000	0.62120	GAG		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			C	54856136	A	C	54856136	3	2	28	1	0	0	0	0	1	0	0	0	15158	304	11	4	2028	4	SPTBN1	2	54856136	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	15577766	54856136	188343237	12	2397										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112839054	112839054	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aatgcttgaaaaagcagtttTttatagtgaataccaaaaca	6	5	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:112839054T>A	ENST00000283206.4	+	8	1166	c.797T>A	c.(796-798)tTt>tAt	p.F266Y		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	266						integral component of membrane (GO:0016021)		p.F266Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						AAAGCAGTTTTTTATAGTGAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	119	116					2																	112839054		2201	4300	6501	112555525	SO:0001583	missense	84910			AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.797T>A	2.37:g.112839054T>A	ENSP00000283206:p.Phe266Tyr		112555525	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	37	CCDS33275.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.464286	0.63513	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.95	5.95	0.96441	.	0.094022	0.85682	N	0.000000	T	0.41419	0.1158	L	0.31420	0.93	0.58432	D	0.999997	B;P	0.36354	0.374;0.549	B;B	0.37346	0.094;0.247	T	0.41752	-0.9491	9	0.52906	T	0.07	-27.6191	9.6208	0.39721	0.1557:0.0:0.0:0.8443	.	265;266	Q96K49-2;Q96K49	.;TM87B_HUMAN	Y	266	.	ENSP00000283206:F266Y	F	+	2	0	TMEM87B	112555525	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.146000	0.71777	2.268000	0.75426	0.533000	0.62120	TTT		0.363	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		A	112839054	T	A	112839054	3	1	28	1	0	0	0	0	1	0	0	0	16250	1841	64	5	827	5	TMEM87B	2	112839054	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	57982918	112839054	130360319	13	2398										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141135749	141135749	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gattttacaaagatgcctacCtcatcagagccatctgcaca	6	12	3	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:141135749C>G	ENST00000389484.3	-	68	11609	c.10638G>C	c.(10636-10638)gaG>gaC	p.E3546D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3546	LDL-receptor class A 26. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.E3546D(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AGATGCCTACCTCATCAGAGC	0.398										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											97	88	91					2																	141135749		2203	4300	6503	140852219	SO:0001630	splice_region_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10638+1G>C	2.37:g.141135749C>G			140852219	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682768	0.88542	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97811	-4.55	5.48	5.48	0.80851	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99342	0.9769	H	0.98646	4.29	0.58432	D	0.999998	D	0.69078	0.997	D	0.79108	0.992	D	0.98476	1.0603	9	.	.	.	.	19.3528	0.94395	0.0:1.0:0.0:0.0	.	3546	Q9NZR2	LRP1B_HUMAN	D	3546;3484	ENSP00000374135:E3546D	.	E	-	3	2	LRP1B	140852219	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.445000	0.80570	2.571000	0.86741	0.591000	0.81541	GAG		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Missense_Mutation	G	141135749	C	G	141135749	5	3	28	1	0	0	0	0	0	0	1	0	8984	695	24	5	3257	5	LRP1B	2	141135749	Splice_Site	SNP	C	TCGA-AG-3601-01A-01W-0833-10	28296695	141135749	102063624	14	2399										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141625248	141625248	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgacattctgccctgtccacTtattggctttggacaatgtg	9	10	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:141625248T>G	ENST00000389484.3	-	27	5461	c.4490A>C	c.(4489-4491)aAg>aCg	p.K1497T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1497					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.K1497T(1)|p.K1497R(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CCCTGTCCACTTATTGGCTTT	0.488										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											2	Substitution - Missense(2)	large_intestine(2)	2											201	177	185					2																	141625248		2203	4300	6503	141341718	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4490A>C	2.37:g.141625248T>G	ENSP00000374135:p.Lys1497Thr		141341718	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190659	0.78789	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.91407	-2.84;-2.84	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.96497	0.8857	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	D	0.97481	1.0047	10	0.72032	D	0.01	.	15.4528	0.75285	0.0:0.0:0.0:1.0	.	680;1497	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	T	1497;1435;642	ENSP00000374135:K1497T;ENSP00000413239:K642T	ENSP00000374135:K1497T	K	-	2	0	LRP1B	141341718	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.942000	0.87708	2.060000	0.61445	0.533000	0.62120	AAG		0.488	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141625248	T	G	141625248	3	3	28	1	0	0	0	0	1	0	0	0	8984	1609	56	4	9569	4	LRP1B	2	141625248	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	489499	141625248	101574125	15	2400										
AGPS	8540	hgsc.bcm.edu	37	chr2	178402821	178402821	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtgggcaagttacggaagcaAtggctaaaggaaagtatctc	13	6	1	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:178402821A>G	ENST00000264167.4	+	20	2021	c.1875A>G	c.(1873-1875)caA>caG	p.Q625Q	AGPS_ENST00000409888.1_Silent_p.Q156Q	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	625					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)	p.Q625Q(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TACGGAAGCAATGGCTAAAGG	0.388																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	2											130	127	128					2																	178402821		2203	4300	6503	178111067	SO:0001819	synonymous_variant	8540			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1875A>G	2.37:g.178402821A>G			178111067	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																				0.388	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			G	178402821	A	G	178402821	2	3	28	1	0	0	0	0	0	0	0	1	394	98	4	4		4	AGPS	2	178402821	Silent	SNP	A	TCGA-AG-3601-01A-01W-0833-10	36777573	178402821	64796552	16	2401										
TTN	7273	hgsc.bcm.edu	37	chr2	179640241	179640241	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tccggtcagaccgttcaattTtgacaccatttttgtaccat	6	11	2	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:179640241T>C	ENST00000591111.1	-	28	6574	c.6350A>G	c.(6349-6351)aAa>aGa	p.K2117R	TTN-AS1_ENST00000584485.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K2071R|TTN_ENST00000342992.6_Missense_Mutation_p.K2117R|TTN_ENST00000460472.2_Missense_Mutation_p.K2071R|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K2071R|TTN_ENST00000589042.1_Missense_Mutation_p.K2117R|TTN_ENST00000360870.5_Missense_Mutation_p.K2117R|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12805	Ig-like 10.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K2071R(2)|p.K2117R(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCGTTCAATTTTGACACCATT	0.498																																																4	Substitution - Missense(4)	large_intestine(4)	2											82	86	85					2																	179640241		2203	4300	6503	179348486	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.6350A>G	2.37:g.179640241T>C	ENSP00000465570:p.Lys2117Arg		179348486	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	7.141	0.581913	0.13749	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	5.33	5.33	0.75918	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55497	0.1924	N	0.16016	0.355	0.20638	N	0.999879	P;P;P;P;P	0.52316	0.669;0.669;0.669;0.669;0.952	B;B;B;B;B	0.43916	0.355;0.355;0.355;0.355;0.436	T	0.55309	-0.8161	9	0.87932	D	0	.	15.3078	0.74008	0.0:0.0:0.0:1.0	.	2071;2071;2071;2117;2117	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	R	2117;2071;2071;2071;2071;2117	ENSP00000343764:K2117R;ENSP00000434586:K2071R;ENSP00000340554:K2071R;ENSP00000352154:K2071R;ENSP00000354117:K2117R	ENSP00000340554:K2071R	K	-	2	0	TTN	179348486	1.000000	0.71417	0.853000	0.33588	0.554000	0.35429	2.531000	0.45650	2.025000	0.59659	0.533000	0.62120	AAA		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179640241	T	C	179640241	3	2	28	1	0	0	0	0	1	0	0	0	16775	1841	64	4	104978	4	TTN	2	179640241	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	1237420	179640241	63559132	17	2402										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802456	185802456	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acgtagacaacattcacattCttattcttcagatgaaagtt	5	8	4	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:185802456C>A	ENST00000302277.6	+	4	2927	c.2333C>A	c.(2332-2334)tCt>tAt	p.S778Y		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	778							metal ion binding (GO:0046872)	p.S778Y(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CATTCACATTCTTATTCTTCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	54	53					2																	185802456		2203	4300	6503	185510701	SO:0001583	missense	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2333C>A	2.37:g.185802456C>A	ENSP00000303252:p.Ser778Tyr		185510701	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.924549	0.52653	.	.	ENSG00000170396	ENST00000302277	T	0.11604	2.76	5.81	3.95	0.45737	.	0.111844	0.40728	N	0.001022	T	0.09905	0.0243	L	0.55481	1.735	0.28660	N	0.906208	B	0.24533	0.105	B	0.20384	0.029	T	0.19516	-1.0303	10	0.30078	T	0.28	-11.5196	5.7976	0.18396	0.1455:0.642:0.1399:0.0726	.	778	Q7Z570	Z804A_HUMAN	Y	778	ENSP00000303252:S778Y	ENSP00000303252:S778Y	S	+	2	0	ZNF804A	185510701	1.000000	0.71417	0.980000	0.43619	0.989000	0.77384	1.478000	0.35442	0.745000	0.32763	0.655000	0.94253	TCT		0.353	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185802456	C	A	185802456	3	1	28	1	0	0	0	0	1	0	0	0	18209	913	32	2	2347	2	ZNF804A	2	185802456	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	6162215	185802456	57396917	18	2403										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627013	187627013	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtaatgactccattttcatcGgaacttcaaggaatttcaga	7	8	3	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:187627013G>A	ENST00000304698.5	+	8	2147	c.1944G>A	c.(1942-1944)tcG>tcA	p.S648S		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	648						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.S648S(1)		NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CATTTTCATCGGAACTTCAAG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	2											103	113	110					2																	187627013		2203	4299	6502	187335258	SO:0001819	synonymous_variant	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1944G>A	2.37:g.187627013G>A			187335258	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																				0.502	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187627013	G	A	187627013	2	1	28	1	0	0	0	0	0	0	0	1	5507	1103	39	1		1	FAM171B	2	187627013	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10	1824557	187627013	55572360	19	2404										
BARD1	580	hgsc.bcm.edu	37	chr2	215593697	215593697	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tggtgtttgaaggttccccaCaaatagaagtagcatccatc	9	9	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:215593697C>A	ENST00000260947.4	-	11	2171	c.2037G>T	c.(2035-2037)ttG>ttT	p.L679F	BARD1_ENST00000449967.2_Missense_Mutation_p.C534F|BARD1_ENST00000432456.1_Missense_Mutation_p.L50F	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	679	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L679F(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AGGTTCCCCACAAATAGAAGT	0.418									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	2											95	83	87					2																	215593697		2203	4300	6503	215301942	SO:0001583	missense	580	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.2037G>T	2.37:g.215593697C>A	ENSP00000260947:p.Leu679Phe		215301942	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.635|2.635	-0.285383|-0.285383	0.05605|0.05605	.|.	.|.	ENSG00000138376|ENSG00000138376	ENST00000449967|ENST00000260947;ENST00000432456	D|T;T	0.82619|0.80480	-1.63|2.68;-1.38	5.91|5.91	-2.13|-2.13	0.07144|0.07144	.|BRCT (3);	.|0.321975	.|0.33980	.|N	.|0.004366	T|T	0.54870|0.54870	0.1885|0.1885	N|N	0.12502|0.12502	0.225|0.225	0.24889|0.24889	N|N	0.992174|0.992174	B|B	0.02656|0.10296	0.0|0.003	B|B	0.01281|0.04013	0.0|0.001	T|T	0.45731|0.45731	-0.9241|-0.9241	8|10	.|0.07482	.|T	.|0.82	-4.8765|-4.8765	8.5623|8.5623	0.33518|0.33518	0.3404:0.479:0.1806:0.0|0.3404:0.479:0.1806:0.0	.|.	534|679	E7EUI3|Q99728	.|BARD1_HUMAN	F|F	534|679;50	ENSP00000406752:C534F|ENSP00000260947:L679F;ENSP00000405020:L50F	.|ENSP00000260947:L679F	C|L	-|-	2|3	0|2	BARD1|BARD1	215301942|215301942	0.144000|0.144000	0.22641|0.22641	0.710000|0.710000	0.30468|0.30468	0.781000|0.781000	0.44180|0.44180	-0.307000|-0.307000	0.08167|0.08167	-0.625000|-0.625000	0.05604|0.05604	0.655000|0.655000	0.94253|0.94253	TGT|TTG		0.418	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		A	215593697	C	A	215593697	3	1	28	1	0	0	0	0	1	0	0	0	1313	477	17	2	300	2	BARD1	2	215593697	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	27966684	215593697	27605676	20	2405										
PAX3	5077	hgsc.bcm.edu	37	chr2	223085004	223085004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgtctgggttggaaggaatcGtgctttggtgtacagtgctt	15	5	1	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:223085004G>A	ENST00000350526.4	-	7	1164	c.1028C>T	c.(1027-1029)aCg>aTg	p.T343M	PAX3_ENST00000392070.2_Missense_Mutation_p.T343M|PAX3_ENST00000336840.6_Missense_Mutation_p.T343M|PAX3_ENST00000344493.4_Missense_Mutation_p.T343M|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000409551.3_Missense_Mutation_p.T342M|PAX3_ENST00000392069.2_Missense_Mutation_p.T343M	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	343					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T343M(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGAAGGAATCGTGCTTTGGTG	0.537			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																Dom	yes		2	2q35	5077	paired box gene 3	yes	M	1	Substitution - Missense(1)	large_intestine(1)	2											262	215	231					2																	223085004		2203	4300	6503	222793248	SO:0001583	missense	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1028C>T	2.37:g.223085004G>A	ENSP00000343052:p.Thr343Met		222793248	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	37	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.901384	0.33535	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000464706;ENST00000555548	D;D;D;D;D;D	0.94280	-3.36;-3.39;-3.35;-3.34;-3.39;-3.34	5.68	4.78	0.61160	.	0.227351	0.44483	D	0.000447	D	0.89143	0.6631	N	0.03608	-0.345	0.80722	D	1	P;P;P;D;P	0.55385	0.918;0.768;0.954;0.971;0.954	B;B;P;P;P	0.54815	0.276;0.178;0.629;0.761;0.454	D	0.90262	0.4301	10	0.38643	T	0.18	.	15.0452	0.71822	0.0:0.4358:0.5642:0.0	.	343;342;343;343;343	P23760;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.	M	343;343;343;343;343;342;60;60	ENSP00000375921:T343M;ENSP00000342092:T343M;ENSP00000343052:T343M;ENSP00000375922:T343M;ENSP00000338767:T343M;ENSP00000386750:T342M	ENSP00000338767:T343M	T	-	2	0	PAX3	222793248	0.996000	0.38824	0.922000	0.36590	0.974000	0.67602	2.073000	0.41519	1.368000	0.46115	0.650000	0.86243	ACG		0.537	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			A	223085004	G	A	223085004	3	1	28	1	0	0	0	0	1	0	0	0	11511	1145	40	1	533	1	PAX3	2	223085004	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	7491307	223085004	20114369	21	2406										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489513	237489513	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttcggcagcattttcttcctCacgtgcatgagcgtggaccg	11	12	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr2:237489513C>T	ENST00000272928.3	+	2	715	c.405C>T	c.(403-405)ctC>ctT	p.L135L		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	135					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.L135L(1)									TTTTCTTCCTCACGTGCATGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	2											266	219	235					2																	237489513		2203	4300	6503	237154252	SO:0001819	synonymous_variant	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.405C>T	2.37:g.237489513C>T			237154252	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	37	CCDS2516.1																																																																																				0.562	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489513	C	T	237489513	2	4	28	1	0	0	0	0	0	0	0	1	4102	813	29	3		3	CXCR7	2	237489513	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	14404509	237489513	5709860	22	2407										
CHL1	10752	hgsc.bcm.edu	37	chr3	424214	424214	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tggaaggtgggaggaactgaCcagagtccaaggaaagaaaa	15	5	0	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr3:424214C>G	ENST00000256509.2	+	18	2678	c.2036C>G	c.(2035-2037)aCc>aGc	p.T679S	CHL1_ENST00000397491.2_Missense_Mutation_p.T663S|CHL1-AS1_ENST00000417612.1_RNA	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.T679S(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GAGGAACTGACCAGAGTCCAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	113	108					3																	424214		2203	4300	6503	399214	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2036C>G	3.37:g.424214C>G	ENSP00000256509:p.Thr679Ser		399214	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	C	8.005	0.756182	0.15846	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.57273	0.41;0.41	4.86	3.0	0.34707	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.567157	0.19880	N	0.103997	T	0.31358	0.0794	N	0.20807	0.61	0.09310	N	1	B;B;B	0.12013	0.005;0.0;0.002	B;B;B	0.24006	0.05;0.007;0.009	T	0.20538	-1.0272	10	0.08381	T	0.77	.	7.5534	0.27810	0.0:0.5929:0.2704:0.1366	.	663;663;679	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	S	679;663	ENSP00000256509:T679S;ENSP00000380628:T663S	ENSP00000256509:T679S	T	+	2	0	CHL1	399214	0.000000	0.05858	0.038000	0.18304	0.751000	0.42716	0.368000	0.20399	1.130000	0.42092	0.591000	0.81541	ACC		0.413	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		G	424214	C	G	424214	3	3	28	1	0	0	0	0	1	0	0	0	3355	507	18	5	2098	5	CHL1	3	424214	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		424214	197598216	23	2408										
ZNF35	7584	hgsc.bcm.edu	37	chr3	44701037	44701037	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aagccatatgagtgtaaagaGtgtgggaaagcctttagttg	13	4	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr3:44701037G>C	ENST00000396056.2	+	4	1417	c.1182G>C	c.(1180-1182)gaG>gaC	p.E394D	RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000296092.3_3'UTR|ZNF35_ENST00000542250.1_Missense_Mutation_p.E234D	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	394					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E394D(1)		large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		AGTGTAAAGAGTGTGGGAAAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	103	100					3																	44701037		2203	4300	6503	44676041	SO:0001583	missense	7584			X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"Zinc fingers, C2H2-type"	13099	protein-coding gene	gene with protein product		194533	"zinc finger protein 35 (clone HF.10)"			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.1182G>C	3.37:g.44701037G>C	ENSP00000379368:p.Glu394Asp		44676041	B2RBU6|Q53Y54|Q96D01	Missense_Mutation	SNP	ENST00000396056.2	37	CCDS2718.2	.	.	.	.	.	.	.	.	.	.	G	15.58	2.875579	0.51695	.	.	ENSG00000169981	ENST00000396056;ENST00000542250	T;T	0.07567	3.18;3.18	5.29	2.3	0.28687	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.144445	0.32218	N	0.006410	T	0.05181	0.0138	N	0.16790	0.44	0.24866	N	0.992317	B	0.10296	0.003	B	0.17098	0.017	T	0.35699	-0.9778	10	0.35671	T	0.21	-22.656	8.5783	0.33612	0.1631:0.1332:0.7037:0.0	.	394	P13682	ZNF35_HUMAN	D	394;234	ENSP00000379368:E394D;ENSP00000443714:E234D	ENSP00000379368:E394D	E	+	3	2	ZNF35	44676041	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-2.480000	0.00983	0.789000	0.33779	0.561000	0.74099	GAG		0.453	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420		C	44701037	G	C	44701037	3	2	28	1	0	0	0	0	1	0	0	0	17901	1020	36	5	1192	5	ZNF35	3	44701037	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	44276823	44701037	153321393	24	2409										
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185146510	185146510	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aagctgctcgaggaccagcaGgaaaaggggatggtacgaac	15	8	0	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr3:185146510G>A	ENST00000265026.3	+	2	475	c.141G>A	c.(139-141)caG>caA	p.Q47Q	MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000443863.1_Intron|MAP3K13_ENST00000424227.1_Silent_p.Q47Q|MAP3K13_ENST00000535426.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.Q47Q(2)|p.E44_L56delEDQQEKGMVRTEL(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AGGACCAGCAGGAAAAGGGGA	0.527																																																3	Substitution - coding silent(2)|Deletion - In frame(1)	large_intestine(2)|breast(1)	3											84	71	76					3																	185146510		2203	4300	6503	186629204	SO:0001819	synonymous_variant	9175			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.141G>A	3.37:g.185146510G>A			186629204		Silent	SNP	ENST00000265026.3	37	CCDS3270.1																																																																																				0.527	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		A	185146510	G	A	185146510	2	1	28	1	0	0	0	0	0	0	0	1	9277	991	35	3		3	MAP3K13	3	185146510	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10	140445473	185146510	12875920	25	2410										
HRG	3273	hgsc.bcm.edu	37	chr3	186389446	186389446	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gccaataccaaagatagtccGgtcctcatagatttctttga	7	10	2	3	rs137953854	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr3:186389446G>A	ENST00000232003.4	+	4	506	c.426G>A	c.(424-426)ccG>ccA	p.P142P		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	142	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.P142P(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		AAGATAGTCCGGTCCTCATAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		0,4406		0,0,2203	91	91	91		426	-10.4	0	3	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HRG	NM_000412.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		142/526	186389446	2,13004	2203	4300	6503	187872140	SO:0001819	synonymous_variant	3273				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.426G>A	3.37:g.186389446G>A			187872140	B9EK35|D3DNU7	Silent	SNP	ENST00000232003.4	37	CCDS3280.1																																																																																				0.448	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		A	186389446	G	A	186389446	2	1	28	1	0	0	0	0	0	0	0	1	7375	1103	39	1		1	HRG	3	186389446	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10	1242936	186389446	11632984	26	2411										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10446851	10446851	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agcttcaaggcaattattttCttccagcggaaacagtttca	7	9	3	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:10446851C>T	ENST00000326756.3	-	3	1540	c.1102G>A	c.(1102-1104)Gaa>Aaa	p.E368K		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	368					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.E368K(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						CAATTATTTTCTTCCAGCGGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											143	147	145					4																	10446851		2203	4300	6503	10055949	SO:0001583	missense	85460			AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1102G>A	4.37:g.10446851C>T	ENSP00000317614:p.Glu368Lys		10055949	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171947	0.78452	.	.	ENSG00000178163	ENST00000326756	T	0.01998	4.51	6.17	6.17	0.99709	.	0.082701	0.49916	D	0.000124	T	0.11879	0.0289	M	0.64997	1.995	0.34629	D	0.719435	D	0.89917	1.0	D	0.79108	0.992	T	0.01245	-1.1407	10	0.38643	T	0.18	-30.3938	19.8676	0.96824	0.0:1.0:0.0:0.0	.	368	Q9C0D4	Z518B_HUMAN	K	368	ENSP00000317614:E368K	ENSP00000317614:E368K	E	-	1	0	ZNF518B	10055949	1.000000	0.71417	0.995000	0.50966	0.702000	0.40608	2.759000	0.47573	2.941000	0.99782	0.655000	0.94253	GAA		0.418	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		T	10446851	C	T	10446851	3	4	28	1	0	0	0	0	1	0	0	0	18002	922	32	3	2126	3	ZNF518B	4	10446851	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		10446851	180707425	27	2412										
ANAPC4	29945	hgsc.bcm.edu	37	chr4	25379130	25379130	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caggagattattttcctggtCtggtcgcccaagcgggatct	12	10	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:25379130C>T	ENST00000315368.3	+	2	223	c.81C>T	c.(79-81)gtC>gtT	p.V27V	ANAPC4_ENST00000510092.1_Silent_p.V27V	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	27					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)	p.V27V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				TTTTCCTGGTCTGGTCGCCCA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	4											36	36	36					4																	25379130		2203	4300	6503	24988228	SO:0001819	synonymous_variant	29945			AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.81C>T	4.37:g.25379130C>T			24988228	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Silent	SNP	ENST00000315368.3	37	CCDS3434.1																																																																																				0.642	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		T	25379130	C	T	25379130	2	4	28	1	0	0	0	0	0	0	0	1	604	900	32	3		3	ANAPC4	4	25379130	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	14932279	25379130	165775146	28	2413										
KDR	3791	hgsc.bcm.edu	37	chr4	55968137	55968137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tggcaggtgtagaggccttcGtcctccttcctcactctgcg	11	14	2	1	rs138304068	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:55968137G>A	ENST00000263923.4	-	15	2488	c.2193C>T	c.(2191-2193)gaC>gaT	p.D731D		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	731	Ig-like C2-type 7.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.D731D(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGAGGCCTTCGTCCTCCTTCC	0.443			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - coding silent(1)	large_intestine(1)	4						G		1,4405	2.1+/-5.4	0,1,2202	130	122	125		2193	-3.3	1	4	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KDR	NM_002253.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		731/1357	55968137	2,13004	2203	4300	6503	55662894	SO:0001819	synonymous_variant	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2193C>T	4.37:g.55968137G>A			55662894	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																				0.443	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55968137	G	A	55968137	2	1	28	1	0	0	0	0	0	0	0	1	8160	1136	40	1		1	KDR	4	55968137	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10	30589007	55968137	135186139	29	2414										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90874346	90874346	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtacaccatcgagtcatttaGtgctcatatttctggatttt	7	8	3	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:90874346G>T	ENST00000394980.1	+	9	3783	c.3464G>T	c.(3463-3465)aGt>aTt	p.S1155I	MMRN1_ENST00000394981.1_Missense_Mutation_p.S458I|MMRN1_ENST00000264790.2_Missense_Mutation_p.S1155I|MMRN1_ENST00000508372.1_Missense_Mutation_p.S897I			Q13201	MMRN1_HUMAN	multimerin 1	1155	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.S1155I(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GAGTCATTTAGTGCTCATATT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											140	138	139					4																	90874346		2203	4300	6503	91093369	SO:0001583	missense	22915			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.3464G>T	4.37:g.90874346G>T	ENSP00000378431:p.Ser1155Ile		91093369	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.927905	0.73327	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981;ENST00000508372	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	5.11	5.11	0.69529	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	D	0.93436	0.7906	M	0.79011	2.435	0.38299	D	0.942916	D;D	0.89917	0.998;1.0	D;D	0.91635	0.988;0.999	D	0.94691	0.7874	10	0.87932	D	0	.	17.6017	0.88027	0.0:0.0:1.0:0.0	.	458;1155	Q13201-2;Q13201	.;MMRN1_HUMAN	I	1155;1155;458;897	ENSP00000378431:S1155I;ENSP00000264790:S1155I;ENSP00000378432:S458I;ENSP00000426461:S897I	ENSP00000264790:S1155I	S	+	2	0	MMRN1	91093369	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	6.297000	0.72757	2.765000	0.95021	0.484000	0.47621	AGT		0.343	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		T	90874346	G	T	90874346	3	4	28	1	0	0	0	0	1	0	0	0	9700	1029	36	2	3494	2	MMRN1	4	90874346	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	34906209	90874346	100279930	30	2415										
UNC5C	8633	hgsc.bcm.edu	37	chr4	96140209	96140209	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tctgccttgctagactctggTtcttcaggctgagggcttca	11	11	5	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:96140209T>G	ENST00000453304.1	-	9	1904	c.1556A>C	c.(1555-1557)aAc>aCc	p.N519T	UNC5C_ENST00000506749.1_Missense_Mutation_p.N538T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	519					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)	p.N519T(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TAGACTCTGGTTCTTCAGGCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	4											146	116	126					4																	96140209		2203	4300	6503	96359232	SO:0001583	missense	8633			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1556A>C	4.37:g.96140209T>G	ENSP00000406022:p.Asn519Thr		96359232	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	T	2.734	-0.263736	0.05754	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796;ENST00000506749	T;T;T	0.57107	0.73;0.42;0.47	5.45	3.05	0.35203	.	0.200947	0.50627	D	0.000105	T	0.21921	0.0528	N	0.02011	-0.69	0.80722	D	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.11329	0.006;0.003;0.003	T	0.04900	-1.0919	10	0.10636	T	0.68	.	9.4215	0.38555	0.0:0.1434:0.0:0.8566	.	519;538;519	A8K385;E0CX15;O95185	.;.;UNC5C_HUMAN	T	519;478;538;538	ENSP00000406022:N519T;ENSP00000426924:N538T;ENSP00000426153:N538T	ENSP00000328673:N478T	N	-	2	0	UNC5C	96359232	0.961000	0.32948	0.993000	0.49108	0.173000	0.22820	0.964000	0.29306	0.387000	0.25024	0.533000	0.62120	AAC		0.522	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		G	96140209	T	G	96140209	3	3	28	1	0	0	0	0	1	0	0	0	17033	1725	60	4	1271	4	UNC5C	4	96140209	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	5265863	96140209	95014067	31	2416										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123301395	123301395	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tccaaggttacgcaagtaacGggtacgacttttttcatttg	9	8	1	0	rs373906340		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:123301395G>A	ENST00000296513.2	+	3	356	c.171G>A	c.(169-171)acG>acA	p.T57T	ADAD1_ENST00000388724.2_Splice_Site_p.T57T|ADAD1_ENST00000388725.2_Splice_Site_p.T39T	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	57					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.T57T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						CGCAAGTAACGGGTACGACTT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											102	88	93					4																	123301395		2203	4300	6503	123520845	SO:0001630	splice_region_variant	132612			AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.172+1G>A	4.37:g.123301395G>A			123520845	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Silent	SNP	ENST00000296513.2	37	CCDS34058.1																																																																																				0.448	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243	Silent	A	123301395	G	A	123301395	5	1	28	1	0	0	0	0	0	0	1	0	231	1130	39	1	173	1	ADAD1	4	123301395	Splice_Site	SNP	G	TCGA-AG-3601-01A-01W-0833-10	27161186	123301395	67852881	32	2417										
SFRP2	6423	hgsc.bcm.edu	37	chr4	154702662	154702662	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gaactctctctgccccttctGccaccgcttcaccgaggtga	8	17	4	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr4:154702662G>C	ENST00000274063.4	-	3	1113	c.829C>G	c.(829-831)Cag>Gag	p.Q277E		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	277	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q277E(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				TGCCCCTTCTGCCACCGCTTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	4											126	98	107					4																	154702662		2203	4300	6503	154922112	SO:0001583	missense	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.829C>G	4.37:g.154702662G>C	ENSP00000274063:p.Gln277Glu		154922112	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	37	CCDS34082.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294891	0.60086	.	.	ENSG00000145423	ENST00000274063	T	0.28666	1.6	5.95	5.95	0.96441	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.000000	0.85682	D	0.000000	T	0.33962	0.0881	L	0.43152	1.355	0.80722	D	1	B	0.28470	0.213	B	0.33960	0.173	T	0.03443	-1.1036	10	0.29301	T	0.29	.	20.3697	0.98890	0.0:0.0:1.0:0.0	.	277	Q96HF1	SFRP2_HUMAN	E	277	ENSP00000274063:Q277E	ENSP00000274063:Q277E	Q	-	1	0	SFRP2	154922112	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.000000	0.93564	2.811000	0.96726	0.655000	0.94253	CAG		0.607	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			C	154702662	G	C	154702662	3	2	28	1	0	0	0	0	1	0	0	0	14199	1328	46	5	62	5	SFRP2	4	154702662	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	31401267	154702662	36451614	33	2418										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492290	71492290	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agagaggaggaatatgagccGgaaaaaatggaagctgaaga	15	3	0	4	rs150527364		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:71492290G>A	ENST00000296755.7	+	5	3406	c.3108G>A	c.(3106-3108)ccG>ccA	p.P1036P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1036					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.P1036P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AATATGAGCCGGAAAAAATGG	0.517																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - coding silent(1)	large_intestine(1)	5						G		0,4406		0,0,2203	153	156	155		3108	-11.7	0	5	dbSNP_134	155	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MAP1B	NM_005909.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		1036/2469	71492290	2,13004	2203	4300	6503	71528046	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3108G>A	5.37:g.71492290G>A			71528046	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.517	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71492290	G	A	71492290	2	1	28	1	0	0	0	0	0	0	0	1	9258	1103	39	1		1	MAP1B	5	71492290	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10		71492290	109422970	34	2419										
PDE8B	8622	hgsc.bcm.edu	37	chr5	76646917	76646917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agggggtttactatgccagaCggaaatccggggacagcatc	14	9	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:76646917C>T	ENST00000264917.5	+	9	1090	c.1045C>T	c.(1045-1047)Cgg>Tgg	p.R349W	PDE8B_ENST00000340978.3_Missense_Mutation_p.R302W|PDE8B_ENST00000333194.4_Missense_Mutation_p.R349W|PDE8B_ENST00000346042.3_Intron|PDE8B_ENST00000342343.4_Missense_Mutation_p.R329W	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	349					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R349W(1)	GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	CTATGCCAGACGGAAATCCGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											113	105	108					5																	76646917		2203	4300	6503	76682673	SO:0001583	missense	8622			AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.1045C>T	5.37:g.76646917C>T	ENSP00000264917:p.Arg349Trp		76682673	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Missense_Mutation	SNP	ENST00000264917.5	37	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354992	0.82243	.	.	ENSG00000113231	ENST00000340978;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000503963	T;D;D;D;D	0.99762	-1.4;-6.67;-6.67;-6.67;-6.67	5.39	4.44	0.53790	PAS (1);PAS fold (1);	0.532223	0.20288	N	0.095316	D	0.99829	0.9923	H	0.96604	3.85	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.72338	0.961;0.921;0.961;0.977	D	0.97450	1.0027	10	0.87932	D	0	.	10.418	0.44333	0.3792:0.6208:0.0:0.0	.	302;349;329;349	O95263-6;O95263-3;O95263-4;O95263	.;.;.;PDE8B_HUMAN	W	302;349;329;349;111	ENSP00000345446:R302W;ENSP00000264917:R349W;ENSP00000345646:R329W;ENSP00000331336:R349W;ENSP00000422861:R111W	ENSP00000264917:R349W	R	+	1	2	PDE8B	76682673	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.215000	0.65241	2.528000	0.85240	0.563000	0.77884	CGG		0.498	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		T	76646917	C	T	76646917	3	4	28	1	0	0	0	0	1	0	0	0	11685	527	19	1	1079	1	PDE8B	5	76646917	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	5154627	76646917	104268343	35	2420										
VCAN	1462	hgsc.bcm.edu	37	chr5	82816870	82816870	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	atcacaagcactgaaggccaAgtttatgcaaccatggaagg	10	9	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:82816870A>C	ENST00000265077.3	+	7	3310	c.2745A>C	c.(2743-2745)caA>caC	p.Q915H	VCAN_ENST00000512590.2_Missense_Mutation_p.Q867H|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.Q915H	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	915	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.Q915H(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	CTGAAGGCCAAGTTTATGCAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											109	105	107					5																	82816870		2203	4300	6503	82852626	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2745A>C	5.37:g.82816870A>C	ENSP00000265077:p.Gln915His		82852626	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	3.722	-0.057413	0.07317	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.20332	2.08;2.08;2.08	5.57	-4.37	0.03633	.	1.862240	0.02458	N	0.086228	T	0.14227	0.0344	L	0.41236	1.265	0.09310	N	1	B;B	0.14805	0.006;0.011	B;B	0.12837	0.008;0.005	T	0.20638	-1.0269	10	0.37606	T	0.19	.	0.4586	0.00512	0.3303:0.1223:0.1894:0.358	.	915;915	P13611-3;P13611	.;CSPG2_HUMAN	H	915;915;867	ENSP00000265077:Q915H;ENSP00000342768:Q915H;ENSP00000425959:Q867H	ENSP00000265077:Q915H	Q	+	3	2	VCAN	82852626	0.000000	0.05858	0.000000	0.03702	0.622000	0.37654	-0.091000	0.11146	-0.495000	0.06659	0.533000	0.62120	CAA		0.428	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82816870	A	C	82816870	3	2	28	1	0	0	0	0	1	0	0	0	17178	69	3	4	2767	4	VCAN	5	82816870	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	6169953	82816870	98098390	36	2421										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101599459	101599459	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acatagccaatagcagggccTaagattgacatagcataacc	8	10	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:101599459T>A	ENST00000310954.6	-	4	1114	c.828A>T	c.(826-828)ttA>ttT	p.L276F		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1									p.L276F(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TAGCAGGGCCTAAGATTGACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											144	137	140					5																	101599459		2203	4300	6503	101627358	SO:0001583	missense	353189			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.828A>T	5.37:g.101599459T>A	ENSP00000309741:p.Leu276Phe		101627358		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.146516	0.37923	.	.	ENSG00000173930	ENST00000310954	T	0.43294	0.95	5.24	-2.88	0.05682	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.122413	0.35495	N	0.003176	T	0.28599	0.0708	L	0.43923	1.385	0.27475	N	0.952762	B	0.17038	0.02	B	0.26310	0.068	T	0.18398	-1.0338	10	0.30078	T	0.28	.	7.34	0.26632	0.2542:0.5297:0.0:0.2161	.	276	Q6ZQN7	SO4C1_HUMAN	F	276	ENSP00000309741:L276F	ENSP00000309741:L276F	L	-	3	2	SLCO4C1	101627358	0.997000	0.39634	0.375000	0.26029	0.778000	0.44026	0.196000	0.17176	-0.436000	0.07254	-0.263000	0.10527	TTA		0.368	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		A	101599459	T	A	101599459	3	1	28	1	0	0	0	0	1	0	0	0	14767	1519	53	5	1386	5	SLCO4C1	5	101599459	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	18782589	101599459	79315801	37	2422										
APC	324	hgsc.bcm.edu	37	chr5	112137036	112137036	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctgagcggcagaatgaaggtCaaggagtgggagaaatcaac	15	6	2	4			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:112137036C>T	ENST00000457016.1	+	8	1170	c.790C>T	c.(790-792)Caa>Taa	p.Q264*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q264*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q264*			P25054	APC_HUMAN	adenomatous polyposis coli	264	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q264*(2)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATGAAGGTCAAGGAGTGGG	0.353		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(2)	large_intestine(2)	5	GRCh37	CM042289	APC	M							88	86	87					5																	112137036		2202	4300	6502	112164935	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.790C>T	5.37:g.112137036C>T	ENSP00000413133:p.Gln264*		112164935	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.145105	0.98675	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.36	5.36	0.76844	.	0.458788	0.24864	N	0.034995	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-2.9982	19.0871	0.93209	0.0:1.0:0.0:0.0	.	.	.	.	X	264;246;264;264;264	.	ENSP00000257430:Q264X	Q	+	1	0	APC	112164935	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.677000	0.68142	2.504000	0.84457	0.585000	0.79938	CAA		0.353	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112137036	C	T	112137036	4	4	28	1	0	0	0	0	0	1	0	0	763	827	29	3	816	3	APC	5	112137036	Nonsense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	10537577	112137036	68778224	38	2423										
APC	324	hgsc.bcm.edu	37	chr5	112175235	112175235	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agaaaagattggaactaggtCagctgaagatcctgtgagcg	13	6	1	5			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:112175235C>A	ENST00000457016.1	+	16	4324	c.3944C>A	c.(3943-3945)tCa>tAa	p.S1315*	APC_ENST00000508376.2_Nonsense_Mutation_p.S1315*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1315*			P25054	APC_HUMAN	adenomatous polyposis coli	1315	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1315*(12)|p.S1315fs*3(2)|p.S1315L(1)|p.?(1)|p.K1192fs*3(1)|p.S1315fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGAACTAGGTCAGCTGAAGAT	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	18	Substitution - Nonsense(12)|Insertion - Frameshift(2)|Deletion - Frameshift(2)|Unknown(1)|Substitution - Missense(1)	large_intestine(16)|soft_tissue(1)|skin(1)	5	GRCh37	CM021066	APC	M							59	61	60					5																	112175235		2202	4300	6502	112203134	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3944C>A	5.37:g.112175235C>A	ENSP00000413133:p.Ser1315*		112203134	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.719660	0.96839	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.642461	0.16403	N	0.215929	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.6185	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1315	.	.	S	+	2	0	APC	112203134	0.319000	0.24607	0.010000	0.14722	0.068000	0.16541	4.424000	0.59868	2.861000	0.98227	0.655000	0.94253	TCA		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175235	C	A	112175235	4	1	28	1	0	0	0	0	0	1	0	0	763	838	29	2	4002	2	APC	5	112175235	Nonsense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	38199	112175235	68740025	39	2424										
APC	324	hgsc.bcm.edu	37	chr5	112178847	112178847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tcccactatagagtataatgAtggaagaccagcaaagcgcc	9	10	0	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:112178847A>G	ENST00000457016.1	+	16	7936	c.7556A>G	c.(7555-7557)gAt>gGt	p.D2519G	APC_ENST00000508376.2_Missense_Mutation_p.D2519G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.D2519G			P25054	APC_HUMAN	adenomatous polyposis coli	2519	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.D2519G(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAGTATAATGATGGAAGACCA	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											96	85	89					5																	112178847		2202	4299	6501	112206746	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.7556A>G	5.37:g.112178847A>G	ENSP00000413133:p.Asp2519Gly		112206746	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534823	0.45073	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.84070	-1.8;-1.8;-1.8	6.07	6.07	0.98685	Adenomatous polyposis coli protein basic domain (1);	0.115400	0.64402	D	0.000016	D	0.82995	0.5158	L	0.44542	1.39	0.53005	D	0.999967	B;P	0.49783	0.008;0.928	B;P	0.53185	0.019;0.72	T	0.82014	-0.0667	9	.	.	.	-22.5307	10.8883	0.46981	0.9305:0.0:0.0695:0.0	.	2521;2519	Q4LE70;P25054	.;APC_HUMAN	G	2519	ENSP00000413133:D2519G;ENSP00000257430:D2519G;ENSP00000427089:D2519G	.	D	+	2	0	APC	112206746	1.000000	0.71417	0.998000	0.56505	0.900000	0.52787	7.425000	0.80255	2.326000	0.78906	0.533000	0.62120	GAT		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112178847	A	G	112178847	3	3	28	1	0	0	0	0	1	0	0	0	763	333	12	4	7614	4	APC	5	112178847	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	3612	112178847	68736413	40	2425										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114462493	114462493	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tatagtaactaaggtaaatgGttgtgaagaatcaaaacagg	10	3	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:114462493G>C	ENST00000282369.3	-	10	2015	c.1894C>G	c.(1894-1896)Cca>Gca	p.P632A	TRIM36_ENST00000513154.1_Missense_Mutation_p.P620A|TRIM36_ENST00000514154.1_Missense_Mutation_p.P477A	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	632	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P632A(1)		breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		AAGGTAAATGGTTGTGAAGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	92	93					5																	114462493		2202	4300	6502	114490392	SO:0001583	missense	55521			AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.1894C>G	5.37:g.114462493G>C	ENSP00000282369:p.Pro632Ala		114490392	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213714	0.79352	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.67523	-0.27;-0.27;-0.27	5.37	5.37	0.77165	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.111231	0.64402	D	0.000007	T	0.77579	0.4151	L	0.45581	1.43	0.80722	D	1	D;D	0.63046	0.992;0.991	P;D	0.72075	0.883;0.976	T	0.74259	-0.3723	10	0.34782	T	0.22	.	19.4818	0.95013	0.0:0.0:1.0:0.0	.	620;632	E9PFI8;Q9NQ86	.;TRI36_HUMAN	A	632;620;477	ENSP00000282369:P632A;ENSP00000423934:P620A;ENSP00000424259:P477A	ENSP00000282369:P632A	P	-	1	0	TRIM36	114490392	1.000000	0.71417	0.253000	0.24343	0.902000	0.53008	9.203000	0.95033	2.658000	0.90341	0.591000	0.81541	CCA		0.378	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		C	114462493	G	C	114462493	3	2	28	1	0	0	0	0	1	0	0	0	16550	1261	44	5	296	5	TRIM36	5	114462493	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	2283646	114462493	66452767	41	2426										
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140175607	140175607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cacaccagaagtctcaataaCgtctctctcacttcccatct	3	16	4	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:140175607C>T	ENST00000526136.1	+	1	1058	c.1058C>T	c.(1057-1059)aCg>aTg	p.T353M	PCDHA2_ENST00000378132.1_Missense_Mutation_p.T353M|PCDHA2_ENST00000520672.2_Missense_Mutation_p.T353M|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	353	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.T353M(2)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCTCAATAACGTCTCTCTCA	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	5											89	76	81					5																	140175607		2203	4300	6503	140155791	SO:0001583	missense	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1058C>T	5.37:g.140175607C>T	ENSP00000431748:p.Thr353Met		140155791	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	c	12.78	2.040551	0.35989	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.60040	0.22;0.22;0.22	3.92	2.03	0.26663	Cadherin (2);Cadherin-like (1);	0.182328	0.25714	U	0.028800	T	0.63885	0.2549	L	0.58101	1.795	0.09310	N	0.999999	D;P;D	0.58970	0.972;0.916;0.984	P;B;P	0.55011	0.686;0.341;0.766	T	0.58781	-0.7576	10	0.66056	D	0.02	.	12.0616	0.53566	0.4487:0.5513:0.0:0.0	.	353;353;353	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	M	353	ENSP00000430584:T353M;ENSP00000367372:T353M;ENSP00000431748:T353M	ENSP00000367372:T353M	T	+	2	0	PCDHA2	140155791	0.000000	0.05858	0.169000	0.22859	0.928000	0.56348	0.209000	0.17435	0.383000	0.24910	0.650000	0.86243	ACG		0.463	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140175607	C	T	140175607	3	4	28	1	0	0	0	0	1	0	0	0	11555	536	19	1	1060	1	PCDHA2	5	140175607	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	25713114	140175607	40739653	42	2427										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432201	140432201	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	attcgagtgggaggaaaagtCacctgcttcctcagagaaga	12	8	2	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:140432201C>T	ENST00000306549.3	+	1	1223	c.1146C>T	c.(1144-1146)gtC>gtT	p.V382V		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	382	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V382V(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGGAAAAGTCACCTGCTTCC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5											111	104	106					5																	140432201		2203	4300	6503	140412385	SO:0001819	synonymous_variant	29930			AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1146C>T	5.37:g.140432201C>T			140412385	Q2M257	Silent	SNP	ENST00000306549.3	37	CCDS4243.1																																																																																				0.502	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		T	140432201	C	T	140432201	2	4	28	1	0	0	0	0	0	0	0	1	11565	813	29	3		3	PCDHB1	5	140432201	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	256594	140432201	40483059	43	2428										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150723758	150723758	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caggatgcccgcgttcttcaCagcgaggggtagtcccagga	14	12	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:150723758C>G	ENST00000335244.4	-	2	364	c.235G>C	c.(235-237)Gtg>Ctg	p.V79L	SLC36A2_ENST00000521967.1_Missense_Mutation_p.V79L	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	79					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)	p.V79L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GCGTTCTTCACAGCGAGGGGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	81	85					5																	150723758		2203	4300	6503	150703951	SO:0001583	missense	153201			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.235G>C	5.37:g.150723758C>G	ENSP00000334223:p.Val79Leu		150703951	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.639229	0.29157	.	.	ENSG00000186335	ENST00000335244;ENST00000521967	T;T	0.02050	4.48;4.48	5.07	0.0823	0.14428	.	0.422514	0.25848	N	0.027914	T	0.02571	0.0078	L	0.53561	1.675	0.80722	D	1	B;B;B	0.19935	0.04;0.005;0.012	B;B;B	0.24006	0.05;0.03;0.033	T	0.46219	-0.9207	10	0.59425	D	0.04	-3.598	4.7318	0.12968	0.1421:0.4588:0.0:0.399	.	79;79;79	B4DMY0;E5RJJ5;Q495M3	.;.;S36A2_HUMAN	L	79	ENSP00000334223:V79L;ENSP00000430535:V79L	ENSP00000334223:V79L	V	-	1	0	SLC36A2	150703951	0.753000	0.28349	0.799000	0.32177	0.468000	0.32798	0.569000	0.23638	0.004000	0.14682	0.650000	0.86243	GTG		0.537	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			G	150723758	C	G	150723758	3	3	28	1	0	0	0	0	1	0	0	0	14631	478	17	5	1252	5	SLC36A2	5	150723758	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	10291557	150723758	30191502	44	2429										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116331	161116331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgggcatgcttgtccactcaAgtttgggagctgtaagttac	12	8	1	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:161116331A>C	ENST00000274545.5	+	5	951	c.518A>C	c.(517-519)aAg>aCg	p.K173T	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.K163T			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	173					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.K173T(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TGTCCACTCAAGTTTGGGAGC	0.393										TCGA Ovarian(5;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	5											123	110	114					5																	161116331		2203	4300	6503	161048909	SO:0001583	missense	2559				CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.518A>C	5.37:g.161116331A>C	ENSP00000274545:p.Lys173Thr		161048909	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.105012|4.105012	0.77096|0.77096	.|.	.|.	ENSG00000145863|ENSG00000145863	ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691|ENST00000520000	T;T;T;T|.	0.80566|.	-1.39;-1.39;-1.39;-1.39|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Neurotransmitter-gated ion-channel ligand-binding (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60843|0.60843	0.2300|0.2300	L|L	0.41356|0.41356	1.27|1.27	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.78314|.	0.991|.	T|T	0.57341|0.57341	-0.7828|-0.7828	10|5	0.87932|.	D|.	0|.	.|.	16.0395|16.0395	0.80654|0.80654	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	173|.	Q16445|.	GBRA6_HUMAN|.	T|R	173;163;120;68|113	ENSP00000274545:K173T;ENSP00000430527:K163T;ENSP00000430212:K120T;ENSP00000427989:K68T|.	ENSP00000274545:K173T|.	K|S	+|+	2|1	0|0	GABRA6|GABRA6	161048909|161048909	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.228000|9.228000	0.95250|0.95250	2.188000|2.188000	0.69820|0.69820	0.533000|0.533000	0.62120|0.62120	AAG|AGT		0.393	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			C	161116331	A	C	161116331	3	2	28	1	0	0	0	0	1	0	0	0	6184	72	3	4	536	4	GABRA6	5	161116331	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	10392573	161116331	19798929	45	2430										
OR2Y1	134083	hgsc.bcm.edu	37	chr5	180166262	180166262	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caaattttccctcacgctcaGaataattgtggatggattgg	9	8	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr5:180166262G>T	ENST00000307832.2	-	1	837	c.797C>A	c.(796-798)tCt>tAt	p.S266Y		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S266Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|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)			CTCACGCTCAGAATAATTGTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											89	101	97					5																	180166262		2203	4300	6503	180098868	SO:0001583	missense	134083			AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"GPCR / Class A : Olfactory receptors"	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.797C>A	5.37:g.180166262G>T	ENSP00000312403:p.Ser266Tyr		180098868	B9EIP1|Q6IFB1|Q96R16	Missense_Mutation	SNP	ENST00000307832.2	37	CCDS34323.1	.	.	.	.	.	.	.	.	.	.	g	14.24	2.476830	0.44044	.	.	ENSG00000174339	ENST00000307832	T	0.00277	8.34	4.41	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.743799	0.11539	N	0.553945	T	0.00754	0.0025	M	0.86097	2.795	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47368	-0.9123	10	0.87932	D	0	.	10.5969	0.45343	0.0965:0.0:0.9035:0.0	.	266	Q8NGV0	OR2Y1_HUMAN	Y	266	ENSP00000312403:S266Y	ENSP00000312403:S266Y	S	-	2	0	OR2Y1	180098868	0.009000	0.17119	0.002000	0.10522	0.002000	0.02628	1.652000	0.37313	1.193000	0.43086	0.511000	0.50034	TCT		0.423	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	XM_068682		T	180166262	G	T	180166262	3	4	28	1	0	0	0	0	1	0	0	0	11066	942	33	2	142	2	OR2Y1	5	180166262	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	19049931	180166262	748998	46	2431										
FARS2	10667	hgsc.bcm.edu	37	chr6	5368874	5368874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gagtaaggccagtcacatctCcagaggccatcagcaccagg	11	13	3	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:5368874C>A	ENST00000324331.6	+	2	407	c.71C>A	c.(70-72)tCc>tAc	p.S24Y	FARS2_ENST00000274680.4_Missense_Mutation_p.S24Y			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	24					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)	p.S24Y(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	AGTCACATCTCCAGAGGCCAT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	63	64					6																	5368874		2203	4300	6503	5313873	SO:0001583	missense	10667			AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	21062	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 2, mitochondrial"	611592	"phenylalanine-tRNA synthetase 1 (mitochondrial)"	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.71C>A	6.37:g.5368874C>A	ENSP00000316335:p.Ser24Tyr		5313873	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	37	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	C	7.624	0.677530	0.14841	.	.	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.71103	-0.54;-0.54	5.45	0.292	0.15737	.	0.608263	0.17019	N	0.190201	T	0.21387	0.0515	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32666	-0.9898	10	0.02654	T	1	-11.682	5.5662	0.17173	0.1176:0.2202:0.5685:0.0938	.	24	O95363	SYFM_HUMAN	Y	24	ENSP00000274680:S24Y;ENSP00000316335:S24Y	ENSP00000274680:S24Y	S	+	2	0	FARS2	5313873	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	0.133000	0.15912	0.348000	0.23949	0.655000	0.94253	TCC		0.572	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567		A	5368874	C	A	5368874	3	1	28	1	0	0	0	0	1	0	0	0	5697	855	30	2	73	2	FARS2	6	5368874	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		5368874	165746193	47	2432										
F13A1	2162	hgsc.bcm.edu	37	chr6	6152175	6152175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cagaaccaactacctgagtgCcacggacctaagagagagaa	10	11	0	4			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:6152175C>T	ENST00000264870.3	-	14	2181	c.1916G>A	c.(1915-1917)gGc>gAc	p.G639D		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	639					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.G639D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TACCTGAGTGCCACGGACCTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											65	58	61					6																	6152175		2203	4300	6503	6097174	SO:0001583	missense	2162			M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1916G>A	6.37:g.6152175C>T	ENSP00000264870:p.Gly639Asp		6097174	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402046	0.83120	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.69806	-0.43	5.37	5.37	0.77165	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.052849	0.85682	D	0.000000	T	0.82047	0.4952	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	D	0.84438	0.0581	10	0.87932	D	0	.	16.6621	0.85243	0.0:1.0:0.0:0.0	.	576;639	F5H080;P00488	.;F13A_HUMAN	D	639;576	ENSP00000264870:G639D	ENSP00000264870:G639D	G	-	2	0	F13A1	6097174	0.965000	0.33210	0.796000	0.32109	0.955000	0.61496	4.293000	0.59037	2.788000	0.95919	0.650000	0.86243	GGC		0.433	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		T	6152175	C	T	6152175	3	4	28	1	0	0	0	0	1	0	0	0	5353	739	26	3	290	3	F13A1	6	6152175	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	783301	6152175	164962892	48	2433										
SLC35B3	51000	hgsc.bcm.edu	37	chr6	8417716	8417716	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tatacaaaaccaattgaataCgaatacaatacctagagcag	5	8	0	2	rs184112854	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:8417716C>T	ENST00000379660.4	-	8	1241	c.792G>A	c.(790-792)tcG>tcA	p.S264S		NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	264					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.S264S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					CAATTGAATACGAATACAATA	0.328													C|||	3	0.000599042	8e-04	0	5008	,	,		15478	0		0.002	False		,,,				2504	0				Melanoma(83;700 1353 9357 11478 30548)											1	Substitution - coding silent(1)	large_intestine(1)	6											69	64	66					6																	8417716		2203	4295	6498	8362715	SO:0001819	synonymous_variant	51000			AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"Solute carriers"	21601	protein-coding gene	gene with protein product	"3' phosphoadenosine 5' phosphosulfate transporter 2"	610845	"chromosome 6 open reading frame 196", "solute carrier family 35, member B3"	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.792G>A	6.37:g.8417716C>T			8362715	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Silent	SNP	ENST00000379660.4	37	CCDS4508.1																																																																																				0.328	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	NM_015948		T	8417716	C	T	8417716	2	4	28	1	0	0	0	0	0	0	0	1	14614	523	19	1		1	SLC35B3	6	8417716	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	2265541	8417716	162697351	49	2434										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24709124	24709124	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tttttcatagtcaccatgatGaaactcaaatttggcctaat	5	8	3	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:24709124G>C	ENST00000378119.4	-	4	2612	c.445C>G	c.(445-447)Cat>Gat	p.H149D	C6orf62_ENST00000540769.1_Missense_Mutation_p.H91D|RP1-30M3.6_ENST00000606921.1_RNA|C6orf62_ENST00000378102.3_Missense_Mutation_p.H120D	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	149						intracellular (GO:0005622)		p.H149D(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						TCACCATGATGAAACTCAAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											141	130	134					6																	24709124		2203	4300	6503	24817103	SO:0001583	missense	81688			AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.445C>G	6.37:g.24709124G>C	ENSP00000367359:p.His149Asp		24817103	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	37	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931312	0.34096	.	.	ENSG00000112308	ENST00000378119;ENST00000540769;ENST00000378102	T;T;T	0.26957	1.7;1.7;1.7	6.08	5.04	0.67666	.	0.087086	0.85682	D	0.000000	T	0.07279	0.0184	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11842	-1.0571	10	0.30854	T	0.27	-16.4881	16.2862	0.82722	0.0729:0.0:0.9271:0.0	.	149	Q9GZU0	CF062_HUMAN	D	149;91;120	ENSP00000367359:H149D;ENSP00000446225:H91D;ENSP00000367342:H120D	ENSP00000367342:H120D	H	-	1	0	C6orf62	24817103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.510000	0.67018	2.894000	0.99253	0.655000	0.94253	CAT		0.363	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		C	24709124	G	C	24709124	3	2	28	1	0	0	0	0	1	0	0	0	2374	1290	45	5	252	5	C6orf62	6	24709124	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	16291408	24709124	146405943	50	2435										
NT5E	4907	hgsc.bcm.edu	37	chr6	86201787	86201787	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agtgtcgagtgcccagttatGaccctctcaaaatggacgag	11	10	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:86201787G>C	ENST00000257770.3	+	8	1502	c.1453G>C	c.(1453-1455)Gac>Cac	p.D485H	NT5E_ENST00000369651.3_Missense_Mutation_p.D435H	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	485					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.D485H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	GCCCAGTTATGACCCTCTCAA	0.423																																					Melanoma(140;797 1765 2035 2752 18208)											1	Substitution - Missense(1)	large_intestine(1)	6											168	159	162					6																	86201787		2203	4300	6503	86258506	SO:0001583	missense	4907			X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"CD molecules"	8021	protein-coding gene	gene with protein product		129190	"5' nucleotidase (CD73)"	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.1453G>C	6.37:g.86201787G>C	ENSP00000257770:p.Asp485His		86258506	B3KQI8|O75520|Q5W116	Missense_Mutation	SNP	ENST00000257770.3	37	CCDS5002.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.388|7.388	0.630201|0.630201	0.14257|0.14257	.|.	.|.	ENSG00000135318|ENSG00000135318	ENST00000257770;ENST00000369651|ENST00000416334	T;T|.	0.54675|.	0.56;0.56|.	5.66|5.66	3.82|3.82	0.43975|0.43975	5&apos (3);-Nucleotidase, C-terminal (3);|.	0.441395|.	0.27043|.	N|.	0.021208|.	T|T	0.15565|0.15565	0.0375|0.0375	N|N	0.20483|0.20483	0.58|0.58	0.26936|0.26936	N|N	0.966365|0.966365	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.08055|.	0.0;0.003|.	T|T	0.23476|0.23476	-1.0187|-1.0187	10|5	0.46703|.	T|.	0.11|.	-11.8537|-11.8537	12.9463|12.9463	0.58373|0.58373	0.1038:0.0:0.8962:0.0|0.1038:0.0:0.8962:0.0	.|.	435;485|.	B3KQI8;P21589|.	.;5NTD_HUMAN|.	H|I	485;435|199	ENSP00000257770:D485H;ENSP00000358665:D435H|.	ENSP00000257770:D485H|.	D|M	+|+	1|3	0|0	NT5E|NT5E	86258506|86258506	1.000000|1.000000	0.71417|0.71417	0.617000|0.617000	0.29091|0.29091	0.006000|0.006000	0.05464|0.05464	4.329000|4.329000	0.59260|0.59260	0.802000|0.802000	0.34089|0.34089	-0.302000|-0.302000	0.09304|0.09304	GAC|ATG		0.423	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1			C	86201787	G	C	86201787	3	2	28	1	0	0	0	0	1	0	0	0	10724	1290	45	5	1483	5	NT5E	6	86201787	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	61492663	86201787	84913280	51	2436										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88170863	88170863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agtggaatgaatgggaattaAgaagaaaagctataaaattg	11	1	0	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:88170863A>G	ENST00000507897.1	+	12	1701	c.1618A>G	c.(1618-1620)Aga>Gga	p.R540G	C6ORF165_ENST00000369562.4_Missense_Mutation_p.R540G|C6orf165_ENST00000506888.1_3'UTR			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	540								p.R540G(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		ATGGGAATTAAGAAGAAAAGC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	60	63					6																	88170863		2203	4298	6501	88227582	SO:0001583	missense	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1618A>G	6.37:g.88170863A>G	ENSP00000426769:p.Arg540Gly		88227582	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.863828	0.71949	.	.	ENSG00000213204	ENST00000369562	T	0.53423	0.62	5.39	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	M	0.90252	3.1	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	T	0.74512	-0.3641	10	0.87932	D	0	.	12.3017	0.54878	0.8588:0.1412:0.0:0.0	.	540	Q8IYR0	CF165_HUMAN	G	540	ENSP00000358575:R540G	ENSP00000358575:R540G	R	+	1	2	C6orf165	88227582	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.908000	0.48750	2.167000	0.68274	0.533000	0.62120	AGA		0.299	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		G	88170863	A	G	88170863	3	3	28	1	0	0	0	0	1	0	0	0	2347	64	3	4	1660	4	C6orf165	6	88170863	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	1969076	88170863	82944204	52	2437										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854294	88854294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	catcaggcaaaacgccaccaCggccttgggcctggtgacaa	11	14	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:88854294C>T	ENST00000537554.1	-	2	4262	c.700G>A	c.(700-702)Gtg>Atg	p.V234M	CNR1_ENST00000549716.1_Missense_Mutation_p.V173M|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000369501.2_Missense_Mutation_p.V234M|CNR1_ENST00000535130.1_Missense_Mutation_p.V234M|CNR1_ENST00000468898.1_Missense_Mutation_p.V201M|CNR1_ENST00000369499.2_Missense_Mutation_p.V234M|CNR1_ENST00000549890.1_Missense_Mutation_p.V234M|CNR1_ENST00000428600.2_Missense_Mutation_p.V234M	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	234					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)	p.V234M(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		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)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	AACGCCACCACGGCCTTGGGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											58	56	57					6																	88854294		2203	4300	6503	88911013	SO:0001583	missense	1268			AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.700G>A	6.37:g.88854294C>T	ENSP00000441046:p.Val234Met		88911013	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	37	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595852	0.46318	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11;1.11;1.11	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	L	0.52573	1.65	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.67900	0.935;0.954	T	0.53683	-0.8404	10	0.72032	D	0.01	.	20.2861	0.98535	0.0:1.0:0.0:0.0	.	201;234	P21554-3;P21554	.;CNR1_HUMAN	M	234;234;234;234;234;201;234;173	ENSP00000358513:V234M;ENSP00000442689:V234M;ENSP00000441046:V234M;ENSP00000358511:V234M;ENSP00000446819:V234M;ENSP00000420188:V201M;ENSP00000412192:V234M;ENSP00000449549:V173M	ENSP00000358511:V234M	V	-	1	0	CNR1	88911013	1.000000	0.71417	0.966000	0.40874	0.056000	0.15407	7.818000	0.86416	2.800000	0.96347	0.655000	0.94253	GTG		0.567	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			T	88854294	C	T	88854294	3	4	28	1	0	0	0	0	1	0	0	0	3637	536	19	1	722	1	CNR1	6	88854294	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	683431	88854294	82260773	53	2438										
GJA1	2697	hgsc.bcm.edu	37	chr6	121768829	121768829	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctcaccaaccgctcccctctCgcctatgtctcctcctgggt	6	20	3	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:121768829C>T	ENST00000282561.3	+	2	993	c.836C>T	c.(835-837)tCg>tTg	p.S279L		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	279					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.S279L(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	GCTCCCCTCTCGCCTATGTCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	6											58	62	61					6																	121768829		2203	4300	6503	121810528	SO:0001583	missense	2697			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.836C>T	6.37:g.121768829C>T	ENSP00000282561:p.Ser279Leu		121810528	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	C	8.078	0.771688	0.16051	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	D	0.82255	-1.59	5.18	5.18	0.71444	.	0.398028	0.22775	N	0.055788	T	0.76919	0.4055	L	0.29908	0.895	0.48571	D	0.999671	D	0.60575	0.988	P	0.52598	0.703	T	0.75698	-0.3227	10	0.33141	T	0.24	.	17.0595	0.86543	0.0:1.0:0.0:0.0	.	279	P17302	CXA1_HUMAN	L	263;279	ENSP00000282561:S279L	ENSP00000282561:S279L	S	+	2	0	GJA1	121810528	1.000000	0.71417	0.552000	0.28243	0.038000	0.13279	5.064000	0.64338	2.694000	0.91930	0.585000	0.79938	TCG		0.507	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		T	121768829	C	T	121768829	3	4	28	1	0	0	0	0	1	0	0	0	6420	893	31	1	838	1	GJA1	6	121768829	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	32914535	121768829	49346238	54	2439										
UTRN	7402	hgsc.bcm.edu	37	chr6	144858824	144858824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgcaaaagagatcaaccaccGaattgggagaaaacctgcaa	9	9	1	2	rs532277544		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:144858824G>A	ENST00000367545.3	+	43	6340	c.6340G>A	c.(6340-6342)Gaa>Aaa	p.E2114K		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2114					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E2114K(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATCAACCACCGAATTGGGAGA	0.408													G|||	1	0.000199681	8e-04	0	5008	,	,		13139	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											147	130	136					6																	144858824		2203	4300	6503	144900517	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.6340G>A	6.37:g.144858824G>A	ENSP00000356515:p.Glu2114Lys		144900517	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883894	0.33255	.	.	ENSG00000152818	ENST00000367545	T	0.37235	1.21	4.77	2.97	0.34412	.	0.496999	0.18562	N	0.137589	T	0.08088	0.0202	N	0.19112	0.55	0.09310	N	0.999995	B	0.11235	0.004	B	0.04013	0.001	T	0.22695	-1.0209	10	0.30078	T	0.28	.	6.8938	0.24245	0.3011:0.0:0.6989:0.0	.	2114	P46939	UTRO_HUMAN	K	2114	ENSP00000356515:E2114K	ENSP00000356515:E2114K	E	+	1	0	UTRN	144900517	0.004000	0.15560	0.003000	0.11579	0.003000	0.03518	1.099000	0.31013	1.319000	0.45190	0.655000	0.94253	GAA		0.408	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144858824	G	A	144858824	3	1	28	1	0	0	0	0	1	0	0	0	17143	1059	37	1	6510	1	UTRN	6	144858824	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	23089995	144858824	26256243	55	2440										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152639268	152639268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtctaatggtctgctggtgaAgttcagtcagttttcctatc	10	8	4	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr6:152639268A>C	ENST00000367255.5	-	86	17121	c.16520T>G	c.(16519-16521)cTt>cGt	p.L5507R	SYNE1_ENST00000265368.4_Missense_Mutation_p.L5507R|SYNE1_ENST00000448038.1_Missense_Mutation_p.L5436R|SYNE1_ENST00000423061.1_Missense_Mutation_p.L5436R|SYNE1_ENST00000356820.4_Missense_Mutation_p.L31R|SYNE1_ENST00000341594.5_Intron	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5507			L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L5507R(3)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTGCTGGTGAAGTTCAGTCAG	0.453										HNSCC(10;0.0054)																																						3	Substitution - Missense(3)	large_intestine(3)	6											266	234	245					6																	152639268		2203	4300	6503	152680961	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16520T>G	6.37:g.152639268A>C	ENSP00000356224:p.Leu5507Arg		152680961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	18.71	3.683137	0.68157	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000356820	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000039	T	0.37404	0.1002	M	0.68952	2.095	0.52099	D	0.999948	D;D;D;D	0.71674	0.998;0.997;0.997;0.998	D;D;D;D	0.71870	0.975;0.944;0.944;0.972	T	0.32693	-0.9897	10	0.08599	T	0.76	.	15.8861	0.79251	1.0:0.0:0.0:0.0	.	5507;5507;5507;5436	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	R	5507;5436;5507;5436;31	ENSP00000356224:L5507R;ENSP00000396024:L5436R;ENSP00000265368:L5507R;ENSP00000390975:L5436R;ENSP00000349276:L31R	ENSP00000265368:L5507R	L	-	2	0	SYNE1	152680961	0.992000	0.36948	0.995000	0.50966	0.771000	0.43674	8.344000	0.90055	2.156000	0.67533	0.533000	0.62120	CTT		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152639268	A	C	152639268	3	2	28	1	0	0	0	0	1	0	0	0	15484	72	3	4	10190	4	SYNE1	6	152639268	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	7780444	152639268	18475799	56	2441										
NPY	4852	hgsc.bcm.edu	37	chr7	24324907	24324907	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tccggactgaccctcgccctGtccctgctcgtgtgcctggg	12	17	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr7:24324907G>T	ENST00000407573.1	+	3	338	c.48G>T	c.(46-48)ctG>ctT	p.L16L	NPY_ENST00000242152.2_Silent_p.L16L|NPY_ENST00000405982.1_Silent_p.L16L			P01303	NPY_HUMAN	neuropeptide Y	16					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)	p.L16L(1)		breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						CCCTCGCCCTGTCCCTGCTCG	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	7											93	77	82					7																	24324907		2203	4300	6503	24291432	SO:0001819	synonymous_variant	4852			K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"Endogenous ligands"	7955	protein-coding gene	gene with protein product	"prepro-neuropeptide Y"	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.48G>T	7.37:g.24324907G>T			24291432		Silent	SNP	ENST00000407573.1	37	CCDS5387.1																																																																																				0.657	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905		T	24324907	G	T	24324907	2	4	28	1	0	0	0	0	0	0	0	1	10638	1364	48	2		2	NPY	7	24324907	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10		24324907	134813756	57	2442										
KBTBD2	25948	hgsc.bcm.edu	37	chr7	32909871	32909871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aggaacttgaccccctgctaTgtagatatcattatcaggag	9	9	2	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr7:32909871T>C	ENST00000304056.4	-	4	1657	c.958A>G	c.(958-960)Ata>Gta	p.I320V	AVL9_ENST00000404479.1_Intron|KBTBD2_ENST00000485611.1_5'Flank	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	320								p.I320V(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			CCCCCTGCTATGTAGATATCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											186	174	178					7																	32909871		2203	4300	6503	32876396	SO:0001583	missense	25948			AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"BTB/POZ domain containing"	21751	protein-coding gene	gene with protein product			"BTB and kelch domain containing 1"	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.958A>G	7.37:g.32909871T>C	ENSP00000302586:p.Ile320Val		32876396	A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Missense_Mutation	SNP	ENST00000304056.4	37	CCDS34614.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326967	0.41197	.	.	ENSG00000170852	ENST00000304056;ENST00000537125	T	0.62364	0.03	5.65	5.65	0.86999	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.60196	0.2250	L	0.47716	1.5	0.58432	D	0.999995	P	0.35745	0.518	P	0.44647	0.456	T	0.55786	-0.8086	10	0.02654	T	1	.	16.1594	0.81686	0.0:0.0:0.0:1.0	.	320	Q8IY47	KBTB2_HUMAN	V	320;127	ENSP00000302586:I320V	ENSP00000302586:I320V	I	-	1	0	KBTBD2	32876396	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.655000	0.83696	2.279000	0.76181	0.402000	0.26972	ATA		0.403	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224		C	32909871	T	C	32909871	3	2	28	1	0	0	0	0	1	0	0	0	8014	1464	51	4	917	4	KBTBD2	7	32909871	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	8584964	32909871	126228792	58	2443										
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94827698	94827698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aaaaaccaggacaagtgagcGaggttgcccagttgataagc	12	8	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr7:94827698G>A	ENST00000433881.1	+	6	2324	c.1792G>A	c.(1792-1794)Gag>Aag	p.E598K	PPP1R9A_ENST00000340694.4_Missense_Mutation_p.E598K|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.E598K|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.E598K|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.E598K|AC002429.5_ENST00000417881.2_RNA|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.E598K			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	598	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)		p.E598K(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			ACAAGTGAGCGAGGTTGCCCA	0.463										HNSCC(28;0.073)																																						1	Substitution - Missense(1)	large_intestine(1)	7											102	100	101					7																	94827698		2203	4300	6503	94665634	SO:0001583	missense	55607			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1792G>A	7.37:g.94827698G>A	ENSP00000398870:p.Glu598Lys		94665634	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	37	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.623980	0.87560	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.21932	2.04;2.03;1.98;2.03;2.02;1.98	5.61	5.61	0.85477	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.50463	0.1617	M	0.76170	2.325	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.999;0.993;0.998	T	0.49679	-0.8914	10	0.87932	D	0	.	20.0173	0.97481	0.0:0.0:1.0:0.0	.	598;598;598;598;598	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	K	598	ENSP00000405514:E598K;ENSP00000344524:E598K;ENSP00000411342:E598K;ENSP00000398870:E598K;ENSP00000289495:E598K;ENSP00000402893:E598K	ENSP00000289495:E598K	E	+	1	0	PPP1R9A	94665634	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	9.718000	0.98758	2.814000	0.96858	0.591000	0.81541	GAG		0.463	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		A	94827698	G	A	94827698	3	1	28	1	0	0	0	0	1	0	0	0	12412	1059	37	1	1810	1	PPP1R9A	7	94827698	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	61917827	94827698	64310965	59	2444										
RELN	5649	hgsc.bcm.edu	37	chr7	103191534	103191534	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ccacaaaggtgcagcttcccAaagtgcacgacctccctcct	7	17	0	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr7:103191534A>G	ENST00000428762.1	-	41	6441	c.6282T>C	c.(6280-6282)ttT>ttC	p.F2094F	RELN_ENST00000424685.2_Silent_p.F2094F|RELN_ENST00000343529.5_Silent_p.F2094F	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2094					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.F2094F(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GCAGCTTCCCAAAGTGCACGA	0.547																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - coding silent(1)	large_intestine(1)	7											56	42	46					7																	103191534		2203	4300	6503	102978770	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6282T>C	7.37:g.103191534A>G			102978770	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.547	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103191534	A	G	103191534	2	3	28	1	0	0	0	0	0	0	0	1	13257	127	5	4		4	RELN	7	103191534	Silent	SNP	A	TCGA-AG-3601-01A-01W-0833-10	8363836	103191534	55947129	60	2445										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121671604	121671604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gcaagtagtgggtttactgaAgaatttgaggtatgatttta	12	2	0	4			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr7:121671604A>C	ENST00000393386.2	+	15	5568	c.5157A>C	c.(5155-5157)gaA>gaC	p.E1719D	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E859D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1719	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E1719D(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GGTTTACTGAAGAATTTGAGG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	7											83	78	80					7																	121671604		2203	4299	6502	121458840	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5157A>C	7.37:g.121671604A>C	ENSP00000377047:p.Glu1719Asp		121458840	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779870	0.49891	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.15017	2.46;2.46	5.91	5.91	0.95273	Protein-tyrosine phosphatase, receptor/non-receptor type (1);	0.073211	0.56097	D	0.000025	T	0.18425	0.0442	L	0.56124	1.755	0.37048	D	0.897477	B;B;B	0.19583	0.001;0.0;0.037	B;B;B	0.15484	0.001;0.001;0.013	T	0.05484	-1.0882	10	0.49607	T	0.09	.	11.4322	0.50047	0.8654:0.0:0.0:0.1346	.	858;859;1719	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	D	1719;859	ENSP00000377047:E1719D;ENSP00000410000:E859D	ENSP00000377047:E1719D	E	+	3	2	PTPRZ1	121458840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.273000	0.33121	2.263000	0.75096	0.528000	0.53228	GAA		0.294	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121671604	A	C	121671604	3	2	28	1	0	0	0	0	1	0	0	0	12851	69	3	4	5215	4	PTPRZ1	7	121671604	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	18480070	121671604	37467059	61	2446										
TNFRSF10D	8793	hgsc.bcm.edu	37	chr8	23003361	23003361	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ggttttcccagtggaactggCagctgattcatttttgcact	10	9	1	1	rs564770894		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr8:23003361C>A	ENST00000312584.3	-	5	650	c.556G>T	c.(556-558)Gcc>Tcc	p.A186S		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	186					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.A186S(1)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GTGGAACTGGCAGCTGATTCA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	8											142	126	131					8																	23003361		2203	4300	6503	23059306	SO:0001583	missense	8793			AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"Tumor necrosis factor receptor superfamily", "CD molecules"	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.556G>T	8.37:g.23003361C>A	ENSP00000310263:p.Ala186Ser		23059306	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	37	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	c	3.996	-0.003512	0.07773	.	.	ENSG00000173530	ENST00000312584	T	0.35789	1.29	1.71	-1.1	0.09872	.	2587.460000	0.00166	N	0.000001	T	0.23249	0.0562	L	0.40543	1.245	0.09310	N	1	P	0.34864	0.473	B	0.28553	0.091	T	0.04607	-1.0939	10	0.14656	T	0.56	.	2.2428	0.04024	0.0:0.2318:0.3143:0.4539	.	186	Q9UBN6	TR10D_HUMAN	S	186	ENSP00000310263:A186S	ENSP00000310263:A186S	A	-	1	0	TNFRSF10D	23059306	0.007000	0.16637	0.001000	0.08648	0.003000	0.03518	0.053000	0.14184	-0.281000	0.09141	-0.379000	0.06801	GCC		0.527	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			A	23003361	C	A	23003361	3	1	28	1	0	0	0	0	1	0	0	0	16322	710	25	2	624	2	TNFRSF10D	8	23003361	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		23003361	123360661	62	2447										
TG	7038	hgsc.bcm.edu	37	chr8	133980166	133980166	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	atggagtccaatgcccagggCtgcagactgatcctgcctca	11	13	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr8:133980166C>A	ENST00000220616.4	+	31	5854	c.5814C>A	c.(5812-5814)ggC>ggA	p.G1938G	TG_ENST00000519543.1_Silent_p.G92G|TG_ENST00000542445.1_Silent_p.G308G|TG_ENST00000377869.1_Silent_p.G1881G	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1938					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.G1938G(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		ATGCCCAGGGCTGCAGACTGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	8											89	76	80					8																	133980166		2203	4300	6503	134049348	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5814C>A	8.37:g.133980166C>A			134049348	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	2.745	-0.261392	0.05791	.	.	ENSG00000042832	ENST00000519178	.	.	.	5.65	3.85	0.44370	.	.	.	.	.	T	0.59865	0.2225	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55642	-0.8109	4	.	.	.	.	9.8174	0.40860	0.1583:0.6896:0.152:0.0	.	.	.	.	M	394	.	.	L	+	1	2	TG	134049348	0.999000	0.42202	0.996000	0.52242	0.253000	0.25986	0.492000	0.22435	0.859000	0.35456	-0.122000	0.15005	CTG		0.522	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133980166	C	A	133980166	2	1	28	1	0	0	0	0	0	0	0	1	15852	784	28	2		2	TG	8	133980166	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	110976805	133980166	12383856	63	2448										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34489429	34489429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aaggacggcggcagcattacCgcgatgaattagtggcaggt	15	8	0	1	rs116938457	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr9:34489429C>T	ENST00000242317.4	+	5	541	c.370C>T	c.(370-372)Cgc>Tgc	p.R124C	DNAI1_ENST00000488369.1_3'UTR	NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	124					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)	p.R124C(1)		autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GCAGCATTACCGCGATGAATT	0.517									Kartagener syndrome				C|||	2	0.000399361	0	0	5008	,	,		17295	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9						C	CYS/ARG	0,4406		0,0,2203	136	117	123		370	6.1	1	9	dbSNP_132	123	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DNAI1	NM_012144.2	180	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	124/700	34489429	3,13003	2203	4300	6503	34479429	SO:0001583	missense	27019	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.370C>T	9.37:g.34489429C>T	ENSP00000242317:p.Arg124Cys		34479429	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.28	3.350415	0.61183	0.0	3.49E-4	ENSG00000122735	ENST00000396929;ENST00000242317;ENST00000437363	T;D	0.81821	1.5;-1.54	6.08	6.08	0.98989	.	0.684347	0.14346	N	0.325391	D	0.85544	0.5721	M	0.67397	2.05	0.80722	D	1	D	0.61697	0.99	P	0.52343	0.696	D	0.85024	0.0913	10	0.56958	D	0.05	.	16.1635	0.81734	0.0:1.0:0.0:0.0	.	124	Q9UI46	DNAI1_HUMAN	C	113;124;113	ENSP00000242317:R124C;ENSP00000395396:R113C	ENSP00000242317:R124C	R	+	1	0	DNAI1	34479429	0.858000	0.29795	0.974000	0.42286	0.241000	0.25554	1.808000	0.38912	2.894000	0.99253	0.655000	0.94253	CGC		0.517	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			T	34489429	C	T	34489429	3	4	28	1	0	0	0	0	1	0	0	0	4620	652	23	1	388	1	DNAI1	9	34489429	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		34489429	106724002	64	2449										
TNC	3371	hgsc.bcm.edu	37	chr9	117788933	117788933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ccgcaggtccacccggagctCgtactgcccctgggctgtga	13	16	0	1	rs140573419	byFrequency	TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr9:117788933C>T	ENST00000350763.4	-	26	6622	c.6211G>A	c.(6211-6213)Gag>Aag	p.E2071K	TNC_ENST00000346706.3_Missense_Mutation_p.E1525K|TNC_ENST00000341037.4_Missense_Mutation_p.E1889K|TNC_ENST00000340094.3_Missense_Mutation_p.E1707K|TNC_ENST00000423613.2_Missense_Mutation_p.E1798K|TNC_ENST00000345230.3_Missense_Mutation_p.E1434K|TNC_ENST00000537320.1_Missense_Mutation_p.E1434K|TNC_ENST00000535648.1_Missense_Mutation_p.E1616K|TNC_ENST00000542877.1_Missense_Mutation_p.E1708K	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	2071	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.E2071K(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ACCCGGAGCTCGTACTGCCCC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	LYS/GLU	0,4406		0,0,2203	74	62	66		6211	5.6	1	9	dbSNP_134	66	3,8597	2.2+/-6.3	0,3,4297	yes	missense	TNC	NM_002160.3	56	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	2071/2202	117788933	3,13003	2203	4300	6503	116828754	SO:0001583	missense	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.6211G>A	9.37:g.117788933C>T	ENSP00000265131:p.Glu2071Lys		116828754	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	36	5.825201	0.96989	0.0	3.49E-4	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.61	5.61	0.85477	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.54679	0.1873	M	0.73598	2.24	0.48901	D	0.999728	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.56426	-0.7981	10	0.72032	D	0.01	.	19.6248	0.95674	0.0:1.0:0.0:0.0	.	1798;2071	E9PC84;P24821	.;TENA_HUMAN	K	1707;1616;1525;1434;2071;1889;1798;1434;1708	ENSP00000344400:E1707K;ENSP00000438152:E1616K;ENSP00000344555:E1525K;ENSP00000345861:E1434K;ENSP00000265131:E2071K;ENSP00000339553:E1889K;ENSP00000411406:E1798K;ENSP00000443478:E1434K;ENSP00000442242:E1708K	ENSP00000344400:E1707K	E	-	1	0	TNC	116828754	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.487000	0.81328	2.631000	0.89168	0.655000	0.94253	GAG		0.557	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117788933	C	T	117788933	3	4	28	1	0	0	0	0	1	0	0	0	16309	893	31	1	406	1	TNC	9	117788933	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	83299504	117788933	23424498	65	2450										
GPR158	57512	hgsc.bcm.edu	37	chr10	25701343	25701343	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ccatcatctccttccaagccCtgtgtatgctgctcgacttc	6	16	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr10:25701343C>T	ENST00000376351.3	+	4	1635	c.1276C>T	c.(1276-1278)Ctg>Ttg	p.L426L		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	426					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L426L(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CTTCCAAGCCCTGTGTATGCT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	10											234	200	212					10																	25701343		2203	4300	6503	25741349	SO:0001819	synonymous_variant	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1276C>T	10.37:g.25701343C>T			25741349	Q6QR81|Q9ULT3	Silent	SNP	ENST00000376351.3	37	CCDS31166.1																																																																																				0.512	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25701343	C	T	25701343	2	4	28	1	0	0	0	0	0	0	0	1	6683	680	24	3		3	GPR158	10	25701343	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10		25701343	109833404	66	2451										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93601073	93601073	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttgcacaatgcatgttcttaTggacattatgaagttgcaga	9	6	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr10:93601073T>C	ENST00000371627.4	+	15	2086	c.1707T>C	c.(1705-1707)taT>taC	p.Y569Y		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	569					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.Y569Y(1)		biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				CATGTTCTTATGGACATTATG	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	10											119	113	115					10																	93601073		2203	4300	6503	93591053	SO:0001819	synonymous_variant	80351			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1707T>C	10.37:g.93601073T>C			93591053	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	37	CCDS7417.1																																																																																				0.318	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		C	93601073	T	C	93601073	2	2	28	1	0	0	0	0	0	0	0	1	16360	1471	51	4		4	TNKS2	10	93601073	Silent	SNP	T	TCGA-AG-3601-01A-01W-0833-10	67899730	93601073	41933674	67	2452										
DNTT	1791	hgsc.bcm.edu	37	chr10	98092166	98092166	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgaaaagctcaggttgcctaGcaggaaggttgatgctttgg	14	6	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr10:98092166G>T	ENST00000371174.2	+	9	1274	c.1172G>T	c.(1171-1173)aGc>aTc	p.S391I	DNTT_ENST00000419175.1_Missense_Mutation_p.S391I			P04053	TDT_HUMAN	DNA nucleotidylexotransferase	391	Mediates interaction with DNTTIP2.				DNA modification (GO:0006304)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA nucleotidylexotransferase activity (GO:0003912)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.S391I(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		AGGTTGCCTAGCAGGAAGGTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											113	111	112					10																	98092166		2203	4300	6503	98082156	SO:0001583	missense	1791			AB046378	CCDS7447.1	10q23-q24	2013-05-21	2013-05-21		ENSG00000107447	ENSG00000107447	2.7.7.31	"DNA polymerases"	2983	protein-coding gene	gene with protein product	"Terminal deoxynucleotidyltransferase"	187410	"deoxynucleotidyltransferase, terminal"				Standard	NM_004088		Approved	TDT	uc001kmf.3	P04053	OTTHUMG00000018832	ENST00000371174.2:c.1172G>T	10.37:g.98092166G>T	ENSP00000360216:p.Ser391Ile		98082156	Q53FH1|Q5W103|Q96E50	Missense_Mutation	SNP	ENST00000371174.2	37	CCDS7447.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.869009	0.72065	.	.	ENSG00000107447	ENST00000419175;ENST00000371174	T;T	0.42513	0.97;0.97	5.81	5.81	0.92471	DNA-directed DNA polymerase X (1);Nucleotidyl transferase domain (1);	0.090322	0.64402	D	0.000001	T	0.66268	0.2772	M	0.78916	2.43	0.45580	D	0.998521	D;D	0.89917	1.0;1.0	D;D	0.71870	0.958;0.975	T	0.67356	-0.5691	10	0.56958	D	0.05	-4.3136	17.5668	0.87922	0.0:0.0:1.0:0.0	.	391;391	P04053-2;P04053	.;TDT_HUMAN	I	391	ENSP00000401169:S391I;ENSP00000360216:S391I	ENSP00000360216:S391I	S	+	2	0	DNTT	98082156	1.000000	0.71417	0.998000	0.56505	0.848000	0.48234	5.823000	0.69272	2.750000	0.94351	0.655000	0.94253	AGC		0.423	DNTT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049607.1	NM_004088		T	98092166	G	T	98092166	3	4	28	1	0	0	0	0	1	0	0	0	4691	971	34	2	1206	2	DNTT	10	98092166	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	4491093	98092166	37442581	68	2453										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108389026	108389026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gtccacctgcacggtcacacGgaaaatgcccacgttctgat	9	14	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr10:108389026G>A	ENST00000263054.6	-	19	2603	c.2596C>T	c.(2596-2598)Cgt>Tgt	p.R866C	SORCS1_ENST00000344440.6_Missense_Mutation_p.R866C|SORCS1_ENST00000369698.1_Missense_Mutation_p.R401C	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	866	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.R866C(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ACGGTCACACGGAAAATGCCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	10											161	116	131					10																	108389026		2203	4300	6503	108379016	SO:0001583	missense	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2596C>T	10.37:g.108389026G>A	ENSP00000263054:p.Arg866Cys		108379016	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097514	0.94197	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.61392	0.11;0.11;0.11	5.82	5.82	0.92795	PKD/Chitinase domain (1);PKD domain (4);	0.082822	0.51477	D	0.000086	T	0.74168	0.3681	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.76071	0.987;0.977;0.982;0.987;0.982	T	0.70680	-0.4805	9	.	.	.	-10.1026	20.1001	0.97870	0.0:0.0:1.0:0.0	.	866;866;866;866;866	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	C	401;866;866	ENSP00000358712:R401C;ENSP00000263054:R866C;ENSP00000345964:R866C	.	R	-	1	0	SORCS1	108379016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.332000	0.59279	2.760000	0.94817	0.655000	0.94253	CGT		0.478	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108389026	G	A	108389026	3	1	28	1	0	0	0	0	1	0	0	0	14967	1116	39	1	1176	1	SORCS1	10	108389026	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	10296860	108389026	27145721	69	2454										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124184459	124184459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgaaattgtaacaacgtctcGaactttctatgtgcaggtaa	8	7	2	1	rs373796370		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr10:124184459G>A	ENST00000368990.3	+	10	925	c.794G>A	c.(793-795)cGa>cAa	p.R265Q	PLEKHA1_ENST00000368989.2_Missense_Mutation_p.R265Q|PLEKHA1_ENST00000368988.1_Missense_Mutation_p.R265Q|PLEKHA1_ENST00000433307.1_Missense_Mutation_p.R265Q|PLEKHA1_ENST00000538022.1_Missense_Mutation_p.R265Q	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	265	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)	p.R265Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				ACAACGTCTCGAACTTTCTAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	103	104	104		794,794,794	5.5	1	10		104	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PLEKHA1	NM_001001974.2,NM_001195608.1,NM_021622.4	43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	265/405,265/335,265/405	124184459	1,13005	2203	4300	6503	124174449	SO:0001583	missense	59338			AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.794G>A	10.37:g.124184459G>A	ENSP00000357986:p.Arg265Gln		124174449	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	37	CCDS7629.1	.	.	.	.	.	.	.	.	.	.	G	35	5.449623	0.96205	0.0	1.16E-4	ENSG00000107679	ENST00000368990;ENST00000368989;ENST00000409427;ENST00000368988;ENST00000538022;ENST00000433307	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.53	5.53	0.82687	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.988;0.997	T	0.48917	-0.8992	10	0.59425	D	0.04	-12.2488	19.4339	0.94783	0.0:0.0:1.0:0.0	.	265;265	B3KQ55;Q9HB21	.;PKHA1_HUMAN	Q	265	ENSP00000357986:R265Q;ENSP00000357985:R265Q;ENSP00000357984:R265Q;ENSP00000438608:R265Q;ENSP00000394416:R265Q	ENSP00000357984:R265Q	R	+	2	0	PLEKHA1	124174449	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.203000	0.95033	2.755000	0.94549	0.650000	0.86243	CGA		0.308	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		A	124184459	G	A	124184459	3	1	28	1	0	0	0	0	1	0	0	0	12086	1058	37	1	828	1	PLEKHA1	10	124184459	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	15795433	124184459	11350288	70	2455										
FAM111B	374393	hgsc.bcm.edu	37	chr11	58877121	58877121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gaattccatgaagactgaagAaaacaagtcatttagcgcta	8	7	1	4			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:58877121A>G	ENST00000343597.3	+	3	214	c.23A>G	c.(22-24)gAa>gGa	p.E8G	FAM111B_ENST00000411426.1_Intron|FAM111B_ENST00000529618.1_Intron	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	8							catalytic activity (GO:0003824)	p.E8G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						AAGACTGAAGAAAACAAGTCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											101	91	94					11																	58877121		2201	4295	6496	58633697	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.23A>G	11.37:g.58877121A>G	ENSP00000341565:p.Glu8Gly		58633697	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	A	9.420	1.082693	0.20309	.	.	ENSG00000189057	ENST00000343597	T	0.40756	1.02	1.46	1.46	0.22682	.	.	.	.	.	T	0.27454	0.0674	L	0.44542	1.39	0.09310	N	0.999997	P	0.40731	0.728	B	0.31495	0.131	T	0.21827	-1.0234	9	0.72032	D	0.01	.	5.0706	0.14604	1.0:0.0:0.0:0.0	.	8	Q6SJ93	F111B_HUMAN	G	8	ENSP00000341565:E8G	ENSP00000341565:E8G	E	+	2	0	FAM111B	58633697	0.196000	0.23350	0.046000	0.18839	0.005000	0.04900	0.725000	0.25970	0.961000	0.38030	0.454000	0.30748	GAA		0.373	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		G	58877121	A	G	58877121	3	3	28	1	0	0	0	0	1	0	0	0	5416	246	9	4	25	4	FAM111B	11	58877121	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10		58877121	76129395	71	2456										
BIRC2	329	hgsc.bcm.edu	37	chr11	102233667	102233667	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tgaaaggccaagagtttgttGatgagattcaaggtagatat	12	3	1	5			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:102233667G>T	ENST00000227758.2	+	4	2435	c.1036G>T	c.(1036-1038)Gat>Tat	p.D346Y	BIRC2_ENST00000532672.1_Missense_Mutation_p.D325Y|BIRC2_ENST00000530675.1_Missense_Mutation_p.D297Y|BIRC2_ENST00000527910.1_3'UTR	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	346					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D346Y(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		AGAGTTTGTTGATGAGATTCA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	11											91	94	93					11																	102233667		2203	4299	6502	101738877	SO:0001583	missense	329			L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.1036G>T	11.37:g.102233667G>T	ENSP00000227758:p.Asp346Tyr		101738877	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	G	9.762	1.170243	0.21621	.	.	ENSG00000110330	ENST00000530675;ENST00000533742;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T;T	0.08634	3.81;3.07;3.81;3.81	5.46	3.56	0.40772	Baculoviral inhibition of apoptosis protein repeat (1);	0.264525	0.45126	D	0.000386	T	0.06462	0.0166	L	0.44542	1.39	0.35238	D	0.777511	P	0.38395	0.629	B	0.31495	0.131	T	0.14980	-1.0453	10	0.49607	T	0.09	-21.8852	7.4647	0.27314	0.1334:0.1507:0.7159:0.0	.	346	Q13490	BIRC2_HUMAN	Y	297;8;346;346;325	ENSP00000431723:D297Y;ENSP00000433851:D8Y;ENSP00000227758:D346Y;ENSP00000434979:D325Y	ENSP00000227758:D346Y	D	+	1	0	BIRC2	101738877	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	1.057000	0.30492	2.568000	0.86640	0.561000	0.74099	GAT		0.259	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		T	102233667	G	T	102233667	3	4	28	1	0	0	0	0	1	0	0	0	1436	1290	45	2	1046	2	BIRC2	11	102233667	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	43356546	102233667	32772849	72	2457										
C11orf57	55216	hgsc.bcm.edu	37	chr11	111952723	111952723	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cagatggggtcacagtggttAtaaagagttataccctgaag	12	6	1	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:111952723A>G	ENST00000280352.9	+	5	974	c.338A>G	c.(337-339)tAt>tGt	p.Y113C	C11orf57_ENST00000532163.1_Missense_Mutation_p.Y84C|C11orf57_ENST00000393047.3_Missense_Mutation_p.Y113C|C11orf57_ENST00000420986.2_Missense_Mutation_p.Y113C|C11orf57_ENST00000530104.1_3'UTR	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	113								p.Y113C(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		CACAGTGGTTATAAAGAGTTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	11											92	89	90					11																	111952723		2201	4296	6497	111457933	SO:0001583	missense	55216			BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.338A>G	11.37:g.111952723A>G	ENSP00000339076:p.Tyr113Cys		111457933	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Missense_Mutation	SNP	ENST00000280352.9	37	CCDS41715.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596716	0.66332	.	.	ENSG00000150776	ENST00000420986;ENST00000532163;ENST00000280352;ENST00000393047;ENST00000525785;ENST00000531378	.	.	.	5.58	5.58	0.84498	.	0.058565	0.64402	D	0.000001	T	0.79155	0.4398	M	0.74881	2.28	0.40301	D	0.978603	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	T	0.82544	-0.0404	9	0.87932	D	0	.	15.7423	0.77910	1.0:0.0:0.0:0.0	.	113;113	Q6ZUT1-2;Q6ZUT1	.;CK057_HUMAN	C	113;84;113;113;84;67	.	ENSP00000339076:Y113C	Y	+	2	0	C11orf57	111457933	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.674000	0.68117	2.107000	0.64212	0.528000	0.53228	TAT		0.313	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		G	111952723	A	G	111952723	3	3	28	1	0	0	0	0	1	0	0	0	1654	449	16	4	352	4	C11orf57	11	111952723	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	9719056	111952723	23053793	73	2458										
MLL	4297	hgsc.bcm.edu	37	chr11	118362633	118362633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gactaccagccatttgctacGctaccggcaggtaggccaag	11	13	0	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:118362633G>A	ENST00000389506.5	+	15	4985	c.4985G>A	c.(4984-4986)cGc>cAc	p.R1662H	KMT2A_ENST00000534358.1_Missense_Mutation_p.R1665H|KMT2A_ENST00000354520.4_Missense_Mutation_p.R1624H			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1662					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R1662H(1)									CATTTGCTACGCTACCGGCAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											35	35	35					11																	118362633		2200	4296	6496	117867843	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.4985G>A	11.37:g.118362633G>A	ENSP00000374157:p.Arg1662His		117867843	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468485	0.84533	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.82619	-1.63;-1.63;-1.56	5.75	5.75	0.90469	Bromodomain (1);	0.000000	0.85682	D	0.000000	D	0.86916	0.6048	L	0.28274	0.84	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.984;0.996	D	0.87120	0.2190	10	0.51188	T	0.08	.	19.9564	0.97221	0.0:0.0:1.0:0.0	.	1665;1662	E9PQG7;Q03164	.;MLL1_HUMAN	H	1665;1662;1624;572	ENSP00000436786:R1665H;ENSP00000374157:R1662H;ENSP00000346516:R1624H	ENSP00000346516:R1624H	R	+	2	0	MLL	117867843	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.671000	0.83941	2.708000	0.92522	0.650000	0.86243	CGC		0.443	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118362633	G	A	118362633	3	1	28	1	0	0	0	0	1	0	0	0	9650	1087	38	1	5043	1	MLL	11	118362633	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	6409910	118362633	16643883	74	2459										
TECTA	7007	hgsc.bcm.edu	37	chr11	120983793	120983793	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tcctgtaggtgaacaccttcCaggccgtcctagtgtccgat	10	13	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:120983793C>A	ENST00000392793.1	+	5	770	c.499C>A	c.(499-501)Cag>Aag	p.Q167K	TECTA_ENST00000264037.2_Missense_Mutation_p.Q167K			O75443	TECTA_HUMAN	tectorin alpha	167	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.Q167K(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GAACACCTTCCAGGCCGTCCT	0.597											OREG0021430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											91	73	79					11																	120983793		2203	4299	6502	120489003	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.499C>A	11.37:g.120983793C>A	ENSP00000376543:p.Gln167Lys	1508	120489003		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	33	5.217965	0.95104	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.91464	-2.85;-2.85	5.26	5.26	0.73747	Nidogen, extracellular domain (3);	0.123890	0.56097	D	0.000035	D	0.97151	0.9069	H	0.96633	3.855	0.53688	D	0.999974	D	0.62365	0.991	D	0.74023	0.982	D	0.98147	1.0439	10	0.87932	D	0	.	19.0783	0.93171	0.0:1.0:0.0:0.0	.	167	O75443	TECTA_HUMAN	K	167	ENSP00000376543:Q167K;ENSP00000264037:Q167K	ENSP00000264037:Q167K	Q	+	1	0	TECTA	120489003	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.619000	0.83057	2.731000	0.93534	0.650000	0.86243	CAG		0.597	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	120983793	C	A	120983793	3	1	28	1	0	0	0	0	1	0	0	0	15786	595	21	2	513	2	TECTA	11	120983793	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	2621160	120983793	14022723	75	2460										
NTM	50863	hgsc.bcm.edu	37	chr11	132082037	132082037	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acttggagacacatctctccCaaaggtaagagaacagtttg	9	9	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr11:132082037C>A	ENST00000374786.1	+	3	1001	c.522C>A	c.(520-522)ccC>ccA	p.P174P	NTM_ENST00000474900.1_3'UTR|NTM_ENST00000427481.2_Silent_p.P165P|NTM_ENST00000539799.1_Silent_p.P174P|NTM_ENST00000374791.3_Silent_p.P174P|NTM_ENST00000425719.2_Silent_p.P174P|NTM_ENST00000374784.1_Silent_p.P174P	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	174	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.P174P(2)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ACATCTCTCCCAAAGGTAAGA	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	11											150	150	150					11																	132082037		2201	4297	6498	131587247	SO:0001819	synonymous_variant	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.522C>A	11.37:g.132082037C>A			131587247	A0MTT2|Q6UXJ3|Q86VJ9	Silent	SNP	ENST00000374786.1	37	CCDS8491.1																																																																																				0.448	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		A	132082037	C	A	132082037	2	1	28	1	0	0	0	0	0	0	0	1	10730	581	21	2		2	NTM	11	132082037	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	11098244	132082037	2924479	76	2461										
BRCA2	675	hgsc.bcm.edu	37	chr13	32914956	32914956	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tattaaagtttctccatatcTctctcaatttcaacaagaca	2	10	4	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr13:32914956T>A	ENST00000380152.3	+	11	6697	c.6464T>A	c.(6463-6465)cTc>cAc	p.L2155H	BRCA2_ENST00000544455.1_Missense_Mutation_p.L2155H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2155					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.L2155H(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCTCCATATCTCTCTCAATTT	0.318			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											39	41	40					13																	32914956		2203	4296	6499	31812956	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6464T>A	13.37:g.32914956T>A	ENSP00000369497:p.Leu2155His		31812956	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	5.578	0.291472	0.10567	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.78595	-1.19;-1.19	4.57	-0.832	0.10785	.	0.909697	0.09164	N	0.839740	T	0.73984	0.3657	L	0.59436	1.845	0.09310	N	1	D	0.58620	0.983	P	0.46975	0.533	T	0.64110	-0.6484	10	0.66056	D	0.02	.	6.0256	0.19652	0.0:0.351:0.1485:0.5004	.	2155	P51587	BRCA2_HUMAN	H	2155	ENSP00000369497:L2155H;ENSP00000439902:L2155H	ENSP00000369497:L2155H	L	+	2	0	BRCA2	31812956	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.741000	0.04855	0.009000	0.14813	-0.353000	0.07706	CTC		0.318	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32914956	T	A	32914956	3	1	28	1	0	0	0	0	1	0	0	0	1502	1551	54	5	6502	5	BRCA2	13	32914956	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10		32914956	82254922	77	2462										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38248466	38248466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	atggatgtagtcctgaagtcCgccatcccacatctgtttaa	8	11	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr13:38248466C>T	ENST00000379705.3	-	5	2130	c.1273G>A	c.(1273-1275)Gga>Aga	p.G425R	TRPC4_ENST00000355779.2_Missense_Mutation_p.G425R|TRPC4_ENST00000358477.2_Missense_Mutation_p.G425R|TRPC4_ENST00000426868.2_Missense_Mutation_p.G425R|TRPC4_ENST00000379681.3_Missense_Mutation_p.G425R|TRPC4_ENST00000494529.1_5'UTR|TRPC4_ENST00000338947.5_Missense_Mutation_p.G252R|TRPC4_ENST00000379673.2_Missense_Mutation_p.G425R|TRPC4_ENST00000379679.1_Missense_Mutation_p.G252R|TRPC4_ENST00000447043.1_Missense_Mutation_p.G425R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	425					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.G425R(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCCTGAAGTCCGCCATCCCAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	13											102	99	100					13																	38248466		2202	4300	6502	37146466	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1273G>A	13.37:g.38248466C>T	ENSP00000369027:p.Gly425Arg		37146466	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897469	0.91962	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000426868;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	D;D;D;D;D;D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	5.16	5.16	0.70880	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99351	0.9772	M	0.86178	2.8	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.99174	1.0865	10	0.87932	D	0	-26.1818	18.9997	0.92828	0.0:1.0:0.0:0.0	.	425;425;425;252;425;425	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	R	425;425;252;252;425;425;425;425;425	ENSP00000369027:G425R;ENSP00000369003:G425R;ENSP00000342580:G252R;ENSP00000369001:G252R;ENSP00000410133:G425R;ENSP00000348025:G425R;ENSP00000351264:G425R;ENSP00000368995:G425R;ENSP00000414316:G425R	ENSP00000342580:G252R	G	-	1	0	TRPC4	37146466	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.776000	0.85560	2.549000	0.85964	0.591000	0.81541	GGA		0.333	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38248466	C	T	38248466	3	4	28	1	0	0	0	0	1	0	0	0	16620	661	23	1	1703	1	TRPC4	13	38248466	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	5333510	38248466	76921412	78	2463										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78474662	78474662	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tttgcctttcttacctcaaaAgttcacatctattgggatca	5	10	5	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr13:78474662A>C	ENST00000334286.5	-	5	1315	c.1079T>G	c.(1078-1080)cTt>cGt	p.L360R	EDNRB_ENST00000446573.1_Missense_Mutation_p.L360R|EDNRB_ENST00000377211.4_Missense_Mutation_p.L450R	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	360					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.L360R(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TTACCTCAAAAGTTCACATCT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	13											78	81	80					13																	78474662		2203	4300	6503	77372663	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1079T>G	13.37:g.78474662A>C	ENSP00000335311:p.Leu360Arg		77372663	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.600478	0.87055	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.73681	-0.77;-0.77;-0.77	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.113669	0.64402	D	0.000009	D	0.88955	0.6578	M	0.91406	3.205	0.58432	D	0.999996	D;B;D	0.89917	1.0;0.185;0.999	D;B;D	0.76575	0.978;0.205;0.988	D	0.91272	0.5045	10	0.72032	D	0.01	-8.8774	16.1323	0.81449	1.0:0.0:0.0:0.0	.	360;450;360	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	R	450;360;360	ENSP00000366416:L450R;ENSP00000403401:L360R;ENSP00000335311:L360R	ENSP00000335311:L360R	L	-	2	0	EDNRB	77372663	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.910000	0.92685	2.277000	0.76020	0.528000	0.53228	CTT		0.413	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78474662	A	C	78474662	3	2	28	1	0	0	0	0	1	0	0	0	4931	72	3	4	382	4	EDNRB	13	78474662	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	40226196	78474662	36695216	79	2464										
C13orf39	196541	hgsc.bcm.edu	37	chr13	103346828	103346828	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cggcgcccaggctgctgcgcGgagctcagacacacgtccat	13	16	1	1	rs559397528		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr13:103346828G>A	ENST00000267273.6	-	1	26	c.21C>T	c.(19-21)tcC>tcT	p.S7S		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	7					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)	p.S7S(1)		breast(1)|large_intestine(3)|lung(2)|skin(1)	7						GCTGCTGCGCGGAGCTCAGAC	0.577													G|||	1	0.000199681	0	0	5008	,	,		9522	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	13											14	16	15					13																	103346828		2201	4299	6500	102144829	SO:0001819	synonymous_variant	196541				CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.21C>T	13.37:g.103346828G>A			102144829		Silent	SNP	ENST00000267273.6	37	CCDS32003.1																																																																																				0.577	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		A	103346828	G	A	103346828	2	1	28	1	0	0	0	0	0	0	0	1	1736	1103	39	1		1	C13orf39	13	103346828	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10	24872166	103346828	11823050	80	2465										
FAM155A	728215	hgsc.bcm.edu	37	chr13	107823115	107823115	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cattctggttcatcattggtTagaaaggtttcataaagccc	8	8	4	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr13:107823115T>A	ENST00000375915.2	-	3	1245	c.1107A>T	c.(1105-1107)ctA>ctT	p.L369L		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	369						integral component of membrane (GO:0016021)		p.L369L(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CATCATTGGTTAGAAAGGTTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	13											143	118	126					13																	107823115		2203	4300	6503	106621116	SO:0001819	synonymous_variant	728215			L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1107A>T	13.37:g.107823115T>A			106621116	B2RUV1|B7Z334	Silent	SNP	ENST00000375915.2	37	CCDS32006.1																																																																																				0.423	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		A	107823115	T	A	107823115	2	1	28	1	0	0	0	0	0	0	0	1	5481	1741	61	5		5	FAM155A	13	107823115	Silent	SNP	T	TCGA-AG-3601-01A-01W-0833-10	4476287	107823115	7346763	81	2466										
AK7	122481	hgsc.bcm.edu	37	chr14	96924524	96924524	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caggagctcctagatggcatCaaggagagcatggagcagaa	14	8	1	3	rs376162440		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr14:96924524C>T	ENST00000267584.4	+	12	1376	c.1332C>T	c.(1330-1332)atC>atT	p.I444I		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	444	Adenylate kinase.|NMPbind. {ECO:0000250}.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)	p.I444I(1)		breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		TAGATGGCATCAAGGAGAGCA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	14						C		0,4406		0,0,2203	117	97	104		1332	2	1	14		104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AK7	NM_152327.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		444/724	96924524	1,13005	2203	4300	6503	95994277	SO:0001819	synonymous_variant	122481			AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1332C>T	14.37:g.96924524C>T			95994277	Q8IYP6	Silent	SNP	ENST00000267584.4	37	CCDS9945.1																																																																																				0.483	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			T	96924524	C	T	96924524	2	4	28	1	0	0	0	0	0	0	0	1	444	816	29	3		3	AK7	14	96924524	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10		96924524	10425016	82	2467										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34536252	34536252	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gcacatgccaagtttacaaaGaggtaacacatgagaaaaaa	8	7	0	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr15:34536252G>A	ENST00000354181.3	-	16	2457	c.1965C>T	c.(1963-1965)ctC>ctT	p.L655L	SLC12A6_ENST00000558589.1_Silent_p.L646L|SLC12A6_ENST00000558667.1_Silent_p.L655L|SLC12A6_ENST00000397702.2_Silent_p.L596L|SLC12A6_ENST00000458406.2_Silent_p.L596L|SLC12A6_ENST00000560611.1_Silent_p.L655L|SLC12A6_ENST00000290209.5_Silent_p.L604L|SLC12A6_ENST00000451844.2_Silent_p.L467L|SLC12A6_ENST00000560164.1_Silent_p.L467L|SLC12A6_ENST00000397707.2_Silent_p.L640L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	655					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)	p.L604L(1)		central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	AGTTTACAAAGAGGTAACACA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	15											120	115	116					15																	34536252		2201	4298	6499	32323544	SO:0001819	synonymous_variant	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.1965C>T	15.37:g.34536252G>A			32323544	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																				0.383	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		A	34536252	G	A	34536252	2	1	28	1	0	0	0	0	0	0	0	1	14424	929	33	3		3	SLC12A6	15	34536252	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10		34536252	67995140	83	2468										
FBN1	2200	hgsc.bcm.edu	37	chr15	48703393	48703393	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttccttttggttgattttaaAgaagccatcttcatttccag	6	8	2	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr15:48703393A>G	ENST00000316623.5	-	66	8865	c.8410T>C	c.(8410-8412)Ttt>Ctt	p.F2804L	FBN1_ENST00000561429.1_5'Flank	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2804					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.F2804L(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTGATTTTAAAGAAGCCATCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											149	144	145					15																	48703393		2198	4297	6495	46490685	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.8410T>C	15.37:g.48703393A>G	ENSP00000325527:p.Phe2804Leu		46490685	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.298512	0.81025	.	.	ENSG00000166147	ENST00000316623	D	0.85702	-2.02	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.91369	0.7277	M	0.78456	2.415	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	D	0.91630	0.5318	10	0.49607	T	0.09	.	14.8921	0.70617	1.0:0.0:0.0:0.0	.	2804	P35555	FBN1_HUMAN	L	2804	ENSP00000325527:F2804L	ENSP00000325527:F2804L	F	-	1	0	FBN1	46490685	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.057000	0.93889	2.247000	0.74100	0.528000	0.53228	TTT		0.413	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			G	48703393	A	G	48703393	3	3	28	1	0	0	0	0	1	0	0	0	5721	72	3	4	209	4	FBN1	15	48703393	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	14167141	48703393	53827999	84	2469										
CYP19A1	1588	hgsc.bcm.edu	37	chr15	51535087	51535087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tggtgatgttataatgtatcGggttcagcatttccaaaacc	9	7	1	1	rs144803182		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr15:51535087G>A	ENST00000396402.1	-	2	176	c.23C>T	c.(22-24)cCg>cTg	p.P8L	CYP19A1_ENST00000260433.2_Missense_Mutation_p.P8L|MIR4713_ENST00000582691.1_RNA|CYP19A1_ENST00000405913.3_Missense_Mutation_p.P8L|CYP19A1_ENST00000559878.1_Missense_Mutation_p.P8L|CYP19A1_ENST00000396404.4_Missense_Mutation_p.P8L|CYP19A1_ENST00000557858.1_Missense_Mutation_p.P8L|RP11-108K3.1_ENST00000559909.1_lincRNA	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	8					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.P8L(2)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	ATAATGTATCGGGTTCAGCAT	0.473																																					Melanoma(142;1016 1807 39614 48966 51721)											2	Substitution - Missense(2)	large_intestine(1)|skin(1)	15											237	208	218					15																	51535087		2196	4293	6489	49322379	SO:0001583	missense	1588			D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"Cytochrome P450s"	2594	protein-coding gene	gene with protein product		107910	"cytochrome P450, subfamily XIX (aromatization of androgens)"	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.23C>T	15.37:g.51535087G>A	ENSP00000379683:p.Pro8Leu		49322379	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	37	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890464	0.52014	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000541721;ENST00000396404;ENST00000420301;ENST00000439712;ENST00000405913;ENST00000453807;ENST00000405011	T;T;T;T;T;T;T	0.79247	-0.54;-0.54;-0.54;1.86;-0.71;-0.67;-1.25	5.01	4.1	0.47936	.	0.338053	0.31589	N	0.007400	T	0.70500	0.3231	L	0.51914	1.62	0.58432	D	0.99999	B;B	0.30114	0.269;0.027	B;B	0.20184	0.028;0.012	T	0.70710	-0.4797	10	0.52906	T	0.07	-1.6078	13.4881	0.61377	0.0753:0.0:0.9247:0.0	.	8;8	Q8IYJ7;P11511	.;CP19A_HUMAN	L	8	ENSP00000379683:P8L;ENSP00000260433:P8L;ENSP00000379685:P8L;ENSP00000390614:P8L;ENSP00000383930:P8L;ENSP00000391139:P8L;ENSP00000384389:P8L	ENSP00000260433:P8L	P	-	2	0	CYP19A1	49322379	0.989000	0.36119	0.823000	0.32752	0.903000	0.53119	1.977000	0.40589	1.334000	0.45468	0.563000	0.77884	CCG		0.473	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1			A	51535087	G	A	51535087	3	1	28	1	0	0	0	0	1	0	0	0	4154	1116	39	1	1524	1	CYP19A1	15	51535087	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	2831694	51535087	50996305	85	2470										
IDH3A	3419	hgsc.bcm.edu	37	chr15	78454583	78454583	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tcctgtcttgcagattgttgAtggagtcgtgcagagtatca	12	7	2	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr15:78454583A>C	ENST00000299518.2	+	6	568	c.485A>C	c.(484-486)gAt>gCt	p.D162A	IDH3A_ENST00000558554.1_Missense_Mutation_p.D127A|IDH3A_ENST00000561366.1_5'Flank|IDH3A_ENST00000441490.2_Missense_Mutation_p.D53A|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000559205.1_Intron	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	162					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.D162A(1)		endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CAGATTGTTGATGGAGTCGTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											128	100	110					15																	78454583		2196	4293	6489	76241638	SO:0001583	missense	3419				CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"H-IDH alpha", "isocitric dehydrogenase", "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "NAD+-specific ICDH", "NAD(H)-specific isocitrate dehydrogenase alpha subunit", "isocitrate dehydrogenase (NAD+) alpha chain"	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.485A>C	15.37:g.78454583A>C	ENSP00000299518:p.Asp162Ala		76241638	D3DW83|Q9H3X0	Missense_Mutation	SNP	ENST00000299518.2	37	CCDS10297.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.796060	0.50208	.	.	ENSG00000166411	ENST00000299518;ENST00000441490	T;T	0.55930	0.49;0.49	5.78	5.78	0.91487	Isopropylmalate dehydrogenase-like domain (2);	0.090091	0.85682	D	0.000000	T	0.56746	0.2006	L	0.51853	1.615	0.80722	D	1	B;B;B	0.27166	0.17;0.009;0.075	B;B;B	0.39339	0.297;0.142;0.217	T	0.57740	-0.7759	10	0.56958	D	0.05	-27.3351	15.2907	0.73865	1.0:0.0:0.0:0.0	.	127;112;162	B4DSY4;B4DJB4;P50213	.;.;IDH3A_HUMAN	A	162;53	ENSP00000299518:D162A;ENSP00000387506:D53A	ENSP00000299518:D162A	D	+	2	0	IDH3A	76241638	1.000000	0.71417	0.993000	0.49108	0.224000	0.24922	9.063000	0.93927	2.210000	0.71456	0.482000	0.46254	GAT		0.542	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		C	78454583	A	C	78454583	3	2	28	1	0	0	0	0	1	0	0	0	7517	333	12	4	507	4	IDH3A	15	78454583	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	26919496	78454583	24076809	86	2471										
CHD2	1106	hgsc.bcm.edu	37	chr15	93498668	93498668	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	tatagatacgggaatatgaaTggattcattcccaaaccaaa	7	7	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr15:93498668T>C	ENST00000394196.4	+	15	2803	c.1735T>C	c.(1735-1737)Tgg>Cgg	p.W579R	CHD2_ENST00000557381.1_Missense_Mutation_p.W579R	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	579	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.W579R(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GGAATATGAATGGATTCATTC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	15											52	48	49					15																	93498668		2195	4297	6492	91299672	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1735T>C	15.37:g.93498668T>C	ENSP00000377747:p.Trp579Arg		91299672	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	T	16.99	3.272771	0.59649	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.92099	-2.97;-2.97	5.38	5.38	0.77491	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.32736	U	0.005704	D	0.93393	0.7893	L	0.38733	1.17	0.80722	D	1	B;D	0.62365	0.015;0.991	B;D	0.65684	0.021;0.937	D	0.94329	0.7560	10	0.87932	D	0	-9.935	15.3851	0.74691	0.0:0.0:0.0:1.0	.	579;579	O14647;O14647-2	CHD2_HUMAN;.	R	579	ENSP00000377747:W579R;ENSP00000451366:W579R	ENSP00000377747:W579R	W	+	1	0	CHD2	91299672	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.033000	0.88852	2.019000	0.59389	0.528000	0.53228	TGG		0.289	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93498668	T	C	93498668	3	2	28	1	0	0	0	0	1	0	0	0	3331	1464	51	4	1793	4	CHD2	15	93498668	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	15044085	93498668	9032724	87	2472										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7629853	7629853	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aacacggaaaacaagtctcaGcccaagcggctgcatgtctc	9	13	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr16:7629853G>A	ENST00000550418.1	+	6	1333	c.345G>A	c.(343-345)caG>caA	p.Q115Q	RBFOX1_ENST00000436368.2_Silent_p.Q135Q|RBFOX1_ENST00000311745.5_Silent_p.Q135Q|RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000552089.1_Silent_p.Q150Q|RBFOX1_ENST00000547372.1_Silent_p.Q158Q|RBFOX1_ENST00000553186.1_Silent_p.Q115Q|RBFOX1_ENST00000547338.1_Silent_p.Q115Q|RBFOX1_ENST00000340209.4_Silent_p.Q120Q|RBFOX1_ENST00000355637.4_Silent_p.Q135Q|RBFOX1_ENST00000422070.4_Silent_p.Q158Q	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	115					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.Q135Q(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						ACAAGTCTCAGCCCAAGCGGC	0.517																																					Ovarian(157;934 2567 15163 39509)											2	Substitution - coding silent(2)	large_intestine(2)	16											140	127	131					16																	7629853		2197	4300	6497	7569854	SO:0001819	synonymous_variant	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.345G>A	16.37:g.7629853G>A			7569854	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	37	CCDS55983.1																																																																																				0.517	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		A	7629853	G	A	7629853	2	1	28	1	0	0	0	0	0	0	0	1	3	962	34	3		3	A2BP1	16	7629853	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10		7629853	82724900	88	2473										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30748693	30748693	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	aggccagcacctaggcctcgAcccactccagcttcagctcc	8	19	1	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr16:30748693A>G	ENST00000262518.4	+	34	7717	c.7332A>G	c.(7330-7332)cgA>cgG	p.R2444R	SRCAP_ENST00000344771.4_Silent_p.R2286R|SRCAP_ENST00000395059.2_Silent_p.R2382R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2444	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.R2444R(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			ctaggcctcgacccactccag	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	16											111	85	94					16																	30748693		2197	4300	6497	30656194	SO:0001819	synonymous_variant	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7332A>G	16.37:g.30748693A>G			30656194	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																				0.592	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30748693	A	G	30748693	2	3	28	1	0	0	0	0	0	0	0	1	15174	262	10	4		4	SRCAP	16	30748693	Silent	SNP	A	TCGA-AG-3601-01A-01W-0833-10	23118840	30748693	59606060	89	2474										
TP53	7157	hgsc.bcm.edu	37	chr17	7577548	7577548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gatgggcctccggttcatgcCgcccatgcaggaactgttac	12	13	1	0	rs28934575|rs397516437		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr17:7577548C>T	ENST00000269305.4	-	7	922	c.733G>A	c.(733-735)Ggc>Agc	p.G245S	TP53_ENST00000420246.2_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S|TP53_ENST00000455263.2_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.G245S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGGTTCATGCCGCCCATGCAG	0.577	G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	420	Substitution - Missense(390)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)|Insertion - Frameshift(1)	large_intestine(119)|lung(51)|breast(38)|ovary(29)|central_nervous_system(27)|upper_aerodigestive_tract(25)|stomach(25)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(22)|urinary_tract(14)|skin(9)|liver(7)|prostate(7)|biliary_tract(5)|bone(5)|pancreas(4)|soft_tissue(3)|vulva(2)|endometrium(2)|kidney(1)|cervix(1)|salivary_gland(1)	17	GRCh37	CM010463|CM900210|CM920674	TP53	M	rs28934575	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	149	112	125	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	733,733,733,733,337,337,337	4.6	1	17	dbSNP_125	125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	56,56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	245/394,245/394,245/347,245/342,113/262,113/210,113/215	7577548	1,13005	2203	4300	6503	7518273	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.733G>A	17.37:g.7577548C>T	ENSP00000269305:p.Gly245Ser		7518273	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	33	5.259904	0.95368	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99894	-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99878	0.9942	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.976;0.992;0.999;0.999;1.0	D	0.96039	0.9023	10	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	rs28934575	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245S;ENSP00000352610:G245S;ENSP00000269305:G245S;ENSP00000398846:G245S;ENSP00000391127:G245S;ENSP00000391478:G245S;ENSP00000425104:G113S;ENSP00000423862:G152S	ENSP00000269305:G245S	G	-	1	0	TP53	7518273	1.000000	0.71417	0.965000	0.40720	0.974000	0.67602	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577548	C	T	7577548	3	4	28	1	0	0	0	0	1	0	0	0	16421	652	23	1	557	1	TP53	17	7577548	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		7577548	73617662	90	2475										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12608480	12608480	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ttcaacaaagaaggacccagGaacaactggctaaccaaggc	9	11	1	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr17:12608480G>T	ENST00000343344.4	+	2	91	c.91G>T	c.(91-93)Gaa>Taa	p.E31*	AC005358.3_ENST00000445508.1_RNA|MYOCD_ENST00000425538.1_Nonsense_Mutation_p.E31*			Q8IZQ8	MYCD_HUMAN	myocardin	31					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.E31*(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AAGGACCCAGGAACAACTGGC	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											131	104	113					17																	12608480		2203	4300	6503	12549205	SO:0001587	stop_gained	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.91G>T	17.37:g.12608480G>T	ENSP00000341835:p.Glu31*		12549205	Q5UBU5|Q8N7Q1	Nonsense_Mutation	SNP	ENST00000343344.4	37	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	G	34	5.402612	0.96030	.	.	ENSG00000141052	ENST00000425538;ENST00000343344	.	.	.	5.16	5.16	0.70880	.	0.055308	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-33.8184	14.3489	0.66685	0.0:0.0:1.0:0.0	.	.	.	.	X	31	.	ENSP00000341835:E31X	E	+	1	0	MYOCD	12549205	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	5.784000	0.68990	2.840000	0.97914	0.655000	0.94253	GAA		0.388	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		T	12608480	G	T	12608480	4	4	28	1	0	0	0	0	0	1	0	0	10117	1175	41	2	97	2	MYOCD	17	12608480	Nonsense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	5030932	12608480	68586730	91	2476										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27002497	27002497	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gaaaaagcttcctggatacaCagacgcgtgagtggggtctg	14	8	1	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr17:27002497C>A	ENST00000314616.6	+	6	900	c.617C>A	c.(616-618)aCa>aAa	p.T206K	SUPT6H_ENST00000347486.4_Missense_Mutation_p.T206K|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	206	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T206K(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCTGGATACACAGACGCGTGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	17											91	83	86					17																	27002497		2203	4300	6503	24026624	SO:0001583	missense	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.617C>A	17.37:g.27002497C>A	ENSP00000319104:p.Thr206Lys		24026624	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135037	0.77662	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	L	0.61387	1.9	0.80722	D	1	P	0.43024	0.798	B	0.37943	0.261	T	0.54193	-0.8330	9	0.10111	T	0.7	-9.4078	20.0953	0.97838	0.0:1.0:0.0:0.0	.	206	Q7KZ85	SPT6H_HUMAN	K	206	.	ENSP00000319104:T206K	T	+	2	0	SUPT6H	24026624	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.084000	0.76866	2.767000	0.95098	0.655000	0.94253	ACA		0.493	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		A	27002497	C	A	27002497	3	1	28	1	0	0	0	0	1	0	0	0	15439	478	17	2	635	2	SUPT6H	17	27002497	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10	14394017	27002497	54192713	92	2477										
CA10	56934	hgsc.bcm.edu	37	chr17	49711002	49711002	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gttctggctgagcaggcgcaAggaatgcatctgaggagaga	16	7	2	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr17:49711002A>C	ENST00000285273.4	-	9	1910	c.799T>G	c.(799-801)Ttg>Gtg	p.L267V	CA10_ENST00000340813.6_Missense_Mutation_p.L273V|CA10_ENST00000451037.2_Missense_Mutation_p.L267V|CA10_ENST00000570565.1_Missense_Mutation_p.L192V|CA10_ENST00000571918.1_5'Flank|CA10_ENST00000442502.2_Missense_Mutation_p.L267V	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	267					brain development (GO:0007420)			p.L267V(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	AGCAGGCGCAAGGAATGCATC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											83	72	76					17																	49711002		2203	4300	6503	47066001	SO:0001583	missense	56934			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.799T>G	17.37:g.49711002A>C	ENSP00000285273:p.Leu267Val		47066001	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.795766	0.50208	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	5.44	3.24	0.37175	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.075450	0.53938	D	0.000045	D	0.85522	0.5716	M	0.93375	3.41	0.45477	D	0.998443	P;P;P	0.51653	0.875;0.947;0.934	P;P;P	0.58210	0.737;0.822;0.835	D	0.85921	0.1446	10	0.66056	D	0.02	.	8.0823	0.30752	0.8331:0.0:0.1669:0.0	.	267;273;192	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	V	267;267;267;273	ENSP00000390666:L267V;ENSP00000285273:L267V;ENSP00000405388:L267V;ENSP00000340363:L273V	ENSP00000285273:L267V	L	-	1	2	CA10	47066001	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.338000	0.43957	0.920000	0.36970	0.533000	0.62120	TTG		0.522	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		C	49711002	A	C	49711002	3	2	28	1	0	0	0	0	1	0	0	0	2517	69	3	4	195	4	CA10	17	49711002	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	22708505	49711002	31484208	93	2478										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6976065	6976065	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	atgcaatctctgtctgcagaCacggcgactttaatctgtag	9	10	3	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr18:6976065C>T	ENST00000389658.3	-	45	6453	c.6360G>A	c.(6358-6360)gtG>gtA	p.V2120V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2120	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.V2120V(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGTCTGCAGACACGGCGACTT	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	18											120	119	119					18																	6976065		2203	4300	6503	6966065	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6360G>A	18.37:g.6976065C>T			6966065		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.453	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6976065	C	T	6976065	2	4	28	1	0	0	0	0	0	0	0	1	8627	465	17	3		3	LAMA1	18	6976065	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10		6976065	71101183	94	2479										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36322257	36322257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctcctcatattcgttcctgaCtcggtcctcttccgaccttc	5	17	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr19:36322257C>T	ENST00000378910.5	-	26	3327	c.3328G>A	c.(3328-3330)Gtc>Atc	p.V1110I	NPHS1_ENST00000353632.6_Missense_Mutation_p.V1070I	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1110					cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.V1110I(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TCGTTCCTGACTCGGTCCTCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											102	97	99					19																	36322257		2203	4300	6503	41014097	SO:0001583	missense	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3328G>A	19.37:g.36322257C>T	ENSP00000368190:p.Val1110Ile		41014097	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	C	3.387	-0.125214	0.06795	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.72725	-0.68;-0.66	5.18	0.35	0.16037	.	0.574722	0.18651	N	0.135013	T	0.44561	0.1299	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.22109	T	0.4	-8.5462	3.9932	0.09546	0.0:0.5008:0.1739:0.3253	.	1110	O60500	NPHN_HUMAN	I	1110;1070	ENSP00000368190:V1110I;ENSP00000343634:V1070I	ENSP00000343634:V1070I	V	-	1	0	NPHS1	41014097	0.019000	0.18553	0.128000	0.21923	0.054000	0.15201	-0.040000	0.12104	0.006000	0.14734	0.442000	0.29010	GTC		0.612	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36322257	C	T	36322257	3	4	28	1	0	0	0	0	1	0	0	0	10613	565	20	3	413	3	NPHS1	19	36322257	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		36322257	22806726	95	2480										
HAS1	3036	hgsc.bcm.edu	37	chr19	52217278	52217278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	actcacggaagtacgacttgGaccagcgtgtctgctggctc	12	12	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr19:52217278G>T	ENST00000222115.1	-	5	1173	c.1139C>A	c.(1138-1140)tCc>tAc	p.S380Y	HAS1_ENST00000594621.1_Silent_p.V209V|HAS1_ENST00000601714.1_Missense_Mutation_p.S387Y|HAS1_ENST00000540069.2_Missense_Mutation_p.S379Y	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	380					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.S380Y(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GTACGACTTGGACCAGCGTGT	0.647																																					NSCLC(132;636 2450 45807 47979)											1	Substitution - Missense(1)	large_intestine(1)	19											50	32	38					19																	52217278		2202	4300	6502	56909090	SO:0001583	missense	3036			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1139C>A	19.37:g.52217278G>T	ENSP00000222115:p.Ser380Tyr		56909090	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	g	15.86	2.958051	0.53400	.	.	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.40225	1.04;1.04	3.22	3.22	0.36961	.	0.135484	0.49916	U	0.000132	T	0.58708	0.2141	M	0.79475	2.455	0.40675	D	0.982257	P;D;D	0.53151	0.948;0.958;0.958	P;P;P	0.58780	0.673;0.845;0.845	T	0.67217	-0.5726	10	0.87932	D	0	-11.6399	12.2907	0.54817	0.0:0.0:1.0:0.0	.	379;380;379	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	Y	379;380	ENSP00000445021:S379Y;ENSP00000222115:S380Y	ENSP00000222115:S380Y	S	-	2	0	HAS1	56909090	1.000000	0.71417	1.000000	0.80357	0.160000	0.22226	5.291000	0.65667	1.816000	0.52996	0.174000	0.16983	TCC		0.647	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		T	52217278	G	T	52217278	3	4	28	1	0	0	0	0	1	0	0	0	6982	1174	41	2	601	2	HAS1	19	52217278	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	15895021	52217278	6911705	96	2481										
TPX2	22974	hgsc.bcm.edu	37	chr20	30370134	30370134	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caaaccaaacaccgtgcacgGgctgtgacctgcaaaagtac	9	13	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr20:30370134G>T	ENST00000300403.6	+	11	1665	c.1137G>T	c.(1135-1137)cgG>cgT	p.R379R	TPX2_ENST00000340513.4_Silent_p.R415R	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	379					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)	p.R379R(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			ACCGTGCACGGGCTGTGACCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	20											113	113	113					20																	30370134		2203	4300	6503	29833795	SO:0001819	synonymous_variant	22974			AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1137G>T	20.37:g.30370134G>T			29833795	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																				0.502	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30370134	G	T	30370134	2	4	28	1	0	0	0	0	0	0	0	1	16472	1219	43	2		2	TPX2	20	30370134	Silent	SNP	G	TCGA-AG-3601-01A-01W-0833-10		30370134	32655386	97	2482										
MMP9	4318	hgsc.bcm.edu	37	chr20	44644971	44644971	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	caggtggaccaagtgggctaCgtgacctatgacatcctgca	12	11	0	2	rs369032528		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr20:44644971C>T	ENST00000372330.3	+	13	2107	c.2088C>T	c.(2086-2088)taC>taT	p.Y696Y	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	696					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y696Y(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	AAGTGGGCTACGTGACCTATG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	20						C		1,4405	2.1+/-5.4	0,1,2202	142	107	119		2088	-0.1	1	20		119	0,8600		0,0,4300	no	coding-synonymous	MMP9	NM_004994.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		696/708	44644971	1,13005	2203	4300	6503	44078378	SO:0001819	synonymous_variant	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.2088C>T	20.37:g.44644971C>T			44078378	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Silent	SNP	ENST00000372330.3	37	CCDS13390.1																																																																																				0.592	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			T	44644971	C	T	44644971	2	4	28	1	0	0	0	0	0	0	0	1	9699	547	19	1		1	MMP9	20	44644971	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	14274837	44644971	18380549	98	2483										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51589849	51589849	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gaggatgccgaggagaaaacAgcaggcacccaagcgggcgg	17	10	0	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr20:51589849A>T	ENST00000371497.5	+	1	904	c.17A>T	c.(16-18)cAg>cTg	p.Q6L		NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	6					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q6L(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			AGGAGAAAACAGCAGGCACCC	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	20											31	30	30					20																	51589849		2000	3962	5962	51023256	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.17A>T	20.37:g.51589849A>T	ENSP00000360552:p.Gln6Leu		51023256	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.451222	0.43531	.	.	ENSG00000182463	ENST00000371497	T	0.14766	2.48	4.42	3.31	0.37934	.	0.648009	0.13913	N	0.354098	T	0.12646	0.0307	L	0.39898	1.24	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.03898	-1.0994	10	0.56958	D	0.05	-10.5365	9.9666	0.41727	0.8478:0.0:0.0:0.1522	.	6	Q9NRE2	TSH2_HUMAN	L	6	ENSP00000360552:Q6L	ENSP00000360552:Q6L	Q	+	2	0	TSHZ2	51023256	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.292000	0.72725	0.704000	0.31869	0.448000	0.29417	CAG		0.706	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		T	51589849	A	T	51589849	3	4	28	1	0	0	0	0	1	0	0	0	16664	188	7	5	19	5	TSHZ2	20	51589849	Missense_Mutation	SNP	A	TCGA-AG-3601-01A-01W-0833-10	6944878	51589849	11435671	99	2484										
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17073367	17073367	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ggggctcctcctcttctggaCtcctcgggctctcccttggg	12	16	3	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chr22:17073367C>A	ENST00000359963.3	-	1	333	c.74G>T	c.(73-75)aGt>aTt	p.S25I		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	25					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)	p.S25I(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTCTTCTGGACTCCTCGGGCT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	22											48	54	52					22																	17073367		2203	4300	6503	15453367	SO:0001583	missense	150160			AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.74G>T	22.37:g.17073367C>A	ENSP00000353048:p.Ser25Ile		15453367	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	2.240	-0.374014	0.05034	.	.	ENSG00000198445	ENST00000359963	T	0.56776	0.44	1.81	0.64	0.17752	.	1.842030	0.03376	U	0.199630	T	0.31827	0.0809	N	0.08118	0	0.09310	N	1	B	0.24186	0.099	B	0.14578	0.011	T	0.18524	-1.0334	10	0.38643	T	0.18	0.4841	5.9635	0.19313	0.0:0.6692:0.3308:0.0	.	25	Q96SF2	TCPQM_HUMAN	I	25	ENSP00000353048:S25I	ENSP00000353048:S25I	S	-	2	0	CCT8L2	15453367	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.196000	0.09532	0.088000	0.17205	0.393000	0.25936	AGT		0.672	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			A	17073367	C	A	17073367	3	1	28	1	0	0	0	0	1	0	0	0	2967	565	20	2	1603	2	CCT8L2	22	17073367	Missense_Mutation	SNP	C	TCGA-AG-3601-01A-01W-0833-10		17073367	34231199	100	2485										
PIR	8544	hgsc.bcm.edu	37	chrX	15509373	15509373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	agagagtaactttcttggagGaccccatatcggagtctaaa	10	8	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:15509373G>A	ENST00000380421.3	-	2	468	c.8C>T	c.(7-9)tCc>tTc	p.S3F	PIR_ENST00000380420.5_Missense_Mutation_p.S3F|PIR_ENST00000476381.1_5'Flank|BMX_ENST00000357607.2_Intron	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	3					monocyte differentiation (GO:0030224)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|quercetin 2,3-dioxygenase activity (GO:0008127)|transcription cofactor activity (GO:0003712)	p.S3F(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					TTTCTTGGAGGACCCCATATC	0.502																																					Ovarian(180;1587 2015 10555 34192 51653)											1	Substitution - Missense(1)	large_intestine(1)	X											100	94	96					X																	15509373		2203	4300	6503	15419294	SO:0001583	missense	8544			Y07868	CCDS14167.1	Xp22.31	2008-02-05			ENSG00000087842	ENSG00000087842			30048	protein-coding gene	gene with protein product		300931				9079676	Standard	NM_003662		Approved		uc004cwv.3	O00625	OTTHUMG00000021176	ENST00000380421.3:c.8C>T	X.37:g.15509373G>A	ENSP00000369786:p.Ser3Phe		15419294	Q5U0G0|Q6FHD2	Missense_Mutation	SNP	ENST00000380421.3	37	CCDS14167.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.676642	0.29783	.	.	ENSG00000087842	ENST00000380420;ENST00000380421	T;T	0.46819	0.86;0.86	5.53	3.56	0.40772	Cupin, RmlC-type (1);	0.714054	0.14036	N	0.345792	T	0.39600	0.1084	L	0.56280	1.765	0.09310	N	1	B	0.33448	0.412	B	0.27887	0.084	T	0.32534	-0.9903	10	0.56958	D	0.05	-23.5092	8.4824	0.33052	0.0:0.152:0.6665:0.1815	.	3	O00625	PIR_HUMAN	F	3	ENSP00000369785:S3F;ENSP00000369786:S3F	ENSP00000369785:S3F	S	-	2	0	PIR	15419294	0.073000	0.21202	0.019000	0.16419	0.212000	0.24457	1.953000	0.40352	1.085000	0.41206	0.600000	0.82982	TCC		0.502	PIR-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055863.1	NM_003662		A	15509373	G	A	15509373	3	1	28	1	0	0	0	0	1	0	0	0	11975	1174	41	3	900	3	PIR	23	15509373	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10		15509373	139761187	101	2486										
PAGE1	8712	hgsc.bcm.edu	37	chrX	49454025	49454025	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctaatggattgcctaccttcCtcaggtgttttcacctcctc	6	14	2	0	rs189247528		TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:49454025C>T	ENST00000376150.3	-	5	546	c.414G>A	c.(412-414)gaG>gaA	p.E138E		NM_003785.3	NP_003776.2	O75459	PAGE1_HUMAN	P antigen family, member 1 (prostate associated)	138					cellular defense response (GO:0006968)			p.E138E(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	7	Ovarian(276;0.236)					GCCTACCTTCCTCAGGTGTTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											118	107	111					X																	49454025		2203	4300	6503	49340979	SO:0001819	synonymous_variant	8712			AF058989	CCDS14327.1	Xp11.23	2009-06-17	2005-01-26	2005-01-27	ENSG00000068985	ENSG00000068985			4107	protein-coding gene	gene with protein product		300288	"G antigen, family B, 1 (prostate associated)"	GAGEB1		9651357, 9724777	Standard	NM_003785		Approved	PAGE-1, GAGE-9, CT16.3	uc004dom.3	O75459	OTTHUMG00000033224	ENST00000376150.3:c.414G>A	X.37:g.49454025C>T			49340979	Q6FGM3|Q9BSS7	Silent	SNP	ENST00000376150.3	37	CCDS14327.1																																																																																				0.473	PAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081210.1			T	49454025	C	T	49454025	2	4	28	1	0	0	0	0	0	0	0	1	11420	680	24	3		3	PAGE1	23	49454025	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	33944652	49454025	105816535	102	2487										
GPR174	84636	hgsc.bcm.edu	37	chrX	78426546	78426546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	accaggccagatggagacaaTacagattttcgatactttat	8	8	0	3			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:78426546T>C	ENST00000276077.1	+	1	78	c.42T>C	c.(40-42)aaT>aaC	p.N14N		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N14N(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						ATGGAGACAATACAGATTTTC	0.383										HNSCC(63;0.18)																																						1	Substitution - coding silent(1)	large_intestine(1)	X											109	92	97					X																	78426546		2203	4300	6503	78313202	SO:0001819	synonymous_variant	84636			AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.42T>C	X.37:g.78426546T>C			78313202	Q2M3F7	Silent	SNP	ENST00000276077.1	37	CCDS14443.1																																																																																				0.383	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		C	78426546	T	C	78426546	2	2	28	1	0	0	0	0	0	0	0	1	6692	1403	49	4		4	GPR174	23	78426546	Silent	SNP	T	TCGA-AG-3601-01A-01W-0833-10	28972521	78426546	76844014	103	2488										
DRP2	1821	hgsc.bcm.edu	37	chrX	100515538	100515538	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	ctgtgcttggaggacatcatGgagaaactccgtcatgcctt	11	10	2	1			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:100515538G>T	ENST00000395209.3	+	24	3329	c.2802G>T	c.(2800-2802)atG>atT	p.M934I	DRP2_ENST00000541709.1_Missense_Mutation_p.M856I|DRP2_ENST00000538510.1_Missense_Mutation_p.M934I|DRP2_ENST00000402866.1_Missense_Mutation_p.M934I	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	934					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.M931I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						AGGACATCATGGAGAAACTCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X											226	185	199					X																	100515538		2203	4300	6503	100402194	SO:0001583	missense	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2802G>T	X.37:g.100515538G>T	ENSP00000378635:p.Met934Ile		100402194	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	G	14.30	2.494249	0.44352	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.06142	3.42;3.42;3.34;3.42	5.05	5.05	0.67936	.	0.040904	0.85682	D	0.000000	T	0.19446	0.0467	M	0.62723	1.935	0.47276	D	0.999374	P	0.45126	0.851	P	0.55391	0.775	T	0.00273	-1.1858	10	0.48119	T	0.1	-14.9202	17.6118	0.88055	0.0:0.0:1.0:0.0	.	934	Q13474	DRP2_HUMAN	I	934;934;856;934	ENSP00000385038:M934I;ENSP00000378635:M934I;ENSP00000444752:M856I;ENSP00000441051:M934I	ENSP00000378635:M934I	M	+	3	0	DRP2	100402194	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.943000	0.63554	2.086000	0.62901	0.436000	0.28706	ATG		0.493	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100515538	G	T	100515538	3	4	28	1	0	0	0	0	1	0	0	0	4775	1348	47	2	2888	2	DRP2	23	100515538	Missense_Mutation	SNP	G	TCGA-AG-3601-01A-01W-0833-10	22088992	100515538	54755022	104	2489										
CHRDL1	91851	hgsc.bcm.edu	37	chrX	109922587	109922587	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	gggttgttctggtcaccagcTtgaagtgaggaagctcctca	13	9	3	2			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:109922587T>G	ENST00000372045.1	-	11	1330	c.1199A>C	c.(1198-1200)aAg>aCg	p.K400T	CHRDL1_ENST00000372042.1_Missense_Mutation_p.K408T|CHRDL1_ENST00000434224.1_Missense_Mutation_p.K327T|CHRDL1_ENST00000444321.2_Missense_Mutation_p.K407T|CHRDL1_ENST00000394797.4_Missense_Mutation_p.K406T|CHRDL1_ENST00000218054.4_Missense_Mutation_p.K406T|CHRDL1_ENST00000482160.1_Missense_Mutation_p.K328T			Q9BU40	CRDL1_HUMAN	chordin-like 1	400					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.K406T(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						GGTCACCAGCTTGAAGTGAGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											182	143	156					X																	109922587		2203	4300	6503	109809243	SO:0001583	missense	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.1199A>C	X.37:g.109922587T>G	ENSP00000361115:p.Lys400Thr		109809243	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Missense_Mutation	SNP	ENST00000372045.1	37		.	.	.	.	.	.	.	.	.	.	T	17.48	3.400552	0.62177	.	.	ENSG00000101938	ENST00000372045;ENST00000434224;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000482160;ENST00000444321	T;T;T;T;T;T;T	0.32753	2.18;1.44;2.18;2.18;2.44;1.44;2.18	5.03	5.03	0.67393	.	0.098405	0.64402	D	0.000002	T	0.41166	0.1147	L	0.27053	0.805	0.47183	D	0.999349	D;D;D;D;D;D	0.71674	0.994;0.998;0.998;0.998;0.998;0.998	D;D;D;D;D;D	0.76071	0.977;0.987;0.987;0.987;0.987;0.981	T	0.18935	-1.0321	9	.	.	.	-15.7162	14.3831	0.66923	0.0:0.0:0.0:1.0	.	328;407;387;400;408;327	B4DMP3;E9PGS5;Q59FB2;Q9BU40;D3DUY6;D3YTA8	.;.;.;CRDL1_HUMAN;.;.	T	400;327;406;406;408;328;407	ENSP00000361115:K400T;ENSP00000389627:K327T;ENSP00000218054:K406T;ENSP00000378276:K406T;ENSP00000361112:K408T;ENSP00000418443:K328T;ENSP00000399739:K407T	.	K	-	2	0	CHRDL1	109809243	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.766000	0.47629	1.932000	0.55993	0.481000	0.45027	AAG		0.453	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		G	109922587	T	G	109922587	3	3	28	1	0	0	0	0	1	0	0	0	3379	1609	56	4	161	4	CHRDL1	23	109922587	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	9407049	109922587	45347973	105	2490										
OCRL	4952	hgsc.bcm.edu	37	chrX	128703310	128703310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	acaaatgttaatcagcttaaTtatcggagtcacatggaact	7	7	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:128703310T>G	ENST00000371113.4	+	15	1701	c.1536T>G	c.(1534-1536)aaT>aaG	p.N512K	OCRL_ENST00000357121.5_Missense_Mutation_p.N512K	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	512	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.N512K(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						ATCAGCTTAATTATCGGAGTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											175	161	166					X																	128703310		2203	4300	6503	128530991	SO:0001583	missense	4952			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.1536T>G	X.37:g.128703310T>G	ENSP00000360154:p.Asn512Lys		128530991	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	T	4.294	0.053743	0.08291	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94966	-3.57;-3.57	5.82	0.354	0.16063	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.534293	0.22268	N	0.062318	T	0.78175	0.4242	N	0.01761	-0.735	0.23820	N	0.996751	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.68872	-0.5294	10	0.06891	T	0.86	.	5.3404	0.15981	0.1478:0.4284:0.0:0.4238	.	512;512	Q01968-2;Q01968	.;OCRL_HUMAN	K	512	ENSP00000360154:N512K;ENSP00000349635:N512K	ENSP00000349635:N512K	N	+	3	2	OCRL	128530991	0.671000	0.27521	0.991000	0.47740	0.964000	0.63967	-0.181000	0.09740	0.022000	0.15160	0.407000	0.27541	AAT		0.418	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128703310	T	G	128703310	3	3	28	1	0	0	0	0	1	0	0	0	10854	1490	52	4	1594	4	OCRL	23	128703310	Missense_Mutation	SNP	T	TCGA-AG-3601-01A-01W-0833-10	18780723	128703310	26567250	106	2491										
GPR101	83550	hgsc.bcm.edu	37	chrX	136112715	136112715	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.13743315508021	1.54466230936819	1.057757885763	0.0968421052631578	0.466258722490609	0	cgactgggtgggaggctctcCgggatgttcactgcctcgac	15	12	2	0			TCGA-AG-3601-01A-01W-0833-10	TCGA-AG-3601-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	bfd52957-b19c-4dca-85ef-7f9f094ad841	e679b932-87eb-47d0-8eff-318986eeba92	g.chrX:136112715C>T	ENST00000298110.1	-	1	1118	c.1119G>A	c.(1117-1119)ccG>ccA	p.P373P		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	373						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.P373P(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GGAGGCTCTCCGGGATGTTCA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	X											218	174	189					X																	136112715		2203	4300	6503	135940381	SO:0001819	synonymous_variant	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1119G>A	X.37:g.136112715C>T			135940381	Q5JSM8|Q8NG93	Silent	SNP	ENST00000298110.1	37	CCDS14662.1																																																																																				0.507	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136112715	C	T	136112715	2	4	28	1	0	0	0	0	0	0	0	1	6642	639	23	1		1	GPR101	23	136112715	Silent	SNP	C	TCGA-AG-3601-01A-01W-0833-10	7409405	136112715	19157845	107	2492										
TXNDC12	51060	hgsc.bcm.edu	37	chr1	52490196	52490196	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ccttacccagaaaaaggattCgtggaatataacccccgtca	7	12	1	1	rs138944221		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr1:52490196C>T	ENST00000371626.4	-	5	1415	c.341G>A	c.(340-342)cGa>cAa	p.R114Q	TXNDC12_ENST00000471493.1_5'UTR	NM_015913.3	NP_056997.1	O95881	TXD12_HUMAN	thioredoxin domain containing 12 (endoplasmic reticulum)	114					cell redox homeostasis (GO:0045454)	endoplasmic reticulum (GO:0005783)	protein-disulfide reductase (glutathione) activity (GO:0019153)	p.R114Q(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7					Glutathione(DB00143)	AAAAAGGATTCGTGGAATATA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	96	89	92		341	5.5	1	1	dbSNP_134	92	0,8600		0,0,4300	no	missense	TXNDC12	NM_015913.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	114/173	52490196	1,13005	2203	4300	6503	52262784	SO:0001583	missense	51060			AF131758	CCDS561.1	1p32.3	2011-10-19			ENSG00000117862	ENSG00000117862		"Protein disulfide isomerases"	24626	protein-coding gene	gene with protein product	"endoplasmic reticulum thioredoxin superfamily member, 18 kDa", "anterior gradient homolog 1 (Xenopus laevis)", "protein disulfide isomerase family A, member 16"	609448				8619474, 9110174	Standard	NM_015913		Approved	TLP19, ERP18, ERP19, hAG-1, AGR1, PDIA16	uc001cti.4	O95881	OTTHUMG00000008629	ENST00000371626.4:c.341G>A	1.37:g.52490196C>T	ENSP00000360688:p.Arg114Gln		52262784	B3KQS0|Q5T1T4|Q96H50	Missense_Mutation	SNP	ENST00000371626.4	37	CCDS561.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186878	0.94923	2.27E-4	0.0	ENSG00000117862	ENST00000371626	T	0.54675	0.56	5.46	5.46	0.80206	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.71581	2.175	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.70004	-0.4991	10	0.37606	T	0.19	.	17.4958	0.87717	0.0:1.0:0.0:0.0	.	114	O95881	TXD12_HUMAN	Q	114	ENSP00000360688:R114Q	ENSP00000360688:R114Q	R	-	2	0	TXNDC12	52262784	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.215000	0.72206	2.550000	0.86006	0.655000	0.94253	CGA		0.413	TXNDC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023818.1	NM_015913		T	52490196	C	T	52490196	3	4	29	1	0	0	0	0	1	0	0	0	16833	884	31	1	189	1	TXNDC12	1	52490196	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		52490196	196760425	1	2493										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157490846	157490846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tgtctcactgcgctgggcccCgaggccattgtcggcctcac	12	16	2	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr1:157490846C>T	ENST00000361835.3	-	11	2633	c.2476G>A	c.(2476-2478)Ggg>Agg	p.G826R	FCRL5_ENST00000356953.4_Missense_Mutation_p.G826R|FCRL5_ENST00000461387.1_5'UTR	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	826	Ig-like C2-type 8.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.G826R(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CGCTGGGCCCCGAGGCCATTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	65	63					1																	157490846		2203	4300	6503	155757470	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2476G>A	1.37:g.157490846C>T	ENSP00000354691:p.Gly826Arg		155757470	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.633977	0.29068	.	.	ENSG00000143297	ENST00000361835;ENST00000356953	T;T	0.14766	2.48;2.48	5.25	2.26	0.28386	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23649	0.0572	H	0.99336	4.52	0.09310	N	0.999996	D;D	0.60160	0.972;0.987	B;P	0.48677	0.422;0.586	T	0.29119	-1.0022	9	0.87932	D	0	.	5.3179	0.15866	0.3625:0.5416:0.0:0.0959	.	826;826	A6NJE8;Q96RD9	.;FCRL5_HUMAN	R	826	ENSP00000354691:G826R;ENSP00000349434:G826R	ENSP00000349434:G826R	G	-	1	0	FCRL5	155757470	0.006000	0.16342	0.013000	0.15412	0.163000	0.22366	1.216000	0.32443	0.316000	0.23135	-0.188000	0.12872	GGG		0.567	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157490846	C	T	157490846	3	4	29	1	0	0	0	0	1	0	0	0	5817	652	23	1	485	1	FCRL5	1	157490846	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	105000650	157490846	91759775	2	2494										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222697016	222697016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	cgggcactggcttgtatttgCacttgcctgggggtgctcgc	15	11	0	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr1:222697016C>T	ENST00000343410.6	-	8	1884	c.1826G>A	c.(1825-1827)tGc>tAc	p.C609Y	HHIPL2_ENST00000473144.1_5'UTR	NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	609					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)	p.C609Y(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CTTGTATTTGCACTTGCCTGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											165	140	148					1																	222697016		2203	4300	6503	220763639	SO:0001583	missense	79802			BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1826G>A	1.37:g.222697016C>T	ENSP00000342118:p.Cys609Tyr		220763639	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	20.6	4.019298	0.75275	.	.	ENSG00000143512	ENST00000343410	T	0.20200	2.09	5.19	5.19	0.71726	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.49745	0.1575	M	0.81942	2.565	0.80722	D	1	D	0.71674	0.998	D	0.67231	0.95	T	0.55988	-0.8053	10	0.87932	D	0	-10.1453	18.3105	0.90197	0.0:1.0:0.0:0.0	.	609	Q6UWX4	HIPL2_HUMAN	Y	609	ENSP00000342118:C609Y	ENSP00000342118:C609Y	C	-	2	0	HHIPL2	220763639	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	6.463000	0.73530	2.397000	0.81536	0.655000	0.94253	TGC		0.517	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222697016	C	T	222697016	3	4	29	1	0	0	0	0	1	0	0	0	7115	710	25	3	356	3	HHIPL2	1	222697016	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	65206170	222697016	26553605	3	2495										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233497916	233497916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gcgagatcgacgtgctggagCgggaacttaacattctgata	13	8	1	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr1:233497916C>T	ENST00000366624.3	+	5	1690	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	MLK4_ENST00000366623.3_Missense_Mutation_p.R477W	NM_032435.2	NP_115811.2												p.R477W(2)									CGTGCTGGAGCGGGAACTTAA	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	1											64	62	62					1																	233497916		2203	4300	6503	231564539	SO:0001583	missense	84451																														ENST00000366624.3:c.1429C>T	1.37:g.233497916C>T	ENSP00000355583:p.Arg477Trp		231564539		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.455729	0.84209	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.12774	2.65;2.65	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.40145	0.1105	M	0.80183	2.485	0.80722	D	1	D;D	0.71674	0.998;0.971	D;P	0.66351	0.943;0.823	T	0.37502	-0.9703	10	0.66056	D	0.02	.	18.2298	0.89931	0.0:1.0:0.0:0.0	.	477;477	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	W	477	ENSP00000355582:R477W;ENSP00000355583:R477W	ENSP00000355582:R477W	R	+	1	2	RP5-862P8.2	231564539	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.760000	0.55235	2.525000	0.85131	0.655000	0.94253	CGG		0.532	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233497916	C	T	233497916	3	4	29	1	0	0	0	0	1	0	0	0	8280	759	27	1	1447	1	KIAA1804	1	233497916	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	10800900	233497916	15752705	4	2496										
APOB	338	hgsc.bcm.edu	37	chr2	21234050	21234050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	taaacggggccattacagaaCggaagacattgctgaaatgc	11	8	0	3	rs199510126		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:21234050C>T	ENST00000233242.1	-	26	5817	c.5690G>A	c.(5689-5691)cGt>cAt	p.R1897H		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1897					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R1897H(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATTACAGAACGGAAGACATT	0.478													C|||	1	0.000199681	0	0	5008	,	,		23181	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											127	119	122					2																	21234050		2203	4300	6503	21087555	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5690G>A	2.37:g.21234050C>T	ENSP00000233242:p.Arg1897His		21087555	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	0.042	-1.282531	0.01398	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00966	5.49	5.67	-2.41	0.06562	.	0.437392	0.21535	N	0.072995	T	0.00468	0.0015	N	0.01729	-0.75	0.58432	D	0.999992	B	0.10296	0.003	B	0.06405	0.002	T	0.55685	-0.8102	10	0.11794	T	0.64	.	13.1172	0.59307	0.0:0.6611:0.0:0.3389	.	1897	P04114	APOB_HUMAN	H	1897	ENSP00000233242:R1897H	ENSP00000233242:R1897H	R	-	2	0	APOB	21087555	0.000000	0.05858	0.334000	0.25495	0.531000	0.34715	-0.148000	0.10219	-0.395000	0.07715	-0.351000	0.07748	CGT		0.478	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21234050	C	T	21234050	3	4	29	1	0	0	0	0	1	0	0	0	785	536	19	1	8017	1	APOB	2	21234050	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		21234050	221965323	5	2497										
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360701	27360701	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tgttagagtggagcctatgaGaaggtgggctggggcctggg	20	5	0	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:27360701G>T	ENST00000335524.3	-	3	1022	c.497C>A	c.(496-498)tCt>tAt	p.S166Y		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		166								p.S166Y(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCCTATGAGAAGGTGGGCT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	57	57					2																	27360701		2203	4300	6503	27214205	SO:0001583	missense	339779																														ENST00000335524.3:c.497C>A	2.37:g.27360701G>T	ENSP00000335017:p.Ser166Tyr		27214205	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	.	.	.	.	.	.	.	.	.	.	g	16.50	3.141319	0.57044	.	.	ENSG00000186143	ENST00000335524	T	0.45276	0.9	4.96	4.07	0.47477	.	0.419266	0.17756	N	0.163052	T	0.48892	0.1525	L	0.32530	0.975	0.22127	N	0.999349	D	0.69078	0.997	D	0.63192	0.912	T	0.35276	-0.9795	10	0.54805	T	0.06	-6.9043	11.2863	0.49224	0.0:0.185:0.815:0.0	.	166	Q53SZ7	CB053_HUMAN	Y	166	ENSP00000335017:S166Y	ENSP00000335017:S166Y	S	-	2	0	C2orf53	27214205	0.994000	0.37717	0.241000	0.24154	0.006000	0.05464	2.396000	0.44468	1.032000	0.39892	0.556000	0.70494	TCT		0.622	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			T	27360701	G	T	27360701	3	4	29	1	0	0	0	0	1	0	0	0	2180	942	33	2	745	2	C2orf53	2	27360701	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	6126651	27360701	215838672	6	2498										
GALNT14	79623	hgsc.bcm.edu	37	chr2	31133781	31133781	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gggtcctcaagagctcaccaTgtcccagtgctggctcatga	11	13	3	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:31133781T>C	ENST00000349752.5	-	15	2284	c.1645A>G	c.(1645-1647)Atg>Gtg	p.M549V	GALNT14_ENST00000486564.1_5'UTR|GALNT14_ENST00000324589.5_Missense_Mutation_p.M554V|GALNT14_ENST00000406653.1_Missense_Mutation_p.M529V|GALNT14_ENST00000420311.2_Missense_Mutation_p.M514V|GALNT14_ENST00000356174.3_Missense_Mutation_p.M516V	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	549	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.M549V(1)		cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					GAGCTCACCATGTCCCAGTGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	100	108					2																	31133781		2203	4300	6503	30987285	SO:0001583	missense	79623			AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"Glycosyltransferase family 2 domain containing"	22946	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 14"	608225	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.1645A>G	2.37:g.31133781T>C	ENSP00000288988:p.Met549Val		30987285	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	T	12.11	1.839087	0.32513	.	.	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	5.26	1.55	0.23275	Ricin B-related lectin (1);Ricin B lectin (2);	0.340043	0.36444	N	0.002594	T	0.32496	0.0831	L	0.47190	1.495	0.31084	N	0.711596	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.10450	0.002;0.005;0.001;0.001	T	0.24941	-1.0146	10	0.59425	D	0.04	.	7.3242	0.26545	0.0:0.076:0.2979:0.626	.	514;554;549;529	F5H263;Q96FL9-3;Q96FL9;B3KV89	.;.;GLT14_HUMAN;.	V	549;554;529;516;514	ENSP00000288988:M549V;ENSP00000314500:M554V;ENSP00000385435:M529V;ENSP00000348497:M516V;ENSP00000415514:M514V	ENSP00000314500:M554V	M	-	1	0	GALNT14	30987285	1.000000	0.71417	0.871000	0.34182	0.985000	0.73830	1.971000	0.40530	0.027000	0.15297	0.533000	0.62120	ATG		0.577	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572		C	31133781	T	C	31133781	3	2	29	1	0	0	0	0	1	0	0	0	6232	1464	51	4	17	4	GALNT14	2	31133781	Missense_Mutation	SNP	T	TCGA-AG-3602-01A-02W-0833-10	3773080	31133781	212065592	7	2499										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74902673	74902673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ggatggacacctccaccgagCagtgcggatcggagctcagc	14	13	1	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:74902673C>T	ENST00000357877.2	+	11	1543	c.1394C>T	c.(1393-1395)gCa>gTa	p.A465V	SEMA4F_ENST00000339773.5_Missense_Mutation_p.A310V|SEMA4F_ENST00000473350.1_3'UTR	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	465	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.A465V(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						CTCCACCGAGCAGTGCGGATC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											119	112	114					2																	74902673		2203	4300	6503	74756181	SO:0001583	missense	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1394C>T	2.37:g.74902673C>T	ENSP00000350547:p.Ala465Val		74756181	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.418910	0.42918	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.27256	1.68;1.68	4.77	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.157215	0.42172	D	0.000758	T	0.26846	0.0657	N	0.05510	-0.035	0.34767	D	0.733289	P;D	0.55605	0.924;0.972	P;D	0.66716	0.646;0.946	T	0.17961	-1.0352	10	0.12103	T	0.63	.	15.3434	0.74314	0.0:1.0:0.0:0.0	.	310;465	O95754-2;O95754	.;SEM4F_HUMAN	V	465;310	ENSP00000350547:A465V;ENSP00000342675:A310V	ENSP00000342675:A310V	A	+	2	0	SEMA4F	74756181	0.962000	0.33011	1.000000	0.80357	0.291000	0.27294	3.849000	0.55910	2.475000	0.83589	0.467000	0.42956	GCA		0.488	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		T	74902673	C	T	74902673	3	4	29	1	0	0	0	0	1	0	0	0	14072	710	25	3	1436	3	SEMA4F	2	74902673	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	43768892	74902673	168296700	8	2500										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103039784	103039784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ttggcttgttgcaggagagcGaattaaaggatttaatattt	11	3	0	1	rs142509174		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:103039784G>A	ENST00000264260.2	+	3	636	c.47G>A	c.(46-48)cGa>cAa	p.R16Q	IL18RAP_ENST00000409369.1_5'UTR	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	16					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R16Q(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						GCAGGAGAGCGAATTAAAGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	251	246	248		47	-0.5	0	2	dbSNP_134	248	0,8600		0,0,4300	no	missense	IL18RAP	NM_003853.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	16/600	103039784	1,13005	2203	4300	6503	102406216	SO:0001583	missense	8807			AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.47G>A	2.37:g.103039784G>A	ENSP00000264260:p.Arg16Gln		102406216	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	37	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210262	0.39003	2.27E-4	0.0	ENSG00000115607	ENST00000264260;ENST00000450855	T	0.02301	4.35	5.67	-0.516	0.11950	.	0.655438	0.15220	N	0.273989	T	0.01730	0.0055	L	0.36672	1.1	0.09310	N	0.999996	P	0.50443	0.935	B	0.34722	0.188	T	0.51252	-0.8729	10	0.38643	T	0.18	.	9.1957	0.37226	0.478:0.0:0.522:0.0	.	16	O95256	I18RA_HUMAN	Q	16	ENSP00000264260:R16Q	ENSP00000264260:R16Q	R	+	2	0	IL18RAP	102406216	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.266000	0.08631	-0.313000	0.08728	0.591000	0.81541	CGA		0.408	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		A	103039784	G	A	103039784	3	1	29	1	0	0	0	0	1	0	0	0	7669	1058	37	1	49	1	IL18RAP	2	103039784	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	28137111	103039784	140159589	9	2501										
DPP10	57628	hgsc.bcm.edu	37	chr2	116520177	116520177	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	atgacatcagatacgtggctCtctcagcaggtacagtatag	10	9	3	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:116520177C>T	ENST00000410059.1	+	12	1584	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	DPP10_ENST00000409163.1_Silent_p.L318L|DPP10_ENST00000393147.2_Silent_p.L372L|DPP10_ENST00000310323.8_Silent_p.L361L	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	368						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.L361L(1)|p.L368L(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						ATACGTGGCTCTCTCAGCAGG	0.348																																																2	Substitution - coding silent(2)	large_intestine(2)	2											195	183	187					2																	116520177		2203	4300	6503	116236647	SO:0001819	synonymous_variant	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1104C>T	2.37:g.116520177C>T			116236647	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																				0.348	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116520177	C	T	116520177	2	4	29	1	0	0	0	0	0	0	0	1	4738	900	32	3		3	DPP10	2	116520177	Silent	SNP	C	TCGA-AG-3602-01A-02W-0833-10	13480393	116520177	126679196	10	2502										
LRP1B	53353	hgsc.bcm.edu	37	chr2	140995732	140995732	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	acatactacctttgttgggtCtatcataaagccaggatcta	7	9	3	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:140995732C>G	ENST00000389484.3	-	89	14520	c.13549G>C	c.(13549-13551)Gac>Cac	p.D4517H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4517					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.D4517H(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		TTTGTTGGGTCTATCATAAAG	0.373										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											170	158	162					2																	140995732		2203	4300	6503	140712202	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13549G>C	2.37:g.140995732C>G	ENSP00000374135:p.Asp4517His		140712202	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.308656|4.308656	0.81247|0.81247	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977	T|.	0.63580|.	-0.05|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.155296|.	0.41712|.	D|.	0.000826|.	T|.	0.61924|.	0.2386|.	L|L	0.56199|0.56199	1.76|1.76	0.46078|0.46078	D|D	0.998853|0.998853	P|.	0.43477|.	0.808|.	P|.	0.48952|.	0.596|.	T|.	0.59883|.	-0.7370|.	10|.	0.72032|.	D|.	0.01|.	.|.	10.5741|10.5741	0.45217|0.45217	0.0:0.8835:0.0:0.1165|0.0:0.8835:0.0:0.1165	.|.	4517|.	Q9NZR2|.	LRP1B_HUMAN|.	H|Y	4517;4455|748	ENSP00000374135:D4517H|.	ENSP00000374135:D4517H|.	D|X	-|-	1|3	0|2	LRP1B|LRP1B	140712202|140712202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.502000|5.502000	0.66956|0.66956	2.596000|2.596000	0.87737|0.87737	0.655000|0.655000	0.94253|0.94253	GAC|TAG		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	140995732	C	G	140995732	3	3	29	1	0	0	0	0	1	0	0	0	8984	913	32	5	262	5	LRP1B	2	140995732	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	24475555	140995732	102203641	11	2503										
LRP2	4036	hgsc.bcm.edu	37	chr2	170127524	170127524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	caaagaaagaaggattccccGaaactggaaccatgacatct	8	10	1	3	rs201860953		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:170127524G>A	ENST00000263816.3	-	16	2495	c.2210C>T	c.(2209-2211)tCg>tTg	p.S737L	LRP2_ENST00000443831.1_Intron	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	737					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S737L(2)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AGGATTCCCCGAAACTGGAAC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2						G	LEU/SER	0,4406		0,0,2203	122	106	111		2210	4.9	0.2	2		111	6,8594	5.0+/-18.6	0,6,4294	yes	missense	LRP2	NM_004525.2	145	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	737/4656	170127524	6,13000	2203	4300	6503	169835770	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2210C>T	2.37:g.170127524G>A	ENSP00000263816:p.Ser737Leu		169835770	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.397079	0.42512	0.0	6.98E-4	ENSG00000081479	ENST00000263816	D	0.90788	-2.73	5.77	4.9	0.64082	Six-bladed beta-propeller, TolB-like (1);	0.101407	0.64402	D	0.000003	T	0.80363	0.4609	N	0.20685	0.6	0.80722	D	1	B	0.33120	0.398	B	0.22152	0.038	T	0.78288	-0.2262	10	0.07813	T	0.8	.	15.2561	0.73585	0.0675:0.0:0.9325:0.0	.	737	P98164	LRP2_HUMAN	L	737	ENSP00000263816:S737L	ENSP00000263816:S737L	S	-	2	0	LRP2	169835770	1.000000	0.71417	0.229000	0.23960	0.126000	0.20510	7.917000	0.87498	1.581000	0.49865	0.655000	0.94253	TCG		0.413	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170127524	G	A	170127524	3	1	29	1	0	0	0	0	1	0	0	0	8985	1059	37	1	12013	1	LRP2	2	170127524	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	29131792	170127524	73071849	12	2504										
STK36	27148	hgsc.bcm.edu	37	chr2	219540759	219540759	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ttatcttctgcagatttgccCgggctatgagcaccaataca	8	11	2	2	rs200288195		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr2:219540759C>T	ENST00000295709.3	+	6	721	c.442C>T	c.(442-444)Cgg>Tgg	p.R148W	STK36_ENST00000392106.2_Missense_Mutation_p.R148W|STK36_ENST00000440309.1_Missense_Mutation_p.R148W|STK36_ENST00000392105.3_Missense_Mutation_p.R148W	NM_015690.4	NP_056505.2			serine/threonine kinase 36									p.R148W(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CAGATTTGCCCGGGCTATGAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	108	107					2																	219540759		2203	4300	6503	219249003	SO:0001583	missense	27148			AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.442C>T	2.37:g.219540759C>T	ENSP00000295709:p.Arg148Trp		219249003		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927971	0.92389	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309;ENST00000424080	T;T;T;T;D	0.84873	1.59;1.59;1.59;1.59;-1.91	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40908	D	0.000985	D	0.92811	0.7714	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92320	0.5865	10	0.87932	D	0	-25.3868	20.8794	0.99867	0.0:1.0:0.0:0.0	.	148;148	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	W	148	ENSP00000295709:R148W;ENSP00000375955:R148W;ENSP00000375954:R148W;ENSP00000394095:R148W;ENSP00000403527:R148W	ENSP00000295709:R148W	R	+	1	2	STK36	219249003	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.829000	0.69316	2.941000	0.99782	0.655000	0.94253	CGG		0.478	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			T	219540759	C	T	219540759	3	4	29	1	0	0	0	0	1	0	0	0	15341	643	23	1	460	1	STK36	2	219540759	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	49413235	219540759	23658614	13	2505										
GALNTL2	117248	hgsc.bcm.edu	37	chr3	16254193	16254193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ccaccctgaggaacagggttCgcattgctgagacctggctg	13	12	0	2	rs191977190		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr3:16254193C>T	ENST00000339732.5	+	6	1818	c.1315C>T	c.(1315-1317)Cgc>Tgc	p.R439C	GALNT15_ENST00000437509.1_Missense_Mutation_p.R439C	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	439					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R439C(1)									GAACAGGGTTCGCATTGCTGA	0.547													C|||	1	0.000199681	0	0	5008	,	,		20618	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											105	101	103					3																	16254193		2203	4300	6503	16229197	SO:0001583	missense	117248			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1315C>T	3.37:g.16254193C>T	ENSP00000344260:p.Arg439Cys		16229197	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.38	3.816623	0.70912	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.61980	0.06;0.06	5.38	3.57	0.40892	.	0.268931	0.36703	N	0.002455	D	0.83083	0.5177	H	0.97659	4.05	0.54753	D	0.99998	D	0.89917	1.0	P	0.61275	0.886	D	0.85842	0.1398	10	0.87932	D	0	.	10.4884	0.44735	0.1337:0.7965:0.0:0.0698	.	439	Q8N3T1	GLTL2_HUMAN	C	439	ENSP00000344260:R439C;ENSP00000395873:R439C	ENSP00000344260:R439C	R	+	1	0	GALNTL2	16229197	0.999000	0.42202	0.663000	0.29738	0.868000	0.49771	4.191000	0.58372	0.627000	0.30340	0.561000	0.74099	CGC		0.547	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		T	16254193	C	T	16254193	3	4	29	1	0	0	0	0	1	0	0	0	6242	884	31	1	1337	1	GALNTL2	3	16254193	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		16254193	181768237	14	2506										
HRASLS	57110	hgsc.bcm.edu	37	chr3	192973513	192973513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ggacttgatcgaagtgttccGtcctggctatcagcactggg	13	10	1	1	rs150318874	byFrequency	TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr3:192973513G>A	ENST00000602513.1	+	2	483	c.74G>A	c.(73-75)cGt>cAt	p.R25H	HRASLS_ENST00000264735.2_Missense_Mutation_p.R130H			Q9HDD0	HRSL1_HUMAN	HRAS-like suppressor	25					ether lipid metabolic process (GO:0046485)|lipid catabolic process (GO:0016042)|peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|nuclear envelope lumen (GO:0005641)|peroxisome (GO:0005777)	phospholipase activity (GO:0004620)|transferase activity (GO:0016740)	p.R25H(1)		breast(1)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	10	all_cancers(143;9.1e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000159)		GAAGTGTTCCGTCCTGGCTAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	198	181	187		74	5.5	1	3	dbSNP_134	187	0,8600		0,0,4300	no	missense	HRASLS	NM_020386.3	29	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	probably-damaging	25/169	192973513	5,13001	2203	4300	6503	194456207	SO:0001583	missense	57110			AB030816	CCDS3303.1, CCDS3303.2	3q29	2008-05-15			ENSG00000127252	ENSG00000127252			14922	protein-coding gene	gene with protein product		606487					Standard	NM_020386		Approved	H-REV107, HRASLS1	uc003fta.4	Q9HDD0	OTTHUMG00000156104	ENST00000602513.1:c.74G>A	3.37:g.192973513G>A	ENSP00000473258:p.Arg25His		194456207	D2KX19	Missense_Mutation	SNP	ENST00000602513.1	37		.	.	.	.	.	.	.	.	.	.	G	26.5	4.742860	0.89573	0.001135	0.0	ENSG00000127252	ENST00000264735	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86343	0.5910	M	0.92604	3.325	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	D	0.88598	0.3148	9	0.66056	D	0.02	0.0	18.5869	0.91192	0.0:0.0:1.0:0.0	.	25	Q9HDD0	HRSL1_HUMAN	H	25	.	ENSP00000264735:R25H	R	+	2	0	HRASLS	194456207	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.095000	0.76952	2.868000	0.98415	0.557000	0.71058	CGT		0.493	HRASLS-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	192973513	G	A	192973513	3	1	29	1	0	0	0	0	1	0	0	0	7370	1145	40	1	76	1	HRASLS	3	192973513	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	176719320	192973513	5048917	15	2507										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66356239	66356239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gacagaggtgtttttcaggcCgctttgccggggaaggtacc	15	9	1	1	rs370503988		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr4:66356239C>T	ENST00000273854.3	-	5	1858	c.1258G>A	c.(1258-1260)Ggc>Agc	p.G420S	EPHA5_ENST00000432638.2_Intron|EPHA5_ENST00000511294.1_Missense_Mutation_p.G420S|EPHA5_ENST00000354839.4_Missense_Mutation_p.G420S	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	420	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.G420S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						TTTTTCAGGCCGCTTTGCCGG	0.502										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4						C	SER/GLY,SER/GLY	0,4406		0,0,2203	125	101	109		1258,1258	6.1	1	4		109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPHA5	NM_004439.5,NM_182472.2	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	420/1038,420/1016	66356239	1,13005	2203	4300	6503	66038834	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1258G>A	4.37:g.66356239C>T	ENSP00000273854:p.Gly420Ser		66038834	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	C	33	5.245266	0.95272	0.0	1.16E-4	ENSG00000145242	ENST00000273854;ENST00000354839;ENST00000511294	T;T;T	0.56275	0.47;0.47;0.47	6.08	6.08	0.98989	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000006	T	0.76983	0.4064	M	0.83012	2.62	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;1.0;1.0	T	0.76206	-0.3044	10	0.51188	T	0.08	.	20.6721	0.99693	0.0:1.0:0.0:0.0	.	420;420;420;420	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	S	420	ENSP00000273854:G420S;ENSP00000346899:G420S;ENSP00000427638:G420S	ENSP00000273854:G420S	G	-	1	0	EPHA5	66038834	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.952000	0.63618	2.894000	0.99253	0.591000	0.81541	GGC		0.502	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66356239	C	T	66356239	3	4	29	1	0	0	0	0	1	0	0	0	5183	652	23	1	1911	1	EPHA5	4	66356239	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		66356239	124798037	16	2508										
ANK2	287	hgsc.bcm.edu	37	chr4	114267166	114267166	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	aacttaaacatcactttgccGatttatacaaaggtatcgta	5	8	1	0	rs183590716		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr4:114267166G>A	ENST00000357077.4	+	35	4412	c.4359G>A	c.(4357-4359)ccG>ccA	p.P1453P	ANK2_ENST00000510275.2_Silent_p.P105P|ANK2_ENST00000264366.6_Silent_p.P1420P|ANK2_ENST00000506722.1_Silent_p.P1444P|ANK2_ENST00000394537.3_Silent_p.P1453P|ANK2_ENST00000509550.1_Silent_p.P629P	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1453	Death 1. {ECO:0000255|PROSITE- ProRule:PRU00064}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.P1453P(2)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TCACTTTGCCGATTTATACAA	0.393													G|||	1	0.000199681	0	0.0014	5008	,	,		19838	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	4											111	99	103					4																	114267166		2203	4300	6503	114486615	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4359G>A	4.37:g.114267166G>A			114486615	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	7.491	0.650674	0.14516	.	.	ENSG00000145362	ENST00000514960;ENST00000504415	.	.	.	5.89	-6.29	0.02013	.	.	.	.	.	T	0.36248	0.0960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39121	-0.9629	4	.	.	.	.	2.3502	0.04281	0.2541:0.1865:0.3769:0.1825	.	.	.	.	N	466;106	.	.	D	+	1	0	ANK2	114486615	0.000000	0.05858	0.176000	0.23000	0.989000	0.77384	-2.212000	0.01225	-1.090000	0.03069	0.585000	0.79938	GAT		0.393	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114267166	G	A	114267166	2	1	29	1	0	0	0	0	0	0	0	1	621	1045	37	1		1	ANK2	4	114267166	Silent	SNP	G	TCGA-AG-3602-01A-02W-0833-10	47910927	114267166	76887110	17	2509										
APC	324	hgsc.bcm.edu	37	chr5	112175328	112175328	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ttctagtttatcttcagaatCagccaggcacaaagctgttg	8	9	4	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr5:112175328C>G	ENST00000457016.1	+	16	4417	c.4037C>G	c.(4036-4038)tCa>tGa	p.S1346*	APC_ENST00000508376.2_Nonsense_Mutation_p.S1346*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1346*			P25054	APC_HUMAN	adenomatous polyposis coli	1346	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1346*(14)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTTCAGAATCAGCCAGGCAC	0.483		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	16	Substitution - Nonsense(14)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(14)|soft_tissue(1)|skin(1)	5											59	63	61					5																	112175328		2202	4300	6502	112203227	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4037C>G	5.37:g.112175328C>G	ENSP00000413133:p.Ser1346*		112203227	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.934355	0.99008	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.386425	0.26734	N	0.022770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.3113	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1346	.	.	S	+	2	0	APC	112203227	0.997000	0.39634	0.940000	0.37924	0.981000	0.71138	5.272000	0.65559	2.861000	0.98227	0.655000	0.94253	TCA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175328	C	G	112175328	4	3	29	1	0	0	0	0	0	1	0	0	763	838	29	5	4095	5	APC	5	112175328	Nonsense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		112175328	68739932	18	2510										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170598234	170598234	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	acaaaccttaaatactggggAagatatgagcctgtaatttc	8	7	0	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr5:170598234A>G	ENST00000523189.1	+	16	1973	c.1809A>G	c.(1807-1809)ggA>ggG	p.G603G	RANBP17_ENST00000521759.1_Intron	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	603					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.G603G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AATACTGGGGAAGATATGAGC	0.313			T	TRD@	ALL																																		Dom	yes		5	5q34	64901	RAN binding protein 17		L	1	Substitution - coding silent(1)	large_intestine(1)	5											134	130	132					5																	170598234		2203	4295	6498	170530839	SO:0001819	synonymous_variant	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1809A>G	5.37:g.170598234A>G			170530839	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																				0.313	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		G	170598234	A	G	170598234	2	3	29	1	0	0	0	0	0	0	0	1	13064	233	9	4		4	RANBP17	5	170598234	Silent	SNP	A	TCGA-AG-3602-01A-02W-0833-10	58422906	170598234	10317026	19	2511										
STK10	6793	hgsc.bcm.edu	37	chr5	171534792	171534792	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tacacgactcaccagtaaggCgtgccgatgaaggaatctcg	11	11	2	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr5:171534792C>T	ENST00000176763.5	-	5	928	c.585G>A	c.(583-585)acG>acA	p.T195T		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	195	Activation segment.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.T195T(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACCAGTAAGGCGTGCCGATGA	0.498											OREG0017039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	5											90	87	88					5																	171534792		2203	4300	6503	171467397	SO:0001819	synonymous_variant	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.585G>A	5.37:g.171534792C>T		1893	171467397	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																				0.498	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		T	171534792	C	T	171534792	2	4	29	1	0	0	0	0	0	0	0	1	15325	755	27	1		1	STK10	5	171534792	Silent	SNP	C	TCGA-AG-3602-01A-02W-0833-10	936558	171534792	9380468	20	2512										
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135260508	135260508	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ccatcgctggagctatcttcCaggtcagcaagtagagtggc	12	11	2	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr6:135260508C>T	ENST00000265605.2	-	4	556	c.488G>A	c.(487-489)tGg>tAg	p.W163*	ALDH8A1_ENST00000367845.2_Nonsense_Mutation_p.W163*|RP11-349J5.2_ENST00000416448.2_RNA|ALDH8A1_ENST00000367847.2_Intron	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	163					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)	p.W163*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		AGCTATCTTCCAGGTCAGCAA	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											95	83	88					6																	135260508		2203	4300	6503	135302201	SO:0001587	stop_gained	64577			AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.488G>A	6.37:g.135260508C>T	ENSP00000265605:p.Trp163*		135302201	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Nonsense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	C	37	6.225861	0.97394	.	.	ENSG00000118514	ENST00000265605;ENST00000367845	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2831	0.94060	0.0:1.0:0.0:0.0	.	.	.	.	X	163	.	ENSP00000265605:W163X	W	-	2	0	ALDH8A1	135302201	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.548000	0.85928	0.563000	0.77884	TGG		0.542	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			T	135260508	C	T	135260508	4	4	29	1	0	0	0	0	0	1	0	0	505	595	21	3	991	3	ALDH8A1	6	135260508	Nonsense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		135260508	35854559	21	2513										
TTLL2	83887	hgsc.bcm.edu	37	chr6	167753657	167753657	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	cttgaagccgctggtttttcGcgttgacgagaccaccccgg	12	13	0	3	rs553495918		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr6:167753657G>A	ENST00000239587.5	+	3	357	c.269G>A	c.(268-270)cGc>cAc	p.R90H		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	90	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)	p.R90H(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CTGGTTTTTCGCGTTGACGAG	0.522													G|||	1	0.000199681	8e-04	0	5008	,	,		19861	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											51	52	51					6																	167753657		2203	4300	6503	167673647	SO:0001583	missense	83887			AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.269G>A	6.37:g.167753657G>A	ENSP00000239587:p.Arg90His		167673647	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598208	0.28445	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02763	4.17	3.37	-0.717	0.11208	.	0.282248	0.26582	N	0.023563	T	0.00784	0.0026	L	0.53617	1.68	0.09310	N	1	P	0.43750	0.816	B	0.29524	0.103	T	0.50874	-0.8776	10	0.72032	D	0.01	.	5.1128	0.14819	0.2806:0.15:0.5694:0.0	.	90	Q9BWV7	TTLL2_HUMAN	H	90;17	ENSP00000239587:R90H	ENSP00000239587:R90H	R	+	2	0	TTLL2	167673647	0.009000	0.17119	0.002000	0.10522	0.008000	0.06430	1.134000	0.31442	-0.319000	0.08652	0.484000	0.47621	CGC		0.522	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167753657	G	A	167753657	3	1	29	1	0	0	0	0	1	0	0	0	16767	1087	38	1	279	1	TTLL2	6	167753657	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	32493149	167753657	3361410	22	2514										
RAMP3	10268	hgsc.bcm.edu	37	chr7	45222943	45222943	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tcccgctgatcgttatacccGtcgttctgactgtcgccatg	9	14	1	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr7:45222943G>A	ENST00000242249.4	+	3	417	c.379G>A	c.(379-381)Gtc>Atc	p.V127I	RAMP3_ENST00000481345.1_Missense_Mutation_p.V127I|RAMP3_ENST00000496212.1_Missense_Mutation_p.V127I	NM_005856.2	NP_005847.1	O60896	RAMP3_HUMAN	receptor (G protein-coupled) activity modifying protein 3	127					calcium ion transport (GO:0006816)|cellular response to estradiol stimulus (GO:0071392)|G-protein coupled receptor signaling pathway involved in heart process (GO:0086103)|intracellular protein transport (GO:0006886)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of receptor recycling (GO:0001921)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.V127I(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	11					Pramlintide(DB01278)	CGTTATACCCGTCGTTCTGAC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	7											130	123	125					7																	45222943		2203	4300	6503	45189468	SO:0001583	missense	10268			AJ001016	CCDS5503.1	7p13-p12	2006-11-21	2006-11-21		ENSG00000122679	ENSG00000122679		"Receptor (G protein-coupled) activity modifying proteins"	9845	protein-coding gene	gene with protein product		605155	"receptor activity modifying protein 3", "receptor (calcitonin) activity modifying protein 3"				Standard	NM_005856		Approved		uc003tnb.3	O60896	OTTHUMG00000023729	ENST00000242249.4:c.379G>A	7.37:g.45222943G>A	ENSP00000242249:p.Val127Ile		45189468	Q7Z2Y1	Missense_Mutation	SNP	ENST00000242249.4	37	CCDS5503.1	.	.	.	.	.	.	.	.	.	.	G	1.747	-0.490277	0.04322	.	.	ENSG00000122679	ENST00000242249;ENST00000481345;ENST00000496212	T;T;T	0.36520	1.25;1.25;1.25	4.37	-0.78	0.10969	.	0.204202	0.41194	N	0.000935	T	0.16471	0.0396	N	0.11789	0.175	0.09310	N	0.999994	P	0.47841	0.901	B	0.40677	0.337	T	0.36311	-0.9753	10	0.22706	T	0.39	-18.4473	8.6703	0.34145	0.4361:0.0:0.5639:0.0	.	127	O60896	RAMP3_HUMAN	I	127	ENSP00000242249:V127I;ENSP00000419012:V127I;ENSP00000418460:V127I	ENSP00000242249:V127I	V	+	1	0	RAMP3	45189468	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	3.751000	0.55165	-0.608000	0.05731	-0.793000	0.03317	GTC		0.622	RAMP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251343.1	NM_005856		A	45222943	G	A	45222943	3	1	29	1	0	0	0	0	1	0	0	0	13060	1145	40	1	389	1	RAMP3	7	45222943	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10		45222943	113915720	23	2515										
CPSF4	10898	hgsc.bcm.edu	37	chr7	99051673	99051673	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ctcccaatcagcagagaaccCcgcaggtcatcggggtcatg	11	14	3	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr7:99051673C>A	ENST00000292476.5	+	7	665	c.655C>A	c.(655-657)Ccg>Acg	p.P219T	CPSF4_ENST00000441580.1_Missense_Mutation_p.P141T|ATP5J2_ENST00000466753.1_Intron|PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000451876.1_Missense_Mutation_p.P161T|ATP5J2-PTCD1_ENST00000413834.1_Intron|CPSF4_ENST00000436336.2_Missense_Mutation_p.P194T|ATP5J2-PTCD1_ENST00000437572.1_Intron			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	219					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P219T(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GCAGAGAACCCCGCAGGTCAT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	7											155	168	163					7																	99051673		2203	4300	6503	98889609	SO:0001583	missense	10898				CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"cleavage and polyadenylation specific factor 4, 30kD subunit"			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.655C>A	7.37:g.99051673C>A	ENSP00000292476:p.Pro219Thr		98889609	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Missense_Mutation	SNP	ENST00000292476.5	37	CCDS5664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.98|14.98	2.697344|2.697344	0.48202|0.48202	.|.	.|.	ENSG00000160917|ENSG00000160917	ENST00000440514|ENST00000436336;ENST00000451876;ENST00000292476;ENST00000441580	.|T;T;T;T	.|0.29655	.|1.98;1.93;1.94;1.56	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.151008|0.151008	0.64402|0.64402	D|D	0.000014|0.000014	T|T	0.24661|0.24661	0.0598|0.0598	L|L	0.27053|0.27053	0.805|0.805	0.58432|0.58432	D|D	0.999994|0.999994	.|B;B;B;B	.|0.06786	.|0.0;0.001;0.001;0.001	.|B;B;B;B	.|0.08055	.|0.0;0.001;0.003;0.001	T|T	0.07424|0.07424	-1.0773|-1.0773	6|10	.|0.14656	.|T	.|0.56	-14.7418|-14.7418	19.7534|19.7534	0.96277|0.96277	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|141;193;219;194	.|B7Z7B0;O95639-3;O95639;O95639-2	.|.;.;CPSF4_HUMAN;.	H|T	100|194;161;219;141	.|ENSP00000395311:P194T;ENSP00000396060:P161T;ENSP00000292476:P219T;ENSP00000402224:P141T	.|ENSP00000292476:P219T	P|P	+|+	2|1	0|0	CPSF4|CPSF4	98889609|98889609	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.841000|0.841000	0.47740|0.47740	5.076000|5.076000	0.64413|0.64413	2.686000|2.686000	0.91538|0.91538	0.655000|0.655000	0.94253|0.94253	CCC|CCG		0.557	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1			A	99051673	C	A	99051673	3	1	29	1	0	0	0	0	1	0	0	0	3834	623	22	2	681	2	CPSF4	7	99051673	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	53828730	99051673	60086990	24	2516										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518637	113518637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	atgttatatttccagtgccaCatttctccctgtcatgtgtc	6	11	2	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr7:113518637C>T	ENST00000284601.3	-	4	2578	c.2510G>A	c.(2509-2511)tGt>tAt	p.C837Y		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	837					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.C837Y(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TCCAGTGCCACATTTCTCCCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											186	167	174					7																	113518637		2203	4300	6503	113305873	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2510G>A	7.37:g.113518637C>T	ENSP00000284601:p.Cys837Tyr		113305873	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.382644	0.01204	.	.	ENSG00000154415	ENST00000284601	T	0.15256	2.44	5.92	-10.5	0.00291	.	2.314490	0.01258	N	0.009080	T	0.08358	0.0208	L	0.36672	1.1	0.09310	N	1	B	0.23490	0.086	B	0.19148	0.024	T	0.31724	-0.9933	10	0.06757	T	0.87	-0.2139	3.1724	0.06556	0.2057:0.3157:0.0732:0.4054	.	837	Q16821	PPR3A_HUMAN	Y	837	ENSP00000284601:C837Y	ENSP00000284601:C837Y	C	-	2	0	PPP1R3A	113305873	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.571000	0.05889	-2.070000	0.00881	-1.284000	0.01376	TGT		0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113518637	C	T	113518637	3	4	29	1	0	0	0	0	1	0	0	0	12405	478	17	3	862	3	PPP1R3A	7	113518637	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	14466964	113518637	45620026	25	2517										
ESYT2	57488	hgsc.bcm.edu	37	chr7	158528258	158528258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tcttcacggcaacgtcgagcGttctcctctgcacttctggt	9	14	5	0	rs145653899	byFrequency	TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr7:158528258G>A	ENST00000251527.5	-	20	2587	c.2522C>T	c.(2521-2523)aCg>aTg	p.T841M	ESYT2_ENST00000435514.2_Missense_Mutation_p.T276M	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	869	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.T841M(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						AACGTCGAGCGTTCTCCTCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7							MET/THR	0,4406		0,0,2203	147	152	150		2522	5.6	0.9	7	dbSNP_134	150	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ESYT2	NM_020728.2	81	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	841/894	158528258	3,13003	2203	4300	6503	158221019	SO:0001583	missense	57488			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2522C>T	7.37:g.158528258G>A	ENSP00000251527:p.Thr841Met		158221019	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.519471	0.44866	0.0	3.49E-4	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514	T;T;T	0.09073	3.02;3.02;3.02	5.59	5.59	0.84812	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048174	0.85682	D	0.000000	T	0.26521	0.0648	L	0.54965	1.715	0.58432	D	0.999999	D;D	0.89917	1.0;0.957	D;P	0.97110	1.0;0.735	T	0.00086	-1.2094	10	0.48119	T	0.1	-17.4245	18.5774	0.91159	0.0:0.0:1.0:0.0	.	841;869	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	M	841;890;832;276	ENSP00000251527:T841M;ENSP00000275418:T832M;ENSP00000411488:T276M	ENSP00000251527:T841M	T	-	2	0	ESYT2	158221019	1.000000	0.71417	0.853000	0.33588	0.007000	0.05969	6.189000	0.72051	2.639000	0.89480	0.655000	0.94253	ACG		0.458	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		A	158528258	G	A	158528258	3	1	29	1	0	0	0	0	1	0	0	0	5278	1145	40	1	171	1	ESYT2	7	158528258	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	45009621	158528258	610405	26	2518										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31812949	31812949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	accgcccaaaaagaaaatgcGgaagacagaaaatggaatgt	10	7	0	3	rs35653460		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr10:31812949G>A	ENST00000320985.10	+	8	2800	c.2690G>A	c.(2689-2691)cGg>cAg	p.R897Q	ZEB1_ENST00000542815.3_Missense_Mutation_p.R830Q|ZEB1_ENST00000446923.2_Missense_Mutation_p.R881Q|ZEB1_ENST00000560721.2_Missense_Mutation_p.R877Q|ZEB1_ENST00000361642.5_Missense_Mutation_p.R898Q			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	897					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R897Q(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AAGAAAATGCGGAAGACAGAA	0.373																																					Ovarian(40;423 959 14296 36701 49589)											1	Substitution - Missense(1)	large_intestine(1)	10						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	111	111	111		2642,2630,2639,2489,2693,2690	4.8	1	10	dbSNP_126	111	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	ZEB1	NM_001128128.2,NM_001174093.1,NM_001174094.1,NM_001174095.1,NM_001174096.1,NM_030751.5	43,43,43,43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	881/1109,877/1105,880/1108,830/1058,898/1126,897/1125	31812949	1,13005	2203	4300	6503	31852955	SO:0001583	missense	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2690G>A	10.37:g.31812949G>A	ENSP00000319248:p.Arg897Gln		31852955	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833834	0.71258	2.27E-4	0.0	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.72	4.8	0.61643	.	0.369405	0.21055	N	0.080939	T	0.14184	0.0343	L	0.27053	0.805	0.37448	D	0.91469	D;P;P;P;P	0.69078	0.997;0.913;0.574;0.913;0.913	D;B;B;B;B	0.64144	0.922;0.174;0.068;0.129;0.089	T	0.12811	-1.0533	10	0.41790	T	0.15	-12.9237	10.1047	0.42526	0.071:0.1383:0.7907:0.0	rs35653460	830;881;877;898;897	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	Q	679;897;898;892;830;897;877;788;881	ENSP00000444282:R679Q;ENSP00000354487:R898Q;ENSP00000444891:R830Q;ENSP00000319248:R897Q;ENSP00000391612:R881Q	ENSP00000319248:R897Q	R	+	2	0	ZEB1	31852955	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.665000	0.68052	1.410000	0.46936	0.585000	0.79938	CGG		0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		A	31812949	G	A	31812949	3	1	29	1	0	0	0	0	1	0	0	0	17662	1116	39	1	2734	1	ZEB1	10	31812949	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10		31812949	103721798	27	2519										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62648035	62648035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tccttacgtgaaaggctttcGtaatctcctggttcatgaag	9	9	2	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr10:62648035G>A	ENST00000337910.5	-	6	1728	c.1391C>T	c.(1390-1392)aCg>aTg	p.T464M	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.T464M	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	464					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.T464M(2)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					AAAGGCTTTCGTAATCTCCTG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	10											111	102	105					10																	62648035		2203	4300	6503	62318041	SO:0001583	missense	9886			AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1391C>T	10.37:g.62648035G>A	ENSP00000338671:p.Thr464Met		62318041		Missense_Mutation	SNP	ENST00000337910.5	37	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.322517	0.81580	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.16743	2.32;2.32	5.71	5.71	0.89125	BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.32771	-0.9894	10	0.49607	T	0.09	.	19.8677	0.96824	0.0:0.0:1.0:0.0	.	464	O94844	RHBT1_HUMAN	M	464	ENSP00000350595:T464M;ENSP00000338671:T464M	ENSP00000338671:T464M	T	-	2	0	RHOBTB1	62318041	1.000000	0.71417	0.943000	0.38184	0.970000	0.65996	9.803000	0.99136	2.709000	0.92574	0.655000	0.94253	ACG		0.507	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			A	62648035	G	A	62648035	3	1	29	1	0	0	0	0	1	0	0	0	13370	1145	40	1	723	1	RHOBTB1	10	62648035	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10	30835086	62648035	72886712	28	2520										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7526002	7526002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	actgccatatggagatatgcGttttaggacactgaatgtca	10	7	1	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr12:7526002G>A	ENST00000313599.3	-	14	3701	c.3644C>T	c.(3643-3645)aCg>aTg	p.T1215M	CD163L1_ENST00000396630.1_Missense_Mutation_p.T1215M|CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Missense_Mutation_p.T1225M			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1215	SRCR 11. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.T1215M(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						GGAGATATGCGTTTTAGGACA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											149	121	130					12																	7526002		2203	4300	6503	7417269	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3644C>T	12.37:g.7526002G>A	ENSP00000315945:p.Thr1215Met		7417269	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	2.333	-0.352846	0.05173	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.37058	1.22;1.22;1.22	2.25	-4.5	0.03493	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.309370	0.06101	N	0.665345	T	0.23926	0.0579	L	0.38838	1.175	0.09310	N	1	B;B	0.21753	0.015;0.06	B;B	0.24848	0.01;0.056	T	0.13953	-1.0490	10	0.27082	T	0.32	.	3.4183	0.07384	0.5963:0.1674:0.132:0.1043	.	1225;1215	E7EVK4;Q9NR16	.;C163B_HUMAN	M	1215;1225;1215	ENSP00000315945:T1215M;ENSP00000393474:T1225M;ENSP00000379871:T1215M	ENSP00000315945:T1215M	T	-	2	0	CD163L1	7417269	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	-1.169000	0.03120	-2.706000	0.00396	-0.693000	0.03709	ACG		0.527	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7526002	G	A	7526002	3	1	29	1	0	0	0	0	1	0	0	0	2974	1145	40	1	741	1	CD163L1	12	7526002	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10		7526002	126325893	29	2521										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	29	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	17872282	25398284	108453611	30	2522										
DHX37	57647	hgsc.bcm.edu	37	chr12	125453485	125453485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tccacccgcagcgtggccgaCatgatgagcagcttgagtgg	14	12	0	3			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr12:125453485C>T	ENST00000308736.2	-	9	1319	c.1221G>A	c.(1219-1221)atG>atA	p.M407I	DHX37_ENST00000544745.1_Missense_Mutation_p.M194I	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	407	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.M407I(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GCGTGGCCGACATGATGAGCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	12											81	60	67					12																	125453485		2203	4300	6503	124019438	SO:0001583	missense	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1221G>A	12.37:g.125453485C>T	ENSP00000311135:p.Met407Ile		124019438	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069997	0.93950	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.10763	2.84;2.84	4.82	4.82	0.62117	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	H	0.98111	4.15	0.80722	D	1	D	0.63880	0.993	D	0.71656	0.974	T	0.71919	-0.4447	10	0.87932	D	0	-4.3043	17.8635	0.88789	0.0:1.0:0.0:0.0	.	407	Q8IY37	DHX37_HUMAN	I	407;194	ENSP00000311135:M407I;ENSP00000439009:M194I	ENSP00000311135:M407I	M	-	3	0	DHX37	124019438	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.239000	0.78182	2.382000	0.81193	0.561000	0.74099	ATG		0.617	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		T	125453485	C	T	125453485	3	4	29	1	0	0	0	0	1	0	0	0	4521	478	17	3	2328	3	DHX37	12	125453485	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	100055201	125453485	8398410	31	2523										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36428647	36428647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tttccttaccctctgcttccGcaggcttcctgggctggtgg	11	14	1	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr13:36428647G>A	ENST00000360631.3	-	6	1235	c.1024C>T	c.(1024-1026)Cgg>Tgg	p.R342W	DCLK1_ENST00000379892.4_Missense_Mutation_p.R342W|DCLK1_ENST00000379893.1_Missense_Mutation_p.R35W|DCLK1_ENST00000255448.4_Missense_Mutation_p.R342W|DCLK1_ENST00000460982.1_5'UTR			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	342					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.R342W(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CTCTGCTTCCGCAGGCTTCCT	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	13											126	105	112					13																	36428647		2203	4300	6503	35326647	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1024C>T	13.37:g.36428647G>A	ENSP00000353846:p.Arg342Trp		35326647	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	26.7	4.758816	0.89843	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893;ENST00000539451;ENST00000379892	T;T;T;T	0.69806	-0.43;-0.42;-0.38;1.6	5.67	5.67	0.87782	.	0.054463	0.64402	D	0.000001	T	0.78761	0.4334	M	0.61703	1.905	0.58432	D	0.999992	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.69479	0.964;0.921;0.964	T	0.80231	-0.1468	10	0.87932	D	0	.	14.5943	0.68395	0.0:0.0:0.8542:0.1458	.	35;342;35	O15075-4;O15075-2;O15075-3	.;.;.	W	34;342;342;35;342;342	ENSP00000255448:R342W;ENSP00000353846:R342W;ENSP00000369223:R35W;ENSP00000369222:R342W	ENSP00000255448:R342W	R	-	1	2	DCLK1	35326647	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.382000	0.52463	2.687000	0.91594	0.655000	0.94253	CGG		0.537	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36428647	G	A	36428647	3	1	29	1	0	0	0	0	1	0	0	0	4297	1086	38	1	1217	1	DCLK1	13	36428647	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10		36428647	78741231	32	2524										
GPR183	1880	hgsc.bcm.edu	37	chr13	99947989	99947989	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ctttttatcttgttgtagcgTagagggtgcaccacagcaat	10	8	1	1	rs530898155	byFrequency	TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr13:99947989T>G	ENST00000376414.4	-	2	494	c.411A>C	c.(409-411)ctA>ctC	p.L137L	UBAC2_ENST00000403766.3_Intron|UBAC2_ENST00000376440.2_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	137					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)	p.L137L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						TGTTGTAGCGTAGAGGGTGCA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	13											161	128	139					13																	99947989		2203	4300	6503	98745990	SO:0001819	synonymous_variant	1880			L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"GPCR / Class A : Orphans"	3128	protein-coding gene	gene with protein product	"EBV-induced G-protein coupled receptor 2"	605741	"Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.411A>C	13.37:g.99947989T>G			98745990	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	37	CCDS9492.1																																																																																				0.438	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		G	99947989	T	G	99947989	2	3	29	1	0	0	0	0	0	0	0	1	6698	1625	57	4		4	GPR183	13	99947989	Silent	SNP	T	TCGA-AG-3602-01A-02W-0833-10	63519342	99947989	15221889	33	2525										
F10	2159	hgsc.bcm.edu	37	chr13	113803789	113803789	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	aggggcttgcccaaggccaaGagccatgccccggaggtcat	14	13	1	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr13:113803789G>A	ENST00000375559.3	+	8	1463	c.1425G>A	c.(1423-1425)aaG>aaA	p.K475K	F10_ENST00000375551.3_3'UTR	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	475					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)	p.K475K(1)		endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	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;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	CCAAGGCCAAGAGCCATGCCC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	13											113	97	103					13																	113803789		2203	4300	6503	112851790	SO:0001819	synonymous_variant	2159				CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.1425G>A	13.37:g.113803789G>A			112851790	Q14340	Silent	SNP	ENST00000375559.3	37	CCDS9530.1																																																																																				0.582	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			A	113803789	G	A	113803789	2	1	29	1	0	0	0	0	0	0	0	1	5349	933	33	3		3	F10	13	113803789	Silent	SNP	G	TCGA-AG-3602-01A-02W-0833-10	13855800	113803789	1366089	34	2526										
ERN2	5347	hgsc.bcm.edu	37	chr16	23702270	23702270	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ggtgcgtgtggaggagcagcCgtgggaagcggtttgtgaag	21	5	0	1	rs377283392		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr16:23702270C>T	ENST00000300093.4	+	0	2227				ERN2_ENST00000457008.2_Missense_Mutation_p.R836Q|CTD-2196E14.5_ENST00000566143.1_RNA|ERN2_ENST00000256797.4_Missense_Mutation_p.R936Q	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1						activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.R936Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		GAGGAGCAGCCGTGGGAAGCG	0.627																																					Colon(12;240 564 27038 33155)											1	Substitution - Missense(1)	large_intestine(1)	16											68	66	66					16																	23702270		2197	4300	6497	23609771	SO:0001628	intergenic_variant	10595				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984		16.37:g.23702270C>T			23609771	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	4.439	0.081159	0.08533	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.29142	1.58;1.58	5.22	-3.28	0.05033	.	0.708209	0.13566	N	0.378434	T	0.14527	0.0351	L	0.28458	0.855	0.22601	N	0.998946	B;B	0.26081	0.141;0.023	B;B	0.19666	0.013;0.026	T	0.25572	-1.0128	10	0.18276	T	0.48	.	4.4086	0.11421	0.24:0.3856:0.0:0.3743	.	836;888	E7ETG2;A5YM65	.;.	Q	936;836	ENSP00000256797:R936Q;ENSP00000413812:R836Q	ENSP00000256797:R936Q	R	-	2	0	ERN2	23609771	0.000000	0.05858	0.028000	0.17463	0.007000	0.05969	-0.248000	0.08854	-0.173000	0.10761	-1.332000	0.01269	CGG		0.627	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		T	23702270	C	T	23702270	1	4	29	0	1	0	0	0	0	0	0	0	5251	652	23	1		1	ERN2	16	23702270	IGR	SNP	C	TCGA-AG-3602-01A-02W-0833-10		23702270	66652483	35	2527										
CDYL2	124359	hgsc.bcm.edu	37	chr16	80654809	80654809	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tctgtggctgcgttgcagagCgctcgccggacttctttcat	12	12	3	1	rs200676958		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr16:80654809C>T	ENST00000570137.2	-	4	1013	c.858G>A	c.(856-858)gcG>gcA	p.A286A	CDYL2_ENST00000562812.1_Silent_p.A287A|CDYL2_ENST00000563890.1_Silent_p.A287A|CDYL2_ENST00000566173.1_Silent_p.A287A	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	286						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.A286A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						CGTTGCAGAGCGCTCGCCGGA	0.557													C|||	1	0.000199681	0	0	5008	,	,		17985	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16						C		0,4406		0,0,2203	48	43	44		858	-10.6	0.2	16		44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDYL2	NM_152342.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		286/507	80654809	1,13005	2203	4300	6503	79212310	SO:0001819	synonymous_variant	124359			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"chromodomain Y-like protein 2"			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.858G>A	16.37:g.80654809C>T			79212310	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																				0.557	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		T	80654809	C	T	80654809	2	4	29	1	0	0	0	0	0	0	0	1	3192	755	27	1		1	CDYL2	16	80654809	Silent	SNP	C	TCGA-AG-3602-01A-02W-0833-10	56952539	80654809	9699944	36	2528										
TP53	7157	hgsc.bcm.edu	37	chr17	7578470	7578470	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	catggcgcggacgcgggtgcCgggcgggggtgtggaatcaa	21	9	1	0	rs137852790|rs137852791|rs137852789		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr17:7578470C>A	ENST00000269305.4	-	5	649	c.460G>T	c.(460-462)Ggc>Tgc	p.G154C	TP53_ENST00000455263.2_Missense_Mutation_p.G154C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.G154C|TP53_ENST00000445888.2_Missense_Mutation_p.G154C|TP53_ENST00000420246.2_Missense_Mutation_p.G154C|TP53_ENST00000413465.2_Missense_Mutation_p.G154C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	154	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in a sporadic cancer; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> I (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> S (in sporadic cancers; somatic mutation).|G -> V (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G154S(9)|p.0?(8)|p.T150fs*16(6)|p.?(5)|p.P152fs*14(5)|p.G154C(4)|p.G154I(3)|p.G154fs*14(2)|p.P153fs*26(2)|p.P153fs*22(2)|p.G154fs*27(2)|p.P151_V173del23(1)|p.G154_R156delGTR(1)|p.G22C(1)|p.Q144_G154del11(1)|p.T57fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.D148fs*23(1)|p.G61C(1)|p.S149fs*72(1)|p.G154fs*22(1)|p.Q144fs*16(1)|p.P153_G154insX(1)|p.T18fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACGCGGGTGCCGGGCGGGGGT	0.612		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	61	Deletion - Frameshift(23)|Substitution - Missense(18)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(2)|Insertion - In frame(1)	large_intestine(9)|stomach(8)|skin(8)|ovary(8)|oesophagus(5)|lung(4)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|liver(2)|cervix(1)|soft_tissue(1)|urinary_tract(1)|pancreas(1)	17	GRCh37	CD090894	TP53	D	rs137852789						50	51	51					17																	7578470		2203	4300	6503	7519195	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.460G>T	17.37:g.7578470C>A	ENSP00000269305:p.Gly154Cys		7519195	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616540	0.46736	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99901	-7.65;-7.65;-7.65;-7.65;-7.65;-7.65;-7.65;-7.65;-7.65	5.59	3.61	0.41365	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.158634	0.56097	D	0.000036	D	0.99878	0.9942	M	0.90759	3.145	0.53688	D	0.999978	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.996;0.997;0.95;0.995;0.999;0.996;0.998	D	0.96970	0.9708	10	0.87932	D	0	-10.7989	10.674	0.45774	0.0:0.8435:0.0:0.1565	.	115;154;154;61;154;154;154	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	154;154;154;154;154;154;143;61;22;61;22;154	ENSP00000410739:G154C;ENSP00000352610:G154C;ENSP00000269305:G154C;ENSP00000398846:G154C;ENSP00000391127:G154C;ENSP00000391478:G154C;ENSP00000425104:G22C;ENSP00000423862:G61C;ENSP00000424104:G154C	ENSP00000269305:G154C	G	-	1	0	TP53	7519195	0.990000	0.36364	0.002000	0.10522	0.004000	0.04260	4.065000	0.57513	0.846000	0.35142	0.655000	0.94253	GGC		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578470	C	A	7578470	3	1	29	1	0	0	0	0	1	0	0	0	16421	652	23	2	838	2	TP53	17	7578470	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		7578470	73616740	37	2529										
MYH1	4619	hgsc.bcm.edu	37	chr17	10409146	10409146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gacctctgtttgaagtctgcAtaaaggattctgcttgggaa	11	7	3	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr17:10409146A>G	ENST00000226207.5	-	19	2251	c.2157T>C	c.(2155-2157)taT>taC	p.Y719Y	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	719	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Y719Y(2)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TGAAGTCTGCATAAAGGATTC	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	17											53	50	51					17																	10409146		2203	4300	6503	10349871	SO:0001819	synonymous_variant	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2157T>C	17.37:g.10409146A>G			10349871	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																				0.408	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10409146	A	G	10409146	2	3	29	1	0	0	0	0	0	0	0	1	10059	224	8	4		4	MYH1	17	10409146	Silent	SNP	A	TCGA-AG-3602-01A-02W-0833-10	2830676	10409146	70786064	38	2530										
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21205470	21205470	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	cacagggagacgtgtggatcTgcatggagctcatggacaca	14	9	2	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr17:21205470T>A	ENST00000342679.4	+	6	664	c.415T>A	c.(415-417)Tgc>Agc	p.C139S	MAP2K3_ENST00000361818.5_Missense_Mutation_p.C110S|MAP2K3_ENST00000316920.6_Missense_Mutation_p.C110S	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.C143S(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CGTGTGGATCTGCATGGAGCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											120	95	104					17																	21205470		2203	4300	6503	21146063	SO:0001583	missense	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.415T>A	17.37:g.21205470T>A	ENSP00000345083:p.Cys139Ser		21146063	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.689565	0.48097	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;T	0.64991	1.12;1.12;-0.13	5.17	5.17	0.71159	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56140	0.1965	L	0.36672	1.1	0.80722	D	1	B	0.23377	0.084	B	0.28139	0.086	T	0.57670	-0.7771	10	0.87932	D	0	-30.6155	15.046	0.71827	0.0:0.0:0.0:1.0	.	139	P46734	MP2K3_HUMAN	S	139;110;110;110;143	ENSP00000345083:C139S;ENSP00000355081:C110S;ENSP00000434068:C110S	ENSP00000319139:C143S	C	+	1	0	MAP2K3	21146063	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.947000	0.87758	1.942000	0.56320	0.533000	0.62120	TGC		0.587	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		A	21205470	T	A	21205470	3	1	29	1	0	0	0	0	1	0	0	0	9268	1580	55	5	437	5	MAP2K3	17	21205470	Missense_Mutation	SNP	T	TCGA-AG-3602-01A-02W-0833-10	10796324	21205470	59989740	39	2531										
MED24	9862	hgsc.bcm.edu	37	chr17	38178692	38178692	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ttctggcgggtggacgcctgTcccttgtgggaggagtagga	18	8	1	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr17:38178692T>G	ENST00000394128.2	-	22	2559	c.2478A>C	c.(2476-2478)ggA>ggC	p.G826G	MED24_ENST00000501516.3_Silent_p.G845G|MED24_ENST00000394126.1_Silent_p.G851G|MED24_ENST00000356271.3_Silent_p.G813G|MED24_ENST00000394127.2_Silent_p.G813G	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	826					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.G826G(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TGGACGCCTGTCCCTTGTGGG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	17											43	40	41					17																	38178692		2203	4300	6503	35432218	SO:0001819	synonymous_variant	9862			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2478A>C	17.37:g.38178692T>G			35432218	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	T	9.097	1.003102	0.19121	.	.	ENSG00000008838	ENST00000422942	.	.	.	5.33	-9.94	0.00449	.	.	.	.	.	T	0.33789	0.0875	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42241	-0.9463	4	.	.	.	-6.4149	2.512	0.04659	0.1516:0.2535:0.3677:0.2273	.	.	.	.	P	81	.	.	T	-	1	0	MED24	35432218	0.009000	0.17119	0.848000	0.33437	0.656000	0.38851	-1.221000	0.02968	-1.527000	0.01758	-0.261000	0.10672	ACA		0.602	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		G	38178692	T	G	38178692	2	3	29	1	0	0	0	0	0	0	0	1	9472	1654	58	4		4	MED24	17	38178692	Silent	SNP	T	TCGA-AG-3602-01A-02W-0833-10	16973222	38178692	43016518	40	2532										
RNF213	57674	hgsc.bcm.edu	37	chr17	78268655	78268655	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gctgcgctcatgctggacagCaccttcagcatcctgcagac	10	15	2	1			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr17:78268655C>G	ENST00000582970.1	+	9	1751	c.1608C>G	c.(1606-1608)agC>agG	p.S536R	RNF213_ENST00000508628.2_Missense_Mutation_p.S585R|RNF213_ENST00000319921.4_Missense_Mutation_p.S536R|RNF213_ENST00000456466.1_Missense_Mutation_p.S536R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	536					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S585R(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TGCTGGACAGCACCTTCAGCA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											109	99	102					17																	78268655		2203	4300	6503	75883250	SO:0001583	missense	57714			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.1608C>G	17.37:g.78268655C>G	ENSP00000464087:p.Ser536Arg		75883250	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	c	3.116	-0.181581	0.06340	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	.	.	.	5.03	0.172	0.15031	.	0.753181	0.11927	N	0.516118	T	0.16811	0.0404	N	0.17674	0.51	0.28672	N	0.905597	B;B	0.11235	0.003;0.004	B;B	0.10450	0.003;0.005	T	0.23476	-1.0187	9	0.20519	T	0.43	-10.6944	0.48	0.00546	0.1816:0.2885:0.1776:0.3523	.	536;536	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	R	536;585;536;536	.	ENSP00000324392:S536R	S	+	3	2	RNF213	75883250	0.001000	0.12720	0.480000	0.27341	0.073000	0.16967	-0.337000	0.07852	0.151000	0.19162	0.457000	0.33378	AGC		0.537	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78268655	C	G	78268655	3	3	29	1	0	0	0	0	1	0	0	0	13514	709	25	5	1789	5	RNF213	17	78268655	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10	40089963	78268655	2926555	41	2533										
SERPINB4	6318	hgsc.bcm.edu	37	chr18	61305192	61305192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ggtcatgcctgagaggtctgCatccccattgaagatattca	10	10	3	3	rs201095674		TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr18:61305192C>T	ENST00000341074.5	-	8	1049	c.934G>A	c.(934-936)Gca>Aca	p.A312T	SERPINB4_ENST00000356424.6_Missense_Mutation_p.A260T	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	312					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A312T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GAGAGGTCTGCATCCCCATTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	18											174	152	159					18																	61305192		2203	4300	6503	59456172	SO:0001583	missense	6318			X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"Serine (or cysteine) peptidase inhibitors"	10570	protein-coding gene	gene with protein product	"squamous cell carcinoma antigen 2"	600518	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.934G>A	18.37:g.61305192C>T	ENSP00000343445:p.Ala312Thr		59456172	A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	CCDS11986.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.275341|4.275341	0.80580|0.80580	.|.	.|.	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424|ENST00000413673	D;D|.	0.87256|.	-2.23;-2.23|.	4.41|4.41	4.41|4.41	0.53225|0.53225	Serpin domain (3);|.	0.173238|.	0.27518|.	N|.	0.019005|.	T|T	0.81341|0.81341	0.4802|0.4802	M|M	0.90483|0.90483	3.12|3.12	0.35153|0.35153	D|D	0.769983|0.769983	D;D;D|.	0.71674|.	0.998;0.998;0.998|.	D;D;D|.	0.67382|.	0.935;0.935;0.951|.	D|D	0.89058|0.89058	0.3460|0.3460	10|5	0.87932|.	D|.	0|.	.|.	16.5216|16.5216	0.84318|0.84318	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	312;312;291|.	Q5K684;P48594;Q9BYF7|.	.;SPB4_HUMAN;.|.	T|I	312;260|292	ENSP00000343445:A312T;ENSP00000348795:A260T|.	ENSP00000343445:A312T|.	A|M	-|-	1|3	0|0	SERPINB4|SERPINB4	59456172|59456172	0.423000|0.423000	0.25482|0.25482	0.281000|0.281000	0.24762|0.24762	0.122000|0.122000	0.20287|0.20287	2.375000|2.375000	0.44283|0.44283	2.431000|2.431000	0.82371|0.82371	0.609000|0.609000	0.83330|0.83330	GCA|ATG		0.498	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		T	61305192	C	T	61305192	3	4	29	1	0	0	0	0	1	0	0	0	14140	710	25	3	242	3	SERPINB4	18	61305192	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		61305192	16772056	42	2534										
FUT3	2525	hgsc.bcm.edu	37	chr19	5844699	5844699	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	gagtggtgtcctgtcgggagGacccactgggagccctaggg	18	10	0	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr19:5844699G>T	ENST00000303225.6	-	3	786	c.152C>A	c.(151-153)tCc>tAc	p.S51Y	FUT3_ENST00000458379.2_Missense_Mutation_p.S51Y|FUT3_ENST00000589918.1_Missense_Mutation_p.S51Y|FUT3_ENST00000589620.1_Missense_Mutation_p.S51Y|FUT3_ENST00000593144.1_5'Flank|AC024592.9_ENST00000589276.1_RNA	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	51					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.S51Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						CTGTCGGGAGGACCCACTGGG	0.617																																					Esophageal Squamous(82;745 1728 24593 44831)											1	Substitution - Missense(1)	large_intestine(1)	19											21	23	22					19																	5844699		2202	4300	6502	5795699	SO:0001583	missense	2525				CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"CD molecules", "Blood group antigens", "Fucosyltransferases"	4014	protein-coding gene	gene with protein product		111100	"fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.152C>A	19.37:g.5844699G>T	ENSP00000305603:p.Ser51Tyr		5795699	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196260	0.38806	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.25250	1.81;1.81	2.33	-0.0794	0.13710	.	1.508160	0.04406	N	0.365254	T	0.40619	0.1124	M	0.61703	1.905	0.09310	N	1	D;D;D;D	0.67145	0.98;0.996;0.98;0.996	P;D;P;D	0.65573	0.873;0.936;0.752;0.936	T	0.31696	-0.9934	10	0.21014	T	0.42	.	4.0367	0.09733	0.1522:0.0:0.6139:0.2339	.	51;51;51;51	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	Y	51	ENSP00000305603:S51Y;ENSP00000416443:S51Y	ENSP00000305603:S51Y	S	-	2	0	FUT3	5795699	0.000000	0.05858	0.000000	0.03702	0.152000	0.21847	0.435000	0.21510	0.221000	0.20879	0.205000	0.17691	TCC		0.617	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		T	5844699	G	T	5844699	3	4	29	1	0	0	0	0	1	0	0	0	6124	1174	41	2	937	2	FUT3	19	5844699	Missense_Mutation	SNP	G	TCGA-AG-3602-01A-02W-0833-10		5844699	53284284	43	2535										
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952078	14952078	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	aggggaccaccgcccagcagCgctactgcaaaatacatcac	9	15	1	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr19:14952078C>T	ENST00000248058.1	-	1	611	c.612G>A	c.(610-612)gcG>gcA	p.A204A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A204A(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					CGCCCAGCAGCGCTACTGCAA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	19											61	59	60					19																	14952078		2203	4300	6503	14813078	SO:0001819	synonymous_variant	390892				CCDS32936.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.612G>A	19.37:g.14952078C>T			14813078	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																				0.453	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		T	14952078	C	T	14952078	2	4	29	1	0	0	0	0	0	0	0	1	11245	755	27	1		1	OR7A10	19	14952078	Silent	SNP	C	TCGA-AG-3602-01A-02W-0833-10	9107379	14952078	44176905	44	2536										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45855080	45855080	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tgcttcggacccaaccacacGctgtaccccatggtcacgcg	9	17	1	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chr21:45855080G>A	ENST00000397928.1	+	28	4486	c.4041G>A	c.(4039-4041)acG>acA	p.T1347T	TRPM2_ENST00000498430.1_3'UTR|snoZ6_ENST00000581669.1_RNA|TRPM2_ENST00000397932.2_Silent_p.T1397T|TRPM2_ENST00000300482.5_Silent_p.T1347T|TRPM2_ENST00000300481.9_Silent_p.T1293T	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1347			T -> M (in dbSNP:rs45589233). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.T1347T(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CCAACCACACGCTGTACCCCA	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	21											81	70	74					21																	45855080		2203	4300	6503	44679508	SO:0001819	synonymous_variant	7226			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.4041G>A	21.37:g.45855080G>A			44679508	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																				0.662	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45855080	G	A	45855080	2	1	29	1	0	0	0	0	0	0	0	1	16626	1074	38	1		1	TRPM2	21	45855080	Silent	SNP	G	TCGA-AG-3602-01A-02W-0833-10		45855080	2274815	45	2537										
YY2	404281	hgsc.bcm.edu	37	chrX	21874924	21874924	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	tggaggaccagttggccctcCcggatagcattgaagacgag	14	10	0	2			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chrX:21874924C>G	ENST00000429584.2	+	1	820	c.322C>G	c.(322-324)Ccg>Gcg	p.P108A	MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000365779.2_Intron|MBTPS2_ENST00000465888.1_3'UTR	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P108A(1)|p.P108>L(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						GTTGGCCCTCCCGGATAGCAT	0.557																																																2	Substitution - Missense(1)|Complex - compound substitution(1)	large_intestine(1)|skin(1)	X											87	70	75					X																	21874924		2203	4300	6503	21784845	SO:0001583	missense	404281			AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.322C>G	X.37:g.21874924C>G	ENSP00000389381:p.Pro108Ala		21784845	B2RP10|Q6Q1S4	Silent	SNP	ENST00000429584.2	37	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325645	0.60743	.	.	ENSG00000230797	ENST00000429584	T	0.12147	2.71	3.99	3.13	0.36017	.	0.069497	0.64402	U	0.000018	T	0.21347	0.0514	M	0.61703	1.905	0.19945	N	0.999948	D	0.58268	0.982	P	0.51415	0.669	T	0.04333	-1.0959	10	0.66056	D	0.02	.	8.8554	0.35225	0.0:0.8853:0.0:0.1147	.	108	O15391	TYY2_HUMAN	A	108	ENSP00000389381:P108A	ENSP00000389381:P108A	P	+	1	0	YY2	21784845	0.058000	0.20735	0.005000	0.12908	0.008000	0.06430	1.830000	0.39131	1.049000	0.40321	0.600000	0.82982	CCG		0.557	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		G	21874924	C	G	21874924	3	3	29	1	0	0	0	0	1	0	0	0	17549	623	22	5	324	5	YY2	23	21874924	Missense_Mutation	SNP	C	TCGA-AG-3602-01A-02W-0833-10		21874924	133395636	46	2538										
RAB40A	142684	hgsc.bcm.edu	37	chrX	102755133	102755133	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0851063829787234	4	1	0.936036036036036	4.32916666666667	0.524747474747475	1	1	0	ctcagtaccttgctcggcctCccgagccaattcatcctgtg	8	16	2	0			TCGA-AG-3602-01A-02W-0833-10	TCGA-AG-3602-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	c261d0ad-5ce8-41b8-9907-9b55015d0a8c	19c61379-5858-4a88-9f7c-ada224980de6	g.chrX:102755133C>T	ENST00000372633.1	-	1	2670	c.552G>A	c.(550-552)ggG>ggA	p.G184G	LL0XNC01-250H12.3_ENST00000445990.1_RNA|RAB40A_ENST00000304236.1_Silent_p.G184G			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	184	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.G184G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						TGCTCGGCCTCCCGAGCCAAT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	X											53	44	48					X																	102755133		2203	4299	6502	102641789	SO:0001819	synonymous_variant	142684			AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"RAB, member RAS oncogene"	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.552G>A	X.37:g.102755133C>T			102641789	O00407|Q17RQ5|Q6DK06|Q8TF06	Silent	SNP	ENST00000372633.1	37	CCDS35357.1																																																																																				0.572	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1			T	102755133	C	T	102755133	2	4	29	1	0	0	0	0	0	0	0	1	12976	842	30	3		3	RAB40A	23	102755133	Silent	SNP	C	TCGA-AG-3602-01A-02W-0833-10	80880209	102755133	52515427	47	2539										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52810593	52810593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gaatgaccaaactgggactaCgtgtgacacttgactcagat	10	9	1	4			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr1:52810593C>T	ENST00000371591.1	+	17	4224	c.4093C>T	c.(4093-4095)Cgt>Tgt	p.R1365C	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.R1306C|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.R1365C	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1365					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)	p.R1365C(1)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						ACTGGGACTACGTGTGACACT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	128	134					1																	52810593		2203	4300	6503	52583181	SO:0001583	missense	9372			AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.4093C>T	1.37:g.52810593C>T	ENSP00000360647:p.Arg1365Cys		52583181	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351164	0.82132	.	.	ENSG00000157077	ENST00000357206;ENST00000287727;ENST00000371591	T;T;T	0.70749	-0.29;-0.51;-0.51	5.16	5.16	0.70880	Domain of unknown function DUF3480 (1);	0.109084	0.64402	D	0.000011	D	0.84306	0.5443	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.988	D	0.86165	0.1596	10	0.87932	D	0	.	13.4251	0.61020	0.1569:0.843:0.0:0.0	.	1306;1365	O95405-2;O95405	.;ZFYV9_HUMAN	C	1306;1365;1365	ENSP00000349737:R1306C;ENSP00000287727:R1365C;ENSP00000360647:R1365C	ENSP00000287727:R1365C	R	+	1	0	ZFYVE9	52583181	0.991000	0.36638	0.987000	0.45799	0.996000	0.88848	2.915000	0.48805	2.676000	0.91093	0.655000	0.94253	CGT		0.458	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		T	52810593	C	T	52810593	3	4	30	1	0	0	0	0	1	0	0	0	17710	536	19	1	4166	1	ZFYVE9	1	52810593	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		52810593	196440028	1	2540										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70225900	70225900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gcctggagatgaccaccaaaCggaaaatcatcggccgtctg	11	12	2	2	rs150507629		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr1:70225900C>T	ENST00000035383.5	+	1	43	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	LRRC7_ENST00000370958.1_Missense_Mutation_p.R43W|LRRC7_ENST00000310961.5_Missense_Mutation_p.R10W|LRRC7_ENST00000415775.2_5'UTR	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	5						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.R5W(2)|p.R43W(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						GACCACCAAACGGAAAATCAT	0.458																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	1						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	38	39	39		13	4.8	1	1	dbSNP_134	39	0,8596		0,0,4298	no	missense	LRRC7	NM_020794.2	101	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	5/1538	70225900	1,13001	2203	4298	6501	69998488	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.13C>T	1.37:g.70225900C>T	ENSP00000035383:p.Arg5Trp		69998488	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.027422	0.75390	2.27E-4	0.0	ENSG00000033122	ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298	T;T;T	0.48522	0.95;1.05;0.81	5.77	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.50684	-0.8799	10	0.87932	D	0	.	12.9121	0.58184	0.3236:0.6764:0.0:0.0	.	5;43	Q96NW7;B1AKT2	LRRC7_HUMAN;.	W	10;43;5;5	ENSP00000309245:R10W;ENSP00000359997:R43W;ENSP00000035383:R5W	ENSP00000035383:R5W	R	+	1	2	LRRC7	69998488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.075000	0.41538	2.729000	0.93468	0.557000	0.71058	CGG		0.458	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70225900	C	T	70225900	3	4	30	1	0	0	0	0	1	0	0	0	9049	527	19	1	15	1	LRRC7	1	70225900	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	17415307	70225900	179024721	2	2541										
TNNI3K	100144878	hgsc.bcm.edu	37	chr1	74957900	74957900	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gcagcattaagaagtcgtttCgaattggaatatgctctaaa	9	6	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr1:74957900C>T	ENST00000294635.4	-	2	89				FPGT-TNNI3K_ENST00000557284.2_Silent_p.F881F|TNNI3K_ENST00000326637.3_Silent_p.F767F|TNNI3K_ENST00000370891.2_Silent_p.F868F			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53							integral component of membrane (GO:0016021)		p.F767F(1)		NS(1)|breast(1)|lung(2)	4						GAAGTCGTTTCGAATTGGAAT	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	1											193	195	194					1																	74957900		2203	4300	6503	74730488	SO:0001627	intron_variant	51086					1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621			25255	protein-coding gene	gene with protein product							Standard			Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.26-8841G>A	1.37:g.74957900C>T			74730488		Silent	SNP	ENST00000294635.4	37																																																																																					0.453	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000026515.2			T	74957900	C	T	74957900	1	4	30	0	1	0	0	0	0	0	0	0	16368	883	31	1		1	TNNI3K	1	74957900	Intron	SNP	C	TCGA-AG-3605-01A-01W-0833-10	4732000	74957900	174292721	3	2542										
TBX15	6913	hgsc.bcm.edu	37	chr1	119427490	119427490	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ctgtgctccatccctgacggCaggtactgcctctctccaaa	8	16	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr1:119427490C>A	ENST00000369429.3	-	8	1683	c.1674G>T	c.(1672-1674)ctG>ctT	p.L558L	TBX15_ENST00000207157.3_Silent_p.L452L			Q96SF7	TBX15_HUMAN	T-box 15	558					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L452L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		TCCCTGACGGCAGGTACTGCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	79	82					1																	119427490		2203	4300	6503	119229013	SO:0001819	synonymous_variant	6913			AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"T-boxes"	11594	protein-coding gene	gene with protein product		604127	"T-box 14"	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1674G>T	1.37:g.119427490C>A			119229013	Q08E76|Q5JT54|Q5T9S7	Silent	SNP	ENST00000369429.3	37																																																																																					0.552	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		A	119427490	C	A	119427490	2	1	30	1	0	0	0	0	0	0	0	1	15691	697	25	2		2	TBX15	1	119427490	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	44469590	119427490	129823131	4	2543										
SMG7	9887	hgsc.bcm.edu	37	chr1	183511583	183511583	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aagaggaaaactgaaaccaaGaaatgcaccttagaaaagtt	8	6	0	4			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr1:183511583G>T	ENST00000347615.2	+	14	1907	c.1788G>T	c.(1786-1788)aaG>aaT	p.K596N	SMG7_ENST00000515829.2_Intron|SMG7_ENST00000507469.1_Intron|SMG7_ENST00000508461.1_Missense_Mutation_p.K554N|SMG7_ENST00000367537.3_Intron|SMG7_ENST00000456731.2_Intron	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	596					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.K596N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CTGAAACCAAGAAATGCACCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	96	97					1																	183511583		2203	4300	6503	181778206	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.1788G>T	1.37:g.183511583G>T	ENSP00000340766:p.Lys596Asn		181778206	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732116	0.69189	.	.	ENSG00000116698	ENST00000508461;ENST00000347615	T;T	0.50548	0.74;0.74	4.66	4.66	0.58398	.	.	.	.	.	T	0.40067	0.1102	L	0.29908	0.895	0.80722	D	1	P;P	0.48407	0.91;0.91	B;B	0.42882	0.401;0.289	T	0.22941	-1.0202	8	.	.	.	.	17.5373	0.87835	0.0:0.0:1.0:0.0	.	554;596	E9PCI0;Q92540	.;SMG7_HUMAN	N	554;596	ENSP00000426915:K554N;ENSP00000340766:K596N	.	K	+	3	2	SMG7	181778206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.896000	0.75665	2.281000	0.76405	0.561000	0.74099	AAG		0.408	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		T	183511583	G	T	183511583	3	4	30	1	0	0	0	0	1	0	0	0	14835	933	33	2	1842	2	SMG7	1	183511583	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	64084093	183511583	65739038	5	2544										
HADHA	3030	hgsc.bcm.edu	37	chr2	26437989	26437989	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	agtcctttggcaaaagtaatTgcaacttcttctaggtattc	7	8	2	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr2:26437989T>C	ENST00000380649.3	-	8	861	c.732A>G	c.(730-732)gcA>gcG	p.A244A	HADHA_ENST00000457468.2_Silent_p.A157A	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	244					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)	p.A157A(1)|p.A244A(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAAGTAATTGCAACTTCTT	0.403																																																2	Substitution - coding silent(2)	large_intestine(2)	2											198	195	196					2																	26437989		2203	4300	6503	26291493	SO:0001819	synonymous_variant	3030			D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.732A>G	2.37:g.26437989T>C			26291493	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	37	CCDS1721.1																																																																																				0.403	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26437989	T	C	26437989	2	2	30	1	0	0	0	0	0	0	0	1	6964	1799	63	4		4	HADHA	2	26437989	Silent	SNP	T	TCGA-AG-3605-01A-01W-0833-10		26437989	216761384	6	2545										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179248000	179248000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aactgatgatccatatgagcGcatggtaataaataactaac	7	7	0	3			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr2:179248000G>A	ENST00000190611.4	+	17	2247	c.1871G>A	c.(1870-1872)cGc>cAc	p.R624H	OSBPL6_ENST00000359685.3_Missense_Mutation_p.R588H|OSBPL6_ENST00000409045.3_Missense_Mutation_p.R593H|OSBPL6_ENST00000409631.1_Missense_Mutation_p.R588H|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R649H|OSBPL6_ENST00000315022.2_Missense_Mutation_p.R628H	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	624					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R624H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CCATATGAGCGCATGGTAATA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											40	40	40					2																	179248000		2203	4300	6503	178956246	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1871G>A	2.37:g.179248000G>A	ENSP00000190611:p.Arg624His		178956246	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	36	5.667358	0.96745	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.87637	0.6227	H	0.99197	4.465	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.996;0.999;0.998;0.998	D	0.91949	0.5569	10	0.87932	D	0	-10.9136	20.5948	0.99439	0.0:0.0:1.0:0.0	.	593;628;588;649;624	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3	.;.;.;.;OSBL6_HUMAN	H	649;588;593;624;588;628	ENSP00000376293:R649H;ENSP00000352713:R588H;ENSP00000387248:R593H;ENSP00000190611:R624H;ENSP00000386885:R588H;ENSP00000318723:R628H	ENSP00000190611:R624H	R	+	2	0	OSBPL6	178956246	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.869000	0.99810	2.873000	0.98535	0.563000	0.77884	CGC		0.483	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		A	179248000	G	A	179248000	3	1	30	1	0	0	0	0	1	0	0	0	11312	1087	38	1	2051	1	OSBPL6	2	179248000	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	152810011	179248000	63951373	7	2546										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180348096	180348096	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	accattttgggtttatttttCgttgcgtctagtgctttgac	9	7	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr2:180348096C>T	ENST00000410066.1	-	6	1176	c.573G>A	c.(571-573)acG>acA	p.T191T	ZNF385B_ENST00000336917.5_Silent_p.T89T|ZNF385B_ENST00000409692.1_Silent_p.T89T|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Silent_p.T115T	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	191	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)	p.T191T(1)		breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GTTTATTTTTCGTTGCGTCTA	0.468																																					Colon(155;204 2491 32774 51842)											1	Substitution - coding silent(1)	large_intestine(1)	2											365	304	325					2																	180348096		2203	4300	6503	180056341	SO:0001819	synonymous_variant	151126			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.573G>A	2.37:g.180348096C>T			180056341	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Silent	SNP	ENST00000410066.1	37	CCDS33339.1																																																																																				0.468	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		T	180348096	C	T	180348096	2	4	30	1	0	0	0	0	0	0	0	1	17916	871	31	1		1	ZNF385B	2	180348096	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	1100096	180348096	62851277	8	2547										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238249123	238249123	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aaggatggcaacagcctcccGaagcgcatcaaaggctcctc	10	14	1	0	rs571287679		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr2:238249123G>A	ENST00000295550.4	-	38	8888	c.8436C>T	c.(8434-8436)ttC>ttT	p.F2812F	COL6A3_ENST00000409809.1_Silent_p.F2606F|COL6A3_ENST00000353578.4_Silent_p.F2606F|COL6A3_ENST00000472056.1_Silent_p.F2205F|COL6A3_ENST00000346358.4_Silent_p.F2612F|COL6A3_ENST00000347401.3_Silent_p.F2611F	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2812	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.F2812F(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		ACAGCCTCCCGAAGCGCATCA	0.547													g|||	1	0.000199681	0	0.0014	5008	,	,		22092	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											75	68	70					2																	238249123		2203	4300	6503	237913862	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8436C>T	2.37:g.238249123G>A			237913862	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238249123	G	A	238249123	2	1	30	1	0	0	0	0	0	0	0	1	3707	1049	37	1		1	COL6A3	2	238249123	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	57901027	238249123	4950250	9	2548										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238296735	238296735	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aattgggagtttctcaaggaGatttacaaggaagtcgagaa	12	4	1	2	rs572430889		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr2:238296735G>T	ENST00000295550.4	-	4	1254	c.802C>A	c.(802-804)Ctc>Atc	p.L268I	COL6A3_ENST00000392004.3_Missense_Mutation_p.L62I|COL6A3_ENST00000409809.1_Missense_Mutation_p.L62I|COL6A3_ENST00000353578.4_Missense_Mutation_p.L62I|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000346358.4_Missense_Mutation_p.L268I|COL6A3_ENST00000347401.3_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	268	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L268I(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TTCTCAAGGAGATTTACAAGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	71	71					2																	238296735		2203	4300	6503	237961474	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.802C>A	2.37:g.238296735G>T	ENSP00000295550:p.Leu268Ile		237961474	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.242330	0.22796	.	.	ENSG00000163359	ENST00000295550;ENST00000353578;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000433762	T;T;T;T;T;D	0.84298	-1.31;-1.31;-1.31;-1.31;-1.31;-1.83	5.43	2.08	0.27032	von Willebrand factor, type A (3);	0.510171	0.16078	U	0.230667	T	0.71517	0.3349	N	0.13371	0.34	0.09310	N	1	B;B;P;B	0.41524	0.007;0.122;0.753;0.007	B;B;B;B	0.42245	0.023;0.2;0.381;0.023	T	0.60556	-0.7240	10	0.27082	T	0.32	.	6.6643	0.23032	0.1654:0.6375:0.1971:0.0	.	268;62;62;268	E9PCV6;E9PGQ9;P12111-2;P12111	.;.;.;CO6A3_HUMAN	I	268;62;62;268;62;268	ENSP00000295550:L268I;ENSP00000315873:L62I;ENSP00000386844:L62I;ENSP00000295546:L268I;ENSP00000375861:L62I;ENSP00000389539:L268I	ENSP00000295550:L268I	L	-	1	0	COL6A3	237961474	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.663000	0.25053	0.602000	0.29896	0.650000	0.86243	CTC		0.453	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238296735	G	T	238296735	3	4	30	1	0	0	0	0	1	0	0	0	3707	942	33	2	8942	2	COL6A3	2	238296735	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	47612	238296735	4902638	10	2549										
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10960098	10960098	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tcagtcctgggttttatggcGtacgagcagggggtacccat	14	9	1	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr3:10960098G>A	ENST00000254488.2	+	8	1146	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	360					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A360A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	GTTTTATGGCGTACGAGCAGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	3											126	103	111					3																	10960098		2203	4300	6503	10935098	SO:0001819	synonymous_variant	6538			S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"Solute carriers"	11044	protein-coding gene	gene with protein product	"GABA transporter 3"	607952	"solute carrier family 6 (neurotransmitter transporter, GABA), member 11"			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1080G>A	3.37:g.10960098G>A			10935098	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																				0.582	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		A	10960098	G	A	10960098	2	1	30	1	0	0	0	0	0	0	0	1	14711	1132	40	1		1	SLC6A11	3	10960098	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10		10960098	187062332	11	2550										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122662372	122662372	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	taggtgaagttagagacccaCggctgcaggtctggtggagg	17	7	1	2	rs566448051		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr3:122662372C>T	ENST00000357599.3	-	4	725	c.339G>A	c.(337-339)ccG>ccA	p.P113P	SEMA5B_ENST00000195173.4_Silent_p.P113P|SEMA5B_ENST00000451055.2_Silent_p.P167P|SEMA5B_ENST00000465147.1_5'UTR	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	113	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.P113P(1)|p.P167P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TAGAGACCCACGGCTGCAGGT	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		16436	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	3											45	54	51					3																	122662372		2203	4300	6503	124145062	SO:0001819	synonymous_variant	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.339G>A	3.37:g.122662372C>T			124145062	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																				0.607	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		T	122662372	C	T	122662372	2	4	30	1	0	0	0	0	0	0	0	1	14075	523	19	1		1	SEMA5B	3	122662372	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	111702274	122662372	75360058	12	2551										
ECE2	9718	hgsc.bcm.edu	37	chr3	183995777	183995777	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cagcgcttctacctatcttgCctacaggtggagcgcattga	10	12	2	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr3:183995777C>T	ENST00000402825.3	+	5	897	c.897C>T	c.(895-897)tgC>tgT	p.C299C	ECE2_ENST00000359140.4_Silent_p.C152C|ECE2_ENST00000404464.3_Silent_p.C181C|ECE2_ENST00000357474.5_Silent_p.C227C|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	299	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.C299C(1)|p.C152C(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACCTATCTTGCCTACAGGTGG	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	3											74	70	71					3																	183995777		2203	4300	6503	185478471	SO:0001819	synonymous_variant	9718			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.897C>T	3.37:g.183995777C>T			185478471	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																				0.567	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		T	183995777	C	T	183995777	2	4	30	1	0	0	0	0	0	0	0	1	4901	747	26	3		3	ECE2	3	183995777	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	61333405	183995777	14026653	13	2552										
CCKAR	886	hgsc.bcm.edu	37	chr4	26483533	26483533	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cgctctgcggaggcggtgtcGtaggcccgccaggcgttggc	18	13	1	0	rs200960240		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr4:26483533G>A	ENST00000295589.3	-	5	1208	c.1014C>T	c.(1012-1014)taC>taT	p.Y338Y		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	338					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)	p.Y338Y(1)		NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	AGGCGGTGTCGTAGGCCCGCC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	4											101	90	94					4																	26483533		2203	4300	6503	26092631	SO:0001819	synonymous_variant	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1014C>T	4.37:g.26483533G>A			26092631	B2R9Z5	Silent	SNP	ENST00000295589.3	37	CCDS3438.1																																																																																				0.597	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			A	26483533	G	A	26483533	2	1	30	1	0	0	0	0	0	0	0	1	2886	1140	40	1		1	CCKAR	4	26483533	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10		26483533	164670743	14	2553										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33643572	33643572	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gcaccacagtgtctggcagaCgttctagaaaacaaattgca	9	10	2	2	rs368041272		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr5:33643572C>T	ENST00000504830.1	-	10	1818	c.1483G>A	c.(1483-1485)Gtc>Atc	p.V495I	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.V495I|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	495	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V495I(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GTCTGGCAGACGTTCTAGAAA	0.443										HNSCC(64;0.19)			C|||	1	0.000199681	0	0.0014	5008	,	,		22119	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	ILE/VAL	0,4406		0,0,2203	117	119	118		1483	2.4	1	5		118	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAMTS12	NM_030955.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	495/1595	33643572	1,13005	2203	4300	6503	33679329	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1483G>A	5.37:g.33643572C>T	ENSP00000422554:p.Val495Ile		33679329	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322277	0.23994	0.0	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59364	0.27;0.27	5.57	2.39	0.29439	.	0.317314	0.32503	N	0.006009	T	0.30727	0.0774	N	0.16862	0.45	0.80722	D	1	P;B	0.35011	0.48;0.05	B;B	0.23716	0.043;0.048	T	0.05517	-1.0880	10	0.21014	T	0.42	.	7.2003	0.25877	0.0:0.5758:0.1341:0.2901	.	495;495	P58397-3;P58397	.;ATS12_HUMAN	I	495	ENSP00000422554:V495I;ENSP00000344847:V495I	ENSP00000344847:V495I	V	-	1	0	ADAMTS12	33679329	0.606000	0.26949	0.994000	0.49952	0.330000	0.28571	0.944000	0.29043	0.721000	0.32231	-0.379000	0.06801	GTC		0.443	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33643572	C	T	33643572	3	4	30	1	0	0	0	0	1	0	0	0	257	536	19	1	3361	1	ADAMTS12	5	33643572	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		33643572	147271688	15	2554										
APC	324	hgsc.bcm.edu	37	chr5	112175423	112175423	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gtccacctgaacactatgttCaggagaccccactcatgttt	7	13	2	2	rs121913329		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr5:112175423C>T	ENST00000457016.1	+	16	4512	c.4132C>T	c.(4132-4134)Cag>Tag	p.Q1378*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1378*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1378*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1378	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1378*(47)|p.Q1378fs*7(2)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.Q1378fs*8(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)|p.Y1376fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACACTATGTTCAGGAGACCCC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	56	Substitution - Nonsense(47)|Deletion - Frameshift(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(49)|stomach(5)|soft_tissue(1)|skin(1)	5											91	87	88					5																	112175423		2202	4300	6502	112203322	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4132C>T	5.37:g.112175423C>T	ENSP00000413133:p.Gln1378*		112203322	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.764727	0.98945	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1139	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1378	.	.	Q	+	1	0	APC	112203322	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	5.761000	0.68801	2.941000	0.99782	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175423	C	T	112175423	4	4	30	1	0	0	0	0	0	1	0	0	763	827	29	3	4190	3	APC	5	112175423	Nonsense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	78531851	112175423	68739837	16	2555										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32184986	32184986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cctggcactgcccaccattgGcacagggagagcttctgcac	11	15	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:32184986G>A	ENST00000375023.3	-	10	1820	c.1682C>T	c.(1681-1683)gCc>gTc	p.A561V	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	561	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.A561V(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCCACCATTGGCACAGGGAGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	57	62					6																	32184986		1511	2709	4220	32292964	SO:0001583	missense	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1682C>T	6.37:g.32184986G>A	ENSP00000364163:p.Ala561Val		32292964	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.263339	0.23051	.	.	ENSG00000204301	ENST00000375023	D	0.88509	-2.39	4.03	4.03	0.46877	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.40385	N	0.001107	T	0.72985	0.3529	N	0.17345	0.48	0.80722	D	1	P;B	0.41498	0.752;0.002	P;B	0.46208	0.507;0.044	T	0.71619	-0.4538	10	0.14656	T	0.56	.	9.3125	0.37915	0.0:0.0:0.7857:0.2143	.	561;561	Q6P3V5;Q99466	.;NOTC4_HUMAN	V	561	ENSP00000364163:A561V	ENSP00000364163:A561V	A	-	2	0	NOTCH4	32292964	0.000000	0.05858	0.960000	0.40013	0.483000	0.33249	0.031000	0.13710	2.233000	0.73108	0.563000	0.77884	GCC		0.627	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32184986	G	A	32184986	3	1	30	1	0	0	0	0	1	0	0	0	10582	1203	42	3	4413	3	NOTCH4	6	32184986	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10		32184986	138930081	17	2556										
HLA-DOA	3111	hgsc.bcm.edu	37	chr6	32975251	32975251	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ccctcagtgacagtttggccGttgcgcagccaggtgatatt	12	11	1	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:32975251G>A	ENST00000229829.5	-	3	525	c.450C>T	c.(448-450)aaC>aaT	p.N150N	HLA-DOA_ENST00000495532.1_5'UTR|HLA-DOA_ENST00000450833.2_Silent_p.N120N	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	150	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)	p.N150N(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						CAGTTTGGCCGTTGCGCAGCC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	6											184	173	177					6																	32975251		1511	2709	4220	33083229	SO:0001819	synonymous_variant	3111			M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.450C>T	6.37:g.32975251G>A			33083229	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																				0.587	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119		A	32975251	G	A	32975251	2	1	30	1	0	0	0	0	0	0	0	1	7221	1136	40	1		1	HLA-DOA	6	32975251	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	790265	32975251	138139816	18	2557										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38919282	38919282	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tcaaattgatgcattggccaAgaaactgaaactgggtaaga	10	6	1	4			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:38919282A>T	ENST00000359357.3	+	80	12040	c.11786A>T	c.(11785-11787)aAg>aTg	p.K3929M	DNAH8_ENST00000441566.1_Missense_Mutation_p.K3893M|RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000449981.2_Missense_Mutation_p.K4146M			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3929	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K3929M(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCATTGGCCAAGAAACTGAAA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	6											160	170	167					6																	38919282		2203	4300	6503	39027260	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11786A>T	6.37:g.38919282A>T	ENSP00000352312:p.Lys3929Met		39027260	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	19.91	3.914797	0.72983	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.10382	2.88;2.88;2.88	5.69	5.69	0.88448	Dynein heavy chain (1);	0.147301	0.64402	D	0.000017	T	0.36663	0.0975	H	0.97732	4.065	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.55547	-0.8124	10	0.87932	D	0	.	8.8291	0.35074	0.8891:0.0:0.1109:0.0	.	3893;3929	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	M	4134;4134;3929;3893	ENSP00000333363:K4134M;ENSP00000352312:K3929M;ENSP00000402294:K3893M	ENSP00000333363:K4134M	K	+	2	0	DNAH8	39027260	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.102000	0.71486	2.296000	0.77279	0.533000	0.62120	AAG		0.398	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38919282	A	T	38919282	3	4	30	1	0	0	0	0	1	0	0	0	4618	72	3	5	12096	5	DNAH8	6	38919282	Missense_Mutation	SNP	A	TCGA-AG-3605-01A-01W-0833-10	5944031	38919282	132195785	19	2558										
IL17F	112744	hgsc.bcm.edu	37	chr6	52101768	52101768	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	acaggggtgacgcaggtgcaGccaacagtcaccagcacctt	12	13	1	1	rs148267766		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:52101768G>T	ENST00000336123.4	-	3	560	c.453C>A	c.(451-453)ggC>ggA	p.G151G		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	151					cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)	p.G151G(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					CGCAGGTGCAGCCAACAGTCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	6											91	80	84					6																	52101768		2203	4300	6503	52209727	SO:0001819	synonymous_variant	112744			AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"Interleukins and interleukin receptors"	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.453C>A	6.37:g.52101768G>T			52209727	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Silent	SNP	ENST00000336123.4	37	CCDS4938.1																																																																																				0.542	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872		T	52101768	G	T	52101768	2	4	30	1	0	0	0	0	0	0	0	1	7659	958	34	2		2	IL17F	6	52101768	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	13182486	52101768	119013299	20	2559										
DDX43	55510	hgsc.bcm.edu	37	chr6	74117253	74117253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aaggtcaaaggaatagacccGgcatgttagttctaactccc	9	10	2	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:74117253G>A	ENST00000370336.4	+	8	1110	c.952G>A	c.(952-954)Ggc>Agc	p.G318S	DDX43_ENST00000479773.1_3'UTR|DDX43_ENST00000539829.1_3'UTR	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	318	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.G318S(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						GAATAGACCCGGCATGTTAGT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											137	147	144					6																	74117253		2203	4300	6503	74173974	SO:0001583	missense	55510				CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.952G>A	6.37:g.74117253G>A	ENSP00000359361:p.Gly318Ser		74173974	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	37	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.605676	0.28623	.	.	ENSG00000080007	ENST00000370336	T	0.14144	2.53	4.91	4.91	0.64330	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.051323	0.85682	D	0.000000	T	0.02571	0.0078	N	0.03253	-0.375	0.80722	D	1	P	0.52170	0.951	B	0.43018	0.405	T	0.28522	-1.0041	10	0.06099	T	0.92	-0.8098	17.2093	0.86926	0.0:0.0:1.0:0.0	.	318	Q9NXZ2	DDX43_HUMAN	S	318	ENSP00000359361:G318S	ENSP00000359361:G318S	G	+	1	0	DDX43	74173974	1.000000	0.71417	0.926000	0.36857	0.006000	0.05464	8.213000	0.89758	2.419000	0.82065	0.655000	0.94253	GGC		0.363	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		A	74117253	G	A	74117253	3	1	30	1	0	0	0	0	1	0	0	0	4369	1116	39	1	982	1	DDX43	6	74117253	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	22015485	74117253	96997814	21	2560										
SIM1	6492	hgsc.bcm.edu	37	chr6	100841378	100841378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cttaccatggatcctgtggaCtgaagcgatgtgaggcatgc	13	9	0	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:100841378C>T	ENST00000369208.3	-	11	2337	c.1555G>A	c.(1555-1557)Gtc>Atc	p.V519I	SIM1_ENST00000262901.4_Missense_Mutation_p.V519I			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	519	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.V519I(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		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)		ATCCTGTGGACTGAAGCGATG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	104	106					6																	100841378		2203	4300	6503	100948099	SO:0001583	missense	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1555G>A	6.37:g.100841378C>T	ENSP00000358210:p.Val519Ile		100948099	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	0.050	-1.252856	0.01457	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.33438	1.41;1.41	5.78	4.0	0.46444	Single-minded, C-terminal (2);	1.083120	0.06897	N	0.805334	T	0.04998	0.0134	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40553	-0.9557	10	0.18276	T	0.48	.	11.1884	0.48671	0.0:0.7994:0.0:0.2006	.	519	P81133	SIM1_HUMAN	I	519	ENSP00000358210:V519I;ENSP00000262901:V519I	ENSP00000262901:V519I	V	-	1	0	SIM1	100948099	0.006000	0.16342	0.004000	0.12327	0.058000	0.15608	1.428000	0.34892	0.781000	0.33589	-0.122000	0.15005	GTC		0.557	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		T	100841378	C	T	100841378	3	4	30	1	0	0	0	0	1	0	0	0	14360	565	20	3	753	3	SIM1	6	100841378	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	26724125	100841378	70273689	22	2561										
PLG	5340	hgsc.bcm.edu	37	chr6	161135915	161135915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gccaggcctgggactctcagAgcccacacgctcatggatac	11	15	2	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr6:161135915A>G	ENST00000308192.9	+	6	700	c.637A>G	c.(637-639)Agc>Ggc	p.S213G		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	213	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S213G(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GGACTCTCAGAGCCCACACGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											64	60	61					6																	161135915		2203	4300	6503	161055905	SO:0001583	missense	5340			M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.637A>G	6.37:g.161135915A>G	ENSP00000308938:p.Ser213Gly		161055905	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	A	10.32	1.318405	0.23994	.	.	ENSG00000122194	ENST00000308192	T	0.62941	-0.01	5.77	3.09	0.35607	Kringle (4);Kringle-like fold (1);	1.076240	0.07322	U	0.877729	T	0.39517	0.1081	M	0.69523	2.12	0.09310	N	1	B	0.30361	0.277	B	0.31390	0.129	T	0.39623	-0.9605	10	0.17369	T	0.5	.	8.3399	0.32237	0.7715:0.0:0.2285:0.0	.	213	P00747	PLMN_HUMAN	G	213	ENSP00000308938:S213G	ENSP00000308938:S213G	S	+	1	0	PLG	161055905	0.167000	0.22975	0.128000	0.21923	0.950000	0.60333	0.840000	0.27600	1.024000	0.39682	0.533000	0.62120	AGC		0.463	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		G	161135915	A	G	161135915	3	3	30	1	0	0	0	0	1	0	0	0	12117	304	11	4	663	4	PLG	6	161135915	Missense_Mutation	SNP	A	TCGA-AG-3605-01A-01W-0833-10	60294537	161135915	9979152	23	2562										
IL6	3569	hgsc.bcm.edu	37	chr7	22769162	22769162	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ctggtgaaaatcatcactggTcttttggagtttgaggtata	11	5	3	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr7:22769162T>G	ENST00000404625.1	+	5	813	c.354T>G	c.(352-354)ggT>ggG	p.G118G	AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000258743.5_Silent_p.G118G|IL6_ENST00000406575.1_Silent_p.G118G|IL6_ENST00000401651.1_Silent_p.G42G|IL6_ENST00000420258.2_Silent_p.G172G|IL6_ENST00000401630.3_Silent_p.G95G|IL6_ENST00000407492.1_Silent_p.G42G			P05231	IL6_HUMAN	interleukin 6	118					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)	p.G118G(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	TCATCACTGGTCTTTTGGAGT	0.423																																					Esophageal Squamous(47;342 1214 13936 33513)											1	Substitution - coding silent(1)	large_intestine(1)	7											158	157	157					7																	22769162		2203	4300	6503	22735687	SO:0001819	synonymous_variant	3569			M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.354T>G	7.37:g.22769162T>G			22735687	Q9UCU2|Q9UCU3|Q9UCU4	Silent	SNP	ENST00000404625.1	37	CCDS5375.1																																																																																				0.423	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		G	22769162	T	G	22769162	2	3	30	1	0	0	0	0	0	0	0	1	7722	1654	58	4		4	IL6	7	22769162	Silent	SNP	T	TCGA-AG-3605-01A-01W-0833-10		22769162	136369501	24	2563										
EPDR1	54749	hgsc.bcm.edu	37	chr7	37989844	37989844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tacagtcaaggattgctatcCtgtccaggaaacctttacca	7	11	1	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr7:37989844C>T	ENST00000199448.4	+	3	900	c.521C>T	c.(520-522)cCt>cTt	p.P174L	EPDR1_ENST00000476620.1_Missense_Mutation_p.P72L|EPDR1_ENST00000559325.1_Missense_Mutation_p.P294L|EPDR1_ENST00000425345.1_Missense_Mutation_p.P113L|EPDR1_ENST00000423717.1_3'UTR	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	174					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)	p.P294L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						GATTGCTATCCTGTCCAGGAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											64	65	64					7																	37989844		2203	4300	6503	37956369	SO:0001583	missense	54749			BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.521C>T	7.37:g.37989844C>T	ENSP00000199448:p.Pro174Leu		37956369	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	37	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956465	0.92726	.	.	ENSG00000086289	ENST00000476620;ENST00000199448;ENST00000425345	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.80864	0.4705	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83423	0.0034	9	0.66056	D	0.02	-8.8292	17.1506	0.86777	0.0:1.0:0.0:0.0	.	113;294	C9JYS3;A4D1W8	.;.	L	72;294;113	.	ENSP00000199448:P294L	P	+	2	0	EPDR1	37956369	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	7.609000	0.82925	2.670000	0.90874	0.655000	0.94253	CCT		0.393	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		T	37989844	C	T	37989844	3	4	30	1	0	0	0	0	1	0	0	0	5176	681	24	3	891	3	EPDR1	7	37989844	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	15220682	37989844	121148819	25	2564										
MRPS24	64951	hgsc.bcm.edu	37	chr7	43908599	43908599	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cagcctttacggtgggcgatGtagtgcggcgcgtgtgcctc	16	11	0	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr7:43908599G>T	ENST00000317534.5	-	3	244	c.183C>A	c.(181-183)taC>taA	p.Y61*	MRPS24_ENST00000467084.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Missense_Mutation_p.H107N	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	61					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.Y61*(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						GGTGGGCGATGTAGTGCGGCG	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											87	79	82					7																	43908599		2203	4300	6503	43875124	SO:0001587	stop_gained	64951			AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"Mitochondrial ribosomal proteins / small subunits"	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.183C>A	7.37:g.43908599G>T	ENSP00000318158:p.Tyr61*		43875124	A4D1U9|P82668|Q96Q23|Q9P047	Nonsense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1	.	.	.	.	.	.	.	.	.	.	G	36	5.656512	0.96724	.	.	ENSG00000062582	ENST00000317534	.	.	.	4.75	2.94	0.34122	.	0.378770	0.30210	N	0.010153	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9231	0.35623	0.1854:0.0:0.8146:0.0	.	.	.	.	X	61	.	ENSP00000318158:Y61X	Y	-	3	2	MRPS24	43875124	1.000000	0.71417	0.992000	0.48379	0.892000	0.51952	1.366000	0.34193	0.425000	0.26087	0.563000	0.77884	TAC		0.607	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014		T	43908599	G	T	43908599	4	4	30	1	0	0	0	0	0	1	0	0	9865	1372	48	2	328	2	MRPS24	7	43908599	Nonsense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	5918755	43908599	115230064	26	2565										
CAV1	857	hgsc.bcm.edu	37	chr7	116166586	116166586	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ccgccctctgcagggacatcTctacaccgttcccatccggg	9	18	2	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr7:116166586T>A	ENST00000341049.2	+	2	316	c.38T>A	c.(37-39)cTc>cAc	p.L13H	CAV1_ENST00000405348.1_5'UTR|CAV1_ENST00000393468.1_5'UTR|CAV1_ENST00000393470.1_Intron|CAV1_ENST00000393467.1_5'UTR	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	13					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.L13H(1)		endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			CAGGGACATCTCTACACCGTT	0.592											OREG0018273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	7											97	79	85					7																	116166586		2203	4300	6503	115953822	SO:0001583	missense	857			AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"caveolin 1, caveolae protein, 22kD"	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.38T>A	7.37:g.116166586T>A	ENSP00000339191:p.Leu13His	1471	115953822	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	37	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512232	0.85389	.	.	ENSG00000105974	ENST00000341049	D	0.94138	-3.36	5.26	5.26	0.73747	.	0.309988	0.31897	N	0.006898	D	0.93304	0.7866	M	0.61703	1.905	0.80722	D	1	D	0.55172	0.97	P	0.49708	0.62	D	0.93683	0.7000	10	0.87932	D	0	-9.3259	11.7718	0.51962	0.0:0.0:0.1469:0.8531	.	13	Q03135	CAV1_HUMAN	H	13	ENSP00000339191:L13H	ENSP00000339191:L13H	L	+	2	0	CAV1	115953822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.510000	0.60455	2.100000	0.63781	0.528000	0.53228	CTC		0.592	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753		A	116166586	T	A	116166586	3	1	30	1	0	0	0	0	1	0	0	0	2699	1551	54	5	44	5	CAV1	7	116166586	Missense_Mutation	SNP	T	TCGA-AG-3605-01A-01W-0833-10	72257987	116166586	42972077	27	2566										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142573294	142573294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tggtcctgggcttgagggggCggtagatgcagcacatggtg	19	7	0	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr7:142573294C>T	ENST00000359396.3	-	8	1294	c.1049G>A	c.(1048-1050)cGc>cAc	p.R350H	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	350					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)	p.R350H(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					CTTGAGGGGGCGGTAGATGCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											127	125	126					7																	142573294		2203	4300	6503	142283416	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1049G>A	7.37:g.142573294C>T	ENSP00000352358:p.Arg350His		142283416	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.697574	0.88830	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	D	0.89485	-2.52	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.95227	0.8452	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95960	0.8961	10	0.72032	D	0.01	-25.3714	16.8604	0.86016	0.0:1.0:0.0:0.0	.	350	Q9H1D0	TRPV6_HUMAN	H	350;182	ENSP00000352358:R350H	ENSP00000310825:R182H	R	-	2	0	TRPV6	142283416	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.299000	0.78831	2.458000	0.83093	0.655000	0.94253	CGC		0.572	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		T	142573294	C	T	142573294	3	4	30	1	0	0	0	0	1	0	0	0	16640	768	27	1	1160	1	TRPV6	7	142573294	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	26406708	142573294	16565369	28	2567										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100514002	100514002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gtaatattggaggaaccagtGgacgtgttagtttatggatg	14	3	0	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr8:100514002G>A	ENST00000358544.2	+	26	4069	c.3958G>A	c.(3958-3960)Gga>Aga	p.G1320R	VPS13B_ENST00000395996.1_Missense_Mutation_p.G1320R|VPS13B_ENST00000357162.2_Missense_Mutation_p.G1320R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1320					protein transport (GO:0015031)			p.G1320R(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGGAACCAGTGGACGTGTTAG	0.428																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											171	167	169					8																	100514002		2203	4300	6503	100583178	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3958G>A	8.37:g.100514002G>A	ENSP00000351346:p.Gly1320Arg		100583178	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.337952	0.41398	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.70516	-0.49;-0.47;-0.16	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.81297	0.4793	L	0.54323	1.7	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.992;0.997;0.992;0.969	T	0.77576	-0.2536	10	0.28530	T	0.3	.	19.1316	0.93410	0.0:0.0:1.0:0.0	.	1319;1320;1320;1320	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	R	1320	ENSP00000349685:G1320R;ENSP00000351346:G1320R;ENSP00000379318:G1320R	ENSP00000349685:G1320R	G	+	1	0	VPS13B	100583178	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.705000	0.84606	2.589000	0.87451	0.557000	0.71058	GGA		0.428	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100514002	G	A	100514002	3	1	30	1	0	0	0	0	1	0	0	0	17230	1349	47	3	4179	3	VPS13B	8	100514002	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10		100514002	45850020	29	2568										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121381608	121381608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gcctggcagccctgggccccCtggctctcctggaccaagag	13	17	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr8:121381608C>A	ENST00000297848.3	+	47	5465	c.5195C>A	c.(5194-5196)cCt>cAt	p.P1732H	COL14A1_ENST00000247781.3_Missense_Mutation_p.P1637H|COL14A1_ENST00000309791.4_Missense_Mutation_p.P1732H	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.P1732H(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			CCTGGGCCCCCTGGCTCTCCT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8											50	54	53					8																	121381608		2203	4300	6503	121450789	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.5195C>A	8.37:g.121381608C>A	ENSP00000297848:p.Pro1732His		121450789		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824671	0.71143	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.94232	-2.66;-2.69;-3.29;-3.38	4.84	4.84	0.62591	.	0.192216	0.46442	D	0.000281	D	0.91586	0.7342	M	0.79343	2.45	0.80722	D	1	P	0.45283	0.855	B	0.35971	0.215	D	0.92338	0.5879	10	0.56958	D	0.05	.	13.4332	0.61068	0.1574:0.8426:0.0:0.0	.	1732	Q05707	COEA1_HUMAN	H	1732;1732;1637;79	ENSP00000311809:P1732H;ENSP00000297848:P1732H;ENSP00000247781:P1637H;ENSP00000403640:P79H	ENSP00000247781:P1637H	P	+	2	0	COL14A1	121450789	0.871000	0.30034	1.000000	0.80357	0.993000	0.82548	3.256000	0.51492	2.618000	0.88619	0.561000	0.74099	CCT		0.577	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121381608	C	A	121381608	3	1	30	1	0	0	0	0	1	0	0	0	3677	681	24	2	5377	2	COL14A1	8	121381608	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	20867606	121381608	24982414	30	2569										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965958	123965958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tattacaaggaccccaaaaaGctctgcgaagaggacttgga	10	9	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr8:123965958G>T	ENST00000314393.4	+	3	3043	c.2208G>T	c.(2206-2208)aaG>aaT	p.K736N		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	736					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.K736N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			ACCCCAAAAAGCTCTGCGAAG	0.532																																					Esophageal Squamous(94;1056 1388 11767 13799 49639)											1	Substitution - Missense(1)	large_intestine(1)	8											94	99	97					8																	123965958		2203	4300	6503	124035139	SO:0001583	missense	22882			AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.2208G>T	8.37:g.123965958G>T	ENSP00000314709:p.Lys736Asn		124035139		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	G	4.636	0.118313	0.08881	.	.	ENSG00000178764	ENST00000314393	T	0.17854	2.25	5.41	0.427	0.16489	.	0.773311	0.12349	N	0.476704	T	0.08223	0.0205	N	0.14661	0.345	0.26053	N	0.981459	B	0.27559	0.181	B	0.21708	0.036	T	0.32719	-0.9896	10	0.34782	T	0.22	-6.6243	5.1858	0.15184	0.2284:0.0942:0.5809:0.0965	.	736	Q9Y6X8	ZHX2_HUMAN	N	736	ENSP00000314709:K736N	ENSP00000314709:K736N	K	+	3	2	ZHX2	124035139	0.912000	0.30974	0.697000	0.30258	0.156000	0.22039	1.373000	0.34272	-0.320000	0.08640	-1.134000	0.01955	AAG		0.532	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		T	123965958	G	T	123965958	3	4	30	1	0	0	0	0	1	0	0	0	17715	962	34	2	2210	2	ZHX2	8	123965958	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	2584350	123965958	22398064	31	2570										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133141552	133141552	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tccatactgaatcagaaatcCcatcccctgtggacgacaga	7	13	1	3			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr8:133141552C>A	ENST00000388996.4	-	15	2996	c.2576G>T	c.(2575-2577)gGg>gTg	p.G859V	KCNQ3_ENST00000519445.1_Missense_Mutation_p.G847V|KCNQ3_ENST00000521134.1_Missense_Mutation_p.G739V	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	859					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.G859V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	ATCAGAAATCCCATCCCCTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	8											77	63	68					8																	133141552		2203	4300	6503	133210734	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2576G>T	8.37:g.133141552C>A	ENSP00000373648:p.Gly859Val		133210734	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657065	0.67586	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	T;T;T	0.48836	0.8;0.8;0.8	5.36	4.46	0.54185	.	0.050052	0.85682	N	0.000000	T	0.49287	0.1548	L	0.55481	1.735	0.80722	D	1	P;P	0.50617	0.777;0.937	P;P	0.46940	0.532;0.532	T	0.47535	-0.9110	10	0.37606	T	0.19	-22.1858	14.263	0.66097	0.15:0.85:0.0:0.0	.	847;859	E7ET42;O43525	.;KCNQ3_HUMAN	V	859;739;847;836;738	ENSP00000373648:G859V;ENSP00000429799:G739V;ENSP00000428790:G847V	ENSP00000373648:G859V	G	-	2	0	KCNQ3	133210734	1.000000	0.71417	0.320000	0.25306	0.987000	0.75469	7.175000	0.77632	1.203000	0.43233	0.561000	0.74099	GGG		0.537	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133141552	C	A	133141552	3	1	30	1	0	0	0	0	1	0	0	0	8105	623	22	2	46	2	KCNQ3	8	133141552	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	9175594	133141552	13222470	32	2571										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35231191	35231191	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tagcagttcgtggtgatcagCcttcctgggaacaggatttc	12	9	1	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr9:35231191C>T	ENST00000378495.3	+	3	349	c.127C>T	c.(127-129)Cct>Tct	p.P43S	UNC13B_ENST00000378496.4_Missense_Mutation_p.P43S|UNC13B_ENST00000396787.1_Missense_Mutation_p.P43S	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	43	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.P43S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TGGTGATCAGCCTTCCTGGGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											134	115	121					9																	35231191		2203	4300	6503	35221191	SO:0001583	missense	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.127C>T	9.37:g.35231191C>T	ENSP00000367756:p.Pro43Ser		35221191	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970917	0.92919	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496	D;D;D	0.93076	-3.16;-3.16;-3.16	5.23	5.23	0.72850	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.96864	0.8976	M	0.82630	2.6	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.97214	0.9873	10	0.87932	D	0	-6.5537	17.6077	0.88044	0.0:1.0:0.0:0.0	.	43;43;43	Q2NKJ5;F8W8M9;O14795	.;.;UN13B_HUMAN	S	43	ENSP00000380006:P43S;ENSP00000367756:P43S;ENSP00000367757:P43S	ENSP00000367756:P43S	P	+	1	0	UNC13B	35221191	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	7.591000	0.82666	2.736000	0.93811	0.644000	0.83932	CCT		0.358	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35231191	C	T	35231191	3	4	30	1	0	0	0	0	1	0	0	0	17025	739	26	3	137	3	UNC13B	9	35231191	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		35231191	105982240	33	2572										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28274019	28274019	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	agcagcatagcaatcttcatCttaatttcactttcaggatc	5	10	5	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr10:28274019C>A	ENST00000305242.5	-	4	596	c.504G>T	c.(502-504)aaG>aaT	p.K168N	ARMC4_ENST00000239715.3_Missense_Mutation_p.K25N|ARMC4_ENST00000537576.1_5'Flank	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	168					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.K168N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						CAATCTTCATCTTAATTTCAC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											74	67	69					10																	28274019		2203	4300	6503	28314025	SO:0001583	missense	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.504G>T	10.37:g.28274019C>A	ENSP00000306410:p.Lys168Asn		28314025	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.401699	0.25291	.	.	ENSG00000169126	ENST00000305242;ENST00000434029;ENST00000239715	T;T;T	0.53423	1.36;0.69;0.62	5.55	2.95	0.34219	.	0.226286	0.42682	D	0.000673	T	0.45816	0.1361	M	0.72118	2.19	0.38496	D	0.948097	P	0.51791	0.948	P	0.45829	0.494	T	0.50268	-0.8848	10	0.52906	T	0.07	-9.1292	4.8429	0.13500	0.0:0.4426:0.0:0.5574	.	168	Q5T2S8	ARMC4_HUMAN	N	168;62;25	ENSP00000306410:K168N;ENSP00000398155:K62N;ENSP00000239715:K25N	ENSP00000239715:K25N	K	-	3	2	ARMC4	28314025	0.996000	0.38824	0.159000	0.22649	0.130000	0.20726	0.755000	0.26405	0.996000	0.38943	0.585000	0.79938	AAG		0.328	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		A	28274019	C	A	28274019	3	1	30	1	0	0	0	0	1	0	0	0	954	912	32	2	2698	2	ARMC4	10	28274019	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		28274019	107260728	34	2573										
NDST2	8509	hgsc.bcm.edu	37	chr10	75562482	75562482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tttgctccggcctagacagcGagtcttaccaccttcaagtc	8	14	2	1	rs372755048		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr10:75562482G>A	ENST00000309979.6	-	14	3032	c.2476C>T	c.(2476-2478)Cgc>Tgc	p.R826C	NDST2_ENST00000299641.4_Missense_Mutation_p.R703C|ZSWIM8-AS1_ENST00000456638.2_RNA|RP11-574K11.31_ENST00000603027.1_Silent_p.L813L			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	826	Heparan sulfate N-sulfotransferase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)	p.R826C(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					CCTAGACAGCGAGTCTTACCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	95	96					10																	75562482		2203	4300	6503	75232488	SO:0001583	missense	8509			U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"Sulfotransferases, membrane-bound"	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.2476C>T	10.37:g.75562482G>A	ENSP00000310657:p.Arg826Cys		75232488	Q2TB32|Q59H89	Missense_Mutation	SNP	ENST00000309979.6	37	CCDS7335.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.654561	0.67472	.	.	ENSG00000166507	ENST00000309979;ENST00000299641;ENST00000429742	D;D;D	0.84223	-1.82;-1.82;-1.82	6.07	6.07	0.98685	Sulfotransferase domain (1);	0.135434	0.52532	D	0.000071	D	0.90466	0.7014	M	0.75615	2.305	0.58432	D	0.999992	D	0.69078	0.997	P	0.60345	0.873	D	0.90900	0.4768	10	0.87932	D	0	.	13.4973	0.61434	0.0:0.0:0.745:0.255	.	826	P52849	NDST2_HUMAN	C	826;703;107	ENSP00000310657:R826C;ENSP00000299641:R703C;ENSP00000392733:R107C	ENSP00000299641:R703C	R	-	1	0	NDST2	75232488	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.717000	0.61923	2.884000	0.98904	0.655000	0.94253	CGC		0.522	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1	NM_003635		A	75562482	G	A	75562482	3	1	30	1	0	0	0	0	1	0	0	0	10287	1058	37	1	183	1	NDST2	10	75562482	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	47288463	75562482	59972265	35	2574										
PPP1R3C	5507	hgsc.bcm.edu	37	chr10	93390113	93390113	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ttctcaaaactcacatttttGactttaacagtccctgtcac	3	12	3	1	rs141426360		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr10:93390113G>T	ENST00000238994.5	-	2	609	c.525C>A	c.(523-525)gtC>gtA	p.V175V		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C									p.V175V(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				TCACATTTTTGACTTTAACAG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	10						T		0,4406		0,0,2203	94	88	90		525	-7.8	0.5	10	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PPP1R3C	NM_005398.4		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		175/318	93390113	1,13005	2203	4300	6503	93380093	SO:0001819	synonymous_variant	5507			Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9293	protein-coding gene	gene with protein product	"Phosphatase 1, regulatory inhibitor subunit 5", "protein targeting to glycogen"	602999	"protein phosphatase 1, regulatory (inhibitor) subunit 3C"	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.525C>A	10.37:g.93390113G>T			93380093		Silent	SNP	ENST00000238994.5	37	CCDS7416.1																																																																																				0.403	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398		T	93390113	G	T	93390113	2	4	30	1	0	0	0	0	0	0	0	1	12407	1277	45	2		2	PPP1R3C	10	93390113	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	17827631	93390113	42144634	36	2575										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64566900	64566900	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cctgcccactcaccggctcaTtcagtgggtcagtttccttc	8	16	4	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr11:64566900T>C	ENST00000294066.2	-	14	1137	c.1046A>G	c.(1045-1047)aAt>aGt	p.N349S	MAP4K2_ENST00000377350.3_Missense_Mutation_p.N349S|MAP4K2_ENST00000468062.1_5'Flank	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	349	PEST2.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.N349S(1)		cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						CACCGGCTCATTCAGTGGGTC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11											90	82	85					11																	64566900		2201	4297	6498	64323476	SO:0001583	missense	5871			BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.1046A>G	11.37:g.64566900T>C	ENSP00000294066:p.Asn349Ser		64323476	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	37	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	T	6.431	0.447568	0.12223	.	.	ENSG00000168067	ENST00000294066;ENST00000377350;ENST00000439069	T;T;T	0.13420	2.59;2.59;2.59	5.14	0.913	0.19354	.	0.552015	0.18737	N	0.132577	T	0.03871	0.0109	N	0.03608	-0.345	0.19945	N	0.999945	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.42015	-0.9476	10	0.08381	T	0.77	.	3.4663	0.07550	0.0:0.2474:0.1995:0.5531	.	349;349	Q86VU3;Q12851	.;M4K2_HUMAN	S	349;349;305	ENSP00000294066:N349S;ENSP00000366567:N349S;ENSP00000403563:N305S	ENSP00000294066:N349S	N	-	2	0	MAP4K2	64323476	0.000000	0.05858	0.222000	0.23844	0.706000	0.40770	-0.528000	0.06193	0.327000	0.23409	0.456000	0.33151	AAT		0.597	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		C	64566900	T	C	64566900	3	2	30	1	0	0	0	0	1	0	0	0	9290	1493	52	4	1492	4	MAP4K2	11	64566900	Missense_Mutation	SNP	T	TCGA-AG-3605-01A-01W-0833-10		64566900	70439616	37	2576										
BBS1	582	hgsc.bcm.edu	37	chr11	66299434	66299434	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ctccataggtgctggtgcttCgagaaggccaaagtgcaccc	12	12	0	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr11:66299434C>T	ENST00000318312.7	+	17	1759	c.1708C>T	c.(1708-1710)Cga>Tga	p.R570*	ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000455748.2_Nonsense_Mutation_p.R473*|BBS1_ENST00000393994.2_3'UTR|CTD-3074O7.11_ENST00000419755.3_Nonsense_Mutation_p.R607*	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	570					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)	p.R570*(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GCTGGTGCTTCGAGAAGGCCA	0.652									Bardet-Biedl syndrome																												GBM(152;173 2612 9770 10137)											1	Substitution - Nonsense(1)	large_intestine(1)	11											43	36	38					11																	66299434		2197	4293	6490	66056010	SO:0001587	stop_gained	582	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1708C>T	11.37:g.66299434C>T	ENSP00000317469:p.Arg570*		66056010	Q32MM9|Q32MN0|Q96SN4	Nonsense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	C	37	6.061050	0.97246	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1274	0.48325	0.1839:0.8161:0.0:0.0	.	.	.	.	X	607;570;473	.	ENSP00000317469:R570X	R	+	1	2	BBS1;CTD-3074O7.11	66056010	0.990000	0.36364	0.992000	0.48379	0.984000	0.73092	2.603000	0.46266	2.682000	0.91365	0.585000	0.79938	CGA		0.652	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			T	66299434	C	T	66299434	4	4	30	1	0	0	0	0	0	1	0	0	1336	876	31	1	1774	1	BBS1	11	66299434	Nonsense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	1732534	66299434	68707082	38	2577										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	30	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		25398281	108453614	39	2578										
FGD4	121512	hgsc.bcm.edu	37	chr12	32755178	32755178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	agaatatgtgaaaggatttgAtaatgcaatggaattggtta	11	1	0	3			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr12:32755178A>G	ENST00000427716.2	+	7	1344	c.920A>G	c.(919-921)gAt>gGt	p.D307G	FGD4_ENST00000266482.3_Missense_Mutation_p.D59G|FGD4_ENST00000534526.2_Missense_Mutation_p.D444G|FGD4_ENST00000531134.1_Missense_Mutation_p.D392G|FGD4_ENST00000525053.1_Missense_Mutation_p.D419G|FGD4_ENST00000546442.1_Missense_Mutation_p.D214G|FGD4_ENST00000381025.3_Missense_Mutation_p.D59G	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	307	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.D307G(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAAGGATTTGATAATGCAATG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											140	145	143					12																	32755178		2203	4300	6503	32646445	SO:0001583	missense	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.920A>G	12.37:g.32755178A>G	ENSP00000394487:p.Asp307Gly		32646445	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425852	0.83667	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000266482;ENST00000546442;ENST00000525053;ENST00000381025	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	4.86	4.86	0.63082	Dbl homology (DH) domain (5);	0.000000	0.53938	D	0.000052	T	0.81861	0.4912	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.996;0.988;1.0;0.977	D	0.85921	0.1446	10	0.87932	D	0	-22.9247	14.7717	0.69684	1.0:0.0:0.0:0.0	.	419;392;307;59	E9PJX4;B7Z493;Q96M96;G3XA97	.;.;FGD4_HUMAN;.	G	444;392;307;59;214;419;59	ENSP00000449273:D444G;ENSP00000431323:D392G;ENSP00000394487:D307G;ENSP00000266482:D59G;ENSP00000446695:D214G;ENSP00000433666:D419G;ENSP00000370413:D59G	ENSP00000266482:D59G	D	+	2	0	FGD4	32646445	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	8.918000	0.92759	1.955000	0.56771	0.533000	0.62120	GAT		0.353	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		G	32755178	A	G	32755178	3	3	30	1	0	0	0	0	1	0	0	0	5854	333	12	4	938	4	FGD4	12	32755178	Missense_Mutation	SNP	A	TCGA-AG-3605-01A-01W-0833-10	7356897	32755178	101096717	40	2579										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58795000	58795000	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	acatcacagtgaaaaaggatCagtgtttagttcgatcattt	8	6	3	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr14:58795000C>T	ENST00000355431.3	+	9	1001	c.628C>T	c.(628-630)Cag>Tag	p.Q210*	ARID4A_ENST00000431317.2_Nonsense_Mutation_p.Q210*|ARID4A_ENST00000348476.3_Nonsense_Mutation_p.Q210*|ARID4A_ENST00000395168.3_Nonsense_Mutation_p.Q210*	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	210					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q210*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GAAAAAGGATCAGTGTTTAGT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											135	130	132					14																	58795000		2203	4295	6498	57864753	SO:0001587	stop_gained	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.628C>T	14.37:g.58795000C>T	ENSP00000347602:p.Gln210*		57864753	Q15991|Q15992|Q15993	Nonsense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	C	39	7.873562	0.98537	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317	.	.	.	5.52	5.52	0.82312	.	0.107199	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-1.8404	19.5157	0.95162	0.0:1.0:0.0:0.0	.	.	.	.	X	210;210;210;173;210	.	ENSP00000344556:Q210X	Q	+	1	0	ARID4A	57864753	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.554000	0.82212	2.631000	0.89168	0.644000	0.83932	CAG		0.313	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		T	58795000	C	T	58795000	4	4	30	1	0	0	0	0	0	1	0	0	919	827	29	3	658	3	ARID4A	14	58795000	Nonsense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		58795000	48554540	41	2580										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57730905	57730905	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cagacctcagtgtgtgtaaaCgttcagagctgcaccaagga	11	10	2	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr15:57730905C>T	ENST00000281282.5	+	2	786	c.708C>T	c.(706-708)aaC>aaT	p.N236N		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	236	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.N236K(1)|p.N236N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TGTGTGTAAACGTTCAGAGCT	0.567																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	15											90	94	93					15																	57730905		2192	4292	6484	55518197	SO:0001819	synonymous_variant	84952			AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.708C>T	15.37:g.57730905C>T			55518197	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Silent	SNP	ENST00000281282.5	37	CCDS10161.1																																																																																				0.567	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		T	57730905	C	T	57730905	2	4	30	1	0	0	0	0	0	0	0	1	3310	535	19	1		1	CGNL1	15	57730905	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10		57730905	44800487	42	2581										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	30	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		7578406	73616804	43	2582										
MYH1	4619	hgsc.bcm.edu	37	chr17	10401083	10401083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cctttgctttttgtccagggCggcacaggcagcatttgtcc	11	12	0	0	rs139860229		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr17:10401083C>T	ENST00000226207.5	-	31	4427	c.4333G>A	c.(4333-4335)Gcc>Acc	p.A1445T	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1445			A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A1445T(2)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TTGTCCAGGGCGGCACAGGCA	0.448																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	17						C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	130	125	127		4333	5.7	1	17	dbSNP_134	127	0,8600		0,0,4300	no	missense	MYH1	NM_005963.3	58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	1445/1940	10401083	2,13004	2203	4300	6503	10341808	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.4333G>A	17.37:g.10401083C>T	ENSP00000226207:p.Ala1445Thr		10341808	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235771	0.39498	4.54E-4	0.0	ENSG00000109061	ENST00000226207;ENST00000379814	D	0.83419	-1.72	5.65	5.65	0.86999	Myosin tail (1);	0.000000	0.42964	U	0.000638	D	0.84714	0.5533	M	0.78456	2.415	0.46701	D	0.999161	B	0.15473	0.013	B	0.15052	0.012	T	0.79976	-0.1576	10	0.42905	T	0.14	.	20.073	0.97731	0.0:1.0:0.0:0.0	.	1445	P12882	MYH1_HUMAN	T	1445;534	ENSP00000226207:A1445T	ENSP00000226207:A1445T	A	-	1	0	MYH1	10341808	0.551000	0.26497	0.966000	0.40874	0.630000	0.37929	1.450000	0.35134	2.811000	0.96726	0.655000	0.94253	GCC		0.448	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10401083	C	T	10401083	3	4	30	1	0	0	0	0	1	0	0	0	10059	768	27	1	1526	1	MYH1	17	10401083	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	2822677	10401083	70794127	44	2583										
STXBP4	252983	hgsc.bcm.edu	37	chr17	53155448	53155448	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tctctgtgcaggaaagtgttCaggatttaaaaaagagaatc	10	5	2	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr17:53155448C>G	ENST00000376352.2	+	14	1405	c.1198C>G	c.(1198-1200)Cag>Gag	p.Q400E	STXBP4_ENST00000434978.2_Missense_Mutation_p.Q378E	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	400					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.Q400E(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						GGAAAGTGTTCAGGATTTAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											82	83	83					17																	53155448		2203	4300	6503	50510447	SO:0001583	missense	252983			BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1198C>G	17.37:g.53155448C>G	ENSP00000365530:p.Gln400Glu		50510447	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	37	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826606	0.32329	.	.	ENSG00000166263	ENST00000376352;ENST00000434978	T;T	0.49432	0.78;0.78	5.33	5.33	0.75918	.	0.159950	0.56097	D	0.000034	T	0.44307	0.1287	M	0.65320	2	0.80722	D	1	B;B	0.32350	0.307;0.366	B;B	0.27170	0.051;0.077	T	0.42666	-0.9438	10	0.45353	T	0.12	-3.1791	13.3593	0.60646	0.1575:0.8425:0.0:0.0	.	378;400	E7EPP7;Q6ZWJ1	.;STXB4_HUMAN	E	400;378	ENSP00000365530:Q400E;ENSP00000391087:Q378E	ENSP00000365530:Q400E	Q	+	1	0	STXBP4	50510447	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	3.872000	0.56085	2.644000	0.89710	0.655000	0.94253	CAG		0.338	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		G	53155448	C	G	53155448	3	3	30	1	0	0	0	0	1	0	0	0	15394	827	29	5	1244	5	STXBP4	17	53155448	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	42754365	53155448	28039762	45	2584										
SLC39A11	201266	hgsc.bcm.edu	37	chr17	70943964	70943964	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tcagacttcttcttcatcaaCgtagagccgaagttcagtgc	8	11	6	2	rs138248966	byFrequency	TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr17:70943964C>T	ENST00000542342.2	-	5	445	c.357G>A	c.(355-357)acG>acA	p.T119T	SLC39A11_ENST00000579732.1_Silent_p.T119T|SLC39A11_ENST00000255559.3_Silent_p.T119T	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	119					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.T119T(1)		endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						TCTTCATCAACGTAGAGCCGA	0.527													C|||	5	0.000998403	0	0	5008	,	,		19344	0.005		0	False		,,,				2504	0				NSCLC(95;736 1527 12296 39625 41839)											1	Substitution - coding silent(1)	large_intestine(1)	17											125	111	116					17																	70943964		2203	4300	6503	68455559	SO:0001819	synonymous_variant	201266			AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"Solute carriers"	14463	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 26"	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.357G>A	17.37:g.70943964C>T			68455559	B2R8H7|Q8WZ81	Silent	SNP	ENST00000542342.2	37	CCDS54160.1																																																																																				0.527	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			T	70943964	C	T	70943964	2	4	30	1	0	0	0	0	0	0	0	1	14651	523	19	1		1	SLC39A11	17	70943964	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	17788516	70943964	10251246	46	2585										
RNF157	114804	hgsc.bcm.edu	37	chr17	74148454	74148454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	accaggtaagcagacctcagAgcacagcttattgtccagtg	10	11	1	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr17:74148454A>G	ENST00000269391.6	-	18	2035	c.1903T>C	c.(1903-1905)Tct>Cct	p.S635P	RNF157_ENST00000319945.6_Missense_Mutation_p.S613P|RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000592748.1_RNA	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	635							zinc ion binding (GO:0008270)	p.S1239P(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CAGACCTCAGAGCACAGCTTA	0.512																																					GBM(186;507 2120 27388 27773 52994)											1	Substitution - Missense(1)	large_intestine(1)	17											287	215	239					17																	74148454		2203	4300	6503	71660049	SO:0001583	missense	114804			AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.1903T>C	17.37:g.74148454A>G	ENSP00000269391:p.Ser635Pro		71660049	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240882	0.39598	.	.	ENSG00000141576	ENST00000269391;ENST00000319945	T;T	0.41758	1.43;0.99	5.71	0.884	0.19182	.	0.147882	0.48286	N	0.000194	T	0.34600	0.0903	L	0.59436	1.845	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.10590	-1.0623	10	0.29301	T	0.29	-4.421	9.5203	0.39131	0.7274:0.0:0.2726:0.0	.	613;635	Q96PX1-2;Q96PX1	.;RN157_HUMAN	P	635;613	ENSP00000269391:S635P;ENSP00000321837:S613P	ENSP00000269391:S635P	S	-	1	0	RNF157	71660049	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	3.553000	0.53713	-0.129000	0.11620	0.533000	0.62120	TCT		0.512	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		G	74148454	A	G	74148454	3	3	30	1	0	0	0	0	1	0	0	0	13491	304	11	4	144	4	RNF157	17	74148454	Missense_Mutation	SNP	A	TCGA-AG-3605-01A-01W-0833-10	3204490	74148454	7046756	47	2586										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55322536	55322536	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	catccttatgtaagaccatcGgccatgcaccagcagtagcc	8	14	0	1	rs374340059		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr18:55322536G>A	ENST00000283684.4	-	22	2820	c.2821C>T	c.(2821-2823)Cga>Tga	p.R941*	RP11-35G9.3_ENST00000592201.1_RNA|ATP8B1_ENST00000536015.1_Nonsense_Mutation_p.R941*|RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	941					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R941*(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				TAAGACCATCGGCCATGCACC	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	18						G	,stop/ARG	0,4406		0,0,2203	160	134	143		,2821	5	1	18		143	1,8599	1.2+/-3.3	0,1,4299	no	intron,stop-gained	ATP8B1,LOC100505549	NM_001242804.1,NM_005603.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	,941/1252	55322536	1,13005	2203	4300	6503	53473534	SO:0001587	stop_gained	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2821C>T	18.37:g.55322536G>A	ENSP00000283684:p.Arg941*		53473534	Q9BTP8	Nonsense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	G	41	8.576052	0.98870	0.0	1.16E-4	ENSG00000081923	ENST00000283684;ENST00000536015	.	.	.	5.9	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2467	0.82448	0.0:0.0:0.8662:0.1338	.	.	.	.	X	941	.	ENSP00000283684:R941X	R	-	1	2	ATP8B1	53473534	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.491000	0.66887	1.489000	0.48450	0.561000	0.74099	CGA		0.433	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		A	55322536	G	A	55322536	4	1	30	1	0	0	0	0	0	1	0	0	1195	1124	39	1	958	1	ATP8B1	18	55322536	Nonsense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10		55322536	22754712	48	2587										
ATG4D	84971	hgsc.bcm.edu	37	chr19	10655509	10655509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gcaagatctccagcatccacCtctgtggccgccgctaccgt	9	17	2	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr19:10655509C>T	ENST00000309469.4	+	2	459	c.286C>T	c.(286-288)Ctc>Ttc	p.L96F	ATG4D_ENST00000540862.1_5'Flank	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	96	Cryptic mitochondrial signal peptide.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)	p.L96F(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CAGCATCCACCTCTGTGGCCG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	80	80					19																	10655509		2203	4300	6503	10516509	SO:0001583	missense	84971			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.286C>T	19.37:g.10655509C>T	ENSP00000311318:p.Leu96Phe		10516509	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410278	0.62399	.	.	ENSG00000130734	ENST00000309469	T	0.48836	0.8	4.4	3.34	0.38264	.	0.524501	0.18714	N	0.133220	T	0.56156	0.1966	M	0.71036	2.16	0.80722	D	1	B;D;P	0.61697	0.391;0.99;0.691	B;P;B	0.54815	0.23;0.761;0.259	T	0.53208	-0.8471	10	0.29301	T	0.29	-29.9552	9.9804	0.41811	0.0:0.7934:0.2066:0.0	.	33;119;96	B4DGM8;B7ZAY9;Q86TL0	.;.;ATG4D_HUMAN	F	96	ENSP00000311318:L96F	ENSP00000311318:L96F	L	+	1	0	ATG4D	10516509	0.845000	0.29573	0.992000	0.48379	0.998000	0.95712	1.452000	0.35156	1.022000	0.39626	0.551000	0.68910	CTC		0.647	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		T	10655509	C	T	10655509	3	4	30	1	0	0	0	0	1	0	0	0	1100	681	24	3	292	3	ATG4D	19	10655509	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10		10655509	48473474	49	2588										
ATP1A3	478	hgsc.bcm.edu	37	chr19	42492205	42492205	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	aagagctgccggcaaaacttGacccactctggggtggtagg	14	10	1	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr19:42492205G>C	ENST00000302102.5	-	4	390	c.240C>G	c.(238-240)gtC>gtG	p.V80V	ATP1A3_ENST00000545399.1_Silent_p.V93V|ATP1A3_ENST00000468774.2_5'Flank|ATP1A3_ENST00000602133.1_Silent_p.V50V|ATP1A3_ENST00000543770.1_Silent_p.V91V	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	80					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.V80V(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						GGCAAAACTTGACCCACTCTG	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	19											110	118	115					19																	42492205		2203	4300	6503	47184045	SO:0001819	synonymous_variant	478				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.240C>G	19.37:g.42492205G>C			47184045	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Silent	SNP	ENST00000302102.5	37	CCDS12594.1																																																																																				0.642	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		C	42492205	G	C	42492205	2	2	30	1	0	0	0	0	0	0	0	1	1131	1277	45	5		5	ATP1A3	19	42492205	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	31836696	42492205	16636778	50	2589										
ZSCAN5A	79149	hgsc.bcm.edu	37	chr19	56733295	56733295	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ttacattgaaagagtctctcGcctgtgtgtgatctcttgtg	10	8	2	3	rs540386597		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr19:56733295G>C	ENST00000587340.1	-	7	1835	c.1140C>G	c.(1138-1140)ggC>ggG	p.G380G	ZSCAN5A_ENST00000587492.1_Silent_p.G234G|ZSCAN5A_ENST00000592355.1_Silent_p.G379G|ZSCAN5A_ENST00000391713.1_Silent_p.G380G|ZSCAN5A_ENST00000254165.3_Silent_p.G263G			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	380					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.G380G(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						AGAGTCTCTCGCCTGTGTGTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	19											67	67	67					19																	56733295		2203	4300	6503	61425107	SO:0001819	synonymous_variant	79149			AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.1140C>G	19.37:g.56733295G>C			61425107	B4DX98|Q49A73|Q53F04|Q8N7B3	Silent	SNP	ENST00000587340.1	37	CCDS12941.1																																																																																				0.517	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		C	56733295	G	C	56733295	2	2	30	1	0	0	0	0	0	0	0	1	18277	1074	38	5		5	ZSCAN5A	19	56733295	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	14241090	56733295	2395688	51	2590										
C20orf3	57136	hgsc.bcm.edu	37	chr20	24950260	24950260	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cgcagctggtccaataaaacTtttacttccctggtcacagt	7	12	1	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr20:24950260T>G	ENST00000217456.2	-	7	1040	c.750A>C	c.(748-750)aaA>aaC	p.K250N	APMAP_ENST00000447138.1_Missense_Mutation_p.K250N	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	250					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)	p.K250N(1)									CCAATAAAACTTTTACTTCCC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	20											95	92	93					20																	24950260		2203	4300	6503	24898260	SO:0001583	missense	57136			AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"chromosome 20 open reading frame 3"	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.750A>C	20.37:g.24950260T>G	ENSP00000217456:p.Lys250Asn		24898260	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.646|6.646	0.487718|0.487718	0.12641|0.12641	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000217456;ENST00000447138|ENST00000451442	T;T|T	0.52057|0.48836	0.68;0.68|0.8	5.68|5.68	-1.46|-1.46	0.08800|0.08800	Strictosidine synthase, conserved region (1);Six-bladed beta-propeller, TolB-like (1);|.	0.285628|0.285628	0.43110|0.43110	D|D	0.000614|0.000614	T|T	0.40272|0.40272	0.1110|0.1110	L|L	0.47016|0.47016	1.485|1.485	0.39898|0.39898	D|D	0.973865|0.973865	B;B;B|.	0.17268|.	0.021;0.002;0.002|.	B;B;B|.	0.14023|.	0.01;0.004;0.01|.	T|T	0.27262|0.27262	-1.0079|-1.0079	10|8	0.41790|0.09843	T|T	0.15|0.71	-13.6284|-13.6284	11.2399|11.2399	0.48964|0.48964	0.0:0.7617:0.0:0.2383|0.0:0.7617:0.0:0.2383	.|.	250;234;250|.	Q9HDC9-2;A2A2F9;Q9HDC9|.	.;.;APMAP_HUMAN|.	N|T	250|235	ENSP00000217456:K250N;ENSP00000415373:K250N|ENSP00000395874:K235T	ENSP00000217456:K250N|ENSP00000395874:K235T	K|K	-|-	3|2	2|0	C20orf3|C20orf3	24898260|24898260	0.893000|0.893000	0.30496|0.30496	0.009000|0.009000	0.14445|0.14445	0.021000|0.021000	0.10359|0.10359	-0.037000|-0.037000	0.12164|0.12164	-0.392000|-0.392000	0.07751|0.07751	-0.912000|-0.912000	0.02778|0.02778	AAA|AAG		0.532	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		G	24950260	T	G	24950260	3	3	30	1	0	0	0	0	1	0	0	0	2115	1606	56	4	512	4	C20orf3	20	24950260	Missense_Mutation	SNP	T	TCGA-AG-3605-01A-01W-0833-10		24950260	38075260	52	2591										
ENTPD6	955	hgsc.bcm.edu	37	chr20	25205904	25205904	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	atgcatggacctcacctacgTcagcctgctactccaggagt	9	14	2	0			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chr20:25205904T>G	ENST00000376652.4	+	14	1470	c.1307T>G	c.(1306-1308)gTc>gGc	p.V436G	ENTPD6_ENST00000360031.2_Missense_Mutation_p.V435G|ENTPD6_ENST00000433259.2_Silent_p.R416R|ENTPD6_ENST00000354989.5_Missense_Mutation_p.V419G|ENTPD6_ENST00000485936.1_3'UTR			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	436					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)	p.V436G(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						CTCACCTACGTCAGCCTGCTA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	20											117	83	94					20																	25205904		2203	4300	6503	25153904	SO:0001583	missense	955			AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1307T>G	20.37:g.25205904T>G	ENSP00000365840:p.Val436Gly		25153904	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.00|14.00	2.404195|2.404195	0.42613|0.42613	.|.	.|.	ENSG00000197586|ENSG00000197586	ENST00000447877;ENST00000376666|ENST00000354989;ENST00000360031;ENST00000376652	.|T;T;T	.|0.12255	.|2.7;2.7;2.7	5.76|5.76	4.66|4.66	0.58398|0.58398	.|.	.|0.253385	.|0.44483	.|D	.|0.000448	T|T	0.28300|0.28300	0.0699|0.0699	L|L	0.61036|0.61036	1.89|1.89	0.40081|0.40081	D|D	0.976138|0.976138	.|P;P;D;D	.|0.61080	.|0.904;0.917;0.989;0.989	.|P;P;P;P	.|0.60345	.|0.664;0.713;0.873;0.873	T|T	0.02424|0.02424	-1.1161|-1.1161	5|10	.|0.87932	.|D	.|0	-14.226|-14.226	9.4365|9.4365	0.38641|0.38641	0.0:0.081:0.0:0.919|0.0:0.081:0.0:0.919	.|.	.|184;419;435;436	.|B4DHS2;O75354-2;Q5QPJ2;O75354	.|.;.;.;ENTP6_HUMAN	A|G	295;274|419;435;436	.|ENSP00000347084:V419G;ENSP00000353131:V435G;ENSP00000365840:V436G	.|ENSP00000347084:V419G	S|V	+|+	1|2	0|0	ENTPD6|ENTPD6	25153904|25153904	1.000000|1.000000	0.71417|0.71417	0.060000|0.060000	0.19600|0.19600	0.023000|0.023000	0.10783|0.10783	5.535000|5.535000	0.67173|0.67173	1.005000|1.005000	0.39183|0.39183	0.460000|0.460000	0.39030|0.39030	TCA|GTC		0.612	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			G	25205904	T	G	25205904	3	3	30	1	0	0	0	0	1	0	0	0	5156	1667	58	4	1364	4	ENTPD6	20	25205904	Missense_Mutation	SNP	T	TCGA-AG-3605-01A-01W-0833-10	255644	25205904	37819616	53	2592										
ARSF	416	hgsc.bcm.edu	37	chrX	3019147	3019147	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ggcaagattcttgatgctatCgatgattttggcctaaggaa	11	6	1	3	rs141074236	byFrequency	TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:3019147C>T	ENST00000381127.1	+	8	1208	c.987C>T	c.(985-987)atC>atT	p.I329I	ARSF_ENST00000359361.2_Silent_p.I329I|ARSF_ENST00000537104.1_Silent_p.I329I	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	329					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.I329I(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		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)				TTGATGCTATCGATGATTTTG	0.418													c|||	25	0.00662252	0.0182	0.0014	3775	,	,		14782	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X						C	,,	73,3762		1,57,14,1574,557	128	106	114		987,987,987	-5.6	0	X	dbSNP_134	114	0,6727		0,0,0,2428,1871	no	coding-synonymous,coding-synonymous,coding-synonymous	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	,,	1,57,14,4002,2428	TT,TC,T,CC,C		0.0,1.9035,0.6912	,,	329/591,329/591,329/591	3019147	73,10489	2203	4299	6502	3029147	SO:0001819	synonymous_variant	416			X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"Arylsulfatase family"	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.987C>T	X.37:g.3019147C>T			3029147	Q8TCC5	Silent	SNP	ENST00000381127.1	37	CCDS14123.1																																																																																				0.418	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			T	3019147	C	T	3019147	2	4	30	1	0	0	0	0	0	0	0	1	992	874	31	1		1	ARSF	23	3019147	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10		3019147	152251413	54	2593										
PHEX	5251	hgsc.bcm.edu	37	chrX	22117215	22117215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	ctccgagaatgtggtggtccGcgtcccgcagtactttaaag	12	11	0	1	rs376461141		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:22117215G>A	ENST00000379374.4	+	9	1590	c.1025G>A	c.(1024-1026)cGc>cAc	p.R342H	PHEX_ENST00000535894.1_Missense_Mutation_p.R245H|PHEX_ENST00000418858.3_Missense_Mutation_p.R45H|PHEX_ENST00000537599.1_Missense_Mutation_p.R342H|PHEX_ENST00000475778.1_3'UTR	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	342					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R342H(1)		breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GTGGTGGTCCGCGTCCCGCAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	HIS/ARG	2,3833		0,2,1630,571	117	107	110		1025	5.5	0.9	X		110	0,6728		0,0,2428,1872	no	missense	PHEX	NM_000444.4	29	0,2,4058,2443	AA,AG,GG,G		0.0,0.0522,0.0189	probably-damaging	342/750	22117215	2,10561	2203	4300	6503	22027136	SO:0001583	missense	5251			U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.1025G>A	X.37:g.22117215G>A	ENSP00000368682:p.Arg342His		22027136	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	37	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076035	0.76415	5.22E-4	0.0	ENSG00000102174	ENST00000379374;ENST00000537599;ENST00000535894;ENST00000418858	T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79	5.46	5.46	0.80206	Peptidase M13 (1);	0.000000	0.85682	D	0.000000	T	0.79335	0.4428	L	0.38531	1.155	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	P;D	0.64042	0.871;0.921	T	0.75889	-0.3158	10	0.24483	T	0.36	.	18.3838	0.90459	0.0:0.0:1.0:0.0	.	342;342	F5GXU4;P78562	.;PHEX_HUMAN	H	342;342;245;45	ENSP00000368682:R342H;ENSP00000440362:R342H;ENSP00000439418:R245H;ENSP00000443531:R45H	ENSP00000368682:R342H	R	+	2	0	PHEX	22027136	1.000000	0.71417	0.938000	0.37757	0.945000	0.59286	7.562000	0.82300	2.282000	0.76494	0.529000	0.55759	CGC		0.448	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		A	22117215	G	A	22117215	3	1	30	1	0	0	0	0	1	0	0	0	11850	1087	38	1	1059	1	PHEX	23	22117215	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	19098068	22117215	133153345	55	2594										
DMD	1756	hgsc.bcm.edu	37	chrX	32456459	32456459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tagggtctgtgccaatatgcGaatctgatttgggttatcct	11	7	2	1	rs143184877	byFrequency	TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:32456459G>A	ENST00000357033.4	-	29	4176	c.3970C>T	c.(3970-3972)Cgc>Tgc	p.R1324C	DMD_ENST00000378677.2_Missense_Mutation_p.R1320C	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1324					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R1319C(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				GCCAATATGCGAATCTGATTT	0.368													G|||	4	0.0010596	0.0023	0.0014	3775	,	,		13294	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	31,3802		1,25,4,1605,567	126	107	113		3946,3970,3601,3958,3601	5.8	1	X	dbSNP_134	113	0,6728		0,0,0,2428,1872	yes	missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	180,180,180,180,180	1,25,4,4033,2439	AA,AG,A,GG,G		0.0,0.8088,0.2935	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1316/3678,1324/3686,1201/3563,1320/3682,1201/3563	32456459	31,10530	2202	4300	6502	32366380	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3970C>T	X.37:g.32456459G>A	ENSP00000354923:p.Arg1324Cys		32366380	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	2	0.0012055455093429777	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	22.3	4.269927	0.80469	0.008088	0.0	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.21361	2.01;2.01	5.82	5.82	0.92795	.	0.000000	0.37178	U	0.002213	T	0.38665	0.1049	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.99	T	0.40308	-0.9570	10	0.87932	D	0	.	13.6182	0.62121	0.0:0.0:0.8451:0.1549	.	1316;1324;1320	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	C	1316;1320;1324;1324;1201	ENSP00000367948:R1320C;ENSP00000354923:R1324C	ENSP00000354923:R1324C	R	-	1	0	DMD	32366380	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.702000	0.68332	2.453000	0.82957	0.600000	0.82982	CGC		0.368	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32456459	G	A	32456459	3	1	30	1	0	0	0	0	1	0	0	0	4591	1058	37	1	7534	1	DMD	23	32456459	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	10339244	32456459	122814101	56	2595										
BCOR	54880	hgsc.bcm.edu	37	chrX	39913169	39913169	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	cagatacttggatgttataaCacggtaagaggggggtctct	13	6	1	2			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:39913169C>G	ENST00000378444.4	-	14	5174	c.4946G>C	c.(4945-4947)tGt>tCt	p.C1649S	BCOR_ENST00000397354.3_Missense_Mutation_p.C1615S|BCOR_ENST00000342274.4_Missense_Mutation_p.C1615S|BCOR_ENST00000378463.1_Missense_Mutation_p.C492S|BCOR_ENST00000378455.4_Missense_Mutation_p.C1597S	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1649	Necessary and sufficient for interaction with PCGF1.				heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.C1615S(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GATGTTATAACACGGTAAGAG	0.478			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		1	Substitution - Missense(1)	large_intestine(1)	X											46	40	42					X																	39913169		2202	4300	6502	39798113	SO:0001583	missense	54880			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4946G>C	X.37:g.39913169C>G	ENSP00000367705:p.Cys1649Ser		39798113	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.713556	0.68730	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	T;T;T;T;T;T;T	0.72167	-0.55;0.82;0.94;0.93;0.88;0.93;-0.63	5.85	5.85	0.93711	.	.	.	.	.	D	0.82522	0.5055	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.91635	0.999;0.989;0.999	T	0.81276	-0.1006	9	0.42905	T	0.14	-12.9757	19.0962	0.93253	0.0:1.0:0.0:0.0	.	1597;1649;1615	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	S	519;492;1597;1615;1649;1615;322	ENSP00000408006:C519S;ENSP00000367724:C492S;ENSP00000367716:C1597S;ENSP00000380512:C1615S;ENSP00000367705:C1649S;ENSP00000345923:C1615S;ENSP00000387552:C322S	ENSP00000345923:C1615S	C	-	2	0	BCOR	39798113	1.000000	0.71417	0.557000	0.28306	0.218000	0.24690	7.487000	0.81328	2.459000	0.83118	0.600000	0.82982	TGT		0.478	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		G	39913169	C	G	39913169	3	3	30	1	0	0	0	0	1	0	0	0	1387	478	17	5	329	5	BCOR	23	39913169	Missense_Mutation	SNP	C	TCGA-AG-3605-01A-01W-0833-10	7456710	39913169	115357391	57	2596										
AKAP4	8852	hgsc.bcm.edu	37	chrX	49958224	49958224	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	atgcaagaatcaatcaaatcGgacacaatctccttggtgtg	8	9	3	1	rs140947270		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:49958224G>A	ENST00000376056.2	-	5	1263	c.1113C>T	c.(1111-1113)tcC>tcT	p.S371S	AKAP4_ENST00000358526.2_Silent_p.S380S|AKAP4_ENST00000376064.3_Silent_p.S371S|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Intron					A kinase (PRKA) anchor protein 4									p.S380S(2)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					CAATCAAATCGGACACAATCT	0.463																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	X						G	,	2,3833		0,1,1,1631,570	70	59	63		1140,1113	-6.4	1	X	dbSNP_134	63	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous	AKAP4	NM_003886.2,NM_139289.1	,	0,1,1,4059,2442	AA,AG,A,GG,G		0.0,0.0522,0.0189	,	380/855,371/846	49958224	2,10561	2203	4300	6503	49844964	SO:0001819	synonymous_variant	8852			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.1113C>T	X.37:g.49958224G>A			49844964		Silent	SNP	ENST00000376056.2	37	CCDS14330.1																																																																																				0.463	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		A	49958224	G	A	49958224	2	1	30	1	0	0	0	0	0	0	0	1	453	1103	39	1		1	AKAP4	23	49958224	Silent	SNP	G	TCGA-AG-3605-01A-01W-0833-10	10045055	49958224	105312336	58	2597										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104984641	104984641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	tatacctgccatgttgaaaaCcgaaatggacggaaacatgc	9	9	0	1			TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:104984641C>T	ENST00000372582.1	+	8	1761	c.1005C>T	c.(1003-1005)aaC>aaT	p.N335N	IL1RAPL2_ENST00000344799.4_Silent_p.N335N	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	335	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.N335N(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATGTTGAAAACCGAAATGGAC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	X											78	68	71					X																	104984641		2203	4300	6503	104871297	SO:0001819	synonymous_variant	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1005C>T	X.37:g.104984641C>T			104871297	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	37	CCDS14517.1																																																																																				0.378	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	104984641	C	T	104984641	2	4	30	1	0	0	0	0	0	0	0	1	7683	506	18	3		3	IL1RAPL2	23	104984641	Silent	SNP	C	TCGA-AG-3605-01A-01W-0833-10	55026417	104984641	50285919	59	2598										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123526026	123526026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	4	1	0.747272727272727	3.73636363636364	0.415151515151515	1	1	0	gaataaacgtcaccaatcccGaaggtgaatatgtgatgttc	9	8	1	2	rs149944014		TCGA-AG-3605-01A-01W-0833-10	TCGA-AG-3605-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	8b2824f8-9cc9-4efc-b2cb-36c236448b43	6ad1bc07-adc9-4336-a3c2-0fd75ee9d9d0	g.chrX:123526026G>A	ENST00000371130.3	-	27	5606	c.5543C>T	c.(5542-5544)tCg>tTg	p.S1848L	TENM1_ENST00000422452.2_Missense_Mutation_p.S1855L|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1848					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S1850L(1)									CACCAATCCCGAAGGTGAATA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	LEU/SER,LEU/SER,LEU/SER	1,3834		0,1,1631,571	94	79	84		5564,5561,5543	5.4	1	X	dbSNP_134	84	0,6726		0,0,2427,1872	no	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	145,145,145	0,1,4058,2443	AA,AG,GG,G		0.0,0.0261,0.0095	benign,benign,benign	1855/2733,1854/2732,1848/2726	123526026	1,10560	2203	4299	6502	123353707	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5543C>T	X.37:g.123526026G>A	ENSP00000360171:p.Ser1848Leu		123353707	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.483113	0.44147	2.61E-4	0.0	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85702	-2.02;-1.99	5.4	5.4	0.78164	.	0.199775	0.45361	D	0.000370	T	0.81602	0.4857	L	0.56769	1.78	0.41845	D	0.99014	B;B;B	0.15141	0.002;0.01;0.012	B;B;B	0.08055	0.001;0.001;0.003	T	0.76782	-0.2832	10	0.28530	T	0.3	.	12.5975	0.56478	0.081:0.0:0.919:0.0	.	1854;1855;1848	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	L	1848;1855	ENSP00000360171:S1848L;ENSP00000403954:S1855L	ENSP00000360171:S1848L	S	-	2	0	ODZ1	123353707	1.000000	0.71417	0.954000	0.39281	0.923000	0.55619	3.940000	0.56599	2.260000	0.74910	0.600000	0.82982	TCG		0.403	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123526026	G	A	123526026	3	1	30	1	0	0	0	0	1	0	0	0	10865	1059	37	1	2654	1	ODZ1	23	123526026	Missense_Mutation	SNP	G	TCGA-AG-3605-01A-01W-0833-10	18541385	123526026	31744534	60	2599										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2082318	2082318	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gacctaatcagagtcatcggGcgcgggagctacgccaaggt	14	11	2	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:2082318G>T	ENST00000400921.2	+	6	911	c.228G>T	c.(226-228)ggG>ggT	p.G76G	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Silent_p.G76G	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	259	OPR.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.G259G(2)		breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	GAGTCATCGGGCGCGGGAGCT	0.517																																																2	Substitution - coding silent(2)	large_intestine(2)	1											79	78	78					1																	2082318		2203	4300	6503	2072178	SO:0001819	synonymous_variant	5590			BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.228G>T	1.37:g.2082318G>T			2072178	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																				0.517	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2082318	G	T	2082318	2	4	31	1	0	0	0	0	0	0	0	1	12551	1190	42	2		2	PRKCZ	1	2082318	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10		2082318	247168303	1	2600										
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35470841	35470841	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tgtccttgcagaagggagctCcgtcacagcagtttttgctt	11	10	1	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:35470841C>G	ENST00000357182.4	-	13	2073	c.1846G>C	c.(1846-1848)Gag>Cag	p.E616Q	ZMYM6_ENST00000487874.1_Missense_Mutation_p.E616Q|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000373340.2_Missense_Mutation_p.E616Q	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	616					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E616Q(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				GAAGGGAGCTCCGTCACAGCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	99	106					1																	35470841		2203	4300	6503	35243428	SO:0001583	missense	9204			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.1846G>C	1.37:g.35470841C>G	ENSP00000349708:p.Glu616Gln		35243428	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	C	3.169	-0.170388	0.06461	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.22336	1.96;3.14	4.8	4.8	0.61643	.	1.542990	0.03394	N	0.202389	T	0.28433	0.0703	L	0.33485	1.01	0.09310	N	1	B;B;B	0.31040	0.165;0.019;0.305	B;B;B	0.39660	0.069;0.03;0.306	T	0.43556	-0.9384	10	0.21014	T	0.42	-0.0065	16.5768	0.84704	0.0:1.0:0.0:0.0	.	519;616;616	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	Q	616	ENSP00000362437:E616Q;ENSP00000349708:E616Q	ENSP00000349708:E616Q	E	-	1	0	ZMYM6	35243428	0.002000	0.14202	0.017000	0.16124	0.145000	0.21501	1.412000	0.34714	2.655000	0.90218	0.484000	0.47621	GAG		0.388	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		G	35470841	C	G	35470841	3	3	31	1	0	0	0	0	1	0	0	0	17743	864	30	5	2147	5	ZMYM6	1	35470841	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	33388523	35470841	213779780	2	2601										
ZNF691	51058	hgsc.bcm.edu	37	chr1	43317084	43317084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ccaggagagctttcggcggcGctcagacctcaccacgcacc	11	17	2	2	rs149242992		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:43317084G>A	ENST00000372506.1	+	4	795	c.455G>A	c.(454-456)cGc>cAc	p.R152H	ZNF691_ENST00000397044.3_Missense_Mutation_p.R183H|ZNF691_ENST00000372507.1_Missense_Mutation_p.R152H|ZNF691_ENST00000372508.3_Missense_Mutation_p.R152H|ZNF691_ENST00000372504.1_Missense_Mutation_p.R174H|ZNF691_ENST00000372502.1_Missense_Mutation_p.R174H	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	183						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R152H(1)		large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTTCGGCGGCGCTCAGACCTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	58	53	55		548,455	3.4	1	1	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF691	NM_001242739.1,NM_015911.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	183/316,152/285	43317084	1,13005	2203	4300	6503	43089671	SO:0001583	missense	51058				CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"Zinc fingers, C2H2-type"	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.455G>A	1.37:g.43317084G>A	ENSP00000361584:p.Arg152His		43089671	A8MXP6|B4DJR7|O95878|Q9NWE8	Missense_Mutation	SNP	ENST00000372506.1	37	CCDS476.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.727974	0.30593	0.0	1.16E-4	ENSG00000164011	ENST00000372508;ENST00000372507;ENST00000372506;ENST00000397044;ENST00000372504;ENST00000372503;ENST00000372502	T;T;T;T;T;T	0.08370	3.1;3.1;3.1;3.1;3.1;3.1	5.31	3.42	0.39159	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.222739	0.32703	N	0.005755	T	0.06600	0.0169	L	0.35542	1.07	0.30646	N	0.755923	B;B	0.11235	0.001;0.004	B;B	0.04013	0.001;0.001	T	0.08330	-1.0727	10	0.44086	T	0.13	-22.0432	7.346	0.26664	0.2798:0.0:0.7202:0.0	.	183;183	B4DJR7;Q5VV52	.;ZN691_HUMAN	H	152;152;152;183;174;183;174	ENSP00000361586:R152H;ENSP00000361585:R152H;ENSP00000361584:R152H;ENSP00000380237:R183H;ENSP00000361582:R174H;ENSP00000361580:R174H	ENSP00000361580:R174H	R	+	2	0	ZNF691	43089671	0.000000	0.05858	1.000000	0.80357	0.970000	0.65996	0.076000	0.14712	0.866000	0.35629	0.561000	0.74099	CGC		0.587	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		A	43317084	G	A	43317084	3	1	31	1	0	0	0	0	1	0	0	0	18135	1087	38	1	457	1	ZNF691	1	43317084	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	7846243	43317084	205933537	3	2602										
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110717556	110717556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gcatcgtggggatggctgtcGttaagggcatccagtcctcg	15	10	0	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:110717556G>A	ENST00000331565.4	+	5	1212	c.727G>A	c.(727-729)Gtt>Att	p.V243I	RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.2_ENST00000440688.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	243					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)	p.V243I(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GATGGCTGTCGTTAAGGGCAT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	65	67					1																	110717556		2203	4300	6503	110519079	SO:0001583	missense	388662				CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.727G>A	1.37:g.110717556G>A	ENSP00000330199:p.Val243Ile		110519079	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	1.290	-0.607888	0.03717	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74106	-0.81	5.27	4.36	0.52297	.	0.251270	0.40818	N	0.001010	T	0.11537	0.0281	N	0.00162	-1.95	0.38906	D	0.957431	B	0.02656	0.0	B	0.04013	0.001	T	0.44329	-0.9335	10	0.02654	T	1	.	6.7558	0.23512	0.3062:0.0:0.6937:0.0	.	243	Q9H1V8	S6A17_HUMAN	I	243	ENSP00000330199:V243I	ENSP00000330199:V243I	V	+	1	0	SLC6A17	110519079	1.000000	0.71417	0.908000	0.35775	0.215000	0.24574	5.038000	0.64177	1.347000	0.45714	0.655000	0.94253	GTT		0.607	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110717556	G	A	110717556	3	1	31	1	0	0	0	0	1	0	0	0	14717	1145	40	1	741	1	SLC6A17	1	110717556	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	67400472	110717556	138533065	4	2603										
EDEM3	80267	hgsc.bcm.edu	37	chr1	184703713	184703713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ctgatacgactacatcgttaTctaaattaacatctcttaaa	3	9	2	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:184703713T>C	ENST00000318130.8	-	5	676	c.410A>G	c.(409-411)gAt>gGt	p.D137G	EDEM3_ENST00000367512.3_Missense_Mutation_p.D94G	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	137					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.D94G(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TACATCGTTATCTAAATTAAC	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	50	49					1																	184703713		2196	4287	6483	182970336	SO:0001583	missense	80267			AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.410A>G	1.37:g.184703713T>C	ENSP00000318147:p.Asp137Gly		182970336	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	37	CCDS1363.2	.	.	.	.	.	.	.	.	.	.	T	26.7	4.763199	0.89932	.	.	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.73789	-0.78;-0.78	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.87684	0.6239	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	D	0.89462	0.3737	10	0.72032	D	0.01	.	16.1678	0.81782	0.0:0.0:0.0:1.0	.	137;94	Q9BZQ6;B7ZLZ2	EDEM3_HUMAN;.	G	137;94	ENSP00000318147:D137G;ENSP00000356482:D94G	ENSP00000318147:D137G	D	-	2	0	EDEM3	182970336	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.562000	0.82300	2.218000	0.71995	0.528000	0.53228	GAT		0.254	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		C	184703713	T	C	184703713	3	2	31	1	0	0	0	0	1	0	0	0	4924	1435	50	4	2452	4	EDEM3	1	184703713	Missense_Mutation	SNP	T	TCGA-AG-3608-01A-01W-0833-10	73986157	184703713	64546908	5	2604										
CFHR5	81494	hgsc.bcm.edu	37	chr1	196964972	196964972	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	atcctaattttataataaacGggcctaagaaaatacaatgt	5	6	0	1	rs201808624		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:196964972G>A	ENST00000256785.4	+	5	842	c.733G>A	c.(733-735)Ggg>Agg	p.G245R	CFHR5_ENST00000367414.5_Missense_Mutation_p.G269R			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	245	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)		p.G245R(1)		NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						TATAATAAACGGGCCTAAGAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	94	102	99		733	3.5	0	1		99	0,8600		0,0,4300	no	missense	CFHR5	NM_030787.3	125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	245/570	196964972	1,13005	2203	4300	6503	195231595	SO:0001583	missense	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.733G>A	1.37:g.196964972G>A	ENSP00000256785:p.Gly245Arg		195231595	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615182	0.46631	2.27E-4	0.0	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.72725	-0.68;-0.68	3.49	3.49	0.39957	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.89044	0.6603	H	0.98199	4.17	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80176	-0.1491	9	0.87932	D	0	.	10.838	0.46698	0.0:0.0:1.0:0.0	.	245	Q9BXR6	FHR5_HUMAN	R	269;245	ENSP00000356384:G269R;ENSP00000256785:G245R	ENSP00000256785:G245R	G	+	1	0	CFHR5	195231595	0.984000	0.35163	0.012000	0.15200	0.001000	0.01503	3.122000	0.50446	1.670000	0.50864	0.544000	0.68410	GGG		0.333	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		A	196964972	G	A	196964972	3	1	31	1	0	0	0	0	1	0	0	0	3294	1116	39	1	751	1	CFHR5	1	196964972	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	12261259	196964972	52285649	6	2605										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208206681	208206681	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	taccttggtggccagtagccGggtcaggtagatctcggaca	14	10	2	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:208206681G>A	ENST00000367033.3	-	28	5795	c.5038C>T	c.(5038-5040)Cgg>Tgg	p.R1680W		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1680					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R1680W(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GCCAGTAGCCGGGTCAGGTAG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	113	117					1																	208206681		2203	4300	6503	206273304	SO:0001583	missense	5362			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.5038C>T	1.37:g.208206681G>A	ENSP00000356000:p.Arg1680Trp		206273304	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087286	0.76642	.	.	ENSG00000076356	ENST00000367033	T	0.19250	2.16	5.53	5.53	0.82687	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.113142	0.64402	D	0.000018	T	0.56934	0.2019	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67711	-0.5600	10	0.87932	D	0	.	14.248	0.66001	0.0:0.0:0.8147:0.1853	.	1680	O75051	PLXA2_HUMAN	W	1680	ENSP00000356000:R1680W	ENSP00000356000:R1680W	R	-	1	2	PLXNA2	206273304	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.275000	0.51639	2.605000	0.88082	0.655000	0.94253	CGG		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208206681	G	A	208206681	3	1	31	1	0	0	0	0	1	0	0	0	12151	1115	39	1	666	1	PLXNA2	1	208206681	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	11241709	208206681	41043940	7	2606										
CAMK1G	57172	hgsc.bcm.edu	37	chr1	209785522	209785522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	caaaggaaagtcctcctactGctctgagcccacactcctca	6	16	2	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:209785522G>A	ENST00000009105.1	+	11	1546	c.1301G>A	c.(1300-1302)tGc>tAc	p.C434Y	CAMK1G_ENST00000361322.2_Missense_Mutation_p.C434Y			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	434						calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.C434Y(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		TCCTCCTACTGCTCTGAGCCC	0.557																																					Ovarian(163;530 1939 9680 28669 48710)											1	Substitution - Missense(1)	large_intestine(1)	1											34	36	36					1																	209785522		2203	4299	6502	207852145	SO:0001583	missense	57172				CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.1301G>A	1.37:g.209785522G>A	ENSP00000009105:p.Cys434Tyr		207852145	Q86UH5|Q9Y3J7	Missense_Mutation	SNP	ENST00000009105.1	37	CCDS1486.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849349	0.51270	.	.	ENSG00000008118	ENST00000009105;ENST00000361322	T;T	0.72394	-0.65;-0.65	5.59	5.59	0.84812	.	0.098157	0.45867	D	0.000333	T	0.60689	0.2288	N	0.24115	0.695	0.51012	D	0.999903	P;P	0.40834	0.73;0.468	B;B	0.39258	0.295;0.154	T	0.63681	-0.6582	10	0.45353	T	0.12	.	17.8704	0.88808	0.0:0.0:1.0:0.0	.	434;434	Q96NX5-2;Q96NX5	.;KCC1G_HUMAN	Y	434	ENSP00000009105:C434Y;ENSP00000354861:C434Y	ENSP00000009105:C434Y	C	+	2	0	CAMK1G	207852145	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.812000	0.55628	2.648000	0.89879	0.650000	0.86243	TGC		0.557	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		A	209785522	G	A	209785522	3	1	31	1	0	0	0	0	1	0	0	0	2604	1319	46	3	1339	3	CAMK1G	1	209785522	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	1578841	209785522	39465099	8	2607										
INTS7	25896	hgsc.bcm.edu	37	chr1	212180626	212180626	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	caaccaaagatgacgctgcaAgcagagtgaaagtgtgcaaa	11	8	0	4			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:212180626A>G	ENST00000366994.3	-	6	826	c.722T>C	c.(721-723)cTt>cCt	p.L241P	INTS7_ENST00000366993.3_Missense_Mutation_p.L241P|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000440600.2_Missense_Mutation_p.L192P|INTS7_ENST00000366992.3_Missense_Mutation_p.L241P	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	241					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)		p.L241P(1)		NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		TGACGCTGCAAGCAGAGTGAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	94	100					1																	212180626		2203	4300	6503	210247249	SO:0001583	missense	25896			AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.722T>C	1.37:g.212180626A>G	ENSP00000355961:p.Leu241Pro		210247249	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.744860	0.89663	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.73469	-0.72;-0.72;-0.72;-0.75	6.04	6.04	0.98038	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86653	0.5984	M	0.77486	2.375	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.88074	0.2802	10	0.87932	D	0	-19.3247	16.5763	0.84648	1.0:0.0:0.0:0.0	.	192;241;241;241	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	P	241;241;241;192	ENSP00000355961:L241P;ENSP00000355960:L241P;ENSP00000355959:L241P;ENSP00000388908:L192P	ENSP00000355959:L241P	L	-	2	0	INTS7	210247249	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	8.649000	0.91067	2.317000	0.78254	0.459000	0.35465	CTT		0.388	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		G	212180626	A	G	212180626	3	3	31	1	0	0	0	0	1	0	0	0	7804	72	3	4	2226	4	INTS7	1	212180626	Missense_Mutation	SNP	A	TCGA-AG-3608-01A-01W-0833-10	2395104	212180626	37069995	9	2608										
EPRS	2058	hgsc.bcm.edu	37	chr1	220193411	220193411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tgttgagatttagccgactaTattcccaaatatatggtttt	7	6	0	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:220193411T>C	ENST00000366923.3	-	10	1537	c.1268A>G	c.(1267-1269)tAt>tGt	p.Y423C		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	423	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)	p.Y423C(1)		breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TAGCCGACTATATTCCCAAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											174	167	169					1																	220193411		2203	4300	6503	218260034	SO:0001583	missense	2058			X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.1268A>G	1.37:g.220193411T>C	ENSP00000355890:p.Tyr423Cys		218260034	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450064	0.84101	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	T	0.23754	1.89	5.82	5.82	0.92795	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.63768	0.2539	H	0.94385	3.53	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.995;0.996;0.992	T	0.75196	-0.3403	10	0.87932	D	0	-21.0339	16.182	0.81915	0.0:0.0:0.0:1.0	.	447;423;423	E7EMN0;Q3KQZ8;P07814	.;.;SYEP_HUMAN	C	423;423;447	ENSP00000355890:Y423C	ENSP00000355890:Y423C	Y	-	2	0	EPRS	218260034	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.484000	0.81180	2.222000	0.72286	0.528000	0.53228	TAT		0.363	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220193411	T	C	220193411	3	2	31	1	0	0	0	0	1	0	0	0	5204	1406	49	4	3362	4	EPRS	1	220193411	Missense_Mutation	SNP	T	TCGA-AG-3608-01A-01W-0833-10	8012785	220193411	29057210	10	2609										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247611785	247611785	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gaaaagcctgagctgaccgtCgtctttgagccttcttggta	11	10	2	3	rs201532680		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:247611785C>A	ENST00000336119.3	+	9	3836	c.3090C>A	c.(3088-3090)gtC>gtA	p.V1030V	NLRP3_ENST00000391827.2_Silent_p.V973V|NLRP3_ENST00000366497.2_Silent_p.V973V|NLRP3_ENST00000391828.3_Silent_p.V1030V|NLRP3_ENST00000366496.2_Silent_p.V973V|NLRP3_ENST00000348069.2_Silent_p.V916V	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	1030					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.V1030V(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AGCTGACCGTCGTCTTTGAGC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											89	89	89					1																	247611785		2203	4300	6503	245678408	SO:0001819	synonymous_variant	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.3090C>A	1.37:g.247611785C>A			245678408	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																				0.502	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247611785	C	A	247611785	2	1	31	1	0	0	0	0	0	0	0	1	10509	871	31	2		2	NLRP3	1	247611785	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10	27418374	247611785	1638836	11	2610										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247614762	247614762	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	aaagttgttcagcacctgccGcccgcagaatggcaattgca	10	12	1	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr1:247614762G>T	ENST00000318749.6	-	1	546	c.523C>A	c.(523-525)Cgg>Agg	p.R175R		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R175W(1)|p.R175R(1)		endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-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)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AGCACCTGCCGCCCGCAGAAT	0.602																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|endometrium(1)	1											55	53	53					1																	247614762		2203	4300	6503	245681385	SO:0001819	synonymous_variant	127623				CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.523C>A	1.37:g.247614762G>T			245681385	B2RP03	Silent	SNP	ENST00000318749.6	37	CCDS31090.1																																																																																				0.602	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		T	247614762	G	T	247614762	2	4	31	1	0	0	0	0	0	0	0	1	11019	1086	38	2		2	OR2B11	1	247614762	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10	2977	247614762	1635859	12	2611										
TPO	7173	hgsc.bcm.edu	37	chr2	1457495	1457495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	cagatggggcgcctccaacaCggccctggcacgatggctcc	13	16	0	1	rs139312937		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr2:1457495C>T	ENST00000345913.4	+	6	603	c.512C>T	c.(511-513)aCg>aTg	p.T171M	TPO_ENST00000346956.3_Missense_Mutation_p.T171M|TPO_ENST00000382198.1_Missense_Mutation_p.T171M|TPO_ENST00000349624.3_Missense_Mutation_p.T171M|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.T171M|TPO_ENST00000329066.4_Missense_Mutation_p.T171M|TPO_ENST00000382201.3_Missense_Mutation_p.T171M	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	171					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.T171M(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GCCTCCAACACGGCCCTGGCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	70	78	75		512,512,512,512,512,512	5.3	1	2	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	81,81,81,81,81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	171/934,171/934,171/877,171/877,171/890,171/761	1457495	1,13005	2203	4300	6503	1436502	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.512C>T	2.37:g.1457495C>T	ENSP00000318820:p.Thr171Met		1436502	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676017	0.67928	0.0	1.16E-4	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T	0.74842	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.88;-0.5;-0.5	5.27	5.27	0.74061	.	0.145775	0.64402	D	0.000010	D	0.85847	0.5792	M	0.70842	2.15	0.80722	D	1	D;D;D;D	0.89917	0.989;1.0;0.989;0.981	P;D;P;P	0.72982	0.538;0.979;0.538;0.668	D	0.87183	0.2229	10	0.72032	D	0.01	-13.2269	18.8829	0.92364	0.0:1.0:0.0:0.0	.	171;171;171;171	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	M	171;171;171;171;171;171;171;171;100	ENSP00000337263:T171M;ENSP00000318820:T171M;ENSP00000263886:T171M;ENSP00000332044:T171M;ENSP00000329869:T171M;ENSP00000371636:T171M;ENSP00000390994:T171M;ENSP00000371633:T171M;ENSP00000405788:T100M	ENSP00000329869:T171M	T	+	2	0	TPO	1436502	0.963000	0.33076	1.000000	0.80357	0.260000	0.26232	2.135000	0.42112	2.438000	0.82558	0.557000	0.71058	ACG		0.587	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1457495	C	T	1457495	3	4	31	1	0	0	0	0	1	0	0	0	16450	536	19	1	530	1	TPO	2	1457495	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		1457495	241741878	13	2612										
TSGA10	80705	hgsc.bcm.edu	37	chr2	99725861	99725861	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ataaaacctacccgggcagtTggtgatgggcgtcttggact	13	9	1	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr2:99725861T>C	ENST00000393483.3	-	6	886	c.42A>G	c.(40-42)ccA>ccG	p.P14P	TSGA10_ENST00000542655.1_Silent_p.P14P|TSGA10_ENST00000355053.4_Silent_p.P14P|TSGA10_ENST00000539964.1_Silent_p.P14P|TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000410001.1_Silent_p.P14P	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	14					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.P14P(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CCCGGGCAGTTGGTGATGGGC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	2											134	125	128					2																	99725861		2203	4300	6503	99092293	SO:0001819	synonymous_variant	80705			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.42A>G	2.37:g.99725861T>C			99092293	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Silent	SNP	ENST00000393483.3	37	CCDS2037.1																																																																																				0.368	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		C	99725861	T	C	99725861	2	2	31	1	0	0	0	0	0	0	0	1	16657	1799	63	4		4	TSGA10	2	99725861	Silent	SNP	T	TCGA-AG-3608-01A-01W-0833-10	98268366	99725861	143473512	14	2613										
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217288358	217288358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tatttcttgtcattgcagatGtcaagaccaggaagtggagc	11	7	3	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr2:217288358G>A	ENST00000357276.4	+	6	1429	c.1099G>A	c.(1099-1101)Gtc>Atc	p.V367I	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.V367I	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	367	HARP 2. {ECO:0000255|PROSITE- ProRule:PRU00800}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.V367I(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CATTGCAGATGTCAAGACCAG	0.373									Schimke Immuno-Osseous Dysplasia																																							1	Substitution - Missense(1)	large_intestine(1)	2											222	210	214					2																	217288358		2203	4300	6503	216996603	SO:0001583	missense	50485	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.1099G>A	2.37:g.217288358G>A	ENSP00000349823:p.Val367Ile		216996603	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.611455	0.28712	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000392128;ENST00000412913	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.44	-0.886	0.10590	HepA-related (1);	2.737020	0.00868	N	0.001996	T	0.53222	0.1783	L	0.29908	0.895	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.13124	-1.0521	10	0.16896	T	0.51	0.629	0.7082	0.00920	0.2391:0.1215:0.2682:0.3711	.	367	Q9NZC9	SMAL1_HUMAN	I	367;367;231;87	ENSP00000349823:V367I;ENSP00000350940:V367I;ENSP00000375974:V231I;ENSP00000390248:V87I	ENSP00000349823:V367I	V	+	1	0	SMARCAL1	216996603	0.991000	0.36638	0.251000	0.24312	0.994000	0.84299	0.636000	0.24644	-0.097000	0.12307	0.655000	0.94253	GTC		0.373	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			A	217288358	G	A	217288358	3	1	31	1	0	0	0	0	1	0	0	0	14810	1377	48	3	1113	3	SMARCAL1	2	217288358	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	117562497	217288358	25911015	15	2614										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219225317	219225317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tcctcatcctccccatggaaCggaagatgagtttgctgaag	10	11	1	3	rs373829179		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr2:219225317C>T	ENST00000289388.3	+	5	426	c.397C>T	c.(397-399)Cgg>Tgg	p.R133W	AC021016.8_ENST00000411433.1_RNA|C2orf62_ENST00000481940.1_3'UTR	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		133					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R133W(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCCATGGAACGGAAGATGAG	0.557													C|||	1	0.000199681	0	0	5008	,	,		17412	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	2						C	TRP/ARG	0,4406		0,0,2203	99	83	89		397	-3.8	0	2		89	1,8599	1.2+/-3.3	0,1,4299	no	missense	C2orf62	NM_198559.1	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	133/388	219225317	1,13005	2203	4300	6503	218933561	SO:0001583	missense	375307																														ENST00000289388.3:c.397C>T	2.37:g.219225317C>T	ENSP00000289388:p.Arg133Trp		218933561		Missense_Mutation	SNP	ENST00000289388.3	37	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.960061	0.34565	0.0	1.16E-4	ENSG00000158428	ENST00000289388	.	.	.	4.36	-3.78	0.04333	.	0.357444	0.26300	N	0.025163	T	0.47248	0.1435	L	0.59436	1.845	0.09310	N	1	D	0.71674	0.998	P	0.53861	0.736	T	0.56202	-0.8018	9	0.87932	D	0	-4.5987	14.6876	0.69059	0.8073:0.1927:0.0:0.0	.	133	Q7Z7H3	CB062_HUMAN	W	133	.	ENSP00000289388:R133W	R	+	1	2	C2orf62	218933561	0.001000	0.12720	0.000000	0.03702	0.114000	0.19823	-0.202000	0.09451	-0.510000	0.06523	-0.165000	0.13383	CGG		0.557	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219225317	C	T	219225317	3	4	31	1	0	0	0	0	1	0	0	0	2187	527	19	1	415	1	C2orf62	2	219225317	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	1936959	219225317	23974056	16	2615										
TRAF3IP1	26146	hgsc.bcm.edu	37	chr2	239237961	239237961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ggacagggagaagaacagagAgcatgacaaacctgagaaaa	13	6	0	5			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr2:239237961A>G	ENST00000373327.4	+	5	1115	c.893A>G	c.(892-894)gAg>gGg	p.E298G	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.E298G|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.E298G	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	298	Abolishes microtubules-binding when missing.|DISC1-interaction domain.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.E298G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		AAGAACAGAGAGCATGACAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2											67	76	73					2																	239237961		2199	4286	6485	238902700	SO:0001583	missense	26146			AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"Intraflagellar transport homologs"	17861	protein-coding gene	gene with protein product	"microtubule interacting protein that associates with TRAF3"	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.893A>G	2.37:g.239237961A>G	ENSP00000362424:p.Glu298Gly		238902700	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.641907	0.29157	.	.	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.15256	2.44;2.44;2.44	4.37	4.37	0.52481	.	0.800459	0.11944	N	0.514359	T	0.17704	0.0425	L	0.44542	1.39	0.32258	N	0.570498	P;B	0.40731	0.728;0.008	B;B	0.39339	0.297;0.012	T	0.11542	-1.0583	10	0.44086	T	0.13	-14.7413	12.1392	0.53989	1.0:0.0:0.0:0.0	.	298;298	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	G	298	ENSP00000375851:E298G;ENSP00000362424:E298G;ENSP00000375852:E298G	ENSP00000362424:E298G	E	+	2	0	TRAF3IP1	238902700	1.000000	0.71417	0.208000	0.23602	0.369000	0.29798	3.397000	0.52572	1.754000	0.51921	0.533000	0.62120	GAG		0.502	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650		G	239237961	A	G	239237961	3	3	31	1	0	0	0	0	1	0	0	0	16480	304	11	4	911	4	TRAF3IP1	2	239237961	Missense_Mutation	SNP	A	TCGA-AG-3608-01A-01W-0833-10	20012644	239237961	3961412	17	2616										
TCTEX1D2	255758	hgsc.bcm.edu	37	chr3	196022935	196022935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	catcccagaaacagcgagaaGccatgctaaaaaatccaaga	7	11	0	3			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr3:196022935G>A	ENST00000325318.5	-	4	458	c.323C>T	c.(322-324)gCt>gTt	p.A108V	RP11-447L10.1_ENST00000431391.1_Intron	NM_152773.4	NP_689986.2	Q8WW35	TC1D2_HUMAN	Tctex1 domain containing 2	108								p.A108V(1)		breast(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	7	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ACAGCGAGAAGCCATGCTAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	97	99					3																	196022935		2203	4300	6503	197507332	SO:0001583	missense	255758			BC021177	CCDS33929.1	3q29	2010-07-19			ENSG00000213123	ENSG00000213123			28482	protein-coding gene	gene with protein product						12477932	Standard	NM_152773		Approved	MGC33212	uc003fwi.3	Q8WW35	OTTHUMG00000155672	ENST00000325318.5:c.323C>T	3.37:g.196022935G>A	ENSP00000324323:p.Ala108Val		197507332	A6NCN5	Missense_Mutation	SNP	ENST00000325318.5	37	CCDS33929.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.424164	0.83667	.	.	ENSG00000213123	ENST00000325318	T	0.37058	1.22	4.95	4.95	0.65309	.	0.223550	0.27581	U	0.018738	T	0.51736	0.1692	M	0.71920	2.185	0.80722	D	1	P	0.49090	0.919	P	0.55749	0.783	T	0.45366	-0.9266	10	0.37606	T	0.19	4.5712	13.8915	0.63742	0.0:0.0:1.0:0.0	.	108	Q8WW35	TC1D2_HUMAN	V	108	ENSP00000324323:A108V	ENSP00000324323:A108V	A	-	2	0	TCTEX1D2	197507332	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.452000	0.73485	2.730000	0.93505	0.655000	0.94253	GCT		0.378	TCTEX1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341166.1	NM_152773		A	196022935	G	A	196022935	3	1	31	1	0	0	0	0	1	0	0	0	15759	971	34	3	113	3	TCTEX1D2	3	196022935	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		196022935	1999495	18	2617										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tttcatgaagatgcatacaaCgcacagtggaagtatgccca	9	9	1	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	114	Substitution - Missense(113)|Unknown(1)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	4											253	218	230					4																	153249384		2203	4300	6503	153468834	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His		153468834	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153249384	C	T	153249384	3	4	31	1	0	0	0	0	1	0	0	0	5788	536	19	1	745	1	FBXW7	4	153249384	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		153249384	37904892	19	2618										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113831789	113831789	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	atggagagctacgacaagcaCgtcacttacaatgctgagcg	11	10	1	2	rs573113551		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr5:113831789C>T	ENST00000512097.3	+	9	2668	c.1650C>T	c.(1648-1650)caC>caT	p.H550H	RP11-492A10.1_ENST00000514115.1_RNA|KCNN2_ENST00000503706.1_Silent_p.H202H|KCNN2_ENST00000264773.3_Silent_p.H550H			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	550					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.H550H(2)|p.H202H(2)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	ACGACAAGCACGTCACTTACA	0.547													c|||	1	0.000199681	0	0	5008	,	,		17795	0.001		0	False		,,,				2504	0															4	Substitution - coding silent(4)	large_intestine(4)	5											120	114	116					5																	113831789		2202	4300	6502	113859688	SO:0001819	synonymous_variant	3781			AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.1650C>T	5.37:g.113831789C>T			113859688	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	37	CCDS4114.1																																																																																				0.547	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113831789	C	T	113831789	2	4	31	1	0	0	0	0	0	0	0	1	8100	535	19	1		1	KCNN2	5	113831789	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10		113831789	67083471	20	2619										
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138223183	138223183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	acaatttaatcattagctccGcaaagctgtcatggaccacg	7	11	2	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr5:138223183G>A	ENST00000302763.7	+	9	1238	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	CTNNA1_ENST00000355078.5_Missense_Mutation_p.R280H|CTNNA1_ENST00000518825.1_Missense_Mutation_p.R383H|CTNNA1_ENST00000540387.1_Missense_Mutation_p.R13H|CTNNA1_ENST00000520400.1_3'UTR	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	383	Interaction with alpha-actinin.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)	p.R383H(1)		NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CATTAGCTCCGCAAAGCTGTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											82	82	82					5																	138223183		2203	4300	6503	138251082	SO:0001583	missense	1495			D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1148G>A	5.37:g.138223183G>A	ENSP00000304669:p.Arg383His		138251082	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	32	5.152145	0.94645	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000518381;ENST00000522013;ENST00000520260;ENST00000523298;ENST00000520865;ENST00000519634;ENST00000517533;ENST00000523685;ENST00000519768;ENST00000517656;ENST00000521683;ENST00000521640;ENST00000519116;ENST00000540387;ENST00000520522	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.58133	0.2101	L	0.50333	1.59	0.80722	D	1	D;D;P	0.76494	0.975;0.999;0.702	P;D;P	0.64506	0.615;0.926;0.483	T	0.54840	-0.8233	10	0.39692	T	0.17	-8.1631	18.4839	0.90821	0.0:0.0:1.0:0.0	.	383;260;383	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	H	280;383;383;368;383;13;13;13;13;13;13;13;13;13;13;13;13;13;13;13	ENSP00000347190:R280H;ENSP00000304669:R383H;ENSP00000427821:R383H;ENSP00000429738:R13H;ENSP00000430379:R13H;ENSP00000429569:R13H;ENSP00000428044:R13H;ENSP00000430841:R13H;ENSP00000428088:R13H;ENSP00000431118:R13H;ENSP00000430240:R13H;ENSP00000430177:R13H;ENSP00000430981:R13H;ENSP00000430623:R13H;ENSP00000428894:R13H;ENSP00000438476:R13H;ENSP00000428710:R13H	ENSP00000304669:R383H	R	+	2	0	CTNNA1	138251082	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.827000	0.99397	2.463000	0.83235	0.655000	0.94253	CGC		0.318	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		A	138223183	G	A	138223183	3	1	31	1	0	0	0	0	1	0	0	0	4018	1087	38	1	1178	1	CTNNA1	5	138223183	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	24391394	138223183	42692077	21	2620										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236291	140236291	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	caactgatggaggcaaacctGaatttaccggatctgtttct	9	9	2	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr5:140236291G>C	ENST00000307360.5	+	1	658	c.658G>C	c.(658-660)Gaa>Caa	p.E220Q	PCDHA10_ENST00000506939.2_Missense_Mutation_p.E220Q|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	220	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E220Q(2)		NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCAAACCTGAATTTACCGG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	5											104	99	101					5																	140236291		2196	4271	6467	140216475	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.658G>C	5.37:g.140236291G>C	ENSP00000304234:p.Glu220Gln		140216475	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	8.606	0.888093	0.17540	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.19669	2.13;2.13	4.29	4.29	0.51040	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.26412	0.0645	L	0.33792	1.035	0.09310	N	1	P;P;P	0.49961	0.744;0.627;0.93	B;B;P	0.53224	0.412;0.317;0.721	T	0.04885	-1.0920	9	0.49607	T	0.09	.	10.8894	0.46988	0.0869:0.0:0.9131:0.0	.	220;220;220	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	Q	220	ENSP00000421030:E220Q;ENSP00000304234:E220Q	ENSP00000304234:E220Q	E	+	1	0	PCDHA10	140216475	0.737000	0.28175	0.134000	0.22075	0.988000	0.76386	0.000000	0.12993	2.383000	0.81215	0.561000	0.74099	GAA		0.433	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		C	140236291	G	C	140236291	3	2	31	1	0	0	0	0	1	0	0	0	11551	1291	45	5	660	5	PCDHA10	5	140236291	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	2013108	140236291	40678969	22	2621										
RAB24	53917	hgsc.bcm.edu	37	chr5	176729591	176729591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	cacctacctcctctaggctgCgcagttccttcacccagaac	6	18	2	1	rs200543182		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr5:176729591C>T	ENST00000303251.6	-	4	739	c.320G>A	c.(319-321)cGc>cAc	p.R107H	PRELID1_ENST00000303204.4_5'Flank|RAB24_ENST00000303270.6_Missense_Mutation_p.R78H|PRELID1_ENST00000503216.1_5'Flank|RAB24_ENST00000393611.2_Missense_Mutation_p.R107H	NM_001031677.2	NP_001026847.1	Q969Q5	RAB24_HUMAN	RAB24, member RAS oncogene family	107					autophagy (GO:0006914)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	autophagic vacuole (GO:0005776)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.R107H(2)				all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCTAGGCTGCGCAGTTCCTT	0.567													C|||	1	0.000199681	0	0	5008	,	,		18452	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	5											122	117	119					5																	176729591		2203	4300	6503	176662197	SO:0001583	missense	53917			AF087904	CCDS34300.1	5q35.3	2009-10-06			ENSG00000169228	ENSG00000169228		"RAB, member RAS oncogene"	9765	protein-coding gene	gene with protein product		612415					Standard	NM_001031677		Approved		uc003mfw.3	Q969Q5	OTTHUMG00000130849	ENST00000303251.6:c.320G>A	5.37:g.176729591C>T	ENSP00000304376:p.Arg107His		176662197	Q7Z4Z7	Missense_Mutation	SNP	ENST00000303251.6	37	CCDS34300.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.37	2.215757	0.39102	.	.	ENSG00000169228	ENST00000393611;ENST00000303251;ENST00000303270	T;T;T	0.70631	-0.5;-0.5;-0.5	5.49	1.18	0.20946	Small GTP-binding protein domain (1);	0.076059	0.52532	U	0.000069	T	0.51890	0.1701	L	0.31120	0.905	0.80722	D	1	B;B	0.30511	0.216;0.282	B;B	0.24269	0.052;0.031	T	0.47368	-0.9123	10	0.87932	D	0	-20.9143	6.7933	0.23711	0.0:0.355:0.0:0.645	.	107;78	Q969Q5;F8W8H5	RAB24_HUMAN;.	H	107;107;78	ENSP00000377235:R107H;ENSP00000304376:R107H;ENSP00000302085:R78H	ENSP00000304376:R107H	R	-	2	0	RAB24	176662197	1.000000	0.71417	0.832000	0.32986	0.494000	0.33585	1.788000	0.38714	0.299000	0.22661	-0.266000	0.10368	CGC		0.567	RAB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253416.1	NM_130781		T	176729591	C	T	176729591	3	4	31	1	0	0	0	0	1	0	0	0	12948	768	27	1	311	1	RAB24	5	176729591	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	36493300	176729591	4185669	23	2622										
MLN	4295	hgsc.bcm.edu	37	chr6	33768863	33768863	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ccataggtgaagatggggacGaaggcttccgtctgggaggc	17	8	1	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr6:33768863G>A	ENST00000430124.2	-	2	143	c.78C>T	c.(76-78)ttC>ttT	p.F26F	MLN_ENST00000266003.5_Silent_p.F26F|MLN_ENST00000507738.1_Silent_p.F26F	NM_001040109.1|NM_001184698.1|NM_002418.2	NP_001035198.1|NP_001171627.1|NP_002409.1	P12872	MOTI_HUMAN	motilin	26					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)	receptor binding (GO:0005102)	p.F26F(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)	6						AGATGGGGACGAAGGCTTCCG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											142	132	135					6																	33768863		2203	4300	6503	33876841	SO:0001819	synonymous_variant	4295				CCDS4786.1, CCDS47412.1, CCDS54993.1	6p21.31	2014-01-30			ENSG00000096395	ENSG00000096395		"Endogenous ligands"	7141	protein-coding gene	gene with protein product	"prepromotilin"	158270					Standard	NM_001184698		Approved		uc003off.1	P12872	OTTHUMG00000014536	ENST00000430124.2:c.78C>T	6.37:g.33768863G>A			33876841	B7ZLR7|E9PDN2|J3KN51|Q2M1L2|Q5T975|Q6NSY7	Silent	SNP	ENST00000430124.2	37	CCDS4786.1																																																																																				0.582	MLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040211.4			A	33768863	G	A	33768863	2	1	31	1	0	0	0	0	0	0	0	1	9661	1049	37	1		1	MLN	6	33768863	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10		33768863	137346204	24	2623										
ROS1	6098	hgsc.bcm.edu	37	chr6	117730797	117730797	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ctgctacagccaacctcacaCgactcccgctgtggaagaca	8	16	1	1	rs55736087	byFrequency	TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr6:117730797C>T	ENST00000368508.3	-	4	435	c.237G>A	c.(235-237)tcG>tcA	p.S79S	ROS1_ENST00000368507.3_Silent_p.S88S|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	79					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S79S(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CAACCTCACACGACTCCCGCT	0.468			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"								c|||	3	0.000599042	8e-04	0	5008	,	,		17634	0		0.001	False		,,,				2504	0.001						Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - coding silent(2)	large_intestine(2)	6						T		6,4400	11.4+/-27.6	0,6,2197	137	115	122		237	-7.3	0.2	6	dbSNP_129	122	32,8568	22.2+/-67.0	0,32,4268	no	coding-synonymous	ROS1	NM_002944.2		0,38,6465	TT,TC,CC		0.3721,0.1362,0.2922		79/2348	117730797	38,12968	2203	4300	6503	117837490	SO:0001819	synonymous_variant	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.237G>A	6.37:g.117730797C>T			117837490	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																				0.468	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			T	117730797	C	T	117730797	2	4	31	1	0	0	0	0	0	0	0	1	13568	523	19	1		1	ROS1	6	117730797	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10	83961934	117730797	53384270	25	2624										
KCND2	3751	hgsc.bcm.edu	37	chr7	120381624	120381624	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ggatccgggcagccaaaagcGgaagcgcaaatgcttacatg	13	10	0	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr7:120381624G>A	ENST00000331113.4	+	3	2280	c.1315G>A	c.(1315-1317)Gga>Aga	p.G439R		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	439					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.G439R(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AGCCAAAAGCGGAAGCGCAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											86	94	91					7																	120381624		2203	4300	6503	120168860	SO:0001583	missense	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1315G>A	7.37:g.120381624G>A	ENSP00000333496:p.Gly439Arg		120168860	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.684736	0.88639	.	.	ENSG00000184408	ENST00000331113	D	0.96940	-4.18	5.62	5.62	0.85841	.	0.073236	0.56097	D	0.000039	D	0.93406	0.7897	L	0.38838	1.175	0.45295	D	0.998294	B	0.28636	0.218	B	0.23852	0.049	D	0.90780	0.4678	9	.	.	.	.	19.662	0.95877	0.0:0.0:1.0:0.0	.	439	Q9NZV8	KCND2_HUMAN	R	439	ENSP00000333496:G439R	.	G	+	1	0	KCND2	120168860	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.157000	0.77461	2.649000	0.89929	0.650000	0.86243	GGA		0.373	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		A	120381624	G	A	120381624	3	1	31	1	0	0	0	0	1	0	0	0	8040	1117	39	1	1325	1	KCND2	7	120381624	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		120381624	38757039	26	2625										
SULF1	23213	hgsc.bcm.edu	37	chr8	70536398	70536398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tggcagatagcagcaacgccGtgggcccacctaccactgtc	11	15	0	1	rs146445328		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr8:70536398G>A	ENST00000260128.4	+	15	2533	c.1816G>A	c.(1816-1818)Gtg>Atg	p.V606M	SULF1_ENST00000419716.3_Missense_Mutation_p.V606M|SULF1_ENST00000402687.4_Missense_Mutation_p.V606M|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000458141.2_Missense_Mutation_p.V606M	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	606					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.V606M(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CAGCAACGCCGTGGGCCCACC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	8											65	61	62					8																	70536398		2203	4300	6503	70698952	SO:0001583	missense	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.1816G>A	8.37:g.70536398G>A	ENSP00000260128:p.Val606Met		70698952	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.959901	0.53400	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	D;D;D;D	0.98968	-5.28;-5.28;-5.28;-5.28	5.25	3.42	0.39159	Extracellular sulfatase, C-terminal (1);Alkaline-phosphatase-like, core domain (1);	0.222920	0.45867	D	0.000332	D	0.96303	0.8794	L	0.47716	1.5	0.36094	D	0.84368	P	0.49862	0.929	B	0.43251	0.413	D	0.95523	0.8596	10	0.23891	T	0.37	.	8.9403	0.35725	0.1286:0.1433:0.728:0.0	.	606	Q8IWU6	SULF1_HUMAN	M	606	ENSP00000403040:V606M;ENSP00000260128:V606M;ENSP00000385704:V606M;ENSP00000390315:V606M	ENSP00000260128:V606M	V	+	1	0	SULF1	70698952	0.896000	0.30565	0.981000	0.43875	0.773000	0.43773	1.332000	0.33805	1.408000	0.46895	0.655000	0.94253	GTG		0.512	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		A	70536398	G	A	70536398	3	1	31	1	0	0	0	0	1	0	0	0	15409	1145	40	1	1858	1	SULF1	8	70536398	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		70536398	75827624	27	2626										
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140437201	140437201	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ttcctgcagctgcacaaagaCgatgtgtttgcaaagctcca	9	11	0	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr9:140437201C>T	ENST00000277531.4	-	6	670	c.484G>A	c.(484-486)Gtc>Atc	p.V162I	AL365502.1_ENST00000580317.1_RNA|PNPLA7_ENST00000406427.1_Missense_Mutation_p.V187I	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	162					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)	p.V162I(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TGCACAAAGACGATGTGTTTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	9											78	71	73					9																	140437201		2203	4300	6503	139557022	SO:0001583	missense	375775			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"Patatin-like phospholipase domain containing"	24768	protein-coding gene	gene with protein product		612122	"chromosome 9 open reading frame 111"	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.484G>A	9.37:g.140437201C>T	ENSP00000277531:p.Val162Ile		139557022	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	37	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.727361	0.30593	.	.	ENSG00000130653	ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090;ENST00000371450	T;T;T	0.42900	0.96;0.96;0.96	4.15	3.24	0.37175	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.289186	0.31834	N	0.006992	T	0.27798	0.0684	L	0.47016	1.485	0.80722	D	1	P;P	0.39250	0.541;0.665	B;B	0.28139	0.064;0.086	T	0.05338	-1.0891	10	0.39692	T	0.17	-29.311	7.3581	0.26731	0.1762:0.7295:0.0:0.0943	.	187;162	Q6ZV29-5;Q6ZV29	.;PLPL7_HUMAN	I	162;187;162;153;187	ENSP00000277531:V162I;ENSP00000384610:V187I;ENSP00000400582:V153I	ENSP00000277531:V162I	V	-	1	0	PNPLA7	139557022	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.197000	0.32211	0.851000	0.35264	0.563000	0.77884	GTC		0.632	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140437201	C	T	140437201	3	4	31	1	0	0	0	0	1	0	0	0	12201	536	19	1	3585	1	PNPLA7	9	140437201	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		140437201	776230	28	2627										
SEPHS1	22929	hgsc.bcm.edu	37	chr10	13361209	13361209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gtggtgcgacctcgatgatcCggggtttgtctatgattctg	14	8	2	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr10:13361209C>T	ENST00000327347.5	-	9	1487	c.1112G>A	c.(1111-1113)cGg>cAg	p.R371Q	SEPHS1_ENST00000378614.4_Missense_Mutation_p.R300Q|SEPHS1_ENST00000537130.1_Missense_Mutation_p.R304Q|SEPHS1_ENST00000545675.1_3'UTR	NM_001195602.1|NM_012247.4	NP_001182531.1|NP_036379.2	P49903	SPS1_HUMAN	selenophosphate synthetase 1	371					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|selenide, water dikinase activity (GO:0004756)	p.R371Q(2)		cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|stomach(1)	16						CTCGATGATCCGGGGTTTGTC	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	10											232	231	232					10																	13361209		2203	4300	6503	13401215	SO:0001583	missense	22929			BC000941	CCDS7098.1, CCDS55702.1, CCDS55703.1	10p14	2006-10-06			ENSG00000086475	ENSG00000086475			19685	protein-coding gene	gene with protein product		600902				7665581	Standard	NM_012247		Approved	SPS, SPS1	uc001imk.3	P49903	OTTHUMG00000017696	ENST00000327347.5:c.1112G>A	10.37:g.13361209C>T	ENSP00000367893:p.Arg371Gln		13401215	B4DWK0|D3DRS9|D6PSQ9|Q5T5U8|Q5T5U9|Q9BVT4	Missense_Mutation	SNP	ENST00000327347.5	37	CCDS7098.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222977	0.58668	.	.	ENSG00000086475	ENST00000327347;ENST00000319684;ENST00000378614;ENST00000537130	T;T;T	0.50813	0.88;0.73;0.89	5.23	5.23	0.72850	AIR synthase-related protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	L	0.51914	1.62	0.80722	D	1	B;B;B;B	0.28128	0.098;0.201;0.201;0.055	B;B;B;B	0.12837	0.003;0.008;0.008;0.003	T	0.43540	-0.9385	10	0.59425	D	0.04	-25.7142	19.197	0.93693	0.0:1.0:0.0:0.0	.	323;371;371;304	B4DLS1;P49903;D3DRS9;B4DWK0	.;SPS1_HUMAN;.;.	Q	371;300;300;304	ENSP00000367893:R371Q;ENSP00000367877:R300Q;ENSP00000442768:R304Q	ENSP00000367887:R300Q	R	-	2	0	SEPHS1	13401215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.605000	0.88082	0.655000	0.94253	CGG		0.483	SEPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046856.1	NM_012247		T	13361209	C	T	13361209	3	4	31	1	0	0	0	0	1	0	0	0	14091	652	23	1	70	1	SEPHS1	10	13361209	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		13361209	122173538	29	2628										
MPP7	143098	hgsc.bcm.edu	37	chr10	28527516	28527516	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ccagtgtcactcccagatccCgttgacaaagctggcatgat	9	13	1	3	rs375446313		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr10:28527516C>T	ENST00000375732.1	-	2	277	c.18G>A	c.(16-18)acG>acA	p.T6T	MPP7_ENST00000375719.3_Silent_p.T6T|MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000540098.1_Silent_p.T6T|MPP7_ENST00000337532.5_Silent_p.T6T|MPP7_ENST00000445954.2_5'UTR			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	6					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)	p.T6T(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						TCCCAGATCCCGTTGACAAAG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	10						C		1,4405	2.1+/-5.4	0,1,2202	148	118	128		18	-12.1	0	10		128	0,8600		0,0,4300	no	coding-synonymous	MPP7	NM_173496.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		6/577	28527516	1,13005	2203	4300	6503	28567522	SO:0001819	synonymous_variant	143098			BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.18G>A	10.37:g.28527516C>T			28567522	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	37	CCDS7158.1																																																																																				0.507	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		T	28527516	C	T	28527516	2	4	31	1	0	0	0	0	0	0	0	1	9769	639	23	1		1	MPP7	10	28527516	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10	15166307	28527516	107007231	30	2629										
LRRC18	474354	hgsc.bcm.edu	37	chr10	50121829	50121829	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ttcaagcctaggttcacagcGcggatgttcttgagttgctt	11	9	3	1	rs144747704	byFrequency	TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr10:50121829G>A	ENST00000374160.3	-	1	448	c.372C>T	c.(370-372)cgC>cgT	p.R124R	RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron|LRRC18_ENST00000298124.3_Silent_p.R124R	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	124						cytoplasm (GO:0005737)		p.R124R(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						GGTTCACAGCGCGGATGTTCT	0.597													G|||	3	0.000599042	0.0023	0	5008	,	,		19139	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10						G	,	7,4399	12.9+/-30.5	0,7,2196	93	90	91		372,	-2	0.4	10	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	0,9,6494	AA,AG,GG		0.0233,0.1589,0.0692	,	124/262,	50121829	9,12997	2203	4300	6503	49791835	SO:0001819	synonymous_variant	474354			AY358137	CCDS31197.1	10q11.23	2011-02-10			ENSG00000165383	ENSG00000165383			23199	protein-coding gene	gene with protein product							Standard	NM_001006939		Approved	UNQ933, MGC34773, UNQ9338, VKGE9338	uc001jhd.3	Q8N456	OTTHUMG00000018182	ENST00000374160.3:c.372C>T	10.37:g.50121829G>A			49791835	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																				0.597	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939		A	50121829	G	A	50121829	2	1	31	1	0	0	0	0	0	0	0	1	9003	1074	38	1		1	LRRC18	10	50121829	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10	21594313	50121829	85412918	31	2630										
LALBA	3906	hgsc.bcm.edu	37	chr12	48963683	48963683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gaactcacattcaggcaaagCgatgcctccataaccatcta	6	13	3	0	rs558586421		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr12:48963683C>T	ENST00000301046.2	-	1	146	c.121G>A	c.(121-123)Gct>Act	p.A41T	LALBA_ENST00000549817.1_Missense_Mutation_p.A41T	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-	41					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)	p.A41T(1)		large_intestine(1)|stomach(2)	3						TCAGGCAAAGCGATGCCTCCA	0.512													C|||	1	0.000199681	8e-04	0	5008	,	,		18410	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											146	118	127					12																	48963683		2203	4300	6503	47249950	SO:0001583	missense	3906				CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.121G>A	12.37:g.48963683C>T	ENSP00000301046:p.Ala41Thr		47249950	Q6FGX0|Q9UDK4	Missense_Mutation	SNP	ENST00000301046.2	37	CCDS8765.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.537366	0.27475	.	.	ENSG00000167531	ENST00000301046;ENST00000549817	T;T	0.68903	1.05;-0.36	5.03	-10.1	0.00402	Lysozyme-like domain (1);	1.580710	0.03950	N	0.288296	T	0.25344	0.0616	N	0.00855	-1.145	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.23691	-1.0181	10	0.48119	T	0.1	-2.197	0.1309	0.00073	0.2746:0.1765:0.2039:0.345	.	41	P00709	LALBA_HUMAN	T	41	ENSP00000301046:A41T;ENSP00000449780:A41T	ENSP00000301046:A41T	A	-	1	0	LALBA	47249950	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.837000	0.04377	-1.455000	0.01923	-0.493000	0.04662	GCT		0.512	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289		T	48963683	C	T	48963683	3	4	31	1	0	0	0	0	1	0	0	0	8626	768	27	1	323	1	LALBA	12	48963683	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		48963683	84888212	32	2631										
GEFT	115557	hgsc.bcm.edu	37	chr12	58007851	58007851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ccccgagagtcttcgaggccGtgacaggattgtgtttggga	15	9	1	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr12:58007851G>A	ENST00000286494.4	+	6	1065	c.605G>A	c.(604-606)cGt>cAt	p.R202H	AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.R241H	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	202	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R202H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						CTTCGAGGCCGTGACAGGATT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	12											103	101	102					12																	58007851		2203	4300	6503	56294118	SO:0001583	missense	115557				CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.605G>A	12.37:g.58007851G>A	ENSP00000286494:p.Arg202His		56294118	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	.	.	.	.	.	.	.	.	.	.	g	29.9	5.045645	0.93685	.	.	ENSG00000240771	ENST00000333972;ENST00000300189;ENST00000286494	T;T	0.62941	-0.01;-0.01	4.83	3.92	0.45320	Dbl homology (DH) domain (5);	0.000000	0.38272	N	0.001754	T	0.62466	0.2430	L	0.38649	1.16	0.50632	D	0.999881	D;D;D	0.71674	0.998;0.995;0.998	P;P;P	0.60609	0.828;0.774;0.877	T	0.64618	-0.6365	10	0.87932	D	0	.	5.8079	0.18450	0.2653:0.0:0.7347:0.0	.	241;202;76	F8W7Z4;Q86VW2;Q96M35	.;ARHGP_HUMAN;.	H	241;76;202	ENSP00000335560:R241H;ENSP00000286494:R202H	ENSP00000286494:R202H	R	+	2	0	ARHGEF25	56294118	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.758000	0.68776	2.410000	0.81850	0.563000	0.77884	CGT		0.567	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		A	58007851	G	A	58007851	3	1	31	1	0	0	0	0	1	0	0	0	6348	1145	40	1	849	1	GEFT	12	58007851	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	9044168	58007851	75844044	33	2632										
RIC8B	55188	hgsc.bcm.edu	37	chr12	107237687	107237687	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gcttattaaccgaatgttccCgagcccatcgaaacatccga	7	13	0	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr12:107237687C>T	ENST00000392839.2	+	6	1229	c.1123C>T	c.(1123-1125)Cga>Tga	p.R375*	RIC8B_ENST00000392837.4_Nonsense_Mutation_p.R375*|RIC8B_ENST00000355478.2_Nonsense_Mutation_p.R335*|RIC8B_ENST00000549643.1_Intron	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	375					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.R375R(1)|p.R375*(1)		kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						CGAATGTTCCCGAGCCCATCG	0.338																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	12											99	94	96					12																	107237687		2203	4300	6503	105761817	SO:0001587	stop_gained	55188			AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.1123C>T	12.37:g.107237687C>T	ENSP00000376583:p.Arg375*		105761817	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Nonsense_Mutation	SNP	ENST00000392839.2	37	CCDS9109.2	.	.	.	.	.	.	.	.	.	.	C	36	5.779204	0.96929	.	.	ENSG00000111785	ENST00000392837;ENST00000392839;ENST00000355478	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.704	14.2787	0.66196	0.1488:0.8512:0.0:0.0	.	.	.	.	X	375;375;335	.	ENSP00000347662:R335X	R	+	1	2	RIC8B	105761817	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.616000	0.36933	2.583000	0.87209	0.557000	0.71058	CGA		0.338	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157		T	107237687	C	T	107237687	4	4	31	1	0	0	0	0	0	1	0	0	13393	644	23	1	1145	1	RIC8B	12	107237687	Nonsense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	49229836	107237687	26614208	34	2633										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109940887	109940887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ggaatattctcaggcctgtcGggggtaaacgggtcgactct	14	9	2	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr12:109940887G>A	ENST00000342494.3	+	14	1937	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R	UBE3B_ENST00000434735.2_Missense_Mutation_p.G448R|UBE3B_ENST00000280774.5_Missense_Mutation_p.G448R|UBE3B_ENST00000535900.1_3'UTR	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	448					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.G448R(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						CAGGCCTGTCGGGGGTAAACG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	12											121	115	117					12																	109940887		2203	4300	6503	108425270	SO:0001583	missense	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1342G>A	12.37:g.109940887G>A	ENSP00000340596:p.Gly448Arg		108425270	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	32	5.161550	0.94727	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.45668	1.24;0.89;1.49;1.24	5.81	5.81	0.92471	.	0.044702	0.85682	N	0.000000	T	0.48370	0.1496	M	0.63428	1.95	0.80722	D	1	D	0.60575	0.988	P	0.44696	0.458	T	0.53358	-0.8450	10	0.66056	D	0.02	-7.5618	18.6619	0.91474	0.0:0.0:1.0:0.0	.	448	Q7Z3V4	UBE3B_HUMAN	R	448	ENSP00000391529:G448R;ENSP00000280774:G448R;ENSP00000443131:G448R;ENSP00000340596:G448R	ENSP00000280774:G448R	G	+	1	0	UBE3B	108425270	1.000000	0.71417	0.956000	0.39512	0.932000	0.56968	8.952000	0.93031	2.741000	0.93983	0.655000	0.94253	GGG		0.522	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		A	109940887	G	A	109940887	3	1	31	1	0	0	0	0	1	0	0	0	16920	1116	39	1	1388	1	UBE3B	12	109940887	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	2703200	109940887	23911008	35	2634										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25744387	25744387	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	agcgcagctgccaccttagcCgcgccctcctggggctcggg	14	17	0	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr13:25744387C>T	ENST00000515384.1	-	1	2038	c.1371G>A	c.(1369-1371)gcG>gcA	p.A457A	AMER2_ENST00000357816.2_Silent_p.A338A|AMER2_ENST00000381853.3_Silent_p.A338A|AMER2-AS1_ENST00000413501.1_lincRNA			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	457			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.A338A(1)|p.A457A(1)									CCACCTTAGCCGCGCCCTCCT	0.652																																																2	Substitution - coding silent(2)	large_intestine(2)	13											24	23	23					13																	25744387		2203	4300	6503	24642387	SO:0001819	synonymous_variant	219287			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1371G>A	13.37:g.25744387C>T			24642387	Q5RL80|Q5VX56|Q8N593|Q96NN5	Silent	SNP	ENST00000515384.1	37	CCDS53859.1																																																																																				0.652	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25744387	C	T	25744387	2	4	31	1	0	0	0	0	0	0	0	1	5438	639	23	1		1	FAM123A	13	25744387	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10		25744387	89425491	36	2635										
FRMD6	122786	hgsc.bcm.edu	37	chr14	52174921	52174921	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gaggctgtccgactggatgaCgtcgctgttcattactacag	12	10	1	1	rs201743850		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr14:52174921C>T	ENST00000344768.5	+	7	880	c.684C>T	c.(682-684)gaC>gaT	p.D228D	FRMD6_ENST00000554167.1_Silent_p.D151D|FRMD6_ENST00000356218.4_Silent_p.D220D|FRMD6_ENST00000395718.2_Silent_p.D220D			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	228	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.D220D(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					GACTGGATGACGTCGCTGTTC	0.393													C|||	1	0.000199681	0	0	5008	,	,		18243	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14											87	75	79					14																	52174921		2203	4300	6503	51244671	SO:0001819	synonymous_variant	122786			BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.684C>T	14.37:g.52174921C>T			51244671	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																				0.393	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		T	52174921	C	T	52174921	2	4	31	1	0	0	0	0	0	0	0	1	6073	535	19	1		1	FRMD6	14	52174921	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10		52174921	55174619	37	2636										
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55215575	55215575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	cctccgcctgcacaaatatgCcgcgcttttctcccagatga	7	16	1	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr14:55215575C>T	ENST00000554335.1	+	5	1685	c.1022C>T	c.(1021-1023)gCc>gTc	p.A341V	SAMD4A_ENST00000357634.3_Missense_Mutation_p.A340V|SAMD4A_ENST00000251091.5_Missense_Mutation_p.A253V|SAMD4A_ENST00000392067.3_Missense_Mutation_p.A341V			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	341	SAM.				negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.A340V(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CACAAATATGCCGCGCTTTTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	51	53					14																	55215575		2193	4283	6476	54285325	SO:0001583	missense	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1022C>T	14.37:g.55215575C>T	ENSP00000452535:p.Ala341Val		54285325	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	32	5.177524	0.94846	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634	T;T;T	0.49139	0.79;0.79;0.79	5.32	5.32	0.75619	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.66915	0.2838	M	0.61703	1.905	0.80722	D	1	P;D	0.76494	0.699;0.999	P;D	0.70227	0.601;0.968	T	0.65421	-0.6172	10	0.48119	T	0.1	-13.4416	19.1782	0.93612	0.0:1.0:0.0:0.0	.	253;341	Q9UPU9-3;Q9UPU9	.;SMAG1_HUMAN	V	341;341;253;252;340	ENSP00000452535:A341V;ENSP00000375919:A341V;ENSP00000350261:A340V	ENSP00000306381:A253V	A	+	2	0	SAMD4A	54285325	1.000000	0.71417	0.934000	0.37439	0.816000	0.46133	7.349000	0.79376	2.769000	0.95229	0.563000	0.77884	GCC		0.547	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55215575	C	T	55215575	3	4	31	1	0	0	0	0	1	0	0	0	13858	739	26	3	1033	3	SAMD4A	14	55215575	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	3040654	55215575	52133965	38	2637										
FNTB	2342	hgsc.bcm.edu	37	chr14	65520041	65520041	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	atgtgctgccagtgccctgcGggggggcttctggataaacc	15	11	1	0	rs149471226	byFrequency	TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr14:65520041G>A	ENST00000246166.2	+	10	1275	c.1041G>A	c.(1039-1041)gcG>gcA	p.A347A	CHURC1-FNTB_ENST00000549987.1_Silent_p.A382A|MAX_ENST00000341653.2_Intron|FNTB_ENST00000542227.1_Silent_p.A301A|FNTB_ENST00000447296.2_Silent_p.A381A	NM_002028.3	NP_002019.1	P49356	FNTB_HUMAN	farnesyltransferase, CAAX box, beta	347					negative regulation of cell proliferation (GO:0008285)|phototransduction, visible light (GO:0007603)|positive regulation of cell cycle (GO:0045787)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|protein farnesylation (GO:0018343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to cytokine (GO:0034097)|response to inorganic substance (GO:0010035)|response to organic cyclic compound (GO:0014070)|rhodopsin mediated signaling pathway (GO:0016056)|wound healing (GO:0042060)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	farnesyltranstransferase activity (GO:0004311)|protein farnesyltransferase activity (GO:0004660)|zinc ion binding (GO:0008270)	p.A347A(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)		AGTGCCCTGCGGGGGGGCTTC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	14						G	,,,	1,4405	2.1+/-5.4	0,1,2202	34	34	34		903,1224,1041,	-10.6	0	14	dbSNP_134	34	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	FNTB,MAX,CHURC1-FNTB	NM_001202558.1,NM_001202559.1,NM_002028.3,NM_197957.2	,,,	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,,,	301/392,408/499,347/438,	65520041	3,13003	2203	4300	6503	64589794	SO:0001819	synonymous_variant	2342				CCDS9769.1	14q23.3	2011-09-28			ENSG00000257365	ENSG00000257365			3785	protein-coding gene	gene with protein product		134636				8276393	Standard	NM_002028		Approved	FPTB		P49356	OTTHUMG00000142811	ENST00000246166.2:c.1041G>A	14.37:g.65520041G>A			64589794	B2RDX6|B4E1A0	Silent	SNP	ENST00000246166.2	37	CCDS9769.1																																																																																				0.597	FNTB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000286392.1	NM_002028		A	65520041	G	A	65520041	2	1	31	1	0	0	0	0	0	0	0	1	5997	1103	39	1		1	FNTB	14	65520041	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10	10304466	65520041	41829499	39	2638										
ENTPD5	957	hgsc.bcm.edu	37	chr14	74439698	74439698	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tcgtaccaccctcagcacttCggcatagcagggctcaaagc	9	15	2	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr14:74439698C>A	ENST00000334696.6	-	13	1235	c.916G>T	c.(916-918)Gaa>Taa	p.E306*	ENTPD5_ENST00000557325.1_Nonsense_Mutation_p.E306*	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	306					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)	p.E306*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CTCAGCACTTCGGCATAGCAG	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											198	196	197					14																	74439698		2203	4300	6503	73509451	SO:0001587	stop_gained	957			AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.916G>T	14.37:g.74439698C>A	ENSP00000335246:p.Glu306*		73509451	A1L4C5|Q96RX0	Nonsense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	.	.	.	.	.	.	.	.	.	.	C	42	9.211031	0.99101	.	.	ENSG00000187097	ENST00000557325;ENST00000334696	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-22.093	19.0466	0.93022	0.0:1.0:0.0:0.0	.	.	.	.	X	306	.	ENSP00000335246:E306X	E	-	1	0	ENTPD5	73509451	1.000000	0.71417	0.966000	0.40874	0.962000	0.63368	7.104000	0.77024	2.744000	0.94065	0.563000	0.77884	GAA		0.567	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		A	74439698	C	A	74439698	4	1	31	1	0	0	0	0	0	1	0	0	5155	893	31	2	386	2	ENTPD5	14	74439698	Nonsense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	8919657	74439698	32909842	40	2639										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25966898	25966898	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ccagttttatctgagaaaatGtactgtatctgtcctaagtc	7	8	2	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr15:25966898G>T	ENST00000356865.6	-	7	1380	c.1269C>A	c.(1267-1269)taC>taA	p.Y423*		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	423					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Y423*(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTGAGAAAATGTACTGTATCT	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											138	125	129					15																	25966898		2203	4300	6503	23517991	SO:0001587	stop_gained	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1269C>A	15.37:g.25966898G>T	ENSP00000349325:p.Tyr423*		23517991	Q4G0S9|Q969I4	Nonsense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	35	5.438841	0.96168	.	.	ENSG00000206190	ENST00000356865	.	.	.	5.53	-1.35	0.09114	.	0.060541	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-31.6891	12.1395	0.53991	0.5848:0.0:0.4152:0.0	.	.	.	.	X	423	.	ENSP00000349325:Y423X	Y	-	3	2	ATP10A	23517991	1.000000	0.71417	0.966000	0.40874	0.344000	0.29017	0.969000	0.29370	-0.568000	0.06038	0.549000	0.68633	TAC		0.428	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25966898	G	T	25966898	4	4	31	1	0	0	0	0	0	1	0	0	1117	1372	48	2	3290	2	ATP10A	15	25966898	Nonsense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		25966898	76564494	41	2640										
CYP11A1	1583	hgsc.bcm.edu	37	chr15	74630994	74630994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	cccagccaaagcccaagttcCggaagtaggtgatgttcttg	11	11	1	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr15:74630994C>T	ENST00000268053.6	-	8	1506	c.1352G>A	c.(1351-1353)cGg>cAg	p.R451Q	CYP11A1_ENST00000419019.2_Missense_Mutation_p.R293Q|CYP11A1_ENST00000358632.4_Missense_Mutation_p.R293Q	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	451					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R451Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	GCCCAAGTTCCGGAAGTAGGT	0.557																																					Esophageal Squamous(87;818 1337 4093 9268 37314)											1	Substitution - Missense(1)	large_intestine(1)	15											164	144	151					15																	74630994		2198	4297	6495	72418047	SO:0001583	missense	1583			AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.1352G>A	15.37:g.74630994C>T	ENSP00000268053:p.Arg451Gln		72418047	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	37	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.149938	0.78001	.	.	ENSG00000140459	ENST00000268053;ENST00000358632;ENST00000419019;ENST00000452422	T;T;T	0.68624	-0.34;-0.34;-0.34	5.14	5.14	0.70334	.	0.214018	0.46758	D	0.000280	T	0.72317	0.3445	L	0.41492	1.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.987	T	0.67277	-0.5711	10	0.21014	T	0.42	-27.3561	12.9989	0.58664	0.0:0.9192:0.0:0.0808	.	421;451	B4DTE5;P05108	.;CP11A_HUMAN	Q	451;293;293;216	ENSP00000268053:R451Q;ENSP00000351455:R293Q;ENSP00000405488:R293Q	ENSP00000268053:R451Q	R	-	2	0	CYP11A1	72418047	0.996000	0.38824	1.000000	0.80357	0.897000	0.52465	0.898000	0.28404	2.389000	0.81357	0.542000	0.68232	CGG		0.557	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			T	74630994	C	T	74630994	3	4	31	1	0	0	0	0	1	0	0	0	4150	652	23	1	221	1	CYP11A1	15	74630994	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	48664096	74630994	27900398	42	2641										
E2F4	1874	hgsc.bcm.edu	37	chr16	67228642	67228642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ctgaagagtgtgagtggtccCattgaggttctgctggtgaa	15	6	1	5			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr16:67228642C>T	ENST00000379378.3	+	6	626	c.567C>T	c.(565-567)ccC>ccT	p.P189P	E2F4_ENST00000564718.1_3'UTR	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	189					blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P189P(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		TGAGTGGTCCCATTGAGGTTC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	16											124	114	118					16																	67228642		2198	4300	6498	65786143	SO:0001819	synonymous_variant	1874			BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.567C>T	16.37:g.67228642C>T			65786143	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	37	CCDS32464.1																																																																																				0.532	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		T	67228642	C	T	67228642	2	4	31	1	0	0	0	0	0	0	0	1	4880	581	21	3		3	E2F4	16	67228642	Silent	SNP	C	TCGA-AG-3608-01A-01W-0833-10		67228642	23126111	43	2642										
TP53	7157	hgsc.bcm.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	31	1	0	0	0	0	1	0	0	0	16421	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		7577539	73617671	44	2643										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42337242	42337242	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	cagaggctgtgaaggatcccCagagcgtgtcaggactgcag	15	10	1	3			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr17:42337242C>G	ENST00000262418.6	-	7	699	c.544G>C	c.(544-546)Ggg>Cgg	p.G182R	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	182	Globular.|Interaction with ANK1. {ECO:0000305}.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.G182R(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GAAGGATCCCCAGAGCGTGTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											91	78	82					17																	42337242		2203	4300	6503	39692768	SO:0001583	missense	6521				CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.544G>C	17.37:g.42337242C>G	ENSP00000262418:p.Gly182Arg		39692768	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	c	19.73	3.882649	0.72410	.	.	ENSG00000004939	ENST00000262418	T	0.67171	-0.25	5.19	5.19	0.71726	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.261736	0.27275	N	0.020114	T	0.69593	0.3128	L	0.37800	1.135	0.25846	N	0.983996	D;P	0.61697	0.99;0.517	P;B	0.58928	0.848;0.229	T	0.62191	-0.6906	10	0.30854	T	0.27	.	14.2885	0.66260	0.0:1.0:0.0:0.0	.	182;182	E2RVJ0;P02730	.;B3AT_HUMAN	R	182	ENSP00000262418:G182R	ENSP00000262418:G182R	G	-	1	0	SLC4A1	39692768	0.004000	0.15560	0.818000	0.32626	0.045000	0.14185	0.170000	0.16663	2.440000	0.82611	0.456000	0.33151	GGG		0.612	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		G	42337242	C	G	42337242	3	3	31	1	0	0	0	0	1	0	0	0	14687	594	21	5	2247	5	SLC4A1	17	42337242	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	34759703	42337242	38857968	45	2644										
FAM38B	63895	hgsc.bcm.edu	37	chr18	10689666	10689666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ttcttaccttctccgactccCgccaacacttcaggatgaat	5	15	3	1			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr18:10689666C>A	ENST00000503781.3	-	45	7144	c.7145G>T	c.(7144-7146)cGg>cTg	p.R2382L	PIEZO2_ENST00000538948.1_Missense_Mutation_p.R339L|PIEZO2_ENST00000302079.6_Missense_Mutation_p.R2382L|PIEZO2_ENST00000285141.4_Missense_Mutation_p.R237L|PIEZO2_ENST00000580640.1_Missense_Mutation_p.R2407L	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2382					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)	p.R2382L(1)|p.R237L(1)									CTCCGACTCCCGCCAACACTT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	18											98	85	90					18																	10689666		2203	4300	6503	10679666	SO:0001583	missense	63895			AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7145G>T	18.37:g.10689666C>A	ENSP00000421377:p.Arg2382Leu		10679666	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Missense_Mutation	SNP	ENST00000503781.3	37		.	.	.	.	.	.	.	.	.	.	C	25.2	4.615439	0.87359	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	T;T;T	0.72282	-0.64;-0.64;-0.64	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000006	D	0.82949	0.5148	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80011	-0.1561	10	0.23302	T	0.38	.	18.0138	0.89232	0.0:1.0:0.0:0.0	.	339	D6RFZ0	.	L	339;2382;339;237	ENSP00000303316:R2382L;ENSP00000443129:R339L;ENSP00000285141:R237L	ENSP00000285141:R237L	R	-	2	0	FAM38B	10679666	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	7.236000	0.78154	2.560000	0.86352	0.643000	0.83706	CGG		0.488	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		A	10689666	C	A	10689666	3	1	31	1	0	0	0	0	1	0	0	0	5574	652	23	2	1145	2	FAM38B	18	10689666	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		10689666	67387582	46	2645										
SMAD2	4087	hgsc.bcm.edu	37	chr18	45374932	45374932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	acctctctgaatttgatgggTctgtaaagccatctacagtg	9	9	3	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr18:45374932T>C	ENST00000402690.2	-	8	1305	c.911A>G	c.(910-912)gAc>gGc	p.D304G	SMAD2_ENST00000586040.1_Missense_Mutation_p.D274G|SMAD2_ENST00000591214.1_Missense_Mutation_p.D274G|SMAD2_ENST00000262160.6_Missense_Mutation_p.D304G|SMAD2_ENST00000356825.4_Missense_Mutation_p.D274G	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	304	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.D304G(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						ATTTGATGGGTCTGTAAAGCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	18											126	114	118					18																	45374932		2203	4300	6503	43628930	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.911A>G	18.37:g.45374932T>C	ENSP00000384449:p.Asp304Gly		43628930		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.866336	0.91511	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.98060	-4.69;-4.69;-4.69	5.81	5.81	0.92471	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98823	0.9603	M	0.87827	2.91	0.80722	D	1	D;D;D	0.89917	1.0;0.988;0.999	D;P;D	0.97110	1.0;0.856;0.988	D	0.99813	1.1042	10	0.87932	D	0	.	16.1773	0.81862	0.0:0.0:0.0:1.0	.	274;274;304	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	G	304;274;304	ENSP00000262160:D304G;ENSP00000349282:D274G;ENSP00000384449:D304G	ENSP00000262160:D304G	D	-	2	0	SMAD2	43628930	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	8.040000	0.89188	2.217000	0.71921	0.482000	0.46254	GAC		0.403	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		C	45374932	T	C	45374932	3	2	31	1	0	0	0	0	1	0	0	0	14795	1667	58	4	508	4	SMAD2	18	45374932	Missense_Mutation	SNP	T	TCGA-AG-3608-01A-01W-0833-10	34685266	45374932	32702316	47	2646										
JAK3	3718	hgsc.bcm.edu	37	chr19	17950354	17950354	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ctacgtgcagccccccatccCagcaggttgccaggagctct	10	17	1	0	rs373774937		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr19:17950354C>A	ENST00000527670.1	-	9	1402	c.1373G>T	c.(1372-1374)tGg>tTg	p.W458L	JAK3_ENST00000526008.1_5'UTR|JAK3_ENST00000534444.1_Missense_Mutation_p.W458L|JAK3_ENST00000458235.1_Missense_Mutation_p.W458L			P52333	JAK3_HUMAN	Janus kinase 3	458	SH2; atypical.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.W458L(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CCCCCCATCCCAGCAGGTTGC	0.622		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	1	Substitution - Missense(1)	large_intestine(1)	19											37	30	32					19																	17950354		2202	4300	6502	17811354	SO:0001583	missense	3718			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1373G>T	19.37:g.17950354C>A	ENSP00000432511:p.Trp458Leu		17811354	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	C	8.707	0.911136	0.17833	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.23552	1.9;1.9;1.9	3.7	3.7	0.42460	SH2 motif (2);	0.307903	0.32218	N	0.006416	T	0.20088	0.0483	L	0.44542	1.39	0.33750	D	0.620571	P;B;B	0.38504	0.634;0.007;0.04	B;B;B	0.33620	0.167;0.009;0.013	T	0.38178	-0.9673	10	0.54805	T	0.06	-3.7306	10.8181	0.46589	0.0:1.0:0.0:0.0	.	458;458;458	B4DK43;P52333-2;P52333	.;.;JAK3_HUMAN	L	458	ENSP00000391676:W458L;ENSP00000432511:W458L;ENSP00000436421:W458L	ENSP00000413248:W458L	W	-	2	0	JAK3	17811354	0.987000	0.35691	0.495000	0.27527	0.091000	0.18340	2.450000	0.44943	1.912000	0.55364	0.455000	0.32223	TGG		0.622	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		A	17950354	C	A	17950354	3	1	31	1	0	0	0	0	1	0	0	0	7960	595	21	2	2061	2	JAK3	19	17950354	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		17950354	41178629	48	2647										
TULP2	7288	hgsc.bcm.edu	37	chr19	49385439	49385439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tttgtccccacgttggtaacGactcagtagcgactcctgtt	9	12	1	0	rs550619669		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr19:49385439G>A	ENST00000221399.3	-	12	1441	c.1297C>T	c.(1297-1299)Cgt>Tgt	p.R433C		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	433					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.R433C(1)		NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CGTTGGTAACGACTCAGTAGC	0.502													G|||	1	0.000199681	0	0	5008	,	,		18950	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											84	72	76					19																	49385439		2203	4300	6503	54077251	SO:0001583	missense	7288			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1297C>T	19.37:g.49385439G>A	ENSP00000221399:p.Arg433Cys		54077251	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398917	0.62177	.	.	ENSG00000104804	ENST00000221399	D	0.96651	-4.08	4.49	4.49	0.54785	Tubby, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.96015	0.8702	M	0.62723	1.935	0.54753	D	0.999984	D	0.69078	0.997	P	0.53266	0.722	D	0.95382	0.8474	10	0.62326	D	0.03	-13.7637	10.2192	0.43188	0.0:0.0:0.802:0.198	.	433	O00295	TULP2_HUMAN	C	433	ENSP00000221399:R433C	ENSP00000221399:R433C	R	-	1	0	TULP2	54077251	0.796000	0.28864	0.550000	0.28217	0.044000	0.14063	2.621000	0.46418	2.494000	0.84150	0.555000	0.69702	CGT		0.502	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		A	49385439	G	A	49385439	3	1	31	1	0	0	0	0	1	0	0	0	16814	1058	37	1	273	1	TULP2	19	49385439	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	31435085	49385439	9743544	49	2648										
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51914441	51914441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tgacgcctgggaagttgagcGtggcataatggagctcctct	14	9	1	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr19:51914441G>A	ENST00000339313.5	-	11	2122	c.2006C>T	c.(2005-2007)aCg>aTg	p.T669M	SIGLEC10_ENST00000436984.2_Missense_Mutation_p.T526M|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.T669M|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.T611M|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.T574M|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.T484M|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.T516M|SIGLEC10_ENST00000442846.3_Missense_Mutation_p.T426M|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.T491M			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	669					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.T611M(1)|p.T669M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GAAGTTGAGCGTGGCATAATG	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	19											168	161	164					19																	51914441		2203	4300	6503	56606253	SO:0001583	missense	89790			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.2006C>T	19.37:g.51914441G>A	ENSP00000345243:p.Thr669Met		56606253	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	14.53	2.562685	0.45694	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313	T;T;T;T;T;T;T;T;T	0.53423	0.94;2.15;1.61;0.78;1.99;1.8;0.62;1.93;0.78	4.55	-2.7	0.06004	.	1.841900	0.02815	N	0.124894	T	0.53367	0.1792	L	0.44542	1.39	0.09310	N	1	D;D;D;D;D;D;D	0.89917	0.993;1.0;0.993;0.996;0.996;0.993;0.981	P;D;P;P;P;P;B	0.66847	0.773;0.947;0.773;0.886;0.886;0.838;0.411	T	0.48833	-0.9000	10	0.66056	D	0.02	.	1.3318	0.02136	0.2085:0.3074:0.3279:0.1562	.	526;484;574;574;516;611;669	C9JM10;E9PL79;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	M	574;491;426;669;516;484;611;526;669	ENSP00000342389:T574M;ENSP00000396742:T491M;ENSP00000395475:T426M;ENSP00000348646:T669M;ENSP00000408387:T516M;ENSP00000431444:T484M;ENSP00000389132:T611M;ENSP00000414324:T526M;ENSP00000345243:T669M	ENSP00000345243:T669M	T	-	2	0	SIGLEC10	56606253	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.283000	0.08433	-0.153000	0.11137	-0.219000	0.12488	ACG		0.552	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		A	51914441	G	A	51914441	3	1	31	1	0	0	0	0	1	0	0	0	14343	1145	40	1	91	1	SIGLEC10	19	51914441	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	2529002	51914441	7214542	50	2649										
TOX2	84969	hgsc.bcm.edu	37	chr20	42682966	42682966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	gagaaaagagaccttcagccGacccaggaaaaaaggccaag	11	10	1	2	rs149594311	byFrequency	TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr20:42682966G>A	ENST00000358131.5	+	5	914	c.706G>A	c.(706-708)Gac>Aac	p.D236N	TOX2_ENST00000372999.1_Missense_Mutation_p.D185N|TOX2_ENST00000341197.4_Missense_Mutation_p.D227N|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000423191.2_Missense_Mutation_p.D185N	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	236					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D185N(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			ACCTTCAGCCGACCCAGGAAA	0.527													G|||	2	0.000399361	0	0.0014	5008	,	,		17026	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20						G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	6,4400	9.9+/-24.2	0,6,2197	25	28	27		553,679,706,553	5.4	0.9	20	dbSNP_134	27	24,8572	16.6+/-54.9	0,24,4274	yes	missense,missense,missense,missense	TOX2	NM_001098796.1,NM_001098797.1,NM_001098798.1,NM_032883.2	23,23,23,23	0,30,6471	AA,AG,GG		0.2792,0.1362,0.2307	probably-damaging,probably-damaging,probably-damaging,probably-damaging	185/465,227/507,236/489,185/465	42682966	30,12972	2203	4298	6501	42116380	SO:0001583	missense	84969			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"granulosa cell HMG box 1"	611163	"chromosome 20 open reading frame 100"	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.706G>A	20.37:g.42682966G>A	ENSP00000350849:p.Asp236Asn		42116380	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Missense_Mutation	SNP	ENST00000358131.5	37	CCDS42875.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	32	5.188325	0.94923	0.001362	0.002792	ENSG00000124191	ENST00000341197;ENST00000423191;ENST00000372999;ENST00000358131;ENST00000435864	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.31	5.44	5.44	0.79542	High mobility group, superfamily (1);	0.767910	0.12144	N	0.495596	T	0.41119	0.1145	L	0.61218	1.895	0.80722	D	1	D;D;P;D;D	0.67145	0.991;0.995;0.94;0.996;0.991	P;P;B;P;P	0.56216	0.627;0.794;0.413;0.646;0.627	T	0.07770	-1.0755	9	.	.	.	.	18.2447	0.89981	0.0:0.0:1.0:0.0	.	105;227;185;236;185	B4DQV8;G3XAC7;A8K1J1;Q96NM4;E1P5X0	.;.;.;TOX2_HUMAN;.	N	227;185;185;236;105	ENSP00000344724:D227N;ENSP00000390278:D185N;ENSP00000362090:D185N;ENSP00000350849:D236N;ENSP00000396777:D105N	.	D	+	1	0	TOX2	42116380	1.000000	0.71417	0.914000	0.36105	0.685000	0.39939	9.869000	0.99810	2.556000	0.86216	0.650000	0.86243	GAC		0.527	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			A	42682966	G	A	42682966	3	1	31	1	0	0	0	0	1	0	0	0	16418	1058	37	1	827	1	TOX2	20	42682966	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		42682966	20342554	51	2650										
CDH26	60437	hgsc.bcm.edu	37	chr20	58574706	58574706	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	acagctgcagcaggacccacGcagggagttaaggtaacatg	13	10	0	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr20:58574706G>A	ENST00000244047.5	+	14	2396	c.2085G>A	c.(2083-2085)acG>acA	p.T695T	CDH26_ENST00000348616.4_Silent_p.T695T|CDH26_ENST00000244049.3_Silent_p.T28T|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000350849.6_Silent_p.T28T			Q8IXH8	CAD26_HUMAN	cadherin 26	695					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T695T(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			CAGGACCCACGCAGGGAGTTA	0.522																																																2	Substitution - coding silent(2)	large_intestine(2)	20											82	79	80					20																	58574706		2203	4300	6503	58008101	SO:0001819	synonymous_variant	60437			AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.2085G>A	20.37:g.58574706G>A			58008101	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37		.	.	.	.	.	.	.	.	.	.	G	1.401	-0.578220	0.03854	.	.	ENSG00000124215	ENST00000370991	.	.	.	2.88	1.93	0.25924	.	.	.	.	.	T	0.27098	0.0664	.	.	.	0.19300	N	0.999976	.	.	.	.	.	.	T	0.19582	-1.0301	4	.	.	.	.	5.8143	0.18484	0.148:0.0:0.852:0.0	.	.	.	.	H	287	.	.	R	+	2	0	CDH26	58008101	0.004000	0.15560	0.007000	0.13788	0.002000	0.02628	1.070000	0.30653	0.805000	0.34159	-0.136000	0.14681	CGC		0.522	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		A	58574706	G	A	58574706	2	1	31	1	0	0	0	0	0	0	0	1	3116	1074	38	1		1	CDH26	20	58574706	Silent	SNP	G	TCGA-AG-3608-01A-01W-0833-10	15891740	58574706	4450814	52	2651										
TCN2	6948	hgsc.bcm.edu	37	chr22	31007025	31007025	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	tctacctgcacagcctcaagCttggttaccagcagtgcctc	8	15	2	0			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr22:31007025C>A	ENST00000215838.3	+	2	726	c.232C>A	c.(232-234)Ctt>Att	p.L78I	TCN2_ENST00000405742.3_Missense_Mutation_p.L78I|TCN2_ENST00000407817.3_Missense_Mutation_p.L78I			P20062	TCO2_HUMAN	transcobalamin II	78					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)	p.L78I(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGCCTCAAGCTTGGTTACCA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											162	146	152					22																	31007025		2203	4300	6503	29337025	SO:0001583	missense	6948				CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"macrocytic anemia"	613441	"transcobalamin II; macrocytic anemia"			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.232C>A	22.37:g.31007025C>A	ENSP00000215838:p.Leu78Ile		29337025	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	.	.	.	.	.	.	.	.	.	.	C	6.832	0.522616	0.13066	.	.	ENSG00000185339	ENST00000215838;ENST00000423350;ENST00000405742;ENST00000407817	T;T;T;T	0.35236	1.33;1.33;1.33;1.32	6.17	1.51	0.23008	.	0.686490	0.15462	N	0.261067	T	0.27489	0.0675	L	0.40543	1.245	0.54753	D	0.999981	B;B;B	0.18166	0.026;0.001;0.001	B;B;B	0.23574	0.047;0.012;0.012	T	0.07966	-1.0745	10	0.33141	T	0.24	-10.0753	8.562	0.33516	0.2781:0.3727:0.3492:0.0	.	78;78;78	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	I	78	ENSP00000215838:L78I;ENSP00000411529:L78I;ENSP00000385914:L78I;ENSP00000384914:L78I	ENSP00000215838:L78I	L	+	1	0	TCN2	29337025	0.412000	0.25392	0.928000	0.36995	0.451000	0.32288	-0.028000	0.12350	0.895000	0.36342	0.655000	0.94253	CTT		0.537	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355		A	31007025	C	A	31007025	3	1	31	1	0	0	0	0	1	0	0	0	15746	797	28	2	238	2	TCN2	22	31007025	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10		31007025	20297541	53	2652										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44074037	44074037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ttctcttgttatcggtccatCgggtttctgagcatcagagt	10	9	3	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chr22:44074037C>T	ENST00000262726.7	-	13	1511	c.1258G>A	c.(1258-1260)Gat>Aat	p.D420N	EFCAB6_ENST00000396231.2_Missense_Mutation_p.D268N|EFCAB6_ENST00000358439.4_Silent_p.P240P	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	420	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.D420N(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATCGGTCCATCGGGTTTCTGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	22											68	67	67					22																	44074037		2203	4300	6503	42405370	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1258G>A	22.37:g.44074037C>T	ENSP00000262726:p.Asp420Asn		42405370	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	3.781	-0.045679	0.07452	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.10099	2.91;2.91	4.96	-2.73	0.05950	EF-hand-like domain (1);	1.430320	0.04009	N	0.297931	T	0.07413	0.0187	N	0.21240	0.645	0.09310	N	1	B	0.22604	0.072	B	0.22753	0.041	T	0.37957	-0.9683	10	0.23891	T	0.37	-0.7381	6.6729	0.23078	0.0:0.4499:0.1205:0.4296	.	420	Q5THR3	EFCB6_HUMAN	N	268;420	ENSP00000379533:D268N;ENSP00000262726:D420N	ENSP00000262726:D420N	D	-	1	0	EFCAB6	42405370	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.145000	0.03194	-0.773000	0.04596	-3.030000	0.00073	GAT		0.323	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	44074037	C	T	44074037	3	4	31	1	0	0	0	0	1	0	0	0	4950	884	31	1	3327	1	EFCAB6	22	44074037	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	13067012	44074037	7230529	54	2653										
DACH2	117154	hgsc.bcm.edu	37	chrX	86069706	86069706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	ttcagctactatgcaaaagcGcctgaagaaggagaaaaaaa	9	7	1	3	rs201550153		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chrX:86069706G>A	ENST00000373125.4	+	10	1553	c.1553G>A	c.(1552-1554)cGc>cAc	p.R518H	DACH2_ENST00000510272.1_Missense_Mutation_p.R299H|DACH2_ENST00000508860.1_Missense_Mutation_p.R351H|DACH2_ENST00000373131.1_Missense_Mutation_p.R505H	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	518	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R518H(1)|p.R505H(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						ATGCAAAAGCGCCTGAAGAAG	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	X						G	HIS/ARG,HIS/ARG,HIS/ARG	0,3835		0,0,1632,571	52	49	50		1514,1052,1553	4.8	1	X		50	2,6726		0,2,2426,1872	yes	missense,missense,missense	DACH2	NM_001139514.1,NM_001139515.1,NM_053281.3	29,29,29	0,2,4058,2443	AA,AG,GG,G		0.0297,0.0,0.0189	probably-damaging,probably-damaging,probably-damaging	505/572,351/433,518/600	86069706	2,10561	2203	4300	6503	85956362	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1553G>A	X.37:g.86069706G>A	ENSP00000362217:p.Arg518His		85956362	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.479378	0.84747	0.0	2.97E-4	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.89617	-2.5;-2.54	4.76	4.76	0.60689	.	0.000000	0.64402	D	0.000003	D	0.94128	0.8117	M	0.76727	2.345	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.996;0.997	D	0.95005	0.8146	10	0.87932	D	0	.	17.002	0.86383	0.0:0.0:1.0:0.0	.	384;518;505;518	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	H	518;505;518;351;299;351;183	ENSP00000362223:R505H;ENSP00000362217:R518H	ENSP00000345134:R518H	R	+	2	0	DACH2	85956362	1.000000	0.71417	0.989000	0.46669	0.860000	0.49131	9.288000	0.96055	1.932000	0.55993	0.415000	0.27848	CGC		0.418	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		A	86069706	G	A	86069706	3	1	31	1	0	0	0	0	1	0	0	0	4227	1087	38	1	1591	1	DACH2	23	86069706	Missense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10		86069706	69200854	55	2654										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104984651	104984651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	atgttgaaaaccgaaatggaCggaaacatgccagtgttttg	11	6	0	1	rs375566296		TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chrX:104984651C>T	ENST00000372582.1	+	8	1771	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.R339W|IL1RAPL2_ENST00000485671.1_3'UTR	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	339	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R339W(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCGAAATGGACGGAAACATGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	TRP/ARG	0,3835		0,0,1632,571	75	64	68		1015	1.7	1	X		68	1,6727		0,1,2427,1872	no	missense	IL1RAPL2	NM_017416.1	101	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging	339/687	104984651	1,10562	2203	4300	6503	104871307	SO:0001583	missense	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1015C>T	X.37:g.104984651C>T	ENSP00000361663:p.Arg339Trp		104871307	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671661	0.67928	0.0	1.49E-4	ENSG00000189108	ENST00000372582;ENST00000344799	T;T	0.77750	-1.12;-1.12	5.61	1.7	0.24286	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000012	D	0.86818	0.6024	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84578	0.0659	10	0.38643	T	0.18	.	14.0838	0.64942	0.5179:0.4821:0.0:0.0	.	339	Q9NP60	IRPL2_HUMAN	W	339	ENSP00000361663:R339W;ENSP00000344976:R339W	ENSP00000344976:R339W	R	+	1	2	IL1RAPL2	104871307	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	2.545000	0.45769	-0.092000	0.12417	0.600000	0.82982	CGG		0.373	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	104984651	C	T	104984651	3	4	31	1	0	0	0	0	1	0	0	0	7683	527	19	1	1041	1	IL1RAPL2	23	104984651	Missense_Mutation	SNP	C	TCGA-AG-3608-01A-01W-0833-10	18914945	104984651	50285909	56	2655										
GPR112	139378	hgsc.bcm.edu	37	chrX	135426910	135426910	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0175438596491228	1	1	0.19031954887218	2.66447368421053	0	1	1	0	aaacgaaatctccatcttcaGaaagcacaaagacaacaaaa	4	10	3	2			TCGA-AG-3608-01A-01W-0833-10	TCGA-AG-3608-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	d1daf7a6-2fce-4178-89b7-248146957a60	e62c9f56-d0da-4cad-a8f5-60dbbe8a0b83	g.chrX:135426910G>T	ENST00000394143.1	+	6	1336	c.1045G>T	c.(1045-1047)Gaa>Taa	p.E349*	GPR112_ENST00000412101.1_Nonsense_Mutation_p.E144*|GPR112_ENST00000370652.1_Nonsense_Mutation_p.E349*|GPR112_ENST00000287534.4_Nonsense_Mutation_p.E286*|GPR112_ENST00000394141.1_Nonsense_Mutation_p.E144*	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	349					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E349*(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TCCATCTTCAGAAAGCACAAA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											89	82	84					X																	135426910		2203	4299	6502	135254576	SO:0001587	stop_gained	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1045G>T	X.37:g.135426910G>T	ENSP00000377699:p.Glu349*		135254576	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Nonsense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	g	27.6	4.842225	0.91197	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	.	.	.	3.95	3.08	0.35506	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	7.3703	0.26798	0.1339:0.0:0.8661:0.0	.	.	.	.	X	349;349;144;286;144	.	ENSP00000287534:E286X	E	+	1	0	GPR112	135254576	0.413000	0.25400	0.010000	0.14722	0.018000	0.09664	2.221000	0.42917	0.758000	0.33059	0.502000	0.49764	GAA		0.383	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135426910	G	T	135426910	4	4	31	1	0	0	0	0	0	1	0	0	6649	943	33	2	1055	2	GPR112	23	135426910	Nonsense_Mutation	SNP	G	TCGA-AG-3608-01A-01W-0833-10	30442259	135426910	19843650	57	2656										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9784120	9784120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ggcattggcgatcggcacagCgacaacatcatgatccgaga	12	11	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:9784120C>T	ENST00000377346.4	+	21	2883	c.2688C>T	c.(2686-2688)agC>agT	p.S896S	PIK3CD_ENST00000536656.1_Silent_p.S920S|PIK3CD_ENST00000361110.2_Silent_p.S920S	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	896	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.S896S(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	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)	Caffeine(DB00201)	ATCGGCACAGCGACAACATCA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	1											179	166	170					1																	9784120		2203	4300	6503	9706707	SO:0001819	synonymous_variant	5293				CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2688C>T	1.37:g.9784120C>T			9706707	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	37	CCDS104.1																																																																																				0.632	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		T	9784120	C	T	9784120	2	4	32	1	0	0	0	0	0	0	0	1	11946	767	27	1		1	PIK3CD	1	9784120	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10		9784120	239466501	1	2657										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118530485	118530485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gtctatcttttctttccagcGttttgaggatgctgtgtgtc	10	8	3	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:118530485G>A	ENST00000336338.5	-	40	5706	c.5641C>T	c.(5641-5643)Cgc>Tgc	p.R1881C		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1881						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.R1881C(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCTTTCCAGCGTTTTGAGGAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											169	153	159					1																	118530485		2203	4300	6503	118332008	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5641C>T	1.37:g.118530485G>A	ENSP00000337804:p.Arg1881Cys		118332008	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	9.572	1.121353	0.20877	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.19394	2.15	4.33	0.569	0.17340	.	1.870170	0.01986	N	0.045190	T	0.13543	0.0328	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	P	0.50896	0.653	T	0.07751	-1.0756	10	0.72032	D	0.01	.	5.2111	0.15316	0.1032:0.0:0.3961:0.5006	.	1881	Q6Q759	SPG17_HUMAN	C	1881;361	ENSP00000337804:R1881C	ENSP00000337804:R1881C	R	-	1	0	SPAG17	118332008	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-0.287000	0.08388	-0.003000	0.14444	0.655000	0.94253	CGC		0.413	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118530485	G	A	118530485	3	1	32	1	0	0	0	0	1	0	0	0	15018	1145	40	1	1066	1	SPAG17	1	118530485	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	108746365	118530485	130720136	2	2658										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145532479	145532479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccttggtcactacctccggcGgcagcgagatcccagctctt	10	16	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:145532479G>A	ENST00000369304.3	+	9	1107	c.932G>A	c.(931-933)cGg>cAg	p.R311Q	ITGA10_ENST00000539363.1_Missense_Mutation_p.R168Q|ITGA10_ENST00000538811.1_Missense_Mutation_p.R180Q|ITGA10_ENST00000481236.1_3'UTR	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	311	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.R311Q(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TACCTCCGGCGGCAGCGAGAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	116	118					1																	145532479		2203	4300	6503	144243836	SO:0001583	missense	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.932G>A	1.37:g.145532479G>A	ENSP00000358310:p.Arg311Gln		144243836	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659554	0.88154	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.54675	0.56;0.56;0.56	5.12	5.12	0.69794	von Willebrand factor, type A (3);	0.150302	0.41938	D	0.000797	T	0.62648	0.2445	M	0.61703	1.905	0.54753	D	0.999983	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.998;0.999	T	0.58763	-0.7579	10	0.33940	T	0.23	.	16.4367	0.83878	0.0:0.0:1.0:0.0	.	277;180;168;311	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	Q	311;277;168;180	ENSP00000358310:R311Q;ENSP00000439894:R168Q;ENSP00000440011:R180Q	ENSP00000358310:R311Q	R	+	2	0	ITGA10	144243836	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	5.161000	0.64935	2.573000	0.86826	0.561000	0.74099	CGG		0.473	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145532479	G	A	145532479	3	1	32	1	0	0	0	0	1	0	0	0	7894	1116	39	1	966	1	ITGA10	1	145532479	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	27001994	145532479	103718142	3	2659										
NBPF14	25832	hgsc.bcm.edu	37	chr1	148004716	148004716	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ggtagttcaaagtacattgaCggagtcgaataacatatatc	9	6	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:148004716C>A	ENST00000369219.1	-	22	2614	c.2598G>T	c.(2596-2598)ccG>ccT	p.P866P				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	866	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.P866P(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					AGTACATTGACGGAGTCGAAT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											133	202	179					1																	148004716		2126	4261	6387	146471340	SO:0001819	synonymous_variant	25832			AK092351		1q21.1	2013-01-17			ENSG00000122497			"neuroblastoma breakpoint family"	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.2598G>T	1.37:g.148004716C>A			146471340	Q5TI23|Q8IX76|Q9UJI9	Silent	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	c	0.518	-0.863374	0.02590	.	.	ENSG00000122497	ENST00000310701	.	.	.	0.445	-0.891	0.10573	.	.	.	.	.	T	0.08179	0.0204	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37596	-0.9699	3	.	.	.	.	.	.	.	.	.	.	.	L	872	.	.	R	-	2	0	NBPF14	146471340	0.023000	0.18921	0.001000	0.08648	0.006000	0.05464	-1.510000	0.02262	-0.810000	0.04375	-1.085000	0.02201	CGT		0.433	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		A	148004716	C	A	148004716	2	1	32	1	0	0	0	0	0	0	0	1	10225	523	19	2		2	NBPF14	1	148004716	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	2472237	148004716	101245905	4	2660										
PEAR1	375033	hgsc.bcm.edu	37	chr1	156876478	156876478	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tgtgacaagccctgcagctgCggcaacaacagctcgtgtga	12	12	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:156876478C>G	ENST00000338302.3	+	7	675	c.450C>G	c.(448-450)tgC>tgG	p.C150W	PEAR1_ENST00000292357.7_Missense_Mutation_p.C150W			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	150					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.C150W(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTGCAGCTGCGGCAACAACA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	96	100					1																	156876478		2203	4300	6503	155143102	SO:0001583	missense	375033			AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.450C>G	1.37:g.156876478C>G	ENSP00000344465:p.Cys150Trp		155143102	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140421	0.56936	.	.	ENSG00000187800	ENST00000338302;ENST00000455314;ENST00000292357	T;T;T	0.67865	-0.29;-0.29;-0.29	4.81	-4.21	0.03812	.	0.000000	0.53938	D	0.000050	D	0.84629	0.5514	H	0.99752	4.75	0.80722	D	1	D;P	0.89917	1.0;0.921	D;P	0.97110	1.0;0.499	D	0.86358	0.1715	10	0.87932	D	0	.	12.5203	0.56056	0.0:0.5987:0.0:0.4013	.	12;150	Q8N780;Q5VY43	.;PEAR1_HUMAN	W	150	ENSP00000344465:C150W;ENSP00000389742:C150W;ENSP00000292357:C150W	ENSP00000292357:C150W	C	+	3	2	PEAR1	155143102	0.032000	0.19561	0.863000	0.33907	0.867000	0.49689	-0.924000	0.03996	-1.082000	0.03101	-0.258000	0.10820	TGC		0.612	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		G	156876478	C	G	156876478	3	3	32	1	0	0	0	0	1	0	0	0	11743	776	27	5	468	5	PEAR1	1	156876478	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	8871762	156876478	92374143	5	2661										
ADAMTS4	9507	hgsc.bcm.edu	37	chr1	161165403	161165403	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atgcatggcttggagttgtcAtggagcatgttgaagacatg	14	5	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:161165403A>T	ENST00000367996.5	-	4	1541	c.1113T>A	c.(1111-1113)caT>caA	p.H371Q	ADAMTS4_ENST00000478394.1_5'UTR	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	371	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)	p.H371Q(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	TGGAGTTGTCATGGAGCATGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	140	149					1																	161165403		2203	4300	6503	159432027	SO:0001583	missense	9507			AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.1113T>A	1.37:g.161165403A>T	ENSP00000356975:p.His371Gln		159432027	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.821988	0.71028	.	.	ENSG00000158859	ENST00000367996	D	0.97161	-4.27	4.77	-0.247	0.13019	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000006	D	0.98409	0.9471	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97820	1.0256	10	0.87932	D	0	.	9.3967	0.38406	0.5493:0.0:0.4507:0.0	.	371	O75173	ATS4_HUMAN	Q	371	ENSP00000356975:H371Q	ENSP00000356975:H371Q	H	-	3	2	ADAMTS4	159432027	0.406000	0.25344	0.995000	0.50966	0.991000	0.79684	-0.086000	0.11233	-0.213000	0.10094	0.459000	0.35465	CAT		0.547	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		T	161165403	A	T	161165403	3	4	32	1	0	0	0	0	1	0	0	0	268	214	8	5	1424	5	ADAMTS4	1	161165403	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	4288925	161165403	88085218	6	2662										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121926	186121926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ttgcccggggcttggattccGatggttctttgctgctagat	13	9	1	1	rs112526907		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:186121926G>A	ENST00000271588.4	+	96	15170	c.14941G>A	c.(14941-14943)Gat>Aat	p.D4981N	HMCN1_ENST00000367492.2_Missense_Mutation_p.D4981N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4981	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.D4981N(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTTGGATTCCGATGGTTCTTT	0.428													G|||	1	0.000199681	0	0	5008	,	,		18974	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											229	205	213					1																	186121926		2203	4300	6503	184388549	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14941G>A	1.37:g.186121926G>A	ENSP00000271588:p.Asp4981Asn		184388549	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.3	4.515396	0.85389	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.35421	1.31;1.31	5.9	5.9	0.94986	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.000000	0.85682	D	0.000000	T	0.55878	0.1948	L	0.42581	1.335	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.51068	-0.8752	10	0.52906	T	0.07	.	20.2789	0.98501	0.0:0.0:1.0:0.0	.	4981	Q96RW7	HMCN1_HUMAN	N	4981	ENSP00000271588:D4981N;ENSP00000356462:D4981N	ENSP00000271588:D4981N	D	+	1	0	HMCN1	184388549	1.000000	0.71417	0.882000	0.34594	0.475000	0.33008	7.676000	0.84012	2.788000	0.95919	0.650000	0.86243	GAT		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186121926	G	A	186121926	3	1	32	1	0	0	0	0	1	0	0	0	7241	1058	37	1	15323	1	HMCN1	1	186121926	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	24956523	186121926	63128695	7	2663										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196285041	196285041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	cctgaagagtgtctgcacgtTcacaatggttttggcatctg	11	9	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:196285041T>C	ENST00000294725.9	-	21	3379	c.2464A>G	c.(2464-2466)Aac>Gac	p.N822D	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000367433.5_Missense_Mutation_p.N798D|KCNT2_ENST00000367431.4_Missense_Mutation_p.N748D|KCNT2_ENST00000609185.1_Missense_Mutation_p.N748D			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	822					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.N822D(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GTCTGCACGTTCACAATGGTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											144	117	126					1																	196285041		2203	4300	6503	194551664	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2464A>G	1.37:g.196285041T>C	ENSP00000294725:p.Asn822Asp		194551664	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.133039	0.77662	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.75477	-0.94;-0.94;-0.94	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000002	D	0.84915	0.5578	M	0.75447	2.3	0.80722	D	1	D;D;D;D;D	0.69078	0.991;0.997;0.992;0.992;0.991	P;D;D;D;P	0.63703	0.776;0.917;0.917;0.917;0.776	D	0.86207	0.1622	10	0.59425	D	0.04	-23.8441	16.2853	0.82717	0.0:0.0:0.0:1.0	.	822;780;798;748;822	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	D	798;748;822	ENSP00000356403:N798D;ENSP00000356401:N748D;ENSP00000294725:N822D	ENSP00000294725:N822D	N	-	1	0	KCNT2	194551664	1.000000	0.71417	0.063000	0.19743	0.841000	0.47740	7.997000	0.88414	2.236000	0.73375	0.528000	0.53228	AAC		0.448	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196285041	T	C	196285041	3	2	32	1	0	0	0	0	1	0	0	0	8113	1783	62	4	975	4	KCNT2	1	196285041	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10	10163115	196285041	52965580	8	2664										
ZBTB41	360023	hgsc.bcm.edu	37	chr1	197160979	197160979	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcgctggtgacaaatatcacActcaaagggcttctcacctg	9	12	3	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:197160979A>T	ENST00000367405.4	-	2	1239	c.1171T>A	c.(1171-1173)Tgt>Agt	p.C391S	ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C391S(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						CAAATATCACACTCAAAGGGC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	73	76					1																	197160979		2203	4300	6503	195427602	SO:0001583	missense	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.1171T>A	1.37:g.197160979A>T	ENSP00000356375:p.Cys391Ser		195427602	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Missense_Mutation	SNP	ENST00000367405.4	37	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.856400	0.91355	.	.	ENSG00000177888	ENST00000367405	D	0.85171	-1.95	5.89	5.89	0.94794	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.294789	0.23821	U	0.044224	D	0.95395	0.8505	H	0.97214	3.96	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.96956	0.9698	10	0.87932	D	0	.	16.3603	0.83259	1.0:0.0:0.0:0.0	.	391	Q5SVQ8	ZBT41_HUMAN	S	391	ENSP00000356375:C391S	ENSP00000356375:C391S	C	-	1	0	ZBTB41	195427602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	2.260000	0.74910	0.529000	0.55759	TGT		0.353	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		T	197160979	A	T	197160979	3	4	32	1	0	0	0	0	1	0	0	0	17582	159	6	5	1594	5	ZBTB41	1	197160979	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	875938	197160979	52089642	9	2665										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198711403	198711403	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	acctatatcggaattgatgcCatgctagaaggcctggaagc	11	9	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:198711403C>A	ENST00000367376.2	+	25	2769	c.2598C>A	c.(2596-2598)gcC>gcA	p.A866A	PTPRC_ENST00000348564.6_Silent_p.A707A|PTPRC_ENST00000352140.3_Silent_p.A818A|PTPRC_ENST00000594404.1_Silent_p.A705A|PTPRC_ENST00000442510.2_Silent_p.A868A	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	866	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A866A(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GAATTGATGCCATGCTAGAAG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	1											232	212	219					1																	198711403		2203	4300	6503	196978026	SO:0001819	synonymous_variant	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2598C>A	1.37:g.198711403C>A			196978026	A8K7W6|Q16614|Q9H0Y6	Silent	SNP	ENST00000367376.2	37																																																																																					0.468	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198711403	C	A	198711403	2	1	32	1	0	0	0	0	0	0	0	1	12834	581	21	2		2	PTPRC	1	198711403	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	1550424	198711403	50539218	10	2666										
DDX59	83479	hgsc.bcm.edu	37	chr1	200635457	200635457	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctcttccttttccttaacttGtagaagatgtttcgctttac	5	10	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:200635457G>A	ENST00000331314.6	-	2	625	c.412C>T	c.(412-414)Caa>Taa	p.Q138*	DDX59_ENST00000367348.3_Nonsense_Mutation_p.Q138*|DDX59_ENST00000447706.2_Nonsense_Mutation_p.Q138*	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	138						cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.Q138*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						TCCTTAACTTGTAGAAGATGT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											97	98	97					1																	200635457		2203	4300	6503	198902080	SO:0001587	stop_gained	83479			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.412C>T	1.37:g.200635457G>A	ENSP00000330460:p.Gln138*		198902080	Q6PJL2|Q8IVW3|Q9H0W3	Nonsense_Mutation	SNP	ENST00000331314.6	37	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858461	0.71834	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314;ENST00000436897	.	.	.	5.09	4.17	0.49024	.	0.473603	0.25711	N	0.028810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-4.9898	14.9352	0.70948	0.0:0.0:0.8556:0.1444	.	.	.	.	X	138	.	ENSP00000330460:Q138X	Q	-	1	0	DDX59	198902080	0.695000	0.27747	0.035000	0.18076	0.854000	0.48673	2.939000	0.48995	1.130000	0.42092	0.555000	0.69702	CAA		0.418	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		A	200635457	G	A	200635457	4	1	32	1	0	0	0	0	0	1	0	0	4382	1386	48	3	1475	3	DDX59	1	200635457	Nonsense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	1924054	200635457	48615164	11	2667										
NFASC	23114	hgsc.bcm.edu	37	chr1	204943415	204943415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gtctcccatccccacactgcGatggtaagttccaggagatc	9	14	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:204943415G>A	ENST00000401399.1	+	12	1587	c.1388G>A	c.(1387-1389)cGa>cAa	p.R463Q	NFASC_ENST00000539706.1_Missense_Mutation_p.R474Q|NFASC_ENST00000360049.4_Missense_Mutation_p.R474Q|NFASC_ENST00000367170.4_Missense_Mutation_p.R463Q|NFASC_ENST00000339876.6_Missense_Mutation_p.R463Q|NFASC_ENST00000513543.1_Missense_Mutation_p.R474Q|NFASC_ENST00000367169.4_Missense_Mutation_p.R463Q|NFASC_ENST00000403080.1_Missense_Mutation_p.R463Q|NFASC_ENST00000367171.4_Missense_Mutation_p.R463Q|NFASC_ENST00000338515.6_Missense_Mutation_p.R463Q|NFASC_ENST00000404907.1_Missense_Mutation_p.R474Q|NFASC_ENST00000338586.6_Missense_Mutation_p.R463Q|NFASC_ENST00000367172.4_Missense_Mutation_p.R463Q|NFASC_ENST00000404076.1_Missense_Mutation_p.R457Q			O94856	NFASC_HUMAN	neurofascin	463	Ig-like C2-type 5.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.R474Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCCACACTGCGATGGTAAGTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	45	52					1																	204943415		2203	4300	6503	203210038	SO:0001583	missense	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1388G>A	1.37:g.204943415G>A	ENSP00000385637:p.Arg463Gln		203210038	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.501656|4.501656	0.85176|0.85176	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.66280	.|-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.000000	.|0.42682	.|D	.|0.000680	T|T	0.63803|0.63803	0.2542|0.2542	N|N	0.10809|0.10809	0.05|0.05	0.80722|0.80722	D|D	1|1	.|D;P;D;P;B;P;D	.|0.89917	.|0.994;0.888;0.999;0.822;0.407;0.661;1.0	.|P;B;D;B;B;B;D	.|0.91635	.|0.804;0.212;0.96;0.212;0.029;0.212;0.999	T|T	0.62656|0.62656	-0.6808|-0.6808	5|10	.|0.20046	.|T	.|0.44	.|.	19.0836|19.0836	0.93192|0.93192	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|474;474;559;463;463;474;463	.|O94856-11;O94856-8;B4DRH7;F8W791;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.;.	N|Q	433|463;463;463;463;463;463;474;474;474;463;463;457;463;474;474;450	.|ENSP00000356140:R463Q;ENSP00000356139:R463Q;ENSP00000356138:R463Q;ENSP00000342128:R463Q;ENSP00000344786:R463Q;ENSP00000343509:R463Q;ENSP00000438614:R474Q;ENSP00000353154:R474Q;ENSP00000356137:R463Q;ENSP00000384875:R463Q;ENSP00000385676:R457Q;ENSP00000385637:R463Q;ENSP00000384061:R474Q;ENSP00000425908:R474Q;ENSP00000415031:R450Q	.|ENSP00000295776:R474Q	D|R	+|+	1|2	0|0	NFASC|NFASC	203210038|203210038	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.938000|0.938000	0.57974|0.57974	9.168000|9.168000	0.94781|0.94781	2.612000|2.612000	0.88384|0.88384	0.585000|0.585000	0.79938|0.79938	GAT|CGA		0.572	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204943415	G	A	204943415	3	1	32	1	0	0	0	0	1	0	0	0	10390	1058	37	1	1485	1	NFASC	1	204943415	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	4307958	204943415	44307206	12	2668										
TMCC2	9911	hgsc.bcm.edu	37	chr1	205241128	205241128	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	caccatcgccaacttcatcaCgcccctcatgaagacacgcc	5	19	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:205241128C>T	ENST00000358024.3	+	5	2395	c.2006C>T	c.(2005-2007)aCg>aTg	p.T669M	TMCC2_ENST00000329800.7_Missense_Mutation_p.T429M|TMCC2_ENST00000545499.1_Missense_Mutation_p.T591M|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000330675.7_Missense_Mutation_p.T444M	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	669						integral component of membrane (GO:0016021)		p.T669M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AACTTCATCACGCCCCTCATG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1											250	189	210					1																	205241128		2203	4300	6503	203507751	SO:0001583	missense	9911			AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"Transmembrane and coiled-coil domain containing"	24239	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 2"			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.2006C>T	1.37:g.205241128C>T	ENSP00000350718:p.Thr669Met		203507751	A2RRH3|B7Z1P7|Q6ZN09	Missense_Mutation	SNP	ENST00000358024.3	37	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418026	0.62622	.	.	ENSG00000133069	ENST00000358024;ENST00000545499;ENST00000330675;ENST00000329800	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.18	4.27	0.50696	.	0.051366	0.85682	D	0.000000	T	0.46367	0.1389	N	0.20401	0.57	0.46874	D	0.999233	D;D;D	0.76494	0.996;0.999;0.999	P;P;D	0.71656	0.789;0.866;0.974	T	0.37056	-0.9722	10	0.29301	T	0.29	.	13.6804	0.62481	0.0:0.9248:0.0:0.0752	.	429;444;669	G5E963;B2RAX5;O75069	.;.;TMCC2_HUMAN	M	669;591;444;429	ENSP00000350718:T669M;ENSP00000437943:T591M;ENSP00000331842:T444M;ENSP00000329436:T429M	ENSP00000329436:T429M	T	+	2	0	TMCC2	203507751	0.998000	0.40836	1.000000	0.80357	0.991000	0.79684	3.889000	0.56212	1.403000	0.46800	0.655000	0.94253	ACG		0.617	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		T	205241128	C	T	205241128	3	4	32	1	0	0	0	0	1	0	0	0	16032	536	19	1	2024	1	TMCC2	1	205241128	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	297713	205241128	44009493	13	2669										
JMJD4	65094	hgsc.bcm.edu	37	chr1	227922372	227922372	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctgcacaagtgccagtctttGaggtagagacagcccctggg	13	11	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:227922372G>A	ENST00000366758.3	-	2	545	c.546C>T	c.(544-546)ctC>ctT	p.L182L	SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|JMJD4_ENST00000485807.1_5'Flank|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Silent_p.L182L	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	182								p.L182L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				GCCAGTCTTTGAGGTAGAGAC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	1											167	145	152					1																	227922372		2203	4300	6503	225988995	SO:0001819	synonymous_variant	65094			AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.546C>T	1.37:g.227922372G>A			225988995	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	37	CCDS1561.1	.	.	.	.	.	.	.	.	.	.	.	11.83	1.756148	0.31137	.	.	ENSG00000081692	ENST00000438896	T	0.48201	0.82	4.55	3.61	0.41365	.	.	.	.	.	T	0.48040	0.1478	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36237	-0.9756	5	.	.	.	-50.7201	8.1223	0.30978	0.0:0.1733:0.6479:0.1789	.	.	.	.	L	175	ENSP00000387830:S175L	.	S	-	2	0	JMJD4	225988995	0.979000	0.34478	1.000000	0.80357	0.994000	0.84299	0.076000	0.14712	0.998000	0.38996	0.555000	0.69702	TCA		0.572	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007		A	227922372	G	A	227922372	2	1	32	1	0	0	0	0	0	0	0	1	7972	1277	45	3		3	JMJD4	1	227922372	Silent	SNP	G	TCGA-AG-3609-01A-02W-0833-10	22681244	227922372	21328249	14	2670										
ERO1LB	56605	hgsc.bcm.edu	37	chr1	236416724	236416724	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ttattttatttattatacctCtggacagggctccacatgac	6	9	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:236416724C>T	ENST00000354619.5	-	3	505	c.304G>A	c.(304-306)Gag>Aag	p.E102K	ERO1LB_ENST00000327333.8_Missense_Mutation_p.E102K	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	102					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)	p.E102K(1)		NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TATTATACCTCTGGACAGGGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											48	46	47					1																	236416724		2203	4300	6503	234483347	SO:0001583	missense	56605			AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.304G>A	1.37:g.236416724C>T	ENSP00000346635:p.Glu102Lys		234483347	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680446	0.68042	.	.	ENSG00000086619	ENST00000354619;ENST00000327333	T;T	0.48201	0.82;0.82	5.65	5.65	0.86999	.	0.155531	0.56097	N	0.000026	T	0.57989	0.2091	M	0.84773	2.715	0.80722	D	1	B;B	0.20550	0.046;0.013	B;B	0.26693	0.04;0.072	T	0.57791	-0.7750	10	0.45353	T	0.12	-4.6606	18.4833	0.90819	0.0:1.0:0.0:0.0	.	102;102	B4DF57;Q86YB8	.;ERO1B_HUMAN	K	102	ENSP00000346635:E102K;ENSP00000377574:E102K	ENSP00000377574:E102K	E	-	1	0	ERO1LB	234483347	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.379000	0.66196	2.662000	0.90505	0.561000	0.74099	GAG		0.383	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		T	236416724	C	T	236416724	3	4	32	1	0	0	0	0	1	0	0	0	5253	922	32	3	1155	3	ERO1LB	1	236416724	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	8494352	236416724	12833897	15	2671										
C1orf101	257044	hgsc.bcm.edu	37	chr1	244681984	244681984	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gaaaagtttattcttcaaatGagaaaatgagaagggggtat	11	2	2	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr1:244681984G>A	ENST00000366534.4	+	8	574	c.520G>A	c.(520-522)Gag>Aag	p.E174K	C1orf101_ENST00000366533.4_Missense_Mutation_p.E174K|C1orf101_ENST00000366531.3_Missense_Mutation_p.E23K|C1orf101_ENST00000473875.1_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	174						CatSper complex (GO:0036128)		p.E174K(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TTCTTCAAATGAGAAAATGAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	1											37	42	40					1																	244681984		2194	4294	6488	242748607	SO:0001583	missense	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.520G>A	1.37:g.244681984G>A	ENSP00000355492:p.Glu174Lys		242748607	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	37	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	G	1.372	-0.585690	0.03827	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000366531	T;T	0.30182	1.54;1.54	4.79	-3.07	0.05363	.	3.065990	0.00610	N	0.000414	T	0.24736	0.0600	L	0.40543	1.245	0.09310	N	1	B;B	0.24426	0.103;0.103	B;B	0.25140	0.058;0.058	T	0.18461	-1.0336	10	0.37606	T	0.19	.	5.4656	0.16642	0.4375:0.303:0.2595:0.0	.	174;174	Q5SY80;Q5SY80-2	CA101_HUMAN;.	K	174;174;174;23	ENSP00000355492:E174K;ENSP00000355491:E174K	ENSP00000355489:E23K	E	+	1	0	C1orf101	242748607	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.127000	0.01315	-0.437000	0.07243	0.650000	0.86243	GAG		0.299	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		A	244681984	G	A	244681984	3	1	32	1	0	0	0	0	1	0	0	0	1982	1291	45	3	550	3	C1orf101	1	244681984	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	8265260	244681984	4568637	16	2672										
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18768433	18768433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gtgattcggattgactgcacGcctcatctgaaagattgtgc	11	9	2	4			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:18768433G>A	ENST00000359846.2	-	3	204	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	NT5C1B_ENST00000600945.1_Missense_Mutation_p.R43C|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.R43C|NT5C1B_ENST00000460052.1_Intron|NT5C1B_ENST00000304081.4_Intron	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	43					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.R43C(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TTGACTGCACGCCTCATCTGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											45	36	39					2																	18768433		2203	4300	6503	18631914	SO:0001583	missense	93034			AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.127C>T	2.37:g.18768433G>A	ENSP00000352904:p.Arg43Cys		18631914	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.209982	0.79240	.	.	ENSG00000250741;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000359846;ENST00000416783	.	.	.	5.39	5.39	0.77823	.	0.473849	0.18290	N	0.145760	T	0.52041	0.1710	N	0.14661	0.345	0.39825	D	0.972898	D;D;D	0.76494	0.999;0.999;0.999	P;P;P	0.58130	0.685;0.685;0.833	T	0.58696	-0.7591	9	0.87932	D	0	-9.291	14.5287	0.67909	0.0:0.0:1.0:0.0	.	43;43;43	B4DZ86;Q96P26;Q96P26-4	.;5NT1B_HUMAN;.	C	43	.	ENSP00000352904:R43C	R	-	1	0	NT5C1B-RDH14;NT5C1B	18631914	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.235000	0.58666	2.809000	0.96659	0.467000	0.42956	CGT		0.567	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			A	18768433	G	A	18768433	3	1	32	1	0	0	0	0	1	0	0	0	10717	1087	38	1	1737	1	NT5C1B	2	18768433	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		18768433	224430940	17	2673										
ALK	238	hgsc.bcm.edu	37	chr2	29450510	29450510	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccatcttccccatccatttcGgggtcattgtttgaggctgc	9	13	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:29450510G>T	ENST00000389048.3	-	17	3750	c.2844C>A	c.(2842-2844)ccC>ccA	p.P948P	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	948					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P948P(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CATCCATTTCGGGGTCATTGT	0.512			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - coding silent(1)	large_intestine(1)	2											183	169	174					2																	29450510		2203	4300	6503	29304014	SO:0001819	synonymous_variant	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2844C>A	2.37:g.29450510G>T			29304014	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.512	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	29450510	G	T	29450510	2	4	32	1	0	0	0	0	0	0	0	1	525	1103	39	2		2	ALK	2	29450510	Silent	SNP	G	TCGA-AG-3609-01A-02W-0833-10	10682077	29450510	213748863	18	2674										
ALK	238	hgsc.bcm.edu	37	chr2	29519818	29519818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gctcaagccttcataggcggCgacatgccagaccatcctgc	10	15	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:29519818C>T	ENST00000389048.3	-	9	2659	c.1753G>A	c.(1753-1755)Gcc>Acc	p.A585T	ALK_ENST00000498037.1_5'UTR|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	585	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A585T(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TCATAGGCGGCGACATGCCAG	0.552			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - Missense(1)	large_intestine(1)	2											150	116	128					2																	29519818		2203	4300	6503	29373322	SO:0001583	missense	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1753G>A	2.37:g.29519818C>T	ENSP00000373700:p.Ala585Thr		29373322	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.471024	0.26423	.	.	ENSG00000171094	ENST00000389048	T	0.02050	4.48	5.2	3.36	0.38483	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.000000	0.45867	U	0.000337	T	0.01558	0.0050	L	0.32530	0.975	0.25576	N	0.986846	P	0.46277	0.875	B	0.30855	0.121	T	0.52895	-0.8514	9	.	.	.	.	7.9422	0.29965	0.0:0.7521:0.1611:0.0868	.	585	Q9UM73	ALK_HUMAN	T	585	ENSP00000373700:A585T	.	A	-	1	0	ALK	29373322	0.622000	0.27085	0.017000	0.16124	0.076000	0.17211	1.078000	0.30754	0.554000	0.29061	0.563000	0.77884	GCC		0.552	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	29519818	C	T	29519818	3	4	32	1	0	0	0	0	1	0	0	0	525	768	27	1	3193	1	ALK	2	29519818	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	69308	29519818	213679555	19	2675										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99013469	99013469	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctgatgaaagacaacctgatCgatgaggagctggccagggc	14	9	0	5			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:99013469C>T	ENST00000272602.2	+	7	1875	c.1836C>T	c.(1834-1836)atC>atT	p.I612I	CNGA3_ENST00000409937.1_Silent_p.I616I|CNGA3_ENST00000436404.2_Silent_p.I594I|CNGA3_ENST00000393504.1_Silent_p.I612I			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	612					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.I612I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						ACAACCTGATCGATGAGGAGC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	2											32	32	32					2																	99013469		2203	4300	6503	98379901	SO:0001819	synonymous_variant	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1836C>T	2.37:g.99013469C>T			98379901	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																				0.607	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	99013469	C	T	99013469	2	4	32	1	0	0	0	0	0	0	0	1	3604	874	31	1		1	CNGA3	2	99013469	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	69493651	99013469	144185904	20	2676										
TMEM182	130827	hgsc.bcm.edu	37	chr2	103431426	103431426	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcatattcagatacatcactAaatcaactgttgccacaagt	5	10	3	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:103431426A>G	ENST00000412401.2	+	5	894	c.689A>G	c.(688-690)tAa>tGa	p.*230*	TMEM182_ENST00000409528.1_Silent_p.*134*|TMEM182_ENST00000409173.1_Silent_p.*187*|TMEM182_ENST00000486293.1_Intron	NM_144632.3	NP_653233.3	Q6ZP80	TM182_HUMAN	transmembrane protein 182	0						integral component of membrane (GO:0016021)		p.*230*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11						ATACATCACTAAATCAACTGT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	2											75	72	73					2																	103431426		2203	4300	6503	102797858	SO:0001819	synonymous_variant	130827			AK054856	CCDS2064.1	2q12.1	2009-08-25			ENSG00000170417	ENSG00000170417			26391	protein-coding gene	gene with protein product						12477932	Standard	NM_144632		Approved	FLJ30294	uc010fjb.3	Q6ZP80	OTTHUMG00000130779	ENST00000412401.2:c.689A>G	2.37:g.103431426A>G			102797858	C9JML7|Q3B7B8|Q53TT9|Q6GMU0|Q8WW45|Q96NR4	Silent	SNP	ENST00000412401.2	37	CCDS2064.1																																																																																				0.348	TMEM182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253293.1	NM_144632		G	103431426	A	G	103431426	2	3	32	1	0	0	0	0	0	0	0	1	16140	369	13	4		4	TMEM182	2	103431426	Silent	SNP	A	TCGA-AG-3609-01A-02W-0833-10	4417957	103431426	139767947	21	2677										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158152266	158152266	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gtttatttaagtagaaagaaAgtggcctgtccagtaatcga	10	5	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:158152266A>T	ENST00000259056.4	+	4	2318	c.1833A>T	c.(1831-1833)aaA>aaT	p.K611N		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	611					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.K611N(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GTAGAAAGAAAGTGGCCTGTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											191	180	184					2																	158152266		2203	4300	6503	157860512	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1833A>T	2.37:g.158152266A>T	ENSP00000259056:p.Lys611Asn		157860512	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863778	0.51482	.	.	ENSG00000136542	ENST00000259056	T	0.58940	0.3	5.63	3.18	0.36537	Glycosyl transferase, family 2 (1);	0.046814	0.85682	D	0.000000	T	0.37999	0.1024	N	0.11201	0.11	0.37179	D	0.903418	P	0.40282	0.711	B	0.41412	0.356	T	0.38542	-0.9656	10	0.44086	T	0.13	.	8.9525	0.35799	0.7664:0.0:0.2336:0.0	.	611	Q7Z7M9	GALT5_HUMAN	N	611	ENSP00000259056:K611N	ENSP00000259056:K611N	K	+	3	2	GALNT5	157860512	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	0.981000	0.29526	0.463000	0.27118	-0.408000	0.06270	AAA		0.378	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		T	158152266	A	T	158152266	3	4	32	1	0	0	0	0	1	0	0	0	6236	69	3	5	1847	5	GALNT5	2	158152266	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	54720840	158152266	85047107	22	2678										
DLX2	1746	hgsc.bcm.edu	37	chr2	172967247	172967247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	agtgcatatcagccactagaCtgtcaaagactccagtcatc	7	12	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:172967247C>T	ENST00000234198.4	-	1	381	c.20G>A	c.(19-21)aGt>aAt	p.S7N	AC104801.1_ENST00000448117.1_lincRNA|DLX2_ENST00000466293.2_Missense_Mutation_p.S7N	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	7					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)	p.S7N(1)		endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			AGCCACTAGACTGTCAAAGAC	0.692																																					GBM(188;775 2993 11256 23072)											1	Substitution - Missense(1)	large_intestine(1)	2											22	20	21					2																	172967247		1928	3737	5665	172675493	SO:0001583	missense	1746			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"Homeoboxes / ANTP class : NKL subclass"	2915	protein-coding gene	gene with protein product		126255	"distal-less homeo box 2"			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.20G>A	2.37:g.172967247C>T	ENSP00000234198:p.Ser7Asn		172675493	B4DMK4|B7ZA14	Missense_Mutation	SNP	ENST00000234198.4	37	CCDS2248.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692815	0.48202	.	.	ENSG00000115844	ENST00000234198;ENST00000466293	D;D	0.92911	-2.6;-3.13	4.51	4.51	0.55191	.	0.047558	0.85682	D	0.000000	T	0.81819	0.4903	N	0.08118	0	0.40406	D	0.979708	B;B	0.24317	0.003;0.101	B;B	0.17098	0.005;0.017	T	0.78795	-0.2064	10	0.32370	T	0.25	-9.9179	11.4959	0.50408	0.0:0.9108:0.0:0.0892	.	7;7	B7ZA14;Q07687	.;DLX2_HUMAN	N	7	ENSP00000234198:S7N;ENSP00000446904:S7N	ENSP00000234198:S7N	S	-	2	0	DLX2	172675493	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.854000	0.27791	2.040000	0.60383	0.561000	0.74099	AGT		0.692	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3			T	172967247	C	T	172967247	3	4	32	1	0	0	0	0	1	0	0	0	4582	565	20	3	978	3	DLX2	2	172967247	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	14814981	172967247	70232126	23	2679										
MYO1B	4430	hgsc.bcm.edu	37	chr2	192255042	192255042	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atcaaaccgaatgataaaaaAgcagcacacatcttcaacga	5	10	3	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:192255042A>T	ENST00000392318.3	+	18	2053	c.1806A>T	c.(1804-1806)aaA>aaT	p.K602N	MYO1B_ENST00000339514.4_Missense_Mutation_p.K602N|MYO1B_ENST00000392316.1_Missense_Mutation_p.K602N|MYO1B_ENST00000439065.2_5'Flank|MYO1B_ENST00000304164.4_Missense_Mutation_p.K602N	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	602	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.K602N(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			ATGATAAAAAAGCAGCACACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											123	121	122					2																	192255042		2203	4300	6503	191963287	SO:0001583	missense	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.1806A>T	2.37:g.192255042A>T	ENSP00000376132:p.Lys602Asn		191963287	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880808	0.72294	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.54	-3.72	0.04411	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93510	0.7929	M	0.85542	2.76	0.80722	D	1	D;D	0.71674	0.998;0.973	D;D	0.69654	0.965;0.913	D	0.92419	0.5944	10	0.62326	D	0.03	.	17.0979	0.86641	0.32:0.0:0.68:0.0	.	602;602	O43795;O43795-2	MYO1B_HUMAN;.	N	602	ENSP00000341903:K602N;ENSP00000376132:K602N;ENSP00000306382:K602N;ENSP00000376130:K602N	ENSP00000306382:K602N	K	+	3	2	MYO1B	191963287	0.992000	0.36948	0.912000	0.35992	0.834000	0.47266	0.360000	0.20250	-0.882000	0.03987	-0.256000	0.11100	AAA		0.428	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		T	192255042	A	T	192255042	3	4	32	1	0	0	0	0	1	0	0	0	10099	69	3	5	1872	5	MYO1B	2	192255042	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	19287795	192255042	50944331	24	2680										
HECW2	57520	hgsc.bcm.edu	37	chr2	197171284	197171284	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gggggagactgtaacagcaaCgtgatcctggatctggaggt	16	7	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:197171284C>T	ENST00000260983.3	-	13	2924	c.2742G>A	c.(2740-2742)acG>acA	p.T914T	HECW2_ENST00000409111.1_Silent_p.T558T	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	914	Interaction with TP73.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.T914T(1)		biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GTAACAGCAACGTGATCCTGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	2											146	131	136					2																	197171284		2203	4300	6503	196879529	SO:0001819	synonymous_variant	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2742G>A	2.37:g.197171284C>T			196879529	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																				0.517	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197171284	C	T	197171284	2	4	32	1	0	0	0	0	0	0	0	1	7064	523	19	1		1	HECW2	2	197171284	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	4916242	197171284	46028089	25	2681										
VIL1	7429	hgsc.bcm.edu	37	chr2	219289054	219289054	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ttggaagcttcttcgatggtGactgctacatcatcctggct	10	10	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr2:219289054G>A	ENST00000248444.5	+	3	218	c.130G>A	c.(130-132)Gac>Aac	p.D44N	VIL1_ENST00000392114.2_Intron|VIL1_ENST00000440053.1_Missense_Mutation_p.D44N	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	44	Core.|Necessary for homodimerization.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)	p.D44N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTCGATGGTGACTGCTACAT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	85	87					2																	219289054		2203	4300	6503	218997298	SO:0001583	missense	7429			X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.130G>A	2.37:g.219289054G>A	ENSP00000248444:p.Asp44Asn		218997298	B2R9A7|Q53S11|Q96AC8	Missense_Mutation	SNP	ENST00000248444.5	37	CCDS2417.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077450	0.94000	.	.	ENSG00000127831	ENST00000248444;ENST00000454069;ENST00000440053	T;T;T	0.26660	1.72;1.72;1.72	4.16	4.16	0.48862	Gelsolin domain (1);	0.000000	0.64402	D	0.000001	T	0.60779	0.2295	M	0.92691	3.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	T	0.72984	-0.4125	10	0.62326	D	0.03	-36.9637	16.6391	0.85068	0.0:0.0:1.0:0.0	.	44;44	Q96AC8;P09327	.;VILI_HUMAN	N	44	ENSP00000248444:D44N;ENSP00000412657:D44N;ENSP00000409270:D44N	ENSP00000248444:D44N	D	+	1	0	VIL1	218997298	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	9.468000	0.97676	2.163000	0.67991	0.313000	0.20887	GAC		0.597	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		A	219289054	G	A	219289054	3	1	32	1	0	0	0	0	1	0	0	0	17204	1290	45	3	136	3	VIL1	2	219289054	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	22117770	219289054	23910319	26	2682										
SPATA12	353324	hgsc.bcm.edu	37	chr3	57108238	57108238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctgacatttactgagggctgCtttgtcaggtccctctctac	9	12	2	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr3:57108238C>T	ENST00000334325.1	+	2	1191	c.516C>T	c.(514-516)tgC>tgT	p.C172C	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	172								p.C172C(1)		large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		CTGAGGGCTGCTTTGTCAGGT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	3											119	117	118					3																	57108238		2202	4300	6502	57083278	SO:0001819	synonymous_variant	353324			AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.516C>T	3.37:g.57108238C>T			57083278	A0AVA8|B2RMW1	Silent	SNP	ENST00000334325.1	37	CCDS2879.1																																																																																				0.483	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727		T	57108238	C	T	57108238	2	4	32	1	0	0	0	0	0	0	0	1	15038	805	28	3		3	SPATA12	3	57108238	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10		57108238	140914192	27	2683										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74350896	74350896	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctttaccttctttccaagagAgttgggctgttgtgtctgta	10	8	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr3:74350896A>C	ENST00000263665.6	-	14	1874	c.1847T>G	c.(1846-1848)cTc>cGc	p.L616R		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	616	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.L616R(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TTTCCAAGAGAGTTGGGCTGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											324	284	298					3																	74350896		2203	4300	6503	74433586	SO:0001583	missense	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1847T>G	3.37:g.74350896A>C	ENSP00000263665:p.Leu616Arg		74433586	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199839	0.79015	.	.	ENSG00000113805	ENST00000263665	T	0.66995	-0.24	5.98	4.8	0.61643	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.067389	0.64402	D	0.000015	D	0.89044	0.6603	H	0.99299	4.505	0.45366	D	0.998351	D	0.89917	1.0	D	0.81914	0.995	D	0.92445	0.5965	10	0.87932	D	0	.	13.379	0.60757	0.8685:0.1315:0.0:0.0	.	616	Q9P232	CNTN3_HUMAN	R	616	ENSP00000263665:L616R	ENSP00000263665:L616R	L	-	2	0	CNTN3	74433586	0.997000	0.39634	0.780000	0.31762	0.995000	0.86356	8.615000	0.90920	1.055000	0.40461	0.482000	0.46254	CTC		0.458	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		C	74350896	A	C	74350896	3	2	32	1	0	0	0	0	1	0	0	0	3648	304	11	4	1275	4	CNTN3	3	74350896	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	17242658	74350896	123671534	28	2684										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89390178	89390178	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aactgcaggtgtgagaataaTtacttccgggcagacaaaga	11	7	0	3			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr3:89390178T>A	ENST00000336596.2	+	4	1152	c.927T>A	c.(925-927)aaT>aaA	p.N309K	EPHA3_ENST00000494014.1_Missense_Mutation_p.N309K|EPHA3_ENST00000452448.2_Missense_Mutation_p.N309K	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	309	Cys-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.N309K(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GTGAGAATAATTACTTCCGGG	0.453										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	large_intestine(1)	3											164	162	163					3																	89390178		2203	4300	6503	89472868	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.927T>A	3.37:g.89390178T>A	ENSP00000337451:p.Asn309Lys		89472868	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466100	0.43839	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	D;D;D	0.97731	-4.51;-4.51;-4.51	6.17	5.01	0.66863	.	0.086238	0.85682	D	0.000000	D	0.95373	0.8498	L	0.51422	1.61	0.54753	D	0.999985	B;B	0.34372	0.451;0.356	B;B	0.36922	0.112;0.236	D	0.92603	0.6093	9	.	.	.	.	8.1682	0.31239	0.0:0.0663:0.136:0.7977	.	309;309	P29320;P29320-2	EPHA3_HUMAN;.	K	309	ENSP00000337451:N309K;ENSP00000399926:N309K;ENSP00000419190:N309K	.	N	+	3	2	EPHA3	89472868	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.685000	0.37659	1.132000	0.42129	0.533000	0.62120	AAT		0.453	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89390178	T	A	89390178	3	1	32	1	0	0	0	0	1	0	0	0	5181	1490	52	5	941	5	EPHA3	3	89390178	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10	15039282	89390178	108632252	29	2685										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132185189	132185189	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aagctcagatctcgtacctgAgaaggatgctgatcggatgc	12	9	2	3			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr3:132185189A>C	ENST00000260818.6	+	19	2263	c.2015A>C	c.(2014-2016)gAg>gCg	p.E672A	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	672					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.E55A(1)|p.E672A(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CTCGTACCTGAGAAGGATGCT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	3											108	105	106					3																	132185189		2203	4300	6503	133667879	SO:0001583	missense	23317			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2015A>C	3.37:g.132185189A>C	ENSP00000260818:p.Glu672Ala		133667879	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.208547	0.58343	.	.	ENSG00000138246	ENST00000260818	T	0.35421	1.31	5.76	5.76	0.90799	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.29458	0.0734	L	0.41824	1.3	0.80722	D	1	P;P	0.43885	0.82;0.816	B;B	0.37198	0.243;0.175	T	0.04635	-1.0937	10	0.28530	T	0.3	.	15.0496	0.71858	1.0:0.0:0.0:0.0	.	672;672	A7E2Y5;O75165	.;DJC13_HUMAN	A	672	ENSP00000260818:E672A	ENSP00000260818:E672A	E	+	2	0	DNAJC13	133667879	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.949000	0.93012	2.192000	0.70111	0.455000	0.32223	GAG		0.393	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132185189	A	C	132185189	3	2	32	1	0	0	0	0	1	0	0	0	4643	304	11	4	2085	4	DNAJC13	3	132185189	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	42795011	132185189	65837241	30	2686										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060622	46060622	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tttccacttatactcaatttCatttttagggtatccatcta	3	9	3	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr4:46060622C>T	ENST00000295452.4	-	6	810	c.643G>A	c.(643-645)Gaa>Aaa	p.E215K		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	215					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.E215K(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TACTCAATTTCATTTTTAGGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	53	54					4																	46060622		2203	4299	6502	45755379	SO:0001583	missense	2565			BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.643G>A	4.37:g.46060622C>T	ENSP00000295452:p.Glu215Lys		45755379	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	37	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667409	0.88348	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.80123	-1.34	5.83	5.83	0.93111	Neurotransmitter-gated ion-channel ligand-binding (3);	0.101306	0.64402	D	0.000003	D	0.85919	0.5809	M	0.64404	1.975	0.58432	D	0.999999	P	0.51791	0.948	P	0.53360	0.724	D	0.86784	0.1981	10	0.87932	D	0	.	19.1642	0.93548	0.0:1.0:0.0:0.0	.	215	Q8N1C3	GBRG1_HUMAN	K	215	ENSP00000295452:E215K	ENSP00000295452:E215K	E	-	1	0	GABRG1	45755379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.747000	0.85070	2.775000	0.95449	0.650000	0.86243	GAA		0.358	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		T	46060622	C	T	46060622	3	4	32	1	0	0	0	0	1	0	0	0	6190	835	29	3	770	3	GABRG1	4	46060622	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10		46060622	145093654	31	2687										
TLL1	7092	hgsc.bcm.edu	37	chr4	166996115	166996115	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tacatgtgtcaatgccgtaaTggatttgtgctacatgacaa	9	7	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr4:166996115T>A	ENST00000061240.2	+	17	2921	c.2274T>A	c.(2272-2274)aaT>aaA	p.N758K	TLL1_ENST00000507499.1_Missense_Mutation_p.N781K	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	758	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.N758K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AATGCCGTAATGGATTTGTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											295	242	260					4																	166996115		2203	4300	6503	167215565	SO:0001583	missense	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2274T>A	4.37:g.166996115T>A	ENSP00000061240:p.Asn758Lys		167215565	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	37	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692981	0.30052	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	D;D	0.96104	-3.91;-3.91	5.72	-1.34	0.09143	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.059985	0.64402	U	0.000005	D	0.83216	0.5206	N	0.03084	-0.415	0.80722	D	1	P;P	0.48911	0.917;0.732	B;B	0.38921	0.285;0.204	T	0.77107	-0.2710	10	0.46703	T	0.11	.	6.3797	0.21527	0.0:0.271:0.1183:0.6106	.	781;758	E9PD25;O43897	.;TLL1_HUMAN	K	758;781	ENSP00000061240:N758K;ENSP00000426082:N781K	ENSP00000061240:N758K	N	+	3	2	TLL1	167215565	0.977000	0.34250	0.850000	0.33497	0.002000	0.02628	0.093000	0.15086	-0.339000	0.08401	-0.417000	0.06048	AAT		0.398	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			A	166996115	T	A	166996115	3	1	32	1	0	0	0	0	1	0	0	0	15984	1461	51	5	2340	5	TLL1	4	166996115	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10	120935493	166996115	24158161	32	2688										
APC	324	hgsc.bcm.edu	37	chr5	112174840	112174840	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	attgattatagtttaaaataTgccacagatattccttcatc	4	7	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:112174840T>A	ENST00000457016.1	+	16	3929	c.3549T>A	c.(3547-3549)taT>taA	p.Y1183*	APC_ENST00000257430.4_Nonsense_Mutation_p.Y1183*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Y1183*			P25054	APC_HUMAN	adenomatous polyposis coli	1183	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Y1183*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTTTAAAATATGCCACAGATA	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											79	85	83					5																	112174840		2197	4296	6493	112202739	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3549T>A	5.37:g.112174840T>A	ENSP00000413133:p.Tyr1183*		112202739	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.884628	0.91814	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	0.83	0.18854	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.8248	10.2282	0.43238	0.0:0.3311:0.0:0.6689	.	.	.	.	X	1183	.	.	Y	+	3	2	APC	112202739	0.032000	0.19561	0.408000	0.26446	0.506000	0.33950	-0.147000	0.10234	0.132000	0.18615	0.533000	0.62120	TAT		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112174840	T	A	112174840	4	1	32	1	0	0	0	0	0	1	0	0	763	1471	51	5	3607	5	APC	5	112174840	Nonsense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10		112174840	68740420	33	2689										
APC	324	hgsc.bcm.edu	37	chr5	112175390	112175390	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctccctccaaaagtggtgctCagacacccaaaagtccacct	6	16	1	1	rs121913328		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:112175390C>T	ENST00000457016.1	+	16	4479	c.4099C>T	c.(4099-4101)Cag>Tag	p.Q1367*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1367*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1367*			P25054	APC_HUMAN	adenomatous polyposis coli	1367	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1367*(26)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGTGGTGCTCAGACACCCAA	0.453	Q1367*(C2BBE1_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	28	Substitution - Nonsense(26)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(26)|soft_tissue(1)|skin(1)	5	GRCh37	CM940072	APC	M	rs121913328						75	73	74					5																	112175390		2202	4300	6502	112203289	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4099C>T	5.37:g.112175390C>T	ENSP00000413133:p.Gln1367*		112203289	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.623019	0.98890	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.166931	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.8965	17.2482	0.87034	0.0:0.8741:0.1259:0.0	.	.	.	.	X	1367	.	.	Q	+	1	0	APC	112203289	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.223000	0.72257	1.603000	0.50134	0.655000	0.94253	CAG		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175390	C	T	112175390	4	4	32	1	0	0	0	0	0	1	0	0	763	827	29	3	4157	3	APC	5	112175390	Nonsense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	550	112175390	68739870	34	2690										
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138714334	138714334	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccgttgcccgtgcccaatagCcccgcgatgatgcagcaaat	10	15	0	1	rs267600365		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:138714334C>T	ENST00000348729.3	-	10	1159	c.1113G>A	c.(1111-1113)ggG>ggA	p.G371G	SLC23A1_ENST00000503919.1_5'Flank|SLC23A1_ENST00000353963.3_Silent_p.G375G	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	371					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)	p.G375G(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	TGCCCAATAGCCCCGCGATGA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	5											63	51	55					5																	138714334		2203	4300	6503	138742233	SO:0001819	synonymous_variant	9963			AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.1113G>A	5.37:g.138714334C>T			138742233	O95191|Q8WWB6|Q9UGH4|Q9UI39	Silent	SNP	ENST00000348729.3	37	CCDS4212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.601|7.601	0.672817|0.672817	0.14776|0.14776	.|.	.|.	ENSG00000170482|ENSG00000170482	ENST00000504513|ENST00000453898	.|.	.|.	.|.	4.71|4.71	-1.74|-1.74	0.08056|0.08056	.|.	.|0.050775	.|0.85682	.|D	.|0.000000	T|T	0.16342|0.16342	0.0393|0.0393	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30937|0.30937	-0.9961|-0.9961	4|6	.|0.05525	.|T	.|0.97	-15.0116|-15.0116	1.9182|1.9182	0.03301|0.03301	0.128:0.3406:0.1254:0.406|0.128:0.3406:0.1254:0.406	.|.	.|.	.|.	.|.	T|D	118|326	.|.	.|ENSP00000406720:G326D	A|G	-|-	1|2	0|0	SLC23A1|SLC23A1	138742233|138742233	0.012000|0.012000	0.17670|0.17670	0.076000|0.076000	0.20297|0.20297	0.701000|0.701000	0.40568|0.40568	-0.779000|-0.779000	0.04659|0.04659	-0.656000|-0.656000	0.05380|0.05380	0.561000|0.561000	0.74099|0.74099	GCT|GGC		0.597	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		T	138714334	C	T	138714334	2	4	32	1	0	0	0	0	0	0	0	1	14499	726	26	3		3	SLC23A1	5	138714334	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	26538944	138714334	42200926	35	2691										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140431259	140431259	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	cgcggggcgcggctggtttcCgagggcaacaaaatgcattt	15	10	0	0	rs538415948		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:140431259C>T	ENST00000306549.3	+	1	281	c.204C>T	c.(202-204)tcC>tcT	p.S68S		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	68	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S68S(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCTGGTTTCCGAGGGCAACA	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		15783	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	5											50	53	52					5																	140431259		2203	4300	6503	140411443	SO:0001819	synonymous_variant	29930			AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.204C>T	5.37:g.140431259C>T			140411443	Q2M257	Silent	SNP	ENST00000306549.3	37	CCDS4243.1																																																																																				0.577	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		T	140431259	C	T	140431259	2	4	32	1	0	0	0	0	0	0	0	1	11565	639	23	1		1	PCDHB1	5	140431259	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	1716925	140431259	40484001	36	2692										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140719701	140719701	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	caccacctgttcactccccgAggatcttccttttaagttag	6	14	2	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:140719701A>G	ENST00000394576.2	+	1	1163	c.1163A>G	c.(1162-1164)gAg>gGg	p.E388G	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	388	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E388G(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACTCCCCGAGGATCTTCCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	80	79					5																	140719701		2203	4300	6503	140699885	SO:0001583	missense	56113			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1163A>G	5.37:g.140719701A>G	ENSP00000378077:p.Glu388Gly		140699885	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	0.011	-1.735444	0.00681	.	.	ENSG00000081853	ENST00000394576	T	0.57752	0.38	5.03	5.03	0.67393	Cadherin (4);Cadherin-like (1);	0.173379	0.26903	U	0.021902	T	0.24431	0.0592	N	0.03324	-0.35	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.16158	-1.0412	10	0.07990	T	0.79	.	9.3279	0.38003	0.9182:0.0:0.0818:0.0	.	388;388	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	G	388	ENSP00000378077:E388G	ENSP00000378077:E388G	E	+	2	0	PCDHGA2	140699885	0.000000	0.05858	0.033000	0.17914	0.005000	0.04900	-0.185000	0.09684	2.025000	0.59659	0.459000	0.35465	GAG		0.428	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140719701	A	G	140719701	3	3	32	1	0	0	0	0	1	0	0	0	11585	304	11	4	1165	4	PCDHGA2	5	140719701	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	288442	140719701	40195559	37	2693										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141335357	141335357	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tgaccctcaacagggctcggGtctgtaagggggggcttccc	15	12	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr5:141335357G>A	ENST00000231484.3	-	1	3270	c.2060C>T	c.(2059-2061)aCc>aTc	p.T687I	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	687	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T687I(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGGCTCGGGTCTGTAAGGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	5											30	28	29					5																	141335357		2203	4300	6503	141315541	SO:0001583	missense	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2060C>T	5.37:g.141335357G>A	ENSP00000231484:p.Thr687Ile		141315541	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.238193	0.39598	.	.	ENSG00000113555	ENST00000231484	T	0.53857	0.6	5.24	4.34	0.51931	Cadherin (4);Cadherin-like (1);	0.055419	0.64402	D	0.000001	T	0.76169	0.3950	M	0.90483	3.12	0.50171	D	0.999854	D	0.76494	0.999	D	0.75484	0.986	T	0.81782	-0.0775	10	0.87932	D	0	.	13.3887	0.60811	0.0:0.159:0.841:0.0	.	687	Q9NPG4	PCD12_HUMAN	I	687	ENSP00000231484:T687I	ENSP00000231484:T687I	T	-	2	0	PCDH12	141315541	1.000000	0.71417	0.899000	0.35326	0.251000	0.25915	4.262000	0.58847	1.387000	0.46486	0.655000	0.94253	ACC		0.592	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141335357	G	A	141335357	3	1	32	1	0	0	0	0	1	0	0	0	11541	1261	44	3	1510	3	PCDH12	5	141335357	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	615656	141335357	39579903	38	2694										
TRIM27	5987	hgsc.bcm.edu	37	chr6	28876838	28876838	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aaatctggaggtgtgatccaAggttcaggaatcctgattct	11	7	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr6:28876838A>T	ENST00000377199.3	-	5	1154	c.798T>A	c.(796-798)ccT>ccA	p.P266P	TRIM27_ENST00000377194.3_Silent_p.P266P|TRIM27_ENST00000498117.1_5'Flank	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	266					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P266P(1)		endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GTGTGATCCAAGGTTCAGGAA	0.388			T	RET	papillary thyroid																																		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	1	Substitution - coding silent(1)	large_intestine(1)	6											79	81	80					6																	28876838		2203	4300	6503	28984817	SO:0001819	synonymous_variant	5987			Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9975	protein-coding gene	gene with protein product		602165	"ret finger protein", "tripartite motif-containing 27"	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.798T>A	6.37:g.28876838A>T			28984817	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Silent	SNP	ENST00000377199.3	37	CCDS4654.1																																																																																				0.388	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950		T	28876838	A	T	28876838	2	4	32	1	0	0	0	0	0	0	0	1	16541	59	3	5		5	TRIM27	6	28876838	Silent	SNP	A	TCGA-AG-3609-01A-02W-0833-10		28876838	142238229	39	2695										
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83763888	83763888	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tgtcttttattatgacttcaCcgcaggattggcaataaaac	7	8	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr6:83763888C>G	ENST00000369747.3	-	3	466	c.344G>C	c.(343-345)gGt>gCt	p.G115A		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	115					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)	p.G115A(1)									TATGACTTCACCGCAGGATTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											105	100	102					6																	83763888		2203	4300	6503	83820607	SO:0001583	missense	90025			AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.344G>C	6.37:g.83763888C>G	ENSP00000358762:p.Gly115Ala		83820607	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	37	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.019871	0.75275	.	.	ENSG00000118420	ENST00000369747	T	0.29917	1.55	5.44	5.44	0.79542	.	0.097576	0.64402	D	0.000002	T	0.46698	0.1406	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.26744	-1.0094	10	0.21014	T	0.42	-22.4018	18.0456	0.89331	0.0:1.0:0.0:0.0	.	115;115	D6RD24;Q7Z6J8	.;UB2CB_HUMAN	A	115	ENSP00000358762:G115A	ENSP00000358762:G115A	G	-	2	0	UBE2CBP	83820607	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	4.852000	0.62904	2.558000	0.86282	0.655000	0.94253	GGT		0.328	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		G	83763888	C	G	83763888	3	3	32	1	0	0	0	0	1	0	0	0	16887	507	18	5	857	5	UBE2CBP	6	83763888	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	54887050	83763888	87351179	40	2696										
REV3L	5980	hgsc.bcm.edu	37	chr6	111678232	111678232	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aatacctctttattatatttGcaatttcatgaaaaagtgcc	4	7	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr6:111678232G>C	ENST00000358835.3	-	19	7623	c.7169C>G	c.(7168-7170)gCa>gGa	p.A2390G	REV3L_ENST00000435970.1_Missense_Mutation_p.A2312G|REV3L_ENST00000368805.1_Missense_Mutation_p.A2390G|REV3L_ENST00000368802.3_Missense_Mutation_p.A2390G			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2390					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.A2312G(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TATTATATTTGCAATTTCATG	0.318								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											85	94	91					6																	111678232		2203	4300	6503	111784925	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7169C>G	6.37:g.111678232G>C	ENSP00000351697:p.Ala2390Gly		111784925	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974989	0.34848	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	5.93	4.96	0.65561	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.371628	0.27851	N	0.017592	T	0.02888	0.0086	L	0.29908	0.895	0.30294	N	0.790105	B	0.22851	0.076	B	0.29440	0.102	T	0.35574	-0.9783	10	0.37606	T	0.19	-0.6038	3.9381	0.09314	0.3165:0.0:0.6835:0.0	.	2390	O60673	DPOLZ_HUMAN	G	2390;2390;2390;2312;463	ENSP00000357792:A2390G;ENSP00000357795:A2390G;ENSP00000351697:A2390G;ENSP00000402003:A2312G	ENSP00000351697:A2390G	A	-	2	0	REV3L	111784925	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	4.564000	0.60830	2.805000	0.96524	0.655000	0.94253	GCA		0.318	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111678232	G	C	111678232	3	2	32	1	0	0	0	0	1	0	0	0	13277	1319	46	5	2283	5	REV3L	6	111678232	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	27914344	111678232	59436835	41	2697										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129591855	129591855	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	actaaaggaacctctgaagaCtgtcaaccctgtgcctgtcc	8	13	2	2	rs144580350		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr6:129591855C>T	ENST00000421865.2	+	17	2458	c.2409C>T	c.(2407-2409)gaC>gaT	p.D803D		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	803	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.D803D(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCTCTGAAGACTGTCAACCCT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	0,4406		0,0,2203	143	132	136		2409,2409	3.8	1	6	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	803/3123,803/3119	129591855	1,13005	2203	4300	6503	129633548	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2409C>T	6.37:g.129591855C>T			129633548	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.423	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129591855	C	T	129591855	2	4	32	1	0	0	0	0	0	0	0	1	8628	564	20	3		3	LAMA2	6	129591855	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	17913623	129591855	41523212	42	2698										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200345	138200345	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	agctggaaacgacgcccctgCtggctgcctgtctcaagctg	12	14	1	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr6:138200345C>G	ENST00000237289.4	+	7	1829	c.1763C>G	c.(1762-1764)gCt>gGt	p.A588G		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	588	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.A588G(2)|p.P587fs*93(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GACGCCCCTGCTGGCTGCCTG	0.617			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	28	Whole gene deletion(25)|Substitution - Missense(2)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(27)|large_intestine(1)	6											48	54	52					6																	138200345		2203	4300	6503	138242038	SO:0001583	missense	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1763C>G	6.37:g.138200345C>G	ENSP00000237289:p.Ala588Gly		138242038	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	9.817	1.184776	0.21870	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.22945	1.93	5.7	5.7	0.88788	.	0.617332	0.18476	N	0.140073	T	0.08582	0.0213	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.11867	-1.0570	10	0.17369	T	0.5	-0.0152	17.9984	0.89191	0.0:1.0:0.0:0.0	.	588	P21580	TNAP3_HUMAN	G	588	ENSP00000237289:A588G	ENSP00000237289:A588G	A	+	2	0	TNFAIP3	138242038	0.002000	0.14202	0.134000	0.22075	0.125000	0.20455	1.441000	0.35035	2.695000	0.91970	0.655000	0.94253	GCT		0.617	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138200345	C	G	138200345	3	3	32	1	0	0	0	0	1	0	0	0	16313	797	28	5	1785	5	TNFAIP3	6	138200345	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	8608490	138200345	32914722	43	2699										
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26236037	26236037	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tcaccagatcctcctctaaaGttacttcctggtcctggtcc	6	15	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:26236037G>T	ENST00000354667.4	-	7	846	c.678C>A	c.(676-678)aaC>aaA	p.N226K	HNRNPA2B1_ENST00000356674.7_Missense_Mutation_p.N214K	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	226	Gly-rich.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)	p.N214K(1)	HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						CTCCTCTAAAGTTACTTCCTG	0.403			T	ETV1	prostate																																		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	1	Substitution - Missense(1)	large_intestine(1)	7											73	71	72					7																	26236037		2203	4300	6503	26202562	SO:0001583	missense	3181			D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"RNA binding motif (RRM) containing"	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.678C>A	7.37:g.26236037G>T	ENSP00000346694:p.Asn226Lys		26202562	A8K064|P22627|Q9UC98|Q9UDJ2	Missense_Mutation	SNP	ENST00000354667.4	37	CCDS43557.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628372	0.46944	.	.	ENSG00000122566	ENST00000354667;ENST00000356674	D;D	0.86097	-2.07;-2.07	6.02	2.76	0.32466	.	0.000000	0.64402	D	0.000001	D	0.85159	0.5633	L	0.56199	1.76	0.28793	N	0.899179	P;P	0.48016	0.904;0.845	P;P	0.52793	0.709;0.515	T	0.78497	-0.2181	10	0.44086	T	0.13	.	8.843	0.35153	0.3737:0.0:0.6263:0.0	.	214;226	P22626-2;P22626	.;ROA2_HUMAN	K	226;214	ENSP00000346694:N226K;ENSP00000349101:N214K	ENSP00000346694:N226K	N	-	3	2	HNRNPA2B1	26202562	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	0.983000	0.29552	0.805000	0.34159	0.650000	0.86243	AAC		0.403	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		T	26236037	G	T	26236037	3	4	32	1	0	0	0	0	1	0	0	0	7280	1020	36	2	403	2	HNRNPA2B1	7	26236037	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		26236037	132902626	44	2700										
C7orf43	55262	hgsc.bcm.edu	37	chr7	99752697	99752697	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcaatcttgtccagagacaaCacagccttgtccgggggcag	12	12	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:99752697C>A	ENST00000316937.3	-	11	1865	c.1680G>T	c.(1678-1680)gtG>gtT	p.V560V	C7orf43_ENST00000498638.1_5'Flank|C7orf43_ENST00000394035.2_Silent_p.V136V|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000419841.1_Silent_p.V328V|C7orf43_ENST00000457641.1_Silent_p.V291V	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	560								p.V560V(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCAGAGACAACACAGCCTTGT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	7											70	68	69					7																	99752697		2203	4300	6503	99590633	SO:0001819	synonymous_variant	55262				CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.1680G>T	7.37:g.99752697C>A			99590633	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Silent	SNP	ENST00000316937.3	37	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	C	4.713	0.132498	0.09032	.	.	ENSG00000146826	ENST00000456769	T	0.55588	0.51	4.67	2.87	0.33458	.	0.210801	0.31415	N	0.007689	T	0.58278	0.2111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57980	-0.7717	7	0.72032	D	0.01	-14.442	7.2211	0.25988	0.0:0.7978:0.0:0.2022	.	.	.	.	F	466	ENSP00000389672:V466F	ENSP00000389672:V466F	V	-	1	0	C7orf43	99590633	0.973000	0.33851	0.907000	0.35723	0.805000	0.45488	-0.032000	0.12266	0.583000	0.29574	-0.224000	0.12420	GTT		0.627	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		A	99752697	C	A	99752697	2	1	32	1	0	0	0	0	0	0	0	1	2399	465	17	2		2	C7orf43	7	99752697	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	73516660	99752697	59385966	45	2701										
RELN	5649	hgsc.bcm.edu	37	chr7	103202326	103202326	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ggcaccctgaggccagtacaAcattatcaatcgcccaggaa	9	13	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:103202326A>G	ENST00000428762.1	-	35	5444	c.5285T>C	c.(5284-5286)gTt>gCt	p.V1762A	RELN_ENST00000424685.2_Missense_Mutation_p.V1762A|RELN_ENST00000343529.5_Missense_Mutation_p.V1762A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1762					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.V1762A(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGCCAGTACAACATTATCAAT	0.453																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											87	75	79					7																	103202326		2203	4300	6503	102989562	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5285T>C	7.37:g.103202326A>G	ENSP00000392423:p.Val1762Ala		102989562	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.001010	0.54254	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.25085	1.82;1.82;1.82	5.78	5.78	0.91487	Neuraminidase (1);	0.000000	0.85682	D	0.000000	T	0.42877	0.1222	M	0.78049	2.395	0.58432	D	0.999994	P;B	0.51147	0.942;0.387	P;B	0.49421	0.61;0.09	T	0.47471	-0.9115	10	0.87932	D	0	.	16.1099	0.81255	1.0:0.0:0.0:0.0	.	1762;1762	P78509-2;P78509	.;RELN_HUMAN	A	1762	ENSP00000392423:V1762A;ENSP00000345694:V1762A;ENSP00000388446:V1762A	ENSP00000345694:V1762A	V	-	2	0	RELN	102989562	1.000000	0.71417	0.857000	0.33713	0.328000	0.28507	8.711000	0.91396	2.215000	0.71742	0.460000	0.39030	GTT		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103202326	A	G	103202326	3	3	32	1	0	0	0	0	1	0	0	0	13257	43	2	4	5221	4	RELN	7	103202326	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	3449629	103202326	55936337	46	2702										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143095520	143095520	+	Missense_Mutation	SNP	A	A	T													0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gttctttcttcaccagtctcAgagacaggcctgacagtgac							TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:143095520A>T	ENST00000275815.3	-	7	1444	c.1358T>A	c.(1357-1359)cTg>cAg	p.L453Q		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	453	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.L453Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				CACCAGTCTCAGAGACAGGCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											51	55	53					7																	143095520		2203	4300	6503	142805642	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1358T>A	7.37:g.143095520A>T	ENSP00000275815:p.Leu453Gln		142805642	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.553819	0.65425	.	.	ENSG00000146904	ENST00000275815	T	0.58797	0.31	5.08	5.08	0.68730	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.145674	0.31784	N	0.007061	T	0.70176	0.3194	M	0.68317	2.08	0.35647	D	0.811499	D	0.71674	0.998	D	0.70487	0.969	T	0.78735	-0.2088	10	0.87932	D	0	.	8.5727	0.33578	0.8284:0.0:0.0:0.1716	.	453	P21709	EPHA1_HUMAN	Q	453	ENSP00000275815:L453Q	ENSP00000275815:L453Q	L	-	2	0	EPHA1	142805642	0.944000	0.32072	1.000000	0.80357	0.980000	0.70556	1.543000	0.36147	2.038000	0.60285	0.533000	0.62120	CTG		0.552	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			T	143095520	A	T	143095520	3	4	32	1	0	0	0	0	1	0	0	0	5178	188	7	5	1620	5	EPHA1	7	143095520	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	39893194	143095520	16043143	47	2703	13	2								
EPHA1	2041	hgsc.bcm.edu	37	chr7	143095525	143095525	+	Silent	SNP	C	C	G													0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ttcttcaccagtctcagagaCaggcctgacagtgactctgg							TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:143095525C>G	ENST00000275815.3	-	7	1439	c.1353G>C	c.(1351-1353)ctG>ctC	p.L451L		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	451	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.L451L(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GTCTCAGAGACAGGCCTGACA	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	7											51	55	54					7																	143095525		2203	4300	6503	142805647	SO:0001819	synonymous_variant	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1353G>C	7.37:g.143095525C>G			142805647	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																				0.547	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			G	143095525	C	G	143095525	2	3	32	1	0	0	0	0	0	0	0	1	5178	465	17	5		5	EPHA1	7	143095525	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	5	143095525	16043138	48	2704	13	2								
ABCF2	10061	hgsc.bcm.edu	37	chr7	150921141	150921141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tcgagtcagatggtagatgtCgatgtgctcagggatgggca	16	6	2	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr7:150921141C>T	ENST00000287844.2	-	4	536	c.427G>A	c.(427-429)Gac>Aac	p.D143N	ABCF2_ENST00000222388.2_Missense_Mutation_p.D143N|ABCF2_ENST00000473874.1_5'Flank	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	143	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)	p.D143N(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGTAGATGTCGATGTGCTCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											116	98	104					7																	150921141		2203	4300	6503	150552074	SO:0001583	missense	10061			AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.427G>A	7.37:g.150921141C>T	ENSP00000287844:p.Asp143Asn		150552074	O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	37	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	C	36	5.636420	0.96693	.	.	ENSG00000033050	ENST00000222388;ENST00000287844;ENST00000468073;ENST00000441774	D;D;T;T	0.92099	-2.92;-2.97;3.9;3.9	5.81	5.81	0.92471	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.96722	0.8930	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.96838	0.9616	10	0.72032	D	0.01	-10.0637	19.0707	0.93134	0.0:1.0:0.0:0.0	.	143;143	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	N	143	ENSP00000222388:D143N;ENSP00000287844:D143N;ENSP00000419720:D143N;ENSP00000395785:D143N	ENSP00000222388:D143N	D	-	1	0	ABCF2	150552074	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.549000	0.82163	2.746000	0.94184	0.655000	0.94253	GAC		0.552	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		T	150921141	C	T	150921141	3	4	32	1	0	0	0	0	1	0	0	0	66	884	31	1	1533	1	ABCF2	7	150921141	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	7825616	150921141	8217522	49	2705										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27646463	27646463	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aaatgcagcatgtacagcatCaccacaggtttctggaagga	10	9	2	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:27646463C>T	ENST00000305188.8	+	7	1469	c.1231C>T	c.(1231-1233)Cac>Tac	p.H411Y	ESCO2_ENST00000397418.2_Missense_Mutation_p.H59Y	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	411					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)	p.H411Y(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		TGTACAGCATCACCACAGGTT	0.408									SC Phocomelia syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	8											123	112	116					8																	27646463		2203	4300	6503	27702382	SO:0001583	missense	157570	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1231C>T	8.37:g.27646463C>T	ENSP00000306999:p.His411Tyr		27702382	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	37	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.943597	0.92593	.	.	ENSG00000171320	ENST00000305188;ENST00000397418	T;T	0.80824	-1.22;-1.42	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.92625	0.7657	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93738	0.7047	10	0.87932	D	0	-11.5793	18.0507	0.89347	0.0:1.0:0.0:0.0	.	411	Q56NI9	ESCO2_HUMAN	Y	411;59	ENSP00000306999:H411Y;ENSP00000380563:H59Y	ENSP00000306999:H411Y	H	+	1	0	ESCO2	27702382	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.137000	0.77295	2.861000	0.98227	0.655000	0.94253	CAC		0.408	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		T	27646463	C	T	27646463	3	4	32	1	0	0	0	0	1	0	0	0	5262	826	29	3	1253	3	ESCO2	8	27646463	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10		27646463	118717559	50	2706										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39564369	39564369	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atagacctccagattgtaaaTtccagtttggttccccaggg	9	10	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:39564369T>A	ENST00000265707.5	+	18	2008	c.1963T>A	c.(1963-1965)Ttc>Atc	p.F655I	ADAM18_ENST00000541111.1_Missense_Mutation_p.F69I|ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.F631I	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	655					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F655I(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			AGATTGTAAATTCCAGTTTGG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	8											95	97	97					8																	39564369		2203	4299	6502	39683526	SO:0001583	missense	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1963T>A	8.37:g.39564369T>A	ENSP00000265707:p.Phe655Ile		39683526	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.776852	0.31411	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.85411	-1.98;-1.98;-1.98	3.58	3.58	0.41010	.	0.169649	0.28515	N	0.015065	T	0.70395	0.3219	N	0.13043	0.29	0.24143	N	0.995721	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.57435	-0.7812	10	0.30854	T	0.27	.	8.8489	0.35188	0.0:0.0:0.0:1.0	.	631;655	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	I	655;631;69	ENSP00000265707:F655I;ENSP00000369195:F631I;ENSP00000444729:F69I	ENSP00000265707:F655I	F	+	1	0	ADAM18	39683526	0.283000	0.24277	0.773000	0.31616	0.953000	0.61014	0.446000	0.21694	1.878000	0.54408	0.528000	0.53228	TTC		0.343	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		A	39564369	T	A	39564369	3	1	32	1	0	0	0	0	1	0	0	0	239	1493	52	5	2033	5	ADAM18	8	39564369	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10	11917906	39564369	106799653	51	2707										
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42286360	42286360	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gccagctcgatcgtgaagccGctgtggggggagcatgagac	17	10	0	2	rs370590168		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:42286360G>A	ENST00000342228.3	-	10	2079	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	SLC20A2_ENST00000520179.1_Splice_Site_p.S570S|SLC20A2_ENST00000520262.1_Splice_Site_p.S570S	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	570					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)	p.S570S(1)		breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			TCGTGAAGCCGCTGTGGGGGG	0.612													g|||	1	0.000199681	8e-04	0	5008	,	,		18029	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						A		1,4405	4.2+/-10.8	0,1,2202	41	35	37		1710	-3.1	0.9	8		37	0,8600		0,0,4300	no	coding-synonymous-near-splice	SLC20A2	NM_006749.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		570/653	42286360	1,13005	2203	4300	6503	42405517	SO:0001630	splice_region_variant	6575				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"Solute carriers"	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1710-1C>T	8.37:g.42286360G>A			42405517		Silent	SNP	ENST00000342228.3	37	CCDS6132.1																																																																																				0.612	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1		Silent	A	42286360	G	A	42286360	5	1	32	1	0	0	0	0	0	0	1	0	14476	1101	38	1	256	1	SLC20A2	8	42286360	Splice_Site	SNP	G	TCGA-AG-3609-01A-02W-0833-10	2721991	42286360	104077662	52	2708										
DPY19L4	286148	hgsc.bcm.edu	37	chr8	95746943	95746943	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atgtatgctctctacttatcAgcataccatgaacggaaatt	6	9	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:95746943A>G	ENST00000414645.2	+	3	312	c.213A>G	c.(211-213)tcA>tcG	p.S71S		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	71						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.S71S(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					TCTACTTATCAGCATACCATG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	8											94	87	89					8																	95746943		2203	4300	6503	95816119	SO:0001819	synonymous_variant	286148				CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.213A>G	8.37:g.95746943A>G			95816119	Q6ZW32|Q6ZW42|Q7Z329	Silent	SNP	ENST00000414645.2	37	CCDS34924.1																																																																																				0.363	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787		G	95746943	A	G	95746943	2	3	32	1	0	0	0	0	0	0	0	1	4754	175	7	4		4	DPY19L4	8	95746943	Silent	SNP	A	TCGA-AG-3609-01A-02W-0833-10	53460583	95746943	50617079	53	2709										
KCNS2	3788	hgsc.bcm.edu	37	chr8	99440991	99440991	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tcttcaagaatgccctaaacCttattgacctcatgtccatc	4	13	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:99440991C>A	ENST00000287042.4	+	2	1134	c.784C>A	c.(784-786)Ctt>Att	p.L262I	KCNS2_ENST00000521839.1_Missense_Mutation_p.L262I	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	262					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.L262I(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TGCCCTAAACCTTATTGACCT	0.522																																					Pancreas(138;844 2489 9202 24627)											1	Substitution - Missense(1)	large_intestine(1)	8											219	214	216					8																	99440991		2203	4300	6503	99510167	SO:0001583	missense	3788			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.784C>A	8.37:g.99440991C>A	ENSP00000287042:p.Leu262Ile		99510167	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	C	0.092	-1.165453	0.01673	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	D;D	0.98178	-4.77;-4.77	6.07	5.02	0.67125	Ion transport (1);	0.229427	0.35291	N	0.003307	D	0.88665	0.6498	N	0.00873	-1.125	0.30479	N	0.772502	B	0.14012	0.009	B	0.12837	0.008	T	0.81499	-0.0905	10	0.02654	T	1	.	8.4706	0.32982	0.1567:0.7338:0.0:0.1095	.	262	Q9ULS6	KCNS2_HUMAN	I	262	ENSP00000287042:L262I;ENSP00000430712:L262I	ENSP00000287042:L262I	L	+	1	0	KCNS2	99510167	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.217000	0.32455	2.884000	0.98904	0.655000	0.94253	CTT		0.522	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		A	99440991	C	A	99440991	3	1	32	1	0	0	0	0	1	0	0	0	8110	681	24	2	786	2	KCNS2	8	99440991	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	3694048	99440991	46923031	54	2710										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113331118	113331118	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	agtcgttctcctaatctgcaCgtcagaattgcattaccaac	6	12	3	1	rs371684642		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr8:113331118C>G	ENST00000297405.5	-	47	7552	c.7308G>C	c.(7306-7308)acG>acC	p.T2436T	CSMD3_ENST00000352409.3_Silent_p.T2366T|CSMD3_ENST00000343508.3_Silent_p.T2396T|CSMD3_ENST00000455883.2_Silent_p.T2332T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2436	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T2436T(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTAATCTGCACGTCAGAATTG	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											108	100	103					8																	113331118		2203	4300	6503	113400294	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7308G>C	8.37:g.113331118C>G			113400294	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113331118	C	G	113331118	2	3	32	1	0	0	0	0	0	0	0	1	3952	523	19	5		5	CSMD3	8	113331118	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	13890127	113331118	33032904	55	2711										
FAM125B	89853	hgsc.bcm.edu	37	chr9	129154394	129154394	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tgcattaaatttattccacgGgattcaacggaagctgcgat	9	8	1	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr9:129154394G>A	ENST00000361171.3	+	5	540	c.459G>A	c.(457-459)cgG>cgA	p.R153R	MVB12B_ENST00000545391.1_Silent_p.R153R|MVB12B_ENST00000436593.3_Silent_p.R138R|MVB12B_ENST00000535766.1_Silent_p.R146R	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	153	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)	p.R153R(1)									TTATTCCACGGGATTCAACGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	9											142	153	149					9																	129154394		2203	4300	6503	128194215	SO:0001819	synonymous_variant	89853			AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 28", "family with sequence similarity 125, member B"	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.459G>A	9.37:g.129154394G>A			128194215	Q8N6S7	Silent	SNP	ENST00000361171.3	37	CCDS35142.1																																																																																				0.458	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525		A	129154394	G	A	129154394	2	1	32	1	0	0	0	0	0	0	0	1	5444	1219	43	3		3	FAM125B	9	129154394	Silent	SNP	G	TCGA-AG-3609-01A-02W-0833-10		129154394	12059037	56	2712										
SUV39H2	79723	hgsc.bcm.edu	37	chr10	14943193	14943193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	cctcgatactcgtcttccccGaatagcattgttttccacaa	5	14	1	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:14943193G>A	ENST00000354919.6	+	5	1058	c.1058G>A	c.(1057-1059)cGa>cAa	p.R353Q	DCLRE1C_ENST00000378289.4_Intron|SUV39H2_ENST00000378325.3_Missense_Mutation_p.R173Q|SUV39H2_ENST00000313519.5_Missense_Mutation_p.R293Q	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	353	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.R293Q(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						CGTCTTCCCCGAATAGCATTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											138	128	131					10																	14943193		2203	4300	6503	14983199	SO:0001583	missense	79723			AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"Chromatin-modifying enzymes / K-methyltransferases"	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.1058G>A	10.37:g.14943193G>A	ENSP00000346997:p.Arg353Gln		14983199	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	37	CCDS53494.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.5|29.5	5.009943|5.009943	0.93346|0.93346	.|.	.|.	ENSG00000152455|ENSG00000152455	ENST00000358298|ENST00000433779;ENST00000378325;ENST00000354919;ENST00000313519	.|D;D;D;D	.|0.81996	.|-1.56;-1.56;-1.56;-1.56	5.87|5.87	5.87|5.87	0.94306|0.94306	.|SET domain (3);	.|0.000000	.|0.64402	.|D	.|0.000008	D|D	0.83894|0.83894	0.5353|0.5353	M|M	0.90082|0.90082	3.085|3.085	0.80722|0.80722	D|D	1|1	.|B;P	.|0.48407	.|0.105;0.91	.|B;B	.|0.28385	.|0.057;0.089	D|D	0.87589|0.87589	0.2489|0.2489	5|10	.|0.52906	.|T	.|0.07	.|.	19.5705|19.5705	0.95413|0.95413	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|353;173	.|Q9H5I1;Q9H5I1-3	.|SUV92_HUMAN;.	K|Q	119|113;173;353;293	.|ENSP00000388968:R113Q;ENSP00000367576:R173Q;ENSP00000346997:R353Q;ENSP00000319208:R293Q	.|ENSP00000319208:R293Q	E|R	+|+	1|2	0|0	SUV39H2|SUV39H2	14983199|14983199	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.522000|9.522000	0.98032|0.98032	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.373	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		A	14943193	G	A	14943193	3	1	32	1	0	0	0	0	1	0	0	0	15452	1058	37	1	888	1	SUV39H2	10	14943193	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		14943193	120591554	57	2713										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31809580	31809580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	caagccaatcttgcatccaaAgaacaagaaacaatcaatgc	5	11	2	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:31809580A>G	ENST00000320985.10	+	7	1427	c.1317A>G	c.(1315-1317)aaA>aaG	p.K439K	ZEB1_ENST00000560721.2_Silent_p.K419K|ZEB1_ENST00000361642.5_Silent_p.K440K|ZEB1_ENST00000446923.2_Silent_p.K423K|ZEB1_ENST00000542815.3_Silent_p.K372K|ZEB1_ENST00000559858.1_3'UTR			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	439					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.K439K(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				TTGCATCCAAAGAACAAGAAA	0.373																																					Ovarian(40;423 959 14296 36701 49589)											1	Substitution - coding silent(1)	large_intestine(1)	10											80	76	77					10																	31809580		2203	4300	6503	31849586	SO:0001819	synonymous_variant	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.1317A>G	10.37:g.31809580A>G			31849586	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Silent	SNP	ENST00000320985.10	37	CCDS7169.1																																																																																				0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		G	31809580	A	G	31809580	2	3	32	1	0	0	0	0	0	0	0	1	17662	69	3	4		4	ZEB1	10	31809580	Silent	SNP	A	TCGA-AG-3609-01A-02W-0833-10	16866387	31809580	103725167	58	2714										
TLL2	7093	hgsc.bcm.edu	37	chr10	98133400	98133400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tcctctgcactgaggcatccGaataaaacctgagaaacata	7	11	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:98133400G>A	ENST00000357947.3	-	19	2840	c.2615C>T	c.(2614-2616)tCg>tTg	p.S872L		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	872	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S872L(2)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TGAGGCATCCGAATAAAACCT	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	10											76	76	76					10																	98133400		2203	4300	6503	98123390	SO:0001583	missense	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2615C>T	10.37:g.98133400G>A	ENSP00000350630:p.Ser872Leu		98123390	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	34	5.362335	0.95877	.	.	ENSG00000095587	ENST00000357947	T	0.47177	0.85	4.85	4.85	0.62838	CUB (5);	0.000000	0.41097	D	0.000957	D	0.82356	0.5019	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89913	0.4053	10	0.87932	D	0	.	17.4922	0.87707	0.0:0.0:1.0:0.0	.	872	Q9Y6L7	TLL2_HUMAN	L	872	ENSP00000350630:S872L	ENSP00000350630:S872L	S	-	2	0	TLL2	98123390	1.000000	0.71417	0.746000	0.31095	0.988000	0.76386	9.601000	0.98297	2.677000	0.91161	0.561000	0.74099	TCG		0.597	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98133400	G	A	98133400	3	1	32	1	0	0	0	0	1	0	0	0	15985	1059	37	1	444	1	TLL2	10	98133400	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	66323820	98133400	37401347	59	2715										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101567923	101567923	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aaggccttcacctccattacCctcttcaatatcctgcgctt	4	16	3	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:101567923C>T	ENST00000370449.4	+	13	1865	c.1752C>T	c.(1750-1752)acC>acT	p.T584T		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	584	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.T584T(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CCTCCATTACCCTCTTCAATA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	10											282	244	257					10																	101567923		2203	4300	6503	101557913	SO:0001819	synonymous_variant	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1752C>T	10.37:g.101567923C>T			101557913	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																				0.488	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		T	101567923	C	T	101567923	2	4	32	1	0	0	0	0	0	0	0	1	53	610	22	3		3	ABCC2	10	101567923	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	3434523	101567923	33966824	60	2716										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102269148	102269148	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcaatcacaggctccttcccCgaagacaggatgtgggtcac	11	13	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:102269148C>T	ENST00000370345.3	-	4	421	c.324G>A	c.(322-324)tcG>tcA	p.S108S	NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000557395.1_Intron|SEC31B_ENST00000451524.1_Silent_p.S108S|SEC31B_ENST00000535773.1_Intron|SEC31B_ENST00000370329.5_Silent_p.S108S	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	108					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)		p.S108S(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GCTCCTTCCCCGAAGACAGGA	0.517											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	10											111	115	114					10																	102269148		2203	4300	6503	102259138	SO:0001819	synonymous_variant	25956			AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.324G>A	10.37:g.102269148C>T		1365	102259138	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																				0.517	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		T	102269148	C	T	102269148	2	4	32	1	0	0	0	0	0	0	0	1	14036	639	23	1		1	SEC31B	10	102269148	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	701225	102269148	33265599	61	2717										
TACC2	10579	hgsc.bcm.edu	37	chr10	123954587	123954587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tgaagaggcatttgagacccCggagtcaacgacccctgtca	11	12	2	3			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:123954587C>T	ENST00000369005.1	+	8	6207	c.5867C>T	c.(5866-5868)cCg>cTg	p.P1956L	TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000369004.3_Missense_Mutation_p.P34L|TACC2_ENST00000334433.3_Missense_Mutation_p.P1956L|TACC2_ENST00000453444.2_Missense_Mutation_p.P1960L|TACC2_ENST00000513429.1_Missense_Mutation_p.P102L|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000515603.1_Missense_Mutation_p.P1911L|TACC2_ENST00000360561.3_Missense_Mutation_p.P34L|TACC2_ENST00000260733.3_Missense_Mutation_p.P34L|TACC2_ENST00000368999.1_Missense_Mutation_p.P34L|TACC2_ENST00000515273.1_Missense_Mutation_p.P1960L|TACC2_ENST00000358010.1_Missense_Mutation_p.P102L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1956	Pro-rich.				astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)	p.P1956L(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TTTGAGACCCCGGAGTCAACG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	102	101					10																	123954587		2203	4300	6503	123944577	SO:0001583	missense	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5867C>T	10.37:g.123954587C>T	ENSP00000358001:p.Pro1956Leu		123944577	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.318606	0.81469	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.52526	0.66;0.66;1.71;2.81;0.66;0.66;1.71;0.66;0.66;0.66;0.66;0.66	4.75	4.75	0.60458	.	0.000000	0.32608	N	0.005872	T	0.65678	0.2714	M	0.62723	1.935	0.58432	D	0.999996	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999;1.0;1.0;0.999	T	0.69544	-0.5117	10	0.87932	D	0	-12.3254	14.7498	0.69516	0.0:1.0:0.0:0.0	.	51;1960;34;1911;34;34;102;1956	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;TACC2_HUMAN	L	1956;102;1960;1911;1956;102;1960;1946;34;34;34;34;51	ENSP00000358001:P1956L;ENSP00000425062:P102L;ENSP00000424467:P1960L;ENSP00000427618:P1911L;ENSP00000334280:P1956L;ENSP00000350701:P102L;ENSP00000395048:P1960L;ENSP00000353763:P34L;ENSP00000357995:P34L;ENSP00000422815:P34L;ENSP00000260733:P34L;ENSP00000420967:P51L	ENSP00000260733:P34L	P	+	2	0	TACC2	123944577	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.166000	0.64965	2.201000	0.70794	0.556000	0.70494	CCG		0.617	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123954587	C	T	123954587	3	4	32	1	0	0	0	0	1	0	0	0	15541	652	23	1	5965	1	TACC2	10	123954587	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	21685439	123954587	11580160	62	2718										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127451878	127451878	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ttttaaccctagcaataacaTcgaagatgacacaattctca	4	10	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:127451878T>A	ENST00000356792.4	+	25	3786	c.3554T>A	c.(3553-3555)aTc>aAc	p.I1185N	C10orf137_ENST00000337623.3_Missense_Mutation_p.I1151N	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		1185					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.I1151N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AGCAATAACATCGAAGATGAC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											85	80	82					10																	127451878		2203	4300	6503	127441868	SO:0001583	missense	26098																														ENST00000356792.4:c.3554T>A	10.37:g.127451878T>A	ENSP00000349244:p.Ile1185Asn		127441868	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	T	7.747	0.702548	0.15172	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	T;T	0.43294	0.95;0.95	5.07	-7.49	0.01355	.	2.061400	0.02006	N	0.046699	T	0.17619	0.0423	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10268	-1.0637	10	0.18276	T	0.48	.	4.1201	0.10101	0.1412:0.3694:0.3485:0.1409	.	1185;532;1151	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	N	1185;1151	ENSP00000349244:I1185N;ENSP00000336727:I1151N	ENSP00000336727:I1151N	I	+	2	0	C10orf137	127441868	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-1.284000	0.02793	-0.885000	0.03971	0.460000	0.39030	ATC		0.433	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			A	127451878	T	A	127451878	3	1	32	1	0	0	0	0	1	0	0	0	1598	1435	50	5	3546	5	C10orf137	10	127451878	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10	3497291	127451878	8082869	63	2719										
EBF3	253738	hgsc.bcm.edu	37	chr10	131638591	131638591	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	acgggcgcgaaggcgctcttCtgtttcactgcggagatgac	14	11	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr10:131638591C>G	ENST00000355311.5	-	15	1749	c.1677G>C	c.(1675-1677)caG>caC	p.Q559H	MIR4297_ENST00000579857.1_RNA|EBF3_ENST00000368648.3_Missense_Mutation_p.Q514H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	559					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q514H(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		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)		AGGCGCTCTTCTGTTTCACTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	10											40	37	38					10																	131638591		2197	4296	6493	131528581	SO:0001583	missense	253738				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.1677G>C	10.37:g.131638591C>G	ENSP00000347463:p.Gln559His		131528581	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.06|16.06	3.016958|3.016958	0.54576|0.54576	.|.	.|.	ENSG00000108001|ENSG00000108001	ENST00000440978|ENST00000355311;ENST00000368648	.|T;T	.|0.58940	.|0.3;0.3	4.53|4.53	3.49|3.49	0.39957|0.39957	.|.	.|0.115769	.|0.64402	.|D	.|0.000009	T|T	0.69708|0.69708	0.3141|0.3141	M|M	0.85542|0.85542	2.76|2.76	0.45318|0.45318	D|D	0.998315|0.998315	.|P	.|0.46952	.|0.887	.|P	.|0.57548	.|0.823	T|T	0.69624|0.69624	-0.5095|-0.5095	5|10	.|0.62326	.|D	.|0.03	-8.7356|-8.7356	4.7854|4.7854	0.13222|0.13222	0.0:0.1954:0.0:0.8046|0.0:0.1954:0.0:0.8046	.|.	.|514	.|Q9H4W6-2	.|.	Q|H	121|559;514	.|ENSP00000347463:Q559H;ENSP00000357637:Q514H	.|ENSP00000347463:Q559H	E|Q	-|-	1|3	0|2	EBF3|EBF3	131528581|131528581	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.296000|2.296000	0.43584|0.43584	0.869000|0.869000	0.35703|0.35703	0.462000|0.462000	0.41574|0.41574	GAA|CAG		0.612	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		G	131638591	C	G	131638591	3	3	32	1	0	0	0	0	1	0	0	0	4893	912	32	5	121	5	EBF3	10	131638591	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	4186713	131638591	3896156	64	2720										
GALNTL4	374378	hgsc.bcm.edu	37	chr11	11454217	11454217	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atctccttgagcagatgtggGggcgtgcgttccatggccga	15	10	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr11:11454217G>A	ENST00000227756.4	-	3	957	c.546C>T	c.(544-546)ccC>ccT	p.P182P		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	182	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.P182P(1)									GCAGATGTGGGGGCGTGCGTT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	11											95	78	84					11																	11454217		2201	4294	6495	11410793	SO:0001819	synonymous_variant	374378			AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"Glycosyltransferase family 2 domain containing"	30488	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 18"	615136	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.546C>T	11.37:g.11454217G>A			11410793	O95903|Q8NDY9	Silent	SNP	ENST00000227756.4	37	CCDS7807.1																																																																																				0.572	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		A	11454217	G	A	11454217	2	1	32	1	0	0	0	0	0	0	0	1	6243	1219	43	3		3	GALNTL4	11	11454217	Silent	SNP	G	TCGA-AG-3609-01A-02W-0833-10		11454217	123552299	65	2721										
WNK1	65125	hgsc.bcm.edu	37	chr12	994296	994296	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tccacatctgagatcgttgtTtctagtacagcactgtatcc	7	11	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr12:994296T>G	ENST00000315939.6	+	19	4969	c.4326T>G	c.(4324-4326)gtT>gtG	p.V1442V	WNK1_ENST00000535572.1_Silent_p.V1195V|WNK1_ENST00000530271.2_Silent_p.V1940V|WNK1_ENST00000537687.1_Silent_p.V1702V|WNK1_ENST00000340908.4_Silent_p.V1035V	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1442					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.V1442V(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AGATCGTTGTTTCTAGTACAG	0.473																																					Colon(19;451 567 6672 12618 28860)											1	Substitution - coding silent(1)	large_intestine(1)	12											142	142	142					12																	994296		2203	4300	6503	864557	SO:0001819	synonymous_variant	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.4326T>G	12.37:g.994296T>G			864557	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																				0.473	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		G	994296	T	G	994296	2	3	32	1	0	0	0	0	0	0	0	1	17417	1828	64	4		4	WNK1	12	994296	Silent	SNP	T	TCGA-AG-3609-01A-02W-0833-10		994296	132857599	66	2722										
RERGL	79785	hgsc.bcm.edu	37	chr12	18242171	18242171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aaggccacttaccttttgtaAcagaaacagatttctcatta	5	9	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr12:18242171A>G	ENST00000229002.2	-	2	253	c.47T>C	c.(46-48)gTt>gCt	p.V16A	RERGL_ENST00000538724.1_Intron|RERGL_ENST00000536890.1_Intron|RERGL_ENST00000541632.1_Intron	NM_024730.2	NP_079006.1	Q9H628	RERGL_HUMAN	RERG/RAS-like	16	Small GTPase-like.				GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)	p.V16A(1)		endometrium(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	17						ACCTTTTGTAACAGAAACAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	76	79					12																	18242171		2202	4297	6499	18133438	SO:0001583	missense	79785			AK026308	CCDS8679.1, CCDS66332.1	12p12.3	2014-08-12			ENSG00000111404	ENSG00000111404			26213	protein-coding gene	gene with protein product						24127187	Standard	NM_001286201		Approved	FLJ22655	uc001rdq.3	Q9H628	OTTHUMG00000168820	ENST00000229002.2:c.47T>C	12.37:g.18242171A>G	ENSP00000229002:p.Val16Ala		18133438		Missense_Mutation	SNP	ENST00000229002.2	37	CCDS8679.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.424419	0.25639	.	.	ENSG00000111404	ENST00000229002	T	0.73897	-0.79	4.26	3.09	0.35607	.	2.034730	0.03094	N	0.160160	T	0.58148	0.2102	N	0.08118	0	0.09310	N	0.999998	B	0.16396	0.017	B	0.17098	0.017	T	0.48875	-0.8996	10	0.36615	T	0.2	.	7.7442	0.28858	0.7742:0.2258:0.0:0.0	.	16	Q9H628	RERGL_HUMAN	A	16	ENSP00000229002:V16A	ENSP00000229002:V16A	V	-	2	0	RERGL	18133438	0.005000	0.15991	0.005000	0.12908	0.146000	0.21551	0.764000	0.26532	0.947000	0.37659	0.383000	0.25322	GTT		0.328	RERGL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401198.1	NM_024730		G	18242171	A	G	18242171	3	3	32	1	0	0	0	0	1	0	0	0	13270	43	2	4	590	4	RERGL	12	18242171	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	17247875	18242171	115609724	67	2723										
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57663139	57663139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tggctgaggcagctgctgacCacgttgggggctataggcca	16	10	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr12:57663139C>A	ENST00000347140.3	-	16	2029	c.1639G>T	c.(1639-1641)Ggt>Tgt	p.G547C	RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Missense_Mutation_p.G561C|R3HDM2_ENST00000441731.2_Missense_Mutation_p.G242C|R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000358907.2_Missense_Mutation_p.G547C|R3HDM2_ENST00000413953.2_Missense_Mutation_p.G274C|R3HDM2_ENST00000403821.2_Missense_Mutation_p.G581C			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	547	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.G208C(1)|p.G547C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						AGCTGCTGACCACGTTGGGGG	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	12											83	88	87					12																	57663139		2203	4300	6503	55949406	SO:0001583	missense	22864			AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1639G>T	12.37:g.57663139C>A	ENSP00000317903:p.Gly547Cys		55949406	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	C	15.70	2.909732	0.52439	.	.	ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.0	3.18	0.36537	.	0.258611	0.36444	N	0.002587	T	0.33527	0.0866	N	0.14661	0.345	0.32778	N	0.502865	D;D;P;P;P	0.55800	0.969;0.973;0.845;0.845;0.924	P;P;B;B;P	0.53146	0.719;0.533;0.43;0.43;0.54	T	0.45687	-0.9244	10	0.59425	D	0.04	-2.6698	6.9105	0.24333	0.0:0.6611:0.0:0.3389	.	274;581;561;547;274	B4DDZ2;B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;.;R3HD2_HUMAN;.	C	274;274;547;561;547;242;312;581	ENSP00000409146:G274C;ENSP00000377400:G274C;ENSP00000317903:G547C;ENSP00000385839:G561C;ENSP00000351784:G547C;ENSP00000408536:G242C;ENSP00000394676:G312C;ENSP00000385169:G581C	ENSP00000317903:G547C	G	-	1	0	R3HDM2	55949406	0.990000	0.36364	1.000000	0.80357	0.999000	0.98932	0.798000	0.27014	0.817000	0.34445	0.655000	0.94253	GGT		0.512	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		A	57663139	C	A	57663139	3	1	32	1	0	0	0	0	1	0	0	0	12925	594	21	2	1327	2	R3HDM2	12	57663139	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	39420968	57663139	76188756	68	2724										
EPYC	1833	hgsc.bcm.edu	37	chr12	91365636	91365636	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	attgttgctaatatcaataaAtgtcaaagtggttggcaatt	8	4	2	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr12:91365636A>C	ENST00000261172.3	-	5	735	c.643T>G	c.(643-645)Ttt>Gtt	p.F215V		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	215					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)	p.F215V(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						ATATCAATAAATGTCAAAGTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	93	96					12																	91365636		2203	4300	6503	89889767	SO:0001583	missense	1833			AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.643T>G	12.37:g.91365636A>C	ENSP00000261172:p.Phe215Val		89889767	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.804185	0.50315	.	.	ENSG00000083782	ENST00000261172;ENST00000551767	T;T	0.02197	4.4;4.4	6.03	6.03	0.97812	.	0.101355	0.64402	D	0.000002	T	0.01835	0.0058	N	0.10707	0.03	0.43924	D	0.996577	B	0.18310	0.027	B	0.22152	0.038	T	0.62263	-0.6891	10	0.15066	T	0.55	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	215	Q99645	EPYC_HUMAN	V	215	ENSP00000261172:F215V;ENSP00000448272:F215V	ENSP00000261172:F215V	F	-	1	0	EPYC	89889767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.083000	0.64456	2.308000	0.77769	0.533000	0.62120	TTT		0.373	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950		C	91365636	A	C	91365636	3	2	32	1	0	0	0	0	1	0	0	0	5214	101	4	4	337	4	EPYC	12	91365636	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10	33702497	91365636	42486259	69	2725										
USPL1	10208	hgsc.bcm.edu	37	chr13	31233051	31233051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	aaatgagctaccatatccaaTtgatattgccagtgagtctg	8	8	1	3			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr13:31233051T>C	ENST00000255304.4	+	9	3179	c.2837T>C	c.(2836-2838)aTt>aCt	p.I946T		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	946					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)	p.I946T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		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)		CCATATCCAATTGATATTGCC	0.413																																					Ovarian(60;318 1180 1554 28110 31601)											1	Substitution - Missense(1)	large_intestine(1)	13											140	141	141					13																	31233051		2203	4300	6503	30131051	SO:0001583	missense	10208			X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2837T>C	13.37:g.31233051T>C	ENSP00000255304:p.Ile946Thr		30131051	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.817283	0.32145	.	.	ENSG00000132952	ENST00000255304	T	0.35605	1.3	5.49	5.49	0.81192	.	0.170192	0.50627	D	0.000112	T	0.51346	0.1669	M	0.66939	2.045	0.27856	N	0.940557	D	0.55605	0.972	P	0.53490	0.727	T	0.54118	-0.8341	10	0.87932	D	0	-16.9825	15.5937	0.76562	0.0:0.0:0.0:1.0	.	946	Q5W0Q7	USPL1_HUMAN	T	946	ENSP00000255304:I946T	ENSP00000255304:I946T	I	+	2	0	USPL1	30131051	1.000000	0.71417	0.018000	0.16275	0.001000	0.01503	3.821000	0.55700	2.084000	0.62774	0.533000	0.62120	ATT		0.413	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		C	31233051	T	C	31233051	3	2	32	1	0	0	0	0	1	0	0	0	17132	1493	52	4	2867	4	USPL1	13	31233051	Missense_Mutation	SNP	T	TCGA-AG-3609-01A-02W-0833-10		31233051	83936827	70	2726										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269535	34269535	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccgcccaaccgggagatctcCaggaacgagtccccctacag	10	17	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr14:34269535C>A	ENST00000356141.4	+	12	2022	c.2022C>A	c.(2020-2022)tcC>tcA	p.S674S	NPAS3_ENST00000346562.2_Silent_p.S642S|NPAS3_ENST00000551492.1_Silent_p.S679S|NPAS3_ENST00000548645.1_Silent_p.S644S|NPAS3_ENST00000357798.5_Silent_p.S661S			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	674					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.S661S(1)|p.S642S(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GGGAGATCTCCAGGAACGAGT	0.637																																																2	Substitution - coding silent(2)	large_intestine(2)	14											70	74	73					14																	34269535		2203	4300	6503	33339286	SO:0001819	synonymous_variant	64067			AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2022C>A	14.37:g.34269535C>A			33339286	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	37	CCDS53891.1																																																																																				0.637	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			A	34269535	C	A	34269535	2	1	32	1	0	0	0	0	0	0	0	1	10595	581	21	2		2	NPAS3	14	34269535	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10		34269535	73080005	71	2727										
CYP46A1	10858	hgsc.bcm.edu	37	chr14	100165832	100165832	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	atgtcaaccaagtacaacaaGgactccaagatgtaccgtgc	8	11	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr14:100165832G>T	ENST00000261835.3	+	4	416	c.312G>T	c.(310-312)aaG>aaT	p.K104N	CYP46A1_ENST00000423126.2_Missense_Mutation_p.K7N	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	104					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.K104N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				AGTACAACAAGGACTCCAAGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	14											301	289	293					14																	100165832		2203	4300	6503	99235585	SO:0001583	missense	10858			AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"Cytochrome P450s"	2641	protein-coding gene	gene with protein product		604087	"cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.312G>T	14.37:g.100165832G>T	ENSP00000261835:p.Lys104Asn		99235585	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	37	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.77|19.77	3.890138|3.890138	0.72524|0.72524	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000380228|ENST00000261835;ENST00000423126	.|T;T	.|0.71934	.|-0.38;-0.61	5.5|5.5	4.61|4.61	0.57282|0.57282	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.81341	.|0.4802	M|M	0.72118|0.72118	2.19|2.19	0.52501|0.52501	D|D	0.999952|0.999952	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.999	.|T	.|0.81986	.|-0.0681	.|10	.|0.54805	.|T	.|0.06	.|.	10.5905|10.5905	0.45306|0.45306	0.0891:0.0:0.9109:0.0|0.0891:0.0:0.9109:0.0	.|.	.|104;75	.|Q9Y6A2;Q59ER2	.|CP46A_HUMAN;.	X|N	91|104;7	.|ENSP00000261835:K104N;ENSP00000405779:K7N	.|ENSP00000261835:K104N	G|K	+|+	1|3	0|2	CYP46A1|CYP46A1	99235585|99235585	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.596000|2.596000	0.46205|0.46205	1.475000|1.475000	0.48197|0.48197	0.643000|0.643000	0.83706|0.83706	GGA|AAG		0.507	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			T	100165832	G	T	100165832	3	4	32	1	0	0	0	0	1	0	0	0	4188	991	35	2	326	2	CYP46A1	14	100165832	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	65896297	100165832	7183708	72	2728										
ATP10A	57194	hgsc.bcm.edu	37	chr15	26026187	26026187	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	agctccgagaagccgcggacCacctgccgccgcttcaggtt	12	16	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr15:26026187C>A	ENST00000356865.6	-	2	744	c.633G>T	c.(631-633)gtG>gtT	p.V211V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	211					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V211V(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGCCGCGGACCACCTGCCGCC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	15											65	68	67					15																	26026187		2203	4300	6503	23577280	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.633G>T	15.37:g.26026187C>A			23577280	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.617	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	26026187	C	A	26026187	2	1	32	1	0	0	0	0	0	0	0	1	1117	581	21	2		2	ATP10A	15	26026187	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10		26026187	76505205	73	2729										
ANPEP	290	hgsc.bcm.edu	37	chr15	90347197	90347197	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gccctcgttcagccacaggtCattccaccactctatggtca	7	16	4	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr15:90347197C>T	ENST00000300060.6	-	7	1529	c.1216G>A	c.(1216-1218)Gac>Aac	p.D406N	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	406	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.D406N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	AGCCACAGGTCATTCCACCAC	0.622																																					NSCLC(30;827 977 2459 19669 26125)											1	Substitution - Missense(1)	large_intestine(1)	15											78	66	70					15																	90347197		2200	4299	6499	88148201	SO:0001583	missense	290			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1216G>A	15.37:g.90347197C>T	ENSP00000300060:p.Asp406Asn		88148201	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	C	33	5.260009	0.95368	.	.	ENSG00000166825	ENST00000300060	T	0.06068	3.35	4.58	4.58	0.56647	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.24586	0.0596	M	0.74467	2.265	0.58432	D	0.999997	D	0.76494	0.999	D	0.76071	0.987	T	0.01169	-1.1430	10	0.72032	D	0.01	.	14.8727	0.70471	0.0:1.0:0.0:0.0	.	406	P15144	AMPN_HUMAN	N	406	ENSP00000300060:D406N	ENSP00000300060:D406N	D	-	1	0	ANPEP	88148201	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.772000	0.85439	2.098000	0.63641	0.313000	0.20887	GAC		0.622	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90347197	C	T	90347197	3	4	32	1	0	0	0	0	1	0	0	0	710	826	29	3	1747	3	ANPEP	15	90347197	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	64321010	90347197	12184195	74	2730										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	32	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		7577094	73618116	75	2731										
KRT15	3866	hgsc.bcm.edu	37	chr17	39674782	39674782	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tttctcattgccagagaggaGaccaccatcgccaccaccaa	7	15	1	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr17:39674782G>C	ENST00000254043.3	-	1	3883	c.298C>G	c.(298-300)Ctc>Gtc	p.L100V	KRT15_ENST00000393976.2_Missense_Mutation_p.L100V|KRT15_ENST00000393974.3_5'UTR|KRT15_ENST00000393981.3_5'Flank	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	100	Gly-rich.|Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.L100V(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				CCAGAGAGGAGaccaccatcg	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											284	272	276					17																	39674782		2203	4300	6503	36928308	SO:0001583	missense	3866				CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"-", "Intermediate filaments type I, keratins (acidic)"	6421	protein-coding gene	gene with protein product	"keratin-15, basic", "keratin-15, beta", "type I cytoskeletal 15", "cytokeratin 15"	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.298C>G	17.37:g.39674782G>C	ENSP00000254043:p.Leu100Val		36928308	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.995910	0.35226	.	.	ENSG00000171346	ENST00000254043;ENST00000393976	D;D	0.93859	-3.3;-3.3	5.07	5.07	0.68467	.	0.000000	0.44483	D	0.000458	D	0.93835	0.8028	L	0.54323	1.7	0.80722	D	1	D	0.58620	0.983	P	0.51016	0.656	D	0.93558	0.6892	10	0.46703	T	0.11	.	18.6371	0.91383	0.0:0.0:1.0:0.0	.	100	P19012	K1C15_HUMAN	V	100	ENSP00000254043:L100V;ENSP00000377546:L100V	ENSP00000254043:L100V	L	-	1	0	KRT15	36928308	0.990000	0.36364	0.996000	0.52242	0.493000	0.33554	2.310000	0.43708	2.653000	0.90120	0.561000	0.74099	CTC		0.582	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275		C	39674782	G	C	39674782	3	2	32	1	0	0	0	0	1	0	0	0	8473	942	33	5	1104	5	KRT15	17	39674782	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	32097688	39674782	41520428	76	2732										
WNT3	7473	hgsc.bcm.edu	37	chr17	44846106	44846106	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcccaccagcaggtcttcacCtcacagctgcccgacagccc	8	20	3	0			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr17:44846106C>T	ENST00000225512.5	-	4	810	c.648G>A	c.(646-648)gaG>gaA	p.E216E		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	216					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.E216E(1)		endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			AGGTCTTCACCTCACAGCTGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	17											79	82	81					17																	44846106		2203	4300	6503	42201275	SO:0001819	synonymous_variant	7473			AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.648G>A	17.37:g.44846106C>T			42201275	Q2M237|Q9H1J9	Silent	SNP	ENST00000225512.5	37	CCDS11505.1																																																																																				0.597	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		T	44846106	C	T	44846106	2	4	32	1	0	0	0	0	0	0	0	1	17428	680	24	3		3	WNT3	17	44846106	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	5171324	44846106	36349104	77	2733										
PRKCA	5578	hgsc.bcm.edu	37	chr17	64492338	64492338	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gtttgctgttttgtggtccaCaagaggtgccatgaatttgt	12	6	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr17:64492338C>A	ENST00000413366.3	+	3	251	c.225C>A	c.(223-225)caC>caA	p.H75Q		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	75					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)	p.H75Q(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	TTGTGGTCCACAAGAGGTGCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											129	114	119					17																	64492338		2203	4300	6503	61922800	SO:0001583	missense	5578				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.225C>A	17.37:g.64492338C>A	ENSP00000408695:p.His75Gln		61922800	B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	37	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.992958	0.74703	.	.	ENSG00000154229	ENST00000413366	D	0.99557	-6.16	5.68	4.69	0.59074	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.088054	0.44902	U	0.000416	D	0.99832	0.9924	H	0.99368	4.535	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.96487	0.9361	10	0.87932	D	0	.	14.3466	0.66668	0.0:0.9265:0.0:0.0735	.	75	P17252	KPCA_HUMAN	Q	75	ENSP00000408695:H75Q	ENSP00000408695:H75Q	H	+	3	2	PRKCA	61922800	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.590000	0.46154	1.505000	0.48720	0.650000	0.86243	CAC		0.383	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1			A	64492338	C	A	64492338	3	1	32	1	0	0	0	0	1	0	0	0	12541	477	17	2	235	2	PRKCA	17	64492338	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	19646232	64492338	16702872	78	2734										
WBP2	23558	hgsc.bcm.edu	37	chr17	73847706	73847706	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	cctttgaaggcttctggcacGttcttcatgtcattgaatgt	9	9	4	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr17:73847706G>A	ENST00000591399.1	-	3	535	c.111C>T	c.(109-111)aaC>aaT	p.N37N	WBP2_ENST00000254806.3_Silent_p.N37N|WBP2_ENST00000585462.1_Silent_p.N15N|WBP2_ENST00000344296.4_Silent_p.N15N|WBP2_ENST00000590450.1_5'UTR|WBP2_ENST00000590221.1_Silent_p.N37N|WBP2_ENST00000433525.2_Silent_p.N37N			Q969T9	WBP2_HUMAN	WW domain binding protein 2	37	GRAM.				cellular response to estrogen stimulus (GO:0071391)|establishment of protein localization (GO:0045184)|positive regulation of gene expression, epigenetic (GO:0045815)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nuclear chromatin (GO:0000790)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)	p.N37N(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTTCTGGCACGTTCTTCATGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	17											319	261	281					17																	73847706		2203	4300	6503	71359301	SO:0001819	synonymous_variant	23558			U79458	CCDS11731.1	17q25	2008-02-01				ENSG00000132471			12738	protein-coding gene	gene with protein product		606962				7644498	Standard	NM_012478		Approved	WBP-2	uc002jps.3	Q969T9		ENST00000591399.1:c.111C>T	17.37:g.73847706G>A			71359301	O95638	Silent	SNP	ENST00000591399.1	37	CCDS11731.1																																																																																				0.493	WBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448862.1	NM_012478		A	73847706	G	A	73847706	2	1	32	1	0	0	0	0	0	0	0	1	17299	1136	40	1		1	WBP2	17	73847706	Silent	SNP	G	TCGA-AG-3609-01A-02W-0833-10	9355368	73847706	7347504	79	2735										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10246814	10246814	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tacctgcttgcccatgggctCggggttggtgacggttgtgc	16	10	0	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr19:10246814C>G	ENST00000340748.4	-	37	4826	c.4591G>C	c.(4591-4593)Gag>Cag	p.E1531Q	DNMT1_ENST00000359526.4_Missense_Mutation_p.E1547Q|DNMT1_ENST00000540357.1_Missense_Mutation_p.E1534Q			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1531	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E1531Q(2)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CCCATGGGCTCGGGGTTGGTG	0.642																																																2	Substitution - Missense(2)	large_intestine(2)	19											41	42	42					19																	10246814		2203	4300	6503	10107814	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4591G>C	19.37:g.10246814C>G	ENSP00000345739:p.Glu1531Gln		10107814	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.077980	0.76528	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.42513	0.97;0.97;0.97	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.59169	0.2174	L	0.54323	1.7	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.51973	-0.8637	10	0.21540	T	0.41	-25.2475	17.5034	0.87738	0.0:1.0:0.0:0.0	.	1534;1547;1531	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	Q	1547;1534;1531;1399	ENSP00000352516:E1547Q;ENSP00000440457:E1534Q;ENSP00000345739:E1531Q	ENSP00000345739:E1531Q	E	-	1	0	DNMT1	10107814	1.000000	0.71417	0.984000	0.44739	0.980000	0.70556	7.377000	0.79668	2.426000	0.82243	0.555000	0.69702	GAG		0.642	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		G	10246814	C	G	10246814	3	3	32	1	0	0	0	0	1	0	0	0	4686	893	31	5	275	5	DNMT1	19	10246814	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10		10246814	48882169	80	2736										
CALR	811	hgsc.bcm.edu	37	chr19	13054418	13054418	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ggcatacgctgaggagtttgGcaacgagacgtggggcgtaa	17	7	0	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr19:13054418G>A	ENST00000316448.5	+	8	1101	c.1028G>A	c.(1027-1029)gGc>gAc	p.G343D	CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000592268.1_5'Flank|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000541222.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	343	C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)	p.G343D(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	GAGGAGTTTGGCAACGAGACG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											154	121	132					19																	13054418		2203	4300	6503	12915418	SO:0001583	missense	811			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1028G>A	19.37:g.13054418G>A	ENSP00000320866:p.Gly343Asp		12915418	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	37	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.421058	0.62622	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	T	0.50813	0.73	5.6	4.56	0.56223	Concanavalin A-like lectin/glucanase (1);	0.054510	0.85682	D	0.000000	T	0.48409	0.1498	L	0.61036	1.89	0.80722	D	1	D	0.54047	0.964	B	0.43867	0.434	T	0.55823	-0.8080	10	0.87932	D	0	-24.7712	12.9742	0.58529	0.0789:0.0:0.9211:0.0	.	343	P27797	CALR_HUMAN	D	343;222	ENSP00000320866:G343D	ENSP00000320866:G343D	G	+	2	0	CALR	12915418	1.000000	0.71417	0.965000	0.40720	0.785000	0.44390	7.706000	0.84615	1.363000	0.46019	0.561000	0.74099	GGC		0.592	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		A	13054418	G	A	13054418	3	1	32	1	0	0	0	0	1	0	0	0	2598	1203	42	3	1058	3	CALR	19	13054418	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	2807604	13054418	46074565	81	2737										
HIPK4	147746	hgsc.bcm.edu	37	chr19	40895718	40895718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccaccatctcgcccgtgctcCgccgccagcccttggctacc	8	22	1	0	rs199527408		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr19:40895718C>T	ENST00000291823.2	-	1	376	c.92G>A	c.(91-93)cGg>cAg	p.R31Q		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	31	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R31Q(2)		breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GCCCGTGCTCCGCCGCCAGCC	0.607													C|||	1	0.000199681	0	0	5008	,	,		16657	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	19											105	84	91					19																	40895718		2203	4300	6503	45587558	SO:0001583	missense	147746			BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.92G>A	19.37:g.40895718C>T	ENSP00000291823:p.Arg31Gln		45587558	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	35	5.526443	0.96431	.	.	ENSG00000160396	ENST00000291823	T	0.65364	-0.15	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43416	D	0.000562	T	0.70753	0.3260	L	0.28740	0.885	0.45662	D	0.99858	D	0.89917	1.0	D	0.87578	0.998	T	0.73780	-0.3875	10	0.72032	D	0.01	.	17.5357	0.87830	0.0:1.0:0.0:0.0	.	31	Q8NE63	HIPK4_HUMAN	Q	31	ENSP00000291823:R31Q	ENSP00000291823:R31Q	R	-	2	0	HIPK4	45587558	0.610000	0.26983	0.984000	0.44739	0.991000	0.79684	5.884000	0.69729	2.673000	0.90976	0.563000	0.77884	CGG		0.607	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		T	40895718	C	T	40895718	3	4	32	1	0	0	0	0	1	0	0	0	7140	652	23	1	1774	1	HIPK4	19	40895718	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	27841300	40895718	18233265	82	2738										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41787095	41787095	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcctttctcctatggctatgGaggcactgggaagaagtcca	12	10	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr19:41787095G>C	ENST00000392006.3	+	7	1087	c.914G>C	c.(913-915)gGa>gCa	p.G305A	HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.G305A|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.G205A|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.G216A|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.G205A|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.G205A|HNRNPUL1_ENST00000378215.4_Intron	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	305	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G305A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TATGGCTATGGAGGCACTGGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											97	76	83					19																	41787095		2203	4300	6503	46478935	SO:0001583	missense	11100			AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.914G>C	19.37:g.41787095G>C	ENSP00000375863:p.Gly305Ala		46478935	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	37	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	G	32	5.189824	0.94923	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000263367	T;T;T	0.68765	-0.35;-0.35;-0.35	5.86	5.86	0.93980	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.80994	0.4731	M	0.79614	2.46	0.58432	D	0.999995	P;P;D;P;D	0.58970	0.94;0.88;0.984;0.763;0.968	P;P;P;P;P	0.60068	0.868;0.758;0.827;0.74;0.853	T	0.80770	-0.1234	10	0.49607	T	0.09	-11.875	18.9646	0.92691	0.0:0.0:1.0:0.0	.	216;205;305;305;205	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2;Q9BUJ2-4	.;.;.;HNRL1_HUMAN;.	A	205;305;216	ENSP00000340857:G205A;ENSP00000375863:G305A;ENSP00000263367:G216A	ENSP00000263367:G216A	G	+	2	0	HNRNPUL1	46478935	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.513000	0.53414	2.771000	0.95319	0.563000	0.77884	GGA		0.502	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		C	41787095	G	C	41787095	3	2	32	1	0	0	0	0	1	0	0	0	7295	1174	41	5	940	5	HNRNPUL1	19	41787095	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	891377	41787095	17341888	83	2739										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31647798	31647798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	acccatccttatcctcaagcGctgcagcacgctcctgggcc	8	18	1	0	rs199515506		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr20:31647798G>A	ENST00000375494.3	+	4	488	c.488G>A	c.(487-489)cGc>cAc	p.R163H	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	163	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.R163H(1)									ATCCTCAAGCGCTGCAGCACG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	20											91	80	84					20																	31647798		2203	4300	6503	31111459	SO:0001583	missense	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.488G>A	20.37:g.31647798G>A	ENSP00000364643:p.Arg163His		31111459	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.549703	0.65311	.	.	ENSG00000186190	ENST00000375494	T	0.04454	3.62	4.79	4.79	0.61399	.	0.444204	0.21454	N	0.074286	T	0.12689	0.0308	L	0.47716	1.5	0.32794	N	0.500816	D	0.71674	0.998	P	0.61070	0.883	T	0.02519	-1.1147	10	0.41790	T	0.15	-16.8523	13.2098	0.59817	0.0:0.0:1.0:0.0	.	163	P59826	BPIB3_HUMAN	H	163	ENSP00000364643:R163H	ENSP00000364643:R163H	R	+	2	0	BPIFB3	31111459	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	3.068000	0.50018	2.481000	0.83766	0.561000	0.74099	CGC		0.637	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		A	31647798	G	A	31647798	3	1	32	1	0	0	0	0	1	0	0	0	2103	1087	38	1	502	1	C20orf185	20	31647798	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		31647798	31377722	84	2740										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198292	52198292	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ggatccgcgtccacggagggCgcttcgccgtgggagtgttt	17	11	0	0	rs374457302		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr20:52198292C>T	ENST00000371471.2	-	2	1499	c.1074G>A	c.(1072-1074)gcG>gcA	p.A358A	ZNF217_ENST00000302342.3_Silent_p.A358A|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	358					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.A358A(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CCACGGAGGGCGCTTCGCCGT	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	20						C		1,4405	2.1+/-5.4	0,1,2202	115	117	117		1074	4.8	0.3	20		117	0,8600		0,0,4300	no	coding-synonymous	ZNF217	NM_006526.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		358/1049	52198292	1,13005	2203	4300	6503	51631699	SO:0001819	synonymous_variant	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1074G>A	20.37:g.52198292C>T			51631699	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																				0.557	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52198292	C	T	52198292	2	4	32	1	0	0	0	0	0	0	0	1	17811	755	27	1		1	ZNF217	20	52198292	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	20550494	52198292	10827228	85	2741										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32508329	32508329	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ccagatcacggtagtgtgcaAaagcaggtctcccatgctca	10	12	3	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chr21:32508329A>T	ENST00000286827.3	-	24	4276	c.3805T>A	c.(3805-3807)Ttg>Atg	p.L1269M	TIAM1_ENST00000541036.1_Missense_Mutation_p.L1209M	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1269	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1269M(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GTAGTGTGCAAAAGCAGGTCT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	21											85	80	82					21																	32508329		2203	4300	6503	31430200	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3805T>A	21.37:g.32508329A>T	ENSP00000286827:p.Leu1269Met		31430200	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589263	0.46110	.	.	ENSG00000156299	ENST00000286827;ENST00000541036	T;T	0.46819	0.86;0.89	5.49	3.02	0.34903	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.64402	D	0.000003	T	0.52821	0.1758	L	0.39397	1.21	0.51012	D	0.999906	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.44360	-0.9333	10	0.23302	T	0.38	.	8.1876	0.31348	0.8148:0.0:0.1852:0.0	.	1209;1209;1269	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	M	1269;1209	ENSP00000286827:L1269M;ENSP00000441570:L1209M	ENSP00000286827:L1269M	L	-	1	2	TIAM1	31430200	0.061000	0.20836	0.958000	0.39756	0.998000	0.95712	0.527000	0.22987	0.964000	0.38108	0.533000	0.62120	TTG		0.488	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32508329	A	T	32508329	3	4	32	1	0	0	0	0	1	0	0	0	15929	11	1	5	994	5	TIAM1	21	32508329	Missense_Mutation	SNP	A	TCGA-AG-3609-01A-02W-0833-10		32508329	15621566	86	2742										
POLA1	5422	hgsc.bcm.edu	37	chrX	24751927	24751927	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gctttcaaagaagtcattgaGaaaaaggtaaagtgctcatt	9	5	3	2			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chrX:24751927G>T	ENST00000379059.3	+	17	1824	c.1809G>T	c.(1807-1809)gaG>gaT	p.E603D	POLA1_ENST00000493342.1_3'UTR|POLA1_ENST00000379068.3_Missense_Mutation_p.E609D	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	603					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.E603D(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	AAGTCATTGAGAAAAAGGTAA	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	X											46	45	45					X																	24751927		2201	4295	6496	24661848	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1809G>T	X.37:g.24751927G>T	ENSP00000368349:p.Glu603Asp		24661848	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	G	6.693	0.496510	0.12762	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.40756	1.02;1.02	4.81	-1.07	0.09968	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.497273	0.24054	N	0.041974	T	0.18173	0.0436	N	0.10809	0.05	0.09310	N	1	B	0.16396	0.017	B	0.20577	0.03	T	0.08994	-1.0695	10	0.38643	T	0.18	0.0	4.0849	0.09943	0.312:0.0:0.2758:0.4122	.	603	P09884	DPOLA_HUMAN	D	609;603	ENSP00000368358:E609D;ENSP00000368349:E603D	ENSP00000368349:E603D	E	+	3	2	POLA1	24661848	0.995000	0.38212	0.000000	0.03702	0.215000	0.24574	0.777000	0.26718	-0.154000	0.11118	0.422000	0.28245	GAG		0.338	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24751927	G	T	24751927	3	4	32	1	0	0	0	0	1	0	0	0	12218	933	33	2	1875	2	POLA1	23	24751927	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10		24751927	130518633	87	2743										
MAOA	4128	hgsc.bcm.edu	37	chrX	43601277	43601277	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gcctacttccctcctgggatCatgactcaatatggaaggta	9	11	2	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chrX:43601277C>G	ENST00000338702.3	+	12	1368	c.1245C>G	c.(1243-1245)atC>atG	p.I415M	MAOA_ENST00000542639.1_Missense_Mutation_p.I282M	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	415					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)	p.I415I(1)|p.I415M(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	CTCCTGGGATCATGACTCAAT	0.463																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|skin(1)	X											95	79	85					X																	43601277		2203	4300	6503	43486221	SO:0001583	missense	4128				CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1245C>G	X.37:g.43601277C>G	ENSP00000340684:p.Ile415Met		43486221	B4DF46|Q16426	Missense_Mutation	SNP	ENST00000338702.3	37	CCDS14260.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.978020	0.53720	.	.	ENSG00000189221	ENST00000338702;ENST00000542639	D;D	0.92397	-3.03;-3.03	5.89	0.0491	0.14288	Amine oxidase (1);	0.043292	0.85682	D	0.000000	D	0.92925	0.7749	M	0.65677	2.01	0.53005	D	0.999968	D	0.55385	0.971	D	0.67382	0.951	D	0.89491	0.3757	10	0.72032	D	0.01	.	4.0196	0.09660	0.4057:0.1795:0.0:0.4148	.	415	P21397	AOFA_HUMAN	M	415;282	ENSP00000340684:I415M;ENSP00000440846:I282M	ENSP00000340684:I415M	I	+	3	3	MAOA	43486221	0.986000	0.35501	0.999000	0.59377	0.883000	0.51084	0.191000	0.17076	0.161000	0.19458	0.529000	0.55759	ATC		0.463	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		G	43601277	C	G	43601277	3	3	32	1	0	0	0	0	1	0	0	0	9255	816	29	5	1291	5	MAOA	23	43601277	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	18849350	43601277	111669283	88	2744										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108691389	108691389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	tcaactggattttatttataCgacgcctaaaacaaacatga	5	8	1	1	rs372111572		TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chrX:108691389C>T	ENST00000218006.2	-	6	1769	c.1478G>A	c.(1477-1479)cGt>cAt	p.R493H		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	493					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.R493H(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						TTTATTTATACGACGCCTAAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	HIS/ARG	0,3835		0,0,0,1632,571	107	92	97		1478	-1.2	0.1	X		97	1,6727		0,0,1,2428,1871	no	missense	GUCY2F	NM_001522.2	29	0,0,1,4060,2442	TT,TC,T,CC,C		0.0149,0.0,0.0095	probably-damaging	493/1109	108691389	1,10562	2203	4300	6503	108578045	SO:0001583	missense	2986			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1478G>A	X.37:g.108691389C>T	ENSP00000218006:p.Arg493His		108578045	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.029703	0.35797	0.0	1.49E-4	ENSG00000101890	ENST00000218006	T	0.79940	-1.32	4.48	-1.18	0.09617	.	0.404244	0.28077	N	0.016697	T	0.73822	0.3636	M	0.66297	2.02	0.31074	N	0.712702	B	0.18968	0.032	B	0.18263	0.021	T	0.64732	-0.6338	10	0.39692	T	0.17	.	9.2131	0.37331	0.0:0.4276:0.0:0.5724	.	493	P51841	GUC2F_HUMAN	H	493	ENSP00000218006:R493H	ENSP00000218006:R493H	R	-	2	0	GUCY2F	108578045	0.008000	0.16893	0.141000	0.22245	0.996000	0.88848	-0.064000	0.11636	-0.435000	0.07264	0.600000	0.82982	CGT		0.398	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108691389	C	T	108691389	3	4	32	1	0	0	0	0	1	0	0	0	6919	536	19	1	1904	1	GUCY2F	23	108691389	Missense_Mutation	SNP	C	TCGA-AG-3609-01A-02W-0833-10	65090112	108691389	46579171	89	2745										
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135579933	135579933	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	gacggcaaggatggtgacacCcagaccgatgccggcggaga	16	11	0	3			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chrX:135579933C>T	ENST00000218364.4	+	1	264	c.90C>T	c.(88-90)acC>acT	p.T30T	HTATSF1_ENST00000535601.1_Silent_p.T30T	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	30					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T30T(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					ATGGTGACACCCAGACCGATG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	X											127	112	117					X																	135579933		2203	4300	6503	135407599	SO:0001819	synonymous_variant	27336			U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.90C>T	X.37:g.135579933C>T			135407599	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	37	CCDS14657.1																																																																																				0.562	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		T	135579933	C	T	135579933	2	4	32	1	0	0	0	0	0	0	0	1	7454	610	22	3		3	HTATSF1	23	135579933	Silent	SNP	C	TCGA-AG-3609-01A-02W-0833-10	26888544	135579933	19690627	90	2746										
MAGEA10	4109	hgsc.bcm.edu	37	chrX	151303310	151303310	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.122222222222222	11	1	1.41968213424152	1.90073145245559	1.29662300632629	0.0995327192661963	0.466258722490609	0	ctgggctccccataaatgagGtgctccatcccatcatacag	8	14	1	1			TCGA-AG-3609-01A-02W-0833-10	TCGA-AG-3609-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	94da44f7-c745-4bfb-bf4d-4bf7d316b6a3	0ce8f81d-3acd-42b8-9188-e42cf9897f47	g.chrX:151303310G>C	ENST00000370323.4	-	4	1099	c.783C>G	c.(781-783)caC>caG	p.H261Q	MAGEA10_ENST00000244096.3_Missense_Mutation_p.H261Q|RP11-1007I13.4_ENST00000509345.2_RNA	NM_001251828.1|NM_021048.4	NP_001238757.1|NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	261	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					nucleus (GO:0005634)		p.H261Q(2)		endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CATAAATGAGGTGCTCCATCC	0.532																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	X											85	80	82					X																	151303310		2203	4300	6503	151053966	SO:0001583	missense	4109				CCDS14705.1	Xq28	2009-03-13			ENSG00000124260	ENSG00000124260			6797	protein-coding gene	gene with protein product	"MAGE-10 antigen", "melanoma-associated antigen 10", "cancer/testis antigen family 1, member 10"	300343		MAGE10		8575766	Standard	NM_001011543		Approved	MGC10599, CT1.10	uc004ffl.3	P43363	OTTHUMG00000024180	ENST00000370323.4:c.783C>G	X.37:g.151303310G>C	ENSP00000359347:p.His261Gln		151053966		Missense_Mutation	SNP	ENST00000370323.4	37	CCDS14705.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837727	0.50951	.	.	ENSG00000124260	ENST00000370323;ENST00000244096	T;T	0.05513	3.43;3.43	2.6	-0.415	0.12355	.	0.000000	0.85682	D	0.000000	T	0.23370	0.0565	H	0.95328	3.655	0.09310	N	1	D	0.64830	0.994	P	0.58520	0.84	T	0.07770	-1.0755	10	0.87932	D	0	.	5.3759	0.16164	0.4739:0.0:0.5261:0.0	.	261	P43363	MAGAA_HUMAN	Q	261	ENSP00000359347:H261Q;ENSP00000244096:H261Q	ENSP00000244096:H261Q	H	-	3	2	MAGEA10	151053966	0.005000	0.15991	0.000000	0.03702	0.547000	0.35210	-0.324000	0.07986	-0.235000	0.09767	0.292000	0.19580	CAC		0.532	MAGEA10-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060916.3	NM_021048		C	151303310	G	C	151303310	3	2	32	1	0	0	0	0	1	0	0	0	9194	1252	44	5	330	5	MAGEA10	23	151303310	Missense_Mutation	SNP	G	TCGA-AG-3609-01A-02W-0833-10	15723377	151303310	3967250	91	2747										
SLC6A9	6536	hgsc.bcm.edu	37	chr1	44463248	44463248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	agtcctggaggcggctggagCcattactgcccacaatgggg	15	11	0	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr1:44463248C>T	ENST00000360584.2	-	14	2281	c.2090G>A	c.(2089-2091)gGc>gAc	p.G697D	SLC6A9_ENST00000372306.3_Intron|SLC6A9_ENST00000372307.3_Intron|SLC6A9_ENST00000357730.2_Missense_Mutation_p.G643D|SLC6A9_ENST00000475075.2_Missense_Mutation_p.G513D|SLC6A9_ENST00000372310.3_Missense_Mutation_p.G624D	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	697					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.G697D(1)|p.G624D(1)		endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	GCGGCTGGAGCCATTACTGCC	0.682																																																2	Substitution - Missense(2)	large_intestine(2)	1											55	67	63					1																	44463248		2203	4300	6503	44235835	SO:0001583	missense	6536			S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.2090G>A	1.37:g.44463248C>T	ENSP00000353791:p.Gly697Asp		44235835	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Missense_Mutation	SNP	ENST00000360584.2	37	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.196109	0.38806	.	.	ENSG00000196517	ENST00000372310;ENST00000475075;ENST00000360584;ENST00000357730	T;T;T;T	0.77229	-0.9;-0.96;-1.08;-0.93	4.92	4.02	0.46733	.	0.801042	0.11771	N	0.531157	T	0.74191	0.3684	L	0.53249	1.67	0.80722	D	1	B;B;B;P	0.36065	0.053;0.049;0.004;0.535	B;B;B;B	0.34722	0.018;0.027;0.003;0.188	T	0.69450	-0.5142	10	0.32370	T	0.25	.	15.2085	0.73198	0.0:0.8583:0.1417:0.0	.	628;624;643;697	B7Z3W8;P48067-2;P48067-3;P48067	.;.;.;SC6A9_HUMAN	D	624;513;697;643	ENSP00000361384:G624D;ENSP00000434460:G513D;ENSP00000353791:G697D;ENSP00000350362:G643D	ENSP00000350362:G643D	G	-	2	0	SLC6A9	44235835	1.000000	0.71417	0.961000	0.40146	0.852000	0.48524	3.382000	0.52463	1.312000	0.45043	-0.167000	0.13348	GGC		0.682	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		T	44463248	C	T	44463248	3	4	33	1	0	0	0	0	1	0	0	0	14728	739	26	3	34	3	SLC6A9	1	44463248	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		44463248	204787373	1	2748										
PGM1	5236	hgsc.bcm.edu	37	chr1	64120046	64120046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tggttctcgaatcgtcttccGactgagcggcactgggagtg	14	10	2	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr1:64120046G>A	ENST00000371084.3	+	10	1721	c.1508G>A	c.(1507-1509)cGa>cAa	p.R503Q	PGM1_ENST00000540265.1_Missense_Mutation_p.R306Q|PGM1_ENST00000371083.4_Missense_Mutation_p.R521Q|RN7SL130P_ENST00000489463.2_RNA|PGM1_ENST00000483707.1_3'UTR	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	503					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)	p.R503Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						ATCGTCTTCCGACTGAGCGGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	77	78					1																	64120046		2203	4300	6503	63892634	SO:0001583	missense	5236			BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1508G>A	1.37:g.64120046G>A	ENSP00000360125:p.Arg503Gln		63892634	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.000268	0.74818	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	D;D;D	0.99042	-5.36;-5.36;-5.36	5.45	3.56	0.40772	Alpha-D-phosphohexomutase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99456	0.9807	H	0.97415	4	0.39937	D	0.974365	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99023	1.0818	10	0.87932	D	0	-17.3083	11.4745	0.50288	0.068:0.1259:0.8061:0.0	.	521;503	P36871-2;P36871	.;PGM1_HUMAN	Q	479;503;306;521	ENSP00000360125:R503Q;ENSP00000443449:R306Q;ENSP00000360124:R521Q	ENSP00000360124:R521Q	R	+	2	0	PGM1	63892634	1.000000	0.71417	0.998000	0.56505	0.292000	0.27327	9.767000	0.98960	0.779000	0.33543	-0.302000	0.09304	CGA		0.537	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		A	64120046	G	A	64120046	3	1	33	1	0	0	0	0	1	0	0	0	11828	1058	37	1	1850	1	PGM1	1	64120046	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	19656798	64120046	185130575	2	2749										
FLG	2312	hgsc.bcm.edu	37	chr1	152286282	152286282	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ccacgagaggaagtctctgcGtgacgagtgcctgattgtct	13	10	2	3	rs375783519		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr1:152286282G>A	ENST00000368799.1	-	3	1115	c.1080C>T	c.(1078-1080)caC>caT	p.H360H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	360	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.H360H(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGTCTCTGCGTGACGAGTGC	0.552									Ichthyosis																																							1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405		0,1,2202	294	286	289		1080	-4.9	0	1		289	1,8599		0,1,4299	no	coding-synonymous	FLG	NM_002016.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		360/4062	152286282	2,13004	2203	4300	6503	150552906	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1080C>T	1.37:g.152286282G>A			150552906	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152286282	G	A	152286282	2	1	33	1	0	0	0	0	0	0	0	1	5941	1136	40	1		1	FLG	1	152286282	Silent	SNP	G	TCGA-AG-3611-01A-01W-0833-10	88166236	152286282	96964339	3	2750										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234527412	234527412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cacatggacattcagggagcGgataatgccctgttgaggaa	13	8	1	1	rs560732693		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr1:234527412G>A	ENST00000040877.1	-	30	4776	c.4777C>T	c.(4777-4779)Cgc>Tgc	p.R1593C	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1593	S-adenosyl-L-methionine binding. {ECO:0000269|PubMed:18412263}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)	p.R1593C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TTCAGGGAGCGGATAATGCCC	0.502													G|||	1	0.000199681	0	0	5008	,	,		14361	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											74	62	66					1																	234527412		2203	4300	6503	232594035	SO:0001583	missense	6894				CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.4777C>T	1.37:g.234527412G>A	ENSP00000040877:p.Arg1593Cys		232594035	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520998	0.85495	.	.	ENSG00000059588	ENST00000040877	T	0.34275	1.37	5.47	5.47	0.80525	tRNA/rRNA methyltransferase, SpoU (1);	0.000000	0.85682	D	0.000000	T	0.72439	0.3460	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80901	-0.1175	10	0.87932	D	0	-6.9886	19.3005	0.94143	0.0:0.0:1.0:0.0	.	1593	Q13395	TARB1_HUMAN	C	1593	ENSP00000040877:R1593C	ENSP00000040877:R1593C	R	-	1	0	TARBP1	232594035	1.000000	0.71417	0.982000	0.44146	0.555000	0.35460	9.829000	0.99411	2.575000	0.86900	0.591000	0.81541	CGC		0.502	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234527412	G	A	234527412	3	1	33	1	0	0	0	0	1	0	0	0	15594	1116	39	1	92	1	TARBP1	1	234527412	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	82241130	234527412	14723209	4	2751										
FAM49A	81553	hgsc.bcm.edu	37	chr2	16734217	16734217	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cagagctctactgaagcattGctcgaatctgtttggaagtt	10	8	2	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr2:16734217G>T	ENST00000381323.3	-	12	1179	c.959C>A	c.(958-960)gCa>gAa	p.A320E	FAM49A_ENST00000355549.2_Missense_Mutation_p.A320E|FAM49A_ENST00000406434.1_Missense_Mutation_p.A320E	NM_030797.3	NP_110424.1	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	320						intracellular (GO:0005622)		p.A320E(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			CTGAAGCATTGCTCGAATCTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											212	185	194					2																	16734217		2203	4300	6503	16597698	SO:0001583	missense	81553			AK001942	CCDS1688.1	2p24.3	2008-02-05			ENSG00000197872	ENSG00000197872			25373	protein-coding gene	gene with protein product							Standard	NM_030797		Approved	DKFZP566A1524, FLJ11080	uc002rck.2	Q9H0Q0	OTTHUMG00000090615	ENST00000381323.3:c.959C>A	2.37:g.16734217G>T	ENSP00000370724:p.Ala320Glu		16597698	B3KNZ1|Q53QW2	Missense_Mutation	SNP	ENST00000381323.3	37	CCDS1688.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151208	0.57151	.	.	ENSG00000197872	ENST00000381323;ENST00000406434;ENST00000355549	T;T;T	0.44881	0.91;0.91;0.91	5.66	5.66	0.87406	.	0.146062	0.64402	D	0.000009	T	0.41696	0.1170	L	0.58101	1.795	0.51233	D	0.999917	B	0.24092	0.097	B	0.23150	0.044	T	0.26985	-1.0087	10	0.13853	T	0.58	-16.9606	19.1332	0.93415	0.0:0.0:1.0:0.0	.	320	Q9H0Q0	FA49A_HUMAN	E	320	ENSP00000370724:A320E;ENSP00000384771:A320E;ENSP00000347744:A320E	ENSP00000347744:A320E	A	-	2	0	FAM49A	16597698	1.000000	0.71417	0.976000	0.42696	0.988000	0.76386	6.597000	0.74118	2.840000	0.97914	0.655000	0.94253	GCA		0.398	FAM49A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207203.2	NM_030797		T	16734217	G	T	16734217	3	4	33	1	0	0	0	0	1	0	0	0	5594	1319	46	2	16	2	FAM49A	2	16734217	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10		16734217	226465156	5	2752										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27479665	27479665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gcccgactcaccttccatgaGgattcgaagaacgtctcgga	10	13	2	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr2:27479665G>A	ENST00000233535.4	-	6	1226	c.874C>T	c.(874-876)Ctc>Ttc	p.L292F	SLC30A3_ENST00000447008.2_Missense_Mutation_p.L287F	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	292					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)	p.L292F(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTTCCATGAGGATTCGAAGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											73	78	76					2																	27479665		2203	4300	6503	27333169	SO:0001583	missense	7781			U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.874C>T	2.37:g.27479665G>A	ENSP00000233535:p.Leu292Phe		27333169	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	37	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	G	33	5.215880	0.95104	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000445870	D;D	0.84873	-1.91;-1.91	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.92763	0.7699	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93574	0.6906	10	0.87932	D	0	-26.2992	16.6997	0.85345	0.0:0.0:1.0:0.0	.	287;292	F5H3B7;Q99726	.;ZNT3_HUMAN	F	292;287;229	ENSP00000233535:L292F;ENSP00000415226:L287F	ENSP00000233535:L292F	L	-	1	0	SLC30A3	27333169	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.739000	0.84976	2.616000	0.88540	0.555000	0.69702	CTC		0.562	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			A	27479665	G	A	27479665	3	1	33	1	0	0	0	0	1	0	0	0	14593	1000	35	3	304	3	SLC30A3	2	27479665	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	10745448	27479665	215719708	6	2753										
SPDYA	245711	hgsc.bcm.edu	37	chr2	29045231	29045231	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tgtttatttcaagagggctaAatttactataagtgagcata	8	4	1	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr2:29045231A>C	ENST00000334056.5	+	5	524	c.335A>C	c.(334-336)aAa>aCa	p.K112T	SPDYA_ENST00000379579.4_Missense_Mutation_p.K112T|SPDYA_ENST00000462832.1_3'UTR	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A									p.K112T(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					AAGAGGGCTAAATTTACTATA	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	2											53	53	53					2																	29045231		2178	4248	6426	28898735	SO:0001583	missense	245711			AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"Speedy homologs"	30613	protein-coding gene	gene with protein product		614029	"speedy homolog 1 (Drosophila)", "speedy homolog A (Xenopus laevis)"	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000334056.5:c.335A>C	2.37:g.29045231A>C	ENSP00000335628:p.Lys112Thr		28898735		Missense_Mutation	SNP	ENST00000334056.5	37	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	A	13.93	2.384279	0.42308	.	.	ENSG00000163806	ENST00000379579;ENST00000334056;ENST00000449210	.	.	.	5.32	4.17	0.49024	.	0.417565	0.23155	U	0.051313	T	0.24314	0.0589	L	0.29908	0.895	0.27599	N	0.949034	P;P	0.39424	0.673;0.491	B;B	0.36608	0.229;0.146	T	0.10405	-1.0631	9	0.48119	T	0.1	-30.8646	7.6914	0.28569	0.7705:0.0:0.2295:0.0	.	112;112	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	T	112	.	ENSP00000335628:K112T	K	+	2	0	SPDYA	28898735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.019000	0.41001	0.968000	0.38212	0.477000	0.44152	AAA		0.264	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	NM_182756		C	29045231	A	C	29045231	3	2	33	1	0	0	0	0	1	0	0	0	15066	14	1	4	345	4	SPDYA	2	29045231	Missense_Mutation	SNP	A	TCGA-AG-3611-01A-01W-0833-10	1565566	29045231	214154142	7	2754										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172641848	172641848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cactaggagacttaaatttcGggagataaaggccaaatttg	10	6	0	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr2:172641848G>A	ENST00000422440.2	-	18	2010	c.1973C>T	c.(1972-1974)cCg>cTg	p.P658L	SLC25A12_ENST00000392592.4_Missense_Mutation_p.P551L	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	658					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)	p.P658L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	CTTAAATTTCGGGAGATAAAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	128	131					2																	172641848		2203	4300	6503	172350094	SO:0001583	missense	8604			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1973C>T	2.37:g.172641848G>A	ENSP00000388658:p.Pro658Leu		172350094	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.008237	0.93346	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	D;D	0.87491	-2.03;-2.26	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.94735	0.8301	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93482	0.6828	10	0.46703	T	0.11	-11.7866	20.8598	0.99761	0.0:0.0:1.0:0.0	.	551;658	B3KR64;O75746	.;CMC1_HUMAN	L	658;551	ENSP00000388658:P658L;ENSP00000376371:P551L	ENSP00000376371:P551L	P	-	2	0	SLC25A12	172350094	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.937000	0.99478	0.650000	0.86243	CCG		0.507	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		A	172641848	G	A	172641848	3	1	33	1	0	0	0	0	1	0	0	0	14511	1116	39	1	67	1	SLC25A12	2	172641848	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	143596617	172641848	70557525	8	2755										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48465392	48465392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ggtggctgtactcggagaggCggcccactgccagcttggct	16	12	0	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr3:48465392C>T	ENST00000358536.4	-	3	898	c.629G>A	c.(628-630)cGc>cAc	p.R210H	PLXNB1_ENST00000296440.6_Missense_Mutation_p.R210H|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Missense_Mutation_p.R210H|PLXNB1_ENST00000456774.1_Missense_Mutation_p.R210H	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	210	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.R210H(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCGGAGAGGCGGCCCACTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	3											23	23	23					3																	48465392		2202	4300	6502	48440396	SO:0001583	missense	5364			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.629G>A	3.37:g.48465392C>T	ENSP00000351338:p.Arg210His		48440396	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	8.615	0.889983	0.17540	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	4.41	2.61	0.31194	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	D	0.000001	T	0.09555	0.0235	M	0.72479	2.2	0.80722	D	1	B;P	0.43909	0.104;0.821	B;B	0.32928	0.041;0.155	T	0.29941	-0.9995	10	0.15499	T	0.54	.	9.2539	0.37571	0.0:0.8237:0.0:0.1763	.	210;210	O43157;O43157-2	PLXB1_HUMAN;.	H	210	ENSP00000296440:R210H;ENSP00000351242:R210H;ENSP00000351338:R210H;ENSP00000414199:R210H	ENSP00000296440:R210H	R	-	2	0	PLXNB1	48440396	1.000000	0.71417	0.998000	0.56505	0.130000	0.20726	4.021000	0.57196	0.327000	0.23409	-0.229000	0.12294	CGC		0.657	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		T	48465392	C	T	48465392	3	4	33	1	0	0	0	0	1	0	0	0	12154	768	27	1	5922	1	PLXNB1	3	48465392	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		48465392	149557038	9	2756										
SLC9A9	285195	hgsc.bcm.edu	37	chr3	143292939	143292939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gaagcactgacctgttaggcCggcagcctcggcagacagga	14	12	0	2	rs544613454		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr3:143292939C>T	ENST00000316549.6	-	8	1199	c.991G>A	c.(991-993)Ggc>Agc	p.G331S		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	331					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)	p.G331S(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						CCTGTTAGGCCGGCAGCCTCG	0.537													C|||	1	0.000199681	0	0	5008	,	,		19456	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											50	49	49					3																	143292939		2203	4300	6503	144775629	SO:0001583	missense	285195			AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.991G>A	3.37:g.143292939C>T	ENSP00000320246:p.Gly331Ser		144775629	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906962	0.92107	.	.	ENSG00000181804	ENST00000316549;ENST00000450105	T	0.25250	1.81	5.39	3.6	0.41247	Cation/H+ exchanger (1);	0.081780	0.51477	N	0.000088	T	0.19685	0.0473	L	0.43152	1.355	0.58432	D	0.999997	P	0.46621	0.881	B	0.39531	0.302	T	0.02736	-1.1117	10	0.18276	T	0.48	.	11.6467	0.51265	0.0:0.8562:0.0:0.1438	.	331	Q8IVB4	SL9A9_HUMAN	S	331;214	ENSP00000320246:G331S	ENSP00000320246:G331S	G	-	1	0	SLC9A9	144775629	0.990000	0.36364	0.925000	0.36789	0.961000	0.63080	2.902000	0.48703	0.651000	0.30788	0.563000	0.77884	GGC		0.537	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		T	143292939	C	T	143292939	3	4	33	1	0	0	0	0	1	0	0	0	14758	652	23	1	982	1	SLC9A9	3	143292939	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10	94827547	143292939	54729491	10	2757										
PPP3CA	5530	hgsc.bcm.edu	37	chr4	101947108	101947108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gttgatggagttaaggttggCgtcagagggcatggcatctc	16	6	2	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr4:101947108C>T	ENST00000394854.3	-	14	2163	c.1480G>A	c.(1480-1482)Gcc>Acc	p.A494T	PPP3CA_ENST00000523694.2_Missense_Mutation_p.A427T|PPP3CA_ENST00000507176.1_Missense_Mutation_p.A396T|PPP3CA_ENST00000512215.1_Missense_Mutation_p.A262T|PPP3CA_ENST00000394853.4_Missense_Mutation_p.A484T|PPP3CA_ENST00000323055.6_Missense_Mutation_p.A442T	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	494					calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)	p.A494T(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		TTAAGGTTGGCGTCAGAGGGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	4											243	226	232					4																	101947108		2203	4300	6503	102166131	SO:0001583	missense	5530				CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.1480G>A	4.37:g.101947108C>T	ENSP00000378323:p.Ala494Thr		102166131	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Missense_Mutation	SNP	ENST00000394854.3	37	CCDS34037.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.554077	0.65425	.	.	ENSG00000138814	ENST00000512215;ENST00000394854;ENST00000323055;ENST00000394853;ENST00000507176;ENST00000523694	T;T;T;T;T;T	0.45668	0.89;2.49;2.5;2.5;2.24;2.5	6.06	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.26882	0.0658	N	0.14661	0.345	0.53005	D	0.999963	P;P;P;P;B;B	0.50710	0.454;0.938;0.454;0.589;0.318;0.318	B;B;B;B;B;B	0.40285	0.075;0.325;0.075;0.157;0.047;0.048	T	0.03829	-1.1000	10	0.20519	T	0.43	-4.6924	15.6511	0.77095	0.0:0.9344:0.0:0.0656	.	494;262;442;484;396;427	Q08209;A8W6Z8;A8W6Z7;Q08209-2;E7ETC2;A1A441	PP2BA_HUMAN;.;.;.;.;.	T	262;494;442;484;396;427	ENSP00000422781:A262T;ENSP00000378323:A494T;ENSP00000320580:A442T;ENSP00000378322:A484T;ENSP00000422990:A396T;ENSP00000429350:A427T	ENSP00000320580:A442T	A	-	1	0	PPP3CA	102166131	1.000000	0.71417	0.977000	0.42913	0.997000	0.91878	3.821000	0.55700	1.570000	0.49709	0.655000	0.94253	GCC		0.493	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		T	101947108	C	T	101947108	3	4	33	1	0	0	0	0	1	0	0	0	12431	768	27	1	89	1	PPP3CA	4	101947108	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		101947108	89207168	11	2758										
GSTCD	79807	hgsc.bcm.edu	37	chr4	106744148	106744148	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cgagctttgaggaagcagcaAcagttgaacaaccttgtcta	10	9	1	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr4:106744148A>G	ENST00000515279.1	+	6	1498	c.1278A>G	c.(1276-1278)caA>caG	p.Q426Q	GSTCD_ENST00000394728.3_Silent_p.Q426Q|GSTCD_ENST00000394730.3_Silent_p.Q339Q|GSTCD_ENST00000515255.1_3'UTR|RP11-45L9.1_ENST00000504955.1_RNA|RP11-45L9.1_ENST00000509003.1_RNA|RP11-45L9.1_ENST00000506527.1_RNA|GSTCD_ENST00000360505.5_Silent_p.Q426Q			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	426						extracellular vesicular exosome (GO:0070062)		p.Q339Q(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		GGAAGCAGCAACAGTTGAACA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	4											186	166	173					4																	106744148		2203	4300	6503	106963597	SO:0001819	synonymous_variant	79807			BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.1278A>G	4.37:g.106744148A>G			106963597	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Silent	SNP	ENST00000515279.1	37	CCDS43257.1																																																																																				0.408	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		G	106744148	A	G	106744148	2	3	33	1	0	0	0	0	0	0	0	1	6856	40	2	4		4	GSTCD	4	106744148	Silent	SNP	A	TCGA-AG-3611-01A-01W-0833-10	4797040	106744148	84410128	12	2759										
CTSO	1519	hgsc.bcm.edu	37	chr4	156849556	156849556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	aagaacttccccaggaattcCgcacaatccaatatggagtg	8	11	0	1	rs138871272		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr4:156849556C>T	ENST00000433477.3	-	7	932	c.863G>A	c.(862-864)cGg>cAg	p.R288Q		NM_001334.2	NP_001325.1	P43235	CATK_HUMAN	cathepsin O	295					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)	p.R288Q(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|prostate(1)	16	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)		CCAGGAATTCCGCACAATCCA	0.348																																					Pancreas(148;2303 2598 8989 35298)											1	Substitution - Missense(1)	large_intestine(1)	4						C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	101	92	95		863	5.6	1	4	dbSNP_134	95	0,8600		0,0,4300	no	missense	CTSO	NM_001334.2	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	288/322	156849556	3,13003	2203	4300	6503	157069006	SO:0001583	missense	1519			X77383	CCDS3794.1	4q32.1	2012-10-03			ENSG00000256043	ENSG00000256043		"Cathepsins"	2542	protein-coding gene	gene with protein product		600550		CTSO1		9790772	Standard	NM_001334		Approved		uc003ipg.3	P43234	OTTHUMG00000161942	ENST00000433477.3:c.863G>A	4.37:g.156849556C>T	ENSP00000414904:p.Arg288Gln		157069006	Q6FHS6	Missense_Mutation	SNP	ENST00000433477.3	37	CCDS3794.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.530247	0.64860	6.81E-4	0.0	ENSG00000256043	ENST00000433477	T	0.34859	1.34	5.56	5.56	0.83823	Peptidase C1A, papain C-terminal (3);	0.194855	0.46442	D	0.000281	T	0.41581	0.1165	L	0.58302	1.8	0.39707	D	0.971271	P	0.50710	0.938	P	0.49953	0.627	T	0.45991	-0.9223	10	0.87932	D	0	.	7.2793	0.26302	0.0:0.7949:0.0:0.2051	.	288	P43234	CATO_HUMAN	Q	288	ENSP00000414904:R288Q	ENSP00000281527:R288Q	R	-	2	0	CTSO	157069006	0.997000	0.39634	0.990000	0.47175	0.744000	0.42396	2.244000	0.43124	2.624000	0.88883	0.650000	0.86243	CGG		0.348	CTSO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366469.1	NM_001334		T	156849556	C	T	156849556	3	4	33	1	0	0	0	0	1	0	0	0	4046	652	23	1	110	1	CTSO	4	156849556	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10	50105408	156849556	34304720	13	2760										
CDH9	1007	hgsc.bcm.edu	37	chr5	26886111	26886111	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ggtgaaattcggattgagagTaaattctggcactggttcaa	12	5	2	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr5:26886111T>A	ENST00000231021.4	-	10	1766	c.1594A>T	c.(1594-1596)Act>Tct	p.T532S		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	532	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T532S(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GGATTGAGAGTAAATTCTGGC	0.308																																					Melanoma(8;187 585 15745 40864 52829)											1	Substitution - Missense(1)	large_intestine(1)	5											70	80	77					5																	26886111		2202	4300	6502	26921868	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1594A>T	5.37:g.26886111T>A	ENSP00000231021:p.Thr532Ser		26921868	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.396701	0.25205	.	.	ENSG00000113100	ENST00000231021	T	0.48201	0.82	5.76	3.92	0.45320	Cadherin (4);Cadherin-like (1);	0.398164	0.26421	N	0.024474	T	0.18383	0.0441	N	0.02916	-0.46	0.23862	N	0.996636	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.15636	-1.0430	9	.	.	.	.	4.0745	0.09897	0.0771:0.137:0.4795:0.3064	.	125;532	B4DFP0;Q9ULB4	.;CADH9_HUMAN	S	532	ENSP00000231021:T532S	.	T	-	1	0	CDH9	26921868	0.591000	0.26824	0.975000	0.42487	0.941000	0.58515	0.238000	0.18004	0.735000	0.32537	-0.644000	0.03951	ACT		0.308	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26886111	T	A	26886111	3	1	33	1	0	0	0	0	1	0	0	0	3123	1638	57	5	787	5	CDH9	5	26886111	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10		26886111	154029149	14	2761										
RAI14	26064	hgsc.bcm.edu	37	chr5	34824362	34824362	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gaagtgagtgtgttggcatcGaaattaaaggaatctgtgaa	13	3	1	2	rs141530324		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr5:34824362G>A	ENST00000265109.3	+	15	2702	c.2415G>A	c.(2413-2415)tcG>tcA	p.S805S	RAI14_ENST00000428746.2_Silent_p.S805S|RAI14_ENST00000515799.1_Silent_p.S808S|RAI14_ENST00000397449.1_Silent_p.S798S|RAI14_ENST00000506376.1_Silent_p.S797S|RAI14_ENST00000503673.1_Silent_p.S805S|RAI14_ENST00000512629.1_Silent_p.S776S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	805						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S805S(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					TGTTGGCATCGAAATTAAAGG	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	5						G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	127	131	130		2415,2415,2328,2391,2424,2415	-11	0	5	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	805/981,805/981,776/952,797/973,808/984,805/981	34824362	1,13005	2203	4300	6503	34860119	SO:0001819	synonymous_variant	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2415G>A	5.37:g.34824362G>A			34860119	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																				0.408	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		A	34824362	G	A	34824362	2	1	33	1	0	0	0	0	0	0	0	1	13045	1045	37	1		1	RAI14	5	34824362	Silent	SNP	G	TCGA-AG-3611-01A-01W-0833-10	7938251	34824362	146090898	15	2762										
APC	324	hgsc.bcm.edu	37	chr5	112164625	112164625	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	aaaagacgttgcgagaagttGgaagtgtgaaagcattgatg	14	3	0	4			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr5:112164625G>T	ENST00000457016.1	+	14	2079	c.1699G>T	c.(1699-1701)Gga>Tga	p.G567*	APC_ENST00000257430.4_Nonsense_Mutation_p.G567*|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.L62F|APC_ENST00000508376.2_Nonsense_Mutation_p.G567*			P25054	APC_HUMAN	adenomatous polyposis coli	567	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.G567*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCGAGAAGTTGGAAGTGTGAA	0.313		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											128	139	135					5																	112164625		2202	4300	6502	112192524	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1699G>T	5.37:g.112164625G>T	ENSP00000413133:p.Gly567*		112192524	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.225014	0.98714	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-22.8304	19.6604	0.95864	0.0:0.0:1.0:0.0	.	.	.	.	X	567;549;567;567;567	.	ENSP00000257430:G567X	G	+	1	0	APC	112192524	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.439000	0.97543	2.648000	0.89879	0.655000	0.94253	GGA		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112164625	G	T	112164625	4	4	33	1	0	0	0	0	0	1	0	0	763	1349	47	2	1749	2	APC	5	112164625	Nonsense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	77340263	112164625	68750635	16	2763										
NDST1	3340	hgsc.bcm.edu	37	chr5	149927842	149927842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ttccatgaggtgattaccgcCggctctgacgcatcctcgaa	10	13	1	3	rs201043334		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr5:149927842C>T	ENST00000261797.6	+	12	2710	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A	NDST1_ENST00000523767.1_Intron	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	736	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.A736A(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGATTACCGCCGGCTCTGACG	0.622													C|||	1	0.000199681	0	0	5008	,	,		17302	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	89	62	71		2208	-9.8	0	5	dbSNP_132	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NDST1	NM_001543.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		736/883	149927842	1,13005	2203	4300	6503	149908035	SO:0001819	synonymous_variant	3340			U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"Sulfotransferases, membrane-bound"	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.2208C>T	5.37:g.149927842C>T			149908035	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																				0.622	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		T	149927842	C	T	149927842	2	4	33	1	0	0	0	0	0	0	0	1	10286	639	23	1		1	NDST1	5	149927842	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10	37763217	149927842	30987418	17	2764										
TMEM14C	51522	hgsc.bcm.edu	37	chr6	10730852	10730852	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tgtttcttttaaacagtttgCtgatggtcgccaaagttgga	10	6	1	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr6:10730852C>T	ENST00000541412.1	+	6	677	c.292C>T	c.(292-294)Ctg>Ttg	p.L98L	TMEM14C_ENST00000229563.5_Silent_p.L98L|TMEM14C_ENST00000467415.1_3'UTR	NM_001165258.1	NP_001158730.1	Q9P0S9	TM14C_HUMAN	transmembrane protein 14C	98					heme biosynthetic process (GO:0006783)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.L98L(1)		large_intestine(2)|lung(3)	5	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)	Epithelial(50;0.246)			AAACAGTTTGCTGATGGTCGC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	6											106	96	99					6																	10730852		2203	4300	6503	10838838	SO:0001819	synonymous_variant	51522			AF151028	CCDS4514.1	6p24.1	2008-02-26	2004-04-16	2004-04-21	ENSG00000111843	ENSG00000111843			20952	protein-coding gene	gene with protein product		615318	"chromosome 6 open reading frame 53"	C6orf53		11042152, 12958361	Standard	NM_016462		Approved	HSPC194, bA421M1.6, NET26	uc021ylj.1	Q9P0S9	OTTHUMG00000014242	ENST00000541412.1:c.292C>T	6.37:g.10730852C>T			10838838	Q5T4I6	Silent	SNP	ENST00000541412.1	37	CCDS4514.1	.	.	.	.	.	.	.	.	.	.	C	7.787	0.710701	0.15239	.	.	ENSG00000111843	ENST00000342277	.	.	.	4.16	4.16	0.48862	.	.	.	.	.	T	0.66915	0.2838	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72763	-0.4195	5	0.87932	D	0	.	13.7188	0.62714	0.0:1.0:0.0:0.0	.	.	.	.	V	97	.	ENSP00000343293:A97V	A	+	2	0	TMEM14C	10838838	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	2.697000	0.47060	2.000000	0.58554	0.455000	0.32223	GCT		0.393	TMEM14C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039829.1	NM_016462		T	10730852	C	T	10730852	2	4	33	1	0	0	0	0	0	0	0	1	16104	796	28	3		3	TMEM14C	6	10730852	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10		10730852	160384215	18	2765										
ME1	4199	hgsc.bcm.edu	37	chr6	84025099	84025099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	acctcttactcttctctgccGtagtccaatgtagagtggat	8	11	3	1	rs141363376	byFrequency	TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr6:84025099G>A	ENST00000369705.3	-	6	750	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	ME1_ENST00000541327.1_Missense_Mutation_p.R46W|ME1_ENST00000543031.1_Missense_Mutation_p.R137W	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	212					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)	p.R212W(1)		NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		CTTCTCTGCCGTAGTCCAATG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	TRP/ARG	0,4406		0,0,2203	102	103	102		634	3.8	0.9	6	dbSNP_134	102	6,8592	4.3+/-15.6	0,6,4293	yes	missense	ME1	NM_002395.4	101	0,6,6496	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	212/573	84025099	6,12998	2203	4299	6502	84081818	SO:0001583	missense	4199			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.634C>T	6.37:g.84025099G>A	ENSP00000358719:p.Arg212Trp		84081818	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Missense_Mutation	SNP	ENST00000369705.3	37	CCDS34492.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.563089	0.65538	0.0	6.98E-4	ENSG00000065833	ENST00000369705;ENST00000541327;ENST00000543031	T;T;T	0.51071	0.72;0.72;0.72	5.76	3.79	0.43588	Malic enzyme, N-terminal (2);	0.044999	0.85682	D	0.000000	T	0.68604	0.3019	H	0.94582	3.555	0.51233	D	0.999912	D	0.89917	1.0	D	0.77004	0.989	T	0.77284	-0.2645	10	0.87932	D	0	-6.1497	10.9295	0.47209	0.0:0.0:0.5255:0.4744	.	212	P48163	MAOX_HUMAN	W	212;46;137	ENSP00000358719:R212W;ENSP00000439912:R46W;ENSP00000446114:R137W	ENSP00000358719:R212W	R	-	1	2	ME1	84081818	1.000000	0.71417	0.853000	0.33588	0.772000	0.43724	3.701000	0.54793	1.419000	0.47118	0.644000	0.83932	CGG		0.313	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1			A	84025099	G	A	84025099	3	1	33	1	0	0	0	0	1	0	0	0	9447	1144	40	1	1120	1	ME1	6	84025099	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	73294247	84025099	87089968	19	2766										
PEX3	8504	hgsc.bcm.edu	37	chr6	143806378	143806378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cagtgaaacacctagtcattTtgttcaggtaagaagaaagc	9	7	2	3			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr6:143806378T>C	ENST00000367591.4	+	11	1094	c.1031T>C	c.(1030-1032)tTt>tCt	p.F344S	RP1-20N2.6_ENST00000591892.1_RNA	NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	344					peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.F344S(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		CCTAGTCATTTTGTTCAGGTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											127	130	129					6																	143806378		2203	4299	6502	143848071	SO:0001583	missense	8504			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.1031T>C	6.37:g.143806378T>C	ENSP00000356563:p.Phe344Ser		143848071	Q6FGP5	Missense_Mutation	SNP	ENST00000367591.4	37	CCDS5199.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.479222	0.63849	.	.	ENSG00000034693	ENST00000367591	T	0.44881	0.91	5.45	5.45	0.79879	.	0.093369	0.85682	D	0.000000	T	0.37100	0.0991	M	0.68952	2.095	0.80722	D	1	B	0.31611	0.331	B	0.39503	0.301	T	0.42207	-0.9465	10	0.62326	D	0.03	-13.0223	14.4996	0.67711	0.0:0.0:0.0:1.0	.	344	P56589	PEX3_HUMAN	S	344	ENSP00000356563:F344S	ENSP00000356563:F344S	F	+	2	0	PEX3	143848071	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.879000	0.75572	2.073000	0.62155	0.528000	0.53228	TTT		0.368	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1			C	143806378	T	C	143806378	3	2	33	1	0	0	0	0	1	0	0	0	11778	1841	64	4	1073	4	PEX3	6	143806378	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10	59781279	143806378	27308689	20	2767										
SOD2	6648	hgsc.bcm.edu	37	chr6	160105983	160105983	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	caaccccaacctgagccttgGacaccaacagatgcagccgt	8	16	0	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr6:160105983G>T	ENST00000546087.1	-	6	2115	c.288C>A	c.(286-288)gtC>gtA	p.V96V	SOD2_ENST00000444946.2_Intron|SOD2_ENST00000367055.4_Silent_p.V142V|SOD2_ENST00000337404.4_Silent_p.V103V|SOD2_ENST00000367054.2_Silent_p.V103V|SOD2_ENST00000538183.2_Silent_p.V142V			P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	142					age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)	p.V142V(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		CTGAGCCTTGGACACCAACAG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	6											141	125	130					6																	160105983		2203	4300	6503	160025973	SO:0001819	synonymous_variant	6648			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	1.15.1.1		11180	protein-coding gene	gene with protein product		147460					Standard	NM_000636		Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.288C>A	6.37:g.160105983G>T			160025973	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	Silent	SNP	ENST00000546087.1	37																																																																																					0.458	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399943.1	NM_000636		T	160105983	G	T	160105983	2	4	33	1	0	0	0	0	0	0	0	1	14958	1161	41	2		2	SOD2	6	160105983	Silent	SNP	G	TCGA-AG-3611-01A-01W-0833-10	16299605	160105983	11009084	21	2768										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47879158	47879158	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	aaccagccctgtcccgtgtgCagctccttcaccatcacgtg	8	17	2	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr7:47879158C>T	ENST00000289672.2	-	36	5705	c.5655G>A	c.(5653-5655)ctG>ctA	p.L1885L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1885	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.L1885L(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GTCCCGTGTGCAGCTCCTTCA	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	7											46	32	37					7																	47879158		2201	4299	6500	47845683	SO:0001819	synonymous_variant	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5655G>A	7.37:g.47879158C>T			47845683	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																				0.657	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47879158	C	T	47879158	2	4	33	1	0	0	0	0	0	0	0	1	11995	697	25	3		3	PKD1L1	7	47879158	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10		47879158	111259505	22	2769										
CUL1	8454	hgsc.bcm.edu	37	chr7	148451114	148451114	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ttcaccagtcaaaccaagcaCgaggagctggagttcctcct	9	13	2	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr7:148451114C>T	ENST00000325222.4	+	3	466	c.187C>T	c.(187-189)Cga>Tga	p.R63*	CUL1_ENST00000409469.1_Nonsense_Mutation_p.R63*|CUL1_ENST00000602748.1_Nonsense_Mutation_p.R63*	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	63				Missing (in Ref. 1; AAC50544). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)		p.R63*(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AAACCAAGCACGAGGAGCTGG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											59	57	58					7																	148451114		2203	4300	6503	148082047	SO:0001587	stop_gained	8454			U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.187C>T	7.37:g.148451114C>T	ENSP00000326804:p.Arg63*		148082047	D3DWG3|O60719|Q08AL6|Q8IYW1	Nonsense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	C	40	8.392545	0.98791	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000543583	.	.	.	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.4878	17.7333	0.88384	0.0:1.0:0.0:0.0	.	.	.	.	X	63;63;21	.	ENSP00000326804:R63X	R	+	1	2	CUL1	148082047	0.995000	0.38212	0.968000	0.41197	0.968000	0.65278	3.332000	0.52083	2.195000	0.70347	0.508000	0.49915	CGA		0.408	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		T	148451114	C	T	148451114	4	4	33	1	0	0	0	0	0	1	0	0	4060	528	19	1	193	1	CUL1	7	148451114	Nonsense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10	100571956	148451114	10687549	23	2770										
MSR1	4481	hgsc.bcm.edu	37	chr8	16026285	16026285	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tgaaatctcatttcctcttcGctgtcatttccttttcccgt	4	13	3	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr8:16026285G>A	ENST00000262101.5	-	4	433	c.312C>T	c.(310-312)agC>agT	p.S104S	MSR1_ENST00000445506.2_Silent_p.S122S|MSR1_ENST00000350896.3_Silent_p.S104S|MSR1_ENST00000381998.4_Silent_p.S104S|MSR1_ENST00000355282.2_Silent_p.S104S|MSR1_ENST00000536385.1_Intron			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	104	Spacer. {ECO:0000305}.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.S104R(2)|p.S104S(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TTTCCTCTTCGCTGTCATTTC	0.398																																																3	Substitution - Missense(2)|Substitution - coding silent(1)	lung(2)|large_intestine(1)	8											228	209	215					8																	16026285		2203	4300	6503	16070656	SO:0001819	synonymous_variant	4481			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.312C>T	8.37:g.16026285G>A			16070656	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	ENST00000262101.5	37	CCDS5995.1																																																																																				0.398	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			A	16026285	G	A	16026285	2	1	33	1	0	0	0	0	0	0	0	1	9916	1078	38	1		1	MSR1	8	16026285	Silent	SNP	G	TCGA-AG-3611-01A-01W-0833-10		16026285	130337737	24	2771										
ATP6V0D2	245972	hgsc.bcm.edu	37	chr8	87153754	87153754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	attgctacgcaataaactatAcaaggtaatggttttcccaa	6	8	0	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr8:87153754A>G	ENST00000285393.3	+	4	699	c.557A>G	c.(556-558)tAc>tGc	p.Y186C	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	186					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)	p.Y186C(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						AATAAACTATACAAGGTAATG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	8											98	98	98					8																	87153754		2203	4300	6503	87222870	SO:0001583	missense	245972			AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"ATPases / V-type"	18266	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.557A>G	8.37:g.87153754A>G	ENSP00000285393:p.Tyr186Cys		87222870		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.798298	0.50208	.	.	ENSG00000147614	ENST00000285393	T	0.34275	1.37	5.29	5.29	0.74685	.	0.074898	0.56097	D	0.000034	T	0.70649	0.3248	H	0.96662	3.86	0.80722	D	1	D	0.65815	0.995	D	0.64237	0.923	T	0.81762	-0.0784	10	0.87932	D	0	-15.2305	14.4429	0.67330	1.0:0.0:0.0:0.0	.	186	Q8N8Y2	VA0D2_HUMAN	C	186	ENSP00000285393:Y186C	ENSP00000285393:Y186C	Y	+	2	0	ATP6V0D2	87222870	1.000000	0.71417	0.999000	0.59377	0.144000	0.21451	8.896000	0.92521	1.997000	0.58415	0.528000	0.53228	TAC		0.333	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565		G	87153754	A	G	87153754	3	3	33	1	0	0	0	0	1	0	0	0	1175	391	14	4	571	4	ATP6V0D2	8	87153754	Missense_Mutation	SNP	A	TCGA-AG-3611-01A-01W-0833-10	71127469	87153754	59210268	25	2772										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37740790	37740790	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tccatgctggaacccctggcCctgcacccaccactggcctt	8	19	0	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr9:37740790C>G	ENST00000539465.1	+	15	2858	c.2265C>G	c.(2263-2265)gcC>gcG	p.A755A	FRMPD1_ENST00000377765.3_Silent_p.A755A|FRMPD1_ENST00000536622.1_Silent_p.A577A|FRMPD1_ENST00000541302.1_Silent_p.A624A|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	755						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.A755A(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		AACCCCTGGCCCTGCACCCAC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	9											36	37	37					9																	37740790		2203	4300	6503	37730790	SO:0001819	synonymous_variant	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.2265C>G	9.37:g.37740790C>G			37730790	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																				0.652	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		G	37740790	C	G	37740790	2	3	33	1	0	0	0	0	0	0	0	1	6076	610	22	5		5	FRMPD1	9	37740790	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10		37740790	103472641	26	2773										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98231267	98231267	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gcggtggtgtagtacacgtgCgtgtgggggtcgtactccgt	18	8	0	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr9:98231267C>T	ENST00000331920.6	-	14	2315	c.2016G>A	c.(2014-2016)acG>acA	p.T672T	PTCH1_ENST00000437951.1_Silent_p.T606T|PTCH1_ENST00000430669.2_Silent_p.T606T|PTCH1_ENST00000429896.2_Silent_p.T521T|PTCH1_ENST00000375274.2_Silent_p.T671T|PTCH1_ENST00000418258.1_Silent_p.T521T|PTCH1_ENST00000421141.1_Silent_p.T521T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	672					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.T672T(4)|p.T671T(3)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGTACACGTGCGTGTGGGGGT	0.627																																																7	Substitution - coding silent(7)	large_intestine(7)	9	GRCh37	CI050947	PTCH1	I							160	147	152					9																	98231267		2203	4300	6503	97271088	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2016G>A	9.37:g.98231267C>T			97271088	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.627	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98231267	C	T	98231267	2	4	33	1	0	0	0	0	0	0	0	1	12764	755	27	1		1	PTCH1	9	98231267	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10	60490477	98231267	42982164	27	2774										
BEND7	222389	hgsc.bcm.edu	37	chr10	13542067	13542067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gtaatttgcttttttatttcCatgctttcatctcctaatgg	5	8	2	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr10:13542067C>T	ENST00000396900.2	-	3	158	c.159G>A	c.(157-159)atG>atA	p.M53I	BEND7_ENST00000378605.3_Start_Codon_SNP_p.M1I|BEND7_ENST00000396898.2_Missense_Mutation_p.M53I|BEND7_ENST00000341083.3_Start_Codon_SNP_p.M1I			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	53						extracellular vesicular exosome (GO:0070062)		p.M1I(2)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						TTTTTATTTCCATGCTTTCAT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	10											95	98	97					10																	13542067		2203	4300	6503	13582073	SO:0001583	missense	222389			BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"BEN domain containing"	23514	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 30"	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.159G>A	10.37:g.13542067C>T	ENSP00000380108:p.Met53Ile		13582073	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Missense_Mutation	SNP	ENST00000396900.2	37		.	.	.	.	.	.	.	.	.	.	C	17.42	3.386354	0.61956	.	.	ENSG00000165626	ENST00000396900;ENST00000341083;ENST00000396898;ENST00000378605	T;T;T;T	0.54866	0.82;0.55;0.86;0.63	5.63	5.63	0.86233	.	0.081003	0.85682	D	0.000000	T	0.52484	0.1737	L	0.58101	1.795	0.43039	D	0.994624	P;P	0.39022	0.627;0.655	B;B	0.35039	0.096;0.194	T	0.59968	-0.7354	10	0.87932	D	0	-22.4437	19.7509	0.96268	0.0:1.0:0.0:0.0	.	53;1	E5RFC0;Q8N7W2-3	.;.	I	53;1;53;1	ENSP00000380108:M53I;ENSP00000345773:M1I;ENSP00000380107:M53I;ENSP00000367868:M1I	ENSP00000345773:M1I	M	-	3	0	BEND7	13582073	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.362000	0.66098	2.693000	0.91896	0.650000	0.86243	ATG		0.388	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		T	13542067	C	T	13542067	3	4	33	1	0	0	0	0	1	0	0	0	1404	594	21	3	1482	3	BEND7	10	13542067	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		13542067	121992680	28	2775										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115947736	115947736	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	aagtcctggaacacttcctaAccaccctaatttcaggctga	6	13	1	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr10:115947736A>C	ENST00000369280.1	+	2	606	c.146A>C	c.(145-147)aAc>aCc	p.N49T	TDRD1_ENST00000369281.2_Missense_Mutation_p.N49T|TDRD1_ENST00000369282.1_Missense_Mutation_p.N49T|TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000251864.2_Missense_Mutation_p.N49T			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	49					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)	p.N49T(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		ACACTTCCTAACCACCCTAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	110	109					10																	115947736		2203	4300	6503	115937726	SO:0001583	missense	56165			AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.146A>C	10.37:g.115947736A>C	ENSP00000358286:p.Asn49Thr		115937726	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	37		.	.	.	.	.	.	.	.	.	.	A	16.09	3.024774	0.54683	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000369280	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.86	2.57	0.30868	.	0.643972	0.14952	N	0.288879	T	0.34803	0.0910	L	0.29908	0.895	0.80722	D	1	P;P;P;P	0.51537	0.666;0.91;0.775;0.946	B;B;B;P	0.48840	0.112;0.388;0.225;0.592	T	0.16808	-1.0390	10	0.87932	D	0	-9.3375	5.5612	0.17144	0.7871:0.0:0.2129:0.0	.	49;49;49;49	Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	TDRD1_HUMAN;.;.;.	T	49	ENSP00000358288:N49T;ENSP00000251864:N49T;ENSP00000358287:N49T;ENSP00000358286:N49T	ENSP00000251864:N49T	N	+	2	0	TDRD1	115937726	0.975000	0.34042	0.995000	0.50966	0.985000	0.73830	0.873000	0.28052	0.964000	0.38108	0.460000	0.39030	AAC		0.378	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			C	115947736	A	C	115947736	3	2	33	1	0	0	0	0	1	0	0	0	15769	43	2	4	148	4	TDRD1	10	115947736	Missense_Mutation	SNP	A	TCGA-AG-3611-01A-01W-0833-10	102405669	115947736	19587011	29	2776										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26743032	26743032	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	agactaggaaggatgccccaAagcggtagacttcagaaggg	14	8	1	3	rs549919551		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr11:26743032A>C	ENST00000396005.3	-	1	539	c.230T>G	c.(229-231)tTt>tGt	p.F77C	SLC5A12_ENST00000280467.6_Missense_Mutation_p.F77C	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	77					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.F77C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GGATGCCCCAAAGCGGTAGAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											92	93	92					11																	26743032		2203	4299	6502	26699608	SO:0001583	missense	159963			BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.230T>G	11.37:g.26743032A>C	ENSP00000379326:p.Phe77Cys		26699608	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	16.60	3.169081	0.57584	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.88046	-2.33;-2.33	5.59	4.44	0.53790	.	0.125321	0.53938	D	0.000059	D	0.93426	0.7903	M	0.89095	3.005	0.47862	D	0.999535	D;D	0.76494	0.991;0.999	D;D	0.73380	0.919;0.98	D	0.93266	0.6647	10	0.87932	D	0	.	10.1519	0.42799	0.6768:0.0:0.0:0.3232	.	77;77	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	C	77	ENSP00000379326:F77C;ENSP00000280467:F77C	ENSP00000280467:F77C	F	-	2	0	SLC5A12	26699608	0.996000	0.38824	1.000000	0.80357	0.852000	0.48524	3.239000	0.51360	0.916000	0.36871	0.477000	0.44152	TTT		0.517	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26743032	A	C	26743032	3	2	33	1	0	0	0	0	1	0	0	0	14701	14	1	4	1686	4	SLC5A12	11	26743032	Missense_Mutation	SNP	A	TCGA-AG-3611-01A-01W-0833-10		26743032	108263484	30	2777										
KRAS	3845	hgsc.bcm.edu	37	chr12	25378561	25378561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tacttacctgtcttgtctttGctgatgtttcaataaaagga	7	7	3	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr12:25378561G>A	ENST00000256078.4	-	4	500	c.437C>T	c.(436-438)gCa>gTa	p.A146V	KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.A146V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146V(20)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TCTTGTCTTTGCTGATGTTTC	0.318		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	20	Substitution - Missense(20)	large_intestine(17)|thyroid(2)|haematopoietic_and_lymphoid_tissue(1)	12											207	188	194					12																	25378561		2203	4300	6503	25269828	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.437C>T	12.37:g.25378561G>A	ENSP00000256078:p.Ala146Val		25269828	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217565	0.95104	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88818	-2.43;-2.43	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.95236	0.8455	M	0.90595	3.13	0.80722	D	1	D;D	0.76494	0.999;0.998	P;D	0.62955	0.802;0.909	D	0.95726	0.8770	10	0.87932	D	0	.	18.7849	0.91951	0.0:0.0:1.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	V	146	ENSP00000308495:A146V;ENSP00000256078:A146V	ENSP00000256078:A146V	A	-	2	0	KRAS	25269828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.795000	0.99099	2.757000	0.94681	0.585000	0.79938	GCA		0.318	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25378561	G	A	25378561	3	1	33	1	0	0	0	0	1	0	0	0	8459	1319	46	3	261	3	KRAS	12	25378561	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10		25378561	108473334	31	2778										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53877728	53877728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tcctcctcatcaccagttccTcttctaggcggtgcagacag	8	15	4	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr12:53877728T>C	ENST00000267079.2	-	9	1451	c.1226A>G	c.(1225-1227)gAg>gGg	p.E409G	MAP3K12_ENST00000547035.1_Missense_Mutation_p.E442G|MAP3K12_ENST00000547488.1_Missense_Mutation_p.E442G|MAP3K12_ENST00000547151.1_5'Flank	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	409	Leucine-zipper 1.		E -> K (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.E409G(1)		NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						CACCAGTTCCTCTTCTAGGCG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	12											192	185	187					12																	53877728		2203	4300	6503	52163995	SO:0001583	missense	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1226A>G	12.37:g.53877728T>C	ENSP00000267079:p.Glu409Gly		52163995	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.910583	0.92107	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	T;T;T	0.79247	-1.23;-1.25;-1.25	4.85	4.85	0.62838	Protein kinase-like domain (1);	0.149661	0.31268	N	0.007941	D	0.84800	0.5552	M	0.66939	2.045	0.80722	D	1	D;D	0.58970	0.984;0.972	P;P	0.61201	0.885;0.771	D	0.86699	0.1928	10	0.87932	D	0	.	13.8578	0.63540	0.0:0.0:0.0:1.0	.	442;409	G3V1Y2;Q12852	.;M3K12_HUMAN	G	409;442;442	ENSP00000267079:E409G;ENSP00000449038:E442G;ENSP00000448689:E442G	ENSP00000267079:E409G	E	-	2	0	MAP3K12	52163995	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.636000	0.83301	2.180000	0.69256	0.379000	0.24179	GAG		0.512	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		C	53877728	T	C	53877728	3	2	33	1	0	0	0	0	1	0	0	0	9276	1551	54	4	1381	4	MAP3K12	12	53877728	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10	28499167	53877728	79974167	32	2779										
TMTC3	160418	hgsc.bcm.edu	37	chr12	88542103	88542103	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tatagaaaagatggctaataTtaacctaaaagaaataacct	5	5	0	3	rs148019384		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr12:88542103T>C	ENST00000266712.6	+	2	231	c.11T>C	c.(10-12)aTt>aCt	p.I4T		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	4					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)		p.I4T(1)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						ATGGCTAATATTAACCTAAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	12						T	THR/ILE	0,4406		0,0,2203	103	100	101		11	5.2	1	12	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense	TMTC3	NM_181783.3	89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	4/915	88542103	1,13005	2203	4300	6503	87066234	SO:0001583	missense	160418				CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.11T>C	12.37:g.88542103T>C	ENSP00000266712:p.Ile4Thr		87066234	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.952042	0.53293	0.0	1.16E-4	ENSG00000139324	ENST00000549011;ENST00000266712;ENST00000551088	T	0.64618	-0.11	5.19	5.19	0.71726	.	0.352416	0.32687	N	0.005767	T	0.52224	0.1721	L	0.36672	1.1	0.46901	D	0.99924	B	0.26547	0.152	B	0.28011	0.085	T	0.47649	-0.9101	10	0.15952	T	0.53	-11.9846	15.3431	0.74314	0.0:0.0:0.0:1.0	.	4	Q6ZXV5-2	.	T	4	ENSP00000266712:I4T	ENSP00000266712:I4T	I	+	2	0	TMTC3	87066234	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	6.947000	0.75959	2.087000	0.62958	0.477000	0.44152	ATT		0.308	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		C	88542103	T	C	88542103	3	2	33	1	0	0	0	0	1	0	0	0	16301	1493	52	4	13	4	TMTC3	12	88542103	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10	34664375	88542103	45309792	33	2780										
GPC5	2262	hgsc.bcm.edu	37	chr13	92380835	92380835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	aacacccacacaaagcccccGttgttcttttgatcagagca	6	14	2	2	rs199631822		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr13:92380835G>A	ENST00000377067.3	+	4	1442	c.1070G>A	c.(1069-1071)cGt>cAt	p.R357H	GPC5_ENST00000483422.1_3'UTR	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	357					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.R357H(1)		NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				CAAAGCCCCCGTTGTTCTTTT	0.408													G|||	1	0.000199681	8e-04	0	5008	,	,		14209	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13											125	129	128					13																	92380835		2203	4300	6503	91178836	SO:0001583	missense	2262			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1070G>A	13.37:g.92380835G>A	ENSP00000366267:p.Arg357His		91178836	B2R726|O60436|Q9BX27	Missense_Mutation	SNP	ENST00000377067.3	37	CCDS9468.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.211	0.800329	0.16397	.	.	ENSG00000179399	ENST00000377067	T	0.55052	0.54	5.88	-2.59	0.06209	.	1.139230	0.06161	N	0.675933	T	0.37073	0.0990	L	0.35854	1.095	0.09310	N	1	B	0.13145	0.007	B	0.13407	0.009	T	0.20739	-1.0266	10	0.15066	T	0.55	-2.7689	6.8158	0.23829	0.4537:0.2053:0.3411:0.0	.	357	P78333	GPC5_HUMAN	H	357	ENSP00000366267:R357H	ENSP00000366267:R357H	R	+	2	0	GPC5	91178836	0.000000	0.05858	0.017000	0.16124	0.985000	0.73830	-0.242000	0.08928	-0.679000	0.05217	-0.259000	0.10710	CGT		0.408	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		A	92380835	G	A	92380835	3	1	33	1	0	0	0	0	1	0	0	0	6621	1145	40	1	1084	1	GPC5	13	92380835	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10		92380835	22789043	34	2781										
NALCN	259232	hgsc.bcm.edu	37	chr13	101762984	101762984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	acttacatcttgagtcaaagTttcaagagattttcccctgc	6	10	3	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr13:101762984T>C	ENST00000251127.6	-	20	2431	c.2350A>G	c.(2350-2352)Act>Gct	p.T784A		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	784					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.T784A(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGAGTCAAAGTTTCAAGAGAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											167	153	158					13																	101762984		2203	4300	6503	100560985	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2350A>G	13.37:g.101762984T>C	ENSP00000251127:p.Thr784Ala		100560985	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.393135	0.25118	.	.	ENSG00000102452	ENST00000251127	D	0.97480	-4.4	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.92743	0.7693	N	0.22421	0.69	0.80722	D	1	B	0.26318	0.146	B	0.26094	0.066	D	0.90583	0.4531	10	0.08381	T	0.77	.	15.6584	0.77162	0.0:0.0:0.0:1.0	.	784	Q8IZF0	NALCN_HUMAN	A	784	ENSP00000251127:T784A	ENSP00000251127:T784A	T	-	1	0	NALCN	100560985	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.106000	0.64143	0.454000	0.30748	ACT		0.373	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		C	101762984	T	C	101762984	3	2	33	1	0	0	0	0	1	0	0	0	10178	1725	60	4	2966	4	NALCN	13	101762984	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10	9382149	101762984	13406894	35	2782										
TMCO3	55002	hgsc.bcm.edu	37	chr13	114193725	114193725	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ggctgtttcctggctggagcGctcgtctcctctcagggccc	13	15	2	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr13:114193725G>A	ENST00000434316.2	+	10	1952	c.1593G>A	c.(1591-1593)gcG>gcA	p.A531A	TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	531						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.A531A(1)		NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TGGCTGGAGCGCTCGTCTCCT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	13											112	91	98					13																	114193725		2203	4300	6503	113241726	SO:0001819	synonymous_variant	55002			BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 11"	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1593G>A	13.37:g.114193725G>A			113241726	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																				0.612	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		A	114193725	G	A	114193725	2	1	33	1	0	0	0	0	0	0	0	1	16036	1074	38	1		1	TMCO3	13	114193725	Silent	SNP	G	TCGA-AG-3611-01A-01W-0833-10	12430741	114193725	976153	36	2783										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25928516	25928516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cctgtccagcaccccagtcaCgagcgggggaagtgacgaga	14	13	1	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr15:25928516C>T	ENST00000356865.6	-	17	3520	c.3409G>A	c.(3409-3411)Gtg>Atg	p.V1137M		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1137					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V1137M(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ACCCCAGTCACGAGCGGGGGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											74	67	69					15																	25928516		2203	4300	6503	23479609	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3409G>A	15.37:g.25928516C>T	ENSP00000349325:p.Val1137Met		23479609	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239248	0.58995	.	.	ENSG00000206190	ENST00000356865	D	0.89050	-2.46	4.81	3.67	0.42095	.	0.113555	0.64402	D	0.000020	T	0.81259	0.4785	L	0.47190	1.495	0.39777	D	0.972249	P	0.51653	0.947	B	0.38616	0.277	T	0.81531	-0.0890	10	0.52906	T	0.07	-31.1609	5.6533	0.17629	0.0:0.6856:0.0:0.3144	.	1137	O60312	AT10A_HUMAN	M	1137	ENSP00000349325:V1137M	ENSP00000349325:V1137M	V	-	1	0	ATP10A	23479609	0.791000	0.28800	0.990000	0.47175	0.589000	0.36550	1.259000	0.32956	2.205000	0.71048	0.655000	0.94253	GTG		0.522	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25928516	C	T	25928516	3	4	33	1	0	0	0	0	1	0	0	0	1117	536	19	1	1110	1	ATP10A	15	25928516	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		25928516	76602876	37	2784										
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21974131	21974131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tcaccacagcaccagaatttCgtcgttgggaagtagctgac	10	11	1	2	rs267604456		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr16:21974131C>T	ENST00000268379.4	+	6	1203	c.439C>T	c.(439-441)Cgt>Tgt	p.R147C	UQCRC2_ENST00000561553.1_Missense_Mutation_p.R147C	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	147					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R147C(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		ACCAGAATTTCGTCGTTGGGA	0.418																																					Colon(123;450 1645 12841 25393 45623)											1	Substitution - Missense(1)	large_intestine(1)	16						C	CYS/ARG	1,4395	2.1+/-5.4	0,1,2197	121	110	114		439	3.9	1	16		114	0,8600		0,0,4300	no	missense	UQCRC2	NM_003366.2	180	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	147/454	21974131	1,12995	2198	4300	6498	21881632	SO:0001583	missense	7385			J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.439C>T	16.37:g.21974131C>T	ENSP00000268379:p.Arg147Cys		21881632	B3KSN4|Q9BQ05	Missense_Mutation	SNP	ENST00000268379.4	37	CCDS10601.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101301	0.76983	2.27E-4	0.0	ENSG00000140740	ENST00000268379	T	0.30448	1.53	4.88	3.86	0.44501	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.55679	-0.8103	10	0.66056	D	0.02	-4.5497	10.5193	0.44910	0.3412:0.6588:0.0:0.0	.	147	P22695	QCR2_HUMAN	C	147	ENSP00000268379:R147C	ENSP00000268379:R147C	R	+	1	0	UQCRC2	21881632	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	3.683000	0.54663	2.411000	0.81874	0.563000	0.77884	CGT		0.418	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366		T	21974131	C	T	21974131	3	4	33	1	0	0	0	0	1	0	0	0	17060	884	31	1	461	1	UQCRC2	16	21974131	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		21974131	68380622	38	2785										
RANBP10	57610	hgsc.bcm.edu	37	chr16	67768939	67768939	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	caggcctacggtggggtagaGgttggcctgaggaggagaat	19	6	0	3			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr16:67768939G>A	ENST00000317506.3	-	6	713	c.598C>T	c.(598-600)Ctc>Ttc	p.L200F	RANBP10_ENST00000602677.1_Missense_Mutation_p.L200F|RANBP10_ENST00000536251.1_5'UTR|RANBP10_ENST00000411657.2_Missense_Mutation_p.L83F|RANBP10_ENST00000602887.1_5'Flank|RANBP10_ENST00000448631.2_Missense_Mutation_p.L144F|RANBP10_ENST00000425512.2_Missense_Mutation_p.L68F	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	200	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.L200F(1)		endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		GTGGGGTAGAGGTTGGCCTGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											49	45	46					16																	67768939		2198	4300	6498	66326440	SO:0001583	missense	57610			AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.598C>T	16.37:g.67768939G>A	ENSP00000316589:p.Leu200Phe		66326440	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	37	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.742944	0.69418	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000411657;ENST00000425512	T;T;T;T	0.74737	-0.87;-0.51;-0.87;-0.87	5.62	2.53	0.30540	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.79907	0.4527	L	0.60845	1.875	0.80722	D	1	D;D;D;D;D	0.89917	0.979;0.99;1.0;1.0;1.0	P;P;D;D;D	0.87578	0.868;0.903;0.998;0.973;0.998	T	0.77054	-0.2730	10	0.48119	T	0.1	-9.3412	6.5959	0.22672	0.2052:0.0:0.6642:0.1306	.	68;200;83;144;200	B4DHL9;B4E1Y2;B4DID0;B4DQH9;Q6VN20	.;.;.;.;RBP10_HUMAN	F	200;144;83;68	ENSP00000316589:L200F;ENSP00000392808:L144F;ENSP00000416460:L83F;ENSP00000410617:L68F	ENSP00000316589:L200F	L	-	1	0	RANBP10	66326440	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.814000	0.48010	0.830000	0.34757	-0.188000	0.12872	CTC		0.592	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		A	67768939	G	A	67768939	3	1	33	1	0	0	0	0	1	0	0	0	13063	1000	35	3	1300	3	RANBP10	16	67768939	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	45794808	67768939	22585814	39	2786										
TP53	7157	hgsc.bcm.edu	37	chr17	7578475	7578475	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cgcggacgcgggtgccgggcGggggtgtggaatcaacccac	19	12	1	0	rs137852790|rs137852791|rs587782705		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr17:7578475G>C	ENST00000269305.4	-	5	644	c.455C>G	c.(454-456)cCg>cGg	p.P152R	TP53_ENST00000445888.2_Missense_Mutation_p.P152R|TP53_ENST00000413465.2_Missense_Mutation_p.P152R|TP53_ENST00000420246.2_Missense_Mutation_p.P152R|TP53_ENST00000359597.4_Missense_Mutation_p.P152R|TP53_ENST00000455263.2_Missense_Mutation_p.P152R|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	152	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1868473}.|P -> Q (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9450901}.|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P152L(66)|p.P152R(8)|p.0?(8)|p.T150fs*16(6)|p.?(5)|p.P153fs*28(5)|p.P152fs*18(5)|p.P152fs*14(5)|p.P152Q(4)|p.P59L(2)|p.P20L(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P59R(1)|p.P20R(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P152fs*27(1)|p.Q144_G154del11(1)|p.Q144fs*16(1)|p.T18fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGTGCCGGGCGGGGGTGTGGA	0.612		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	132	Substitution - Missense(84)|Deletion - Frameshift(25)|Whole gene deletion(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)	large_intestine(22)|central_nervous_system(18)|upper_aerodigestive_tract(15)|oesophagus(10)|skin(9)|haematopoietic_and_lymphoid_tissue(8)|ovary(8)|prostate(8)|urinary_tract(7)|stomach(6)|bone(5)|breast(4)|lung(3)|liver(3)|vulva(2)|soft_tissue(2)|thyroid(1)|adrenal_gland(1)	17	GRCh37	CM941327	TP53	M							51	52	52					17																	7578475		2203	4300	6503	7519200	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.455C>G	17.37:g.7578475G>C	ENSP00000269305:p.Pro152Arg		7519200	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.463848	0.63513	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99885	-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5	5.59	5.59	0.84812	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.91768	3.24	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.998;1.0;0.996;0.999;0.998;0.994	D	0.96400	0.9296	10	0.87932	D	0	-5.4688	17.4784	0.87667	0.0:0.0:1.0:0.0	.	113;152;152;59;152;152;152	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	152;152;152;152;152;152;141;59;20;59;20;152	ENSP00000410739:P152R;ENSP00000352610:P152R;ENSP00000269305:P152R;ENSP00000398846:P152R;ENSP00000391127:P152R;ENSP00000391478:P152R;ENSP00000425104:P20R;ENSP00000423862:P59R;ENSP00000424104:P152R	ENSP00000269305:P152R	P	-	2	0	TP53	7519200	1.000000	0.71417	0.940000	0.37924	0.022000	0.10575	7.901000	0.87382	2.804000	0.96469	0.655000	0.94253	CCG		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578475	G	C	7578475	3	2	33	1	0	0	0	0	1	0	0	0	16421	1116	39	5	843	5	TP53	17	7578475	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10		7578475	73616735	40	2787										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901476	51901476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gacattttttgagatttatgGgggcaaggtgtatgatttgt	13	2	0	2			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr17:51901476G>A	ENST00000268919.4	+	1	1238	c.1082G>A	c.(1081-1083)gGg>gAg	p.G361E		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	361	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G361E(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAGATTTATGGGGGCAAGGTG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	17											100	103	102					17																	51901476		2203	4300	6503	49256475	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1082G>A	17.37:g.51901476G>A	ENSP00000268919:p.Gly361Glu		49256475	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466328	0.84425	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.17213	2.29	5.73	5.73	0.89815	Kinesin, motor domain (4);	0.000000	0.46758	D	0.000265	T	0.48537	0.1505	M	0.88241	2.94	0.49798	D	0.999826	D	0.58970	0.984	P	0.61477	0.889	T	0.54057	-0.8350	10	0.72032	D	0.01	.	19.2577	0.93952	0.0:0.0:1.0:0.0	.	361	Q8N4N8	KIF2B_HUMAN	E	361;249	ENSP00000268919:G361E	ENSP00000268919:G361E	G	+	2	0	KIF2B	49256475	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.567000	0.60850	2.854000	0.98071	0.655000	0.94253	GGG		0.463	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		A	51901476	G	A	51901476	3	1	33	1	0	0	0	0	1	0	0	0	8319	1232	43	3	1084	3	KIF2B	17	51901476	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	44323001	51901476	29293734	41	2788										
CDH2	1000	hgsc.bcm.edu	37	chr18	25573481	25573481	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	caccgtcatggcagtaaactCtggaggattgtcattgacat	10	9	3	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr18:25573481C>T	ENST00000269141.3	-	8	1564	c.1141G>A	c.(1141-1143)Gag>Aag	p.E381K	CDH2_ENST00000399380.3_Missense_Mutation_p.E350K	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	381	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.E381K(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GCAGTAAACTCTGGAGGATTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	18											294	252	266					18																	25573481		2203	4300	6503	23827479	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1141G>A	18.37:g.25573481C>T	ENSP00000269141:p.Glu381Lys		23827479	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.029895	0.93575	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.61040	0.14;0.14	5.87	5.87	0.94306	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.62146	0.2404	N	0.21282	0.65	0.80722	D	1	P;D	0.89917	0.91;1.0	P;D	0.83275	0.489;0.996	T	0.50499	-0.8821	10	0.02654	T	1	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	350;381	A8MWK3;P19022	.;CADH2_HUMAN	K	381;350	ENSP00000269141:E381K;ENSP00000382312:E350K	ENSP00000269141:E381K	E	-	1	0	CDH2	23827479	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	GAG		0.438	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25573481	C	T	25573481	3	4	33	1	0	0	0	0	1	0	0	0	3111	922	32	3	1615	3	CDH2	18	25573481	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		25573481	52503767	42	2789										
DTNA	1837	hgsc.bcm.edu	37	chr18	32459673	32459673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	gagctaccacaagtaccatgCgtggcgacatgtgagtatct	11	10	1	1	rs368868084		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr18:32459673C>T	ENST00000399113.3	+	19	2071	c.2071C>T	c.(2071-2073)Cgt>Tgt	p.R691C	DTNA_ENST00000444659.1_Missense_Mutation_p.R691C|DTNA_ENST00000591182.1_Missense_Mutation_p.R339C|DTNA_ENST00000598142.1_Missense_Mutation_p.R634C|DTNA_ENST00000598334.1_Missense_Mutation_p.R631C|DTNA_ENST00000590831.2_Missense_Mutation_p.R117C|DTNA_ENST00000556414.3_Missense_Mutation_p.R343C|DTNA_ENST00000283365.9_Missense_Mutation_p.R634C|DTNA_ENST00000269190.7_Missense_Mutation_p.R692C|DTNA_ENST00000269192.7_Missense_Mutation_p.R400C|DTNA_ENST00000399097.3_Missense_Mutation_p.R339C|DTNA_ENST00000595022.1_Missense_Mutation_p.R631C|DTNA_ENST00000399121.5_Missense_Mutation_p.R638C|DTNA_ENST00000601125.1_Missense_Mutation_p.R313C			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	691					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R339C(1)|p.R691C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						AAGTACCATGCGTGGCGACAT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	18											66	60	62					18																	32459673		2203	4300	6503	30713671	SO:0001583	missense	1837			U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.2071C>T	18.37:g.32459673C>T	ENSP00000382064:p.Arg691Cys		30713671	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	37	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.887499	0.52014	.	.	ENSG00000134769	ENST00000399119;ENST00000283365;ENST00000399114;ENST00000269190;ENST00000399097;ENST00000399121;ENST00000444659;ENST00000399113;ENST00000269192;ENST00000450377;ENST00000556414	T;T;T;T	0.19938	2.12;2.11;2.12;2.12	5.12	5.12	0.69794	.	0.294672	0.34725	N	0.003727	T	0.27241	0.0668	N	0.19112	0.55	0.41755	D	0.989684	D;D;D;D;D;D;D;D;D	0.71674	0.995;0.992;0.966;0.986;0.997;0.998;0.988;0.988;0.993	P;P;B;P;P;P;B;B;P	0.55824	0.707;0.785;0.258;0.614;0.656;0.768;0.265;0.265;0.453	T	0.05716	-1.0868	10	0.72032	D	0.01	-4.3178	17.0969	0.86637	0.0:1.0:0.0:0.0	.	343;400;381;691;634;339;638;642;634	B4DIU8;B4DIR0;B7Z3X3;Q9Y4J8;F5H5C1;Q9Y4J8-6;E9PEH8;Q59GK7;Q9Y4J8-2	.;.;.;DTNA_HUMAN;.;.;.;.;.	C	634;634;638;692;339;691;691;691;400;339;343	ENSP00000283365:R634C;ENSP00000269190:R692C;ENSP00000405819:R691C;ENSP00000382064:R691C	ENSP00000269190:R692C	R	+	1	0	DTNA	30713671	1.000000	0.71417	0.950000	0.38849	0.077000	0.17291	5.523000	0.67099	2.545000	0.85829	0.655000	0.94253	CGT		0.433	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		T	32459673	C	T	32459673	3	4	33	1	0	0	0	0	1	0	0	0	4799	768	27	1	2235	1	DTNA	18	32459673	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10	6886192	32459673	45617575	43	2790										
CDH22	64405	hgsc.bcm.edu	37	chr20	44869868	44869868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	agatggtgtacttgatggccCcgtcaccctcgtctgagtcg	12	12	2	3			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr20:44869868C>T	ENST00000372262.3	-	2	684	c.284G>A	c.(283-285)gGg>gAg	p.G95E	CDH22_ENST00000537909.1_Missense_Mutation_p.G95E	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	95	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G95E(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CTTGATGGCCCCGTCACCCTC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	20											62	53	56					20																	44869868		2203	4300	6503	44303275	SO:0001583	missense	64405			AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.284G>A	20.37:g.44869868C>T	ENSP00000361336:p.Gly95Glu		44303275	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.571666	0.86542	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.60672	0.17;0.17	4.42	4.42	0.53409	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.79131	0.4394	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83439	0.0042	10	0.72032	D	0.01	.	16.5845	0.84724	0.0:1.0:0.0:0.0	.	95	Q9UJ99	CAD22_HUMAN	E	95	ENSP00000361336:G95E;ENSP00000437790:G95E	ENSP00000361336:G95E	G	-	2	0	CDH22	44303275	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	7.320000	0.79064	2.475000	0.83589	0.455000	0.32223	GGG		0.597	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		T	44869868	C	T	44869868	3	4	33	1	0	0	0	0	1	0	0	0	3113	623	22	3	2242	3	CDH22	20	44869868	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10		44869868	18155652	44	2791										
CSE1L	1434	hgsc.bcm.edu	37	chr20	47711485	47711485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tcacttcacaagttgtctacCgcctgtccaggaagggtaag	10	11	3	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr20:47711485C>T	ENST00000262982.2	+	24	2934	c.2811C>T	c.(2809-2811)acC>acT	p.T937T	CSE1L_ENST00000469700.1_3'UTR|CSE1L_ENST00000396192.3_Silent_p.T881T|CSE1L_ENST00000542325.1_Silent_p.T720T	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	937					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)	p.T937T(2)		breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AGTTGTCTACCGCCTGTCCAG	0.438																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	20											69	64	66					20																	47711485		2203	4300	6503	47144892	SO:0001819	synonymous_variant	1434			U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.2811C>T	20.37:g.47711485C>T			47144892	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	37	CCDS13412.1																																																																																				0.438	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		T	47711485	C	T	47711485	2	4	33	1	0	0	0	0	0	0	0	1	3936	639	23	1		1	CSE1L	20	47711485	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10	2841617	47711485	15314035	45	2792										
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47865967	47865967	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	tcttggttgctccgcactagCgagaggaggatgatgtcatt	13	8	2	2	rs146287599		TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr20:47865967C>T	ENST00000396105.1	-	14	3840	c.3594G>A	c.(3592-3594)tcG>tcA	p.S1198S	ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000371752.1_Silent_p.S1198S	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1198							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S1198S(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TCCGCACTAGCGAGAGGAGGA	0.532													C|||	1	0.000199681	0	0	5008	,	,		21437	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	20						C		1,4405	2.1+/-5.4	0,1,2202	182	162	169		3594	-12.1	0	20	dbSNP_134	169	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ZNFX1	NM_021035.2		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		1198/1919	47865967	6,13000	2203	4300	6503	47299374	SO:0001819	synonymous_variant	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.3594G>A	20.37:g.47865967C>T			47299374	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Silent	SNP	ENST00000396105.1	37	CCDS13417.1																																																																																				0.532	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		T	47865967	C	T	47865967	2	4	33	1	0	0	0	0	0	0	0	1	18244	755	27	1		1	ZNFX1	20	47865967	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10	154482	47865967	15159553	46	2793										
MYT1	4661	hgsc.bcm.edu	37	chr20	62842648	62842648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ccgggttgtaccctcaccacCgcagcctttctggctgtccc	9	18	2	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chr20:62842648C>T	ENST00000328439.1	+	8	1745	c.1381C>T	c.(1381-1383)Cgc>Tgc	p.R461C	MYT1_ENST00000536311.1_Missense_Mutation_p.R461C|MYT1_ENST00000360149.4_Missense_Mutation_p.R163C	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R461C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CCCTCACCACCGCAGCCTTTC	0.557																																					GBM(59;481 1041 20555 21139 33705)											1	Substitution - Missense(1)	large_intestine(1)	20											136	102	114					20																	62842648		2203	4300	6503	62313092	SO:0001583	missense	4661			M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1381C>T	20.37:g.62842648C>T	ENSP00000327465:p.Arg461Cys		62313092	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.500982	0.64298	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.59906	0.44;0.23;0.25	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.79240	0.4412	M	0.90814	3.15	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.83617	0.0137	10	0.87932	D	0	-25.8002	13.071	0.59061	0.1607:0.8393:0.0:0.0	.	461;461;163	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	C	163;461;461	ENSP00000353269:R163C;ENSP00000327465:R461C;ENSP00000442412:R461C	ENSP00000327465:R461C	R	+	1	0	MYT1	62313092	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.656000	0.61483	2.298000	0.77334	0.563000	0.77884	CGC		0.557	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62842648	C	T	62842648	3	4	33	1	0	0	0	0	1	0	0	0	10136	652	23	1	1403	1	MYT1	20	62842648	Missense_Mutation	SNP	C	TCGA-AG-3611-01A-01W-0833-10	14976681	62842648	182872	47	2794										
ZNF645	158506	hgsc.bcm.edu	37	chrX	22292068	22292068	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ccagctctaaccacgacctaCgatccatcatctggatatat	5	14	3	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chrX:22292068C>T	ENST00000323684.1	+	1	1004	c.960C>T	c.(958-960)taC>taT	p.Y320Y		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	320	Pro-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.Y320Y(1)		cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						CCACGACCTACGATCCATCAT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	X											131	106	114					X																	22292068		2203	4300	6503	22201989	SO:0001819	synonymous_variant	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.960C>T	X.37:g.22292068C>T			22201989	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																				0.458	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		T	22292068	C	T	22292068	2	4	33	1	0	0	0	0	0	0	0	1	18100	547	19	1		1	ZNF645	23	22292068	Silent	SNP	C	TCGA-AG-3611-01A-01W-0833-10		22292068	132978492	48	2795										
SRPX	8406	hgsc.bcm.edu	37	chrX	38009100	38009100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	ctttgtccatgccatgcttaTccactagcaccatactgaag	6	13	0	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chrX:38009100T>C	ENST00000378533.3	-	10	1365	c.1259A>G	c.(1258-1260)gAt>gGt	p.D420G	SRPX_ENST00000343800.6_Missense_Mutation_p.D407G|SRPX_ENST00000479015.1_5'UTR|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_Missense_Mutation_p.D400G|SRPX_ENST00000432886.2_Missense_Mutation_p.D361G|SRPX_ENST00000538295.1_Silent_p.G379G	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	420					autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.D420G(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GCCATGCTTATCCACTAGCAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X											145	90	109					X																	38009100		2202	4300	6502	37894044	SO:0001583	missense	8406			U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"sushi-repeat-containing protein, X chromosome", "sushi-repeat-containing protein, X-linked"			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.1259A>G	X.37:g.38009100T>C	ENSP00000367794:p.Asp420Gly		37894044	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.684166	0.88639	.	.	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000378533;ENST00000343800	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.40862	0.1134	L	0.31207	0.915	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.995;0.999	T	0.32798	-0.9893	10	0.87932	D	0	-18.4398	15.4637	0.75381	0.0:0.0:0.0:1.0	.	361;400;420	B4DQH5;G3V1L0;P78539	.;.;SRPX_HUMAN	G	400;361;420;407	ENSP00000440758:D400G;ENSP00000411165:D361G;ENSP00000367794:D420G;ENSP00000339211:D407G	ENSP00000339211:D407G	D	-	2	0	SRPX	37894044	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.626000	0.83164	2.036000	0.60181	0.486000	0.48141	GAT		0.493	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		C	38009100	T	C	38009100	3	2	33	1	0	0	0	0	1	0	0	0	15203	1435	50	4	139	4	SRPX	23	38009100	Missense_Mutation	SNP	T	TCGA-AG-3611-01A-01W-0833-10	15717032	38009100	117261460	49	2796										
OPHN1	4983	hgsc.bcm.edu	37	chrX	67283720	67283720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	cttgtggtgggccaggggccGgggagctggtctctttatgt	18	8	1	0			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chrX:67283720G>A	ENST00000355520.5	-	21	2775	c.2134C>T	c.(2134-2136)Cgg>Tgg	p.R712W	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Intron	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	712	Pro-rich.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.R712W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						GCCAGGGGCCGGGGAGCTGGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	X											24	20	22					X																	67283720		2195	4281	6476	67200445	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.2134C>T	X.37:g.67283720G>A	ENSP00000347710:p.Arg712Trp		67200445	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.065129	0.55432	.	.	ENSG00000079482	ENST00000355520	T	0.53423	0.62	5.04	1.54	0.23209	.	0.291572	0.30338	N	0.009848	T	0.45796	0.1360	N	0.19112	0.55	0.20196	N	0.999924	D	0.76494	0.999	P	0.60609	0.877	T	0.37430	-0.9706	10	0.66056	D	0.02	.	10.2416	0.43316	0.0:0.0:0.3508:0.6492	.	712	O60890	OPHN1_HUMAN	W	712	ENSP00000347710:R712W	ENSP00000347710:R712W	R	-	1	2	OPHN1	67200445	0.912000	0.30974	0.267000	0.24556	0.821000	0.46438	0.776000	0.26704	0.364000	0.24374	0.506000	0.49869	CGG		0.577	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		A	67283720	G	A	67283720	3	1	33	1	0	0	0	0	1	0	0	0	10906	1115	39	1	290	1	OPHN1	23	67283720	Missense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	29274620	67283720	87986840	50	2797										
AMOT	154796	hgsc.bcm.edu	37	chrX	112022804	112022804	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0196078431372549	1	1	0.203181905309565	0	0.214792299898683	1	1	0	agtttgggtactgcagtctcGgctgcctgtcttggagtgag	15	8	2	1			TCGA-AG-3611-01A-01W-0833-10	TCGA-AG-3611-10A-01W-0833-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	53fdb7ba-3c64-4b8b-9e2f-d3fd97769aa1	21a5b4f1-926e-4801-8bd4-0124c5f5f8f8	g.chrX:112022804G>A	ENST00000524145.1	-	11	2652	c.2578C>T	c.(2578-2580)Cga>Tga	p.R860*	MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371962.1_Nonsense_Mutation_p.R628*|AMOT_ENST00000304758.1_Nonsense_Mutation_p.R451*|AMOT_ENST00000371959.3_Nonsense_Mutation_p.R860*			Q4VCS5	AMOT_HUMAN	angiomotin	860					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)	p.R451*(1)|p.R860*(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						CTGCAGTCTCGGCTGCCTGTC	0.592																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											105	73	84					X																	112022804		2203	4300	6503	111909460	SO:0001587	stop_gained	154796			AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2578C>T	X.37:g.112022804G>A	ENSP00000429013:p.Arg860*		111909460	Q504X5|Q9HD27|Q9UPT1	Nonsense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	G	38	6.802785	0.97849	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000432214	.	.	.	5.5	5.5	0.81552	.	0.126462	0.51477	D	0.000089	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-3.5806	12.0864	0.53700	0.0:0.0:0.7087:0.2913	.	.	.	.	X	451;860;628;860;100	.	ENSP00000305557:R451X	R	-	1	2	AMOT	111909460	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.741000	0.38238	2.305000	0.77605	0.529000	0.55759	CGA		0.592	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		A	112022804	G	A	112022804	4	1	33	1	0	0	0	0	0	1	0	0	582	1124	39	1	684	1	AMOT	23	112022804	Nonsense_Mutation	SNP	G	TCGA-AG-3611-01A-01W-0833-10	44739084	112022804	43247756	51	2798										
UBR4	23352	hgsc.bcm.edu	37	chr1	19488941	19488941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tcagcctgggaatcttcctcTtccaccgccaactcctccac	5	19	3	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr1:19488941T>C	ENST00000375254.3	-	35	4956	c.4929A>G	c.(4927-4929)gaA>gaG	p.E1643E	UBR4_ENST00000375217.2_Silent_p.E1643E|UBR4_ENST00000375226.2_Silent_p.E1643E|UBR4_ENST00000375267.2_Silent_p.E1643E	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1643					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E1643E(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AATCTTCCTCTTCCACCGCCA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											132	122	126					1																	19488941		2203	4300	6503	19361528	SO:0001819	synonymous_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.4929A>G	1.37:g.19488941T>C			19361528	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.502	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19488941	T	C	19488941	2	2	34	1	0	0	0	0	0	0	0	1	16944	1606	56	4		4	UBR4	1	19488941	Silent	SNP	T	TCGA-AG-3612-01A-01W-0833-10		19488941	229761680	1	2799										
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85498583	85498583	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtccagtgttaagttcagttTattttctgctggtgtcccaa	9	8	2	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr1:85498583T>G	ENST00000370589.2	-	5	659	c.607A>C	c.(607-609)Aaa>Caa	p.K203Q	MCOLN3_ENST00000341115.4_Missense_Mutation_p.K147Q|MCOLN3_ENST00000370587.1_Missense_Mutation_p.K203Q|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	203					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K203Q(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		AAGTTCAGTTTATTTTCTGCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											261	252	255					1																	85498583		2203	4300	6503	85271171	SO:0001583	missense	55283			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.607A>C	1.37:g.85498583T>G	ENSP00000359621:p.Lys203Gln		85271171	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.608081	0.28623	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115;ENST00000370587	T;T;T	0.57273	0.41;0.41;0.41	5.53	5.53	0.82687	.	0.243503	0.40469	N	0.001096	T	0.20007	0.0481	L	0.29908	0.895	0.34095	D	0.661221	B;B;B;B	0.33694	0.295;0.141;0.365;0.421	B;B;B;B	0.31751	0.122;0.114;0.135;0.095	T	0.07558	-1.0766	10	0.12103	T	0.63	1.5112	11.4312	0.50041	0.135:0.0:0.0:0.865	.	203;203;147;203	A8K841;B1ANB7;Q8TDD5-2;Q8TDD5	.;.;.;MCLN3_HUMAN	Q	203;203;147;147;203	ENSP00000359621:K203Q;ENSP00000342698:K147Q;ENSP00000359619:K203Q	ENSP00000304843:K203Q	K	-	1	0	MCOLN3	85271171	0.436000	0.25586	0.993000	0.49108	0.968000	0.65278	1.926000	0.40084	2.096000	0.63516	0.528000	0.53228	AAA		0.408	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85498583	T	G	85498583	3	3	34	1	0	0	0	0	1	0	0	0	9427	1763	61	4	1090	4	MCOLN3	1	85498583	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	66009642	85498583	163752038	2	2800										
DPYD	1806	hgsc.bcm.edu	37	chr1	98187122	98187122	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gggtccctcttcagtggcatAtaaattgcatccacctacac	7	13	2	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr1:98187122A>C	ENST00000370192.3	-	5	527	c.427T>G	c.(427-429)Tat>Gat	p.Y143D	DPYD_ENST00000423006.2_Missense_Mutation_p.Y106D|DPYD_ENST00000306031.5_Missense_Mutation_p.Y143D|DPYD_ENST00000474241.1_5'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	143					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.Y143D(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TCAGTGGCATATAAATTGCAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	118	121					1																	98187122		2203	4299	6502	97959710	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.427T>G	1.37:g.98187122A>C	ENSP00000359211:p.Tyr143Asp		97959710	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.515664	0.44763	.	.	ENSG00000188641	ENST00000370192;ENST00000423006;ENST00000306031	T;T;T	0.80824	-1.42;-1.42;-1.42	5.88	3.59	0.41128	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.189289	0.47852	D	0.000205	T	0.68183	0.2973	M	0.70595	2.14	0.45962	D	0.998788	P;P	0.38922	0.651;0.599	B;B	0.39706	0.307;0.271	T	0.65615	-0.6125	10	0.36615	T	0.2	-2.7339	9.774	0.40607	0.8591:0.0:0.1409:0.0	.	143;143	E9PFN1;Q12882	.;DPYD_HUMAN	D	143;106;143	ENSP00000359211:Y143D;ENSP00000398884:Y106D;ENSP00000307107:Y143D	ENSP00000307107:Y143D	Y	-	1	0	DPYD	97959710	1.000000	0.71417	0.870000	0.34147	0.985000	0.73830	4.967000	0.63722	0.491000	0.27793	-0.280000	0.10049	TAT		0.428	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		C	98187122	A	C	98187122	3	2	34	1	0	0	0	0	1	0	0	0	4756	449	16	4	2769	4	DPYD	1	98187122	Missense_Mutation	SNP	A	TCGA-AG-3612-01A-01W-0833-10	12688539	98187122	151063499	3	2801										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182027037	182027037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ggcctccccaccatcttcatCgtcactctctaagttcatgc	5	17	5	0	rs144839806		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr1:182027037C>T	ENST00000339948.3	-	2	316	c.109G>A	c.(109-111)Gat>Aat	p.D37N		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	37					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D37N(1)		breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CCATCTTCATCGTCACTCTCT	0.577																																					NSCLC(71;908 1374 5429 20458 35642)											1	Substitution - Missense(1)	large_intestine(1)	1						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	97	91	93		109	2.8	0.2	1	dbSNP_134	93	0,8600		0,0,4300	no	missense	ZNF648	NM_001009992.1	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	37/569	182027037	1,13005	2203	4300	6503	180293660	SO:0001583	missense	127665			AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.109G>A	1.37:g.182027037C>T	ENSP00000344129:p.Asp37Asn		180293660	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.297595	0.40694	2.27E-4	0.0	ENSG00000179930	ENST00000339948	T	0.09073	3.02	2.76	2.76	0.32466	.	.	.	.	.	T	0.05686	0.0149	N	0.24115	0.695	0.20196	N	0.99993	P	0.35328	0.495	B	0.22601	0.04	T	0.30534	-0.9975	9	0.62326	D	0.03	.	11.7128	0.51635	0.0:1.0:0.0:0.0	.	37	Q5T619	ZN648_HUMAN	N	37	ENSP00000344129:D37N	ENSP00000344129:D37N	D	-	1	0	ZNF648	180293660	0.000000	0.05858	0.224000	0.23877	0.014000	0.08584	-0.425000	0.07017	1.864000	0.54056	0.655000	0.94253	GAT		0.577	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		T	182027037	C	T	182027037	3	4	34	1	0	0	0	0	1	0	0	0	18102	884	31	1	1601	1	ZNF648	1	182027037	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	83839915	182027037	67223584	4	2802										
OR2T10	127069	hgsc.bcm.edu	37	chr1	248756878	248756878	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aagtctatgagtgagagctgGtttataaagaagtacatggg	13	3	1	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr1:248756878G>T	ENST00000330500.2	-	1	222	c.192C>A	c.(190-192)aaC>aaA	p.N64K	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N64K(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGAGAGCTGGTTTATAAAGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	89	86					1																	248756878		2049	4236	6285	246823501	SO:0001583	missense	127069				CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"GPCR / Class A : Olfactory receptors"	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.192C>A	1.37:g.248756878G>T	ENSP00000329210:p.Asn64Lys		246823501	B2RNK7	Missense_Mutation	SNP	ENST00000330500.2	37	CCDS31121.1	.	.	.	.	.	.	.	.	.	.	.	8.329	0.825977	0.16749	.	.	ENSG00000184022	ENST00000330500	T	0.00388	7.59	2.34	-0.0309	0.13912	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00144	0.0004	N	0.02802	-0.49	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.37079	-0.9721	9	0.87932	D	0	.	2.2657	0.04078	0.3362:0.0:0.279:0.3848	.	64	Q8NGZ9	O2T10_HUMAN	K	64	ENSP00000329210:N64K	ENSP00000329210:N64K	N	-	3	2	OR2T10	246823501	0.000000	0.05858	0.267000	0.24556	0.909000	0.53808	-1.502000	0.02279	0.179000	0.19938	0.441000	0.28932	AAC		0.423	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097139.1	NM_001004693		T	248756878	G	T	248756878	3	4	34	1	0	0	0	0	1	0	0	0	11048	1252	44	2	749	2	OR2T10	1	248756878	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	66729841	248756878	493743	5	2803										
DYSF	8291	hgsc.bcm.edu	37	chr2	71896834	71896834	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tggaggttcattttccccttCgactacctgccagctgagca	9	13	1	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr2:71896834C>T	ENST00000258104.3	+	50	5902	c.5625C>T	c.(5623-5625)ttC>ttT	p.F1875F	DYSF_ENST00000429174.2_Silent_p.F1896F|DYSF_ENST00000409762.1_Silent_p.F1892F|DYSF_ENST00000410041.1_Silent_p.F1893F|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Silent_p.F1906F|DYSF_ENST00000409366.1_Silent_p.F1897F|DYSF_ENST00000409744.1_Silent_p.F1883F|DYSF_ENST00000394120.2_Silent_p.F1876F|DYSF_ENST00000409582.3_Silent_p.F1913F|DYSF_ENST00000409651.1_Silent_p.F1907F|DYSF_ENST00000410020.3_Silent_p.F1914F	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1875	C2 7. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.F1875F(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TTTTCCCCTTCGACTACCTGC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	2											190	155	167					2																	71896834		2203	4300	6503	71750342	SO:0001819	synonymous_variant	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5625C>T	2.37:g.71896834C>T			71750342	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																				0.502	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71896834	C	T	71896834	2	4	34	1	0	0	0	0	0	0	0	1	4870	883	31	1		1	DYSF	2	71896834	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10		71896834	171302539	6	2804										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179236884	179236884	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gaatgctgaactaaggagtcGgttgaacagaatacattcag	11	6	1	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr2:179236884G>T	ENST00000190611.4	+	14	1695	c.1319G>T	c.(1318-1320)cGg>cTg	p.R440L	OSBPL6_ENST00000357080.4_Intron|OSBPL6_ENST00000409045.3_Missense_Mutation_p.R409L|OSBPL6_ENST00000409631.1_Intron|OSBPL6_ENST00000315022.2_Missense_Mutation_p.R444L|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R465L|OSBPL6_ENST00000359685.3_Intron	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	440					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R440L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CTAAGGAGTCGGTTGAACAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	135	134					2																	179236884		2203	4300	6503	178945130	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1319G>T	2.37:g.179236884G>T	ENSP00000190611:p.Arg440Leu		178945130	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	35	5.525989	0.96431	.	.	ENSG00000079156	ENST00000392505;ENST00000409045;ENST00000190611;ENST00000315022	T;T;T;T	0.14640	2.5;2.55;2.52;2.49	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.32466	0.0830	L	0.61218	1.895	0.80722	D	1	P;D;D;P	0.61697	0.949;0.99;0.99;0.915	P;P;P;B	0.58660	0.66;0.843;0.843;0.35	T	0.00334	-1.1809	10	0.37606	T	0.19	-15.714	19.8529	0.96746	0.0:0.0:1.0:0.0	.	409;444;465;440	Q9BZF3-4;Q9BZF3-3;Q9BZF3-5;Q9BZF3	.;.;.;OSBL6_HUMAN	L	465;409;440;444	ENSP00000376293:R465L;ENSP00000387248:R409L;ENSP00000190611:R440L;ENSP00000318723:R444L	ENSP00000190611:R440L	R	+	2	0	OSBPL6	178945130	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	9.152000	0.94680	2.755000	0.94549	0.655000	0.94253	CGG		0.328	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		T	179236884	G	T	179236884	3	4	34	1	0	0	0	0	1	0	0	0	11312	1116	39	2	1487	2	OSBPL6	2	179236884	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	107340050	179236884	63962489	7	2805										
TFPI	7035	hgsc.bcm.edu	37	chr2	188343482	188343482	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aggcgttcagaaagacttggTaaatatgagccgcattcttc	10	8	2	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr2:188343482T>A	ENST00000233156.3	-	6	923				TFPI_ENST00000392365.1_Intron|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000339091.4_Missense_Mutation_p.Y226F|TFPI_ENST00000409676.1_Missense_Mutation_p.Y226F|AC007319.1_ENST00000453517.1_RNA	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)						blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y226F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	AAAGACTTGGTAAATATGAGC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											149	132	138					2																	188343482		2203	4300	6503	188051727	SO:0001627	intron_variant	7035				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.628+5368A>T	2.37:g.188343482T>A			188051727	O95103|Q53TS4	Missense_Mutation	SNP	ENST00000233156.3	37	CCDS2294.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892504	0.72524	.	.	ENSG00000003436	ENST00000409676;ENST00000339091	T;T	0.66638	-0.22;-0.22	4.72	0.975	0.19721	.	.	.	.	.	T	0.72946	0.3524	.	.	.	0.80722	D	1	D	0.61697	0.99	P	0.58266	0.836	T	0.69518	-0.5124	8	0.52906	T	0.07	.	8.1202	0.30967	0.0:0.3451:0.0:0.6549	.	226	P10646-2	.	F	226	ENSP00000386344:Y226F;ENSP00000342306:Y226F	ENSP00000342306:Y226F	Y	-	2	0	TFPI	188051727	1.000000	0.71417	0.994000	0.49952	0.943000	0.58893	0.422000	0.21296	-0.077000	0.12752	0.455000	0.32223	TAC		0.343	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		A	188343482	T	A	188343482	1	1	34	0	1	0	0	0	0	0	0	0	15847	1638	57	5		5	TFPI	2	188343482	Intron	SNP	T	TCGA-AG-3612-01A-01W-0833-10	9106598	188343482	54855891	8	2806										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209190426	209190426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	acatagcacaacagcttgccCggcgggtctcccttgtgctt	10	14	1	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr2:209190426C>T	ENST00000264380.4	+	20	3049	c.2891C>T	c.(2890-2892)cCg>cTg	p.P964L		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	964					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.P964L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACAGCTTGCCCGGCGGGTCTC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	65	65					2																	209190426		2203	4300	6503	208898671	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2891C>T	2.37:g.209190426C>T	ENSP00000264380:p.Pro964Leu		208898671	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	6.701	0.498060	0.12762	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.27890	1.64;1.81	6.07	4.22	0.49857	.	0.284775	0.28187	N	0.016268	T	0.23926	0.0579	L	0.56769	1.78	0.52099	D	0.999943	B;B	0.28880	0.226;0.031	B;B	0.17098	0.017;0.006	T	0.05533	-1.0879	10	0.21014	T	0.42	-1.1002	6.4434	0.21863	0.1432:0.6971:0.0:0.1596	.	964;908	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	L	964;540;908	ENSP00000264380:P964L;ENSP00000405736:P908L	ENSP00000264380:P964L	P	+	2	0	PIKFYVE	208898671	0.000000	0.05858	0.381000	0.26106	0.040000	0.13550	0.619000	0.24388	0.830000	0.34757	0.650000	0.86243	CCG		0.502	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209190426	C	T	209190426	3	4	34	1	0	0	0	0	1	0	0	0	11955	652	23	1	2976	1	PIKFYVE	2	209190426	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	20846944	209190426	34008947	9	2807										
MAP2	4133	hgsc.bcm.edu	37	chr2	210559149	210559149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ccttccagccaccacacctgCactggagaaagccccttgct	7	18	0	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr2:210559149C>T	ENST00000360351.4	+	7	2761	c.2255C>T	c.(2254-2256)gCa>gTa	p.A752V	MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.A748V|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	752					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.A752V(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	ACCACACCTGCACTGGAGAAA	0.468																																					Pancreas(27;423 979 28787 29963)											1	Substitution - Missense(1)	large_intestine(1)	2											70	70	70					2																	210559149		2203	4300	6503	210267394	SO:0001583	missense	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.2255C>T	2.37:g.210559149C>T	ENSP00000353508:p.Ala752Val		210267394	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842336	0.71488	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.25579	1.79;1.79	5.96	5.04	0.67666	MAP2/Tau projection (1);	0.000000	0.64402	D	0.000006	T	0.46425	0.1392	L	0.56769	1.78	0.51233	D	0.999917	D;D	0.69078	0.996;0.997	P;D	0.65323	0.892;0.934	T	0.39078	-0.9631	10	0.87932	D	0	-20.4248	16.6757	0.85278	0.0:0.8706:0.1294:0.0	.	748;752	P11137-3;P11137	.;MAP2_HUMAN	V	752;748	ENSP00000353508:A752V;ENSP00000392164:A748V	ENSP00000353508:A752V	A	+	2	0	MAP2	210267394	0.997000	0.39634	0.889000	0.34880	0.703000	0.40648	3.582000	0.53921	2.833000	0.97629	0.650000	0.86243	GCA		0.468	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210559149	C	T	210559149	3	4	34	1	0	0	0	0	1	0	0	0	9265	710	25	3	2269	3	MAP2	2	210559149	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	1368723	210559149	32640224	10	2808										
BOC	91653	hgsc.bcm.edu	37	chr3	112991422	112991422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	caccggctacaacaagacgcGcttcctgctgagcaacctcc	8	17	0	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr3:112991422G>A	ENST00000495514.1	+	7	1537	c.833G>A	c.(832-834)cGc>cAc	p.R278H	BOC_ENST00000273395.4_Missense_Mutation_p.R278H|BOC_ENST00000355385.3_Missense_Mutation_p.R278H			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	278	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.R278H(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			AACAAGACGCGCTTCCTGCTG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	3											133	127	129					3																	112991422		2203	4300	6503	114474112	SO:0001583	missense	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.833G>A	3.37:g.112991422G>A	ENSP00000418663:p.Arg278His		114474112	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594470	0.66219	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.68479	-0.33;-0.33;-0.33	5.92	5.92	0.95590	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.104866	0.64402	D	0.000003	T	0.61236	0.2331	L	0.42632	1.34	0.54753	D	0.99998	P;P	0.37083	0.525;0.581	B;B	0.36845	0.098;0.234	T	0.56208	-0.8017	10	0.15066	T	0.55	.	20.3213	0.98679	0.0:0.0:1.0:0.0	.	278;278	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	H	278	ENSP00000418663:R278H;ENSP00000273395:R278H;ENSP00000347546:R278H	ENSP00000273395:R278H	R	+	2	0	BOC	114474112	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.170000	0.71920	2.810000	0.96702	0.650000	0.86243	CGC		0.642	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		A	112991422	G	A	112991422	3	1	34	1	0	0	0	0	1	0	0	0	1482	1087	38	1	851	1	BOC	3	112991422	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10		112991422	85031008	11	2809										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098766	133098766	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tgatgctgacccccaatcccGatggacccccctcacaggct	8	18	1	2	rs372281436		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr3:133098766G>T	ENST00000321871.6	+	4	421	c.211G>T	c.(211-213)Gat>Tat	p.D71Y	TMEM108_ENST00000393130.3_Missense_Mutation_p.D71Y|TMEM108_ENST00000515826.1_Missense_Mutation_p.D71Y|TMEM108_ENST00000508711.1_Intron	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	71	Pro-rich.					integral component of membrane (GO:0016021)		p.D71Y(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CCCCAATCCCGATGGACCCCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	97	98					3																	133098766		2203	4300	6503	134581456	SO:0001583	missense	66000			AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.211G>T	3.37:g.133098766G>T	ENSP00000324651:p.Asp71Tyr		134581456	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	g	1.725	-0.495606	0.04291	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000514894;ENST00000512662;ENST00000512137;ENST00000511555;ENST00000515826;ENST00000510183	T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	3.8	1.88	0.25563	.	0.189876	0.25771	N	0.028407	T	0.48822	0.1521	L	0.51422	1.61	0.09310	N	1	P;D	0.55172	0.57;0.97	B;P	0.54664	0.364;0.758	T	0.36114	-0.9761	10	0.62326	D	0.03	-0.9379	5.5797	0.17243	0.2822:0.0:0.7178:0.0	.	71;71	E9PB58;Q6UXF1	.;TM108_HUMAN	Y	71;71;22;22;71;71;71;71	ENSP00000324651:D71Y;ENSP00000376838:D71Y;ENSP00000422072:D22Y;ENSP00000427447:D22Y;ENSP00000426301:D71Y;ENSP00000422196:D71Y;ENSP00000423338:D71Y;ENSP00000421486:D71Y	ENSP00000324651:D71Y	D	+	1	0	TMEM108	134581456	0.000000	0.05858	0.014000	0.15608	0.035000	0.12851	-0.258000	0.08733	0.342000	0.23796	-0.261000	0.10672	GAT		0.622	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133098766	G	T	133098766	3	4	34	1	0	0	0	0	1	0	0	0	16063	1058	37	2	217	2	TMEM108	3	133098766	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	20107344	133098766	64923664	12	2810										
TTC14	151613	hgsc.bcm.edu	37	chr3	180322377	180322377	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aggtgtaattagctctgaagAgcttcctttatactacaggt	9	7	1	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr3:180322377A>T	ENST00000296015.4	+	5	815	c.683A>T	c.(682-684)gAg>gTg	p.E228V	RP11-496B10.3_ENST00000472596.1_lincRNA|TTC14_ENST00000382584.4_Missense_Mutation_p.E228V|TTC14_ENST00000412756.2_Missense_Mutation_p.E228V	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	228							RNA binding (GO:0003723)	p.E228V(1)		endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			AGCTCTGAAGAGCTTCCTTTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											58	58	58					3																	180322377		2203	4295	6498	181805071	SO:0001583	missense	151613			AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.683A>T	3.37:g.180322377A>T	ENSP00000296015:p.Glu228Val		181805071	G5E9X0|Q6UWJ7|Q8TF22	Missense_Mutation	SNP	ENST00000296015.4	37	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.936033	0.92458	.	.	ENSG00000163728	ENST00000296015;ENST00000412756;ENST00000382584;ENST00000492617;ENST00000495660	T;T	0.51325	0.73;0.71	5.71	5.71	0.89125	.	0.094536	0.64402	D	0.000001	T	0.52125	0.1715	L	0.27053	0.805	0.80722	D	1	D;P;P	0.67145	0.996;0.95;0.938	P;P;P	0.57548	0.823;0.719;0.502	T	0.57004	-0.7885	10	0.87932	D	0	-18.1689	15.9836	0.80130	1.0:0.0:0.0:0.0	.	228;228;228	Q96N46-2;G5E9X0;Q96N46	.;.;TTC14_HUMAN	V	228;228;228;128;128	ENSP00000296015:E228V;ENSP00000372027:E228V	ENSP00000296015:E228V	E	+	2	0	TTC14	181805071	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.108000	0.94275	2.185000	0.69588	0.528000	0.53228	GAG		0.343	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		T	180322377	A	T	180322377	3	4	34	1	0	0	0	0	1	0	0	0	16721	304	11	5	701	5	TTC14	3	180322377	Missense_Mutation	SNP	A	TCGA-AG-3612-01A-01W-0833-10	47223611	180322377	17700053	13	2811										
CPZ	8532	hgsc.bcm.edu	37	chr4	8608503	8608503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ggacgagcgggaggcagaacGcgcagaacctggatctgaac	16	10	1	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr4:8608503G>A	ENST00000360986.4	+	6	1120	c.946G>A	c.(946-948)Gcg>Acg	p.A316T	CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000382480.2_Missense_Mutation_p.A179T|CPZ_ENST00000315782.6_Missense_Mutation_p.A305T	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	316					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.A316T(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GAGGCAGAACGCGCAGAACCT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	4											70	69	69					4																	8608503		2203	4300	6503	8659403	SO:0001583	missense	8532			U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.946G>A	4.37:g.8608503G>A	ENSP00000354255:p.Ala316Thr		8659403	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	g	17.95	3.513537	0.64522	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	T;T;T	0.03889	3.77;3.77;3.77	3.31	2.33	0.28932	Peptidase M14, carboxypeptidase A (2);	0.202783	0.41605	U	0.000853	T	0.12178	0.0296	M	0.87038	2.855	0.80722	D	1	D;P	0.59767	0.986;0.868	P;B	0.47102	0.537;0.319	T	0.10965	-1.0607	10	0.52906	T	0.07	-20.6085	11.0173	0.47696	0.0:0.0:0.8005:0.1995	.	305;316	Q66K79-2;Q66K79	.;CBPZ_HUMAN	T	316;179;305	ENSP00000354255:A316T;ENSP00000371920:A179T;ENSP00000315074:A305T	ENSP00000315074:A305T	A	+	1	0	CPZ	8659403	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.549000	0.67261	1.672000	0.50884	0.450000	0.29827	GCG		0.657	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8608503	G	A	8608503	3	1	34	1	0	0	0	0	1	0	0	0	3845	1087	38	1	968	1	CPZ	4	8608503	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10		8608503	182545773	14	2812										
STIM2	57620	hgsc.bcm.edu	37	chr4	27019361	27019361	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gctaaacctcctggatcattAgccagaagcagcagcctgtg	10	12	1	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr4:27019361A>C	ENST00000467011.1	+	11	1943	c.1518A>C	c.(1516-1518)ttA>ttC	p.L506F	STIM2_ENST00000467087.1_Missense_Mutation_p.L506F|STIM2_ENST00000237364.5_Missense_Mutation_p.L593F|STIM2_ENST00000412829.2_Missense_Mutation_p.L593F|STIM2_ENST00000382009.3_Missense_Mutation_p.L601F|STIM2_ENST00000465503.1_Missense_Mutation_p.L514F	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	506					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)	p.L593F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				CTGGATCATTAGCCAGAAGCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	4											149	147	148					4																	27019361		2203	4300	6503	26628459	SO:0001583	missense	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.1518A>C	4.37:g.27019361A>C	ENSP00000419383:p.Leu506Phe		26628459	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314109	0.60414	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503;ENST00000473519;ENST00000477474	T;T;T;T;T;T;D;D	0.83075	-1.26;-1.28;-1.29;-1.27;-1.31;-1.24;-1.68;-1.68	5.68	2.02	0.26589	.	0.084168	0.50627	D	0.000116	D	0.85173	0.5636	L	0.55990	1.75	0.49687	D	0.999815	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.85130	0.994;0.994;0.994;0.997	T	0.79983	-0.1573	10	0.37606	T	0.19	.	4.7338	0.12977	0.5322:0.0:0.3309:0.137	.	506;593;601;593	Q9P246;A6H8L7;E9PGD0;F5GXJ4	STIM2_HUMAN;.;.;.	F	506;601;593;506;593;514;214;108	ENSP00000419073:L506F;ENSP00000371439:L601F;ENSP00000237364:L593F;ENSP00000419383:L506F;ENSP00000404812:L593F;ENSP00000417569:L514F;ENSP00000420113:L214F;ENSP00000419536:L108F	ENSP00000237364:L593F	L	+	3	2	STIM2	26628459	1.000000	0.71417	0.815000	0.32552	0.712000	0.41017	1.343000	0.33930	0.123000	0.18342	0.528000	0.53228	TTA		0.552	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		C	27019361	A	C	27019361	3	2	34	1	0	0	0	0	1	0	0	0	15323	417	15	4	1588	4	STIM2	4	27019361	Missense_Mutation	SNP	A	TCGA-AG-3612-01A-01W-0833-10	18410858	27019361	164134915	15	2813										
HTN3	3347	hgsc.bcm.edu	37	chr4	70896510	70896510	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tctcatgctttccatgactgTaagtatatctggaagtttta	7	7	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr4:70896510T>A	ENST00000530128.1	+	2	126		c.e2+2		HTN3_ENST00000526767.1_Splice_Site|HTN3_ENST00000381057.3_Splice_Site			P15516	HIS3_HUMAN	histatin 3						biomineral tissue development (GO:0031214)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.?(1)		breast(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	8						TCCATGACTGTAAGTATATCT	0.333																																																1	Unknown(1)	large_intestine(1)	4											112	109	110					4																	70896510		2203	4298	6501	70931099	SO:0001630	splice_region_variant	3347				CCDS33999.1	4q13	2008-08-29							5284	protein-coding gene	gene with protein product		142702					Standard	NM_000200		Approved	HIS2	uc003hew.2	P15516		ENST00000530128.1:c.51+2T>A	4.37:g.70896510T>A			70931099	Q16243|Q502Z1	Splice_Site	SNP	ENST00000530128.1	37	CCDS33999.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.095107	0.36952	.	.	ENSG00000205649	ENST00000526767;ENST00000530128;ENST00000381057	.	.	.	2.62	2.62	0.31277	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.1135	0.25403	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HTN3	70931099	1.000000	0.71417	0.998000	0.56505	0.280000	0.26924	2.719000	0.47244	1.459000	0.47892	0.413000	0.27773	.		0.333	HTN3-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387375.1	NM_000200	Intron	A	70896510	T	A	70896510	5	1	34	1	0	0	0	0	0	0	1	0	7456	1652	57	5	55	5	HTN3	4	70896510	Splice_Site	SNP	T	TCGA-AG-3612-01A-01W-0833-10	43877149	70896510	120257766	16	2814										
TRIML2	205860	hgsc.bcm.edu	37	chr4	189012815	189012815	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tcggtccccatcaccgacccCgtgagcaagactttctctcc	7	18	2	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr4:189012815C>T	ENST00000512729.1	-	7	1250	c.876G>A	c.(874-876)acG>acA	p.T292T	TRIML2_ENST00000326754.3_Silent_p.T317T	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	292	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.T292T(1)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		TCACCGACCCCGTGAGCAAGA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	4											142	152	149					4																	189012815		2203	4300	6503	189249809	SO:0001819	synonymous_variant	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.876G>A	4.37:g.189012815C>T			189249809	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																				0.572	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		T	189012815	C	T	189012815	2	4	34	1	0	0	0	0	0	0	0	1	16591	639	23	1		1	TRIML2	4	189012815	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	118116305	189012815	2141461	17	2815										
LIFR	3977	hgsc.bcm.edu	37	chr5	38486060	38486060	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tgggatatgtcagtaatattCttaacttttatgtcagaacg	8	5	3	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr5:38486060C>G	ENST00000263409.4	-	17	2520	c.2358G>C	c.(2356-2358)aaG>aaC	p.K786N	LIFR_ENST00000453190.2_Missense_Mutation_p.K786N	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	786	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.K786N(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					CAGTAATATTCTTAACTTTTA	0.398			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	1	Substitution - Missense(1)	large_intestine(1)	5											88	83	85					5																	38486060		2203	4300	6503	38521817	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2358G>C	5.37:g.38486060C>G	ENSP00000263409:p.Lys786Asn		38521817	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457793	0.43634	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.58358	0.34;0.34	5.43	4.56	0.56223	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.44350	0.1289	M	0.73962	2.25	0.37877	D	0.93025	P	0.42409	0.779	B	0.35182	0.197	T	0.48479	-0.9032	10	0.23891	T	0.37	-21.3193	5.729	0.18028	0.1407:0.6467:0.1363:0.0764	.	786	P42702	LIFR_HUMAN	N	786	ENSP00000263409:K786N;ENSP00000398368:K786N	ENSP00000263409:K786N	K	-	3	2	LIFR	38521817	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.244000	0.32778	1.280000	0.44463	0.563000	0.77884	AAG		0.398	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		G	38486060	C	G	38486060	3	3	34	1	0	0	0	0	1	0	0	0	8803	912	32	5	951	5	LIFR	5	38486060	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		38486060	142429200	18	2816										
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79855019	79855019	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tttataggatagttcttcctCtggtgtaatatcctggagct	9	7	2	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr5:79855019C>G	ENST00000338682.3	-	5	1492	c.820G>C	c.(820-822)Gag>Cag	p.E274Q		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	274						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E274Q(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		AGTTCTTCCTCTGGTGTAATA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											60	64	62					5																	79855019		2203	4300	6503	79890775	SO:0001583	missense	340120				CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"Ankyrin repeat domain containing"	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.820G>C	5.37:g.79855019C>G	ENSP00000339802:p.Glu274Gln		79890775	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236898	0.79800	.	.	ENSG00000189127	ENST00000338682	T	0.22539	1.95	5.96	5.96	0.96718	.	0.181275	0.34291	N	0.004083	T	0.35885	0.0947	M	0.66939	2.045	0.40692	D	0.9824	D	0.60575	0.988	P	0.53313	0.723	T	0.08659	-1.0711	10	0.62326	D	0.03	-25.3487	13.2531	0.60062	0.0:0.924:0.0:0.076	.	274	A5PLL1	AN34B_HUMAN	Q	274	ENSP00000339802:E274Q	ENSP00000339802:E274Q	E	-	1	0	ANKRD34B	79890775	0.991000	0.36638	0.997000	0.53966	0.991000	0.79684	3.239000	0.51360	2.832000	0.97577	0.655000	0.94253	GAG		0.483	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		G	79855019	C	G	79855019	3	3	34	1	0	0	0	0	1	0	0	0	663	922	32	5	728	5	ANKRD34B	5	79855019	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	41368959	79855019	101060241	19	2817										
APC	324	hgsc.bcm.edu	37	chr5	112175507	112175507	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gttcgattgccagctccgttCagagtgaaccatgcagtgga	12	10	1	2	rs587782518		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr5:112175507C>T	ENST00000457016.1	+	16	4596	c.4216C>T	c.(4216-4218)Cag>Tag	p.Q1406*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1406*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1406*			P25054	APC_HUMAN	adenomatous polyposis coli	1406	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1406*(15)|p.Q1406fs*11(1)|p.?(1)|p.K1192fs*3(1)|p.I1401fs*2(1)|p.Y1376fs*41(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCTCCGTTCAGAGTGAACC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(15)|Deletion - Frameshift(3)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(18)|soft_tissue(1)|skin(1)	5	GRCh37	CI084250|CM023011	APC	I|M							113	105	108					5																	112175507		2202	4300	6502	112203406	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4216C>T	5.37:g.112175507C>T	ENSP00000413133:p.Gln1406*		112203406	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.658788	0.98903	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.187376	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.0613	15.6825	0.77381	0.0:0.8637:0.1363:0.0	.	.	.	.	X	1406	.	.	Q	+	1	0	APC	112203406	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.175000	0.77632	1.615000	0.50252	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175507	C	T	112175507	4	4	34	1	0	0	0	0	0	1	0	0	763	827	29	3	4274	3	APC	5	112175507	Nonsense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	32320488	112175507	68739753	20	2818										
FAT2	2196	hgsc.bcm.edu	37	chr5	150930323	150930323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cttgatctatggcctggactCgcaggagctctacccctggc	11	14	2	1	rs200746707		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr5:150930323C>T	ENST00000261800.5	-	7	4418	c.4406G>A	c.(4405-4407)cGa>cAa	p.R1469Q		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1469	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1469Q(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCCTGGACTCGCAGGAGCTC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG	0,4406		0,0,2203	103	85	91		4406	0.1	0.1	5		91	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FAT2	NM_001447.2	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1469/4350	150930323	2,13004	2203	4300	6503	150910516	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.4406G>A	5.37:g.150930323C>T	ENSP00000261800:p.Arg1469Gln		150910516	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	2.128	-0.399693	0.04865	0.0	2.33E-4	ENSG00000086570	ENST00000261800	T	0.52526	0.66	5.0	0.112	0.14623	Cadherin (3);Cadherin-like (1);	0.426434	0.19824	N	0.105241	T	0.18509	0.0444	N	0.03917	-0.325	0.32026	N	0.600197	B	0.16802	0.019	B	0.17098	0.017	T	0.41142	-0.9525	10	0.02654	T	1	.	10.5163	0.44892	0.0:0.5245:0.0:0.4755	.	1469	Q9NYQ8	FAT2_HUMAN	Q	1469	ENSP00000261800:R1469Q	ENSP00000261800:R1469Q	R	-	2	0	FAT2	150910516	0.045000	0.20229	0.132000	0.22025	0.678000	0.39670	0.126000	0.15769	-0.315000	0.08703	0.655000	0.94253	CGA		0.537	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150930323	C	T	150930323	3	4	34	1	0	0	0	0	1	0	0	0	5709	884	31	1	8711	1	FAT2	5	150930323	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	38754816	150930323	29984937	21	2819										
ADAM19	8728	hgsc.bcm.edu	37	chr5	156918659	156918659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cccactgtcgatactgccccCgtggcccggtgtgttgcaga	12	15	0	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr5:156918659C>T	ENST00000517905.1	-	18	2103	c.2059G>A	c.(2059-2061)Ggg>Agg	p.G687R	ADAM19_ENST00000257527.4_Missense_Mutation_p.G687R|ADAM19_ENST00000430702.2_Missense_Mutation_p.G420R|ADAM19_ENST00000394020.1_Missense_Mutation_p.G689R			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	687					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G688R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	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)			ATACTGCCCCCGTGGCCCGGT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5											21	22	22					5																	156918659		2202	4299	6501	156851237	SO:0001583	missense	8728			AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"ADAM metallopeptidase domain containing"	197	protein-coding gene	gene with protein product	"meltrin beta"	603640	"a disintegrin and metalloproteinase domain 19 (meltrin beta)"			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.2059G>A	5.37:g.156918659C>T	ENSP00000428654:p.Gly687Arg		156851237	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.629763	0.87660	.	.	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	D;D;D;D	0.99051	-5.37;-5.37;-5.37;-5.37	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000010	D	0.99530	0.9832	H	0.95079	3.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.98029	1.0375	10	0.87932	D	0	.	18.1389	0.89631	0.0:1.0:0.0:0.0	.	687;687;420	Q9H013-2;Q9H013;E9PD32	.;ADA19_HUMAN;.	R	420;687;689;687	ENSP00000414088:G420R;ENSP00000257527:G687R;ENSP00000377588:G689R;ENSP00000428654:G687R	ENSP00000257527:G687R	G	-	1	0	ADAM19	156851237	1.000000	0.71417	0.892000	0.35008	0.565000	0.35776	7.818000	0.86416	2.286000	0.76751	0.563000	0.77884	GGG		0.637	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		T	156918659	C	T	156918659	3	4	34	1	0	0	0	0	1	0	0	0	240	652	23	1	721	1	ADAM19	5	156918659	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	5988336	156918659	23996601	22	2820										
SLC17A4	10050	hgsc.bcm.edu	37	chr6	25777143	25777143	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tcttctgccatcagcagcttCtgtgaatcaggagcccttgt	9	12	5	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr6:25777143C>A	ENST00000377905.4	+	10	1343	c.1224C>A	c.(1222-1224)ttC>ttA	p.F408L	SLC17A4_ENST00000397076.2_Missense_Mutation_p.F206L|SLC17A4_ENST00000439485.2_Missense_Mutation_p.F178L	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	408					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)	p.F408L(1)		breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TCAGCAGCTTCTGTGAATCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											134	119	124					6																	25777143		2203	4300	6503	25885122	SO:0001583	missense	10050			AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"Solute carriers"	10932	protein-coding gene	gene with protein product		604216	"solute carrier family 17 (sodium phosphate), member 4"			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1224C>A	6.37:g.25777143C>A	ENSP00000367137:p.Phe408Leu		25885122	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.238262	0.22711	.	.	ENSG00000146039	ENST00000377905;ENST00000439485;ENST00000397076	T;T;T	0.69040	0.39;0.53;-0.37	5.62	3.71	0.42584	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.121880	0.06752	N	0.780235	T	0.27169	0.0666	L	0.33189	0.99	0.18873	N	0.999987	B;B;B	0.15473	0.0;0.013;0.0	B;B;B	0.19391	0.001;0.025;0.006	T	0.36890	-0.9729	10	0.02654	T	1	.	6.7938	0.23715	0.0:0.6783:0.2254:0.0963	.	178;206;408	E7EPE8;E7EU17;Q9Y2C5	.;.;S17A4_HUMAN	L	408;178;206	ENSP00000367137:F408L;ENSP00000391345:F178L;ENSP00000380266:F206L	ENSP00000367137:F408L	F	+	3	2	SLC17A4	25885122	0.622000	0.27085	0.066000	0.19879	0.895000	0.52256	1.509000	0.35780	1.516000	0.48900	0.650000	0.86243	TTC		0.517	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1			A	25777143	C	A	25777143	3	1	34	1	0	0	0	0	1	0	0	0	14456	912	32	2	1258	2	SLC17A4	6	25777143	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		25777143	145337924	23	2821										
BAI3	577	hgsc.bcm.edu	37	chr6	69666543	69666543	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aacatttctttcagccaatgGtcaatggaatcagtggggtc	10	8	4	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr6:69666543G>A	ENST00000370598.1	+	8	2188	c.1367G>A	c.(1366-1368)gGt>gAt	p.G456D		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	456	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G456D(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TCAGCCAATGGTCAATGGAAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											160	161	160					6																	69666543		2203	4300	6503	69723264	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1367G>A	6.37:g.69666543G>A	ENSP00000359630:p.Gly456Asp		69723264	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.931796	0.92389	.	.	ENSG00000135298	ENST00000370598	T	0.62364	0.03	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.82139	0.4972	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.85554	0.1223	10	0.87932	D	0	.	19.6195	0.95650	0.0:0.0:1.0:0.0	.	456	O60242	BAI3_HUMAN	D	456	ENSP00000359630:G456D	ENSP00000359630:G456D	G	+	2	0	BAI3	69723264	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.420000	0.97426	2.710000	0.92621	0.650000	0.86243	GGT		0.438	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69666543	G	A	69666543	3	1	34	1	0	0	0	0	1	0	0	0	1301	1261	44	3	1389	3	BAI3	6	69666543	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	43889400	69666543	101448524	24	2822										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101110342	101110342	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aatttctgtcctgccgaagcAttcctgcatgatgaatacta	7	10	1	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr6:101110342A>T	ENST00000369162.2	-	15	2701	c.2357T>A	c.(2356-2358)aTg>aAg	p.M786K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	786	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.M786K(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CTGCCGAAGCATTCCTGCATG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											90	89	89					6																	101110342		2203	4299	6502	101217063	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2357T>A	6.37:g.101110342A>T	ENSP00000358159:p.Met786Lys		101217063	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495279	0.85069	.	.	ENSG00000112249	ENST00000369162	T	0.76968	-1.06	5.52	5.52	0.82312	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.90868	0.7131	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93702	0.7016	10	0.87932	D	0	.	15.9507	0.79835	1.0:0.0:0.0:0.0	.	786	Q8N3C0	HELC1_HUMAN	K	786	ENSP00000358159:M786K	ENSP00000358159:M786K	M	-	2	0	ASCC3	101217063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.203000	0.95033	2.232000	0.73038	0.528000	0.53228	ATG		0.398	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101110342	A	T	101110342	3	4	34	1	0	0	0	0	1	0	0	0	1034	217	8	5	4363	5	ASCC3	6	101110342	Missense_Mutation	SNP	A	TCGA-AG-3612-01A-01W-0833-10	31443799	101110342	70004725	25	2823										
AIM1	202	hgsc.bcm.edu	37	chr6	106968273	106968273	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ccaccaactctcccagcagcGgaaatcacttagccactcct	5	18	2	0	rs201201445	byFrequency	TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr6:106968273G>A	ENST00000369066.3	+	2	2453	c.1966G>A	c.(1966-1968)Gga>Aga	p.G656R		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.G656R(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TCCCAGCAGCGGAAATCACTT	0.517													G|||	2	0.000399361	0	0	5008	,	,		19198	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	6											51	49	50					6																	106968273		2203	4300	6503	107074966	SO:0001583	missense	202			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1966G>A	6.37:g.106968273G>A	ENSP00000358062:p.Gly656Arg		107074966	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.258	-1.001738	0.02128	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.68765	-0.35	5.45	-0.999	0.10208	.	1.007710	0.07983	N	0.985969	T	0.13072	0.0317	N	0.02916	-0.46	0.09310	N	0.999996	B	0.09022	0.002	B	0.04013	0.001	T	0.18366	-1.0339	10	0.10902	T	0.67	.	4.9282	0.13903	0.4548:0.1703:0.3749:0.0	.	656	Q9Y4K1	AIM1_HUMAN	R	1064;656	ENSP00000358062:G656R	ENSP00000285105:G1064R	G	+	1	0	AIM1	107074966	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.077000	0.11394	-0.167000	0.10871	-0.793000	0.03317	GGA		0.517	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106968273	G	A	106968273	3	1	34	1	0	0	0	0	1	0	0	0	430	1117	39	1	1972	1	AIM1	6	106968273	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	5857931	106968273	64146794	26	2824										
ROS1	6098	hgsc.bcm.edu	37	chr6	117715385	117715385	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tctatggagatagaagaaatTaatcctgaacctctgtaaaa	7	6	2	4			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr6:117715385T>A	ENST00000368508.3	-	10	1302	c.1104A>T	c.(1102-1104)ttA>ttT	p.L368F	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.L377F	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	368					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L368F(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TAGAAGAAATTAATCCTGAAC	0.368			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - Missense(2)	large_intestine(2)	6											52	55	54					6																	117715385		2202	4300	6502	117822078	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1104A>T	6.37:g.117715385T>A	ENSP00000357494:p.Leu368Phe		117822078	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.322541	0.23994	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91124	-2.79;-2.79	5.12	-1.31	0.09230	.	0.898111	0.09327	N	0.817477	T	0.70771	0.3262	L	0.44542	1.39	0.23685	N	0.997115	B	0.12013	0.005	B	0.10450	0.005	T	0.58880	-0.7558	10	0.56958	D	0.05	.	0.8758	0.01223	0.2163:0.308:0.2392:0.2365	.	368	P08922	ROS1_HUMAN	F	368;377	ENSP00000357494:L368F;ENSP00000357493:L377F	ENSP00000357493:L377F	L	-	3	2	ROS1	117822078	0.097000	0.21791	0.920000	0.36463	0.949000	0.60115	-0.114000	0.10757	-0.089000	0.12484	0.528000	0.53228	TTA		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117715385	T	A	117715385	3	1	34	1	0	0	0	0	1	0	0	0	13568	1751	61	5	6075	5	ROS1	6	117715385	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	10747112	117715385	53399682	27	2825										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31890286	31890286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtggaaattgttggtggttcCggtatgctcgtagtcatgga	15	5	1	0	rs559775895		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr7:31890286C>T	ENST00000396191.1	-	8	1275	c.820G>A	c.(820-822)Gga>Aga	p.G274R	PDE1C_ENST00000396182.2_Missense_Mutation_p.G274R|PDE1C_ENST00000396184.3_Missense_Mutation_p.G274R|PDE1C_ENST00000321453.7_Missense_Mutation_p.G274R|PDE1C_ENST00000396193.1_Missense_Mutation_p.G334R	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	274	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.G274R(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TTGGTGGTTCCGGTATGCTCG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	7											204	181	189					7																	31890286		2203	4300	6503	31856811	SO:0001583	missense	5137			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.820G>A	7.37:g.31890286C>T	ENSP00000379494:p.Gly274Arg		31856811	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	c	35	5.545009	0.96488	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	D;D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42;-4.42	5.91	5.91	0.95273	Metal-dependent phosphohydrolase, HD domain (1);-cyclic nucleotide phosphodiesterase, conserved site (1);5&apos (3);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (3);	0.000000	0.85682	D	0.000000	D	0.99199	0.9722	H	0.97918	4.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98847	1.0757	10	0.87932	D	0	.	19.9008	0.96985	0.0:1.0:0.0:0.0	.	274;334;274	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	R	334;274;274;274;274	ENSP00000379496:G334R;ENSP00000379494:G274R;ENSP00000318105:G274R;ENSP00000379487:G274R;ENSP00000379485:G274R	ENSP00000318105:G274R	G	-	1	0	PDE1C	31856811	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.818000	0.86416	2.805000	0.96524	0.651000	0.88453	GGA		0.448	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			T	31890286	C	T	31890286	3	4	34	1	0	0	0	0	1	0	0	0	11666	661	23	1	1124	1	PDE1C	7	31890286	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		31890286	127248377	28	2826										
AKR1D1	6718	hgsc.bcm.edu	37	chr7	137792252	137792252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cagcagctcaaattgttttgCgtttcaacatccagcgaggg	10	10	2	0	rs267606650		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr7:137792252C>T	ENST00000242375.3	+	7	823	c.781C>T	c.(781-783)Cgt>Tgt	p.R261C	AKR1D1_ENST00000468877.2_3'UTR|AKR1D1_ENST00000432161.1_Missense_Mutation_p.R261C|AKR1D1_ENST00000411726.2_Missense_Mutation_p.R220C	NM_005989.3	NP_005980.1	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	261			R -> C (in CBAS2). {ECO:0000269|PubMed:15030995}.		androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|C21-steroid hormone metabolic process (GO:0008207)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|steroid binding (GO:0005496)	p.R261C(2)		endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	23					Azelaic Acid(DB00548)|Finasteride(DB01216)	AATTGTTTTGCGTTTCAACAT	0.373																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7	GRCh37	CM044568	AKR1D1	M							146	136	140					7																	137792252		2203	4300	6503	137442792	SO:0001583	missense	6718			Z28339	CCDS5846.1, CCDS55169.1, CCDS55170.1	7q32-q33	2012-12-04	2012-12-04		ENSG00000122787	ENSG00000122787	1.3.99.6	"Aldo-keto reductases"	388	protein-coding gene	gene with protein product	"delta 4-3-ketosteroid-5-beta-reductase"	604741	"aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)"	SRD5B1		7508385, 10343119	Standard	NM_005989		Approved		uc003vtz.3	P51857	OTTHUMG00000155787	ENST00000242375.3:c.781C>T	7.37:g.137792252C>T	ENSP00000242375:p.Arg261Cys		137442792	A1L4P6|A8K060|B4DPN3|B4DPN8	Missense_Mutation	SNP	ENST00000242375.3	37	CCDS5846.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103412	0.76983	.	.	ENSG00000122787	ENST00000432161;ENST00000411726;ENST00000242375	T;T;T	0.29142	1.58;1.58;1.58	5.55	5.55	0.83447	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.68495	0.3007	H	0.95645	3.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.984	T	0.77624	-0.2518	10	0.87932	D	0	.	17.0553	0.86532	0.0:1.0:0.0:0.0	.	220;261;261	B4DPN8;B4DPN3;P51857	.;.;AK1D1_HUMAN	C	261;220;261	ENSP00000389197:R261C;ENSP00000402374:R220C;ENSP00000242375:R261C	ENSP00000242375:R261C	R	+	1	0	AKR1D1	137442792	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.151000	0.58105	2.894000	0.99253	0.591000	0.81541	CGT		0.373	AKR1D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341637.1	NM_005989		T	137792252	C	T	137792252	3	4	34	1	0	0	0	0	1	0	0	0	473	768	27	1	807	1	AKR1D1	7	137792252	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	105901966	137792252	21346411	29	2827										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142627221	142627221	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cctccatcagcaccaaggccGcctccaagttgtcatagagg	9	15	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr7:142627221G>T	ENST00000265310.1	-	3	629	c.281C>A	c.(280-282)gCg>gAg	p.A94E	TRPV5_ENST00000442623.1_Missense_Mutation_p.A94E	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	94					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.A94E(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CACCAAGGCCGCCTCCAAGTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	7											73	73	73					7																	142627221		2203	4300	6503	142337343	SO:0001583	missense	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.281C>A	7.37:g.142627221G>T	ENSP00000265310:p.Ala94Glu		142337343	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748289	0.69533	.	.	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	T;T;T	0.66995	0.57;-0.24;-0.2	4.3	3.42	0.39159	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.80265	0.4591	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.81914	0.987;0.995	T	0.81439	-0.0932	10	0.54805	T	0.06	-16.145	11.4912	0.50381	0.0895:0.0:0.9105:0.0	.	94;94	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	E	94;88;94	ENSP00000265310:A94E;ENSP00000406361:A88E;ENSP00000406572:A94E	ENSP00000265310:A94E	A	-	2	0	TRPV5	142337343	1.000000	0.71417	0.700000	0.30305	0.818000	0.46254	4.257000	0.58816	1.167000	0.42706	-0.657000	0.03884	GCG		0.547	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142627221	G	T	142627221	3	4	34	1	0	0	0	0	1	0	0	0	16639	1087	38	2	1960	2	TRPV5	7	142627221	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	4834969	142627221	16511442	30	2828										
SMARCD3	6604	hgsc.bcm.edu	37	chr7	150936210	150936210	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	taggtgttgcgcacaaccagCgactgctccagctcctgcct	10	15	0	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr7:150936210C>T	ENST00000262188.8	-	13	1841	c.1431G>A	c.(1429-1431)tcG>tcA	p.S477S	SMARCD3_ENST00000356800.2_Silent_p.S464S|MIR671_ENST00000390183.1_RNA|SMARCD3_ENST00000477169.1_5'Flank|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000392811.2_Silent_p.S464S	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	477					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.S464S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCACAACCAGCGACTGCTCCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	7											124	122	122					7																	150936210		2203	4300	6503	150567143	SO:0001819	synonymous_variant	6604			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60C", "Swp73-like protein", "SWI/SNF complex 60 kDa subunit C", "60kDa BRG-1/Brm associated factor subunit c"	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.1431G>A	7.37:g.150936210C>T			150567143	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Silent	SNP	ENST00000262188.8	37	CCDS34780.1																																																																																				0.577	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		T	150936210	C	T	150936210	2	4	34	1	0	0	0	0	0	0	0	1	14816	755	27	1		1	SMARCD3	7	150936210	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	8308989	150936210	8202453	31	2829										
STC1	6781	hgsc.bcm.edu	37	chr8	23702526	23702526	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtgtcttcatcacattccagCaggcttcggacaagtctgtt	9	11	4	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr8:23702526C>T	ENST00000290271.2	-	4	784	c.501G>A	c.(499-501)ctG>ctA	p.L167L	STC1_ENST00000524323.1_Silent_p.L98L	NM_003155.2	NP_003146.1	P52823	STC1_HUMAN	stanniocalcin 1	167					bone development (GO:0060348)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cAMP (GO:0071320)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hypoxia (GO:0071456)|chondrocyte proliferation (GO:0035988)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endothelial cell morphogenesis (GO:0001886)|growth plate cartilage axis specification (GO:0003421)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of renal phosphate excretion (GO:1903403)|ossification (GO:0001503)|positive regulation of calcium ion import (GO:0090280)|regulation of anion transport (GO:0044070)|regulation of cardiac muscle cell contraction (GO:0086004)|response to vitamin D (GO:0033280)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.L167L(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CACATTCCAGCAGGCTTCGGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	8											141	128	133					8																	23702526		2203	4300	6503	23758471	SO:0001819	synonymous_variant	6781				CCDS6043.1	8p22-p12	2008-06-23			ENSG00000159167	ENSG00000159167			11373	protein-coding gene	gene with protein product		601185		STC		9480753	Standard	NM_003155		Approved		uc003xdw.1	P52823	OTTHUMG00000097853	ENST00000290271.2:c.501G>A	8.37:g.23702526C>T			23758471	B4DN22|Q71UE5	Silent	SNP	ENST00000290271.2	37	CCDS6043.1																																																																																				0.532	STC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215143.1			T	23702526	C	T	23702526	2	4	34	1	0	0	0	0	0	0	0	1	15314	697	25	3		3	STC1	8	23702526	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10		23702526	122661496	32	2830										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24359065	24359065	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cagataaggactgagccaatCctgccagaaattcatttcct	7	11	1	3	rs143083584		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr8:24359065C>A	ENST00000175238.6	+	20	2267	c.2184C>A	c.(2182-2184)atC>atA	p.I728I	ADAM7_ENST00000380789.1_Silent_p.I728I|RP11-624C23.1_ENST00000519689.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Silent_p.I500I|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	728						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.I728I(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CTGAGCCAATCCTGCCAGAAA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	8						C		1,4405	2.1+/-5.4	0,1,2202	81	82	81		2184	0.7	0	8	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	ADAM7	NM_003817.2		0,1,6502	AA,AC,CC		0.0,0.0227,0.0077		728/755	24359065	1,13005	2203	4300	6503	24414955	SO:0001819	synonymous_variant	8756			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.2184C>A	8.37:g.24359065C>A			24414955	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	37	CCDS6045.1																																																																																				0.368	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		A	24359065	C	A	24359065	2	1	34	1	0	0	0	0	0	0	0	1	251	845	30	2		2	ADAM7	8	24359065	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	656539	24359065	122004957	33	2831										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28573810	28573810	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gagctgtgcgaggtgaagcaCgtgctggatctgtgccgcat	16	9	1	1	rs200105783	byFrequency	TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr8:28573810C>T	ENST00000220562.4	+	3	1136	c.234C>T	c.(232-234)caC>caT	p.H78H	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	78					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.H78H(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		AGGTGAAGCACGTGCTGGATC	0.597													C|||	2	0.000399361	0.0015	0	5008	,	,		20435	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						C		1,4405	2.1+/-5.4	0,1,2202	95	90	92		234	-4.9	0.9	8		92	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	EXTL3	NM_001440.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		78/920	28573810	2,13004	2203	4300	6503	28629729	SO:0001819	synonymous_variant	2137			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.234C>T	8.37:g.28573810C>T			28629729	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	37	CCDS6070.1																																																																																				0.597	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28573810	C	T	28573810	2	4	34	1	0	0	0	0	0	0	0	1	5340	535	19	1		1	EXTL3	8	28573810	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	4214745	28573810	117790212	34	2832										
UBR5	51366	hgsc.bcm.edu	37	chr8	103341610	103341610	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gaatacagagccccaatacaGatgaattttgttccatccta	6	10	0	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr8:103341610G>A	ENST00000520539.1	-	10	1722	c.1116C>T	c.(1114-1116)atC>atT	p.I372I	UBR5_ENST00000220959.4_Silent_p.I372I|UBR5_ENST00000521922.1_Silent_p.I366I	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	372					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.I372I(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			CCCCAATACAGATGAATTTTG	0.358																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - coding silent(1)	large_intestine(1)	8											103	113	109					8																	103341610		2202	4300	6502	103410786	SO:0001819	synonymous_variant	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.1116C>T	8.37:g.103341610G>A			103410786	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																				0.358	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103341610	G	A	103341610	2	1	34	1	0	0	0	0	0	0	0	1	16945	932	33	3		3	UBR5	8	103341610	Silent	SNP	G	TCGA-AG-3612-01A-01W-0833-10	74767800	103341610	43022412	35	2833										
SAMD12	401474	hgsc.bcm.edu	37	chr8	119391878	119391878	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tgtaagatgtgctgccggagGttctcctgggcaatccccat	12	11	1	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr8:119391878G>A	ENST00000314727.4	-	4	520	c.384C>T	c.(382-384)aaC>aaT	p.N128N	SAMD12_ENST00000527515.1_5'Flank|SAMD12_ENST00000409003.4_Silent_p.N128N|AC023590.1_ENST00000430457.1_Intron	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	128	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.							p.N128N(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			GCTGCCGGAGGTTCTCCTGGG	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	8											147	131	136					8																	119391878		2203	4300	6503	119461059	SO:0001819	synonymous_variant	401474			AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"Sterile alpha motif (SAM) domain containing"	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.384C>T	8.37:g.119391878G>A			119461059	Q0P502	Silent	SNP	ENST00000314727.4	37	CCDS6325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.642|9.642	1.139157|1.139157	0.21205|0.21205	.|.	.|.	ENSG00000177570|ENSG00000177570	ENST00000453675|ENST00000526765	.|.	.|.	.|.	6.17|6.17	4.39|4.39	0.52855|0.52855	.|.	.|.	.|.	.|.	.|.	T|T	0.61362|0.61362	0.2341|0.2341	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57871|0.57871	-0.7736|-0.7736	4|4	.|.	.|.	.|.	-13.1067|-13.1067	10.1023|10.1023	0.42513|0.42513	0.202:0.0:0.798:0.0|0.202:0.0:0.798:0.0	.|.	.|.	.|.	.|.	S|I	115|143	.|.	.|.	P|T	-|-	1|2	0|0	SAMD12|SAMD12	119461059|119461059	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	2.428000|2.428000	0.44749|0.44749	0.942000|0.942000	0.37525|0.37525	-0.136000|-0.136000	0.14681|0.14681	CCT|ACC		0.483	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506		A	119391878	G	A	119391878	2	1	34	1	0	0	0	0	0	0	0	1	13854	1252	44	3		3	SAMD12	8	119391878	Silent	SNP	G	TCGA-AG-3612-01A-01W-0833-10	16050268	119391878	26972144	36	2834										
PTPDC1	138639	hgsc.bcm.edu	37	chr9	96859681	96859681	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tatatttgtgcgggcaaagcGacccaattccatacaaacca	7	11	0	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr9:96859681G>T	ENST00000375360.3	+	7	1011	c.671G>T	c.(670-672)cGa>cTa	p.R224L	PTPDC1_ENST00000288976.3_Missense_Mutation_p.R276L	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	224	Tyrosine-protein phosphatase.				cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R276Q(1)|p.R224L(1)|p.R276L(1)|p.R224Q(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						CGGGCAAAGCGACCCAATTCC	0.413																																																4	Substitution - Missense(4)	large_intestine(4)	9											79	77	77					9																	96859681		2203	4300	6503	95899502	SO:0001583	missense	138639			BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	30184	protein-coding gene	gene with protein product	"protein tyrosine phosphatase PTP9Q22"					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.671G>T	9.37:g.96859681G>T	ENSP00000364509:p.Arg224Leu		95899502	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	.	27.7	4.857074	0.91433	.	.	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.50548	0.74;0.74	5.55	5.55	0.83447	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.81959	0.4933	H	0.98388	4.22	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.89000	0.3421	10	0.87932	D	0	-10.6174	18.4793	0.90806	0.0:0.0:1.0:0.0	.	278;276;278;224	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	L	224;276	ENSP00000364509:R224L;ENSP00000288976:R276L	ENSP00000288976:R276L	R	+	2	0	PTPDC1	95899502	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.269000	0.95684	2.610000	0.88304	0.591000	0.81541	CGA		0.413	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		T	96859681	G	T	96859681	3	4	34	1	0	0	0	0	1	0	0	0	12808	1058	37	2	935	2	PTPDC1	9	96859681	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10		96859681	44353750	37	2835										
GOLGA2	2801	hgsc.bcm.edu	37	chr9	131030738	131030738	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtgagactggcaccaggggaAgggacaccgccaggtaacac	15	11	0	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr9:131030738A>C	ENST00000421699.2	-	3	285	c.273T>G	c.(271-273)ccT>ccG	p.P91P	GOLGA2_ENST00000609374.1_Silent_p.P79P	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	91					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.P79P(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						CACCAGGGGAAGGGACACCGC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	9											94	67	76					9																	131030738		2203	4300	6503	130070559	SO:0001819	synonymous_variant	2801			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.273T>G	9.37:g.131030738A>C			130070559	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	CCDS6896.2	.	.	.	.	.	.	.	.	.	.	a	5.824	0.336341	0.11013	.	.	ENSG00000167110	ENST00000458730	.	.	.	5.63	0.721	0.18219	.	.	.	.	.	T	0.24314	0.0589	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	4.5307	0.12004	0.609:0.162:0.2289:0.0	.	.	.	.	V	51	.	.	F	-	1	0	GOLGA2	130070559	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.114000	0.15520	0.394000	0.25230	-0.263000	0.10527	TTC		0.567	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		C	131030738	A	C	131030738	2	2	34	1	0	0	0	0	0	0	0	1	6572	59	3	4		4	GOLGA2	9	131030738	Silent	SNP	A	TCGA-AG-3612-01A-01W-0833-10	34171057	131030738	10182693	38	2836										
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011768	138011768	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cacgagctaccccaagcgcaGcgccggggaggccttcatca	12	16	2	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr9:138011768G>C	ENST00000371793.3	+	6	1453	c.1202G>C	c.(1201-1203)aGc>aCc	p.S401T	OLFM1_ENST00000371796.3_Missense_Mutation_p.S374T|OLFM1_ENST00000252854.4_Missense_Mutation_p.S383T	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	401	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)	p.S383T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		CCCAAGCGCAGCGCCGGGGAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	9											74	63	67					9																	138011768		2203	4300	6503	137151589	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.1202G>C	9.37:g.138011768G>C	ENSP00000360858:p.Ser401Thr		137151589	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	G	24.3	4.511282	0.85389	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.90004	-2.6;-2.6;-2.6	4.7	4.7	0.59300	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	D	0.94355	0.8185	M	0.79614	2.46	0.80722	D	1	D;D	0.65815	0.992;0.995	D;D	0.76071	0.987;0.969	D	0.95205	0.8320	10	0.87932	D	0	.	17.6361	0.88122	0.0:0.0:1.0:0.0	.	401;383	Q99784;Q6IMJ8	NOE1_HUMAN;.	T	383;374;401	ENSP00000252854:S383T;ENSP00000360861:S374T;ENSP00000360858:S401T	ENSP00000252854:S383T	S	+	2	0	OLFM1	137151589	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.571000	0.98176	2.166000	0.68216	0.491000	0.48974	AGC		0.617	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		C	138011768	G	C	138011768	3	2	34	1	0	0	0	0	1	0	0	0	10883	971	34	5	1180	5	OLFM1	9	138011768	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	6981030	138011768	3201663	39	2837										
RSU1	6251	hgsc.bcm.edu	37	chr10	16796931	16796931	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ttgttgtacgtcaagtccagAacctcaagagctggcaggga	12	9	2	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:16796931A>T	ENST00000377921.3	-	4	640	c.339T>A	c.(337-339)gtT>gtA	p.V113V	RSU1_ENST00000602389.1_Silent_p.V60V|RSU1_ENST00000345264.5_Silent_p.V113V|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	113					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)		p.V113V(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		TCAAGTCCAGAACCTCAAGAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	10											82	91	88					10																	16796931		2203	4300	6503	16836937	SO:0001819	synonymous_variant	6251			AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.339T>A	10.37:g.16796931A>T			16836937	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																				0.448	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724		T	16796931	A	T	16796931	2	4	34	1	0	0	0	0	0	0	0	1	13753	233	9	5		5	RSU1	10	16796931	Silent	SNP	A	TCGA-AG-3612-01A-01W-0833-10		16796931	118737816	40	2838										
CUBN	8029	hgsc.bcm.edu	37	chr10	16992025	16992025	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aggggcgcgtcttcgtggccGccatccaaaatttctacaaa	10	12	2	0	rs565623595		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:16992025G>A	ENST00000377833.4	-	34	5120	c.5055C>T	c.(5053-5055)ggC>ggT	p.G1685G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1685	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.G1685G(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTCGTGGCCGCCATCCAAAA	0.448													g|||	1	0.000199681	0	0	5008	,	,		16066	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	10											74	67	69					10																	16992025		2203	4300	6503	17032031	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5055C>T	10.37:g.16992025G>A			17032031	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16992025	G	A	16992025	2	1	34	1	0	0	0	0	0	0	0	1	4057	1074	38	1		1	CUBN	10	16992025	Silent	SNP	G	TCGA-AG-3612-01A-01W-0833-10	195094	16992025	118542722	41	2839										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45485159	45485159	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ttcgcactctacatcgttcaCgagtctgggggtaagtacct	10	11	3	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:45485159C>T	ENST00000340258.5	+	8	788	c.675C>T	c.(673-675)caC>caT	p.H225H	RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000334940.6_Silent_p.H234H|RASSF4_ENST00000374417.2_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)	p.H225H(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						ACATCGTTCACGAGTCTGGGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	10											138	109	119					10																	45485159		2203	4300	6503	44805165	SO:0001819	synonymous_variant	83937			BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.675C>T	10.37:g.45485159C>T			44805165	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	37	CCDS7208.1																																																																																				0.547	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		T	45485159	C	T	45485159	2	4	34	1	0	0	0	0	0	0	0	1	13125	535	19	1		1	RASSF4	10	45485159	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	28493134	45485159	90049588	42	2840										
SFTPD	6441	hgsc.bcm.edu	37	chr10	81706265	81706265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ctctctcccatcccgtccatCgcgaccaggcaggccactct	7	20	2	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:81706265C>T	ENST00000372292.3	-	2	191	c.151G>A	c.(151-153)Gat>Aat	p.D51N		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	51	Collagen-like.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)	p.D51N(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	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)			TCCCGTCCATCGCGACCAGGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10											80	70	73					10																	81706265		2203	4300	6503	81696245	SO:0001583	missense	6441			L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"Collectins"	10803	protein-coding gene	gene with protein product		178635	"surfactant, pulmonary-associated protein D"	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.151G>A	10.37:g.81706265C>T	ENSP00000361366:p.Asp51Asn		81696245	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075409	0.76415	.	.	ENSG00000133661	ENST00000372292;ENST00000444384	D;D	0.90504	-2.68;-2.68	5.53	4.63	0.57726	.	0.000000	0.64402	D	0.000016	D	0.86493	0.5946	L	0.50993	1.605	0.35204	D	0.774514	P	0.46784	0.884	B	0.40165	0.321	D	0.87726	0.2576	10	0.28530	T	0.3	-16.3504	11.9983	0.53216	0.0:0.915:0.0:0.085	.	51	P35247	SFTPD_HUMAN	N	51;64	ENSP00000361366:D51N;ENSP00000394325:D64N	ENSP00000361366:D51N	D	-	1	0	SFTPD	81696245	0.958000	0.32768	0.853000	0.33588	0.540000	0.34992	2.138000	0.42140	1.336000	0.45506	0.655000	0.94253	GAT		0.607	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1			T	81706265	C	T	81706265	3	4	34	1	0	0	0	0	1	0	0	0	14230	884	31	1	1004	1	SFTPD	10	81706265	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	36221106	81706265	53828482	43	2841										
KIF11	3832	hgsc.bcm.edu	37	chr10	94353174	94353174	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tctgcgaagaagaaagaggaGaaggggaagaacatccaggt	15	5	1	5			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:94353174G>A	ENST00000260731.3	+	1	132	c.42G>A	c.(40-42)gaG>gaA	p.E14E		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	14					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)	p.E14E(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGAAAGAGGAGAAGGGGAAGA	0.637																																					Colon(47;212 1003 2764 4062 8431)											1	Substitution - coding silent(1)	large_intestine(1)	10											76	66	70					10																	94353174		2203	4300	6503	94343154	SO:0001819	synonymous_variant	3832			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.42G>A	10.37:g.94353174G>A			94343154	A0AV49|B2RMV3|Q15716|Q5VWX0	Silent	SNP	ENST00000260731.3	37	CCDS7422.1																																																																																				0.637	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		A	94353174	G	A	94353174	2	1	34	1	0	0	0	0	0	0	0	1	8293	933	33	3		3	KIF11	10	94353174	Silent	SNP	G	TCGA-AG-3612-01A-01W-0833-10	12646909	94353174	41181573	44	2842										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101567927	101567927	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ccttcacctccattaccctcTtcaatatcctgcgctttccc	2	19	3	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr10:101567927T>A	ENST00000370449.4	+	13	1869	c.1756T>A	c.(1756-1758)Ttc>Atc	p.F586I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	586	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.F586I(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CATTACCCTCTTCAATATCCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	10											272	236	248					10																	101567927		2203	4300	6503	101557917	SO:0001583	missense	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1756T>A	10.37:g.101567927T>A	ENSP00000359478:p.Phe586Ile		101557917	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608367	0.87258	.	.	ENSG00000023839	ENST00000370449	T	0.12984	2.63	5.73	5.73	0.89815	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	T	0.45856	0.1363	M	0.90542	3.125	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.54323	-0.8311	10	0.54805	T	0.06	-22.5997	15.9985	0.80270	0.0:0.0:0.0:1.0	.	586	Q92887	MRP2_HUMAN	I	586	ENSP00000359478:F586I	ENSP00000359478:F586I	F	+	1	0	ABCC2	101557917	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	6.295000	0.72744	2.183000	0.69458	0.459000	0.35465	TTC		0.478	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101567927	T	A	101567927	3	1	34	1	0	0	0	0	1	0	0	0	53	1609	56	5	1806	5	ABCC2	10	101567927	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	7214753	101567927	33966820	45	2843										
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371516	55371516	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aacagccatgagaatgaggaCaaagatctccatgcagccaa	9	10	1	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr11:55371516C>A	ENST00000302231.4	-	1	358	c.334G>T	c.(334-336)Gtc>Ttc	p.V112F		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V112F(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						AGAATGAGGACAAAGATCTCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	86	92					11																	55371516		2179	4005	6184	55128092	SO:0001583	missense	219429			AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.334G>T	11.37:g.55371516C>A	ENSP00000306651:p.Val112Phe		55128092	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.733093	0.30684	.	.	ENSG00000172188	ENST00000302231	T	0.01133	5.29	4.34	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.155734	0.29799	U	0.011169	T	0.01870	0.0059	L	0.31294	0.92	0.09310	N	0.999995	D	0.58620	0.983	P	0.56563	0.801	T	0.48422	-0.9037	10	0.87932	D	0	.	4.8604	0.13581	0.0:0.6262:0.1756:0.1981	.	112	Q6IEV9	OR4CB_HUMAN	F	112	ENSP00000306651:V112F	ENSP00000306651:V112F	V	-	1	0	OR4C11	55128092	0.000000	0.05858	0.950000	0.38849	0.235000	0.25334	-3.615000	0.00414	0.563000	0.29222	0.478000	0.44815	GTC		0.428	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		A	55371516	C	A	55371516	3	1	34	1	0	0	0	0	1	0	0	0	11076	478	17	2	600	2	OR4C11	11	55371516	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		55371516	79635000	46	2844										
CLECL1	160365	hgsc.bcm.edu	37	chr12	9875397	9875397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	atgatttatggacagtagaaAagttgaaagaaactggaaga	11	2	0	5			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr12:9875397A>G	ENST00000327839.3	-	2	363	c.329T>C	c.(328-330)tTt>tCt	p.F110S		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.F110S(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						GACAGTAGAAAAGTTGAAAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											55	51	52					12																	9875397		2203	4299	6502	9766664	SO:0001583	missense	160365			AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.329T>C	12.37:g.9875397A>G	ENSP00000331766:p.Phe110Ser		9766664		Missense_Mutation	SNP	ENST00000327839.3	37	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.357|3.357	-0.131378|-0.131378	0.06753|0.06753	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000542530|ENST00000327839	T|T	0.15139|0.15952	2.45|2.38	2.49|2.49	-0.559|-0.559	0.11792|0.11792	.|.	.|.	.|.	.|.	.|.	T|T	0.10895|0.10895	0.0266|0.0266	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.36016|0.36016	-0.9765|-0.9765	6|8	.|.	.|.	.|.	.|.	2.8791|2.8791	0.05641|0.05641	0.311:0.2443:0.4447:0.0|0.311:0.2443:0.4447:0.0	.|.	.|110	.|Q8IZS7	.|CLCL1_HUMAN	L|S	62|110	ENSP00000438981:F62L|ENSP00000331766:F110S	.|.	F|F	-|-	1|2	0|0	CLECL1|CLECL1	9766664|9766664	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.547000|-0.547000	0.06055|0.06055	-0.135000|-0.135000	0.11495|0.11495	-0.244000|-0.244000	0.11960|0.11960	TTT|TTT		0.328	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		G	9875397	A	G	9875397	3	3	34	1	0	0	0	0	1	0	0	0	3529	14	1	4	178	4	CLECL1	12	9875397	Missense_Mutation	SNP	A	TCGA-AG-3612-01A-01W-0833-10		9875397	123976498	47	2845										
VDR	7421	hgsc.bcm.edu	37	chr12	48238710	48238710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ccgggggcgggtggcggcagCggatgtacgtctgcagtgtg	21	9	1	0	rs376903517		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr12:48238710C>T	ENST00000395324.2	-	10	1371	c.1103G>A	c.(1102-1104)cGc>cAc	p.R368H	VDR_ENST00000535672.1_Missense_Mutation_p.R336H|VDR_ENST00000549336.1_Missense_Mutation_p.R368H|VDR_ENST00000550325.1_Missense_Mutation_p.R418H|VDR_ENST00000229022.3_Missense_Mutation_p.R368H			P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	368	Ligand-binding.				bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R368H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2)	22		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GTGGCGGCAGCGGATGTACGT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											103	112	109					12																	48238710		2203	4299	6502	46524977	SO:0001583	missense	7421			J03258	CCDS8757.1, CCDS55820.1	12q12-q14	2014-06-13				ENSG00000111424		"Nuclear hormone receptors"	12679	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 163"	601769				1662663	Standard	NM_001017536		Approved	NR1I1, PPP1R163	uc001rql.3	P11473		ENST00000395324.2:c.1103G>A	12.37:g.48238710C>T	ENSP00000378734:p.Arg368His		46524977	B2R5Q1|G3V1V9|Q5PSV3	Missense_Mutation	SNP	ENST00000395324.2	37	CCDS8757.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258548	0.39896	.	.	ENSG00000111424	ENST00000395324;ENST00000229022;ENST00000549336;ENST00000550325;ENST00000535672	D;D;D;D;D	0.96685	-4.09;-4.09;-4.09;-4.09;-4.09	4.05	4.05	0.47172	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.177032	0.50627	D	0.000109	D	0.94843	0.8334	M	0.73962	2.25	0.49299	D	0.99977	B;B;B	0.20671	0.017;0.015;0.047	B;B;B	0.21546	0.022;0.035;0.024	D	0.93182	0.6575	10	0.51188	T	0.08	.	10.6927	0.45882	0.1912:0.8088:0.0:0.0	.	336;368;418	B4DRV7;P11473;G3V1V9	.;VDR_HUMAN;.	H	368;368;368;418;336	ENSP00000378734:R368H;ENSP00000229022:R368H;ENSP00000449573:R368H;ENSP00000447173:R418H;ENSP00000442145:R336H	ENSP00000229022:R368H	R	-	2	0	VDR	46524977	0.999000	0.42202	1.000000	0.80357	0.523000	0.34469	1.000000	0.29770	2.268000	0.75426	0.462000	0.41574	CGC		0.632	VDR-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406433.1			T	48238710	C	T	48238710	3	4	34	1	0	0	0	0	1	0	0	0	17189	768	27	1	184	1	VDR	12	48238710	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	38363313	48238710	85613185	48	2846										
GPN3	51184	hgsc.bcm.edu	37	chr12	110897524	110897524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	acaatcaaaaaggatatagtCgtcctctacatggccaagac	7	10	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr12:110897524C>T	ENST00000228827.3	-	3	363	c.301G>A	c.(301-303)Gac>Aac	p.D101N	GPN3_ENST00000543199.1_Missense_Mutation_p.D140N|GPN3_ENST00000537466.2_Missense_Mutation_p.D111N|GPN3_ENST00000552180.1_5'Flank	NM_016301.3	NP_057385.3			GPN-loop GTPase 3									p.D101N(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						AGGATATAGTCGTCCTCTACA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											140	133	135					12																	110897524		2203	4300	6503	109381907	SO:0001583	missense	51184			BC008416	CCDS9147.1, CCDS53830.1, CCDS53831.1	12q24.11	2012-12-18	2008-04-30	2008-04-30	ENSG00000111231	ENSG00000111231		"GPN-loop GTPases"	30186	protein-coding gene	gene with protein product			"ATP binding domain 1 family, member C"	ATPBD1C		12975309	Standard	NM_016301		Approved	MGC14560	uc021rdu.1	Q9UHW5	OTTHUMG00000169524	ENST00000228827.3:c.301G>A	12.37:g.110897524C>T	ENSP00000228827:p.Asp101Asn		109381907		Missense_Mutation	SNP	ENST00000228827.3	37	CCDS9147.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888394	0.91814	.	.	ENSG00000111231	ENST00000228827;ENST00000543199;ENST00000537466;ENST00000550974	T;T;T;T	0.25250	1.81;1.81;1.81;1.81	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.55162	0.1903	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.55692	-0.8101	10	0.87932	D	0	-20.9086	20.089	0.97809	0.0:1.0:0.0:0.0	.	111;101	Q9UHW5-2;Q9UHW5	.;GPN3_HUMAN	N	101;140;111;79	ENSP00000228827:D101N;ENSP00000442770:D140N;ENSP00000443068:D111N;ENSP00000447480:D79N	ENSP00000228827:D101N	D	-	1	0	GPN3	109381907	1.000000	0.71417	0.997000	0.53966	0.476000	0.33039	7.356000	0.79445	2.765000	0.95021	0.591000	0.81541	GAC		0.418	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301		T	110897524	C	T	110897524	3	4	34	1	0	0	0	0	1	0	0	0	6639	884	31	1	577	1	GPN3	12	110897524	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	62658814	110897524	22954371	49	2847										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36744713	36744713	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtctggcccaacccagaagtGcagtgccgagggagaagctt	14	11	1	2	rs550456759		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr13:36744713G>A	ENST00000379881.3	-	10	1300	c.1212C>T	c.(1210-1212)tgC>tgT	p.C404C	SOHLH2_ENST00000554962.1_Silent_p.C481C|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.C481C	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	404					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.C404C(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		ACCCAGAAGTGCAGTGCCGAG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	13											84	71	75					13																	36744713		2203	4300	6503	35642713	SO:0001819	synonymous_variant	54937			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1212C>T	13.37:g.36744713G>A			35642713	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																				0.517	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		A	36744713	G	A	36744713	2	1	34	1	0	0	0	0	0	0	0	1	14961	1311	46	3		3	SOHLH2	13	36744713	Silent	SNP	G	TCGA-AG-3612-01A-01W-0833-10		36744713	78425165	50	2848										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265931	39265931	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tgtccatcacgtctttcactCagctgcaactggctggaaac	8	13	4	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr13:39265931C>T	ENST00000280481.7	+	1	4666	c.4450C>T	c.(4450-4452)Cag>Tag	p.Q1484*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1484					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q1484*(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GTCTTTCACTCAGCTGCAACT	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											90	77	82					13																	39265931		2203	4300	6503	38163931	SO:0001587	stop_gained	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4450C>T	13.37:g.39265931C>T	ENSP00000280481:p.Gln1484*		38163931	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	46	12.324773	0.99657	.	.	ENSG00000150893	ENST00000280481	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0826	0.97783	0.0:1.0:0.0:0.0	.	.	.	.	X	1484	.	ENSP00000280481:Q1484X	Q	+	1	0	FREM2	38163931	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.814000	0.86154	2.746000	0.94184	0.655000	0.94253	CAG		0.483	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39265931	C	T	39265931	4	4	34	1	0	0	0	0	0	1	0	0	6064	827	29	3	4452	3	FREM2	13	39265931	Nonsense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	2521218	39265931	75903947	51	2849										
RNF219	79596	hgsc.bcm.edu	37	chr13	79213138	79213138	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ggatccagaatagttttgatCtgtgactccaagctgagatt	10	7	1	4			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr13:79213138C>A	ENST00000282003.6	-	4	427	c.369G>T	c.(367-369)caG>caT	p.Q123H		NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	123							zinc ion binding (GO:0008270)	p.Q123H(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		TAGTTTTGATCTGTGACTCCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											133	128	129					13																	79213138		2203	4300	6503	78111139	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.369G>T	13.37:g.79213138C>A	ENSP00000282003:p.Gln123His		78111139	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.152490	0.38021	.	.	ENSG00000152193	ENST00000282003	.	.	.	5.38	2.5	0.30297	.	0.191546	0.45867	D	0.000321	T	0.30634	0.0771	N	0.17082	0.46	0.35911	D	0.831126	B	0.26775	0.159	B	0.19148	0.024	T	0.30736	-0.9968	9	0.42905	T	0.14	-4.7486	7.2706	0.26254	0.1209:0.6784:0.0:0.2007	.	123	Q5W0B1	RN219_HUMAN	H	123	.	ENSP00000282003:Q123H	Q	-	3	2	RNF219	78111139	0.991000	0.36638	1.000000	0.80357	0.993000	0.82548	0.287000	0.18920	1.272000	0.44329	0.655000	0.94253	CAG		0.383	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79213138	C	A	79213138	3	1	34	1	0	0	0	0	1	0	0	0	13519	912	32	2	1823	2	RNF219	13	79213138	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	39947207	79213138	35956740	52	2850										
UBR1	197131	hgsc.bcm.edu	37	chr15	43294805	43294805	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ggggatcacagtattgcacaGagatttgcaaagagggcaaa	13	6	1	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr15:43294805G>C	ENST00000290650.4	-	32	3685	c.3607C>G	c.(3607-3609)Ctg>Gtg	p.L1203V	UBR1_ENST00000382177.2_3'UTR|UBR1_ENST00000568782.1_5'Flank	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1203					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L1203V(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GTATTGCACAGAGATTTGCAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											71	68	69					15																	43294805		2203	4299	6502	41082097	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3607C>G	15.37:g.43294805G>C	ENSP00000290650:p.Leu1203Val		41082097	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534188	0.45073	.	.	ENSG00000159459	ENST00000290650	T	0.64085	-0.08	5.29	2.31	0.28768	Zinc finger, RING/FYVE/PHD-type (1);	0.162619	0.42053	N	0.000773	T	0.61274	0.2334	M	0.77313	2.365	0.80722	D	1	B	0.21452	0.056	B	0.20577	0.03	T	0.64002	-0.6509	10	0.72032	D	0.01	-16.322	11.2436	0.48982	0.2639:0.0:0.7361:0.0	.	1203	Q8IWV7	UBR1_HUMAN	V	1203	ENSP00000290650:L1203V	ENSP00000290650:L1203V	L	-	1	2	UBR1	41082097	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.781000	0.55394	0.791000	0.33826	0.460000	0.39030	CTG		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43294805	G	C	43294805	3	2	34	1	0	0	0	0	1	0	0	0	16941	933	33	5	1706	5	UBR1	15	43294805	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10		43294805	59236587	53	2851										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9858209	9858209	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tggcacgtggcccgatttgaCgtttctgaaatgtcagagtg	13	8	2	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr16:9858209C>T	ENST00000396573.2	-	14	3501	c.3192G>A	c.(3190-3192)acG>acA	p.T1064T	GRIN2A_ENST00000535259.1_Silent_p.T907T|GRIN2A_ENST00000396575.2_Silent_p.T1064T|GRIN2A_ENST00000562109.1_Silent_p.T1064T|GRIN2A_ENST00000404927.2_Silent_p.T1064T|GRIN2A_ENST00000330684.3_Silent_p.T1064T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1064					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.T1064T(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCCGATTTGACGTTTCTGAAA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	16											131	127	128					16																	9858209		2197	4300	6497	9765710	SO:0001819	synonymous_variant	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3192G>A	16.37:g.9858209C>T			9765710	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.502	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9858209	C	T	9858209	2	4	34	1	0	0	0	0	0	0	0	1	6800	523	19	1		1	GRIN2A	16	9858209	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10		9858209	80496544	54	2852										
TP53	7157	hgsc.bcm.edu	37	chr17	7577509	7577509	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ggctcctgacctggagtcttCcagtgtgatgatggtgagga	15	8	1	4	rs121912652		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr17:7577509C>A	ENST00000269305.4	-	7	961	c.772G>T	c.(772-774)Gaa>Taa	p.E258*	TP53_ENST00000420246.2_Nonsense_Mutation_p.E258*|TP53_ENST00000455263.2_Nonsense_Mutation_p.E258*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E258*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E258*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E258*|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E258K(40)|p.E258*(15)|p.E258Q(9)|p.0?(8)|p.?(1)|p.E258fs*85(1)|p.E258>XX(1)|p.E258fs*71(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)|p.T256fs*87(1)|p.E258L(1)|p.E258fs*87(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGGAGTCTTCCAGTGTGATG	0.587		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	82	Substitution - Missense(50)|Substitution - Nonsense(15)|Whole gene deletion(8)|Deletion - Frameshift(5)|Deletion - In frame(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(14)|urinary_tract(10)|upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|skin(7)|lung(6)|oesophagus(5)|central_nervous_system(4)|breast(4)|ovary(4)|bone(4)|stomach(2)|liver(2)|thyroid(1)|soft_tissue(1)|peritoneum(1)|biliary_tract(1)|endometrium(1)|pancreas(1)	17	GRCh37	CM900213	TP53	M	rs121912652						137	97	111					17																	7577509		2203	4300	6503	7518234	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.772G>T	17.37:g.7577509C>A	ENSP00000269305:p.Glu258*		7518234	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.891139	0.52014	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	4.62	3.62	0.41486	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-21.9865	12.6215	0.56605	0.0:0.8318:0.1682:0.0	.	.	.	.	X	258;258;258;258;258;258;247;126	.	ENSP00000269305:E258X	E	-	1	0	TP53	7518234	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	7.609000	0.82925	1.266000	0.44231	0.462000	0.41574	GAA		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577509	C	A	7577509	4	1	34	1	0	0	0	0	0	1	0	0	16421	864	30	2	518	2	TP53	17	7577509	Nonsense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		7577509	73617701	55	2853										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7702525	7702525	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtgcagaacaacctgcacatCgtgctctgcctcagccccat	8	16	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr17:7702525C>T	ENST00000572933.1	+	56	10124	c.8664C>T	c.(8662-8664)atC>atT	p.I2888I	DNAH2_ENST00000389173.2_Silent_p.I2888I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2888	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I2888I(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				ACCTGCACATCGTGCTCTGCC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											109	87	95					17																	7702525		2203	4300	6503	7643250	SO:0001819	synonymous_variant	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.8664C>T	17.37:g.7702525C>T			7643250	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																				0.592	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7702525	C	T	7702525	2	4	34	1	0	0	0	0	0	0	0	1	4613	874	31	1		1	DNAH2	17	7702525	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	125016	7702525	73492685	56	2854										
SLFN12	55106	hgsc.bcm.edu	37	chr17	33738414	33738414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	tcattcttctgaaagcaatcTataccgattatctggtatag	6	8	5	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr17:33738414T>C	ENST00000394562.1	-	6	2203	c.1680A>G	c.(1678-1680)atA>atG	p.I560M	SLFN12_ENST00000460530.1_5'UTR|RP11-686D22.8_ENST00000587012.1_RNA|SLFN12_ENST00000304905.5_Missense_Mutation_p.I560M|SLFN12_ENST00000452764.3_Missense_Mutation_p.I560M			Q8IYM2	SLN12_HUMAN	schlafen family member 12	560							ATP binding (GO:0005524)	p.I560M(1)		breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GAAAGCAATCTATACCGATTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	17											51	55	54					17																	33738414		2203	4300	6503	30762527	SO:0001583	missense	55106			AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.1680A>G	17.37:g.33738414T>C	ENSP00000378063:p.Ile560Met		30762527	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	T	9.717	1.158632	0.21454	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03801	3.8;3.8;3.8	2.75	-3.75	0.04372	.	.	.	.	.	T	0.02119	0.0066	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44620	-0.9316	9	0.33141	T	0.24	.	3.694	0.08357	0.2032:0.4815:0.0:0.3154	.	560	Q8IYM2	SLN12_HUMAN	M	560	ENSP00000378063:I560M;ENSP00000302077:I560M;ENSP00000394903:I560M	ENSP00000302077:I560M	I	-	3	3	SLFN12	30762527	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.161000	0.03144	-1.014000	0.03379	0.164000	0.16699	ATA		0.353	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		C	33738414	T	C	33738414	3	2	34	1	0	0	0	0	1	0	0	0	14771	1512	53	4	60	4	SLFN12	17	33738414	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	26035889	33738414	47456796	57	2855										
SERPINB5	5268	hgsc.bcm.edu	37	chr18	61166415	61166415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ttctgtatgggaaacattgaCagtatcaattgtaagatcat	8	5	3	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr18:61166415C>A	ENST00000382771.4	+	6	922	c.630C>A	c.(628-630)gaC>gaA	p.D210E	SERPINB5_ENST00000464346.1_3'UTR	NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	210					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D210E(1)		kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						GAAACATTGACAGTATCAATT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											131	113	119					18																	61166415		2203	4300	6503	59317395	SO:0001583	missense	5268			U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"Serine (or cysteine) peptidase inhibitors"	8949	protein-coding gene	gene with protein product	"protease inhibitor 5 (maspin)"	154790	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.630C>A	18.37:g.61166415C>A	ENSP00000372221:p.Asp210Glu		59317395	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	.	.	.	.	.	.	.	.	.	.	C	1.308	-0.602884	0.03744	.	.	ENSG00000206075	ENST00000382771	T	0.16743	2.32	5.03	-10.1	0.00402	Serpin domain (3);	0.277161	0.35235	N	0.003354	T	0.02848	0.0085	N	0.03050	-0.425	0.24412	N	0.994654	B	0.10296	0.003	B	0.13407	0.009	T	0.32079	-0.9920	10	0.02654	T	1	.	3.5112	0.07709	0.1031:0.0886:0.2188:0.5894	.	210	P36952	SPB5_HUMAN	E	210	ENSP00000372221:D210E	ENSP00000372221:D210E	D	+	3	2	SERPINB5	59317395	0.007000	0.16637	0.000000	0.03702	0.846000	0.48090	-1.441000	0.02409	-1.537000	0.01736	0.511000	0.50034	GAC		0.418	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639		A	61166415	C	A	61166415	3	1	34	1	0	0	0	0	1	0	0	0	14141	477	17	2	648	2	SERPINB5	18	61166415	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		61166415	16910833	58	2856			1	3		2	2	16	N	G_C	3.488679e-05
SERPINB5	5268	hgsc.bcm.edu	37	chr18	61166430	61166430	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	attgacagtatcaattgtaaGatcatagagcttccttttca	6	7	3	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr18:61166430G>C	ENST00000382771.4	+	6	937	c.645G>C	c.(643-645)aaG>aaC	p.K215N	SERPINB5_ENST00000464346.1_3'UTR	NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	215					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.K215N(1)		kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						TCAATTGTAAGATCATAGAGC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	18											130	112	118					18																	61166430		2203	4300	6503	59317410	SO:0001583	missense	5268			U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"Serine (or cysteine) peptidase inhibitors"	8949	protein-coding gene	gene with protein product	"protease inhibitor 5 (maspin)"	154790	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.645G>C	18.37:g.61166430G>C	ENSP00000372221:p.Lys215Asn		59317410	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.611281	0.28712	.	.	ENSG00000206075	ENST00000382771	D	0.85556	-2.0	5.14	3.33	0.38152	Serpin domain (3);	0.360177	0.29396	N	0.012278	T	0.81856	0.4911	M	0.70275	2.135	0.42499	D	0.992925	B	0.25312	0.123	B	0.20767	0.031	T	0.77983	-0.2382	10	0.66056	D	0.02	.	7.928	0.29887	0.141:0.2479:0.6111:0.0	.	215	P36952	SPB5_HUMAN	N	215	ENSP00000372221:K215N	ENSP00000372221:K215N	K	+	3	2	SERPINB5	59317410	1.000000	0.71417	0.767000	0.31495	0.773000	0.43773	0.857000	0.27831	0.663000	0.31027	-0.416000	0.06073	AAG		0.428	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639		C	61166430	G	C	61166430	3	2	34	1	0	0	0	0	1	0	0	0	14141	933	33	5	663	5	SERPINB5	18	61166430	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10	15	61166430	16910818	59	2857			1	3		2	2	16	N	G_C	3.488679e-05
ZNF146	7705	hgsc.bcm.edu	37	chr19	36728063	36728063	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	atacaggggagaagccctatGgttgtaatgaatgtgggaaa	14	4	0	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr19:36728063G>T	ENST00000443387.2	+	4	1713	c.721G>T	c.(721-723)Ggt>Tgt	p.G241C	ZNF565_ENST00000355114.5_Intron|ZNF146_ENST00000456324.1_Missense_Mutation_p.G241C	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	241	Interaction with TERF2IP.				regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G241C(1)		kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					GAAGCCCTATGGTTGTAATGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											122	112	115					19																	36728063		2203	4300	6503	41419903	SO:0001583	missense	7705			X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"Zinc fingers, C2H2-type"	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.721G>T	19.37:g.36728063G>T	ENSP00000392095:p.Gly241Cys		41419903	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	37	CCDS12492.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405784	0.42715	.	.	ENSG00000167635	ENST00000443387;ENST00000456324	T;T	0.16324	2.35;2.35	4.48	4.48	0.54585	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40818	N	0.001015	T	0.22936	0.0554	N	0.21448	0.665	0.21984	N	0.999438	D	0.89917	1.0	D	0.97110	1.0	T	0.05835	-1.0861	10	0.87932	D	0	-5.3835	5.8534	0.18707	0.0951:0.0:0.7122:0.1927	.	241	Q15072	OZF_HUMAN	C	241	ENSP00000392095:G241C;ENSP00000400391:G241C	ENSP00000392095:G241C	G	+	1	0	ZNF146	41419903	0.000000	0.05858	1.000000	0.80357	0.891000	0.51852	-1.343000	0.02642	2.780000	0.95670	0.561000	0.74099	GGT		0.448	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145		T	36728063	G	T	36728063	3	4	34	1	0	0	0	0	1	0	0	0	17772	1348	47	2	723	2	ZNF146	19	36728063	Missense_Mutation	SNP	G	TCGA-AG-3612-01A-01W-0833-10		36728063	22400920	60	2858										
MRPS12	6183	hgsc.bcm.edu	37	chr19	39423124	39423124	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gtggtcctgtgcacgtttacCcgcaagccgaagaagcccaa	11	13	0	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr19:39423124C>A	ENST00000407800.2	+	2	542	c.201C>A	c.(199-201)acC>acA	p.T67T	SARS2_ENST00000221431.6_5'Flank|SARS2_ENST00000600042.1_5'Flank|CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000430193.3_5'Flank|MRPS12_ENST00000308018.4_Silent_p.T67T|SARS2_ENST00000594171.1_5'Flank|MRPS12_ENST00000402029.3_Silent_p.T67T|CTC-360G5.9_ENST00000599320.1_lincRNA|SARS2_ENST00000448145.2_Intron	NM_021107.1	NP_066930.1	O15235	RT12_HUMAN	mitochondrial ribosomal protein S12	67					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T67T(1)		endometrium(1)|large_intestine(1)	2	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GCACGTTTACCCGCAAGCCGA	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	19											51	49	50					19																	39423124		2203	4300	6503	44114964	SO:0001819	synonymous_variant	6183			Y11681	CCDS12525.1	19q13.1-q13.2	2012-09-13			ENSG00000128626	ENSG00000128626		"Mitochondrial ribosomal proteins / small subunits"	10380	protein-coding gene	gene with protein product		603021		RPMS12		9545647, 9790755	Standard	NM_021107		Approved	RPS12, RPSM12	uc002oke.3	O15235		ENST00000407800.2:c.201C>A	19.37:g.39423124C>A			44114964	Q53X98	Silent	SNP	ENST00000407800.2	37	CCDS12525.1																																																																																				0.682	MRPS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463154.1			A	39423124	C	A	39423124	2	1	34	1	0	0	0	0	0	0	0	1	9853	610	22	2		2	MRPS12	19	39423124	Silent	SNP	C	TCGA-AG-3612-01A-01W-0833-10	2695061	39423124	19705859	61	2859										
RPS16	6217	hgsc.bcm.edu	37	chr19	39924346	39924346	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	caccaccctttacacggacaCggatgtctacaccagcaaat	6	15	1	0			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr19:39924346C>A	ENST00000251453.3	-	3	258	c.206G>T	c.(205-207)cGt>cTt	p.R69L	RPS16_ENST00000599539.1_Missense_Mutation_p.R69L|RPS16_ENST00000339471.4_Missense_Mutation_p.R69L|RPS16_ENST00000601655.1_Missense_Mutation_p.R52L	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	69					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.R69L(1)		central_nervous_system(1)|large_intestine(2)|lung(2)|skin(2)	7	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;4.14e-26)|all cancers(26;2.68e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TACACGGACACGGATGTCTAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											92	71	78					19																	39924346		2203	4300	6503	44616186	SO:0001583	missense	6217			M60854	CCDS12535.1	19q13.1	2011-04-05				ENSG00000105193		"S ribosomal proteins"	10396	protein-coding gene	gene with protein product	"40S ribosomal protein S16"	603675				2016298, 9582194	Standard	XM_005259137		Approved	S16	uc002olk.3	P62249		ENST00000251453.3:c.206G>T	19.37:g.39924346C>A	ENSP00000251453:p.Arg69Leu		44616186	B2RDD5|P17008	Missense_Mutation	SNP	ENST00000251453.3	37	CCDS12535.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.058575	0.76074	.	.	ENSG00000105193	ENST00000251453;ENST00000339471	.	.	.	5.14	5.14	0.70334	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.79034	0.4378	M	0.83312	2.635	0.80722	D	1	D;B	0.57571	0.98;0.008	P;B	0.62885	0.908;0.125	T	0.81269	-0.1009	8	.	.	.	-7.9873	16.0972	0.81135	0.0:1.0:0.0:0.0	.	69;69	Q6IPX4;P62249	.;RS16_HUMAN	L	69	.	.	R	-	2	0	RPS16	44616186	1.000000	0.71417	0.939000	0.37840	0.835000	0.47333	4.468000	0.60162	2.372000	0.80975	0.643000	0.83706	CGT		0.562	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020		A	39924346	C	A	39924346	3	1	34	1	0	0	0	0	1	0	0	0	13664	536	19	2	246	2	RPS16	19	39924346	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	501222	39924346	19204637	62	2860										
FCAR	2204	hgsc.bcm.edu	37	chr19	55396680	55396680	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gcctttcatatctgccaaatCgagtcctgtgattcccttgg	8	12	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr19:55396680C>T	ENST00000355524.3	+	3	114	c.104C>T	c.(103-105)tCg>tTg	p.S35L	FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.S35L|FCAR_ENST00000469767.1_Missense_Mutation_p.S35L|FCAR_ENST00000391726.3_Missense_Mutation_p.S23L|FCAR_ENST00000391724.3_Missense_Mutation_p.S23L|FCAR_ENST00000391725.3_Missense_Mutation_p.S35L|FCAR_ENST00000353758.4_Intron|FCAR_ENST00000359272.4_Missense_Mutation_p.S23L|FCAR_ENST00000391723.3_Missense_Mutation_p.S23L	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	35					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.S35L(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		TCTGCCAAATCGAGTCCTGTG	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	19											67	65	66					19																	55396680		2203	4300	6503	60088492	SO:0001583	missense	2204			X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.104C>T	19.37:g.55396680C>T	ENSP00000347714:p.Ser35Leu		60088492	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.934890	0.34189	.	.	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000359272;ENST00000391723;ENST00000391724	T;T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;2.76;2.76	3.19	2.1	0.27182	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.788741	0.10353	N	0.684825	T	0.18341	0.0440	M	0.61703	1.905	0.09310	N	1	D;D;D;D;D;D;D;D	0.69078	0.995;0.959;0.973;0.997;0.98;0.989;0.994;0.981	P;P;P;P;P;P;P;P	0.51101	0.659;0.607;0.529;0.636;0.467;0.452;0.588;0.56	T	0.12811	-1.0533	10	0.87932	D	0	.	7.3977	0.26946	0.2597:0.7403:0.0:0.0	.	23;23;23;23;35;35;35;35	Q92588;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071;P24071-4	.;.;.;.;.;.;FCAR_HUMAN;.	L	35;23;35;35;35;23;23;23	ENSP00000375606:S23L;ENSP00000347714:S35L;ENSP00000375605:S35L;ENSP00000338257:S35L;ENSP00000352218:S23L;ENSP00000375603:S23L;ENSP00000375604:S23L	ENSP00000338257:S35L	S	+	2	0	FCAR	60088492	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.083000	0.30815	0.852000	0.35287	0.563000	0.77884	TCG		0.498	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		T	55396680	C	T	55396680	3	4	34	1	0	0	0	0	1	0	0	0	5792	893	31	1	114	1	FCAR	19	55396680	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	15472334	55396680	3732303	63	2861										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953007	56953007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	aataagaaatgattggcggcCgaaaactttactacatttat	7	6	0	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr19:56953007C>T	ENST00000504904.3	-	7	2076	c.1357G>A	c.(1357-1359)Ggc>Agc	p.G453S	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.G581S|ZNF667_ENST00000292069.6_Missense_Mutation_p.G453S			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	453					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G453S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		GATTGGCGGCCGAAAACTTTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											49	50	50					19																	56953007		2203	4300	6503	61644819	SO:0001583	missense	63934				CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1357G>A	19.37:g.56953007C>T	ENSP00000439402:p.Gly453Ser		61644819	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	C	0.516	-0.864405	0.02590	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518;ENST00000360227	T;T;T	0.07114	3.22;3.22;3.22	5.03	2.81	0.32909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45126	D	0.000386	T	0.01730	0.0055	N	0.01424	-0.875	0.09310	N	0.99999	P;P	0.39665	0.682;0.682	B;B	0.29716	0.106;0.106	T	0.40757	-0.9546	10	0.02654	T	1	-9.6494	6.2343	0.20754	0.0:0.7729:0.0:0.2271	.	581;453	E7EPS0;Q5HYK9	.;ZN667_HUMAN	S	581;453;453;235;168	ENSP00000344699:G581S;ENSP00000439402:G453S;ENSP00000292069:G453S	ENSP00000292069:G453S	G	-	1	0	ZNF667	61644819	0.000000	0.05858	0.899000	0.35326	0.001000	0.01503	0.312000	0.19397	1.339000	0.45563	-0.140000	0.14226	GGC		0.368	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		T	56953007	C	T	56953007	3	4	34	1	0	0	0	0	1	0	0	0	18113	652	23	1	479	1	ZNF667	19	56953007	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	1556327	56953007	2175976	64	2862										
SUN5	140732	hgsc.bcm.edu	37	chr20	31590400	31590400	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	agtatatacgtacacacacaTcccagcatgcactgagtcag	7	12	1	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr20:31590400T>A	ENST00000356173.3	-	3	296	c.204A>T	c.(202-204)ggA>ggT	p.G68G	SUN5_ENST00000375519.2_Silent_p.G68G|SUN5_ENST00000375523.3_Intron	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5	68					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.G68G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						TACACACACATCCCAGCATGC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	20											196	143	161					20																	31590400		2203	4300	6503	31054061	SO:0001819	synonymous_variant	140732			AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"testis and spermatogenesis related gene 4"	613942	"sperm associated antigen 4-like"	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.204A>T	20.37:g.31590400T>A			31054061	A6NJ82|Q5T9R0	Silent	SNP	ENST00000356173.3	37	CCDS13209.1																																																																																				0.552	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675		A	31590400	T	A	31590400	2	1	34	1	0	0	0	0	0	0	0	1	15433	1422	50	5		5	SUN5	20	31590400	Silent	SNP	T	TCGA-AG-3612-01A-01W-0833-10		31590400	31435120	65	2863										
KCNB1	3745	hgsc.bcm.edu	37	chr20	47990392	47990392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gcgagtgggcagaggggctaCggggctggggatactctcca	19	9	1	1	rs376490656		TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr20:47990392C>T	ENST00000371741.4	-	2	1871	c.1705G>A	c.(1705-1707)Gta>Ata	p.V569I		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	569					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)	p.V569I(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	AGAGGGGCTACGGGGCTGGGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	ILE/VAL	0,4406		0,0,2203	97	86	90		1705	-0.3	0	20		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNB1	NM_004975.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	569/859	47990392	1,13005	2203	4300	6503	47423799	SO:0001583	missense	3745			AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1705G>A	20.37:g.47990392C>T	ENSP00000360806:p.Val569Ile		47423799	Q14193	Missense_Mutation	SNP	ENST00000371741.4	37	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	C	4.218	0.039215	0.08148	0.0	1.16E-4	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.22945	1.93	6.07	-0.292	0.12839	.	2.114130	0.01750	N	0.029865	T	0.22399	0.0540	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31223	-0.9951	10	0.36615	T	0.2	.	11.1674	0.48552	0.0:0.4126:0.0:0.5874	.	569	Q14721	KCNB1_HUMAN	I	569;524	ENSP00000360806:V569I	ENSP00000360806:V569I	V	-	1	0	KCNB1	47423799	0.000000	0.05858	0.006000	0.13384	0.711000	0.40976	-0.038000	0.12144	-0.248000	0.09583	0.655000	0.94253	GTA		0.522	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		T	47990392	C	T	47990392	3	4	34	1	0	0	0	0	1	0	0	0	8033	536	19	1	875	1	KCNB1	20	47990392	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	16399992	47990392	15035128	66	2864										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62044879	62044879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	ctcgatgacgtccatcacgtCgtagggccgcaggctctcct	11	15	2	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chr20:62044879C>T	ENST00000359125.2	-	15	1861	c.1687G>A	c.(1687-1689)Gac>Aac	p.D563N	KCNQ2_ENST00000344462.4_Missense_Mutation_p.D532N|KCNQ2_ENST00000359689.1_Missense_Mutation_p.D563N|KCNQ2_ENST00000357249.2_Missense_Mutation_p.D545N|KCNQ2_ENST00000360480.3_Missense_Mutation_p.D535N|KCNQ2_ENST00000370224.1_Missense_Mutation_p.D535N|KCNQ2_ENST00000354587.3_Missense_Mutation_p.D535N	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	563					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.D563N(2)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCCATCACGTCGTAGGGCCGC	0.642																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	20											111	100	104					20																	62044879		2203	4300	6503	61515323	SO:0001583	missense	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1687G>A	20.37:g.62044879C>T	ENSP00000352035:p.Asp563Asn		61515323	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	c	26.7	4.758246	0.89843	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	D;D;D;D;D;D;D;D;D;D	0.99886	-7.52;-7.52;-7.52;-7.52;-7.52;-7.52;-7.52;-7.52;-7.52;-7.52	4.99	4.99	0.66335	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.054789	0.64402	D	0.000001	D	0.99894	0.9949	M	0.87547	2.89	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	D	0.96075	0.9049	10	0.87932	D	0	-21.3948	18.2551	0.90017	0.0:1.0:0.0:0.0	.	535;545;532;563	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	N	545;563;533;535;563;532;535;523;535;535	ENSP00000349789:D545N;ENSP00000352035:D563N;ENSP00000359246:D533N;ENSP00000346601:D535N;ENSP00000352718:D563N;ENSP00000399612:D532N;ENSP00000353668:D535N;ENSP00000339611:D523N;ENSP00000359244:D535N;ENSP00000359242:D535N	ENSP00000339611:D523N	D	-	1	0	KCNQ2	61515323	1.000000	0.71417	0.600000	0.28864	0.493000	0.33554	7.660000	0.83776	2.323000	0.78572	0.556000	0.70494	GAC		0.642	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		T	62044879	C	T	62044879	3	4	34	1	0	0	0	0	1	0	0	0	8104	884	31	1	943	1	KCNQ2	20	62044879	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	14054487	62044879	980641	67	2865										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5821193	5821193	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	cgttcttggaaaagttacaaCtgaagagctcggtgggaccg	13	8	1	2			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chrX:5821193C>A	ENST00000381095.3	-	5	2153	c.1526G>T	c.(1525-1527)aGt>aTt	p.S509I	NLGN4X_ENST00000275857.6_Missense_Mutation_p.S509I|NLGN4X_ENST00000381093.2_Missense_Mutation_p.S529I|NLGN4X_ENST00000381092.1_Missense_Mutation_p.S509I|NLGN4X_ENST00000538097.1_Missense_Mutation_p.S509I	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	509					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.S509I(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						AAAGTTACAACTGAAGAGCTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	90	96					X																	5821193		2203	4300	6503	5831193	SO:0001583	missense	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1526G>T	X.37:g.5821193C>A	ENSP00000370485:p.Ser509Ile		5831193	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	37	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	C	9.460	1.092826	0.20471	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25	3.8	3.8	0.43715	Carboxylesterase, type B (1);	.	.	.	.	T	0.56514	0.1990	L	0.39566	1.225	0.32066	N	0.595033	B;B;B	0.23990	0.095;0.047;0.008	B;B;B	0.31101	0.088;0.124;0.053	T	0.62845	-0.6768	9	0.72032	D	0.01	.	5.4324	0.16460	0.0:0.7351:0.0:0.2649	.	566;509;529	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	I	509;529;509;509;509	ENSP00000370485:S509I;ENSP00000370483:S529I;ENSP00000275857:S509I;ENSP00000370482:S509I;ENSP00000439203:S509I	ENSP00000275857:S509I	S	-	2	0	NLGN4X	5831193	1.000000	0.71417	1.000000	0.80357	0.526000	0.34562	1.336000	0.33850	1.512000	0.48834	0.513000	0.50165	AGT		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5821193	C	A	5821193	3	1	34	1	0	0	0	0	1	0	0	0	10495	565	20	2	932	2	NLGN4X	23	5821193	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10		5821193	149449367	68	2866										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148936	34148936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gcgagtggagactggacctcCgacgtgtcttgggatgttcc	15	10	1	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chrX:34148936C>T	ENST00000346193.3	-	1	1511	c.1460G>A	c.(1459-1461)cGg>cAg	p.R487Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	487								p.R487Q(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						ACTGGACCTCCGACGTGTCTT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	X											47	54	51					X																	34148936		2192	4286	6478	34058857	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1460G>A	X.37:g.34148936C>T	ENSP00000345029:p.Arg487Gln		34058857	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	9.489	1.100058	0.20552	.	.	ENSG00000185448	ENST00000346193	T	0.16196	2.36	0.446	0.446	0.16602	.	.	.	.	.	T	0.10380	0.0254	N	0.24115	0.695	0.09310	N	1	D	0.62365	0.991	P	0.44811	0.461	T	0.23762	-1.0179	8	0.13470	T	0.59	.	.	.	.	.	487	Q5JRC9	FA47A_HUMAN	Q	487	ENSP00000345029:R487Q	ENSP00000345029:R487Q	R	-	2	0	FAM47A	34058857	0.022000	0.18835	0.006000	0.13384	0.016000	0.09150	0.010000	0.13242	0.435000	0.26365	0.183000	0.17082	CGG		0.642	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148936	C	T	34148936	3	4	34	1	0	0	0	0	1	0	0	0	5588	652	23	1	919	1	FAM47A	23	34148936	Missense_Mutation	SNP	C	TCGA-AG-3612-01A-01W-0833-10	28327743	34148936	121121624	69	2867										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35985861	35985861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	gcactcacaatcatcgctcaTgtgaagagccagtgaaggat	10	10	3	3			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chrX:35985861T>C	ENST00000297866.5	+	10	1792	c.1726T>C	c.(1726-1728)Tgt>Cgt	p.C576R		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	576								p.C576R(2)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						TCATCGCTCATGTGAAGAGCC	0.433													T|||	1	0.000264901	8e-04	0	3775	,	,		9084	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	X											126	94	105					X																	35985861		2202	4300	6502	35895782	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1726T>C	X.37:g.35985861T>C	ENSP00000297866:p.Cys576Arg		35895782	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	1.603	-0.526150	0.04141	.	.	ENSG00000165164	ENST00000297866	T	0.12879	2.64	5.35	-2.03	0.07365	.	1.723700	0.02720	N	0.113892	T	0.06188	0.0160	N	0.12182	0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.22556	-1.0213	10	0.14656	T	0.56	-24.162	0.3028	0.00275	0.3888:0.1361:0.1986:0.2765	.	576	Q6ZTR5	CX022_HUMAN	R	576	ENSP00000297866:C576R	ENSP00000297866:C576R	C	+	1	0	CXorf22	35895782	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.269000	0.18589	-0.869000	0.04052	-1.266000	0.01441	TGT		0.433	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35985861	T	C	35985861	3	2	34	1	0	0	0	0	1	0	0	0	4108	1464	51	4	1764	4	CXorf22	23	35985861	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	1836925	35985861	119284699	70	2868										
GPR112	139378	hgsc.bcm.edu	37	chrX	135431746	135431746	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	acccttcattatcaacatctTtaagagctatcacttccaca	2	13	4	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chrX:135431746T>C	ENST00000394143.1	+	6	6172	c.5881T>C	c.(5881-5883)Tta>Cta	p.L1961L	GPR112_ENST00000370652.1_Silent_p.L1961L|GPR112_ENST00000412101.1_Silent_p.L1756L|GPR112_ENST00000287534.4_Silent_p.L1898L|GPR112_ENST00000394141.1_Silent_p.L1756L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1961					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L1961L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ATCAACATCTTTAAGAGCTAT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	X											105	100	101					X																	135431746		2203	4299	6502	135259412	SO:0001819	synonymous_variant	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5881T>C	X.37:g.135431746T>C			135259412	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																				0.413	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135431746	T	C	135431746	2	2	34	1	0	0	0	0	0	0	0	1	6649	1838	64	4		4	GPR112	23	135431746	Silent	SNP	T	TCGA-AG-3612-01A-01W-0833-10	99445885	135431746	19838814	71	2869										
MCF2	4168	hgsc.bcm.edu	37	chrX	138701838	138701838	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.111111111111111	8	1	1.37029337029337	5.34414414414414	0.785903550609433	1	1	0	agccagttctgcttgttggtTtaatagaaattcaacttcag	8	7	3	1			TCGA-AG-3612-01A-01W-0833-10	TCGA-AG-3612-10A-01W-0833-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	93a27bfa-33be-4eec-863e-5c85a11493e2	e350ce5e-3bd3-4c1a-a212-a3b2294e180c	g.chrX:138701838T>G	ENST00000370576.4	-	7	924	c.715A>C	c.(715-717)Aac>Cac	p.N239H	MCF2_ENST00000520602.1_Missense_Mutation_p.N299H|MCF2_ENST00000370578.4_Missense_Mutation_p.N384H|MCF2_ENST00000536274.1_Missense_Mutation_p.N200H|MCF2_ENST00000338585.6_Missense_Mutation_p.N239H|MCF2_ENST00000370573.4_Missense_Mutation_p.N239H|MCF2_ENST00000414978.1_Missense_Mutation_p.N299H|MCF2_ENST00000519895.1_Missense_Mutation_p.N299H	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	239					apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N239H(1)|p.N299H(1)		NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					GCTTGTTGGTTTAATAGAAAT	0.289																																																2	Substitution - Missense(2)	large_intestine(2)	X											37	35	35					X																	138701838		2202	4282	6484	138529504	SO:0001583	missense	4168				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.715A>C	X.37:g.138701838T>G	ENSP00000359608:p.Asn239His		138529504	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.553508	0.45487	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.2	2.49	0.30216	.	1.080410	0.06815	N	0.791067	T	0.41994	0.1183	L	0.36672	1.1	0.09310	N	1	P;P;P;P;P;P;P;P	0.50943	0.79;0.939;0.867;0.79;0.681;0.79;0.94;0.79	P;P;P;P;P;P;P;P	0.53062	0.492;0.525;0.6;0.492;0.6;0.492;0.717;0.492	T	0.25676	-1.0125	10	0.48119	T	0.1	.	2.3296	0.04232	0.0:0.213:0.2928:0.4942	.	299;384;200;239;239;384;239;239	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	H	299;239;200;384;299;299;239;239	ENSP00000427745:N299H;ENSP00000359608:N239H;ENSP00000438155:N200H;ENSP00000359610:N384H;ENSP00000397055:N299H;ENSP00000430276:N299H;ENSP00000359605:N239H;ENSP00000342204:N239H	ENSP00000342204:N239H	N	-	1	0	MCF2	138529504	0.151000	0.22747	0.010000	0.14722	0.182000	0.23217	1.540000	0.36115	0.711000	0.32018	-0.378000	0.06908	AAC		0.289	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		G	138701838	T	G	138701838	3	3	34	1	0	0	0	0	1	0	0	0	9408	1841	64	4	2218	4	MCF2	23	138701838	Missense_Mutation	SNP	T	TCGA-AG-3612-01A-01W-0833-10	3270092	138701838	16568722	72	2870										
PTPRU	10076	broad.mit.edu	37	chr1	29642617	29642617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cacctacaaggagatgatccGcattgatcctcagagtaatt	8	10	1	4			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:29642617G>A	ENST00000345512.3	+	25	3626	c.3497G>A	c.(3496-3498)cGc>cAc	p.R1166H	PTPRU_ENST00000428026.2_Missense_Mutation_p.R1153H|PTPRU_ENST00000356870.3_Missense_Mutation_p.R1162H|PTPRU_ENST00000460170.2_Missense_Mutation_p.R1162H|PTPRU_ENST00000323874.8_Missense_Mutation_p.R1162H|PTPRU_ENST00000373779.3_Missense_Mutation_p.R1156H	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1166					canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R1166H(2)|p.R1162H(2)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GAGATGATCCGCATTGATCCT	0.527																																																4	Substitution - Missense(4)	endometrium(3)|large_intestine(1)	1											146	108	120					1																	29642617		2203	4300	6503	29515204	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3497G>A	1.37:g.29642617G>A	ENSP00000334941:p.Arg1166His		29515204	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425034	0.83667	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52	4.51	4.51	0.55191	.	0.076076	0.52532	D	0.000079	T	0.29288	0.0729	M	0.75264	2.295	0.45066	D	0.998085	D;D;D;D;D	0.64830	0.994;0.994;0.994;0.99;0.99	P;P;P;P;P	0.57846	0.828;0.828;0.828;0.677;0.677	T	0.01030	-1.1475	9	.	.	.	.	10.3953	0.44196	0.0899:0.0:0.9101:0.0	.	1153;1162;1156;1162;1166	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	H	1166;1156;1162;1162;1153;1162	ENSP00000334941:R1166H;ENSP00000362884:R1156H;ENSP00000349333:R1162H;ENSP00000314987:R1162H;ENSP00000392332:R1153H;ENSP00000432906:R1162H	.	R	+	2	0	PTPRU	29515204	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.603000	0.67619	2.498000	0.84270	0.561000	0.74099	CGC		0.527	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29642617	G	A	29642617	3	1	35	1	0	0	0	0	1	0	0	0	12850	1087	38	1	3617	1	PTPRU	1	29642617	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10		29642617	219608004	1	2871										
KPNA6	23633	broad.mit.edu	37	chr1	32623933	32623933	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tggatcggttcgtggagtttCtgaagaggaatgagaattgt	15	3	1	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:32623933C>A	ENST00000373625.3	+	5	490	c.397C>A	c.(397-399)Ctg>Atg	p.L133M	KPNA6_ENST00000469790.1_3'UTR|KPNA6_ENST00000545542.1_Missense_Mutation_p.L138M|KPNA6_ENST00000537234.1_Missense_Mutation_p.L130M	NM_012316.4	NP_036448.1	O60684	IMA7_HUMAN	karyopherin alpha 6 (importin alpha 7)	133					maternal process involved in female pregnancy (GO:0060135)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.L133M(1)		large_intestine(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				CGTGGAGTTTCTGAAGAGGAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	170	169					1																	32623933		2203	4300	6503	32396520	SO:0001583	missense	23633			AF060543	CCDS352.1	1p35.1	2013-02-14			ENSG00000025800	ENSG00000025800		"Importins", "Armadillo repeat containing"	6399	protein-coding gene	gene with protein product		610563				10523667	Standard	NM_012316		Approved	IPOA7, KPNA7, MGC17918, FLJ11249	uc001bug.3	O60684	OTTHUMG00000004333	ENST00000373625.3:c.397C>A	1.37:g.32623933C>A	ENSP00000362728:p.Leu133Met		32396520	B2RDC7|D3DPP5|Q5VVU3	De_novo_Start_OutOfFrame	SNP	ENST00000373625.3	37	CCDS352.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789092	0.70337	.	.	ENSG00000025800	ENST00000373625;ENST00000373617;ENST00000537234;ENST00000545542;ENST00000446515	D;D;D;T	0.83837	-1.77;-1.77;-1.77;0.5	5.21	4.29	0.51040	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90731	0.7091	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.97110	1.0;1.0;0.985	D	0.91561	0.5264	10	0.59425	D	0.04	-6.0512	14.1683	0.65493	0.0:0.927:0.0:0.073	.	138;138;133	F5GYL8;B4DWX3;O60684	.;.;IMA7_HUMAN	M	133;107;130;138;84	ENSP00000362728:L133M;ENSP00000444930:L130M;ENSP00000440609:L138M;ENSP00000415677:L84M	ENSP00000362719:L107M	L	+	1	2	KPNA6	32396520	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.192000	0.50989	1.335000	0.45486	0.561000	0.74099	CTG		0.403	KPNA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012527.4	NM_012316		A	32623933	C	A	32623933	3	1	35	1	0	0	0	0	1	0	0	0	8455	912	32	2	415	2	KPNA6	1	32623933	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	2981316	32623933	216626688	2	2872										
LPPR5	163404	broad.mit.edu	37	chr1	99422174	99422174	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tgaacacataccaagaaatcGgacagttcggcgcaccagcg	10	12	0	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:99422174G>A	ENST00000263177.4	-	2	582	c.361C>T	c.(361-363)Cga>Tga	p.R121*	LPPR5_ENST00000370188.3_Nonsense_Mutation_p.R121*	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		121						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.R121*(2)									CCAAGAAATCGGACAGTTCGG	0.358																																																2	Substitution - Nonsense(2)	large_intestine(1)|central_nervous_system(1)	1											55	59	58					1																	99422174		2202	4300	6502	99194762	SO:0001587	stop_gained	163404																														ENST00000263177.4:c.361C>T	1.37:g.99422174G>A	ENSP00000263177:p.Arg121*		99194762	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Nonsense_Mutation	SNP	ENST00000263177.4	37	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	G	38	6.889546	0.97912	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	.	.	.	4.74	3.8	0.43715	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.9165	0.52767	0.0:0.0:0.5615:0.4385	.	.	.	.	X	121	.	ENSP00000263177:R121X	R	-	1	2	AL161744.1	99194762	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.382000	0.44345	1.064000	0.40671	0.591000	0.81541	CGA		0.358	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			A	99422174	G	A	99422174	4	1	35	1	0	0	0	0	0	1	0	0	8957	1124	39	1	624	1	LPPR5	1	99422174	Nonsense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	66798241	99422174	149828447	3	2873										
CDC14A	8556	broad.mit.edu	37	chr1	100933607	100933607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttgcttggattagaatatgcCggccaggctctattatagga	11	7	1	1	rs148737918		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:100933607C>T	ENST00000336454.3	+	10	1289	c.934C>T	c.(934-936)Cgg>Tgg	p.R312W	CDC14A_ENST00000361544.6_Missense_Mutation_p.R312W|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000370124.3_Missense_Mutation_p.R312W|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000544534.1_Missense_Mutation_p.R312W|CDC14A_ENST00000542213.1_Missense_Mutation_p.R254W	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	312	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R312W(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		TAGAATATGCCGGCCAGGCTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	161	165	163		934,934,934	5	1	1	dbSNP_134	163	0,8600		0,0,4300	no	missense,missense,missense	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	312/595,312/624,312/384	100933607	1,13005	2203	4300	6503	100706195	SO:0001583	missense	8556			AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.934C>T	1.37:g.100933607C>T	ENSP00000336739:p.Arg312Trp		100706195	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	37	CCDS769.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.219878	0.58560	2.27E-4	0.0	ENSG00000079335	ENST00000542213;ENST00000361544;ENST00000370124;ENST00000336454;ENST00000544534	T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45	4.96	4.96	0.65561	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.82226	0.4991	H	0.99746	4.745	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.89360	0.3667	10	0.87932	D	0	-7.6366	13.2024	0.59776	0.1594:0.8406:0.0:0.0	.	254;312;312;312;312	F5H7B3;A6MA65;Q9UNH5;Q9UNH5-2;Q52LH9	.;.;CC14A_HUMAN;.;.	W	254;312;312;312;312	ENSP00000442640:R254W;ENSP00000354916:R312W;ENSP00000359142:R312W;ENSP00000336739:R312W;ENSP00000442543:R312W	ENSP00000336739:R312W	R	+	1	2	CDC14A	100706195	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	1.949000	0.40313	2.290000	0.77057	0.591000	0.81541	CGG		0.418	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		T	100933607	C	T	100933607	3	4	35	1	0	0	0	0	1	0	0	0	3062	643	23	1	972	1	CDC14A	1	100933607	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1511433	100933607	148317014	4	2874										
VCAM1	7412	broad.mit.edu	37	chr1	101196837	101196837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	taagctgcaaggttcctagcGtgtacccccttgaccggctg	11	13	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:101196837G>A	ENST00000294728.2	+	6	1389	c.1288G>A	c.(1288-1290)Gtg>Atg	p.V430M	VCAM1_ENST00000370115.1_Intron|VCAM1_ENST00000347652.2_Missense_Mutation_p.V338M|VCAM1_ENST00000370119.4_Missense_Mutation_p.V368M	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	430	Ig-like C2-type 5.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)	p.V430M(2)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	GGTTCCTAGCGTGTACCCCCT	0.468																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	1											68	71	70					1																	101196837		2203	4300	6503	100969425	SO:0001583	missense	7412			M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1288G>A	1.37:g.101196837G>A	ENSP00000294728:p.Val430Met		100969425	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581859	0.46006	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728	T;T;T	0.26957	1.7;1.7;1.7	5.52	4.58	0.56647	Immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.126553	0.52532	D	0.000063	T	0.44540	0.1298	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	T	0.26744	-1.0094	10	0.41790	T	0.15	-19.2323	13.2468	0.60028	0.0746:0.0:0.9254:0.0	.	368;338;430	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	M	368;338;430	ENSP00000359137:V368M;ENSP00000304611:V338M;ENSP00000294728:V430M	ENSP00000294728:V430M	V	+	1	0	VCAM1	100969425	1.000000	0.71417	0.968000	0.41197	0.025000	0.11179	6.029000	0.70895	2.873000	0.98535	0.563000	0.77884	GTG		0.468	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		A	101196837	G	A	101196837	3	1	35	1	0	0	0	0	1	0	0	0	17177	1145	40	1	1310	1	VCAM1	1	101196837	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	263230	101196837	148053784	5	2875										
SPAG17	200162	broad.mit.edu	37	chr1	118629592	118629592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tgctctgggggatggctcccGcagactgggtgggacgagat	18	9	1	2	rs139343615	byFrequency	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:118629592G>A	ENST00000336338.5	-	11	1464	c.1399C>T	c.(1399-1401)Cgg>Tgg	p.R467W		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	467						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.R467W(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GATGGCTCCCGCAGACTGGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	125	121	123		1399	1.6	0.2	1	dbSNP_134	123	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	101	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	possibly-damaging	467/2224	118629592	4,13002	2203	4300	6503	118431115	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1399C>T	1.37:g.118629592G>A	ENSP00000337804:p.Arg467Trp		118431115	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632467	0.46944	9.08E-4	0.0	ENSG00000155761	ENST00000336338	T	0.18502	2.21	4.76	1.59	0.23543	.	1.188320	0.05901	N	0.630029	T	0.05227	0.0139	L	0.29908	0.895	0.22521	N	0.999025	D	0.56968	0.978	B	0.40101	0.319	T	0.35919	-0.9769	10	0.66056	D	0.02	.	8.6773	0.34187	0.0:0.5932:0.3206:0.0862	.	467	Q6Q759	SPG17_HUMAN	W	467	ENSP00000337804:R467W	ENSP00000337804:R467W	R	-	1	2	SPAG17	118431115	0.000000	0.05858	0.241000	0.24154	0.829000	0.46940	-0.079000	0.11357	0.690000	0.31570	0.563000	0.77884	CGG		0.517	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118629592	G	A	118629592	3	1	35	1	0	0	0	0	1	0	0	0	15018	1086	38	1	5424	1	SPAG17	1	118629592	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	17432755	118629592	130621029	6	2876										
MTX1	4580	broad.mit.edu	37	chr1	155182266	155182266	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cctttcccctcaacttcttcCtgcctggccgcatgcagcgg	8	18	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:155182266C>G	ENST00000368376.3	+	5	968	c.862C>G	c.(862-864)Ctg>Gtg	p.L288V	MTX1_ENST00000495589.1_3'UTR|MTX1_ENST00000609421.1_Missense_Mutation_p.L139V|MTX1_ENST00000316721.4_Missense_Mutation_p.L257V|GBAP1_ENST00000486869.1_RNA|RP11-263K19.6_ENST00000455788.1_RNA	NM_002455.3	NP_002446.2	Q13505	MTX1_HUMAN	metaxin 1	288					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)		p.L288V(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)			CAACTTCTTCCTGCCTGGCCG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	46	46					1																	155182266		2203	4297	6500	153448890	SO:0001583	missense	4580				CCDS1100.1, CCDS1101.1	1q21	2008-07-18			ENSG00000173171	ENSG00000173171			7504	protein-coding gene	gene with protein product		600605		MTX		7753840	Standard	XM_006711338		Approved	MTXN	uc001fjb.3	Q13505	OTTHUMG00000035708	ENST00000368376.3:c.862C>G	1.37:g.155182266C>G	ENSP00000357360:p.Leu288Val		153448890	B1AVR9|B1AVS0|B2R9P4|Q9BUU3	Missense_Mutation	SNP	ENST00000368376.3	37	CCDS1100.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.75|14.75	2.629138|2.629138	0.46944|0.46944	.|.	.|.	ENSG00000173171|ENSG00000173171	ENST00000368376;ENST00000316721|ENST00000424959	T;T|.	0.33438|.	1.44;1.41|.	4.61|4.61	3.69|3.69	0.42338|0.42338	Glutathione S-transferase, C-terminal-like (1);|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.47377|0.47377	0.1442|0.1442	L|L	0.56340|0.56340	1.77|1.77	0.40726|0.40726	D|D	0.982701|0.982701	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.997;0.999|.	T|T	0.45644|0.45644	-0.9247|-0.9247	10|5	0.52906|.	T|.	0.07|.	-9.1266|-9.1266	10.4309|10.4309	0.44407|0.44407	0.0:0.9024:0.0:0.0976|0.0:0.9024:0.0:0.0976	.|.	257;288|.	Q13505-2;Q13505|.	.;MTX1_HUMAN|.	V|R	288;257|150	ENSP00000357360:L288V;ENSP00000317106:L257V|.	ENSP00000317106:L257V|.	L|P	+|+	1|2	2|0	MTX1|MTX1	153448890|153448890	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.053000|1.053000	0.30442|0.30442	1.049000|1.049000	0.40321|0.40321	0.563000|0.563000	0.77884|0.77884	CTG|CCT		0.557	MTX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086844.1	NM_198883		G	155182266	C	G	155182266	3	3	35	1	0	0	0	0	1	0	0	0	9997	680	24	5	880	5	MTX1	1	155182266	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	36552674	155182266	94068355	7	2877										
FCRLA	84824	broad.mit.edu	37	chr1	161681039	161681039	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cagccaagccagtttttgaaGgggacctgctggttctgcgc	13	11	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:161681039G>A	ENST00000236938.6	+	3	567	c.325G>A	c.(325-327)Ggg>Agg	p.G109R	FCRLA_ENST00000367959.2_Missense_Mutation_p.G115R|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000540926.1_Missense_Mutation_p.G98R|FCRLA_ENST00000349527.4_Missense_Mutation_p.G92R|FCRLA_ENST00000309691.6_Intron|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367950.1_Intron|FCRLA_ENST00000367957.2_Intron|FCRLA_ENST00000294796.4_Intron|FCRLA_ENST00000540521.1_Intron|FCRLA_ENST00000546024.1_Intron|FCRLA_ENST00000367953.3_Missense_Mutation_p.G98R|FCRLA_ENST00000350710.3_Intron	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	92	Ig-like C2-type 1.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.G92R(1)		breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			AGTTTTTGAAGGGGACCTGCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1											36	39	38					1																	161681039		2203	4300	6503	159947663	SO:0001583	missense	84824			AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18504	protein-coding gene	gene with protein product		606891	"Fc receptor-like and mucin-like 1"	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.325G>A	1.37:g.161681039G>A	ENSP00000236938:p.Gly109Arg		159947663	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092924	0.56075	.	.	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000540926;ENST00000349527;ENST00000367953	T;T;T;T;T	0.01484	4.84;4.84;4.84;4.84;4.84	4.99	4.99	0.66335	.	0.000000	0.46442	D	0.000286	T	0.11537	0.0281	H	0.96111	3.77	0.43003	D	0.994521	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	T	0.00875	-1.1531	10	0.87932	D	0	.	13.6413	0.62253	0.0:0.0:1.0:0.0	.	115;109	A6NC03;Q7L513-9	.;.	R	109;115;98;92;98	ENSP00000236938:G109R;ENSP00000356936:G115R;ENSP00000446380:G98R;ENSP00000294798:G92R;ENSP00000356930:G98R	ENSP00000236938:G109R	G	+	1	0	FCRLA	159947663	1.000000	0.71417	1.000000	0.80357	0.203000	0.24098	4.487000	0.60293	2.568000	0.86640	0.655000	0.94253	GGG		0.617	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738		A	161681039	G	A	161681039	3	1	35	1	0	0	0	0	1	0	0	0	5819	1000	35	3	357	3	FCRLA	1	161681039	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	6498773	161681039	87569582	8	2878										
ZNF648	127665	broad.mit.edu	37	chr1	182025960	182025960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agcgaactcccggtcgcaggCggggcagcggaagggcttgg	19	11	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:182025960C>T	ENST00000339948.3	-	2	1393	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A396T(1)		breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CGGTCGCAGGCGGGGCAGCGG	0.721																																					NSCLC(71;908 1374 5429 20458 35642)											1	Substitution - Missense(1)	large_intestine(1)	1											17	18	17					1																	182025960		2159	4220	6379	180292583	SO:0001583	missense	127665			AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.1186G>A	1.37:g.182025960C>T	ENSP00000344129:p.Ala396Thr		180292583	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	C	9.855	1.194752	0.22037	.	.	ENSG00000179930	ENST00000339948	T	0.18016	2.24	2.81	-0.706	0.11249	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05410	0.0143	N	0.02334	-0.595	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.34054	-0.9844	9	0.49607	T	0.09	.	1.5293	0.02532	0.2051:0.2796:0.3727:0.1426	.	396	Q5T619	ZN648_HUMAN	T	396	ENSP00000344129:A396T	ENSP00000344129:A396T	A	-	1	0	ZNF648	180292583	0.000000	0.05858	0.092000	0.20876	0.992000	0.81027	0.655000	0.24933	-0.134000	0.11516	0.561000	0.74099	GCC		0.721	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		T	182025960	C	T	182025960	3	4	35	1	0	0	0	0	1	0	0	0	18102	768	27	1	524	1	ZNF648	1	182025960	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	20344921	182025960	67224661	9	2879										
KDM5B	10765	broad.mit.edu	37	chr1	202705510	202705510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gtgtgtctaacactggcacaCgtcctccagcctaataagtc	8	13	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:202705510C>T	ENST00000367265.3	-	21	4259	c.3095G>A	c.(3094-3096)cGt>cAt	p.R1032H	KDM5B_ENST00000367264.2_Missense_Mutation_p.R1068H	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1032					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R1032H(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						CACTGGCACACGTCCTCCAGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	75	77					1																	202705510		2203	4300	6503	200972133	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3095G>A	1.37:g.202705510C>T	ENSP00000356234:p.Arg1032His		200972133	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.134007	0.37630	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.40756	1.02;1.02;1.02	5.66	5.66	0.87406	Lysine-specific demethylase-like domain (1);	0.098509	0.64402	D	0.000002	T	0.28830	0.0715	N	0.16602	0.42	0.58432	D	0.99999	D;B	0.53885	0.963;0.024	B;B	0.42692	0.395;0.018	T	0.10520	-1.0626	10	0.02654	T	1	-20.0717	20.1253	0.97977	0.0:1.0:0.0:0.0	.	1068;1032	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	H	1032;874;1068;874	ENSP00000356234:R1032H;ENSP00000356233:R1068H;ENSP00000235790:R874H	ENSP00000235790:R874H	R	-	2	0	KDM5B	200972133	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	2.832000	0.97577	0.655000	0.94253	CGT		0.413	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		T	202705510	C	T	202705510	3	4	35	1	0	0	0	0	1	0	0	0	8155	536	19	1	1567	1	KDM5B	1	202705510	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	20679550	202705510	46545111	10	2880										
DYRK3	8444	broad.mit.edu	37	chr1	206821586	206821586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tctcctgaaacaccacgggcGcagttcaaccaaggtcattg	9	13	3	1	rs200323668		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:206821586G>A	ENST00000367109.2	+	3	1211	c.1043G>A	c.(1042-1044)cGc>cAc	p.R348H	DYRK3_ENST00000367106.1_Missense_Mutation_p.R328H|DYRK3_ENST00000367108.3_Missense_Mutation_p.R328H|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	348	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.R348H(2)|p.R313H(2)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CACCACGGGCGCAGTTCAACC	0.458																																					Melanoma(164;427 2622 26826 51707)											4	Substitution - Missense(4)	large_intestine(2)|lung(2)	1						G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	89	96	94		983,1043	4.2	0.9	1		94	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DYRK3	NM_001004023.1,NM_003582.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	328/569,348/589	206821586	1,13005	2203	4300	6503	204888209	SO:0001583	missense	8444			Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1043G>A	1.37:g.206821586G>A	ENSP00000356076:p.Arg348His		204888209	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	37	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990623	0.35131	0.0	1.16E-4	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000367106	T;T;T	0.20463	2.07;2.07;2.07	5.17	4.24	0.50183	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050585	0.85682	D	0.000000	T	0.27027	0.0662	L	0.31578	0.945	0.80722	D	1	B;D	0.65815	0.139;0.995	B;P	0.54965	0.043;0.765	T	0.02037	-1.1225	10	0.45353	T	0.12	.	14.1405	0.65316	0.0:0.0:0.8488:0.1512	.	348;328	O43781;O43781-2	DYRK3_HUMAN;.	H	348;328;328	ENSP00000356076:R348H;ENSP00000356075:R328H;ENSP00000356073:R328H	ENSP00000356073:R328H	R	+	2	0	DYRK3	204888209	1.000000	0.71417	0.874000	0.34290	0.810000	0.45777	7.760000	0.85248	1.376000	0.46267	0.448000	0.29417	CGC		0.458	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		A	206821586	G	A	206821586	3	1	35	1	0	0	0	0	1	0	0	0	4868	1087	38	1	1074	1	DYRK3	1	206821586	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	4116076	206821586	42429035	11	2881										
MARK1	4139	broad.mit.edu	37	chr1	220826465	220826465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	caacccagagagtgcctgctGcttccccatctgctcacagt	8	16	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:220826465G>T	ENST00000366917.4	+	16	2025	c.1759G>T	c.(1759-1761)Gct>Tct	p.A587S	MARK1_ENST00000366918.4_Missense_Mutation_p.A565S|MARK1_ENST00000402574.1_Missense_Mutation_p.A452S					MAP/microtubule affinity-regulating kinase 1									p.A587S(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		AGTGCCTGCTGCTTCCCCATC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	68	72					1																	220826465		2203	4300	6503	218893088	SO:0001583	missense	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1759G>T	1.37:g.220826465G>T	ENSP00000355884:p.Ala587Ser		218893088		Missense_Mutation	SNP	ENST00000366917.4	37	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874248	0.51695	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.36699	1.24;1.24;1.24	4.64	3.71	0.42584	.	0.249867	0.40064	N	0.001190	T	0.33059	0.0850	L	0.49126	1.545	0.37674	D	0.923245	B;B;B;B	0.15141	0.012;0.004;0.001;0.004	B;B;B;B	0.12837	0.005;0.008;0.001;0.004	T	0.20739	-1.0266	10	0.23891	T	0.37	.	15.0605	0.71947	0.0:0.1428:0.8572:0.0	.	587;452;587;565	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	S	452;565;587	ENSP00000386017:A452S;ENSP00000355885:A565S;ENSP00000355884:A587S	ENSP00000355884:A587S	A	+	1	0	MARK1	218893088	1.000000	0.71417	0.718000	0.30602	0.997000	0.91878	3.454000	0.52986	1.037000	0.40024	0.462000	0.41574	GCT		0.468	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220826465	G	T	220826465	3	4	35	1	0	0	0	0	1	0	0	0	9342	1319	46	2	1821	2	MARK1	1	220826465	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	14004879	220826465	28424156	12	2882										
MARK1	4139	broad.mit.edu	37	chr1	220826676	220826676	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tggtataataagcaaaatcaCatccaaatttgttcgcaggt	7	7	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:220826676C>T	ENST00000366917.4	+	16	2236	c.1970C>T	c.(1969-1971)aCa>aTa	p.T657I	MARK1_ENST00000366918.4_Missense_Mutation_p.T635I|MARK1_ENST00000402574.1_Missense_Mutation_p.T522I					MAP/microtubule affinity-regulating kinase 1									p.T657I(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		AGCAAAATCACATCCAAATTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	64	63					1																	220826676		2203	4300	6503	218893299	SO:0001583	missense	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1970C>T	1.37:g.220826676C>T	ENSP00000355884:p.Thr657Ile		218893299		Missense_Mutation	SNP	ENST00000366917.4	37	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404548	0.83230	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.74315	-0.83;-0.63;0.44	5.34	4.4	0.53042	.	0.000000	0.85682	D	0.000000	D	0.85936	0.5813	M	0.87269	2.87	0.52501	D	0.999954	P;P;D;P	0.58268	0.955;0.504;0.982;0.816	P;B;P;P	0.59703	0.709;0.356;0.862;0.614	D	0.88890	0.3345	10	0.87932	D	0	.	16.07	0.80919	0.0:0.8662:0.1338:0.0	.	657;522;657;635	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	I	522;635;657	ENSP00000386017:T522I;ENSP00000355885:T635I;ENSP00000355884:T657I	ENSP00000355884:T657I	T	+	2	0	MARK1	218893299	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	7.578000	0.82498	2.506000	0.84524	0.462000	0.41574	ACA		0.383	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220826676	C	T	220826676	3	4	35	1	0	0	0	0	1	0	0	0	9342	478	17	3	2032	3	MARK1	1	220826676	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	211	220826676	28423945	13	2883										
WNT3A	89780	broad.mit.edu	37	chr1	228210497	228210497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gagatcatgcccagcgtggcCgagggcatcaagattggcat	14	10	2	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr1:228210497C>T	ENST00000284523.1	+	2	279	c.201C>T	c.(199-201)gcC>gcT	p.A67A	WNT3A_ENST00000366753.2_Silent_p.A67A	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	67					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)	p.A67A(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				CCAGCGTGGCCGAGGGCATCA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	1											58	55	56					1																	228210497		2203	4300	6503	226277120	SO:0001819	synonymous_variant	89780			AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.201C>T	1.37:g.228210497C>T			226277120	Q3SY79|Q3SY80|Q969P2	Silent	SNP	ENST00000284523.1	37	CCDS1564.1																																																																																				0.672	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		T	228210497	C	T	228210497	2	4	35	1	0	0	0	0	0	0	0	1	17429	639	23	1		1	WNT3A	1	228210497	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	7383821	228210497	21040124	14	2884										
C2orf39	92749	broad.mit.edu	37	chr2	26624929	26624929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttgtccacccagattctcgcGccctcggtccactccgacaa	7	18	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:26624929G>A	ENST00000288710.2	+	1	146	c.72G>A	c.(70-72)gcG>gcA	p.A24A		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	24					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.A24A(1)									AGATTCTCGCGCCCTCGGTCC	0.701																																																1	Substitution - coding silent(1)	large_intestine(1)	2											34	30	31					2																	26624929		2203	4300	6503	26478433	SO:0001819	synonymous_variant	92749			AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.72G>A	2.37:g.26624929G>A			26478433	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Silent	SNP	ENST00000288710.2	37	CCDS1723.1																																																																																				0.701	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		A	26624929	G	A	26624929	2	1	35	1	0	0	0	0	0	0	0	1	2170	1074	38	1		1	C2orf39	2	26624929	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10		26624929	216574444	15	2885										
PRKCE	5581	broad.mit.edu	37	chr2	45879362	45879363	+	Nonsense_Mutation	DNP	CA	CA	AG													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	actttccttctcgacccctaCattgccctcaatgtggacga							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:45879362_45879363CA>AG	ENST00000306156.3	+	1	450_451	c.123_124CA>AG	c.(121-126)taCAtt>taAGtt	p.41_42YI>*V		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	41	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)	p.Y41>?(1)	MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	TCGACCCCTACATTGCCCTCAA	0.609																																																1	Complex(1)	large_intestine(1)	2																																								45732867	SO:0001587	stop_gained	5581				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	Exception_encountered	2.37:g.45879362_45879363delinsAG	ENSP00000306124:p.Y41_I42delins*V		45732866	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Nonsense_Mutation	DNP	ENST00000306156.3	37	CCDS1824.1																																																																																				0.609	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			AG	45879363	CA	AG	45879362	4	1	35	1	0	0	0	0	0	1	0	0	12545	489	17	2	125	2	PRKCE	2	45879362	Nonsense_Mutation	DNP	CA	TCGA-AG-3726-01A-02W-0899-10	19254433	45879362	197320011	16	2886										
CYP26B1	56603	broad.mit.edu	37	chr2	72359497	72359497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cgggggaaggtccgtgtggcCagctcaaagcggctggtgct	18	10	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:72359497C>T	ENST00000001146.2	-	6	1601	c.1398G>A	c.(1396-1398)ctG>ctA	p.L466L	CYP26B1_ENST00000412253.1_Silent_p.L275L|CYP26B1_ENST00000546307.1_Silent_p.L391L	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	466					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)	p.L466L(1)		breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						TCCGTGTGGCCAGCTCAAAGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	2											48	42	44					2																	72359497		2203	4300	6503	72213005	SO:0001819	synonymous_variant	56603				CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1398G>A	2.37:g.72359497C>T			72213005	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Silent	SNP	ENST00000001146.2	37	CCDS1919.1																																																																																				0.647	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		T	72359497	C	T	72359497	2	4	35	1	0	0	0	0	0	0	0	1	4162	581	21	3		3	CYP26B1	2	72359497	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	26480135	72359497	170839876	17	2887										
GPR45	11250	broad.mit.edu	37	chr2	105859240	105859240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tctacgccaccagcacctgcGtcctgtggctcagttacctc	8	17	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:105859240G>A	ENST00000258456.1	+	1	1041	c.925G>A	c.(925-927)Gtc>Atc	p.V309I		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V309I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						CAGCACCTGCGTCCTGTGGCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	134	135					2																	105859240		2203	4300	6503	105225672	SO:0001583	missense	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.925G>A	2.37:g.105859240G>A	ENSP00000258456:p.Val309Ile		105225672	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.392572	0.25118	.	.	ENSG00000135973	ENST00000258456	T	0.71222	-0.55	4.63	-1.89	0.07689	GPCR, rhodopsin-like superfamily (1);	0.306652	0.30911	N	0.008634	T	0.49115	0.1538	N	0.22421	0.69	0.18873	N	0.999986	B	0.15473	0.013	B	0.11329	0.006	T	0.30851	-0.9964	10	0.18710	T	0.47	-18.1173	10.3933	0.44185	0.5306:0.0:0.4694:0.0	.	309	Q9Y5Y3	GPR45_HUMAN	I	309	ENSP00000258456:V309I	ENSP00000258456:V309I	V	+	1	0	GPR45	105225672	0.040000	0.19996	0.611000	0.29010	0.983000	0.72400	0.362000	0.20284	-0.504000	0.06577	-0.464000	0.05259	GTC		0.567	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		A	105859240	G	A	105859240	3	1	35	1	0	0	0	0	1	0	0	0	6716	1145	40	1	927	1	GPR45	2	105859240	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	33499743	105859240	137340133	18	2888										
CXCR4	7852	broad.mit.edu	37	chr2	136873184	136873184	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctgccttgcataggaagttcCcaaagtaccagtttgccacg	9	12	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:136873184C>G	ENST00000241393.3	-	2	418	c.314G>C	c.(313-315)gGg>gCg	p.G105A	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.G109A	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	105					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)	p.G109A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	TAGGAAGTTCCCAAAGTACCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	2											146	136	140					2																	136873184		2203	4300	6503	136589654	SO:0001583	missense	7852			AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	2561	protein-coding gene	gene with protein product		162643	"chemokine (C-X-C motif), receptor 4 (fusin)"			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.314G>C	2.37:g.136873184C>G	ENSP00000241393:p.Gly105Ala		136589654	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.96|15.96	2.986497|2.986497	0.53934|0.53934	.|.	.|.	ENSG00000121966|ENSG00000121966	ENST00000409817;ENST00000241393|ENST00000537957	T;T|.	0.50548|.	0.74;0.74|.	5.79|5.79	5.79|5.79	0.91817|0.91817	GPCR, rhodopsin-like superfamily (1);|.	0.095449|0.095449	0.64402|0.64402	D|D	0.000001|0.000001	D|D	0.85682|0.85682	0.5753|0.5753	H|H	0.94542|0.94542	3.55|3.55	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.984|.	D;P|.	0.76071|.	0.987;0.479|.	D|D	0.88851|0.88851	0.3319|0.3319	10|7	0.87932|0.87932	D|D	0|0	.|.	13.2582|13.2582	0.60091|0.60091	0.0:0.9279:0.0:0.0721|0.0:0.9279:0.0:0.0721	.|.	105;109|.	P61073;P61073-2|.	CXCR4_HUMAN;.|.	A|R	109;105|9	ENSP00000386884:G109A;ENSP00000241393:G105A|.	ENSP00000241393:G105A|ENSP00000440311:G9R	G|G	-|-	2|1	0|0	CXCR4|CXCR4	136589654|136589654	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.426000|0.426000	0.31534|0.31534	6.091000|6.091000	0.71406|0.71406	2.734000|2.734000	0.93682|0.93682	0.655000|0.655000	0.94253|0.94253	GGG|GGA		0.542	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			G	136873184	C	G	136873184	3	3	35	1	0	0	0	0	1	0	0	0	4099	623	22	5	748	5	CXCR4	2	136873184	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	31013944	136873184	106326189	19	2889										
CALCRL	10203	broad.mit.edu	37	chr2	188223964	188223964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	attgtaatataagcttctagCaatggcatgtatacaagcag	8	6	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:188223964C>A	ENST00000409998.1	-	12	1598	c.817G>T	c.(817-819)Gct>Tct	p.A273S	AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.A273S|CALCRL_ENST00000410068.1_Missense_Mutation_p.A273S|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	273					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)	p.A273S(1)		endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			AAGCTTCTAGCAATGGCATGT	0.239																																																1	Substitution - Missense(1)	large_intestine(1)	2											21	23	22					2																	188223964		2184	4286	6470	187932209	SO:0001583	missense	10203			U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"GPCR / Class B : Calcitonin receptors"	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.817G>T	2.37:g.188223964C>A	ENSP00000386972:p.Ala273Ser		187932209	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572613	0.65765	.	.	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.36878	1.23;1.23;1.23	5.5	5.5	0.81552	GPCR, family 2-like (1);	0.087235	0.48286	D	0.000193	T	0.41073	0.1143	L	0.49699	1.58	0.80722	D	1	B	0.21520	0.057	B	0.32342	0.144	T	0.21724	-1.0237	10	0.46703	T	0.11	.	18.3984	0.90507	0.0:1.0:0.0:0.0	.	273	Q16602	CALRL_HUMAN	S	273	ENSP00000376177:A273S;ENSP00000386972:A273S;ENSP00000387190:A273S	ENSP00000376177:A273S	A	-	1	0	CALCRL	187932209	1.000000	0.71417	0.997000	0.53966	0.831000	0.47069	5.865000	0.69583	2.599000	0.87857	0.655000	0.94253	GCT		0.239	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		A	188223964	C	A	188223964	3	1	35	1	0	0	0	0	1	0	0	0	2586	710	25	2	588	2	CALCRL	2	188223964	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	51350780	188223964	54975409	20	2890										
ALS2CR8	79800	broad.mit.edu	37	chr2	203846818	203846818	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttgcagttacaaccaaggtaCacctctcctgatgaatcacc	6	13	2	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:203846818C>T	ENST00000402905.3	+	15	2034	c.1713C>T	c.(1711-1713)taC>taT	p.Y571Y	WDR12_ENST00000477723.1_Intron|CARF_ENST00000320443.8_Silent_p.Y571Y|CARF_ENST00000545262.1_Silent_p.Y495Y|CARF_ENST00000438828.2_Silent_p.Y571Y|CARF_ENST00000428585.1_Silent_p.Y495Y|CARF_ENST00000545253.1_Silent_p.Y483Y|CARF_ENST00000414439.1_Silent_p.Y469Y	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	571					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y571Y(1)									AACCAAGGTACACCTCTCCTG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	2											60	55	57					2																	203846818		1844	4107	5951	203555063	SO:0001819	synonymous_variant	79800			AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1713C>T	2.37:g.203846818C>T			203555063	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Silent	SNP	ENST00000402905.3	37	CCDS42801.1																																																																																				0.368	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		T	203846818	C	T	203846818	2	4	35	1	0	0	0	0	0	0	0	1	555	489	17	3		3	ALS2CR8	2	203846818	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	15622854	203846818	39352555	21	2891										
NRP2	8828	broad.mit.edu	37	chr2	206610611	206610611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aggtgctgggctgtgactggAcaggtaagatgacatttcct	14	7	0	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:206610611A>G	ENST00000357785.5	+	10	1814	c.1783A>G	c.(1783-1785)Aca>Gca	p.T595A	NRP2_ENST00000360409.3_Missense_Mutation_p.T595A|NRP2_ENST00000357118.4_Missense_Mutation_p.T595A|NRP2_ENST00000272849.3_Missense_Mutation_p.T595A|NRP2_ENST00000412873.2_Missense_Mutation_p.T595A|NRP2_ENST00000540178.1_Missense_Mutation_p.T595A|NRP2_ENST00000540841.1_Missense_Mutation_p.T595A			Q99435	NELL2_HUMAN	neuropilin 2	288	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T595A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						CTGTGACTGGACAGGTAAGAT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	94	96					2																	206610611		2203	4300	6503	206318856	SO:0001583	missense	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1783A>G	2.37:g.206610611A>G	ENSP00000350432:p.Thr595Ala		206318856	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.643941	0.29246	.	.	ENSG00000118257	ENST00000360409;ENST00000540178;ENST00000540841;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849	D;D;D;D;D;D;D	0.98889	-5.21;-5.21;-5.21;-5.21;-5.21;-5.21;-5.21	5.62	4.47	0.54385	.	0.097167	0.64402	D	0.000001	D	0.95771	0.8624	L	0.43152	1.355	0.80722	D	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	D	0.91694	0.5368	10	0.15952	T	0.53	-5.5747	7.4701	0.27344	0.7852:0.1428:0.072:0.0	.	595;595;595;595;595	O60462-2;O60462-3;O60462;O60462-4;O60462-5	.;.;NRP2_HUMAN;.;.	A	595	ENSP00000353582:T595A;ENSP00000439658:T595A;ENSP00000439261:T595A;ENSP00000349632:T595A;ENSP00000350432:T595A;ENSP00000407626:T595A;ENSP00000272849:T595A	ENSP00000272849:T595A	T	+	1	0	NRP2	206318856	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	3.672000	0.54583	0.962000	0.38057	-0.250000	0.11733	ACA		0.617	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			G	206610611	A	G	206610611	3	3	35	1	0	0	0	0	1	0	0	0	10692	275	10	4	1848	4	NRP2	2	206610611	Missense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	2763793	206610611	36588762	22	2892										
INPP5D	3635	broad.mit.edu	37	chr2	234078674	234078674	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gctttttccttgcattaggcGaaaccaaaactatatgaaca	6	9	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:234078674G>A	ENST00000359570.5	+	17	1619	c.1619G>A	c.(1618-1620)cGa>cAa	p.R540Q	INPP5D_ENST00000450745.1_Missense_Mutation_p.R304Q|INPP5D_ENST00000455936.2_Missense_Mutation_p.R304Q|INPP5D_ENST00000538935.1_Missense_Mutation_p.R539Q			Q92835	SHIP1_HUMAN	inositol polyphosphate-5-phosphatase, 145kDa	552					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|determination of adult lifespan (GO:0008340)|immunoglobulin mediated immune response (GO:0016064)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of bone resorption (GO:0045779)|negative regulation of immune response (GO:0050777)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of neutrophil differentiation (GO:0045659)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of signal transduction (GO:0009968)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of erythrocyte differentiation (GO:0045648)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|membrane (GO:0016020)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)	p.R552Q(2)		central_nervous_system(1)|ovary(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		TGCATTAGGCGAAACCAAAAC	0.547																																					NSCLC(82;1215 1426 16163 20348 41018)											2	Substitution - Missense(2)	large_intestine(2)	2											138	144	142					2																	234078674		2058	4184	6242	233742738	SO:0001583	missense	3635			U57650	CCDS74672.1	2q37.1	2013-02-14	2002-08-29		ENSG00000168918	ENSG00000168918		"SH2 domain containing"	6079	protein-coding gene	gene with protein product		601582	"inositol polyphosphate-5-phosphatase, 145kD"			8643691, 8874179	Standard	NM_001017915		Approved	SHIP, hp51CN	uc010zmp.2	Q92835	OTTHUMG00000133688	ENST00000359570.5:c.1619G>A	2.37:g.234078674G>A	ENSP00000352575:p.Arg540Gln		233742738	O00145|Q13544|Q13545|Q6P5A4|Q92656|Q9UE80	Missense_Mutation	SNP	ENST00000359570.5	37		.	.	.	.	.	.	.	.	.	.	G	31	5.076865	0.94000	.	.	ENSG00000168918	ENST00000359570;ENST00000538935;ENST00000450745;ENST00000455936;ENST00000435188;ENST00000415617;ENST00000445964	D;D;D;D;D;D;D	0.98747	-5.11;-5.11;-5.11;-5.11;-5.11;-5.11;-5.11	4.75	4.75	0.60458	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.134765	0.48767	D	0.000178	D	0.99127	0.9699	.	.	.	0.51767	D	0.999932	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.943	D	0.99698	1.1003	9	0.87932	D	0	.	17.7644	0.88473	0.0:0.0:1.0:0.0	.	551;552	Q92835-2;Q92835	.;SHIP1_HUMAN	Q	540;539;304;304;173;173;173	ENSP00000352575:R540Q;ENSP00000441010:R539Q;ENSP00000407916:R304Q;ENSP00000404610:R304Q;ENSP00000400151:R173Q;ENSP00000397421:R173Q;ENSP00000405338:R173Q	ENSP00000352575:R540Q	R	+	2	0	INPP5D	233742738	1.000000	0.71417	0.904000	0.35570	0.790000	0.44656	9.356000	0.97091	2.192000	0.70111	0.561000	0.74099	CGA		0.547	INPP5D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001017915		A	234078674	G	A	234078674	3	1	35	1	0	0	0	0	1	0	0	0	7777	1058	37	1	1221	1	INPP5D	2	234078674	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	27468063	234078674	9120699	23	2893										
DGKD	8527	broad.mit.edu	37	chr2	234372907	234372907	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	caccccgtggctctgccagtCcgcagagcccggcgacgaag	13	17	1	1	rs575794923		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr2:234372907C>A	ENST00000264057.2	+	27	3296	c.3284C>A	c.(3283-3285)tCc>tAc	p.S1095Y	DGKD_ENST00000409813.3_Missense_Mutation_p.S1051Y	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	1095					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S1095Y(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	CTCTGCCAGTCCGCAGAGCCC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	2											39	47	44					2																	234372907		2203	4300	6503	234037646	SO:0001583	missense	8527			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.3284C>A	2.37:g.234372907C>A	ENSP00000264057:p.Ser1095Tyr		234037646	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	C	0.073	-1.197712	0.01594	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.79940	-1.15;-1.32	4.92	0.965	0.19661	.	0.953100	0.08685	N	0.908918	T	0.66458	0.2791	N	0.19112	0.55	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.12156	0.002;0.007	T	0.55623	-0.8112	10	0.54805	T	0.06	.	6.5207	0.22272	0.0:0.4576:0.0:0.5424	.	1051;1095	Q16760-2;Q16760	.;DGKD_HUMAN	Y	1095;1051	ENSP00000264057:S1095Y;ENSP00000386455:S1051Y	ENSP00000264057:S1095Y	S	+	2	0	DGKD	234037646	0.335000	0.24748	0.052000	0.19188	0.016000	0.09150	2.148000	0.42235	0.328000	0.23435	-0.312000	0.09012	TCC		0.642	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		A	234372907	C	A	234372907	3	1	35	1	0	0	0	0	1	0	0	0	4478	855	30	2	3414	2	DGKD	2	234372907	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	294233	234372907	8826466	24	2894										
GRM7	2917	broad.mit.edu	37	chr3	7340412	7340412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ccgtgagaatcccccaggaaCgcaaagacaggaccattgac	10	13	0	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:7340412C>T	ENST00000357716.4	+	3	1052	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C	GRM7_ENST00000403881.1_Missense_Mutation_p.R260C|GRM7_ENST00000389336.4_Missense_Mutation_p.R260C|GRM7_ENST00000402647.2_Missense_Mutation_p.R260C|GRM7_ENST00000486284.1_Missense_Mutation_p.R260C	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	260					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.R260C(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CCCCCAGGAACGCAAAGACAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											83	82	82					3																	7340412		2203	4299	6502	7315412	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.778C>T	3.37:g.7340412C>T	ENSP00000350348:p.Arg260Cys		7315412	Q8NFS2|Q8NFS3|Q8NFS4	De_novo_Start_OutOfFrame	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.900503	0.72754	.	.	ENSG00000196277	ENST00000448328;ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492	D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	5.32	5.32	0.75619	Extracellular ligand-binding receptor (1);	0.122178	0.56097	D	0.000025	D	0.82995	0.5158	L	0.39898	1.24	0.80722	D	1	D;D;P	0.64830	0.993;0.994;0.773	P;P;B	0.51895	0.555;0.683;0.279	T	0.83056	-0.0150	10	0.44086	T	0.13	.	16.1106	0.81261	0.0:1.0:0.0:0.0	.	260;260;260	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	C	52;260;260;260;260;260;260;260	ENSP00000393799:R52C;ENSP00000350348:R260C;ENSP00000417536:R260C;ENSP00000373987:R260C;ENSP00000385664:R260C;ENSP00000384585:R260C	ENSP00000350348:R260C	R	+	1	0	GRM7	7315412	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	3.900000	0.56295	2.648000	0.89879	0.650000	0.86243	CGC		0.463	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7340412	C	T	7340412	3	4	35	1	0	0	0	0	1	0	0	0	6823	536	19	1	788	1	GRM7	3	7340412	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		7340412	190682018	25	2895										
KCNH8	131096	broad.mit.edu	37	chr3	19554600	19554600	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggggatcttcttcgcgcaacAagaaggttggaagcaataaa	12	7	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:19554600A>C	ENST00000328405.2	+	13	2484	c.2218A>C	c.(2218-2220)Aag>Cag	p.K740Q		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	740					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.K740Q(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						TTCGCGCAACAAGAAGGTTGG	0.542																																					NSCLC(124;1625 1765 8018 24930 42026)											1	Substitution - Missense(1)	large_intestine(1)	3											79	68	72					3																	19554600		2203	4300	6503	19529604	SO:0001583	missense	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2218A>C	3.37:g.19554600A>C	ENSP00000328813:p.Lys740Gln		19529604	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.088807	0.36855	.	.	ENSG00000183960	ENST00000328405	D	0.98649	-5.05	5.78	5.78	0.91487	.	0.000000	0.32671	U	0.005787	D	0.96602	0.8891	L	0.44542	1.39	0.80722	D	1	B	0.23128	0.08	B	0.20384	0.029	D	0.95271	0.8377	9	.	.	.	.	14.3553	0.66733	1.0:0.0:0.0:0.0	.	740	Q96L42	KCNH8_HUMAN	Q	740	ENSP00000328813:K740Q	.	K	+	1	0	KCNH8	19529604	1.000000	0.71417	0.575000	0.28536	0.839000	0.47603	6.021000	0.70832	2.205000	0.71048	0.477000	0.44152	AAG		0.542	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		C	19554600	A	C	19554600	3	2	35	1	0	0	0	0	1	0	0	0	8059	131	5	4	2268	4	KCNH8	3	19554600	Missense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	12214188	19554600	178467830	26	2896										
VILL	50853	broad.mit.edu	37	chr3	38048437	38048437	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tctctcccctgcccagttctAtctctcagactctgacttcc	4	18	5	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:38048437A>C	ENST00000283713.6	+	20	2728	c.2462A>C	c.(2461-2463)tAt>tCt	p.Y821S	VILL_ENST00000383759.2_Missense_Mutation_p.Y821S|VILL_ENST00000465644.1_Missense_Mutation_p.Y539S			O15195	VILL_HUMAN	villin-like	821	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.				actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.Y821S(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GCCCAGTTCTATCTCTCAGAC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											178	188	185					3																	38048437		2203	4300	6503	38023441	SO:0001583	missense	50853				CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.2462A>C	3.37:g.38048437A>C	ENSP00000283713:p.Tyr821Ser		38023441	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	37	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	a	19.73	3.881434	0.72294	.	.	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.27256	2.06;2.06;1.68	3.96	3.96	0.45880	Villin headpiece (5);	0.269718	0.37809	N	0.001932	T	0.54983	0.1892	M	0.88105	2.93	0.44469	D	0.997409	D	0.76494	0.999	D	0.79108	0.992	T	0.63501	-0.6623	10	0.54805	T	0.06	-8.6343	12.973	0.58524	1.0:0.0:0.0:0.0	.	821	O15195	VILL_HUMAN	S	821;821;807;539	ENSP00000283713:Y821S;ENSP00000373266:Y821S;ENSP00000422096:Y539S	ENSP00000283713:Y821S	Y	+	2	0	VILL	38023441	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.549000	0.73900	1.807000	0.52817	0.529000	0.55759	TAT		0.557	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		C	38048437	A	C	38048437	3	2	35	1	0	0	0	0	1	0	0	0	17205	449	16	4	2536	4	VILL	3	38048437	Missense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	18493837	38048437	159973993	27	2897										
MYRIP	25924	broad.mit.edu	37	chr3	40285980	40285980	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gtatggactggagacccagcTgactgagctagaagatgccg	14	9	0	5			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:40285980T>A	ENST00000302541.6	+	13	2486	c.2144T>A	c.(2143-2145)cTg>cAg	p.L715Q	MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000425621.1_Missense_Mutation_p.L650Q|MYRIP_ENST00000444716.1_Missense_Mutation_p.L715Q|MYRIP_ENST00000539167.1_Missense_Mutation_p.L528Q|MYRIP_ENST00000396217.3_Missense_Mutation_p.L626Q	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	715	Actin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)	p.L715Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		GAGACCCAGCTGACTGAGCTA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	67	68					3																	40285980		2203	4300	6503	40260984	SO:0001583	missense	25924			AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.2144T>A	3.37:g.40285980T>A	ENSP00000301972:p.Leu715Gln		40260984	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.517639	0.85495	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.3	5.3	0.74995	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.000000	0.64402	D	0.000005	T	0.61527	0.2354	M	0.67397	2.05	0.50171	D	0.999857	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.62048	-0.6936	9	.	.	.	.	13.4832	0.61348	0.0:0.0:0.0:1.0	.	626;650;715	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	Q	715;715;650;626;528	ENSP00000398665:L715Q;ENSP00000301972:L715Q;ENSP00000389323:L650Q;ENSP00000379519:L626Q;ENSP00000438297:L528Q	.	L	+	2	0	MYRIP	40260984	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.576000	0.82467	2.141000	0.66446	0.533000	0.62120	CTG		0.582	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		A	40285980	T	A	40285980	3	1	35	1	0	0	0	0	1	0	0	0	10130	1580	55	5	2190	5	MYRIP	3	40285980	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10	2237543	40285980	157736450	28	2898										
TRAK1	22906	broad.mit.edu	37	chr3	42244137	42244138	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	acccactgagagcatcatgtCcctgggcacgcactcccgct							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:42244137_42244138CC>AA	ENST00000327628.5	+	13	2037_2038	c.1637_1638CC>AA	c.(1636-1638)tCC>tAA	p.S546*	TRAK1_ENST00000396175.1_Nonsense_Mutation_p.S488*|TRAK1_ENST00000341421.3_Nonsense_Mutation_p.S488*|TRAK1_ENST00000449246.1_Nonsense_Mutation_p.S472*|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	546					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S488>?(2)|p.S546>?(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						AGCATCATGTCCCTGGGCACGC	0.624																																					GBM(44;195 884 22595 31865 41850)											3	Complex(3)	large_intestine(3)	3																																								42219142	SO:0001587	stop_gained	22906				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	Exception_encountered	3.37:g.42244137_42244138delinsAA	ENSP00000328998:p.Ser546*		42219141	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Nonsense_Mutation	DNP	ENST00000327628.5	37	CCDS43072.1																																																																																				0.624	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		AA	42244138	CC	AA	42244137	4	1	35	1	0	0	0	0	0	1	0	0	16489	855	30	2	1803	2	TRAK1	3	42244137	Nonsense_Mutation	DNP	CC	TCGA-AG-3726-01A-02W-0899-10	1958157	42244137	155778293	29	2899										
ZNF197	10168	broad.mit.edu	37	chr3	44685501	44685501	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aggggagaaaccctatgggtGtaatgattgtagtaaagttt	13	3	0	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:44685501G>C	ENST00000396058.1	+	5	3046	c.2879G>C	c.(2878-2880)tGt>tCt	p.C960S	ZNF197_ENST00000383744.4_Intron|ZNF197_ENST00000344387.4_Missense_Mutation_p.C960S|ZNF197_ENST00000383745.2_Intron|RP11-944L7.4_ENST00000457331.1_RNA			O14709	ZN197_HUMAN	zinc finger protein 197	960					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C960S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		CCCTATGGGTGTAATGATTGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											63	69	67					3																	44685501		2203	4300	6503	44660505	SO:0001583	missense	10168			AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.2879G>C	3.37:g.44685501G>C	ENSP00000379370:p.Cys960Ser		44660505	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	37	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.593955	0.66219	.	.	ENSG00000186448	ENST00000344387;ENST00000396058	D;D	0.85171	-1.95;-1.95	4.07	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94447	0.8213	H	0.95187	3.635	0.44454	D	0.997382	D	0.89917	1.0	D	0.91635	0.999	D	0.96078	0.9051	9	0.87932	D	0	.	15.5545	0.76180	0.0:0.0:1.0:0.0	.	960	O14709	ZN197_HUMAN	S	960	ENSP00000345809:C960S;ENSP00000379370:C960S	ENSP00000345809:C960S	C	+	2	0	ZNF197	44660505	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.476000	0.81055	2.252000	0.74401	0.557000	0.71058	TGT		0.368	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		C	44685501	G	C	44685501	3	2	35	1	0	0	0	0	1	0	0	0	17798	1377	48	5	2897	5	ZNF197	3	44685501	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	2441364	44685501	153336929	30	2900										
BSN	8927	broad.mit.edu	37	chr3	49689416	49689417	+	Missense_Mutation	DNP	AT	AT	CC													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tcagacgactttggcagccaAttgaggcacgactatgtgga							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:49689416_49689417AT>CC	ENST00000296452.4	+	5	2541_2542	c.2427_2428AT>CC	c.(2425-2430)caATtg>caCCtg	p.Q809H		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	809					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.Q809>?(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TTGGCAGCCAATTGAGGCACGA	0.599																																																1	Complex(1)	large_intestine(1)	3																																								49664421	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	Exception_encountered	3.37:g.49689416_49689417delinsCC	ENSP00000296452:p.Gln809His		49664420	O43161|Q7LGH3	Missense_Mutation	DNP	ENST00000296452.4	37	CCDS2800.1																																																																																				0.599	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		CC	49689417	AT	CC	49689416	3	2	35	1	0	0	0	0	1	0	0	0	1533	98	4	4	2445	4	BSN	3	49689416	Missense_Mutation	DNP	AT	TCGA-AG-3726-01A-02W-0899-10	5003915	49689416	148333014	31	2901										
IFT57	55081	broad.mit.edu	37	chr3	107941064	107941065	+	Missense_Mutation	DNP	CG	CG	TT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cacgaacatgtggtaggccgCgccgggcccccgctccaaga							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:107941064_107941065CG>TT	ENST00000264538.3	-	1	352_353	c.105_106CG>AA	c.(103-108)ggCGcg>ggAAcg	p.A36T		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	36					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)	p.G35>?(1)		kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			TGGTAGGCCGCGCCGGGCCCCC	0.649																																																1	Complex(1)	large_intestine(1)	3																																								109423755	SO:0001583	missense	55081			AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.105_106delinsTT	3.37:g.107941064_107941065delinsTT	ENSP00000264538:p.Ala36Thr		109423754	Q96DA9	Missense_Mutation	DNP	ENST00000264538.3	37	CCDS2951.1																																																																																				0.649	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		TT	107941065	CG	TT	107941064	3	4	35	1	0	0	0	0	1	0	0	0	7583	768	27	1	1227	1	IFT57	3	107941064	Missense_Mutation	DNP	CG	TCGA-AG-3726-01A-02W-0899-10	58251648	107941064	90081366	32	2902										
ABTB1	80325	broad.mit.edu	37	chr3	127395267	127395267	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gagtgtcgtggttctcaggcAcccactggtatgtcccttca	11	12	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:127395267A>T	ENST00000232744.8	+	5	559	c.473A>T	c.(472-474)cAc>cTc	p.H158L	ABTB1_ENST00000393363.3_Missense_Mutation_p.H16L|ABTB1_ENST00000453791.2_Missense_Mutation_p.H16L|ABTB1_ENST00000468137.1_Missense_Mutation_p.H16L					ankyrin repeat and BTB (POZ) domain containing 1									p.H158L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						GTTCTCAGGCACCCACTGGTA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	3											152	114	127					3																	127395267		2203	4300	6503	128877957	SO:0001583	missense	80325			AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.473A>T	3.37:g.127395267A>T	ENSP00000232744:p.His158Leu		128877957		Missense_Mutation	SNP	ENST00000232744.8	37	CCDS3045.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.307579	0.60305	.	.	ENSG00000114626	ENST00000361019;ENST00000393363;ENST00000232744;ENST00000453791;ENST00000468137	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	4.58	4.58	0.56647	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.56978	0.2022	N	0.10685	0.025	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.71414	0.939;0.973	T	0.53585	-0.8418	10	0.10111	T	0.7	-22.2876	13.9857	0.64334	1.0:0.0:0.0:0.0	.	158;133	Q969K4;Q969K4-3	ABTB1_HUMAN;.	L	63;16;158;16;16	ENSP00000377030:H16L;ENSP00000232744:H158L;ENSP00000412684:H16L;ENSP00000417366:H16L	ENSP00000232744:H158L	H	+	2	0	ABTB1	128877957	1.000000	0.71417	0.830000	0.32933	0.176000	0.22953	7.236000	0.78154	1.706000	0.51276	0.459000	0.35465	CAC		0.567	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027		T	127395267	A	T	127395267	3	4	35	1	0	0	0	0	1	0	0	0	102	159	6	5	491	5	ABTB1	3	127395267	Missense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	19454203	127395267	70627163	33	2903										
PLSCR5	389158	broad.mit.edu	37	chr3	146307458	146307458	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	acaaagagaaaacaggcaccGatcattgctgctttgactgt	9	9	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr3:146307458G>A	ENST00000443512.1	-	6	1762	c.759C>T	c.(757-759)atC>atT	p.I253I	PLSCR5_ENST00000492200.1_Silent_p.I253I|PLSCR5-AS1_ENST00000473817.1_RNA|PLSCR5_ENST00000482567.1_Silent_p.I241I	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	253								p.I253I(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						AACAGGCACCGATCATTGCTG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	3											146	137	140					3																	146307458		1901	4121	6022	147790148	SO:0001819	synonymous_variant	389158			AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.759C>T	3.37:g.146307458G>A			147790148	B2RXK5	Silent	SNP	ENST00000443512.1	37	CCDS46931.1																																																																																				0.383	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670		A	146307458	G	A	146307458	2	1	35	1	0	0	0	0	0	0	0	1	12144	1048	37	1		1	PLSCR5	3	146307458	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	18912191	146307458	51714972	34	2904										
ATP10D	57205	broad.mit.edu	37	chr4	47593390	47593391	+	Missense_Mutation	DNP	GA	GA	TC													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctggaccctccaaaggtaaaGaaagctagataccctccttg							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr4:47593390_47593391GA>TC	ENST00000273859.3	+	23	4542_4543	c.4273_4274GA>TC	c.(4273-4275)GAa>TCa	p.E1425S		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1425					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.E1425>?(1)		NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CAAAGGTAAAGAAAGCTAGATA	0.416																																																1	Complex(1)	large_intestine(1)	4																																								47288148	SO:0001583	missense	57205			AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	Exception_encountered	4.37:g.47593390_47593391delinsTC	ENSP00000273859:p.Glu1425Ser		47288147	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	DNP	ENST00000273859.3	37	CCDS3476.1																																																																																				0.416	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		TC	47593391	GA	TC	47593390	3	4	35	1	0	0	0	0	1	0	0	0	1119	943	33	2	4359	2	ATP10D	4	47593390	Missense_Mutation	DNP	GA	TCGA-AG-3726-01A-02W-0899-10		47593390	143560886	35	2905										
INTU	27152	broad.mit.edu	37	chr4	128628017	128628017	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gatctgacaatggttgtgaaGgtggagaagatgatggcttt	15	3	1	5			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr4:128628017G>C	ENST00000335251.6	+	12	2267	c.2164G>C	c.(2164-2166)Ggt>Cgt	p.G722R		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	722					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)		p.G722R(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TGGTTGTGAAGGTGGAGAAGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	4											222	223	223					4																	128628017		2203	4300	6503	128847467	SO:0001583	missense	27152			BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2164G>C	4.37:g.128628017G>C	ENSP00000334003:p.Gly722Arg		128847467	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494636	0.64186	.	.	ENSG00000164066	ENST00000335251	.	.	.	4.92	4.92	0.64577	.	0.251667	0.39083	N	0.001471	T	0.70718	0.3256	L	0.59436	1.845	0.80722	D	1	P	0.47962	0.903	P	0.51806	0.68	T	0.74090	-0.3777	9	0.72032	D	0.01	-3.9062	18.6723	0.91516	0.0:0.0:1.0:0.0	.	722	Q9ULD6	PDZD6_HUMAN	R	722	.	ENSP00000334003:G722R	G	+	1	0	INTU	128847467	1.000000	0.71417	0.782000	0.31804	0.191000	0.23601	8.612000	0.90909	2.717000	0.92951	0.650000	0.86243	GGT		0.468	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		C	128628017	G	C	128628017	3	2	35	1	0	0	0	0	1	0	0	0	7807	1000	35	5	2210	5	INTU	4	128628017	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	81034627	128628017	62526259	36	2906										
SMAD1	4086	broad.mit.edu	37	chr4	146435885	146435885	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gttgatgctttggtgaaaaaActgaagaaaaagaaaggtgc	12	3	0	5			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr4:146435885A>G	ENST00000515385.1	+	2	662	c.120A>G	c.(118-120)aaA>aaG	p.K40K	SMAD1_ENST00000302085.4_Silent_p.K40K|RP11-301H24.4_ENST00000513542.1_RNA|SMAD1_ENST00000394092.2_Silent_p.K40K|SMAD1_ENST00000515527.1_3'UTR			Q15797	SMAD1_HUMAN	SMAD family member 1	40	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.|Poly-Lys.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)	p.K40K(1)		endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					TGGTGAAAAAACTGAAGAAAA	0.483																																					Pancreas(182;1287 2092 10326 35158 50562)											1	Substitution - coding silent(1)	large_intestine(1)	4											78	77	77					4																	146435885		2203	4300	6503	146655335	SO:0001819	synonymous_variant	4086			U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365		"SMADs"	6767	protein-coding gene	gene with protein product		601595	"MAD, mothers against decapentaplegic homolog 1 (Drosophila)", "SMAD, mothers against DPP homolog 1 (Drosophila)"	MADH1		8653785, 8673135	Standard	NM_005900		Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.120A>G	4.37:g.146435885A>G			146655335	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	Silent	SNP	ENST00000515385.1	37	CCDS3765.1																																																																																				0.483	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365467.1	NM_005900		G	146435885	A	G	146435885	2	3	35	1	0	0	0	0	0	0	0	1	14794	40	2	4		4	SMAD1	4	146435885	Silent	SNP	A	TCGA-AG-3726-01A-02W-0899-10	17807868	146435885	44718391	37	2907										
C4orf41	60684	broad.mit.edu	37	chr4	184601385	184601385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cagcatactatgcccaggagCggaaacagcttgcaaaaacc	9	12	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr4:184601385C>T	ENST00000334690.6	+	10	1280	c.1078C>T	c.(1078-1080)Cgg>Tgg	p.R360W	TRAPPC11_ENST00000357207.4_Missense_Mutation_p.R360W	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	360					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.R360W(1)									TGCCCAGGAGCGGAAACAGCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											118	117	117					4																	184601385		2203	4300	6503	184838379	SO:0001583	missense	60684				CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"Trafficking protein particle complex"	25751	protein-coding gene	gene with protein product	"gryzun homolog (Drosophila)", "foie gras homolog (zebrafish)"	614138	"chromosome 4 open reading frame 41"	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.1078C>T	4.37:g.184601385C>T	ENSP00000335371:p.Arg360Trp		184838379	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072598	0.76415	.	.	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109	.	.	.	5.96	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.84257	0.5432	M	0.86864	2.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87530	0.2452	9	0.87932	D	0	.	16.5523	0.84475	0.1317:0.8683:0.0:0.0	.	360;360	Q7Z392;Q7Z392-3	TPC11_HUMAN;.	W	360	.	ENSP00000335371:R360W	R	+	1	2	C4orf41	184838379	0.976000	0.34144	1.000000	0.80357	0.962000	0.63368	2.008000	0.40893	1.513000	0.48852	-0.188000	0.12872	CGG		0.388	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942		T	184601385	C	T	184601385	3	4	35	1	0	0	0	0	1	0	0	0	2276	759	27	1	1112	1	C4orf41	4	184601385	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	38165500	184601385	6552891	38	2908										
PIK3R1	5295	broad.mit.edu	37	chr5	67589586	67589591	+	In_Frame_Del	DEL	ATGAAT	ATGAAT	-													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agctgtagggaaaaaattacAtgaatataacactcagtttc					rs17852841		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	ATGAAT	ATGAAT	ATGAAT	-	ATGAAT	ATGAAT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:67589586_67589591delATGAAT	ENST00000521381.1	+	11	1965_1970	c.1349_1354delATGAAT	c.(1348-1356)catgaatat>cat	p.EY451del	PIK3R1_ENST00000523872.1_In_Frame_Del_p.EY88del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.EY181del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.EY151del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.EY451del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.EY451del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.EY451del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	451			E -> K (in dbSNP:rs17852841). {ECO:0000269|PubMed:15489334}.		B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.H450_E451del(2)|p.G446_Y452>VI(1)|p.Y152N(1)|p.0?(1)|p.?(1)|p.Y452N(1)|p.Y182N(1)|p.E451_Y452del(1)|p.N453_T454insN(1)|p.E451_Y452delEY(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAAAAATTACATGAATATAACACTCA	0.277			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	11	Deletion - In frame(4)|Substitution - Missense(3)|Insertion - In frame(1)|Unknown(1)|Whole gene deletion(1)|Complex - deletion inframe(1)	endometrium(5)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|lung(1)	5																																								67625347	SO:0001651	inframe_deletion	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1349_1354delATGAAT	5.37:g.67589586_67589591delATGAAT	ENSP00000428056:p.Glu451_Tyr452del		67625342	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	37	CCDS3993.1																																																																																				0.277	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		-	67589591	ATGAAT	-	67589586	7	5	35	1	0	1	0	1	0	0	0	0	11949	217	8	0	1517	0	PIK3R1	5	67589586	In_Frame_Del	DEL	ATGAAT	TCGA-AG-3726-01A-02W-0899-10		67589586	113325674	39	2909										
VCAN	1462	broad.mit.edu	37	chr5	82818043	82818043	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gaggcctttggacctcaggcGctttctacgccacagccccc	10	17	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:82818043G>A	ENST00000265077.3	+	7	4483	c.3918G>A	c.(3916-3918)gcG>gcA	p.A1306A	VCAN_ENST00000342785.4_Silent_p.A1306A|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Silent_p.A1258A|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1306	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.A1306A(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	GACCTCAGGCGCTTTCTACGC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											60	61	61					5																	82818043		2203	4300	6503	82853799	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.3918G>A	5.37:g.82818043G>A			82853799	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.448	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82818043	G	A	82818043	2	1	35	1	0	0	0	0	0	0	0	1	17178	1074	38	1		1	VCAN	5	82818043	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	15228457	82818043	98097217	40	2910										
EPB41L4A	64097	broad.mit.edu	37	chr5	111575392	111575392	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	taacgtatggatccaaacttGctgagttttcttgacagtga	9	7	1	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:111575392G>T	ENST00000261486.5	-	11	1206	c.930C>A	c.(928-930)agC>agA	p.S310R	RP11-526F3.1_ENST00000504004.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	310						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.S310R(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ATCCAAACTTGCTGAGTTTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											135	119	124					5																	111575392		1823	4070	5893	111603291	SO:0001583	missense	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.930C>A	5.37:g.111575392G>T	ENSP00000261486:p.Ser310Arg		111603291	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.441477	0.63067	.	.	ENSG00000129595	ENST00000261486	D	0.87334	-2.24	5.59	4.72	0.59763	FERM adjacent (FA) (1);	0.103551	0.64402	D	0.000002	T	0.80954	0.4723	N	0.19112	0.55	0.41165	D	0.986127	B	0.32010	0.351	B	0.36534	0.227	T	0.81754	-0.0788	10	0.72032	D	0.01	.	13.7115	0.62672	0.076:0.0:0.924:0.0	.	310	Q9HCS5	E41LA_HUMAN	R	310	ENSP00000261486:S310R	ENSP00000261486:S310R	S	-	3	2	EPB41L4A	111603291	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.281000	0.65609	1.495000	0.48549	0.655000	0.94253	AGC		0.353	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			T	111575392	G	T	111575392	3	4	35	1	0	0	0	0	1	0	0	0	5168	1310	46	2	1182	2	EPB41L4A	5	111575392	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	28757349	111575392	69339868	41	2911										
APC	324	broad.mit.edu	37	chr5	112173290	112173290	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	actgtctacaaactttattaCaacacttaaaatctcatagt	2	9	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:112173290C>T	ENST00000457016.1	+	16	2379	c.1999C>T	c.(1999-2001)Caa>Taa	p.Q667*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q667*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q667*			P25054	APC_HUMAN	adenomatous polyposis coli	667	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.Q667*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AACTTTATTACAACACTTAAA	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5	GRCh37	HM060574	APC	M							67	69	69					5																	112173290		2202	4300	6502	112201189	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1999C>T	5.37:g.112173290C>T	ENSP00000413133:p.Gln667*		112201189	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.807428	0.96967	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.99	5.99	0.97316	.	0.051053	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-13.6268	20.4777	0.99188	0.0:1.0:0.0:0.0	.	.	.	.	X	667;649;667;667;667	.	ENSP00000257430:Q667X	Q	+	1	0	APC	112201189	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.840000	0.97914	0.655000	0.94253	CAA		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173290	C	T	112173290	4	4	35	1	0	0	0	0	0	1	0	0	763	479	17	3	2057	3	APC	5	112173290	Nonsense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	597898	112173290	68741970	42	2912										
APC	324	broad.mit.edu	37	chr5	112175136	112175136	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttcattatcatctttgtcatCagctgaagatgaaataggat	7	6	5	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:112175136C>G	ENST00000457016.1	+	16	4225	c.3845C>G	c.(3844-3846)tCa>tGa	p.S1282*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1282*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1282*			P25054	APC_HUMAN	adenomatous polyposis coli	1282	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1282*(4)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTTTGTCATCAGCTGAAGAT	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Substitution - Nonsense(4)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											54	56	55					5																	112175136		2202	4300	6502	112203035	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3845C>G	5.37:g.112175136C>G	ENSP00000413133:p.Ser1282*		112203035	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	7.998517	0.98602	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.056000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6145	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1282	.	.	S	+	2	0	APC	112203035	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.861000	0.98227	0.655000	0.94253	TCA		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175136	C	G	112175136	4	3	35	1	0	0	0	0	0	1	0	0	763	838	29	5	3903	5	APC	5	112175136	Nonsense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1846	112175136	68740124	43	2913										
PCDHB11	56125	broad.mit.edu	37	chr5	140580521	140580521	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttccggaagacctcccattcGtgctaaaatcttcagttgag	8	11	2	2	rs201835076		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:140580521G>A	ENST00000354757.3	+	1	1174	c.1174G>A	c.(1174-1176)Gtg>Atg	p.V392M	PCDHB11_ENST00000536699.1_Missense_Mutation_p.V27M	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	392	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.V392M(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTCCCATTCGTGCTAAAATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											115	115	115					5																	140580521		2203	4300	6503	140560705	SO:0001583	missense	56125			AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1174G>A	5.37:g.140580521G>A	ENSP00000346802:p.Val392Met		140560705	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.853054	0.32699	.	.	ENSG00000197479	ENST00000536699;ENST00000354757;ENST00000536825	T;T	0.60672	0.17;4.64	2.52	-5.04	0.02964	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.48554	0.1506	L	0.53617	1.68	0.09310	N	1	P	0.39940	0.696	B	0.42343	0.384	T	0.46843	-0.9162	9	0.51188	T	0.08	.	6.0648	0.19858	0.2939:0.3788:0.3273:0.0	.	392	Q9Y5F2	PCDBB_HUMAN	M	27;392;80	ENSP00000440344:V27M;ENSP00000346802:V392M	ENSP00000346802:V392M	V	+	1	0	PCDHB11	140560705	0.000000	0.05858	0.000000	0.03702	0.942000	0.58702	-6.600000	0.00060	-1.295000	0.02357	0.306000	0.20318	GTG		0.453	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		A	140580521	G	A	140580521	3	1	35	1	0	0	0	0	1	0	0	0	11567	1145	40	1	1176	1	PCDHB11	5	140580521	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	28405385	140580521	40334739	44	2914										
JAKMIP2	9832	broad.mit.edu	37	chr5	147040726	147040726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cagtttccgggcctcctcccGggcctcaatggtgagcgctg	13	15	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:147040726G>A	ENST00000265272.5	-	3	879	c.412C>T	c.(412-414)Cgg>Tgg	p.R138W	JAKMIP2_ENST00000507386.1_Missense_Mutation_p.R138W|JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R96W	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	138						Golgi apparatus (GO:0005794)		p.R138W(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCCTCCCGGGCCTCAATG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											107	110	109					5																	147040726		2203	4300	6503	147020919	SO:0001583	missense	9832			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.412C>T	5.37:g.147040726G>A	ENSP00000265272:p.Arg138Trp		147020919	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327169	0.81690	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.46451	0.87;0.87;0.87	4.67	4.67	0.58626	.	0.112717	0.64402	D	0.000016	T	0.61400	0.2344	M	0.69823	2.125	0.50313	D	0.99986	D;D;D;D	0.71674	0.997;0.998;0.998;0.998	P;P;P;P	0.59643	0.807;0.861;0.861;0.861	T	0.66712	-0.5854	10	0.72032	D	0.01	.	18.4503	0.90702	0.0:0.0:1.0:0.0	.	96;138;138;138	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	W	138;138;96;138	ENSP00000421398:R138W;ENSP00000265272:R138W;ENSP00000328989:R96W	ENSP00000265272:R138W	R	-	1	2	JAKMIP2	147020919	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.068000	0.57534	2.529000	0.85273	0.563000	0.77884	CGG		0.567	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		A	147040726	G	A	147040726	3	1	35	1	0	0	0	0	1	0	0	0	7962	1115	39	1	2096	1	JAKMIP2	5	147040726	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	6460205	147040726	33874534	45	2915										
SPINK7	84651	broad.mit.edu	37	chr5	147693673	147693674	+	Missense_Mutation	DNP	GC	GC	TA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tatgacacaggtggactgcaGcatttacaagaagtatccag							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:147693673_147693674GC>TA	ENST00000274565.4	+	3	159_160	c.98_99GC>TA	c.(97-99)aGC>aTA	p.S33I	SPINK7_ENST00000523535.1_Missense_Mutation_p.S7I|SPINK7_ENST00000514394.1_3'UTR|RP11-373N22.3_ENST00000501695.3_RNA	NM_032566.2	NP_115955.1	P58062	ISK7_HUMAN	serine peptidase inhibitor, Kazal type 7 (putative)	33	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S33>?(1)		large_intestine(2)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGACTGCAGCATTTACAAGA	0.475																																																1	Complex(1)	large_intestine(1)	5																																								147673867	SO:0001583	missense	84651				CCDS4289.1	5q32	2011-08-31			ENSG00000145879	ENSG00000145879		"Serine peptidase inhibitors, Kazal type"	24643	protein-coding gene	gene with protein product	"esophagus cancer related gene 2"					12646258, 12970870	Standard	NM_032566		Approved	ECG2, ECRG2	uc003lpd.3	P58062	OTTHUMG00000163522	Exception_encountered	5.37:g.147693673_147693674delinsTA	ENSP00000274565:p.Ser33Ile		147673866	Q32LY0	Missense_Mutation	DNP	ENST00000274565.4	37	CCDS4289.1																																																																																				0.475	SPINK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251944.5	NM_032566		TA	147693674	GC	TA	147693673	3	4	35	1	0	0	0	0	1	0	0	0	15103	971	34	2	108	2	SPINK7	5	147693673	Missense_Mutation	DNP	GC	TCGA-AG-3726-01A-02W-0899-10	652947	147693673	33221587	46	2916										
PPARGC1B	133522	broad.mit.edu	37	chr5	149200080	149200080	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atgccagcgactttgactcgGccacctgctttggggagctg	13	12	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:149200080G>A	ENST00000309241.5	+	2	195	c.163G>A	c.(163-165)Gcc>Acc	p.A55T	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.A55T|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.A55T|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.A30T	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	55	Abolishes DNA transcriptional activity when missing.				actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)	p.A55T(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CTTTGACTCGGCCACCTGCTT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	99	101					5																	149200080		2203	4300	6503	149180273	SO:0001583	missense	133522			AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.163G>A	5.37:g.149200080G>A	ENSP00000312649:p.Ala55Thr		149180273	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	g	14.75	2.628494	0.46944	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.08984	3.05;3.03;3.04;3.07	5.76	4.88	0.63580	.	0.212561	0.49916	D	0.000134	T	0.16557	0.0398	L	0.47716	1.5	0.34487	D	0.70454	D;B;B;D;P	0.89917	1.0;0.208;0.208;1.0;0.851	D;B;B;D;P	0.87578	0.998;0.068;0.068;0.996;0.493	T	0.07328	-1.0778	10	0.10902	T	0.67	-26.6019	8.7486	0.34602	0.2112:0.0:0.7888:0.0	.	34;34;55;55;55	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	T	55;55;55;30	ENSP00000353638:A55T;ENSP00000377855:A55T;ENSP00000312649:A55T;ENSP00000384403:A30T	ENSP00000312649:A55T	A	+	1	0	PPARGC1B	149180273	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	4.496000	0.60360	2.724000	0.93272	0.651000	0.88453	GCC		0.582	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149200080	G	A	149200080	3	1	35	1	0	0	0	0	1	0	0	0	12332	1203	42	3	176	3	PPARGC1B	5	149200080	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	1506407	149200080	31715180	47	2917										
TCOF1	6949	broad.mit.edu	37	chr5	149771711	149771712	+	Missense_Mutation	DNP	CC	CC	TA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gaggaagatggtgaagggccCcagggggccaagtcagccca							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:149771711_149771712CC>TA	ENST00000504761.2	+	21	3489_3490	c.3489_3490CC>TA	c.(3487-3492)ccCCag>ccTAag	p.Q1164K	TCOF1_ENST00000323668.7_Missense_Mutation_p.Q1087K|TCOF1_ENST00000445265.2_Missense_Mutation_p.Q1087K|TCOF1_ENST00000513346.1_Missense_Mutation_p.Q1163K|TCOF1_ENST00000451292.1_Missense_Mutation_p.Q1201K|TCOF1_ENST00000377797.3_Missense_Mutation_p.Q1164K|TCOF1_ENST00000439160.2_Missense_Mutation_p.Q1126K			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1164					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.P1086>?(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGAAGGGCCCCAGGGGGCCAA	0.619																																																1	Complex(1)	large_intestine(1)	5	GRCh37	CM023461	TCOF1	M																																				149751905	SO:0001583	missense	6949				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	Exception_encountered	5.37:g.149771711_149771712delinsTA	ENSP00000421655:p.Gln1164Lys		149751904	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	DNP	ENST00000504761.2	37	CCDS54936.1																																																																																				0.619	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		TA	149771712	CC	TA	149771711	3	4	35	1	0	0	0	0	1	0	0	0	15747	610	22	3	3593	3	TCOF1	5	149771711	Missense_Mutation	DNP	CC	TCGA-AG-3726-01A-02W-0899-10	571631	149771711	31143549	48	2918										
NDST1	3340	broad.mit.edu	37	chr5	149919654	149919654	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cctggagcagatcagcatctTcatgacgcacctgtccaact	8	14	3	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:149919654T>G	ENST00000261797.6	+	8	2079	c.1577T>G	c.(1576-1578)tTc>tGc	p.F526C	NDST1_ENST00000523767.1_Missense_Mutation_p.F526C	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	526	Heparan sulfate N-deacetylase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.F526C(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATCAGCATCTTCATGACGCAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	85	92					5																	149919654		2203	4300	6503	149899847	SO:0001583	missense	3340			U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"Sulfotransferases, membrane-bound"	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.1577T>G	5.37:g.149919654T>G	ENSP00000261797:p.Phe526Cys		149899847	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	37	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497782	0.85069	.	.	ENSG00000070614	ENST00000523767;ENST00000261797	T;T	0.61859	0.07;0.48	5.37	5.37	0.77165	.	0.042255	0.85682	D	0.000000	T	0.79598	0.4473	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.74674	0.984;0.927	D	0.84098	0.0394	10	0.87932	D	0	.	15.6753	0.77311	0.0:0.0:0.0:1.0	.	526;526	E7EVJ3;P52848	.;NDST1_HUMAN	C	526	ENSP00000428604:F526C;ENSP00000261797:F526C	ENSP00000261797:F526C	F	+	2	0	NDST1	149899847	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.991000	0.88244	2.155000	0.67459	0.460000	0.39030	TTC		0.612	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		G	149919654	T	G	149919654	3	3	35	1	0	0	0	0	1	0	0	0	10286	1783	62	4	1603	4	NDST1	5	149919654	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10	147943	149919654	30995606	49	2919										
RARS	5917	broad.mit.edu	37	chr5	167943865	167943865	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tgctgacctttcccataaccGgttgaatgactacatcttct	6	12	2	3	rs369398935		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr5:167943865G>T	ENST00000231572.3	+	13	1589	c.1535G>T	c.(1534-1536)cGg>cTg	p.R512L	RARS_ENST00000538719.1_Missense_Mutation_p.R306L	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	512					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R512L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		TCCCATAACCGGTTGAATGAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											211	200	204					5																	167943865		2203	4300	6503	167876443	SO:0001583	missense	5917			BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1535G>T	5.37:g.167943865G>T	ENSP00000231572:p.Arg512Leu		167876443	B2RBS9|Q53GY4|Q9BWA1	Missense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	g	24.0	4.476577	0.84640	.	.	ENSG00000113643	ENST00000231572;ENST00000538719	T;T	0.67865	-0.06;-0.29	5.97	5.09	0.68999	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.85691	0.5755	M	0.91920	3.255	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.89426	0.3713	10	0.87932	D	0	-15.6789	17.243	0.87019	0.0:0.1258:0.8742:0.0	.	512	P54136	SYRC_HUMAN	L	512;306	ENSP00000231572:R512L;ENSP00000439108:R306L	ENSP00000231572:R512L	R	+	2	0	RARS	167876443	1.000000	0.71417	0.899000	0.35326	0.744000	0.42396	9.452000	0.97615	1.514000	0.48869	-0.181000	0.13052	CGG		0.418	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		T	167943865	G	T	167943865	3	4	35	1	0	0	0	0	1	0	0	0	13095	1116	39	2	1585	2	RARS	5	167943865	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	18024211	167943865	12971395	50	2920										
DAAM2	23500	broad.mit.edu	37	chr6	39847198	39847198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cgtcccactcaggaaaaagcGtgtcccccagccttctcacc	7	18	2	0	rs181701991	byFrequency	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr6:39847198G>A	ENST00000398904.2	+	14	1972	c.1790G>A	c.(1789-1791)cGt>cAt	p.R597H	DAAM2_ENST00000274867.4_Missense_Mutation_p.R597H|DAAM2_ENST00000538976.1_Missense_Mutation_p.R597H|RP11-61I13.3_ENST00000607675.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	597	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.R597H(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					AGGAAAAAGCGTGTCCCCCAG	0.632													G|||	12	0.00239617	0	0.0014	5008	,	,		14562	0.006		0.001	False		,,,				2504	0.0041															1	Substitution - Missense(1)	large_intestine(1)	6											71	73	72					6																	39847198		1974	4133	6107	39955176	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1790G>A	6.37:g.39847198G>A	ENSP00000381876:p.Arg597His		39955176	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	1	0.0013192612137203166	G	10.93	1.490231	0.26686	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.18016	2.24;2.24;2.24	5.15	-1.29	0.09288	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.620813	0.16621	N	0.206470	T	0.09291	0.0229	N	0.22421	0.69	0.09310	N	0.999999	D;D	0.76494	0.992;0.999	B;D	0.64877	0.35;0.93	T	0.14392	-1.0474	10	0.59425	D	0.04	.	6.6426	0.22917	0.4393:0.2235:0.3372:0.0	.	597;597	G5EA45;Q86T65	.;DAAM2_HUMAN	H	597	ENSP00000274867:R597H;ENSP00000381876:R597H;ENSP00000437808:R597H	ENSP00000274867:R597H	R	+	2	0	DAAM2	39955176	0.997000	0.39634	0.844000	0.33320	0.028000	0.11728	1.290000	0.33319	-0.108000	0.12066	-0.157000	0.13467	CGT		0.632	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39847198	G	A	39847198	3	1	35	1	0	0	0	0	1	0	0	0	4222	1145	40	1	1840	1	DAAM2	6	39847198	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10		39847198	131267869	51	2921										
PGC	5225	broad.mit.edu	37	chr6	41712141	41712141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agcccagcactcactgcaggCctggctctggcagtagacag	12	14	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr6:41712141C>T	ENST00000373025.3	-	3	384	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	PGC_ENST00000425343.2_Missense_Mutation_p.A108T	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	108					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)	p.A108T(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TCACTGCAGGCCTGGCTCTGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	62	61					6																	41712141		2203	4300	6503	41820119	SO:0001583	missense	5225				CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.322G>A	6.37:g.41712141C>T	ENSP00000362116:p.Ala108Thr		41820119	B4DVZ3|Q5T3D7|Q5T3D8	Missense_Mutation	SNP	ENST00000373025.3	37	CCDS4859.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821681	0.50633	.	.	ENSG00000096088	ENST00000373025;ENST00000425343	T;T	0.60672	0.17;0.17	4.65	3.79	0.43588	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.063203	0.64402	N	0.000010	T	0.72391	0.3454	M	0.88377	2.95	0.44175	D	0.996986	D	0.89917	1.0	D	0.79784	0.993	T	0.79014	-0.1976	10	0.87932	D	0	.	12.4447	0.55645	0.0:0.9174:0.0:0.0826	.	108	P20142	PEPC_HUMAN	T	108	ENSP00000362116:A108T;ENSP00000405094:A108T	ENSP00000362116:A108T	A	-	1	0	PGC	41820119	1.000000	0.71417	0.999000	0.59377	0.011000	0.07611	4.216000	0.58540	1.203000	0.43233	-0.225000	0.12378	GCC		0.612	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			T	41712141	C	T	41712141	3	4	35	1	0	0	0	0	1	0	0	0	11816	739	26	3	1181	3	PGC	6	41712141	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1864943	41712141	129402926	52	2922										
COL12A1	1303	broad.mit.edu	37	chr6	75828815	75828815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	catcctgggaccgaccgtccGtgaccacaaccaacacctta	7	17	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr6:75828815G>A	ENST00000322507.8	-	46	7607	c.7298C>T	c.(7297-7299)aCg>aTg	p.T2433M	COL12A1_ENST00000483888.2_Missense_Mutation_p.T2433M|COL12A1_ENST00000345356.6_Missense_Mutation_p.T1269M|COL12A1_ENST00000416123.2_Missense_Mutation_p.T2433M	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2433	VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.T2433M(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCGACCGTCCGTGACCACAAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											132	131	131					6																	75828815		1979	4167	6146	75885535	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.7298C>T	6.37:g.75828815G>A	ENSP00000325146:p.Thr2433Met		75885535	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261183	0.80246	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	5.78	5.78	0.91487	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.96571	0.8881	H	0.96301	3.8	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97195	0.9860	10	0.87932	D	0	.	20.0175	0.97485	0.0:0.0:1.0:0.0	.	1269;2433	Q99715-2;Q99715	.;COCA1_HUMAN	M	2433;71;2433;1269;2433;2433	ENSP00000325146:T2433M;ENSP00000399812:T71M;ENSP00000305147:T1269M;ENSP00000412864:T2433M;ENSP00000421216:T2433M	ENSP00000325146:T2433M	T	-	2	0	COL12A1	75885535	1.000000	0.71417	0.968000	0.41197	0.435000	0.31806	9.869000	0.99810	2.730000	0.93505	0.650000	0.86243	ACG		0.488	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75828815	G	A	75828815	3	1	35	1	0	0	0	0	1	0	0	0	3675	1145	40	1	1977	1	COL12A1	6	75828815	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	34116674	75828815	95286252	53	2923										
COL12A1	1303	broad.mit.edu	37	chr6	75855840	75855840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctttgggtcttgttggctctGtgtccttaacaggtttgtat	11	7	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr6:75855840G>A	ENST00000322507.8	-	24	4847	c.4538C>T	c.(4537-4539)aCa>aTa	p.T1513I	COL12A1_ENST00000483888.2_Missense_Mutation_p.T1513I|COL12A1_ENST00000345356.6_Missense_Mutation_p.T349I|COL12A1_ENST00000416123.2_Missense_Mutation_p.T1513I	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1513	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.T1513I(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGTTGGCTCTGTGTCCTTAAC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											122	118	119					6																	75855840		1952	4155	6107	75912560	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4538C>T	6.37:g.75855840G>A	ENSP00000325146:p.Thr1513Ile		75912560	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500463	0.64298	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.19	4.29	0.51040	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.253027	0.33253	N	0.005102	T	0.48295	0.1492	M	0.76002	2.32	0.32147	N	0.584756	P;P	0.48016	0.676;0.904	B;P	0.48063	0.429;0.565	T	0.54443	-0.8293	10	0.46703	T	0.11	.	15.4227	0.75025	0.0:0.1397:0.8603:0.0	.	349;1513	Q99715-2;Q99715	.;COCA1_HUMAN	I	1513;1513;349;1513;1513	ENSP00000325146:T1513I;ENSP00000305147:T349I;ENSP00000412864:T1513I;ENSP00000421216:T1513I	ENSP00000325146:T1513I	T	-	2	0	COL12A1	75912560	1.000000	0.71417	0.002000	0.10522	0.006000	0.05464	6.554000	0.73923	1.129000	0.42072	0.655000	0.94253	ACA		0.433	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75855840	G	A	75855840	3	1	35	1	0	0	0	0	1	0	0	0	3675	1377	48	3	4825	3	COL12A1	6	75855840	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	27025	75855840	95259227	54	2924										
CASP8AP2	9994	broad.mit.edu	37	chr6	90577280	90577281	+	RNA	DNP	GT	GT	AG													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aagtaaagataatgtgtgtaGtgtagaaaagagcaagccct					rs544986776		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr6:90577280_90577281GT>AG	ENST00000551025.1	+	0	5708_5709									caspase 8 associated protein 2									p.S1424>?(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AATGTGTGTAGTGTAGAAAAGA	0.411																																					Colon(187;1656 2025 17045 31481 39901)											1	Complex(1)	large_intestine(1)	6																																								90634002			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212	Exception_encountered	6.37:g.90577280_90577281delinsAG			90634001		Missense_Mutation	DNP	ENST00000551025.1	37																																																																																					0.411	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		AG	90577281	GT	AG	90577280	1	1	35	0	1	0	0	0	0	0	0	0	2684	1029	36	3		3	CASP8AP2	6	90577280	RNA	DNP	GT	TCGA-AG-3726-01A-02W-0899-10	14721440	90577280	80537787	55	2925										
CHST12	55501	broad.mit.edu	37	chr7	2473376	2473376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agctccgcttccccccgagcTaccggaacaggaccgccagc	10	19	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr7:2473376T>C	ENST00000258711.6	+	2	1237	c.1102T>C	c.(1102-1104)Tac>Cac	p.Y368H		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	368					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)	p.Y368H(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CCCCCCGAGCTACCGGAACAG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	7											29	32	31					7																	2473376		2203	4300	6503	2439902	SO:0001583	missense	55501			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.1102T>C	7.37:g.2473376T>C	ENSP00000258711:p.Tyr368His		2439902	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	T	6.367	0.435895	0.12104	.	.	ENSG00000136213	ENST00000258711	T	0.21543	2.0	5.15	5.15	0.70609	.	0.466235	0.24691	N	0.036387	T	0.17959	0.0431	L	0.38692	1.165	0.43259	D	0.995192	B	0.20261	0.043	B	0.19666	0.026	T	0.05354	-1.0890	10	0.16420	T	0.52	-16.5209	14.9757	0.71269	0.0:0.0:0.0:1.0	.	368	Q9NRB3	CHSTC_HUMAN	H	368	ENSP00000258711:Y368H	ENSP00000258711:Y368H	Y	+	1	0	CHST12	2439902	1.000000	0.71417	0.988000	0.46212	0.963000	0.63663	3.975000	0.56859	1.957000	0.56846	0.459000	0.35465	TAC		0.642	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		C	2473376	T	C	2473376	3	2	35	1	0	0	0	0	1	0	0	0	3406	1522	53	4	1104	4	CHST12	7	2473376	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10		2473376	156665287	56	2926										
MOGAT3	346606	broad.mit.edu	37	chr7	100843714	100843714	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttgggtgtgtcccagtccacAtagagccacaccaagtaaaa	9	11	0	1	rs149668601	byFrequency	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr7:100843714A>G	ENST00000223114.4	-	2	358	c.192T>C	c.(190-192)taT>taC	p.Y64Y	MOGAT3_ENST00000379423.3_Silent_p.Y64Y|MOGAT3_ENST00000440203.2_Silent_p.Y64Y	NM_178176.2	NP_835470.1	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	64					glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)	p.Y64Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3)	22	Lung NSC(181;0.168)|all_lung(186;0.215)					CCCAGTCCACATAGAGCCACA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	7											75	77	76					7																	100843714		2203	4300	6503	100630434	SO:0001819	synonymous_variant	346606			AY229854	CCDS5714.1, CCDS75643.1	7q22	2012-09-06			ENSG00000106384	ENSG00000106384	2.3.1.20, 2.3.1.22		23249	protein-coding gene	gene with protein product		610184				12618427, 14970677	Standard	XM_005250309		Approved	DC7, MGAT3	uc003uyc.3	Q86VF5	OTTHUMG00000023328	ENST00000223114.4:c.192T>C	7.37:g.100843714A>G			100630434	Q496A6|Q496A7|Q496A8|Q9UDW7	Silent	SNP	ENST00000223114.4	37	CCDS5714.1																																																																																				0.587	MOGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059649.3	NM_178176		G	100843714	A	G	100843714	2	3	35	1	0	0	0	0	0	0	0	1	9726	224	8	4		4	MOGAT3	7	100843714	Silent	SNP	A	TCGA-AG-3726-01A-02W-0899-10	98370338	100843714	58294949	57	2927										
ARMC10	83787	broad.mit.edu	37	chr7	102738813	102738813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gattcttcttcgagtacttaCgctatttcagaatataaaga	6	7	3	2	rs150955727	byFrequency	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr7:102738813C>T	ENST00000323716.3	+	7	1237	c.845C>T	c.(844-846)aCg>aTg	p.T282M	ARMC10_ENST00000454559.1_Missense_Mutation_p.T188M|ARMC10_ENST00000441711.2_Missense_Mutation_p.T247M|ARMC10_ENST00000428183.2_Missense_Mutation_p.T223M|ARMC10_ENST00000541300.1_Missense_Mutation_p.T164M|ARMC10_ENST00000425331.1_Missense_Mutation_p.T223M	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	282					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.T282M(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						CGAGTACTTACGCTATTTCAG	0.363													C|||	2	0.000399361	0.0015	0	5008	,	,		19465	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	5,4401	4.2+/-10.8	0,5,2198	103	89	94		740,668,668,563,491,845	4.5	0.7	7	dbSNP_134	94	0,8598		0,0,4299	no	missense,missense,missense,missense,missense,missense	ARMC10	NM_001161009.2,NM_001161010.2,NM_001161011.2,NM_001161012.2,NM_001161013.2,NM_031905.4	81,81,81,81,81,81	0,5,6497	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	247/309,223/285,223/285,188/250,164/226,282/344	102738813	5,12999	2203	4299	6502	102526049	SO:0001583	missense	83787			AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.845C>T	7.37:g.102738813C>T	ENSP00000319412:p.Thr282Met		102526049	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	37	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.501547	0.64298	0.001135	0.0	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153;ENST00000431642	T;T;T;T;T;T;T;T	0.49432	1.41;1.41;1.41;1.41;1.52;1.52;0.78;1.52	5.42	4.48	0.54585	Armadillo-type fold (1);	0.288557	0.40818	N	0.001011	T	0.61540	0.2355	M	0.72894	2.215	0.09310	N	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.99;0.998;0.978;0.998;0.999;0.995;0.991	T	0.55761	-0.8090	10	0.62326	D	0.03	-7.4805	5.3834	0.16204	0.0:0.6594:0.1779:0.1627	.	223;164;188;210;223;247;282	B4DWJ8;F5GX65;Q8N2F6-4;C9J5N7;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;.;ARM10_HUMAN	M	282;223;247;188;223;164;210;124	ENSP00000319412:T282M;ENSP00000396654:T223M;ENSP00000413619:T247M;ENSP00000405612:T188M;ENSP00000397969:T223M;ENSP00000440463:T164M;ENSP00000398201:T210M;ENSP00000406840:T124M	ENSP00000319412:T282M	T	+	2	0	ARMC10	102526049	0.093000	0.21703	0.717000	0.30585	0.966000	0.64601	0.571000	0.23669	2.709000	0.92574	0.591000	0.81541	ACG		0.363	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		T	102738813	C	T	102738813	3	4	35	1	0	0	0	0	1	0	0	0	951	536	19	1	871	1	ARMC10	7	102738813	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1895099	102738813	56399850	58	2928										
FLNC	2318	broad.mit.edu	37	chr7	128470916	128470916	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cggctcatcgcgctgctcgaGgtgctcagccagaagcgcat	13	14	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr7:128470916G>T	ENST00000325888.8	+	1	486	c.225G>T	c.(223-225)gaG>gaT	p.E75D	FLNC_ENST00000346177.6_Missense_Mutation_p.E75D	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	75	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.E75D(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CGCTGCTCGAGGTGCTCAGCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	7											51	52	52					7																	128470916		2203	4300	6503	128258152	SO:0001583	missense	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.225G>T	7.37:g.128470916G>T	ENSP00000327145:p.Glu75Asp		128258152	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860687	0.71834	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.66815	-0.23;-0.23	4.49	3.59	0.41128	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	T	0.70806	0.3266	M	0.83774	2.66	0.40987	D	0.98482	B;B	0.27732	0.133;0.187	B;B	0.35931	0.108;0.214	T	0.73049	-0.4105	10	0.87932	D	0	.	10.651	0.45649	0.0986:0.0:0.9014:0.0	.	75;75	Q14315-2;Q14315	.;FLNC_HUMAN	D	75	ENSP00000327145:E75D;ENSP00000344002:E75D	ENSP00000327145:E75D	E	+	3	2	FLNC	128258152	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.385000	0.52485	0.979000	0.38497	0.561000	0.74099	GAG		0.647	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128470916	G	T	128470916	3	4	35	1	0	0	0	0	1	0	0	0	5954	991	35	2	227	2	FLNC	7	128470916	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	25732103	128470916	30667747	59	2929										
CNTNAP2	26047	broad.mit.edu	37	chr7	147869340	147869340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tctgtcattcccaggtggtgCtgggggccagcagggcttcc	15	12	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr7:147869340C>T	ENST00000361727.3	+	18	3296	c.2780C>T	c.(2779-2781)gCt>gTt	p.A927V	CNTNAP2_ENST00000538075.1_5'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	927	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.A927V(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CCAGGTGGTGCTGGGGGCCAG	0.502										HNSCC(39;0.1)																																						1	Substitution - Missense(1)	large_intestine(1)	7											53	54	54					7																	147869340		2203	4300	6503	147500273	SO:0001583	missense	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.2780C>T	7.37:g.147869340C>T	ENSP00000354778:p.Ala927Val		147500273	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518481	0.85495	.	.	ENSG00000174469	ENST00000361727	T	0.76060	-0.99	5.45	4.57	0.56435	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.063306	0.64402	D	0.000007	T	0.67353	0.2884	L	0.39633	1.23	0.80722	D	1	B	0.33345	0.409	B	0.38264	0.269	T	0.62320	-0.6879	10	0.22109	T	0.4	.	12.7302	0.57193	0.0:0.9201:0.0:0.0799	.	927	Q9UHC6	CNTP2_HUMAN	V	927	ENSP00000354778:A927V	ENSP00000354778:A927V	A	+	2	0	CNTNAP2	147500273	1.000000	0.71417	0.230000	0.23976	0.981000	0.71138	7.683000	0.84093	1.304000	0.44892	0.655000	0.94253	GCT		0.502	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	147869340	C	T	147869340	3	4	35	1	0	0	0	0	1	0	0	0	3653	797	28	3	2850	3	CNTNAP2	7	147869340	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	19398424	147869340	11269323	60	2930										
CSMD1	64478	broad.mit.edu	37	chr8	3855603	3855603	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggagatggagctgctggtccCgcgtaaggttcctccgcagg	16	11	0	1	rs544220269		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr8:3855603C>T	ENST00000520002.1	-	5	1195	c.640G>A	c.(640-642)Ggg>Agg	p.G214R	CSMD1_ENST00000537824.1_Missense_Mutation_p.G214R|CSMD1_ENST00000539096.1_Missense_Mutation_p.G214R|CSMD1_ENST00000602723.1_Missense_Mutation_p.G214R|CSMD1_ENST00000542608.1_Missense_Mutation_p.G214R|CSMD1_ENST00000602557.1_Missense_Mutation_p.G214R|CSMD1_ENST00000400186.3_Missense_Mutation_p.G214R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	214	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.G214R(1)		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)		CTGCTGGTCCCGCGTAAGGTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	8											33	36	35					8																	3855603		2090	4253	6343	3843011	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.640G>A	8.37:g.3855603C>T	ENSP00000430733:p.Gly214Arg		3843011	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	20.6	4.015093	0.75161	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29	5.45	5.45	0.79879	.	0.000000	0.26832	U	0.022270	T	0.48021	0.1477	M	0.87381	2.88	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.45220	-0.9276	10	0.25751	T	0.34	-17.6909	18.2724	0.90072	0.0:1.0:0.0:0.0	.	214	E5RIG2	.	R	214;214;76;214;214;214	ENSP00000383047:G214R;ENSP00000430733:G214R;ENSP00000441462:G214R;ENSP00000446243:G214R;ENSP00000441675:G214R	ENSP00000320445:G76R	G	-	1	0	CSMD1	3843011	1.000000	0.71417	0.156000	0.22583	0.337000	0.28794	7.626000	0.83164	2.551000	0.86045	0.655000	0.94253	GGG		0.572	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3855603	C	T	3855603	3	4	35	1	0	0	0	0	1	0	0	0	3950	652	23	1	10131	1	CSMD1	8	3855603	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		3855603	142508419	61	2931										
C8orf41	80185	broad.mit.edu	37	chr8	33369725	33369726	+	Missense_Mutation	DNP	CC	CC	AT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggcccgtctgccatgcagggCcgaccagggaattcttagca							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr8:33369725_33369726CC>AT	ENST00000431156.2	-	2	1024_1025	c.406_407GG>AT	c.(406-408)GGc>ATc	p.G136I	TTI2_ENST00000360742.5_Missense_Mutation_p.G136I|TTI2_ENST00000520636.1_Missense_Mutation_p.G136I|SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000519356.1_5'Flank	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	136								p.G136>?(1)									CCATGCAGGGCCGACCAGGGAA	0.535																																																1	Complex(1)	large_intestine(1)	8																																								33489268	SO:0001583	missense	80185			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.406_407delinsAT	8.37:g.33369725_33369726delinsAT	ENSP00000411169:p.Gly136Ile		33489267	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	DNP	ENST00000431156.2	37	CCDS6090.1																																																																																				0.535	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		AT	33369726	CC	AT	33369725	3	1	35	1	0	0	0	0	1	0	0	0	2433	739	26	2	1147	2	C8orf41	8	33369725	Missense_Mutation	DNP	CC	TCGA-AG-3726-01A-02W-0899-10	29514122	33369725	112994297	62	2932										
ADCY8	114	broad.mit.edu	37	chr8	131848609	131848609	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gcatagatggcaatcatgatCagcagcactgccagcttcag	10	11	3	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr8:131848609C>A	ENST00000286355.5	-	12	4681	c.2589G>T	c.(2587-2589)ctG>ctT	p.L863L	ADCY8_ENST00000377928.3_Silent_p.L732L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	863					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.L863L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CAATCATGATCAGCAGCACTG	0.537										HNSCC(32;0.087)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											167	128	141					8																	131848609		2203	4300	6503	131917791	SO:0001819	synonymous_variant	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2589G>T	8.37:g.131848609C>A			131917791		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																				0.537	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131848609	C	A	131848609	2	1	35	1	0	0	0	0	0	0	0	1	300	813	29	2		2	ADCY8	8	131848609	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	98478884	131848609	14515413	63	2933										
BNC2	54796	broad.mit.edu	37	chr9	16436676	16436676	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ccgaattaaatctttatctcGgttattccttagcataggca	6	9	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr9:16436676G>A	ENST00000380672.4	-	6	1573	c.1516C>T	c.(1516-1518)Cga>Tga	p.R506*	BNC2_ENST00000380666.2_Nonsense_Mutation_p.R506*|BNC2_ENST00000545497.1_Nonsense_Mutation_p.R411*|BNC2_ENST00000380667.2_Nonsense_Mutation_p.R439*	NM_017637.5	NP_060107.3			basonuclin 2									p.R506*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		TCTTTATCTCGGTTATTCCTT	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											97	96	97					9																	16436676		2203	4300	6503	16426676	SO:0001587	stop_gained	54796			AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.1516C>T	9.37:g.16436676G>A	ENSP00000370047:p.Arg506*		16426676		Nonsense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	G	37	6.344417	0.97489	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	.	.	.	5.88	3.99	0.46301	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.566	13.9861	0.64337	0.0:0.0:0.6027:0.3973	.	.	.	.	X	506;463;439;411;332;506;506	.	ENSP00000370041:R506X	R	-	1	2	BNC2	16426676	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.822000	0.55708	0.768000	0.33290	-0.169000	0.13324	CGA		0.502	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16436676	G	A	16436676	4	1	35	1	0	0	0	0	0	1	0	0	1476	1124	39	1	1791	1	BNC2	9	16436676	Nonsense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10		16436676	124776755	64	2934										
PRUNE2	158471	broad.mit.edu	37	chr9	79325540	79325541	+	Missense_Mutation	DNP	TG	TG	AC													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cctgacaaaagtgaactggaTgaataattagacatgttggt							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	TG	TG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr9:79325540_79325541TG>AC	ENST00000376718.3	-	8	1772_1773	c.1649_1650CA>GT	c.(1648-1650)tCA>tGT	p.S550C	PRUNE2_ENST00000428286.1_Missense_Mutation_p.S191C	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	550	Poly-Ser.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.S550>?(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GTGAACTGGATGAATAATTAGA	0.49																																																1	Complex(1)	large_intestine(1)	9																																								78515361	SO:0001583	missense	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.1649_1650delinsAC	9.37:g.79325540_79325541delinsAC	ENSP00000365908:p.Ser550Cys		78515360	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	DNP	ENST00000376718.3	37	CCDS47982.1																																																																																				0.49	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		AC	79325541	TG	AC	79325540	3	1	35	1	0	0	0	0	1	0	0	0	12675	1451	51	5	7664	5	PRUNE2	9	79325540	Missense_Mutation	DNP	TG	TCGA-AG-3726-01A-02W-0899-10	62888864	79325540	61887891	65	2935										
COL27A1	85301	broad.mit.edu	37	chr9	117063736	117063736	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tccctccagggattgcaaggTccgagggtgagtgggctggg	18	9	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr9:117063736T>A	ENST00000356083.3	+	54	5194	c.4803T>A	c.(4801-4803)ggT>ggA	p.G1601G		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1601	Collagen-like 16.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.G1601G(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GATTGCAAGGTCCGAGGGTGA	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	9											39	42	41					9																	117063736		2203	4300	6503	116103557	SO:0001819	synonymous_variant	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4803T>A	9.37:g.117063736T>A			116103557	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																				0.682	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117063736	T	A	117063736	2	1	35	1	0	0	0	0	0	0	0	1	3691	1654	58	5		5	COL27A1	9	117063736	Silent	SNP	T	TCGA-AG-3726-01A-02W-0899-10	37738196	117063736	24149695	66	2936										
TNC	3371	broad.mit.edu	37	chr9	117849445	117849445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gtgacagttgcctggacattCgggctcagagcagttggggc	16	9	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr9:117849445C>T	ENST00000350763.4	-	3	976	c.565G>A	c.(565-567)Gaa>Aaa	p.E189K	TNC_ENST00000423613.2_Missense_Mutation_p.E189K|TNC_ENST00000346706.3_Missense_Mutation_p.E189K|TNC_ENST00000535648.1_Missense_Mutation_p.E189K|TNC_ENST00000345230.3_Missense_Mutation_p.E189K|TNC_ENST00000542877.1_Missense_Mutation_p.E189K|TNC_ENST00000537320.1_Missense_Mutation_p.E189K|TNC_ENST00000341037.4_Missense_Mutation_p.E189K|TNC_ENST00000340094.3_Missense_Mutation_p.E189K	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	189	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.E189K(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCTGGACATTCGGGCTCAGAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	9											103	92	96					9																	117849445		2203	4300	6503	116889266	SO:0001583	missense	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.565G>A	9.37:g.117849445C>T	ENSP00000265131:p.Glu189Lys		116889266	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.244052	0.39697	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;2.81;2.81;2.81;2.81	5.19	5.19	0.71726	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.432977	0.26931	N	0.021778	T	0.06234	0.0161	N	0.20304	0.555	0.09310	N	1	P;B	0.46656	0.882;0.149	B;B	0.37888	0.26;0.03	T	0.37384	-0.9708	10	0.27785	T	0.31	.	8.9179	0.35592	0.0:0.7689:0.1507:0.0805	.	189;189	E9PC84;P24821	.;TENA_HUMAN	K	189	ENSP00000344400:E189K;ENSP00000438152:E189K;ENSP00000344555:E189K;ENSP00000345861:E189K;ENSP00000265131:E189K;ENSP00000339553:E189K;ENSP00000411406:E189K;ENSP00000443478:E189K;ENSP00000442242:E189K	ENSP00000344400:E189K	E	-	1	0	TNC	116889266	0.563000	0.26594	0.253000	0.24343	0.931000	0.56810	2.652000	0.46682	2.586000	0.87340	0.467000	0.42956	GAA		0.622	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117849445	C	T	117849445	3	4	35	1	0	0	0	0	1	0	0	0	16309	893	31	1	6144	1	TNC	9	117849445	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	785709	117849445	23363986	67	2937										
CARD9	64170	broad.mit.edu	37	chr9	139264271	139264272	+	Frame_Shift_Del	DEL	GG	GG	-													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atgcggtccttgtacatcttGgagtccttacgtagtgccag					rs189645633		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr9:139264271_139264272delGG	ENST00000371732.5	-	7	1172_1173	c.1007_1008delCC	c.(1006-1008)tccfs	p.S336fs	CARD9_ENST00000315908.7_Frame_Shift_Del_p.S336fs|CARD9_ENST00000371734.3_Frame_Shift_Del_p.S336fs|CARD9_ENST00000460290.1_5'Flank	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	336					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)	p.S336fs*1(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGTACATCTTGGAGTCCTTACG	0.639																																																1	Deletion - Frameshift(1)	large_intestine(1)	9																																								138384093	SO:0001589	frameshift_variant	64170			AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.1007_1008delCC	9.37:g.139264271_139264272delGG	ENSP00000360797:p.Ser336fs		138384092	Q5SXM5|Q5SXM6|Q9H854	Frame_Shift_Del	DEL	ENST00000371732.5	37	CCDS6997.1																																																																																				0.639	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813		-	139264272	GG	-	139264271	7	5	35	1	0	1	0	1	0	0	0	0	2658	1335	47	0	683	0	CARD9	9	139264271	Frame_Shift_Del	DEL	GG	TCGA-AG-3726-01A-02W-0899-10	21414826	139264271	1949160	68	2938										
DNAJC1	64215	broad.mit.edu	37	chr10	22292227	22292227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggtctccgctctcccagccgCgcgccggcgccacggcggcc	14	21	2	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr10:22292227C>T	ENST00000376980.3	-	1	427	c.137G>A	c.(136-138)cGc>cAc	p.R46H	DNAJC1_ENST00000376946.1_Missense_Mutation_p.R46H	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	46					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R46H(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				CTCCCAgccgcgcgccggcgc	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	10											18	15	16					10																	22292227		2112	4147	6259	22332233	SO:0001583	missense	64215			AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.137G>A	10.37:g.22292227C>T	ENSP00000366179:p.Arg46His		22332233	B0YIZ8|Q5VX89|Q9H6B8	Missense_Mutation	SNP	ENST00000376980.3	37	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.304801	0.40795	.	.	ENSG00000136770	ENST00000376980;ENST00000376946	T;T	0.63417	-0.04;1.49	4.12	2.17	0.27698	.	0.724746	0.13468	N	0.385657	T	0.37625	0.1010	N	0.11927	0.2	0.25771	N	0.984839	B	0.06786	0.001	B	0.01281	0.0	T	0.19582	-1.0301	10	0.18710	T	0.47	.	6.3115	0.21166	0.0:0.7639:0.0:0.2361	.	46	Q96KC8	DNJC1_HUMAN	H	46	ENSP00000366179:R46H;ENSP00000366145:R46H	ENSP00000366145:R46H	R	-	2	0	DNAJC1	22332233	0.951000	0.32395	0.994000	0.49952	0.958000	0.62258	0.307000	0.19296	0.435000	0.26365	0.585000	0.79938	CGC		0.706	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		T	22292227	C	T	22292227	3	4	35	1	0	0	0	0	1	0	0	0	4639	768	27	1	1575	1	DNAJC1	10	22292227	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		22292227	113242520	69	2939										
SORCS3	22986	broad.mit.edu	37	chr10	106974307	106974307	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tcggggcctccatgtggtgaCgaccgatgggcggctggtgg	19	10	0	1	rs201415126		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr10:106974307C>T	ENST00000369701.3	+	18	2710	c.2483C>T	c.(2482-2484)aCg>aTg	p.T828M	SORCS3_ENST00000369699.4_Missense_Mutation_p.T114M	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	828	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.T828M(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CATGTGGTGACGACCGATGGG	0.587																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - Missense(1)	large_intestine(1)	10							MET/THR	0,4406		0,0,2203	58	53	55		2483	5	0.9	10		55	1,8599	1.2+/-3.3	0,1,4299	no	missense	SORCS3	NM_014978.1	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	828/1223	106974307	1,13005	2203	4300	6503	106964297	SO:0001583	missense	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2483C>T	10.37:g.106974307C>T	ENSP00000358715:p.Thr828Met		106964297	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	c	19.42	3.823419	0.71143	0.0	1.16E-4	ENSG00000156395	ENST00000369701;ENST00000369699	T;T	0.69561	-0.41;-0.41	5.89	4.99	0.66335	PKD domain (1);	0.000000	0.85682	D	0.000000	T	0.79179	0.4402	M	0.62723	1.935	0.49915	D	0.999836	D	0.89917	1.0	D	0.87578	0.998	T	0.79179	-0.1910	9	.	.	.	.	15.1529	0.72717	0.0:0.9324:0.0:0.0676	.	828	Q9UPU3	SORC3_HUMAN	M	828;114	ENSP00000358715:T828M;ENSP00000358713:T114M	.	T	+	2	0	SORCS3	106964297	1.000000	0.71417	0.900000	0.35374	0.992000	0.81027	5.768000	0.68858	1.500000	0.48636	0.558000	0.71614	ACG		0.587	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106974307	C	T	106974307	3	4	35	1	0	0	0	0	1	0	0	0	14969	536	19	1	2553	1	SORCS3	10	106974307	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	84682080	106974307	28560440	70	2940										
TCF7L2	6934	broad.mit.edu	37	chr10	114901010	114901011	+	Missense_Mutation	DNP	GC	GC	TT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cacgcctcttatcacgtacaGcaatgaacacttcacgccgg							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr10:114901010_114901011GC>TT	ENST00000355995.4	+	6	1127_1128	c.620_621GC>TT	c.(619-621)aGC>aTT	p.S207I	TCF7L2_ENST00000536810.1_Missense_Mutation_p.S207I|TCF7L2_ENST00000543371.1_Missense_Mutation_p.S207I|TCF7L2_ENST00000369395.1_Missense_Mutation_p.S232I|TCF7L2_ENST00000369397.4_Missense_Mutation_p.S184I|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000349937.2_Missense_Mutation_p.S207I|TCF7L2_ENST00000534894.1_Missense_Mutation_p.S207I|TCF7L2_ENST00000352065.5_Missense_Mutation_p.S184I|TCF7L2_ENST00000538897.1_Missense_Mutation_p.S207I|TCF7L2_ENST00000545257.1_Missense_Mutation_p.S207I|TCF7L2_ENST00000355717.4_Missense_Mutation_p.S231I			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	207	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S231>?(1)|p.S207>?(1)|p.S184>?(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ATCACGTACAGCAATGAACACT	0.564			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	3	Complex(3)	large_intestine(3)	10																																								114891001	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	Exception_encountered	10.37:g.114901010_114901011delinsTT	ENSP00000348274:p.Ser207Ile		114891000	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	DNP	ENST00000355995.4	37																																																																																					0.564	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		TT	114901011	GC	TT	114901010	3	4	35	1	0	0	0	0	1	0	0	0	15737	971	34	2	787	2	TCF7L2	10	114901010	Missense_Mutation	DNP	GC	TCGA-AG-3726-01A-02W-0899-10	7926703	114901010	20633737	71	2941										
DCLRE1A	9937	broad.mit.edu	37	chr10	115612743	115612743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctgacaacctgcatttccaaGgggcacttcatggtccttca	8	13	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr10:115612743G>A	ENST00000361384.2	-	1	1116	c.199C>T	c.(199-201)Ctt>Ttt	p.L67F	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.L67F|DCLRE1A_ENST00000476112.1_5'Flank|NHLRC2_ENST00000369301.3_5'Flank	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	67	Nuclear localization region.				mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)		p.L67F(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		GCATTTCCAAGGGGCACTTCA	0.433								Other identified genes with known or suspected DNA repair function																																								1	Substitution - Missense(1)	large_intestine(1)	10											201	196	198					10																	115612743		2203	4300	6503	115602733	SO:0001583	missense	9937				CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.199C>T	10.37:g.115612743G>A	ENSP00000355185:p.Leu67Phe		115602733	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	37	CCDS7584.1	.	.	.	.	.	.	.	.	.	.	G	6.728	0.503078	0.12822	.	.	ENSG00000198924	ENST00000361384;ENST00000369305	D;D	0.96365	-3.99;-3.99	5.59	1.0	0.19881	.	0.925721	0.08862	N	0.882918	D	0.92577	0.7642	L	0.46157	1.445	0.09310	N	1	B	0.25048	0.117	B	0.20184	0.028	D	0.83970	0.0326	10	0.39692	T	0.17	-0.697	5.287	0.15706	0.2852:0.1554:0.5594:0.0	.	67	Q6PJP8	DCR1A_HUMAN	F	67	ENSP00000355185:L67F;ENSP00000358311:L67F	ENSP00000355185:L67F	L	-	1	0	DCLRE1A	115602733	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.093000	0.15086	0.291000	0.22468	0.557000	0.71058	CTT		0.433	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		A	115612743	G	A	115612743	3	1	35	1	0	0	0	0	1	0	0	0	4300	1000	35	3	2959	3	DCLRE1A	10	115612743	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	711733	115612743	19922004	72	2942										
ART5	116969	broad.mit.edu	37	chr11	3661063	3661064	+	Missense_Mutation	DNP	AG	AG	GC													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agcaagttgttagagagaagAgggtggcattaccaaatctg							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:3661063_3661064AG>GC	ENST00000397068.3	-	2	987_988	c.595_596CT>GC	c.(595-597)CTc>GCc	p.L199A	ART5_ENST00000359918.4_Missense_Mutation_p.L199A|ART5_ENST00000397067.3_Intron|TRPC2_ENST00000526541.1_RNA	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	199					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)	p.L199>?(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		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)		TAGAGAGAAGAGGGTGGCATTA	0.55																																																1	Complex(1)	large_intestine(1)	11																																								3617640	SO:0001583	missense	116969			Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.595_596delinsGC	11.37:g.3661063_3661064delinsGC	ENSP00000380258:p.Leu199Ala		3617639	C9IYG7|Q6UX84|Q86W02	Missense_Mutation	DNP	ENST00000397068.3	37	CCDS7743.1																																																																																				0.55	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017		GC	3661064	AG	GC	3661063	3	3	35	1	0	0	0	0	1	0	0	0	1001	304	11	4	291	4	ART5	11	3661063	Missense_Mutation	DNP	AG	TCGA-AG-3726-01A-02W-0899-10		3661063	131345453	73	2943										
ARNTL	406	broad.mit.edu	37	chr11	13397168	13397168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tacattttcagttttacagaCgagagaaaaaattacaacta	5	6	1	2	rs370345058		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:13397168C>T	ENST00000403290.1	+	15	1539	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	ARNTL_ENST00000401424.1_Missense_Mutation_p.T352M|ARNTL_ENST00000403510.3_Missense_Mutation_p.T351M|ARNTL_ENST00000403482.3_Missense_Mutation_p.T393M|ARNTL_ENST00000389707.4_Missense_Mutation_p.T394M|ARNTL_ENST00000389708.3_Missense_Mutation_p.T395M|ARNTL_ENST00000361003.4_Missense_Mutation_p.T277M|ARNTL_ENST00000396441.3_Missense_Mutation_p.T394M			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	395	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.T394M(2)		breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		GTTTTACAGACGAGAGAAAAA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	11						C	MET/THR,MET/THR,MET/THR	2,4398	4.2+/-10.8	0,2,2198	40	41	41		1181,1052,1181	5.4	0.9	11		41	0,8584		0,0,4292	no	missense,missense,missense	ARNTL	NM_001178.4,NM_001030273.1,NM_001030272.1	81,81,81	0,2,6490	TT,TC,CC		0.0,0.0455,0.0154	benign,benign,benign	394/626,351/583,394/626	13397168	2,12982	2200	4292	6492	13353744	SO:0001583	missense	406			D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1184C>T	11.37:g.13397168C>T	ENSP00000384517:p.Thr395Met		13353744	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	De_novo_Start_OutOfFrame	SNP	ENST00000403290.1	37		.	.	.	.	.	.	.	.	.	.	C	13.79	2.342650	0.41498	4.55E-4	0.0	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000389708;ENST00000403510;ENST00000339640;ENST00000403482	T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.4	5.4	0.78164	PAS fold-3 (1);PAS (2);	0.092020	0.85682	D	0.000000	T	0.14399	0.0348	N	0.22421	0.69	0.43874	D	0.996489	B;B;B;B;B;B	0.27192	0.002;0.171;0.008;0.004;0.004;0.081	B;B;B;B;B;B	0.20184	0.004;0.027;0.01;0.006;0.003;0.028	T	0.04467	-1.0949	10	0.46703	T	0.11	.	18.7646	0.91866	0.0:1.0:0.0:0.0	.	277;393;352;395;394;351	O00327-4;O00327-7;O00327-1;O00327;O00327-8;A2I2N6	.;.;.;BMAL1_HUMAN;.;.	M	394;394;352;395;277;395;351;351;393	ENSP00000379718:T394M;ENSP00000374357:T394M;ENSP00000385915:T352M;ENSP00000384517:T395M;ENSP00000354278:T277M;ENSP00000374358:T395M;ENSP00000385581:T351M;ENSP00000385897:T393M	ENSP00000340289:T351M	T	+	2	0	ARNTL	13353744	1.000000	0.71417	0.947000	0.38551	0.884000	0.51177	5.587000	0.67510	2.510000	0.84645	0.555000	0.69702	ACG		0.323	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		T	13397168	C	T	13397168	3	4	35	1	0	0	0	0	1	0	0	0	968	536	19	1	1238	1	ARNTL	11	13397168	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	9736105	13397168	121609348	74	2944										
OR4A5	81318	broad.mit.edu	37	chr11	51412212	51412212	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atctataaatgacaggcaggCaaggaagaaatacattgggg	12	5	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:51412212C>A	ENST00000319760.6	-	1	236	c.184G>T	c.(184-186)Gcc>Tcc	p.A62S		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A62S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				GACAGGCAGGCAAGGAAGAAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											61	59	60					11																	51412212		2201	4296	6497	51268788	SO:0001583	missense	81318			AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.184G>T	11.37:g.51412212C>A	ENSP00000367664:p.Ala62Ser		51268788	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	1.038	-0.679875	0.03353	.	.	ENSG00000221840	ENST00000319760	T	0.01084	5.36	1.93	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.643454	0.13420	N	0.389205	T	0.00666	0.0022	N	0.04090	-0.28	0.18873	N	0.999989	B	0.28128	0.201	B	0.31245	0.126	T	0.48603	-0.9021	10	0.10636	T	0.68	.	6.4367	0.21827	0.0:0.6895:0.3105:0.0	.	62	Q8NH83	OR4A5_HUMAN	S	62	ENSP00000367664:A62S	ENSP00000367664:A62S	A	-	1	0	OR4A5	51268788	0.000000	0.05858	0.837000	0.33122	0.025000	0.11179	-1.678000	0.01942	1.394000	0.46624	0.162000	0.16502	GCC		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51412212	C	A	51412212	3	1	35	1	0	0	0	0	1	0	0	0	11074	710	25	2	767	2	OR4A5	11	51412212	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	38015044	51412212	83594304	75	2945										
PLCB3	5331	broad.mit.edu	37	chr11	64033794	64033794	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ccggcttctccagggagaagAaggagctgcagaagatcctg	14	10	1	4			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:64033794A>T	ENST00000540288.1	+	28	3377	c.3274A>T	c.(3274-3276)Aag>Tag	p.K1092*	PLCB3_ENST00000279230.6_Nonsense_Mutation_p.K1092*|PLCB3_ENST00000325234.5_Nonsense_Mutation_p.K1025*	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1092				REKKELQKILDRKRHNSISEAKMRDKHKKEA -> SWPSWP RSVRSSGRGSPRRSAGACWARCRRG (in Ref. 2; CAA85776). {ECO:0000305}.	inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.K1092*(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CAGGGAGAAGAAGGAGCTGCA	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											59	64	62					11																	64033794		2201	4297	6498	63790370	SO:0001587	stop_gained	5331			Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.3274A>T	11.37:g.64033794A>T	ENSP00000443631:p.Lys1092*		63790370	A5PKZ6|G5E960|Q8N1A4	Nonsense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	A	41	8.631788	0.98892	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	.	.	.	5.17	5.17	0.71159	.	0.653399	0.16815	N	0.198407	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9879	0.64348	1.0:0.0:0.0:0.0	.	.	.	.	X	1092;1092;1025	.	ENSP00000279230:K1092X	K	+	1	0	PLCB3	63790370	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.908000	0.75730	1.959000	0.56917	0.454000	0.30748	AAG		0.587	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			T	64033794	A	T	64033794	4	4	35	1	0	0	0	0	0	1	0	0	12060	247	9	5	3384	5	PLCB3	11	64033794	Nonsense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	12621582	64033794	70972722	76	2946										
CUL5	8065	broad.mit.edu	37	chr11	107965671	107965672	+	Missense_Mutation	DNP	GT	GT	AG													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	attctacaaaaaaaatcataGtggtagaaaattacattggc							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:107965671_107965672GT>AG	ENST00000393094.2	+	15	2316_2317	c.1700_1701GT>AG	c.(1699-1701)aGT>aAG	p.S567K		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	567					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)	p.S567>?(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		AAAAATCATAGTGGTAGAAAAT	0.381																																																1	Complex(1)	large_intestine(1)	11																																								107470882	SO:0001583	missense	8065			X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	Exception_encountered	11.37:g.107965671_107965672delinsAG	ENSP00000376808:p.Ser567Lys		107470881	A8K960|O14766|Q9BZC6	Missense_Mutation	DNP	ENST00000393094.2	37	CCDS31668.1																																																																																				0.381	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			AG	107965672	GT	AG	107965671	3	1	35	1	0	0	0	0	1	0	0	0	4065	1029	36	3	1758	3	CUL5	11	107965671	Missense_Mutation	DNP	GT	TCGA-AG-3726-01A-02W-0899-10	43931877	107965671	27040845	77	2947										
ZBTB16	7704	broad.mit.edu	37	chr11	114112927	114112927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tctgtctgctgtgtgggaagCgcttccaggcgcagagcgca	15	11	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:114112927C>T	ENST00000335953.4	+	5	1872	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	ZBTB16_ENST00000535379.1_3'UTR|RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000392996.2_Missense_Mutation_p.R498C	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	498					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R498C(1)		central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GTGTGGGAAGCGCTTCCAGGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											81	56	65					11																	114112927		2201	4296	6497	113618137	SO:0001583	missense	7704			Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1492C>T	11.37:g.114112927C>T	ENSP00000338157:p.Arg498Cys		113618137	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	C	32	5.180751	0.94846	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.52295	0.67;0.67	5.33	5.33	0.75918	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	L	0.60845	1.875	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.67998	-0.5525	10	0.62326	D	0.03	-8.8717	19.4129	0.94683	0.0:1.0:0.0:0.0	.	498	Q05516	ZBT16_HUMAN	C	498;498;375	ENSP00000338157:R498C;ENSP00000376721:R498C	ENSP00000309507:R375C	R	+	1	0	ZBTB16	113618137	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	4.754000	0.62191	2.652000	0.90054	0.655000	0.94253	CGC		0.612	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		T	114112927	C	T	114112927	3	4	35	1	0	0	0	0	1	0	0	0	17565	768	27	1	1506	1	ZBTB16	11	114112927	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	6147256	114112927	20893589	78	2948										
OR10G7	390265	broad.mit.edu	37	chr11	123909245	123909245	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tcaatatggtctggacagcaGagtgcagagagccactgagc	13	9	2	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:123909245G>A	ENST00000330487.5	-	1	472	c.464C>T	c.(463-465)tCt>tTt	p.S155F		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S155F(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CTGGACAGCAGAGTGCAGAGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11											138	135	136					11																	123909245		2200	4297	6497	123414455	SO:0001583	missense	390265			AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"GPCR / Class A : Olfactory receptors"	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.464C>T	11.37:g.123909245G>A	ENSP00000329689:p.Ser155Phe		123414455	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.734653	0.48939	.	.	ENSG00000182634	ENST00000330487	T	0.44881	0.91	3.24	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.347872	0.20989	N	0.082077	T	0.64549	0.2608	M	0.87269	2.87	0.34183	D	0.671209	D	0.67145	0.996	D	0.76575	0.988	T	0.75789	-0.3194	10	0.87932	D	0	.	8.6875	0.34247	0.1098:0.0:0.8902:0.0	.	155	Q8NGN6	O10G7_HUMAN	F	155	ENSP00000329689:S155F	ENSP00000329689:S155F	S	-	2	0	OR10G7	123414455	0.003000	0.15002	1.000000	0.80357	0.825000	0.46686	1.272000	0.33109	1.826000	0.53198	0.455000	0.32223	TCT		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		A	123909245	G	A	123909245	3	1	35	1	0	0	0	0	1	0	0	0	10933	942	33	3	475	3	OR10G7	11	123909245	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	9796318	123909245	11097271	79	2949										
ROBO3	64221	broad.mit.edu	37	chr11	124750355	124750355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gcagaccaagcttcctgtccCggggccagggcaccagcaca	12	16	0	1	rs374478103		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:124750355C>T	ENST00000397801.1	+	27	4192	c.4000C>T	c.(4000-4002)Cgg>Tgg	p.R1334W	ROBO3_ENST00000543966.1_Missense_Mutation_p.R97W|ROBO3_ENST00000538940.1_Missense_Mutation_p.R1312W|ROBO3_ENST00000525482.1_3'UTR	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	1334					axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)		p.R1334W(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		CTTCCTGTCCCGGGGCCAGGG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	TRP/ARG	0,4020		0,0,2010	25	30	28		4000	4.7	0.8	11		28	1,8377		0,1,4188	no	missense	ROBO3	NM_022370.3	101	0,1,6198	TT,TC,CC		0.0119,0.0,0.0081	probably-damaging	1334/1387	124750355	1,12397	2010	4189	6199	124255565	SO:0001583	missense	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.4000C>T	11.37:g.124750355C>T	ENSP00000380903:p.Arg1334Trp		124255565		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117955	0.56505	0.0	1.19E-4	ENSG00000154134	ENST00000397801;ENST00000538940;ENST00000543966	T;T;T	0.72942	-0.7;-0.69;0.4	5.62	4.7	0.59300	.	0.556287	0.13801	N	0.361808	T	0.77246	0.4102	L	0.58101	1.795	0.36107	D	0.844566	D	0.76494	0.999	P	0.54210	0.745	T	0.82212	-0.0569	10	0.87932	D	0	.	14.2659	0.66118	0.2709:0.7291:0.0:0.0	.	1334	Q96MS0	ROBO3_HUMAN	W	1334;1312;97	ENSP00000380903:R1334W;ENSP00000441797:R1312W;ENSP00000438799:R97W	ENSP00000380903:R1334W	R	+	1	2	ROBO3	124255565	0.997000	0.39634	0.809000	0.32408	0.415000	0.31203	0.781000	0.26774	1.356000	0.45884	0.655000	0.94253	CGG		0.662	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		T	124750355	C	T	124750355	3	4	35	1	0	0	0	0	1	0	0	0	13552	643	23	1	4106	1	ROBO3	11	124750355	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	841110	124750355	10256161	80	2950										
OPCML	4978	broad.mit.edu	37	chr11	132527122	132527122	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tattgaccaggatgatcacaCgagggtctatggaccacttg	11	9	2	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr11:132527122C>T	ENST00000331898.7	-	2	838	c.260G>A	c.(259-261)cGt>cAt	p.R87H	OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Missense_Mutation_p.R87H|OPCML_ENST00000524381.1_Missense_Mutation_p.R80H|OPCML_ENST00000374778.4_Missense_Mutation_p.R46H	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	87	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.R87H(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GATGATCACACGAGGGTCTAT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											231	169	190					11																	132527122		2201	4297	6498	132032332	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.260G>A	11.37:g.132527122C>T	ENSP00000330862:p.Arg87His		132032332	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	De_novo_Start_OutOfFrame	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	32	5.192401	0.94960	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000541867	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.92	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.058301	0.64402	N	0.000001	T	0.75361	0.3839	H	0.96365	3.81	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.999	D	0.84226	0.0464	10	0.87932	D	0	-5.6923	15.0633	0.71973	0.0:0.9322:0.0:0.0678	.	87;80;87;87	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	H	87;80;46;87	ENSP00000330862:R87H;ENSP00000434750:R80H;ENSP00000363910:R46H;ENSP00000445496:R87H	ENSP00000330862:R87H	R	-	2	0	OPCML	132032332	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	7.764000	0.85297	1.521000	0.48983	0.655000	0.94253	CGT		0.532	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132527122	C	T	132527122	3	4	35	1	0	0	0	0	1	0	0	0	10905	536	19	1	801	1	OPCML	11	132527122	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	7776767	132527122	2479394	81	2951										
TAS2R10	50839	broad.mit.edu	37	chr12	10978857	10978857	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aaaatgaagatgccttccacTacacgtagcatatctgctaa	6	10	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:10978857T>A	ENST00000240619.2	-	1	100	c.12A>T	c.(10-12)gtA>gtT	p.V4V		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	4					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.V4V(1)		breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						TGCCTTCCACTACACGTAGCA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	12											77	69	72					12																	10978857		2202	4296	6498	10870124	SO:0001819	synonymous_variant	50839			AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.12A>T	12.37:g.10978857T>A			10870124	Q3MIM9|Q6NTD9	Silent	SNP	ENST00000240619.2	37	CCDS8634.1																																																																																				0.403	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			A	10978857	T	A	10978857	2	1	35	1	0	0	0	0	0	0	0	1	15605	1509	53	5		5	TAS2R10	12	10978857	Silent	SNP	T	TCGA-AG-3726-01A-02W-0899-10		10978857	122873038	82	2952										
LRP6	4040	broad.mit.edu	37	chr12	12284793	12284793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctgatttgtcctggcagtttGcatctccattgcatcggagg	11	10	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:12284793G>A	ENST00000261349.4	-	18	4008	c.3932C>T	c.(3931-3933)gCa>gTa	p.A1311V	LRP6_ENST00000543091.1_Missense_Mutation_p.A1266V|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000540415.1_5'UTR	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1311	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A1311V(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CTGGCAGTTTGCATCTCCATT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	12											152	122	132					12																	12284793		2203	4300	6503	12176060	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3932C>T	12.37:g.12284793G>A	ENSP00000261349:p.Ala1311Val		12176060	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.276820	0.40294	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.95518	-3.73;-3.73	5.92	5.92	0.95590	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000010	D	0.92430	0.7597	L	0.31065	0.9	0.45762	D	0.998651	B;B	0.02656	0.0;0.0	B;B	0.10450	0.002;0.005	D	0.87155	0.2211	10	0.28530	T	0.3	.	20.3081	0.98638	0.0:0.0:1.0:0.0	.	1266;1311	F5H7J9;O75581	.;LRP6_HUMAN	V	1311;1266	ENSP00000261349:A1311V;ENSP00000442472:A1266V	ENSP00000261349:A1311V	A	-	2	0	LRP6	12176060	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.035000	0.57297	2.795000	0.96236	0.655000	0.94253	GCA		0.463	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12284793	G	A	12284793	3	1	35	1	0	0	0	0	1	0	0	0	8991	1319	46	3	933	3	LRP6	12	12284793	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	1305936	12284793	121567102	83	2953										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	35	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	13113491	25398284	108453611	84	2954										
BHLHE41	79365	broad.mit.edu	37	chr12	26276012	26276012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ccagctctcaaaccgggagaGgtattgcaagacttctttgg	11	10	2	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:26276012G>A	ENST00000242728.4	-	5	783	c.436C>T	c.(436-438)Ctc>Ttc	p.L146F	RP11-283G6.3_ENST00000545819.1_RNA|RP11-283G6.3_ENST00000535914.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	146	Orange. {ECO:0000255|PROSITE- ProRule:PRU00380}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)	p.L146F(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						AACCGGGAGAGGTATTGCAAG	0.582											OREG0021711	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											25	27	26					12																	26276012		2203	4300	6503	26167279	SO:0001583	missense	79365			AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.436C>T	12.37:g.26276012G>A	ENSP00000242728:p.Leu146Phe	785	26167279	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	37	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238760	0.79800	.	.	ENSG00000123095	ENST00000242728;ENST00000540731	T	0.72725	-0.68	2.85	2.85	0.33270	Orange subgroup (1);Orange (2);	0.000000	0.64402	U	0.000013	D	0.82449	0.5039	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85111	0.0963	10	0.87932	D	0	-9.0858	12.6715	0.56870	0.0:0.0:1.0:0.0	.	146	Q9C0J9	BHE41_HUMAN	F	146	ENSP00000242728:L146F	ENSP00000242728:L146F	L	-	1	0	BHLHE41	26167279	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	6.898000	0.75676	1.598000	0.50083	0.467000	0.42956	CTC		0.582	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		A	26276012	G	A	26276012	3	1	35	1	0	0	0	0	1	0	0	0	1425	1000	35	3	1016	3	BHLHE41	12	26276012	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	877728	26276012	107575883	85	2955										
KLHDC5	57542	broad.mit.edu	37	chr12	27950731	27950731	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gtgacgtccacattcgcaagCagcagatggtgtctgtggaa	13	9	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:27950731C>A	ENST00000381271.2	+	3	1461	c.1150C>A	c.(1150-1152)Cag>Aag	p.Q384K	RP11-860B13.3_ENST00000543527.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	384					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.Q384K(1)									CATTCGCAAGCAGCAGATGGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12											153	148	150					12																	27950731		2203	4300	6503	27841998	SO:0001583	missense	57542			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"Kelch-like"	29252	protein-coding gene	gene with protein product			"kelch domain containing 5"	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.1150C>A	12.37:g.27950731C>A	ENSP00000370671:p.Gln384Lys		27841998	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858775	0.91433	.	.	ENSG00000087448	ENST00000381271	T	0.65916	-0.18	5.29	5.29	0.74685	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.70500	0.3231	L	0.51422	1.61	0.58432	D	0.999995	D	0.63880	0.993	D	0.70935	0.971	T	0.64580	-0.6374	10	0.02654	T	1	.	17.9151	0.88947	0.0:1.0:0.0:0.0	.	384	Q9P2K6	KLDC5_HUMAN	K	384	ENSP00000370671:Q384K	ENSP00000370671:Q384K	Q	+	1	0	KLHDC5	27841998	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.270000	0.78493	2.452000	0.82932	0.561000	0.74099	CAG		0.547	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		A	27950731	C	A	27950731	3	1	35	1	0	0	0	0	1	0	0	0	8380	711	25	2	1160	2	KLHDC5	12	27950731	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1674719	27950731	105901164	86	2956										
KRT7	3855	broad.mit.edu	37	chr12	52642412	52642413	+	Missense_Mutation	DNP	TG	TG	AA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggtggcagtagcagtggcggTggcattgggctgaccctcgg							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	TG	TG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:52642412_52642413TG>AA	ENST00000331817.5	+	9	1461_1462	c.1278_1279TG>AA	c.(1276-1281)ggTGgc>ggAAgc	p.G427S	KRT7_ENST00000552322.1_3'UTR|RP3-416H24.1_ENST00000546686.1_RNA|KRT121P_ENST00000529785.1_RNA|KRT86_ENST00000544024.1_5'Flank	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	427	Tail.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.G426>?(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	GCAGTGGCGGTGGCATTGGGCT	0.614																																																1	Complex(1)	large_intestine(1)	12																																								50928680	SO:0001583	missense	3855				CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"-", "Intermediate filaments type II, keratins (basic)"	6445	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 7", "cytokeratin 7", "sarcolectin", "keratin, 55K type II cytoskeletal"	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	Exception_encountered	12.37:g.52642412_52642413delinsAA	ENSP00000329243:p.Gly427Ser		50928679	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	DNP	ENST00000331817.5	37	CCDS8822.1																																																																																				0.614	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		AA	52642413	TG	AA	52642412	3	1	35	1	0	0	0	0	1	0	0	0	8504	1683	59	5	1312	5	KRT7	12	52642412	Missense_Mutation	DNP	TG	TCGA-AG-3726-01A-02W-0899-10	24691681	52642412	81209483	87	2957										
KRT86	3892	broad.mit.edu	37	chr12	52699515	52699515	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cgcaccaaggaggagatcaaCgagctgaaccgcatgatcca	11	12	1	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:52699515C>T	ENST00000423955.2	+	8	1147	c.969C>T	c.(967-969)aaC>aaT	p.N323N	KRT86_ENST00000293525.5_Silent_p.N323N|KRT86_ENST00000544024.1_Silent_p.N323N|RP11-845M18.6_ENST00000552441.1_RNA			O43790	KRT86_HUMAN	keratin 86	323	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.N323N(1)		breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGAGATCAACGAGCTGAACC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	12											128	113	118					12																	52699515		2203	4300	6503	50985782	SO:0001819	synonymous_variant	3892			X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"-", "Intermediate filaments type II, keratins (basic)"	6463	protein-coding gene	gene with protein product	"hard keratin type II 6"	601928	"keratin, hair, basic, 6 (monilethrix)"	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.969C>T	12.37:g.52699515C>T			50985782	P78387	Silent	SNP	ENST00000423955.2	37	CCDS41785.1																																																																																				0.592	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		T	52699515	C	T	52699515	2	4	35	1	0	0	0	0	0	0	0	1	8521	535	19	1		1	KRT86	12	52699515	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	57103	52699515	81152380	88	2958										
ERBB3	2065	broad.mit.edu	37	chr12	56494864	56494864	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggagtctgcagtttctgggaGcagtgaacggtgcccccgtc	15	11	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:56494864G>A	ENST00000267101.3	+	27	3661	c.3221G>A	c.(3220-3222)aGc>aAc	p.S1074N	ERBB3_ENST00000450146.2_Missense_Mutation_p.S431N|RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000549832.1_Missense_Mutation_p.S194N|ERBB3_ENST00000553131.1_Missense_Mutation_p.S315N|ERBB3_ENST00000415288.2_Missense_Mutation_p.S1015N	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1074					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)	p.S1074N(1)		central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			GTTTCTGGGAGCAGTGAACGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											34	32	33					12																	56494864		2203	4300	6503	54781131	SO:0001583	missense	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3221G>A	12.37:g.56494864G>A	ENSP00000267101:p.Ser1074Asn		54781131	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.337484	0.00224	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.78481	-1.05;-0.96;-1.04;-1.18;-0.91	5.39	1.49	0.22878	.	0.464806	0.21330	N	0.076316	T	0.53626	0.1808	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.004;0.008;0.002	B;B;B	0.16289	0.015;0.007;0.007	T	0.39542	-0.9609	10	0.33940	T	0.23	.	6.4261	0.21770	0.1564:0.2824:0.5612:0.0	.	1015;194;1074	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	N	1074;431;1015;197;315;194	ENSP00000267101:S1074N;ENSP00000399178:S431N;ENSP00000408340:S1015N;ENSP00000449129:S315N;ENSP00000448729:S194N	ENSP00000267101:S1074N	S	+	2	0	ERBB3	54781131	0.009000	0.17119	0.000000	0.03702	0.042000	0.13812	1.098000	0.31000	0.100000	0.17581	0.655000	0.94253	AGC		0.468	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			A	56494864	G	A	56494864	3	1	35	1	0	0	0	0	1	0	0	0	5221	971	34	3	3458	3	ERBB3	12	56494864	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	3795349	56494864	77357031	89	2959										
SLC17A8	246213	broad.mit.edu	37	chr12	100751241	100751241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aaggaaggagtgaagaacgcCgtgggagattctttgggaat	16	4	1	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:100751241C>T	ENST00000323346.5	+	1	385	c.72C>T	c.(70-72)gcC>gcT	p.A24A	SLC17A8_ENST00000392989.3_Silent_p.A24A	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	24					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.A24A(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						TGAAGAACGCCGTGGGAGATT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											78	88	84					12																	100751241		2203	4300	6503	99275372	SO:0001819	synonymous_variant	246213			AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.72C>T	12.37:g.100751241C>T			99275372	B3KXZ6|B7ZKV4|Q17RQ8	Silent	SNP	ENST00000323346.5	37	CCDS9077.1																																																																																				0.408	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		T	100751241	C	T	100751241	2	4	35	1	0	0	0	0	0	0	0	1	14460	639	23	1		1	SLC17A8	12	100751241	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	44256377	100751241	33100654	90	2960										
SLC5A8	160728	broad.mit.edu	37	chr12	101581229	101581229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atggtacctggaatatagggCgagcccacaaaacactgagc	11	10	0	1	rs377445681		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:101581229C>T	ENST00000536262.2	-	7	1456	c.898G>A	c.(898-900)Gcc>Acc	p.A300T		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8									p.A300T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GAATATAGGGCGAGCCCACAA	0.453																																					GBM(60;420 1056 13605 22380 47675)											1	Substitution - Missense(1)	large_intestine(1)	12						C	THR/ALA	0,4406		0,0,2203	113	104	107		898	3.5	1	12		107	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC5A8	NM_145913.3	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	300/611	101581229	1,13005	2203	4300	6503	100105360	SO:0001583	missense	160728			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.898G>A	12.37:g.101581229C>T	ENSP00000445340:p.Ala300Thr		100105360		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	C	7.110	0.575850	0.13623	0.0	1.16E-4	ENSG00000256870	ENST00000536262	D	0.87809	-2.3	5.35	3.46	0.39613	.	0.227900	0.46442	D	0.000294	T	0.77903	0.4200	N	0.16368	0.405	0.35630	D	0.810134	B	0.21381	0.055	B	0.22753	0.041	T	0.73748	-0.3885	10	0.33940	T	0.23	.	14.2763	0.66181	0.3865:0.6135:0.0:0.0	.	300	Q8N695	SC5A8_HUMAN	T	300	ENSP00000445340:A300T	ENSP00000445340:A300T	A	-	1	0	SLC5A8	100105360	0.000000	0.05858	0.968000	0.41197	0.102000	0.19082	-0.479000	0.06567	0.582000	0.29556	-0.535000	0.04281	GCC		0.453	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		T	101581229	C	T	101581229	3	4	35	1	0	0	0	0	1	0	0	0	14708	768	27	1	970	1	SLC5A8	12	101581229	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	829988	101581229	32270666	91	2961										
HNF1A	6927	broad.mit.edu	37	chr12	121426705	121426706	+	Missense_Mutation	DNP	GG	GG	AA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cacaacatcccacagcgggaGgtggtcgataccactggcct							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:121426705_121426706GG>AA	ENST00000257555.6	+	2	622_623	c.396_397GG>AA	c.(394-399)gaGGtg>gaAAtg	p.V133M	HNF1A_ENST00000544413.1_Missense_Mutation_p.V133M|HNF1A_ENST00000400024.2_Missense_Mutation_p.V133M|HNF1A_ENST00000402929.1_Missense_Mutation_p.V133M|HNF1A_ENST00000541395.1_Missense_Mutation_p.V133M|HNF1A_ENST00000543427.1_Missense_Mutation_p.V16M|HNF1A_ENST00000538626.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	133			V -> M (in MODY3).		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E132>?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACAGCGGGAGGTGGTCGATAC	0.619									Hepatic Adenoma, Familial Clustering of																																							1	Complex(1)	large_intestine(1)	12	GRCh37	CM002110|CM082851|CM082870	HNF1A	M																																				119911089	SO:0001583	missense	6927	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	Exception_encountered	12.37:g.121426705_121426706delinsAA	ENSP00000257555:p.Val133Met		119911088	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	DNP	ENST00000257555.6	37	CCDS9209.1																																																																																				0.619	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		AA	121426706	GG	AA	121426705	3	1	35	1	0	0	0	0	1	0	0	0	7272	991	35	3	402	3	HNF1A	12	121426705	Missense_Mutation	DNP	GG	TCGA-AG-3726-01A-02W-0899-10	19845476	121426705	12425190	92	2962										
GPR109B	8843	broad.mit.edu	37	chr12	123201276	123201276	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aagtgatcctgcagatggtgCcgattcatgagtgcagctag	13	8	1	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr12:123201276C>T	ENST00000528880.2	-	1	163	c.9G>A	c.(7-9)cgG>cgA	p.R3R	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	3					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R3R(3)		endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	GCAGATGGTGCCGATTCATGA	0.542																																																3	Substitution - coding silent(3)	large_intestine(3)	12											80	69	73					12																	123201276		2203	4300	6503	121767229	SO:0001819	synonymous_variant	8843			D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	16824	protein-coding gene	gene with protein product		606039	"G protein-coupled receptor 109B"	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.9G>A	12.37:g.123201276C>T			121767229	A8K4G5|B2R830|E9PI97|Q8NGE4	Silent	SNP	ENST00000528880.2	37	CCDS53842.1																																																																																				0.542	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018		T	123201276	C	T	123201276	2	4	35	1	0	0	0	0	0	0	0	1	6646	726	26	3		3	GPR109B	12	123201276	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1774571	123201276	10650619	93	2963										
MYH6	4624	broad.mit.edu	37	chr14	23869923	23869924	+	Missense_Mutation	DNP	AG	AG	GT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggggtcccaactcacgtcgaAgatctcgaagccagcgatgt							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr14:23869923_23869924AG>GT	ENST00000356287.3	-	12	1433_1434	c.1404_1405CT>AC	c.(1402-1407)atCTtc>atACtc	p.F469L	MYH6_ENST00000405093.3_Missense_Mutation_p.F469L			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	469	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.I468>?(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CTCACGTCGAAGATCTCGAAGC	0.559																																																1	Complex(1)	large_intestine(1)	14																																								22939764	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1404_1405delinsGT	14.37:g.23869923_23869924delinsGT	ENSP00000348634:p.Phe469Leu		22939763	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	DNP	ENST00000356287.3	37	CCDS9600.1																																																																																				0.559	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			GT	23869924	AG	GT	23869923	3	3	35	1	0	0	0	0	1	0	0	0	10068	72	3	4	4522	4	MYH6	14	23869923	Missense_Mutation	DNP	AG	TCGA-AG-3726-01A-02W-0899-10		23869923	83479617	94	2964										
CCDC88C	440193	broad.mit.edu	37	chr14	91744454	91744454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gcggccgagggcgttgcgtcCcggtgtgctggcttcccggg	19	13	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr14:91744454C>T	ENST00000389857.6	-	29	4956	c.4870G>A	c.(4870-4872)Gga>Aga	p.G1624R	CCDC88C_ENST00000331194.7_Missense_Mutation_p.G148R	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1624					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.G1624R(1)|p.G148R(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GCGTTGCGTCCCGGTGTGCTG	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	14											16	20	19					14																	91744454		2046	4182	6228	90814207	SO:0001583	missense	440193				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.4870G>A	14.37:g.91744454C>T	ENSP00000374507:p.Gly1624Arg		90814207	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.694600	0.30052	.	.	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.42513	2.56;0.97	5.44	4.44	0.53790	.	0.502367	0.16523	U	0.210720	T	0.50429	0.1615	L	0.51422	1.61	0.09310	N	1	P;D;D	0.67145	0.893;0.996;0.996	B;D;D	0.63381	0.361;0.914;0.914	T	0.40646	-0.9552	10	0.51188	T	0.08	-28.5025	6.1509	0.20310	0.0:0.8418:0.0:0.1582	.	1624;148;74	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	R	1624;148;148	ENSP00000374507:G1624R;ENSP00000330332:G148R	ENSP00000330332:G148R	G	-	1	0	CCDC88C	90814207	0.001000	0.12720	0.101000	0.21167	0.047000	0.14425	0.475000	0.22164	2.550000	0.86006	0.462000	0.41574	GGA		0.687	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91744454	C	T	91744454	3	4	35	1	0	0	0	0	1	0	0	0	2871	632	22	3	1224	3	CCDC88C	14	91744454	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	67874531	91744454	15605086	95	2965										
SERPINA9	327657	broad.mit.edu	37	chr14	94936084	94936084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gctctttgtggaggaagggcGggggtatgcactgggggcat	20	6	1	0	rs370139069		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr14:94936084G>A	ENST00000380365.3	-	2	172	c.94C>T	c.(94-96)Cgc>Tgc	p.R32C	SERPINA9_ENST00000337425.5_Missense_Mutation_p.R50C|SERPINA9_ENST00000298845.7_Missense_Mutation_p.R50C|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000448305.2_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	32					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R50C(2)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GAGGAAGGGCGGGGGTATGCA	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	14						G	CYS/ARG,CYS/ARG	3,4045		0,3,2021	80	83	82		148,148	-4.6	0	14		82	0,8346		0,0,4173	no	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	180,180	0,3,6194	AA,AG,GG		0.0,0.0741,0.0242	benign,benign	50/336,50/436	94936084	3,12391	2024	4173	6197	94005837	SO:0001583	missense	327657			AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"Serine (or cysteine) peptidase inhibitors"	15995	protein-coding gene	gene with protein product		615677	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.94C>T	14.37:g.94936084G>A	ENSP00000369723:p.Arg32Cys		94005837	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		.	.	.	.	.	.	.	.	.	.	G	9.277	1.047155	0.19827	7.41E-4	0.0	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.87571	-2.27;-2.27;-2.27	3.99	-4.58	0.03410	Serpin domain (1);	6.324830	0.00424	U	0.000062	T	0.72503	0.3468	N	0.08118	0	0.09310	N	0.999997	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.0	T	0.62656	-0.6808	10	0.87932	D	0	.	4.5267	0.11985	0.5484:0.0:0.2345:0.2171	.	32;50;50	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	C	50;50;32	ENSP00000298845:R50C;ENSP00000337133:R50C;ENSP00000369723:R32C	ENSP00000298845:R50C	R	-	1	0	SERPINA9	94005837	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	0.163000	0.16520	-0.508000	0.06540	0.313000	0.20887	CGC		0.557	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739		A	94936084	G	A	94936084	3	1	35	1	0	0	0	0	1	0	0	0	14132	1116	39	1	1175	1	SERPINA9	14	94936084	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	3191630	94936084	12413456	96	2966										
TRAF3	7187	broad.mit.edu	37	chr14	103371896	103371896	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tggccgtttaagcagaaagtGacactcatgctgatggatca	11	8	2	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr14:103371896G>T	ENST00000560371.1	+	11	1699	c.1482G>T	c.(1480-1482)gtG>gtT	p.V494V	TRAF3_ENST00000539721.1_Silent_p.V411V|TRAF3_ENST00000347662.4_Silent_p.V469V|TRAF3_ENST00000392745.2_Silent_p.V494V|TRAF3_ENST00000351691.5_Silent_p.V469V	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	494	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V494V(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		AGCAGAAAGTGACACTCATGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	14											188	171	177					14																	103371896		2203	4300	6503	102441649	SO:0001819	synonymous_variant	7187			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1482G>T	14.37:g.103371896G>T			102441649	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																				0.542	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725		T	103371896	G	T	103371896	2	4	35	1	0	0	0	0	0	0	0	1	16479	1277	45	2		2	TRAF3	14	103371896	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	8435812	103371896	3977644	97	2967										
PLD4	122618	broad.mit.edu	37	chr14	105397224	105397224	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cttctcatctcacttcaaccGtttccagcccttccacggcc	4	19	3	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr14:105397224G>C	ENST00000392593.4	+	7	1031	c.863G>C	c.(862-864)cGt>cCt	p.R288P	PLD4_ENST00000553861.1_5'Flank|PLD4_ENST00000540372.1_Missense_Mutation_p.R295P	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	288					glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)	p.R271P(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			CACTTCAACCGTTTCCAGCCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	14											108	115	112					14																	105397224		1896	4114	6010	104468269	SO:0001583	missense	122618				CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 175"	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.863G>C	14.37:g.105397224G>C	ENSP00000376372:p.Arg288Pro		104468269	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	37	CCDS9995.2	.	.	.	.	.	.	.	.	.	.	G	5.753	0.323389	0.10900	.	.	ENSG00000166428	ENST00000540372;ENST00000392593	T;T	0.23754	1.89;1.89	4.46	0.463	0.16700	Phospholipase D/viral envelope (1);	0.521663	0.19822	N	0.105285	T	0.27866	0.0686	L	0.55834	1.745	0.28182	N	0.928118	P;B	0.44044	0.825;0.079	P;B	0.50490	0.642;0.111	T	0.10683	-1.0619	10	0.36615	T	0.2	-10.1406	4.4432	0.11584	0.3354:0.0:0.5189:0.1457	.	295;288	F5H2B5;Q96BZ4	.;PLD4_HUMAN	P	295;288	ENSP00000438677:R295P;ENSP00000376372:R288P	ENSP00000376372:R288P	R	+	2	0	PLD4	104468269	0.101000	0.21875	0.227000	0.23927	0.271000	0.26615	1.459000	0.35234	-0.133000	0.11537	-0.169000	0.13324	CGT		0.577	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790		C	105397224	G	C	105397224	3	2	35	1	0	0	0	0	1	0	0	0	12079	1145	40	5	885	5	PLD4	14	105397224	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	2025328	105397224	1952316	98	2968										
NIPA2	81614	broad.mit.edu	37	chr15	23006754	23006754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cgcgccgattacagagcagaTtgttatgtacacaagaatgt	10	8	0	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:23006754T>C	ENST00000337451.3	-	8	1162	c.550A>G	c.(550-552)Atc>Gtc	p.I184V	NIPA2_ENST00000398013.3_Missense_Mutation_p.I184V|NIPA2_ENST00000398014.2_Missense_Mutation_p.I184V|NIPA2_ENST00000359727.4_Missense_Mutation_p.I165V|NIPA2_ENST00000539711.2_Missense_Mutation_p.I165V	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	184						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)	p.I165V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		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;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		ACAGAGCAGATTGTTATGTAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											75	66	69					15																	23006754		2203	4300	6503	20558195	SO:0001583	missense	81614			AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.550A>G	15.37:g.23006754T>C	ENSP00000337618:p.Ile184Val		20558195	F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	37	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.788159	0.70337	.	.	ENSG00000140157	ENST00000337451;ENST00000398014;ENST00000359727;ENST00000539711;ENST00000398013	D;D;D;D	0.92249	-2.73;-2.73;-2.73;-3.0	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.92662	0.7668	M	0.66560	2.04	0.80722	D	1	B;P	0.40578	0.421;0.722	B;P	0.45946	0.421;0.498	D	0.91832	0.5476	10	0.35671	T	0.21	-3.113	15.9649	0.79961	0.0:0.0:0.0:1.0	.	165;184	F8W7Y8;Q8N8Q9	.;NIPA2_HUMAN	V	184;184;165;184;165	ENSP00000337618:I184V;ENSP00000381096:I184V;ENSP00000352762:I165V;ENSP00000437746:I184V	ENSP00000337618:I184V	I	-	1	0	NIPA2	20558195	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.932000	0.87634	2.232000	0.73038	0.533000	0.62120	ATC		0.502	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922		C	23006754	T	C	23006754	3	2	35	1	0	0	0	0	1	0	0	0	10454	1493	52	4	536	4	NIPA2	15	23006754	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10		23006754	79524638	99	2969										
SLC30A4	7782	broad.mit.edu	37	chr15	45814167	45814168	+	Missense_Mutation	DNP	AG	AG	TC													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ggcaacacaactcacctacaAgttctccaatcatgaaaagc							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:45814167_45814168AG>TC	ENST00000261867.4	-	2	699_700	c.385_386CT>GA	c.(385-387)CTt>GAt	p.L129D	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	129					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)	p.L129>?(1)		endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		CTCACCTACAAGTTCTCCAATC	0.441																																																1	Complex(1)	large_intestine(1)	15																																								43601460	SO:0001583	missense	7782				CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.385_386delinsTC	15.37:g.45814167_45814168delinsTC	ENSP00000261867:p.Leu129Asp		43601459	Q8TC39	Missense_Mutation	DNP	ENST00000261867.4	37	CCDS10125.1																																																																																				0.441	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			TC	45814168	AG	TC	45814167	3	4	35	1	0	0	0	0	1	0	0	0	14594	72	3	5	931	5	SLC30A4	15	45814167	Missense_Mutation	DNP	AG	TCGA-AG-3726-01A-02W-0899-10	22807413	45814167	56717225	100	2970										
IGDCC4	57722	broad.mit.edu	37	chr15	65703604	65703604	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tccagcggcagcagcccccaGgctacagtttagcactgcag	11	15	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:65703604G>C	ENST00000352385.2	-	2	384	c.175C>G	c.(175-177)Ctg>Gtg	p.L59V		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	59	Ig-like C2-type 1.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L59V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GCAGCCCCCAGGCTACAGTTT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	15											38	35	36					15																	65703604		2201	4299	6500	63490657	SO:0001583	missense	57722				CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.175C>G	15.37:g.65703604G>C	ENSP00000319623:p.Leu59Val		63490657	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	G	0.207	-1.039700	0.02013	.	.	ENSG00000103742	ENST00000352385	T	0.74632	-0.86	5.19	1.18	0.20946	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.257299	0.32190	N	0.006446	T	0.48077	0.1480	N	0.05510	-0.035	0.34214	D	0.674587	B	0.31026	0.304	B	0.26310	0.068	T	0.47837	-0.9086	10	0.30854	T	0.27	-11.4112	8.0142	0.30372	0.3321:0.0:0.6679:0.0	.	59	Q8TDY8	IGDC4_HUMAN	V	59	ENSP00000319623:L59V	ENSP00000319623:L59V	L	-	1	2	IGDCC4	63490657	1.000000	0.71417	0.181000	0.23098	0.143000	0.21401	4.981000	0.63819	-0.031000	0.13781	-0.253000	0.11424	CTG		0.642	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		C	65703604	G	C	65703604	3	2	35	1	0	0	0	0	1	0	0	0	7590	991	35	5	3653	5	IGDCC4	15	65703604	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	19889437	65703604	36827788	101	2971										
CSK	1445	broad.mit.edu	37	chr15	75094753	75094753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gcccgcccgcagtctatgaaGtcatgaagaactgctggcac	11	13	2	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:75094753G>A	ENST00000220003.9	+	13	1981	c.1252G>A	c.(1252-1254)Gtc>Atc	p.V418I	CSK_ENST00000567571.1_Missense_Mutation_p.V418I|CSK_ENST00000309470.9_Missense_Mutation_p.V418I|CSK_ENST00000439220.2_Missense_Mutation_p.V418I	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)	p.V418I(1)		central_nervous_system(1)|lung(2)	3						AGTCTATGAAGTCATGAAGAA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	15											63	71	68					15																	75094753		2197	4296	6493	72881806	SO:0001583	missense	1445				CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"SH2 domain containing"	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.1252G>A	15.37:g.75094753G>A	ENSP00000220003:p.Val418Ile		72881806	Q2M3N2|Q6FGZ6	Missense_Mutation	SNP	ENST00000220003.9	37	CCDS10269.1	.	.	.	.	.	.	.	.	.	.	G	4.175	0.031078	0.08101	.	.	ENSG00000103653	ENST00000220003;ENST00000439220;ENST00000451345;ENST00000309470	T;T;T	0.33216	1.42;1.42;1.42	4.28	4.28	0.50868	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.168211	0.41712	D	0.000840	T	0.09642	0.0237	N	0.01679	-0.765	0.48901	D	0.999722	B	0.02656	0.0	B	0.06405	0.002	T	0.19877	-1.0292	10	0.05436	T	0.98	-30.6387	10.9679	0.47422	0.0:0.0:0.8128:0.1872	.	418	P41240	CSK_HUMAN	I	418;418;367;418	ENSP00000220003:V418I;ENSP00000414764:V418I;ENSP00000438808:V418I	ENSP00000220003:V418I	V	+	1	0	CSK	72881806	0.508000	0.26154	0.995000	0.50966	0.799000	0.45148	0.669000	0.25142	2.218000	0.71995	0.563000	0.77884	GTC		0.637	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383		A	75094753	G	A	75094753	3	1	35	1	0	0	0	0	1	0	0	0	3949	1029	36	3	1298	3	CSK	15	75094753	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	9391149	75094753	27436639	102	2972										
POLG	5428	broad.mit.edu	37	chr15	89872218	89872218	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctgggacttctggccttgctTtgtggggggctggaccttgt	16	9	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:89872218T>G	ENST00000268124.5	-	4	1312	c.979A>C	c.(979-981)Aag>Cag	p.K327Q	POLG_ENST00000442287.2_Missense_Mutation_p.K327Q	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	327					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)	p.K327Q(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TGGCCTTGCTTTGTGGGGGGC	0.607								DNA polymerases (catalytic subunits)																													Colon(73;648 1203 11348 18386 27782)											1	Substitution - Missense(1)	large_intestine(1)	15											88	78	81					15																	89872218		2200	4299	6499	87673222	SO:0001583	missense	5428			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.979A>C	15.37:g.89872218T>G	ENSP00000268124:p.Lys327Gln		87673222	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	T	2.774	-0.254971	0.05829	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.92149	-2.98;-2.98	6.06	1.7	0.24286	Ribonuclease H-like (1);	0.665958	0.16084	N	0.230382	D	0.83156	0.5193	N	0.19112	0.55	0.25471	N	0.987828	B	0.02656	0.0	B	0.04013	0.001	T	0.65874	-0.6062	10	0.15499	T	0.54	-2.2493	10.9052	0.47076	0.0:0.2064:0.4381:0.3555	.	327	P54098	DPOG1_HUMAN	Q	327	ENSP00000268124:K327Q;ENSP00000399851:K327Q	ENSP00000268124:K327Q	K	-	1	0	POLG	87673222	0.987000	0.35691	0.002000	0.10522	0.017000	0.09413	1.470000	0.35354	0.359000	0.24239	-0.213000	0.12676	AAG		0.607	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		G	89872218	T	G	89872218	3	3	35	1	0	0	0	0	1	0	0	0	12231	1850	64	4	2820	4	POLG	15	89872218	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10	14777465	89872218	12659174	103	2973										
CRTC3	64784	broad.mit.edu	37	chr15	91169107	91169107	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctaaccaacctccactactcGacacccctgccagcctccct	3	22	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr15:91169107G>T	ENST00000268184.6	+	10	853	c.849G>T	c.(847-849)tcG>tcT	p.S283S	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Silent_p.S283S			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	283					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.S283S(1)	CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			TCCACTACTCGACACCCCTGC	0.542			T	MAML2	salivary gland mucoepidermoid																																		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	1	Substitution - coding silent(1)	large_intestine(1)	15											278	275	276					15																	91169107		2198	4298	6496	88970111	SO:0001819	synonymous_variant	64784				CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.849G>T	15.37:g.91169107G>T			88970111	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Silent	SNP	ENST00000268184.6	37	CCDS32331.1																																																																																				0.542	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		T	91169107	G	T	91169107	2	4	35	1	0	0	0	0	0	0	0	1	3907	1045	37	2		2	CRTC3	15	91169107	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	1296889	91169107	11362285	104	2974										
SETD6	79918	broad.mit.edu	37	chr16	58552125	58552125	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atggtgacagttcgtgaggcAgcattacagggtgagtgtat	15	5	0	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr16:58552125A>G	ENST00000219315.4	+	6	1013	c.963A>G	c.(961-963)gcA>gcG	p.A321A	SETD6_ENST00000394266.4_Silent_p.A252A|SETD6_ENST00000310682.2_Silent_p.A297A|SETD6_ENST00000418480.1_3'UTR			Q8TBK2	SETD6_HUMAN	SET domain containing 6	321					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)	p.A297A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						TTCGTGAGGCAGCATTACAGG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	16											140	119	126					16																	58552125		2198	4300	6498	57109626	SO:0001819	synonymous_variant	79918			AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.963A>G	16.37:g.58552125A>G			57109626	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																				0.418	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		G	58552125	A	G	58552125	2	3	35	1	0	0	0	0	0	0	0	1	14172	175	7	4		4	SETD6	16	58552125	Silent	SNP	A	TCGA-AG-3726-01A-02W-0899-10		58552125	31802628	105	2975										
MYBBP1A	10514	broad.mit.edu	37	chr17	4455909	4455909	+	Frame_Shift_Del	DEL	T	T	-													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cggcaggatctcctgcaatgTggccttcgagacctaaggat							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:4455909delT	ENST00000254718.4	-	6	880	c.574delA	c.(574-576)acafs	p.T192fs	MYBBP1A_ENST00000381556.2_Frame_Shift_Del_p.T192fs			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	192	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)	p.T192fs*14(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TCCTGCAATGTGGCCTTCGAG	0.567																																																1	Deletion - Frameshift(1)	large_intestine(1)	17											54	48	50					17																	4455909		2203	4300	6503	4402658	SO:0001589	frameshift_variant	10514			AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.574delA	17.37:g.4455909delT	ENSP00000254718:p.Thr192fs		4402658	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Frame_Shift_Del	DEL	ENST00000254718.4	37	CCDS11046.1																																																																																				0.567	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		-	4455909	T	-	4455909	7	5	35	1	0	1	0	1	0	0	0	0	10038	1696	59	0	3536	0	MYBBP1A	17	4455909	Frame_Shift_Del	DEL	T	TCGA-AG-3726-01A-02W-0899-10		4455909	76739301	106	2976										
PITPNM3	83394	broad.mit.edu	37	chr17	6441380	6441380	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tttcgaaggtgccagggggcAccgccgcccgggggaggacc	18	13	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:6441380A>T	ENST00000262483.8	-	2	132	c.45T>A	c.(43-45)ggT>ggA	p.G15G	PITPNM3_ENST00000421306.3_Silent_p.G15G	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	15					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.G15G(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GCCAGGGGGCACCGCCGCCCG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	17											37	36	36					17																	6441380		2203	4300	6503	6382104	SO:0001819	synonymous_variant	83394			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.45T>A	17.37:g.6441380A>T			6382104	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																				0.552	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		T	6441380	A	T	6441380	2	4	35	1	0	0	0	0	0	0	0	1	11983	146	6	5		5	PITPNM3	17	6441380	Silent	SNP	A	TCGA-AG-3726-01A-02W-0899-10	1985471	6441380	74753830	107	2977										
TP53	7157	broad.mit.edu	37	chr17	7577081	7577081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctttcttgcggagattctctTcctctgtgcgccggtctctc	9	14	4	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:7577081T>C	ENST00000269305.4	-	8	1046	c.857A>G	c.(856-858)gAa>gGa	p.E286G	TP53_ENST00000445888.2_Missense_Mutation_p.E286G|TP53_ENST00000455263.2_Missense_Mutation_p.E286G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.E286G|TP53_ENST00000359597.4_Missense_Mutation_p.E286G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E286G(18)|p.E286V(9)|p.0?(8)|p.?(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.E286A(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAGATTCTCTTCCTCTGTGCG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	51	Substitution - Missense(28)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	large_intestine(9)|liver(6)|haematopoietic_and_lymphoid_tissue(5)|upper_aerodigestive_tract(4)|lung(4)|breast(4)|bone(4)|stomach(3)|central_nervous_system(3)|urinary_tract(3)|oesophagus(2)|ovary(2)|soft_tissue(1)|skin(1)	17	GRCh37	CM920679	TP53	M							95	81	86					17																	7577081		2203	4300	6503	7517806	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.857A>G	17.37:g.7577081T>C	ENSP00000269305:p.Glu286Gly		7517806	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.431106	0.62844	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99859	-7.24;-7.24;-7.24;-7.24;-7.24;-7.24	5.12	4.04	0.47022	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99857	0.9933	M	0.92077	3.27	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.81914	0.992;0.989;0.992;0.995	D	0.97429	1.0014	10	0.87932	D	0	-23.2961	9.0226	0.36209	0.0:0.0873:0.0:0.9127	.	286;286;286;286	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	G	286;286;286;286;286;275;154	ENSP00000352610:E286G;ENSP00000269305:E286G;ENSP00000398846:E286G;ENSP00000391127:E286G;ENSP00000391478:E286G;ENSP00000425104:E154G	ENSP00000269305:E286G	E	-	2	0	TP53	7517806	1.000000	0.71417	0.970000	0.41538	0.305000	0.27757	7.447000	0.80620	0.965000	0.38133	-0.379000	0.06801	GAA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577081	T	C	7577081	3	2	35	1	0	0	0	0	1	0	0	0	16421	1783	62	4	429	4	TP53	17	7577081	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10	1135701	7577081	73618129	108	2978										
HDAC5	10014	broad.mit.edu	37	chr17	42169092	42169092	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aggtgtgagttggtgacagtGaccgtggcctgcagccctag	16	9	0	3			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:42169092G>T	ENST00000393622.2	-	10	1471	c.1140C>A	c.(1138-1140)gtC>gtA	p.V380V	HDAC5_ENST00000586802.1_Silent_p.V380V|HDAC5_ENST00000336057.5_Silent_p.V380V|HDAC5_ENST00000225983.6_Silent_p.V381V	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	380					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.V380V(1)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TGGTGACAGTGACCGTGGCCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	17											159	131	141					17																	42169092		2203	4300	6503	39524618	SO:0001819	synonymous_variant	10014			AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.1140C>A	17.37:g.42169092G>T			39524618	C9JFV9|O60340|O60528|Q96DY4	Silent	SNP	ENST00000393622.2	37	CCDS45696.1																																																																																				0.587	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		T	42169092	G	T	42169092	2	4	35	1	0	0	0	0	0	0	0	1	7031	1277	45	2		2	HDAC5	17	42169092	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	34592011	42169092	39026118	109	2979										
MYCBPAP	84073	broad.mit.edu	37	chr17	48603500	48603501	+	Missense_Mutation	DNP	CA	CA	GT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gagtggggaccaagagtcctCagcggaagagcatcatggag							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:48603500_48603501CA>GT	ENST00000323776.5	+	14	2332_2333	c.2170_2171CA>GT	c.(2170-2172)CAg>GTg	p.Q724V	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.Q687V	NM_032133.4	NP_115509.4			MYCBP associated protein									p.Q687>?(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			CAAGAGTCCTCAGCGGAAGAGC	0.624																																																1	Complex(1)	large_intestine(1)	17																																								45958500	SO:0001583	missense	84073			BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	Exception_encountered	17.37:g.48603500_48603501delinsGT	ENSP00000323184:p.Gln724Val		45958499		Missense_Mutation	DNP	ENST00000323776.5	37	CCDS32680.2																																																																																				0.624	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		GT	48603501	CA	GT	48603500	3	3	35	1	0	0	0	0	1	0	0	0	10049	827	29	5	2224	5	MYCBPAP	17	48603500	Missense_Mutation	DNP	CA	TCGA-AG-3726-01A-02W-0899-10	6434408	48603500	32591710	110	2980										
CD79B	974	broad.mit.edu	37	chr17	62007479	62007479	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gccctggtagacctccgaggTgttgttgcacttctgctgac	12	12	1	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr17:62007479T>C	ENST00000006750.3	-	3	477	c.385A>G	c.(385-387)Acc>Gcc	p.T129A	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_Missense_Mutation_p.T130A	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	129	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.T129A(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						ACCTCCGAGGTGTTGTTGCAC	0.602			"Mis, O"		DLBCL																																		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	1	Substitution - Missense(1)	large_intestine(1)	17											111	89	96					17																	62007479		2203	4300	6503	59361211	SO:0001583	missense	974			L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1699	protein-coding gene	gene with protein product		147245	"CD79B antigen (immunoglobulin-associated beta)"	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.385A>G	17.37:g.62007479T>C	ENSP00000006750:p.Thr129Ala		59361211	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	2.603	-0.292535	0.05568	.	.	ENSG00000007312	ENST00000392795;ENST00000006750	T;T	0.76316	-1.01;-1.01	4.21	-8.17	0.01057	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.989320	0.00855	N	0.001879	T	0.61160	0.2325	L	0.35854	1.095	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56798	-0.7919	10	0.05833	T	0.94	1.1638	8.6672	0.34127	0.0:0.5552:0.1299:0.3149	.	129	P40259	CD79B_HUMAN	A	130;129	ENSP00000376544:T130A;ENSP00000006750:T129A	ENSP00000006750:T129A	T	-	1	0	CD79B	59361211	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.015000	0.00313	-1.539000	0.01732	-1.202000	0.01658	ACC		0.602	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			C	62007479	T	C	62007479	3	2	35	1	0	0	0	0	1	0	0	0	3043	1696	59	4	320	4	CD79B	17	62007479	Missense_Mutation	SNP	T	TCGA-AG-3726-01A-02W-0899-10	13403979	62007479	19187731	111	2981										
TAF4B	6875	broad.mit.edu	37	chr18	23866438	23866438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttcacaaccagctgggattcCacaggcagttcaagtcaagc	9	12	3	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr18:23866438C>T	ENST00000269142.5	+	7	2563	c.1565C>T	c.(1564-1566)cCa>cTa	p.P522L	TAF4B_ENST00000400466.2_Missense_Mutation_p.P522L|TAF4B_ENST00000578121.1_Missense_Mutation_p.P522L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	522	Nuclear export signal.|Required for interaction with P65/RELA.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P522L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GCTGGGATTCCACAGGCAGTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	18											54	52	53					18																	23866438		1823	4083	5906	22120436	SO:0001583	missense	6875			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1565C>T	18.37:g.23866438C>T	ENSP00000269142:p.Pro522Leu		22120436	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.752479	0.31046	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T	0.24723	1.92;1.84	5.28	5.28	0.74379	.	0.809542	0.11469	N	0.560980	T	0.22513	0.0543	L	0.29908	0.895	0.39196	D	0.963057	P;P	0.48764	0.915;0.845	B;B	0.44315	0.446;0.421	T	0.02301	-1.1180	10	0.16896	T	0.51	-6.447	12.8986	0.58113	0.1622:0.8378:0.0:0.0	.	522;522	Q92750;A4PBF7	TAF4B_HUMAN;.	L	520;522;522	ENSP00000269142:P522L;ENSP00000383314:P522L	ENSP00000269142:P522L	P	+	2	0	TAF4B	22120436	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	1.533000	0.36040	2.483000	0.83821	0.557000	0.71058	CCA		0.438	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23866438	C	T	23866438	3	4	35	1	0	0	0	0	1	0	0	0	15566	594	21	3	1591	3	TAF4B	18	23866438	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		23866438	54210810	112	2982										
ACAA2	10449	broad.mit.edu	37	chr18	47323934	47323934	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tcccacacgcaaaccaacatGccttgccaaatatatagcat	4	14	0	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr18:47323934G>C	ENST00000285093.10	-	3	689	c.214C>G	c.(214-216)Cat>Gat	p.H72D	ACAA2_ENST00000587994.1_Missense_Mutation_p.H69D|RP11-886H22.1_ENST00000590532.2_3'UTR|ACAA2_ENST00000589432.1_Missense_Mutation_p.H17D	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	72					cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)	p.H72D(1)		large_intestine(2)|lung(7)|ovary(1)	10						AAACCAACATGCCTTGCCAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	18											55	58	57					18																	47323934		2203	4300	6503	45577932	SO:0001583	missense	10449			D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"mitochondrial 3-oxoacyl-Coenzyme A thiolase"	604770	"acetyl-Coenzyme A acyltransferase 2"			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.214C>G	18.37:g.47323934G>C	ENSP00000285093:p.His72Asp		45577932	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	37	CCDS11939.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021762	0.75275	.	.	ENSG00000167315	ENST00000285093	D	0.90004	-2.6	5.78	5.78	0.91487	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.95529	0.8547	M	0.86805	2.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.994	D	0.95605	0.8666	10	0.87932	D	0	-23.2864	20.0086	0.97443	0.0:0.0:1.0:0.0	.	72;72	B2RB23;P42765	.;THIM_HUMAN	D	72	ENSP00000285093:H72D	ENSP00000285093:H72D	H	-	1	0	ACAA2	45577932	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	9.405000	0.97313	2.717000	0.92951	0.655000	0.94253	CAT		0.393	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111		C	47323934	G	C	47323934	3	2	35	1	0	0	0	0	1	0	0	0	105	1319	46	5	1011	5	ACAA2	18	47323934	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	23457496	47323934	30753314	113	2983										
SLC25A23	79085	broad.mit.edu	37	chr19	6457532	6457533	+	Missense_Mutation	DNP	GC	GC	AA													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	acctgtgcaaaattttctcaGcctgctccagcgagatggaa							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:6457532_6457533GC>AA	ENST00000301454.4	-	3	458_459	c.352_353GC>TT	c.(352-354)GCt>TTt	p.A118F	SLC25A23_ENST00000334510.5_Missense_Mutation_p.A118F|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	118	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)	p.A118>?(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						AATTTTCTCAGCCTGCTCCAGC	0.559																																																1	Complex(1)	large_intestine(1)	19																																								6408533	SO:0001583	missense	79085			AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.352_353delinsAA	19.37:g.6457532_6457533delinsAA	ENSP00000301454:p.Ala118Phe		6408532	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	DNP	ENST00000301454.4	37	CCDS32882.1																																																																																				0.559	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		AA	6457533	GC	AA	6457532	3	1	35	1	0	0	0	0	1	0	0	0	14523	971	34	3	1085	3	SLC25A23	19	6457532	Missense_Mutation	DNP	GC	TCGA-AG-3726-01A-02W-0899-10		6457532	52671451	114	2984										
ZNF121	7675	broad.mit.edu	37	chr19	9677159	9677159	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ttagtaaggcctgagcgcccAgcgaaggctcttccacattc	10	13	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:9677159A>T	ENST00000586602.1	-	6	1046	c.630T>A	c.(628-630)gcT>gcA	p.A210A	ZNF121_ENST00000320451.6_Silent_p.A210A			P58317	ZN121_HUMAN	zinc finger protein 121	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A210A(1)		breast(3)|kidney(4)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	24						CTGAGCGCCCAGCGAAGGCTC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	19											47	48	48					19																	9677159		2203	4300	6503	9538159	SO:0001819	synonymous_variant	7675			M99593	CCDS32902.1	19p13.2	2013-01-08	2006-08-22			ENSG00000197961		"Zinc fingers, C2H2-type"	12904	protein-coding gene	gene with protein product		194628	"zinc finger protein 121 (clone ZHC32)"	D19S204		8468057	Standard	NM_001008727		Approved	ZHC32, ZNF20	uc010xkp.1	P58317		ENST00000586602.1:c.630T>A	19.37:g.9677159A>T			9538159		Silent	SNP	ENST00000586602.1	37																																																																																					0.418	ZNF121-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000449910.1	NM_001008727		T	9677159	A	T	9677159	2	4	35	1	0	0	0	0	0	0	0	1	17758	175	7	5		5	ZNF121	19	9677159	Silent	SNP	A	TCGA-AG-3726-01A-02W-0899-10	3219627	9677159	49451824	115	2985										
ECSIT	51295	broad.mit.edu	37	chr19	11618839	11618839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctgggggggatctgctgcacCtgttgagtctttgggcaaag	16	8	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:11618839C>T	ENST00000270517.7	-	5	898	c.763G>A	c.(763-765)Ggt>Agt	p.G255S	ECSIT_ENST00000591104.1_Missense_Mutation_p.G255S|ECSIT_ENST00000588998.1_Missense_Mutation_p.G41S|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000252440.7_Missense_Mutation_p.G255S|ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000592312.1_Missense_Mutation_p.G139S|ECSIT_ENST00000417981.2_Missense_Mutation_p.G41S|CTC-398G3.6_ENST00000585656.1_5'Flank|ZNF653_ENST00000593191.1_5'Flank	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	255					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.G255S(1)		kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						TCTGCTGCACCTGTTGAGTCT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	111	108					19																	11618839		2203	4300	6503	11479839	SO:0001583	missense	51295			BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.763G>A	19.37:g.11618839C>T	ENSP00000270517:p.Gly255Ser		11479839	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	C	9.416	1.081692	0.20309	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.75154	-0.91;1.53;-0.91	3.81	0.257	0.15574	.	1.103950	0.06786	N	0.786203	T	0.61739	0.2371	L	0.34521	1.04	0.09310	N	1	B;B;B	0.16802	0.019;0.019;0.005	B;B;B	0.20767	0.031;0.01;0.004	T	0.45411	-0.9263	10	0.31617	T	0.26	-1.3712	6.0847	0.19960	0.0:0.6054:0.0:0.3946	.	41;255;255	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	S	255;41;255	ENSP00000270517:G255S;ENSP00000412712:G41S;ENSP00000252440:G255S	ENSP00000252440:G255S	G	-	1	0	ECSIT	11479839	0.000000	0.05858	0.003000	0.11579	0.089000	0.18198	0.942000	0.29017	0.004000	0.14682	0.561000	0.74099	GGT		0.557	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		T	11618839	C	T	11618839	3	4	35	1	0	0	0	0	1	0	0	0	4911	681	24	3	548	3	ECSIT	19	11618839	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	1941680	11618839	47510144	116	2986										
MLL4	9757	broad.mit.edu	37	chr19	36210409	36210410	+	Missense_Mutation	DNP	CA	CA	GT													0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	tcagatgaagatgtggccccCagttccctgcgctctgcgct							TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:36210409_36210410CA>GT	ENST00000222270.7	+	2	402_403	c.402_403CA>GT	c.(400-405)ccCAgt>ccGTgt	p.S135C	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_Missense_Mutation_p.S135C|KMT2B_ENST00000420124.1_Missense_Mutation_p.S135C	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	135					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P134>?(1)									ATGTGGCCCCCAGTTCCCTGCG	0.569																																																1	Complex(1)	large_intestine(1)	19																																								40902250	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	Exception_encountered	19.37:g.36210409_36210410delinsGT	ENSP00000222270:p.Ser135Cys		40902249	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	DNP	ENST00000222270.7	37	CCDS46055.1																																																																																				0.569	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		GT	36210410	CA	GT	36210409	3	3	35	1	0	0	0	0	1	0	0	0	9653	581	21	5	408	5	MLL4	19	36210409	Missense_Mutation	DNP	CA	TCGA-AG-3726-01A-02W-0899-10	24591570	36210409	22918574	117	2987										
MAP3K10	4294	broad.mit.edu	37	chr19	40704296	40704296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ccacagtcctgatcctggagGccatcgagaaccacaacctc	8	16	0	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:40704296G>A	ENST00000253055.3	+	2	985	c.697G>A	c.(697-699)Gcc>Acc	p.A233T	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)	p.A233T(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GATCCTGGAGGCCATCGAGAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	73	78					19																	40704296		2203	4300	6503	45396136	SO:0001583	missense	4294			X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.697G>A	19.37:g.40704296G>A	ENSP00000253055:p.Ala233Thr		45396136	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845818	0.51164	.	.	ENSG00000130758	ENST00000253055	T	0.74737	-0.87	5.08	4.03	0.46877	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.194452	0.44483	D	0.000441	T	0.50360	0.1611	N	0.05259	-0.085	0.37719	D	0.924844	B	0.19445	0.036	B	0.25987	0.065	T	0.50947	-0.8767	10	0.27082	T	0.32	.	7.1451	0.25579	0.1878:0.0:0.8122:0.0	.	233	Q02779	M3K10_HUMAN	T	233	ENSP00000253055:A233T	ENSP00000253055:A233T	A	+	1	0	MAP3K10	45396136	0.999000	0.42202	1.000000	0.80357	0.962000	0.63368	1.934000	0.40163	2.549000	0.85964	0.306000	0.20318	GCC		0.627	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40704296	G	A	40704296	3	1	35	1	0	0	0	0	1	0	0	0	9274	1203	42	3	703	3	MAP3K10	19	40704296	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	4493887	40704296	18424687	118	2988										
BCAM	4059	broad.mit.edu	37	chr19	45317529	45317529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cagccccagcccggagtataCgcttttccgccttcaggtga	10	15	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:45317529C>T	ENST00000270233.6	+	7	927	c.905C>T	c.(904-906)aCg>aTg	p.T302M	BCAM_ENST00000589651.1_Missense_Mutation_p.T302M	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	302	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)	p.T302M(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCGGAGTATACGCTTTTCCGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19	GRCh37	CM033644	BCAM	M							37	39	38					19																	45317529		2203	4300	6503	50009369	SO:0001583	missense	4059			X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.905C>T	19.37:g.45317529C>T	ENSP00000270233:p.Thr302Met		50009369	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	5.994	0.367393	0.11352	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.13778	2.56;2.56	3.98	-0.528	0.11905	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10337	0.0253	L	0.56199	1.76	0.09310	N	1	B	0.34226	0.443	B	0.25140	0.058	T	0.23084	-1.0198	9	0.34782	T	0.22	-2.0869	5.9639	0.19315	0.0:0.5205:0.0:0.4795	.	302	P50895	BCAM_HUMAN	M	302	ENSP00000270233:T302M;ENSP00000375817:T302M	ENSP00000270233:T302M	T	+	2	0	BCAM	50009369	0.068000	0.21057	0.008000	0.14137	0.537000	0.34900	0.197000	0.17197	0.093000	0.17368	-0.379000	0.06801	ACG		0.647	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45317529	C	T	45317529	3	4	35	1	0	0	0	0	1	0	0	0	1345	536	19	1	931	1	BCAM	19	45317529	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	4613233	45317529	13811454	119	2989										
CCDC155	147872	broad.mit.edu	37	chr19	49912498	49912498	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agagtgggctggaccgagctGctacccccatcgctgggctt	14	13	0	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:49912498G>T	ENST00000447857.3	+	14	1309	c.1104G>T	c.(1102-1104)ctG>ctT	p.L368L		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	368						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L368L(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						GGACCGAGCTGCTACCCCCAT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											54	59	57					19																	49912498		2008	4175	6183	54604310	SO:0001819	synonymous_variant	147872				CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1104G>T	19.37:g.49912498G>T			54604310	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																				0.612	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		T	49912498	G	T	49912498	2	4	35	1	0	0	0	0	0	0	0	1	2794	1306	46	2		2	CCDC155	19	49912498	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	4594969	49912498	9216485	120	2990										
ZNF83	55769	broad.mit.edu	37	chr19	53117118	53117118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cttgccacatttgttacattCgtaaggtttttctccagtat	6	9	1	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr19:53117118C>T	ENST00000597597.1	-	2	2953	c.700G>A	c.(700-702)Gaa>Aaa	p.E234K	ZNF83_ENST00000545872.1_Missense_Mutation_p.E234K|ZNF83_ENST00000536937.1_Missense_Mutation_p.E234K|ZNF83_ENST00000301096.3_Missense_Mutation_p.E234K|ZNF83_ENST00000541777.2_Missense_Mutation_p.E234K|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000544146.1_Missense_Mutation_p.E234K|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000391789.4_Missense_Mutation_p.E234K			P51522	ZNF83_HUMAN	zinc finger protein 83	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E234K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TTGTTACATTCGTAAGGTTTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											85	77	80					19																	53117118		2203	4300	6503	57808930	SO:0001583	missense	55769			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.700G>A	19.37:g.53117118C>T	ENSP00000472619:p.Glu234Lys		57808930	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	N	0.009	-1.857421	0.00558	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;3.28	1.7	0.653	0.17828	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06005	0.0156	N	0.03224	-0.385	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.39231	-0.9624	9	0.02654	T	1	.	2.6726	0.05071	0.2252:0.1504:0.0:0.6244	.	234;234	P51522-2;P51522	.;ZNF83_HUMAN	K	234	ENSP00000445993:E234K;ENSP00000301096:E234K;ENSP00000445470:E234K;ENSP00000440713:E234K;ENSP00000439681:E234K;ENSP00000375666:E234K	ENSP00000301096:E234K	E	-	1	0	ZNF83	57808930	0.000000	0.05858	0.077000	0.20336	0.020000	0.10135	-1.889000	0.01614	0.111000	0.17947	-0.600000	0.04104	GAA		0.388	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		T	53117118	C	T	53117118	3	4	35	1	0	0	0	0	1	0	0	0	18222	893	31	1	854	1	ZNF83	19	53117118	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	3204620	53117118	6011865	121	2991										
CBFA2T2	9139	broad.mit.edu	37	chr20	32211008	32211008	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	agtacctggctcagcacgaaCaccttctgctcaacacaagc	7	15	3	0			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr20:32211008C>G	ENST00000346541.3	+	6	1162	c.625C>G	c.(625-627)Cac>Gac	p.H209D	CBFA2T2_ENST00000397800.1_Missense_Mutation_p.H180D|CBFA2T2_ENST00000344201.3_Missense_Mutation_p.H180D|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.H180D|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.H219D|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.H209D|CBFA2T2_ENST00000397798.2_Missense_Mutation_p.H180D|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.H200D	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	209					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.H209D(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						TCAGCACGAACACCTTCTGCT	0.602																																					Esophageal Squamous(174;142 1955 14837 21276 28041)											1	Substitution - Missense(1)	large_intestine(1)	20											127	107	114					20																	32211008		2203	4300	6503	31674669	SO:0001583	missense	9139			AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.625C>G	20.37:g.32211008C>G	ENSP00000262653:p.His209Asp		31674669	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	37	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916151	0.92178	.	.	ENSG00000078699	ENST00000375279;ENST00000342704;ENST00000344201;ENST00000346541;ENST00000397800;ENST00000397798;ENST00000359606	T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.64159	0.2573	L	0.60455	1.87	0.80722	D	1	D;D	0.67145	0.993;0.996	D;D	0.77557	0.977;0.99	T	0.61317	-0.7087	10	0.56958	D	0.05	-2.5888	20.547	0.99278	0.0:1.0:0.0:0.0	.	209;200	O43439;F8W6D7	MTG8R_HUMAN;.	D	209;200;180;209;180;180;219	ENSP00000364428:H209D;ENSP00000345810:H200D;ENSP00000341865:H180D;ENSP00000262653:H209D;ENSP00000380902:H180D;ENSP00000380900:H180D;ENSP00000352622:H219D	ENSP00000345810:H200D	H	+	1	0	CBFA2T2	31674669	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.816000	0.86201	2.850000	0.98022	0.650000	0.86243	CAC		0.602	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		G	32211008	C	G	32211008	3	3	35	1	0	0	0	0	1	0	0	0	2703	478	17	5	681	5	CBFA2T2	20	32211008	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		32211008	30814512	122	2992										
MATN4	8785	broad.mit.edu	37	chr20	43932919	43932919	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctcctggatgaggtcgaaggActctacgaggaagacgtgct	14	9	1	2	rs549592281		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr20:43932919A>G	ENST00000372754.1	-	2	600	c.592T>C	c.(592-594)Tcc>Ccc	p.S198P	MATN4_ENST00000372756.1_Missense_Mutation_p.S198P|MATN4_ENST00000342716.4_Missense_Mutation_p.S198P|MATN4_ENST00000353917.5_Missense_Mutation_p.S198P|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000537548.1_Missense_Mutation_p.S198P|MATN4_ENST00000360607.6_Missense_Mutation_p.S198P|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000372751.4_Intron|RBPJL_ENST00000372743.1_5'Flank			O95460	MATN4_HUMAN	matrilin 4	198	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)		p.S198P(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				AGGTCGAAGGACTCTACGAGG	0.622													A|||	1	0.000199681	8e-04	0	5008	,	,		17054	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											49	48	48					20																	43932919		2202	4297	6499	43366333	SO:0001583	missense	8785			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.592T>C	20.37:g.43932919A>G	ENSP00000361840:p.Ser198Pro		43366333	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	37		.	.	.	.	.	.	.	.	.	.	A	18.50	3.637000	0.67130	.	.	ENSG00000124159	ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132	T;T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31;-1.31	4.81	2.43	0.29744	.	0.167016	0.28828	N	0.014020	D	0.87912	0.6297	M	0.83223	2.63	0.80722	D	1	P;D;D	0.89917	0.879;1.0;0.998	P;D;D	0.91635	0.637;0.999;0.994	D	0.85665	0.1291	10	0.72032	D	0.01	.	7.2652	0.26226	0.7045:0.1511:0.0:0.1444	.	198;198;198	A6NNA4;O95460-4;O95460-2	.;.;.	P	198	ENSP00000361840:S198P;ENSP00000361842:S198P;ENSP00000243983:S198P;ENSP00000353819:S198P;ENSP00000343164:S198P;ENSP00000440328:S198P	ENSP00000255132:S198P	S	-	1	0	MATN4	43366333	1.000000	0.71417	0.954000	0.39281	0.994000	0.84299	2.502000	0.45398	0.291000	0.22468	0.379000	0.24179	TCC		0.622	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			G	43932919	A	G	43932919	3	3	35	1	0	0	0	0	1	0	0	0	9366	275	10	4	1185	4	MATN4	20	43932919	Missense_Mutation	SNP	A	TCGA-AG-3726-01A-02W-0899-10	11721911	43932919	19092601	123	2993										
SAMSN1	64092	broad.mit.edu	37	chr21	15893508	15893508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gttttgataaagaattattcCgaaaacgatcgaaattccca	6	7	0	2	rs199748093		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr21:15893508C>T	ENST00000400566.1	-	2	173	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	SAMSN1_ENST00000285670.2_Missense_Mutation_p.R99Q|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	31					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)	p.R31Q(2)|p.R99Q(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		AGAATTATTCCGAAAACGATC	0.299																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	21						C	GLN/ARG	1,3603		0,1,1801	38	36	36		92	5.5	1	21		36	0,8126		0,0,4063	yes	missense	SAMSN1	NM_022136.3	43	0,1,5864	TT,TC,CC		0.0,0.0277,0.0085	probably-damaging	31/374	15893508	1,11729	1802	4063	5865	14815379	SO:0001583	missense	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.92G>A	21.37:g.15893508C>T	ENSP00000383411:p.Arg31Gln		14815379	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826551	0.90955	2.77E-4	0.0	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.50001	0.76;0.76	5.48	5.48	0.80851	.	0.111985	0.56097	D	0.000022	T	0.70850	0.3271	M	0.78916	2.43	0.41089	D	0.985589	D;D	0.89917	0.999;1.0	P;D	0.73380	0.889;0.98	T	0.73091	-0.4092	10	0.54805	T	0.06	-13.6929	19.3408	0.94340	0.0:1.0:0.0:0.0	.	99;31	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	Q	99;31	ENSP00000285670:R99Q;ENSP00000383411:R31Q	ENSP00000285670:R99Q	R	-	2	0	SAMSN1	14815379	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	5.338000	0.65947	2.555000	0.86185	0.557000	0.71058	CGG		0.299	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			T	15893508	C	T	15893508	3	4	35	1	0	0	0	0	1	0	0	0	13867	652	23	1	1057	1	SAMSN1	21	15893508	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10		15893508	32236387	124	2994										
RWDD2B	10069	broad.mit.edu	37	chr21	30380383	30380383	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atctccatgacaatgtttttGcaggaatgcagtcagatctg	9	8	3	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr21:30380383G>T	ENST00000493196.1	-	4	524	c.424C>A	c.(424-426)Caa>Aaa	p.Q142K	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	142	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.							p.Q142K(1)		endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						CAATGTTTTTGCAGGAATGCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	21											64	63	63					21																	30380383		2203	4300	6503	29302254	SO:0001583	missense	10069			AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.424C>A	21.37:g.30380383G>T	ENSP00000418693:p.Gln142Lys		29302254		Missense_Mutation	SNP	ENST00000493196.1	37	CCDS13582.1	.	.	.	.	.	.	.	.	.	.	G	2.128	-0.399721	0.04865	.	.	ENSG00000156253	ENST00000493196	T	0.21191	2.02	5.38	5.38	0.77491	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.458779	0.23208	N	0.050717	T	0.12433	0.0302	N	0.17872	0.535	0.19775	N	0.99996	B;B	0.11235	0.0;0.004	B;B	0.17433	0.001;0.018	T	0.23691	-1.0181	10	0.05436	T	0.98	-19.5931	13.4227	0.61007	0.0:0.0:0.7496:0.2504	.	142;142	Q53FD2;P57060	.;RWD2B_HUMAN	K	142	ENSP00000418693:Q142K	ENSP00000418693:Q142K	Q	-	1	0	RWDD2B	29302254	0.972000	0.33761	0.747000	0.31113	0.958000	0.62258	1.035000	0.30216	2.793000	0.96121	0.655000	0.94253	CAA		0.408	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			T	30380383	G	T	30380383	3	4	35	1	0	0	0	0	1	0	0	0	13793	1328	46	2	543	2	RWDD2B	21	30380383	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10	14486875	30380383	17749512	125	2995										
CCT8	10694	broad.mit.edu	37	chr21	30445900	30445900	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aagcccggagccttgggaacGtgaagcgccatggccagcct	14	13	0	1	rs16983693		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr21:30445900G>A	ENST00000286788.4	-	1	218	c.12C>T	c.(10-12)caC>caT	p.H4H	CCT8_ENST00000542732.1_5'Flank|CCT8_ENST00000540844.1_De_novo_Start_InFrame|CCT8_ENST00000470450.1_5'UTR	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	4			H -> Q (in dbSNP:rs16983693).		'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)	p.H4H(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						CCTTGGGAACGTGAAGCGCCA	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	21											84	75	78					21																	30445900		2203	4300	6503	29367771	SO:0001819	synonymous_variant	10694			Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"Heat Shock Proteins / Chaperonins"	1623	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 112"	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.12C>T	21.37:g.30445900G>A			29367771	A6NN54|B4DEM7|B4DQH4|Q4VBP8	De_novo_Start_InFrame	SNP	ENST00000286788.4	37	CCDS33528.1																																																																																				0.627	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			A	30445900	G	A	30445900	2	1	35	1	0	0	0	0	0	0	0	1	2966	1136	40	1		1	CCT8	21	30445900	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	65517	30445900	17683995	126	2996										
SNRPD3	6634	broad.mit.edu	37	chr22	24967917	24967917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	aagaggacgtggaatgggacGtggaaacatctttcaaaagc	13	6	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr22:24967917G>A	ENST00000215829.3	+	4	940	c.353G>A	c.(352-354)cGt>cAt	p.R118H	SNRPD3_ENST00000402849.1_Intron	NM_001278656.1|NM_004175.3	NP_001265585.1|NP_004166.1	P62318	SMD3_HUMAN	small nuclear ribonucleoprotein D3 polypeptide 18kDa	118	5 X 2 AA tandem repeats of [RM]-G.|Arg/Lys-rich (basic).				gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	enzyme binding (GO:0019899)|histone pre-mRNA DCP binding (GO:0071208)|poly(A) RNA binding (GO:0044822)	p.R118H(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6						GGAATGGGACGTGGAAACATC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	22											106	95	99					22																	24967917		2203	4300	6503	23297917	SO:0001583	missense	6634			U15009	CCDS13828.1	22q11.23	2011-10-11	2002-08-29		ENSG00000100028	ENSG00000100028			11160	protein-coding gene	gene with protein product		601062	"small nuclear ribonucleoprotein D3 polypeptide (18kD)"			1701240, 7527560	Standard	NM_004175		Approved	SMD3, Sm-D3	uc003aam.1	P62318	OTTHUMG00000150727	ENST00000215829.3:c.353G>A	22.37:g.24967917G>A	ENSP00000215829:p.Arg118His		23297917	B4DJP7|B5BU13|P43331	Missense_Mutation	SNP	ENST00000215829.3	37	CCDS13828.1	.	.	.	.	.	.	.	.	.	.	G	32	5.173155	0.94807	.	.	ENSG00000100028	ENST00000215829	T	0.44881	0.91	5.99	4.98	0.66077	Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.100571	0.64402	D	0.000001	T	0.35335	0.0928	L	0.38175	1.15	0.80722	D	1	B	0.09022	0.002	B	0.01281	0.0	T	0.10800	-1.0614	10	0.49607	T	0.09	.	14.2783	0.66194	0.071:0.0:0.929:0.0	.	118	P62318	SMD3_HUMAN	H	118	ENSP00000215829:R118H	ENSP00000385994:R118H	R	+	2	0	SNRPD3	23297917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.771000	0.74996	1.549000	0.49425	0.655000	0.94253	CGT		0.448	SNRPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319813.1	NM_004175		A	24967917	G	A	24967917	3	1	35	1	0	0	0	0	1	0	0	0	14903	1145	40	1	363	1	SNRPD3	22	24967917	Missense_Mutation	SNP	G	TCGA-AG-3726-01A-02W-0899-10		24967917	26336649	127	2997										
SULT4A1	25830	broad.mit.edu	37	chr22	44225070	44225070	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	gccagctgctccaccatcgtCaccaggtcctggaagacaag	10	15	1	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chr22:44225070C>A	ENST00000330884.4	-	6	732	c.612G>T	c.(610-612)gtG>gtT	p.V204V	SULT4A1_ENST00000249130.5_Silent_p.V204V|SULT4A1_ENST00000540422.1_Silent_p.V91V	NM_014351.3	NP_055166.1	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	204					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)	p.V204V(1)		kidney(1)|large_intestine(3)|lung(4)|ovary(1)	9		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		CCACCATCGTCACCAGGTCCT	0.622											OREG0026620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	22											24	20	21					22																	44225070		2198	4279	6477	42556403	SO:0001819	synonymous_variant	25830			AF188698	CCDS14051.1	22q13.2	2012-11-05			ENSG00000130540	ENSG00000130540		"Sulfotransferases, cytosolic"	14903	protein-coding gene	gene with protein product		608359				10698717	Standard	NM_014351		Approved	SULTX3, hBR-STL-1	uc003bee.1	Q9BR01	OTTHUMG00000141314	ENST00000330884.4:c.612G>T	22.37:g.44225070C>A		922	42556403	B2R7N3|O43728	Silent	SNP	ENST00000330884.4	37	CCDS14051.1																																																																																				0.622	SULT4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280660.2	NM_014351		A	44225070	C	A	44225070	2	1	35	1	0	0	0	0	0	0	0	1	15422	813	29	2		2	SULT4A1	22	44225070	Silent	SNP	C	TCGA-AG-3726-01A-02W-0899-10	19257153	44225070	7079496	128	2998										
WWC3	55841	broad.mit.edu	37	chrX	10094280	10094280	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	atccccgtgcattccagcgcGttgacactgaagtcacttca	8	14	2	2			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chrX:10094280G>A	ENST00000380861.4	+	15	2431	c.2040G>A	c.(2038-2040)gcG>gcA	p.A680A	WWC3_ENST00000454666.1_Silent_p.A680A	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	680	C2.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.A680A(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						ATTCCAGCGCGTTGACACTGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	X											138	117	124					X																	10094280		2203	4300	6503	10054280	SO:0001819	synonymous_variant	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2040G>A	X.37:g.10094280G>A			10054280	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																				0.577	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10094280	G	A	10094280	2	1	35	1	0	0	0	0	0	0	0	1	17453	1132	40	1		1	WWC3	23	10094280	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10		10094280	145176280	129	2999										
DMD	1756	broad.mit.edu	37	chrX	32563361	32563361	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	ctcttgagcatgctttaccaGgatctgttcccttgtggtca	9	11	3	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chrX:32563361G>A	ENST00000357033.4	-	17	2289	c.2083C>T	c.(2083-2085)Ctg>Ttg	p.L695L	DMD_ENST00000288447.4_Silent_p.L687L|DMD_ENST00000378677.2_Silent_p.L691L	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	695					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L691L(1)|p.L690L(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				TGCTTTACCAGGATCTGTTCC	0.458																																																2	Substitution - coding silent(2)	large_intestine(2)	X											277	199	225					X																	32563361		2202	4300	6502	32473282	SO:0001819	synonymous_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2083C>T	X.37:g.32563361G>A			32473282	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																				0.458	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32563361	G	A	32563361	2	1	35	1	0	0	0	0	0	0	0	1	4591	991	35	3		3	DMD	23	32563361	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	22469081	32563361	122707199	130	3000										
POU3F4	5456	broad.mit.edu	37	chrX	82764015	82764015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	actgtatggtaacgtgttctCgcagaccaccatctgcaggt	10	11	2	1			TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chrX:82764015C>T	ENST00000373200.2	+	1	747	c.683C>T	c.(682-684)tCg>tTg	p.S228L	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	228	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S228L(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						AACGTGTTCTCGCAGACCACC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CM056683	POU3F4	M							81	62	69					X																	82764015		2203	4300	6503	82650671	SO:0001583	missense	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.683C>T	X.37:g.82764015C>T	ENSP00000362296:p.Ser228Leu		82650671	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	37	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487647	0.84854	.	.	ENSG00000196767	ENST00000373200	D	0.87491	-2.26	5.07	5.07	0.68467	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96579	0.9429	10	0.87932	D	0	.	17.4614	0.87620	0.0:1.0:0.0:0.0	.	228	P49335	PO3F4_HUMAN	L	228	ENSP00000362296:S228L	ENSP00000362296:S228L	S	+	2	0	POU3F4	82650671	1.000000	0.71417	0.973000	0.42090	0.979000	0.70002	7.579000	0.82511	2.244000	0.73946	0.525000	0.51046	TCG		0.532	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82764015	C	T	82764015	3	4	35	1	0	0	0	0	1	0	0	0	12308	893	31	1	685	1	POU3F4	23	82764015	Missense_Mutation	SNP	C	TCGA-AG-3726-01A-02W-0899-10	50200654	82764015	72506545	131	3001										
CDR1	1038	broad.mit.edu	37	chrX	139866052	139866052	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	2	1	0.231867283950617	0.927469135802469	0.132495590828924	1	1	0	cccaacaatccaagtcttccGgataatttgggtcttcctga	7	12	2	1	rs146276960		TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3726-01A-02W-0899-10	TCGA-AG-3726-10A-01W-0901-10	g.chrX:139866052G>A	ENST00000370532.2	-	1	671	c.480C>T	c.(478-480)tcC>tcT	p.S160S		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	160	6 X 6 AA approximate repeats.							p.S160S(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CAAGTCTTCCGGATAATTTGG	0.443													G|||	1	0.000264901	0	0	3775	,	,		15094	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X						G		1,3832		0,1,1630,571	134	140	138		480	-7	0	X	dbSNP_134	138	1,6727		0,1,2427,1872	no	coding-synonymous	CDR1	NM_004065.2		0,2,4057,2443	AA,AG,GG,G		0.0149,0.0261,0.0189		160/263	139866052	2,10559	2202	4300	6502	139693718	SO:0001819	synonymous_variant	1038				CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.480C>T	X.37:g.139866052G>A			139693718	Q5JXH6	Silent	SNP	ENST00000370532.2	37	CCDS14670.1																																																																																				0.443	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		A	139866052	G	A	139866052	2	1	35	1	0	0	0	0	0	0	0	1	3177	1103	39	1		1	CDR1	23	139866052	Silent	SNP	G	TCGA-AG-3726-01A-02W-0899-10	57102037	139866052	15404508	132	3002										
MACF1	23499	broad.mit.edu	37	chr1	39823509	39823509	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aaccatcagaaattggaaacTtagtaaaggacaagttgaag	9	5	1	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:39823509T>G	ENST00000372915.3	+	44	11989	c.11902T>G	c.(11902-11904)Tta>Gta	p.L3968V	MACF1_ENST00000567887.1_Missense_Mutation_p.L4000V|MACF1_ENST00000564288.1_Missense_Mutation_p.L3963V|MACF1_ENST00000361689.2_Missense_Mutation_p.L1901V|MACF1_ENST00000317713.7_Missense_Mutation_p.L1901V|MACF1_ENST00000289893.4_Missense_Mutation_p.L2403V|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Missense_Mutation_p.L1901V|MACF1_ENST00000539005.1_Missense_Mutation_p.L1901V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3968					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.L2403V(1)|p.L1901V(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			AATTGGAAACTTAGTAAAGGA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	1											74	70	71					1																	39823509		2203	4300	6503	39596096	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11902T>G	1.37:g.39823509T>G	ENSP00000362006:p.Leu3968Val		39596096	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.20|11.20	1.569278|1.569278	0.28003|0.28003	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.34472	.|1.36;1.36;1.36;1.36;1.36;1.36	6.07|6.07	2.48|2.48	0.30137|0.30137	.|.	0.283763|0.283763	0.25055|0.25055	N|N	0.033500|0.033500	T|T	0.19765|0.19765	0.0475|0.0475	L|L	0.35723|0.35723	1.085|1.085	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.33212	.|0.402;0.04;0.009;0.003	.|B;B;B;B	.|0.36335	.|0.222;0.051;0.026;0.029	T|T	0.19745|0.19745	-1.0296|-1.0296	6|10	.|0.02654	.|T	.|1	.|.	1.8268|1.8268	0.03122|0.03122	0.1351:0.1467:0.1407:0.5775|0.1351:0.1467:0.1407:0.5775	.|.	.|3968;1901;1901;1866	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	R|V	1034|1901;3968;1901;1901;1901;2403	.|ENSP00000439537:L1901V;ENSP00000362006:L3968V;ENSP00000354573:L1901V;ENSP00000313438:L1901V;ENSP00000444364:L1901V;ENSP00000289893:L2403V	.|ENSP00000289893:L2403V	L|L	+|+	2|1	0|2	MACF1|MACF1	39596096|39596096	0.522000|0.522000	0.26266|0.26266	0.996000|0.996000	0.52242|0.52242	0.987000|0.987000	0.75469|0.75469	1.003000|1.003000	0.29809|0.29809	0.508000|0.508000	0.28173|0.28173	0.533000|0.533000	0.62120|0.62120	CTT|TTA		0.428	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39823509	T	G	39823509	3	3	36	1	0	0	0	0	1	0	0	0	9174	1606	56	4	12010	4	MACF1	1	39823509	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10		39823509	209427112	1	3003										
GBP5	115362	broad.mit.edu	37	chr1	89726432	89726432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ttattaacagtcctctgggcGtgctggagctcactgagaag	12	9	2	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:89726432G>A	ENST00000370459.3	-	11	1843	c.1716C>T	c.(1714-1716)caC>caT	p.H572H	GBP5_ENST00000343435.5_Silent_p.H572H|RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000471171.1_5'UTR			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	572	Required for tetramerization. {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.H572H(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TCCTCTGGGCGTGCTGGAGCT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	1											203	185	191					1																	89726432		2203	4300	6503	89499020	SO:0001819	synonymous_variant	115362			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1716C>T	1.37:g.89726432G>A			89499020	B2RCE1|Q86TM5	Silent	SNP	ENST00000370459.3	37	CCDS722.1																																																																																				0.408	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		A	89726432	G	A	89726432	2	1	36	1	0	0	0	0	0	0	0	1	6297	1136	40	1		1	GBP5	1	89726432	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	49902923	89726432	159524189	2	3004										
ZNF326	284695	broad.mit.edu	37	chr1	90473060	90473060	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cggaatagccttgactctttCggaggtagaaaccagggcgg	14	9	1	2	rs142094932		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:90473060C>T	ENST00000340281.4	+	5	509	c.366C>T	c.(364-366)ttC>ttT	p.F122F	ZNF326_ENST00000370447.3_Intron|ZNF326_ENST00000455342.2_Intron	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	122	Gly-rich.|Mediates transcriptional activation. {ECO:0000250}.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.F122F(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		TTGACTCTTTCGGAGGTAGAA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		1,4405	2.1+/-5.4	0,1,2202	140	150	147		366	4.9	1	1	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous	ZNF326	NM_182976.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		122/583	90473060	1,13005	2203	4300	6503	90245648	SO:0001819	synonymous_variant	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.366C>T	1.37:g.90473060C>T			90245648	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	37	CCDS727.1																																																																																				0.493	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90473060	C	T	90473060	2	4	36	1	0	0	0	0	0	0	0	1	17885	883	31	1		1	ZNF326	1	90473060	Silent	SNP	C	TCGA-AG-3727-01A-01W-0899-10	746628	90473060	158777561	3	3005										
BRDT	676	broad.mit.edu	37	chr1	92442915	92442915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gactccataactactatgacGttgtcaaaaatccgatggat	7	9	1	1	rs142308966		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:92442915G>A	ENST00000362005.3	+	7	1352	c.934G>A	c.(934-936)Gtt>Att	p.V312I	BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000394530.3_Missense_Mutation_p.V266I|BRDT_ENST00000402388.1_Missense_Mutation_p.V312I|BRDT_ENST00000370389.2_Missense_Mutation_p.V239I|BRDT_ENST00000399546.2_Missense_Mutation_p.V312I	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	312	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)	p.V312I(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		CTACTATGACGTTGTCAAAAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	70	69					1																	92442915		2203	4294	6497	92215503	SO:0001583	missense	676			AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.934G>A	1.37:g.92442915G>A	ENSP00000354568:p.Val312Ile		92215503	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	.	.	.	.	.	.	.	.	.	.	A	2.047	-0.418568	0.04766	.	.	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71	5.88	-0.779	0.10973	Bromodomain (5);Bromodomain, conserved site (1);	0.641330	0.15262	N	0.271734	T	0.02230	0.0069	N	0.02765	-0.5	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.45220	-0.9276	10	0.02654	T	1	-2.2149	13.4445	0.61134	0.4227:0.0:0.5773:0.0	.	266;266;316;312	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	I	312;239;312;312;266;312;312	ENSP00000354568:V312I;ENSP00000359416:V239I;ENSP00000387822:V312I;ENSP00000378038:V266I;ENSP00000404969:V312I;ENSP00000384051:V312I	ENSP00000354568:V312I	V	+	1	0	BRDT	92215503	0.920000	0.31207	0.015000	0.15790	0.920000	0.55202	1.123000	0.31308	-0.349000	0.08274	-0.972000	0.02603	GTT		0.323	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		A	92442915	G	A	92442915	3	1	36	1	0	0	0	0	1	0	0	0	1511	1145	40	1	952	1	BRDT	1	92442915	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	1969855	92442915	156807706	4	3006										
SYPL2	284612	broad.mit.edu	37	chr1	110018224	110018224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tctttgctattttcgccttcGggtcctgtggctcctacagc	9	13	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:110018224G>A	ENST00000369872.3	+	3	367	c.151G>A	c.(151-153)Ggg>Agg	p.G51R	SYPL2_ENST00000401021.3_Missense_Mutation_p.G51R|SYPL2_ENST00000475497.1_3'UTR	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	51	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)	p.G51R(1)		breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		TTTCGCCTTCGGGTCCTGTGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	67	65					1																	110018224		1963	4145	6108	109819747	SO:0001583	missense	284612			AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"mitsugumin-29"					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.151G>A	1.37:g.110018224G>A	ENSP00000358888:p.Gly51Arg		109819747	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Missense_Mutation	SNP	ENST00000369872.3	37	CCDS41365.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879282	0.91740	.	.	ENSG00000143028	ENST00000401021;ENST00000369872	T;T	0.34472	1.36;1.36	5.87	5.87	0.94306	Marvel (1);MARVEL-like domain (1);	0.048597	0.85682	D	0.000000	T	0.49983	0.1589	L	0.52573	1.65	0.52099	D	0.999942	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.979;0.975	T	0.48328	-0.9045	10	0.87932	D	0	.	18.9775	0.92743	0.0:0.0:1.0:0.0	.	51;51;51	B4DYR7;Q5VXT5;Q5VXT5-2	.;SYPL2_HUMAN;.	R	51	ENSP00000383805:G51R;ENSP00000358888:G51R	ENSP00000358888:G51R	G	+	1	0	SYPL2	109819747	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.119000	0.77145	2.785000	0.95823	0.655000	0.94253	GGG		0.542	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030191.1	NM_001006603		A	110018224	G	A	110018224	3	1	36	1	0	0	0	0	1	0	0	0	15502	1116	39	1	161	1	SYPL2	1	110018224	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	17575309	110018224	139232397	5	3007										
MAN1A2	10905	broad.mit.edu	37	chr1	117944820	117944820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tctcacagggaagaggaagaAcgtctgagaaataaaattcg	11	6	2	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:117944820A>G	ENST00000356554.3	+	2	1050	c.315A>G	c.(313-315)gaA>gaG	p.E105E	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	105					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.E105E(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		AAGAGGAAGAACGTCTGAGAA	0.348																																					Ovarian(33;199 881 8228 13687 31538)											1	Substitution - coding silent(1)	large_intestine(1)	1											59	63	62					1																	117944820		2200	4299	6499	117746343	SO:0001819	synonymous_variant	10905			AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.315A>G	1.37:g.117944820A>G			117746343	Q9H510	Silent	SNP	ENST00000356554.3	37	CCDS895.1																																																																																				0.348	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		G	117944820	A	G	117944820	2	3	36	1	0	0	0	0	0	0	0	1	9241	40	2	4		4	MAN1A2	1	117944820	Silent	SNP	A	TCGA-AG-3727-01A-01W-0899-10	7926596	117944820	131305801	6	3008										
FCGR2C	2214	broad.mit.edu	37	chr1	161569551	161569551	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gacgatgataaaaacatctaCctgactcttcctcccaacga	5	13	2	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:161569551C>T	ENST00000540048.1	-	2	94				FCGR2C_ENST00000543859.1_RNA|FCGR2C_ENST00000466542.2_RNA|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AAAACATCTACCTGACTCTTC	0.453																																																0			1											54	54	54					1																	161569551		2190	4293	6483	159836175	SO:0001627	intron_variant	9103			BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+30606G>A	1.37:g.161569551C>T			159836175	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000540048.1	37																																																																																					0.453	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569		T	161569551	C	T	161569551	1	4	36	0	1	0	0	0	0	0	0	0	5802	518	18	3		3	FCGR2C	1	161569551	Intron	SNP	C	TCGA-AG-3727-01A-01W-0899-10	43624731	161569551	87681070	7	3009										
KIAA1804	84451	broad.mit.edu	37	chr1	233497907	233497907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tggcagagcgcgagatcgacGtgctggagcgggaacttaac	16	9	0	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr1:233497907G>A	ENST00000366624.3	+	5	1681	c.1420G>A	c.(1420-1422)Gtg>Atg	p.V474M	MLK4_ENST00000366623.3_Missense_Mutation_p.V474M	NM_032435.2	NP_115811.2												p.V474M(2)									CGAGATCGACGTGCTGGAGCG	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	1											59	58	58					1																	233497907		2203	4300	6503	231564530	SO:0001583	missense	84451																														ENST00000366624.3:c.1420G>A	1.37:g.233497907G>A	ENSP00000355583:p.Val474Met		231564530		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720169	0.68844	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.76060	-0.87;-0.99	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000002	T	0.81093	0.4751	M	0.65975	2.015	0.80722	D	1	D;D	0.63880	0.975;0.993	P;P	0.61003	0.636;0.882	T	0.79482	-0.1785	10	0.35671	T	0.21	.	11.6727	0.51411	0.0808:0.0:0.9192:0.0	.	474;474	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	M	474	ENSP00000355582:V474M;ENSP00000355583:V474M	ENSP00000355582:V474M	V	+	1	0	RP5-862P8.2	231564530	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.610000	0.74178	2.525000	0.85131	0.655000	0.94253	GTG		0.542	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			A	233497907	G	A	233497907	3	1	36	1	0	0	0	0	1	0	0	0	8280	1145	40	1	1438	1	KIAA1804	1	233497907	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	71928356	233497907	15752714	8	3010										
TBC1D8	11138	broad.mit.edu	37	chr2	101654162	101654162	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	atgcttgttgaatgaaacacGagtgaagcctgcacagcaag	11	8	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr2:101654162G>T	ENST00000376840.4	-	8	1238	c.1239C>A	c.(1237-1239)ctC>ctA	p.L413L	TBC1D8_ENST00000409318.1_Silent_p.L428L			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	413					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.L428L(1)|p.L413L(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						AATGAAACACGAGTGAAGCCT	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	2											96	98	97					2																	101654162		1990	4178	6168	101020594	SO:0001819	synonymous_variant	11138			AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1239C>A	2.37:g.101654162G>T			101020594	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																				0.468	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		T	101654162	G	T	101654162	2	4	36	1	0	0	0	0	0	0	0	1	15664	1045	37	2		2	TBC1D8	2	101654162	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10		101654162	141545211	9	3011										
HOXD12	3238	broad.mit.edu	37	chr2	176965450	176965450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	acaggcgtatgaagaagaagCgcgtggtgcttcgggagcag	17	7	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr2:176965450C>T	ENST00000406506.2	+	2	847	c.775C>T	c.(775-777)Cgc>Tgc	p.R259C	HOXD12_ENST00000404162.2_3'UTR			P35452	HXD12_HUMAN	homeobox D12	259					embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)	p.R259C(1)		central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		GAAGAAGAAGCGCGTGGTGCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											37	38	38					2																	176965450		1982	4195	6177	176673696	SO:0001583	missense	3238				CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"Homeoboxes / ANTP class : HOXL subclass"	5135	protein-coding gene	gene with protein product		142988	"homeo box D12"	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.775C>T	2.37:g.176965450C>T	ENSP00000385586:p.Arg259Cys		176673696	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Missense_Mutation	SNP	ENST00000406506.2	37	CCDS46456.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.658983	0.67586	.	.	ENSG00000170178	ENST00000406506	D	0.96745	-4.11	5.76	3.72	0.42706	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98362	0.9456	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99671	1.0996	10	0.87932	D	0	.	15.2119	0.73230	0.3498:0.6502:0.0:0.0	.	259	P35452	HXD12_HUMAN	C	259	ENSP00000385586:R259C	ENSP00000385586:R259C	R	+	1	0	HOXD12	176673696	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.900000	0.39828	1.375000	0.46248	0.655000	0.94253	CGC		0.572	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193		T	176965450	C	T	176965450	3	4	36	1	0	0	0	0	1	0	0	0	7342	768	27	1	781	1	HOXD12	2	176965450	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	75311288	176965450	66233923	10	3012										
ZDBF2	57683	broad.mit.edu	37	chr2	207172207	207172207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tggcttcaaagagaaaagcaCgctgaattccaaggtagaag	11	7	1	3	rs370841894	byFrequency	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr2:207172207C>T	ENST00000374423.3	+	5	3341	c.2955C>T	c.(2953-2955)caC>caT	p.H985H		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	985							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.H985H(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GAGAAAAGCACGCTGAATTCC	0.393													C|||	4	0.000798722	0.0023	0	5008	,	,		19470	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	2						C		6,3754		0,6,1874	77	76	76		2955	-4.3	0	2		76	0,8214		0,0,4107	no	coding-synonymous	ZDBF2	NM_020923.1		0,6,5981	TT,TC,CC		0.0,0.1596,0.0501		985/2355	207172207	6,11968	1880	4107	5987	206880452	SO:0001819	synonymous_variant	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2955C>T	2.37:g.207172207C>T			206880452	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																				0.393	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207172207	C	T	207172207	2	4	36	1	0	0	0	0	0	0	0	1	17638	535	19	1		1	ZDBF2	2	207172207	Silent	SNP	C	TCGA-AG-3727-01A-01W-0899-10	30206757	207172207	36027166	11	3013										
SMARCAL1	50485	broad.mit.edu	37	chr2	217279488	217279488	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aagagaatcgacaaaaggctCtggcccgcagagctgagaag	13	9	1	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr2:217279488C>G	ENST00000357276.4	+	3	391	c.61C>G	c.(61-63)Ctg>Gtg	p.L21V	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.L21V|AC098820.2_ENST00000457694.1_RNA	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	21	Mediates interaction with RPA2.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.L21V(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		ACAAAAGGCTCTGGCCCGCAG	0.493									Schimke Immuno-Osseous Dysplasia																																							1	Substitution - Missense(1)	large_intestine(1)	2											87	99	95					2																	217279488		2203	4300	6503	216987733	SO:0001583	missense	50485	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.61C>G	2.37:g.217279488C>G	ENSP00000349823:p.Leu21Val		216987733	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.773596	0.69992	.	.	ENSG00000138375	ENST00000430374;ENST00000357276;ENST00000444508;ENST00000358207;ENST00000434435	T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89	5.64	4.75	0.60458	.	0.000000	0.64402	D	0.000008	T	0.33118	0.0852	L	0.27053	0.805	0.32921	D	0.515838	D	0.76494	0.999	D	0.75020	0.985	T	0.47262	-0.9131	10	0.87932	D	0	-12.1314	7.196	0.25853	0.0:0.7391:0.0:0.2609	.	21	Q9NZC9	SMAL1_HUMAN	V	21	ENSP00000405077:L21V;ENSP00000349823:L21V;ENSP00000398969:L21V;ENSP00000350940:L21V;ENSP00000402967:L21V	ENSP00000349823:L21V	L	+	1	2	SMARCAL1	216987733	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	0.793000	0.26944	1.359000	0.45940	0.563000	0.77884	CTG		0.493	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			G	217279488	C	G	217279488	3	3	36	1	0	0	0	0	1	0	0	0	14810	912	32	5	63	5	SMARCAL1	2	217279488	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	10107281	217279488	25919885	12	3014										
C2orf62	375307	broad.mit.edu	37	chr2	219227497	219227497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cttctttcccctggagctcaAtcaagggcttcatctcagag	8	13	5	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr2:219227497A>G	ENST00000289388.3	+	6	531	c.502A>G	c.(502-504)Atc>Gtc	p.I168V	C2orf62_ENST00000481940.1_Intron	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		168					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.I168V(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGAGCTCAATCAAGGGCTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	79	81					2																	219227497		2203	4300	6503	218935741	SO:0001583	missense	375307																														ENST00000289388.3:c.502A>G	2.37:g.219227497A>G	ENSP00000289388:p.Ile168Val		218935741		Missense_Mutation	SNP	ENST00000289388.3	37	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	A	6.077	0.382523	0.11524	.	.	ENSG00000158428	ENST00000289388	.	.	.	4.55	-5.01	0.02991	.	0.835022	0.10742	N	0.639322	T	0.26412	0.0645	L	0.44542	1.39	0.09310	N	1	B	0.20780	0.048	B	0.21708	0.036	T	0.23583	-1.0184	9	0.44086	T	0.13	-18.4332	2.2888	0.04133	0.189:0.4382:0.1536:0.2191	.	168	Q7Z7H3	CB062_HUMAN	V	168	.	ENSP00000289388:I168V	I	+	1	0	C2orf62	218935741	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.068000	0.11561	-1.194000	0.02684	-0.290000	0.09829	ATC		0.597	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			G	219227497	A	G	219227497	3	3	36	1	0	0	0	0	1	0	0	0	2187	101	4	4	524	4	C2orf62	2	219227497	Missense_Mutation	SNP	A	TCGA-AG-3727-01A-01W-0899-10	1948009	219227497	23971876	13	3015										
APPL1	26060	broad.mit.edu	37	chr3	57303587	57303587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aggacttggaagaacaaagtCggttgatagctgcttccagt	12	7	0	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr3:57303587C>T	ENST00000288266.3	+	22	2149	c.2002C>T	c.(2002-2004)Cgg>Tgg	p.R668W	ASB14_ENST00000487349.1_3'UTR|ASB14_ENST00000389601.3_3'UTR	NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	668					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.R668W(2)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGAACAAAGTCGGTTGATAGC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	3											109	104	106					3																	57303587		2203	4300	6503	57278627	SO:0001583	missense	26060			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.2002C>T	3.37:g.57303587C>T	ENSP00000288266:p.Arg668Trp		57278627	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862194	0.71949	.	.	ENSG00000157500	ENST00000288266	T	0.11495	2.77	5.65	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.23806	0.0576	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.02009	-1.1230	10	0.87932	D	0	.	16.1283	0.81408	0.1347:0.8653:0.0:0.0	.	668	Q9UKG1	DP13A_HUMAN	W	668	ENSP00000288266:R668W	ENSP00000288266:R668W	R	+	1	2	APPL1	57278627	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.679000	0.68160	1.468000	0.48064	0.563000	0.77884	CGG		0.423	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57303587	C	T	57303587	3	4	36	1	0	0	0	0	1	0	0	0	817	875	31	1	2088	1	APPL1	3	57303587	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		57303587	140718843	14	3016										
KALRN	8997	broad.mit.edu	37	chr3	123987813	123987813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ggatgtggagggctctcggcGgctcattgacgaacacacac	14	11	2	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr3:123987813G>A	ENST00000240874.3	+	5	831	c.674G>A	c.(673-675)cGg>cAg	p.R225Q	KALRN_ENST00000460856.1_Missense_Mutation_p.R225Q|KALRN_ENST00000360013.3_Missense_Mutation_p.R225Q	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	225					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R225Q(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GGCTCTCGGCGGCTCATTGAC	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	3											30	30	30					3																	123987813		2203	4300	6503	125470503	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.674G>A	3.37:g.123987813G>A	ENSP00000240874:p.Arg225Gln		125470503	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.7|24.7	4.555073|4.555073	0.86231|0.86231	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000448253;ENST00000354186|ENST00000460856;ENST00000240874;ENST00000360013	.|T;T;T	.|0.40756	.|1.02;1.02;1.02	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.37571|0.37571	0.1008|0.1008	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.39181	.|0.197;0.663;0.501	.|B;B;B	.|0.28232	.|0.04;0.041;0.087	T|T	0.30592|0.30592	-0.9973|-0.9973	5|10	.|0.13108	.|T	.|0.6	.|.	19.5125|19.5125	0.95148|0.95148	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|225;225;225	.|C9IZQ6;O60229;O60229-2	.|.;KALRN_HUMAN;.	S|Q	253;203|225	.|ENSP00000418611:R225Q;ENSP00000240874:R225Q;ENSP00000353109:R225Q	.|ENSP00000240874:R225Q	G|R	+|+	1|2	0|0	KALRN|KALRN	125470503|125470503	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	5.636000|5.636000	0.67848|0.67848	2.840000|2.840000	0.97914|0.97914	0.655000|0.655000	0.94253|0.94253	GGC|CGG		0.627	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	123987813	G	A	123987813	3	1	36	1	0	0	0	0	1	0	0	0	7996	1116	39	1	692	1	KALRN	3	123987813	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	66684226	123987813	74034617	15	3017										
PPP2R2C	5522	broad.mit.edu	37	chr4	6382753	6382753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ccgctggaagatgacgacccGgccgcccttgtcacctgtgg	13	15	1	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr4:6382753G>A	ENST00000382599.4	-	2	355	c.139C>T	c.(139-141)Cgg>Tgg	p.R47W	PPP2R2C_ENST00000515571.1_Missense_Mutation_p.R30W|PPP2R2C_ENST00000507294.1_Missense_Mutation_p.R40W|PPP2R2C_ENST00000314348.8_5'UTR|PPP2R2C_ENST00000335585.5_Missense_Mutation_p.R47W|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.R40W			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	47					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.R47W(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						ATGACGACCCGGCCGCCCTTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	4											45	36	39					4																	6382753		2203	4300	6503	6433654	SO:0001583	missense	5522			AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.139C>T	4.37:g.6382753G>A	ENSP00000372042:p.Arg47Trp		6433654	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	37		.	.	.	.	.	.	.	.	.	.	G	21.0	4.077310	0.76415	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	4.02	3.15	0.36227	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.70149	-0.4951	10	0.87932	D	0	-33.236	12.2817	0.54767	0.0:0.0:0.8293:0.1707	.	40;143;47;30;47	B7Z3Y1;Q59GC6;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;.;2ABG_HUMAN;.;.	W	47;40;30;47;40	ENSP00000335083:R47W;ENSP00000423649:R40W;ENSP00000422374:R30W;ENSP00000372042:R47W;ENSP00000425247:R40W	ENSP00000335083:R47W	R	-	1	2	PPP2R2C	6433654	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.742000	0.55097	0.997000	0.38969	0.462000	0.41574	CGG		0.647	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		A	6382753	G	A	6382753	3	1	36	1	0	0	0	0	1	0	0	0	12420	1115	39	1	1236	1	PPP2R2C	4	6382753	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10		6382753	184771523	16	3018										
TEC	7006	broad.mit.edu	37	chr4	48165756	48165756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gtttgatttctttcccgttaCgtaattacttgggatatatc	7	7	1	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr4:48165756C>T	ENST00000381501.3	-	8	857	c.700G>A	c.(700-702)Gta>Ata	p.V234I		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	234	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.V234I(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						TTTCCCGTTACGTAATTACTT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	62	64					4																	48165756		2188	4269	6457	47860513	SO:0001583	missense	7006			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.700G>A	4.37:g.48165756C>T	ENSP00000370912:p.Val234Ile		47860513	B7ZKZ6|Q3MIS5	Missense_Mutation	SNP	ENST00000381501.3	37	CCDS3481.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719590	0.68844	.	.	ENSG00000135605	ENST00000381501	T	0.29142	1.58	5.69	5.69	0.88448	Src homology-3 domain (3);	0.129327	0.51477	D	0.000096	T	0.58878	0.2153	M	0.75447	2.3	0.48696	D	0.999698	D	0.89917	1.0	D	0.80764	0.994	T	0.59295	-0.7481	10	0.59425	D	0.04	.	19.7977	0.96492	0.0:1.0:0.0:0.0	.	234	P42680	TEC_HUMAN	I	234	ENSP00000370912:V234I	ENSP00000370912:V234I	V	-	1	0	TEC	47860513	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.626000	0.67777	2.692000	0.91855	0.491000	0.48974	GTA		0.279	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			T	48165756	C	T	48165756	3	4	36	1	0	0	0	0	1	0	0	0	15781	536	19	1	1239	1	TEC	4	48165756	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	41783003	48165756	142988520	17	3019										
MMAA	166785	broad.mit.edu	37	chr4	146575272	146575272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cactgaaattactccgcaaaCgttcacaagtctggaaacca	6	12	2	1	rs141974563		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr4:146575272C>T	ENST00000281317.5	+	6	2156	c.946C>T	c.(946-948)Cgt>Tgt	p.R316C	MMAA_ENST00000541599.1_Missense_Mutation_p.R35C	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	316					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.R316C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACTCCGCAAACGTTCACAAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	CYS/ARG	0,4406		0,0,2203	153	142	146		946	4.6	1	4	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	missense	MMAA	NM_172250.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	316/419	146575272	1,13005	2203	4300	6503	146794722	SO:0001583	missense	166785			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.946C>T	4.37:g.146575272C>T	ENSP00000281317:p.Arg316Cys		146794722	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230880	0.79688	0.0	1.16E-4	ENSG00000151611	ENST00000281317;ENST00000537246;ENST00000541599	D;D	0.90504	-2.68;-2.68	5.49	4.64	0.57946	.	0.172614	0.53938	D	0.000056	D	0.95689	0.8598	M	0.89095	3.005	0.58432	D	0.999996	D	0.89917	1.0	D	0.72075	0.976	D	0.96201	0.9145	10	0.72032	D	0.01	-11.7306	14.4595	0.67440	0.0:0.9289:0.0:0.0711	.	316	Q8IVH4	MMAA_HUMAN	C	316;316;35	ENSP00000281317:R316C;ENSP00000442284:R35C	ENSP00000281317:R316C	R	+	1	0	MMAA	146794722	1.000000	0.71417	0.957000	0.39632	0.982000	0.71751	3.485000	0.53208	1.312000	0.45043	0.650000	0.86243	CGT		0.423	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			T	146575272	C	T	146575272	3	4	36	1	0	0	0	0	1	0	0	0	9669	536	19	1	964	1	MMAA	4	146575272	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	98409516	146575272	44579004	18	3020										
PRMT10	90826	broad.mit.edu	37	chr4	148594942	148594942	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	accagtttgcaacacgataaAaattctcctttgcatcactg	5	11	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr4:148594942A>C	ENST00000322396.6	-	3	664	c.422T>G	c.(421-423)tTt>tGt	p.F141C	PRMT10_ENST00000541232.1_Missense_Mutation_p.F28C	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		141	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)	p.F141C(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						AACACGATAAAAATTCTCCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											94	95	94					4																	148594942		2203	4300	6503	148814392	SO:0001583	missense	90826																														ENST00000322396.6:c.422T>G	4.37:g.148594942A>C	ENSP00000314396:p.Phe141Cys		148814392	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.341358	0.81911	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.63255	-0.03;1.75	5.37	5.37	0.77165	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.74989	0.3789	L	0.57536	1.79	0.58432	D	0.999996	D	0.89917	1.0	D	0.70487	0.969	T	0.75448	-0.3314	10	0.45353	T	0.12	.	15.3765	0.74610	1.0:0.0:0.0:0.0	.	141	Q6P2P2	ANM10_HUMAN	C	141;28	ENSP00000314396:F141C;ENSP00000439508:F28C	ENSP00000314396:F141C	F	-	2	0	PRMT10	148814392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.948000	0.93006	2.045000	0.60652	0.533000	0.62120	TTT		0.393	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			C	148594942	A	C	148594942	3	2	36	1	0	0	0	0	1	0	0	0	12570	14	1	4	2155	4	PRMT10	4	148594942	Missense_Mutation	SNP	A	TCGA-AG-3727-01A-01W-0899-10	2019670	148594942	42559334	19	3021										
C5orf42	65250	broad.mit.edu	37	chr5	37183070	37183070	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ttcctatactgccaaaagtgTttagtgctaaaggaagatct	8	7	1	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:37183070T>C	ENST00000508244.1	-	25	5306	c.5213A>G	c.(5212-5214)aAc>aGc	p.N1738S	C5orf42_ENST00000274258.7_Missense_Mutation_p.N619S|C5orf42_ENST00000425232.2_Missense_Mutation_p.N1738S			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1738						integral component of membrane (GO:0016021)		p.N619S(1)|p.N1738S(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GCCAAAAGTGTTTAGTGCTAA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	5											106	102	103					5																	37183070		2203	4300	6503	37218827	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5213A>G	5.37:g.37183070T>C	ENSP00000421690:p.Asn1738Ser		37218827	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787445	0.31593	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.19	-1.48	0.08745	.	1.276180	0.05435	N	0.546714	T	0.08891	0.0220	N	0.14661	0.345	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.005	T	0.34254	-0.9836	10	0.27785	T	0.31	.	3.1076	0.06347	0.1093:0.3522:0.1126:0.426	.	1738;619	E9PH94;Q9H799	.;CE042_HUMAN	S	1738;1738;619;786;619	ENSP00000421690:N1738S;ENSP00000389014:N1738S;ENSP00000274258:N619S;ENSP00000424223:N786S	ENSP00000274258:N619S	N	-	2	0	C5orf42	37218827	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	0.082000	0.14847	-0.522000	0.06417	-0.256000	0.11100	AAC		0.378	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37183070	T	C	37183070	3	2	36	1	0	0	0	0	1	0	0	0	2307	1725	60	4	4488	4	C5orf42	5	37183070	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10		37183070	143732190	20	3022										
APC	324	broad.mit.edu	37	chr5	112175174	112175174	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gatgtaatcagacgacacagGaagcagattctgctaatacc	9	9	2	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:112175174G>T	ENST00000457016.1	+	16	4263	c.3883G>T	c.(3883-3885)Gaa>Taa	p.E1295*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1295*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1295*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1295	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1295*(4)|p.T1293fs*2(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GACGACACAGGAAGCAGATTC	0.378		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Substitution - Nonsense(4)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(5)|soft_tissue(1)|skin(1)	5											55	57	56					5																	112175174		2202	4300	6502	112203073	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3883G>T	5.37:g.112175174G>T	ENSP00000413133:p.Glu1295*		112203073	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	38	6.678343	0.97755	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	3.87	0.44632	.	0.307464	0.33691	N	0.004641	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.0118	10.9173	0.47144	0.0711:0.1319:0.797:0.0	.	.	.	.	X	1295	.	.	E	+	1	0	APC	112203073	0.969000	0.33509	0.998000	0.56505	0.989000	0.77384	1.129000	0.31381	1.497000	0.48584	0.655000	0.94253	GAA		0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175174	G	T	112175174	4	4	36	1	0	0	0	0	0	1	0	0	763	1175	41	2	3941	2	APC	5	112175174	Nonsense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	74992104	112175174	68740086	21	3023										
MCC	4163	broad.mit.edu	37	chr5	112406861	112406861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	caccagcatgctcatcctctCggcattgcttttacattcct	5	15	2	0	rs578122540		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:112406861C>T	ENST00000302475.4	-	10	1848	c.1285G>A	c.(1285-1287)Gag>Aag	p.E429K	MCC_ENST00000408903.3_Missense_Mutation_p.E619K|MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Missense_Mutation_p.E366K	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	429					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.E429K(1)|p.E619K(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CTCATCCTCTCGGCATTGCTT	0.488													C|||	1	0.000199681	0	0.0014	5008	,	,		19792	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	5											269	224	239					5																	112406861		2202	4300	6502	112434760	SO:0001583	missense	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1285G>A	5.37:g.112406861C>T	ENSP00000305617:p.Glu429Lys		112434760	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304452	0.81136	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.57595	0.39;0.39;0.39	4.93	4.93	0.64822	Usher syndrome type-1C protein-binding protein 1, PDZ domain (1);	0.000000	0.85682	D	0.000000	T	0.68879	0.3049	L	0.52905	1.665	0.80722	D	1	D;P;D;D	0.76494	0.996;0.911;0.995;0.999	D;P;D;D	0.71656	0.974;0.635;0.97;0.911	T	0.71935	-0.4442	10	0.72032	D	0.01	-25.2469	18.4994	0.90876	0.0:1.0:0.0:0.0	.	429;391;619;429	B7Z6G0;B3KTX0;P23508-2;P23508	.;.;.;CRCM_HUMAN	K	429;366;619	ENSP00000305617:E429K;ENSP00000421615:E366K;ENSP00000386227:E619K	ENSP00000305617:E429K	E	-	1	0	MCC	112434760	1.000000	0.71417	0.309000	0.25155	0.951000	0.60555	6.180000	0.71981	2.449000	0.82847	0.591000	0.81541	GAG		0.488	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		T	112406861	C	T	112406861	3	4	36	1	0	0	0	0	1	0	0	0	9403	893	31	1	1236	1	MCC	5	112406861	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	231687	112406861	68508399	22	3024										
PCDHB8	56128	broad.mit.edu	37	chr5	140558277	140558277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	agcactggatggtggctctcCgcccagatctggcactgctc	12	14	2	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:140558277C>T	ENST00000239444.2	+	1	907	c.662C>T	c.(661-663)cCg>cTg	p.P221L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	221	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P221L(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGGCTCTCCGCCCAGATCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	135	125					5																	140558277		2203	4297	6500	140538461	SO:0001583	missense	56128			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.662C>T	5.37:g.140558277C>T	ENSP00000239444:p.Pro221Leu		140538461	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	c	13.10	2.136943	0.37728	.	.	ENSG00000120322	ENST00000239444	T	0.57436	0.4	4.25	3.36	0.38483	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.75722	0.3888	H	0.97240	3.965	0.43678	D	0.996112	D	0.60160	0.987	P	0.54401	0.751	T	0.82784	-0.0286	9	0.66056	D	0.02	.	12.0568	0.53540	0.0:0.9123:0.0:0.0877	.	221	Q9UN66	PCDB8_HUMAN	L	221	ENSP00000239444:P221L	ENSP00000239444:P221L	P	+	2	0	PCDHB8	140538461	1.000000	0.71417	0.789000	0.31954	0.150000	0.21749	4.629000	0.61290	0.740000	0.32651	0.585000	0.79938	CCG		0.522	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140558277	C	T	140558277	3	4	36	1	0	0	0	0	1	0	0	0	11579	652	23	1	664	1	PCDHB8	5	140558277	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	28151416	140558277	40356983	23	3025										
PCDHB13	56123	broad.mit.edu	37	chr5	140593773	140593773	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cttttgggcttatctctggcGggcgcggcggaacctagaag	15	10	1	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:140593773G>A	ENST00000341948.4	+	1	265	c.78G>A	c.(76-78)gcG>gcA	p.A26A		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	26					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A26A(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TATCTCTGGCGGGCGCGGCGG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	5											22	22	22					5																	140593773		2192	4272	6464	140573957	SO:0001819	synonymous_variant	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.78G>A	5.37:g.140593773G>A			140573957	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																				0.522	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		A	140593773	G	A	140593773	2	1	36	1	0	0	0	0	0	0	0	1	11569	1103	39	1		1	PCDHB13	5	140593773	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	35496	140593773	40321487	24	3026										
PCDHGA3	56112	broad.mit.edu	37	chr5	140725113	140725113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gggcgcccctgtcctccttcGtctctatcaactccaacact	6	18	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:140725113G>A	ENST00000253812.6	+	1	1513	c.1513G>A	c.(1513-1515)Gtc>Atc	p.V505I	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	505	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V505I(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCTCCTTCGTCTCTATCAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	79	76					5																	140725113		2115	4263	6378	140705297	SO:0001583	missense	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1513G>A	5.37:g.140725113G>A	ENSP00000253812:p.Val505Ile		140705297	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	7.652	0.683080	0.14907	.	.	ENSG00000254245	ENST00000253812	T	0.60920	0.15	5.36	-3.5	0.04710	Cadherin (4);Cadherin-like (1);	0.000000	0.30338	U	0.009846	T	0.28167	0.0695	N	0.13198	0.31	0.09310	N	1	B;B	0.23891	0.093;0.051	B;B	0.23716	0.048;0.044	T	0.07751	-1.0756	10	0.27785	T	0.31	.	2.5247	0.04689	0.3725:0.1919:0.3386:0.0969	.	505;505	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	I	505	ENSP00000253812:V505I	ENSP00000253812:V505I	V	+	1	0	PCDHGA3	140705297	0.000000	0.05858	0.006000	0.13384	0.858000	0.48976	-0.554000	0.06006	-1.035000	0.03291	0.563000	0.77884	GTC		0.552	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		A	140725113	G	A	140725113	3	1	36	1	0	0	0	0	1	0	0	0	11586	1145	40	1	1515	1	PCDHGA3	5	140725113	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	131340	140725113	40190147	25	3027										
KIF4B	285643	broad.mit.edu	37	chr5	154393469	154393469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aagagtggcactgcgttgtcGccctctggtccccaaagaga	12	12	1	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr5:154393469G>A	ENST00000435029.4	+	1	210	c.50G>A	c.(49-51)cGc>cAc	p.R17H		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.R17H(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGCGTTGTCGCCCTCTGGTC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	5											123	116	118					5																	154393469		2203	4300	6503	154373662	SO:0001583	missense	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.50G>A	5.37:g.154393469G>A	ENSP00000387875:p.Arg17His		154373662		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	g	18.22	3.576762	0.65878	.	.	ENSG00000226650	ENST00000435029	D	0.85171	-1.95	1.48	1.48	0.22813	Kinesin, motor domain (4);	.	.	.	.	D	0.95149	0.8428	H	0.99719	4.725	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.93917	0.7202	9	0.87932	D	0	.	8.8832	0.35387	0.0:0.0:1.0:0.0	.	17	Q2VIQ3	KIF4B_HUMAN	H	17	ENSP00000387875:R17H	ENSP00000387875:R17H	R	+	2	0	KIF4B	154373662	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	4.834000	0.62774	1.138000	0.42230	0.563000	0.77884	CGC		0.542	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			A	154393469	G	A	154393469	3	1	36	1	0	0	0	0	1	0	0	0	8325	1087	38	1	52	1	KIF4B	5	154393469	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	13668356	154393469	26521791	26	3028										
KLC4	89953	broad.mit.edu	37	chr6	43034792	43034792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	atgatgcccttagcatccggGagagcaccttgggacctgac	12	12	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr6:43034792G>A	ENST00000394056.2	+	7	1345	c.850G>A	c.(850-852)Gag>Aag	p.E284K	KLC4_ENST00000259708.3_Missense_Mutation_p.E302K|KLC4_ENST00000453940.2_Missense_Mutation_p.E207K|KLC4_ENST00000479388.1_Missense_Mutation_p.E284K|KLC4_ENST00000347162.5_Missense_Mutation_p.E284K|KLC4_ENST00000458460.2_Missense_Mutation_p.E284K|KLC4_ENST00000394058.1_Missense_Mutation_p.E284K			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	284						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.E284K(1)		endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			TAGCATCCGGGAGAGCACCTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	94	100					6																	43034792		2203	4300	6503	43142770	SO:0001583	missense	89953			AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.850G>A	6.37:g.43034792G>A	ENSP00000377620:p.Glu284Lys		43142770	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	G	36	5.840966	0.97009	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000470728;ENST00000458460;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T;T;T	0.79554	-0.06;-1.28;-0.07;-0.07;-0.06;-0.06;-0.06;-0.06	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000006	D	0.83372	0.5240	L	0.41492	1.28	0.58432	D	0.999999	P;D;D;D	0.69078	0.517;0.996;0.991;0.997	B;D;D;D	0.78314	0.399;0.989;0.991;0.951	T	0.79624	-0.1726	10	0.31617	T	0.26	-12.365	19.9271	0.97107	0.0:0.0:1.0:0.0	.	207;302;284;284	B4DME9;Q9NSK0-3;Q9NSK0;Q96EG6	.;.;KLC4_HUMAN;.	K	284;207;262;284;302;284;284;284	ENSP00000340221:E284K;ENSP00000395806:E207K;ENSP00000417652:E262K;ENSP00000410358:E284K;ENSP00000259708:E302K;ENSP00000418031:E284K;ENSP00000377620:E284K;ENSP00000377622:E284K	ENSP00000259708:E302K	E	+	1	0	KLC4	43142770	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.782000	0.99034	2.809000	0.96659	0.557000	0.71058	GAG		0.557	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		A	43034792	G	A	43034792	3	1	36	1	0	0	0	0	1	0	0	0	8357	1175	41	3	926	3	KLC4	6	43034792	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10		43034792	128080275	27	3029										
MAP7	9053	broad.mit.edu	37	chr6	136742910	136742911	+	Frame_Shift_Ins	INS	-	-	TA													0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gcggctggaggcatttttctINStatcttgcactttgtagctg							TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr6:136742910_136742911insTA	ENST00000354570.3	-	2	504_505	c.94_95insTA	c.(94-96)aagfs	p.K32fs	MAP7_ENST00000432797.2_5'UTR|MAP7_ENST00000454590.1_Frame_Shift_Ins_p.K54fs|MAP7_ENST00000544465.1_Frame_Shift_Ins_p.K17fs|MAP7_ENST00000438100.2_Frame_Shift_Ins_p.K54fs	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	32					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.K32fs*51(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		GGCATTTTTCTTATCTTGCACT	0.381																																																1	Insertion - Frameshift(1)	large_intestine(1)	6																																								136784604	SO:0001589	frameshift_variant	9053			X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.93_94dupTA	6.37:g.136742911_136742912dupTA	ENSP00000346581:p.Lys32fs		136784603	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Frame_Shift_Ins	INS	ENST00000354570.3	37	CCDS5178.1																																																																																				0.381	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		TA	136742911	-	TA	136742910	7	5	36	1	0	1	1	0	0	0	0	0	9296	1609	56	0	2222	0	MAP7	6	136742910	Frame_Shift_Ins	INS	-	TCGA-AG-3727-01A-01W-0899-10	93708118	136742910	34372157	28	3030										
CARD11	84433	broad.mit.edu	37	chr7	2946435	2946435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tctccttcagccggcacacgCgcaggaactcctcctccgtc	8	19	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr7:2946435C>T	ENST00000396946.4	-	25	3705	c.3302G>A	c.(3301-3303)cGc>cAc	p.R1101H		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1101	Guanylate kinase-like.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.R1094H(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CCGGCACACGCGCAGGAACTC	0.672			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	1	Substitution - Missense(1)	large_intestine(1)	7											51	41	45					7																	2946435		2203	4300	6503	2912961	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.3302G>A	7.37:g.2946435C>T	ENSP00000380150:p.Arg1101His		2912961	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	15.65	2.897137	0.52121	.	.	ENSG00000198286	ENST00000396946	T	0.18338	2.22	3.86	2.95	0.34219	.	0.081921	0.43579	D	0.000553	T	0.18882	0.0453	L	0.50333	1.59	0.39646	D	0.970398	D	0.64830	0.994	P	0.47162	0.54	T	0.03086	-1.1074	10	0.72032	D	0.01	-22.1086	8.3646	0.32378	0.0:0.756:0.1536:0.0904	.	1101	Q9BXL7	CAR11_HUMAN	H	1101	ENSP00000380150:R1101H	ENSP00000380150:R1101H	R	-	2	0	CARD11	2912961	0.657000	0.27393	0.991000	0.47740	0.707000	0.40811	1.312000	0.33574	1.704000	0.51252	0.511000	0.50034	CGC		0.672	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2946435	C	T	2946435	3	4	36	1	0	0	0	0	1	0	0	0	2651	768	27	1	166	1	CARD11	7	2946435	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		2946435	156192228	29	3031										
STK31	56164	broad.mit.edu	37	chr7	23810649	23810649	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aggtgatgcagacaaggagaTaatttcaaatacatatagtc	9	5	1	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr7:23810649T>A	ENST00000355870.3	+	14	1858	c.1739T>A	c.(1738-1740)aTa>aAa	p.I580K	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.I557K|STK31_ENST00000433467.2_Missense_Mutation_p.I580K|STK31_ENST00000428484.1_Missense_Mutation_p.I557K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	580						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)	p.I580K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GACAAGGAGATAATTTCAAAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											173	173	173					7																	23810649		2203	4300	6503	23777174	SO:0001583	missense	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1739T>A	7.37:g.23810649T>A	ENSP00000348132:p.Ile580Lys		23777174	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454972	0.84209	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.76316	-1.01;0.72;-1.0;-1.0	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86789	0.6017	M	0.68952	2.095	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	D	0.88241	0.2910	10	0.87932	D	0	-7.733	15.2746	0.73732	0.0:0.0:0.0:1.0	.	580;580	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	580;580;557;557	ENSP00000348132:I580K;ENSP00000411852:I580K;ENSP00000346660:I557K;ENSP00000406146:I557K	ENSP00000346660:I557K	I	+	2	0	STK31	23777174	1.000000	0.71417	0.971000	0.41717	0.978000	0.69477	4.974000	0.63771	2.083000	0.62718	0.528000	0.53228	ATA		0.358	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		A	23810649	T	A	23810649	3	1	36	1	0	0	0	0	1	0	0	0	15335	1406	49	5	1793	5	STK31	7	23810649	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	20864214	23810649	135328014	30	3032										
TFR2	7036	broad.mit.edu	37	chr7	100218697	100218697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cacggcccatgaagatgtggCggaacggggagtcggctggc	18	10	0	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr7:100218697C>T	ENST00000462107.1	-	19	2476	c.2189G>A	c.(2188-2190)cGc>cAc	p.R730H	TFR2_ENST00000544242.1_Missense_Mutation_p.R271H|TFR2_ENST00000223051.3_Missense_Mutation_p.R730H|TFR2_ENST00000431692.1_3'UTR			Q9UP52	TFR2_HUMAN	transferrin receptor 2	730					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)	p.R730H(2)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	GAAGATGTGGCGGAACGGGGA	0.682																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	7											16	18	18					7																	100218697		2162	4264	6426	100056633	SO:0001583	missense	7036			AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.2189G>A	7.37:g.100218697C>T	ENSP00000420525:p.Arg730His		100056633	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	37	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	C	35	5.484930	0.96323	.	.	ENSG00000106327	ENST00000223051;ENST00000462107;ENST00000544242	T;T;T	0.68479	-0.33;-0.33;-0.33	5.39	5.39	0.77823	Transferrin receptor-like, dimerisation domain (3);	0.000000	0.85682	D	0.000000	T	0.80711	0.4675	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81892	-0.0724	10	0.87932	D	0	-22.1464	16.7045	0.85368	0.0:1.0:0.0:0.0	.	730	Q9UP52	TFR2_HUMAN	H	730;730;271	ENSP00000223051:R730H;ENSP00000420525:R730H;ENSP00000443656:R271H	ENSP00000223051:R730H	R	-	2	0	TFR2	100056633	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.993000	0.76245	2.810000	0.96702	0.650000	0.86243	CGC		0.682	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		T	100218697	C	T	100218697	3	4	36	1	0	0	0	0	1	0	0	0	15850	768	27	1	220	1	TFR2	7	100218697	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	76408048	100218697	58919966	31	3033										
SLC37A3	84255	broad.mit.edu	37	chr7	140051177	140051177	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	attcggctcatattcgtcttCattttcaccaccattaatta	3	11	4	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr7:140051177C>T	ENST00000326232.9	-	9	981	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K	SLC37A3_ENST00000340308.3_Missense_Mutation_p.E260K|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000447932.2_Missense_Mutation_p.E260K	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	260					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.E260K(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					TATTCGTCTTCATTTTCACCA	0.428																																					Esophageal Squamous(133;211 1716 4665 11387 37873)											1	Substitution - Missense(1)	large_intestine(1)	7											169	156	160					7																	140051177		2203	4300	6503	139697646	SO:0001583	missense	84255			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"Solute carriers"	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.778G>A	7.37:g.140051177C>T	ENSP00000321498:p.Glu260Lys		139697646	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.312637|4.312637	0.81358|0.81358	.|.	.|.	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232|ENST00000485734	T;T;T|.	0.18960|.	2.18;2.44;2.44|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.298518|.	0.38272|.	N|.	0.001756|.	T|T	0.66376|0.66376	0.2783|0.2783	L|L	0.39245|0.39245	1.2|1.2	0.80722|0.80722	D|D	1|1	B;B;B|.	0.23058|.	0.006;0.079;0.015|.	B;B;B|.	0.17433|.	0.007;0.011;0.018|.	T|T	0.61893|0.61893	-0.6969|-0.6969	10|5	0.08599|.	T|.	0.76|.	-38.7391|-38.7391	18.7136|18.7136	0.91667|0.91667	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	260;260;260|.	Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;SPX3_HUMAN|.	K|I	260|38	ENSP00000343358:E260K;ENSP00000397481:E260K;ENSP00000321498:E260K|.	ENSP00000321498:E260K|.	E|M	-|-	1|3	0|0	SLC37A3|SLC37A3	139697646|139697646	1.000000|1.000000	0.71417|0.71417	0.949000|0.949000	0.38748|0.38748	0.642000|0.642000	0.38348|0.38348	5.941000|5.941000	0.70195|0.70195	2.575000|2.575000	0.86900|0.86900	0.563000|0.563000	0.77884|0.77884	GAA|ATG		0.428	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		T	140051177	C	T	140051177	3	4	36	1	0	0	0	0	1	0	0	0	14636	835	29	3	883	3	SLC37A3	7	140051177	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	39832480	140051177	19087486	32	3034										
DKK4	27121	broad.mit.edu	37	chr8	42232377	42232377	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ctgcatgtgtgccatcttgcTcatcaagctgcctttctaat	7	12	4	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr8:42232377T>G	ENST00000220812.2	-	3	503	c.317A>C	c.(316-318)gAg>gCg	p.E106A		NM_014420.2	NP_055235.1	Q9UBT3	DKK4_HUMAN	dickkopf WNT signaling pathway inhibitor 4	106					multicellular organismal development (GO:0007275)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)		p.E106A(1)		NS(1)|endometrium(1)|large_intestine(7)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|Lung(22;0.00597)|LUSC - Lung squamous cell carcinoma(45;0.024)			GCCATCTTGCTCATCAAGCTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											263	238	246					8																	42232377		2203	4300	6503	42351534	SO:0001583	missense	27121			AF177397	CCDS6130.1	8p11.2-p11.1	2013-05-15	2013-05-15		ENSG00000104371	ENSG00000104371			2894	protein-coding gene	gene with protein product		605417	"dickkopf (Xenopus laevis) homolog 4", "dickkopf homolog 4 (Xenopus laevis)"			10570958, 11701963	Standard	NM_014420		Approved		uc003xpb.3	Q9UBT3	OTTHUMG00000164167	ENST00000220812.2:c.317A>C	8.37:g.42232377T>G	ENSP00000220812:p.Glu106Ala		42351534	Q3KNX0|Q9Y4C3	Missense_Mutation	SNP	ENST00000220812.2	37	CCDS6130.1	.	.	.	.	.	.	.	.	.	.	T	4.677	0.125787	0.08931	.	.	ENSG00000104371	ENST00000543914;ENST00000220812	T	0.30981	1.51	5.3	-1.52	0.08637	.	0.384718	0.25065	N	0.033401	T	0.09949	0.0244	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.15263	-1.0443	10	0.19590	T	0.45	-12.8825	0.9355	0.01344	0.1515:0.2665:0.157:0.425	.	106	Q9UBT3	DKK4_HUMAN	A	106	ENSP00000220812:E106A	ENSP00000220812:E106A	E	-	2	0	DKK4	42351534	0.013000	0.17824	0.000000	0.03702	0.001000	0.01503	-0.012000	0.12699	-0.429000	0.07329	-0.256000	0.11100	GAG		0.453	DKK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377563.1			G	42232377	T	G	42232377	3	3	36	1	0	0	0	0	1	0	0	0	4558	1551	54	4	365	4	DKK4	8	42232377	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10		42232377	104131645	33	3035										
MOS	4342	broad.mit.edu	37	chr8	57026217	57026217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	atcgtggcgcagccttgctaCgttgagctcagcccagaaac	11	13	1	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr8:57026217C>T	ENST00000311923.1	-	1	324	c.325G>A	c.(325-327)Gta>Ata	p.V109I		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	109	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|chromatin organization (GO:0006325)|establishment of meiotic spindle orientation (GO:0051296)|MAPK cascade (GO:0000165)|meiotic spindle organization (GO:0000212)|negative regulation of metaphase/anaphase transition of meiotic cell cycle (GO:1902103)|protein autophosphorylation (GO:0046777)|regulation of meiosis (GO:0040020)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)	p.V109I(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(12)|ovary(1)|urinary_tract(2)	22			Epithelial(17;0.00117)|all cancers(17;0.00879)			AGCCTTGCTACGTTGAGCTCA	0.592																																					Esophageal Squamous(124;373 2870 4778)											1	Substitution - Missense(1)	large_intestine(1)	8											113	103	106					8																	57026217		2203	4300	6503	57188771	SO:0001583	missense	4342				CCDS6164.1	8q11	2012-10-02			ENSG00000172680	ENSG00000172680			7199	protein-coding gene	gene with protein product		190060				9552420	Standard	NM_005372		Approved		uc011leb.2	P00540	OTTHUMG00000164299	ENST00000311923.1:c.325G>A	8.37:g.57026217C>T	ENSP00000310722:p.Val109Ile		57188771	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	37	CCDS6164.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.305306	0.40795	.	.	ENSG00000172680	ENST00000311923	T	0.64085	-0.08	5.47	-5.19	0.02832	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.560526	0.16507	N	0.211404	T	0.37128	0.0992	N	0.03304	-0.355	0.20074	N	0.999938	B	0.16166	0.016	B	0.17979	0.02	T	0.02860	-1.1101	10	0.25106	T	0.35	.	21.0975	0.99946	0.0:0.8848:0.0:0.1152	.	109	P00540	MOS_HUMAN	I	109	ENSP00000310722:V109I	ENSP00000310722:V109I	V	-	1	0	MOS	57188771	1.000000	0.71417	0.022000	0.16811	0.892000	0.51952	0.861000	0.27885	-0.923000	0.03785	0.551000	0.68910	GTA		0.592	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372		T	57026217	C	T	57026217	3	4	36	1	0	0	0	0	1	0	0	0	9742	536	19	1	718	1	MOS	8	57026217	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	14793840	57026217	89337805	34	3036										
MSC	9242	broad.mit.edu	37	chr8	72755898	72755898	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	accaggttcactgggtgcacGtagccgttctcatagcggtc	12	12	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr8:72755898G>A	ENST00000325509.4	-	1	805	c.516C>T	c.(514-516)taC>taT	p.Y172Y	RP11-383H13.1_ENST00000537896.1_Missense_Mutation_p.V88I|RP11-383H13.1_ENST00000524152.1_5'UTR|MSC_ENST00000518440.1_5'Flank|RP11-383H13.1_ENST00000521467.1_Intron	NM_005098.3	NP_005089.2	O60682	MUSC_HUMAN	musculin	172					branchiomeric skeletal muscle development (GO:0014707)|diaphragm development (GO:0060539)|palate development (GO:0060021)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.Y172Y(1)		endometrium(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(4)|skin(2)	26	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			CTGGGTGCACGTAGCCGTTCT	0.662											OREG0018826	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	8											35	38	37					8																	72755898		2200	4298	6498	72918452	SO:0001819	synonymous_variant	9242				CCDS43746.1	8q13.3	2013-06-07	2010-04-28		ENSG00000178860	ENSG00000178860		"Basic helix-loop-helix proteins"	7321	protein-coding gene	gene with protein product	"activated B-cell factor-1"	603628	"musculin (activated B-cell factor-1)"			9584154, 10198176	Standard	NM_005098		Approved	ABF-1, bHLHa22	uc003xyx.1	O60682	OTTHUMG00000164489	ENST00000325509.4:c.516C>T	8.37:g.72755898G>A		1140	72918452	O75946|Q53XZ2|Q9BRE7	Silent	SNP	ENST00000325509.4	37	CCDS43746.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.345920	0.41599	.	.	ENSG00000235531	ENST00000537896	.	.	.	5.07	2.28	0.28536	.	.	.	.	.	T	0.62998	0.2474	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61133	-0.7124	5	0.87932	D	0	.	7.7727	0.29019	0.3266:0.0:0.6734:0.0	.	.	.	.	I	88	.	ENSP00000440866:V88I	V	+	1	0	RP11-383H13.1	72918452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.574000	0.46016	0.175000	0.19841	0.555000	0.69702	GTA		0.662	MSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378974.1	NM_005098		A	72755898	G	A	72755898	2	1	36	1	0	0	0	0	0	0	0	1	9898	1140	40	1		1	MSC	8	72755898	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	15729681	72755898	73608124	35	3037										
B4GALT1	2683	broad.mit.edu	37	chr9	33166779	33166779	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gcagcggggactcctcagggCaggcgggcagcgacagtgcg	19	12	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:33166779C>A	ENST00000379731.4	-	1	575	c.389G>T	c.(388-390)tGc>tTc	p.C130F	RP11-326F20.5_ENST00000426270.1_RNA|B4GALT1_ENST00000535206.1_Missense_Mutation_p.C130F|RP11-326F20.5_ENST00000442432.1_RNA	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	130					acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)	p.C130F(1)		endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	CTCCTCAGGGCAGGCGGGCAG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	9											19	26	24					9																	33166779		2194	4278	6472	33156779	SO:0001583	missense	2683			X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2.4.1.22	"Beta 4-glycosyltransferases"	924	protein-coding gene	gene with protein product		137060		GGTB2		9597550	Standard	NM_001497		Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.389G>T	9.37:g.33166779C>A	ENSP00000369055:p.Cys130Phe		33156779	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	Missense_Mutation	SNP	ENST00000379731.4	37	CCDS6535.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805347	0.70682	.	.	ENSG00000086062	ENST00000535206;ENST00000379731;ENST00000541701	T;T	0.25085	1.82;1.82	4.33	3.41	0.39046	.	0.224065	0.47852	D	0.000218	T	0.57725	0.2073	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65397	-0.6178	10	0.87932	D	0	-15.1055	7.4702	0.27344	0.0:0.8808:0.0:0.1192	.	130	P15291	B4GT1_HUMAN	F	130;130;87	ENSP00000440341:C130F;ENSP00000369055:C130F	ENSP00000369055:C130F	C	-	2	0	B4GALT1	33156779	0.936000	0.31750	0.994000	0.49952	0.839000	0.47603	1.551000	0.36233	2.101000	0.63845	0.455000	0.32223	TGC		0.687	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052039.1	NM_001497		A	33166779	C	A	33166779	3	1	36	1	0	0	0	0	1	0	0	0	1271	710	25	2	831	2	B4GALT1	9	33166779	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		33166779	108046652	36	3038										
TMEFF1	8577	broad.mit.edu	37	chr9	103310154	103310154	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gcaagaacaaattgatataaGgcatcttggtcattgcacag	9	7	2	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:103310154G>T	ENST00000374879.4	+	6	1121	c.689G>T	c.(688-690)aGg>aTg	p.R230M	MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.K193N|TMEFF1_ENST00000334943.6_Missense_Mutation_p.R191M	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	230	Kazal-like 2. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R230M(1)		NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				ATTGATATAAGGCATCTTGGT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	9											126	119	121					9																	103310154		2203	4299	6502	102349975	SO:0001583	missense	8577			U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.689G>T	9.37:g.103310154G>T	ENSP00000364013:p.Arg230Met		102349975	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	37	CCDS6750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.710690|2.710690	0.48517|0.48517	.|.	.|.	ENSG00000251349|ENSG00000241697	ENST00000502978|ENST00000334943;ENST00000374879	.|T;T	.|0.04194	.|3.68;3.68	5.98|5.98	5.98|5.98	0.97165|0.97165	.|Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	.|0.046510	.|0.85682	.|D	.|0.000000	T|T	0.06234|0.06234	0.0161|0.0161	N|N	0.20766|0.20766	0.605|0.605	0.47407|0.47407	D|D	0.999414|0.999414	.|B;D	.|0.54207	.|0.056;0.965	.|B;P	.|0.51135	.|0.063;0.66	T|T	0.51084|0.51084	-0.8750|-0.8750	5|10	.|0.29301	.|T	.|0.29	-18.2008|-18.2008	11.245|11.245	0.48991|0.48991	0.0824:0.0:0.9176:0.0|0.0824:0.0:0.9176:0.0	.|.	.|230;191	.|Q8IYR6;Q8IYR6-2	.|TEFF1_HUMAN;.	N|M	193|191;230	.|ENSP00000334447:R191M;ENSP00000364013:R230M	.|ENSP00000334447:R191M	K|R	+|+	3|2	2|0	C9orf30-TMEFF1|TMEFF1	102349975|102349975	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.298000|5.298000	0.65710|0.65710	2.838000|2.838000	0.97847|0.97847	0.591000|0.591000	0.81541|0.81541	AAG|AGG		0.323	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		T	103310154	G	T	103310154	3	4	36	1	0	0	0	0	1	0	0	0	16052	1000	35	2	711	2	TMEFF1	9	103310154	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	70143375	103310154	37903277	37	3039										
SVEP1	79987	broad.mit.edu	37	chr9	113241943	113241943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ccagggtcgtctcaaatgctTcagaaaacttcttcatcaga	7	11	5	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:113241943T>C	ENST00000401783.2	-	13	2795	c.2459A>G	c.(2458-2460)gAa>gGa	p.E820G	SVEP1_ENST00000302728.8_Missense_Mutation_p.E820G|SVEP1_ENST00000374461.1_Missense_Mutation_p.E797G|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.E797G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	820					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.E820G(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CTCAAATGCTTCAGAAAACTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											254	244	247					9																	113241943		1847	4087	5934	112281764	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.2459A>G	9.37:g.113241943T>C	ENSP00000384917:p.Glu820Gly		112281764	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268952	0.40095	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.79247	-1.1;-1.11;-1.25;1.08	5.62	4.46	0.54185	.	0.298786	0.38326	N	0.001722	T	0.65616	0.2708	L	0.31664	0.95	0.29366	N	0.864323	B;B;B	0.23442	0.085;0.0;0.001	B;B;B	0.19666	0.026;0.001;0.002	T	0.56842	-0.7912	10	0.25751	T	0.34	.	12.2795	0.54755	0.0:0.0:0.1472:0.8528	.	820;820;820	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	G	820;797;820;797	ENSP00000384917:E820G;ENSP00000363593:E797G;ENSP00000304118:E820G;ENSP00000363585:E797G	ENSP00000304118:E820G	E	-	2	0	SVEP1	112281764	0.999000	0.42202	0.985000	0.45067	0.894000	0.52154	3.584000	0.53936	0.941000	0.37499	0.455000	0.32223	GAA		0.378	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113241943	T	C	113241943	3	2	36	1	0	0	0	0	1	0	0	0	15459	1783	62	4	8400	4	SVEP1	9	113241943	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	9931789	113241943	27971488	38	3040										
ASTN2	23245	broad.mit.edu	37	chr9	119976945	119976945	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcttctgggggatgcggcgaCgcttctgccaacgtcgctgg	15	12	3	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:119976945C>T	ENST00000313400.4	-	3	807	c.707G>A	c.(706-708)cGt>cAt	p.R236H	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.R236H|ASTN2_ENST00000373996.3_Missense_Mutation_p.R236H			O75129	ASTN2_HUMAN	astrotactin 2	236					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R236H(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GATGCGGCGACGCTTCTGCCA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											55	51	52					9																	119976945		2203	4300	6503	119016766	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.707G>A	9.37:g.119976945C>T	ENSP00000314038:p.Arg236His		119016766	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	26.1	4.709341	0.89018	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.15372	2.49;2.49;2.43	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000002	T	0.24890	0.0604	L	0.27053	0.805	0.53005	D	0.999964	D;D;D	0.71674	0.996;0.994;0.998	P;P;P	0.62382	0.681;0.483;0.901	T	0.00942	-1.1506	9	.	.	.	-10.8852	13.3768	0.60743	0.0:0.9237:0.0:0.0763	.	236;236;236	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	H	236	ENSP00000314038:R236H;ENSP00000363108:R236H;ENSP00000354504:R236H	.	R	-	2	0	ASTN2	119016766	1.000000	0.71417	0.954000	0.39281	0.838000	0.47535	6.050000	0.71063	2.599000	0.87857	0.655000	0.94253	CGT		0.637	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119976945	C	T	119976945	3	4	36	1	0	0	0	0	1	0	0	0	1066	536	19	1	3471	1	ASTN2	9	119976945	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	6735002	119976945	21236486	39	3041										
TRAF2	7186	broad.mit.edu	37	chr9	139815531	139815531	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	attggcctcaaggacctggcGatggctgacttggagcagaa	14	9	1	2	rs146825488	byFrequency	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:139815531G>A	ENST00000247668.2	+	9	1054	c.1002G>A	c.(1000-1002)gcG>gcA	p.A334A	TRAF2_ENST00000536468.1_Silent_p.A334A|TRAF2_ENST00000359662.3_Silent_p.A386A	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	334					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A334A(1)		breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	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)		AGGACCTGGCGATGGCTGACT	0.612													G|||	27	0.00539137	0.0197	0	5008	,	,		19428	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9						G		49,4357	50.9+/-86.3	1,47,2155	85	64	71		1002	-5.6	1	9	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAF2	NM_021138.3		1,48,6454	AA,AG,GG		0.0116,1.1121,0.3844		334/502	139815531	50,12956	2203	4300	6503	138935352	SO:0001819	synonymous_variant	7186			U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"RING-type (C3HC4) zinc fingers"	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.1002G>A	9.37:g.139815531G>A			138935352	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																				0.612	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		A	139815531	G	A	139815531	2	1	36	1	0	0	0	0	0	0	0	1	16478	1045	37	1		1	TRAF2	9	139815531	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	19838586	139815531	1397900	40	3042										
CACNA1B	774	broad.mit.edu	37	chr9	140919528	140919528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	atgcagacaatcagcggaacGtcactcgcatgggcagtcag	12	11	3	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr9:140919528G>A	ENST00000371372.1	+	20	3335	c.3190G>A	c.(3190-3192)Gtc>Atc	p.V1064I	CACNA1B_ENST00000371367.5_Missense_Mutation_p.V48I|CACNA1B_ENST00000545473.1_Missense_Mutation_p.V48I|CACNA1B_ENST00000371363.1_Missense_Mutation_p.V1064I|CACNA1B_ENST00000371355.4_Missense_Mutation_p.V1065I|CACNA1B_ENST00000277551.2_Missense_Mutation_p.V1064I|CACNA1B_ENST00000371357.1_Missense_Mutation_p.V1065I|CACNA1B_ENST00000277549.5_Missense_Mutation_p.V256I	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1064					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.V1064I(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCAGCGGAACGTCACTCGCAT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											72	81	78					9																	140919528		2172	4263	6435	140039349	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.3190G>A	9.37:g.140919528G>A	ENSP00000360423:p.Val1064Ile		140039349	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.473424	0.63737	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355;ENST00000371367;ENST00000545473	T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.02	5.02	0.67125	.	11.358800	0.00166	N	0.000000	T	0.34454	0.0898	L	0.37630	1.12	0.33656	D	0.609106	B;B;P	0.38335	0.414;0.414;0.627	B;B;B	0.24394	0.034;0.034;0.053	T	0.50898	-0.8773	10	0.05959	T	0.93	.	18.3374	0.90293	0.0:0.0:1.0:0.0	.	1064;1065;1064	B1AQK4;B1AQK7;B1AQK6	.;.;.	I	1064;1064;256;1064;1065;1065;48;48	ENSP00000360423:V1064I;ENSP00000277551:V1064I;ENSP00000277549:V256I;ENSP00000360414:V1064I;ENSP00000360408:V1065I;ENSP00000360406:V1065I;ENSP00000360418:V48I;ENSP00000441232:V48I	ENSP00000277549:V256I	V	+	1	0	CACNA1B	140039349	1.000000	0.71417	0.983000	0.44433	0.878000	0.50629	4.545000	0.60698	2.327000	0.79052	0.561000	0.74099	GTC		0.592	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140919528	G	A	140919528	3	1	36	1	0	0	0	0	1	0	0	0	2545	1145	40	1	3268	1	CACNA1B	9	140919528	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	1103997	140919528	293903	41	3043										
CSTF2T	23283	broad.mit.edu	37	chr10	53458361	53458361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	accaccaggagtcacgggtcCgcgaggtataggagctctag	14	11	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr10:53458361C>T	ENST00000331173.4	-	1	994	c.949G>A	c.(949-951)Gga>Aga	p.G317R	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	317	Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G317R(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				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)		GTCACGGGTCCGCGAGGTATA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	10											72	68	70					10																	53458361		2203	4300	6503	53128367	SO:0001583	missense	23283			AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.949G>A	10.37:g.53458361C>T	ENSP00000332444:p.Gly317Arg		53128367	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	37	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169805	0.78452	.	.	ENSG00000177613	ENST00000331173	T	0.22539	1.95	4.7	4.7	0.59300	.	0.449653	0.22819	N	0.055255	T	0.41994	0.1183	L	0.55481	1.735	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	T	0.13737	-1.0498	10	0.52906	T	0.07	-7.9329	15.5353	0.75998	0.0:1.0:0.0:0.0	.	317	Q9H0L4	CSTFT_HUMAN	R	317	ENSP00000332444:G317R	ENSP00000332444:G317R	G	-	1	0	CSTF2T	53128367	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.116000	0.71571	2.613000	0.88420	0.655000	0.94253	GGA		0.567	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		T	53458361	C	T	53458361	3	4	36	1	0	0	0	0	1	0	0	0	3991	661	23	1	905	1	CSTF2T	10	53458361	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		53458361	82076386	42	3044										
COL13A1	1305	broad.mit.edu	37	chr10	71700761	71700761	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cagggagcttcaggtttggaCggcaggcctgggccaccggt	17	11	1	0	rs374512468		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr10:71700761C>T	ENST00000398978.3	+	34	2355	c.1863C>T	c.(1861-1863)gaC>gaT	p.D621D	COL13A1_ENST00000398964.3_Silent_p.D592D|COL13A1_ENST00000357811.3_Intron|COL13A1_ENST00000398971.3_Silent_p.D606D|COL13A1_ENST00000356340.3_Silent_p.D621D|COL13A1_ENST00000517713.1_Intron|COL13A1_ENST00000354547.3_Silent_p.D599D|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000398966.3_Silent_p.D599D|COL13A1_ENST00000398969.3_Silent_p.D549D|COL13A1_ENST00000398974.3_Silent_p.D609D|COL13A1_ENST00000398972.3_Silent_p.D607D|COL13A1_ENST00000522165.1_Intron|COL13A1_ENST00000398973.3_Intron|COL13A1_ENST00000520267.1_Silent_p.D549D|COL13A1_ENST00000398968.3_Silent_p.D602D	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1									p.D621D(1)|p.D604D(1)		endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CAGGTTTGGACGGCAGGCCTG	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	10						C	,,,,,	0,4062		0,0,2031	203	225	218		1863,1647,,1797,,	4.9	1	10		218	1,8339		0,1,4169	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,intron	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	0,1,6200	TT,TC,CC		0.012,0.0,0.0081	,,,,,	621/718,549/646,,599/696,,	71700761	1,12401	2031	4170	6201	71370767	SO:0001819	synonymous_variant	1305			AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1863C>T	10.37:g.71700761C>T			71370767		Silent	SNP	ENST00000398978.3	37	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	C	8.814	0.936051	0.18206	0.0	1.2E-4	ENSG00000197467	ENST00000398975	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	T	0.73853	0.3640	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73720	-0.3894	4	.	.	.	-13.1173	18.095	0.89487	0.0:1.0:0.0:0.0	.	.	.	.	M	151	.	.	T	+	2	0	COL13A1	71370767	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.110000	0.71535	2.259000	0.74868	0.655000	0.94253	ACG		0.582	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71700761	C	T	71700761	2	4	36	1	0	0	0	0	0	0	0	1	3676	535	19	1		1	COL13A1	10	71700761	Silent	SNP	C	TCGA-AG-3727-01A-01W-0899-10	18242400	71700761	63833986	43	3045										
FAM24B	196792	broad.mit.edu	37	chr10	124608836	124608836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cacacattctatatccttcaCagcactgcagggcaggacaa	7	13	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr10:124608836C>T	ENST00000368898.3	-	4	502	c.212G>A	c.(211-213)tGt>tAt	p.C71Y	FAM24B_ENST00000462859.1_5'UTR|CUZD1_ENST00000545804.1_Intron|FAM24B_ENST00000368896.1_Missense_Mutation_p.C71Y|CUZD1_ENST00000368904.1_De_novo_Start_OutOfFrame	NM_152644.2	NP_689857.2	Q8N5W8	FA24B_HUMAN	family with sequence similarity 24, member B	71						extracellular region (GO:0005576)		p.C71Y(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.136)|COAD - Colon adenocarcinoma(40;0.141)		ATATCCTTCACAGCACTGCAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	10											146	122	130					10																	124608836		2203	4300	6503	124598826	SO:0001583	missense	50624			BC031343	CCDS31303.1	10q26.13	2004-05-27			ENSG00000213185	ENSG00000213185			23475	protein-coding gene	gene with protein product						12477932	Standard	NM_152644		Approved	MGC45962, AC073585.2	uc021qai.1	Q8N5W8	OTTHUMG00000019194	ENST00000368898.3:c.212G>A	10.37:g.124608836C>T	ENSP00000357894:p.Cys71Tyr		124598826	Q5JPG1	De_novo_Start_OutOfFrame	SNP	ENST00000368898.3	37	CCDS31303.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.736144	0.30774	.	.	ENSG00000213185	ENST00000368898;ENST00000368896	T;T	0.50548	0.74;0.74	3.12	2.2	0.27929	.	0.169266	0.28700	N	0.014426	T	0.40196	0.1107	.	.	.	0.09310	N	1	P	0.44946	0.846	B	0.43445	0.42	T	0.26224	-1.0109	9	0.56958	D	0.05	.	7.7345	0.28806	0.248:0.752:0.0:0.0	.	71	Q8N5W8	FA24B_HUMAN	Y	71	ENSP00000357894:C71Y;ENSP00000357892:C71Y	ENSP00000357892:C71Y	C	-	2	0	FAM24B	124598826	0.787000	0.28750	0.004000	0.12327	0.001000	0.01503	1.526000	0.35964	0.853000	0.35312	0.467000	0.42956	TGT		0.502	FAM24B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050825.1	NM_152644		T	124608836	C	T	124608836	3	4	36	1	0	0	0	0	1	0	0	0	5564	478	17	3	76	3	FAM24B	10	124608836	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	52908075	124608836	10925911	44	3046										
INSC	387755	broad.mit.edu	37	chr11	15267467	15267467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cttctccccaggctgctctgCgtagattggctggggtctgc	13	13	3	1	rs199686458		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr11:15267467C>T	ENST00000379554.3	+	13	1667	c.1621C>T	c.(1621-1623)Cgt>Tgt	p.R541C	INSC_ENST00000525218.1_Missense_Mutation_p.R452C|INSC_ENST00000379556.3_Missense_Mutation_p.R494C|INSC_ENST00000528567.1_Missense_Mutation_p.A520V|INSC_ENST00000530161.1_Missense_Mutation_p.R494C|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000424273.1_Missense_Mutation_p.R452C	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	541					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)		p.R541C(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GGCTGCTCTGCGTAGATTGGC	0.542													C|||	1	0.000199681	0	0.0014	5008	,	,		19461	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						C	CYS/ARG,CYS/ARG	0,4102		0,0,2051	111	113	113		1621,1480	5.2	1	11		113	2,8356		0,2,4177	yes	missense,missense	INSC	NM_001031853.3,NM_001042536.1	180,180	0,2,6228	TT,TC,CC		0.0239,0.0,0.0161	probably-damaging,probably-damaging	541/580,494/533	15267467	2,12458	2051	4179	6230	15224043	SO:0001583	missense	387755			AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1621C>T	11.37:g.15267467C>T	ENSP00000368872:p.Arg541Cys		15224043	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.4|22.4	4.282012|4.282012	0.80692|0.80692	0.0|0.0	2.39E-4|2.39E-4	ENSG00000188487|ENSG00000188487	ENST00000528567|ENST00000379554;ENST00000379556;ENST00000424273;ENST00000530161;ENST00000525218	T|T;T;T;T;T	0.32988|0.50001	1.43|0.76;0.76;0.76;0.76;0.76	6.17|6.17	5.21|5.21	0.72293|0.72293	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64305|0.64305	0.2586|0.2586	L|L	0.53249|0.53249	1.67|1.67	0.58432|0.58432	D|D	0.999995|0.999995	P|D;D;D	0.52170|0.89917	0.951|1.0;1.0;1.0	B|D;D;D	0.40134|0.91635	0.32|0.999;0.996;0.999	T|T	0.64837|0.64837	-0.6313|-0.6313	9|10	0.87932|0.87932	D|D	0|0	-16.2309|-16.2309	15.3417|15.3417	0.74303|0.74303	0.1403:0.8597:0.0:0.0|0.1403:0.8597:0.0:0.0	.|.	520|529;452;541	A0PJX5|Q1MX18-5;Q1MX18-4;Q1MX18	.|.;.;INSC_HUMAN	V|C	520|541;494;452;494;452	ENSP00000435022:A520V|ENSP00000368872:R541C;ENSP00000368874:R494C;ENSP00000389161:R452C;ENSP00000436194:R494C;ENSP00000436113:R452C	ENSP00000435022:A520V|ENSP00000368872:R541C	A|R	+|+	2|1	0|0	INSC|INSC	15224043|15224043	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.726000|2.726000	0.47302|0.47302	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.542	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		T	15267467	C	T	15267467	3	4	36	1	0	0	0	0	1	0	0	0	7785	768	27	1	1671	1	INSC	11	15267467	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		15267467	119739049	45	3047										
ZNHIT2	741	broad.mit.edu	37	chr11	64883979	64883979	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ggggcctccccaaagccgctCcagctccccagtgagggcgg	14	17	0	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr11:64883979C>A	ENST00000310597.4	-	1	1191	c.1147G>T	c.(1147-1149)Gag>Tag	p.E383*	AP003068.12_ENST00000527789.1_RNA	NM_014205.2	NP_055020.1	Q9UHR6	ZNHI2_HUMAN	zinc finger, HIT-type containing 2	383							metal ion binding (GO:0046872)	p.E383*(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						CAAAGCCGCTCCAGCTCCCCA	0.627																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											58	63	61					11																	64883979		2201	4297	6498	64640555	SO:0001587	stop_gained	741				CCDS8094.1	11q13	2012-08-08	2010-09-15	2004-07-14	ENSG00000174276	ENSG00000174276		"Zinc fingers, HIT-type"	1177	protein-coding gene	gene with protein product		604575	"chromosome 11 open reading frame 5", "zinc finger, HIT domain containing 2"	C11orf5			Standard	NM_014205		Approved	FON	uc001ocw.3	Q9UHR6	OTTHUMG00000165604	ENST00000310597.4:c.1147G>T	11.37:g.64883979C>A	ENSP00000308548:p.Glu383*		64640555	Q3SY14|Q8IUV0	Nonsense_Mutation	SNP	ENST00000310597.4	37	CCDS8094.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096386	0.56075	.	.	ENSG00000174276	ENST00000310597	.	.	.	4.79	4.79	0.61399	.	0.286130	0.28077	U	0.016688	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-14.8125	13.1907	0.59709	0.0:1.0:0.0:0.0	.	.	.	.	X	383	.	ENSP00000308548:E383X	E	-	1	0	ZNHIT2	64640555	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	2.923000	0.48868	2.482000	0.83794	0.561000	0.74099	GAG		0.627	ZNHIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385260.1	NM_014205		A	64883979	C	A	64883979	4	1	36	1	0	0	0	0	0	1	0	0	18246	864	30	2	68	2	ZNHIT2	11	64883979	Nonsense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	49616512	64883979	70122537	46	3048										
ENDOD1	23052	broad.mit.edu	37	chr11	94861651	94861651	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aatacagattaccttgattcTgattaccaaagaggacagct	7	8	1	4			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr11:94861651T>G	ENST00000278505.4	+	2	529	c.411T>G	c.(409-411)tcT>tcG	p.S137S		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	137						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S137S(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				ACCTTGATTCTGATTACCAAA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	11											112	112	112					11																	94861651		2009	4172	6181	94501299	SO:0001819	synonymous_variant	23052			BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.411T>G	11.37:g.94861651T>G			94501299	A8K6K8|Q6GQY5|Q8TAQ8	Silent	SNP	ENST00000278505.4	37	CCDS41699.1																																																																																				0.488	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		G	94861651	T	G	94861651	2	3	36	1	0	0	0	0	0	0	0	1	5127	1567	55	4		4	ENDOD1	11	94861651	Silent	SNP	T	TCGA-AG-3727-01A-01W-0899-10	29977672	94861651	40144865	47	3049										
ATM	472	broad.mit.edu	37	chr11	108115600	108115600	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tggctgtcaactttcgaattCgagtgtgtgaattaggagat	12	5	1	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr11:108115600C>T	ENST00000452508.2	+	8	937	c.748C>T	c.(748-750)Cga>Tga	p.R250*	ATM_ENST00000278616.4_Nonsense_Mutation_p.R250*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	250			R -> Q. {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R250*(4)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTTTCGAATTCGAGTGTGTGA	0.338			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	4	Substitution - Nonsense(4)	large_intestine(2)|kidney(2)	11	GRCh37	CM030188|CS991299	ATM	M|S							123	114	117					11																	108115600		2200	4298	6498	107620810	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.748C>T	11.37:g.108115600C>T	ENSP00000388058:p.Arg250*		107620810	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	38	6.953864	0.97960	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	.	.	.	5.33	3.43	0.39272	.	0.499073	0.19940	N	0.102677	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6503	0.45645	0.1323:0.7986:0.0:0.0691	.	.	.	.	X	250	.	ENSP00000278616:R250X	R	+	1	2	ATM	107620810	1.000000	0.71417	0.203000	0.23512	0.947000	0.59692	2.176000	0.42500	0.725000	0.32318	0.650000	0.86243	CGA		0.338	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108115600	C	T	108115600	4	4	36	1	0	0	0	0	0	1	0	0	1110	876	31	1	770	1	ATM	11	108115600	Nonsense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	13253949	108115600	26890916	48	3050										
OPCML	4978	broad.mit.edu	37	chr11	132307150	132307150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tttactttccgcacatcgggCgcagcgacatcgttcaacgc	9	14	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr11:132307150C>T	ENST00000331898.7	-	4	1208	c.630G>A	c.(628-630)gcG>gcA	p.A210A	OPCML_ENST00000524381.1_Silent_p.A203A|OPCML_ENST00000541867.1_Silent_p.A210A|OPCML_ENST00000374778.4_Silent_p.A169A|OPCML_ENST00000529038.1_5'UTR	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	210	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.A210A(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GCACATCGGGCGCAGCGACAT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	11											129	113	118					11																	132307150		2201	4297	6498	131812360	SO:0001819	synonymous_variant	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.630G>A	11.37:g.132307150C>T			131812360	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Silent	SNP	ENST00000331898.7	37	CCDS8492.1																																																																																				0.552	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132307150	C	T	132307150	2	4	36	1	0	0	0	0	0	0	0	1	10905	755	27	1		1	OPCML	11	132307150	Silent	SNP	C	TCGA-AG-3727-01A-01W-0899-10	24191550	132307150	2699366	49	3051										
KRAS	3845	broad.mit.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	36	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		25398281	108453614	50	3052										
FMNL3	91010	broad.mit.edu	37	chr12	50052249	50052249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gcacagactggcgcgcagagCgagcgaggctgttggtgaag	18	9	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:50052249C>T	ENST00000293590.5	-	6	814	c.581G>A	c.(580-582)cGc>cAc	p.R194H	FMNL3_ENST00000352151.5_Intron|FMNL3_ENST00000335154.5_Missense_Mutation_p.R194H|FMNL3_ENST00000550488.1_Missense_Mutation_p.R194H			Q8IVF7	FMNL3_HUMAN	formin-like 3	194	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)	p.R194H(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GCGCGCAGAGCGAGCGAGGCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	12											52	60	57					12																	50052249		2141	4241	6382	48338516	SO:0001583	missense	91010			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.581G>A	12.37:g.50052249C>T	ENSP00000293590:p.Arg194His		48338516	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	ENST00000293590.5	37		.	.	.	.	.	.	.	.	.	.	C	23.2	4.383307	0.82792	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000293590	T;T;T	0.81078	-1.45;-1.45;-1.45	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.90058	0.6895	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.90068	0.4161	10	0.44086	T	0.13	.	17.409	0.87480	0.0:1.0:0.0:0.0	.	194	Q8IVF7-3	.	H	194	ENSP00000335655:R194H;ENSP00000447479:R194H;ENSP00000293590:R194H	ENSP00000293590:R194H	R	-	2	0	FMNL3	48338516	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.805000	0.69143	2.507000	0.84556	0.467000	0.42956	CGC		0.627	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		T	50052249	C	T	50052249	3	4	36	1	0	0	0	0	1	0	0	0	5972	768	27	1	2586	1	FMNL3	12	50052249	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	24653968	50052249	83799646	51	3053										
CAND1	55832	broad.mit.edu	37	chr12	67700368	67700368	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ttccacggcttaaggggtacTtgatatcaggtaggtatcta	11	7	2	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:67700368T>A	ENST00000545606.1	+	10	3357	c.2920T>A	c.(2920-2922)Ttg>Atg	p.L974M		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	974					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.L974M(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAAGGGGTACTTGATATCAGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											73	75	74					12																	67700368		2203	4300	6503	65986635	SO:0001583	missense	55832				CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.2920T>A	12.37:g.67700368T>A	ENSP00000442318:p.Leu974Met		65986635	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	37	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.770060	0.49680	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000544619	T;T	0.38401	1.14;1.14	5.76	5.76	0.90799	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	0.978;1.0	D;D	0.80764	0.923;0.994	T	0.67734	-0.5594	9	.	.	.	-6.7556	16.0706	0.80928	0.0:0.0:0.0:1.0	.	806;974	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	M	974;974;514	ENSP00000442318:L974M;ENSP00000444089:L514M	.	L	+	1	2	CAND1	65986635	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.632000	0.46511	2.191000	0.70037	0.482000	0.46254	TTG		0.368	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67700368	T	A	67700368	3	1	36	1	0	0	0	0	1	0	0	0	2621	1606	56	5	2958	5	CAND1	12	67700368	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	17648119	67700368	66151527	52	3054										
MYF5	4617	broad.mit.edu	37	chr12	81111115	81111115	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cggaaggcagccactatgcgCgagcggaggcgcctgaagaa	16	11	0	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:81111115C>T	ENST00000228644.3	+	1	425	c.273C>T	c.(271-273)cgC>cgT	p.R91R		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	91	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.R91R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						CCACTATGCGCGAGCGGAGGC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	12											45	41	42					12																	81111115		2203	4299	6502	79635246	SO:0001819	synonymous_variant	4617				CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.273C>T	12.37:g.81111115C>T			79635246	Q6ISR9	Silent	SNP	ENST00000228644.3	37	CCDS9020.1																																																																																				0.612	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		T	81111115	C	T	81111115	2	4	36	1	0	0	0	0	0	0	0	1	10057	755	27	1		1	MYF5	12	81111115	Silent	SNP	C	TCGA-AG-3727-01A-01W-0899-10	13410747	81111115	52740780	53	3055										
SSH1	54434	broad.mit.edu	37	chr12	109205065	109205065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcaaggtggattttcgtgtcGctccacagtcggagaaccat	11	10	1	1	rs542173852		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:109205065G>A	ENST00000326495.5	-	6	534	c.441C>T	c.(439-441)agC>agT	p.S147S	SSH1_ENST00000360239.3_5'UTR|SSH1_ENST00000326470.5_Silent_p.S158S|SSH1_ENST00000546812.1_5'UTR|SSH1_ENST00000551165.1_Silent_p.S147S	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	147					actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S147S(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTTTCGTGTCGCTCCACAGTC	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		23716	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											178	145	156					12																	109205065		2203	4300	6503	107729194	SO:0001819	synonymous_variant	54434			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.441C>T	12.37:g.109205065G>A			107729194	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1																																																																																				0.493	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		A	109205065	G	A	109205065	2	1	36	1	0	0	0	0	0	0	0	1	15223	1078	38	1		1	SSH1	12	109205065	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	28093950	109205065	24646830	54	3056										
HSPB8	26353	broad.mit.edu	37	chr12	119617203	119617203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ggactctcccctctcctctcGcctgctggatgatggctttg	10	15	3	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:119617203G>A	ENST00000281938.2	+	1	757	c.86G>A	c.(85-87)cGc>cAc	p.R29H	RP11-64B16.3_ENST00000538405.1_RNA|RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	29					cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.R29H(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTCTCCTCTCGCCTGCTGGAT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	12											114	130	125					12																	119617203		2203	4300	6503	118101586	SO:0001583	missense	26353			AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"Heat shock proteins / HSPB"	30171	protein-coding gene	gene with protein product		608014	"heat shock 27kDa protein 8"			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.86G>A	12.37:g.119617203G>A	ENSP00000281938:p.Arg29His		118101586	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	37	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	30	5.057370	0.93846	.	.	ENSG00000152137	ENST00000281938	D	0.90324	-2.65	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.90728	0.7090	L	0.61036	1.89	0.80722	D	1	D	0.56746	0.977	P	0.47206	0.541	D	0.90679	0.4604	9	.	.	.	.	17.2157	0.86943	0.0:0.0:1.0:0.0	.	29	Q9UJY1	HSPB8_HUMAN	H	29	ENSP00000281938:R29H	.	R	+	2	0	HSPB8	118101586	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.143000	0.77348	2.294000	0.77228	0.563000	0.77884	CGC		0.657	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365		A	119617203	G	A	119617203	3	1	36	1	0	0	0	0	1	0	0	0	7444	1087	38	1	88	1	HSPB8	12	119617203	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	10412138	119617203	14234692	55	3057										
ANAPC5	51433	broad.mit.edu	37	chr12	121766193	121766193	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	agctctgacaggctgtgtttCcagtgcaggaggtcggagtc	15	9	1	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr12:121766193C>T	ENST00000261819.3	-	10	1351	c.1230G>A	c.(1228-1230)tgG>tgA	p.W410*	ANAPC5_ENST00000535482.1_Nonsense_Mutation_p.W76*|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000344395.4_Nonsense_Mutation_p.W298*|ANAPC5_ENST00000441917.2_Nonsense_Mutation_p.W298*|ANAPC5_ENST00000541887.1_Nonsense_Mutation_p.W397*	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	410					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.W410*(1)		breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGCTGTGTTTCCAGTGCAGGA	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											149	114	126					12																	121766193		2203	4300	6503	120250576	SO:0001587	stop_gained	51433			AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.1230G>A	12.37:g.121766193C>T	ENSP00000261819:p.Trp410*		120250576	E9PFB2|Q8N4H7|Q9BQD4	Nonsense_Mutation	SNP	ENST00000261819.3	37	CCDS9220.1	.	.	.	.	.	.	.	.	.	.	C	37	6.627967	0.97718	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000535482;ENST00000544314;ENST00000344395	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	19.3813	0.94536	0.0:1.0:0.0:0.0	.	.	.	.	X	298;397;410;76;12;298	.	ENSP00000261819:W410X	W	-	3	0	ANAPC5	120250576	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.077000	0.76814	2.824000	0.97209	0.655000	0.94253	TGG		0.562	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			T	121766193	C	T	121766193	4	4	36	1	0	0	0	0	0	1	0	0	605	856	30	3	1069	3	ANAPC5	12	121766193	Nonsense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	2148990	121766193	12085702	56	3058										
SAP18	10284	broad.mit.edu	37	chr13	21721351	21721351	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ggagattggcagcaccatgtCtggcagaaaggggactgatg	16	7	1	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr13:21721351C>A	ENST00000607003.1	+	4	364	c.332C>A	c.(331-333)tCt>tAt	p.S111Y	SAP18_ENST00000382533.4_Missense_Mutation_p.S130Y			O00422	SAP18_HUMAN	Sin3A-associated protein, 18kDa	111	Involved in splicing regulation activity.				mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)	p.S111Y(1)		kidney(1)|large_intestine(1)|lung(4)	6		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)		AGCACCATGTCTGGCAGAAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											105	104	105					13																	21721351		2203	4300	6503	20619351	SO:0001583	missense	10284			U96915	CCDS9295.2	13q12.11	2008-02-05	2006-02-02		ENSG00000150459	ENSG00000150459			10530	protein-coding gene	gene with protein product		602949	"sin3A-associated protein, 18kDa"			9150135	Standard	NM_005870		Approved	SAP18p, 2HOR0202, MGC27131	uc001uns.3	O00422	OTTHUMG00000016535	ENST00000607003.1:c.332C>A	13.37:g.21721351C>A	ENSP00000475925:p.Ser111Tyr		20619351	B2R494|Q2TTR4|Q6IAW9|Q8N606|Q9UF14	Missense_Mutation	SNP	ENST00000607003.1	37		.	.	.	.	.	.	.	.	.	.	C	23.6	4.434471	0.83776	.	.	ENSG00000150459	ENST00000382533	.	.	.	5.87	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.83046	0.5169	M	0.87456	2.885	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82750	-0.0303	9	0.22109	T	0.4	-12.752	16.4939	0.84209	0.1319:0.8681:0.0:0.0	.	111	O00422	SAP18_HUMAN	Y	130	.	ENSP00000371973:S130Y	S	+	2	0	SAP18	20619351	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.640000	0.83355	1.475000	0.48197	0.655000	0.94253	TCT		0.438	SAP18-009	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470725.1	NM_005870		A	21721351	C	A	21721351	3	1	36	1	0	0	0	0	1	0	0	0	13869	913	32	2	403	2	SAP18	13	21721351	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		21721351	93448527	57	3059										
PABPC3	5042	broad.mit.edu	37	chr13	25670809	25670809	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tgaaagagctattaaaaaaaTgaacggaatgctcctaaatg	8	5	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr13:25670809T>G	ENST00000281589.3	+	1	510	c.473T>G	c.(472-474)aTg>aGg	p.M158R		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	158	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)	p.M158R(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		ATTAAAAAAATGAACGGAATG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											117	116	116					13																	25670809		2203	4300	6503	24568809	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.473T>G	13.37:g.25670809T>G	ENSP00000281589:p.Met158Arg		24568809	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473409	0.43942	.	.	ENSG00000151846	ENST00000281589	T	0.17854	2.25	0.546	0.546	0.17196	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.56097	U	0.000023	T	0.38558	0.1045	M	0.87456	2.885	0.49483	D	0.999796	D	0.76494	0.999	D	0.76071	0.987	T	0.19484	-1.0304	10	0.87932	D	0	.	5.327	0.15913	0.0:1.0E-4:0.0:0.9999	.	158	Q9H361	PABP3_HUMAN	R	158	ENSP00000281589:M158R	ENSP00000281589:M158R	M	+	2	0	PABPC3	24568809	1.000000	0.71417	0.583000	0.28640	0.125000	0.20455	3.874000	0.56101	0.469000	0.27268	0.254000	0.18369	ATG		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		G	25670809	T	G	25670809	3	3	36	1	0	0	0	0	1	0	0	0	11396	1464	51	4	475	4	PABPC3	13	25670809	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	3949458	25670809	89499069	58	3060										
SLITRK1	114798	broad.mit.edu	37	chr13	84454048	84454048	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gcacaattgtgcaggagcacTcccaggggtttccgtggagg	15	10	0	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr13:84454048T>A	ENST00000377084.2	-	1	2480	c.1595A>T	c.(1594-1596)gAg>gTg	p.E532V		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	532	LRRCT 2.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.E532V(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GCAGGAGCACTCCCAGGGGTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	13											54	54	54					13																	84454048		2203	4300	6503	83352049	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1595A>T	13.37:g.84454048T>A	ENSP00000366288:p.Glu532Val		83352049	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.409862	0.42715	.	.	ENSG00000178235	ENST00000377084	T	0.50813	0.73	5.22	5.22	0.72569	Cysteine-rich flanking region, C-terminal (1);	0.051933	0.64402	D	0.000001	T	0.49558	0.1564	L	0.54323	1.7	0.54753	D	0.999986	B	0.22983	0.078	B	0.34536	0.185	T	0.50833	-0.8781	10	0.54805	T	0.06	-15.6625	14.208	0.65746	0.0:0.0:0.0:1.0	.	532	Q96PX8	SLIK1_HUMAN	V	532	ENSP00000366288:E532V	ENSP00000366288:E532V	E	-	2	0	SLITRK1	83352049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.104000	0.64026	0.533000	0.62120	GAG		0.547	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454048	T	A	84454048	3	1	36	1	0	0	0	0	1	0	0	0	14779	1551	54	5	499	5	SLITRK1	13	84454048	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	58783239	84454048	30715830	59	3061										
RASGRP1	10125	broad.mit.edu	37	chr15	38800144	38800144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cggtgcactctccataggctCgccggtaattgtcgtagttt	11	11	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr15:38800144C>T	ENST00000310803.5	-	9	1202	c.1025G>A	c.(1024-1026)cGa>cAa	p.R342Q	RASGRP1_ENST00000558164.1_Missense_Mutation_p.R342Q|RASGRP1_ENST00000561180.1_Missense_Mutation_p.R393Q|RASGRP1_ENST00000559830.1_Missense_Mutation_p.R342Q|RASGRP1_ENST00000450598.2_Missense_Mutation_p.R342Q|RASGRP1_ENST00000539159.1_Missense_Mutation_p.R294Q|RP11-102L12.2_ENST00000560231.1_RNA	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	342	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.R342Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TCCATAGGCTCGCCGGTAATT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											55	54	55					15																	38800144		2026	4185	6211	36587436	SO:0001583	missense	10125			AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1025G>A	15.37:g.38800144C>T	ENSP00000310244:p.Arg342Gln		36587436	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	37	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646740	0.67358	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.13	5.13	0.70059	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.249894	0.38217	N	0.001767	T	0.25901	0.0631	N	0.20328	0.56	0.53005	D	0.999963	B;P;P;P	0.50819	0.113;0.766;0.817;0.939	B;B;B;B	0.43155	0.016;0.392;0.317;0.41	T	0.03651	-1.1016	10	0.48119	T	0.1	-10.6811	18.782	0.91937	0.0:1.0:0.0:0.0	.	342;342;342;342	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	Q	342;342;342;342;294;342;342	ENSP00000310244:R342Q;ENSP00000388540:R342Q;ENSP00000444762:R294Q;ENSP00000413105:R342Q	ENSP00000310244:R342Q	R	-	2	0	RASGRP1	36587436	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.799000	0.62517	2.653000	0.90120	0.561000	0.74099	CGA		0.532	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		T	38800144	C	T	38800144	3	4	36	1	0	0	0	0	1	0	0	0	13111	884	31	1	1404	1	RASGRP1	15	38800144	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		38800144	63731248	60	3062										
MAPKBP1	23005	broad.mit.edu	37	chr15	42103107	42103107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ggttgtgttgttcaatccccGgaaacacaaacagcaccaca	8	12	1	0	rs201805153		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr15:42103107G>A	ENST00000456763.2	+	4	429	c.233G>A	c.(232-234)cGg>cAg	p.R78Q	MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R78Q|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R78Q|MAPKBP1_ENST00000260357.7_5'UTR|MAPKBP1_ENST00000507762.1_3'UTR|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.R78Q	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	78								p.R78Q(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TTCAATCCCCGGAAACACAAA	0.557													g|||	1	0.000199681	0	0	5008	,	,		18824	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											167	152	157					15																	42103107		2203	4300	6503	39890399	SO:0001583	missense	23005			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.233G>A	15.37:g.42103107G>A	ENSP00000393099:p.Arg78Gln		39890399	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	18.27	3.587896	0.66105	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000456763;ENST00000514566;ENST00000510535	T;T;T;T;T	0.56941	5.04;0.43;5.04;5.04;2.32	5.03	4.1	0.47936	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.221418	0.41294	D	0.000906	T	0.36663	0.0975	L	0.27053	0.805	0.80722	D	1	B;P;B	0.36990	0.066;0.577;0.176	B;B;B	0.29942	0.024;0.109;0.052	T	0.40327	-0.9569	10	0.51188	T	0.08	-19.5738	13.8788	0.63670	0.0747:0.0:0.9253:0.0	.	78;78;78	O60336-2;O60336;O60336-6	.;MABP1_HUMAN;.	Q	78	ENSP00000397570:R78Q;ENSP00000221214:R78Q;ENSP00000393099:R78Q;ENSP00000426154:R78Q;ENSP00000422132:R78Q	ENSP00000221214:R78Q	R	+	2	0	MAPKBP1	39890399	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.247000	0.43151	2.608000	0.88229	0.655000	0.94253	CGG		0.557	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42103107	G	A	42103107	3	1	36	1	0	0	0	0	1	0	0	0	9322	1116	39	1	243	1	MAPKBP1	15	42103107	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	3302963	42103107	60428285	61	3063										
MYO1E	4643	broad.mit.edu	37	chr15	59464132	59464132	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	agatccgttctatctcgattTtccgcttcaggacttctttc	6	12	4	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr15:59464132T>A	ENST00000288235.4	-	22	2843	c.2444A>T	c.(2443-2445)aAa>aTa	p.K815I	MIR2116_ENST00000517221.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	815	Myosin tail. {ECO:0000255}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.K815I(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TATCTCGATTTTCCGCTTCAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											151	132	139					15																	59464132		2191	4291	6482	57251424	SO:0001583	missense	4643			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2444A>T	15.37:g.59464132T>A	ENSP00000288235:p.Lys815Ile		57251424	Q14778	Missense_Mutation	SNP	ENST00000288235.4	37	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.479844	0.26511	.	.	ENSG00000157483	ENST00000288235	T	0.39787	1.06	5.05	-0.29	0.12847	Myosin tail 2 (1);	0.386506	0.29980	N	0.010704	T	0.64046	0.2563	M	0.88979	2.995	0.21473	N	0.999675	P	0.45126	0.851	D	0.64506	0.926	T	0.58255	-0.7668	10	0.72032	D	0.01	.	10.0207	0.42041	0.0:0.4447:0.0:0.5553	.	815	Q12965	MYO1E_HUMAN	I	815	ENSP00000288235:K815I	ENSP00000288235:K815I	K	-	2	0	MYO1E	57251424	0.003000	0.15002	0.191000	0.23289	0.369000	0.29798	0.095000	0.15127	-0.201000	0.10284	-0.366000	0.07423	AAA		0.542	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59464132	T	A	59464132	3	1	36	1	0	0	0	0	1	0	0	0	10102	1841	64	5	910	5	MYO1E	15	59464132	Missense_Mutation	SNP	T	TCGA-AG-3727-01A-01W-0899-10	17361025	59464132	43067260	62	3064										
GRIN2A	2903	broad.mit.edu	37	chr16	10031934	10031934	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tgcagcggtggttaggatgcCaatgccgtccctcactctcg	12	13	2	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr16:10031934C>T	ENST00000396573.2	-	4	1198	c.889G>A	c.(889-891)Ggc>Agc	p.G297S	GRIN2A_ENST00000566670.1_5'Flank|GRIN2A_ENST00000404927.2_Missense_Mutation_p.G297S|GRIN2A_ENST00000330684.3_Missense_Mutation_p.G297S|GRIN2A_ENST00000396575.2_Missense_Mutation_p.G297S|GRIN2A_ENST00000535259.1_Missense_Mutation_p.G140S|GRIN2A_ENST00000562109.1_Missense_Mutation_p.G297S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	297					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.G297S(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTTAGGATGCCAATGCCGTCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											89	68	75					16																	10031934		2197	4300	6497	9939435	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.889G>A	16.37:g.10031934C>T	ENSP00000379818:p.Gly297Ser		9939435	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	c	22.0	4.233296	0.79688	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.05382	3.45;3.45;3.45;3.45;3.45	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.06371	0.0164	L	0.28274	0.84	0.58432	D	0.999997	B;B;P	0.37423	0.235;0.277;0.594	B;B;B	0.35859	0.09;0.145;0.212	T	0.50171	-0.8859	9	.	.	.	.	18.0961	0.89490	0.0:1.0:0.0:0.0	.	140;297;297	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	S	297;297;140;297;297	ENSP00000379818:G297S;ENSP00000385872:G297S;ENSP00000441572:G140S;ENSP00000332549:G297S;ENSP00000379820:G297S	.	G	-	1	0	GRIN2A	9939435	1.000000	0.71417	0.997000	0.53966	0.553000	0.35397	5.905000	0.69893	2.582000	0.87167	0.561000	0.74099	GGC		0.572	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	10031934	C	T	10031934	3	4	36	1	0	0	0	0	1	0	0	0	6800	594	21	3	3549	3	GRIN2A	16	10031934	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		10031934	80322819	63	3065										
MYH1	4619	broad.mit.edu	37	chr17	10404045	10404045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	actcagttgatcttctagagCgcggcacatcttttcaaggt	9	10	5	2	rs142605633	byFrequency	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:10404045C>T	ENST00000226207.5	-	28	3857	c.3763G>A	c.(3763-3765)Gct>Act	p.A1255T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1255					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A1255T(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TCTTCTAGAGCGCGGCACATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	THR/ALA	0,4406		0,0,2203	146	129	135		3763	3.1	0.1	17	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	yes	missense	MYH1	NM_005963.3	58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1255/1940	10404045	2,13004	2203	4300	6503	10344770	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3763G>A	17.37:g.10404045C>T	ENSP00000226207:p.Ala1255Thr		10344770	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	2.155	-0.393510	0.04899	0.0	2.33E-4	ENSG00000109061	ENST00000226207	D	0.82433	-1.61	5.45	3.12	0.35913	Myosin tail (1);	0.320500	0.22216	N	0.063022	T	0.47930	0.1472	N	0.00468	-1.46	0.26872	N	0.967733	B	0.02656	0.0	B	0.04013	0.001	T	0.49103	-0.8974	10	0.02654	T	1	.	9.6684	0.39998	0.0:0.2075:0.0:0.7925	.	1255	P12882	MYH1_HUMAN	T	1255	ENSP00000226207:A1255T	ENSP00000226207:A1255T	A	-	1	0	MYH1	10344770	0.018000	0.18449	0.146000	0.22360	0.752000	0.42762	0.160000	0.16462	0.445000	0.26639	-0.300000	0.09419	GCT		0.453	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10404045	C	T	10404045	3	4	36	1	0	0	0	0	1	0	0	0	10059	768	27	1	2108	1	MYH1	17	10404045	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		10404045	70791165	64	3066										
MAP2K4	6416	broad.mit.edu	37	chr17	11998898	11998898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcattcttttccagagaattCggtcaacagtggatgaaaaa	8	7	3	2	rs375500789		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:11998898C>T	ENST00000353533.5	+	4	463	c.400C>T	c.(400-402)Cgg>Tgg	p.R134W	MAP2K4_ENST00000415385.3_Missense_Mutation_p.R145W|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	134	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.R134W(2)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		CCAGAGAATTCGGTCAACAGT	0.338			"D, Mis, N"		"pancreatic, breast, colorectal"																																		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	13	Whole gene deletion(10)|Substitution - Missense(2)|Unknown(1)	breast(4)|ovary(4)|large_intestine(2)|biliary_tract(1)|skin(1)|pancreas(1)	17											112	109	110					17																	11998898		2203	4300	6503	11939623	SO:0001583	missense	6416			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.400C>T	17.37:g.11998898C>T	ENSP00000262445:p.Arg134Trp		11939623	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600257	0.46423	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.66815	-0.23;-0.23	5.97	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83454	0.5258	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.997	D	0.85848	0.1402	10	0.87932	D	0	.	14.9277	0.70893	0.1438:0.8562:0.0:0.0	.	6;145;134	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	W	134;145;111;6	ENSP00000262445:R134W;ENSP00000410402:R145W	ENSP00000262445:R134W	R	+	1	2	MAP2K4	11939623	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.735000	0.62051	2.835000	0.97688	0.591000	0.81541	CGG		0.338	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	11998898	C	T	11998898	3	4	36	1	0	0	0	0	1	0	0	0	9269	875	31	1	414	1	MAP2K4	17	11998898	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	1594853	11998898	69196312	65	3067										
DLX4	1748	broad.mit.edu	37	chr17	48050478	48050478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ccccggaaccctccgagcggCgccctcaggcccccgccaaa	10	22	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:48050478C>T	ENST00000240306.3	+	2	620	c.325C>T	c.(325-327)Cgc>Tgc	p.R109C	DLX4_ENST00000411890.2_Missense_Mutation_p.R37C|DLX4_ENST00000503410.1_3'UTR	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	109					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R109C(1)		central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CTCCGAGCGGCGCCCTCAGGC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	17											27	34	31					17																	48050478		2203	4300	6503	45405477	SO:0001583	missense	1748				CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"Homeoboxes / ANTP class : NKL subclass"	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.325C>T	17.37:g.48050478C>T	ENSP00000240306:p.Arg109Cys		45405477	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	37	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.242043	0.39598	.	.	ENSG00000108813	ENST00000240306;ENST00000411890	D;D	0.95724	-2.96;-3.79	4.65	1.36	0.22044	Homeodomain-related (1);Homeodomain-like (1);	.	.	.	.	D	0.93180	0.7828	M	0.76328	2.33	0.09310	N	1	B;B	0.15141	0.012;0.004	B;B	0.10450	0.005;0.002	D	0.87008	0.2121	9	0.72032	D	0.01	-1.378	4.5273	0.11988	0.1943:0.6023:0.0:0.2034	.	37;109	Q92988-2;Q92988	.;DLX4_HUMAN	C	109;37	ENSP00000240306:R109C;ENSP00000410622:R37C	ENSP00000240306:R109C	R	+	1	0	DLX4	45405477	0.173000	0.23056	0.000000	0.03702	0.011000	0.07611	2.384000	0.44362	0.437000	0.26423	0.655000	0.94253	CGC		0.667	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			T	48050478	C	T	48050478	3	4	36	1	0	0	0	0	1	0	0	0	4584	768	27	1	398	1	DLX4	17	48050478	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	36051580	48050478	33144732	66	3068										
TMEM49	81671	broad.mit.edu	37	chr17	57812727	57812727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcagtgaatgaaaagaagagGagggagcgggaagaaaggca	17	3	1	5			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:57812727G>T	ENST00000262291.4	+	3	415	c.105G>T	c.(103-105)agG>agT	p.R35S	VMP1_ENST00000539763.1_Intron|VMP1_ENST00000537567.1_5'UTR|VMP1_ENST00000545362.1_Missense_Mutation_p.R35S|VMP1_ENST00000536180.1_5'UTR	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	35					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)		p.R35S(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						AAAAGAAGAGGAGGGAGCGGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											82	76	78					17																	57812727		2203	4300	6503	55167509	SO:0001583	missense	81671				CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"ectopic P-granules autophagy protein 3 homolog (C. elegans)", "transport and golgi organization 5 homolog (Drosophila)"	611753	"transmembrane protein 49"	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.105G>T	17.37:g.57812727G>T	ENSP00000262291:p.Arg35Ser		55167509	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	37	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.684381	0.29872	.	.	ENSG00000062716	ENST00000262291;ENST00000545362	.	.	.	5.46	1.1	0.20463	.	0.144593	0.64402	D	0.000005	T	0.29190	0.0726	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.03795	-1.1003	9	0.21540	T	0.41	-4.5525	4.9922	0.14220	0.4528:0.1555:0.3917:0.0	.	35;35	F5H2J3;Q96GC9	.;VMP1_HUMAN	S	35	.	ENSP00000262291:R35S	R	+	3	2	VMP1	55167509	1.000000	0.71417	0.993000	0.49108	0.934000	0.57294	2.241000	0.43097	0.350000	0.24002	0.591000	0.81541	AGG		0.388	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		T	57812727	G	T	57812727	3	4	36	1	0	0	0	0	1	0	0	0	16212	1165	41	2	111	2	TMEM49	17	57812727	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	9762249	57812727	23382483	67	3069										
ABCA10	10349	broad.mit.edu	37	chr17	67149983	67149983	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tctctgtaccgtgaaatactGagagcagcatcttctttgcc	8	11	3	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:67149983G>A	ENST00000269081.4	-	33	4863	c.3954C>T	c.(3952-3954)ctC>ctT	p.L1318L	ABCA10_ENST00000519732.1_5'UTR|ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1318	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L1318L(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GTGAAATACTGAGAGCAGCAT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	17											159	166	163					17																	67149983		2203	4300	6503	64661578	SO:0001819	synonymous_variant	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3954C>T	17.37:g.67149983G>A			64661578	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																				0.408	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		A	67149983	G	A	67149983	2	1	36	1	0	0	0	0	0	0	0	1	29	1277	45	3		3	ABCA10	17	67149983	Silent	SNP	G	TCGA-AG-3727-01A-01W-0899-10	9337256	67149983	14045227	68	3070										
LLGL2	3993	broad.mit.edu	37	chr17	73565329	73565329	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cctttgacccctacagtgatGacccccggctgggcatccag	10	16	0	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr17:73565329G>A	ENST00000392550.3	+	14	1621	c.1504G>A	c.(1504-1506)Gac>Aac	p.D502N	LLGL2_ENST00000577200.1_Missense_Mutation_p.D502N|LLGL2_ENST00000167462.5_Missense_Mutation_p.D502N	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	502					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)	p.D502N(1)		NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTACAGTGATGACCCCCGGCT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	17											60	64	63					17																	73565329		2203	4300	6503	71076924	SO:0001583	missense	3993			X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1504G>A	17.37:g.73565329G>A	ENSP00000376333:p.Asp502Asn		71076924	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462049	0.43736	.	.	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.46819	0.86;0.86	5.29	3.29	0.37713	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.69602	0.3129	M	0.85542	2.76	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.997;0.999;1.0;1.0	T	0.73164	-0.4069	10	0.87932	D	0	-14.5691	11.982	0.53125	0.1423:0.0:0.8577:0.0	.	129;491;491;502;502	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	N	502;502;491	ENSP00000167462:D502N;ENSP00000376333:D502N	ENSP00000167462:D502N	D	+	1	0	LLGL2	71076924	1.000000	0.71417	0.149000	0.22428	0.990000	0.78478	9.807000	0.99171	0.615000	0.30124	0.555000	0.69702	GAC		0.672	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		A	73565329	G	A	73565329	3	1	36	1	0	0	0	0	1	0	0	0	8858	1290	45	3	1589	3	LLGL2	17	73565329	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	6415346	73565329	7629881	69	3071										
THOC1	9984	broad.mit.edu	37	chr18	252542	252542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aggctctgaaaactcaccacGttgttggagcttcctcgtct	9	12	3	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr18:252542G>A	ENST00000261600.6	-	9	681	c.674C>T	c.(673-675)aCg>aTg	p.T225M	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	225					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.T225M(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				AACTCACCACGTTGTTGGAGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											145	136	139					18																	252542		1867	4102	5969	242542	SO:0001583	missense	9984			AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"THO complex subunits"	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.674C>T	18.37:g.252542G>A	ENSP00000261600:p.Thr225Met		242542	B2RBP6|Q15219|Q64I72|Q64I73	Missense_Mutation	SNP	ENST00000261600.6	37	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.136087	0.56936	.	.	ENSG00000079134	ENST00000261600	.	.	.	5.44	3.55	0.40652	.	0.221642	0.45606	D	0.000356	T	0.51126	0.1656	M	0.67397	2.05	0.34241	D	0.677694	P;P	0.48407	0.851;0.91	B;P	0.45037	0.429;0.467	T	0.65249	-0.6214	9	0.49607	T	0.09	.	8.8745	0.35337	0.0:0.3448:0.5317:0.1236	.	225;225	Q96FV9-2;Q96FV9	.;THOC1_HUMAN	M	225	.	ENSP00000261600:T225M	T	-	2	0	THOC1	242542	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.490000	0.45294	2.714000	0.92807	0.650000	0.86243	ACG		0.398	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		A	252542	G	A	252542	3	1	36	1	0	0	0	0	1	0	0	0	15903	1145	40	1	1351	1	THOC1	18	252542	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10		252542	77824706	70	3072										
RALBP1	10928	broad.mit.edu	37	chr18	9524700	9524700	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gatggtctaacatggccacgAtgcccacgctgccagagacc	11	14	1	1			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr18:9524700A>C	ENST00000019317.4	+	5	1385	c.1162A>C	c.(1162-1164)Atg>Ctg	p.M388L	RALBP1_ENST00000383432.3_Missense_Mutation_p.M388L			Q15311	RBP1_HUMAN	ralA binding protein 1	388					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)	p.M388L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	CATGGCCACGATGCCCACGCT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	18											53	46	48					18																	9524700		2203	4300	6503	9514700	SO:0001583	missense	10928			L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.1162A>C	18.37:g.9524700A>C	ENSP00000019317:p.Met388Leu		9514700	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.051620	0.55218	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.09630	2.96;2.96	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.10766	0.0263	L	0.34521	1.04	0.54753	D	0.999985	B	0.18968	0.032	B	0.23419	0.046	T	0.16394	-1.0404	10	0.23891	T	0.37	0.2236	15.9209	0.79570	1.0:0.0:0.0:0.0	.	388	Q15311	RBP1_HUMAN	L	388	ENSP00000019317:M388L;ENSP00000372924:M388L	ENSP00000019317:M388L	M	+	1	0	RALBP1	9514700	1.000000	0.71417	0.943000	0.38184	0.988000	0.76386	9.109000	0.94291	2.210000	0.71456	0.533000	0.62120	ATG		0.532	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		C	9524700	A	C	9524700	3	2	36	1	0	0	0	0	1	0	0	0	13049	333	12	4	1176	4	RALBP1	18	9524700	Missense_Mutation	SNP	A	TCGA-AG-3727-01A-01W-0899-10	9272158	9524700	68552548	71	3073										
SHC2	25759	broad.mit.edu	37	chr19	434833	434834	+	Frame_Shift_Ins	INS	-	-	C													0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ctccaaagagtcctcctcgtINSccccccaggccgactcctcc							TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr19:434833_434834insC	ENST00000264554.6	-	8	984_985	c.985_986insG	c.(985-987)gacfs	p.D329fs		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	329	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)		p.D690fs*107(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|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)		GTCCTCCTCGTCCCCCCAGGCC	0.663																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								385834	SO:0001589	frameshift_variant	25759			AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.986dupG	19.37:g.434839_434839dupC	ENSP00000264554:p.Asp329fs		385833	O60230|Q9NPL5|Q9UCX4	Frame_Shift_Ins	INS	ENST00000264554.6	37	CCDS45891.1																																																																																				0.663	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			C	434834	-	C	434833	7	5	36	1	0	1	1	0	0	0	0	0	14308	1667	58	0	782	0	SHC2	19	434833	Frame_Shift_Ins	INS	-	TCGA-AG-3727-01A-01W-0899-10		434833	58694150	72	3074										
SEMA6B	10501	broad.mit.edu	37	chr19	4554434	4554434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	taaactccatcgcaatctccCggaagaagaagtagacatgg	9	10	1	3	rs370318420		TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr19:4554434C>T	ENST00000586582.1	-	9	1047	c.737G>A	c.(736-738)cGg>cAg	p.R246Q	SEMA6B_ENST00000586965.1_Missense_Mutation_p.R246Q|SEMA6B_ENST00000301293.3_Missense_Mutation_p.R246Q	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	246	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R246Q(1)		breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCAATCTCCCGGAAGAAGAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19							GLN/ARG	0,4406		0,0,2203	87	75	79		737	3.8	1	19		79	1,8597		0,1,4298	no	missense	SEMA6B	NM_032108.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	246/889	4554434	1,13003	2203	4299	6502	4505434	SO:0001583	missense	10501			AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"Semaphorins"	10739	protein-coding gene	gene with protein product	"Sema VIb", "semaphorin Z", "semaphorin VIB"	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.737G>A	19.37:g.4554434C>T	ENSP00000467290:p.Arg246Gln		4505434	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	26.9	4.785328	0.90282	0.0	1.16E-4	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.12569	2.67	3.77	3.77	0.43336	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	U	0.000000	T	0.48840	0.1522	H	0.95539	3.685	0.37960	D	0.932958	D;D	0.89917	0.999;1.0	P;D	0.97110	0.888;1.0	T	0.69300	-0.5181	10	0.66056	D	0.02	.	14.3189	0.66470	0.0:1.0:0.0:0.0	.	246;246	B4DT36;Q9H3T3	.;SEM6B_HUMAN	Q	246	ENSP00000301293:R246Q	ENSP00000301292:R246Q	R	-	2	0	SEMA6B	4505434	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	7.487000	0.81328	1.956000	0.56807	0.298000	0.19748	CGG		0.562	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		T	4554434	C	T	4554434	3	4	36	1	0	0	0	0	1	0	0	0	14077	652	23	1	1965	1	SEMA6B	19	4554434	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	4119601	4554434	54574549	73	3075										
ARHGEF18	23370	broad.mit.edu	37	chr19	7511947	7511947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	agttttcaggtgaaaatgggGagagaatgaaagaaaagtac	13	2	1	4			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr19:7511947G>A	ENST00000359920.6	+	5	1319	c.1066G>A	c.(1066-1068)Gag>Aag	p.E356K	ARHGEF18_ENST00000319670.9_Missense_Mutation_p.E198K|CTD-2207O23.3_ENST00000593531.1_Silent_p.G313G	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	356	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E198K(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TGAAAATGGGGAGAGAATGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	79	79					19																	7511947		2203	4300	6503	7417947	SO:0001583	missense	23370			AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1066G>A	19.37:g.7511947G>A	ENSP00000352995:p.Glu356Lys		7417947	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425360	0.83667	.	.	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.68903	-0.36;-0.36	4.85	4.85	0.62838	Dbl homology (DH) domain (5);	0.105878	0.41097	D	0.000953	T	0.75895	0.3912	M	0.90650	3.135	0.58432	D	0.999999	P	0.40602	0.723	B	0.42625	0.393	T	0.81940	-0.0703	10	0.62326	D	0.03	-18.7463	15.4853	0.75560	0.0:0.0:1.0:0.0	.	356	Q6ZSZ5	ARHGI_HUMAN	K	198;356	ENSP00000319200:E198K;ENSP00000352995:E356K	ENSP00000319200:E198K	E	+	1	0	ARHGEF18	7417947	1.000000	0.71417	0.984000	0.44739	0.838000	0.47535	7.878000	0.87231	2.235000	0.73313	0.561000	0.74099	GAG		0.353	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		A	7511947	G	A	7511947	3	1	36	1	0	0	0	0	1	0	0	0	901	1175	41	3	1084	3	ARHGEF18	19	7511947	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	2957513	7511947	51617036	74	3076										
CASP14	23581	broad.mit.edu	37	chr19	15163075	15163075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	aaggagaaatgagcaatccgCggtctttggaagaggtaggc	15	6	1	3	rs77227419	byFrequency	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr19:15163075C>T	ENST00000427043.3	+	2	321	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	AC004699.1_ENST00000411269.1_RNA|CASP14_ENST00000221740.1_Missense_Mutation_p.R5W	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	5					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.R5W(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						GAGCAATCCGCGGTCTTTGGA	0.502													C|||	9	0.00179712	0.0068	0	5008	,	,		16614	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	19						C	TRP/ARG	17,4389		0,17,2186	89	74	79		13	-0.8	0	19	dbSNP_131	79	0,8600		0,0,4300	yes	missense	CASP14	NM_012114.2	101	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	probably-damaging	5/243	15163075	17,12989	2203	4300	6503	15024075	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.13C>T	19.37:g.15163075C>T	ENSP00000393417:p.Arg5Trp		15024075	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	.	11.21	1.572012	0.28092	0.003858	0.0	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.02944	4.1;4.1	4.2	-0.76	0.11041	.	4.671220	0.00166	N	0.000014	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	D	0.56968	0.978	B	0.38106	0.265	T	0.29212	-1.0019	10	0.59425	D	0.04	.	1.9888	0.03442	0.3634:0.3547:0.1773:0.1047	.	5	P31944	CASPE_HUMAN	W	5	ENSP00000393417:R5W;ENSP00000221740:R5W	ENSP00000221740:R5W	R	+	1	2	CASP14	15024075	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.245000	0.18142	0.082000	0.17018	0.491000	0.48974	CGG		0.502	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15163075	C	T	15163075	3	4	36	1	0	0	0	0	1	0	0	0	2676	759	27	1	15	1	CASP14	19	15163075	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	7651128	15163075	43965908	75	3077										
SIGLEC12	89858	broad.mit.edu	37	chr19	52003321	52003321	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	ctgtgggtccccaaggaggaGgaatcgaccgtgggtatcct	15	10	0	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr19:52003321G>T	ENST00000291707.3	-	2	716	c.661C>A	c.(661-663)Ctc>Atc	p.L221I	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.L103I	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	221	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.L221I(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCAAGGAGGAGGAATCGACCG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											131	120	124					19																	52003321		2203	4300	6503	56695133	SO:0001583	missense	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.661C>A	19.37:g.52003321G>T	ENSP00000291707:p.Leu221Ile		56695133	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	1.228	-0.624914	0.03636	.	.	ENSG00000254521	ENST00000291707	T	0.64803	-0.12	0.735	-0.466	0.12153	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	1.117400	0.07015	U	0.825818	T	0.44307	0.1287	N	0.02916	-0.46	0.09310	N	1	D;B	0.58268	0.982;0.391	P;B	0.55871	0.786;0.257	T	0.31861	-0.9928	10	0.23302	T	0.38	.	3.1203	0.06388	0.3517:0.0:0.6483:0.0	.	221;103	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	I	221	ENSP00000291707:L221I	ENSP00000291707:L221I	L	-	1	0	SIGLEC12	56695133	0.003000	0.15002	0.003000	0.11579	0.015000	0.08874	-0.444000	0.06854	-0.121000	0.11787	0.399000	0.26434	CTC		0.542	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		T	52003321	G	T	52003321	3	4	36	1	0	0	0	0	1	0	0	0	14345	1000	35	2	1154	2	SIGLEC12	19	52003321	Missense_Mutation	SNP	G	TCGA-AG-3727-01A-01W-0899-10	36840246	52003321	7125662	76	3078										
SSTR4	6754	broad.mit.edu	37	chr20	23016359	23016359	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	tcgctacgccaagatgaagaCggctaccaacatctacctgc	8	14	1	3			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chr20:23016359C>T	ENST00000255008.3	+	1	303	c.239C>T	c.(238-240)aCg>aTg	p.T80M	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	80					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.T80M(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					AAGATGAAGACGGCTACCAAC	0.632																																					Esophageal Squamous(15;850 1104 16640)											1	Substitution - Missense(1)	large_intestine(1)	20											128	135	133					20																	23016359		2203	4300	6503	22964359	SO:0001583	missense	6754				CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.239C>T	20.37:g.23016359C>T	ENSP00000255008:p.Thr80Met		22964359	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.223631	0.79576	.	.	ENSG00000132671	ENST00000255008	T	0.46819	0.86	3.58	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000005	T	0.74222	0.3688	M	0.92970	3.365	0.58432	D	0.999995	D	0.89917	1.0	D	0.79784	0.993	T	0.82368	-0.0492	10	0.87932	D	0	.	14.3291	0.66541	0.0:1.0:0.0:0.0	.	80	P31391	SSR4_HUMAN	M	80	ENSP00000255008:T80M	ENSP00000255008:T80M	T	+	2	0	SSTR4	22964359	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.256000	0.65468	1.811000	0.52892	0.561000	0.74099	ACG		0.632	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			T	23016359	C	T	23016359	3	4	36	1	0	0	0	0	1	0	0	0	15239	536	19	1	241	1	SSTR4	20	23016359	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10		23016359	40009161	77	3079										
KLHL34	257240	broad.mit.edu	37	chrX	21675045	21675046	+	Frame_Shift_Ins	INS	-	-	C													0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	accacctcccgtgccctgcgINScccccccaccaacaagatgc					rs139183650	byFrequency	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chrX:21675045_21675046insC	ENST00000379499.2	-	1	1402_1403	c.861_862insG	c.(859-864)gggcgcfs	p.R288fs		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	288						extracellular space (GO:0005615)		p.R288fs*9(1)		cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						CGTGCCCTGCGCCCCCCCACCA	0.693																																																1	Insertion - Frameshift(1)	large_intestine(1)	X																																								21584967	SO:0001589	frameshift_variant	257240			AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"Kelch-like", "BTB/POZ domain containing"	26634	protein-coding gene	gene with protein product			"kelch-like 34 (Drosophila)"				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.862dupG	X.37:g.21675052_21675052dupC	ENSP00000368813:p.Arg288fs		21584966		Frame_Shift_Ins	INS	ENST00000379499.2	37	CCDS14199.1																																																																																				0.693	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		C	21675046	-	C	21675045	7	5	36	1	0	1	1	0	0	0	0	0	8408	1087	38	0	1076	0	KLHL34	23	21675045	Frame_Shift_Ins	INS	-	TCGA-AG-3727-01A-01W-0899-10		21675045	133595515	78	3080										
TRPC5	7224	broad.mit.edu	37	chrX	111155953	111155953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gacaagcaatttgatgatttCgtagttgttggtgtgggcag	14	4	0	2			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chrX:111155953C>T	ENST00000262839.2	-	3	1384	c.466G>A	c.(466-468)Gaa>Aaa	p.E156K		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	156					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.E156K(2)		biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTGATGATTTCGTAGTTGTTG	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	X											121	102	109					X																	111155953		2203	4300	6503	111042609	SO:0001583	missense	7224			AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"Voltage-gated ion channels / Transient receptor potential cation channels"	12337	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 159"	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.466G>A	X.37:g.111155953C>T	ENSP00000262839:p.Glu156Lys		111042609	B2RP53|O75233|Q5JXY8|Q9Y514	Missense_Mutation	SNP	ENST00000262839.2	37	CCDS14561.1	.	.	.	.	.	.	.	.	.	.	C	34	5.319307	0.95682	.	.	ENSG00000072315	ENST00000262839	T	0.68479	-0.33	5.43	5.43	0.79202	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	D	0.82678	0.5089	M	0.78344	2.41	0.80722	D	1	D;D	0.76494	0.995;0.999	P;D	0.76071	0.905;0.987	D	0.85118	0.0967	10	0.87932	D	0	-27.7824	18.2995	0.90158	0.0:1.0:0.0:0.0	.	157;156	Q59G51;Q9UL62	.;TRPC5_HUMAN	K	156	ENSP00000262839:E156K	ENSP00000262839:E156K	E	-	1	0	TRPC5	111042609	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.818000	0.86416	2.260000	0.74910	0.529000	0.55759	GAA		0.512	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		T	111155953	C	T	111155953	3	4	36	1	0	0	0	0	1	0	0	0	16622	893	31	1	2491	1	TRPC5	23	111155953	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	89480908	111155953	44114607	79	3081										
SLC25A43	203427	broad.mit.edu	37	chrX	118587023	118587023	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	cgaagcctaaaaaaccaactCtataaaatggaatggaacta	6	8	1	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chrX:118587023C>A	ENST00000217909.7	+	5	1365	c.1021C>A	c.(1021-1023)Cta>Ata	p.L341I	SLC25A43_ENST00000488158.1_3'UTR|SLC25A43_ENST00000336249.7_3'UTR	NM_145305.2	NP_660348.2	Q8WUT9	S2543_HUMAN	solute carrier family 25, member 43	341					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.L341I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	9						AAAACCAACTCTATAAAATGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											64	65	64					X																	118587023		2203	4300	6503	118471051	SO:0001583	missense	203427			BC019584	CCDS14577.1	Xq24	2013-05-22			ENSG00000077713	ENSG00000077713		"Solute carriers"	30557	protein-coding gene	gene with protein product		300641				16949250	Standard	NM_145305		Approved		uc004erd.3	Q8WUT9	OTTHUMG00000022272	ENST00000217909.7:c.1021C>A	X.37:g.118587023C>A	ENSP00000217909:p.Leu341Ile		118471051	O75854|Q8N9L5	Missense_Mutation	SNP	ENST00000217909.7	37	CCDS14577.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057170	0.36277	.	.	ENSG00000077713	ENST00000217909;ENST00000326714	T	0.79554	-1.28	5.24	1.1	0.20463	.	.	.	.	.	T	0.66127	0.2758	L	0.33485	1.01	0.51767	D	0.999936	B	0.16166	0.016	B	0.15870	0.014	T	0.59752	-0.7395	9	0.66056	D	0.02	.	3.1673	0.06540	0.1198:0.5402:0.1158:0.2241	.	341	Q8WUT9	S2543_HUMAN	I	341;289	ENSP00000217909:L341I	ENSP00000217909:L341I	L	+	1	2	SLC25A43	118471051	0.024000	0.19004	0.826000	0.32828	0.523000	0.34469	-0.206000	0.09398	0.408000	0.25621	0.600000	0.82982	CTA		0.423	SLC25A43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058028.1	NM_145305		A	118587023	C	A	118587023	3	1	36	1	0	0	0	0	1	0	0	0	14545	912	32	2	1039	2	SLC25A43	23	118587023	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	7431070	118587023	36683537	80	3082										
RHOXF2	727940	broad.mit.edu	37	chrX	119211113	119211113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.51965811965812	7.14529914529915	0.39696106362773	0.545454545454546	1	0	gccatctttttcttctccgcCgccatctttttcttctccgc	4	17	6	0			TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3727-01A-01W-0899-10	TCGA-AG-3727-10A-01W-0901-10	g.chrX:119211113C>T	ENST00000371402.2	-	2	409	c.220G>A	c.(220-222)Ggc>Agc	p.G74S	RP4-755D9.1_ENST00000553843.1_RNA	NM_001099685.1	NP_001093155.1	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2B	74					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G74S(1)		kidney(1)|large_intestine(2)|skin(3)|upper_aerodigestive_tract(1)	7						TCTTCTCCGCCGCCATCTTTT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	X											14	17	16					X																	119211113		1929	3759	5688	119095141	SO:0001583	missense	727940				CCDS43985.1	Xq24	2011-06-20			ENSG00000203989	ENSG00000203989		"Homeoboxes / PRD class"	33519	protein-coding gene	gene with protein product							Standard	NM_001099685		Approved		uc004esj.4	P0C7M4	OTTHUMG00000022288	ENST00000371402.2:c.220G>A	X.37:g.119211113C>T	ENSP00000360455:p.Gly74Ser		119095141		Missense_Mutation	SNP	ENST00000371402.2	37	CCDS43985.1	.	.	.	.	.	.	.	.	.	.	-	14.07	2.425452	0.43020	.	.	ENSG00000203989	ENST00000371402	D	0.91686	-2.89	1.81	0.878	0.19150	.	.	.	.	.	D	0.89663	0.6780	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79579	-0.1745	9	0.16420	T	0.52	.	5.5064	0.16856	0.0:0.6505:0.3495:0.0	.	74	P0C7M4	RHF2B_HUMAN	S	74	ENSP00000360455:G74S	ENSP00000360455:G74S	G	-	1	0	RHOXF2B	119095141	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.436000	0.06922	0.213000	0.20722	0.488000	0.48403	GGC		0.592	RHOXF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058081.2	NM_001099685		T	119211113	C	T	119211113	3	4	36	1	0	0	0	0	1	0	0	0	13385	652	23	1	658	1	RHOXF2	23	119211113	Missense_Mutation	SNP	C	TCGA-AG-3727-01A-01W-0899-10	624090	119211113	36059447	81	3083										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1421550	1421550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccaggaacaccaagaagaacCggggcctgtacaggcacatc	11	13	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:1421550C>T	ENST00000308647.7	+	10	1140	c.1024C>T	c.(1024-1026)Cgg>Tgg	p.R342W		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	342						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)	p.R342W(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CAAGAAGAACCGGGGCCTGTA	0.647																																																1	Substitution - Missense(1)	endometrium(1)	1											81	89	86					1																	1421550		2203	4299	6502	1411413	SO:0001583	missense	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1024C>T	1.37:g.1421550C>T	ENSP00000311766:p.Arg342Trp		1411413	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	9.510	1.105557	0.20632	.	.	ENSG00000160072	ENST00000360489;ENST00000378737;ENST00000308647	D	0.94966	-3.57	2.26	-2.86	0.05717	.	0.616433	0.16127	N	0.228367	D	0.94420	0.8205	M	0.73217	2.22	0.48830	D	0.999719	D;D	0.76494	0.999;0.997	P;P	0.61275	0.886;0.696	D	0.90218	0.4269	10	0.72032	D	0.01	.	4.022	0.09670	0.5905:0.1843:0.2252:0.0	.	296;342	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	W	237;159;342	ENSP00000311766:R342W	ENSP00000311766:R342W	R	+	1	2	ATAD3B	1411413	0.141000	0.22595	0.015000	0.15790	0.001000	0.01503	0.777000	0.26718	-0.801000	0.04427	-1.027000	0.02421	CGG		0.647	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1421550	C	T	1421550	3	4	37	1	0	0	0	0	1	0	0	0	1075	643	23	1	1062	1	ATAD3B	1	1421550	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10		1421550	247829071	1	3084										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23395124	23395124	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	catcaactagacttcaatgtCctcaataataagcctgtgtc	5	11	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:23395124C>T	ENST00000356634.3	+	9	1349	c.1200C>T	c.(1198-1200)gtC>gtT	p.V400V	KDM1A_ENST00000400181.4_Silent_p.V424V|KDM1A_ENST00000542151.1_Silent_p.V424V|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	400	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						ACTTCAATGTCCTCAATAATA	0.383																																																0			1											101	85	90					1																	23395124		2203	4300	6503	23267711	SO:0001819	synonymous_variant	0			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1200C>T	1.37:g.23395124C>T			23267711	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																				0.383	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		T	23395124	C	T	23395124	2	4	37	1	0	0	0	0	0	0	0	1	8143	842	30	3		3	KDM1A	1	23395124	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	21973574	23395124	225855497	2	3085										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105552	27105552	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctccttgtagaatatttccgAcgatgcctgattgagatctt	8	9	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:27105552A>G	ENST00000324856.7	+	20	5534	c.5163A>G	c.(5161-5163)cgA>cgG	p.R1721R	ARID1A_ENST00000457599.2_Silent_p.R1504R|ARID1A_ENST00000374152.2_Silent_p.R1338R|ARID1A_ENST00000540690.1_Silent_p.R49R	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1721					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		AATATTTCCGACGATGCCTGA	0.438			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											182	200	194					1																	27105552		2203	4300	6503	26978139	SO:0001819	synonymous_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5163A>G	1.37:g.27105552A>G			26978139	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	7.472	0.646786	0.14516	.	.	ENSG00000117713	ENST00000430799	.	.	.	4.71	-0.765	0.11023	.	.	.	.	.	T	0.42988	0.1227	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26780	-1.0093	4	.	.	.	-6.2012	3.4497	0.07494	0.4185:0.0:0.2933:0.2882	.	.	.	.	A	618	.	.	T	+	1	0	ARID1A	26978139	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.866000	0.27954	0.057000	0.16193	0.482000	0.46254	ACG		0.438	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27105552	A	G	27105552	2	3	37	1	0	0	0	0	0	0	0	1	913	262	10	4		4	ARID1A	1	27105552	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	3710428	27105552	222145069	3	3086										
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33945203	33945203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gttcctgactatcttgcctaGggaggtccagacctgggtgc	13	11	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:33945203G>A	ENST00000361328.3	+	2	467	c.314G>A	c.(313-315)aGg>aAg	p.R105K	ZSCAN20_ENST00000373413.2_Missense_Mutation_p.R105K|ZSCAN20_ENST00000480917.1_3'UTR	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	105	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ATCTTGCCTAGGGAGGTCCAG	0.617																																																0			1											38	42	41					1																	33945203		2202	4300	6502	33717790	SO:0001583	missense	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.314G>A	1.37:g.33945203G>A	ENSP00000355053:p.Arg105Lys		33717790	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	G	5.293	0.239466	0.10023	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.03982	3.74	4.97	-1.63	0.08345	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.954791	0.08671	N	0.910918	T	0.02610	0.0079	L	0.31065	0.9	0.20703	N	0.999861	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.10450	0.003;0.005;0.003	T	0.47156	-0.9139	10	0.02654	T	1	-1.4394	1.4869	0.02449	0.4132:0.1385:0.3065:0.1419	.	105;105;105	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	K	105;105;105;39;39	ENSP00000362512:R105K	ENSP00000324450:R105K	R	+	2	0	ZSCAN20	33717790	0.000000	0.05858	0.597000	0.28824	0.974000	0.67602	-0.340000	0.07821	-0.497000	0.06641	0.637000	0.83480	AGG		0.617	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		A	33945203	G	A	33945203	3	1	37	1	0	0	0	0	1	0	0	0	18271	1000	35	3	316	3	ZSCAN20	1	33945203	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	6839651	33945203	215305418	4	3087										
AGBL4	84871	hgsc.bcm.edu	37	chr1	49128842	49128842	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	accttggcacacaaatgatgAgggtgtttcccctgggtgga	13	9	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:49128842A>G	ENST00000371839.1	-	7	822	c.706T>C	c.(706-708)Tca>Cca	p.S236P	AGBL4_ENST00000371838.1_Missense_Mutation_p.S236P|AGBL4_ENST00000334103.7_5'UTR	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	236					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.S236A(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		ACAAATGATGAGGGTGTTTCC	0.493																																																1	Substitution - Missense(1)	breast(1)	1											181	179	179					1																	49128842		2034	4186	6220	48901429	SO:0001583	missense	84871			AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 6"					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.706T>C	1.37:g.49128842A>G	ENSP00000360905:p.Ser236Pro		48901429	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.985204	0.74474	.	.	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000371838	T;T	0.12879	2.64;2.64	5.51	5.51	0.81932	Peptidase M14, carboxypeptidase A (1);	0.052765	0.85682	D	0.000000	T	0.42426	0.1202	M	0.86740	2.835	0.80722	D	1	D;D;D	0.57899	0.958;0.981;0.981	P;D;D	0.69142	0.563;0.953;0.962	T	0.44832	-0.9302	9	.	.	.	-21.0301	15.0959	0.72235	1.0:0.0:0.0:0.0	.	248;81;236	Q5VU57-2;B1AMW2;Q5VU57	.;.;CBPC6_HUMAN	P	236;230;236	ENSP00000360905:S236P;ENSP00000360904:S236P	.	S	-	1	0	AGBL4	48901429	1.000000	0.71417	0.999000	0.59377	0.892000	0.51952	5.655000	0.67981	2.216000	0.71823	0.533000	0.62120	TCA		0.493	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		G	49128842	A	G	49128842	3	3	37	1	0	0	0	0	1	0	0	0	377	304	11	4	837	4	AGBL4	1	49128842	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	15183639	49128842	200121779	5	3088										
USP24	23358	hgsc.bcm.edu	37	chr1	55591073	55591073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cacggacaactgtcggtaggAtgacttttctggggtaccac	12	10	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:55591073A>G	ENST00000294383.6	-	34	3879	c.3880T>C	c.(3880-3882)Tcc>Ccc	p.S1294P	USP24_ENST00000407756.1_Missense_Mutation_p.S1134P	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1294					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.S1211T(1)		breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TGTCGGTAGGATGACTTTTCT	0.463																																																1	Substitution - Missense(1)	ovary(1)	1											169	159	162					1																	55591073		1927	4140	6067	55363661	SO:0001583	missense	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.3880T>C	1.37:g.55591073A>G	ENSP00000294383:p.Ser1294Pro		55363661	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810148	0.70797	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02709	4.21;4.19	5.13	5.13	0.70059	.	0.052612	0.85682	D	0.000000	T	0.02929	0.0087	L	0.34521	1.04	0.58432	D	0.999991	P	0.38922	0.651	B	0.30855	0.121	T	0.58352	-0.7651	10	0.45353	T	0.12	.	14.9324	0.70926	1.0:0.0:0.0:0.0	.	1134	B7WPF4	.	P	1294;1134	ENSP00000294383:S1294P;ENSP00000385700:S1134P	ENSP00000294383:S1294P	S	-	1	0	USP24	55363661	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	8.923000	0.92808	1.938000	0.56188	0.460000	0.39030	TCC		0.463	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55591073	A	G	55591073	3	3	37	1	0	0	0	0	1	0	0	0	17095	333	12	4	4122	4	USP24	1	55591073	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	6462231	55591073	193659548	6	3089										
USP24	23358	hgsc.bcm.edu	37	chr1	55623038	55623038	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtgctatcttctattagtttGgttacctaaaaagataagat	7	5	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:55623038G>A	ENST00000294383.6	-	11	1232	c.1233C>T	c.(1231-1233)acC>acT	p.T411T	USP24_ENST00000407756.1_Silent_p.T299T	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	411					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CTATTAGTTTGGTTACCTAAA	0.284																																																0			1											67	63	64					1																	55623038		1807	4063	5870	55395626	SO:0001819	synonymous_variant	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1233C>T	1.37:g.55623038G>A			55395626	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																				0.284	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55623038	G	A	55623038	2	1	37	1	0	0	0	0	0	0	0	1	17095	1335	47	3		3	USP24	1	55623038	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	31965	55623038	193627583	7	3090										
RBMXL1	494115	hgsc.bcm.edu	37	chr1	89449223	89449223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tacttcttggaggtgggggcGgtccatgtctacctctttca	12	10	4	0	rs530375965	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:89449223G>A	ENST00000321792.5	-	2	714	c.287C>T	c.(286-288)cCg>cTg	p.P96L	CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000399794.2_Missense_Mutation_p.P96L|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	96					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										AGGTGGGGGCGGTCCATGTCT	0.512											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	3	0.000599042	0	0	5008	,	,		17899	0		0	False		,,,				2504	0.0031															0			1											92	97	95					1																	89449223		2203	4300	6503	89221811	SO:0001583	missense	56267			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"RNA binding motif (RRM) containing"	25073	protein-coding gene	gene with protein product	"kynurenine aminotransferase III"					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.287C>T	1.37:g.89449223G>A	ENSP00000318415:p.Pro96Leu	1267	89221811		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	9.954	1.220967	0.22457	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.73897	-0.79;-0.79	1.76	0.688	0.18027	.	0.000000	0.85682	U	0.000000	T	0.40815	0.1132	L	0.39898	1.24	0.34839	D	0.740515	B	0.27351	0.176	B	0.16722	0.016	T	0.09930	-1.0652	10	0.54805	T	0.06	-5.7204	5.0541	0.14524	0.0:0.0:0.6507:0.3493	.	96	Q96E39	RBMXL_HUMAN	L	96	ENSP00000318415:P96L;ENSP00000446099:P96L	ENSP00000318415:P96L	P	-	2	0	RBMXL1	89221811	1.000000	0.71417	0.132000	0.22025	0.147000	0.21601	4.379000	0.59575	0.042000	0.15717	0.306000	0.20318	CCG		0.512	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		A	89449223	G	A	89449223	3	1	37	1	0	0	0	0	1	0	0	0	13190	1116	39	1	889	1	RBMXL1	1	89449223	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	33826185	89449223	159801398	8	3091										
GFI1	2672	hgsc.bcm.edu	37	chr1	92944146	92944146	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aagggcctttttagctcaccAgtgtggatgaaagtgtgttt	12	6	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:92944146A>G	ENST00000370332.1	-	6	1407	c.1089T>C	c.(1087-1089)acT>acC	p.T363T	GFI1_ENST00000427103.1_Splice_Site_p.T363T|GFI1_ENST00000294702.5_Splice_Site_p.T363T	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	363					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.T363T(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		TTAGCTCACCAGTGTGGATGA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											189	163	172					1																	92944146		2203	4300	6503	92716734	SO:0001630	splice_region_variant	2672			U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"Zinc fingers, C2H2-type"	4237	protein-coding gene	gene with protein product		600871	"growth factor independent 1"	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.1090+1T>C	1.37:g.92944146A>G			92716734	Q8N564	Silent	SNP	ENST00000370332.1	37	CCDS30773.1																																																																																				0.507	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263	Silent	G	92944146	A	G	92944146	5	3	37	1	0	0	0	0	0	0	1	0	6359	202	7	4	187	4	GFI1	1	92944146	Splice_Site	SNP	A	TCGA-AG-3731-01A-11D-1733-10	3494923	92944146	156306475	9	3092										
AGL	178	hgsc.bcm.edu	37	chr1	100343239	100343239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agaacttatttgctggggagAcagtgttaaattacgctatg	11	5	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:100343239A>G	ENST00000294724.4	+	12	1944	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	AGL_ENST00000370163.3_Missense_Mutation_p.D489G|AGL_ENST00000361522.4_Missense_Mutation_p.D472G|AGL_ENST00000370165.3_Missense_Mutation_p.D489G|AGL_ENST00000361915.3_Missense_Mutation_p.D489G|AGL_ENST00000361302.3_Missense_Mutation_p.D473G|AGL_ENST00000370161.2_Missense_Mutation_p.D473G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGCTGGGGAGACAGTGTTAAA	0.363																																																0			1											102	99	100					1																	100343239		2203	4300	6503	100115827	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1466A>G	1.37:g.100343239A>G	ENSP00000294724:p.Asp489Gly		100115827	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838082	0.91117	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12;-3.12;-3.12	5.97	5.97	0.96955	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97687	1.0176	10	0.87932	D	0	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	472;473;489	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	489;489;489;489;473;473;472	ENSP00000355106:D489G;ENSP00000359184:D489G;ENSP00000359182:D489G;ENSP00000294724:D489G;ENSP00000354971:D473G;ENSP00000359180:D473G;ENSP00000354635:D472G	ENSP00000294724:D489G	D	+	2	0	AGL	100115827	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.896000	0.92521	2.288000	0.76882	0.533000	0.62120	GAC		0.363	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100343239	A	G	100343239	3	3	37	1	0	0	0	0	1	0	0	0	384	275	10	4	1577	4	AGL	1	100343239	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	7399093	100343239	148907382	10	3093										
C1orf162	128346	hgsc.bcm.edu	37	chr1	112020640	112020640	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggggaatcacttacctatgcCagcacaactttcaaactctc	6	13	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:112020640C>T	ENST00000343534.5	+	6	613	c.363C>T	c.(361-363)gcC>gcT	p.A121A	C1orf162_ENST00000464591.1_3'UTR|C1orf162_ENST00000369718.3_Silent_p.A96A	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	121						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		TTACCTATGCCAGCACAACTT	0.438																																																0			1											103	98	100					1																	112020640		2203	4300	6503	111822163	SO:0001819	synonymous_variant	128346			BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.363C>T	1.37:g.112020640C>T			111822163	Q5QNZ1	Silent	SNP	ENST00000343534.5	37	CCDS837.1																																																																																				0.438	C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1	NM_174896		T	112020640	C	T	112020640	2	4	37	1	0	0	0	0	0	0	0	1	2016	581	21	3		3	C1orf162	1	112020640	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	11677401	112020640	137229981	11	3094										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206712	116206712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggtccgcattttggactctcGggaccggaattaccagggca	13	11	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:116206712G>A	ENST00000355485.2	+	4	906	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	VANGL1_ENST00000369509.1_Missense_Mutation_p.R212Q|VANGL1_ENST00000310260.3_Missense_Mutation_p.R212Q|VANGL1_ENST00000369510.4_Missense_Mutation_p.R210Q	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	212					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGGACTCTCGGGACCGGAAT	0.517																																																0			1											195	197	196					1																	116206712		2203	4300	6503	116008235	SO:0001583	missense	81839			AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.635G>A	1.37:g.116206712G>A	ENSP00000347672:p.Arg212Gln		116008235	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274091	0.40194	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.73	4.82	0.62117	.	0.120688	0.64402	D	0.000018	T	0.51449	0.1675	N	0.25890	0.77	0.39974	D	0.974838	B;B	0.15930	0.012;0.015	B;B	0.15052	0.007;0.012	T	0.50939	-0.8768	10	0.21014	T	0.42	2.8345	9.7263	0.40333	0.197:0.0:0.803:0.0	.	210;212	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	Q	212;210;212;212	ENSP00000347672:R212Q;ENSP00000358523:R210Q;ENSP00000310800:R212Q;ENSP00000358522:R212Q	ENSP00000310800:R212Q	R	+	2	0	VANGL1	116008235	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.819000	0.62664	1.582000	0.49881	-0.142000	0.14014	CGG		0.517	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116206712	G	A	116206712	3	1	37	1	0	0	0	0	1	0	0	0	17159	1116	39	1	645	1	VANGL1	1	116206712	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4186072	116206712	133043909	12	3095										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380779	147380779	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acctgggcctgaaggggatcCggtctgccttgaagaggcct	15	11	1	3	rs140512440		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:147380779C>T	ENST00000369235.1	+	1	697	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	GJA8_ENST00000240986.4_Missense_Mutation_p.R233W			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	233					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GAAGGGGATCCGGTCTGCCTT	0.557													C|||	1	0.000199681	0	0	5008	,	,		17208	0		0	False		,,,				2504	0.001				Melanoma(76;1255 1795 8195 52096)											0			1						C	TRP/ARG	0,4406		0,0,2203	83	75	78		697	4.4	0.5	1	dbSNP_134	78	2,8598	2.2+/-6.3	0,2,4298	no	missense	GJA8	NM_005267.4	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	233/434	147380779	2,13004	2203	4300	6503	145847403	SO:0001583	missense	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.697C>T	1.37:g.147380779C>T	ENSP00000358238:p.Arg233Trp		145847403	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	37	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	c	16.89	3.246117	0.59103	0.0	2.33E-4	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.97831	-4.56;-4.56	4.4	4.4	0.53042	.	0.065730	0.64402	D	0.000007	D	0.97170	0.9075	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.65573	0.936	D	0.98521	1.0623	10	0.87932	D	0	.	17.1387	0.86747	0.0:1.0:0.0:0.0	.	233	P48165	CXA8_HUMAN	W	233	ENSP00000240986:R233W;ENSP00000358238:R233W	ENSP00000240986:R233W	R	+	1	2	GJA8	145847403	1.000000	0.71417	0.520000	0.27837	0.478000	0.33099	5.842000	0.69417	2.267000	0.75376	0.313000	0.20887	CGG		0.557	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380779	C	T	147380779	3	4	37	1	0	0	0	0	1	0	0	0	6425	643	23	1	699	1	GJA8	1	147380779	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	31174067	147380779	101869842	13	3096										
FLG2	388698	hgsc.bcm.edu	37	chr1	152324056	152324056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tctgtccatgagtagttccgTgtctctcatgaactgaggat	10	9	3	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:152324056T>C	ENST00000388718.5	-	3	6278	c.6206A>G	c.(6205-6207)cAc>cGc	p.H2069R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2069					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTAGTTCCGTGTCTCTCATG	0.532																																																0			1											549	483	506					1																	152324056		2203	4300	6503	150590680	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6206A>G	1.37:g.152324056T>C	ENSP00000373370:p.His2069Arg		150590680	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	4.716	0.133155	0.09032	.	.	ENSG00000143520	ENST00000388718	T	0.03635	3.86	4.32	3.21	0.36854	.	.	.	.	.	T	0.01156	0.0038	L	0.50333	1.59	0.09310	N	1	B	0.15930	0.015	B	0.12156	0.007	T	0.47861	-0.9084	9	0.11485	T	0.65	.	6.0272	0.19662	0.0:0.1144:0.0:0.8856	.	2069	Q5D862	FILA2_HUMAN	R	2069	ENSP00000373370:H2069R	ENSP00000373370:H2069R	H	-	2	0	FLG2	150590680	0.021000	0.18746	0.167000	0.22817	0.006000	0.05464	1.485000	0.35519	1.961000	0.56991	0.524000	0.50904	CAC		0.532	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		C	152324056	T	C	152324056	3	2	37	1	0	0	0	0	1	0	0	0	5942	1696	59	4	973	4	FLG2	1	152324056	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	4943277	152324056	96926565	14	3097										
LCE2B	26239	hgsc.bcm.edu	37	chr1	152659458	152659458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gttcccctgcagtctcttctTgctgtggtcccatctctggg	10	14	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:152659458T>C	ENST00000368780.3	+	2	193	c.139T>C	c.(139-141)Tgc>Cgc	p.C47R	LCE2B_ENST00000417924.2_Missense_Mutation_p.C47R	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	47	Cys-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTCTCTTCTTGCTGTGGTCC	0.622																																																0			1											139	149	146					1																	152659458		2203	4300	6503	150926082	SO:0001583	missense	26239			BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"Late cornified envelopes"	16610	protein-coding gene	gene with protein product		612610	"small proline rich-like (epidermal differentiation complex) 1B"	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.139T>C	1.37:g.152659458T>C	ENSP00000357769:p.Cys47Arg		150926082	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	.	.	.	.	.	.	.	.	.	.	T	0.305	-0.971704	0.02215	.	.	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.05382	3.45;3.45	2.26	2.26	0.28386	.	.	.	.	.	T	0.12518	0.0304	M	0.82323	2.585	0.41513	D	0.988354	D	0.62365	0.991	D	0.68039	0.955	T	0.01198	-1.1421	9	0.87932	D	0	.	6.3311	0.21270	0.0:0.0:0.0:1.0	.	47	O14633	LCE2B_HUMAN	R	47	ENSP00000414043:C47R;ENSP00000357769:C47R	ENSP00000357769:C47R	C	+	1	0	LCE2B	150926082	0.910000	0.30920	0.805000	0.32314	0.027000	0.11550	0.988000	0.29616	1.029000	0.39812	0.260000	0.18958	TGC		0.622	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357		C	152659458	T	C	152659458	3	2	37	1	0	0	0	0	1	0	0	0	8688	1812	63	4	141	4	LCE2B	1	152659458	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	335402	152659458	96591163	15	3098										
LMNA	4000	hgsc.bcm.edu	37	chr1	156106818	156106818	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gaaggctgggcaggtggtgaCggtgagtggcagggcgcttg	22	6	0	2	rs200466188		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:156106818C>T	ENST00000368300.4	+	8	1699	c.1487C>T	c.(1486-1488)aCg>aTg	p.T496M	LMNA_ENST00000392353.3_Splice_Site_p.T415M|LMNA_ENST00000368297.1_Splice_Site_p.T415M|LMNA_ENST00000448611.2_Splice_Site_p.T384M|LMNA_ENST00000368301.2_Splice_Site_p.T496M|LMNA_ENST00000347559.2_Splice_Site_p.T496M|LMNA_ENST00000473598.2_Splice_Site_p.T397M|LMNA_ENST00000361308.4_Splice_Site_p.T496M|LMNA_ENST00000368299.3_Splice_Site_p.T496M|LMNA_ENST00000496738.1_3'UTR	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	496	LTD.|Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CAGGTGGTGACGGTGAGTGGC	0.597									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																																							0			1											48	49	48					1																	156106818		2203	4300	6503	154373442	SO:0001630	splice_region_variant	4000	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1488+1C>T	1.37:g.156106818C>T			154373442	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Missense_Mutation	SNP	ENST00000368300.4	37	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.814232	0.90790	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000448611;ENST00000368297;ENST00000473598;ENST00000392353;ENST00000508500	D;D;D;D;D;D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05	5.4	5.4	0.78164	Intermediate filament, C-terminal (1);	0.000000	0.56097	D	0.000029	D	0.99196	0.9721	M	0.87547	2.89	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;0.997;1.0;0.999;0.999;0.999;0.998;1.0	D	0.99376	1.0921	10	0.59425	D	0.04	.	16.7143	0.85394	0.0:1.0:0.0:0.0	.	152;384;496;397;415;496;496;496	B4DFR3;E7EUI9;Q6UYC3;D6RAQ3;Q5TCI8;P02545;P02545-3;P02545-2	.;.;.;.;.;LMNA_HUMAN;.;.	M	496;496;496;496;496;384;415;397;415;122	ENSP00000357284:T496M;ENSP00000292304:T496M;ENSP00000355292:T496M;ENSP00000357283:T496M;ENSP00000357282:T496M;ENSP00000395597:T384M;ENSP00000357280:T415M;ENSP00000421821:T397M;ENSP00000376164:T415M;ENSP00000424977:T122M	ENSP00000292304:T496M	T	+	2	0	LMNA	154373442	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.448000	0.80631	2.797000	0.96272	0.655000	0.94253	ACG		0.597	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Missense_Mutation	T	156106818	C	T	156106818	5	4	37	1	0	0	0	0	0	0	1	0	8872	550	19	1	1517	1	LMNA	1	156106818	Splice_Site	SNP	C	TCGA-AG-3731-01A-11D-1733-10	3447360	156106818	93143803	16	3099										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183111876	183111876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caatctggaggacatcaggaAgaccttaccatctggctgct	10	11	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:183111876A>G	ENST00000258341.4	+	28	5038	c.4781A>G	c.(4780-4782)aAg>aGg	p.K1594R	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1594	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.K1594T(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GACATCAGGAAGACCTTACCA	0.522																																																1	Substitution - Missense(1)	ovary(1)	1											126	110	115					1																	183111876		2203	4300	6503	181378499	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4781A>G	1.37:g.183111876A>G	ENSP00000258341:p.Lys1594Arg		181378499	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	A	9.320	1.057726	0.19907	.	.	ENSG00000135862	ENST00000258341	T	0.30448	1.53	5.57	3.28	0.37604	.	0.159267	0.53938	N	0.000041	T	0.22627	0.0546	L	0.35723	1.085	0.39737	D	0.971694	B	0.14805	0.011	B	0.08055	0.003	T	0.05084	-1.0907	10	0.36615	T	0.2	.	9.517	0.39111	0.8577:0.0:0.1423:0.0	.	1594	P11047	LAMC1_HUMAN	R	1594	ENSP00000258341:K1594R	ENSP00000258341:K1594R	K	+	2	0	LAMC1	181378499	1.000000	0.71417	0.973000	0.42090	0.997000	0.91878	5.465000	0.66725	0.415000	0.25817	0.533000	0.62120	AAG		0.522	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		G	183111876	A	G	183111876	3	3	37	1	0	0	0	0	1	0	0	0	8636	72	3	4	4891	4	LAMC1	1	183111876	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	27005058	183111876	66138745	17	3100										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200972809	200972809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtcctggttcactaccacctTgttcttgatgttgcgggccc	10	13	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:200972809T>C	ENST00000422435.2	-	8	1433	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	KIF21B_ENST00000332129.2_Missense_Mutation_p.K373E|KIF21B_ENST00000461742.2_Missense_Mutation_p.K373E|KIF21B_ENST00000360529.5_Missense_Mutation_p.K373E	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	373					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						ACTACCACCTTGTTCTTGATG	0.542																																																0			1											193	148	163					1																	200972809		2203	4300	6503	199239432	SO:0001583	missense	23046			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1117A>G	1.37:g.200972809T>C	ENSP00000411831:p.Lys373Glu		199239432	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	t	24.2	4.502713	0.85176	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.19	5.19	0.71726	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.81964	0.4934	M	0.86178	2.8	0.58432	D	0.999996	D;D;P;D	0.56746	0.961;0.961;0.816;0.977	P;P;B;P	0.51974	0.489;0.489;0.188;0.686	D	0.85109	0.0962	10	0.87932	D	0	.	11.1258	0.48317	0.0:0.0:0.1544:0.8455	.	373;373;373;373	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	E	373	ENSP00000328494:K373E;ENSP00000353724:K373E;ENSP00000433808:K373E;ENSP00000411831:K373E	ENSP00000328494:K373E	K	-	1	0	KIF21B	199239432	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.939000	0.63526	1.959000	0.56917	0.524000	0.50904	AAG		0.542	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200972809	T	C	200972809	3	2	37	1	0	0	0	0	1	0	0	0	8310	1821	63	4	3865	4	KIF21B	1	200972809	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	17860933	200972809	48277812	18	3101										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205277835	205277838	+	Frame_Shift_Del	DEL	CACG	CACG	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctggcatactccatgacgatCacgatcttgctgctgttctc					rs116063043		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CACG	CACG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:205277835_205277838delCACG	ENST00000367157.3	-	3	501_504	c.375_378delCGTG	c.(373-378)atcgtgfs	p.IV127fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCATGACGATCACGATCTTGCTGC	0.593																																																0			1																																								203544461	SO:0001589	frameshift_variant	81788			AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.375_378delCGTG	1.37:g.205277835_205277838delCACG	ENSP00000356125:p.Ile127fs		203544458		Frame_Shift_Del	DEL	ENST00000367157.3	37	CCDS1453.1																																																																																				0.593	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		-	205277838	CACG	-	205277835	7	5	37	1	0	1	0	1	0	0	0	0	10744	813	29	0	1528	0	NUAK2	1	205277835	Frame_Shift_Del	DEL	CACG	TCGA-AG-3731-01A-11D-1733-10	4305026	205277835	43972786	19	3102										
RAB7L1	8934	hgsc.bcm.edu	37	chr1	205739922	205739922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttctgtccaacctgtgaaacCgttctctttactgaaccggt	7	12	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:205739922C>T	ENST00000367139.3	-	5	742	c.439G>A	c.(439-441)Ggt>Agt	p.G147S	RAB7L1_ENST00000446390.2_Missense_Mutation_p.G123S|RAB7L1_ENST00000414729.1_Missense_Mutation_p.G147S|RAB7L1_ENST00000437324.2_Missense_Mutation_p.G75S|RAB7L1_ENST00000235932.4_Missense_Mutation_p.G147S|RAB7L1_ENST00000468887.1_5'UTR	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		147					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CCTGTGAAACCGTTCTCTTTA	0.428																																					Pancreas(25;658 872 27763 34889 38531)											0			1											160	129	139					1																	205739922		2203	4300	6503	204006545	SO:0001583	missense	8934																														ENST00000367139.3:c.439G>A	1.37:g.205739922C>T	ENSP00000356107:p.Gly147Ser		204006545	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	37	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868480	0.91587	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	D;D;T;D;D	0.81821	-1.54;-1.54;-0.74;-1.54;-1.54	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.82655	0.5084	L	0.43554	1.36	0.49582	D	0.999801	P;D	0.60160	0.886;0.987	B;P	0.53593	0.195;0.73	D	0.84571	0.0655	10	0.72032	D	0.01	-10.8692	17.0021	0.86384	0.0:1.0:0.0:0.0	.	123;147	B4E1K3;O14966	.;RAB7L_HUMAN	S	147;147;75;123;147	ENSP00000356107:G147S;ENSP00000235932:G147S;ENSP00000416613:G75S;ENSP00000389899:G123S;ENSP00000402910:G147S	ENSP00000235932:G147S	G	-	1	0	RAB7L1	204006545	1.000000	0.71417	0.935000	0.37517	0.908000	0.53690	5.420000	0.66441	2.619000	0.88677	0.561000	0.74099	GGT		0.428	RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1			T	205739922	C	T	205739922	3	4	37	1	0	0	0	0	1	0	0	0	12992	652	23	1	180	1	RAB7L1	1	205739922	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	462087	205739922	43510699	20	3103										
HHAT	55733	hgsc.bcm.edu	37	chr1	210577849	210577849	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aacgagtactacctgctgcaGttcacgctgaccgttcgctg	10	13	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:210577849G>A	ENST00000367010.1	+	6	737	c.510G>A	c.(508-510)caG>caA	p.Q170Q	HHAT_ENST00000413764.2_Silent_p.Q170Q|HHAT_ENST00000545781.1_Silent_p.Q107Q|HHAT_ENST00000261458.3_Silent_p.Q170Q|HHAT_ENST00000545154.1_Silent_p.Q171Q|HHAT_ENST00000308852.6_Silent_p.Q125Q|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000391905.3_Silent_p.Q170Q|HHAT_ENST00000537898.1_Silent_p.Q105Q	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	170					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		ACCTGCTGCAGTTCACGCTGA	0.542																																																0			1											109	88	95					1																	210577849		2203	4300	6503	208644472	SO:0001819	synonymous_variant	55733			AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.510G>A	1.37:g.210577849G>A			208644472	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Silent	SNP	ENST00000367010.1	37	CCDS1495.1																																																																																				0.542	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		A	210577849	G	A	210577849	2	1	37	1	0	0	0	0	0	0	0	1	7110	1020	36	3		3	HHAT	1	210577849	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4837927	210577849	38672772	21	3104										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072213	240072213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgtccctggtcaaggagaagAaagcggcccagaccctcagt	12	12	2	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr1:240072213A>G	ENST00000255380.4	+	5	2241	c.1462A>G	c.(1462-1464)Aaa>Gaa	p.K488E		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	488					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAAGGAGAAGAAAGCGGCCCA	0.507																																																0			1											135	129	131					1																	240072213		2203	4300	6503	238138836	SO:0001583	missense	1131			U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1462A>G	1.37:g.240072213A>G	ENSP00000255380:p.Lys488Glu		238138836	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.142363	0.77888	.	.	ENSG00000133019	ENST00000255380	T	0.42131	0.98	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66848	0.2831	M	0.86097	2.795	0.80722	D	1	D	0.59767	0.986	P	0.62014	0.897	T	0.73065	-0.4100	10	0.87932	D	0	-18.1655	16.2343	0.82363	1.0:0.0:0.0:0.0	.	488	P20309	ACM3_HUMAN	E	488	ENSP00000255380:K488E	ENSP00000255380:K488E	K	+	1	0	CHRM3	238138836	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.339000	0.96797	2.234000	0.73211	0.533000	0.62120	AAA		0.507	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		G	240072213	A	G	240072213	3	3	37	1	0	0	0	0	1	0	0	0	3384	247	9	4	1464	4	CHRM3	1	240072213	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	29494364	240072213	9178408	22	3105										
KCNS3	3790	hgsc.bcm.edu	37	chr2	18113666	18113666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgtaggcattgtggtgagcgAtcctgactccacagatgctt	12	9	0	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:18113666A>G	ENST00000403915.1	+	3	1842	c.1391A>G	c.(1390-1392)gAt>gGt	p.D464G	KCNS3_ENST00000304101.4_Missense_Mutation_p.D464G|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	464					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTGGTGAGCGATCCTGACTCC	0.453																																																0			2											123	112	116					2																	18113666		2203	4300	6503	17977147	SO:0001583	missense	3790			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1391A>G	2.37:g.18113666A>G	ENSP00000385968:p.Asp464Gly		17977147	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.425329	0.25639	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.97209	-4.29;-4.29	6.07	6.07	0.98685	.	0.658090	0.16144	N	0.227590	D	0.92740	0.7692	N	0.22421	0.69	0.46279	D	0.998965	B	0.02656	0.0	B	0.01281	0.0	D	0.88473	0.3063	10	0.21540	T	0.41	.	10.8883	0.46981	0.9305:0.0:0.0695:0.0	.	464	Q9BQ31	KCNS3_HUMAN	G	464	ENSP00000385968:D464G;ENSP00000305824:D464G	ENSP00000305824:D464G	D	+	2	0	KCNS3	17977147	0.843000	0.29541	0.408000	0.26446	0.981000	0.71138	2.481000	0.45215	2.326000	0.78906	0.533000	0.62120	GAT		0.453	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		G	18113666	A	G	18113666	3	3	37	1	0	0	0	0	1	0	0	0	8111	333	12	4	1393	4	KCNS3	2	18113666	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10		18113666	225085707	23	3106										
SULT6B1	391365	hgsc.bcm.edu	37	chr2	37398688	37398688	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aatttgctccccagttagaaAgaatcccaagaactcagcaa	6	11	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:37398688A>G	ENST00000535679.1	-	6	669	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	SULT6B1_ENST00000407963.1_Missense_Mutation_p.F186L|SULT6B1_ENST00000379149.2_Missense_Mutation_p.F120L|SULT6B1_ENST00000260637.3_Missense_Mutation_p.F186L			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	224						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)	p.F186I(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCAGTTAGAAAGAATCCCAAG	0.428																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											113	112	112					2																	37398688		2203	4300	6503	37252192	SO:0001583	missense	391365			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"Sulfotransferases, cytosolic"	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.670T>C	2.37:g.37398688A>G	ENSP00000444081:p.Phe224Leu		37252192	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		.	.	.	.	.	.	.	.	.	.	A	11.20	1.569186	0.28003	.	.	ENSG00000138068	ENST00000535679;ENST00000379149;ENST00000260637;ENST00000407963	T;T;T;T	0.11063	2.81;2.81;2.81;2.81	4.87	4.87	0.63330	Sulfotransferase domain (1);	0.462043	0.24518	N	0.037832	T	0.06554	0.0168	N	0.14661	0.345	0.24110	N	0.995844	B	0.11235	0.004	B	0.08055	0.003	T	0.25363	-1.0134	10	0.39692	T	0.17	.	8.6963	0.34298	0.9105:0.0:0.0895:0.0	.	224	Q6IMI4	ST6B1_HUMAN	L	224;120;186;186	ENSP00000444081:F224L;ENSP00000368444:F120L;ENSP00000260637:F186L;ENSP00000384950:F186L	ENSP00000260637:F186L	F	-	1	0	SULT6B1	37252192	1.000000	0.71417	0.972000	0.41901	0.217000	0.24651	2.353000	0.44089	2.041000	0.60428	0.482000	0.46254	TTT		0.428	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		G	37398688	A	G	37398688	3	3	37	1	0	0	0	0	1	0	0	0	15423	72	3	4	249	4	SULT6B1	2	37398688	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	19285022	37398688	205800685	24	3107										
REG3A	5068	hgsc.bcm.edu	37	chr2	79384717	79384717	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cctgtgcttctcgacaggctCgcacagtggccggggcttga	14	13	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:79384717C>T	ENST00000409839.3	-	5	477	c.441G>A	c.(439-441)gcG>gcA	p.A147A	REG3A_ENST00000393878.1_Silent_p.A147A|AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Silent_p.A147A	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	147	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						TCGACAGGCTCGCACAGTGGC	0.527																																																0			2											103	104	104					2																	79384717		2203	4300	6503	79238225	SO:0001819	synonymous_variant	5068			S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"pancreatitis-associated protein"	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.441G>A	2.37:g.79384717C>T			79238225		Silent	SNP	ENST00000409839.3	37	CCDS1965.1																																																																																				0.527	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580		T	79384717	C	T	79384717	2	4	37	1	0	0	0	0	0	0	0	1	13249	871	31	1		1	REG3A	2	79384717	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	41986029	79384717	163814656	25	3108										
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85554536	85554577	+	In_Frame_Del	DEL	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acccgacttgctagtgctgcCtttttgggtctttgcctccg					rs1044964|rs1044965		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENST00000409232.3	-	2	339_380	c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	c.(277-321)gacagctccaacaagtcgggtgcggaggcaaagacccaaaaaggc>ggc	p.DSSNKSGAEAKTQK93del	TGOLN2_ENST00000444342.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000409015.1_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000398263.2_In_Frame_Del_p.DSSNKSGAEAKTQK93del|TGOLN2_ENST00000377386.3_In_Frame_Del_p.DSSNKSGAEAKTQK93del			O43493	TGON2_HUMAN	trans-golgi network protein 2	93	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTAGTGCTGCCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGTCTTTTTGGGT	0.57																																																0			2																																								85408088	SO:0001651	inframe_deletion	10618			AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.278_319delACAGCTCCAACAAGTCGGGTGCGGAGGCAAAGACCCAAAAAG	2.37:g.85554536_85554577delCTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	ENSP00000386443:p.Asp93_Lys106del		85408047	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	In_Frame_Del	DEL	ENST00000409232.3	37	CCDS56126.1																																																																																				0.57	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		-	85554577	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	-	85554536	7	5	37	1	0	1	0	1	0	0	0	0	15875	681	24	0	1006	0	TGOLN2	2	85554536	In_Frame_Del	DEL	CTTTTTGGGTCTTTGCCTCCGCACCCGACTTGTTGGAGCTGT	TCGA-AG-3731-01A-11D-1733-10	6169819	85554536	157644837	26	3109										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102456283	102456283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctttttcacttcttacaggtCgaagaagttttttagtttta	6	6	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:102456283C>T	ENST00000347699.4	+	10	776	c.776C>T	c.(775-777)tCg>tTg	p.S259L	MAP4K4_ENST00000425019.1_Missense_Mutation_p.S259L|MAP4K4_ENST00000413150.2_Missense_Mutation_p.S259L|MAP4K4_ENST00000350198.4_Missense_Mutation_p.S259L|MAP4K4_ENST00000302217.5_Intron|MAP4K4_ENST00000350878.4_Missense_Mutation_p.S239L|MAP4K4_ENST00000324219.4_Missense_Mutation_p.S259L|MAP4K4_ENST00000456652.1_Intron	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.S259L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTTACAGGTCGAAGAAGTTT	0.378																																																1	Substitution - Missense(1)	lung(1)	2											68	57	60					2																	102456283		1822	4082	5904	101822715	SO:0001583	missense	9448			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.776C>T	2.37:g.102456283C>T	ENSP00000314363:p.Ser259Leu		101822715	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.499809	0.85176	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000413150;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;2.09	5.71	5.71	0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68201	0.2975	M	0.93939	3.475	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.982;0.993;1.0;0.978;0.989	D;D;D;D;D;B;B;D;B;B	0.79108	0.992;0.991;0.988;0.969;0.963;0.289;0.376;0.97;0.191;0.384	T	0.76650	-0.2881	10	0.87932	D	0	.	19.8484	0.96730	0.0:1.0:0.0:0.0	.	239;259;259;239;259;259;259;259;259;259	B7Z388;B7Z3V5;E7ENQ1;E7ESS2;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;.;M4K4_HUMAN;.;.;.;.	L	259;259;259;259;259;221;239	ENSP00000392830:S259L;ENSP00000313644:S259L;ENSP00000281111:S259L;ENSP00000389752:S259L;ENSP00000314363:S259L;ENSP00000409720:S221L;ENSP00000343658:S239L	ENSP00000313644:S259L	S	+	2	0	MAP4K4	101822715	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.776000	0.85560	2.684000	0.91462	0.655000	0.94253	TCG		0.378	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		T	102456283	C	T	102456283	3	4	37	1	0	0	0	0	1	0	0	0	9292	893	31	1	814	1	MAP4K4	2	102456283	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	16901747	102456283	140743090	27	3110										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141625386	141625386	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgttccatcatagagggctGaataaatagcatctgaccta	8	8	2	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:141625386G>C	ENST00000389484.3	-	27	5323	c.4352C>G	c.(4351-4353)tCa>tGa	p.S1451*		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1451					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ATAGAGGGCTGAATAAATAGC	0.383										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											73	77	76					2																	141625386		2202	4300	6502	141341856	SO:0001587	stop_gained	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4352C>G	2.37:g.141625386G>C	ENSP00000374135:p.Ser1451*		141341856	Q8WY29|Q8WY30|Q8WY31	Nonsense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	51	18.016610	0.99897	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	.	.	.	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	19.6932	0.96010	0.0:0.0:1.0:0.0	.	.	.	.	X	1451;1389;596	.	ENSP00000374135:S1451X	S	-	2	0	LRP1B	141341856	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.744000	0.98853	2.664000	0.90586	0.655000	0.94253	TCA		0.383	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141625386	G	C	141625386	4	2	37	1	0	0	0	0	0	1	0	0	8984	1294	45	5	9707	5	LRP1B	2	141625386	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	39169103	141625386	101573987	28	3111										
LRP2	4036	hgsc.bcm.edu	37	chr2	170026297	170026297	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acacaatgtccacttgtacaCtgaaaatattcaggatggca	7	9	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:170026297C>T	ENST00000263816.3	-	60	11697	c.11412G>A	c.(11410-11412)caG>caA	p.Q3804Q		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3804	LDL-receptor class A 33. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CACTTGTACACTGAAAATATT	0.438																																																0			2											151	125	134					2																	170026297		2203	4300	6503	169734543	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11412G>A	2.37:g.170026297C>T			169734543	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170026297	C	T	170026297	2	4	37	1	0	0	0	0	0	0	0	1	8985	564	20	3		3	LRP2	2	170026297	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	28400911	170026297	73173076	29	3112										
LRP2	4036	hgsc.bcm.edu	37	chr2	170147488	170147488	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tctcttggggaacatttatgAacatcatgaggaccgctttc	9	9	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:170147488A>G	ENST00000263816.3	-	8	1074	c.789T>C	c.(787-789)gtT>gtC	p.V263V	LRP2_ENST00000443831.1_Silent_p.V263V	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	263					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AACATTTATGAACATCATGAG	0.463																																																0			2											111	109	109					2																	170147488		2203	4300	6503	169855734	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.789T>C	2.37:g.170147488A>G			169855734	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170147488	A	G	170147488	2	3	37	1	0	0	0	0	0	0	0	1	8985	233	9	4		4	LRP2	2	170147488	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	121191	170147488	73051885	30	3113										
ZAK	51776	hgsc.bcm.edu	37	chr2	174034552	174034552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggcagaaatactcagtgtccTcagtcacagaaacatcatcc	7	12	4	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:174034552T>C	ENST00000375213.3	+	3	257	c.179T>C	c.(178-180)cTc>cCc	p.L60P	MLTK_ENST00000338983.3_Missense_Mutation_p.L60P|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000431503.2_5'UTR|MLTK_ENST00000539448.1_Missense_Mutation_p.L60P|MLTK_ENST00000409176.2_Missense_Mutation_p.L60P|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000419609.1_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		60	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CTCAGTGTCCTCAGTCACAGA	0.333																																																0			2											139	134	136					2																	174034552		2203	4300	6503	173742798	SO:0001583	missense	51776																														ENST00000375213.3:c.179T>C	2.37:g.174034552T>C	ENSP00000364361:p.Leu60Pro		173742798	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814709	0.70912	.	.	ENSG00000091436	ENST00000539448;ENST00000409176;ENST00000338983;ENST00000375213;ENST00000422149	D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98	5.67	5.67	0.87782	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96962	0.9008	M	0.92459	3.31	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.999;0.991	D	0.97896	1.0300	10	0.87932	D	0	.	15.5783	0.76410	0.0:0.0:0.0:1.0	.	60;60;60;60	Q9NYL2-2;Q9NYL2;D4Q8H0;Q9NYL2-3	.;MLTK_HUMAN;.;.	P	60	ENSP00000439414:L60P;ENSP00000387259:L60P;ENSP00000340257:L60P;ENSP00000364361:L60P;ENSP00000411923:L60P	ENSP00000340257:L60P	L	+	2	0	AC013461.1	173742798	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.334000	0.79224	2.152000	0.67230	0.455000	0.32223	CTC		0.333	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			C	174034552	T	C	174034552	3	2	37	1	0	0	0	0	1	0	0	0	17552	1551	54	4	185	4	ZAK	2	174034552	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	3887064	174034552	69164821	31	3114										
TTN	7273	hgsc.bcm.edu	37	chr2	179585116	179585116	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtccatgtatacaaacctttGaacttgacagagcaagaaca	7	9	0	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:179585116G>C	ENST00000591111.1	-	78	22646	c.22422C>G	c.(22420-22422)ttC>ttG	p.F7474L	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.F7791L|TTN_ENST00000342992.6_Missense_Mutation_p.F6547L|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	13029					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACAAACCTTTGAACTTGACAG	0.413																																																0			2											139	131	133					2																	179585116		1900	4121	6021	179293361	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22422C>G	2.37:g.179585116G>C	ENSP00000465570:p.Phe7474Leu		179293361	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	12.58	1.979761	0.34942	.	.	ENSG00000155657	ENST00000342992	T	0.39406	1.08	5.91	5.03	0.67393	Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.20577	0.0495	N	0.02539	-0.55	0.80722	D	1	B	0.12013	0.005	B	0.12837	0.008	T	0.06338	-1.0832	9	0.87932	D	0	.	11.0129	0.47673	0.1414:0.0:0.8586:0.0	.	7474	Q8WZ42	TITIN_HUMAN	L	6547	ENSP00000343764:F6547L	ENSP00000343764:F6547L	F	-	3	2	TTN	179293361	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.055000	0.49916	1.498000	0.48600	0.650000	0.86243	TTC		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179585116	G	C	179585116	3	2	37	1	0	0	0	0	1	0	0	0	16775	1281	45	5	81288	5	TTN	2	179585116	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	5550564	179585116	63614257	32	3115										
HECW2	57520	hgsc.bcm.edu	37	chr2	197298107	197298107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	accgcatctggggatttcgaCgcctcacaaaaagcaggtgc	11	12	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:197298107C>T	ENST00000260983.3	-	2	223	c.41G>A	c.(40-42)cGt>cAt	p.R14H		NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	14					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GGGATTTCGACGCCTCACAAA	0.557																																																0			2											70	63	65					2																	197298107		2203	4300	6503	197006352	SO:0001583	missense	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.41G>A	2.37:g.197298107C>T	ENSP00000260983:p.Arg14His		197006352	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066800	0.93898	.	.	ENSG00000138411	ENST00000260983;ENST00000452031;ENST00000427457	T	0.58797	0.31	5.27	5.27	0.74061	.	0.067263	0.64402	D	0.000013	T	0.75391	0.3843	M	0.69823	2.125	0.54753	D	0.999988	D	0.89917	1.0	D	0.78314	0.991	T	0.72629	-0.4235	10	0.35671	T	0.21	.	19.0714	0.93138	0.0:1.0:0.0:0.0	.	14	Q9P2P5	HECW2_HUMAN	H	14	ENSP00000260983:R14H	ENSP00000260983:R14H	R	-	2	0	HECW2	197006352	1.000000	0.71417	0.997000	0.53966	0.931000	0.56810	7.127000	0.77210	2.736000	0.93811	0.561000	0.74099	CGT		0.557	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197298107	C	T	197298107	3	4	37	1	0	0	0	0	1	0	0	0	7064	536	19	1	4789	1	HECW2	2	197298107	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	17712991	197298107	45901266	33	3116										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215807721	215807721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	taatggccaacctggtacagAgagcttcacattcttccatg	8	11	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr2:215807721A>G	ENST00000272895.7	-	50	7583	c.7364T>C	c.(7363-7365)cTc>cCc	p.L2455P	ABCA12_ENST00000389661.4_Missense_Mutation_p.L2137P|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2455	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		CCTGGTACAGAGAGCTTCACA	0.383																																					Ovarian(66;664 1488 5121 34295)											0			2											123	105	111					2																	215807721		2203	4300	6503	215515966	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7364T>C	2.37:g.215807721A>G	ENSP00000272895:p.Leu2455Pro		215515966	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528545	0.85706	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.98028	-4.67;-4.67	5.65	5.65	0.86999	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.56097	D	0.000033	D	0.99230	0.9732	H	0.97564	4.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98908	1.0779	10	0.87932	D	0	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	2455;2137	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	2455;2137	ENSP00000272895:L2455P;ENSP00000374312:L2137P	ENSP00000272895:L2455P	L	-	2	0	ABCA12	215515966	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.971000	0.93419	2.276000	0.75962	0.528000	0.53228	CTC		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215807721	A	G	215807721	3	3	37	1	0	0	0	0	1	0	0	0	30	304	11	4	439	4	ABCA12	2	215807721	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	18509614	215807721	27391652	34	3117										
NGLY1	55768	hgsc.bcm.edu	37	chr3	25761660	25761660	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaatataagcaaaagatgatCcttcctttcgggccaaatat	6	8	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:25761660C>A	ENST00000280700.5	-	11	1794	c.1634G>T	c.(1633-1635)gGa>gTa	p.G545V	NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000417874.2_Missense_Mutation_p.G503V|NGLY1_ENST00000467224.1_5'UTR|NGLY1_ENST00000428257.1_Missense_Mutation_p.G527V|NGLY1_ENST00000396649.3_Intron	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	545	PAW. {ECO:0000255|PROSITE- ProRule:PRU00731}.				glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						AAAAGATGATCCTTCCTTTCG	0.358																																																0			3											70	68	68					3																	25761660		2203	4300	6503	25736664	SO:0001583	missense	55768			AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1634G>T	3.37:g.25761660C>A	ENSP00000280700:p.Gly545Val		25736664	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Missense_Mutation	SNP	ENST00000280700.5	37	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615578	0.87359	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000308710;ENST00000417874	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.79	5.79	0.91817	Peptide N glycanase, PAW domain (3);Galactose-binding domain-like (1);	0.044965	0.85682	D	0.000000	T	0.66499	0.2795	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.69661	-0.5085	10	0.87932	D	0	-25.1316	20.0402	0.97587	0.0:1.0:0.0:0.0	.	503;527;545	B4DJE9;Q96IV0-2;Q96IV0	.;.;NGLY1_HUMAN	V	527;545;524;503	ENSP00000387430:G527V;ENSP00000280700:G545V;ENSP00000307980:G524V;ENSP00000389888:G503V	ENSP00000280700:G545V	G	-	2	0	NGLY1	25736664	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.696000	0.61774	2.750000	0.94351	0.563000	0.77884	GGA		0.358	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			A	25761660	C	A	25761660	3	1	37	1	0	0	0	0	1	0	0	0	10429	855	30	2	338	2	NGLY1	3	25761660	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10		25761660	172260770	35	3118										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36871126	36871126	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgactgacaggatcagaatgTtgaccagccgagtcatcgcc	11	11	2	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:36871126T>C	ENST00000429976.2	-	22	8853	c.8606A>G	c.(8605-8607)aAc>aGc	p.N2869S	TRANK1_ENST00000301807.6_Missense_Mutation_p.N2319S|TRANK1_ENST00000428977.2_Missense_Mutation_p.N2319S	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2869							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GATCAGAATGTTGACCAGCCG	0.483																																																0			3											92	94	93					3																	36871126		2075	4208	6283	36846130	SO:0001583	missense	0			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.8606A>G	3.37:g.36871126T>C	ENSP00000416168:p.Asn2869Ser		36846130	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	11.00	1.510046	0.27036	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.30448	1.53;1.95;1.53	5.17	0.0217	0.14130	.	0.807151	0.10197	U	0.703837	T	0.18130	0.0435	L	0.27053	0.805	0.09310	N	1	B	0.23937	0.094	B	0.19666	0.026	T	0.24728	-1.0152	10	0.51188	T	0.08	.	3.7329	0.08500	0.1537:0.2583:0.0:0.588	.	2869	O15050	TRNK1_HUMAN	S	2319;2869;2319	ENSP00000416826:N2319S;ENSP00000416168:N2869S;ENSP00000301807:N2319S	ENSP00000301807:N2319S	N	-	2	0	TRANK1	36846130	0.000000	0.05858	0.000000	0.03702	0.802000	0.45316	-0.264000	0.08658	0.057000	0.16193	0.459000	0.35465	AAC		0.483	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		C	36871126	T	C	36871126	3	2	37	1	0	0	0	0	1	0	0	0	16494	1725	60	4	179	4	TRANK1	3	36871126	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	11109466	36871126	161151304	36	3119										
GRM2	2912	hgsc.bcm.edu	37	chr3	51746730	51746730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgagctagaggctcgtgcccGcaacatctgtgtggccacct	12	13	1	2	rs147501226		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:51746730G>A	ENST00000395052.3	+	3	926	c.692G>A	c.(691-693)cGc>cAc	p.R231H	GRM2_ENST00000475478.1_Intron|GRM2_ENST00000442933.2_Missense_Mutation_p.R231H	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	231					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GCTCGTGCCCGCAACATCTGT	0.622													G|||	1	0.000199681	0	0	5008	,	,		15266	0		0	False		,,,				2504	0.001															0			3											57	54	55					3																	51746730		2203	4300	6503	51721770	SO:0001583	missense	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.692G>A	3.37:g.51746730G>A	ENSP00000378492:p.Arg231His		51721770	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187530	0.38609	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.84800	-1.9;-1.9	5.25	3.42	0.39159	Extracellular ligand-binding receptor (1);	0.094462	0.40064	N	0.001188	T	0.80204	0.4580	L	0.59436	1.845	0.80722	D	1	B	0.26602	0.154	B	0.27170	0.077	T	0.73833	-0.3858	10	0.21540	T	0.41	.	10.0298	0.42094	0.0718:0.0:0.7893:0.1388	.	231	Q14416	GRM2_HUMAN	H	231	ENSP00000378492:R231H;ENSP00000408906:R231H	ENSP00000296479:R231H	R	+	2	0	GRM2	51721770	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	8.022000	0.88759	1.356000	0.45884	-0.175000	0.13238	CGC		0.622	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			A	51746730	G	A	51746730	3	1	37	1	0	0	0	0	1	0	0	0	6818	1087	38	1	698	1	GRM2	3	51746730	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	14875604	51746730	146275700	37	3120										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108330154	108330154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	taagaagttcttacaagaagAtttttccttccaaactatgc	5	8	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:108330154A>G	ENST00000361582.3	+	4	466	c.236A>G	c.(235-237)gAt>gGt	p.D79G	DZIP3_ENST00000463306.1_Missense_Mutation_p.D79G	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	79					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						TTACAAGAAGATTTTTCCTTC	0.328																																																0			3											71	74	73					3																	108330154		2203	4300	6503	109812844	SO:0001583	missense	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.236A>G	3.37:g.108330154A>G	ENSP00000355028:p.Asp79Gly		109812844	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	37	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516279	0.44763	.	.	ENSG00000198919	ENST00000393969;ENST00000361582;ENST00000479138;ENST00000463306	T;T	0.19250	2.16;2.16	5.02	3.86	0.44501	.	0.336984	0.25851	N	0.027897	T	0.14141	0.0342	L	0.27053	0.805	0.31401	N	0.676648	B	0.16603	0.018	B	0.14023	0.01	T	0.05084	-1.0907	10	0.72032	D	0.01	-10.4218	8.1869	0.31343	0.7788:0.2212:0.0:0.0	.	79	Q86Y13	DZIP3_HUMAN	G	79	ENSP00000355028:D79G;ENSP00000419981:D79G	ENSP00000355028:D79G	D	+	2	0	DZIP3	109812844	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.532000	0.36029	2.101000	0.63845	0.528000	0.53228	GAT		0.328	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		G	108330154	A	G	108330154	3	3	37	1	0	0	0	0	1	0	0	0	4876	333	12	4	246	4	DZIP3	3	108330154	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	56583424	108330154	89692276	38	3121										
GATA2	2624	hgsc.bcm.edu	37	chr3	128205664	128205664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	accgtgcgcggggctgtaggAgacgcgcgcccgcgcgtgag	19	13	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:128205664A>G	ENST00000341105.2	-	2	542	c.211T>C	c.(211-213)Tcc>Ccc	p.S71P	GATA2_ENST00000430265.2_Missense_Mutation_p.S71P|RP11-475N22.4_ENST00000464242.1_RNA|GATA2_ENST00000487848.1_Missense_Mutation_p.S71P|RP11-475N22.4_ENST00000473958.1_RNA|RP11-475N22.4_ENST00000468377.1_RNA	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	71					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		GGGCTGTAGGAGACGCGCGCC	0.692			Mis		AML(CML blast transformation)																																		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	0			3											30	30	30					3																	128205664		2201	4298	6499	129688354	SO:0001583	missense	2624			AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"GATA zinc finger domain containing"	4171	protein-coding gene	gene with protein product		137295	"GATA-binding protein 2"			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.211T>C	3.37:g.128205664A>G	ENSP00000345681:p.Ser71Pro		129688354	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.528384	0.44969	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848;ENST00000492608	D;D;D	0.97232	-4.3;-4.3;-4.3	4.74	4.74	0.60224	.	0.094180	0.46758	D	0.000270	D	0.96340	0.8806	M	0.70275	2.135	0.48830	D	0.999715	P;B	0.46220	0.874;0.0	P;B	0.44990	0.466;0.003	D	0.95498	0.8575	10	0.35671	T	0.21	-15.1408	14.2339	0.65911	1.0:0.0:0.0:0.0	.	71;71	P23769-2;P23769	.;GATA2_HUMAN	P	71	ENSP00000345681:S71P;ENSP00000400259:S71P;ENSP00000417074:S71P	ENSP00000345681:S71P	S	-	1	0	GATA2	129688354	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	2.849000	0.48286	1.756000	0.51951	0.260000	0.18958	TCC		0.692	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638		G	128205664	A	G	128205664	3	3	37	1	0	0	0	0	1	0	0	0	6274	304	11	4	1251	4	GATA2	3	128205664	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	19875510	128205664	69816766	39	3122										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130300560	130300560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gctgtgaggtgggcacagagActcaggtcagtgtggctttt	16	7	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:130300560A>G	ENST00000358511.6	+	8	3734	c.3703A>G	c.(3703-3705)Act>Gct	p.T1235A	COL6A6_ENST00000453409.2_Missense_Mutation_p.T1235A	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1235	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGGCACAGAGACTCAGGTCAG	0.448																																																0			3											98	96	97					3																	130300560		2018	4175	6193	131783250	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3703A>G	3.37:g.130300560A>G	ENSP00000351310:p.Thr1235Ala		131783250	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.666675	0.47677	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.38887	1.11;1.11	6.06	6.06	0.98353	von Willebrand factor, type A (2);	.	.	.	.	T	0.32556	0.0833	N	0.24115	0.695	0.28237	N	0.925854	P	0.52463	0.953	P	0.47603	0.551	T	0.07233	-1.0783	9	0.08179	T	0.78	.	11.5702	0.50829	0.8509:0.1491:0.0:0.0	.	1235	A6NMZ7	CO6A6_HUMAN	A	1235	ENSP00000351310:T1235A;ENSP00000399236:T1235A	ENSP00000351310:T1235A	T	+	1	0	COL6A6	131783250	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.558000	0.45879	2.324000	0.78689	0.533000	0.62120	ACT		0.448	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130300560	A	G	130300560	3	3	37	1	0	0	0	0	1	0	0	0	3709	275	10	4	3733	4	COL6A6	3	130300560	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	2094896	130300560	67721870	40	3123										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128637	147128637	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aagtcgtgcaacaaaactttCagcaccatgcacgagctagt	8	11	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:147128637C>G	ENST00000282928.4	+	1	1467	c.738C>G	c.(736-738)ttC>ttG	p.F246L		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	246					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						ACAAAACTTTCAGCACCATGC	0.572																																																0			3											93	86	89					3																	147128637		2203	4300	6503	148611327	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.738C>G	3.37:g.147128637C>G	ENSP00000282928:p.Phe246Leu		148611327	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905112	0.52333	.	.	ENSG00000152977	ENST00000282928	T	0.49432	0.78	3.86	2.96	0.34315	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.89840	3.065	0.58432	D	0.999999	P	0.41710	0.76	P	0.60286	0.872	T	0.76410	-0.2969	10	0.87932	D	0	.	14.6385	0.68706	0.0:0.918:0.0:0.082	.	246	Q15915	ZIC1_HUMAN	L	246	ENSP00000282928:F246L	ENSP00000282928:F246L	F	+	3	2	ZIC1	148611327	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.334000	0.33827	0.237000	0.21200	-1.134000	0.01955	TTC		0.572	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		G	147128637	C	G	147128637	3	3	37	1	0	0	0	0	1	0	0	0	17717	825	29	5	740	5	ZIC1	3	147128637	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	16828077	147128637	50893793	41	3124										
DHX36	170506	hgsc.bcm.edu	37	chr3	154032850	154032850	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	actacctgcatttcaatataCcgaaggtcattttttttctt	4	9	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:154032850C>T	ENST00000496811.1	-	3	668	c.588G>A	c.(586-588)cgG>cgA	p.R196R	DHX36_ENST00000329463.5_Silent_p.R196R|DHX36_ENST00000544526.1_Silent_p.R196R|DHX36_ENST00000308361.6_Silent_p.R196R	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	196					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCAATATACCGAAGGTCAT	0.308																																																0			3											31	34	33					3																	154032850		2192	4286	6478	155515544	SO:0001819	synonymous_variant	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.588G>A	3.37:g.154032850C>T			155515544	B2RB00|Q70JU3|Q8IYE5|Q9P240	Silent	SNP	ENST00000496811.1	37	CCDS3171.1																																																																																				0.308	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		T	154032850	C	T	154032850	2	4	37	1	0	0	0	0	0	0	0	1	4520	494	18	3		3	DHX36	3	154032850	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	6904213	154032850	43989580	42	3125										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951995	178951995	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gccagaactacaatcttttgAtgacattgcatacattcgaa	6	9	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:178951995A>G	ENST00000263967.3	+	21	3207	c.3050A>G	c.(3049-3051)gAt>gGt	p.D1017G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1017	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D1017V(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAATCTTTTGATGACATTGCA	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	lung(1)	3											107	95	98					3																	178951995		1879	4117	5996	180434689	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3050A>G	3.37:g.178951995A>G	ENSP00000263967:p.Asp1017Gly		180434689	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.897876	0.72639	.	.	ENSG00000121879	ENST00000263967	T	0.80824	-1.42	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.82098	0.4963	L	0.35288	1.05	0.80722	D	1	D	0.65815	0.995	P	0.56700	0.804	T	0.82131	-0.0609	10	0.42905	T	0.14	-22.9512	16.635	0.85050	1.0:0.0:0.0:0.0	.	1017	P42336	PK3CA_HUMAN	G	1017	ENSP00000263967:D1017G	ENSP00000263967:D1017G	D	+	2	0	PIK3CA	180434689	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.798000	0.91888	2.330000	0.79161	0.477000	0.44152	GAT		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951995	A	G	178951995	3	3	37	1	0	0	0	0	1	0	0	0	11944	333	12	4	3128	4	PIK3CA	3	178951995	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	24919145	178951995	19070435	43	3126										
FBXO45	200933	hgsc.bcm.edu	37	chr3	196311032	196311032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aagaattcgagtcatcttggAcatggaagataagactttag	10	5	2	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr3:196311032A>G	ENST00000311630.6	+	3	1001	c.704A>G	c.(703-705)gAc>gGc	p.D235G	FBXO45_ENST00000440469.1_Missense_Mutation_p.D56G	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GTCATCTTGGACATGGAAGAT	0.408																																																0			3											135	129	131					3																	196311032		1838	4087	5925	197795429	SO:0001583	missense	200933			AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.704A>G	3.37:g.196311032A>G	ENSP00000310332:p.Asp235Gly		197795429	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918358	0.73098	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	D;D	0.82526	-1.62;-1.62	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95098	0.8228	10	0.87932	D	0	-16.4144	15.0971	0.72244	1.0:0.0:0.0:0.0	.	235	P0C2W1	FBSP1_HUMAN	G	56;235	ENSP00000389868:D56G;ENSP00000310332:D235G	ENSP00000310332:D235G	D	+	2	0	FBXO45	197795429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.500000	0.90498	2.212000	0.71576	0.460000	0.39030	GAC		0.408	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			G	196311032	A	G	196311032	3	3	37	1	0	0	0	0	1	0	0	0	5773	275	10	4	714	4	FBXO45	3	196311032	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	17359037	196311032	1711398	44	3127										
POLN	353497	hgsc.bcm.edu	37	chr4	2209942	2209942	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cttgttttctctgacaaattAttatatgtaatatgttttct	4	5	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:2209942A>G	ENST00000511885.2	-	5	839	c.486T>C	c.(484-486)aaT>aaC	p.N162N	POLN_ENST00000515357.1_5'UTR|POLN_ENST00000382865.1_Silent_p.N162N			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	162					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			CTGACAAATTATTATATGTAA	0.313								DNA polymerases (catalytic subunits)																																								0			4											66	66	66					4																	2209942		2203	4300	6503	2179740	SO:0001819	synonymous_variant	353497			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"DNA polymerases"	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.486T>C	4.37:g.2209942A>G			2179740	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1																																																																																				0.313	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		G	2209942	A	G	2209942	2	3	37	1	0	0	0	0	0	0	0	1	12238	446	16	4		4	POLN	4	2209942	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10		2209942	188944334	45	3128										
GUF1	60558	hgsc.bcm.edu	37	chr4	44685325	44685325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtttgatattccaagtgatgAatgtattaaggtaaaatacg	9	3	0	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:44685325A>G	ENST00000281543.5	+	6	853	c.659A>G	c.(658-660)gAa>gGa	p.E220G	GUF1_ENST00000506793.1_3'UTR	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CCAAGTGATGAATGTATTAAG	0.299																																																0			4											60	65	63					4																	44685325		2202	4294	6496	44380082	SO:0001583	missense	60558				CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.659A>G	4.37:g.44685325A>G	ENSP00000281543:p.Glu220Gly		44380082		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.355053	0.82243	.	.	ENSG00000151806	ENST00000281543	T	0.76186	-1.0	5.18	5.18	0.71444	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.155195	0.56097	D	0.000026	T	0.80717	0.4676	M	0.66506	2.035	0.80722	D	1	D	0.52996	0.957	P	0.54431	0.752	T	0.82236	-0.0557	10	0.52906	T	0.07	-22.1232	14.222	0.65833	1.0:0.0:0.0:0.0	.	220	Q8N442	GUF1_HUMAN	G	220	ENSP00000281543:E220G	ENSP00000281543:E220G	E	+	2	0	GUF1	44380082	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.782000	0.91809	1.952000	0.56665	0.455000	0.32223	GAA		0.299	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		G	44685325	A	G	44685325	3	3	37	1	0	0	0	0	1	0	0	0	6920	246	9	4	681	4	GUF1	4	44685325	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	42475383	44685325	146468951	46	3129										
KIT	3815	hgsc.bcm.edu	37	chr4	55593649	55593649	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaacaattatgtttacatagAcccaacacaacttccttatg	3	10	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:55593649A>G	ENST00000288135.5	+	11	1812	c.1715A>G	c.(1714-1716)gAc>gGc	p.D572G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	572					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y570_L576del(9)|p.V560_L576del(4)|p.Y553_T574>S(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.W557_P573>S(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I571_L576del(2)|p.Y568_T574del(2)|p.Y568_L576>CV(1)|p.I563_D572del(1)|p.N564_T574del(1)|p.K558_Q575del(1)|p.V569_D572del(1)|p.V569_L576del(1)|p.M552_T574>TESA(1)|p.571_572>GE(1)|p.Q556_T574del(1)|p.Q556_D572>PS(1)|p.E561_P577del(1)|p.I571_N587del(1)|p.Q556_D572del(1)|p.N564_P573>T(1)|p.V569_L576>G(1)|p.K558_L576>NV(1)|p.V559_P573>A(1)|p.V569_Q575del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.K558_D572del(1)|p.Q556_D572>H(1)|p.N567_L576>E(1)|p.M552_D572del(1)|p.E562_P573del(1)|p.D572A(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.N567_P573del(1)|p.Y570_L576delYIDPTQL(1)|p.N564_P573>TS(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTTTACATAGACCCAACACAA	0.408		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	66	Deletion - In frame(49)|Complex - deletion inframe(15)|Substitution - Missense(1)|Complex - insertion inframe(1)	soft_tissue(60)|skin(3)|haematopoietic_and_lymphoid_tissue(2)|testis(1)	4											77	77	77					4																	55593649		2203	4300	6503	55288406	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1715A>G	4.37:g.55593649A>G	ENSP00000288135:p.Asp572Gly		55288406	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.629174	0.87560	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.97404	-4.37;-4.37	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000003	D	0.98579	0.9525	M	0.88105	2.93	0.80722	D	1	D;D;D	0.64830	0.976;0.994;0.99	P;D;D	0.68039	0.477;0.955;0.93	D	0.99544	1.0964	10	0.87932	D	0	.	16.6003	0.84812	1.0:0.0:0.0:0.0	.	79;568;572	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	G	572;568	ENSP00000288135:D572G;ENSP00000390987:D568G	ENSP00000288135:D572G	D	+	2	0	KIT	55288406	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	9.150000	0.94667	2.319000	0.78375	0.533000	0.62120	GAC		0.408	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55593649	A	G	55593649	3	3	37	1	0	0	0	0	1	0	0	0	8350	275	10	4	1757	4	KIT	4	55593649	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	10908324	55593649	135560627	47	3130										
AASDH	132949	hgsc.bcm.edu	37	chr4	57221472	57221472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcctctccagcttctgagaaCtgtcaatgatggaaacgctt	8	11	3	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:57221472C>T	ENST00000205214.6	-	6	1159	c.979G>A	c.(979-981)Gtt>Att	p.V327I	AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000602986.1_Missense_Mutation_p.V174I|AASDH_ENST00000502617.1_Missense_Mutation_p.V327I|AASDH_ENST00000513376.1_Missense_Mutation_p.V227I|AASDH_ENST00000510762.1_5'UTR|AASDH_ENST00000451613.1_Missense_Mutation_p.V327I	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	327					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CTTCTGAGAACTGTCAATGAT	0.403																																																0			4											130	120	123					4																	57221472		2203	4300	6503	56916229	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.979G>A	4.37:g.57221472C>T	ENSP00000205214:p.Val327Ile		56916229	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	5.624	0.299750	0.10622	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.68	2.99	0.34606	AMP-dependent synthetase/ligase (1);	0.470851	0.24158	N	0.041019	T	0.31979	0.0814	L	0.43554	1.36	0.09310	N	1	B;B;B;B	0.25719	0.132;0.11;0.11;0.016	B;B;B;B	0.25614	0.026;0.037;0.037;0.062	T	0.18777	-1.0326	10	0.39692	T	0.17	-2.6129	7.7383	0.28827	0.0:0.6636:0.1271:0.2094	.	174;327;327;327	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	I	327;227;327;174;327	ENSP00000205214:V327I;ENSP00000423760:V227I;ENSP00000409656:V327I;ENSP00000421171:V327I	ENSP00000205214:V327I	V	-	1	0	AASDH	56916229	0.107000	0.21998	0.134000	0.22075	0.074000	0.17049	0.757000	0.26433	0.736000	0.32559	0.650000	0.86243	GTT		0.403	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57221472	C	T	57221472	3	4	37	1	0	0	0	0	1	0	0	0	22	565	20	3	2357	3	AASDH	4	57221472	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1627823	57221472	133932804	48	3131										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170717	90170717	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	actcacaggacacctgatctTtgctgctactgaggacgcct	9	13	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:90170717T>C	ENST00000609438.1	-	2	1063	c.545A>G	c.(544-546)aAa>aGa	p.K182R	GPRIN3_ENST00000333209.4_Missense_Mutation_p.K182R	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	182										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CACCTGATCTTTGCTGCTACT	0.512																																																0			4											132	123	126					4																	90170717		2203	4300	6503	90389740	SO:0001583	missense	285513			AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.545A>G	4.37:g.90170717T>C	ENSP00000476603:p.Lys182Arg		90389740	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.593311	0.46214	.	.	ENSG00000185477	ENST00000333209	T	0.11169	2.8	5.05	5.05	0.67936	.	0.690951	0.11930	N	0.515804	T	0.11024	0.0269	L	0.27053	0.805	0.09310	N	1	P	0.36909	0.573	B	0.39217	0.294	T	0.24261	-1.0165	10	0.40728	T	0.16	-1.6179	13.8113	0.63266	0.0:0.0:0.0:1.0	.	182	Q6ZVF9	GRIN3_HUMAN	R	182	ENSP00000328672:K182R	ENSP00000328672:K182R	K	-	2	0	GPRIN3	90389740	0.001000	0.12720	0.200000	0.23457	0.142000	0.21351	0.988000	0.29616	2.242000	0.73789	0.528000	0.53228	AAA		0.512	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		C	90170717	T	C	90170717	3	2	37	1	0	0	0	0	1	0	0	0	6752	1841	64	4	1789	4	GPRIN3	4	90170717	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	32949245	90170717	100983559	49	3132										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113351613	113351613	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atttttcccagaatatccgtGgcacgtgtttattgtcctac	7	10	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:113351613G>T	ENST00000458497.1	+	11	1189	c.910G>T	c.(910-912)Ggc>Tgc	p.G304C	ALPK1_ENST00000504176.2_Missense_Mutation_p.G226C|ALPK1_ENST00000177648.9_Missense_Mutation_p.G304C	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	304							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GAATATCCGTGGCACGTGTTT	0.388																																																0			4											62	64	63					4																	113351613		2203	4300	6503	113571062	SO:0001583	missense	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.910G>T	4.37:g.113351613G>T	ENSP00000398048:p.Gly304Cys		113571062	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.774904	0.70107	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.56776	0.44;0.44;0.44	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.75384	0.3842	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.77381	-0.2609	10	0.87932	D	0	-22.5725	19.8968	0.96969	0.0:0.0:1.0:0.0	.	226;226;304	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	C	304;304;226	ENSP00000398048:G304C;ENSP00000177648:G304C;ENSP00000426044:G226C	ENSP00000177648:G304C	G	+	1	0	ALPK1	113571062	1.000000	0.71417	0.995000	0.50966	0.387000	0.30353	9.361000	0.97122	2.691000	0.91804	0.655000	0.94253	GGC		0.388	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		T	113351613	G	T	113351613	3	4	37	1	0	0	0	0	1	0	0	0	544	1348	47	2	944	2	ALPK1	4	113351613	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	23180896	113351613	77802663	50	3133										
METTL14	57721	hgsc.bcm.edu	37	chr4	119631268	119631268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgtacagaagaaattgagagActtcgaccaaaatcgcctcc	8	10	0	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:119631268A>C	ENST00000388822.5	+	11	1349	c.1182A>C	c.(1180-1182)agA>agC	p.R394S	METTL14_ENST00000506780.1_Missense_Mutation_p.R356S			Q9HCE5	MET14_HUMAN	methyltransferase like 14	394					mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						AAATTGAGAGACTTCGACCAA	0.478																																																0			4											84	85	85					4																	119631268		2203	4300	6503	119850716	SO:0001583	missense	57721			AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.1182A>C	4.37:g.119631268A>C	ENSP00000373474:p.Arg394Ser		119850716	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	37	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	A	9.804	1.181391	0.21787	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.62	1.88	0.25563	.	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	L	0.32530	0.975	0.58432	D	0.999995	B;B	0.28880	0.205;0.226	B;B	0.19148	0.013;0.024	T	0.08848	-1.0702	9	0.08381	T	0.77	-0.6427	9.1099	0.36720	0.6824:0.0:0.3176:0.0	.	356;394	D6RBL4;Q9HCE5	.;MTL14_HUMAN	S	394;356	.	ENSP00000373474:R394S	R	+	3	2	METTL14	119850716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.519000	0.35888	0.387000	0.25024	0.528000	0.53228	AGA		0.478	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		C	119631268	A	C	119631268	3	2	37	1	0	0	0	0	1	0	0	0	9528	272	10	4	1224	4	METTL14	4	119631268	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	6279655	119631268	71523008	51	3134										
DCLK2	166614	hgsc.bcm.edu	37	chr4	151160899	151160899	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgatttctgtttcaggtgtgTgaatatcctgatggaaccaa	10	6	2	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:151160899T>C	ENST00000296550.7	+	11	2326	c.1572T>C	c.(1570-1572)tgT>tgC	p.C524C	DCLK2_ENST00000506325.1_Silent_p.C523C|DCLK2_ENST00000302176.8_Silent_p.C541C	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	524	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.C524W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TTCAGGTGTGTGAATATCCTG	0.428																																					GBM(195;186 2215 13375 16801 37459)											1	Substitution - Missense(1)	ovary(1)	4											129	131	130					4																	151160899		2203	4300	6503	151380349	SO:0001819	synonymous_variant	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"doublecortin and CaM kinase-like 2"	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1572T>C	4.37:g.151160899T>C			151380349	C9J5Q9|Q59GC8|Q8N399	Silent	SNP	ENST00000296550.7	37	CCDS34076.1																																																																																				0.428	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260		C	151160899	T	C	151160899	2	2	37	1	0	0	0	0	0	0	0	1	4298	1702	59	4		4	DCLK2	4	151160899	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	31529631	151160899	39993377	52	3135										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245398	153245398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttttaactgtagaatctgcaTtcccagagacaagaatattg	7	7	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:153245398T>C	ENST00000281708.4	-	11	3022	c.1793A>G	c.(1792-1794)aAt>aGt	p.N598S	FBXW7_ENST00000296555.5_Missense_Mutation_p.N480S|FBXW7_ENST00000603548.1_Missense_Mutation_p.N598S|FBXW7_ENST00000603841.1_Missense_Mutation_p.N598S|FBXW7_ENST00000393956.3_Missense_Mutation_p.N422S|FBXW7_ENST00000263981.5_Missense_Mutation_p.N518S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	598					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGAATCTGCATTCCCAGAGAC	0.388			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											130	119	123					4																	153245398		2203	4300	6503	153464848	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1793A>G	4.37:g.153245398T>C	ENSP00000281708:p.Asn598Ser		153464848	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033104	0.75504	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.21022	0.0506	N	0.00069	-2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.997;0.997	T	0.67722	-0.5597	10	0.35671	T	0.21	-27.2537	15.5099	0.75772	0.0:0.0:0.0:1.0	.	422;598;480;518	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	S	598;480;518;422	ENSP00000281708:N598S;ENSP00000296555:N480S;ENSP00000263981:N518S;ENSP00000377528:N422S	ENSP00000263981:N518S	N	-	2	0	FBXW7	153464848	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.060000	0.61445	0.533000	0.62120	AAT		0.388	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153245398	T	C	153245398	3	2	37	1	0	0	0	0	1	0	0	0	5788	1493	52	4	338	4	FBXW7	4	153245398	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	2084499	153245398	37908878	53	3136										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249460	153249460	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccacactttgagtgtccgatCtgtagatccactaatgatga	8	10	1	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:153249460C>A	ENST00000281708.4	-	9	2547	c.1318G>T	c.(1318-1320)Gat>Tat	p.D440Y	FBXW7_ENST00000296555.5_Missense_Mutation_p.D322Y|FBXW7_ENST00000603548.1_Missense_Mutation_p.D440Y|FBXW7_ENST00000603841.1_Missense_Mutation_p.D440Y|FBXW7_ENST00000393956.3_Missense_Mutation_p.D264Y|FBXW7_ENST00000263981.5_Missense_Mutation_p.D360Y	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	440					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)|p.D440N(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGTGTCCGATCTGTAGATCCA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	2	Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	4											310	262	278					4																	153249460		2203	4300	6503	153468910	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1318G>T	4.37:g.153249460C>A	ENSP00000281708:p.Asp440Tyr		153468910	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574255	0.86542	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.97682	0.9240	H	0.99783	4.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.98877	1.0768	10	0.87932	D	0	-22.1701	20.2787	0.98501	0.0:1.0:0.0:0.0	.	264;440;322;360	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	Y	440;322;360;264	ENSP00000281708:D440Y;ENSP00000296555:D322Y;ENSP00000263981:D360Y;ENSP00000377528:D264Y	ENSP00000263981:D360Y	D	-	1	0	FBXW7	153468910	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	GAT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249460	C	A	153249460	3	1	37	1	0	0	0	0	1	0	0	0	5788	913	32	2	821	2	FBXW7	4	153249460	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	4062	153249460	37904816	54	3137										
FBXO8	26269	hgsc.bcm.edu	37	chr4	175158655	175158655	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agcagcgcgacgggtatttcGaataaattccctttttgaca	9	9	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:175158655G>A	ENST00000393674.2	-	6	1730	c.868C>T	c.(868-870)Cga>Tga	p.R290*	FBXO8_ENST00000503293.1_Nonsense_Mutation_p.R249*	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	290					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		CGGGTATTTCGAATAAATTCC	0.388																																																0			4											90	91	91					4																	175158655		2203	4300	6503	175395230	SO:0001587	stop_gained	26269			AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"F-boxes /  "other""	13587	protein-coding gene	gene with protein product		605649	"F-box only protein 8"			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.868C>T	4.37:g.175158655G>A	ENSP00000377280:p.Arg290*		175395230	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Nonsense_Mutation	SNP	ENST00000393674.2	37	CCDS3820.1	.	.	.	.	.	.	.	.	.	.	G	43	10.161063	0.99350	.	.	ENSG00000164117	ENST00000393674;ENST00000503293;ENST00000296517	.	.	.	5.72	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7393	0.62838	0.0:0.0:0.7197:0.2803	.	.	.	.	X	290;249;203	.	ENSP00000296517:R203X	R	-	1	2	FBXO8	175395230	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.300000	0.59079	1.394000	0.46624	0.655000	0.94253	CGA		0.388	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180		A	175158655	G	A	175158655	4	1	37	1	0	0	0	0	0	1	0	0	5780	1066	37	1	95	1	FBXO8	4	175158655	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	21909195	175158655	15995621	55	3138										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175896768	175896768	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cccccaatatcacagccctcCggatgtggtgattcctgtga	9	14	1	2	rs544557652		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:175896768C>T	ENST00000359240.3	+	5	762	c.92C>T	c.(91-93)cCg>cTg	p.P31L	ADAM29_ENST00000514159.1_Missense_Mutation_p.P31L|ADAM29_ENST00000445694.1_Missense_Mutation_p.P31L|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000404450.4_Missense_Mutation_p.P31L	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	31			P -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P31L(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CACAGCCCTCCGGATGTGGTG	0.517																																					Ovarian(140;1727 1835 21805 25838 41440)											2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	4											82	81	81					4																	175896768		2203	4300	6503	176133343	SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.92C>T	4.37:g.175896768C>T	ENSP00000352177:p.Pro31Leu		176133343	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	7.389	0.630296	0.14257	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000502940;ENST00000502305;ENST00000404450;ENST00000514159	T;T;T;D;T;T	0.81579	4.66;4.66;0.9;-1.51;4.66;4.66	4.36	1.46	0.22682	.	.	.	.	.	D	0.85124	0.5625	M	0.71206	2.165	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.71580	-0.4550	8	.	.	.	.	2.5819	0.04820	0.1935:0.5128:0.1878:0.1059	.	31	Q9UKF5	ADA29_HUMAN	L	31	ENSP00000352177:P31L;ENSP00000414544:P31L;ENSP00000427674:P31L;ENSP00000422537:P31L;ENSP00000384229:P31L;ENSP00000423517:P31L	.	P	+	2	0	ADAM29	176133343	0.003000	0.15002	0.098000	0.21074	0.004000	0.04260	0.096000	0.15147	0.156000	0.19299	0.637000	0.83480	CCG		0.517	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				T	175896768	C	T	175896768	3	4	37	1	0	0	0	0	1	0	0	0	247	652	23	1	94	1	ADAM29	4	175896768	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	738113	175896768	15257508	56	3139										
FAT1	2195	hgsc.bcm.edu	37	chr4	187540871	187540871	+	Frame_Shift_Del	DEL	A	A	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cagatgcctcagacagggtcAccgcataagactgctgagca							TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr4:187540871delA	ENST00000441802.2	-	10	7078	c.6869delT	c.(6868-6870)gtgfs	p.V2290fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2290	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGACAGGGTCACCGCATAAGA	0.453										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											94	97	96					4																	187540871		1991	4160	6151	187777865	SO:0001589	frameshift_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6869delT	4.37:g.187540871delA	ENSP00000406229:p.Val2290fs		187777865		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																				0.453	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187540871	A	-	187540871	7	5	37	1	0	1	0	1	0	0	0	0	5708	159	6	0	6969	0	FAT1	4	187540871	Frame_Shift_Del	DEL	A	TCGA-AG-3731-01A-11D-1733-10	11644103	187540871	3613405	57	3140										
RIOK2	55781	hgsc.bcm.edu	37	chr5	96507042	96507042	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	catgatttgcaagtttgacaAttagttccatagcttcatca	6	8	2	2	rs147608663		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:96507042A>G	ENST00000283109.3	-	6	715	c.647T>C	c.(646-648)aTt>aCt	p.I216T	RIOK2_ENST00000508447.1_Missense_Mutation_p.I216T|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	216			I -> T (in a renal clear cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I216T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		AAGTTTGACAATTAGTTCCAT	0.338																																																1	Substitution - Missense(1)	kidney(1)	5						A	THR/ILE,THR/ILE	3,4403	6.2+/-15.9	0,3,2200	106	98	101		647,647	5.1	1	5	dbSNP_134	101	0,8600		0,0,4300	no	missense,missense	RIOK2	NM_001159749.1,NM_018343.2	89,89	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging,probably-damaging	216/475,216/553	96507042	3,13003	2203	4300	6503	96532798	SO:0001583	missense	55781			AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"RIO kinase 2 (yeast)"				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.647T>C	5.37:g.96507042A>G	ENSP00000283109:p.Ile216Thr		96532798	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148761	0.78001	6.81E-4	0.0	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.08984	3.03;3.03	5.06	5.06	0.68205	Protein kinase-like domain (1);RIO-like kinase (1);	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.992	T	0.48127	-0.9062	10	0.87932	D	0	-0.2874	14.4605	0.67445	1.0:0.0:0.0:0.0	.	216;216	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	T	216	ENSP00000283109:I216T;ENSP00000420932:I216T	ENSP00000283109:I216T	I	-	2	0	RIOK2	96532798	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.586000	0.90806	1.900000	0.55004	0.482000	0.46254	ATT		0.338	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343		G	96507042	A	G	96507042	3	3	37	1	0	0	0	0	1	0	0	0	13415	101	4	4	1059	4	RIOK2	5	96507042	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10		96507042	84408218	58	3141										
APC	324	hgsc.bcm.edu	37	chr5	112128143	112128143	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggtttcttgttttattttagCgaagaatagccagaattcag	9	5	2	2	rs62619935		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:112128143C>T	ENST00000457016.1	+	7	1026	c.646C>T	c.(646-648)Cga>Tga	p.R216*	APC_ENST00000257430.4_Splice_Site_p.R216*|APC_ENST00000508376.2_Splice_Site_p.R216*			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R216*(12)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATTTTAGCGAAGAATAGC	0.323		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	12	Substitution - Nonsense(12)	large_intestine(12)	5	GRCh37	CM992133	APC	M	rs62619935						52	51	51					5																	112128143		2202	4300	6502	112156042	SO:0001630	splice_region_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.646-1C>T	5.37:g.112128143C>T			112156042	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.466758	0.98302	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	2.99	0.34606	.	0.630262	0.16042	N	0.232387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2274	1.7088	0.02888	0.2899:0.3634:0.2259:0.1208	rs62619935	.	.	.	X	216	.	.	R	+	1	2	APC	112156042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.662000	0.25038	1.304000	0.44892	-0.158000	0.13435	CGA		0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation	T	112128143	C	T	112128143	5	4	37	1	0	0	0	0	0	0	1	0	763	782	27	1	668	1	APC	5	112128143	Splice_Site	SNP	C	TCGA-AG-3731-01A-11D-1733-10	15621101	112128143	68787117	59	3142										
APC	324	hgsc.bcm.edu	37	chr5	112170692	112170692	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agtgccttatggaatttgtcAgcacattgcactgagaataa	9	7	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:112170692A>G	ENST00000457016.1	+	15	2168	c.1788A>G	c.(1786-1788)tcA>tcG	p.S596S	APC_ENST00000257430.4_Silent_p.S596S|APC_ENST00000508376.2_Silent_p.S596S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	596	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGAATTTGTCAGCACATTGCA	0.393		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											197	162	174					5																	112170692		2202	4300	6502	112198591	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1788A>G	5.37:g.112170692A>G			112198591	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.393	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112170692	A	G	112170692	2	3	37	1	0	0	0	0	0	0	0	1	763	175	7	4		4	APC	5	112170692	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	42549	112170692	68744568	60	3143										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131042147	131042147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caaacttgttgtttggctgcGtcgccaacgtcgctggtagc	12	11	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:131042147G>A	ENST00000510461.1	-	9	966	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	FNIP1_ENST00000307968.7_Missense_Mutation_p.R263C|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307954.8_Missense_Mutation_p.R246C|FNIP1_ENST00000511848.1_Missense_Mutation_p.R291C	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	291					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		GTTTGGCTGCGTCGCCAACGT	0.443																																																0			5											100	94	96					5																	131042147		2203	4300	6503	131070046	SO:0001583	missense	96459			DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.871C>T	5.37:g.131042147G>A	ENSP00000421985:p.Arg291Cys		131070046	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.924336	0.92319	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.41400	2.01;1.8;1.72;1.0	5.6	4.7	0.59300	.	.	.	.	.	T	0.67785	0.2930	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.998;0.999	T	0.74544	-0.3630	9	0.87932	D	0	-5.6888	15.9298	0.79651	0.0:0.0:0.8638:0.1361	.	291;291;263;291	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	C	263;246;51;291;291	ENSP00000309266:R263C;ENSP00000310453:R246C;ENSP00000421985:R291C;ENSP00000425619:R291C	ENSP00000310453:R246C	R	-	1	0	FNIP1	131070046	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.910000	0.87451	1.434000	0.47414	0.591000	0.81541	CGC		0.443	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		A	131042147	G	A	131042147	3	1	37	1	0	0	0	0	1	0	0	0	5994	1145	40	1	2669	1	FNIP1	5	131042147	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	18871455	131042147	49873113	61	3144										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167966	140167966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcggcgctggtggatgtcaaCgtgtacctgatcatcgccat	13	11	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:140167966C>T	ENST00000504120.2	+	1	2091	c.2091C>T	c.(2089-2091)aaC>aaT	p.N697N	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Silent_p.N697N	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	697					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGATGTCAACGTGTACCTGA	0.667																																																0			5											56	55	55					5																	140167966		2203	4299	6502	140148150	SO:0001819	synonymous_variant	56147			AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2091C>T	5.37:g.140167966C>T			140148150	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																				0.667	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		T	140167966	C	T	140167966	2	4	37	1	0	0	0	0	0	0	0	1	11550	535	19	1		1	PCDHA1	5	140167966	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	9125819	140167966	40747294	62	3145										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182445	140182445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acgtgacgctgcaggtgttcGtgctggacgagaacgacaac	14	10	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr5:140182445G>A	ENST00000522353.2	+	1	1663	c.1663G>A	c.(1663-1665)Gtg>Atg	p.V555M	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.V555M|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	555	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGTGTTCGTGCTGGACGA	0.692																																																0			5											93	93	93					5																	140182445		2203	4298	6501	140162629	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1663G>A	5.37:g.140182445G>A	ENSP00000429808:p.Val555Met		140162629	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	15.47	2.841798	0.51057	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.68181	-0.31;-0.31	4.5	4.5	0.54988	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.37623	U	0.002008	D	0.83202	0.5203	M	0.89904	3.07	0.27208	N	0.959983	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.77292	-0.2642	10	0.87932	D	0	.	11.1965	0.48715	0.0859:0.0:0.9141:0.0	.	555;555	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	M	555	ENSP00000429808:V555M;ENSP00000434086:V555M	ENSP00000429808:V555M	V	+	1	0	PCDHA3	140162629	0.980000	0.34600	1.000000	0.80357	0.696000	0.40369	2.784000	0.47774	2.237000	0.73441	0.306000	0.20318	GTG		0.692	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140182445	G	A	140182445	3	1	37	1	0	0	0	0	1	0	0	0	11556	1145	40	1	1665	1	PCDHA3	5	140182445	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	14479	140182445	40732815	63	3146										
HIST1H4A	8359	hgsc.bcm.edu	37	chr6	26022177	26022177	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccatggacgtggtctacgcgCttaagcgccagggacgcacc	13	14	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:26022177C>T	ENST00000359907.3	+	1	271	c.271C>T	c.(271-273)Ctt>Ttt	p.L91F		NM_003538.3	NP_003529.1	P62805	H4_HUMAN	histone cluster 1, H4a	91					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|skin(1)	2						GGTCTACGCGCTTAAGCGCCA	0.557																																																0			6											99	85	90					6																	26022177		2203	4300	6503	26130156	SO:0001583	missense	8359			X60481	CCDS4571.1	6p22.1	2011-01-27	2006-10-11	2003-03-07	ENSG00000196176	ENSG00000278637		"Histones / Replication-dependent"	4781	protein-coding gene	gene with protein product		602822	"H4 histone family, member A", "histone 1, H4a"	H4FA		9119399, 12408966	Standard	NM_003538		Approved		uc003nfq.3	P62805	OTTHUMG00000014419	ENST00000359907.3:c.271C>T	6.37:g.26022177C>T	ENSP00000352980:p.Leu91Phe		26130156	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000359907.3	37	CCDS4571.1	.	.	.	.	.	.	.	.	.	.	c	19.49	3.837513	0.71373	.	.	ENSG00000196176	ENST00000359907	T	0.70986	-0.53	3.97	3.97	0.46021	.	.	.	.	.	T	0.71500	0.3347	.	.	.	0.47778	D	0.99951	.	.	.	.	.	.	T	0.72001	-0.4422	5	.	.	.	.	15.9333	0.79683	0.0:1.0:0.0:0.0	.	.	.	.	F	91	ENSP00000352980:L91F	.	L	+	1	0	HIST1H4A	26130156	1.000000	0.71417	1.000000	0.80357	0.152000	0.21847	4.718000	0.61930	2.134000	0.65973	0.655000	0.94253	CTT		0.557	HIST1H4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040081.1	NM_003538		T	26022177	C	T	26022177	3	4	37	1	0	0	0	0	1	0	0	0	7186	797	28	3	273	3	HIST1H4A	6	26022177	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10		26022177	145092890	64	3147										
MAS1L	116511	hgsc.bcm.edu	37	chr6	29454673	29454673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cctctggcttatctgctaacGcccgttggagaatcactctg	9	13	4	1	rs566796111	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:29454673G>A	ENST00000377127.3	-	1	1065	c.1007C>T	c.(1006-1008)gCg>gTg	p.A336V		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	336					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A336V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						ATCTGCTAACGCCCGTTGGAG	0.493													G|||	2	0.000399361	0.0015	0	5008	,	,		17088	0		0	False		,,,				2504	0				NSCLC(153;755 1987 3859 11251 32945)											1	Substitution - Missense(1)	large_intestine(1)	6											137	138	138					6																	29454673		2203	4300	6503	29562652	SO:0001583	missense	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.1007C>T	6.37:g.29454673G>A	ENSP00000366331:p.Ala336Val		29562652	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	G	8.581	0.882339	0.17467	.	.	ENSG00000204687	ENST00000377127	T	0.36878	1.23	2.23	0.27	0.15635	.	.	.	.	.	T	0.10680	0.0261	L	0.45285	1.41	0.09310	N	1	B	0.27700	0.186	B	0.29942	0.109	T	0.33033	-0.9884	9	0.44086	T	0.13	.	2.6171	0.04907	0.2894:0.0:0.4883:0.2223	.	336	P35410	MAS1L_HUMAN	V	336	ENSP00000366331:A336V	ENSP00000366331:A336V	A	-	2	0	MAS1L	29562652	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.361000	0.07612	-0.075000	0.12798	-0.364000	0.07487	GCG		0.493	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		A	29454673	G	A	29454673	3	1	37	1	0	0	0	0	1	0	0	0	9351	1087	38	1	131	1	MAS1L	6	29454673	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	3432496	29454673	141660394	65	3148										
MICA	100507436	hgsc.bcm.edu	37	chr6	31379840	31379840	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgacctggcgtcaggatgggGtatctttgagccacgacacc	13	11	2	2	rs41540613	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:31379840G>T	ENST00000449934.2	+	4	784	c.730G>T	c.(730-732)Gta>Tta	p.V244L	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCAGGATGGGGTATCTTTGAG	0.592																																																0			6											18	18	18					6																	31379840		692	1591	2283	31487819	SO:0001583	missense	4276			L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"Immunoglobulin superfamily / C1-set domain containing"	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.730G>T	6.37:g.31379840G>T	ENSP00000413079:p.Val244Leu		31487819		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	g	8.834	0.940646	0.18281	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02944	4.1;4.1	2.52	-1.02	0.10135	.	2.098610	0.03122	U	0.163877	T	0.01061	0.0035	L	0.52364	1.645	0.09310	N	1	B;B	0.32382	0.368;0.036	B;B	0.35688	0.208;0.092	T	0.44967	-0.9293	10	0.34782	T	0.22	.	0.3146	0.00293	0.2776:0.2026:0.3136:0.2061	.	106;244	Q5SS58;Q96QC4	.;.	L	106;244;201;244;135	ENSP00000413079:V244L;ENSP00000402410:V135L	ENSP00000365394:V244L	V	+	1	0	MICA	31487819	0.070000	0.21116	0.000000	0.03702	0.013000	0.08279	0.375000	0.20518	-0.001000	0.14495	0.444000	0.29173	GTA		0.592	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519		T	31379840	G	T	31379840	3	4	37	1	0	0	0	0	1	0	0	0	9598	1261	44	2	744	2	MICA	6	31379840	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	1925167	31379840	139735227	66	3149										
C6orf25	80740	hgsc.bcm.edu	37	chr6	31691923	31691923	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cacgcctttcccccagggtcCgtgtatccccagctcctgat	8	18	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:31691923C>T	ENST00000375819.2	-	0	0				C6orf25_ENST00000480039.1_Silent_p.S138S|LY6G6C_ENST00000495859.1_5'Flank|DDAH2_ENST00000480913.1_5'Flank|C6orf25_ENST00000375810.4_Silent_p.S138S|C6orf25_ENST00000375809.3_Silent_p.S138S|C6orf25_ENST00000375805.2_Intron	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C							anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|large_intestine(1)|lung(1)|skin(1)	4						CCCCAGGGTCCGTGTATCCCC	0.667																																																0			6											39	28	32					6																	31691923		1509	2709	4218	31799902	SO:0001631	upstream_gene_variant	80739				CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"chromosome 6 open reading frame 24"	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251		6.37:g.31691923C>T	Exception_encountered		31799902	Q5SRS8|Q8IY94	Silent	SNP	ENST00000375819.2	37	CCDS4714.1																																																																																				0.667	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2			T	31691923	C	T	31691923	1	4	37	0	1	0	0	0	0	0	0	0	2366	639	23	1		1	C6orf25	6	31691923	5'Flank	SNP	C	TCGA-AG-3731-01A-11D-1733-10	312083	31691923	139423144	67	3150										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50682843	50682843	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttccagatacgtcacgacggAtcaaacagctaccgtttgat	8	11	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:50682843A>G	ENST00000008391.3	+	2	282	c.54A>G	c.(52-54)ggA>ggG	p.G18G		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GTCACGACGGATCAAACAGCT	0.527																																																0			6											118	96	103					6																	50682843		2203	4300	6503	50790802	SO:0001819	synonymous_variant	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.54A>G	6.37:g.50682843A>G			50790802		Silent	SNP	ENST00000008391.3	37	CCDS4933.1																																																																																				0.527	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		G	50682843	A	G	50682843	2	3	37	1	0	0	0	0	0	0	0	1	15829	320	12	4		4	TFAP2D	6	50682843	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	18990920	50682843	120432224	68	3151										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128297824	128297824	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgttagattgcatatcctaAaaatccggttgatcacatca	6	8	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:128297824A>T	ENST00000368215.3	-	27	3943	c.3944T>A	c.(3943-3945)tTt>tAt	p.F1315Y	PTPRK_ENST00000532331.1_Missense_Mutation_p.F1338Y|PTPRK_ENST00000368207.3_Missense_Mutation_p.F1348Y|PTPRK_ENST00000368210.3_Missense_Mutation_p.F1334Y|PTPRK_ENST00000368226.4_Missense_Mutation_p.F1316Y|PTPRK_ENST00000368227.3_Missense_Mutation_p.F1333Y|PTPRK_ENST00000368213.5_Missense_Mutation_p.F1322Y			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	1315	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GCATATCCTAAAAATCCGGTT	0.423																																																0			6											98	80	86					6																	128297824		2203	4300	6503	128339517	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.3944T>A	6.37:g.128297824A>T	ENSP00000357198:p.Phe1315Tyr		128339517	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	A	31	5.084202	0.94100	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207	T;T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36;2.36	5.56	5.56	0.83823	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	M	0.91972	3.26	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.991;0.989	D;D;D;D	0.91635	0.999;0.999;0.982;0.969	T	0.57659	-0.7773	10	0.87932	D	0	.	15.9985	0.80270	1.0:0.0:0.0:0.0	.	1338;1322;1315;1316	B7ZMG0;Q15262-3;Q15262;Q15262-2	.;.;PTPRK_HUMAN;.	Y	1316;1333;1338;1322;1334;1315;1348	ENSP00000357209:F1316Y;ENSP00000357210:F1333Y;ENSP00000432973:F1338Y;ENSP00000357196:F1322Y;ENSP00000357193:F1334Y;ENSP00000357198:F1315Y;ENSP00000357190:F1348Y	ENSP00000357190:F1348Y	F	-	2	0	PTPRK	128339517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.237000	0.73441	0.533000	0.62120	TTT		0.423	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			T	128297824	A	T	128297824	3	4	37	1	0	0	0	0	1	0	0	0	12842	14	1	5	391	5	PTPRK	6	128297824	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	77614981	128297824	42817243	69	3152										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152712587	152712587	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggagtttctctttggtcattCtaagtaggttctggtggctt	12	6	4	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:152712587C>G	ENST00000367255.5	-	52	8430	c.7829G>C	c.(7828-7830)aGa>aCa	p.R2610T	SYNE1_ENST00000265368.4_Missense_Mutation_p.R2610T|SYNE1_ENST00000448038.1_Missense_Mutation_p.R2617T|SYNE1_ENST00000341594.5_Missense_Mutation_p.R2649T|SYNE1_ENST00000423061.1_Missense_Mutation_p.R2617T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2610					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTGGTCATTCTAAGTAGGTT	0.582										HNSCC(10;0.0054)																																						0			6											62	61	61					6																	152712587		2203	4300	6503	152754280	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.7829G>C	6.37:g.152712587C>G	ENSP00000356224:p.Arg2610Thr		152754280	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024271	0.35701	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54479	0.66;0.64;0.57;0.64;0.77	5.91	4.11	0.48088	.	0.094910	0.44688	D	0.000422	T	0.19127	0.0459	L	0.29908	0.895	0.80722	D	1	P;P;P;P	0.43094	0.799;0.611;0.611;0.682	B;B;B;B	0.39531	0.205;0.159;0.159;0.302	T	0.03887	-1.0995	10	0.14252	T	0.57	.	5.9398	0.19186	0.0:0.7034:0.0:0.2966	.	2593;2610;2610;2617	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	T	2610;2617;2610;2617;2649	ENSP00000356224:R2610T;ENSP00000396024:R2617T;ENSP00000265368:R2610T;ENSP00000390975:R2617T;ENSP00000341887:R2649T	ENSP00000265368:R2610T	R	-	2	0	SYNE1	152754280	0.996000	0.38824	0.333000	0.25482	0.926000	0.56050	2.959000	0.49153	2.793000	0.96121	0.655000	0.94253	AGA		0.582	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152712587	C	G	152712587	3	3	37	1	0	0	0	0	1	0	0	0	15484	913	32	5	19017	5	SYNE1	6	152712587	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	24414763	152712587	18402480	70	3153										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152776694	152776694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gactgttggtttccacatgcTtcttccaatctccagttttc	6	12	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:152776694T>C	ENST00000367255.5	-	24	3360	c.2759A>G	c.(2758-2760)aAg>aGg	p.K920R	SYNE1_ENST00000265368.4_Missense_Mutation_p.K920R|SYNE1_ENST00000367248.3_Missense_Mutation_p.K910R|SYNE1_ENST00000367253.4_Missense_Mutation_p.K920R|SYNE1_ENST00000448038.1_Missense_Mutation_p.K927R|SYNE1_ENST00000495090.2_Missense_Mutation_p.K487R|SYNE1_ENST00000341594.5_Missense_Mutation_p.K986R|SYNE1_ENST00000413186.2_Missense_Mutation_p.K920R|SYNE1_ENST00000423061.1_Missense_Mutation_p.K927R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	920					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCCACATGCTTCTTCCAATC	0.433										HNSCC(10;0.0054)																																						0			6											117	115	116					6																	152776694		2203	4300	6503	152818387	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.2759A>G	6.37:g.152776694T>C	ENSP00000356224:p.Lys920Arg		152818387	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	16.24	3.068351	0.55539	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090	T;T;T;T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.39;1.32;1.32;1.32;1.32	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000015	T	0.37571	0.1008	L	0.52364	1.645	0.80722	D	1	D;B;B;B;D;B;P	0.69078	0.997;0.397;0.281;0.423;0.993;0.397;0.454	D;B;B;B;P;B;B	0.63957	0.92;0.093;0.103;0.138;0.876;0.093;0.137	T	0.13926	-1.0491	10	0.14656	T	0.56	.	15.5657	0.76290	0.0:0.0:0.0:1.0	.	903;920;487;910;920;920;927	B3W695;Q8NF91;F5H422;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.;.	R	920;927;920;927;986;920;910;920;487	ENSP00000356224:K920R;ENSP00000396024:K927R;ENSP00000265368:K920R;ENSP00000390975:K927R;ENSP00000341887:K986R;ENSP00000356222:K920R;ENSP00000356217:K910R;ENSP00000414510:K920R;ENSP00000438508:K487R	ENSP00000265368:K920R	K	-	2	0	SYNE1	152818387	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.910000	0.56371	2.069000	0.61940	0.533000	0.62120	AAG		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152776694	T	C	152776694	3	2	37	1	0	0	0	0	1	0	0	0	15484	1609	56	4	24199	4	SYNE1	6	152776694	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	64107	152776694	18338373	71	3154										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159457675	159457675	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcgtccagcgagctgctggaGaaggctttgagaaccagtgc	15	10	0	2	rs201570448		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:159457675G>C	ENST00000367066.3	-	10	1711	c.1380C>G	c.(1378-1380)ttC>ttG	p.F460L	RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.F282L|RP1-111C20.4_ENST00000607796.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	460					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGCTGCTGGAGAAGGCTTTGA	0.572																																																0			6											84	96	92					6																	159457675		2203	4300	6503	159377663	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1380C>G	6.37:g.159457675G>C	ENSP00000356033:p.Phe460Leu		159377663	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	6.603	0.479673	0.12581	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000539071	T;T	0.15603	2.41;2.67	6.05	4.23	0.50019	.	1.573710	0.02913	N	0.136931	T	0.04452	0.0122	L	0.35414	1.06	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44081	-0.9351	10	0.07813	T	0.8	-0.69	7.4384	0.27169	0.1443:0.1703:0.6854:0.0	.	460	Q8N103	TAGAP_HUMAN	L	460;282;125	ENSP00000356033:F460L;ENSP00000322650:F282L	ENSP00000322650:F282L	F	-	3	2	TAGAP	159377663	0.891000	0.30450	0.039000	0.18376	0.853000	0.48598	0.660000	0.25009	0.807000	0.34208	0.650000	0.86243	TTC		0.572	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		C	159457675	G	C	159457675	3	2	37	1	0	0	0	0	1	0	0	0	15576	933	33	5	819	5	TAGAP	6	159457675	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	6680981	159457675	11657392	72	3155										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160517551	160517551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctgtttcttccaccatcttcTtccactgtgaccctctggtg	6	15	4	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr6:160517551T>C	ENST00000356956.1	+	45	6884	c.6736T>C	c.(6736-6738)Ttc>Ctc	p.F2246L	RP11-288H12.3_ENST00000569097.1_RNA|IGF2R_ENST00000475584.1_3'UTR	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2246					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CACCATCTTCTTCCACTGTGA	0.552																																																0			6											263	206	226					6																	160517551		2203	4300	6503	160437541	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6736T>C	6.37:g.160517551T>C	ENSP00000349437:p.Phe2246Leu		160437541	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	33	5.255695	0.95336	.	.	ENSG00000197081	ENST00000356956	T	0.05996	3.36	5.69	5.69	0.88448	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.20373	0.0490	M	0.85710	2.77	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.01639	-1.1306	10	0.44086	T	0.13	-4.6091	15.9393	0.79743	0.0:0.0:0.0:1.0	.	2246	P11717	MPRI_HUMAN	L	2246	ENSP00000349437:F2246L	ENSP00000349437:F2246L	F	+	1	0	IGF2R	160437541	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.929000	0.70096	2.162000	0.67917	0.533000	0.62120	TTC		0.552	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160517551	T	C	160517551	3	2	37	1	0	0	0	0	1	0	0	0	7597	1609	56	4	6914	4	IGF2R	6	160517551	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	1059876	160517551	10597516	73	3156										
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378715	31378715	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcctcctcttcttctttctcGgtttcttctccaggggccct	6	16	6	0	rs563979318		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:31378715G>A	ENST00000297142.3	-	2	490	c.168C>T	c.(166-168)acC>acT	p.T56T		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	56	Poly-Glu.				cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						cttctttctcggtttcttctc	0.458													G|||	1	0.000199681	0	0	5008	,	,		16244	0.001		0	False		,,,				2504	0															0			7											181	179	179					7																	31378715		2203	4300	6503	31345240	SO:0001819	synonymous_variant	63974			AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.168C>T	7.37:g.31378715G>A			31345240	Q548T9|Q9H3H6	Silent	SNP	ENST00000297142.3	37	CCDS5434.1																																																																																				0.458	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31378715	G	A	31378715	2	1	37	1	0	0	0	0	0	0	0	1	10382	1103	39	1		1	NEUROD6	7	31378715	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10		31378715	127759948	74	3157										
AMPH	273	hgsc.bcm.edu	37	chr7	38534123	38534123	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agcttcatggaggcctcctgCatgcctagtgttggagagaa	13	9	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:38534123C>A	ENST00000356264.2	-	4	425	c.210G>T	c.(208-210)atG>atT	p.M70I	AMPH_ENST00000325590.5_Missense_Mutation_p.M70I|AMPH_ENST00000428293.2_Missense_Mutation_p.M70I	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	70	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						AGGCCTCCTGCATGCCTAGTG	0.473																																																0			7											149	130	137					7																	38534123		2203	4300	6503	38500648	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.210G>T	7.37:g.38534123C>A	ENSP00000348602:p.Met70Ile		38500648	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238839	0.95240	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000544070	T;T;T	0.60548	0.18;0.18;0.18	6.07	6.07	0.98685	BAR (3);	0.000000	0.85682	D	0.000000	T	0.76428	0.3986	M	0.87180	2.865	0.80722	D	1	P;D	0.55605	0.877;0.972	B;P	0.56514	0.361;0.8	T	0.79708	-0.1690	10	0.72032	D	0.01	-30.9676	17.5761	0.87949	0.0:1.0:0.0:0.0	.	70;70	P49418-2;P49418	.;AMPH_HUMAN	I	70	ENSP00000317441:M70I;ENSP00000348602:M70I;ENSP00000390734:M70I	ENSP00000317441:M70I	M	-	3	0	AMPH	38500648	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.991000	0.76232	2.885000	0.99019	0.655000	0.94253	ATG		0.473	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38534123	C	A	38534123	3	1	37	1	0	0	0	0	1	0	0	0	588	710	25	2	1949	2	AMPH	7	38534123	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	7155408	38534123	120604540	75	3158										
EGFR	1956	hgsc.bcm.edu	37	chr7	55249087	55249087	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atcacgcagctcatgcccttCggctgcctcctggactatgt	9	15	2	0	rs375332959		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:55249087C>T	ENST00000275493.2	+	20	2562	c.2385C>T	c.(2383-2385)ttC>ttT	p.F795F	EGFR_ENST00000454757.2_Silent_p.F742F|EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Silent_p.F750F	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	795	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCATGCCCTTCGGCTGCCTCC	0.587		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7						C		1,4405	2.1+/-5.4	0,1,2202	95	82	86		2385	-5.8	0.5	7		86	0,8600		0,0,4300	no	coding-synonymous	EGFR	NM_005228.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		795/1211	55249087	1,13005	2203	4300	6503	55216581	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2385C>T	7.37:g.55249087C>T			55216581	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.587	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55249087	C	T	55249087	2	4	37	1	0	0	0	0	0	0	0	1	4978	883	31	1		1	EGFR	7	55249087	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	16714964	55249087	103889576	76	3159										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84644426	84644426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	catttccatcccaggcacagTaggggtctctggcaagacaa	10	12	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:84644426T>C	ENST00000284136.6	-	14	1695	c.1652A>G	c.(1651-1653)tAc>tGc	p.Y551C	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	551	PSI.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCAGGCACAGTAGGGGTCTCT	0.468																																					Ovarian(63;442 1191 17318 29975 31528)											0			7											132	119	124					7																	84644426		2203	4300	6503	84482362	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1652A>G	7.37:g.84644426T>C	ENSP00000284136:p.Tyr551Cys		84482362	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597799	0.87055	.	.	ENSG00000153993	ENST00000284136	T	0.38240	1.15	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.73458	0.3589	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83406	0.0025	10	0.87932	D	0	.	16.0459	0.80720	0.0:0.0:0.0:1.0	.	551	O95025	SEM3D_HUMAN	C	551	ENSP00000284136:Y551C	ENSP00000284136:Y551C	Y	-	2	0	SEMA3D	84482362	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.196000	0.70406	0.459000	0.35465	TAC		0.468	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		C	84644426	T	C	84644426	3	2	37	1	0	0	0	0	1	0	0	0	14064	1638	57	4	697	4	SEMA3D	7	84644426	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	29395339	84644426	74494237	77	3160										
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92760879	92760879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaagtgtgcttgcctgcttgGacctgcacatgcgcttgtac	11	11	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:92760879G>A	ENST00000318238.4	-	5	5622	c.4406C>T	c.(4405-4407)tCc>tTc	p.S1469F	SAMD9L_ENST00000411955.1_Missense_Mutation_p.S1469F|SAMD9L_ENST00000437805.1_Missense_Mutation_p.S1469F	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1469					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGCCTGCTTGGACCTGCACAT	0.398																																																0			7											150	140	144					7																	92760879		2203	4300	6503	92598815	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4406C>T	7.37:g.92760879G>A	ENSP00000326247:p.Ser1469Phe		92598815	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398691	0.42512	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.24908	1.83;1.83;1.83	5.22	4.26	0.50523	.	0.251965	0.32518	N	0.005995	T	0.27697	0.0681	L	0.56769	1.78	0.26349	N	0.977236	B	0.15473	0.013	B	0.14578	0.011	T	0.21008	-1.0258	10	0.72032	D	0.01	-7.544	14.055	0.64761	0.0851:0.0:0.9149:0.0	.	1469	Q8IVG5	SAM9L_HUMAN	F	1469;1469;1469;291	ENSP00000326247:S1469F;ENSP00000405760:S1469F;ENSP00000408796:S1469F	ENSP00000326247:S1469F	S	-	2	0	SAMD9L	92598815	0.014000	0.17966	0.986000	0.45419	0.848000	0.48234	1.075000	0.30716	2.716000	0.92895	0.467000	0.42956	TCC		0.398	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92760879	G	A	92760879	3	1	37	1	0	0	0	0	1	0	0	0	13864	1174	41	3	352	3	SAMD9L	7	92760879	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	8116453	92760879	66377784	78	3161										
CALCR	799	hgsc.bcm.edu	37	chr7	93055880	93055880	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aattttgaattgggcccattGgcgcttcacggtggtttgga	13	7	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:93055880G>A	ENST00000394441.1	-	13	1528	c.1213C>T	c.(1213-1215)Caa>Taa	p.Q405*	CALCR_ENST00000421592.1_Nonsense_Mutation_p.Q421*|CALCR_ENST00000359558.2_Nonsense_Mutation_p.Q439*|CALCR_ENST00000360249.4_Nonsense_Mutation_p.Q421*|CALCR_ENST00000426151.1_Nonsense_Mutation_p.Q405*	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	439					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TGGGCCCATTGGCGCTTCACG	0.532																																																0			7											35	40	39					7																	93055880		2203	4300	6503	92893816	SO:0001587	stop_gained	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1213C>T	7.37:g.93055880G>A	ENSP00000377959:p.Gln405*		92893816	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Nonsense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	G	33	5.286164	0.95517	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	13.8286	0.63366	0.0:0.0:1.0:0.0	.	.	.	.	X	439;421;421;405;405	.	ENSP00000352561:Q439X	Q	-	1	0	CALCR	92893816	1.000000	0.71417	0.954000	0.39281	0.304000	0.27724	7.279000	0.78599	2.728000	0.93425	0.585000	0.79938	CAA		0.532	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		A	93055880	G	A	93055880	4	1	37	1	0	0	0	0	0	1	0	0	2585	1357	47	3	215	3	CALCR	7	93055880	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	295001	93055880	66082783	79	3162										
TRIP6	7205	hgsc.bcm.edu	37	chr7	100470316	100470316	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caggtcaggaggagactgtgAgaattgttgctctggatcga	15	6	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:100470316A>T	ENST00000200457.4	+	8	1609	c.1249A>T	c.(1249-1251)Aga>Tga	p.R417*	SRRT_ENST00000388793.4_5'Flank|SRRT_ENST00000432932.1_5'Flank|SRRT_ENST00000347433.4_5'Flank|SRRT_ENST00000457580.2_5'Flank	NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	417	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGAGACTGTGAGAATTGTTGC	0.572																																																0			7											149	110	123					7																	100470316		2203	4300	6503	100308252	SO:0001587	stop_gained	7205			L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.1249A>T	7.37:g.100470316A>T	ENSP00000200457:p.Arg417*		100308252	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Nonsense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	.	.	.	.	.	.	.	.	.	.	A	38	6.924247	0.97940	.	.	ENSG00000087077	ENST00000200457	.	.	.	4.61	0.809	0.18725	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0889	0.53713	0.5529:0.4471:0.0:0.0	.	.	.	.	X	417	.	ENSP00000200457:R417X	R	+	1	2	TRIP6	100308252	0.998000	0.40836	0.993000	0.49108	0.986000	0.74619	0.694000	0.25512	0.245000	0.21373	0.460000	0.39030	AGA		0.572	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		T	100470316	A	T	100470316	4	4	37	1	0	0	0	0	0	1	0	0	16599	296	11	5	1279	5	TRIP6	7	100470316	Nonsense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	7414436	100470316	58668347	80	3163										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107816967	107816967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaaacttatatcgagtgctgAaatttaaattttttaaagtc	5	4	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:107816967A>G	ENST00000425651.2	-	24	3058	c.3059T>C	c.(3058-3060)tTc>tCc	p.F1020S	NRCAM_ENST00000413765.2_Missense_Mutation_p.F1001S|NRCAM_ENST00000379028.3_Missense_Mutation_p.F1020S|NRCAM_ENST00000379024.4_Missense_Mutation_p.F1001S|NRCAM_ENST00000379022.4_Missense_Mutation_p.F1020S|NRCAM_ENST00000351718.4_Missense_Mutation_p.F1004S	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1020	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TCGAGTGCTGAAATTTAAATT	0.363																																																0			7											112	113	113					7																	107816967		2203	4300	6503	107604203	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3059T>C	7.37:g.107816967A>G	ENSP00000401244:p.Phe1020Ser		107604203	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.523389	0.27299	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5	5.62	3.08	0.35506	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.441828	0.28971	N	0.013550	T	0.25005	0.0607	N	0.02674	-0.535	0.36472	D	0.867304	B;B;B;B;B	0.16603	0.018;0.0;0.0;0.0;0.007	B;B;B;B;B	0.18561	0.022;0.003;0.004;0.003;0.001	T	0.10753	-1.0616	10	0.32370	T	0.25	.	9.3702	0.38250	0.4325:0.0:0.0:0.5675	.	1020;1001;1001;1004;1020	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	S	1020;1020;1001;1020;1004;1001;1020;1020	ENSP00000368314:F1020S;ENSP00000407858:F1001S;ENSP00000325269:F1004S;ENSP00000368310:F1001S;ENSP00000401244:F1020S;ENSP00000368308:F1020S	ENSP00000325269:F1004S	F	-	2	0	NRCAM	107604203	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.076000	0.50081	0.922000	0.37019	0.528000	0.53228	TTC		0.363	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		G	107816967	A	G	107816967	3	3	37	1	0	0	0	0	1	0	0	0	10675	246	9	4	913	4	NRCAM	7	107816967	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	7346651	107816967	51321696	81	3164										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117432610	117432610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcttcttcgtttctcagcggAgagttcctcttctaattcat	7	11	5	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:117432610A>G	ENST00000160373.3	-	4	731	c.640T>C	c.(640-642)Tcc>Ccc	p.S214P	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	214					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TTCTCAGCGGAGAGTTCCTCT	0.478																																																0			7											136	123	127					7																	117432610		2203	4300	6503	117219846	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.640T>C	7.37:g.117432610A>G	ENSP00000160373:p.Ser214Pro		117219846	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	A	7.250	0.603130	0.13939	.	.	ENSG00000077063	ENST00000160373	T	0.66099	-0.19	5.77	0.123	0.14709	.	0.534645	0.20899	N	0.083674	T	0.62865	0.2463	M	0.77820	2.39	0.19775	N	0.999952	P	0.36944	0.574	B	0.40228	0.323	T	0.58891	-0.7556	10	0.48119	T	0.1	0.8091	12.078	0.53655	0.3391:0.571:0.0:0.0899	.	214	Q8WZ74	CTTB2_HUMAN	P	214	ENSP00000160373:S214P	ENSP00000160373:S214P	S	-	1	0	CTTNBP2	117219846	0.994000	0.37717	0.150000	0.22450	0.019000	0.09904	1.203000	0.32284	0.141000	0.18875	0.528000	0.53228	TCC		0.478	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117432610	A	G	117432610	3	3	37	1	0	0	0	0	1	0	0	0	4051	304	11	4	4431	4	CTTNBP2	7	117432610	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	9615643	117432610	41706053	82	3165										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138763338	138763338	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cacagatggtcaagacaaatTtcctctgagtcatgatcatc	7	10	4	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:138763338T>G	ENST00000242351.5	-	5	1849	c.1533A>C	c.(1531-1533)gaA>gaC	p.E511D	ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.E511D|ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.E633D	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	511					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CAAGACAAATTTCCTCTGAGT	0.388																																																0			7											135	116	123					7																	138763338		2203	4300	6503	138413878	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1533A>C	7.37:g.138763338T>G	ENSP00000242351:p.Glu511Asp		138413878	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.68|12.68	2.009873|2.009873	0.35415|0.35415	.|.	.|.	ENSG00000105939|ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247|ENST00000460845	T;T;T|.	0.23147|.	2.99;2.96;1.92|.	5.05|5.05	1.27|1.27	0.21489|0.21489	Zinc finger, CCCH-type (1);|.	0.993989|.	0.08164|.	N|.	0.987971|.	T|T	0.59307|0.59307	0.2184|0.2184	M|M	0.83012|0.83012	2.62|2.62	0.33722|0.33722	D|D	0.617178|0.617178	B;B|.	0.25904|.	0.004;0.137|.	B;B|.	0.23852|.	0.016;0.049|.	T|T	0.64829|0.64829	-0.6315|-0.6315	10|5	0.56958|.	D|.	0.05|.	.|.	3.1164|3.1164	0.06376|0.06376	0.0:0.2544:0.2226:0.5229|0.0:0.2544:0.2226:0.5229	.|.	511;511|.	Q7Z2W4-2;Q7Z2W4|.	.;ZCCHV_HUMAN|.	D|H	511;633;511;271|76	ENSP00000242351:E511D;ENSP00000418385:E633D;ENSP00000419855:E511D|.	ENSP00000242351:E511D|.	E|N	-|-	3|1	2|0	ZC3HAV1|ZC3HAV1	138413878|138413878	0.322000|0.322000	0.24634|0.24634	0.964000|0.964000	0.40570|0.40570	0.658000|0.658000	0.38924|0.38924	-0.024000|-0.024000	0.12435|0.12435	0.382000|0.382000	0.24878|0.24878	0.519000|0.519000	0.50382|0.50382	GAA|AAT		0.388	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		G	138763338	T	G	138763338	3	3	37	1	0	0	0	0	1	0	0	0	17614	1838	64	4	1215	4	ZC3HAV1	7	138763338	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	21330728	138763338	20375325	83	3166										
BRAF	673	hgsc.bcm.edu	37	chr7	140500173	140500173	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaaccatacccaatagagtcCgaggcgggtgcggaagggga	15	9	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:140500173C>T	ENST00000288602.6	-	7	1029	c.969G>A	c.(967-969)tcG>tcA	p.S323S		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	323					activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CAATAGAGTCCGAGGCGGGTG	0.483		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											137	112	120					7																	140500173		2203	4300	6503	140146642	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.969G>A	7.37:g.140500173C>T			140146642	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1																																																																																				0.483	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140500173	C	T	140500173	2	4	37	1	0	0	0	0	0	0	0	1	1499	639	23	1		1	BRAF	7	140500173	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1736835	140500173	18638490	84	3167										
TAS2R3	50831	hgsc.bcm.edu	37	chr7	141464569	141464571	+	In_Frame_Del	DEL	TCT	TCT	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggcctcctactctttgctcaTcttctccctggggaggcaca							TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	TCT	TCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr7:141464569_141464571delTCT	ENST00000247879.2	+	1	673_675	c.611_613delTCT	c.(610-615)atcttc>atc	p.F205del	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	205					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					TCTTTGCTCATCTTCTCCCTGGG	0.512																																																0			7																																								141111040	SO:0001651	inframe_deletion	50831			AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.611_613delTCT	7.37:g.141464572_141464574delTCT	ENSP00000247879:p.Phe205del		141111038	A4D1U2|Q645W2|Q75MV6	In_Frame_Del	DEL	ENST00000247879.2	37	CCDS5867.1																																																																																				0.512	TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1			-	141464571	TCT	-	141464569	7	5	37	1	0	1	0	1	0	0	0	0	15611	1435	50	0	613	0	TAS2R3	7	141464569	In_Frame_Del	DEL	TCT	TCGA-AG-3731-01A-11D-1733-10	964396	141464569	17674094	85	3168										
ADRA1A	148	hgsc.bcm.edu	37	chr8	26722324	26722324	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cgtgactgagtgcaggtgtcGgtgacaggctacggagagga	18	7	0	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:26722324G>A	ENST00000519229.1	-	1	169	c.163C>T	c.(163-165)Cga>Tga	p.R55*	ADRA1A_ENST00000276393.4_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380581.2_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380587.1_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380586.1_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380582.3_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000358857.5_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000354550.4_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380573.3_Nonsense_Mutation_p.R55*|ADRA1A_ENST00000380572.3_Nonsense_Mutation_p.R55*			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	125				MTFRDLLSVSFEGPRPDSSAGGSSAGGGGGSAGGAAPSEGP AVGGVPGGAGGGGGVVGAGSGEDNRSSAGEPGSAGAGGDVN G -> MAAALRSVMMAGYLSEWRTPTYRSTEMVQRLRMEAV QHSTS (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	TGCAGGTGTCGGTGACAGGCT	0.587																																																0			8											255	266	262					8																	26722324		2203	4300	6503	26778241	SO:0001587	stop_gained	148			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"GPCR / Class A : Adrenoceptors : alpha"	277	protein-coding gene	gene with protein product		104221	"adrenergic, alpha-1A-, receptor"	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.163C>T	8.37:g.26722324G>A	ENSP00000430793:p.Arg55*		26778241	Q9NPY0	Nonsense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	G	40	8.009688	0.98607	.	.	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	.	.	.	4.83	4.83	0.62350	.	0.067670	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9988	0.58664	0.0:0.0:0.7953:0.2047	.	.	.	.	X	55	.	ENSP00000276393:R55X	R	-	1	2	ADRA1A	26778241	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.116000	0.41930	2.365000	0.80145	0.563000	0.77884	CGA		0.587	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303		A	26722324	G	A	26722324	4	1	37	1	0	0	0	0	0	1	0	0	334	1124	39	1	1536	1	ADRA1A	8	26722324	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		26722324	119641698	86	3169										
PNOC	5368	hgsc.bcm.edu	37	chr8	28186709	28186709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgtgacctgctgctgctcaGtctcttctccagtgtgttca	9	12	4	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:28186709G>A	ENST00000301908.3	+	2	243	c.35G>A	c.(34-36)aGt>aAt	p.S12N	RP11-380I10.4_ENST00000521731.1_RNA	NM_006228.3	NP_006219.1	Q13519	PNOC_HUMAN	prepronociceptin	12					neuropeptide signaling pathway (GO:0007218)|sensory perception (GO:0007600)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5		Ovarian(32;0.000953)		KIRC - Kidney renal clear cell carcinoma(542;0.104)|Kidney(114;0.125)|Colorectal(74;0.145)|BRCA - Breast invasive adenocarcinoma(99;0.245)		CTGCTGCTCAGTCTCTTCTCC	0.552																																																0			8											164	137	146					8																	28186709		2203	4300	6503	28242628	SO:0001583	missense	5368				CCDS6066.1, CCDS64862.1	8p21	2013-02-26			ENSG00000168081	ENSG00000168081		"Endogenous ligands"	9163	protein-coding gene	gene with protein product	"nocistatin"	601459				8710928, 10101606	Standard	XM_005273532		Approved	PPNOC	uc003xgp.3	Q13519	OTTHUMG00000102125	ENST00000301908.3:c.35G>A	8.37:g.28186709G>A	ENSP00000301908:p.Ser12Asn		28242628	B7Z749|Q6FH16	Missense_Mutation	SNP	ENST00000301908.3	37	CCDS6066.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036041	0.54896	.	.	ENSG00000168081	ENST00000518479;ENST00000301908	T;T	0.78364	0.74;-1.17	4.57	4.57	0.56435	.	0.307857	0.34245	N	0.004121	T	0.72277	0.3440	L	0.54323	1.7	0.80722	D	1	P	0.45044	0.849	B	0.39617	0.305	T	0.76495	-0.2938	10	0.56958	D	0.05	-14.4077	13.025	0.58810	0.0:0.0:1.0:0.0	.	12	Q13519	PNOC_HUMAN	N	12	ENSP00000428059:S12N;ENSP00000301908:S12N	ENSP00000301908:S12N	S	+	2	0	PNOC	28242628	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.977000	0.49297	2.526000	0.85167	0.491000	0.48974	AGT		0.552	PNOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219964.2	NM_006228		A	28186709	G	A	28186709	3	1	37	1	0	0	0	0	1	0	0	0	12193	1029	36	3	37	3	PNOC	8	28186709	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	1464385	28186709	118177313	87	3170										
PLAG1	5324	hgsc.bcm.edu	37	chr8	57079860	57079860	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acataccttacaggtgaggtCaccacttgttgcggcatgca	10	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:57079860C>T	ENST00000316981.3	-	5	924	c.445G>A	c.(445-447)Gac>Aac	p.D149N	PLAG1_ENST00000423799.2_Missense_Mutation_p.D67N|PLAG1_ENST00000429357.2_Missense_Mutation_p.D149N	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	149	Decreased nuclear import with localization in the nucleus but also in the cytoplasm.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CAGGTGAGGTCACCACTTGTT	0.463			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	0			8											117	90	99					8																	57079860		2203	4300	6503	57242414	SO:0001583	missense	5324			U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.445G>A	8.37:g.57079860C>T	ENSP00000325546:p.Asp149Asn		57242414	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	37	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477940	0.84747	.	.	ENSG00000181690	ENST00000316981;ENST00000423799;ENST00000429357	T;T;T	0.27557	1.66;3.39;1.66	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	N	0.17564	0.495	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.40327	-0.9569	10	0.46703	T	0.11	-22.9455	19.5003	0.95091	0.0:1.0:0.0:0.0	.	149	Q6DJT9	PLAG1_HUMAN	N	149;67;149	ENSP00000325546:D149N;ENSP00000404067:D67N;ENSP00000416537:D149N	ENSP00000325546:D149N	D	-	1	0	PLAG1	57242414	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.818000	0.86416	2.594000	0.87642	0.585000	0.79938	GAC		0.463	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		T	57079860	C	T	57079860	3	4	37	1	0	0	0	0	1	0	0	0	12049	826	29	3	1061	3	PLAG1	8	57079860	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	28893151	57079860	89284162	88	3171										
GGH	8836	hgsc.bcm.edu	37	chr8	63951237	63951237	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	accgatgatgggcttcttggCggtgtcgccgtggggtctag	17	9	2	1	rs11545077	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:63951237C>T	ENST00000260118.6	-	1	493	c.91G>A	c.(91-93)Gcc>Acc	p.A31T		NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)	31	Gamma-glutamyl hydrolase. {ECO:0000255|PROSITE-ProRule:PRU00607}.		A -> T (in dbSNP:rs11545077).		glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)			breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	GGCTTCTTGGCGGTGTCGCCG	0.726													C|||	1005	0.200679	0.1051	0.2046	5008	,	,		11929	0.2183		0.2505	False		,,,				2504	0.2577															0			8						C	THR/ALA	573,3819		35,503,1658	15	15	15		91	-8	0	8	dbSNP_120	15	2151,6439		264,1623,2408	yes	missense	GGH	NM_003878.2	58	299,2126,4066	TT,TC,CC		25.0407,13.0464,20.9829	benign	31/319	63951237	2724,10258	2196	4295	6491	64113791	SO:0001583	missense	8836			U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.91G>A	8.37:g.63951237C>T	ENSP00000260118:p.Ala31Thr		64113791		Missense_Mutation	SNP	ENST00000260118.6	37	CCDS6177.1	443	0.20283882783882784	46	0.09349593495934959	74	0.20441988950276244	127	0.22202797202797203	196	0.25857519788918204	C	8.288	0.817065	0.16607	0.130464	0.250407	ENSG00000137563	ENST00000260118	T	0.21543	2.0	4.08	-7.97	0.01139	.	0.792035	0.11203	N	0.588636	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.26408	T	0.33	-13.8596	0.7201	0.00939	0.2962:0.13:0.3164:0.2574	rs11545077;rs13270305;rs58961784;rs13270305	31	Q92820	GGH_HUMAN	T	31	ENSP00000260118:A31T	ENSP00000260118:A31T	A	-	1	0	GGH	64113791	0.000000	0.05858	0.000000	0.03702	0.653000	0.38743	-1.288000	0.02783	-1.754000	0.01321	0.313000	0.20887	GCC		0.726	GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378453.1			T	63951237	C	T	63951237	3	4	37	1	0	0	0	0	1	0	0	0	6377	768	27	1	901	1	GGH	8	63951237	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	6871377	63951237	82412785	89	3172										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86035726	86035726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atataacttctgaaagtgacTatggaaacagaaaagaatgc	8	5	1	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:86035726T>C	ENST00000360375.3	+	7	1158	c.1009T>C	c.(1009-1011)Tat>Cat	p.Y337H	LRRCC1_ENST00000414626.2_Missense_Mutation_p.Y317H	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	337					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TGAAAGTGACTATGGAAACAG	0.323																																																0			8											81	81	81					8																	86035726		1806	4071	5877	86222978	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1009T>C	8.37:g.86035726T>C	ENSP00000353538:p.Tyr337His		86222978	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	T	8.252	0.809206	0.16537	.	.	ENSG00000133739	ENST00000426019;ENST00000360375;ENST00000414626	T;T	0.31769	1.48;1.48	5.83	4.64	0.57946	.	1.012730	0.07950	N	0.980698	T	0.23014	0.0556	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.15473	0.013;0.007;0.013;0.005	B;B;B;B	0.18561	0.022;0.011;0.012;0.005	T	0.39461	-0.9613	10	0.14252	T	0.57	0.1053	3.718	0.08445	0.1214:0.0682:0.2528:0.5576	.	244;317;244;337	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	H	244;337;317	ENSP00000353538:Y337H;ENSP00000394695:Y317H	ENSP00000353538:Y337H	Y	+	1	0	LRRCC1	86222978	0.028000	0.19301	0.383000	0.26132	0.995000	0.86356	1.656000	0.37355	1.000000	0.39049	0.528000	0.53228	TAT		0.323	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		C	86035726	T	C	86035726	3	2	37	1	0	0	0	0	1	0	0	0	9055	1522	53	4	1035	4	LRRCC1	8	86035726	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	22084489	86035726	60328296	90	3173										
PSKH2	85481	hgsc.bcm.edu	37	chr8	87081681	87081681	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctttacctggcaaggacccgGgggtcgaacttggctcggaa	14	11	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:87081681G>A	ENST00000276616.2	-	1	245	c.171C>T	c.(169-171)ccC>ccT	p.P57P	PSKH2_ENST00000517981.1_Intron	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	57							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			CAAGGACCCGGGGGTCGAACT	0.672																																																0			8											15	19	18					8																	87081681		2201	4297	6498	87150797	SO:0001819	synonymous_variant	85481			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.171C>T	8.37:g.87081681G>A			87150797	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																				0.672	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		A	87081681	G	A	87081681	2	1	37	1	0	0	0	0	0	0	0	1	12699	1219	43	3		3	PSKH2	8	87081681	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	1045955	87081681	59282341	91	3174										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93026961	93026963	+	In_Frame_Del	DEL	GAA	GAA	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gattagccagagaggaggagGaagaagaggaaggcccattg							TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:93026961_93026963delGAA	ENST00000523629.1	-	4	766_768	c.312_314delTTC	c.(310-315)tcttcc>tcc	p.104_105SS>S	RUNX1T1_ENST00000518844.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000520724.1_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000521553.1_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000436581.2_In_Frame_Del_p.115_116SS>S|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000396218.1_In_Frame_Del_p.77_78SS>S|RUNX1T1_ENST00000422361.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000360348.2_In_Frame_Del_p.67_68SS>S|RUNX1T1_ENST00000265814.3_In_Frame_Del_p.104_105SS>S	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	104	Poly-Ser.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGAGGAGGAGGAAGAAGAGGAAG	0.542																																																0			8																																								93096139	SO:0001651	inframe_deletion	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.312_314delTTC	8.37:g.93026964_93026966delGAA	ENSP00000428543:p.Ser108del		93096137	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	In_Frame_Del	DEL	ENST00000523629.1	37	CCDS6256.1																																																																																				0.542	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		-	93026963	GAA	-	93026961	7	5	37	1	0	1	0	1	0	0	0	0	13784	1174	41	0	1536	0	RUNX1T1	8	93026961	In_Frame_Del	DEL	GAA	TCGA-AG-3731-01A-11D-1733-10	5945280	93026961	53337061	92	3175										
PLEKHF2	79666	hgsc.bcm.edu	37	chr8	96166991	96166991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcctttaaatgatatgtctgAtgatgatgacgatgatgata	9	4	1	7			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:96166991A>G	ENST00000315367.3	+	2	960	c.719A>G	c.(718-720)gAt>gGt	p.D240G	PLEKHF2_ENST00000519516.1_Missense_Mutation_p.D240G	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	240					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					GATATGTCTGATGATGATGAC	0.433																																																0			8											77	74	75					8																	96166991		2203	4300	6503	96236167	SO:0001583	missense	79666			AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"Zinc fingers, FYVE domain containing", "Pleckstrin homology (PH) domain containing"	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.719A>G	8.37:g.96166991A>G	ENSP00000322373:p.Asp240Gly		96236167		Missense_Mutation	SNP	ENST00000315367.3	37	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103495	0.37145	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	T;T	0.81078	-1.45;-1.45	5.81	5.81	0.92471	.	0.090894	0.64402	D	0.000001	T	0.76962	0.4061	N	0.08118	0	0.80722	D	1	D	0.57571	0.98	P	0.57009	0.811	T	0.81387	-0.0956	10	0.51188	T	0.08	-19.809	16.179	0.81887	1.0:0.0:0.0:0.0	.	240	Q9H8W4	PKHF2_HUMAN	G	240	ENSP00000322373:D240G;ENSP00000427792:D240G	ENSP00000322373:D240G	D	+	2	0	PLEKHF2	96236167	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	8.590000	0.90821	2.225000	0.72522	0.455000	0.32223	GAT		0.433	PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613		G	96166991	A	G	96166991	3	3	37	1	0	0	0	0	1	0	0	0	12098	333	12	4	721	4	PLEKHF2	8	96166991	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	3140030	96166991	50197031	93	3176										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101237453	101237453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caaattggcgggagaagctgTcacctattcctgctgtgcct	11	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:101237453T>C	ENST00000388798.2	+	14	1932	c.1741T>C	c.(1741-1743)Tca>Cca	p.S581P	SPAG1_ENST00000523302.1_3'UTR|SPAG1_ENST00000251809.3_Missense_Mutation_p.S581P	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	581					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GGAGAAGCTGTCACCTATTCC	0.453																																																0			8											63	59	61					8																	101237453		2203	4300	6503	101306629	SO:0001583	missense	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1741T>C	8.37:g.101237453T>C	ENSP00000373450:p.Ser581Pro		101306629	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.410763	0.42817	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.59772	0.24;0.24	5.46	-1.44	0.08856	.	0.281448	0.39985	N	0.001218	T	0.23572	0.0570	N	0.02685	-0.53	0.27830	N	0.941496	B	0.06786	0.001	B	0.08055	0.003	T	0.35126	-0.9801	10	0.02654	T	1	-0.0026	11.0949	0.48139	0.0:0.6141:0.0:0.3859	.	581	Q07617	SPAG1_HUMAN	P	581	ENSP00000251809:S581P;ENSP00000373450:S581P	ENSP00000251809:S581P	S	+	1	0	SPAG1	101306629	0.598000	0.26882	0.986000	0.45419	0.993000	0.82548	0.578000	0.23773	-0.170000	0.10816	0.528000	0.53228	TCA		0.453	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101237453	T	C	101237453	3	2	37	1	0	0	0	0	1	0	0	0	15014	1667	58	4	1791	4	SPAG1	8	101237453	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	5070462	101237453	45126569	94	3177										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101299869	101299869	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggattaaaccgttcagtacaTtctgggcaactaatattaac	7	8	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:101299869T>C	ENST00000519449.1	-	3	850	c.534A>G	c.(532-534)gaA>gaG	p.E178E	RNF19A_ENST00000341084.2_Silent_p.E178E	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	178					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			GTTCAGTACATTCTGGGCAAC	0.358																																																0			8											120	124	122					8																	101299869		2203	4300	6503	101369045	SO:0001819	synonymous_variant	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.534A>G	8.37:g.101299869T>C			101369045	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Silent	SNP	ENST00000519449.1	37	CCDS6286.1																																																																																				0.358	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		C	101299869	T	C	101299869	2	2	37	1	0	0	0	0	0	0	0	1	13507	1490	52	4		4	RNF19A	8	101299869	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	62416	101299869	45064153	95	3178										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113402946	113402946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccacacacaattcagattgtTgtcataaggctcagggtatc	8	10	3	1	rs375988803	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:113402946T>C	ENST00000297405.5	-	36	6125	c.5881A>G	c.(5881-5883)Aac>Gac	p.N1961D	CSMD3_ENST00000352409.3_Missense_Mutation_p.N1891D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1857D|CSMD3_ENST00000343508.3_Missense_Mutation_p.N1921D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1961	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTCAGATTGTTGTCATAAGGC	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	8	0.00159744	0	0	5008	,	,		17211	0		0	False		,,,				2504	0.0082															0			8											90	84	86					8																	113402946		2203	4300	6503	113472122	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5881A>G	8.37:g.113402946T>C	ENSP00000297405:p.Asn1961Asp		113472122	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608830	0.87258	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.14	5.14	0.70334	CUB (5);	0.000000	0.85682	D	0.000000	T	0.51024	0.1650	L	0.56396	1.775	0.52099	D	0.999942	D;P;D	0.76494	0.999;0.948;0.999	D;D;D	0.85130	0.997;0.93;0.986	T	0.44952	-0.9294	10	0.36615	T	0.2	.	15.1178	0.72416	0.0:0.0:0.0:1.0	.	1857;1961;1921	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1921;1961;1231;1857;1891	ENSP00000345799:N1921D;ENSP00000297405:N1961D;ENSP00000341558:N1231D;ENSP00000412263:N1857D;ENSP00000343124:N1891D	ENSP00000297405:N1961D	N	-	1	0	CSMD3	113472122	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.857000	0.86963	2.162000	0.67917	0.383000	0.25322	AAC		0.408	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113402946	T	C	113402946	3	2	37	1	0	0	0	0	1	0	0	0	3952	1812	63	4	5386	4	CSMD3	8	113402946	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	12103077	113402946	32961076	96	3179										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145625387	145625387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gggggaggggctcacatctcGccgcccttgagggagatgac	17	11	2	3	rs144467510	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr8:145625387G>A	ENST00000349769.3	-	10	1120	c.1026C>T	c.(1024-1026)ggC>ggT	p.G342G	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	342					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CTCACATCTCGCCGCCCTTGA	0.672													G|||	5	0.000998403	0.0038	0	5008	,	,		8530	0		0	False		,,,				2504	0				NSCLC(133;1088 1848 27708 34777 35269)											0			8						G		9,4395		0,9,2193	25	21	23		1026	-11.3	0	8	dbSNP_134	23	0,8596		0,0,4298	no	coding-synonymous	CPSF1	NM_013291.2		0,9,6491	AA,AG,GG		0.0,0.2044,0.0692		342/1444	145625387	9,12991	2202	4298	6500	145596195	SO:0001819	synonymous_variant	29894			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1026C>T	8.37:g.145625387G>A			145596195	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																				0.672	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		A	145625387	G	A	145625387	2	1	37	1	0	0	0	0	0	0	0	1	3830	1074	38	1		1	CPSF1	8	145625387	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	32222441	145625387	738635	97	3180										
C9orf68	55064	hgsc.bcm.edu	37	chr9	4661998	4661998	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aggtagaccccgaggtacacAtcttgtttgccaggcaggaa	12	10	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:4661998A>G	ENST00000454239.2	-	3	323	c.78T>C	c.(76-78)gaT>gaC	p.D26D	SPATA6L_ENST00000381890.5_Silent_p.D26D|PPAPDC2_ENST00000381883.2_5'Flank|SPATA6L_ENST00000475086.1_Silent_p.D26D|SPATA6L_ENST00000223517.5_5'UTR|SPATA6L_ENST00000381895.5_5'UTR			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	26																	CGAGGTACACATCTTGTTTGC	0.433											OREG0019084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			9											84	78	80					9																	4661998		1882	4113	5995	4651998	SO:0001819	synonymous_variant	55064			AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 68"	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.78T>C	9.37:g.4661998A>G		620	4651998	B4DIY4|Q5JVJ5|Q8IY90	Silent	SNP	ENST00000454239.2	37																																																																																					0.433	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985		G	4661998	A	G	4661998	2	3	37	1	0	0	0	0	0	0	0	1	2497	214	8	4		4	C9orf68	9	4661998	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10		4661998	136551433	98	3181										
TLN1	7094	hgsc.bcm.edu	37	chr9	35703799	35703799	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gagttctttagctgccacacAgcagggtcatctccaacttt	8	12	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:35703799A>G	ENST00000314888.9	-	47	6683	c.6330T>C	c.(6328-6330)gcT>gcC	p.A2110A	TLN1_ENST00000540444.1_Silent_p.A2004A|TLN1_ENST00000464379.1_5'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2110					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTGCCACACAGCAGGGTCAT	0.493																																																0			9											96	89	91					9																	35703799		2203	4300	6503	35693799	SO:0001819	synonymous_variant	7094			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6330T>C	9.37:g.35703799A>G			35693799	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																				0.493	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		G	35703799	A	G	35703799	2	3	37	1	0	0	0	0	0	0	0	1	15986	175	7	4		4	TLN1	9	35703799	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	31041801	35703799	105509632	99	3182										
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666272	117666272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caagaggaaaggtgcttgtaTctatgtactggaatgtatcc	11	6	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:117666272T>C	ENST00000223795.2	-	4	757	c.644A>G	c.(643-645)gAt>gGt	p.D215G	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	215					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						GGTGCTTGTATCTATGTACTG	0.418																																																0			9											248	226	233					9																	117666272		2203	4300	6503	116706093	SO:0001583	missense	944			L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.644A>G	9.37:g.117666272T>C	ENSP00000223795:p.Asp215Gly		116706093	O43404	Missense_Mutation	SNP	ENST00000223795.2	37	CCDS6810.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448623	0.43531	.	.	ENSG00000106952	ENST00000223795	D	0.95272	-3.66	5.78	5.78	0.91487	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.104923	0.46442	D	0.000281	D	0.94112	0.8112	L	0.27053	0.805	0.38783	D	0.95481	D	0.63046	0.992	P	0.61477	0.889	D	0.95188	0.8305	10	0.56958	D	0.05	-13.2654	13.6253	0.62161	0.0:0.0:0.0:1.0	.	215	P32971	TNFL8_HUMAN	G	215	ENSP00000223795:D215G	ENSP00000223795:D215G	D	-	2	0	TNFSF8	116706093	1.000000	0.71417	1.000000	0.80357	0.111000	0.19643	4.057000	0.57455	2.203000	0.70933	0.533000	0.62120	GAT		0.418	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			C	117666272	T	C	117666272	3	2	37	1	0	0	0	0	1	0	0	0	16350	1435	50	4	64	4	TNFSF8	9	117666272	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	81962473	117666272	23547159	100	3183										
TOR1A	1861	hgsc.bcm.edu	37	chr9	132576475	132576475	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ataatcaatgaggttccggtCaattaagctgctgtgccaga	10	8	2	2	rs17849354		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:132576475C>T	ENST00000351698.4	-	5	823	c.775G>A	c.(775-777)Gac>Aac	p.D259N		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	259	Interaction with KLC1.			D -> H (in Ref. 3; AAP35577 and 5; AAH00674). {ECO:0000305}.	ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				AGGTTCCGGTCAATTAAGCTG	0.493																																																0			9											93	89	90					9																	132576475		2203	4300	6503	131616296	SO:0001583	missense	1861			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"dystonia 1, torsion (autosomal dominant; torsin A)"	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.775G>A	9.37:g.132576475C>T	ENSP00000345719:p.Asp259Asn		131616296	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634665	0.87660	.	.	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.29655	1.56	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.51907	0.1702	M	0.73753	2.245	0.58432	D	0.999999	D	0.59357	0.985	P	0.57468	0.821	T	0.56908	-0.7901	10	0.59425	D	0.04	-11.0018	17.2642	0.87081	0.0:1.0:0.0:0.0	.	259	O14656	TOR1A_HUMAN	N	228;259	ENSP00000345719:D259N	ENSP00000345719:D259N	D	-	1	0	TOR1A	131616296	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.690000	0.68241	2.297000	0.77311	0.561000	0.74099	GAC		0.493	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113		T	132576475	C	T	132576475	3	4	37	1	0	0	0	0	1	0	0	0	16411	826	29	3	227	3	TOR1A	9	132576475	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	14910203	132576475	8636956	101	3184										
NUP214	8021	hgsc.bcm.edu	37	chr9	134098264	134098264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cactggcactttcagctctgGaggaggaagtgtggcatccc	13	11	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr9:134098264G>A	ENST00000359428.5	+	32	5993	c.5849G>A	c.(5848-5850)gGa>gAa	p.G1950E	NUP214_ENST00000411637.2_Missense_Mutation_p.G1940E|NUP214_ENST00000451030.1_Missense_Mutation_p.G1951E|NUP214_ENST00000483497.2_Missense_Mutation_p.G776E			P35658	NU214_HUMAN	nucleoporin 214kDa	1950	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCAGCTCTGGAGGAGGAAGT	0.443			T	"DEK, SET, ABL1"	"AML, T-ALL"																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0			9											120	111	114					9																	134098264		2203	4300	6503	133088085	SO:0001583	missense	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5849G>A	9.37:g.134098264G>A	ENSP00000352400:p.Gly1950Glu		133088085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070750	0.93950	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497	T;T;T;T	0.69435	0.1;0.12;0.11;-0.4	5.71	5.71	0.89125	.	0.000000	0.40554	N	0.001076	T	0.67429	0.2892	N	0.08118	0	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.72265	-0.4344	10	0.45353	T	0.12	-12.9455	16.9975	0.86372	0.0:0.0:1.0:0.0	.	776;1544;1940;1950	B7ZAV2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	E	1950;1940;1951;1929;1544;1379;776	ENSP00000352400:G1950E;ENSP00000396576:G1940E;ENSP00000405014:G1951E;ENSP00000436793:G776E	ENSP00000352400:G1950E	G	+	2	0	NUP214	133088085	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.060000	0.93907	2.700000	0.92200	0.655000	0.94253	GGA		0.443	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134098264	G	A	134098264	3	1	37	1	0	0	0	0	1	0	0	0	10793	1174	41	3	5975	3	NUP214	9	134098264	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	1521789	134098264	7115167	102	3185										
GTPBP4	23560	hgsc.bcm.edu	37	chr10	1042096	1042096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtatggcgactctctctaccGctgcaaacagctgaagcgtg	11	12	2	1	rs374244248		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:1042096G>A	ENST00000360803.4	+	4	456	c.374G>A	c.(373-375)cGc>cAc	p.R125H	GTPBP4_ENST00000545048.1_Missense_Mutation_p.R78H|GTPBP4_ENST00000538293.1_Missense_Mutation_p.R9H|GTPBP4_ENST00000491635.1_3'UTR	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	125					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		TCTCTCTACCGCTGCAAACAG	0.433																																																0			10							HIS/ARG	0,4406		0,0,2203	77	59	65		374	5.5	1	10		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	GTPBP4	NM_012341.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/635	1042096	1,13005	2203	4300	6503	1032096	SO:0001583	missense	23560			AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"G protein-binding protein CRFG", " GTP-binding protein"					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.374G>A	10.37:g.1042096G>A	ENSP00000354040:p.Arg125His		1032096	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	37	CCDS31132.1	.	.	.	.	.	.	.	.	.	.	g	29.2	4.989192	0.93106	0.0	1.16E-4	ENSG00000107937	ENST00000360803;ENST00000538293;ENST00000360059;ENST00000545048	T;T;T;T	0.40756	2.53;1.02;2.53;2.53	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.75170	0.3813	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81938	-0.0704	10	0.87932	D	0	-1.384	19.4919	0.95054	0.0:0.0:1.0:0.0	.	125	Q9BZE4	NOG1_HUMAN	H	125;9;78;78	ENSP00000354040:R125H;ENSP00000444277:R9H;ENSP00000353168:R78H;ENSP00000445473:R78H	ENSP00000353168:R78H	R	+	2	0	GTPBP4	1032096	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	9.595000	0.98260	2.615000	0.88500	0.550000	0.68814	CGC		0.433	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341		A	1042096	G	A	1042096	3	1	37	1	0	0	0	0	1	0	0	0	6903	1087	38	1	388	1	GTPBP4	10	1042096	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		1042096	134492651	103	3186										
UCMA	221044	hgsc.bcm.edu	37	chr10	13276241	13276241	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gagaagcaagacagcaggacGgcctgtctccaagtcatctt	11	11	3	2	rs187657704	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:13276241G>A	ENST00000378681.3	-	1	90	c.18C>T	c.(16-18)gcC>gcT	p.A6A	UCMA_ENST00000463405.2_Silent_p.A6A	NM_145314.1	NP_660357.2	Q8WVF2	UCMA_HUMAN	upper zone of growth plate and cartilage matrix associated	6					negative regulation of osteoblast differentiation (GO:0045668)	aggresome (GO:0016235)|extracellular space (GO:0005615)|perinuclear region of cytoplasm (GO:0048471)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9						ACAGCAGGACGGCCTGTCTCC	0.582													G|||	2	0.000399361	0	0	5008	,	,		15154	0.001		0.001	False		,,,				2504	0															0			10											77	59	65					10																	13276241		2203	4300	6503	13316247	SO:0001819	synonymous_variant	221044			BC018068	CCDS31147.1	10p13	2009-03-25	2009-03-25	2009-03-25	ENSG00000165623	ENSG00000165623			25205	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 49"	C10orf49		12477932	Standard	NM_145314		Approved		uc001imd.3	Q8WVF2	OTTHUMG00000017692	ENST00000378681.3:c.18C>T	10.37:g.13276241G>A			13316247		Silent	SNP	ENST00000378681.3	37	CCDS31147.1																																																																																				0.582	UCMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046843.2	NM_145314		A	13276241	G	A	13276241	2	1	37	1	0	0	0	0	0	0	0	1	16966	1103	39	1		1	UCMA	10	13276241	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	12234145	13276241	122258506	104	3187										
CHAT	1103	hgsc.bcm.edu	37	chr10	50835688	50835688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgttgtcattaatttccgccGtctcagtgagggggatctgt	12	8	3	1	rs200176236		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:50835688G>A	ENST00000337653.2	+	7	1121	c.968G>A	c.(967-969)cGt>cAt	p.R323H	CHAT_ENST00000351556.3_Missense_Mutation_p.R205H|CHAT_ENST00000339797.1_Missense_Mutation_p.R205H|CHAT_ENST00000395559.2_Missense_Mutation_p.R205H|CHAT_ENST00000395562.2_Missense_Mutation_p.R241H|CHAT_ENST00000455728.2_Missense_Mutation_p.R205H	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	323					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.R323H(2)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	AATTTCCGCCGTCTCAGTGAG	0.512																																																2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	10											216	182	194					10																	50835688		2203	4300	6503	50505694	SO:0001583	missense	10044			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.968G>A	10.37:g.50835688G>A	ENSP00000337103:p.Arg323His		50505694	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	34	5.387473	0.95988	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.88952	0.6577	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	0.986;1.0	B;D	0.72338	0.37;0.977	D	0.87755	0.2594	10	0.44086	T	0.13	-10.1192	19.6873	0.95984	0.0:0.0:1.0:0.0	.	205;323	F8W8I2;P28329	.;CLAT_HUMAN	H	205;205;205;323;241;205	ENSP00000343486:R205H;ENSP00000345878:R205H;ENSP00000378926:R205H;ENSP00000337103:R323H;ENSP00000378929:R241H;ENSP00000390521:R205H	ENSP00000337103:R323H	R	+	2	0	CHAT	50505694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.647000	0.89833	0.579000	0.79373	CGT		0.512	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50835688	G	A	50835688	3	1	37	1	0	0	0	0	1	0	0	0	3319	1145	40	1	1038	1	CHAT	10	50835688	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	37559447	50835688	84699059	105	3188										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624271	89624271	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gttagcagaaacaaaaggagAtatcaagaggatggattcga	12	4	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:89624271A>G	ENST00000371953.3	+	1	1402	c.45A>G	c.(43-45)agA>agG	p.R15R	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	15	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		R -> S (in glioma). {ECO:0000269|PubMed:9090379}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.R15S(3)|p.R15fs*23(1)|p.R14fs*26(1)|p.R15fs*28(1)|p.Y16fs*27(1)|p.R15fs*9(1)|p.N12fs*6(1)|p.R14_D22del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ACAAAAGGAGATATCAAGAGG	0.478		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	60	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(4)|Substitution - Missense(3)|Insertion - Frameshift(2)|Deletion - In frame(1)	central_nervous_system(14)|prostate(14)|skin(7)|lung(6)|endometrium(3)|ovary(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|large_intestine(1)|urinary_tract(1)|kidney(1)	10											186	177	180					10																	89624271		2203	4300	6503	89614251	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.45A>G	10.37:g.89624271A>G			89614251	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.478	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89624271	A	G	89624271	2	3	37	1	0	0	0	0	0	0	0	1	12772	330	12	4		4	PTEN	10	89624271	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	38788583	89624271	45910476	106	3189										
MKI67	4288	hgsc.bcm.edu	37	chr10	129903302	129903302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acctcctgctggtttgggtgTgtccatagctttccctactg	10	12	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr10:129903302T>C	ENST00000368654.3	-	13	7177	c.6802A>G	c.(6802-6804)Aca>Gca	p.T2268A	MKI67_ENST00000368653.3_Missense_Mutation_p.T1908A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2268	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGTTTGGGTGTGTCCATAGCT	0.473																																																0			10											301	273	282					10																	129903302		2203	4300	6503	129793292	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6802A>G	10.37:g.129903302T>C	ENSP00000357643:p.Thr2268Ala		129793292	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053516	0.36181	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03065	4.06;4.06	2.91	0.477	0.16784	.	0.419884	0.17486	N	0.172501	T	0.06325	0.0163	M	0.63843	1.955	0.09310	N	1	P;D;D	0.55800	0.762;0.961;0.973	B;P;P	0.56163	0.348;0.793;0.754	T	0.22977	-1.0201	10	0.08599	T	0.76	.	2.4224	0.04451	0.3502:0.0:0.21:0.4398	.	2267;1908;2268	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	2268;1908;2267	ENSP00000357643:T2268A;ENSP00000357642:T1908A	ENSP00000357642:T1908A	T	-	1	0	MKI67	129793292	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.759000	0.01808	0.301000	0.22738	0.533000	0.62120	ACA		0.473	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129903302	T	C	129903302	3	2	37	1	0	0	0	0	1	0	0	0	9628	1696	59	4	2980	4	MKI67	10	129903302	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	40279031	129903302	5631445	107	3190										
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3143293	3143293	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctgagcagctgccgtgtggcGcgcttcttctcctgccggta	13	14	2	1	rs11828515	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:3143293G>A	ENST00000263650.7	-	5	495	c.336C>T	c.(334-336)cgC>cgT	p.R112R	OSBPL5_ENST00000348039.5_Silent_p.R112R|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000525498.1_Silent_p.R64R|OSBPL5_ENST00000389989.3_Silent_p.R112R	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	112					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		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)		GCCGTGTGGCGCGCTTCTTCT	0.682													G|||	18	0.00359425	0.0136	0	5008	,	,		15914	0		0	False		,,,				2504	0															0			11						G	,,	32,4348		0,32,2158	43	35	38		336,336,336	-8.3	0	11	dbSNP_120	38	0,8582		0,0,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	,,	0,32,6449	AA,AG,GG		0.0,0.7306,0.2469	,,	112/812,112/880,112/812	3143293	32,12930	2190	4291	6481	3099869	SO:0001819	synonymous_variant	114879			AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.336C>T	11.37:g.3143293G>A			3099869	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																				0.682	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			A	3143293	G	A	3143293	2	1	37	1	0	0	0	0	0	0	0	1	11311	1074	38	1		1	OSBPL5	11	3143293	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10		3143293	131863223	108	3191										
OR52B6	340980	hgsc.bcm.edu	37	chr11	5603051	5603051	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cccgttatttatggagtgagGactaagccaatactggaagg	12	7	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:5603051G>A	ENST00000345043.2	+	1	945	c.945G>A	c.(943-945)agG>agA	p.R315R	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGGAGTGAGGACTAAGCCAA	0.438																																																0			11											196	175	182					11																	5603051		1915	4130	6045	5559627	SO:0001819	synonymous_variant	340980			AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.945G>A	11.37:g.5603051G>A			5559627	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																				0.438	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		A	5603051	G	A	5603051	2	1	37	1	0	0	0	0	0	0	0	1	11144	1165	41	3		3	OR52B6	11	5603051	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	2459758	5603051	129403465	109	3192										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17418522	17418522	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caccggcttcagggagctgtCgtagcgcacgctcaggttct	13	13	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:17418522C>T	ENST00000389817.3	-	33	4128	c.4060G>A	c.(4060-4062)Gac>Aac	p.D1354N	ABCC8_ENST00000302539.4_Missense_Mutation_p.D1355N			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1354	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.D1354N(1)|p.D1354Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	AGGGAGCTGTCGTAGCGCACG	0.632																																																2	Substitution - Missense(2)	ovary(1)|lung(1)	11											130	104	113					11																	17418522		2200	4293	6493	17375098	SO:0001583	missense	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4060G>A	11.37:g.17418522C>T	ENSP00000374467:p.Asp1354Asn		17375098	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.046357|4.046357	0.75846|0.75846	.|.	.|.	ENSG00000006071|ENSG00000006071	ENST00000389817;ENST00000302539|ENST00000528374	D;D|.	0.90504|.	-2.68;-2.68|.	4.83|4.83	4.83|4.83	0.62350|0.62350	ABC transporter-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56202|0.56202	0.1969|0.1969	L|L	0.28014|0.28014	0.82|0.82	0.80722|0.80722	D|D	1|1	B|.	0.26318|.	0.146|.	B|.	0.17433|.	0.018|.	T|T	0.52403|0.52403	-0.8580|-0.8580	10|5	0.42905|.	T|.	0.14|.	.|.	18.2867|18.2867	0.90117|0.90117	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1354|.	Q09428|.	ABCC8_HUMAN|.	N|Q	1354;1355|181	ENSP00000374467:D1354N;ENSP00000303960:D1355N|.	ENSP00000303960:D1355N|.	D|R	-|-	1|2	0|0	ABCC8|ABCC8	17375098|17375098	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.924000|0.924000	0.55760|0.55760	5.983000|5.983000	0.70540|0.70540	2.386000|2.386000	0.81285|0.81285	0.555000|0.555000	0.69702|0.69702	GAC|CGA		0.632	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		T	17418522	C	T	17418522	3	4	37	1	0	0	0	0	1	0	0	0	58	884	31	1	713	1	ABCC8	11	17418522	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	11815471	17418522	117587994	110	3193										
FLRT1	28992	hgsc.bcm.edu	37	chr11	63884784	63884784	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gggtgaaggcacgggcggccGtggtcaacgtgcggggcctc	20	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:63884784G>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.V349M	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						ACGGGCGGCCGTGGTCAACGT	0.632																																																0			11											51	51	51					11																	63884784		2201	4297	6498	63641360	SO:0001627	intron_variant	23769			AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33926C>T	11.37:g.63884784G>A			63641360	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827920	0.50845	.	.	ENSG00000126500	ENST00000246841	T	0.02498	4.27	4.84	4.84	0.62591	Cysteine-rich flanking region, C-terminal (1);	0.394868	0.24052	N	0.041987	T	0.08358	0.0208	M	0.64997	1.995	0.39604	D	0.969782	D	0.71674	0.998	P	0.51550	0.673	T	0.33497	-0.9866	10	0.33141	T	0.24	-25.1881	17.0921	0.86625	0.0:0.0:1.0:0.0	.	321	Q9NZU1	FLRT1_HUMAN	M	349	ENSP00000246841:V349M	ENSP00000246841:V349M	V	+	1	0	FLRT1	63641360	0.992000	0.36948	0.990000	0.47175	0.889000	0.51656	2.162000	0.42367	2.395000	0.81488	0.555000	0.69702	GTG		0.632	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63884784	G	A	63884784	1	1	37	0	1	0	0	0	0	0	0	0	5957	1145	40	1		1	FLRT1	11	63884784	Intron	SNP	G	TCGA-AG-3731-01A-11D-1733-10	46466262	63884784	71121732	111	3194										
MEN1	4221	hgsc.bcm.edu	37	chr11	64571900	64571900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tctgcacttgcgactgtgccGtgagttgcagcttgatggcg	14	10	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64571900G>A	ENST00000337652.1	-	10	2257	c.1754C>T	c.(1753-1755)aCg>aTg	p.T585M	MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000377326.3_Missense_Mutation_p.T580M|MEN1_ENST00000377316.2_Missense_Mutation_p.T525M|MEN1_ENST00000443283.1_Missense_Mutation_p.T585M|MEN1_ENST00000377321.1_Missense_Mutation_p.T545M|MEN1_ENST00000394376.1_Missense_Mutation_p.T585M|MEN1_ENST00000377313.1_Missense_Mutation_p.T585M|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000394374.2_Missense_Mutation_p.T585M|MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000315422.4_Missense_Mutation_p.T580M|MEN1_ENST00000312049.6_Missense_Mutation_p.T580M|MEN1_ENST00000478548.1_5'UTR	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	585					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.T580R(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CGACTGTGCCGTGAGTTGCAG	0.542			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	parathyroid(1)	11											240	215	223					11																	64571900		2201	4297	6498	64328476	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1754C>T	11.37:g.64571900G>A	ENSP00000337088:p.Thr585Met		64328476	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940959	0.73557	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313	D;D;D;D;D;D;D;D;D;D	0.99598	-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26	4.67	4.67	0.58626	.	0.111153	0.64402	D	0.000014	D	0.99477	0.9814	M	0.65975	2.015	0.58432	D	0.999995	D;P;D	0.89917	1.0;0.834;1.0	D;B;D	0.87578	0.996;0.337;0.998	D	0.98272	1.0504	10	0.87932	D	0	-10.9542	15.5063	0.75743	0.0:0.0:1.0:0.0	.	580;545;585	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	M	525;545;580;580;580;585;585;585;585;585	ENSP00000366533:T525M;ENSP00000366538:T545M;ENSP00000366543:T580M;ENSP00000308975:T580M;ENSP00000323747:T580M;ENSP00000337088:T585M;ENSP00000377901:T585M;ENSP00000377899:T585M;ENSP00000396940:T585M;ENSP00000366530:T585M	ENSP00000308975:T580M	T	-	2	0	MEN1	64328476	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	8.325000	0.90007	2.327000	0.79052	0.555000	0.69702	ACG		0.542	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			A	64571900	G	A	64571900	3	1	37	1	0	0	0	0	1	0	0	0	9502	1145	40	1	97	1	MEN1	11	64571900	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	687116	64571900	70434616	112	3195										
MEN1	4221	hgsc.bcm.edu	37	chr11	64574511	64574511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agagggtgagtgggtctggcCggccaggggtgggctccagc	21	9	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64574511C>T	ENST00000337652.1	-	6	1402	c.899G>A	c.(898-900)cGg>cAg	p.R300Q	MEN1_ENST00000377326.3_Missense_Mutation_p.R295Q|MEN1_ENST00000377316.2_Missense_Mutation_p.R295Q|MEN1_ENST00000443283.1_Missense_Mutation_p.R300Q|MEN1_ENST00000377321.1_Missense_Mutation_p.R260Q|MEN1_ENST00000394376.1_Missense_Mutation_p.R300Q|MEN1_ENST00000377313.1_Missense_Mutation_p.R300Q|MEN1_ENST00000394374.2_Missense_Mutation_p.R300Q|MEN1_ENST00000315422.4_Missense_Mutation_p.R295Q|MEN1_ENST00000312049.6_Missense_Mutation_p.R295Q|MEN1_ENST00000478548.1_5'Flank	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	300	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.R295L(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TGGGTCTGGCCGGCCAGGGGT	0.627			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	lung(1)	11											49	55	53					11																	64574511		2201	4297	6498	64331087	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.899G>A	11.37:g.64574511C>T	ENSP00000337088:p.Arg300Gln		64331087	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482561	0.84747	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873	D;D;D;D;D;D;D;D;D;D;D	0.99369	-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78;-5.78	4.24	4.24	0.50183	.	0.072223	0.52532	D	0.000076	D	0.98305	0.9438	L	0.49126	1.545	0.37982	D	0.933627	P;P;P	0.50710	0.923;0.706;0.938	B;B;P	0.47162	0.405;0.124;0.54	D	0.99933	1.1335	10	0.72032	D	0.01	-27.2369	14.501	0.67722	0.0:1.0:0.0:0.0	.	295;260;300	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	Q	295;260;295;295;295;300;300;300;300;300;295	ENSP00000366533:R295Q;ENSP00000366538:R260Q;ENSP00000366543:R295Q;ENSP00000308975:R295Q;ENSP00000323747:R295Q;ENSP00000337088:R300Q;ENSP00000377901:R300Q;ENSP00000377899:R300Q;ENSP00000396940:R300Q;ENSP00000366530:R300Q;ENSP00000413944:R295Q	ENSP00000308975:R295Q	R	-	2	0	MEN1	64331087	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.567000	0.60850	2.080000	0.62538	0.462000	0.41574	CGG		0.627	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			T	64574511	C	T	64574511	3	4	37	1	0	0	0	0	1	0	0	0	9502	652	23	1	968	1	MEN1	11	64574511	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	2611	64574511	70432005	113	3196										
MEN1	4221	hgsc.bcm.edu	37	chr11	64577457	64577457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccagaaaatgctccacgaagCccagcaccaaggaaaggagc	10	13	0	1	rs386134248		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:64577457C>T	ENST00000337652.1	-	2	628	c.125G>A	c.(124-126)gGc>gAc	p.G42D	MEN1_ENST00000377326.3_Missense_Mutation_p.G42D|MEN1_ENST00000377316.2_Missense_Mutation_p.G42D|MEN1_ENST00000443283.1_Missense_Mutation_p.G42D|MEN1_ENST00000377321.1_Missense_Mutation_p.G42D|MEN1_ENST00000394376.1_Missense_Mutation_p.G42D|MEN1_ENST00000377313.1_Missense_Mutation_p.G42D|MEN1_ENST00000394374.2_Missense_Mutation_p.G42D|MEN1_ENST00000315422.4_Missense_Mutation_p.G42D|MEN1_ENST00000312049.6_Missense_Mutation_p.G42D	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	42			G -> D (in MEN1). {ECO:0000269|PubMed:12112656, ECO:0000269|PubMed:9463336}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.E30_F47>D(1)|p.L22_P59del(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CTCCACGAAGCCCAGCACCAA	0.672			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	2	Complex - deletion inframe(1)|Deletion - In frame(1)	parathyroid(2)	11	GRCh37	CM981250	MEN1	M							46	48	47					11																	64577457		2192	4292	6484	64334033	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.125G>A	11.37:g.64577457C>T	ENSP00000337088:p.Gly42Asp		64334033	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857404	0.91433	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626;ENST00000429702;ENST00000424912	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99773	-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72	4.89	3.98	0.46160	.	0.000000	0.85682	D	0.000000	D	0.99603	0.9856	M	0.67397	2.05	0.58432	D	0.999999	D;B;D	0.89917	1.0;0.028;1.0	D;B;D	0.97110	1.0;0.016;1.0	D	0.98091	1.0409	10	0.87932	D	0	-30.7605	11.2371	0.48946	0.0:0.9096:0.0:0.0904	.	42;42;42	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	D	42	ENSP00000366533:G42D;ENSP00000366538:G42D;ENSP00000366543:G42D;ENSP00000308975:G42D;ENSP00000323747:G42D;ENSP00000337088:G42D;ENSP00000377901:G42D;ENSP00000377899:G42D;ENSP00000396940:G42D;ENSP00000366530:G42D;ENSP00000413944:G42D;ENSP00000394933:G42D;ENSP00000411218:G42D;ENSP00000402752:G42D;ENSP00000388016:G42D	ENSP00000308975:G42D	G	-	2	0	MEN1	64334033	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.464000	0.66719	1.191000	0.43056	0.462000	0.41574	GGC		0.672	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			T	64577457	C	T	64577457	3	4	37	1	0	0	0	0	1	0	0	0	9502	739	26	3	1758	3	MEN1	11	64577457	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	2946	64577457	70429059	114	3197										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349195	65349195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggcatgccctcaggaagggaCagaagcccatggagctaggc	15	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:65349195C>T	ENST00000309295.4	+	9	1317	c.1052C>T	c.(1051-1053)aCa>aTa	p.T351I		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	351						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGGAAGGGACAGAAGCCCAT	0.602																																																0			11											22	25	24					11																	65349195		1911	4104	6015	65105771	SO:0001583	missense	254102			AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1052C>T	11.37:g.65349195C>T	ENSP00000312671:p.Thr351Ile		65105771	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501541	0.26861	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.81163	-0.23;-1.46	4.13	-0.573	0.11742	.	0.813010	0.10520	N	0.665133	T	0.78052	0.4223	L	0.36672	1.1	0.34121	D	0.664121	D	0.65815	0.995	P	0.56278	0.795	T	0.77778	-0.2460	10	0.87932	D	0	.	5.253	0.15532	0.0:0.4692:0.3132:0.2176	.	351	Q8N3D4	EH1L1_HUMAN	I	351	ENSP00000312671:T351I;ENSP00000431996:T351I	ENSP00000312671:T351I	T	+	2	0	EHBP1L1	65105771	0.151000	0.22747	0.976000	0.42696	0.238000	0.25445	0.494000	0.22467	0.301000	0.22738	-0.367000	0.07326	ACA		0.602	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		T	65349195	C	T	65349195	3	4	37	1	0	0	0	0	1	0	0	0	4987	478	17	3	1086	3	EHBP1L1	11	65349195	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	771738	65349195	69657321	115	3198										
TYR	7299	hgsc.bcm.edu	37	chr11	88924500	88924500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaggctcccctcttcagctgAtgtagaattttgcctgagtt	9	10	2	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:88924500A>G	ENST00000263321.5	+	2	1452	c.950A>G	c.(949-951)gAt>gGt	p.D317G	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	317					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.D317A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	TCTTCAGCTGATGTAGAATTT	0.448																																																1	Substitution - Missense(1)	ovary(1)	11											120	117	118					11																	88924500		2201	4299	6500	88564148	SO:0001583	missense	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.950A>G	11.37:g.88924500A>G	ENSP00000263321:p.Asp317Gly		88564148	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.635987	0.87760	.	.	ENSG00000077498	ENST00000263321	D	0.97480	-4.4	5.59	5.59	0.84812	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.197051	0.52532	D	0.000062	D	0.98485	0.9495	M	0.91249	3.19	0.58432	D	0.999999	D	0.56746	0.977	P	0.59703	0.862	D	0.99327	1.0908	9	.	.	.	.	15.7688	0.78149	1.0:0.0:0.0:0.0	.	317	P14679	TYRO_HUMAN	G	317	ENSP00000263321:D317G	.	D	+	2	0	TYR	88564148	1.000000	0.71417	0.969000	0.41365	0.970000	0.65996	8.771000	0.91751	2.134000	0.65973	0.533000	0.62120	GAT		0.448	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		G	88924500	A	G	88924500	3	3	37	1	0	0	0	0	1	0	0	0	16853	333	12	4	956	4	TYR	11	88924500	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	23575305	88924500	46082016	116	3199										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100179135	100179135	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcaaggcgacaagtgtgtctGtgtcagagattcttgttgca	12	7	4	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:100179135G>T	ENST00000524871.1	+	21	2955	c.2665G>T	c.(2665-2667)Gtg>Ttg	p.V889L	CNTN5_ENST00000418526.2_Missense_Mutation_p.V815L|CNTN5_ENST00000527185.1_Missense_Mutation_p.V889L|CNTN5_ENST00000528682.1_Missense_Mutation_p.V889L|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000279463.3_Missense_Mutation_p.V889L	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	889	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		AAGTGTGTCTGTGTCAGAGAT	0.383																																																0			11											77	76	76					11																	100179135		1883	4115	5998	99684345	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.2665G>T	11.37:g.100179135G>T	ENSP00000435637:p.Val889Leu		99684345	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960201	0.53400	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.56611	2.33;0.45;0.45;0.45;0.45	5.69	0.605	0.17553	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.446700	0.26251	N	0.025450	T	0.34395	0.0896	N	0.17082	0.46	0.33590	D	0.601012	B;B	0.30146	0.228;0.27	B;B	0.31812	0.058;0.136	T	0.40924	-0.9537	10	0.66056	D	0.02	.	9.9907	0.41870	0.331:0.0:0.669:0.0	.	815;889	O94779-2;O94779	.;CNTN5_HUMAN	L	889;889;889;815;889	ENSP00000433575:V889L;ENSP00000436185:V889L;ENSP00000435637:V889L;ENSP00000393229:V815L;ENSP00000279463:V889L	ENSP00000279463:V889L	V	+	1	0	CNTN5	99684345	1.000000	0.71417	0.987000	0.45799	0.994000	0.84299	1.557000	0.36299	-0.058000	0.13177	0.591000	0.81541	GTG		0.383	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	100179135	G	T	100179135	3	4	37	1	0	0	0	0	1	0	0	0	3650	1377	48	2	2739	2	CNTN5	11	100179135	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	11254635	100179135	34827381	117	3200										
ATM	472	hgsc.bcm.edu	37	chr11	108117712	108117712	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgcttatgaatcaacaaaatGgagaagtattttatacaact	6	5	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr11:108117712G>A	ENST00000452508.2	+	9	1112	c.923G>A	c.(922-924)tGg>tAg	p.W308*	ATM_ENST00000278616.4_Nonsense_Mutation_p.W308*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	308					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.W308*(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCAACAAAATGGAGAAGTATT	0.313			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	11											44	47	46					11																	108117712		2200	4294	6494	107622922	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.923G>A	11.37:g.108117712G>A	ENSP00000388058:p.Trp308*		107622922	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	40	8.432389	0.98808	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4005	0.94627	0.0:0.0:1.0:0.0	.	.	.	.	X	308	.	ENSP00000278616:W308X	W	+	2	0	ATM	107622922	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.254000	0.95512	2.591000	0.87537	0.655000	0.94253	TGG		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108117712	G	A	108117712	4	1	37	1	0	0	0	0	0	1	0	0	1110	1357	47	3	949	3	ATM	11	108117712	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	7938577	108117712	26888804	118	3201										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2788865	2788865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtcgcctccctcgccccgccGgctaccccagcacggtcagc	10	22	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:2788865G>A	ENST00000347598.4	+	44	5491	c.5491G>A	c.(5491-5493)Ggc>Agc	p.G1831S	CACNA1C_ENST00000399644.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G1800S|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G1803S|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G1783S|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G1811S|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G1789S|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399641.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G1791S|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G1783S|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G1808S|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G1802S|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G1802S|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G1824S|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G1783S|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G1802S|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G1791S	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1831					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCGCCCCGCCGGCTACCCCAG	0.677																																																0			12											41	49	46					12																	2788865		2054	4198	6252	2659126	SO:0001583	missense	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5491G>A	12.37:g.2788865G>A	ENSP00000266376:p.Gly1831Ser		2659126	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	5.139	0.211285	0.09757	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95949	-3.8;-3.79;-3.79;-3.8;-3.79;-3.81;-3.7;-3.75;-3.79;-3.73;-3.72;-3.79;-3.85;-3.72;-3.63;-3.85;-3.8;-3.79;-3.78;-3.73;-3.78;-3.86	5.06	3.19	0.36642	.	2.241760	0.01598	N	0.021892	D	0.92051	0.7481	L	0.41573	1.285	0.26335	N	0.977457	B;P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.50710	0.003;0.938;0.0;0.004;0.005;0.004;0.003;0.008;0.001;0.003;0.004;0.0;0.003;0.012;0.001;0.003;0.003;0.001;0.004;0.003;0.001;0.004;0.004;0.0;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.43225	0.002;0.412;0.001;0.003;0.01;0.005;0.002;0.01;0.001;0.002;0.006;0.001;0.003;0.01;0.001;0.004;0.003;0.005;0.006;0.004;0.001;0.007;0.007;0.001;0.002	T	0.82649	-0.0353	10	0.15952	T	0.53	.	3.0471	0.06157	0.1067:0.3219:0.4061:0.1652	.	474;1824;1780;1831;1783;1802;1783;1800;1811;1783;1803;1783;1743;1831;1783;1783;1783;1791;1789;1791;1772;1802;1802;1783;1783	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	1808;1783;1783;1811;1783;1802;1802;1791;1783;1831;1803;1783;1824;1800;1783;1789;1802;1783;1783;1783;1783;1791;1613	ENSP00000336982:G1808S;ENSP00000382563:G1783S;ENSP00000382552:G1783S;ENSP00000382547:G1811S;ENSP00000382506:G1783S;ENSP00000382530:G1802S;ENSP00000382546:G1802S;ENSP00000382500:G1791S;ENSP00000382549:G1783S;ENSP00000266376:G1831S;ENSP00000382515:G1803S;ENSP00000382510:G1783S;ENSP00000341092:G1824S;ENSP00000382537:G1800S;ENSP00000329877:G1783S;ENSP00000382557:G1789S;ENSP00000385724:G1802S;ENSP00000382512:G1783S;ENSP00000382542:G1783S;ENSP00000382526:G1783S;ENSP00000385896:G1783S;ENSP00000382504:G1791S	ENSP00000323129:G1613S	G	+	1	0	CACNA1C	2659126	0.981000	0.34729	0.048000	0.18961	0.022000	0.10575	2.143000	0.42187	0.506000	0.28125	0.305000	0.20034	GGC		0.677	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2788865	G	A	2788865	3	1	37	1	0	0	0	0	1	0	0	0	2546	1116	39	1	5896	1	CACNA1C	12	2788865	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		2788865	131063030	119	3202										
ENO2	2026	hgsc.bcm.edu	37	chr12	7028820	7028820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgctgcctcagagttttatcGtgatggcaaatatgacttgg	11	7	1	3	rs151259229		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:7028820G>A	ENST00000535366.1	+	7	1384	c.758G>A	c.(757-759)cGt>cAt	p.R253H	ENO2_ENST00000541477.1_Missense_Mutation_p.R253H|ENO2_ENST00000229277.1_Missense_Mutation_p.R253H|ENO2_ENST00000538763.1_Missense_Mutation_p.R210H|ENO2_ENST00000544774.1_Missense_Mutation_p.R210H|ENO2_ENST00000545045.2_Missense_Mutation_p.R134H			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	253					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GAGTTTTATCGTGATGGCAAA	0.527													g|||	1	0.000199681	8e-04	0	5008	,	,		-128	0		0	False		,,,				2504	0															0			12							HIS/ARG	0,4406		0,0,2203	168	134	145		758	5.2	1	12	dbSNP_134	145	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ENO2	NM_001975.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	253/435	7028820	1,13005	2203	4300	6503	6899081	SO:0001583	missense	2026			M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.758G>A	12.37:g.7028820G>A	ENSP00000437402:p.Arg253His		6899081	B7Z2X9|Q96J33	Missense_Mutation	SNP	ENST00000535366.1	37	CCDS8570.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	18.57	3.652762	0.67472	0.0	1.16E-4	ENSG00000111674	ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000535366;ENST00000545045	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	5.23	5.23	0.72850	Enolase, C-terminal (1);	0.152089	0.64402	D	0.000010	T	0.31199	0.0789	M	0.73319	2.225	0.80722	D	1	B;B	0.23128	0.08;0.031	B;B	0.27715	0.082;0.013	T	0.13548	-1.0505	10	0.72032	D	0.01	-9.7732	18.8056	0.92035	0.0:0.0:1.0:0.0	.	210;253	B7Z2X9;P09104	.;ENOG_HUMAN	H	253;253;210;210;253;134	ENSP00000438873:R253H;ENSP00000229277:R253H;ENSP00000441490:R210H;ENSP00000446195:R210H;ENSP00000437402:R253H;ENSP00000438062:R134H	ENSP00000229277:R253H	R	+	2	0	ENO2	6899081	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	3.953000	0.56699	2.447000	0.82792	0.543000	0.68304	CGT		0.527	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1			A	7028820	G	A	7028820	3	1	37	1	0	0	0	0	1	0	0	0	5135	1145	40	1	784	1	ENO2	12	7028820	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4239955	7028820	126823075	120	3203										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	37	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	18369464	25398284	108453611	121	3204										
HOXC8	3224	hgsc.bcm.edu	37	chr12	54404943	54404943	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gaactagaaaaggagtttctCtttaatccttatttgacacg	7	7	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:54404943C>G	ENST00000040584.4	+	2	744	c.507C>G	c.(505-507)ctC>ctG	p.L169L	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	169					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						AGGAGTTTCTCTTTAATCCTT	0.498																																					GBM(197;701 2226 7002 18822 41696)											0			12											88	84	85					12																	54404943		2203	4300	6503	52691210	SO:0001819	synonymous_variant	3224			X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.507C>G	12.37:g.54404943C>G			52691210	A8K4J4|O15221|O15362	Silent	SNP	ENST00000040584.4	37	CCDS8870.1																																																																																				0.498	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			G	54404943	C	G	54404943	2	3	37	1	0	0	0	0	0	0	0	1	7337	900	32	5		5	HOXC8	12	54404943	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	29006659	54404943	79446952	122	3205										
YEATS4	8089	hgsc.bcm.edu	37	chr12	69753758	69753758	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cttccgtgggacaatatgttCaagagaatggccgaatttgg	12	7	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:69753758C>G	ENST00000247843.2	+	1	276	c.6C>G	c.(4-6)ttC>ttG	p.F2L	YEATS4_ENST00000548020.1_Missense_Mutation_p.F2L	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4	2					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			ACAATATGTTCAAGAGAATGG	0.687																																																0			12											29	33	32					12																	69753758		2203	4300	6503	68040025	SO:0001583	missense	8089			AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.6C>G	12.37:g.69753758C>G	ENSP00000247843:p.Phe2Leu		68040025	Q9NQD0	Missense_Mutation	SNP	ENST00000247843.2	37	CCDS8990.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574102	0.86542	.	.	ENSG00000127337	ENST00000247843;ENST00000548020;ENST00000552955	.	.	.	5.31	5.31	0.75309	.	0.044747	0.85682	D	0.000000	T	0.39226	0.1070	N	0.08118	0	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.21895	-1.0232	8	.	.	.	-6.3934	19.1698	0.93572	0.0:1.0:0.0:0.0	.	2	O95619	YETS4_HUMAN	L	2	.	.	F	+	3	2	YEATS4	68040025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.965000	0.49200	2.761000	0.94854	0.563000	0.77884	TTC		0.687	YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530		G	69753758	C	G	69753758	3	3	37	1	0	0	0	0	1	0	0	0	17513	825	29	5	8	5	YEATS4	12	69753758	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	15348815	69753758	64098137	123	3206										
BEST3	144453	hgsc.bcm.edu	37	chr12	70091550	70091550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atccaaaaaaagttgcatttGctactttactggagtaagtg	8	6	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:70091550G>A	ENST00000330891.5	-	2	255	c.29C>T	c.(28-30)gCa>gTa	p.A10V	BEST3_ENST00000331471.4_Missense_Mutation_p.A10V|BEST3_ENST00000533674.1_Intron|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000266661.4_Intron|BEST3_ENST00000553096.1_Intron|BEST3_ENST00000551160.1_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	10					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			AGTTGCATTTGCTACTTTACT	0.343																																																0			12											110	107	108					12																	70091550		1828	4089	5917	68377817	SO:0001583	missense	144453			AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.29C>T	12.37:g.70091550G>A	ENSP00000332413:p.Ala10Val		68377817	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	G	35	5.495272	0.96355	.	.	ENSG00000127325	ENST00000331471;ENST00000330891;ENST00000548658	D;D;D	0.98732	-5.1;-5.1;-5.1	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.99447	0.9804	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.982	D	0.98604	1.0660	10	0.87932	D	0	-18.1199	20.1535	0.98095	0.0:0.0:1.0:0.0	.	10;10	Q8N1M1;Q8N1M1-1	BEST3_HUMAN;.	V	10	ENSP00000329064:A10V;ENSP00000332413:A10V;ENSP00000446575:A10V	ENSP00000332413:A10V	A	-	2	0	BEST3	68377817	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.764000	0.94973	0.650000	0.86243	GCA		0.343	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		A	70091550	G	A	70091550	3	1	37	1	0	0	0	0	1	0	0	0	1407	1319	46	3	2013	3	BEST3	12	70091550	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	337792	70091550	63760345	124	3207										
ATP2B1	490	hgsc.bcm.edu	37	chr12	89997555	89997555	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	acccaaaatattcttcatcaTtgtacgtgagatgagaggct	8	8	3	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:89997555T>C	ENST00000428670.3	-	17	3238	c.2782A>G	c.(2782-2784)Atg>Gtg	p.M928V	ATP2B1_ENST00000359142.3_Missense_Mutation_p.M928V|ATP2B1_ENST00000393164.2_Missense_Mutation_p.M671V|ATP2B1_ENST00000348959.3_Missense_Mutation_p.M928V|ATP2B1_ENST00000261173.2_Missense_Mutation_p.M928V			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	928					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TTCTTCATCATTGTACGTGAG	0.413																																																0			12											132	122	126					12																	89997555		2203	4300	6503	88521686	SO:0001583	missense	490			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.2782A>G	12.37:g.89997555T>C	ENSP00000392043:p.Met928Val		88521686	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395123	0.83011	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.98185	0.9400	M	0.88512	2.96	0.80722	D	1	P;D;D	0.69078	0.917;0.968;0.997	D;P;D	0.64042	0.915;0.8;0.921	D	0.99129	1.0852	10	0.87932	D	0	-27.3567	16.3634	0.83296	0.0:0.0:0.0:1.0	.	928;928;928	P20020-3;P20020-2;P20020-6	.;.;.	V	928;928;928;928;671	ENSP00000261173:M928V;ENSP00000343599:M928V;ENSP00000352054:M928V;ENSP00000392043:M928V;ENSP00000376869:M671V	ENSP00000261173:M928V	M	-	1	0	ATP2B1	88521686	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.997000	0.88414	2.324000	0.78689	0.533000	0.62120	ATG		0.413	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	89997555	T	C	89997555	3	2	37	1	0	0	0	0	1	0	0	0	1140	1493	52	4	1058	4	ATP2B1	12	89997555	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	19906005	89997555	43854340	125	3208										
LUM	4060	hgsc.bcm.edu	37	chr12	91502182	91502182	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtctggctatctgattgaagCtcaagtcaaggtattcgagt	11	7	4	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:91502182C>G	ENST00000266718.4	-	2	1029	c.575G>C	c.(574-576)aGc>aCc	p.S192T	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	192					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						CTGATTGAAGCTCAAGTCAAG	0.433																																																0			12											138	134	135					12																	91502182		2203	4300	6503	90026313	SO:0001583	missense	4060			BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.575G>C	12.37:g.91502182C>G	ENSP00000266718:p.Ser192Thr		90026313	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	37	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735252	0.69189	.	.	ENSG00000139329	ENST00000266718	T	0.61627	0.09	5.6	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.68595	0.3018	L	0.60012	1.86	0.58432	D	0.999997	D	0.54601	0.967	P	0.58391	0.838	T	0.69636	-0.5092	10	0.45353	T	0.12	-10.3664	15.6021	0.76634	0.1386:0.8614:0.0:0.0	.	192	P51884	LUM_HUMAN	T	192	ENSP00000266718:S192T	ENSP00000266718:S192T	S	-	2	0	LUM	90026313	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.487000	0.81328	1.311000	0.45024	0.557000	0.71058	AGC		0.433	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		G	91502182	C	G	91502182	3	3	37	1	0	0	0	0	1	0	0	0	9114	797	28	5	449	5	LUM	12	91502182	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1504627	91502182	42349713	126	3209										
CHST11	50515	hgsc.bcm.edu	37	chr12	105151178	105151178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cggcaccaagatcatcaaacGccagcggaagaacgccaccc	9	16	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:105151178G>A	ENST00000303694.5	+	3	1095	c.656G>A	c.(655-657)cGc>cAc	p.R219H	CHST11_ENST00000549260.1_Missense_Mutation_p.R214H	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	219					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						ATCATCAAACGCCAGCGGAAG	0.582																																																0			12											121	104	110					12																	105151178		2203	4300	6503	103675308	SO:0001583	missense	50515			AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"Sulfotransferases, membrane-bound"	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.656G>A	12.37:g.105151178G>A	ENSP00000305725:p.Arg219His		103675308	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	37	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976433	0.92982	.	.	ENSG00000171310	ENST00000549260;ENST00000303694	T;T	0.75154	-0.91;-0.91	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.86698	0.5995	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.977;0.995	D	0.86448	0.1771	10	0.46703	T	0.11	-29.1637	19.2155	0.93776	0.0:0.0:1.0:0.0	.	214;219	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	H	214;219	ENSP00000450004:R214H;ENSP00000305725:R219H	ENSP00000305725:R219H	R	+	2	0	CHST11	103675308	1.000000	0.71417	0.956000	0.39512	0.978000	0.69477	8.004000	0.88535	2.553000	0.86117	0.655000	0.94253	CGC		0.582	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		A	105151178	G	A	105151178	3	1	37	1	0	0	0	0	1	0	0	0	3405	1087	38	1	666	1	CHST11	12	105151178	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	13648996	105151178	28700717	127	3210										
CORO1C	23603	hgsc.bcm.edu	37	chr12	109046145	109046145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gaatgtgttgaggtagtggaCgtacggggattcatccgtga	16	5	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr12:109046145C>T	ENST00000261401.3	-	8	1076	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	CORO1C_ENST00000549384.1_Intron|CORO1C_ENST00000420959.2_Missense_Mutation_p.V355I|CORO1C_ENST00000549772.1_Missense_Mutation_p.V308I|CORO1C_ENST00000421578.2_Missense_Mutation_p.V197I|CORO1C_ENST00000541050.1_Missense_Mutation_p.V302I	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	302					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						AGGTAGTGGACGTACGGGGAT	0.468																																																0			12											201	178	186					12																	109046145		2203	4300	6503	107570274	SO:0001583	missense	23603			BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"Coronins", "WD repeat domain containing"	2254	protein-coding gene	gene with protein product		605269	"coronin, actin-binding protein, 1C"			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.904G>A	12.37:g.109046145C>T	ENSP00000261401:p.Val302Ile		107570274	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Missense_Mutation	SNP	ENST00000261401.3	37	CCDS9120.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641882	0.67244	.	.	ENSG00000110880	ENST00000261401;ENST00000541050;ENST00000421578;ENST00000549772;ENST00000420959	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);Domain of unknown function DUF1900 (1);	0.228765	0.43747	D	0.000540	T	0.29389	0.0732	L	0.31065	0.9	0.80722	D	1	B;B;B	0.24483	0.052;0.104;0.052	B;B;B	0.29716	0.047;0.106;0.032	T	0.03453	-1.1035	10	0.30078	T	0.28	-17.0323	20.0716	0.97726	0.0:1.0:0.0:0.0	.	265;355;302	B4DMH3;A7MAP1;Q9ULV4	.;.;COR1C_HUMAN	I	302;302;197;308;355	ENSP00000261401:V302I;ENSP00000438341:V302I;ENSP00000415554:V197I;ENSP00000447534:V308I;ENSP00000394496:V355I	ENSP00000261401:V302I	V	-	1	0	CORO1C	107570274	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	6.042000	0.70996	2.741000	0.93983	0.585000	0.79938	GTC		0.468	CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325		T	109046145	C	T	109046145	3	4	37	1	0	0	0	0	1	0	0	0	3761	536	19	1	536	1	CORO1C	12	109046145	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	3894967	109046145	24805750	128	3211										
LRCH1	23143	hgsc.bcm.edu	37	chr13	47260086	47260086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tttgacttttcctgcaacaaAgtgctcgtgattccaatttg	7	9	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:47260086A>G	ENST00000389798.3	+	5	929	c.732A>G	c.(730-732)aaA>aaG	p.K244K	LRCH1_ENST00000389797.3_Silent_p.K244K|LRCH1_ENST00000311191.6_Silent_p.K244K	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	244										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CCTGCAACAAAGTGCTCGTGA	0.368																																																0			13											61	56	58					13																	47260086		2203	4300	6503	46158087	SO:0001819	synonymous_variant	23143			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.732A>G	13.37:g.47260086A>G			46158087	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Silent	SNP	ENST00000389798.3	37	CCDS31972.1																																																																																				0.368	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		G	47260086	A	G	47260086	2	3	37	1	0	0	0	0	0	0	0	1	8961	69	3	4		4	LRCH1	13	47260086	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10		47260086	67909792	129	3212										
HTR2A	3356	hgsc.bcm.edu	37	chr13	47466659	47466659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agaggtgcatgatggaggccGtggagaagagcacgtccagg	18	7	0	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:47466659G>A	ENST00000378688.4	-	2	610	c.479C>T	c.(478-480)aCg>aTg	p.T160M	HTR2A_ENST00000543956.1_Missense_Mutation_p.T76M|HTR2A_ENST00000542664.1_Missense_Mutation_p.T160M			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	160	Agonist binding. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GATGGAGGCCGTGGAGAAGAG	0.572																																																0			13											187	178	181					13																	47466659		2203	4300	6503	46364660	SO:0001583	missense	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.479C>T	13.37:g.47466659G>A	ENSP00000367959:p.Thr160Met		46364660	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	G	34	5.291601	0.95546	.	.	ENSG00000102468	ENST00000378688;ENST00000543956;ENST00000542664	T;T;T	0.74421	2.43;-0.84;2.43	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.91925	0.7443	H	0.97240	3.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93711	0.7024	10	0.87932	D	0	.	19.848	0.96722	0.0:0.0:1.0:0.0	.	76;160	F5GWE8;P28223	.;5HT2A_HUMAN	M	160;76;160	ENSP00000367959:T160M;ENSP00000441861:T76M;ENSP00000437737:T160M	ENSP00000367959:T160M	T	-	2	0	HTR2A	46364660	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.860000	0.99555	2.937000	0.99478	0.650000	0.86243	ACG		0.572	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		A	47466659	G	A	47466659	3	1	37	1	0	0	0	0	1	0	0	0	7462	1145	40	1	944	1	HTR2A	13	47466659	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	206573	47466659	67703219	130	3213										
RB1	5925	hgsc.bcm.edu	37	chr13	49027203	49027203	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gatcaccttgaatctgcttgTcctcttaatcttcctctcca	4	14	5	1	rs145310579	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:49027203T>C	ENST00000267163.4	+	18	1908	c.1770T>C	c.(1768-1770)tgT>tgC	p.C590C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	590	Pocket; binds T and E1A.|Spacer.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.C590C(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AATCTGCTTGTCCTCTTAATC	0.328		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			T|||	2	0.000399361	0	0.0014	5008	,	,		19059	0		0.001	False		,,,				2504	0					yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	26	Whole gene deletion(15)|Unknown(10)|Substitution - coding silent(1)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13						T		0,4406		0,0,2203	121	113	116		1770	3.4	1	13	dbSNP_134	116	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	RB1	NM_000321.2		0,3,6500	CC,CT,TT		0.0349,0.0,0.0231		590/929	49027203	3,13003	2203	4300	6503	47925204	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1770T>C	13.37:g.49027203T>C			47925204	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.328	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	49027203	T	C	49027203	2	2	37	1	0	0	0	0	0	0	0	1	13135	1673	58	4		4	RB1	13	49027203	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	1560544	49027203	66142675	131	3214										
KPNA3	3839	hgsc.bcm.edu	37	chr13	50307151	50307151	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tttcttcttggggaacatttCtctttttcaataagtgttca	6	7	5	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:50307151C>G	ENST00000261667.3	-	3	560	c.146G>C	c.(145-147)aGa>aCa	p.R49T		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	49	IBB. {ECO:0000255|PROSITE- ProRule:PRU00561}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		GGGAACATTTCTCTTTTTCAA	0.284																																																0			13											122	123	122					13																	50307151		2202	4295	6497	49205152	SO:0001583	missense	3839			D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"Importins", "Armadillo repeat containing"	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.146G>C	13.37:g.50307151C>G	ENSP00000261667:p.Arg49Thr		49205152	O00191|O43195|Q5JVM9|Q96AA7	Missense_Mutation	SNP	ENST00000261667.3	37	CCDS9421.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354162	0.82243	.	.	ENSG00000102753	ENST00000261667	T	0.78126	-1.15	5.77	5.77	0.91146	Importin-alpha, importin-beta-binding domain (2);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93135	0.6536	10	0.87932	D	0	-12.7609	19.9795	0.97321	0.0:1.0:0.0:0.0	.	49	O00505	IMA3_HUMAN	T	49	ENSP00000261667:R49T	ENSP00000261667:R49T	R	-	2	0	KPNA3	49205152	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.738000	0.68613	2.720000	0.93068	0.650000	0.86243	AGA		0.284	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267		G	50307151	C	G	50307151	3	3	37	1	0	0	0	0	1	0	0	0	8452	913	32	5	1479	5	KPNA3	13	50307151	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1279948	50307151	64862727	132	3215										
CARKD	55739	hgsc.bcm.edu	37	chr13	111277575	111277575	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtgttctgtgccagtgcggcCgcacctgtgattaaggccta	13	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr13:111277575C>T	ENST00000309957.2	+	4	350	c.336C>T	c.(334-336)gcC>gcT	p.A112A	CARKD_ENST00000470164.2_Intron|CARKD_ENST00000397191.4_Intron|CARKD_ENST00000458711.2_Intron|CARKD_ENST00000424185.2_Intron	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						CCAGTGCGGCCGCACCTGTGA	0.627																																																0			13											83	69	74					13																	111277575		2203	4300	6503	110075576	SO:0001819	synonymous_variant	55739			AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.336C>T	13.37:g.111277575C>T			110075576		Silent	SNP	ENST00000309957.2	37	CCDS9513.1																																																																																				0.627	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210		T	111277575	C	T	111277575	2	4	37	1	0	0	0	0	0	0	0	1	2660	639	23	1		1	CARKD	13	111277575	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	60970424	111277575	3892303	133	3216										
OR4K5	79317	hgsc.bcm.edu	37	chr14	20389054	20389054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agaccatatctttcagtggcTgcatagcccaaattttcttt	6	10	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:20389054T>C	ENST00000315915.4	+	1	314	c.289T>C	c.(289-291)Tgc>Cgc	p.C97R		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCAGTGGCTGCATAGCCCA	0.428																																																0			14											251	268	263					14																	20389054		2203	4299	6502	19458894	SO:0001583	missense	79317			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"GPCR / Class A : Olfactory receptors"	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.289T>C	14.37:g.20389054T>C	ENSP00000319511:p.Cys97Arg		19458894	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	19.61	3.859049	0.71834	.	.	ENSG00000176281	ENST00000315915	T	0.00545	6.67	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000036	T	0.04363	0.0120	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00420	-1.1750	10	0.87932	D	0	.	11.614	0.51078	0.0:0.0:0.0:1.0	.	97	Q8NGD3	OR4K5_HUMAN	R	97	ENSP00000319511:C97R	ENSP00000319511:C97R	C	+	1	0	OR4K5	19458894	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.152000	0.77419	1.838000	0.53458	0.533000	0.62120	TGC		0.428	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483		C	20389054	T	C	20389054	3	2	37	1	0	0	0	0	1	0	0	0	11104	1580	55	4	291	4	OR4K5	14	20389054	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10		20389054	86960486	134	3217										
CHD8	57680	hgsc.bcm.edu	37	chr14	21870224	21870224	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aacttggagccttcatcatcTtcctccatgatggctgcata	7	12	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:21870224T>C	ENST00000557364.1	-	20	4217	c.3954A>G	c.(3952-3954)gaA>gaG	p.E1318E	CHD8_ENST00000430710.3_Silent_p.E1039E|CHD8_ENST00000399982.2_Silent_p.E1318E|CHD8_ENST00000555962.1_5'UTR			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1318					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTTCATCATCTTCCTCCATGA	0.388																																																0			14											142	135	137					14																	21870224		2027	4222	6249	20940064	SO:0001819	synonymous_variant	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.3954A>G	14.37:g.21870224T>C			20940064	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	T	6.292	0.422062	0.11928	.	.	ENSG00000100888	ENST00000555935	.	.	.	6.17	5.03	0.67393	.	.	.	.	.	T	0.60183	0.2249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57694	-0.7767	4	.	.	.	-22.9691	9.2637	0.37627	0.0:0.1448:0.0:0.8552	.	.	.	.	G	544	.	.	R	-	1	2	CHD8	20940064	0.995000	0.38212	1.000000	0.80357	0.999000	0.98932	0.377000	0.20552	1.148000	0.42385	0.533000	0.62120	AGA		0.388	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		C	21870224	T	C	21870224	2	2	37	1	0	0	0	0	0	0	0	1	3337	1606	56	4		4	CHD8	14	21870224	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	1481170	21870224	85479316	135	3218										
SLC35F4	341880	hgsc.bcm.edu	37	chr14	58056021	58056021	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaaacataatgttccagtttGttgaaaaccaagtcatgaaa	6	6	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:58056021G>A	ENST00000339762.6	-	3	607	c.608C>T	c.(607-609)aCa>aTa	p.T203I	SLC35F4_ENST00000556826.1_Missense_Mutation_p.T167I|SLC35F4_ENST00000554729.1_Missense_Mutation_p.T44I			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	203					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GTTCCAGTTTGTTGAAAACCA	0.343																																																0			14											99	99	99					14																	58056021		1845	4089	5934	57125774	SO:0001583	missense	341880					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"Solute carriers"	19845	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 36"	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.608C>T	14.37:g.58056021G>A	ENSP00000342518:p.Thr203Ile		57125774	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		.	.	.	.	.	.	.	.	.	.	G	21.0	4.087633	0.76642	.	.	ENSG00000151812	ENST00000556826;ENST00000339762;ENST00000554729	T;T;T	0.54479	0.62;0.57;0.69	5.92	5.92	0.95590	.	0.041863	0.85682	D	0.000000	T	0.73822	0.3636	M	0.74647	2.275	0.80722	D	1	D	0.69078	0.997	D	0.69479	0.964	T	0.73927	-0.3828	10	0.59425	D	0.04	-14.8536	20.3167	0.98654	0.0:0.0:1.0:0.0	.	203	A4IF30	S35F4_HUMAN	I	167;203;44	ENSP00000452086:T167I;ENSP00000342518:T203I;ENSP00000451990:T44I	ENSP00000342518:T203I	T	-	2	0	SLC35F4	57125774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.058000	0.76676	2.809000	0.96659	0.557000	0.71058	ACA		0.343	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260		A	58056021	G	A	58056021	3	1	37	1	0	0	0	0	1	0	0	0	14628	1377	48	3	981	3	SLC35F4	14	58056021	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	36185797	58056021	49293519	136	3219										
GPHN	10243	hgsc.bcm.edu	37	chr14	67525469	67525470	+	Frame_Shift_Ins	INS	-	-	C													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcacagtcctggagatgactINSccggtgcttgggacagaaat							TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:67525469_67525470insC	ENST00000315266.5	+	10	2132_2133	c.1011_1012insC	c.(1012-1014)ccgfs	p.P338fs	GPHN_ENST00000459628.1_Frame_Shift_Ins_p.P353fs|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000543237.1_Frame_Shift_Ins_p.P384fs|GPHN_ENST00000478722.1_Frame_Shift_Ins_p.P371fs|GPHN_ENST00000305960.9_Frame_Shift_Ins_p.P307fs	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	338	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		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)		TGGAGATGACTCCGGTGCTTGG	0.406			T	MLL	AL																																		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	0			14																																								66595223	SO:0001589	frameshift_variant	10243			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1013dupC	14.37:g.67525471_67525471dupC	ENSP00000312771:p.Pro338fs		66595222	Q9H4E9|Q9P2G2	Frame_Shift_Ins	INS	ENST00000315266.5	37	CCDS32103.1																																																																																				0.406	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67525470	-	C	67525469	7	5	37	1	0	1	1	0	0	0	0	0	6630	1538	54	0	1152	0	GPHN	14	67525469	Frame_Shift_Ins	INS	-	TCGA-AG-3731-01A-11D-1733-10	9469448	67525469	39824071	137	3220										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68268904	68268904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctggtgtgagtttacacagaGggcatagatggcatacttca	12	7	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:68268904G>A	ENST00000347230.4	-	10	1669	c.1531C>T	c.(1531-1533)Ctc>Ttc	p.L511F	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.L511F	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	511					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TTTACACAGAGGGCATAGATG	0.547																																																0			14											143	128	133					14																	68268904		2203	4300	6503	67338657	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.1531C>T	14.37:g.68268904G>A	ENSP00000251119:p.Leu511Phe		67338657	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791400	0.70452	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.36699	1.4;1.24	5.83	4.93	0.64822	.	0.230823	0.35646	N	0.003061	T	0.48840	0.1522	L	0.60455	1.87	0.43919	D	0.996563	D;D;D	0.63046	0.973;0.992;0.986	P;P;P	0.60068	0.811;0.868;0.741	T	0.45323	-0.9269	10	0.42905	T	0.14	-9.9359	9.6924	0.40136	0.0696:0.0:0.7883:0.142	.	511;511;511	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	F	511;490;511	ENSP00000251119:L511F;ENSP00000450603:L511F	ENSP00000251119:L511F	L	-	1	0	ZFYVE26	67338657	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.505000	0.53356	1.447000	0.47661	-0.182000	0.12963	CTC		0.547	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68268904	G	A	68268904	3	1	37	1	0	0	0	0	1	0	0	0	17707	1000	35	3	6220	3	ZFYVE26	14	68268904	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	743435	68268904	39080636	138	3221										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70989383	70989383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agcaaccaaaggaagaaggcAcaatagtgacaggtaacgca	11	8	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:70989383A>G	ENST00000256389.3	-	2	2486	c.2242T>C	c.(2242-2244)Tgc>Cgc	p.C748R	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	698					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		GGAAGAAGGCACAATAGTGAC	0.393																																																0			14											225	188	201					14																	70989383		2203	4300	6503	70059136	SO:0001583	missense	8748			AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2242T>C	14.37:g.70989383A>G	ENSP00000256389:p.Cys748Arg		70059136	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	A	8.748	0.920573	0.17982	.	.	ENSG00000134007	ENST00000256389	T	0.00912	5.55	3.66	3.66	0.41972	.	3.514400	0.01092	U	0.005201	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	0.999994	P	0.36144	0.539	B	0.22880	0.042	T	0.44267	-0.9339	10	0.23891	T	0.37	.	6.584	0.22610	0.7863:0.0:0.0:0.2137	.	698	O43506	ADA20_HUMAN	R	748	ENSP00000256389:C748R	ENSP00000256389:C748R	C	-	1	0	ADAM20	70059136	0.014000	0.17966	0.032000	0.17829	0.066000	0.16364	1.280000	0.33202	1.441000	0.47550	0.477000	0.44152	TGC		0.393	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			G	70989383	A	G	70989383	3	3	37	1	0	0	0	0	1	0	0	0	242	159	6	4	92	4	ADAM20	14	70989383	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	2720479	70989383	36360157	139	3222										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77845074	77845074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtattctgtaggaaacgatgAgctagagcaccgtgagccta	12	8	1	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr14:77845074A>G	ENST00000216471.4	+	1	1599	c.1313A>G	c.(1312-1314)gAg>gGg	p.E438G	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	438										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGAAACGATGAGCTAGAGCAC	0.393																																																0			14											71	68	69					14																	77845074		2203	4300	6503	76914827	SO:0001583	missense	0			AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1313A>G	14.37:g.77845074A>G	ENSP00000216471:p.Glu438Gly		76914827	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.775707	0.49786	.	.	ENSG00000100583	ENST00000216471	T	0.20881	2.04	4.7	3.57	0.40892	.	.	.	.	.	T	0.26846	0.0657	L	0.58810	1.83	0.09310	N	1	P	0.51791	0.948	P	0.48815	0.591	T	0.11591	-1.0581	9	0.62326	D	0.03	0.2598	6.5641	0.22503	0.8928:0.0:0.1072:0.0	.	438	Q9P1V8	SAM15_HUMAN	G	438	ENSP00000216471:E438G	ENSP00000216471:E438G	E	+	2	0	SAMD15	76914827	0.004000	0.15560	0.004000	0.12327	0.004000	0.04260	1.769000	0.38522	0.860000	0.35481	0.454000	0.30748	GAG		0.393	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		G	77845074	A	G	77845074	3	3	37	1	0	0	0	0	1	0	0	0	1763	304	11	4	1315	4	C14orf174	14	77845074	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	6855691	77845074	29504466	140	3223										
EPB42	2038	hgsc.bcm.edu	37	chr15	43499591	43499591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctgctggggtcagccccagcGtcccctccttgactgctctg	11	17	2	1	rs115972761	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:43499591G>A	ENST00000441366.2	-	9	1349	c.1124C>T	c.(1123-1125)aCg>aTg	p.T375M	EPB42_ENST00000300215.3_Missense_Mutation_p.T405M|EPB42_ENST00000563128.1_5'Flank|EPB42_ENST00000540029.1_Missense_Mutation_p.T297M	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	375					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		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;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		CAGCCCCAGCGTCCCCTCCTT	0.582													G|||	2	0.000399361	0.0015	0	5008	,	,		15600	0		0	False		,,,				2504	0															0			15											66	53	58					15																	43499591		2203	4299	6502	41286883	SO:0001583	missense	2038			M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"Transglutaminases"	3381	protein-coding gene	gene with protein product	"Erythrocyte surface protein band 4.2"	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.1124C>T	15.37:g.43499591G>A	ENSP00000396616:p.Thr375Met		41286883	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	37	CCDS45249.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.005	0.555666	0.13436	.	.	ENSG00000166947	ENST00000300215;ENST00000540029;ENST00000441366	T;T;T	0.51071	0.72;0.72;0.72	6.02	-12.0	0.00017	.	1.311570	0.04307	N	0.348294	T	0.28333	0.0700	L	0.51422	1.61	0.09310	N	1	B;B;B;B	0.27823	0.029;0.068;0.19;0.068	B;B;B;B	0.16289	0.005;0.006;0.015;0.006	T	0.08330	-1.0727	10	0.38643	T	0.18	4.7421	1.2729	0.02025	0.4301:0.1641:0.1298:0.276	.	297;375;405;375	F5H563;B7Z4C3;P16452-2;P16452	.;.;.;EPB42_HUMAN	M	405;297;375	ENSP00000300215:T405M;ENSP00000444699:T297M;ENSP00000396616:T375M	ENSP00000300215:T405M	T	-	2	0	EPB42	41286883	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.186000	0.03070	-2.622000	0.00439	-0.769000	0.03391	ACG		0.582	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		A	43499591	G	A	43499591	3	1	37	1	0	0	0	0	1	0	0	0	5171	1145	40	1	971	1	EPB42	15	43499591	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		43499591	59031801	141	3224										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54557568	54557568	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttcagtggtttctgcacaggGtctacaggcaaaagataaaa	10	7	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:54557568G>T	ENST00000260323.11	+	9	3692	c.3692G>T	c.(3691-3693)gGt>gTt	p.G1231V	UNC13C_ENST00000545554.1_Missense_Mutation_p.G1231V|UNC13C_ENST00000537900.1_Missense_Mutation_p.G1229V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1231	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCTGCACAGGGTCTACAGGCA	0.303																																																0			15											51	46	48					15																	54557568		1806	4059	5865	52344860	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3692G>T	15.37:g.54557568G>T	ENSP00000260323:p.Gly1231Val		52344860	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092843	0.76756	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.73575	-0.76;-0.76;-0.76	5.04	5.04	0.67666	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050091	0.85682	D	0.000000	D	0.87811	0.6271	M	0.86097	2.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89771	0.3954	10	0.87932	D	0	.	17.722	0.88355	0.0:0.0:1.0:0.0	.	1231;1231	F5H090;Q8NB66	.;UN13C_HUMAN	V	1231;1231;1229	ENSP00000260323:G1231V;ENSP00000438156:G1231V;ENSP00000442569:G1229V	ENSP00000260323:G1231V	G	+	2	0	UNC13C	52344860	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.794000	0.99096	2.487000	0.83934	0.591000	0.81541	GGT		0.303	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54557568	G	T	54557568	3	4	37	1	0	0	0	0	1	0	0	0	17026	1261	44	2	3722	2	UNC13C	15	54557568	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	11057977	54557568	47973824	142	3225										
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57910378	57910378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgaaagaagagatgaactacAtcaaagatgtgagccattta	9	5	1	6			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:57910378A>G	ENST00000267853.5	+	3	404	c.310A>G	c.(310-312)Atc>Gtc	p.I104V	GCOM1_ENST00000574161.1_Missense_Mutation_p.I104V|GCOM1_ENST00000380561.2_Missense_Mutation_p.I104V|GCOM1_ENST00000572390.1_Missense_Mutation_p.I104V|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000396180.1_Missense_Mutation_p.I104V|GCOM1_ENST00000587652.1_Missense_Mutation_p.I104V|GCOM1_ENST00000380568.3_Missense_Mutation_p.I104V|GCOM1_ENST00000380569.2_Missense_Mutation_p.I104V|GCOM1_ENST00000380560.2_Missense_Mutation_p.I104V|MYZAP_ENST00000380565.4_Missense_Mutation_p.I104V			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	104					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											GATGAACTACATCAAAGATGT	0.413																																																0			15											166	149	155					15																	57910378		2192	4292	6484	55697670	SO:0001583	missense	145781			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.310A>G	15.37:g.57910378A>G	ENSP00000267853:p.Ile104Val		55697670	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956280	0.73902	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.36340	1.26;1.42;1.47;1.64;1.26;1.26;1.26	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.55242	0.1908	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	D;D;D;D	0.81914	0.99;0.99;0.99;0.995	T	0.48758	-0.9007	10	0.15066	T	0.55	-21.5521	15.8048	0.78491	1.0:0.0:0.0:0.0	.	104;104;104;104	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	V	104	ENSP00000369943:I104V;ENSP00000369935:I104V;ENSP00000379483:I104V;ENSP00000369933:I104V;ENSP00000267853:I104V;ENSP00000369939:I104V;ENSP00000369942:I104V	ENSP00000267853:I104V	I	+	1	0	GCOM1	55697670	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.025000	0.76449	2.371000	0.80710	0.533000	0.62120	ATC		0.413	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		G	57910378	A	G	57910378	3	3	37	1	0	0	0	0	1	0	0	0	6324	217	8	4	320	4	GCOM1	15	57910378	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	3352810	57910378	44621014	143	3226										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72260362	72260362	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cttttccagcataatgttttAtaatgaaagcaggctccatc	6	9	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:72260362A>T	ENST00000356056.5	-	13	2421	c.1949T>A	c.(1948-1950)aTa>aAa	p.I650K	MYO9A_ENST00000566885.1_Missense_Mutation_p.I245K|MYO9A_ENST00000444904.1_Missense_Mutation_p.I631K|MYO9A_ENST00000424560.1_Missense_Mutation_p.I650K|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000564571.1_Missense_Mutation_p.I650K	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	650	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATAATGTTTTATAATGAAAGC	0.383																																																0			15											126	124	125					15																	72260362		2199	4297	6496	70047416	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.1949T>A	15.37:g.72260362A>T	ENSP00000348349:p.Ile650Lys		70047416	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.787098	0.90367	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	T;T;T	0.78364	-1.17;-1.17;-1.17	5.13	5.13	0.70059	Myosin head, motor domain (2);	.	.	.	.	D	0.92107	0.7498	H	0.97240	3.965	0.80722	D	1	D;D;D;D	0.76494	0.999;0.995;0.995;0.998	D;D;D;D	0.79108	0.982;0.929;0.929;0.992	D	0.94786	0.7958	9	0.87932	D	0	.	14.9176	0.70810	1.0:0.0:0.0:0.0	.	631;650;631;650	B2RTY4-2;B2RTY4-3;B7WP69;B2RTY4	.;.;.;MYO9A_HUMAN	K	650;650;631;631;650	ENSP00000348349:I650K;ENSP00000399162:I650K;ENSP00000398250:I631K	ENSP00000261864:I631K	I	-	2	0	MYO9A	70047416	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.231000	0.95317	1.917000	0.55516	0.455000	0.32223	ATA		0.383	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72260362	A	T	72260362	3	4	37	1	0	0	0	0	1	0	0	0	10114	449	16	5	5817	5	MYO9A	15	72260362	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	14349984	72260362	30271030	144	3227										
ISLR	3671	hgsc.bcm.edu	37	chr15	74467645	74467645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccgcagcctccgtgctctgcGctcgctgcaactcaaccaca	8	19	2	0	rs149796219		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:74467645G>A	ENST00000249842.3	+	2	803	c.446G>A	c.(445-447)cGc>cAc	p.R149H	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Missense_Mutation_p.R149H	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	149					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)		p.R149H(1)		central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						CGTGCTCTGCGCTCGCTGCAA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	73	72	72		446,446	3.1	0.9	15	dbSNP_134	72	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	ISLR	NM_005545.3,NM_201526.1	29,29	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	149/429,149/429	74467645	1,12989	2198	4297	6495	72254698	SO:0001583	missense	3671			AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.446G>A	15.37:g.74467645G>A	ENSP00000249842:p.Arg149His		72254698		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885881	0.51908	0.0	1.16E-4	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.58506	0.33;0.33	4.05	3.11	0.35812	.	0.125517	0.28431	U	0.015369	T	0.61999	0.2392	L	0.39898	1.24	0.43579	D	0.995915	D	0.89917	1.0	D	0.67231	0.95	T	0.60342	-0.7282	10	0.56958	D	0.05	.	7.4589	0.27283	0.0911:0.1698:0.739:0.0	.	149	O14498	ISLR_HUMAN	H	149	ENSP00000249842:R149H;ENSP00000378550:R149H	ENSP00000249842:R149H	R	+	2	0	ISLR	72254698	1.000000	0.71417	0.880000	0.34516	0.312000	0.27988	4.800000	0.62524	0.672000	0.31204	0.313000	0.20887	CGC		0.622	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		A	74467645	G	A	74467645	3	1	37	1	0	0	0	0	1	0	0	0	7879	1087	38	1	448	1	ISLR	15	74467645	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	2207283	74467645	28063747	145	3228										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83346498	83346498	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gccgatgttagttgcacagcGtccaatggcctggattgtgg	14	9	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:83346498G>A	ENST00000261722.3	-	12	1510	c.1303C>T	c.(1303-1305)Cgc>Tgc	p.R435C	AP3B2_ENST00000535359.1_Missense_Mutation_p.R435C|RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535348.1_Missense_Mutation_p.R403C	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	435					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			GTTGCACAGCGTCCAATGGCC	0.537																																																0			15											47	50	49					15																	83346498		2115	4232	6347	81143553	SO:0001583	missense	8120			U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.1303C>T	15.37:g.83346498G>A	ENSP00000261722:p.Arg435Cys		81143553	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083481	0.76642	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.28454	1.61;1.61;1.61	4.98	1.62	0.23740	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.097447	0.64402	D	0.000006	T	0.62648	0.2445	H	0.96175	3.78	0.80722	D	1	B;D;D	0.89917	0.018;1.0;1.0	B;D;D	0.91635	0.016;0.999;0.993	T	0.66945	-0.5795	10	0.87932	D	0	-12.5333	8.099	0.30846	0.1646:0.0:0.7018:0.1336	.	403;435;435	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	C	435;403;435	ENSP00000261722:R435C;ENSP00000438721:R403C;ENSP00000440984:R435C	ENSP00000261722:R435C	R	-	1	0	AP3B2	81143553	1.000000	0.71417	0.964000	0.40570	0.998000	0.95712	5.441000	0.66569	0.602000	0.29896	0.655000	0.94253	CGC		0.537	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			A	83346498	G	A	83346498	3	1	37	1	0	0	0	0	1	0	0	0	745	1145	40	1	2005	1	AP3B2	15	83346498	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	8878853	83346498	19184894	146	3229										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84566668	84566668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgttctgtgtattaaccaccGcggagagcatgttgggggct	14	8	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:84566668G>A	ENST00000286744.5	+	14	1750	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R509H	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	509	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			ATTAACCACCGCGGAGAGCAT	0.458																																																0			15											148	122	131					15																	84566668		2203	4300	6503	82357672	SO:0001583	missense	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1526G>A	15.37:g.84566668G>A	ENSP00000286744:p.Arg509His		82357672	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.552246	0.27739	.	.	ENSG00000156218	ENST00000286744	T	0.61040	0.14	5.24	-5.95	0.02241	.	0.351880	0.29087	N	0.013189	T	0.36413	0.0966	L	0.38953	1.18	0.09310	N	1	B;B	0.19073	0.033;0.005	B;B	0.22152	0.038;0.007	T	0.11131	-1.0600	10	0.45353	T	0.12	.	5.3902	0.16240	0.3496:0.0:0.3829:0.2675	.	509;509	P82987-2;P82987	.;ATL3_HUMAN	H	509	ENSP00000286744:R509H	ENSP00000286744:R509H	R	+	2	0	ADAMTSL3	82357672	0.047000	0.20315	0.000000	0.03702	0.395000	0.30598	0.726000	0.25984	-1.036000	0.03287	-0.880000	0.02959	CGC		0.458	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		A	84566668	G	A	84566668	3	1	37	1	0	0	0	0	1	0	0	0	276	1087	38	1	1576	1	ADAMTSL3	15	84566668	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	1220170	84566668	17964724	147	3230										
ISG20	3669	hgsc.bcm.edu	37	chr15	89195465	89195465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cactgacaggctgttgtggcGtgaggccaagctggaccact	14	11	0	2	rs549880749		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr15:89195465G>A	ENST00000306072.5	+	3	711	c.353G>A	c.(352-354)cGt>cAt	p.R118H	ISG20_ENST00000560741.1_Missense_Mutation_p.R118H|ISG20_ENST00000560746.1_3'UTR	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	118					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			CTGTTGTGGCGTGAGGCCAAG	0.592																																																0			15											162	133	143					15																	89195465		2200	4299	6499	86996469	SO:0001583	missense	3669			X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"interferon stimulated gene (20kD)"			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.353G>A	15.37:g.89195465G>A	ENSP00000306565:p.Arg118His		86996469	O00441|O00586	Missense_Mutation	SNP	ENST00000306072.5	37	CCDS10345.1	.	.	.	.	.	.	.	.	.	.	G	4.007	-0.001342	0.07819	.	.	ENSG00000172183	ENST00000306072;ENST00000546338	T	0.24908	1.83	4.58	-4.59	0.03400	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.771688	0.12177	N	0.492459	T	0.17916	0.0430	L	0.39245	1.2	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.18681	-1.0329	10	0.33940	T	0.23	-9.4457	11.8782	0.52560	0.8125:0.0:0.1875:0.0	.	118	Q96AZ6	ISG20_HUMAN	H	118;126	ENSP00000306565:R118H	ENSP00000306565:R118H	R	+	2	0	ISG20	86996469	0.000000	0.05858	0.001000	0.08648	0.186000	0.23388	-1.156000	0.03160	-0.847000	0.04168	-0.339000	0.08088	CGT		0.592	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201		A	89195465	G	A	89195465	3	1	37	1	0	0	0	0	1	0	0	0	7875	1145	40	1	359	1	ISG20	15	89195465	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4628797	89195465	13335927	148	3231										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3788618	3788618	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctcatggtaaacggctgtgcGgaggcaacgtggccggaaga	16	9	1	1	rs398124146		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:3788618G>T	ENST00000262367.5	-	26	5145	c.4336C>A	c.(4336-4338)Cgc>Agc	p.R1446S	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1446C(6)|p.R1446G(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACGGCTGTGCGGAGGCAACGT	0.413			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	16											75	68	71					16																	3788618		2197	4300	6497	3728619	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4336C>A	16.37:g.3788618G>T	ENSP00000262367:p.Arg1446Ser		3728619	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.58	3.424625	0.62733	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93763	-3.28;-3.28	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97732	0.9256	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98886	1.0771	10	0.72032	D	0.01	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	S	1446;1476;1408;35	ENSP00000262367:R1446S;ENSP00000371502:R1408S	ENSP00000262367:R1446S	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC		0.413	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3788618	G	T	3788618	3	4	37	1	0	0	0	0	1	0	0	0	3867	1116	39	2	3016	2	CREBBP	16	3788618	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		3788618	86566135	149	3232										
CIITA	4261	hgsc.bcm.edu	37	chr16	11001528	11001528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgtggctggctctgagtggcGaaatcaaggacaaggagctc	15	8	2	1	rs548646642	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:11001528G>A	ENST00000324288.8	+	11	2312	c.2179G>A	c.(2179-2181)Gaa>Aaa	p.E727K	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	727					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TCTGAGTGGCGAAATCAAGGA	0.622			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	0			16											60	65	64					16																	11001528		2197	4300	6497	10909029	SO:0001583	missense	4261			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2179G>A	16.37:g.11001528G>A	ENSP00000316328:p.Glu727Lys		10909029	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	5.722	0.317775	0.10845	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.73789	-0.78	5.47	4.48	0.54585	.	0.352334	0.24366	N	0.039142	T	0.71584	0.3357	L	0.56769	1.78	0.33576	D	0.599176	P;B;P;P	0.51351	0.535;0.019;0.878;0.944	B;B;B;B	0.43508	0.189;0.006;0.422;0.262	T	0.79235	-0.1887	10	0.39692	T	0.17	.	13.2692	0.60152	0.0:0.3048:0.6952:0.0	.	727;727;679;727	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	K	727;679	ENSP00000316328:E727K	ENSP00000316328:E727K	E	+	1	0	CIITA	10909029	0.998000	0.40836	0.015000	0.15790	0.006000	0.05464	3.885000	0.56182	1.235000	0.43724	0.655000	0.94253	GAA		0.622	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	11001528	G	A	11001528	3	1	37	1	0	0	0	0	1	0	0	0	3434	1059	37	1	2221	1	CIITA	16	11001528	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	7212910	11001528	79353225	150	3233										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24816116	24816116	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	caaatagtgcactacctaacCaggcccttggctccatagca	7	14	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:24816116C>G	ENST00000395799.3	+	13	4057	c.3928C>G	c.(3928-3930)Cag>Gag	p.Q1310E	TNRC6A_ENST00000315183.7_Intron|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1310	Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACTACCTAACCAGGCCCTTGG	0.443																																																0			16											135	126	129					16																	24816116		2197	4300	6497	24723617	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.3928C>G	16.37:g.24816116C>G	ENSP00000379144:p.Gln1310Glu		24723617	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840489	0.51057	.	.	ENSG00000090905	ENST00000395799	T	0.13307	2.6	5.82	5.82	0.92795	.	0.269312	0.32719	N	0.005737	T	0.30386	0.0763	L	0.50333	1.59	0.80722	D	1	P	0.49447	0.924	P	0.62298	0.9	T	0.00754	-1.1580	10	0.15066	T	0.55	-4.8507	20.0989	0.97860	0.0:1.0:0.0:0.0	.	1310	Q8NDV7	TNR6A_HUMAN	E	1310	ENSP00000379144:Q1310E	ENSP00000379144:Q1310E	Q	+	1	0	TNRC6A	24723617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.368000	0.66133	2.764000	0.94973	0.650000	0.86243	CAG		0.443	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24816116	C	G	24816116	3	3	37	1	0	0	0	0	1	0	0	0	16379	595	21	5	3978	5	TNRC6A	16	24816116	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	13814588	24816116	65538637	151	3234										
GIYD1	445329	hgsc.bcm.edu	37	chr16	29466211	29466211	+	5'Flank	DEL	A	A	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	agcagcacaatgggggccgcAaaaaaggcggggcctggcgg							TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:29466211delA	ENST00000395400.3	+	0	0				SLX1B_ENST00000330181.5_Frame_Shift_Del_p.K51fs|BOLA2_ENST00000330978.3_5'UTR|SULT1A4_ENST00000344620.6_5'Flank|SNX29P2_ENST00000398878.3_lincRNA|SLX1B-SULT1A4_ENST00000564950.1_RNA|SLX1B_ENST00000351581.4_Frame_Shift_Del_p.K51fs|RP11-345J4.5_ENST00000565417.1_5'Flank			P0DMN0	ST1A4_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4						catecholamine metabolic process (GO:0006584)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	aryl sulfotransferase activity (GO:0004062)										TGGGGGCCGCAAAAAAGGCGG	0.697																																																0			16																																								29373712	SO:0001631	upstream_gene_variant	0			L34160	CCDS32427.1	16p11.2	2013-05-10			ENSG00000213648	ENSG00000213648	2.8.2.1	"Sulfotransferases, cytosolic"	30004	protein-coding gene	gene with protein product		615819				15358107, 15752422	Standard	NM_001017390		Approved		uc002dxk.3	P0DMN0	OTTHUMG00000170468		16.37:g.29466211delA	Exception_encountered		29373712	B4DNV0|O95603|P50224|Q1ET66|Q6ZWJ5	Frame_Shift_Del	DEL	ENST00000395400.3	37	CCDS32427.1																																																																																				0.697	SULT1A4-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001017389		-	29466211	A	-	29466211	6	5	37	0	1	1	0	1	0	0	0	0	6418	131	5	0		0	GIYD1	16	29466211	5'Flank	DEL	A	TCGA-AG-3731-01A-11D-1733-10	4650095	29466211	60888542	152	3235										
MMP2	4313	hgsc.bcm.edu	37	chr16	55518020	55518020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gagcgatgtgaccccactgcGgttttctcgaatccatgatg	11	11	1	2	rs368486758		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:55518020G>A	ENST00000219070.4	+	3	982	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	MMP2_ENST00000570308.1_Missense_Mutation_p.R82Q|MMP2_ENST00000437642.2_Missense_Mutation_p.R108Q|MMP2_ENST00000543485.1_Missense_Mutation_p.R82Q	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	158	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	ACCCCACTGCGGTTTTCTCGA	0.557																																																0			16						G	GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	150	121	131		323,473	2.7	0.7	16		131	0,8600		0,0,4300	no	missense,missense	MMP2	NM_001127891.1,NM_004530.4	43,43	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	108/611,158/661	55518020	1,12995	2198	4300	6498	54075521	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.473G>A	16.37:g.55518020G>A	ENSP00000219070:p.Arg158Gln		54075521	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424160	0.25639	2.27E-4	0.0	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.21031	2.03;2.03;2.03	4.72	2.72	0.32119	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.431251	0.26635	N	0.023290	T	0.11707	0.0285	N	0.16602	0.42	0.09310	N	1	B;B	0.15719	0.003;0.014	B;B	0.08055	0.003;0.002	T	0.19063	-1.0317	10	0.42905	T	0.14	.	8.2601	0.31779	0.2443:0.0:0.7557:0.0	.	108;158	E9PE45;P08253	.;MMP2_HUMAN	Q	158;82;108	ENSP00000219070:R158Q;ENSP00000444143:R82Q;ENSP00000394237:R108Q	ENSP00000219070:R158Q	R	+	2	0	MMP2	54075521	0.000000	0.05858	0.721000	0.30653	0.984000	0.73092	0.383000	0.20651	1.122000	0.41944	0.455000	0.32223	CGG		0.557	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			A	55518020	G	A	55518020	3	1	37	1	0	0	0	0	1	0	0	0	9688	1116	39	1	490	1	MMP2	16	55518020	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	26051809	55518020	34836733	153	3236										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687915	61687915	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctcctccttcatcatcgtagCgaatgatgttttctcgaacg	7	12	3	1	rs146063486	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:61687915C>T	ENST00000577390.1	-	12	2951	c.1997G>A	c.(1996-1998)cGc>cAc	p.R666H	CDH8_ENST00000577730.1_Missense_Mutation_p.R666H|CDH8_ENST00000299345.6_Missense_Mutation_p.R666H	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	666					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATCATCGTAGCGAATGATGTT	0.408													C|||	2	0.000399361	0	0	5008	,	,		17903	0		0.002	False		,,,				2504	0															0			16						C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	120	112	115		1997	5.7	1	16	dbSNP_134	115	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CDH8	NM_001796.4	29	0,21,6482	TT,TC,CC		0.1744,0.1362,0.1615	probably-damaging	666/800	61687915	21,12985	2203	4300	6503	60245416	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1997G>A	16.37:g.61687915C>T	ENSP00000462701:p.Arg666His		60245416	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	29.5	5.012465	0.93346	0.001362	0.001744	ENSG00000150394	ENST00000299345	T	0.76316	-1.01	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.105154	0.64402	D	0.000002	T	0.80929	0.4718	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	D	0.66716	0.946	T	0.80236	-0.1466	10	0.38643	T	0.18	.	18.8311	0.92139	0.0:1.0:0.0:0.0	.	666	P55286	CADH8_HUMAN	H	666	ENSP00000299345:R666H	ENSP00000299345:R666H	R	-	2	0	CDH8	60245416	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.046000	0.71029	2.679000	0.91253	0.655000	0.94253	CGC		0.408	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61687915	C	T	61687915	3	4	37	1	0	0	0	0	1	0	0	0	3122	768	27	1	406	1	CDH8	16	61687915	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	6169895	61687915	28666838	154	3237										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67681232	67681234	+	In_Frame_Del	DEL	ATG	ATG	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tctcagaacagattctgcacAtgatgagtcagtcatcacac					rs201801777		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATG	ATG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:67681232_67681234delATG	ENST00000334583.6	+	10	1046_1048	c.718_720delATG	c.(718-720)atgdel	p.M241del	RLTPR_ENST00000545661.1_In_Frame_Del_p.M241del	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	241					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GATTCTGCACATGATGAGTCAGT	0.645																																																0			16																																								66238735	SO:0001651	inframe_deletion	146206			AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.718_720delATG	16.37:g.67681235_67681237delATG	ENSP00000334958:p.Met241del		66238733	B8X2Z3	In_Frame_Del	DEL	ENST00000334583.6	37	CCDS45513.1																																																																																				0.645	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		-	67681234	ATG	-	67681232	7	5	37	1	0	1	0	1	0	0	0	0	13431	217	8	0	756	0	RLTPR	16	67681232	In_Frame_Del	DEL	ATG	TCGA-AG-3731-01A-11D-1733-10	5993317	67681232	22673521	155	3238										
CDH1	999	hgsc.bcm.edu	37	chr16	68846134	68846134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgatcacagtcactgacaccAacgataatcctccgatcttc	5	14	3	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr16:68846134A>G	ENST00000261769.5	+	8	1296	c.1105A>G	c.(1105-1107)Aac>Gac	p.N369D	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Missense_Mutation_p.N369D|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	369	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.N369D(1)|p.S337_T379del(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACTGACACCAACGATAATCC	0.463			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	3	Substitution - Missense(1)|Unknown(1)|Deletion - In frame(1)	stomach(2)|breast(1)	16											182	139	154					16																	68846134		2198	4300	6498	67403635	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1105A>G	16.37:g.68846134A>G	ENSP00000261769:p.Asn369Asp		67403635	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810509	0.70797	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.75821	-0.97;-0.17	5.72	5.72	0.89469	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.53938	D	0.000041	D	0.89350	0.6690	M	0.92169	3.28	0.53005	D	0.999963	D;D	0.89917	0.997;1.0	D;D	0.91635	0.991;0.999	D	0.91857	0.5496	10	0.87932	D	0	.	15.6694	0.77262	1.0:0.0:0.0:0.0	.	369;369	Q9UII8;P12830	.;CADH1_HUMAN	D	369	ENSP00000261769:N369D;ENSP00000414946:N369D	ENSP00000261769:N369D	N	+	1	0	CDH1	67403635	1.000000	0.71417	0.928000	0.36995	0.058000	0.15608	7.112000	0.77086	2.190000	0.69967	0.454000	0.30748	AAC		0.463	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68846134	A	G	68846134	3	3	37	1	0	0	0	0	1	0	0	0	3101	130	5	4	1135	4	CDH1	16	68846134	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	1164902	68846134	21508619	156	3239										
ALOX15	246	hgsc.bcm.edu	37	chr17	4542791	4542791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtaacaagggaacctgacctCgtccccggctccggggccct	12	16	0	1	rs139214774		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:4542791C>T	ENST00000570836.1	-	3	367	c.271G>A	c.(271-273)Gag>Aag	p.E91K	ALOX15_ENST00000574640.1_Missense_Mutation_p.E52K|ALOX15_ENST00000545513.1_Missense_Mutation_p.E113K|ALOX15_ENST00000293761.3_Missense_Mutation_p.E91K			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	91	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		AACCTGACCTCGTCCCCGGCT	0.652																																																0			17						C	LYS/GLU	0,4406		0,0,2203	48	50	49		271	2.7	0.1	17	dbSNP_134	49	1,8599		0,1,4299	no	missense	ALOX15	NM_001140.3	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	91/663	4542791	1,13005	2203	4300	6503	4489540	SO:0001583	missense	246			M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"Arachidonate lipoxygenases"	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.271G>A	17.37:g.4542791C>T	ENSP00000458832:p.Glu91Lys		4489540	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	.	.	.	.	.	.	.	.	.	.	C	7.363	0.625227	0.14257	0.0	1.16E-4	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.62498	0.02;0.02	4.81	2.73	0.32206	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.593720	0.16110	N	0.229141	T	0.49779	0.1577	L	0.48362	1.52	0.09310	N	1	B;B;B	0.17667	0.023;0.007;0.016	B;B;B	0.13407	0.005;0.002;0.009	T	0.34179	-0.9839	10	0.25751	T	0.34	-19.0055	7.0033	0.24821	0.0:0.7282:0.1736:0.0981	.	113;52;91	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	K	91;113	ENSP00000293761:E91K;ENSP00000439855:E113K	ENSP00000293761:E91K	E	-	1	0	ALOX15	4489540	0.167000	0.22975	0.119000	0.21687	0.136000	0.21042	1.951000	0.40333	0.407000	0.25591	0.561000	0.74099	GAG		0.652	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2			T	4542791	C	T	4542791	3	4	37	1	0	0	0	0	1	0	0	0	538	893	31	1	1769	1	ALOX15	17	4542791	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10		4542791	76652419	157	3240										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5445208	5445208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tagcttgcagctcggctgtcTcagtctctggcaaaggtgtt	12	10	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:5445208T>C	ENST00000572272.1	-	6	2667	c.2668A>G	c.(2668-2670)Aga>Gga	p.R890G	NLRP1_ENST00000262467.5_Missense_Mutation_p.R890G|NLRP1_ENST00000354411.3_Missense_Mutation_p.R890G|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000345221.3_Missense_Mutation_p.R890G|NLRP1_ENST00000269280.4_Missense_Mutation_p.R890G|NLRP1_ENST00000577119.1_Missense_Mutation_p.R890G			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	890					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CTCGGCTGTCTCAGTCTCTGG	0.587																																																0			17											101	81	88					17																	5445208		2203	4300	6503	5385932	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2668A>G	17.37:g.5445208T>C	ENSP00000460475:p.Arg890Gly		5385932	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.234869	0.22626	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56	2.01	2.01	0.26516	.	0.933482	0.08723	N	0.903207	T	0.14527	0.0351	M	0.64676	1.99	0.09310	N	1	B;B;B;B;B;B	0.31548	0.328;0.16;0.137;0.009;0.037;0.015	B;B;B;B;B;B	0.28011	0.085;0.056;0.075;0.006;0.014;0.008	T	0.24870	-1.0148	10	0.56958	D	0.05	.	6.0548	0.19804	0.0:0.0:0.0:1.0	.	156;890;890;890;890;890	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	G	890;890;890;890;890;156	ENSP00000442029:R890G;ENSP00000262467:R890G;ENSP00000269280:R890G;ENSP00000346390:R890G;ENSP00000324366:R890G	ENSP00000262467:R890G	R	-	1	2	NLRP1	5385932	0.008000	0.16893	0.014000	0.15608	0.019000	0.09904	0.346000	0.19997	1.211000	0.43351	0.454000	0.30748	AGA		0.587	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		C	5445208	T	C	5445208	3	2	37	1	0	0	0	0	1	0	0	0	10502	1559	54	4	1876	4	NLRP1	17	5445208	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	902417	5445208	75750002	158	3241										
TP53	7157	hgsc.bcm.edu	37	chr17	7579591	7579591	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcttgggacggcaagggggaCtgtagatgggtgaaaagagc	19	5	0	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:7579591C>T	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	17	GRCh37	CS971912	TP53	S							141	137	138					17																	7579591		2203	4300	6503	7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>A	17.37:g.7579591C>T			7520316	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.702	0.498192	0.12762	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40380	D	0.979434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7579591	C	T	7579591	5	4	37	1	0	0	0	0	0	0	1	0	16421	579	20	3	1206	3	TP53	17	7579591	Splice_Site	SNP	C	TCGA-AG-3731-01A-11D-1733-10	2134383	7579591	73615619	159	3242										
ODF4	146852	hgsc.bcm.edu	37	chr17	8248732	8248732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcgagttggaaaggaatgtaTccatccccataggctggagc	12	9	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:8248732T>C	ENST00000328248.2	+	2	714	c.526T>C	c.(526-528)Tcc>Ccc	p.S176P	ODF4_ENST00000584943.1_Missense_Mutation_p.S61P	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	176					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)		p.S176T(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						AAGGAATGTATCCATCCCCAT	0.517																																																1	Substitution - Missense(1)	ovary(1)	17											292	254	267					17																	8248732		2203	4300	6503	8189457	SO:0001583	missense	146852			AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"cancer/testis antigen 136"	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.526T>C	17.37:g.8248732T>C	ENSP00000331086:p.Ser176Pro		8189457	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	.	.	.	.	.	.	.	.	.	.	T	1.687	-0.505050	0.04261	.	.	ENSG00000184650	ENST00000328248	T	0.28069	1.63	4.59	2.18	0.27775	.	0.000000	0.38663	N	0.001606	T	0.16599	0.0399	N	0.17082	0.46	0.09310	N	1	P	0.44816	0.844	B	0.42319	0.383	T	0.08391	-1.0724	10	0.62326	D	0.03	-8.8169	3.6185	0.08086	0.1916:0.1042:0.0:0.7042	.	176	Q2M2E3	ODFP4_HUMAN	P	176	ENSP00000331086:S176P	ENSP00000331086:S176P	S	+	1	0	ODF4	8189457	0.086000	0.21541	0.019000	0.16419	0.047000	0.14425	1.871000	0.39539	0.888000	0.36160	0.460000	0.39030	TCC		0.517	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1			C	8248732	T	C	8248732	3	2	37	1	0	0	0	0	1	0	0	0	10864	1435	50	4	532	4	ODF4	17	8248732	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	669141	8248732	72946478	160	3243										
MYH4	4622	hgsc.bcm.edu	37	chr17	10351935	10351935	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gaatgattacagtgactcacGttgtaagttcttattctctc	7	8	3	2	rs545963911	byFrequency	TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:10351935G>A	ENST00000255381.2	-	32	4641	c.4531C>T	c.(4531-4533)Cag>Tag	p.Q1511*	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1511					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AGTGACTCACGTTGTAAGTTC	0.378													G|||	2	0.000399361	8e-04	0	5008	,	,		20564	0		0	False		,,,				2504	0.001															0			17											99	100	99					17																	10351935		2203	4300	6503	10292660	SO:0001630	splice_region_variant	4622				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4531+1C>T	17.37:g.10351935G>A			10292660		Nonsense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	41	8.891088	0.98992	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.34	5.34	0.76211	.	0.000000	0.35772	U	0.002987	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3996	0.94623	0.0:0.0:1.0:0.0	.	.	.	.	X	1511	.	.	Q	-	1	0	MYH4	10292660	0.895000	0.30542	0.998000	0.56505	0.594000	0.36715	1.244000	0.32778	2.666000	0.90696	0.655000	0.94253	CAG		0.378	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	Nonsense_Mutation	A	10351935	G	A	10351935	5	1	37	1	0	0	0	0	0	0	1	0	10067	1159	40	1	1324	1	MYH4	17	10351935	Splice_Site	SNP	G	TCGA-AG-3731-01A-11D-1733-10	2103203	10351935	70843275	161	3244										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11872712	11872712	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcagataagcaggactgccgCagtgtctattcctgtcctgt	11	11	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:11872712C>T	ENST00000262442.4	+	69	13397	c.13329C>T	c.(13327-13329)cgC>cgT	p.R4443R	DNAH9_ENST00000454412.2_Silent_p.R4367R|DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Silent_p.R755R|RP11-1096G20.5_ENST00000580270.1_RNA	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4443			R -> C (in dbSNP:rs9913494).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		AGGACTGCCGCAGTGTCTATT	0.517																																																0			17											106	90	95					17																	11872712		2203	4300	6503	11813437	SO:0001819	synonymous_variant	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.13329C>T	17.37:g.11872712C>T			11813437	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.517	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11872712	C	T	11872712	2	4	37	1	0	0	0	0	0	0	0	1	4619	697	25	3		3	DNAH9	17	11872712	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1520777	11872712	69322498	162	3245										
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15611544	15611544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gaagcttgagagaaaagcccCcaaaagcagctattcaggtg	11	9	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:15611544C>T	ENST00000464847.2	+	4	870	c.317C>T	c.(316-318)cCc>cTc	p.P106L	ZNF286A_ENST00000395894.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000395893.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000472486.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000421016.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000585194.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000413242.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000581529.1_3'UTR|ZNF286A_ENST00000583566.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000593105.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000580259.1_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P106L(2)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		AGAAAAGCCCCCAAAAGCAGC	0.403																																																2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	17											57	58	57					17																	15611544		2203	4300	6503	15552269	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.317C>T	17.37:g.15611544C>T	ENSP00000464218:p.Pro106Leu		15552269	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	c	11.26	1.587257	0.28268	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.08282	3.47;3.11;5.43;5.59	4.85	3.84	0.44239	Krueppel-associated box (1);	30.442900	0.00744	N	0.001035	T	0.06280	0.0162	N	0.10685	0.025	0.09310	N	1	B	0.27498	0.18	B	0.21546	0.035	T	0.31696	-0.9934	10	0.27785	T	0.31	-0.0869	10.6557	0.45673	0.2079:0.7921:0.0:0.0	.	106	Q9HBT8	Z286A_HUMAN	L	106;96;106;106	ENSP00000397163:P106L;ENSP00000408168:P96L;ENSP00000379231:P106L;ENSP00000379230:P106L	ENSP00000435872:P106L	P	+	2	0	ZNF286A	15552269	0.000000	0.05858	0.003000	0.11579	0.188000	0.23474	0.417000	0.21214	1.321000	0.45227	0.563000	0.77884	CCC		0.403	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15611544	C	T	15611544	3	4	37	1	0	0	0	0	1	0	0	0	17862	623	22	3	331	3	ZNF286A	17	15611544	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	3738832	15611544	65583666	163	3246										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20163524	20163524	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtgtggaaagaaaagaccctCtggcagccttggcccgggaa	14	10	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:20163524C>G	ENST00000261503.5	+	12	2908	c.2857C>G	c.(2857-2859)Ctg>Gtg	p.L953V	SPECC1_ENST00000536879.1_Missense_Mutation_p.L293V|SPECC1_ENST00000395527.4_Missense_Mutation_p.L953V|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395530.2_Missense_Mutation_p.L872V	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	953					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AAAAGACCCTCTGGCAGCCTT	0.443																																																0			17											89	93	92					17																	20163524		2203	4300	6503	20104116	SO:0001583	missense	92521			AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.2857C>G	17.37:g.20163524C>G	ENSP00000261503:p.Leu953Val		20104116	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109202	0.56398	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000536879;ENST00000395527	T;D	0.95205	-0.35;-3.64	4.31	4.31	0.51392	.	0.000000	0.64402	D	0.000004	D	0.94915	0.8356	L	0.43152	1.355	0.51767	D	0.999931	D;D;D	0.89917	1.0;0.999;0.997	D;D;D	0.87578	0.998;0.997;0.965	D	0.94244	0.7487	10	0.87932	D	0	-11.4805	8.2976	0.31995	0.0:0.893:0.0:0.107	.	953;872;953	A8MV89;Q5M775-4;Q5M775	.;.;CYTSB_HUMAN	V	953;953;293;872	ENSP00000261503:L953V;ENSP00000438294:L293V	ENSP00000261503:L953V	L	+	1	2	SPECC1	20104116	0.051000	0.20477	0.999000	0.59377	0.994000	0.84299	0.320000	0.19540	2.399000	0.81585	0.655000	0.94253	CTG		0.443	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20163524	C	G	20163524	3	3	37	1	0	0	0	0	1	0	0	0	4216	912	32	5	2969	5	CYTSB	17	20163524	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	4551980	20163524	61031686	164	3247										
PCGF2	7703	hgsc.bcm.edu	37	chr17	36895858	36895858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cctgatgctcagcagcggccGggttttatggacctgcacgt	13	12	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:36895858G>A	ENST00000580830.1	-	5	891	c.190C>T	c.(190-192)Cgg>Tgg	p.R64W	PCGF2_ENST00000581345.1_Missense_Mutation_p.R64W|PCGF2_ENST00000585100.1_Missense_Mutation_p.R64W|PCGF2_ENST00000578109.1_Missense_Mutation_p.R10W|PCGF2_ENST00000579882.1_Missense_Mutation_p.R64W|PCGF2_ENST00000360797.2_Missense_Mutation_p.R64W			P35227	PCGF2_HUMAN	polycomb group ring finger 2	64					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R64W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					AGCAGCGGCCGGGTTTTATGG	0.617																																																1	Substitution - Missense(1)	central_nervous_system(1)	17											145	117	127					17																	36895858		2203	4300	6503	34149384	SO:0001583	missense	7703			D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.190C>T	17.37:g.36895858G>A	ENSP00000461961:p.Arg64Trp		34149384	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	37	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.421315	0.25639	.	.	ENSG00000056661	ENST00000360797	T	0.43294	0.95	4.56	2.5	0.30297	Zinc finger, RING/FYVE/PHD-type (1);	0.070142	0.64402	D	0.000017	T	0.42449	0.1203	M	0.68952	2.095	0.40076	D	0.976072	D	0.62365	0.991	P	0.44860	0.462	T	0.42766	-0.9432	10	0.46703	T	0.11	-9.2425	11.0498	0.47880	0.0:0.0:0.6189:0.3811	.	64	P35227	PCGF2_HUMAN	W	64	ENSP00000354033:R64W	ENSP00000354033:R64W	R	-	1	2	PCGF2	34149384	0.009000	0.17119	0.520000	0.27837	0.916000	0.54674	0.548000	0.23314	0.478000	0.27488	0.491000	0.48974	CGG		0.617	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		A	36895858	G	A	36895858	3	1	37	1	0	0	0	0	1	0	0	0	11606	1115	39	1	876	1	PCGF2	17	36895858	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	16732334	36895858	44299352	165	3248										
GJC1	10052	hgsc.bcm.edu	37	chr17	42882687	42882687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gagcccatcttcccgaatccGtcgtcggccatcatgcttag	9	15	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:42882687G>A	ENST00000426548.1	-	3	768	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W	GJC1_ENST00000592524.1_Missense_Mutation_p.R167W|GJC1_ENST00000590758.1_Missense_Mutation_p.R167W|GJC1_ENST00000330514.4_Missense_Mutation_p.R167W	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	167					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				TCCCGAATCCGTCGTCGGCCA	0.463																																																0			17											205	185	192					17																	42882687		2203	4300	6503	40238213	SO:0001583	missense	125111			U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"Ion channels / Gap junction proteins (connexins)"	4280	protein-coding gene	gene with protein product	"connexin 45"	608655	"gap junction protein, alpha 7, 45kDa"	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.499C>T	17.37:g.42882687G>A	ENSP00000411528:p.Arg167Trp		40238213	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	37	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.327755	0.60743	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.98280	-4.84;-4.84	5.52	5.52	0.82312	.	0.060473	0.64402	D	0.000002	D	0.98782	0.9590	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.99201	1.0873	10	0.40728	T	0.16	.	18.419	0.90582	0.0:0.0:1.0:0.0	.	167	P36383	CXG1_HUMAN	W	167	ENSP00000411528:R167W;ENSP00000333193:R167W	ENSP00000333193:R167W	R	-	1	2	GJC1	40238213	1.000000	0.71417	0.247000	0.24249	0.815000	0.46073	6.590000	0.74085	2.581000	0.87130	0.514000	0.50259	CGG		0.463	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497		A	42882687	G	A	42882687	3	1	37	1	0	0	0	0	1	0	0	0	6434	1144	40	1	695	1	GJC1	17	42882687	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	5986829	42882687	38312523	166	3249										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48735832	48735832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ccagcgctggctttctctccCgcctgtttttctggtggttc	10	14	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:48735832C>T	ENST00000285238.8	+	6	729	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C	ABCC3_ENST00000427699.1_Missense_Mutation_p.R217C	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	217					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.L215_F219delLSRLF(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CTTTCTCTCCCGCCTGTTTTT	0.582																																																1	Deletion - In frame(1)	prostate(1)	17											128	118	121					17																	48735832		2203	4300	6503	46090831	SO:0001583	missense	8714			Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.649C>T	17.37:g.48735832C>T	ENSP00000285238:p.Arg217Cys		46090831	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.716134	0.68844	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.93247	-3.19;-3.19	5.92	4.96	0.65561	.	0.158362	0.42964	D	0.000632	D	0.96849	0.8971	M	0.92691	3.335	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	P;D	0.72338	0.852;0.977	D	0.96712	0.9526	10	0.66056	D	0.02	-14.056	8.5005	0.33154	0.2579:0.6706:0.0:0.0715	.	217;217	O15438;O15438-5	MRP3_HUMAN;.	C	217	ENSP00000395160:R217C;ENSP00000285238:R217C	ENSP00000285238:R217C	R	+	1	0	ABCC3	46090831	0.028000	0.19301	1.000000	0.80357	0.985000	0.73830	1.110000	0.31147	1.515000	0.48885	0.561000	0.74099	CGC		0.582	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		T	48735832	C	T	48735832	3	4	37	1	0	0	0	0	1	0	0	0	54	652	23	1	671	1	ABCC3	17	48735832	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	5853145	48735832	32459378	167	3250										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49048080	49048080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgacatacccattcggaagtCgatgtagccctctcctccac	7	15	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr17:49048080C>T	ENST00000262013.7	-	29	4046	c.3838G>A	c.(3838-3840)Gac>Aac	p.D1280N	SPAG9_ENST00000357122.4_Missense_Mutation_p.D1266N|SPAG9_ENST00000505279.1_Missense_Mutation_p.D1270N|SPAG9_ENST00000510283.1_Missense_Mutation_p.D1136N	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1280					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ATTCGGAAGTCGATGTAGCCC	0.493																																																0			17											126	102	110					17																	49048080		2203	4300	6503	46403079	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3838G>A	17.37:g.49048080C>T	ENSP00000262013:p.Asp1280Asn		46403079	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.531065	0.64972	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	T;T;T;T	0.39056	1.13;1.1;1.14;1.14	6.17	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.65207	0.2669	M	0.70842	2.15	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;P;D;D	0.97110	0.964;0.886;1.0;1.0	T	0.69435	-0.5146	10	0.66056	D	0.02	-18.5972	17.0955	0.86634	0.1278:0.8722:0.0:0.0	.	1270;1280;1266;1136	O60271-2;O60271;O60271-4;E7ENU2	.;JIP4_HUMAN;.;.	N	1280;1037;1027;1136;1270;1266;878	ENSP00000262013:D1280N;ENSP00000423165:D1136N;ENSP00000426900:D1270N;ENSP00000349636:D1266N	ENSP00000262013:D1280N	D	-	1	0	SPAG9	46403079	1.000000	0.71417	0.953000	0.39169	0.026000	0.11368	7.333000	0.79214	1.615000	0.50252	-0.169000	0.13324	GAC		0.493	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		T	49048080	C	T	49048080	3	4	37	1	0	0	0	0	1	0	0	0	15024	884	31	1	135	1	SPAG9	17	49048080	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	312248	49048080	32147130	168	3251										
MIB1	57534	hgsc.bcm.edu	37	chr18	19348680	19348680	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggagtggactggcagtgggaAgatcaagatggaggaaatgg	19	3	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:19348680A>T	ENST00000261537.6	+	3	762	c.498A>T	c.(496-498)gaA>gaT	p.E166D	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	166	MIB/HERC2 2. {ECO:0000255|PROSITE- ProRule:PRU00749}.				blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GGCAGTGGGAAGATCAAGATG	0.418																																																0			18											83	80	81					18																	19348680		2203	4300	6503	17602678	SO:0001583	missense	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.498A>T	18.37:g.19348680A>T	ENSP00000261537:p.Glu166Asp		17602678	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.556376	0.65425	.	.	ENSG00000101752	ENST00000261537	T	0.37235	1.21	5.0	3.83	0.44106	Mib-herc2 (2);	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	L	0.33189	0.99	0.54753	D	0.999982	P	0.40032	0.699	P	0.58928	0.848	T	0.13308	-1.0514	10	0.17832	T	0.49	-19.7346	10.7948	0.46453	0.924:0.0:0.076:0.0	.	166	Q86YT6	MIB1_HUMAN	D	166	ENSP00000261537:E166D	ENSP00000261537:E166D	E	+	3	2	MIB1	17602678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.876000	0.63079	1.870000	0.54199	0.533000	0.62120	GAA		0.418	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		T	19348680	A	T	19348680	3	4	37	1	0	0	0	0	1	0	0	0	9596	69	3	5	508	5	MIB1	18	19348680	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10		19348680	58728568	169	3252										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575112	48575112	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gcccgtctctggaggtggccTgatcttcacaaaaatgaact	10	11	3	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:48575112T>C	ENST00000342988.3	+	3	844	c.306T>C	c.(304-306)ccT>ccC	p.P102P	SMAD4_ENST00000398417.2_Silent_p.P102P|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Silent_p.P102P|SMAD4_ENST00000452201.2_Silent_p.P102P	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	102	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGTGGCCTGATCTTCACA	0.388																																																40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											161	147	152					18																	48575112		2203	4300	6503	46829110	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.306T>C	18.37:g.48575112T>C			46829110	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.388	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48575112	T	C	48575112	2	2	37	1	0	0	0	0	0	0	0	1	14797	1567	55	4		4	SMAD4	18	48575112	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	29226432	48575112	29502136	170	3253										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591809	48591809	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atagctcctgagtattggtgTtccattgcttactttgaaat	8	7	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:48591809T>C	ENST00000342988.3	+	9	1510	c.972T>C	c.(970-972)tgT>tgC	p.C324C	SMAD4_ENST00000398417.2_Silent_p.C324C|SMAD4_ENST00000588745.1_Silent_p.C228C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	324	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.W323fs*11(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGTATTGGTGTTCCATTGCTT	0.413																																																39	Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|small_intestine(1)|oesophagus(1)	18											248	214	225					18																	48591809		2203	4300	6503	46845807	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.972T>C	18.37:g.48591809T>C			46845807	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48591809	T	C	48591809	2	2	37	1	0	0	0	0	0	0	0	1	14797	1731	60	4		4	SMAD4	18	48591809	Silent	SNP	T	TCGA-AG-3731-01A-11D-1733-10	16697	48591809	29485439	171	3254										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56204708	56204708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gattttctcctgtggcacctTcactagctgtgtgtgaaatg	10	9	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:56204708T>C	ENST00000361673.3	-	5	2924	c.2711A>G	c.(2710-2712)gAa>gGa	p.E904G	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	904						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGTGGCACCTTCACTAGCTGT	0.512																																																0			18											78	78	78					18																	56204708		2203	4300	6503	54355688	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2711A>G	18.37:g.56204708T>C	ENSP00000354991:p.Glu904Gly		54355688	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	T	12.43	1.935262	0.34189	.	.	ENSG00000198796	ENST00000361673	T	0.48522	0.81	5.43	1.84	0.25277	.	0.414085	0.22635	N	0.057527	T	0.34513	0.0900	L	0.41824	1.3	0.09310	N	1	B;B	0.23735	0.09;0.014	B;B	0.26310	0.068;0.008	T	0.20240	-1.0281	10	0.38643	T	0.18	-1.5835	6.3066	0.21141	0.0:0.2867:0.0:0.7133	.	904;904	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	G	904	ENSP00000354991:E904G	ENSP00000354991:E904G	E	-	2	0	ALPK2	54355688	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	0.276000	0.18716	0.384000	0.24942	0.482000	0.46254	GAA		0.512	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56204708	T	C	56204708	3	2	37	1	0	0	0	0	1	0	0	0	545	1783	62	4	3837	4	ALPK2	18	56204708	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	7612899	56204708	21872540	172	3255										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178966	65178966	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aaagactctctccttttaaaTtttctttttttgtccttatt	2	8	2	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:65178966T>A	ENST00000310045.7	-	2	4383	c.2910A>T	c.(2908-2910)aaA>aaT	p.K970N	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	960					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TCCTTTTAAATTTTCTTTTTT	0.378																																																0			18											43	50	47					18																	65178966		2183	4286	6469	63329946	SO:0001583	missense	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2910A>T	18.37:g.65178966T>A	ENSP00000310565:p.Lys970Asn		63329946	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	T	9.044	0.990304	0.18966	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	D	0.81996	-1.56	5.17	2.81	0.32909	Sulfotransferase domain (1);	0.081233	0.46758	U	0.000274	T	0.79907	0.4527	L	0.40543	1.245	0.19300	N	0.99997	P	0.42078	0.77	P	0.48598	0.583	T	0.71397	-0.4605	10	0.72032	D	0.01	-21.7788	8.2308	0.31597	0.0:0.2936:0.0:0.7064	.	960	Q8IZU8	DSEL_HUMAN	N	970;960	ENSP00000310565:K970N	ENSP00000310565:K970N	K	-	3	2	DSEL	63329946	0.098000	0.21812	0.693000	0.30195	0.407000	0.30961	0.391000	0.20784	0.806000	0.34183	0.460000	0.39030	AAA		0.378	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65178966	T	A	65178966	3	1	37	1	0	0	0	0	1	0	0	0	4786	1490	52	5	762	5	DSEL	18	65178966	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	8974258	65178966	12898282	173	3256										
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66678184	66678184	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgaaaggaattactgaaccTtcaacatgcctactataaac	5	9	1	2	rs567681416		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr18:66678184T>C	ENST00000360242.5	+	7	1394	c.1277T>C	c.(1276-1278)cTt>cCt	p.L426P	CCDC102B_ENST00000584156.1_Missense_Mutation_p.L426P|CCDC102B_ENST00000319445.6_Missense_Mutation_p.L426P	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	426										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				TTACTGAACCTTCAACATGCC	0.323																																																0			18											62	60	61					18																	66678184		2203	4300	6503	64829164	SO:0001583	missense	79839			AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 14", "aminoacylase 1-like"	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1277T>C	18.37:g.66678184T>C	ENSP00000353377:p.Leu426Pro		64829164	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	.	.	.	.	.	.	.	.	.	.	T	9.106	1.005407	0.19199	.	.	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.22539	1.95;1.95	5.4	4.21	0.49690	.	0.466449	0.18234	N	0.147474	T	0.38719	0.1051	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	T	0.06197	-1.0840	10	0.31617	T	0.26	-3.7455	8.4266	0.32733	0.174:0.0:0.0:0.826	.	426	Q68D86	C102B_HUMAN	P	426	ENSP00000316237:L426P;ENSP00000353377:L426P	ENSP00000316237:L426P	L	+	2	0	CCDC102B	64829164	0.980000	0.34600	0.178000	0.23040	0.822000	0.46500	2.526000	0.45607	0.844000	0.35094	0.528000	0.53228	CTT		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		C	66678184	T	C	66678184	3	2	37	1	0	0	0	0	1	0	0	0	2743	1609	56	4	1299	4	CCDC102B	18	66678184	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	1499218	66678184	11399064	174	3257										
REXO1	57455	hgsc.bcm.edu	37	chr19	1827578	1827578	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cttctccacaggccgccctcGgcccttgtccttggtcttgt	9	17	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:1827578G>A	ENST00000170168.4	-	2	1304	c.1210C>T	c.(1210-1212)Cga>Tga	p.R404*	REXO1_ENST00000587524.1_5'Flank	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	404						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		GGCCGCCCTCGGCCCTTGTCC	0.672																																																0			19											14	17	16					19																	1827578		2194	4273	6467	1778578	SO:0001587	stop_gained	57455			AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1210C>T	19.37:g.1827578G>A	ENSP00000170168:p.Arg404*		1778578	Q9ULT2	Nonsense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080879	0.76528	.	.	ENSG00000079313	ENST00000170168	.	.	.	4.12	1.8	0.24995	.	1.275950	0.05319	N	0.526203	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-1.0924	2.5034	0.04639	0.1731:0.1454:0.5129:0.1685	.	.	.	.	X	404	.	ENSP00000170168:R404X	R	-	1	2	REXO1	1778578	0.000000	0.05858	0.001000	0.08648	0.225000	0.24961	0.552000	0.23376	0.942000	0.37525	-0.273000	0.10243	CGA		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		A	1827578	G	A	1827578	4	1	37	1	0	0	0	0	0	1	0	0	13278	1124	39	1	2515	1	REXO1	19	1827578	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10		1827578	57301405	175	3258										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2396635	2396635	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gggagacctcggactatcacCgcacgctgacgcccaccctg	11	17	1	2	rs552048658		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:2396635C>T	ENST00000332578.3	+	2	241	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	81					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		GGACTATCACCGCACGCTGAC	0.662													C|||	1	0.000199681	0	0	5008	,	,		12114	0.001		0	False		,,,				2504	0															0			19											28	24	25					19																	2396635		2203	4299	6502	2347635	SO:0001583	missense	360200			AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.241C>T	19.37:g.2396635C>T	ENSP00000330264:p.Arg81Cys		2347635	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.971224	0.53614	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.90788	-2.73	3.98	1.58	0.23477	.	0.119241	0.36932	N	0.002337	D	0.92331	0.7567	M	0.65498	2.005	0.19945	N	0.999941	D;D	0.89917	0.999;1.0	P;D	0.69824	0.826;0.966	D	0.83490	0.0069	10	0.72032	D	0.01	.	5.5525	0.17099	0.194:0.6968:0.0:0.1092	.	81;81	Q7Z410;E7EMP4	TMPS9_HUMAN;.	C	81	ENSP00000330264:R81C	ENSP00000330264:R81C	R	+	1	0	TMPRSS9	2347635	0.003000	0.15002	0.034000	0.17996	0.002000	0.02628	0.065000	0.14466	0.798000	0.33994	-0.266000	0.10368	CGC		0.662	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2396635	C	T	2396635	3	4	37	1	0	0	0	0	1	0	0	0	16292	652	23	1	247	1	TMPRSS9	19	2396635	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	569057	2396635	56732348	176	3259										
XAB2	56949	hgsc.bcm.edu	37	chr19	7690922	7690922	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gagatgaggtcgcacagctcGtgccacagctgcagggcatg	15	11	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:7690922G>T	ENST00000358368.4	-	6	703	c.666C>A	c.(664-666)caC>caA	p.H222Q	XAB2_ENST00000534844.1_Missense_Mutation_p.H219Q	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	222					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CGCACAGCTCGTGCCACAGCT	0.672								Direct reversal of damage;Nucleotide excision repair (NER)																																								0			19											55	53	54					19																	7690922		2203	4300	6503	7596922	SO:0001583	missense	56949			AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.666C>A	19.37:g.7690922G>T	ENSP00000351137:p.His222Gln		7596922	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	37	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301505	0.23736	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.62498	0.02;0.02	4.61	-1.35	0.09114	.	0.065141	0.64402	D	0.000012	T	0.30324	0.0761	N	0.03608	-0.345	0.44956	D	0.997971	B	0.09022	0.002	B	0.09377	0.004	T	0.02202	-1.1196	10	0.25751	T	0.34	-45.9916	7.5803	0.27961	0.6209:0.0:0.3791:0.0	.	222	Q9HCS7	SYF1_HUMAN	Q	222;219	ENSP00000351137:H222Q;ENSP00000438225:H219Q	ENSP00000351137:H222Q	H	-	3	2	XAB2	7596922	0.177000	0.23109	0.997000	0.53966	0.968000	0.65278	-0.545000	0.06069	-0.024000	0.13941	-0.266000	0.10368	CAC		0.672	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		T	7690922	G	T	7690922	3	4	37	1	0	0	0	0	1	0	0	0	17458	1136	40	2	1957	2	XAB2	19	7690922	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	5294287	7690922	51438061	177	3260										
ZNF490	57474	hgsc.bcm.edu	37	chr19	12691348	12691348	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cgtgcacgtgcaaagactttGagtaactgaaggctttacca	10	9	0	3			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:12691348G>C	ENST00000311437.6	-	5	1663	c.1541C>G	c.(1540-1542)tCa>tGa	p.S514*	CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.Q148E|ZNF490_ENST00000465656.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						CAAAGACTTTGAGTAACTGAA	0.383																																																0			19											181	162	168					19																	12691348		2203	4300	6503	12552348	SO:0001587	stop_gained	57474			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"Zinc fingers, C2H2-type", "-"	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1541C>G	19.37:g.12691348G>C	ENSP00000311521:p.Ser514*		12552348		Nonsense_Mutation	SNP	ENST00000311437.6	37	CCDS12272.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575083	0.45902	.	.	ENSG00000188033	ENST00000311437	.	.	.	0.832	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.29708	N	0.839658	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	3.9343	0.09299	0.4162:0.0:0.5838:0.0	.	.	.	.	X	514	.	ENSP00000311521:S514X	S	-	2	0	ZNF490	12552348	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.549000	0.06041	-0.512000	0.06505	0.313000	0.20887	TCA		0.383	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		C	12691348	G	C	12691348	4	2	37	1	0	0	0	0	0	1	0	0	17980	1294	45	5	52	5	ZNF490	19	12691348	Nonsense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	5000426	12691348	46437635	178	3261										
AKAP8	10270	hgsc.bcm.edu	37	chr19	15469828	15469828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atgtctgttgttcaaaacacTcttagccacatggagactgg	9	9	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:15469828T>C	ENST00000269701.2	-	13	1633	c.1573A>G	c.(1573-1575)Agt>Ggt	p.S525G		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	525					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						TTCAAAACACTCTTAGCCACA	0.403																																					GBM(190;1671 2163 3274 27186 30476)											0			19											161	145	150					19																	15469828		2203	4300	6503	15330828	SO:0001583	missense	10270			Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"A-kinase anchor proteins"	378	protein-coding gene	gene with protein product	"A-kinase anchor protein, 95kDa"	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1573A>G	19.37:g.15469828T>C	ENSP00000269701:p.Ser525Gly		15330828		Missense_Mutation	SNP	ENST00000269701.2	37	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879773	0.72294	.	.	ENSG00000105127	ENST00000269701	T	0.50813	0.73	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000015	T	0.51143	0.1657	L	0.47190	1.495	0.80722	D	1	P	0.52842	0.956	P	0.49799	0.622	T	0.54820	-0.8236	10	0.72032	D	0.01	-25.2211	13.7399	0.62840	0.0:0.0:0.0:1.0	.	525	O43823	AKAP8_HUMAN	G	525	ENSP00000269701:S525G	ENSP00000269701:S525G	S	-	1	0	AKAP8	15330828	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	6.284000	0.72652	2.234000	0.73211	0.460000	0.39030	AGT		0.403	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		C	15469828	T	C	15469828	3	2	37	1	0	0	0	0	1	0	0	0	457	1551	54	4	513	4	AKAP8	19	15469828	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	2778480	15469828	43659155	179	3262										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20002521	20002521	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tatggaaaagtctttcataaGttttcaaattcaaacacata	4	6	4	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:20002521G>A	ENST00000589717.1	+	4	557	c.465G>A	c.(463-465)aaG>aaA	p.K155K	ZNF253_ENST00000355650.4_Silent_p.K79K|CTC-559E9.8_ENST00000585571.1_RNA|AC011477.1_ENST00000578823.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	155					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTTTCATAAGTTTTCAAATT	0.308																																																0			19											43	45	44					19																	20002521		2058	4240	6298	19863521	SO:0001819	synonymous_variant	56242			AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.465G>A	19.37:g.20002521G>A			19863521	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																				0.308	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		A	20002521	G	A	20002521	2	1	37	1	0	0	0	0	0	0	0	1	17836	1020	36	3		3	ZNF253	19	20002521	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4532693	20002521	39126462	180	3263										
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807776	20807776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tccagtatgaattatcttatGtgtagtaagggttgaggacc	11	5	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:20807776G>A	ENST00000601440.1	-	4	1053	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						ATTATCTTATGTGTAGTAAGG	0.368																																																0			19											85	94	91					19																	20807776		2180	4288	6468	20599616	SO:0001583	missense	199777			BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.907C>T	19.37:g.20807776G>A	ENSP00000469958:p.His303Tyr		20599616	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	11.32	1.604238	0.28534	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	T	0.67523	-0.27	0.865	0.865	0.19074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.83825	0.5338	H	0.95884	3.735	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	T	0.82184	-0.0583	9	0.72032	D	0.01	.	7.1124	0.25399	0.0:0.0:1.0:0.0	.	303	Q68DY1	ZN626_HUMAN	Y	303;227;303	ENSP00000445201:H303Y	ENSP00000445201:H303Y	H	-	1	0	ZNF626	20599616	1.000000	0.71417	0.306000	0.25113	0.305000	0.27757	6.564000	0.73969	0.277000	0.22141	0.282000	0.19409	CAT		0.368	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		A	20807776	G	A	20807776	3	1	37	1	0	0	0	0	1	0	0	0	18089	1377	48	3	683	3	ZNF626	19	20807776	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	805255	20807776	38321207	181	3264										
TMEM91	641649	hgsc.bcm.edu	37	chr19	41884236	41884236	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tggacagccctagtcttcgtGagcttcaacagcctctgctg	10	13	3	1	rs192256295		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:41884236G>C	ENST00000392002.2	+	2	682	c.22G>C	c.(22-24)Gag>Cag	p.E8Q	CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000436170.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000447302.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000544232.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000539627.1_Missense_Mutation_p.E8Q|TMEM91_ENST00000413014.2_Missense_Mutation_p.E8Q|TMEM91_ENST00000356385.4_Missense_Mutation_p.E8Q|CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000604123.1_Missense_Mutation_p.E65Q|TMEM91_ENST00000542945.1_Missense_Mutation_p.E8Q|BCKDHA_ENST00000595085.1_Missense_Mutation_p.E8Q	NM_001098821.1	NP_001092291.1	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91	8					hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						TAGTCTTCGTGAGCTTCAACA	0.547																																																0			19											67	66	67					19																	41884236		1881	4116	5997	46576076	SO:0001583	missense	641649			AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16							32393	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 6"					12477932	Standard	NM_001098824		Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000392002.2:c.22G>C	19.37:g.41884236G>C	ENSP00000375859:p.Glu8Gln		46576076	C9J9D1|C9JZ62|C9K046|Q6P434	Missense_Mutation	SNP	ENST00000392002.2	37	CCDS42571.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432733	0.43224	.	.	ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000142046;ENSG00000255730	ENST00000539627;ENST00000413014;ENST00000392002;ENST00000436170;ENST00000447302;ENST00000544232;ENST00000542945;ENST00000537354;ENST00000342187;ENST00000356385;ENST00000540732	D;D	0.99113	-4.33;-5.44	4.44	4.44	0.53790	.	0.000000	0.39759	N	0.001274	D	0.97108	0.9055	L	0.27053	0.805	0.09310	N	1	P;P;P;P;B;P;P	0.52061	0.917;0.917;0.917;0.917;0.13;0.629;0.95	B;B;B;B;B;B;P	0.46718	0.401;0.401;0.326;0.401;0.102;0.137;0.525	D	0.93403	0.6762	10	0.56958	D	0.05	.	12.7892	0.57523	0.0:0.0:1.0:0.0	.	8;8;8;8;8;8;8	C9J9D1;C9JZ62;C9K046;Q6P434;F5H5P2;Q6ZNR0;F5GWC9	.;.;.;.;.;TMM91_HUMAN;.	Q	8	ENSP00000375859:E8Q;ENSP00000443246:E8Q	ENSP00000443246:E8Q	E	+	1	0	CTC-435M10.3;TMEM91	46576076	0.553000	0.26513	0.270000	0.24601	0.242000	0.25591	3.821000	0.55700	2.488000	0.83962	0.561000	0.74099	GAG		0.547	TMEM91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398302.2			C	41884236	G	C	41884236	3	2	37	1	0	0	0	0	1	0	0	0	16259	1291	45	5	24	5	TMEM91	19	41884236	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	21076460	41884236	17244747	182	3265										
BCL3	602	hgsc.bcm.edu	37	chr19	45262731	45262731	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tcaccctcccagtctcccccCagggacccccctggattccc	6	23	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:45262731C>A	ENST00000164227.5	+	9	1468	c.1224C>A	c.(1222-1224)ccC>ccA	p.P408P		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	408	Pro/Ser-rich.				antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				AGTCTCCCCCCAGGGACCCCC	0.627			T	IGH@	CLL																																		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	0			19											190	205	200					19																	45262731		2203	4300	6503	49954571	SO:0001819	synonymous_variant	602			M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"Ankyrin repeat domain containing"	998	protein-coding gene	gene with protein product	"B-cell lymphoma 3-encoded protein", "B-cell leukemia/lymphoma 3", "chronic lymphatic leukemia protein"	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1224C>A	19.37:g.45262731C>A			49954571		Silent	SNP	ENST00000164227.5	37	CCDS12642.2																																																																																				0.627	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178		A	45262731	C	A	45262731	2	1	37	1	0	0	0	0	0	0	0	1	1376	581	21	2		2	BCL3	19	45262731	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	3378495	45262731	13866252	183	3266										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48922494	48922494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cactcccttgtccccagagcCctacagccccgccgtgtggg	10	19	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:48922494C>T	ENST00000263269.3	+	8	1827	c.1739C>T	c.(1738-1740)cCc>cTc	p.P580L		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	580					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TCCCCAGAGCCCTACAGCCCC	0.577																																																0			19											121	85	97					19																	48922494		2203	4300	6503	53614306	SO:0001583	missense	2906			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1739C>T	19.37:g.48922494C>T	ENSP00000263269:p.Pro580Leu		53614306		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	C	29.4	4.999137	0.93227	.	.	ENSG00000105464	ENST00000263269	T	0.56941	0.43	4.33	4.33	0.51752	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.79305	0.4423	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85509	0.1196	10	0.87932	D	0	.	16.1361	0.81490	0.0:1.0:0.0:0.0	.	580	O15399	NMDE4_HUMAN	L	580	ENSP00000263269:P580L	ENSP00000263269:P580L	P	+	2	0	GRIN2D	53614306	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.605000	0.82844	2.421000	0.82119	0.655000	0.94253	CCC		0.577	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			T	48922494	C	T	48922494	3	4	37	1	0	0	0	0	1	0	0	0	6803	623	22	3	1765	3	GRIN2D	19	48922494	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	3659763	48922494	10206489	184	3267										
ZNF547	284306	hgsc.bcm.edu	37	chr19	57889115	57889115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tggagttccacactcattacAcatcagagggttcacactgg	9	11	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:57889115A>G	ENST00000282282.3	+	4	921	c.771A>G	c.(769-771)acA>acG	p.T257T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	257					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CACTCATTACACATCAGAGGG	0.433																																																0			19											125	114	118					19																	57889115		2203	4300	6503	62580927	SO:0001819	synonymous_variant	284306			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.771A>G	19.37:g.57889115A>G			62580927	A8K5Z9|Q96NC4	Silent	SNP	ENST00000282282.3	37	CCDS33131.1																																																																																				0.433	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		G	57889115	A	G	57889115	2	3	37	1	0	0	0	0	0	0	0	1	18018	146	6	4		4	ZNF547	19	57889115	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	8966621	57889115	1239868	185	3268										
ZNF134	7693	hgsc.bcm.edu	37	chr19	58131715	58131715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggtacacaccatggactgaaActtcacacatgtggggcatg	11	10	1	1	rs373945795		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr19:58131715A>G	ENST00000396161.5	+	3	538	c.228A>G	c.(226-228)aaA>aaG	p.K76K	ZNF134_ENST00000597975.1_3'UTR	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		ATGGACTGAAACTTCACACAT	0.478																																																0			19						A		1,4087		0,1,2043	103	100	101		228	1.8	0	19		101	0,8446		0,0,4223	no	coding-synonymous	ZNF134	NM_003435.3		0,1,6266	GG,GA,AA		0.0,0.0245,0.0080		76/428	58131715	1,12533	2044	4223	6267	62823527	SO:0001819	synonymous_variant	7693			U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"Zinc fingers, C2H2-type"	12918	protein-coding gene	gene with protein product		604076	"zinc finger protein 134 (clone pHZ-15)"			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.228A>G	19.37:g.58131715A>G			62823527	Q9Y4B2	Silent	SNP	ENST00000396161.5	37	CCDS42638.1																																																																																				0.478	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		G	58131715	A	G	58131715	2	3	37	1	0	0	0	0	0	0	0	1	17763	40	2	4		4	ZNF134	19	58131715	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	242600	58131715	997268	186	3269										
PCNA	5111	hgsc.bcm.edu	37	chr20	5099470	5099470	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttatcttcggcccttagtgtAatgatatcttcattgccggc	8	10	3	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:5099470A>T	ENST00000379160.3	-	3	506	c.264T>A	c.(262-264)atT>atA	p.I88I	SNORA26_ENST00000391215.1_RNA|PCNA_ENST00000379143.5_Silent_p.I88I	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	88	Interaction with NUDT15.				base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CCCTTAGTGTAATGATATCTT	0.428								DNA polymerases (catalytic subunits)																																								0			20											225	218	220					20																	5099470		2203	4300	6503	5047470	SO:0001819	synonymous_variant	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.264T>A	20.37:g.5099470A>T			5047470	B2R897|D3DW02	Silent	SNP	ENST00000379160.3	37	CCDS13087.1																																																																																				0.428	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			T	5099470	A	T	5099470	2	4	37	1	0	0	0	0	0	0	0	1	11619	358	13	5		5	PCNA	20	5099470	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10		5099470	57926050	187	3270										
LRRN4	164312	hgsc.bcm.edu	37	chr20	6022178	6022178	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gtgtcttccccgctgaggccGgggcaccggcaccgccaccg	14	18	1	1	rs555054750		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:6022178G>T	ENST00000378858.4	-	5	1937	c.1713C>A	c.(1711-1713)ccC>ccA	p.P571P		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	571					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						CGCTGAGGCCGGGGCACCGGC	0.697																																																0			20											56	63	60					20																	6022178		2202	4298	6500	5970178	SO:0001819	synonymous_variant	164312			AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"Fibronectin type III domain containing"	16208	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 75"	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.1713C>A	20.37:g.6022178G>T			5970178	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	37	CCDS13097.1																																																																																				0.697	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		T	6022178	G	T	6022178	2	4	37	1	0	0	0	0	0	0	0	1	9066	1103	39	2		2	LRRN4	20	6022178	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	922708	6022178	57003342	188	3271										
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30729599	30729599	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	aacctgcctgtggccacccgGctggagctctactccaaccg	10	17	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:30729599G>A	ENST00000398022.2	+	5	664	c.429G>A	c.(427-429)cgG>cgA	p.R143R	TM9SF4_ENST00000217315.5_Silent_p.R126R	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	143						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TGGCCACCCGGCTGGAGCTCT	0.577																																																0			20											104	118	114					20																	30729599		2203	4300	6503	30193260	SO:0001819	synonymous_variant	9777			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.429G>A	20.37:g.30729599G>A			30193260	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	37	CCDS13196.2																																																																																				0.577	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		A	30729599	G	A	30729599	2	1	37	1	0	0	0	0	0	0	0	1	16019	1190	42	3		3	TM9SF4	20	30729599	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	24707421	30729599	32295921	189	3272										
ERGIC3	51614	hgsc.bcm.edu	37	chr20	34136262	34136262	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	cgtcactccctgccctacagGtgctgtaacacctgtgaaga	9	14	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:34136262G>A	ENST00000348547.2	+	6	539	c.462G>A	c.(460-462)aaG>aaA	p.K154K	ERGIC3_ENST00000447986.1_Splice_Site_p.K154K|ERGIC3_ENST00000482338.1_3'UTR|ERGIC3_ENST00000357394.4_Splice_Site_p.K154K|ERGIC3_ENST00000279052.6_Splice_Site_p.K154K	NM_015966.2	NP_057050.1	Q9Y282	ERGI3_HUMAN	ERGIC and golgi 3	154					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)	16	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			TGCCCTACAGGTGCTGTAACA	0.557																																																0			20											58	55	56					20																	34136262		2203	4300	6503	33599676	SO:0001630	splice_region_variant	51614			AF077030	CCDS13257.1, CCDS13258.1	20q11.22	2013-09-19	2006-01-19	2006-01-19	ENSG00000125991	ENSG00000125991			15927	protein-coding gene	gene with protein product			"serologically defined breast cancer antigen 84", "chromosome 20 open reading frame 47"	SDBCAG84, C20orf47		10810093	Standard	NM_015966		Approved	CGI-54, PRO0989, NY-BR-84, Erv46	uc002xcs.3	Q9Y282	OTTHUMG00000032346	ENST00000348547.2:c.462-1G>A	20.37:g.34136262G>A			33599676	Q5JWS3|Q6ZWP7|Q9H276|Q9P1L3	Silent	SNP	ENST00000348547.2	37	CCDS13257.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	10.51|10.51	1.371023|1.371023	0.24771|0.24771	.|.	.|.	ENSG00000125991|ENSG00000125991	ENST00000416206|ENST00000413587	.|.	.|.	.|.	4.74|4.74	2.38|2.38	0.29361|0.29361	.|.	.|.	.|.	.|.	.|.	T|T	0.55878|0.55878	0.1948|0.1948	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50709|0.50709	-0.8796|-0.8796	4|4	.|.	.|.	.|.	.|.	7.7232|7.7232	0.28744|0.28744	0.2267:0.1292:0.644:0.0|0.2267:0.1292:0.644:0.0	.|.	.|.	.|.	.|.	N|M	153|156	.|.	.|.	S|V	+|+	2|1	0|0	ERGIC3|ERGIC3	33599676|33599676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.831000|0.831000	0.47069|0.47069	1.628000|1.628000	0.37060|0.37060	1.006000|1.006000	0.39211|0.39211	-0.354000|-0.354000	0.07668|0.07668	AGT|GTG		0.557	ERGIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078880.2	NM_015966	Silent	A	34136262	G	A	34136262	5	1	37	1	0	0	0	0	0	0	1	0	5238	1275	44	3	484	3	ERGIC3	20	34136262	Splice_Site	SNP	G	TCGA-AG-3731-01A-11D-1733-10	3406663	34136262	28889258	190	3273										
BCAS1	8537	hgsc.bcm.edu	37	chr20	52645320	52645320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgatccaagggatgaatctgCggcttggtctccggtacgtc	13	10	2	2	rs201371925		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:52645320C>T	ENST00000395961.3	-	4	500	c.334G>A	c.(334-336)Gca>Aca	p.A112T	BCAS1_ENST00000371435.2_Missense_Mutation_p.A112T|BCAS1_ENST00000411563.1_Missense_Mutation_p.A15T|BCAS1_ENST00000371440.3_Missense_Mutation_p.A112T	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	112						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GATGAATCTGCGGCTTGGTCT	0.532																																																0			20											71	68	69					20																	52645320		2203	4300	6503	52078727	SO:0001583	missense	8537			AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.334G>A	20.37:g.52645320C>T	ENSP00000379290:p.Ala112Thr		52078727	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	C	1.524	-0.546098	0.04024	.	.	ENSG00000064787	ENST00000371440;ENST00000395961;ENST00000371435;ENST00000411563	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	5.11	-3.93	0.04143	.	0.785958	0.11479	N	0.559912	T	0.00784	0.0026	N	0.00142	-2.005	0.09310	N	0.999999	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.38520	-0.9657	10	0.02654	T	1	-0.4969	4.5089	0.11901	0.5014:0.2285:0.0:0.2701	.	15;112;112;112;112;112	B4E2C4;B2RCQ5;O75363-2;G3XAF7;A0AVG7;O75363	.;.;.;.;.;BCAS1_HUMAN	T	112;112;112;15	ENSP00000360495:A112T;ENSP00000379290:A112T;ENSP00000360490:A112T;ENSP00000397442:A15T	ENSP00000360490:A112T	A	-	1	0	BCAS1	52078727	0.082000	0.21442	0.548000	0.28192	0.660000	0.38997	-0.061000	0.11693	-1.046000	0.03246	-0.414000	0.06135	GCA		0.532	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		T	52645320	C	T	52645320	3	4	37	1	0	0	0	0	1	0	0	0	1351	768	27	1	1456	1	BCAS1	20	52645320	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	18509058	52645320	10380200	191	3274										
VAPB	9217	hgsc.bcm.edu	37	chr20	56993271	56993271	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctgtctcattctacaggtccCttcaccgatgttgtcaccac	6	15	4	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr20:56993271C>T	ENST00000475243.1	+	2	401	c.63C>T	c.(61-63)ccC>ccT	p.P21P	VAPB_ENST00000265619.2_3'UTR|VAPB_ENST00000395802.3_Silent_p.P21P	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	21	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			CTACAGGTCCCTTCACCGATG	0.448																																																0			20											138	126	130					20																	56993271		2203	4300	6503	56426677	SO:0001819	synonymous_variant	9217			AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.63C>T	20.37:g.56993271C>T			56426677	A2A2F2|O95293|Q9P0H0	Silent	SNP	ENST00000475243.1	37	CCDS33498.1																																																																																				0.448	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2			T	56993271	C	T	56993271	2	4	37	1	0	0	0	0	0	0	0	1	17162	668	24	3		3	VAPB	20	56993271	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	4347951	56993271	6032249	192	3275										
BAGE	85319	hgsc.bcm.edu	37	chr21	11098733	11098733	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gccatcttactgctccggccGccatcttactgctccagccc	7	19	2	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr21:11098733G>A	ENST00000470054.1	-	0	192							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgctccggccgccatcttact	0.632																																																0			21											104	151	135					21																	11098733		2124	4261	6385	10120604			574			AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11098733G>A			10120604	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																					0.632	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		A	11098733	G	A	11098733	1	1	37	0	1	0	0	0	0	0	0	0	1292	1087	38	1		1	BAGE	21	11098733	RNA	SNP	G	TCGA-AG-3731-01A-11D-1733-10		11098733	37031162	193	3276										
ADORA2A	135	hgsc.bcm.edu	37	chr22	24836656	24836656	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atgctaggttggaacaactgCggtcagccaaaggagggcaa	14	8	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:24836656C>T	ENST00000337539.7	+	3	897	c.438C>T	c.(436-438)tgC>tgT	p.C146C	ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A_ENST00000496497.1_3'UTR|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	146					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GGAACAACTGCGGTCAGCCAA	0.587																																																0			22											189	184	186					22																	24836656		2203	4300	6503	23166656	SO:0001819	synonymous_variant	135			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.438C>T	22.37:g.24836656C>T			23166656	B2R7E0	Silent	SNP	ENST00000337539.7	37	CCDS13826.1																																																																																				0.587	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24836656	C	T	24836656	2	4	37	1	0	0	0	0	0	0	0	1	327	776	27	1		1	ADORA2A	22	24836656	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10		24836656	26467910	194	3277										
THOC5	8563	hgsc.bcm.edu	37	chr22	29921864	29921864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gatcagctccatggcagttgTcactttggcttttactgtca	9	10	3	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:29921864T>C	ENST00000490103.1	-	12	1260	c.1138A>G	c.(1138-1140)Aca>Gca	p.T380A	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.T380A|THOC5_ENST00000397872.1_Missense_Mutation_p.T380A|THOC5_ENST00000397873.2_Missense_Mutation_p.T380A	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	380			T -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATGGCAGTTGTCACTTTGGCT	0.507																																																0			22											193	154	167					22																	29921864		2203	4300	6503	28251864	SO:0001583	missense	8563			AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1138A>G	22.37:g.29921864T>C	ENSP00000420306:p.Thr380Ala		28251864	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.441|8.441	0.850758|0.850758	0.17034|0.17034	.|.	.|.	ENSG00000100296|ENSG00000100296	ENST00000443089|ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	.|T;T;T;T	.|0.23147	.|1.92;1.92;1.92;1.92	6.07|6.07	5.03|5.03	0.67393|0.67393	.|.	.|0.198934	.|0.56097	.|D	.|0.000039	T|T	0.17323|0.17323	0.0416|0.0416	L|L	0.34521|0.34521	1.04|1.04	0.35455|0.35455	D|D	0.796031|0.796031	.|B	.|0.20164	.|0.042	.|B	.|0.21917	.|0.037	T|T	0.17930|0.17930	-1.0353|-1.0353	5|10	.|0.11485	.|T	.|0.65	-11.7893|-11.7893	8.6602|8.6602	0.34088|0.34088	0.1285:0.0:0.1348:0.7367|0.1285:0.0:0.1348:0.7367	.|.	.|380	.|Q13769	.|THOC5_HUMAN	G|A	250|380	.|ENSP00000420306:T380A;ENSP00000380970:T380A;ENSP00000380969:T380A;ENSP00000380971:T380A	.|ENSP00000380969:T380A	D|T	-|-	2|1	0|0	THOC5|THOC5	28251864|28251864	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.390000|0.390000	0.30446|0.30446	2.973000|2.973000	0.49264|0.49264	1.093000|1.093000	0.41377|0.41377	-0.333000|-0.333000	0.08304|0.08304	GAC|ACA		0.507	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		C	29921864	T	C	29921864	3	2	37	1	0	0	0	0	1	0	0	0	15907	1667	58	4	949	4	THOC5	22	29921864	Missense_Mutation	SNP	T	TCGA-AG-3731-01A-11D-1733-10	5085208	29921864	21382702	195	3278										
SGSM3	27352	hgsc.bcm.edu	37	chr22	40802178	40802178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctgggacctgtttttctacgAgggctcccgggtgctgttcc	13	12	1	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:40802178A>G	ENST00000248929.9	+	9	1100	c.911A>G	c.(910-912)gAg>gGg	p.E304G	SGSM3_ENST00000454798.2_Missense_Mutation_p.E237G	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						TTTTTCTACGAGGGCTCCCGG	0.627																																																0			22											83	73	76					22																	40802178		2203	4300	6503	39132124	SO:0001583	missense	27352			AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.911A>G	22.37:g.40802178A>G	ENSP00000248929:p.Glu304Gly		39132124		Missense_Mutation	SNP	ENST00000248929.9	37	CCDS14002.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628349	0.87560	.	.	ENSG00000100359	ENST00000457767;ENST00000248929;ENST00000545416;ENST00000454798	T;T;T	0.15487	2.42;2.42;2.42	4.85	4.85	0.62838	Rab-GAP/TBC domain (4);	0.107661	0.64402	D	0.000006	T	0.46521	0.1397	H	0.94183	3.505	0.58432	D	0.999993	P;B;P;P;P	0.50443	0.51;0.29;0.921;0.935;0.935	B;B;P;P;P	0.54174	0.312;0.375;0.735;0.744;0.744	T	0.63341	-0.6659	10	0.72032	D	0.01	.	15.1445	0.72641	1.0:0.0:0.0:0.0	.	241;237;304;304;304	B4DVE3;B4DMS2;Q96HU1-2;B9A6J5;Q96HU1	.;.;.;.;SGSM3_HUMAN	G	237;304;247;237	ENSP00000399249:E237G;ENSP00000248929:E304G;ENSP00000390998:E237G	ENSP00000248929:E304G	E	+	2	0	SGSM3	39132124	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	5.648000	0.67930	2.129000	0.65627	0.260000	0.18958	GAG		0.627	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		G	40802178	A	G	40802178	3	3	37	1	0	0	0	0	1	0	0	0	14261	304	11	4	941	4	SGSM3	22	40802178	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	10880314	40802178	10502388	196	3279										
PHF21B	112885	hgsc.bcm.edu	37	chr22	45312408	45312408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggctgggctggggttcttgaCgctgaccacggtggccttct	16	11	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:45312408C>T	ENST00000313237.5	-	4	466	c.316G>A	c.(316-318)Gtc>Atc	p.V106I	PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000404079.2_Missense_Mutation_p.V94I|PHF21B_ENST00000396103.3_Missense_Mutation_p.V106I|PHF21B_ENST00000447824.3_Missense_Mutation_p.V94I	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	106							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		GGGTTCTTGACGCTGACCACG	0.697																																																0			22											43	47	46					22																	45312408		2202	4300	6502	43691072	SO:0001583	missense	112885			AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"Zinc fingers, PHD-type"	25161	protein-coding gene	gene with protein product			"PHD finger protein 4"	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.316G>A	22.37:g.45312408C>T	ENSP00000324403:p.Val106Ile		43691072	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	37	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	C	3.658	-0.070121	0.07228	.	.	ENSG00000056487	ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000420689	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.21	0.465	0.16711	.	0.325833	0.28718	N	0.014369	T	0.06371	0.0164	N	0.02916	-0.46	0.19575	N	0.999966	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.41805	-0.9488	10	0.02654	T	1	-24.1219	9.6005	0.39601	0.0:0.263:0.0:0.737	.	94;106;94;106	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2	.;.;.;PF21B_HUMAN	I	106;106;94;94;94	ENSP00000324403:V106I;ENSP00000379410:V106I;ENSP00000385105:V94I;ENSP00000388619:V94I;ENSP00000401294:V94I	ENSP00000324403:V106I	V	-	1	0	PHF21B	43691072	1.000000	0.71417	0.959000	0.39883	0.982000	0.71751	1.657000	0.37366	-0.238000	0.09724	-0.982000	0.02568	GTC		0.697	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415		T	45312408	C	T	45312408	3	4	37	1	0	0	0	0	1	0	0	0	11865	536	19	1	1319	1	PHF21B	22	45312408	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	4510230	45312408	5992158	197	3280										
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50538027	50538027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttctctctggagagtgtgtgCgaaggtatgctcaggggtct	15	7	4	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chr22:50538027C>T	ENST00000262794.5	+	3	521	c.438C>T	c.(436-438)tgC>tgT	p.C146C	MOV10L1_ENST00000395858.3_Silent_p.C146C|MOV10L1_ENST00000540615.1_Silent_p.C126C|MOV10L1_ENST00000545383.1_Silent_p.C146C|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000475190.1_3'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	146					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		AGAGTGTGTGCGAAGGTATGC	0.512																																																0			22											113	94	101					22																	50538027		2203	4300	6503	48880154	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.438C>T	22.37:g.50538027C>T			48880154	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.512	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50538027	C	T	50538027	2	4	37	1	0	0	0	0	0	0	0	1	9749	776	27	1		1	MOV10L1	22	50538027	Silent	SNP	C	TCGA-AG-3731-01A-11D-1733-10	5225619	50538027	766539	198	3281										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12734761	12734761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgtgaagagcttccaggccgCggaggggatcgaggaacccc	16	11	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12734761C>T	ENST00000380682.1	+	15	2689	c.2183C>T	c.(2182-2184)gCg>gTg	p.A728V		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	728					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.A728V(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TTCCAGGCCGCGGAGGGGATC	0.547																																																1	Substitution - Missense(1)	ovary(1)	X											106	108	107					X																	12734761		2203	4300	6503	12644682	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2183C>T	X.37:g.12734761C>T	ENSP00000370057:p.Ala728Val		12644682	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192817	0.38707	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.27104	1.69	5.71	5.71	0.89125	.	0.304412	0.35870	N	0.002934	T	0.28234	0.0697	M	0.63428	1.95	0.09310	N	1	B;B	0.31459	0.324;0.324	B;B	0.23852	0.049;0.049	T	0.16394	-1.0404	10	0.22706	T	0.39	.	18.8648	0.92287	0.0:1.0:0.0:0.0	.	720;728	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	V	728;719;717	ENSP00000370057:A728V	ENSP00000304583:A717V	A	+	2	0	FRMPD4	12644682	0.519000	0.26242	0.005000	0.12908	0.097000	0.18754	5.634000	0.67833	2.402000	0.81655	0.600000	0.82982	GCG		0.547	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12734761	C	T	12734761	3	4	37	1	0	0	0	0	1	0	0	0	6078	768	27	1	2241	1	FRMPD4	23	12734761	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10		12734761	142535799	199	3282										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937316	12937316	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgcagagtgcagcaatcgtCgactacaggaagttccccaa	10	11	0	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12937316C>T	ENST00000218032.6	+	2	244	c.157C>T	c.(157-159)Cga>Tga	p.R53*	TLR8_ENST00000311912.5_Nonsense_Mutation_p.R71*	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	53					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.R71*(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGCAATCGTCGACTACAGGA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											100	91	94					X																	12937316		2203	4300	6503	12847237	SO:0001587	stop_gained	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.157C>T	X.37:g.12937316C>T	ENSP00000218032:p.Arg53*		12847237	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Nonsense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116415	0.56505	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	.	.	.	5.17	3.37	0.38596	.	0.824012	0.09906	N	0.740514	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.859	0.41103	0.0:0.7852:0.1368:0.078	.	.	.	.	X	53;71	.	ENSP00000218032:R53X	R	+	1	2	TLR8	12847237	0.032000	0.19561	0.000000	0.03702	0.160000	0.22226	2.131000	0.42074	0.410000	0.25675	0.523000	0.50628	CGA		0.413	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		T	12937316	C	T	12937316	4	4	37	1	0	0	0	0	0	1	0	0	15996	876	31	1	163	1	TLR8	23	12937316	Nonsense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	202555	12937316	142333244	200	3283										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938669	12938669	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ggccaaaccaatttgaaaatCttcctgacattgcctgttta	6	10	1	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:12938669C>A	ENST00000218032.6	+	2	1597	c.1510C>A	c.(1510-1512)Ctt>Att	p.L504I	TLR8_ENST00000311912.5_Missense_Mutation_p.L522I	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	504					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	ATTTGAAAATCTTCCTGACAT	0.373																																																0			X											47	45	45					X																	12938669		2203	4300	6503	12848590	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1510C>A	X.37:g.12938669C>A	ENSP00000218032:p.Leu504Ile		12848590	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	2.979	-0.210730	0.06140	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	D;D	0.82526	-1.62;-1.62	5.97	3.56	0.40772	.	0.184908	0.26099	N	0.026349	T	0.76919	0.4055	M	0.66939	2.045	0.09310	N	1	B;B	0.31581	0.329;0.329	B;B	0.27887	0.084;0.084	T	0.70839	-0.4763	10	0.72032	D	0.01	.	4.8411	0.13491	0.1348:0.2705:0.0:0.5947	.	504;522	Q9NR97;D1CS70	TLR8_HUMAN;.	I	504;522	ENSP00000218032:L504I;ENSP00000312082:L522I	ENSP00000218032:L504I	L	+	1	0	TLR8	12848590	0.009000	0.17119	0.019000	0.16419	0.136000	0.21042	0.348000	0.20031	0.877000	0.35895	-0.340000	0.08031	CTT		0.373	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12938669	C	A	12938669	3	1	37	1	0	0	0	0	1	0	0	0	15996	913	32	2	1516	2	TLR8	23	12938669	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	1353	12938669	142331891	201	3284										
MAP7D2	256714	hgsc.bcm.edu	37	chrX	20033383	20033383	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgctcaatctgcagcataatCtgttctctctcgagacgcat	7	12	5	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:20033383C>G	ENST00000379651.3	-	11	1602	c.1584G>C	c.(1582-1584)caG>caC	p.Q528H	MIR23C_ENST00000579846.1_RNA|MAP7D2_ENST00000443379.3_Missense_Mutation_p.Q483H|MAP7D2_ENST00000379643.5_Missense_Mutation_p.Q569H|MAP7D2_ENST00000543767.1_Missense_Mutation_p.Q413H|MAP7D2_ENST00000452324.3_Missense_Mutation_p.Q476H	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	528					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						GCAGCATAATCTGTTCTCTCT	0.458																																																0			X											196	148	164					X																	20033383		2203	4300	6503	19943304	SO:0001583	missense	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1584G>C	X.37:g.20033383C>G	ENSP00000368972:p.Gln528His		19943304	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878461	0.51801	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	5.6	2.34	0.29019	.	0.000000	0.64402	D	0.000003	T	0.45175	0.1329	M	0.78637	2.42	0.39036	D	0.960034	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.996	D;D;D;D;D	0.81914	0.986;0.976;0.976;0.995;0.968	T	0.41520	-0.9504	10	0.66056	D	0.02	-14.5599	5.7878	0.18343	0.0:0.5608:0.1606:0.2787	.	483;476;569;528;413	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	H	528;569;413;483;211;476	ENSP00000368972:Q528H;ENSP00000368964:Q569H;ENSP00000440691:Q413H;ENSP00000388239:Q483H;ENSP00000413301:Q476H	ENSP00000368964:Q569H	Q	-	3	2	MAP7D2	19943304	0.362000	0.24980	1.000000	0.80357	0.714000	0.41099	-0.375000	0.07475	0.512000	0.28257	0.508000	0.49915	CAG		0.458	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		G	20033383	C	G	20033383	3	3	37	1	0	0	0	0	1	0	0	0	9298	912	32	5	634	5	MAP7D2	23	20033383	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	7094714	20033383	135237177	202	3285										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149658	34149693	+	In_Frame_Del	DEL	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	-													0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	atgggaggccccgggcggatAtgggacactccagtctctgg					rs367563899|rs201090915|rs201363312|rs373732464		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENST00000346193.3	-	1	754_789	c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	c.(703-738)ctccgcccggagcctccagagactggagtgtcccatdel	p.LRPEPPETGVSH235del		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	235	Pro-rich.							p.L235_H246delLRPEPPETGVSH(1)|p.P240P(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CCGGGCGGATATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAGATGGGACACT	0.627														5	0.0013245	0	0	3775	,	,		15035	0		0.004	False		,,,				2504	0.001															2	Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|lung(1)	X								33,3667		0,20,13,1562,523						-0.3	0			32	98,6373		2,62,32,2290,1731	no	coding	FAM47A	NM_203408.3		2,82,45,3852,2254	A1A1,A1R,A1,RR,R		1.5144,0.8919,1.288				131,10040				34059614	SO:0001651	inframe_deletion	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	X.37:g.34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENSP00000345029:p.Leu235_His246del		34059579	A8K8I9|Q8TAA0	In_Frame_Del	DEL	ENST00000346193.3	37	CCDS43926.1																																																																																				0.627	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		-	34149693	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	-	34149658	7	5	37	1	0	1	0	1	0	0	0	0	5588	446	16	0	1641	0	FAM47A	23	34149658	In_Frame_Del	DEL	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	TCGA-AG-3731-01A-11D-1733-10	14116275	34149658	121120902	203	3286										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37026939	37026939	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctactacaggtactgaaaccGctggaccctgagaggaagct	11	11	0	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:37026939G>A	ENST00000358047.3	+	1	508	c.456G>A	c.(454-456)ccG>ccA	p.P152P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	152										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TACTGAAACCGCTGGACCCTG	0.557																																																0			X											64	56	59					X																	37026939		2202	4300	6502	36936860	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.456G>A	X.37:g.37026939G>A			36936860	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.557	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37026939	G	A	37026939	2	1	37	1	0	0	0	0	0	0	0	1	5590	1074	38	1		1	FAM47C	23	37026939	Silent	SNP	G	TCGA-AG-3731-01A-11D-1733-10	2877281	37026939	118243621	204	3287										
WNK3	65267	hgsc.bcm.edu	37	chrX	54334413	54334413	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	actcagaataaggatactccGatgtggccatttccagcata	8	10	1	1			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:54334413G>A	ENST00000375159.2	-	4	1030	c.1031C>T	c.(1030-1032)tCg>tTg	p.S344L	WNK3_ENST00000354646.2_Missense_Mutation_p.S344L|WNK3_ENST00000375169.3_Missense_Mutation_p.S344L			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	344	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AGGATACTCCGATGTGGCCAT	0.388																																																0			X											170	147	155					X																	54334413		2203	4300	6503	54351138	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1031C>T	X.37:g.54334413G>A	ENSP00000364301:p.Ser344Leu		54351138	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.941565	0.73557	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.23552	1.9;1.9;1.9	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000175	T	0.24122	0.0584	N	0.02181	-0.65	0.47511	D	0.999446	P;D	0.61080	0.934;0.989	P;P	0.61397	0.731;0.888	T	0.51787	-0.8661	10	0.56958	D	0.05	-5.7368	17.083	0.86603	0.0:0.0:1.0:0.0	.	344;344	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	L	344	ENSP00000364312:S344L;ENSP00000346667:S344L;ENSP00000364301:S344L	ENSP00000346667:S344L	S	-	2	0	WNK3	54351138	1.000000	0.71417	0.898000	0.35279	0.333000	0.28666	9.757000	0.98924	2.386000	0.81285	0.544000	0.68410	TCG		0.388	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		A	54334413	G	A	54334413	3	1	37	1	0	0	0	0	1	0	0	0	17419	1059	37	1	4451	1	WNK3	23	54334413	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	17307474	54334413	100936147	205	3288										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118971919	118971919	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tacggcgctcttcttcttgcCgcttcagcctctctctttct	6	16	7	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:118971919C>A	ENST00000276201.2	-	10	1172	c.1103G>T	c.(1102-1104)cGg>cTg	p.R368L	UPF3B_ENST00000345865.2_Missense_Mutation_p.R355L|UPF3B_ENST00000478840.1_5'Flank	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	368	Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						TTCTTCTTGCCGCTTCAGCCT	0.473																																																0			X											148	126	134					X																	118971919		2203	4300	6503	118855947	SO:0001583	missense	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.1103G>T	X.37:g.118971919C>A	ENSP00000276201:p.Arg368Leu		118855947	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.480885	0.44044	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	T;T	0.79454	-1.19;-1.27	5.59	5.59	0.84812	.	0.215397	0.47852	D	0.000211	T	0.76392	0.3981	M	0.63843	1.955	0.53005	D	0.999968	P;P	0.51933	0.949;0.914	P;P	0.48114	0.567;0.448	T	0.72798	-0.4184	10	0.13853	T	0.58	.	11.1005	0.48170	0.0:0.9145:0.0:0.0855	.	355;368	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	L	368;355	ENSP00000276201:R368L;ENSP00000245418:R355L	ENSP00000276201:R368L	R	-	2	0	UPF3B	118855947	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.688000	0.46984	2.360000	0.80028	0.526000	0.51066	CGG		0.473	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			A	118971919	C	A	118971919	3	1	37	1	0	0	0	0	1	0	0	0	17046	652	23	2	356	2	UPF3B	23	118971919	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	64637506	118971919	36298641	206	3289										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517987	123517987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	gccctaggctggacttactcGcgacacgtcgcccaagccca	10	17	0	0	rs372260419		TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:123517987G>A	ENST00000371130.3	-	29	6836	c.6773C>T	c.(6772-6774)gCg>gTg	p.A2258V	TENM1_ENST00000422452.2_Missense_Mutation_p.A2265V|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2258					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A2260V(1)									GGACTTACTCGCGACACGTCG	0.458																																																1	Substitution - Missense(1)	ovary(1)	X						G	VAL/ALA,VAL/ALA,VAL/ALA	1,3834		0,1,1631,571	99	95	96		6794,6791,6773	5.7	1	X		96	0,6728		0,0,2428,1872	no	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	64,64,64	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	possibly-damaging,possibly-damaging,possibly-damaging	2265/2733,2264/2732,2258/2726	123517987	1,10562	2203	4300	6503	123345668	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6773C>T	X.37:g.123517987G>A	ENSP00000360171:p.Ala2258Val		123345668	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249756	0.80024	2.61E-4	0.0	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86769	-2.17;-2.13	5.66	5.66	0.87406	.	0.051235	0.85682	D	0.000000	D	0.91489	0.7313	L	0.53561	1.675	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.63793	0.918;0.692;0.647	D	0.91220	0.5006	10	0.48119	T	0.1	.	18.6847	0.91559	0.0:0.0:1.0:0.0	.	2264;2265;2258	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	2258;2265	ENSP00000360171:A2258V;ENSP00000403954:A2265V	ENSP00000360171:A2258V	A	-	2	0	ODZ1	123345668	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.022000	0.88759	2.356000	0.79943	0.600000	0.82982	GCG		0.458	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123517987	G	A	123517987	3	1	37	1	0	0	0	0	1	0	0	0	10865	1087	38	1	1416	1	ODZ1	23	123517987	Missense_Mutation	SNP	G	TCGA-AG-3731-01A-11D-1733-10	4546068	123517987	31752573	207	3290										
GPR112	139378	hgsc.bcm.edu	37	chrX	135430849	135430849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ttgtaaaaaccgttcccaccAccattatggctgggatagtg	9	10	0	0			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:135430849A>G	ENST00000394143.1	+	6	5275	c.4984A>G	c.(4984-4986)Acc>Gcc	p.T1662A	GPR112_ENST00000370652.1_Missense_Mutation_p.T1662A|GPR112_ENST00000412101.1_Missense_Mutation_p.T1457A|GPR112_ENST00000394141.1_Missense_Mutation_p.T1457A|GPR112_ENST00000287534.4_Missense_Mutation_p.T1599A	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1662					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CGTTCCCACCACCATTATGGC	0.478																																																0			X											153	153	153					X																	135430849		2203	4300	6503	135258515	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4984A>G	X.37:g.135430849A>G	ENSP00000377699:p.Thr1662Ala		135258515	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	17.27	3.346207	0.61073	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.37915	1.21;1.21;1.17;1.28;1.17	3.39	-5.38	0.02673	.	.	.	.	.	T	0.23926	0.0579	L	0.32530	0.975	0.09310	N	1	P;P;P	0.49783	0.928;0.597;0.646	P;B;B	0.46975	0.533;0.242;0.162	T	0.16041	-1.0416	9	0.62326	D	0.03	.	0.8592	0.01189	0.2145:0.3331:0.122:0.3304	.	1599;1457;1662	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	A	1662;1662;1457;1599;1457	ENSP00000377699:T1662A;ENSP00000359686:T1662A;ENSP00000416526:T1457A;ENSP00000287534:T1599A;ENSP00000377697:T1457A	ENSP00000287534:T1599A	T	+	1	0	GPR112	135258515	0.000000	0.05858	0.000000	0.03702	0.611000	0.37282	0.220000	0.17660	-0.631000	0.05560	0.347000	0.21830	ACC		0.478	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135430849	A	G	135430849	3	3	37	1	0	0	0	0	1	0	0	0	6649	159	6	4	4994	4	GPR112	23	135430849	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	11912862	135430849	19839711	208	3291										
FGF13	2258	hgsc.bcm.edu	37	chrX	137717737	137717737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	ctcggcctgactgctgctgaCggtatatcattgatgaatat	10	9	1	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:137717737C>T	ENST00000315930.6	-	4	1143	c.482G>A	c.(481-483)cGt>cAt	p.R161H	FGF13_ENST00000305414.4_Missense_Mutation_p.R108H|FGF13_ENST00000541469.1_Missense_Mutation_p.R115H|FGF13_ENST00000441825.2_Missense_Mutation_p.R142H|FGF13_ENST00000370603.3_Missense_Mutation_p.R171H	NM_004114.3	NP_004105.1	Q92913	FGF13_HUMAN	fibroblast growth factor 13	161	Mediates interaction with sodium channels.				cell-cell signaling (GO:0007267)|cerebral cortex cell migration (GO:0021795)|establishment of neuroblast polarity (GO:0045200)|hippocampus development (GO:0021766)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|microtubule polymerization (GO:0046785)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of microtubule depolymerization (GO:0007026)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|positive regulation of protein kinase activity (GO:0045860)|protein localization to plasma membrane (GO:0072659)|signal transduction (GO:0007165)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|filopodium (GO:0030175)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|microtubule (GO:0005874)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-tubulin binding (GO:0048487)|growth factor activity (GO:0008083)|ion channel binding (GO:0044325)|microtubule binding (GO:0008017)|protein kinase activator activity (GO:0030295)|sodium channel regulator activity (GO:0017080)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	24	Acute lymphoblastic leukemia(192;0.000127)					CTGCTGCTGACGGTATATCAT	0.398																																																0			X											153	128	136					X																	137717737		2203	4300	6503	137545403	SO:0001583	missense	2258			BC034340	CCDS14664.1, CCDS14665.1, CCDS55511.1	Xq26.3	2008-02-05			ENSG00000129682	ENSG00000129682			3670	protein-coding gene	gene with protein product	"fibroblast growth factor homologous factor 2"	300070				8790420	Standard	NM_033642		Approved	FHF2, FGF2	uc011mwj.2	Q92913	OTTHUMG00000022532	ENST00000315930.6:c.482G>A	X.37:g.137717737C>T	ENSP00000322390:p.Arg161His		137545403	B1AK18|B7Z4M7|B7Z8N0|D3DWH4|O95830|Q9NZH9|Q9NZI0	Missense_Mutation	SNP	ENST00000315930.6	37	CCDS14665.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995021	0.93167	.	.	ENSG00000129682	ENST00000315930;ENST00000305414;ENST00000441825;ENST00000370603;ENST00000541469;ENST00000436198;ENST00000455663	T;T;T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.82495	0.5049	M	0.75150	2.29	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.977;0.987;0.96;0.992	D	0.83631	0.0145	10	0.87932	D	0	.	18.5888	0.91200	0.0:1.0:0.0:0.0	.	115;171;108;161	B7Z8N0;B7Z4M7;Q92913-2;Q92913	.;.;.;FGF13_HUMAN	H	161;108;142;171;115;171;177	ENSP00000322390:R161H;ENSP00000303391:R108H;ENSP00000409276:R142H;ENSP00000359635:R171H;ENSP00000437903:R115H;ENSP00000396198:R171H;ENSP00000406916:R177H	ENSP00000303391:R108H	R	-	2	0	FGF13	137545403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.618000	0.88619	0.600000	0.82982	CGT		0.398	FGF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058534.2	NM_004114		T	137717737	C	T	137717737	3	4	37	1	0	0	0	0	1	0	0	0	5861	536	19	1	263	1	FGF13	23	137717737	Missense_Mutation	SNP	C	TCGA-AG-3731-01A-11D-1733-10	2286888	137717737	17552823	209	3292										
FMR1	2332	hgsc.bcm.edu	37	chrX	147011728	147011728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tgcgcactaagttgtctctgAtaatgagaaatgaagaagct	10	6	1	4			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:147011728A>G	ENST00000370475.4	+	7	723	c.595A>G	c.(595-597)Ata>Gta	p.I199V	FMR1_ENST00000370470.1_Missense_Mutation_p.I199V|FMR1_ENST00000439526.2_Missense_Mutation_p.I199V|FMR1_ENST00000370477.1_Missense_Mutation_p.I199V|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000370471.3_Missense_Mutation_p.I199V|FMR1_ENST00000334557.6_Missense_Mutation_p.I199V|FMR1_ENST00000218200.8_Missense_Mutation_p.I199V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	199					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GTTGTCTCTGATAATGAGAAA	0.413									Fragile X syndrome																																							0			X											137	114	122					X																	147011728		2203	4300	6503	146819420	SO:0001583	missense	2477	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.595A>G	X.37:g.147011728A>G	ENSP00000359506:p.Ile199Val		146819420	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314123	0.40996	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.55588	1.28;0.51;1.28;1.28;1.58;1.29;1.3	5.06	5.06	0.68205	.	0.097230	0.85682	D	0.000000	T	0.42944	0.1225	L	0.36672	1.1	0.80722	D	1	B;B;B;B;B	0.31009	0.002;0.155;0.06;0.303;0.166	B;B;B;B;B	0.29353	0.007;0.065;0.031;0.076;0.101	T	0.36866	-0.9730	10	0.40728	T	0.16	-32.2746	13.1966	0.59743	1.0:0.0:0.0:0.0	.	199;199;115;199;199	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	V	199	ENSP00000218200:I199V;ENSP00000359502:I199V;ENSP00000359508:I199V;ENSP00000359506:I199V;ENSP00000355115:I199V;ENSP00000395923:I199V;ENSP00000359501:I199V	ENSP00000218200:I199V	I	+	1	0	FMR1	146819420	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.095000	0.76952	1.778000	0.52293	0.486000	0.48141	ATA		0.413	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		G	147011728	A	G	147011728	3	3	37	1	0	0	0	0	1	0	0	0	5979	333	12	4	621	4	FMR1	23	147011728	Missense_Mutation	SNP	A	TCGA-AG-3731-01A-11D-1733-10	9293991	147011728	8258832	210	3293										
PASD1	139135	hgsc.bcm.edu	37	chrX	150842517	150842517	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0663507109004739	14	1	0.847870597870598	5.76205936920223	0.138606239121703	0.000965052278614514	0.0196227296651618	0	tttcccataacttcagactcAaccataagcaccctggagac	5	14	2	2			TCGA-AG-3731-01A-11D-1733-10	TCGA-AG-3731-11A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f3974a1-e0c1-4b51-a363-73938d0c2b00	20617e67-8a2d-4150-86d7-1c1a5854adf3	g.chrX:150842517A>G	ENST00000370357.4	+	15	2279	c.2034A>G	c.(2032-2034)tcA>tcG	p.S678S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	678						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.S678S(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CTTCAGACTCAACCATAAGCA	0.498																																																1	Substitution - coding silent(1)	ovary(1)	X											128	115	119					X																	150842517		2203	4300	6503	150593173	SO:0001819	synonymous_variant	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2034A>G	X.37:g.150842517A>G			150593173	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																				0.498	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		G	150842517	A	G	150842517	2	3	37	1	0	0	0	0	0	0	0	1	11502	117	5	4		4	PASD1	23	150842517	Silent	SNP	A	TCGA-AG-3731-01A-11D-1733-10	3830789	150842517	4428043	211	3294										
MFN2	9927	hgsc.bcm.edu	37	chr1	12065963	12065963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gggccccaagaacagccgtcGggccttgatgggctacaatg	14	12	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:12065963G>A	ENST00000235329.5	+	15	2013	c.1691G>A	c.(1690-1692)cGg>cAg	p.R564Q	MFN2_ENST00000444836.1_Missense_Mutation_p.R564Q	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	564					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AACAGCCGTCGGGCCTTGATG	0.552																																																0			1											97	94	95					1																	12065963		2203	4300	6503	11988550	SO:0001583	missense	9927			AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.1691G>A	1.37:g.12065963G>A	ENSP00000235329:p.Arg564Gln		11988550	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Missense_Mutation	SNP	ENST00000235329.5	37	CCDS30587.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958166	0.92726	.	.	ENSG00000116688	ENST00000444836;ENST00000235329;ENST00000376337	T;T	0.69435	-0.4;-0.4	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.67961	0.2949	L	0.60455	1.87	0.80722	D	1	P	0.52463	0.953	P	0.47786	0.557	T	0.64356	-0.6427	10	0.18710	T	0.47	-31.8458	17.3618	0.87353	0.0:0.0:1.0:0.0	.	564	O95140	MFN2_HUMAN	Q	564;564;262	ENSP00000416338:R564Q;ENSP00000235329:R564Q	ENSP00000235329:R564Q	R	+	2	0	MFN2	11988550	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.166000	0.94766	2.656000	0.90262	0.561000	0.74099	CGG		0.552	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		A	12065963	G	A	12065963	3	1	38	1	0	0	0	0	1	0	0	0	9554	1116	39	1	1741	1	MFN2	1	12065963	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10		12065963	237184658	1	3295										
FBLIM1	54751	hgsc.bcm.edu	37	chr1	16091648	16091649	+	Frame_Shift_Ins	INS	-	-	G													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	acacccgaggctggcttggcINSggggaggcccagcccctgga					rs201442626		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:16091648_16091649insG	ENST00000375766.3	+	3	810_811	c.170_171insG	c.(169-174)gcggggfs	p.AG57fs	FBLIM1_ENST00000400773.1_Frame_Shift_Ins_p.AG57fs|FBLIM1_ENST00000375771.1_Frame_Shift_Ins_p.AG57fs|FBLIM1_ENST00000441801.2_Frame_Shift_Ins_p.AG57fs|FBLIM1_ENST00000332305.5_Frame_Shift_Ins_p.AG57fs	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	57	Filamin-binding.|Intrinsically disordered.|Pro-rich.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)	p.A57A(1)		large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|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;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		GCTGGCTTGGCGGGGAGGCCCA	0.673																																																1	Substitution - coding silent(1)	lung(1)	1																																								15964236	SO:0001589	frameshift_variant	54751				CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.174dupG	1.37:g.16091652_16091652dupG	ENSP00000364921:p.Ala57fs		15964235	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Frame_Shift_Ins	INS	ENST00000375766.3	37	CCDS163.1																																																																																				0.673	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215		G	16091649	-	G	16091648	7	5	38	1	0	1	1	0	0	0	0	0	5716	768	27	0	172	0	FBLIM1	1	16091648	Frame_Shift_Ins	INS	-	TCGA-AG-3732-01A-11D-1657-10	4025685	16091648	233158973	2	3296										
USP48	84196	hgsc.bcm.edu	37	chr1	22021624	22021624	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgctttctcaccacgaacttTtctatgtcgcatacttcggc	6	13	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:22021624T>C	ENST00000308271.9	-	23	3466	c.2818A>G	c.(2818-2820)Aaa>Gaa	p.K940E	USP48_ENST00000374732.3_Intron|USP48_ENST00000529637.1_Missense_Mutation_p.K952E|USP48_ENST00000400301.1_Intron	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	940	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CCACGAACTTTTCTATGTCGC	0.378																																																0			1											162	154	157					1																	22021624		2203	4299	6502	21894211	SO:0001583	missense	84196			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2818A>G	1.37:g.22021624T>C	ENSP00000309262:p.Lys940Glu		21894211	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	37	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.146896	0.77888	.	.	ENSG00000090686	ENST00000308271;ENST00000529637	T;T	0.05996	3.36;3.37	5.95	5.95	0.96441	Ubiquitin supergroup (1);	0.000000	0.85682	D	0.000000	T	0.22322	0.0538	M	0.62723	1.935	0.80722	D	1	D;B;D;P	0.67145	0.993;0.204;0.996;0.9	D;B;D;B	0.76071	0.953;0.075;0.987;0.344	T	0.00184	-1.1944	10	0.42905	T	0.14	.	15.2477	0.73517	0.0:0.0:0.0:1.0	.	952;940;65;940	B7ZKS7;B7ZKS3;Q86UV5-6;Q86UV5	.;.;.;UBP48_HUMAN	E	940;952	ENSP00000309262:K940E;ENSP00000431949:K952E	ENSP00000309262:K940E	K	-	1	0	USP48	21894211	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	6.734000	0.74801	2.279000	0.76181	0.533000	0.62120	AAA		0.378	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		C	22021624	T	C	22021624	3	2	38	1	0	0	0	0	1	0	0	0	17119	1850	64	4	309	4	USP48	1	22021624	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	5929976	22021624	227228997	3	3297										
KHDRBS1	10657	hgsc.bcm.edu	37	chr1	32504197	32504197	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caaagttacgaaggctacgaAggctattacagccagagtca	10	9	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:32504197A>G	ENST00000327300.7	+	7	1319	c.1152A>G	c.(1150-1152)gaA>gaG	p.E384E	KHDRBS1_ENST00000492989.1_Silent_p.E345E|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1											endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				AAGGCTACGAAGGCTATTACA	0.403																																					Ovarian(173;401 1982 12359 31110 42403)											0			1											132	116	122					1																	32504197		2203	4300	6503	32276784	SO:0001819	synonymous_variant	10657			U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"GAP-associated tyrosine phosphoprotein p62 (Sam68)"	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.1152A>G	1.37:g.32504197A>G			32276784		Silent	SNP	ENST00000327300.7	37	CCDS350.1																																																																																				0.403	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		G	32504197	A	G	32504197	2	3	38	1	0	0	0	0	0	0	0	1	8167	69	3	4		4	KHDRBS1	1	32504197	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	10482573	32504197	216746424	4	3298										
DMAP1	55929	hgsc.bcm.edu	37	chr1	44684098	44684098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cagccgccgctttgacctgcGttttgttgttatccatgacc	9	13	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:44684098G>A	ENST00000372289.2	+	4	772	c.509G>A	c.(508-510)cGt>cAt	p.R170H	DMAP1_ENST00000361745.6_Missense_Mutation_p.R170H|DMAP1_ENST00000315913.5_Missense_Mutation_p.R170H|DMAP1_ENST00000488433.1_3'UTR	NM_019100.4	NP_061973.1	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	170	SANT.				chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription factor import into nucleus (GO:0042993)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|RNA polymerase II repressing transcription factor binding (GO:0001103)|transcription corepressor activity (GO:0003714)			breast(1)|cervix(1)|endometrium(6)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(166;0.155)					TTTGACCTGCGTTTTGTTGTT	0.522											OREG0013437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			1											166	138	147					1																	44684098		2203	4300	6503	44456685	SO:0001583	missense	55929			AB037846	CCDS509.1	1p34	2009-07-13			ENSG00000178028	ENSG00000178028			18291	protein-coding gene	gene with protein product		605077				10888872, 10718198	Standard	XM_005271039		Approved	DNMAP1, FLJ11543, KIAA1425, DNMTAP1, EAF2, MEAF2, SWC4	uc001clq.1	Q9NPF5	OTTHUMG00000007577	ENST00000372289.2:c.509G>A	1.37:g.44684098G>A	ENSP00000361363:p.Arg170His	925	44456685	A8K001|D3DPY8|Q0JSM4|Q5TG41|Q7Z3H7|Q9H0S8|Q9P2C2	Missense_Mutation	SNP	ENST00000372289.2	37	CCDS509.1	.	.	.	.	.	.	.	.	.	.	G	35	5.429903	0.96131	.	.	ENSG00000178028	ENST00000361745;ENST00000446292;ENST00000372283;ENST00000440641;ENST00000437511;ENST00000315913;ENST00000372289;ENST00000372290	.	.	.	5.26	5.26	0.73747	SANT domain, DNA binding (1);	0.050298	0.85682	D	0.000000	D	0.83635	0.5297	M	0.82433	2.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.85183	0.1005	9	0.62326	D	0.03	-12.9847	19.0611	0.93093	0.0:0.0:1.0:0.0	.	160;170	B4DQG8;Q9NPF5	.;DMAP1_HUMAN	H	170;170;196;170;196;170;170;131	.	ENSP00000312697:R170H	R	+	2	0	DMAP1	44456685	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.218000	0.95166	2.735000	0.93741	0.655000	0.94253	CGT		0.522	DMAP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020027.3	NM_019100		A	44684098	G	A	44684098	3	1	38	1	0	0	0	0	1	0	0	0	4587	1145	40	1	523	1	DMAP1	1	44684098	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	12179901	44684098	204566523	5	3299										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67795363	67795363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagagatgagggactggtacTgcttaatcgactcagatatc	12	7	1	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:67795363T>C	ENST00000262345.1	+	6	1398	c.758T>C	c.(757-759)cTg>cCg	p.L253P	IL12RB2_ENST00000371000.1_Missense_Mutation_p.L253P|IL12RB2_ENST00000544434.1_Missense_Mutation_p.L253P|IL12RB2_ENST00000541374.1_Missense_Mutation_p.L253P	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	253	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						GGACTGGTACTGCTTAATCGA	0.418																																																0			1											141	134	136					1																	67795363		2203	4300	6503	67567951	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.758T>C	1.37:g.67795363T>C	ENSP00000262345:p.Leu253Pro		67567951	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.343756	0.41498	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.2	3.99	0.46301	Fibronectin, type III (3);Immunoglobulin-like fold (1);	1.301510	0.04683	N	0.412781	T	0.57460	0.2055	L	0.45228	1.405	0.51233	D	0.999914	D;D;D;D	0.71674	0.966;0.998;0.98;0.976	P;P;P;P	0.62560	0.641;0.904;0.731;0.454	T	0.55010	-0.8207	10	0.62326	D	0.03	-3.8341	8.6662	0.34123	0.0:0.0:0.1928:0.8072	.	253;253;253;253	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	P	253	ENSP00000262345:L253P;ENSP00000360039:L253P;ENSP00000445276:L253P;ENSP00000442443:L253P	ENSP00000262345:L253P	L	+	2	0	IL12RB2	67567951	0.014000	0.17966	0.902000	0.35471	0.361000	0.29550	0.722000	0.25925	2.093000	0.63338	0.459000	0.35465	CTG		0.418	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67795363	T	C	67795363	3	2	38	1	0	0	0	0	1	0	0	0	7648	1580	55	4	776	4	IL12RB2	1	67795363	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	23111265	67795363	181455258	6	3300										
AK5	26289	hgsc.bcm.edu	37	chr1	77876727	77876727	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cagcatggcagttgacaacaAgttatttccaaacaaagagg	9	8	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:77876727A>T	ENST00000354567.2	+	7	1216	c.953A>T	c.(952-954)aAg>aTg	p.K318M	AK5_ENST00000344720.5_Missense_Mutation_p.K292M	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	318					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						GTTGACAACAAGTTATTTCCA	0.463																																																0			1											136	110	119					1																	77876727		2203	4300	6503	77649315	SO:0001583	missense	26289			AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"Adenylate kinases"	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.953A>T	1.37:g.77876727A>T	ENSP00000346577:p.Lys318Met		77649315	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Missense_Mutation	SNP	ENST00000354567.2	37	CCDS675.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.882271	0.72294	.	.	ENSG00000154027	ENST00000354567;ENST00000344720	T;T	0.72505	-0.64;-0.66	4.92	4.92	0.64577	.	0.120286	0.56097	D	0.000039	T	0.67211	0.2869	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.67635	-0.5620	10	0.33940	T	0.23	-4.9288	13.9557	0.64147	1.0:0.0:0.0:0.0	.	318	Q9Y6K8	KAD5_HUMAN	M	318;292	ENSP00000346577:K318M;ENSP00000341430:K292M	ENSP00000341430:K292M	K	+	2	0	AK5	77649315	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.618000	0.61211	2.199000	0.70637	0.533000	0.62120	AAG		0.463	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858		T	77876727	A	T	77876727	3	4	38	1	0	0	0	0	1	0	0	0	443	72	3	5	979	5	AK5	1	77876727	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	10081364	77876727	171373894	7	3301										
SORT1	6272	hgsc.bcm.edu	37	chr1	109897063	109897063	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agtgagaggatgaaaagggaGatctgtttgcacaaaattct	12	4	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:109897063G>A	ENST00000256637.6	-	5	692	c.634C>T	c.(634-636)Ctc>Ttc	p.L212F	SORT1_ENST00000482236.1_5'Flank|SORT1_ENST00000538502.1_Missense_Mutation_p.L76F	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	212					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		TGAAAAGGGAGATCTGTTTGC	0.418																																																0			1											153	146	148					1																	109897063		2203	4300	6503	109698586	SO:0001583	missense	6272			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.634C>T	1.37:g.109897063G>A	ENSP00000256637:p.Leu212Phe		109698586	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411288	0.83340	.	.	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.39997	1.05;1.05	5.11	5.11	0.69529	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	M	0.69823	2.125	0.58432	D	0.99999	D;D	0.89917	0.999;1.0	D;D	0.81914	0.982;0.995	T	0.61013	-0.7148	10	0.59425	D	0.04	-13.6701	17.6652	0.88201	0.0:0.0:1.0:0.0	.	76;212	B4DWI3;Q99523	.;SORT_HUMAN	F	212;76	ENSP00000256637:L212F;ENSP00000438597:L76F	ENSP00000256637:L212F	L	-	1	0	SORT1	109698586	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.952000	0.63618	2.515000	0.84797	0.655000	0.94253	CTC		0.418	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959		A	109897063	G	A	109897063	3	1	38	1	0	0	0	0	1	0	0	0	14972	942	33	3	1925	3	SORT1	1	109897063	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	32020336	109897063	139353558	8	3302										
RPTN	126638	hgsc.bcm.edu	37	chr1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cttgtctctcaggctgactgTggtgggaatctctgtcttgt					rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152129101	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	152129066	7	5	38	1	0	1	0	1	0	0	0	0	13701	1696	59	0	1849	0	RPTN	1	152129066	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TCGA-AG-3732-01A-11D-1657-10	42232003	152129066	97121555	9	3303										
SMG7	9887	hgsc.bcm.edu	37	chr1	183502837	183502837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttcttggcatcctgtgcaagTgtcctctacagaatgagtct	9	10	3	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:183502837T>C	ENST00000347615.2	+	10	1152	c.1033T>C	c.(1033-1035)Tgt>Cgt	p.C345R	SMG7_ENST00000456731.2_Missense_Mutation_p.C303R|SMG7_ENST00000507469.1_Missense_Mutation_p.C345R|SMG7_ENST00000508461.1_Missense_Mutation_p.C303R|SMG7_ENST00000515829.2_Missense_Mutation_p.C345R|SMG7_ENST00000367537.3_Missense_Mutation_p.C374R	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	345					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CCTGTGCAAGTGTCCTCTACA	0.413																																																0			1											77	79	78					1																	183502837		2203	4300	6503	181769460	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.1033T>C	1.37:g.183502837T>C	ENSP00000340766:p.Cys345Arg		181769460	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.849936	0.32699	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76;1.76	5.6	5.6	0.85130	.	0.179903	0.53938	D	0.000044	T	0.16599	0.0399	N	0.17345	0.48	0.80722	D	1	B;B;B;B;B;B	0.13145	0.002;0.002;0.001;0.001;0.002;0.007	B;B;B;B;B;B	0.13407	0.009;0.006;0.003;0.003;0.004;0.008	T	0.08659	-1.0711	10	0.11485	T	0.65	-0.1554	15.7929	0.78380	0.0:0.0:0.0:1.0	.	303;374;303;345;345;345	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	R	303;374;303;303;345;345;345	ENSP00000407629:C303R;ENSP00000356507:C374R;ENSP00000426915:C303R;ENSP00000388390:C303R;ENSP00000340766:C345R;ENSP00000425133:C345R;ENSP00000421358:C345R	ENSP00000340766:C345R	C	+	1	0	SMG7	181769460	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.524000	0.60552	2.123000	0.65237	0.533000	0.62120	TGT		0.413	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		C	183502837	T	C	183502837	3	2	38	1	0	0	0	0	1	0	0	0	14835	1696	59	4	1071	4	SMG7	1	183502837	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	31373771	183502837	65747784	10	3304										
CDC73	79577	hgsc.bcm.edu	37	chr1	193094254	193094254	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tatttcaggactggaaaggaAggccaacccagagagtacta	11	8	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:193094254A>G	ENST00000367435.3	+	2	328	c.144A>G	c.(142-144)gaA>gaG	p.E48E		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	48					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						CTGGAAAGGAAGGCCAACCCA	0.363																																																0			1											132	130	130					1																	193094254		2203	4300	6503	191360877	SO:0001819	synonymous_variant	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.144A>G	1.37:g.193094254A>G			191360877	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Silent	SNP	ENST00000367435.3	37	CCDS1382.1																																																																																				0.363	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		G	193094254	A	G	193094254	2	3	38	1	0	0	0	0	0	0	0	1	3091	69	3	4		4	CDC73	1	193094254	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	9591417	193094254	56156367	11	3305										
ASPM	259266	hgsc.bcm.edu	37	chr1	197111702	197111702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtcgaagagggtgttacctcGtttttataactcttagattt	9	6	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:197111702G>A	ENST00000367409.4	-	3	1936	c.1680C>T	c.(1678-1680)aaC>aaT	p.N560N	ASPM_ENST00000294732.7_Silent_p.N560N	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	560					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GTGTTACCTCGTTTTTATAAC	0.323																																																0			1											99	106	104					1																	197111702		2203	4300	6503	195378325	SO:0001819	synonymous_variant	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1680C>T	1.37:g.197111702G>A			195378325	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																				0.323	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197111702	G	A	197111702	2	1	38	1	0	0	0	0	0	0	0	1	1057	1136	40	1		1	ASPM	1	197111702	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	4017448	197111702	52138919	12	3306										
CR1	1378	hgsc.bcm.edu	37	chr1	207790003	207790003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atattccctatggaaaagaaAtatcttacgcatgcgacacc	6	10	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:207790003A>G	ENST00000367049.4	+	41	6745	c.6745A>G	c.(6745-6747)Ata>Gta	p.I2249V	CR1_ENST00000400960.2_Missense_Mutation_p.I1799V|CR1_ENST00000367051.1_Missense_Mutation_p.I1799V|CR1_ENST00000367052.1_Missense_Mutation_p.I1799V|CR1_ENST00000367053.1_Missense_Mutation_p.I1799V	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1799					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.I1804V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TGGAAAAGAAATATCTTACGC	0.473																																																1	Substitution - Missense(1)	ovary(1)	1											135	130	131					1																	207790003		1891	4111	6002	205856626	SO:0001583	missense	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6745A>G	1.37:g.207790003A>G	ENSP00000356016:p.Ile2249Val		205856626	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.958013	0.00049	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	4.15	-8.3	0.01005	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.24470	0.0593	N	0.00801	-1.175	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.17098	0.001;0.017	T	0.50759	-0.8790	9	0.02654	T	1	.	23.1927	0.99980	0.1514:0.0:0.8486:0.0	rs55770942	1799;2249	P17927;E9PDY4	CR1_HUMAN;.	V	1799;1799;1799;1799;2249	ENSP00000356019:I1799V;ENSP00000356018:I1799V;ENSP00000356020:I1799V;ENSP00000383744:I1799V;ENSP00000356016:I2249V	ENSP00000356016:I2249V	I	+	1	0	CR1	205856626	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-2.738000	0.00800	-2.855000	0.00329	-1.192000	0.01694	ATA		0.473	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		G	207790003	A	G	207790003	3	3	38	1	0	0	0	0	1	0	0	0	3846	101	4	4	6907	4	CR1	1	207790003	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	10678301	207790003	41460618	13	3307										
EPRS	2058	hgsc.bcm.edu	37	chr1	220152937	220152955	+	Frame_Shift_Del	DEL	TAAATGATGTGATGTTCCT	TAAATGATGTGATGTTCCT	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	attttggaaaaattctgcccTaaatgatgtgatgttcctcc							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TAAATGATGTGATGTTCCT	TAAATGATGTGATGTTCCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:220152937_220152955delTAAATGATGTGATGTTCCT	ENST00000366923.3	-	27	3983_4001	c.3714_3732delAGGAACATCACATCATTTA	c.(3712-3732)ggaggaacatcacatcatttafs	p.GGTSHHL1238fs		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1238	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)	p.G1239A(1)		breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AATTCTGCCCTAAATGATGTGATGTTCCTCCCTAAAATA	0.352																																																1	Substitution - Missense(1)	lung(1)	1																																								218219578	SO:0001589	frameshift_variant	2058			X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3714_3732delAGGAACATCACATCATTTA	1.37:g.220152937_220152955delTAAATGATGTGATGTTCCT	ENSP00000355890:p.Gly1238fs		218219560	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Frame_Shift_Del	DEL	ENST00000366923.3	37	CCDS31027.1																																																																																				0.352	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		-	220152955	TAAATGATGTGATGTTCCT	-	220152937	7	5	38	1	0	1	0	1	0	0	0	0	5204	1519	53	0	830	0	EPRS	1	220152937	Frame_Shift_Del	DEL	TAAATGATGTGATGTTCCT	TCGA-AG-3732-01A-11D-1657-10	12362934	220152937	29097684	14	3308										
RYR2	6262	hgsc.bcm.edu	37	chr1	237777661	237777661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgttccctgatgagaacaaaAaacacggccttccagggatc	9	11	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:237777661A>G	ENST00000366574.2	+	37	5550	c.5233A>G	c.(5233-5235)Aaa>Gaa	p.K1745E	RYR2_ENST00000542537.1_Missense_Mutation_p.K1729E|RYR2_ENST00000360064.6_Missense_Mutation_p.K1743E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1745	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGAGAACAAAAAACACGGCCT	0.517																																																0			1											65	65	65					1																	237777661		2048	4201	6249	235844284	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5233A>G	1.37:g.237777661A>G	ENSP00000355533:p.Lys1745Glu		235844284	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.255930	0.22965	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.73363	-0.74;-0.74;-0.74	5.43	4.26	0.50523	.	0.000000	0.64402	D	0.000006	T	0.58623	0.2135	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.48163	-0.9059	10	0.11794	T	0.64	.	10.2702	0.43479	0.9155:0.0:0.0845:0.0	.	1745	Q92736	RYR2_HUMAN	E	1745;1743;1729	ENSP00000355533:K1745E;ENSP00000353174:K1743E;ENSP00000443798:K1729E	ENSP00000353174:K1743E	K	+	1	0	RYR2	235844284	1.000000	0.71417	0.940000	0.37924	0.850000	0.48378	4.224000	0.58593	0.851000	0.35264	0.528000	0.53228	AAA		0.517	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237777661	A	G	237777661	3	3	38	1	0	0	0	0	1	0	0	0	13806	15	1	4	5379	4	RYR2	1	237777661	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	17624724	237777661	11472960	15	3309										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	38	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-AG-3732-01A-11D-1657-10	2593253	240370914	8879707	16	3310										
FH	2271	hgsc.bcm.edu	37	chr1	241663880	241663880	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcagcctggctgagtgtaacAcatttttaatctttgagtga	10	7	1	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr1:241663880A>G	ENST00000366560.3	-	9	1285	c.1247T>C	c.(1246-1248)gTg>gCg	p.V416A		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	416					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TGAGTGTAACACATTTTTAAT	0.428			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	0			1											66	64	64					1																	241663880		2203	4300	6503	239730503	SO:0001583	missense	3949	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1247T>C	1.37:g.241663880A>G	ENSP00000355518:p.Val416Ala		239730503	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	37	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	A	19.28	3.796993	0.70567	.	.	ENSG00000091483	ENST00000366560	D	0.92099	-2.97	5.71	5.71	0.89125	L-Aspartase-like (1);	0.120226	0.56097	D	0.000028	D	0.93592	0.7954	M	0.87381	2.88	0.80722	D	1	P	0.39696	0.683	B	0.42112	0.376	D	0.94248	0.7491	10	0.87932	D	0	-2.1797	13.9333	0.64010	1.0:0.0:0.0:0.0	.	416	P07954	FUMH_HUMAN	A	416	ENSP00000355518:V416A	ENSP00000355518:V416A	V	-	2	0	FH	239730503	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.059000	0.76684	2.178000	0.69098	0.533000	0.62120	GTG		0.428	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		G	241663880	A	G	241663880	3	3	38	1	0	0	0	0	1	0	0	0	5894	159	6	4	293	4	FH	1	241663880	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	1292966	241663880	7586741	17	3311										
GLI2	2736	hgsc.bcm.edu	37	chr2	121736047	121736047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	catccacggggagaagaaggAgtttgtgtgccgctggcagg	17	8	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:121736047A>G	ENST00000452319.1	+	10	1466	c.1406A>G	c.(1405-1407)gAg>gGg	p.E469G	GLI2_ENST00000361492.4_Missense_Mutation_p.E469G|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Missense_Mutation_p.E141G					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GAGAAGAAGGAGTTTGTGTGC	0.642																																																0			2											152	147	149					2																	121736047		2203	4300	6503	121452517	SO:0001583	missense	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1406A>G	2.37:g.121736047A>G	ENSP00000390436:p.Glu469Gly		121452517		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760512	0.69763	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	D;D;D	0.91521	-2.86;-2.86;-2.86	4.03	4.03	0.46877	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.114584	0.64402	D	0.000017	D	0.94085	0.8104	M	0.72479	2.2	0.58432	D	0.999997	P;D;P;P;B	0.71674	0.514;0.998;0.589;0.891;0.195	B;D;B;B;B	0.70935	0.058;0.971;0.042;0.385;0.049	D	0.94675	0.7860	10	0.87932	D	0	.	13.398	0.60865	1.0:0.0:0.0:0.0	.	469;452;124;124;141	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	G	469;469;141	ENSP00000390436:E469G;ENSP00000354586:E469G;ENSP00000312694:E141G	ENSP00000312694:E141G	E	+	2	0	GLI2	121452517	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.036000	0.93758	1.823000	0.53134	0.402000	0.26972	GAG		0.642	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		G	121736047	A	G	121736047	3	3	38	1	0	0	0	0	1	0	0	0	6458	304	11	4	1440	4	GLI2	2	121736047	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10		121736047	121463326	18	3312										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520172	131520172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caagactgaggacttggcctCgctggcggccgaggggaaaa	16	10	0	2	rs139544644		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:131520172C>T	ENST00000423981.1	+	2	637	c.527C>T	c.(526-528)tCg>tTg	p.S176L	AMER3_ENST00000321420.4_Missense_Mutation_p.S176L	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	176					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										GACTTGGCCTCGCTGGCGGCC	0.642																																																0			2						C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	1,4401	2.1+/-5.4	0,1,2200	47	51	50		527,527,527,527	4	0	2	dbSNP_134	50	0,8586		0,0,4293	no	missense,missense,missense,missense	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	145,145,145,145	0,1,6493	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	176/862,176/862,176/862,176/862	131520172	1,12987	2201	4293	6494	131236642	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.527C>T	2.37:g.131520172C>T	ENSP00000392700:p.Ser176Leu		131236642	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.203645	0.00296	2.27E-4	0.0	ENSG00000178171	ENST00000321420;ENST00000458606;ENST00000423981	T;T	0.44083	0.93;0.93	5.09	3.97	0.46021	.	1.118290	0.06631	N	0.759122	T	0.27349	0.0671	L	0.29908	0.895	0.09310	N	1	P	0.38767	0.646	B	0.35655	0.207	T	0.07404	-1.0774	10	0.02654	T	1	.	9.0084	0.36127	0.0:0.8595:0.0:0.1405	.	176	Q8N944	F123C_HUMAN	L	176	ENSP00000314914:S176L;ENSP00000392700:S176L	ENSP00000314914:S176L	S	+	2	0	FAM123C	131236642	0.006000	0.16342	0.022000	0.16811	0.004000	0.04260	2.074000	0.41529	2.536000	0.85505	0.561000	0.74099	TCG		0.642	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		T	131520172	C	T	131520172	3	4	38	1	0	0	0	0	1	0	0	0	5440	893	31	1	529	1	FAM123C	2	131520172	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	9784125	131520172	111679201	19	3313										
SCN3A	6328	hgsc.bcm.edu	37	chr2	166012311	166012311	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cagtagtcttgagtcatgagTcgaaatagagacaggaaagc	12	6	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:166012311T>C	ENST00000360093.3	-	10	1625	c.1134A>G	c.(1132-1134)cgA>cgG	p.R378R	SCN3A_ENST00000283254.7_Silent_p.R378R|SCN3A_ENST00000409101.3_Silent_p.R378R	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	378					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGTCATGAGTCGAAATAGAG	0.408																																																0			2											107	103	104					2																	166012311		2203	4300	6503	165720557	SO:0001819	synonymous_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1134A>G	2.37:g.166012311T>C			165720557	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																					0.408	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	166012311	T	C	166012311	2	2	38	1	0	0	0	0	0	0	0	1	13955	1654	58	4		4	SCN3A	2	166012311	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	34492139	166012311	77187062	20	3314										
HOXD10	3236	hgsc.bcm.edu	37	chr2	176981954	176981954	+	Silent	SNP	C	C	T													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tcggccgaggtcccttcgtaCcagaggctggtccctgagtc							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:176981954C>T	ENST00000249501.4	+	1	648	c.393C>T	c.(391-393)taC>taT	p.Y131Y	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	131					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TCCCTTCGTACCAGAGGCTGG	0.517																																																0			2											139	156	150					2																	176981954		2203	4300	6503	176690200	SO:0001819	synonymous_variant	3236				CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"Homeoboxes / ANTP class : HOXL subclass"	5133	protein-coding gene	gene with protein product		142984	"homeo box D10"	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.393C>T	2.37:g.176981954C>T			176690200	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																				0.517	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2			T	176981954	C	T	176981954	2	4	38	1	0	0	0	0	0	0	0	1	7340	518	18	3		3	HOXD10	2	176981954	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	10969643	176981954	66217419	21	3315	14	2								
HOXD10	3236	hgsc.bcm.edu	37	chr2	176981956	176981956	+	Missense_Mutation	SNP	A	A	T													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggccgaggtcccttcgtaccAgaggctggtccctgagtctt							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:176981956A>T	ENST00000249501.4	+	1	650	c.395A>T	c.(394-396)cAg>cTg	p.Q132L	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	132					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		CCTTCGTACCAGAGGCTGGTC	0.517																																																0			2											137	154	148					2																	176981956		2203	4300	6503	176690202	SO:0001583	missense	3236				CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"Homeoboxes / ANTP class : HOXL subclass"	5133	protein-coding gene	gene with protein product		142984	"homeo box D10"	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.395A>T	2.37:g.176981956A>T	ENSP00000249501:p.Gln132Leu		176690202	Q6NT10	Missense_Mutation	SNP	ENST00000249501.4	37	CCDS2266.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.153677	0.38021	.	.	ENSG00000128710	ENST00000249501	T	0.31247	1.5	5.99	5.99	0.97316	.	0.107337	0.64402	D	0.000003	T	0.36771	0.0979	M	0.68317	2.08	0.45035	D	0.998051	B	0.11235	0.004	B	0.14578	0.011	T	0.10847	-1.0612	10	0.54805	T	0.06	.	16.4892	0.84195	1.0:0.0:0.0:0.0	.	132	P28358	HXD10_HUMAN	L	132	ENSP00000249501:Q132L	ENSP00000249501:Q132L	Q	+	2	0	HOXD10	176690202	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.608000	0.74168	2.296000	0.77279	0.533000	0.62120	CAG		0.517	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2			T	176981956	A	T	176981956	3	4	38	1	0	0	0	0	1	0	0	0	7340	188	7	5	397	5	HOXD10	2	176981956	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	2	176981956	66217417	22	3316	14	2								
FN1	2335	hgsc.bcm.edu	37	chr2	216251569	216251569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggtctcccactgaagtgctcGggatgatggcggatcctgta	14	10	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:216251569G>A	ENST00000359671.1	-	27	4447	c.4182C>T	c.(4180-4182)ccC>ccT	p.P1394P	FN1_ENST00000336916.4_Silent_p.P1394P|FN1_ENST00000346544.3_Silent_p.P1394P|FN1_ENST00000357009.2_Silent_p.P1394P|FN1_ENST00000421182.1_Silent_p.P1394P|FN1_ENST00000345488.5_Silent_p.P1394P|FN1_ENST00000357867.4_Silent_p.P1394P|FN1_ENST00000446046.1_Silent_p.P1394P|FN1_ENST00000443816.1_Silent_p.P1394P|FN1_ENST00000356005.4_Silent_p.P1394P|FN1_ENST00000354785.4_Silent_p.P1485P|FN1_ENST00000323926.6_Silent_p.P1485P|FN1_ENST00000432072.2_Silent_p.P1485P			P02751	FINC_HUMAN	fibronectin 1	1394	Cell-attachment.|Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	TGAAGTGCTCGGGATGATGGC	0.532																																																0			2											91	82	85					2																	216251569		2203	4300	6503	215959814	SO:0001819	synonymous_variant	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4182C>T	2.37:g.216251569G>A			215959814	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																					0.532	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216251569	G	A	216251569	2	1	38	1	0	0	0	0	0	0	0	1	5981	1103	39	1		1	FN1	2	216251569	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	39269613	216251569	26947804	23	3317										
SPEG	10290	hgsc.bcm.edu	37	chr2	220355198	220355198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaacgttcgtggccaagatcGtgccctatgctgccgagggc	14	12	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:220355198G>A	ENST00000312358.7	+	37	9121	c.8989G>A	c.(8989-8991)Gtg>Atg	p.V2997M	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2997	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGCCAAGATCGTGCCCTATGC	0.667																																																0			2											41	48	46					2																	220355198		2125	4226	6351	220063442	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8989G>A	2.37:g.220355198G>A	ENSP00000311684:p.Val2997Met		220063442	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.027249	0.54683	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.41400	1.0	4.64	4.64	0.57946	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.36778	N	0.002408	T	0.46889	0.1416	N	0.20574	0.59	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.49908	-0.8889	10	0.87932	D	0	.	10.9133	0.47120	0.0868:0.0:0.9132:0.0	.	2997	Q15772	SPEG_HUMAN	M	2997	ENSP00000311684:V2997M	ENSP00000265327:V2997M	V	+	1	0	SPEG	220063442	0.998000	0.40836	0.982000	0.44146	0.986000	0.74619	2.609000	0.46317	2.417000	0.82017	0.591000	0.81541	GTG		0.667	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220355198	G	A	220355198	3	1	38	1	0	0	0	0	1	0	0	0	15075	1145	40	1	9147	1	SPEG	2	220355198	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	4103629	220355198	22844175	24	3318										
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622413	234622413	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atctgtgtggctgttccgagGggactttgtgatggattacc	14	7	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:234622413G>A	ENST00000373414.3	+	1	776	c.776G>A	c.(775-777)gGg>gAg	p.G259E	UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.G259E|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000373424.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	259			G -> R (in dbSNP:rs3892170).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		CTGTTCCGAGGGGACTTTGTG	0.522																																																0			2											152	159	157					2																	234622413		2203	4299	6502	234287152	SO:0001583	missense	54579			M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.776G>A	2.37:g.234622413G>A	ENSP00000362513:p.Gly259Glu		234287152	B8K294	Missense_Mutation	SNP	ENST00000373414.3	37	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	G	0.371	-0.933817	0.02340	.	.	ENSG00000240224	ENST00000373414	T	0.61510	0.1	4.73	-2.87	0.05700	.	1.728100	0.02944	N	0.140911	T	0.46639	0.1403	L	0.51914	1.62	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.15052	0.012;0.012	T	0.25257	-1.0137	10	0.52906	T	0.07	.	0.5971	0.00738	0.3505:0.1945:0.2579:0.197	.	259;259	Q5DSZ9;P35504	.;UD15_HUMAN	E	259	ENSP00000362513:G259E	ENSP00000362513:G259E	G	+	2	0	UGT1A5	234287152	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-2.561000	0.00921	-0.427000	0.07350	-2.205000	0.00302	GGG		0.522	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		A	234622413	G	A	234622413	3	1	38	1	0	0	0	0	1	0	0	0	16988	1232	43	3	778	3	UGT1A5	2	234622413	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	14267215	234622413	8576960	25	3319										
HJURP	55355	hgsc.bcm.edu	37	chr2	234750096	234750096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cctgggactcaggcaatattCccgatgaagctgatcaaatc	9	11	2	2	rs546977139		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr2:234750096C>T	ENST00000411486.2	-	8	1395	c.1330G>A	c.(1330-1332)Gaa>Aaa	p.E444K	HJURP_ENST00000441687.1_Missense_Mutation_p.E359K|HJURP_ENST00000432087.1_Missense_Mutation_p.E390K|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	444					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.E444K(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		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)		AGGCAATATTCCCGATGAAGC	0.532													C|||	1	0.000199681	0	0	5008	,	,		17779	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	ovary(1)	2											98	98	98					2																	234750096		2203	4300	6503	234414835	SO:0001583	missense	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1330G>A	2.37:g.234750096C>T	ENSP00000414109:p.Glu444Lys		234414835	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.777771	0.49786	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.61627	0.09;0.09;0.09;0.09	4.35	0.601	0.17529	Holliday junction regulator protein family C-terminal repeat (1);	0.674446	0.14356	N	0.324774	T	0.49081	0.1536	L	0.61218	1.895	0.09310	N	1	B;B;B	0.32862	0.336;0.15;0.387	B;B;B	0.31016	0.044;0.044;0.123	T	0.45454	-0.9260	10	0.87932	D	0	-14.6442	6.5845	0.22612	0.0:0.6012:0.0:0.3988	.	359;390;444	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	K	444;390;359;359	ENSP00000414109:E444K;ENSP00000407208:E390K;ENSP00000401944:E359K;ENSP00000393253:E359K	ENSP00000414109:E444K	E	-	1	0	HJURP	234414835	0.005000	0.15991	0.002000	0.10522	0.007000	0.05969	0.565000	0.23578	0.093000	0.17368	-0.793000	0.03317	GAA		0.532	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		T	234750096	C	T	234750096	3	4	38	1	0	0	0	0	1	0	0	0	7210	864	30	3	924	3	HJURP	2	234750096	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	127683	234750096	8449277	26	3320										
IL17RC	84818	hgsc.bcm.edu	37	chr3	9970142	9970142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctgccagccactggtcccacCgctttcctgggagaacgtca	10	16	1	1	rs151311782		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:9970142C>T	ENST00000295981.3	+	11	1462	c.1244C>T	c.(1243-1245)cCg>cTg	p.P415L	IL17RC_ENST00000403601.3_Missense_Mutation_p.P344L|IL17RC_ENST00000455057.1_Missense_Mutation_p.P329L|IL17RC_ENST00000413608.1_Missense_Mutation_p.P344L|IL17RC_ENST00000383812.4_Missense_Mutation_p.P329L|IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000416074.2_Missense_Mutation_p.P200L	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	415					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CTGGTCCCACCGCTTTCCTGG	0.672													C|||	1	0.000199681	0	0	5008	,	,		15542	0.001		0	False		,,,				2504	0															0			3						C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	52	61	58		1031,1031,986,986,1031,1244	1.7	0	3	dbSNP_134	58	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	98,98,98,98,98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	344/708,344/691,329/689,329/706,344/721,415/792	9970142	1,13005	2203	4300	6503	9945142	SO:0001583	missense	84818			BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1244C>T	3.37:g.9970142C>T	ENSP00000295981:p.Pro415Leu		9945142	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.559297	0.27827	2.27E-4	0.0	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39;2.39;2.39;2.39	5.0	1.73	0.24493	.	0.415062	0.20560	N	0.089932	T	0.31482	0.0798	M	0.61703	1.905	0.09310	N	0.999999	B;D;B;B;D;D;B;D;D	0.89917	0.095;0.999;0.033;0.033;1.0;1.0;0.055;1.0;1.0	B;P;B;B;D;D;B;D;D	0.87578	0.029;0.876;0.005;0.005;0.933;0.933;0.011;0.998;0.97	T	0.04454	-1.0950	10	0.72032	D	0.01	-14.4235	4.6959	0.12804	0.3697:0.5191:0.0:0.1112	.	329;200;329;344;344;344;329;415;344	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	L	329;304;415;319;344;200;329;344	ENSP00000373323:P329L;ENSP00000414609:P304L;ENSP00000295981:P415L;ENSP00000401128:P319L;ENSP00000384969:P344L;ENSP00000395315:P200L;ENSP00000407894:P329L;ENSP00000396064:P344L	ENSP00000295981:P415L	P	+	2	0	IL17RC	9945142	0.000000	0.05858	0.010000	0.14722	0.017000	0.09413	-0.075000	0.11431	0.511000	0.28236	-0.378000	0.06908	CCG		0.672	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9970142	C	T	9970142	3	4	38	1	0	0	0	0	1	0	0	0	7662	652	23	1	1286	1	IL17RC	3	9970142	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10		9970142	188052288	27	3321										
VHL	7428	hgsc.bcm.edu	37	chr3	10191594	10191594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agaccacccaaatgtgcagaAagacctggagcggctgacac	11	12	0	4			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:10191594A>G	ENST00000256474.2	+	3	1427	c.587A>G	c.(586-588)aAa>aGa	p.K196R	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.K155R	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	196					cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.K196fs*18(2)|p.P192fs*3(1)|p.N193fs*>16(1)|p.K196fs*4(1)|p.K196fs*17(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AATGTGCAGAAAGACCTGGAG	0.498		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	6	Deletion - Frameshift(6)	kidney(6)	3											72	65	68					3																	10191594		2203	4300	6503	10166594	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.587A>G	3.37:g.10191594A>G	ENSP00000256474:p.Lys196Arg		10166594	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785064	0.90282	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99815	-6.9;-6.9	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.170647	0.50627	D	0.000101	D	0.99518	0.9828	L	0.41236	1.265	0.37190	D	0.90387	D;D	0.64830	0.994;0.983	D;P	0.63703	0.917;0.775	D	0.98306	1.0521	10	0.44086	T	0.13	-2.7872	12.9354	0.58311	1.0:0.0:0.0:0.0	.	155;196	P40337-2;P40337	.;VHL_HUMAN	R	196;155;114	ENSP00000256474:K196R;ENSP00000344757:K155R	ENSP00000256474:K196R	K	+	2	0	VHL	10166594	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	3.954000	0.56708	2.209000	0.71365	0.533000	0.62120	AAA		0.498	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191594	A	G	10191594	3	3	38	1	0	0	0	0	1	0	0	0	17202	14	1	4	597	4	VHL	3	10191594	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	221452	10191594	187830836	28	3322										
FGD5	152273	hgsc.bcm.edu	37	chr3	14861729	14861729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	accaaagctggggctgcgtgCggaggagaaccccatggtgg	17	10	0	1	rs374659688		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:14861729C>T	ENST00000285046.5	+	1	1261	c.1151C>T	c.(1150-1152)gCg>gTg	p.A384V	FGD5_ENST00000543601.1_Missense_Mutation_p.A143V	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	384					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GGGCTGCGTGCGGAGGAGAAC	0.602																																																0			3						C	VAL/ALA	0,3858		0,0,1929	36	39	38		1151	-0.1	0	3		38	1,8273		0,1,4136	no	missense	FGD5	NM_152536.3	64	0,1,6065	TT,TC,CC		0.0121,0.0,0.0082	benign	384/1463	14861729	1,12131	1929	4137	6066	14836733	SO:0001583	missense	152273			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1151C>T	3.37:g.14861729C>T	ENSP00000285046:p.Ala384Val		14836733	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	C	8.526	0.869910	0.17322	0.0	1.21E-4	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.74947	-0.89;-0.74	4.52	-0.0954	0.13641	.	1.151570	0.06481	N	0.732823	T	0.50633	0.1627	N	0.11560	0.145	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.04013	0.001;0.001	T	0.28681	-1.0036	10	0.18276	T	0.48	-2.3995	4.6679	0.12675	0.1779:0.4198:0.0:0.4022	.	143;384	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	V	384;143	ENSP00000285046:A384V;ENSP00000445949:A143V	ENSP00000285046:A384V	A	+	2	0	FGD5	14836733	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.925000	0.03992	0.037000	0.15575	0.491000	0.48974	GCG		0.602	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		T	14861729	C	T	14861729	3	4	38	1	0	0	0	0	1	0	0	0	5855	768	27	1	1153	1	FGD5	3	14861729	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	4670135	14861729	183160701	29	3323										
FGD5	152273	hgsc.bcm.edu	37	chr3	14862025	14862025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agaacaccagcacgagggtcCggccccactctgggaaggtg	14	13	1	1	rs560710091		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:14862025C>T	ENST00000285046.5	+	1	1557	c.1447C>T	c.(1447-1449)Cgg>Tgg	p.R483W	FGD5_ENST00000543601.1_Missense_Mutation_p.R242W	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	483					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CACGAGGGTCCGGCCCCACTC	0.632													C|||	1	0.000199681	0	0	5008	,	,		16776	0.001		0	False		,,,				2504	0															0			3											43	48	46					3																	14862025		1964	4138	6102	14837029	SO:0001583	missense	152273			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1447C>T	3.37:g.14862025C>T	ENSP00000285046:p.Arg483Trp		14837029	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.541270	0.27563	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	D;T	0.82344	-1.6;-1.37	4.86	2.96	0.34315	.	0.000000	0.49916	D	0.000123	T	0.78355	0.4270	M	0.73598	2.24	0.44918	D	0.997937	P;P	0.50066	0.707;0.931	B;B	0.38428	0.102;0.273	T	0.76061	-0.3097	10	0.87932	D	0	-17.4118	7.1843	0.25791	0.5161:0.3989:0.0:0.085	.	242;483	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	W	483;242	ENSP00000285046:R483W;ENSP00000445949:R242W	ENSP00000285046:R483W	R	+	1	2	FGD5	14837029	0.995000	0.38212	0.526000	0.27913	0.025000	0.11179	0.681000	0.25320	0.401000	0.25424	0.650000	0.86243	CGG		0.632	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		T	14862025	C	T	14862025	3	4	38	1	0	0	0	0	1	0	0	0	5855	643	23	1	1449	1	FGD5	3	14862025	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	296	14862025	183160405	30	3324										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19436738	19436738	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	actccttgcacactggatggCgtgtatctggtacgtcattg	11	10	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:19436738C>T	ENST00000328405.2	+	7	1378	c.1112C>T	c.(1111-1113)gCg>gTg	p.A371V	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_Missense_Mutation_p.A12V	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	371					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						CACTGGATGGCGTGTATCTGG	0.458																																					NSCLC(124;1625 1765 8018 24930 42026)											0			3											174	148	157					3																	19436738		2203	4300	6503	19411742	SO:0001583	missense	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1112C>T	3.37:g.19436738C>T	ENSP00000328813:p.Ala371Val		19411742	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	36	5.661999	0.96734	.	.	ENSG00000183960	ENST00000328405;ENST00000537696	D;T	0.98666	-5.06;1.36	5.79	5.79	0.91817	Ion transport (1);	0.000000	0.31358	U	0.007786	D	0.99363	0.9776	M	0.91972	3.26	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99004	1.0812	9	.	.	.	.	20.0326	0.97545	0.0:1.0:0.0:0.0	.	12;371;371	B7Z2I7;B7Z398;Q96L42	.;.;KCNH8_HUMAN	V	371;12	ENSP00000328813:A371V;ENSP00000446294:A12V	.	A	+	2	0	KCNH8	19411742	1.000000	0.71417	0.985000	0.45067	0.923000	0.55619	7.818000	0.86416	2.732000	0.93576	0.557000	0.71058	GCG		0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19436738	C	T	19436738	3	4	38	1	0	0	0	0	1	0	0	0	8059	768	27	1	1138	1	KCNH8	3	19436738	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	4574713	19436738	178585692	31	3325										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266114	41266114	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctggactctggaatccattcTggtgccactaccacagctcc	8	15	2	0	rs121913416		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:41266114T>C	ENST00000349496.5	+	3	391	c.111T>C	c.(109-111)tcT>tcC	p.S37S	CTNNB1_ENST00000396185.3_Silent_p.S37S|CTNNB1_ENST00000405570.1_Silent_p.S37S|CTNNB1_ENST00000396183.3_Silent_p.S37S|CTNNB1_ENST00000453024.1_Silent_p.S30S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S37S(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.S37_A39>S(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GAATCCATTCTGGTGCCACTA	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	132	Deletion - In frame(102)|Complex - deletion inframe(19)|Unknown(7)|Deletion - Frameshift(3)|Substitution - coding silent(1)	liver(98)|large_intestine(19)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|kidney(1)	3											92	78	82					3																	41266114		2203	4300	6503	41241118	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.111T>C	3.37:g.41266114T>C			41241118	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266114	T	C	41266114	2	2	38	1	0	0	0	0	0	0	0	1	4022	1567	55	4		4	CTNNB1	3	41266114	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	21829376	41266114	156756316	32	3326										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266142	41266142	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctaccacagctccttctctgAgtggtaaaggcaatcctgag	9	12	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:41266142A>G	ENST00000349496.5	+	3	419	c.139A>G	c.(139-141)Agt>Ggt	p.S47G	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S47G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S47G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S47G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S40G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	47					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.L46_S47del(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S47G(1)|p.H24_M131del(1)|p.S47C(1)|p.A21_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCCTTCTCTGAGTGGTAAAGG	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	124	Deletion - In frame(95)|Complex - deletion inframe(20)|Unknown(7)|Substitution - Missense(2)	liver(89)|large_intestine(16)|stomach(7)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|skin(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	3											81	72	75					3																	41266142		2203	4300	6503	41241146	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.139A>G	3.37:g.41266142A>G	ENSP00000344456:p.Ser47Gly		41241146	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752623	0.69533	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	L	0.59436	1.845	0.80722	D	1	B	0.23442	0.085	B	0.25291	0.059	T	0.48080	-0.9066	10	0.87932	D	0	-16.8827	16.3453	0.83126	1.0:0.0:0.0:0.0	.	47	P35222	CTNB1_HUMAN	G	40;47;47;47;47;40;47;47;47	ENSP00000400508:S40G;ENSP00000385604:S47G;ENSP00000412219:S47G;ENSP00000379486:S47G;ENSP00000344456:S47G;ENSP00000411226:S40G;ENSP00000379488:S47G;ENSP00000409302:S47G;ENSP00000401599:S47G	ENSP00000344456:S47G	S	+	1	0	CTNNB1	41241146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	AGT		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266142	A	G	41266142	3	3	38	1	0	0	0	0	1	0	0	0	4022	304	11	4	145	4	CTNNB1	3	41266142	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	28	41266142	156756288	33	3327										
PLA1A	51365	hgsc.bcm.edu	37	chr3	119327670	119327670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atttattagaacccttctgcGtgcaacgaatgctaatgtga	8	8	1	2	rs61733987	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:119327670G>A	ENST00000273371.4	+	3	401	c.329G>A	c.(328-330)cGt>cAt	p.R110H	PLA1A_ENST00000495992.1_Missense_Mutation_p.R110H|PLA1A_ENST00000488919.1_5'UTR|PLA1A_ENST00000494440.1_Missense_Mutation_p.R94H	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	110			R -> H (in dbSNP:rs61733987). {ECO:0000269|PubMed:12436198}.		lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ACCCTTCTGCGTGCAACGAAT	0.438													G|||	77	0.0153754	0.0091	0.0288	5008	,	,		21644	0.002		0.0239	False		,,,				2504	0.0194															0			3						G	HIS/ARG,,HIS/ARG	40,4366	43.8+/-77.6	1,38,2164	180	179	179		329,,329	-7.8	0	3	dbSNP_129	179	258,8342	100.6+/-161.9	6,246,4048	yes	missense,utr-5,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	29,,29	7,284,6212	AA,AG,GG		3.0,0.9079,2.2913	possibly-damaging,,possibly-damaging	110/441,,110/457	119327670	298,12708	2203	4300	6503	120810360	SO:0001583	missense	51365			AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.329G>A	3.37:g.119327670G>A	ENSP00000273371:p.Arg110His		120810360	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	35	0.016025641025641024	4	0.008130081300813009	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	1.976	-0.435335	0.04669	0.009079	0.03	ENSG00000144837	ENST00000273371;ENST00000495992;ENST00000494440	D;D;D	0.91295	-2.71;-2.82;-2.71	5.17	-7.8	0.01214	Lipase, N-terminal (1);	0.896444	0.09888	N	0.742779	T	0.69351	0.3101	L	0.54863	1.705	0.18873	N	0.999985	B;B	0.19583	0.037;0.003	B;B	0.11329	0.006;0.004	T	0.61773	-0.6994	10	0.37606	T	0.19	-0.1671	11.6367	0.51209	0.679:0.0:0.2269:0.0941	rs61733987	110;110	Q53H76-3;Q53H76	.;PLA1A_HUMAN	H	110;110;94	ENSP00000273371:R110H;ENSP00000417326:R110H;ENSP00000418793:R94H	ENSP00000273371:R110H	R	+	2	0	PLA1A	120810360	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.684000	0.05173	-2.554000	0.00477	-1.325000	0.01285	CGT		0.438	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			A	119327670	G	A	119327670	3	1	38	1	0	0	0	0	1	0	0	0	12019	1145	40	1	339	1	PLA1A	3	119327670	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	78061528	119327670	78694760	34	3328										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121416549	121416549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctcagctctggataataaatTtagctgttctttaagagtct	7	7	4	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:121416549T>C	ENST00000340645.5	-	13	2931	c.2806A>G	c.(2806-2808)Aat>Gat	p.N936D	GOLGB1_ENST00000393667.3_Missense_Mutation_p.N941D	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	936					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GATAATAAATTTAGCTGTTCT	0.363																																																0			3											87	97	93					3																	121416549		2203	4298	6501	122899239	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2806A>G	3.37:g.121416549T>C	ENSP00000341848:p.Asn936Asp		122899239	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022651	0.35701	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	T;T;T	0.24350	2.45;2.45;1.86	5.35	5.35	0.76521	.	0.167956	0.42294	D	0.000725	T	0.27384	0.0672	L	0.47716	1.5	0.31180	N	0.702217	P;P;P;P;P	0.49559	0.571;0.925;0.873;0.925;0.629	B;P;B;P;B	0.47162	0.229;0.54;0.291;0.54;0.213	T	0.10917	-1.0609	10	0.13853	T	0.58	.	13.3329	0.60500	0.0:0.0:0.0:1.0	.	861;900;941;941;936	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	D	936;941;900;748	ENSP00000341848:N936D;ENSP00000377275:N941D;ENSP00000418231:N900D	ENSP00000341848:N936D	N	-	1	0	GOLGB1	122899239	0.860000	0.29831	0.994000	0.49952	0.972000	0.66771	3.547000	0.53663	2.244000	0.73946	0.533000	0.62120	AAT		0.363	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121416549	T	C	121416549	3	2	38	1	0	0	0	0	1	0	0	0	6585	1841	64	4	7013	4	GOLGB1	3	121416549	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	2088879	121416549	76605881	35	3329										
XRN1	54464	hgsc.bcm.edu	37	chr3	142144096	142144098	+	In_Frame_Del	DEL	TGG	TGG	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	taaaccataaagacagtgtcTggtgtttggatcatgatctg							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TGG	TGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:142144096_142144098delTGG	ENST00000264951.4	-	5	710_712	c.593_595delCCA	c.(592-597)accaga>aga	p.T198del	XRN1_ENST00000392981.2_In_Frame_Del_p.T198del|XRN1_ENST00000544157.1_Intron|XRN1_ENST00000463916.1_In_Frame_Del_p.T198del	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	198					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AGACAGTGTCTGGTGTTTGGATC	0.3																																																0			3																																								143626788	SO:0001651	inframe_deletion	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.593_595delCCA	3.37:g.142144096_142144098delTGG	ENSP00000264951:p.Thr198del		143626786	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	In_Frame_Del	DEL	ENST00000264951.4	37	CCDS3123.1																																																																																				0.3	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		-	142144098	TGG	-	142144096	7	5	38	1	0	1	0	1	0	0	0	0	17499	1588	55	0	4677	0	XRN1	3	142144096	In_Frame_Del	DEL	TGG	TCGA-AG-3732-01A-11D-1657-10	20727547	142144096	55878334	36	3330										
FAM194A	131831	hgsc.bcm.edu	37	chr3	150403601	150403601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggtggtccgatgctgggtaaCgttcttagagaaggctcgaa	15	7	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:150403601C>T	ENST00000295910.6	-	6	763	c.711G>A	c.(709-711)acG>acA	p.T237T	FAM194A_ENST00000491361.1_Silent_p.T91T	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TGCTGGGTAACGTTCTTAGAG	0.373																																																0			3											120	112	115					3																	150403601		2203	4300	6503	151886291	SO:0001819	synonymous_variant	0																														ENST00000295910.6:c.711G>A	3.37:g.150403601C>T			151886291		Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																				0.373	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			T	150403601	C	T	150403601	2	4	38	1	0	0	0	0	0	0	0	1	5542	523	19	1		1	FAM194A	3	150403601	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	8259505	150403601	47618829	37	3331										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910746	184910746	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggattcaacattcgattcccCacaaatccaaaacagttgcc	5	13	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr3:184910746C>T	ENST00000231887.3	-	7	1515	c.1440G>A	c.(1438-1440)gtG>gtA	p.V480V	EHHADH_ENST00000456310.1_Silent_p.V384V|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	480	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)	p.V480V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TTCGATTCCCCACAAATCCAA	0.413																																																1	Substitution - coding silent(1)	ovary(1)	3											108	109	109					3																	184910746		2203	4300	6503	186393440	SO:0001819	synonymous_variant	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1440G>A	3.37:g.184910746C>T			186393440	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	37	CCDS33901.1																																																																																				0.413	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			T	184910746	C	T	184910746	2	4	38	1	0	0	0	0	0	0	0	1	4993	581	21	3		3	EHHADH	3	184910746	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	34507145	184910746	13111684	38	3332										
AFAP1	60312	hgsc.bcm.edu	37	chr4	7776610	7776610	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgcttctacccggttcttgcCatacttgtactgggcagcat	9	12	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:7776610C>G	ENST00000360265.4	-	13	1900	c.1666G>C	c.(1666-1668)Ggc>Cgc	p.G556R	AFAP1_ENST00000420658.1_Missense_Mutation_p.G640R|AFAP1_ENST00000358461.2_Missense_Mutation_p.G556R|AFAP1_ENST00000382543.3_Missense_Mutation_p.G640R|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000513842.1_5'UTR			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	556						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CGGTTCTTGCCATACTTGTAC	0.493																																																0			4											96	104	102					4																	7776610		2203	4300	6503	7827510	SO:0001583	missense	60312			AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1666G>C	4.37:g.7776610C>G	ENSP00000353402:p.Gly556Arg		7827510	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595452	0.86953	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.69895	0.3162	M	0.87547	2.89	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77381	-0.2609	10	0.72032	D	0.01	-39.0433	17.4991	0.87727	0.0:1.0:0.0:0.0	.	640;556	E9PDT7;Q8N556	.;AFAP1_HUMAN	R	556;640;556;640	ENSP00000353402:G556R;ENSP00000410689:G640R;ENSP00000351245:G556R;ENSP00000371983:G640R	ENSP00000351245:G556R	G	-	1	0	AFAP1	7827510	1.000000	0.71417	0.976000	0.42696	0.947000	0.59692	6.735000	0.74806	2.108000	0.64289	0.655000	0.94253	GGC		0.493	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		G	7776610	C	G	7776610	3	3	38	1	0	0	0	0	1	0	0	0	353	594	21	5	542	5	AFAP1	4	7776610	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10		7776610	183377666	39	3333										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82065433	82065433	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttcaggtttgccacatatccTtcaaggtatttttgcagctc	7	10	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:82065433T>C	ENST00000395578.1	-	10	1322	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000418486.2_Silent_p.E402E|PRKG2_ENST00000264399.1_Silent_p.E402E			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	402					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CCACATATCCTTCAAGGTATT	0.408																																																0			4											173	160	164					4																	82065433		2203	4300	6503	82284457	SO:0001819	synonymous_variant	5593			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1206A>G	4.37:g.82065433T>C			82284457	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																				0.408	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		C	82065433	T	C	82065433	2	2	38	1	0	0	0	0	0	0	0	1	12557	1606	56	4		4	PRKG2	4	82065433	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	74288823	82065433	109088843	40	3334										
HPSE	10855	hgsc.bcm.edu	37	chr4	84231914	84231914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tctttcttcgaggctgaccaAcatcaggaccatagagtttt	8	10	3	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:84231914A>G	ENST00000405413.2	-	6	939	c.803T>C	c.(802-804)gTt>gCt	p.V268A	HPSE_ENST00000311412.5_Missense_Mutation_p.V268A|HPSE_ENST00000512196.1_Missense_Mutation_p.V268A|HPSE_ENST00000513463.1_Missense_Mutation_p.V210A	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	268					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	AGGCTGACCAACATCAGGACC	0.388																																																0			4											208	201	203					4																	84231914		2203	4300	6503	84450938	SO:0001583	missense	10855			AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.803T>C	4.37:g.84231914A>G	ENSP00000384262:p.Val268Ala		84450938	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848191	0.71603	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.11	5.11	0.69529	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.643383	0.16294	N	0.220767	T	0.49440	0.1557	L	0.56769	1.78	0.40041	D	0.975656	P;P;D	0.56746	0.892;0.95;0.977	B;P;P	0.54270	0.389;0.716;0.747	T	0.49890	-0.8891	10	0.49607	T	0.09	-2.178	14.7198	0.69297	1.0:0.0:0.0:0.0	.	268;210;268	E9PCA9;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	A	268;268;268;210	ENSP00000308107:V268A;ENSP00000384262:V268A;ENSP00000423265:V268A;ENSP00000421365:V210A	ENSP00000308107:V268A	V	-	2	0	HPSE	84450938	0.886000	0.30341	0.292000	0.24919	0.927000	0.56198	8.002000	0.88514	2.143000	0.66587	0.477000	0.44152	GTT		0.388	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84231914	A	G	84231914	3	3	38	1	0	0	0	0	1	0	0	0	7365	43	2	4	860	4	HPSE	4	84231914	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	2166481	84231914	106922362	41	3335										
ANK2	287	hgsc.bcm.edu	37	chr4	114279170	114279170	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gatgaaagttttcactttttCcaaattggtcaagaatccag	7	7	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:114279170C>T	ENST00000357077.4	+	38	9449	c.9396C>T	c.(9394-9396)ttC>ttT	p.F3132F	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Silent_p.F3099F|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3132					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TTCACTTTTTCCAAATTGGTC	0.448																																																0			4											41	45	44					4																	114279170		2202	4299	6501	114498619	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9396C>T	4.37:g.114279170C>T			114498619	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.448	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114279170	C	T	114279170	2	4	38	1	0	0	0	0	0	0	0	1	621	854	30	3		3	ANK2	4	114279170	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	30047256	114279170	76875106	42	3336										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153258969	153258969	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tttacctctttagggagcaaTgaaatgaagtctcgttgaaa	9	6	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:153258969T>C	ENST00000281708.4	-	5	2075	c.846A>G	c.(844-846)tcA>tcG	p.S282S	RP11-461L13.2_ENST00000605147.1_RNA|FBXW7_ENST00000393956.3_Silent_p.S106S|FBXW7_ENST00000296555.5_Silent_p.S164S|FBXW7_ENST00000603841.1_Silent_p.S282S|FBXW7_ENST00000263981.5_Silent_p.S202S|FBXW7_ENST00000603548.1_Silent_p.S282S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	282	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TAGGGAGCAATGAAATGAAGT	0.338			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											171	166	168					4																	153258969		2203	4300	6503	153478419	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.846A>G	4.37:g.153258969T>C			153478419	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.338	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153258969	T	C	153258969	2	2	38	1	0	0	0	0	0	0	0	1	5788	1451	51	4		4	FBXW7	4	153258969	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	38979799	153258969	37895307	43	3337										
FAT1	2195	hgsc.bcm.edu	37	chr4	187630478	187630478	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tccgtggcgctgactcttgcGatactggtccttatagctgt	11	11	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr4:187630478G>A	ENST00000441802.2	-	2	713	c.504C>T	c.(502-504)atC>atT	p.I168I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	168	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TGACTCTTGCGATACTGGTCC	0.453										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											183	190	188					4																	187630478		2173	4280	6453	187867472	SO:0001819	synonymous_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.504C>T	4.37:g.187630478G>A			187867472		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.453	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187630478	G	A	187630478	2	1	38	1	0	0	0	0	0	0	0	1	5708	1048	37	1		1	FAT1	4	187630478	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	34371509	187630478	3523798	44	3338										
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867093	7867093	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atgaccctgcagacaacttcAggatccaacgtgaggcacac	9	13	1	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:7867093A>G	ENST00000264669.5	-	2	1240	c.1104T>C	c.(1102-1104)ccT>ccC	p.P368P	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000341013.6_5'Flank|FASTKD3_ENST00000513658.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	368					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.P368P(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AGACAACTTCAGGATCCAACG	0.458																																																1	Substitution - coding silent(1)	ovary(1)	5											72	71	72					5																	7867093		2203	4300	6503	7920093	SO:0001819	synonymous_variant	79072			AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1104T>C	5.37:g.7867093A>G			7920093	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																				0.458	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867093	A	G	7867093	2	3	38	1	0	0	0	0	0	0	0	1	5706	175	7	4		4	FASTKD3	5	7867093	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10		7867093	173048167	45	3339										
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36035970	36035970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atagggcttgaggtgcgtcgCgccccctgtctggaggacgt	16	11	1	1	rs200458466		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:36035970C>T	ENST00000282507.3	-	7	1503	c.1402G>A	c.(1402-1404)Gcg>Acg	p.A468T	UGT3A2_ENST00000513300.1_Missense_Mutation_p.A434T|UGT3A2_ENST00000545528.1_Missense_Mutation_p.A166T	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	468					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.A468T(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGGTGCGTCGCGCCCCCTGTC	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		16335	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	5											50	45	46					5																	36035970		2203	4300	6503	36071727	SO:0001583	missense	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.1402G>A	5.37:g.36035970C>T	ENSP00000282507:p.Ala468Thr		36071727	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.574251	0.28092	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.71579	-0.58;-0.58;-0.25	2.74	1.84	0.25277	.	0.364632	0.19685	U	0.108411	T	0.74535	0.3729	M	0.74258	2.255	0.09310	N	1	D;D	0.67145	0.978;0.996	P;P	0.55577	0.74;0.779	T	0.64672	-0.6352	10	0.87932	D	0	.	4.8123	0.13349	0.217:0.6619:0.0:0.1211	.	434;468	E9PFK7;Q3SY77	.;UD3A2_HUMAN	T	468;434;166	ENSP00000282507:A468T;ENSP00000427404:A434T;ENSP00000445367:A166T	ENSP00000282507:A468T	A	-	1	0	UGT3A2	36071727	0.003000	0.15002	0.003000	0.11579	0.000000	0.00434	1.274000	0.33132	0.689000	0.31550	-0.309000	0.09137	GCG		0.632	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		T	36035970	C	T	36035970	3	4	38	1	0	0	0	0	1	0	0	0	17004	768	27	1	173	1	UGT3A2	5	36035970	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	28168877	36035970	144879290	46	3340										
F2RL2	2151	hgsc.bcm.edu	37	chr5	75913456	75913456	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttctggtttttgacatgagaAaataaaggaatggatctaag	10	3	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:75913456A>C	ENST00000296641.4	-	2	1279	c.1076T>G	c.(1075-1077)tTt>tGt	p.F359C	IQGAP2_ENST00000502745.1_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.F337C|IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000396234.3_Intron|IQGAP2_ENST00000379730.3_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	359					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		TGACATGAGAAAATAAAGGAA	0.363																																																0			5											103	101	102					5																	75913456		2203	4300	6503	75949212	SO:0001583	missense	2151			U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"GPCR / Class A : Protease activated receptors"	3539	protein-coding gene	gene with protein product	"proteinase-activated receptor-3"	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.1076T>G	5.37:g.75913456A>C	ENSP00000296641:p.Phe359Cys		75949212	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.724010	0.48728	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.37584	1.19;1.19	5.0	2.49	0.30216	.	0.126185	0.56097	D	0.000038	T	0.27765	0.0683	L	0.45352	1.415	0.39048	D	0.960264	B	0.26547	0.152	B	0.24269	0.052	T	0.08166	-1.0735	10	0.48119	T	0.1	-12.3456	8.3495	0.32295	0.7307:0.1379:0.0:0.1314	.	359	O00254	PAR3_HUMAN	C	359;337	ENSP00000296641:F359C;ENSP00000426703:F337C	ENSP00000296641:F359C	F	-	2	0	F2RL2	75949212	1.000000	0.71417	0.989000	0.46669	0.945000	0.59286	3.386000	0.52492	0.295000	0.22570	0.460000	0.39030	TTT		0.363	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			C	75913456	A	C	75913456	3	2	38	1	0	0	0	0	1	0	0	0	5358	14	1	4	52	4	F2RL2	5	75913456	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	39877486	75913456	105001804	47	3341										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80390708	80390708	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcaagtgtttgggcacctggAttttaaaatagtggtggagc	14	5	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:80390708A>T	ENST00000265080.4	+	12	1719	c.1652A>T	c.(1651-1653)gAt>gTt	p.D551V		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	551	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		GGGCACCTGGATTTTAAAATA	0.458																																																0			5											118	121	120					5																	80390708		2203	4300	6503	80426464	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.1652A>T	5.37:g.80390708A>T	ENSP00000265080:p.Asp551Val		80426464	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861162	0.91433	.	.	ENSG00000113319	ENST00000265080	T	0.25912	1.77	5.93	5.93	0.95920	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	M	0.78801	2.425	0.80722	D	1	D	0.63046	0.992	P	0.59056	0.851	T	0.53982	-0.8361	10	0.87932	D	0	.	16.0219	0.80503	1.0:0.0:0.0:0.0	.	551	O14827	RGRF2_HUMAN	V	551	ENSP00000265080:D551V	ENSP00000265080:D551V	D	+	2	0	RASGRF2	80426464	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	8.920000	0.92779	2.267000	0.75376	0.528000	0.53228	GAT		0.458	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		T	80390708	A	T	80390708	3	4	38	1	0	0	0	0	1	0	0	0	13110	333	12	5	1698	5	RASGRF2	5	80390708	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	4477252	80390708	100524552	48	3342										
APC	324	hgsc.bcm.edu	37	chr5	112179182	112179182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atagtacttctcagaccgttTcctcaggtgctacaaatggt	8	10	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:112179182T>C	ENST00000457016.1	+	16	8271	c.7891T>C	c.(7891-7893)Tcc>Ccc	p.S2631P	APC_ENST00000508376.2_Missense_Mutation_p.S2631P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S2631P			P25054	APC_HUMAN	adenomatous polyposis coli	2631	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAGACCGTTTCCTCAGGTGC	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											92	102	99					5																	112179182		2202	4298	6500	112207081	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.7891T>C	5.37:g.112179182T>C	ENSP00000413133:p.Ser2631Pro		112207081	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	10.48	1.362344	0.24684	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89552	-2.53;-2.53;-2.53	6.17	6.17	0.99709	.	0.304311	0.34853	N	0.003624	D	0.90013	0.6882	N	0.24115	0.695	0.41624	D	0.988984	D;D	0.71674	0.998;0.995	D;D	0.75484	0.986;0.979	D	0.89353	0.3662	9	.	.	.	-2.3313	15.3933	0.74767	0.0:0.0:0.0:1.0	.	2633;2631	Q4LE70;P25054	.;APC_HUMAN	P	2631	ENSP00000413133:S2631P;ENSP00000257430:S2631P;ENSP00000427089:S2631P	.	S	+	1	0	APC	112207081	0.990000	0.36364	0.998000	0.56505	0.843000	0.47879	2.087000	0.41653	2.371000	0.80710	0.533000	0.62120	TCC		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112179182	T	C	112179182	3	2	38	1	0	0	0	0	1	0	0	0	763	1783	62	4	7949	4	APC	5	112179182	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	31788474	112179182	68736078	49	3343										
CCDC112	153733	hgsc.bcm.edu	37	chr5	114611077	114611077	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaagttctggtgatcataatCatcccaggcaccttgtcgcc	8	12	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:114611077C>T	ENST00000512261.1	-	7	921	c.505G>A	c.(505-507)Gat>Aat	p.D169N	CCDC112_ENST00000503027.1_5'UTR|CCDC112_ENST00000379611.5_Missense_Mutation_p.D252N|CCDC112_ENST00000506442.1_Missense_Mutation_p.D169N|CCDC112_ENST00000395557.4_Missense_Mutation_p.D169N			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112	169										endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		TGATCATAATCATCCCAGGCA	0.403																																																0			5											141	141	141					5																	114611077		2202	4300	6502	114638976	SO:0001583	missense	153733			BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.505G>A	5.37:g.114611077C>T	ENSP00000423712:p.Asp169Asn		114638976	Q6A334	Missense_Mutation	SNP	ENST00000512261.1	37	CCDS4117.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568977	0.65765	.	.	ENSG00000164221	ENST00000379611;ENST00000512261;ENST00000506442;ENST00000395557	T;T;T;T	0.21361	2.01;2.19;2.2;2.19	5.96	5.08	0.68730	.	0.299407	0.40818	N	0.001016	T	0.27559	0.0677	L	0.59436	1.845	0.25538	N	0.987201	B;B;P	0.37276	0.328;0.328;0.589	B;B;B	0.39258	0.232;0.232;0.295	T	0.14448	-1.0472	10	0.66056	D	0.02	-9.1493	16.3735	0.83374	0.133:0.867:0.0:0.0	.	169;252;169	D6RF76;Q8NEF3-2;Q8NEF3	.;.;CC112_HUMAN	N	252;169;169;169	ENSP00000368931:D252N;ENSP00000423712:D169N;ENSP00000424876:D169N;ENSP00000378925:D169N	ENSP00000368931:D252N	D	-	1	0	CCDC112	114638976	1.000000	0.71417	0.862000	0.33874	0.995000	0.86356	1.994000	0.40757	1.475000	0.48197	0.655000	0.94253	GAT		0.403	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370999.1	NM_152549		T	114611077	C	T	114611077	3	4	38	1	0	0	0	0	1	0	0	0	2755	826	29	3	855	3	CCDC112	5	114611077	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	2431895	114611077	66304183	50	3344										
RAD50	10111	hgsc.bcm.edu	37	chr5	131976422	131976422	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aacgttctgcctcaactgtgGcatcattgccttggatgagc	10	11	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:131976422G>T	ENST00000265335.6	+	24	4064	c.3677G>T	c.(3676-3678)gGc>gTc	p.G1226V	AC004041.2_ENST00000417516.1_RNA|AC004041.2_ENST00000435042.1_RNA|RAD50_ENST00000378823.3_Missense_Mutation_p.G1087V|AC004041.2_ENST00000457489.1_RNA|AC004041.2_ENST00000458509.1_RNA			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1226	Ala/Asp-rich (DA-box).				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCAACTGTGGCATCATTGCC	0.483								Homologous recombination																																								0			5											253	219	230					5																	131976422		2203	4300	6503	132004321	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3677G>T	5.37:g.131976422G>T	ENSP00000265335:p.Gly1226Val		132004321	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.324717|5.324717	0.95708|0.95708	.|.	.|.	ENSG00000113522|ENSG00000113522	ENST00000378823;ENST00000265335|ENST00000455677	T;T|.	0.03663|.	3.85;3.85|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.053054|.	0.85682|.	N|.	0.000000|.	T|T	0.58004|0.58004	0.2092|0.2092	N|N	0.25144|0.25144	0.715|0.715	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.48055|0.48055	-0.9068|-0.9068	10|5	0.87932|.	D|.	0|.	-10.0375|-10.0375	20.8598|20.8598	0.99761|0.99761	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1226|.	Q92878|.	RAD50_HUMAN|.	V|C	1087;1226|104	ENSP00000368100:G1087V;ENSP00000265335:G1226V|.	ENSP00000265335:G1226V|.	G|W	+|+	2|3	0|0	RAD50|RAD50	132004321|132004321	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.917000|0.917000	0.54804|0.54804	9.209000|9.209000	0.95087|0.95087	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GGC|TGG		0.483	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131976422	G	T	131976422	3	4	38	1	0	0	0	0	1	0	0	0	13021	1203	42	2	3771	2	RAD50	5	131976422	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	17365345	131976422	48938838	51	3345										
GABRP	2568	hgsc.bcm.edu	37	chr5	170239185	170239185	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaaaccccagtaatgttgatCactattccaaactactgttt	4	10	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr5:170239185C>T	ENST00000518525.1	+	11	1710	c.1246C>T	c.(1246-1248)Cac>Tac	p.H416Y	GABRP_ENST00000519385.1_3'UTR|GABRP_ENST00000265294.4_Missense_Mutation_p.H416Y			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	416			H -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TAATGTTGATCACTATTCCAA	0.348																																																0			5											120	110	114					5																	170239185		2203	4300	6503	170171763	SO:0001583	missense	2568			U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4089	protein-coding gene	gene with protein product	"GABA(A) receptor, pi"	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1246C>T	5.37:g.170239185C>T	ENSP00000430100:p.His416Tyr		170171763	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549247	0.45383	.	.	ENSG00000094755	ENST00000518525;ENST00000265294	T;T	0.81415	-1.49;-1.49	5.74	4.87	0.63330	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.234387	0.41396	D	0.000893	T	0.66499	0.2795	N	0.08118	0	0.23063	N	0.998356	B	0.16166	0.016	B	0.12837	0.008	T	0.61686	-0.7012	10	0.87932	D	0	.	15.8208	0.78644	0.1372:0.8628:0.0:0.0	.	416	O00591	GBRP_HUMAN	Y	416	ENSP00000430100:H416Y;ENSP00000265294:H416Y	ENSP00000265294:H416Y	H	+	1	0	GABRP	170171763	0.179000	0.23135	0.996000	0.52242	0.874000	0.50279	1.600000	0.36762	1.402000	0.46780	0.655000	0.94253	CAC		0.348	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		T	170239185	C	T	170239185	3	4	38	1	0	0	0	0	1	0	0	0	6193	826	29	3	1280	3	GABRP	5	170239185	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	38262763	170239185	10676075	52	3346										
IP6K3	117283	hgsc.bcm.edu	37	chr6	33694526	33694535	+	Frame_Shift_Del	DEL	GGTACTCGGA	GGTACTCGGA	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	acgatgccgcttgttctctgGgtactcggagcacaggcggg					rs576578939		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	GGTACTCGGA	GGTACTCGGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:33694526_33694535delGGTACTCGGA	ENST00000293756.4	-	4	888_897	c.562_571delTCCGAGTACC	c.(562-573)tccgagtacccafs	p.SEYP188fs	IP6K3_ENST00000451316.1_Frame_Shift_Del_p.SEYP188fs	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	188					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						TTGTTCTCTGGGTACTCGGAGCACAGGCGG	0.61																																																0			6																																								33802513	SO:0001589	frameshift_variant	117283			AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.562_571delTCCGAGTACC	6.37:g.33694526_33694535delGGTACTCGGA	ENSP00000293756:p.Ser188fs		33802504	Q96MQ9	Frame_Shift_Del	DEL	ENST00000293756.4	37	CCDS34435.1																																																																																				0.61	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		-	33694535	GGTACTCGGA	-	33694526	7	5	38	1	0	1	0	1	0	0	0	0	7811	1232	43	0	673	0	IP6K3	6	33694526	Frame_Shift_Del	DEL	GGTACTCGGA	TCGA-AG-3732-01A-11D-1657-10		33694526	137420541	53	3347										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38773335	38773335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgaagctaatattgtgaatgAgtttgatactcatgataaag	9	3	1	5			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:38773335A>G	ENST00000359357.3	+	21	2716	c.2462A>G	c.(2461-2463)gAg>gGg	p.E821G	DNAH8_ENST00000449981.2_Missense_Mutation_p.E1038G|DNAH8_ENST00000441566.1_Missense_Mutation_p.E821G			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	821					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATTGTGAATGAGTTTGATACT	0.313																																																0			6											97	94	95					6																	38773335		2203	4300	6503	38881313	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2462A>G	6.37:g.38773335A>G	ENSP00000352312:p.Glu821Gly		38881313	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	9.509	1.105201	0.20632	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.26223	1.78;1.78;1.75	5.45	4.26	0.50523	.	1.086810	0.06911	N	0.807661	T	0.06690	0.0171	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.38520	-0.9657	10	0.23302	T	0.38	.	9.7228	0.40313	0.8454:0.0:0.0:0.1546	.	821	Q96JB1	DYH8_HUMAN	G	1026;1026;821;821	ENSP00000333363:E1026G;ENSP00000352312:E821G;ENSP00000402294:E821G	ENSP00000333363:E1026G	E	+	2	0	DNAH8	38881313	0.799000	0.28903	0.008000	0.14137	0.200000	0.23975	2.658000	0.46733	0.975000	0.38392	0.533000	0.62120	GAG		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38773335	A	G	38773335	3	3	38	1	0	0	0	0	1	0	0	0	4618	304	11	4	2536	4	DNAH8	6	38773335	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	5078809	38773335	132341732	54	3348										
GPR115	221393	hgsc.bcm.edu	37	chr6	47682172	47682172	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atgtcctccaaatcgatgacCgacaaagttctggactacat	7	11	1	1	rs367867105		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:47682172C>T	ENST00000283303.2	+	6	1449	c.1191C>T	c.(1189-1191)acC>acT	p.T397T	RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Silent_p.T454T|GPR115_ENST00000327753.3_Silent_p.T397T	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	397					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						AATCGATGACCGACAAAGTTC	0.483																																					GBM(22;431 510 9010 26644 32828)											0			6						C		0,4406		0,0,2203	154	119	131		1191	-10.5	0	6		131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR115	NM_153838.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		397/696	47682172	1,13005	2203	4300	6503	47790131	SO:0001819	synonymous_variant	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1191C>T	6.37:g.47682172C>T			47790131	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	37	CCDS4922.2																																																																																				0.483	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		T	47682172	C	T	47682172	2	4	38	1	0	0	0	0	0	0	0	1	6652	639	23	1		1	GPR115	6	47682172	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	8908837	47682172	123432895	55	3349										
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245445	137245445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctctgttcattgccggcgtgGtggtgaacaccctgggctct	13	12	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:137245445G>A	ENST00000331858.4	+	2	1027	c.862G>A	c.(862-864)Gtg>Atg	p.V288M		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	288					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)		p.V288M(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		TGCCGGCGTGGTGGTGAACAC	0.592																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											75	69	71					6																	137245445		2203	4300	6503	137287138	SO:0001583	missense	340146				CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.862G>A	6.37:g.137245445G>A	ENSP00000333591:p.Val288Met		137287138	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036939	0.75617	.	.	ENSG00000182747	ENST00000331858	T	0.66099	-0.19	5.68	5.68	0.88126	Domain of unknown function DUF250 (1);	0.064498	0.64402	D	0.000010	T	0.70552	0.3237	L	0.55481	1.735	0.53005	D	0.999965	D	0.65815	0.995	D	0.65323	0.934	T	0.68887	-0.5290	10	0.48119	T	0.1	-22.3154	19.7951	0.96477	0.0:0.0:1.0:0.0	.	288	Q5M8T2	S35D3_HUMAN	M	288	ENSP00000333591:V288M	ENSP00000333591:V288M	V	+	1	0	SLC35D3	137287138	1.000000	0.71417	0.986000	0.45419	0.917000	0.54804	9.765000	0.98953	2.698000	0.92095	0.561000	0.74099	GTG		0.592	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		A	137245445	G	A	137245445	3	1	38	1	0	0	0	0	1	0	0	0	14620	1261	44	3	868	3	SLC35D3	6	137245445	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	89563273	137245445	33869622	56	3350										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200294	138200294	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtcagatccctcgcggctcgTccggagcccctccccgcatt	10	19	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:138200294T>C	ENST00000237289.4	+	7	1778	c.1712T>C	c.(1711-1713)gTc>gCc	p.V571A		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	571	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TCGCGGCTCGTCCGGAGCCCC	0.637			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	6											55	60	58					6																	138200294		2203	4300	6503	138241987	SO:0001583	missense	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1712T>C	6.37:g.138200294T>C	ENSP00000237289:p.Val571Ala		138241987	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	T	1.273	-0.612529	0.03690	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.21031	2.03	5.84	-1.59	0.08453	.	1.311420	0.04429	N	0.368847	T	0.02767	0.0083	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39542	-0.9609	10	0.22706	T	0.39	-21.4622	6.2662	0.20928	0.0:0.3595:0.2674:0.3731	.	571	P21580	TNAP3_HUMAN	A	571	ENSP00000237289:V571A	ENSP00000237289:V571A	V	+	2	0	TNFAIP3	138241987	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.047000	0.14056	-0.093000	0.12396	-1.235000	0.01560	GTC		0.637	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			C	138200294	T	C	138200294	3	2	38	1	0	0	0	0	1	0	0	0	16313	1667	58	4	1734	4	TNFAIP3	6	138200294	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	954849	138200294	32914773	57	3351										
UST	10090	hgsc.bcm.edu	37	chr6	149285594	149285594	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aacatcattagagaccccgtCaaccggttcttatccaacta	5	13	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:149285594C>T	ENST00000367463.4	+	5	679	c.576C>T	c.(574-576)gtC>gtT	p.V192V	RP11-162J8.2_ENST00000413845.1_RNA	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	192					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		GAGACCCCGTCAACCGGTTCT	0.498																																																0			6											104	95	98					6																	149285594		2203	4300	6503	149327287	SO:0001819	synonymous_variant	10090			AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.576C>T	6.37:g.149285594C>T			149327287	B2RCX6	Silent	SNP	ENST00000367463.4	37	CCDS5213.1																																																																																				0.498	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		T	149285594	C	T	149285594	2	4	38	1	0	0	0	0	0	0	0	1	17133	813	29	3		3	UST	6	149285594	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	11085300	149285594	21829473	58	3352										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152462343	152462343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atgctacgcactcaccagccGtttgggtttcggtactatgc	10	12	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr6:152462343G>A	ENST00000367255.5	-	139	25842	c.25241C>T	c.(25240-25242)aCg>aTg	p.T8414M	SYNE1_ENST00000341594.5_Missense_Mutation_p.T8026M|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000265368.4_Missense_Mutation_p.T8414M|SYNE1_ENST00000539504.1_Missense_Mutation_p.T569M|SYNE1_ENST00000423061.1_Missense_Mutation_p.T8366M|SYNE1_ENST00000356820.4_Missense_Mutation_p.T2938M|SYNE1_ENST00000448038.1_Missense_Mutation_p.T8366M|SYNE1_ENST00000354674.4_Missense_Mutation_p.T592M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8414					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.T8414M(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCACCAGCCGTTTGGGTTTC	0.478										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											173	149	157					6																	152462343		2203	4300	6503	152504036	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25241C>T	6.37:g.152462343G>A	ENSP00000356224:p.Thr8414Met		152504036	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654955	0.47467	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.56611	0.54;4.6;1.45;0.53;0.45;0.53;0.66;2.56;1.61;4.6	5.84	3.13	0.36017	.	0.113562	0.39759	N	0.001275	T	0.57504	0.2058	M	0.70595	2.14	0.40467	D	0.980307	D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;0.918	P;P;D;D;B	0.68621	0.855;0.855;0.959;0.912;0.39	T	0.60193	-0.7311	10	0.48119	T	0.1	.	11.5613	0.50778	0.1857:0.0:0.8143:0.0	.	8414;8414;8366;8366;616	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	M	8414;569;1060;8366;8414;8366;8026;2938;599;594;1359;592	ENSP00000356224:T8414M;ENSP00000441052:T569M;ENSP00000356226:T1060M;ENSP00000396024:T8366M;ENSP00000265368:T8414M;ENSP00000390975:T8366M;ENSP00000341887:T8026M;ENSP00000349276:T2938M;ENSP00000356220:T1359M;ENSP00000346701:T592M	ENSP00000265368:T8414M	T	-	2	0	SYNE1	152504036	1.000000	0.71417	0.886000	0.34754	0.287000	0.27160	3.615000	0.54167	0.391000	0.25143	-1.008000	0.02478	ACG		0.478	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152462343	G	A	152462343	3	1	38	1	0	0	0	0	1	0	0	0	15484	1145	40	1	1184	1	SYNE1	6	152462343	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	3176749	152462343	18652724	59	3353										
SFRP4	6424	hgsc.bcm.edu	37	chr7	37955773	37955773	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aggcagctcgtcgcaggccaGgctttcgggccagctgtggt	16	12	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:37955773G>C	ENST00000436072.2	-	1	744	c.367C>G	c.(367-369)Ctg>Gtg	p.L123V	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	123	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TCGCAGGCCAGGCTTTCGGGC	0.637																																																0			7											56	51	53					7																	37955773		2203	4300	6503	37922298	SO:0001583	missense	6424			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.367C>G	7.37:g.37955773G>C	ENSP00000410715:p.Leu123Val		37922298	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Missense_Mutation	SNP	ENST00000436072.2	37	CCDS5453.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810107	0.70797	.	.	ENSG00000106483	ENST00000436072;ENST00000446575	D	0.83591	-1.74	4.28	4.28	0.50868	Frizzled domain (5);	0.082585	0.51477	D	0.000089	D	0.91703	0.7377	M	0.86343	2.81	0.44129	D	0.996912	D	0.89917	1.0	D	0.87578	0.998	D	0.92686	0.6162	10	0.52906	T	0.07	.	15.6407	0.76997	0.0:0.0:1.0:0.0	.	123	Q6FHJ7	SFRP4_HUMAN	V	123;120	ENSP00000410715:L123V	ENSP00000410715:L123V	L	-	1	2	SFRP4	37922298	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.297000	0.65704	2.205000	0.71048	0.650000	0.86243	CTG		0.637	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		C	37955773	G	C	37955773	3	2	38	1	0	0	0	0	1	0	0	0	14200	991	35	5	697	5	SFRP4	7	37955773	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10		37955773	121182890	60	3354										
PSPH	5723	hgsc.bcm.edu	37	chr7	56079456	56079456	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agctgtacgacaatggatgtTattcttccagttctcccagc	8	11	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:56079456T>C	ENST00000395471.3	-	8	1482	c.677A>G	c.(676-678)tAa>tGa	p.*226*	PSPH_ENST00000275605.3_Silent_p.*226*|PSPH_ENST00000459834.1_5'UTR			P78330	SERB_HUMAN	phosphoserine phosphatase	0					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CAATGGATGTTATTCTTCCAG	0.373																																																0			7											108	90	96					7																	56079456		2203	4300	6503	56046950	SO:0001819	synonymous_variant	5723			Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.677A>G	7.37:g.56079456T>C			56046950	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																				0.373	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577		C	56079456	T	C	56079456	2	2	38	1	0	0	0	0	0	0	0	1	12751	1761	61	4		4	PSPH	7	56079456	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	18123683	56079456	103059207	61	3355										
EIF4H	7458	hgsc.bcm.edu	37	chr7	73609165	73609165	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agccgcttcagagatggcccTcccctccgtggatccaacat	9	16	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:73609165T>C	ENST00000265753.8	+	6	703	c.564T>C	c.(562-564)ccT>ccC	p.P188P	EIF4H_ENST00000353999.6_Silent_p.P168P	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	188					cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|sexual reproduction (GO:0019953)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|lung(2)|prostate(1)	4						GAGATGGCCCTCCCCTCCGTG	0.617																																																0			7											42	47	46					7																	73609165		2203	4300	6503	73247101	SO:0001819	synonymous_variant	7458				CCDS5564.1, CCDS5565.1	7q11.23	2013-02-12	2006-11-27	2006-11-27	ENSG00000106682	ENSG00000106682		"RNA binding motif (RRM) containing"	12741	protein-coding gene	gene with protein product		603431	"Williams-Beuren syndrome chromosome region 1"	WBSCR1		9516461, 15078951	Standard	NM_022170		Approved	WSCR1, KIAA0038	uc003uad.1	Q15056	OTTHUMG00000023025	ENST00000265753.8:c.564T>C	7.37:g.73609165T>C			73247101	A8K3R1|D3DXF6|D3DXF8	Silent	SNP	ENST00000265753.8	37	CCDS5564.1																																																																																				0.617	EIF4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252375.2	NM_022170		C	73609165	T	C	73609165	2	2	38	1	0	0	0	0	0	0	0	1	5052	1538	54	4		4	EIF4H	7	73609165	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	17529709	73609165	85529498	62	3356										
CROT	54677	hgsc.bcm.edu	37	chr7	87011450	87011450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tcattttcattgtggatgagAaagttttaaatgacatcaac	7	5	3	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:87011450A>G	ENST00000331536.3	+	12	1308	c.1123A>G	c.(1123-1125)Aaa>Gaa	p.K375E	CROT_ENST00000419147.2_Missense_Mutation_p.K403E|CROT_ENST00000442291.1_Missense_Mutation_p.K375E	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	375					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)	p.K375E(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TGTGGATGAGAAAGTTTTAAA	0.318																																																1	Substitution - Missense(1)	ovary(1)	7											68	69	68					7																	87011450		2203	4298	6501	86849386	SO:0001583	missense	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.1123A>G	7.37:g.87011450A>G	ENSP00000331981:p.Lys375Glu		86849386	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	.	.	.	.	.	.	.	.	.	.	A	9.246	1.039426	0.19669	.	.	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.88586	-2.4;-2.4;-2.4	5.3	5.3	0.74995	.	0.095061	0.64402	D	0.000001	T	0.80813	0.4695	N	0.25647	0.755	0.49130	D	0.999753	B;B	0.21452	0.056;0.028	B;B	0.23419	0.046;0.013	T	0.74618	-0.3605	10	0.02654	T	1	-27.0211	15.5342	0.75990	1.0:0.0:0.0:0.0	.	403;375	E7EQF2;Q9UKG9	.;OCTC_HUMAN	E	403;375;375	ENSP00000413575:K403E;ENSP00000331981:K375E;ENSP00000411983:K375E	ENSP00000331981:K375E	K	+	1	0	CROT	86849386	1.000000	0.71417	0.992000	0.48379	0.386000	0.30323	6.767000	0.74975	2.134000	0.65973	0.383000	0.25322	AAA		0.318	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		G	87011450	A	G	87011450	3	3	38	1	0	0	0	0	1	0	0	0	3900	247	9	4	1249	4	CROT	7	87011450	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	13402285	87011450	72127213	63	3357										
SRI	6717	hgsc.bcm.edu	37	chr7	87838725	87838725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tctttccattggtgctgtatCgttttgcaattgaattcaca	7	8	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:87838725C>T	ENST00000265729.2	-	6	492	c.440G>A	c.(439-441)cGa>cAa	p.R147Q	SRI_ENST00000431660.1_Missense_Mutation_p.R132Q|SRI_ENST00000394641.3_Missense_Mutation_p.R132Q|SRI_ENST00000490437.1_Missense_Mutation_p.R104Q|SRI_ENST00000419179.1_Missense_Mutation_p.R107Q	NM_003130.3	NP_003121.1	P30626	SORCN_HUMAN	sorcin	147	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				action potential (GO:0001508)|calcium ion transport (GO:0006816)|cytoplasmic sequestering of transcription factor (GO:0042994)|heart development (GO:0007507)|intracellular sequestering of iron ion (GO:0006880)|muscle organ development (GO:0007517)|negative regulation of heart rate (GO:0010459)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|proteolysis (GO:0006508)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart contraction (GO:0008016)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of relaxation of muscle (GO:1901077)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of striated muscle contraction (GO:0006942)|signal transduction (GO:0007165)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|ion channel binding (GO:0044325)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(14;0.00202)					GGTGCTGTATCGTTTTGCAAT	0.428																																																0			7											183	153	163					7																	87838725		2203	4300	6503	87676661	SO:0001583	missense	6717			M32886	CCDS5612.1, CCDS47638.1, CCDS59063.1	7q21.1	2014-09-17			ENSG00000075142	ENSG00000075142		"EF-hand domain containing"	11292	protein-coding gene	gene with protein product		182520				2901906	Standard	NM_001256891		Approved		uc003ujq.2	P30626	OTTHUMG00000157267	ENST00000265729.2:c.440G>A	7.37:g.87838725C>T	ENSP00000265729:p.Arg147Gln		87676661	A8MTH6|B4DKK2|D6W5Q0	Missense_Mutation	SNP	ENST00000265729.2	37	CCDS5612.1	.	.	.	.	.	.	.	.	.	.	C	37	6.048351	0.97236	.	.	ENSG00000075142	ENST00000265729;ENST00000419179;ENST00000490437;ENST00000394641;ENST00000431660	T;T;T;T;T	0.71461	-0.57;0.85;-0.57;-0.57;-0.57	5.87	5.87	0.94306	EF-hand-like domain (1);	0.000000	0.64402	D	0.000001	D	0.86431	0.5931	M	0.82193	2.58	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.996;1.0;1.0;1.0	D	0.87242	0.2267	10	0.87932	D	0	.	20.1861	0.98216	0.0:1.0:0.0:0.0	.	132;107;104;132;147	B4DKK2;B4DHQ6;C9J0K6;A8MTH6;P30626	.;.;.;.;SORCN_HUMAN	Q	147;107;104;132;132	ENSP00000265729:R147Q;ENSP00000397609:R107Q;ENSP00000418512:R104Q;ENSP00000378137:R132Q;ENSP00000391148:R132Q	ENSP00000265729:R147Q	R	-	2	0	SRI	87676661	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	7.729000	0.84864	2.774000	0.95407	0.655000	0.94253	CGA		0.428	SRI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253680.1	NM_003130		T	87838725	C	T	87838725	3	4	38	1	0	0	0	0	1	0	0	0	15188	884	31	1	168	1	SRI	7	87838725	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	827275	87838725	71299938	64	3358										
CDK14	5218	hgsc.bcm.edu	37	chr7	90492574	90492574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggagacgctgacacttgtgtTtgaatatgtggtaagtaaaa	12	4	0	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:90492574T>C	ENST00000380050.3	+	6	760	c.629T>C	c.(628-630)tTt>tCt	p.F210S	CDK14_ENST00000406263.1_Missense_Mutation_p.F164S|CDK14_ENST00000436577.2_Missense_Mutation_p.F81S|CDK14_ENST00000265741.3_Missense_Mutation_p.F192S			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						ACACTTGTGTTTGAATATGTG	0.303																																					GBM(83;1228 1256 8311 16577 31299)											0			7											76	72	73					7																	90492574		2203	4299	6502	90330510	SO:0001583	missense	0				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.629T>C	7.37:g.90492574T>C	ENSP00000369390:p.Phe210Ser		90330510	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	37		.	.	.	.	.	.	.	.	.	.	T	23.5	4.419806	0.83559	.	.	ENSG00000058091	ENST00000380050;ENST00000265741;ENST00000406263;ENST00000436577	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81740	0.4886	M	0.86864	2.845	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.995;0.998;0.996	D	0.85421	0.1143	10	0.87932	D	0	-17.2422	15.3825	0.74669	0.0:0.0:0.0:1.0	.	81;192;210	E7EUK8;O94921-2;O94921	.;.;CDK14_HUMAN	S	210;192;164;81	ENSP00000369390:F210S;ENSP00000265741:F192S;ENSP00000385034:F164S;ENSP00000398936:F81S	ENSP00000265741:F192S	F	+	2	0	CDK14	90330510	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.581000	0.82535	2.028000	0.59812	0.528000	0.53228	TTT		0.303	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		C	90492574	T	C	90492574	3	2	38	1	0	0	0	0	1	0	0	0	3136	1841	64	4	593	4	CDK14	7	90492574	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	2653849	90492574	68646089	65	3359										
TRIM56	81844	hgsc.bcm.edu	37	chr7	100730765	100730765	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcggccgcgtccgctgccccGagtgccgcgagacagtgcct	15	17	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:100730765G>T	ENST00000306085.6	+	3	469	c.172G>T	c.(172-174)Gag>Tag	p.E58*		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	58					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CCGCTGCCCCGAGTGCCGCGA	0.677																																					Ovarian(89;1092 1379 22756 38989 39611)											0			7											36	46	43					7																	100730765		2125	4232	6357	100517485	SO:0001587	stop_gained	81844			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.172G>T	7.37:g.100730765G>T	ENSP00000305161:p.Glu58*		100517485	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Nonsense_Mutation	SNP	ENST00000306085.6	37	CCDS43625.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308744	0.60305	.	.	ENSG00000169871	ENST00000306085;ENST00000412507	.	.	.	3.95	3.95	0.45737	.	0.000000	0.45361	D	0.000363	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	11.7795	0.52006	0.0:0.0:1.0:0.0	.	.	.	.	X	58	.	ENSP00000305161:E58X	E	+	1	0	TRIM56	100517485	0.990000	0.36364	0.925000	0.36789	0.013000	0.08279	2.188000	0.42612	2.478000	0.83669	0.655000	0.94253	GAG		0.677	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		T	100730765	G	T	100730765	4	4	38	1	0	0	0	0	0	1	0	0	16570	1059	37	2	174	2	TRIM56	7	100730765	Nonsense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	10238191	100730765	58407898	66	3360										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107704330	107704330	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cggctgcaggactctggatcGgttacatctatgttgttgtt	12	8	2	0	rs538631774		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:107704330G>T	ENST00000388781.3	-	22	3020	c.2937C>A	c.(2935-2937)acC>acA	p.T979T	LAMB4_ENST00000388780.3_Silent_p.T979T|LAMB4_ENST00000205386.4_Silent_p.T979T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	979	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.T979T(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ACTCTGGATCGGTTACATCTA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	7											173	161	165					7																	107704330		2203	4300	6503	107491566	SO:0001819	synonymous_variant	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2937C>A	7.37:g.107704330G>T			107491566	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																				0.502	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		T	107704330	G	T	107704330	2	4	38	1	0	0	0	0	0	0	0	1	8635	1103	39	2		2	LAMB4	7	107704330	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	6973565	107704330	51434333	67	3361										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342385	122342385	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtcccctggtgagacatgggAaatactttactgcccgtacc	10	12	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:122342385A>T	ENST00000434824.1	-	1	636	c.420T>A	c.(418-420)ttT>ttA	p.F140L	RNF148_ENST00000447240.1_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	140	PA.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						GAGACATGGGAAATACTTTAC	0.448																																																0			7											280	272	274					7																	122342385		1988	4165	6153	122129621	SO:0001583	missense	378925			BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.420T>A	7.37:g.122342385A>T	ENSP00000388207:p.Phe140Leu		122129621	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	37	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.227346	0.39399	.	.	ENSG00000235631	ENST00000434824	T	0.07114	3.22	4.95	1.23	0.21249	Protease-associated domain, PA (1);	.	.	.	.	T	0.07728	0.0194	L	0.39633	1.23	0.80722	D	1	B	0.20780	0.048	B	0.29440	0.102	T	0.28004	-1.0057	9	0.25106	T	0.35	.	8.7197	0.34434	0.6907:0.0:0.3093:0.0	.	140	Q8N7C7	RN148_HUMAN	L	140	ENSP00000388207:F140L	ENSP00000388207:F140L	F	-	3	2	RNF148	122129621	0.997000	0.39634	0.998000	0.56505	0.959000	0.62525	0.811000	0.27198	0.030000	0.15379	0.454000	0.30748	TTT		0.448	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		T	122342385	A	T	122342385	3	4	38	1	0	0	0	0	1	0	0	0	13486	243	9	5	501	5	RNF148	7	122342385	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	14638055	122342385	36796278	68	3362										
FSCN3	29999	hgsc.bcm.edu	37	chr7	127235526	127235526	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgcgtttccaccggaacagcAagtggaccctccagtgccta	10	14	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:127235526A>G	ENST00000265825.5	+	2	529	c.310A>G	c.(310-312)Aag>Gag	p.K104E	FSCN3_ENST00000420086.2_5'UTR|GCC1_ENST00000497650.1_5'Flank	NM_020369.2	NP_065102.1	Q9NQT6	FSCN3_HUMAN	fascin actin-bundling protein 3, testicular	104						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30						CCGGAACAGCAAGTGGACCCT	0.557																																																0			7											155	116	129					7																	127235526		2203	4300	6503	127022762	SO:0001583	missense	29999				CCDS34746.1	7q31.3	2014-02-03	2014-02-03		ENSG00000106328	ENSG00000106328		"Fascins"	3961	protein-coding gene	gene with protein product		615800	"fascin (Strongylocentrotus purpuratus) homolog 3 (actin-bundling protein, testicular)", "fascin homolog 3, actin-bundling protein, testicular (Strongylocentrotus purpuratus)"			11925108	Standard	NM_020369		Approved		uc003vmd.2	Q9NQT6	OTTHUMG00000022935	ENST00000265825.5:c.310A>G	7.37:g.127235526A>G	ENSP00000265825:p.Lys104Glu		127022762	A4D0Z2|A6NLL7|B2RA62|B4DU68	Missense_Mutation	SNP	ENST00000265825.5	37	CCDS34746.1	.	.	.	.	.	.	.	.	.	.	A	18.34	3.602463	0.66445	.	.	ENSG00000106328	ENST00000265825	T	0.24723	1.84	5.59	4.42	0.53409	Fascin domain (1);Actin cross-linking (1);	0.087565	0.49916	D	0.000132	T	0.32255	0.0823	L	0.57536	1.79	0.80722	D	1	P	0.40000	0.698	P	0.45753	0.492	T	0.06463	-1.0825	10	0.66056	D	0.02	-42.6881	9.9401	0.41576	0.8289:0.1711:0.0:0.0	.	104	Q9NQT6	FSCN3_HUMAN	E	104	ENSP00000265825:K104E	ENSP00000265825:K104E	K	+	1	0	FSCN3	127022762	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	2.088000	0.41663	1.038000	0.40049	0.533000	0.62120	AAG		0.557	FSCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059256.2	NM_020369		G	127235526	A	G	127235526	3	3	38	1	0	0	0	0	1	0	0	0	6088	131	5	4	316	4	FSCN3	7	127235526	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	4893141	127235526	31903137	69	3363										
TNPO3	23534	hgsc.bcm.edu	37	chr7	128655105	128655105	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtgcgccgattagctccaatTcgtaaggaacgactatgtac	10	10	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:128655105T>C	ENST00000265388.5	-	4	623	c.480A>G	c.(478-480)cgA>cgG	p.R160R	TNPO3_ENST00000482320.1_Silent_p.R94R|TNPO3_ENST00000393245.1_Silent_p.R160R|TNPO3_ENST00000471166.1_Silent_p.R160R|TNPO3_ENST00000471234.1_Silent_p.R160R			Q9Y5L0	TNPO3_HUMAN	transportin 3	160					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TAGCTCCAATTCGTAAGGAAC	0.378																																					Pancreas(147;583 2585 39696 52331)											0			7											114	105	108					7																	128655105		2203	4300	6503	128442341	SO:0001819	synonymous_variant	23534			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.480A>G	7.37:g.128655105T>C			128442341	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	37	CCDS5809.1																																																																																				0.378	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		C	128655105	T	C	128655105	2	2	38	1	0	0	0	0	0	0	0	1	16376	1770	62	4		4	TNPO3	7	128655105	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	1419579	128655105	30483558	70	3364										
MLL3	58508	hgsc.bcm.edu	37	chr7	151859570	151859570	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tacttctgaatttgcatacgTctgttgatttggagttgctt	9	6	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr7:151859570T>C	ENST00000262189.6	-	43	11310	c.11092A>G	c.(11092-11094)Acg>Gcg	p.T3698A	KMT2C_ENST00000355193.2_Missense_Mutation_p.T3698A	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3698			T -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.T3698S(1)									TTTGCATACGTCTGTTGATTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											243	245	244					7																	151859570		2203	4300	6503	151490503	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11092A>G	7.37:g.151859570T>C	ENSP00000262189:p.Thr3698Ala		151490503	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.498|8.498	0.863573|0.863573	0.17250|0.17250	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193;ENST00000424877	.|D;D;D	.|0.87809	.|-1.59;-1.61;-2.3	5.51|5.51	-3.92|-3.92	0.04155|0.04155	.|.	.|0.507408	.|0.16272	.|U	.|0.221726	T|T	0.71592|0.71592	0.3358|0.3358	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.0;0.001;0.001	T|T	0.55598|0.55598	-0.8116|-0.8116	5|10	.|0.31617	.|T	.|0.26	.|.	0.9915|0.9915	0.01458|0.01458	0.3754:0.2125:0.0953:0.3168|0.3754:0.2125:0.0953:0.3168	.|.	.|3698;2759;3698	.|Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	.|MLL3_HUMAN;.;.	G|A	1203|3698;3698;284	.|ENSP00000262189:T3698A;ENSP00000347325:T3698A;ENSP00000410411:T284A	.|ENSP00000262189:T3698A	D|T	-|-	2|1	0|0	MLL3|MLL3	151490503|151490503	0.061000|0.061000	0.20836|0.20836	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	0.167000|0.167000	0.16602|0.16602	-0.451000|-0.451000	0.07097|0.07097	-1.437000|-1.437000	0.01076|0.01076	GAC|ACG		0.473	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151859570	T	C	151859570	3	2	38	1	0	0	0	0	1	0	0	0	9652	1667	58	4	3711	4	MLL3	7	151859570	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	23204465	151859570	7279093	71	3365										
HOOK3	84376	hgsc.bcm.edu	37	chr8	42814397	42814397	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aagaaaactacagaggaactAaatgaagctttgtcagcaaa	8	6	1	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr8:42814397A>G	ENST00000307602.4	+	8	755	c.555A>G	c.(553-555)ctA>ctG	p.L185L		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	185					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.L185L(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CAGAGGAACTAAATGAAGCTT	0.343			T	RET	papillary thyroid																																		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - coding silent(1)	ovary(1)	8											106	106	106					8																	42814397		2203	4300	6503	42933554	SO:0001819	synonymous_variant	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.555A>G	8.37:g.42814397A>G			42933554	D3DSY8|Q8NBH0|Q9BY13	Silent	SNP	ENST00000307602.4	37	CCDS6139.1																																																																																				0.343	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		G	42814397	A	G	42814397	2	3	38	1	0	0	0	0	0	0	0	1	7305	349	13	4		4	HOOK3	8	42814397	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10		42814397	103549625	72	3366										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53570340	53570340	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aattcttctaagggacaaacTgcaggacataagggatcctg	10	8	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr8:53570340T>C	ENST00000025008.5	-	15	2572	c.2049A>G	c.(2047-2049)gcA>gcG	p.A683A	RB1CC1_ENST00000539297.1_Silent_p.A683A|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Silent_p.A683A	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	683					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				AGGGACAAACTGCAGGACATA	0.423																																					GBM(180;1701 2102 13475 42023 52570)											0			8											98	99	99					8																	53570340		2203	4300	6503	53732893	SO:0001819	synonymous_variant	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2049A>G	8.37:g.53570340T>C			53732893	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																				0.423	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		C	53570340	T	C	53570340	2	2	38	1	0	0	0	0	0	0	0	1	13136	1567	55	4		4	RB1CC1	8	53570340	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	10755943	53570340	92793682	73	3367										
ASPH	444	hgsc.bcm.edu	37	chr8	62430095	62430095	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaggacccatacttggtctcGttggcacatcgaatcttgca	10	11	2	0	rs554349058		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr8:62430095G>A	ENST00000379454.4	-	24	2305	c.2118C>T	c.(2116-2118)aaC>aaT	p.N706N	ASPH_ENST00000541428.1_Silent_p.N677N	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	706					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	ACTTGGTCTCGTTGGCACATC	0.512													G|||	1	0.000199681	0	0.0014	5008	,	,		20083	0		0	False		,,,				2504	0															0			8											174	124	141					8																	62430095		2203	4300	6503	62592649	SO:0001819	synonymous_variant	444			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.2118C>T	8.37:g.62430095G>A			62592649	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Silent	SNP	ENST00000379454.4	37	CCDS34898.1																																																																																				0.512	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		A	62430095	G	A	62430095	2	1	38	1	0	0	0	0	0	0	0	1	1054	1136	40	1		1	ASPH	8	62430095	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	8859755	62430095	83933927	74	3368										
PLEKHF2	79666	hgsc.bcm.edu	37	chr8	96166992	96166992	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cctttaaatgatatgtctgaTgatgatgacgatgatgatag	10	4	1	7			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr8:96166992T>C	ENST00000315367.3	+	2	961	c.720T>C	c.(718-720)gaT>gaC	p.D240D	PLEKHF2_ENST00000519516.1_Silent_p.D240D	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	240					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					ATATGTCTGATGATGATGACG	0.438																																																0			8											77	74	75					8																	96166992		2203	4300	6503	96236168	SO:0001819	synonymous_variant	79666			AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"Zinc fingers, FYVE domain containing", "Pleckstrin homology (PH) domain containing"	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.720T>C	8.37:g.96166992T>C			96236168		Silent	SNP	ENST00000315367.3	37	CCDS6267.1																																																																																				0.438	PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613		C	96166992	T	C	96166992	2	2	38	1	0	0	0	0	0	0	0	1	12098	1461	51	4		4	PLEKHF2	8	96166992	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	33736897	96166992	50197030	75	3369										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109240604	109240604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttctctgctgaagagactgaAgtggagaactcacagactaa	10	8	2	5			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr8:109240604A>G	ENST00000220849.5	-	7	676	c.614T>C	c.(613-615)cTt>cCt	p.L205P	EIF3E_ENST00000519030.1_Missense_Mutation_p.L112P|EIF3E_ENST00000519517.1_5'UTR|RP11-35G22.1_ENST00000520037.1_RNA	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E									p.L205H(1)	EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			AAGAGACTGAAGTGGAGAACT	0.348																																					GBM(15;360 410 8460 34179 52246)											1	Substitution - Missense(1)	ovary(1)	8											74	74	74					8																	109240604		2203	4300	6503	109309780	SO:0001583	missense	3646			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.614T>C	8.37:g.109240604A>G	ENSP00000220849:p.Leu205Pro		109309780		Missense_Mutation	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403034	0.83230	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.50277	0.75;0.75;0.75	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.73946	0.3652	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.971	T	0.79902	-0.1607	10	0.87932	D	0	-11.5618	15.9153	0.79512	1.0:0.0:0.0:0.0	.	205;205	B2R806;P60228	.;EIF3E_HUMAN	P	205;112;78	ENSP00000220849:L205P;ENSP00000428796:L112P;ENSP00000430839:L78P	ENSP00000220849:L205P	L	-	2	0	EIF3E	109309780	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	9.287000	0.95975	2.213000	0.71641	0.477000	0.44152	CTT		0.348	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		G	109240604	A	G	109240604	3	3	38	1	0	0	0	0	1	0	0	0	5028	72	3	4	751	4	EIF3E	8	109240604	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	13073612	109240604	37123418	76	3370										
KANK1	23189	hgsc.bcm.edu	37	chr9	738304	738304	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaggttctgtctgaacacccTccagcacgagtggttccgcg	12	13	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr9:738304T>C	ENST00000382303.1	+	12	4005	c.3353T>C	c.(3352-3354)cTc>cCc	p.L1118P	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.L1118P|KANK1_ENST00000382293.3_Missense_Mutation_p.L960P	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1118					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		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)		CTGAACACCCTCCAGCACGAG	0.498																																																0			9											77	57	64					9																	738304		2203	4300	6503	728304	SO:0001583	missense	23189			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3353T>C	9.37:g.738304T>C	ENSP00000371740:p.Leu1118Pro		728304	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.532102	0.85812	.	.	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293;ENST00000382289;ENST00000382286	T;T;T	0.42513	0.97;0.97;1.02	5.73	5.73	0.89815	.	0.138628	0.32314	N	0.006273	T	0.56262	0.1973	L	0.48642	1.525	0.80722	D	1	P;D;D	0.58620	0.947;0.983;0.972	P;P;P	0.61800	0.894;0.732;0.804	T	0.58470	-0.7631	10	0.87932	D	0	13.4839	16.3265	0.82983	0.0:0.0:0.0:1.0	.	164;30;1118	F5H7I5;Q5W0W2;Q14678	.;.;KANK1_HUMAN	P	1118;164;1118;960;96;30	ENSP00000371740:L1118P;ENSP00000371734:L1118P;ENSP00000371730:L960P	ENSP00000371723:L30P	L	+	2	0	KANK1	728304	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	7.608000	0.82898	2.313000	0.78055	0.455000	0.32223	CTC		0.498	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		C	738304	T	C	738304	3	2	38	1	0	0	0	0	1	0	0	0	7997	1551	54	4	3379	4	KANK1	9	738304	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10		738304	140475127	77	3371										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13119559	13119559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaacgtcttccccattcaccAttaatatctggtctccctgc	5	15	4	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr9:13119559A>G	ENST00000319217.7	-	39	5568	c.5321T>C	c.(5320-5322)aTg>aCg	p.M1774T	MPDZ_ENST00000538841.1_Missense_Mutation_p.M633T|MPDZ_ENST00000381022.2_Missense_Mutation_p.M1774T|MPDZ_ENST00000546205.1_Missense_Mutation_p.M1788T|MPDZ_ENST00000541093.1_Missense_Mutation_p.M8T|MPDZ_ENST00000447879.1_Missense_Mutation_p.M1741T|MPDZ_ENST00000536827.1_Missense_Mutation_p.M1741T|MPDZ_ENST00000381015.4_Missense_Mutation_p.M1774T|MPDZ_ENST00000541718.1_Missense_Mutation_p.M1774T	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1774	PDZ 11. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CCCATTCACCATTAATATCTG	0.418																																																0			9											154	151	152					9																	13119559		1904	4136	6040	13109559	SO:0001583	missense	84708			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.5321T>C	9.37:g.13119559A>G	ENSP00000320006:p.Met1774Thr		13109559	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	A	1.163	-0.643222	0.03531	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000541093;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T;T	0.40756	1.02;1.72;1.72;1.02;1.72;1.02;1.02;1.72;1.02;1.02;1.02	6.03	-1.03	0.10102	PDZ/DHR/GLGF (4);	0.339838	0.25138	N	0.032848	T	0.19167	0.0460	N	0.12182	0.205	0.29713	N	0.83923	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.002;0.002;0.001;0.001	T	0.20405	-1.0276	10	0.18276	T	0.48	.	8.367	0.32393	0.4261:0.1196:0.4543:0.0	.	1741;633;479;1741;1654;1774;1774;467	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970;B3KRN5	.;.;.;.;.;.;MPDZ_HUMAN;.	T	1774;1774;1774;315;8;710;633;1741;1741;1774;1654;1788	ENSP00000320006:M1774T;ENSP00000439807:M1774T;ENSP00000370410:M1774T;ENSP00000415964:M315T;ENSP00000445259:M8T;ENSP00000444230:M710T;ENSP00000444717:M633T;ENSP00000444151:M1741T;ENSP00000415208:M1741T;ENSP00000370403:M1774T;ENSP00000446358:M1788T	ENSP00000320006:M1774T	M	-	2	0	MPDZ	13109559	0.919000	0.31177	0.244000	0.24202	0.351000	0.29236	1.915000	0.39976	-0.422000	0.07405	-0.313000	0.08912	ATG		0.418	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		G	13119559	A	G	13119559	3	3	38	1	0	0	0	0	1	0	0	0	9752	217	8	4	836	4	MPDZ	9	13119559	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	12381255	13119559	128093872	78	3372										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543970	32543970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agaagcatttcgttcccttgTcagagttgtacggtagcgaa	11	8	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr9:32543970T>C	ENST00000360538.2	-	3	669	c.553A>G	c.(553-555)Aca>Gca	p.T185A	TOPORS_ENST00000379858.1_Missense_Mutation_p.T120A	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	185	E3 ubiquitin-protein ligase activity.|Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CGTTCCCTTGTCAGAGTTGTA	0.463																																																0			9											135	116	122					9																	32543970		2203	4300	6503	32533970	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.553A>G	9.37:g.32543970T>C	ENSP00000353735:p.Thr185Ala		32533970	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316678	0.40996	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18657	2.2;2.21	5.21	5.21	0.72293	.	0.000000	0.47455	D	0.000234	T	0.31638	0.0803	L	0.55481	1.735	0.39957	D	0.974616	D	0.58620	0.983	P	0.51016	0.656	T	0.11084	-1.0602	10	0.62326	D	0.03	-15.1247	14.3756	0.66874	0.0:0.0:0.0:1.0	.	185	Q9NS56	TOPRS_HUMAN	A	185;120	ENSP00000353735:T185A;ENSP00000369187:T120A	ENSP00000353735:T185A	T	-	1	0	TOPORS	32533970	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	7.610000	0.82949	2.092000	0.63282	0.460000	0.39030	ACA		0.463	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543970	T	C	32543970	3	2	38	1	0	0	0	0	1	0	0	0	16410	1667	58	4	2588	4	TOPORS	9	32543970	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	19424411	32543970	108669461	79	3373										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98248027	98248027	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccgagtccaggtgttgtaggAgcgcttctgtggtcaggaca	15	9	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr9:98248027A>G	ENST00000331920.6	-	3	823	c.524T>C	c.(523-525)cTc>cCc	p.L175P	PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000437951.1_Missense_Mutation_p.L109P|PTCH1_ENST00000421141.1_Missense_Mutation_p.L24P|PTCH1_ENST00000468211.2_Missense_Mutation_p.L109P|PTCH1_ENST00000418258.1_Missense_Mutation_p.L24P|PTCH1_ENST00000430669.2_Missense_Mutation_p.L109P|PTCH1_ENST00000429896.2_Missense_Mutation_p.L24P|PTCH1_ENST00000375274.2_Missense_Mutation_p.L174P	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	175			L -> P (in BCNS; sporadic BCC). {ECO:0000269|PubMed:8658145}.		brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GTGTTGTAGGAGCGCTTCTGT	0.507																																																0			9											193	199	197					9																	98248027		2203	4300	6503	97287848	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.524T>C	9.37:g.98248027A>G	ENSP00000332353:p.Leu175Pro		97287848	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.041598	0.55003	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000553011;ENST00000551845;ENST00000547672;ENST00000546820;ENST00000468211;ENST00000551630	D;D;D;D;D;D;D;D;D;D;D;D;T	0.97553	-2.21;-4.36;-4.19;-4.19;-4.36;-4.19;-4.43;-3.05;-3.05;-3.05;-3.05;-2.21;0.77	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.98394	0.9466	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.99564	1.0969	10	0.87932	D	0	-28.3253	16.2449	0.82437	1.0:0.0:0.0:0.0	.	109;174;175	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	P	175;109;24;24;109;24;174;24;24;24;24;109;24	ENSP00000332353:L175P;ENSP00000389744:L109P;ENSP00000399981:L24P;ENSP00000396135:L24P;ENSP00000410287:L109P;ENSP00000414823:L24P;ENSP00000364423:L174P;ENSP00000447797:L24P;ENSP00000447008:L24P;ENSP00000447878:L24P;ENSP00000448843:L24P;ENSP00000449745:L109P;ENSP00000450131:L24P	ENSP00000332353:L175P	L	-	2	0	PTCH1	97287848	1.000000	0.71417	0.409000	0.26459	0.020000	0.10135	8.962000	0.93254	2.241000	0.73720	0.482000	0.46254	CTC		0.507	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		G	98248027	A	G	98248027	3	3	38	1	0	0	0	0	1	0	0	0	12764	304	11	4	3903	4	PTCH1	9	98248027	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	65704057	98248027	42965404	80	3374										
OR1J2	26740	hgsc.bcm.edu	37	chr9	125273262	125273262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccttcacacccccatgtactTcttcctcagccacttggctc	4	19	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr9:125273262T>C	ENST00000335302.5	+	1	182	c.182T>C	c.(181-183)tTc>tCc	p.F61S		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						CCCATGTACTTCTTCCTCAGC	0.517																																																0			9											268	206	227					9																	125273262		2203	4300	6503	124313083	SO:0001583	missense	26740				CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.182T>C	9.37:g.125273262T>C	ENSP00000335575:p.Phe61Ser		124313083	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694793	0.88830	.	.	ENSG00000197233	ENST00000335302;ENST00000444856	T	0.00557	6.62	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37012	U	0.002285	T	0.02929	0.0087	M	0.91612	3.225	0.32759	N	0.505352	D	0.57899	0.981	D	0.67231	0.95	T	0.01702	-1.1292	10	0.72032	D	0.01	.	13.9092	0.63855	0.0:0.0:0.0:1.0	.	61	Q8NGS2	OR1J2_HUMAN	S	61	ENSP00000335575:F61S	ENSP00000335575:F61S	F	+	2	0	OR1J2	124313083	0.362000	0.24980	1.000000	0.80357	0.991000	0.79684	2.606000	0.46291	2.132000	0.65825	0.529000	0.55759	TTC		0.517	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			C	125273262	T	C	125273262	3	2	38	1	0	0	0	0	1	0	0	0	10991	1783	62	4	184	4	OR1J2	9	125273262	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	27025235	125273262	15940169	81	3375										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22657452	22657452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caagaaagcagctgcctttgTgttacgagcagttggtaaac	11	8	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:22657452T>C	ENST00000376624.3	+	4	459	c.317T>C	c.(316-318)gTg>gCg	p.V106A	SPAG6_ENST00000376601.1_Intron|SPAG6_ENST00000538630.1_Missense_Mutation_p.V81A|SPAG6_ENST00000313311.6_Missense_Mutation_p.V106A|SPAG6_ENST00000376603.2_Missense_Mutation_p.V182A|RP11-301N24.3_ENST00000422675.1_RNA	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	106			V -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						GCTGCCTTTGTGTTACGAGCA	0.418																																																0			10											104	97	99					10																	22657452		2203	4300	6503	22697458	SO:0001583	missense	9576			AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.317T>C	10.37:g.22657452T>C	ENSP00000365811:p.Val106Ala		22697458	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	37	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	T	32	5.169334	0.94768	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311;ENST00000435326	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;1.24	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.052283	0.85682	D	0.000000	T	0.76557	0.4004	M	0.88310	2.945	0.80722	D	1	P;P;D;P	0.55172	0.795;0.812;0.97;0.89	P;P;P;P	0.57152	0.539;0.551;0.814;0.539	T	0.81484	-0.0912	10	0.62326	D	0.03	-22.2157	15.9771	0.80076	0.0:0.0:0.0:1.0	.	81;182;106;106	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	A	106;182;81;106;182	ENSP00000365811:V106A;ENSP00000365788:V182A;ENSP00000441325:V81A;ENSP00000323599:V106A;ENSP00000406594:V182A	ENSP00000323599:V106A	V	+	2	0	SPAG6	22697458	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.665000	0.83852	2.165000	0.68154	0.533000	0.62120	GTG		0.418	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			C	22657452	T	C	22657452	3	2	38	1	0	0	0	0	1	0	0	0	15021	1696	59	4	331	4	SPAG6	10	22657452	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10		22657452	112877295	82	3376										
PDSS1	23590	hgsc.bcm.edu	37	chr10	27024245	27024247	+	In_Frame_Del	DEL	TTC	TTC	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaaaaatgtaggaatagcttTtcaggttagtatgcttttta							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TTC	TTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:27024245_27024247delTTC	ENST00000376215.5	+	9	961_963	c.908_910delTTC	c.(907-912)tttcag>tag	p.303_304FQ>*	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_Intron	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	303					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						GGAATAGCTTTTCAGGTTAGTAT	0.429																																																0			10																																								27064253	SO:0001651	inframe_deletion	23590			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"coenzyme Q1 homolog (yeast)"	607429	"trans-prenyltransferase"	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.908_910delTTC	10.37:g.27024245_27024247delTTC	ENSP00000365388:p.Phe303_Gln304delins*		27064251	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	In_Frame_Del	DEL	ENST00000376215.5	37	CCDS31168.1																																																																																				0.429	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1			-	27024247	TTC	-	27024245	7	5	38	1	0	1	0	1	0	0	0	0	11724	1841	64	0	942	0	PDSS1	10	27024245	In_Frame_Del	DEL	TTC	TCGA-AG-3732-01A-11D-1657-10	4366793	27024245	108510502	83	3377	15	2								
PDSS1	23590	hgsc.bcm.edu	37	chr10	27024250	27024251	+	Splice_Site	DEL	GT	GT	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atgtaggaatagcttttcagGttagtatgctttttatttgt							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:27024250_27024251delGT	ENST00000376215.5	+	9	965		c.e9+1		PDSS1_ENST00000470978.1_Splice_Site|PDSS1_ENST00000376203.5_Intron	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1						isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						AGCTTTTCAGGTTAGTATGCTT	0.426																																																0			10																																								27064257	SO:0001630	splice_region_variant	23590			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"coenzyme Q1 homolog (yeast)"	607429	"trans-prenyltransferase"	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.912+1GT>-	10.37:g.27024250_27024251delGT			27064256	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Frame_Shift_Del	DEL	ENST00000376215.5	37	CCDS31168.1																																																																																				0.426	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		Intron	-	27024251	GT	-	27024250	8	5	38	1	0	1	0	1	0	0	1	0	11724	1275	44	0	947	0	PDSS1	10	27024250	Splice_Site	DEL	GT	TCGA-AG-3732-01A-11D-1657-10	5	27024250	108510497	84	3378	15	2								
ZEB1	6935	hgsc.bcm.edu	37	chr10	31812949	31812949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	accgcccaaaaagaaaatgcGgaagacagaaaatggaatgt	10	7	0	3	rs35653460		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:31812949G>A	ENST00000320985.10	+	8	2800	c.2690G>A	c.(2689-2691)cGg>cAg	p.R897Q	ZEB1_ENST00000560721.2_Missense_Mutation_p.R877Q|ZEB1_ENST00000446923.2_Missense_Mutation_p.R881Q|ZEB1_ENST00000542815.3_Missense_Mutation_p.R830Q|ZEB1_ENST00000361642.5_Missense_Mutation_p.R898Q			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	897					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R897Q(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AAGAAAATGCGGAAGACAGAA	0.373																																					Ovarian(40;423 959 14296 36701 49589)											1	Substitution - Missense(1)	large_intestine(1)	10						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	111	111	111		2642,2630,2639,2489,2693,2690	4.8	1	10	dbSNP_126	111	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	ZEB1	NM_001128128.2,NM_001174093.1,NM_001174094.1,NM_001174095.1,NM_001174096.1,NM_030751.5	43,43,43,43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	881/1109,877/1105,880/1108,830/1058,898/1126,897/1125	31812949	1,13005	2203	4300	6503	31852955	SO:0001583	missense	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2690G>A	10.37:g.31812949G>A	ENSP00000319248:p.Arg897Gln		31852955	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833834	0.71258	2.27E-4	0.0	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.72	4.8	0.61643	.	0.369405	0.21055	N	0.080939	T	0.14184	0.0343	L	0.27053	0.805	0.37448	D	0.91469	D;P;P;P;P	0.69078	0.997;0.913;0.574;0.913;0.913	D;B;B;B;B	0.64144	0.922;0.174;0.068;0.129;0.089	T	0.12811	-1.0533	10	0.41790	T	0.15	-12.9237	10.1047	0.42526	0.071:0.1383:0.7907:0.0	rs35653460	830;881;877;898;897	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	Q	679;897;898;892;830;897;877;788;881	ENSP00000444282:R679Q;ENSP00000354487:R898Q;ENSP00000444891:R830Q;ENSP00000319248:R897Q;ENSP00000391612:R881Q	ENSP00000319248:R897Q	R	+	2	0	ZEB1	31852955	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.665000	0.68052	1.410000	0.46936	0.585000	0.79938	CGG		0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		A	31812949	G	A	31812949	3	1	38	1	0	0	0	0	1	0	0	0	17662	1116	39	1	2734	1	ZEB1	10	31812949	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	4788699	31812949	103721798	85	3379										
CSGALNACT2	55454	hgsc.bcm.edu	37	chr10	43678937	43678937	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tggtcttcagggaggaaataGagacgcatcttcataaacag	11	7	4	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:43678937G>A	ENST00000374466.3	+	8	1911	c.1576G>A	c.(1576-1578)Gag>Aag	p.E526K		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	526					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GGAGGAAATAGAGACGCATCT	0.463																																																0			10											104	100	101					10																	43678937		2203	4300	6503	42998943	SO:0001583	missense	55454			AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1576G>A	10.37:g.43678937G>A	ENSP00000363590:p.Glu526Lys		42998943	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	36	5.814143	0.96975	.	.	ENSG00000169826	ENST00000374466	T	0.24538	1.85	5.87	5.87	0.94306	.	0.088022	0.85682	D	0.000000	T	0.53174	0.1780	M	0.73962	2.25	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.32613	-0.9900	10	0.30854	T	0.27	-18.2922	20.5827	0.99408	0.0:0.0:1.0:0.0	.	526	Q8N6G5	CGAT2_HUMAN	K	526	ENSP00000363590:E526K	ENSP00000363590:E526K	E	+	1	0	CSGALNACT2	42998943	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.434000	0.80377	2.941000	0.99782	0.655000	0.94253	GAG		0.463	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		A	43678937	G	A	43678937	3	1	38	1	0	0	0	0	1	0	0	0	3945	943	33	3	1602	3	CSGALNACT2	10	43678937	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	11865988	43678937	91855810	86	3380										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717639	89717639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttgtggtctgccagctaaagGtgaagatatattcctccaat	9	8	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:89717639G>A	ENST00000371953.3	+	7	2021	c.664G>A	c.(664-666)Gtg>Atg	p.V222M	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	222	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.Q214fs*1(1)|p.?(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CCAGCTAAAGGTGAAGATATA	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	49	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	10											139	121	127					10																	89717639		2203	4300	6503	89707619	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.664G>A	10.37:g.89717639G>A	ENSP00000361021:p.Val222Met		89707619	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936685	0.92458	.	.	ENSG00000171862	ENST00000371953	D	0.85411	-1.98	5.67	5.67	0.87782	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.92136	0.7507	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91161	0.4961	9	.	.	.	-2.0154	19.7712	0.96366	0.0:0.0:1.0:0.0	.	222	P60484	PTEN_HUMAN	M	222	ENSP00000361021:V222M	.	V	+	1	0	PTEN	89707619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.429000	0.97481	2.677000	0.91161	0.585000	0.79938	GTG		0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89717639	G	A	89717639	3	1	38	1	0	0	0	0	1	0	0	0	12772	1261	44	3	690	3	PTEN	10	89717639	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	46038702	89717639	45817108	87	3381										
SLK	9748	hgsc.bcm.edu	37	chr10	105762748	105762748	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaggaagttcctattaaagaAatagttgaaatgaatgaaat	8	2	0	4			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:105762748A>G	ENST00000369755.3	+	9	2357	c.1812A>G	c.(1810-1812)gaA>gaG	p.E604E	SLK_ENST00000335753.4_Silent_p.E604E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	604	Glu-rich.		E -> Q (in an ovarian serous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CTATTAAAGAAATAGTTGAAA	0.378																																					NSCLC(111;540 1651 1927 4474 17706)											0			10											35	37	36					10																	105762748		2203	4300	6503	105752738	SO:0001819	synonymous_variant	9748				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1812A>G	10.37:g.105762748A>G			105752738	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Silent	SNP	ENST00000369755.3	37	CCDS7553.1																																																																																				0.378	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105762748	A	G	105762748	2	3	38	1	0	0	0	0	0	0	0	1	14785	11	1	4		4	SLK	10	105762748	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	16045109	105762748	29771999	88	3382										
VWA2	340706	hgsc.bcm.edu	37	chr10	116032537	116032537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggaacttgctctgaaataccTtctgcacagagggttgcctg	11	10	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr10:116032537T>C	ENST00000392982.3	+	6	660	c.410T>C	c.(409-411)cTt>cCt	p.L137P	VWA2_ENST00000603594.1_Missense_Mutation_p.L137P			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	137	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.L137R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CTGAAATACCTTCTGCACAGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	10											112	109	110					10																	116032537		2203	4300	6503	116022527	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.410T>C	10.37:g.116032537T>C	ENSP00000376708:p.Leu137Pro		116022527	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	T	14.42	2.530212	0.45073	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.83837	-1.77	4.83	3.67	0.42095	von Willebrand factor, type A (3);	0.341394	0.27323	N	0.019887	D	0.90099	0.6907	M	0.87547	2.89	0.53005	D	0.999964	D;D	0.69078	0.997;0.996	D;D	0.67103	0.949;0.914	D	0.88651	0.3182	10	0.48119	T	0.1	.	9.2493	0.37545	0.1612:0.0:0.0:0.8388	.	137;137	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	P	137	ENSP00000376708:L137P	ENSP00000298715:L137P	L	+	2	0	VWA2	116022527	1.000000	0.71417	0.998000	0.56505	0.371000	0.29859	5.402000	0.66332	0.656000	0.30886	0.533000	0.62120	CTT		0.537	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		C	116032537	T	C	116032537	3	2	38	1	0	0	0	0	1	0	0	0	17279	1609	56	4	428	4	VWA2	10	116032537	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	10269789	116032537	19502210	89	3383										
OR52E4	390081	hgsc.bcm.edu	37	chr11	5906021	5906021	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	catttgtgtttctcattctgCgtctgccattctgtgggcat	9	10	4	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:5906021C>T	ENST00000316987.2	+	1	521	c.499C>T	c.(499-501)Cgt>Tgt	p.R167C		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R167G(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTCATTCTGCGTCTGCCATT	0.453																																																1	Substitution - Missense(1)	lung(1)	11											154	140	145					11																	5906021		2201	4296	6497	5862597	SO:0001583	missense	390081			AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.499C>T	11.37:g.5906021C>T	ENSP00000321426:p.Arg167Cys		5862597	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.661888	0.47572	.	.	ENSG00000180974	ENST00000316987	T	0.00188	8.59	5.15	0.874	0.19124	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000210	T	0.00468	0.0015	M	0.86953	2.85	0.09310	N	0.999999	D	0.69078	0.997	D	0.66716	0.946	T	0.44817	-0.9303	10	0.87932	D	0	.	5.7145	0.17952	0.4898:0.3415:0.0:0.1687	.	167	Q8NGH9	O52E4_HUMAN	C	167	ENSP00000321426:R167C	ENSP00000321426:R167C	R	+	1	0	OR52E4	5862597	0.000000	0.05858	0.016000	0.15963	0.913000	0.54294	-0.034000	0.12225	-0.017000	0.14103	0.643000	0.83706	CGT		0.453	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		T	5906021	C	T	5906021	3	4	38	1	0	0	0	0	1	0	0	0	11147	768	27	1	501	1	OR52E4	11	5906021	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10		5906021	129100495	90	3384										
METT5D1	196074	hgsc.bcm.edu	37	chr11	28135031	28135031	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaagcccgggagcaaacagaTcaaactcaagcccaggagtt	11	11	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:28135031T>C	ENST00000407364.3	+	3	502	c.150T>C	c.(148-150)gaT>gaC	p.D50D	METTL15_ENST00000303459.6_Silent_p.D50D|METTL15_ENST00000403099.1_Silent_p.D50D|METTL15_ENST00000379199.2_Silent_p.D50D|METTL15_ENST00000342303.5_Silent_p.D50D|METTL15_ENST00000406787.3_Silent_p.D50D			A6NJ78	MET15_HUMAN	methyltransferase like 15	50							methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						AGCAAACAGATCAAACTCAAG	0.383																																																0			11											52	60	57					11																	28135031		2202	4299	6501	28091607	SO:0001819	synonymous_variant	196074			AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"methyltransferase 5 domain containing 1"	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.150T>C	11.37:g.28135031T>C			28091607	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Silent	SNP	ENST00000407364.3	37	CCDS44559.1																																																																																				0.383	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636		C	28135031	T	C	28135031	2	2	38	1	0	0	0	0	0	0	0	1	9522	1432	50	4		4	METT5D1	11	28135031	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	22229010	28135031	106871485	91	3385										
CREB3L1	90993	hgsc.bcm.edu	37	chr11	46329480	46329481	+	Frame_Shift_Ins	INS	-	-	C													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgccccctcggccatggctgINSccgcggccgccatggccacc							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:46329480_46329481insC	ENST00000529193.1	+	3	896_897	c.445_446insC	c.(445-447)gccfs	p.A149fs	CREB3L1_ENST00000288400.3_Frame_Shift_Ins_p.A149fs			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	149	Poly-Ala.				regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		GGCCATGGCTGCCGCGGCCGCC	0.683			T	FUS	myxofibrosarcoma																																Pancreas(3;159 194 19597 26278 47995)		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	0			11																																								46286057	SO:0001589	frameshift_variant	90993				CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.447dupC	11.37:g.46329482_46329482dupC	ENSP00000434939:p.Ala149fs		46286056	Q8N2D5|Q96CP0	Frame_Shift_Ins	INS	ENST00000529193.1	37	CCDS53620.1																																																																																				0.683	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854		C	46329481	-	C	46329480	7	5	38	1	0	1	1	0	0	0	0	0	3862	1319	46	0	455	0	CREB3L1	11	46329480	Frame_Shift_Ins	INS	-	TCGA-AG-3732-01A-11D-1657-10	18194449	46329480	88677036	92	3386										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418738	55418738	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tactgtaatggcctatgatcGttatgtggctatctgtaaac	9	7	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:55418738G>A	ENST00000312422.2	+	1	359	c.359G>A	c.(358-360)cGt>cAt	p.R120H		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GCCTATGATCGTTATGTGGCT	0.428																																																0			11											205	173	184					11																	55418738		2181	4039	6220	55175314	SO:0001583	missense	219431			BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.359G>A	11.37:g.55418738G>A	ENSP00000310337:p.Arg120His		55175314	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757293	0.49468	.	.	ENSG00000174982	ENST00000312422	T	0.77489	-1.1	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000150	T	0.81564	0.4849	M	0.86420	2.815	0.47511	D	0.99944	B	0.21452	0.056	B	0.16289	0.015	T	0.80471	-0.1368	10	0.59425	D	0.04	.	17.6575	0.88182	0.0:0.0:1.0:0.0	.	120	Q8NH73	OR4S2_HUMAN	H	120	ENSP00000310337:R120H	ENSP00000310337:R120H	R	+	2	0	OR4S2	55175314	0.998000	0.40836	0.986000	0.45419	0.323000	0.28346	6.549000	0.73900	2.512000	0.84698	0.549000	0.68633	CGT		0.428	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		A	55418738	G	A	55418738	3	1	38	1	0	0	0	0	1	0	0	0	11114	1145	40	1	361	1	OR4S2	11	55418738	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	9089258	55418738	79587778	93	3387										
P2RX3	5024	hgsc.bcm.edu	37	chr11	57118272	57118272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttaagatcggctgggtgtgcGacttggacaaggcctgggac	16	8	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:57118272G>A	ENST00000263314.2	+	8	776	c.742G>A	c.(742-744)Gac>Aac	p.D248N		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	248					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CTGGGTGTGCGACTTGGACAA	0.597																																																0			11											90	75	80					11																	57118272		2201	4296	6497	56874848	SO:0001583	missense	5024			Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.742G>A	11.37:g.57118272G>A	ENSP00000263314:p.Asp248Asn		56874848	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.739924	0.69304	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.05649	3.41	5.83	5.83	0.93111	.	0.049050	0.85682	D	0.000000	T	0.05364	0.0142	N	0.16790	0.44	0.80722	D	1	P	0.34892	0.474	B	0.36567	0.228	T	0.49011	-0.8983	10	0.09338	T	0.73	-37.9877	17.0318	0.86463	0.0:0.0:1.0:0.0	.	248	P56373	P2RX3_HUMAN	N	248	ENSP00000263314:D248N	ENSP00000263314:D248N	D	+	1	0	P2RX3	56874848	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	5.315000	0.65810	2.761000	0.94854	0.650000	0.86243	GAC		0.597	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559		A	57118272	G	A	57118272	3	1	38	1	0	0	0	0	1	0	0	0	11372	1058	37	1	772	1	P2RX3	11	57118272	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	1699534	57118272	77888244	94	3388										
RTN3	10313	hgsc.bcm.edu	37	chr11	63523611	63523611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttgatcactatgttggcatcGcccgagatcagaccaagtca	9	11	3	3	rs140229299	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:63523611G>A	ENST00000377819.5	+	8	3176	c.3022G>A	c.(3022-3024)Gcc>Acc	p.A1008T	RTN3_ENST00000354497.4_Silent_p.S126S|RTN3_ENST00000339997.4_Missense_Mutation_p.A989T|RTN3_ENST00000537981.1_Missense_Mutation_p.A212T|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Missense_Mutation_p.A231T|RTN3_ENST00000540798.1_Missense_Mutation_p.A896T	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	1008	Interaction with FADD.|Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A989T(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TGTTGGCATCGCCCGAGATCA	0.408																																																1	Substitution - Missense(1)	ovary(1)	11						G	THR/ALA,THR/ALA,THR/ALA,	0,4402		0,0,2201	202	176	185		634,2965,691,	4.4	1	11	dbSNP_134	185	3,8593	3.0+/-9.4	0,3,4295	yes	missense,missense,missense,intron	RTN3	NM_006054.2,NM_201428.1,NM_201429.1,NM_201430.1	58,58,58,	0,3,6496	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,	212/237,989/1014,231/256,	63523611	3,12995	2201	4298	6499	63280187	SO:0001583	missense	10313			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.3022G>A	11.37:g.63523611G>A	ENSP00000367050:p.Ala1008Thr		63280187	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701249	0.88924	0.0	3.49E-4	ENSG00000133318	ENST00000356000;ENST00000377819;ENST00000339997;ENST00000540798;ENST00000537981	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.28	4.36	0.52297	.	0.400023	0.26680	N	0.023041	T	0.56352	0.1979	L	0.53249	1.67	0.23923	N	0.996458	D;D;D;D;D	0.65815	0.991;0.987;0.988;0.984;0.995	P;P;P;P;P	0.57101	0.79;0.813;0.75;0.667;0.682	T	0.51474	-0.8701	10	0.66056	D	0.02	-0.6239	11.4294	0.50032	0.088:0.0:0.912:0.0	.	896;1008;212;989;231	F5H774;O95197;O95197-3;O95197-2;O95197-4	.;RTN3_HUMAN;.;.;.	T	231;1008;989;896;212	ENSP00000348279:A231T;ENSP00000367050:A1008T;ENSP00000344106:A989T;ENSP00000442733:A896T;ENSP00000440874:A212T	ENSP00000344106:A989T	A	+	1	0	RTN3	63280187	0.920000	0.31207	0.964000	0.40570	0.992000	0.81027	4.841000	0.62824	1.233000	0.43693	0.555000	0.69702	GCC		0.408	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		A	63523611	G	A	63523611	3	1	38	1	0	0	0	0	1	0	0	0	13764	1087	38	1	3052	1	RTN3	11	63523611	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	6405339	63523611	71482905	95	3389										
GPR152	390212	hgsc.bcm.edu	37	chr11	67219092	67219092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgtggctgagctgtgggatcCgatcgtggctggagtgtggg	20	6	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:67219092C>T	ENST00000312457.2	-	1	1108	c.1104G>A	c.(1102-1104)tcG>tcA	p.S368S	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	368						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CTGTGGGATCCGATCGTGGCT	0.617																																					Pancreas(102;800 1581 2723 7382 33622)											0			11											51	47	49					11																	67219092		2200	4295	6495	66975668	SO:0001819	synonymous_variant	390212			AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.1104G>A	11.37:g.67219092C>T			66975668	Q0VD88|Q86SM0	Silent	SNP	ENST00000312457.2	37	CCDS8165.1																																																																																				0.617	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			T	67219092	C	T	67219092	2	4	38	1	0	0	0	0	0	0	0	1	6678	639	23	1		1	GPR152	11	67219092	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	3695481	67219092	67787424	96	3390										
CHRDL2	25884	hgsc.bcm.edu	37	chr11	74424489	74424489	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggctgggggcagtggacaggCggacagtggaggcggtaaca	21	7	0	0	rs555934347		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:74424489C>T	ENST00000376332.3	-	3	727	c.231G>A	c.(229-231)ccG>ccA	p.P77P	CHRDL2_ENST00000263671.5_Silent_p.P77P|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	77	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					AGTGGACAGGCGGACAGTGGA	0.587													C|||	1	0.000199681	0	0	5008	,	,		19171	0		0	False		,,,				2504	0.001															0			11											103	88	93					11																	74424489		2200	4293	6493	74102137	SO:0001819	synonymous_variant	25884			AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.231G>A	11.37:g.74424489C>T			74102137	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Silent	SNP	ENST00000376332.3	37																																																																																					0.587	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1			T	74424489	C	T	74424489	2	4	38	1	0	0	0	0	0	0	0	1	3380	755	27	1		1	CHRDL2	11	74424489	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	7205397	74424489	60582027	97	3391										
CLNS1A	1207	hgsc.bcm.edu	37	chr11	77333633	77333633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaaagcattccttctaatctCtccagtgtggcttggccttc	8	12	2	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:77333633C>A	ENST00000525428.1	-	5	648	c.558G>T	c.(556-558)gaG>gaT	p.E186D	CLNS1A_ENST00000263309.3_Missense_Mutation_p.E152D|CLNS1A_ENST00000532069.1_Missense_Mutation_p.E116D|CLNS1A_ENST00000528364.1_Missense_Mutation_p.E186D|CLNS1A_ENST00000525064.1_Intron	NM_001293.2	NP_001284.1	P54105	ICLN_HUMAN	chloride channel, nucleotide-sensitive, 1A	186					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	5	all_cancers(14;5.43e-17)|all_epithelial(13;1.78e-19)		Epithelial(5;1.02e-48)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CTTCTAATCTCTCCAGTGTGG	0.433																																																0			11											130	112	118					11																	77333633		2200	4292	6492	77011281	SO:0001583	missense	1207			U17899	CCDS8252.1	11q13.5-q14	2008-05-02							2080	protein-coding gene	gene with protein product		602158		CLCI		7887970, 8975725	Standard	NM_001293		Approved	ICln	uc001oyk.3	P54105		ENST00000525428.1:c.558G>T	11.37:g.77333633C>A	ENSP00000433919:p.Glu186Asp		77011281	B2RCS9|Q0VDK6|Q9NRD2|Q9NRD3	Missense_Mutation	SNP	ENST00000525428.1	37	CCDS8252.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411149	0.83340	.	.	ENSG00000074201	ENST00000525428;ENST00000263309;ENST00000532069;ENST00000528364	D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78	4.9	4.9	0.64082	.	0.048315	0.85682	D	0.000000	D	0.98112	0.9377	M	0.66939	2.045	0.53005	D	0.99996	B;D	0.62365	0.217;0.991	B;P	0.55508	0.121;0.777	D	0.97805	1.0247	10	0.19147	T	0.46	-10.2334	18.4196	0.90586	0.0:1.0:0.0:0.0	.	116;186	E9PMI6;P54105	.;ICLN_HUMAN	D	186;152;116;186	ENSP00000433919:E186D;ENSP00000263309:E152D;ENSP00000434963:E116D;ENSP00000434311:E186D	ENSP00000263309:E152D	E	-	3	2	CLNS1A	77011281	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.476000	0.66793	2.419000	0.82065	0.655000	0.94253	GAG		0.433	CLNS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382156.2	NM_001293		A	77333633	C	A	77333633	3	1	38	1	0	0	0	0	1	0	0	0	3554	912	32	2	163	2	CLNS1A	11	77333633	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	2909144	77333633	57672883	98	3392										
ME3	10873	hgsc.bcm.edu	37	chr11	86152477	86152477	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttgtgtttgtacgcgtagtcGagaacctagagaaaaacatg	11	6	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:86152477G>A	ENST00000393324.3	-	14	1912	c.1659C>T	c.(1657-1659)ctC>ctT	p.L553L	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000543262.1_Silent_p.L553L|ME3_ENST00000359636.2_Silent_p.L553L	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	553					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.L553L(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				ACGCGTAGTCGAGAACCTAGA	0.493																																																1	Substitution - coding silent(1)	ovary(1)	11											159	149	152					11																	86152477		2202	4299	6501	85830125	SO:0001819	synonymous_variant	56110			X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1659C>T	11.37:g.86152477G>A			85830125	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																				0.493	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2			A	86152477	G	A	86152477	2	1	38	1	0	0	0	0	0	0	0	1	9449	1045	37	1		1	ME3	11	86152477	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	8818844	86152477	48854039	99	3393										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100211914	100211914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccgtcataccattagccaacGaatctgaagttgtgggttac	9	10	2	1	rs201638465		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:100211914G>A	ENST00000524871.1	+	23	3297	c.3007G>A	c.(3007-3009)Gaa>Aaa	p.E1003K	CNTN5_ENST00000279463.3_Missense_Mutation_p.E1003K|CNTN5_ENST00000418526.2_Missense_Mutation_p.E929K|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000528682.1_Missense_Mutation_p.E1003K	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1003	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		ATTAGCCAACGAATCTGAAGT	0.433																																																0			11											139	137	137					11																	100211914		1866	4109	5975	99717124	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.3007G>A	11.37:g.100211914G>A	ENSP00000435637:p.Glu1003Lys		99717124	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703237	0.88924	.	.	ENSG00000149972	ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.83312	2.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.74523	-0.3637	9	.	.	.	.	18.288	0.90120	0.0:0.0:1.0:0.0	.	929;1003	O94779-2;O94779	.;CNTN5_HUMAN	K	1003;1003;929;1003	ENSP00000436185:E1003K;ENSP00000435637:E1003K;ENSP00000393229:E929K;ENSP00000279463:E1003K	.	E	+	1	0	CNTN5	99717124	1.000000	0.71417	0.978000	0.43139	0.872000	0.50106	8.972000	0.93424	2.566000	0.86566	0.655000	0.94253	GAA		0.433	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	100211914	G	A	100211914	3	1	38	1	0	0	0	0	1	0	0	0	3650	1059	37	1	3089	1	CNTN5	11	100211914	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	14059437	100211914	34794602	100	3394										
MMP27	64066	hgsc.bcm.edu	37	chr11	102564712	102564712	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cggctgcatctattttcttcAcacgtcctggaaaacctaat	6	12	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:102564712A>G	ENST00000260229.4	-	8	1209	c.1118T>C	c.(1117-1119)gTg>gCg	p.V373A		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	373					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V373E(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TATTTTCTTCACACGTCCTGG	0.418																																																1	Substitution - Missense(1)	ovary(1)	11											150	142	145					11																	102564712		2203	4299	6502	102069922	SO:0001583	missense	64066			AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1118T>C	11.37:g.102564712A>G	ENSP00000260229:p.Val373Ala		102069922	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.453162	0.63290	.	.	ENSG00000137675	ENST00000260229	T	0.15372	2.43	4.79	3.64	0.41730	Hemopexin/matrixin (2);	0.287996	0.24532	N	0.037706	T	0.40473	0.1118	M	0.85299	2.745	0.44432	D	0.997355	D	0.56035	0.974	P	0.62089	0.898	T	0.41610	-0.9499	10	0.72032	D	0.01	.	10.6059	0.45394	0.9123:0.0:0.0877:0.0	.	373	Q9H306	MMP27_HUMAN	A	373	ENSP00000260229:V373A	ENSP00000260229:V373A	V	-	2	0	MMP27	102069922	0.934000	0.31675	0.994000	0.49952	0.493000	0.33554	6.909000	0.75735	1.996000	0.58369	0.533000	0.62120	GTG		0.418	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		G	102564712	A	G	102564712	3	3	38	1	0	0	0	0	1	0	0	0	9694	159	6	4	435	4	MMP27	11	102564712	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	2352798	102564712	32441804	101	3395										
MMP8	4317	hgsc.bcm.edu	37	chr11	102593393	102593393	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cttggtaattggtagaacttTtccaggtagtcctggacaaa	10	7	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:102593393T>C	ENST00000236826.3	-	2	212	c.114A>G	c.(112-114)gaA>gaG	p.E38E		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	38					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	GGTAGAACTTTTCCAGGTAGT	0.423																																																0			11											88	86	87					11																	102593393		2203	4298	6501	102098603	SO:0001819	synonymous_variant	4317			J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.114A>G	11.37:g.102593393T>C			102098603	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	.	.	.	.	.	.	.	.	.	.	T	8.001	0.755376	0.15846	.	.	ENSG00000118113	ENST00000438475	.	.	.	5.99	2.14	0.27477	.	.	.	.	.	T	0.31420	0.0796	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	T	0.23048	-1.0199	4	.	.	.	.	5.7122	0.17941	0.1148:0.2987:0.0:0.5865	.	.	.	.	E	14	.	.	K	-	1	0	MMP8	102098603	0.000000	0.05858	0.076000	0.20297	0.985000	0.73830	-1.055000	0.03493	0.094000	0.17404	0.533000	0.62120	AAA		0.423	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		C	102593393	T	C	102593393	2	2	38	1	0	0	0	0	0	0	0	1	9698	1838	64	4		4	MMP8	11	102593393	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	28681	102593393	32413123	102	3396										
ATM	472	hgsc.bcm.edu	37	chr11	108106551	108106551	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tggtgtgaaatatctcagcaAcagtggttaggtatgttttg	12	4	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr11:108106551A>G	ENST00000452508.2	+	6	675	c.486A>G	c.(484-486)caA>caG	p.Q162Q	ATM_ENST00000278616.4_Silent_p.Q162Q			Q13315	ATM_HUMAN	ATM serine/threonine kinase	162					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TATCTCAGCAACAGTGGTTAG	0.363			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											233	234	234					11																	108106551		2201	4298	6499	107611761	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.486A>G	11.37:g.108106551A>G			107611761	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.363	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108106551	A	G	108106551	2	3	38	1	0	0	0	0	0	0	0	1	1110	40	2	4		4	ATM	11	108106551	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	5513158	108106551	26899965	103	3397										
KRT85	3891	hgsc.bcm.edu	37	chr12	52761098	52761098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gggcggcgctgatgcagcagCggttgccagttttgggggcc	19	10	0	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr12:52761098C>T	ENST00000257901.3	-	1	167	c.92G>A	c.(91-93)cGc>cAc	p.R31H	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	31	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GATGCAGCAGCGGTTGCCAGT	0.672																																																0			12											27	29	28					12																	52761098		2203	4300	6503	51047365	SO:0001583	missense	3891			X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.92G>A	12.37:g.52761098C>T	ENSP00000257901:p.Arg31His		51047365	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995596	0.35226	.	.	ENSG00000135443	ENST00000257901	D	0.82893	-1.66	4.63	4.63	0.57726	.	0.000000	0.56097	D	0.000029	T	0.77212	0.4097	L	0.38953	1.18	0.80722	D	1	B	0.14438	0.01	B	0.15052	0.012	T	0.71626	-0.4536	10	0.30854	T	0.27	.	18.0305	0.89282	0.0:1.0:0.0:0.0	.	31	P78386	KRT85_HUMAN	H	31	ENSP00000257901:R31H	ENSP00000257901:R31H	R	-	2	0	KRT85	51047365	0.265000	0.24102	1.000000	0.80357	0.950000	0.60333	2.165000	0.42396	2.548000	0.85928	0.561000	0.74099	CGC		0.672	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		T	52761098	C	T	52761098	3	4	38	1	0	0	0	0	1	0	0	0	8520	768	27	1	1467	1	KRT85	12	52761098	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10		52761098	81090797	104	3398										
UTP20	27340	hgsc.bcm.edu	37	chr12	101745882	101745882	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gattattggagccatttgcaAacatctctcttggtcagcgt	9	9	3	0	rs140657361	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr12:101745882A>G	ENST00000261637.4	+	39	5108	c.4934A>G	c.(4933-4935)aAa>aGa	p.K1645R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1645			K -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.K1645I(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GCCATTTGCAAACATCTCTCT	0.363																																																1	Substitution - Missense(1)	breast(1)	12											141	138	139					12																	101745882		2203	4300	6503	100270013	SO:0001583	missense	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4934A>G	12.37:g.101745882A>G	ENSP00000261637:p.Lys1645Arg		100270013	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	A	6.509	0.462068	0.12342	.	.	ENSG00000120800	ENST00000261637	T	0.63913	-0.07	5.84	-4.48	0.03515	Armadillo-type fold (1);	0.385429	0.30219	N	0.010136	T	0.22322	0.0538	N	0.00972	-1.085	0.23454	N	0.997649	B	0.02656	0.0	B	0.01281	0.0	T	0.42189	-0.9466	10	0.06365	T	0.9	-5.1064	12.194	0.54286	0.2276:0.1101:0.6623:0.0	.	1645	O75691	UTP20_HUMAN	R	1645	ENSP00000261637:K1645R	ENSP00000261637:K1645R	K	+	2	0	UTP20	100270013	0.481000	0.25941	0.965000	0.40720	0.953000	0.61014	0.551000	0.23361	-0.341000	0.08376	-0.250000	0.11733	AAA		0.363	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101745882	A	G	101745882	3	3	38	1	0	0	0	0	1	0	0	0	17139	14	1	4	5088	4	UTP20	12	101745882	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	48984784	101745882	32106013	105	3399										
CRY1	1407	hgsc.bcm.edu	37	chr12	107393837	107393837	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gaattcgcattcattcgaggTctttcaaaatttgccaccca	6	11	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr12:107393837T>C	ENST00000008527.5	-	6	1575	c.708A>G	c.(706-708)agA>agG	p.R236R		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	236					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.R236R(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						TCATTCGAGGTCTTTCAAAAT	0.353																																																1	Substitution - coding silent(1)	ovary(1)	12											73	74	74					12																	107393837		2203	4300	6503	105917967	SO:0001819	synonymous_variant	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.708A>G	12.37:g.107393837T>C			105917967		Silent	SNP	ENST00000008527.5	37	CCDS9112.1																																																																																				0.353	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		C	107393837	T	C	107393837	2	2	38	1	0	0	0	0	0	0	0	1	3909	1664	58	4		4	CRY1	12	107393837	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	5647955	107393837	26458058	106	3400										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20638636	20638636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgaatttttattaccacctgTttttggcgaagaatatgagg	9	5	0	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr13:20638636T>C	ENST00000382874.2	+	20	3273	c.3083T>C	c.(3082-3084)gTt>gCt	p.V1028A	ZMYM2_ENST00000382871.2_Missense_Mutation_p.V1028A|ZMYM2_ENST00000382869.3_Missense_Mutation_p.V1028A	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1028					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		TTACCACCTGTTTTTGGCGAA	0.338																																																0			13											118	108	111					13																	20638636		1821	4087	5908	19536636	SO:0001583	missense	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3083T>C	13.37:g.20638636T>C	ENSP00000372327:p.Val1028Ala		19536636	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483847	0.26598	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382870	T	0.17691	2.26	5.52	4.32	0.51571	.	0.107103	0.64402	D	0.000006	T	0.12732	0.0309	L	0.43152	1.355	0.80722	D	1	B	0.32781	0.384	B	0.26517	0.07	T	0.05582	-1.0876	10	0.11182	T	0.66	-17.314	12.1044	0.53803	0.1288:0.0:0.0:0.8712	.	1028	Q9UBW7	ZMYM2_HUMAN	A	1028;1028;1026;1026;406	ENSP00000372322:V1028A	ENSP00000372322:V1028A	V	+	2	0	ZMYM2	19536636	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.789000	0.69029	0.997000	0.38969	0.533000	0.62120	GTT		0.338	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		C	20638636	T	C	20638636	3	2	38	1	0	0	0	0	1	0	0	0	17739	1725	60	4	3149	4	ZMYM2	13	20638636	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10		20638636	94531242	107	3401										
NALCN	259232	hgsc.bcm.edu	37	chr13	101759859	101759859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cgttgaagcgtgctcggaccAccacccggcaaaagtttctg	11	13	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr13:101759859A>G	ENST00000251127.6	-	22	2639	c.2558T>C	c.(2557-2559)gTg>gCg	p.V853A		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	853					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGCTCGGACCACCACCCGGCA	0.498																																																0			13											129	112	118					13																	101759859		2203	4300	6503	100557860	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2558T>C	13.37:g.101759859A>G	ENSP00000251127:p.Val853Ala		100557860	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993415	0.74703	.	.	ENSG00000102452	ENST00000251127	D	0.97688	-4.49	5.61	5.61	0.85477	.	0.116529	0.64402	D	0.000017	D	0.93488	0.7922	N	0.08118	0	0.80722	D	1	B	0.16396	0.017	B	0.18263	0.021	D	0.90318	0.4342	10	0.72032	D	0.01	.	15.8226	0.78667	1.0:0.0:0.0:0.0	.	853	Q8IZF0	NALCN_HUMAN	A	853	ENSP00000251127:V853A	ENSP00000251127:V853A	V	-	2	0	NALCN	100557860	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.233000	0.95337	2.126000	0.65437	0.528000	0.53228	GTG		0.498	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		G	101759859	A	G	101759859	3	3	38	1	0	0	0	0	1	0	0	0	10178	159	6	4	2750	4	NALCN	13	101759859	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	81121223	101759859	13410019	108	3402										
SLC25A21	89874	hgsc.bcm.edu	37	chr14	37154057	37154057	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttttggcaacatcaaaagggAtgttaatgactgaggctatt	10	5	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:37154057A>G	ENST00000331299.5	-	8	1192	c.677T>C	c.(676-678)aTc>aCc	p.I226T	SLC25A21_ENST00000555449.1_Missense_Mutation_p.I226T	NM_030631.3	NP_085134.1	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	226					cellular nitrogen compound metabolic process (GO:0034641)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|pancreas(1)|prostate(1)|skin(1)	9	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		ATCAAAAGGGATGTTAATGAC	0.393																																																0			14											138	132	134					14																	37154057		2203	4300	6503	36223808	SO:0001583	missense	89874			AJ278148	CCDS9663.1, CCDS55913.1	14q13.3	2014-01-28	2012-03-29		ENSG00000183032	ENSG00000183032		"Solute carriers"	14411	protein-coding gene	gene with protein product		607571	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"			11083877	Standard	NM_030631		Approved	ODC1, ODC	uc001wtz.2	Q9BQT8	OTTHUMG00000140250	ENST00000331299.5:c.677T>C	14.37:g.37154057A>G	ENSP00000329452:p.Ile226Thr		36223808	A8K0L0|G3V4L5|Q3MJ99	Missense_Mutation	SNP	ENST00000331299.5	37	CCDS9663.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356141	0.61293	.	.	ENSG00000183032	ENST00000555449;ENST00000331299	T;T	0.76839	-1.05;-1.05	5.67	5.67	0.87782	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.72684	0.3491	N	0.16201	0.385	0.80722	D	1	P	0.50943	0.94	P	0.58391	0.838	T	0.68519	-0.5387	10	0.02654	T	1	-12.3715	16.1842	0.81939	1.0:0.0:0.0:0.0	.	226	Q9BQT8	ODC_HUMAN	T	226	ENSP00000451873:I226T;ENSP00000329452:I226T	ENSP00000329452:I226T	I	-	2	0	SLC25A21	36223808	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.850000	0.92190	2.283000	0.76528	0.533000	0.62120	ATC		0.393	SLC25A21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276732.2	NM_030631		G	37154057	A	G	37154057	3	3	38	1	0	0	0	0	1	0	0	0	14521	333	12	4	239	4	SLC25A21	14	37154057	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10		37154057	70195483	109	3403										
KLHDC2	23588	hgsc.bcm.edu	37	chr14	50245175	50245175	+	Frame_Shift_Del	DEL	A	A	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgatcatgtacatattttagAtactgaaacatttacctgga							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:50245175delA	ENST00000298307.5	+	6	1457	c.596delA	c.(595-597)gatfs	p.D199fs	KLHDC2_ENST00000554589.1_Frame_Shift_Del_p.D199fs|KLHDC2_ENST00000557247.1_Frame_Shift_Del_p.D199fs	NM_014315.2	NP_055130.1	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	199						nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	all_epithelial(31;0.000959)|Breast(41;0.0117)					CATATTTTAGATACTGAAACA	0.348																																																0			14											46	50	49					14																	50245175		2203	4298	6501	49314925	SO:0001589	frameshift_variant	23588			AK001771	CCDS9693.1	14q21.3	2003-01-15			ENSG00000165516	ENSG00000165516			20231	protein-coding gene	gene with protein product		611280				11384994	Standard	NM_014315		Approved	HCLP-1, LCP	uc001wwx.3	Q9Y2U9	OTTHUMG00000140288	ENST00000298307.5:c.596delA	14.37:g.50245175delA	ENSP00000298307:p.Asp199fs		49314925	B3KPF9|Q6IAF0|Q86TY9	Frame_Shift_Del	DEL	ENST00000298307.5	37	CCDS9693.1																																																																																				0.348	KLHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276869.1			-	50245175	A	-	50245175	7	5	38	1	0	1	0	1	0	0	0	0	8377	333	12	0	618	0	KLHDC2	14	50245175	Frame_Shift_Del	DEL	A	TCGA-AG-3732-01A-11D-1657-10	13091118	50245175	57104365	110	3404										
NID2	22795	hgsc.bcm.edu	37	chr14	52509009	52509009	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtccacatcagtgaagtgcaCgggtgtatggcccacgtgga	14	10	1	1	rs149213118	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:52509009C>T	ENST00000216286.5	-	7	1638	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	NID2_ENST00000541773.1_Missense_Mutation_p.V494M	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	547	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTGAAGTGCACGGGTGTATGG	0.577																																																0			14						C	MET/VAL	0,4406		0,0,2203	138	140	140		1639	5.3	0.9	14	dbSNP_134	140	3,8597	3.0+/-9.4	0,3,4297	no	missense	NID2	NM_007361.3	21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	547/1376	52509009	3,13003	2203	4300	6503	51578759	SO:0001583	missense	22795			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1639G>A	14.37:g.52509009C>T	ENSP00000216286:p.Val547Met		51578759	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225977	0.58668	0.0	3.49E-4	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.35973	1.28;1.28	6.17	5.29	0.74685	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.052456	0.85682	N	0.000000	T	0.63721	0.2535	M	0.84326	2.69	0.44409	D	0.997322	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.996;1.0;0.999	T	0.69903	-0.5019	10	0.72032	D	0.01	.	14.9824	0.71321	0.0:0.9317:0.0:0.0683	.	141;494;549;547	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	M	547;141;494;549	ENSP00000216286:V547M;ENSP00000443730:V494M	ENSP00000216286:V547M	V	-	1	0	NID2	51578759	1.000000	0.71417	0.909000	0.35828	0.007000	0.05969	4.641000	0.61375	1.620000	0.50308	0.655000	0.94253	GTG		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52509009	C	T	52509009	3	4	38	1	0	0	0	0	1	0	0	0	10446	536	19	1	2552	1	NID2	14	52509009	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	2263834	52509009	54840531	111	3405										
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64989449	64989449	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagaatatgaggccccctaaCaacagcagtccagtacaaga	9	11	0	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:64989449C>G	ENST00000554015.1	+	4	1658	c.1227C>G	c.(1225-1227)aaC>aaG	p.N409K	RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Missense_Mutation_p.N409K|ZBTB1_ENST00000358738.3_Missense_Mutation_p.N409K			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	409					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		GGCCCCCTAACAACAGCAGTC	0.423																																																0			14											56	55	55					14																	64989449		2203	4300	6503	64059202	SO:0001583	missense	22890			AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1227C>G	14.37:g.64989449C>G	ENSP00000451000:p.Asn409Lys		64059202	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	37	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	C	7.936	0.741754	0.15642	.	.	ENSG00000126804	ENST00000554015;ENST00000358738;ENST00000394712	T;T;T	0.09163	3.01;3.6;3.01	5.91	4.02	0.46733	.	0.249755	0.34828	N	0.003647	T	0.06826	0.0174	N	0.24115	0.695	0.35662	D	0.812638	B;B	0.15473	0.013;0.008	B;B	0.16289	0.015;0.007	T	0.18178	-1.0345	10	0.06236	T	0.91	-15.3631	12.3647	0.55222	0.0:0.8578:0.0:0.1422	.	409;409	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	K	409	ENSP00000451000:N409K;ENSP00000351587:N409K;ENSP00000378201:N409K	ENSP00000351587:N409K	N	+	3	2	ZBTB1	64059202	0.663000	0.27448	0.951000	0.38953	0.983000	0.72400	1.243000	0.32767	0.760000	0.33108	0.655000	0.94253	AAC		0.423	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			G	64989449	C	G	64989449	3	3	38	1	0	0	0	0	1	0	0	0	17561	477	17	5	1229	5	ZBTB1	14	64989449	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	12480440	64989449	42360091	112	3406										
C14orf118	55668	hgsc.bcm.edu	37	chr14	76644340	76644340	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cttttctttagaaagaataaAgcgttggcttctgattttcc	7	7	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:76644340A>G	ENST00000261530.7	+	7	1128	c.1062A>G	c.(1060-1062)aaA>aaG	p.K354K	GPATCH2L_ENST00000312858.5_Intron|GPATCH2L_ENST00000553588.1_5'Flank	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	354								p.K354N(1)									GAAAGAATAAAGCGTTGGCTT	0.348																																																1	Substitution - Missense(1)	ovary(1)	14											173	181	178					14																	76644340		2203	4300	6503	75714093	SO:0001819	synonymous_variant	55668			AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 118"	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.1062A>G	14.37:g.76644340A>G			75714093	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Silent	SNP	ENST00000261530.7	37	CCDS9848.1																																																																																				0.348	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		G	76644340	A	G	76644340	2	3	38	1	0	0	0	0	0	0	0	1	1745	69	3	4		4	C14orf118	14	76644340	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	11654891	76644340	30705200	113	3407										
RAGE	5891	hgsc.bcm.edu	37	chr14	102698923	102698923	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cctggtgggcggcgattctcTcatcgggatcataggccacc	13	13	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:102698923T>C	ENST00000361847.2	-	9	1046	c.815A>G	c.(814-816)gAg>gGg	p.E272G	MOK_ENST00000522874.1_Missense_Mutation_p.E271G|MOK_ENST00000524370.1_Missense_Mutation_p.R5G|MOK_ENST00000524214.1_Missense_Mutation_p.E242G|MOK_ENST00000193029.6_Missense_Mutation_p.E38G|MOK_ENST00000522867.1_Missense_Mutation_p.R5G|MOK_ENST00000523231.1_Missense_Mutation_p.R5G|MOK_ENST00000522534.1_Missense_Mutation_p.R5G|MOK_ENST00000561150.1_Missense_Mutation_p.R5G|MOK_ENST00000517966.1_Missense_Mutation_p.R5G|MOK_ENST00000520266.1_Intron|MOK_ENST00000519058.1_Missense_Mutation_p.R5G	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										GGCGATTCTCTCATCGGGATC	0.542																																																0			14											149	151	150					14																	102698923		2203	4300	6503	101768676	SO:0001583	missense	5891			AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"renal tumor antigen"	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.815A>G	14.37:g.102698923T>C	ENSP00000355304:p.Glu272Gly		101768676	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.65|12.65	2.002688|2.002688	0.35320|0.35320	.|.	.|.	ENSG00000080823|ENSG00000080823	ENST00000193029;ENST00000522874;ENST00000361847;ENST00000524214|ENST00000519058	T;T;T;T|.	0.67345|.	0.87;-0.26;-0.26;-0.26|.	5.5|5.5	3.12|3.12	0.35913|0.35913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.308209|.	0.34178|.	N|.	0.004183|.	T|T	0.62270|0.62270	0.2414|0.2414	M|M	0.67625|0.67625	2.065|2.065	0.42157|0.42157	D|D	0.991586|0.991586	B;B|.	0.28026|.	0.198;0.122|.	B;B|.	0.31337|.	0.128;0.128|.	T|T	0.57590|0.57590	-0.7785|-0.7785	10|5	0.87932|.	D|.	0|.	-1.6855|-1.6855	8.632|8.632	0.33926|0.33926	0.1279:0.0:0.1342:0.7379|0.1279:0.0:0.1342:0.7379	.|.	242;272|.	E7ERR8;Q9UQ07|.	.;MOK_HUMAN|.	G|G	38;271;272;242|5	ENSP00000193029:E38G;ENSP00000429469:E271G;ENSP00000355304:E272G;ENSP00000428942:E242G|.	ENSP00000193029:E38G|.	E|R	-|-	2|1	0|2	RAGE|RAGE	101768676|101768676	1.000000|1.000000	0.71417|0.71417	0.045000|0.045000	0.18777|0.18777	0.943000|0.943000	0.58893|0.58893	4.530000|4.530000	0.60595|0.60595	0.379000|0.379000	0.24794|0.24794	0.379000|0.379000	0.24179|0.24179	GAG|AGA		0.542	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3			C	102698923	T	C	102698923	3	2	38	1	0	0	0	0	1	0	0	0	13043	1551	54	4	460	4	RAGE	14	102698923	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	26054583	102698923	4650617	114	3408										
CKB	1152	hgsc.bcm.edu	37	chr14	103988688	103988688	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cgtccagcgtgaagccgctcGgcgtgctcttggcgcgcagc	15	15	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr14:103988688G>C	ENST00000348956.2	-	2	500	c.143C>G	c.(142-144)cCg>cGg	p.P48R	RP11-600F24.7_ENST00000568177.1_RNA	NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	48	Phosphagen kinase N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00842}.				cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	GAAGCCGCTCGGCGTGCTCTT	0.726																																					Esophageal Squamous(186;2492 2823 49929 50127)											0			14											51	49	49					14																	103988688		2202	4299	6501	103058441	SO:0001583	missense	1152				CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.143C>G	14.37:g.103988688G>C	ENSP00000299198:p.Pro48Arg		103058441	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Missense_Mutation	SNP	ENST00000348956.2	37	CCDS9981.1	.	.	.	.	.	.	.	.	.	.	G	33	5.204135	0.95033	.	.	ENSG00000166165	ENST00000348956;ENST00000428256;ENST00000553878;ENST00000557530	T;T;T	0.64618	-0.11;-0.11;-0.11	4.24	4.24	0.50183	ATP:guanido phosphotransferase, N-terminal (4);	0.058300	0.64402	D	0.000001	T	0.81912	0.4923	M	0.91249	3.19	0.80722	D	1	D	0.61080	0.989	P	0.62649	0.905	D	0.87273	0.2287	10	0.87932	D	0	0.0112	16.853	0.85999	0.0:0.0:1.0:0.0	.	48	P12277	KCRB_HUMAN	R	48;48;48;19	ENSP00000299198:P48R;ENSP00000451904:P48R;ENSP00000451611:P19R	ENSP00000299198:P48R	P	-	2	0	CKB	103058441	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	9.053000	0.93860	2.203000	0.70933	0.306000	0.20318	CCG		0.726	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1			C	103988688	G	C	103988688	3	2	38	1	0	0	0	0	1	0	0	0	3452	1116	39	5	1030	5	CKB	14	103988688	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	1289765	103988688	3360852	115	3409										
LRRC57	255252	hgsc.bcm.edu	37	chr15	42839667	42839667	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	acggcagctctctaaggtgaTtgttgtttaggcttagcgtc	12	8	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:42839667T>C	ENST00000323443.2	-	3	651	c.284A>G	c.(283-285)aAt>aGt	p.N95S	LRRC57_ENST00000397130.3_Missense_Mutation_p.N95S|HAUS2_ENST00000260372.3_5'Flank|HAUS2_ENST00000568876.1_5'Flank|HAUS2_ENST00000568846.2_5'Flank|LRRC57_ENST00000563454.1_Missense_Mutation_p.N95S			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	95						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		TCTAAGGTGATTGTTGTTTAG	0.448																																																0			15											93	87	89					15																	42839667		2203	4299	6502	40626959	SO:0001583	missense	255252			AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.284A>G	15.37:g.42839667T>C	ENSP00000326817:p.Asn95Ser		40626959	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	37	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.146713	0.77888	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.72615	-0.67;-0.67	5.63	4.44	0.53790	.	0.042164	0.85682	D	0.000000	T	0.80093	0.4560	M	0.85777	2.775	0.80722	D	1	P	0.52692	0.955	P	0.52424	0.698	D	0.84036	0.0362	10	0.87932	D	0	.	12.6822	0.56928	0.0:0.0:0.1374:0.8626	.	95	Q8N9N7	LRC57_HUMAN	S	95	ENSP00000326817:N95S;ENSP00000380319:N95S	ENSP00000326817:N95S	N	-	2	0	LRRC57	40626959	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.791000	0.69045	2.281000	0.76405	0.533000	0.62120	AAT		0.448	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		C	42839667	T	C	42839667	3	2	38	1	0	0	0	0	1	0	0	0	9042	1493	52	4	447	4	LRRC57	15	42839667	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10		42839667	59691725	116	3410										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52517287	52517287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	attacctgcttcttacatctTcaatgtcatagctttcgaga	5	10	4	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:52517287T>C	ENST00000261839.7	-	27	3511	c.3350A>G	c.(3349-3351)gAa>gGa	p.E1117G		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1117						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TCTTACATCTTCAATGTCATA	0.318																																																0			15											138	121	127					15																	52517287		1848	4092	5940	50304579	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.3350A>G	15.37:g.52517287T>C	ENSP00000261839:p.Glu1117Gly		50304579	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.531660	0.45073	.	.	ENSG00000128833	ENST00000261839	T	0.17691	2.26	5.89	4.75	0.60458	.	0.185758	0.44688	D	0.000427	T	0.12689	0.0308	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.04522	-1.0945	10	0.41790	T	0.15	.	12.5123	0.56013	0.0:0.0:0.2631:0.7369	.	1117	Q9NQX4	MYO5C_HUMAN	G	1117	ENSP00000261839:E1117G	ENSP00000261839:E1117G	E	-	2	0	MYO5C	50304579	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	3.258000	0.51507	1.021000	0.39600	0.533000	0.62120	GAA		0.318	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		C	52517287	T	C	52517287	3	2	38	1	0	0	0	0	1	0	0	0	10110	1783	62	4	1938	4	MYO5C	15	52517287	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	9677620	52517287	50014105	117	3411										
TBC1D21	161514	hgsc.bcm.edu	37	chr15	74178503	74178503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccttcctggaccccgtgtttGctgagcacctaagtgagtgg	12	12	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:74178503G>A	ENST00000300504.2	+	7	747	c.664G>A	c.(664-666)Gct>Act	p.A222T	TBC1D21_ENST00000535547.2_Missense_Mutation_p.A186T|TBC1D21_ENST00000562056.1_Missense_Mutation_p.A185T	NM_153356.1	NP_699187.1	Q8IYX1	TBC21_HUMAN	TBC1 domain family, member 21	222	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.A222P(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	17						CCCCGTGTTTGCTGAGCACCT	0.592																																																1	Substitution - Missense(1)	ovary(1)	15											186	128	148					15																	74178503		2198	4297	6495	71965556	SO:0001583	missense	161514			BC033516	CCDS10252.1, CCDS66822.1	15q24	2013-07-09			ENSG00000167139	ENSG00000167139			28536	protein-coding gene	gene with protein product	"male germ cell-specific expressed, containing a RabGAP domain"					21128978	Standard	XR_243080		Approved	MGC34741, MgcRabGAP	uc002avz.3	Q8IYX1	OTTHUMG00000137594	ENST00000300504.2:c.664G>A	15.37:g.74178503G>A	ENSP00000300504:p.Ala222Thr		71965556	B9A6M2	Missense_Mutation	SNP	ENST00000300504.2	37	CCDS10252.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957521	0.53400	.	.	ENSG00000167139	ENST00000300504;ENST00000535547	T;T	0.22743	1.94;1.94	4.78	4.78	0.61160	Rab-GAP/TBC domain (5);	0.000000	0.52532	D	0.000078	T	0.19565	0.0470	L	0.29908	0.895	0.39627	D	0.97012	P;B	0.40398	0.716;0.124	B;B	0.44133	0.442;0.19	T	0.04347	-1.0958	10	0.24483	T	0.36	.	13.6457	0.62279	0.0:0.0:1.0:0.0	.	186;222	B9A6M2;Q8IYX1	.;TBC21_HUMAN	T	222;186	ENSP00000300504:A222T;ENSP00000439325:A186T	ENSP00000300504:A222T	A	+	1	0	TBC1D21	71965556	1.000000	0.71417	0.987000	0.45799	0.820000	0.46376	1.798000	0.38814	2.371000	0.80710	0.536000	0.68110	GCT		0.592	TBC1D21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268994.1	NM_153356		A	74178503	G	A	74178503	3	1	38	1	0	0	0	0	1	0	0	0	15649	1319	46	3	690	3	TBC1D21	15	74178503	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	21661216	74178503	28352889	118	3412										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77057314	77057314	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaactcaccctttctaacaaTttctgaagcttcaatgtttt	3	10	4	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:77057314T>C	ENST00000563290.1	-	14	1808	c.1713A>G	c.(1711-1713)aaA>aaG	p.K571K	SCAPER_ENST00000324767.7_Silent_p.K571K|SCAPER_ENST00000538941.2_Silent_p.K325K			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	571	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TTTCTAACAATTTCTGAAGCT	0.343																																																0			15											79	69	72					15																	77057314		1794	4054	5848	74844369	SO:0001819	synonymous_variant	49855			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1713A>G	15.37:g.77057314T>C			74844369	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																				0.343	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		C	77057314	T	C	77057314	2	2	38	1	0	0	0	0	0	0	0	1	13915	1490	52	4		4	SCAPER	15	77057314	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	2878811	77057314	25474078	119	3413										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91017007	91017007	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	atcggttagcttacctgcgcTcccacaaagatgaagttgta	9	10	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:91017007T>C	ENST00000268182.5	+	20	2534	c.2410T>C	c.(2410-2412)Tcc>Ccc	p.S804P	IQGAP1_ENST00000560738.1_Missense_Mutation_p.S232P	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	804	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTACCTGCGCTCCCACAAAGA	0.433																																																0			15											95	84	88					15																	91017007		2198	4298	6496	88818011	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2410T>C	15.37:g.91017007T>C	ENSP00000268182:p.Ser804Pro		88818011	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148181	0.37923	.	.	ENSG00000140575	ENST00000268182	D	0.95238	-3.65	5.91	0.468	0.16732	.	0.298649	0.32357	N	0.006218	D	0.89354	0.6691	L	0.27053	0.805	0.28569	N	0.910734	B	0.26744	0.158	B	0.27262	0.078	T	0.78342	-0.2241	10	0.31617	T	0.26	-5.5698	16.4491	0.83973	0.0:0.0:0.7237:0.2762	.	804	P46940	IQGA1_HUMAN	P	804	ENSP00000268182:S804P	ENSP00000268182:S804P	S	+	1	0	IQGAP1	88818011	1.000000	0.71417	0.981000	0.43875	0.634000	0.38068	3.279000	0.51670	0.096000	0.17463	0.533000	0.62120	TCC		0.433	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		C	91017007	T	C	91017007	3	2	38	1	0	0	0	0	1	0	0	0	7835	1551	54	4	2488	4	IQGAP1	15	91017007	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	13959693	91017007	11514385	120	3414										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91026787	91026787	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gataatgcccacttaagcatCattaatgaatatctttccca	4	10	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:91026787C>A	ENST00000268182.5	+	29	3874	c.3750C>A	c.(3748-3750)atC>atA	p.I1250I	IQGAP1_ENST00000560738.1_Silent_p.I678I	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1250	C1.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ACTTAAGCATCATTAATGAAT	0.423																																																0			15											81	76	78					15																	91026787		2198	4298	6496	88827791	SO:0001819	synonymous_variant	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.3750C>A	15.37:g.91026787C>A			88827791	A7MBM3	Silent	SNP	ENST00000268182.5	37	CCDS10362.1																																																																																				0.423	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		A	91026787	C	A	91026787	2	1	38	1	0	0	0	0	0	0	0	1	7835	816	29	2		2	IQGAP1	15	91026787	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	9780	91026787	11504605	121	3415										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101566295	101566295	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcactctgccgctccccctcCggctccagggccacaggctt	10	20	1	0	rs370178353		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr15:101566295C>T	ENST00000388948.3	+	17	2717	c.2358C>T	c.(2356-2358)tcC>tcT	p.S786S	LRRK1_ENST00000284395.5_Silent_p.S783S	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	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)			GCTCCCCCTCCGGCTCCAGGG	0.597																																																0			15						T		1,4205		0,1,2102	65	74	71		2358	-9.4	0	15		71	0,8444		0,0,4222	no	coding-synonymous	LRRK1	NM_024652.3		0,1,6324	TT,TC,CC		0.0,0.0238,0.0079		786/2016	101566295	1,12649	2103	4222	6325	99383818	SO:0001819	synonymous_variant	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.2358C>T	15.37:g.101566295C>T			99383818		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																				0.597	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101566295	C	T	101566295	2	4	38	1	0	0	0	0	0	0	0	1	9061	639	23	1		1	LRRK1	15	101566295	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	10539508	101566295	965097	122	3416										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1260600	1260600	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caggagcgggtcttcctcagCgtctccaattacatcttcac	8	14	5	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:1260600C>T	ENST00000348261.5	+	20	4235	c.3987C>T	c.(3985-3987)agC>agT	p.S1329S	CACNA1H_ENST00000565831.1_Silent_p.S1329S|CACNA1H_ENST00000358590.4_Silent_p.S1329S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1329					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TCTTCCTCAGCGTCTCCAATT	0.672																																																0			16											32	36	35					16																	1260600		1998	4163	6161	1200601	SO:0001819	synonymous_variant	8912			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.3987C>T	16.37:g.1260600C>T			1200601	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																				0.672	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1260600	C	T	1260600	2	4	38	1	0	0	0	0	0	0	0	1	2551	767	27	1		1	CACNA1H	16	1260600	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10		1260600	89094153	123	3417										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3647924	3647924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtcctcggacggtgcctcgtCcaccttccgcctcttccgtg	10	18	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:3647924C>T	ENST00000294008.3	-	6	1880	c.1240G>A	c.(1240-1242)Gac>Aac	p.D414N		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	414	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GGTGCCTCGTCCACCTTCCGC	0.597								Direct reversal of damage																																								0			16											84	80	81					16																	3647924		2197	4300	6497	3587925	SO:0001583	missense	0			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1240G>A	16.37:g.3647924C>T	ENSP00000294008:p.Asp414Asn		3587925	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	0.108	-1.142433	0.01728	.	.	ENSG00000188827	ENST00000294008	T	0.20200	2.09	3.63	-2.32	0.06745	.	1.541050	0.03830	N	0.268953	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.23726	-1.0180	10	0.10902	T	0.67	.	3.4271	0.07414	0.1819:0.3515:0.0:0.4666	.	414	Q8IY92	SLX4_HUMAN	N	414	ENSP00000294008:D414N	ENSP00000294008:D414N	D	-	1	0	SLX4	3587925	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.936000	0.03946	-0.117000	0.11872	0.655000	0.94253	GAC		0.597	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3647924	C	T	3647924	3	4	38	1	0	0	0	0	1	0	0	0	1543	855	30	3	4304	3	BTBD12	16	3647924	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	2387324	3647924	86706829	124	3418										
THUMPD1	55623	hgsc.bcm.edu	37	chr16	20753048	20753048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caggctgagtagtctgctggGcaggggccgccatggtgtgc	18	10	1	1	rs368837394		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:20753048G>A	ENST00000381337.2	-	1	358	c.14C>T	c.(13-15)gCc>gTc	p.A5V	THUMPD1_ENST00000396083.2_Missense_Mutation_p.A5V|THUMPD1_ENST00000431224.2_Missense_Mutation_p.A91V|AC004381.7_ENST00000565498.1_RNA	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	5							poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						AGTCTGCTGGGCAGGGGCCGC	0.662																																																0			16						G	VAL/ALA	0,4370		0,0,2185	8	9	8		14	-6.4	0	16		8	1,8581		0,1,4290	no	missense	THUMPD1	NM_017736.3	64	0,1,6475	AA,AG,GG		0.0117,0.0,0.0077	benign	5/354	20753048	1,12951	2185	4291	6476	20660549	SO:0001583	missense	55623			BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.14C>T	16.37:g.20753048G>A	ENSP00000370741:p.Ala5Val		20660549	Q9BWC3	Missense_Mutation	SNP	ENST00000381337.2	37	CCDS10588.1	.	.	.	.	.	.	.	.	.	.	G	6.050	0.377633	0.11466	0.0	1.17E-4	ENSG00000066654	ENST00000381337;ENST00000431224;ENST00000396083	T;T;T	0.50813	0.94;0.73;0.94	5.61	-6.39	0.01951	.	0.702261	0.13356	N	0.394037	T	0.32466	0.0830	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31138	-0.9954	10	0.19147	T	0.46	.	13.2025	0.59776	0.1594:0.1232:0.7174:0.0	.	5	Q9NXG2	THUM1_HUMAN	V	5;91;5	ENSP00000370741:A5V;ENSP00000392282:A91V;ENSP00000379392:A5V	ENSP00000370741:A5V	A	-	2	0	THUMPD1	20660549	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.166000	0.09954	-0.754000	0.04715	-0.837000	0.03062	GCC		0.662	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736		A	20753048	G	A	20753048	3	1	38	1	0	0	0	0	1	0	0	0	15921	1203	42	3	1063	3	THUMPD1	16	20753048	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	17105124	20753048	69601705	125	3419										
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25251325	25251325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctctccagtgtgtattctccGatgttctcgaaatctcgtac	7	12	4	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:25251325G>A	ENST00000328086.7	-	7	3519	c.2716C>T	c.(2716-2718)Cgg>Tgg	p.R906W	CTD-2547G23.2_ENST00000569456.1_RNA	NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	906					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TGTATTCTCCGATGTTCTCGA	0.458																																																0			16											97	84	89					16																	25251325		2197	4300	6497	25158826	SO:0001583	missense	342357			AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.2716C>T	16.37:g.25251325G>A	ENSP00000331626:p.Arg906Trp		25158826	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725457	0.30593	.	.	ENSG00000155592	ENST00000328086	T	0.18810	2.19	5.43	5.43	0.79202	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.438734	0.20673	N	0.087800	T	0.39937	0.1097	M	0.87682	2.9	0.26774	N	0.969735	D;D	0.67145	0.993;0.996	P;P	0.51101	0.545;0.659	T	0.47114	-0.9142	10	0.48119	T	0.1	-5.7995	12.3085	0.54915	0.0:0.1697:0.8303:0.0	.	702;906	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	W	906	ENSP00000331626:R906W	ENSP00000331626:R906W	R	-	1	2	ZKSCAN2	25158826	0.905000	0.30787	0.563000	0.28383	0.023000	0.10783	1.766000	0.38491	2.824000	0.97209	0.655000	0.94253	CGG		0.458	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		A	25251325	G	A	25251325	3	1	38	1	0	0	0	0	1	0	0	0	17726	1057	37	1	191	1	ZKSCAN2	16	25251325	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	4498277	25251325	65103428	126	3420										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30733516	30733525	+	Frame_Shift_Del	DEL	ACCTCTCACC	ACCTCTCACC	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gctaatgcagggggaagcaaAcctctcaccttccaaatcca							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	ACCTCTCACC	ACCTCTCACC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:30733516_30733525delACCTCTCACC	ENST00000262518.4	+	22	4000_4009	c.3615_3624delACCTCTCACC	c.(3613-3624)aaacctctcaccfs	p.KPLT1205fs	SRCAP_ENST00000344771.4_Frame_Shift_Del_p.KPLT1109fs|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.KPLT1205fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1205	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGGGAAGCAAACCTCTCACCTTCCAAATCC	0.571																																																0			16																																								30641026	SO:0001589	frameshift_variant	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3615_3624delACCTCTCACC	16.37:g.30733516_30733525delACCTCTCACC	ENSP00000262518:p.Lys1205fs		30641017	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	37	CCDS10689.2																																																																																				0.571	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30733525	ACCTCTCACC	-	30733516	7	5	38	1	0	1	0	1	0	0	0	0	15174	40	2	0	3693	0	SRCAP	16	30733516	Frame_Shift_Del	DEL	ACCTCTCACC	TCGA-AG-3732-01A-11D-1657-10	5482191	30733516	59621237	127	3421										
LCAT	3931	hgsc.bcm.edu	37	chr16	67977993	67977993	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	acccactgccatggggagccGggcggccccattccagccct	12	18	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:67977993G>A	ENST00000264005.5	-	1	41	c.12C>T	c.(10-12)ccC>ccT	p.P4P	SLC12A4_ENST00000422611.2_3'UTR|CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	4					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		ATGGGGAGCCGGGCGGCCCCA	0.687																																																0			16											10	11	11					16																	67977993		1926	3788	5714	66535494	SO:0001819	synonymous_variant	3931				CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.12C>T	16.37:g.67977993G>A			66535494	Q53XQ3	Silent	SNP	ENST00000264005.5	37	CCDS10854.1																																																																																				0.687	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			A	67977993	G	A	67977993	2	1	38	1	0	0	0	0	0	0	0	1	8680	1103	39	1		1	LCAT	16	67977993	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	37244477	67977993	22376760	128	3422										
CDH1	999	hgsc.bcm.edu	37	chr16	68772219	68772219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggtctcctcttggctctgccAggagccggagccctgccacc	12	17	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:68772219A>G	ENST00000261769.5	+	2	259	c.68A>G	c.(67-69)cAg>cGg	p.Q23R	CDH1_ENST00000422392.2_Missense_Mutation_p.Q23R	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	23					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.V17fs*1(3)|p.?(2)|p.W20fs*7(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TGGCTCTGCCAGGAGCCGGAG	0.677			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	6	Deletion - Frameshift(4)|Unknown(2)	breast(6)	16											14	17	16					16																	68772219		1773	3321	5094	67329720	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.68A>G	16.37:g.68772219A>G	ENSP00000261769:p.Gln23Arg		67329720	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	5.625	0.300043	0.10622	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.53857	0.6;0.61	4.76	2.42	0.29668	Cadherin-like (1);	0.000000	0.34652	N	0.003783	T	0.40145	0.1105	L	0.57536	1.79	0.21579	N	0.999631	B;B	0.26400	0.148;0.148	B;B	0.22601	0.04;0.04	T	0.22347	-1.0219	10	0.16420	T	0.52	.	5.2451	0.15493	0.6334:0.1873:0.0:0.1793	.	23;23	Q9UII8;P12830	.;CADH1_HUMAN	R	23	ENSP00000261769:Q23R;ENSP00000414946:Q23R	ENSP00000261769:Q23R	Q	+	2	0	CDH1	67329720	1.000000	0.71417	0.960000	0.40013	0.249000	0.25844	2.121000	0.41977	0.283000	0.22279	0.460000	0.39030	CAG		0.677	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68772219	A	G	68772219	3	3	38	1	0	0	0	0	1	0	0	0	3101	188	7	4	74	4	CDH1	16	68772219	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	794226	68772219	21582534	129	3423										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76556103	76556103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgacaccaaagacacagcccGcccccgctgatgggcatgtc	10	16	0	3	rs376451733		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:76556103G>A	ENST00000476707.1	+	16	2852	c.2713G>A	c.(2713-2715)Gcc>Acc	p.A905T	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.A853T|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.A829T|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.A901T			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	902	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GACACAGCCCGCCCCCGCTGA	0.488																																																0			16						G	THR/ALA,THR/ALA	0,4084		0,0,2042	77	81	79		2703,2485	4.9	0.3	16		79	1,8409		0,1,4204	no	missense,missense	CNTNAP4	NM_033401.3,NM_138994.3	58,58	0,1,6246	AA,AG,GG		0.0119,0.0,0.0080	benign,benign	902/1309,829/1236	76556103	1,12493	2042	4205	6247	75113604	SO:0001583	missense	85445			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.2713G>A	16.37:g.76556103G>A	ENSP00000417628:p.Ala905Thr		75113604	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	G	9.330	1.060285	0.19987	0.0	1.19E-4	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	4.87	4.87	0.63330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.41396	D	0.000887	T	0.41351	0.1155	.	.	.	0.43421	D	0.995579	P;P;B	0.45240	0.854;0.582;0.426	B;B;B	0.42738	0.396;0.13;0.102	T	0.15867	-1.0422	9	0.31617	T	0.26	.	11.9643	0.53025	0.0795:0.0:0.9205:0.0	.	829;905;902	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	T	901;853;829;905	ENSP00000306893:A901T;ENSP00000439733:A853T;ENSP00000418741:A829T;ENSP00000417628:A905T	ENSP00000306893:A901T	A	+	1	0	CNTNAP4	75113604	1.000000	0.71417	0.274000	0.24659	0.010000	0.07245	5.481000	0.66826	2.678000	0.91216	0.655000	0.94253	GCC		0.488	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		A	76556103	G	A	76556103	3	1	38	1	0	0	0	0	1	0	0	0	3655	1087	38	1	2783	1	CNTNAP4	16	76556103	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	7783884	76556103	13798650	130	3424										
CDH15	1013	hgsc.bcm.edu	37	chr16	89259992	89259992	+	Frame_Shift_Del	DEL	A	A	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgtcctcaactacgatgagcAaggaggcggggaggaggacc							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr16:89259992delA	ENST00000289746.2	+	12	2035	c.1970delA	c.(1969-1971)caafs	p.Q657fs		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	657					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		TACGATGAGCAAGGAGGCGGG	0.662																																																0			16											22	20	21					16																	89259992		2176	4286	6462	87787493	SO:0001589	frameshift_variant	1013			D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1970delA	16.37:g.89259992delA	ENSP00000289746:p.Gln657fs		87787493		Frame_Shift_Del	DEL	ENST00000289746.2	37	CCDS10976.1																																																																																				0.662	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		-	89259992	A	-	89259992	7	5	38	1	0	1	0	1	0	0	0	0	3106	130	5	0	2016	0	CDH15	16	89259992	Frame_Shift_Del	DEL	A	TCGA-AG-3732-01A-11D-1657-10	12703889	89259992	1094761	131	3425										
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7385827	7385840	+	Frame_Shift_Del	DEL	CTGGACTCTGGACA	CTGGACTCTGGACA	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	actaatcatcattgtgggacCtggactctggacactacagg					rs372476896|rs548321934		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	CTGGACTCTGGACA	CTGGACTCTGGACA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:7385827_7385840delCTGGACTCTGGACA	ENST00000412468.2	+	2	639_652	c.524_537delCTGGACTCTGGACA	c.(523-537)cctggactctggacafs	p.PGLWT175fs	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	175						integral component of membrane (GO:0016021)											ATTGTGGGACCTGGACTCTGGACACTACAGGAGG	0.603																																																0			17																																								7326564	SO:0001589	frameshift_variant	643664				CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.524_537delCTGGACTCTGGACA	17.37:g.7385827_7385840delCTGGACTCTGGACA	ENSP00000396523:p.Pro175fs		7326551		Frame_Shift_Del	DEL	ENST00000412468.2	37	CCDS45603.1																																																																																				0.603	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		-	7385840	CTGGACTCTGGACA	-	7385827	7	5	38	1	0	1	0	1	0	0	0	0	561	681	24	0	530	0	AMAC1L3	17	7385827	Frame_Shift_Del	DEL	CTGGACTCTGGACA	TCGA-AG-3732-01A-11D-1657-10		7385827	73809383	132	3426										
TP53	7157	hgsc.bcm.edu	37	chr17	7576918	7576918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gggagaggagctggtgttgtTgggcagtgctaggaaagagg	21	3	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:7576918T>C	ENST00000269305.4	-	9	1117	c.928A>G	c.(928-930)Aac>Gac	p.N310D	TP53_ENST00000420246.2_Missense_Mutation_p.N310D|TP53_ENST00000359597.4_Missense_Mutation_p.N310D|TP53_ENST00000455263.2_Missense_Mutation_p.N310D|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.N310D	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	310	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		N -> I (in a sporadic cancer; somatic mutation).|N -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(3)|p.A307fs*34(1)|p.N310fs*27(1)|p.N310L(1)|p.P309fs*26(1)|p.L308fs*15(1)|p.L308fs*31(1)|p.N310D(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGGTGTTGTTGGGCAGTGCT	0.488		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	18	Whole gene deletion(8)|Deletion - Frameshift(4)|Unknown(3)|Substitution - Missense(2)|Insertion - Frameshift(1)	bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|large_intestine(1)|stomach(1)|lung(1)|oesophagus(1)|liver(1)	17											135	122	126					17																	7576918		2203	4300	6503	7517643	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.928A>G	17.37:g.7576918T>C	ENSP00000269305:p.Asn310Asp		7517643	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	8.971	0.972950	0.18736	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99722	-5.72;-5.46;-5.72;-5.72;-5.46;-6.53	5.16	4.08	0.47627	.	2.455720	0.01918	N	0.040315	D	0.98213	0.9409	N	0.16743	0.435	0.09310	N	0.999992	B;B;B;B	0.20988	0.007;0.05;0.0;0.004	B;B;B;B	0.20767	0.026;0.031;0.0;0.012	D	0.98036	1.0379	10	0.11794	T	0.64	-12.5551	8.9375	0.35708	0.0:0.0:0.2035:0.7965	.	310;310;310;310	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	D	310;310;310;310;310;299;178	ENSP00000352610:N310D;ENSP00000269305:N310D;ENSP00000398846:N310D;ENSP00000391127:N310D;ENSP00000391478:N310D;ENSP00000425104:N178D	ENSP00000269305:N310D	N	-	1	0	TP53	7517643	0.005000	0.15991	0.079000	0.20413	0.230000	0.25150	0.172000	0.16704	0.985000	0.38656	0.459000	0.35465	AAC		0.488	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7576918	T	C	7576918	3	2	38	1	0	0	0	0	1	0	0	0	16421	1812	63	4	354	4	TP53	17	7576918	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	191091	7576918	73618292	133	3427										
TP53	7157	hgsc.bcm.edu	37	chr17	7578436	7578439	+	Frame_Shift_Del	DEL	TGCT	TGCT	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	cctccgtcatgtgctgtgacTgcttgtagatggccatggcg							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TGCT	TGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:7578436_7578439delTGCT	ENST00000269305.4	-	5	680_683	c.491_494delAGCA	c.(490-495)aagcagfs	p.KQ164fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.KQ164fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.KQ164fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.KQ164fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.KQ164fs|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000445888.2_Frame_Shift_Del_p.KQ164fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	164	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		K -> E (in sporadic cancers; somatic mutation).|K -> M (in sporadic cancers; somatic mutation).|K -> N (in sporadic cancers; somatic mutation).|K -> Q (in sporadic cancers; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q165*(24)|p.0?(8)|p.K164N(6)|p.K164M(4)|p.Q165L(3)|p.Q165R(2)|p.Q165P(2)|p.K164K(2)|p.K164fs*5(2)|p.K164fs*3(2)|p.K164T(2)|p.V157_C176del20(1)|p.Y163fs*1(1)|p.Q165E(1)|p.Y163_Q165delYKQ(1)|p.P151_V173del23(1)|p.S149fs*72(1)|p.K164_Q165insXXX(1)|p.Q165fs*16(1)|p.K164fs*17(1)|p.Q165fs*4(1)|p.Q165del(1)|p.K164R(1)|p.Q165_M169delQSQHM(1)|p.Y163fs*14(1)|p.A159_Q167delAMAIYKQSQ(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGCTGTGACTGCTTGTAGATGGC	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	72	Substitution - Nonsense(24)|Substitution - Missense(21)|Deletion - Frameshift(8)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(2)|Substitution - coding silent(2)|Insertion - In frame(1)	oesophagus(15)|breast(11)|large_intestine(7)|haematopoietic_and_lymphoid_tissue(7)|lung(5)|upper_aerodigestive_tract(4)|stomach(4)|soft_tissue(4)|central_nervous_system(4)|bone(4)|salivary_gland(2)|pancreas(2)|urinary_tract(1)|skin(1)|prostate(1)	17																																								7519164	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.491_494delAGCA	17.37:g.7578436_7578439delTGCT	ENSP00000269305:p.Lys164fs		7519161	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7578439	TGCT	-	7578436	7	5	38	1	0	1	0	1	0	0	0	0	16421	1580	55	0	804	0	TP53	17	7578436	Frame_Shift_Del	DEL	TGCT	TCGA-AG-3732-01A-11D-1657-10	1518	7578436	73616774	134	3428										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29161960	29161960	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagataccagactctacaatGtcaatttgtgttccttctga	7	9	3	3	rs60663953|rs80170526|rs398102309|rs72427574	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:29161960G>T	ENST00000321990.4	+	2	1239	c.861G>T	c.(859-861)atG>atT	p.M287I	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	287					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ACTCTACAATGTCAATTTGTG	0.348																																																0			17											40	40	40					17																	29161960		2195	4274	6469	26186086	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.861G>T	17.37:g.29161960G>T	ENSP00000313171:p.Met287Ile		26186086	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	5.215	0.225221	0.09916	.	.	ENSG00000176208	ENST00000321990	T	0.18810	2.19	5.61	0.154	0.14901	.	1.134440	0.06347	N	0.709245	T	0.15435	0.0372	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33445	-0.9868	10	0.45353	T	0.12	.	6.4897	0.22109	0.3734:0.0:0.5153:0.1114	.	287;287	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	I	287	ENSP00000313171:M287I	ENSP00000313171:M287I	M	+	3	0	ATAD5	26186086	0.003000	0.15002	0.005000	0.12908	0.767000	0.43475	0.774000	0.26675	-0.077000	0.12752	0.655000	0.94253	ATG		0.348	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29161960	G	T	29161960	3	4	38	1	0	0	0	0	1	0	0	0	1077	1377	48	2	867	2	ATAD5	17	29161960	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	21583524	29161960	52033250	135	3429										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37879794	37879794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccaccccctcaccccagctgGtggagccgctgacacctagc	9	20	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:37879794G>T	ENST00000269571.5	+	18	2248	c.2089G>T	c.(2089-2091)Gtg>Ttg	p.V697L	MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584450.1_Missense_Mutation_p.V697L|ERBB2_ENST00000541774.1_Missense_Mutation_p.V682L|ERBB2_ENST00000445658.2_Missense_Mutation_p.V421L|ERBB2_ENST00000540147.1_Missense_Mutation_p.V667L|ERBB2_ENST00000584601.1_Missense_Mutation_p.V667L|ERBB2_ENST00000406381.2_Missense_Mutation_p.V667L			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	697					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	ACCCCAGCTGGTGGAGCCGCT	0.672		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	0			17											36	39	38					17																	37879794		2202	4299	6501	35133320	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2089G>T	17.37:g.37879794G>T	ENSP00000269571:p.Val697Leu		35133320	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	17.10	3.304268	0.60305	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.75938	-0.98;-0.98;-0.97;-0.98;-0.98	4.97	4.97	0.65823	.	.	.	.	.	D	0.83695	0.5310	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.999	D	0.84356	0.0535	9	0.51188	T	0.08	.	17.8613	0.88781	0.0:0.0:1.0:0.0	.	421;682;697	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	L	667;682;421;697;667	ENSP00000385185:V667L;ENSP00000446466:V682L;ENSP00000404047:V421L;ENSP00000269571:V697L;ENSP00000443562:V667L	ENSP00000269571:V697L	V	+	1	0	ERBB2	35133320	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.996000	0.88334	2.317000	0.78254	0.561000	0.74099	GTG		0.672	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37879794	G	T	37879794	3	4	38	1	0	0	0	0	1	0	0	0	5219	1261	44	2	2159	2	ERBB2	17	37879794	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	8717834	37879794	43315416	136	3430										
CDC6	990	hgsc.bcm.edu	37	chr17	38447589	38447589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgtgagactattcaagcaagAaggtttgttcttacatggca	10	6	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:38447589A>G	ENST00000209728.4	+	3	929	c.458A>G	c.(457-459)gAa>gGa	p.E153G		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	153					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						TTCAAGCAAGAAGGTTTGTTC	0.408																																																0			17											84	87	86					17																	38447589		2203	4300	6503	35701115	SO:0001583	missense	990			U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.458A>G	17.37:g.38447589A>G	ENSP00000209728:p.Glu153Gly		35701115	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712008	0.48517	.	.	ENSG00000094804	ENST00000209728	T	0.53640	0.61	5.86	4.76	0.60689	.	0.253355	0.45126	D	0.000395	T	0.43366	0.1244	L	0.59436	1.845	0.45464	D	0.998435	B	0.19073	0.033	B	0.13407	0.009	T	0.25572	-1.0128	10	0.26408	T	0.33	-2.1609	12.3968	0.55389	0.8592:0.1408:0.0:0.0	.	153	Q99741	CDC6_HUMAN	G	153	ENSP00000209728:E153G	ENSP00000209728:E153G	E	+	2	0	CDC6	35701115	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.682000	0.54656	1.101000	0.41535	0.528000	0.53228	GAA		0.408	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			G	38447589	A	G	38447589	3	3	38	1	0	0	0	0	1	0	0	0	3089	246	9	4	464	4	CDC6	17	38447589	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	567795	38447589	42747621	137	3431										
OTOP3	347741	hgsc.bcm.edu	37	chr17	72938094	72938095	+	In_Frame_Ins	INS	-	-	TCT													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caagtcacagctggaccttgINStcttctctgtcatcgagatg							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr17:72938094_72938095insTCT	ENST00000328801.4	+	3	589_590	c.589_590insTCT	c.(589-591)gtc>gTCTtc	p.198_199insF		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	198			S -> P (in dbSNP:rs1542752).			integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					GCTGGACCTTGTCTTCTCTGTC	0.559																																																0			17																																								70449690	SO:0001652	inframe_insertion	347741			BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.593_595dupTCT	17.37:g.72938098_72938100dupTCT	ENSP00000328090:p.Phe198_Phe198dup		70449689		In_Frame_Ins	INS	ENST00000328801.4	37	CCDS11709.1																																																																																				0.559	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		TCT	72938095	-	TCT	72938094	7	5	38	1	0	1	1	0	0	0	0	0	11338	1377	48	0	599	0	OTOP3	17	72938094	In_Frame_Ins	INS	-	TCGA-AG-3732-01A-11D-1657-10	34490505	72938094	8257116	138	3432										
ESCO1	114799	hgsc.bcm.edu	37	chr18	19144171	19144171	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gttgtgtacttactataatcAactgtttttcatcagttttc	5	7	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr18:19144171A>T	ENST00000269214.5	-	7	2751	c.1814T>A	c.(1813-1815)tTg>tAg	p.L605*		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	605					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TACTATAATCAACTGTTTTTC	0.328																																																0			18											112	104	107					18																	19144171		2202	4298	6500	17398169	SO:0001587	stop_gained	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.1814T>A	18.37:g.19144171A>T	ENSP00000269214:p.Leu605*		17398169	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Nonsense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	A	46	12.759586	0.99694	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	.	.	.	4.78	4.78	0.61160	.	0.222293	0.31061	N	0.008335	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.6669	8.511	0.33217	0.9121:0.0:0.0879:0.0	.	.	.	.	X	605	.	ENSP00000269214:L605X	L	-	2	0	ESCO1	17398169	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.068000	0.57534	1.922000	0.55676	0.533000	0.62120	TTG		0.328	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		T	19144171	A	T	19144171	4	4	38	1	0	0	0	0	0	1	0	0	5261	131	5	5	732	5	ESCO1	18	19144171	Nonsense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10		19144171	58933077	139	3433										
KIAA1328	57536	hgsc.bcm.edu	37	chr18	34647215	34647215	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggtcatagacttgctgcagaTcgtgttcatgacagccatcc	10	11	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr18:34647215T>C	ENST00000280020.5	+	7	961	c.939T>C	c.(937-939)gaT>gaC	p.D313D	KIAA1328_ENST00000591619.1_Silent_p.D309D|KIAA1328_ENST00000435985.2_Silent_p.D29D|KIAA1328_ENST00000586135.1_Silent_p.D29D|KIAA1328_ENST00000543923.1_Silent_p.D205D|KIAA1328_ENST00000586501.1_Silent_p.D29D	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	313										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		TTGCTGCAGATCGTGTTCATG	0.458																																																0			18											111	106	108					18																	34647215		2097	4217	6314	32901213	SO:0001819	synonymous_variant	57536			AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.939T>C	18.37:g.34647215T>C			32901213	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																				0.458	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		C	34647215	T	C	34647215	2	2	38	1	0	0	0	0	0	0	0	1	8246	1432	50	4		4	KIAA1328	18	34647215	Silent	SNP	T	TCGA-AG-3732-01A-11D-1657-10	15503044	34647215	43430033	140	3434										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43450590	43450590	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggtccttccatggcagtttcCggtacgtgctatggaaagcg	13	10	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr18:43450590C>A	ENST00000282041.5	-	36	6201	c.6167G>T	c.(6166-6168)cGg>cTg	p.R2056L	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2056			R -> W (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.R2056Q(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGGCAGTTTCCGGTACGTGCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	18											106	107	107					18																	43450590		1993	4170	6163	41704588	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.6167G>T	18.37:g.43450590C>A	ENSP00000282041:p.Arg2056Leu		41704588	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	9.582	1.123745	0.20959	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.08458	3.09	6.03	-12.1	0.00011	.	.	.	.	.	T	0.05090	0.0136	N	0.08118	0	0.09310	N	1	B	0.30973	0.302	B	0.31946	0.138	T	0.55854	-0.8075	9	0.08179	T	0.78	-0.1748	29.0522	0.99999	0.0:0.8579:0.0:0.1421	.	2056	Q9HCE0	EPG5_HUMAN	L	2056;931	ENSP00000282041:R2056L	ENSP00000282041:R2056L	R	-	2	0	EPG5	41704588	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-1.613000	0.02059	-2.940000	0.00297	-0.880000	0.02959	CGG		0.517	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43450590	C	A	43450590	3	1	38	1	0	0	0	0	1	0	0	0	8270	652	23	2	1608	2	KIAA1632	18	43450590	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	8803375	43450590	34626658	141	3435										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575670	48575670	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctttaaacaattaagatctcTcaggattaacactgcagagt	6	8	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr18:48575670T>C	ENST00000342988.3	+	4	968	c.430T>C	c.(430-432)Tca>Cca	p.S144P	SMAD4_ENST00000398417.2_Missense_Mutation_p.S144P|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.S144P|SMAD4_ENST00000452201.2_Missense_Mutation_p.S144P	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	144					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TTAAGATCTCTCAGGATTAAC	0.294																																																40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18	GRCh37	CD064639	SMAD4	D							183	164	171					18																	48575670		2202	4298	6500	46829668	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.430T>C	18.37:g.48575670T>C	ENSP00000341551:p.Ser144Pro		46829668	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.364470	0.82463	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	T;D;D	0.97731	-1.18;-4.51;-4.51	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.97536	0.9193	M	0.64170	1.965	0.51482	D	0.99992	D	0.55605	0.972	P	0.52386	0.697	D	0.97417	1.0006	10	0.46703	T	0.11	.	15.3535	0.74409	0.0:0.0:0.0:1.0	.	144	Q13485	SMAD4_HUMAN	P	144	ENSP00000409551:S144P;ENSP00000341551:S144P;ENSP00000381452:S144P	ENSP00000341551:S144P	S	+	1	0	SMAD4	46829668	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.017000	0.64047	2.267000	0.75376	0.477000	0.44152	TCA		0.294	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48575670	T	C	48575670	3	2	38	1	0	0	0	0	1	0	0	0	14797	1551	54	4	440	4	SMAD4	18	48575670	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	5125080	48575670	29501578	142	3436										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591866	48591866	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagacatttaaggttccttcAagctgccctattgttactgt	8	9	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr18:48591866A>G	ENST00000342988.3	+	9	1567	c.1029A>G	c.(1027-1029)tcA>tcG	p.S343S	SMAD4_ENST00000398417.2_Silent_p.S343S|SMAD4_ENST00000588745.1_Silent_p.S247S	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	343	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.F339_S343del(2)|p.?(2)|p.S344fs*41(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGGTTCCTTCAAGCTGCCCTA	0.433																																																41	Whole gene deletion(36)|Deletion - In frame(2)|Unknown(2)|Insertion - Frameshift(1)	pancreas(27)|large_intestine(5)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											257	220	232					18																	48591866		2203	4300	6503	46845864	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1029A>G	18.37:g.48591866A>G			46845864	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.433	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48591866	A	G	48591866	2	3	38	1	0	0	0	0	0	0	0	1	14797	117	5	4		4	SMAD4	18	48591866	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	16196	48591866	29485382	143	3437										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15067369	15067369	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggttccggtgagtgacgaggAagtagatgaggggaaggaca	19	4	0	4			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr19:15067369A>T	ENST00000221742.3	-	6	1095	c.1088T>A	c.(1087-1089)tTc>tAc	p.F363Y	SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000430939.2_Missense_Mutation_p.F299Y	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	363					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						AGTGACGAGGAAGTAGATGAG	0.607																																																0			19											180	141	154					19																	15067369		2203	4300	6503	14928369	SO:0001583	missense	6511				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1088T>A	19.37:g.15067369A>T	ENSP00000221742:p.Phe363Tyr		14928369	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	a	17.81	3.481251	0.63849	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.62941	-0.01;0.25	3.96	3.96	0.45880	.	0.159067	0.64402	D	0.000020	T	0.69672	0.3137	L	0.54863	1.705	0.80722	D	1	P;B	0.48589	0.912;0.402	P;B	0.59012	0.85;0.213	T	0.71517	-0.4569	10	0.56958	D	0.05	-16.2113	11.1006	0.48172	1.0:0.0:0.0:0.0	.	299;363	E7EV13;P48664	.;EAA4_HUMAN	Y	299;363	ENSP00000409386:F299Y;ENSP00000221742:F363Y	ENSP00000221742:F363Y	F	-	2	0	SLC1A6	14928369	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.907000	0.92634	1.805000	0.52779	0.482000	0.46254	TTC		0.607	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15067369	A	T	15067369	3	4	38	1	0	0	0	0	1	0	0	0	14473	246	9	5	622	5	SLC1A6	19	15067369	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10		15067369	44061614	144	3438										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23837045	23837045	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	aaagttctgtcacattcttgAcatttgtagagtttctcaca	6	8	4	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr19:23837045A>G	ENST00000359788.4	-	4	858	c.690T>C	c.(688-690)tgT>tgC	p.C230C	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	230					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CACATTCTTGACATTTGTAGA	0.308																																																0			19											50	53	52					19																	23837045		2201	4296	6497	23628885	SO:0001819	synonymous_variant	171392				CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.690T>C	19.37:g.23837045A>G			23628885	Q8N211	Silent	SNP	ENST00000359788.4	37	CCDS32981.1																																																																																				0.308	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		G	23837045	A	G	23837045	2	3	38	1	0	0	0	0	0	0	0	1	18121	273	10	4		4	ZNF675	19	23837045	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	8769676	23837045	35291938	145	3439										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805292	39805292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ctgcgacctcaggaagagccCgtcgggcgggagtttatgca	15	11	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr19:39805292C>T	ENST00000248668.4	-	1	684	c.685G>A	c.(685-687)Ggg>Agg	p.G229R	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	229						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			AGGAAGAGCCCGTCGGGCGGG	0.662																																																0			19											23	28	26					19																	39805292		2113	4238	6351	44497132	SO:0001583	missense	57622			BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.685G>A	19.37:g.39805292C>T	ENSP00000248668:p.Gly229Arg		44497132	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	37	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008429	0.35415	.	.	ENSG00000128011	ENST00000248668	T	0.55234	0.53	4.3	4.3	0.51218	.	0.000000	0.42172	D	0.000751	T	0.28665	0.0710	N	0.08118	0	0.31115	N	0.709509	D	0.53619	0.961	B	0.40134	0.32	T	0.33650	-0.9860	10	0.59425	D	0.04	.	7.9909	0.30239	0.0:0.8896:0.0:0.1104	.	229	Q9P244	LRFN1_HUMAN	R	229	ENSP00000248668:G229R	ENSP00000248668:G229R	G	-	1	0	LRFN1	44497132	0.009000	0.17119	0.952000	0.39060	0.777000	0.43975	1.629000	0.37071	2.234000	0.73211	0.491000	0.48974	GGG		0.662	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		T	39805292	C	T	39805292	3	4	38	1	0	0	0	0	1	0	0	0	8966	652	23	1	1638	1	LRFN1	19	39805292	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	15968247	39805292	19323691	146	3440										
LIG1	3978	hgsc.bcm.edu	37	chr19	48657140	48657140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ggggctcaccttcctcctccTtcttcctcttggcttctctg	7	17	4	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr19:48657140T>C	ENST00000263274.7	-	6	874	c.455A>G	c.(454-456)aAg>aGg	p.K152R	LIG1_ENST00000536218.1_Intron|LIG1_ENST00000599165.1_Intron|LIG1_ENST00000427526.2_Missense_Mutation_p.K122R	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	152			K -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ttcctcctccttcttcctctt	0.577								Nucleotide excision repair (NER)																																								0			19											196	113	141					19																	48657140		2203	4300	6503	53348952	SO:0001583	missense	26018				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.455A>G	19.37:g.48657140T>C	ENSP00000263274:p.Lys152Arg		53348952	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	6.386	0.439422	0.12104	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526	T;T	0.58506	0.44;0.33	3.99	2.94	0.34122	.	0.866238	0.10215	N	0.701604	T	0.48714	0.1515	L	0.54323	1.7	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.28839	-1.0031	10	0.18710	T	0.47	-18.4584	7.3918	0.26913	0.0:0.0:0.2229:0.7771	.	122;152	B4DTU4;P18858	.;DNLI1_HUMAN	R	152;184;122	ENSP00000263274:K152R;ENSP00000442841:K122R	ENSP00000263274:K152R	K	-	2	0	LIG1	53348952	0.292000	0.24362	0.892000	0.35008	0.244000	0.25665	1.067000	0.30616	0.837000	0.34925	0.496000	0.49642	AAG		0.577	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48657140	T	C	48657140	3	2	38	1	0	0	0	0	1	0	0	0	8804	1609	56	4	2396	4	LIG1	19	48657140	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	8851848	48657140	10471843	147	3441										
ANGPT4	51378	hgsc.bcm.edu	37	chr20	858965	858965	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgctccccagctgggtctccGaagccctatagggaggggag	15	12	1	0	rs112090528	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr20:858965G>A	ENST00000381922.3	-	7	1161	c.1059C>T	c.(1057-1059)ttC>ttT	p.F353F	ANGPT4_ENST00000546022.1_Silent_p.F353F	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	353	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						CTGGGTCTCCGAAGCCCTATA	0.632																																					Pancreas(181;481 2077 3259 31286 49856)											0			20						G		3,4403	6.2+/-15.9	0,3,2200	30	29	29		1059	0.6	1	20	dbSNP_132	29	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ANGPT4	NM_015985.2		0,5,6498	AA,AG,GG		0.0233,0.0681,0.0384		353/504	858965	5,13001	2203	4300	6503	806965	SO:0001819	synonymous_variant	51378			AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1059C>T	20.37:g.858965G>A			806965	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																				0.632	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		A	858965	G	A	858965	2	1	38	1	0	0	0	0	0	0	0	1	612	1049	37	1		1	ANGPT4	20	858965	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10		858965	62166555	148	3442										
PAK7	57144	hgsc.bcm.edu	37	chr20	9546754	9546754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	catgggacaccctggagggcTgctggtcggaggaggagccc	18	11	0	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr20:9546754T>C	ENST00000378429.3	-	6	1814	c.1268A>G	c.(1267-1269)cAg>cGg	p.Q423R	PAK7_ENST00000353224.5_Missense_Mutation_p.Q423R|PAK7_ENST00000378423.1_Missense_Mutation_p.Q423R	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	423	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			CCTGGAGGGCTGCTGGTCGGA	0.622																																																0			20											57	58	58					20																	9546754		2203	4300	6503	9494754	SO:0001583	missense	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1268A>G	20.37:g.9546754T>C	ENSP00000367686:p.Gln423Arg		9494754	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527991	0.64860	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.72725	-0.68;-0.68;-0.68	5.66	4.55	0.56014	.	0.109437	0.64402	D	0.000004	T	0.66307	0.2776	M	0.62723	1.935	0.58432	D	0.999995	B;B	0.18610	0.029;0.029	B;B	0.13407	0.009;0.009	T	0.60239	-0.7302	9	.	.	.	.	12.9957	0.58646	0.0:0.0:0.1348:0.8651	.	423;423	B0AZM9;Q9P286	.;PAK7_HUMAN	R	423;423;423;371	ENSP00000367686:Q423R;ENSP00000322957:Q423R;ENSP00000367679:Q423R	.	Q	-	2	0	PAK7	9494754	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.907000	0.63300	0.949000	0.37715	0.477000	0.44152	CAG		0.622	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			C	9546754	T	C	9546754	3	2	38	1	0	0	0	0	1	0	0	0	11436	1580	55	4	915	4	PAK7	20	9546754	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	8687789	9546754	53478766	149	3443										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45221138	45221138	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcgaaaatgaaccaggagccGaaattcaccacgtcacactg	9	12	2	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr20:45221138G>A	ENST00000279027.4	-	6	843	c.825C>T	c.(823-825)ttC>ttT	p.F275F	SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000413164.2_Intron|SLC13A3_ENST00000472148.1_Silent_p.F228F|SLC13A3_ENST00000396360.1_Silent_p.F228F|SLC13A3_ENST00000372121.1_Intron|SLC13A3_ENST00000495082.1_Silent_p.F228F|SLC13A3_ENST00000290317.5_Silent_p.F228F	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	275					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ACCAGGAGCCGAAATTCACCA	0.562																																																0			20											137	104	115					20																	45221138		2203	4300	6503	44654545	SO:0001819	synonymous_variant	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.825C>T	20.37:g.45221138G>A			44654545	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.460264	0.26248	.	.	ENSG00000158296	ENST00000450298	.	.	.	5.69	-5.52	0.02560	.	.	.	.	.	T	0.65626	0.2709	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67906	-0.5549	4	.	.	.	-29.6292	16.999	0.86376	0.8746:0.0:0.1254:0.0	.	.	.	.	W	105	.	.	R	-	1	2	SLC13A3	44654545	0.906000	0.30813	0.772000	0.31596	0.987000	0.75469	0.087000	0.14958	-0.899000	0.03901	-0.812000	0.03155	CGG		0.562	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45221138	G	A	45221138	2	1	38	1	0	0	0	0	0	0	0	1	14430	1049	37	1		1	SLC13A3	20	45221138	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	35674384	45221138	17804382	150	3444										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484421	57484421	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tcaggacctgcttcgctgccGtgtcctgacttctggaatct	10	13	3	1	rs121913495		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr20:57484421G>T	ENST00000371085.3	+	8	1026	c.602G>T	c.(601-603)cGt>cTt	p.R201L	GNAS_ENST00000371100.4_Missense_Mutation_p.R844L|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186L|GNAS_ENST00000354359.7_Missense_Mutation_p.R202L|GNAS_ENST00000371102.4_Missense_Mutation_p.R830L|GNAS_ENST00000306090.10_Missense_Mutation_p.R187L|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000371095.3_Missense_Mutation_p.R187L	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CTTCGCTGCCGTGTCCTGACT	0.423			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	88	Substitution - Missense(88)	pancreas(28)|large_intestine(19)|thyroid(12)|pituitary(12)|liver(6)|biliary_tract(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|stomach(1)|small_intestine(1)|ovary(1)	20											80	78	79					20																	57484421		2203	4300	6503	56917816	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.602G>T	20.37:g.57484421G>T	ENSP00000360126:p.Arg201Leu		56917816	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	37	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	G	34	5.392054	0.95988	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99458	-5.93;-5.93;-5.93;-5.93;-5.93;-2.97;-5.93	5.53	5.53	0.82687	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.98965	4.385	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.91635	0.99;0.983;0.95;0.999	D	0.96812	0.9597	10	0.87932	D	0	.	19.4606	0.94915	0.0:0.0:1.0:0.0	.	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	L	844;830;187;201;202;186;187	ENSP00000360141:R844L;ENSP00000360143:R830L;ENSP00000360136:R187L;ENSP00000360126:R201L;ENSP00000346328:R202L;ENSP00000265620:R186L;ENSP00000304472:R187L	ENSP00000265620:R186L	R	+	2	0	GNAS	56917816	1.000000	0.71417	0.963000	0.40424	0.936000	0.57629	9.291000	0.96070	2.596000	0.87737	0.563000	0.77884	CGT		0.423	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57484421	G	T	57484421	3	4	38	1	0	0	0	0	1	0	0	0	6530	1145	40	2	3449	2	GNAS	20	57484421	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	12263283	57484421	5541099	151	3445										
TAF4	6874	hgsc.bcm.edu	37	chr20	60589624	60589624	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tgtacggtggagatctggacGggaggggcacttgtgggggt	21	5	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr20:60589624G>A	ENST00000252996.4	-	2	1499	c.1500C>T	c.(1498-1500)ccC>ccT	p.P500P	TAF4_ENST00000609045.1_5'Flank	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	500					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			AGATCTGGACGGGAGGGGCAC	0.667																																																0			20											49	43	45					20																	60589624		2203	4299	6502	60023019	SO:0001819	synonymous_variant	6874			Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1500C>T	20.37:g.60589624G>A			60023019	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Silent	SNP	ENST00000252996.4	37	CCDS33500.1																																																																																				0.667	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60589624	G	A	60589624	2	1	38	1	0	0	0	0	0	0	0	1	15565	1103	39	1		1	TAF4	20	60589624	Silent	SNP	G	TCGA-AG-3732-01A-11D-1657-10	3105203	60589624	2435896	152	3446										
USP25	29761	hgsc.bcm.edu	37	chr21	17250153	17250153	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gcagaactcttcgaatctggAgaggatcgagaagtaaacaa	11	7	2	3			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr21:17250153A>G	ENST00000285679.6	+	23	3207	c.2838A>G	c.(2836-2838)ggA>ggG	p.G946G	USP25_ENST00000351097.5_Silent_p.G341G|USP25_ENST00000400183.2_Silent_p.G1016G|USP25_ENST00000285681.2_Silent_p.G978G	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	946					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		TCGAATCTGGAGAGGATCGAG	0.328																																																0			21											92	93	93					21																	17250153		2203	4300	6503	16172024	SO:0001819	synonymous_variant	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2838A>G	21.37:g.17250153A>G			16172024	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																				0.328	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17250153	A	G	17250153	2	3	38	1	0	0	0	0	0	0	0	1	17096	291	11	4		4	USP25	21	17250153	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10		17250153	30879742	153	3447										
APP	351	hgsc.bcm.edu	37	chr21	27484438	27484438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caatctggggttcagccagcAggccagcattaccatcagtg	11	12	3	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr21:27484438A>G	ENST00000346798.3	-	2	116	c.83T>C	c.(82-84)cTg>cCg	p.L28P	APP_ENST00000474136.1_5'UTR|APP_ENST00000357903.3_Missense_Mutation_p.L28P|APP_ENST00000439274.2_Intron|APP_ENST00000348990.5_Missense_Mutation_p.L28P|APP_ENST00000358918.3_Missense_Mutation_p.L28P|APP_ENST00000354192.3_Intron|APP_ENST00000440126.3_Missense_Mutation_p.L23P|APP_ENST00000359726.3_Missense_Mutation_p.L28P|APP_ENST00000448388.2_5'UTR	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	28					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TTCAGCCAGCAGGCCAGCATT	0.488																																																0			21											119	106	111					21																	27484438		2203	4300	6503	26406309	SO:0001583	missense	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.83T>C	21.37:g.27484438A>G	ENSP00000284981:p.Leu28Pro		26406309	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.318766	0.81469	.	.	ENSG00000142192	ENST00000346798;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000440126	D;D;D;D;D;D	0.96427	-2.05;-4.01;-2.07;-1.91;-4.01;-2.09	5.44	5.44	0.79542	Amyloidogenic glycoprotein, heparin-binding (1);Amyloidogenic glycoprotein, extracellular (1);	0.000000	0.64402	D	0.000001	D	0.97476	0.9174	M	0.61703	1.905	0.80722	D	1	D;B;D;D;D	0.89917	1.0;0.111;0.999;0.996;0.998	D;B;D;D;D	0.91635	0.999;0.086;0.985;0.968;0.988	D	0.97603	1.0124	10	0.46703	T	0.11	-15.0248	15.1534	0.72720	1.0:0.0:0.0:0.0	.	28;23;28;28;28	P05067-2;B4DII8;P05067-4;P05067-8;P05067	.;.;.;.;A4_HUMAN	P	28;28;28;28;28;23	ENSP00000284981:L28P;ENSP00000345463:L28P;ENSP00000350578:L28P;ENSP00000351796:L28P;ENSP00000352760:L28P;ENSP00000387483:L23P	ENSP00000284981:L28P	L	-	2	0	APP	26406309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.051000	0.76627	2.047000	0.60756	0.533000	0.62120	CTG		0.488	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		G	27484438	A	G	27484438	3	3	38	1	0	0	0	0	1	0	0	0	815	188	7	4	2297	4	APP	21	27484438	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	10234285	27484438	20645457	154	3448										
KRTAP8-1	337879	hgsc.bcm.edu	37	chr21	32185378	32185378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	caaatggcgagtatctcctgTagccgaaagccccacagccg	10	14	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr21:32185378T>C	ENST00000329621.4	-	1	192	c.161A>G	c.(160-162)tAc>tGc	p.Y54C		NM_175857.3	NP_787053.1	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1	54	12 X 2 AA repeats of G-[YCGS].					intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(1)|lung(4)	6						GTATCTCCTGTAGCCGAAAGC	0.562																																																0			21											87	82	83					21																	32185378		2203	4300	6503	31107249	SO:0001583	missense	337879			AJ457064	CCDS13607.1	21q22.1	2006-03-13			ENSG00000183640	ENSG00000183640		"Keratin associated proteins"	18935	protein-coding gene	gene with protein product						12359730	Standard	NM_175857		Approved	KAP8.1	uc002you.3	Q8IUC2	OTTHUMG00000057771	ENST00000329621.4:c.161A>G	21.37:g.32185378T>C	ENSP00000332805:p.Tyr54Cys		31107249	Q3LI57	Missense_Mutation	SNP	ENST00000329621.4	37	CCDS13607.1	.	.	.	.	.	.	.	.	.	.	T	3.877	-0.026674	0.07589	.	.	ENSG00000183640	ENST00000329621	T	0.15718	2.4	5.56	4.39	0.52855	.	0.000000	0.46442	D	0.000295	T	0.36744	0.0978	.	.	.	0.36452	D	0.866163	D	0.89917	1.0	D	0.81914	0.995	T	0.39272	-0.9622	9	0.42905	T	0.14	-1.0634	9.0834	0.36565	0.1633:0.0:0.0:0.8367	.	54	Q8IUC2	KRA81_HUMAN	C	54	ENSP00000332805:Y54C	ENSP00000332805:Y54C	Y	-	2	0	KRTAP8-1	31107249	0.950000	0.32346	0.968000	0.41197	0.209000	0.24338	0.223000	0.17719	1.020000	0.39573	-0.336000	0.08194	TAC		0.562	KRTAP8-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128223.1			C	32185378	T	C	32185378	3	2	38	1	0	0	0	0	1	0	0	0	8594	1638	57	4	34	4	KRTAP8-1	21	32185378	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	4700940	32185378	15944517	155	3449										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41423988	41424001	+	Frame_Shift_Del	DEL	TGCCTCTCCAAAGT	TGCCTCTCCAAAGT	-													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gtcagggacttctgcttagcTgcctctccaaagtcagcatc					rs374542622		TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	TGCCTCTCCAAAGT	TGCCTCTCCAAAGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr21:41423988_41424001delTGCCTCTCCAAAGT	ENST00000400454.1	-	30	5546_5559	c.5069_5082delACTTTGGAGAGGCA	c.(5068-5082)gactttggagaggcafs	p.DFGEA1690fs		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1690					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D1690A(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TCTGCTTAGCTGCCTCTCCAAAGTCAGCATCCGT	0.547																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - Missense(1)	ovary(1)	21																																								40345871	SO:0001589	frameshift_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5069_5082delACTTTGGAGAGGCA	21.37:g.41423988_41424001delTGCCTCTCCAAAGT	ENSP00000383303:p.Asp1690fs		40345858	O60468	Frame_Shift_Del	DEL	ENST00000400454.1	37	CCDS42929.1																																																																																				0.547	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		-	41424001	TGCCTCTCCAAAGT	-	41423988	7	5	38	1	0	1	0	1	0	0	0	0	4779	1567	55	0	972	0	DSCAM	21	41423988	Frame_Shift_Del	DEL	TGCCTCTCCAAAGT	TCGA-AG-3732-01A-11D-1657-10	9238610	41423988	6705907	156	3450										
NF2	4771	hgsc.bcm.edu	37	chr22	30038189	30038189	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tctcccttgttgctcctttcAggtaaagaagcagattttag	8	9	2	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr22:30038189A>G	ENST00000338641.4	+	4	804		c.e4-1		NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000413209.2_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(5)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TGCTCCTTTCAGGTAAAGAAG	0.507			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	5	Unknown(5)	soft_tissue(2)|meninges(1)|large_intestine(1)|stomach(1)	22											87	81	83					22																	30038189		2203	4300	6503	28368189	SO:0001630	splice_region_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.364-1A>G	22.37:g.30038189A>G			28368189	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.625773	0.87560	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5249	0.75894	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28368189	1.000000	0.71417	0.993000	0.49108	0.979000	0.70002	9.136000	0.94489	2.075000	0.62263	0.533000	0.62120	.		0.507	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	G	30038189	A	G	30038189	5	3	38	1	0	0	0	0	0	0	1	0	10388	202	7	4	376	4	NF2	22	30038189	Splice_Site	SNP	A	TCGA-AG-3732-01A-11D-1657-10		30038189	21266377	157	3451										
EP300	2033	hgsc.bcm.edu	37	chr22	41569718	41569718	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagtaggggcaacaagaagaAacccgggatgcccaatgtat	13	8	0	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr22:41569718A>G	ENST00000263253.7	+	29	5928	c.4709A>G	c.(4708-4710)aAa>aGa	p.K1570R	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1570	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AACAAGAAGAAACCCGGGATG	0.448			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											153	161	158					22																	41569718		2203	4300	6503	39899664	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4709A>G	22.37:g.41569718A>G	ENSP00000263253:p.Lys1570Arg		39899664	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.341006	0.81911	.	.	ENSG00000100393	ENST00000263253	D	0.93659	-3.26	5.52	5.52	0.82312	.	0.000000	0.48767	D	0.000171	D	0.96713	0.8927	M	0.83692	2.655	0.46131	D	0.998889	D	0.76494	0.999	D	0.83275	0.996	D	0.96837	0.9615	10	0.51188	T	0.08	-13.6072	15.643	0.77020	1.0:0.0:0.0:0.0	.	1570	Q09472	EP300_HUMAN	R	1570	ENSP00000263253:K1570R	ENSP00000263253:K1570R	K	+	2	0	EP300	39899664	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.237000	0.95368	2.094000	0.63399	0.533000	0.62120	AAA		0.448	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41569718	A	G	41569718	3	3	38	1	0	0	0	0	1	0	0	0	5161	14	1	4	4823	4	EP300	22	41569718	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	11531529	41569718	9734848	158	3452										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42293161	42293161	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agctccgtgctcaagtccgcCctgggtaagcacctgcgggt	13	14	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr22:42293161C>T	ENST00000361204.4	+	14	2767	c.2601C>T	c.(2599-2601)gcC>gcT	p.A867A	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	867					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TCAAGTCCGCCCTGGGTAAGC	0.567																																																0			22											35	35	35					22																	42293161		2203	4300	6503	40623107	SO:0001819	synonymous_variant	6721			U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2601C>T	22.37:g.42293161C>T			40623107	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Silent	SNP	ENST00000361204.4	37	CCDS14023.1																																																																																				0.567	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42293161	C	T	42293161	2	4	38	1	0	0	0	0	0	0	0	1	15181	610	22	3		3	SREBF2	22	42293161	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	723443	42293161	9011405	159	3453										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45767392	45767392	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttctttaattcttcgttgtcGttccttgattccttcactca	4	11	4	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chr22:45767392G>A	ENST00000357450.4	-	14	2271	c.2272C>T	c.(2272-2274)Cga>Tga	p.R758*	SMC1B_ENST00000404354.3_Nonsense_Mutation_p.R758*	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	758			R -> Q (in dbSNP:rs9614653).		meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTTCGTTGTCGTTCCTTGATT	0.284																																																0			22											102	92	95					22																	45767392		1814	4070	5884	44146056	SO:0001587	stop_gained	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2272C>T	22.37:g.45767392G>A	ENSP00000350036:p.Arg758*		44146056	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Nonsense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	G	35	5.427948	0.96131	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	.	.	.	5.66	3.5	0.40072	.	0.228496	0.29995	N	0.010671	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	6.2413	0.20793	0.0962:0.0:0.6123:0.2915	.	.	.	.	X	758	.	ENSP00000350036:R758X	R	-	1	2	SMC1B	44146056	0.960000	0.32886	0.966000	0.40874	0.311000	0.27955	2.622000	0.46427	1.394000	0.46624	0.655000	0.94253	CGA		0.284	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		A	45767392	G	A	45767392	4	1	38	1	0	0	0	0	0	1	0	0	14819	1153	40	1	1483	1	SMC1B	22	45767392	Nonsense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	3474231	45767392	5537174	160	3454										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938160	12938160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agcctctggggcatttttaaCgatgctgccccgcttagaaa	10	11	1	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:12938160C>T	ENST00000218032.6	+	2	1088	c.1001C>T	c.(1000-1002)aCg>aTg	p.T334M	TLR8_ENST00000311912.5_Missense_Mutation_p.T352M	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	334					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	GCATTTTTAACGATGCTGCCC	0.368																																																0			X											68	71	70					X																	12938160		2200	4294	6494	12848081	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1001C>T	X.37:g.12938160C>T	ENSP00000218032:p.Thr334Met		12848081	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	7.186	0.590625	0.13812	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.00995	5.46;5.46	5.29	2.52	0.30459	.	0.183248	0.26297	N	0.025182	T	0.02888	0.0086	M	0.80508	2.5	0.09310	N	1	D;D	0.76494	0.999;0.999	P;P	0.58577	0.841;0.841	T	0.38001	-0.9681	10	0.36615	T	0.2	.	4.1868	0.10402	0.2246:0.4626:0.0:0.3127	.	334;352	Q9NR97;D1CS70	TLR8_HUMAN;.	M	334;352	ENSP00000218032:T334M;ENSP00000312082:T352M	ENSP00000218032:T334M	T	+	2	0	TLR8	12848081	0.000000	0.05858	0.030000	0.17652	0.151000	0.21798	-0.613000	0.05610	0.542000	0.28846	-0.192000	0.12808	ACG		0.368	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		T	12938160	C	T	12938160	3	4	38	1	0	0	0	0	1	0	0	0	15996	536	19	1	1007	1	TLR8	23	12938160	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10		12938160	142332400	161	3455										
SYTL5	94122	hgsc.bcm.edu	37	chrX	37893211	37893211	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gagaaggaaatgatcctgggCgtcctaaagagagatgaata	13	5	0	5	rs73632432	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:37893211C>T	ENST00000357972.5	+	2	615	c.69C>T	c.(67-69)ggC>ggT	p.G23G	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Silent_p.G23G|SYTL5_ENST00000456733.2_Silent_p.G23G			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	23	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						TGATCCTGGGCGTCCTAAAGA	0.373													c|||	14	0.00370861	0.0106	0	3775	,	,		15299	0		0	False		,,,				2504	0															0			X						T	,,	43,3790		0,32,11,1599,560	76	68	70		69,69,69	0.5	1	X	dbSNP_130	70	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	0,32,11,4027,2432	TT,TC,T,CC,C		0.0,1.1218,0.4072	,,	23/753,23/731,23/731	37893211	43,10518	2202	4300	6502	37778155	SO:0001819	synonymous_variant	94122				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"exophilin 9"						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.69C>T	X.37:g.37893211C>T			37778155	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																				0.373	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		T	37893211	C	T	37893211	2	4	38	1	0	0	0	0	0	0	0	1	15525	755	27	1		1	SYTL5	23	37893211	Silent	SNP	C	TCGA-AG-3732-01A-11D-1657-10	24955051	37893211	117377349	162	3456										
WDR13	64743	hgsc.bcm.edu	37	chrX	48457274	48457274	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	agcgctacgggcccctctccGagccaggcagtgctcgtgcc	13	17	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:48457274G>A	ENST00000218056.5	+	2	716	c.211G>A	c.(211-213)Gag>Aag	p.E71K	WDR13_ENST00000492715.1_3'UTR|WDR13_ENST00000376729.5_Missense_Mutation_p.E71K	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	71						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						GCCCCTCTCCGAGCCAGGCAG	0.672																																																0			X											24	19	21					X																	48457274		2203	4296	6499	48342218	SO:0001583	missense	64743			AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.211G>A	X.37:g.48457274G>A	ENSP00000218056:p.Glu71Lys		48342218	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	37	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800191	0.70567	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.73789	-0.78;-0.78	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.64649	0.2617	M	0.65498	2.005	0.58432	D	0.999999	P	0.50710	0.938	B	0.32465	0.146	T	0.66492	-0.5910	10	0.16896	T	0.51	-11.6698	13.6403	0.62246	0.0:0.0:1.0:0.0	.	71	Q9H1Z4	WDR13_HUMAN	K	71	ENSP00000365919:E71K;ENSP00000218056:E71K	ENSP00000218056:E71K	E	+	1	0	WDR13	48342218	1.000000	0.71417	0.774000	0.31636	0.955000	0.61496	8.822000	0.92013	2.081000	0.62600	0.523000	0.50628	GAG		0.672	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			A	48457274	G	A	48457274	3	1	38	1	0	0	0	0	1	0	0	0	17315	1059	37	1	217	1	WDR13	23	48457274	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	10564063	48457274	106813286	163	3457										
WNK3	65267	hgsc.bcm.edu	37	chrX	54265376	54265376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ccagctttttaatttgcgagTccaggatttcttgctaatag	8	8	1	0			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:54265376T>C	ENST00000375159.2	-	17	3807	c.3808A>G	c.(3808-3810)Act>Gct	p.T1270A	WNK3_ENST00000375169.3_Intron|WNK3_ENST00000354646.2_Missense_Mutation_p.T1270A			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1270					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AATTTGCGAGTCCAGGATTTC	0.453																																																0			X											80	70	73					X																	54265376		2203	4300	6503	54282101	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3808A>G	X.37:g.54265376T>C	ENSP00000364301:p.Thr1270Ala		54282101	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.810068	0.32053	.	.	ENSG00000196632	ENST00000354646;ENST00000375159	T;T	0.74002	-0.8;-0.8	5.02	5.02	0.67125	.	0.126294	0.34986	N	0.003534	T	0.55497	0.1924	N	0.19112	0.55	0.30162	N	0.802128	B	0.23891	0.093	B	0.21917	0.037	T	0.50972	-0.8764	10	0.19147	T	0.46	-9.9764	7.7853	0.29089	0.0:0.0976:0.0:0.9024	.	1270	Q9BYP7	WNK3_HUMAN	A	1270	ENSP00000346667:T1270A;ENSP00000364301:T1270A	ENSP00000346667:T1270A	T	-	1	0	WNK3	54282101	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.208000	0.65203	1.672000	0.50884	0.437000	0.28790	ACT		0.453	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		C	54265376	T	C	54265376	3	2	38	1	0	0	0	0	1	0	0	0	17419	1667	58	4	1622	4	WNK3	23	54265376	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	5808102	54265376	101005184	164	3458										
SLC16A2	6567	hgsc.bcm.edu	37	chrX	73751291	73751291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tcaaaggatgttcaagaaagAgcagagagattccagcaagg	12	6	2	4			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:73751291A>G	ENST00000587091.1	+	6	1700	c.1523A>G	c.(1522-1524)gAg>gGg	p.E508G	SLC16A2_ENST00000276033.5_Missense_Mutation_p.E582G	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	508					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	TTCAAGAAAGAGCAGAGAGAT	0.547																																																0			X											106	92	97					X																	73751291		2203	4300	6503	73668016	SO:0001583	missense	6567				CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"Solute carriers"	10923	protein-coding gene	gene with protein product		300095	"solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)", "Allan-Herndon-Dudley syndrome", "solute carrier family 16 (monocarboxylic acid transporters), member 2", "mental retardation, X-linked 22", "solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.1523A>G	X.37:g.73751291A>G	ENSP00000465734:p.Glu508Gly		73668016	Q7Z797	Missense_Mutation	SNP	ENST00000587091.1	37	CCDS14426.2	.	.	.	.	.	.	.	.	.	.	A	12.67	2.008991	0.35415	.	.	ENSG00000147100	ENST00000276033	T	0.11712	2.75	5.3	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.775103	0.12099	N	0.499630	T	0.07728	0.0194	N	0.17082	0.46	0.30984	N	0.722118	B	0.12013	0.005	B	0.15052	0.012	T	0.05903	-1.0857	10	0.45353	T	0.12	.	9.7488	0.40464	0.9179:0.0:0.0821:0.0	.	508	P36021	MOT8_HUMAN	G	582	ENSP00000276033:E582G	ENSP00000276033:E582G	E	+	2	0	SLC16A2	73668016	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.510000	0.60455	1.770000	0.52166	0.430000	0.28490	GAG		0.547	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3			G	73751291	A	G	73751291	3	3	38	1	0	0	0	0	1	0	0	0	14445	304	11	4	1767	4	SLC16A2	23	73751291	Missense_Mutation	SNP	A	TCGA-AG-3732-01A-11D-1657-10	19485915	73751291	81519269	165	3459										
ATP7A	538	hgsc.bcm.edu	37	chrX	77284798	77284799	+	Frame_Shift_Ins	INS	-	-	A													0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	gataatacgatttgctttccINSaagcctctatcacagttctg							TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:77284798_77284799insA	ENST00000341514.6	+	15	3123_3124	c.2968_2969insA	c.(2968-2970)caafs	p.Q990fs	ATP7A_ENST00000343533.5_Frame_Shift_Ins_p.Q912fs|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	990					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATTTGCTTTCCAAGCCTCTATC	0.431																																																0			X																																								77171455	SO:0001589	frameshift_variant	538			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2970dupA	X.37:g.77284800_77284800dupA	ENSP00000345728:p.Gln990fs		77171454	B1AT72|O00227|O00745|Q9BYY8	Frame_Shift_Ins	INS	ENST00000341514.6	37	CCDS35339.1																																																																																				0.431	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		A	77284799	-	A	77284798	7	5	38	1	0	1	1	0	0	0	0	0	1191	595	21	0	3022	0	ATP7A	23	77284798	Frame_Shift_Ins	INS	-	TCGA-AG-3732-01A-11D-1657-10	3533507	77284798	77985762	166	3460										
ODZ1	10178	hgsc.bcm.edu	37	chrX	124029955	124029955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	tccacattcttagtgcatggTcaggtgaggcagcaccttct	10	11	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:124029955T>C	ENST00000371130.3	-	2	416	c.353A>G	c.(352-354)gAc>gGc	p.D118G	TENM1_ENST00000422452.2_Missense_Mutation_p.D118G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	118	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TAGTGCATGGTCAGGTGAGGC	0.502																																																0			X											277	225	242					X																	124029955		2203	4300	6503	123857636	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.353A>G	X.37:g.124029955T>C	ENSP00000360171:p.Asp118Gly		123857636	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665041	0.47677	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.30714	1.52;1.52	5.56	5.56	0.83823	Teneurin intracellular, N-terminal (2);	0.240686	0.33309	N	0.005054	T	0.25082	0.0609	N	0.22421	0.69	0.44789	D	0.997792	B;B;B	0.16396	0.017;0.017;0.017	B;B;B	0.22152	0.038;0.038;0.038	T	0.04178	-1.0971	10	0.72032	D	0.01	.	14.9145	0.70785	0.0:0.0:0.0:1.0	.	118;118;118	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	G	118	ENSP00000360171:D118G;ENSP00000403954:D118G	ENSP00000360171:D118G	D	-	2	0	ODZ1	123857636	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	3.853000	0.55941	1.972000	0.57404	0.486000	0.48141	GAC		0.502	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	124029955	T	C	124029955	3	2	38	1	0	0	0	0	1	0	0	0	10865	1667	58	4	7969	4	ODZ1	23	124029955	Missense_Mutation	SNP	T	TCGA-AG-3732-01A-11D-1657-10	46745157	124029955	31240605	167	3461										
GPR112	139378	hgsc.bcm.edu	37	chrX	135427606	135427606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttattgatgctgaagctacaCgtacagccttaactcctgaa	7	10	0	3	rs151008495	byFrequency	TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:135427606C>T	ENST00000394143.1	+	6	2032	c.1741C>T	c.(1741-1743)Cgt>Tgt	p.R581C	GPR112_ENST00000412101.1_Missense_Mutation_p.R376C|GPR112_ENST00000287534.4_Missense_Mutation_p.R518C|GPR112_ENST00000394141.1_Missense_Mutation_p.R376C|GPR112_ENST00000370652.1_Missense_Mutation_p.R581C	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	581					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TGAAGCTACACGTACAGCCTT	0.428																																																0			X							CYS/ARG	2,3833		0,2,0,1630,571	105	84	91		1741	-3.5	0	X	dbSNP_134	91	7,6721		0,5,2,2423,1870	yes	missense	GPR112	NM_153834.3	180	0,7,2,4053,2441	TT,TC,T,CC,C		0.104,0.0522,0.0852	benign	581/3081	135427606	9,10554	2203	4300	6503	135255272	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1741C>T	X.37:g.135427606C>T	ENSP00000377699:p.Arg581Cys		135255272	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	8.639	0.895545	0.17686	5.22E-4	0.00104	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.32023	1.5;1.5;1.47;1.61;1.47	3.56	-3.46	0.04767	.	.	.	.	.	T	0.09024	0.0223	N	0.08118	0	0.09310	N	1	P;B;B	0.39748	0.686;0.067;0.277	B;B;B	0.17098	0.017;0.004;0.005	T	0.16100	-1.0414	9	0.54805	T	0.06	.	3.2266	0.06734	0.3175:0.2416:0.0:0.4409	.	518;376;581	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	C	581;581;376;518;376	ENSP00000377699:R581C;ENSP00000359686:R581C;ENSP00000416526:R376C;ENSP00000287534:R518C;ENSP00000377697:R376C	ENSP00000287534:R518C	R	+	1	0	GPR112	135255272	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.616000	0.05591	-0.924000	0.03780	-0.613000	0.04052	CGT		0.428	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135427606	C	T	135427606	3	4	38	1	0	0	0	0	1	0	0	0	6649	536	19	1	1751	1	GPR112	23	135427606	Missense_Mutation	SNP	C	TCGA-AG-3732-01A-11D-1657-10	11397651	135427606	19842954	168	3462										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905479	144905479	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	ttttctcacctgcccgtgaaAggggttctggatcagctccc	10	13	3	1			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:144905479A>G	ENST00000370490.1	+	1	5791	c.1536A>G	c.(1534-1536)aaA>aaG	p.K512K	SLITRK2_ENST00000447897.2_Silent_p.K512K|SLITRK2_ENST00000413937.2_Silent_p.K512K|SLITRK2_ENST00000428560.2_Silent_p.K512K|SLITRK2_ENST00000434188.2_Silent_p.K512K			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	512					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.K512N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TGCCCGTGAAAGGGGTTCTGG	0.507																																																1	Substitution - Missense(1)	ovary(1)	X											73	77	76					X																	144905479		2203	4300	6503	144713171	SO:0001819	synonymous_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1536A>G	X.37:g.144905479A>G			144713171	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																				0.507	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		G	144905479	A	G	144905479	2	3	38	1	0	0	0	0	0	0	0	1	14780	69	3	4		4	SLITRK2	23	144905479	Silent	SNP	A	TCGA-AG-3732-01A-11D-1657-10	9477873	144905479	10365081	169	3463										
F8	2157	hgsc.bcm.edu	37	chrX	154159114	154159114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297619047619048	5	1	0.573727933541018	0	0.612624742594646	0.020979020979021	0.170629370629371	0	acctaccactctctgttgacGatacattttttccccatgaa	4	13	1	2			TCGA-AG-3732-01A-11D-1657-10	TCGA-AG-3732-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9a627bd7-6de9-42dd-8e31-7a1985e9d9a3	7c5a47b4-4ea6-42cc-8e3f-8150c231f796	g.chrX:154159114G>A	ENST00000360256.4	-	14	3151	c.2951C>T	c.(2950-2952)tCg>tTg	p.S984L		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	984	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTCTGTTGACGATACATTTTT	0.363																																																0			X											71	70	71					X																	154159114		2203	4299	6502	153812308	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.2951C>T	X.37:g.154159114G>A	ENSP00000353393:p.Ser984Leu		153812308	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.242647	0.00022	.	.	ENSG00000185010	ENST00000360256	D	0.99214	-5.57	5.07	-6.94	0.01633	.	1.487810	0.04065	N	0.307122	D	0.94978	0.8375	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	D	0.93750	0.7058	10	0.18710	T	0.47	-0.0037	11.0531	0.47903	0.242:0.111:0.647:0.0	.	984	P00451	FA8_HUMAN	L	984	ENSP00000353393:S984L	ENSP00000353393:S984L	S	-	2	0	F8	153812308	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.104000	0.10923	-2.125000	0.00821	-3.173000	0.00056	TCG		0.363	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			A	154159114	G	A	154159114	3	1	38	1	0	0	0	0	1	0	0	0	5363	1059	37	1	4184	1	F8	23	154159114	Missense_Mutation	SNP	G	TCGA-AG-3732-01A-11D-1657-10	9253635	154159114	1111446	170	3464										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3413261	3413262	+	Frame_Shift_Ins	INS	-	-	G													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aacccagtggggcagcggcaINSggcccccgtggccgcatcac							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:3413261_3413262insG	ENST00000356575.4	-	29	3925_3926	c.3699_3700insC	c.(3697-3702)gcctgcfs	p.C1234fs	MEGF6_ENST00000294599.4_Frame_Shift_Ins_p.C999fs	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1234	EGF-like 22. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GGGCAGCGGCAGGCCCCCGTGG	0.688																																					Ovarian(73;978 3658)											0			1																																								3403122	SO:0001589	frameshift_variant	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3700dupC	1.37:g.3413263_3413263dupG	ENSP00000348982:p.Cys1234fs		3403121	Q4AC86|Q5VV39	Frame_Shift_Ins	INS	ENST00000356575.4	37	CCDS41237.1																																																																																				0.688	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		G	3413262	-	G	3413261	7	5	39	1	0	1	1	0	0	0	0	0	9492	188	7	0	961	0	MEGF6	1	3413261	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10		3413261	245837360	1	3465										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18807550	18807550	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggcaaggtggtgctgtcagcCgctgccctgctcctggtgac	15	13	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:18807550C>A	ENST00000400664.1	+	1	127	c.75C>A	c.(73-75)gcC>gcA	p.A25A		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	25						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGCTGTCAGCCGCTGCCCTGC	0.642																																																0			1											40	46	44					1																	18807550		2062	4216	6278	18680137	SO:0001819	synonymous_variant	127707			AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.75C>A	1.37:g.18807550C>A			18680137	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																				0.642	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		A	18807550	C	A	18807550	2	1	39	1	0	0	0	0	0	0	0	1	8381	639	23	2		2	KLHDC7A	1	18807550	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	15394289	18807550	230443071	2	3466										
HPCA	3208	hgsc.bcm.edu	37	chr1	33354678	33354678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	caacttctttccctatggtgAcgcctccaagtttgccgagc	8	14	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:33354678A>G	ENST00000373467.3	+	2	281	c.179A>G	c.(178-180)gAc>gGc	p.D60G	HPCA_ENST00000480118.1_3'UTR	NM_002143.2	NP_002134.2	P84074	HPCA_HUMAN	hippocalcin	60	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				inner ear development (GO:0048839)		actin binding (GO:0003779)|calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CCCTATGGTGACGCCTCCAAG	0.537																																																0			1											122	107	112					1																	33354678		2203	4300	6503	33127265	SO:0001583	missense	3208			BC001777	CCDS370.1	1p35-p34.2	2013-01-10			ENSG00000121905	ENSG00000121905		"EF-hand domain containing"	5144	protein-coding gene	gene with protein product		142622				8166736, 9931466	Standard	NM_002143		Approved		uc001bwh.3	P84074	OTTHUMG00000004017	ENST00000373467.3:c.179A>G	1.37:g.33354678A>G	ENSP00000362566:p.Asp60Gly		33127265	B2R9T3|D3DPQ7|P32076|P41211|P70510	Missense_Mutation	SNP	ENST00000373467.3	37	CCDS370.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376287	0.82682	.	.	ENSG00000121905	ENST00000373467	T	0.30714	1.52	5.22	5.22	0.72569	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.60274	0.2256	M	0.91872	3.25	0.80722	D	1	D	0.60575	0.988	P	0.60949	0.881	T	0.70490	-0.4857	10	0.87932	D	0	.	14.3821	0.66919	1.0:0.0:0.0:0.0	.	60	P84074	HPCA_HUMAN	G	60	ENSP00000362566:D60G	ENSP00000362566:D60G	D	+	2	0	HPCA	33127265	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.053000	0.93860	2.333000	0.79357	0.533000	0.62120	GAC		0.537	HPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011480.1	NM_002143		G	33354678	A	G	33354678	3	3	39	1	0	0	0	0	1	0	0	0	7350	275	10	4	181	4	HPCA	1	33354678	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	14547128	33354678	215895943	3	3467										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42045588	42045588	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aaacttatgcaccaaccagcGtaaacagaggacctcctatc	6	13	0	1	rs138363884	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:42045588G>A	ENST00000372583.1	-	4	5766	c.4881C>T	c.(4879-4881)taC>taT	p.Y1627Y	HIVEP3_ENST00000429157.2_Silent_p.Y1627Y|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Silent_p.Y1627Y|HIVEP3_ENST00000247584.5_Silent_p.Y1627Y	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1627					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ACCAACCAGCGTAAACAGAGG	0.473																																																0			1						G	,	0,4406		0,0,2203	142	117	125		4881,4881	4.7	1	1	dbSNP_134	125	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	,	1627/2406,1627/2407	42045588	7,12999	2203	4300	6503	41818175	SO:0001819	synonymous_variant	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.4881C>T	1.37:g.42045588G>A			41818175	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																				0.473	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	42045588	G	A	42045588	2	1	39	1	0	0	0	0	0	0	0	1	7209	1140	40	1		1	HIVEP3	1	42045588	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	8690910	42045588	207205033	4	3468										
WDR78	79819	hgsc.bcm.edu	37	chr1	67359090	67359090	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aacatcagttccatttatgtCaaatacctgttaaaaatggt	5	7	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:67359090C>A	ENST00000371026.3	-	3	407	c.352G>T	c.(352-354)Gac>Tac	p.D118Y	WDR78_ENST00000371023.3_Missense_Mutation_p.D118Y|WDR78_ENST00000371022.3_Missense_Mutation_p.D118Y|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	118					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CCATTTATGTCAAATACCTGT	0.338																																																0			1											111	107	109					1																	67359090		2203	4300	6503	67131678	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.352G>T	1.37:g.67359090C>A	ENSP00000360065:p.Asp118Tyr		67131678	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625795	0.46840	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	D;T;T	0.81659	-1.52;-0.07;-0.62	5.17	4.26	0.50523	.	0.047632	0.85682	D	0.000000	D	0.83764	0.5325	M	0.69823	2.125	0.42547	D	0.99309	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.71656	0.971;0.974;0.974	D	0.85926	0.1449	10	0.87932	D	0	-28.5313	10.1303	0.42674	0.0:0.9065:0.0:0.0935	.	118;118;118	Q5TAD8;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	Y	118	ENSP00000360065:D118Y;ENSP00000360062:D118Y;ENSP00000360061:D118Y	ENSP00000360061:D118Y	D	-	1	0	WDR78	67131678	0.940000	0.31905	0.065000	0.19835	0.002000	0.02628	2.377000	0.44300	1.312000	0.45043	0.650000	0.86243	GAC		0.338	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		A	67359090	C	A	67359090	3	1	39	1	0	0	0	0	1	0	0	0	17368	826	29	2	2311	2	WDR78	1	67359090	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	25313502	67359090	181891531	5	3469										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060606	111060606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tccaccatgaagaaagggtcGgtgaacatggtctgggagag	15	7	1	4	rs142311370	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:111060606G>A	ENST00000369771.2	-	1	1191	c.804C>T	c.(802-804)acC>acT	p.T268T		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	268					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	AGAAAGGGTCGGTGAACATGG	0.552													A|||	4	0.000798722	0	0.0014	5008	,	,		21380	0		0	False		,,,				2504	0.0031															0			1						A		1,4405	826.1+/-416.6	0,1,2202	191	150	164		804	-11.6	0.1	1	dbSNP_134	164	9,8591	818.9+/-406.8	0,9,4291	no	coding-synonymous	KCNA10	NM_005549.2		0,10,6493	AA,AG,GG		0.1047,0.0227,0.0769		268/512	111060606	10,12996	2203	4300	6503	110862129	SO:0001819	synonymous_variant	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.804C>T	1.37:g.111060606G>A			110862129		Silent	SNP	ENST00000369771.2	37	CCDS826.1																																																																																				0.552	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		A	111060606	G	A	111060606	2	1	39	1	0	0	0	0	0	0	0	1	8023	1103	39	1		1	KCNA10	1	111060606	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	43701516	111060606	138190015	6	3470										
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957138	111957138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggatttctttttttagagaaAgaggacttgtttgaggggtt	13	2	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:111957138A>G	ENST00000369732.3	-	11	2040	c.1985T>C	c.(1984-1986)cTt>cCt	p.L662P		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	662			L -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.L662H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TTTTAGAGAAAGAGGACTTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	66	64					1																	111957138		2203	4300	6503	111758661	SO:0001583	missense	5016			U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1985T>C	1.37:g.111957138A>G	ENSP00000358747:p.Leu662Pro		111758661	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.342821	0.41498	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.06449	3.3	4.92	-4.54	0.03452	.	14.586000	0.00166	N	0.000009	T	0.01558	0.0050	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.49390	-0.8945	10	0.87932	D	0	.	8.6962	0.34298	0.2698:0.153:0.5772:0.0	.	662;726	Q12889;Q59HH5	OVGP1_HUMAN;.	P	662;726;470	ENSP00000358747:L662P	ENSP00000358743:L726P	L	-	2	0	OVGP1	111758661	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.100000	0.10990	-0.749000	0.04747	-0.472000	0.04984	CTT		0.448	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		G	111957138	A	G	111957138	3	3	39	1	0	0	0	0	1	0	0	0	11356	72	3	4	55	4	OVGP1	1	111957138	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	896532	111957138	137293483	7	3471										
ST7L	54879	hgsc.bcm.edu	37	chr1	113161717	113161717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aacagctgcggcttcacccaCgccgccacggtccgccatct	9	19	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:113161717C>T	ENST00000358039.4	-	1	323	c.19G>A	c.(19-21)Gtg>Atg	p.V7M	ST7L_ENST00000343210.7_Missense_Mutation_p.V7M|ST7L_ENST00000360743.4_Missense_Mutation_p.V7M|ST7L_ENST00000544629.1_Missense_Mutation_p.V7M|ST7L_ENST00000369668.2_Missense_Mutation_p.V7M|ST7L_ENST00000490067.1_Missense_Mutation_p.V7M|ST7L_ENST00000538187.1_5'Flank|CAPZA1_ENST00000263168.3_5'Flank|ST7L_ENST00000463235.1_Intron|ST7L_ENST00000369666.1_Missense_Mutation_p.V7M|ST7L_ENST00000543570.1_Missense_Mutation_p.V7M|ST7L_ENST00000369669.1_5'Flank	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	7					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTCACCCACGCCGCCACGG	0.682																																																0			1											18	18	18					1																	113161717		2196	4282	6478	112963240	SO:0001583	missense	54879			AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.19G>A	1.37:g.113161717C>T	ENSP00000350734:p.Val7Met		112963240	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	C	6.768	0.510616	0.12883	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000544629;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000543570	T;T;T;T;T;T;T;T	0.32023	2.44;2.45;2.19;2.44;2.2;2.2;2.18;1.47	5.18	-1.44	0.08856	.	1.533070	0.03499	N	0.217775	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B;B	0.27594	0.058;0.182;0.096;0.096;0.096;0.096;0.096;0.058	B;B;B;B;B;B;B;B	0.21360	0.01;0.015;0.034;0.023;0.023;0.034;0.018;0.015	T	0.28332	-1.0047	10	0.46703	T	0.11	21.0369	5.4488	0.16550	0.4216:0.3578:0.2206:0.0	.	7;7;7;7;7;7;7;7	B7Z8V6;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;.;.;.;ST7L_HUMAN	M	7	ENSP00000350734:V7M;ENSP00000353972:V7M;ENSP00000445499:V7M;ENSP00000417140:V7M;ENSP00000358682:V7M;ENSP00000345312:V7M;ENSP00000358680:V7M;ENSP00000444088:V7M	ENSP00000345312:V7M	V	-	1	0	ST7L	112963240	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.183000	0.09712	-0.060000	0.13132	-0.264000	0.10439	GTG		0.682	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			T	113161717	C	T	113161717	3	4	39	1	0	0	0	0	1	0	0	0	15269	536	19	1	1807	1	ST7L	1	113161717	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	1204579	113161717	136088904	8	3472										
BCL2L15	440603	hgsc.bcm.edu	37	chr1	114429214	114429214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagaagcttccaattctccgTtgaactggtcacccaacatc	6	14	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:114429214T>C	ENST00000393316.3	-	2	365	c.194A>G	c.(193-195)aAc>aGc	p.N65S	AP4B1-AS1_ENST00000419536.1_RNA|BCL2L15_ENST00000488450.1_Intron|BCL2L15_ENST00000471267.1_Missense_Mutation_p.N65S|BCL2L15_ENST00000393320.3_Intron	NM_001010922.2	NP_001010922.1	Q5TBC7	B2L15_HUMAN	BCL2-like 15	65					apoptotic process (GO:0006915)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)	9	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-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)		CAATTCTCCGTTGAACTGGTC	0.423																																																0			1											129	112	118					1																	114429214		2203	4300	6503	114230737	SO:0001583	missense	440603				CCDS30809.1	1p13.2	2014-03-07			ENSG00000188761	ENSG00000188761			33624	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 178"	C1orf178		12700646, 15961081, 16690252, 17412810	Standard	NM_001010922		Approved	Bfk, FLJ22588	uc001edw.3	Q5TBC7	OTTHUMG00000011940	ENST00000393316.3:c.194A>G	1.37:g.114429214T>C	ENSP00000376992:p.Asn65Ser		114230737	A0PJY6|A8K074|I6LA82	Missense_Mutation	SNP	ENST00000393316.3	37	CCDS30809.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.500187	0.44455	.	.	ENSG00000188761	ENST00000393316;ENST00000471267	T;T	0.04119	3.7;3.7	5.48	5.48	0.80851	.	0.051302	0.85682	D	0.000000	T	0.08670	0.0215	M	0.72118	2.19	0.40732	D	0.982752	D	0.59357	0.985	P	0.54270	0.747	T	0.01185	-1.1425	10	0.87932	D	0	.	13.1044	0.59239	0.0:0.0:0.0:1.0	.	65	Q5TBC7	B2L15_HUMAN	S	65	ENSP00000376992:N65S;ENSP00000417458:N65S	ENSP00000376992:N65S	N	-	2	0	BCL2L15	114230737	0.998000	0.40836	0.702000	0.30337	0.002000	0.02628	4.112000	0.57845	2.094000	0.63399	0.528000	0.53228	AAC		0.423	BCL2L15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033026.2	NM_001010922		C	114429214	T	C	114429214	3	2	39	1	0	0	0	0	1	0	0	0	1374	1725	60	4	309	4	BCL2L15	1	114429214	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	1267497	114429214	134821407	9	3473										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145536014	145536014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcagacatgaggttcaccgcAtcactggatgaatggactgc	11	10	3	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:145536014A>G	ENST00000369304.3	+	17	2281	c.2106A>G	c.(2104-2106)gcA>gcG	p.A702A	ITGA10_ENST00000538811.1_Silent_p.A571A|ITGA10_ENST00000539363.1_Silent_p.A559A	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	702			A -> T (in dbSNP:rs35515885).		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGTTCACCGCATCACTGGATG	0.542																																																0			1											149	140	143					1																	145536014		2203	4300	6503	144247371	SO:0001819	synonymous_variant	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2106A>G	1.37:g.145536014A>G			144247371	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Silent	SNP	ENST00000369304.3	37	CCDS918.1																																																																																				0.542	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		G	145536014	A	G	145536014	2	3	39	1	0	0	0	0	0	0	0	1	7894	204	8	4		4	ITGA10	1	145536014	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	31106800	145536014	103714607	10	3474										
SPRR2E	6704	hgsc.bcm.edu	37	chr1	153066109	153066109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtgggcagggctgtggacacTttggtggtgggcagggctca	20	7	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:153066109T>C	ENST00000368751.1	-	2	193	c.119A>G	c.(118-120)aAg>aGg	p.K40R	SPRR2B_ENST00000368752.4_Intron|SPRR2E_ENST00000368750.3_Missense_Mutation_p.K40R			P22531	SPR2E_HUMAN	small proline-rich protein 2E	40	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGTGGACACTTTGGTGGTGG	0.622																																																0			1											151	148	149					1																	153066109		2203	4298	6501	151332733	SO:0001583	missense	6704			AF333955	CCDS30866.1	1q21-q22	2008-02-05			ENSG00000203785	ENSG00000203785			11265	protein-coding gene	gene with protein product						8325635	Standard	NM_001024209		Approved		uc001fbh.3	P22531	OTTHUMG00000014397	ENST00000368751.1:c.119A>G	1.37:g.153066109T>C	ENSP00000357740:p.Lys40Arg		151332733	Q5T9T4|Q96RM2	Missense_Mutation	SNP	ENST00000368751.1	37	CCDS30866.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483727	0.26598	.	.	ENSG00000203785	ENST00000368751;ENST00000368750	T;T	0.32753	1.44;1.44	4.3	1.89	0.25635	.	0.942785	0.08679	N	0.909641	T	0.05181	0.0138	.	.	.	0.09310	N	1	P	0.36909	0.573	B	0.33521	0.165	T	0.35599	-0.9782	9	0.21014	T	0.42	.	3.6516	0.08205	0.191:0.1085:0.0:0.7004	.	40	P22531	SPR2E_HUMAN	R	40	ENSP00000357740:K40R;ENSP00000357739:K40R	ENSP00000357739:K40R	K	-	2	0	SPRR2E	151332733	0.166000	0.22962	0.005000	0.12908	0.446000	0.32137	0.850000	0.27737	0.088000	0.17205	0.333000	0.21579	AAG		0.622	SPRR2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040054.1			C	153066109	T	C	153066109	3	2	39	1	0	0	0	0	1	0	0	0	15139	1609	56	4	103	4	SPRR2E	1	153066109	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	7530095	153066109	96184512	11	3475										
CREB3L4	148327	hgsc.bcm.edu	37	chr1	153941071	153941071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aggatatcttctcgacaggaTccgtcctggagctgggactc	12	11	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:153941071T>C	ENST00000368607.3	+	2	336	c.70T>C	c.(70-72)Tcc>Ccc	p.S24P	CREB3L4_ENST00000368600.3_Missense_Mutation_p.S24P|CREB3L4_ENST00000271889.4_Missense_Mutation_p.S24P|CREB3L4_ENST00000368603.1_Missense_Mutation_p.S24P|RP11-422P24.10_ENST00000608147.1_RNA|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000368601.1_Missense_Mutation_p.S24P|CREB3L4_ENST00000405694.3_5'UTR	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	24					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	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)			CTCGACAGGATCCGTCCTGGA	0.632																																																0			1											64	66	65					1																	153941071		2203	4300	6503	152207695	SO:0001583	missense	148327			AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"basic leucine zipper proteins"	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.70T>C	1.37:g.153941071T>C	ENSP00000357596:p.Ser24Pro		152207695	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	37	CCDS1056.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.163709	0.38217	.	.	ENSG00000143578	ENST00000449724;ENST00000368607;ENST00000271889;ENST00000368601;ENST00000368603;ENST00000368600;ENST00000431292	T;T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3;1.3	4.05	2.9	0.33743	.	0.441406	0.19606	N	0.110280	T	0.34221	0.0890	L	0.50333	1.59	0.80722	D	1	D;B;B	0.67145	0.996;0.001;0.003	D;B;B	0.65573	0.936;0.001;0.002	T	0.10636	-1.0621	10	0.44086	T	0.13	.	7.6103	0.28126	0.0:0.0:0.2173:0.7827	.	24;24;24	B4E2G3;Q5T4L0;Q8TEY5	.;.;CR3L4_HUMAN	P	24	ENSP00000391847:S24P;ENSP00000357596:S24P;ENSP00000271889:S24P;ENSP00000357590:S24P;ENSP00000357592:S24P;ENSP00000357589:S24P;ENSP00000402308:S24P	ENSP00000271889:S24P	S	+	1	0	CREB3L4	152207695	0.695000	0.27747	0.992000	0.48379	0.654000	0.38779	-0.206000	0.09398	0.864000	0.35578	0.459000	0.35465	TCC		0.632	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898		C	153941071	T	C	153941071	3	2	39	1	0	0	0	0	1	0	0	0	3865	1435	50	4	72	4	CREB3L4	1	153941071	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	874962	153941071	95309550	12	3476										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156503657	156503657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gggcaatgcagtcctggtgcTccagcaacagctgcaggacg	14	12	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:156503657T>C	ENST00000361170.2	-	31	3894	c.3884A>G	c.(3883-3885)gAg>gGg	p.E1295G		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1295					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTCCTGGTGCTCCAGCAACAG	0.592																																																0			1											62	51	55					1																	156503657		2203	4300	6503	154770281	SO:0001583	missense	128239			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3884A>G	1.37:g.156503657T>C	ENSP00000354451:p.Glu1295Gly		154770281	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.550571	0.65311	.	.	ENSG00000183856	ENST00000361170	T	0.55760	0.5	4.99	4.99	0.66335	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.059563	0.64402	D	0.000001	T	0.68210	0.2976	M	0.82716	2.605	0.58432	D	0.999999	D	0.76494	0.999	D	0.75484	0.986	T	0.74137	-0.3762	10	0.72032	D	0.01	-25.7785	13.9408	0.64054	0.0:0.0:0.0:1.0	.	1295	Q86VI3	IQGA3_HUMAN	G	1295	ENSP00000354451:E1295G	ENSP00000354451:E1295G	E	-	2	0	IQGAP3	154770281	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	7.825000	0.86693	2.225000	0.72522	0.379000	0.24179	GAG		0.592	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		C	156503657	T	C	156503657	3	2	39	1	0	0	0	0	1	0	0	0	7837	1551	54	4	1043	4	IQGAP3	1	156503657	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	2562586	156503657	92746964	13	3477										
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517533	158517533	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tagcggtcaaaggccatgatAgcaagaaggatgtactcagt	12	7	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:158517533A>T	ENST00000302617.3	-	1	362	c.363T>A	c.(361-363)gcT>gcA	p.A121A		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AGGCCATGATAGCAAGAAGGA	0.463																																																0			1											129	112	118					1																	158517533		2202	4300	6502	156784157	SO:0001819	synonymous_variant	391112			BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.363T>A	1.37:g.158517533A>T			156784157	Q6IFS0	Silent	SNP	ENST00000302617.3	37	CCDS30899.1																																																																																				0.463	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517533	A	T	158517533	2	4	39	1	0	0	0	0	0	0	0	1	11244	407	15	5		5	OR6Y1	1	158517533	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	2013876	158517533	90733088	14	3478										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158609792	158609792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgttccttcagctgttccagTtgctcctaacccaaggagag	9	12	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:158609792T>C	ENST00000368147.4	-	34	4923	c.4743A>G	c.(4741-4743)caA>caG	p.Q1581Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1581					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.Q1581H(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GCTGTTCCAGTTGCTCCTAAC	0.473																																																1	Substitution - Missense(1)	breast(1)	1											165	147	153					1																	158609792		1936	4144	6080	156876416	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4743A>G	1.37:g.158609792T>C			156876416	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158609792	T	C	158609792	2	2	39	1	0	0	0	0	0	0	0	1	15155	1722	60	4		4	SPTA1	1	158609792	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	92259	158609792	90640829	15	3479										
SLAMF1	6504	hgsc.bcm.edu	37	chr1	160607154	160607154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggcctgcttcggatggatcaAgagacactattttgttctcg	11	9	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:160607154A>G	ENST00000302035.6	-	2	591	c.242T>C	c.(241-243)cTt>cCt	p.L81P	SLAMF1_ENST00000235739.5_Missense_Mutation_p.L81P|SLAMF1_ENST00000355199.3_Missense_Mutation_p.L81P|SLAMF1_ENST00000538290.1_Missense_Mutation_p.L81P	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	81	Ig-like V-type.		L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGATGGATCAAGAGACACTAT	0.443																																																0			1											192	155	167					1																	160607154		2203	4300	6503	158873778	SO:0001583	missense	6504			U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.242T>C	1.37:g.160607154A>G	ENSP00000306190:p.Leu81Pro		158873778	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.476699	0.84640	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	4.19	4.19	0.49359	Signaling lymphocytic activation molecule, N-terminal (2);	1.325950	0.04873	N	0.446248	T	0.58609	0.2134	L	0.49126	1.545	0.39721	D	0.971476	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.51164	-0.8740	10	0.45353	T	0.12	-0.6847	9.9336	0.41537	1.0:0.0:0.0:0.0	.	81;81	B4E2E4;Q13291	.;SLAF1_HUMAN	P	81	ENSP00000306190:L81P;ENSP00000235739:L81P;ENSP00000438406:L81P;ENSP00000347333:L81P	ENSP00000235739:L81P	L	-	2	0	SLAMF1	158873778	0.602000	0.26916	0.407000	0.26434	0.960000	0.62799	3.598000	0.54038	2.117000	0.64856	0.402000	0.26972	CTT		0.443	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			G	160607154	A	G	160607154	3	3	39	1	0	0	0	0	1	0	0	0	14404	72	3	4	789	4	SLAMF1	1	160607154	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1997362	160607154	88643467	16	3480										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161018480	161018480	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcccatttctcctcagcaacTtgatcttcctgggccccttg	6	16	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:161018480T>C	ENST00000368013.3	-	12	2651	c.2331A>G	c.(2329-2331)caA>caG	p.Q777Q	USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368015.1_Silent_p.Q600Q|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368016.3_Intron	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	777	Glu-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCTCAGCAACTTGATCTTCCT	0.488																																																0			1											208	207	207					1																	161018480		2203	4300	6503	159285104	SO:0001819	synonymous_variant	257106			AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.2331A>G	1.37:g.161018480T>C			159285104	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																				0.488	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		C	161018480	T	C	161018480	2	2	39	1	0	0	0	0	0	0	0	1	879	1606	56	4		4	ARHGAP30	1	161018480	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	411326	161018480	88232141	17	3481										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067183	190067183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggtcgtgtcataatccattgTgtttggcaatttggcattaa	10	6	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:190067183T>C	ENST00000367462.3	-	8	2497	c.2266A>G	c.(2266-2268)Aca>Gca	p.T756A	BRINP3_ENST00000534846.1_Missense_Mutation_p.T654A	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	756					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TAATCCATTGTGTTTGGCAAT	0.403																																																0			1											149	146	147					1																	190067183		2203	4300	6503	188333806	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.2266A>G	1.37:g.190067183T>C	ENSP00000356432:p.Thr756Ala		188333806	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	5.904	0.350860	0.11182	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.16324	2.61;2.35	5.59	5.59	0.84812	.	0.182240	0.48286	D	0.000181	T	0.06826	0.0174	N	0.01352	-0.895	0.30227	N	0.796255	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.12167	-1.0558	10	0.30078	T	0.28	.	13.7173	0.62705	0.0:0.0:0.0:1.0	.	654;756	B7Z260;Q76B58	.;FAM5C_HUMAN	A	756;654	ENSP00000356432:T756A;ENSP00000438022:T654A	ENSP00000356432:T756A	T	-	1	0	FAM5C	188333806	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.997000	0.40786	2.122000	0.65172	0.455000	0.32223	ACA		0.403	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		C	190067183	T	C	190067183	3	2	39	1	0	0	0	0	1	0	0	0	5613	1696	59	4	38	4	FAM5C	1	190067183	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	29048703	190067183	59183438	18	3482										
PRSS38	339501	hgsc.bcm.edu	37	chr1	228005072	228005072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gccctggtgcagctgaagacCcgcattgtgttttctgagtc	12	11	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:228005072C>T	ENST00000366757.3	+	3	498	c.474C>T	c.(472-474)acC>acT	p.T158T		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AGCTGAAGACCCGCATTGTGT	0.562																																																0			1											185	154	164					1																	228005072		2203	4300	6503	226071695	SO:0001819	synonymous_variant	0				CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.474C>T	1.37:g.228005072C>T			226071695	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																				0.562	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228005072	C	T	228005072	2	4	39	1	0	0	0	0	0	0	0	1	12661	610	22	3		3	PRSS38	1	228005072	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	37937889	228005072	21245549	19	3483										
WDR64	128025	hgsc.bcm.edu	37	chr1	241959600	241959600	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agatttcttccactgattggCgtagaagcccaaaaggactc	9	10	1	3	rs145395572	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:241959600C>T	ENST00000366552.2	+	26	3297	c.3090C>T	c.(3088-3090)ggC>ggT	p.G1030G	WDR64_ENST00000437684.2_Silent_p.G863G	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	1030										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			CACTGATTGGCGTAGAAGCCC	0.398																																																0			1						C		0,4406		0,0,2203	106	95	99		3090	-3.5	0.1	1	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR64	NM_144625.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1030/1082	241959600	1,13005	2203	4300	6503	240026223	SO:0001819	synonymous_variant	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.3090C>T	1.37:g.241959600C>T			240026223	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	C	0.037	-1.301197	0.01364	0.0	1.16E-4	ENSG00000162843	ENST00000425826	.	.	.	5.22	-3.48	0.04739	.	.	.	.	.	T	0.24967	0.0606	.	.	.	0.32247	N	0.571996	.	.	.	.	.	.	T	0.39251	-0.9623	4	.	.	.	-8.6668	1.7104	0.02891	0.1284:0.2559:0.1316:0.4841	.	.	.	.	V	509	.	.	A	+	2	0	WDR64	240026223	0.007000	0.16637	0.096000	0.21009	0.005000	0.04900	-1.093000	0.03362	-0.431000	0.07307	-1.195000	0.01675	GCG		0.398	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241959600	C	T	241959600	2	4	39	1	0	0	0	0	0	0	0	1	17355	755	27	1		1	WDR64	1	241959600	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	13954528	241959600	7291021	20	3484										
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737880	248737880	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agaagtacatgggggtgtggAggcggggctctgagtggatg	21	4	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:248737880A>G	ENST00000328782.2	-	1	200	c.179T>C	c.(178-180)cTc>cCc	p.L60P		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGGGTGTGGAGGCGGGGCTC	0.567																																																0			1											16	20	18					1																	248737880		2093	4233	6326	246804503	SO:0001583	missense	127068			BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.179T>C	1.37:g.248737880A>G	ENSP00000330904:p.Leu60Pro		246804503	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	21.6	4.168660	0.78339	.	.	ENSG00000183310	ENST00000328782	T	0.14893	2.47	2.35	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.55641	0.1933	H	0.98951	4.38	0.53688	D	0.999977	D	0.89917	1.0	D	0.97110	1.0	T	0.66677	-0.5863	9	0.87932	D	0	.	9.2015	0.37260	1.0:0.0:0.0:0.0	.	60	Q8NGX1	O2T34_HUMAN	P	60	ENSP00000330904:L60P	ENSP00000330904:L60P	L	-	2	0	OR2T34	246804503	1.000000	0.71417	0.251000	0.24312	0.855000	0.48748	6.765000	0.74965	0.956000	0.37904	0.324000	0.21423	CTC		0.567	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		G	248737880	A	G	248737880	3	3	39	1	0	0	0	0	1	0	0	0	11056	304	11	4	781	4	OR2T34	1	248737880	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	6778280	248737880	512741	21	3485										
ZNF672	79894	hgsc.bcm.edu	37	chr1	249141646	249141646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcacgggctgctgacctccGagcgcacaggcgcacgcatg	14	15	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr1:249141646G>A	ENST00000306562.3	+	4	919	c.173G>A	c.(172-174)cGa>cAa	p.R58Q		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	58					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GCTGACCTCCGAGCGCACAGG	0.637																																																0			1											30	22	25					1																	249141646		2198	4298	6496	247108269	SO:0001583	missense	79894			AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"Zinc fingers, C2H2-type"	26179	protein-coding gene	gene with protein product	"hypothetical protein FLJ22301"					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.173G>A	1.37:g.249141646G>A	ENSP00000421915:p.Arg58Gln		247108269	Q96H65|Q96IM3|Q9H6G5	Missense_Mutation	SNP	ENST00000306562.3	37	CCDS1638.1	.	.	.	.	.	.	.	.	.	.	G	4.488	0.090434	0.08632	.	.	ENSG00000171161	ENST00000306562;ENST00000428515;ENST00000306576	T;T	0.50813	2.06;0.73	3.83	2.92	0.33932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.28589	U	0.014816	T	0.36496	0.0969	L	0.42744	1.35	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.19910	-1.0291	10	0.27785	T	0.31	.	9.5935	0.39561	0.1054:0.0:0.8946:0.0	.	58	Q499Z4	ZN672_HUMAN	Q	58	ENSP00000421915:R58Q;ENSP00000427021:R58Q	ENSP00000421915:R58Q	R	+	2	0	ZNF672	247108269	0.000000	0.05858	0.158000	0.22627	0.064000	0.16182	-0.591000	0.05753	0.969000	0.38237	-0.137000	0.14449	CGA		0.637	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836		A	249141646	G	A	249141646	3	1	39	1	0	0	0	0	1	0	0	0	18118	1058	37	1	175	1	ZNF672	1	249141646	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	403766	249141646	108975	22	3486										
DDX1	1653	hgsc.bcm.edu	37	chr2	15760383	15760383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcgatgtaaagaaactgtccGagaagataatgcattttcct	8	7	0	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:15760383G>A	ENST00000381341.2	+	18	1647	c.1258G>A	c.(1258-1260)Gag>Aag	p.E420K	DDX1_ENST00000233084.3_Missense_Mutation_p.E420K			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	420	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)	p.E420K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		GAAACTGTCCGAGAAGATAAT	0.368																																																1	Substitution - Missense(1)	ovary(1)	2											130	126	128					2																	15760383		2203	4300	6503	15677834	SO:0001583	missense	1653			X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1258G>A	2.37:g.15760383G>A	ENSP00000370745:p.Glu420Lys		15677834	B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	37	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141873	0.94560	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	T;T	0.04454	3.62;3.62	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.06735	0.0172	N	0.17872	0.535	0.80722	D	1	D	0.61697	0.99	P	0.46659	0.523	T	0.46992	-0.9151	10	0.33141	T	0.24	-29.4035	20.6525	0.99598	0.0:0.0:1.0:0.0	.	420	Q92499	DDX1_HUMAN	K	420;420;404	ENSP00000370745:E420K;ENSP00000233084:E420K	ENSP00000233084:E420K	E	+	1	0	DDX1	15677834	1.000000	0.71417	0.995000	0.50966	0.436000	0.31835	9.869000	0.99810	2.890000	0.99128	0.585000	0.79938	GAG		0.368	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		A	15760383	G	A	15760383	3	1	39	1	0	0	0	0	1	0	0	0	4347	1059	37	1	1324	1	DDX1	2	15760383	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		15760383	227438990	23	3487										
APOB	338	hgsc.bcm.edu	37	chr2	21232202	21232202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtgtatcttctagggtctctCggaatttggccttcatgtga	11	8	4	1	rs554045156		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:21232202C>T	ENST00000233242.1	-	26	7665	c.7538G>A	c.(7537-7539)cGa>cAa	p.R2513Q		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2513					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGGGTCTCTCGGAATTTGGC	0.433													C|||	1	0.000199681	0	0	5008	,	,		21389	0		0	False		,,,				2504	0.001															0			2											126	107	113					2																	21232202		2203	4300	6503	21085707	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7538G>A	2.37:g.21232202C>T	ENSP00000233242:p.Arg2513Gln		21085707	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	2.948	-0.217300	0.06101	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00651	5.97	5.08	-0.328	0.12690	.	0.718713	0.12483	N	0.464943	T	0.00271	0.0008	N	0.01188	-0.97	0.80722	D	1	B	0.12013	0.005	B	0.01281	0.0	T	0.46884	-0.9159	10	0.16896	T	0.51	.	3.5646	0.07895	0.2792:0.2257:0.0:0.4951	.	2513	P04114	APOB_HUMAN	Q	2513	ENSP00000233242:R2513Q	ENSP00000233242:R2513Q	R	-	2	0	APOB	21085707	0.611000	0.26992	0.997000	0.53966	0.912000	0.54170	0.083000	0.14871	0.251000	0.21505	-0.379000	0.06801	CGA		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21232202	C	T	21232202	3	4	39	1	0	0	0	0	1	0	0	0	785	884	31	1	6169	1	APOB	2	21232202	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5471819	21232202	221967171	24	3488										
CAD	790	hgsc.bcm.edu	37	chr2	27459632	27459632	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcaggccctaggccagatcGggccagcccctcctttgaag	12	15	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:27459632G>T	ENST00000403525.1	+	26	4285	c.4141G>T	c.(4141-4143)Ggg>Tgg	p.G1381W	CAD_ENST00000264705.4_Missense_Mutation_p.G1444W			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGCCAGATCGGGCCAGCCCC	0.537																																																0			2											115	111	113					2																	27459632		2203	4300	6503	27313136	SO:0001583	missense	1677			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4141G>T	2.37:g.27459632G>T	ENSP00000384510:p.Gly1381Trp		27313136	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	27.2	4.807082	0.90623	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.87029	-2.2;-2.2	5.58	5.58	0.84498	Methylglyoxal synthase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92163	0.7515	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.917;1.0	D	0.91034	0.4866	10	0.39692	T	0.17	-16.0693	18.128	0.89592	0.0:0.0:1.0:0.0	.	1381;1444	F8VPD4;P27708	.;PYR1_HUMAN	W	1444;1381	ENSP00000264705:G1444W;ENSP00000384510:G1381W	ENSP00000264705:G1444W	G	+	1	0	CAD	27313136	1.000000	0.71417	0.955000	0.39395	0.959000	0.62525	7.199000	0.77831	2.622000	0.88805	0.561000	0.74099	GGG		0.537	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			T	27459632	G	T	27459632	3	4	39	1	0	0	0	0	1	0	0	0	2571	1116	39	2	4436	2	CAD	2	27459632	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	6227430	27459632	215739741	25	3489										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452439	43452440	+	Frame_Shift_Ins	INS	-	-	C													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggcacttttcgccgtacttgINScacgtgccgctctcctcgaa							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:43452439_43452440insC	ENST00000282388.3	-	2	796_797	c.503_504insG	c.(502-504)tgcfs	p.C168fs	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	168					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				CGCCGTACTTGCACGTGCCGCT	0.634																																																0			2																																								43305944	SO:0001589	frameshift_variant	678			X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.504dupG	2.37:g.43452440_43452440dupC	ENSP00000282388:p.Cys168fs		43305943	Q53TB4|Q9BSJ3	Frame_Shift_Ins	INS	ENST00000282388.3	37	CCDS1811.1																																																																																				0.634	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		C	43452440	-	C	43452439	7	5	39	1	0	1	1	0	0	0	0	0	17686	1311	46	0	984	0	ZFP36L2	2	43452439	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	15992807	43452439	199746934	26	3490										
C2orf3	6936	hgsc.bcm.edu	37	chr2	75933720	75933720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aaccctgatcatccttacttTctgaggagtgatgtatttta	7	8	2	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:75933720T>C	ENST00000321027.3	-	2	456	c.323A>G	c.(322-324)gAa>gGa	p.E108G	GCFC2_ENST00000409857.3_Missense_Mutation_p.E108G|GCFC2_ENST00000541687.1_Missense_Mutation_p.E108G|GCFC2_ENST00000470503.1_Missense_Mutation_p.E108G	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	108					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										ATCCTTACTTTCTGAGGAGTG	0.343																																																0			2											115	110	112					2																	75933720		2203	4300	6503	75787228	SO:0001583	missense	6936			AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.323A>G	2.37:g.75933720T>C	ENSP00000318690:p.Glu108Gly		75787228	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	T	7.345	0.621783	0.14193	.	.	ENSG00000005436	ENST00000321027;ENST00000541687;ENST00000409857;ENST00000442309	T;T;T;T	0.36520	2.26;1.31;2.32;1.25	4.04	2.81	0.32909	.	0.859599	0.10079	N	0.718680	T	0.28234	0.0697	L	0.35723	1.085	0.27688	N	0.946206	B;B	0.20052	0.041;0.009	B;B	0.20767	0.031;0.005	T	0.24548	-1.0157	10	0.45353	T	0.12	-1.2405	6.9668	0.24627	0.0:0.1137:0.0:0.8863	.	108;108	A4UHQ8;P16383	.;GCF_HUMAN	G	108	ENSP00000318690:E108G;ENSP00000437767:E108G;ENSP00000386552:E108G;ENSP00000415831:E108G	ENSP00000318690:E108G	E	-	2	0	C2orf3	75787228	0.895000	0.30542	0.945000	0.38365	0.072000	0.16883	0.402000	0.20965	0.614000	0.30107	0.528000	0.53228	GAA		0.343	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		C	75933720	T	C	75933720	3	2	39	1	0	0	0	0	1	0	0	0	2168	1783	62	4	2086	4	C2orf3	2	75933720	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	32481281	75933720	167265653	27	3491										
AMMECR1L	83607	hgsc.bcm.edu	37	chr2	128627062	128627062	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acctcaggtaaatatgtggcTgtgcgtttgacacctttttc	9	9	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:128627062T>C	ENST00000272647.5	-	6	950	c.690A>G	c.(688-690)acA>acG	p.T230T	AMMECR1L_ENST00000393001.1_Silent_p.T230T	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	230	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		AATATGTGGCTGTGCGTTTGA	0.388																																																0			2											148	131	137					2																	128627062		2203	4300	6503	128343532	SO:0001819	synonymous_variant	83607				CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"AMME chromosomal region gene 1-like"				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.690A>G	2.37:g.128627062T>C			128343532	B4E276	Silent	SNP	ENST00000272647.5	37	CCDS2152.1																																																																																				0.388	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445		C	128627062	T	C	128627062	2	2	39	1	0	0	0	0	0	0	0	1	579	1567	55	4		4	AMMECR1L	2	128627062	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	52693342	128627062	114572311	28	3492										
ACMSD	130013	hgsc.bcm.edu	37	chr2	135630172	135630172	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acagatgctttggttcatgaTcctctgtccctcaagctgtt	8	11	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:135630172T>A	ENST00000356140.5	+	8	946	c.810T>A	c.(808-810)gaT>gaA	p.D270E	AC016725.4_ENST00000413962.1_RNA|ACMSD_ENST00000283054.4_Missense_Mutation_p.D212E|AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000392928.1_Missense_Mutation_p.D212E|AC016725.4_ENST00000537615.1_RNA|AC016725.4_ENST00000428857.1_RNA	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	270					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		TGGTTCATGATCCTCTGTCCC	0.502																																																0			2											162	140	148					2																	135630172		2203	4300	6503	135346642	SO:0001583	missense	130013			AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.810T>A	2.37:g.135630172T>A	ENSP00000348459:p.Asp270Glu		135346642	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	37	CCDS2173.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091205	0.76756	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.66	3.32	0.38043	.	0.000000	0.85682	D	0.000000	T	0.70509	0.3232	M	0.87682	2.9	0.58432	D	0.999999	B;P	0.35433	0.198;0.501	B;P	0.45377	0.23;0.478	T	0.69359	-0.5166	9	0.40728	T	0.16	-18.0802	8.4879	0.33082	0.0:0.2795:0.0:0.7205	.	212;270	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	E	270;212;212	.	ENSP00000283054:D212E	D	+	3	2	ACMSD	135346642	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.023000	0.41040	0.991000	0.38814	0.477000	0.44152	GAT		0.502	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			A	135630172	T	A	135630172	3	1	39	1	0	0	0	0	1	0	0	0	144	1432	50	5	840	5	ACMSD	2	135630172	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	7003110	135630172	107569201	29	3493										
TTN	7273	hgsc.bcm.edu	37	chr2	179560732	179560732	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cttcttcccattcctcgtgaActtcttttttagcttctacc	3	14	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:179560732A>T	ENST00000591111.1	-	112	30340	c.30116T>A	c.(30115-30117)gTt>gAt	p.V10039D	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V10356D|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9112D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ttcctcgtgaacttctttttt	0.413																																																0			2											181	158	166					2																	179560732		1483	3194	4677	179268977	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30116T>A	2.37:g.179560732A>T	ENSP00000465570:p.Val10039Asp		179268977	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	12.47	1.946360	0.34377	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.68624	-0.34	5.78	4.52	0.55395	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.62441	0.2428	L	0.57536	1.79	0.09310	N	0.999999	B;P	0.36837	0.023;0.571	B;B	0.36464	0.021;0.225	T	0.60826	-0.7186	9	0.87932	D	0	.	9.5697	0.39420	0.8326:0.0:0.0:0.1674	.	10039;10039	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	D	9112;234	ENSP00000343764:V9112D	ENSP00000343764:V9112D	V	-	2	0	TTN	179268977	0.289000	0.24334	0.246000	0.24233	0.785000	0.44390	1.849000	0.39318	2.204000	0.70986	0.528000	0.53228	GTT		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179560732	A	T	179560732	3	4	39	1	0	0	0	0	1	0	0	0	16775	43	2	5	73458	5	TTN	2	179560732	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	43930560	179560732	63638641	30	3494										
ANO7	50636	hgsc.bcm.edu	37	chr2	242148982	242148982	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	accccatcacgggtgaggacGagccctacttccctgagagg	12	14	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr2:242148982G>A	ENST00000274979.8	+	13	1556	c.1453G>A	c.(1453-1455)Gag>Aag	p.E485K	ANO7_ENST00000402430.3_Missense_Mutation_p.E484K	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	485					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GGGTGAGGACGAGCCCTACTT	0.701																																																0			2											36	39	38					2																	242148982		2203	4299	6502	241797655	SO:0001583	missense	50636			AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1453G>A	2.37:g.242148982G>A	ENSP00000274979:p.Glu485Lys		241797655	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477806	0.84640	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	T;T	0.67523	-0.27;-0.27	3.61	3.61	0.41365	.	0.163928	0.38272	N	0.001741	T	0.77903	0.4200	M	0.77103	2.36	0.44711	D	0.997707	D	0.60160	0.987	P	0.58172	0.834	T	0.82382	-0.0485	10	0.87932	D	0	.	14.1015	0.65059	0.0:0.0:1.0:0.0	.	485	Q6IWH7	ANO7_HUMAN	K	485;484	ENSP00000274979:E485K;ENSP00000385418:E484K	ENSP00000274979:E485K	E	+	1	0	ANO7	241797655	1.000000	0.71417	0.809000	0.32408	0.469000	0.32828	7.964000	0.87933	1.578000	0.49821	0.306000	0.20318	GAG		0.701	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		A	242148982	G	A	242148982	3	1	39	1	0	0	0	0	1	0	0	0	702	1059	37	1	1575	1	ANO7	2	242148982	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	62588250	242148982	1050391	31	3495										
IL17RC	84818	hgsc.bcm.edu	37	chr3	9970121	9970121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcgggctccgggtggggaccCctgccagccactggtcccac	15	17	0	0	rs115419420	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:9970121C>T	ENST00000295981.3	+	11	1441	c.1223C>T	c.(1222-1224)cCc>cTc	p.P408L	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000455057.1_Missense_Mutation_p.P322L|IL17RC_ENST00000383812.4_Missense_Mutation_p.P322L|IL17RC_ENST00000413608.1_Missense_Mutation_p.P337L|IL17RC_ENST00000416074.2_Missense_Mutation_p.P193L|IL17RC_ENST00000403601.3_Missense_Mutation_p.P337L	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	408					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGTGGGGACCCCTGCCAGCCA	0.682													C|||	77	0.0153754	0.0174	0.0173	5008	,	,		14342	0		0.0398	False		,,,				2504	0.002															0			3						C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	123,4283	81.4+/-119.9	1,121,2081	34	42	39		1010,1010,965,965,1010,1223	2.7	1	3	dbSNP_132	39	324,8276	108.2+/-168.9	6,312,3982	yes	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	98,98,98,98,98,98	7,433,6063	TT,TC,CC		3.7674,2.7916,3.4369	benign,benign,benign,benign,benign,benign	337/708,337/691,322/689,322/706,337/721,408/792	9970121	447,12559	2203	4300	6503	9945121	SO:0001583	missense	84818			BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1223C>T	3.37:g.9970121C>T	ENSP00000295981:p.Pro408Leu		9945121	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	51	0.023351648351648352	8	0.016260162601626018	5	0.013812154696132596	0	0.0	38	0.05013192612137203	C	9.485	1.099131	0.20552	0.027916	0.037674	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66	4.96	2.73	0.32206	.	0.270585	0.26812	N	0.022371	T	0.01061	0.0035	L	0.39633	1.23	0.41034	D	0.985174	B;B;B;B;B;B;B;P;B	0.43094	0.015;0.016;0.009;0.009;0.016;0.016;0.015;0.799;0.009	B;B;B;B;B;B;B;B;B	0.38562	0.016;0.013;0.007;0.007;0.01;0.01;0.016;0.276;0.02	T	0.28522	-1.0041	10	0.02654	T	1	-17.4595	5.5033	0.16840	0.0:0.7134:0.0:0.2866	.	322;193;322;337;337;337;322;408;337	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	L	322;297;408;312;337;193;322;337	ENSP00000373323:P322L;ENSP00000414609:P297L;ENSP00000295981:P408L;ENSP00000401128:P312L;ENSP00000384969:P337L;ENSP00000395315:P193L;ENSP00000407894:P322L;ENSP00000396064:P337L	ENSP00000295981:P408L	P	+	2	0	IL17RC	9945121	0.941000	0.31946	0.992000	0.48379	0.108000	0.19459	0.855000	0.27805	1.222000	0.43521	0.549000	0.68633	CCC		0.682	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9970121	C	T	9970121	3	4	39	1	0	0	0	0	1	0	0	0	7662	623	22	3	1265	3	IL17RC	3	9970121	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		9970121	188052309	32	3496										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19295236	19295236	+	Frame_Shift_Del	DEL	C	C	-													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgcgagcttgctggatttgCccgaactgaagtcatgcaga							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:19295236delC	ENST00000328405.2	+	2	433	c.167delC	c.(166-168)gccfs	p.A56fs		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	56	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						GCTGGATTTGCCCGAACTGAA	0.458																																					NSCLC(124;1625 1765 8018 24930 42026)											0			3											176	182	180					3																	19295236		2203	4300	6503	19270240	SO:0001589	frameshift_variant	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.167delC	3.37:g.19295236delC	ENSP00000328813:p.Ala56fs		19270240	B7Z2I7|Q59GQ6	Frame_Shift_Del	DEL	ENST00000328405.2	37	CCDS2632.1																																																																																				0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		-	19295236	C	-	19295236	7	5	39	1	0	1	0	1	0	0	0	0	8059	739	26	0	173	0	KCNH8	3	19295236	Frame_Shift_Del	DEL	C	TCGA-AG-3742-01A-11D-1657-10	9325115	19295236	178727194	33	3497										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266159	41266159	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgagtggtaaaggcaatccTgaggaagaggatgtggatac	15	5	0	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:41266159T>C	ENST00000349496.5	+	3	436	c.156T>C	c.(154-156)ccT>ccC	p.P52P	CTNNB1_ENST00000396185.3_Silent_p.P52P|CTNNB1_ENST00000453024.1_Silent_p.P45P|CTNNB1_ENST00000405570.1_Silent_p.P52P|CTNNB1_ENST00000396183.3_Silent_p.P52P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	52					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		AAGGCAATCCTGAGGAAGAGG	0.478		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	111	Deletion - In frame(88)|Complex - deletion inframe(16)|Unknown(7)	liver(82)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											74	68	70					3																	41266159		2203	4300	6503	41241163	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.156T>C	3.37:g.41266159T>C			41241163	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266159	T	C	41266159	2	2	39	1	0	0	0	0	0	0	0	1	4022	1567	55	4		4	CTNNB1	3	41266159	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	21970923	41266159	156756271	34	3498										
UBA7	7318	hgsc.bcm.edu	37	chr3	49845298	49845299	+	Frame_Shift_Ins	INS	-	-	C													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acagctccaggcccaacaggINScctgccacagctgctgtagt							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:49845298_49845299insC	ENST00000333486.3	-	21	2743_2744	c.2585_2586insG	c.(2584-2586)ggcfs	p.G862fs	MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	862					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GGCCCAACAGGCCTGCCACAGC	0.569																																																0			3																																								49820303	SO:0001589	frameshift_variant	7318			BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.2586dupG	3.37:g.49845300_49845300dupC	ENSP00000333266:p.Gly862fs		49820302	Q9BRB2	Frame_Shift_Ins	INS	ENST00000333486.3	37	CCDS2805.1																																																																																				0.569	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		C	49845299	-	C	49845298	7	5	39	1	0	1	1	0	0	0	0	0	16873	1190	42	0	468	0	UBA7	3	49845298	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	8579139	49845298	148177132	35	3499										
GPR15	2838	hgsc.bcm.edu	37	chr3	98251220	98251220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggagctcctacatgatctccGtcaatatgcactgcagtgtc	9	12	2	1	rs189514169		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:98251220G>A	ENST00000284311.3	+	1	478	c.343G>A	c.(343-345)Gtc>Atc	p.V115I		NM_005290.1	NP_005281.1	P49685	GPR15_HUMAN	G protein-coupled receptor 15	115					G-protein coupled receptor signaling pathway (GO:0007186)|T cell migration (GO:0072678)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		CATGATCTCCGTCAATATGCA	0.512													G|||	1	0.000199681	0	0.0014	5008	,	,		21318	0		0	False		,,,				2504	0															0			3						G	ILE/VAL	0,4406		0,0,2203	79	74	76		343	4	0.9	3		76	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GPR15	NM_005290.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	115/361	98251220	1,13005	2203	4300	6503	99733910	SO:0001583	missense	2838				CCDS2931.1	3q11.2-q13.1	2014-01-30			ENSG00000154165	ENSG00000154165		"GPCR / Class A : Orphans"	4469	protein-coding gene	gene with protein product		601166				8838812	Standard	NM_005290		Approved		uc011bgy.3	P49685	OTTHUMG00000160017	ENST00000284311.3:c.343G>A	3.37:g.98251220G>A	ENSP00000284311:p.Val115Ile		99733910	Q3MIL4|Q6ISN6	Missense_Mutation	SNP	ENST00000284311.3	37	CCDS2931.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	20.3	3.970768	0.74246	0.0	1.16E-4	ENSG00000154165	ENST00000284311	T	0.72835	-0.69	4.83	3.96	0.45880	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000303	T	0.77532	0.4144	L	0.48260	1.515	0.41665	D	0.989207	D	0.89917	1.0	D	0.79108	0.992	T	0.78858	-0.2038	10	0.62326	D	0.03	-26.6571	11.0385	0.47816	0.0909:0.0:0.9091:0.0	.	115	P49685	GPR15_HUMAN	I	115	ENSP00000284311:V115I	ENSP00000284311:V115I	V	+	1	0	GPR15	99733910	1.000000	0.71417	0.887000	0.34795	0.944000	0.59088	5.267000	0.65530	1.410000	0.46936	0.591000	0.81541	GTC		0.512	GPR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358907.1			A	98251220	G	A	98251220	3	1	39	1	0	0	0	0	1	0	0	0	6675	1145	40	1	345	1	GPR15	3	98251220	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	48405922	98251220	99771210	36	3500										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126751257	126751257	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgcgcttctgggtgaacgtGatcaagaacccacagtttgt	11	10	2	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:126751257G>T	ENST00000393409.2	+	29	5259	c.5259G>T	c.(5257-5259)gtG>gtT	p.V1753V	PLXNA1_ENST00000251772.4_Silent_p.V1730V|PLXNA1_ENST00000505278.1_3'UTR	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1753					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GGGTGAACGTGATCAAGAACC	0.602																																																0			3											116	106	109					3																	126751257		2203	4300	6503	128233947	SO:0001819	synonymous_variant	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.5259G>T	3.37:g.126751257G>T			128233947		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																				0.602	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126751257	G	T	126751257	2	4	39	1	0	0	0	0	0	0	0	1	12150	1277	45	2		2	PLXNA1	3	126751257	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	28500037	126751257	71271173	37	3501										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140277686	140277686	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aaaaccgaagcccccggggaCgtgaaaaccacaggtacagg	12	12	0	1	rs144701273	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:140277686C>T	ENST00000458420.3	+	12	2218	c.2028C>T	c.(2026-2028)gaC>gaT	p.D676D		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	676					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.D676D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CCCCCGGGGACGTGAAAACCA	0.498										HNSCC(16;0.037)			C|||	10	0.00199681	0.0053	0.0014	5008	,	,		19045	0		0	False		,,,				2504	0.002				GBM(45;858 913 3709 36904 37282)											1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	3						C		19,4387	25.3+/-52.1	0,19,2184	39	43	42		2028	-3	0	3	dbSNP_134	42	0,8600		0,0,4300	no	coding-synonymous	CLSTN2	NM_022131.2		0,19,6484	TT,TC,CC		0.0,0.4312,0.1461		676/956	140277686	19,12987	2203	4300	6503	141760376	SO:0001819	synonymous_variant	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2028C>T	3.37:g.140277686C>T			141760376	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																				0.498	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140277686	C	T	140277686	2	4	39	1	0	0	0	0	0	0	0	1	3568	535	19	1		1	CLSTN2	3	140277686	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	13526429	140277686	57744744	38	3502										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916725	178916725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tagtgactttagaatgcctcCgtgaggctacattaataacc	8	9	0	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:178916725C>T	ENST00000263967.3	+	2	269	c.112C>T	c.(112-114)Cgt>Tgt	p.R38C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	38	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.		R -> H (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity; may disrupt the interaction between the PI3K-ABD domain and the N-terminal lobe of PI3K/PI4K kinase domain possibly affecting the conformation of the kinase domain).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R38G(1)|p.R38S(1)|p.R38C(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGAATGCCTCCGTGAGGCTAC	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Substitution - Missense(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	3											76	74	75					3																	178916725		1845	4085	5930	180399419	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.112C>T	3.37:g.178916725C>T	ENSP00000263967:p.Arg38Cys		180399419	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909863	0.72983	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.73363	-0.74;-0.74	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.84019	0.5380	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.82665	-0.0345	9	.	.	.	-9.214	19.2635	0.93977	0.0:1.0:0.0:0.0	.	38	P42336	PK3CA_HUMAN	C	38	ENSP00000263967:R38C;ENSP00000417479:R38C	.	R	+	1	0	PIK3CA	180399419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.642000	0.67888	2.547000	0.85894	0.555000	0.69702	CGT		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916725	C	T	178916725	3	4	39	1	0	0	0	0	1	0	0	0	11944	652	23	1	114	1	PIK3CA	3	178916725	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	38639039	178916725	19105705	39	3503										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178921450	178921450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gccatcttattccagacgcaTttccacagctacaccatata	4	14	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:178921450T>C	ENST00000263967.3	+	5	1089	c.932T>C	c.(931-933)aTt>aCt	p.I311T		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	311					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCAGACGCATTTCCACAGCT	0.388		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											116	112	113					3																	178921450		1868	4100	5968	180404144	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.932T>C	3.37:g.178921450T>C	ENSP00000263967:p.Ile311Thr		180404144	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574499	0.28092	.	.	ENSG00000121879	ENST00000263967	T	0.71579	-0.58	5.25	5.25	0.73442	.	0.076087	0.64402	D	0.000002	T	0.50497	0.1619	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46857	-0.9161	10	0.17832	T	0.49	-10.2287	15.4533	0.75294	0.0:0.0:0.0:1.0	.	311	P42336	PK3CA_HUMAN	T	311	ENSP00000263967:I311T	ENSP00000263967:I311T	I	+	2	0	PIK3CA	180404144	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.571000	0.82399	2.120000	0.65058	0.383000	0.25322	ATT		0.388	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178921450	T	C	178921450	3	2	39	1	0	0	0	0	1	0	0	0	11944	1493	52	4	946	4	PIK3CA	3	178921450	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	4725	178921450	19100980	40	3504										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936095	178936095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tctctctgaaatcactgagcAggagaaagattttctatgga	9	7	4	4	rs397517201		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr3:178936095A>G	ENST00000263967.3	+	10	1794	c.1637A>G	c.(1636-1638)cAg>cGg	p.Q546R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	546	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		Q -> E (in BC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> K (in OC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> P (found in an anaplastic astrocytoma sample; unknown pathological significance). {ECO:0000269|PubMed:15289301}.|Q -> R (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q546R(30)|p.Q546P(18)|p.Q546L(5)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATCACTGAGCAGGAGAAAGAT	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	53	Substitution - Missense(53)	endometrium(18)|breast(17)|large_intestine(10)|central_nervous_system(3)|prostate(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	3											61	61	61					3																	178936095		1813	4072	5885	180418789	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1637A>G	3.37:g.178936095A>G	ENSP00000263967:p.Gln546Arg		180418789	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332178	0.81801	.	.	ENSG00000121879	ENST00000263967	T	0.63417	-0.04	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75657	0.3879	M	0.64404	1.975	0.80722	D	1	D	0.63046	0.992	D	0.65323	0.934	T	0.76782	-0.2832	10	0.52906	T	0.07	-14.2064	16.1026	0.81194	1.0:0.0:0.0:0.0	.	546	P42336	PK3CA_HUMAN	R	546	ENSP00000263967:Q546R	ENSP00000263967:Q546R	Q	+	2	0	PIK3CA	180418789	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	CAG		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936095	A	G	178936095	3	3	39	1	0	0	0	0	1	0	0	0	11944	188	7	4	1671	4	PIK3CA	3	178936095	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	14645	178936095	19086335	41	3505										
ZNF595	152687	hgsc.bcm.edu	37	chr4	60044	60044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgagacagcagccaaaccccCaggtaggtgagactgaatga	12	10	0	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:60044C>T	ENST00000509152.2	+	3	409	c.224C>T	c.(223-225)cCa>cTa	p.P75L	ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_Missense_Mutation_p.P75L			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	75	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GCCAAACCCCCAGGTAGGTGA	0.498																																																0			4											104	111	109					4																	60044		2174	4296	6470	50044	SO:0001583	missense	255403			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.224C>T	4.37:g.60044C>T	ENSP00000434858:p.Pro75Leu		50044		Missense_Mutation	SNP	ENST00000509152.2	37		.	.	.	.	.	.	.	.	.	.	C	13.64	2.296181	0.40594	.	.	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.01034	5.42;5.52	0.681	0.681	0.17986	Krueppel-associated box (2);	.	.	.	.	T	0.04048	0.0113	.	.	.	0.36552	D	0.87191	D;D	0.89917	0.983;1.0	P;D	0.85130	0.656;0.997	T	0.42899	-0.9424	7	0.87932	D	0	.	.	.	.	.	75;75	Q8IYB9;Q3SXZ3	ZN595_HUMAN;ZN718_HUMAN	L	75	ENSP00000434858:P75L;ENSP00000437878:P75L	ENSP00000434858:P75L	P	+	2	0	ZNF595	50044	0.011000	0.17503	0.188000	0.23233	0.234000	0.25298	0.061000	0.14366	0.655000	0.30866	0.484000	0.47621	CCA		0.498	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524		T	60044	C	T	60044	3	4	39	1	0	0	0	0	1	0	0	0	18064	594	21	3	234	3	ZNF595	4	60044	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		60044	191094232	42	3506										
PIGG	54872	hgsc.bcm.edu	37	chr4	533022	533022	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cacgtacatcgttttggtgaCatctctgcgttatcatttat	7	9	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:533022C>A	ENST00000453061.2	+	13	2922	c.2816C>A	c.(2815-2817)aCa>aAa	p.T939K	PIGG_ENST00000310340.5_Missense_Mutation_p.T931K|PIGG_ENST00000383028.4_Missense_Mutation_p.T806K|PIGG_ENST00000504346.1_Missense_Mutation_p.T850K|PIGG_ENST00000296306.7_3'UTR	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	939					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						GTTTTGGTGACATCTCTGCGT	0.393																																																0			4											191	168	176					4																	533022		2203	4300	6503	523022	SO:0001583	missense	54872				CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"Phosphatidylinositol glycan anchor biosynthesis"	25985	protein-coding gene	gene with protein product			"phosphatidylinositol glycan, class G"			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2816C>A	4.37:g.533022C>A	ENSP00000415203:p.Thr939Lys		523022	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.875396	0.91664	.	.	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000453065	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.91	5.91	0.95273	.	0.212372	0.48286	D	0.000197	T	0.65544	0.2701	M	0.87547	2.89	0.80722	D	1	D;D;D	0.63880	0.993;0.989;0.993	P;P;P	0.57620	0.79;0.672;0.824	T	0.67169	-0.5738	10	0.41790	T	0.15	-16.5418	17.7902	0.88550	0.0:1.0:0.0:0.0	.	806;939;931	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	K	931;939;850;806;95	ENSP00000311750:T931K;ENSP00000415203:T939K;ENSP00000424800:T850K;ENSP00000372494:T806K	ENSP00000311750:T931K	T	+	2	0	PIGG	523022	1.000000	0.71417	0.959000	0.39883	0.769000	0.43574	6.747000	0.74872	2.813000	0.96785	0.655000	0.94253	ACA		0.393	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733		A	533022	C	A	533022	3	1	39	1	0	0	0	0	1	0	0	0	11919	478	17	2	2866	2	PIGG	4	533022	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	472978	533022	190621254	43	3507										
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25262148	25262148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcttgtttgttttgaaagacAggggcaatgataattggtta	11	3	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:25262148A>G	ENST00000264864.6	+	6	1102	c.913A>G	c.(913-915)Agg>Ggg	p.R305G	PI4K2B_ENST00000512921.1_Missense_Mutation_p.R209G	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	305	PI3K/PI4K.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				TTTGAAAGACAGGGGCAATGA	0.299																																																0			4											116	124	121					4																	25262148		2203	4299	6502	24871246	SO:0001583	missense	55300			AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.913A>G	4.37:g.25262148A>G	ENSP00000264864:p.Arg305Gly		24871246	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	37	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.656056	0.67586	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	D;D	0.98914	-5.23;-5.23	5.76	5.76	0.90799	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.046975	0.85682	D	0.000000	D	0.99369	0.9778	H	0.97806	4.08	0.80722	D	1	D	0.54207	0.965	P	0.61533	0.89	D	0.98681	1.0692	10	0.87932	D	0	-8.3356	11.7544	0.51868	0.7317:0.2683:0.0:0.0	.	305	Q8TCG2	P4K2B_HUMAN	G	209;305;274	ENSP00000423373:R209G;ENSP00000264864:R305G	ENSP00000264864:R305G	R	+	1	2	PI4K2B	24871246	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.184000	0.42575	2.323000	0.78572	0.528000	0.53228	AGG		0.299	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		G	25262148	A	G	25262148	3	3	39	1	0	0	0	0	1	0	0	0	11903	179	7	4	935	4	PI4K2B	4	25262148	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	24729126	25262148	165892128	44	3508										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40104123	40104123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acccattaccttcacattcaGttttgaacgagtccaagtgt	6	11	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:40104123G>A	ENST00000261435.6	+	4	1074	c.658G>A	c.(658-660)Gtt>Att	p.V220I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	220					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTCACATTCAGTTTTGAACGA	0.333																																																0			4											44	46	45					4																	40104123		2187	4297	6484	39780518	SO:0001583	missense	55728			AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.658G>A	4.37:g.40104123G>A	ENSP00000261435:p.Val220Ile		39780518	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	G	8.367	0.834379	0.16820	.	.	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.80393	-1.37;-1.37	5.53	2.77	0.32553	.	1.146900	0.06266	N	0.694850	T	0.72104	0.3419	L	0.32530	0.975	0.09310	N	1	B;B	0.25904	0.137;0.085	B;B	0.24269	0.052;0.023	T	0.53272	-0.8462	10	0.20046	T	0.44	-1.538	10.9171	0.47142	0.0:0.2644:0.5982:0.1373	.	220;220	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	I	220;140;140	ENSP00000261435:V220I;ENSP00000422057:V140I	ENSP00000261435:V220I	V	+	1	0	N4BP2	39780518	0.020000	0.18652	0.000000	0.03702	0.002000	0.02628	0.279000	0.18771	0.395000	0.25257	0.650000	0.86243	GTT		0.333	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		A	40104123	G	A	40104123	3	1	39	1	0	0	0	0	1	0	0	0	10140	1029	36	3	664	3	N4BP2	4	40104123	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	14841975	40104123	151050153	45	3509										
KIT	3815	hgsc.bcm.edu	37	chr4	55592092	55592092	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gggccaccgtttggaaagctAgtggttcagagttctataga	13	7	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:55592092A>G	ENST00000288135.5	+	9	1513	c.1416A>G	c.(1414-1416)ctA>ctG	p.L472L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	472	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L472L(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTGGAAAGCTAGTGGTTCAGA	0.448		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - coding silent(1)	genital_tract(1)	4											121	109	113					4																	55592092		2203	4300	6503	55286849	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1416A>G	4.37:g.55592092A>G			55286849	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.448	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55592092	A	G	55592092	2	3	39	1	0	0	0	0	0	0	0	1	8350	407	15	4		4	KIT	4	55592092	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	15487969	55592092	135562184	46	3510										
TACR3	6870	hgsc.bcm.edu	37	chr4	104640303	104640303	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acctgtccaccgcaatggccGtcatggagtagatgctggcg	13	12	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:104640303G>A	ENST00000304883.2	-	1	670	c.530C>T	c.(529-531)aCg>aTg	p.T177M		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	177					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		CGCAATGGCCGTCATGGAGTA	0.507																																																0			4											52	50	50					4																	104640303		2203	4300	6503	104859752	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.530C>T	4.37:g.104640303G>A	ENSP00000303325:p.Thr177Met		104859752	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058659	0.55325	.	.	ENSG00000169836	ENST00000304883	T	0.74002	-0.8	5.14	5.14	0.70334	GPCR, rhodopsin-like superfamily (1);	0.212960	0.48767	D	0.000179	D	0.84009	0.5378	M	0.74258	2.255	0.58432	D	0.999994	D	0.69078	0.997	P	0.62184	0.899	T	0.82481	-0.0436	10	0.29301	T	0.29	.	17.6101	0.88050	0.0:0.0:1.0:0.0	.	177	P29371	NK3R_HUMAN	M	177	ENSP00000303325:T177M	ENSP00000303325:T177M	T	-	2	0	TACR3	104859752	1.000000	0.71417	0.963000	0.40424	0.431000	0.31685	9.319000	0.96338	2.386000	0.81285	0.591000	0.81541	ACG		0.507	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		A	104640303	G	A	104640303	3	1	39	1	0	0	0	0	1	0	0	0	15546	1145	40	1	887	1	TACR3	4	104640303	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	49048211	104640303	86513973	47	3511										
FAT4	79633	hgsc.bcm.edu	37	chr4	126411432	126411432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcaaagctggaagtcctgcGgggcatgtctgtgttctgag	15	8	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:126411432G>A	ENST00000394329.3	+	17	13468	c.13455G>A	c.(13453-13455)gcG>gcA	p.A4485A	FAT4_ENST00000335110.5_Silent_p.A2726A	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4485					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GAAGTCCTGCGGGGCATGTCT	0.622																																																0			4											88	86	86					4																	126411432		2203	4300	6503	126630882	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13455G>A	4.37:g.126411432G>A			126630882	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.622	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126411432	G	A	126411432	2	1	39	1	0	0	0	0	0	0	0	1	5711	1103	39	1		1	FAT4	4	126411432	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	21771129	126411432	64742844	48	3512										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148594895	148594895	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	attcctcttggtgtcattaaGcatgataaagtgccagcgtt	9	8	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:148594895G>T	ENST00000322396.6	-	3	711	c.469C>A	c.(469-471)Ctt>Att	p.L157I	PRMT10_ENST00000541232.1_Missense_Mutation_p.L44I	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		157	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						GTGTCATTAAGCATGATAAAG	0.398																																																0			4											103	102	102					4																	148594895		2203	4300	6503	148814345	SO:0001583	missense	90826																														ENST00000322396.6:c.469C>A	4.37:g.148594895G>T	ENSP00000314396:p.Leu157Ile		148814345	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017865	0.93404	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.26518	1.73;1.73	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.52256	0.1723	M	0.66297	2.02	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.52779	-0.8530	10	0.66056	D	0.02	.	19.2339	0.93850	0.0:0.0:1.0:0.0	.	157	Q6P2P2	ANM10_HUMAN	I	157;44	ENSP00000314396:L157I;ENSP00000439508:L44I	ENSP00000314396:L157I	L	-	1	0	PRMT10	148814345	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.461000	0.97646	2.548000	0.85928	0.655000	0.94253	CTT		0.398	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			T	148594895	G	T	148594895	3	4	39	1	0	0	0	0	1	0	0	0	12570	971	34	2	2108	2	PRMT10	4	148594895	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	22183463	148594895	42559381	49	3513										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245446	153245446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gttccattccacttgttaacGactggtgccctgttaacgtg	9	11	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr4:153245446G>A	ENST00000281708.4	-	11	2974	c.1745C>T	c.(1744-1746)tCg>tTg	p.S582L	FBXW7_ENST00000393956.3_Missense_Mutation_p.S406L|FBXW7_ENST00000263981.5_Missense_Mutation_p.S502L|FBXW7_ENST00000296555.5_Missense_Mutation_p.S464L|FBXW7_ENST00000603841.1_Missense_Mutation_p.S582L|FBXW7_ENST00000603548.1_Missense_Mutation_p.S582L	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	582			S -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.S582L(10)|p.S502L(2)|p.S343L(2)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTTGTTAACGACTGGTGCCC	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	15	Substitution - Missense(14)|Unknown(1)	large_intestine(14)|haematopoietic_and_lymphoid_tissue(1)	4											150	126	134					4																	153245446		2203	4300	6503	153464896	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1745C>T	4.37:g.153245446G>A	ENSP00000281708:p.Ser582Leu		153464896	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429316	0.62844	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.81179	2.53	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.99;0.993;0.988;0.988	T	0.66480	-0.5913	10	0.39692	T	0.17	-9.1133	19.838	0.96666	0.0:0.0:1.0:0.0	.	406;582;464;502	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	L	582;464;502;406	ENSP00000281708:S582L;ENSP00000296555:S464L;ENSP00000263981:S502L;ENSP00000377528:S406L	ENSP00000263981:S502L	S	-	2	0	FBXW7	153464896	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.869000	0.99810	2.692000	0.91855	0.650000	0.86243	TCG		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153245446	G	A	153245446	3	1	39	1	0	0	0	0	1	0	0	0	5788	1059	37	1	386	1	FBXW7	4	153245446	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	4650551	153245446	37908830	50	3514										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13717498	13717498	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aaagtccgcttggttaaattCgtaggggatattccacccca	9	10	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:13717498C>A	ENST00000265104.4	-	73	12735	c.12631G>T	c.(12631-12633)Gaa>Taa	p.E4211*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4211	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGGTTAAATTCGTAGGGGATA	0.542									Kartagener syndrome																																							0			5											71	63	66					5																	13717498		2203	4300	6503	13770498	SO:0001587	stop_gained	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12631G>T	5.37:g.13717498C>A	ENSP00000265104:p.Glu4211*		13770498	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	54	23.268893	0.99954	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.45	4.58	0.56647	.	0.101878	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	13.8576	0.63537	0.0:0.9268:0.0:0.0732	.	.	.	.	X	4211	.	ENSP00000265104:E4211X	E	-	1	0	DNAH5	13770498	1.000000	0.71417	0.956000	0.39512	0.935000	0.57460	7.798000	0.85924	1.301000	0.44836	0.655000	0.94253	GAA		0.542	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13717498	C	A	13717498	4	1	39	1	0	0	0	0	0	1	0	0	4615	893	31	2	1271	2	DNAH5	5	13717498	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		13717498	167197762	51	3515										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13894787	13894787	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcaaaagtgttttctaaataAgcctcaatattcagtgatgt	7	6	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:13894787A>G	ENST00000265104.4	-	16	2507	c.2403T>C	c.(2401-2403)gcT>gcC	p.A801A	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	801	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTTCTAAATAAGCCTCAATAT	0.403									Kartagener syndrome																																							0			5											126	119	122					5																	13894787		2203	4300	6503	13947787	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2403T>C	5.37:g.13894787A>G			13947787	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13894787	A	G	13894787	2	3	39	1	0	0	0	0	0	0	0	1	4615	59	3	4		4	DNAH5	5	13894787	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	177289	13894787	167020473	52	3516										
CDH18	1016	hgsc.bcm.edu	37	chr5	19838903	19838903	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aggatctggtcccatatgttCttctaaaacaaagaactgat	7	8	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:19838903C>T	ENST00000507958.1	-	5	1183	c.193G>A	c.(193-195)Gaa>Aaa	p.E65K	CDH18_ENST00000511273.1_Missense_Mutation_p.E65K|CDH18_ENST00000274170.4_Missense_Mutation_p.E65K|CDH18_ENST00000502796.1_Missense_Mutation_p.E65K|CDH18_ENST00000382275.1_Missense_Mutation_p.E65K|CDH18_ENST00000506372.1_Missense_Mutation_p.E65K			Q13634	CAD18_HUMAN	cadherin 18, type 2	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E65*(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CCCATATGTTCTTCTAAAACA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											141	123	129					5																	19838903		2203	4300	6503	19874660	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.193G>A	5.37:g.19838903C>T	ENSP00000425093:p.Glu65Lys		19874660	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459777	0.96240	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.00565	6.56;6.56;6.56;6.56;6.56;6.56;6.56	5.93	5.93	0.95920	Cadherin (1);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.04815	0.0130	H	0.96111	3.77	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.78314	0.965;0.991	T	0.01323	-1.1385	9	.	.	.	.	18.9006	0.92440	0.0:1.0:0.0:0.0	.	65;65	B4DHG6;Q13634	.;CAD18_HUMAN	K	65;65;65;65;65;65;11;65	ENSP00000371710:E65K;ENSP00000425093:E65K;ENSP00000274170:E65K;ENSP00000424931:E65K;ENSP00000422138:E65K;ENSP00000427383:E11K;ENSP00000425854:E65K	.	E	-	1	0	CDH18	19874660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.452000	0.80683	2.805000	0.96524	0.655000	0.94253	GAA		0.398	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19838903	C	T	19838903	3	4	39	1	0	0	0	0	1	0	0	0	3109	922	32	3	2223	3	CDH18	5	19838903	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5944116	19838903	161076357	53	3517										
ENC1	8507	hgsc.bcm.edu	37	chr5	73931301	73931301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtacactttgcagccaatcGcacatgcactaaactctttt	5	12	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:73931301G>A	ENST00000302351.4	-	2	2140	c.1010C>T	c.(1009-1011)gCg>gTg	p.A337V	ENC1_ENST00000510316.1_Missense_Mutation_p.A264V|ENC1_ENST00000537006.1_Missense_Mutation_p.A337V	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	337					multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		GCAGCCAATCGCACATGCACT	0.483																																																0			5											121	131	128					5																	73931301		2203	4300	6503	73967057	SO:0001583	missense	8507			AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"Kelch-like", "BTB/POZ domain containing"	3345	protein-coding gene	gene with protein product	"kelch-like family member 37"	605173	"ectodermal-neural cortex 1 (with BTB-like domain)"	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1010C>T	5.37:g.73931301G>A	ENSP00000306356:p.Ala337Val		73967057	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	37	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.515857	0.85495	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.72615	-0.67;-0.67;-0.67	5.89	5.89	0.94794	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.69869	0.3159	N	0.25647	0.755	0.80722	D	1	D	0.56287	0.975	P	0.56127	0.792	T	0.62015	-0.6943	10	0.06625	T	0.88	.	20.2566	0.98424	0.0:0.0:1.0:0.0	.	337	O14682	ENC1_HUMAN	V	337;264;337	ENSP00000306356:A337V;ENSP00000423804:A264V;ENSP00000446289:A337V	ENSP00000306356:A337V	A	-	2	0	ENC1	73967057	1.000000	0.71417	0.964000	0.40570	0.985000	0.73830	9.869000	0.99810	2.793000	0.96121	0.561000	0.74099	GCG		0.483	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633		A	73931301	G	A	73931301	3	1	39	1	0	0	0	0	1	0	0	0	5126	1087	38	1	763	1	ENC1	5	73931301	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	54092398	73931301	106983959	54	3518										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102474135	102474135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgaaggtattttacttcctcGttatgctattttgaaccgtg	8	7	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:102474135G>A	ENST00000358359.3	+	5	958	c.449G>A	c.(448-450)cGt>cAt	p.R150H	PPIP5K2_ENST00000414217.1_Missense_Mutation_p.R150H|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.R150H	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	150					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TTACTTCCTCGTTATGCTATT	0.363																																																0			5											97	95	96					5																	102474135		2202	4299	6501	102502034	SO:0001583	missense	23262			AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.449G>A	5.37:g.102474135G>A	ENSP00000351126:p.Arg150His		102502034	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	37		.	.	.	.	.	.	.	.	.	.	G	34	5.333969	0.95758	.	.	ENSG00000145725	ENST00000321521;ENST00000507921;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000507310	T;T;T;T	0.16196	2.37;3.05;2.36;2.37	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.47322	0.1439	M	0.91090	3.175	0.80722	D	1	D;D;D	0.67145	0.974;0.996;0.994	P;P;P	0.59595	0.764;0.86;0.803	T	0.61143	-0.7122	10	0.87932	D	0	.	16.5739	0.84632	0.0:0.0:1.0:0.0	.	72;150;150	D6RBU4;O43314-2;O43314	.;.;VIP2_HUMAN	H	150;72;150;150;150;80	ENSP00000313070:R150H;ENSP00000422525:R72H;ENSP00000351126:R150H;ENSP00000416016:R150H	ENSP00000313070:R150H	R	+	2	0	PPIP5K2	102502034	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.199000	0.95003	2.413000	0.81919	0.585000	0.79938	CGT		0.363	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		A	102474135	G	A	102474135	3	1	39	1	0	0	0	0	1	0	0	0	12367	1145	40	1	463	1	PPIP5K2	5	102474135	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	28542834	102474135	78441125	55	3519										
APC	324	hgsc.bcm.edu	37	chr5	112162891	112162891	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	actacagtattacactaagaCgatatgctggaatggctttg	9	7	0	1	rs137854580		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:112162891C>T	ENST00000457016.1	+	12	1875	c.1495C>T	c.(1495-1497)Cga>Tga	p.R499*	APC_ENST00000257430.4_Nonsense_Mutation_p.R499*|CTC-554D6.1_ENST00000520401.1_5'Flank|APC_ENST00000508376.2_Nonsense_Mutation_p.R499*			P25054	APC_HUMAN	adenomatous polyposis coli	499	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R499*(5)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TACACTAAGACGATATGCTGG	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Substitution - Nonsense(5)|Unknown(1)	large_intestine(5)|skin(1)	5	GRCh37	CM930023	APC	M	rs137854580						135	123	127					5																	112162891		2202	4300	6502	112190790	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1495C>T	5.37:g.112162891C>T	ENSP00000413133:p.Arg499*		112190790	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.025077	0.98616	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.85	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3767	14.9298	0.70906	0.2732:0.7267:0.0:0.0	.	.	.	.	X	499;481;499;499;499	.	ENSP00000257430:R499X	R	+	1	2	APC	112190790	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.513000	0.35823	1.461000	0.47929	0.655000	0.94253	CGA		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112162891	C	T	112162891	4	4	39	1	0	0	0	0	0	1	0	0	763	528	19	1	1537	1	APC	5	112162891	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	9688756	112162891	68752369	56	3520										
APC	324	hgsc.bcm.edu	37	chr5	112173603	112173603	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agatgctcagcacttatcagAaacttttgacaatatagaca	6	8	2	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:112173603A>G	ENST00000457016.1	+	16	2692	c.2312A>G	c.(2311-2313)gAa>gGa	p.E771G	APC_ENST00000257430.4_Missense_Mutation_p.E771G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.E771G			P25054	APC_HUMAN	adenomatous polyposis coli	771	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E771G(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CACTTATCAGAAACTTTTGAC	0.388		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											58	59	59					5																	112173603		2202	4300	6502	112201502	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2312A>G	5.37:g.112173603A>G	ENSP00000413133:p.Glu771Gly		112201502	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.773064	0.69992	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;T;D;D;T	0.92249	-3.0;0.88;-3.0;-3.0;0.88	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.95611	0.8573	M	0.71581	2.175	0.80722	D	1	D;D	0.63046	0.992;0.992	D;D	0.70016	0.936;0.967	D	0.95788	0.8822	10	0.72032	D	0.01	-23.7975	16.8061	0.85666	1.0:0.0:0.0:0.0	.	773;771	Q4LE70;P25054	.;APC_HUMAN	G	771;753;771;771;771	ENSP00000413133:E771G;ENSP00000423224:E753G;ENSP00000257430:E771G;ENSP00000427089:E771G;ENSP00000423828:E771G	ENSP00000257430:E771G	E	+	2	0	APC	112201502	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	GAA		0.388	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173603	A	G	112173603	3	3	39	1	0	0	0	0	1	0	0	0	763	246	9	4	2370	4	APC	5	112173603	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	10712	112173603	68741657	57	3521										
APC	324	hgsc.bcm.edu	37	chr5	112174743	112174743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgaacgttactctgaagaagAacagcatgaagaagaagaga	11	5	1	8			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:112174743A>G	ENST00000457016.1	+	16	3832	c.3452A>G	c.(3451-3453)gAa>gGa	p.E1151G	APC_ENST00000257430.4_Missense_Mutation_p.E1151G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.E1151G			P25054	APC_HUMAN	adenomatous polyposis coli	1151	Asp/Glu-rich (acidic).|Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTGAAGAAGAACAGCATGAA	0.328		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											61	60	60					5																	112174743		2202	4300	6502	112202642	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3452A>G	5.37:g.112174743A>G	ENSP00000413133:p.Glu1151Gly		112202642	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.909575	0.52439	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48	5.76	4.6	0.57074	.	0.071969	0.56097	N	0.000029	D	0.89615	0.6766	L	0.27053	0.805	0.46521	D	0.999088	B;D	0.76494	0.0;0.999	B;D	0.81914	0.0;0.995	D	0.88663	0.3190	10	0.44086	T	0.13	-11.3568	11.7089	0.51614	0.931:0.0:0.069:0.0	.	1153;1151	Q4LE70;P25054	.;APC_HUMAN	G	1151;1133;1151;1151;1151	ENSP00000413133:E1151G;ENSP00000423224:E1133G;ENSP00000257430:E1151G;ENSP00000427089:E1151G;ENSP00000423828:E1151G	ENSP00000257430:E1151G	E	+	2	0	APC	112202642	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.297000	0.72757	1.021000	0.39600	0.533000	0.62120	GAA		0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174743	A	G	112174743	3	3	39	1	0	0	0	0	1	0	0	0	763	246	9	4	3510	4	APC	5	112174743	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1140	112174743	68740517	58	3522										
APC	324	hgsc.bcm.edu	37	chr5	112175678	112175678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aagcacctactgctgaaaagAgagagagtggacctaagcaa	11	8	0	3	rs387906235		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:112175678A>G	ENST00000457016.1	+	16	4767	c.4387A>G	c.(4387-4389)Aga>Gga	p.R1463G	APC_ENST00000257430.4_Missense_Mutation_p.R1463G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.R1463G			P25054	APC_HUMAN	adenomatous polyposis coli	1463	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1464fs*8(8)|p.S1465fs*3(8)|p.R1463*(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.K1462fs*5(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGCTGAAAAGAGAGAGAGTGG	0.453		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	21	Deletion - Frameshift(18)|Substitution - Nonsense(1)|Unknown(1)|Complex - frameshift(1)	large_intestine(17)|thyroid(1)|NS(1)|soft_tissue(1)|skin(1)	5											84	79	81					5																	112175678		2202	4300	6502	112203577	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4387A>G	5.37:g.112175678A>G	ENSP00000413133:p.Arg1463Gly		112203577	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	8.392	0.839860	0.16891	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89617	-2.54;-2.54;-2.54	5.96	3.49	0.39957	.	0.094899	0.64402	D	0.000001	D	0.82852	0.5127	L	0.40543	1.245	0.39935	D	0.974336	B;B	0.23735	0.09;0.09	B;B	0.16722	0.016;0.016	T	0.74968	-0.3483	9	.	.	.	-16.6113	12.9433	0.58359	0.7447:0.2553:0.0:0.0	.	1465;1463	Q4LE70;P25054	.;APC_HUMAN	G	1463	ENSP00000413133:R1463G;ENSP00000257430:R1463G;ENSP00000427089:R1463G	.	R	+	1	2	APC	112203577	1.000000	0.71417	0.995000	0.50966	0.659000	0.38960	3.477000	0.53151	0.457000	0.26962	-0.321000	0.08615	AGA		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175678	A	G	112175678	3	3	39	1	0	0	0	0	1	0	0	0	763	296	11	4	4445	4	APC	5	112175678	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	935	112175678	68739582	59	3523										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129070665	129070665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aggaatgcagtcccgtgtaaTccaatgcatgcataagatca	9	9	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:129070665T>C	ENST00000274487.4	+	22	3480	c.3335T>C	c.(3334-3336)aTc>aCc	p.I1112T	ADAMTS19_ENST00000509467.1_3'UTR|CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	1112	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		TCCCGTGTAATCCAATGCATG	0.383																																																0			5											102	101	101					5																	129070665		2203	4300	6503	129098564	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.3335T>C	5.37:g.129070665T>C	ENSP00000274487:p.Ile1112Thr		129098564		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120656	0.77323	.	.	ENSG00000145808	ENST00000274487	T	0.50548	0.74	4.26	4.26	0.50523	.	0.280714	0.28001	N	0.016983	T	0.52224	0.1721	L	0.37800	1.135	0.50632	D	0.999888	D	0.63046	0.992	P	0.58013	0.831	T	0.48736	-0.9009	9	.	.	.	.	14.4332	0.67264	0.0:0.0:0.0:1.0	.	1112	Q8TE59	ATS19_HUMAN	T	1112	ENSP00000274487:I1112T	.	I	+	2	0	ADAMTS19	129098564	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.279000	0.78599	2.149000	0.67028	0.477000	0.44152	ATC		0.383	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	129070665	T	C	129070665	3	2	39	1	0	0	0	0	1	0	0	0	264	1435	50	4	3421	4	ADAMTS19	5	129070665	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	16894987	129070665	51844595	60	3524										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209752	140209752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gccgcgggcccagaggcggcGctggtggatgtcaacgtgta	18	11	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:140209752G>A	ENST00000529310.1	+	1	2190	c.2076G>A	c.(2074-2076)gcG>gcA	p.A692A	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	692					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGGCGGCGCTGGTGGATG	0.672																																																0			5											46	50	48					5																	140209752		2201	4293	6494	140189936	SO:0001819	synonymous_variant	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2076G>A	5.37:g.140209752G>A			140189936	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																				0.672	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140209752	G	A	140209752	2	1	39	1	0	0	0	0	0	0	0	1	11559	1074	38	1		1	PCDHA6	5	140209752	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	11139087	140209752	40705508	61	3525										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250778	140250778	+	Frame_Shift_Del	DEL	T	T	-													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcgctggtggatgtcaacgTgtacctgatcatcgccatct							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:140250778delT	ENST00000398640.2	+	1	2090	c.2090delT	c.(2089-2091)gtgfs	p.V697fs	PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	697					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGTCAACGTGTACCTGATC	0.657																																																0			5											45	47	46					5																	140250778		2203	4299	6502	140230962	SO:0001589	frameshift_variant	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2090delT	5.37:g.140250778delT	ENSP00000381636:p.Val697fs		140230962	B2RN58|O75279	Frame_Shift_Del	DEL	ENST00000398640.2	37	CCDS47284.1																																																																																				0.657	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		-	140250778	T	-	140250778	7	5	39	1	0	1	0	1	0	0	0	0	11552	1696	59	0	2092	0	PCDHA11	5	140250778	Frame_Shift_Del	DEL	T	TCGA-AG-3742-01A-11D-1657-10	41026	140250778	40664482	62	3526										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140755454	140755454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acagagactcgggccagaacGcctggctgtcctaccgcctg	12	15	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:140755454G>A	ENST00000517434.1	+	1	1804	c.1804G>A	c.(1804-1806)Gcc>Acc	p.A602T	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	602	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCCAGAACGCCTGGCTGTC	0.697																																																0			5											32	40	37					5																	140755454		2200	4293	6493	140735638	SO:0001583	missense	56109			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1804G>A	5.37:g.140755454G>A	ENSP00000429601:p.Ala602Thr		140735638	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	20.5	3.997278	0.74818	.	.	ENSG00000253731	ENST00000517434	T	0.60797	0.16	4.75	2.95	0.34219	Cadherin (4);Cadherin-like (1);	0.000000	0.30901	U	0.008642	T	0.78432	0.4282	M	0.92268	3.29	0.29298	N	0.868864	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.983	T	0.74763	-0.3555	10	0.87932	D	0	.	9.6554	0.39923	0.0739:0.0:0.7846:0.1414	.	602;602	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	T	602	ENSP00000429601:A602T	ENSP00000429601:A602T	A	+	1	0	PCDHGA6	140735638	1.000000	0.71417	0.970000	0.41538	0.945000	0.59286	4.686000	0.61700	0.718000	0.32166	0.558000	0.71614	GCC		0.697	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		A	140755454	G	A	140755454	3	1	39	1	0	0	0	0	1	0	0	0	11589	1087	38	1	1806	1	PCDHGA6	5	140755454	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	504676	140755454	40159806	63	3527										
GRPEL2	134266	hgsc.bcm.edu	37	chr5	148730567	148730567	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tttctgaagaatcggagcctGaggaccaaaagctcactctg	10	10	3	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:148730567G>T	ENST00000329271.3	+	4	510	c.400G>T	c.(400-402)Gag>Tag	p.E134*	GRPEL2_ENST00000507562.1_3'UTR|GRPEL2-AS1_ENST00000521295.1_RNA|GRPEL2_ENST00000416916.2_Silent_p.L106L	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	134					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCGGAGCCTGAGGACCAAAA	0.483																																																0			5											95	97	96					5																	148730567		2203	4300	6503	148710760	SO:0001587	stop_gained	134266			AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.400G>T	5.37:g.148730567G>T	ENSP00000329558:p.Glu134*		148710760	B4DFA6|Q49AJ6	Nonsense_Mutation	SNP	ENST00000329271.3	37	CCDS4295.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269979	0.40095	.	.	ENSG00000164284	ENST00000329271	.	.	.	5.95	4.13	0.48395	.	0.499437	0.20114	N	0.098942	.	.	.	.	.	.	0.53688	D	0.999978	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-16.1984	5.8756	0.18826	0.1501:0.3358:0.5141:0.0	.	.	.	.	X	134	.	ENSP00000329558:E134X	E	+	1	0	GRPEL2	148710760	0.414000	0.25408	0.870000	0.34147	0.014000	0.08584	3.534000	0.53568	0.801000	0.34066	0.655000	0.94253	GAG		0.483	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		T	148730567	G	T	148730567	4	4	39	1	0	0	0	0	0	1	0	0	6828	1291	45	2	414	2	GRPEL2	5	148730567	Nonsense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	7975113	148730567	32184693	64	3528										
GRM6	2916	hgsc.bcm.edu	37	chr5	178413956	178413956	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccgggcgcatctccgttctcGttgaacatcacaggggttcc	11	14	3	1	rs143351800	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr5:178413956G>A	ENST00000517717.1	-	8	1421	c.1383C>T	c.(1381-1383)aaC>aaT	p.N461N	GRM6_ENST00000231188.5_Silent_p.N461N|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	461					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		CTCCGTTCTCGTTGAACATCA	0.662													G|||	5	0.000998403	0	0.0014	5008	,	,		17812	0.003		0.001	False		,,,				2504	0															0			5						G		0,4406		0,0,2203	66	57	60		1383	-7.3	0.9	5	dbSNP_134	60	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GRM6	NM_000843.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		461/878	178413956	2,13004	2203	4300	6503	178346562	SO:0001819	synonymous_variant	2916			U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1383C>T	5.37:g.178413956G>A			178346562		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																				0.662	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			A	178413956	G	A	178413956	2	1	39	1	0	0	0	0	0	0	0	1	6822	1136	40	1		1	GRM6	5	178413956	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	29683389	178413956	2501304	65	3529										
FOXF2	2295	hgsc.bcm.edu	37	chr6	1390681	1390681	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agctgcctaagggcctcgggCggcccggcaagggccactac	15	15	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:1390681C>T	ENST00000259806.1	+	1	613	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	167					embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		GGGCCTCGGGCGGCCCGGCAA	0.667																																																0			6											46	56	53					6																	1390681		2202	4300	6502	1335680	SO:0001583	missense	2295			U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"Forkhead boxes"	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.499C>T	6.37:g.1390681C>T	ENSP00000259806:p.Arg167Trp		1335680	Q5TGJ1|Q9UQ85	Missense_Mutation	SNP	ENST00000259806.1	37	CCDS4472.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941817	0.73557	.	.	ENSG00000137273	ENST00000259806	D	0.95724	-3.79	4.53	3.65	0.41850	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	D	0.000001	D	0.97210	0.9088	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97427	1.0013	10	0.87932	D	0	.	11.0223	0.47726	0.3352:0.6648:0.0:0.0	.	167	Q12947	FOXF2_HUMAN	W	167	ENSP00000259806:R167W	ENSP00000259806:R167W	R	+	1	2	FOXF2	1335680	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.780000	0.26760	0.898000	0.36418	0.536000	0.68110	CGG		0.667	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1			T	1390681	C	T	1390681	3	4	39	1	0	0	0	0	1	0	0	0	6025	759	27	1	501	1	FOXF2	6	1390681	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		1390681	169724386	66	3530										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31933753	31933753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tatcctgctctgcaagggccGagtgcccgagatggcagacc	13	13	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:31933753G>A	ENST00000375394.2	+	18	2278	c.2165G>A	c.(2164-2166)cGa>cAa	p.R722Q	SKIV2L_ENST00000544581.1_Missense_Mutation_p.R529Q	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	722	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TGCAAGGGCCGAGTGCCCGAG	0.662																																																0			6											28	24	26					6																	31933753		1509	2708	4217	32041732	SO:0001583	missense	6499				CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.2165G>A	6.37:g.31933753G>A	ENSP00000364543:p.Arg722Gln		32041732	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	37	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806760	0.50421	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.46063	1.01;0.88	5.34	5.34	0.76211	Helicase, C-terminal (1);	0.117336	0.56097	D	0.000022	T	0.07593	0.0191	N	0.08118	0	0.34074	D	0.658782	P	0.51791	0.948	B	0.33254	0.16	T	0.06023	-1.0850	10	0.26408	T	0.33	-9.2184	8.2915	0.31960	0.17:0.0:0.83:0.0	.	722	Q15477	SKIV2_HUMAN	Q	722;564;529	ENSP00000364543:R722Q;ENSP00000442645:R529Q	ENSP00000364543:R722Q	R	+	2	0	SKIV2L	32041732	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.623000	0.54224	2.494000	0.84150	0.655000	0.94253	CGA		0.662	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31933753	G	A	31933753	3	1	39	1	0	0	0	0	1	0	0	0	14396	1058	37	1	2235	1	SKIV2L	6	31933753	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	30543072	31933753	139181314	67	3531										
KHDC1	80759	hgsc.bcm.edu	37	chr6	73951352	73951352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cggttccacttatcctgggaGccaaagacaggtctccagtg	11	12	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:73951352G>A	ENST00000370384.3	-	5	1114	c.614C>T	c.(613-615)gCt>gTt	p.A205V	RP11-257K9.8_ENST00000423730.3_Intron|KHDC1_ENST00000257765.5_Missense_Mutation_p.A132V	NM_001251874.1	NP_001238803.1	Q4VXA5	KHDC1_HUMAN	KH homology domain containing 1	205						integral component of membrane (GO:0016021)	RNA binding (GO:0003723)			large_intestine(1)|lung(4)|skin(1)	6						TATCCTGGGAGCCAAAGACAG	0.527																																																0			6											114	119	117					6																	73951352		2056	4182	6238	74008073	SO:0001583	missense	80759				CCDS43480.1, CCDS59027.1	6q13	2014-05-15	2007-11-13	2007-11-13	ENSG00000135314	ENSG00000135314			21366	protein-coding gene	gene with protein product		611688	"chromosome 6 open reading frame 148"	C6orf148		17913455	Standard	NM_030568		Approved	MGC10818, bA257K9.4, NDG1	uc003pgn.4	Q4VXA5	OTTHUMG00000015030	ENST00000370384.3:c.614C>T	6.37:g.73951352G>A	ENSP00000359411:p.Ala205Val		74008073	Q5JSQ7|Q8WTV2|Q96NQ5	Missense_Mutation	SNP	ENST00000370384.3	37	CCDS59027.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.630726	0.28978	.	.	ENSG00000135314	ENST00000257765;ENST00000370384	T	0.32272	1.46	1.99	1.07	0.20283	.	.	.	.	.	T	0.04770	0.0129	N	0.22421	0.69	0.09310	N	1	P	0.44659	0.84	B	0.37692	0.256	T	0.20140	-1.0284	9	0.08381	T	0.77	.	6.2543	0.20865	0.0:0.3173:0.6827:0.0	.	205	Q4VXA5	KHDC1_HUMAN	V	132;205	ENSP00000359411:A205V	ENSP00000257765:A132V	A	-	2	0	KHDC1	74008073	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	0.523000	0.22925	0.375000	0.24679	0.561000	0.74099	GCT		0.527	KHDC1-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000148103.2	NM_030568		A	73951352	G	A	73951352	3	1	39	1	0	0	0	0	1	0	0	0	8165	971	34	3	103	3	KHDC1	6	73951352	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	42017599	73951352	97163715	68	3532										
PHIP	55023	hgsc.bcm.edu	37	chr6	79692787	79692787	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctttctttggtggctgcagaTtaattcctgcatctgctgtc	9	10	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:79692787T>C	ENST00000275034.4	-	23	2752	c.2585A>G	c.(2584-2586)aAt>aGt	p.N862S	PHIP_ENST00000479165.1_5'Flank	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	862					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TGGCTGCAGATTAATTCCTGC	0.363																																																0			6											108	110	109					6																	79692787		2203	4300	6503	79749506	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2585A>G	6.37:g.79692787T>C	ENSP00000275034:p.Asn862Ser		79749506	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349165	0.82132	.	.	ENSG00000146247	ENST00000275034	T	0.53857	0.6	5.12	5.12	0.69794	.	0.064417	0.64402	D	0.000007	T	0.46852	0.1414	M	0.64080	1.96	0.80722	D	1	P;P	0.51791	0.948;0.948	P;P	0.48738	0.588;0.588	T	0.49093	-0.8975	9	.	.	.	-21.882	14.092	0.64998	0.0:0.0:0.0:1.0	.	862;862	A7J992;Q8WWQ0	.;PHIP_HUMAN	S	862	ENSP00000275034:N862S	.	N	-	2	0	PHIP	79749506	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	7.694000	0.84235	1.921000	0.55644	0.383000	0.25322	AAT		0.363	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79692787	T	C	79692787	3	2	39	1	0	0	0	0	1	0	0	0	11873	1493	52	4	2952	4	PHIP	6	79692787	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	5741435	79692787	91422280	69	3533										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599122	136599122	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcgattgtctttgcaggactTcttcgtgaagggatgtgatg	14	6	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:136599122T>C	ENST00000531224.1	-	4	1149	c.897A>G	c.(895-897)agA>agG	p.R299R	BCLAF1_ENST00000527536.1_Silent_p.R299R|BCLAF1_ENST00000527759.1_Silent_p.R297R|BCLAF1_ENST00000530767.1_Silent_p.R299R|BCLAF1_ENST00000353331.4_Silent_p.R297R|BCLAF1_ENST00000392348.2_Silent_p.R297R	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	299					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TTGCAGGACTTCTTCGTGAAG	0.468																																					Colon(142;1534 1789 5427 7063 28491)											0			6											86	77	80					6																	136599122		2203	4300	6503	136640815	SO:0001819	synonymous_variant	9774			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.897A>G	6.37:g.136599122T>C			136640815	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Silent	SNP	ENST00000531224.1	37	CCDS5177.1																																																																																				0.468	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		C	136599122	T	C	136599122	2	2	39	1	0	0	0	0	0	0	0	1	1384	1780	62	4		4	BCLAF1	6	136599122	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	56906335	136599122	34515945	70	3534										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138198220	138198220	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tttttttccttagaaatccgAgctgttccacttgttaacag	6	9	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:138198220A>G	ENST00000237289.4	+	6	879	c.813A>G	c.(811-813)cgA>cgG	p.R271R	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	271	TRAF-binding.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TAGAAATCCGAGCTGTTCCAC	0.323			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	6											65	73	70					6																	138198220		2203	4300	6503	138239913	SO:0001819	synonymous_variant	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.813A>G	6.37:g.138198220A>G			138239913	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																				0.323	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138198220	A	G	138198220	2	3	39	1	0	0	0	0	0	0	0	1	16313	291	11	4		4	TNFAIP3	6	138198220	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1599098	138198220	32916847	71	3535										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143090731	143090731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cttgatgatgtaagcttgccGgttccaggcctatgcatagc	11	10	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:143090731G>A	ENST00000367604.1	-	4	5784	c.5145C>T	c.(5143-5145)acC>acT	p.T1715T	HIVEP2_ENST00000012134.2_Silent_p.T1715T|HIVEP2_ENST00000367603.2_Silent_p.T1715T			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1715					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TAAGCTTGCCGGTTCCAGGCC	0.433																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											0			6											116	107	110					6																	143090731		1869	4122	5991	143132424	SO:0001819	synonymous_variant	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5145C>T	6.37:g.143090731G>A			143132424	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																				0.433	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			A	143090731	G	A	143090731	2	1	39	1	0	0	0	0	0	0	0	1	7208	1103	39	1		1	HIVEP2	6	143090731	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	4892511	143090731	28024336	72	3536										
ULBP2	80328	hgsc.bcm.edu	37	chr6	150267608	150267608	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gatgggcagatcttcctcctCtttgactcagagaagagaat	10	9	3	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:150267608C>G	ENST00000367351.3	+	3	523	c.450C>G	c.(448-450)ctC>ctG	p.L150L		NM_025217.2	NP_079493.1	Q9BZM5	N2DL2_HUMAN	UL16 binding protein 2	150	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular space (GO:0005615)	natural killer cell lectin-like receptor binding (GO:0046703)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		TCTTCCTCCTCTTTGACTCAG	0.493																																																0			6											247	222	230					6																	150267608		2203	4300	6503	150309301	SO:0001819	synonymous_variant	80328			AF304378	CCDS5222.1	6q25	2008-04-11			ENSG00000131015	ENSG00000131015			14894	protein-coding gene	gene with protein product		605698				11239445	Standard	NM_025217		Approved	RAET1H	uc003qno.3	Q9BZM5	OTTHUMG00000015803	ENST00000367351.3:c.450C>G	6.37:g.150267608C>G			150309301	Q5VUN4	Silent	SNP	ENST00000367351.3	37	CCDS5222.1																																																																																				0.493	ULBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042669.1			G	150267608	C	G	150267608	2	3	39	1	0	0	0	0	0	0	0	1	17013	900	32	5		5	ULBP2	6	150267608	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	7176877	150267608	20847459	73	3537										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152485384	152485384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagctctgactcgatgtgagCgagccaggtcctcaggctgc	13	13	2	2	rs372990463		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:152485384C>T	ENST00000367255.5	-	131	24305	c.23704G>A	c.(23704-23706)Gct>Act	p.A7902T	SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000423061.1_Missense_Mutation_p.A7831T|SYNE1_ENST00000448038.1_Missense_Mutation_p.A7831T|SYNE1_ENST00000341594.5_Missense_Mutation_p.A7514T|SYNE1_ENST00000356820.4_Missense_Mutation_p.A2426T|SYNE1_ENST00000539504.1_Missense_Mutation_p.A57T|SYNE1_ENST00000354674.4_Missense_Mutation_p.A57T|SYNE1_ENST00000265368.4_Missense_Mutation_p.A7902T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7902					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCGATGTGAGCGAGCCAGGTC	0.502										HNSCC(10;0.0054)																																						0			6						C	THR/ALA,THR/ALA	0,4406		0,0,2203	103	92	96		23491,23704	3.4	1	6		96	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SYNE1	NM_033071.3,NM_182961.3	58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	7831/8750,7902/8798	152485384	2,13004	2203	4300	6503	152527077	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23704G>A	6.37:g.152485384C>T	ENSP00000356224:p.Ala7902Thr		152527077	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998983	0.74818	0.0	2.33E-4	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.26	3.37	0.38596	.	0.252994	0.27549	N	0.018862	T	0.36744	0.0978	N	0.22421	0.69	0.42346	D	0.992356	D;D;D;D;P	0.71674	0.985;0.998;0.998;0.998;0.896	P;D;P;D;B	0.64321	0.821;0.924;0.876;0.924;0.378	T	0.34976	-0.9807	10	0.56958	D	0.05	.	9.5516	0.39313	0.142:0.7837:0.0:0.0743	.	7902;7902;7831;7831;104	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	T	7902;57;548;7831;7902;7831;7514;2426;64;59;824;57	ENSP00000356224:A7902T;ENSP00000441052:A57T;ENSP00000356226:A548T;ENSP00000396024:A7831T;ENSP00000265368:A7902T;ENSP00000390975:A7831T;ENSP00000341887:A7514T;ENSP00000349276:A2426T;ENSP00000356220:A824T;ENSP00000346701:A57T	ENSP00000265368:A7902T	A	-	1	0	SYNE1	152527077	0.775000	0.28604	0.965000	0.40720	0.856000	0.48823	1.510000	0.35790	1.219000	0.43474	-0.225000	0.12378	GCT		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152485384	C	T	152485384	3	4	39	1	0	0	0	0	1	0	0	0	15484	768	27	1	2826	1	SYNE1	6	152485384	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	2217776	152485384	18629683	74	3538										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152629718	152629718	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gagctccttctatcagttgcTggagatgtttcatttcttgc	9	9	4	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr6:152629718T>C	ENST00000367255.5	-	91	17853	c.17252A>G	c.(17251-17253)cAg>cGg	p.Q5751R	SYNE1_ENST00000423061.1_Missense_Mutation_p.Q5680R|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q5680R|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q5363R|SYNE1_ENST00000356820.4_Missense_Mutation_p.Q275R|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q5751R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5751					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TATCAGTTGCTGGAGATGTTT	0.393										HNSCC(10;0.0054)																																						0			6											185	166	173					6																	152629718		2203	4300	6503	152671411	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.17252A>G	6.37:g.152629718T>C	ENSP00000356224:p.Gln5751Arg		152671411	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	17.19	3.325235	0.60743	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74	5.96	4.8	0.61643	.	0.100348	0.44483	N	0.000460	T	0.18718	0.0449	L	0.32530	0.975	0.58432	D	0.999993	B;B;B	0.20368	0.044;0.044;0.036	B;B;B	0.25405	0.06;0.06;0.059	T	0.06552	-1.0820	10	0.13853	T	0.58	.	12.1123	0.53846	0.0:0.0668:0.0:0.9332	.	5751;5751;5680	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	R	5751;5680;5751;5680;5363;275	ENSP00000356224:Q5751R;ENSP00000396024:Q5680R;ENSP00000265368:Q5751R;ENSP00000390975:Q5680R;ENSP00000341887:Q5363R;ENSP00000349276:Q275R	ENSP00000265368:Q5751R	Q	-	2	0	SYNE1	152671411	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.304000	0.72800	1.076000	0.40961	0.533000	0.62120	CAG		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152629718	T	C	152629718	3	2	39	1	0	0	0	0	1	0	0	0	15484	1580	55	4	9438	4	SYNE1	6	152629718	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	144334	152629718	18485349	75	3539										
CRHR2	1395	hgsc.bcm.edu	37	chr7	30693202	30693202	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagcggtgccacctcttcctCacggctgagcgcacctgtgg	12	16	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:30693202C>T	ENST00000471646.1	-	12	1527	c.1110G>A	c.(1108-1110)gtG>gtA	p.V370V	CRHR2_ENST00000506074.2_3'UTR|CRHR2_ENST00000341843.4_Silent_p.V356V|CRHR2_ENST00000348438.4_Silent_p.V397V	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	370					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACCTCTTCCTCACGGCTGAGC	0.632																																																0			7											107	93	97					7																	30693202		2203	4300	6503	30659727	SO:0001819	synonymous_variant	1395				CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.1110G>A	7.37:g.30693202C>T			30659727	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Silent	SNP	ENST00000471646.1	37	CCDS5429.1																																																																																				0.632	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3			T	30693202	C	T	30693202	2	4	39	1	0	0	0	0	0	0	0	1	3878	813	29	3		3	CRHR2	7	30693202	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10		30693202	128445461	76	3540										
EGFR	1956	hgsc.bcm.edu	37	chr7	55241674	55241674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aagctctcttgaggatcttgAaggaaactgaattcaaaaag	9	6	3	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:55241674A>G	ENST00000275493.2	+	18	2299	c.2122A>G	c.(2122-2124)Aag>Gag	p.K708E	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.K663E|EGFR_ENST00000454757.2_Missense_Mutation_p.K655E	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	708					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.K708E(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GAGGATCTTGAAGGAAACTGA	0.562		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	1	Substitution - Missense(1)	ovary(1)	7											88	91	90					7																	55241674		2203	4300	6503	55209168	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2122A>G	7.37:g.55241674A>G	ENSP00000275493:p.Lys708Glu		55209168	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.980676	0.92982	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.62232	0.04;0.04;0.04	5.83	5.83	0.93111	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.78578	0.4305	M	0.74258	2.255	0.58432	D	0.999999	P;D	0.89917	0.621;1.0	B;D	0.72338	0.267;0.977	T	0.81234	-0.1025	10	0.87932	D	0	.	15.0123	0.71557	1.0:0.0:0.0:0.0	.	663;708	Q504U8;P00533	.;EGFR_HUMAN	E	663;578;708;655	ENSP00000415559:K663E;ENSP00000275493:K708E;ENSP00000395243:K655E	ENSP00000275493:K708E	K	+	1	0	EGFR	55209168	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.306000	0.96204	2.215000	0.71742	0.460000	0.39030	AAG		0.562	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55241674	A	G	55241674	3	3	39	1	0	0	0	0	1	0	0	0	4978	247	9	4	2456	4	EGFR	7	55241674	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	24548472	55241674	103896989	77	3541										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188404	57188404	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acattcctcacatctatatgGtttctctccagtatgaatta	4	10	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:57188404G>T	ENST00000331162.4	-	5	988	c.718C>A	c.(718-720)Cca>Aca	p.P240T		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			CATCTATATGGTTTCTCTCCA	0.398																																																0			7											21	23	22					7																	57188404		2011	4194	6205	57192346	SO:0001583	missense	90827			AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.718C>A	7.37:g.57188404G>T	ENSP00000333776:p.Pro240Thr		57192346		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	g	11.10	1.540410	0.27563	.	.	ENSG00000185177	ENST00000331162	T	0.16897	2.31	0.946	0.946	0.19549	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21718	0.0523	M	0.82193	2.58	0.34411	D	0.696371	P	0.36086	0.536	B	0.35899	0.213	T	0.30475	-0.9977	9	0.72032	D	0.01	.	7.3305	0.26580	0.0:0.0:1.0:0.0	.	240	Q96JC4	ZN479_HUMAN	T	240	ENSP00000333776:P240T	ENSP00000333776:P240T	P	-	1	0	ZNF479	57192346	0.995000	0.38212	0.118000	0.21660	0.077000	0.17291	3.756000	0.55205	0.399000	0.25367	0.400000	0.26472	CCA		0.398	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		T	57188404	G	T	57188404	3	4	39	1	0	0	0	0	1	0	0	0	17972	1261	44	2	860	2	ZNF479	7	57188404	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	1946730	57188404	101950259	78	3542										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70880968	70880968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gaagagggaaggcctgatccGcgctcgcattgagggctgga	17	9	0	3	rs367865697		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:70880968G>A	ENST00000333538.5	+	4	1317	c.683G>A	c.(682-684)cGc>cAc	p.R228H	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	228	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				GGCCTGATCCGCGCTCGCATT	0.572																																																0			7						G	HIS/ARG	0,4406		0,0,2203	91	78	82		683	5	1	7		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	WBSCR17	NM_022479.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	228/599	70880968	1,13005	2203	4300	6503	70518904	SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.683G>A	7.37:g.70880968G>A	ENSP00000329654:p.Arg228His		70518904	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	35	5.466726	0.96257	0.0	1.16E-4	ENSG00000185274	ENST00000333538	T	0.61980	0.06	5.04	5.04	0.67666	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.79885	0.4523	M	0.87180	2.865	0.80722	D	1	D	0.58620	0.983	P	0.58820	0.846	D	0.84356	0.0535	10	0.87932	D	0	.	17.3775	0.87396	0.0:0.0:1.0:0.0	.	228	Q6IS24	GLTL3_HUMAN	H	228	ENSP00000329654:R228H	ENSP00000329654:R228H	R	+	2	0	WBSCR17	70518904	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.378000	0.97191	2.351000	0.79841	0.462000	0.41574	CGC		0.572	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	70880968	G	A	70880968	3	1	39	1	0	0	0	0	1	0	0	0	17304	1087	38	1	697	1	WBSCR17	7	70880968	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	13692564	70880968	88257695	79	3543										
ZP3	7784	hgsc.bcm.edu	37	chr7	76062905	76062905	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgtttgtggaccactgcgtGgccacaccgacaccagacca	10	14	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:76062905G>A	ENST00000394857.3	+	4	712	c.654G>A	c.(652-654)gtG>gtA	p.V218V	ZP3_ENST00000416245.1_Silent_p.V42V|ZP3_ENST00000336517.4_Silent_p.V167V	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	218	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						ACCACTGCGTGGCCACACCGA	0.597																																																0			7											125	108	113					7																	76062905		2203	4300	6503	75900841	SO:0001819	synonymous_variant	7784			M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"Zona pellucida glycoproteins"	13189	protein-coding gene	gene with protein product		182889	"zona pellucida glycoprotein 3A (sperm receptor)"	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.654G>A	7.37:g.76062905G>A			75900841	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	G	6.631	0.484872	0.12641	.	.	ENSG00000188372	ENST00000394860	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.6654	16.7058	0.85371	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	.	W	+	2	0	ZP3	75900841	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	6.318000	0.72866	2.534000	0.85438	0.655000	0.94253	TGG		0.597	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			A	76062905	G	A	76062905	2	1	39	1	0	0	0	0	0	0	0	1	18256	1335	47	3		3	ZP3	7	76062905	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	5181937	76062905	83075758	80	3544										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963747	88963747	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	actgtattttgattttaagcTttctcggaacacaaaggaag	8	6	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:88963747T>C	ENST00000333190.4	+	4	2060	c.1451T>C	c.(1450-1452)cTt>cCt	p.L484P		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	484							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GATTTTAAGCTTTCTCGGAAC	0.423										HNSCC(36;0.09)																																						0			7											50	50	50					7																	88963747		2203	4299	6502	88801683	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1451T>C	7.37:g.88963747T>C	ENSP00000329638:p.Leu484Pro		88801683	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.787441	0.49997	.	.	ENSG00000182348	ENST00000333190	T	0.06933	3.24	5.49	1.6	0.23607	.	0.442309	0.21471	N	0.073982	T	0.19967	0.0480	M	0.76328	2.33	0.58432	D	0.999992	D	0.64830	0.994	P	0.60173	0.87	T	0.00978	-1.1493	10	0.72032	D	0.01	-6.9896	6.8767	0.24151	0.2373:0.0:0.2223:0.5404	.	484	A4D1E1	Z804B_HUMAN	P	484	ENSP00000329638:L484P	ENSP00000329638:L484P	L	+	2	0	ZNF804B	88801683	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.967000	0.29344	0.518000	0.28383	0.533000	0.62120	CTT		0.423	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88963747	T	C	88963747	3	2	39	1	0	0	0	0	1	0	0	0	18210	1609	56	4	1465	4	ZNF804B	7	88963747	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	12900842	88963747	70174916	81	3545										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94048862	94048862	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgctggagccacaggtgaccGggtaagcatgcattttcact	12	10	1	1	rs34147460	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:94048862G>A	ENST00000297268.6	+	34	2549	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	693			Missing (in OI2). {ECO:0000269|PubMed:1339453}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ACAGGTGACCGGGTAAGCATG	0.473										HNSCC(75;0.22)			G|||	4	0.000798722	0	0	5008	,	,		17032	0.001		0.003	False		,,,				2504	0															0			7						G	GLN/ARG	0,4406		0,0,2203	164	153	157		2078	5.5	1	7	dbSNP_126	157	12,8588	9.8+/-36.6	0,12,4288	yes	missense-near-splice	COL1A2	NM_000089.3	43	0,12,6491	AA,AG,GG		0.1395,0.0,0.0923	possibly-damaging	693/1367	94048862	12,12994	2203	4300	6503	93886798	SO:0001630	splice_region_variant	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2079+1G>A	7.37:g.94048862G>A			93886798	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	17.98	3.521458	0.64747	0.0	0.001395	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93604	-3.25	5.53	5.53	0.82687	.	0.059760	0.64402	D	0.000002	D	0.89125	0.6626	L	0.31526	0.94	0.47245	D	0.999369	P	0.42908	0.793	B	0.35931	0.214	D	0.90002	0.4115	10	0.56958	D	0.05	.	19.4491	0.94860	0.0:0.0:1.0:0.0	rs34147460	693	P08123	CO1A2_HUMAN	Q	693;694	ENSP00000297268:R693Q	ENSP00000297268:R693Q	R	+	2	0	COL1A2	93886798	0.151000	0.22747	1.000000	0.80357	0.971000	0.66376	0.670000	0.25157	2.781000	0.95711	0.650000	0.86243	CGG		0.473	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	Missense_Mutation	A	94048862	G	A	94048862	5	1	39	1	0	0	0	0	0	0	1	0	3684	1130	39	1	2212	1	COL1A2	7	94048862	Splice_Site	SNP	G	TCGA-AG-3742-01A-11D-1657-10	5085115	94048862	65089801	82	3546										
NPTX2	4885	hgsc.bcm.edu	37	chr7	98257797	98257797	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atatgggaccgcgtccttcgCgcacaagaaattgtcaacat	9	11	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:98257797C>T	ENST00000265634.3	+	5	1317	c.1152C>T	c.(1150-1152)cgC>cgT	p.R384R		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	384	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			GCGTCCTTCGCGCACAAGAAA	0.562																																																0			7											98	77	84					7																	98257797		2203	4300	6503	98095733	SO:0001819	synonymous_variant	4885				CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1152C>T	7.37:g.98257797C>T			98095733	A4D267|Q86XV7|Q96G70	Silent	SNP	ENST00000265634.3	37	CCDS5657.1																																																																																				0.562	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		T	98257797	C	T	98257797	2	4	39	1	0	0	0	0	0	0	0	1	10634	755	27	1		1	NPTX2	7	98257797	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4208935	98257797	60880866	83	3547										
MUC17	140453	hgsc.bcm.edu	37	chr7	100677278	100677278	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcatgccaacctcaacttatAgtgaaggaagaactccttta	7	10	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:100677278A>G	ENST00000306151.4	+	3	2645	c.2581A>G	c.(2581-2583)Agt>Ggt	p.S861G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	861	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTCAACTTATAGTGAAGGAAG	0.483																																																0			7											298	284	289					7																	100677278		2203	4300	6503	100463998	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2581A>G	7.37:g.100677278A>G	ENSP00000302716:p.Ser861Gly		100463998	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.041	-1.283412	0.01398	.	.	ENSG00000169876	ENST00000306151	T	0.02552	4.25	1.14	-2.29	0.06805	.	.	.	.	.	T	0.01222	0.0040	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45101	-0.9284	9	0.18710	T	0.47	.	4.631	0.12502	0.3832:0.179:0.4378:0.0	.	861	Q685J3	MUC17_HUMAN	G	861	ENSP00000302716:S861G	ENSP00000302716:S861G	S	+	1	0	MUC17	100463998	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.628000	0.05515	-2.401000	0.00578	-1.281000	0.01382	AGT		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100677278	A	G	100677278	3	3	39	1	0	0	0	0	1	0	0	0	10004	420	15	4	2591	4	MUC17	7	100677278	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	2419481	100677278	58461385	84	3548										
FOXP2	93986	hgsc.bcm.edu	37	chr7	114268710	114268710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acaagcccttctccaacaacAgcaggctgtcatgctgcagc	8	15	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:114268710A>G	ENST00000393494.2	+	4	653	c.374A>G	c.(373-375)cAg>cGg	p.Q125R	AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000408937.3_Missense_Mutation_p.Q150R|FOXP2_ENST00000393489.3_Missense_Mutation_p.Q33R|FOXP2_ENST00000350908.4_Missense_Mutation_p.Q125R|FOXP2_ENST00000459666.1_3'UTR|FOXP2_ENST00000390668.3_Missense_Mutation_p.Q149R|FOXP2_ENST00000378237.3_Missense_Mutation_p.Q125R|FOXP2_ENST00000360232.4_Missense_Mutation_p.Q125R|FOXP2_ENST00000393498.2_Missense_Mutation_p.Q125R|FOXP2_ENST00000393491.3_Missense_Mutation_p.Q33R|FOXP2_ENST00000393500.3_Missense_Mutation_p.Q33R|FOXP2_ENST00000403559.4_Missense_Mutation_p.Q125R			O15409	FOXP2_HUMAN	forkhead box P2	125	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q150L(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						CTCCAACAACAGCAGGCTGTC	0.502																																																1	Substitution - Missense(1)	lung(1)	7											206	164	178					7																	114268710		2203	4300	6503	114055946	SO:0001583	missense	93986			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.374A>G	7.37:g.114268710A>G	ENSP00000377132:p.Gln125Arg		114055946	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.556279	0.65425	.	.	ENSG00000128573	ENST00000393500;ENST00000324462;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000393489;ENST00000360232;ENST00000452963;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T;T	0.70631	-0.5;1.57;1.55;1.59;1.57;1.57;1.36;1.57;1.55;1.36	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.84257	0.5432	M	0.80183	2.485	0.80722	D	1	P;P;P;P;P;P;P;P	0.48294	0.851;0.851;0.851;0.908;0.908;0.851;0.908;0.908	P;P;P;P;D;P;D;P	0.64144	0.775;0.775;0.775;0.888;0.922;0.775;0.922;0.888	D	0.86314	0.1688	10	0.87932	D	0	.	16.0681	0.80903	1.0:0.0:0.0:0.0	.	125;125;33;125;149;125;150;150	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4;O15409-5	.;.;.;.;.;FOXP2_HUMAN;.;.	R	33;125;125;150;125;125;125;125;33;125;125;149;33	ENSP00000377137:Q33R;ENSP00000377132:Q125R;ENSP00000386200:Q150R;ENSP00000385069:Q125R;ENSP00000265436:Q125R;ENSP00000367482:Q125R;ENSP00000377129:Q33R;ENSP00000353367:Q125R;ENSP00000375084:Q149R;ENSP00000377130:Q33R	ENSP00000319424:Q125R	Q	+	2	0	FOXP2	114055946	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.188000	0.69820	0.528000	0.53228	CAG		0.502	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		G	114268710	A	G	114268710	3	3	39	1	0	0	0	0	1	0	0	0	6046	188	7	4	463	4	FOXP2	7	114268710	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	13591432	114268710	44869953	85	3549										
CALD1	800	hgsc.bcm.edu	37	chr7	134613584	134613584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gagcccgacaggaacggctgCggcagaagcaggaggaagaa	17	9	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:134613584C>T	ENST00000361675.2	+	4	380	c.151C>T	c.(151-153)Cgg>Tgg	p.R51W	CALD1_ENST00000422748.1_Missense_Mutation_p.R51W|CALD1_ENST00000417172.1_Missense_Mutation_p.R51W|CALD1_ENST00000424922.1_Missense_Mutation_p.R45W|CALD1_ENST00000393118.2_Missense_Mutation_p.R45W|CALD1_ENST00000543443.1_Missense_Mutation_p.R56W|CALD1_ENST00000495522.1_Missense_Mutation_p.R45W|CALD1_ENST00000361901.2_Missense_Mutation_p.R51W|CALD1_ENST00000361388.2_Missense_Mutation_p.R51W			Q05682	CALD1_HUMAN	caldesmon 1	51	Myosin and calmodulin-binding. {ECO:0000250}.				cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GGAACGGCTGCGGCAGAAGCA	0.577																																																0			7											57	53	54					7																	134613584		2203	4300	6503	134264124	SO:0001583	missense	800			M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.151C>T	7.37:g.134613584C>T	ENSP00000354826:p.Arg51Trp		134264124	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427199	0.62733	.	.	ENSG00000122786	ENST00000417172;ENST00000436461;ENST00000361388;ENST00000422748;ENST00000454108;ENST00000361675;ENST00000361901;ENST00000445569;ENST00000435928;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.55	4.65	0.58169	.	0.169667	0.27362	N	0.019715	T	0.70988	0.3287	M	0.76328	2.33	0.38957	D	0.958474	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.994;0.997;0.994;0.994;0.994;0.994;0.999;0.997	T	0.76170	-0.3057	10	0.87932	D	0	-13.5091	12.6149	0.56571	0.3002:0.6998:0.0:0.0	.	56;51;45;45;51;51;51;51	F5H1Z9;A8K0X1;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682;Q9NYG1	.;.;.;.;.;.;CALD1_HUMAN;.	W	51;51;51;51;51;51;51;65;51;45;45;45;56	ENSP00000398826:R51W;ENSP00000411476:R51W;ENSP00000355000:R51W;ENSP00000395710:R51W;ENSP00000401988:R51W;ENSP00000354826:R51W;ENSP00000354513:R51W;ENSP00000390926:R65W;ENSP00000416611:R51W;ENSP00000376826:R45W;ENSP00000393621:R45W;ENSP00000419673:R45W;ENSP00000445641:R56W	ENSP00000355000:R51W	R	+	1	2	CALD1	134264124	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.490000	0.35573	1.284000	0.44531	0.561000	0.74099	CGG		0.577	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		T	134613584	C	T	134613584	3	4	39	1	0	0	0	0	1	0	0	0	2587	759	27	1	214	1	CALD1	7	134613584	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	20344874	134613584	24525079	86	3550										
ZNF467	168544	hgsc.bcm.edu	37	chr7	149462747	149462747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aatcaagtgcgtcttcttgcGaaagcgcttctcgcattccg	9	12	4	0	rs560346109		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:149462747G>A	ENST00000302017.3	-	5	1257	c.844C>T	c.(844-846)Cgc>Tgc	p.R282C	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTCTTCTTGCGAAAGCGCTTC	0.627													G|||	1	0.000199681	0	0.0014	5008	,	,		15086	0		0	False		,,,				2504	0															0			7											39	24	29					7																	149462747		2203	4300	6503	149093680	SO:0001583	missense	168544			BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"Zinc fingers, C2H2-type"	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.844C>T	7.37:g.149462747G>A	ENSP00000304769:p.Arg282Cys		149093680		Missense_Mutation	SNP	ENST00000302017.3	37	CCDS5899.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447502	0.63178	.	.	ENSG00000181444	ENST00000302017	T	0.08282	3.11	4.34	3.46	0.39613	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33515	U	0.004836	T	0.16300	0.0392	L	0.39020	1.185	0.41829	D	0.990063	D	0.89917	1.0	D	0.75484	0.986	T	0.01252	-1.1405	10	0.54805	T	0.06	-26.804	8.0576	0.30614	0.088:0.0:0.755:0.157	.	282	Q7Z7K2	ZN467_HUMAN	C	282	ENSP00000304769:R282C	ENSP00000304769:R282C	R	-	1	0	ZNF467	149093680	0.040000	0.19996	0.997000	0.53966	0.991000	0.79684	0.147000	0.16202	0.798000	0.33994	0.462000	0.41574	CGC		0.627	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		A	149462747	G	A	149462747	3	1	39	1	0	0	0	0	1	0	0	0	17966	1058	37	1	947	1	ZNF467	7	149462747	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	14849163	149462747	9675916	87	3551										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149559230	149559231	+	Frame_Shift_Ins	INS	-	-	G													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gctctgctggaggagtggctINSgggcctgaaaaccattgccc							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr7:149559230_149559231insG	ENST00000223210.4	+	7	3226_3227	c.2981_2982insG	c.(2980-2985)ctgggcfs	p.LG994fs	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	994					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						GAGGAGTGGCTGGGCCTGAAAA	0.574																																																0			7																																								149190164	SO:0001589	frameshift_variant	643641			AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2984dupG	7.37:g.149559233_149559233dupG	ENSP00000223210:p.Leu994fs		149190163	A0AUL8	Frame_Shift_Ins	INS	ENST00000223210.4	37	CCDS47741.1																																																																																				0.574	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		G	149559231	-	G	149559230	7	5	39	1	0	1	1	0	0	0	0	0	18234	1580	55	0	3007	0	ZNF862	7	149559230	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	96483	149559230	9579433	88	3552										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25246747	25246747	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atcaagtcgtcccccaagcaGtgtatcctttccggggggag	12	12	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:25246747G>T	ENST00000276440.7	+	41	4316	c.4272G>T	c.(4270-4272)caG>caT	p.Q1424H		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1424	DHR-2.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CCCCCAAGCAGTGTATCCTTT	0.567																																					Pancreas(145;34 1887 3271 10937 30165)											0			8											102	92	96					8																	25246747		2203	4300	6503	25302664	SO:0001630	splice_region_variant	80005				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.4273+1G>T	8.37:g.25246747G>T			25302664	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.209291	0.39003	.	.	ENSG00000147459	ENST00000276440	T	0.06933	3.24	5.21	3.42	0.39159	.	0.346217	0.30602	N	0.009275	T	0.32194	0.0821	M	0.91510	3.215	0.58432	D	0.999994	D;P;D	0.76494	0.999;0.95;0.981	D;P;P	0.74023	0.982;0.64;0.741	T	0.09357	-1.0678	10	0.87932	D	0	.	8.9265	0.35643	0.2261:0.0:0.7739:0.0	.	213;1414;1424	Q6ZP32;D3DSS6;Q9H7D0	.;.;DOCK5_HUMAN	H	1424	ENSP00000276440:Q1424H	ENSP00000276440:Q1424H	Q	+	3	2	DOCK5	25302664	1.000000	0.71417	1.000000	0.80357	0.086000	0.17979	3.550000	0.53691	0.699000	0.31761	-0.266000	0.10368	CAG		0.567	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	Missense_Mutation	T	25246747	G	T	25246747	5	4	39	1	0	0	0	0	0	0	1	0	4701	1043	36	2	4434	2	DOCK5	8	25246747	Splice_Site	SNP	G	TCGA-AG-3742-01A-11D-1657-10		25246747	121117275	89	3553										
IDO1	3620	hgsc.bcm.edu	37	chr8	39780140	39780140	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttcttcctggtctctctattGgtggaaatagcagctgcttc	9	10	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:39780140G>A	ENST00000518237.1	+	6	1146	c.507G>A	c.(505-507)ttG>ttA	p.L169L	RP11-44K6.4_ENST00000522970.1_RNA|RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Silent_p.L169L	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	169					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	TCTCTCTATTGGTGGAAATAG	0.408																																																0			8											153	140	144					8																	39780140		1863	4115	5978	39899297	SO:0001819	synonymous_variant	3620			M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.507G>A	8.37:g.39780140G>A			39899297	Q540B4	Silent	SNP	ENST00000518237.1	37	CCDS47847.1																																																																																				0.408	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		A	39780140	G	A	39780140	2	1	39	1	0	0	0	0	0	0	0	1	7522	1339	47	3		3	IDO1	8	39780140	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	14533393	39780140	106583882	90	3554										
CYP7B1	9420	hgsc.bcm.edu	37	chr8	65509289	65509289	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tagtttagtcctatgggcttAtcatcaattatttctaaatc	5	7	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:65509289A>G	ENST00000310193.3	-	6	1604	c.1431T>C	c.(1429-1431)gaT>gaC	p.D477D	CYP7B1_ENST00000523954.1_Intron	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	477					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				CTATGGGCTTATCATCAATTA	0.323																																																0			8											50	53	52					8																	65509289		2201	4300	6501	65671843	SO:0001819	synonymous_variant	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.1431T>C	8.37:g.65509289A>G			65671843	B2RN07|Q9UNF5	Silent	SNP	ENST00000310193.3	37	CCDS6180.1																																																																																				0.323	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			G	65509289	A	G	65509289	2	3	39	1	0	0	0	0	0	0	0	1	4203	446	16	4		4	CYP7B1	8	65509289	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	25729149	65509289	80854733	91	3555										
RPL7	6129	hgsc.bcm.edu	37	chr8	74204636	74204636	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	taagcttcctccttgcctttCgaagctgaaaaccaataatc	5	12	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:74204636C>T	ENST00000352983.2	-	3	413	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	RPL7_ENST00000396465.1_Missense_Mutation_p.R3Q|RPL7_ENST00000487500.1_5'Flank|RPL7_ENST00000396467.1_Missense_Mutation_p.R3Q|RDH10_ENST00000240285.5_5'Flank|RPL7_ENST00000396466.1_Missense_Mutation_p.R3Q			P18124	RL7_HUMAN	ribosomal protein L7	43	4 X 12 AA tandem repeats.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(64;0.0954)		Epithelial(68;0.0193)|all cancers(69;0.0766)|BRCA - Breast invasive adenocarcinoma(89;0.134)			CCTTGCCTTTCGAAGCTGAAA	0.343																																																0			8											36	40	39					8																	74204636		2181	4277	6458	74367190	SO:0001583	missense	6129			L16557	CCDS6212.1	8q13.3	2011-04-06			ENSG00000147604	ENSG00000147604		"L ribosomal proteins"	10363	protein-coding gene	gene with protein product		604166				8360149, 8441630	Standard	XM_006716463		Approved	humL7-1, L7	uc003xzg.3	P18124	OTTHUMG00000134312	ENST00000352983.2:c.128G>A	8.37:g.74204636C>T	ENSP00000339795:p.Arg43Gln		74367190	A8K504|Q15289|Q3KQU0|Q5I0X1|Q6IBM9	Missense_Mutation	SNP	ENST00000352983.2	37	CCDS6212.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616888	0.46736	.	.	ENSG00000147604	ENST00000396467;ENST00000352983;ENST00000396466;ENST00000396465;ENST00000435330;ENST00000431653	.	.	.	4.5	4.5	0.54988	Ribosomal protein L30, N-terminal (1);	0.078538	0.52532	U	0.000069	T	0.41190	0.1148	N	0.13140	0.3	0.48288	D	0.999621	B	0.24483	0.104	B	0.19391	0.025	T	0.24261	-1.0165	9	0.22706	T	0.39	.	17.4563	0.87608	0.0:1.0:0.0:0.0	.	43	P18124	RL7_HUMAN	Q	3;43;3;3;3;3	.	ENSP00000339795:R43Q	R	-	2	0	RPL7	74367190	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.435000	0.52849	2.332000	0.79248	0.586000	0.80456	CGA		0.343	RPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259287.1	NM_000971		T	74204636	C	T	74204636	3	4	39	1	0	0	0	0	1	0	0	0	13636	884	31	1	634	1	RPL7	8	74204636	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	8695347	74204636	72159386	92	3556										
SYBU	55638	hgsc.bcm.edu	37	chr8	110587791	110587793	+	Missense_Mutation	TNP	CTA	CTA	TAT													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttctgtggtggtggctgtcaCtatctcatcgaacaaatctg							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C|T|A	C|T|A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:110587791_110587793CTA>TAT	ENST00000422135.1	-	8	1849_1851	c.1334_1336TAG>ATA	c.(1333-1338)aTAGtg>aATAtg	p.445_446IV>NM	SYBU_ENST00000408889.3_Missense_Mutation_p.326_327IV>NM|SYBU_ENST00000533065.1_Missense_Mutation_p.326_327IV>NM|SYBU_ENST00000532779.1_Missense_Mutation_p.377_378IV>NM|SYBU_ENST00000276646.9_Missense_Mutation_p.445_446IV>NM|SYBU_ENST00000528331.1_Missense_Mutation_p.326_327IV>NM|SYBU_ENST00000533895.1_Missense_Mutation_p.444_445IV>NM|SYBU_ENST00000446070.2_Missense_Mutation_p.444_445IV>NM|SYBU_ENST00000529690.1_Missense_Mutation_p.315_316IV>NM|SYBU_ENST00000433638.1_Missense_Mutation_p.445_446IV>NM|SYBU_ENST00000528647.1_Missense_Mutation_p.444_445IV>NM|SYBU_ENST00000533171.1_Missense_Mutation_p.445_446IV>NM|SYBU_ENST00000408908.2_Missense_Mutation_p.445_446IV>NM|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000440310.1_Missense_Mutation_p.445_446IV>NM|SYBU_ENST00000399066.3_Missense_Mutation_p.442_443IV>NM|SYBU_ENST00000424158.2_Missense_Mutation_p.450_451IV>NM|SYBU_ENST00000529175.1_Missense_Mutation_p.239_240IV>NM|SYBU_ENST00000419099.1_Missense_Mutation_p.444_445IV>NM	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	445					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						GTGGCTGTCACTATCTCATCGAA	0.557																																																0			8																																								110656967|110656968|110656969	SO:0001583	missense	55638			AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"syntaphilin-like"	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1334_1336TAG>ATA	8.37:g.110587791CTA>TAT	ENSP00000407118:p.I445_V446delinsNM		110656967|110656968|110656969	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Missense_Mutation|Silent|Missense_Mutation	SNP	ENST00000422135.1	37	CCDS47912.1																																																																																				0.557	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		TAT	110587793	CTA	TAT	110587791	3	4	39	1	0	0	0	0	1	0	0	0	15466	565	20	3	659	3	SYBU	8	110587791	Missense_Mutation	TNP	CTA	TCGA-AG-3742-01A-11D-1657-10	36383155	110587791	35776231	93	3557										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144943713	144943713	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccacaggcaggccttcaccgCcggctgctcggcgacctggg	14	17	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr8:144943713C>G	ENST00000525985.1	-	2	3780	c.3709G>C	c.(3709-3711)Gcg>Ccg	p.A1237P				P58107	EPIPL_HUMAN	epiplakin 1	1237						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	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)			GCCTTCACCGCCGGCTGCTCG	0.706																																																0			8											5	6	6					8																	144943713		1875	3956	5831	145015701	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.3709G>C	8.37:g.144943713C>G	ENSP00000436337:p.Ala1237Pro		145015701	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	11.83	1.755995	0.31137	.	.	ENSG00000227184	ENST00000525985	T	0.70045	-0.45	4.4	0.512	0.16994	.	.	.	.	.	T	0.35653	0.0939	N	0.08118	0	0.09310	N	1	P	0.44578	0.838	B	0.35550	0.205	T	0.18745	-1.0327	9	0.30078	T	0.28	.	3.8512	0.08955	0.1593:0.4795:0.0:0.3613	.	1237	E9PPU0	.	P	1237	ENSP00000436337:A1237P	ENSP00000436337:A1237P	A	-	1	0	EPPK1	145015701	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.258000	0.08733	-0.099000	0.12263	0.462000	0.41574	GCG		0.706	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144943713	C	G	144943713	3	3	39	1	0	0	0	0	1	0	0	0	5203	739	26	5	3557	5	EPPK1	8	144943713	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	34355922	144943713	1420309	94	3558										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718826	2718826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cgggcgagggccaccaacgcGgccagacggtgggcagcgtg	19	13	0	1	rs566426805		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:2718826G>A	ENST00000382082.3	+	1	1325	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	363					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.G363C(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CCACCAACGCGGCCAGACGGT	0.677																																																1	Substitution - Missense(1)	kidney(1)	9											85	76	79					9																	2718826		2203	4299	6502	2708826	SO:0001583	missense	169522			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1087G>A	9.37:g.2718826G>A	ENSP00000371514:p.Gly363Ser		2708826	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.016|3.016	-0.202931|-0.202931	0.06219|0.06219	.|.	.|.	ENSG00000168263|ENSG00000168263	ENST00000382082|ENST00000423608	D|.	0.96940|.	-4.18|.	5.07|5.07	-1.74|-1.74	0.08056|0.08056	Ion transport (1);|.	0.888331|.	0.09828|.	N|.	0.750577|.	T|T	0.25680|0.25680	0.0625|0.0625	N|N	0.21373|0.21373	0.66|0.66	0.09310|0.09310	N|N	1|1	B|.	0.26081|.	0.141|.	B|.	0.15484|.	0.013|.	T|T	0.34700|0.34700	-0.9818|-0.9818	10|6	0.39692|0.87932	T|D	0.17|0	.|.	7.0073|7.0073	0.24844|0.24844	0.3208:0.1076:0.5716:0.0|0.3208:0.1076:0.5716:0.0	.|.	363|.	Q8TDN2|.	KCNV2_HUMAN|.	S|Q	363|313	ENSP00000371514:G363S|.	ENSP00000371514:G363S|ENSP00000409635:R313Q	G|R	+|+	1|2	0|0	KCNV2|KCNV2	2708826|2708826	0.184000|0.184000	0.23200|0.23200	0.008000|0.008000	0.14137|0.14137	0.190000|0.190000	0.23558|0.23558	0.542000|0.542000	0.23222|0.23222	-0.319000|-0.319000	0.08652|0.08652	0.563000|0.563000	0.77884|0.77884	GGC|CGG		0.677	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		A	2718826	G	A	2718826	3	1	39	1	0	0	0	0	1	0	0	0	8116	1116	39	1	1089	1	KCNV2	9	2718826	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		2718826	138494605	95	3559										
FREM1	158326	hgsc.bcm.edu	37	chr9	14868843	14868843	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gatggcaaacttcaggtcatCtcctgacaggaaggcagagt	12	9	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:14868843C>T	ENST00000380880.3	-	2	916	c.133G>A	c.(133-135)Gat>Aat	p.D45N	FREM1_ENST00000422223.2_Missense_Mutation_p.D45N|FREM1_ENST00000380881.4_Missense_Mutation_p.D45N			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	45					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTCAGGTCATCTCCTGACAGG	0.557																																																0			9											49	51	50					9																	14868843		2005	4180	6185	14858843	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.133G>A	9.37:g.14868843C>T	ENSP00000370262:p.Asp45Asn		14858843	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	7.199	0.593042	0.13875	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.09630	2.97;2.96;2.96	5.36	5.36	0.76844	.	0.340632	0.34555	N	0.003878	T	0.08358	0.0208	L	0.31420	0.93	0.28960	N	0.889914	B	0.17268	0.021	B	0.15052	0.012	T	0.19745	-1.0296	10	0.14656	T	0.56	-5.564	12.4376	0.55608	0.0:0.9233:0.0:0.0767	.	45	Q5H8C1	FREM1_HUMAN	N	45	ENSP00000370263:D45N;ENSP00000412940:D45N;ENSP00000370262:D45N	ENSP00000370257:D45N	D	-	1	0	FREM1	14858843	0.753000	0.28349	0.304000	0.25085	0.302000	0.27658	3.661000	0.54503	2.521000	0.84997	0.563000	0.77884	GAT		0.557	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14868843	C	T	14868843	3	4	39	1	0	0	0	0	1	0	0	0	6063	913	32	3	6600	3	FREM1	9	14868843	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	12150017	14868843	126344588	96	3560										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19063006	19063006	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcattacagtcttttctcacCtcttctaccagatgatcttg	4	12	6	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:19063006C>T	ENST00000380502.3	-	14	2096	c.1629G>A	c.(1627-1629)gaG>gaA	p.E543E	SCARNA8_ENST00000515924.1_RNA|HAUS6_ENST00000380496.1_Splice_Site_p.E407E	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	543					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTTTTCTCACCTCTTCTACCA	0.418																																																0			9											162	147	152					9																	19063006		2203	4300	6503	19053006	SO:0001630	splice_region_variant	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1629+1G>A	9.37:g.19063006C>T			19053006	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																				0.418	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	Silent	T	19063006	C	T	19063006	5	4	39	1	0	0	0	0	0	0	1	0	6991	695	24	3	1254	3	HAUS6	9	19063006	Splice_Site	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4194163	19063006	122150425	97	3561										
DNAJB5	25822	hgsc.bcm.edu	37	chr9	34996273	34996273	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cccctctaggcctgaagaccGgcggtggcacatcaggtggc	14	14	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:34996273G>A	ENST00000541010.1	+	2	3235	c.223G>A	c.(223-225)Ggc>Agc	p.G75S	DNAJB5_ENST00000453597.3_Missense_Mutation_p.G189S|DNAJB5_ENST00000454002.2_Missense_Mutation_p.G147S|DNAJB5_ENST00000545841.1_Missense_Mutation_p.G75S|DNAJB5_ENST00000335998.3_Missense_Mutation_p.G109S|DNAJB5_ENST00000312316.5_Missense_Mutation_p.G75S			O75953	DNJB5_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 5	75					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(32;0.00575)			CCTGAAGACCGGCGGTGGCAC	0.592																																																0			9											36	36	36					9																	34996273		2203	4299	6502	34986273	SO:0001583	missense	25822			AF088982	CCDS35007.1, CCDS47959.1, CCDS47960.1, CCDS47960.2	9p	2011-09-02			ENSG00000137094	ENSG00000137094		"Heat shock proteins / DNAJ (HSP40)"	14887	protein-coding gene	gene with protein product		611328				10570961, 11147971	Standard	NM_001135004		Approved	Hsc40	uc003zvs.4	O75953	OTTHUMG00000019840	ENST00000541010.1:c.223G>A	9.37:g.34996273G>A	ENSP00000443151:p.Gly75Ser		34986273	B3KN14|B4DSA6|J3KQM9|J3KR08|Q5T656|Q8TDR7|Q96EM4	Missense_Mutation	SNP	ENST00000541010.1	37	CCDS35007.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529786	0.64860	.	.	ENSG00000137094	ENST00000453597;ENST00000335998;ENST00000378751;ENST00000312316;ENST00000541010;ENST00000454002;ENST00000545841;ENST00000539059;ENST00000443266	T;T;T;T;T;T;T;T	0.73363	0.01;0.1;-0.02;-0.02;0.05;-0.02;-0.74;-0.58	5.35	4.45	0.53987	Heat shock protein DnaJ, N-terminal (2);	0.096440	0.64402	D	0.000001	T	0.68531	0.3011	L	0.48174	1.505	0.80722	D	1	D;P	0.57257	0.979;0.724	B;B	0.43536	0.423;0.295	T	0.69339	-0.5171	10	0.36615	T	0.2	.	13.5344	0.61639	0.0744:0.0:0.9256:0.0	.	147;75	B4DSA6;O75953	.;DNJB5_HUMAN	S	189;109;75;75;75;147;75;111;75	ENSP00000404079:G189S;ENSP00000337626:G109S;ENSP00000312517:G75S;ENSP00000443151:G75S;ENSP00000413684:G147S;ENSP00000441999:G75S;ENSP00000445536:G111S;ENSP00000396332:G75S	ENSP00000312517:G75S	G	+	1	0	DNAJB5	34986273	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	7.752000	0.85141	1.636000	0.50526	-0.136000	0.14681	GGC		0.592	DNAJB5-008	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401397.1			A	34996273	G	A	34996273	3	1	39	1	0	0	0	0	1	0	0	0	4634	1116	39	1	449	1	DNAJB5	9	34996273	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	15933267	34996273	106217158	98	3562										
MELK	9833	hgsc.bcm.edu	37	chr9	36671030	36671030	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	attggatctcaaccaagcacAtatggaggagactccaaaaa	8	9	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:36671030A>G	ENST00000298048.2	+	16	1725	c.1541A>G	c.(1540-1542)cAt>cGt	p.H514R	MELK_ENST00000543751.1_Missense_Mutation_p.H482R|MELK_ENST00000541717.1_Missense_Mutation_p.H473R|MELK_ENST00000536860.1_Missense_Mutation_p.H466R|MELK_ENST00000536329.1_Missense_Mutation_p.H443R|MELK_ENST00000538311.1_Missense_Mutation_p.H320R|MELK_ENST00000545008.1_Missense_Mutation_p.H443R|MELK_ENST00000536987.1_Missense_Mutation_p.H383R	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	514	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			AACCAAGCACATATGGAGGAG	0.507																																					Ovarian(82;980 1317 7225 14391 18624)											0			9											102	100	101					9																	36671030		2203	4300	6503	36661030	SO:0001583	missense	9833			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1541A>G	9.37:g.36671030A>G	ENSP00000298048:p.His514Arg		36661030	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726511	0.48833	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.70986	-0.34;0.64;0.43;0.96;0.34;-0.53;-0.35;-0.34	5.95	5.95	0.96441	.	0.203413	0.51477	D	0.000085	T	0.75561	0.3866	M	0.65498	2.005	0.58432	D	0.999998	P;P;B;B;D;B;B	0.53462	0.868;0.835;0.005;0.004;0.96;0.325;0.001	P;P;B;B;P;B;B	0.52514	0.448;0.576;0.015;0.016;0.701;0.272;0.004	T	0.72232	-0.4353	10	0.10377	T	0.69	-10.8298	16.4237	0.83790	1.0:0.0:0.0:0.0	.	434;443;466;473;443;482;514	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	R	514;320;383;443;466;443;473;482	ENSP00000298048:H514R;ENSP00000438226:H320R;ENSP00000439184:H383R;ENSP00000445452:H443R;ENSP00000439792:H466R;ENSP00000443550:H443R;ENSP00000437804:H473R;ENSP00000441596:H482R	ENSP00000298048:H514R	H	+	2	0	MELK	36661030	1.000000	0.71417	0.934000	0.37439	0.981000	0.71138	6.700000	0.74619	2.279000	0.76181	0.533000	0.62120	CAT		0.507	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36671030	A	G	36671030	3	3	39	1	0	0	0	0	1	0	0	0	9500	217	8	4	1599	4	MELK	9	36671030	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1674757	36671030	104542401	99	3563										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98231179	98231179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtggagctggtgctctctgGgctctggcagctgagggtgt	18	8	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:98231179G>A	ENST00000331920.6	-	14	2403	c.2104C>T	c.(2104-2106)Cca>Tca	p.P702S	PTCH1_ENST00000430669.2_Missense_Mutation_p.P636S|PTCH1_ENST00000429896.2_Missense_Mutation_p.P551S|PTCH1_ENST00000437951.1_Missense_Mutation_p.P636S|PTCH1_ENST00000421141.1_Missense_Mutation_p.P551S|PTCH1_ENST00000418258.1_Missense_Mutation_p.P551S|PTCH1_ENST00000375274.2_Missense_Mutation_p.P701S	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	702					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GTGCTCTCTGGGCTCTGGCAG	0.632																																																0			9											98	99	99					9																	98231179		2203	4300	6503	97271000	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2104C>T	9.37:g.98231179G>A	ENSP00000332353:p.Pro702Ser		97271000	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.350707	0.41599	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32;-3.32;-3.32;-3.32	4.8	4.8	0.61643	.	0.109676	0.64402	D	0.000006	D	0.88422	0.6432	N	0.20986	0.625	0.58432	D	0.999993	B;B;B;B	0.31274	0.317;0.08;0.035;0.014	B;B;B;B	0.33454	0.164;0.029;0.029;0.022	D	0.85585	0.1242	10	0.17832	T	0.49	-15.8702	18.1128	0.89541	0.0:0.0:1.0:0.0	.	551;636;701;702	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	S	702;636;551;551;138;636;551;701	ENSP00000332353:P702S;ENSP00000389744:P636S;ENSP00000399981:P551S;ENSP00000396135:P551S;ENSP00000410287:P636S;ENSP00000414823:P551S;ENSP00000364423:P701S	ENSP00000332353:P702S	P	-	1	0	PTCH1	97271000	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	4.813000	0.62620	2.501000	0.84356	0.551000	0.68910	CCA		0.632	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98231179	G	A	98231179	3	1	39	1	0	0	0	0	1	0	0	0	12764	1232	43	3	2279	3	PTCH1	9	98231179	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	61560149	98231179	42982252	100	3564										
GPR21	2844	hgsc.bcm.edu	37	chr9	125797414	125797414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtcctggcacaccgactcctActtcaccctgttcatcgtga	7	16	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:125797414A>G	ENST00000373642.1	+	1	609	c.569A>G	c.(568-570)tAc>tGc	p.Y190C	RABGAP1_ENST00000373643.5_Intron|RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373647.4_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	190					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.Y190C(1)		endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						ACCGACTCCTACTTCACCCTG	0.507																																																1	Substitution - Missense(1)	ovary(1)	9											151	134	140					9																	125797414		2203	4300	6503	124837235	SO:0001583	missense	2844			BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"GPCR / Class A : Orphans"	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.569A>G	9.37:g.125797414A>G	ENSP00000362746:p.Tyr190Cys		124837235	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	37	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	A	10.46	1.356498	0.24598	.	.	ENSG00000188394	ENST00000373642;ENST00000412269	T	0.74315	-0.83	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.536026	0.17626	U	0.167554	T	0.81786	0.4896	L	0.58354	1.805	0.22479	N	0.999064	D	0.71674	0.998	D	0.63113	0.911	T	0.74532	-0.3634	10	0.66056	D	0.02	-13.2237	12.124	0.53907	0.8569:0.1431:0.0:0.0	.	190	Q99679	GPR21_HUMAN	C	190	ENSP00000362746:Y190C	ENSP00000362746:Y190C	Y	+	2	0	GPR21	124837235	0.964000	0.33143	0.997000	0.53966	0.798000	0.45092	2.294000	0.43567	2.075000	0.62263	0.383000	0.25322	TAC		0.507	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294		G	125797414	A	G	125797414	3	3	39	1	0	0	0	0	1	0	0	0	6701	391	14	4	571	4	GPR21	9	125797414	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	27566235	125797414	15416017	101	3565										
HSPA5	3309	hgsc.bcm.edu	37	chr9	128001075	128001075	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagaatcttccaacactttcTggacgggcttcatagtagac	8	11	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:128001075T>C	ENST00000324460.6	-	6	1231	c.1028A>G	c.(1027-1029)cAg>cGg	p.Q343R	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	343					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	CAACACTTTCTGGACGGGCTT	0.388										Prostate(1;0.17)																																						0			9											72	71	71					9																	128001075		2203	4300	6503	127040896	SO:0001583	missense	3309				CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"Heat shock proteins / HSP70"	5238	protein-coding gene	gene with protein product		138120	"heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.1028A>G	9.37:g.128001075T>C	ENSP00000324173:p.Gln343Arg		127040896	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Missense_Mutation	SNP	ENST00000324460.6	37	CCDS6863.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852733	0.71719	.	.	ENSG00000044574	ENST00000324460	T	0.00958	5.5	4.23	4.23	0.50019	.	0.000000	0.85682	D	0.000000	T	0.01029	0.0034	N	0.04355	-0.22	0.80722	D	1	P	0.34662	0.462	P	0.44394	0.448	T	0.76011	-0.3115	10	0.87932	D	0	-25.2689	12.5216	0.56062	0.0:0.0:0.0:1.0	.	343	P11021	GRP78_HUMAN	R	343	ENSP00000324173:Q343R	ENSP00000324173:Q343R	Q	-	2	0	HSPA5	127040896	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.036000	0.88901	1.536000	0.49237	0.460000	0.39030	CAG		0.388	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			C	128001075	T	C	128001075	3	2	39	1	0	0	0	0	1	0	0	0	7435	1580	55	4	948	4	HSPA5	9	128001075	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	2203661	128001075	13212356	102	3566										
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139694861	139694861	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atcatccgccagctggagaaCaacatcgagaagacaatgat	9	10	1	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr9:139694861C>G	ENST00000338005.6	+	5	494	c.459C>G	c.(457-459)aaC>aaG	p.N153K	RP11-216L13.18_ENST00000471502.1_RNA|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.N183K|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		153										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AGCTGGAGAACAACATCGAGA	0.607																																																0			9											40	46	44					9																	139694861		2050	4185	6235	138814682	SO:0001583	missense	84960																														ENST00000338005.6:c.459C>G	9.37:g.139694861C>G	ENSP00000338013:p.Asn153Lys		138814682	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867585	0.72065	.	.	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.38722	1.12	4.19	3.29	0.37713	.	0.000000	0.45126	U	0.000388	T	0.55242	0.1908	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.49934	-0.8886	10	0.29301	T	0.29	-31.7025	8.2154	0.31507	0.0:0.8856:0.0:0.1144	.	153	Q5T5S1	K1984_HUMAN	K	153	ENSP00000338013:N153K	ENSP00000338013:N153K	N	+	3	2	KIAA1984	138814682	0.999000	0.42202	1.000000	0.80357	0.866000	0.49608	0.342000	0.19926	0.751000	0.32900	-0.704000	0.03662	AAC		0.607	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			G	139694861	C	G	139694861	3	3	39	1	0	0	0	0	1	0	0	0	8287	477	17	5	477	5	KIAA1984	9	139694861	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	11693786	139694861	1518570	103	3567										
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30315078	30315078	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctcttctccttttgtgctgcCggatgctccttctcttccct	6	16	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr10:30315078C>T	ENST00000375377.1	-	3	4100	c.3999G>A	c.(3997-3999)ccG>ccA	p.P1333P		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	1333					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TTTGTGCTGCCGGATGCTCCT	0.547																																																0			10											125	122	123					10																	30315078		2037	4201	6238	30355084	SO:0001819	synonymous_variant	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.3999G>A	10.37:g.30315078C>T			30355084	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																				0.547	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30315078	C	T	30315078	2	4	39	1	0	0	0	0	0	0	0	1	8255	639	23	1		1	KIAA1462	10	30315078	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10		30315078	105219669	104	3568										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49658681	49658681	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atgccggggaccaggcccggCgcgggcacattgtcgtaggt	17	12	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr10:49658681C>T	ENST00000249601.4	-	9	1787	c.1491G>A	c.(1489-1491)gcG>gcA	p.A497A	ARHGAP22_ENST00000477708.2_Silent_p.A330A|ARHGAP22_ENST00000417912.2_Silent_p.A513A|ARHGAP22_ENST00000417247.2_Silent_p.A407A|ARHGAP22_ENST00000435790.2_Silent_p.A503A|ARHGAP22_ENST00000374170.1_Silent_p.A338A|ARHGAP22_ENST00000374172.1_Silent_p.A388A	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	497	Ser-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCAGGCCCGGCGCGGGCACAT	0.716																																																0			10											8	10	9					10																	49658681		2059	4028	6087	49328687	SO:0001819	synonymous_variant	58504			AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1491G>A	10.37:g.49658681C>T			49328687	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Silent	SNP	ENST00000249601.4	37	CCDS7227.1																																																																																				0.716	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49658681	C	T	49658681	2	4	39	1	0	0	0	0	0	0	0	1	872	755	27	1		1	ARHGAP22	10	49658681	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	19343603	49658681	85876066	105	3569										
P4HA1	5033	hgsc.bcm.edu	37	chr10	74804762	74804762	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgctaattctgtaatgtacCgtctccaagtctcctgttat	6	10	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr10:74804762C>T	ENST00000307116.2	-	9	1241	c.1125G>A	c.(1123-1125)acG>acA	p.T375T	P4HA1_ENST00000412021.2_Silent_p.T375T|P4HA1_ENST00000373008.2_Intron|P4HA1_ENST00000440381.1_Intron|P4HA1_ENST00000263556.3_Intron|P4HA1_ENST00000394890.2_Silent_p.T375T			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	375					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGTAATGTACCGTCTCCAAGT	0.373																																					Colon(147;367 2405 2662 52127)											0			10											144	143	143					10																	74804762		1875	4102	5977	74474768	SO:0001819	synonymous_variant	5033				CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.1125G>A	10.37:g.74804762C>T			74474768	C9JL12|Q15082|Q15083|Q5VSQ5	Silent	SNP	ENST00000307116.2	37																																																																																					0.373	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		T	74804762	C	T	74804762	2	4	39	1	0	0	0	0	0	0	0	1	11387	639	23	1		1	P4HA1	10	74804762	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	25146081	74804762	60729985	106	3570										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105204330	105204330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttcagctgggggatgcagagCgggccaaagccatttttgag	15	8	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr10:105204330C>T	ENST00000369797.3	+	35	5429	c.5335C>T	c.(5335-5337)Cgg>Tgg	p.R1779W		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1779					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.R1779W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GGATGCAGAGCGGGCCAAAGC	0.547																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											134	107	116					10																	105204330		2203	4300	6503	105194320	SO:0001583	missense	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5335C>T	10.37:g.105204330C>T	ENSP00000358812:p.Arg1779Trp		105194320	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210380	0.79240	.	.	ENSG00000148843	ENST00000369797	T	0.56275	0.47	5.57	4.65	0.58169	Tetratricopeptide-like helical (1);Suppressor of forked (1);Tetratricopeptide repeat-containing (1);	0.242285	0.39407	N	0.001369	T	0.77384	0.4122	M	0.89715	3.055	0.52501	D	0.999954	D	0.89917	1.0	D	0.78314	0.991	T	0.83241	-0.0058	10	0.87932	D	0	-20.5552	15.6725	0.77289	0.1383:0.8617:0.0:0.0	.	1779	Q14690	RRP5_HUMAN	W	1779	ENSP00000358812:R1779W	ENSP00000358812:R1779W	R	+	1	2	PDCD11	105194320	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	3.116000	0.50399	1.315000	0.45114	0.561000	0.74099	CGG		0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105204330	C	T	105204330	3	4	39	1	0	0	0	0	1	0	0	0	11648	759	27	1	5469	1	PDCD11	10	105204330	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	30399568	105204330	30330417	107	3571										
WDR11	55717	hgsc.bcm.edu	37	chr10	122633433	122633433	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agcatccactcatgtgaagtCaagtaagtatgtcattgtga	9	7	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr10:122633433C>A	ENST00000263461.6	+	11	1800	c.1554C>A	c.(1552-1554)gtC>gtA	p.V518V		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CATGTGAAGTCAAGTAAGTAT	0.368																																																0			10											159	128	138					10																	122633433		2203	4300	6503	122623423	SO:0001819	synonymous_variant	55717			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1554C>A	10.37:g.122633433C>A			122623423	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																				0.368	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			A	122633433	C	A	122633433	2	1	39	1	0	0	0	0	0	0	0	1	17313	813	29	2		2	WDR11	10	122633433	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	17429103	122633433	12901314	108	3572										
MUC6	4588	hgsc.bcm.edu	37	chr11	1024980	1024980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acagcgggctctccttccacGagttcaccaactccagctcg	8	17	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:1024980G>A	ENST00000421673.2	-	24	3139	c.3089C>T	c.(3088-3090)tCg>tTg	p.S1030L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1030	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTCCTTCCACGAGTTCACCAA	0.632																																																0			11											38	46	44					11																	1024980		2123	4235	6358	1014980	SO:0001583	missense	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3089C>T	11.37:g.1024980G>A	ENSP00000406861:p.Ser1030Leu		1014980	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665984	0.67700	.	.	ENSG00000184956	ENST00000421673	T	0.32272	1.46	3.88	2.95	0.34219	von Willebrand factor, type D domain (1);	0.000000	0.28834	U	0.013988	T	0.62122	0.2402	M	0.91459	3.21	0.31755	N	0.634118	D	0.89917	1.0	D	0.87578	0.998	T	0.74774	-0.3551	10	0.87932	D	0	.	13.7916	0.63146	0.0:0.1548:0.8452:0.0	.	1030	Q6W4X9	MUC6_HUMAN	L	1030	ENSP00000406861:S1030L	ENSP00000406861:S1030L	S	-	2	0	MUC6	1014980	0.997000	0.39634	0.990000	0.47175	0.904000	0.53231	2.795000	0.47861	0.968000	0.38212	0.561000	0.74099	TCG		0.632	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1024980	G	A	1024980	3	1	39	1	0	0	0	0	1	0	0	0	10010	1059	37	1	4270	1	MUC6	11	1024980	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		1024980	133981536	109	3573										
OR52E2	119678	hgsc.bcm.edu	37	chr11	5080595	5080595	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgatccctctgaggttgatcCagaagattccaagcatctta	8	10	2	5			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:5080595C>T	ENST00000321522.2	-	1	262	c.263G>A	c.(262-264)tGg>tAg	p.W88*		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		GAGGTTGATCCAGAAGATTCC	0.498																																																0			11											88	81	83					11																	5080595		2201	4298	6499	5037171	SO:0001587	stop_gained	119678			AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"GPCR / Class A : Olfactory receptors"	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.263G>A	11.37:g.5080595C>T	ENSP00000322088:p.Trp88*		5037171		Nonsense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747714	0.30955	.	.	ENSG00000176787	ENST00000321522	.	.	.	3.77	2.82	0.32997	.	0.000000	0.49916	D	0.000135	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0125	0.53295	0.175:0.825:0.0:0.0	.	.	.	.	X	88	.	ENSP00000322088:W88X	W	-	2	0	OR52E2	5037171	0.000000	0.05858	0.989000	0.46669	0.136000	0.21042	-1.150000	0.03178	1.148000	0.42385	0.650000	0.86243	TGG		0.498	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		T	5080595	C	T	5080595	4	4	39	1	0	0	0	0	0	1	0	0	11146	595	21	3	717	3	OR52E2	11	5080595	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4055615	5080595	129925921	110	3574										
TRIM34	53840	hgsc.bcm.edu	37	chr11	5653741	5653741	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agcagctgtcctgtgtgtggTatcagttactcatttgaaca	10	8	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:5653741T>C	ENST00000514226.1	+	2	517	c.180T>C	c.(178-180)ggT>ggC	p.G60G	TRIM34_ENST00000429814.2_Silent_p.G60G|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Silent_p.G414G|TRIM6-TRIM34_ENST00000457787.2_Silent_p.G60G	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	60					positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGTGTGTGGTATCAGTTACT	0.512																																																0			11											141	127	132					11																	5653741		2201	4297	6498	5610317	SO:0001819	synonymous_variant	445372			AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10063	protein-coding gene	gene with protein product		605684	"tripartite motif-containing 34"	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.180T>C	11.37:g.5653741T>C			5610317	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Silent	SNP	ENST00000514226.1	37	CCDS31391.1																																																																																				0.512	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827		C	5653741	T	C	5653741	2	2	39	1	0	0	0	0	0	0	0	1	16548	1625	57	4		4	TRIM34	11	5653741	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	573146	5653741	129352775	111	3575										
CCKBR	887	hgsc.bcm.edu	37	chr11	6292409	6292409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cacccaggccaagctgctggCtaagaagcgcgtggtgcgaa	14	12	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:6292409C>T	ENST00000334619.2	+	5	1173	c.980C>T	c.(979-981)gCt>gTt	p.A327V	CCKBR_ENST00000525462.1_Missense_Mutation_p.A396V|CCKBR_ENST00000532396.1_3'UTR|CCKBR_ENST00000532715.1_Missense_Mutation_p.A243V	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	327					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		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)	AAGCTGCTGGCTAAGAAGCGC	0.612																																																0			11											137	114	122					11																	6292409		2201	4296	6497	6248985	SO:0001583	missense	887			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.980C>T	11.37:g.6292409C>T	ENSP00000335544:p.Ala327Val		6248985	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858533	0.91433	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.72942	-0.7;-0.7;-0.7	4.86	4.86	0.63082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86070	0.5845	M	0.87547	2.89	0.54753	D	0.999981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.991;0.996	D	0.88643	0.3177	10	0.87932	D	0	.	16.7176	0.85400	0.0:1.0:0.0:0.0	.	396;261;327	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	V	327;243;396	ENSP00000335544:A327V;ENSP00000432079:A243V;ENSP00000435534:A396V	ENSP00000335544:A327V	A	+	2	0	CCKBR	6248985	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	7.604000	0.82830	2.513000	0.84729	0.557000	0.71058	GCT		0.612	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		T	6292409	C	T	6292409	3	4	39	1	0	0	0	0	1	0	0	0	2887	797	28	3	998	3	CCKBR	11	6292409	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	638668	6292409	128714107	112	3576										
STK33	65975	hgsc.bcm.edu	37	chr11	8414133	8414133	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgttccttggcttggagtcAcaggggttttctccatttct	10	10	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:8414133A>G	ENST00000447869.1	-	12	2387	c.1469T>C	c.(1468-1470)gTg>gCg	p.V490A	STK33_ENST00000473980.1_5'UTR|STK33_ENST00000358872.3_Missense_Mutation_p.V303A|STK33_ENST00000534493.1_Missense_Mutation_p.V449A|STK33_ENST00000315204.1_Missense_Mutation_p.V490A|STK33_ENST00000396673.1_Missense_Mutation_p.V424A|STK33_ENST00000396672.1_Missense_Mutation_p.V490A			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	490					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GCTTGGAGTCACAGGGGTTTT	0.473																																																0			11											207	194	198					11																	8414133		2201	4296	6497	8370709	SO:0001583	missense	65975			AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.1469T>C	11.37:g.8414133A>G	ENSP00000416750:p.Val490Ala		8370709	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.366636	0.24771	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000396673;ENST00000444064;ENST00000534493	T;T;T;T;T;T;T	0.71222	-0.5;-0.5;-0.5;-0.55;-0.54;2.0;-0.49	6.17	-8.88	0.00789	.	1.107710	0.06944	N	0.813365	T	0.38427	0.1040	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.32161	-0.9917	10	0.07813	T	0.8	.	2.2138	0.03955	0.2295:0.2426:0.3507:0.1772	.	490	Q9BYT3	STK33_HUMAN	A	490;490;490;303;424;179;449	ENSP00000416750:V490A;ENSP00000320754:V490A;ENSP00000379905:V490A;ENSP00000351743:V303A;ENSP00000379906:V424A;ENSP00000415688:V179A;ENSP00000436418:V449A	ENSP00000320754:V490A	V	-	2	0	STK33	8370709	0.000000	0.05858	0.000000	0.03702	0.147000	0.21601	-0.721000	0.04963	-1.769000	0.01297	-0.316000	0.08728	GTG		0.473	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		G	8414133	A	G	8414133	3	3	39	1	0	0	0	0	1	0	0	0	15339	159	6	4	79	4	STK33	11	8414133	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	2121724	8414133	126592383	113	3577										
KCNC1	3746	hgsc.bcm.edu	37	chr11	17757798	17757798	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cactgcccagccgacgtgtgCgggccgctctacgaggagga	15	14	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:17757798C>T	ENST00000379472.3	+	1	279	c.249C>T	c.(247-249)tgC>tgT	p.C83C	KCNC1_ENST00000265969.6_Silent_p.C83C	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	83					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	CCGACGTGTGCGGGCCGCTCT	0.677																																																0			11											43	43	43					11																	17757798		2200	4292	6492	17714374	SO:0001819	synonymous_variant	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.249C>T	11.37:g.17757798C>T			17714374	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																				0.677	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		T	17757798	C	T	17757798	2	4	39	1	0	0	0	0	0	0	0	1	8035	776	27	1		1	KCNC1	11	17757798	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	9343665	17757798	117248718	114	3578										
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159319	18159319	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctggtttttttatgtgtggtTctctgtgggtccagcctggt	13	7	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:18159319T>C	ENST00000396275.2	+	3	931	c.570T>C	c.(568-570)gtT>gtC	p.V190V		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TATGTGTGGTTCTCTGTGGGT	0.507																																																0			11											143	132	136					11																	18159319		2200	4293	6493	18115895	SO:0001819	synonymous_variant	117195				CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.570T>C	11.37:g.18159319T>C			18115895	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	37	CCDS7830.1																																																																																				0.507	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		C	18159319	T	C	18159319	2	2	39	1	0	0	0	0	0	0	0	1	9798	1770	62	4		4	MRGPRX3	11	18159319	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	401521	18159319	116847197	115	3579										
LUZP2	338645	hgsc.bcm.edu	37	chr11	24750801	24750801	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcagctgacaaagacatcaaGagaacttgatggaattaaag	9	6	2	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:24750801G>T	ENST00000336930.6	+	2	215	c.149G>T	c.(148-150)aGa>aTa	p.R50I	LUZP2_ENST00000531187.1_3'UTR|LUZP2_ENST00000533227.1_5'UTR			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	50						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						AAGACATCAAGAGAACTTGAT	0.408																																																0			11											72	74	73					11																	24750801		2203	4299	6502	24707377	SO:0001583	missense	338645			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.149G>T	11.37:g.24750801G>T	ENSP00000336817:p.Arg50Ile		24707377	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970933	0.74246	.	.	ENSG00000187398	ENST00000336930;ENST00000529015	T;T	0.23147	1.92;1.92	5.98	3.12	0.35913	.	0.126562	0.64402	D	0.000019	T	0.30070	0.0753	L	0.44542	1.39	0.80722	D	1	D	0.53885	0.963	P	0.52343	0.696	T	0.02567	-1.1140	10	0.56958	D	0.05	-14.3361	9.0632	0.36447	0.2372:0.0:0.7628:0.0	.	50	Q86TE4	LUZP2_HUMAN	I	50	ENSP00000336817:R50I;ENSP00000437032:R50I	ENSP00000336817:R50I	R	+	2	0	LUZP2	24707377	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.099000	0.50267	0.871000	0.35750	0.650000	0.86243	AGA		0.408	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		T	24750801	G	T	24750801	3	4	39	1	0	0	0	0	1	0	0	0	9116	942	33	2	155	2	LUZP2	11	24750801	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	6591482	24750801	110255715	116	3580										
OR4X1	390113	hgsc.bcm.edu	37	chr11	48285591	48285591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cacctcccccatgtatttctTtctcagctacttatcctttg	3	15	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:48285591T>C	ENST00000320048.1	+	1	179	c.179T>C	c.(178-180)tTt>tCt	p.F60S		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						ATGTATTTCTTTCTCAGCTAC	0.473																																																0			11											150	136	141					11																	48285591		2201	4298	6499	48242167	SO:0001583	missense	390113			AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"GPCR / Class A : Olfactory receptors"	14854	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily X, member 1"				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.179T>C	11.37:g.48285591T>C	ENSP00000321506:p.Phe60Ser		48242167	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.511757	0.64522	.	.	ENSG00000176567	ENST00000320048	T	0.14640	2.49	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.55986	0.1955	H	0.99650	4.68	0.28316	N	0.922447	D	0.76494	0.999	D	0.67725	0.953	T	0.66324	-0.5952	9	0.72032	D	0.01	.	11.6949	0.51538	0.0:0.0:0.0:1.0	.	60	Q8NH49	OR4X1_HUMAN	S	60	ENSP00000321506:F60S	ENSP00000321506:F60S	F	+	2	0	OR4X1	48242167	0.985000	0.35326	1.000000	0.80357	0.601000	0.36947	5.900000	0.69853	1.914000	0.55421	0.460000	0.39030	TTT		0.473	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		C	48285591	T	C	48285591	3	2	39	1	0	0	0	0	1	0	0	0	11115	1841	64	4	181	4	OR4X1	11	48285591	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	23534790	48285591	86720925	117	3581										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56057872	56057872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggaattaattttcaggatggTagagagaatggacacatagg	13	3	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:56057872T>C	ENST00000313022.2	-	1	694	c.667A>G	c.(667-669)Acc>Gcc	p.T223A		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					TTCAGGATGGTAGAGAGAATG	0.403																																																0			11											139	128	132					11																	56057872		2201	4294	6495	55814448	SO:0001583	missense	219469			AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.667A>G	11.37:g.56057872T>C	ENSP00000323595:p.Thr223Ala		55814448	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.807011	0.00074	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.00029	8.91	3.81	2.67	0.31697	GPCR, rhodopsin-like superfamily (1);	0.117893	0.39020	N	0.001497	T	0.00073	0.0002	N	0.10837	0.055	0.09310	N	1	B	0.12013	0.005	B	0.22880	0.042	T	0.23797	-1.0178	10	0.02654	T	1	.	6.8232	0.23868	0.0:0.2622:0.0:0.7378	.	223	Q8NGG4	OR8H1_HUMAN	A	223;219	ENSP00000323595:T223A	ENSP00000323595:T223A	T	-	1	0	OR8H1	55814448	0.000000	0.05858	0.011000	0.14972	0.003000	0.03518	-0.305000	0.08188	0.603000	0.29913	-0.350000	0.07774	ACC		0.403	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		C	56057872	T	C	56057872	3	2	39	1	0	0	0	0	1	0	0	0	11268	1638	57	4	270	4	OR8H1	11	56057872	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	7772281	56057872	78948644	118	3582										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344266	56344267	+	Missense_Mutation	DNP	CA	CA	TG													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aggcctaaactgcaattttaCaaaaggattttcccctaatc					rs201834242		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C|A	C|A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:56344266_56344267CA>TG	ENST00000526812.2	-	1	996_997	c.931_932TG>CA	c.(931-933)TGt>CAt	p.C311H		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TGCAATTTTACAAAAGGATTTT	0.361																																																0			11																																								56100842|56100843	SO:0001583	missense	390167			BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.931_932delinsTG	11.37:g.56344266_56344267delinsTG	ENSP00000436004:p.Cys311His		56100842|56100843	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1																																																																																				0.361	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		TG	56344267	CA	TG	56344266	3	4	39	1	0	0	0	0	1	0	0	0	11204	478	17	3	19	3	OR5M10	11	56344266	Missense_Mutation	DNP	CA	TCGA-AG-3742-01A-11D-1657-10	286394	56344266	78662250	119	3583										
PLAC1L	219990	hgsc.bcm.edu	37	chr11	59811097	59811097	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atgagtttatatatcttgttCgtgattgtggcatcaggaca	10	5	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:59811097C>T	ENST00000278855.2	+	2	405	c.220C>T	c.(220-222)Cgt>Tgt	p.R74C	PLAC1L_ENST00000532905.1_Missense_Mutation_p.R43C	NM_173801.3	NP_776162.2	Q86WS3	OOSP2_HUMAN		74						extracellular region (GO:0005576)				breast(1)|lung(9)|ovary(2)|prostate(2)|skin(1)	15						ATATCTTGTTCGTGATTGTGG	0.343																																																0			11											81	79	80					11																	59811097		2201	4295	6496	59567673	SO:0001583	missense	219990																														ENST00000278855.2:c.220C>T	11.37:g.59811097C>T	ENSP00000278855:p.Arg74Cys		59567673	E9PJA4|Q8N9U6	Missense_Mutation	SNP	ENST00000278855.2	37	CCDS7979.1	.	.	.	.	.	.	.	.	.	.	C	8.537	0.872255	0.17322	.	.	ENSG00000149507	ENST00000278855;ENST00000532905	D;D	0.82344	-1.6;-1.6	3.4	-6.81	0.01704	.	4.023620	0.00735	N	0.000965	T	0.64114	0.2569	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56565	-0.7958	10	0.39692	T	0.17	1.3025	5.9635	0.19313	0.2724:0.1427:0.0:0.5849	.	74	Q86WS3	PLACL_HUMAN	C	74;43	ENSP00000278855:R74C;ENSP00000433831:R43C	ENSP00000278855:R74C	R	+	1	0	PLAC1L	59567673	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.293000	0.01145	-2.076000	0.00875	-0.262000	0.10625	CGT		0.343	PLAC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394411.1			T	59811097	C	T	59811097	3	4	39	1	0	0	0	0	1	0	0	0	12044	884	31	1	226	1	PLAC1L	11	59811097	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	3466831	59811097	75195419	120	3584										
FADS2	9415	hgsc.bcm.edu	37	chr11	61632668	61632668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	caacttacacaagatcgcccCgctggtgaagtctctatgtg	9	12	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:61632668C>T	ENST00000278840.4	+	11	1832	c.1202C>T	c.(1201-1203)cCg>cTg	p.P401L	FADS2_ENST00000257261.6_Missense_Mutation_p.P379L|FADS2_ENST00000522056.1_Missense_Mutation_p.P370L	NM_004265.2	NP_004256.1	O95864	FADS2_HUMAN	fatty acid desaturase 2	401					alpha-linolenic acid metabolic process (GO:0036109)|linoleic acid metabolic process (GO:0043651)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			breast(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20					Alpha-Linolenic Acid(DB00132)	AAGATCGCCCCGCTGGTGAAG	0.602																																																0			11											76	58	64					11																	61632668		2202	4299	6501	61389244	SO:0001583	missense	9415			AF084559	CCDS8012.1, CCDS60807.1, CCDS60808.1	11q12.2	2013-01-25			ENSG00000134824	ENSG00000134824	1.14.19.3	"Fatty acid desaturases"	3575	protein-coding gene	gene with protein product	"delta-6-desaturase"	606149		LLCDL2			Standard	NM_004265		Approved	FADSD6, D6D, TU13, DES6, SLL0262	uc001nsl.1	O95864	OTTHUMG00000163794	ENST00000278840.4:c.1202C>T	11.37:g.61632668C>T	ENSP00000278840:p.Pro401Leu		61389244	A8K2M6|B7Z634|Q6MZQ7|Q96H07|Q96SV8|Q9H3G3|Q9Y3X4	Missense_Mutation	SNP	ENST00000278840.4	37	CCDS8012.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545599	0.86022	.	.	ENSG00000134824	ENST00000257261;ENST00000522056;ENST00000278840	T;T;T	0.20738	2.05;2.05;2.05	4.66	4.66	0.58398	Fatty acid desaturase, type 1 (1);	0.000000	0.56097	D	0.000031	T	0.54415	0.1857	M	0.90252	3.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.81914	0.982;0.995;0.985	T	0.65635	-0.6120	10	0.66056	D	0.02	0.3691	16.6753	0.85277	0.0:1.0:0.0:0.0	.	370;401;379	B7Z634;O95864;O95864-2	.;FADS2_HUMAN;.	L	379;370;401	ENSP00000257261:P379L;ENSP00000429500:P370L;ENSP00000278840:P401L	ENSP00000257261:P379L	P	+	2	0	FADS2	61389244	1.000000	0.71417	0.939000	0.37840	0.764000	0.43329	6.444000	0.73452	2.294000	0.77228	0.313000	0.20887	CCG		0.602	FADS2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375586.2	NM_004265		T	61632668	C	T	61632668	3	4	39	1	0	0	0	0	1	0	0	0	5382	652	23	1	1244	1	FADS2	11	61632668	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	1821571	61632668	73373848	121	3585										
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62996902	62996902	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgagtcgaatgggatggagaTtctcaggagggcatcctggc	16	7	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:62996902T>C	ENST00000306494.6	-	1	222	c.223A>G	c.(223-225)Atc>Gtc	p.I75V	SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						GGGATGGAGATTCTCAGGAGG	0.512																																																0			11											136	123	128					11																	62996902		2201	4298	6499	62753478	SO:0001583	missense	387601			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.223A>G	11.37:g.62996902T>C	ENSP00000307443:p.Ile75Val		62753478		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	T	2.154	-0.393762	0.04899	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.35236	1.32	3.7	-4.11	0.03928	Major facilitator superfamily domain (1);	0.737600	0.12650	N	0.450490	T	0.23532	0.0569	L	0.41027	1.25	0.42943	D	0.994357	B;B	0.31705	0.028;0.336	B;B	0.31442	0.04;0.13	T	0.16541	-1.0399	10	0.16896	T	0.51	.	10.8094	0.46538	0.0:0.5974:0.0:0.4026	.	73;75	A4IF29;Q6T423	.;S22AP_HUMAN	V	75	ENSP00000307443:I75V	ENSP00000307443:I75V	I	-	1	0	SLC22A25	62753478	0.000000	0.05858	0.973000	0.42090	0.604000	0.37047	-1.311000	0.02723	-0.668000	0.05296	0.386000	0.25728	ATC		0.512	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		C	62996902	T	C	62996902	3	2	39	1	0	0	0	0	1	0	0	0	14491	1493	52	4	1456	4	SLC22A25	11	62996902	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	1364234	62996902	72009614	122	3586										
FAM86C	55199	hgsc.bcm.edu	37	chr11	71507139	71507139	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gctgcctgccgggagcaccaGcgggctcctcaattctacat	11	15	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:71507139G>C	ENST00000359244.4	+	4	361	c.338G>C	c.(337-339)aGc>aCc	p.S113T	FAM86C1_ENST00000346333.6_Missense_Mutation_p.S79T|FAM86C1_ENST00000426628.2_Missense_Mutation_p.S106T	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	113										lung(1)	1						GGGAGCACCAGCGGGCTCCTC	0.627																																																0			11											70	77	75					11																	71507139		2200	4293	6493	71184787	SO:0001583	missense	55199			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.338G>C	11.37:g.71507139G>C	ENSP00000352182:p.Ser113Thr		71184787	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	.	.	.	.	.	.	.	.	.	.	.	8.217	0.801675	0.16397	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.24723	1.89;2.23;1.88;1.84	0.906	0.906	0.19314	.	.	.	.	.	T	0.11239	0.0274	N	0.24115	0.695	0.09310	N	1	B;P;P	0.35493	0.006;0.505;0.505	B;B;B	0.27500	0.003;0.08;0.08	T	0.20874	-1.0262	9	0.12103	T	0.63	.	5.193	0.15220	0.0:0.0:1.0:0.0	.	106;79;113	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	T	79;113;106;79	ENSP00000325662:S79T;ENSP00000352182:S113T;ENSP00000391329:S106T;ENSP00000436598:S79T	ENSP00000325662:S79T	S	+	2	0	FAM86C1	71184787	0.000000	0.05858	0.007000	0.13788	0.087000	0.18053	0.249000	0.18216	0.793000	0.33875	0.184000	0.17185	AGC		0.627	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		C	71507139	G	C	71507139	3	2	39	1	0	0	0	0	1	0	0	0	5665	971	34	5	437	5	FAM86C	11	71507139	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	8510237	71507139	63499377	123	3587										
CAPN5	726	hgsc.bcm.edu	37	chr11	76830139	76830139	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcatccagcagcggccaaagCggtctacgcgccgggagggc	16	14	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:76830139C>T	ENST00000278559.3	+	9	1420	c.1231C>T	c.(1231-1233)Cgg>Tgg	p.R411W	CAPN5_ENST00000456580.2_Missense_Mutation_p.R451W|CAPN5_ENST00000529629.1_Missense_Mutation_p.R411W|CAPN5_ENST00000531028.1_Intron	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	411	Domain III.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GCGGCCAAAGCGGTCTACGCG	0.592																																																0			11											79	64	69					11																	76830139		2200	4292	6492	76507787	SO:0001583	missense	726				CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1231C>T	11.37:g.76830139C>T	ENSP00000278559:p.Arg411Trp		76507787	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135947	0.77662	.	.	ENSG00000149260	ENST00000278559;ENST00000360841;ENST00000529629;ENST00000456580;ENST00000544318	D;D;D	0.90261	-2.64;-2.64;-2.64	5.22	5.22	0.72569	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.052633	0.64402	D	0.000001	D	0.96522	0.8865	H	0.96015	3.755	0.53688	D	0.999978	D;D;D;D	0.89917	0.996;1.0;0.999;0.987	P;D;D;P	0.76575	0.872;0.988;0.978;0.802	D	0.97032	0.9751	10	0.87932	D	0	.	11.9311	0.52847	0.2739:0.7261:0.0:0.0	.	449;451;451;411	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	W	411;451;411;451;451	ENSP00000278559:R411W;ENSP00000432332:R411W;ENSP00000409996:R451W	ENSP00000278559:R411W	R	+	1	2	CAPN5	76507787	0.230000	0.23740	0.974000	0.42286	0.835000	0.47333	0.727000	0.25999	2.603000	0.88011	0.655000	0.94253	CGG		0.592	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		T	76830139	C	T	76830139	3	4	39	1	0	0	0	0	1	0	0	0	2635	759	27	1	1261	1	CAPN5	11	76830139	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5323000	76830139	58176377	124	3588										
DLG2	1740	hgsc.bcm.edu	37	chr11	83770481	83770481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	caccgctttactgtgggaaaCctctgacacatcaacctcat	6	14	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:83770481C>T	ENST00000532653.1	-	6	783	c.481G>A	c.(481-483)Gtt>Att	p.V161I	DLG2_ENST00000280241.8_Missense_Mutation_p.V200I|DLG2_ENST00000418306.2_Missense_Mutation_p.V110I|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000398301.2_Missense_Mutation_p.V200I|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000543673.1_Missense_Mutation_p.V266I|DLG2_ENST00000376104.2_Missense_Mutation_p.V266I|DLG2_ENST00000330014.6_Missense_Mutation_p.V100I|DLG2_ENST00000531015.1_Missense_Mutation_p.V128I|DLG2_ENST00000398309.2_Missense_Mutation_p.V161I|DLG2_ENST00000524982.1_Missense_Mutation_p.V161I			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.V161F(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				CTGTGGGAAACCTCTGACACA	0.468																																																1	Substitution - Missense(1)	ovary(1)	11											89	81	84					11																	83770481		1916	4151	6067	83448129	SO:0001583	missense	4355			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.481G>A	11.37:g.83770481C>T	ENSP00000435849:p.Val161Ile		83448129	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.398531	0.96030	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301;ENST00000398299	T;T;T;T;T;T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63;1.63;1.63;1.63;1.63;1.63	5.17	5.17	0.71159	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000019	T	0.50222	0.1603	L	0.48218	1.51	0.80722	D	1	D;D;P;D;D;D;P;D	0.76494	0.992;0.998;0.89;0.999;0.981;0.99;0.864;0.99	D;D;P;D;D;D;P;D	0.83275	0.995;0.994;0.571;0.996;0.937;0.984;0.731;0.991	T	0.39354	-0.9618	9	.	.	.	.	18.6643	0.91483	0.0:1.0:0.0:0.0	.	128;161;161;100;200;266;161;110	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	I	161;266;110;266;200;100;161;161;266;128;200;78	ENSP00000381355:V161I;ENSP00000365272:V266I;ENSP00000402275:V110I;ENSP00000441994:V266I;ENSP00000280241:V200I;ENSP00000381353:V100I;ENSP00000432894:V161I;ENSP00000435849:V161I;ENSP00000433848:V128I;ENSP00000381346:V200I;ENSP00000381344:V78I	.	V	-	1	0	DLG2	83448129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.420000	0.82092	0.460000	0.39030	GTT		0.468	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		T	83770481	C	T	83770481	3	4	39	1	0	0	0	0	1	0	0	0	4566	507	18	3	2253	3	DLG2	11	83770481	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	6940342	83770481	51236035	125	3589										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85445096	85445096	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tggtcttgcagttaaaacttCtgaatgagaatgcagcccat	9	8	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:85445096C>G	ENST00000528231.1	-	6	1550	c.1273G>C	c.(1273-1275)Gaa>Caa	p.E425Q	SYTL2_ENST00000527523.1_Missense_Mutation_p.E377Q|SYTL2_ENST00000389960.4_Missense_Mutation_p.E425Q|SYTL2_ENST00000524452.1_Missense_Mutation_p.E425Q|SYTL2_ENST00000316356.4_Missense_Mutation_p.E426Q	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	425					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GTTAAAACTTCTGAATGAGAA	0.368																																																0			11											151	144	146					11																	85445096		2203	4299	6502	85122744	SO:0001583	missense	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1273G>C	11.37:g.85445096C>G	ENSP00000431701:p.Glu425Gln		85122744	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	6.755	0.508073	0.12883	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.34859	1.39;1.47;1.44;1.34;1.39	6.08	3.11	0.35812	.	.	.	.	.	T	0.28896	0.0717	L	0.51422	1.61	0.09310	N	0.999997	B;B;B;B;B	0.32573	0.376;0.376;0.259;0.376;0.045	B;B;B;B;B	0.29942	0.109;0.109;0.051;0.109;0.019	T	0.15065	-1.0450	8	.	.	.	.	6.7323	0.23390	0.0:0.5747:0.2762:0.1491	.	377;425;425;426;283	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	Q	425;426;425;377;425	ENSP00000374610:E425Q;ENSP00000318803:E426Q;ENSP00000431701:E425Q;ENSP00000434010:E377Q;ENSP00000435238:E425Q	.	E	-	1	0	SYTL2	85122744	0.203000	0.23435	0.003000	0.11579	0.232000	0.25224	1.046000	0.30354	0.411000	0.25702	0.655000	0.94253	GAA		0.368	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		G	85445096	C	G	85445096	3	3	39	1	0	0	0	0	1	0	0	0	15522	922	32	5	4064	5	SYTL2	11	85445096	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	1674615	85445096	49561420	126	3590										
GPR83	10888	hgsc.bcm.edu	37	chr11	94113833	94113833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggccacagagatgatgaggaGgggcaggatgtagagcagga	19	5	0	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:94113833G>A	ENST00000243673.2	-	4	925	c.754C>T	c.(754-756)Ctc>Ttc	p.L252F	GPR83_ENST00000539203.2_Missense_Mutation_p.L210F	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	252					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ATGATGAGGAGGGGCAGGATG	0.567																																																0			11											80	75	76					11																	94113833		2201	4298	6499	93753481	SO:0001583	missense	10888			AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.754C>T	11.37:g.94113833G>A	ENSP00000243673:p.Leu252Phe		93753481	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	37	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.410176	0.62399	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.40476	1.03;1.03	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	M	0.77616	2.38	0.80722	D	1	D	0.71674	0.998	D	0.71656	0.974	T	0.60026	-0.7343	10	0.20046	T	0.44	.	17.7794	0.88519	0.0:0.0:1.0:0.0	.	252	Q9NYM4	GPR83_HUMAN	F	252;210	ENSP00000243673:L252F;ENSP00000441550:L210F	ENSP00000243673:L252F	L	-	1	0	GPR83	93753481	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	6.504000	0.73704	2.535000	0.85469	0.655000	0.94253	CTC		0.567	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		A	94113833	G	A	94113833	3	1	39	1	0	0	0	0	1	0	0	0	6733	1000	35	3	521	3	GPR83	11	94113833	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	8668737	94113833	40892683	127	3591										
ATM	472	hgsc.bcm.edu	37	chr11	108142043	108142043	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tattttaaaccatgtccttcAtgtagtgaaaaacctaggtc	6	8	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:108142043A>G	ENST00000452508.2	+	21	3176	c.2987A>G	c.(2986-2988)cAt>cGt	p.H996R	ATM_ENST00000278616.4_Missense_Mutation_p.H996R			Q13315	ATM_HUMAN	ATM serine/threonine kinase	996					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.H996L(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CATGTCCTTCATGTAGTGAAA	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	liver(1)	11											180	172	174					11																	108142043		2201	4298	6499	107647253	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2987A>G	11.37:g.108142043A>G	ENSP00000388058:p.His996Arg		107647253	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	9.913	1.210122	0.22289	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.66280	-0.2;-0.2;-0.2	5.5	-7.9	0.01169	Armadillo-type fold (1);	0.317850	0.39210	N	0.001435	T	0.51041	0.1651	L	0.57536	1.79	0.09310	N	0.999996	B	0.06786	0.001	B	0.06405	0.002	T	0.36359	-0.9751	10	0.22706	T	0.39	.	18.6793	0.91541	0.1386:0.7932:0.0682:0.0	.	996	Q13315	ATM_HUMAN	R	996	ENSP00000435747:H996R;ENSP00000278616:H996R;ENSP00000388058:H996R	ENSP00000278616:H996R	H	+	2	0	ATM	107647253	0.012000	0.17670	0.008000	0.14137	0.334000	0.28698	0.194000	0.17135	-0.859000	0.04105	0.459000	0.35465	CAT		0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108142043	A	G	108142043	3	3	39	1	0	0	0	0	1	0	0	0	1110	217	8	4	3061	4	ATM	11	108142043	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	14028210	108142043	26864473	128	3592										
ATM	472	hgsc.bcm.edu	37	chr11	108202754	108202754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtgcctaaacaaagctctcAgcttgatgaggtatttggat	10	7	1	2	rs587779867		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:108202754A>G	ENST00000452508.2	+	53	7967	c.7778A>G	c.(7777-7779)cAg>cGg	p.Q2593R	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.Q2593R			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2593					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CAAAGCTCTCAGCTTGATGAG	0.338			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											71	70	71					11																	108202754		2201	4298	6499	107707964	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7778A>G	11.37:g.108202754A>G	ENSP00000388058:p.Gln2593Arg		107707964	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	8.047	0.765211	0.15914	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.79141	-1.24;-1.24	5.44	4.28	0.50868	Armadillo-type fold (1);	0.157662	0.64402	D	0.000020	T	0.67795	0.2931	L	0.45581	1.43	0.80722	D	1	B	0.28552	0.215	B	0.24155	0.051	T	0.62338	-0.6875	10	0.38643	T	0.18	.	8.1909	0.31368	0.7279:0.1391:0.0:0.133	.	2593	Q13315	ATM_HUMAN	R	2593	ENSP00000278616:Q2593R;ENSP00000388058:Q2593R	ENSP00000278616:Q2593R	Q	+	2	0	ATM	107707964	0.997000	0.39634	1.000000	0.80357	0.567000	0.35839	1.617000	0.36943	0.855000	0.35359	0.443000	0.29094	CAG		0.338	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108202754	A	G	108202754	3	3	39	1	0	0	0	0	1	0	0	0	1110	188	7	4	7980	4	ATM	11	108202754	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	60711	108202754	26803762	129	3593										
HTR3A	3359	hgsc.bcm.edu	37	chr11	113860381	113860381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tggcccgagactggctgcgcGtgggctccgtgctggacaag	17	12	0	1	rs34111946	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:113860381G>A	ENST00000504030.2	+	9	1778	c.1333G>A	c.(1333-1335)Gtg>Atg	p.V445M	HTR3A_ENST00000535865.1_Missense_Mutation_p.V189M|HTR3A_ENST00000355556.2_Missense_Mutation_p.V483M|HTR3A_ENST00000299961.5_Missense_Mutation_p.V430M|HTR3A_ENST00000375498.2_Missense_Mutation_p.V451M|HTR3A_ENST00000506841.2_Missense_Mutation_p.V477M			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	445	HA-stretch.				cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	CTGGCTGCGCGTGGGCTCCGT	0.612													G|||	2	0.000399361	0	0	5008	,	,		17034	0.002		0	False		,,,				2504	0															0			11						G	MET/VAL,MET/VAL,MET/VAL	1,4401	2.1+/-5.4	0,1,2200	77	71	73		1351,1288,1447	5.7	1	11	dbSNP_126	73	0,8592		0,0,4296	no	missense,missense,missense	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	21,21,21	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	451/485,430/464,483/517	113860381	1,12993	2201	4296	6497	113365591	SO:0001583	missense	3359			D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.1333G>A	11.37:g.113860381G>A	ENSP00000424189:p.Val445Met		113365591	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	G	20.1	3.936011	0.73442	2.27E-4	0.0	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000535865;ENST00000299961	D;T;D;T;D;D	0.87412	-2.25;1.98;-2.25;1.98;-2.25;-2.25	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.93416	0.7900	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.976;0.997	D	0.93607	0.6935	10	0.62326	D	0.03	-25.58	15.353	0.74405	0.0:0.1389:0.8611:0.0	rs34111946	430;483;451	B4DSY6;G5E986;Q7KZM7	.;.;.	M	445;483;451;477;189;430	ENSP00000424189:V445M;ENSP00000347754:V483M;ENSP00000364648:V451M;ENSP00000424776:V477M;ENSP00000437776:V189M;ENSP00000299961:V430M	ENSP00000299961:V430M	V	+	1	0	HTR3A	113365591	1.000000	0.71417	0.963000	0.40424	0.444000	0.32077	6.310000	0.72830	2.710000	0.92621	0.655000	0.94253	GTG		0.612	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		A	113860381	G	A	113860381	3	1	39	1	0	0	0	0	1	0	0	0	7465	1145	40	1	1503	1	HTR3A	11	113860381	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	5657627	113860381	21146135	130	3594										
CBL	867	hgsc.bcm.edu	37	chr11	119149247	119149247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aaggtcagggctgtcctttcTgccgatgtgaaattaaaggt	12	7	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:119149247T>C	ENST00000264033.4	+	9	1631	c.1255T>C	c.(1255-1257)Tgc>Cgc	p.C419R		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	419	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G397_I429del(1)|p.C419R(1)|p.E366_K477del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CTGTCCTTTCTGCCGATGTGA	0.438			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	3	Deletion - In frame(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(3)	11											125	122	123					11																	119149247		2199	4295	6494	118654457	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1255T>C	11.37:g.119149247T>C	ENSP00000264033:p.Cys419Arg		118654457	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.635166	0.67130	.	.	ENSG00000110395	ENST00000264033	D	0.99167	-5.51	5.96	5.96	0.96718	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.99691	0.9883	H	0.99626	4.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97048	0.9762	10	0.87932	D	0	-42.5012	16.4484	0.83959	0.0:0.0:0.0:1.0	.	419	P22681	CBL_HUMAN	R	419	ENSP00000264033:C419R	ENSP00000264033:C419R	C	+	1	0	CBL	118654457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	TGC		0.438	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119149247	T	C	119149247	3	2	39	1	0	0	0	0	1	0	0	0	2706	1580	55	4	1289	4	CBL	11	119149247	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	5288866	119149247	15857269	131	3595										
PANX3	116337	hgsc.bcm.edu	37	chr11	124489410	124489410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agggctgctaagtgatgagaCccatgtccccaatctgatca	10	11	2	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr11:124489410C>T	ENST00000284288.2	+	4	825	c.758C>T	c.(757-759)aCc>aTc	p.T253I		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	253					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		AGTGATGAGACCCATGTCCCC	0.473																																																0			11											123	108	113					11																	124489410		2201	4299	6500	123994620	SO:0001583	missense	116337			AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"Ion channels / Pannexins"	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.758C>T	11.37:g.124489410C>T	ENSP00000284288:p.Thr253Ile		123994620		Missense_Mutation	SNP	ENST00000284288.2	37	CCDS8447.1	.	.	.	.	.	.	.	.	.	.	C	8.628	0.892908	0.17613	.	.	ENSG00000154143	ENST00000284288	T	0.29655	1.56	5.39	1.8	0.24995	.	0.695263	0.15091	N	0.281094	T	0.13756	0.0333	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14337	-1.0476	10	0.48119	T	0.1	-9.3293	5.5826	0.17258	0.1418:0.6024:0.0:0.2558	.	253	Q96QZ0	PANX3_HUMAN	I	253	ENSP00000284288:T253I	ENSP00000284288:T253I	T	+	2	0	PANX3	123994620	0.020000	0.18652	0.586000	0.28679	0.709000	0.40893	0.871000	0.28023	1.266000	0.44231	0.561000	0.74099	ACC		0.473	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			T	124489410	C	T	124489410	3	4	39	1	0	0	0	0	1	0	0	0	11453	507	18	3	772	3	PANX3	11	124489410	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5340163	124489410	10517106	132	3596										
PZP	5858	hgsc.bcm.edu	37	chr12	9354931	9354931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttaccagttcatttcgagggCgaaaattttcatccacggag	9	9	2	0	rs369009345		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:9354931C>T	ENST00000261336.2	-	4	492	c.464G>A	c.(463-465)cGc>cAc	p.R155H	PZP_ENST00000381997.2_Missense_Mutation_p.R24H	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	155					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						ATTTCGAGGGCGAAAATTTTC	0.428																																					Melanoma(125;1402 1695 4685 34487 38571)											0			12						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	92	80	84		464	-3.7	0	12		84	0,8600		0,0,4300	no	missense	PZP	NM_002864.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	155/1483	9354931	1,13005	2203	4300	6503	9246198	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.464G>A	12.37:g.9354931C>T	ENSP00000261336:p.Arg155His		9246198	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	0.071	-1.202722	0.01581	2.27E-4	0.0	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.74421	-0.84;-0.84	2.44	-3.66	0.04489	Alpha-2-macroglobulin, N-terminal (1);	0.847105	0.09858	N	0.746585	T	0.42562	0.1208	N	0.05414	-0.055	0.09310	N	1	B;B	0.12013	0.005;0.002	B;B	0.12837	0.008;0.004	T	0.38650	-0.9651	10	0.05833	T	0.94	.	4.19	0.10416	0.0:0.4492:0.2195:0.3313	.	24;155	P20742-2;P20742	.;PZP_HUMAN	H	155;24	ENSP00000261336:R155H;ENSP00000371427:R24H	ENSP00000261336:R155H	R	-	2	0	PZP	9246198	0.000000	0.05858	0.012000	0.15200	0.492000	0.33523	-1.934000	0.01552	-0.756000	0.04703	-0.691000	0.03719	CGC		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9354931	C	T	9354931	3	4	39	1	0	0	0	0	1	0	0	0	12906	768	27	1	4116	1	PZP	12	9354931	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		9354931	124496964	133	3597										
KLRF1	51348	hgsc.bcm.edu	37	chr12	9985930	9985930	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtattgctaaaatgccaaaaAggaagttgttcaaatgccac	8	7	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:9985930A>G	ENST00000279544.3	+	3	280	c.216A>G	c.(214-216)aaA>aaG	p.K72K	KLRF1_ENST00000537723.1_Silent_p.K72K|KLRF1_ENST00000324214.4_Intron|KLRF1_ENST00000354855.3_Intron	NM_016523.1	NP_057607	Q9NZS2	KLRF1_HUMAN	killer cell lectin-like receptor subfamily F, member 1	72					cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|MHC class I receptor activity (GO:0032393)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)	13						AATGCCAAAAAGGAAGTTGTT	0.358																																																0			12											109	104	105					12																	9985930		1859	4098	5957	9877197	SO:0001819	synonymous_variant	51348			AF175206	CCDS41750.1	12p13.31	2011-08-30			ENSG00000150045	ENSG00000150045		"Killer cell lectin-like receptors", "C-type lectin domain containing"	13342	protein-coding gene	gene with protein product		605029				10671213	Standard	NM_001291823		Approved	CLEC5C, NKp80	uc021qux.1	Q9NZS2		ENST00000279544.3:c.216A>G	12.37:g.9985930A>G			9877197	Q4KMT5|Q96PR2|Q96PR3|Q9NZS1	Silent	SNP	ENST00000279544.3	37	CCDS41750.1																																																																																				0.358	KLRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399535.1	NM_016523		G	9985930	A	G	9985930	2	3	39	1	0	0	0	0	0	0	0	1	8441	69	3	4		4	KLRF1	12	9985930	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	630999	9985930	123865965	134	3598										
LRP6	4040	hgsc.bcm.edu	37	chr12	12311913	12311913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgtcgagatgagtgaaagaCgaggatgtccatcacataat	11	7	1	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:12311913C>T	ENST00000261349.4	-	12	2717	c.2641G>A	c.(2641-2643)Gtc>Atc	p.V881I	LRP6_ENST00000543091.1_Missense_Mutation_p.V881I	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	881	Beta-propeller 3.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.V881L(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GAGTGAAAGACGAGGATGTCC	0.537																																																1	Substitution - Missense(1)	central_nervous_system(1)	12											226	159	181					12																	12311913		2203	4300	6503	12203180	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.2641G>A	12.37:g.12311913C>T	ENSP00000261349:p.Val881Ile		12203180	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106476	0.94292	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91351	-2.83;-2.83	6.02	6.02	0.97574	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.53938	D	0.000042	D	0.92941	0.7754	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.984;0.999	D;D	0.76575	0.973;0.988	D	0.88959	0.3392	10	0.15499	T	0.54	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	881;881	F5H7J9;O75581	.;LRP6_HUMAN	I	881	ENSP00000261349:V881I;ENSP00000442472:V881I	ENSP00000261349:V881I	V	-	1	0	LRP6	12203180	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	7.487000	0.81328	2.865000	0.98341	0.655000	0.94253	GTC		0.537	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12311913	C	T	12311913	3	4	39	1	0	0	0	0	1	0	0	0	8991	536	19	1	2248	1	LRP6	12	12311913	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	2325983	12311913	121539982	135	3599										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380275	25380275	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctcattgcactgtactcctcTtgacctgctgtgtcgagaat	8	12	2	2	rs17851045		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:25380275T>G	ENST00000256078.4	-	3	246	c.183A>C	c.(181-183)caA>caC	p.Q61H	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61H|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61H(153)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TGTACTCCTCTTGACCTGCTG	0.423	Q61H(CL11_LARGE_INTESTINE)|Q61H(HS766T_PANCREAS)|Q61H(NCIH1155_LUNG)|Q61H(NCIH460_LUNG)|Q61H(T3M4_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	153	Substitution - Missense(153)	large_intestine(74)|lung(26)|pancreas(18)|haematopoietic_and_lymphoid_tissue(9)|endometrium(7)|soft_tissue(3)|biliary_tract(3)|liver(3)|cervix(2)|skin(2)|kidney(2)|stomach(1)|small_intestine(1)|ovary(1)|NS(1)	12											109	98	102					12																	25380275		2203	4300	6503	25271542	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.183A>C	12.37:g.25380275T>G	ENSP00000256078:p.Gln61His		25271542	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.133750	0.77662	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.84146	-1.81;-1.81	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.87265	0.6134	M	0.91140	3.18	0.80722	D	1	B;B	0.33413	0.411;0.09	B;B	0.32724	0.092;0.151	D	0.87829	0.2643	10	0.72032	D	0.01	.	9.9836	0.41828	0.0:0.0752:0.0:0.9248	.	61;61	P01116-2;P01116	.;RASK_HUMAN	H	61	ENSP00000308495:Q61H;ENSP00000256078:Q61H	ENSP00000256078:Q61H	Q	-	3	2	KRAS	25271542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.240000	0.43088	2.326000	0.78906	0.533000	0.62120	CAA		0.423	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		G	25380275	T	G	25380275	3	3	39	1	0	0	0	0	1	0	0	0	8459	1606	56	4	519	4	KRAS	12	25380275	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	13068362	25380275	108471620	136	3600										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244264	46244264	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccaggacagatcccttcaggCactcctgttacagtaattca	7	13	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:46244264C>T	ENST00000334344.6	+	15	2530	c.2358C>T	c.(2356-2358)ggC>ggT	p.G786G	ARID2_ENST00000444670.1_Silent_p.G396G|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Silent_p.G637G|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	786					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCCTTCAGGCACTCCTGTTA	0.448			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0			12											88	77	81					12																	46244264		2203	4300	6503	44530531	SO:0001819	synonymous_variant	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2358C>T	12.37:g.46244264C>T			44530531	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																				0.448	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46244264	C	T	46244264	2	4	39	1	0	0	0	0	0	0	0	1	915	697	25	3		3	ARID2	12	46244264	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	20863989	46244264	87607631	137	3601										
LASS5	91012	hgsc.bcm.edu	37	chr12	50536911	50536911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtcctgattcctccgatggCgaaaccagcattggattttt	9	10	0	1	rs547919626	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:50536911C>T	ENST00000317551.6	-	3	504	c.380G>A	c.(379-381)cGc>cAc	p.R127H	CERS5_ENST00000422340.2_Missense_Mutation_p.R69H	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	127					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CCTCCGATGGCGAAACCAGCA	0.483													C|||	3	0.000599042	0	0	5008	,	,		19728	0.003		0	False		,,,				2504	0															0			12											214	222	219					12																	50536911		2203	4300	6503	48823178	SO:0001583	missense	91012				CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.380G>A	12.37:g.50536911C>T	ENSP00000325485:p.Arg127His		48823178	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	37	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.513457|5.513457	0.96402|0.96402	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000547800|ENST00000551005;ENST00000317551;ENST00000422340	.|D;D;D	.|0.96041	.|-3.89;-3.89;-3.89	4.52|4.52	4.52|4.52	0.55395|0.55395	.|Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97892|0.97892	0.9307|0.9307	M|M	0.86740|0.86740	2.835|2.835	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.986;0.999	.|D;P;P	.|0.97110	.|1.0;0.771;0.886	D|D	0.98113|0.98113	1.0421|1.0421	6|10	0.22109|0.51188	T|T	0.4|0.08	-8.9486|-8.9486	17.8139|17.8139	0.88625|0.88625	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|69;127;46	.|B4DV54;Q8N5B7;F8W0U5	.|.;CERS5_HUMAN;.	T|H	62|46;127;69	.|ENSP00000447556:R46H;ENSP00000325485:R127H;ENSP00000389050:R69H	ENSP00000407896:A92T|ENSP00000325485:R127H	A|R	-|-	1|2	0|0	CERS5|CERS5	48823178|48823178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.625000|7.625000	0.83145|0.83145	2.514000|2.514000	0.84764|0.84764	0.650000|0.650000	0.86243|0.86243	GCC|CGC		0.483	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		T	50536911	C	T	50536911	3	4	39	1	0	0	0	0	1	0	0	0	8664	768	27	1	830	1	LASS5	12	50536911	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4292647	50536911	83314984	138	3602										
SCN8A	6334	hgsc.bcm.edu	37	chr12	52162736	52162736	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acgatggggaaatgaacaacCtccagatctcagtgatccgt	10	10	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:52162736C>A	ENST00000354534.6	+	17	3167	c.2989C>A	c.(2989-2991)Ctc>Atc	p.L997I	SCN8A_ENST00000545061.1_Missense_Mutation_p.L997I	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	997					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	AATGAACAACCTCCAGATCTC	0.537																																																0			12											94	93	93					12																	52162736		2045	4206	6251	50449003	SO:0001583	missense	6334			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.2989C>A	12.37:g.52162736C>A	ENSP00000346534:p.Leu997Ile		50449003	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678849	0.68042	.	.	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D	0.87650	-2.28;-2.28;-2.28	4.66	3.74	0.42951	Sodium ion transport-associated (1);	0.152963	0.44097	D	0.000496	D	0.91700	0.7376	M	0.83118	2.625	0.58432	D	0.999999	D;D	0.69078	0.997;0.99	D;P	0.63877	0.919;0.874	D	0.90325	0.4347	10	0.31617	T	0.26	.	10.4679	0.44618	0.0:0.8339:0.0:0.1661	.	997;997	F8VWM7;Q9UQD0	.;SCN8A_HUMAN	I	997;997;997;910	ENSP00000346534:L997I;ENSP00000440360:L997I;ENSP00000347255:L997I	ENSP00000346534:L997I	L	+	1	0	SCN8A	50449003	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	3.925000	0.56484	1.502000	0.48669	0.563000	0.77884	CTC		0.537	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52162736	C	A	52162736	3	1	39	1	0	0	0	0	1	0	0	0	13961	681	24	2	3051	2	SCN8A	12	52162736	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	1625825	52162736	81689159	139	3603										
OR6C1	390321	hgsc.bcm.edu	37	chr12	55714819	55714819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcacactgcttgtttttactTcttggctggtttcattctta	7	9	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:55714819T>C	ENST00000379668.2	+	1	474	c.436T>C	c.(436-438)Tct>Cct	p.S146P		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						TGTTTTTACTTCTTGGCTGGT	0.408																																																0			12											45	43	43					12																	55714819		2203	4300	6503	54001086	SO:0001583	missense	390321			AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.436T>C	12.37:g.55714819T>C	ENSP00000368990:p.Ser146Pro		54001086	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	37	CCDS31818.1	.	.	.	.	.	.	.	.	.	.	t	13.72	2.320298	0.41096	.	.	ENSG00000205330	ENST00000379668	T	0.38887	1.11	4.62	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000047	T	0.60011	0.2236	M	0.73753	2.245	0.09310	N	1	D	0.53745	0.962	D	0.69142	0.962	T	0.51718	-0.8670	10	0.52906	T	0.07	.	10.0589	0.42261	0.0:0.0:0.4769:0.5231	.	146	Q96RD1	OR6C1_HUMAN	P	146	ENSP00000368990:S146P	ENSP00000368990:S146P	S	+	1	0	OR6C1	54001086	0.000000	0.05858	0.007000	0.13788	0.697000	0.40408	0.413000	0.21148	0.766000	0.33244	0.374000	0.22700	TCT		0.408	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		C	55714819	T	C	55714819	3	2	39	1	0	0	0	0	1	0	0	0	11221	1783	62	4	438	4	OR6C1	12	55714819	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	3552083	55714819	78137076	140	3604										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59271440	59271440	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtgtatttcccagcatcacTgacatctgagtccacaataa	6	11	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:59271440T>A	ENST00000320743.3	-	15	2564	c.2278A>T	c.(2278-2280)Agt>Tgt	p.S760C	LRIG3_ENST00000379141.4_Missense_Mutation_p.S700C	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	760	Ig-like C2-type 3.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CCAGCATCACTGACATCTGAG	0.498			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0			12											179	167	171					12																	59271440		2203	4300	6503	57557707	SO:0001583	missense	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2278A>T	12.37:g.59271440T>A	ENSP00000326759:p.Ser760Cys		57557707	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.070454	0.55539	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.39056	1.1;1.1	5.59	1.65	0.23941	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.165643	0.28706	N	0.014410	T	0.61565	0.2357	M	0.92367	3.3	0.24923	N	0.991961	D;D	0.60160	0.98;0.987	P;P	0.58013	0.831;0.75	T	0.55554	-0.8123	9	.	.	.	.	6.3634	0.21441	0.0:0.5334:0.0:0.4666	.	700;760	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	C	700;760	ENSP00000368436:S700C;ENSP00000326759:S760C	.	S	-	1	0	LRIG3	57557707	0.995000	0.38212	0.553000	0.28255	0.323000	0.28346	4.960000	0.63673	0.502000	0.28037	0.533000	0.62120	AGT		0.498	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59271440	T	A	59271440	3	1	39	1	0	0	0	0	1	0	0	0	8975	1580	55	5	1101	5	LRIG3	12	59271440	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	3556621	59271440	74580455	141	3605										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80663931	80663931	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atgaattagcaacgccctctGctggtaagatcttaaaagat	8	8	2	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:80663931G>C	ENST00000547103.1	+	22	2494	c.2488G>C	c.(2488-2490)Gct>Cct	p.A830P	OTOGL_ENST00000458043.2_Missense_Mutation_p.A830P			Q3ZCN5	OTOGL_HUMAN	otogelin-like	830					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						AACGCCCTCTGCTGGTAAGAT	0.393											OREG0011204|OREG0022007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)|type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip); Conservation found by scanning with a motif model																																				0			12											94	92	92					12																	80663931		1935	4130	6065	79188062	SO:0001583	missense	283310			AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.2488G>C	12.37:g.80663931G>C	ENSP00000447211:p.Ala830Pro	1200	79188062	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		.	.	.	.	.	.	.	.	.	.	G	13.22	2.171707	0.38315	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.16324	2.35;2.35	5.22	-2.25	0.06888	.	.	.	.	.	T	0.04272	0.0118	N	0.01146	-0.985	0.26190	N	0.979591	.	.	.	.	.	.	T	0.40059	-0.9583	7	0.26408	T	0.33	.	5.5944	0.17319	0.2351:0.3366:0.4283:0.0	.	.	.	.	P	830	ENSP00000447211:A830P;ENSP00000400895:A830P	ENSP00000400895:A830P	A	+	1	0	OTOGL	79188062	0.997000	0.39634	0.994000	0.49952	0.969000	0.65631	0.298000	0.19120	-0.199000	0.10317	-0.312000	0.09012	GCT		0.393	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80663931	G	C	80663931	3	2	39	1	0	0	0	0	1	0	0	0	1711	1319	46	5	2574	5	C12orf64	12	80663931	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	21392491	80663931	53187964	142	3606										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85450452	85450452	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tccaaagatgtaagagaaaaCgtaatattacaagaaaaaga	7	4	0	4	rs550886780	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:85450452C>T	ENST00000393217.2	+	8	1942	c.1881C>T	c.(1879-1881)aaC>aaT	p.N627N		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	627										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TAAGAGAAAACGTAATATTAC	0.284													C|||	6	0.00119808	0	0	5008	,	,		17342	0		0	False		,,,				2504	0.0061															0			12											29	31	30					12																	85450452		2197	4295	6492	83974583	SO:0001819	synonymous_variant	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1881C>T	12.37:g.85450452C>T			83974583	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	37	CCDS41816.1																																																																																				0.284	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85450452	C	T	85450452	2	4	39	1	0	0	0	0	0	0	0	1	9058	535	19	1		1	LRRIQ1	12	85450452	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4786521	85450452	48401443	143	3607										
UNG	7374	hgsc.bcm.edu	37	chr12	109536404	109536404	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tttggagagagctggaagaaGcacctcagcggggagttcgg	17	7	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:109536404G>A	ENST00000242576.2	+	2	406	c.300G>A	c.(298-300)aaG>aaA	p.K100K	UNG_ENST00000336865.2_Silent_p.K91K	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						GCTGGAAGAAGCACCTCAGCG	0.572								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																																							0			12											43	50	48					12																	109536404		2200	4289	6489	108020787	SO:0001819	synonymous_variant	7374	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.300G>A	12.37:g.109536404G>A			108020787		Silent	SNP	ENST00000242576.2	37	CCDS9124.1																																																																																				0.572	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		A	109536404	G	A	109536404	2	1	39	1	0	0	0	0	0	0	0	1	17039	962	34	3		3	UNG	12	109536404	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	24085952	109536404	24315491	144	3608										
OAS3	4940	hgsc.bcm.edu	37	chr12	113403675	113403675	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccgagatcatctccgagatcCgagcccagctggaggcatgt	12	13	2	2	rs61942233	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:113403675C>T	ENST00000228928.7	+	12	2709	c.2530C>T	c.(2530-2532)Cga>Tga	p.R844*	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	844	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CTCCGAGATCCGAGCCCAGCT	0.587													C|||	26	0.00519169	0.0015	0.0058	5008	,	,		21143	0		0.0109	False		,,,				2504	0.0092															0			12						C	stop/ARG	18,3980		0,18,1981	33	38	36		2530	3.2	0.9	12	dbSNP_129	36	141,8229		4,133,4048	yes	stop-gained	OAS3	NM_006187.2		4,151,6029	TT,TC,CC		1.6846,0.4502,1.2856		844/1088	113403675	159,12209	1999	4185	6184	111888058	SO:0001587	stop_gained	4940			AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"2'-5'-oligoadenylate synthetase 3 (100 kD)"			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2530C>T	12.37:g.113403675C>T	ENSP00000228928:p.Arg844*		111888058	Q2HJ14|Q9H3P5	Nonsense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	14	0.00641025641025641	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	38	7.264510	0.98171	0.004502	0.016846	ENSG00000111331	ENST00000228928;ENST00000323881	.	.	.	5.16	3.16	0.36331	.	0.615122	0.12178	U	0.492349	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7356	0.40386	0.377:0.623:0.0:0.0	rs61942233	.	.	.	X	844;843	.	ENSP00000228928:R844X	R	+	1	2	OAS3	111888058	0.003000	0.15002	0.854000	0.33618	0.178000	0.23041	0.025000	0.13577	1.126000	0.42016	0.655000	0.94253	CGA		0.587	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			T	113403675	C	T	113403675	4	4	39	1	0	0	0	0	0	1	0	0	10832	644	23	1	2576	1	OAS3	12	113403675	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	3867271	113403675	20448220	145	3609										
C12orf43	64897	hgsc.bcm.edu	37	chr12	121454184	121454184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgctccaagccccaagccgGcattgccgcctcgcggcacc	10	19	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:121454184G>A	ENST00000288757.3	-	1	116	c.94C>T	c.(94-96)Ccg>Tcg	p.P32S	C12orf43_ENST00000445832.3_Missense_Mutation_p.P2S|C12orf43_ENST00000539736.1_Missense_Mutation_p.P32S|C12orf43_ENST00000537817.1_Missense_Mutation_p.P2S|C12orf43_ENST00000366211.2_5'UTR|C12orf43_ENST00000536407.2_Missense_Mutation_p.P32S	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	32										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCCCAAGCCGGCATTGCCGCC	0.637																																																0			12											39	39	39					12																	121454184		2203	4300	6503	119938567	SO:0001583	missense	64897			AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.94C>T	12.37:g.121454184G>A	ENSP00000288757:p.Pro32Ser		119938567	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.47|12.47	1.947255|1.947255	0.34377|0.34377	.|.	.|.	ENSG00000157895|ENSG00000157895	ENST00000536407|ENST00000445832;ENST00000288757;ENST00000537817;ENST00000539736;ENST00000538296	.|T;T;T;T;T	.|0.71461	.|0.19;0.83;-0.42;0.81;-0.57	5.06|5.06	4.18|4.18	0.49190|0.49190	.|.	.|0.350255	.|0.28349	.|N	.|0.015671	T|T	0.74366|0.74366	0.3707|0.3707	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	.|B;D;B;P	.|0.63046	.|0.221;0.992;0.221;0.947	.|B;P;B;P	.|0.56865	.|0.15;0.808;0.15;0.676	T|T	0.74822|0.74822	-0.3534|-0.3534	5|10	.|0.51188	.|T	.|0.08	-12.8822|-12.8822	9.5491|9.5491	0.39299|0.39299	0.0955:0.0:0.9045:0.0|0.0955:0.0:0.9045:0.0	.|.	.|32;2;32;32	.|G5EA44;F5H7W8;B4DWJ9;Q96C57	.|.;.;.;CL043_HUMAN	V|S	36|2;32;2;32;2	.|ENSP00000409788:P2S;ENSP00000288757:P32S;ENSP00000442224:P2S;ENSP00000437803:P32S;ENSP00000442041:P2S	.|ENSP00000288757:P32S	A|P	-|-	2|1	0|0	C12orf43|C12orf43	119938567|119938567	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.022000|0.022000	0.10575|0.10575	2.996000|2.996000	0.49449|0.49449	1.494000|1.494000	0.48533|0.48533	0.655000|0.655000	0.94253|0.94253	GCC|CCG		0.637	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895		A	121454184	G	A	121454184	3	1	39	1	0	0	0	0	1	0	0	0	1693	1203	42	3	718	3	C12orf43	12	121454184	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	8050509	121454184	12397711	146	3610										
ABCB9	23457	hgsc.bcm.edu	37	chr12	123430600	123430600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cccagacgtagtacatgtagGcagctgcctccttcctgttc	9	14	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:123430600G>A	ENST00000542678.1	-	6	4061	c.1223C>T	c.(1222-1224)gCc>gTc	p.A408V	ABCB9_ENST00000541983.1_5'Flank|ABCB9_ENST00000344275.7_Missense_Mutation_p.A408V|ABCB9_ENST00000442028.2_Missense_Mutation_p.A408V|ABCB9_ENST00000540285.1_Missense_Mutation_p.A408V|ABCB9_ENST00000346530.5_Missense_Mutation_p.A408V|ABCB9_ENST00000392439.3_Missense_Mutation_p.A408V|ABCB9_ENST00000280560.8_Missense_Mutation_p.A408V|ABCB9_ENST00000442833.2_Missense_Mutation_p.A408V			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	408	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		GTACATGTAGGCAGCTGCCTC	0.602																																					Ovarian(49;786 1333 9175 38236)											0			12											88	65	73					12																	123430600		2203	4300	6503	121996553	SO:0001583	missense	23457			U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1223C>T	12.37:g.123430600G>A	ENSP00000440288:p.Ala408Val		121996553	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407787	0.62399	.	.	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028;ENST00000542448;ENST00000540971;ENST00000536976;ENST00000546077	D;D;D;D;D;D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	5.0	5.0	0.66597	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88190	0.6370	L	0.31752	0.955	0.80722	D	1	P;D;P;P;P	0.54397	0.597;0.966;0.587;0.532;0.95	B;P;B;B;P	0.55303	0.401;0.747;0.326;0.155;0.773	D	0.85132	0.0975	10	0.15066	T	0.55	-36.1287	17.9177	0.88957	0.0:0.0:1.0:0.0	.	408;408;190;408;408	B4E2J0;Q9NP78-3;B3KNJ8;Q9NP78-2;Q9NP78	.;.;.;.;ABCB9_HUMAN	V	408;408;408;408;408;408;34;114;170;65	ENSP00000280560:A408V;ENSP00000441734:A408V;ENSP00000280559:A408V;ENSP00000376234:A408V;ENSP00000440288:A408V;ENSP00000394898:A408V;ENSP00000440244:A34V;ENSP00000441086:A114V;ENSP00000443433:A170V;ENSP00000443224:A65V	ENSP00000280560:A408V	A	-	2	0	ABCB9	121996553	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	9.828000	0.99408	2.309000	0.77851	0.561000	0.74099	GCC		0.602	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		A	123430600	G	A	123430600	3	1	39	1	0	0	0	0	1	0	0	0	48	1203	42	3	1105	3	ABCB9	12	123430600	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	1976416	123430600	10421295	147	3611										
ULK1	8408	hgsc.bcm.edu	37	chr12	132400633	132400633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcagtcctgccggaacctgCggggctcacccaagctgccc	12	17	1	0	rs142452051		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr12:132400633C>T	ENST00000321867.4	+	19	2158	c.1807C>T	c.(1807-1809)Cgg>Tgg	p.R603W	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	603					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CCGGAACCTGCGGGGCTCACC	0.701													C|||	1	0.000199681	0	0	5008	,	,		14441	0		0	False		,,,				2504	0.001															0			12						C	TRP/ARG	2,4398	4.2+/-10.8	0,2,2198	27	32	31		1807	4.7	1	12	dbSNP_134	31	1,8587	1.2+/-3.3	0,1,4293	no	missense	ULK1	NM_003565.2	101	0,3,6491	TT,TC,CC		0.0116,0.0455,0.0231	probably-damaging	603/1051	132400633	3,12985	2200	4294	6494	130966586	SO:0001583	missense	8408			AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.1807C>T	12.37:g.132400633C>T	ENSP00000324560:p.Arg603Trp		130966586	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468489	0.63625	4.55E-4	1.16E-4	ENSG00000177169	ENST00000321867	T	0.39787	1.06	5.62	4.65	0.58169	.	0.066330	0.56097	D	0.000024	T	0.62405	0.2425	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.68353	0.957	T	0.64980	-0.6279	10	0.59425	D	0.04	-21.5144	15.683	0.77388	0.2192:0.7807:0.0:0.0	.	603	O75385	ULK1_HUMAN	W	603	ENSP00000324560:R603W	ENSP00000324560:R603W	R	+	1	2	ULK1	130966586	1.000000	0.71417	0.999000	0.59377	0.568000	0.35870	1.507000	0.35758	2.653000	0.90120	0.655000	0.94253	CGG		0.701	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132400633	C	T	132400633	3	4	39	1	0	0	0	0	1	0	0	0	17015	759	27	1	1881	1	ULK1	12	132400633	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	8970033	132400633	1451262	148	3612										
GPR12	2835	hgsc.bcm.edu	37	chr13	27333439	27333439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gaggcagttccagcccatgaCgggcagcagccccaggcaga	14	14	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr13:27333439C>T	ENST00000381436.2	-	1	988	c.526G>A	c.(526-528)Gtc>Atc	p.V176I	GPR12_ENST00000405846.3_Missense_Mutation_p.V176I			P47775	GPR12_HUMAN	G protein-coupled receptor 12	176					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		CAGCCCATGACGGGCAGCAGC	0.597																																																0			13											51	47	48					13																	27333439		2203	4300	6503	26231439	SO:0001583	missense	2835			U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.526G>A	13.37:g.27333439C>T	ENSP00000370844:p.Val176Ile		26231439	Q5T8P3	Missense_Mutation	SNP	ENST00000381436.2	37	CCDS9319.1	.	.	.	.	.	.	.	.	.	.	C	3.117	-0.181320	0.06380	.	.	ENSG00000132975	ENST00000405846;ENST00000381436	T;T	0.36520	1.25;1.25	5.36	0.721	0.18219	GPCR, rhodopsin-like superfamily (1);	0.236354	0.42964	N	0.000627	T	0.16342	0.0393	N	0.11892	0.195	0.21841	N	0.999511	B	0.19073	0.033	B	0.19946	0.027	T	0.32134	-0.9918	10	0.07813	T	0.8	.	9.6996	0.40178	0.0:0.4994:0.0:0.5006	.	176	P47775	GPR12_HUMAN	I	176	ENSP00000384932:V176I;ENSP00000370844:V176I	ENSP00000370844:V176I	V	-	1	0	GPR12	26231439	0.001000	0.12720	0.292000	0.24919	0.946000	0.59487	0.002000	0.13061	-0.184000	0.10567	-0.224000	0.12420	GTC		0.597	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			T	27333439	C	T	27333439	3	4	39	1	0	0	0	0	1	0	0	0	6655	536	19	1	482	1	GPR12	13	27333439	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		27333439	87836439	149	3613										
RB1	5925	hgsc.bcm.edu	37	chr13	49033926	49033926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gacccttttccagcacacccTgcagaatgagtatgaactca	7	13	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr13:49033926T>C	ENST00000267163.4	+	20	2201	c.2063T>C	c.(2062-2064)cTg>cCg	p.L688P		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	688	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.L688P(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAGCACACCCTGCAGAATGAG	0.443		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	27	Whole gene deletion(15)|Unknown(11)|Substitution - Missense(1)	bone(10)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|eye(2)|adrenal_gland(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13	GRCh37	CM074471	RB1	M							87	82	83					13																	49033926		2203	4300	6503	47931927	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2063T>C	13.37:g.49033926T>C	ENSP00000267163:p.Leu688Pro		47931927	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379557	0.82682	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.94000	-3.33	5.48	5.48	0.80851	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.64402	D	0.000007	D	0.97328	0.9126	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98283	1.0509	10	0.87932	D	0	-7.9392	15.5642	0.76277	0.0:0.0:0.0:1.0	.	688	P06400	RB_HUMAN	P	667;688	ENSP00000267163:L688P	ENSP00000267163:L688P	L	+	2	0	RB1	47931927	1.000000	0.71417	0.990000	0.47175	0.905000	0.53344	7.698000	0.84413	2.086000	0.62901	0.477000	0.44152	CTG		0.443	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	49033926	T	C	49033926	3	2	39	1	0	0	0	0	1	0	0	0	13135	1580	55	4	2141	4	RB1	13	49033926	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	21700487	49033926	66135952	150	3614										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86368486	86368486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	attttcctgttccaaaagacTtctttggagatgttttgcat	7	7	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr13:86368486T>C	ENST00000400286.2	-	2	2756	c.2158A>G	c.(2158-2160)Agt>Ggt	p.S720G		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	720					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.S720C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TCCAAAAGACTTCTTTGGAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											294	284	287					13																	86368486		1871	4112	5983	85266487	SO:0001583	missense	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.2158A>G	13.37:g.86368486T>C	ENSP00000383143:p.Ser720Gly		85266487	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.231399	0.39399	.	.	ENSG00000184564	ENST00000400286	T	0.58060	0.36	5.84	5.84	0.93424	.	0.000000	0.85682	U	0.000000	T	0.33990	0.0882	N	0.08118	0	0.45403	D	0.998384	B	0.26081	0.141	B	0.25614	0.062	T	0.18429	-1.0337	10	0.27785	T	0.31	-7.7815	15.0542	0.71901	0.0:0.0:0.0:1.0	.	720	Q9H5Y7	SLIK6_HUMAN	G	720	ENSP00000383143:S720G	ENSP00000383143:S720G	S	-	1	0	SLITRK6	85266487	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.763000	0.62257	2.228000	0.72767	0.533000	0.62120	AGT		0.398	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		C	86368486	T	C	86368486	3	2	39	1	0	0	0	0	1	0	0	0	14784	1609	56	4	371	4	SLITRK6	13	86368486	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	37334560	86368486	28801392	151	3615										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103510653	103510653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctttcataatcctcaagcgaTagatattgagtctgaggact	8	8	3	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr13:103510653T>C	ENST00000355739.4	+	6	1980	c.557T>C	c.(556-558)aTa>aCa	p.I186T	ERCC5_ENST00000535557.1_Missense_Mutation_p.I186T|BIVM-ERCC5_ENST00000602836.1_Silent_p.D611D	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	186					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)	p.I186T(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CCTCAAGCGATAGATATTGAG	0.363			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	1	Substitution - Missense(1)	ovary(1)	13											94	95	95					13																	103510653		2203	4300	6503	102308654	SO:0001583	missense	2073	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.557T>C	13.37:g.103510653T>C	ENSP00000347978:p.Ile186Thr		102308654	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.166924	0.57476	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557;ENST00000375955	T;T	0.17854	2.25;2.25	5.31	5.31	0.75309	.	0.252736	0.41500	D	0.000871	T	0.32164	0.0820	M	0.73962	2.25	0.47737	D	0.999502	P;D;P	0.54964	0.956;0.969;0.829	P;P;B	0.50049	0.629;0.462;0.322	T	0.15206	-1.0445	10	0.72032	D	0.01	-9.7192	15.2802	0.73778	0.0:0.0:0.0:1.0	.	186;186;611	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	T	611;186;186;18	ENSP00000347978:I186T;ENSP00000442117:I186T	ENSP00000347978:I186T	I	+	2	0	ERCC5	102308654	1.000000	0.71417	0.817000	0.32601	0.935000	0.57460	7.384000	0.79751	2.000000	0.58554	0.533000	0.62120	ATA		0.363	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			C	103510653	T	C	103510653	3	2	39	1	0	0	0	0	1	0	0	0	5229	1406	49	4	579	4	ERCC5	13	103510653	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	17142167	103510653	11659225	152	3616										
NOVA1	4857	hgsc.bcm.edu	37	chr14	27064655	27064655	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cttagacagcttgatggtggCtccagtttctttttgcaact	9	9	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr14:27064655C>A	ENST00000344429.5	-	2	244	c.241G>T	c.(241-243)Gcc>Tcc	p.A81S	NOVA1_ENST00000551754.1_5'UTR|NOVA1_ENST00000539517.2_Missense_Mutation_p.A81S|NOVA1_ENST00000465357.2_Missense_Mutation_p.A81S|RP11-483C6.1_ENST00000572358.1_RNA|NOVA1_ENST00000547619.1_Missense_Mutation_p.A81S|NOVA1_ENST00000574031.1_Missense_Mutation_p.A81S|NOVA1_ENST00000267422.7_5'UTR|NOVA1-AS1_ENST00000547786.1_RNA	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	81	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		TTGATGGTGGCTCCAGTTTCT	0.428																																																0			14											169	159	163					14																	27064655		2203	4300	6503	26134495	SO:0001583	missense	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.241G>T	14.37:g.27064655C>A	ENSP00000342387:p.Ala81Ser		26134495	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	37	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.895610	0.72639	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000449198;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14;1.14	4.86	3.96	0.45880	.	0.469026	0.18861	N	0.129132	T	0.54095	0.1837	L	0.56396	1.775	0.80722	D	1	D;B;B	0.62365	0.991;0.041;0.033	D;B;B	0.63597	0.916;0.022;0.013	T	0.57923	-0.7727	10	0.72032	D	0.01	-1.8263	14.8854	0.70564	0.1446:0.8554:0.0:0.0	.	81;81;81	P51513-2;D3DS81;P51513-4	.;.;.	S	81;81;40;44;81;81	ENSP00000447391:A81S;ENSP00000438875:A81S;ENSP00000408914:A40S;ENSP00000449185:A44S;ENSP00000342387:A81S;ENSP00000448157:A81S	ENSP00000342387:A81S	A	-	1	0	NOVA1	26134495	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.729000	0.84864	1.169000	0.42739	0.561000	0.74099	GCC		0.428	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		A	27064655	C	A	27064655	3	1	39	1	0	0	0	0	1	0	0	0	10585	797	28	2	1329	2	NOVA1	14	27064655	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10		27064655	80284885	153	3617										
MIA2	117153	hgsc.bcm.edu	37	chr14	39722337	39722337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgatgtttatgatttcatgAattctgcattttcaccaatt	5	6	3	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr14:39722337A>G	ENST00000280082.3	+	6	2048	c.1849A>G	c.(1849-1851)Aat>Gat	p.N617D	RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.N544D	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	0					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		TGATTTCATGAATTCTGCATT	0.274																																																0			14											78	85	83					14																	39722337		2201	4291	6492	38792088	SO:0001583	missense	117153			BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1849A>G	14.37:g.39722337A>G	ENSP00000280082:p.Asn617Asp		38792088	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.336854	0.41398	.	.	ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000553728	T;T	0.52983	0.64;3.14	5.09	3.94	0.45596	.	1.370910	0.05175	N	0.500184	T	0.35856	0.0946	.	.	.	0.39364	D	0.965979	B	0.09022	0.002	B	0.12156	0.007	T	0.05733	-1.0867	8	.	.	.	.	8.5466	0.33426	0.91:0.0:0.09:0.0	.	617	Q96PC5-2	.	D	617;544	ENSP00000280082:N617D;ENSP00000452252:N544D	.	N	+	1	0	MIA2;RP11-407N17.3	38792088	0.184000	0.23200	0.944000	0.38274	0.843000	0.47879	1.565000	0.36386	0.889000	0.36185	0.477000	0.44152	AAT		0.274	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39722337	A	G	39722337	3	3	39	1	0	0	0	0	1	0	0	0	9594	246	9	4	1871	4	MIA2	14	39722337	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	12657682	39722337	67627203	154	3618										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72055681	72055681	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aacaccaccactggagcttcCgcagctgccgtggcatcctt	9	16	0	0	rs144648264	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr14:72055681C>T	ENST00000555818.1	+	2	1440	c.1092C>T	c.(1090-1092)tcC>tcT	p.S364S	SIPA1L1_ENST00000381232.3_Silent_p.S364S|SIPA1L1_ENST00000358550.2_Silent_p.S364S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	364					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CTGGAGCTTCCGCAGCTGCCG	0.478													C|||	6	0.00119808	0	0.0014	5008	,	,		19320	0		0.005	False		,,,				2504	0															0			14						C		1,4405	2.1+/-5.4	0,1,2202	57	60	59		1092	-2.3	0.7	14	dbSNP_134	59	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	SIPA1L1	NM_015556.1		0,13,6490	TT,TC,CC		0.1395,0.0227,0.1		364/1805	72055681	13,12993	2203	4300	6503	71125434	SO:0001819	synonymous_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1092C>T	14.37:g.72055681C>T			71125434	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.478	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72055681	C	T	72055681	2	4	39	1	0	0	0	0	0	0	0	1	14366	639	23	1		1	SIPA1L1	14	72055681	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	32333344	72055681	35293859	155	3619										
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77797491	77797491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcttggaggccttccaggtgTctcacccctgccggcagcca	11	16	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr14:77797491T>C	ENST00000556627.1	+	8	654	c.523T>C	c.(523-525)Tct>Cct	p.S175P	GSTZ1_ENST00000361389.4_Missense_Mutation_p.S147P|GSTZ1_ENST00000393734.1_Missense_Mutation_p.S147P|GSTZ1_ENST00000349555.3_Missense_Mutation_p.S160P|GSTZ1_ENST00000557053.1_Missense_Mutation_p.S105P|GSTZ1_ENST00000554279.1_Missense_Mutation_p.S188P|GSTZ1_ENST00000216465.5_Missense_Mutation_p.S202P|GSTZ1_ENST00000557639.1_Missense_Mutation_p.S147P|GSTZ1_ENST00000553586.1_Missense_Mutation_p.S203P			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	202	GST C-terminal.				cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CTTCCAGGTGTCTCACCCCTG	0.597																																																0			14											74	66	68					14																	77797491		2203	4300	6503	76867244	SO:0001583	missense	2954			U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"Glutathione S-transferases / Soluble"	4643	protein-coding gene	gene with protein product	"maleylacetoacetate isomerase"	603758	"glutathione transferase zeta 1"			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.523T>C	14.37:g.77797491T>C	ENSP00000450487:p.Ser175Pro		76867244	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		.	.	.	.	.	.	.	.	.	.	T	17.24	3.339081	0.60963	.	.	ENSG00000100577	ENST00000216465;ENST00000361389;ENST00000554279;ENST00000557639;ENST00000349555;ENST00000556627;ENST00000557053;ENST00000393734;ENST00000553586	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.48	-0.259	0.12971	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.312207	0.41605	D	0.000853	T	0.48370	0.1496	M	0.81802	2.56	0.49687	D	0.999814	P;P	0.49635	0.865;0.926	P;P	0.47015	0.52;0.534	T	0.56438	-0.7979	10	0.87932	D	0	1.2504	11.6251	0.51139	0.6426:0.0:0.0:0.3574	.	160;202	A6NED0;O43708	.;MAAI_HUMAN	P	202;147;188;147;160;175;105;147;203	ENSP00000216465:S202P;ENSP00000354959:S147P;ENSP00000452498:S188P;ENSP00000451927:S147P;ENSP00000314404:S160P;ENSP00000450487:S175P;ENSP00000451150:S105P;ENSP00000377335:S147P;ENSP00000451976:S203P	ENSP00000216465:S202P	S	+	1	0	GSTZ1	76867244	1.000000	0.71417	0.992000	0.48379	0.865000	0.49528	2.185000	0.42584	-0.244000	0.09639	-1.966000	0.00469	TCT		0.597	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		C	77797491	T	C	77797491	3	2	39	1	0	0	0	0	1	0	0	0	6869	1667	58	4	638	4	GSTZ1	14	77797491	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	5741810	77797491	29552049	156	3620										
SIN3A	25942	hgsc.bcm.edu	37	chr15	75702229	75702229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgcggatctggcagccattcTggctgggcctctgcggcttg	15	12	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr15:75702229T>C	ENST00000394947.3	-	8	1579	c.1265A>G	c.(1264-1266)cAg>cGg	p.Q422R	SIN3A_ENST00000360439.4_Missense_Mutation_p.Q422R|SIN3A_ENST00000394949.4_Missense_Mutation_p.Q422R	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GCAGCCATTCTGGCTGGGCCT	0.493																																																0			15											132	131	131					15																	75702229		2197	4294	6491	73489282	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1265A>G	15.37:g.75702229T>C	ENSP00000378402:p.Gln422Arg		73489282		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.138552	0.77775	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.44482	0.92;0.92;0.92	5.93	5.93	0.95920	.	0.098406	0.64402	D	0.000001	T	0.54967	0.1891	L	0.46157	1.445	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	T	0.46331	-0.9199	10	0.15499	T	0.54	-20.2558	15.5755	0.76380	0.0:0.0:0.0:1.0	.	422	Q96ST3	SIN3A_HUMAN	R	422	ENSP00000378402:Q422R;ENSP00000378403:Q422R;ENSP00000353622:Q422R	ENSP00000353622:Q422R	Q	-	2	0	SIN3A	73489282	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.039000	0.88947	2.281000	0.76405	0.533000	0.62120	CAG		0.493	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		C	75702229	T	C	75702229	3	2	39	1	0	0	0	0	1	0	0	0	14362	1580	55	4	2612	4	SIN3A	15	75702229	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10		75702229	26829163	157	3621										
MEFV	4210	hgsc.bcm.edu	37	chr16	3293889	3293889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cctgagcgccaatcagctccGgaactacggagaaaaatcag	10	12	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:3293889G>A	ENST00000219596.1	-	9	1802	c.1763C>T	c.(1762-1764)cCg>cTg	p.P588L	MEFV_ENST00000536379.1_Missense_Mutation_p.P377L|MEFV_ENST00000541159.1_Silent_p.S435S|MEFV_ENST00000339854.4_Missense_Mutation_p.P408L	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	588	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AATCAGCTCCGGAACTACGGA	0.512																																																0			16											45	47	46					16																	3293889		2197	4300	6497	3233890	SO:0001583	missense	4210			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1763C>T	16.37:g.3293889G>A	ENSP00000219596:p.Pro588Leu		3233890	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	G	1.606	-0.525162	0.04141	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379	T;T;T	0.66638	-0.22;0.21;0.21	4.83	0.551	0.17225	B30.2/SPRY domain (1);	0.788758	0.11219	N	0.586891	T	0.49575	0.1565	L	0.42245	1.32	0.09310	N	0.999998	B	0.26147	0.143	B	0.06405	0.002	T	0.30592	-0.9973	10	0.31617	T	0.26	-22.9385	3.4443	0.07474	0.1912:0.0:0.4512:0.3576	.	588	O15553	MEFV_HUMAN	L	588;588;408;377	ENSP00000219596:P588L;ENSP00000339639:P408L;ENSP00000445079:P377L	ENSP00000219596:P588L	P	-	2	0	MEFV	3233890	0.886000	0.30341	0.280000	0.24747	0.022000	0.10575	1.942000	0.40243	0.307000	0.22880	-0.136000	0.14681	CCG		0.512	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		A	3293889	G	A	3293889	3	1	39	1	0	0	0	0	1	0	0	0	9489	1116	39	1	590	1	MEFV	16	3293889	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		3293889	87060864	158	3622										
CPPED1	55313	hgsc.bcm.edu	37	chr16	12758911	12758911	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcagatgacaccaccatgtcGaggttctggtaggtaccccc	11	13	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:12758911G>A	ENST00000381774.4	-	4	1017	c.777C>T	c.(775-777)ctC>ctT	p.L259L	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Silent_p.L117L	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	259						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						CCACCATGTCGAGGTTCTGGT	0.572																																																0			16											53	54	54					16																	12758911		1974	4174	6148	12666412	SO:0001819	synonymous_variant	55313			AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"complete S transactivated protein 1"	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.777C>T	16.37:g.12758911G>A			12666412	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Silent	SNP	ENST00000381774.4	37	CCDS42120.1																																																																																				0.572	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340		A	12758911	G	A	12758911	2	1	39	1	0	0	0	0	0	0	0	1	3828	1045	37	1		1	CPPED1	16	12758911	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	9465022	12758911	77595842	159	3623										
ACSM5	54988	hgsc.bcm.edu	37	chr16	20432711	20432711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagctacggactgggttttgTggccagcggaaggtaccaga	15	9	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:20432711T>C	ENST00000331849.4	+	5	902	c.755T>C	c.(754-756)gTg>gCg	p.V252A		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	252					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						CTGGGTTTTGTGGCCAGCGGA	0.587																																																0			16											29	28	29					16																	20432711		2203	4299	6502	20340212	SO:0001583	missense	54988				CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"Acyl-CoA synthetase family"	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.755T>C	16.37:g.20432711T>C	ENSP00000327916:p.Val252Ala		20340212	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	T	3.756	-0.050686	0.07407	.	.	ENSG00000183549	ENST00000331849	T	0.40225	1.04	4.43	2.18	0.27775	AMP-dependent synthetase/ligase (1);	0.244718	0.27720	N	0.018136	T	0.19208	0.0461	N	0.12471	0.22	0.25481	N	0.987735	B	0.02656	0.0	B	0.06405	0.002	T	0.19811	-1.0294	10	0.11794	T	0.64	-13.6763	6.9392	0.24483	0.0:0.2632:0.0:0.7368	.	252	Q6NUN0	ACSM5_HUMAN	A	252	ENSP00000327916:V252A	ENSP00000327916:V252A	V	+	2	0	ACSM5	20340212	0.000000	0.05858	1.000000	0.80357	0.926000	0.56050	-0.328000	0.07945	0.802000	0.34089	0.533000	0.62120	GTG		0.587	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888		C	20432711	T	C	20432711	3	2	39	1	0	0	0	0	1	0	0	0	187	1696	59	4	769	4	ACSM5	16	20432711	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	7673800	20432711	69922042	160	3624										
OTOA	146183	hgsc.bcm.edu	37	chr16	21734241	21734241	+	Frame_Shift_Del	DEL	T	T	-													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttcaggttaattgtttggcgTggaaatactgggaagtttcc							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:21734241delT	ENST00000286149.4	+	17	1865	c.1864delT	c.(1864-1866)tggfs	p.W622fs	OTOA_ENST00000388957.3_Frame_Shift_Del_p.W284fs|OTOA_ENST00000388958.3_Frame_Shift_Del_p.W608fs|OTOA_ENST00000388956.4_Frame_Shift_Del_p.W529fs			Q7RTW8	OTOAN_HUMAN	otoancorin	622					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		TTGTTTGGCGTGGAAATACTG	0.448																																																0			16											116	102	107					16																	21734241		2198	4300	6498	21641742	SO:0001589	frameshift_variant	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1864delT	16.37:g.21734241delT	ENSP00000286149:p.Trp622fs		21641742	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Frame_Shift_Del	DEL	ENST00000286149.4	37																																																																																					0.448	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			-	21734241	T	-	21734241	7	5	39	1	0	1	0	1	0	0	0	0	11333	1696	59	0	1934	0	OTOA	16	21734241	Frame_Shift_Del	DEL	T	TCGA-AG-3742-01A-11D-1657-10	1301530	21734241	68620512	161	3625										
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25251333	25251333	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgtgtattctccgatgttctCgaaatctcgtacagttattg	8	8	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:25251333C>A	ENST00000328086.7	-	7	3511	c.2708G>T	c.(2707-2709)cGa>cTa	p.R903L	CTD-2547G23.2_ENST00000569456.1_RNA	NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	903					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		CCGATGTTCTCGAAATCTCGT	0.453																																																0			16											98	86	90					16																	25251333		2197	4300	6497	25158834	SO:0001583	missense	342357			AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.2708G>T	16.37:g.25251333C>A	ENSP00000331626:p.Arg903Leu		25158834	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.628438	0.28978	.	.	ENSG00000155592	ENST00000328086	T	0.20738	2.05	5.43	5.43	0.79202	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.152246	0.31648	N	0.007294	T	0.12390	0.0301	L	0.31420	0.93	0.09310	N	1	P;P	0.47910	0.772;0.902	B;B	0.37943	0.133;0.261	T	0.22382	-1.0218	10	0.07175	T	0.84	-12.0503	12.3085	0.54915	0.0:0.8303:0.1697:0.0	.	699;903	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	L	903	ENSP00000331626:R903L	ENSP00000331626:R903L	R	-	2	0	ZKSCAN2	25158834	0.000000	0.05858	0.947000	0.38551	0.009000	0.06853	-0.642000	0.05427	2.824000	0.97209	0.655000	0.94253	CGA		0.453	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		A	25251333	C	A	25251333	3	1	39	1	0	0	0	0	1	0	0	0	17726	884	31	2	199	2	ZKSCAN2	16	25251333	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	3517092	25251333	65103420	162	3626										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31434699	31434699	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aacctcagccagcgagatctGgccatcagcattaacttctg	8	13	4	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:31434699G>C	ENST00000389202.2	+	25	2935	c.2886G>C	c.(2884-2886)ctG>ctC	p.L962L		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	962					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGCGAGATCTGGCCATCAGCA	0.552																																																0			16											161	138	146					16																	31434699		2197	4300	6497	31342200	SO:0001819	synonymous_variant	3681			U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2886G>C	16.37:g.31434699G>C			31342200	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																				0.552	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		C	31434699	G	C	31434699	2	2	39	1	0	0	0	0	0	0	0	1	7905	1335	47	5		5	ITGAD	16	31434699	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	6183366	31434699	58920054	163	3627										
SNX20	124460	hgsc.bcm.edu	37	chr16	50707891	50707891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccctgaacgtcttcagcagcGctttctggagcttcgcgaag	11	13	3	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:50707891G>A	ENST00000330943.4	-	4	548	c.377C>T	c.(376-378)gCg>gTg	p.A126V	SNX20_ENST00000300590.3_Intron|RP11-401P9.5_ENST00000570241.2_RNA|RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000423026.2_Intron	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	126	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						CTTCAGCAGCGCTTTCTGGAG	0.562																																																0			16											81	73	76					16																	50707891		2198	4300	6498	49265392	SO:0001583	missense	124460			AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"Sorting nexins"	30390	protein-coding gene	gene with protein product	"selectin ligand interactor cytoplasmic 1"	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.377C>T	16.37:g.50707891G>A	ENSP00000332062:p.Ala126Val		49265392	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Missense_Mutation	SNP	ENST00000330943.4	37	CCDS10745.1	.	.	.	.	.	.	.	.	.	.	G	9.690	1.151584	0.21371	.	.	ENSG00000167208	ENST00000330943	T	0.39592	1.07	5.53	-7.27	0.01461	Phox homologous domain (5);	1.170640	0.05870	N	0.624431	T	0.22085	0.0532	N	0.26092	0.79	0.09310	N	1	P	0.36733	0.567	B	0.28465	0.09	T	0.13575	-1.0504	10	0.29301	T	0.29	-1.7733	9.1687	0.37067	0.0:0.4352:0.304:0.2608	.	126	Q7Z614	SNX20_HUMAN	V	126	ENSP00000332062:A126V	ENSP00000332062:A126V	A	-	2	0	SNX20	49265392	0.008000	0.16893	0.000000	0.03702	0.126000	0.20510	0.169000	0.16641	-1.682000	0.01446	0.561000	0.74099	GCG		0.562	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337		A	50707891	G	A	50707891	3	1	39	1	0	0	0	0	1	0	0	0	14929	1087	38	1	720	1	SNX20	16	50707891	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	19273192	50707891	39646862	164	3628										
RBL2	5934	hgsc.bcm.edu	37	chr16	53488674	53488674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aggaaattgggactctctcaAggtgtctgaacgctggttca	12	8	4	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:53488674A>G	ENST00000262133.6	+	8	1236	c.1099A>G	c.(1099-1101)Agg>Ggg	p.R367G	RBL2_ENST00000544545.1_Missense_Mutation_p.R151G|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	367					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GACTCTCTCAAGGTGTCTGAA	0.443																																																0			16											113	110	111					16																	53488674		2198	4300	6498	52046175	SO:0001583	missense	5934			X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1099A>G	16.37:g.53488674A>G	ENSP00000262133:p.Arg367Gly		52046175	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.085702	0.36758	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.89552	-2.53;-2.12;-1.85	5.5	4.23	0.50019	.	0.168455	0.51477	D	0.000097	D	0.85221	0.5647	L	0.57536	1.79	0.09310	N	0.999992	B;P;P;P	0.48764	0.001;0.761;0.65;0.915	B;B;B;B	0.36922	0.003;0.191;0.191;0.236	T	0.77496	-0.2566	10	0.72032	D	0.01	-9.1175	13.3417	0.60549	0.4993:0.5007:0.0:0.0	.	151;367;77;367	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	G	367;293;77;151	ENSP00000262133:R367G;ENSP00000443744:R293G;ENSP00000444685:R151G	ENSP00000262133:R367G	R	+	1	2	RBL2	52046175	0.718000	0.27976	0.723000	0.30687	0.932000	0.56968	1.339000	0.33885	0.696000	0.31696	0.454000	0.30748	AGG		0.443	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		G	53488674	A	G	53488674	3	3	39	1	0	0	0	0	1	0	0	0	13147	63	3	4	1129	4	RBL2	16	53488674	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	2780783	53488674	36866079	165	3629										
CDH11	1009	hgsc.bcm.edu	37	chr16	64984824	64984824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtgttggtgctactcatgggCgggatgccgccatcgctgat	15	10	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:64984824C>T	ENST00000268603.4	-	12	2355	c.1740G>A	c.(1738-1740)ccG>ccA	p.P580P	CDH11_ENST00000394156.3_Silent_p.P580P|CDH11_ENST00000566827.1_Silent_p.P454P	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	580	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TACTCATGGGCGGGATGCCGC	0.602			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																													Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	0			16											105	89	94					16																	64984824		2203	4300	6503	63542325	SO:0001819	synonymous_variant	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1740G>A	16.37:g.64984824C>T			63542325	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.602	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	64984824	C	T	64984824	2	4	39	1	0	0	0	0	0	0	0	1	3103	755	27	1		1	CDH11	16	64984824	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	11496150	64984824	25369929	166	3630										
FANCA	2175	hgsc.bcm.edu	37	chr16	89849483	89849483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gagggagcggtacttgccggGaaccaggggtgggtggagaa	21	6	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr16:89849483G>A	ENST00000389301.3	-	16	1528	c.1498C>T	c.(1498-1500)Ccc>Tcc	p.P500S	FANCA_ENST00000568369.1_Missense_Mutation_p.P500S	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	500					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.P500A(1)		breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		TACTTGCCGGGAACCAGGGGT	0.597			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	1	Substitution - Missense(1)	ovary(1)	16											178	137	151					16																	89849483		2198	4300	6498	88376984	SO:0001583	missense	2175	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1498C>T	16.37:g.89849483G>A	ENSP00000373952:p.Pro500Ser		88376984	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.793253	0.50102	.	.	ENSG00000187741	ENST00000389301	D	0.86230	-2.09	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000007	D	0.92512	0.7622	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91766	0.5424	10	0.44086	T	0.13	-25.2563	18.4531	0.90711	0.0:0.0:1.0:0.0	.	500;500	B4DRI7;O15360	.;FANCA_HUMAN	S	500	ENSP00000373952:P500S	ENSP00000373952:P500S	P	-	1	0	FANCA	88376984	1.000000	0.71417	0.140000	0.22221	0.043000	0.13939	5.001000	0.63946	2.599000	0.87857	0.555000	0.69702	CCC		0.597	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			A	89849483	G	A	89849483	3	1	39	1	0	0	0	0	1	0	0	0	5681	1174	41	3	2981	3	FANCA	16	89849483	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	24864659	89849483	505270	167	3631										
METT10D	79066	hgsc.bcm.edu	37	chr17	2323838	2323838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tccaggagttttctatggccGttaggaaaaggctgacttcc	11	9	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:2323838G>A	ENST00000263092.6	-	10	1242	c.1115C>T	c.(1114-1116)aCg>aTg	p.T372M	METTL16_ENST00000538844.1_Missense_Mutation_p.T154M|METTL16_ENST00000571669.2_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	372							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						TTCTATGGCCGTTAGGAAAAG	0.473																																																0			17											66	67	66					17																	2323838		1851	4095	5946	2270588	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1115C>T	17.37:g.2323838G>A	ENSP00000263092:p.Thr372Met		2270588	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.368500	0.82463	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.53423	0.76;0.62	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.68044	0.2958	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	T	0.70673	-0.4807	10	0.72032	D	0.01	-12.239	16.9366	0.86204	0.0:0.0:1.0:0.0	.	372	Q86W50	MET16_HUMAN	M	372;52;154	ENSP00000263092:T372M;ENSP00000443633:T154M	ENSP00000263092:T372M	T	-	2	0	METTL16	2270588	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.447000	0.97595	2.588000	0.87417	0.655000	0.94253	ACG		0.473	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		A	2323838	G	A	2323838	3	1	39	1	0	0	0	0	1	0	0	0	9520	1145	40	1	577	1	METT10D	17	2323838	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		2323838	78871372	168	3632										
C17orf74	201243	hgsc.bcm.edu	37	chr17	7329758	7329758	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agcggccgcagaactacagaCaaatcccccatagccactca	7	16	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:7329758C>T	ENST00000333870.3	+	3	522	c.448C>T	c.(448-450)Caa>Taa	p.Q150*	C17orf74_ENST00000574034.1_Intron|RP11-104H15.7_ENST00000575310.1_RNA	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	150						integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				GAACTACAGACAAATCCCCCA	0.592																																																0			17											88	96	93					17																	7329758		1991	4160	6151	7270482	SO:0001587	stop_gained	201243			BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.448C>T	17.37:g.7329758C>T	ENSP00000328061:p.Gln150*		7270482		Nonsense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.556577	0.45487	.	.	ENSG00000184560	ENST00000333870	.	.	.	4.0	0.628	0.17681	.	2.617620	0.01695	N	0.026850	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	-8.5383	9.8278	0.40923	0.5881:0.4119:0.0:0.0	.	.	.	.	X	150	.	ENSP00000328061:Q150X	Q	+	1	0	C17orf74	7270482	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.034000	0.12225	0.050000	0.15949	-0.336000	0.08194	CAA		0.592	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		T	7329758	C	T	7329758	4	4	39	1	0	0	0	0	0	1	0	0	1884	479	17	3	458	3	C17orf74	17	7329758	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5005920	7329758	73865452	169	3633										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	39	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	247362	7577120	73618090	170	3634										
NF1	4763	hgsc.bcm.edu	37	chr17	29664408	29664408	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gagaccaagcaagttttgagActcagtctgacagagttctc	10	9	3	4			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:29664408A>G	ENST00000358273.4	+	43	6833	c.6450A>G	c.(6448-6450)agA>agG	p.R2150R	NF1_ENST00000417592.2_5'Flank|NF1_ENST00000444181.2_5'Flank|NF1_ENST00000356175.3_Silent_p.R2129R	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2150					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.R2150S(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAGTTTTGAGACTCAGTCTGA	0.368			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(8)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											86	75	79					17																	29664408		2203	4300	6503	26688534	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.6450A>G	17.37:g.29664408A>G			26688534	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29664408	A	G	29664408	2	3	39	1	0	0	0	0	0	0	0	1	10387	272	10	4		4	NF1	17	29664408	Silent	SNP	A	TCGA-AG-3742-01A-11D-1657-10	22087288	29664408	51530802	171	3635										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43553015	43553016	+	Frame_Shift_Ins	INS	-	-	C													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	catcaggccatcgttcagggINSccagccgcagccatgcccgg							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:43553015_43553016insC	ENST00000430334.3	-	4	506_507	c.373_374insG	c.(373-375)gccfs	p.A125fs	PLEKHM1_ENST00000421073.2_Frame_Shift_Ins_p.A36fs	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	125	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					ATCGTTCAGGGCCAGCCGCAGC	0.614																																																0			17																																								40908799	SO:0001589	frameshift_variant	9842			X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.374dupG	17.37:g.43553017_43553017dupC	ENSP00000389913:p.Ala125fs		40908798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Frame_Shift_Ins	INS	ENST00000430334.3	37	CCDS32671.1																																																																																				0.614	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		C	43553016	-	C	43553015	7	5	39	1	0	1	1	0	0	0	0	0	12111	1203	42	0	2832	0	PLEKHM1	17	43553015	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	13888607	43553015	37642195	172	3636										
TRIM25	7706	hgsc.bcm.edu	37	chr17	54969505	54969505	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggccggtagttctgaggcatCtcagccacagaagctactgt	12	11	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:54969505C>A	ENST00000316881.4	-	9	1498	c.1449G>T	c.(1447-1449)gaG>gaT	p.E483D	TRIM25_ENST00000573108.1_5'Flank|MIR3614_ENST00000581261.1_RNA|RP11-670E13.5_ENST00000574826.1_RNA|TRIM25_ENST00000537230.1_Missense_Mutation_p.E483D	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	483	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					TCTGAGGCATCTCAGCCACAG	0.522																																																0			17											68	69	69					17																	54969505		2203	4300	6503	52324504	SO:0001583	missense	7706			D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1449G>T	17.37:g.54969505C>A	ENSP00000323889:p.Glu483Asp		52324504		Missense_Mutation	SNP	ENST00000316881.4	37	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.481649	0.01027	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.11385	2.78;2.78	4.84	-6.29	0.02013	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.635159	0.14702	N	0.303534	T	0.01695	0.0054	N	0.01134	-0.995	0.09310	N	0.999999	B	0.09022	0.002	B	0.08055	0.003	T	0.39482	-0.9612	10	0.08837	T	0.75	.	0.4776	0.00542	0.2332:0.2745:0.2231:0.2692	.	483	Q14258	TRI25_HUMAN	D	483	ENSP00000323889:E483D;ENSP00000445961:E483D	ENSP00000323889:E483D	E	-	3	2	TRIM25	52324504	0.000000	0.05858	0.001000	0.08648	0.369000	0.29798	-2.351000	0.01092	-0.722000	0.04922	-0.416000	0.06073	GAG		0.522	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		A	54969505	C	A	54969505	3	1	39	1	0	0	0	0	1	0	0	0	16539	912	32	2	447	2	TRIM25	17	54969505	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	11416490	54969505	26225705	173	3637										
KIF19	124602	hgsc.bcm.edu	37	chr17	72341014	72341014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgaccgtgcgccagcgcagcCgggtcaagaacatcttgcag	13	13	2	2	rs145463528	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr17:72341014C>T	ENST00000389916.4	+	7	835	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	233	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CCAGCGCAGCCGGGTCAAGAA	0.687													C|||	2	0.000399361	0	0	5008	,	,		16886	0.002		0	False		,,,				2504	0															0			17											30	32	31					17																	72341014		2200	4298	6498	69852609	SO:0001583	missense	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.697C>T	17.37:g.72341014C>T	ENSP00000374566:p.Arg233Trp		69852609	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	C	18.83	3.707819	0.68615	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.75938	-0.98;-0.98	5.49	2.24	0.28232	Kinesin, motor domain (4);	.	.	.	.	T	0.81475	0.4830	M	0.87827	2.91	0.50467	D	0.999872	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.993;0.998;0.978;0.978	T	0.83109	-0.0124	9	0.87932	D	0	.	8.7635	0.34689	0.2637:0.6636:0.0:0.0727	.	233;191;191;233	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	W	191;233	ENSP00000449134:R191W;ENSP00000374566:R233W	ENSP00000374566:R233W	R	+	1	2	KIF19	69852609	1.000000	0.71417	0.967000	0.41034	0.369000	0.29798	2.745000	0.47459	0.636000	0.30508	0.556000	0.70494	CGG		0.687	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72341014	C	T	72341014	3	4	39	1	0	0	0	0	1	0	0	0	8303	643	23	1	723	1	KIF19	17	72341014	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	17371509	72341014	8854196	174	3638										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8824820	8824820	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	accccacccctgtctccagaCgacctcaagtacatcgagga	7	17	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr18:8824820C>T	ENST00000306329.11	+	13	4269	c.4269C>T	c.(4267-4269)gaC>gaT	p.D1423D	SOGA2_ENST00000517570.1_Silent_p.D1063D|SOGA2_ENST00000359865.3_Silent_p.D1104D|SOGA2_ENST00000306285.7_Silent_p.D429D|SOGA2_ENST00000400050.3_Silent_p.D1063D|SOGA2_ENST00000518815.1_Silent_p.D429D														p.D1104D(1)									TGTCTCCAGACGACCTCAAGT	0.612																																																1	Substitution - coding silent(1)	prostate(1)	18											79	68	72					18																	8824820		2203	4300	6503	8814820	SO:0001819	synonymous_variant	23255																														ENST00000306329.11:c.4269C>T	18.37:g.8824820C>T			8814820		Silent	SNP	ENST00000306329.11	37																																																																																					0.612	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8824820	C	T	8824820	2	4	39	1	0	0	0	0	0	0	0	1	8215	535	19	1		1	KIAA0802	18	8824820	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10		8824820	69252428	175	3639										
KCTD1	284252	hgsc.bcm.edu	37	chr18	24035775	24035775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cgtccgcctcagttcccgccGaaggacgtattcgctgaact	10	15	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr18:24035775G>A	ENST00000408011.3	-	5	1265	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	KCTD1_ENST00000317932.7_Missense_Mutation_p.R236W|KCTD1_ENST00000417602.1_Missense_Mutation_p.R844W|KCTD1_ENST00000580059.1_Missense_Mutation_p.R236W|KCTD1_ENST00000579973.1_Missense_Mutation_p.R236W	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1	236					negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			AGTTCCCGCCGAAGGACGTAT	0.537																																																0			18											84	83	83					18																	24035775		2203	4300	6503	22289773	SO:0001583	missense	284252			AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"potassium channel tetramerisation domain containing 1"	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.706C>T	18.37:g.24035775G>A	ENSP00000384367:p.Arg236Trp		22289773	A8K1F5	Missense_Mutation	SNP	ENST00000408011.3	37	CCDS11888.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.331034	0.60853	.	.	ENSG00000134504	ENST00000317932;ENST00000417602;ENST00000408011	T;T;T	0.78364	-0.76;-1.17;-0.76	5.98	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.68302	0.2986	N	0.22421	0.69	0.58432	D	0.999999	D	0.54207	0.965	P	0.46452	0.517	T	0.67837	-0.5567	10	0.38643	T	0.18	.	11.7396	0.51786	0.0:0.0:0.6243:0.3757	.	236	Q719H9	KCTD1_HUMAN	W	236;844;236	ENSP00000314831:R236W;ENSP00000408405:R844W;ENSP00000384367:R236W	ENSP00000314831:R236W	R	-	1	2	KCTD1	22289773	0.998000	0.40836	0.999000	0.59377	0.934000	0.57294	1.569000	0.36428	2.837000	0.97791	0.591000	0.81541	CGG		0.537	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091		A	24035775	G	A	24035775	3	1	39	1	0	0	0	0	1	0	0	0	8117	1057	37	1	71	1	KCTD1	18	24035775	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	15210955	24035775	54041473	176	3640										
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43253775	43253775	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagacgcacctcctcgccatCgcctgcggtaggtactcccc	9	19	0	1	rs139049054		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr18:43253775C>T	ENST00000255226.6	+	18	3321	c.2505C>T	c.(2503-2505)atC>atT	p.I835I	SLC14A2_ENST00000586448.1_Silent_p.I835I|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000589658.1_Silent_p.I312I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	835					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCTCGCCATCGCCTGCGGTA	0.443													C|||	1	0.000199681	8e-04	0	5008	,	,		4049	0		0	False		,,,				2504	0															0			18						C	,	3,4403	6.2+/-15.9	0,3,2200	87	73	78		2505,2505	-4.3	0.8	18	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC14A2	NM_001242692.1,NM_007163.3	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	835/921,835/921	43253775	3,13003	2203	4300	6503	41507773	SO:0001819	synonymous_variant	8170			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.2505C>T	18.37:g.43253775C>T			41507773	A8K8Q7|Q2TBD6|Q96PH5	Silent	SNP	ENST00000255226.6	37	CCDS11924.1																																																																																				0.443	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43253775	C	T	43253775	2	4	39	1	0	0	0	0	0	0	0	1	14434	874	31	1		1	SLC14A2	18	43253775	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	19218000	43253775	34823473	177	3641										
STARD6	147323	hgsc.bcm.edu	37	chr18	51851219	51851219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcatttctgtctggacaaacAtcactagtttggaatatgct	7	8	4	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr18:51851219A>G	ENST00000581310.1	-	9	879	c.506T>C	c.(505-507)aTg>aCg	p.M169T	STARD6_ENST00000307844.3_Missense_Mutation_p.M169T|STARD6_ENST00000580990.2_Missense_Mutation_p.M45T			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	169	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)	p.M169T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)	8				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		CTGGACAAACATCACTAGTTT	0.333																																																1	Substitution - Missense(1)	ovary(1)	18											114	111	112					18																	51851219		2202	4300	6502	50105217	SO:0001583	missense	147323			AF480305	CCDS11955.1	18q21.2	2011-09-12	2007-08-16		ENSG00000174448	ENSG00000174448		"StAR-related lipid transfer (START) domain containing"	18066	protein-coding gene	gene with protein product		607051	"START domain containing 6"			12011452	Standard	NM_139171		Approved		uc010xdt.2	P59095	OTTHUMG00000132702	ENST00000581310.1:c.506T>C	18.37:g.51851219A>G	ENSP00000462349:p.Met169Thr		50105217		Missense_Mutation	SNP	ENST00000581310.1	37	CCDS11955.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438064	0.25900	.	.	ENSG00000174448	ENST00000307844	T	0.78595	-1.19	5.53	5.53	0.82687	Lipid-binding START (3);START-like domain (1);	0.350903	0.29515	N	0.011932	T	0.66327	0.2778	L	0.27053	0.805	0.28573	N	0.910505	P	0.37914	0.611	B	0.37731	0.257	T	0.63225	-0.6685	10	0.32370	T	0.25	.	12.0438	0.53469	1.0:0.0:0.0:0.0	.	169	P59095	STAR6_HUMAN	T	169	ENSP00000310814:M169T	ENSP00000310814:M169T	M	-	2	0	STARD6	50105217	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.927000	0.63440	2.090000	0.63153	0.338000	0.21704	ATG		0.333	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171		G	51851219	A	G	51851219	3	3	39	1	0	0	0	0	1	0	0	0	15300	217	8	4	159	4	STARD6	18	51851219	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	8597444	51851219	26226029	178	3642										
GNA15	2769	hgsc.bcm.edu	37	chr19	3150215	3150215	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcggccatgcagtggctgtgGagggatgccggcatccgggc	19	11	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:3150215G>A	ENST00000262958.3	+	3	675	c.417G>A	c.(415-417)tgG>tgA	p.W139*	AC005264.2_ENST00000587587.1_RNA	NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein), alpha 15 (Gq class)	139					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		AGTGGCTGTGGAGGGATGCCG	0.632																																																0			19											74	76	75					19																	3150215		2203	4299	6502	3101215	SO:0001587	stop_gained	2769				CCDS12104.1	19p13.3	2008-07-16				ENSG00000060558			4383	protein-coding gene	gene with protein product		139314				1302014	Standard	NM_002068		Approved	GNA16	uc002lxf.2	P30679		ENST00000262958.3:c.417G>A	19.37:g.3150215G>A	ENSP00000262958:p.Trp139*		3101215	E9KL40|E9KL47|O75247|Q53XK2	Nonsense_Mutation	SNP	ENST00000262958.3	37	CCDS12104.1	.	.	.	.	.	.	.	.	.	.	G	34	5.380957	0.95945	.	.	ENSG00000060558	ENST00000262958	.	.	.	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.363	0.44006	0.0:0.0:1.0:0.0	.	.	.	.	X	139	.	ENSP00000262958:W139X	W	+	3	0	GNA15	3101215	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	5.391000	0.66266	1.786000	0.52430	0.313000	0.20887	TGG		0.632	GNA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452320.2	NM_002068		A	3150215	G	A	3150215	4	1	39	1	0	0	0	0	0	1	0	0	6523	1183	41	3	427	3	GNA15	19	3150215	Nonsense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		3150215	55978768	179	3643										
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495678	6495679	+	Frame_Shift_Ins	INS	-	-	G													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agggcccggtactgctggctINSgccccggctggtcaggggtg							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:6495678_6495679insG	ENST00000264071.2	-	4	1202_1203	c.831_832insC	c.(829-834)ggcagcfs	p.S278fs	TUBB4A_ENST00000540257.1_Frame_Shift_Ins_p.S278fs|CTD-2396E7.10_ENST00000596027.1_RNA|CTD-2396E7.9_ENST00000599292.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	278					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										TACTGCTGGCTGCCCCGGCTGG	0.668																																																0			19																																								6446679	SO:0001589	frameshift_variant	10382			AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.832dupC	19.37:g.6495679_6495679dupG	ENSP00000264071:p.Ser278fs		6446678	B3KQP4|Q969E5	Frame_Shift_Ins	INS	ENST00000264071.2	37	CCDS12168.1																																																																																				0.668	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		G	6495679	-	G	6495678	7	5	39	1	0	1	1	0	0	0	0	0	16798	1580	55	0	506	0	TUBB4	19	6495678	Frame_Shift_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	3345463	6495678	52633305	180	3644										
FBN3	84467	hgsc.bcm.edu	37	chr19	8209823	8209823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agcggttgggcccaatgcagCgacccccattgtggcagccg	14	14	0	0	rs554641249		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:8209823C>T	ENST00000600128.1	-	6	893	c.479G>A	c.(478-480)cGc>cAc	p.R160H	FBN3_ENST00000270509.2_Missense_Mutation_p.R160H|FBN3_ENST00000601739.1_Missense_Mutation_p.R160H			Q75N90	FBN3_HUMAN	fibrillin 3	160	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCCAATGCAGCGACCCCCATT	0.622													C|||	1	0.000199681	0	0	5008	,	,		16220	0.001		0	False		,,,				2504	0															0			19											47	36	40					19																	8209823		2201	4300	6501	8115823	SO:0001583	missense	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.479G>A	19.37:g.8209823C>T	ENSP00000470498:p.Arg160His		8115823	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	c	16.21	3.058579	0.55325	.	.	ENSG00000142449	ENST00000270509	D	0.88201	-2.35	3.94	3.94	0.45596	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	U	0.000001	D	0.86678	0.5990	M	0.65975	2.015	0.41587	D	0.98877	B	0.29432	0.244	B	0.21151	0.033	D	0.86693	0.1924	10	0.49607	T	0.09	.	14.905	0.70711	0.0:1.0:0.0:0.0	.	160	Q75N90	FBN3_HUMAN	H	160	ENSP00000270509:R160H	ENSP00000270509:R160H	R	-	2	0	FBN3	8115823	1.000000	0.71417	1.000000	0.80357	0.374000	0.29953	4.237000	0.58681	1.934000	0.56057	0.313000	0.20887	CGC		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8209823	C	T	8209823	3	4	39	1	0	0	0	0	1	0	0	0	5723	768	27	1	8186	1	FBN3	19	8209823	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	1714145	8209823	50919160	181	3645										
MUC16	94025	hgsc.bcm.edu	37	chr19	9059278	9059278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gtgagttcctggccaggaggCtgtgcttgatgagtccaagg	16	8	0	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:9059278C>T	ENST00000397910.4	-	3	28371	c.28168G>A	c.(28168-28170)Gcc>Acc	p.A9390T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9392	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGCCAGGAGGCTGTGCTTGAT	0.527																																																0			19											132	130	131					19																	9059278		2011	4173	6184	8920278	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28168G>A	19.37:g.9059278C>T	ENSP00000381008:p.Ala9390Thr		8920278	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	7.664	0.685513	0.14973	.	.	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.1	0.98	0.19750	.	.	.	.	.	T	0.16896	0.0406	L	0.29908	0.895	.	.	.	B	0.27823	0.19	B	0.28139	0.086	T	0.20874	-1.0262	8	0.87932	D	0	.	5.0379	0.14443	0.0:0.8162:0.0:0.1838	.	9390	B5ME49	.	T	9390	ENSP00000381008:A9390T	ENSP00000381008:A9390T	A	-	1	0	MUC16	8920278	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.748000	0.04818	0.423000	0.26033	0.306000	0.20318	GCC		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9059278	C	T	9059278	3	4	39	1	0	0	0	0	1	0	0	0	10003	797	28	3	15683	3	MUC16	19	9059278	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	849455	9059278	50069705	182	3646										
JAK3	3718	hgsc.bcm.edu	37	chr19	17945506	17945506	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cttgggggccggcagctgctGccggtcctcataaaattgga	14	11	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:17945506G>A	ENST00000527670.1	-	16	2253	c.2224C>T	c.(2224-2226)Cag>Tag	p.Q742*	JAK3_ENST00000534444.1_Nonsense_Mutation_p.Q742*|JAK3_ENST00000458235.1_Nonsense_Mutation_p.Q742*			P52333	JAK3_HUMAN	Janus kinase 3	742	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGCAGCTGCTGCCGGTCCTCA	0.587		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	0			19											48	59	55					19																	17945506		2203	4300	6503	17806506	SO:0001587	stop_gained	3718			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2224C>T	19.37:g.17945506G>A	ENSP00000432511:p.Gln742*		17806506	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Nonsense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	38	7.271270	0.98179	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	.	.	.	4.8	2.5	0.30297	.	0.657301	0.15520	N	0.258075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-6.3658	7.8871	0.29656	0.0:0.3502:0.482:0.1678	.	.	.	.	X	742	.	ENSP00000391676:Q742X	Q	-	1	0	JAK3	17806506	0.395000	0.25254	0.253000	0.24343	0.882000	0.50991	3.403000	0.52615	0.365000	0.24400	0.484000	0.47621	CAG		0.587	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		A	17945506	G	A	17945506	4	1	39	1	0	0	0	0	0	1	0	0	7960	1328	46	3	1182	3	JAK3	19	17945506	Nonsense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	8886228	17945506	41183477	183	3647										
ZNF529	57711	hgsc.bcm.edu	37	chr19	37038372	37038372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccttacatgcataaggtttcTcaccagtgtgaattctctga	7	10	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:37038372T>C	ENST00000591340.1	-	5	1246	c.1088A>G	c.(1087-1089)gAg>gGg	p.E363G	ZNF529_ENST00000334116.7_Missense_Mutation_p.E258G	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					ATAAGGTTTCTCACCAGTGTG	0.393																																																0			19											58	64	62					19																	37038372		2196	4297	6493	41730212	SO:0001583	missense	57711			AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"Zinc fingers, C2H2-type", "-"	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1088A>G	19.37:g.37038372T>C	ENSP00000465578:p.Glu363Gly		41730212	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	37	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521512	0.64747	.	.	ENSG00000186020	ENST00000334116	.	.	.	3.19	3.19	0.36642	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.62245	0.2412	L	0.58669	1.825	0.30688	N	0.751634	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.62412	-0.6860	8	0.87932	D	0	.	10.5474	0.45068	0.0:0.0:0.0:1.0	.	258;330	Q6P280-2;Q6P280	.;ZN529_HUMAN	G	363	.	ENSP00000334695:E363G	E	-	2	0	ZNF529	41730212	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.442000	0.52900	1.312000	0.45043	0.482000	0.46254	GAG		0.393	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		C	37038372	T	C	37038372	3	2	39	1	0	0	0	0	1	0	0	0	18009	1551	54	4	607	4	ZNF529	19	37038372	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	19092866	37038372	22090611	184	3648										
ARHGEF1	9138	hgsc.bcm.edu	37	chr19	42398314	42398314	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acgccattggcctgtacatgCgccaccttggggtgcggacc	13	14	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:42398314C>T	ENST00000354532.3	+	9	827	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C	ARHGEF1_ENST00000378152.4_Missense_Mutation_p.R209C|ARHGEF1_ENST00000347545.4_Missense_Mutation_p.R194C|ARHGEF1_ENST00000337665.4_Missense_Mutation_p.R242C|ARHGEF1_ENST00000599846.1_Missense_Mutation_p.R227C	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	227	RGSL.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		CCTGTACATGCGCCACCTTGG	0.567																																																0			19											104	66	79					19																	42398314		2203	4299	6502	47090154	SO:0001583	missense	9138			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"Rho guanine nucleotide exchange factors"	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.679C>T	19.37:g.42398314C>T	ENSP00000346532:p.Arg227Cys		47090154	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Missense_Mutation	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613138	0.66672	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000316079;ENST00000337665;ENST00000378152	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86	3.89	3.89	0.44902	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.130576	0.46758	D	0.000267	D	0.86276	0.5894	L	0.36672	1.1	0.47183	D	0.999349	D;D;D;D;D	0.89917	0.992;0.988;0.963;0.984;1.0	P;P;B;P;D	0.67103	0.729;0.471;0.431;0.511;0.949	D	0.86586	0.1857	10	0.87932	D	0	-20.0193	9.1847	0.37163	0.2172:0.7828:0.0:0.0	.	209;242;194;227;287	Q6NX52;Q92888-3;Q92888-2;Q92888;Q8NF33	.;.;.;ARHG1_HUMAN;.	C	227;194;263;242;209	ENSP00000346532:R227C;ENSP00000344429:R194C;ENSP00000337261:R242C;ENSP00000367394:R209C	ENSP00000323044:R263C	R	+	1	0	ARHGEF1	47090154	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.964000	0.49192	2.201000	0.70794	0.484000	0.47621	CGC		0.567	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		T	42398314	C	T	42398314	3	4	39	1	0	0	0	0	1	0	0	0	893	768	27	1	758	1	ARHGEF1	19	42398314	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5359942	42398314	16730669	185	3649										
PSG11	5680	hgsc.bcm.edu	37	chr19	43529004	43529004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cactgtatgccggtccatatAtaattatttgaccgtctact	6	10	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:43529004A>G	ENST00000401740.1	-	2	372	c.269T>C	c.(268-270)aTa>aCa	p.I90T	PSG11_ENST00000306322.7_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.I90T|PSG11_ENST00000403486.1_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	90	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CGGTCCATATATAATTATTTG	0.448																																																0			19											207	199	202					19																	43529004		2199	4298	6497	48220844	SO:0001583	missense	5680			U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.269T>C	19.37:g.43529004A>G	ENSP00000384995:p.Ile90Thr		48220844	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	a	0.001	-3.962015	0.00002	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.63255	-0.03;-0.03	0.929	-1.86	0.07760	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39253	0.1071	L	0.31120	0.905	0.09310	N	1	B	0.20368	0.044	B	0.24006	0.05	T	0.31779	-0.9931	9	0.07175	T	0.84	.	2.9487	0.05854	0.2272:0.0:0.4317:0.3411	.	90	Q9UQ72	PSG11_HUMAN	T	90	ENSP00000319140:I90T;ENSP00000384995:I90T	ENSP00000319140:I90T	I	-	2	0	PSG11	48220844	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.271000	0.02828	-2.960000	0.00290	-1.412000	0.01120	ATA		0.448	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		G	43529004	A	G	43529004	3	3	39	1	0	0	0	0	1	0	0	0	12688	449	16	4	754	4	PSG11	19	43529004	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1130690	43529004	15599979	186	3650										
NUCB1	4924	hgsc.bcm.edu	37	chr19	49409126	49409126	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctgctcaaggccaagatggaCgccgagcaggatcccagtga	13	12	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:49409126C>T	ENST00000405315.4	+	4	694	c.360C>T	c.(358-360)gaC>gaT	p.D120D	NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000407032.1_Silent_p.D120D|NUCB1_ENST00000263273.5_Silent_p.D120D	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	120						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		CCAAGATGGACGCCGAGCAGG	0.657																																																0			19											31	29	29					19																	49409126		2203	4300	6503	54100938	SO:0001819	synonymous_variant	4924			BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.360C>T	19.37:g.49409126C>T			54100938	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	37	CCDS12740.1																																																																																				0.657	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		T	49409126	C	T	49409126	2	4	39	1	0	0	0	0	0	0	0	1	10749	535	19	1		1	NUCB1	19	49409126	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5880122	49409126	9719857	187	3651										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54724541	54724541	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cctggtacttatgagctccgTacattgatctcagacgcagt	9	11	1	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:54724541T>C	ENST00000391750.1	-	7	1251	c.1115A>G	c.(1114-1116)tAc>tGc	p.Y372C	LILRB3_ENST00000424807.1_Missense_Mutation_p.Y372C|LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000270464.5_Missense_Mutation_p.Y372C|LILRA6_ENST00000391735.3_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.Y372C|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.Y372C|LILRB3_ENST00000245620.9_Missense_Mutation_p.Y372C|LILRB3_ENST00000346401.6_Missense_Mutation_p.Y372C			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	372	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATGAGCTCCGTACATTGATCT	0.567																																																0			19											72	53	59					19																	54724541		2199	4190	6389	59416353	SO:0001583	missense	79168			U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1115A>G	19.37:g.54724541T>C	ENSP00000375630:p.Tyr372Cys		59416353	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	T	9.448	1.089820	0.20390	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.03124	4.04;4.04;4.04;4.04;4.04;4.04;4.04	2.7	-4.21	0.03812	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.532280	0.01726	N	0.028563	T	0.12092	0.0294	M	0.76002	2.32	0.09310	N	0.999997	P;D;P;D;D;D	0.71674	0.951;0.998;0.867;0.996;0.992;0.998	D;D;P;D;D;P	0.69479	0.926;0.927;0.535;0.94;0.964;0.818	T	0.41052	-0.9530	10	0.42905	T	0.14	.	0.6038	0.00749	0.331:0.1267:0.3112:0.2311	.	372;372;372;372;372;372	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	C	372	ENSP00000375630:Y372C;ENSP00000412771:Y372C;ENSP00000345184:Y372C;ENSP00000245620:Y372C;ENSP00000384274:Y372C;ENSP00000390120:Y372C;ENSP00000270464:Y372C	ENSP00000270464:Y372C	Y	-	2	0	LILRB3;LILRA6	59416353	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.780000	0.00773	-1.130000	0.02914	0.397000	0.26171	TAC		0.567	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		C	54724541	T	C	54724541	3	2	39	1	0	0	0	0	1	0	0	0	8815	1638	57	4	815	4	LILRB3	19	54724541	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	5315415	54724541	4404442	188	3652										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55086381	55086381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ccgtgggtggtcctgggccaTcttctccgtgggccccgtga	15	14	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:55086381T>C	ENST00000251377.3	+	5	669	c.536T>C	c.(535-537)aTc>aCc	p.I179T	LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.I179T|LILRA2_ENST00000391738.3_Missense_Mutation_p.I179T|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391737.1_Missense_Mutation_p.I167T			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	179	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		TCCTGGGCCATCTTCTCCGTG	0.567																																																0			19											161	150	154					19																	55086381		2203	4300	6503	59778193	SO:0001583	missense	11027			U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.536T>C	19.37:g.55086381T>C	ENSP00000251377:p.Ile179Thr		59778193	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.714193	0.30413	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.02323	4.34;4.34;4.34;4.34;4.34	2.93	-1.36	0.09085	Immunoglobulin-like fold (1);	0.746744	0.11359	N	0.572090	T	0.02610	0.0079	L	0.27053	0.805	0.09310	N	1	B;B;B;P	0.40431	0.0;0.122;0.013;0.717	B;P;B;P	0.46796	0.026;0.455;0.032;0.527	T	0.40098	-0.9581	9	.	.	.	.	0.4469	0.00495	0.2127:0.1394:0.2172:0.4307	.	179;167;179;179	E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;LIRA2_HUMAN;.	T	179;179;179;179;167	ENSP00000388131:I179T;ENSP00000251377:I179T;ENSP00000375618:I179T;ENSP00000251376:I179T;ENSP00000375617:I167T	.	I	+	2	0	LILRA2	59778193	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.077000	0.11394	-0.093000	0.12396	0.416000	0.27883	ATC		0.567	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			C	55086381	T	C	55086381	3	2	39	1	0	0	0	0	1	0	0	0	8808	1435	50	4	550	4	LILRA2	19	55086381	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	361840	55086381	4042602	189	3653										
KIR2DL1	3811	hgsc.bcm.edu	37	chr19	55284980	55284980	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggccaacttctccatcagtcGcatgacgcaagacctggcag	10	14	2	2	rs543746914		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:55284980G>A	ENST00000538269.1	+	2	61				KIR2DL3_ENST00000434419.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.R89H|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.R89H|KIR3DL1_ENST00000541392.1_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.R89H(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TCCATCAGTCGCATGACGCAA	0.537													.|||	1	0.000199681	0	0	5008	,	,		18723	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	prostate(1)	19											254	223	233					19																	55284980		2178	4210	6388	59976792	SO:0001627	intron_variant	3802			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-44009G>A	19.37:g.55284980G>A			59976792	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37		.	.	.	.	.	.	.	.	.	.	a	7.047	0.563636	0.13498	.	.	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.23147	1.92;1.92	1.24	0.114	0.14639	.	.	.	.	.	T	0.12263	0.0298	N	0.11756	0.17	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.25187	-1.0139	9	0.66056	D	0.02	.	3.5284	0.07768	0.2873:0.4304:0.2823:0.0	.	89;89	Q6IST4;Q6H2H3	.;.	H	89	ENSP00000336769:R89H;ENSP00000291633:R89H	ENSP00000291633:R89H	R	+	2	0	KIR2DL1	59976792	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.081000	0.14823	-0.274000	0.09232	-2.943000	0.00086	CGC		0.537	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		A	55284980	G	A	55284980	1	1	39	0	1	0	0	0	0	0	0	0	8337	1087	38	1		1	KIR2DL1	19	55284980	Intron	SNP	G	TCGA-AG-3742-01A-11D-1657-10	198599	55284980	3844003	190	3654										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55693158	55693158	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgggcctggatggcggccacGttctcgtagatgaggttttc	15	9	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr19:55693158G>A	ENST00000376350.3	-	20	3334	c.3312C>T	c.(3310-3312)aaC>aaT	p.N1104N	SYT5_ENST00000354308.3_5'Flank|PTPRH_ENST00000263434.5_Silent_p.N926N|SYT5_ENST00000537500.1_5'Flank|SYT5_ENST00000590851.1_5'Flank	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1104					apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TGGCGGCCACGTTCTCGTAGA	0.607																																																0			19											137	129	132					19																	55693158		2203	4300	6503	60384970	SO:0001819	synonymous_variant	5794				CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.3312C>T	19.37:g.55693158G>A			60384970	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	37	CCDS33110.1																																																																																				0.607	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55693158	G	A	55693158	2	1	39	1	0	0	0	0	0	0	0	1	12840	1136	40	1		1	PTPRH	19	55693158	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	408178	55693158	3435825	191	3655										
TRIB3	57761	hgsc.bcm.edu	37	chr20	368896	368896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggagcccgaggagggcgggcGggcctaccaggccctgcact	18	14	0	0	rs143437909	byFrequency	TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:368896G>A	ENST00000217233.3	+	2	795	c.242G>A	c.(241-243)cGg>cAg	p.R81Q	TRIB3_ENST00000422053.2_Missense_Mutation_p.R108Q	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	81	Interaction with DDIT3/CHOP.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		GAGGGCGGGCGGGCCTACCAG	0.667													G|||	3	0.000599042	0.0023	0	5008	,	,		16649	0		0	False		,,,				2504	0				Melanoma(101;421 2374 19538)											0			20						G	GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	36	38	37		242	3.5	0.3	20	dbSNP_134	37	0,8598		0,0,4299	no	missense	TRIB3	NM_021158.3	43	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign	81/359	368896	4,13000	2203	4299	6502	316896	SO:0001583	missense	57761			AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"chromosome 20 open reading frame 97", "tribbles homolog 3 (Drosophila)"	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.242G>A	20.37:g.368896G>A	ENSP00000217233:p.Arg81Gln		316896	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Missense_Mutation	SNP	ENST00000217233.3	37	CCDS12997.1	.	.	.	.	.	.	.	.	.	.	G	9.562	1.118704	0.20877	9.08E-4	0.0	ENSG00000101255	ENST00000217233;ENST00000449710;ENST00000422053	T;T;T	0.20069	2.1;2.18;2.1	4.49	3.54	0.40534	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.592033	0.12998	N	0.421918	T	0.12561	0.0305	L	0.28344	0.845	0.09310	N	1	B;B	0.30511	0.084;0.282	B;B	0.18871	0.013;0.023	T	0.17349	-1.0372	10	0.38643	T	0.18	-10.6178	6.9455	0.24516	0.2054:0.0:0.7946:0.0	.	108;81	B4DMM9;Q96RU7	.;TRIB3_HUMAN	Q	81;81;108	ENSP00000217233:R81Q;ENSP00000391873:R81Q;ENSP00000415416:R108Q	ENSP00000217233:R81Q	R	+	2	0	TRIB3	316896	0.000000	0.05858	0.269000	0.24586	0.292000	0.27327	0.219000	0.17641	1.103000	0.41568	-0.291000	0.09656	CGG		0.667	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158		A	368896	G	A	368896	3	1	39	1	0	0	0	0	1	0	0	0	16524	1116	39	1	244	1	TRIB3	20	368896	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		368896	62656624	192	3656										
TMC2	117532	hgsc.bcm.edu	37	chr20	2593939	2593939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgtgcggttcatgaactacTgctggtgctgggacttggag	15	7	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:2593939T>C	ENST00000358864.1	+	14	1858	c.1843T>C	c.(1843-1845)Tgc>Cgc	p.C615R	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	615					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CATGAACTACTGCTGGTGCTG	0.483																																																0			20											209	165	180					20																	2593939		2203	4300	6503	2541939	SO:0001583	missense	117532			AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1843T>C	20.37:g.2593939T>C	ENSP00000351732:p.Cys615Arg		2541939	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	T	21.3	4.128400	0.77549	.	.	ENSG00000149488	ENST00000358864	T	0.68181	-0.31	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.78616	0.4311	M	0.62154	1.92	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.80750	-0.1243	10	0.72032	D	0.01	-20.9487	12.857	0.57890	0.0:0.0:0.0:1.0	.	446;447;615;615	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	R	615	ENSP00000351732:C615R	ENSP00000351732:C615R	C	+	1	0	TMC2	2541939	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.783000	0.85696	1.992000	0.58205	0.533000	0.62120	TGC		0.483	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			C	2593939	T	C	2593939	3	2	39	1	0	0	0	0	1	0	0	0	16024	1580	55	4	1897	4	TMC2	20	2593939	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	2225043	2593939	60431581	193	3657										
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18143316	18143316	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tatactcccgtgagcatctaCgaggaaaagctgctgctcaa	9	11	2	1	rs577238938		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:18143316C>T	ENST00000435364.3	+	6	1739	c.1398C>T	c.(1396-1398)taC>taT	p.Y466Y	CSRP2BP_ENST00000489634.2_Silent_p.Y338Y|CSRP2BP_ENST00000377681.3_Silent_p.Y465Y	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	466					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						TGAGCATCTACGAGGAAAAGC	0.517																																																0			20											61	60	60					20																	18143316		2203	4300	6503	18091316	SO:0001819	synonymous_variant	57325			AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1398C>T	20.37:g.18143316C>T			18091316	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Silent	SNP	ENST00000435364.3	37	CCDS13133.1																																																																																				0.517	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		T	18143316	C	T	18143316	2	4	39	1	0	0	0	0	0	0	0	1	3974	547	19	1		1	CSRP2BP	20	18143316	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	15549377	18143316	44882204	194	3658										
XKR7	343702	hgsc.bcm.edu	37	chr20	30584381	30584381	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagaaggtgctgcgggactcGcgggacgacaagcggccgct	17	12	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:30584381G>A	ENST00000562532.2	+	3	1035	c.861G>A	c.(859-861)tcG>tcA	p.S287S		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	287						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TGCGGGACTCGCGGGACGACA	0.701																																																0			20											28	28	28					20																	30584381		2203	4300	6503	30048042	SO:0001819	synonymous_variant	343702			AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 7", "chromosome 20 open reading frame 159"	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.861G>A	20.37:g.30584381G>A			30048042	Q9NUG5	Silent	SNP	ENST00000562532.2	37	CCDS33459.1																																																																																				0.701	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718		A	30584381	G	A	30584381	2	1	39	1	0	0	0	0	0	0	0	1	17476	1074	38	1		1	XKR7	20	30584381	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	12441065	30584381	32441139	195	3659										
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35575190	35575190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atcaagacaaggcagtaatgCgcctgtgatttcattttcta	8	8	3	2	rs141599277		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:35575190C>T	ENST00000262878.4	-	2	425	c.226G>A	c.(226-228)Gca>Aca	p.A76T	SAMHD1_ENST00000373694.5_5'UTR	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	76	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				GGCAGTAATGCGCCTGTGATT	0.323																																																0			20											79	77	77					20																	35575190		2203	4300	6503	35008604	SO:0001583	missense	25939			AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.226G>A	20.37:g.35575190C>T	ENSP00000262878:p.Ala76Thr		35008604	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	C	1.881	-0.457856	0.04508	.	.	ENSG00000101347	ENST00000262878	T	0.43294	0.95	4.32	0.7	0.18099	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.957832	0.08632	N	0.916839	T	0.31389	0.0795	L	0.55834	1.745	0.23043	N	0.998383	B	0.15719	0.014	B	0.08055	0.003	T	0.29882	-0.9997	10	0.23302	T	0.38	-1.1196	1.6004	0.02672	0.5537:0.1818:0.0972:0.1673	.	76	Q9Y3Z3	SAMH1_HUMAN	T	76	ENSP00000262878:A76T	ENSP00000262878:A76T	A	-	1	0	SAMHD1	35008604	0.008000	0.16893	0.182000	0.23118	0.456000	0.32438	-0.002000	0.12924	0.003000	0.14656	-1.479000	0.00991	GCA		0.323	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		T	35575190	C	T	35575190	3	4	39	1	0	0	0	0	1	0	0	0	13865	768	27	1	1714	1	SAMHD1	20	35575190	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	4990809	35575190	27450330	196	3660										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36869092	36869092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ctccggggtcacagagggttGcctctgccctctcaagaatg	12	13	3	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:36869092G>T	ENST00000279024.4	-	3	1712	c.1441C>A	c.(1441-1443)Caa>Aaa	p.Q481K		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	481										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				ACAGAGGGTTGCCTCTGCCCT	0.572																																																0			20											78	81	80					20																	36869092		2203	4300	6503	36302506	SO:0001583	missense	85449			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1441C>A	20.37:g.36869092G>T	ENSP00000279024:p.Gln481Lys		36302506	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.946534	0.00475	.	.	ENSG00000149633	ENST00000279024;ENST00000373398	T	0.06068	3.35	4.85	2.83	0.33086	.	1.283900	0.05508	N	0.559640	T	0.07638	0.0192	L	0.60455	1.87	0.20926	N	0.999825	B	0.12013	0.005	B	0.09377	0.004	T	0.51498	-0.8698	10	0.06099	T	0.92	.	7.5989	0.28065	0.0:0.1902:0.6279:0.1819	.	481	Q5JYT7	K1755_HUMAN	K	481;28	ENSP00000279024:Q481K	ENSP00000279024:Q481K	Q	-	1	0	KIAA1755	36302506	0.004000	0.15560	0.560000	0.28344	0.058000	0.15608	1.323000	0.33701	0.600000	0.29862	-0.169000	0.13324	CAA		0.572	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36869092	G	T	36869092	3	4	39	1	0	0	0	0	1	0	0	0	8278	1328	46	2	2209	2	KIAA1755	20	36869092	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	1293902	36869092	26156428	197	3661										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46279839	46279839	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	cagcagcagcagcagcaacaGcagcagcagcagcagcagca	12	14	0	0	rs147879509|rs2664555|rs397778717|rs3830809		TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr20:46279839G>A	ENST00000371998.3	+	20	3956	c.3765G>A	c.(3763-3765)caG>caA	p.Q1255Q	NCOA3_ENST00000341724.6_Silent_p.Q1181Q|NCOA3_ENST00000372004.3_Silent_p.Q1251Q|NCOA3_ENST00000371997.3_Silent_p.Q1246Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1255	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1255delQ(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcaacagcagcagcagc	0.557																																																1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	20											41	44	43					20																	46279839		2202	4300	6502	45713246	SO:0001819	synonymous_variant	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3765G>A	20.37:g.46279839G>A			45713246	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																				0.557	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		A	46279839	G	A	46279839	2	1	39	1	0	0	0	0	0	0	0	1	10261	962	34	3		3	NCOA3	20	46279839	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	9410747	46279839	16745681	198	3662										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35237600	35237600	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gggctgccctgatccagcagAagacggatgaggccccagac	14	13	0	5			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr21:35237600A>C	ENST00000381318.3	+	32	4324	c.4036A>C	c.(4036-4038)Aag>Cag	p.K1346Q	AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399367.3_Missense_Mutation_p.K1341Q|ITSN1_ENST00000381285.4_Missense_Mutation_p.K1346Q|ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000437442.2_Missense_Mutation_p.K1341Q	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1346	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GATCCAGCAGAAGACGGATGA	0.597																																																0			21											21	20	20					21																	35237600		2203	4298	6501	34159470	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4036A>C	21.37:g.35237600A>C	ENSP00000370719:p.Lys1346Gln		34159470	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.3|27.3	4.823225|4.823225	0.90873|0.90873	.|.	.|.	ENSG00000205726|ENSG00000205726	ENST00000381284|ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	.|T;T;T;T	.|0.29397	.|1.57;1.57;1.57;1.57	5.91|5.91	5.91|5.91	0.95273|0.95273	.|Dbl homology (DH) domain (5);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.53981|0.53981	0.1830|0.1830	M|M	0.64404|0.64404	1.975|1.975	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;D;D	.|0.85130	.|0.997;0.955;0.955	T|T	0.52653|0.52653	-0.8547|-0.8547	5|10	.|0.49607	.|T	.|0.09	.|.	16.3364|16.3364	0.83064|0.83064	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1341;1341;1346	.|A8CTY3;A8CTX8;Q15811	.|.;.;ITSN1_HUMAN	A|Q	81|1346;1346;1275;1341;1341	.|ENSP00000370719:K1346Q;ENSP00000370685:K1346Q;ENSP00000382301:K1341Q;ENSP00000387377:K1341Q	.|ENSP00000370685:K1346Q	E|K	+|+	2|1	0|0	ITSN1|ITSN1	34159470|34159470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	8.758000|8.758000	0.91663|0.91663	2.252000|2.252000	0.74401|0.74401	0.528000|0.528000	0.53228|0.53228	GAA|AAG		0.597	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		C	35237600	A	C	35237600	3	2	39	1	0	0	0	0	1	0	0	0	7947	247	9	4	4164	4	ITSN1	21	35237600	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10		35237600	12892295	199	3663										
ZNF70	7621	hgsc.bcm.edu	37	chr22	24086478	24086478	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acaaaaggctttcccacagaGatcgcactcgtgaggtttct	9	11	1	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr22:24086478G>A	ENST00000341976.3	-	2	1310	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L284V(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TTCCCACAGAGATCGCACTCG	0.517																																																1	Substitution - Missense(1)	ovary(1)	22											85	79	81					22																	24086478		2203	4300	6503	22416478	SO:0001583	missense	7621			X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"Zinc fingers, C2H2-type"	13140	protein-coding gene	gene with protein product		194544	"zinc finger protein 70 (Cos17)"			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.850C>T	22.37:g.24086478G>A	ENSP00000339314:p.Leu284Phe		22416478		Missense_Mutation	SNP	ENST00000341976.3	37	CCDS13812.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335442	0.41398	.	.	ENSG00000187792	ENST00000341976	T	0.09073	3.02	3.34	2.27	0.28462	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07413	0.0187	L	0.36672	1.1	0.09310	N	1	B	0.12630	0.006	B	0.16722	0.016	T	0.29610	-1.0006	9	0.87932	D	0	-24.3909	6.037	0.19712	0.0:0.2126:0.5688:0.2185	.	284	Q9UC06	ZNF70_HUMAN	F	284	ENSP00000339314:L284F	ENSP00000339314:L284F	L	-	1	0	ZNF70	22416478	0.000000	0.05858	0.663000	0.29738	0.908000	0.53690	0.058000	0.14301	0.930000	0.37217	0.456000	0.33151	CTC		0.517	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916		A	24086478	G	A	24086478	3	1	39	1	0	0	0	0	1	0	0	0	18142	942	33	3	494	3	ZNF70	22	24086478	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		24086478	27218088	200	3664										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26743766	26743766	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttctcacacggagttggtgcGgggagccagaatcacctacc	12	12	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr22:26743766G>A	ENST00000248933.6	+	11	2389	c.2294G>A	c.(2293-2295)cGg>cAg	p.R765Q	SEZ6L_ENST00000529632.2_Missense_Mutation_p.R765Q|SEZ6L_ENST00000404234.3_Missense_Mutation_p.R765Q|SEZ6L_ENST00000343706.4_Missense_Mutation_p.R765Q|SEZ6L_ENST00000411842.2_5'UTR|SEZ6L_ENST00000360929.3_Missense_Mutation_p.R765Q|SEZ6L_ENST00000403121.1_Missense_Mutation_p.R538Q|SEZ6L_ENST00000402979.1_Missense_Mutation_p.R538Q			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	765	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GAGTTGGTGCGGGGAGCCAGA	0.557																																																0			22											82	78	79					22																	26743766		2203	4300	6503	25073766	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2294G>A	22.37:g.26743766G>A	ENSP00000248933:p.Arg765Gln		25073766	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.525395	0.85600	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	4.88	2.8	0.32819	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000008	T	0.63189	0.2490	N	0.21508	0.67	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.998;0.998;0.999	T	0.58853	-0.7563	10	0.33940	T	0.23	.	10.1572	0.42829	0.1601:0.0:0.8399:0.0	.	765;765;538;765;765;765;765	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	Q	765;765;765;765;765;538;538	ENSP00000384772:R765Q;ENSP00000437037:R765Q;ENSP00000354185:R765Q;ENSP00000248933:R765Q;ENSP00000342661:R765Q;ENSP00000384838:R538Q;ENSP00000384733:R538Q	ENSP00000248933:R765Q	R	+	2	0	SEZ6L	25073766	1.000000	0.71417	0.404000	0.26397	0.967000	0.64934	7.266000	0.78452	0.668000	0.31126	0.655000	0.94253	CGG		0.557	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26743766	G	A	26743766	3	1	39	1	0	0	0	0	1	0	0	0	14180	1116	39	1	2336	1	SEZ6L	22	26743766	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	2657288	26743766	24560800	201	3665										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32162610	32162610	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tggaattaacttttaaggatCagtatattggccgtggggat	12	4	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr22:32162610C>T	ENST00000382112.3	+	5	389	c.319C>T	c.(319-321)Cag>Tag	p.Q107*	DEPDC5_ENST00000400242.3_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.Q107*|DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.Q107*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	107					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.Q107*(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TTTTAAGGATCAGTATATTGG	0.353																																																1	Substitution - Nonsense(1)	ovary(1)	22											196	205	202					22																	32162610		2155	4273	6428	30492610	SO:0001587	stop_gained	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.319C>T	22.37:g.32162610C>T	ENSP00000371546:p.Gln107*		30492610	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	C	36	5.633922	0.96682	.	.	ENSG00000100150	ENST00000535622;ENST00000400242;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.	.	.	5.42	4.39	0.52855	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.9192	0.63921	0.0:0.8466:0.1534:0.0	.	.	.	.	X	107	.	ENSP00000266091:Q107X	Q	+	1	0	DEPDC5	30492610	1.000000	0.71417	0.997000	0.53966	0.890000	0.51754	7.058000	0.76676	1.266000	0.44231	0.655000	0.94253	CAG		0.353	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32162610	C	T	32162610	4	4	39	1	0	0	0	0	0	1	0	0	4453	827	29	3	337	3	DEPDC5	22	32162610	Nonsense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	5418844	32162610	19141956	202	3666										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46654129	46654129	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttgatcctcttctttcttttGaatattctgatttcatcttc	3	9	6	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr22:46654129G>A	ENST00000253255.5	-	1	5090	c.5091C>T	c.(5089-5091)ttC>ttT	p.F1697F		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1697					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.F1697F(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TCTTTCTTTTGAATATTCTGA	0.418																																																1	Substitution - coding silent(1)	ovary(1)	22											192	156	168					22																	46654129		2203	4300	6503	45032793	SO:0001819	synonymous_variant	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5091C>T	22.37:g.46654129G>A			45032793	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																				0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46654129	G	A	46654129	2	1	39	1	0	0	0	0	0	0	0	1	12001	1281	45	3		3	PKDREJ	22	46654129	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	14491519	46654129	4650437	203	3667										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50662947	50662947	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tggggccactcaccactcagTgcactcaggaccctggatgc	11	15	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chr22:50662947T>C	ENST00000248846.5	-	11	2162	c.2058A>G	c.(2056-2058)gcA>gcG	p.A686A	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Silent_p.A686A			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	686					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		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)		CACCACTCAGTGCACTCAGGA	0.537																																																0			22											106	116	113					22																	50662947		2203	4300	6503	49005074	SO:0001819	synonymous_variant	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.2058A>G	22.37:g.50662947T>C			49005074	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																				0.537	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		C	50662947	T	C	50662947	2	2	39	1	0	0	0	0	0	0	0	1	16810	1683	59	4		4	TUBGCP6	22	50662947	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	4008818	50662947	641619	204	3668										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18606247	18606247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcttttctacagtaatcctcGcttccatgggctccgggtaa	9	12	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:18606247G>A	ENST00000379989.3	+	10	1013	c.728G>A	c.(727-729)cGc>cAc	p.R243H	CDKL5_ENST00000379996.3_Missense_Mutation_p.R243H	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					AGTAATCCTCGCTTCCATGGG	0.403																																																0			X											160	157	158					X																	18606247		2203	4300	6503	18516168	SO:0001583	missense	6792			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.728G>A	X.37:g.18606247G>A	ENSP00000369325:p.Arg243His		18516168	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769578	0.90020	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.44083	0.93;0.93	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.044170	0.85682	D	0.000000	T	0.52980	0.1768	N	0.20685	0.6	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	T	0.54990	-0.8210	10	0.51188	T	0.08	-17.0545	19.5557	0.95347	0.0:0.0:1.0:0.0	.	243	O76039	CDKL5_HUMAN	H	243	ENSP00000369332:R243H;ENSP00000369325:R243H	ENSP00000369325:R243H	R	+	2	0	CDKL5	18516168	1.000000	0.71417	0.958000	0.39756	0.836000	0.47400	6.357000	0.73051	2.574000	0.86865	0.583000	0.79449	CGC		0.403	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		A	18606247	G	A	18606247	3	1	39	1	0	0	0	0	1	0	0	0	3163	1087	38	1	758	1	CDKL5	23	18606247	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10		18606247	136664313	205	3669										
MAOA	4128	hgsc.bcm.edu	37	chrX	43601226	43601227	+	In_Frame_Ins	INS	-	-	GAG													0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atgaagagaagaactggtgtINSgaggagcagtactctggggg							TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:43601226_43601227insGAG	ENST00000338702.3	+	12	1317_1318	c.1194_1195insGAG	c.(1195-1197)gag>GAGgag	p.399_399E>EE	MAOA_ENST00000542639.1_In_Frame_Ins_p.266_266E>EE	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	399					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	AGAACTGGTGTGAGGAGCAGTA	0.455																																																0			X																																								43486171	SO:0001652	inframe_insertion	4128				CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1198_1200dupGAG	X.37:g.43601230_43601232dupGAG	ENSP00000340684:p.Glu400dup		43486170	B4DF46|Q16426	In_Frame_Ins	INS	ENST00000338702.3	37	CCDS14260.1																																																																																				0.455	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		GAG	43601227	-	GAG	43601226	7	5	39	1	0	1	1	0	0	0	0	0	9255	1702	59	0	1240	0	MAOA	23	43601226	In_Frame_Ins	INS	-	TCGA-AG-3742-01A-11D-1657-10	24994979	43601226	111669334	206	3670										
DGKK	139189	hgsc.bcm.edu	37	chrX	50114798	50114798	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ttattcatggcatccagggcGctttgtagtgcagtctcatc	10	10	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:50114798G>A	ENST00000376025.2	-	0	3595							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					CATCCAGGGCGCTTTGTAGTG	0.443																																																0			X											120	108	112					X																	50114798		1980	4148	6128	50131538			139189			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50114798G>A			50131538	B2RP91	Missense_Mutation	SNP	ENST00000376025.2	37																																																																																					0.443	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742		A	50114798	G	A	50114798	1	1	39	0	1	0	0	0	0	0	0	0	4483	1078	38	1		1	DGKK	23	50114798	RNA	SNP	G	TCGA-AG-3742-01A-11D-1657-10	6513572	50114798	105155762	207	3671										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54777505	54777505	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gaaccccaggtggggtagttGcagggtactgggatgcctgt	17	8	0	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:54777505G>T	ENST00000218436.6	-	12	3690	c.3661C>A	c.(3661-3663)Caa>Aaa	p.Q1221K		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1221					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TGGGGTAGTTGCAGGGTACTG	0.637																																																0			X											31	24	26					X																	54777505		2199	4297	6496	54794230	SO:0001583	missense	347365			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3661C>A	X.37:g.54777505G>T	ENSP00000218436:p.Gln1221Lys		54794230	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690552	0.29962	.	.	ENSG00000102313	ENST00000218436	T	0.11712	2.75	3.58	1.31	0.21738	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.654529	0.13434	U	0.388198	T	0.14141	0.0342	M	0.70595	2.14	0.22827	N	0.998685	B	0.14438	0.01	B	0.15484	0.013	T	0.17531	-1.0366	10	0.42905	T	0.14	.	11.4543	0.50171	0.0:0.0:0.6637:0.3362	.	1221	Q6UXX5	ITH5L_HUMAN	K	1221	ENSP00000218436:Q1221K	ENSP00000218436:Q1221K	Q	-	1	0	ITIH5L	54794230	1.000000	0.71417	0.708000	0.30435	0.632000	0.37999	2.427000	0.44740	0.365000	0.24400	0.287000	0.19450	CAA		0.637	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		T	54777505	G	T	54777505	3	4	39	1	0	0	0	0	1	0	0	0	7929	1328	46	2	288	2	ITIH5L	23	54777505	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	4662707	54777505	100493055	208	3672										
ALAS2	212	hgsc.bcm.edu	37	chrX	55042055	55042055	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcttatgcataattccatcaCgctccccaatcccagcgccc	4	18	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:55042055C>T	ENST00000330807.5	-	8	1261	c.1124G>A	c.(1123-1125)cGt>cAt	p.R375H	ALAS2_ENST00000498636.1_5'UTR|ALAS2_ENST00000396198.3_Missense_Mutation_p.R362H|ALAS2_ENST00000335854.4_Missense_Mutation_p.R338H	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	375			R -> C (in XLSA; significantly reduced activity). {ECO:0000269|PubMed:21309041}.		cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	AATTCCATCACGCTCCCCAAT	0.517																																																0			X											95	84	88					X																	55042055		2203	4300	6503	55058780	SO:0001583	missense	212				CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"sideroblastic/hypochromic anemia"	301300	"aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.1124G>A	X.37:g.55042055C>T	ENSP00000332369:p.Arg375His		55058780	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Missense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934925	0.92458	.	.	ENSG00000158578	ENST00000330807;ENST00000396198;ENST00000335854	D;D;D	0.91464	-2.85;-2.85;-2.85	5.75	5.75	0.90469	Aminotransferase, class I/classII (1);Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.92309	0.7560	L	0.31926	0.97	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.993;0.993	D	0.90425	0.4420	10	0.25751	T	0.34	-8.2479	17.8507	0.88746	0.0:1.0:0.0:0.0	.	338;362;375	A8K6C4;Q5JZF5;P22557	.;.;HEM0_HUMAN	H	375;362;338	ENSP00000332369:R375H;ENSP00000379501:R362H;ENSP00000337131:R338H	ENSP00000332369:R375H	R	-	2	0	ALAS2	55058780	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.576000	0.86940	0.594000	0.82650	CGT		0.517	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		T	55042055	C	T	55042055	3	4	39	1	0	0	0	0	1	0	0	0	485	536	19	1	655	1	ALAS2	23	55042055	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	264550	55042055	100228505	209	3673										
STARD8	9754	hgsc.bcm.edu	37	chrX	67943553	67943553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggtgctgcatcgtgttctccGggagcgggccctctgggatg	17	11	2	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:67943553G>A	ENST00000252336.6	+	12	3017	c.2645G>A	c.(2644-2646)cGg>cAg	p.R882Q	STARD8_ENST00000374599.3_Missense_Mutation_p.R962Q|STARD8_ENST00000374597.3_Missense_Mutation_p.R882Q	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	882	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						CGTGTTCTCCGGGAGCGGGCC	0.657																																																0			X											19	21	20					X																	67943553		2188	4280	6468	67860278	SO:0001583	missense	9754			D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.2645G>A	X.37:g.67943553G>A	ENSP00000252336:p.Arg882Gln		67860278	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178285	0.78564	.	.	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.30182	1.54;1.54;1.54	4.44	3.57	0.40892	Lipid-binding START (3);START-like domain (1);	0.000000	0.64402	D	0.000011	T	0.56381	0.1981	M	0.86953	2.85	0.47341	D	0.999395	D;D	0.89917	0.999;1.0	D;D	0.77557	0.943;0.99	T	0.59920	-0.7363	10	0.72032	D	0.01	.	8.9995	0.36072	0.1103:0.0:0.8897:0.0	.	962;882	Q92502-2;Q92502	.;STAR8_HUMAN	Q	882;962;882	ENSP00000252336:R882Q;ENSP00000363727:R962Q;ENSP00000363725:R882Q	ENSP00000252336:R882Q	R	+	2	0	STARD8	67860278	1.000000	0.71417	0.679000	0.29978	0.987000	0.75469	4.158000	0.58150	0.890000	0.36211	0.600000	0.82982	CGG		0.657	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		A	67943553	G	A	67943553	3	1	39	1	0	0	0	0	1	0	0	0	15302	1116	39	1	2935	1	STARD8	23	67943553	Missense_Mutation	SNP	G	TCGA-AG-3742-01A-11D-1657-10	12901498	67943553	87327007	210	3674										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216071	78216071	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aagatgggtagcaacagtacCagcactgctgagatttactg	11	8	0	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:78216071C>T	ENST00000171757.2	+	4	334	c.54C>T	c.(52-54)acC>acT	p.T18T	P2RY10_ENST00000475374.1_3'UTR|P2RY10_ENST00000544091.1_Silent_p.T18T	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						GCAACAGTACCAGCACTGCTG	0.378																																																0			X											142	110	121					X																	78216071		2203	4300	6503	78102727	SO:0001819	synonymous_variant	27334			AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.54C>T	X.37:g.78216071C>T			78102727	D3DTE5|Q4VBN7|Q86V16	Silent	SNP	ENST00000171757.2	37	CCDS14442.1																																																																																				0.378	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			T	78216071	C	T	78216071	2	4	39	1	0	0	0	0	0	0	0	1	11378	581	21	3		3	P2RY10	23	78216071	Silent	SNP	C	TCGA-AG-3742-01A-11D-1657-10	10272518	78216071	77054489	211	3675										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79945493	79945493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atcgaagtaagacatcagttAcaattttagctgctttaact	6	7	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:79945493A>G	ENST00000373275.4	-	32	3917	c.3701T>C	c.(3700-3702)gTa>gCa	p.V1234A	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1234					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.V1234G(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						GACATCAGTTACAATTTTAGC	0.323																																																1	Substitution - Missense(1)	ovary(1)	X											86	73	78					X																	79945493		2203	4300	6503	79832149	SO:0001583	missense	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.3701T>C	X.37:g.79945493A>G	ENSP00000362372:p.Val1234Ala		79832149	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497006	0.85069	.	.	ENSG00000165288	ENST00000373275	T	0.19532	2.14	4.44	4.44	0.53790	Bromodomain (3);	0.000000	0.85682	D	0.000000	T	0.43478	0.1249	M	0.79926	2.475	0.58432	D	0.999997	D	0.63880	0.993	P	0.60012	0.867	T	0.45220	-0.9276	9	.	.	.	-11.3827	13.1253	0.59351	1.0:0.0:0.0:0.0	.	1234	Q6RI45	BRWD3_HUMAN	A	1234	ENSP00000362372:V1234A	.	V	-	2	0	BRWD3	79832149	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.705000	0.91357	1.738000	0.51689	0.481000	0.45027	GTA		0.323	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		G	79945493	A	G	79945493	3	3	39	1	0	0	0	0	1	0	0	0	1529	391	14	4	1747	4	BRWD3	23	79945493	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	1729422	79945493	75325067	212	3676										
ZNF711	7552	hgsc.bcm.edu	37	chrX	84526278	84526278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	atttggtgatgagagggagcTtcaacgccatctggatttgt	13	6	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:84526278T>C	ENST00000373165.3	+	9	2036	c.1730T>C	c.(1729-1731)cTt>cCt	p.L577P	ZNF711_ENST00000276123.3_Missense_Mutation_p.L577P|ZNF711_ENST00000395402.1_Missense_Mutation_p.L585P|ZNF711_ENST00000542798.1_Missense_Mutation_p.L419P|ZNF711_ENST00000360700.4_Missense_Mutation_p.L623P	NM_021998.4	NP_068838.3	Q9Y462	ZN711_HUMAN	zinc finger protein 711	577				L -> P (in Ref. 3; BAG61766). {ECO:0000305}.	positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(3)|skin(4)	28						GAGAGGGAGCTTCAACGCCAT	0.408																																																0			X											79	63	68					X																	84526278		2201	4298	6499	84412934	SO:0001583	missense	7552			BC006349	CCDS35344.1	Xq21.1	2014-02-19	2006-06-29	2006-06-29	ENSG00000147180	ENSG00000147180		"Zinc fingers, C2H2-type"	13128	protein-coding gene	gene with protein product		314990	"zinc finger protein 6 (CMPX1)", "zinc finger protein 6"	ZNF6		19377476	Standard	XM_005262186		Approved	CMPX1, ZNF4, ZNF5, dJ75N13.1, Zfp711, MRX97	uc004eeo.3	Q9Y462	OTTHUMG00000021933	ENST00000373165.3:c.1730T>C	X.37:g.84526278T>C	ENSP00000362260:p.Leu577Pro		84412934	B4DSV4|Q6NX42|Q9Y4J6	Missense_Mutation	SNP	ENST00000373165.3	37	CCDS35344.1	.	.	.	.	.	.	.	.	.	.	T	11.34	1.609816	0.28712	.	.	ENSG00000147180	ENST00000395402;ENST00000373165;ENST00000276123;ENST00000360700;ENST00000542798	T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72	5.3	2.93	0.34026	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.189536	0.25529	N	0.030048	T	0.41604	0.1166	H	0.96208	3.785	0.80722	D	1	B;B	0.18968	0.032;0.0	B;B	0.21360	0.034;0.001	T	0.45498	-0.9257	10	0.87932	D	0	-2.2071	8.5625	0.33520	0.0:0.1589:0.0:0.8411	.	623;577	Q9Y462-3;Q9Y462	.;ZN711_HUMAN	P	585;577;577;623;419	ENSP00000378798:L585P;ENSP00000362260:L577P;ENSP00000276123:L577P;ENSP00000353922:L623P;ENSP00000442071:L419P	ENSP00000276123:L577P	L	+	2	0	ZNF711	84412934	1.000000	0.71417	0.971000	0.41717	0.986000	0.74619	5.060000	0.64312	0.678000	0.31325	0.417000	0.27973	CTT		0.408	ZNF711-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057388.2	NM_021998		C	84526278	T	C	84526278	3	2	39	1	0	0	0	0	1	0	0	0	18155	1609	56	4	1756	4	ZNF711	23	84526278	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	4580785	84526278	70744282	213	3677										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86888868	86888868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	ggaattacgtagccagtatgTcaactcctagaagcacagtt	9	9	1	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:86888868T>C	ENST00000373119.4	+	8	1814	c.1669T>C	c.(1669-1671)Tca>Cca	p.S557P	KLHL4_ENST00000373114.4_Missense_Mutation_p.S557P	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	557						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						AGCCAGTATGTCAACTCCTAG	0.423																																																0			X											165	131	142					X																	86888868		2203	4300	6503	86775524	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1669T>C	X.37:g.86888868T>C	ENSP00000362211:p.Ser557Pro		86775524	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.013234	0.54468	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.58652	0.32;0.32	4.72	3.51	0.40186	Galactose oxidase, beta-propeller (1);	0.072240	0.64402	D	0.000019	T	0.60881	0.2303	L	0.33339	1.005	0.80722	D	1	D;B	0.53745	0.962;0.077	P;B	0.62885	0.908;0.099	T	0.61088	-0.7133	10	0.87932	D	0	.	9.0941	0.36629	0.1661:0.0:0.0:0.8339	.	557;557	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	P	557	ENSP00000362211:S557P;ENSP00000362206:S557P	ENSP00000362206:S557P	S	+	1	0	KLHL4	86775524	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	5.588000	0.67517	0.603000	0.29913	0.412000	0.27726	TCA		0.423	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			C	86888868	T	C	86888868	3	2	39	1	0	0	0	0	1	0	0	0	8412	1667	58	4	1699	4	KLHL4	23	86888868	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	2362590	86888868	68381692	214	3678										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99551677	99551677	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	acatctttcccaaaggttgcGaaagtccgtttggtggggcc	12	10	1	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:99551677G>A	ENST00000373034.4	-	6	4720	c.3045C>T	c.(3043-3045)ttC>ttT	p.F1015F	PCDH19_ENST00000420881.2_Silent_p.F967F|PCDH19_ENST00000255531.7_Silent_p.F968F|PCDH19_ENST00000464981.1_5'Flank	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1015					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F1015F(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CAAAGGTTGCGAAAGTCCGTT	0.562																																																1	Substitution - coding silent(1)	breast(1)	X											81	80	81					X																	99551677		2126	4212	6338	99438333	SO:0001819	synonymous_variant	57575			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3045C>T	X.37:g.99551677G>A			99438333	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																				0.562	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99551677	G	A	99551677	2	1	39	1	0	0	0	0	0	0	0	1	11545	1049	37	1		1	PCDH19	23	99551677	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	12662809	99551677	55718883	215	3679										
NRK	203447	hgsc.bcm.edu	37	chrX	105159726	105159726	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	gcattgtgtctttaaggttcAagagagatctccttctgtgc	10	8	4	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:105159726A>T	ENST00000243300.9	+	15	2657	c.2354A>T	c.(2353-2355)cAa>cTa	p.Q785L	NRK_ENST00000428173.2_Missense_Mutation_p.Q786L	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	785					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						TTTAAGGTTCAAGAGAGATCT	0.328										HNSCC(51;0.14)																																						0			X											115	100	104					X																	105159726		1853	4075	5928	105046382	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2354A>T	X.37:g.105159726A>T	ENSP00000434830:p.Gln785Leu		105046382	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	a	10.57	1.387347	0.25031	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.77358	-1.07;-1.09	5.09	0.911	0.19343	.	0.742320	0.11786	N	0.529731	T	0.68550	0.3013	N	0.24115	0.695	0.31403	N	0.676453	P;P	0.50819	0.939;0.596	P;B	0.51193	0.662;0.107	T	0.66972	-0.5788	10	0.72032	D	0.01	.	3.7559	0.08585	0.5178:0.2571:0.2251:0.0	.	453;785	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	L	785;786	ENSP00000434830:Q785L;ENSP00000438378:Q786L	ENSP00000434830:Q785L	Q	+	2	0	NRK	105046382	1.000000	0.71417	0.026000	0.17262	0.124000	0.20399	1.732000	0.38146	0.211000	0.20683	-0.326000	0.08463	CAA		0.328	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105159726	A	T	105159726	3	4	39	1	0	0	0	0	1	0	0	0	10686	130	5	5	2412	5	NRK	23	105159726	Missense_Mutation	SNP	A	TCGA-AG-3742-01A-11D-1657-10	5608049	105159726	50110834	216	3680										
VSIG1	340547	hgsc.bcm.edu	37	chrX	107319439	107319439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	aagaaattctaagaccatcgCggaacttgagtaagccttca	8	9	2	3			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:107319439C>T	ENST00000217957.5	+	6	938	c.821C>T	c.(820-822)gCg>gTg	p.A274V	VSIG1_ENST00000415430.3_Missense_Mutation_p.A310V	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	274						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						AAGACCATCGCGGAACTTGAG	0.403																																																0			X											166	143	151					X																	107319439		2203	4300	6503	107206095	SO:0001583	missense	340547			BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.821C>T	X.37:g.107319439C>T	ENSP00000217957:p.Ala274Val		107206095	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	C	6.523	0.464676	0.12402	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.40756	1.02;1.02	4.61	4.61	0.57282	.	2.341010	0.02190	N	0.061246	T	0.33527	0.0866	L	0.36672	1.1	0.09310	N	1	P;P	0.35226	0.491;0.491	B;B	0.22753	0.041;0.041	T	0.20739	-1.0266	10	0.29301	T	0.29	.	9.4469	0.38703	0.2284:0.7716:0.0:0.0	.	310;274	C9J4P2;Q86XK7	.;VSIG1_HUMAN	V	310;274	ENSP00000402219:A310V;ENSP00000217957:A274V	ENSP00000217957:A274V	A	+	2	0	VSIG1	107206095	0.117000	0.22190	0.013000	0.15412	0.008000	0.06430	2.635000	0.46537	2.284000	0.76573	0.600000	0.82982	GCG		0.403	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607		T	107319439	C	T	107319439	3	4	39	1	0	0	0	0	1	0	0	0	17262	768	27	1	955	1	VSIG1	23	107319439	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	2159713	107319439	47951121	217	3681										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118220751	118220751	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tctgcgagggaggggctcttTtcagtcgaactccaaaaagc	12	10	3	0			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:118220751T>G	ENST00000402510.2	-	11	4441	c.4442A>C	c.(4441-4443)aAa>aCa	p.K1481T		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1481										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						AGGGGCTCTTTTCAGTCGAAC	0.448																																																0			X											70	68	69					X																	118220751		1893	4099	5992	118104779	SO:0001583	missense	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4442A>C	X.37:g.118220751T>G	ENSP00000384670:p.Lys1481Thr		118104779	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.58|13.58	2.279451|2.279451	0.40294|0.40294	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.13657	.|2.57	5.13|5.13	-0.121|-0.121	0.13535|0.13535	.|.	.|.	.|.	.|.	.|.	T|T	0.08980|0.08980	0.0222|0.0222	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|P	.|0.36535	.|0.557	.|B	.|0.35607	.|0.206	T|T	0.26643|0.26643	-1.0097|-1.0097	5|9	.|0.51188	.|T	.|0.08	.|.	8.2378|8.2378	0.31636|0.31636	0.0:0.494:0.0:0.506|0.0:0.494:0.0:0.506	.|.	.|1481	.|Q9ULL0	.|K1210_HUMAN	D|T	887|1481	.|ENSP00000384670:K1481T	.|ENSP00000384670:K1481T	E|K	-|-	3|2	2|0	KIAA1210|RP13-347D8.6	118104779|118104779	0.014000|0.014000	0.17966|0.17966	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	0.153000|0.153000	0.16323|0.16323	-0.261000|-0.261000	0.09405|0.09405	-1.230000|-1.230000	0.01575|0.01575	GAA|AAA		0.448	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118220751	T	G	118220751	3	3	39	1	0	0	0	0	1	0	0	0	8235	1841	64	4	703	4	KIAA1210	23	118220751	Missense_Mutation	SNP	T	TCGA-AG-3742-01A-11D-1657-10	10901312	118220751	37049809	218	3682										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130409618	130409618	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	agctgcattgaagtggcttcTccttctttgtgcagaatgta	10	8	2	2			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:130409618T>C	ENST00000361420.3	-	16	3097	c.3018A>G	c.(3016-3018)ggA>ggG	p.G1006G	IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Silent_p.G997G|IGSF1_ENST00000370904.1_Silent_p.G997G|IGSF1_ENST00000370903.3_Silent_p.G1011G			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	1006	Ig-like C2-type 10.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)	p.G1006G(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						AAGTGGCTTCTCCTTCTTTGT	0.532																																																1	Substitution - coding silent(1)	lung(1)	X											120	103	109					X																	130409618		2203	4300	6503	130237299	SO:0001819	synonymous_variant	3547			AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.3018A>G	X.37:g.130409618T>C			130237299	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	37	CCDS14629.1																																																																																				0.532	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			C	130409618	T	C	130409618	2	2	39	1	0	0	0	0	0	0	0	1	7617	1538	54	4		4	IGSF1	23	130409618	Silent	SNP	T	TCGA-AG-3742-01A-11D-1657-10	12188867	130409618	24860942	219	3683										
FLNA	2316	hgsc.bcm.edu	37	chrX	153592920	153592920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tgggtggaagtcctggggcgCgtcacggatgtcagccatga	17	9	2	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:153592920C>T	ENST00000369850.3	-	13	2232	c.1996G>A	c.(1996-1998)Gcg>Acg	p.A666T	FLNA_ENST00000360319.4_Missense_Mutation_p.A666T|FLNA_ENST00000422373.1_Missense_Mutation_p.A666T|FLNA_ENST00000344736.4_Missense_Mutation_p.A666T	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	666					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCCTGGGGCGCGTCACGGATG	0.627																																																0			X											38	43	42					X																	153592920		2170	4234	6404	153246114	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1996G>A	X.37:g.153592920C>T	ENSP00000358866:p.Ala666Thr		153246114	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.335861	0.41398	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.91996	-2.1;-2.1;-2.95;-2.95	4.95	4.95	0.65309	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.076257	0.51477	D	0.000086	D	0.93452	0.7911	L	0.54323	1.7	0.80722	D	1	B;D	0.63046	0.069;0.992	B;P	0.54965	0.111;0.765	D	0.93591	0.6921	10	0.49607	T	0.09	.	17.4666	0.87634	0.0:1.0:0.0:0.0	.	666;666	P21333-2;P21333	.;FLNA_HUMAN	T	666;639;666;666;666	ENSP00000353467:A666T;ENSP00000416926:A666T;ENSP00000358866:A666T;ENSP00000358863:A666T	ENSP00000358863:A666T	A	-	1	0	FLNA	153246114	0.996000	0.38824	0.110000	0.21437	0.580000	0.36256	3.082000	0.50128	2.049000	0.60858	0.525000	0.51046	GCG		0.627	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153592920	C	T	153592920	3	4	39	1	0	0	0	0	1	0	0	0	5952	768	27	1	6091	1	FLNA	23	153592920	Missense_Mutation	SNP	C	TCGA-AG-3742-01A-11D-1657-10	23183302	153592920	1677640	220	3684										
CTAG2	30848	hgsc.bcm.edu	37	chrX	153881592	153881592	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0361990950226244	8	1	0.496641289744738	2.05751391465677	0.39640176337424	0.208695652173913	0.66867542651632	0	tcctgcgcagaagcggcaccGccatgcggaccccgcggggc	15	17	0	1			TCGA-AG-3742-01A-11D-1657-10	TCGA-AG-3742-11A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	48f3fa65-c79b-4f86-8d30-a692d0d5521b	17d4fb78-6e64-4aaf-b136-e270b18076b3	g.chrX:153881592G>A	ENST00000247306.4	-	1	261	c.198C>T	c.(196-198)ggC>ggT	p.G66G	CTAG2_ENST00000369585.3_Silent_p.G66G	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	66	Gly-rich.					centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AAGCGGCACCGCCATGCGGAC	0.721																																																0			X											20	21	20					X																	153881592		2185	4279	6464	153534786	SO:0001819	synonymous_variant	30848			AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"CTL-recognized antigen on melanoma", "LAGE-1a protein", "cancer/testis antigen family 6, member 2a", "cancer/testis antigen family 6, member 2b"	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.198C>T	X.37:g.153881592G>A			153534786	O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Silent	SNP	ENST00000247306.4	37	CCDS14759.1																																																																																				0.721	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061176.1	NM_020994		A	153881592	G	A	153881592	2	1	39	1	0	0	0	0	0	0	0	1	3997	1074	38	1		1	CTAG2	23	153881592	Silent	SNP	G	TCGA-AG-3742-01A-11D-1657-10	288672	153881592	1388968	221	3685										
UBR4	23352	broad.mit.edu	37	chr1	19499450	19499450	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttatgaggatcagtctcagcAgccatcttagaaaaatgctc	8	9	3	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:19499450A>T	ENST00000375254.3	-	25	3456	c.3429T>A	c.(3427-3429)gcT>gcA	p.A1143A	UBR4_ENST00000375226.2_Silent_p.A1143A|UBR4_ENST00000375267.2_Silent_p.A1143A|UBR4_ENST00000375217.2_Silent_p.A1143A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1143					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A1143A(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAGTCTCAGCAGCCATCTTAG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											89	83	85					1																	19499450		2203	4300	6503	19372037	SO:0001819	synonymous_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3429T>A	1.37:g.19499450A>T			19372037	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.498	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19499450	A	T	19499450	2	4	40	1	0	0	0	0	0	0	0	1	16944	175	7	5		5	UBR4	1	19499450	Silent	SNP	A	TCGA-AG-3878-01A-02W-0899-10		19499450	229751171	1	3686										
USP48	84196	broad.mit.edu	37	chr1	22021580	22021580	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgaattttcaattcttttaaCgtctgattagcagaaacgag	7	6	3	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:22021580C>T	ENST00000308271.9	-	23	3510	c.2862G>A	c.(2860-2862)acG>acA	p.T954T	USP48_ENST00000529637.1_Silent_p.T966T|USP48_ENST00000374732.3_Intron|USP48_ENST00000400301.1_Intron	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	954	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.T954T(1)		NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATTCTTTTAACGTCTGATTAG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	1											114	112	113					1																	22021580		2203	4299	6502	21894167	SO:0001819	synonymous_variant	84196			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2862G>A	1.37:g.22021580C>T			21894167	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																				0.368	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		T	22021580	C	T	22021580	2	4	40	1	0	0	0	0	0	0	0	1	17119	523	19	1		1	USP48	1	22021580	Silent	SNP	C	TCGA-AG-3878-01A-02W-0899-10	2522130	22021580	227229041	2	3687										
ARID1A	8289	broad.mit.edu	37	chr1	27087880	27087880	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctttgtctggagcaggcaacCagatgccacctcggccaccc	10	16	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:27087880C>T	ENST00000324856.7	+	6	2538	c.2167C>T	c.(2167-2169)Cag>Tag	p.Q723*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q723*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q340*|RN7SL501P_ENST00000578818.1_RNA	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	723					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q723*(2)|p.N722fs*18(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		AGCAGGCAACCAGATGCCACC	0.498			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	3	Substitution - Nonsense(2)|Deletion - Frameshift(1)	ovary(1)|large_intestine(1)|breast(1)	1											78	73	75					1																	27087880		2203	4300	6503	26960467	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2167C>T	1.37:g.27087880C>T	ENSP00000320485:p.Gln723*		26960467	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	39	7.398777	0.98258	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	.	.	.	5.33	5.33	0.75918	.	0.247263	0.42294	D	0.000725	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-6.6748	19.2079	0.93742	0.0:1.0:0.0:0.0	.	.	.	.	X	723;723;340	.	ENSP00000320485:Q723X	Q	+	1	0	ARID1A	26960467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.586000	0.67503	2.768000	0.95171	0.655000	0.94253	CAG		0.498	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27087880	C	T	27087880	4	4	40	1	0	0	0	0	0	1	0	0	913	595	21	3	2189	3	ARID1A	1	27087880	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	5066300	27087880	222162741	3	3688										
TRNAU1AP	54952	broad.mit.edu	37	chr1	28887240	28887240	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gaaaccccttccaggagccaCacctgtaaggacatttagat	8	12	0	1	rs370368589		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:28887240C>A	ENST00000373830.3	+	3	247	c.221C>A	c.(220-222)aCa>aAa	p.T74K	TRNAU1AP_ENST00000495995.1_3'UTR	NM_017846.4	NP_060316.1	Q9NX07	TSAP1_HUMAN	tRNA selenocysteine 1 associated protein 1	74	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				selenocysteine incorporation (GO:0001514)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T74K(1)		breast(1)|endometrium(2)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	8						CCAGGAGCCACACCTGTAAGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	59	60					1																	28887240		2203	4300	6503	28759827	SO:0001583	missense	54952				CCDS324.1	1p35.3	2013-02-12	2008-09-05	2008-09-05	ENSG00000180098	ENSG00000180098		"RNA binding motif (RRM) containing"	30813	protein-coding gene	gene with protein product			"tRNA selenocysteine associated protein 1"	TRSPAP1		10606267, 16230358	Standard	NM_017846		Approved	SECP43, FLJ20503	uc001bqi.3	Q9NX07	OTTHUMG00000003653	ENST00000373830.3:c.221C>A	1.37:g.28887240C>A	ENSP00000362936:p.Thr74Lys		28759827	Q86SU7	Missense_Mutation	SNP	ENST00000373830.3	37	CCDS324.1	.	.	.	.	.	.	.	.	.	.	c	15.02	2.709305	0.48517	.	.	ENSG00000180098	ENST00000373830	T	0.05513	3.43	5.46	4.53	0.55603	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.209732	0.48767	D	0.000169	T	0.12817	0.0311	L	0.31207	0.915	0.43408	D	0.99554	D	0.64830	0.994	P	0.61592	0.891	T	0.03068	-1.1076	10	0.51188	T	0.08	.	13.1987	0.59754	0.0:0.8396:0.1604:0.0	.	74	Q9NX07	TSAP1_HUMAN	K	74	ENSP00000362936:T74K	ENSP00000362936:T74K	T	+	2	0	TRNAU1AP	28759827	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.030000	0.49720	1.277000	0.44412	0.552000	0.68991	ACA		0.388	TRNAU1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010346.1	NM_017846		A	28887240	C	A	28887240	3	1	40	1	0	0	0	0	1	0	0	0	16612	478	17	2	231	2	TRNAU1AP	1	28887240	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	1799360	28887240	220363381	4	3689										
PABPC4	8761	broad.mit.edu	37	chr1	40034517	40034517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gtttcaactgttcaaatttcCgttttaactctgcctgccgt	6	11	3	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:40034517C>T	ENST00000372857.3	-	6	1625	c.833G>A	c.(832-834)cGg>cAg	p.R278Q	PABPC4_ENST00000372856.3_Missense_Mutation_p.R278Q|PABPC4_ENST00000372862.3_Missense_Mutation_p.R278Q|PABPC4_ENST00000372858.3_Missense_Mutation_p.R278Q|SNORA55_ENST00000364587.1_RNA|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000529216.1_5'Flank	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	278					blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)	p.R278Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTCAAATTTCCGTTTTAACTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											225	207	213					1																	40034517		2203	4300	6503	39807104	SO:0001583	missense	8761			U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.833G>A	1.37:g.40034517C>T	ENSP00000361948:p.Arg278Gln		39807104	B1ANQ8|Q4VC03|Q6P0N3	Missense_Mutation	SNP	ENST00000372857.3	37	CCDS438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.279888|6.279888	0.97440|0.97440	.|.	.|.	ENSG00000090621|ENSG00000090621	ENST00000421687;ENST00000527718;ENST00000474378|ENST00000372862;ENST00000372858;ENST00000372857;ENST00000372856	.|T;T;T;T	.|0.06142	.|3.34;3.34;3.34;3.34	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.21468|0.21468	0.0517|0.0517	M|M	0.64630|0.64630	1.985|1.985	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P;P	.|0.69078	.|0.997;0.942;0.922	.|P;B;B	.|0.58172	.|0.834;0.328;0.409	T|T	0.00004|0.00004	-1.2562|-1.2562	5|10	.|0.62326	.|D	.|0.03	.|.	20.5948|20.5948	0.99439|0.99439	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|278;278;278	.|Q13310;Q13310-2;Q4VC03	.|PABP4_HUMAN;.;.	R|Q	180;5;191|278	.|ENSP00000361953:R278Q;ENSP00000361949:R278Q;ENSP00000361948:R278Q;ENSP00000361947:R278Q	.|ENSP00000361947:R278Q	G|R	-|-	1|2	0|0	PABPC4|PABPC4	39807104|39807104	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.818000|7.818000	0.86416|0.86416	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	GGA|CGG		0.413	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		T	40034517	C	T	40034517	3	4	40	1	0	0	0	0	1	0	0	0	11397	652	23	1	1189	1	PABPC4	1	40034517	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	11147277	40034517	209216104	5	3690										
C1orf43	25912	broad.mit.edu	37	chr1	154184827	154184827	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctcactcagggcctcctgatAgcgtaggtactcattctggc	10	13	4	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:154184827A>T	ENST00000368521.5	-	6	733	c.535T>A	c.(535-537)Tat>Aat	p.Y179N	C1orf43_ENST00000368516.1_Missense_Mutation_p.Y145N|C1orf43_ENST00000368518.1_Missense_Mutation_p.Y179N|C1orf43_ENST00000350592.3_Missense_Mutation_p.Y145N|C1orf43_ENST00000368519.1_Missense_Mutation_p.Y161N|C1orf43_ENST00000362076.4_Missense_Mutation_p.Y127N	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	179						integral component of membrane (GO:0016021)	coenzyme binding (GO:0050662)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)	p.Y145N(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					GCCTCCTGATAGCGTAGGTAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											150	143	145					1																	154184827		2203	4300	6503	152451451	SO:0001583	missense	25912			AF077036	CCDS1061.1, CCDS1062.1, CCDS41404.1, CCDS72924.1	1q21.2	2012-06-25			ENSG00000143612	ENSG00000143612			29876	protein-coding gene	gene with protein product						11042152, 11230159	Standard	XM_005245077		Approved	NICE-3, DKFZp586G1722	uc001fei.2	Q9BWL3	OTTHUMG00000035981	ENST00000368521.5:c.535T>A	1.37:g.154184827A>T	ENSP00000357507:p.Tyr179Asn		152451451	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	37	CCDS41404.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974469	0.74246	.	.	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	5.39	0.77823	Dehydrogenase, multihelical (1);	0.057471	0.64402	D	0.000001	T	0.73377	0.3579	M	0.76838	2.35	0.80722	D	1	P;D;P;P	0.60575	0.919;0.988;0.904;0.934	P;D;B;P	0.65773	0.504;0.938;0.364;0.637	T	0.78094	-0.2338	9	0.87932	D	0	-27.3306	14.7453	0.69485	1.0:0.0:0.0:0.0	.	145;179;127;145	Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;CA043_HUMAN;.;.	N	145;179;127;161;179;145	.	ENSP00000271925:Y145N	Y	-	1	0	C1orf43	152451451	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.091000	0.76923	2.270000	0.75569	0.477000	0.44152	TAT		0.522	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449		T	154184827	A	T	154184827	3	4	40	1	0	0	0	0	1	0	0	0	2046	420	15	5	234	5	C1orf43	1	154184827	Missense_Mutation	SNP	A	TCGA-AG-3878-01A-02W-0899-10	114150310	154184827	95065794	6	3691										
HMCN1	83872	broad.mit.edu	37	chr1	186092153	186092153	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	aagcccatcacgttatcctgTgaagcagatggcctccctcc	8	15	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:186092153T>G	ENST00000271588.4	+	81	12529	c.12300T>G	c.(12298-12300)tgT>tgG	p.C4100W	HMCN1_ENST00000367492.2_Missense_Mutation_p.C4100W	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4100	Ig-like C2-type 40.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.C4100W(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CGTTATCCTGTGAAGCAGATG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	93	100					1																	186092153		2203	4300	6503	184358776	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12300T>G	1.37:g.186092153T>G	ENSP00000271588:p.Cys4100Trp		184358776	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.861640	0.32884	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.85484	-1.99;-1.99	5.85	0.931	0.19460	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94922	0.8358	H	0.99336	4.52	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93543	0.6879	10	0.72032	D	0.01	.	10.757	0.46243	0.0:0.4004:0.0:0.5996	.	4100	Q96RW7	HMCN1_HUMAN	W	4100	ENSP00000271588:C4100W;ENSP00000356462:C4100W	ENSP00000271588:C4100W	C	+	3	2	HMCN1	184358776	1.000000	0.71417	0.310000	0.25168	0.001000	0.01503	1.332000	0.33805	-0.079000	0.12707	-0.256000	0.11100	TGT		0.458	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186092153	T	G	186092153	3	3	40	1	0	0	0	0	1	0	0	0	7241	1702	59	4	12622	4	HMCN1	1	186092153	Missense_Mutation	SNP	T	TCGA-AG-3878-01A-02W-0899-10	31907326	186092153	63158468	7	3692										
OR14C36	127066	broad.mit.edu	37	chr1	248512497	248512497	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgaactctcgaatctgcatcCagatgacactggcctcccta	7	14	2	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr1:248512497C>T	ENST00000317861.1	+	1	421	c.421C>T	c.(421-423)Cag>Tag	p.Q141*		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	141			Q -> R (in dbSNP:rs28448343).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q141*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						AATCTGCATCCAGATGACACT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											107	93	98					1																	248512497		2203	4300	6503	246579120	SO:0001587	stop_gained	127066			BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"GPCR / Class A : Olfactory receptors"	15026	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BF, member 1"	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.421C>T	1.37:g.248512497C>T	ENSP00000324534:p.Gln141*		246579120	Q6IEZ6	Nonsense_Mutation	SNP	ENST00000317861.1	37	CCDS31112.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.313507	0.40996	.	.	ENSG00000177174	ENST00000317861	.	.	.	4.05	3.14	0.36123	.	0.581781	0.14757	N	0.300211	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	3.7756	0.08659	0.2463:0.5513:0.0:0.2024	.	.	.	.	X	141	.	ENSP00000324534:Q141X	Q	+	1	0	OR14C36	246579120	0.000000	0.05858	0.001000	0.08648	0.399000	0.30720	-0.403000	0.07214	0.947000	0.37659	-0.531000	0.04308	CAG		0.522	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918		T	248512497	C	T	248512497	4	4	40	1	0	0	0	0	0	1	0	0	10977	595	21	3	423	3	OR14C36	1	248512497	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	62420344	248512497	738124	8	3693										
ZNF638	27332	broad.mit.edu	37	chr2	71661885	71661885	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttaacagaaattcatggccaAgcaaagaaaggaaaaggagc	10	6	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr2:71661885A>G	ENST00000409544.1	+	28	6515	c.5885A>G	c.(5884-5886)aAg>aGg	p.K1962R	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Missense_Mutation_p.K902R|ZNF638_ENST00000264447.4_Missense_Mutation_p.K1962R	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1962					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K1962R(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTCATGGCCAAGCAAAGAAAG	0.333																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	2											66	77	73					2																	71661885		2203	4300	6503	71515393	SO:0001583	missense	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5885A>G	2.37:g.71661885A>G	ENSP00000386433:p.Lys1962Arg		71515393	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.647161	0.47258	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.35605	1.3;1.3;1.74	6.08	4.75	0.60458	.	0.100063	0.44483	D	0.000441	T	0.39436	0.1078	N	0.17631	0.505	0.80722	D	1	D;B	0.71674	0.998;0.06	D;B	0.78314	0.991;0.018	T	0.13019	-1.0525	10	0.30078	T	0.28	-13.5376	8.7169	0.34416	0.905:0.0:0.095:0.0	.	1941;1962	Q14966-3;Q14966	.;ZN638_HUMAN	R	1962;1962;902	ENSP00000264447:K1962R;ENSP00000386433:K1962R;ENSP00000386813:K902R	ENSP00000264447:K1962R	K	+	2	0	ZNF638	71515393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.990000	0.40717	2.333000	0.79357	0.482000	0.46254	AAG		0.333	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71661885	A	G	71661885	3	3	40	1	0	0	0	0	1	0	0	0	18094	72	3	4	5991	4	ZNF638	2	71661885	Missense_Mutation	SNP	A	TCGA-AG-3878-01A-02W-0899-10		71661885	171537488	9	3694										
GAD1	2571	broad.mit.edu	37	chr2	171686107	171686107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	accgggatgcccgcttccggCgcacagagactgacttctct	11	15	1	2	rs373042715	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr2:171686107C>T	ENST00000358196.3	+	4	818	c.268C>T	c.(268-270)Cgc>Tgc	p.R90C	GAD1_ENST00000344257.5_Missense_Mutation_p.R90C|GAD1_ENST00000375272.1_Missense_Mutation_p.R90C|GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	90					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.R90C(3)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CCGCTTCCGGCGCACAGAGAC	0.532													C|||	3	0.000599042	8e-04	0.0014	5008	,	,		11741	0.001		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	2						C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	62	71	68		268,268	5.4	1	2		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GAD1	NM_000817.2,NM_013445.3	180,180	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	possibly-damaging,possibly-damaging	90/595,90/225	171686107	3,13003	2203	4300	6503	171394353	SO:0001583	missense	2571				CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.268C>T	2.37:g.171686107C>T	ENSP00000350928:p.Arg90Cys		171394353	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.954013	0.92660	4.54E-4	1.16E-4	ENSG00000128683	ENST00000358196;ENST00000375272;ENST00000344257;ENST00000455008;ENST00000456864	T;T;T;D;T	0.82526	2.15;0.22;0.22;-1.62;-1.47	5.37	5.37	0.77165	.	0.093423	0.85682	D	0.000000	D	0.86314	0.5903	M	0.61703	1.905	0.80722	D	1	P;D	0.67145	0.927;0.996	P;P	0.53185	0.485;0.72	D	0.87932	0.2711	10	0.87932	D	0	-3.9982	14.7874	0.69813	0.1449:0.8551:0.0:0.0	.	90;90	Q99259;Q99259-3	DCE1_HUMAN;.	C	90	ENSP00000350928:R90C;ENSP00000364421:R90C;ENSP00000341167:R90C;ENSP00000405917:R90C;ENSP00000394255:R90C	ENSP00000341167:R90C	R	+	1	0	GAD1	171394353	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.448000	0.60027	2.483000	0.83821	0.542000	0.68232	CGC		0.532	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171686107	C	T	171686107	3	4	40	1	0	0	0	0	1	0	0	0	6198	768	27	1	278	1	GAD1	2	171686107	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	100024222	171686107	71513266	10	3695										
HIBCH	26275	broad.mit.edu	37	chr2	191077702	191077702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	catacaagcttgacttagccGatactccatagttagtactt	6	10	0	1	rs569593420		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr2:191077702G>A	ENST00000359678.5	-	12	1285	c.991C>T	c.(991-993)Cgg>Tgg	p.R331W	HIBCH_ENST00000410045.1_Missense_Mutation_p.R108W|HIBCH_ENST00000486981.1_5'UTR|HIBCH_ENST00000392332.3_Missense_Mutation_p.R331W	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	331					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)	p.R331W(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			TGACTTAGCCGATACTCCATA	0.318													G|||	1	0.000199681	8e-04	0	5008	,	,		18131	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											87	89	88					2																	191077702		2202	4300	6502	190785947	SO:0001583	missense	26275			U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.991C>T	2.37:g.191077702G>A	ENSP00000352706:p.Arg331Trp		190785947	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	37	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.612291	0.66672	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000410045;ENST00000416732;ENST00000409820	T;T;T;T;T	0.77098	-0.72;-0.72;-1.07;-1.07;-1.07	5.01	4.06	0.47325	.	0.167565	0.51477	D	0.000093	D	0.89343	0.6688	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90910	0.4775	10	0.87932	D	0	-7.4197	12.3873	0.55338	0.0:0.0:0.8217:0.1783	.	331;331	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	W	331;331;108;82;111	ENSP00000376144:R331W;ENSP00000352706:R331W;ENSP00000386274:R108W;ENSP00000399263:R82W;ENSP00000387098:R111W	ENSP00000352706:R331W	R	-	1	2	HIBCH	190785947	1.000000	0.71417	0.974000	0.42286	0.987000	0.75469	1.689000	0.37700	2.594000	0.87642	0.563000	0.77884	CGG		0.318	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			A	191077702	G	A	191077702	3	1	40	1	0	0	0	0	1	0	0	0	7121	1057	37	1	181	1	HIBCH	2	191077702	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	19391595	191077702	52121671	11	3696										
RBM44	375316	broad.mit.edu	37	chr2	238726684	238726684	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gagacattactccaaccctgTaaagattgtcaaacttcctg	6	11	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr2:238726684T>C	ENST00000409864.1	+	3	1379	c.1125T>C	c.(1123-1125)tgT>tgC	p.C375C	RBM44_ENST00000316997.4_Silent_p.C375C|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	374						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.C375C(2)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TCCAACCCTGTAAAGATTGTC	0.368																																																2	Substitution - coding silent(2)	large_intestine(2)	2											61	62	62					2																	238726684		1845	4097	5942	238391423	SO:0001819	synonymous_variant	375316			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1125T>C	2.37:g.238726684T>C			238391423	A0AUW3	Silent	SNP	ENST00000409864.1	37	CCDS46554.1																																																																																				0.368	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		C	238726684	T	C	238726684	2	2	40	1	0	0	0	0	0	0	0	1	13175	1644	57	4		4	RBM44	2	238726684	Silent	SNP	T	TCGA-AG-3878-01A-02W-0899-10	47648982	238726684	4472689	12	3697										
TTC21A	199223	broad.mit.edu	37	chr3	39162536	39162536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tagtgtgtagtttcatcgagCgcaccttcatggccaccccc	9	14	2	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr3:39162536C>T	ENST00000431162.2	+	9	1107	c.973C>T	c.(973-975)Cgc>Tgc	p.R325C	TTC21A_ENST00000440121.1_Missense_Mutation_p.R276C|TTC21A_ENST00000301819.6_Missense_Mutation_p.R325C			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	325								p.R325C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTTCATCGAGCGCACCTTCAT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											148	141	144					3																	39162536		1997	4168	6165	39137540	SO:0001583	missense	199223			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.973C>T	3.37:g.39162536C>T	ENSP00000398211:p.Arg325Cys		39137540	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898155	0.52227	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.55930	1.26;0.49;0.49	5.95	5.95	0.96441	.	0.155263	0.46442	D	0.000293	T	0.73544	0.3600	M	0.79926	2.475	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.984;0.965	T	0.76203	-0.3045	10	0.87932	D	0	-19.2157	14.6398	0.68714	0.1462:0.8538:0.0:0.0	.	276;325;325	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	C	325;317;325;276	ENSP00000301819:R325C;ENSP00000398211:R325C;ENSP00000410882:R276C	ENSP00000301819:R325C	R	+	1	0	TTC21A	39137540	1.000000	0.71417	0.998000	0.56505	0.140000	0.21249	1.908000	0.39907	2.825000	0.97269	0.655000	0.94253	CGC		0.517	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39162536	C	T	39162536	3	4	40	1	0	0	0	0	1	0	0	0	16727	768	27	1	1007	1	TTC21A	3	39162536	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		39162536	158859894	13	3698										
VPRBP	9730	broad.mit.edu	37	chr3	51450463	51450463	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttacctcaatgacagcaagaTagcagtctttggtgtctgta	9	8	3	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr3:51450463T>C	ENST00000335891.5	-	14	2756	c.2747A>G	c.(2746-2748)tAt>tGt	p.Y916C				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1365					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)	p.Y1369C(1)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		GACAGCAAGATAGCAGTCTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	104	106					3																	51450463		1870	4109	5979	51425503	SO:0001583	missense	9730			AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2747A>G	3.37:g.51450463T>C	ENSP00000338857:p.Tyr916Cys		51425503	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	T	20.9	4.067177	0.76301	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	T;T	0.01406	4.93;4.93	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.06050	0.0157	L	0.46157	1.445	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.35126	-0.9801	10	0.59425	D	0.04	-15.0477	15.7584	0.78054	0.0:0.0:0.0:1.0	.	1365	Q9Y4B6	VPRBP_HUMAN	C	936;916	ENSP00000393183:Y936C;ENSP00000338857:Y916C	ENSP00000338857:Y916C	Y	-	2	0	VPRBP	51425503	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.135000	0.66039	0.533000	0.62120	TAT		0.408	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		C	51450463	T	C	51450463	3	2	40	1	0	0	0	0	1	0	0	0	17225	1406	49	4	445	4	VPRBP	3	51450463	Missense_Mutation	SNP	T	TCGA-AG-3878-01A-02W-0899-10	12287927	51450463	146571967	14	3699										
MYLK	4638	broad.mit.edu	37	chr3	123366087	123366087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tcacatctccaggaccatgaCgatgttggccttttcttcaa	7	12	4	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr3:123366087C>T	ENST00000475616.1	-	24	4602	c.4603G>A	c.(4603-4605)Gtc>Atc	p.V1535I	MYLK_ENST00000360304.3_Missense_Mutation_p.V1535I|MYLK_ENST00000346322.5_Missense_Mutation_p.V1466I|MYLK_ENST00000360772.3_Missense_Mutation_p.V1535I|MYLK_ENST00000359169.1_Missense_Mutation_p.V1535I|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000354792.5_Missense_Mutation_p.V335I			Q15746	MYLK_HUMAN	myosin light chain kinase	1535	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.V1535I(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		AGGACCATGACGATGTTGGCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	96	102					3																	123366087		2203	4300	6503	124848777	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.4603G>A	3.37:g.123366087C>T	ENSP00000418335:p.Val1535Ile		124848777	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.859367	0.91433	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.40767	0.1130	N	0.11341	0.13	0.53688	D	0.999972	P;D;D;D;P	0.60575	0.76;0.988;0.972;0.96;0.89	B;P;B;P;P	0.53912	0.364;0.593;0.309;0.737;0.705	T	0.45264	-0.9273	9	0.49607	T	0.09	.	19.3887	0.94570	0.0:1.0:0.0:0.0	.	1535;1466;1535;1466;1535	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	I	1535;1535;1535;1466;335;1535	ENSP00000354004:V1535I;ENSP00000353452:V1535I;ENSP00000352088:V1535I;ENSP00000320622:V1466I;ENSP00000346846:V335I;ENSP00000418335:V1535I	ENSP00000320622:V1466I	V	-	1	0	MYLK	124848777	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.071000	0.71229	2.571000	0.86741	0.655000	0.94253	GTC		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		T	123366087	C	T	123366087	3	4	40	1	0	0	0	0	1	0	0	0	10086	536	19	1	1173	1	MYLK	3	123366087	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	71915624	123366087	74656343	15	3700										
CP	84343	broad.mit.edu	37	chr3	148894089	148894089	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	attccagcatgaatgtggtcGgtcacatggcagtggagtaa	13	7	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr3:148894089G>A	ENST00000296051.2	+	0	4665				CP_ENST00000264613.6_Silent_p.T1043T	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3						organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.T1043T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			GAATGTGGTCGGTCACATGGC	0.383									Hermansky-Pudlak syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	3											125	115	118					3																	148894089		2203	4299	6502	150376779	SO:0001628	intergenic_variant	1356	Familial Cancer Database	HPS, HPS1-8	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548		3.37:g.148894089G>A			150376779	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																				0.383	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		A	148894089	G	A	148894089	1	1	40	0	1	0	0	0	0	0	0	0	3793	1103	39	1		1	CP	3	148894089	IGR	SNP	G	TCGA-AG-3878-01A-02W-0899-10	25528002	148894089	49128341	16	3701										
PIK3CA	5290	broad.mit.edu	37	chr3	178936092	178936092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tcctctctctgaaatcactgAgcaggagaaagattttctat	7	9	4	4	rs121913274		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr3:178936092A>G	ENST00000263967.3	+	10	1791	c.1634A>G	c.(1633-1635)gAg>gGg	p.E545G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545A(96)|p.E545G(78)|p.E545V(4)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAAATCACTGAGCAGGAGAAA	0.353	E545A(AGS_STOMACH)|E545G(KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	178	Substitution - Missense(178)	breast(40)|large_intestine(39)|ovary(30)|endometrium(17)|skin(9)|urinary_tract(8)|upper_aerodigestive_tract(4)|central_nervous_system(4)|oesophagus(4)|stomach(4)|liver(4)|thyroid(3)|soft_tissue(3)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|NS(1)|eye(1)|pancreas(1)|prostate(1)|pituitary(1)	3											61	61	61					3																	178936092		1813	4072	5885	180418786	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1634A>G	3.37:g.178936092A>G	ENSP00000263967:p.Glu545Gly		180418786	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704887	0.88924	.	.	ENSG00000121879	ENST00000263967	T	0.64438	-0.1	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77046	0.4073	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.76675	-0.2872	10	0.41790	T	0.15	-25.7963	16.1026	0.81194	1.0:0.0:0.0:0.0	.	545	P42336	PK3CA_HUMAN	G	545	ENSP00000263967:E545G	ENSP00000263967:E545G	E	+	2	0	PIK3CA	180418786	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936092	A	G	178936092	3	3	40	1	0	0	0	0	1	0	0	0	11944	304	11	4	1668	4	PIK3CA	3	178936092	Missense_Mutation	SNP	A	TCGA-AG-3878-01A-02W-0899-10	30042003	178936092	19086338	17	3702										
LYAR	55646	broad.mit.edu	37	chr4	4285362	4285362	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gcttaccagaaatctttaccGcagtcaatgcaagaaaggca	8	10	2	2	rs528236112		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:4285362G>A	ENST00000343470.4	-	3	348	c.108C>T	c.(106-108)tgC>tgT	p.C36C	LYAR_ENST00000452476.1_Silent_p.C36C	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	36						nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.C36C(1)		endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AATCTTTACCGCAGTCAATGC	0.393													G|||	1	0.000199681	0	0	5008	,	,		19333	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	4											91	82	85					4																	4285362		2203	4300	6503	4336263	SO:0001819	synonymous_variant	55646			AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.108C>T	4.37:g.4285362G>A			4336263	D3DVS4|Q6FI78|Q9NYS1	Silent	SNP	ENST00000343470.4	37	CCDS3374.1																																																																																				0.393	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		A	4285362	G	A	4285362	2	1	40	1	0	0	0	0	0	0	0	1	9133	1079	38	1		1	LYAR	4	4285362	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10		4285362	186868914	18	3703										
CEP135	9662	broad.mit.edu	37	chr4	56830455	56830455	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttcagattgagctaagagaaCgagagatagaacgactgtca	11	6	2	5			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:56830455C>T	ENST00000257287.4	+	7	839	c.715C>T	c.(715-717)Cga>Tga	p.R239*		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	239					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)	p.R239*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					GCTAAGAGAACGAGAGATAGA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											143	142	142					4																	56830455		2203	4300	6503	56525212	SO:0001587	stop_gained	9662			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.715C>T	4.37:g.56830455C>T	ENSP00000257287:p.Arg239*		56525212	B2RMY0|O75130|Q58F25|Q9H8H7	Nonsense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	C	38	6.869953	0.97901	.	.	ENSG00000174799	ENST00000257287	.	.	.	5.36	4.51	0.55191	.	0.505809	0.20650	N	0.088222	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	14.3209	0.66487	0.2835:0.7165:0.0:0.0	.	.	.	.	X	239	.	ENSP00000257287:R239X	R	+	1	2	CEP135	56525212	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	1.291000	0.33330	1.368000	0.46115	0.655000	0.94253	CGA		0.363	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56830455	C	T	56830455	4	4	40	1	0	0	0	0	0	1	0	0	3253	528	19	1	737	1	CEP135	4	56830455	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	52545093	56830455	134323821	19	3704										
ENAM	10117	broad.mit.edu	37	chr4	71508261	71508261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ggaacgtaaacaagtagctcGtccaggaaatccagtttatc	9	9	0	0	rs143134915		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:71508261G>A	ENST00000396073.3	+	9	1399	c.1118G>A	c.(1117-1119)cGt>cAt	p.R373H	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	373					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.R373H(2)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CAAGTAGCTCGTCCAGGAAAT	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	HIS/ARG	0,4406		0,0,2203	110	115	113		1118	-1.5	0	4	dbSNP_134	113	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ENAM	NM_031889.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	373/1143	71508261	1,13005	2203	4300	6503	71727125	SO:0001583	missense	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1118G>A	4.37:g.71508261G>A	ENSP00000379383:p.Arg373His		71727125	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	G	6.130	0.392297	0.11638	0.0	1.16E-4	ENSG00000132464	ENST00000396073	T	0.33216	1.42	5.83	-1.46	0.08800	.	0.946121	0.08814	N	0.889824	T	0.17789	0.0427	L	0.31752	0.955	0.09310	N	1	B	0.21753	0.06	B	0.20384	0.029	T	0.28364	-1.0046	10	0.41790	T	0.15	0.5722	1.9369	0.03339	0.3596:0.1205:0.3964:0.1236	.	373	Q9NRM1	ENAM_HUMAN	H	373	ENSP00000379383:R373H	ENSP00000379383:R373H	R	+	2	0	ENAM	71727125	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.433000	0.06948	-0.336000	0.08438	0.655000	0.94253	CGT		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		A	71508261	G	A	71508261	3	1	40	1	0	0	0	0	1	0	0	0	5125	1145	40	1	1148	1	ENAM	4	71508261	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	14677806	71508261	119646015	20	3705										
ADH1A	124	broad.mit.edu	37	chr4	100208722	100208722	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	atggaaaaatgtatttcaccTtaatacgaacttcatgggcc	7	8	2	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:100208722T>A	ENST00000209668.2	-	2	232	c.119A>T	c.(118-120)aAg>aTg	p.K40M	ADH1A_ENST00000511656.1_5'UTR|RP11-696N14.1_ENST00000500358.2_RNA	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide	40					alcohol metabolic process (GO:0006066)|drug metabolic process (GO:0017144)|ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)	p.K40M(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)	25				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Ethanol(DB00898)|Fomepizole(DB01213)	GTATTTCACCTTAATACGAAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											56	55	55					4																	100208722		2203	4300	6503	100427745	SO:0001630	splice_region_variant	124			M12963	CCDS3648.1	4q23	2009-12-04			ENSG00000187758	ENSG00000187758	1.1.1.1	"Alcohol dehydrogenases"	249	protein-coding gene	gene with protein product		103700		ADH1		3006456	Standard	NM_000667		Approved		uc003hur.2	P07327	OTTHUMG00000131026	ENST00000209668.2:c.120+1A>T	4.37:g.100208722T>A			100427745	A8K3E3|Q17R68	Missense_Mutation	SNP	ENST00000209668.2	37	CCDS3648.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.941830	0.73557	.	.	ENSG00000187758	ENST00000209668	T	0.04360	3.64	4.25	4.25	0.50352	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.35913	0.0948	H	0.98466	4.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59573	-0.7429	10	0.87932	D	0	-13.7977	13.3387	0.60533	0.0:0.0:0.0:1.0	.	40	P07327	ADH1A_HUMAN	M	40	ENSP00000209668:K40M	ENSP00000209668:K40M	K	-	2	0	ADH1A	100427745	1.000000	0.71417	0.997000	0.53966	0.797000	0.45037	7.162000	0.77515	1.532000	0.49169	0.377000	0.23210	AAG		0.343	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	NM_000667	Missense_Mutation	A	100208722	T	A	100208722	5	1	40	1	0	0	0	0	0	0	1	0	307	1623	56	5	1040	5	ADH1A	4	100208722	Splice_Site	SNP	T	TCGA-AG-3878-01A-02W-0899-10	28700461	100208722	90945554	21	3706										
TET2	54790	broad.mit.edu	37	chr4	106157490	106157490	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tattcaaaatcaagcgagttCgagactcataatgtccaaat	6	8	3	1	rs144220888		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:106157490C>T	ENST00000540549.1	+	3	3251	c.2391C>T	c.(2389-2391)ttC>ttT	p.F797F	TET2_ENST00000545826.1_Silent_p.F797F|TET2_ENST00000305737.2_Silent_p.F797F|TET2_ENST00000394764.1_Silent_p.F797F|TET2_ENST00000413648.2_Silent_p.F797F|TET2_ENST00000513237.1_Silent_p.F818F|TET2_ENST00000380013.4_Silent_p.F797F			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	797	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.F797F(2)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CAAGCGAGTTCGAGACTCATA	0.373			"Mis N, F"		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	2	Substitution - coding silent(2)	large_intestine(2)	4						C	,	4,4400	8.1+/-20.4	0,4,2198	57	61	60		2391,2391	4.1	1	4	dbSNP_134	60	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	TET2	NM_001127208.2,NM_017628.4	,	0,4,6497	TT,TC,CC		0.0,0.0908,0.0308	,	797/2003,797/1166	106157490	4,12998	2202	4299	6501	106376939	SO:0001819	synonymous_variant	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.2391C>T	4.37:g.106157490C>T			106376939	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																				0.373	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106157490	C	T	106157490	2	4	40	1	0	0	0	0	0	0	0	1	15809	883	31	1		1	TET2	4	106157490	Silent	SNP	C	TCGA-AG-3878-01A-02W-0899-10	5948768	106157490	84996786	22	3707										
SEC24B	10427	broad.mit.edu	37	chr4	110384789	110384789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ggctgtagcgaacaacaaccCaaccattactggtaggttga	10	10	0	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:110384789C>T	ENST00000265175.5	+	2	921	c.866C>T	c.(865-867)cCa>cTa	p.P289L	SEC24B_ENST00000504968.2_Missense_Mutation_p.P320L|SEC24B_ENST00000399100.2_Missense_Mutation_p.P289L	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	289					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.P289L(2)		breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		AACAACAACCCAACCATTACT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	4											65	64	64					4																	110384789		2013	4196	6209	110604238	SO:0001583	missense	10427			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.866C>T	4.37:g.110384789C>T	ENSP00000265175:p.Pro289Leu		110604238	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.799620	0.31869	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.79247	-1.07;-1.25;-1.24	5.57	4.73	0.59995	.	2.527880	0.01230	N	0.008326	T	0.70919	0.3279	N	0.24115	0.695	0.34675	D	0.724115	B;B;B;B	0.34290	0.0;0.0;0.447;0.0	B;B;B;B	0.32533	0.0;0.0;0.147;0.0	T	0.57376	-0.7822	10	0.46703	T	0.11	-5.5693	11.9041	0.52701	0.3344:0.6655:0.0:0.0	.	239;320;289;289	B4DTM6;B7ZKM8;O95487-2;O95487	.;.;.;SC24B_HUMAN	L	320;289;289	ENSP00000428564:P320L;ENSP00000382051:P289L;ENSP00000265175:P289L	ENSP00000265175:P289L	P	+	2	0	SEC24B	110604238	0.868000	0.29978	0.084000	0.20598	0.067000	0.16453	1.674000	0.37544	1.346000	0.45694	0.591000	0.81541	CCA		0.418	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			T	110384789	C	T	110384789	3	4	40	1	0	0	0	0	1	0	0	0	14032	594	21	3	872	3	SEC24B	4	110384789	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	4227299	110384789	80769487	23	3708										
AP1AR	55435	broad.mit.edu	37	chr4	113186912	113186912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	caggaccagaagatgacttcGaatcttgtttgagaaatatg	10	6	1	4			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:113186912G>A	ENST00000274000.5	+	8	818	c.463G>A	c.(463-465)Gaa>Aaa	p.E155K	AP1AR_ENST00000309703.6_Missense_Mutation_p.E122K	NM_018569.4	NP_061039.3	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated regulatory protein	155					cellular protein localization (GO:0034613)|negative regulation of cell motility (GO:2000146)|negative regulation of receptor recycling (GO:0001920)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|transport vesicle (GO:0030133)	AP-1 adaptor complex binding (GO:0035650)|kinesin binding (GO:0019894)	p.E155K(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	9						AGATGACTTCGAATCTTGTTT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	76	75					4																	113186912		2202	4295	6497	113406361	SO:0001583	missense	55435			AL136628	CCDS3696.1, CCDS47125.1	4q25	2009-09-28	2009-09-25	2009-09-25	ENSG00000138660	ENSG00000138660			28808	protein-coding gene	gene with protein product	"gamma1-adaptin brefeldin A resistance"	610851	"chromosome 4 open reading frame 16"	C4orf16		15775984	Standard	NM_018569		Approved	PRO0971, 2C18, gamma-BAR	uc003iaj.4	Q63HQ0	OTTHUMG00000132849	ENST00000274000.5:c.463G>A	4.37:g.113186912G>A	ENSP00000274000:p.Glu155Lys		113406361	B2RCV7|Q96GG6|Q9H0V0|Q9P1L4	Missense_Mutation	SNP	ENST00000274000.5	37	CCDS3696.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.412879	0.83340	.	.	ENSG00000138660	ENST00000274000;ENST00000309703	T;T	0.56776	0.44;0.57	5.99	5.99	0.97316	.	0.146987	0.64402	D	0.000010	T	0.51398	0.1672	L	0.50333	1.59	0.49798	D	0.999821	P;P	0.52577	0.954;0.954	B;B	0.39840	0.311;0.311	T	0.57843	-0.7741	10	0.72032	D	0.01	-11.418	20.4777	0.99188	0.0:0.0:1.0:0.0	.	122;155	Q63HQ0-2;Q63HQ0	.;AP1AR_HUMAN	K	155;122	ENSP00000274000:E155K;ENSP00000309023:E122K	ENSP00000274000:E155K	E	+	1	0	AP1AR	113406361	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.689000	0.61723	2.840000	0.97914	0.655000	0.94253	GAA		0.289	AP1AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256323.2	NM_018569		A	113186912	G	A	113186912	3	1	40	1	0	0	0	0	1	0	0	0	730	1059	37	1	493	1	AP1AR	4	113186912	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	2802123	113186912	77967364	24	3709										
FAT4	79633	broad.mit.edu	37	chr4	126411514	126411514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctgccatcgtgggcagctgcGcaaccgtcttggccctcctg	12	16	1	0	rs369929089		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr4:126411514G>A	ENST00000394329.3	+	17	13550	c.13537G>A	c.(13537-13539)Gca>Aca	p.A4513T	FAT4_ENST00000335110.5_Missense_Mutation_p.A2754T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4513					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A4456T(1)|p.A4513T(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGGCAGCTGCGCAACCGTCTT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	63	62	63		13537	5.2	0.2	4		63	0,8600		0,0,4300	no	missense	FAT4	NM_024582.4	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	4513/4982	126411514	1,13005	2203	4300	6503	126630964	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13537G>A	4.37:g.126411514G>A	ENSP00000377862:p.Ala4513Thr		126630964	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419827	0.83559	2.27E-4	0.0	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.78816	-0.98;-1.21	5.17	5.17	0.71159	.	0.000000	0.34110	U	0.004259	D	0.86301	0.5900	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	D	0.84986	0.0891	10	0.35671	T	0.21	.	17.6678	0.88208	0.0:0.0:1.0:0.0	.	2754;4513;4512	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	T	4513;2754	ENSP00000377862:A4513T;ENSP00000335169:A2754T	ENSP00000335169:A2754T	A	+	1	0	FAT4	126630964	1.000000	0.71417	0.156000	0.22583	0.945000	0.59286	9.502000	0.97981	2.395000	0.81488	0.561000	0.74099	GCA		0.567	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126411514	G	A	126411514	3	1	40	1	0	0	0	0	1	0	0	0	5711	1087	38	1	13603	1	FAT4	4	126411514	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	13224602	126411514	64742762	25	3710										
RIOK2	55781	broad.mit.edu	37	chr5	96498917	96498917	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	caactgacgtttcaccttctGtttcaccagttcctggaaag	7	12	3	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr5:96498917G>A	ENST00000283109.3	-	10	1575	c.1507C>T	c.(1507-1509)Cag>Tag	p.Q503*	CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	503	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.Q503*(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		TTCACCTTCTGTTTCACCAGT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											106	94	98					5																	96498917		2202	4299	6501	96524673	SO:0001587	stop_gained	55781			AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"RIO kinase 2 (yeast)"				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1507C>T	5.37:g.96498917G>A	ENSP00000283109:p.Gln503*		96524673	D6RDI3|Q9NUT0	Nonsense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.1|22.1	4.240904|4.240904	0.79912|0.79912	.|.	.|.	ENSG00000058729|ENSG00000058729	ENST00000283109|ENST00000511293	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.116786|.	0.64402|.	D|.	0.000014|.	.|T	.|0.71350	.|0.3329	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69691	.|-0.5077	.|4	0.09843|.	T|.	0.71|.	-10.1184|-10.1184	15.0797|15.0797	0.72106|0.72106	0.0:0.0:0.8576:0.1424|0.0:0.0:0.8576:0.1424	.|.	.|.	.|.	.|.	X|I	503|109	.|.	ENSP00000283109:Q503X|.	Q|T	-|-	1|2	0|0	RIOK2|RIOK2	96524673|96524673	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.491000|4.491000	0.60326|0.60326	2.605000|2.605000	0.88082|0.88082	0.655000|0.655000	0.94253|0.94253	CAG|ACA		0.343	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343		A	96498917	G	A	96498917	4	1	40	1	0	0	0	0	0	1	0	0	13415	1386	48	3	155	3	RIOK2	5	96498917	Nonsense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10		96498917	84416343	26	3711										
APC	324	broad.mit.edu	37	chr5	112170691	112170691	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gagtgccttatggaatttgtCagcacattgcactgagaata	10	7	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr5:112170691C>G	ENST00000457016.1	+	15	2167	c.1787C>G	c.(1786-1788)tCa>tGa	p.S596*	APC_ENST00000257430.4_Nonsense_Mutation_p.S596*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.S596*			P25054	APC_HUMAN	adenomatous polyposis coli	596	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S596*(3)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGAATTTGTCAGCACATTGC	0.388		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Substitution - Nonsense(3)|Unknown(1)	large_intestine(3)|skin(1)	5	GRCh37	CM056295	APC	M							194	160	172					5																	112170691		2202	4300	6502	112198590	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1787C>G	5.37:g.112170691C>G	ENSP00000413133:p.Ser596*		112198590	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	7.218231	0.98143	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.4015	20.3409	0.98764	0.0:1.0:0.0:0.0	.	.	.	.	X	596;578;596;596;596	.	ENSP00000257430:S596X	S	+	2	0	APC	112198590	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.814000	0.96858	0.655000	0.94253	TCA		0.388	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112170691	C	G	112170691	4	3	40	1	0	0	0	0	0	1	0	0	763	838	29	5	1841	5	APC	5	112170691	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	15671774	112170691	68744569	27	3712										
DMXL1	1657	broad.mit.edu	37	chr5	118468902	118468902	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctgtgataaaatggtaccaaActcaagttttacatcattat	5	7	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr5:118468902A>C	ENST00000311085.8	+	11	1471	c.1391A>C	c.(1390-1392)aAc>aCc	p.N464T	DMXL1_ENST00000539542.1_Missense_Mutation_p.N464T	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	464								p.N464T(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		ATGGTACCAAACTCAAGTTTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											137	131	133					5																	118468902		2202	4300	6502	118496801	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1391A>C	5.37:g.118468902A>C	ENSP00000309690:p.Asn464Thr		118496801		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.597909	0.00857	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.44482	0.92;0.92;2.67	5.32	-0.886	0.10590	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.652897	0.16636	N	0.205876	T	0.16727	0.0402	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.13407	0.009;0.001	T	0.29212	-1.0019	10	0.09843	T	0.71	-0.7233	7.1146	0.25409	0.5407:0.1159:0.3434:0.0	.	464;464	F5H269;Q9Y485	.;DMXL1_HUMAN	T	464	ENSP00000427692:N464T;ENSP00000309690:N464T;ENSP00000439479:N464T	ENSP00000309690:N464T	N	+	2	0	DMXL1	118496801	0.795000	0.28851	0.727000	0.30756	0.085000	0.17905	1.782000	0.38654	0.060000	0.16281	0.482000	0.46254	AAC		0.343	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118468902	A	C	118468902	3	2	40	1	0	0	0	0	1	0	0	0	4605	43	2	4	1433	4	DMXL1	5	118468902	Missense_Mutation	SNP	A	TCGA-AG-3878-01A-02W-0899-10	6298211	118468902	62446358	28	3713										
KIAA0141	9812	broad.mit.edu	37	chr5	141318178	141318178	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ccctgctagcaggaacctcaCgcctaccacatgcctcgagc	8	18	1	0	rs10056676	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr5:141318178C>T	ENST00000432126.2	+	12	1536	c.1402C>T	c.(1402-1404)Cgc>Tgc	p.R468C	KIAA0141_ENST00000194118.4_Missense_Mutation_p.R468C	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	468			R -> C (in dbSNP:rs10056676).		extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)		p.R468C(1)		endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAACCTCACGCCTACCACA	0.612													C|||	18	0.00359425	0.0121	0.0029	5008	,	,		18657	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	CYS/ARG,CYS/ARG	71,4335	64.7+/-102.0	0,71,2132	117	112	114		1402,1402	-4	0	5	dbSNP_119	114	0,8600		0,0,4300	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	180,180	0,71,6432	TT,TC,CC		0.0,1.6114,0.5459	benign,benign	468/516,468/516	141318178	71,12935	2203	4300	6503	141298362	SO:0001583	missense	9812			BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1402C>T	5.37:g.141318178C>T	ENSP00000396225:p.Arg468Cys		141298362	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	5.470	0.271844	0.10349	0.016114	0.0	ENSG00000081791	ENST00000432126;ENST00000194118	T;T	0.12361	2.69;2.69	5.11	-4.02	0.04034	.	1.226240	0.05604	N	0.576815	T	0.01905	0.0060	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35649	-0.9780	10	0.51188	T	0.08	2.1945	2.346	0.04271	0.1049:0.1918:0.271:0.4323	rs10056676;rs52806441;rs10056676	468	Q14154	DELE_HUMAN	C	468	ENSP00000396225:R468C;ENSP00000194118:R468C	ENSP00000194118:R468C	R	+	1	0	KIAA0141	141298362	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-2.209000	0.01228	-1.244000	0.02516	-0.140000	0.14226	CGC		0.612	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141318178	C	T	141318178	3	4	40	1	0	0	0	0	1	0	0	0	8177	536	19	1	1448	1	KIAA0141	5	141318178	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	22849276	141318178	39597082	29	3714										
GABRB2	2561	broad.mit.edu	37	chr5	160757890	160757890	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ggcttgccctctgaatttacCttgttgacatccaggcgcat	9	12	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr5:160757890C>A	ENST00000393959.1	-	8	1076	c.1077G>T	c.(1075-1077)aaG>aaT	p.K359N	GABRB2_ENST00000353437.6_Splice_Site_p.K359N|GABRB2_ENST00000517901.1_Splice_Site_p.K296N|GABRB2_ENST00000520240.1_Splice_Site_p.K359N|GABRB2_ENST00000274547.2_Splice_Site_p.K359N|GABRB2_ENST00000517547.1_Splice_Site_p.K199N			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	359					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.K359N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	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)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGAATTTACCTTGTTGACAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	5											111	112	112					5																	160757890		2203	4300	6503	160690468	SO:0001630	splice_region_variant	2561				CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1077+1G>T	5.37:g.160757890C>A			160690468	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	37	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829802	0.91036	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	D;D;D;D;D;D	0.87029	-2.2;-2.2;-1.81;-1.81;-1.81;-1.81	5.26	5.26	0.73747	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.64402	D	0.000008	D	0.83266	0.5217	N	0.17248	0.465	0.80722	D	1	P;P;B;P	0.41008	0.642;0.607;0.254;0.735	B;B;B;P	0.46585	0.258;0.41;0.201;0.521	T	0.81682	-0.0822	9	.	.	.	.	18.8686	0.92303	0.0:1.0:0.0:0.0	.	199;296;359;359	B7Z279;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	N	359;359;359;359;296;199	ENSP00000377531:K359N;ENSP00000274547:K359N;ENSP00000274546:K359N;ENSP00000429320:K359N;ENSP00000430532:K296N;ENSP00000429750:K199N	.	K	-	3	2	GABRB2	160690468	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.524000	0.81866	2.451000	0.82905	0.563000	0.77884	AAG		0.488	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1		Missense_Mutation	A	160757890	C	A	160757890	5	1	40	1	0	0	0	0	0	0	1	0	6186	695	24	2	473	2	GABRB2	5	160757890	Splice_Site	SNP	C	TCGA-AG-3878-01A-02W-0899-10	19439712	160757890	20157370	30	3715										
PGBD1	84547	broad.mit.edu	37	chr6	28269508	28269508	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gtatccctatcacctgtgttTtgatagcttctttacaagtg	7	9	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr6:28269508T>G	ENST00000405948.2	+	7	2297	c.1877T>G	c.(1876-1878)tTt>tGt	p.F626C	PGBD1_ENST00000259883.3_Missense_Mutation_p.F626C	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	626						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F626C(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						CACCTGTGTTTTGATAGCTTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											151	148	149					6																	28269508		2203	4300	6503	28377487	SO:0001583	missense	84547			D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1877T>G	6.37:g.28269508T>G	ENSP00000385213:p.Phe626Cys		28377487	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.879874	0.51801	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.19669	2.13;2.13	4.66	4.66	0.58398	.	0.000000	0.37761	N	0.001945	T	0.31575	0.0801	M	0.73962	2.25	0.33197	D	0.551638	D	0.56035	0.974	D	0.67548	0.952	T	0.19484	-1.0304	10	0.54805	T	0.06	-15.7673	10.6791	0.45804	0.0:0.0:0.0:1.0	.	626	Q96JS3	PGBD1_HUMAN	C	626	ENSP00000385213:F626C;ENSP00000259883:F626C	ENSP00000259883:F626C	F	+	2	0	PGBD1	28377487	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.339000	0.59322	2.087000	0.62958	0.533000	0.62120	TTT		0.433	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			G	28269508	T	G	28269508	3	3	40	1	0	0	0	0	1	0	0	0	11811	1841	64	4	1899	4	PGBD1	6	28269508	Missense_Mutation	SNP	T	TCGA-AG-3878-01A-02W-0899-10		28269508	142845559	31	3716										
PTK7	5754	broad.mit.edu	37	chr6	43111358	43111358	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cagagatggaatgcctcaacGgtgaggggccctggacgggg	18	9	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr6:43111358G>A	ENST00000230419.4	+	14	2472	c.2251G>A	c.(2251-2253)Ggt>Agt	p.G751S	PTK7_ENST00000481273.1_Splice_Site_p.G759S|PTK7_ENST00000345201.2_Splice_Site_p.G711S|PTK7_ENST00000349241.2_Splice_Site_p.G621S|PTK7_ENST00000352931.2_Splice_Site_p.G695S	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	751					actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G751S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			ATGCCTCAACGGTGAGGGGCC	0.682											OREG0017450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	6											21	20	20					6																	43111358		2203	4300	6503	43219336	SO:0001630	splice_region_variant	5754			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2251+1G>A	6.37:g.43111358G>A		913	43219336	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	SNP	ENST00000230419.4	37	CCDS4884.1	.	.	.	.	.	.	.	.	.	.	G	35	5.544043	0.96488	.	.	ENSG00000112655	ENST00000230419;ENST00000349241;ENST00000352931;ENST00000345201;ENST00000481273	T;T;T;T;T	0.73897	-0.69;-0.79;-0.66;-0.71;-0.71	5.51	5.51	0.81932	.	0.051101	0.85682	D	0.000000	D	0.82692	0.5092	M	0.70595	2.14	0.80722	D	1	P;D;D;D;D	0.89917	0.883;0.984;1.0;0.992;1.0	B;P;D;P;D	0.76575	0.195;0.864;0.988;0.864;0.984	T	0.83146	-0.0106	10	0.52906	T	0.07	.	16.607	0.84832	0.0:0.0:1.0:0.0	.	759;621;711;695;751	E9PFZ5;Q13308-3;Q13308-2;Q13308-4;Q13308	.;.;.;.;PTK7_HUMAN	S	751;621;695;711;759	ENSP00000230419:G751S;ENSP00000325462:G621S;ENSP00000326029:G695S;ENSP00000325992:G711S;ENSP00000418754:G759S	ENSP00000230418:G751S	G	+	1	0	PTK7	43219336	1.000000	0.71417	0.991000	0.47740	0.808000	0.45660	9.317000	0.96327	2.593000	0.87608	0.655000	0.94253	GGT		0.682	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		Missense_Mutation	A	43111358	G	A	43111358	5	1	40	1	0	0	0	0	0	0	1	0	12800	1130	39	1	2305	1	PTK7	6	43111358	Splice_Site	SNP	G	TCGA-AG-3878-01A-02W-0899-10	14841850	43111358	128003709	32	3717										
UTRN	7402	broad.mit.edu	37	chr6	144780475	144780475	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	aggctgtagaggatcgtcaaCaacatctagagaatggtaaa	11	6	2	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr6:144780475C>G	ENST00000367545.3	+	20	2692	c.2692C>G	c.(2692-2694)Caa>Gaa	p.Q898E		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	898	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.Q898E(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GGATCGTCAACAACATCTAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	67	67					6																	144780475		2203	4300	6503	144822168	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2692C>G	6.37:g.144780475C>G	ENSP00000356515:p.Gln898Glu		144822168	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	4.939	0.174366	0.09391	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.34472	1.36	5.44	1.16	0.20824	.	0.448236	0.18750	N	0.132209	T	0.11836	0.0288	L	0.32530	0.975	0.25797	N	0.984556	B	0.24882	0.113	B	0.20767	0.031	T	0.23583	-1.0184	10	0.62326	D	0.03	.	11.4709	0.50268	0.4481:0.4424:0.1096:0.0	.	898	P46939	UTRO_HUMAN	E	898	ENSP00000356515:Q898E	ENSP00000356499:Q898E	Q	+	1	0	UTRN	144822168	0.100000	0.21855	0.014000	0.15608	0.010000	0.07245	0.480000	0.22244	0.291000	0.22468	-0.188000	0.12872	CAA		0.453	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144780475	C	G	144780475	3	3	40	1	0	0	0	0	1	0	0	0	17143	479	17	5	2770	5	UTRN	6	144780475	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	101669117	144780475	26334592	33	3718										
DAGLB	221955	broad.mit.edu	37	chr7	6476076	6476076	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	acccaggcagcccccagagaGgcccagaccatctctggaaa	10	16	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr7:6476076G>A	ENST00000297056.6	-	3	505	c.336C>T	c.(334-336)gcC>gcT	p.A112A	DAGLB_ENST00000436575.1_Silent_p.A71A|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000428902.2_Intron|DAGLB_ENST00000425398.2_Silent_p.A112A|DAGLB_ENST00000479922.2_5'UTR	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	112					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A112A(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		CCCCCAGAGAGGCCCAGACCA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	7											100	100	100					7																	6476076		2203	4300	6503	6442601	SO:0001819	synonymous_variant	221955			AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.336C>T	7.37:g.6476076G>A			6442601	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																				0.532	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		A	6476076	G	A	6476076	2	1	40	1	0	0	0	0	0	0	0	1	4233	987	35	3		3	DAGLB	7	6476076	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10		6476076	152662587	34	3719										
GNAI1	2770	broad.mit.edu	37	chr7	79840384	79840384	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgtgtagcactgagtgactaCgacctggttctagctgaaga	12	8	1	4	rs71555062	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr7:79840384C>T	ENST00000351004.3	+	6	1063	c.690C>T	c.(688-690)taC>taT	p.Y230Y	GNAI1_ENST00000457358.2_Silent_p.Y178Y	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	230					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.Y230Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						TGAGTGACTACGACCTGGTTC	0.443													C|||	2	0.000399361	0	0.0014	5008	,	,		16716	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C		0,4406		0,0,2203	133	109	117		690	1.7	1	7	dbSNP_130	117	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	GNAI1	NM_002069.5		0,19,6484	TT,TC,CC		0.2209,0.0,0.1461		230/355	79840384	19,12987	2203	4300	6503	79678320	SO:0001819	synonymous_variant	2770			AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.690C>T	7.37:g.79840384C>T			79678320	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																				0.443	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		T	79840384	C	T	79840384	2	4	40	1	0	0	0	0	0	0	0	1	6524	547	19	1		1	GNAI1	7	79840384	Silent	SNP	C	TCGA-AG-3878-01A-02W-0899-10	73364308	79840384	79298279	35	3720										
ZKSCAN1	7586	broad.mit.edu	37	chr7	99631011	99631011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	catcacgcggggagacaacaGgaagatcccagaaagagttt	12	9	1	4			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr7:99631011G>A	ENST00000324306.6	+	6	1117	c.883G>A	c.(883-885)Gga>Aga	p.G295R	ZKSCAN1_ENST00000535170.1_Missense_Mutation_p.G82R|ZKSCAN1_ENST00000426572.1_Missense_Mutation_p.G259R	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	295	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G295R(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GGAGACAACAGGAAGATCCCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											68	71	70					7																	99631011		2203	4300	6503	99468947	SO:0001583	missense	7586			X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"Zinc fingers, C2H2-type", "-", "-", "-"	13101	protein-coding gene	gene with protein product		601260	"zinc finger protein 36 (KOX 18)"	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.883G>A	7.37:g.99631011G>A	ENSP00000323148:p.Gly295Arg		99468947	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	ENST00000324306.6	37	CCDS34698.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.835130	0.32421	.	.	ENSG00000106261	ENST00000324306;ENST00000426572;ENST00000535170	T;T;T	0.07908	3.27;3.23;3.15	5.64	3.8	0.43715	Krueppel-associated box (1);	0.123556	0.37095	N	0.002246	T	0.06188	0.0160	N	0.22421	0.69	0.40536	D	0.980974	B	0.24533	0.105	B	0.23150	0.044	T	0.30475	-0.9977	10	0.51188	T	0.08	.	8.9863	0.35997	0.0805:0.1502:0.7693:0.0	.	295	P17029	ZKSC1_HUMAN	R	295;259;82	ENSP00000323148:G295R;ENSP00000409172:G259R;ENSP00000443508:G82R	ENSP00000323148:G295R	G	+	1	0	ZKSCAN1	99468947	0.000000	0.05858	0.289000	0.24876	0.042000	0.13812	0.744000	0.26245	0.894000	0.36317	0.650000	0.86243	GGA		0.463	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		A	99631011	G	A	99631011	3	1	40	1	0	0	0	0	1	0	0	0	17725	1001	35	3	901	3	ZKSCAN1	7	99631011	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	19790627	99631011	59507652	36	3721										
OR9A4	130075	broad.mit.edu	37	chr7	141619594	141619594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cccttcgggatggggtgaaaCgctgctgtcaactattcagg	13	10	2	1	rs540557231		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr7:141619594C>T	ENST00000548136.1	+	1	978	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R307C(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					TGGGGTGAAACGCTGCTGTCA	0.423													C|||	1	0.000199681	0	0	5008	,	,		20070	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	7											95	96	96					7																	141619594		2051	4235	6286	141266063	SO:0001583	missense	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.919C>T	7.37:g.141619594C>T	ENSP00000448789:p.Arg307Cys		141266063	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	37	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	C	7.805	0.714374	0.15306	.	.	ENSG00000258083	ENST00000548136	T	0.35048	1.33	3.71	0.723	0.18231	.	.	.	.	.	T	0.27384	0.0672	L	0.42008	1.315	0.09310	N	1	B	0.16603	0.018	B	0.15870	0.014	T	0.27262	-1.0079	9	0.72032	D	0.01	-0.0715	5.0256	0.14383	0.2739:0.543:0.0:0.1831	.	307	Q8NGU2	OR9A4_HUMAN	C	307	ENSP00000448789:R307C	ENSP00000386148:R307C	R	+	1	0	OR9A4	141266063	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.007000	0.12810	-0.207000	0.10187	-1.094000	0.02160	CGC		0.423	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		T	141619594	C	T	141619594	3	4	40	1	0	0	0	0	1	0	0	0	11280	536	19	1	921	1	OR9A4	7	141619594	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	41988583	141619594	17519069	37	3722										
CSMD1	64478	broad.mit.edu	37	chr8	2823354	2823354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tttggtacagcgaatagtggCggatgtgactgcttccatga	13	7	0	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr8:2823354C>T	ENST00000520002.1	-	60	9781	c.9226G>A	c.(9226-9228)Gcc>Acc	p.A3076T	CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Missense_Mutation_p.A3076T|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000537824.1_Missense_Mutation_p.A3075T|CSMD1_ENST00000602723.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3076	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.A3075T(1)|p.A2804T(1)		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)		CGAATAGTGGCGGATGTGACT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	8											64	75	72					8																	2823354		2061	4207	6268	2810761	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9226G>A	8.37:g.2823354C>T	ENSP00000430733:p.Ala3076Thr		2810761	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.331|2.331	-0.353339|-0.353339	0.05173|0.05173	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000520002;ENST00000318252;ENST00000537824|ENST00000335551	T;T|.	0.65916|.	-0.18;-0.18|.	5.42|5.42	-10.8|-10.8	0.00216|0.00216	Complement control module (2);Sushi/SCR/CCP (3);|.	1.204620|.	0.05789|.	N|.	0.609964|.	T|T	0.17704|0.17704	0.0425|0.0425	L|L	0.28556|0.28556	0.865|0.865	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.13407|.	0.001;0.009|.	T|T	0.07121|0.07121	-1.0789|-1.0789	10|5	0.14252|.	T|.	0.57|.	.|.	3.0968|3.0968	0.06312|0.06312	0.563:0.0925:0.2293:0.1152|0.563:0.0925:0.2293:0.1152	.|.	3076;3076|.	E5RIG2;Q96PZ7|.	.;CSMD1_HUMAN|.	T|H	3076;2937;3075|2492	ENSP00000430733:A3076T;ENSP00000441462:A3075T|.	ENSP00000320445:A2937T|.	A|R	-|-	1|2	0|0	CSMD1|CSMD1	2810761|2810761	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.021000|-0.021000	0.12504|0.12504	-3.028000|-3.028000	0.00267|0.00267	-0.181000|-0.181000	0.13052|0.13052	GCC|CGC		0.473	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2823354	C	T	2823354	3	4	40	1	0	0	0	0	1	0	0	0	3950	768	27	1	1519	1	CSMD1	8	2823354	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		2823354	143540668	38	3723										
CRISPLD1	83690	broad.mit.edu	37	chr8	75928888	75928888	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gtccatgacacccatgtccgGacaagatcagatgatagtag	10	10	1	4			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr8:75928888G>A	ENST00000262207.4	+	7	1284	c.816G>A	c.(814-816)cgG>cgA	p.R272R	CRISPLD1_ENST00000523524.1_Silent_p.R84R|CRISPLD1_ENST00000517786.1_Silent_p.R86R	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	272					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)		p.R272R(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			CCCATGTCCGGACAAGATCAG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	8											167	176	173					8																	75928888		2203	4300	6503	76091443	SO:0001819	synonymous_variant	83690			AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.816G>A	8.37:g.75928888G>A			76091443	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	37	CCDS6219.1																																																																																				0.393	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		A	75928888	G	A	75928888	2	1	40	1	0	0	0	0	0	0	0	1	3888	1161	41	3		3	CRISPLD1	8	75928888	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10	73105534	75928888	70435134	39	3724										
NIPAL2	79815	broad.mit.edu	37	chr8	99217377	99217377	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gatgctatcatgatgataaaCatgatatagaaaatggggta	10	3	1	4	rs148824821		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr8:99217377C>A	ENST00000341166.3	-	7	1008	c.753G>T	c.(751-753)atG>atT	p.M251I	NIPAL2_ENST00000430223.2_Missense_Mutation_p.M251I|NIPAL2_ENST00000520545.1_5'UTR	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	251						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)	p.M251I(1)		cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						TGATGATAAACATGATATAGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	8											101	97	98					8																	99217377		2203	4300	6503	99286553	SO:0001583	missense	79815			AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.753G>T	8.37:g.99217377C>A	ENSP00000339256:p.Met251Ile		99286553	A2RTY8	Missense_Mutation	SNP	ENST00000341166.3	37	CCDS6278.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049608	0.75846	.	.	ENSG00000104361	ENST00000430223;ENST00000341166	D;D	0.90069	-2.61;-2.61	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	D	0.91690	0.7373	M	0.82056	2.57	0.47547	D	0.999451	B;P	0.47191	0.1;0.891	B;P	0.48952	0.11;0.596	D	0.92923	0.6357	10	0.62326	D	0.03	-13.5324	15.5035	0.75719	0.0:1.0:0.0:0.0	.	251;251	A2RTY8;Q9H841	.;NPAL2_HUMAN	I	251	ENSP00000407087:M251I;ENSP00000339256:M251I	ENSP00000339256:M251I	M	-	3	0	NIPAL2	99286553	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.411000	0.80078	2.058000	0.61347	0.462000	0.41574	ATG		0.378	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759		A	99217377	C	A	99217377	3	1	40	1	0	0	0	0	1	0	0	0	10456	478	17	2	377	2	NIPAL2	8	99217377	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	23288489	99217377	47146645	40	3725										
ABRA	137735	broad.mit.edu	37	chr8	107782168	107782168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctccatgtccttctggcaggCggggtggcgactttggggca	16	11	1	0	rs140322632		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr8:107782168C>T	ENST00000311955.3	-	1	305	c.251G>A	c.(250-252)cGc>cAc	p.R84H		NM_139166.4	NP_631905.1			actin-binding Rho activating protein									p.R84H(1)		breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			TTCTGGCAGGCGGGGTGGCGA	0.547													C|||	1	0.000199681	0	0	5008	,	,		18664	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	96	96	96		251	-10.2	0	8	dbSNP_134	96	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABRA	NM_139166.4	29	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	benign	84/382	107782168	3,13003	2203	4300	6503	107851344	SO:0001583	missense	137735			AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.251G>A	8.37:g.107782168C>T	ENSP00000311436:p.Arg84His		107851344		Missense_Mutation	SNP	ENST00000311955.3	37	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	C	2.433	-0.330347	0.05314	4.54E-4	1.16E-4	ENSG00000174429	ENST00000311955	D	0.92858	-3.12	5.12	-10.2	0.00374	.	1.154450	0.06089	N	0.663379	T	0.74321	0.3701	N	0.08118	0	0.09310	N	1	P	0.44344	0.833	B	0.32289	0.143	T	0.76299	-0.3010	10	0.45353	T	0.12	.	5.6274	0.17490	0.1249:0.2087:0.0866:0.5798	.	84	Q8N0Z2	ABRA_HUMAN	H	84	ENSP00000311436:R84H	ENSP00000311436:R84H	R	-	2	0	ABRA	107851344	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.530000	0.06179	-3.777000	0.00108	-0.910000	0.02820	CGC		0.547	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		T	107782168	C	T	107782168	3	4	40	1	0	0	0	0	1	0	0	0	100	768	27	1	902	1	ABRA	8	107782168	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	8564791	107782168	38581854	41	3726										
MAMDC2	256691	broad.mit.edu	37	chr9	72659528	72659528	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctcgccggtgccctcgacctGcccgctgggtcctgtgcctt	12	18	0	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr9:72659528G>T	ENST00000377182.4	+	2	680	c.63G>T	c.(61-63)ctG>ctT	p.L21L		NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	21					peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)	p.L21L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						CCCTCGACCTGCCCGCTGGGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	9											44	39	41					9																	72659528		2032	3907	5939	71849348	SO:0001819	synonymous_variant	256691			BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.63G>T	9.37:g.72659528G>T			71849348	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	37	CCDS6631.1																																																																																				0.617	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		T	72659528	G	T	72659528	2	4	40	1	0	0	0	0	0	0	0	1	9233	1306	46	2		2	MAMDC2	9	72659528	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10		72659528	68553903	42	3727										
FLJ46321	389763	broad.mit.edu	37	chr9	84606147	84606147	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctcccaccacatcacattgaGagagtggagtccagcctcca	8	15	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr9:84606147G>T	ENST00000344803.2	+	4	809	c.762G>T	c.(760-762)gaG>gaT	p.E254D		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	254					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.E254D(1)									ATCACATTGAGAGAGTGGAGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											261	241	247					9																	84606147		1927	4125	6052	83795967	SO:0001583	missense	389763				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.762G>T	9.37:g.84606147G>T	ENSP00000341988:p.Glu254Asp		83795967		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	7.851	0.724002	0.15439	.	.	ENSG00000214929	ENST00000344803	T	0.04758	3.56	2.96	1.06	0.20224	.	1.877400	0.02681	N	0.109670	T	0.02267	0.0070	N	0.02539	-0.55	0.09310	N	1	B	0.18610	0.029	B	0.14023	0.01	T	0.40720	-0.9548	10	0.13853	T	0.58	-0.0634	5.2593	0.15563	0.2836:0.0:0.7164:0.0	.	254	Q6ZQQ2	F75D1_HUMAN	D	254	ENSP00000341988:E254D	ENSP00000341988:E254D	E	+	3	2	FAM75D1	83795967	0.008000	0.16893	0.001000	0.08648	0.001000	0.01503	0.368000	0.20399	0.302000	0.22762	-0.145000	0.13849	GAG		0.517	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84606147	G	T	84606147	3	4	40	1	0	0	0	0	1	0	0	0	5951	933	33	2	776	2	FLJ46321	9	84606147	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	11946619	84606147	56607284	43	3728										
FGD3	89846	broad.mit.edu	37	chr9	95738899	95738900	+	Frame_Shift_Ins	INS	-	-	C													0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cagccaggtcccgaaggtcaINSccccccaggaggaggcggac							TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr9:95738899_95738900insC	ENST00000375482.3	+	3	857_858	c.361_362insC	c.(361-363)accfs	p.T121fs	FGD3_ENST00000337352.6_Frame_Shift_Ins_p.T121fs|FGD3_ENST00000416701.2_Frame_Shift_Ins_p.T121fs|FGD3_ENST00000468206.1_3'UTR	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	121					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.Q123fs*10(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						CCCGAAGGTCACCCCCCAGGAG	0.658																																																2	Insertion - Frameshift(2)	large_intestine(2)	9																																								94778721	SO:0001589	frameshift_variant	89846			AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.367dupC	9.37:g.95738905_95738905dupC	ENSP00000364631:p.Thr121fs		94778720	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Frame_Shift_Ins	INS	ENST00000375482.3	37	CCDS43849.1																																																																																				0.658	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		C	95738900	-	C	95738899	7	5	40	1	0	1	1	0	0	0	0	0	5853	159	6	0	363	0	FGD3	9	95738899	Frame_Shift_Ins	INS	-	TCGA-AG-3878-01A-02W-0899-10	11132752	95738899	45474532	44	3729										
DBC1	1620	broad.mit.edu	37	chr9	121971143	121971143	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttctgcaggtcccagtcattGccccagtgctgatggatgct	11	12	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr9:121971143G>T	ENST00000265922.3	-	7	1460	c.999C>A	c.(997-999)ggC>ggA	p.G333G	BRINP1_ENST00000482797.1_5'UTR	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	333					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.G333G(1)									CCCAGTCATTGCCCCAGTGCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	9											138	119	126					9																	121971143		2203	4300	6503	121010964	SO:0001819	synonymous_variant	1620			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.999C>A	9.37:g.121971143G>T			121010964	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																				0.542	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121971143	G	T	121971143	2	4	40	1	0	0	0	0	0	0	0	1	4253	1306	46	2		2	DBC1	9	121971143	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10	26232244	121971143	19242288	45	3730										
STRBP	55342	broad.mit.edu	37	chr9	125909188	125909188	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gatggtcctgaggcttcataTgttgtgccatccacatctac	9	11	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr9:125909188T>G	ENST00000348403.5	-	13	1713	c.1284A>C	c.(1282-1284)acA>acC	p.T428T	STRBP_ENST00000360998.3_Silent_p.T414T|STRBP_ENST00000447404.2_Silent_p.T428T	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	428	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.T428T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						AGGCTTCATATGTTGTGCCAT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	9											154	140	145					9																	125909188		2203	4300	6503	124949009	SO:0001819	synonymous_variant	55342			AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1284A>C	9.37:g.125909188T>G			124949009	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	ENST00000348403.5	37	CCDS6851.1																																																																																				0.438	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			G	125909188	T	G	125909188	2	3	40	1	0	0	0	0	0	0	0	1	15366	1451	51	4		4	STRBP	9	125909188	Silent	SNP	T	TCGA-AG-3878-01A-02W-0899-10	3938045	125909188	15304243	46	3731										
NRG3	10718	broad.mit.edu	37	chr10	84738833	84738833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gaccagcatatcagcaactcGaagaatcaaggatcccagac	8	12	2	2	rs564020344		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr10:84738833G>A	ENST00000404547.1	+	8	1540	c.1540G>A	c.(1540-1542)Gaa>Aaa	p.E514K	NRG3_ENST00000404576.2_Missense_Mutation_p.E318K|NRG3_ENST00000545131.1_Missense_Mutation_p.E164K|NRG3_ENST00000372142.2_Missense_Mutation_p.E293K|NRG3_ENST00000556918.1_Missense_Mutation_p.E344K|NRG3_ENST00000537893.1_Missense_Mutation_p.E164K|NRG3_ENST00000372141.2_Missense_Mutation_p.E514K			P56975	NRG3_HUMAN	neuregulin 3	514					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.E514K(2)|p.E293K(2)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TCAGCAACTCGAAGAATCAAG	0.493													G|||	1	0.000199681	0	0	5008	,	,		18551	0		0	False		,,,				2504	0.001															4	Substitution - Missense(4)	urinary_tract(2)|large_intestine(2)	10											109	91	97					10																	84738833		2203	4300	6503	84728813	SO:0001583	missense	10718			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1540G>A	10.37:g.84738833G>A	ENSP00000384796:p.Glu514Lys		84728813	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768186	0.90020	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.52295	1.44;1.27;1.28;0.67;0.67;0.67;0.67	5.79	5.79	0.91817	.	0.153130	0.44902	D	0.000403	T	0.64649	0.2617	L	0.50333	1.59	0.50313	D	0.999864	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.992;0.913;0.994;0.992	T	0.63875	-0.6538	10	0.59425	D	0.04	-0.0016	17.6117	0.88055	0.0:0.0:1.0:0.0	.	513;514;293;514	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	K	514;514;513;293;318;344;164;164	ENSP00000361214:E514K;ENSP00000384796:E514K;ENSP00000361215:E293K;ENSP00000385804:E318K;ENSP00000451376:E344K;ENSP00000441201:E164K;ENSP00000440377:E164K	ENSP00000361214:E514K	E	+	1	0	NRG3	84728813	0.998000	0.40836	0.960000	0.40013	0.761000	0.43186	2.977000	0.49297	2.759000	0.94783	0.558000	0.71614	GAA		0.493	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		A	84738833	G	A	84738833	3	1	40	1	0	0	0	0	1	0	0	0	10680	1059	37	1	1738	1	NRG3	10	84738833	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10		84738833	50795914	47	3732										
TLX1	3195	broad.mit.edu	37	chr10	102893975	102893975	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ccccccaagaagaagaagccGcgcacgtccttcacacgcct	8	18	1	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr10:102893975G>A	ENST00000370196.6	+	2	2654	c.612G>A	c.(610-612)ccG>ccA	p.P204P	TLX1_ENST00000467928.2_Silent_p.P204P|RP11-31L23.3_ENST00000411459.1_RNA			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	204					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.P204P(2)		breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AGAAGAAGCCGCGCACGTCCT	0.647			T	"TRB@, TRD@"	T-ALL																																		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	10											49	51	50					10																	102893975		2199	4297	6496	102883965	SO:0001819	synonymous_variant	3195			M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"Homeoboxes / ANTP class : NKL subclass"	5056	protein-coding gene	gene with protein product	"Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)", "homeo box 11 (T-cell lymphoma 3-associated breakpoint)"	186770	"homeo box 11 (T-cell lymphoma 3-associated breakpoint)", "T-cell leukemia, homeobox 1"	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.612G>A	10.37:g.102893975G>A			102883965	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Silent	SNP	ENST00000370196.6	37	CCDS7510.1																																																																																				0.647	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		A	102893975	G	A	102893975	2	1	40	1	0	0	0	0	0	0	0	1	15998	1074	38	1		1	TLX1	10	102893975	Silent	SNP	G	TCGA-AG-3878-01A-02W-0899-10	18155142	102893975	32640772	48	3733										
MS4A14	84689	broad.mit.edu	37	chr11	60183412	60183412	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgaagacttgccatcccaagCtctaccagtagaaggcctgt	9	12	1	3	rs139364741	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr11:60183412C>A	ENST00000300187.6	+	5	1248	c.971C>A	c.(970-972)gCt>gAt	p.A324D	MS4A14_ENST00000531787.1_Missense_Mutation_p.A212D|MS4A14_ENST00000531783.1_Missense_Mutation_p.A357D|MS4A14_ENST00000395005.2_Missense_Mutation_p.A307D|MS4A14_ENST00000395001.1_3'UTR	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	324						integral component of membrane (GO:0016021)		p.A324D(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CCATCCCAAGCTCTACCAGTA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											102	94	97					11																	60183412		2203	4300	6503	59939988	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.971C>A	11.37:g.60183412C>A	ENSP00000300187:p.Ala324Asp		59939988	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.281727	0.40394	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.33216	1.42;2.64;1.43;3.01	3.74	-0.28	0.12886	.	4.640210	0.00465	N	0.000117	T	0.37919	0.1021	L	0.27053	0.805	0.09310	N	1	D;D	0.65815	0.995;0.991	D;P	0.63877	0.919;0.831	T	0.19418	-1.0306	10	0.66056	D	0.02	-0.7115	3.6017	0.08027	0.0:0.4773:0.1912:0.3315	.	307;324	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	D	212;324;307;357	ENSP00000437222:A212D;ENSP00000300187:A324D;ENSP00000378453:A307D;ENSP00000433761:A357D	ENSP00000300187:A324D	A	+	2	0	MS4A14	59939988	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.274000	0.08537	-0.042000	0.13535	-0.182000	0.12963	GCT		0.468	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			A	60183412	C	A	60183412	3	1	40	1	0	0	0	0	1	0	0	0	9888	797	28	2	989	2	MS4A14	11	60183412	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		60183412	74823104	49	3734										
TMEM216	51259	broad.mit.edu	37	chr11	61161436	61161436	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	atcttggaattgaagtaattCgcctgttttttggtaagtgt	10	4	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr11:61161436C>A	ENST00000515837.2	+	3	1162	c.217C>A	c.(217-219)Cgc>Agc	p.R73S	TMEM216_ENST00000334888.5_Missense_Mutation_p.R73S|TMEM216_ENST00000398979.3_Missense_Mutation_p.R12S			Q9P0N5	TM216_HUMAN	transmembrane protein 216	73			R -> C (in JBTS2). {ECO:0000269|PubMed:20512146, ECO:0000269|PubMed:22282472}.|R -> H (in JBTS2 and MKS2). {ECO:0000269|PubMed:20512146, ECO:0000269|PubMed:22282472}.|R -> L (in JBTS2). {ECO:0000269|PubMed:20036350, ECO:0000269|PubMed:20512146, ECO:0000269|PubMed:22282472}.		cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.R73S(1)		endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TGAAGTAATTCGCCTGTTTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											204	198	200					11																	61161436		1928	4130	6058	60918012	SO:0001583	missense	51259				CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"cerebello-oculo-renal syndrome 2", "Meckel syndrome, type 2"	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.217C>A	11.37:g.61161436C>A	ENSP00000440638:p.Arg73Ser		60918012	A8MZ23|B7Z8N1	Missense_Mutation	SNP	ENST00000515837.2	37	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985216	0.74474	.	.	ENSG00000187049	ENST00000515837;ENST00000334888;ENST00000398979	D;D;D	0.94184	-3.37;-3.37;-3.37	5.95	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.96380	0.8819	M	0.86864	2.845	0.51767	D	0.999939	D;P	0.67145	0.996;0.924	D;P	0.66602	0.945;0.593	D	0.96215	0.9156	10	0.87932	D	0	-7.3836	11.5558	0.50748	0.2579:0.7421:0.0:0.0	.	66;12	Q9P0N5;Q9P0N5-2	TM216_HUMAN;.	S	73;73;12	ENSP00000440638:R73S;ENSP00000334844:R73S;ENSP00000381950:R12S	ENSP00000334844:R73S	R	+	1	0	TMEM216	60918012	0.579000	0.26725	0.185000	0.23176	0.881000	0.50899	0.878000	0.28126	2.824000	0.97209	0.655000	0.94253	CGC		0.403	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499		A	61161436	C	A	61161436	3	1	40	1	0	0	0	0	1	0	0	0	16178	884	31	2	227	2	TMEM216	11	61161436	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	978024	61161436	73845080	50	3735										
NTM	50863	broad.mit.edu	37	chr11	132177693	132177693	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	acgtggccgcgcccgtggtaCggagagtaaaggtcaccgtg	16	11	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr11:132177693C>T	ENST00000374786.1	+	4	1116	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W	NTM_ENST00000374791.3_Missense_Mutation_p.R213W|NTM_ENST00000374784.1_Missense_Mutation_p.R213W|NTM_ENST00000425719.2_Missense_Mutation_p.R213W|NTM_ENST00000427481.2_Missense_Mutation_p.R204W|NTM_ENST00000539799.1_Missense_Mutation_p.R213W|NTM_ENST00000474900.1_3'UTR	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	213	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R213W(2)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						GCCCGTGGTACGGAGAGTAAA	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	11											83	72	76					11																	132177693		2201	4297	6498	131682903	SO:0001583	missense	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.637C>T	11.37:g.132177693C>T	ENSP00000363918:p.Arg213Trp		131682903	A0MTT2|Q6UXJ3|Q86VJ9	De_novo_Start_OutOfFrame	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547537	0.65311	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.78	4.82	0.62117	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.046634	0.85682	D	0.000000	D	0.82852	0.5127	M	0.82433	2.59	0.49582	D	0.999802	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.81914	0.995;0.995;0.995;0.993;0.988;0.988	D	0.85003	0.0901	10	0.87932	D	0	-20.1674	16.8142	0.85729	0.1289:0.8711:0.0:0.0	.	213;204;213;213;213;213	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	W	213;213;204;213;213;213	ENSP00000363923:R213W;ENSP00000437668:R213W;ENSP00000416320:R204W;ENSP00000363918:R213W;ENSP00000396722:R213W;ENSP00000363916:R213W	ENSP00000363916:R213W	R	+	1	2	NTM	131682903	0.991000	0.36638	0.969000	0.41365	0.207000	0.24258	2.989000	0.49393	2.894000	0.99253	0.591000	0.81541	CGG		0.582	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		T	132177693	C	T	132177693	3	4	40	1	0	0	0	0	1	0	0	0	10730	527	19	1	737	1	NTM	11	132177693	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	71016257	132177693	2828823	51	3736										
LRP6	4040	broad.mit.edu	37	chr12	12397416	12397416	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	agttttgttaaattctgttcGtttaatggcttcttcgctga	8	6	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:12397416G>A	ENST00000261349.4	-	2	305	c.229C>T	c.(229-231)Cga>Tga	p.R77*	LRP6_ENST00000543091.1_Nonsense_Mutation_p.R77*	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	77	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R77*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AATTCTGTTCGTTTAATGGCT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											113	98	103					12																	12397416		2203	4300	6503	12288683	SO:0001587	stop_gained	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.229C>T	12.37:g.12397416G>A	ENSP00000261349:p.Arg77*		12288683	Q17RZ2	Nonsense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	37	6.195739	0.97367	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	.	.	.	5.04	5.04	0.67666	.	0.000000	0.43110	U	0.000609	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1892	0.59700	0.0:0.0:0.7209:0.2791	.	.	.	.	X	77	.	ENSP00000261349:R77X	R	-	1	2	LRP6	12288683	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.068000	0.50018	2.627000	0.88993	0.460000	0.39030	CGA		0.438	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12397416	G	A	12397416	4	1	40	1	0	0	0	0	0	1	0	0	8991	1153	40	1	4700	1	LRP6	12	12397416	Nonsense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10		12397416	121454479	52	3737										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	40	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	13000868	25398284	108453611	53	3738										
SFRS2IP	9169	broad.mit.edu	37	chr12	46315944	46315944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	aaccagatttgccactttagTagaatttacttctccactct	4	11	2	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:46315944T>C	ENST00000369367.3	-	15	4512	c.4279A>G	c.(4279-4281)Act>Gct	p.T1427A	SCAF11_ENST00000549162.1_Missense_Mutation_p.T1235A|SCAF11_ENST00000419565.2_Missense_Mutation_p.T1427A|SCAF11_ENST00000550629.1_Intron|SCAF11_ENST00000465950.1_Missense_Mutation_p.T1112A	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1427					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.T1427A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GCCACTTTAGTAGAATTTACT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	80	81					12																	46315944		2203	4300	6503	44602211	SO:0001583	missense	9169			Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.4279A>G	12.37:g.46315944T>C	ENSP00000358374:p.Thr1427Ala		44602211	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	6.998	0.554372	0.13374	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565	T;T;T;T	0.60424	0.19;2.36;0.19;2.36	5.12	-0.315	0.12746	.	0.331079	0.25344	N	0.031353	T	0.26484	0.0647	N	0.11560	0.145	0.23043	N	0.998386	B	0.17268	0.021	B	0.12156	0.007	T	0.19679	-1.0298	10	0.07030	T	0.85	-6.5488	5.1434	0.14971	0.1846:0.522:0.0:0.2933	.	1427	Q99590	SCAFB_HUMAN	A	1112;1427;1235;1427	ENSP00000449812:T1112A;ENSP00000358374:T1427A;ENSP00000448864:T1235A;ENSP00000413036:T1427A	ENSP00000358374:T1427A	T	-	1	0	SCAF11	44602211	0.764000	0.28473	0.997000	0.53966	0.999000	0.98932	0.469000	0.22067	0.065000	0.16485	0.533000	0.62120	ACT		0.373	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		C	46315944	T	C	46315944	3	2	40	1	0	0	0	0	1	0	0	0	14214	1638	57	4	116	4	SFRS2IP	12	46315944	Missense_Mutation	SNP	T	TCGA-AG-3878-01A-02W-0899-10	20917660	46315944	87535951	54	3739										
KRT84	3890	broad.mit.edu	37	chr12	52775176	52775176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	accaggcctcagcatcagccCggctgcgcctggccacctcc	10	20	2	0	rs113837792	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:52775176C>T	ENST00000257951.3	-	5	1112	c.1046G>A	c.(1045-1047)cGg>cAg	p.R349Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	349	Coil 2.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.R349Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGCATCAGCCCGGCTGCGCCT	0.572													C|||	2	0.000399361	0.0015	0	5008	,	,		19649	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	128	125	126		1046	4.5	1	12	dbSNP_132	126	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT84	NM_033045.3	43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	349/601	52775176	2,13004	2203	4300	6503	51061443	SO:0001583	missense	3890			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1046G>A	12.37:g.52775176C>T	ENSP00000257951:p.Arg349Gln		51061443	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	32	5.141118	0.94560	2.27E-4	1.16E-4	ENSG00000161849	ENST00000257951	T	0.75154	-0.91	5.41	4.51	0.55191	Filament (1);	0.000000	0.44285	D	0.000469	T	0.79845	0.4516	L	0.58101	1.795	0.30864	N	0.733259	D	0.69078	0.997	P	0.59012	0.85	T	0.79860	-0.1625	10	0.59425	D	0.04	.	11.8705	0.52517	0.0:0.8612:0.0:0.1388	.	349	Q9NSB2	KRT84_HUMAN	Q	349	ENSP00000257951:R349Q	ENSP00000257951:R349Q	R	-	2	0	KRT84	51061443	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	3.345000	0.52182	2.537000	0.85549	0.563000	0.77884	CGG		0.572	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		T	52775176	C	T	52775176	3	4	40	1	0	0	0	0	1	0	0	0	8519	652	23	1	776	1	KRT84	12	52775176	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	6459232	52775176	81076719	55	3740										
KRT74	121391	broad.mit.edu	37	chr12	52967420	52967420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tccaaggctatagaggctccGactgccaaagccagcgccag	11	14	0	1	rs569075312		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:52967420G>A	ENST00000305620.2	-	1	189	c.142C>T	c.(142-144)Cgg>Tgg	p.R48W	KRT74_ENST00000549343.1_Missense_Mutation_p.R48W	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	48	Gly-rich.|Head.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)	p.R48W(1)		kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		TAGAGGCTCCGACTGCCAAAG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	12											51	56	54					12																	52967420		2203	4300	6503	51253687	SO:0001583	missense	121391			BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"-", "Intermediate filaments type II, keratins (basic)"	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.142C>T	12.37:g.52967420G>A	ENSP00000307240:p.Arg48Trp		51253687	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.244369	0.22796	.	.	ENSG00000170484	ENST00000549343;ENST00000305620	T;T	0.44482	0.92;0.92	4.51	2.53	0.30540	.	0.551628	0.13621	N	0.374428	T	0.49064	0.1535	M	0.88704	2.975	0.09310	N	1	B	0.22983	0.078	B	0.20184	0.028	T	0.50406	-0.8832	10	0.87932	D	0	.	9.7644	0.40552	0.0:0.1141:0.4203:0.4655	.	48	Q7RTS7	K2C74_HUMAN	W	48	ENSP00000447447:R48W;ENSP00000307240:R48W	ENSP00000307240:R48W	R	-	1	2	KRT74	51253687	0.000000	0.05858	0.070000	0.20053	0.687000	0.40016	-0.184000	0.09698	0.515000	0.28320	0.561000	0.74099	CGG		0.597	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053		A	52967420	G	A	52967420	3	1	40	1	0	0	0	0	1	0	0	0	8508	1057	37	1	1483	1	KRT74	12	52967420	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	192244	52967420	80884475	56	3741										
SRGAP1	57522	broad.mit.edu	37	chr12	64383725	64383725	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gttgtctccagtgaactgctGgtatttgctcctgaaccaag	10	10	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr12:64383725G>A	ENST00000355086.3	+	3	823	c.299G>A	c.(298-300)tGg>tAg	p.W100*	SRGAP1_ENST00000543397.1_Nonsense_Mutation_p.W60*|SRGAP1_ENST00000357825.3_Nonsense_Mutation_p.W100*	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	100	F-BAR domain.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.W100*(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GTGAACTGCTGGTATTTGCTC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											162	142	149					12																	64383725		2203	4300	6503	62669992	SO:0001587	stop_gained	57522			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.299G>A	12.37:g.64383725G>A	ENSP00000347198:p.Trp100*		62669992	Q9H8A3|Q9P2P2	Nonsense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	50	16.970259	0.99876	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	.	.	.	5.61	5.61	0.85477	.	0.000000	0.33875	U	0.004466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0269	0.97525	0.0:0.0:1.0:0.0	.	.	.	.	X	100;100;60	.	.	W	+	2	0	SRGAP1	62669992	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.694000	0.98686	2.816000	0.96949	0.561000	0.74099	TGG		0.423	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64383725	G	A	64383725	4	1	40	1	0	0	0	0	0	1	0	0	15184	1357	47	3	309	3	SRGAP1	12	64383725	Nonsense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	11416305	64383725	69468170	57	3742										
FLT1	2321	broad.mit.edu	37	chr13	29041214	29041214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tttagttatgctcagcctttCgctttccttactcaccattt	4	12	2	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr13:29041214C>T	ENST00000282397.4	-	3	465	c.214G>A	c.(214-216)Gaa>Aaa	p.E72K	FLT1_ENST00000539099.1_Missense_Mutation_p.E72K|FLT1_ENST00000541932.1_Missense_Mutation_p.E72K	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	72	Ig-like C2-type 1.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.E72K(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTCAGCCTTTCGCTTTCCTTA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											206	190	196					13																	29041214		2203	4300	6503	27939214	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.214G>A	13.37:g.29041214C>T	ENSP00000282397:p.Glu72Lys		27939214	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	4.041	0.005280	0.07866	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000450836;ENST00000539099	T;T;T	0.63580	-0.05;-0.05;-0.05	5.7	-1.01	0.10169	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.477149	0.23690	N	0.045526	T	0.16342	0.0393	N	0.00230	-1.795	0.20926	N	0.999827	B;B;B;B;B	0.06786	0.001;0.001;0.0;0.001;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.0	T	0.39941	-0.9589	10	0.05525	T	0.97	.	5.517	0.16912	0.0:0.2063:0.2704:0.5233	.	72;72;72;72;72	P17948-4;P17948-3;B5A924;P17948-2;P17948	.;.;.;.;VGFR1_HUMAN	K	72	ENSP00000282397:E72K;ENSP00000437631:E72K;ENSP00000442630:E72K	ENSP00000282397:E72K	E	-	1	0	FLT1	27939214	0.512000	0.26186	0.231000	0.23993	0.880000	0.50808	0.141000	0.16076	-0.369000	0.08028	-1.027000	0.02421	GAA		0.438	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			T	29041214	C	T	29041214	3	4	40	1	0	0	0	0	1	0	0	0	5960	893	31	1	4177	1	FLT1	13	29041214	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		29041214	86128664	58	3743										
NBEA	26960	broad.mit.edu	37	chr13	36006464	36006464	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	atgatcttcgtcgaaggagaCgatttgttcgcaatgcattt	10	7	1	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr13:36006464C>T	ENST00000400445.3	+	39	6772	c.6238C>T	c.(6238-6240)Cga>Tga	p.R2080*	NBEA_ENST00000540320.1_Nonsense_Mutation_p.R2080*|NBEA_ENST00000310336.4_Nonsense_Mutation_p.R2080*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.R2077*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2080					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R2080*(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TCGAAGGAGACGATTTGTTCG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											121	108	112					13																	36006464		1904	4111	6015	34904464	SO:0001587	stop_gained	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6238C>T	13.37:g.36006464C>T	ENSP00000383295:p.Arg2080*		34904464	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	50	16.923632	0.99875	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	.	.	.	5.72	1.37	0.22104	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.3795	0.87401	0.5126:0.4874:0.0:0.0	.	.	.	.	X	2080;2080;2077;2080;707	.	ENSP00000308534:R2080X	R	+	1	2	NBEA	34904464	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	1.084000	0.30828	0.289000	0.22422	-0.181000	0.13052	CGA		0.393	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	36006464	C	T	36006464	4	4	40	1	0	0	0	0	0	1	0	0	10217	528	19	1	6392	1	NBEA	13	36006464	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	6965250	36006464	79163414	59	3744										
KCNH5	27133	broad.mit.edu	37	chr14	63473091	63473091	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ttgagatacctactgtttttCttgtacagaagaacttcaaa	6	7	2	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr14:63473091C>A	ENST00000322893.7	-	3	565	c.297G>T	c.(295-297)aaG>aaT	p.K99N	KCNH5_ENST00000420622.2_Missense_Mutation_p.K99N|KCNH5_ENST00000394968.1_Missense_Mutation_p.K41N|KCNH5_ENST00000394964.2_Missense_Mutation_p.K41N	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	99	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.K99N(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TACTGTTTTTCTTGTACAGAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	14											87	85	86					14																	63473091		2202	4299	6501	62542844	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.297G>T	14.37:g.63473091C>A	ENSP00000321427:p.Lys99Asn		62542844	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463220	0.63513	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.99652	-6.3;-6.3;-6.3;-6.3	5.35	2.26	0.28386	PAS-associated, C-terminal (1);PAS (1);PAS fold (1);	0.097389	0.64402	D	0.000001	D	0.99441	0.9802	M	0.86178	2.8	0.80722	D	1	P;D;D;D	0.57257	0.604;0.958;0.958;0.979	P;P;P;D	0.64410	0.524;0.682;0.682;0.925	D	0.99790	1.1031	10	0.87932	D	0	.	8.1947	0.31389	0.0:0.7192:0.0:0.2808	.	41;41;99;99	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	N	99;99;41;41	ENSP00000321427:K99N;ENSP00000395439:K99N;ENSP00000378419:K41N;ENSP00000378415:K41N	ENSP00000321427:K99N	K	-	3	2	KCNH5	62542844	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.596000	0.24044	0.197000	0.20387	0.655000	0.94253	AAG		0.338	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63473091	C	A	63473091	3	1	40	1	0	0	0	0	1	0	0	0	8056	912	32	2	2739	2	KCNH5	14	63473091	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		63473091	43876449	60	3745										
DYNC1H1	1778	broad.mit.edu	37	chr14	102461408	102461408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gatgctaggatcaaacatgaCggaattccattcccagatct	8	10	2	2	rs587780331		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr14:102461408C>T	ENST00000360184.4	+	14	3583	c.3419C>T	c.(3418-3420)aCg>aTg	p.T1140M		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1140	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.T1140M(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TCAAACATGACGGAATTCCAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											116	105	109					14																	102461408		2203	4300	6503	101531161	SO:0001583	missense	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3419C>T	14.37:g.102461408C>T	ENSP00000348965:p.Thr1140Met		101531161	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570587	0.65765	.	.	ENSG00000197102	ENST00000360184	T	0.77489	-1.1	5.84	5.84	0.93424	.	0.158283	0.56097	D	0.000021	T	0.68504	0.3008	L	0.36672	1.1	0.58432	D	0.999992	P	0.42556	0.783	B	0.30401	0.115	T	0.71530	-0.4565	10	0.46703	T	0.11	.	20.1346	0.98019	0.0:1.0:0.0:0.0	.	1140	Q14204	DYHC1_HUMAN	M	1140	ENSP00000348965:T1140M	ENSP00000348965:T1140M	T	+	2	0	DYNC1H1	101531161	1.000000	0.71417	0.966000	0.40874	0.979000	0.70002	4.877000	0.63086	2.763000	0.94921	0.557000	0.71058	ACG		0.453	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102461408	C	T	102461408	3	4	40	1	0	0	0	0	1	0	0	0	4852	536	19	1	3473	1	DYNC1H1	14	102461408	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	38988317	102461408	4888132	61	3746										
KLC1	3831	broad.mit.edu	37	chr14	104136612	104136612	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gtaaaagagctctggaaatcCgagaaaaggtacaaaagaag	11	5	1	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr14:104136612C>T	ENST00000348520.6	+	7	1298	c.979C>T	c.(979-981)Cga>Tga	p.R327*	KLC1_ENST00000246489.7_Nonsense_Mutation_p.R327*|KLC1_ENST00000452929.2_Nonsense_Mutation_p.R327*|KLC1_ENST00000554280.1_Nonsense_Mutation_p.R327*|KLC1_ENST00000557575.1_Nonsense_Mutation_p.R327*|KLC1_ENST00000334553.6_Nonsense_Mutation_p.R327*|KLC1_ENST00000347839.6_Nonsense_Mutation_p.R327*|KLC1_ENST00000445352.4_Nonsense_Mutation_p.R325*|KLC1_ENST00000389744.4_Nonsense_Mutation_p.R327*|KLC1_ENST00000553286.1_Nonsense_Mutation_p.R327*|KLC1_ENST00000557450.1_Nonsense_Mutation_p.R327*|KLC1_ENST00000380038.3_Nonsense_Mutation_p.R327*|RP11-73M18.2_ENST00000472726.2_Nonsense_Mutation_p.R499*|KLC1_ENST00000555836.1_Nonsense_Mutation_p.R327*	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	327					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R327*(2)	KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				TCTGGAAATCCGAGAAAAGGT	0.408																																																2	Substitution - Nonsense(2)	large_intestine(1)|NS(1)	14											77	86	83					14																	104136612		2203	4300	6503	103206365	SO:0001587	stop_gained	3831			AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"Tetratricopeptide (TTC) repeat domain containing"	6387	protein-coding gene	gene with protein product		600025	"kinesin 2 60/70kDa", "kinesin 2"	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.979C>T	14.37:g.104136612C>T	ENSP00000341154:p.Arg327*		103206365	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Nonsense_Mutation	SNP	ENST00000348520.6	37	CCDS41996.1	.	.	.	.	.	.	.	.	.	.	C	36	5.794577	0.96952	.	.	ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000256500	ENST00000348520;ENST00000443396;ENST00000380038;ENST00000389744;ENST00000557575;ENST00000553286;ENST00000347839;ENST00000555836;ENST00000334553;ENST00000246489;ENST00000557450;ENST00000554280;ENST00000452929;ENST00000445352;ENST00000472726	.	.	.	5.44	-6.85	0.01681	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0588	23.2919	0.99981	0.2014:0.7986:0.0:0.0	.	.	.	.	X	327;327;327;327;327;327;327;327;327;327;327;327;327;325;499	.	ENSP00000246489:R327X	R	+	1	2	KLC1;RP11-73M18.2	103206365	0.040000	0.19996	0.794000	0.32065	0.731000	0.41821	-0.497000	0.06428	-1.409000	0.02038	-0.485000	0.04761	CGA		0.408	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552		T	104136612	C	T	104136612	4	4	40	1	0	0	0	0	0	1	0	0	8354	644	23	1	1001	1	KLC1	14	104136612	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	1675204	104136612	3212928	62	3747										
C15orf2	23742	broad.mit.edu	37	chr15	24921536	24921536	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cagatcgaaggggaggatgaCgagaaaaggaccccccttag	14	9	0	3	rs368120585		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr15:24921536C>T	ENST00000329468.2	+	1	996	c.522C>T	c.(520-522)gaC>gaT	p.D174D		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	174					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.D174D(2)									GGGAGGATGACGAGAAAAGGA	0.622																																																2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	15						C		1,4405		0,1,2202	48	41	43		522	-5.4	0	15		43	0,8600		0,0,4300	no	coding-synonymous	C15orf2	NM_018958.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		174/1157	24921536	1,13005	2203	4300	6503	22472629	SO:0001819	synonymous_variant	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.522C>T	15.37:g.24921536C>T			22472629		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.622	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921536	C	T	24921536	2	4	40	1	0	0	0	0	0	0	0	1	1788	535	19	1		1	C15orf2	15	24921536	Silent	SNP	C	TCGA-AG-3878-01A-02W-0899-10		24921536	77609856	63	3748										
DMXL2	23312	broad.mit.edu	37	chr15	51839564	51839564	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgaggtataattgaagacttCcaaccagtcataggatacca	8	8	1	3			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr15:51839564C>T	ENST00000251076.5	-	7	896	c.609G>A	c.(607-609)tgG>tgA	p.W203*	DMXL2_ENST00000543779.2_Nonsense_Mutation_p.W203*|DMXL2_ENST00000560421.1_5'UTR|DMXL2_ENST00000449909.3_Nonsense_Mutation_p.W203*	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	203						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.W203*(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTGAAGACTTCCAACCAGTCA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											87	86	86					15																	51839564		2195	4292	6487	49626856	SO:0001587	stop_gained	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.609G>A	15.37:g.51839564C>T	ENSP00000251076:p.Trp203*		49626856	B2RTR3|B7ZMH3|F5GWF1|O94938	Nonsense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428615	0.83667	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3281	0.94270	0.0:1.0:0.0:0.0	.	.	.	.	X	203	.	ENSP00000251076:W203X	W	-	3	0	DMXL2	49626856	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.398000	0.79919	2.588000	0.87417	0.585000	0.79938	TGG		0.343	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51839564	C	T	51839564	4	4	40	1	0	0	0	0	0	1	0	0	4606	856	30	3	8652	3	DMXL2	15	51839564	Nonsense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	26918028	51839564	50691828	64	3749										
ANPEP	290	broad.mit.edu	37	chr15	90344715	90344715	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	atcggggtcaaggaggaagtGctcctgggaaagggtccccg	17	9	1	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr15:90344715G>T	ENST00000300060.6	-	11	2006	c.1693C>A	c.(1693-1695)Cac>Aac	p.H565N	ANPEP_ENST00000558177.1_5'UTR	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	565	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.H565N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	AGGAGGAAGTGCTCCTGGGAA	0.607																																					NSCLC(30;827 977 2459 19669 26125)											1	Substitution - Missense(1)	large_intestine(1)	15											108	101	103					15																	90344715		2200	4299	6499	88145719	SO:0001583	missense	290			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1693C>A	15.37:g.90344715G>T	ENSP00000300060:p.His565Asn		88145719	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860715	0.91433	.	.	ENSG00000166825	ENST00000300060	T	0.01258	5.09	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.12987	0.0315	H	0.94658	3.565	0.54753	D	0.999983	D	0.67145	0.996	D	0.67900	0.954	T	0.01225	-1.1413	10	0.62326	D	0.03	.	16.374	0.83379	0.0:0.0:1.0:0.0	.	565	P15144	AMPN_HUMAN	N	565	ENSP00000300060:H565N	ENSP00000300060:H565N	H	-	1	0	ANPEP	88145719	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	9.411000	0.97342	2.474000	0.83562	0.655000	0.94253	CAC		0.607	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90344715	G	T	90344715	3	4	40	1	0	0	0	0	1	0	0	0	710	1319	46	2	1254	2	ANPEP	15	90344715	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	38505151	90344715	12186677	65	3750										
PHKG2	5261	broad.mit.edu	37	chr16	30762584	30762584	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cacacatccttcgccaggtcGccggccacccccacatcagt	7	20	1	0	rs535265672		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr16:30762584G>A	ENST00000563588.1	+	3	492	c.253G>A	c.(253-255)Gcc>Acc	p.A85T	PHKG2_ENST00000424889.3_Missense_Mutation_p.A85T|RP11-2C24.4_ENST00000483578.1_lincRNA|PHKG2_ENST00000328273.7_Missense_Mutation_p.A85T	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	85	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.A85T(1)		ovary(1)|skin(1)	2			Colorectal(24;0.198)			TCGCCAGGTCGCCGGCCACCC	0.622													G|||	1	0.000199681	0	0.0014	5008	,	,		18015	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											69	69	69					16																	30762584		2197	4300	6497	30670085	SO:0001583	missense	5261			S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.253G>A	16.37:g.30762584G>A	ENSP00000455607:p.Ala85Thr		30670085	A8K0C7|B4DEB7|E9PEU3|P11800	Missense_Mutation	SNP	ENST00000563588.1	37	CCDS10690.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249464	0.59212	.	.	ENSG00000156873	ENST00000328273;ENST00000424889	T;T	0.71579	-0.12;-0.58	4.85	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44285	D	0.000471	T	0.59459	0.2195	N	0.21448	0.665	0.38093	D	0.937014	D;P;P	0.59767	0.986;0.556;0.647	P;B;B	0.48738	0.588;0.175;0.075	T	0.57516	-0.7798	10	0.17369	T	0.5	-11.0908	10.5423	0.45039	0.0:0.0:0.6978:0.3022	.	77;85;85	Q16221;P15735;P15735-2	.;PHKG2_HUMAN;.	T	85	ENSP00000329968:A85T;ENSP00000388571:A85T	ENSP00000329968:A85T	A	+	1	0	PHKG2	30670085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.068000	0.41471	2.514000	0.84764	0.655000	0.94253	GCC		0.622	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294		A	30762584	G	A	30762584	3	1	40	1	0	0	0	0	1	0	0	0	11878	1087	38	1	259	1	PHKG2	16	30762584	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10		30762584	59592169	66	3751										
ZFHX3	463	broad.mit.edu	37	chr16	72831260	72831260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ggaagtgaggaaggagggtgGggttaaacagctgagactgg	20	3	0	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr16:72831260G>T	ENST00000268489.5	-	9	5993	c.5321C>A	c.(5320-5322)cCc>cAc	p.P1774H	ZFHX3_ENST00000397992.5_Missense_Mutation_p.P860H	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1774					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P1774H(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AAGGAGGGTGGGGTTAAACAG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	16											91	93	92					16																	72831260		2198	4300	6498	71388761	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5321C>A	16.37:g.72831260G>T	ENSP00000268489:p.Pro1774His		71388761	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.554492	0.27739	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	D;D	0.92099	-2.97;-2.85	6.17	5.22	0.72569	.	0.000000	0.49916	D	0.000134	D	0.94338	0.8180	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	D	0.94932	0.8083	10	0.87932	D	0	.	15.565	0.76284	0.0655:0.0:0.9345:0.0	.	1774	Q15911	ZFHX3_HUMAN	H	1774;860	ENSP00000268489:P1774H;ENSP00000438926:P860H	ENSP00000268489:P1774H	P	-	2	0	ZFHX3	71388761	1.000000	0.71417	1.000000	0.80357	0.519000	0.34347	9.858000	0.99539	1.636000	0.50526	-0.136000	0.14681	CCC		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72831260	G	T	72831260	3	4	40	1	0	0	0	0	1	0	0	0	17673	1232	43	2	5798	2	ZFHX3	16	72831260	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	42068676	72831260	17523493	67	3752										
KIAA1609	57707	broad.mit.edu	37	chr16	84529306	84529306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	taccttttggacttctctggCcttcacgggaccttctgtgg	10	12	3	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr16:84529306C>A	ENST00000343629.6	-	3	549	c.367G>T	c.(367-369)Gcc>Tcc	p.A123S	RP11-517C16.4_ENST00000568771.1_RNA|TLDC1_ENST00000535580.1_Missense_Mutation_p.A96S|TLDC1_ENST00000561807.1_5'UTR	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	123						lysosomal membrane (GO:0005765)		p.A123S(1)									ACTTCTCTGGCCTTCACGGGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											95	91	93					16																	84529306		2200	4300	6500	83086807	SO:0001583	missense	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.367G>T	16.37:g.84529306C>A	ENSP00000343635:p.Ala123Ser		83086807	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	C	4.413	0.076422	0.08485	.	.	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.15487	2.42;2.42	4.46	3.5	0.40072	.	0.692235	0.14112	N	0.340675	T	0.16642	0.0400	M	0.63428	1.95	0.09310	N	1	P;B	0.34587	0.458;0.083	B;B	0.31869	0.137;0.02	T	0.13818	-1.0495	10	0.18276	T	0.48	-11.456	9.7275	0.40342	0.0:0.8987:0.0:0.1013	.	96;123	F5GWS3;Q6P9B6	.;K1609_HUMAN	S	123;96	ENSP00000343635:A123S;ENSP00000441997:A96S	ENSP00000343635:A123S	A	-	1	0	KIAA1609	83086807	0.456000	0.25744	0.021000	0.16686	0.064000	0.16182	3.104000	0.50306	1.141000	0.42275	0.563000	0.77884	GCC		0.532	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		A	84529306	C	A	84529306	3	1	40	1	0	0	0	0	1	0	0	0	8268	739	26	2	1027	2	KIAA1609	16	84529306	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	11698046	84529306	5825447	68	3753										
TGIF1	7050	broad.mit.edu	37	chr18	3457365	3457366	+	Frame_Shift_Ins	INS	-	-	T													0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	taccgatatgatttcaggtcINStgtaactggttcatcaacgc							TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr18:3457365_3457366insT	ENST00000330513.5	+	3	936_937	c.633_634insT	c.(634-636)tgtfs	p.C212fs	TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000405385.3_Frame_Shift_Ins_p.C63fs|TGIF1_ENST00000407501.2_Frame_Shift_Ins_p.C83fs|TGIF1_ENST00000472042.1_Frame_Shift_Ins_p.C63fs|TGIF1_ENST00000548489.2_Frame_Shift_Ins_p.C97fs|TGIF1_ENST00000343820.5_Frame_Shift_Ins_p.C83fs|TGIF1_ENST00000400167.2_Frame_Shift_Ins_p.C63fs|TGIF1_ENST00000401449.1_Frame_Shift_Ins_p.C63fs|TGIF1_ENST00000345133.5_Frame_Shift_Ins_p.C63fs|TGIF1_ENST00000551541.1_Frame_Shift_Ins_p.C63fs	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	212					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.C212fs*2(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GATTTCAGGTCTGTAACTGGTT	0.485																																																1	Insertion - Frameshift(1)	large_intestine(1)	18																																								3447366	SO:0001589	frameshift_variant	7050			X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"Homeoboxes / TALE class"	11776	protein-coding gene	gene with protein product		602630	"TGFB-induced factor (TALE family homeobox)"	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.634dupT	18.37:g.3457366_3457366dupT	ENSP00000327959:p.Cys212fs		3447365	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Frame_Shift_Ins	INS	ENST00000330513.5	37	CCDS11834.1																																																																																				0.485	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		T	3457366	-	T	3457365	7	5	40	1	0	1	1	0	0	0	0	0	15864	900	32	0	725	0	TGIF1	18	3457365	Frame_Shift_Ins	INS	-	TCGA-AG-3878-01A-02W-0899-10		3457365	74619883	69	3754										
MOCOS	55034	broad.mit.edu	37	chr18	33780275	33780275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	cttctacatcccgaggcagtCggtagctcagaggtaacctt	10	12	2	1	rs77940522	byFrequency	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr18:33780275C>T	ENST00000261326.5	+	4	950	c.929C>T	c.(928-930)tCg>tTg	p.S310L		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase									p.S310L(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCGAGGCAGTCGGTAGCTCAG	0.567													C|||	2	0.000399361	0	0	5008	,	,		19961	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											39	36	37					18																	33780275		2203	4300	6503	32034273	SO:0001583	missense	55034			AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.929C>T	18.37:g.33780275C>T	ENSP00000261326:p.Ser310Leu		32034273		Missense_Mutation	SNP	ENST00000261326.5	37	CCDS11919.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	10.50	1.367718	0.24771	.	.	ENSG00000075643	ENST00000261326	D	0.87029	-2.2	5.34	5.34	0.76211	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.312643	0.34959	N	0.003557	D	0.87943	0.6305	M	0.80746	2.51	0.09310	N	1	P	0.39116	0.66	B	0.38428	0.273	T	0.82440	-0.0456	10	0.37606	T	0.19	-1.9638	16.5317	0.84362	0.0:1.0:0.0:0.0	.	310	Q96EN8	MOCOS_HUMAN	L	310	ENSP00000261326:S310L	ENSP00000261326:S310L	S	+	2	0	MOCOS	32034273	0.843000	0.29541	0.302000	0.25058	0.023000	0.10783	4.093000	0.57714	2.509000	0.84616	0.561000	0.74099	TCG		0.567	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			T	33780275	C	T	33780275	3	4	40	1	0	0	0	0	1	0	0	0	9719	893	31	1	943	1	MOCOS	18	33780275	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	30322910	33780275	44296973	70	3755										
LMAN1	3998	broad.mit.edu	37	chr18	57013171	57013171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	caggctgcccttggaggtcgGggtggcccttctggaattcc	15	12	1	0			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr18:57013171G>A	ENST00000251047.5	-	8	1652	c.935C>T	c.(934-936)cCc>cTc	p.P312L	LMAN1_ENST00000587940.1_5'Flank	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	312					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.P312L(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TTGGAGGTCGGGGTGGCCCTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	18											130	129	130					18																	57013171		2203	4300	6503	55164151	SO:0001583	missense	3998			X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.935C>T	18.37:g.57013171G>A	ENSP00000251047:p.Pro312Leu		55164151	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	G	32	5.125831	0.94429	.	.	ENSG00000074695	ENST00000251047	D	0.99259	-5.64	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.99432	0.9799	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99226	1.0880	10	0.72032	D	0.01	-13.2985	19.4527	0.94873	0.0:0.0:1.0:0.0	.	312	P49257	LMAN1_HUMAN	L	312	ENSP00000251047:P312L	ENSP00000251047:P312L	P	-	2	0	LMAN1	55164151	1.000000	0.71417	0.980000	0.43619	0.988000	0.76386	9.434000	0.97515	2.696000	0.92011	0.655000	0.94253	CCC		0.468	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		A	57013171	G	A	57013171	3	1	40	1	0	0	0	0	1	0	0	0	8860	1232	43	3	621	3	LMAN1	18	57013171	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	23232896	57013171	21064077	71	3756										
SIN3B	23309	broad.mit.edu	37	chr19	16973225	16973225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ggtaaaagagctgtccttcgCgccacccatgagcgacagat	11	12	0	3	rs369206489		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr19:16973225C>T	ENST00000248054.5	+	9	1142	c.1121C>T	c.(1120-1122)gCg>gTg	p.A374V	SIN3B_ENST00000379803.1_Missense_Mutation_p.A374V|SIN3B_ENST00000595541.1_5'Flank					SIN3 transcription regulator family member B									p.A374V(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CTGTCCTTCGCGCCACCCATG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	74	75	75		1121	4.6	0.2	19		75	0,8600		0,0,4300	no	missense	SIN3B	NM_015260.2	64	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	374/1163	16973225	3,13003	2203	4300	6503	16834225	SO:0001583	missense	23309			AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1121C>T	19.37:g.16973225C>T	ENSP00000248054:p.Ala374Val		16834225		Missense_Mutation	SNP	ENST00000248054.5	37		.	.	.	.	.	.	.	.	.	.	C	8.633	0.894193	0.17613	6.81E-4	0.0	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.46063	0.88;0.9	4.63	4.63	0.57726	.	0.166715	0.52532	D	0.000068	T	0.18467	0.0443	N	0.03608	-0.345	0.30721	N	0.748263	B;B	0.27286	0.174;0.024	B;B	0.22152	0.038;0.006	T	0.12192	-1.0557	10	0.13108	T	0.6	-4.7297	12.0059	0.53259	0.0:0.915:0.0:0.085	.	374;374	O75182-2;O75182	.;SIN3B_HUMAN	V	374	ENSP00000369131:A374V;ENSP00000248054:A374V	ENSP00000248054:A374V	A	+	2	0	SIN3B	16834225	0.477000	0.25909	0.248000	0.24265	0.187000	0.23431	1.451000	0.35145	2.121000	0.65114	0.561000	0.74099	GCG		0.517	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		T	16973225	C	T	16973225	3	4	40	1	0	0	0	0	1	0	0	0	14363	768	27	1	1155	1	SIN3B	19	16973225	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		16973225	42155758	72	3757										
KIAA1683	80726	broad.mit.edu	37	chr19	18377810	18377811	+	Missense_Mutation	DNP	GC	GC	AT													0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	atgatgggcggggacagaagGcggttctcttccggatgctg					rs201565974		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr19:18377810_18377811GC>AT	ENST00000600328.3	-	3	732_733	c.539_540GC>AT	c.(538-540)cGC>cAT	p.R180H	KIAA1683_ENST00000392413.4_Missense_Mutation_p.R180H|KIAA1683_ENST00000600359.3_Missense_Mutation_p.R134H			Q9H0B3	K1683_HUMAN	KIAA1683	180						mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R180>?(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGGACAGAAGGCGGTTCTCTTC	0.604																																																1	Complex(1)	large_intestine(1)	19																																								18238811	SO:0001583	missense	80726			AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.539_540delinsAT	19.37:g.18377810_18377811delinsAT	ENSP00000470780:p.Arg180His		18238810	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	DNP	ENST00000600328.3	37	CCDS32958.1																																																																																				0.604	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			AT	18377811	GC	AT	18377810	3	1	40	1	0	0	0	0	1	0	0	0	8272	1190	42	3	3571	3	KIAA1683	19	18377810	Missense_Mutation	DNP	GC	TCGA-AG-3878-01A-02W-0899-10	1404585	18377810	40751173	73	3758										
HRC	3270	broad.mit.edu	37	chr19	49658072	49658072	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	tgctcagctgagtcttccgtGtcttcactcccgtggcctct	9	15	5	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr19:49658072G>T	ENST00000252825.4	-	1	609	c.423C>A	c.(421-423)gaC>gaA	p.D141E	TRPM4_ENST00000427978.2_5'Flank|TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.D141E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	141	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.D141E(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGTCTTCCGTGTCTTCACTCC	0.597																																					Melanoma(37;75 1097 24567 25669 30645)											1	Substitution - Missense(1)	large_intestine(1)	19											181	131	148					19																	49658072		2203	4300	6503	54349884	SO:0001583	missense	3270				CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.423C>A	19.37:g.49658072G>T	ENSP00000252825:p.Asp141Glu		54349884	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.237427	0.22711	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.06068	3.35	2.6	-5.2	0.02823	.	.	.	.	.	T	0.03477	0.0100	N	0.26130	0.795	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.41484	-0.9506	9	0.27082	T	0.32	-0.3231	3.3907	0.07287	0.6102:0.1271:0.1354:0.1272	.	141	P23327	SRCH_HUMAN	E	141;111	ENSP00000252825:D141E	ENSP00000252825:D141E	D	-	3	2	HRC	54349884	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.296000	0.02762	-1.880000	0.01125	0.462000	0.41574	GAC		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49658072	G	T	49658072	3	4	40	1	0	0	0	0	1	0	0	0	7373	1368	48	2	1700	2	HRC	19	49658072	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	31280262	49658072	9470911	74	3759										
MYH14	79784	broad.mit.edu	37	chr19	50764793	50764793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	acagagcaagatcttcttccGggctggggtcctggcccagc	13	13	2	2			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr19:50764793G>A	ENST00000596571.1	+	18	2363	c.2363G>A	c.(2362-2364)cGg>cAg	p.R788Q	MYH14_ENST00000425460.1_Missense_Mutation_p.R796Q|MYH14_ENST00000440075.2_Missense_Mutation_p.R829Q|MYH14_ENST00000262269.8_Missense_Mutation_p.R829Q|MYH14_ENST00000376970.2_Missense_Mutation_p.R821Q|MYH14_ENST00000601313.1_Missense_Mutation_p.R829Q|MYH14_ENST00000598205.1_Missense_Mutation_p.R796Q			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	788	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R788Q(1)|p.R829Q(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ATCTTCTTCCGGGCTGGGGTC	0.642																																																2	Substitution - Missense(2)	large_intestine(2)	19											37	42	40					19																	50764793		2063	4222	6285	55456605	SO:0001583	missense	79784			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2363G>A	19.37:g.50764793G>A	ENSP00000472819:p.Arg788Gln		55456605	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	33	5.209325	0.95069	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52	4.48	4.48	0.54585	Myosin head, motor domain (2);	.	.	.	.	D	0.86556	0.5961	H	0.96111	3.77	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;P;P	0.57679	0.825;0.76;0.775	D	0.90828	0.4714	9	0.72032	D	0.01	.	15.0404	0.71785	0.0:0.0:1.0:0.0	.	829;788;796	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	Q	788;829;821;796;788;829	ENSP00000406273:R829Q;ENSP00000366169:R821Q;ENSP00000407879:R796Q;ENSP00000262269:R829Q	ENSP00000262269:R829Q	R	+	2	0	MYH14	55456605	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.327000	0.96396	2.508000	0.84585	0.555000	0.69702	CGG		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		A	50764793	G	A	50764793	3	1	40	1	0	0	0	0	1	0	0	0	10063	1116	39	1	2564	1	MYH14	19	50764793	Missense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10	1106721	50764793	8364190	75	3760										
SULF2	55959	broad.mit.edu	37	chr20	46290537	46290537	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ccaggtccatgtttcgagtcCgggggttacactgcttgtaa	12	10	0	0	rs533810544		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr20:46290537C>T	ENST00000359930.4	-	18	3325	c.2474G>A	c.(2473-2475)cGg>cAg	p.R825Q	SULF2_ENST00000361612.4_Missense_Mutation_p.R825Q|SULF2_ENST00000467815.1_Missense_Mutation_p.R825Q|SULF2_ENST00000484875.1_Missense_Mutation_p.R825Q	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	825					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.R825Q(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTTTCGAGTCCGGGGGTTACA	0.562													C|||	1	0.000199681	0	0	5008	,	,		21083	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	20											151	124	133					20																	46290537		2203	4300	6503	45723944	SO:0001583	missense	55959			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2474G>A	20.37:g.46290537C>T	ENSP00000353007:p.Arg825Gln		45723944	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.2|26.2	4.717761|4.717761	0.89205|0.89205	.|.	.|.	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.22945	.|1.93;1.93;1.93;1.93	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.168662	.|0.47455	.|D	.|0.000232	T|T	0.29061|0.29061	0.0722|0.0722	L|L	0.49778|0.49778	1.585|1.585	0.52501|0.52501	D|D	0.999958|0.999958	.|B;B	.|0.22746	.|0.074;0.009	.|B;B	.|0.17433	.|0.018;0.006	T|T	0.04281|0.04281	-1.0963|-1.0963	5|10	.|0.54805	.|T	.|0.06	-23.6604|-23.6604	19.0961|19.0961	0.93251|0.93251	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|825;825	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	R|Q	180|825;825;825;244;825	.|ENSP00000353007:R825Q;ENSP00000418290:R825Q;ENSP00000354662:R825Q;ENSP00000418442:R825Q	.|ENSP00000353007:R825Q	G|R	-|-	1|2	0|0	SULF2|SULF2	45723944|45723944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.759000|5.759000	0.68785|0.68785	2.506000|2.506000	0.84524|0.84524	0.462000|0.462000	0.41574|0.41574	GGA|CGG		0.562	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		T	46290537	C	T	46290537	3	4	40	1	0	0	0	0	1	0	0	0	15410	652	23	1	154	1	SULF2	20	46290537	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10		46290537	16734983	76	3761										
HSPA13	6782	broad.mit.edu	37	chr21	15750652	15750652	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	ctttaacttcaacaatagtcGagagccaacatattctgggg	8	9	2	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr21:15750652G>A	ENST00000285667.3	-	3	515	c.448C>T	c.(448-450)Cga>Tga	p.R150*	HSPA13_ENST00000478035.1_5'Flank|HSPA13_ENST00000544452.1_Intron	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	150						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)	p.R150*(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AACAATAGTCGAGAGCCAACA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											99	89	93					21																	15750652		2203	4300	6503	14672523	SO:0001587	stop_gained	6782				CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.448C>T	21.37:g.15750652G>A	ENSP00000285667:p.Arg150*		14672523	B2R616|Q8NE40	Nonsense_Mutation	SNP	ENST00000285667.3	37	CCDS13567.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881422	0.91740	.	.	ENSG00000155304	ENST00000285667	.	.	.	5.88	4.94	0.65067	.	0.111621	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-15.6822	13.9143	0.63887	0.0:0.0:0.6495:0.3505	.	.	.	.	X	150	.	ENSP00000285667:R150X	R	-	1	2	HSPA13	14672523	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.218000	0.51192	1.337000	0.45525	0.655000	0.94253	CGA		0.393	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			A	15750652	G	A	15750652	4	1	40	1	0	0	0	0	0	1	0	0	7427	1066	37	1	979	1	HSPA13	21	15750652	Nonsense_Mutation	SNP	G	TCGA-AG-3878-01A-02W-0899-10		15750652	32379243	77	3762										
TIAM1	7074	broad.mit.edu	37	chr21	32502559	32502559	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gccaaagctcgaacctgcagCgcttccgtggggatcatgtg	13	12	1	0	rs145341566		TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr21:32502559C>T	ENST00000286827.3	-	26	4488	c.4017G>A	c.(4015-4017)gcG>gcA	p.A1339A	TIAM1_ENST00000541036.1_Silent_p.A1279A	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1339	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A1339A(5)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GAACCTGCAGCGCTTCCGTGG	0.488																																																5	Substitution - coding silent(5)	large_intestine(4)|breast(1)	21						C		0,4406		0,0,2203	180	178	179		4017	-10.5	0.4	21	dbSNP_134	179	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TIAM1	NM_003253.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1339/1592	32502559	1,13005	2203	4300	6503	31424430	SO:0001819	synonymous_variant	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.4017G>A	21.37:g.32502559C>T			31424430	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.488	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32502559	C	T	32502559	2	4	40	1	0	0	0	0	0	0	0	1	15929	755	27	1		1	TIAM1	21	32502559	Silent	SNP	C	TCGA-AG-3878-01A-02W-0899-10	16751907	32502559	15627336	78	3763										
HLCS	3141	broad.mit.edu	37	chr21	38269293	38269293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	gaaggcctccatgttggtcaCcacaggtatacaagatgggg	13	9	1	1			TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chr21:38269293C>T	ENST00000399120.1	-	7	2548	c.1318G>A	c.(1318-1320)Gtg>Atg	p.V440M	HLCS_ENST00000336648.4_Missense_Mutation_p.V440M|HLCS_ENST00000482273.1_5'UTR	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	440					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)	p.V440M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	ATGTTGGTCACCACAGGTATA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	21											112	103	106					21																	38269293		2203	4300	6503	37191163	SO:0001583	missense	3141				CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.1318G>A	21.37:g.38269293C>T	ENSP00000382071:p.Val440Met		37191163	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	37	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.647433	0.29246	.	.	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98329	-4.87;-4.87	5.12	0.129	0.14739	.	0.503651	0.21429	N	0.074698	D	0.96993	0.9018	M	0.72118	2.19	0.41747	D	0.989645	P	0.52170	0.951	P	0.50537	0.643	D	0.93469	0.6817	10	0.34782	T	0.22	.	5.5661	0.17170	0.1248:0.4675:0.0:0.4077	.	440	P50747	BPL1_HUMAN	M	440	ENSP00000382071:V440M;ENSP00000338387:V440M	ENSP00000338387:V440M	V	-	1	0	HLCS	37191163	0.515000	0.26210	0.048000	0.18961	0.055000	0.15305	-0.038000	0.12144	-0.183000	0.10585	-0.251000	0.11542	GTG		0.438	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			T	38269293	C	T	38269293	3	4	40	1	0	0	0	0	1	0	0	0	7234	507	18	3	886	3	HLCS	21	38269293	Missense_Mutation	SNP	C	TCGA-AG-3878-01A-02W-0899-10	5766734	38269293	9860602	79	3764										
BCOR	54880	broad.mit.edu	37	chrX	39932209	39932210	+	Frame_Shift_Del	DEL	AC	AC	-													0.0125	1	1	0.131592292089249	3.35560344827586	0	1	1	0	caagcttgtcgcttttgacaAcagtcttcccttgattccag							TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	AC	AC	AC	-	AC	AC	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3878-01A-02W-0899-10	TCGA-AG-3878-10A-01W-0901-10	g.chrX:39932209_39932210delAC	ENST00000378444.4	-	4	2617_2618	c.2389_2390delGT	c.(2389-2391)gttfs	p.V798fs	BCOR_ENST00000342274.4_Frame_Shift_Del_p.V798fs|BCOR_ENST00000397354.3_Frame_Shift_Del_p.V798fs|BCOR_ENST00000378455.4_Frame_Shift_Del_p.V798fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	798					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.V797fs*19(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GCTTTTGACAACAGTCTTCCCT	0.475			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		1	Deletion - Frameshift(1)	large_intestine(1)	X																																								39817154	SO:0001589	frameshift_variant	54880			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.2389_2390delGT	X.37:g.39932209_39932210delAC	ENSP00000367705:p.Val798fs		39817153	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	ENST00000378444.4	37	CCDS48093.1																																																																																				0.475	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		-	39932210	AC	-	39932209	7	5	40	1	0	1	0	1	0	0	0	0	1387	43	2	0	2925	0	BCOR	23	39932209	Frame_Shift_Del	DEL	AC	TCGA-AG-3878-01A-02W-0899-10		39932209	115338351	80	3765										
NBPF1	55672	broad.mit.edu	37	chr1	16892277	16892277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gcaagacttcaggctctactGcctccagcagctccctgctg	9	16	2	1	rs368729374		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:16892277G>A	ENST00000430580.2	-	27	3802	c.2915C>T	c.(2914-2916)gCa>gTa	p.A972V		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	972	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)									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)		AGGCTCTACTGCCTCCAGCAG	0.498																																																0			1											20	16	18					1																	16892277		1476	2583	4059	16764864	SO:0001583	missense	55672			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"neuroblastoma breakpoint family"	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2915C>T	1.37:g.16892277G>A	ENSP00000474456:p.Ala972Val		16764864	Q8N4E8|Q9C0H0	Missense_Mutation	SNP	ENST00000430580.2	37																																																																																					0.498	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940		A	16892277	G	A	16892277	3	1	41	1	0	0	0	0	1	0	0	0	10222	1319	46	3	516	3	NBPF1	1	16892277	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10		16892277	232358344	1	3766										
RHD	6007	broad.mit.edu	37	chr1	25627527	25627527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gcctgccaaagcctctacccGagggaacggaggataaagat	12	11	1	1	rs17418091		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:25627527G>A	ENST00000328664.4	+	4	732	c.577G>A	c.(577-579)Gag>Aag	p.E193K	RHD_ENST00000568195.1_Missense_Mutation_p.E193K|RHD_ENST00000454452.2_Missense_Mutation_p.E193K|RHD_ENST00000417538.2_Missense_Mutation_p.E193K|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000342055.5_Missense_Mutation_p.E193K|RHD_ENST00000423810.2_Missense_Mutation_p.E193K|RHD_ENST00000357542.4_Missense_Mutation_p.E193K	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	193			E -> K (in dbSNP:rs17418091).			integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)	p.E193K(1)		breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCTCTACCCGAGGGAACGGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	LYS/GLU,LYS/GLU	0,4242		0,0,2121	215	148	172		577,577	-7.9	0	1	dbSNP_123	172	1,7479		0,1,3739	no	missense,missense	RHD	NM_001127691.1,NM_016124.3	56,56	0,1,5860	AA,AG,GG		0.0134,0.0,0.0085	benign,benign	193/322,193/418	25627527	1,11721	2121	3740	5861	25500114	SO:0001583	missense	6007			AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"CD molecules", "Blood group antigens"	10009	protein-coding gene	gene with protein product		111680	"Rhesus blood group, D antigen", "Rh blood group, D antigen"	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.577G>A	1.37:g.25627527G>A	ENSP00000331871:p.Glu193Lys		25500114	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Missense_Mutation	SNP	ENST00000328664.4	37	CCDS262.1	.	.	.	.	.	.	.	.	.	.	.	0.240	-1.014575	0.02095	0.0	1.34E-4	ENSG00000187010	ENST00000328664;ENST00000419831;ENST00000454452;ENST00000342055;ENST00000357542;ENST00000417538;ENST00000423810	T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1	3.95	-7.89	0.01174	Ammonium transporter AmtB-like (3);	3.503140	0.00766	N	0.001164	T	0.05227	0.0139	N	0.01505	-0.83	0.09310	N	1	B;B;B;B;B;B;B;B	0.11235	0.001;0.0;0.004;0.001;0.0;0.001;0.002;0.0	B;B;B;B;B;B;B;B	0.13407	0.002;0.001;0.009;0.002;0.001;0.001;0.006;0.001	T	0.21008	-1.0258	10	0.05959	T	0.93	8.0803	3.0402	0.06135	0.1981:0.1136:0.4646:0.2237	rs17418091	193;193;193;193;193;193;193;193	B4DLT8;Q5XLT1;Q5XLS9;Q5XLT2;Q5XLT3;E7EVW1;Q5XLT0;Q02161	.;.;.;.;.;.;.;RHD_HUMAN	K	193	ENSP00000331871:E193K;ENSP00000413849:E193K;ENSP00000339577:E193K;ENSP00000350150:E193K;ENSP00000396420:E193K;ENSP00000399640:E193K	ENSP00000331871:E193K	E	+	1	0	RHD	25500114	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.842000	0.04354	-3.458000	0.00159	-2.434000	0.00213	GAG		0.527	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124		A	25627527	G	A	25627527	3	1	41	1	0	0	0	0	1	0	0	0	13364	1059	37	1	591	1	RHD	1	25627527	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	8735250	25627527	223623094	2	3767										
NCDN	23154	broad.mit.edu	37	chr1	36030904	36030904	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tcacagtcccacgtggcgcgGgccaccccgggctcagacca	12	18	2	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:36030904G>C	ENST00000373243.2	+	7	2213	c.1830G>C	c.(1828-1830)cgG>cgC	p.R610R	NCDN_ENST00000373253.3_Silent_p.R593R|NCDN_ENST00000356090.4_Silent_p.R610R	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	610					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.R593R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACGTGGCGCGGGCCACCCCGG	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	1											95	100	99					1																	36030904		2203	4300	6503	35803491	SO:0001819	synonymous_variant	23154			AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.1830G>C	1.37:g.36030904G>C			35803491	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Silent	SNP	ENST00000373243.2	37	CCDS392.1																																																																																				0.637	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		C	36030904	G	C	36030904	2	2	41	1	0	0	0	0	0	0	0	1	10245	1219	43	5		5	NCDN	1	36030904	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	10403377	36030904	213219717	3	3768										
LRRIQ3	127255	broad.mit.edu	37	chr1	74507367	74507367	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atatcactaaatgttcggagTttcataccagctctttgtgg	8	8	3	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:74507367T>A	ENST00000395089.1	-	6	1247	c.1248A>T	c.(1246-1248)aaA>aaT	p.K416N	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.K416N			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	416								p.K416N(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						ATGTTCGGAGTTTCATACCAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											140	127	131					1																	74507367		1844	4082	5926	74279955	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1248A>T	1.37:g.74507367T>A	ENSP00000378524:p.Lys416Asn		74279955	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490794	0.26774	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.09538	2.97;2.97	5.77	-3.32	0.04973	.	0.638626	0.13858	N	0.357873	T	0.01189	0.0039	L	0.32530	0.975	0.09310	N	1	B	0.32829	0.386	B	0.24269	0.052	T	0.46596	-0.9180	10	0.13470	T	0.59	.	0.7247	0.00946	0.3595:0.1498:0.123:0.3678	.	416	A6PVS8	LRIQ3_HUMAN	N	416	ENSP00000378524:K416N;ENSP00000346414:K416N	ENSP00000346414:K416N	K	-	3	2	LRRIQ3	74279955	0.550000	0.26489	0.016000	0.15963	0.157000	0.22087	0.100000	0.15231	-0.356000	0.08187	0.477000	0.44152	AAA		0.368	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		A	74507367	T	A	74507367	3	1	41	1	0	0	0	0	1	0	0	0	9059	1722	60	5	634	5	LRRIQ3	1	74507367	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	38476463	74507367	174743254	4	3769										
FNBP1L	54874	broad.mit.edu	37	chr1	94000447	94000447	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gccaagggcaaattgtggctCtttggaaagaagccaaaggt	13	7	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:94000447C>T	ENST00000271234.7	+	9	1123	c.972C>T	c.(970-972)ctC>ctT	p.L324L	FNBP1L_ENST00000370256.4_Silent_p.L324L|FNBP1L_ENST00000604705.1_Silent_p.L324L|FNBP1L_ENST00000370253.2_Silent_p.L324L|FNBP1L_ENST00000260506.8_Silent_p.L324L	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	324	Interaction with CDC42.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.L324L(1)		breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		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)		AATTGTGGCTCTTTGGAAAGA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	1											39	37	38					1																	94000447		1856	4093	5949	93773035	SO:0001819	synonymous_variant	54874				CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.972C>T	1.37:g.94000447C>T			93773035	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Silent	SNP	ENST00000271234.7	37	CCDS53343.1																																																																																				0.388	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		T	94000447	C	T	94000447	2	4	41	1	0	0	0	0	0	0	0	1	5985	900	32	3		3	FNBP1L	1	94000447	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10	19493080	94000447	155250174	5	3770										
SPTA1	6708	broad.mit.edu	37	chr1	158595941	158595941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atctatcaatctcacctgttTtgccagaagagtgaggaagt	9	8	3	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:158595941T>C	ENST00000368147.4	-	42	6085	c.5905A>G	c.(5905-5907)Aaa>Gaa	p.K1969E		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1969					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.K1969E(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTCACCTGTTTTGCCAGAAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	113	114					1																	158595941		1918	4122	6040	156862565	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5905A>G	1.37:g.158595941T>C	ENSP00000357129:p.Lys1969Glu		156862565	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435329	0.62955	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.57273	0.41;0.41	4.93	4.93	0.64822	.	0.245199	0.20991	N	0.082023	T	0.67543	0.2904	M	0.83774	2.66	0.37530	D	0.917887	D	0.89917	1.0	D	0.91635	0.999	T	0.74472	-0.3654	10	0.87932	D	0	.	12.577	0.56369	0.0:0.0:0.0:1.0	.	1969	P02549	SPTA1_HUMAN	E	1969;1966	ENSP00000357130:K1969E;ENSP00000357129:K1966E	ENSP00000357129:K1966E	K	-	1	0	SPTA1	156862565	1.000000	0.71417	0.999000	0.59377	0.258000	0.26162	5.820000	0.69250	2.068000	0.61886	0.460000	0.39030	AAA		0.388	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158595941	T	C	158595941	3	2	41	1	0	0	0	0	1	0	0	0	15155	1850	64	4	1398	4	SPTA1	1	158595941	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	64595494	158595941	90654680	6	3771										
KLHL20	27252	broad.mit.edu	37	chr1	173720985	173720985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tgatgagctaaacgttcgcaGtgaagaacaagtgttcaatg	11	6	1	4			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:173720985G>A	ENST00000209884.4	+	4	816	c.680G>A	c.(679-681)aGt>aAt	p.S227N	KLHL20_ENST00000546011.1_Missense_Mutation_p.S38N	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	227	BACK.				cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)	p.S227N(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						AACGTTCGCAGTGAAGAACAA	0.398																																					GBM(159;862 2695 6559 23041)											1	Substitution - Missense(1)	large_intestine(1)	1											105	93	97					1																	173720985		2203	4300	6503	171987608	SO:0001583	missense	27252			AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"Kelch-like", "BTB/POZ domain containing"	25056	protein-coding gene	gene with protein product			"kelch-like 20 (Drosophila)"			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.680G>A	1.37:g.173720985G>A	ENSP00000209884:p.Ser227Asn		171987608	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	37	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888183	0.52014	.	.	ENSG00000076321	ENST00000546011;ENST00000209884	T;T	0.70045	-0.45;-0.45	5.38	5.38	0.77491	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.53126	0.1777	L	0.58969	1.84	0.80722	D	1	B;B	0.29378	0.243;0.131	B;B	0.24974	0.054;0.057	T	0.57423	-0.7814	10	0.46703	T	0.11	.	17.892	0.88875	0.0:0.0:1.0:0.0	.	38;227	B4DUR0;Q9Y2M5	.;KLH20_HUMAN	N	38;227	ENSP00000443121:S38N;ENSP00000209884:S227N	ENSP00000209884:S227N	S	+	2	0	KLHL20	171987608	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.404000	0.97306	2.490000	0.84030	0.591000	0.81541	AGT		0.398	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		A	173720985	G	A	173720985	3	1	41	1	0	0	0	0	1	0	0	0	8396	1029	36	3	690	3	KLHL20	1	173720985	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	15125044	173720985	75529636	7	3772										
DYRK3	8444	broad.mit.edu	37	chr1	206821697	206821697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agaaatcatcttaggaagccGctacagcacaccaattgaca	7	11	2	2	rs200229954		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:206821697G>A	ENST00000367109.2	+	3	1322	c.1154G>A	c.(1153-1155)cGc>cAc	p.R385H	DYRK3_ENST00000367106.1_Missense_Mutation_p.R365H|DYRK3_ENST00000367108.3_Missense_Mutation_p.R365H|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.R350H(1)|p.R385H(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TTAGGAAGCCGCTACAGCACA	0.473																																					Melanoma(164;427 2622 26826 51707)											2	Substitution - Missense(2)	large_intestine(2)	1											86	93	91					1																	206821697		2203	4300	6503	204888320	SO:0001583	missense	8444			Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1154G>A	1.37:g.206821697G>A	ENSP00000356076:p.Arg385His		204888320	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	37	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.339621	0.81911	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000367106	T;T;T	0.65549	-0.16;-0.16;-0.16	5.3	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	N	0.21240	0.645	0.80722	D	1	D;D	0.76494	0.997;0.999	D;P	0.63793	0.918;0.907	T	0.71286	-0.4638	10	0.72032	D	0.01	.	18.1141	0.89545	0.0:0.0:1.0:0.0	.	385;365	O43781;O43781-2	DYRK3_HUMAN;.	H	385;365;365	ENSP00000356076:R385H;ENSP00000356075:R365H;ENSP00000356073:R365H	ENSP00000356073:R365H	R	+	2	0	DYRK3	204888320	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	7.807000	0.86032	2.760000	0.94817	0.549000	0.68633	CGC		0.473	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		A	206821697	G	A	206821697	3	1	41	1	0	0	0	0	1	0	0	0	4868	1087	38	1	1185	1	DYRK3	1	206821697	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	33100712	206821697	42428924	8	3773										
OBSCN	84033	broad.mit.edu	37	chr1	228482576	228482576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agctgagcaaggcggcccccGtggagtggaggaaggggtct	19	9	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:228482576G>A	ENST00000422127.1	+	43	11535	c.11491G>A	c.(11491-11493)Gtg>Atg	p.V3831M	OBSCN_ENST00000570156.2_Missense_Mutation_p.V4260M|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.V3831M|OBSCN_ENST00000366707.4_Missense_Mutation_p.V950M|OBSCN_ENST00000359599.6_Missense_Mutation_p.V2678M|OBSCN_ENST00000366709.4_Missense_Mutation_p.V950M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3831	Ig-like 39.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.V4114M(1)|p.V3885M(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCGGCCCCCGTGGAGTGGAG	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	1											112	116	115					1																	228482576		1982	4146	6128	226549199	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11491G>A	1.37:g.228482576G>A	ENSP00000409493:p.Val3831Met		226549199	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015207	0.75161	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	5.22	5.22	0.72569	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.90841	0.7123	M	0.90870	3.155	0.51767	D	0.999938	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92243	0.5802	10	0.66056	D	0.02	.	18.973	0.92722	0.0:0.0:1.0:0.0	.	3831;3831	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	M	3831;3831;950;950;2678	ENSP00000284548:V3831M;ENSP00000409493:V3831M;ENSP00000355668:V950M;ENSP00000355670:V950M;ENSP00000352613:V2678M	ENSP00000284548:V3831M	V	+	1	0	OBSCN	226549199	1.000000	0.71417	0.955000	0.39395	0.003000	0.03518	9.527000	0.98044	2.720000	0.93068	0.563000	0.77884	GTG		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228482576	G	A	228482576	3	1	41	1	0	0	0	0	1	0	0	0	10843	1145	40	1	11657	1	OBSCN	1	228482576	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	21660879	228482576	20768045	9	3774										
FMN2	56776	broad.mit.edu	37	chr1	240492661	240492661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tcctttatgaactgtcactaAtccccaacttttcagagcga	5	12	2	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr1:240492661A>G	ENST00000319653.9	+	10	4560	c.4330A>G	c.(4330-4332)Atc>Gtc	p.I1444V	FMN2_ENST00000545751.1_Missense_Mutation_p.I40V	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1444	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.I1587V(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACTGTCACTAATCCCCAACTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											165	154	158					1																	240492661		2203	4300	6503	238559284	SO:0001583	missense	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4330A>G	1.37:g.240492661A>G	ENSP00000318884:p.Ile1444Val		238559284	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	A	26.6	4.752857	0.89753	.	.	ENSG00000155816	ENST00000319653;ENST00000441342;ENST00000545751;ENST00000537355	T;T;T	0.18502	2.21;2.21;2.21	5.65	5.65	0.86999	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.64402	D	0.000014	T	0.34832	0.0911	L	0.42581	1.335	0.80722	D	1	P;B;D;D	0.76494	0.592;0.421;0.999;0.999	B;B;D;D	0.85130	0.306;0.31;0.997;0.995	T	0.02282	-1.1183	10	0.44086	T	0.13	.	15.8761	0.79162	1.0:0.0:0.0:0.0	.	40;90;73;1444	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	V	1444;90;40;71	ENSP00000318884:I1444V;ENSP00000388922:I90V;ENSP00000437918:I40V	ENSP00000318884:I1444V	I	+	1	0	FMN2	238559284	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.288000	0.96055	2.139000	0.66308	0.533000	0.62120	ATC		0.353	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		G	240492661	A	G	240492661	3	3	41	1	0	0	0	0	1	0	0	0	5969	101	4	4	4368	4	FMN2	1	240492661	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10	12010085	240492661	8757960	10	3775										
POLR1B	84172	broad.mit.edu	37	chr2	113333220	113333220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtagtcgcagtgacactatcGatactgtttctgtgccttat	9	9	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr2:113333220G>A	ENST00000263331.5	+	15	3902	c.3322G>A	c.(3322-3324)Gat>Aat	p.D1108N	POLR1B_ENST00000417433.2_Missense_Mutation_p.D1052N|POLR1B_ENST00000541869.1_Missense_Mutation_p.D1146N|POLR1B_ENST00000409894.3_Missense_Mutation_p.D925N|POLR1B_ENST00000537335.1_Missense_Mutation_p.D897N	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	1108					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.D1108N(1)		breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						TGACACTATCGATACTGTTTC	0.433																																					Ovarian(16;256 576 9537 23969 41147)											1	Substitution - Missense(1)	large_intestine(1)	2											131	117	122					2																	113333220		2203	4300	6503	113049691	SO:0001583	missense	84172			AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.3322G>A	2.37:g.113333220G>A	ENSP00000263331:p.Asp1108Asn		113049691	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.455806	0.63401	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.37	5.37	0.77165	RNA polymerase Rpb2, domain 7 (1);	0.302177	0.39985	N	0.001204	T	0.69106	0.3074	L	0.43923	1.385	0.40330	D	0.978916	P;B;B;P	0.46064	0.872;0.007;0.007;0.827	B;B;B;B	0.40982	0.234;0.005;0.016;0.345	T	0.70219	-0.4932	10	0.33141	T	0.24	-35.4586	17.9067	0.88920	0.0:0.0:1.0:0.0	.	1146;925;1052;1108	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	N	1108;1146;925;897;1052	ENSP00000263331:D1108N;ENSP00000444136:D1146N;ENSP00000387143:D925N;ENSP00000437914:D897N;ENSP00000405358:D1052N	ENSP00000263331:D1108N	D	+	1	0	POLR1B	113049691	1.000000	0.71417	0.937000	0.37676	0.985000	0.73830	6.254000	0.72460	2.507000	0.84556	0.557000	0.71058	GAT		0.433	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		A	113333220	G	A	113333220	3	1	41	1	0	0	0	0	1	0	0	0	12241	1058	37	1	3380	1	POLR1B	2	113333220	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10		113333220	129866153	11	3776										
SATB2	23314	broad.mit.edu	37	chr2	200173513	200173513	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tcagggggaagctggaccacGtgttgcatgcgttcgctgtg	16	9	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr2:200173513G>A	ENST00000417098.1	-	10	2526	c.1710C>T	c.(1708-1710)caC>caT	p.H570H	SATB2_ENST00000457245.1_Silent_p.H570H|SATB2_ENST00000443023.1_Silent_p.H511H|SATB2_ENST00000260926.5_Silent_p.H570H|SATB2_ENST00000428695.1_Silent_p.H452H	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	570					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.H570H(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GCTGGACCACGTGTTGCATGC	0.607																																					Colon(30;262 767 11040 24421 36230)											2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	2											162	133	143					2																	200173513		2203	4300	6503	199881758	SO:0001819	synonymous_variant	23314			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1710C>T	2.37:g.200173513G>A			199881758	A8K5Z8|Q3ZB87|Q4V763	Silent	SNP	ENST00000417098.1	37	CCDS2327.1																																																																																				0.607	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		A	200173513	G	A	200173513	2	1	41	1	0	0	0	0	0	0	0	1	13891	1136	40	1		1	SATB2	2	200173513	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	86840293	200173513	43025860	12	3777										
SNED1	25992	broad.mit.edu	37	chr2	241988533	241988533	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tacctctgcgtctgccacacCgaccacaatgccagccactg	7	18	2	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr2:241988533C>T	ENST00000310397.8	+	11	1599	c.1599C>T	c.(1597-1599)acC>acT	p.T533T	SNED1_ENST00000469006.1_3'UTR|SNED1_ENST00000342631.6_Silent_p.T533T|SNED1_ENST00000405547.3_Silent_p.T533T|SNED1_ENST00000401884.1_Silent_p.T533T|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	533					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.T533T(1)		NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|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;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TCTGCCACACCGACCACAATG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	2											17	22	21					2																	241988533		2061	4178	6239	241637206	SO:0001819	synonymous_variant	25992			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1599C>T	2.37:g.241988533C>T			241637206	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.422|8.422	0.846688|0.846688	0.16963|0.16963	.|.	.|.	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	5.09|5.09	-10.2|-10.2	0.00374|0.00374	.|.	.|.	.|.	.|.	.|.	T|.	0.41834|.	0.1176|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.50734|.	-0.8793|.	4|.	.|.	.|.	.|.	.|.	5.3|5.3	0.15773|0.15773	0.3374:0.1178:0.4338:0.111|0.3374:0.1178:0.4338:0.111	.|.	.|.	.|.	.|.	L|X	191|230	.|.	.|.	P|R	+|+	2|1	0|2	SNED1|SNED1	241637206|241637206	0.000000|0.000000	0.05858|0.05858	0.254000|0.254000	0.24359|0.24359	0.985000|0.985000	0.73830|0.73830	-6.121000|-6.121000	0.00080|0.00080	-2.954000|-2.954000	0.00292|0.00292	0.563000|0.563000	0.77884|0.77884	CCG|CGA		0.632	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	241988533	C	T	241988533	2	4	41	1	0	0	0	0	0	0	0	1	14882	639	23	1		1	SNED1	2	241988533	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10	41815020	241988533	1210840	13	3778										
DAZL	1618	broad.mit.edu	37	chr3	16638500	16638500	+	Frame_Shift_Del	DEL	T	T	-													0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tctttttgtactcacataaaTtttgtttcctgattgcaggg							TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:16638500delT	ENST00000399444.2	-	5	646	c.353delA	c.(352-354)aatfs	p.N118fs	DAZL_ENST00000250863.8_Frame_Shift_Del_p.N138fs	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like	118	Homodimerization. {ECO:0000250}.				female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.N118fs*41(1)	RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						CTCACATAAATTTTGTTTCCT	0.289																																																1	Deletion - Frameshift(1)	large_intestine(1)	3											69	68	68					3																	16638500		1969	4195	6164	16613504	SO:0001589	frameshift_variant	1618			BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"RNA binding motif (RRM) containing"	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.353delA	3.37:g.16638500delT	ENSP00000382373:p.Asn118fs		16613504	O15396|Q5HYB4|Q92909	Frame_Shift_Del	DEL	ENST00000399444.2	37	CCDS43059.1																																																																																				0.289	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351		-	16638500	T	-	16638500	7	5	41	1	0	1	0	1	0	0	0	0	4252	1493	52	0	562	0	DAZL	3	16638500	Frame_Shift_Del	DEL	T	TCGA-AG-3881-01A-01W-0899-10		16638500	181383930	14	3779										
CTNNB1	1499	broad.mit.edu	37	chr3	41275654	41275654	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctgttggattgattcgaaatCttgccctttgtcccgcaaat	8	10	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:41275654C>T	ENST00000349496.5	+	10	1829	c.1549C>T	c.(1549-1551)Ctt>Ttt	p.L517F	CTNNB1_ENST00000396183.3_Missense_Mutation_p.L517F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.L517F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L517F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.L510F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	517					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.L517F(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GATTCGAAATCTTGCCCTTTG	0.458		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	3											155	136	142					3																	41275654		2203	4300	6503	41250658	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1549C>T	3.37:g.41275654C>T	ENSP00000344456:p.Leu517Phe		41250658	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457254	0.84317	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66	5.96	5.96	0.96718	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88897	0.6562	M	0.94101	3.495	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.73708	0.941;0.981	D	0.90257	0.4298	10	0.62326	D	0.03	-16.2857	20.422	0.99049	0.0:1.0:0.0:0.0	.	445;517	B4DSW9;P35222	.;CTNB1_HUMAN	F	517;517;517;510;517	ENSP00000385604:L517F;ENSP00000379486:L517F;ENSP00000344456:L517F;ENSP00000411226:L510F;ENSP00000379488:L517F	ENSP00000344456:L517F	L	+	1	0	CTNNB1	41250658	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.964000	0.63701	2.832000	0.97577	0.655000	0.94253	CTT		0.458	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41275654	C	T	41275654	3	4	41	1	0	0	0	0	1	0	0	0	4022	913	32	3	1583	3	CTNNB1	3	41275654	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	24637154	41275654	156746776	15	3780										
ALS2CL	259173	broad.mit.edu	37	chr3	46713452	46713452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	actcccggcccaataccctcGacaccgtgccctcaatttcc	5	20	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:46713452G>A	ENST00000318962.4	-	24	2689	c.2606C>T	c.(2605-2607)tCg>tTg	p.S869L	ALS2CL_ENST00000383742.3_Missense_Mutation_p.S216L|ALS2CL_ENST00000415953.1_Missense_Mutation_p.S869L	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	869	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S869L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CAATACCCTCGACACCGTGCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	3											121	101	108					3																	46713452		2203	4300	6503	46688456	SO:0001583	missense	259173			AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2606C>T	3.37:g.46713452G>A	ENSP00000313670:p.Ser869Leu		46688456	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854134	0.32791	.	.	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.32753	1.44;1.44;1.44	4.76	3.88	0.44766	Vacuolar sorting protein 9 (2);	0.000000	0.56097	D	0.000040	T	0.36991	0.0987	N	0.21373	0.66	0.34981	D	0.754087	D	0.89917	1.0	D	0.87578	0.998	T	0.43845	-0.9366	10	0.29301	T	0.29	.	10.6094	0.45412	0.0941:0.0:0.9059:0.0	.	869	Q60I27	AL2CL_HUMAN	L	869;869;216	ENSP00000313670:S869L;ENSP00000413223:S869L;ENSP00000373248:S216L	ENSP00000313670:S869L	S	-	2	0	ALS2CL	46688456	1.000000	0.71417	0.760000	0.31359	0.027000	0.11550	4.398000	0.59697	1.221000	0.43506	0.650000	0.86243	TCG		0.637	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		A	46713452	G	A	46713452	3	1	41	1	0	0	0	0	1	0	0	0	551	1059	37	1	267	1	ALS2CL	3	46713452	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	5437798	46713452	151308978	16	3781										
FSTL1	11167	broad.mit.edu	37	chr3	120128473	120128473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ccagccactggatgatgcgaCgtcggagctcatcacggttg	13	12	2	1	rs554312023		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:120128473C>T	ENST00000295633.3	-	6	724	c.368G>A	c.(367-369)cGt>cAt	p.R123H	FSTL1_ENST00000424703.2_Missense_Mutation_p.R88H	NM_007085.4	NP_009016.1	Q12841	FSTL1_HUMAN	follistatin-like 1	123					BMP signaling pathway (GO:0030509)|response to starvation (GO:0042594)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R123H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(1)	20				GBM - Glioblastoma multiforme(114;0.189)		GATGATGCGACGTCGGAGCTC	0.502													C|||	1	0.000199681	8e-04	0	5008	,	,		22184	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											94	88	90					3																	120128473		2203	4300	6503	121611163	SO:0001583	missense	11167			U06863	CCDS2998.1	3q13.33	2013-01-10			ENSG00000163430	ENSG00000163430		"EF-hand domain containing"	3972	protein-coding gene	gene with protein product		605547				7957230, 9786430	Standard	NM_007085		Approved	FRP, FSL1	uc003eds.3	Q12841	OTTHUMG00000159440	ENST00000295633.3:c.368G>A	3.37:g.120128473C>T	ENSP00000295633:p.Arg123His		121611163	A8K523|B4DTT5|D3DN90|Q549Z0	Missense_Mutation	SNP	ENST00000295633.3	37	CCDS2998.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870192	0.51588	.	.	ENSG00000163430	ENST00000295633;ENST00000539471;ENST00000424703;ENST00000469005	T;T;T	0.23950	2.4;1.88;2.44	5.24	3.45	0.39498	.	0.341398	0.34507	N	0.003916	T	0.19327	0.0464	L	0.38175	1.15	0.40669	D	0.98219	B;B	0.24483	0.104;0.051	B;B	0.15052	0.011;0.012	T	0.04140	-1.0974	10	0.42905	T	0.14	-9.9698	10.6484	0.45634	0.0:0.8459:0.0:0.1541	.	88;123	B4DTT5;Q12841	.;FSTL1_HUMAN	H	123;66;88;123	ENSP00000295633:R123H;ENSP00000394355:R88H;ENSP00000418505:R123H	ENSP00000295633:R123H	R	-	2	0	FSTL1	121611163	0.005000	0.15991	0.999000	0.59377	0.992000	0.81027	0.611000	0.24268	0.614000	0.30107	-0.136000	0.14681	CGT		0.502	FSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355399.1	NM_007085		T	120128473	C	T	120128473	3	4	41	1	0	0	0	0	1	0	0	0	6096	536	19	1	582	1	FSTL1	3	120128473	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	73415021	120128473	77893957	17	3782										
ACAD9	28976	broad.mit.edu	37	chr3	128616497	128616497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ggagcgatgcagcctcaatcCggagcagagccacactaagt	12	12	1	1	rs377547811		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:128616497C>T	ENST00000308982.7	+	6	658	c.577C>T	c.(577-579)Cgg>Tgg	p.R193W	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	193						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.R193W(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						AGCCTCAATCCGGAGCAGAGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	142	101	115		577	4.8	1	3		115	2,8598	2.2+/-6.3	0,2,4298	no	missense	ACAD9	NM_014049.4	101	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	probably-damaging	193/622	128616497	5,13001	2203	4300	6503	130099187	SO:0001583	missense	28976			AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.577C>T	3.37:g.128616497C>T	ENSP00000312618:p.Arg193Trp		130099187	D3DNB8|Q8WXX3	Missense_Mutation	SNP	ENST00000308982.7	37	CCDS3053.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919819	0.52653	6.81E-4	2.33E-4	ENSG00000177646	ENST00000308982;ENST00000334167	D	0.99113	-5.44	5.67	4.79	0.61399	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.675448	0.16256	N	0.222461	D	0.99180	0.9716	M	0.91196	3.185	0.20307	N	0.999917	D;D	0.64830	0.987;0.994	P;P	0.55011	0.766;0.713	D	0.96843	0.9619	10	0.87932	D	0	.	13.5417	0.61679	0.1661:0.8339:0.0:0.0	.	70;193	Q9H9W4;Q9H845	.;ACAD9_HUMAN	W	193;60	ENSP00000312618:R193W	ENSP00000312618:R193W	R	+	1	2	ACAD9	130099187	1.000000	0.71417	0.961000	0.40146	0.198000	0.23893	2.045000	0.41250	1.366000	0.46076	0.555000	0.69702	CGG		0.498	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		T	128616497	C	T	128616497	3	4	41	1	0	0	0	0	1	0	0	0	111	643	23	1	599	1	ACAD9	3	128616497	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	8488024	128616497	69405933	18	3783										
RAB6B	51560	broad.mit.edu	37	chr3	133583485	133583485	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtaatcagagacgtcttcccGactgcaaaacaacaaggaga	9	10	2	2	rs373466732		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr3:133583485G>A	ENST00000285208.4	-	2	421	c.72C>T	c.(70-72)gtC>gtT	p.V24V	RAB6B_ENST00000469959.1_Splice_Site_p.V24V|RAB6B_ENST00000486858.1_Splice_Site_p.V11V|RAB6B_ENST00000543906.1_Splice_Site_p.V24V	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	24					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.V24V(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	11						ACGTCTTCCCGACTGCAAAAC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		0,4406		0,0,2203	208	177	187		72	-2.5	1	3		187	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	RAB6B	NM_016577.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		24/209	133583485	1,13005	2203	4300	6503	135066175	SO:0001630	splice_region_variant	51560			AF166492	CCDS3082.1	3q22.1	2008-05-15			ENSG00000154917	ENSG00000154917		"RAB, member RAS oncogene"	14902	protein-coding gene	gene with protein product		615852					Standard	NM_016577		Approved		uc003epy.3	Q9NRW1	OTTHUMG00000159749	ENST00000285208.4:c.71-1C>T	3.37:g.133583485G>A			135066175	B2R5Z9|B7Z337|D3DND3|Q92929	Silent	SNP	ENST00000285208.4	37	CCDS3082.1																																																																																				0.473	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1		Silent	A	133583485	G	A	133583485	5	1	41	1	0	0	0	0	0	0	1	0	12989	1072	37	1	582	1	RAB6B	3	133583485	Splice_Site	SNP	G	TCGA-AG-3881-01A-01W-0899-10	4966988	133583485	64438945	19	3784										
FRYL	285527	broad.mit.edu	37	chr4	48549744	48549744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ttaataagtgcagaagcaggCgtttacaatgttcatacacc	8	8	1	1	rs372020475		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:48549744C>T	ENST00000503238.1	-	38	4930	c.4931G>A	c.(4930-4932)cGc>cAc	p.R1644H	FRYL_ENST00000358350.4_Missense_Mutation_p.R1644H|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.R1644H			O94915	FRYL_HUMAN	FRY-like	1644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.R1644H(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						CAGAAGCAGGCGTTTACAATG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	HIS/ARG	0,3750		0,0,1875	86	82	83		4931	5.5	1	4		83	1,8197		0,1,4098	no	missense	FRYL	NM_015030.1	29	0,1,5973	TT,TC,CC		0.0122,0.0,0.0084	benign	1644/3014	48549744	1,11947	1875	4099	5974	48244501	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.4931G>A	4.37:g.48549744C>T	ENSP00000426064:p.Arg1644His		48244501	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.963991	0.53507	0.0	1.22E-4	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810	T;T;T	0.04917	3.53;3.53;3.53	5.53	5.53	0.82687	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.10981	0.0268	M	0.66939	2.045	0.80722	D	1	B;P;P	0.47350	0.021;0.894;0.87	B;B;B	0.42593	0.019;0.392;0.33	T	0.01512	-1.1336	10	0.45353	T	0.12	.	13.7137	0.62682	0.0:0.9264:0.0:0.0736	.	475;1644;1644	Q6ZR29;O94915;F5GX82	.;FRYL_HUMAN;.	H	1644	ENSP00000426064:R1644H;ENSP00000351113:R1644H;ENSP00000441114:R1644H	ENSP00000351113:R1644H	R	-	2	0	FRYL	48244501	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	5.735000	0.68587	2.596000	0.87737	0.460000	0.39030	CGC		0.398	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48549744	C	T	48549744	3	4	41	1	0	0	0	0	1	0	0	0	6083	768	27	1	4206	1	FRYL	4	48549744	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		48549744	142604532	20	3785										
LPHN3	23284	broad.mit.edu	37	chr4	62936364	62936364	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctctctctataccagcatgcCgacactggctggtgtggccg	11	14	2	0	rs371830824		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:62936364C>T	ENST00000514591.1	+	25	4477	c.4148C>T	c.(4147-4149)cCg>cTg	p.P1383L	LPHN3_ENST00000508693.1_3'UTR|LPHN3_ENST00000514996.1_Missense_Mutation_p.P1417L|LPHN3_ENST00000514157.1_3'UTR|LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000507164.1_3'UTR|LPHN3_ENST00000506746.1_Missense_Mutation_p.P1485L|LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.P1383L|RP11-84A1.3_ENST00000509461.1_RNA|RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000507625.1_Missense_Mutation_p.P1442L|LPHN3_ENST00000506720.1_Missense_Mutation_p.P1494L|LPHN3_ENST00000509896.1_3'UTR|LPHN3_ENST00000508946.1_Missense_Mutation_p.P1426L|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000511324.1_3'UTR|LPHN3_ENST00000506700.1_3'UTR			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1361					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.P1383L(1)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						ACCAGCATGCCGACACTGGCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	LEU/PRO	1,1383		0,1,691	23	30	28		4148	5.4	1	4		28	0,3182		0,0,1591	no	missense	LPHN3	NM_015236.4	98	0,1,2282	TT,TC,CC		0.0,0.0723,0.0219	probably-damaging	1383/1470	62936364	1,4565	692	1591	2283	62618959	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.4148C>T	4.37:g.62936364C>T	ENSP00000422533:p.Pro1383Leu		62618959	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972159	0.74246	7.23E-4	0.0	ENSG00000150471	ENST00000514591;ENST00000545650;ENST00000295349;ENST00000507625;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T	0.79033	-1.18;-1.18;-1.23;-0.9;-0.93;-0.94;-0.92	5.39	5.39	0.77823	GPCR, family 2, latrophilin, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88040	0.6330	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88960	0.3393	10	0.87932	D	0	.	19.1541	0.93503	0.0:1.0:0.0:0.0	.	1383;1361	E9PE04;Q9HAR2	.;LPHN3_HUMAN	L	1383;1383;1361;1442;1426;1494;1485;1417	ENSP00000422533:P1383L;ENSP00000439831:P1383L;ENSP00000421372:P1442L;ENSP00000421627:P1426L;ENSP00000420931:P1494L;ENSP00000425884:P1485L;ENSP00000424258:P1417L	ENSP00000295349:P1361L	P	+	2	0	LPHN3	62618959	1.000000	0.71417	0.956000	0.39512	0.970000	0.65996	5.680000	0.68168	2.535000	0.85469	0.591000	0.81541	CCG		0.537	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62936364	C	T	62936364	3	4	41	1	0	0	0	0	1	0	0	0	8946	652	23	1	4238	1	LPHN3	4	62936364	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	14386620	62936364	128217912	21	3786										
UGT2A3	79799	broad.mit.edu	37	chr4	69816848	69816848	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	caaaactgaaagcattgaatTttttactctttccagaaagg	6	7	1	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:69816848T>C	ENST00000251566.4	-	1	661	c.631A>G	c.(631-633)Aat>Gat	p.N211D	UGT2A3_ENST00000420231.2_5'UTR	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	211					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.N211D(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AGCATTGAATTTTTTACTCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											52	53	53					4																	69816848		2203	4299	6502	69851437	SO:0001583	missense	79799				CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.631A>G	4.37:g.69816848T>C	ENSP00000251566:p.Asn211Asp		69851437	Q9H6S4	Missense_Mutation	SNP	ENST00000251566.4	37	CCDS3525.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.919144	0.52546	.	.	ENSG00000135220	ENST00000251566	T	0.73363	-0.74	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.90652	0.7068	H	0.98238	4.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93270	0.6651	10	0.87932	D	0	.	12.2413	0.54544	0.0:0.0:0.0:1.0	.	211	Q6UWM9	UD2A3_HUMAN	D	211	ENSP00000251566:N211D	ENSP00000251566:N211D	N	-	1	0	UGT2A3	69851437	1.000000	0.71417	0.810000	0.32431	0.029000	0.11900	6.329000	0.72920	1.996000	0.58369	0.482000	0.46254	AAT		0.393	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		C	69816848	T	C	69816848	3	2	41	1	0	0	0	0	1	0	0	0	16995	1841	64	4	976	4	UGT2A3	4	69816848	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	6880484	69816848	121337428	22	3787										
POU4F2	5458	broad.mit.edu	37	chr4	147560536	147560536	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gcagtggcagcagcggcggcGggggctcggaggctatgcgg	22	10	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:147560536G>T	ENST00000281321.3	+	1	492	c.244G>T	c.(244-246)Ggg>Tgg	p.G82W	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	82	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.G82W(1)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					cagcggcggcgggggcTCGGA	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	4											13	17	16					4																	147560536		2146	4239	6385	147779986	SO:0001583	missense	5458			U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.244G>T	4.37:g.147560536G>T	ENSP00000281321:p.Gly82Trp		147779986	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	37	CCDS34074.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.184756	0.57909	.	.	ENSG00000151615	ENST00000281321	D	0.90385	-2.66	4.78	4.78	0.61160	.	0.483231	0.19289	N	0.117942	D	0.91257	0.7244	N	0.22421	0.69	0.42466	D	0.992803	D	0.89917	1.0	D	0.87578	0.998	D	0.91803	0.5453	10	0.66056	D	0.02	.	13.2213	0.59890	0.0:0.0:1.0:0.0	.	82	Q12837	PO4F2_HUMAN	W	82	ENSP00000281321:G82W	ENSP00000281321:G82W	G	+	1	0	POU4F2	147779986	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	2.409000	0.44583	2.481000	0.83766	0.561000	0.74099	GGG		0.677	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		T	147560536	G	T	147560536	3	4	41	1	0	0	0	0	1	0	0	0	12310	1116	39	2	246	2	POU4F2	4	147560536	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	77743688	147560536	43593740	23	3788										
FBXW7	55294	broad.mit.edu	37	chr4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tttcatgaagatgcatacaaCgcacagtggaagtatgccca	9	9	1	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	114	Substitution - Missense(113)|Unknown(1)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	4											253	218	230					4																	153249384		2203	4300	6503	153468834	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His		153468834	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153249384	C	T	153249384	3	4	41	1	0	0	0	0	1	0	0	0	5788	536	19	1	745	1	FBXW7	4	153249384	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	5688848	153249384	37904892	24	3789										
C4orf41	60684	broad.mit.edu	37	chr4	184587552	184587552	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtggaaagaaaagcagtctgAgtgcgccaccagagtggaaa	14	7	1	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:184587552A>C	ENST00000334690.6	+	3	549	c.347A>C	c.(346-348)gAg>gCg	p.E116A	TRAPPC11_ENST00000357207.4_Missense_Mutation_p.E116A	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	116					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.E116A(1)									AAGCAGTCTGAGTGCGCCACC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	112	113					4																	184587552		2203	4300	6503	184824546	SO:0001583	missense	60684				CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"Trafficking protein particle complex"	25751	protein-coding gene	gene with protein product	"gryzun homolog (Drosophila)", "foie gras homolog (zebrafish)"	614138	"chromosome 4 open reading frame 41"	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.347A>C	4.37:g.184587552A>C	ENSP00000335371:p.Glu116Ala		184824546	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986849	0.74589	.	.	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.57272	0.2042	L	0.56280	1.765	0.80722	D	1	P;P	0.45715	0.787;0.865	B;B	0.43478	0.241;0.421	T	0.58707	-0.7589	9	0.39692	T	0.17	.	15.6867	0.77415	1.0:0.0:0.0:0.0	.	116;116	Q7Z392;Q7Z392-3	TPC11_HUMAN;.	A	116	.	ENSP00000335371:E116A	E	+	2	0	C4orf41	184824546	1.000000	0.71417	0.293000	0.24932	0.993000	0.82548	9.158000	0.94723	2.109000	0.64355	0.460000	0.39030	GAG		0.478	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942		C	184587552	A	C	184587552	3	2	41	1	0	0	0	0	1	0	0	0	2276	304	11	4	353	4	C4orf41	4	184587552	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10	31338168	184587552	6566724	25	3790										
SORBS2	8470	broad.mit.edu	37	chr4	186545170	186545170	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ttcacggagcagatcacctcGgagttcatcaggtccttgcg	11	12	4	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr4:186545170G>A	ENST00000284776.7	-	13	1910	c.1401C>T	c.(1399-1401)tcC>tcT	p.S467S	SORBS2_ENST00000431808.1_Silent_p.S467S|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000355634.5_Silent_p.S567S|SORBS2_ENST00000418609.1_Silent_p.S371S|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000498125.1_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	467					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.S467S(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		AGATCACCTCGGAGTTCATCA	0.592																																					Esophageal Squamous(153;41 2433 9491 36028)											1	Substitution - coding silent(1)	large_intestine(1)	4											98	89	92					4																	186545170		2203	4300	6503	186782164	SO:0001819	synonymous_variant	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1401C>T	4.37:g.186545170G>A			186782164	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																				0.592	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		A	186545170	G	A	186545170	2	1	41	1	0	0	0	0	0	0	0	1	14965	1103	39	1		1	SORBS2	4	186545170	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	1957618	186545170	4609106	26	3791										
PAPD7	11044	broad.mit.edu	37	chr5	6739912	6739912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agctgctggagcaagccctgCggaagcacaacgtggctgag	15	11	0	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr5:6739912C>T	ENST00000230859.6	+	4	334	c.205C>T	c.(205-207)Cgg>Tgg	p.R69W		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	299	Ala-rich.				double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.R69W(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GCAAGCCCTGCGGAAGCACAA	0.587																																					NSCLC(7;212 333 5667 23379 46547)											1	Substitution - Missense(1)	large_intestine(1)	5											94	79	84					5																	6739912		2203	4300	6503	6792912	SO:0001583	missense	11044			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.205C>T	5.37:g.6739912C>T	ENSP00000230859:p.Arg69Trp		6792912	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	37	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028173	0.54790	.	.	ENSG00000112941	ENST00000230859	T	0.50001	0.76	5.14	5.14	0.70334	Nucleotidyl transferase domain (1);	0.130709	0.45126	D	0.000396	T	0.47673	0.1458	M	0.78916	2.43	0.50813	D	0.999893	P;P	0.42961	0.795;0.629	B;B	0.36922	0.236;0.112	T	0.56920	-0.7899	10	0.59425	D	0.04	-9.9064	11.9054	0.52708	0.2982:0.7018:0.0:0.0	.	69;69	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	W	69	ENSP00000230859:R69W	ENSP00000230859:R69W	R	+	1	2	PAPD7	6792912	0.977000	0.34250	1.000000	0.80357	0.999000	0.98932	1.912000	0.39946	2.379000	0.81126	0.655000	0.94253	CGG		0.587	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		T	6739912	C	T	6739912	3	4	41	1	0	0	0	0	1	0	0	0	11457	759	27	1	215	1	PAPD7	5	6739912	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		6739912	174175348	27	3792										
NUP155	9631	broad.mit.edu	37	chr5	37304852	37304852	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aagatttacctgtagcagctTatctgcaaggtcgacttgta	9	8	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr5:37304852T>G	ENST00000231498.3	-	27	3354	c.3151A>C	c.(3151-3153)Aag>Cag	p.K1051Q	NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000513532.1_Missense_Mutation_p.K987Q|NUP155_ENST00000381843.2_Missense_Mutation_p.K992Q	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1051					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.K1051Q(1)		endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGTAGCAGCTTATCTGCAAGG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											125	129	128					5																	37304852		2203	4300	6503	37340609	SO:0001583	missense	9631			AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.3151A>C	5.37:g.37304852T>G	ENSP00000231498:p.Lys1051Gln		37340609	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	37	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.492599	0.84962	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.77620	-1.1;-1.1;-1.11	5.54	5.54	0.83059	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.042164	0.85682	D	0.000000	D	0.83385	0.5243	L	0.59436	1.845	0.80722	D	1	D;P	0.60160	0.987;0.615	P;P	0.61003	0.882;0.536	T	0.80953	-0.1152	10	0.23891	T	0.37	-3.2149	15.6762	0.77326	0.0:0.0:0.0:1.0	.	987;1051	E9PF10;O75694	.;NU155_HUMAN	Q	1051;992;1013;987	ENSP00000231498:K1051Q;ENSP00000371265:K992Q;ENSP00000422019:K987Q	ENSP00000231498:K1051Q	K	-	1	0	NUP155	37340609	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	5.880000	0.69698	2.102000	0.63906	0.533000	0.62120	AAG		0.318	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		G	37304852	T	G	37304852	3	3	41	1	0	0	0	0	1	0	0	0	10787	1763	61	4	1060	4	NUP155	5	37304852	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	30564940	37304852	143610408	28	3793										
C7	730	broad.mit.edu	37	chr5	40981662	40981662	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cagcataaggccttgtgctgCggaaacccagtaggctcctg	12	12	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr5:40981662C>T	ENST00000313164.9	+	18	2878	c.2519C>T	c.(2518-2520)gCg>gTg	p.A840V		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	840	Factor I module (FIM) 2.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.A840V(1)					Ovarian(839;0.0112)				CCTTGTGCTGCGGAAACCCAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											46	47	46					5																	40981662		2040	4204	6244	41017419	SO:0001583	missense	730			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.2519C>T	5.37:g.40981662C>T	ENSP00000322061:p.Ala840Val		41017419	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	c	13.06	2.125489	0.37533	.	.	ENSG00000112936	ENST00000313164	T	0.64260	-0.09	5.74	-5.23	0.02798	Factor I / membrane attack complex (1);	1.556280	0.03611	N	0.234835	T	0.48607	0.1509	L	0.50333	1.59	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21109	-1.0255	10	0.46703	T	0.11	1.2935	0.658	0.00838	0.1938:0.2244:0.2745:0.3073	.	840	P10643	CO7_HUMAN	V	840	ENSP00000322061:A840V	ENSP00000322061:A840V	A	+	2	0	C7	41017419	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.236000	0.00546	-1.157000	0.02815	-1.944000	0.00493	GCG		0.587	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			T	40981662	C	T	40981662	3	4	41	1	0	0	0	0	1	0	0	0	2381	768	27	1	2589	1	C7	5	40981662	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	3676810	40981662	139933598	29	3794										
GPR98	84059	broad.mit.edu	37	chr5	90072351	90072351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtcatctaggcacatcctcaTtggggaaccctcagcaaaat	8	12	4	0	rs370746571		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr5:90072351T>C	ENST00000405460.2	+	61	12581	c.12485T>C	c.(12484-12486)aTt>aCt	p.I4162T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4162	Calx-beta 28. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.I4162T(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CACATCCTCATTGGGGAACCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5						T	THR/ILE	1,3805		0,1,1902	118	117	117		12485	5.1	0.7	5		117	0,8266		0,0,4133	no	missense	GPR98	NM_032119.3	89	0,1,6035	CC,CT,TT		0.0,0.0263,0.0083	probably-damaging	4162/6307	90072351	1,12071	1903	4133	6036	90108107	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12485T>C	5.37:g.90072351T>C	ENSP00000384582:p.Ile4162Thr		90108107	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.295754	0.40594	2.63E-4	0.0	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27256	1.68	5.13	5.13	0.70059	.	0.143828	0.64402	D	0.000010	T	0.24890	0.0604	M	0.62723	1.935	0.80722	D	1	P	0.39480	0.675	B	0.28553	0.091	T	0.10042	-1.0647	10	0.54805	T	0.06	.	14.9054	0.70715	0.0:0.0:0.0:1.0	.	4162	Q8WXG9	GPR98_HUMAN	T	4162	ENSP00000384582:I4162T	ENSP00000296619:I4162T	I	+	2	0	GPR98	90108107	1.000000	0.71417	0.725000	0.30721	0.138000	0.21146	6.944000	0.75940	2.055000	0.61198	0.519000	0.50382	ATT		0.393	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90072351	T	C	90072351	3	2	41	1	0	0	0	0	1	0	0	0	6742	1493	52	4	12727	4	GPR98	5	90072351	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	49090689	90072351	90842909	30	3795										
APC	324	broad.mit.edu	37	chr5	112175390	112175390	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctccctccaaaagtggtgctCagacacccaaaagtccacct	6	16	1	1	rs121913328		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr5:112175390C>T	ENST00000457016.1	+	16	4479	c.4099C>T	c.(4099-4101)Cag>Tag	p.Q1367*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1367*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1367*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1367	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1367*(26)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGTGGTGCTCAGACACCCAA	0.453	Q1367*(C2BBE1_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	28	Substitution - Nonsense(26)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(26)|soft_tissue(1)|skin(1)	5	GRCh37	CM940072	APC	M	rs121913328						75	73	74					5																	112175390		2202	4300	6502	112203289	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4099C>T	5.37:g.112175390C>T	ENSP00000413133:p.Gln1367*		112203289	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.623019	0.98890	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.166931	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.8965	17.2482	0.87034	0.0:0.8741:0.1259:0.0	.	.	.	.	X	1367	.	.	Q	+	1	0	APC	112203289	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.223000	0.72257	1.603000	0.50134	0.655000	0.94253	CAG		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175390	C	T	112175390	4	4	41	1	0	0	0	0	0	1	0	0	763	827	29	3	4157	3	APC	5	112175390	Nonsense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	22103039	112175390	68739870	31	3796										
DAAM2	23500	broad.mit.edu	37	chr6	39846311	39846311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cccgggagtcccaggagctgCgccaggctcggggacaagtg	17	13	0	0	rs375733561		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr6:39846311C>T	ENST00000398904.2	+	13	1674	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	DAAM2_ENST00000538976.1_Missense_Mutation_p.R498C|DAAM2_ENST00000274867.4_Missense_Mutation_p.R498C			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	498					actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.R498C(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCAGGAGCTGCGCCAGGCTCG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	CYS/ARG,CYS/ARG	0,4022		0,0,2011	26	32	30		1492,1492	4.5	1	6		30	1,8345		0,1,4172	no	missense,missense	DAAM2	NM_001201427.1,NM_015345.3	180,180	0,1,6183	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging	498/1069,498/1068	39846311	1,12367	2011	4173	6184	39954289	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1492C>T	6.37:g.39846311C>T	ENSP00000381876:p.Arg498Cys		39954289	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439366	0.83885	0.0	1.2E-4	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.76186	-1.0;-1.0;-1.0	5.46	4.53	0.55603	.	0.115379	0.64402	D	0.000020	T	0.74786	0.3762	L	0.53249	1.67	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.59288	0.855;0.719	T	0.77043	-0.2734	10	0.59425	D	0.04	.	12.6434	0.56721	0.2879:0.7121:0.0:0.0	.	498;498	G5EA45;Q86T65	.;DAAM2_HUMAN	C	498	ENSP00000274867:R498C;ENSP00000381876:R498C;ENSP00000437808:R498C	ENSP00000274867:R498C	R	+	1	0	DAAM2	39954289	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.211000	0.51137	2.552000	0.86080	0.555000	0.69702	CGC		0.567	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39846311	C	T	39846311	3	4	41	1	0	0	0	0	1	0	0	0	4222	768	27	1	1538	1	DAAM2	6	39846311	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		39846311	131268756	32	3797										
CRISP1	167	broad.mit.edu	37	chr6	49819777	49819777	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agggcgttgtgtatattaacGatctcttcttgtacatttgg	10	6	2	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr6:49819777G>A	ENST00000335847.4	-	3	233	c.132C>T	c.(130-132)atC>atT	p.I44I	CRISP1_ENST00000329411.5_Silent_p.I44I|CRISP1_ENST00000355791.2_Silent_p.I44I|CRISP1_ENST00000505118.1_Silent_p.I44I|CRISP1_ENST00000536021.1_Silent_p.I44I|CRISP1_ENST00000507853.1_Silent_p.I44I	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	44					binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)	p.I44I(2)		endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					GTATATTAACGATCTCTTCTT	0.378																																																2	Substitution - coding silent(2)	large_intestine(1)|skin(1)	6											204	195	198					6																	49819777		2203	4300	6503	49927736	SO:0001819	synonymous_variant	167			D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.132C>T	6.37:g.49819777G>A			49927736	B5BU98|O00698|Q13248|Q14082|Q96SF6	Silent	SNP	ENST00000335847.4	37	CCDS4931.1																																																																																				0.378	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		A	49819777	G	A	49819777	2	1	41	1	0	0	0	0	0	0	0	1	3885	1048	37	1		1	CRISP1	6	49819777	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	9973466	49819777	121295290	33	3798										
FAM83B	222584	broad.mit.edu	37	chr6	54735195	54735195	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aagaatttcttgtccaggaaCgagtttcagactttcttgct	8	8	3	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr6:54735195C>T	ENST00000306858.7	+	2	267	c.151C>T	c.(151-153)Cga>Tga	p.R51*		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	51								p.R51*(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TGTCCAGGAACGAGTTTCAGA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											110	112	111					6																	54735195		2203	4300	6503	54843154	SO:0001587	stop_gained	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.151C>T	6.37:g.54735195C>T	ENSP00000304078:p.Arg51*		54843154	Q2M1P3|Q96DQ2	Nonsense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346733	0.95807	.	.	ENSG00000168143	ENST00000306858	.	.	.	5.41	3.44	0.39384	.	0.130688	0.47852	D	0.000212	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3111	8.3839	0.32488	0.3443:0.5395:0.1163:0.0	.	.	.	.	X	51	.	ENSP00000304078:R51X	R	+	1	2	FAM83B	54843154	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	1.096000	0.30976	1.358000	0.45922	0.460000	0.39030	CGA		0.388	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		T	54735195	C	T	54735195	4	4	41	1	0	0	0	0	0	1	0	0	5653	528	19	1	153	1	FAM83B	6	54735195	Nonsense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	4915418	54735195	116379872	34	3799										
PDE10A	10846	broad.mit.edu	37	chr6	165808723	165808723	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	acaaaaattccaggccacatGttttcaaaaggaccaatgtc	6	10	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr6:165808723G>T	ENST00000366882.1	-	16	1576	c.1422C>A	c.(1420-1422)aaC>aaA	p.N474K	PDE10A_ENST00000354448.4_Missense_Mutation_p.N474K|PDE10A_ENST00000539869.2_Missense_Mutation_p.N484K			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	474					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.N474K(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	CAGGCCACATGTTTTCAAAAG	0.338																																					Esophageal Squamous(22;308 615 5753 12038 40624)											1	Substitution - Missense(1)	large_intestine(1)	6											73	72	72					6																	165808723		2203	4300	6503	165728713	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1422C>A	6.37:g.165808723G>T	ENSP00000355847:p.Asn474Lys		165728713	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	G	6.598	0.478612	0.12521	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.75367	-0.93;-0.93	5.57	2.57	0.30868	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.298435	0.40144	N	0.001180	T	0.34337	0.0894	N	0.22421	0.69	0.36488	D	0.868235	B;B	0.18461	0.028;0.001	B;B	0.15870	0.014;0.0	T	0.12993	-1.0526	10	0.19590	T	0.45	.	4.3443	0.11126	0.2602:0.0:0.5511:0.1887	.	484;474	Q9ULW9;Q9Y233	.;PDE10_HUMAN	K	474;502;484;474;473	ENSP00000355847:N474K;ENSP00000346435:N474K	ENSP00000341187:N484K	N	-	3	2	PDE10A	165728713	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.519000	0.22862	1.363000	0.46019	0.650000	0.86243	AAC		0.338	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165808723	G	T	165808723	3	4	41	1	0	0	0	0	1	0	0	0	11661	1368	48	2	949	2	PDE10A	6	165808723	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	111073528	165808723	5306344	35	3800										
PMS2	5395	broad.mit.edu	37	chr7	6017218	6017219	+	Splice_Site	DNP	CC	CC	TG													0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agccaggctttctttacttaCcgacttccggcaggctctgg							TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:6017218_6017219CC>TG	ENST00000265849.7	-	14	2550_2551	c.2445_2446GG>CA	c.(2443-2448)tcGGtg>tcCAtg	p.V816M	PMS2_ENST00000382321.4_Splice_Site_p.V415M|PMS2_ENST00000441476.2_Splice_Site_p.V710M	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	816					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.?(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TCTTTACTTACCGACTTCCGGC	0.554			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	1	Unknown(1)	large_intestine(1)	7																																								5983745	SO:0001630	splice_region_variant	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2445_2446delinsTG	7.37:g.6017218_6017219delinsTG			5983744	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Splice_Site	DNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.554	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	Missense_Mutation	TG	6017219	CC	TG	6017218	5	4	41	1	0	0	0	0	0	0	1	0	12174	521	18	3	150	3	PMS2	7	6017218	Splice_Site	DNP	CC	TCGA-AG-3881-01A-01W-0899-10		6017218	153121445	36	3801										
DPY19L1	23333	broad.mit.edu	37	chr7	34994377	34994377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cagttccaaataaccaaaaaCatccttgaataacctaaaca	2	11	0	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:34994377C>T	ENST00000310974.4	-	13	1178	c.1034G>A	c.(1033-1035)tGt>tAt	p.C345Y	DPY19L1_ENST00000462134.2_5'Flank	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	345						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.C345Y(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TAACCAAAAACATCCTTGAAT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	7											25	21	22					7																	34994377		1790	4035	5825	34960902	SO:0001583	missense	23333			AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1034G>A	7.37:g.34994377C>T	ENSP00000308695:p.Cys345Tyr		34960902	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	C	4.819	0.152202	0.09185	.	.	ENSG00000173852	ENST00000310974;ENST00000446375	T;T	0.53423	0.62;0.62	5.17	5.17	0.71159	.	0.362487	0.32357	N	0.006209	T	0.36248	0.0960	L	0.47716	1.5	0.38355	D	0.944442	P	0.43885	0.82	B	0.39119	0.291	T	0.35076	-0.9803	10	0.02654	T	1	-10.3169	14.0434	0.64690	0.0:1.0:0.0:0.0	.	345	Q2PZI1	D19L1_HUMAN	Y	345;115	ENSP00000308695:C345Y;ENSP00000400510:C115Y	ENSP00000308695:C345Y	C	-	2	0	DPY19L1	34960902	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	1.713000	0.37951	2.687000	0.91594	0.591000	0.81541	TGT		0.279	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			T	34994377	C	T	34994377	3	4	41	1	0	0	0	0	1	0	0	0	4751	478	17	3	1033	3	DPY19L1	7	34994377	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	28977159	34994377	124144286	37	3802										
C7orf10	79783	broad.mit.edu	37	chr7	40228168	40228168	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	catattatctcagtgttaacCgaaataaaaaagtaagaata	5	5	1	1	rs137852862	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:40228168C>T	ENST00000335693.4	+	4	345	c.322C>T	c.(322-324)Cga>Tga	p.R108*	C7orf10_ENST00000540834.1_Nonsense_Mutation_p.R101*|C7orf10_ENST00000309930.5_Nonsense_Mutation_p.R108*|C7orf10_ENST00000401647.2_Nonsense_Mutation_p.R108*	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		108					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)	p.R108*(2)		endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						CAGTGTTAACCGAAATAAAAA	0.333													C|||	2	0.000399361	0	0.0014	5008	,	,		14957	0		0.001	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(2)	7	GRCh37	CM085299	C7orf10	M	rs137852862	C	stop/ARG,stop/ARG,stop/ARG,stop/ARG	1,3661		0,1,1830	49	50	49	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	322,322,322,322	4.9	1	7	dbSNP_133	49	1,8155		0,1,4077	yes	stop-gained,stop-gained,stop-gained,stop-gained	C7orf10	NM_001193311.1,NM_001193312.1,NM_001193313.1,NM_024728.2	,,,	0,2,5907	TT,TC,CC		0.0123,0.0273,0.0169	,,,	108/472,108/398,108/446,108/435	40228168	2,11816	1831	4078	5909	40194693	SO:0001587	stop_gained	79783																														ENST00000335693.4:c.322C>T	7.37:g.40228168C>T	ENSP00000338475:p.Arg108*		40194693	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Nonsense_Mutation	SNP	ENST00000335693.4	37	CCDS55105.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	21.7|21.7	4.183373|4.183373	0.78677|0.78677	2.73E-4|2.73E-4	1.23E-4|1.23E-4	ENSG00000175600|ENSG00000175600	ENST00000413931|ENST00000309930;ENST00000401647;ENST00000335693;ENST00000540834	.|.	.|.	.|.	5.77|5.77	4.88|4.88	0.63580|0.63580	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.33118|.	0.0852|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35871|.	-0.9771|.	3|.	.|0.02654	.|T	.|1	-7.2377|-7.2377	12.5126|12.5126	0.56013|0.56013	0.4117:0.5883:0.0:0.0|0.4117:0.5883:0.0:0.0	.|.	.|.	.|.	.|.	L|X	119|108;108;108;101	.|.	.|ENSP00000312054:R108X	P|R	+|+	2|1	0|2	C7orf10|C7orf10	40194693|40194693	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.990000|0.990000	0.78478|0.78478	1.308000|1.308000	0.33528|0.33528	1.539000|1.539000	0.49286|0.49286	0.585000|0.585000	0.79938|0.79938	CCG|CGA		0.333	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1			T	40228168	C	T	40228168	4	4	41	1	0	0	0	0	0	1	0	0	2382	644	23	1	336	1	C7orf10	7	40228168	Nonsense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	5233791	40228168	118910495	38	3803										
SRCRB4D	136853	broad.mit.edu	37	chr7	76019551	76019551	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cgccaggggctgcgagggccTggccacagcccagctggcgg	18	15	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:76019551T>A	ENST00000275560.3	-	11	1900	c.1553A>T	c.(1552-1554)cAg>cTg	p.Q518L	SRCRB4D_ENST00000492979.2_5'UTR	NM_080744.1	NP_542782.1												p.Q518L(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						TGCGAGGGCCTGGCCACAGCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	7											43	41	42					7																	76019551		2202	4300	6502	75857487	SO:0001583	missense	136853																														ENST00000275560.3:c.1553A>T	7.37:g.76019551T>A	ENSP00000275560:p.Gln518Leu		75857487		Missense_Mutation	SNP	ENST00000275560.3	37	CCDS5585.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.070976	0.36566	.	.	ENSG00000146700	ENST00000275560	T	0.44083	0.93	5.81	0.805	0.18703	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.425454	0.25795	N	0.028248	T	0.23094	0.0558	N	0.13168	0.305	0.27635	N	0.94789	B	0.20164	0.042	B	0.32022	0.139	T	0.18745	-1.0327	10	0.25106	T	0.35	.	5.359	0.16077	0.0:0.2734:0.2582:0.4684	.	518	Q8WTU2	SRB4D_HUMAN	L	518	ENSP00000275560:Q518L	ENSP00000275560:Q518L	Q	-	2	0	SRCRB4D	75857487	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	-0.404000	0.07205	0.123000	0.18342	-0.256000	0.11100	CAG		0.652	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3			A	76019551	T	A	76019551	3	1	41	1	0	0	0	0	1	0	0	0	15176	1580	55	5	178	5	SRCRB4D	7	76019551	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	35791383	76019551	83119112	39	3804										
SAMD9L	219285	broad.mit.edu	37	chr7	92765029	92765029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	attatctaattgtcccggatCatgattgtcactttcagggg	9	8	4	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:92765029C>A	ENST00000318238.4	-	5	1472	c.256G>T	c.(256-258)Gat>Tat	p.D86Y	SAMD9L_ENST00000437805.1_Missense_Mutation_p.D86Y|SAMD9L_ENST00000411955.1_Missense_Mutation_p.D86Y	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	86					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.D86Y(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGTCCCGGATCATGATTGTCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											130	145	140					7																	92765029		2203	4300	6503	92602965	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.256G>T	7.37:g.92765029C>A	ENSP00000326247:p.Asp86Tyr		92602965	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.973799	0.53720	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.14144	2.53;2.53;2.53	4.5	0.0108	0.14084	.	0.653293	0.13839	N	0.359152	T	0.20577	0.0495	L	0.51422	1.61	0.09310	N	1	D;P	0.60160	0.987;0.785	P;P	0.55303	0.773;0.465	T	0.09357	-1.0678	10	0.66056	D	0.02	-6.9358	8.4698	0.32977	0.0:0.5326:0.0:0.4674	.	86;86	Q8IVG5-2;Q8IVG5	.;SAM9L_HUMAN	Y	86	ENSP00000326247:D86Y;ENSP00000405760:D86Y;ENSP00000408796:D86Y	ENSP00000326247:D86Y	D	-	1	0	SAMD9L	92602965	0.000000	0.05858	0.012000	0.15200	0.052000	0.14988	-0.478000	0.06575	0.050000	0.15949	0.460000	0.39030	GAT		0.373	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92765029	C	A	92765029	3	1	41	1	0	0	0	0	1	0	0	0	13864	826	29	2	4502	2	SAMD9L	7	92765029	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	16745478	92765029	66373634	40	3805										
AKR1B15	441282	broad.mit.edu	37	chr7	134260639	134260639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gccactccaagggcatcaccGttacggcctacagccccctg	9	18	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:134260639G>A	ENST00000457545.2	+	8	963	c.703G>A	c.(703-705)Gtt>Att	p.V235I	AKR1B15_ENST00000423958.1_Missense_Mutation_p.V207I	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	235							oxidoreductase activity (GO:0016491)	p.V253I(1)|p.V207I(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						GGGCATCACCGTTACGGCCTA	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	7											73	60	64					7																	134260639		2202	4298	6500	133911179	SO:0001583	missense	441282				CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.703G>A	7.37:g.134260639G>A	ENSP00000389289:p.Val235Ile		133911179	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	G	2.857	-0.237039	0.05944	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.23348	1.91;1.91	3.87	1.06	0.20224	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.17408	0.0418	L	0.41236	1.265	0.44462	D	0.997391	B;P	0.35481	0.344;0.504	B;B	0.35470	0.094;0.203	T	0.07868	-1.0750	9	0.17832	T	0.49	.	8.0939	0.30816	0.2791:0.0:0.7209:0.0	.	207;235	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	I	235;207	ENSP00000389289:V235I;ENSP00000397009:V207I	ENSP00000397009:V207I	V	+	1	0	AKR1B15	133911179	0.666000	0.27475	0.007000	0.13788	0.014000	0.08584	0.930000	0.28858	0.021000	0.15133	-0.255000	0.11280	GTT		0.488	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			A	134260639	G	A	134260639	3	1	41	1	0	0	0	0	1	0	0	0	468	1145	40	1	725	1	AKR1B15	7	134260639	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	41495610	134260639	24878024	41	3806										
C7orf29	113763	broad.mit.edu	37	chr7	150028109	150028109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atctgtgggagaatgagaccGttggagcccaggatgacccc	14	10	1	3	rs370437244		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr7:150028109G>A	ENST00000343855.4	+	1	1172	c.616G>A	c.(616-618)Gtt>Att	p.V206I	LRRC61_ENST00000323078.7_Intron|LRRC61_ENST00000359623.4_Intron|LRRC61_ENST00000493307.1_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	206								p.V206I(1)									GAATGAGACCGTTGGAGCCCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	,,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	44	48	46		,,616	-2	0	7		46	0,8600		0,0,4300	no	intron,intron,missense	LRRC61,C7orf29	NM_001142928.1,NM_023942.2,NM_138434.2	,,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,benign	,,206/237	150028109	1,13005	2203	4300	6503	149659042	SO:0001583	missense	113763			BC011406	CCDS5900.1	7q35	2013-05-03	2013-05-03	2013-05-03	ENSG00000188707	ENSG00000188707			21720	protein-coding gene	gene with protein product		615252	"chromosome 7 open reading frame 29"	C7orf29		23533661	Standard	NM_138434		Approved			Q96FA7	OTTHUMG00000158328	ENST00000343855.4:c.616G>A	7.37:g.150028109G>A	ENSP00000343242:p.Val206Ile		149659042		Missense_Mutation	SNP	ENST00000343855.4	37	CCDS5900.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.281545	0.00251	2.27E-4	0.0	ENSG00000188707	ENST00000343855	.	.	.	4.18	-1.95	0.07548	.	0.618525	0.12505	N	0.463038	T	0.18257	0.0438	N	0.12182	0.205	0.09310	N	1	B	0.14805	0.011	B	0.09377	0.004	T	0.32798	-0.9893	9	0.05525	T	0.97	.	9.9295	0.41514	0.6495:0.0:0.3505:0.0	.	206	Q96FA7	CG029_HUMAN	I	206	.	ENSP00000343242:V206I	V	+	1	0	C7orf29	149659042	0.000000	0.05858	0.030000	0.17652	0.084000	0.17831	0.134000	0.15932	-0.347000	0.08299	-1.034000	0.02401	GTT		0.582	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434		A	150028109	G	A	150028109	3	1	41	1	0	0	0	0	1	0	0	0	2391	1145	40	1	618	1	C7orf29	7	150028109	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	15767470	150028109	9110554	42	3807										
SLC30A8	169026	broad.mit.edu	37	chr8	118183325	118183325	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aaagagcttattttagcagtCgacggggtgctgtctgtgca	13	7	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr8:118183325C>T	ENST00000456015.2	+	7	882	c.882C>T	c.(880-882)gtC>gtT	p.V294V	SLC30A8_ENST00000427715.2_Silent_p.V245V|SLC30A8_ENST00000521243.1_Silent_p.V245V|SLC30A8_ENST00000519688.1_Silent_p.V245V	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	294					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.V294V(2)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TTTTAGCAGTCGACGGGGTGC	0.443																																					Ovarian(162;1202 1922 6011 16223 52092)											2	Substitution - coding silent(2)	large_intestine(2)	8											171	157	162					8																	118183325		2203	4300	6503	118252506	SO:0001819	synonymous_variant	169026				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.882C>T	8.37:g.118183325C>T			118252506	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Silent	SNP	ENST00000456015.2	37	CCDS6322.1																																																																																				0.443	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		T	118183325	C	T	118183325	2	4	41	1	0	0	0	0	0	0	0	1	14598	871	31	1		1	SLC30A8	8	118183325	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10		118183325	28180697	43	3808										
MTBP	27085	broad.mit.edu	37	chr8	121463513	121463513	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aatgtttgggtgctgttgagTgttttgaagaagaagacagt	14	2	0	5			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr8:121463513T>G	ENST00000305949.1	+	4	421	c.376T>G	c.(376-378)Tgt>Ggt	p.C126G		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	126					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)		p.C126G(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGCTGTTGAGTGTTTTGAAGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											106	110	108					8																	121463513		2203	4299	6502	121532694	SO:0001583	missense	27085				CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.376T>G	8.37:g.121463513T>G	ENSP00000303398:p.Cys126Gly		121532694	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	T	7.985	0.752000	0.15778	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.17	3.94	0.45596	.	0.288882	0.34986	N	0.003533	T	0.36690	0.0976	L	0.60455	1.87	0.27439	N	0.953762	P;P	0.46784	0.884;0.792	B;B	0.43658	0.426;0.194	T	0.18493	-1.0335	9	0.11794	T	0.64	-15.1118	9.1094	0.36718	0.2464:0.0:0.0:0.7536	.	126;126	Q96DY7;B4DUR5	MTBP_HUMAN;.	G	126	.	ENSP00000303398:C126G	C	+	1	0	MTBP	121532694	0.997000	0.39634	0.994000	0.49952	0.995000	0.86356	2.505000	0.45424	1.937000	0.56155	0.523000	0.50628	TGT		0.313	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		G	121463513	T	G	121463513	3	3	41	1	0	0	0	0	1	0	0	0	9942	1696	59	4	390	4	MTBP	8	121463513	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	3280188	121463513	24900509	44	3809										
FAM83A	84985	broad.mit.edu	37	chr8	124195326	124195326	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	catccaggcccaggccagggAgcccccgtgtcccccagaca	11	19	0	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr8:124195326A>G	ENST00000518448.1	+	2	2244	c.230A>G	c.(229-231)gAg>gGg	p.E77G	FAM83A_ENST00000536633.1_Missense_Mutation_p.E77G|RP11-539E17.5_ENST00000522383.1_RNA|U3_ENST00000408534.1_RNA|FAM83A_ENST00000276699.6_Missense_Mutation_p.E77G|FAM83A_ENST00000546351.1_Missense_Mutation_p.E77G|FAM83A_ENST00000522648.1_Missense_Mutation_p.E77G|FAM83A_ENST00000318462.6_Missense_Mutation_p.E77G			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	77								p.E77G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGCCAGGGAGCCCCCGTGT	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	8											40	38	39					8																	124195326		2203	4300	6503	124264507	SO:0001583	missense	84985			BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.230A>G	8.37:g.124195326A>G	ENSP00000428876:p.Glu77Gly		124264507	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	.	.	.	.	.	.	.	.	.	.	A	9.920	1.211912	0.22289	.	.	ENSG00000147689	ENST00000518448;ENST00000546351;ENST00000536633;ENST00000318462;ENST00000522648;ENST00000276699	T;T;T;T;T;T	0.12255	2.7;2.87;2.7;2.7;2.87;2.7	5.46	2.97	0.34412	.	0.536026	0.19922	N	0.103067	T	0.11879	0.0289	M	0.62016	1.91	0.27238	N	0.959212	B;B;B	0.12013	0.001;0.005;0.004	B;B;B	0.12156	0.004;0.004;0.007	T	0.24693	-1.0153	10	0.20519	T	0.43	-17.4172	3.6791	0.08304	0.6614:0.1367:0.071:0.131	.	77;77;77	Q86UY5-2;Q86UY5-3;Q86UY5	.;.;FA83A_HUMAN	G	77	ENSP00000428876:E77G;ENSP00000440565:E77G;ENSP00000445218:E77G;ENSP00000323034:E77G;ENSP00000427979:E77G;ENSP00000276699:E77G	ENSP00000276699:E77G	E	+	2	0	FAM83A	124264507	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	2.485000	0.45250	0.906000	0.36621	0.459000	0.35465	GAG		0.662	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899		G	124195326	A	G	124195326	3	3	41	1	0	0	0	0	1	0	0	0	5652	304	11	4	232	4	FAM83A	8	124195326	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10	2731813	124195326	22168696	45	3810										
TRAPPC9	83696	broad.mit.edu	37	chr8	141285900	141285900	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atatttcatcaccagaagaaGgttgcaatgaatgtgcagat	9	6	2	4			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr8:141285900G>T	ENST00000438773.2	-	15	2268	c.2135C>A	c.(2134-2136)cCt>cAt	p.P712H	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.P810H|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.P703H	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	712					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)		p.P810H(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						ACCAGAAGAAGGTTGCAATGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	8											67	63	65					8																	141285900		2203	4300	6503	141355082	SO:0001583	missense	83696			BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2135C>A	8.37:g.141285900G>T	ENSP00000405060:p.Pro712His		141355082	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829930	0.71258	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	4.43	4.43	0.53597	.	0.061273	0.64402	D	0.000003	T	0.74207	0.3686	L	0.51422	1.61	0.50813	D	0.999899	D;D;D;D	0.89917	0.996;1.0;0.994;0.999	D;D;P;D	0.77557	0.915;0.99;0.892;0.927	T	0.74945	-0.3491	9	0.45353	T	0.12	.	17.2723	0.87105	0.0:0.0:1.0:0.0	.	810;712;703;810	A6NIF0;Q96Q05;Q96Q05-3;Q96Q05-2	.;TPPC9_HUMAN;.;.	H	810;703;712	.	ENSP00000373978:P703H	P	-	2	0	TRAPPC9	141355082	1.000000	0.71417	0.414000	0.26521	0.981000	0.71138	5.368000	0.66133	2.299000	0.77371	0.650000	0.86243	CCT		0.338	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	141285900	G	T	141285900	3	4	41	1	0	0	0	0	1	0	0	0	16505	1000	35	2	1347	2	TRAPPC9	8	141285900	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	17090574	141285900	5078122	46	3811										
PTPRD	5789	broad.mit.edu	37	chr9	8471084	8471084	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cacaattattatgtagtaacCtctgcacaagaatgaataga	6	7	1	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr9:8471084C>A	ENST00000381196.4	-	28	3958	c.3415G>T	c.(3415-3417)Ggt>Tgt	p.G1139C	PTPRD_ENST00000397617.3_Splice_Site_p.G718C|PTPRD_ENST00000397606.3_Splice_Site_p.G718C|PTPRD_ENST00000486161.1_Splice_Site_p.G728C|PTPRD_ENST00000355233.5_Splice_Site_p.G728C|PTPRD_ENST00000356435.5_Splice_Site_p.G1139C|PTPRD_ENST00000397611.3_Splice_Site_p.G725C|PTPRD_ENST00000540109.1_Splice_Site_p.G1139C|PTPRD_ENST00000358503.5_Splice_Site_p.G1117C|PTPRD_ENST00000537002.1_Splice_Site_p.G725C|PTPRD_ENST00000360074.4_Splice_Site_p.G1126C	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1139					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G610C(1)|p.G1139C(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		ATGTAGTAACCTCTGCACAAG	0.388										TSP Lung(15;0.13)																																						2	Substitution - Missense(2)	large_intestine(2)	9											104	102	103					9																	8471084		2203	4300	6503	8461084	SO:0001630	splice_region_variant	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3414-1G>T	9.37:g.8471084C>A			8461084	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.399741	0.83120	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.72	5.72	0.89469	.	0.221960	0.45126	D	0.000397	T	0.54647	0.1871	N	0.19112	0.55	0.58432	D	0.999994	P;P;D;P;B;P;P;D;P	0.61080	0.747;0.897;0.984;0.776;0.0;0.903;0.801;0.989;0.7	P;B;P;B;B;P;P;P;B	0.57204	0.497;0.338;0.689;0.258;0.012;0.631;0.694;0.815;0.067	T	0.50083	-0.8869	9	.	.	.	.	19.4857	0.95027	0.0:1.0:0.0:0.0	.	718;723;728;728;725;725;1126;1139;1139	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	C	1139;1139;1126;1117;728;718;725;725;610;1139;728;718	ENSP00000370593:G1139C;ENSP00000348812:G1139C;ENSP00000353187:G1126C;ENSP00000351293:G1117C;ENSP00000347373:G728C;ENSP00000380741:G718C;ENSP00000380735:G725C;ENSP00000440515:G725C;ENSP00000438164:G1139C;ENSP00000417093:G728C;ENSP00000380731:G718C	.	G	-	1	0	PTPRD	8461084	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.447000	0.66606	2.711000	0.92665	0.655000	0.94253	GGT		0.388	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		Missense_Mutation	A	8471084	C	A	8471084	5	1	41	1	0	0	0	0	0	0	1	0	12836	695	24	2	2452	2	PTPRD	9	8471084	Splice_Site	SNP	C	TCGA-AG-3881-01A-01W-0899-10		8471084	132742347	47	3812										
COL27A1	85301	broad.mit.edu	37	chr9	117062385	117062385	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atgggcttcccaggaatggcAggtctcttcggacccaaggt	13	11	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr9:117062385A>T	ENST00000356083.3	+	50	5011	c.4620A>T	c.(4618-4620)gcA>gcT	p.A1540A		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1540	Collagen-like 15.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.A1540A(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CAGGAATGGCAGGTCTCTTCG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	9											126	114	118					9																	117062385		2203	4300	6503	116102206	SO:0001819	synonymous_variant	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4620A>T	9.37:g.117062385A>T			116102206	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																				0.542	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		T	117062385	A	T	117062385	2	4	41	1	0	0	0	0	0	0	0	1	3691	175	7	5		5	COL27A1	9	117062385	Silent	SNP	A	TCGA-AG-3881-01A-01W-0899-10	108591301	117062385	24151046	48	3813										
STXBP1	6812	broad.mit.edu	37	chr9	130444800	130444800	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atgagatgcgctgcgcctacGaggtgacccaggccaacgga	14	12	0	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr9:130444800G>C	ENST00000373299.1	+	18	1778	c.1663G>C	c.(1663-1665)Gag>Cag	p.E555Q	STXBP1_ENST00000481942.1_3'UTR|STXBP1_ENST00000373302.3_Missense_Mutation_p.E555Q	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	555					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)	p.E555Q(2)		breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CTGCGCCTACGAGGTGACCCA	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	9											97	77	84					9																	130444800		2203	4300	6503	129484621	SO:0001583	missense	6812			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.1663G>C	9.37:g.130444800G>C	ENSP00000362396:p.Glu555Gln		129484621	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	37	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	34	5.372786	0.95923	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299	T;T	0.78595	-1.19;-1.19	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.86401	0.5924	M	0.71920	2.185	0.80722	D	1	D;D	0.67145	0.996;0.995	D;P	0.63877	0.919;0.868	D	0.86327	0.1696	10	0.49607	T	0.09	-24.127	17.1696	0.86826	0.0:0.0:1.0:0.0	.	555;555	P61764;P61764-2	STXB1_HUMAN;.	Q	509;555;387;555	ENSP00000362399:E555Q;ENSP00000362396:E555Q	ENSP00000362396:E555Q	E	+	1	0	STXBP1	129484621	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.731000	0.98807	2.644000	0.89710	0.561000	0.74099	GAG		0.622	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		C	130444800	G	C	130444800	3	2	41	1	0	0	0	0	1	0	0	0	15391	1059	37	5	1733	5	STXBP1	9	130444800	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	13382415	130444800	10768631	49	3814										
COL5A1	1289	broad.mit.edu	37	chr9	137712036	137712036	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ggcgaccgtggtctccctggCccccagggctcctccggtcc	13	19	1	0	rs552985514		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr9:137712036C>A	ENST00000371817.3	+	58	4935	c.4521C>A	c.(4519-4521)ggC>ggA	p.G1507G		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1507	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.G1507G(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GTCTCCCTGGCCCCCAGGGCT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	77	79					9																	137712036		2203	4300	6503	136851857	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4521C>A	9.37:g.137712036C>A			136851857	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.617	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137712036	C	A	137712036	2	1	41	1	0	0	0	0	0	0	0	1	3702	726	26	2		2	COL5A1	9	137712036	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10	7267236	137712036	3501395	50	3815										
CUBN	8029	broad.mit.edu	37	chr10	17142210	17142210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agttgtccatggattctaacCggaaaaaagtgaaagtgata	10	5	1	2	rs145380076		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr10:17142210C>T	ENST00000377833.4	-	14	1624	c.1559G>A	c.(1558-1560)cGg>cAg	p.R520Q		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	520	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.R520Q(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGATTCTAACCGGAAAAAAGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											70	72	71					10																	17142210		2203	4300	6503	17182216	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1559G>A	10.37:g.17142210C>T	ENSP00000367064:p.Arg520Gln		17182216	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	0.390	-0.924062	0.02377	.	.	ENSG00000107611	ENST00000377833	T	0.17370	2.28	5.51	-1.31	0.09230	CUB (5);	0.577503	0.14251	N	0.331463	T	0.04272	0.0118	N	0.02142	-0.665	0.47153	D	0.999338	B	0.13594	0.008	B	0.09377	0.004	T	0.44267	-0.9339	10	0.07482	T	0.82	.	5.8002	0.18410	0.11:0.2577:0.0:0.6323	.	520	O60494	CUBN_HUMAN	Q	520	ENSP00000367064:R520Q	ENSP00000367064:R520Q	R	-	2	0	CUBN	17182216	0.493000	0.26035	0.009000	0.14445	0.095000	0.18619	0.769000	0.26604	-0.519000	0.06444	-0.312000	0.09012	CGG		0.383	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17142210	C	T	17142210	3	4	41	1	0	0	0	0	1	0	0	0	4057	652	23	1	9528	1	CUBN	10	17142210	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		17142210	118392537	51	3816										
YME1L1	10730	broad.mit.edu	37	chr10	27443118	27443118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctggcttacctggggttgcaCcgtgctcgacaaggaaaaca	12	11	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr10:27443118C>T	ENST00000326799.3	-	1	170	c.22G>A	c.(22-24)Gtg>Atg	p.V8M	MASTL_ENST00000375946.4_5'Flank|YME1L1_ENST00000477432.1_Missense_Mutation_p.V8M|MASTL_ENST00000375940.4_5'Flank|MASTL_ENST00000342386.6_5'Flank|YME1L1_ENST00000375972.3_Missense_Mutation_p.V8M|YME1L1_ENST00000376016.3_Missense_Mutation_p.V8M	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	8					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.V8M(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						TGGGGTTGCACCGTGCTCGAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	10											58	50	52					10																	27443118		2198	4292	6490	27483124	SO:0001583	missense	10730			AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.22G>A	10.37:g.27443118C>T	ENSP00000318480:p.Val8Met		27483124	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	37	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968336	0.53614	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000427324	D;D;D	0.94687	-3.26;-3.49;-3.26	5.9	5.9	0.94986	.	0.207799	0.41001	D	0.000963	D	0.95014	0.8386	L	0.27053	0.805	0.34146	D	0.666924	B;D;P;P	0.89917	0.435;1.0;0.859;0.498	B;D;B;B	0.91635	0.088;0.999;0.329;0.216	D	0.96953	0.9696	10	0.62326	D	0.03	-0.3865	15.7665	0.78131	0.0:1.0:0.0:0.0	.	8;8;8;8	B4DNM1;Q6PJ89;Q96TA2-2;Q96TA2	.;.;.;YMEL1_HUMAN	M	8	ENSP00000365184:V8M;ENSP00000318480:V8M;ENSP00000365139:V8M	ENSP00000318480:V8M	V	-	1	0	YME1L1	27483124	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	3.781000	0.55394	2.786000	0.95864	0.561000	0.74099	GTG		0.627	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		T	27443118	C	T	27443118	3	4	41	1	0	0	0	0	1	0	0	0	17527	507	18	3	2379	3	YME1L1	10	27443118	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	10300908	27443118	108091629	52	3817										
PDCD11	22984	broad.mit.edu	37	chr10	105172894	105172894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tgagggcctgcatcctttgcGtccatcctcgaaccagagtt	10	13	0	2	rs148850392	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr10:105172894G>A	ENST00000369797.3	+	9	1094	c.1000G>A	c.(1000-1002)Gtc>Atc	p.V334I		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	334	S1 motif 3. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.V334I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CATCCTTTGCGTCCATCCTCG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	111	91	98		1000	2.5	0.2	10	dbSNP_134	98	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PDCD11	NM_014976.1	29	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	probably-damaging	334/1872	105172894	12,12994	2203	4300	6503	105162884	SO:0001583	missense	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1000G>A	10.37:g.105172894G>A	ENSP00000358812:p.Val334Ile		105162884	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	8.701	0.909814	0.17833	2.27E-4	0.001279	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.19105	2.17	5.47	2.49	0.30216	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.315524	0.33813	N	0.004530	T	0.19685	0.0473	M	0.62154	1.92	0.09310	N	1	B	0.18968	0.032	B	0.10450	0.005	T	0.23190	-1.0195	10	0.22706	T	0.39	-9.325	9.5711	0.39429	0.3434:0.0:0.6566:0.0	.	334	Q14690	RRP5_HUMAN	I	334	ENSP00000358812:V334I	ENSP00000358812:V334I	V	+	1	0	PDCD11	105162884	0.000000	0.05858	0.179000	0.23059	0.674000	0.39518	-0.165000	0.09968	0.250000	0.21479	0.467000	0.42956	GTC		0.597	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			A	105172894	G	A	105172894	3	1	41	1	0	0	0	0	1	0	0	0	11648	1145	40	1	1030	1	PDCD11	10	105172894	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	77729776	105172894	30361853	53	3818										
TRIM5	85363	broad.mit.edu	37	chr11	5701072	5701072	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cgctcacaaagccagcaaatGaccttcccgtcctcctgaca	6	17	1	2	rs536510027	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:5701072G>T	ENST00000380034.3	-	2	592	c.336C>A	c.(334-336)gtC>gtA	p.V112V	TRIM5_ENST00000396855.3_Silent_p.V112V|TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000396847.3_Silent_p.V112V|TRIM5_ENST00000396853.4_Silent_p.V112V|TRIM5_ENST00000305836.5_Silent_p.V112V|TRIM5_ENST00000380027.1_Silent_p.V112V	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	112			V -> F (in dbSNP:rs11601507). {ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V112V(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		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)		GCCAGCAAATGACCTTCCCGT	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	11											172	150	157					11																	5701072		2201	4297	6498	5657648	SO:0001819	synonymous_variant	85363			AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16276	protein-coding gene	gene with protein product	"tripartite motif protein TRIM5", "tripartite motif protein TRIM"	608487	"tripartite motif-containing 5"			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.336C>A	11.37:g.5701072G>T			5657648	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Silent	SNP	ENST00000380034.3	37	CCDS31393.1																																																																																				0.547	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034		T	5701072	G	T	5701072	2	4	41	1	0	0	0	0	0	0	0	1	16565	1277	45	2		2	TRIM5	11	5701072	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10		5701072	129305444	54	3819										
CHKA	1119	broad.mit.edu	37	chr11	67832022	67832022	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	caagcaacatttcttcttttAtaatggatttttcttcagta	4	7	4	0	rs145358463		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:67832022A>C	ENST00000265689.4	-	10	1228	c.1202T>G	c.(1201-1203)aTa>aGa	p.I401R	CHKA_ENST00000533728.1_5'Flank|CHKA_ENST00000356135.5_Missense_Mutation_p.I383R	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	401					CDP-choline pathway (GO:0006657)|choline metabolic process (GO:0019695)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline binding (GO:0033265)|choline kinase activity (GO:0004103)|cholinesterase activity (GO:0004104)|drug binding (GO:0008144)|ethanolamine kinase activity (GO:0004305)|signal transducer activity (GO:0004871)	p.I401R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13					Choline(DB00122)	TTCTTCTTTTATAATGGATTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	11											67	69	68					11																	67832022		2199	4291	6490	67588598	SO:0001583	missense	1119			D10704	CCDS8178.1, CCDS8179.1	11q13.1	2008-02-05	2004-04-19	2004-04-21	ENSG00000110721	ENSG00000110721	2.7.1.32		1937	protein-coding gene	gene with protein product		118491	"choline kinase"	CHK		1618328, 15003397	Standard	NM_001277		Approved	CKI	uc001onj.3	P35790	OTTHUMG00000167424	ENST00000265689.4:c.1202T>G	11.37:g.67832022A>C	ENSP00000265689:p.Ile401Arg		67588598	Q8NE29	Missense_Mutation	SNP	ENST00000265689.4	37	CCDS8178.1	.	.	.	.	.	.	.	.	.	.	A	5.918	0.353404	0.11182	.	.	ENSG00000110721	ENST00000265689;ENST00000356135	T;T	0.65549	-0.16;-0.16	5.67	4.55	0.56014	Protein kinase-like domain (1);	0.378221	0.29760	N	0.011276	T	0.43700	0.1259	N	0.17674	0.51	0.45634	D	0.998566	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.21008	-1.0258	10	0.16896	T	0.51	-10.847	10.8192	0.46595	0.925:0.0:0.075:0.0	.	383;401	P35790-2;P35790	.;CHKA_HUMAN	R	401;383	ENSP00000265689:I401R;ENSP00000348454:I383R	ENSP00000265689:I401R	I	-	2	0	CHKA	67588598	0.151000	0.22747	0.637000	0.29366	0.504000	0.33889	3.433000	0.52834	0.990000	0.38787	0.533000	0.62120	ATA		0.299	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277		C	67832022	A	C	67832022	3	2	41	1	0	0	0	0	1	0	0	0	3353	449	16	4	183	4	CHKA	11	67832022	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10	62130950	67832022	67174494	55	3820										
GRM5	2915	broad.mit.edu	37	chr11	88301104	88301104	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aaggcaggcaaacaccacagCtgcaatgggttcagggtcac	12	11	2	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:88301104C>G	ENST00000305447.4	-	7	1896	c.1747G>C	c.(1747-1749)Gct>Cct	p.A583P	GRM5_ENST00000455756.2_Missense_Mutation_p.A583P|GRM5_ENST00000305432.5_Missense_Mutation_p.A583P|GRM5_ENST00000393297.1_Missense_Mutation_p.A583P|GRM5_ENST00000418177.2_Missense_Mutation_p.A583P	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	583					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.A583P(1)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	AACACCACAGCTGCAATGGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											64	61	62					11																	88301104		2201	4299	6500	87940752	SO:0001583	missense	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1747G>C	11.37:g.88301104C>G	ENSP00000306138:p.Ala583Pro		87940752	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	C	12.75	2.031338	0.35797	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.88431	-2.34;-2.35;-2.35;-2.34;-2.38	5.71	5.71	0.89125	GPCR, family 3, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91385	0.7282	L	0.28556	0.865	0.80722	D	1	D;B	0.89917	1.0;0.355	D;B	0.87578	0.998;0.057	D	0.89795	0.3971	9	.	.	.	.	19.8631	0.96790	0.0:1.0:0.0:0.0	.	583;583	P41594-2;P41594	.;GRM5_HUMAN	P	583	ENSP00000402912:A583P;ENSP00000405690:A583P;ENSP00000305905:A583P;ENSP00000306138:A583P;ENSP00000376975:A583P	.	A	-	1	0	GRM5	87940752	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.999000	0.70665	2.709000	0.92574	0.655000	0.94253	GCT		0.493	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		G	88301104	C	G	88301104	3	3	41	1	0	0	0	0	1	0	0	0	6821	797	28	5	1903	5	GRM5	11	88301104	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	20469082	88301104	46705412	56	3821										
ATP5L	10632	broad.mit.edu	37	chr11	118279754	118279754	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tggtggccactgaggtgttgAtgtggttttatgtcggagag	17	4	0	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:118279754A>T	ENST00000300688.3	+	3	765	c.253A>T	c.(253-255)Atg>Ttg	p.M85L	ATP5L_ENST00000524422.1_Intron|ATP5L_ENST00000529770.1_3'UTR	NM_006476.4	NP_006467.4	O75964	ATP5L_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G	85					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)	p.M85L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)	7	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;3.07e-05)		TGAGGTGTTGATGTGGTTTTA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											113	105	107					11																	118279754		2200	4296	6496	117784964	SO:0001583	missense	10632			AF092124	CCDS8397.1	11q23.3	2012-10-12	2010-06-11		ENSG00000167283	ENSG00000167283		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	14247	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G"			11230166, 11042152	Standard	NR_033759		Approved	ATP5JG	uc001psx.3	O75964		ENST00000300688.3:c.253A>T	11.37:g.118279754A>T	ENSP00000300688:p.Met85Leu		117784964	A8K0K3|Q96BV6|Q9UBZ7	Missense_Mutation	SNP	ENST00000300688.3	37	CCDS8397.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406729	0.62399	.	.	ENSG00000167283	ENST00000300688	.	.	.	5.9	4.77	0.60923	.	0.103637	0.85682	D	0.000000	T	0.70316	0.3210	M	0.87900	2.915	0.80722	D	1	B	0.27380	0.177	B	0.35312	0.2	T	0.64504	-0.6392	9	0.11485	T	0.65	-14.4277	11.6151	0.51086	0.9303:0.0:0.0697:0.0	.	85	O75964	ATP5L_HUMAN	L	85	.	ENSP00000300688:M85L	M	+	1	0	ATP5L	117784964	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.552000	0.90682	1.056000	0.40484	0.528000	0.53228	ATG		0.323	ATP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389220.1	NM_006476		T	118279754	A	T	118279754	3	4	41	1	0	0	0	0	1	0	0	0	1161	333	12	5	263	5	ATP5L	11	118279754	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10	29978650	118279754	16726762	57	3822										
OR10G4	390264	broad.mit.edu	37	chr11	123887117	123887117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cattttctacactgtgctgaCgccccttctcaaccctgttg	6	15	2	1	rs201358968	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:123887117C>T	ENST00000320891.4	+	1	836	c.836C>T	c.(835-837)aCg>aTg	p.T279M		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T279M(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		ACTGTGCTGACGCCCCTTCTC	0.473													-|||	2	0.000399361	0	0.0029	5008	,	,		19664	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	11						C	MET/THR	0,4402		0,0,2201	108	93	98		836	2.6	0.5	11		98	3,8595		0,3,4296	yes	missense	OR10G4	NM_001004462.1	81	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	279/312	123887117	3,12997	2201	4299	6500	123392327	SO:0001583	missense	390264			AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"GPCR / Class A : Olfactory receptors"	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.836C>T	11.37:g.123887117C>T	ENSP00000325076:p.Thr279Met		123392327	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	.	.	.	.	.	.	.	.	.	.	N	11.01	1.513019	0.27123	0.0	3.49E-4	ENSG00000254737	ENST00000320891	T	0.38401	1.14	3.48	2.56	0.30785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40640	N	0.001050	T	0.62429	0.2427	M	0.90309	3.105	0.22996	N	0.998452	D	0.76494	0.999	D	0.72338	0.977	T	0.56275	-0.8006	10	0.87932	D	0	.	10.2744	0.43501	0.0:0.8997:0.0:0.1003	.	279	Q8NGN3	O10G4_HUMAN	M	279	ENSP00000325076:T279M	ENSP00000325076:T279M	T	+	2	0	OR10G4	123392327	0.000000	0.05858	0.491000	0.27477	0.069000	0.16628	0.831000	0.27476	0.809000	0.34255	0.580000	0.79431	ACG		0.473	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		T	123887117	C	T	123887117	3	4	41	1	0	0	0	0	1	0	0	0	10932	536	19	1	838	1	OR10G4	11	123887117	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	5607363	123887117	11119399	58	3823										
NCAPD3	23310	broad.mit.edu	37	chr11	134054798	134054798	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	attctccagcagacactcacCagtcactttgtcccgggtgc	8	15	3	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr11:134054798C>G	ENST00000534548.2	-	18	2399	c.2335G>C	c.(2335-2337)Gat>Cat	p.D779H	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	779					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)	p.D779H(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		AGACACTCACCAGTCACTTTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											298	308	305					11																	134054798		2201	4297	6498	133560008	SO:0001630	splice_region_variant	23310			AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.2335+1G>C	11.37:g.134054798C>G			133560008	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483981	0.84854	.	.	ENSG00000151503	ENST00000534548	T	0.66995	-0.24	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.353901	0.35124	N	0.003422	T	0.72977	0.3528	M	0.65975	2.015	0.80722	D	1	D	0.65815	0.995	P	0.53185	0.72	T	0.73148	-0.4074	9	.	.	.	-6.3925	12.6481	0.56746	0.0:0.9246:0.0:0.0754	.	779	P42695	CNDD3_HUMAN	H	779	ENSP00000433681:D779H	.	D	-	1	0	NCAPD3	133560008	1.000000	0.71417	0.969000	0.41365	0.931000	0.56810	4.838000	0.62803	2.775000	0.95449	0.655000	0.94253	GAT		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation	G	134054798	C	G	134054798	5	3	41	1	0	0	0	0	0	0	1	0	10237	608	21	5	2233	5	NCAPD3	11	134054798	Splice_Site	SNP	C	TCGA-AG-3881-01A-01W-0899-10	10167681	134054798	951718	59	3824										
CDCA3	83461	broad.mit.edu	37	chr12	6958846	6958846	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cacctgtttggaggggaactCagtctggttccaaggtggca	14	9	2	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:6958846C>G	ENST00000538862.2	-	4	1328	c.427G>C	c.(427-429)Gag>Cag	p.E143Q	CDCA3_ENST00000540683.1_Missense_Mutation_p.E143Q|CDCA3_ENST00000229265.6_Missense_Mutation_p.E118Q|USP5_ENST00000229268.8_5'Flank|CDCA3_ENST00000604599.1_5'Flank|CDCA3_ENST00000422785.3_Missense_Mutation_p.E143Q|USP5_ENST00000389231.5_5'Flank|CDCA3_ENST00000535406.1_Missense_Mutation_p.E143Q			Q99618	CDCA3_HUMAN	cell division cycle associated 3	143					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.E143Q(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(1)|stomach(1)	8						GAGGGGAACTCAGTCTGGTTC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											69	72	71					12																	6958846		2203	4300	6503	6829107	SO:0001583	missense	83461			BG354576	CCDS8565.1, CCDS73428.1	12p13.31	2010-07-20				ENSG00000111665			14624	protein-coding gene	gene with protein product	"trigger of mitotic entry 1"	607749				9074930, 12188893	Standard	XR_242988		Approved	TOME-1, GRCC8	uc001qrg.2	Q99618		ENST00000538862.2:c.427G>C	12.37:g.6958846C>G	ENSP00000442068:p.Glu143Gln		6829107	A8K5V6|D3DUS6	Missense_Mutation	SNP	ENST00000538862.2	37	CCDS8565.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.257111	0.39896	.	.	ENSG00000237240;ENSG00000111665;ENSG00000111665;ENSG00000111665;ENSG00000111665	ENST00000422785;ENST00000229265;ENST00000538862;ENST00000535406;ENST00000540683	.	.	.	5.34	2.48	0.30137	.	0.284743	0.32386	N	0.006162	T	0.41858	0.1177	M	0.65975	2.015	0.09310	N	0.999998	B;B	0.20550	0.046;0.043	B;B	0.27796	0.081;0.083	T	0.32613	-0.9900	9	0.32370	T	0.25	-10.2716	5.5531	0.17101	0.0:0.6623:0.1628:0.1749	.	143;143	Q99618;F8WDL1	CDCA3_HUMAN;.	Q	143;118;143;143;143	.	ENSP00000229265:E118Q	E	-	1	0	U47924.25;CDCA3	6829107	1.000000	0.71417	0.179000	0.23059	0.446000	0.32137	1.101000	0.31037	0.461000	0.27071	-0.157000	0.13467	GAG		0.552	CDCA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401940.2	NM_031299		G	6958846	C	G	6958846	3	3	41	1	0	0	0	0	1	0	0	0	3093	835	29	5	391	5	CDCA3	12	6958846	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		6958846	126893049	60	3825										
EPS8	2059	broad.mit.edu	37	chr12	15818787	15818787	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ggcgcaggggcaggagctctGggtggaggcggtatactagg	21	7	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:15818787G>A	ENST00000281172.5	-	8	1075	c.639C>T	c.(637-639)ccC>ccT	p.P213P	EPS8_ENST00000543612.1_Silent_p.P213P|EPS8_ENST00000543523.1_Silent_p.P213P	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	213					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)	p.P213P(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CAGGAGCTCTGGGTGGAGGCG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	12											48	50	49					12																	15818787		2203	4300	6503	15710054	SO:0001819	synonymous_variant	2059			U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.639C>T	12.37:g.15818787G>A			15710054	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																				0.493	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			A	15818787	G	A	15818787	2	1	41	1	0	0	0	0	0	0	0	1	5207	1335	47	3		3	EPS8	12	15818787	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	8859941	15818787	118033108	61	3826										
METTL7A	25840	broad.mit.edu	37	chr12	51323839	51323839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gagctggaaggccctggagcGggccagcttctctaagctga	15	11	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:51323839G>A	ENST00000548553.1	+	3	1622	c.641G>A	c.(640-642)cGg>cAg	p.R214Q	METTL7A_ENST00000332160.4_Missense_Mutation_p.R214Q			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	214						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)	p.R214Q(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GCCCTGGAGCGGGCCAGCTTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	79	79					12																	51323839		2203	4300	6503	49610106	SO:0001583	missense	25840				CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.641G>A	12.37:g.51323839G>A	ENSP00000448785:p.Arg214Gln		49610106	Q9H7R3|Q9UHZ7|Q9Y422	Missense_Mutation	SNP	ENST00000548553.1	37	CCDS8804.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.441835	0.25900	.	.	ENSG00000185432	ENST00000548553;ENST00000332160;ENST00000433599	T;T	0.18338	2.22;2.22	5.61	-4.74	0.03249	.	1.731360	0.03088	N	0.159399	T	0.10852	0.0265	N	0.16016	0.355	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31943	-0.9925	10	0.13853	T	0.58	-8.1188	14.7983	0.69894	0.6438:0.0:0.3562:0.0	.	214	Q9H8H3	MET7A_HUMAN	Q	214;214;145	ENSP00000448785:R214Q;ENSP00000331787:R214Q	ENSP00000331787:R214Q	R	+	2	0	METTL7A	49610106	0.000000	0.05858	0.001000	0.08648	0.849000	0.48306	-0.491000	0.06474	-1.200000	0.02662	0.655000	0.94253	CGG		0.547	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		A	51323839	G	A	51323839	3	1	41	1	0	0	0	0	1	0	0	0	9535	1116	39	1	647	1	METTL7A	12	51323839	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	35505052	51323839	82528056	62	3827										
RDH16	8608	broad.mit.edu	37	chr12	57345981	57345981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tccatgcagttggtcaccaaCgacagatcctgtgtgcactt	9	12	1	1	rs372244884		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:57345981C>T	ENST00000398138.3	-	4	1642	c.786G>A	c.(784-786)tcG>tcA	p.S262S	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	262					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)	p.S262S(2)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						TGGTCACCAACGACAGATCCT	0.502													C|||	1	0.000199681	8e-04	0	5008	,	,		22190	0		0	False		,,,				2504	0				GBM(179;741 2921 43105 45298)											2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	12						C		1,4251		0,1,2125	90	100	97		786	0.1	0	12		97	0,8496		0,0,4248	no	coding-synonymous	RDH16	NM_003708.3		0,1,6373	TT,TC,CC		0.0,0.0235,0.0078		262/318	57345981	1,12747	2126	4248	6374	55632248	SO:0001819	synonymous_variant	8608				CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29674	protein-coding gene	gene with protein product	"microsomal NAD+ dependent retinol dehydrogenase 4", "short chain dehydrogenase/reductase family 9C, member 8"		"retinol dehydrogenase 16 (all-trans and 13-cis)"			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.786G>A	12.37:g.57345981C>T			55632248	Q9UNV2	Silent	SNP	ENST00000398138.3	37	CCDS41797.1																																																																																				0.502	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708		T	57345981	C	T	57345981	2	4	41	1	0	0	0	0	0	0	0	1	13231	523	19	1		1	RDH16	12	57345981	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10	6022142	57345981	76505914	63	3828										
SLC6A15	55117	broad.mit.edu	37	chr12	85255570	85255570	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	atctcgctcggtatttttccGtgaatgaggcttgtatcatc	9	9	2	2	rs140619291	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:85255570G>A	ENST00000266682.5	-	12	2575	c.2034C>T	c.(2032-2034)caC>caT	p.H678H	SLC6A15_ENST00000309283.7_3'UTR|SLC6A15_ENST00000552192.1_Silent_p.H571H	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	678					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.H678H(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						GTATTTTTCCGTGAATGAGGC	0.433													G|||	3	0.000599042	0	0	5008	,	,		17036	0.003		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						G	,	2,4404	4.2+/-10.8	0,2,2201	122	119	120		1713,2034	-5.1	1	12	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC6A15	NM_001146335.1,NM_182767.4	,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	,	571/624,678/731	85255570	3,13003	2203	4300	6503	83779701	SO:0001819	synonymous_variant	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.2034C>T	12.37:g.85255570G>A			83779701	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																				0.433	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		A	85255570	G	A	85255570	2	1	41	1	0	0	0	0	0	0	0	1	14715	1136	40	1		1	SLC6A15	12	85255570	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	27909589	85255570	48596325	64	3829										
C12orf42	374470	broad.mit.edu	37	chr12	103695938	103695938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aaagggcctgtgaacaaaccGtatggaaacgccgggttggg	15	8	0	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:103695938G>A	ENST00000378113.2	-	6	1256	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	C12orf42_ENST00000315192.8_Intron|C12orf42_ENST00000548048.1_Missense_Mutation_p.T277M|C12orf42_ENST00000548883.1_Missense_Mutation_p.T344M	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	344								p.T344M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						TGAACAAACCGTATGGAAACG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	12											55	62	60					12																	103695938		1839	4082	5921	102220068	SO:0001583	missense	374470			AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.1031C>T	12.37:g.103695938G>A	ENSP00000367353:p.Thr344Met		102220068	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	37	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614632	0.28712	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113	T;T;T	0.58210	0.35;0.35;0.35	5.06	-2.38	0.06622	.	0.843870	0.09924	N	0.738078	T	0.33702	0.0872	L	0.29908	0.895	0.25549	N	0.987105	P	0.46578	0.88	B	0.41894	0.369	T	0.23084	-1.0198	10	0.52906	T	0.07	-1.7934	2.1918	0.03901	0.1673:0.1325:0.1206:0.5795	.	344	Q96LP6	CL042_HUMAN	M	344;277;344	ENSP00000447908:T344M;ENSP00000449362:T277M;ENSP00000367353:T344M	ENSP00000367353:T344M	T	-	2	0	C12orf42	102220068	1.000000	0.71417	0.987000	0.45799	0.222000	0.24845	0.833000	0.27504	-0.284000	0.09102	0.655000	0.94253	ACG		0.562	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		A	103695938	G	A	103695938	3	1	41	1	0	0	0	0	1	0	0	0	1692	1145	40	1	55	1	C12orf42	12	103695938	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	18440368	103695938	30155957	65	3830										
GCN1L1	10985	broad.mit.edu	37	chr12	120591164	120591164	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tagctggcatcattgggcgcGttcttcaggaactcctcgaa	11	11	3	0	rs148374886	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:120591164G>A	ENST00000300648.6	-	33	3927	c.3915C>T	c.(3913-3915)aaC>aaT	p.N1305N	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1305					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)	p.N1305N(1)		NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CATTGGGCGCGTTCTTCAGGA	0.562													G|||	6	0.00119808	0.0045	0	5008	,	,		20875	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						G		8,4176		0,8,2084	70	75	73		3915	-7.2	0.6	12	dbSNP_134	73	0,8438		0,0,4219	no	coding-synonymous	GCN1L1	NM_006836.1		0,8,6303	AA,AG,GG		0.0,0.1912,0.0634		1305/2672	120591164	8,12614	2092	4219	6311	119075547	SO:0001819	synonymous_variant	10985			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3915C>T	12.37:g.120591164G>A			119075547	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																				0.562	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120591164	G	A	120591164	2	1	41	1	0	0	0	0	0	0	0	1	6319	1136	40	1		1	GCN1L1	12	120591164	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	16895226	120591164	13260731	66	3831										
DNAH10	196385	broad.mit.edu	37	chr12	124272483	124272483	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gatcggtgggagtttgaccgGaagcggctgttcgagaggac	18	7	0	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr12:124272483G>T	ENST00000409039.3	+	10	1396	c.1371G>T	c.(1369-1371)cgG>cgT	p.R457R		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	457	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R457R(1)|p.R275R(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGTTTGACCGGAAGCGGCTGT	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	12											53	43	46					12																	124272483		2203	4300	6503	122838436	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1371G>T	12.37:g.124272483G>T			122838436	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.597	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124272483	G	T	124272483	2	4	41	1	0	0	0	0	0	0	0	1	4609	1161	41	2		2	DNAH10	12	124272483	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	3681319	124272483	9579412	67	3832										
RB1	5925	broad.mit.edu	37	chr13	49033946	49033946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tgcagaatgagtatgaactcAtgagagacaggcatttggac	12	6	1	5			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr13:49033946A>G	ENST00000267163.4	+	20	2221	c.2083A>G	c.(2083-2085)Atg>Gtg	p.M695V		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	695	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.M695V(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GTATGAACTCATGAGAGACAG	0.413		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	27	Whole gene deletion(15)|Unknown(11)|Substitution - Missense(1)	bone(10)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13											80	74	76					13																	49033946		2203	4300	6503	47931947	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2083A>G	13.37:g.49033946A>G	ENSP00000267163:p.Met695Val		47931947	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596761	0.86953	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.91740	-2.9	5.48	5.48	0.80851	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.95159	0.8431	M	0.73319	2.225	0.80722	D	1	D	0.65815	0.995	D	0.63488	0.915	D	0.95650	0.8706	10	0.87932	D	0	-17.3092	15.5642	0.76277	1.0:0.0:0.0:0.0	.	695	P06400	RB_HUMAN	V	674;695	ENSP00000267163:M695V	ENSP00000267163:M695V	M	+	1	0	RB1	47931947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.005000	0.76323	2.086000	0.62901	0.477000	0.44152	ATG		0.413	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	49033946	A	G	49033946	3	3	41	1	0	0	0	0	1	0	0	0	13135	217	8	4	2161	4	RB1	13	49033946	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10		49033946	66135932	68	3833										
ATP10A	57194	broad.mit.edu	37	chr15	25924611	25924611	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tgtccatctgcaagctgctcCgtccgggagaactgtaagac	11	12	1	2	rs149560828		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr15:25924611C>A	ENST00000356865.6	-	21	4488	c.4377G>T	c.(4375-4377)acG>acT	p.T1459T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1459					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.T1459T(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CAAGCTGCTCCGTCCGGGAGA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	15											54	54	54					15																	25924611		2203	4300	6503	23475704	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4377G>T	15.37:g.25924611C>A			23475704	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.572	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25924611	C	A	25924611	2	1	41	1	0	0	0	0	0	0	0	1	1117	639	23	2		2	ATP10A	15	25924611	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10		25924611	76606781	69	3834										
KIAA1024	23251	broad.mit.edu	37	chr15	79749974	79749974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gacctgtgcacctctggtcaGggcaagtacagtgacaggca	13	11	2	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr15:79749974G>T	ENST00000305428.3	+	2	1560	c.1485G>T	c.(1483-1485)caG>caT	p.Q495H		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	495						integral component of membrane (GO:0016021)		p.Q495H(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						CCTCTGGTCAGGGCAAGTACA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	15											96	79	85					15																	79749974		2196	4293	6489	77537029	SO:0001583	missense	23251			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.1485G>T	15.37:g.79749974G>T	ENSP00000307461:p.Gln495His		77537029	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.334886	0.24253	.	.	ENSG00000169330	ENST00000305428	T	0.33865	1.39	4.92	3.99	0.46301	.	0.496732	0.23600	N	0.046442	T	0.35913	0.0948	M	0.65975	2.015	0.36637	D	0.876634	P	0.46277	0.875	P	0.44732	0.459	T	0.41910	-0.9482	9	.	.	.	.	4.5655	0.12184	0.0882:0.1527:0.6017:0.1574	.	495	Q9UPX6	K1024_HUMAN	H	495	ENSP00000307461:Q495H	.	Q	+	3	2	KIAA1024	77537029	0.994000	0.37717	0.989000	0.46669	0.106000	0.19336	1.026000	0.30103	1.032000	0.39892	0.491000	0.48974	CAG		0.537	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		T	79749974	G	T	79749974	3	4	41	1	0	0	0	0	1	0	0	0	8226	991	35	2	1487	2	KIAA1024	15	79749974	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	53825363	79749974	22781418	70	3835										
ZNF629	23361	broad.mit.edu	37	chr16	30793957	30793957	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	cacttgtgcggcttggctccCggcggcggggtcagcaggga	18	12	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr16:30793957C>T	ENST00000262525.4	-	3	1899	c.1692G>A	c.(1690-1692)ccG>ccA	p.P564P	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	564					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P564P(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GCTTGGCTCCCGGCGGCGGGG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	16											28	28	28					16																	30793957		1964	4112	6076	30701458	SO:0001819	synonymous_variant	23361			AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.1692G>A	16.37:g.30793957C>T			30701458	Q15938	Silent	SNP	ENST00000262525.4	37	CCDS45463.1																																																																																				0.647	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		T	30793957	C	T	30793957	2	4	41	1	0	0	0	0	0	0	0	1	18092	639	23	1		1	ZNF629	16	30793957	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10		30793957	59560796	71	3836										
HYDIN	54768	broad.mit.edu	37	chr16	71008137	71008137	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	tggccccctgtgggtcaaatCtcacttcaaatatttccgtt	7	12	3	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr16:71008137C>G	ENST00000393567.2	-	33	5126	c.4976G>C	c.(4975-4977)aGa>aCa	p.R1659T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1659					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R1610T(1)|p.R1658T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGGTCAAATCTCACTTCAAA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	16											18	18	18					16																	71008137		1818	4064	5882	69565638	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4976G>C	16.37:g.71008137C>G	ENSP00000377197:p.Arg1659Thr		69565638	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	4.376	0.069264	0.08436	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00753	5.74	4.81	2.76	0.32466	.	0.283844	0.16109	U	0.229207	T	0.00754	0.0025	L	0.33137	0.985	0.80722	D	1	P	0.37330	0.59	B	0.38954	0.286	T	0.69910	-0.5017	10	0.11794	T	0.64	.	7.092	0.25289	0.0:0.7041:0.0:0.2959	.	1658	F8WD23	.	T	1659;1658	ENSP00000377197:R1659T	ENSP00000313052:R1658T	R	-	2	0	HYDIN	69565638	0.548000	0.26473	0.998000	0.56505	0.274000	0.26718	1.233000	0.32648	1.085000	0.41206	0.505000	0.49811	AGA		0.458	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	71008137	C	G	71008137	3	3	41	1	0	0	0	0	1	0	0	0	7488	913	32	5	10605	5	HYDIN	16	71008137	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	40214180	71008137	19346616	72	3837										
OVCA2	124641	broad.mit.edu	37	chr17	1946040	1946040	+	Frame_Shift_Del	DEL	T	T	-													0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ggcacaggcactgaacaggcTggggccttttgacggccttc							TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:1946040delT	ENST00000572195.1	+	2	341	c.326delT	c.(325-327)ctgfs	p.L109fs	DPH1_ENST00000263083.6_3'UTR|RP11-667K14.3_ENST00000572790.1_lincRNA|DPH1_ENST00000570477.1_3'UTR|RP11-667K14.4_ENST00000572404.1_RNA	NM_080822.2	NP_543012.1	Q8WZ82	OVCA2_HUMAN	ovarian tumor suppressor candidate 2	109					metabolic process (GO:0008152)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)	p.L109fs*16(1)									CTGAACAGGCTGGGGCCTTTT	0.642											OREG0024078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Deletion - Frameshift(1)	large_intestine(1)	17											48	46	46					17																	1946040		2203	4300	6503	1892790	SO:0001589	frameshift_variant	124641			AF321875	CCDS11015.1	17p13.3	2012-10-08			ENSG00000262664	ENSG00000262664			24203	protein-coding gene	gene with protein product	"candidate tumor suppressor in ovarian cancer 2"	607896				11979432, 8616839, 16368187	Standard	NM_080822		Approved		uc002ftx.3	Q8WZ82	OTTHUMG00000132471	ENST00000572195.1:c.326delT	17.37:g.1946040delT	ENSP00000461388:p.Leu109fs	599	1892790	Q86XN3|Q8IW87|Q9UCX9	Frame_Shift_Del	DEL	ENST00000572195.1	37	CCDS11015.1																																																																																				0.642	OVCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255636.5	NM_080822		-	1946040	T	-	1946040	7	5	41	1	0	1	0	1	0	0	0	0	11353	1580	55	0	332	0	OVCA2	17	1946040	Frame_Shift_Del	DEL	T	TCGA-AG-3881-01A-01W-0899-10		1946040	79249170	73	3838										
MYH3	4621	broad.mit.edu	37	chr17	10541653	10541653	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctccagccgctcgctcagctCctccagctcccgggcatagt	9	19	1	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:10541653C>A	ENST00000583535.1	-	27	3523	c.3436G>T	c.(3436-3438)Gag>Tag	p.E1146*	MYH3_ENST00000226209.7_Nonsense_Mutation_p.E1146*	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1146					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.E1146*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCGCTCAGCTCCTCCAGCTCC	0.637																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											34	36	35					17																	10541653		2203	4300	6503	10482378	SO:0001587	stop_gained	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.3436G>T	17.37:g.10541653C>A	ENSP00000464317:p.Glu1146*		10482378	Q15492	Nonsense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	43	10.238455	0.99366	.	.	ENSG00000109063	ENST00000226209	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.661	0.95871	0.0:1.0:0.0:0.0	.	.	.	.	X	1146	.	ENSP00000226209:E1146X	E	-	1	0	MYH3	10482378	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.776000	0.85560	2.714000	0.92807	0.563000	0.77884	GAG		0.637	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10541653	C	A	10541653	4	1	41	1	0	0	0	0	0	1	0	0	10066	864	30	2	2446	2	MYH3	17	10541653	Nonsense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	8595613	10541653	70653557	74	3839										
VTN	7448	broad.mit.edu	37	chr17	26695960	26695960	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agggccaaggctgcatccacGttgtccgggatgccatcgaa	13	12	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:26695960G>A	ENST00000226218.4	-	5	1377	c.759C>T	c.(757-759)aaC>aaT	p.N253N	SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|CTB-96E2.2_ENST00000555059.2_5'Flank|SARM1_ENST00000457710.3_5'Flank|VTN_ENST00000536498.1_De_novo_Start_InFrame|TMEM199_ENST00000509083.1_Intron	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	253					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.N253N(1)		kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	CTGCATCCACGTTGTCCGGGA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											96	92	93					17																	26695960		2203	4300	6503	23720087	SO:0001819	synonymous_variant	7448			BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"Endogenous ligands"	12724	protein-coding gene	gene with protein product	"serum spreading factor", "somatomedin B", "complement S-protein"	193190	"vitronectin (serum spreading factor, somatomedin B, complement S-protein)"			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.759C>T	17.37:g.26695960G>A			23720087	B2R7G0|P01141|Q9BSH7	Silent	SNP	ENST00000226218.4	37	CCDS11229.1																																																																																				0.592	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638		A	26695960	G	A	26695960	2	1	41	1	0	0	0	0	0	0	0	1	17277	1136	40	1		1	VTN	17	26695960	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	16154307	26695960	54499250	75	3840										
C17orf47	284083	broad.mit.edu	37	chr17	56620511	56620511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gaactgtcacatggtgagttGgctctactgactgtacccct	10	11	2	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:56620511G>A	ENST00000321691.3	-	1	1218	c.1037C>T	c.(1036-1038)cCa>cTa	p.P346L	RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_5'Flank|SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580769.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	346								p.P346L(1)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATGGTGAGTTGGCTCTACTGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											137	121	127					17																	56620511		2203	4300	6503	53975510	SO:0001583	missense	284083				CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1037C>T	17.37:g.56620511G>A	ENSP00000354874:p.Pro346Leu		53975510	Q8N821	Missense_Mutation	SNP	ENST00000321691.3	37	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	G	7.998	0.754683	0.15778	.	.	ENSG00000181013	ENST00000321691	T	0.28666	1.6	4.21	0.633	0.17712	.	1.621520	0.03943	N	0.287162	T	0.14700	0.0355	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19128	-1.0315	10	0.27785	T	0.31	-0.1284	2.0739	0.03619	0.1149:0.2:0.4799:0.2052	.	346	Q8NEP4	CQ047_HUMAN	L	346	ENSP00000354874:P346L	ENSP00000354874:P346L	P	-	2	0	C17orf47	53975510	0.000000	0.05858	0.001000	0.08648	0.044000	0.14063	0.024000	0.13555	0.453000	0.26858	0.462000	0.41574	CCA		0.532	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		A	56620511	G	A	56620511	3	1	41	1	0	0	0	0	1	0	0	0	1863	1348	47	3	683	3	C17orf47	17	56620511	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	29924551	56620511	24574699	76	3841										
SCN4A	6329	broad.mit.edu	37	chr17	62049740	62049740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gagcaccttgatggccccgcGcctgactacgctgaaggggc	14	14	0	3	rs150158100	byFrequency	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:62049740G>A	ENST00000435607.1	-	2	440	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	CTC-264K15.6_ENST00000577329.1_lincRNA|SCN4A_ENST00000578147.1_Missense_Mutation_p.R122C	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	122					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R122C(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGGCCCCGCGCCTGACTACG	0.612													G|||	2	0.000399361	0	0	5008	,	,		21174	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											64	68	66					17																	62049740		2155	4262	6417	59403472	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.364C>T	17.37:g.62049740G>A	ENSP00000396320:p.Arg122Cys		59403472	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.04	2.415786	0.42817	.	.	ENSG00000007314	ENST00000435607	D	0.97186	-4.28	4.23	3.24	0.37175	.	0.190420	0.45606	D	0.000353	D	0.98257	0.9423	M	0.91561	3.22	0.58432	D	0.999998	D	0.89917	1.0	D	0.63033	0.91	D	0.98352	1.0544	10	0.87932	D	0	.	10.3651	0.44019	0.0:0.0:0.5026:0.4974	.	122	P35499	SCN4A_HUMAN	C	122	ENSP00000396320:R122C	ENSP00000396320:R122C	R	-	1	0	SCN4A	59403472	1.000000	0.71417	0.864000	0.33941	0.208000	0.24298	4.663000	0.61532	0.965000	0.38133	0.313000	0.20887	CGC		0.612	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62049740	G	A	62049740	3	1	41	1	0	0	0	0	1	0	0	0	13957	1087	38	1	5238	1	SCN4A	17	62049740	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	5429229	62049740	19145470	77	3842										
RNF213	57674	broad.mit.edu	37	chr17	78319745	78319745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctctgaggagatgatctgccGtttggagtcagctggtttgg	15	7	3	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr17:78319745G>A	ENST00000582970.1	+	29	7753	c.7610G>A	c.(7609-7611)cGt>cAt	p.R2537H	RNF213_ENST00000336301.6_Missense_Mutation_p.R610H|RNF213_ENST00000508628.2_Missense_Mutation_p.R2586H	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2537					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R610H(1)|p.R2586H(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ATGATCTGCCGTTTGGAGTCA	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	17											85	82	83					17																	78319745		2203	4300	6503	75934340	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.7610G>A	17.37:g.78319745G>A	ENSP00000464087:p.Arg2537His		75934340	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255469	0.22965	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.23950	1.88	5.13	5.13	0.70059	ATPase, AAA+ type, core (1);	0.063927	0.64402	D	0.000010	T	0.56217	0.1970	M	0.82517	2.595	0.44927	D	0.997946	D	0.71674	0.998	D	0.74023	0.982	T	0.61898	-0.6968	10	0.72032	D	0.01	.	18.7595	0.91845	0.0:0.0:1.0:0.0	.	610	Q63HN8	RN213_HUMAN	H	2537;2586;610	ENSP00000338218:R610H	ENSP00000338218:R610H	R	+	2	0	RNF213	75934340	1.000000	0.71417	0.154000	0.22540	0.039000	0.13416	7.647000	0.83462	2.646000	0.89796	0.655000	0.94253	CGT		0.562	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78319745	G	A	78319745	3	1	41	1	0	0	0	0	1	0	0	0	13514	1145	40	1	8039	1	RNF213	17	78319745	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	16270005	78319745	2875465	78	3843										
MEP1B	4225	broad.mit.edu	37	chr18	29782965	29782965	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	aactatatatcagtgttcaaGggcagtgggtaagttgcaga	12	5	2	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr18:29782965G>A	ENST00000269202.6	+	6	407	c.360G>A	c.(358-360)aaG>aaA	p.K120K	MEP1B_ENST00000581447.1_Silent_p.K120K	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	120	Metalloprotease.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K120K(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CAGTGTTCAAGGGCAGTGGGT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	18											81	79	80					18																	29782965		1904	4134	6038	28036963	SO:0001819	synonymous_variant	4225			X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.360G>A	18.37:g.29782965G>A			28036963	B7ZM35|B9EGL6|Q670J1	Silent	SNP	ENST00000269202.6	37	CCDS45846.1																																																																																				0.423	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		A	29782965	G	A	29782965	2	1	41	1	0	0	0	0	0	0	0	1	9506	991	35	3		3	MEP1B	18	29782965	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10		29782965	48294283	79	3844										
CCDC159	126075	broad.mit.edu	37	chr19	11460668	11460668	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gctcctgcgatgtgaacttgAgtcactcaagagccagttac	10	11	2	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:11460668A>T	ENST00000588790.1	+	5	557	c.110A>T	c.(109-111)gAg>gTg	p.E37V	CCDC159_ENST00000458408.1_Missense_Mutation_p.E37V			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	152								p.E37V(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						TGTGAACTTGAGTCACTCAAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											56	58	57					19																	11460668		1933	4135	6068	11321668	SO:0001583	missense	126075			BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.110A>T	19.37:g.11460668A>T	ENSP00000468232:p.Glu37Val		11321668	B4DEG3|B4DWR8|B4E133|B7ZAM4	Missense_Mutation	SNP	ENST00000588790.1	37	CCDS45976.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.992153	0.54041	.	.	ENSG00000183401	ENST00000458408;ENST00000427879	T	0.53206	0.63	5.49	5.49	0.81192	.	.	.	.	.	T	0.63558	0.2521	L	0.59436	1.845	0.34556	D	0.711837	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.998;0.999	D;D;D;D;D	0.72075	0.975;0.943;0.976;0.943;0.976	T	0.73920	-0.3830	9	0.52906	T	0.07	-31.7045	13.1113	0.59275	1.0:0.0:0.0:0.0	.	152;152;36;37;37	P0C7I6;P0C7I6-4;P0C7I6-3;P0C7I6-2;P0C7I6-5	CC159_HUMAN;.;.;.;.	V	37;152	ENSP00000402239:E37V	ENSP00000390400:E152V	E	+	2	0	CCDC159	11321668	1.000000	0.71417	1.000000	0.80357	0.087000	0.18053	4.900000	0.63252	2.079000	0.62486	0.533000	0.62120	GAG		0.592	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503		T	11460668	A	T	11460668	3	4	41	1	0	0	0	0	1	0	0	0	2797	304	11	5	120	5	CCDC159	19	11460668	Missense_Mutation	SNP	A	TCGA-AG-3881-01A-01W-0899-10		11460668	47668315	80	3845										
CCDC159	126075	broad.mit.edu	37	chr19	11461550	11461550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtggggcatggagcagggccGgcaggagctgtatggggccc	21	9	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:11461550G>A	ENST00000588790.1	+	7	740	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	CCDC159_ENST00000458408.1_Missense_Mutation_p.R98Q			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	213								p.R98Q(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						GAGCAGGGCCGGCAGGAGCTG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											10	14	13					19																	11461550		1997	4074	6071	11322550	SO:0001583	missense	126075			BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.293G>A	19.37:g.11461550G>A	ENSP00000468232:p.Arg98Gln		11322550	B4DEG3|B4DWR8|B4E133|B7ZAM4	Missense_Mutation	SNP	ENST00000588790.1	37	CCDS45976.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.272620	0.23221	.	.	ENSG00000183401	ENST00000458408;ENST00000427879	T	0.45668	0.89	5.05	-8.88	0.00789	.	.	.	.	.	T	0.15176	0.0366	N	0.05124	-0.11	0.09310	N	1	B;B;B;B;B	0.19706	0.038;0.011;0.038;0.001;0.038	B;B;B;B;B	0.10450	0.005;0.002;0.003;0.001;0.003	T	0.20638	-1.0269	9	0.48119	T	0.1	-15.9405	3.3957	0.07304	0.3334:0.1043:0.4574:0.105	.	213;213;97;98;98	P0C7I6;P0C7I6-4;P0C7I6-3;P0C7I6-2;P0C7I6-5	CC159_HUMAN;.;.;.;.	Q	98;213	ENSP00000402239:R98Q	ENSP00000390400:R213Q	R	+	2	0	CCDC159	11322550	0.000000	0.05858	0.269000	0.24586	0.501000	0.33797	-1.230000	0.02942	-1.524000	0.01764	-1.305000	0.01319	CGG		0.662	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503		A	11461550	G	A	11461550	3	1	41	1	0	0	0	0	1	0	0	0	2797	1116	39	1	311	1	CCDC159	19	11461550	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	882	11461550	47667433	81	3846										
CNN1	1264	broad.mit.edu	37	chr19	11660241	11660241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agaccagcctctggaccaggCgaccatcagcctgcagatgg	12	14	2	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:11660241C>T	ENST00000252456.2	+	6	816	c.605C>T	c.(604-606)gCg>gTg	p.A202V	CNN1_ENST00000535659.2_Missense_Mutation_p.A152V|CNN1_ENST00000544952.1_Missense_Mutation_p.A182V|CNN1_ENST00000592923.1_Missense_Mutation_p.A152V	NM_001299.4	NP_001290.2	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle	202					actomyosin structure organization (GO:0031032)|regulation of smooth muscle contraction (GO:0006940)	cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)		p.A202V(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9						CTGGACCAGGCGACCATCAGC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	19											42	43	43					19																	11660241		2203	4300	6503	11521241	SO:0001583	missense	1264			U37019	CCDS12263.1	19p13.2-p13.1	2008-07-16				ENSG00000130176			2155	protein-coding gene	gene with protein product		600806				8526917, 9332369	Standard	XM_005259741		Approved	SMCC, Sm-Calp	uc002msc.1	P51911		ENST00000252456.2:c.605C>T	19.37:g.11660241C>T	ENSP00000252456:p.Ala202Val		11521241	B2R868|B4DUX6|O00638|Q15416|Q8IY93|Q99438	Missense_Mutation	SNP	ENST00000252456.2	37	CCDS12263.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888931	0.91814	.	.	ENSG00000130176	ENST00000252456;ENST00000535659;ENST00000544952	T;T;T	0.33865	1.39;1.39;1.39	5.21	5.21	0.72293	.	0.053759	0.85682	D	0.000000	T	0.35740	0.0942	L	0.39898	1.24	0.48395	D	0.999646	P	0.50943	0.94	B	0.43251	0.413	T	0.26710	-1.0095	10	0.66056	D	0.02	-48.1972	17.5118	0.87762	0.0:1.0:0.0:0.0	.	202	P51911	CNN1_HUMAN	V	202;152;182	ENSP00000252456:A202V;ENSP00000442031:A152V;ENSP00000437470:A182V	ENSP00000252456:A202V	A	+	2	0	CNN1	11521241	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	5.602000	0.67612	2.442000	0.82660	0.471000	0.43371	GCG		0.682	CNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458854.1	NM_001299		T	11660241	C	T	11660241	3	4	41	1	0	0	0	0	1	0	0	0	3615	768	27	1	627	1	CNN1	19	11660241	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10	198691	11660241	47468742	82	3847										
NOTCH3	4854	broad.mit.edu	37	chr19	15290210	15290210	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gacaggagcagagatagcggGccacgaggtcaatgcatgaa	15	8	1	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:15290210G>T	ENST00000263388.2	-	21	3500	c.3425C>A	c.(3424-3426)gCc>gAc	p.A1142D		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1142	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.A1142D(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GAGATAGCGGGCCACGAGGTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	83	86					19																	15290210		2203	4300	6503	15151210	SO:0001583	missense	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3425C>A	19.37:g.15290210G>T	ENSP00000263388:p.Ala1142Asp		15151210	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709091	0.68615	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.92048	-2.96	4.3	3.22	0.36961	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.87541	0.6203	N	0.15975	0.35	0.39945	D	0.974462	B;P	0.38110	0.025;0.618	B;P	0.47251	0.019;0.542	D	0.87179	0.2226	9	0.48119	T	0.1	.	10.3836	0.44125	0.0:0.4689:0.5311:0.0	.	1093;1142	Q59FL3;Q9UM47	.;NOTC3_HUMAN	D	1142;1092	ENSP00000263388:A1142D	ENSP00000263388:A1142D	A	-	2	0	NOTCH3	15151210	0.000000	0.05858	1.000000	0.80357	0.875000	0.50365	0.930000	0.28858	1.934000	0.56057	0.561000	0.74099	GCC		0.607	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15290210	G	T	15290210	3	4	41	1	0	0	0	0	1	0	0	0	10581	1203	42	2	3592	2	NOTCH3	19	15290210	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	3629969	15290210	43838773	83	3848										
OR10H2	26538	broad.mit.edu	37	chr19	15839060	15839060	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ctgtgcgtcctctcagtctcCgagatcctctacaccgtggc	9	16	3	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:15839060C>T	ENST00000305899.3	+	1	227	c.207C>T	c.(205-207)tcC>tcT	p.S69S		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S69S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCTCAGTCTCCGAGATCCTCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	19											210	170	183					19																	15839060		2203	4300	6503	15700060	SO:0001819	synonymous_variant	26538			AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.207C>T	19.37:g.15839060C>T			15700060	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																				0.627	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			T	15839060	C	T	15839060	2	4	41	1	0	0	0	0	0	0	0	1	10937	639	23	1		1	OR10H2	19	15839060	Silent	SNP	C	TCGA-AG-3881-01A-01W-0899-10	548850	15839060	43289923	84	3849										
OR10H1	26539	broad.mit.edu	37	chr19	15918641	15918641	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gccacggtgtagaggatctcGgagacggagagggcgcacag	18	9	1	3			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:15918641G>A	ENST00000334920.2	-	1	295	c.207C>T	c.(205-207)tcC>tcT	p.S69S		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S69S(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						AGAGGATCTCGGAGACGGAGA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	19											92	84	87					19																	15918641		2196	4286	6482	15779641	SO:0001819	synonymous_variant	26539			AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.207C>T	19.37:g.15918641G>A			15779641	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																				0.637	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			A	15918641	G	A	15918641	2	1	41	1	0	0	0	0	0	0	0	1	10936	1103	39	1		1	OR10H1	19	15918641	Silent	SNP	G	TCGA-AG-3881-01A-01W-0899-10	79581	15918641	43210342	85	3850										
PLEKHA4	57664	broad.mit.edu	37	chr19	49368858	49368858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gtggatcttgtttactgcccGggtgggcttctgaggagaga	16	7	2	2	rs201547716		TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:49368858G>A	ENST00000263265.6	-	3	649	c.94C>T	c.(94-96)Cgg>Tgg	p.R32W	PLEKHA4_ENST00000355496.5_Missense_Mutation_p.R32W	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	32						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)	p.R32W(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TTTACTGCCCGGGTGGGCTTC	0.597													G|||	1	0.000199681	0	0	5008	,	,		16811	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											89	70	76					19																	49368858		2203	4300	6503	54060670	SO:0001583	missense	57664			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.94C>T	19.37:g.49368858G>A	ENSP00000263265:p.Arg32Trp		54060670	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.35	3.810631	0.70797	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.20598	2.63;2.06	5.04	2.79	0.32731	.	0.000000	0.50627	D	0.000112	T	0.43077	0.1231	M	0.70595	2.14	0.37784	D	0.927104	D;D	0.89917	1.0;1.0	D;D	0.78314	0.984;0.991	T	0.49560	-0.8927	10	0.87932	D	0	.	12.1172	0.53872	0.0:0.0:0.6892:0.3107	.	32;32	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	W	32	ENSP00000263265:R32W;ENSP00000347683:R32W	ENSP00000263265:R32W	R	-	1	2	PLEKHA4	54060670	0.270000	0.24152	0.990000	0.47175	0.992000	0.81027	0.785000	0.26830	0.575000	0.29434	0.563000	0.77884	CGG		0.597	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			A	49368858	G	A	49368858	3	1	41	1	0	0	0	0	1	0	0	0	12089	1115	39	1	2317	1	PLEKHA4	19	49368858	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	33450217	49368858	9760125	86	3851										
ZNF160	90338	broad.mit.edu	37	chr19	53572104	53572104	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ttacacttgtaaggtttctcTccagaatgaattccccgatg	7	10	1	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr19:53572104T>A	ENST00000429604.1	-	7	2098	c.1683A>T	c.(1681-1683)ggA>ggT	p.G561G	ZNF160_ENST00000601421.1_Silent_p.G525G|ZNF160_ENST00000599056.1_Silent_p.G561G|ZNF160_ENST00000418871.1_Silent_p.G561G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	561					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G561G(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		AAGGTTTCTCTCCAGAATGAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	19											83	85	84					19																	53572104		2203	4300	6503	58263916	SO:0001819	synonymous_variant	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1683A>T	19.37:g.53572104T>A			58263916	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	37	CCDS12859.1																																																																																				0.398	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		A	53572104	T	A	53572104	2	1	41	1	0	0	0	0	0	0	0	1	17778	1538	54	5		5	ZNF160	19	53572104	Silent	SNP	T	TCGA-AG-3881-01A-01W-0899-10	4203246	53572104	5556879	87	3852										
CENPB	1059	broad.mit.edu	37	chr20	3766001	3766001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	agcaggcggctatgtccgaaGgctccactgcctgccaggcg	14	14	0	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr20:3766001G>A	ENST00000379751.4	-	1	1336	c.1130C>T	c.(1129-1131)cCt>cTt	p.P377L	CDC25B_ENST00000344256.6_5'Flank|CDC25B_ENST00000379598.5_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	377					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)	p.P377L(1)		kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						TATGTCCGAAGGCTCCACTGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	20											13	12	12					20																	3766001		2199	4297	6496	3714001	SO:0001583	missense	1059			X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"centromere protein B (80kD)"			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.1130C>T	20.37:g.3766001G>A	ENSP00000369075:p.Pro377Leu		3714001	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	37	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	g	17.57	3.422358	0.62622	.	.	ENSG00000125817	ENST00000379751	T	0.43294	0.95	4.52	4.52	0.55395	.	0.624337	0.13186	U	0.407128	T	0.47967	0.1474	L	0.28400	0.85	0.42066	D	0.991189	D	0.54601	0.967	P	0.57960	0.83	T	0.47302	-0.9128	10	0.66056	D	0.02	-5.005	12.7498	0.57302	0.0:0.0:1.0:0.0	.	377	P07199	CENPB_HUMAN	L	377	ENSP00000369075:P377L	ENSP00000369075:P377L	P	-	2	0	CENPB	3714001	0.994000	0.37717	0.984000	0.44739	0.952000	0.60782	2.986000	0.49370	2.064000	0.61679	0.479000	0.44913	CCT		0.642	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		A	3766001	G	A	3766001	3	1	41	1	0	0	0	0	1	0	0	0	3233	1000	35	3	673	3	CENPB	20	3766001	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10		3766001	59259519	88	3853										
CCDC117	150275	broad.mit.edu	37	chr22	29182240	29182240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gaactgaactgttttcggaaCctcggccaacagggatgtct	11	10	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr22:29182240C>T	ENST00000249064.4	+	5	942	c.766C>T	c.(766-768)Cct>Tct	p.P256S	CCDC117_ENST00000443309.2_Missense_Mutation_p.P124S|CCDC117_ENST00000421503.2_Missense_Mutation_p.P181S|CCDC117_ENST00000448492.2_Missense_Mutation_p.P238S	NM_001284263.1|NM_001284265.1|NM_173510.2	NP_001271192.1|NP_001271194.1|NP_775781.1	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	256								p.P256S(1)		breast(1)|kidney(1)|large_intestine(4)|upper_aerodigestive_tract(1)	7						GTTTTCGGAACCTCGGCCAAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	22											93	89	90					22																	29182240		2203	4300	6503	27512240	SO:0001583	missense	150275			AK091133	CCDS13846.1, CCDS63435.1, CCDS63436.1	22q12.1	2006-06-27			ENSG00000159873	ENSG00000159873			26599	protein-coding gene	gene with protein product						12477932	Standard	NM_001284263		Approved	FLJ33814	uc003aeb.3	Q8IWD4	OTTHUMG00000151091	ENST00000249064.4:c.766C>T	22.37:g.29182240C>T	ENSP00000249064:p.Pro256Ser		27512240	A8K0F1|B7Z2V1|B7Z860|Q6ICA7|Q8N278	Missense_Mutation	SNP	ENST00000249064.4	37	CCDS13846.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.716721	0.48622	.	.	ENSG00000159873	ENST00000249064;ENST00000448492;ENST00000421503;ENST00000443309	T;T;T;T	0.31247	1.51;1.52;1.5;1.53	5.94	4.87	0.63330	.	0.273852	0.36002	N	0.002854	T	0.15392	0.0371	N	0.19112	0.55	0.30464	N	0.773998	P;P;P	0.38597	0.639;0.639;0.639	B;B;B	0.30029	0.11;0.11;0.11	T	0.07290	-1.0780	10	0.28530	T	0.3	.	9.0311	0.36260	0.0:0.7641:0.1526:0.0833	.	181;238;256	B7Z2V1;B7Z860;Q8IWD4	.;.;CC117_HUMAN	S	256;238;181;124	ENSP00000249064:P256S;ENSP00000389478:P238S;ENSP00000387827:P181S;ENSP00000399363:P124S	ENSP00000249064:P256S	P	+	1	0	CCDC117	27512240	1.000000	0.71417	0.997000	0.53966	0.447000	0.32167	1.603000	0.36794	2.816000	0.96949	0.561000	0.74099	CCT		0.438	CCDC117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321258.1	NM_173510		T	29182240	C	T	29182240	3	4	41	1	0	0	0	0	1	0	0	0	2760	507	18	3	784	3	CCDC117	22	29182240	Missense_Mutation	SNP	C	TCGA-AG-3881-01A-01W-0899-10		29182240	22122326	89	3854										
EIF3D	8664	broad.mit.edu	37	chr22	36908574	36908574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	ccgggccaacttgtagctgtTgttcttcagctccgtggcaa	11	12	2	0			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr22:36908574T>C	ENST00000216190.8	-	13	1652	c.1282A>G	c.(1282-1284)Aac>Gac	p.N428D	EIF3D_ENST00000541106.1_Missense_Mutation_p.N379D|EIF3D_ENST00000478547.1_5'Flank|EIF3D_ENST00000405442.1_Missense_Mutation_p.N428D	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D									p.N428D(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						TTGTAGCTGTTGTTCTTCAGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											105	89	94					22																	36908574		2203	4300	6503	35238520	SO:0001583	missense	8664			U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.1282A>G	22.37:g.36908574T>C	ENSP00000216190:p.Asn428Asp		35238520		Missense_Mutation	SNP	ENST00000216190.8	37	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048789	0.93740	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000426531;ENST00000458572	.	.	.	5.52	5.52	0.82312	.	0.167930	0.64402	D	0.000005	D	0.85613	0.5737	M	0.92169	3.28	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.74348	0.978;0.983	D	0.89171	0.3537	9	0.87932	D	0	-0.5557	15.8129	0.78578	0.0:0.0:0.0:1.0	.	379;428	B4DVY1;O15371	.;EIF3D_HUMAN	D	428;413;379;428;81;115	.	ENSP00000216190:N428D	N	-	1	0	EIF3D	35238520	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.432000	0.80349	2.318000	0.78349	0.523000	0.50628	AAC		0.567	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1			C	36908574	T	C	36908574	3	2	41	1	0	0	0	0	1	0	0	0	5027	1812	63	4	376	4	EIF3D	22	36908574	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10	7726334	36908574	14395992	90	3855										
CACNA1I	8911	broad.mit.edu	37	chr22	40015370	40015370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	acctgtcagccatccgcaccGtgcgcgtcctgaggcccctc	10	19	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chr22:40015370G>A	ENST00000402142.3	+	4	538	c.538G>A	c.(538-540)Gtg>Atg	p.V180M	CACNA1I_ENST00000401624.1_Missense_Mutation_p.V180M|CACNA1I_ENST00000400164.3_Missense_Mutation_p.V180M|CACNA1I_ENST00000407673.1_Missense_Mutation_p.V180M|CACNA1I_ENST00000404898.1_Missense_Mutation_p.V180M|CACNA1I_ENST00000336649.4_Missense_Mutation_p.V180M	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	180					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.V180M(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CATCCGCACCGTGCGCGTCCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											111	114	113					22																	40015370		2190	4279	6469	38345316	SO:0001583	missense	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.538G>A	22.37:g.40015370G>A	ENSP00000385019:p.Val180Met		38345316	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	-	17.60	3.430234	0.62844	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02;-5.02	5.11	5.11	0.69529	Ion transport (1);	0.154977	0.41938	D	0.000791	D	0.98451	0.9484	M	0.67625	2.065	0.51233	D	0.999919	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.98871	1.0766	10	0.10636	T	0.68	.	17.3138	0.87217	0.0:0.0:1.0:0.0	.	180;180;180;180	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	M	180	ENSP00000385019:V180M;ENSP00000384093:V180M;ENSP00000383887:V180M;ENSP00000385680:V180M;ENSP00000337829:V180M;ENSP00000383028:V180M	ENSP00000337829:V180M	V	+	1	0	CACNA1I	38345316	1.000000	0.71417	0.989000	0.46669	0.179000	0.23085	7.102000	0.77005	2.405000	0.81733	0.556000	0.70494	GTG		0.612	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40015370	G	A	40015370	3	1	41	1	0	0	0	0	1	0	0	0	2552	1145	40	1	552	1	CACNA1I	22	40015370	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	3106796	40015370	11289196	91	3856										
HCCS	3052	broad.mit.edu	37	chrX	11139874	11139874	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	acgtccgtcctgccttagatTcactttcggcagtatgggac	10	12	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chrX:11139874T>A	ENST00000321143.4	+	7	953	c.751T>A	c.(751-753)Tca>Aca	p.S251T	ARHGAP6_ENST00000534860.1_Intron|HCCS_ENST00000380763.3_Missense_Mutation_p.S251T|HCCS_ENST00000380762.4_Missense_Mutation_p.S251T	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	251					organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)	p.S251T(1)		kidney(1)|large_intestine(3)|lung(3)	7						TGCCTTAGATTCACTTTCGGC	0.433																																					Ovarian(86;1338 1347 1462 10340 37882)											1	Substitution - Missense(1)	large_intestine(1)	X											129	103	112					X																	11139874		2203	4300	6503	11049795	SO:0001583	missense	3052				CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"cytochrome c heme-lyase"	300056	"holocytochrome c synthase (cytochrome c heme-lyase)", "microphthalamia with linear skin defects"	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.751T>A	X.37:g.11139874T>A	ENSP00000326579:p.Ser251Thr		11049795	B3KUS1|Q502X8	Missense_Mutation	SNP	ENST00000321143.4	37	CCDS14139.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.938298	0.73557	.	.	ENSG00000004961	ENST00000321143;ENST00000380763;ENST00000380762	D;D;D	0.82711	-1.64;-1.64;-1.64	5.74	5.74	0.90152	.	0.112740	0.64402	D	0.000007	D	0.88089	0.6343	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86844	0.2019	10	0.35671	T	0.21	-6.6141	8.3086	0.32058	0.1785:0.0:0.0:0.8215	.	251	P53701	CCHL_HUMAN	T	251	ENSP00000326579:S251T;ENSP00000370140:S251T;ENSP00000370139:S251T	ENSP00000326579:S251T	S	+	1	0	HCCS	11049795	1.000000	0.71417	0.131000	0.22000	0.861000	0.49209	5.653000	0.67967	1.917000	0.55516	0.486000	0.48141	TCA		0.433	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			A	11139874	T	A	11139874	3	1	41	1	0	0	0	0	1	0	0	0	7011	1783	62	5	773	5	HCCS	23	11139874	Missense_Mutation	SNP	T	TCGA-AG-3881-01A-01W-0899-10		11139874	144130686	92	3857										
SLC7A3	84889	broad.mit.edu	37	chrX	70146731	70146731	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	attccactgctcaccaagcaAtgaggaacaaacatagacaa	6	11	1	2			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chrX:70146731A>G	ENST00000374299.3	-	9	1591	c.1447T>C	c.(1447-1449)Ttg>Ctg	p.L483L	SLC7A3_ENST00000298085.4_Silent_p.L483L			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	483					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)	p.L483L(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	TCACCAAGCAATGAGGAACAA	0.478													A|||	1	0.000264901	8e-04	0	3775	,	,		15919	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											82	71	74					X																	70146731		2203	4300	6503	70063456	SO:0001819	synonymous_variant	84889			AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"Solute carriers"	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1447T>C	X.37:g.70146731A>G			70063456	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	37	CCDS14404.1																																																																																				0.478	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803		G	70146731	A	G	70146731	2	3	41	1	0	0	0	0	0	0	0	1	14735	98	4	4		4	SLC7A3	23	70146731	Silent	SNP	A	TCGA-AG-3881-01A-01W-0899-10	59006857	70146731	85123829	93	3858										
GPR174	84636	broad.mit.edu	37	chrX	78427423	78427423	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	gaagacggctttcaagacaaGatttgcatgacagcatccaa	9	9	1	4			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chrX:78427423G>T	ENST00000276077.1	+	1	955	c.919G>T	c.(919-921)Gat>Tat	p.D307Y		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D307Y(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						TTCAAGACAAGATTTGCATGA	0.403										HNSCC(63;0.18)																																						1	Substitution - Missense(1)	large_intestine(1)	X											110	93	99					X																	78427423		2203	4300	6503	78314079	SO:0001583	missense	84636			AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.919G>T	X.37:g.78427423G>T	ENSP00000276077:p.Asp307Tyr		78314079	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	37	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	g	13.21	2.170609	0.38315	.	.	ENSG00000147138	ENST00000276077	T	0.62639	0.01	5.25	5.25	0.73442	.	0.483859	0.22638	N	0.057493	T	0.45736	0.1357	N	0.08118	0	0.49687	D	0.999813	B	0.32010	0.351	B	0.32624	0.149	T	0.52660	-0.8546	10	0.59425	D	0.04	.	16.358	0.83243	0.0:0.0:1.0:0.0	.	307	Q9BXC1	GP174_HUMAN	Y	307	ENSP00000276077:D307Y	ENSP00000276077:D307Y	D	+	1	0	GPR174	78314079	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	8.346000	0.90060	2.172000	0.68678	0.534000	0.68092	GAT		0.403	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		T	78427423	G	T	78427423	3	4	41	1	0	0	0	0	1	0	0	0	6692	942	33	2	921	2	GPR174	23	78427423	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	8280692	78427423	76843137	94	3859										
ODZ1	10178	broad.mit.edu	37	chrX	123514919	123514919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	attgagaatggcagcaagccGcctgctatcttcattggcta	10	10	2	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chrX:123514919G>A	ENST00000371130.3	-	31	7708	c.7645C>T	c.(7645-7647)Cgg>Tgg	p.R2549W	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.R2556W	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2549					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R2551W(2)|p.R2551G(1)									GCAGCAAGCCGCCTGCTATCT	0.438																																																3	Substitution - Missense(3)	large_intestine(2)|upper_aerodigestive_tract(1)	X											77	73	74					X																	123514919		2203	4300	6503	123342600	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7645C>T	X.37:g.123514919G>A	ENSP00000360171:p.Arg2549Trp		123342600	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.104619	0.56291	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86366	-2.11;-2.08	5.83	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.92260	0.7545	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.993;0.998;0.987	D	0.92731	0.6200	10	0.72032	D	0.01	.	15.4756	0.75478	0.0:0.0:0.8606:0.1394	.	2555;2556;2549	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	W	2549;2556	ENSP00000360171:R2549W;ENSP00000403954:R2556W	ENSP00000360171:R2549W	R	-	1	2	ODZ1	123342600	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.531000	0.67148	1.204000	0.43247	0.600000	0.82982	CGG		0.438	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123514919	G	A	123514919	3	1	41	1	0	0	0	0	1	0	0	0	10865	1086	38	1	536	1	ODZ1	23	123514919	Missense_Mutation	SNP	G	TCGA-AG-3881-01A-01W-0899-10	45087496	123514919	31755641	95	3860										
SLITRK2	84631	broad.mit.edu	37	chrX	144904613	144904613	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.693537414965986	2.77414965986395	0.462358276643991	1	1	0	catggaattgcacttgtgacTtacttcctctcaaggcctgg	9	11	1	1			TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3881-01A-01W-0899-10	TCGA-AG-3881-10A-01W-0901-10	g.chrX:144904613T>C	ENST00000370490.1	+	1	4925	c.670T>C	c.(670-672)Tta>Cta	p.L224L	SLITRK2_ENST00000413937.2_Silent_p.L224L|SLITRK2_ENST00000428560.2_Silent_p.L224L|SLITRK2_ENST00000434188.2_Silent_p.L224L|SLITRK2_ENST00000447897.2_Silent_p.L224L			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	224	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.L224L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CACTTGTGACTTACTTCCTCT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	X											127	116	120					X																	144904613		2203	4300	6503	144712305	SO:0001819	synonymous_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.670T>C	X.37:g.144904613T>C			144712305	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																				0.463	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		C	144904613	T	C	144904613	2	2	41	1	0	0	0	0	0	0	0	1	14780	1606	56	4		4	SLITRK2	23	144904613	Silent	SNP	T	TCGA-AG-3881-01A-01W-0899-10	21389694	144904613	10365947	96	3861										
AADACL4	343066	broad.mit.edu	37	chr1	12726161	12726161	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtgggcagatcagatcttccCcggatccgggctcaggttct	13	12	4	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:12726161C>T	ENST00000376221.1	+	4	639	c.639C>T	c.(637-639)ccC>ccT	p.P213P		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	213						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.P213P(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		CAGATCTTCCCCGGATCCGGG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	1											80	84	83					1																	12726161		2203	4300	6503	12648748	SO:0001819	synonymous_variant	343066				CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.639C>T	1.37:g.12726161C>T			12648748		Silent	SNP	ENST00000376221.1	37	CCDS30590.1																																																																																				0.567	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630		T	12726161	C	T	12726161	2	4	42	1	0	0	0	0	0	0	0	1	13	610	22	3		3	AADACL4	1	12726161	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10		12726161	236524460	1	3862										
CD5L	922	broad.mit.edu	37	chr1	157804386	157804386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cctcccacatcccagctgccGgcacaccacctttgcggccc	7	22	0	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:157804386G>A	ENST00000368174.4	-	4	625	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	177	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.R177W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CCCAGCTGCCGGCACACCACC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	83	84					1																	157804386		2203	4300	6503	156071010	SO:0001583	missense	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.529C>T	1.37:g.157804386G>A	ENSP00000357156:p.Arg177Trp		156071010	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.258210	0.59321	.	.	ENSG00000073754	ENST00000368174	T	0.44482	0.92	5.13	4.19	0.49359	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.552418	0.15335	N	0.267793	T	0.62624	0.2443	H	0.94808	3.585	0.28548	N	0.911747	D	0.89917	1.0	D	0.80764	0.994	T	0.62969	-0.6741	10	0.87932	D	0	.	10.3736	0.44068	0.0:0.0:0.6292:0.3708	.	177	O43866	CD5L_HUMAN	W	177	ENSP00000357156:R177W	ENSP00000357156:R177W	R	-	1	2	CD5L	156071010	0.017000	0.18338	1.000000	0.80357	0.630000	0.37929	0.105000	0.15333	1.324000	0.45282	0.655000	0.94253	CGG		0.597	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157804386	G	A	157804386	3	1	42	1	0	0	0	0	1	0	0	0	3033	1115	39	1	526	1	CD5L	1	157804386	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	145078225	157804386	91446235	2	3863										
CD1B	910	broad.mit.edu	37	chr1	158300707	158300707	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	aagttacctttagaccaaggCttcaggaatatggcagtgcc	10	9	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:158300707C>A	ENST00000368168.3	-	2	314	c.207G>T	c.(205-207)aaG>aaT	p.K69N		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	69					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.K69N(1)		breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					TAGACCAAGGCTTCAGGAATA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											258	251	253					1																	158300707		2203	4300	6503	156567331	SO:0001583	missense	910			M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.207G>T	1.37:g.158300707C>A	ENSP00000357150:p.Lys69Asn		156567331	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	37	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.99|13.99	2.402338|2.402338	0.42613|0.42613	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.06933	.|3.24	4.01|4.01	2.01|2.01	0.26516|0.26516	.|MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.159685	.|0.29501	.|N	.|0.011966	T|T	0.11665|0.11665	0.0284|0.0284	M|M	0.88979|0.88979	2.995|2.995	0.24533|0.24533	N|N	0.994108|0.994108	.|P;P	.|0.49783	.|0.928;0.872	.|P;P	.|0.57846	.|0.828;0.46	T|T	0.06197|0.06197	-1.0840|-1.0840	5|10	.|0.40728	.|T	.|0.16	-19.1782|-19.1782	5.5834|5.5834	0.17262|0.17262	0.0:0.7269:0.0:0.2731|0.0:0.7269:0.0:0.2731	.|.	.|69;69	.|B4E0D2;P29016	.|.;CD1B_HUMAN	S|N	37|69	.|ENSP00000357150:K69N	.|ENSP00000357150:K69N	A|K	-|-	1|3	0|2	CD1B|CD1B	156567331|156567331	0.854000|0.854000	0.29725|0.29725	0.995000|0.995000	0.50966|0.50966	0.444000|0.444000	0.32077|0.32077	0.126000|0.126000	0.15769|0.15769	0.390000|0.390000	0.25115|0.25115	0.655000|0.655000	0.94253|0.94253	GCC|AAG		0.458	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		A	158300707	C	A	158300707	3	1	42	1	0	0	0	0	1	0	0	0	2981	796	28	2	814	2	CD1B	1	158300707	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	496321	158300707	90949914	3	3864										
SPTA1	6708	broad.mit.edu	37	chr1	158619701	158619701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cagctgccgctgttcatctgCaagcctctgcaaagaacccc	8	16	3	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:158619701C>A	ENST00000368147.4	-	25	3694	c.3514G>T	c.(3514-3516)Gca>Tca	p.A1172S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1172					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.A1172S(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGTTCATCTGCAAGCCTCTGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											29	29	29					1																	158619701		1839	4097	5936	156886325	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3514G>T	1.37:g.158619701C>A	ENSP00000357129:p.Ala1172Ser		156886325	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507713	0.85282	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.54479	0.57;0.57	5.08	5.08	0.68730	.	0.000000	0.32120	N	0.006560	T	0.54334	0.1852	M	0.66506	2.035	0.48185	D	0.999601	P	0.45474	0.859	P	0.52646	0.705	T	0.48614	-0.9020	10	0.27082	T	0.32	.	17.2337	0.86992	0.0:1.0:0.0:0.0	.	1172	P02549	SPTA1_HUMAN	S	1172	ENSP00000357130:A1172S;ENSP00000357129:A1172S	ENSP00000357129:A1172S	A	-	1	0	SPTA1	156886325	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	6.743000	0.74848	2.621000	0.88768	0.650000	0.86243	GCA		0.463	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158619701	C	A	158619701	3	1	42	1	0	0	0	0	1	0	0	0	15155	710	25	2	3857	2	SPTA1	1	158619701	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	318994	158619701	90630920	4	3865										
DUSP27	92235	broad.mit.edu	37	chr1	167096368	167096368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tgcgttctggtctgcagaccCctcagtcagcgctgatgggg	14	12	4	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:167096368C>T	ENST00000361200.2	+	6	2166	c.2000C>T	c.(1999-2001)cCc>cTc	p.P667L	DUSP27_ENST00000443333.1_Missense_Mutation_p.P667L|DUSP27_ENST00000271385.5_Missense_Mutation_p.P667L|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	667					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.P667L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						TCTGCAGACCCCTCAGTCAGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											45	43	43					1																	167096368		2203	4300	6503	165362992	SO:0001583	missense	92235			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2000C>T	1.37:g.167096368C>T	ENSP00000354483:p.Pro667Leu		165362992	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	5.657	0.305801	0.10733	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03860	3.78;3.78;3.78	5.1	2.17	0.27698	.	0.994205	0.08162	N	0.988299	T	0.01940	0.0061	L	0.59436	1.845	0.18873	N	0.999988	B	0.31680	0.335	B	0.22386	0.039	T	0.44802	-0.9304	10	0.87932	D	0	-2.4805	6.5076	0.22204	0.0:0.6483:0.1349:0.2168	.	667	Q5VZP5	DUS27_HUMAN	L	667	ENSP00000354483:P667L;ENSP00000271385:P667L;ENSP00000404874:P667L	ENSP00000271385:P667L	P	+	2	0	DUSP27	165362992	0.277000	0.24220	0.015000	0.15790	0.231000	0.25187	2.294000	0.43567	0.527000	0.28560	-0.163000	0.13421	CCC		0.637	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167096368	C	T	167096368	3	4	42	1	0	0	0	0	1	0	0	0	4835	623	22	3	2018	3	DUSP27	1	167096368	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	8476667	167096368	82154253	5	3866										
FAM5C	339479	broad.mit.edu	37	chr1	190068184	190068184	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gacacgtgcacgagtgcgtcTcttctgaaaagctgcctagg	12	11	2	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:190068184T>A	ENST00000367462.3	-	8	1496	c.1265A>T	c.(1264-1266)gAg>gTg	p.E422V	BRINP3_ENST00000534846.1_Missense_Mutation_p.E320V	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	422				E -> K (in Ref. 3; AAD09521). {ECO:0000305}.	cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.E422V(1)									CGAGTGCGTCTCTTCTGAAAA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	39	43					1																	190068184		2203	4300	6503	188334807	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1265A>T	1.37:g.190068184T>A	ENSP00000356432:p.Glu422Val		188334807	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300141	0.60195	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	D;D	0.87729	-2.29;-2.29	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.89329	0.6684	L	0.58101	1.795	0.58432	D	0.999997	D;P	0.54964	0.969;0.948	P;P	0.53185	0.72;0.529	D	0.90300	0.4329	10	0.72032	D	0.01	.	13.8296	0.63373	0.0:0.0:0.0:1.0	.	320;422	B7Z260;Q76B58	.;FAM5C_HUMAN	V	422;320	ENSP00000356432:E422V;ENSP00000438022:E320V	ENSP00000356432:E422V	E	-	2	0	FAM5C	188334807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.104000	0.71498	2.146000	0.66826	0.482000	0.46254	GAG		0.547	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190068184	T	A	190068184	3	1	42	1	0	0	0	0	1	0	0	0	5613	1551	54	5	1039	5	FAM5C	1	190068184	Missense_Mutation	SNP	T	TCGA-AG-3882-01A-01W-0899-10	22971816	190068184	59182437	6	3867										
HIST3H2BB	128312	broad.mit.edu	37	chr1	228645872	228645872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gctcctgcgcccaagaagggTtctaaaaaggctgtcaccaa	10	12	2	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:228645872T>C	ENST00000369160.2	+	1	65	c.42T>C	c.(40-42)ggT>ggC	p.G14G	HIST3H2A_ENST00000366695.2_5'Flank	NM_175055.2	NP_778225.1	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	14					chromatin organization (GO:0006325)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G14G(1)		skin(1)	1		Prostate(94;0.183)				CCAAGAAGGGTTCTAAAAAGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	1											74	76	75					1																	228645872		2203	4300	6503	226712495	SO:0001819	synonymous_variant	128312			AY131981	CCDS1574.1	1q42.13	2011-01-27	2006-10-11		ENSG00000196890	ENSG00000196890		"Histones / Replication-dependent"	20514	protein-coding gene	gene with protein product		615046	"histone 3, H2bb"			12408966	Standard	NM_175055		Approved		uc001hsz.3	Q8N257	OTTHUMG00000040045	ENST00000369160.2:c.42T>C	1.37:g.228645872T>C			226712495	A4FU05|Q3ZCP6|Q5TA30	Silent	SNP	ENST00000369160.2	37	CCDS1574.1																																																																																				0.547	HIST3H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096597.1	NM_175055		C	228645872	T	C	228645872	2	2	42	1	0	0	0	0	0	0	0	1	7204	1712	60	4		4	HIST3H2BB	1	228645872	Silent	SNP	T	TCGA-AG-3882-01A-01W-0899-10	38577688	228645872	20604749	7	3868										
FMN2	56776	broad.mit.edu	37	chr1	240371836	240371836	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cccctctgcttcctgtatcaGgccctccactcctcccacaa	4	21	2	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr1:240371836G>T	ENST00000319653.9	+	5	3954	c.3724G>T	c.(3724-3726)Ggc>Tgc	p.G1242C		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1242	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1385C(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCCTGTATCAGGCCCTCCACT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	43	44					1																	240371836		2203	4300	6503	238438459	SO:0001583	missense	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3724G>T	1.37:g.240371836G>T	ENSP00000318884:p.Gly1242Cys		238438459	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	g	4.743	0.138141	0.09083	.	.	ENSG00000155816	ENST00000319653	T	0.59364	0.27	4.26	4.26	0.50523	Actin-binding FH2 (1);Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	0.412914	0.19399	U	0.115222	T	0.70736	0.3258	M	0.61703	1.905	0.54753	D	0.999986	D	0.89917	1.0	D	0.68943	0.961	T	0.70392	-0.4884	9	.	.	.	.	13.4923	0.61402	0.0:0.1577:0.8423:0.0	.	1242	Q9NZ56	FMN2_HUMAN	C	1242	ENSP00000318884:G1242C	.	G	+	1	0	FMN2	238438459	0.001000	0.12720	0.115000	0.21578	0.395000	0.30598	0.434000	0.21494	2.203000	0.70933	0.472000	0.43445	GGC		0.582	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371836	G	T	240371836	3	4	42	1	0	0	0	0	1	0	0	0	5969	1000	35	2	3742	2	FMN2	1	240371836	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	11725964	240371836	8878785	8	3869										
DYSF	8291	broad.mit.edu	37	chr2	71883368	71883368	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	taacaccttcaagctgtaccGgggcaagacgcaggaggaga	13	10	1	2	rs191383034	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr2:71883368G>A	ENST00000258104.3	+	42	4863	c.4586G>A	c.(4585-4587)cGg>cAg	p.R1529Q	DYSF_ENST00000410041.1_Missense_Mutation_p.R1547Q|DYSF_ENST00000409762.1_Missense_Mutation_p.R1546Q|DYSF_ENST00000413539.2_Missense_Mutation_p.R1560Q|DYSF_ENST00000409744.1_Missense_Mutation_p.R1537Q|DYSF_ENST00000410020.3_Missense_Mutation_p.R1568Q|DYSF_ENST00000409651.1_Missense_Mutation_p.R1561Q|DYSF_ENST00000394120.2_Missense_Mutation_p.R1530Q|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409366.1_Missense_Mutation_p.R1551Q|DYSF_ENST00000409582.3_Missense_Mutation_p.R1567Q|DYSF_ENST00000429174.2_Missense_Mutation_p.R1550Q	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1529					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R1529Q(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						AAGCTGTACCGGGGCAAGACG	0.512													G|||	3	0.000599042	0	0	5008	,	,		21952	0		0.001	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	2											273	269	271					2																	71883368		2203	4300	6503	71736876	SO:0001583	missense	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4586G>A	2.37:g.71883368G>A	ENSP00000258104:p.Arg1529Gln		71736876	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	31	5.064173	0.93898	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.85955	-2.05;-2.04;-2.01;-2.02;-2.05;-2.04;-2.05;-2.02;-2.02;-2.01;-2.04	5.39	4.52	0.55395	.	0.178183	0.47852	N	0.000210	D	0.90007	0.6880	M	0.62154	1.92	0.48087	D	0.999582	B;D;D;D;D;D;D;D;P;D;D;D;D;D;D	0.89917	0.044;1.0;1.0;1.0;1.0;0.999;1.0;0.999;0.884;1.0;0.998;0.998;0.999;1.0;0.999	B;D;D;D;D;D;D;D;P;D;D;P;D;D;D	0.77004	0.084;0.964;0.964;0.964;0.964;0.976;0.985;0.976;0.541;0.964;0.989;0.868;0.964;0.964;0.922	D	0.89631	0.3855	10	0.46703	T	0.11	-35.0765	12.1972	0.54305	0.0823:0.0:0.9177:0.0	.	293;1561;1568;1551;1516;1547;1537;1546;1536;1560;1567;1550;1515;1530;1529	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	Q	1560;1546;1567;1550;1529;1561;1530;1537;1551;1568;1547	ENSP00000407046:R1560Q;ENSP00000387137:R1546Q;ENSP00000386547:R1567Q;ENSP00000398305:R1550Q;ENSP00000258104:R1529Q;ENSP00000386683:R1561Q;ENSP00000377678:R1530Q;ENSP00000386285:R1537Q;ENSP00000386512:R1551Q;ENSP00000386881:R1568Q;ENSP00000386617:R1547Q	ENSP00000258104:R1529Q	R	+	2	0	DYSF	71736876	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.699000	0.84547	1.509000	0.48786	0.655000	0.94253	CGG		0.512	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71883368	G	A	71883368	3	1	42	1	0	0	0	0	1	0	0	0	4870	1116	39	1	5011	1	DYSF	2	71883368	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		71883368	171316005	9	3870										
CNTNAP5	129684	broad.mit.edu	37	chr2	125521251	125521251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	taaatttatgttttgcaggaCaaatgatactggctttcttt	7	5	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr2:125521251C>T	ENST00000431078.1	+	15	2598	c.2234C>T	c.(2233-2235)aCa>aTa	p.T745I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	745	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.T745I(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TTTTGCAGGACAAATGATACT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	67	69					2																	125521251		1839	4081	5920	125237721	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2234C>T	2.37:g.125521251C>T	ENSP00000399013:p.Thr745Ile		125237721	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.066256	0.36470	.	.	ENSG00000155052	ENST00000431078	T	0.13420	2.59	5.24	4.36	0.52297	.	0.281428	0.24599	N	0.037153	T	0.14743	0.0356	L	0.51422	1.61	0.33902	D	0.638687	B	0.09022	0.002	B	0.10450	0.005	T	0.07597	-1.0764	10	0.36615	T	0.2	.	13.1459	0.59461	0.0:0.9225:0.0:0.0775	.	745	Q8WYK1	CNTP5_HUMAN	I	745	ENSP00000399013:T745I	ENSP00000399013:T745I	T	+	2	0	CNTNAP5	125237721	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.751000	0.62169	1.364000	0.46038	0.655000	0.94253	ACA		0.398	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125521251	C	T	125521251	3	4	42	1	0	0	0	0	1	0	0	0	3656	478	17	3	2292	3	CNTNAP5	2	125521251	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	53637883	125521251	117678122	10	3871										
SSB	6741	broad.mit.edu	37	chr2	170667734	170667734	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gaaagggtaataaagctgccCagcctgggtctggtaaagga	14	7	1	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr2:170667734C>A	ENST00000409333.1	+	11	1286	c.1039C>A	c.(1039-1041)Cag>Aag	p.Q347K	METTL5_ENST00000409837.1_Intron|SSB_ENST00000260956.4_Missense_Mutation_p.Q347K			P05455	LA_HUMAN	Sjogren syndrome antigen B (autoantigen La)	347					histone mRNA metabolic process (GO:0008334)|tRNA modification (GO:0006400)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)	p.Q347K(1)		endometrium(3)|large_intestine(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						TAAAGCTGCCCAGCCTGGGTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	70	70					2																	170667734		2203	4300	6503	170375980	SO:0001583	missense	6741				CCDS2237.1	2q31.1	2014-02-14		2005-06-16	ENSG00000138385	ENSG00000138385		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	11316	protein-coding gene	gene with protein product	"La ribonucleoprotein domain family, member 3"	109090					Standard	NM_003142		Approved	LARP3, La, La/SSB	uc002ufk.3	P05455	OTTHUMG00000132212	ENST00000409333.1:c.1039C>A	2.37:g.170667734C>A	ENSP00000386636:p.Gln347Lys		170375980	Q15367|Q53XJ4	Missense_Mutation	SNP	ENST00000409333.1	37	CCDS2237.1	.	.	.	.	.	.	.	.	.	.	C	4.173	0.030736	0.08101	.	.	ENSG00000138385	ENST00000260956;ENST00000409333	T;T	0.40476	1.03;1.03	4.67	3.78	0.43462	.	0.405138	0.26514	N	0.023958	T	0.29850	0.0746	L	0.44542	1.39	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.07481	-1.0770	10	0.06494	T	0.89	1.0372	10.496	0.44777	0.0:0.9072:0.0:0.0928	.	347	P05455	LA_HUMAN	K	347	ENSP00000260956:Q347K;ENSP00000386636:Q347K	ENSP00000260956:Q347K	Q	+	1	0	SSB	170375980	0.797000	0.28877	0.770000	0.31555	0.993000	0.82548	1.394000	0.34509	1.073000	0.40885	0.460000	0.39030	CAG		0.388	SSB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333316.1	NM_003142		A	170667734	C	A	170667734	3	1	42	1	0	0	0	0	1	0	0	0	15217	595	21	2	1077	2	SSB	2	170667734	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	45146483	170667734	72531639	11	3872										
TTN	7273	broad.mit.edu	37	chr2	179470279	179470279	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	agatgtggttgggcagagtcGcttgttaactctttcaaagt	12	6	2	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr2:179470279G>A	ENST00000591111.1	-	229	49044	c.48820C>T	c.(48820-48822)Cga>Tga	p.R16274*	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R17915*|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.R15347*|TTN_ENST00000460472.2_Nonsense_Mutation_p.R8850*|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R8975*|TTN_ENST00000342175.6_Nonsense_Mutation_p.R9042*			Q8WZ42	TITIN_HUMAN	titin	16274	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R15347*(1)|p.R9042*(1)|p.R8850*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGCAGAGTCGCTTGTTAACT	0.433																																																3	Substitution - Nonsense(3)	large_intestine(3)	2											151	145	147					2																	179470279		1918	4118	6036	179178524	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48820C>T	2.37:g.179470279G>A	ENSP00000465570:p.Arg16274*		179178524	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	59	38.396451	0.99984	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.87	-3.6	0.04570	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	22.2861	0.99969	0.0:0.0:0.1325:0.8675	.	.	.	.	X	15347;8850;9042;8975;8850	.	ENSP00000340554:R9042X	R	-	1	2	TTN	179178524	0.005000	0.15991	0.269000	0.24586	0.007000	0.05969	-0.004000	0.12878	-0.650000	0.05423	-0.182000	0.12963	CGA		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179470279	G	A	179470279	4	1	42	1	0	0	0	0	0	1	0	0	16775	1095	38	1	54286	1	TTN	2	179470279	Nonsense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	8802545	179470279	63729094	12	3873										
TTN	7273	broad.mit.edu	37	chr2	179579278	179579278	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	acagtagatatgtcactgagCttcttcacaaatcttggtgg	9	8	4	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr2:179579278C>A	ENST00000591111.1	-	89	25496	c.25272G>T	c.(25270-25272)aaG>aaT	p.K8424N	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K8741N|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K7497N|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12595	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K7497N(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTCACTGAGCTTCTTCACAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	41	43					2																	179579278		1843	4106	5949	179287523	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25272G>T	2.37:g.179579278C>A	ENSP00000465570:p.Lys8424Asn		179287523	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.44	1.938775	0.34189	.	.	ENSG00000155657	ENST00000342992	T	0.68765	-0.35	5.96	0.826	0.18829	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.69079	0.3071	M	0.77313	2.365	0.80722	D	1	P	0.37573	0.6	P	0.45610	0.487	T	0.65709	-0.6102	9	0.87932	D	0	.	6.1298	0.20199	0.0:0.4533:0.1226:0.4241	.	8424	Q8WZ42	TITIN_HUMAN	N	7497	ENSP00000343764:K7497N	ENSP00000343764:K7497N	K	-	3	2	TTN	179287523	0.988000	0.35896	0.991000	0.47740	0.966000	0.64601	0.256000	0.18351	-0.127000	0.11661	0.655000	0.94253	AAG		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179579278	C	A	179579278	3	1	42	1	0	0	0	0	1	0	0	0	16775	796	28	2	78394	2	TTN	2	179579278	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	108999	179579278	63620095	13	3874										
VGLL4	9686	broad.mit.edu	37	chr3	11684941	11684941	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cagaatgccgatattgttgtTcatcttgtccaagtactgat	8	8	2	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr3:11684941T>G	ENST00000430365.2	-	1	457	c.52A>C	c.(52-54)Aac>Cac	p.N18H	VGLL4_ENST00000404339.1_Intron|VGLL4_ENST00000273038.3_Intron	NM_001128219.1	NP_001121691.1	Q14135	VGLL4_HUMAN	vestigial-like family member 4	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.N18H(1)		NS(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		ATATTGTTGTTCATCTTGTCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											203	194	197					3																	11684941		1568	3582	5150	11659941	SO:0001583	missense	9686			D50911	CCDS2606.1, CCDS46754.1, CCDS46755.1, CCDS46756.1, CCDS68342.1, CCDS68343.1	3p25.2	2014-03-03	2014-03-03		ENSG00000144560	ENSG00000144560			28966	protein-coding gene	gene with protein product			"vestigial like 4 (Drosophila)"			8590280, 15140898	Standard	NM_001284390		Approved	KIAA0121	uc010hdx.1	Q14135	OTTHUMG00000129739	ENST00000430365.2:c.52A>C	3.37:g.11684941T>G	ENSP00000404251:p.Asn18His		11659941	B4DTS7|J3KN68|Q7L5V0|Q9BQ78	Missense_Mutation	SNP	ENST00000430365.2	37	CCDS46754.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.549815	0.86127	.	.	ENSG00000144560	ENST00000430365	T	0.50813	0.73	5.63	5.63	0.86233	.	.	.	.	.	T	0.62986	0.2473	L	0.59436	1.845	0.80722	D	1	D	0.67145	0.996	D	0.63877	0.919	T	0.66060	-0.6017	9	0.72032	D	0.01	.	14.441	0.67318	0.0:0.0:0.0:1.0	.	18	G5E9M7	.	H	18	ENSP00000404251:N18H	ENSP00000404251:N18H	N	-	1	0	VGLL4	11659941	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.131000	0.77243	2.145000	0.66743	0.533000	0.62120	AAC		0.473	VGLL4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339133.1	NM_014667		G	11684941	T	G	11684941	3	3	42	1	0	0	0	0	1	0	0	0	17201	1783	62	4	882	4	VGLL4	3	11684941	Missense_Mutation	SNP	T	TCGA-AG-3882-01A-01W-0899-10		11684941	186337489	14	3875										
PHLDB2	90102	broad.mit.edu	37	chr3	111681012	111681012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gaaatctgaattttataaccGcacagcatctgaatcaaatg	6	8	3	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr3:111681012G>A	ENST00000431670.2	+	13	3341	c.2930G>A	c.(2929-2931)cGc>cAc	p.R977H	PHLDB2_ENST00000393925.3_Missense_Mutation_p.R977H|PHLDB2_ENST00000495180.1_Missense_Mutation_p.R468H|PHLDB2_ENST00000470699.2_3'UTR|PHLDB2_ENST00000481953.1_Missense_Mutation_p.R934H|PHLDB2_ENST00000412622.1_Missense_Mutation_p.R934H|PHLDB2_ENST00000393923.3_Missense_Mutation_p.R961H	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	977						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)		p.R934H(1)|p.R977H(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TTTTATAACCGCACAGCATCT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	3											125	122	123					3																	111681012		2203	4300	6503	113163702	SO:0001583	missense	90102				CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2930G>A	3.37:g.111681012G>A	ENSP00000405405:p.Arg977His		113163702	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	37	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085975	0.94100	.	.	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49;0.49;0.49	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	L	0.55743	1.74	0.58432	D	0.999999	P;D;D;D;D	0.89917	0.95;1.0;1.0;1.0;1.0	B;D;D;D;D	0.74674	0.313;0.962;0.972;0.984;0.984	T	0.69277	-0.5187	10	0.72032	D	0.01	.	17.3945	0.87441	0.0:0.0:1.0:0.0	.	96;468;977;934;961	Q658P8;E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;.;PHLB2_HUMAN;.;.	H	961;977;934;934;977;934;468	ENSP00000377500:R961H;ENSP00000405405:R977H;ENSP00000405292:R934H;ENSP00000418296:R934H;ENSP00000377502:R977H;ENSP00000418319:R934H;ENSP00000420303:R468H	ENSP00000377500:R961H	R	+	2	0	PHLDB2	113163702	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.802000	0.91910	2.840000	0.97914	0.655000	0.94253	CGC		0.398	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		A	111681012	G	A	111681012	3	1	42	1	0	0	0	0	1	0	0	0	11883	1087	38	1	3061	1	PHLDB2	3	111681012	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	99996071	111681012	86341418	15	3876										
GSK3B	2932	broad.mit.edu	37	chr3	119582401	119582401	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ggcagttggtgtatactccaGcagacggctacacagtgcaa	12	10	0	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr3:119582401G>T	ENST00000264235.8	-	9	1943	c.961C>A	c.(961-963)Ctg>Atg	p.L321M	GSK3B_ENST00000316626.5_Missense_Mutation_p.L334M|GSK3B_ENST00000473886.1_5'UTR	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	321	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)	p.L334M(2)		endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	GTATACTCCAGCAGACGGCTA	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	3											95	87	90					3																	119582401		2203	4300	6503	121065091	SO:0001583	missense	2932			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.961C>A	3.37:g.119582401G>T	ENSP00000264235:p.Leu321Met		121065091	D3DN89|Q9BWH3|Q9UL47	Missense_Mutation	SNP	ENST00000264235.8	37	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862379	0.71949	.	.	ENSG00000082701	ENST00000264235;ENST00000316626;ENST00000539838	T;T	0.73575	-0.76;-0.76	5.03	3.25	0.37280	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84606	0.5509	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85517	0.1201	10	0.87932	D	0	-5.8294	11.72	0.51677	0.1407:0.0:0.8593:0.0	.	321;334	P49841;P49841-2	GSK3B_HUMAN;.	M	321;334;38	ENSP00000264235:L321M;ENSP00000324806:L334M	ENSP00000264235:L321M	L	-	1	2	GSK3B	121065091	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.462000	0.45049	0.830000	0.34757	0.650000	0.86243	CTG		0.443	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2			T	119582401	G	T	119582401	3	4	42	1	0	0	0	0	1	0	0	0	6845	962	34	2	313	2	GSK3B	3	119582401	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	7901389	119582401	78440029	16	3877										
MASP1	5648	broad.mit.edu	37	chr3	186978589	186978589	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gcggcaggagcagtagtagcCgccaatgtagttgtggcagt	16	8	0	0	rs115241263	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr3:186978589C>T	ENST00000337774.5	-	4	876	c.487G>A	c.(487-489)Ggc>Agc	p.G163S	MASP1_ENST00000392470.2_Missense_Mutation_p.G137S|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000169293.6_Missense_Mutation_p.G163S|MASP1_ENST00000392472.2_Missense_Mutation_p.G50S|MASP1_ENST00000296280.6_Missense_Mutation_p.G163S	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	163	EGF-like; calcium-binding.|Homodimerization. {ECO:0000250}.|Interaction with FCN2.|Interaction with MBL2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.G163S(2)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		CAGTAGTAGCCGCCAATGTAG	0.547													C|||	3	0.000599042	0.0023	0	5008	,	,		17272	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	3											156	112	127					3																	186978589		2203	4300	6503	188461283	SO:0001583	missense	5648			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.487G>A	3.37:g.186978589C>T	ENSP00000336792:p.Gly163Ser		188461283	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	37	CCDS33907.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.270470	0.95429	.	.	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000392472;ENST00000541896;ENST00000169293;ENST00000392470;ENST00000392475	D;D;D;D;D;D	0.97016	-2.48;-2.48;-2.48;-2.48;-2.48;-4.21	5.57	5.57	0.84162	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.000000	0.85682	D	0.000000	D	0.93680	0.7981	N	0.11341	0.13	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;P;D;D;D	0.97110	0.993;0.902;1.0;0.996;0.994	D	0.92089	0.5679	10	0.15952	T	0.53	.	18.9138	0.92496	0.0:1.0:0.0:0.0	.	137;163;50;163;163	F8W876;P48740-3;P48740-4;P48740-2;P48740	.;.;.;.;MASP1_HUMAN	S	163;163;50;50;163;137;170	ENSP00000336792:G163S;ENSP00000296280:G163S;ENSP00000376264:G50S;ENSP00000169293:G163S;ENSP00000376262:G137S;ENSP00000376267:G170S	ENSP00000169293:G163S	G	-	1	0	MASP1	188461283	1.000000	0.71417	0.953000	0.39169	0.814000	0.46013	5.869000	0.69613	2.778000	0.95560	0.650000	0.86243	GGC		0.547	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		T	186978589	C	T	186978589	3	4	42	1	0	0	0	0	1	0	0	0	9352	652	23	1	2609	1	MASP1	3	186978589	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	67396188	186978589	11043841	17	3878										
CPZ	8532	broad.mit.edu	37	chr4	8603130	8603130	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtctgccagcccgccttcgaCgccattgacatggcctggcc	11	17	1	1	rs143569240		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr4:8603130C>T	ENST00000360986.4	+	3	576	c.402C>T	c.(400-402)gaC>gaT	p.D134D	CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000315782.6_Silent_p.D123D|CPZ_ENST00000429646.2_5'Flank|CPZ_ENST00000506287.1_3'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	134	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.D134D(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCGCCTTCGACGCCATTGACA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	4						C	,,	0,4400		0,0,2200	26	30	29		402,,369	-1.2	1	4	dbSNP_134	29	1,8589		0,1,4294	no	coding-synonymous,utr-5,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,,	134/653,,123/642	8603130	1,12989	2200	4295	6495	8654030	SO:0001819	synonymous_variant	8532			U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.402C>T	4.37:g.8603130C>T			8654030	O00520|Q96MX2	De_novo_Start_OutOfFrame	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																				0.672	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8603130	C	T	8603130	2	4	42	1	0	0	0	0	0	0	0	1	3845	535	19	1		1	CPZ	4	8603130	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10		8603130	182551146	18	3879										
GK2	2712	broad.mit.edu	37	chr4	80328567	80328567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	agcacatttgtcctactaatGcagcacattggtcccccaaa	6	13	0	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr4:80328567G>T	ENST00000358842.3	-	1	805	c.788C>A	c.(787-789)gCa>gAa	p.A263E		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	0					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.A263E(1)		autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						TCCTACTAATGCAGCACATTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											107	99	102					4																	80328567		2203	4300	6503	80547591	SO:0001583	missense	2712			BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"Glycerol kinases"	4291	protein-coding gene	gene with protein product		600148	"glycerol kinase pseudogene 2"	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.788C>A	4.37:g.80328567G>T	ENSP00000351706:p.Ala263Glu		80547591	Q7Z4Q4	Missense_Mutation	SNP	ENST00000358842.3	37	CCDS3585.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885668	0.72410	.	.	ENSG00000196475	ENST00000358842	T	0.58358	0.34	3.92	3.92	0.45320	Carbohydrate kinase, FGGY, N-terminal (1);	0.115696	0.64402	D	0.000020	T	0.79587	0.4471	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85688	0.1305	10	0.87932	D	0	-17.8303	14.2359	0.65927	0.0:0.0:1.0:0.0	.	263	Q14410	GLPK2_HUMAN	E	263	ENSP00000351706:A263E	ENSP00000351706:A263E	A	-	2	0	GK2	80547591	1.000000	0.71417	0.998000	0.56505	0.878000	0.50629	6.976000	0.76135	2.496000	0.84212	0.585000	0.79938	GCA		0.448	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214		T	80328567	G	T	80328567	3	4	42	1	0	0	0	0	1	0	0	0	6441	1319	46	2	877	2	GK2	4	80328567	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	71725437	80328567	110825709	19	3880										
TACR3	6870	broad.mit.edu	37	chr4	104510948	104510948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tgaaacttgggtctcttggcGttgctcttttcttccgactg	10	10	3	1	rs200736098		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr4:104510948G>A	ENST00000304883.2	-	5	1429	c.1289C>T	c.(1288-1290)aCg>aTg	p.T430M	RP11-297P16.3_ENST00000512401.1_RNA|RP11-297P16.3_ENST00000502936.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	430					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.T430M(2)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		GTCTCTTGGCGTTGCTCTTTT	0.502																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											221	206	211					4																	104510948		2203	4300	6503	104730397	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1289C>T	4.37:g.104510948G>A	ENSP00000303325:p.Thr430Met		104730397	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	G	4.907	0.168570	0.09339	.	.	ENSG00000169836	ENST00000304883	T	0.64260	-0.09	5.54	0.22	0.15279	.	0.953048	0.08759	N	0.898048	T	0.48519	0.1504	L	0.44542	1.39	0.09310	N	1	P	0.36027	0.533	B	0.26310	0.068	T	0.20806	-1.0264	10	0.46703	T	0.11	.	9.2084	0.37304	0.4127:0.0:0.5873:0.0	.	430	P29371	NK3R_HUMAN	M	430	ENSP00000303325:T430M	ENSP00000303325:T430M	T	-	2	0	TACR3	104730397	0.740000	0.28207	0.000000	0.03702	0.010000	0.07245	4.451000	0.60047	-0.305000	0.08831	-0.469000	0.05056	ACG		0.502	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		A	104510948	G	A	104510948	3	1	42	1	0	0	0	0	1	0	0	0	15546	1145	40	1	112	1	TACR3	4	104510948	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	24182381	104510948	86643328	20	3881										
TTC29	83894	broad.mit.edu	37	chr4	147724621	147724621	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tgccttaccagtaactggatCaggttcaatgttacctctgc	8	11	3	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr4:147724621C>T	ENST00000325106.4	-	11	1544	c.1318G>A	c.(1318-1320)Gat>Aat	p.D440N	TTC29_ENST00000513335.1_Missense_Mutation_p.D466N|TTC29_ENST00000398886.4_Missense_Mutation_p.D466N|TTC29_ENST00000506019.1_5'Flank	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	440								p.D440N(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GTAACTGGATCAGGTTCAATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											99	96	97					4																	147724621		1913	4138	6051	147944071	SO:0001583	missense	83894			AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.1318G>A	4.37:g.147724621C>T	ENSP00000316740:p.Asp440Asn		147944071	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.875882	0.33162	.	.	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000504425	T;T;T;T	0.26067	1.76;1.76;1.79;1.79	5.84	3.17	0.36434	.	0.548979	0.19903	N	0.103472	T	0.40743	0.1129	L	0.58101	1.795	0.09310	N	1	B;D;B	0.63046	0.441;0.992;0.441	B;P;B	0.59357	0.087;0.856;0.087	T	0.21314	-1.0249	10	0.72032	D	0.01	-7.9086	11.1844	0.48646	0.0:0.6762:0.2585:0.0653	.	440;466;440	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	N	466;466;440;440	ENSP00000423505:D466N;ENSP00000381861:D466N;ENSP00000316740:D440N;ENSP00000425778:D440N	ENSP00000316740:D440N	D	-	1	0	TTC29	147944071	0.972000	0.33761	0.001000	0.08648	0.059000	0.15707	2.342000	0.43992	0.362000	0.24319	-0.211000	0.12701	GAT		0.383	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		T	147724621	C	T	147724621	3	4	42	1	0	0	0	0	1	0	0	0	16736	826	29	3	121	3	TTC29	4	147724621	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	43213673	147724621	43429655	21	3882										
MRPS36	92259	broad.mit.edu	37	chr5	68513666	68513666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tctcgggggtcatgatgggcAgcaagatggcgtctgctagt	16	8	3	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr5:68513666A>G	ENST00000256441.4	+	1	80	c.10A>G	c.(10-12)Agc>Ggc	p.S4G	MRPS36_ENST00000602380.1_5'UTR|MRPS36_ENST00000512880.1_5'UTR|MRPS36_ENST00000507022.1_3'UTR	NM_033281.5	NP_150597.1	P82909	RT36_HUMAN	mitochondrial ribosomal protein S36	4					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)	p.S4G(1)		NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(1)|urinary_tract(1)	7		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.04e-56)|Epithelial(20;8.79e-53)|all cancers(19;2.01e-48)|Lung(70;0.0176)		CATGATGGGCAGCAAGATGGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	5											117	100	106					5																	68513666		2203	4300	6503	68549422	SO:0001583	missense	92259				CCDS34174.1	5q13.2	2013-09-20			ENSG00000134056	ENSG00000134056		"Mitochondrial ribosomal proteins / small subunits"	16631	protein-coding gene	gene with protein product		611996				11279123	Standard	NM_033281		Approved	DC47, MRP-S36	uc003jvq.3	P82909	OTTHUMG00000162443	ENST00000256441.4:c.10A>G	5.37:g.68513666A>G	ENSP00000256441:p.Ser4Gly		68549422	Q9H2H4	Missense_Mutation	SNP	ENST00000256441.4	37	CCDS34174.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757962	0.89843	.	.	ENSG00000134056	ENST00000256441	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.53481	0.1799	N	0.11756	0.17	0.80722	D	1	D	0.67145	0.996	D	0.73380	0.98	T	0.58668	-0.7596	9	0.49607	T	0.09	-4.3697	12.8836	0.58030	1.0:0.0:0.0:0.0	.	4	P82909	RT36_HUMAN	G	4	.	ENSP00000256441:S4G	S	+	1	0	MRPS36	68549422	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.429000	0.59901	2.293000	0.77203	0.528000	0.53228	AGC		0.647	MRPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368940.1	NM_033281		G	68513666	A	G	68513666	3	3	42	1	0	0	0	0	1	0	0	0	9875	188	7	4	12	4	MRPS36	5	68513666	Missense_Mutation	SNP	A	TCGA-AG-3882-01A-01W-0899-10		68513666	112401594	22	3883										
APC	324	broad.mit.edu	37	chr5	112164663	112164664	+	Frame_Shift_Ins	INS	-	-	A													0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tggaatgtgctttagaagttINSaaaaaggtacctttgaaaac							TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr5:112164663_112164664insA	ENST00000457016.1	+	14	2117_2118	c.1737_1738insA	c.(1738-1740)aaafs	p.K580fs	CTC-554D6.1_ENST00000520401.1_Frame_Shift_Ins_p.LK75fs|APC_ENST00000257430.4_Frame_Shift_Ins_p.K580fs|APC_ENST00000508376.2_Frame_Shift_Ins_p.K580fs			P25054	APC_HUMAN	adenomatous polyposis coli	580	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E582fs*20(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTTTAGAAGTTAAAAAGGTACC	0.342		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Insertion - Frameshift(1)	large_intestine(1)|skin(1)	5																																								112192563	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1742dupA	5.37:g.112164668_112164668dupA	ENSP00000413133:p.Lys580fs		112192562	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.342	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112164664	-	A	112164663	7	5	42	1	0	1	1	0	0	0	0	0	763	1741	61	0	1787	0	APC	5	112164663	Frame_Shift_Ins	INS	-	TCGA-AG-3882-01A-01W-0899-10	43650997	112164663	68750597	23	3884										
PRDM1	639	broad.mit.edu	37	chr6	106553539	106553539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ccttctcctttaccggggccGccgccagcatgaaggacaag	11	15	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr6:106553539G>A	ENST00000369096.4	+	5	1738	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	PRDM1_ENST00000369091.2_Missense_Mutation_p.A466T|PRDM1_ENST00000369089.3_Missense_Mutation_p.A368T	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	502					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A466T(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		TACCGGGGCCGCCGCCAGCAT	0.672			"D, N, Mis, F, S"		DLBCL																																		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	1	Substitution - Missense(1)	large_intestine(1)	6											23	29	27					6																	106553539		2201	4294	6495	106660232	SO:0001583	missense	639				CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1504G>A	6.37:g.106553539G>A	ENSP00000358092:p.Ala502Thr		106660232	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005472	0.74932	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	T;T;T	0.08634	3.09;3.08;3.07	5.74	5.74	0.90152	.	0.191274	0.56097	N	0.000030	T	0.16811	0.0404	L	0.52364	1.645	0.45330	D	0.998326	D;D	0.89917	1.0;0.999	D;P	0.74348	0.983;0.851	T	0.01245	-1.1407	10	0.32370	T	0.25	-23.5711	19.9279	0.97110	0.0:0.0:1.0:0.0	.	368;502	Q86WM7;O75626	.;PRDM1_HUMAN	T	466;502;465;368	ENSP00000358087:A466T;ENSP00000358092:A502T;ENSP00000358085:A368T	ENSP00000358085:A368T	A	+	1	0	PRDM1	106660232	1.000000	0.71417	0.194000	0.23346	0.823000	0.46562	6.291000	0.72719	2.715000	0.92844	0.655000	0.94253	GCC		0.672	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			A	106553539	G	A	106553539	3	1	42	1	0	0	0	0	1	0	0	0	12484	1087	38	1	1535	1	PRDM1	6	106553539	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		106553539	64561528	24	3885										
C6orf97	80129	broad.mit.edu	37	chr6	151914317	151914317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ccgaacttggctttgacatgCggctggacgtggttttagct	13	9	0	1	rs550166524		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr6:151914317C>T	ENST00000239374.7	+	8	1468	c.1369C>T	c.(1369-1371)Cgg>Tgg	p.R457W	CCDC170_ENST00000367290.5_Missense_Mutation_p.R457W	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	457								p.R457W(1)									CTTTGACATGCGGCTGGACGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											105	97	99					6																	151914317		1915	4139	6054	151956010	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1369C>T	6.37:g.151914317C>T	ENSP00000239374:p.Arg457Trp		151956010	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.262719	0.59431	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09350	2.99;2.99	5.87	4.09	0.47781	.	0.277720	0.34777	N	0.003697	T	0.15262	0.0368	M	0.75447	2.3	0.42436	D	0.992693	D	0.76494	0.999	P	0.59221	0.854	T	0.01195	-1.1422	10	0.48119	T	0.1	-1.4138	9.9802	0.41809	0.29:0.643:0.0:0.0671	.	457	Q8IYT3	CF097_HUMAN	W	457	ENSP00000239374:R457W;ENSP00000356259:R457W	ENSP00000239374:R457W	R	+	1	2	C6orf97	151956010	1.000000	0.71417	1.000000	0.80357	0.448000	0.32197	1.863000	0.39459	0.927000	0.37143	-0.127000	0.14921	CGG		0.443	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		T	151914317	C	T	151914317	3	4	42	1	0	0	0	0	1	0	0	0	2380	759	27	1	1399	1	C6orf97	6	151914317	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	45360778	151914317	19200750	25	3886										
C7orf28A	51622	broad.mit.edu	37	chr7	5940194	5940194	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gaagaaaatttctggatggtCatggtatttacatacacagt	9	5	2	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr7:5940194C>T	ENST00000325974.6	+	3	375	c.309C>T	c.(307-309)gtC>gtT	p.V103V	CCZ1_ENST00000537980.1_Intron	NM_015622.5	NP_056437.4	P86791	CCZ1_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog (S. cerevisiae)	103						lysosome (GO:0005764)|membrane (GO:0016020)		p.V103V(1)		large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	6						TCTGGATGGTCATGGTATTTA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	7											12	13	13					7																	5940194		2063	4194	6257	5906720	SO:0001819	synonymous_variant	51622			AF151801	CCDS34597.1	7p22.1	2014-02-13	2010-06-29	2010-06-29	ENSG00000122674	ENSG00000122674			21691	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 28A"	C7orf28A		10810093, 20305638	Standard	NM_015622		Approved	CGI-43, CCZ1A	uc003spf.3	P86791	OTTHUMG00000155502	ENST00000325974.6:c.309C>T	7.37:g.5940194C>T			5906720	A2RU45|O95766|Q9UG65|Q9Y359	Silent	SNP	ENST00000325974.6	37	CCDS34597.1																																																																																				0.363	CCZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340391.1	NM_015622		T	5940194	C	T	5940194	2	4	42	1	0	0	0	0	0	0	0	1	2389	813	29	3		3	C7orf28A	7	5940194	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10		5940194	153198469	26	3887										
WNT2	7472	broad.mit.edu	37	chr7	116918295	116918295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gcagtcctgacagcgcacggCgcagcaccagtggaacttac	12	14	0	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr7:116918295C>T	ENST00000265441.3	-	5	1296	c.997G>A	c.(997-999)Gcc>Acc	p.A333T		NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	333					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.A333T(1)		breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CAGCGCACGGCGCAGCACCAG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											154	109	124					7																	116918295		2203	4300	6503	116705531	SO:0001583	missense	7472			X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.997G>A	7.37:g.116918295C>T	ENSP00000265441:p.Ala333Thr		116705531	A4D0V1|Q75N05|Q9UDP9	Missense_Mutation	SNP	ENST00000265441.3	37	CCDS5771.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.770547	0.49680	.	.	ENSG00000105989	ENST00000265441	T	0.75477	-0.94	5.87	5.87	0.94306	.	0.051249	0.85682	D	0.000000	T	0.60261	0.2255	N	0.20328	0.56	0.50813	D	0.999896	B;B	0.32573	0.376;0.376	B;B	0.31101	0.124;0.124	T	0.59820	-0.7382	10	0.34782	T	0.22	.	14.0901	0.64984	0.1502:0.8498:0.0:0.0	.	333;333	A4D0V1;P09544	.;WNT2_HUMAN	T	333	ENSP00000265441:A333T	ENSP00000265441:A333T	A	-	1	0	WNT2	116705531	1.000000	0.71417	0.979000	0.43373	0.982000	0.71751	4.676000	0.61627	2.780000	0.95670	0.655000	0.94253	GCC		0.602	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		T	116918295	C	T	116918295	3	4	42	1	0	0	0	0	1	0	0	0	17426	768	27	1	89	1	WNT2	7	116918295	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	110978101	116918295	42220368	27	3888										
HIATL1	84641	broad.mit.edu	37	chr9	97221572	97221572	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	aacacagtaacagcagcagcGgcagcctgaccaacacccca	8	16	0	1	rs199783937		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr9:97221572G>A	ENST00000375344.3	+	12	1668	c.1399G>A	c.(1399-1401)Ggc>Agc	p.G467S	HIATL1_ENST00000428393.2_3'UTR	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	467					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.G467S(1)		endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				CAGCAGCAGCGGCAGCCTGAC	0.493																																					Pancreas(77;1260 1915 1973 10423)											1	Substitution - Missense(1)	large_intestine(1)	9						G	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	72	68	69		1399	3.5	0.7	9		69	0,8600		0,0,4300	yes	missense	HIATL1	NM_032558.2	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	467/507	97221572	1,13005	2203	4300	6503	96261393	SO:0001583	missense	84641			AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.1399G>A	9.37:g.97221572G>A	ENSP00000364493:p.Gly467Ser		96261393	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Missense_Mutation	SNP	ENST00000375344.3	37	CCDS6710.2	.	.	.	.	.	.	.	.	.	.	G	8.392	0.840045	0.16891	2.27E-4	0.0	ENSG00000148110	ENST00000375344	T	0.29397	1.57	4.4	3.5	0.40072	.	0.000000	0.49916	D	0.000129	T	0.15176	0.0366	N	0.20530	0.585	0.80722	D	1	B	0.17465	0.022	B	0.13407	0.009	T	0.06698	-1.0812	10	0.08599	T	0.76	-1.2896	6.9161	0.24361	0.206:0.0:0.794:0.0	.	467	Q5SR56	HIAL1_HUMAN	S	467	ENSP00000364493:G467S	ENSP00000364493:G467S	G	+	1	0	HIATL1	96261393	1.000000	0.71417	0.657000	0.29651	0.488000	0.33401	3.803000	0.55560	1.211000	0.43351	0.609000	0.83330	GGC		0.493	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558		A	97221572	G	A	97221572	3	1	42	1	0	0	0	0	1	0	0	0	7119	1116	39	1	1445	1	HIATL1	9	97221572	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		97221572	43991859	28	3889										
COL5A1	1289	broad.mit.edu	37	chr9	137716501	137716501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ccaggcatccaggacgcggcGgaacatcgacgccagccagc	13	16	0	0	rs531431738		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr9:137716501G>A	ENST00000371817.3	+	62	5168	c.4754G>A	c.(4753-4755)cGg>cAg	p.R1585Q		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1585	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.R1585Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGGACGCGGCGGAACATCGAC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											59	50	53					9																	137716501		2203	4300	6503	136856322	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4754G>A	9.37:g.137716501G>A	ENSP00000360882:p.Arg1585Gln		136856322	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.594917	0.66219	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	D	0.90004	-2.6	4.34	4.34	0.51931	.	0.000000	0.64402	U	0.000003	D	0.91586	0.7342	M	0.85197	2.74	0.37805	D	0.927828	D	0.63880	0.993	P	0.47299	0.543	D	0.93986	0.7262	10	0.51188	T	0.08	.	17.2645	0.87083	0.0:0.0:1.0:0.0	.	1585	P20908	CO5A1_HUMAN	Q	1585;122	ENSP00000360882:R1585Q	ENSP00000347458:R122Q	R	+	2	0	COL5A1	136856322	1.000000	0.71417	0.927000	0.36925	0.713000	0.41058	9.671000	0.98627	2.129000	0.65627	0.545000	0.68477	CGG		0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137716501	G	A	137716501	3	1	42	1	0	0	0	0	1	0	0	0	3702	1116	39	1	5000	1	COL5A1	9	137716501	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	40494929	137716501	3496930	29	3890										
FBXW4	6468	broad.mit.edu	37	chr10	103427654	103427655	+	Missense_Mutation	DNP	GC	GC	AT													0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ctcccttacctgagtaatggGctgatagcaatggaccagac							TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr10:103427654_103427655GC>AT	ENST00000331272.7	-	5	1376_1377	c.758_759GC>AT	c.(757-759)aGC>aAT	p.S253N		NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	253					cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)		p.S253>?(1)		breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		TGAGTAATGGGCTGATAGCAAT	0.47																																																1	Complex(1)	large_intestine(1)	10																																								103417645	SO:0001583	missense	6468			AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"F-boxes / WD-40 domains", "WD repeat domain containing"	10847	protein-coding gene	gene with protein product		608071	"split hand/foot malformation (ectrodactyly) type 3", "F-box and WD-40 domain protein 4"	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.758_759delinsAT	10.37:g.103427654_103427655delinsAT	ENSP00000359149:p.Ser253Asn		103417644	Q5SVS1|Q96IM6	Missense_Mutation	DNP	ENST00000331272.7	37	CCDS31271.1																																																																																				0.47	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039		AT	103427655	GC	AT	103427654	3	1	42	1	0	0	0	0	1	0	0	0	5786	1194	42	3	499	3	FBXW4	10	103427654	Missense_Mutation	DNP	GC	TCGA-AG-3882-01A-01W-0899-10		103427654	32107093	30	3891										
SORCS3	22986	broad.mit.edu	37	chr10	107007076	107007076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tattggcaatgtcatcaagcGagctctggttaaagtaagtt	10	6	3	0			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr10:107007076G>A	ENST00000369701.3	+	22	3319	c.3092G>A	c.(3091-3093)cGa>cAa	p.R1031Q	SORCS3_ENST00000369699.4_3'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1031					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.R1031Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GTCATCAAGCGAGCTCTGGTT	0.378																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - Missense(1)	large_intestine(1)	10											121	119	120					10																	107007076		2203	4300	6503	106997066	SO:0001583	missense	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3092G>A	10.37:g.107007076G>A	ENSP00000358715:p.Arg1031Gln		106997066	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.826145	0.50739	.	.	ENSG00000156395	ENST00000369701	T	0.15139	2.45	5.5	1.19	0.21007	.	0.516807	0.19807	N	0.105624	T	0.13200	0.0320	L	0.48642	1.525	0.30356	N	0.784259	B	0.21381	0.055	B	0.11329	0.006	T	0.15065	-1.0450	9	.	.	.	.	8.6496	0.34027	0.348:0.0:0.652:0.0	.	1031	Q9UPU3	SORC3_HUMAN	Q	1031	ENSP00000358715:R1031Q	.	R	+	2	0	SORCS3	106997066	0.999000	0.42202	0.951000	0.38953	0.996000	0.88848	1.597000	0.36729	0.265000	0.21872	0.650000	0.86243	CGA		0.378	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	107007076	G	A	107007076	3	1	42	1	0	0	0	0	1	0	0	0	14969	1058	37	1	3178	1	SORCS3	10	107007076	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	3579422	107007076	28527671	31	3892										
TCF7L2	6934	broad.mit.edu	37	chr10	114925333	114925333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ggagaaaaaaaaagtgcgttCgctacatacaaggtgaaggc	12	6	0	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr10:114925333C>T	ENST00000355995.4	+	15	1969	c.1462C>T	c.(1462-1464)Cgc>Tgc	p.R488C	TCF7L2_ENST00000543371.1_Missense_Mutation_p.R471C|TCF7L2_ENST00000352065.5_3'UTR|TCF7L2_ENST00000369397.4_Missense_Mutation_p.R465C|TCF7L2_ENST00000545257.1_Missense_Mutation_p.R488C|TCF7L2_ENST00000369389.1_Silent_p.F157F|TCF7L2_ENST00000542695.1_Missense_Mutation_p.R204C|TCF7L2_ENST00000369386.1_3'UTR|TCF7L2_ENST00000536810.1_Missense_Mutation_p.R471C|TCF7L2_ENST00000538897.1_Silent_p.F463F|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000355717.4_Silent_p.F470F			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	488	Promoter-specific activation domain.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R465C(3)|p.R471C(2)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		AAAGTGCGTTCGCTACATACA	0.532			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	5	Substitution - Missense(5)	large_intestine(5)	10											100	107	105					10																	114925333		2203	4300	6503	114915323	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1462C>T	10.37:g.114925333C>T	ENSP00000348274:p.Arg488Cys		114915323	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	C	31	5.096063	0.94197	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000369397;ENST00000542695;ENST00000277945	D;D;D;D;D;D;D	0.99329	-5.21;-5.21;-5.2;-5.19;-5.21;-5.24;-5.75	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	D	0.99375	0.9780	M	0.74647	2.275	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;1.0;0.997;0.999;0.999;0.999;0.983	P;D;P;P;P;P;B	0.85130	0.8;0.997;0.634;0.791;0.77;0.857;0.405	D	0.99457	1.0942	10	0.87932	D	0	-33.6256	19.3381	0.94329	0.0:1.0:0.0:0.0	.	488;359;403;448;448;471;465	Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ8;C6ZRK5;Q9NQB0-7;Q6FHW4	TF7L2_HUMAN;.;.;.;.;.;.	C	488;488;471;471;465;204;188	ENSP00000348274:R488C;ENSP00000440547:R488C;ENSP00000444972:R471C;ENSP00000446238:R471C;ENSP00000358404:R465C;ENSP00000443883:R204C;ENSP00000277945:R188C	ENSP00000277945:R188C	R	+	1	0	TCF7L2	114915323	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.558000	0.86282	0.655000	0.94253	CGC		0.532	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114925333	C	T	114925333	3	4	42	1	0	0	0	0	1	0	0	0	15737	884	31	1	1742	1	TCF7L2	10	114925333	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	7918257	114925333	20609414	32	3893										
SLC1A2	6506	broad.mit.edu	37	chr11	35333789	35333789	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gttttcagggaagagatttcGaataaggtccaggaaggcat	13	5	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr11:35333789G>A	ENST00000278379.3	-	4	799	c.517C>T	c.(517-519)Cga>Tga	p.R173*	SLC1A2_ENST00000606205.1_Nonsense_Mutation_p.R173*|SLC1A2_ENST00000395753.1_Nonsense_Mutation_p.R164*|SLC1A2_ENST00000395750.1_Nonsense_Mutation_p.R164*	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	173					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.R173*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			AAGAGATTTCGAATAAGGTCC	0.493																																					NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)											1	Substitution - Nonsense(1)	large_intestine(1)	11											211	204	207					11																	35333789		2202	4298	6500	35290365	SO:0001587	stop_gained	6506			AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.517C>T	11.37:g.35333789G>A	ENSP00000278379:p.Arg173*		35290365	B4DQE9|Q14417|Q541G6|U3KQQ4	Nonsense_Mutation	SNP	ENST00000278379.3	37	CCDS31459.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722963	0.89298	.	.	ENSG00000110436	ENST00000278379;ENST00000395750;ENST00000395753;ENST00000449068	.	.	.	5.66	3.68	0.42216	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7246	14.0878	0.64971	0.0:0.0:0.5567:0.4433	.	.	.	.	X	173;164;164;169	.	ENSP00000278379:R173X	R	-	1	2	SLC1A2	35290365	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.084000	0.50143	0.631000	0.30412	0.462000	0.41574	CGA		0.493	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		A	35333789	G	A	35333789	4	1	42	1	0	0	0	0	0	1	0	0	14469	1066	37	1	1239	1	SLC1A2	11	35333789	Nonsense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		35333789	99672727	33	3894										
LRRK2	120892	broad.mit.edu	37	chr12	40716270	40716270	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ttaatgatggtgaagaacatCaaaaaatcttacttgatgac	7	5	2	5	rs72547980	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr12:40716270C>A	ENST00000298910.7	+	37	5525	c.5467C>A	c.(5467-5469)Caa>Aaa	p.Q1823K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1823					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.Q1786K(1)|p.Q1823K(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TGAAGAACATCAAAAAATCTT	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	12						C	LYS/GLN	2,4404	4.2+/-10.8	0,2,2201	116	116	116		5467	3.7	1	12	dbSNP_130	116	0,8600		0,0,4300	no	missense	LRRK2	NM_198578.3	53	0,2,6501	AA,AC,CC		0.0,0.0454,0.0154	benign	1823/2528	40716270	2,13004	2203	4300	6503	39002537	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5467C>A	12.37:g.40716270C>A	ENSP00000298910:p.Gln1823Lys		39002537	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539342	0.27475	4.54E-4	0.0	ENSG00000188906	ENST00000298910	T	0.72051	-0.62	5.58	3.73	0.42828	.	0.151473	0.49916	D	0.000124	T	0.45236	0.1332	N	0.08118	0	0.34446	D	0.700174	B;B	0.14012	0.004;0.009	B;B	0.08055	0.002;0.003	T	0.48139	-0.9061	10	0.15499	T	0.54	.	8.8358	0.35111	0.2622:0.669:0.0:0.0687	.	1823;1823	Q17RV3;Q5S007	.;LRRK2_HUMAN	K	1823	ENSP00000298910:Q1823K	ENSP00000298910:Q1823K	Q	+	1	0	LRRK2	39002537	0.998000	0.40836	0.999000	0.59377	0.748000	0.42578	0.608000	0.24223	1.334000	0.45468	-0.158000	0.13435	CAA		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40716270	C	A	40716270	3	1	42	1	0	0	0	0	1	0	0	0	9062	827	29	2	5613	2	LRRK2	12	40716270	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10		40716270	93135625	34	3895										
NELL2	4753	broad.mit.edu	37	chr12	44913930	44913930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	aagggtctgtgacacagcgcGggcagcactcattctctggg	14	11	3	1	rs141156235		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr12:44913930G>A	ENST00000429094.2	-	19	2762	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	NELL2_ENST00000551601.1_Missense_Mutation_p.P705L|NELL2_ENST00000549027.1_Missense_Mutation_p.P752L|NELL2_ENST00000452445.2_Missense_Mutation_p.P753L|NELL2_ENST00000333837.4_Missense_Mutation_p.P776L|NELL2_ENST00000395487.2_Missense_Mutation_p.P752L|NELL2_ENST00000437801.2_Missense_Mutation_p.P803L	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	753	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P753L(1)|p.P803L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		GACACAGCGCGGGCAGCACTC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	12						G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	93	77	82		2408,2258,2255,2327,2258	3.3	0.7	12	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	NELL2	NM_001145107.1,NM_001145108.1,NM_001145109.1,NM_001145110.1,NM_006159.2	98,98,98,98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	803/867,753/817,752/816,776/840,753/817	44913930	1,13005	2203	4300	6503	43200197	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2258C>T	12.37:g.44913930G>A	ENSP00000390680:p.Pro753Leu		43200197	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.319157	0.81469	0.0	1.16E-4	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	T;T;T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71	5.21	3.34	0.38264	von Willebrand factor, type C (4);	0.238554	0.43416	D	0.000580	D	0.85401	0.5688	H	0.94734	3.575	0.80722	D	1	P;D;D;D;D	0.76494	0.727;0.998;0.999;0.973;0.994	B;P;P;P;P	0.60117	0.212;0.869;0.766;0.463;0.869	D	0.87160	0.2214	10	0.59425	D	0.04	0.2169	12.0246	0.53362	0.0:0.1316:0.7313:0.1371	.	776;803;705;753;752	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	L	752;753;705;753;752;776;803	ENSP00000378866:P752L;ENSP00000390680:P753L;ENSP00000449332:P705L;ENSP00000394612:P753L;ENSP00000447927:P752L;ENSP00000327988:P776L;ENSP00000416341:P803L	ENSP00000327988:P776L	P	-	2	0	NELL2	43200197	1.000000	0.71417	0.655000	0.29622	0.899000	0.52679	4.861000	0.62969	0.545000	0.28902	0.650000	0.86243	CCG		0.542	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		A	44913930	G	A	44913930	3	1	42	1	0	0	0	0	1	0	0	0	10365	1116	39	1	200	1	NELL2	12	44913930	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	4197660	44913930	88937965	35	3896										
RNFT2	84900	broad.mit.edu	37	chr12	117287165	117287165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cctgtggctggaccgtgagcGcacctgcccgctctgccgct	13	17	1	1	rs571206253	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr12:117287165G>A	ENST00000257575.4	+	11	1480	c.1247G>A	c.(1246-1248)cGc>cAc	p.R416H	RNFT2_ENST00000392549.2_Missense_Mutation_p.R416H|RNFT2_ENST00000319176.7_Intron|RNFT2_ENST00000551251.1_Intron|RNFT2_ENST00000407967.3_Intron			Q96EX2	RNFT2_HUMAN	ring finger protein, transmembrane 2	416						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R416H(1)		endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		GACCGTGAGCGCACCTGCCCG	0.652													G|||	4	0.000798722	8e-04	0	5008	,	,		14831	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	12											18	22	21					12																	117287165		2111	4111	6222	115771548	SO:0001583	missense	84900			AK027533	CCDS9180.2, CCDS44987.1	12q24.22	2013-01-09	2008-02-26	2008-02-26	ENSG00000135119	ENSG00000135119		"RING-type (C3HC4) zinc fingers"	25905	protein-coding gene	gene with protein product			"transmembrane protein 118"	TMEM118		12477932	Standard	NM_032814		Approved	FLJ14627	uc009zwn.3	Q96EX2	OTTHUMG00000150882	ENST00000257575.4:c.1247G>A	12.37:g.117287165G>A	ENSP00000257575:p.Arg416His		115771548	E9PAM7|Q96SU5	Missense_Mutation	SNP	ENST00000257575.4	37	CCDS44987.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258200	0.80246	.	.	ENSG00000135119	ENST00000257575;ENST00000392549	T;T	0.44482	0.92;0.92	5.19	4.19	0.49359	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.28234	0.0697	N	0.21240	0.645	0.44946	D	0.997961	B	0.13594	0.008	B	0.12837	0.008	T	0.05599	-1.0875	9	0.45353	T	0.12	-5.2798	9.0244	0.36220	0.2367:0.0:0.7633:0.0	.	416	Q96EX2	RNFT2_HUMAN	H	416	ENSP00000257575:R416H;ENSP00000376332:R416H	ENSP00000257575:R416H	R	+	2	0	RNFT2	115771548	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.485000	0.53208	1.010000	0.39314	0.549000	0.68633	CGC		0.652	RNFT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320417.1	NM_032814		A	117287165	G	A	117287165	3	1	42	1	0	0	0	0	1	0	0	0	13539	1087	38	1	1285	1	RNFT2	12	117287165	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	72373235	117287165	16564730	36	3897										
PIWIL1	9271	broad.mit.edu	37	chr12	130840103	130840103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtgttaaatttacagaaacgAtaatgttcaaagggagcttc	9	5	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr12:130840103A>G	ENST00000245255.3	+	12	1567	c.1295A>G	c.(1294-1296)gAt>gGt	p.D432G		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	432					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.D432G(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		TACAGAAACGATAATGTTCAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											184	190	188					12																	130840103		2203	4300	6503	129406056	SO:0001583	missense	9271			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1295A>G	12.37:g.130840103A>G	ENSP00000245255:p.Asp432Gly		129406056	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720974	0.30503	.	.	ENSG00000125207	ENST00000245255	T	0.11495	2.77	5.39	5.39	0.77823	Ribonuclease H-like (1);	0.321079	0.37906	N	0.001898	T	0.10895	0.0266	L	0.40543	1.245	0.34477	D	0.703455	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.10989	-1.0606	10	0.27785	T	0.31	-27.1637	14.6233	0.68602	1.0:0.0:0.0:0.0	.	432;432	Q96J94;Q96J94-2	PIWL1_HUMAN;.	G	432	ENSP00000245255:D432G	ENSP00000245255:D432G	D	+	2	0	PIWIL1	129406056	0.996000	0.38824	0.768000	0.31515	0.902000	0.53008	2.972000	0.49256	2.046000	0.60703	0.529000	0.55759	GAT		0.408	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			G	130840103	A	G	130840103	3	3	42	1	0	0	0	0	1	0	0	0	11988	333	12	4	1337	4	PIWIL1	12	130840103	Missense_Mutation	SNP	A	TCGA-AG-3882-01A-01W-0899-10	13552938	130840103	3011792	37	3898										
ZMYM2	7750	broad.mit.edu	37	chr13	20660013	20660013	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ttttatttgcaaccagaatgCtctagttctacagatagccc	6	10	2	2	rs370286795		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr13:20660013C>T	ENST00000382874.2	+	26	4183	c.3993C>T	c.(3991-3993)tgC>tgT	p.C1331C	ZMYM2_ENST00000382871.2_Silent_p.C1331C|ZMYM2_ENST00000382869.3_Silent_p.C1331C	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.C1331C(1)		large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		AACCAGAATGCTCTAGTTCTA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	13						C	,,,	1,3667		0,1,1833	92	86	88		3993,3993,3993,3993	1.9	1	13		88	0,8164		0,0,4082	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZMYM2	NM_001190964.1,NM_001190965.1,NM_003453.3,NM_197968.2	,,,	0,1,5915	TT,TC,CC		0.0,0.0273,0.0085	,,,	1331/1378,1331/1378,1331/1378,1331/1378	20660013	1,11831	1834	4082	5916	19558013	SO:0001819	synonymous_variant	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3993C>T	13.37:g.20660013C>T			19558013	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	37	CCDS45016.1																																																																																				0.388	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		T	20660013	C	T	20660013	2	4	42	1	0	0	0	0	0	0	0	1	17739	805	28	3		3	ZMYM2	13	20660013	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10		20660013	94509865	38	3899										
FREM2	341640	broad.mit.edu	37	chr13	39271918	39271918	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tgttctattttgcagttgaaGatggtggtaagtattcccct	10	6	1	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr13:39271918G>A	ENST00000280481.7	+	2	5473	c.5257G>A	c.(5257-5259)Gat>Aat	p.D1753N		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1753					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1753N(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGCAGTTGAAGATGGTGGTAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											172	151	158					13																	39271918		2203	4300	6503	38169918	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5257G>A	13.37:g.39271918G>A	ENSP00000280481:p.Asp1753Asn		38169918	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	35	5.583019	0.96578	.	.	ENSG00000150893	ENST00000280481	T	0.35973	1.28	6.06	6.06	0.98353	.	0.044558	0.85682	D	0.000000	T	0.74673	0.3747	H	0.97186	3.955	0.80722	D	1	D	0.71674	0.998	D	0.69307	0.963	T	0.82502	-0.0425	10	0.87932	D	0	.	20.6282	0.99521	0.0:0.0:1.0:0.0	.	1753	Q5SZK8	FREM2_HUMAN	N	1753	ENSP00000280481:D1753N	ENSP00000280481:D1753N	D	+	1	0	FREM2	38169918	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.439000	0.97543	2.871000	0.98454	0.655000	0.94253	GAT		0.393	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39271918	G	A	39271918	3	1	42	1	0	0	0	0	1	0	0	0	6064	942	33	3	5263	3	FREM2	13	39271918	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	18611905	39271918	75897960	39	3900										
KLF12	11278	broad.mit.edu	37	chr13	74420000	74420000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cccatcctccaaaagcggcaCgacaatagtgttgttcacat	7	13	1	0	rs375091947	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr13:74420000C>T	ENST00000377669.2	-	3	660	c.634G>A	c.(634-636)Gtg>Atg	p.V212M	KLF12_ENST00000472022.1_5'UTR|KLF12_ENST00000377666.4_Missense_Mutation_p.V212M	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	212					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.V212M(1)		central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		AAAAGCGGCACGACAATAGTG	0.473													C|||	2	0.000399361	0	0	5008	,	,		21075	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	13						C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	124	105	111		634	6	1	13		111	0,8600		0,0,4300	no	missense	KLF12	NM_007249.4	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	212/403	74420000	1,13005	2203	4300	6503	73318001	SO:0001583	missense	11278			AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.634G>A	13.37:g.74420000C>T	ENSP00000366897:p.Val212Met		73318001	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.380842	0.42207	2.27E-4	0.0	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.01548	4.78;4.78	6.02	6.02	0.97574	.	0.061548	0.64402	D	0.000003	T	0.02533	0.0077	L	0.51914	1.62	0.49299	D	0.999774	P	0.50443	0.935	B	0.34242	0.178	T	0.61941	-0.6959	10	0.38643	T	0.18	.	19.1188	0.93353	0.0:1.0:0.0:0.0	.	212	Q9Y4X4	KLF12_HUMAN	M	212	ENSP00000366897:V212M;ENSP00000366894:V212M	ENSP00000344057:V212M	V	-	1	0	KLF12	73318001	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.632000	0.61311	2.865000	0.98341	0.655000	0.94253	GTG		0.473	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		T	74420000	C	T	74420000	3	4	42	1	0	0	0	0	1	0	0	0	8361	536	19	1	594	1	KLF12	13	74420000	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	35148082	74420000	40749878	40	3901										
SYT16	83851	broad.mit.edu	37	chr14	62536483	62536483	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gcagaaaccaaaattcagccGttcgttgttgacacacggag	10	10	1	2	rs190756776	byFrequency	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr14:62536483G>T	ENST00000430451.2	+	2	883	c.686G>T	c.(685-687)cGt>cTt	p.R229L	SYT16_ENST00000446982.2_Missense_Mutation_p.R229L|RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	229					exocytosis (GO:0006887)			p.R229L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		AAATTCAGCCGTTCGTTGTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											117	119	118					14																	62536483		1975	4150	6125	61606236	SO:0001583	missense	83851			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.686G>T	14.37:g.62536483G>T	ENSP00000394700:p.Arg229Leu		61606236	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.591064	0.46214	.	.	ENSG00000139973	ENST00000446982;ENST00000430451	T;T	0.39406	1.08;3.5	5.4	-5.3	0.02738	.	1.577760	0.03166	N	0.170079	T	0.37019	0.0988	L	0.43152	1.355	0.09310	N	0.999998	P;B	0.43352	0.804;0.037	B;B	0.38264	0.269;0.009	T	0.52675	-0.8544	10	0.48119	T	0.1	-0.3326	15.5637	0.76273	0.6632:0.0:0.3368:0.0	.	229;229	B4DZH2;Q17RD7	.;SYT16_HUMAN	L	229	ENSP00000388023:R229L;ENSP00000394700:R229L	ENSP00000394700:R229L	R	+	2	0	SYT16	61606236	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.154000	0.03166	-0.937000	0.03719	0.655000	0.94253	CGT		0.473	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62536483	G	T	62536483	3	4	42	1	0	0	0	0	1	0	0	0	15511	1145	40	2	692	2	SYT16	14	62536483	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		62536483	44813057	41	3902										
MTHFD1	4522	broad.mit.edu	37	chr14	64920543	64920543	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gatgacattgaattacttccCgaagctcaacacaaagctga	7	10	1	3			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr14:64920543C>T	ENST00000545908.1	+	25	2926	c.2697C>T	c.(2695-2697)ccC>ccT	p.P899P	ZBTB25_ENST00000555220.1_Intron|ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000556284.1_3'UTR|MTHFD1_ENST00000216605.8_Silent_p.P843P			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	843	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)	p.P843P(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	AATTACTTCCCGAAGCTCAAC	0.433																																					Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)											1	Substitution - coding silent(1)	large_intestine(1)	14											169	134	146					14																	64920543		2203	4300	6503	63990296	SO:0001819	synonymous_variant	4522			J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2697C>T	14.37:g.64920543C>T			63990296	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Silent	SNP	ENST00000545908.1	37																																																																																					0.433	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			T	64920543	C	T	64920543	2	4	42	1	0	0	0	0	0	0	0	1	9957	639	23	1		1	MTHFD1	14	64920543	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10	2384060	64920543	42428997	42	3903										
XRCC3	7517	broad.mit.edu	37	chr14	104165200	104165201	+	Frame_Shift_Ins	INS	-	-	G													0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	atcgtgtaggaacaggaggaINSggggggcaggtggggggcag							TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr14:104165200_104165201insG	ENST00000553264.1	-	8	1771_1772	c.975_976insC	c.(973-978)ccctccfs	p.S326fs	XRCC3_ENST00000555055.1_Frame_Shift_Ins_p.S326fs|XRCC3_ENST00000352127.7_Frame_Shift_Ins_p.S326fs|KLC1_ENST00000557450.1_Intron|XRCC3_ENST00000554974.1_Frame_Shift_Ins_p.S121fs|KLC1_ENST00000334553.6_Intron|RP11-73M18.8_ENST00000602422.1_RNA|KLC1_ENST00000554280.1_Intron|KLC1_ENST00000555836.1_Intron|XRCC3_ENST00000554913.1_Frame_Shift_Ins_p.S326fs|KLC1_ENST00000452929.2_Intron|KLC1_ENST00000348520.6_Intron|XRCC3_ENST00000445556.1_Frame_Shift_Ins_p.S326fs			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	326					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.S326fs*>22(1)		endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		GAACAGGAGGAGGGGGGCAGGT	0.688								Direct reversal of damage;Homologous recombination																																								1	Insertion - Frameshift(1)	large_intestine(1)	14																																								103234954	SO:0001589	frameshift_variant	7517			AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"RAD51-like"	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.976dupC	14.37:g.104165206_104165206dupG	ENSP00000451974:p.Ser326fs		103234953	O43568|Q9BU18	Frame_Shift_Ins	INS	ENST00000553264.1	37	CCDS9984.1																																																																																				0.688	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432		G	104165201	-	G	104165200	7	5	42	1	0	1	1	0	0	0	0	0	17494	304	11	0	68	0	XRCC3	14	104165200	Frame_Shift_Ins	INS	-	TCGA-AG-3882-01A-01W-0899-10	39244657	104165200	3184340	43	3904										
LACTB	114294	broad.mit.edu	37	chr15	63433525	63433525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtcttgtcaacacaccttacGtggataactcctataaatgg	7	10	2	0	rs566925626		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr15:63433525G>A	ENST00000261893.4	+	6	1237	c.1165G>A	c.(1165-1167)Gtg>Atg	p.V389M	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	389						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.V389M(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CACACCTTACGTGGATAACTC	0.373													G|||	1	0.000199681	0	0	5008	,	,		19972	0.001		0	False		,,,				2504	0				Melanoma(85;443 1381 6215 27308 35583)											1	Substitution - Missense(1)	large_intestine(1)	15											141	135	137					15																	63433525		2203	4300	6503	61220578	SO:0001583	missense	114294			AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1165G>A	15.37:g.63433525G>A	ENSP00000261893:p.Val389Met		61220578	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401993	0.83120	.	.	ENSG00000103642	ENST00000261893	T	0.45276	0.9	5.64	5.64	0.86602	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.000000	0.85682	D	0.000000	T	0.64204	0.2577	M	0.76002	2.32	0.80722	D	1	D	0.71674	0.998	D	0.63033	0.91	T	0.63166	-0.6698	10	0.48119	T	0.1	-16.2437	19.0467	0.93022	0.0:0.0:1.0:0.0	.	389	P83111	LACTB_HUMAN	M	389	ENSP00000261893:V389M	ENSP00000261893:V389M	V	+	1	0	LACTB	61220578	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.498000	0.97972	2.817000	0.96982	0.563000	0.77884	GTG		0.373	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		A	63433525	G	A	63433525	3	1	42	1	0	0	0	0	1	0	0	0	8619	1145	40	1	1191	1	LACTB	15	63433525	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		63433525	39097867	44	3905										
ITGAL	3683	broad.mit.edu	37	chr16	30521753	30521753	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cttctgtccagggcattatcTtgcaatgtgagctctcccat	8	12	3	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr16:30521753T>A	ENST00000356798.6	+	22	2760	c.2580T>A	c.(2578-2580)tcT>tcA	p.S860S	ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.S776S	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	860					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.S860S(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGGCATTATCTTGCAATGTGA	0.562																																					NSCLC(110;1462 1641 3311 33990 49495)											1	Substitution - coding silent(1)	large_intestine(1)	16											130	116	120					16																	30521753		2197	4300	6497	30429254	SO:0001819	synonymous_variant	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.2580T>A	16.37:g.30521753T>A			30429254	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.562	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			A	30521753	T	A	30521753	2	1	42	1	0	0	0	0	0	0	0	1	7907	1596	56	5		5	ITGAL	16	30521753	Silent	SNP	T	TCGA-AG-3882-01A-01W-0899-10		30521753	59833000	45	3906										
TP53	7157	broad.mit.edu	37	chr17	7577106	7577106	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tgtgcgccggtctctcccagGacaggcacaaacacgcacct	10	16	1	0	rs17849781		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr17:7577106G>C	ENST00000269305.4	-	8	1021	c.832C>G	c.(832-834)Cct>Gct	p.P278A	TP53_ENST00000445888.2_Missense_Mutation_p.P278A|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P278A|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.P278A|TP53_ENST00000420246.2_Missense_Mutation_p.P278A	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	278	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation; dbSNP:rs17849781). {ECO:0000269|PubMed:15489334}.|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:9450901}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P278S(55)|p.P278A(24)|p.P278T(23)|p.0?(8)|p.P278F(3)|p.P278fs*67(3)|p.?(2)|p.P278fs*28(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.F270_D281del12(1)|p.C275fs*67(1)|p.V274_P278del(1)|p.S269fs*21(1)|p.C277_P278insXXXXXXX(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTCTCCCAGGACAGGCACAA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	131	Substitution - Missense(105)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Insertion - Frameshift(2)|Unknown(2)|Insertion - In frame(1)	upper_aerodigestive_tract(19)|breast(18)|skin(16)|large_intestine(14)|oesophagus(11)|lung(11)|central_nervous_system(7)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|ovary(4)|bone(4)|kidney(3)|endometrium(3)|urinary_tract(3)|soft_tissue(2)|pancreas(2)|eye(1)|biliary_tract(1)|liver(1)|prostate(1)	17	GRCh37	CM011015|CM052927	TP53	M	rs17849781						72	62	65					17																	7577106		2203	4300	6503	7517831	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.832C>G	17.37:g.7577106G>C	ENSP00000269305:p.Pro278Ala		7517831	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.954842	0.92726	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99880	-7.46;-7.46;-7.46;-7.46;-7.46;-7.46	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.050655	0.85682	D	0.000000	D	0.99894	0.9949	M	0.88570	2.965	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.97110	0.992;1.0;0.991;0.988	D	0.96234	0.9170	10	0.72032	D	0.01	-13.7877	16.1198	0.81342	0.0:0.0:1.0:0.0	rs17849781	278;278;278;278	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	A	278;278;278;278;278;267;146	ENSP00000352610:P278A;ENSP00000269305:P278A;ENSP00000398846:P278A;ENSP00000391127:P278A;ENSP00000391478:P278A;ENSP00000425104:P146A	ENSP00000269305:P278A	P	-	1	0	TP53	7517831	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.573000	0.98181	2.667000	0.90743	0.462000	0.41574	CCT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577106	G	C	7577106	3	2	42	1	0	0	0	0	1	0	0	0	16421	1174	41	5	454	5	TP53	17	7577106	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		7577106	73618104	46	3907										
MRC2	9902	broad.mit.edu	37	chr17	60742200	60742200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtccttgctcctgggggcccGcaccagcaacatatccaagc	10	16	0	0	rs370889422		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr17:60742200G>A	ENST00000303375.5	+	2	812	c.410G>A	c.(409-411)cGc>cAc	p.R137H		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	137	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)	p.R137H(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CTGGGGGCCCGCACCAGCAAC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	HIS/ARG	0,4406		0,0,2203	59	55	57		410	3.7	0.9	17		57	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRC2	NM_006039.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	137/1480	60742200	1,13005	2203	4300	6503	58095932	SO:0001583	missense	9902			AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.410G>A	17.37:g.60742200G>A	ENSP00000307513:p.Arg137His		58095932	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.856718	0.32791	0.0	1.16E-4	ENSG00000011028	ENST00000303375	T	0.29917	1.55	4.7	3.66	0.41972	Ricin B-related lectin (1);Ricin B lectin (1);	0.389653	0.27172	N	0.020593	T	0.22704	0.0548	L	0.36672	1.1	0.58432	D	0.999996	D	0.53151	0.958	B	0.42214	0.38	T	0.01081	-1.1458	10	0.33141	T	0.24	-11.1172	9.8054	0.40791	0.1694:0.0:0.8306:0.0	.	137	Q9UBG0	MRC2_HUMAN	H	137	ENSP00000307513:R137H	ENSP00000307513:R137H	R	+	2	0	MRC2	58095932	0.986000	0.35501	0.928000	0.36995	0.282000	0.26991	2.048000	0.41278	2.450000	0.82876	0.561000	0.74099	CGC		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60742200	G	A	60742200	3	1	42	1	0	0	0	0	1	0	0	0	9788	1087	38	1	416	1	MRC2	17	60742200	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	53165094	60742200	20453010	47	3908										
EMILIN2	84034	broad.mit.edu	37	chr18	2885079	2885079	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	caagaaggtcccaaagacccCgtgaagaccctccgccccac	8	18	0	4			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr18:2885079C>T	ENST00000254528.3	+	3	534	c.375C>T	c.(373-375)ccC>ccT	p.P125P		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	125					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.P125P(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		CCAAAGACCCCGTGAAGACCC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	18											87	82	84					18																	2885079		2203	4300	6503	2875079	SO:0001819	synonymous_variant	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.375C>T	18.37:g.2885079C>T			2875079	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																				0.502	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2885079	C	T	2885079	2	4	42	1	0	0	0	0	0	0	0	1	5107	639	23	1		1	EMILIN2	18	2885079	Silent	SNP	C	TCGA-AG-3882-01A-01W-0899-10		2885079	75192169	48	3909										
DNMT1	1786	broad.mit.edu	37	chr19	10248656	10248656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	cggacatcgtgtctcgcaccGtgatggtccggaaaggaccc	13	13	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:10248656G>A	ENST00000340748.4	-	35	4332	c.4097C>T	c.(4096-4098)aCg>aTg	p.T1366M	DNMT1_ENST00000589538.1_5'Flank|DNMT1_ENST00000359526.4_Missense_Mutation_p.T1382M|DNMT1_ENST00000540357.1_Missense_Mutation_p.T1366M			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1366	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.T1366M(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	GTCTCGCACCGTGATGGTCCG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	34	36					19																	10248656		2203	4300	6503	10109656	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4097C>T	19.37:g.10248656G>A	ENSP00000345739:p.Thr1366Met		10109656	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.152228	0.78001	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.53640	0.61;0.61;0.61	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.81123	0.4757	H	0.98133	4.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.996;0.998	D	0.88505	0.3085	10	0.87932	D	0	-31.4871	17.6482	0.88154	0.0:0.0:1.0:0.0	.	1366;1382;1366	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	M	1382;1366;1366;1234	ENSP00000352516:T1382M;ENSP00000440457:T1366M;ENSP00000345739:T1366M	ENSP00000345739:T1366M	T	-	2	0	DNMT1	10109656	1.000000	0.71417	0.984000	0.44739	0.450000	0.32258	9.416000	0.97383	2.446000	0.82766	0.655000	0.94253	ACG		0.622	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		A	10248656	G	A	10248656	3	1	42	1	0	0	0	0	1	0	0	0	4686	1145	40	1	777	1	DNMT1	19	10248656	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		10248656	48880327	49	3910										
ZNF382	84911	broad.mit.edu	37	chr19	37100906	37100906	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ctagaccctgctcagaaggcGctttacagggatgtgatgtt	12	9	1	3			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:37100906G>A	ENST00000292928.2	+	3	203	c.90G>A	c.(88-90)gcG>gcA	p.A30A	ZNF382_ENST00000439428.1_Silent_p.A29A|ZNF382_ENST00000423582.1_Intron|ZNF382_ENST00000435416.1_Silent_p.A30A	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.|Mediates interaction with TRIM28. {ECO:0000250}.|Represses transcription. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A30A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CTCAGAAGGCGCTTTACAGGG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	19											161	146	151					19																	37100906		2203	4300	6503	41792746	SO:0001819	synonymous_variant	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.90G>A	19.37:g.37100906G>A			41792746	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Silent	SNP	ENST00000292928.2	37	CCDS33004.1																																																																																				0.463	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		A	37100906	G	A	37100906	2	1	42	1	0	0	0	0	0	0	0	1	17912	1074	38	1		1	ZNF382	19	37100906	Silent	SNP	G	TCGA-AG-3882-01A-01W-0899-10	26852250	37100906	22028077	50	3911										
LIPE	3991	broad.mit.edu	37	chr19	42914515	42914515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	atgcagcgtgacatactcccGgaggaagtcggcggtgagcc	15	11	0	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:42914515G>A	ENST00000244289.4	-	2	1639	c.1363C>T	c.(1363-1365)Cgg>Tgg	p.R455W	LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE_ENST00000602000.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	455					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)	p.R455W(1)		breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				ACATACTCCCGGAGGAAGTCG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											29	29	29					19																	42914515		2202	4300	6502	47606355	SO:0001583	missense	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.1363C>T	19.37:g.42914515G>A	ENSP00000244289:p.Arg455Trp		47606355	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.998092	0.35226	.	.	ENSG00000079435	ENST00000244289	T	0.32988	1.43	4.2	0.417	0.16421	Hormone-sensitive lipase, N-terminal (1);	0.376195	0.23752	N	0.044913	T	0.46229	0.1382	L	0.60455	1.87	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.938	T	0.36648	-0.9739	10	0.72032	D	0.01	-3.5008	12.0114	0.53289	0.0:0.0:0.4296:0.5704	.	455;455	A8K8W7;Q05469	.;LIPS_HUMAN	W	455	ENSP00000244289:R455W	ENSP00000244289:R455W	R	-	1	2	LIPE	47606355	0.043000	0.20138	0.371000	0.25978	0.243000	0.25628	0.543000	0.23237	0.465000	0.27167	0.455000	0.32223	CGG		0.652	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		A	42914515	G	A	42914515	3	1	42	1	0	0	0	0	1	0	0	0	8845	1115	39	1	1903	1	LIPE	19	42914515	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	5813609	42914515	16214468	51	3912										
ZNF235	9310	broad.mit.edu	37	chr19	44792182	44792182	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	tatgaagattaaagctcaaaCtaaagcacttaccacactca	4	10	2	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:44792182C>G	ENST00000291182.4	-	5	1508	c.1406G>C	c.(1405-1407)aGt>aCt	p.S469T	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	469					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S469T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				AAAGCTCAAACTAAAGCACTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											113	110	111					19																	44792182		2203	4300	6503	49484022	SO:0001583	missense	9310			X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"Zinc fingers, C2H2-type", "-"	12866	protein-coding gene	gene with protein product		604749	"zinc finger protein homologous to Zfp93 in mouse"	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.1406G>C	19.37:g.44792182C>G	ENSP00000291182:p.Ser469Thr		49484022	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892935	0.33442	.	.	ENSG00000159917	ENST00000391957;ENST00000291182	T	0.17854	2.25	4.8	3.74	0.42951	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000129	T	0.15305	0.0369	N	0.10809	0.05	0.09310	N	0.999991	D;D	0.57899	0.977;0.981	P;P	0.59424	0.776;0.857	T	0.13845	-1.0494	10	0.21540	T	0.41	.	8.7209	0.34441	0.0:0.7556:0.1557:0.0887	.	465;469	Q14590-2;Q14590	.;ZN235_HUMAN	T	469	ENSP00000291182:S469T	ENSP00000291182:S469T	S	-	2	0	ZNF235	49484022	0.000000	0.05858	0.900000	0.35374	0.972000	0.66771	-0.619000	0.05572	2.385000	0.81259	0.462000	0.41574	AGT		0.388	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			G	44792182	C	G	44792182	3	3	42	1	0	0	0	0	1	0	0	0	17827	565	20	5	814	5	ZNF235	19	44792182	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	1877667	44792182	14336801	52	3913										
EXOC3L2	90332	broad.mit.edu	37	chr19	45730933	45730933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ccctcacctcagtggggggcCgcagttgaccagggcgatgg	16	13	2	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:45730933C>T	ENST00000252482.3	-	4	418	c.391G>A	c.(391-393)Ggc>Agc	p.G131S	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.G131S			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	131					exocytosis (GO:0006887)	exocyst (GO:0000145)		p.G131S(1)		endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		AGTGGGGGGCCGCAGTTGACC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											77	73	74					19																	45730933		2203	4300	6503	50422773	SO:0001583	missense	90332			AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.391G>A	19.37:g.45730933C>T	ENSP00000252482:p.Gly131Ser		50422773	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.722239	0.48728	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.05925	3.37;3.37	5.07	3.97	0.46021	.	0.060613	0.64402	D	0.000004	T	0.15565	0.0375	L	0.57536	1.79	0.33107	D	0.540038	D	0.89917	1.0	D	0.67103	0.949	T	0.05500	-1.0881	10	0.19590	T	0.45	.	9.9665	0.41727	0.2023:0.7977:0.0:0.0	.	131	Q2M3D2	EX3L2_HUMAN	S	131	ENSP00000252482:G131S;ENSP00000400713:G131S	ENSP00000252482:G131S	G	-	1	0	EXOC3L2	50422773	0.998000	0.40836	0.986000	0.45419	0.803000	0.45373	4.482000	0.60257	2.376000	0.81061	0.491000	0.48974	GGC		0.602	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		T	45730933	C	T	45730933	3	4	42	1	0	0	0	0	1	0	0	0	5318	652	23	1	862	1	EXOC3L2	19	45730933	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	938751	45730933	13398050	53	3914										
PRKCG	5582	broad.mit.edu	37	chr19	54395022	54395022	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ccagaccctcggaacctgacGaaacagaagacccgaacggt	10	14	0	4	rs553245210		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr19:54395022G>A	ENST00000263431.3	+	6	906	c.624G>A	c.(622-624)acG>acA	p.T208T	PRKCG_ENST00000542049.1_Silent_p.T95T|PRKCG_ENST00000536044.1_Silent_p.T208T|PRKCG_ENST00000540413.1_Silent_p.T208T	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	208	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.T208T(2)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	GGAACCTGACGAAACAGAAGA	0.522													G|||	1	0.000199681	8e-04	0	5008	,	,		17926	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	19											142	115	124					19																	54395022		2203	4300	6503	59086834	SO:0001819	synonymous_variant	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.624G>A	19.37:g.54395022G>A			59086834	B7Z8Q0	Silent	SNP	ENST00000263431.3	37	CCDS12867.1																																																																																				0.522	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54395022	G	A	54395022	2	1	42	1	0	0	0	0	0	0	0	1	12546	1045	37	1		1	PRKCG	19	54395022	Silent	SNP	G	TCGA-AG-3882-01A-01W-0899-10	8664089	54395022	4733961	54	3915										
PTPRT	11122	broad.mit.edu	37	chr20	40727112	40727112	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	acagaggagcagttgtaatcGaacaccagcctccagaagtc	10	11	0	2	rs376065743		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr20:40727112G>A	ENST00000373187.1	-	27	3794	c.3795C>T	c.(3793-3795)ttC>ttT	p.F1265F	PTPRT_ENST00000373190.1_Silent_p.F1264F|PTPRT_ENST00000356100.2_Silent_p.F1274F|PTPRT_ENST00000373201.1_Silent_p.F1255F|PTPRT_ENST00000373193.3_Silent_p.F1268F|PTPRT_ENST00000373184.1_Silent_p.F1275F|PTPRT_ENST00000373198.4_Silent_p.F1284F			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1265	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.F1287F(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGTTGTAATCGAACACCAGCC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	20											73	78	77					20																	40727112		2103	4240	6343	40160526	SO:0001819	synonymous_variant	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3795C>T	20.37:g.40727112G>A			40160526	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																				0.592	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40727112	G	A	40727112	2	1	42	1	0	0	0	0	0	0	0	1	12849	1049	37	1		1	PTPRT	20	40727112	Silent	SNP	G	TCGA-AG-3882-01A-01W-0899-10		40727112	22298408	55	3916										
COL18A1	80781	broad.mit.edu	37	chr21	46901899	46901899	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	acccccaggccctccgggaaGagaggggcccccaggaagga	15	15	0	1	rs373536407		TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chr21:46901899G>A	ENST00000359759.4	+	13	2900	c.2879G>A	c.(2878-2880)aGa>aAa	p.R960K	COL18A1_ENST00000355480.5_Missense_Mutation_p.R725K|COL18A1_ENST00000400337.2_Missense_Mutation_p.R545K			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	960	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.R725K(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CCTCCGGGAAGAGAGGGGCCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	21											31	38	35					21																	46901899		1867	4092	5959	45726327	SO:0001583	missense	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2879G>A	21.37:g.46901899G>A	ENSP00000352798:p.Arg960Lys		45726327	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	G	0.077	-1.189983	0.01607	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.93366	-3.13;-3.21;-3.21	3.83	-4.57	0.03421	.	1.360120	0.04823	N	0.437224	T	0.80358	0.4608	N	0.02960	-0.455	0.09310	N	0.999993	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.74247	-0.3727	10	0.05959	T	0.93	.	11.4664	0.50241	0.7423:0.0:0.2577:0.0	.	960;725;545	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	K	545;545;725;960;960	ENSP00000383191:R545K;ENSP00000347665:R725K;ENSP00000352798:R960K	ENSP00000347665:R725K	R	+	2	0	COL18A1	45726327	0.000000	0.05858	0.297000	0.24988	0.407000	0.30961	-0.624000	0.05540	-1.536000	0.01738	-1.626000	0.00786	AGA		0.607	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46901899	G	A	46901899	3	1	42	1	0	0	0	0	1	0	0	0	3681	942	33	3	3043	3	COL18A1	21	46901899	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		46901899	1227996	56	3917										
TLR8	51311	broad.mit.edu	37	chrX	12939149	12939149	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	aagcattccttaatttgccaGcgagtctcactgaactacat	6	11	1	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chrX:12939149G>A	ENST00000218032.6	+	2	2077	c.1990G>A	c.(1990-1992)Gcg>Acg	p.A664T	TLR8_ENST00000311912.5_Missense_Mutation_p.A682T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	664					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.A682T(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TAATTTGCCAGCGAGTCTCAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											53	54	54					X																	12939149		2203	4298	6501	12849070	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1990G>A	X.37:g.12939149G>A	ENSP00000218032:p.Ala664Thr		12849070	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	0.507	-0.868246	0.02590	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56611	0.45;0.45	5.82	-0.669	0.11388	.	2.781830	0.01516	N	0.018171	T	0.35682	0.0940	N	0.20986	0.625	0.09310	N	1	B;B	0.28584	0.216;0.216	B;B	0.31390	0.129;0.129	T	0.09952	-1.0651	10	0.29301	T	0.29	.	0.4773	0.00542	0.219:0.3007:0.2226:0.2576	.	664;682	Q9NR97;D1CS70	TLR8_HUMAN;.	T	664;682	ENSP00000218032:A664T;ENSP00000312082:A682T	ENSP00000218032:A664T	A	+	1	0	TLR8	12849070	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.066000	0.01385	-0.015000	0.14150	-0.216000	0.12614	GCG		0.388	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12939149	G	A	12939149	3	1	42	1	0	0	0	0	1	0	0	0	15996	971	34	3	1996	3	TLR8	23	12939149	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10		12939149	142331411	57	3918										
CNKSR2	22866	broad.mit.edu	37	chrX	21627280	21627280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gtcttctcatgaggagtttcGccaggaagtaactgggagca	13	8	2	1			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chrX:21627280G>A	ENST00000379510.3	+	20	2273	c.2237G>A	c.(2236-2238)cGc>cAc	p.R746H	CNKSR2_ENST00000543067.1_Missense_Mutation_p.R697H|CNKSR2_ENST00000425654.2_Missense_Mutation_p.R716H|CNKSR2_ENST00000279451.4_Missense_Mutation_p.R746H	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	746					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.R746H(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						GAGGAGTTTCGCCAGGAAGTA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	X											74	73	73					X																	21627280		2203	4300	6503	21537201	SO:0001583	missense	22866			AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.2237G>A	X.37:g.21627280G>A	ENSP00000368824:p.Arg746His		21537201	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	37	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.336613	0.41398	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.21191	2.34;2.02;2.04;2.37	5.28	5.28	0.74379	.	0.049583	0.85682	D	0.000000	T	0.29126	0.0724	L	0.33485	1.01	0.51482	D	0.999926	P;B;D;D	0.60160	0.564;0.163;0.979;0.987	B;B;B;P	0.52856	0.097;0.027;0.363;0.711	T	0.01920	-1.1247	10	0.51188	T	0.08	-13.6897	17.9342	0.89007	0.0:0.0:1.0:0.0	.	716;697;338;746	B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2	.;.;.;CNKR2_HUMAN	H	716;697;746;746	ENSP00000397906:R716H;ENSP00000444633:R697H;ENSP00000279451:R746H;ENSP00000368824:R746H	ENSP00000279451:R746H	R	+	2	0	CNKSR2	21537201	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.339000	0.65953	2.168000	0.68352	0.506000	0.49869	CGC		0.512	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		A	21627280	G	A	21627280	3	1	42	1	0	0	0	0	1	0	0	0	3613	1087	38	1	2315	1	CNKSR2	23	21627280	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	8688131	21627280	133643280	58	3919										
CXorf59	286464	broad.mit.edu	37	chrX	36116960	36116960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gccagaatttttgcttgaacCagaagattataagaggtgga	11	5	0	5			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chrX:36116960C>T	ENST00000313548.4	+	6	878	c.692C>T	c.(691-693)cCa>cTa	p.P231L		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	231						integral component of membrane (GO:0016021)		p.P231L(1)									TTGCTTGAACCAGAAGATTAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	X											41	38	39					X																	36116960		2201	4291	6492	36026881	SO:0001583	missense	286464			AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.692C>T	X.37:g.36116960C>T	ENSP00000324767:p.Pro231Leu		36026881		Missense_Mutation	SNP	ENST00000313548.4	37	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	c	1.277	-0.611496	0.03690	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	5.52	3.76	0.43208	.	0.328640	0.25305	N	0.031629	T	0.43456	0.1248	L	0.52364	1.645	0.32586	N	0.52778	B	0.31077	0.307	B	0.28385	0.089	T	0.51052	-0.8754	9	0.34782	T	0.22	-3.2584	9.5525	0.39319	0.0:0.8238:0.0:0.1762	.	231	Q8N9S7	CX059_HUMAN	L	231	.	ENSP00000324767:P231L	P	+	2	0	CXorf59	36026881	0.807000	0.29009	0.553000	0.28255	0.071000	0.16799	0.818000	0.27295	0.622000	0.30249	0.579000	0.79373	CCA		0.294	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		T	36116960	C	T	36116960	3	4	42	1	0	0	0	0	1	0	0	0	4121	594	21	3	710	3	CXorf59	23	36116960	Missense_Mutation	SNP	C	TCGA-AG-3882-01A-01W-0899-10	14489680	36116960	119153600	59	3920										
MCF2	4168	broad.mit.edu	37	chrX	138708853	138708853	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	gaactgacagctccttcagtGtcaggcacttccagatttgt	9	11	2	2			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chrX:138708853G>T	ENST00000370576.4	-	5	710	c.501C>A	c.(499-501)gaC>gaA	p.D167E	MCF2_ENST00000414978.1_Missense_Mutation_p.D227E|MCF2_ENST00000519895.1_Missense_Mutation_p.D227E|MCF2_ENST00000370573.4_Missense_Mutation_p.D167E|MCF2_ENST00000370578.4_Missense_Mutation_p.D312E|MCF2_ENST00000536274.1_Missense_Mutation_p.D128E|MCF2_ENST00000338585.6_Missense_Mutation_p.D167E|MCF2_ENST00000520602.1_Missense_Mutation_p.D227E	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	167					apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D227E(1)|p.D167E(1)		NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					CTCCTTCAGTGTCAGGCACTT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	X											155	141	146					X																	138708853		2203	4300	6503	138536519	SO:0001583	missense	4168				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.501C>A	X.37:g.138708853G>T	ENSP00000359608:p.Asp167Glu		138536519	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	g	0.268	-0.994677	0.02145	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	4.56	2.65	0.31530	.	0.719811	0.14022	N	0.346734	T	0.30008	0.0751	L	0.54323	1.7	0.09310	N	1	B;B;B;B;B;B;B;B	0.26002	0.004;0.139;0.001;0.001;0.008;0.002;0.082;0.005	B;B;B;B;B;B;B;B	0.23574	0.017;0.021;0.016;0.007;0.039;0.011;0.047;0.017	T	0.35871	-0.9771	10	0.02654	T	1	.	6.518	0.22258	0.3485:0.0:0.6515:0.0	.	227;312;128;167;167;312;167;167	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	E	227;167;128;312;227;227;167;167	ENSP00000427745:D227E;ENSP00000359608:D167E;ENSP00000438155:D128E;ENSP00000359610:D312E;ENSP00000397055:D227E;ENSP00000430276:D227E;ENSP00000359605:D167E;ENSP00000342204:D167E	ENSP00000342204:D167E	D	-	3	2	MCF2	138536519	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-0.070000	0.11523	0.261000	0.21753	0.597000	0.82753	GAC		0.373	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		T	138708853	G	T	138708853	3	4	42	1	0	0	0	0	1	0	0	0	9408	1368	48	2	2440	2	MCF2	23	138708853	Missense_Mutation	SNP	G	TCGA-AG-3882-01A-01W-0899-10	102591893	138708853	16561707	60	3921										
PASD1	139135	broad.mit.edu	37	chrX	150840874	150840874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	0.739787520574592	0	0.77772534214252	0.0476190476190476	0.29047619047619	0	ggaagaagtggcaggggcagAtgctacagaaagagccagag	17	6	0	5			TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3882-01A-01W-0899-10	TCGA-AG-3882-10A-01W-0901-10	g.chrX:150840874A>G	ENST00000370357.4	+	14	1902	c.1657A>G	c.(1657-1659)Atg>Gtg	p.M553V		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	553						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.M553V(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					gcaggggcagatgctacagaa	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	X											63	58	60					X																	150840874		2203	4300	6503	150591530	SO:0001583	missense	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1657A>G	X.37:g.150840874A>G	ENSP00000359382:p.Met553Val		150591530	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	A	2.704	-0.270300	0.05716	.	.	ENSG00000166049	ENST00000370357	T	0.17213	2.29	1.14	-2.29	0.06805	.	.	.	.	.	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.11329	0.006	T	0.30060	-0.9991	9	0.66056	D	0.02	.	2.75	0.05277	0.3687:0.3895:0.2418:0.0	.	553	Q8IV76	PASD1_HUMAN	V	553	ENSP00000359382:M553V	ENSP00000359382:M553V	M	+	1	0	PASD1	150591530	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.827000	0.04424	-1.165000	0.02786	-0.461000	0.05368	ATG		0.537	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		G	150840874	A	G	150840874	3	3	42	1	0	0	0	0	1	0	0	0	11502	333	12	4	1707	4	PASD1	23	150840874	Missense_Mutation	SNP	A	TCGA-AG-3882-01A-01W-0899-10	12132021	150840874	4429686	61	3922										
ELAVL4	1996	broad.mit.edu	37	chr1	50666847	50666847	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	accaacaaagcccacaagtcCtgaatttcccattcttactt	3	14	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:50666847C>A	ENST00000371823.4	+	7	1364	c.1140C>A	c.(1138-1140)tcC>tcA	p.S380S	ELAVL4_ENST00000448907.2_Silent_p.S369S|ELAVL4_ENST00000371827.1_Silent_p.S366S|ELAVL4_ENST00000371824.1_Silent_p.S366S|ELAVL4_ENST00000371819.1_Silent_p.S371S|ELAVL4_ENST00000371821.1_Silent_p.S385S|ELAVL4_ENST00000357083.4_Silent_p.S383S	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4	380					mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.S380S(1)|p.S383S(1)		NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						CCCACAAGTCCTGAATTTCCC	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	1											20	20	20					1																	50666847		2195	4288	6483	50439434	SO:0001819	synonymous_variant	1996			AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"RNA binding motif (RRM) containing"	3315	protein-coding gene	gene with protein product	"Hu antigen D"	168360	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.1140C>A	1.37:g.50666847C>A			50439434	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Silent	SNP	ENST00000371823.4	37	CCDS553.1																																																																																				0.443	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952		A	50666847	C	A	50666847	2	1	43	1	0	0	0	0	0	0	0	1	5065	668	24	2		2	ELAVL4	1	50666847	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10		50666847	198583774	1	3923										
IFI44L	10964	broad.mit.edu	37	chr1	79093736	79093736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atatggttgaaagatgcagcCgtcagggatgtactataaca	11	6	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:79093736C>T	ENST00000370751.5	+	2	315	c.136C>T	c.(136-138)Cgt>Tgt	p.R46C	IFI44L_ENST00000342282.3_Intron|IFI44L_ENST00000476521.1_Intron	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	46					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)		p.R7C(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						AAGATGCAGCCGTCAGGGATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	79	79					1																	79093736		2203	4300	6503	78866324	SO:0001583	missense	10964			AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.136C>T	1.37:g.79093736C>T	ENSP00000359787:p.Arg46Cys		78866324	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	37	CCDS687.2	.	.	.	.	.	.	.	.	.	.	C	6.305	0.424379	0.11928	.	.	ENSG00000137959	ENST00000452835;ENST00000370751;ENST00000450498	T;T;T	0.32515	1.45;3.07;2.48	3.41	-6.83	0.01693	.	1.843670	0.03430	N	0.207711	T	0.02418	0.0074	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16512	-1.0400	10	0.35671	T	0.21	5.3548	0.8249	0.01118	0.4079:0.2237:0.113:0.2554	.	46	Q53G44	IF44L_HUMAN	C	46;46;23	ENSP00000409914:R46C;ENSP00000359787:R46C;ENSP00000400784:R23C	ENSP00000359787:R46C	R	+	1	0	IFI44L	78866324	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.650000	0.00203	-1.778000	0.01282	-0.718000	0.03613	CGT		0.363	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		T	79093736	C	T	79093736	3	4	43	1	0	0	0	0	1	0	0	0	7539	652	23	1	138	1	IFI44L	1	79093736	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	28426889	79093736	170156885	2	3924										
MOV10	4343	broad.mit.edu	37	chr1	113235545	113235545	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cagaaccccaggctgctcacGctggaggtcagggctcagat	13	13	3	2	rs114735246	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:113235545G>A	ENST00000413052.2	+	7	1524	c.1134G>A	c.(1132-1134)acG>acA	p.T378T	MOV10_ENST00000369645.1_Silent_p.T378T|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.T322T|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000357443.2_Silent_p.T378T	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	378					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.T378T(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GGCTGCTCACGCTGGAGGTCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1											25	23	24					1																	113235545		2203	4300	6503	113037068	SO:0001819	synonymous_variant	4343			AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1134G>A	1.37:g.113235545G>A			113037068	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																				0.592	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		A	113235545	G	A	113235545	2	1	43	1	0	0	0	0	0	0	0	1	9748	1074	38	1		1	MOV10	1	113235545	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	34141809	113235545	136015076	3	3925										
FLG	2312	broad.mit.edu	37	chr1	152282954	152282954	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gctgtttcgtgcctgctcatGgcgggatccttgtcttcctc	11	13	2	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:152282954G>T	ENST00000368799.1	-	3	4443	c.4408C>A	c.(4408-4410)Cat>Aat	p.H1470N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1470	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.H1470N(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTGCTCATGGCGGGATCCT	0.572									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											287	276	280					1																	152282954		2203	4300	6503	150549578	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4408C>A	1.37:g.152282954G>T	ENSP00000357789:p.His1470Asn		150549578	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	4.371	0.068358	0.08436	.	.	ENSG00000143631	ENST00000368799	T	0.04015	3.73	3.61	1.69	0.24217	.	.	.	.	.	T	0.01454	0.0047	L	0.56769	1.78	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.46541	-0.9184	9	0.16420	T	0.52	.	4.1035	0.10025	0.1236:0.0:0.646:0.2303	.	1470	P20930	FILA_HUMAN	N	1470	ENSP00000357789:H1470N	ENSP00000357789:H1470N	H	-	1	0	FLG	150549578	0.001000	0.12720	0.001000	0.08648	0.031000	0.12232	0.685000	0.25378	0.863000	0.35553	-0.255000	0.11280	CAT		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152282954	G	T	152282954	3	4	43	1	0	0	0	0	1	0	0	0	5941	1348	47	2	7781	2	FLG	1	152282954	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	39047409	152282954	96967667	4	3926										
CEP350	9857	broad.mit.edu	37	chr1	180047703	180047703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tgctgttgaatatgtaccatCcgagtctataggacaggagc	11	8	1	1	rs149801617	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:180047703C>T	ENST00000367607.3	+	29	6291	c.5873C>T	c.(5872-5874)tCc>tTc	p.S1958F		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1958					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S1958F(1)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TATGTACCATCCGAGTCTATA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	PHE/SER	0,4406		0,0,2203	60	59	60		5873	5.3	0.3	1	dbSNP_134	60	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CEP350	NM_014810.4	155	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging	1958/3118	180047703	4,13002	2203	4300	6503	178314326	SO:0001583	missense	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.5873C>T	1.37:g.180047703C>T	ENSP00000356579:p.Ser1958Phe		178314326	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.281263	0.59758	0.0	4.65E-4	ENSG00000135837	ENST00000367607	T	0.54675	0.56	5.31	5.31	0.75309	.	0.313987	0.23063	N	0.052351	T	0.60971	0.2310	L	0.57536	1.79	0.25756	N	0.985002	D;P	0.53885	0.963;0.94	P;P	0.51266	0.642;0.664	T	0.57081	-0.7872	9	.	.	.	.	17.5204	0.87786	0.0:1.0:0.0:0.0	.	1958;1958	E7EU22;Q5VT06	.;CE350_HUMAN	F	1958	ENSP00000356579:S1958F	.	S	+	2	0	CEP350	178314326	0.442000	0.25633	0.278000	0.24718	0.392000	0.30506	2.535000	0.45685	2.649000	0.89929	0.591000	0.81541	TCC		0.443	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180047703	C	T	180047703	3	4	43	1	0	0	0	0	1	0	0	0	3260	855	30	3	5983	3	CEP350	1	180047703	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	27764749	180047703	69202918	5	3927										
ANGEL2	90806	broad.mit.edu	37	chr1	213181764	213181764	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tcctaggatcttcgttttttCtttatcatggctacatatat	5	8	3	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:213181764C>G	ENST00000366962.3	-	3	584	c.430G>C	c.(430-432)Gaa>Caa	p.E144Q	ANGEL2_ENST00000360506.2_5'UTR|ANGEL2_ENST00000544555.1_5'UTR|ANGEL2_ENST00000535388.1_5'UTR|ANGEL2_ENST00000540642.1_Missense_Mutation_p.E18Q	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	144								p.E144Q(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		TTCGTTTTTTCTTTATCATGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											133	129	130					1																	213181764		2203	4300	6503	211248387	SO:0001583	missense	90806			AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.430G>C	1.37:g.213181764C>G	ENSP00000355929:p.Glu144Gln		211248387	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Missense_Mutation	SNP	ENST00000366962.3	37	CCDS1512.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.206721	0.39003	.	.	ENSG00000174606	ENST00000366962;ENST00000540642;ENST00000310246	T;T	0.30981	1.86;1.51	5.76	5.76	0.90799	.	0.597438	0.18263	N	0.146549	T	0.27098	0.0664	L	0.29908	0.895	0.80722	D	1	B;B;B	0.32968	0.068;0.392;0.041	B;B;B	0.36666	0.126;0.23;0.043	T	0.03910	-1.0993	10	0.24483	T	0.36	-7.6566	15.4858	0.75564	0.0:1.0:0.0:0.0	.	18;122;144	F5H476;Q96AL9;Q5VTE6	.;.;ANGE2_HUMAN	Q	144;18;122	ENSP00000355929:E144Q;ENSP00000446124:E18Q	ENSP00000309755:E122Q	E	-	1	0	ANGEL2	211248387	1.000000	0.71417	0.992000	0.48379	0.294000	0.27393	3.922000	0.56462	2.706000	0.92434	0.655000	0.94253	GAA		0.323	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		G	213181764	C	G	213181764	3	3	43	1	0	0	0	0	1	0	0	0	609	922	32	5	1232	5	ANGEL2	1	213181764	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	33134061	213181764	36068857	6	3928										
SPATA17	128153	broad.mit.edu	37	chr1	217804761	217804761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gcaagctaggtcgtcgactgTaggaaatcagtactacttta	10	8	1	0	rs143300149	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:217804761T>C	ENST00000366933.4	+	1	96	c.41T>C	c.(40-42)gTa>gCa	p.V14A	GPATCH2_ENST00000366934.3_5'Flank|GPATCH2_ENST00000366935.3_5'Flank	NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	14						cytoplasm (GO:0005737)		p.V14A(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TCGTCGACTGTAGGAAATCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1						T	ALA/VAL	10,4396	16.8+/-37.8	0,10,2193	94	84	87		41	4.5	0	1	dbSNP_134	87	0,8600		0,0,4300	yes	missense	SPATA17	NM_138796.2	64	0,10,6493	CC,CT,TT		0.0,0.227,0.0769	benign	14/362	217804761	10,12996	2203	4300	6503	215871384	SO:0001583	missense	128153			AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.41T>C	1.37:g.217804761T>C	ENSP00000355900:p.Val14Ala		215871384	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.423711	0.43020	0.00227	0.0	ENSG00000162814	ENST00000366933	T	0.71817	-0.6	4.47	4.47	0.54385	.	1.635520	0.03548	N	0.225053	T	0.66944	0.2841	L	0.36672	1.1	0.09310	N	1	B	0.19817	0.039	B	0.19946	0.027	T	0.54576	-0.8273	10	0.66056	D	0.02	-0.0091	11.5437	0.50681	0.0:0.0:0.0:1.0	.	14	Q96L03	SPT17_HUMAN	A	14	ENSP00000355900:V14A	ENSP00000355900:V14A	V	+	2	0	SPATA17	215871384	0.007000	0.16637	0.010000	0.14722	0.069000	0.16628	1.921000	0.40035	2.003000	0.58678	0.533000	0.62120	GTA		0.517	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		C	217804761	T	C	217804761	3	2	43	1	0	0	0	0	1	0	0	0	15041	1638	57	4	43	4	SPATA17	1	217804761	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	4622997	217804761	31445860	7	3929										
C1orf35	79169	broad.mit.edu	37	chr1	228289097	228289099	+	In_Frame_Del	DEL	TTC	TTC	-													0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gccgcctgtgctctttgtctTtcttcttcttctctttcttg					rs370819690		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	TTC	TTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr1:228289097_228289099delTTC	ENST00000272139.4	-	7	843_845	c.609_611delGAA	c.(607-612)aagaaa>aaa	p.203_204KK>K	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	203	Lys-rich.						poly(A) RNA binding (GO:0044822)	p.K204delK(1)		large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CTCTTTGTCTttcttcttcttct	0.517																																																1	Deletion - In frame(1)	large_intestine(1)	1																																								226355722	SO:0001651	inframe_deletion	79169			AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"multiple myeloma tumor-associated protein 2"					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.609_611delGAA	1.37:g.228289106_228289108delTTC	ENSP00000272139:p.Lys204del		226355720	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	In_Frame_Del	DEL	ENST00000272139.4	37	CCDS1566.1																																																																																				0.517	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		-	228289099	TTC	-	228289097	7	5	43	1	0	1	0	1	0	0	0	0	2044	1841	64	0	188	0	C1orf35	1	228289097	In_Frame_Del	DEL	TTC	TCGA-AG-3883-01A-02W-0899-10	10484336	228289097	20961524	8	3930										
ALLC	55821	broad.mit.edu	37	chr2	3727534	3727534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cgtggacgtttcttacttcaCgggagattacgctcctcgag	11	11	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:3727534C>T	ENST00000252505.3	+	5	410	c.248C>T	c.(247-249)aCg>aTg	p.T83M		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	102					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)	p.T83M(2)		breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		TCTTACTTCACGGGAGATTAC	0.532										HNSCC(21;0.051)																																						2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	2											137	144	142					2																	3727534		2075	4214	6289	3705409	SO:0001583	missense	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.248C>T	2.37:g.3727534C>T	ENSP00000252505:p.Thr83Met		3705409	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	C	8.179	0.793502	0.16327	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.77	-3.07	0.05363	Allantoicase domain (1);Galactose-binding domain-like (1);	0.782013	0.12462	N	0.466774	T	0.31389	0.0795	M	0.64260	1.97	0.09310	N	1	P	0.52170	0.951	P	0.44696	0.458	T	0.18713	-1.0328	9	0.59425	D	0.04	-6.5612	4.4518	0.11624	0.2443:0.378:0.0:0.3777	.	102	Q8N6M5	ALLC_HUMAN	M	83	.	ENSP00000252505:T83M	T	+	2	0	ALLC	3705409	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.173000	0.09854	-0.616000	0.05671	-1.268000	0.01426	ACG		0.532	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			T	3727534	C	T	3727534	3	4	43	1	0	0	0	0	1	0	0	0	534	536	19	1	262	1	ALLC	2	3727534	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		3727534	239471839	9	3931										
TET3	200424	broad.mit.edu	37	chr2	74328441	74328441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccactctggaggacggctgcGaggcaaaccgtggagcccct	14	14	1	0	rs201185906	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:74328441G>A	ENST00000409262.3	+	9	4121	c.4121G>A	c.(4120-4122)cGa>cAa	p.R1374Q		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1374					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.R651Q(1)|p.R1374Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGACGGCTGCGAGGCAAACCG	0.682													G|||	8	0.00159744	0.0061	0	5008	,	,		17849	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2						G	GLN/ARG	17,3803		0,17,1893	24	30	28		4121	4.1	1	2		28	0,8238		0,0,4119	yes	missense	TET3	NM_144993.1	43	0,17,6012	AA,AG,GG		0.0,0.445,0.141	probably-damaging	1374/1661	74328441	17,12041	1910	4119	6029	74181949	SO:0001583	missense	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.4121G>A	2.37:g.74328441G>A	ENSP00000386869:p.Arg1374Gln		74181949	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.96	1.498062	0.26861	0.00445	0.0	ENSG00000187605	ENST00000409262;ENST00000233310	T	0.11277	2.79	5.08	4.13	0.48395	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	0.263863	0.26265	N	0.025375	T	0.07007	0.0178	L	0.36672	1.1	0.26915	N	0.966814	D	0.58268	0.982	P	0.48795	0.59	T	0.14868	-1.0457	10	0.13853	T	0.58	.	7.6298	0.28232	0.0:0.1647:0.6421:0.1932	.	1374	O43151	TET3_HUMAN	Q	1374	ENSP00000386869:R1374Q	ENSP00000233310:R1374Q	R	+	2	0	TET3	74181949	0.831000	0.29352	0.991000	0.47740	0.973000	0.67179	2.448000	0.44926	2.639000	0.89480	0.655000	0.94253	CGA		0.682	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			A	74328441	G	A	74328441	3	1	43	1	0	0	0	0	1	0	0	0	15810	1058	37	1	4155	1	TET3	2	74328441	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	70600907	74328441	168870932	10	3932										
EDAR	10913	broad.mit.edu	37	chr2	109522822	109522822	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atctttttcctccggctttgAatctgtgaaaaagagtcgag	9	8	2	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:109522822A>C	ENST00000258443.2	-	11	1396	c.966T>G	c.(964-966)atT>atG	p.I322M	EDAR_ENST00000376651.1_Missense_Mutation_p.I354M|EDAR_ENST00000409271.1_Missense_Mutation_p.I354M	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	322					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.I322M(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						TCCGGCTTTGAATCTGTGAAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											72	71	71					2																	109522822		2203	4300	6503	108889254	SO:0001583	missense	10913			AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"Tumor necrosis factor receptor superfamily"	2895	protein-coding gene	gene with protein product		604095	"ectodysplasin 1, anhidrotic receptor"	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.966T>G	2.37:g.109522822A>C	ENSP00000258443:p.Ile322Met		108889254	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Missense_Mutation	SNP	ENST00000258443.2	37	CCDS2081.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.361360	0.24684	.	.	ENSG00000135960	ENST00000409271;ENST00000258443;ENST00000376651	D;D;D	0.92149	-2.98;-2.92;-2.98	5.39	3.09	0.35607	.	0.537275	0.19530	N	0.112073	D	0.90010	0.6881	M	0.67953	2.075	0.53688	D	0.999973	P;B	0.42409	0.779;0.435	P;B	0.45037	0.467;0.372	D	0.86274	0.1663	10	0.87932	D	0	-11.4592	2.46	0.04538	0.4277:0.0:0.2233:0.3491	.	354;322	E9PC98;Q9UNE0	.;EDAR_HUMAN	M	354;322;354	ENSP00000386371:I354M;ENSP00000258443:I322M;ENSP00000365839:I354M	ENSP00000258443:I322M	I	-	3	3	EDAR	108889254	1.000000	0.71417	0.999000	0.59377	0.186000	0.23388	1.086000	0.30853	0.385000	0.24970	0.379000	0.24179	ATT		0.517	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			C	109522822	A	C	109522822	3	2	43	1	0	0	0	0	1	0	0	0	4916	242	9	4	388	4	EDAR	2	109522822	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	35194381	109522822	133676551	11	3933										
PTPN18	26469	broad.mit.edu	37	chr2	131128792	131128792	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aattgtgccccactctacgaCgatgccctcttcctccggac	7	17	2	0	rs551564117		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:131128792C>T	ENST00000175756.5	+	12	1046	c.945C>T	c.(943-945)gaC>gaT	p.D315D	PTPN18_ENST00000347849.3_Silent_p.D208D	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	315					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.D315D(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					CACTCTACGACGATGCCCTCT	0.617													C|||	1	0.000199681	8e-04	0	5008	,	,		16110	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											92	88	89					2																	131128792		2203	4300	6503	130845262	SO:0001819	synonymous_variant	26469			X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.945C>T	2.37:g.131128792C>T			130845262	B4E1E6|Q53P42	Silent	SNP	ENST00000175756.5	37	CCDS2161.1																																																																																				0.617	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			T	131128792	C	T	131128792	2	4	43	1	0	0	0	0	0	0	0	1	12819	535	19	1		1	PTPN18	2	131128792	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	21605970	131128792	112070581	12	3934										
LRP1B	53353	broad.mit.edu	37	chr2	141359136	141359136	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cagtgtgtctggtgatggatGaggtggtagagcttgtccag	17	5	1	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:141359136G>T	ENST00000389484.3	-	42	7843	c.6872C>A	c.(6871-6873)tCa>tAa	p.S2291*		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2291					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S2291*(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		GGTGATGGATGAGGTGGTAGA	0.498										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Nonsense(1)	large_intestine(1)	2											145	121	129					2																	141359136		2203	4300	6503	141075606	SO:0001587	stop_gained	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6872C>A	2.37:g.141359136G>T	ENSP00000374135:p.Ser2291*		141075606	Q8WY29|Q8WY30|Q8WY31	Nonsense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	53	21.406506	0.99940	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7339	0.91746	0.0:0.0:1.0:0.0	.	.	.	.	X	2291;2229	.	ENSP00000374135:S2291X	S	-	2	0	LRP1B	141075606	1.000000	0.71417	0.995000	0.50966	0.880000	0.50808	7.836000	0.86788	2.491000	0.84063	0.561000	0.74099	TCA		0.498	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141359136	G	T	141359136	4	4	43	1	0	0	0	0	0	1	0	0	8984	1294	45	2	7127	2	LRP1B	2	141359136	Nonsense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	10230344	141359136	101840237	13	3935										
ZEB2	9839	broad.mit.edu	37	chr2	145157726	145157726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tcttgatattgtttctcattCggccatttacagagattaaa	6	7	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:145157726C>T	ENST00000558170.2	-	8	2212	c.1028G>A	c.(1027-1029)cGa>cAa	p.R343Q	ZEB2_ENST00000539609.3_Missense_Mutation_p.R319Q|ZEB2_ENST00000303660.4_Missense_Mutation_p.R343Q|ZEB2_ENST00000409487.3_Missense_Mutation_p.R343Q	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	343					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.R343Q(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GTTTCTCATTCGGCCATTTAC	0.413																																					Melanoma(33;1235 1264 5755 16332)											1	Substitution - Missense(1)	large_intestine(1)	2											57	57	57					2																	145157726		2203	4300	6503	144874196	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.1028G>A	2.37:g.145157726C>T	ENSP00000454157:p.Arg343Gln		144874196	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000892	0.74818	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	T;T;T;T;T	0.15834	2.4;2.39;2.39;2.57;2.57	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.40015	0.1100	L	0.49126	1.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.997;0.998	D;D;D;D	0.91635	0.999;0.987;0.968;0.992	T	0.08722	-1.0708	10	0.87932	D	0	-5.3533	19.7156	0.96119	0.0:1.0:0.0:0.0	.	319;208;342;343	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	Q	338;319;343;343;343;343	ENSP00000443792:R319Q;ENSP00000302501:R343Q;ENSP00000386854:R343Q;ENSP00000395496:R343Q;ENSP00000376601:R343Q	ENSP00000302501:R343Q	R	-	2	0	ZEB2	144874196	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.658000	0.90341	0.655000	0.94253	CGA		0.413	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		T	145157726	C	T	145157726	3	4	43	1	0	0	0	0	1	0	0	0	17663	884	31	1	2628	1	ZEB2	2	145157726	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	3798590	145157726	98041647	14	3936										
COBLL1	22837	broad.mit.edu	37	chr2	165555960	165555960	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cttcaagtttcttatactgtCaactaccttctttccattgc	3	12	4	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:165555960C>G	ENST00000392717.2	-	12	1745	c.1741G>C	c.(1741-1743)Gac>Cac	p.D581H	COBLL1_ENST00000194871.6_Missense_Mutation_p.D609H|COBLL1_ENST00000409184.3_Missense_Mutation_p.D542H|COBLL1_ENST00000342193.4_Missense_Mutation_p.D543H|COBLL1_ENST00000375458.2_Missense_Mutation_p.D504H|COBLL1_ENST00000491126.2_5'Flank			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	581						extracellular vesicular exosome (GO:0070062)		p.D543H(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CTTATACTGTCAACTACCTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											221	211	215					2																	165555960		2203	4300	6503	165264206	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1741G>C	2.37:g.165555960C>G	ENSP00000376478:p.Asp581His		165264206	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	C	14.05	2.419938	0.42918	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	4.83	3.96	0.45880	.	0.095320	0.45126	D	0.000392	T	0.47414	0.1444	L	0.29908	0.895	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.71656	0.947;0.947;0.974	T	0.27571	-1.0070	9	0.72032	D	0.01	-6.9244	8.2552	0.31751	0.0:0.7573:0.1563:0.0864	.	581;609;542	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	H	504;543;542;581;609	.	ENSP00000194871:D609H	D	-	1	0	COBLL1	165264206	0.895000	0.30542	0.018000	0.16275	0.001000	0.01503	2.111000	0.41883	1.160000	0.42584	-0.136000	0.14681	GAC		0.353	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		G	165555960	C	G	165555960	3	3	43	1	0	0	0	0	1	0	0	0	3660	826	29	5	1889	5	COBLL1	2	165555960	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	20398234	165555960	77643413	15	3937										
SCN9A	6335	broad.mit.edu	37	chr2	167163057	167163057	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtccggtgggttattcatggTcataaatatgcagtttgtca	11	6	3	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:167163057T>C	ENST00000409435.1	-	3	429	c.430A>G	c.(430-432)Acc>Gcc	p.T144A	SCN9A_ENST00000303354.6_Missense_Mutation_p.T145A|SCN9A_ENST00000409672.1_Missense_Mutation_p.T144A|SCN9A_ENST00000375387.4_Missense_Mutation_p.T145A			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	144					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.T144A(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTATTCATGGTCATAAATATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	83	83					2																	167163057		1935	4186	6121	166871303	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.430A>G	2.37:g.167163057T>C	ENSP00000386330:p.Thr144Ala		166871303	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	t	15.57	2.873121	0.51695	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.97232	-4.3;-4.3;-4.3;-4.3;-4.3;-4.3	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000004	D	0.96071	0.8720	L	0.45352	1.415	0.80722	D	1	P;B;B	0.35208	0.49;0.423;0.001	B;B;B	0.44044	0.209;0.439;0.006	D	0.95098	0.8228	10	0.29301	T	0.29	.	16.4447	0.83919	0.0:0.0:0.0:1.0	.	144;144;145	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	A	144;145;145;144;9;9	ENSP00000386306:T144A;ENSP00000364536:T145A;ENSP00000304748:T145A;ENSP00000386330:T144A;ENSP00000413212:T9A;ENSP00000393141:T9A	ENSP00000304748:T145A	T	-	1	0	SCN9A	166871303	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	8.040000	0.89188	2.284000	0.76573	0.528000	0.53228	ACC		0.363	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		C	167163057	T	C	167163057	3	2	43	1	0	0	0	0	1	0	0	0	13962	1667	58	4	5599	4	SCN9A	2	167163057	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	1607097	167163057	76036316	16	3938										
LRP2	4036	broad.mit.edu	37	chr2	170066101	170066101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tgagctgctaaaatcacaccAataaataaagccagaggaca	7	9	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:170066101A>G	ENST00000263816.3	-	38	6616	c.6331T>C	c.(6331-6333)Tgg>Cgg	p.W2111R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2111					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.W2111R(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AAATCACACCAATAAATAAAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	95	98					2																	170066101		2203	4300	6503	169774347	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.6331T>C	2.37:g.170066101A>G	ENSP00000263816:p.Trp2111Arg		169774347	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.551814	0.65311	.	.	ENSG00000081479	ENST00000263816	D	0.91843	-2.92	5.88	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.96636	0.8902	M	0.92691	3.335	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.96662	0.9490	10	0.87932	D	0	.	11.7462	0.51821	0.9313:0.0:0.0687:0.0	.	2111	P98164	LRP2_HUMAN	R	2111	ENSP00000263816:W2111R	ENSP00000263816:W2111R	W	-	1	0	LRP2	169774347	1.000000	0.71417	0.998000	0.56505	0.475000	0.33008	9.281000	0.95811	1.042000	0.40150	0.533000	0.62120	TGG		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170066101	A	G	170066101	3	3	43	1	0	0	0	0	1	0	0	0	8985	130	5	4	7804	4	LRP2	2	170066101	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	2903044	170066101	73133272	17	3939										
SMARCAL1	50485	broad.mit.edu	37	chr2	217279945	217279945	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tctggccaaaccaaagagttCccaagagacaccagctcatt	7	13	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:217279945C>A	ENST00000357276.4	+	3	848	c.518C>A	c.(517-519)tCc>tAc	p.S173Y	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.S173Y|AC098820.2_ENST00000457694.1_RNA	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	173					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.S173Y(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CCAAAGAGTTCCCAAGAGACA	0.507									Schimke Immuno-Osseous Dysplasia																																							1	Substitution - Missense(1)	large_intestine(1)	2											110	109	109					2																	217279945		2203	4300	6503	216988190	SO:0001583	missense	50485	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.518C>A	2.37:g.217279945C>A	ENSP00000349823:p.Ser173Tyr		216988190	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	9.989	1.230306	0.22542	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128	D;D;T;D	0.87491	-2.26;-2.26;1.21;-2.26	5.23	1.72	0.24424	.	0.823449	0.11058	N	0.604240	T	0.73606	0.3608	N	0.19112	0.55	0.09310	N	1	P	0.38582	0.638	B	0.34242	0.178	T	0.63695	-0.6579	10	0.52906	T	0.07	-0.4036	3.8125	0.08802	0.1558:0.5174:0.0:0.3268	.	173	Q9NZC9	SMAL1_HUMAN	Y	173;173;72;37	ENSP00000349823:S173Y;ENSP00000350940:S173Y;ENSP00000392997:S72Y;ENSP00000375974:S37Y	ENSP00000349823:S173Y	S	+	2	0	SMARCAL1	216988190	0.005000	0.15991	0.004000	0.12327	0.258000	0.26162	0.880000	0.28159	0.101000	0.17610	0.591000	0.81541	TCC		0.507	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			A	217279945	C	A	217279945	3	1	43	1	0	0	0	0	1	0	0	0	14810	855	30	2	520	2	SMARCAL1	2	217279945	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	47213844	217279945	25919428	18	3940										
SLC4A3	6508	broad.mit.edu	37	chr2	220497093	220497093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cgtggaggaggagacggagcGctgggggaagccccatgttg	20	8	0	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:220497093G>A	ENST00000358055.3	+	8	1582	c.1070G>A	c.(1069-1071)cGc>cAc	p.R357H	SLC4A3_ENST00000373762.3_Missense_Mutation_p.R384H|SLC4A3_ENST00000373760.2_Missense_Mutation_p.R357H|SLC4A3_ENST00000317151.3_Missense_Mutation_p.R357H|SLC4A3_ENST00000497589.1_3'UTR|SLC4A3_ENST00000273063.6_Missense_Mutation_p.R384H			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	357					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.R384H(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAGACGGAGCGCTGGGGGAAG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	57	57					2																	220497093		2203	4300	6503	220205337	SO:0001583	missense	6508				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1070G>A	2.37:g.220497093G>A	ENSP00000350756:p.Arg357His		220205337	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	G	35	5.442946	0.96187	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151;ENST00000413743	T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	3.96	3.96	0.45880	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	T	0.80369	0.4610	M	0.90252	3.1	0.80722	D	1	P;P	0.41710	0.76;0.717	P;B	0.45406	0.479;0.347	D	0.85973	0.1478	10	0.66056	D	0.02	.	16.546	0.84445	0.0:0.0:1.0:0.0	.	357;384	P48751;P48751-3	B3A3_HUMAN;.	H	357;357;384;384;357;159	ENSP00000350756:R357H;ENSP00000362865:R357H;ENSP00000273063:R384H;ENSP00000362867:R384H;ENSP00000314006:R357H;ENSP00000414722:R159H	ENSP00000273063:R384H	R	+	2	0	SLC4A3	220205337	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.601000	0.98297	2.185000	0.69588	0.561000	0.74099	CGC		0.667	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220497093	G	A	220497093	3	1	43	1	0	0	0	0	1	0	0	0	14692	1087	38	1	1177	1	SLC4A3	2	220497093	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	3217148	220497093	22702280	19	3941										
KIAA1486	57624	broad.mit.edu	37	chr2	226516187	226516187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	attaggccggtctgcgtcgaCgtcaggtgtgcctcctccat	12	13	2	0	rs568027472		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:226516187C>T	ENST00000272907.6	+	6	2281	c.1868C>T	c.(1867-1869)aCg>aTg	p.T623M		NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	623					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.T623M(1)									TCTGCGTCGACGTCAGGTGTG	0.498													C|||	1	0.000199681	8e-04	0	5008	,	,		19906	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											196	198	198					2																	226516187		2133	4253	6386	226224431	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1868C>T	2.37:g.226516187C>T	ENSP00000272907:p.Thr623Met		226224431	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.182407	0.57800	.	.	ENSG00000144460	ENST00000272907	T	0.34859	1.34	5.92	5.02	0.67125	.	9.088210	0.00682	N	0.000686	T	0.55337	0.1914	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.17684	-1.0361	10	0.87932	D	0	-0.0062	16.2369	0.82380	0.1338:0.8662:0.0:0.0	.	137;623	Q9P242-3;Q9P242	.;K1486_HUMAN	M	623	ENSP00000272907:T623M	ENSP00000272907:T623M	T	+	2	0	KIAA1486	226224431	1.000000	0.71417	0.944000	0.38274	0.805000	0.45488	5.677000	0.68142	1.448000	0.47680	0.557000	0.71058	ACG		0.498	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226516187	C	T	226516187	3	4	43	1	0	0	0	0	1	0	0	0	8258	536	19	1	1886	1	KIAA1486	2	226516187	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	6019094	226516187	16683186	20	3942										
GIGYF2	26058	broad.mit.edu	37	chr2	233671231	233671231	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	taatcaggagatggcagaatGgtttcaggcgggctatttta	13	5	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr2:233671231G>A	ENST00000409547.1	+	17	1981	c.1670G>A	c.(1669-1671)tGg>tAg	p.W557*	GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.W579*|GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.W579*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.W578*|GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.W557*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.W551*|GIGYF2_ENST00000452341.2_Nonsense_Mutation_p.W388*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	557	GYF. {ECO:0000255|PROSITE- ProRule:PRU00101}.|Required for GRB10-binding. {ECO:0000250}.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.W557*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		ATGGCAGAATGGTTTCAGGCG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											187	183	185					2																	233671231		2203	4300	6503	233379475	SO:0001587	stop_gained	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1670G>A	2.37:g.233671231G>A	ENSP00000386537:p.Trp557*		233379475	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	41	8.991942	0.99029	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.9441	20.1551	0.98106	0.0:0.0:1.0:0.0	.	.	.	.	X	579;500;557;579;557;557;500;551;578;551;388	.	ENSP00000362664:W557X	W	+	2	0	GIGYF2	233379475	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.807000	0.99171	2.760000	0.94817	0.655000	0.94253	TGG		0.388	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233671231	G	A	233671231	4	1	43	1	0	0	0	0	0	1	0	0	6398	1357	47	3	1790	3	GIGYF2	2	233671231	Nonsense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	7155044	233671231	9528142	21	3943										
C3orf20	84077	broad.mit.edu	37	chr3	14724602	14724602	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccaccatggcccgtcaggtgCgcacccaccaggagaccctg	11	18	1	1	rs370846039		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:14724602C>T	ENST00000253697.3	+	3	834	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	C3orf20_ENST00000435614.1_Missense_Mutation_p.R6C|C3orf20_ENST00000412910.1_Missense_Mutation_p.R6C	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	128						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R128C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCGTCAGGTGCGCACCCACCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	56	54	55		16,16,382	-2.5	0	3		55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	6/783,6/783,128/905	14724602	1,13005	2203	4300	6503	14699606	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.382C>T	3.37:g.14724602C>T	ENSP00000253697:p.Arg128Cys		14699606	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.128011	0.37533	0.0	1.16E-4	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08896	3.35;3.04;3.04	4.87	-2.48	0.06423	.	0.744664	0.11535	N	0.554290	T	0.03305	0.0096	N	0.08118	0	0.09310	N	1	P	0.45044	0.849	B	0.41723	0.365	T	0.31916	-0.9926	10	0.66056	D	0.02	-0.3814	0.4093	0.00438	0.279:0.2487:0.1263:0.3459	.	128	Q8ND61	CC020_HUMAN	C	128;6;6	ENSP00000253697:R128C;ENSP00000402933:R6C;ENSP00000396081:R6C	ENSP00000253697:R128C	R	+	1	0	C3orf20	14699606	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.103000	0.03329	-0.168000	0.10853	0.467000	0.42956	CGC		0.617	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14724602	C	T	14724602	3	4	43	1	0	0	0	0	1	0	0	0	2219	768	27	1	384	1	C3orf20	3	14724602	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		14724602	183297828	22	3944										
GALNTL2	117248	broad.mit.edu	37	chr3	16216964	16216964	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctggtggccgtggccttaccCcaggccagaaggaaccagag	14	13	0	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:16216964C>T	ENST00000339732.5	+	1	809	c.306C>T	c.(304-306)ccC>ccT	p.P102P	GALNT15_ENST00000437509.1_Silent_p.P102P|GALNT15_ENST00000470031.1_3'UTR	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	102					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.P102P(1)									TGGCCTTACCCCAGGCCAGAA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	3											38	40	39					3																	16216964		2203	4300	6503	16191968	SO:0001819	synonymous_variant	117248			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.306C>T	3.37:g.16216964C>T			16191968	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Silent	SNP	ENST00000339732.5	37	CCDS33711.1																																																																																				0.617	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		T	16216964	C	T	16216964	2	4	43	1	0	0	0	0	0	0	0	1	6242	610	22	3		3	GALNTL2	3	16216964	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	1492362	16216964	181805466	23	3945										
XIRP1	165904	broad.mit.edu	37	chr3	39229333	39229333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cttcctgccgggtgatgcccCgcaccacgtcgatggtactg	12	15	0	1	rs370513707		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:39229333C>T	ENST00000340369.3	-	2	1832	c.1604G>A	c.(1603-1605)cGg>cAg	p.R535Q	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.R535Q	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	535	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.R535Q(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGTGATGCCCCGCACCACGTC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	64	61	62		1604,1604	4.3	1	3		62	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	535/1122,535/1844	39229333	1,13005	2203	4300	6503	39204337	SO:0001583	missense	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1604G>A	3.37:g.39229333C>T	ENSP00000343140:p.Arg535Gln		39204337	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.007634	0.54361	0.0	1.16E-4	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.06768	3.26;3.63	5.17	4.3	0.51218	.	0.063724	0.64402	D	0.000009	T	0.08935	0.0221	M	0.66297	2.02	0.80722	D	1	P;P	0.42039	0.74;0.769	B;B	0.27608	0.075;0.081	T	0.08166	-1.0735	10	0.72032	D	0.01	.	11.6304	0.51171	0.0:0.913:0.0:0.087	.	535;535	Q702N8;Q702N8-2	XIRP1_HUMAN;.	Q	535	ENSP00000379550:R535Q;ENSP00000343140:R535Q	ENSP00000343140:R535Q	R	-	2	0	XIRP1	39204337	0.998000	0.40836	0.991000	0.47740	0.982000	0.71751	2.393000	0.44442	1.325000	0.45301	0.655000	0.94253	CGG		0.622	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39229333	C	T	39229333	3	4	43	1	0	0	0	0	1	0	0	0	17469	652	23	1	3931	1	XIRP1	3	39229333	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	23012369	39229333	158793097	24	3946										
NSUN3	63899	broad.mit.edu	37	chr3	93802973	93802973	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agatactaacatctccatcaTgctggcaatatgctgtcctg	7	11	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:93802973T>G	ENST00000314622.4	+	3	356	c.145T>G	c.(145-147)Tgc>Ggc	p.C49G		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	49							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.C49G(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						ATCTCCATCATGCTGGCAATA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											46	46	46					3																	93802973		2203	4300	6503	95285663	SO:0001583	missense	63899			BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"NOP2/Sun domain containing"	26208	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 3", "NOL1/NOP2/Sun domain family, member 3"			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.145T>G	3.37:g.93802973T>G	ENSP00000318986:p.Cys49Gly		95285663	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	37	CCDS2927.1	.	.	.	.	.	.	.	.	.	.	T	9.827	1.187291	0.21870	.	.	ENSG00000178694	ENST00000314622	T	0.21734	1.99	5.81	3.39	0.38822	.	0.290828	0.39985	N	0.001210	T	0.14056	0.0340	L	0.39898	1.24	0.09310	N	0.999995	B	0.20671	0.047	B	0.16722	0.016	T	0.32561	-0.9902	10	0.15066	T	0.55	-0.0942	6.5114	0.22224	0.0:0.0853:0.2912:0.6235	.	49	Q9H649	NSUN3_HUMAN	G	49	ENSP00000318986:C49G	ENSP00000318986:C49G	C	+	1	0	NSUN3	95285663	0.977000	0.34250	0.071000	0.20095	0.688000	0.40055	1.984000	0.40658	0.434000	0.26340	0.533000	0.62120	TGC		0.338	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072		G	93802973	T	G	93802973	3	3	43	1	0	0	0	0	1	0	0	0	10710	1464	51	4	155	4	NSUN3	3	93802973	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	54573640	93802973	104219457	25	3947										
OR5H2	79310	broad.mit.edu	37	chr3	98002174	98002174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gaacaattcactatgcatacGgctgttagccttctcatttt	6	10	2	0	rs149368502		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:98002174G>A	ENST00000355273.2	+	1	443	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R148Q(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						CTATGCATACGGCTGTTAGCC	0.363													G|||	1	0.000199681	8e-04	0	5008	,	,		20735	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	111	101	104		443	-2	0	3	dbSNP_134	104	0,8600		0,0,4300	no	missense	OR5H2	NM_001005482.1	43	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	148/315	98002174	3,13003	2203	4300	6503	99484864	SO:0001583	missense	79310				CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.443G>A	3.37:g.98002174G>A	ENSP00000347418:p.Arg148Gln		99484864	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.613815	0.00835	6.81E-4	0.0	ENSG00000197938	ENST00000355273	T	0.00076	8.76	3.03	-2.05	0.07321	GPCR, rhodopsin-like superfamily (1);	0.989423	0.08190	N	0.984084	T	0.00039	0.0001	N	0.01284	-0.91	0.09310	N	1	B	0.24483	0.104	B	0.19391	0.025	T	0.00512	-1.1696	10	0.15499	T	0.54	.	8.2254	0.31566	0.5652:0.0:0.4348:0.0	.	148	Q8NGV7	OR5H2_HUMAN	Q	148	ENSP00000347418:R148Q	ENSP00000347418:R148Q	R	+	2	0	OR5H2	99484864	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.155000	0.00284	-0.441000	0.07201	-0.474000	0.04947	CGG		0.363	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			A	98002174	G	A	98002174	3	1	43	1	0	0	0	0	1	0	0	0	11193	1116	39	1	445	1	OR5H2	3	98002174	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	4199201	98002174	100020256	26	3948										
SLC15A2	6565	broad.mit.edu	37	chr3	121634083	121634083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtttgtttcaggcagaggaaCggactagatacttctcagtc	11	8	2	2	rs371451053		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:121634083C>T	ENST00000489711.1	+	6	926	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	SLC15A2_ENST00000295605.2_Missense_Mutation_p.R149W	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	180					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)	p.R180W(1)		NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GGCAGAGGAACGGACTAGATA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	177	154	162		445,538	3.5	1	3		162	0,8600		0,0,4300	no	missense,missense	SLC15A2	NM_001145998.1,NM_021082.3	101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	149/699,180/730	121634083	1,13005	2203	4300	6503	123116773	SO:0001583	missense	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.538C>T	3.37:g.121634083C>T	ENSP00000417085:p.Arg180Trp		123116773	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.151922	0.38021	2.27E-4	0.0	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605;ENST00000469013	T;T;T	0.70282	-0.47;-0.47;-0.47	5.41	3.49	0.39957	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.83792	0.5331	M	0.89095	3.005	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.993	D	0.84877	0.0828	10	0.66056	D	0.02	-15.5201	8.4495	0.32862	0.1623:0.7517:0.0:0.086	.	149;180	B4E2A7;Q16348	.;S15A2_HUMAN	W	180;142;149;118	ENSP00000417085:R180W;ENSP00000295605:R149W;ENSP00000418704:R118W	ENSP00000295605:R149W	R	+	1	2	SLC15A2	123116773	1.000000	0.71417	1.000000	0.80357	0.186000	0.23388	1.812000	0.38952	1.526000	0.49068	-0.229000	0.12294	CGG		0.458	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		T	121634083	C	T	121634083	3	4	43	1	0	0	0	0	1	0	0	0	14436	527	19	1	560	1	SLC15A2	3	121634083	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	23631909	121634083	76388347	27	3949										
CEP70	80321	broad.mit.edu	37	chr3	138216928	138216928	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aatgctgggaaaaattcctcGtgttcttccaatttgtagat	8	7	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:138216928G>A	ENST00000264982.3	-	17	1943	c.1677C>T	c.(1675-1677)caC>caT	p.H559H	CEP70_ENST00000542237.1_Silent_p.H539H|CEP70_ENST00000489254.1_Silent_p.H407H|CEP70_ENST00000484888.1_Silent_p.H559H	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	559					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.H559H(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						AAAATTCCTCGTGTTCTTCCA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	3											110	105	107					3																	138216928		2203	4300	6503	139699618	SO:0001819	synonymous_variant	80321			AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1677C>T	3.37:g.138216928G>A			139699618	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Silent	SNP	ENST00000264982.3	37	CCDS3102.1																																																																																				0.333	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		A	138216928	G	A	138216928	2	1	43	1	0	0	0	0	0	0	0	1	3265	1136	40	1		1	CEP70	3	138216928	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	16582845	138216928	59805502	28	3950										
MAP3K13	9175	broad.mit.edu	37	chr3	185183578	185183578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	actatgagcggaagcttgagCgggcgaataatttatacatg	12	6	0	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr3:185183578C>T	ENST00000265026.3	+	9	1766	c.1432C>T	c.(1432-1434)Cgg>Tgg	p.R478W	MAP3K13_ENST00000443863.1_Missense_Mutation_p.R334W|MAP3K13_ENST00000446828.1_Missense_Mutation_p.R271W|MAP3K13_ENST00000424227.1_Missense_Mutation_p.R478W|MAP3K13_ENST00000535426.1_Missense_Mutation_p.R334W	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.R478W(2)|p.R478R(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GAAGCTTGAGCGGGCGAATAA	0.478																																																3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(3)	3											139	143	142					3																	185183578		2203	4300	6503	186666272	SO:0001583	missense	9175			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.1432C>T	3.37:g.185183578C>T	ENSP00000265026:p.Arg478Trp		186666272		Missense_Mutation	SNP	ENST00000265026.3	37	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.873817	0.72180	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026;ENST00000420577	T;T;T;T;T;T	0.80566	-1.39;-1.35;-1.25;-1.25;-1.35;-1.05	4.97	2.95	0.34219	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	D	0.83243	0.5212	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.996;0.997	D	0.84993	0.0895	10	0.72032	D	0.01	.	13.4974	0.61434	0.3171:0.6829:0.0:0.0	.	334;271;478	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	W	271;478;334;334;478;223	ENSP00000411483:R271W;ENSP00000399910:R478W;ENSP00000409325:R334W;ENSP00000439257:R334W;ENSP00000265026:R478W;ENSP00000415712:R223W	ENSP00000265026:R478W	R	+	1	2	MAP3K13	186666272	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.491000	0.22419	2.309000	0.77851	0.655000	0.94253	CGG		0.478	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		T	185183578	C	T	185183578	3	4	43	1	0	0	0	0	1	0	0	0	9277	759	27	1	1462	1	MAP3K13	3	185183578	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	46966650	185183578	12838852	29	3951										
ENPEP	2028	broad.mit.edu	37	chr4	111469392	111469392	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aagtatctcaaaagggaagaGaattttttaccatggcagag	10	5	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr4:111469392G>T	ENST00000265162.5	+	14	2403	c.2061G>T	c.(2059-2061)gaG>gaT	p.E687D		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	687					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E687D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		AAAGGGAAGAGAATTTTTTAC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											86	90	89					4																	111469392		2202	4300	6502	111688841	SO:0001583	missense	2028			L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.2061G>T	4.37:g.111469392G>T	ENSP00000265162:p.Glu687Asp		111688841	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	3.055	-0.194448	0.06259	.	.	ENSG00000138792	ENST00000265162	T	0.04758	3.56	5.65	-1.77	0.07982	.	0.823917	0.11230	N	0.585730	T	0.02455	0.0075	N	0.21545	0.675	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.48281	-0.9049	10	0.13470	T	0.59	.	2.1527	0.03804	0.5107:0.112:0.163:0.2144	.	687	Q07075	AMPE_HUMAN	D	687	ENSP00000265162:E687D	ENSP00000265162:E687D	E	+	3	2	ENPEP	111688841	0.000000	0.05858	0.000000	0.03702	0.299000	0.27559	-0.297000	0.08276	0.042000	0.15717	0.655000	0.94253	GAG		0.323	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			T	111469392	G	T	111469392	3	4	43	1	0	0	0	0	1	0	0	0	5141	933	33	2	2115	2	ENPEP	4	111469392	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		111469392	79684884	30	3952										
FAT4	79633	broad.mit.edu	37	chr4	126398366	126398366	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aggtatcagatctctagaacCaatccttcagagaagaggac	9	9	3	4			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr4:126398366C>A	ENST00000394329.3	+	13	12363	c.12350C>A	c.(12349-12351)cCa>cAa	p.P4117Q	FAT4_ENST00000335110.5_Missense_Mutation_p.P2380Q	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4117	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P4117Q(2)|p.P4082Q(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCTCTAGAACCAATCCTTCAG	0.393																																																4	Substitution - Missense(4)	cervix(2)|large_intestine(2)	4											167	172	170					4																	126398366		2203	4300	6503	126617816	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12350C>A	4.37:g.126398366C>A	ENSP00000377862:p.Pro4117Gln		126617816	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	17.15	3.316718	0.60524	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.76968	-1.06;-1.06	5.6	5.6	0.85130	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.34314	U	0.004068	D	0.85323	0.5670	L	0.60067	1.865	0.58432	D	0.999997	D;D;P	0.55385	0.971;0.967;0.9	P;P;P	0.60012	0.718;0.867;0.718	D	0.85287	0.1065	10	0.54805	T	0.06	.	19.6182	0.95643	0.0:1.0:0.0:0.0	.	2380;4117;4117	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	Q	4117;2380	ENSP00000377862:P4117Q;ENSP00000335169:P2380Q	ENSP00000335169:P2380Q	P	+	2	0	FAT4	126617816	1.000000	0.71417	0.142000	0.22268	0.122000	0.20287	5.614000	0.67695	2.626000	0.88956	0.650000	0.86243	CCA		0.393	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126398366	C	A	126398366	3	1	43	1	0	0	0	0	1	0	0	0	5711	594	21	2	12400	2	FAT4	4	126398366	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	14928974	126398366	64755910	31	3953										
DCLK2	166614	broad.mit.edu	37	chr4	151119175	151119175	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atgtcgtgtcctgaagtcatCttattctcgatcctcagctg	8	11	4	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr4:151119175C>G	ENST00000296550.7	+	4	1635	c.881C>G	c.(880-882)tCt>tGt	p.S294C	DCLK2_ENST00000506325.1_Missense_Mutation_p.S294C|DCLK2_ENST00000507694.1_3'UTR|DCLK2_ENST00000302176.8_Missense_Mutation_p.S294C	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	294	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S294C(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					CTGAAGTCATCTTATTCTCGA	0.398																																					GBM(195;186 2215 13375 16801 37459)											2	Substitution - Missense(2)	large_intestine(2)	4											123	117	119					4																	151119175		2203	4300	6503	151338625	SO:0001583	missense	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"doublecortin and CaM kinase-like 2"	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.881C>G	4.37:g.151119175C>G	ENSP00000296550:p.Ser294Cys		151338625	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265673	0.80358	.	.	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.69435	-0.38;-0.38;-0.4	5.52	4.67	0.58626	Doublecortin domain (1);	0.059906	0.64402	D	0.000002	T	0.76407	0.3983	M	0.66939	2.045	0.46011	D	0.99881	P;D;P	0.65815	0.941;0.995;0.943	P;P;P	0.58970	0.849;0.847;0.711	T	0.76484	-0.2942	10	0.39692	T	0.17	.	14.6743	0.68967	0.1466:0.8534:0.0:0.0	.	294;294;294	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	C	294	ENSP00000296550:S294C;ENSP00000427235:S294C;ENSP00000303887:S294C	ENSP00000296550:S294C	S	+	2	0	DCLK2	151338625	0.984000	0.35163	0.996000	0.52242	0.995000	0.86356	4.752000	0.62176	1.316000	0.45131	0.643000	0.83706	TCT		0.398	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260		G	151119175	C	G	151119175	3	3	43	1	0	0	0	0	1	0	0	0	4298	913	32	5	895	5	DCLK2	4	151119175	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	24720809	151119175	40035101	32	3954										
SFRP2	6423	broad.mit.edu	37	chr4	154702786	154702786	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctgtctttgagccacagcacCgatttcttcaggtccctttc	7	14	3	1	rs143701440		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr4:154702786C>T	ENST00000274063.4	-	3	989	c.705G>A	c.(703-705)tcG>tcA	p.S235S		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	235	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S235S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				GCCACAGCACCGATTTCTTCA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	4						C		2,4404	4.2+/-10.8	0,2,2201	214	174	188		705	-8.1	0.7	4	dbSNP_134	188	0,8600		0,0,4300	no	coding-synonymous	SFRP2	NM_003013.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		235/296	154702786	2,13004	2203	4300	6503	154922236	SO:0001819	synonymous_variant	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.705G>A	4.37:g.154702786C>T			154922236	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1																																																																																				0.512	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			T	154702786	C	T	154702786	2	4	43	1	0	0	0	0	0	0	0	1	14199	639	23	1		1	SFRP2	4	154702786	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	3583611	154702786	36451490	33	3955										
DCHS2	54798	broad.mit.edu	37	chr4	155156339	155156339	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tggctggcttctgctgtttcGgcagtcaccatcacatcagt	10	12	4	0	rs568618708	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr4:155156339G>A	ENST00000357232.4	-	25	8099	c.8100C>T	c.(8098-8100)gcC>gcT	p.A2700A		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2700					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A2700A(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGCTGTTTCGGCAGTCACCA	0.547													G|||	7	0.00139776	8e-04	0	5008	,	,		18801	0		0	False		,,,				2504	0.0061															1	Substitution - coding silent(1)	large_intestine(1)	4											86	75	79					4																	155156339		2203	4300	6503	155375789	SO:0001819	synonymous_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8100C>T	4.37:g.155156339G>A			155375789	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.547	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156339	G	A	155156339	2	1	43	1	0	0	0	0	0	0	0	1	4294	1103	39	1		1	DCHS2	4	155156339	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	453553	155156339	35997937	34	3956										
CDH10	1008	broad.mit.edu	37	chr5	24537631	24537631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cttctgttaatagcttgtgcGcgtagagtataaaaggcctt	10	7	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:24537631G>A	ENST00000264463.4	-	3	891	c.384C>T	c.(382-384)cgC>cgT	p.R128R		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	128	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R128R(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TAGCTTGTGCGCGTAGAGTAT	0.413										HNSCC(23;0.051)																																						1	Substitution - coding silent(1)	large_intestine(1)	5											158	146	150					5																	24537631		2203	4300	6503	24573388	SO:0001819	synonymous_variant	1008			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.384C>T	5.37:g.24537631G>A			24573388	Q9ULB3	Silent	SNP	ENST00000264463.4	37	CCDS3892.1																																																																																				0.413	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		A	24537631	G	A	24537631	2	1	43	1	0	0	0	0	0	0	0	1	3102	1074	38	1		1	CDH10	5	24537631	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10		24537631	156377629	35	3957										
NUP155	9631	broad.mit.edu	37	chr5	37307497	37307497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ggatcttttttctctgcagcCgtaagagaaagttccaccac	8	11	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:37307497C>T	ENST00000231498.3	-	25	3008	c.2805G>A	c.(2803-2805)acG>acA	p.T935T	NUP155_ENST00000513532.1_Silent_p.T871T|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Silent_p.T876T	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	935					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.T935T(1)		endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCTCTGCAGCCGTAAGAGAAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	5											94	87	90					5																	37307497		2203	4300	6503	37343254	SO:0001819	synonymous_variant	9631			AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.2805G>A	5.37:g.37307497C>T			37343254	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																				0.398	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		T	37307497	C	T	37307497	2	4	43	1	0	0	0	0	0	0	0	1	10787	639	23	1		1	NUP155	5	37307497	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	12769866	37307497	143607763	36	3958										
VCAN	1462	broad.mit.edu	37	chr5	82834175	82834175	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	caccaacacagtctgaaaggGaaatgacagattctactcct	7	11	2	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:82834175G>T	ENST00000265077.3	+	8	5918	c.5353G>T	c.(5353-5355)Gaa>Taa	p.E1785*	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Nonsense_Mutation_p.E798*|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1785	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.E1785*(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	GTCTGAAAGGGAAATGACAGA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											60	64	63					5																	82834175		2203	4299	6502	82869931	SO:0001587	stop_gained	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5353G>T	5.37:g.82834175G>T	ENSP00000265077:p.Glu1785*		82869931	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	47	13.586169	0.99751	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	.	.	.	5.7	3.86	0.44501	.	0.295688	0.29438	N	0.012144	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	5.2013	0.15267	0.1717:0.0:0.6554:0.1729	.	.	.	.	X	1785;798;798	.	ENSP00000265077:E1785X	E	+	1	0	VCAN	82869931	0.207000	0.23482	0.005000	0.12908	0.064000	0.16182	1.172000	0.31908	1.362000	0.46000	0.655000	0.94253	GAA		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82834175	G	T	82834175	4	4	43	1	0	0	0	0	0	1	0	0	17178	1175	41	2	5379	2	VCAN	5	82834175	Nonsense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	45526678	82834175	98081085	37	3959										
APC	324	broad.mit.edu	37	chr5	112151204	112151204	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atttttagggttcaactacaCgaatggaccatgaaacagcc	8	9	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:112151204C>T	ENST00000457016.1	+	9	1227	c.847C>T	c.(847-849)Cga>Tga	p.R283*	APC_ENST00000257430.4_Nonsense_Mutation_p.R283*|APC_ENST00000508376.2_Nonsense_Mutation_p.R283*			P25054	APC_HUMAN	adenomatous polyposis coli	283	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R283*(11)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCAACTACACGAATGGACCA	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	11	Substitution - Nonsense(11)	large_intestine(11)	5	GRCh37	CM920030	APC	M							108	98	102					5																	112151204		2202	4300	6502	112179103	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.847C>T	5.37:g.112151204C>T	ENSP00000413133:p.Arg283*		112179103	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381748	0.98786	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	4.22	0.49857	.	0.134048	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.044	12.9775	0.58546	0.2942:0.7058:0.0:0.0	.	.	.	.	X	283;265;283;283;283	.	ENSP00000257430:R283X	R	+	1	2	APC	112179103	1.000000	0.71417	0.953000	0.39169	0.976000	0.68499	5.216000	0.65246	1.244000	0.43870	0.650000	0.86243	CGA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112151204	C	T	112151204	4	4	43	1	0	0	0	0	0	1	0	0	763	528	19	1	877	1	APC	5	112151204	Nonsense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	29317029	112151204	68764056	38	3960										
AQPEP	206338	broad.mit.edu	37	chr5	115298789	115298789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	actgcgagcgcgccgaggtgCggggacccctttccccgggc	16	16	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:115298789C>T	ENST00000357872.4	+	1	599	c.475C>T	c.(475-477)Cgg>Tgg	p.R159W	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		159						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R159W(1)									CGCCGAGGTGCGGGGACCCCT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	5											27	30	29					5																	115298789		2201	4299	6500	115326688	SO:0001583	missense	206338																														ENST00000357872.4:c.475C>T	5.37:g.115298789C>T	ENSP00000350541:p.Arg159Trp		115326688	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	13.70	2.315203	0.40996	.	.	ENSG00000172901	ENST00000357872	T	0.02944	4.1	4.77	2.93	0.34026	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.292930	0.05810	N	0.613772	T	0.02970	0.0088	L	0.28694	0.88	0.43047	D	0.994649	B	0.26081	0.141	B	0.22880	0.042	T	0.35549	-0.9784	10	0.36615	T	0.2	.	5.2309	0.15422	0.2033:0.6879:0.0:0.1088	.	159	Q6Q4G3	AMPQ_HUMAN	W	159	ENSP00000350541:R159W	ENSP00000350541:R159W	R	+	1	2	AC010282.1	115326688	0.618000	0.27051	0.719000	0.30619	0.927000	0.56198	0.799000	0.27028	0.398000	0.25338	0.650000	0.86243	CGG		0.677	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115298789	C	T	115298789	3	4	43	1	0	0	0	0	1	0	0	0	834	759	27	1	477	1	AQPEP	5	115298789	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	3147585	115298789	65616471	39	3961										
PCDHB7	56129	broad.mit.edu	37	chr5	140552510	140552510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gggctggcgccgaaccgcttCggtattttgtggcggaggaa	17	9	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr5:140552510C>T	ENST00000231137.3	+	1	268	c.94C>T	c.(94-96)Cgg>Tgg	p.R32W		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	32					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R32W(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAACCGCTTCGGTATTTTGT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	5											149	136	140					5																	140552510		2203	4300	6503	140532694	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.94C>T	5.37:g.140552510C>T	ENSP00000231137:p.Arg32Trp		140532694	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.970935	0.34754	.	.	ENSG00000113212	ENST00000231137	T	0.33216	1.42	4.79	1.86	0.25419	Cadherin, N-terminal (1);	.	.	.	.	T	0.47581	0.1453	H	0.95328	3.655	0.09310	N	1	B	0.22604	0.072	B	0.24848	0.056	T	0.50206	-0.8855	9	0.72032	D	0.01	.	10.9176	0.47146	0.1372:0.5982:0.2646:0.0	.	32	Q9Y5E2	PCDB7_HUMAN	W	32	ENSP00000231137:R32W	ENSP00000231137:R32W	R	+	1	2	PCDHB7	140532694	0.000000	0.05858	0.427000	0.26684	0.654000	0.38779	1.016000	0.29976	0.134000	0.18681	-0.181000	0.13052	CGG		0.522	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		T	140552510	C	T	140552510	3	4	43	1	0	0	0	0	1	0	0	0	11578	875	31	1	96	1	PCDHB7	5	140552510	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	25253721	140552510	40362750	40	3962										
HIST1H2AG	8969	broad.mit.edu	37	chr6	27100950	27100950	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccgtgggccgagtgcaccgcCtgctccgcaaaggcaactat	12	15	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:27100950C>T	ENST00000359193.2	+	1	119	c.100C>T	c.(100-102)Ctg>Ttg	p.L34L	HIST1H2BJ_ENST00000339812.2_5'Flank|HIST1H2BJ_ENST00000607124.1_5'Flank|HIST1H2BJ_ENST00000541790.1_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	34						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.L34L(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	17						AGTGCACCGCCTGCTCCGCAA	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	6											32	37	35					6																	27100950		2203	4300	6503	27208929	SO:0001819	synonymous_variant	8969			L19778	CCDS4619.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196787	ENSG00000196787		"Histones / Replication-dependent"	4737	protein-coding gene	gene with protein product		615012	"H2A histone family, member P", "histone 1, H2ag"	H2AFP		8179821, 12408966	Standard	NM_021064		Approved	pH2A/f, H2A/p, H2A.1b	uc003niw.3	P0C0S8	OTTHUMG00000014469	ENST00000359193.2:c.100C>T	6.37:g.27100950C>T			27208929	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000359193.2	37	CCDS4619.1																																																																																				0.667	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		T	27100950	C	T	27100950	2	4	43	1	0	0	0	0	0	0	0	1	7154	680	24	3		3	HIST1H2AG	6	27100950	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10		27100950	144014117	41	3963										
CPNE5	57699	broad.mit.edu	37	chr6	36714185	36714185	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccacctaccagtgggaactcGtgggacactctgccatccgg	11	15	1	0	rs137962210	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:36714185G>A	ENST00000244751.2	-	16	1812	c.1188C>T	c.(1186-1188)caC>caT	p.H396H	CPNE5_ENST00000459703.1_5'UTR|CPNE5_ENST00000393189.2_Silent_p.H104H	NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	396	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.H396H(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						GTGGGAACTCGTGGGACACTC	0.632													G|||	13	0.00259585	0.0098	0	5008	,	,		15828	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						G		24,4382	31.7+/-61.6	0,24,2179	86	77	80		1188	-7.1	0.6	6	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	CPNE5	NM_020939.1		0,24,6479	AA,AG,GG		0.0,0.5447,0.1845		396/594	36714185	24,12982	2203	4300	6503	36822163	SO:0001819	synonymous_variant	57699			H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.1188C>T	6.37:g.36714185G>A			36822163	Q7Z6C8	Silent	SNP	ENST00000244751.2	37	CCDS4825.1																																																																																				0.632	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		A	36714185	G	A	36714185	2	1	43	1	0	0	0	0	0	0	0	1	3821	1136	40	1		1	CPNE5	6	36714185	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	9613235	36714185	134400882	42	3964										
KIF6	221458	broad.mit.edu	37	chr6	39328285	39328285	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tccaccttcagggctttcagGcgagtgaacattgttttata	9	9	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:39328285G>A	ENST00000287152.7	-	18	2062	c.1968C>T	c.(1966-1968)cgC>cgT	p.R656R	KIF6_ENST00000541946.1_Silent_p.R107R|KIF6_ENST00000373215.3_Silent_p.R639R|KIF6_ENST00000229913.5_Silent_p.R107R|KIF6_ENST00000394362.1_Silent_p.R107R|KIF6_ENST00000538893.1_Silent_p.R600R|KIF6_ENST00000373216.3_Silent_p.R656R|KIF6_ENST00000373213.4_Silent_p.R495R	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	656					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R656R(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GGGCTTTCAGGCGAGTGAACA	0.527																																																2	Substitution - coding silent(2)	large_intestine(2)	6											96	85	88					6																	39328285		2203	4300	6503	39436263	SO:0001819	synonymous_variant	221458			AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1968C>T	6.37:g.39328285G>A			39436263	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Silent	SNP	ENST00000287152.7	37	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308339	0.23821	.	.	ENSG00000164627	ENST00000458470	.	.	.	4.47	2.63	0.31362	.	.	.	.	.	T	0.47135	0.1429	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43972	-0.9358	4	.	.	.	.	10.617	0.45456	0.1707:0.0:0.8293:0.0	.	.	.	.	V	548	.	.	A	-	2	0	KIF6	39436263	1.000000	0.71417	0.826000	0.32828	0.983000	0.72400	2.512000	0.45485	1.014000	0.39417	0.462000	0.41574	GCC		0.527	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		A	39328285	G	A	39328285	2	1	43	1	0	0	0	0	0	0	0	1	8329	1190	42	3		3	KIF6	6	39328285	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	2614100	39328285	131786782	43	3965										
SLC22A7	10864	broad.mit.edu	37	chr6	43271893	43271893	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aagcttacttatggggggatCgccctgctggctgccggcac	14	12	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:43271893C>T	ENST00000372585.5	+	10	1598	c.1503C>T	c.(1501-1503)atC>atT	p.I501I	SLC22A7_ENST00000372589.3_Silent_p.I499I|SLC22A7_ENST00000372574.3_Silent_p.I499I|ZNF318_ENST00000607252.1_5'Flank	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	501					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.I501I(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	ATGGGGGGATCGCCCTGCTGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	6											62	71	68					6																	43271893		2203	4299	6502	43379871	SO:0001819	synonymous_variant	10864			AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.1503C>T	6.37:g.43271893C>T			43379871	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	37	CCDS4893.2																																																																																				0.652	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			T	43271893	C	T	43271893	2	4	43	1	0	0	0	0	0	0	0	1	14496	874	31	1		1	SLC22A7	6	43271893	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	3943608	43271893	127843174	44	3966										
HMGCLL1	54511	broad.mit.edu	37	chr6	55443836	55443836	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctgaggcagtgcttcaccgcGgatggcacattccccatggc	12	14	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:55443836G>A	ENST00000398661.2	-	1	149	c.18C>T	c.(16-18)tcC>tcT	p.S6S	HMGCLL1_ENST00000370850.2_Silent_p.S6S|HMGCLL1_ENST00000274901.4_Silent_p.S6S|HMGCLL1_ENST00000508459.1_Silent_p.S6S|HMGCLL1_ENST00000358072.5_Silent_p.S6S|HMGCLL1_ENST00000308161.4_Silent_p.S6S|HMGCLL1_ENST00000428842.1_Silent_p.S6S	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	6					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.S6S(2)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			GCTTCACCGCGGATGGCACAT	0.687																																					Ovarian(35;840 893 7837 15538 42887)											2	Substitution - coding silent(2)	large_intestine(2)	6											21	23	23					6																	55443836		1993	4146	6139	55551795	SO:0001819	synonymous_variant	54511			AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.18C>T	6.37:g.55443836G>A			55551795	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Silent	SNP	ENST00000398661.2	37	CCDS43475.1																																																																																				0.687	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383		A	55443836	G	A	55443836	2	1	43	1	0	0	0	0	0	0	0	1	7251	1103	39	1		1	HMGCLL1	6	55443836	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	12171943	55443836	115671231	45	3967										
KCNQ5	56479	broad.mit.edu	37	chr6	73787159	73787159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	acagatcctccgcatggtgcGcatggaccgaaggggaggca	15	11	0	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:73787159G>A	ENST00000370398.1	+	4	840	c.731G>A	c.(730-732)cGc>cAc	p.R244H	KCNQ5_ENST00000342056.2_Missense_Mutation_p.R244H|KCNQ5_ENST00000403813.2_Missense_Mutation_p.R244H|KCNQ5_ENST00000414165.2_Missense_Mutation_p.R244H|KCNQ5_ENST00000355194.4_Missense_Mutation_p.R244H|KCNQ5_ENST00000355635.3_Missense_Mutation_p.R244H|KCNQ5_ENST00000402622.2_Missense_Mutation_p.R244H|KCNQ5_ENST00000370392.1_Missense_Mutation_p.R244H	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	244			R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)	p.R244H(2)		breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	CGCATGGTGCGCATGGACCGA	0.438																																					GBM(142;1375 1859 14391 23261 44706)											2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	6											80	77	78					6																	73787159		2203	4300	6503	73843880	SO:0001583	missense	56479			AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.731G>A	6.37:g.73787159G>A	ENSP00000359425:p.Arg244His		73843880	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.844706	0.91197	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000370392;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94	5.84	5.84	0.93424	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98346	0.9451	L	0.48174	1.505	0.80722	D	1	D;D;D;D;D;D	0.89917	0.985;1.0;0.995;0.989;1.0;1.0	P;D;D;P;D;D	0.87578	0.766;0.998;0.919;0.887;0.958;0.99	D	0.98098	1.0413	10	0.40728	T	0.16	.	20.1438	0.98071	0.0:0.0:1.0:0.0	.	244;244;244;244;244;244	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82;Q9NR82-4	.;.;.;.;KCNQ5_HUMAN;.	H	244	ENSP00000345055:R244H;ENSP00000347326:R244H;ENSP00000359425:R244H;ENSP00000359419:R244H;ENSP00000385501:R244H;ENSP00000347853:R244H;ENSP00000384453:R244H;ENSP00000409861:R244H	ENSP00000345055:R244H	R	+	2	0	KCNQ5	73843880	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.768000	0.95171	0.650000	0.86243	CGC		0.438	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		A	73787159	G	A	73787159	3	1	43	1	0	0	0	0	1	0	0	0	8107	1087	38	1	745	1	KCNQ5	6	73787159	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	18343323	73787159	97327908	46	3968										
DDX43	55510	broad.mit.edu	37	chr6	74123769	74123769	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atggagatagagaacagagaGatcgggagaaagcattagag	15	3	0	6			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:74123769G>T	ENST00000370336.4	+	13	1731	c.1573G>T	c.(1573-1575)Gat>Tat	p.D525Y	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	525	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.D525Y(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						AGAACAGAGAGATCGGGAGAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	59	60					6																	74123769		2203	4300	6503	74180490	SO:0001583	missense	55510				CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1573G>T	6.37:g.74123769G>T	ENSP00000359361:p.Asp525Tyr		74180490	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	37	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675384	0.47781	.	.	ENSG00000080007	ENST00000370336	T	0.76186	-1.0	4.6	4.6	0.57074	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81678	0.4873	L	0.60845	1.875	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83659	0.0160	10	0.87932	D	0	-20.4045	17.532	0.87817	0.0:0.0:1.0:0.0	.	525	Q9NXZ2	DDX43_HUMAN	Y	525	ENSP00000359361:D525Y	ENSP00000359361:D525Y	D	+	1	0	DDX43	74180490	1.000000	0.71417	0.358000	0.25811	0.027000	0.11550	6.978000	0.76147	2.523000	0.85059	0.655000	0.94253	GAT		0.363	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		T	74123769	G	T	74123769	3	4	43	1	0	0	0	0	1	0	0	0	4369	942	33	2	1623	2	DDX43	6	74123769	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	336610	74123769	96991298	47	3969										
COL12A1	1303	broad.mit.edu	37	chr6	75912479	75912479	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agcagggccgcgcccagggcGgcaagcgctgggggaagcct	19	13	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:75912479G>A	ENST00000322507.8	-	2	339	c.30C>T	c.(28-30)gcC>gcT	p.A10A	COL12A1_ENST00000345356.6_Silent_p.A10A|COL12A1_ENST00000416123.2_Silent_p.A10A|COL12A1_ENST00000483888.2_Silent_p.A10A	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	10					cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.A10A(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CGCCCAGGGCGGCAAGCGCTG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	6											39	40	40					6																	75912479		1815	3885	5700	75969199	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.30C>T	6.37:g.75912479G>A			75969199	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.567	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75912479	G	A	75912479	2	1	43	1	0	0	0	0	0	0	0	1	3675	1103	39	1		1	COL12A1	6	75912479	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	1788710	75912479	95202588	48	3970										
TTK	7272	broad.mit.edu	37	chr6	80724229	80724229	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tctggtgtcagatgaaaagaGttctgaacttattattactg	9	5	3	4	rs200901836		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:80724229G>T	ENST00000369798.2	+	10	1145	c.1034G>T	c.(1033-1035)aGt>aTt	p.S345I	TTK_ENST00000515751.1_3'UTR|TTK_ENST00000230510.3_Missense_Mutation_p.S345I|TTK_ENST00000509894.1_Missense_Mutation_p.S345I	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	345					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.S329I(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		GATGAAAAGAGTTCTGAACTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	6											78	85	82					6																	80724229		2203	4295	6498	80780948	SO:0001583	missense	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1034G>T	6.37:g.80724229G>T	ENSP00000358813:p.Ser345Ile		80780948	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439843	0.43326	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	T;T;T	0.70164	-0.46;-0.46;-0.45	5.29	3.5	0.40072	.	0.128026	0.64402	D	0.000001	T	0.49440	0.1557	M	0.66939	2.045	0.39613	D	0.969902	P;P	0.35033	0.481;0.481	B;B	0.36922	0.236;0.213	T	0.55296	-0.8163	10	0.72032	D	0.01	.	8.0829	0.30754	0.187:0.0:0.813:0.0	.	345;345	P33981;A8K8U5	TTK_HUMAN;.	I	345	ENSP00000422936:S345I;ENSP00000230510:S345I;ENSP00000358813:S345I	ENSP00000230510:S345I	S	+	2	0	TTK	80780948	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	2.526000	0.45607	0.720000	0.32209	0.585000	0.79938	AGT		0.308	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			T	80724229	G	T	80724229	3	4	43	1	0	0	0	0	1	0	0	0	16760	1029	36	2	1068	2	TTK	6	80724229	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	4811750	80724229	90390838	49	3971										
FHL5	9457	broad.mit.edu	37	chr6	97058624	97058624	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aagtgtgtagcctgttccaaAcccattagtggtgagttctt	10	8	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:97058624A>T	ENST00000326771.2	+	6	1061	c.681A>T	c.(679-681)aaA>aaT	p.K227N	FHL5_ENST00000541107.1_Missense_Mutation_p.K227N	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	227	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.K227N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		CCTGTTCCAAACCCATTAGTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											147	142	144					6																	97058624		2203	4300	6503	97165345	SO:0001583	missense	9457			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.681A>T	6.37:g.97058624A>T	ENSP00000326022:p.Lys227Asn		97165345	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.989922	0.35131	.	.	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.88975	-2.45;-2.45	5.98	2.07	0.26955	Zinc finger, LIM-type (5);	0.000000	0.48286	D	0.000188	T	0.78272	0.4257	M	0.71036	2.16	0.51012	D	0.999905	B	0.20368	0.044	B	0.27608	0.081	T	0.70425	-0.4875	10	0.14252	T	0.57	.	10.4658	0.44607	0.604:0.0:0.396:0.0	.	227	Q5TD97	FHL5_HUMAN	N	227	ENSP00000442357:K227N;ENSP00000326022:K227N	ENSP00000326022:K227N	K	+	3	2	FHL5	97165345	0.098000	0.21812	0.999000	0.59377	0.752000	0.42762	-0.376000	0.07465	0.455000	0.26910	0.528000	0.53228	AAA		0.383	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		T	97058624	A	T	97058624	3	4	43	1	0	0	0	0	1	0	0	0	5900	40	2	5	695	5	FHL5	6	97058624	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	16334395	97058624	74056443	50	3972										
C6orf174	387104	broad.mit.edu	37	chr6	127834114	127834114	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agctgttgcctcagtttctcAttttcatcttctgttgttgt	7	9	5	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:127834114A>T	ENST00000525778.1	-	4	2152	c.1407T>A	c.(1405-1407)aaT>aaA	p.N469K	SOGA3_ENST00000556132.1_Missense_Mutation_p.N469K|SOGA3_ENST00000368268.2_Missense_Mutation_p.N469K|SOGA3_ENST00000465909.2_Missense_Mutation_p.N469K|SOGA3_ENST00000481848.2_Missense_Mutation_p.N469K			Q5TF21	SOGA3_HUMAN	SOGA family member 3	469					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.N469K(1)									TCAGTTTCTCATTTTCATCTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											167	146	153					6																	127834114		1834	4093	5927	127875807	SO:0001583	missense	387104			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1407T>A	6.37:g.127834114A>T	ENSP00000434570:p.Asn469Lys		127875807		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.218996	0.58560	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.52	3.13	0.36017	.	0.000000	0.85682	D	0.000000	T	0.50820	0.1638	M	0.80982	2.52	0.54753	D	0.999988	P	0.51537	0.946	D	0.64506	0.926	T	0.55774	-0.8088	10	0.56958	D	0.05	-11.4719	9.7051	0.40211	0.859:0.0:0.141:0.0	.	469	Q5TF21	CF174_HUMAN	K	469	ENSP00000451768:N469K;ENSP00000357251:N469K;ENSP00000434570:N469K;ENSP00000435559:N469K	ENSP00000435559:N469K	N	-	3	2	C6orf174	127875807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.423000	0.34837	1.033000	0.39918	0.533000	0.62120	AAT		0.338	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		T	127834114	A	T	127834114	3	4	43	1	0	0	0	0	1	0	0	0	2351	214	8	5	1452	5	C6orf174	6	127834114	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	30775490	127834114	43280953	51	3973										
BCLAF1	9774	broad.mit.edu	37	chr6	136588205	136588205	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctttggggtatattctggatCccattcctcttccttcggtc	8	12	2	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:136588205C>G	ENST00000531224.1	-	11	2758	c.2506G>C	c.(2506-2508)Gat>Cat	p.D836H	BCLAF1_ENST00000353331.4_Intron|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527759.1_Missense_Mutation_p.D834H|BCLAF1_ENST00000031135.9_Missense_Mutation_p.D54H|BCLAF1_ENST00000527536.1_Intron|BCLAF1_ENST00000530767.1_Missense_Mutation_p.D663H|BCLAF1_ENST00000392348.2_Intron	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	836					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.D836H(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TATTCTGGATCCCATTCCTCT	0.408																																					Colon(142;1534 1789 5427 7063 28491)											1	Substitution - Missense(1)	large_intestine(1)	6											141	136	138					6																	136588205		2203	4300	6503	136629898	SO:0001583	missense	9774			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2506G>C	6.37:g.136588205C>G	ENSP00000435210:p.Asp836His		136629898	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.9|23.9	4.468880|4.468880	0.84533|0.84533	.|.	.|.	ENSG00000029363|ENSG00000029363	ENST00000531224;ENST00000530767;ENST00000527759;ENST00000031135|ENST00000534762	T;T;T;T|.	0.65732|.	1.46;1.34;1.45;-0.17|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.64402|.	D|.	0.000003|.	T|T	0.49898|0.49898	0.1584|0.1584	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D;P|.	0.89917|.	1.0;1.0;0.821|.	D;D;P|.	0.83275|.	0.996;0.996;0.651|.	T|T	0.38478|0.38478	-0.9659|-0.9659	10|5	0.87932|.	D|.	0|.	-8.722|-8.722	20.3812|20.3812	0.98933|0.98933	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	834;836;663|.	Q9NYF8-2;Q9NYF8;Q9NYF8-4|.	.;BCLF1_HUMAN;.|.	H|A	836;663;834;54|102	ENSP00000435210:D836H;ENSP00000436501:D663H;ENSP00000434826:D834H;ENSP00000031135:D54H|.	ENSP00000031135:D54H|.	D|G	-|-	1|2	0|0	BCLAF1|BCLAF1	136629898|136629898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.672000|6.672000	0.74477|0.74477	2.821000|2.821000	0.97095|0.97095	0.650000|0.650000	0.86243|0.86243	GAT|GGA		0.408	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		G	136588205	C	G	136588205	3	3	43	1	0	0	0	0	1	0	0	0	1384	855	30	5	268	5	BCLAF1	6	136588205	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	8754091	136588205	34526862	52	3974										
KIAA1244	57221	broad.mit.edu	37	chr6	138607916	138607916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atcaaccccactgactggtcGaatggcggggagctccaaag	12	12	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:138607916G>A	ENST00000251691.4	+	16	2814	c.2648G>A	c.(2647-2649)cGa>cAa	p.R883Q		NM_020340.4	NP_065073.3			KIAA1244									p.R812Q(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CTGACTGGTCGAATGGCGGGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	121	119					6																	138607916		2203	4300	6503	138649609	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2648G>A	6.37:g.138607916G>A	ENSP00000251691:p.Arg883Gln		138649609		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	26.4	4.729650	0.89390	.	.	ENSG00000112379	ENST00000251691	T	0.18338	2.22	5.25	5.25	0.73442	.	0.052856	0.64402	D	0.000001	T	0.27241	0.0668	M	0.62723	1.935	0.58432	D	0.999996	D	0.89917	1.0	P	0.59546	0.859	T	0.00412	-1.1755	10	0.33940	T	0.23	-23.4399	19.037	0.92983	0.0:0.0:1.0:0.0	.	883	Q5TH69	BIG3_HUMAN	Q	883	ENSP00000251691:R883Q	ENSP00000251691:R883Q	R	+	2	0	KIAA1244	138649609	1.000000	0.71417	0.732000	0.30844	0.634000	0.38068	9.017000	0.93651	2.738000	0.93877	0.655000	0.94253	CGA		0.557	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138607916	G	A	138607916	3	1	43	1	0	0	0	0	1	0	0	0	8238	1058	37	1	2710	1	KIAA1244	6	138607916	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	2019711	138607916	32507151	53	3975										
AGPAT4	56895	broad.mit.edu	37	chr6	161574408	161574408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	caagctcctcacggtgatggCgaagcccttggttcgtggca	13	12	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr6:161574408C>T	ENST00000320285.4	-	5	846	c.634G>A	c.(634-636)Gcc>Acc	p.A212T	AGPAT4_ENST00000457520.2_Intron|AGPAT4_ENST00000366908.5_3'UTR|AGPAT4_ENST00000366911.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	212					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.A212T(2)		endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		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)		ACGGTGATGGCGAAGCCCTTG	0.622											OREG0017775	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	6											94	69	77					6																	161574408		2203	4300	6503	161494398	SO:0001583	missense	56895			AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20885	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, delta"	614795	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.634G>A	6.37:g.161574408C>T	ENSP00000314036:p.Ala212Thr	1817	161494398	B4DSF9|Q5TEF0	Missense_Mutation	SNP	ENST00000320285.4	37	CCDS5280.1	.	.	.	.	.	.	.	.	.	.	C	5.808	0.333347	0.11013	.	.	ENSG00000026652	ENST00000320285	D	0.93426	-3.22	4.82	3.96	0.45880	Phospholipid/glycerol acyltransferase (2);	0.316586	0.34676	N	0.003763	T	0.65144	0.2663	N	0.01219	-0.95	0.80722	D	1	P	0.51653	0.947	B	0.42030	0.373	T	0.78677	-0.2111	10	0.02654	T	1	-15.6488	13.2004	0.59765	0.0:0.923:0.0:0.077	.	212	Q9NRZ5	PLCD_HUMAN	T	212	ENSP00000314036:A212T	ENSP00000314036:A212T	A	-	1	0	AGPAT4	161494398	0.999000	0.42202	0.338000	0.25549	0.901000	0.52897	3.935000	0.56560	1.273000	0.44346	0.555000	0.69702	GCC		0.622	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133		T	161574408	C	T	161574408	3	4	43	1	0	0	0	0	1	0	0	0	389	768	27	1	522	1	AGPAT4	6	161574408	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	22966492	161574408	9540659	54	3976										
FOXK1	221937	broad.mit.edu	37	chr7	4796634	4796634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cttccctgcagaattctatcCggcacaacctctctttgaac	5	15	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr7:4796634C>T	ENST00000328914.4	+	5	1060	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	FOXK1_ENST00000446823.1_Missense_Mutation_p.R191W	NM_001037165.1	NP_001032242.1			forkhead box K1									p.R354W(2)|p.R332W(2)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GAATTCTATCCGGCACAACCT	0.522																																																4	Substitution - Missense(4)	large_intestine(4)	7											78	79	78					7																	4796634		2203	4300	6503	4763160	SO:0001583	missense	221937			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1060C>T	7.37:g.4796634C>T	ENSP00000328720:p.Arg354Trp		4763160		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191421	0.78902	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.98135	-4.74;-4.74	5.8	5.8	0.92144	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);Transcription factor, fork head, conserved site (1);	0.059857	0.64402	D	0.000003	D	0.99378	0.9781	H	0.98996	4.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98393	1.0564	10	0.87932	D	0	.	19.0512	0.93046	0.0:1.0:0.0:0.0	.	354;191	P85037;P85037-2	FOXK1_HUMAN;.	W	191;118;354;237	ENSP00000394442:R191W;ENSP00000328720:R354W	ENSP00000328720:R354W	R	+	1	2	FOXK1	4763160	1.000000	0.71417	0.986000	0.45419	0.991000	0.79684	3.933000	0.56545	2.735000	0.93741	0.655000	0.94253	CGG		0.522	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			T	4796634	C	T	4796634	3	4	43	1	0	0	0	0	1	0	0	0	6033	643	23	1	1078	1	FOXK1	7	4796634	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		4796634	154342029	55	3977										
ZNF277	11179	broad.mit.edu	37	chr7	111982761	111982761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	atgctttgaaacaaagcagtAttttgaaccagttgctacta	7	7	0	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr7:111982761A>G	ENST00000361822.3	+	12	1459	c.1330A>G	c.(1330-1332)Att>Gtt	p.I444V	AC004112.4_ENST00000431064.1_RNA|AC004112.4_ENST00000411413.1_RNA	NM_021994.2	NP_068834.2	Q9NRM2	ZN277_HUMAN	zinc finger protein 277	444					cellular response to hydrogen peroxide (GO:0070301)|regulation of cellular senescence (GO:2000772)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.I444V(1)		breast(4)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	15						ACAAAGCAGTATTTTGAACCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											68	65	66					7																	111982761		2203	4300	6503	111769997	SO:0001583	missense	11179			AF209198	CCDS5755.2	7q31.1	2012-10-05	2007-10-23	2007-10-23	ENSG00000198839	ENSG00000198839			13070	protein-coding gene	gene with protein product		605465	"zinc finger protein (C2H2 type) 277", "zinc finger protein 277 pseudogene"	ZNF277P		10860669, 16213364, 16395595	Standard	NM_021994		Approved	NRIF4	uc003vge.2	Q9NRM2	OTTHUMG00000150209	ENST00000361822.3:c.1330A>G	7.37:g.111982761A>G	ENSP00000354501:p.Ile444Val		111769997	Q75MZ2|Q75MZ3|Q8WY14	Missense_Mutation	SNP	ENST00000361822.3	37	CCDS5755.2	.	.	.	.	.	.	.	.	.	.	A	3.942	-0.014063	0.07681	.	.	ENSG00000198839	ENST00000361822;ENST00000421864	T	0.25912	1.77	6.06	-0.0844	0.13690	.	0.392379	0.28694	N	0.014442	T	0.07728	0.0194	N	0.02247	-0.625	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42068	-0.9473	10	0.02654	T	1	-8.0492	11.5111	0.50494	0.4427:0.0:0.5573:0.0	.	444	Q9NRM2	ZN277_HUMAN	V	444;112	ENSP00000354501:I444V	ENSP00000354501:I444V	I	+	1	0	ZNF277	111769997	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	0.715000	0.25822	0.183000	0.20059	0.533000	0.62120	ATT		0.353	ZNF277-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316843.2	NM_021994		G	111982761	A	G	111982761	3	3	43	1	0	0	0	0	1	0	0	0	17851	449	16	4	1376	4	ZNF277	7	111982761	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	107186127	111982761	47155902	56	3978										
PTPRZ1	5803	broad.mit.edu	37	chr7	121699922	121699922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agatgatcaatctgatgaggCcaggagtctttgctgacatt	11	7	3	5			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr7:121699922C>T	ENST00000393386.2	+	29	7198	c.6787C>T	c.(6787-6789)Cca>Tca	p.P2263S	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.P1396S	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2263	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P2263S(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCTGATGAGGCCAGGAGTCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											113	102	106					7																	121699922		2203	4300	6503	121487158	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6787C>T	7.37:g.121699922C>T	ENSP00000377047:p.Pro2263Ser		121487158	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	32	5.176597	0.94846	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.13420	2.59;2.59	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000001	T	0.41396	0.1157	M	0.72479	2.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.998	T	0.06881	-1.0802	10	0.87932	D	0	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	1402;1396;2263	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	S	2263;1396	ENSP00000377047:P2263S;ENSP00000410000:P1396S	ENSP00000377047:P2263S	P	+	1	0	PTPRZ1	121487158	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	CCA		0.413	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121699922	C	T	121699922	3	4	43	1	0	0	0	0	1	0	0	0	12851	739	26	3	6901	3	PTPRZ1	7	121699922	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	9717161	121699922	37438741	57	3979										
SCARA5	286133	broad.mit.edu	37	chr8	27824005	27824005	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ggacagcatgcttcagggccGacagggaccccagctgggta	15	12	1	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:27824005G>T	ENST00000354914.3	-	3	652	c.167C>A	c.(166-168)tCg>tAg	p.S56*	SCARA5_ENST00000518030.1_Intron|SCARA5_ENST00000301906.4_Intron|SCARA5_ENST00000524352.1_Nonsense_Mutation_p.S56*|SCARA5_ENST00000380385.2_Nonsense_Mutation_p.S56*	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	56					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)	p.S56*(1)		central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CTTCAGGGCCGACAGGGACCC	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											97	103	101					8																	27824005		2203	4300	6503	27879924	SO:0001587	stop_gained	286133			AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.167C>A	8.37:g.27824005G>T	ENSP00000346990:p.Ser56*		27879924	Q6UXZ1|Q7Z4A1|Q8N4Z7	Nonsense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	G	42	9.285645	0.99125	.	.	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000524352	.	.	.	5.93	5.93	0.95920	.	0.269718	0.30584	N	0.009305	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8364	0.78801	0.0:0.0:1.0:0.0	.	.	.	.	X	56	.	ENSP00000346990:S56X	S	-	2	0	SCARA5	27879924	1.000000	0.71417	0.987000	0.45799	0.873000	0.50193	5.403000	0.66338	2.814000	0.96858	0.563000	0.77884	TCG		0.527	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		T	27824005	G	T	27824005	4	4	43	1	0	0	0	0	0	1	0	0	13917	1059	37	2	1348	2	SCARA5	8	27824005	Nonsense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		27824005	118540017	58	3980										
C8orf80	389643	broad.mit.edu	37	chr8	27922074	27922074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtccctcttgctgttgaagtCgcctgtgcctgggatgtcca	12	12	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:27922074C>T	ENST00000413272.2	-	7	1028	c.886G>A	c.(886-888)Gac>Aac	p.D296N	NUGGC_ENST00000341513.6_Missense_Mutation_p.D296N	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	296					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D296N(1)									CTGTTGAAGTCGCCTGTGCCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8											76	79	78					8																	27922074		2060	4187	6247	27977993	SO:0001583	missense	389643			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.886G>A	8.37:g.27922074C>T	ENSP00000408697:p.Asp296Asn		27977993	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	C	29.4	4.999497	0.93227	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	D;D	0.96856	-4.15;-4.15	6.08	6.08	0.98989	Dynamin, GTPase domain (1);	0.000000	0.64402	D	0.000002	D	0.98210	0.9408	M	0.85630	2.765	0.40611	D	0.981678	D	0.89917	1.0	D	0.97110	1.0	D	0.99187	1.0869	10	0.87932	D	0	-25.5178	16.1754	0.81847	0.0:1.0:0.0:0.0	.	296	Q68CJ6	SLIP_HUMAN	N	296	ENSP00000408697:D296N;ENSP00000345031:D296N	ENSP00000345031:D296N	D	-	1	0	C8orf80	27977993	0.996000	0.38824	0.974000	0.42286	0.998000	0.95712	4.482000	0.60257	2.895000	0.99335	0.650000	0.86243	GAC		0.507	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		T	27922074	C	T	27922074	3	4	43	1	0	0	0	0	1	0	0	0	2445	884	31	1	1556	1	C8orf80	8	27922074	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	98069	27922074	118441948	59	3981										
NRG1	3084	broad.mit.edu	37	chr8	32505455	32505456	+	Intron	DEL	AG	AG	-													0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctgagaggttgcctcaactcAgagaaaatctgcattgtccc					rs371797228	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:32505455_32505456delAG	ENST00000405005.3	+	5	502				NRG1_ENST00000338921.4_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520502.2_Frame_Shift_Del_p.E74fs|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000287842.3_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.K75fs*30(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		GCCTCAACTCAGAGAAAATCTG	0.574																																																1	Deletion - Frameshift(1)	large_intestine(1)	8																																								32624998	SO:0001627	intron_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31052AG>-	8.37:g.32505457_32505458delAG			32624997	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Frame_Shift_Del	DEL	ENST00000405005.3	37	CCDS6085.1																																																																																				0.574	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			-	32505456	AG	-	32505455	6	5	43	0	1	1	0	1	0	0	0	0	10678	175	7	0		0	NRG1	8	32505455	Intron	DEL	AG	TCGA-AG-3883-01A-02W-0899-10	4583381	32505455	113858567	60	3982										
PXDNL	137902	broad.mit.edu	37	chr8	52287284	52287284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtcaatgtcacctggagagcCgtacaacctggaacagagac	11	11	2	2	rs371171299		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:52287284C>T	ENST00000356297.4	-	18	3665	c.3565G>A	c.(3565-3567)Ggc>Agc	p.G1189S	PXDNL_ENST00000543296.1_Missense_Mutation_p.G1189S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1189					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.G388S(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CCTGGAGAGCCGTACAACCTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	SER/GLY	1,4059		0,1,2029	57	57	57		3565	-6.1	0	8		57	0,8392		0,0,4196	no	missense	PXDNL	NM_144651.4	56	0,1,6225	TT,TC,CC		0.0,0.0246,0.0080	probably-damaging	1189/1464	52287284	1,12451	2030	4196	6226	52449837	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3565G>A	8.37:g.52287284C>T	ENSP00000348645:p.Gly1189Ser		52449837	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179707	0.57800	2.46E-4	0.0	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.76186	-1.0;-1.0	4.46	-6.1	0.02138	.	1.052750	0.07566	N	0.917801	T	0.73877	0.3643	M	0.67700	2.07	0.09310	N	1	D	0.59357	0.985	P	0.54499	0.754	T	0.67581	-0.5634	10	0.62326	D	0.03	.	2.8393	0.05524	0.1125:0.3251:0.1107:0.4516	.	1189	A1KZ92	PXDNL_HUMAN	S	1189	ENSP00000348645:G1189S;ENSP00000444865:G1189S	ENSP00000348645:G1189S	G	-	1	0	PXDNL	52449837	0.063000	0.20901	0.000000	0.03702	0.000000	0.00434	0.818000	0.27295	-2.171000	0.00775	-1.740000	0.00687	GGC		0.473	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52287284	C	T	52287284	3	4	43	1	0	0	0	0	1	0	0	0	12885	652	23	1	850	1	PXDNL	8	52287284	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	19781829	52287284	94076738	61	3983										
KCNB2	9312	broad.mit.edu	37	chr8	73480197	73480197	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cacgagagcctcctggaagtGtgcgacgactataatctgaa	11	10	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:73480197G>C	ENST00000523207.1	+	2	816	c.228G>C	c.(226-228)gtG>gtC	p.V76V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	76					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.V76V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TCCTGGAAGTGTGCGACGACT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	8											83	81	81					8																	73480197		2203	4300	6503	73642751	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.228G>C	8.37:g.73480197G>C			73642751	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.532	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73480197	G	C	73480197	2	2	43	1	0	0	0	0	0	0	0	1	8034	1364	48	5		5	KCNB2	8	73480197	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	21192913	73480197	72883825	62	3984										
GDF6	392255	broad.mit.edu	37	chr8	97156898	97156898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gggagtcaatttggtgggcaCgcagcagctgggcggggtgg	21	7	1	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:97156898C>T	ENST00000287020.5	-	2	1360	c.1261G>A	c.(1261-1263)Gtg>Atg	p.V421M		NM_001001557.2	NP_001001557.1	Q6KF10	GDF6_HUMAN	growth differentiation factor 6	421					activin receptor signaling pathway (GO:0032924)|apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|growth (GO:0040007)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal cell apoptotic process (GO:1990009)	extracellular space (GO:0005615)		p.V421M(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27	Breast(36;2.67e-05)					TTGGTGGGCACGCAGCAGCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	8											72	76	75					8																	97156898		2203	4300	6503	97226074	SO:0001583	missense	392255				CCDS34926.1	8q22.1	2014-01-29			ENSG00000156466	ENSG00000156466			4221	protein-coding gene	gene with protein product		601147	"segmentation syndrome 1"	SGM1		10022976, 18425797	Standard	NM_001001557		Approved	BMP13, KFS, KFS1	uc003yhp.3	Q6KF10	OTTHUMG00000164710	ENST00000287020.5:c.1261G>A	8.37:g.97156898C>T	ENSP00000287020:p.Val421Met		97226074	Q6PI58	Missense_Mutation	SNP	ENST00000287020.5	37	CCDS34926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.528248|4.528248	0.85706|0.85706	.|.	.|.	ENSG00000156466|ENSG00000156466	ENST00000435084|ENST00000287020	.|D	.|0.90261	.|-2.64	4.95|4.95	4.95|4.95	0.65309|0.65309	.|Transforming growth factor-beta, C-terminal (3);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.96818|0.96818	0.8961|0.8961	H|H	0.95780|0.95780	3.72|3.72	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	D|D	0.97907|0.97907	1.0306|1.0306	6|10	0.87932|0.87932	D|D	0|0	.|.	17.1426|17.1426	0.86758|0.86758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|421	.|Q6KF10	.|GDF6_HUMAN	H|M	337|421	.|ENSP00000287020:V421M	ENSP00000412749:R337H|ENSP00000287020:V421M	R|V	-|-	2|1	0|0	GDF6|GDF6	97226074|97226074	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.604000|7.604000	0.82830|0.82830	2.567000|2.567000	0.86603|0.86603	0.650000|0.650000	0.86243|0.86243	CGT|GTG		0.607	GDF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379862.2	NM_001001557		T	97156898	C	T	97156898	3	4	43	1	0	0	0	0	1	0	0	0	6337	536	19	1	110	1	GDF6	8	97156898	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	23676701	97156898	49207124	63	3985										
RGS22	26166	broad.mit.edu	37	chr8	101075803	101075803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tatgagaaatacaccagtccGccctgctctctggtccagcg	9	14	1	1	rs370599090		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:101075803G>A	ENST00000360863.6	-	8	1387	c.1193C>T	c.(1192-1194)gCg>gTg	p.A398V	RGS22_ENST00000523287.1_Missense_Mutation_p.A217V|RGS22_ENST00000523437.1_Missense_Mutation_p.A386V	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	398					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.A398V(1)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			ACACCAGTCCGCCCTGCTCTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	VAL/ALA	0,3772		0,0,1886	145	133	137		1193	4.8	0.9	8		137	1,8209		0,1,4104	no	missense	RGS22	NM_015668.3	64	0,1,5990	AA,AG,GG		0.0122,0.0,0.0083	probably-damaging	398/1265	101075803	1,11981	1886	4105	5991	101144979	SO:0001583	missense	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.1193C>T	8.37:g.101075803G>A	ENSP00000354109:p.Ala398Val		101144979	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065152	0.36470	0.0	1.22E-4	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.63096	-0.02;-0.02;-0.02	5.68	4.79	0.61399	Regulator of G protein signalling superfamily (1);	0.270973	0.30667	N	0.009127	T	0.74696	0.3750	M	0.66939	2.045	0.30693	N	0.751126	D;D;D	0.76494	0.997;0.997;0.999	P;P;P	0.59825	0.734;0.734;0.864	T	0.77422	-0.2594	10	0.54805	T	0.06	.	16.8092	0.85715	0.0:0.1289:0.8711:0.0	.	386;398;217	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	V	398;386;217;386	ENSP00000354109:A398V;ENSP00000429382:A217V;ENSP00000428212:A386V	ENSP00000354109:A398V	A	-	2	0	RGS22	101144979	1.000000	0.71417	0.903000	0.35520	0.009000	0.06853	4.255000	0.58804	1.496000	0.48567	0.650000	0.86243	GCG		0.368	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101075803	G	A	101075803	3	1	43	1	0	0	0	0	1	0	0	0	13342	1087	38	1	2681	1	RGS22	8	101075803	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	3918905	101075803	45288219	64	3986										
ZHX2	22882	broad.mit.edu	37	chr8	123964739	123964739	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agaagaggtggaggaggcccGgaagaagatgttcaacggca	17	6	1	4			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr8:123964739G>A	ENST00000314393.4	+	3	1824	c.989G>A	c.(988-990)cGg>cAg	p.R330Q		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	330	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R330Q(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GAGGAGGCCCGGAAGAAGATG	0.602																																					Esophageal Squamous(94;1056 1388 11767 13799 49639)											1	Substitution - Missense(1)	large_intestine(1)	8											96	82	87					8																	123964739		2203	4300	6503	124033920	SO:0001583	missense	22882			AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.989G>A	8.37:g.123964739G>A	ENSP00000314709:p.Arg330Gln		124033920		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956298	0.92726	.	.	ENSG00000178764	ENST00000314393	T	0.64991	-0.13	5.84	5.84	0.93424	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.82245	0.4995	M	0.82323	2.585	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.83693	0.0178	10	0.87932	D	0	-23.7383	20.1363	0.98032	0.0:0.0:1.0:0.0	.	330	Q9Y6X8	ZHX2_HUMAN	Q	330	ENSP00000314709:R330Q	ENSP00000314709:R330Q	R	+	2	0	ZHX2	124033920	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.476000	0.97823	2.774000	0.95407	0.484000	0.47621	CGG		0.602	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123964739	G	A	123964739	3	1	43	1	0	0	0	0	1	0	0	0	17715	1116	39	1	991	1	ZHX2	8	123964739	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	22888936	123964739	22399283	65	3987										
VLDLR	7436	broad.mit.edu	37	chr9	2651465	2651465	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	caaaagatacgaacacaacaGaaatttcagcaactagtgga	7	8	1	2	rs143836414		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:2651465G>T	ENST00000382100.3	+	16	2658	c.2302G>T	c.(2302-2304)Gaa>Taa	p.E768*	VLDLR_ENST00000382099.2_Intron	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	768	Clustered O-linked oligosaccharides.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.E768*(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		GAACACAACAGAAATTTCAGC	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											90	82	85					9																	2651465		2203	4300	6503	2641465	SO:0001587	stop_gained	7436				CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.2302G>T	9.37:g.2651465G>T	ENSP00000371532:p.Glu768*		2641465	B2RMZ7|D3DRH6|Q5VVF6	Nonsense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	G	41	9.147817	0.99080	.	.	ENSG00000147852	ENST00000382100;ENST00000382092	.	.	.	5.26	2.25	0.28309	.	0.426300	0.19874	N	0.104121	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	7.423	0.27083	0.1533:0.137:0.7097:0.0	.	.	.	.	X	768;647	.	ENSP00000371524:E647X	E	+	1	0	VLDLR	2641465	1.000000	0.71417	0.977000	0.42913	0.998000	0.95712	2.436000	0.44819	0.710000	0.31997	0.591000	0.81541	GAA		0.408	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		T	2651465	G	T	2651465	4	4	43	1	0	0	0	0	0	1	0	0	17214	943	33	2	2364	2	VLDLR	9	2651465	Nonsense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		2651465	138561966	66	3988										
ERMP1	79956	broad.mit.edu	37	chr9	5797837	5797837	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctgttgcttcaaaagtcaatTttatagaatcccaaggtgtc	7	8	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:5797837T>G	ENST00000339450.5	-	13	2455	c.2366A>C	c.(2365-2367)aAa>aCa	p.K789T	ERMP1_ENST00000381506.3_3'UTR|ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000543230.1_Missense_Mutation_p.K367T	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	789						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.K789T(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		AAAAGTCAATTTTATAGAATC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											111	125	120					9																	5797837		2203	4300	6503	5787837	SO:0001583	missense	79956			AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.2366A>C	9.37:g.5797837T>G	ENSP00000340427:p.Lys789Thr		5787837	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.583738	0.28268	.	.	ENSG00000099219	ENST00000339450;ENST00000543230	T	0.45668	0.89	5.77	3.48	0.39840	.	0.182174	0.64402	D	0.000018	T	0.23410	0.0566	L	0.29908	0.895	0.80722	D	1	P	0.40000	0.698	B	0.29353	0.101	T	0.04413	-1.0953	10	0.45353	T	0.12	-12.8392	7.0648	0.25145	0.0:0.3448:0.0:0.6552	.	789	Q7Z2K6	ERMP1_HUMAN	T	789;367	ENSP00000340427:K789T	ENSP00000340427:K789T	K	-	2	0	ERMP1	5787837	1.000000	0.71417	0.920000	0.36463	0.413000	0.31143	1.485000	0.35519	1.025000	0.39708	0.383000	0.25322	AAA		0.363	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		G	5797837	T	G	5797837	3	3	43	1	0	0	0	0	1	0	0	0	5249	1841	64	4	360	4	ERMP1	9	5797837	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	3146372	5797837	135415594	67	3989										
PSIP1	11168	broad.mit.edu	37	chr9	15469306	15469306	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tttttaatctcagcatgtatCctttgaagtcgagaatccat	6	8	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:15469306C>T	ENST00000380733.4	-	12	1405	c.1062G>A	c.(1060-1062)agG>agA	p.R354R	PSIP1_ENST00000380738.4_Silent_p.R354R			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	354					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)	p.R354R(1)		breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		CAGCATGTATCCTTTGAAGTC	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	9											56	60	59					9																	15469306		2199	4282	6481	15459306	SO:0001819	synonymous_variant	11168			AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1062G>A	9.37:g.15469306C>T			15459306	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Silent	SNP	ENST00000380733.4	37	CCDS6479.1																																																																																				0.279	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		T	15469306	C	T	15469306	2	4	43	1	0	0	0	0	0	0	0	1	12697	854	30	3		3	PSIP1	9	15469306	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	9671469	15469306	125744125	68	3990										
FAM75A3	727830	broad.mit.edu	37	chr9	40701736	40701736	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtagggcggaggcggaggccCagaggcaggatgaaaaacca	18	8	0	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:40701736C>T	ENST00000356699.5	+	2	245	c.216C>T	c.(214-216)ccC>ccT	p.P72P	RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	72					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.P72P(2)									GGCGGAGGCCCAGAGGCAGGA	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	9											1	1	1					9																	40701736		291	740	1031	40691736	SO:0001819	synonymous_variant	727830					9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A3"	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.216C>T	9.37:g.40701736C>T			40691736		Silent	SNP	ENST00000356699.5	37	CCDS47969.1																																																																																				0.532	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124		T	40701736	C	T	40701736	2	4	43	1	0	0	0	0	0	0	0	1	5640	581	21	3		3	FAM75A3	9	40701736	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	25232430	40701736	100511695	69	3991										
ASTN2	23245	broad.mit.edu	37	chr9	119976958	119976958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gcggcgacgcttctgccaacGtcgctgggcgtacagcgcca	14	15	1	0	rs138260564		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:119976958G>A	ENST00000313400.4	-	3	794	c.694C>T	c.(694-696)Cgt>Tgt	p.R232C	ASTN2_ENST00000361209.2_Missense_Mutation_p.R232C|ASTN2_ENST00000361477.3_De_novo_Start_OutOfFrame|ASTN2_ENST00000373996.3_Missense_Mutation_p.R232C			O75129	ASTN2_HUMAN	astrotactin 2	232					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R232C(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TTCTGCCAACGTCGCTGGGCG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	48	46	46		694	5.5	1	9	dbSNP_134	46	0,8600		0,0,4300	no	missense	ASTN2	NM_014010.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	232/1289	119976958	1,13005	2203	4300	6503	119016779	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.694C>T	9.37:g.119976958G>A	ENSP00000314038:p.Arg232Cys		119016779	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	19.63	3.863558	0.71949	2.27E-4	0.0	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.15139	2.53;2.53;2.45	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.29850	0.0746	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.993	T	0.02966	-1.1088	9	.	.	.	-21.1878	19.0397	0.92993	0.0:0.0:1.0:0.0	.	232;232;232	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	C	232	ENSP00000314038:R232C;ENSP00000363108:R232C;ENSP00000354504:R232C	.	R	-	1	0	ASTN2	119016779	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	9.757000	0.98924	2.599000	0.87857	0.655000	0.94253	CGT		0.632	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119976958	G	A	119976958	3	1	43	1	0	0	0	0	1	0	0	0	1066	1145	40	1	3484	1	ASTN2	9	119976958	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	79275222	119976958	21236473	70	3992										
ODF2	4957	broad.mit.edu	37	chr9	131262485	131262485	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtttggggatggtccctattCcaccttcctgactagctctc	9	13	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:131262485C>A	ENST00000434106.3	+	21	2804	c.2441C>A	c.(2440-2442)tCc>tAc	p.S814Y	ODF2_ENST00000351030.3_Missense_Mutation_p.S809Y|ODF2_ENST00000372807.5_Missense_Mutation_p.S809Y|ODF2_ENST00000444119.2_Missense_Mutation_p.S790Y|ODF2_ENST00000604420.1_Missense_Mutation_p.S814Y|ODF2_ENST00000393527.3_Missense_Mutation_p.S790Y	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	814					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.S790Y(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GGTCCCTATTCCACCTTCCTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	9											252	203	219					9																	131262485		2203	4300	6503	130302306	SO:0001583	missense	4957			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2441C>A	9.37:g.131262485C>A	ENSP00000403453:p.Ser814Tyr		130302306	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	C	8.967	0.971891	0.18736	.	.	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.25085	1.83;1.82;1.82	5.5	2.33	0.28932	.	0.484833	0.18083	N	0.152232	T	0.18467	0.0443	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31351	0.086;0.25;0.32;0.073	B;B;B;B	0.38056	0.086;0.115;0.264;0.06	T	0.32079	-0.9920	10	0.72032	D	0.01	-1.467	16.076	0.80969	0.0:0.5051:0.4948:0.0	.	809;159;814;790	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	Y	809;814;790	ENSP00000342581:S809Y;ENSP00000361882:S814Y;ENSP00000307781:S790Y	ENSP00000307781:S790Y	S	+	2	0	ODF2	130302306	0.001000	0.12720	0.207000	0.23584	0.191000	0.23601	0.348000	0.20031	0.610000	0.30035	0.561000	0.74099	TCC		0.572	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			A	131262485	C	A	131262485	3	1	43	1	0	0	0	0	1	0	0	0	10858	855	30	2	2637	2	ODF2	9	131262485	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	11285527	131262485	9950946	71	3993										
USP20	10868	broad.mit.edu	37	chr9	132642547	132642547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tcgaagccgagacgcgggccGtgtgatctgctgggctagtc	16	11	1	2	rs374645414		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr9:132642547G>A	ENST00000315480.4	+	25	2898	c.2740G>A	c.(2740-2742)Gtg>Atg	p.V914M	USP20_ENST00000472108.1_3'UTR|USP20_ENST00000372429.3_Missense_Mutation_p.V914M|USP20_ENST00000358355.1_Missense_Mutation_p.V914M			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	914					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.V914M(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GACGCGGGCCGTGTGATCTGC	0.637													G|||	1	0.000199681	0	0	5008	,	,		14703	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9						G	MET/VAL,MET/VAL,MET/VAL	1,4197		0,1,2098	16	22	20		2740,2740,2740	-0.5	0.2	9		20	0,8424		0,0,4212	no	missense,missense,missense	USP20	NM_001008563.3,NM_001110303.2,NM_006676.6	21,21,21	0,1,6310	AA,AG,GG		0.0,0.0238,0.0079	benign,benign,benign	914/915,914/915,914/915	132642547	1,12621	2099	4212	6311	131682368	SO:0001583	missense	10868			AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2740G>A	9.37:g.132642547G>A	ENSP00000313811:p.Val914Met		131682368	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	9.391	1.075501	0.20227	2.38E-4	0.0	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.21031	2.03;2.03;2.03	5.01	-0.505	0.11993	.	0.706629	0.12690	N	0.447267	T	0.11410	0.0278	L	0.29908	0.895	0.22213	N	0.999284	B	0.32604	0.377	B	0.24269	0.052	T	0.16070	-1.0415	10	0.72032	D	0.01	.	4.4527	0.11628	0.0716:0.2454:0.4365:0.2464	.	914	Q9Y2K6	UBP20_HUMAN	M	914	ENSP00000361506:V914M;ENSP00000313811:V914M;ENSP00000351122:V914M	ENSP00000313811:V914M	V	+	1	0	USP20	131682368	0.570000	0.26651	0.160000	0.22671	0.001000	0.01503	0.913000	0.28611	-0.422000	0.07405	-0.253000	0.11424	GTG		0.637	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			A	132642547	G	A	132642547	3	1	43	1	0	0	0	0	1	0	0	0	17092	1145	40	1	2830	1	USP20	9	132642547	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	1380062	132642547	8570884	72	3994										
MYO3A	53904	broad.mit.edu	37	chr10	26241162	26241162	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtttttaaagtattgaataaGaaaaatggccaaaaagcagc	8	4	0	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:26241162G>T	ENST00000265944.5	+	3	289	c.123G>T	c.(121-123)aaG>aaT	p.K41N	MYO3A_ENST00000376302.1_Missense_Mutation_p.K41N|MYO3A_ENST00000543632.1_Missense_Mutation_p.K41N|MYO3A_ENST00000376301.1_Missense_Mutation_p.K41N	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	41	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K41N(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TATTGAATAAGAAAAATGGCC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											62	67	65					10																	26241162		2203	4298	6501	26281168	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.123G>T	10.37:g.26241162G>T	ENSP00000265944:p.Lys41Asn		26281168	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033313	0.75504	.	.	ENSG00000095777	ENST00000265944;ENST00000376302;ENST00000543632;ENST00000376301	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	6.01	6.01	0.97437	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042794	0.85682	D	0.000000	T	0.81380	0.4810	M	0.63843	1.955	0.80722	D	1	D;D;P;D	0.89917	1.0;1.0;0.927;0.988	D;D;P;D	0.87578	0.996;0.998;0.759;0.948	T	0.79401	-0.1819	10	0.49607	T	0.09	.	20.5041	0.99208	0.0:0.0:1.0:0.0	.	41;41;41;41	F5H0U9;Q0VD65;Q8NEV4;Q4G0X2	.;.;MYO3A_HUMAN;.	N	41	ENSP00000265944:K41N;ENSP00000365479:K41N;ENSP00000445909:K41N;ENSP00000365478:K41N	ENSP00000265944:K41N	K	+	3	2	MYO3A	26281168	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.879000	0.56138	2.855000	0.98099	0.536000	0.68110	AAG		0.313	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26241162	G	T	26241162	3	4	43	1	0	0	0	0	1	0	0	0	10106	933	33	2	125	2	MYO3A	10	26241162	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		26241162	109293585	73	3995										
JMJD1C	221037	broad.mit.edu	37	chr10	64973553	64973553	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agtgggaagtaaatgagggtGatgaacagcatggtgtggac	17	3	0	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:64973553G>A	ENST00000399262.2	-	8	2592	c.2374C>T	c.(2374-2376)Cac>Tac	p.H792Y	JMJD1C_ENST00000399251.1_Missense_Mutation_p.H573Y|JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000542921.1_Missense_Mutation_p.H610Y|JMJD1C_ENST00000402544.1_Missense_Mutation_p.H573Y	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	792					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)	p.H792Y(1)|p.H573Y(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AAATGAGGGTGATGAACAGCA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	10											87	82	84					10																	64973553		2146	4253	6399	64643559	SO:0001583	missense	221037			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2374C>T	10.37:g.64973553G>A	ENSP00000382204:p.His792Tyr		64643559	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.612177	0.66672	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.73	5.73	0.89815	.	0.052068	0.85682	D	0.000000	T	0.72087	0.3417	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.77557	0.99;0.99	T	0.72940	-0.4139	10	0.72032	D	0.01	-8.2269	19.9036	0.96999	0.0:0.0:1.0:0.0	.	792;610	Q15652;A0T124	JHD2C_HUMAN;.	Y	792;573;573;610	ENSP00000382204:H792Y;ENSP00000384990:H573Y;ENSP00000382195:H573Y;ENSP00000444682:H610Y	ENSP00000382195:H573Y	H	-	1	0	JMJD1C	64643559	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.096000	0.94182	2.706000	0.92434	0.655000	0.94253	CAC		0.507	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		A	64973553	G	A	64973553	3	1	43	1	0	0	0	0	1	0	0	0	7971	1290	45	3	5324	3	JMJD1C	10	64973553	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	38732391	64973553	70561194	74	3996										
TLX1	3195	broad.mit.edu	37	chr10	102893953	102893953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tcacccctatcagaaccggaCgccccccaagaagaagaagc	8	16	2	4			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:102893953C>T	ENST00000370196.6	+	2	2632	c.590C>T	c.(589-591)aCg>aTg	p.T197M	TLX1_ENST00000467928.2_Missense_Mutation_p.T197M|TLX1_ENST00000533319.1_3'UTR|RP11-31L23.3_ENST00000411459.1_RNA			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	197					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.T197M(1)		breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CAGAACCGGACGCCCCCCAAG	0.627			T	"TRB@, TRD@"	T-ALL																																		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	1	Substitution - Missense(1)	large_intestine(1)	10											51	52	52					10																	102893953		2200	4299	6499	102883943	SO:0001583	missense	3195			M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"Homeoboxes / ANTP class : NKL subclass"	5056	protein-coding gene	gene with protein product	"Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)", "homeo box 11 (T-cell lymphoma 3-associated breakpoint)"	186770	"homeo box 11 (T-cell lymphoma 3-associated breakpoint)", "T-cell leukemia, homeobox 1"	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.590C>T	10.37:g.102893953C>T	ENSP00000359215:p.Thr197Met		102883943	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Missense_Mutation	SNP	ENST00000370196.6	37	CCDS7510.1	.	.	.	.	.	.	.	.	.	.	C	35	5.416598	0.96092	.	.	ENSG00000107807	ENST00000370196;ENST00000463716;ENST00000467928	D;D	0.95788	-3.73;-3.81	5.85	5.85	0.93711	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97598	0.9213	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97672	1.0167	10	0.66056	D	0.02	.	20.1775	0.98187	0.0:1.0:0.0:0.0	.	197	P31314	TLX1_HUMAN	M	197;209;197	ENSP00000359215:T197M;ENSP00000434914:T197M	ENSP00000359215:T197M	T	+	2	0	TLX1	102883943	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.759000	0.85235	2.771000	0.95319	0.561000	0.74099	ACG		0.627	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		T	102893953	C	T	102893953	3	4	43	1	0	0	0	0	1	0	0	0	15998	536	19	1	596	1	TLX1	10	102893953	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	37920400	102893953	32640794	75	3997										
TACC2	10579	broad.mit.edu	37	chr10	123846509	123846509	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccagcttcagacaagcttctGggtccagcagggctgacctg	12	13	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:123846509G>T	ENST00000369005.1	+	4	4834	c.4494G>T	c.(4492-4494)ctG>ctT	p.L1498L	TACC2_ENST00000334433.3_Silent_p.L1498L|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.L1498L|TACC2_ENST00000515603.1_Silent_p.L1498L|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.L1498L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1498					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)	p.L1498L(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ACAAGCTTCTGGGTCCAGCAG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	10											45	45	45					10																	123846509		2203	4300	6503	123836499	SO:0001819	synonymous_variant	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4494G>T	10.37:g.123846509G>T			123836499	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																				0.602	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123846509	G	T	123846509	2	4	43	1	0	0	0	0	0	0	0	1	15541	1335	47	2		2	TACC2	10	123846509	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	20952556	123846509	11688238	76	3998										
ADAM12	8038	broad.mit.edu	37	chr10	127824202	127824202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tgctgaatcagaatatccccGtacatgtccatggtagtaac	8	10	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:127824202G>A	ENST00000368679.4	-	5	685	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	ADAM12_ENST00000368676.4_Missense_Mutation_p.R126W	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	126					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R126W(2)		biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GAATATCCCCGTACATGTCCA	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	10											149	114	126					10																	127824202		2203	4300	6503	127814192	SO:0001583	missense	8038			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.376C>T	10.37:g.127824202G>A	ENSP00000357668:p.Arg126Trp		127814192	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725479	0.68959	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	T;T;T	0.06849	3.25;3.25;3.25	4.17	4.17	0.49024	Peptidase M12B, propeptide (1);	0.430200	0.22565	N	0.058411	T	0.22126	0.0533	M	0.70787	2.145	0.20821	N	0.999849	D;D;D;D;D	0.67145	0.996;0.995;0.995;0.995;0.989	P;P;P;P;P	0.56916	0.809;0.711;0.711;0.711;0.72	T	0.02326	-1.1176	10	0.87932	D	0	.	13.7996	0.63192	0.0:0.0:1.0:0.0	.	123;123;126;123;126	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	W	126;126;123	ENSP00000357668:R126W;ENSP00000357665:R126W;ENSP00000391268:R123W	ENSP00000357665:R126W	R	-	1	2	ADAM12	127814192	0.995000	0.38212	0.236000	0.24074	0.087000	0.18053	4.273000	0.58914	2.158000	0.67659	0.491000	0.48974	CGG		0.473	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			A	127824202	G	A	127824202	3	1	43	1	0	0	0	0	1	0	0	0	236	1144	40	1	2537	1	ADAM12	10	127824202	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	3977693	127824202	7710545	77	3999										
C10orf90	118611	broad.mit.edu	37	chr10	128114641	128114641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tcttttttctttttaacttcCggcaagttatcatagattct	4	8	4	1	rs200783026		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr10:128114641C>T	ENST00000284694.7	-	8	2100	c.1980G>A	c.(1978-1980)ccG>ccA	p.P660P	C10orf90_ENST00000454341.1_Silent_p.P563P|C10orf90_ENST00000356858.3_Silent_p.P613P|C10orf90_ENST00000480379.1_Silent_p.P64P|C10orf90_ENST00000544758.1_Silent_p.P757P	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	660	ALMS motif. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.P660P(2)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TTTTAACTTCCGGCAAGTTAT	0.453													C|||	1	0.000199681	0	0.0014	5008	,	,		20975	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	10											96	95	96					10																	128114641		2203	4300	6503	128104631	SO:0001819	synonymous_variant	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1980G>A	10.37:g.128114641C>T			128104631	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	9.752	1.167857	0.21621	.	.	ENSG00000154493	ENST00000424927	.	.	.	4.8	-8.71	0.00848	.	.	.	.	.	T	0.32496	0.0831	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.41088	-0.9528	4	.	.	.	-19.2912	1.1129	0.01708	0.2405:0.1406:0.1778:0.4411	.	.	.	.	Q	203	.	.	R	-	2	0	C10orf90	128104631	0.198000	0.23374	0.712000	0.30502	0.996000	0.88848	-0.765000	0.04730	-1.469000	0.01890	0.655000	0.94253	CGG		0.453	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128114641	C	T	128114641	2	4	43	1	0	0	0	0	0	0	0	1	1627	639	23	1		1	C10orf90	10	128114641	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	290439	128114641	7420106	78	4000										
COPB1	1315	broad.mit.edu	37	chr11	14515886	14515886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cctgaagaggtagcacaaaaCgaatgatggtcatcagaagt	11	7	2	4			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:14515886C>T	ENST00000249923.3	-	3	491	c.191G>A	c.(190-192)cGt>cAt	p.R64H	PSMA1_ENST00000555531.1_3'UTR|COPB1_ENST00000439561.2_Missense_Mutation_p.R64H|PSMA1_ENST00000419365.2_3'UTR	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	64					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.R64H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						TAGCACAAAACGAATGATGGT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	11											106	104	104					11																	14515886		2200	4294	6494	14472462	SO:0001583	missense	1315			BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.191G>A	11.37:g.14515886C>T	ENSP00000249923:p.Arg64His		14472462	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	C	35	5.521894	0.96416	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234;ENST00000529866;ENST00000534771	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.58	5.58	0.84498	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63438	0.2511	H	0.94423	3.535	0.80722	D	1	D	0.69078	0.997	D	0.65010	0.931	T	0.74728	-0.3567	10	0.87932	D	0	-5.1216	19.5796	0.95461	0.0:1.0:0.0:0.0	.	64	P53618	COPB_HUMAN	H	64	ENSP00000249923:R64H;ENSP00000397873:R64H;ENSP00000436383:R64H;ENSP00000431530:R64H;ENSP00000436401:R64H	ENSP00000249923:R64H	R	-	2	0	COPB1	14472462	1.000000	0.71417	0.987000	0.45799	0.999000	0.98932	7.818000	0.86416	2.624000	0.88883	0.655000	0.94253	CGT		0.363	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		T	14515886	C	T	14515886	3	4	43	1	0	0	0	0	1	0	0	0	3734	536	19	1	2750	1	COPB1	11	14515886	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		14515886	120490630	79	4001										
SOX6	55553	broad.mit.edu	37	chr11	16007817	16007817	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ttgcttatactccccaatccGaagctttttgccatcaacaa	4	13	1	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:16007817G>A	ENST00000352083.6	-	15	2193	c.2116C>T	c.(2116-2118)Cgg>Tgg	p.R706W	SOX6_ENST00000528252.1_Missense_Mutation_p.R679W|SOX6_ENST00000527619.1_Missense_Mutation_p.R682W|SOX6_ENST00000316399.6_Missense_Mutation_p.R686W|SOX6_ENST00000528429.1_Missense_Mutation_p.R706W|SOX6_ENST00000396356.3_Missense_Mutation_p.R686W			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	706					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R686W(2)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						TCCCCAATCCGAAGCTTTTTG	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	11											214	202	206					11																	16007817		2200	4294	6494	15964393	SO:0001583	missense	55553			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.2116C>T	11.37:g.16007817G>A	ENSP00000339876:p.Arg706Trp		15964393	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	G	28.7	4.941914	0.92526	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429	T;T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27;0.27	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.79621	0.4477	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.995	T	0.81965	-0.0691	10	0.87932	D	0	.	19.6107	0.95606	0.0:0.0:1.0:0.0	.	686;706;682	P35712-3;P35712;P35712-2	.;SOX6_HUMAN;.	W	686;706;686;679;682;706	ENSP00000324948:R686W;ENSP00000339876:R706W;ENSP00000379644:R686W;ENSP00000432134:R679W;ENSP00000434455:R682W;ENSP00000433233:R706W	ENSP00000324948:R686W	R	-	1	2	SOX6	15964393	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.029000	0.88807	2.648000	0.89879	0.655000	0.94253	CGG		0.478	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		A	16007817	G	A	16007817	3	1	43	1	0	0	0	0	1	0	0	0	14992	1057	37	1	378	1	SOX6	11	16007817	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	1491931	16007817	118998699	80	4002										
SOX6	55553	broad.mit.edu	37	chr11	16208370	16208370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aaggtccatttgctgccgttGtttctcaatttgtgacgctg	10	9	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:16208370G>T	ENST00000352083.6	-	5	744	c.667C>A	c.(667-669)Caa>Aaa	p.Q223K	SOX6_ENST00000528252.1_Missense_Mutation_p.Q223K|SOX6_ENST00000527619.1_Missense_Mutation_p.Q226K|SOX6_ENST00000316399.6_Missense_Mutation_p.Q223K|SOX6_ENST00000528429.1_Missense_Mutation_p.Q223K|SOX6_ENST00000396356.3_Missense_Mutation_p.Q223K			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	223	Gln-rich.				astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.Q223K(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						TGCTGCCGTTGTTTCTCAATT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											208	195	200					11																	16208370		2200	4294	6494	16164946	SO:0001583	missense	55553			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.667C>A	11.37:g.16208370G>T	ENSP00000339876:p.Gln223Lys		16164946	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	G	27.1	4.800870	0.90538	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429	D;D;D;D;D;D	0.99121	-5.41;-5.35;-5.41;-5.45;-5.45;-5.35	5.73	5.73	0.89815	.	0.055575	0.85682	D	0.000000	D	0.99278	0.9748	M	0.82193	2.58	0.80722	D	1	D;P;P	0.63046	0.992;0.855;0.917	P;P;D	0.63488	0.798;0.474;0.915	D	0.99589	1.0975	10	0.87932	D	0	.	19.8956	0.96956	0.0:0.0:1.0:0.0	.	223;223;226	P35712-3;P35712;P35712-2	.;SOX6_HUMAN;.	K	223;223;223;223;226;223	ENSP00000324948:Q223K;ENSP00000339876:Q223K;ENSP00000379644:Q223K;ENSP00000432134:Q223K;ENSP00000434455:Q226K;ENSP00000433233:Q223K	ENSP00000324948:Q223K	Q	-	1	0	SOX6	16164946	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.708000	0.92522	0.563000	0.77884	CAA		0.522	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		T	16208370	G	T	16208370	3	4	43	1	0	0	0	0	1	0	0	0	14992	1386	48	2	1909	2	SOX6	11	16208370	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	200553	16208370	118798146	81	4003										
OR4C15	81309	broad.mit.edu	37	chr11	55322396	55322396	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gggggtagcctggacaggggGcctcttgcattccatgatac	15	10	1	1	rs193168035	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:55322396G>T	ENST00000314644.2	+	1	614	c.614G>T	c.(613-615)gGc>gTc	p.G205V		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G205V(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						TGGACAGGGGGCCTCTTGCAT	0.468										HNSCC(20;0.049)																																						1	Substitution - Missense(1)	large_intestine(1)	11											93	89	90					11																	55322396		2201	4296	6497	55078972	SO:0001583	missense	81309			BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.614G>T	11.37:g.55322396G>T	ENSP00000324958:p.Gly205Val		55078972	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.224451	0.39300	.	.	ENSG00000181939	ENST00000314644	T	0.39056	1.1	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.70168	0.3193	M	0.88906	2.99	0.40906	D	0.984193	D	0.89917	1.0	D	0.97110	1.0	T	0.77008	-0.2747	9	0.87932	D	0	.	16.0842	0.81025	0.0:0.0:1.0:0.0	.	151	Q8NGM1	OR4CF_HUMAN	V	205	ENSP00000324958:G205V	ENSP00000324958:G205V	G	+	2	0	OR4C15	55078972	0.966000	0.33281	0.956000	0.39512	0.484000	0.33280	1.919000	0.40015	2.665000	0.90641	0.385000	0.25706	GGC		0.468	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		T	55322396	G	T	55322396	3	4	43	1	0	0	0	0	1	0	0	0	11079	1203	42	2	616	2	OR4C15	11	55322396	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	39114026	55322396	79684120	82	4004										
OR8H1	219469	broad.mit.edu	37	chr11	56058005	56058005	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gctaaaattggagacgtgtcGcagaaaaagtgacgaactac	11	7	0	3	rs374019056		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:56058005G>A	ENST00000313022.2	-	1	561	c.534C>T	c.(532-534)tgC>tgT	p.C178C		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C178C(1)		NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					GAGACGTGTCGCAGAAAAAGT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	11						G		0,4402		0,0,2201	115	104	108		534	1.4	0.9	11		108	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	OR8H1	NM_001005199.1		0,1,6496	AA,AG,GG		0.0116,0.0,0.0077		178/312	56058005	1,12993	2201	4296	6497	55814581	SO:0001819	synonymous_variant	219469			AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.534C>T	11.37:g.56058005G>A			55814581	B2RNI7|Q6IFC5	Silent	SNP	ENST00000313022.2	37	CCDS31526.1																																																																																				0.438	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		A	56058005	G	A	56058005	2	1	43	1	0	0	0	0	0	0	0	1	11268	1079	38	1		1	OR8H1	11	56058005	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	735609	56058005	78948511	83	4005										
OR5A2	219981	broad.mit.edu	37	chr11	59190126	59190126	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cccacagaagacaaagtactGagtggcacagccaacaaagg	10	11	0	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:59190126G>T	ENST00000302040.4	-	1	323	c.301C>A	c.(301-303)Cag>Aag	p.Q101K		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q101K(1)		large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						ACAAAGTACTGAGTGGCACAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											81	78	79					11																	59190126		2201	4295	6496	58946702	SO:0001583	missense	219981			AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"GPCR / Class A : Olfactory receptors"	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.301C>A	11.37:g.59190126G>T	ENSP00000303834:p.Gln101Lys		58946702	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	37	CCDS31560.1	.	.	.	.	.	.	.	.	.	.	G	37	6.089241	0.97271	.	.	ENSG00000172324	ENST00000302040	T	0.00462	7.26	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33553	U	0.004785	T	0.03136	0.0092	H	0.97732	4.065	0.43499	D	0.995742	D	0.69078	0.997	D	0.81914	0.995	T	0.02505	-1.1149	10	0.72032	D	0.01	.	17.1743	0.86837	0.0:0.0:1.0:0.0	.	101	Q8NGI9	OR5A2_HUMAN	K	101	ENSP00000303834:Q101K	ENSP00000303834:Q101K	Q	-	1	0	OR5A2	58946702	1.000000	0.71417	0.200000	0.23457	0.887000	0.51463	6.298000	0.72763	2.740000	0.93945	0.585000	0.79938	CAG		0.512	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954		T	59190126	G	T	59190126	3	4	43	1	0	0	0	0	1	0	0	0	11171	1299	45	2	675	2	OR5A2	11	59190126	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	3132121	59190126	75816390	84	4006										
ZP1	22917	broad.mit.edu	37	chr11	60640728	60640728	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cctgctcctatgacccagccCggccccctgcggcttgagct	10	19	0	2	rs151198562		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:60640728C>T	ENST00000278853.5	+	7	1206	c.1206C>T	c.(1204-1206)ccC>ccT	p.P402P		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	402	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)		p.P402P(1)		breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						TGACCCAGCCCGGCCCCCTGC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	11																																								60397304	SO:0001819	synonymous_variant	22917			BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1206C>T	11.37:g.60640728C>T			60397304		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																				0.602	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		T	60640728	C	T	60640728	2	4	43	1	0	0	0	0	0	0	0	1	18254	639	23	1		1	ZP1	11	60640728	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	1450602	60640728	74365788	85	4007										
DAGLA	747	broad.mit.edu	37	chr11	61505220	61505220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tggttctgggcaaagacctcGtccccaggtgagtccttggc	13	12	1	2	rs377269260		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:61505220G>A	ENST00000257215.5	+	15	1692	c.1576G>A	c.(1576-1578)Gtc>Atc	p.V526I		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	526					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.V526I(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CAAAGACCTCGTCCCCAGGTG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	ILE/VAL	1,4403	2.1+/-5.4	0,1,2201	142	116	125		1576	4.1	0.9	11		125	0,8598		0,0,4299	no	missense	DAGLA	NM_006133.2	29	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	526/1043	61505220	1,13001	2202	4299	6501	61261796	SO:0001583	missense	747			AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1576G>A	11.37:g.61505220G>A	ENSP00000257215:p.Val526Ile		61261796	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	g	12.54	1.967413	0.34754	2.27E-4	0.0	ENSG00000134780	ENST00000257215	T	0.37752	1.18	4.11	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.56001	0.1956	L	0.59912	1.85	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.58020	-0.7710	10	0.45353	T	0.12	-32.4334	16.7773	0.85555	0.0:0.0:1.0:0.0	.	526	Q9Y4D2	DGLA_HUMAN	I	526	ENSP00000257215:V526I	ENSP00000257215:V526I	V	+	1	0	DAGLA	61261796	1.000000	0.71417	0.943000	0.38184	0.144000	0.21451	9.352000	0.97076	2.036000	0.60181	0.299000	0.19835	GTC		0.622	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61505220	G	A	61505220	3	1	43	1	0	0	0	0	1	0	0	0	4232	1145	40	1	1630	1	DAGLA	11	61505220	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	864492	61505220	73501296	86	4008										
INTS4	92105	broad.mit.edu	37	chr11	77612476	77612476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccacatcttaccctcgtgtaGttcgtgctgttactataagt	7	11	1	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:77612476G>A	ENST00000534064.1	-	18	2253	c.2219C>T	c.(2218-2220)aCt>aTt	p.T740I	AAMDC_ENST00000532481.1_Intron|INTS4_ENST00000535943.1_Missense_Mutation_p.T115I	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	740					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.T740I(1)	INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			CCCTCGTGTAGTTCGTGCTGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											214	192	199					11																	77612476		2200	4292	6492	77290124	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.2219C>T	11.37:g.77612476G>A	ENSP00000434466:p.Thr740Ile		77290124	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765153	0.49574	.	.	ENSG00000149262	ENST00000534064;ENST00000535943	.	.	.	4.64	4.64	0.57946	.	0.169167	0.51477	D	0.000085	T	0.28599	0.0708	N	0.08118	0	0.42164	D	0.991612	P	0.48911	0.917	B	0.41135	0.348	T	0.09465	-1.0673	9	0.21014	T	0.42	-11.1084	16.2184	0.82243	0.0:0.0:1.0:0.0	.	740	Q96HW7	INT4_HUMAN	I	740;115	.	ENSP00000434466:T740I	T	-	2	0	INTS4	77290124	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.769000	0.74985	2.572000	0.86782	0.460000	0.39030	ACT		0.413	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77612476	G	A	77612476	3	1	43	1	0	0	0	0	1	0	0	0	7801	1029	36	3	696	3	INTS4	11	77612476	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	16107256	77612476	57394040	87	4009										
GRIA4	2893	broad.mit.edu	37	chr11	105623916	105623916	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tggatcactacgaatggaacTgttttgtcttcctgtatgac	9	8	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:105623916T>A	ENST00000530497.1	+	3	457	c.457T>A	c.(457-459)Tgt>Agt	p.C153S	GRIA4_ENST00000393125.2_Missense_Mutation_p.C153S|GRIA4_ENST00000393127.2_Missense_Mutation_p.C153S|GRIA4_ENST00000525187.1_Missense_Mutation_p.C153S|GRIA4_ENST00000428631.2_Missense_Mutation_p.C153S|GRIA4_ENST00000282499.5_Missense_Mutation_p.C153S			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	153					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.C153S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CGAATGGAACTGTTTTGTCTT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	11											148	129	136					11																	105623916		2202	4299	6501	105129126	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.457T>A	11.37:g.105623916T>A	ENSP00000435775:p.Cys153Ser		105129126	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.332138	0.41297	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000531011;ENST00000530497;ENST00000525187	T;T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	5.51	3.17	0.36434	Extracellular ligand-binding receptor (1);	0.342781	0.29362	N	0.012367	T	0.49047	0.1534	N	0.01874	-0.695	0.28672	N	0.905573	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.31861	-0.9928	10	0.22706	T	0.39	.	1.9833	0.03431	0.2321:0.2391:0.0:0.5289	.	153;153;183;153	P48058;G3V164;Q59GL7;Q86XE8	GRIA4_HUMAN;.;.;.	S	153	ENSP00000376833:C153S;ENSP00000282499:C153S;ENSP00000376835:C153S;ENSP00000415551:C153S;ENSP00000432443:C153S;ENSP00000435775:C153S;ENSP00000432180:C153S	ENSP00000282499:C153S	C	+	1	0	GRIA4	105129126	0.992000	0.36948	1.000000	0.80357	0.993000	0.82548	1.083000	0.30815	0.892000	0.36259	0.533000	0.62120	TGT		0.433	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105623916	T	A	105623916	3	1	43	1	0	0	0	0	1	0	0	0	6791	1580	55	5	467	5	GRIA4	11	105623916	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	28011440	105623916	29382600	88	4010										
CWF19L2	143884	broad.mit.edu	37	chr11	107263597	107263597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agactgatctgttctgacaaGgattacttcttgctggtctt	9	8	4	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:107263597G>A	ENST00000282251.5	-	11	1669	c.1642C>T	c.(1642-1644)Ctt>Ttt	p.L548F	CWF19L2_ENST00000433523.1_Missense_Mutation_p.L548F	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	548							catalytic activity (GO:0003824)	p.L394F(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		GTTCTGACAAGGATTACTTCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	11											100	95	97					11																	107263597		2201	4298	6499	106768807	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1642C>T	11.37:g.107263597G>A	ENSP00000282251:p.Leu548Phe		106768807	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	G	25.0	4.590972	0.86851	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.36520	1.25;1.25	6.16	6.16	0.99307	.	0.064941	0.64402	D	0.000006	T	0.65544	0.2701	M	0.84846	2.72	0.58432	D	0.999999	D	0.71674	0.998	D	0.69307	0.963	T	0.68127	-0.5491	10	0.72032	D	0.01	-13.2786	18.3537	0.90348	0.0:0.0:1.0:0.0	.	548	Q2TBE0	C19L2_HUMAN	F	548	ENSP00000282251:L548F;ENSP00000387533:L548F	ENSP00000282251:L548F	L	-	1	0	CWF19L2	106768807	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.066000	0.76734	2.937000	0.99478	0.650000	0.86243	CTT		0.338	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		A	107263597	G	A	107263597	3	1	43	1	0	0	0	0	1	0	0	0	4078	1000	35	3	1074	3	CWF19L2	11	107263597	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	1639681	107263597	27742919	89	4011										
DSCAML1	57453	broad.mit.edu	37	chr11	117332233	117332233	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	acgccattgagggtgctgcgCgggggctctgaccaggagat	17	10	1	3	rs572641245	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:117332233C>T	ENST00000321322.6	-	18	3526	c.3525G>A	c.(3523-3525)ccG>ccA	p.P1175P	DSCAML1_ENST00000527706.1_Silent_p.P905P	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1115	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.P1175P(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	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)		GGGTGCTGCGCGGGGGCTCTG	0.627													C|||	4	0.000798722	0	0.0058	5008	,	,		17297	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11											73	74	74					11																	117332233		2201	4296	6497	116837443	SO:0001819	synonymous_variant	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.3525G>A	11.37:g.117332233C>T			116837443	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.627	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117332233	C	T	117332233	2	4	43	1	0	0	0	0	0	0	0	1	4780	755	27	1		1	DSCAML1	11	117332233	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	10068636	117332233	17674283	90	4012										
TMEM25	84866	broad.mit.edu	37	chr11	118403707	118403707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cctcctggttgtcctgtttgCcctggtgcgtgccaacccgc	11	16	0	0	rs75184401		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr11:118403707C>T	ENST00000313236.5	+	4	511	c.458C>T	c.(457-459)gCc>gTc	p.A153V	TMEM25_ENST00000524725.1_Missense_Mutation_p.A153V|TMEM25_ENST00000533102.1_Missense_Mutation_p.A153V|TMEM25_ENST00000442938.2_Missense_Mutation_p.A153V|TMEM25_ENST00000354064.7_Missense_Mutation_p.A49V|TMEM25_ENST00000529001.1_3'UTR|RP11-770J1.3_ENST00000532597.1_RNA|RP11-770J1.3_ENST00000528578.1_RNA|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000556583.1_RNA|TMEM25_ENST00000354284.4_Missense_Mutation_p.A153V|TMEM25_ENST00000359862.4_Missense_Mutation_p.A153V|TMEM25_ENST00000544878.1_Intron|TMEM25_ENST00000411589.2_Missense_Mutation_p.A153V	NM_032780.3	NP_116169.2	Q86YD3	TMM25_HUMAN	transmembrane protein 25	153						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A153V(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		GTCCTGTTTGCCCTGGTGCGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	89	87					11																	118403707		2200	4295	6495	117908917	SO:0001583	missense	84866			AK075437	CCDS8398.1, CCDS44745.1, CCDS44746.1, CCDS44747.1, CCDS44748.1	11q23.3	2013-01-11			ENSG00000149582	ENSG00000149582		"Immunoglobulin superfamily / C2-set domain containing"	25890	protein-coding gene	gene with protein product		613934				15254712, 12975309	Standard	NM_001144034		Approved	FLJ14399	uc010rye.2	Q86YD3	OTTHUMG00000166339	ENST00000313236.5:c.458C>T	11.37:g.118403707C>T	ENSP00000315635:p.Ala153Val		117908917	A8K8J4|B0YJA6|B0YJA7|B0YJA9|G5E9U4|Q6UW89|Q86UA7|Q8NBL5|Q96KA6|Q96MW9	Missense_Mutation	SNP	ENST00000313236.5	37	CCDS8398.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.296117|4.296117	0.81025|0.81025	.|.	.|.	ENSG00000149582|ENSG00000149582	ENST00000411589;ENST00000442938;ENST00000359862;ENST00000354284;ENST00000533137;ENST00000354064;ENST00000533102;ENST00000313236;ENST00000524725|ENST00000526973	T;T;T;T;T;T;T;T;T|.	0.31769|.	2.2;2.19;2.2;2.17;2.2;1.48;2.14;2.19;2.2|.	5.97|5.97	5.97|5.97	0.96955|0.96955	Immunoglobulin-like fold (1);|.	0.054186|.	0.64402|.	D|.	0.000001|.	T|T	0.45975|0.45975	0.1369|0.1369	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	P;P;P;P;P;P;B;P|.	0.45715|.	0.533;0.787;0.787;0.865;0.663;0.714;0.211;0.607|.	B;B;B;P;B;B;B;B|.	0.46585|.	0.102;0.219;0.322;0.521;0.206;0.213;0.106;0.223|.	T|T	0.33879|0.33879	-0.9851|-0.9851	10|5	0.23891|.	T|.	0.37|.	-26.8481|-26.8481	8.7879|8.7879	0.34832|0.34832	0.0:0.8417:0.0:0.1583|0.0:0.8417:0.0:0.1583	.|.	153;153;153;153;153;153;49;153|.	Q86YD3;B7Z4E4;Q8NBL5;G5E9U4;Q86YD3-4;E9PKP3;Q86YD3-3;Q86YD3-2|.	TMM25_HUMAN;.;.;.;.;.;.;.|.	V|S	153;153;153;153;121;49;153;153;153|37	ENSP00000411882:A153V;ENSP00000416071:A153V;ENSP00000352924:A153V;ENSP00000346237:A153V;ENSP00000433938:A121V;ENSP00000278959:A49V;ENSP00000431548:A153V;ENSP00000315635:A153V;ENSP00000431205:A153V|.	ENSP00000315635:A153V|.	A|P	+|+	2|1	0|0	TMEM25|TMEM25	117908917|117908917	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.311000|3.311000	0.51919|0.51919	2.837000|2.837000	0.97791|0.97791	0.655000|0.655000	0.94253|0.94253	GCC|CCC		0.597	TMEM25-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389266.1	NM_032780		T	118403707	C	T	118403707	3	4	43	1	0	0	0	0	1	0	0	0	16189	739	26	3	468	3	TMEM25	11	118403707	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	1071474	118403707	16602809	91	4013										
TAS2R9	50835	broad.mit.edu	37	chr12	10962223	10962223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tgaaaaggtgataccacataTcatcattctttggaacacta	6	8	3	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:10962223T>C	ENST00000240691.2	-	1	544	c.452A>G	c.(451-453)gAt>gGt	p.D151G	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	151					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)	p.D151G(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						ATACCACATATCATCATTCTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											54	56	55					12																	10962223		2203	4300	6503	10853490	SO:0001583	missense	50835			AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.452A>G	12.37:g.10962223T>C	ENSP00000240691:p.Asp151Gly		10853490	Q502V7|Q50KT0|Q50KT1|Q645W9	Missense_Mutation	SNP	ENST00000240691.2	37	CCDS8633.1	.	.	.	.	.	.	.	.	.	.	T	8.559	0.877409	0.17395	.	.	ENSG00000121381	ENST00000240691	T	0.00724	5.78	4.33	-7.61	0.01299	GPCR, rhodopsin-like superfamily (1);	2.077890	0.03346	U	0.195499	T	0.00784	0.0026	L	0.28458	0.855	0.09310	N	1	B	0.21309	0.054	B	0.16289	0.015	T	0.36578	-0.9742	10	0.26408	T	0.33	.	11.3565	0.49620	0.1064:0.5951:0.0:0.2985	.	151	Q9NYW1	TA2R9_HUMAN	G	151	ENSP00000240691:D151G	ENSP00000240691:D151G	D	-	2	0	TAS2R9	10853490	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.162000	0.10012	-2.032000	0.00926	-2.057000	0.00402	GAT		0.353	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1			C	10962223	T	C	10962223	3	2	43	1	0	0	0	0	1	0	0	0	15627	1435	50	4	490	4	TAS2R9	12	10962223	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10		10962223	122889672	92	4014										
PIK3C2G	5288	broad.mit.edu	37	chr12	18762480	18762480	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ttttatcaggtgagaagtttCcagacaagaagcctaaggtg	11	6	1	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:18762480C>A	ENST00000266497.5	+	29	4014	c.3976C>A	c.(3976-3978)Cca>Aca	p.P1326T	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.P1326T|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.P1367T			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1326					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.P1326T(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TGAGAAGTTTCCAGACAAGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	41	41					12																	18762480		1856	4097	5953	18653747	SO:0001583	missense	5288			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3976C>A	12.37:g.18762480C>A	ENSP00000266497:p.Pro1326Thr		18653747	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	C	4.585	0.108715	0.08780	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.60920	0.16;0.16;0.15	4.02	0.0809	0.14422	C2 calcium/lipid-binding domain, CaLB (1);	0.920458	0.08957	N	0.869228	T	0.26846	0.0657	N	0.03608	-0.345	0.19945	N	0.999947	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.15052	0.005;0.012;0.005	T	0.22871	-1.0204	10	0.09590	T	0.72	-0.1118	4.9436	0.13978	0.0:0.3892:0.3979:0.2129	.	1366;1367;1326	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	T	1326;1326;1367	ENSP00000404845:P1326T;ENSP00000266497:P1326T;ENSP00000445381:P1367T	ENSP00000266497:P1326T	P	+	1	0	PIK3C2G	18653747	0.000000	0.05858	0.306000	0.25113	0.886000	0.51366	-1.104000	0.03326	0.007000	0.14760	-0.253000	0.11424	CCA		0.353	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18762480	C	A	18762480	3	1	43	1	0	0	0	0	1	0	0	0	11942	855	30	2	4090	2	PIK3C2G	12	18762480	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	7800257	18762480	115089415	93	4015										
AMN1	196394	broad.mit.edu	37	chr12	31841957	31841957	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	taacctgttatcaaggggcaTccatggaagagtaatatacg	10	7	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:31841957T>C	ENST00000281471.6	-	6	852	c.687A>G	c.(685-687)ggA>ggG	p.G229G	AMN1_ENST00000536761.1_Silent_p.G211G|AMN1_ENST00000542781.1_Silent_p.G29G|AMN1_ENST00000541931.1_Silent_p.G29G|AMN1_ENST00000537562.1_Silent_p.G211G	NM_001113402.1|NM_001278411.1|NM_001278412.1	NP_001106873.1|NP_001265340.1|NP_001265341.1	Q8IY45	AMN1_HUMAN	antagonist of mitotic exit network 1 homolog (S. cerevisiae)	229								p.G229G(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	7	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			TCAAGGGGCATCCATGGAAGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	12											91	86	88					12																	31841957		1909	4129	6038	31733224	SO:0001819	synonymous_variant	196394				CCDS44858.1, CCDS61089.1	12p11.21	2010-07-19			ENSG00000151743	ENSG00000151743			27281	protein-coding gene	gene with protein product							Standard	NM_001113402		Approved		uc001rkq.4	Q8IY45	OTTHUMG00000169192	ENST00000281471.6:c.687A>G	12.37:g.31841957T>C			31733224	B7Z7J3|Q6NVU4|Q86X98	Silent	SNP	ENST00000281471.6	37	CCDS44858.1																																																																																				0.403	AMN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402807.2	NR_004854		C	31841957	T	C	31841957	2	2	43	1	0	0	0	0	0	0	0	1	581	1422	50	4		4	AMN1	12	31841957	Silent	SNP	T	TCGA-AG-3883-01A-02W-0899-10	13079477	31841957	102009938	94	4016										
KRT82	3888	broad.mit.edu	37	chr12	52788908	52788908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gcccccattgctcctgaggaCgccagtgctgaggacaggcg	14	14	0	2	rs149755657		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:52788908C>T	ENST00000257974.2	-	9	1470	c.1393G>A	c.(1393-1395)Gtc>Atc	p.V465I	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	465	Tail.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.V465I(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		CTCCTGAGGACGCCAGTGCTG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	54	47	49		1393	0.9	0	12	dbSNP_134	49	0,8600		0,0,4300	no	missense	KRT82	NM_033033.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	465/514	52788908	1,13005	2203	4300	6503	51075175	SO:0001583	missense	3888			Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"-", "Intermediate filaments type II, keratins (basic)"	6459	protein-coding gene	gene with protein product	"hard keratin type II 2"	601078	"keratin, hair, basic, 2"	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1393G>A	12.37:g.52788908C>T	ENSP00000257974:p.Val465Ile		51075175		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	.	.	.	.	.	.	.	.	.	.	C	0.918	-0.716728	0.03206	2.27E-4	0.0	ENSG00000161850	ENST00000257974	D	0.82344	-1.6	4.73	0.85	0.18980	.	1.675130	0.03601	N	0.233328	T	0.67097	0.2857	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.52756	-0.8533	10	0.22706	T	0.39	.	6.8571	0.24046	0.0:0.6053:0.0:0.3947	.	465	Q9NSB4	KRT82_HUMAN	I	465	ENSP00000257974:V465I	ENSP00000257974:V465I	V	-	1	0	KRT82	51075175	0.000000	0.05858	0.024000	0.17045	0.041000	0.13682	-1.471000	0.02344	-0.043000	0.13513	-0.258000	0.10820	GTC		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52788908	C	T	52788908	3	4	43	1	0	0	0	0	1	0	0	0	8517	536	19	1	152	1	KRT82	12	52788908	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	20946951	52788908	81062987	95	4017										
KIAA0748	9840	broad.mit.edu	37	chr12	55356420	55356420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccttggctggatgggtttccGtattggtggctggtagacta	15	7	0	1	rs148518799	byFrequency	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:55356420G>A	ENST00000449076.1	-	9	1394	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M	TESPA1_ENST00000316577.8_Missense_Mutation_p.T421M|TESPA1_ENST00000532804.1_Missense_Mutation_p.T283M|TESPA1_ENST00000524622.1_Missense_Mutation_p.T283M|TESPA1_ENST00000531122.1_Missense_Mutation_p.T283M|TESPA1_ENST00000524959.1_5'Flank	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	421					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.T283M(1)									ATGGGTTTCCGTATTGGTGGC	0.498													G|||	2	0.000399361	8e-04	0	5008	,	,		20022	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	MET/THR,MET/THR	0,3924		0,0,1962	147	150	149		1262,1262	-2.7	0	12	dbSNP_134	149	2,8284		0,2,4141	yes	missense,missense	KIAA0748	NM_001098815.1,NM_001136030.1	81,81	0,2,6103	AA,AG,GG		0.0241,0.0,0.0164	benign,benign	421/522,421/522	55356420	2,12208	1962	4143	6105	53642687	SO:0001583	missense	9840			AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.1262C>T	12.37:g.55356420G>A	ENSP00000400892:p.Thr421Met		53642687	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	37	CCDS44913.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	1.146	-0.647973	0.03506	0.0	2.41E-4	ENSG00000135426	ENST00000524622;ENST00000528240;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000531122	T;T;T;T;T	0.46819	0.86;0.86;0.87;0.87;0.86	3.92	-2.7	0.06004	.	1.095960	0.06924	N	0.809818	T	0.22360	0.0539	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17623	-1.0363	10	0.66056	D	0.02	-0.2781	1.1899	0.01862	0.4406:0.0968:0.1697:0.293	.	421	A2RU30	K0748_HUMAN	M	283;21;283;421;421;283	ENSP00000435622:T283M;ENSP00000432030:T283M;ENSP00000400892:T421M;ENSP00000312679:T421M;ENSP00000433098:T283M	ENSP00000312679:T421M	T	-	2	0	KIAA0748	53642687	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.240000	0.18042	-0.531000	0.06340	-2.158000	0.00328	ACG		0.498	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		A	55356420	G	A	55356420	3	1	43	1	0	0	0	0	1	0	0	0	8211	1145	40	1	311	1	KIAA0748	12	55356420	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	2567512	55356420	78495475	96	4018										
MSRB3	253827	broad.mit.edu	37	chr12	65722310	65722310	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tctgtttatttatcagtgccTttgaaggagaatacacacat	7	7	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:65722310T>A	ENST00000355192.3	+	3	337	c.211T>A	c.(211-213)Ttt>Att	p.F71I	MSRB3_ENST00000308259.5_Missense_Mutation_p.F64I|MSRB3_ENST00000540804.1_Missense_Mutation_p.F71I|MSRB3_ENST00000535664.1_Missense_Mutation_p.F64I	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	71					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)	p.F64I(1)|p.F71I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		TATCAGTGCCTTTGAAGGAGA	0.269																																																2	Substitution - Missense(2)	large_intestine(2)	12											116	118	118					12																	65722310		2203	4296	6499	64008577	SO:0001583	missense	253827			BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"deafness, autosomal recessive 74"	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.211T>A	12.37:g.65722310T>A	ENSP00000347324:p.Phe71Ile		64008577	B4DR19|B7ZAQ0|Q6UXS2	Missense_Mutation	SNP	ENST00000355192.3	37	CCDS8973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.01|18.01	3.527491|3.527491	0.64860|0.64860	.|.	.|.	ENSG00000174099|ENSG00000174099	ENST00000355192;ENST00000308259;ENST00000540804;ENST00000535664;ENST00000538045;ENST00000535239|ENST00000541189;ENST00000446731	T;T;T;T;T;T|.	0.79749|.	-1.3;-1.3;-1.1;-1.3;-1.1;-1.3|.	5.22|5.22	5.22|5.22	0.72569|0.72569	Mss4-like (1);Methionine sulphoxide reductase B (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88865|0.88865	0.6553|0.6553	H|H	0.98542|0.98542	4.26|4.26	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.995|.	D;D|.	0.76575|.	0.981;0.988|.	D|D	0.93170|0.93170	0.6565|0.6565	9|5	.|.	.|.	.|.	.|.	15.3886|15.3886	0.74723|0.74723	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	71;64|.	Q8IXL7;Q8IXL7-2|.	MSRB3_HUMAN;.|.	I|H	71;64;71;64;64;64|79;22	ENSP00000347324:F71I;ENSP00000312274:F64I;ENSP00000437623:F71I;ENSP00000441650:F64I;ENSP00000442620:F64I;ENSP00000445843:F64I|.	.|.	F|L	+|+	1|2	0|0	MSRB3|MSRB3	64008577|64008577	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	6.757000|6.757000	0.74924|0.74924	2.106000|2.106000	0.64143|0.64143	0.455000|0.455000	0.32223|0.32223	TTT|CTT		0.269	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		A	65722310	T	A	65722310	3	1	43	1	0	0	0	0	1	0	0	0	9919	1609	56	5	301	5	MSRB3	12	65722310	Missense_Mutation	SNP	T	TCGA-AG-3883-01A-02W-0899-10	10365890	65722310	68129585	97	4019										
NAV3	89795	broad.mit.edu	37	chr12	78415551	78415551	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cattcagaaaatgaaggtacCgctttaccatcggctgactc	8	11	1	3	rs368619435		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:78415551C>T	ENST00000397909.2	+	9	2105	c.1932C>T	c.(1930-1932)acC>acT	p.T644T	NAV3_ENST00000266692.7_Silent_p.T644T|NAV3_ENST00000228327.6_Silent_p.T644T|NAV3_ENST00000536525.2_Silent_p.T644T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	644						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.T644T(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ATGAAGGTACCGCTTTACCAT	0.408										HNSCC(70;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12						C		0,4030		0,0,2015	108	109	108		1932	-2.3	1	12		108	1,8391		0,1,4195	no	coding-synonymous	NAV3	NM_014903.4		0,1,6210	TT,TC,CC		0.0119,0.0,0.0081		644/2364	78415551	1,12421	2015	4196	6211	76939682	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1932C>T	12.37:g.78415551C>T			76939682	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																					0.408	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78415551	C	T	78415551	2	4	43	1	0	0	0	0	0	0	0	1	10215	639	23	1		1	NAV3	12	78415551	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	12693241	78415551	55436344	98	4020										
TMEM132D	121256	broad.mit.edu	37	chr12	129566495	129566495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cacaaactgcgtcaggacccGcaccatggcgtgctggtact	11	14	1	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr12:129566495G>A	ENST00000422113.2	-	7	2058	c.1732C>T	c.(1732-1734)Cgg>Tgg	p.R578W	TMEM132D_ENST00000389441.4_Missense_Mutation_p.R116W	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	578					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.R578W(2)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		GTCAGGACCCGCACCATGGCG	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	12											45	47	47					12																	129566495		2203	4299	6502	128132448	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1732C>T	12.37:g.129566495G>A	ENSP00000408581:p.Arg578Trp		128132448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787869	0.70337	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.55588	0.51;0.51	4.72	3.76	0.43208	.	0.101204	0.42964	D	0.000622	T	0.74741	0.3756	M	0.88105	2.93	0.44619	D	0.997599	D;D	0.89917	1.0;1.0	D;D	0.85130	0.984;0.997	T	0.79671	-0.1706	9	.	.	.	-44.7815	12.9732	0.58524	0.0:0.0:0.7201:0.2798	.	578;116	Q14C87;Q14C87-2	T132D_HUMAN;.	W	116;578	ENSP00000374092:R116W;ENSP00000408581:R578W	.	R	-	1	2	TMEM132D	128132448	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.775000	0.47702	2.149000	0.67028	0.561000	0.74099	CGG		0.652	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	129566495	G	A	129566495	3	1	43	1	0	0	0	0	1	0	0	0	16086	1086	38	1	1579	1	TMEM132D	12	129566495	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	51150944	129566495	4285400	99	4021										
TUBA3C	7278	broad.mit.edu	37	chr13	19752431	19752431	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aggtcgacgatctccttgccGatggtgtaatggcctctggc	13	11	2	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr13:19752431G>A	ENST00000400113.3	-	3	434	c.330C>T	c.(328-330)atC>atT	p.I110I		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	110					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.I110I(2)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCTCCTTGCCGATGGTGTAAT	0.542																																																2	Substitution - coding silent(2)	large_intestine(2)	13											222	188	200					13																	19752431		2203	4300	6503	18650431	SO:0001819	synonymous_variant	7278			AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"Tubulins"	12408	protein-coding gene	gene with protein product		602528	"tubulin, alpha 2"	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.330C>T	13.37:g.19752431G>A			18650431	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																				0.542	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001		A	19752431	G	A	19752431	2	1	43	1	0	0	0	0	0	0	0	1	16786	1048	37	1		1	TUBA3C	13	19752431	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10		19752431	95417447	100	4022										
RBM26	64062	broad.mit.edu	37	chr13	79932499	79932499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ggaacttttctaagttcaagCttggtattttcatttccaaa	6	7	3	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr13:79932499C>A	ENST00000438737.2	-	11	2039	c.1599G>T	c.(1597-1599)aaG>aaT	p.K533N	RBM26_ENST00000438724.1_Missense_Mutation_p.K533N|RBM26_ENST00000267229.7_Missense_Mutation_p.K533N			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	533	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K533N(2)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		TAAGTTCAAGCTTGGTATTTT	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	13											78	82	81					13																	79932499		2202	4300	6502	78830500	SO:0001583	missense	64062			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.1599G>T	13.37:g.79932499C>A	ENSP00000387531:p.Lys533Asn		78830500	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Missense_Mutation	SNP	ENST00000438737.2	37		.	.	.	.	.	.	.	.	.	.	C	17.65	3.441065	0.63067	.	.	ENSG00000139746	ENST00000267229;ENST00000438737;ENST00000327303;ENST00000438724	T;T	0.50813	0.73;0.73	5.14	2.7	0.31948	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	L	0.49640	1.575	0.58432	D	0.999996	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.994;0.996	T	0.53885	-0.8375	9	.	.	.	-22.9164	9.1056	0.36696	0.0:0.1511:0.0:0.8489	.	533;533;533	Q5T8P6-2;Q5T8P6;Q5T8P6-3	.;RBM26_HUMAN;.	N	533;534;533;533	ENSP00000267229:K533N;ENSP00000390222:K533N	.	K	-	3	2	RBM26	78830500	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.763000	0.38461	0.893000	0.36288	-0.483000	0.04790	AAG		0.328	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		A	79932499	C	A	79932499	3	1	43	1	0	0	0	0	1	0	0	0	13163	796	28	2	1387	2	RBM26	13	79932499	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	60180068	79932499	35237379	101	4023										
TPP2	7174	broad.mit.edu	37	chr13	103268839	103268839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aatttgatgttgccaacaacGgctcttctcaagttggtgct	9	9	2	1	rs202026163		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr13:103268839G>A	ENST00000376065.4	+	4	520	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TPP2_ENST00000376052.3_Missense_Mutation_p.G162S	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	162	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.G162S(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGCCAACAACGGCTCTTCTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	13											87	92	90					13																	103268839		2203	4300	6503	102066840	SO:0001583	missense	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.484G>A	13.37:g.103268839G>A	ENSP00000365233:p.Gly162Ser		102066840	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	5.997	0.367897	0.11352	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.55	2.91	0.33838	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.356145	0.32459	N	0.006067	T	0.16428	0.0395	N	0.13043	0.29	0.26312	N	0.977801	B	0.02656	0.0	B	0.04013	0.001	T	0.26815	-1.0092	9	0.08381	T	0.77	.	6.7401	0.23431	0.1165:0.0:0.3537:0.5298	.	162	P29144	TPP2_HUMAN	S	162	.	ENSP00000365220:G162S	G	+	1	0	TPP2	102066840	0.996000	0.38824	0.304000	0.25085	0.959000	0.62525	3.295000	0.51794	0.633000	0.30452	0.585000	0.79938	GGC		0.413	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			A	103268839	G	A	103268839	3	1	43	1	0	0	0	0	1	0	0	0	16452	1116	39	1	498	1	TPP2	13	103268839	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	23336340	103268839	11901039	102	4024										
NGB	58157	broad.mit.edu	37	chr14	77735634	77735634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	actggcggcagttgtactggAagaggggcagcaggtcaggc	18	8	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr14:77735634A>G	ENST00000298352.4	-	2	499	c.125T>C	c.(124-126)tTc>tCc	p.F42S		NM_021257.3	NP_067080.1	Q9NPG2	NGB_HUMAN	neuroglobin	42	Globin.				apoptotic process (GO:0006915)|oxygen transport (GO:0015671)	mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.F42S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0273)		GTTGTACTGGAAGAGGGGCAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	14											43	31	35					14																	77735634		2097	4097	6194	76805387	SO:0001583	missense	58157			AJ245946	CCDS9856.1	14q24.3	2014-06-13			ENSG00000165553	ENSG00000165553			14077	protein-coding gene	gene with protein product		605304				11029004, 17210637	Standard	NM_021257		Approved		uc001xtg.1	Q9NPG2	OTTHUMG00000171558	ENST00000298352.4:c.125T>C	14.37:g.77735634A>G	ENSP00000298352:p.Phe42Ser		76805387		Missense_Mutation	SNP	ENST00000298352.4	37	CCDS9856.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082876	0.76642	.	.	ENSG00000165553	ENST00000298352	D	0.99850	-7.16	4.88	2.48	0.30137	Globin-like (1);Globin, structural domain (1);	0.100795	0.64402	D	0.000001	D	0.99576	0.9847	M	0.78637	2.42	0.49130	D	0.999754	D	0.65815	0.995	P	0.58873	0.847	D	0.99167	1.0863	10	0.87932	D	0	-31.1297	5.4088	0.16336	0.7296:0.1774:0.0929:0.0	.	42	Q9NPG2	NGB_HUMAN	S	42	ENSP00000298352:F42S	ENSP00000298352:F42S	F	-	2	0	NGB	76805387	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.237000	0.65360	0.230000	0.21059	0.459000	0.35465	TTC		0.627	NGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414194.1	NM_021257		G	77735634	A	G	77735634	3	3	43	1	0	0	0	0	1	0	0	0	10423	246	9	4	342	4	NGB	14	77735634	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10		77735634	29613906	103	4025										
GJD2	57369	broad.mit.edu	37	chr15	35045073	35045073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agcgggagatgccttcctgcCttctgagcttggattttgat	12	9	1	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr15:35045073C>T	ENST00000290374.4	-	2	1048	c.572G>A	c.(571-573)aGg>aAg	p.R191K	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	191					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)	p.R191K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		GCCTTCCTGCCTTCTGAGCTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	15											131	138	136					15																	35045073		2201	4298	6499	32832365	SO:0001583	missense	57369			AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"Ion channels / Gap junction proteins (connexins)"	19154	protein-coding gene	gene with protein product	"connexin 36"	607058	"gap junction protein, alpha 9, 36kDa"	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.572G>A	15.37:g.35045073C>T	ENSP00000290374:p.Arg191Lys		32832365	Q2M241|Q9P2R0	Missense_Mutation	SNP	ENST00000290374.4	37	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.214092	0.58452	.	.	ENSG00000159248	ENST00000290374	D	0.97976	-4.64	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.94742	0.8303	L	0.34521	1.04	0.80722	D	1	P	0.35612	0.512	B	0.35073	0.195	D	0.92756	0.6220	10	0.02654	T	1	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	191	Q9UKL4	CXD2_HUMAN	K	191	ENSP00000290374:R191K	ENSP00000290374:R191K	R	-	2	0	GJD2	32832365	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.890000	0.99128	0.650000	0.86243	AGG		0.478	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			T	35045073	C	T	35045073	3	4	43	1	0	0	0	0	1	0	0	0	6437	681	24	3	397	3	GJD2	15	35045073	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		35045073	67486319	104	4026										
FBN1	2200	broad.mit.edu	37	chr15	48802322	48802322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gccatctgtgttgatgcagcGtccattattgcagatccggc	11	11	1	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr15:48802322G>A	ENST00000316623.5	-	14	2088	c.1633C>T	c.(1633-1635)Cgc>Tgc	p.R545C		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	545	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		R -> C (in MFS). {ECO:0000269|PubMed:11700157, ECO:0000269|PubMed:9338581}.		extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R545C(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTGATGCAGCGTCCATTATTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15	GRCh37	CD040176|CM970507	FBN1	D|M							102	90	94					15																	48802322		2197	4296	6493	46589614	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1633C>T	15.37:g.48802322G>A	ENSP00000325527:p.Arg545Cys		46589614	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120406	0.94385	.	.	ENSG00000166147	ENST00000316623	D	0.92199	-2.99	5.5	5.5	0.81552	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96932	0.8998	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96721	0.9532	10	0.48119	T	0.1	.	18.3167	0.90224	0.0:0.0:1.0:0.0	.	545	P35555	FBN1_HUMAN	C	545	ENSP00000325527:R545C	ENSP00000325527:R545C	R	-	1	0	FBN1	46589614	1.000000	0.71417	0.861000	0.33841	0.946000	0.59487	7.939000	0.87685	2.736000	0.93811	0.591000	0.81541	CGC		0.358	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48802322	G	A	48802322	3	1	43	1	0	0	0	0	1	0	0	0	5721	1145	40	1	7194	1	FBN1	15	48802322	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	13757249	48802322	53729070	105	4027										
SLTM	79811	broad.mit.edu	37	chr15	59186662	59186662	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gaaatcagctgtccatgcagCtcagtgcgatgaagatgtgc	12	9	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr15:59186662C>T	ENST00000380516.2	-	10	1434	c.1347G>A	c.(1345-1347)gaG>gaA	p.E449E	SLTM_ENST00000536328.1_Silent_p.E18E|AC025918.2_ENST00000452467.1_RNA	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	449	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E449E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTCCATGCAGCTCAGTGCGAT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	15											147	136	139					15																	59186662		2192	4292	6484	56973954	SO:0001819	synonymous_variant	79811			BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.1347G>A	15.37:g.59186662C>T			56973954	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000380516.2	37	CCDS10168.2																																																																																				0.418	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		T	59186662	C	T	59186662	2	4	43	1	0	0	0	0	0	0	0	1	14791	796	28	3		3	SLTM	15	59186662	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	10384340	59186662	43344730	106	4028										
CDH3	1001	broad.mit.edu	37	chr16	68679313	68679315	+	In_Frame_Del	DEL	CTC	CTC	-													0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctcgtggacctctcgcgtctCtcctccttctccaggtactc							TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr16:68679313_68679315delCTC	ENST00000264012.4	+	1	575_577	c.31_33delCTC	c.(31-33)ctcdel	p.L14del	CDH3_ENST00000581171.1_5'UTR|CDH3_ENST00000429102.2_In_Frame_Del_p.L14del|RP11-615I2.2_ENST00000562172.1_RNA	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	14					adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L11delL(1)|p.?(1)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCTCGCGTCTCTCCTCCTTCTCC	0.719																																																2	Unknown(1)|Deletion - In frame(1)	large_intestine(1)|breast(1)	16								15,4249		7,1,2124						0.7	0.1			48	22,8232		9,4,4114	no	coding	CDH3	NM_001793.4		16,5,6238	A1A1,A1R,RR		0.2665,0.3518,0.2956				37,12481				67236816	SO:0001651	inframe_deletion	1001			X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"Cadherins / Major cadherins"	1762	protein-coding gene	gene with protein product		114021	"cadherin 3, P-cadherin (placental)"			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.31_33delCTC	16.37:g.68679316_68679318delCTC	ENSP00000264012:p.Leu14del		67236814	B2R6F4|Q05DI6	In_Frame_Del	DEL	ENST00000264012.4	37	CCDS10868.1																																																																																				0.719	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		-	68679315	CTC	-	68679313	7	5	43	1	0	1	0	1	0	0	0	0	3117	913	32	0	33	0	CDH3	16	68679313	In_Frame_Del	DEL	CTC	TCGA-AG-3883-01A-02W-0899-10		68679313	21675440	107	4029										
NTN1	9423	broad.mit.edu	37	chr17	9086250	9086250	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aagagatccctgtagcgccgCcgacgactgcagccagcagc	12	15	0	1	rs376278603		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr17:9086250C>A	ENST00000173229.2	+	5	1482	c.1375C>A	c.(1375-1377)Ccg>Acg	p.P459T	NTN1_ENST00000538852.1_Missense_Mutation_p.P459T|NTN1_ENST00000546090.1_Missense_Mutation_p.P459T	NM_004822.2	NP_004813.2	O95631	NET1_HUMAN	netrin 1	459					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|establishment of nucleus localization (GO:0040023)|inner ear morphogenesis (GO:0042472)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of axon extension (GO:0030517)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of cell proliferation (GO:0008284)|regulation of cell migration (GO:0030334)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.P459T(1)	NTN1/ACLY(2)	central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(5)	13						TGTAGCGCCGCCGACGACTGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	THR/PRO	0,4406		0,0,2203	96	104	101		1375	5.8	0.2	17		101	2,8598	2.2+/-6.3	0,2,4298	no	missense	NTN1	NM_004822.2	38	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	benign	459/605	9086250	2,13004	2203	4300	6503	9026975	SO:0001583	missense	9423			U75586	CCDS11148.1	17p13-p12	2013-03-01			ENSG00000065320	ENSG00000065320		"Netrins"	8029	protein-coding gene	gene with protein product	"Netrin-1"	601614				9950216	Standard	NM_004822		Approved	NTN1L	uc002glw.4	O95631	OTTHUMG00000130257	ENST00000173229.2:c.1375C>A	17.37:g.9086250C>A	ENSP00000173229:p.Pro459Thr		9026975	E9KL51	Missense_Mutation	SNP	ENST00000173229.2	37	CCDS11148.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469735	0.26423	0.0	2.33E-4	ENSG00000065320	ENST00000173229;ENST00000538852;ENST00000546090;ENST00000436734	T;T;T;T	0.33654	1.4;1.4;1.4;2.84	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.37785	0.1016	M	0.67953	2.075	0.80722	D	1	B	0.26512	0.151	B	0.24269	0.052	T	0.37888	-0.9686	10	0.06625	T	0.88	.	20.1195	0.97955	0.0:1.0:0.0:0.0	.	459	O95631	NET1_HUMAN	T	459;459;459;79	ENSP00000173229:P459T;ENSP00000443259:P459T;ENSP00000441611:P459T;ENSP00000389375:P79T	ENSP00000173229:P459T	P	+	1	0	NTN1	9026975	1.000000	0.71417	0.192000	0.23308	0.025000	0.11179	7.016000	0.76393	2.759000	0.94783	0.650000	0.86243	CCG		0.567	NTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252583.1			A	9086250	C	A	9086250	3	1	43	1	0	0	0	0	1	0	0	0	10731	739	26	2	1389	2	NTN1	17	9086250	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		9086250	72108960	108	4030										
EXOC7	23265	broad.mit.edu	37	chr17	74085270	74085270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	cgggacctgtatcagggagtCgaaggtcttcttctggtggt	15	8	4	0	rs372862629		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr17:74085270C>T	ENST00000335146.7	-	9	1239	c.1186G>A	c.(1186-1188)Gac>Aac	p.D396N	EXOC7_ENST00000589210.1_Missense_Mutation_p.D345N|EXOC7_ENST00000411744.2_Missense_Mutation_p.D337N|EXOC7_ENST00000467929.2_Missense_Mutation_p.D304N|EXOC7_ENST00000405575.4_Missense_Mutation_p.D368N|EXOC7_ENST00000332065.5_Missense_Mutation_p.D314N|EXOC7_ENST00000607838.1_Missense_Mutation_p.D368N			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	396					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)		p.D345N(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			ATCAGGGAGTCGAAGGTCTTC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	88	95	93		1033,1186,1009,1102,940	5	0.9	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	EXOC7	NM_001013839.2,NM_001145297.2,NM_001145298.2,NM_001145299.2,NM_015219.3	23,23,23,23,23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	345/685,396/736,337/677,368/708,314/654	74085270	1,13005	2203	4300	6503	71596865	SO:0001583	missense	23265			BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1186G>A	17.37:g.74085270C>T	ENSP00000334100:p.Asp396Asn		71596865	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	C	32	5.162196	0.94727	0.0	1.16E-4	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.98	4.98	0.66077	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;0.971;1.0;0.998;0.999;0.991;0.998	D;P;D;P;D;P;P	0.75484	0.928;0.484;0.986;0.865;0.939;0.732;0.863	T	0.71919	-0.4447	9	0.17369	T	0.5	-29.4878	18.2619	0.90038	0.0:1.0:0.0:0.0	.	337;368;304;304;396;314;345	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	N	314;234;368;396;345;304;337	.	ENSP00000333806:D314N	D	-	1	0	EXOC7	71596865	1.000000	0.71417	0.900000	0.35374	0.960000	0.62799	5.665000	0.68052	2.300000	0.77407	0.557000	0.71058	GAC		0.632	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		T	74085270	C	T	74085270	3	4	43	1	0	0	0	0	1	0	0	0	5323	884	31	1	1069	1	EXOC7	17	74085270	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	64999020	74085270	7109940	109	4031										
CYGB	114757	broad.mit.edu	37	chr17	74527682	74527682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gactcggcaggcgtgcttccGcagctgggggctccgctcca	15	15	0	0	rs373180768		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr17:74527682G>A	ENST00000293230.5	-	2	597	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	PRCD_ENST00000592432.1_Intron|CYGB_ENST00000590175.1_Missense_Mutation_p.R14W|CYGB_ENST00000589342.1_Missense_Mutation_p.R79W|CYGB_ENST00000589145.1_Missense_Mutation_p.R14W|CYGB_ENST00000586160.1_5'Flank	NM_134268.4	NP_599030.1	Q8WWM9	CYGB_HUMAN	cytoglobin	79	Globin.				oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)	p.R79W(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)	7						GCGTGCTTCCGCAGCTGGGGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	64	64	64		235	5.4	1	17		64	0,8600		0,0,4300	no	missense	CYGB	NM_134268.3	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	79/191	74527682	1,13005	2203	4300	6503	72039277	SO:0001583	missense	114757			AJ315162	CCDS11746.1	17q25	2008-07-18				ENSG00000161544			16505	protein-coding gene	gene with protein product	"stellate cell activation-associated protein", "histoglobin"	608759				11919282	Standard	NM_134268		Approved	HGB, STAP	uc002jru.2	Q8WWM9		ENST00000293230.5:c.235C>T	17.37:g.74527682G>A	ENSP00000293230:p.Arg79Trp		72039277	Q541Y7|Q8N2X5	Missense_Mutation	SNP	ENST00000293230.5	37	CCDS11746.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.288743	0.80914	2.27E-4	0.0	ENSG00000161544	ENST00000293230	D	0.93712	-3.27	5.4	5.4	0.78164	Globin-like (1);Globin, structural domain (1);	0.000000	0.85682	D	0.000000	D	0.97532	0.9192	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98252	1.0494	10	0.87932	D	0	-11.1779	19.1688	0.93569	0.0:0.0:1.0:0.0	.	79	Q8WWM9	CYGB_HUMAN	W	79	ENSP00000293230:R79W	ENSP00000293230:R79W	R	-	1	2	CYGB	72039277	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.182000	0.58310	2.536000	0.85505	0.462000	0.41574	CGG		0.607	CYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450590.1	NM_134268		A	74527682	G	A	74527682	3	1	43	1	0	0	0	0	1	0	0	0	4145	1086	38	1	349	1	CYGB	17	74527682	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	442412	74527682	6667528	110	4032										
MIB1	57534	broad.mit.edu	37	chr18	19429197	19429197	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gtccttctatgattagtaatGattctgaaaccttagaagag	8	6	2	5			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr18:19429197G>T	ENST00000261537.6	+	17	2698	c.2434G>T	c.(2434-2436)Gat>Tat	p.D812Y	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	812					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D812Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GATTAGTAATGATTCTGAAAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											200	200	200					18																	19429197		2203	4300	6503	17683195	SO:0001583	missense	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.2434G>T	18.37:g.19429197G>T	ENSP00000261537:p.Asp812Tyr		17683195	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.900294	0.52227	.	.	ENSG00000101752	ENST00000261537	T	0.38240	1.15	5.33	5.33	0.75918	.	0.048325	0.85682	D	0.000000	T	0.41305	0.1153	N	0.08118	0	0.54753	D	0.999988	D	0.61697	0.99	D	0.70487	0.969	T	0.48328	-0.9045	10	0.36615	T	0.2	-20.6605	19.042	0.93004	0.0:0.0:1.0:0.0	.	812	Q86YT6	MIB1_HUMAN	Y	812	ENSP00000261537:D812Y	ENSP00000261537:D812Y	D	+	1	0	MIB1	17683195	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.391000	0.79828	2.494000	0.84150	0.585000	0.79938	GAT		0.348	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		T	19429197	G	T	19429197	3	4	43	1	0	0	0	0	1	0	0	0	9596	1290	45	2	2500	2	MIB1	18	19429197	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		19429197	58648051	111	4033										
ACTL9	284382	broad.mit.edu	37	chr19	8807881	8807881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccagcaggactggaaggcgcGcagggaggccaggatggagc	19	10	0	0			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr19:8807881G>A	ENST00000324436.3	-	1	1291	c.1171C>T	c.(1171-1173)Cgc>Tgc	p.R391C		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	391						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R391C(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						TGGAAGGCGCGCAGGGAGGCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											37	39	38					19																	8807881		2203	4299	6502	8668881	SO:0001583	missense	284382				CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.1171C>T	19.37:g.8807881G>A	ENSP00000316674:p.Arg391Cys		8668881	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	g	10.61	1.399657	0.25291	.	.	ENSG00000181786	ENST00000324436	T	0.08193	3.12	4.51	2.23	0.28157	.	0.317190	0.22565	N	0.058402	T	0.12220	0.0297	L	0.29908	0.895	0.35755	D	0.81972	D	0.76494	0.999	P	0.60886	0.88	T	0.17684	-1.0361	10	0.87932	D	0	.	6.1475	0.20293	0.0884:0.0:0.5749:0.3367	.	391	Q8TC94	ACTL9_HUMAN	C	391	ENSP00000316674:R391C	ENSP00000316674:R391C	R	-	1	0	ACTL9	8668881	0.013000	0.17824	0.431000	0.26735	0.759000	0.43091	0.742000	0.26216	0.564000	0.29238	0.457000	0.33378	CGC		0.652	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525		A	8807881	G	A	8807881	3	1	43	1	0	0	0	0	1	0	0	0	203	1087	38	1	83	1	ACTL9	19	8807881	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10		8807881	50321102	112	4034										
ZNF808	388558	broad.mit.edu	37	chr19	53050783	53050783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agggacgcttgactttcaggGatgtggctatagaattctca	12	7	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr19:53050783G>A	ENST00000359798.4	+	4	262	c.82G>A	c.(82-84)Gat>Aat	p.D28N		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GACTTTCAGGGATGTGGCTAT	0.413																																																0			19											119	127	124					19																	53050783		2203	4300	6503	57742595	SO:0001583	missense	388558			CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.82G>A	19.37:g.53050783G>A	ENSP00000352846:p.Asp28Asn		57742595	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	16.81	3.226060	0.58668	.	.	ENSG00000198482	ENST00000359798;ENST00000465448;ENST00000461779;ENST00000461321	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	2.29	2.29	0.28610	Krueppel-associated box (4);	.	.	.	.	T	0.49012	0.1532	H	0.98866	4.355	0.23798	N	0.996816	D	0.89917	1.0	D	0.97110	1.0	T	0.50092	-0.8868	9	0.87932	D	0	.	11.2779	0.49178	0.0:0.0:1.0:0.0	.	28	Q8N4W9	ZN808_HUMAN	N	28	ENSP00000352846:D28N;ENSP00000419291:D28N;ENSP00000417727:D28N;ENSP00000418696:D28N	ENSP00000352846:D28N	D	+	1	0	ZNF808	57742595	0.997000	0.39634	0.050000	0.19076	0.255000	0.26057	4.374000	0.59543	1.090000	0.41315	0.174000	0.16983	GAT		0.413	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		A	53050783	G	A	53050783	3	1	43	1	0	0	0	0	1	0	0	0	18212	1174	41	3	88	3	ZNF808	19	53050783	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	44242902	53050783	6078200	113	4035										
PDYN	5173	broad.mit.edu	37	chr20	1961096	1961096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	acttgagcttgggacgaatgCgccgcaagaagcccccatag	12	12	0	2	rs373922212		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr20:1961096C>T	ENST00000217305.2	-	4	863	c.638G>A	c.(637-639)cGc>cAc	p.R213H	PDYN_ENST00000539905.1_Missense_Mutation_p.R213H|PDYN_ENST00000540134.1_Missense_Mutation_p.R213H|RP4-684O24.5_ENST00000446562.1_RNA	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	213					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.R213H(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GGGACGAATGCGCCGCAAGAA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	102	112	108		638,638,638,638,638	5	1	20		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	PDYN	NM_001190892.1,NM_001190898.2,NM_001190899.2,NM_001190900.1,NM_024411.4	29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	213/255,213/255,213/255,213/255,213/255	1961096	1,13005	2203	4300	6503	1909096	SO:0001583	missense	5173				CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.638G>A	20.37:g.1961096C>T	ENSP00000217305:p.Arg213His		1909096	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	.	.	.	.	.	.	.	.	.	.	C	31	5.093258	0.94149	0.0	1.16E-4	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	D;D;D	0.83419	-1.72;-1.72;-1.72	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.92189	0.7523	M	0.89095	3.005	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.93235	0.6621	10	0.66056	D	0.02	-19.9746	15.8394	0.78835	0.0:1.0:0.0:0.0	.	213	P01213	PDYN_HUMAN	H	213	ENSP00000440185:R213H;ENSP00000442259:R213H;ENSP00000217305:R213H	ENSP00000217305:R213H	R	-	2	0	PDYN	1909096	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.347000	0.73004	2.603000	0.88011	0.313000	0.20887	CGC		0.592	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			T	1961096	C	T	1961096	3	4	43	1	0	0	0	0	1	0	0	0	11730	768	27	1	130	1	PDYN	20	1961096	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		1961096	61064424	114	4036										
SLC24A3	57419	broad.mit.edu	37	chr20	19665779	19665779	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aacagcagggcttataccaaCggggaatctgaggtggccat	13	9	1	1	rs370751183		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr20:19665779C>T	ENST00000328041.6	+	12	1295	c.1098C>T	c.(1096-1098)aaC>aaT	p.N366N		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	366					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.N366N(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CTTATACCAACGGGGAATCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	20						C		2,4404	4.2+/-10.8	0,2,2201	84	84	84		1098	-0.6	1	20		84	0,8600		0,0,4300	no	coding-synonymous	SLC24A3	NM_020689.3		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		366/645	19665779	2,13004	2203	4300	6503	19613779	SO:0001819	synonymous_variant	57419			AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1098C>T	20.37:g.19665779C>T			19613779	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	37	CCDS13140.1																																																																																				0.517	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689		T	19665779	C	T	19665779	2	4	43	1	0	0	0	0	0	0	0	1	14504	535	19	1		1	SLC24A3	20	19665779	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	17704683	19665779	43359741	115	4037										
SSTR4	6754	broad.mit.edu	37	chr20	23016830	23016830	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ctacctgctcatcgtgggcaAgatgcgcgccgtggccctgc	13	15	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr20:23016830A>T	ENST00000255008.3	+	1	774	c.710A>T	c.(709-711)aAg>aTg	p.K237M	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	237					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.K237M(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					ATCGTGGGCAAGATGCGCGCC	0.647																																					Esophageal Squamous(15;850 1104 16640)											1	Substitution - Missense(1)	large_intestine(1)	20											78	86	83					20																	23016830		2172	4285	6457	22964830	SO:0001583	missense	6754				CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.710A>T	20.37:g.23016830A>T	ENSP00000255008:p.Lys237Met		22964830	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179737	0.57800	.	.	ENSG00000132671	ENST00000255008	T	0.38887	1.11	3.6	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.082939	0.43416	U	0.000570	T	0.68476	0.3005	M	0.91090	3.175	0.44155	D	0.996957	D	0.76494	0.999	D	0.75484	0.986	T	0.75436	-0.3318	10	0.87932	D	0	.	11.1475	0.48438	1.0:0.0:0.0:0.0	.	237	P31391	SSR4_HUMAN	M	237	ENSP00000255008:K237M	ENSP00000255008:K237M	K	+	2	0	SSTR4	22964830	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.495000	0.60353	1.481000	0.48307	0.533000	0.62120	AAG		0.647	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			T	23016830	A	T	23016830	3	4	43	1	0	0	0	0	1	0	0	0	15239	72	3	5	712	5	SSTR4	20	23016830	Missense_Mutation	SNP	A	TCGA-AG-3883-01A-02W-0899-10	3351051	23016830	40008690	116	4038										
NFATC2	4773	broad.mit.edu	37	chr20	50048703	50048703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	gaccgggggtccgtttttggCggctctttggctcgtggcat	16	10	1	0	rs553983994		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr20:50048703C>T	ENST00000396009.3	-	9	2842	c.2623G>A	c.(2623-2625)Gcc>Acc	p.A875T	NFATC2_ENST00000610033.1_Missense_Mutation_p.A656T|NFATC2_ENST00000609507.1_Missense_Mutation_p.A656T|NFATC2_ENST00000609943.1_Missense_Mutation_p.A855T|NFATC2_ENST00000414705.1_Missense_Mutation_p.A855T|NFATC2_ENST00000371564.3_Missense_Mutation_p.A875T	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	875					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A875T(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CCGTTTTTGGCGGCTCTTTGG	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		16243	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											97	97	97					20																	50048703		2203	4300	6503	49482110	SO:0001583	missense	4773			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2623G>A	20.37:g.50048703C>T	ENSP00000379330:p.Ala875Thr		49482110	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485399	0.44147	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.15139	2.45;2.46;2.46	5.42	3.5	0.40072	.	0.453535	0.24174	N	0.040870	T	0.09992	0.0245	L	0.36672	1.1	0.31734	N	0.636613	B;B;B;B	0.31859	0.343;0.291;0.011;0.343	B;B;B;B	0.18871	0.021;0.023;0.002;0.023	T	0.20472	-1.0274	10	0.16896	T	0.51	-11.7881	7.1212	0.25446	0.1376:0.7199:0.0:0.1426	.	855;855;875;875	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	T	875;875;855	ENSP00000360619:A875T;ENSP00000379330:A875T;ENSP00000396471:A855T	ENSP00000360619:A875T	A	-	1	0	NFATC2	49482110	0.784000	0.28713	0.998000	0.56505	0.970000	0.65996	0.888000	0.28268	0.667000	0.31107	-0.216000	0.12614	GCC		0.582	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		T	50048703	C	T	50048703	3	4	43	1	0	0	0	0	1	0	0	0	10393	768	27	1	210	1	NFATC2	20	50048703	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10	27031873	50048703	12976817	117	4039										
NCAM2	4685	broad.mit.edu	37	chr21	22656525	22656525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tctttgcagcgattggtgaaCctgaaagtatagattggtat	11	5	1	3			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr21:22656525C>T	ENST00000400546.1	+	3	391	c.142C>T	c.(142-144)Cct>Tct	p.P48S	NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000535285.1_Missense_Mutation_p.P73S|NCAM2_ENST00000486367.1_3'UTR	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	48	Ig-like C2-type 1.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P48S(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GATTGGTGAACCTGAAAGTAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	21											111	99	103					21																	22656525		1829	4076	5905	21578396	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.142C>T	21.37:g.22656525C>T	ENSP00000383392:p.Pro48Ser		21578396	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290429	0.59976	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	T;T	0.41758	0.99;0.99	5.73	5.73	0.89815	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.097389	0.64402	D	0.000001	T	0.67344	0.2883	M	0.92784	3.345	0.45762	D	0.998658	D;P	0.56746	0.977;0.927	P;P	0.56960	0.81;0.743	T	0.74948	-0.3490	10	0.62326	D	0.03	-13.3019	14.1145	0.65144	0.0:0.8496:0.1504:0.0	.	73;48	B7Z841;O15394	.;NCAM2_HUMAN	S	48;73	ENSP00000383392:P48S;ENSP00000441887:P73S	ENSP00000383392:P48S	P	+	1	0	NCAM2	21578396	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.487000	0.35540	2.713000	0.92767	0.591000	0.81541	CCT		0.333	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22656525	C	T	22656525	3	4	43	1	0	0	0	0	1	0	0	0	10234	507	18	3	152	3	NCAM2	21	22656525	Missense_Mutation	SNP	C	TCGA-AG-3883-01A-02W-0899-10		22656525	25473370	118	4040										
LSS	4047	broad.mit.edu	37	chr21	47611069	47611069	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tacagctgggagaagcggccGagggcccagatggggaagat	18	8	0	3	rs372838581		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr21:47611069G>A	ENST00000397728.3	-	22	2226	c.2148C>T	c.(2146-2148)ctC>ctT	p.L716L	AP001468.58_ENST00000415026.1_RNA|LSS_ENST00000457828.2_Silent_p.L636L|LSS_ENST00000522411.1_Silent_p.L705L|LSS_ENST00000356396.4_Silent_p.L716L	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	716					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)	p.L716L(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					AGAAGCGGCCGAGGGCCCAGA	0.562																																					Pancreas(114;955 2313 34923 50507)											1	Substitution - coding silent(1)	large_intestine(1)	21						G	,,,	0,4406		0,0,2203	99	98	98		2148,2115,1908,2148	-11.1	0	21		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	716/733,705/722,636/653,716/733	47611069	1,13005	2203	4300	6503	46435497	SO:0001819	synonymous_variant	4047			U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.2148C>T	21.37:g.47611069G>A			46435497	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																				0.562	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47611069	G	A	47611069	2	1	43	1	0	0	0	0	0	0	0	1	9094	1045	37	1		1	LSS	21	47611069	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10	24954544	47611069	518826	119	4041										
MED15	51586	broad.mit.edu	37	chr22	20920885	20920885	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ccaccaattcagcagccaccGatgcagcagccacagcctcc	7	19	1	0	rs201812389		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chr22:20920885G>A	ENST00000263205.7	+	7	891	c.822G>A	c.(820-822)ccG>ccA	p.P274P	MED15_ENST00000542773.1_Silent_p.P79P|MED15_ENST00000425759.2_Silent_p.P163P|MED15_ENST00000406969.1_Silent_p.P248P|MED15_ENST00000382974.2_Silent_p.P203P|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000541476.1_Silent_p.P248P|MED15_ENST00000292733.7_Silent_p.P274P	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	274	Pro-rich.			Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.P274P(2)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	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)			AGCAGCCACCGATGCAGCAGC	0.647													G|||	1	0.000199681	8e-04	0	5008	,	,		14998	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	22											63	70	68					22																	20920885		2203	4299	6502	19250885	SO:0001819	synonymous_variant	51586			AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"trinucleotide repeat containing 7", "PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.822G>A	22.37:g.20920885G>A			19250885	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	CCDS33602.1																																																																																				0.647	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		A	20920885	G	A	20920885	2	1	43	1	0	0	0	0	0	0	0	1	9463	1045	37	1		1	MED15	22	20920885	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10		20920885	30383681	120	4042										
NLGN4X	57502	broad.mit.edu	37	chrX	5821678	5821678	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	tgggggtcgtctgggatgacGtcgccgtcgatcaccggccc	16	13	2	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chrX:5821678G>A	ENST00000381095.3	-	5	1668	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	NLGN4X_ENST00000381092.1_Silent_p.D347D|NLGN4X_ENST00000538097.1_Silent_p.D347D|NLGN4X_ENST00000381093.2_Silent_p.D367D|NLGN4X_ENST00000275857.6_Silent_p.D347D	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	347					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.D347D(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						CTGGGATGACGTCGCCGTCGA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	X											133	92	106					X																	5821678		2203	4300	6503	5831678	SO:0001819	synonymous_variant	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1041C>T	X.37:g.5821678G>A			5831678	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.587	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5821678	G	A	5821678	2	1	43	1	0	0	0	0	0	0	0	1	10495	1136	40	1		1	NLGN4X	23	5821678	Silent	SNP	G	TCGA-AG-3883-01A-02W-0899-10		5821678	149448882	121	4043										
DACH2	117154	broad.mit.edu	37	chrX	85769338	85769338	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	agtgttgcaggaaaatgcccGccttctgacccatgcagtcc	10	13	1	1			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chrX:85769338G>A	ENST00000373125.4	+	3	584	c.584G>A	c.(583-585)cGc>cAc	p.R195H	DACH2_ENST00000510272.1_5'UTR|DACH2_ENST00000508860.1_Missense_Mutation_p.R28H|DACH2_ENST00000373131.1_Missense_Mutation_p.R182H	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	195					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R182H(2)|p.R195H(2)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						GAAAATGCCCGCCTTCTGACC	0.468																																																4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	X											54	46	49					X																	85769338		2203	4300	6503	85655994	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.584G>A	X.37:g.85769338G>A	ENSP00000362217:p.Arg195His		85655994	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	5.896	0.349361	0.11182	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000400297	D;D	0.83163	-1.69;-1.68	4.88	4.01	0.46588	.	0.170292	0.41194	D	0.000921	T	0.65165	0.2665	N	0.20766	0.605	0.80722	D	1	P;B;P	0.45902	0.868;0.181;0.735	B;B;B	0.34452	0.09;0.183;0.109	T	0.62053	-0.6935	10	0.12430	T	0.62	.	12.126	0.53917	0.0857:0.0:0.9143:0.0	.	61;182;195	Q1RMF5;Q96NX9-2;Q96NX9	.;.;DACH2_HUMAN	H	195;182;195;28;28	ENSP00000362223:R182H;ENSP00000362217:R195H	ENSP00000345134:R195H	R	+	2	0	DACH2	85655994	0.999000	0.42202	0.992000	0.48379	0.987000	0.75469	2.924000	0.48876	0.834000	0.34852	0.506000	0.49869	CGC		0.468	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		A	85769338	G	A	85769338	3	1	43	1	0	0	0	0	1	0	0	0	4227	1087	38	1	594	1	DACH2	23	85769338	Missense_Mutation	SNP	G	TCGA-AG-3883-01A-02W-0899-10	79947660	85769338	69501222	122	4044										
PCDH11X	27328	broad.mit.edu	37	chrX	91137944	91137944	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	actattgaaatctgcagtgaGatataactttctaggaacaa	7	6	2	2			TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chrX:91137944G>T	ENST00000373094.1	+	2	3878				PCDH11X_ENST00000361655.2_Intron|PCDH11X_ENST00000373088.1_Intron|PCDH11X_ENST00000504220.2_Intron|PCDH11X_ENST00000395337.2_Missense_Mutation_p.E1024D|PCDH11X_ENST00000373097.1_Intron|PCDH11X_ENST00000298274.8_Intron|PCDH11X_ENST00000406881.1_Intron	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked						homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1024D(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						TCTGCAGTGAGATATAACTTT	0.318																																					NSCLC(38;925 1092 2571 38200 45895)											1	Substitution - Missense(1)	large_intestine(1)	X											144	129	134					X																	91137944		2203	4299	6502	91024600	SO:0001627	intron_variant	27328			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3033+3672G>T	X.37:g.91137944G>T			91024600	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.852726	0.32699	.	.	ENSG00000102290	ENST00000395337	T	0.52295	0.67	3.42	2.55	0.30701	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.80722	D	1	P	0.42871	0.792	B	0.43301	0.415	T	0.29579	-1.0007	8	0.02654	T	1	.	5.498	0.16813	0.1558:0.0:0.8442:0.0	.	1024	Q9BZA7-2	.	D	1024	ENSP00000378746:E1024D	ENSP00000378746:E1024D	E	+	3	2	PCDH11X	91024600	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	1.090000	0.30902	0.807000	0.34208	0.523000	0.50628	GAG		0.318	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91137944	G	T	91137944	1	4	43	0	1	0	0	0	0	0	0	0	11539	933	33	2		2	PCDH11X	23	91137944	Intron	SNP	G	TCGA-AG-3883-01A-02W-0899-10	5368606	91137944	64132616	123	4045										
IL1RAPL2	26280	broad.mit.edu	37	chrX	104993063	104993063	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	ttgaattgatgctcttctacAggcagcactttggagctgat	10	8	2	3	rs372925400		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chrX:104993063A>C	ENST00000372582.1	+	9	1915	c.1159A>C	c.(1159-1161)Agg>Cgg	p.R387R	IL1RAPL2_ENST00000344799.4_Silent_p.R387R|IL1RAPL2_ENST00000485671.1_3'UTR	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	387					central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R387R(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GCTCTTCTACAGGCAGCACTT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	X						A		0,3835		0,0,1632,571	115	92	100		1159	-2.9	0.9	X		100	1,6727		0,1,2427,1872	no	coding-synonymous	IL1RAPL2	NM_017416.1		0,1,4059,2443	CC,CA,AA,A		0.0149,0.0,0.0095		387/687	104993063	1,10562	2203	4300	6503	104879719	SO:0001819	synonymous_variant	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1159A>C	X.37:g.104993063A>C			104879719	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	37	CCDS14517.1																																																																																				0.413	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		C	104993063	A	C	104993063	2	2	43	1	0	0	0	0	0	0	0	1	7683	179	7	4		4	IL1RAPL2	23	104993063	Silent	SNP	A	TCGA-AG-3883-01A-02W-0899-10	13855119	104993063	50277497	124	4046										
MAGEC2	51438	broad.mit.edu	37	chrX	141291474	141291474	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.04	5	1	0.444364161849711	4.47919075144509	0.188995390356333	1	1	0	aaagaggagcagcaggagctCagaggactctgggaaggacc	16	8	2	2	rs528011223		TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3883-01A-02W-0899-10	TCGA-AG-3883-10A-01W-0901-10	g.chrX:141291474C>T	ENST00000247452.3	-	3	647	c.300G>A	c.(298-300)ctG>ctA	p.L100L		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	100	Ser-rich.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.L100L(1)		NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAGGAGCTCAgaggactct	0.572										HNSCC(46;0.14)																																						1	Substitution - coding silent(1)	large_intestine(1)	X											72	67	69					X																	141291474		2203	4300	6503	141119140	SO:0001819	synonymous_variant	51438			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.300G>A	X.37:g.141291474C>T			141119140	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Silent	SNP	ENST00000247452.3	37	CCDS14678.1																																																																																				0.572	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		T	141291474	C	T	141291474	2	4	43	1	0	0	0	0	0	0	0	1	9211	813	29	3		3	MAGEC2	23	141291474	Silent	SNP	C	TCGA-AG-3883-01A-02W-0899-10	36298411	141291474	13979086	125	4047										
PADI1	29943	hgsc.bcm.edu	37	chr1	17555207	17555207	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acagccaggggagcaggagaTcaagttctatgtggaggggc	17	7	2	1	rs371985846		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:17555207T>A	ENST00000375471.4	+	7	832	c.740T>A	c.(739-741)aTc>aAc	p.I247N		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	247					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		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)	GAGCAGGAGATCAAGTTCTAT	0.572																																					Esophageal Squamous(80;414 1257 4580 27746 50832)											0			1											142	145	144					1																	17555207		2203	4300	6503	17427794	SO:0001583	missense	29943			AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.740T>A	1.37:g.17555207T>A	ENSP00000364620:p.Ile247Asn		17427794	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	T	6.452	0.451601	0.12223	.	.	ENSG00000142623	ENST00000375471	T	0.14766	2.48	4.44	4.44	0.53790	Protein-arginine deiminase (PAD), central domain (2);	0.628414	0.16721	N	0.202243	T	0.17746	0.0426	L	0.50333	1.59	0.80722	D	1	P	0.50369	0.934	P	0.47206	0.541	T	0.02208	-1.1195	10	0.29301	T	0.29	-17.4383	11.6905	0.51512	0.0:0.0:0.0:1.0	.	247	Q9ULC6	PADI1_HUMAN	N	247	ENSP00000364620:I247N	ENSP00000364620:I247N	I	+	2	0	PADI1	17427794	0.002000	0.14202	0.473000	0.27253	0.046000	0.14306	0.370000	0.20433	1.859000	0.53934	0.459000	0.35465	ATC		0.572	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		A	17555207	T	A	17555207	3	1	44	1	0	0	0	0	1	0	0	0	11408	1435	50	5	766	5	PADI1	1	17555207	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		17555207	231695414	1	4048										
AKR7A2	8574	hgsc.bcm.edu	37	chr1	19633531	19633531	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcagcccagctattcccaaaGaagcggcccacaggctgttt	9	14	1	1	rs2231202	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:19633531G>A	ENST00000235835.3	-	5	774	c.753C>T	c.(751-753)ttC>ttT	p.F251F	RNU6-1099P_ENST00000363533.1_RNA	NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	251					carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TATTCCCAAAGAAGCGGCCCA	0.602													G|||	6	0.00119808	0.0038	0.0014	5008	,	,		13940	0		0	False		,,,				2504	0															0			1						G		17,4389	24.3+/-50.5	0,17,2186	100	108	105		753	4.3	1	1	dbSNP_98	105	0,8600		0,0,4300	no	coding-synonymous	AKR7A2	NM_003689.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		251/360	19633531	17,12989	2203	4300	6503	19506118	SO:0001819	synonymous_variant	8574			AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"Aldo-keto reductases"	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.753C>T	1.37:g.19633531G>A			19506118	O75749|Q5TG63	Silent	SNP	ENST00000235835.3	37	CCDS194.1																																																																																				0.602	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689		A	19633531	G	A	19633531	2	1	44	1	0	0	0	0	0	0	0	1	475	933	33	3		3	AKR7A2	1	19633531	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	2078324	19633531	229617090	2	4049										
PAFAH2	5051	hgsc.bcm.edu	37	chr1	26303229	26303229	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtggcccctccaaatgaatgTcccatcacagccacacggct	8	16	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:26303229T>C	ENST00000374282.3	-	8	881	c.702A>G	c.(700-702)ggA>ggG	p.G234G	PAFAH2_ENST00000374284.1_Silent_p.G234G	NM_000437.3	NP_000428.2	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2, 40kDa	234					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|phospholipid binding (GO:0005543)			NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	9		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		CAAATGAATGTCCCATCACAG	0.493																																																0			1											94	80	85					1																	26303229		2203	4300	6503	26175816	SO:0001819	synonymous_variant	5051			D87845	CCDS270.1	1p34.3	2008-09-19	2002-08-29		ENSG00000158006	ENSG00000158006			8579	protein-coding gene	gene with protein product		602344	"platelet-activating factor acetylhydrolase 2 (40kD)"			8955149, 9494101	Standard	NM_000437		Approved	HSD-PLA2	uc001bld.4	Q99487	OTTHUMG00000007437	ENST00000374282.3:c.702A>G	1.37:g.26303229T>C			26175816	D3DPK1|O15458|Q5SY02	Silent	SNP	ENST00000374282.3	37	CCDS270.1																																																																																				0.493	PAFAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019544.1	NM_000437		C	26303229	T	C	26303229	2	2	44	1	0	0	0	0	0	0	0	1	11418	1654	58	4		4	PAFAH2	1	26303229	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	6669698	26303229	222947392	3	4050										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32262288	32262288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctggaagtctgcacggctccTtctgttgctgctcaatgata	10	11	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:32262288T>C	ENST00000360482.2	-	10	2303	c.2174A>G	c.(2173-2175)aAg>aGg	p.K725R	SPOCD1_ENST00000373648.2_3'UTR|SPOCD1_ENST00000257100.3_Missense_Mutation_p.K218R|SPOCD1_ENST00000533231.1_Missense_Mutation_p.K725R	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	725	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		GCACGGCTCCTTCTGTTGCTG	0.567																																																0			1											145	137	140					1																	32262288		2203	4300	6503	32034875	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2174A>G	1.37:g.32262288T>C	ENSP00000353670:p.Lys725Arg		32034875	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	T	8.531	0.870903	0.17322	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231	T;T;T;T	0.45276	0.9;1.92;0.93;1.91	4.34	1.64	0.23874	Transcription elongation factor S-II, central domain (1);	.	.	.	.	T	0.15869	0.0382	N	0.05078	-0.115	0.80722	D	1	B;B;B;B	0.22746	0.039;0.074;0.007;0.044	B;B;B;B	0.25140	0.01;0.058;0.006;0.036	T	0.14254	-1.0479	9	0.05959	T	0.93	-11.2123	4.7501	0.13056	0.0:0.3215:0.0:0.6785	.	69;725;162;725	Q6ZMY3-4;Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;.;SPOC1_HUMAN	R	218;725;123;162;725	ENSP00000257100:K218R;ENSP00000353670:K725R;ENSP00000399778:K162R;ENSP00000435851:K725R	ENSP00000257100:K218R	K	-	2	0	SPOCD1	32034875	0.988000	0.35896	0.996000	0.52242	0.808000	0.45660	0.107000	0.15375	0.644000	0.30656	0.379000	0.24179	AAG		0.567	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		C	32262288	T	C	32262288	3	2	44	1	0	0	0	0	1	0	0	0	15117	1609	56	4	1504	4	SPOCD1	1	32262288	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	5959059	32262288	216988333	4	4051										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34666527	34666527	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccgcccaagaaacctacatgTccagccgagaagaacttgct	8	14	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:34666527T>C	ENST00000488417.1	+	3	1284	c.1164T>C	c.(1162-1164)tgT>tgC	p.C388C	C1orf94_ENST00000373374.3_Silent_p.C198C	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	388										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				AACCTACATGTCCAGCCGAGA	0.607																																																0			1											55	55	55					1																	34666527		2203	4300	6503	34439114	SO:0001819	synonymous_variant	84970			AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1164T>C	1.37:g.34666527T>C			34439114	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																				0.607	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		C	34666527	T	C	34666527	2	2	44	1	0	0	0	0	0	0	0	1	2077	1673	58	4		4	C1orf94	1	34666527	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	2404239	34666527	214584094	5	4052										
CLSPN	63967	hgsc.bcm.edu	37	chr1	36213602	36213602	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtcttaggctctggggaggCgttatacagatcctgggaat	14	7	2	1	rs561888056		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:36213602C>G	ENST00000318121.3	-	14	2590	c.2533G>C	c.(2533-2535)Gcc>Ccc	p.A845P	CLSPN_ENST00000251195.5_Missense_Mutation_p.A845P|CLSPN_ENST00000520551.1_Missense_Mutation_p.A792P|CLSPN_ENST00000373220.3_Missense_Mutation_p.A781P	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	845					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTGGGGAGGCGTTATACAGA	0.448																																																0			1											224	234	231					1																	36213602		2203	4300	6503	35986189	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.2533G>C	1.37:g.36213602C>G	ENSP00000312995:p.Ala845Pro		35986189	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.640477	0.47153	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.31769	1.48;1.5;1.6;1.59	5.69	4.78	0.61160	.	0.053886	0.85682	D	0.000000	T	0.51398	0.1672	L	0.60455	1.87	0.52099	D	0.99994	D;P	0.89917	1.0;0.837	D;B	0.79784	0.993;0.353	T	0.52675	-0.8544	10	0.54805	T	0.06	-2.2542	14.8584	0.70359	0.0:0.9309:0.0:0.0691	.	781;845	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	P	845;845;781;792	ENSP00000251195:A845P;ENSP00000312995:A845P;ENSP00000362317:A781P;ENSP00000428848:A792P	ENSP00000251195:A845P	A	-	1	0	CLSPN	35986189	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.011000	0.40922	1.409000	0.46915	0.563000	0.77884	GCC		0.448	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		G	36213602	C	G	36213602	3	3	44	1	0	0	0	0	1	0	0	0	3566	768	27	5	1534	5	CLSPN	1	36213602	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1547075	36213602	213037019	6	4053										
MACF1	23499	hgsc.bcm.edu	37	chr1	39913186	39913186	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	caactggctcactctagcagAgcagagtttaaacatcgctt	8	11	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:39913186A>G	ENST00000372915.3	+	80	19472	c.19385A>G	c.(19384-19386)gAg>gGg	p.E6462G	MACF1_ENST00000564288.1_Missense_Mutation_p.E6563G|MACF1_ENST00000317713.7_Missense_Mutation_p.E4504G|MACF1_ENST00000361689.2_Missense_Mutation_p.E4504G|MACF1_ENST00000289893.4_Missense_Mutation_p.E5006G|MACF1_ENST00000545844.1_Missense_Mutation_p.E4504G|MACF1_ENST00000567887.1_Missense_Mutation_p.E6600G|MACF1_ENST00000539005.1_Missense_Mutation_p.E4374G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6462			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACTCTAGCAGAGCAGAGTTTA	0.408																																																0			1											95	96	96					1																	39913186		2203	4300	6503	39685773	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.19385A>G	1.37:g.39913186A>G	ENSP00000362006:p.Glu6462Gly		39685773	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	A	28.2	4.903802	0.92035	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.74574	0.3734	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.79787	-0.1656	10	0.87932	D	0	.	16.6277	0.84984	1.0:0.0:0.0:0.0	.	6462;4504	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	G	4504;6462;4504;4504;4374;5006	ENSP00000439537:E4504G;ENSP00000362006:E6462G;ENSP00000354573:E4504G;ENSP00000313438:E4504G;ENSP00000444364:E4374G;ENSP00000289893:E5006G	ENSP00000289893:E5006G	E	+	2	0	MACF1	39685773	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.330000	0.79161	0.528000	0.53228	GAG		0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39913186	A	G	39913186	3	3	44	1	0	0	0	0	1	0	0	0	9174	304	11	4	19968	4	MACF1	1	39913186	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	3699584	39913186	209337435	7	4054										
HPCAL4	51440	hgsc.bcm.edu	37	chr1	40149642	40149642	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agcatctccaggcgcgtgatGcgcccgtcgccgtccaggtc	13	16	1	1	rs784634	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:40149642G>T	ENST00000372844.3	-	3	736	c.345C>A	c.(343-345)cgC>cgA	p.R115R		NM_001282396.1|NM_001282397.1|NM_016257.2	NP_001269325.1|NP_001269326.1|NP_057341.1	Q9UM19	HPCL4_HUMAN	hippocalcin like 4	115	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				central nervous system development (GO:0007417)|signal transduction (GO:0007165)	intracellular (GO:0005622)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|lung(5)|stomach(1)	8	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)			GGCGCGTGATGCGCCCGTCGC	0.692													G|||	4288	0.85623	0.9191	0.8256	5008	,	,		12058	0.8165		0.825	False		,,,				2504	0.8661															0			1						G		3857,547	762.6+/-413.1	1694,469,39	40	42	41		345	3.5	1	1	dbSNP_86	41	6936,1664	729.4+/-406.7	2788,1360,152	no	coding-synonymous	HPCAL4	NM_016257.2		4482,1829,191	TT,TG,GG		19.3488,12.4205,17.0025		115/192	40149642	10793,2211	2202	4300	6502	39922229	SO:0001819	synonymous_variant	51440			AB001105	CCDS441.1, CCDS72761.1	1p34.2	2013-01-10			ENSG00000116983	ENSG00000116983		"EF-hand domain containing"	18212	protein-coding gene	gene with protein product						10520747	Standard	NM_016257		Approved	HLP4, DKFZp761G122	uc001cdr.3	Q9UM19	OTTHUMG00000009246	ENST00000372844.3:c.345C>A	1.37:g.40149642G>T			39922229	B2R5U2|D3DPU1|Q5TG97|Q8N611	Silent	SNP	ENST00000372844.3	37	CCDS441.1																																																																																				0.692	HPCAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025640.1	NM_016257		T	40149642	G	T	40149642	2	4	44	1	0	0	0	0	0	0	0	1	7352	1306	46	2		2	HPCAL4	1	40149642	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	236456	40149642	209100979	8	4055										
SLFNL1	200172	hgsc.bcm.edu	37	chr1	41481845	41481845	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gctgctggagctgctccttcTccatcatcagcgccttcatc	8	16	4	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:41481845T>C	ENST00000359345.1	-	4	3733	c.1157A>G	c.(1156-1158)gAg>gGg	p.E386G	SLFNL1_ENST00000397197.2_Missense_Mutation_p.E338G|SLFNL1_ENST00000372613.2_Missense_Mutation_p.E338G|SLFNL1_ENST00000439569.2_Missense_Mutation_p.E386G|SLFNL1_ENST00000372611.1_Missense_Mutation_p.E327G|SLFNL1_ENST00000302946.8_Missense_Mutation_p.E386G	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	386							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				CTGCTCCTTCTCCATCATCAG	0.642																																																0			1											93	84	87					1																	41481845		2203	4300	6503	41254432	SO:0001583	missense	200172			BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1157A>G	1.37:g.41481845T>C	ENSP00000352299:p.Glu386Gly		41254432	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.239922	0.58995	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.37915	1.37;1.17;1.5;1.37;1.37;1.17	5.25	5.25	0.73442	.	0.000000	0.49916	D	0.000130	T	0.47728	0.1461	L	0.34521	1.04	0.36682	D	0.879113	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.996	T	0.57974	-0.7718	10	0.87932	D	0	-35.3513	11.5599	0.50769	0.0:0.0:0.0:1.0	.	338;327;386	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	G	386;338;327;386;386;338	ENSP00000304401:E386G;ENSP00000361696:E338G;ENSP00000361694:E327G;ENSP00000352299:E386G;ENSP00000398938:E386G;ENSP00000380381:E338G	ENSP00000304401:E386G	E	-	2	0	SLFNL1	41254432	1.000000	0.71417	0.925000	0.36789	0.373000	0.29922	4.572000	0.60886	1.991000	0.58162	0.459000	0.35465	GAG		0.642	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990		C	41481845	T	C	41481845	3	2	44	1	0	0	0	0	1	0	0	0	14775	1551	54	4	70	4	SLFNL1	1	41481845	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	1332203	41481845	207768776	9	4056										
AK5	26289	hgsc.bcm.edu	37	chr1	77752792	77752792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	actaaatggaggacagtcacGgagatcctttctaagaaatg	10	7	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:77752792G>A	ENST00000354567.2	+	2	490	c.227G>A	c.(226-228)cGg>cAg	p.R76Q	AK5_ENST00000317704.4_3'UTR|AK5_ENST00000344720.5_Missense_Mutation_p.R50Q	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	76					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						GGACAGTCACGGAGATCCTTT	0.368																																																0			1											71	70	70					1																	77752792		2203	4300	6503	77525380	SO:0001583	missense	26289			AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"Adenylate kinases"	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.227G>A	1.37:g.77752792G>A	ENSP00000346577:p.Arg76Gln		77525380	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Missense_Mutation	SNP	ENST00000354567.2	37	CCDS675.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939429	0.92526	.	.	ENSG00000154027	ENST00000354567;ENST00000344720;ENST00000478407	T;T;D	0.83914	-0.62;-0.67;-1.78	5.59	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.78748	0.4332	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;0.957	P;B	0.59546	0.859;0.223	T	0.78033	-0.2362	10	0.38643	T	0.18	-0.7307	14.2613	0.66088	0.0717:0.0:0.9283:0.0	.	76;76	Q9Y6K8;Q8N291	KAD5_HUMAN;.	Q	76;50;50	ENSP00000346577:R76Q;ENSP00000341430:R50Q;ENSP00000434409:R50Q	ENSP00000341430:R50Q	R	+	2	0	AK5	77525380	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.583000	0.82559	2.809000	0.96659	0.650000	0.86243	CGG		0.368	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858		A	77752792	G	A	77752792	3	1	44	1	0	0	0	0	1	0	0	0	443	1116	39	1	233	1	AK5	1	77752792	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	36270947	77752792	171497829	10	4057										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86252103	86252103	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tttactcctggaggacctggAgccccagcaagacctgttct	10	13	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:86252103A>G	ENST00000370571.2	-	48	4359	c.3993T>C	c.(3991-3993)gcT>gcC	p.A1331A	COL24A1_ENST00000436319.1_Silent_p.A1331A	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1331	Collagen-like 15.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		GAGGACCTGGAGCCCCAGCAA	0.463																																																0			1											88	91	90					1																	86252103		1835	4083	5918	86024691	SO:0001819	synonymous_variant	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3993T>C	1.37:g.86252103A>G			86024691	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																				0.463	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		G	86252103	A	G	86252103	2	3	44	1	0	0	0	0	0	0	0	1	3689	291	11	4		4	COL24A1	1	86252103	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	8499311	86252103	162998518	11	4058										
AGL	178	hgsc.bcm.edu	37	chr1	100343239	100343239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agaacttatttgctggggagAcagtgttaaattacgctatg	11	5	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:100343239A>G	ENST00000294724.4	+	12	1944	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	AGL_ENST00000361915.3_Missense_Mutation_p.D489G|AGL_ENST00000361302.3_Missense_Mutation_p.D473G|AGL_ENST00000370163.3_Missense_Mutation_p.D489G|AGL_ENST00000370161.2_Missense_Mutation_p.D473G|AGL_ENST00000370165.3_Missense_Mutation_p.D489G|AGL_ENST00000361522.4_Missense_Mutation_p.D472G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGCTGGGGAGACAGTGTTAAA	0.363																																																0			1											102	99	100					1																	100343239		2203	4300	6503	100115827	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1466A>G	1.37:g.100343239A>G	ENSP00000294724:p.Asp489Gly		100115827	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838082	0.91117	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12;-3.12;-3.12	5.97	5.97	0.96955	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97687	1.0176	10	0.87932	D	0	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	472;473;489	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	489;489;489;489;473;473;472	ENSP00000355106:D489G;ENSP00000359184:D489G;ENSP00000359182:D489G;ENSP00000294724:D489G;ENSP00000354971:D473G;ENSP00000359180:D473G;ENSP00000354635:D472G	ENSP00000294724:D489G	D	+	2	0	AGL	100115827	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.896000	0.92521	2.288000	0.76882	0.533000	0.62120	GAC		0.363	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100343239	A	G	100343239	3	3	44	1	0	0	0	0	1	0	0	0	384	275	10	4	1577	4	AGL	1	100343239	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	14091136	100343239	148907382	12	4059										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111146297	111146297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcctacagttgtcatggagaCgactgcccaccagaaggcat	11	12	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:111146297C>T	ENST00000485317.1	-	3	1781	c.1108G>A	c.(1108-1110)Gtc>Atc	p.V370I	KCNA2_ENST00000369770.3_Intron|KCNA2_ENST00000440270.1_Missense_Mutation_p.V370I|KCNA2_ENST00000316361.4_Missense_Mutation_p.V370I|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	370					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	GTCATGGAGACGACTGCCCAC	0.517																																					Pancreas(18;568 735 10587 23710 36357)											0			1											51	54	53					1																	111146297		2203	4300	6503	110947820	SO:0001583	missense	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.1108G>A	1.37:g.111146297C>T	ENSP00000433109:p.Val370Ile		110947820	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800235	0.70567	.	.	ENSG00000177301	ENST00000485317;ENST00000440270;ENST00000316361	D;D;D	0.97620	-4.46;-4.46;-4.46	5.71	5.71	0.89125	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97436	0.9161	L	0.46741	1.465	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96260	0.9190	10	0.32370	T	0.25	.	19.857	0.96762	0.0:1.0:0.0:0.0	.	370	P16389	KCNA2_HUMAN	I	370	ENSP00000433109:V370I;ENSP00000415257:V370I;ENSP00000314520:V370I	ENSP00000314520:V370I	V	-	1	0	KCNA2	110947820	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.770000	0.85390	2.703000	0.92315	0.655000	0.94253	GTC		0.517	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		T	111146297	C	T	111146297	3	4	44	1	0	0	0	0	1	0	0	0	8024	536	19	1	395	1	KCNA2	1	111146297	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	10803058	111146297	138104324	13	4060										
SLC16A1	6566	hgsc.bcm.edu	37	chr1	113460045	113460045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccgcaaagaaatactgaattCgaggtcttattggctttgtg	10	7	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:113460045C>T	ENST00000538576.1	-	4	1814	c.983G>A	c.(982-984)cGa>cAa	p.R328Q	SLC16A1_ENST00000369626.3_Missense_Mutation_p.R328Q|SLC16A1_ENST00000433570.4_Missense_Mutation_p.R328Q	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	328					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	ATACTGAATTCGAGGTCTTAT	0.453																																																0			1											61	50	54					1																	113460045		2203	4300	6503	113261568	SO:0001583	missense	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.983G>A	1.37:g.113460045C>T	ENSP00000441065:p.Arg328Gln		113261568	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080583	0.76528	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.56	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.053038	0.64402	D	0.000001	T	0.68137	0.2968	M	0.85630	2.765	0.42796	D	0.993912	D;D	0.71674	0.996;0.998	P;D	0.65773	0.87;0.938	T	0.74080	-0.3780	10	0.59425	D	0.04	.	10.4687	0.44624	0.0:0.8501:0.0:0.1499	.	328;328	Q49A45;P53985	.;MOT1_HUMAN	Q	328	ENSP00000358640:R328Q;ENSP00000441065:R328Q;ENSP00000416167:R328Q;ENSP00000445061:R328Q	ENSP00000358640:R328Q	R	-	2	0	SLC16A1	113261568	0.962000	0.33011	0.998000	0.56505	0.902000	0.53008	2.039000	0.41193	1.481000	0.48307	0.563000	0.77884	CGA		0.453	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		T	113460045	C	T	113460045	3	4	44	1	0	0	0	0	1	0	0	0	14439	884	31	1	527	1	SLC16A1	1	113460045	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	2313748	113460045	135790576	14	4061										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131472	150131472	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cttctggcagaggttcagggActgggagatgggaagcgaaa	17	6	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:150131472A>G	ENST00000369124.4	+	6	1262	c.984A>G	c.(982-984)ggA>ggG	p.G328G	PLEKHO1_ENST00000025469.6_Silent_p.G294G|PLEKHO1_ENST00000369126.1_Silent_p.G145G	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	328	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTTCAGGGACTGGGAGATG	0.642																																																0			1											52	57	56					1																	150131472		2203	4300	6503	148398096	SO:0001819	synonymous_variant	51177			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.984A>G	1.37:g.150131472A>G			148398096	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Silent	SNP	ENST00000369124.4	37	CCDS945.1																																																																																				0.642	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		G	150131472	A	G	150131472	2	3	44	1	0	0	0	0	0	0	0	1	12115	262	10	4		4	PLEKHO1	1	150131472	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	36671427	150131472	99119149	15	4062										
LCE3A	353142	hgsc.bcm.edu	37	chr1	152595447	152595447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtgactcaggcagcagctgcGctcggagctgggcccacagc	15	14	1	1	rs375349290		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:152595447G>A	ENST00000335674.1	-	1	132	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C		NM_178431.1	NP_848518.1	Q5TA76	LCE3A_HUMAN	late cornified envelope 3A	45					keratinization (GO:0031424)					endometrium(1)|lung(5)	6	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGCAGCTGCGCTCGGAGCTG	0.657																																																0			1											47	50	49					1																	152595447		2203	4300	6503	150862071	SO:0001583	missense	353142				CCDS1017.1	1q21.3	2008-02-05			ENSG00000185962	ENSG00000185962		"Late cornified envelopes"	29461	protein-coding gene	gene with protein product		612613				11698679	Standard	NM_178431		Approved	LEP13	uc010pdt.2	Q5TA76	OTTHUMG00000012397	ENST00000335674.1:c.133C>T	1.37:g.152595447G>A	ENSP00000335006:p.Arg45Cys		150862071		Missense_Mutation	SNP	ENST00000335674.1	37	CCDS1017.1	.	.	.	.	.	.	.	.	.	.	C	8.887	0.953125	0.18431	.	.	ENSG00000185962	ENST00000335674	T	0.03553	3.89	3.61	1.65	0.23941	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.09310	N	1	B	0.23058	0.079	B	0.10450	0.005	T	0.48031	-0.9070	8	0.56958	D	0.05	.	4.2341	0.10616	0.0:0.5864:0.1897:0.2239	.	45	Q5TA76	LCE3A_HUMAN	C	45	ENSP00000335006:R45C	ENSP00000335006:R45C	R	-	1	0	LCE3A	150862071	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.720000	0.04969	0.014000	0.14944	-0.786000	0.03341	CGC		0.657	LCE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034517.2	NM_178431		A	152595447	G	A	152595447	3	1	44	1	0	0	0	0	1	0	0	0	8691	1087	38	1	139	1	LCE3A	1	152595447	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	2463975	152595447	96655174	16	4063										
SPRR3	6707	hgsc.bcm.edu	37	chr1	152975543	152975543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctttaccccaccacctcagcTtcaacagcagcaggtgaaac	6	16	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:152975543T>C	ENST00000295367.4	+	2	89	c.47T>C	c.(46-48)cTt>cCt	p.L16P	SPRR3_ENST00000331860.3_Missense_Mutation_p.L16P|SPRR3_ENST00000542696.1_Missense_Mutation_p.L16P	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	16					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCACCTCAGCTTCAACAGCAG	0.488																																																0			1											86	82	84					1																	152975543		2203	4300	6503	151242167	SO:0001583	missense	6707			AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.47T>C	1.37:g.152975543T>C	ENSP00000295367:p.Leu16Pro		151242167	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	.	.	.	.	.	.	.	.	.	.	T	9.780	1.175172	0.21704	.	.	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.17370	2.5;2.28;2.5;2.34	4.49	-1.91	0.07641	.	.	.	.	.	T	0.01627	0.0052	N	0.01800	-0.715	0.19300	N	0.999975	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.47381	-0.9122	9	0.29301	T	0.29	.	8.7832	0.34804	0.0:0.3031:0.0:0.6969	.	16;16	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	P	16	ENSP00000330391:L16P;ENSP00000402016:L16P;ENSP00000295367:L16P;ENSP00000441477:L16P	ENSP00000295367:L16P	L	+	2	0	SPRR3	151242167	0.000000	0.05858	0.001000	0.08648	0.867000	0.49689	-1.227000	0.02950	-0.229000	0.09854	-0.376000	0.06991	CTT		0.488	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416		C	152975543	T	C	152975543	3	2	44	1	0	0	0	0	1	0	0	0	15142	1609	56	4	49	4	SPRR3	1	152975543	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	380096	152975543	96275078	17	4064										
LELP1	149018	hgsc.bcm.edu	37	chr1	153177339	153177339	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aagtgcccatgggaaaagtgTccagcaccacccaagtgcct	10	13	0	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:153177339T>C	ENST00000368747.1	+	2	266	c.156T>C	c.(154-156)tgT>tgC	p.C52C		NM_001010857.1	NP_001010857.1	Q5T871	LELP1_HUMAN	late cornified envelope-like proline-rich 1	52	Cys/Pro-rich.									NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(9)|ovary(1)|pancreas(1)|prostate(1)	19	all_lung(78;3.51e-31)|Lung NSC(65;1.34e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGGAAAAGTGTCCAGCACCAC	0.562																																																0			1											181	148	159					1																	153177339		2203	4300	6503	151443963	SO:0001819	synonymous_variant	149018				CCDS30869.1	1q21.3	2008-02-05			ENSG00000203784	ENSG00000203784			32046	protein-coding gene	gene with protein product		611042					Standard	NM_001010857		Approved		uc001fbl.4	Q5T871	OTTHUMG00000013935	ENST00000368747.1:c.156T>C	1.37:g.153177339T>C			151443963	A1L4E1	Silent	SNP	ENST00000368747.1	37	CCDS30869.1																																																																																				0.562	LELP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039104.1	NM_001010857		C	153177339	T	C	153177339	2	2	44	1	0	0	0	0	0	0	0	1	8740	1673	58	4		4	LELP1	1	153177339	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	201796	153177339	96073282	18	4065										
NES	10763	hgsc.bcm.edu	37	chr1	156640308	156640308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcttccaggatcggggtgtaCgttgggctgggggagaccag	18	8	1	1	rs3748571	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:156640308C>T	ENST00000368223.3	-	4	3804	c.3672G>A	c.(3670-3672)acG>acA	p.T1224T		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1224	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCGGGGTGTACGTTGGGCTGG	0.652													C|||	1123	0.224241	0.0159	0.2882	5008	,	,		17214	0.2946		0.3032	False		,,,				2504	0.3067															0			1						C		278,4128	154.8+/-188.1	8,262,1933	79	78	79		3672	-6.6	0	1	dbSNP_107	79	2455,6145	399.5+/-346.5	350,1755,2195	no	coding-synonymous	NES	NM_006617.1		358,2017,4128	TT,TC,CC		28.5465,6.3096,21.0134		1224/1622	156640308	2733,10273	2203	4300	6503	154906932	SO:0001819	synonymous_variant	10763			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3672G>A	1.37:g.156640308C>T			154906932	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																				0.652	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156640308	C	T	156640308	2	4	44	1	0	0	0	0	0	0	0	1	10368	523	19	1		1	NES	1	156640308	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	3462969	156640308	92610313	19	4066										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158582696	158582696	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atcactggacttgatgttttCtgactccttgtcaatcagga	8	9	4	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:158582696C>T	ENST00000368147.4	-	51	7225	c.7045G>A	c.(7045-7047)Gaa>Aaa	p.E2349K	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2349	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGATGTTTTCTGACTCCTTG	0.473																																																0			1											107	102	104					1																	158582696		1949	4148	6097	156849320	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.7045G>A	1.37:g.158582696C>T	ENSP00000357129:p.Glu2349Lys		156849320	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	35	5.461592	0.96240	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.22336	1.96;1.96	5.39	5.39	0.77823	EF-hand-like domain (1);	0.000000	0.32624	N	0.005851	T	0.39989	0.1099	M	0.71036	2.16	0.58432	D	0.999999	D	0.71674	0.998	D	0.74348	0.983	T	0.17837	-1.0356	10	0.72032	D	0.01	.	17.8981	0.88895	0.0:1.0:0.0:0.0	.	2349	P02549	SPTA1_HUMAN	K	2349;2346	ENSP00000357130:E2349K;ENSP00000357129:E2346K	ENSP00000357129:E2346K	E	-	1	0	SPTA1	156849320	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	6.962000	0.76048	2.795000	0.96236	0.655000	0.94253	GAA		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158582696	C	T	158582696	3	4	44	1	0	0	0	0	1	0	0	0	15155	922	32	3	222	3	SPTA1	1	158582696	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1942388	158582696	90667925	20	4067										
ACTN2	88	hgsc.bcm.edu	37	chr1	236924324	236924324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctttgccccagggtgaagccGaatttgcccgcattatgacc	10	13	0	2	rs145450474		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:236924324G>A	ENST00000366578.4	+	20	2543	c.2377G>A	c.(2377-2379)Gaa>Aaa	p.E793K	ACTN2_ENST00000542672.1_Missense_Mutation_p.E793K|ACTN2_ENST00000546208.1_Missense_Mutation_p.E287K	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	793	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	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)			GGGTGAAGCCGAATTTGCCCG	0.512																																																0			1						G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	179	145	156		2377	5.8	1	1	dbSNP_134	156	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACTN2	NM_001103.2	56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	793/895	236924324	2,13004	2203	4300	6503	234990947	SO:0001583	missense	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2377G>A	1.37:g.236924324G>A	ENSP00000355537:p.Glu793Lys		234990947	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851598	0.97023	2.27E-4	1.16E-4	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000546208;ENST00000545611	D;D;D	0.84223	-1.82;-1.82;-1.82	5.78	5.78	0.91487	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.94430	0.8208	M	0.91354	3.2	0.80722	D	1	D;P;D;D	0.89917	1.0;0.727;1.0;0.978	D;B;D;D	0.87578	0.998;0.256;0.998;0.921	D	0.94925	0.8077	10	0.87932	D	0	.	20.0197	0.97489	0.0:0.0:1.0:0.0	.	578;793;563;793	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	K	793;793;287;562	ENSP00000443495:E793K;ENSP00000355537:E793K;ENSP00000438384:E287K	ENSP00000355537:E793K	E	+	1	0	ACTN2	234990947	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	9.831000	0.99420	2.718000	0.92993	0.655000	0.94253	GAA		0.512	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236924324	G	A	236924324	3	1	44	1	0	0	0	0	1	0	0	0	205	1059	37	1	2455	1	ACTN2	1	236924324	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	78341628	236924324	12326297	21	4068										
RYR2	6262	hgsc.bcm.edu	37	chr1	237666672	237666672	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tccttgttatgaagctgttcTgccaaaagaaaagttgaaag	9	6	1	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:237666672T>C	ENST00000366574.2	+	22	2797	c.2480T>C	c.(2479-2481)cTg>cCg	p.L827P	RYR2_ENST00000542537.1_Missense_Mutation_p.L811P|RYR2_ENST00000360064.6_Missense_Mutation_p.L825P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	827					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAAGCTGTTCTGCCAAAAGAA	0.488																																																0			1											89	90	90					1																	237666672		1942	4137	6079	235733295	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2480T>C	1.37:g.237666672T>C	ENSP00000355533:p.Leu827Pro		235733295	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614381	0.87359	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97186	-4.28;-4.25;-4.27	5.86	5.86	0.93980	.	0.000000	0.48767	D	0.000171	D	0.98388	0.9464	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99187	1.0869	10	0.59425	D	0.04	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	827	Q92736	RYR2_HUMAN	P	827;825;811	ENSP00000355533:L827P;ENSP00000353174:L825P;ENSP00000443798:L811P	ENSP00000353174:L825P	L	+	2	0	RYR2	235733295	0.998000	0.40836	0.997000	0.53966	0.968000	0.65278	7.990000	0.88215	2.367000	0.80283	0.528000	0.53228	CTG		0.488	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237666672	T	C	237666672	3	2	44	1	0	0	0	0	1	0	0	0	13806	1580	55	4	2566	4	RYR2	1	237666672	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	742348	237666672	11583949	22	4069										
WDR64	128025	hgsc.bcm.edu	37	chr1	241886616	241886616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	caggagatgataaggtcatcCggttgtggcaccccaatatc	11	10	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:241886616C>T	ENST00000366552.2	+	9	1249	c.1042C>T	c.(1042-1044)Cgg>Tgg	p.R348W	WDR64_ENST00000437684.2_Missense_Mutation_p.R348W	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	348										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TAAGGTCATCCGGTTGTGGCA	0.443																																																0			1											108	100	103					1																	241886616		2203	4300	6503	239953239	SO:0001583	missense	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1042C>T	1.37:g.241886616C>T	ENSP00000355510:p.Arg348Trp		239953239	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	C	14.83	2.653764	0.47362	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.43688	1.97;0.94;4.85	4.7	3.71	0.42584	.	0.133058	0.33553	N	0.004794	T	0.61489	0.2351	M	0.73598	2.24	0.36875	D	0.889129	D	0.89917	1.0	D	0.91635	0.999	T	0.70428	-0.4874	10	0.87932	D	0	-10.0835	11.161	0.48516	0.1839:0.8161:0.0:0.0	.	68	D1MPS4	.	W	348;348;119	ENSP00000355510:R348W;ENSP00000402446:R348W;ENSP00000406656:R119W	ENSP00000355510:R348W	R	+	1	2	WDR64	239953239	1.000000	0.71417	0.833000	0.33012	0.363000	0.29612	2.807000	0.47955	2.308000	0.77769	0.563000	0.77884	CGG		0.443	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241886616	C	T	241886616	3	4	44	1	0	0	0	0	1	0	0	0	17355	643	23	1	1076	1	WDR64	1	241886616	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	4219944	241886616	7364005	23	4070										
ZNF669	79862	hgsc.bcm.edu	37	chr1	247264093	247264094	+	Frame_Shift_Del	DEL	CC	CC	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggtctttctccagtgtgagtCctttcatgcgtcttaaaaga							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:247264093_247264094delCC	ENST00000343381.6	-	4	1149_1150	c.977_978delGG	c.(976-978)aggfs	p.R326fs	ZNF669_ENST00000448299.2_Frame_Shift_Del_p.R240fs|ZNF669_ENST00000358785.4_3'UTR	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	326					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CAGTGTGAGTCCTTTCATGCGT	0.406																																																0			1																																								245330717	SO:0001589	frameshift_variant	79862				CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"Zinc fingers, C2H2-type", "-"	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.977_978delGG	1.37:g.247264093_247264094delCC	ENSP00000342818:p.Arg326fs		245330716	B3KP94|Q5VT39|Q9H9Q6	Frame_Shift_Del	DEL	ENST00000343381.6	37	CCDS31088.1																																																																																				0.406	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804		-	247264094	CC	-	247264093	7	5	44	1	0	1	0	1	0	0	0	0	18115	854	30	0	420	0	ZNF669	1	247264093	Frame_Shift_Del	DEL	CC	TCGA-AG-3885-01A-01W-0899-10	5377477	247264093	1986528	24	4071										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55831123	55831123	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aagaaacttacctgacaaatTttttcccagatctcatcaca	3	11	2	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:55831123T>G	ENST00000345102.5	-	3	589	c.288A>C	c.(286-288)aaA>aaC	p.K96N	SMEK2_ENST00000407823.3_Missense_Mutation_p.K96N|SMEK2_ENST00000272313.5_Missense_Mutation_p.K96N	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	96	WH1.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CCTGACAAATTTTTTCCCAGA	0.323																																																0			2											61	63	62					2																	55831123		2202	4300	6502	55684627	SO:0001583	missense	57223			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.288A>C	2.37:g.55831123T>G	ENSP00000339769:p.Lys96Asn		55684627	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	37	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832188	0.71258	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.46451	0.87;0.87;0.87	5.58	5.58	0.84498	Pleckstrin homology-type (1);	0.043066	0.85682	D	0.000000	T	0.48554	0.1506	L	0.51422	1.61	0.80722	D	1	D;D;P	0.56287	0.975;0.975;0.516	P;P;B	0.57468	0.791;0.821;0.281	T	0.38757	-0.9646	10	0.15066	T	0.55	-16.8615	10.8841	0.46957	0.0:0.0735:0.0:0.9265	.	96;96;96	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3	.;P4R3B_HUMAN;.	N	96	ENSP00000272313:K96N;ENSP00000385912:K96N;ENSP00000339769:K96N	ENSP00000272313:K96N	K	-	3	2	SMEK2	55684627	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.485000	0.45250	2.110000	0.64415	0.482000	0.46254	AAA		0.323	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55831123	T	G	55831123	3	3	44	1	0	0	0	0	1	0	0	0	14831	1838	64	4	2321	4	SMEK2	2	55831123	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		55831123	187368250	25	4072										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85529702	85529702	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cacttctcccccggctccccTcccacccacctctccccaga	3	26	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:85529702T>C	ENST00000282111.3	+	5	896	c.621T>C	c.(619-621)ccT>ccC	p.P207P		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	207	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CCGGCTCCCCTCCCACCCACC	0.572																																																0			2											82	85	84					2																	85529702		2203	4300	6503	85383213	SO:0001819	synonymous_variant	83439			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.621T>C	2.37:g.85529702T>C			85383213	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	37	CCDS1971.1																																																																																				0.572	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		C	85529702	T	C	85529702	2	2	44	1	0	0	0	0	0	0	0	1	15736	1538	54	4		4	TCF7L1	2	85529702	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	29698579	85529702	157669671	26	4073										
MGAT4A	11320	hgsc.bcm.edu	37	chr2	99342737	99342737	+	Frame_Shift_Del	DEL	G	G	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atgtagtataccaagacaaaGtaaggaaggaagtgataaat							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:99342737delG	ENST00000264968.3	-	1	422	c.59delC	c.(58-60)actfs	p.T20fs	MGAT4A_ENST00000495056.2_Frame_Shift_Del_p.T20fs|MGAT4A_ENST00000409391.1_Frame_Shift_Del_p.T20fs|MGAT4A_ENST00000393487.1_Frame_Shift_Del_p.T20fs			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	20					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						CCAAGACAAAGTAAGGAAGGA	0.408																																																0			2											124	111	115					2																	99342737		2203	4300	6503	98709169	SO:0001589	frameshift_variant	11320			AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7047	protein-coding gene	gene with protein product		604623	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.59delC	2.37:g.99342737delG	ENSP00000264968:p.Thr20fs		98709169	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Frame_Shift_Del	DEL	ENST00000264968.3	37	CCDS2036.1																																																																																				0.408	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214		-	99342737	G	-	99342737	7	5	44	1	0	1	0	1	0	0	0	0	9575	1029	36	0	1710	0	MGAT4A	2	99342737	Frame_Shift_Del	DEL	G	TCGA-AG-3885-01A-01W-0899-10	13813035	99342737	143856636	27	4074										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167330824	167330824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agccgcattgaatctgaagaTtgttctatttttatttaata	6	5	2	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:167330824T>C	ENST00000409855.1	-	3	391	c.265A>G	c.(265-267)Atc>Gtc	p.I89V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	89					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AATCTGAAGATTGTTCTATTT	0.313																																																0			2											51	48	49					2																	167330824		1758	3949	5707	167039070	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.265A>G	2.37:g.167330824T>C	ENSP00000386796:p.Ile89Val		167039070		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.131703	0.37630	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98567	-4.6;-4.6;-5.0	4.52	2.06	0.26882	.	0.113548	0.38272	N	0.001743	D	0.97328	0.9126	M	0.93062	3.375	0.27687	N	0.946238	B	0.10296	0.003	B	0.10450	0.005	D	0.94362	0.7588	10	0.66056	D	0.02	.	4.1325	0.10156	0.149:0.171:0.0:0.6799	.	89	Q01118	SCN7A_HUMAN	V	89	ENSP00000386796:I89V;ENSP00000413699:I89V;ENSP00000403846:I89V	ENSP00000259060:I89V	I	-	1	0	SCN7A	167039070	1.000000	0.71417	0.974000	0.42286	0.871000	0.50021	3.196000	0.51020	0.332000	0.23536	0.383000	0.25322	ATC		0.313	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			C	167330824	T	C	167330824	3	2	44	1	0	0	0	0	1	0	0	0	13960	1493	52	4	4875	4	SCN7A	2	167330824	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	67988087	167330824	75868549	28	4075										
XIRP2	129446	hgsc.bcm.edu	37	chr2	167760306	167760306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggattccctgagcagtcggcGcaggattgaacgcttttcca	12	11	0	2	rs553364503		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:167760306G>A	ENST00000409728.1	+	2	403	c.314G>A	c.(313-315)cGc>cAc	p.R105H	XIRP2_ENST00000420519.1_Missense_Mutation_p.R105H|XIRP2_ENST00000409756.2_Missense_Mutation_p.R105H|XIRP2_ENST00000409195.1_Missense_Mutation_p.R105H|XIRP2_ENST00000295237.9_Missense_Mutation_p.R105H|XIRP2_ENST00000409043.1_Missense_Mutation_p.R105H	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGCAGTCGGCGCAGGATTGAA	0.512													G|||	1	0.000199681	0	0	5008	,	,		20520	0		0	False		,,,				2504	0.001															0			2											116	118	117					2																	167760306		2030	4161	6191	167468552	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.314G>A	2.37:g.167760306G>A	ENSP00000386619:p.Arg105His		167468552	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198409	0.38806	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	D;D;T;D;D;T	0.83163	-1.68;-1.69;3.7;-1.68;-1.69;3.7	5.12	5.12	0.69794	.	.	.	.	.	D	0.89757	0.6807	.	.	.	0.31070	N	0.713156	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	D	0.88217	0.2894	8	0.48119	T	0.1	-2.224	14.0425	0.64684	0.0:0.0:1.0:0.0	.	105;105	A4UGR9-4;A4UGR9-6	.;.	H	105	ENSP00000386454:R105H;ENSP00000386619:R105H;ENSP00000386840:R105H;ENSP00000386724:R105H;ENSP00000415541:R105H;ENSP00000295237:R105H	ENSP00000295237:R105H	R	+	2	0	XIRP2	167468552	1.000000	0.71417	0.993000	0.49108	0.295000	0.27426	2.351000	0.44071	2.390000	0.81377	0.655000	0.94253	CGC		0.512	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	167760306	G	A	167760306	3	1	44	1	0	0	0	0	1	0	0	0	17470	1087	38	1	316	1	XIRP2	2	167760306	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	429482	167760306	75439067	29	4076										
TTN	7273	hgsc.bcm.edu	37	chr2	179471982	179471982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ttctggatcagaccagttaaGtagacacatttttctgtttg	8	7	3	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:179471982G>C	ENST00000591111.1	-	228	48648	c.48424C>G	c.(48424-48426)Ctt>Gtt	p.L16142V	TTN_ENST00000589042.1_Missense_Mutation_p.L17783V|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L15215V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L8718V|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L8843V|TTN_ENST00000342175.6_Missense_Mutation_p.L8910V			Q8WZ42	TITIN_HUMAN	titin	16142	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACCAGTTAAGTAGACACATT	0.358																																																0			2											119	110	112					2																	179471982		1854	4102	5956	179180227	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48424C>G	2.37:g.179471982G>C	ENSP00000465570:p.Leu16142Val		179180227	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.95	1.790922	0.31685	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.99	5.99	0.97316	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73110	0.3545	L	0.46567	1.45	0.53005	D	0.999968	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.73135	-0.4078	9	0.87932	D	0	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	8718;8843;8910;16142	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	15215;8718;8910;8843;8718	ENSP00000343764:L15215V;ENSP00000434586:L8718V;ENSP00000340554:L8910V;ENSP00000352154:L8843V	ENSP00000340554:L8910V	L	-	1	0	TTN	179180227	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.646000	0.74348	2.840000	0.97914	0.655000	0.94253	CTT		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179471982	G	C	179471982	3	2	44	1	0	0	0	0	1	0	0	0	16775	1029	36	5	54686	5	TTN	2	179471982	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	11711676	179471982	63727391	30	4077										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197990136	197990136	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcccagtgcagagcacgccgGtccttcttgtcaaatgcatt	10	13	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:197990136G>A	ENST00000328737.2	-	6	520	c.444C>T	c.(442-444)gaC>gaT	p.D148D	ANKRD44_ENST00000282272.8_Silent_p.D165D|ANKRD44_ENST00000539527.1_Silent_p.D101D|ANKRD44_ENST00000337207.5_Silent_p.D148D|ANKRD44_ENST00000409153.1_Silent_p.D173D|ANKRD44_ENST00000450567.1_Silent_p.D148D|ANKRD44_ENST00000409919.1_Silent_p.D173D			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	173										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GAGCACGCCGGTCCTTCTTGT	0.418																																																0			2											127	118	121					2																	197990136		2203	4300	6503	197698381	SO:0001819	synonymous_variant	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.444C>T	2.37:g.197990136G>A			197698381	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																					0.418	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	197990136	G	A	197990136	2	1	44	1	0	0	0	0	0	0	0	1	672	1252	44	3		3	ANKRD44	2	197990136	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	18518154	197990136	45209237	31	4078										
CLK1	1195	hgsc.bcm.edu	37	chr2	201728889	201728889	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gaaccccagcaaatccccccTcaacggggagcctcgccttt	8	18	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:201728889T>C	ENST00000321356.4	-	1	136				CLK1_ENST00000492793.1_Intron|CLK1_ENST00000434813.2_Missense_Mutation_p.R21G|Y_RNA_ENST00000516950.1_RNA	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1						cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						AAATCCCCCCTCAACGGGGAG	0.637																																																0			2											60	55	57					2																	201728889		692	1591	2283	201437134	SO:0001627	intron_variant	78989			L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.0+397A>G	2.37:g.201728889T>C			201437134	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	.	.	.	.	.	.	.	.	.	.	T	3.630	-0.075828	0.07184	.	.	ENSG00000013441	ENST00000434813	T	0.70399	-0.48	1.8	-3.61	0.04556	.	.	.	.	.	T	0.41926	0.1180	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11275	-1.0594	9	0.87932	D	0	.	0.3931	0.00414	0.3209:0.1709:0.136:0.3721	.	21	B4DFW7	.	G	21	ENSP00000394734:R21G	ENSP00000394734:R21G	R	-	1	2	CLK1	201437134	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-6.303000	0.00071	-2.763000	0.00369	-0.765000	0.03448	AGG		0.637	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			C	201728889	T	C	201728889	1	2	44	0	1	0	0	0	0	0	0	0	3542	1550	54	4		4	CLK1	2	201728889	Intron	SNP	T	TCGA-AG-3885-01A-01W-0899-10	3738753	201728889	41470484	32	4079										
NRP2	8828	hgsc.bcm.edu	37	chr2	206608150	206608150	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aaaggtgtcatcatccagggAgcccgcggaggagacagtat	14	9	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:206608150A>G	ENST00000357785.5	+	9	1546	c.1515A>G	c.(1513-1515)ggA>ggG	p.G505G	NRP2_ENST00000355117.4_Silent_p.G505G|NRP2_ENST00000540841.1_Silent_p.G505G|NRP2_ENST00000412873.2_Silent_p.G505G|NRP2_ENST00000360409.3_Silent_p.G505G|NRP2_ENST00000417189.1_Silent_p.G505G|NRP2_ENST00000540178.1_Silent_p.G505G|NRP2_ENST00000357118.4_Silent_p.G505G|NRP2_ENST00000272849.3_Silent_p.G505G			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						TCATCCAGGGAGCCCGCGGAG	0.562																																																0			2											68	72	71					2																	206608150		2203	4300	6503	206316395	SO:0001819	synonymous_variant	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1515A>G	2.37:g.206608150A>G			206316395	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																				0.562	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			G	206608150	A	G	206608150	2	3	44	1	0	0	0	0	0	0	0	1	10692	291	11	4		4	NRP2	2	206608150	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	4879261	206608150	36591223	33	4080										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253148	238253148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cactttcctcattaggaatcCgttcctcacacgcttaaatg	5	13	2	0	rs545819982		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:238253148C>T	ENST00000295550.4	-	36	7965	c.7513G>A	c.(7513-7515)Gga>Aga	p.G2505R	COL6A3_ENST00000353578.4_Missense_Mutation_p.G2299R|COL6A3_ENST00000472056.1_Missense_Mutation_p.G1898R|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2304R|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2299R|COL6A3_ENST00000346358.4_Missense_Mutation_p.G2305R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2505	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		ATTAGGAATCCGTTCCTCACA	0.507													C|||	1	0.000199681	0	0	5008	,	,		22006	0		0	False		,,,				2504	0.001															0			2											138	131	133					2																	238253148		2203	4300	6503	237917887	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7513G>A	2.37:g.238253148C>T	ENSP00000295550:p.Gly2505Arg		237917887	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322322	0.23994	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34;2.34	4.87	4.87	0.63330	von Willebrand factor, type A (3);	0.000000	0.52532	D	0.000073	T	0.47469	0.1447	M	0.82193	2.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.981	T	0.53294	-0.8459	10	0.59425	D	0.04	.	18.4072	0.90539	0.0:1.0:0.0:0.0	.	1898;1898;2299;2505	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	R	2505;2304;2299;1898;2299;2305	ENSP00000295550:G2505R;ENSP00000315609:G2304R;ENSP00000315873:G2299R;ENSP00000418285:G1898R;ENSP00000386844:G2299R;ENSP00000295546:G2305R	ENSP00000295550:G2505R	G	-	1	0	COL6A3	237917887	1.000000	0.71417	0.076000	0.20297	0.134000	0.20937	7.632000	0.83247	2.396000	0.81511	0.655000	0.94253	GGA		0.507	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238253148	C	T	238253148	3	4	44	1	0	0	0	0	1	0	0	0	3707	661	23	1	2056	1	COL6A3	2	238253148	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	31644998	238253148	4946225	34	4081										
PRR21	643905	hgsc.bcm.edu	37	chr2	240981464	240981464	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cgtgggtgaagaggcatggaCgaagggccgtgggtgaagag	21	5	0	4	rs113555849	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:240981464C>G	ENST00000408934.1	-	1	935	c.936G>C	c.(934-936)tcG>tcC	p.S312S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	312	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GAGGCATGGACGAAGGGCCGT	0.607													N|||	3	0.000599042	8e-04	0	5008	,	,		18021	0		0.002	False		,,,				2504	0															0			2											75	67	70					2																	240981464		2203	4298	6501	240630137	SO:0001819	synonymous_variant	643905			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.936G>C	2.37:g.240981464C>G			240630137		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																				0.607	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		G	240981464	C	G	240981464	2	3	44	1	0	0	0	0	0	0	0	1	12626	523	19	5		5	PRR21	2	240981464	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	2728316	240981464	2217909	35	4082										
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38307447	38307447	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtgttctcaacttcctgtcTcccttctacttttttgccca	4	14	3	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:38307447T>C	ENST00000311856.4	+	1	145	c.96T>C	c.(94-96)tcT>tcC	p.S32S	SLC22A13_ENST00000450935.2_5'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	32					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		ACTTCCTGTCTCCCTTCTACT	0.498																																																0			3											219	183	195					3																	38307447		2203	4300	6503	38282451	SO:0001819	synonymous_variant	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.96T>C	3.37:g.38307447T>C			38282451	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																				0.498	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38307447	T	C	38307447	2	2	44	1	0	0	0	0	0	0	0	1	14481	1538	54	4		4	SLC22A13	3	38307447	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10		38307447	159714983	36	4083										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52430526	52430526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gaagtcctatagtagccttgGtgaagacttcctcaactcct	8	11	1	2	rs12163565	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:52430526G>A	ENST00000420323.2	+	71	11663	c.11402G>A	c.(11401-11403)gGt>gAt	p.G3801D		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3866	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		AGTAGCCTTGGTGAAGACTTC	0.602													G|||	831	0.165935	0.0219	0.1239	5008	,	,		17097	0.2927		0.1978	False		,,,				2504	0.227															0			3						G	ASP/GLY	203,4047		10,183,1932	52	57	56		11402	2.3	0.7	3	dbSNP_120	56	1603,6875		158,1287,2794	yes	missense	DNAH1	NM_015512.4	94	168,1470,4726	AA,AG,GG		18.9078,4.7765,14.1892	benign	3801/4266	52430526	1806,10922	2125	4239	6364	52405566	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11402G>A	3.37:g.52430526G>A	ENSP00000401514:p.Gly3801Asp		52405566	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	363	0.1662087912087912	15	0.03048780487804878	52	0.143646408839779	144	0.2517482517482518	152	0.20052770448548812	G	0.006	-2.059211	0.00386	0.047765	0.189078	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.07327	3.2	4.35	2.35	0.29111	.	0.375043	0.26684	N	0.023037	T	0.00012	0.0000	N	0.00602	-1.34	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.47018	-0.9149	9	0.02654	T	1	.	10.1318	0.42682	0.0878:0.1423:0.7698:0.0	rs12163565;rs52793948;rs57160821;rs12163565	3801;3866	C9JXH6;Q9P2D7-2	.;.	D	3801;554	ENSP00000401514:G3801D	ENSP00000273600:G554D	G	+	2	0	DNAH1	52405566	0.985000	0.35326	0.712000	0.30502	0.148000	0.21650	1.873000	0.39558	1.034000	0.39945	0.491000	0.48974	GGT		0.602	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52430526	G	A	52430526	3	1	44	1	0	0	0	0	1	0	0	0	4608	1261	44	3	11680	3	DNAH1	3	52430526	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	14123079	52430526	145591904	37	4084										
CHDH	55349	hgsc.bcm.edu	37	chr3	53854534	53854534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gagccactccagaccaatgcAgaccttccgcaggggcttct	10	15	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:53854534A>G	ENST00000315251.6	-	6	1524	c.1087T>C	c.(1087-1089)Tgc>Cgc	p.C363R		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	363					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	AGACCAATGCAGACCTTCCGC	0.557																																																0			3											165	156	159					3																	53854534		2203	4300	6503	53829574	SO:0001583	missense	55349			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1087T>C	3.37:g.53854534A>G	ENSP00000319851:p.Cys363Arg		53829574	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	A	0.371	-0.933873	0.02340	.	.	ENSG00000016391	ENST00000315251	T	0.39229	1.09	5.26	-4.36	0.03645	.	0.669254	0.15227	N	0.273657	T	0.08268	0.0206	N	0.00138	-2.015	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.43228	-0.9404	10	0.24483	T	0.36	-2.0244	8.5686	0.33556	0.1814:0.0838:0.6259:0.1089	.	363	Q8NE62	CHDH_HUMAN	R	363	ENSP00000319851:C363R	ENSP00000319851:C363R	C	-	1	0	CHDH	53829574	0.348000	0.24861	0.002000	0.10522	0.021000	0.10359	0.496000	0.22499	-0.677000	0.05231	-1.054000	0.02325	TGC		0.557	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		G	53854534	A	G	53854534	3	3	44	1	0	0	0	0	1	0	0	0	3339	188	7	4	713	4	CHDH	3	53854534	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	1424008	53854534	144167896	38	4085										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130095335	130095335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcagttcattggcgggtcccTgcagataggaaaggctcttc	12	10	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:130095335T>C	ENST00000432398.2	+	3	817	c.323T>C	c.(322-324)cTg>cCg	p.L108P	COL6A5_ENST00000265379.6_Missense_Mutation_p.L108P	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	108	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GGCGGGTCCCTGCAGATAGGA	0.502																																																0			3											48	45	46					3																	130095335		692	1591	2283	131578025	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.323T>C	3.37:g.130095335T>C	ENSP00000390895:p.Leu108Pro		131578025	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	T	9.534	1.111567	0.20714	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77489	-1.1;-1.1	5.14	3.98	0.46160	.	.	.	.	.	T	0.80486	0.4632	L	0.58302	1.8	0.42961	D	0.994402	D	0.52996	0.957	P	0.55667	0.781	T	0.80360	-0.1415	9	0.46703	T	0.11	.	9.6991	0.40175	0.0:0.0843:0.0:0.9157	.	108	A8TX70-2	.	P	108	ENSP00000390895:L108P;ENSP00000265379:L108P	ENSP00000265379:L108P	L	+	2	0	COL6A5	131578025	0.952000	0.32445	0.996000	0.52242	0.089000	0.18198	2.997000	0.49457	2.064000	0.61679	0.455000	0.32223	CTG		0.502	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		C	130095335	T	C	130095335	3	2	44	1	0	0	0	0	1	0	0	0	3708	1580	55	4	329	4	COL6A5	3	130095335	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	76240801	130095335	67927095	39	4086										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130318628	130318628	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gaggctggccaggcccccccGggacaccaggctccagaaga	14	16	0	2	rs376262924		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:130318628G>C	ENST00000358511.6	+	19	4658	c.4627G>C	c.(4627-4629)Ggg>Cgg	p.G1543R	COL6A6_ENST00000453409.2_Missense_Mutation_p.G1543R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1543	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AGGCCCCCCCGGGACACCAGG	0.502																																																0			3											45	49	48					3																	130318628		1849	4100	5949	131801318	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4627G>C	3.37:g.130318628G>C	ENSP00000351310:p.Gly1543Arg		131801318	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247298	0.80024	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.99637	-6.29;-6.29	5.79	5.79	0.91817	.	.	.	.	.	D	0.99684	0.9881	M	0.91090	3.175	0.42268	D	0.992041	D	0.89917	1.0	D	0.91635	0.999	D	0.97789	1.0237	9	0.87932	D	0	.	15.5401	0.76035	0.0:0.0:1.0:0.0	.	1543	A6NMZ7	CO6A6_HUMAN	R	1543	ENSP00000351310:G1543R;ENSP00000399236:G1543R	ENSP00000351310:G1543R	G	+	1	0	COL6A6	131801318	1.000000	0.71417	0.883000	0.34634	0.919000	0.55068	4.888000	0.63164	2.733000	0.93635	0.655000	0.94253	GGG		0.502	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130318628	G	C	130318628	3	2	44	1	0	0	0	0	1	0	0	0	3709	1116	39	5	4701	5	COL6A6	3	130318628	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	223293	130318628	67703802	40	4087										
LRRC15	131578	hgsc.bcm.edu	37	chr3	194081016	194081016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctgggagatgtggttgttggAcaggtagagtctctggaggt	18	4	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:194081016A>G	ENST00000347624.3	-	2	842	c.757T>C	c.(757-759)Tcc>Ccc	p.S253P	LRRC15_ENST00000428839.1_Missense_Mutation_p.S259P|LRRC15_ENST00000439944.2_Missense_Mutation_p.S259P	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	253					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TGGTTGTTGGACAGGTAGAGT	0.552																																																0			3											157	169	165					3																	194081016		2203	4300	6503	195562311	SO:0001583	missense	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.757T>C	3.37:g.194081016A>G	ENSP00000306276:p.Ser253Pro		195562311	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610476	0.66558	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.12361	2.69;2.69;2.69	5.15	5.15	0.70609	.	0.088290	0.49305	D	0.000153	T	0.44030	0.1274	M	0.89095	3.005	0.47949	D	0.999556	D;D	0.89917	1.0;0.976	D;P	0.79784	0.993;0.775	T	0.51872	-0.8650	10	0.54805	T	0.06	.	15.2753	0.73737	1.0:0.0:0.0:0.0	.	253;259	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	P	253;259;259	ENSP00000306276:S253P;ENSP00000389128:S259P;ENSP00000413707:S259P	ENSP00000306276:S253P	S	-	1	0	LRRC15	195562311	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.335000	0.72949	2.074000	0.62210	0.533000	0.62120	TCC		0.552	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			G	194081016	A	G	194081016	3	3	44	1	0	0	0	0	1	0	0	0	8999	275	10	4	992	4	LRRC15	3	194081016	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	63762388	194081016	3941414	41	4088										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20512134	20512134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcagacgtttggaacagaacAcaatcaaagtcatccctcct	7	12	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:20512134A>G	ENST00000504154.1	+	10	1183	c.931A>G	c.(931-933)Aca>Gca	p.T311A	SLIT2_ENST00000503823.1_Missense_Mutation_p.T311A|SLIT2_ENST00000273739.5_Missense_Mutation_p.T315A|SLIT2_ENST00000503837.1_Missense_Mutation_p.T315A	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	311					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GGAACAGAACACAATCAAAGT	0.318																																																0			4											104	113	110					4																	20512134		2203	4300	6503	20121232	SO:0001583	missense	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.931A>G	4.37:g.20512134A>G	ENSP00000422591:p.Thr311Ala		20121232	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	8.767	0.924957	0.18056	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.5	2.94	0.34122	.	0.122223	0.56097	D	0.000026	T	0.19287	0.0463	N	0.00991	-1.07	0.25653	N	0.98608	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23583	-1.0184	10	0.13108	T	0.6	.	8.9132	0.35565	0.1266:0.0:0.1289:0.7445	.	311;311	O94813-3;O94813	.;SLIT2_HUMAN	A	311;311;315;315;315	ENSP00000427548:T311A;ENSP00000422591:T311A;ENSP00000273739:T315A;ENSP00000422261:T315A	ENSP00000273739:T315A	T	+	1	0	SLIT2	20121232	0.993000	0.37304	0.998000	0.56505	0.951000	0.60555	1.035000	0.30216	0.345000	0.23873	-0.429000	0.05907	ACA		0.318	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			G	20512134	A	G	20512134	3	3	44	1	0	0	0	0	1	0	0	0	14777	159	6	4	969	4	SLIT2	4	20512134	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10		20512134	170642142	42	4089										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46930361	46930361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggcatatttgtctattttacTtgtgccagatccagaaggtg	10	7	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:46930361T>C	ENST00000264318.3	-	9	2528	c.1546A>G	c.(1546-1548)Agt>Ggt	p.S516G		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	516			S -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S516R(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TCTATTTTACTTGTGCCAGAT	0.433																																					Ovarian(6;283 369 8234 12290 33402)											1	Substitution - Missense(1)	breast(1)	4											132	128	129					4																	46930361		2203	4300	6503	46625118	SO:0001583	missense	2557				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1546A>G	4.37:g.46930361T>C	ENSP00000264318:p.Ser516Gly		46625118	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.826322	0.90955	.	.	ENSG00000109158	ENST00000264318	D	0.84800	-1.9	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90521	0.7030	L	0.54323	1.7	0.51233	D	0.999913	D	0.89917	1.0	D	0.91635	0.999	D	0.91388	0.5133	10	0.87932	D	0	.	15.3777	0.74625	0.0:0.0:0.0:1.0	.	516	P48169	GBRA4_HUMAN	G	516	ENSP00000264318:S516G	ENSP00000264318:S516G	S	-	1	0	GABRA4	46625118	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.950000	0.87804	2.232000	0.73038	0.528000	0.53228	AGT		0.433	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			C	46930361	T	C	46930361	3	2	44	1	0	0	0	0	1	0	0	0	6182	1609	56	4	122	4	GABRA4	4	46930361	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	26418227	46930361	144223915	43	4090										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536019	88536019	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agcaacagcagcgatagcagTgacagcagcaacagcagtga	12	10	0	2	rs554265208	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88536019T>C	ENST00000282478.7	+	4	2238	c.2205T>C	c.(2203-2205)agT>agC	p.S735S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S735S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	735	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcgatagcagtgacagcagca	0.502													t|||	10	0.00199681	0	0	5008	,	,		33236	0		0.007	False		,,,				2504	0.0031															0			4											65	73	70					4																	88536019		1654	2937	4591	88755043	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2205T>C	4.37:g.88536019T>C			88755043	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88536019	T	C	88536019	2	2	44	1	0	0	0	0	0	0	0	1	4793	1693	59	4		4	DSPP	4	88536019	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	41605658	88536019	102618257	44	4091										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537357	88537357	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agtgacagcagcaatagcagTgatagcagcgacagcagtga	13	8	0	3	rs146317878	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88537357T>C	ENST00000282478.7	+	4	3576	c.3543T>C	c.(3541-3543)agT>agC	p.S1181S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1181S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1181	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcaatagcagtgatagcagcg	0.567													t|||	285	0.0569089	0.0091	0.0879	5008	,	,		25184	0.003		0.168	False		,,,				2504	0.0409															0			4						C		80,3200		0,80,1560	55	74	67		3543	1.2	0	4	dbSNP_134	67	750,5074		47,656,2209	no	coding-synonymous	DSPP	NM_014208.3		47,736,3769	CC,CT,TT		12.8777,2.439,9.1169		1181/1302	88537357	830,8274	1640	2912	4552	88756381	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3543T>C	4.37:g.88537357T>C			88756381	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537357	T	C	88537357	2	2	44	1	0	0	0	0	0	0	0	1	4793	1693	59	4		4	DSPP	4	88537357	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	1338	88537357	102616919	45	4092										
MEPE	56955	hgsc.bcm.edu	37	chr4	88766391	88766391	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcctaagtcaactgggaataAagggtttgaggatggagatg	14	4	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88766391A>G	ENST00000424957.3	+	4	444	c.371A>G	c.(370-372)aAa>aGa	p.K124R	MEPE_ENST00000560249.1_Missense_Mutation_p.K11R|MEPE_ENST00000497649.2_Missense_Mutation_p.K100R|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000540395.1_Missense_Mutation_p.K11R|MEPE_ENST00000361056.3_Missense_Mutation_p.K124R|MEPE_ENST00000511670.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.K155R	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	124					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		ACTGGGAATAAAGGGTTTGAG	0.383																																																0			4											73	72	72					4																	88766391		2203	4300	6503	88985415	SO:0001583	missense	56955			AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.371A>G	4.37:g.88766391A>G	ENSP00000416984:p.Lys124Arg		88985415	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	A	8.394	0.840329	0.16891	.	.	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.46063	4.27;0.89;0.88;0.89;4.27	4.84	-2.05	0.07321	.	1.784080	0.02498	N	0.090183	T	0.31638	0.0803	L	0.39397	1.21	0.09310	N	1	B	0.13145	0.007	B	0.16289	0.015	T	0.09640	-1.0665	10	0.21540	T	0.41	-0.5334	5.4758	0.16695	0.3619:0.1929:0.4452:0.0	.	124	Q9NQ76	MEPE_HUMAN	R	124;124;155;100;11;124	ENSP00000416984:K124R;ENSP00000378534:K155R;ENSP00000422747:K100R;ENSP00000443491:K11R;ENSP00000354341:K124R	ENSP00000354341:K124R	K	+	2	0	MEPE	88985415	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.457000	0.06745	-0.171000	0.10797	0.533000	0.62120	AAA		0.383	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			G	88766391	A	G	88766391	3	3	44	1	0	0	0	0	1	0	0	0	9508	14	1	4	381	4	MEPE	4	88766391	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	229034	88766391	102387885	46	4093										
ANK2	287	hgsc.bcm.edu	37	chr4	114120225	114120225	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acaagcagaagttgtcaaagTtcttgttaaggaaggagcca	11	6	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:114120225T>G	ENST00000357077.4	+	4	397	c.344T>G	c.(343-345)gTt>gGt	p.V115G	ANK2_ENST00000506722.1_Missense_Mutation_p.V94G|ANK2_ENST00000264366.6_Missense_Mutation_p.V115G|ANK2_ENST00000394537.3_Missense_Mutation_p.V115G	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	115					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GTTGTCAAAGTTCTTGTTAAG	0.358																																																0			4											130	129	130					4																	114120225		2203	4300	6503	114339674	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.344T>G	4.37:g.114120225T>G	ENSP00000349588:p.Val115Gly		114339674	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561769	0.65538	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000508613;ENST00000343056	T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.82	5.82	0.92795	Ankyrin repeat-containing domain (3);	0.000000	0.46145	D	0.000307	T	0.77308	0.4111	M	0.72894	2.215	0.80722	D	1	D;P;D;D;D	0.62365	0.967;0.82;0.977;0.991;0.969	P;B;D;P;P	0.65684	0.901;0.433;0.937;0.844;0.792	T	0.78971	-0.1993	10	0.56958	D	0.05	.	15.858	0.79000	0.0:0.0:0.0:1.0	.	115;115;115;94;94	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	G	94;94;94;130;115;115;115;130;94	ENSP00000423799:V94G;ENSP00000421011:V94G;ENSP00000421067:V94G;ENSP00000424722:V130G;ENSP00000378044:V115G;ENSP00000349588:V115G;ENSP00000264366:V115G;ENSP00000422900:V130G	ENSP00000264366:V115G	V	+	2	0	ANK2	114339674	1.000000	0.71417	0.982000	0.44146	0.991000	0.79684	7.443000	0.80521	2.232000	0.73038	0.528000	0.53228	GTT		0.358	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114120225	T	G	114120225	3	3	44	1	0	0	0	0	1	0	0	0	621	1725	60	4	383	4	ANK2	4	114120225	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	25353834	114120225	77034051	47	4094										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247289	153247289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gccatcatattgaacacagcGgactgctgcaacatgaccca	8	13	1	2	rs149680468		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:153247289G>A	ENST00000281708.4	-	10	2742	c.1513C>T	c.(1513-1515)Cgc>Tgc	p.R505C	FBXW7_ENST00000263981.5_Missense_Mutation_p.R425C|FBXW7_ENST00000603841.1_Missense_Mutation_p.R505C|FBXW7_ENST00000296555.5_Missense_Mutation_p.R387C|FBXW7_ENST00000393956.3_Missense_Mutation_p.R329C|FBXW7_ENST00000603548.1_Missense_Mutation_p.R505C	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	505			R -> L (in an ovarian cancer cell line). {ECO:0000269|PubMed:11565033, ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R505C(60)|p.R505G(18)|p.R425C(14)|p.R266C(13)|p.R425G(9)|p.R266G(9)|p.R387G(6)|p.R387C(3)|p.R505S(3)|p.R387S(1)|p.?(1)|p.R425S(1)|p.R266S(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAACACAGCGGACTGCTGCA	0.468			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	139	Substitution - Missense(138)|Unknown(1)	haematopoietic_and_lymphoid_tissue(44)|large_intestine(26)|endometrium(20)|urinary_tract(15)|lung(15)|upper_aerodigestive_tract(8)|skin(8)|ovary(2)|biliary_tract(1)	4											167	156	160					4																	153247289		2203	4300	6503	153466739	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1513C>T	4.37:g.153247289G>A	ENSP00000281708:p.Arg505Cys		153466739	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.722220	0.68959	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.72	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.101576	0.64402	D	0.000001	T	0.78679	0.4321	M	0.75085	2.285	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.81858	-0.0739	10	0.87932	D	0	-12.0024	15.0746	0.72066	0.0681:0.0:0.9319:0.0	.	329;505;387;425	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	C	505;387;425;329	ENSP00000281708:R505C;ENSP00000296555:R387C;ENSP00000263981:R425C;ENSP00000377528:R329C	ENSP00000263981:R425C	R	-	1	0	FBXW7	153466739	1.000000	0.71417	1.000000	0.80357	0.556000	0.35491	9.772000	0.98984	1.559000	0.49555	-0.145000	0.13849	CGC		0.468	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153247289	G	A	153247289	3	1	44	1	0	0	0	0	1	0	0	0	5788	1116	39	1	622	1	FBXW7	4	153247289	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	39127064	153247289	37906987	48	4095										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156634454	156634454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcctgaagaagaggctggggAagctgaaggctacccttgag	16	8	0	5			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:156634454A>G	ENST00000296518.7	+	7	1500	c.1291A>G	c.(1291-1293)Aag>Gag	p.K431E	GUCY1A3_ENST00000506455.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.K431E|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.K173E|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.K431E			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	431					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GAGGCTGGGGAAGCTGAAGGC	0.522																																																0			4											82	85	84					4																	156634454		2203	4300	6503	156853904	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1291A>G	4.37:g.156634454A>G	ENSP00000296518:p.Lys431Glu		156853904	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.849746	0.91277	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000002	D	0.92825	0.7718	L	0.56199	1.76	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.79108	0.992;0.992	D	0.92083	0.5674	10	0.39692	T	0.17	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	431;431	B3KU69;Q02108	.;GCYA3_HUMAN	E	431;431;431;431;173;431;431	ENSP00000424361:K431E;ENSP00000421493:K431E;ENSP00000426968:K431E;ENSP00000412201:K431E;ENSP00000377418:K173E;ENSP00000296518:K431E;ENSP00000426040:K431E	ENSP00000296518:K431E	K	+	1	0	GUCY1A3	156853904	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	8.930000	0.92872	2.308000	0.77769	0.533000	0.62120	AAG		0.522	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			G	156634454	A	G	156634454	3	3	44	1	0	0	0	0	1	0	0	0	6915	247	9	4	1324	4	GUCY1A3	4	156634454	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	3387165	156634454	34519822	49	4096										
NEK1	4750	hgsc.bcm.edu	37	chr4	170345770	170345770	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aaggaattcttgtttttattTtttggtggtaaatgcgagtg	11	2	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:170345770T>C	ENST00000439128.2	-	29	3712	c.3072A>G	c.(3070-3072)aaA>aaG	p.K1024K	NEK1_ENST00000507142.1_Silent_p.K1052K|NEK1_ENST00000511633.1_Silent_p.K1008K|NEK1_ENST00000510533.1_Silent_p.K980K|NEK1_ENST00000512193.1_Silent_p.K955K	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1024					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TGTTTTTATTTTTTGGTGGTA	0.383																																																0			4											82	80	80					4																	170345770		1837	4083	5920	170582345	SO:0001819	synonymous_variant	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.3072A>G	4.37:g.170345770T>C			170582345	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																				0.383	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			C	170345770	T	C	170345770	2	2	44	1	0	0	0	0	0	0	0	1	10352	1838	64	4		4	NEK1	4	170345770	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	13711316	170345770	20808506	50	4097										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183594202	183594202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aaaataacaccatagattccGgagaacttgatattggccga	8	8	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:183594202G>A	ENST00000511685.1	+	7	1279	c.1156G>A	c.(1156-1158)Gga>Aga	p.G386R	TENM3_ENST00000406950.2_Missense_Mutation_p.G386R			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	386					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G386*(1)|p.G386R(1)									CATAGATTCCGGAGAACTTGA	0.363																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	4											35	33	33					4																	183594202		1811	4083	5894	183831196	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1156G>A	4.37:g.183594202G>A	ENSP00000424226:p.Gly386Arg		183831196	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862373	0.91511	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.40225	1.04;1.04	4.91	4.91	0.64330	.	.	.	.	.	T	0.67306	0.2879	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71361	-0.4616	9	0.87932	D	0	.	18.7292	0.91728	0.0:0.0:1.0:0.0	.	386	Q9P273	TEN3_HUMAN	R	386	ENSP00000424226:G386R;ENSP00000385276:G386R	ENSP00000385276:G386R	G	+	1	0	ODZ3	183831196	1.000000	0.71417	0.993000	0.49108	0.977000	0.68977	9.351000	0.97073	2.720000	0.93068	0.558000	0.71614	GGA		0.363	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183594202	G	A	183594202	3	1	44	1	0	0	0	0	1	0	0	0	10867	1117	39	1	1178	1	ODZ3	4	183594202	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	13248432	183594202	7560074	51	4098										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183696126	183696126	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggctccctcagaattatctaCgccagtggcctggactcaca	9	14	3	1	rs145946924	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:183696126C>T	ENST00000511685.1	+	24	5247	c.5124C>T	c.(5122-5124)taC>taT	p.Y1708Y	RP11-18D7.2_ENST00000513255.1_RNA|TENM3_ENST00000406950.2_Silent_p.Y1708Y			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1708					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GAATTATCTACGCCAGTGGCC	0.463													C|||	29	0.00579073	0	0.0288	5008	,	,		18933	0		0	False		,,,				2504	0.0092															0			4						C		2,3756		0,2,1877	40	40	40		5124	-5.2	0.5	4	dbSNP_134	40	6,8226		0,6,4110	no	coding-synonymous	ODZ3	NM_001080477.1		0,8,5987	TT,TC,CC		0.0729,0.0532,0.0667		1708/2700	183696126	8,11982	1879	4116	5995	183933120	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5124C>T	4.37:g.183696126C>T			183933120	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.463	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183696126	C	T	183696126	2	4	44	1	0	0	0	0	0	0	0	1	10867	547	19	1		1	ODZ3	4	183696126	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	101924	183696126	7458150	52	4099										
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36049170	36049170	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atgttccttgatggtgttgtCaaatgtagactgcatgtgct	11	6	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:36049170C>T	ENST00000282507.3	-	4	765	c.664G>A	c.(664-666)Gac>Aac	p.D222N	UGT3A2_ENST00000513300.1_Missense_Mutation_p.D188N|UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000545528.1_Intron	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	222					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATGGTGTTGTCAAATGTAGAC	0.438																																																0			5											146	147	147					5																	36049170		2203	4300	6503	36084927	SO:0001583	missense	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.664G>A	5.37:g.36049170C>T	ENSP00000282507:p.Asp222Asn		36084927	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035139	0.75617	.	.	ENSG00000168671	ENST00000282507;ENST00000513300	T;T	0.61510	0.1;0.1	3.45	3.45	0.39498	.	0.485483	0.19185	N	0.120581	T	0.70193	0.3196	M	0.74467	2.265	0.80722	D	1	B;D	0.59767	0.418;0.986	B;P	0.57502	0.206;0.822	T	0.73780	-0.3875	10	0.48119	T	0.1	.	14.8735	0.70478	0.0:1.0:0.0:0.0	.	188;222	E9PFK7;Q3SY77	.;UD3A2_HUMAN	N	222;188	ENSP00000282507:D222N;ENSP00000427404:D188N	ENSP00000282507:D222N	D	-	1	0	UGT3A2	36084927	0.902000	0.30710	0.016000	0.15963	0.268000	0.26511	1.898000	0.39809	2.242000	0.73789	0.655000	0.94253	GAC		0.438	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		T	36049170	C	T	36049170	3	4	44	1	0	0	0	0	1	0	0	0	17004	826	29	3	923	3	UGT3A2	5	36049170	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10		36049170	144866090	53	4100										
GZMA	3001	hgsc.bcm.edu	37	chr5	54404152	54404152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	caatgatcgaaatcactataAttttaaccctgtgattggaa	6	7	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:54404152A>G	ENST00000274306.6	+	4	592	c.557A>G	c.(556-558)aAt>aGt	p.N186S		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	186	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AATCACTATAATTTTAACCCT	0.423																																																0			5											80	81	80					5																	54404152		2203	4300	6503	54439909	SO:0001583	missense	3001				CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.557A>G	5.37:g.54404152A>G	ENSP00000274306:p.Asn186Ser		54439909	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	37	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	A	8.920	0.960938	0.18583	.	.	ENSG00000145649	ENST00000274306	D	0.88277	-2.36	5.93	4.77	0.60923	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.700801	0.15720	N	0.247943	T	0.77791	0.4183	L	0.35723	1.085	0.09310	N	1	P	0.39352	0.669	B	0.28709	0.093	T	0.65747	-0.6093	10	0.06365	T	0.9	.	9.837	0.40975	0.859:0.0:0.141:0.0	.	186	P12544	GRAA_HUMAN	S	186	ENSP00000274306:N186S	ENSP00000274306:N186S	N	+	2	0	GZMA	54439909	0.898000	0.30612	0.681000	0.30009	0.109000	0.19521	3.512000	0.53407	1.067000	0.40740	-0.250000	0.11733	AAT		0.423	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144		G	54404152	A	G	54404152	3	3	44	1	0	0	0	0	1	0	0	0	6936	101	4	4	571	4	GZMA	5	54404152	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	18354982	54404152	126511108	54	4101										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58270649	58270649	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtcactgcagctagtgtcttCttccacttgactgccactgt	8	13	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:58270649C>T	ENST00000340635.6	-	15	2447	c.2272G>A	c.(2272-2274)Gaa>Aaa	p.E758K	PDE4D_ENST00000360047.5_Missense_Mutation_p.E622K|PDE4D_ENST00000358923.6_Missense_Mutation_p.E456K|PDE4D_ENST00000405755.2_Missense_Mutation_p.E636K|PDE4D_ENST00000317118.8_Missense_Mutation_p.E467K|PDE4D_ENST00000502484.2_Missense_Mutation_p.E697K|PDE4D_ENST00000546160.1_Missense_Mutation_p.E697K|PDE4D_ENST00000507116.1_Missense_Mutation_p.E694K|PDE4D_ENST00000503258.1_Missense_Mutation_p.E628K	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	758					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CTAGTGTCTTCTTCCACTTGA	0.483																																																0			5											269	273	272					5																	58270649		1984	4161	6145	58306406	SO:0001583	missense	5144				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2272G>A	5.37:g.58270649C>T	ENSP00000345502:p.Glu758Lys		58306406	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	37	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.890084	0.52014	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000358923;ENST00000317118;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160	T;T;T;T;T;T;T;T;T	0.67345	-0.26;-0.24;-0.24;-0.04;-0.05;-0.24;-0.24;-0.25;-0.25	5.22	5.22	0.72569	.	0.159021	0.47455	D	0.000234	T	0.74543	0.3730	L	0.42245	1.32	0.80722	D	1	D;P;D;B;B;D;B;B	0.56035	0.974;0.956;0.974;0.003;0.103;0.974;0.202;0.108	D;D;D;B;B;D;B;B	0.70487	0.969;0.931;0.969;0.003;0.058;0.969;0.138;0.089	T	0.66156	-0.5994	10	0.11182	T	0.66	.	18.9581	0.92668	0.0:1.0:0.0:0.0	.	697;758;694;621;636;628;533;467	Q08499-11;Q08499;Q08499-6;Q08499-2;Q08499-9;Q08499-10;Q08499-4;Q08499-8	.;PDE4D_HUMAN;.;.;.;.;.;.	K	758;627;622;694;456;467;628;636;697;697	ENSP00000345502:E758K;ENSP00000353152:E622K;ENSP00000424852:E694K;ENSP00000351800:E456K;ENSP00000321739:E467K;ENSP00000425605:E628K;ENSP00000384806:E636K;ENSP00000423094:E697K;ENSP00000442734:E697K	ENSP00000321739:E467K	E	-	1	0	PDE4D	58306406	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.095000	0.76952	2.728000	0.93425	0.655000	0.94253	GAA		0.483	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			T	58270649	C	T	58270649	3	4	44	1	0	0	0	0	1	0	0	0	11673	922	32	3	161	3	PDE4D	5	58270649	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	3866497	58270649	122644611	55	4102										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031477	79031477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gaaaaaaagaaatctcaggcGattcagaggaaatgaacata	9	5	2	3	rs377265303		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:79031477G>A	ENST00000446378.2	+	2	6920	c.6889G>A	c.(6889-6891)Gat>Aat	p.D2297N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2297					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AATCTCAGGCGATTCAGAGGA	0.338																																																0			5						G	ASN/ASP	1,3651		0,1,1825	91	89	89		6889	-1.8	0	5		89	0,8158		0,0,4079	no	missense	CMYA5	NM_153610.3	23	0,1,5904	AA,AG,GG		0.0,0.0274,0.0085	benign	2297/4070	79031477	1,11809	1826	4079	5905	79067233	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6889G>A	5.37:g.79031477G>A	ENSP00000394770:p.Asp2297Asn		79067233	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.676871	0.00102	2.74E-4	0.0	ENSG00000164309	ENST00000446378	T	0.16597	2.33	6.02	-1.84	0.07809	.	2.353210	0.01435	N	0.014865	T	0.10294	0.0252	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30736	-0.9968	10	0.02654	T	1	.	8.1801	0.31305	0.2042:0.0:0.4518:0.344	.	2297	Q8N3K9	CMYA5_HUMAN	N	2297	ENSP00000394770:D2297N	ENSP00000394770:D2297N	D	+	1	0	CMYA5	79067233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.127000	0.15790	-0.357000	0.08175	-2.337000	0.00247	GAT		0.338	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79031477	G	A	79031477	3	1	44	1	0	0	0	0	1	0	0	0	3596	1058	37	1	6895	1	CMYA5	5	79031477	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	20760828	79031477	101883783	56	4103										
PCSK1	5122	hgsc.bcm.edu	37	chr5	95729007	95729007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctcctccaactcatccctccGgccccctacgctgctgctgc	6	22	1	0	rs200614230	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:95729007G>A	ENST00000311106.3	-	14	2197	c.1960C>T	c.(1960-1962)Cgg>Tgg	p.R654W	PCSK1_ENST00000508626.1_Missense_Mutation_p.R607W|PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	654					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCATCCCTCCGGCCCCCTACG	0.547													G|||	2	0.000399361	0	0	5008	,	,		17878	0		0.001	False		,,,				2504	0.001															0			5											67	71	70					5																	95729007		2203	4300	6503	95754763	SO:0001583	missense	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1960C>T	5.37:g.95729007G>A	ENSP00000308024:p.Arg654Trp		95754763	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	12.07	1.826852	0.32329	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.68903	-0.21;-0.36	5.62	1.9	0.25705	.	0.359981	0.32918	N	0.005481	T	0.45236	0.1332	L	0.36672	1.1	0.09310	N	1	P;P	0.44260	0.561;0.83	B;B	0.28638	0.092;0.075	T	0.41360	-0.9513	10	0.66056	D	0.02	-5.6154	7.2964	0.26395	0.0:0.0811:0.4678:0.4511	.	607;654	E9PHA1;P29120	.;NEC1_HUMAN	W	654;607	ENSP00000308024:R654W;ENSP00000421600:R607W	ENSP00000308024:R654W	R	-	1	2	PCSK1	95754763	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.042000	0.13949	0.081000	0.16988	-0.262000	0.10625	CGG		0.547	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		A	95729007	G	A	95729007	3	1	44	1	0	0	0	0	1	0	0	0	11631	1115	39	1	305	1	PCSK1	5	95729007	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	16697530	95729007	85186253	57	4104										
APC	324	hgsc.bcm.edu	37	chr5	112174366	112174366	+	Frame_Shift_Del	DEL	A	A	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggagaactagatacaccaatAaattatagtcttaaatattc							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112174366delA	ENST00000457016.1	+	16	3455	c.3075delA	c.(3073-3075)atafs	p.I1025fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.I1025fs|APC_ENST00000508376.2_Frame_Shift_Del_p.I1025fs			P25054	APC_HUMAN	adenomatous polyposis coli	1025	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATACACCAATAAATTATAGTC	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											71	76	74					5																	112174366		2202	4299	6501	112202265	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3075delA	5.37:g.112174366delA	ENSP00000413133:p.Ile1025fs		112202265	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112174366	A	-	112174366	7	5	44	1	0	1	0	1	0	0	0	0	763	352	13	0	3133	0	APC	5	112174366	Frame_Shift_Del	DEL	A	TCGA-AG-3885-01A-01W-0899-10	16445359	112174366	68740894	58	4105			1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175410	112175410	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cagacacccaaaagtccaccTgaacactatgttcaggagac	7	13	1	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175410T>C	ENST00000457016.1	+	16	4499	c.4119T>C	c.(4117-4119)ccT>ccC	p.P1373P	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.P1373P|APC_ENST00000508376.2_Silent_p.P1373P			P25054	APC_HUMAN	adenomatous polyposis coli	1373	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1374fs*2(1)|p.E1374fs*1(1)|p.P1373fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGTCCACCTGAACACTATG	0.453		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Insertion - Frameshift(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD011100	APC	D							83	80	81					5																	112175410		2202	4300	6502	112203309	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4119T>C	5.37:g.112175410T>C			112203309	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175410	T	C	112175410	2	2	44	1	0	0	0	0	0	0	0	1	763	1567	55	4		4	APC	5	112175410	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	1044	112175410	68739850	59	4106			1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175474	112175475	+	Missense_Mutation	DNP	AG	AG	GT													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cttctgtcagttcacttgatAgttttgagagtcgttcgatt					rs137854578		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A|G	A|G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175474_112175475AG>GT	ENST00000457016.1	+	16	4563_4564	c.4183_4184AG>GT	c.(4183-4185)AGt>GTt	p.S1395V	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1395V|APC_ENST00000508376.2_Missense_Mutation_p.S1395V			P25054	APC_HUMAN	adenomatous polyposis coli	1395	Ser-rich.		S -> C (in hepatoblastoma). {ECO:0000269|PubMed:8764128}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1395C(3)|p.E1397fs*1(2)|p.S1395fs*19(2)|p.Y1376fs*41(1)|p.?(1)|p.D1394fs*20(1)|p.K1192fs*3(1)|p.S1395fs*20(1)|p.?fs(1)|p.D1394fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCACTTGATAGTTTTGAGAGT	0.475		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	14	Deletion - Frameshift(7)|Substitution - Missense(3)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(9)|liver(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD972010|CP995074	APC	D|X	rs137854578																																			112203373|112203374	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	Exception_encountered	5.37:g.112175474_112175475delinsGT	ENSP00000413133:p.Ser1395Val		112203373|112203374	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.475	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		GT	112175475	AG	GT	112175474	3	3	44	1	0	0	0	0	1	0	0	0	763	420	15	4	4241	4	APC	5	112175474	Missense_Mutation	DNP	AG	TCGA-AG-3885-01A-01W-0899-10	64	112175474	68739786	60	4107	16	2	1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175475	112175476	+	Frame_Shift_Ins	INS	-	-	T													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tctgtcagttcacttgatagINSttttgagagtcgttcgattg							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175475_112175476insT	ENST00000457016.1	+	16	4564_4565	c.4184_4185insT	c.(4183-4188)agttttfs	p.SF1395fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Ins_p.SF1395fs|APC_ENST00000508376.2_Frame_Shift_Ins_p.SF1395fs			P25054	APC_HUMAN	adenomatous polyposis coli	1395	Ser-rich.		S -> C (in hepatoblastoma). {ECO:0000269|PubMed:8764128}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1397fs*1(2)|p.S1395fs*19(2)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.?fs(1)|p.F1396fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCACTTGATAGTTTTGAGAGTC	0.475		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	9	Deletion - Frameshift(5)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(7)|soft_tissue(1)|skin(1)	5	GRCh37	CD972010	APC	D																																				112203375	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4188dupT	5.37:g.112175479_112175479dupT	ENSP00000413133:p.Ser1395fs		112203374	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.475	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175476	-	T	112175475	7	5	44	1	0	1	1	0	0	0	0	0	763	1029	36	0	4242	0	APC	5	112175475	Frame_Shift_Ins	INS	-	TCGA-AG-3885-01A-01W-0899-10	1	112175475	68739785	61	4108	16	2	1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175682	112175682	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acctactgctgaaaagagagAgagtggacctaagcaagctg	12	8	0	3	rs112961968		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175682A>G	ENST00000457016.1	+	16	4771	c.4391A>G	c.(4390-4392)gAg>gGg	p.E1464G	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.E1464G|APC_ENST00000508376.2_Missense_Mutation_p.E1464G			P25054	APC_HUMAN	adenomatous polyposis coli	1464	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1464fs*8(29)|p.?(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.S1465fs*4(1)|p.S1465fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAAGAGAGAGAGTGGACCT	0.453		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	34	Deletion - Frameshift(31)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(21)|stomach(5)|small_intestine(3)|thyroid(1)|soft_tissue(1)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CD972012	APC	D	rs112961968						84	79	81					5																	112175682		2202	4300	6502	112203581	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4391A>G	5.37:g.112175682A>G	ENSP00000413133:p.Glu1464Gly		112203581	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121479	0.37436	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90676	-2.71;-2.71;-2.71	6.16	5.01	0.66863	.	0.103794	0.64402	D	0.000004	D	0.83289	0.5222	N	0.25647	0.755	0.48830	D	0.999711	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.76181	-0.3053	9	.	.	.	-16.9486	12.0784	0.53657	0.9336:0.0:0.0664:0.0	.	1466;1464	Q4LE70;P25054	.;APC_HUMAN	G	1464	ENSP00000413133:E1464G;ENSP00000257430:E1464G;ENSP00000427089:E1464G	.	E	+	2	0	APC	112203581	1.000000	0.71417	0.990000	0.47175	0.750000	0.42670	8.585000	0.90802	1.157000	0.42530	0.528000	0.53228	GAG		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175682	A	G	112175682	3	3	44	1	0	0	0	0	1	0	0	0	763	304	11	4	4449	4	APC	5	112175682	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	207	112175682	68739578	62	4109			1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175730	112175730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgctgcagttcagagggtccAggttcttccagatgctgata	12	9	2	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175730A>G	ENST00000457016.1	+	16	4819	c.4439A>G	c.(4438-4440)cAg>cGg	p.Q1480R	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1480R|APC_ENST00000508376.2_Missense_Mutation_p.Q1480R			P25054	APC_HUMAN	adenomatous polyposis coli	1480	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGAGGGTCCAGGTTCTTCCA	0.453		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Unknown(1)|Complex - frameshift(1)|Deletion - Frameshift(1)	thyroid(1)|soft_tissue(1)|skin(1)	5											72	72	72					5																	112175730		2202	4300	6502	112203629	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4439A>G	5.37:g.112175730A>G	ENSP00000413133:p.Gln1480Arg		112203629	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.041642	0.35989	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89681	-2.55;-2.55;-2.55	6.16	6.16	0.99307	.	0.059477	0.64402	D	0.000002	D	0.90909	0.7143	L	0.34521	1.04	0.54753	D	0.999981	D;D	0.60160	0.987;0.967	D;D	0.67725	0.953;0.932	D	0.89997	0.4112	9	.	.	.	-8.2076	16.8061	0.85666	1.0:0.0:0.0:0.0	.	1482;1480	Q4LE70;P25054	.;APC_HUMAN	R	1480	ENSP00000413133:Q1480R;ENSP00000257430:Q1480R;ENSP00000427089:Q1480R	.	Q	+	2	0	APC	112203629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.425000	0.80255	2.367000	0.80283	0.528000	0.53228	CAG		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175730	A	G	112175730	3	3	44	1	0	0	0	0	1	0	0	0	763	188	7	4	4497	4	APC	5	112175730	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	48	112175730	68739530	63	4110			1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
APC	324	hgsc.bcm.edu	37	chr5	112175944	112175944	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcaaatgaaaaccaagagaaAgaggcagaaaaaactattga	8	5	1	5			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175944A>G	ENST00000457016.1	+	16	5033	c.4653A>G	c.(4651-4653)aaA>aaG	p.K1551K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.K1551K|APC_ENST00000508376.2_Silent_p.K1551K			P25054	APC_HUMAN	adenomatous polyposis coli	1551	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACCAAGAGAAAGAGGCAGAAA	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											78	85	83					5																	112175944		2202	4300	6502	112203843	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4653A>G	5.37:g.112175944A>G			112203843	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175944	A	G	112175944	2	3	44	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112175944	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	214	112175944	68739316	64	4111			1	4		7	6	1579	N	T_AG_A_-	7.569343e-13
SLC4A9	83697	hgsc.bcm.edu	37	chr5	139747350	139747350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcttctgtgtggctgtgctgAtgctactcacatcagcgctt	10	11	4	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:139747350A>G	ENST00000230993.6	+	16	2328	c.2293A>G	c.(2293-2295)Atg>Gtg	p.M765V	SLC4A9_ENST00000432095.2_Missense_Mutation_p.M727V|SLC4A9_ENST00000507527.1_Missense_Mutation_p.M765V|SLC4A9_ENST00000506757.2_Missense_Mutation_p.M741V|SLC4A9_ENST00000506545.1_Missense_Mutation_p.M678V	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	765	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTGTGCTGATGCTACTCAC	0.587																																																0			5											49	51	50					5																	139747350		2095	4217	6312	139727534	SO:0001583	missense	83697			AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2293A>G	5.37:g.139747350A>G	ENSP00000230993:p.Met765Val		139727534	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	37	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	A	11.58	1.681351	0.29872	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	5.12	1.24	0.21308	Bicarbonate transporter, C-terminal (1);	0.521018	0.20725	N	0.086823	T	0.67887	0.2941	L	0.41415	1.275	0.31044	N	0.715927	B;B;B;B	0.20550	0.003;0.046;0.037;0.037	B;B;B;B	0.30029	0.008;0.11;0.037;0.037	T	0.63646	-0.6590	10	0.49607	T	0.09	.	7.7721	0.29015	0.6691:0.2623:0.0686:0.0	.	678;765;727;741	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	V	765;741;727;678;765	ENSP00000230993:M765V;ENSP00000424424:M741V;ENSP00000410056:M727V;ENSP00000422855:M678V;ENSP00000427661:M765V	ENSP00000230993:M765V	M	+	1	0	SLC4A9	139727534	1.000000	0.71417	0.968000	0.41197	0.889000	0.51656	2.841000	0.48223	0.130000	0.18549	0.482000	0.46254	ATG		0.587	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		G	139747350	A	G	139747350	3	3	44	1	0	0	0	0	1	0	0	0	14697	333	12	4	2283	4	SLC4A9	5	139747350	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	27571406	139747350	41167910	65	4112										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141335623	141335624	+	Frame_Shift_Ins	INS	-	-	A													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtcagtgcccgctgggcccINSaagccattgggagtctcgat							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:141335623_141335624insA	ENST00000231484.3	-	1	3003_3004	c.1793_1794insT	c.(1792-1794)ttgfs	p.L598fs	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	598					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCTGGGCCCAAGCCATTGGG	0.604																																																0			5																																								141315808	SO:0001589	frameshift_variant	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1794dupT	5.37:g.141335625_141335625dupA	ENSP00000231484:p.Leu598fs		141315807	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Frame_Shift_Ins	INS	ENST00000231484.3	37	CCDS4269.1																																																																																				0.604	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141335624	-	A	141335623	7	5	44	1	0	1	1	0	0	0	0	0	11541	593	21	0	1776	0	PCDH12	5	141335623	Frame_Shift_Ins	INS	-	TCGA-AG-3885-01A-01W-0899-10	1588273	141335623	39579637	66	4113										
PCYOX1L	78991	hgsc.bcm.edu	37	chr5	148743642	148743642	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtgggcaggagcgccatcttCggcggggagcacttcatgct	16	11	2	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:148743642C>T	ENST00000274569.4	+	3	401	c.339C>T	c.(337-339)ttC>ttT	p.F113F	PCYOX1L_ENST00000514349.1_Silent_p.F23F	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	113					prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCATCTTCGGCGGGGAGC	0.622																																					Ovarian(62;1136 1477 27277 27495)											0			5											102	99	100					5																	148743642		2203	4300	6503	148723835	SO:0001819	synonymous_variant	78991				CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.339C>T	5.37:g.148743642C>T			148723835	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Silent	SNP	ENST00000274569.4	37	CCDS4296.1																																																																																				0.622	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028		T	148743642	C	T	148743642	2	4	44	1	0	0	0	0	0	0	0	1	11640	883	31	1		1	PCYOX1L	5	148743642	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	7408019	148743642	32171618	67	4114										
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149216623	149216623	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	actcctggtcaccagccactCgaaggaacttcaggtatgaa	9	12	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:149216623C>T	ENST00000309241.5	+	8	2637	c.2605C>T	c.(2605-2607)Cga>Tga	p.R869*	PPARGC1B_ENST00000394320.3_Nonsense_Mutation_p.R869*|PPARGC1B_ENST00000403750.1_Nonsense_Mutation_p.R805*|PPARGC1B_ENST00000360453.4_Nonsense_Mutation_p.R830*	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	869					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			ACCAGCCACTCGAAGGAACTT	0.652																																																0			5											61	71	68					5																	149216623		2203	4300	6503	149196816	SO:0001587	stop_gained	133522			AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2605C>T	5.37:g.149216623C>T	ENSP00000312649:p.Arg869*		149196816	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Nonsense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.541765|7.541765	0.98348|0.98348	.|.	.|.	ENSG00000155846|ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750|ENST00000434684	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.213744|.	0.32901|.	N|.	0.005520|.	.|T	.|0.65729	.|0.2719	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69247	.|-0.5195	.|3	0.02654|.	T|.	1|.	-7.9394|-7.9394	14.1067|14.1067	0.65093|0.65093	0.1592:0.8408:0.0:0.0|0.1592:0.8408:0.0:0.0	.|.	.|.	.|.	.|.	X|L	830;869;869;805|555	.|.	ENSP00000312649:R869X|.	R|S	+|+	1|2	2|0	PPARGC1B|PPARGC1B	149196816|149196816	0.958000|0.958000	0.32768|0.32768	0.259000|0.259000	0.24435|0.24435	0.730000|0.730000	0.41778|0.41778	0.924000|0.924000	0.28777|0.28777	2.747000|2.747000	0.94245|0.94245	0.462000|0.462000	0.41574|0.41574	CGA|TCG		0.652	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		T	149216623	C	T	149216623	4	4	44	1	0	0	0	0	0	1	0	0	12332	876	31	1	2642	1	PPARGC1B	5	149216623	Nonsense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	472981	149216623	31698637	68	4115										
CCNJL	79616	hgsc.bcm.edu	37	chr5	159680550	159680550	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aagggctgcagcggttggtaCggggtgtggagggatgagcc	21	6	0	1	rs141268151		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:159680550C>T	ENST00000393977.3	-	7	1428	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P	CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000257536.7_Silent_p.P333P	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	381						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCGGTTGGTACGGGGTGTGGA	0.637																																																0			5											74	81	79					5																	159680550		2121	4240	6361	159613128	SO:0001819	synonymous_variant	79616			BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.1143G>A	5.37:g.159680550C>T			159613128	Q6ZN43|Q9H7W8	Silent	SNP	ENST00000393977.3	37	CCDS4350.2																																																																																				0.637	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565		T	159680550	C	T	159680550	2	4	44	1	0	0	0	0	0	0	0	1	2935	523	19	1		1	CCNJL	5	159680550	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	10463927	159680550	21234710	69	4116										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161300148	161300148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tacaatagatgtatttttccGtcaaagctggaaggatgaaa	9	5	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:161300148G>A	ENST00000428797.2	+	6	636	c.281G>A	c.(280-282)cGt>cAt	p.R94H	GABRA1_ENST00000393943.4_Missense_Mutation_p.R94H|GABRA1_ENST00000420560.1_Missense_Mutation_p.R94H|GABRA1_ENST00000437025.2_Missense_Mutation_p.R94H|GABRA1_ENST00000444819.1_Missense_Mutation_p.R94H|GABRA1_ENST00000023897.6_Missense_Mutation_p.R94H	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	94					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R94H(2)|p.R94L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	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;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GTATTTTTCCGTCAAAGCTGG	0.373																																																3	Substitution - Missense(3)	urinary_tract(1)|ovary(1)|lung(1)	5											91	98	96					5																	161300148		2203	4300	6503	161232726	SO:0001583	missense	2554				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.281G>A	5.37:g.161300148G>A	ENSP00000393097:p.Arg94His		161232726	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	35	5.525396	0.96431	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819;ENST00000519621	T;T;T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35;-1.35;-1.35	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.107484	0.64402	D	0.000008	D	0.91133	0.7208	M	0.84585	2.705	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	D	0.91782	0.5436	10	0.87932	D	0	.	19.9462	0.97183	0.0:0.0:1.0:0.0	.	94	P14867	GBRA1_HUMAN	H	94	ENSP00000023897:R94H;ENSP00000393097:R94H;ENSP00000377517:R94H;ENSP00000415441:R94H;ENSP00000408041:R94H;ENSP00000414232:R94H;ENSP00000430435:R94H	ENSP00000023897:R94H	R	+	2	0	GABRA1	161232726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.717000	0.92951	0.585000	0.79938	CGT		0.373	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161300148	G	A	161300148	3	1	44	1	0	0	0	0	1	0	0	0	6179	1145	40	1	295	1	GABRA1	5	161300148	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	1619598	161300148	19615112	70	4117										
LCP2	3937	hgsc.bcm.edu	37	chr5	169697858	169697858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctcttcctcctcattgggggActcatagtctccatcatcct	6	15	5	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:169697858A>G	ENST00000046794.5	-	7	1003	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P		NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	130					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	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)		TCATTGGGGGACTCATAGTCT	0.537																																																0			5											73	89	84					5																	169697858		2132	4245	6377	169630436	SO:0001583	missense	3937				CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.388T>C	5.37:g.169697858A>G	ENSP00000046794:p.Ser130Pro		169630436	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484390	0.84854	.	.	ENSG00000043462	ENST00000046794	T	0.52526	0.66	5.4	5.4	0.78164	.	0.348432	0.30869	N	0.008715	T	0.64724	0.2624	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.65479	-0.6158	9	.	.	.	-29.6851	12.1086	0.53825	1.0:0.0:0.0:0.0	.	130	Q13094	LCP2_HUMAN	P	130	ENSP00000046794:S130P	.	S	-	1	0	LCP2	169630436	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.406000	0.52637	2.164000	0.68074	0.533000	0.62120	TCC		0.537	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169697858	A	G	169697858	3	3	44	1	0	0	0	0	1	0	0	0	8714	275	10	4	1273	4	LCP2	5	169697858	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	8397710	169697858	11217402	71	4118										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520243	176520243	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctgtgctcctgctgctggccGggctgtatcgagggcaggcg	17	12	0	0	rs351855	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:176520243G>A	ENST00000292408.4	+	9	1407	c.1162G>A	c.(1162-1164)Ggg>Agg	p.G388R	FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000292410.3_Intron|FGFR4_ENST00000393637.1_Intron|FGFR4_ENST00000502906.1_Missense_Mutation_p.G388R	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	388			G -> R (prolonged FGFR4 activity, increased cell motility and tumor cell invasion, possibly due to increased stability of the protease MMP14; dbSNP:rs351855). {ECO:0000269|PubMed:11781352, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.8}.		alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	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)		Palifermin(DB00039)|Ponatinib(DB08901)	GCTGCTGGCCGGGCTGTATCG	0.711										TSP Lung(9;0.080)			G|||	1500	0.299521	0.1097	0.3098	5008	,	,		12765	0.4633		0.2942	False		,,,				2504	0.3855															0			5	GRCh37	CM023917	FGFR4	M	rs351855	G	ARG/GLY,,ARG/GLY	567,3839	240.9+/-251.5	34,499,1670	35	32	33	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1162,,1162	4.3	0.9	5	dbSNP_79	33	2583,6011	393.4+/-344.3	429,1725,2143	yes	missense,intron,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	125,,125	463,2224,3813	AA,AG,GG		30.0559,12.8688,24.2308	possibly-damaging,,possibly-damaging	388/803,,388/803	176520243	3150,9850	2203	4297	6500	176452849	SO:0001583	missense	2264			AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1162G>A	5.37:g.176520243G>A	ENSP00000292408:p.Gly388Arg		176452849	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	661|661	0.30265567765567764|0.30265567765567764	61|61	0.12398373983739837|0.12398373983739837	123|123	0.3397790055248619|0.3397790055248619	258|258	0.45104895104895104|0.45104895104895104	219|219	0.28891820580474936|0.28891820580474936	G|G	19.01|19.01	3.743077|3.743077	0.69418|0.69418	0.128688|0.128688	0.300559|0.300559	ENSG00000160867|ENSG00000160867	ENST00000292408;ENST00000502906;ENST00000377207|ENST00000511076	D;D|.	0.82984|.	-1.67;-1.67|.	4.29|4.29	4.29|4.29	0.51040|0.51040	.|.	0.316526|.	0.32753|.	N|.	0.005687|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	P|P	1.0|1.0	D|.	0.71674|.	0.998|.	P|.	0.52481|.	0.7|.	T|T	0.50338|0.50338	-0.8840|-0.8840	9|4	0.59425|.	D|.	0.04|.	.|.	11.2123|11.2123	0.48806|0.48806	0.0906:0.0:0.9094:0.0|0.0906:0.0:0.9094:0.0	rs351855;rs56695235;rs351855|rs351855;rs56695235;rs351855	388|.	P22455|.	FGFR4_HUMAN|.	R|Q	388;388;616|23	ENSP00000292408:G388R;ENSP00000424960:G388R|.	ENSP00000292408:G388R|.	G|R	+|+	1|2	0|0	FGFR4|FGFR4	176452849|176452849	0.995000|0.995000	0.38212|0.38212	0.911000|0.911000	0.35937|0.35937	0.721000|0.721000	0.41392|0.41392	4.235000|4.235000	0.58666|0.58666	2.233000|2.233000	0.73108|0.73108	0.561000|0.561000	0.74099|0.74099	GGG|CGG		0.711	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			A	176520243	G	A	176520243	3	1	44	1	0	0	0	0	1	0	0	0	5887	1116	39	1	1192	1	FGFR4	5	176520243	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	6822385	176520243	4395017	72	4119										
FARS2	10667	hgsc.bcm.edu	37	chr6	5771573	5771573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcacgtaccgccacatggaaCggactctgtcccagagagag	11	13	2	2	rs145697325		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:5771573C>T	ENST00000324331.6	+	7	1603	c.1267C>T	c.(1267-1269)Cgg>Tgg	p.R423W	FARS2_ENST00000274680.4_Missense_Mutation_p.R423W			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	423	FDX-ACB. {ECO:0000255|PROSITE- ProRule:PRU00778}.				gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	CCACATGGAACGGACTCTGTC	0.587																																																0			6											173	130	144					6																	5771573		2203	4300	6503	5716572	SO:0001583	missense	10667			AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	21062	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 2, mitochondrial"	611592	"phenylalanine-tRNA synthetase 1 (mitochondrial)"	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.1267C>T	6.37:g.5771573C>T	ENSP00000316335:p.Arg423Trp		5716572	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	37	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.621024	0.66787	.	.	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.79352	-1.26;-1.26	5.81	2.71	0.32032	Phenylalanyl-tRNA synthetase, beta subunit, ferrodoxin-fold anticodon-binding (5);	0.000000	0.64402	D	0.000002	D	0.88066	0.6337	M	0.93638	3.44	0.52099	D	0.999948	D	0.89917	1.0	D	0.91635	0.999	D	0.90661	0.4590	10	0.72032	D	0.01	-36.8389	13.5071	0.61489	0.4852:0.5148:0.0:0.0	.	423	O95363	SYFM_HUMAN	W	423	ENSP00000274680:R423W;ENSP00000316335:R423W	ENSP00000274680:R423W	R	+	1	2	FARS2	5716572	1.000000	0.71417	0.980000	0.43619	0.778000	0.44026	1.436000	0.34980	0.756000	0.33013	0.655000	0.94253	CGG		0.587	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567		T	5771573	C	T	5771573	3	4	44	1	0	0	0	0	1	0	0	0	5697	527	19	1	1289	1	FARS2	6	5771573	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10		5771573	165343494	73	4120										
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910759	29910759	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccagtcacagactgaccgagTggacctggggaccctgcgcg	14	14	1	2	rs1071742	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:29910759T>A	ENST00000396634.1	+	4	640	c.299T>A	c.(298-300)gTg>gAg	p.V100E	HLA-A_ENST00000376809.5_Missense_Mutation_p.V100E|HLA-A_ENST00000376806.5_Missense_Mutation_p.V100E|HLA-A_ENST00000376802.2_Missense_Mutation_p.V100E			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	100	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACTGACCGAGTGGACCTGGGG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	1111	0.221845	0.2345	0.2522	5008	,	,		10249	0.2222		0.1938	False		,,,				2504	0.2117															0			6											60	64	63					6																	29910759		2194	4284	6478	30018738	SO:0001583	missense	3105	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.299T>A	6.37:g.29910759T>A	ENSP00000379873:p.Val100Glu		30018738	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	345	0.15796703296703296	79	0.16056910569105692	84	0.23204419889502761	95	0.1660839160839161	87	0.11477572559366754	.	5.377	0.254742	0.10185	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00695	5.83;5.83;5.83;5.83	3.33	-6.67	0.01783	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	15.776400	0.01836	U	0.034989	T	0.00271	0.0008	L	0.58428	1.81	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.002	T	0.46898	-0.9158	10	0.30854	T	0.27	.	0.4643	0.00521	0.2856:0.2905:0.146:0.2778	rs1071742;rs2231002;rs3129019;rs3173422;rs3200152;rs3200155;rs9256981;rs17423971;rs41551313	100;100;100;100;100	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	E	100	ENSP00000379873:V100E;ENSP00000366002:V100E;ENSP00000366005:V100E;ENSP00000365998:V100E	ENSP00000348012:V100E	V	+	2	0	HLA-A	30018738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.538000	0.00938	-1.834000	0.01193	-3.111000	0.00062	GTG		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		A	29910759	T	A	29910759	3	1	44	1	0	0	0	0	1	0	0	0	7216	1696	59	5	305	5	HLA-A	6	29910759	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	24139186	29910759	141204308	74	4121										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954491	30954491	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctccagtggggccagcacagCcaccaactctgagtccagca	10	16	1	1	rs34126344	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:30954491C>T	ENST00000376296.3	+	2	780	c.539C>T	c.(538-540)gCc>gTc	p.A180V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	180	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> V (in Ref. 4; CAQ07653). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCAGCACAGCCACCAACTCT	0.607													C|||	312	0.0623003	0.0166	0.0994	5008	,	,		27275	0.1319		0.0596	False		,,,				2504	0.0286															0			6						C	VAL/ALA	162,4244	108.6+/-147.0	1,160,2042	159	151	154		539	1.9	0	6	dbSNP_126	154	585,8015	155.4+/-209.4	23,539,3738	no	missense	MUC21	NM_001010909.2	64	24,699,5780	TT,TC,CC		6.8023,3.6768,5.7435	benign	180/567	30954491	747,12259	2203	4300	6503	31062470	SO:0001583	missense	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.539C>T	6.37:g.30954491C>T	ENSP00000365473:p.Ala180Val		31062470	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	148	0.06776556776556776	10	0.02032520325203252	30	0.08287292817679558	62	0.10839160839160839	46	0.06068601583113457	C	9.071	0.996786	0.19043	0.036768	0.068023	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02787	4.16	3.72	1.89	0.25635	.	.	.	.	.	T	0.00695	0.0023	N	0.19112	0.55	0.80722	P	0.0	B	0.33044	0.395	B	0.36289	0.221	T	0.49725	-0.8909	7	.	.	.	-0.31	3.2061	0.06666	0.2079:0.5615:0.0:0.2305	rs34126344	180	Q5SSG8	MUC21_HUMAN	V	180	ENSP00000365473:A180V	.	A	+	2	0	MUC21	31062470	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	0.279000	0.18771	0.360000	0.24265	0.485000	0.47835	GCC		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954491	C	T	30954491	3	4	44	1	0	0	0	0	1	0	0	0	10007	739	26	3	545	3	MUC21	6	30954491	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1043732	30954491	140160576	75	4122										
LY6G6D	58530	hgsc.bcm.edu	37	chr6	31685453	31685453	+	Missense_Mutation	SNP	G	G	T													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgggagacgtgacttatccaGcccacagggactgctacctg							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:31685453G>T	ENST00000375825.3	+	3	274	c.274G>T	c.(274-276)Gcc>Tcc	p.A92S	LY6G6F_ENST00000556581.1_Missense_Mutation_p.A341S|MEGT1_ENST00000503322.1_Missense_Mutation_p.A341S	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	92	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						GACTTATCCAGCCCACAGGGA	0.602																																																0			6											156	158	158					6																	31685453		2203	4300	6503	31793432	SO:0001583	missense	259215				CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"chromosome 6 open reading frame 23"	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.274G>T	6.37:g.31685453G>T	ENSP00000364985:p.Ala92Ser		31793432	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Missense_Mutation	SNP	ENST00000375825.3	37	CCDS34404.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	7.565|7.565	0.665501|0.665501	0.14710|0.14710	.|.	.|.	ENSG00000204424;ENSG00000250641;ENSG00000244355|ENSG00000244355	ENST00000556581;ENST00000503322;ENST00000375825|ENST00000375824	T;T;T|T	0.69685|0.37058	2.53;2.53;-0.42|1.22	5.54|5.54	0.0731|0.0731	0.14389|0.14389	.|.	1.740850|.	0.03400|.	N|.	0.203239|.	T|T	0.08447|0.08447	0.0210|0.0210	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.09377|.	0.004;0.004|.	T|T	0.29305|0.29305	-1.0016|-1.0016	10|7	0.54805|0.72032	T|D	0.06|0.01	.|.	3.99|3.99	0.09533|0.09533	0.6057:0.0:0.2494:0.1449|0.6057:0.0:0.2494:0.1449	.|.	92;341|.	O95868;Q9NZJ1|.	LY66D_HUMAN;.|.	S|I	341;341;92|132	ENSP00000452432:A341S;ENSP00000421232:A341S;ENSP00000364985:A92S|ENSP00000364984:S132I	ENSP00000364985:A92S|ENSP00000364984:S132I	A|S	+|+	1|2	0|0	LY6G6D;XXbac-BPG32J3.19;LY6G6F|LY6G6D	31793432|31793432	0.042000|0.042000	0.20092|0.20092	0.024000|0.024000	0.17045|0.17045	0.240000|0.240000	0.25518|0.25518	0.426000|0.426000	0.21363|0.21363	0.072000|0.072000	0.16694|0.16694	-0.792000|-0.792000	0.03331|0.03331	GCC|AGC		0.602	LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2			T	31685453	G	T	31685453	3	4	44	1	0	0	0	0	1	0	0	0	9125	971	34	2	284	2	LY6G6D	6	31685453	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	730962	31685453	139429614	76	4123	17	2								
LY6G6D	58530	hgsc.bcm.edu	37	chr6	31685455	31685455	+	Silent	SNP	C	C	A													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggagacgtgacttatccagcCcacagggactgctacctggg							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:31685455C>A	ENST00000375825.3	+	3	276	c.276C>A	c.(274-276)gcC>gcA	p.A92A	LY6G6F_ENST00000556581.1_Silent_p.A341A|MEGT1_ENST00000503322.1_Silent_p.A341A	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	92	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						CTTATCCAGCCCACAGGGACT	0.602																																																0			6											155	157	156					6																	31685455		2203	4300	6503	31793434	SO:0001819	synonymous_variant	259215				CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"chromosome 6 open reading frame 23"	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.276C>A	6.37:g.31685455C>A			31793434	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Silent	SNP	ENST00000375825.3	37	CCDS34404.1	.	.	.	.	.	.	.	.	.	.	c	12.93	2.084495	0.36758	.	.	ENSG00000244355	ENST00000375824	T	0.38240	1.15	5.54	1.65	0.23941	.	.	.	.	.	T	0.17195	0.0413	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	T	0.24870	-1.0148	6	0.87932	D	0	.	4.6608	0.12641	0.1502:0.5976:0.0:0.2522	.	.	.	.	T	133	ENSP00000364984:P133T	ENSP00000364984:P133T	P	+	1	0	LY6G6D	31793434	0.262000	0.24073	0.091000	0.20842	0.329000	0.28539	0.403000	0.20982	0.284000	0.22305	0.645000	0.84053	CCA		0.602	LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2			A	31685455	C	A	31685455	2	1	44	1	0	0	0	0	0	0	0	1	9125	610	22	2		2	LY6G6D	6	31685455	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	2	31685455	139429612	77	4124	17	2								
MAPK13	5603	hgsc.bcm.edu	37	chr6	36106492	36106492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cttccaggccaaatcctacaTccagtccctgccacagaccc	5	19	0	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:36106492T>C	ENST00000211287.4	+	10	1038	c.776T>C	c.(775-777)aTc>aCc	p.I259T	MAPK13_ENST00000373761.6_Missense_Mutation_p.I249T|MAPK13_ENST00000373759.1_Silent_p.H130H|MAPK13_ENST00000373766.5_Silent_p.H208H|Z95152.1_ENST00000408816.1_RNA	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						AAATCCTACATCCAGTCCCTG	0.597																																																0			6											58	60	59					6																	36106492		2203	4300	6503	36214470	SO:0001583	missense	5603			Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.776T>C	6.37:g.36106492T>C	ENSP00000211287:p.Ile259Thr		36214470	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Missense_Mutation	SNP	ENST00000211287.4	37	CCDS4818.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145620	0.77888	.	.	ENSG00000156711	ENST00000373761;ENST00000211287	T;T	0.43688	0.94;0.94	5.25	5.25	0.73442	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000017	T	0.45657	0.1353	M	0.62209	1.925	0.80722	D	1	P	0.45126	0.851	P	0.53809	0.735	T	0.51309	-0.8722	10	0.87932	D	0	-29.7119	14.3162	0.66452	0.0:0.0:0.0:1.0	.	259	O15264	MK13_HUMAN	T	249;259	ENSP00000362866:I249T;ENSP00000211287:I259T	ENSP00000211287:I259T	I	+	2	0	MAPK13	36214470	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.717000	0.84732	1.976000	0.57569	0.397000	0.26171	ATC		0.597	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1			C	36106492	T	C	36106492	3	2	44	1	0	0	0	0	1	0	0	0	9305	1435	50	4	814	4	MAPK13	6	36106492	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	4421037	36106492	135008575	78	4125										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39034026	39034026	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atcatctacacggtgggctaCgcactctccttctctgctct	7	15	5	0	rs200564025		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:39034026C>T	ENST00000373256.4	+	5	499	c.456C>T	c.(454-456)taC>taT	p.Y152Y		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	152					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.Y152Y(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	CGGTGGGCTACGCACTCTCCT	0.617																																																1	Substitution - coding silent(1)	endometrium(1)	6											176	130	146					6																	39034026		2203	4300	6503	39142004	SO:0001819	synonymous_variant	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.456C>T	6.37:g.39034026C>T			39142004	Q2M229|Q99669	Silent	SNP	ENST00000373256.4	37	CCDS4839.1																																																																																				0.617	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			T	39034026	C	T	39034026	2	4	44	1	0	0	0	0	0	0	0	1	6472	547	19	1		1	GLP1R	6	39034026	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	2927534	39034026	132081041	79	4126										
POLH	5429	hgsc.bcm.edu	37	chr6	43550100	43550100	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggttgctctcgtggacatggActgtttttttgttcaagtgg	13	6	2	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:43550100A>G	ENST00000372236.4	+	2	339	c.44A>G	c.(43-45)gAc>gGc	p.D15G	POLH_ENST00000535400.1_Intron|POLH_ENST00000372226.1_Missense_Mutation_p.D15G	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GTGGACATGGACTGTTTTTTT	0.418								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																																							0			6											234	217	222					6																	43550100		2203	4300	6503	43658078	SO:0001583	missense	10721	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.44A>G	6.37:g.43550100A>G	ENSP00000361310:p.Asp15Gly		43658078	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.840285	0.91117	.	.	ENSG00000170734	ENST00000372236;ENST00000372226	D;D	0.83755	-1.76;-1.76	5.56	5.56	0.83823	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.000000	0.85682	D	0.000000	D	0.93298	0.7864	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95253	0.8361	10	0.87932	D	0	0.3493	14.2865	0.66249	1.0:0.0:0.0:0.0	.	15	Q9Y253	POLH_HUMAN	G	15	ENSP00000361310:D15G;ENSP00000361300:D15G	ENSP00000361300:D15G	D	+	2	0	POLH	43658078	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.613000	0.82986	2.245000	0.73994	0.454000	0.30748	GAC		0.418	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502		G	43550100	A	G	43550100	3	3	44	1	0	0	0	0	1	0	0	0	12233	275	10	4	46	4	POLH	6	43550100	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	4516074	43550100	127564967	80	4127										
PREP	5550	hgsc.bcm.edu	37	chr6	105736747	105736747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgaacattggaatcttcgtaCcatccttgctagggtagaaa	9	8	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:105736747C>T	ENST00000369110.3	-	11	1532	c.1340G>A	c.(1339-1341)gGt>gAt	p.G447D		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	447					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AATCTTCGTACCATCCTTGCT	0.353																																																0			6											111	106	108					6																	105736747		2203	4300	6503	105843440	SO:0001583	missense	5550				CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1340G>A	6.37:g.105736747C>T	ENSP00000358106:p.Gly447Asp		105843440	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739413	0.89573	.	.	ENSG00000085377	ENST00000369110	T	0.65549	-0.16	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.74015	0.3661	H	0.95365	3.66	0.80722	D	1	P	0.40731	0.728	B	0.42882	0.401	T	0.81167	-0.1056	10	0.62326	D	0.03	-20.1991	20.2469	0.98398	0.0:1.0:0.0:0.0	.	447	P48147	PPCE_HUMAN	D	447	ENSP00000358106:G447D	ENSP00000358106:G447D	G	-	2	0	PREP	105843440	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.757000	0.68766	2.781000	0.95711	0.555000	0.69702	GGT		0.353	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			T	105736747	C	T	105736747	3	4	44	1	0	0	0	0	1	0	0	0	12508	507	18	3	812	3	PREP	6	105736747	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	62186647	105736747	65378320	81	4128										
MCM9	254394	hgsc.bcm.edu	37	chr6	119252789	119252789	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aactgggtaatgagcatcttCatccctttccttcaagatta	6	10	3	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:119252789C>T	ENST00000316316.6	-	2	386	c.100G>A	c.(100-102)Gaa>Aaa	p.E34K	MCM9_ENST00000316068.3_Missense_Mutation_p.E34K	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	34					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGAGCATCTTCATCCCTTTCC	0.398																																																0			6											129	116	121					6																	119252789		2203	4300	6503	119294488	SO:0001583	missense	254394			BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.100G>A	6.37:g.119252789C>T	ENSP00000314505:p.Glu34Lys		119294488	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613254	0.87359	.	.	ENSG00000111877	ENST00000316316;ENST00000316068;ENST00000425154;ENST00000505446	T;T;T;T	0.04275	3.66;3.66;3.66;3.66	5.91	5.91	0.95273	.	.	.	.	.	T	0.03695	0.0105	M	0.64997	1.995	0.80722	D	1	P	0.38504	0.634	B	0.33620	0.167	T	0.51220	-0.8733	9	0.19147	T	0.46	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	34	Q9NXL9-2	.	K	34	ENSP00000314505:E34K;ENSP00000312870:E34K;ENSP00000394776:E34K;ENSP00000426890:E34K	ENSP00000312870:E34K	E	-	1	0	MCM9	119294488	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.707000	0.68370	2.793000	0.96121	0.655000	0.94253	GAA		0.398	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255		T	119252789	C	T	119252789	3	4	44	1	0	0	0	0	1	0	0	0	9424	835	29	3	1099	3	MCM9	6	119252789	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	13516042	119252789	51862278	82	4129										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121625558	121625558	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggagcttctttctgatattcAtttagaagacgaacctacaa	7	8	3	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:121625558A>T	ENST00000398212.2	-	8	937	c.888T>A	c.(886-888)aaT>aaA	p.N296K	TBC1D32_ENST00000275159.6_Missense_Mutation_p.N296K	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	296					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCTGATATTCATTTAGAAGAC	0.368																																																0			6											83	80	81					6																	121625558		1817	4083	5900	121667257	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.888T>A	6.37:g.121625558A>T	ENSP00000381270:p.Asn296Lys		121667257	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392106	0.62066	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.23552	1.9;1.9	5.05	2.56	0.30785	.	0.053903	0.64402	D	0.000001	T	0.33030	0.0849	M	0.75264	2.295	0.43330	D	0.995361	D	0.76494	0.999	D	0.65874	0.939	T	0.14364	-1.0475	10	0.66056	D	0.02	.	9.5036	0.39033	0.8523:0.0:0.1477:0.0	.	296	Q96NH3	BROMI_HUMAN	K	296	ENSP00000275159:N296K;ENSP00000381270:N296K	ENSP00000275159:N296K	N	-	3	2	C6orf170	121667257	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.895000	0.48648	0.226000	0.20979	0.528000	0.53228	AAT		0.368	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121625558	A	T	121625558	3	4	44	1	0	0	0	0	1	0	0	0	2350	214	8	5	2985	5	C6orf170	6	121625558	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	2372769	121625558	49489509	83	4130										
PDE7B	27115	hgsc.bcm.edu	37	chr6	136429947	136429947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	attcattgacttccgcctacTtaacagtgagtaatcaagtg	7	9	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:136429947T>C	ENST00000308191.6	+	3	464	c.161T>C	c.(160-162)cTt>cCt	p.L54P	RP13-143G15.4_ENST00000417643.1_RNA|RP13-143G15.4_ENST00000591521.1_RNA|RP13-143G15.4_ENST00000585946.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	54					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	TTCCGCCTACTTAACAGTGAG	0.433																																																0			6											105	104	104					6																	136429947		2203	4300	6503	136471640	SO:0001583	missense	27115			AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"Phosphodiesterases"	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.161T>C	6.37:g.136429947T>C	ENSP00000310661:p.Leu54Pro		136471640	Q5W154	Missense_Mutation	SNP	ENST00000308191.6	37	CCDS5175.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049803	0.75846	.	.	ENSG00000171408	ENST00000308191;ENST00000367787	T	0.73897	-0.79	5.97	5.97	0.96955	.	3.163210	0.00424	N	0.000070	T	0.77260	0.4104	L	0.58101	1.795	0.80722	D	1	D;P	0.54397	0.966;0.929	P;P	0.54629	0.641;0.757	T	0.62034	-0.6939	10	0.37606	T	0.19	.	13.9684	0.64223	0.0:0.0:0.0:1.0	.	106;54	A1E5M1;Q9NP56	.;PDE7B_HUMAN	P	54;190	ENSP00000310661:L54P	ENSP00000310661:L54P	L	+	2	0	PDE7B	136471640	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.757000	0.62213	2.281000	0.76405	0.528000	0.53228	CTT		0.433	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1			C	136429947	T	C	136429947	3	2	44	1	0	0	0	0	1	0	0	0	11683	1609	56	4	171	4	PDE7B	6	136429947	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	14804389	136429947	34685120	84	4131										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5363928	5363928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agtcttggttgggttcaaagTcctcctcggctgccatgctc	11	12	2	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:5363928T>C	ENST00000430969.1	-	21	6707	c.6359A>G	c.(6358-6360)gAc>gGc	p.D2120G	TNRC18_ENST00000399537.4_Missense_Mutation_p.D2120G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2120							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGTTCAAAGTCCTCCTCGGC	0.637																																																0			7											46	49	48					7																	5363928		1568	3581	5149	5330454	SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.6359A>G	7.37:g.5363928T>C	ENSP00000395538:p.Asp2120Gly		5330454	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.97|18.97	3.735255|3.735255	0.69189|0.69189	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000455076	T;T|.	0.23147|.	1.92;1.92|.	4.07|4.07	4.07|4.07	0.47477|0.47477	.|.	.|.	.|.	.|.	.|.	T|T	0.51075|0.51075	0.1653|0.1653	L|L	0.28115|0.28115	0.83|0.83	0.43330|0.43330	D|D	0.995362|0.995362	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.46498|0.46498	-0.9187|-0.9187	9|5	0.66056|.	D|.	0.02|.	.|.	12.9664|12.9664	0.58485|0.58485	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2120|.	O15417|.	TNC18_HUMAN|.	G|A	2120|168	ENSP00000382452:D2120G;ENSP00000395538:D2120G|.	ENSP00000382452:D2120G|.	D|T	-|-	2|1	0|0	TNRC18|TNRC18	5330454|5330454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.566000|0.566000	0.35808|0.35808	7.178000|7.178000	0.77657|0.77657	1.614000|1.614000	0.50241|0.50241	0.260000|0.260000	0.18958|0.18958	GAC|ACT		0.637	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5363928	T	C	5363928	3	2	44	1	0	0	0	0	1	0	0	0	16378	1667	58	4	2587	4	TNRC18	7	5363928	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		5363928	153774735	85	4132										
C7orf26	79034	hgsc.bcm.edu	37	chr7	6634106	6634106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtgaggttagccaaggcccTtgtagatgactactgctgtt	12	8	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:6634106T>C	ENST00000344417.5	+	3	722	c.455T>C	c.(454-456)cTt>cCt	p.L152P	C7orf26_ENST00000472693.1_3'UTR|C7orf26_ENST00000359073.5_Missense_Mutation_p.L133P	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	152										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		GCCAAGGCCCTTGTAGATGAC	0.527																																																0			7											243	218	226					7																	6634106		2203	4300	6503	6600631	SO:0001583	missense	79034			BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.455T>C	7.37:g.6634106T>C	ENSP00000340220:p.Leu152Pro		6600631	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	37	CCDS5353.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404955	0.62288	.	.	ENSG00000146576	ENST00000344417;ENST00000359073	T;T	0.53206	0.63;0.63	4.66	4.66	0.58398	.	0.065009	0.56097	D	0.000023	T	0.63628	0.2527	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.67055	-0.5767	10	0.87932	D	0	-22.1337	12.6786	0.56908	0.0:0.0:0.0:1.0	.	133;152	Q96N11-2;Q96N11	.;CG026_HUMAN	P	152;133	ENSP00000340220:L152P;ENSP00000351974:L133P	ENSP00000340220:L152P	L	+	2	0	C7orf26	6600631	1.000000	0.71417	0.948000	0.38648	0.986000	0.74619	7.931000	0.87625	2.033000	0.60031	0.533000	0.62120	CTT		0.527	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		C	6634106	T	C	6634106	3	2	44	1	0	0	0	0	1	0	0	0	2387	1609	56	4	465	4	C7orf26	7	6634106	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	1270178	6634106	152504557	86	4133										
SP4	6671	hgsc.bcm.edu	37	chr7	21470070	21470070	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cagtcgtttcaactccagtcAgggcagacgattcagaccat	9	12	3	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:21470070A>G	ENST00000222584.3	+	3	1505	c.1287A>G	c.(1285-1287)tcA>tcG	p.S429S		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	429					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						AACTCCAGTCAGGGCAGACGA	0.473																																																0			7											118	118	118					7																	21470070		2203	4300	6503	21436595	SO:0001819	synonymous_variant	6671				CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1287A>G	7.37:g.21470070A>G			21436595	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																				0.473	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		G	21470070	A	G	21470070	2	3	44	1	0	0	0	0	0	0	0	1	15003	175	7	4		4	SP4	7	21470070	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	14835964	21470070	137668593	87	4134										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21737770	21737770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgaaggttttgtggatgcgcGtgcattagcccgaaagttca	13	7	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:21737770G>A	ENST00000409508.3	+	36	6150	c.6119G>A	c.(6118-6120)cGt>cAt	p.R2040H	DNAH11_ENST00000328843.6_Missense_Mutation_p.R2047H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2047	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTGGATGCGCGTGCATTAGCC	0.418									Kartagener syndrome																																							0			7																																								21704295	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.6119G>A	7.37:g.21737770G>A	ENSP00000475939:p.Arg2040His		21704295	Q9UJ82	Silent	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	15.56	2.869856	0.51588	.	.	ENSG00000105877	ENST00000328843	T	0.11821	2.74	5.33	5.33	0.75918	.	0.072264	0.51477	D	0.000095	T	0.40694	0.1127	.	.	.	0.53005	D	0.999962	D	0.76494	0.999	D	0.68943	0.961	T	0.32025	-0.9922	9	0.72032	D	0.01	.	19.0193	0.92906	0.0:0.0:1.0:0.0	.	2047	Q96DT5	DYH11_HUMAN	H	2047	ENSP00000330671:R2047H	ENSP00000330671:R2047H	R	+	2	0	DNAH11	21704295	0.688000	0.27680	0.105000	0.21289	0.028000	0.11728	3.849000	0.55910	2.493000	0.84123	0.655000	0.94253	CGT		0.418	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21737770	G	A	21737770	3	1	44	1	0	0	0	0	1	0	0	0	4610	1145	40	1	6283	1	DNAH11	7	21737770	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	267700	21737770	137400893	88	4135										
DDC	1644	hgsc.bcm.edu	37	chr7	50605570	50605570	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	caccttacctggatcactccTcccccttctccagctttctc	3	20	3	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:50605570T>C	ENST00000444124.2	-	4	623	c.423A>G	c.(421-423)ggA>ggG	p.G141G	DDC_ENST00000357936.5_Silent_p.G141G|DDC_ENST00000426377.1_Intron|DDC_ENST00000431062.1_Silent_p.G141G|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000380984.4_Silent_p.G141G|DDC_ENST00000489162.1_5'UTR	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	141	2 X approximate tandem repeats.				catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	GGATCACTCCTCCCCCTTCTC	0.557																																																0			7											118	109	112					7																	50605570		2203	4300	6503	50573064	SO:0001819	synonymous_variant	1644				CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.423A>G	7.37:g.50605570T>C			50573064	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1																																																																																				0.557	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			C	50605570	T	C	50605570	2	2	44	1	0	0	0	0	0	0	0	1	4331	1538	54	4		4	DDC	7	50605570	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	28867800	50605570	108533093	89	4136										
POM121	9883	hgsc.bcm.edu	37	chr7	72413443	72413443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cgggagccaacccccagcccGcatttggggccgctgagggg	16	15	0	1	rs62463429	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:72413443G>A	ENST00000434423.2	+	11	2911	c.2911G>A	c.(2911-2913)Gca>Aca	p.A971T	POM121_ENST00000358357.3_Missense_Mutation_p.A706T|POM121_ENST00000446813.1_Missense_Mutation_p.A706T|POM121_ENST00000257622.4_Missense_Mutation_p.A706T|POM121_ENST00000395270.1_Missense_Mutation_p.A706T			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	971	Pore side. {ECO:0000255}.			A -> T (in Ref. 3; BAB14097). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCCCCAGCCCGCATTTGGGGC	0.642																																																0			7											13	19	17					7																	72413443		2073	4153	6226	72051379	SO:0001583	missense	22932			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2911G>A	7.37:g.72413443G>A	ENSP00000405562:p.Ala971Thr		72051379	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		806	0.36904761904761907	111	0.22560975609756098	135	0.3729281767955801	269	0.47027972027972026	291	0.3839050131926121	G	0.019	-1.453214	0.01071	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.06849	3.25;3.27;3.25;3.27;3.54	2.33	-4.66	0.03329	.	1.040150	0.07705	N	0.941009	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B;B	0.23650	0.089;0.008	B;B	0.16722	0.016;0.004	T	0.45396	-0.9264	9	0.25106	T	0.35	.	10.3771	0.44088	0.524:0.0:0.476:0.0	rs62463429	706;971	A8MXF9;Q96HA1	.;P121A_HUMAN	T	706;706;706;706;971	ENSP00000393020:A706T;ENSP00000257622:A706T;ENSP00000378687:A706T;ENSP00000351124:A706T;ENSP00000405562:A971T	ENSP00000257622:A706T	A	+	1	0	POM121	72051379	0.000000	0.05858	0.055000	0.19348	0.038000	0.13279	-1.922000	0.01568	-1.455000	0.01923	-1.195000	0.01675	GCA		0.642	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			A	72413443	G	A	72413443	3	1	44	1	0	0	0	0	1	0	0	0	12270	1087	38	1	2154	1	POM121	7	72413443	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	21807873	72413443	86725220	90	4137										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98460916	98460916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcggtagaggtgggcgtcagCgggcagggccaggctgccgt	21	10	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:98460916C>T	ENST00000416379.2	-	2	197	c.193G>A	c.(193-195)Gct>Act	p.A65T	TMEM130_ENST00000339375.4_Missense_Mutation_p.A65T|TMEM130_ENST00000450876.1_5'UTR|TMEM130_ENST00000546258.1_Missense_Mutation_p.A46T|TMEM130_ENST00000345589.4_Intron			Q8N3G9	TM130_HUMAN	transmembrane protein 130	65						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A65T(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGGGCGTCAGCGGGCAGGGCC	0.642																																																1	Substitution - Missense(1)	urinary_tract(1)	7											54	50	51					7																	98460916		2203	4300	6503	98298852	SO:0001583	missense	222865				CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.193G>A	7.37:g.98460916C>T	ENSP00000413163:p.Ala65Thr		98298852	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Missense_Mutation	SNP	ENST00000416379.2	37	CCDS47650.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.799256	0.00617	.	.	ENSG00000166448	ENST00000416379;ENST00000339375;ENST00000546258	T;T;T	0.12569	2.67;2.67;2.67	4.28	-3.09	0.05331	.	0.877727	0.09755	N	0.760081	T	0.03520	0.0101	N	0.01576	-0.805	0.09310	N	1	B;B;B	0.10296	0.001;0.001;0.003	B;B;B	0.04013	0.001;0.001;0.001	T	0.44847	-0.9301	10	0.12766	T	0.61	-6.2021	5.9152	0.19052	0.0:0.4178:0.1431:0.4391	.	65;46;65	Q8N3G9-2;B7Z2F1;Q8N3G9	.;.;TM130_HUMAN	T	65;65;46	ENSP00000413163:A65T;ENSP00000341256:A65T;ENSP00000445869:A46T	ENSP00000341256:A65T	A	-	1	0	TMEM130	98298852	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-3.422000	0.00476	-0.814000	0.04352	0.505000	0.49811	GCT		0.642	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		T	98460916	C	T	98460916	3	4	44	1	0	0	0	0	1	0	0	0	16082	768	27	1	1142	1	TMEM130	7	98460916	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	26047473	98460916	60677747	91	4138										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112424142	112424142	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tttccatctttcagttactgAaagtccactaaaataaatgt	4	8	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:112424142A>G	ENST00000312814.6	-	2	1299	c.739T>C	c.(739-741)Tca>Cca	p.S247P	TMEM168_ENST00000454074.1_Missense_Mutation_p.S247P	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	247						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.S247T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						TCAGTTACTGAAAGTCCACTA	0.348																																																1	Substitution - Missense(1)	central_nervous_system(1)	7											100	111	107					7																	112424142		2203	4300	6503	112211378	SO:0001583	missense	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.739T>C	7.37:g.112424142A>G	ENSP00000323068:p.Ser247Pro		112211378	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.768042	0.69878	.	.	ENSG00000146802	ENST00000312814;ENST00000454074	.	.	.	6.06	6.06	0.98353	.	0.246149	0.42294	D	0.000740	T	0.73118	0.3546	L	0.55481	1.735	0.80722	D	1	D	0.69078	0.997	P	0.59487	0.858	T	0.75402	-0.3330	9	0.72032	D	0.01	-27.2205	16.6245	0.84952	1.0:0.0:0.0:0.0	.	247	Q9H0V1	TM168_HUMAN	P	247	.	ENSP00000323068:S247P	S	-	1	0	TMEM168	112211378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.353000	0.79414	2.323000	0.78572	0.528000	0.53228	TCA		0.348	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		G	112424142	A	G	112424142	3	3	44	1	0	0	0	0	1	0	0	0	16122	246	9	4	1370	4	TMEM168	7	112424142	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	13963226	112424142	46714521	92	4139										
MKLN1	4289	hgsc.bcm.edu	37	chr7	131155643	131155643	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gatccccttagtgctctgaaAtatttacaaaatgatcttta	5	8	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:131155643A>G	ENST00000352689.6	+	16	2011	c.1971A>G	c.(1969-1971)aaA>aaG	p.K657K	MKLN1_ENST00000498778.1_3'UTR|MKLN1_ENST00000421797.2_Silent_p.K565K	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	657					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					GTGCTCTGAAATATTTACAAA	0.323																																																0			7											72	76	75					7																	131155643		2203	4297	6500	130806183	SO:0001819	synonymous_variant	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1971A>G	7.37:g.131155643A>G			130806183	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Silent	SNP	ENST00000352689.6	37	CCDS34754.1																																																																																				0.323	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		G	131155643	A	G	131155643	2	3	44	1	0	0	0	0	0	0	0	1	9633	98	4	4		4	MKLN1	7	131155643	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	18731501	131155643	27983020	93	4140										
BRAF	673	hgsc.bcm.edu	37	chr7	140453170	140453170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aaaatcacctatttttactgTgaggtcttcatgaagaaata	6	6	3	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:140453170T>C	ENST00000288602.6	-	15	1825	c.1765A>G	c.(1765-1767)Aca>Gca	p.T589A		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	589	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ATTTTTACTGTGAGGTCTTCA	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											98	94	95					7																	140453170		2203	4300	6503	140099639	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1765A>G	7.37:g.140453170T>C	ENSP00000288602:p.Thr589Ala		140099639	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.616302	0.87359	.	.	ENSG00000157764	ENST00000288602	D	0.98958	-5.27	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98451	0.9484	L	0.49640	1.575	0.80722	D	1	P	0.35780	0.52	P	0.51701	0.677	D	0.99846	1.1066	10	0.87932	D	0	.	15.9326	0.79675	0.0:0.0:0.0:1.0	.	589	P15056	BRAF_HUMAN	A	589	ENSP00000288602:T589A	ENSP00000288602:T589A	T	-	1	0	BRAF	140099639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.921000	0.87530	2.169000	0.68431	0.529000	0.55759	ACA		0.383	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140453170	T	C	140453170	3	2	44	1	0	0	0	0	1	0	0	0	1499	1696	59	4	551	4	BRAF	7	140453170	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	9297527	140453170	18685493	94	4141										
GIMAP5	55340	hgsc.bcm.edu	37	chr7	150439391	150439391	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tggccagcccgtgtttgagtCcaagctgagggcccagtcag	14	12	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:150439391C>G	ENST00000358647.3	+	3	531	c.164C>G	c.(163-165)tCc>tGc	p.S55C	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	55	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)	p.S55Y(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGTTTGAGTCCAAGCTGAGG	0.562																																																1	Substitution - Missense(1)	central_nervous_system(1)	7											90	76	80					7																	150439391		2203	4300	6503	150070324	SO:0001583	missense	0			AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"GTPases, IMAP"	18005	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 5"	608086	"immune associated nucleotide 4 like 1 (mouse)"	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.164C>G	7.37:g.150439391C>G	ENSP00000351473:p.Ser55Cys		150070324	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Missense_Mutation	SNP	ENST00000358647.3	37	CCDS5907.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111174	0.37242	.	.	ENSG00000196329	ENST00000358647;ENST00000447239	T	0.11712	2.75	4.35	4.35	0.52113	AIG1 (1);	0.063252	0.64402	D	0.000003	T	0.34135	0.0887	M	0.84326	2.69	0.09310	N	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.09530	-1.0670	10	0.66056	D	0.02	.	12.225	0.54455	0.0:1.0:0.0:0.0	.	55	Q96F15	GIMA5_HUMAN	C	55;91	ENSP00000351473:S55C	ENSP00000351473:S55C	S	+	2	0	GIMAP5	150070324	0.000000	0.05858	0.982000	0.44146	0.285000	0.27093	0.614000	0.24314	2.251000	0.74343	0.655000	0.94253	TCC		0.562	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384		G	150439391	C	G	150439391	3	3	44	1	0	0	0	0	1	0	0	0	6402	855	30	5	170	5	GIMAP5	7	150439391	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	9986221	150439391	8699272	95	4142										
DLC1	10395	hgsc.bcm.edu	37	chr8	13356870	13356870	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcatctttaggggggtcaggTttccttcgttgctgagcaat	12	8	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:13356870T>C	ENST00000276297.4	-	2	1120	c.711A>G	c.(709-711)aaA>aaG	p.K237K	DLC1_ENST00000511869.1_Silent_p.K237K|DLC1_ENST00000316609.5_Silent_p.K237K	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	237					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.K237N(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GGGGGTCAGGTTTCCTTCGTT	0.403																																																1	Substitution - Missense(1)	lung(1)	8											155	156	155					8																	13356870		2203	4300	6503	13401241	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.711A>G	8.37:g.13356870T>C			13401241	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.403	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13356870	T	C	13356870	2	2	44	1	0	0	0	0	0	0	0	1	4561	1722	60	4		4	DLC1	8	13356870	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10		13356870	133007152	96	4143										
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19190463	19190468	+	Splice_Site	DEL	CAGAGA	CAGAGA	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tttgtttgtgtgtttgtttgCagagaatggcaaatcggttc					rs529179009		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CAGAGA	CAGAGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:19190463_19190468delCAGAGA	ENST00000265807.3	+	3	592_595	c.181_184delCAGAGA	c.(181-186)cagaga>ga	p.QR61del	SH2D4A_ENST00000519207.1_Splice_Site_p.QR61del|SH2D4A_ENST00000518040.1_Splice_Site_p.QR16del	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	61					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TGTTTGTTTGCAGAGAATGGCAAATC	0.364																																																0			8																																								19234748	SO:0001630	splice_region_variant	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.182-1CAGAGA>-	8.37:g.19190463_19190468delCAGAGA			19234743	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Frame_Shift_Del	DEL	ENST00000265807.3	37	CCDS6009.1																																																																																				0.364	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	In_Frame_Del	-	19190468	CAGAGA	-	19190463	8	5	44	1	0	1	0	1	0	0	1	0	14272	725	25	0		0	SH2D4A	8	19190463	Splice_Site	DEL	CAGAGA	TCGA-AG-3885-01A-01W-0899-10	5833593	19190463	127173559	97	4144										
CLVS1	157807	hgsc.bcm.edu	37	chr8	62212613	62212613	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acgtacagatgatgccttcaTcctgagatttctccgagcca	8	12	2	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:62212613T>C	ENST00000519846.1	+	3	699	c.227T>C	c.(226-228)aTc>aCc	p.I76T	CLVS1_ENST00000518592.1_Intron|RP11-787D18.1_ENST00000518064.1_RNA|RP11-787D18.1_ENST00000521801.1_RNA|CLVS1_ENST00000325897.4_Missense_Mutation_p.I76T			Q8IUQ0	CLVS1_HUMAN	clavesin 1	76					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						GATGCCTTCATCCTGAGATTT	0.458																																																0			8											113	96	102					8																	62212613		2203	4300	6503	62375167	SO:0001583	missense	0			AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"retinaldehyde binding protein 1-like 1"	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.227T>C	8.37:g.62212613T>C	ENSP00000428402:p.Ile76Thr		62375167	B2R7M5|C8UZT3|Q8NB32	Missense_Mutation	SNP	ENST00000519846.1	37	CCDS6176.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384999	0.82792	.	.	ENSG00000177182	ENST00000522621;ENST00000519846;ENST00000325897	D;D	0.85702	-2.02;-2.02	5.79	5.79	0.91817	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.048550	0.85682	N	0.000000	D	0.89760	0.6808	L	0.48642	1.525	0.80722	D	1	D;D;D	0.71674	0.998;0.971;0.998	D;P;D	0.71184	0.94;0.901;0.972	D	0.90766	0.4668	10	0.87932	D	0	0.203	16.1303	0.81428	0.0:0.0:0.0:1.0	.	76;76;76	E5RK22;Q8IUQ0;Q8IUQ0-2	.;CLVS1_HUMAN;.	T	76	ENSP00000428402:I76T;ENSP00000325506:I76T	ENSP00000325506:I76T	I	+	2	0	CLVS1	62375167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.218000	0.71995	0.533000	0.62120	ATC		0.458	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519		C	62212613	T	C	62212613	3	2	44	1	0	0	0	0	1	0	0	0	3577	1435	50	4	229	4	CLVS1	8	62212613	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	43022150	62212613	84151409	98	4145										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72935336	72935336	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgctgtttttccaggagaaaAgtaagatccttcagcctaaa	8	8	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:72935336A>G	ENST00000262209.4	-	27	3372	c.3165T>C	c.(3163-3165)acT>acC	p.T1055T	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	1055					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CCAGGAGAAAAGTAAGATCCT	0.373																																																0			8											88	79	82					8																	72935336		2203	4300	6503	73097890	SO:0001819	synonymous_variant	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.3165T>C	8.37:g.72935336A>G			73097890	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																				0.373	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		G	72935336	A	G	72935336	2	3	44	1	0	0	0	0	0	0	0	1	16617	59	3	4		4	TRPA1	8	72935336	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	10722723	72935336	73428686	99	4146										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13192158	13192158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ttagctcaatatcacataagTccaggctatccaattctgat	5	10	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:13192158T>C	ENST00000319217.7	-	15	2187	c.1940A>G	c.(1939-1941)gAc>gGc	p.D647G	MPDZ_ENST00000546205.1_Missense_Mutation_p.D647G|MPDZ_ENST00000536827.1_Missense_Mutation_p.D647G|MPDZ_ENST00000541718.1_Missense_Mutation_p.D647G|MPDZ_ENST00000381022.2_Missense_Mutation_p.D647G|MPDZ_ENST00000447879.1_Missense_Mutation_p.D647G|MPDZ_ENST00000381015.4_Missense_Mutation_p.D647G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	647					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		ATCACATAAGTCCAGGCTATC	0.388																																																0			9											120	113	116					9																	13192158		1919	4132	6051	13182158	SO:0001583	missense	84708			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1940A>G	9.37:g.13192158T>C	ENSP00000320006:p.Asp647Gly		13182158	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.00|14.00	2.406213|2.406213	0.42715|0.42715	.|.	.|.	ENSG00000107186|ENSG00000107186	ENST00000399902|ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000546205	.|T;T;T;T;T;T;T	.|0.10960	.|2.87;2.82;2.82;2.82;2.86;2.87;2.87	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.139921	.|0.32416	.|N	.|0.006125	.|T	.|0.06005	.|0.0156	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.34615	.|0.179;0.459;0.459	.|B;B;B	.|0.33960	.|0.084;0.115;0.173	.|T	.|0.47959	.|-0.9076	.|10	.|0.18276	.|T	.|0.48	.|.	8.0925|8.0925	0.30809|0.30809	0.0:0.093:0.0:0.907|0.0:0.093:0.0:0.907	.|.	.|647;647;647	.|B7ZMI4;O75970-3;O75970-2	.|.;.;.	.|G	-1|647	.|ENSP00000320006:D647G;ENSP00000439807:D647G;ENSP00000370410:D647G;ENSP00000444151:D647G;ENSP00000415208:D647G;ENSP00000370403:D647G;ENSP00000446358:D647G	.|ENSP00000320006:D647G	.|D	-|-	.|2	.|0	MPDZ|MPDZ	13182158|13182158	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.983000|0.983000	0.72400|0.72400	1.278000|1.278000	0.33179|0.33179	2.199000|2.199000	0.70637|0.70637	0.533000|0.533000	0.62120|0.62120	.|GAC		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13192158	T	C	13192158	3	2	44	1	0	0	0	0	1	0	0	0	9752	1667	58	4	4313	4	MPDZ	9	13192158	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		13192158	128021273	100	4147										
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15422893	15422893	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cgaacatggctgaaggaagcCgaggtggccctacgtgtagc	15	10	0	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:15422893C>T	ENST00000380821.3	+	1	192	c.16C>T	c.(16-18)Cga>Tga	p.R6*		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	6					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		TGAAGGAAGCCGAGGTGGCCC	0.612																																																0			9											27	24	25					9																	15422893		2109	4170	6279	15412893	SO:0001587	stop_gained	6619			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.16C>T	9.37:g.15422893C>T	ENSP00000370200:p.Arg6*		15412893	D3DRI8|Q2VPI6|Q5T285	Nonsense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809522	0.90707	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	.	.	.	4.86	-3.17	0.05202	.	2.010380	0.02238	N	0.065449	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9315	0.4719	0.00533	0.2577:0.2913:0.1262:0.3248	.	.	.	.	X	6	.	ENSP00000370185:R6X	R	+	1	2	SNAPC3	15412893	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.646000	0.05403	-0.536000	0.06298	-0.379000	0.06801	CGA		0.612	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		T	15422893	C	T	15422893	4	4	44	1	0	0	0	0	0	1	0	0	14873	644	23	1	18	1	SNAPC3	9	15422893	Nonsense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	2230735	15422893	125790538	101	4148										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15848930	15848930	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aatcacatgagagcagtagaAaatacgcttcacaaggtact	8	8	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:15848930A>C	ENST00000380701.3	+	23	3781	c.3453A>C	c.(3451-3453)gaA>gaC	p.E1151D	CCDC171_ENST00000297641.3_Missense_Mutation_p.E1151D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1151																	GAGCAGTAGAAAATACGCTTC	0.299																																																0			9											79	87	85					9																	15848930		2201	4294	6495	15838930	SO:0001583	missense	203238			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3453A>C	9.37:g.15848930A>C	ENSP00000370077:p.Glu1151Asp		15838930	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.14|19.14	3.769386|3.769386	0.69992|0.69992	.|.	.|.	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701;ENST00000359391|ENST00000449575;ENST00000432954	T;T|.	0.69561|.	-0.41;-0.41|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.050681|.	0.85682|.	D|.	0.000000|.	T|T	0.55097|0.55097	0.1899|0.1899	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;P;D|.	0.55385|.	0.971;0.952;0.971|.	P;P;P|.	0.50934|.	0.654;0.452;0.654|.	T|T	0.51834|0.51834	-0.8655|-0.8655	10|5	0.62326|.	D|.	0.03|.	-18.9668|-18.9668	14.6699|14.6699	0.68937|0.68937	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1159;418;1151|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	D|T	1151;418;1151;5|391;205	ENSP00000297641:E1151D;ENSP00000370077:E1151D|.	ENSP00000297641:E1151D|.	E|K	+|+	3|2	2|0	C9orf93|C9orf93	15838930|15838930	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.628000|0.628000	0.37860|0.37860	2.614000|2.614000	0.46359|0.46359	2.274000|2.274000	0.75844|0.75844	0.477000|0.477000	0.44152|0.44152	GAA|AAA		0.299	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15848930	A	C	15848930	3	2	44	1	0	0	0	0	1	0	0	0	2512	11	1	4	3539	4	C9orf93	9	15848930	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	426037	15848930	125364501	102	4149										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21974593	21974593	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tttttccggagaatcgaagcGctacctgattccaattcccc	7	13	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:21974593G>A	ENST00000304494.5	-	1	421				CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000579122.1_Intron|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000498124.1_Intron|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000446177.1_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000579755.1_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A						cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(10)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GAATCGAAGCGCTACCTGATT	0.607		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1327	Whole gene deletion(1316)|Unknown(10)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(277)|skin(167)|central_nervous_system(162)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|oesophagus(48)|upper_aerodigestive_tract(47)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											162	186	178					9																	21974593		2203	4300	6503	21964593	SO:0001627	intron_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.150+83C>T	9.37:g.21974593G>A			21964593	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Silent	SNP	ENST00000304494.5	37	CCDS6510.1																																																																																				0.607	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		A	21974593	G	A	21974593	1	1	44	0	1	0	0	0	0	0	0	0	3167	1078	38	1		1	CDKN2A	9	21974593	Intron	SNP	G	TCGA-AG-3885-01A-01W-0899-10	6125663	21974593	119238838	103	4150										
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99064377	99064377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gatgaagaactgttccaggaCgtcccccatggctgcactca	10	13	1	2	rs377018679		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:99064377C>T	ENST00000375263.3	-	1	57	c.10G>A	c.(10-12)Gtc>Atc	p.V4I	HSD17B3_ENST00000375262.2_Missense_Mutation_p.V4I	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	4					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				TGTTCCAGGACGTCCCCCATG	0.567																																																0			9						C	ILE/VAL	0,4406		0,0,2203	85	74	78		10	-2.2	0	9		78	3,8597	3.0+/-9.4	0,3,4297	no	missense	HSD17B3	NM_000197.1	29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	4/311	99064377	3,13003	2203	4300	6503	98104198	SO:0001583	missense	3293				CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.10G>A	9.37:g.99064377C>T	ENSP00000364412:p.Val4Ile		98104198	Q5U0Q6	Missense_Mutation	SNP	ENST00000375263.3	37	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	C	2.860	-0.236340	0.05944	0.0	3.49E-4	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.84800	-1.9;-1.9	4.55	-2.25	0.06888	.	0.928961	0.09089	N	0.850088	T	0.61726	0.2370	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.52193	-0.8608	10	0.05959	T	0.93	-11.1653	1.3859	0.02240	0.2015:0.3857:0.2466:0.1662	.	4;4	Q5U0Q6;P37058	.;DHB3_HUMAN	I	4	ENSP00000364412:V4I;ENSP00000364411:V4I	ENSP00000364411:V4I	V	-	1	0	HSD17B3	98104198	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.660000	0.05317	-0.242000	0.09667	-0.794000	0.03295	GTC		0.567	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		T	99064377	C	T	99064377	3	4	44	1	0	0	0	0	1	0	0	0	7406	536	19	1	966	1	HSD17B3	9	99064377	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	77089784	99064377	42149054	104	4151										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767414	105767414	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agcaaaaaaggtaaaaaggaTgcagagaagggcaaagactc	12	5	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:105767414T>C	ENST00000374798.3	+	5	571	c.501T>C	c.(499-501)gaT>gaC	p.D167D	CYLC2_ENST00000487798.1_Silent_p.D167D	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	167	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				gtaaaaaggatgcagagaagg	0.333																																																0			9											71	68	69					9																	105767414		2203	4300	6503	104807235	SO:0001819	synonymous_variant	1539			Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.501T>C	9.37:g.105767414T>C			104807235	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	37	CCDS35085.1																																																																																				0.333	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		C	105767414	T	C	105767414	2	2	44	1	0	0	0	0	0	0	0	1	4148	1461	51	4		4	CYLC2	9	105767414	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	6703037	105767414	35446017	105	4152										
SURF6	6838	hgsc.bcm.edu	37	chr9	136199466	136199466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccaccacctcctgggcctccGtggcctcctcagccttcctg	8	21	1	0	rs886089	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:136199466G>A	ENST00000372022.4	-	4	789	c.524C>T	c.(523-525)aCg>aTg	p.T175M	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	175			T -> M (in dbSNP:rs886089).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		CTGGGCCTCCGTGGCCTCCTC	0.657													G|||	1407	0.28095	0.0386	0.3501	5008	,	,		15252	0.2986		0.3569	False		,,,				2504	0.4632															0			9						G	MET/THR	372,4034	184.0+/-211.4	20,332,1851	88	92	90		524	-8.3	0	9	dbSNP_86	90	3017,5583	460.5+/-365.2	543,1931,1826	yes	missense	SURF6	NM_006753.4	81	563,2263,3677	AA,AG,GG		35.0814,8.443,26.0572	possibly-damaging	175/362	136199466	3389,9617	2203	4300	6503	135189287	SO:0001583	missense	6838			AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"surfeit locus protein 6"	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.524C>T	9.37:g.136199466G>A	ENSP00000361092:p.Thr175Met		135189287	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	584	0.2673992673992674	31	0.06300813008130081	122	0.3370165745856354	154	0.2692307692307692	277	0.3654353562005277	G	8.549	0.875047	0.17395	0.08443	0.350814	ENSG00000148296	ENST00000372022	T	0.14516	2.5	4.14	-8.28	0.01013	.	1.762280	0.02976	N	0.145022	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.31191	0.125	T	0.25847	-1.0120	9	0.48119	T	0.1	.	1.6707	0.02811	0.2994:0.1487:0.0953:0.4565	rs886089;rs886089	175	O75683	SURF6_HUMAN	M	175	ENSP00000361092:T175M	ENSP00000361092:T175M	T	-	2	0	SURF6	135189287	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.892000	0.01610	-3.813000	0.00104	-1.250000	0.01514	ACG		0.657	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753		A	136199466	G	A	136199466	3	1	44	1	0	0	0	0	1	0	0	0	15445	1145	40	1	569	1	SURF6	9	136199466	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	30432052	136199466	5013965	106	4153										
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20568635	20568635	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtgttttctgtttcagagaCgcccaagcagatggcctgcg	12	10	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:20568635C>T	ENST00000377252.4	+	14	2318	c.1477C>T	c.(1477-1479)Cgc>Tgc	p.R493C	PLXDC2_ENST00000377242.3_Missense_Mutation_p.R444C|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	493					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R493C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						GTTTCAGAGACGCCCAAGCAG	0.393																																																1	Substitution - Missense(1)	stomach(1)	10											78	77	77					10																	20568635		2203	4300	6503	20608641	SO:0001583	missense	84898			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.1477C>T	10.37:g.20568635C>T	ENSP00000366460:p.Arg493Cys		20608641	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460213	0.84317	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	T;T	0.56103	0.48;0.74	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.75496	0.3857	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.76836	-0.2812	10	0.87932	D	0	.	20.2406	0.98372	0.0:1.0:0.0:0.0	.	444;493	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	C	493;444;356;479	ENSP00000366460:R493C;ENSP00000366450:R444C	ENSP00000366446:R356C	R	+	1	0	PLXDC2	20608641	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.133000	0.77259	2.857000	0.98124	0.650000	0.86243	CGC		0.393	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20568635	C	T	20568635	3	4	44	1	0	0	0	0	1	0	0	0	12149	536	19	1	1531	1	PLXDC2	10	20568635	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10		20568635	114966112	107	4154										
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24909794	24909794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atttccagacttaagtaaaaTtccagaaggttccagtgatc	7	8	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:24909794T>C	ENST00000396432.2	-	9	1516	c.1030A>G	c.(1030-1032)Att>Gtt	p.I344V	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.I131V	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	343					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TTAAGTAAAATTCCAGAAGGT	0.423																																																0			10											101	102	101					10																	24909794		2203	4300	6503	24949800	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.1030A>G	10.37:g.24909794T>C	ENSP00000379709:p.Ile344Val		24949800	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	3.444	-0.113424	0.06881	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.42131	2.94;3.02;0.98;0.99	5.6	0.35	0.16037	.	0.974264	0.08495	N	0.937347	T	0.22859	0.0552	N	0.17674	0.51	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.28004	-1.0057	10	0.12103	T	0.63	.	5.4131	0.16358	0.1193:0.2689:0.0:0.6118	.	334;343	F8W9U9;Q5T5U3	.;RHG21_HUMAN	V	344;333;131;334;344;179	ENSP00000379709:I344V;ENSP00000365604:I131V;ENSP00000365592:I334V;ENSP00000405018:I344V	ENSP00000365604:I131V	I	-	1	0	ARHGAP21	24949800	0.537000	0.26386	0.024000	0.17045	0.973000	0.67179	0.876000	0.28092	0.106000	0.17784	0.528000	0.53228	ATT		0.423	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24909794	T	C	24909794	3	2	44	1	0	0	0	0	1	0	0	0	871	1493	52	4	4918	4	ARHGAP21	10	24909794	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	4341159	24909794	110624953	108	4155										
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	61004855	61004855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tatgcagccatctgtcaaggAtaacagtggtagccatggct	11	9	2	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:61004855A>G	ENST00000373880.4	+	5	899	c.635A>G	c.(634-636)gAt>gGt	p.D212G	PHYHIPL_ENST00000373878.3_Missense_Mutation_p.D186G	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	212						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						TCTGTCAAGGATAACAGTGGT	0.428																																																0			10											70	64	66					10																	61004855		2203	4300	6503	60674861	SO:0001583	missense	84457			AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"Fibronectin type III domain containing"	29378	protein-coding gene	gene with protein product			"phytanoyl-CoA hydroxylase interacting protein-like"			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.635A>G	10.37:g.61004855A>G	ENSP00000362987:p.Asp212Gly		60674861	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Missense_Mutation	SNP	ENST00000373880.4	37	CCDS7254.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.690835	0.68271	.	.	ENSG00000165443	ENST00000373880;ENST00000373878	T;T	0.42131	1.38;0.98	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.69196	0.3084	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.74850	-0.3524	10	0.87932	D	0	-15.652	16.1968	0.82036	1.0:0.0:0.0:0.0	.	186;212	Q96FC7-2;Q96FC7	.;PHIPL_HUMAN	G	212;186	ENSP00000362987:D212G;ENSP00000362985:D186G	ENSP00000362985:D186G	D	+	2	0	PHYHIPL	60674861	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.225000	0.72522	0.533000	0.62120	GAT		0.428	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		G	61004855	A	G	61004855	3	3	44	1	0	0	0	0	1	0	0	0	11898	333	12	4	685	4	PHYHIPL	10	61004855	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	36095061	61004855	74529892	109	4156										
PTEN	5728	hgsc.bcm.edu	37	chr10	89685281	89685281	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgttttaaggtttttggattCaaagcataaaaaccattaca	6	5	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:89685281C>T	ENST00000371953.3	+	3	1533	c.176C>T	c.(175-177)tCa>tTa	p.S59L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	59	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.S59*(4)|p.Y27fs*1(2)|p.R55fs*2(1)|p.S59L(1)|p.V54fs*29(1)|p.R55_L70>S(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTTTTGGATTCAAAGCATAAA	0.254		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	59	Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(6)|Substitution - Nonsense(4)|Complex - deletion inframe(1)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|lung(7)|skin(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|urinary_tract(2)|breast(2)|soft_tissue(1)	10	GRCh37	CM043772	PTEN	M							31	33	33					10																	89685281		2182	4276	6458	89675261	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.176C>T	10.37:g.89685281C>T	ENSP00000361021:p.Ser59Leu		89675261	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.515368	0.64634	.	.	ENSG00000171862	ENST00000371953	D	0.98419	-4.92	5.46	5.46	0.80206	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	L	0.50993	1.605	0.80722	D	1	B	0.22346	0.068	B	0.24006	0.05	D	0.94948	0.8097	9	.	.	.	-6.4254	19.2989	0.94134	0.0:1.0:0.0:0.0	.	59	P60484	PTEN_HUMAN	L	59	ENSP00000361021:S59L	.	S	+	2	0	PTEN	89675261	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.244000	0.78228	2.563000	0.86464	0.655000	0.94253	TCA		0.254	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89685281	C	T	89685281	3	4	44	1	0	0	0	0	1	0	0	0	12772	838	29	3	186	3	PTEN	10	89685281	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	28680426	89685281	45849466	110	4157										
CH25H	9023	hgsc.bcm.edu	37	chr10	90966639	90966639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aggtgccacacgaagaactcCatgtcgaagagtagcaggca	12	10	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:90966639C>T	ENST00000371852.2	-	1	432	c.411G>A	c.(409-411)atG>atA	p.M137I		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	137					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		CGAAGAACTCCATGTCGAAGA	0.632																																																0			10											75	73	74					10																	90966639		2203	4300	6503	90956619	SO:0001583	missense	9023			AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"Fatty acid hydroxylase domain containing"	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.411G>A	10.37:g.90966639C>T	ENSP00000360918:p.Met137Ile		90956619	B2RBY3	Missense_Mutation	SNP	ENST00000371852.2	37	CCDS7400.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.249706	0.22880	.	.	ENSG00000138135	ENST00000371852	D	0.83163	-1.69	5.3	0.197	0.15164	Fatty acid hydroxylase (1);	0.810877	0.11339	N	0.574289	T	0.54143	0.1840	N	0.01576	-0.805	0.22017	N	0.99941	B	0.06786	0.001	B	0.08055	0.003	T	0.43940	-0.9360	10	0.13470	T	0.59	-7.1466	6.2913	0.21061	0.2708:0.2328:0.4964:0.0	.	137	O95992	CH25H_HUMAN	I	137	ENSP00000360918:M137I	ENSP00000360918:M137I	M	-	3	0	CH25H	90956619	0.994000	0.37717	0.143000	0.22291	0.960000	0.62799	0.317000	0.19487	-0.143000	0.11334	-0.171000	0.13296	ATG		0.632	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956		T	90966639	C	T	90966639	3	4	44	1	0	0	0	0	1	0	0	0	3313	594	21	3	411	3	CH25H	10	90966639	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1281358	90966639	44568108	111	4158										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411935	6411935	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	actcctttggatgggcctggTgctggcgctggcgctggcgc	17	12	0	0	rs550365194|rs550067660|rs1050228|rs71056748|rs558809956|rs3838786	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:6411935T>C	ENST00000342245.4	+	1	275	c.107T>C	c.(106-108)gTg>gCg	p.V36A	SMPD1_ENST00000527275.1_Missense_Mutation_p.V36A|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000299397.3_Missense_Mutation_p.V36A|SMPD1_ENST00000356761.2_Missense_Mutation_p.V36A	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	36			V -> A (in dbSNP:rs1050228). {ECO:0000269|PubMed:1740330}.	Missing (in Ref. 4; CAA42584). {ECO:0000305}.	cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ATGGGCctggtgctggcgctg	0.706													T|||	2811	0.561302	0.202	0.6729	5008	,	,		11441	0.8075		0.5905	False		,,,				2504	0.684															0			11						T	ALA/VAL,ALA/VAL	1052,3322		158,736,1293	14	16	15		107,107	0.7	0	11	dbSNP_86	15	4795,3693		1471,1853,920	no	missense,missense	SMPD1	NM_000543.4,NM_001007593.2	64,64	1629,2589,2213	CC,CT,TT		43.5085,24.0512,45.4595	benign,benign	36/632,36/631	6411935	5847,7015	2187	4244	6431	6368511	SO:0001583	missense	6609			AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.107T>C	11.37:g.6411935T>C	ENSP00000340409:p.Val36Ala		6368511	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	37	CCDS44531.1	1284	0.5879120879120879	106	0.21544715447154472	226	0.6243093922651933	466	0.8146853146853147	486	0.6411609498680739	T	9.778	1.174552	0.21704	0.240512	0.564915	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09350	2.99;2.99;3.0;3.0	4.16	0.672	0.17935	.	0.945921	0.08638	N	0.915970	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12243	-1.0555	9	0.19590	T	0.45	.	7.0836	0.25245	0.0:0.3281:0.4874:0.1844	rs1050228;rs2450945;rs3190530;rs11544729;rs12417689;rs16912853	36;36	E9PKS3;G3XAB5	.;.	A	36	ENSP00000299397:V36A;ENSP00000349203:V36A;ENSP00000340409:V36A;ENSP00000435350:V36A	ENSP00000299397:V36A	V	+	2	0	SMPD1	6368511	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	0.500000	0.22562	0.243000	0.21327	-0.445000	0.05633	GTG		0.706	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		C	6411935	T	C	6411935	3	2	44	1	0	0	0	0	1	0	0	0	14841	1696	59	4	109	4	SMPD1	11	6411935	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		6411935	128594581	112	4159										
LMO2	4005	hgsc.bcm.edu	37	chr11	33881081	33881081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	catctcataggcacgaatccGcttgtcacaggatgcgcaga	10	12	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:33881081G>A	ENST00000395833.3	-	3	727	c.298C>T	c.(298-300)Cgg>Tgg	p.R100W	LMO2_ENST00000257818.2_Missense_Mutation_p.R169W	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	100	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						GCACGAATCCGCTTGTCACAG	0.488			T	TRD@	T-ALL																																		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	0			11											98	89	92					11																	33881081		2202	4298	6500	33837657	SO:0001583	missense	4005			X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"T-cell translocation gene 2", "rhombotin-like 1"	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.298C>T	11.37:g.33881081G>A	ENSP00000379175:p.Arg100Trp		33837657	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	37	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479767	0.44044	.	.	ENSG00000135363	ENST00000395833;ENST00000257818	D;D	0.87103	-2.21;-2.21	5.29	4.38	0.52667	Zinc finger, LIM-type (5);	0.052193	0.85682	N	0.000000	D	0.91290	0.7254	L	0.54323	1.7	0.58432	D	0.999999	D;D	0.89917	0.997;1.0	D;D	0.68353	0.957;0.957	D	0.92114	0.5698	10	0.66056	D	0.02	.	15.813	0.78578	0.0:0.0:0.8628:0.1372	.	169;100	P25791-3;P25791	.;RBTN2_HUMAN	W	100;169	ENSP00000379175:R100W;ENSP00000257818:R169W	ENSP00000257818:R169W	R	-	1	2	LMO2	33837657	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.023000	0.57211	1.391000	0.46566	-0.196000	0.12772	CGG		0.488	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574		A	33881081	G	A	33881081	3	1	44	1	0	0	0	0	1	0	0	0	8876	1086	38	1	182	1	LMO2	11	33881081	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	27469146	33881081	101125435	113	4160										
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606641	55606641	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctgctctacacagttgccatCtcccagaaactctgtgccat	6	15	3	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:55606641C>A	ENST00000378396.1	+	1	414	c.414C>A	c.(412-414)atC>atA	p.I138I		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CAGTTGCCATCTCCCAGAAAC	0.458																																																0			11											121	110	113					11																	55606641		2201	4296	6497	55363217	SO:0001819	synonymous_variant	390144			AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"GPCR / Class A : Olfactory receptors"	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.414C>A	11.37:g.55606641C>A			55363217	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																				0.458	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		A	55606641	C	A	55606641	2	1	44	1	0	0	0	0	0	0	0	1	11187	903	32	2		2	OR5D16	11	55606641	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	21725560	55606641	79399875	114	4161										
SLC25A45	283130	hgsc.bcm.edu	37	chr11	65147382	65147382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	catgcaatcaacgatgccccGgtaggtggtctgggtctgca	13	11	3	0	rs377005228		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:65147382G>A	ENST00000527174.1	-	3	164	c.109C>T	c.(109-111)Cgg>Tgg	p.R37W	SLC25A45_ENST00000360662.3_Intron|SLC25A45_ENST00000534028.1_Intron|SLC25A45_ENST00000398802.1_Missense_Mutation_p.R37W|SLC25A45_ENST00000294187.6_5'UTR|SLC25A45_ENST00000526432.1_Missense_Mutation_p.R37W|SLC25A45_ENST00000377152.2_5'UTR|SLC25A45_ENST00000417511.2_5'UTR			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	37					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						ACGATGCCCCGGTAGGTGGTC	0.627																																																0			11						G	,TRP/ARG	0,4102		0,0,2051	61	68	66		,109	4.4	1	11		66	3,8393		0,3,4195	no	utr-5,missense	SLC25A45	NM_001077241.1,NM_182556.2	,101	0,3,6246	AA,AG,GG		0.0357,0.0,0.024	,probably-damaging	,37/289	65147382	3,12495	2051	4198	6249	64903958	SO:0001583	missense	283130			BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"Solute carriers"	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.109C>T	11.37:g.65147382G>A	ENSP00000435489:p.Arg37Trp		64903958	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896045	0.72639	0.0	3.57E-4	ENSG00000162241	ENST00000527174;ENST00000398802;ENST00000526432;ENST00000530936	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	4.38	4.38	0.52667	Mitochondrial carrier domain (2);	.	.	.	.	D	0.88687	0.6504	M	0.89904	3.07	0.80722	D	1	D;D	0.67145	0.996;0.995	P;P	0.55303	0.761;0.773	D	0.91161	0.4961	9	0.66056	D	0.02	.	14.4776	0.67557	0.0:0.0:1.0:0.0	.	37;37	E9PJQ3;Q8N413	.;S2545_HUMAN	W	37	ENSP00000435489:R37W;ENSP00000381782:R37W;ENSP00000435547:R37W;ENSP00000431642:R37W	ENSP00000381782:R37W	R	-	1	2	SLC25A45	64903958	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	5.116000	0.64661	2.251000	0.74343	0.561000	0.74099	CGG		0.627	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		A	65147382	G	A	65147382	3	1	44	1	0	0	0	0	1	0	0	0	14547	1115	39	1	773	1	SLC25A45	11	65147382	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	9540741	65147382	69859134	115	4162										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68566756	68566756	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtccaagaccgacagcaaaaTcttgagcaagtgctgtcatc	9	11	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:68566756T>G	ENST00000265641.5	-	6	777	c.623A>C	c.(622-624)gAt>gCt	p.D208A	CPT1A_ENST00000538994.1_5'Flank|CPT1A_ENST00000539743.1_Missense_Mutation_p.D208A|CPT1A_ENST00000376618.2_Missense_Mutation_p.D208A|CPT1A_ENST00000540367.1_Missense_Mutation_p.D208A	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	208					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GACAGCAAAATCTTGAGCAAG	0.408																																																0			11											100	98	99					11																	68566756		2200	4294	6494	68323332	SO:0001583	missense	1374			L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.623A>C	11.37:g.68566756T>G	ENSP00000265641:p.Asp208Ala		68323332	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	37	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	t	16.42	3.118742	0.56505	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.90937	0.7151	M	0.66378	2.025	0.80722	D	1	B;P;P	0.48911	0.363;0.88;0.917	B;P;P	0.51945	0.196;0.685;0.557	D	0.91130	0.4937	10	0.49607	T	0.09	.	14.1003	0.65051	0.0:0.0:0.0:1.0	.	208;208;208	B2RAQ8;P50416;P50416-2	.;CPT1A_HUMAN;.	A	208	ENSP00000439084:D208A;ENSP00000365803:D208A;ENSP00000265641:D208A;ENSP00000446108:D208A	ENSP00000265641:D208A	D	-	2	0	CPT1A	68323332	1.000000	0.71417	0.364000	0.25888	0.075000	0.17131	7.636000	0.83301	1.742000	0.51746	0.379000	0.24179	GAT		0.408	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		G	68566756	T	G	68566756	3	3	44	1	0	0	0	0	1	0	0	0	3837	1435	50	4	1794	4	CPT1A	11	68566756	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	3419374	68566756	66439760	116	4163										
SLC36A4	120103	hgsc.bcm.edu	37	chr11	92895991	92895991	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atccccatgccaatattcaaCgcttgagggaaacgctttga	8	11	1	2	rs34525400	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:92895991C>T	ENST00000326402.4	-	9	1048	c.918G>A	c.(916-918)gcG>gcA	p.A306A	SLC36A4_ENST00000529184.1_Silent_p.A171A	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	306					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAATATTCAACGCTTGAGGGA	0.323													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		15291	0		0	False		,,,				2504	0															0			11						C		99,4303	78.3+/-116.7	1,97,2103	92	90	91		918	-2.9	0.2	11	dbSNP_126	91	0,8596		0,0,4298	no	coding-synonymous	SLC36A4	NM_152313.2		1,97,6401	TT,TC,CC		0.0,2.249,0.7617		306/505	92895991	99,12899	2201	4298	6499	92535639	SO:0001819	synonymous_variant	120103			AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.918G>A	11.37:g.92895991C>T			92535639	Q86X30|Q8IVM5|Q8N8S6	Silent	SNP	ENST00000326402.4	37	CCDS8291.1																																																																																				0.323	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2			T	92895991	C	T	92895991	2	4	44	1	0	0	0	0	0	0	0	1	14633	523	19	1		1	SLC36A4	11	92895991	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	24329235	92895991	42110525	117	4164										
CASP5	838	hgsc.bcm.edu	37	chr11	104869632	104869632	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtggtgttgaagaacagaaaGcaatgaagtccttctcctcg	11	8	1	4	rs531060230		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:104869632G>T	ENST00000260315.3	-	7	1075	c.1076C>A	c.(1075-1077)gCt>gAt	p.A359D	CASP5_ENST00000393141.2_Missense_Mutation_p.A372D|CASP5_ENST00000526056.1_Missense_Mutation_p.A372D|CASP5_ENST00000531367.1_Missense_Mutation_p.A217D|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Missense_Mutation_p.A217D|CASP5_ENST00000444749.2_Missense_Mutation_p.A301D			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	359					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		AGAACAGAAAGCAATGAAGTC	0.448																																																0			11											143	133	136					11																	104869632		2202	4299	6501	104374842	SO:0001583	missense	838				CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"Caspases"	1506	protein-coding gene	gene with protein product		602665	"caspase 5, apoptosis-related cysteine protease"			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.1076C>A	11.37:g.104869632G>T	ENSP00000260315:p.Ala359Asp		104374842	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	G	10.31	1.315384	0.23908	.	.	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	3.66	1.73	0.24493	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.288882	0.33110	N	0.005266	T	0.46229	0.1382	M	0.92555	3.32	0.58432	D	0.999999	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	D;D;D;D	0.79108	0.967;0.976;0.992;0.981	T	0.36187	-0.9758	10	0.87932	D	0	.	2.3071	0.04177	0.1113:0.1936:0.4962:0.1989	.	217;301;359;372	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	D	372;217;359;301;372;217	ENSP00000376849:A372D;ENSP00000398130:A217D;ENSP00000260315:A359D;ENSP00000388365:A301D;ENSP00000436877:A372D;ENSP00000434471:A217D	ENSP00000260315:A359D	A	-	2	0	CASP5	104374842	0.131000	0.22433	0.895000	0.35142	0.022000	0.10575	1.481000	0.35476	0.330000	0.23485	-0.311000	0.09066	GCT		0.448	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347		T	104869632	G	T	104869632	3	4	44	1	0	0	0	0	1	0	0	0	2680	971	34	2	240	2	CASP5	11	104869632	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	11973641	104869632	30136884	118	4165										
ATM	472	hgsc.bcm.edu	37	chr11	108170479	108170479	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgggagaagtgggtcctataGatttctctaccatagctata	10	7	1	2	rs121434217		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:108170479G>T	ENST00000452508.2	+	35	5233	c.5044G>T	c.(5044-5046)Gat>Tat	p.D1682Y	ATM_ENST00000278616.4_Missense_Mutation_p.D1682Y			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1682			D -> H (in T-prolymphocytic leukemia). {ECO:0000269|PubMed:9288106}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1682Y(2)|p.D1682H(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GGGTCCTATAGATTTCTCTAC	0.358			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	11											132	139	136					11																	108170479		2201	4298	6499	107675689	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5044G>T	11.37:g.108170479G>T	ENSP00000388058:p.Asp1682Tyr		107675689	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805415	0.70682	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73047	-0.71;-0.71	5.2	4.28	0.50868	Armadillo-type fold (1);	0.044055	0.85682	D	0.000000	T	0.82029	0.4948	M	0.74258	2.255	0.46564	D	0.999107	D	0.89917	1.0	D	0.87578	0.998	T	0.83316	-0.0020	10	0.87932	D	0	.	10.8473	0.46751	0.1519:0.0:0.8481:0.0	.	1682	Q13315	ATM_HUMAN	Y	1682	ENSP00000278616:D1682Y;ENSP00000388058:D1682Y	ENSP00000278616:D1682Y	D	+	1	0	ATM	107675689	1.000000	0.71417	0.993000	0.49108	0.952000	0.60782	2.926000	0.48892	1.180000	0.42898	0.650000	0.86243	GAT		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108170479	G	T	108170479	3	4	44	1	0	0	0	0	1	0	0	0	1110	942	33	2	5174	2	ATM	11	108170479	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	3300847	108170479	26836037	119	4166										
ATM	472	hgsc.bcm.edu	37	chr11	108186757	108186757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gactacgaacatatgaacacGaagcaatgtggggcaaagcc	11	9	0	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:108186757G>A	ENST00000452508.2	+	43	6304	c.6115G>A	c.(6115-6117)Gaa>Aaa	p.E2039K	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.E2039K			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2039	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.E2039K(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATATGAACACGAAGCAATGTG	0.398			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											103	93	96					11																	108186757		2201	4298	6499	107691967	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.6115G>A	11.37:g.108186757G>A	ENSP00000388058:p.Glu2039Lys		107691967	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819217	0.71028	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02015	4.5;4.5	5.24	5.24	0.73138	PIK-related kinase (1);Armadillo-type fold (1);	0.213177	0.48767	D	0.000164	T	0.12987	0.0315	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	T	0.00376	-1.1779	10	0.49607	T	0.09	.	17.0101	0.86404	0.0:0.0:1.0:0.0	.	2039	Q13315	ATM_HUMAN	K	2039	ENSP00000278616:E2039K;ENSP00000388058:E2039K	ENSP00000278616:E2039K	E	+	1	0	ATM	107691967	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	9.101000	0.94219	2.447000	0.82792	0.305000	0.20034	GAA		0.398	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108186757	G	A	108186757	3	1	44	1	0	0	0	0	1	0	0	0	1110	1059	37	1	6277	1	ATM	11	108186757	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	16278	108186757	26819759	120	4167										
UPK2	7379	hgsc.bcm.edu	37	chr11	118827131	118827131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggctctgctgtccccaggggCtgcaggtctcttccatctct	11	15	3	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:118827131C>A	ENST00000264031.2	+	1	106	c.71C>A	c.(70-72)gCt>gAt	p.A24D	UPK2_ENST00000534788.1_Intron|RP11-158I9.7_ENST00000584831.1_RNA	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2	24					epithelial cell differentiation (GO:0030855)|membrane organization (GO:0061024)|multicellular organismal development (GO:0007275)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		TCCCCAGGGGCTGCAGGTCTC	0.637																																																0			11											59	51	54					11																	118827131		2200	4295	6495	118332341	SO:0001583	missense	7379			Y13645	CCDS8404.1	11q23	2008-07-21				ENSG00000110375			12579	protein-coding gene	gene with protein product	"uroplakin II", "uroplakin-2"	611558				9515818, 9846985	Standard	NM_006760		Approved	UP2, UPII, MGC138598	uc001puh.3	O00526		ENST00000264031.2:c.71C>A	11.37:g.118827131C>A	ENSP00000264031:p.Ala24Asp		118332341	B0YJ92|O00457|Q53YV0	Missense_Mutation	SNP	ENST00000264031.2	37	CCDS8404.1	.	.	.	.	.	.	.	.	.	.	C	8.795	0.931585	0.18131	.	.	ENSG00000110375	ENST00000264031	T	0.36878	1.23	5.22	3.38	0.38709	.	0.644480	0.14496	N	0.316013	T	0.37183	0.0994	L	0.54323	1.7	0.19775	N	0.999959	P	0.42456	0.78	B	0.43123	0.409	T	0.17899	-1.0354	10	0.66056	D	0.02	-0.8848	9.8206	0.40880	0.0:0.8851:0.0:0.1149	.	24	O00526	UPK2_HUMAN	D	24	ENSP00000264031:A24D	ENSP00000264031:A24D	A	+	2	0	UPK2	118332341	0.799000	0.28903	0.688000	0.30117	0.097000	0.18754	0.884000	0.28214	0.795000	0.33922	-1.073000	0.02249	GCT		0.637	UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389311.1	NM_006760		A	118827131	C	A	118827131	3	1	44	1	0	0	0	0	1	0	0	0	17049	797	28	2	73	2	UPK2	11	118827131	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	10640374	118827131	16179385	121	4168										
NTM	50863	hgsc.bcm.edu	37	chr11	132016335	132016335	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cagaacgtggatgtgtatgaCgagggcccttacacctgctc	12	11	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:132016335C>A	ENST00000374786.1	+	2	806	c.327C>A	c.(325-327)gaC>gaA	p.D109E	NTM_ENST00000374791.3_Missense_Mutation_p.D109E|NTM_ENST00000425719.2_Missense_Mutation_p.D109E|NTM_ENST00000427481.2_Missense_Mutation_p.D100E|NTM_ENST00000374784.1_Missense_Mutation_p.D109E|NTM_ENST00000539799.1_Missense_Mutation_p.D109E	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	109	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ATGTGTATGACGAGGGCCCTT	0.577																																																0			11											172	118	136					11																	132016335		2201	4297	6498	131521545	SO:0001583	missense	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.327C>A	11.37:g.132016335C>A	ENSP00000363918:p.Asp109Glu		131521545	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.139607	0.77775	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.58	-3.24	0.05094	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.045498	0.85682	D	0.000000	T	0.69459	0.3113	M	0.90977	3.165	0.43021	D	0.994577	P;P;D;P;P;D	0.54047	0.933;0.539;0.964;0.539;0.935;0.964	P;P;P;P;P;P	0.61722	0.893;0.893;0.881;0.893;0.766;0.829	T	0.72360	-0.4317	10	0.87932	D	0	-30.9792	10.0169	0.42020	0.102:0.2652:0.0:0.6328	.	109;100;109;109;109;109	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	E	109;109;100;100;109;109;109	ENSP00000363923:D109E;ENSP00000437668:D109E;ENSP00000448104:D100E;ENSP00000416320:D100E;ENSP00000363918:D109E;ENSP00000396722:D109E;ENSP00000363916:D109E	ENSP00000363916:D109E	D	+	3	2	NTM	131521545	0.673000	0.27539	0.906000	0.35671	0.987000	0.75469	-0.050000	0.11904	-0.734000	0.04843	-0.137000	0.14449	GAC		0.577	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		A	132016335	C	A	132016335	3	1	44	1	0	0	0	0	1	0	0	0	10730	535	19	2	419	2	NTM	11	132016335	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	13189204	132016335	2990181	122	4169										
DCP1B	196513	hgsc.bcm.edu	37	chr12	2062353	2062353	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgctgctgctgctgctgctgGtggagagtctgcggaggctc	17	10	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:2062353G>C	ENST00000280665.6	-	7	832	c.753C>G	c.(751-753)caC>caG	p.H251Q	DCP1B_ENST00000540622.1_Missense_Mutation_p.H125Q|DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_Missense_Mutation_p.H149Q	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	251				H -> HQ (in Ref. 1; AAN62764, 2; BAB71118 and 4; AAH15368/AAH43437). {ECO:0000305}.	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			gctgctgctgGTGGAGAGTCT	0.552																																																0			12											36	42	40					12																	2062353		2203	4300	6503	1932614	SO:0001583	missense	196513			AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.753C>G	12.37:g.2062353G>C	ENSP00000280665:p.His251Gln		1932614	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Missense_Mutation	SNP	ENST00000280665.6	37	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.346987	0.01266	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	T;T;T	0.17054	2.32;2.31;2.3	4.5	0.369	0.16151	.	1.548950	0.03620	N	0.236163	T	0.16769	0.0403	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.41822	-0.9487	10	0.12766	T	0.61	0.002	15.1763	0.72913	0.0:0.5449:0.4551:0.0	.	149;251	B4DRD1;Q8IZD4	.;DCP1B_HUMAN	Q	251;149;125	ENSP00000280665:H251Q;ENSP00000380358:H149Q;ENSP00000444374:H125Q	ENSP00000280665:H251Q	H	-	3	2	DCP1B	1932614	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.086000	0.11233	-0.095000	0.12351	-0.835000	0.03068	CAC		0.552	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2062353	G	C	2062353	3	2	44	1	0	0	0	0	1	0	0	0	4305	1252	44	5	1112	5	DCP1B	12	2062353	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10		2062353	131789542	123	4170										
KRAS	3845	hgsc.bcm.edu	37	chr12	25378647	25378647	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gttctagaaggcaaatcacaTttatttcctactaggaccat	6	9	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:25378647T>A	ENST00000256078.4	-	4	414	c.351A>T	c.(349-351)aaA>aaT	p.K117N	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.K117N	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	117			K -> N (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.K117N(9)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCAAATCACATTTATTTCCTA	0.358		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	9	Substitution - Missense(9)	large_intestine(8)|haematopoietic_and_lymphoid_tissue(1)	12											164	149	154					12																	25378647		2202	4299	6501	25269914	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.351A>T	12.37:g.25378647T>A	ENSP00000256078:p.Lys117Asn		25269914	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.959738	0.74016	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.94650	-3.48;-2.31	5.52	0.583	0.17417	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.98448	0.9483	H	0.99940	5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.976;0.998	D	0.96017	0.9006	10	0.72032	D	0.01	.	9.1263	0.36816	0.0:0.4112:0.0:0.5888	.	117;117	P01116-2;P01116	.;RASK_HUMAN	N	117	ENSP00000308495:K117N;ENSP00000256078:K117N	ENSP00000256078:K117N	K	-	3	2	KRAS	25269914	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.664000	0.25068	0.131000	0.18576	0.477000	0.44152	AAA		0.358	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25378647	T	A	25378647	3	1	44	1	0	0	0	0	1	0	0	0	8459	1490	52	5	347	5	KRAS	12	25378647	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	23316294	25378647	108473248	124	4171										
KRT3	3850	hgsc.bcm.edu	37	chr12	53184999	53185000	+	Frame_Shift_Ins	INS	-	-	CGCC													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggaggctcacctgtactcctINScgccctccagcagcttgcgg					rs57872071		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:53184999_53185000insCGCC	ENST00000417996.2	-	7	1599_1600	c.1525_1526insGGCG	c.(1525-1527)gagfs	p.E509fs	KRT3_ENST00000309505.3_Frame_Shift_Ins_p.E509fs	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	509	Coil 2.|Rod.		E -> K (in MECD; dbSNP:rs57872071). {ECO:0000269|PubMed:9171831}.		epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						CCTGTACTCCTCGCCCTCCAGC	0.609																																																0			12	GRCh37	CM970845	KRT3	M	rs57872071																																			51471267	SO:0001589	frameshift_variant	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1522_1525dupGGCG	12.37:g.53185000_53185003dupCGCC	ENSP00000413479:p.Glu509fs		51471266	A6NIS2|Q701L8	Frame_Shift_Ins	INS	ENST00000417996.2	37	CCDS44895.1																																																																																				0.609	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		CGCC	53185000	-	CGCC	53184999	7	5	44	1	0	1	1	0	0	0	0	0	8487	1551	54	0	372	0	KRT3	12	53184999	Frame_Shift_Ins	INS	-	TCGA-AG-3885-01A-01W-0899-10	27806352	53184999	80666896	125	4172										
KRT4	3851	hgsc.bcm.edu	37	chr12	53207603	53207603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccaccaaagccaccagtgccAaagcctccagcacccccaaa	5	20	0	0	rs7135148		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:53207603A>G	ENST00000551956.1	-	1	732	c.240T>C	c.(238-240)ttT>ttC	p.F80F	KRT4_ENST00000293774.4_Silent_p.F154F|KRT4_ENST00000458244.2_Silent_p.F60F			P19013	K2C4_HUMAN	keratin 4	80	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CACCAGTGCCAAAGCCTCCAG	0.602																																					Pancreas(190;284 2995 41444 45903)											0			12											82	99	94					12																	53207603		2119	4253	6372	51493870	SO:0001819	synonymous_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"-", "Intermediate filaments type II, keratins (basic)"	6441	protein-coding gene	gene with protein product	"cytokeratin 4", "keratin, type II cytoskeletal 4"	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240T>C	12.37:g.53207603A>G			51493870	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																				0.602	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272		G	53207603	A	G	53207603	2	3	44	1	0	0	0	0	0	0	0	1	8498	127	5	4		4	KRT4	12	53207603	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	22604	53207603	80644292	126	4173										
C12orf52	84934	hgsc.bcm.edu	37	chr12	113629545	113629545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccctggtgacttccagggctCgctcagttagcatttcagtg	11	12	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:113629545C>T	ENST00000548278.1	+	4	1425	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C	C12orf52_ENST00000549621.1_Missense_Mutation_p.R245C|C12orf52_ENST00000552495.1_Missense_Mutation_p.R269C|RP11-545P7.4_ENST00000552525.1_RNA	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		245	Interaction with tubulin.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)			large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						TTCCAGGGCTCGCTCAGTTAG	0.587																																																0			12											57	56	56					12																	113629545		2203	4300	6503	112113928	SO:0001583	missense	84934																														ENST00000548278.1:c.733C>T	12.37:g.113629545C>T	ENSP00000449841:p.Arg245Cys		112113928	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	37	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	C	3.887	-0.024704	0.07589	.	.	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000266813	T;T;T	0.33654	1.42;1.42;1.4	4.89	-1.67	0.08238	.	0.498586	0.17804	N	0.161448	T	0.17874	0.0429	N	0.19112	0.55	0.09310	N	0.999992	B;B	0.14438	0.01;0.005	B;B	0.06405	0.002;0.002	T	0.10086	-1.0645	10	0.35671	T	0.21	0.4668	5.5682	0.17182	0.0:0.3153:0.4226:0.2621	.	269;245	F8VRG5;Q96K30	.;RITA_HUMAN	C	245;245;269;245;242	ENSP00000448289:R245C;ENSP00000449841:R245C;ENSP00000448680:R269C	ENSP00000266813:R242C	R	+	1	0	C12orf52	112113928	0.089000	0.21612	0.002000	0.10522	0.061000	0.15899	0.392000	0.20801	-0.563000	0.06078	-0.165000	0.13383	CGC		0.587	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1			T	113629545	C	T	113629545	3	4	44	1	0	0	0	0	1	0	0	0	1701	884	31	1	739	1	C12orf52	12	113629545	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	60421942	113629545	20222350	127	4174										
WDR66	144406	hgsc.bcm.edu	37	chr12	122359392	122359392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agaggaaaacgggcgaggagGaaggggaggaggaggggaag	24	2	0	1	rs114531812		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:122359392G>A	ENST00000288912.4	+	2	1035	c.181G>A	c.(181-183)Gaa>Aaa	p.E61K	WDR66_ENST00000397454.2_Missense_Mutation_p.E61K	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	61	Glu-rich.		E -> G (in dbSNP:rs12824001).				calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		gggcgaggaggaaggggagga	0.468																																					Esophageal Squamous(85;849 1794 49757 52143)											0			12											51	54	53					12																	122359392		1941	4124	6065	120843775	SO:0001583	missense	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.181G>A	12.37:g.122359392G>A	ENSP00000288912:p.Glu61Lys		120843775	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839198	0.32513	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.12984	2.69;2.63	2.92	-1.07	0.09968	.	.	.	.	.	T	0.07593	0.0191	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	9	0.42905	T	0.14	.	3.4144	0.07371	0.3738:0.2278:0.3984:0.0	.	61	Q8TBY9	WDR66_HUMAN	K	61	ENSP00000288912:E61K;ENSP00000380595:E61K	ENSP00000288912:E61K	E	+	1	0	WDR66	120843775	0.000000	0.05858	0.000000	0.03702	0.263000	0.26337	-0.063000	0.11655	-0.231000	0.09825	0.313000	0.20887	GAA		0.468	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		A	122359392	G	A	122359392	3	1	44	1	0	0	0	0	1	0	0	0	17357	1175	41	3	183	3	WDR66	12	122359392	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	8729847	122359392	11492503	128	4175										
ELF1	1997	hgsc.bcm.edu	37	chr13	41515327	41515327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctggacttgaagatactctcGaccggctggtttgattccta	10	10	1	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:41515327G>A	ENST00000239882.3	-	8	1300	c.986C>T	c.(985-987)tCg>tTg	p.S329L	ELF1_ENST00000442101.1_Missense_Mutation_p.S305L|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	329					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		AGATACTCTCGACCGGCTGGT	0.428																																																0			13											118	126	123					13																	41515327		2203	4300	6503	40413327	SO:0001583	missense	84337			M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.986C>T	13.37:g.41515327G>A	ENSP00000239882:p.Ser329Leu		40413327	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167161	0.38217	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.54479	0.57;0.57	5.47	5.47	0.80525	.	0.214873	0.41605	D	0.000847	T	0.40067	0.1102	L	0.34521	1.04	0.52099	D	0.999949	P;P	0.43750	0.669;0.816	B;B	0.27380	0.057;0.079	T	0.49551	-0.8928	10	0.62326	D	0.03	.	19.6893	0.95993	0.0:0.0:1.0:0.0	.	305;329	E9PDQ9;P32519	.;ELF1_HUMAN	L	305;71;329	ENSP00000405580:S305L;ENSP00000239882:S329L	ENSP00000239882:S329L	S	-	2	0	ELF1	40413327	1.000000	0.71417	0.726000	0.30738	0.026000	0.11368	6.515000	0.73751	2.729000	0.93468	0.655000	0.94253	TCG		0.428	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		A	41515327	G	A	41515327	3	1	44	1	0	0	0	0	1	0	0	0	5066	1059	37	1	881	1	ELF1	13	41515327	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10		41515327	73654551	129	4176										
ALG11	440138	hgsc.bcm.edu	37	chr13	52586597	52586597	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggtgcctgtgcaagttgttgAggtgagcagccggtcgtgtg	18	7	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:52586597A>G	ENST00000521508.1	+	1	48	c.43A>G	c.(43-45)Agg>Ggg	p.R15G	ATP7B_ENST00000242839.4_5'Flank|ATP7B_ENST00000400366.3_5'Flank|ATP7B_ENST00000448424.2_5'Flank|ATP7B_ENST00000400370.3_5'Flank|ATP7B_ENST00000344297.5_5'Flank|ATP7B_ENST00000418097.2_5'Flank|ALG11_ENST00000523764.1_Splice_Site_p.R15G	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	15					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		CAAGTTGTTGAGGTGAGCAGC	0.562																																																0			13											95	87	89					13																	52586597		2203	4300	6503	51484598	SO:0001630	splice_region_variant	440138			AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"Glycosyltransferase group 1 domain containing"	32456	protein-coding gene	gene with protein product	"GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"	613666	"asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)", "asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.44+1A>G	13.37:g.52586597A>G			51484598	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	37	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.313977	0.23908	.	.	ENSG00000253710	ENST00000523764;ENST00000521508	T;T	0.78126	0.77;-1.15	5.1	3.89	0.44902	.	0.000000	0.85682	U	0.000000	T	0.77061	0.4075	M	0.79123	2.44	0.53005	D	0.999964	P	0.46706	0.883	B	0.42827	0.399	T	0.78013	-0.2370	10	0.72032	D	0.01	.	8.8967	0.35470	0.7294:0.2706:0.0:0.0	.	15	Q2TAA5	ALG11_HUMAN	G	15	ENSP00000429497:R15G;ENSP00000430236:R15G	ENSP00000430236:R15G	R	+	1	2	ALG11	51484598	1.000000	0.71417	0.994000	0.49952	0.245000	0.25701	2.461000	0.45040	0.984000	0.38629	0.482000	0.46254	AGG		0.562	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	Missense_Mutation	G	52586597	A	G	52586597	5	3	44	1	0	0	0	0	0	0	1	0	513	318	11	4	45	4	ALG11	13	52586597	Splice_Site	SNP	A	TCGA-AG-3885-01A-01W-0899-10	11071270	52586597	62583281	130	4177										
COMMD6	170622	hgsc.bcm.edu	37	chr13	76111932	76111932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atccagcggcggctcgctggAcgcctccatgggcagcgtct	14	15	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:76111932A>G	ENST00000377615.3	-	2	174	c.10T>C	c.(10-12)Tcc>Ccc	p.S4P	COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000355801.4_Missense_Mutation_p.S4P|COMMD6_ENST00000377619.5_5'Flank|COMMD6_ENST00000406936.3_Missense_Mutation_p.S4P			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6	4					negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		GGCTCGCTGGACGCCTCCATG	0.632																																																0			13											73	74	74					13																	76111932		2203	4300	6503	75009933	SO:0001583	missense	170622			AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.10T>C	13.37:g.76111932A>G	ENSP00000366841:p.Ser4Pro		75009933	A6NF28|B7ZLN0|Q5TBK4	Missense_Mutation	SNP	ENST00000377615.3	37	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	a	10.52	1.373613	0.24857	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000355801	T;T;T	0.48201	0.86;0.86;0.82	4.52	-4.63	0.03359	.	0.970579	0.08519	N	0.933780	T	0.25938	0.0632	.	.	.	0.09310	N	1	B;P	0.35982	0.072;0.531	B;B	0.31812	0.018;0.136	T	0.17258	-1.0375	9	0.48119	T	0.1	.	2.4675	0.04556	0.2416:0.1375:0.0846:0.5362	.	4;4	Q7Z4G1;Q7Z4G1-2	COMD6_HUMAN;.	P	4	ENSP00000385660:S4P;ENSP00000366841:S4P;ENSP00000348054:S4P	ENSP00000348054:S4P	S	-	1	0	COMMD6	75009933	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.282000	0.08445	-0.626000	0.05596	-3.262000	0.00049	TCC		0.632	COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023		G	76111932	A	G	76111932	3	3	44	1	0	0	0	0	1	0	0	0	3726	275	10	4	306	4	COMMD6	13	76111932	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	23525335	76111932	39057946	131	4178										
NALCN	259232	hgsc.bcm.edu	37	chr13	101717772	101717772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtacctcaggacatcatggaAggtgacgtcgccgccattgt	12	11	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:101717772A>G	ENST00000251127.6	-	40	4669	c.4588T>C	c.(4588-4590)Ttc>Ctc	p.F1530L		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1530					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACATCATGGAAGGTGACGTCG	0.552																																																0			13											154	125	135					13																	101717772		2203	4300	6503	100515773	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4588T>C	13.37:g.101717772A>G	ENSP00000251127:p.Phe1530Leu		100515773	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918562	0.92249	.	.	ENSG00000102452	ENST00000251127	D	0.98684	-5.07	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.98745	0.9578	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99892	1.1137	10	0.59425	D	0.04	.	15.9883	0.80179	1.0:0.0:0.0:0.0	.	1530	Q8IZF0	NALCN_HUMAN	L	1530	ENSP00000251127:F1530L	ENSP00000251127:F1530L	F	-	1	0	NALCN	100515773	1.000000	0.71417	0.977000	0.42913	0.829000	0.46940	8.956000	0.93066	2.172000	0.68678	0.533000	0.62120	TTC		0.552	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		G	101717772	A	G	101717772	3	3	44	1	0	0	0	0	1	0	0	0	10178	72	3	4	648	4	NALCN	13	101717772	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	25605840	101717772	13452106	132	4179										
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55636179	55636179	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggtagtctcctttatacctcGtttatattcacaatcatcaa	4	10	4	0	rs565083852		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:55636179G>A	ENST00000247191.2	-	12	1702	c.1486C>T	c.(1486-1488)Cga>Tga	p.R496*	DLGAP5_ENST00000395425.2_Nonsense_Mutation_p.R496*	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	496					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TTTATACCTCGTTTATATTCA	0.363													G|||	1	0.000199681	0	0	5008	,	,		16074	0.001		0	False		,,,				2504	0															0			14											116	105	109					14																	55636179		2203	4300	6503	54705932	SO:0001587	stop_gained	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1486C>T	14.37:g.55636179G>A	ENSP00000247191:p.Arg496*		54705932	A8MTM6|B4DRM8|Q86T11|Q8NG58	Nonsense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531200	0.85706	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	.	.	.	5.85	2.93	0.34026	.	0.242538	0.42420	D	0.000720	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1119	0.42568	0.1297:0.1155:0.7548:0.0	.	.	.	.	X	496	.	ENSP00000247191:R496X	R	-	1	2	DLGAP5	54705932	0.996000	0.38824	0.101000	0.21167	0.009000	0.06853	2.861000	0.48380	0.897000	0.36392	-0.140000	0.14226	CGA		0.363	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55636179	G	A	55636179	4	1	44	1	0	0	0	0	0	1	0	0	4574	1153	40	1	1181	1	DLGAP5	14	55636179	Nonsense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10		55636179	51713361	133	4180										
C14orf50	145376	hgsc.bcm.edu	37	chr14	65054959	65054959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcatcaagtagacgtcagatTcccagccgagatgcaaaagc	9	11	3	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:65054959T>C	ENST00000298705.1	+	11	1124	c.1028T>C	c.(1027-1029)tTc>tCc	p.F343S	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	343					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GACGTCAGATTCCCAGCCGAG	0.488																																																0			14											98	95	96					14																	65054959		2203	4300	6503	64124712	SO:0001583	missense	145376				CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.1028T>C	14.37:g.65054959T>C	ENSP00000298705:p.Phe343Ser		64124712	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	T	10.25	1.298445	0.23650	.	.	ENSG00000165807	ENST00000298705	T	0.31247	1.5	5.03	-2.4	0.06583	.	1.132860	0.06558	N	0.746156	T	0.19644	0.0472	L	0.47716	1.5	0.09310	N	1	B	0.29805	0.257	B	0.24155	0.051	T	0.23868	-1.0176	10	0.24483	T	0.36	3.0E-4	1.588	0.02648	0.469:0.0903:0.1464:0.2943	.	343	Q96LQ0	PPR36_HUMAN	S	343	ENSP00000298705:F343S	ENSP00000298705:F343S	F	+	2	0	C14orf50	64124712	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.544000	0.06077	-0.187000	0.10516	-0.258000	0.10820	TTC		0.488	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		C	65054959	T	C	65054959	3	2	44	1	0	0	0	0	1	0	0	0	1781	1783	62	4	1070	4	C14orf50	14	65054959	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	9418780	65054959	42294581	134	4181										
SFRS5	6430	hgsc.bcm.edu	37	chr14	70234923	70234923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	actaaatccagcggccagggAgaaggacgtggaaagattct	13	8	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:70234923A>G	ENST00000553521.1	+	3	1503	c.50A>G	c.(49-51)gAg>gGg	p.E17G	SRSF5_ENST00000553635.1_Missense_Mutation_p.E17G|SRSF5_ENST00000554021.1_Missense_Mutation_p.E17G|SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000451983.2_Missense_Mutation_p.E17G|SRSF5_ENST00000555349.1_Missense_Mutation_p.E17G|SRSF5_ENST00000553548.1_Missense_Mutation_p.E17G|SRSF5_ENST00000557154.1_Missense_Mutation_p.E17G|SRSF5_ENST00000394366.2_Missense_Mutation_p.E17G			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	17	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						GCGGCCAGGGAGAAGGACGTG	0.428																																																0			14											157	170	165					14																	70234923		2203	4300	6503	69304676	SO:0001583	missense	0			AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.50A>G	14.37:g.70234923A>G	ENSP00000452123:p.Glu17Gly		69304676	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	37	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757652	0.89843	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000553548;ENST00000553369;ENST00000557154;ENST00000451983;ENST00000553635;ENST00000555349;ENST00000554021	T;T;T;T;T;T;T;T;T	0.80214	1.91;1.91;-1.35;-1.35;1.91;-1.35;1.91;-1.35;-1.35	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.89473	0.6725	M	0.73430	2.235	0.80722	D	1	P;P;D	0.89917	0.531;0.73;1.0	P;P;D	0.87578	0.614;0.652;0.998	D	0.90582	0.4530	10	0.87932	D	0	.	16.2453	0.82441	1.0:0.0:0.0:0.0	.	17;17;17	Q13243-3;Q6FGE0;Q13243	.;.;SRSF5_HUMAN	G	17	ENSP00000452123:E17G;ENSP00000377892:E17G;ENSP00000452400:E17G;ENSP00000452449:E17G;ENSP00000451088:E17G;ENSP00000402734:E17G;ENSP00000451391:E17G;ENSP00000452090:E17G;ENSP00000450918:E17G	ENSP00000377892:E17G	E	+	2	0	SRSF5	69304676	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.306000	0.78905	2.241000	0.73720	0.533000	0.62120	GAG		0.428	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		G	70234923	A	G	70234923	3	3	44	1	0	0	0	0	1	0	0	0	14217	304	11	4	52	4	SFRS5	14	70234923	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	5179964	70234923	37114617	135	4182										
RTL1	388015	hgsc.bcm.edu	37	chr14	101350472	101350472	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtaaggtcagttggcagagTacgatgaactcgtggaattc	13	6	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:101350472T>C	ENST00000534062.1	-	1	712	c.654A>G	c.(652-654)gtA>gtG	p.V218V	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	218					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GTTGGCAGAGTACGATGAACT	0.493																																																0			14											133	109	116					14																	101350472		692	1591	2283	100420225	SO:0001819	synonymous_variant	388015				CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.654A>G	14.37:g.101350472T>C			100420225	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																				0.493	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		C	101350472	T	C	101350472	2	2	44	1	0	0	0	0	0	0	0	1	13761	1625	57	4		4	RTL1	14	101350472	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	31115549	101350472	5999068	136	4183										
MGA	23269	hgsc.bcm.edu	37	chr15	42041775	42041775	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ataaaaagagagcaagaaacGaagaaggttctacagtcaga	10	5	2	4			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:42041775G>A	ENST00000570161.1	+	16	5970	c.5970G>A	c.(5968-5970)acG>acA	p.T1990T	MGA_ENST00000219905.7_Silent_p.T1990T|MGA_ENST00000545763.1_Silent_p.T1781T|MGA_ENST00000389936.4_Silent_p.T1951T|MGA_ENST00000566586.1_Silent_p.T1781T			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGCAAGAAACGAAGAAGGTTC	0.413																																																0			15											67	66	66					15																	42041775		1850	4090	5940	39829067	SO:0001819	synonymous_variant	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5970G>A	15.37:g.42041775G>A			39829067	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																				0.413	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42041775	G	A	42041775	2	1	44	1	0	0	0	0	0	0	0	1	9570	1045	37	1		1	MGA	15	42041775	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10		42041775	60489617	137	4184										
NARG2	79664	hgsc.bcm.edu	37	chr15	60720652	60720652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgttgtgttgtggtatccagTgatttcggtggaaaagtaca	13	4	0	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:60720652T>C	ENST00000261520.4	-	15	3030	c.2796A>G	c.(2794-2796)tcA>tcG	p.S932S	NARG2_ENST00000439632.1_Silent_p.S795S	NM_024611.4	NP_078887.2												p.S932S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TGGTATCCAGTGATTTCGGTG	0.373																																																1	Substitution - coding silent(1)	lung(1)	15											136	129	132					15																	60720652		2203	4300	6503	58507944	SO:0001819	synonymous_variant	79664																														ENST00000261520.4:c.2796A>G	15.37:g.60720652T>C			58507944		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																				0.373	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			C	60720652	T	C	60720652	2	2	44	1	0	0	0	0	0	0	0	1	10199	1683	59	4		4	NARG2	15	60720652	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	18678877	60720652	41810740	138	4185										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65623923	65623923	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcctggcactggcctgtgatGagcccgcactgttctcggcc	13	15	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:65623923G>T	ENST00000327987.4	-	8	1474	c.1223C>A	c.(1222-1224)tCa>tAa	p.S408*	IGDCC3_ENST00000559231.1_5'UTR	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	408	Ig-like C2-type 4.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGCCTGTGATGAGCCCGCACT	0.612																																																0			15											42	41	41					15																	65623923		2201	4299	6500	63410976	SO:0001587	stop_gained	9543			AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1223C>A	15.37:g.65623923G>T	ENSP00000332773:p.Ser408*		63410976	O95215	Nonsense_Mutation	SNP	ENST00000327987.4	37	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679380	0.88542	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	.	.	.	4.92	4.92	0.64577	.	0.063209	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.8131	18.1374	0.89624	0.0:0.0:1.0:0.0	.	.	.	.	X	408;271	.	ENSP00000332773:S408X	S	-	2	0	IGDCC3	63410976	1.000000	0.71417	0.888000	0.34837	0.235000	0.25334	7.831000	0.86748	2.241000	0.73720	0.655000	0.94253	TCA		0.612	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		T	65623923	G	T	65623923	4	4	44	1	0	0	0	0	0	1	0	0	7589	1294	45	2	1249	2	IGDCC3	15	65623923	Nonsense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	4903271	65623923	36907469	139	4186										
NR2E3	10002	hgsc.bcm.edu	37	chr15	72105929	72105929	+	RNA	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ttccgggcattggcggtggaCccccacggagtttgcctgca	14	13	0	0	rs139176226|rs11351249|rs398027866		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:72105929C>A	ENST00000398840.2	+	0	1138							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						TGGCGGTGGACCCCCACGGAG	0.607																																																0			15											6	5	5					15																	72105929		1758	3851	5609	69892983			10002				CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"Nuclear hormone receptors"	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72105929C>A			69892983	B6ZGU0|Q9UHM4	Missense_Mutation	SNP	ENST00000398840.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.549|1.549	-0.539623|-0.539623	0.04053|0.04053	.|.	.|.	ENSG00000031544|ENSG00000031544	ENST00000326995;ENST00000398840|ENST00000326995;ENST00000398840	.|.	.|.	.|.	.|.	.|.	.|.	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.597438	.|0.17891	.|N	.|0.158507	.|T	.|0.74824	.|0.3767	M|M	0.88570|0.88570	2.965|2.965	.|.	.|.	.|.	.|D	.|0.67145	.|0.996	.|D	.|0.73380	.|0.98	.|T	.|0.78897	.|-0.2023	.|6	.|0.87932	.|D	.|0	.|.	.|.	.|.	.|.	.|.	.|316	.|Q9Y5X4	.|NR2E3_HUMAN	.|E	-1|228;316	.|.	.|ENSP00000317199:D228E	.|D	+|+	.|3	.|2	NR2E3|NR2E3	69892983|69892983	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.857000|0.857000	0.48899|0.48899	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|GAC		0.607	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		A	72105929	C	A	72105929	1	1	44	0	1	0	0	0	0	0	0	0	10657	506	18	2		2	NR2E3	15	72105929	RNA	SNP	C	TCGA-AG-3885-01A-01W-0899-10	6482006	72105929	30425463	140	4187										
CRABP1	1381	hgsc.bcm.edu	37	chr15	78640277	78640277	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcttctctgcagacgtttggCgccgatgacgtggtctgcac	12	12	3	2	rs201099878		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:78640277C>T	ENST00000299529.6	+	4	477	c.372C>T	c.(370-372)ggC>ggT	p.G124G		NM_004378.2	NP_004369.1	P29762	RABP1_HUMAN	cellular retinoic acid binding protein 1	124					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|lung(4)|skin(1)	6					Alitretinoin(DB00523)|Tretinoin(DB00755)	AGACGTTTGGCGCCGATGACG	0.478													C|||	1	0.000199681	0	0	5008	,	,		18987	0		0.001	False		,,,				2504	0				Ovarian(146;578 3231 38536)											0			15											165	147	153					15																	78640277		2196	4293	6489	76427332	SO:0001819	synonymous_variant	1381				CCDS10301.1	15q24	2013-03-01	2001-11-28		ENSG00000166426	ENSG00000166426		"Fatty acid binding protein family"	2338	protein-coding gene	gene with protein product		180230	"cellular retinoic acid-binding protein 1"	RBP5		9154115	Standard	NM_004378		Approved	CRABP, CRABP-I, CRABPI	uc002bdp.2	P29762	OTTHUMG00000143862	ENST00000299529.6:c.372C>T	15.37:g.78640277C>T			76427332	Q6IAY7|Q8WTV5	Silent	SNP	ENST00000299529.6	37	CCDS10301.1																																																																																				0.478	CRABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290110.2	NM_004378		T	78640277	C	T	78640277	2	4	44	1	0	0	0	0	0	0	0	1	3849	755	27	1		1	CRABP1	15	78640277	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	6534348	78640277	23891115	141	4188										
TMED3	23423	hgsc.bcm.edu	37	chr15	79614396	79614396	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gacgcattaccggctgcgggAggcccaggaccgggcccgag	17	14	0	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:79614396A>G	ENST00000299705.5	+	3	682	c.494A>G	c.(493-495)gAg>gGg	p.E165G	TMED3_ENST00000424155.2_Intron|TMED3_ENST00000558562.1_3'UTR|TMED3_ENST00000536821.1_Intron	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	165					protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						CGGCTGCGGGAGGCCCAGGAC	0.582																																																0			15											72	69	70					15																	79614396		2196	4293	6489	77401451	SO:0001583	missense	23423			BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 22", "transmembrane emp24 domain containing 3"	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.494A>G	15.37:g.79614396A>G	ENSP00000299705:p.Glu165Gly		77401451	A8K069|B4DN05|Q2T9F8	Missense_Mutation	SNP	ENST00000299705.5	37	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.944788	0.92593	.	.	ENSG00000166557	ENST00000299705	T	0.28454	1.61	4.86	4.86	0.63082	GOLD (1);	0.062952	0.64402	D	0.000007	T	0.66809	0.2827	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77520	-0.2557	10	0.87932	D	0	-31.98	12.4554	0.55702	1.0:0.0:0.0:0.0	.	165	Q9Y3Q3	TMED3_HUMAN	G	165	ENSP00000299705:E165G	ENSP00000299705:E165G	E	+	2	0	TMED3	77401451	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.813000	0.75231	2.029000	0.59856	0.482000	0.46254	GAG		0.582	TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364		G	79614396	A	G	79614396	3	3	44	1	0	0	0	0	1	0	0	0	16044	304	11	4	504	4	TMED3	15	79614396	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	974119	79614396	22916996	142	4189										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100252738	100252738	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcagcagcagcagcagcagcAgcagccgccgccaccaccgc	12	19	0	0	rs560400205|rs201861701	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:100252738A>C	ENST00000557785.1	+	11	1605	c.1256A>C	c.(1255-1257)cAg>cCg	p.Q419P	MEF2A_ENST00000557942.1_Missense_Mutation_p.Q427P|MEF2A_ENST00000558812.1_Missense_Mutation_p.Q359P|MEF2A_ENST00000449277.2_Missense_Mutation_p.Q351P|MEF2A_ENST00000453228.2_Missense_Mutation_p.Q419P|MEF2A_ENST00000354410.5_Missense_Mutation_p.Q421P|MEF2A_ENST00000338042.6_Missense_Mutation_p.Q428P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	429					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			cagcagcagcagcagcCGCCG	0.637																																																0			15																																								98070261	SO:0001583	missense	4205				CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1256A>C	15.37:g.100252738A>C	ENSP00000453441:p.Gln419Pro		98070261	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	37	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.790689	0.00077	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T	0.07800	3.16;3.16;3.16	0.337	0.337	0.15966	.	.	.	.	.	T	0.08802	0.0218	N	0.08118	0	0.18873	N	0.999989	B;B;B;D;B;D	0.53462	0.0;0.0;0.0;0.96;0.001;0.96	B;B;B;D;B;D	0.64237	0.0;0.0;0.0;0.923;0.0;0.923	T	0.40776	-0.9545	8	0.23891	T	0.37	.	.	.	.	.	429;359;340;419;421;427	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	P	419;421;428;359	ENSP00000404110:Q419P;ENSP00000346389:Q421P;ENSP00000337202:Q428P	ENSP00000337202:Q428P	Q	+	2	0	MEF2A	98070261	0.962000	0.33011	0.021000	0.16686	0.081000	0.17604	-0.272000	0.08560	0.353000	0.24079	0.342000	0.21767	CAG		0.637	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			C	100252738	A	C	100252738	3	2	44	1	0	0	0	0	1	0	0	0	9485	188	7	4	1460	4	MEF2A	15	100252738	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	20638342	100252738	2278654	143	4190										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11214599	11214599	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tccaggcttggctggggagtGgtcaagtttgcaggcctatt	15	8	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:11214599G>A	ENST00000409790.1	+	20	2474	c.2244G>A	c.(2242-2244)gtG>gtA	p.V748V	CLEC16A_ENST00000409552.3_Silent_p.V730V|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCTGGGGAGTGGTCAAGTTTG	0.532																																																1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	16											110	113	112					16																	11214599		2062	4203	6265	11122100	SO:0001819	synonymous_variant	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2244G>A	16.37:g.11214599G>A			11122100		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																				0.532	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11214599	G	A	11214599	2	1	44	1	0	0	0	0	0	0	0	1	3506	1335	47	3		3	CLEC16A	16	11214599	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10		11214599	79140154	144	4191										
COG7	91949	hgsc.bcm.edu	37	chr16	23436075	23436075	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggaaggaatgtttacgtaggTgggggagcagtgccatctcc	16	7	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:23436075T>G	ENST00000307149.5	-	7	1189	c.1004A>C	c.(1003-1005)cAc>cCc	p.H335P		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	335					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		TTTACGTAGGTGGGGGAGCAG	0.567																																																0			16											99	106	104					16																	23436075		2197	4300	6497	23343576	SO:0001583	missense	91949			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1004A>C	16.37:g.23436075T>G	ENSP00000305442:p.His335Pro		23343576	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	T	9.838	1.190124	0.21954	.	.	ENSG00000168434	ENST00000307149	T	0.42513	0.97	5.31	3.07	0.35406	.	0.398252	0.32343	N	0.006238	T	0.26159	0.0638	N	0.22421	0.69	0.37382	D	0.912064	B	0.02656	0.0	B	0.01281	0.0	T	0.09314	-1.0680	10	0.30078	T	0.28	-14.5543	8.7063	0.34356	0.0:0.1543:0.0:0.8457	.	335	P83436	COG7_HUMAN	P	335	ENSP00000305442:H335P	ENSP00000305442:H335P	H	-	2	0	COG7	23343576	1.000000	0.71417	0.020000	0.16555	0.469000	0.32828	3.263000	0.51546	0.356000	0.24157	0.482000	0.46254	CAC		0.567	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			G	23436075	T	G	23436075	3	3	44	1	0	0	0	0	1	0	0	0	3669	1696	59	4	1352	4	COG7	16	23436075	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	12221476	23436075	66918678	145	4192										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30507513	30507513	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gctctgacagacatcaacggCgatgggctggtagacgtggc	15	10	2	3	rs148420170	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:30507513C>T	ENST00000356798.6	+	14	1779	c.1599C>T	c.(1597-1599)ggC>ggT	p.G533G	ITGAL_ENST00000433423.2_Intron|RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000358164.5_Silent_p.G450G|ITGAL_ENST00000568012.1_3'UTR	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	533					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	ACATCAACGGCGATGGGCTGG	0.622													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		15652	0		0	False		,,,				2504	0				NSCLC(110;1462 1641 3311 33990 49495)											0			16						C	,	6,4388	11.4+/-27.6	0,6,2191	88	97	94		1350,1599	2.8	0.9	16	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	0,7,6490	TT,TC,CC		0.0116,0.1365,0.0539	,	450/1087,533/1171	30507513	7,12987	2197	4300	6497	30415014	SO:0001819	synonymous_variant	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1599C>T	16.37:g.30507513C>T			30415014	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.622	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30507513	C	T	30507513	2	4	44	1	0	0	0	0	0	0	0	1	7907	755	27	1		1	ITGAL	16	30507513	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	7071438	30507513	59847240	146	4193										
BCKDK	10295	hgsc.bcm.edu	37	chr16	31121793	31121793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggaatccgcatgttggccacGcatcacctggcgctgcatga	12	13	1	1	rs14235	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:31121793G>A	ENST00000394951.1	+	8	1238	c.615G>A	c.(613-615)acG>acA	p.T205T	BCKDK_ENST00000287507.3_Silent_p.T205T|BCKDK_ENST00000219794.6_Silent_p.T205T|BCKDK_ENST00000394950.3_Silent_p.T205T|AC135050.1_ENST00000517000.2_RNA			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	205	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						TGTTGGCCACGCATCACCTGG	0.567													G|||	1799	0.359225	0.0893	0.3833	5008	,	,		18067	0.8849		0.3817	False		,,,				2504	0.1421															0			16						G	,	592,3802	255.8+/-260.9	44,504,1649	62	63	63		615,615	-9	0.9	16	dbSNP_52	63	3344,5256	492.2+/-373.3	638,2068,1594	no	coding-synonymous,coding-synonymous	BCKDK	NM_001122957.1,NM_005881.2	,	682,2572,3243	AA,AG,GG		38.8837,13.4729,30.2909	,	205/366,205/413	31121793	3936,9058	2197	4300	6497	31029294	SO:0001819	synonymous_variant	10295			AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.615G>A	16.37:g.31121793G>A			31029294	A8MY43|Q6FGL4|Q96G95|Q96IN5	Silent	SNP	ENST00000394951.1	37	CCDS10705.1																																																																																				0.567	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881		A	31121793	G	A	31121793	2	1	44	1	0	0	0	0	0	0	0	1	1362	1074	38	1		1	BCKDK	16	31121793	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	614280	31121793	59232960	147	4194										
MMP2	4313	hgsc.bcm.edu	37	chr16	55539301	55539301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acctgaagctggagaaccaaAgtctgaagagcgtgaagttt	12	7	1	5			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:55539301A>G	ENST00000219070.4	+	13	2439	c.1930A>G	c.(1930-1932)Agt>Ggt	p.S644G	MMP2_ENST00000570308.1_Missense_Mutation_p.S568G|MMP2_ENST00000437642.2_Missense_Mutation_p.S594G|MMP2_ENST00000543485.1_Missense_Mutation_p.S568G	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	644	Required for inhibitor TIMP2 binding.		S -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	GGAGAACCAAAGTCTGAAGAG	0.537																																																0			16											168	163	165					16																	55539301		2198	4300	6498	54096802	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.1930A>G	16.37:g.55539301A>G	ENSP00000219070:p.Ser644Gly		54096802	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906323	0.52333	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.02606	4.23;4.23;4.23	5.38	5.38	0.77491	Hemopexin/matrixin (2);	0.163087	0.64402	D	0.000002	T	0.04907	0.0132	L	0.42245	1.32	0.80722	D	1	P;P	0.43169	0.8;0.647	B;B	0.43950	0.437;0.122	T	0.54846	-0.8232	10	0.32370	T	0.25	.	14.3832	0.66926	1.0:0.0:0.0:0.0	.	594;644	E9PE45;P08253	.;MMP2_HUMAN	G	644;568;594	ENSP00000219070:S644G;ENSP00000444143:S568G;ENSP00000394237:S594G	ENSP00000219070:S644G	S	+	1	0	MMP2	54096802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.196000	0.89725	2.050000	0.60909	0.460000	0.39030	AGT		0.537	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			G	55539301	A	G	55539301	3	3	44	1	0	0	0	0	1	0	0	0	9688	72	3	4	1987	4	MMP2	16	55539301	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	24417508	55539301	34815452	148	4195										
CES7	221223	hgsc.bcm.edu	37	chr16	55890317	55890317	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tttgtatcagatggagggcaAgggacttgttggagccactg	15	6	1	1	rs199767426		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:55890317A>G	ENST00000290567.9	-	9	1218	c.1097T>C	c.(1096-1098)cTt>cCt	p.L366P	CES5A_ENST00000521992.1_Missense_Mutation_p.L395P|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000319165.9_Missense_Mutation_p.L366P|CES5A_ENST00000518005.1_Missense_Mutation_p.L260P|CES5A_ENST00000520435.1_Missense_Mutation_p.L336P	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	366						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						ATGGAGGGCAAGGGACTTGTT	0.527																																																0			16											149	125	133					16																	55890317		2198	4300	6498	54447818	SO:0001583	missense	0			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1097T>C	16.37:g.55890317A>G	ENSP00000290567:p.Leu366Pro		54447818	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	11.51	1.659670	0.29515	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.18	2.09	0.27110	Carboxylesterase, type B (1);	1.293400	0.05941	N	0.636938	T	0.69260	0.3091	L	0.41906	1.305	0.26833	N	0.968533	D;D	0.58970	0.984;0.966	P;P	0.60541	0.876;0.735	T	0.54549	-0.8277	10	0.32370	T	0.25	.	4.5993	0.12345	0.8456:0.0:0.1544:0.0	.	366;366	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	P	395;366;260;366;336;146	ENSP00000428864:L395P;ENSP00000324271:L366P;ENSP00000428571:L260P;ENSP00000290567:L366P;ENSP00000428887:L336P	ENSP00000290567:L366P	L	-	2	0	CES5A	54447818	0.000000	0.05858	0.214000	0.23707	0.118000	0.20060	0.801000	0.27055	0.633000	0.30452	0.369000	0.22263	CTT		0.527	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		G	55890317	A	G	55890317	3	3	44	1	0	0	0	0	1	0	0	0	3278	72	3	4	650	4	CES7	16	55890317	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	351016	55890317	34464436	149	4196										
DPEP2	64174	hgsc.bcm.edu	37	chr16	68021778	68021778	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ttccacttgtctgaagacccGcagcaggtttccacgaagga	10	12	1	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:68021778G>T	ENST00000572888.1	-	9	1833	c.1183C>A	c.(1183-1185)Cgg>Agg	p.R395R	DPEP2_ENST00000393847.1_Silent_p.R395R|DPEP2_ENST00000412757.2_Silent_p.R395R			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	395					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		CTGAAGACCCGCAGCAGGTTT	0.567																																																0			16											129	129	129					16																	68021778		2198	4300	6498	66579279	SO:0001819	synonymous_variant	64174			AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.1183C>A	16.37:g.68021778G>T			66579279	B2RCF8|Q6UX92|Q8TC95	Silent	SNP	ENST00000572888.1	37	CCDS10857.1																																																																																				0.567	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355		T	68021778	G	T	68021778	2	4	44	1	0	0	0	0	0	0	0	1	4725	1086	38	2		2	DPEP2	16	68021778	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	12131461	68021778	22332975	150	4197										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70841910	70841910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cactggcttcagtgcctcccTggcctcctggggctgcatta	11	15	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:70841910T>C	ENST00000393567.2	-	86	15089	c.14939A>G	c.(14938-14940)cAg>cGg	p.Q4980R		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4980					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AGTGCCTCCCTGGCCTCCTGG	0.532																																																0			16											61	63	62					16																	70841910		1982	4150	6132	69399411	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14939A>G	16.37:g.70841910T>C	ENSP00000377197:p.Gln4980Arg		69399411	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444244	0.63067	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00882	5.58	5.91	5.91	0.95273	.	0.339335	0.16344	U	0.218528	T	0.03011	0.0089	M	0.75447	2.3	0.80722	D	1	P	0.47762	0.9	P	0.52454	0.699	T	0.63888	-0.6535	10	0.17369	T	0.5	.	11.9385	0.52886	0.1301:0.0:0.0:0.8699	.	4979	F8WD23	.	R	4980;4979	ENSP00000377197:Q4980R	ENSP00000313052:Q4979R	Q	-	2	0	HYDIN	69399411	0.892000	0.30473	0.997000	0.53966	0.593000	0.36681	1.145000	0.31577	2.254000	0.74563	0.533000	0.62120	CAG		0.532	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	70841910	T	C	70841910	3	2	44	1	0	0	0	0	1	0	0	0	7488	1580	55	4	430	4	HYDIN	16	70841910	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	2820132	70841910	19512843	151	4198										
KIAA0174	9798	hgsc.bcm.edu	37	chr16	71956517	71956517	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gatggaacggtgccaatgccCatgcccatgcccatgcctat	10	14	0	0	rs549750934|rs372825060	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:71956517C>A	ENST00000378799.6	+	7	1049	c.693C>A	c.(691-693)ccC>ccA	p.P231P	IST1_ENST00000538850.1_Silent_p.P83P|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000535424.1_Silent_p.P244P|IST1_ENST00000544564.1_Silent_p.P231P|IST1_ENST00000541571.2_Silent_p.P231P|IST1_ENST00000378798.5_Silent_p.P231P|IST1_ENST00000606369.1_Silent_p.P83P|IST1_ENST00000329908.8_Silent_p.P231P|RP11-498D10.5_ENST00000567146.1_RNA			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	229	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										tgccaatgcccatgcccatgc	0.498																																																0			16											102	70	81					16																	71956517		2198	4300	6498	70514018	SO:0001819	synonymous_variant	9798			BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"KIAA0174"	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.693C>A	16.37:g.71956517C>A			70514018	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Silent	SNP	ENST00000378799.6	37	CCDS59272.1	.	.	.	.	.	.	.	.	.	.	C	7.943	0.743115	0.15642	.	.	ENSG00000182149	ENST00000541848	.	.	.	5.54	-4.88	0.03113	.	0.046113	0.85682	D	0.000000	T	0.58750	0.2144	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	T	0.60454	-0.7260	6	0.62326	D	0.03	-2.7071	8.7497	0.34609	0.1145:0.2195:0.0:0.666	.	.	.	.	Q	118	.	ENSP00000437499:P118Q	P	+	2	0	KIAA0174	70514018	0.000000	0.05858	0.488000	0.27440	0.917000	0.54804	-3.886000	0.00342	-0.979000	0.03529	-0.122000	0.15005	CCA		0.498	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761		A	71956517	C	A	71956517	2	1	44	1	0	0	0	0	0	0	0	1	8179	581	21	2		2	KIAA0174	16	71956517	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1114607	71956517	18398236	152	4199										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77334230	77334230	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gcaggtctttttgtggctggTggagttccattcatgacctt	12	8	2	1	rs201338151	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:77334230T>G	ENST00000282849.5	-	17	3022	c.2604A>C	c.(2602-2604)ccA>ccC	p.P868P		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	868	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TTGTGGCTGGTGGAGTTCCAT	0.458																																																0			16											145	122	130					16																	77334230		2198	4300	6498	75891731	SO:0001819	synonymous_variant	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2604A>C	16.37:g.77334230T>G			75891731	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																				0.458	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			G	77334230	T	G	77334230	2	3	44	1	0	0	0	0	0	0	0	1	263	1683	59	4		4	ADAMTS18	16	77334230	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	5377713	77334230	13020523	153	4200										
CDH13	1012	hgsc.bcm.edu	37	chr16	83711906	83711906	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acgtctcctacggccccagcTccacagccaccgtccacatc	6	21	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:83711906T>C	ENST00000566620.1	+	10	1668	c.1378T>C	c.(1378-1380)Tcc>Ccc	p.S460P	CDH13_ENST00000428848.3_Missense_Mutation_p.S421P|CDH13_ENST00000268613.10_Missense_Mutation_p.S507P	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	460	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CGGCCCCAGCTCCACAGCCAC	0.562																																																0			16											83	90	88					16																	83711906		2096	4215	6311	82269407	SO:0001583	missense	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1378T>C	16.37:g.83711906T>C	ENSP00000454435:p.Ser460Pro		82269407	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.393670	0.83011	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000540531	T	0.55760	0.5	4.81	4.81	0.61882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74092	0.3671	M	0.84773	2.715	0.80722	D	1	P;P;D	0.76494	0.908;0.722;0.999	P;P;D	0.81914	0.737;0.519;0.995	T	0.78914	-0.2016	9	0.66056	D	0.02	.	13.5579	0.61770	0.0:0.0:0.0:1.0	.	421;507;460	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	P	507;460;421;162;150	ENSP00000268613:S507P	ENSP00000268613:S507P	S	+	1	0	CDH13	82269407	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.387000	0.79785	1.809000	0.52856	0.482000	0.46254	TCC		0.562	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		C	83711906	T	C	83711906	3	2	44	1	0	0	0	0	1	0	0	0	3105	1551	54	4	1416	4	CDH13	16	83711906	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	6377676	83711906	6642847	154	4201										
INPP5K	51763	hgsc.bcm.edu	37	chr17	1416807	1416807	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctgctccacgagtcattaaaGgcagcatcggaaaggaggct	12	10	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:1416807G>A	ENST00000421807.2	-	3	589	c.201C>T	c.(199-201)gcC>gcT	p.A67A	INPP5K_ENST00000406424.4_5'UTR|INPP5K_ENST00000542125.1_Silent_p.A67A|INPP5K_ENST00000320345.6_5'UTR|INPP5K_ENST00000397335.3_Intron	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	67	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						AGTCATTAAAGGCAGCATCGG	0.512																																																0			17											212	193	200					17																	1416807		2203	4300	6503	1363557	SO:0001819	synonymous_variant	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.201C>T	17.37:g.1416807G>A			1363557	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																				0.512	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			A	1416807	G	A	1416807	2	1	44	1	0	0	0	0	0	0	0	1	7781	987	35	3		3	INPP5K	17	1416807	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10		1416807	79778403	155	4202										
TP53	7157	hgsc.bcm.edu	37	chr17	7577080	7577080	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cctttcttgcggagattctcTtcctctgtgcgccggtctct	9	14	4	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577080T>C	ENST00000269305.4	-	8	1047	c.858A>G	c.(856-858)gaA>gaG	p.E286E	TP53_ENST00000420246.2_Silent_p.E286E|TP53_ENST00000455263.2_Silent_p.E286E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Silent_p.E286E|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Silent_p.E286E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(2)|p.E286D(2)|p.E286fs*17(2)|p.E286E(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAGATTCTCTTCCTCTGTGC	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	27	Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)|Substitution - Missense(2)|Substitution - coding silent(2)	liver(5)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|breast(3)|stomach(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|pancreas(1)	17											96	82	87					17																	7577080		2203	4300	6503	7517805	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.858A>G	17.37:g.7577080T>C			7517805	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577080	T	C	7577080	2	2	44	1	0	0	0	0	0	0	0	1	16421	1606	56	4		4	TP53	17	7577080	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	6160273	7577080	73618130	156	4203			2	5		4	3	495	N	T_C_A	4.723448e-06
TP53	7157	hgsc.bcm.edu	37	chr17	7577153	7577153	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgttccgtcccagtagattaCcactactcaggataggaaaa	8	10	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577153C>A	ENST00000269305.4	-	8	974	c.785G>T	c.(784-786)gGt>gTt	p.G262V	TP53_ENST00000420246.2_Missense_Mutation_p.G262V|TP53_ENST00000455263.2_Missense_Mutation_p.G262V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.G262V|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.G262V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	262	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> C (in a sporadic cancer; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> S (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation). {ECO:0000269|Ref.23}.|GN -> PD (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G262V(19)|p.0?(8)|p.G262D(4)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262fs*83(2)|p.G262_S269delGNLLGRNS(2)|p.G262del(2)|p.G262H(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGTAGATTACCACTACTCAG	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	46	Substitution - Missense(24)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(4)|Unknown(3)|Complex - deletion inframe(1)	lung(8)|large_intestine(5)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(5)|ovary(5)|upper_aerodigestive_tract(4)|bone(4)|endometrium(2)|urinary_tract(2)|pancreas(2)|eye(1)|liver(1)|breast(1)|stomach(1)	17											40	37	38					17																	7577153		2203	4299	6502	7517878	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.785G>T	17.37:g.7577153C>A	ENSP00000269305:p.Gly262Val		7517878	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565296	0.86439	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99957	-9.0;-9.0;-9.0;-9.0;-9.0;-9.0	5.03	5.03	0.67393	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	M	0.90977	3.165	0.80722	D	1	D;P;D;D	0.89917	1.0;0.819;0.999;1.0	D;P;D;D	0.83275	0.996;0.537;0.996;0.992	D	0.95599	0.8661	10	0.87932	D	0	-15.6281	15.9038	0.79403	0.0:1.0:0.0:0.0	.	262;262;262;262	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	262;262;262;262;262;251;130	ENSP00000352610:G262V;ENSP00000269305:G262V;ENSP00000398846:G262V;ENSP00000391127:G262V;ENSP00000391478:G262V;ENSP00000425104:G130V	ENSP00000269305:G262V	G	-	2	0	TP53	7517878	1.000000	0.71417	0.951000	0.38953	0.085000	0.17905	7.572000	0.82409	2.619000	0.88677	0.462000	0.41574	GGT		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577153	C	A	7577153	3	1	44	1	0	0	0	0	1	0	0	0	16421	507	18	2	501	2	TP53	17	7577153	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	73	7577153	73618057	157	4204			2	5		4	3	495	N	T_C_A	4.723448e-06
TP53	7157	hgsc.bcm.edu	37	chr17	7577571	7577571	+	Missense_Mutation	SNP	A	A	G													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccatgcaggaactgttacacAtgtagttgtagtggatggtg							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577571A>G	ENST00000269305.4	-	7	899	c.710T>C	c.(709-711)aTg>aCg	p.M237T	TP53_ENST00000420246.2_Missense_Mutation_p.M237T|TP53_ENST00000455263.2_Missense_Mutation_p.M237T|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.M237T|TP53_ENST00000413465.2_Missense_Mutation_p.M237T|TP53_ENST00000445888.2_Missense_Mutation_p.M237T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	237	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		M -> I (in LFS; germline mutation and in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.M237K(11)|p.0?(8)|p.?(5)|p.M237_N239delMCN(4)|p.M237R(3)|p.M237T(2)|p.M237fs*10(2)|p.Y236_M237delYM(1)|p.H233fs*6(1)|p.M144K(1)|p.M144_N146delMCN(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.H233_C242del10(1)|p.M237fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACTGTTACACATGTAGTTGTA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	43	Substitution - Missense(17)|Whole gene deletion(8)|Deletion - In frame(8)|Deletion - Frameshift(5)|Unknown(5)	ovary(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(4)|endometrium(4)|bone(4)|upper_aerodigestive_tract(3)|lung(3)|breast(3)|central_nervous_system(2)|pancreas(2)|stomach(1)|urinary_tract(1)|prostate(1)	17											130	102	111					17																	7577571		2203	4300	6503	7518296	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.710T>C	17.37:g.7577571A>G	ENSP00000269305:p.Met237Thr		7518296	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.930451	0.73327	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99815	-6.9;-6.9;-6.9;-6.9;-6.9;-6.9;-6.9;-6.9	4.09	4.09	0.47781	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	M	0.86953	2.85	0.58432	D	0.999997	D;P;D;D;D;D	0.89917	1.0;0.647;1.0;1.0;0.999;1.0	D;B;D;D;D;D	0.97110	1.0;0.408;1.0;1.0;1.0;1.0	D	0.96910	0.9666	10	0.87932	D	0	-32.6033	11.6823	0.51466	1.0:0.0:0.0:0.0	.	237;237;144;237;237;237	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	T	237;237;237;237;237;237;226;144;105;144	ENSP00000410739:M237T;ENSP00000352610:M237T;ENSP00000269305:M237T;ENSP00000398846:M237T;ENSP00000391127:M237T;ENSP00000391478:M237T;ENSP00000425104:M105T;ENSP00000423862:M144T	ENSP00000269305:M237T	M	-	2	0	TP53	7518296	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.021000	0.93673	2.074000	0.62210	0.379000	0.24179	ATG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577571	A	G	7577571	3	3	44	1	0	0	0	0	1	0	0	0	16421	217	8	4	580	4	TP53	17	7577571	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	418	7577571	73617639	158	4205	18	2	2	5		4	3	495	N	T_C_A	4.723448e-06
TP53	7157	hgsc.bcm.edu	37	chr17	7577574	7577574	+	Missense_Mutation	SNP	T	T	C													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgcaggaactgttacacatgTagttgtagtggatggtggta							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577574T>C	ENST00000269305.4	-	7	896	c.707A>G	c.(706-708)tAc>tGc	p.Y236C	TP53_ENST00000420246.2_Missense_Mutation_p.Y236C|TP53_ENST00000455263.2_Missense_Mutation_p.Y236C|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Missense_Mutation_p.Y236C|TP53_ENST00000413465.2_Missense_Mutation_p.Y236C|TP53_ENST00000445888.2_Missense_Mutation_p.Y236C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	236	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y236C(61)|p.0?(8)|p.?(5)|p.Y143C(5)|p.Y236del(4)|p.Y236S(3)|p.Y236_M237delYM(1)|p.I232_Y236delIHYNY(1)|p.H233fs*6(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.Y236fs*4(1)|p.H233_C242del10(1)|p.N235_Y236delNY(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTTACACATGTAGTTGTAGTG	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	94	Substitution - Missense(69)|Deletion - In frame(9)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	breast(13)|ovary(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|biliary_tract(6)|stomach(6)|oesophagus(6)|upper_aerodigestive_tract(5)|central_nervous_system(5)|urinary_tract(5)|pancreas(5)|prostate(4)|bone(4)|liver(2)|large_intestine(2)|soft_tissue(1)|endometrium(1)	17	GRCh37	CM004907	TP53	M							126	100	109					17																	7577574		2203	4300	6503	7518299	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.707A>G	17.37:g.7577574T>C	ENSP00000269305:p.Tyr236Cys		7518299	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173261	0.57584	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99801	-6.81;-6.81;-6.81;-6.81;-6.81;-6.81;-6.81;-6.81	4.09	0.528	0.17089	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.335105	0.32884	N	0.005532	D	0.99582	0.9849	M	0.74258	2.255	0.44570	D	0.997534	D;D;D;D;D;D	0.89917	0.998;0.982;1.0;0.998;0.999;1.0	D;P;D;D;D;D	0.81914	0.974;0.898;0.99;0.985;0.992;0.995	D	0.99253	1.0888	10	0.87932	D	0	-12.7522	10.2884	0.43581	0.222:0.0:0.0:0.778	.	236;236;143;236;236;236	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	C	236;236;236;236;236;236;225;143;104;143	ENSP00000410739:Y236C;ENSP00000352610:Y236C;ENSP00000269305:Y236C;ENSP00000398846:Y236C;ENSP00000391127:Y236C;ENSP00000391478:Y236C;ENSP00000425104:Y104C;ENSP00000423862:Y143C	ENSP00000269305:Y236C	Y	-	2	0	TP53	7518299	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	1.502000	0.35704	0.034000	0.15491	0.379000	0.24179	TAC		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577574	T	C	7577574	3	2	44	1	0	0	0	0	1	0	0	0	16421	1638	57	4	583	4	TP53	17	7577574	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	3	7577574	73617636	159	4206	18	2	2	5		4	3	495	N	T_C_A	4.723448e-06
LLGL1	3996	hgsc.bcm.edu	37	chr17	18137141	18137141	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tggtcctgctggtggctgccAgcgacatagcagccctgggc	15	13	0	0	rs2290505	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:18137141A>G	ENST00000316843.4	+	5	538	c.442A>G	c.(442-444)Agc>Ggc	p.S148G		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	148			S -> G (in dbSNP:rs2290505). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7542763, ECO:0000269|PubMed:8565641}.		axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GGTGGCTGCCAGCGACATAGC	0.632													G|||	3918	0.782348	0.848	0.7493	5008	,	,		11652	0.6786		0.7614	False		,,,				2504	0.8456															0			17						G	GLY/SER	3690,716	298.1+/-285.1	1556,578,69	89	80	83		442	2.6	0	17	dbSNP_100	83	6459,2141	365.6+/-334.0	2422,1615,263	yes	missense	LLGL1	NM_004140.3	56	3978,2193,332	GG,GA,AA		24.8953,16.2506,21.9668	benign	148/1065	18137141	10149,2857	2203	4300	6503	18077866	SO:0001583	missense	3996				CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"WD repeat domain containing"	6628	protein-coding gene	gene with protein product		600966	"lethal giant larvae (Drosophila) homolog 1"	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.442A>G	17.37:g.18137141A>G	ENSP00000321537:p.Ser148Gly		18077866	A7MBM7|O00188|Q58F11|Q86UK6	Missense_Mutation	SNP	ENST00000316843.4	37	CCDS32586.1	1650	0.7554945054945055	406	0.8252032520325203	274	0.7569060773480663	402	0.7027972027972028	568	0.7493403693931399	G	0.008	-1.867144	0.00547	0.837494	0.751047	ENSG00000131899	ENST00000316843	T	0.05139	3.49	5.87	2.63	0.31362	WD40 repeat-like-containing domain (1);	0.357650	0.36444	N	0.002589	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	9	0.16896	T	0.51	-8.2838	7.0524	0.25081	0.2156:0.0:0.6055:0.1788	rs2290505;rs58954283;rs2290505	148	Q15334	L2GL1_HUMAN	G	148	ENSP00000321537:S148G	ENSP00000321537:S148G	S	+	1	0	LLGL1	18077866	0.002000	0.14202	0.001000	0.08648	0.033000	0.12548	-0.023000	0.12456	0.428000	0.26173	-0.748000	0.03510	AGC		0.632	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3			G	18137141	A	G	18137141	3	3	44	1	0	0	0	0	1	0	0	0	8857	188	7	4	460	4	LLGL1	17	18137141	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	10559567	18137141	63058069	160	4207										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319767	21319767	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aacaagttcctgctgcccagCgccaactccttctgctacga	7	16	1	0	rs1612176	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:21319767C>T	ENST00000583088.1	+	3	2008	c.1113C>T	c.(1111-1113)agC>agT	p.S371S	KCNJ12_ENST00000331718.5_Silent_p.S371S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	371				S -> R (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGCTGCCCAGCGCCAACTCCT	0.607										Prostate(3;0.18)																																						0			17																																								21260360	SO:0001819	synonymous_variant	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1113C>T	17.37:g.21319767C>T			21260360	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				0.607	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21319767	C	T	21319767	2	4	44	1	0	0	0	0	0	0	0	1	8067	767	27	1		1	KCNJ12	17	21319767	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	3182626	21319767	59875443	161	4208										
KLHL11	55175	hgsc.bcm.edu	37	chr17	40011144	40011144	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctcagagcatgtctctccacTgcgtcagcgaccaacttgac	8	15	3	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:40011144T>G	ENST00000319121.3	-	2	1035	c.975A>C	c.(973-975)gcA>gcC	p.A325A		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	325										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				GTCTCTCCACTGCGTCAGCGA	0.483																																																0			17											105	95	98					17																	40011144		2203	4300	6503	37264670	SO:0001819	synonymous_variant	55175				CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.975A>C	17.37:g.40011144T>G			37264670		Silent	SNP	ENST00000319121.3	37	CCDS11411.1																																																																																				0.483	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		G	40011144	T	G	40011144	2	3	44	1	0	0	0	0	0	0	0	1	8388	1567	55	4		4	KLHL11	17	40011144	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	18691377	40011144	41184066	162	4209										
MYST2	11143	hgsc.bcm.edu	37	chr17	47869354	47869354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cacatcccgacgatctgctcGagtcacccgctcctcagcca	7	19	3	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:47869354G>A	ENST00000259021.4	+	2	402	c.122G>A	c.(121-123)cGa>cAa	p.R41Q	KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000454930.2_Missense_Mutation_p.R41Q|KAT7_ENST00000509773.1_Missense_Mutation_p.R41Q|KAT7_ENST00000424009.2_Missense_Mutation_p.R41Q|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000510819.1_Missense_Mutation_p.R41Q	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	41	Ser-rich.			Missing (in Ref. 5; BAG57945). {ECO:0000305}.|R -> Q (in Ref. 5; BAG57346). {ECO:0000305}.	chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGATCTGCTCGAGTCACCCGC	0.498																																																0			17											108	99	102					17																	47869354		2203	4300	6503	45224353	SO:0001583	missense	11143			AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.122G>A	17.37:g.47869354G>A	ENSP00000259021:p.Arg41Gln		45224353	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542729	0.85917	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009	.	.	.	5.82	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	L	0.48642	1.525	0.80722	D	1	B;B;B;D;D	0.76494	0.147;0.079;0.079;0.999;0.999	B;B;B;D;D	0.72625	0.006;0.003;0.003;0.978;0.975	T	0.68550	-0.5379	9	0.42905	T	0.14	-8.7342	14.3568	0.66742	0.0715:0.0:0.9285:0.0	.	41;41;41;41;41	B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;KAT7_HUMAN;.	Q	41	.	ENSP00000259021:R41Q	R	+	2	0	KAT7	45224353	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	9.448000	0.97600	1.475000	0.48197	0.650000	0.86243	CGA		0.498	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		A	47869354	G	A	47869354	3	1	44	1	0	0	0	0	1	0	0	0	10133	1058	37	1	128	1	MYST2	17	47869354	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	7858210	47869354	33325856	163	4210										
MED13	9969	hgsc.bcm.edu	37	chr17	60060307	60060307	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccaccagctccacgaggagtCcgaggagtccttggagtcct	12	14	0	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:60060307C>A	ENST00000397786.2	-	16	3133	c.3057G>T	c.(3055-3057)cgG>cgT	p.R1019R		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1019					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CACGAGGAGTCCGAGGAGTCC	0.517																																																0			17											66	68	67					17																	60060307		1920	4130	6050	57415089	SO:0001819	synonymous_variant	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.3057G>T	17.37:g.60060307C>A			57415089	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																				0.517	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60060307	C	A	60060307	2	1	44	1	0	0	0	0	0	0	0	1	9460	842	30	2		2	MED13	17	60060307	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	12190953	60060307	21134903	164	4211										
PRKCA	5578	hgsc.bcm.edu	37	chr17	64800031	64800031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctttgacaagttcttcacacGaggacagcccgtcttaacac	7	13	3	1	rs140466753		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:64800031G>A	ENST00000413366.3	+	17	1921	c.1895G>A	c.(1894-1896)cGa>cAa	p.R632Q		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	632	AGC-kinase C-terminal.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	TTCTTCACACGAGGACAGCCC	0.473																																																0			17						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	147	125	132		1895	4.6	0.9	17	dbSNP_134	132	0,8600		0,0,4300	no	missense	PRKCA	NM_002737.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	632/673	64800031	1,13005	2203	4300	6503	62230493	SO:0001583	missense	5578				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1895G>A	17.37:g.64800031G>A	ENSP00000408695:p.Arg632Gln		62230493	B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	37	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834989	0.32421	2.27E-4	0.0	ENSG00000154229	ENST00000413366	T	0.57436	0.4	5.57	4.6	0.57074	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.000000	0.64402	D	0.000001	T	0.48352	0.1495	L	0.52011	1.625	0.52099	D	0.999944	B	0.19583	0.037	B	0.14023	0.01	T	0.46965	-0.9153	10	0.56958	D	0.05	.	14.3942	0.67001	0.0707:0.0:0.9293:0.0	.	632	P17252	KPCA_HUMAN	Q	632	ENSP00000408695:R632Q	ENSP00000408695:R632Q	R	+	2	0	PRKCA	62230493	1.000000	0.71417	0.940000	0.37924	0.307000	0.27823	9.414000	0.97362	1.363000	0.46019	-0.136000	0.14681	CGA		0.473	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1			A	64800031	G	A	64800031	3	1	44	1	0	0	0	0	1	0	0	0	12541	1058	37	1	1961	1	PRKCA	17	64800031	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	4739724	64800031	16395179	165	4212										
SDK2	54549	hgsc.bcm.edu	37	chr17	71382658	71382658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtcattggtcgccttcactCggaacttgtaggacgtgaag	12	9	2	1	rs368464336		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:71382658C>T	ENST00000392650.3	-	31	4424	c.4424G>A	c.(4423-4425)cGa>cAa	p.R1475Q	SDK2_ENST00000388726.3_Missense_Mutation_p.R1475Q	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1475	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CGCCTTCACTCGGAACTTGTA	0.587																																																0			17						C	GLN/ARG	0,4390		0,0,2195	65	48	54		4424	4.1	1	17		54	1,8549		0,1,4274	no	missense	SDK2	NM_001144952.1	43	0,1,6469	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	1475/2173	71382658	1,12939	2195	4275	6470	68894253	SO:0001583	missense	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4424G>A	17.37:g.71382658C>T	ENSP00000376421:p.Arg1475Gln		68894253	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.020236	0.75275	0.0	1.17E-4	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.59772	0.24;0.24;0.24	5.08	4.12	0.48240	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77143	0.4087	M	0.85542	2.76	0.50171	D	0.999855	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.80469	-0.1369	10	0.62326	D	0.03	.	13.1413	0.59436	0.0:0.9216:0.0:0.0784	.	1475;1475;1475	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	Q	1099;1475;1475;651;1475	ENSP00000376421:R1475Q;ENSP00000373378:R1475Q;ENSP00000407098:R651Q	ENSP00000324967:R1475Q	R	-	2	0	SDK2	68894253	1.000000	0.71417	0.996000	0.52242	0.314000	0.28054	7.742000	0.85008	1.154000	0.42482	-0.192000	0.12808	CGA		0.587	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		T	71382658	C	T	71382658	3	4	44	1	0	0	0	0	1	0	0	0	14006	884	31	1	2154	1	SDK2	17	71382658	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	6582627	71382658	9812552	166	4213										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73747128	73747128	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cagctgagctgggctgagccGgctgagaccaacggtgagat	16	10	0	4	rs61735289	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:73747128G>A	ENST00000200181.3	+	30	3916	c.3729G>A	c.(3727-3729)ccG>ccA	p.P1243P	ITGB4_ENST00000339591.3_Silent_p.P1243P|ITGB4_ENST00000579662.1_Silent_p.P1243P|ITGB4_ENST00000449880.2_Silent_p.P1243P|ITGB4_ENST00000450894.3_Silent_p.P1243P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1243	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGCTGAGCCGGCTGAGACCA	0.597													G|||	76	0.0151757	0.0015	0.0173	5008	,	,		22177	0		0.0348	False		,,,				2504	0.0276															0			17						G	,,	30,4376	35.2+/-66.4	0,30,2173	92	85	88		3729,3729,3729	-10.7	0	17	dbSNP_129	88	323,8277	114.2+/-174.2	6,311,3983	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	6,341,6156	AA,AG,GG		3.7558,0.6809,2.7141	,,	1243/1823,1243/1806,1243/1753	73747128	353,12653	2203	4300	6503	71258723	SO:0001819	synonymous_variant	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3729G>A	17.37:g.73747128G>A			71258723	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																				0.597	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73747128	G	A	73747128	2	1	44	1	0	0	0	0	0	0	0	1	7918	1103	39	1		1	ITGB4	17	73747128	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	2364470	73747128	7448082	167	4214										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591811	48591812	+	Frame_Shift_Del	DEL	CC	CC	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agctcctgagtattggtgttCcattgcttactttgaaatgg							TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr18:48591811_48591812delCC	ENST00000342988.3	+	9	1512_1513	c.974_975delCC	c.(973-975)tccfs	p.S325fs	SMAD4_ENST00000398417.2_Frame_Shift_Del_p.S325fs|SMAD4_ENST00000588745.1_Frame_Shift_Del_p.S229fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	325	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.W323fs*11(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TATTGGTGTTCCATTGCTTACT	0.421																																																39	Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|small_intestine(1)|oesophagus(1)	18																																								46845810	SO:0001589	frameshift_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.974_975delCC	18.37:g.48591811_48591812delCC	ENSP00000341551:p.Ser325fs		46845809	A8K405	Frame_Shift_Del	DEL	ENST00000342988.3	37	CCDS11950.1																																																																																				0.421	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		-	48591812	CC	-	48591811	7	5	44	1	0	1	0	1	0	0	0	0	14797	855	30	0	1004	0	SMAD4	18	48591811	Frame_Shift_Del	DEL	CC	TCGA-AG-3885-01A-01W-0899-10		48591811	29485437	168	4215										
ATP9B	374868	hgsc.bcm.edu	37	chr18	77063654	77063654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agcggctgcacctgggcaccGtgtcctatggcgccgacacg	14	15	0	0	rs201117656		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr18:77063654G>A	ENST00000426216.2	+	14	1479	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	ATP9B_ENST00000307671.7_Missense_Mutation_p.V488M	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	488					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CCTGGGCACCGTGTCCTATGG	0.552													G|||	1	0.000199681	0	0.0014	5008	,	,		17828	0		0	False		,,,				2504	0															0			18											90	80	83					18																	77063654		2203	4300	6503	75164642	SO:0001583	missense	374868			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1462G>A	18.37:g.77063654G>A	ENSP00000398076:p.Val488Met		75164642	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	19.34	3.808632	0.70797	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	T;T	0.65364	-0.15;-0.15	4.94	4.94	0.65067	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.063082	0.64402	D	0.000007	T	0.78059	0.4224	M	0.71581	2.175	0.80722	D	1	D;D	0.60575	0.988;0.985	D;D	0.66847	0.947;0.911	T	0.79455	-0.1796	10	0.52906	T	0.07	.	18.5557	0.91083	0.0:0.0:1.0:0.0	.	488;488	O43861;O43861-2	ATP9B_HUMAN;.	M	488	ENSP00000398076:V488M;ENSP00000304500:V488M	ENSP00000304500:V488M	V	+	1	0	ATP9B	75164642	1.000000	0.71417	0.637000	0.29366	0.564000	0.35744	9.057000	0.93889	2.435000	0.82474	0.655000	0.94253	GTG		0.552	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531		A	77063654	G	A	77063654	3	1	44	1	0	0	0	0	1	0	0	0	1200	1145	40	1	1516	1	ATP9B	18	77063654	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	28471843	77063654	1013594	169	4216										
MOBKL2A	126308	hgsc.bcm.edu	37	chr19	2078488	2078488	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agctcgaagcgctgggtgccTggctcaaacttgcgcttggg	15	11	1	0	rs2074894	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:2078488T>C	ENST00000357066.3	-	3	451	c.72A>G	c.(70-72)ccA>ccG	p.P24P	MOB3A_ENST00000592280.1_Silent_p.P24P|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	24						intracellular (GO:0005622)	metal ion binding (GO:0046872)										GCTGGGTGCCTGGCTCAAACT	0.627													C|||	1973	0.39397	0.6528	0.2507	5008	,	,		16431	0.1835		0.329	False		,,,				2504	0.4294															0			19						C		2793,1613	497.7+/-363.9	887,1019,297	55	57	56		72	-8.5	0	19	dbSNP_96	56	2932,5668	665.8+/-402.3	506,1920,1874	no	coding-synonymous	MOB3A	NM_130807.2		1393,2939,2171	CC,CT,TT		34.093,36.6092,44.0181		24/218	2078488	5725,7281	2203	4300	6503	2029488	SO:0001819	synonymous_variant	126308			AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.72A>G	19.37:g.2078488T>C			2029488	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																				0.627	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		C	2078488	T	C	2078488	2	2	44	1	0	0	0	0	0	0	0	1	9714	1567	55	4		4	MOBKL2A	19	2078488	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10		2078488	57050495	170	4217										
MRPL4	51073	hgsc.bcm.edu	37	chr19	10363280	10363280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcccggtacccactcatcgaCgcccagtgcaggcctgggtc	11	17	1	0	rs45520838	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:10363280C>T	ENST00000253099.6	+	3	465	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	MRPL4_ENST00000588502.1_Missense_Mutation_p.R59C|MRPL4_ENST00000307422.5_Missense_Mutation_p.R60C|MRPL4_ENST00000590669.1_Missense_Mutation_p.R60C|MRPL4_ENST00000393733.2_Missense_Mutation_p.R60C|CTD-2369P2.5_ENST00000592893.1_RNA	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	60					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		CACTCATCGACGCCCAGTGCA	0.682													C|||	9	0.00179712	0	0.0029	5008	,	,		16320	0		0.006	False		,,,				2504	0.001															0			19						C	CYS/ARG,CYS/ARG,CYS/ARG	3,4403		0,3,2200	37	41	39		178,178,178	1.4	0	19	dbSNP_127	39	44,8556		0,44,4256	yes	missense,missense,missense	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	180,180,180	0,47,6456	TT,TC,CC		0.5116,0.0681,0.3614	probably-damaging,probably-damaging,probably-damaging	60/312,60/312,60/264	10363280	47,12959	2203	4300	6503	10224280	SO:0001583	missense	51073			AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"Mitochondrial ribosomal proteins / large subunits"	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.178C>T	19.37:g.10363280C>T	ENSP00000253099:p.Arg60Cys		10224280	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.21	3.572904	0.65765	6.81E-4	0.005116	ENSG00000105364	ENST00000253099;ENST00000307422;ENST00000393733	.	.	.	4.89	1.37	0.22104	.	0.341831	0.30118	N	0.010366	T	0.31575	0.0801	L	0.47716	1.5	0.09310	N	1	D;D	0.71674	0.998;0.989	P;P	0.59825	0.864;0.613	T	0.08513	-1.0718	9	0.59425	D	0.04	-19.6719	3.669	0.08266	0.3659:0.443:0.0:0.1911	rs45520838	60;60	Q9BYD3-2;Q9BYD3	.;RM04_HUMAN	C	60	.	ENSP00000253099:R60C	R	+	1	0	MRPL4	10224280	0.177000	0.23109	0.014000	0.15608	0.044000	0.14063	0.602000	0.24134	0.650000	0.30769	-0.320000	0.08662	CGC		0.682	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1			T	10363280	C	T	10363280	3	4	44	1	0	0	0	0	1	0	0	0	9833	536	19	1	188	1	MRPL4	19	10363280	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	8284792	10363280	48765703	171	4218										
FDX1L	112812	hgsc.bcm.edu	37	chr19	10421229	10421229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcttgggcagggtgaattccGctccttccagctccggtgtc	12	13	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:10421229G>A	ENST00000393708.3	-	5	503	c.485C>T	c.(484-486)gCg>gTg	p.A162V	ZGLP1_ENST00000403903.3_5'Flank|FDX1L_ENST00000494368.1_Missense_Mutation_p.A27V|FDX1L_ENST00000541276.1_3'UTR|ZGLP1_ENST00000403352.1_5'Flank|FDX1L_ENST00000492239.1_5'UTR|CTD-2369P2.10_ENST00000452032.2_3'UTR	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	162	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			GGTGAATTCCGCTCCTTCCAG	0.592																																																0			19											127	102	111					19																	10421229		2203	4300	6503	10282229	SO:0001583	missense	112812			AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.485C>T	19.37:g.10421229G>A	ENSP00000377311:p.Ala162Val		10282229	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	37	CCDS32905.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534889	0.27475	.	.	ENSG00000167807	ENST00000393708	.	.	.	4.25	2.02	0.26589	Beta-grasp fold, ferredoxin-type (1);Ferredoxin (2);	0.350657	0.29544	N	0.011852	T	0.16300	0.0392	N	0.05158	-0.105	0.20489	N	0.999894	B	0.15141	0.012	B	0.09377	0.004	T	0.16837	-1.0389	9	0.41790	T	0.15	-2.5169	8.0535	0.30591	0.2087:0.0:0.7913:0.0	.	162	Q6P4F2	ADXL_HUMAN	V	162	.	ENSP00000377311:A162V	A	-	2	0	FDX1L	10282229	0.982000	0.34865	0.756000	0.31282	0.964000	0.63967	2.177000	0.42509	0.738000	0.32606	0.555000	0.69702	GCG		0.592	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2			A	10421229	G	A	10421229	3	1	44	1	0	0	0	0	1	0	0	0	5824	1087	38	1	70	1	FDX1L	19	10421229	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	57949	10421229	48707754	172	4219										
ACP5	54	hgsc.bcm.edu	37	chr19	11687604	11687604	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtcatggtttccggctagcaCgtaccagggcactttgcgaa	12	11	1	0	rs148219285		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:11687604C>T	ENST00000592828.1	-	5	718	c.316G>A	c.(316-318)Gtg>Atg	p.V106M	ACP5_ENST00000590420.1_Intron|ACP5_ENST00000433365.2_Missense_Mutation_p.V106M|ACP5_ENST00000218758.5_Missense_Mutation_p.V106M|ACP5_ENST00000412435.2_Missense_Mutation_p.V106M	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	106					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						CCGGCTAGCACGTACCAGGGC	0.572													C|||	1	0.000199681	0	0	5008	,	,		19155	0.001		0	False		,,,				2504	0															0			19						C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	171	157	162		316,316,316,316	3.8	1	19	dbSNP_134	162	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	21,21,21,21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign	106/326,106/326,106/326,106/326	11687604	3,13003	2203	4300	6503	11548604	SO:0001583	missense	54			X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"tartrate-resistant acid phosphatase"	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.316G>A	19.37:g.11687604C>T	ENSP00000468767:p.Val106Met		11548604	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Missense_Mutation	SNP	ENST00000592828.1	37	CCDS12265.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	13.64	2.298854	0.40694	0.0	3.49E-4	ENSG00000102575	ENST00000218758;ENST00000412435;ENST00000433365	D;D;D	0.85629	-2.01;-2.01;-2.01	4.87	3.82	0.43975	Metallophosphoesterase domain (1);	0.060473	0.64402	D	0.000003	D	0.82508	0.5052	L	0.49571	1.57	0.80722	D	1	D	0.55800	0.973	P	0.48227	0.571	T	0.80984	-0.1138	10	0.51188	T	0.08	-18.9338	7.8633	0.29522	0.0:0.7462:0.1652:0.0886	.	106	P13686	PPA5_HUMAN	M	106	ENSP00000218758:V106M;ENSP00000392374:V106M;ENSP00000413456:V106M	ENSP00000218758:V106M	V	-	1	0	ACP5	11548604	0.937000	0.31787	0.991000	0.47740	0.007000	0.05969	1.984000	0.40658	1.021000	0.39600	-0.175000	0.13238	GTG		0.572	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1			T	11687604	C	T	11687604	3	4	44	1	0	0	0	0	1	0	0	0	164	536	19	1	673	1	ACP5	19	11687604	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	1266375	11687604	47441379	173	4220										
ZNF43	7594	hgsc.bcm.edu	37	chr19	21992107	21992108	+	Missense_Mutation	DNP	GC	GC	AA													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ttttttttatgtgtagtaagGcgtgaggaccaattaaagac					rs201159112		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:21992107_21992108GC>AA	ENST00000354959.4	-	4	900_901	c.731_732GC>TT	c.(730-732)cGC>cTT	p.R244L	ZNF43_ENST00000594012.1_Missense_Mutation_p.R238L|ZNF43_ENST00000595461.1_Missense_Mutation_p.R238L|ZNF43_ENST00000598381.1_Missense_Mutation_p.R238L	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	244			R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GTGTAGTAAGGCGTGAGGACCA	0.347																																																0			19																																								21783947|21783948	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.731_732delinsAA	19.37:g.21992107_21992108delinsAA	ENSP00000347045:p.Arg244Leu		21783947|21783948	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent|Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2																																																																																				0.347	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		AA	21992108	GC	AA	21992107	3	1	44	1	0	0	0	0	1	0	0	0	17942	1190	42	3	1701	3	ZNF43	19	21992107	Missense_Mutation	DNP	GC	TCGA-AG-3885-01A-01W-0899-10	10304503	21992107	37136876	174	4221										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40420087	40420087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccaaagtccgtgcgcacgacGgcatccctgccctgtcggaa	11	16	0	0	rs12460562	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:40420087G>A	ENST00000221347.6	-	6	2914	c.2907C>T	c.(2905-2907)gcC>gcT	p.A969A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	969	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			TGCGCACGACGGCATCCCTGC	0.597													G|||	694	0.138578	0.0129	0.3329	5008	,	,		20473	0.0417		0.1998	False		,,,				2504	0.2076															0			19						G		208,4198	126.6+/-163.6	7,194,2002	62	58	60		2907	-9.7	0	19	dbSNP_120	60	1795,6805	321.8+/-315.3	192,1411,2697	no	coding-synonymous	FCGBP	NM_003890.2		199,1605,4699	AA,AG,GG		20.8721,4.7208,15.4006		969/5406	40420087	2003,11003	2203	4300	6503	45111927	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.2907C>T	19.37:g.40420087G>A			45111927	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40420087	G	A	40420087	2	1	44	1	0	0	0	0	0	0	0	1	5797	1103	39	1		1	FCGBP	19	40420087	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	18427980	40420087	18708896	175	4222										
CYP2S1	29785	hgsc.bcm.edu	37	chr19	41709382	41709382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acgtgaggagctgaatcgggAgctgggggctggccaggcac	19	9	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:41709382A>G	ENST00000310054.4	+	7	1220	c.1004A>G	c.(1003-1005)gAg>gGg	p.E335G	CYP2S1_ENST00000542619.1_Missense_Mutation_p.E60G	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	335					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						CTGAATCGGGAGCTGGGGGCT	0.667																																																0			19											32	31	31					19																	41709382		2202	4300	6502	46401222	SO:0001583	missense	29785			AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"Cytochrome P450s"	15654	protein-coding gene	gene with protein product		611529	"cytochrome P450, subfamily IIS, polypeptide 1"			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.1004A>G	19.37:g.41709382A>G	ENSP00000308032:p.Glu335Gly		46401222	Q9BZ66	Missense_Mutation	SNP	ENST00000310054.4	37	CCDS12573.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.989338	0.53934	.	.	ENSG00000167600	ENST00000301173;ENST00000310054;ENST00000542619	T;T	0.68181	-0.31;-0.31	5.02	3.93	0.45458	.	0.420777	0.22160	N	0.063798	T	0.73225	0.3560	L	0.55481	1.735	0.29838	N	0.829493	B;D	0.71674	0.093;0.998	B;D	0.67382	0.102;0.951	T	0.69544	-0.5117	10	0.87932	D	0	.	7.343	0.26648	0.6839:0.0:0.0:0.3161	.	60;335	B4DJI0;Q96SQ9	.;CP2S1_HUMAN	G	335;335;60	ENSP00000308032:E335G;ENSP00000445299:E60G	ENSP00000301173:E335G	E	+	2	0	CYP2S1	46401222	0.999000	0.42202	0.998000	0.56505	0.721000	0.41392	1.901000	0.39838	1.896000	0.54893	0.449000	0.29647	GAG		0.667	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1			G	41709382	A	G	41709382	3	3	44	1	0	0	0	0	1	0	0	0	4180	304	11	4	1030	4	CYP2S1	19	41709382	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	1289295	41709382	17419601	176	4223										
HAS1	3036	hgsc.bcm.edu	37	chr19	52217338	52217338	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agggcgtctctgagtagcagCgggacctggaggtgtacctg	17	9	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:52217338C>T	ENST00000222115.1	-	5	1113	c.1079G>A	c.(1078-1080)cGc>cAc	p.R360H	HAS1_ENST00000540069.2_Missense_Mutation_p.R359H|HAS1_ENST00000594621.1_Silent_p.P189P|HAS1_ENST00000601714.1_Missense_Mutation_p.R367H	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	360					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGAGTAGCAGCGGGACCTGGA	0.632																																					NSCLC(132;636 2450 45807 47979)											0			19											30	20	23					19																	52217338		2202	4297	6499	56909150	SO:0001583	missense	3036			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1079G>A	19.37:g.52217338C>T	ENSP00000222115:p.Arg360His		56909150	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	2.471|2.471	-0.321898|-0.321898	0.05386|0.05386	.|.	.|.	ENSG00000105509|ENSG00000105509	ENST00000376737|ENST00000540069;ENST00000222115	.|T;T	.|0.43294	.|0.95;0.95	2.98|2.98	2.98|2.98	0.34508|0.34508	.|.	.|0.159749	.|0.38111	.|U	.|0.001811	T|T	0.30727|0.30727	0.0774|0.0774	M|M	0.63428|0.63428	1.95|1.95	0.26810|0.26810	N|N	0.969013|0.969013	.|P;P;P	.|0.36048	.|0.478;0.534;0.534	.|B;B;B	.|0.31547	.|0.052;0.132;0.132	T|T	0.09400|0.09400	-1.0676|-1.0676	6|10	0.56958|0.15499	D|T	0.05|0.54	.|.	6.0486|6.0486	0.19773|0.19773	0.0:0.8529:0.0:0.1471|0.0:0.8529:0.0:0.1471	.|.	.|359;360;359	.|G3V1S7;Q92839;Q8IYH3	.|.;HAS1_HUMAN;.	T|H	173|359;360	.|ENSP00000445021:R359H;ENSP00000222115:R360H	ENSP00000365927:A173T|ENSP00000222115:R360H	A|R	-|-	1|2	0|0	HAS1|HAS1	56909150|56909150	0.614000|0.614000	0.27017|0.27017	0.893000|0.893000	0.35052|0.35052	0.020000|0.020000	0.10135|0.10135	1.058000|1.058000	0.30504|0.30504	1.693000|1.693000	0.51124|0.51124	0.174000|0.174000	0.16983|0.16983	GCT|CGC		0.632	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		T	52217338	C	T	52217338	3	4	44	1	0	0	0	0	1	0	0	0	6982	768	27	1	661	1	HAS1	19	52217338	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	10507956	52217338	6911645	177	4224										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53116934	53117017	+	In_Frame_Del	DEL	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	-													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	acttgtgactgaagaccttgCcacactcattacatttgtaa					rs78562523|rs573424533|rs561268356|rs575275768|rs542853549|rs7248435|rs201794892|rs557033862|rs144905073|rs560464978|rs199821089|rs201460258|rs542573550|rs201157018|rs199590691|rs556550175|rs367946778|rs146207784|rs200250390|rs7247691|rs7247690|rs113015820|rs75857698|rs78207921|rs140513277	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENST00000597597.1	-	2	3054_3137	c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	c.(799-885)ggaaaggtcttccatcatatttcacaccttgcacaacatcagagaatccacactggagagaaaccttacaaatgtaatgagtgtggc>ggc	p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G	ZNF83_ENST00000536937.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000391789.4_Splice_Site_p.KV268del|ZNF83_ENST00000545872.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000541777.2_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000301096.3_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000544146.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G			P51522	ZNF83_HUMAN	zinc finger protein 83	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GAAGACCTTGCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTTCCACATACAT	0.405																																																0			19							,,,,,,,,	1161,3099		263,635,1232					,,,,,,,,	-2.2	0			87	1473,6779		168,1137,2821	no	coding,coding-near-splice,coding-near-splice,coding-near-splice,coding-near-splice,coding,coding,coding,coding	ZNF83	NM_018300.3,NM_001242538.1,NM_001242531.1,NM_001105554.1,NM_001105553.1,NM_001105552.1,NM_001105551.1,NM_001105550.1,NM_001105549.1	,,,,,,,,	431,1772,4053	A1A1,A1R,RR		17.8502,27.2535,21.0518	,,,,,,,,	,,,,,,,,		2634,9878				57808829	SO:0001651	inframe_deletion	55769			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	19.37:g.53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENSP00000472619:p.Gly267_Cys294del		57808746	A8MT75|Q3ZCX0|Q6PI08	In_Frame_Del	DEL	ENST00000597597.1	37	CCDS12854.1																																																																																				0.405	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		-	53117017	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	-	53116934	7	5	44	1	0	1	0	1	0	0	0	0	18222	739	26	0	670	0	ZNF83	19	53116934	In_Frame_Del	DEL	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	TCGA-AG-3885-01A-01W-0899-10	899596	53116934	6012049	178	4225										
ZNF329	79673	hgsc.bcm.edu	37	chr19	58639353	58639353	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	caccggctgggaccctccctGctatggagtctctgatgtac	11	14	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:58639353G>A	ENST00000598312.1	-	4	1751	c.1518C>T	c.(1516-1518)agC>agT	p.S506S	ZNF329_ENST00000358067.4_Silent_p.S506S	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		GACCCTCCCTGCTATGGAGTC	0.512																																																0			19											134	129	131					19																	58639353		2203	4300	6503	63331165	SO:0001819	synonymous_variant	79673			AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"Zinc fingers, C2H2-type"	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1518C>T	19.37:g.58639353G>A			63331165	B3KR32|Q9H9R7	Silent	SNP	ENST00000598312.1	37	CCDS12972.1																																																																																				0.512	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620		A	58639353	G	A	58639353	2	1	44	1	0	0	0	0	0	0	0	1	17886	1310	46	3		3	ZNF329	19	58639353	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	5522419	58639353	489630	179	4226										
CST9	128822	hgsc.bcm.edu	37	chr20	23586266	23586266	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cctttctgtccatgctatccTccctccatgaactcaggacg	6	16	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:23586266T>C	ENST00000376971.3	-	1	247	c.236A>G	c.(235-237)gAg>gGg	p.E79G		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	79						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					CATGCTATCCTCCCTCCATGA	0.532																																																0			20											249	179	203					20																	23586266		2203	4300	6503	23534266	SO:0001583	missense	128822			AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.236A>G	20.37:g.23586266T>C	ENSP00000366170:p.Glu79Gly		23534266	B2RP76|Q8TD53	Missense_Mutation	SNP	ENST00000376971.3	37	CCDS33450.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022710	0.35701	.	.	ENSG00000173335	ENST00000376971	T	0.22134	1.97	2.85	1.68	0.24146	Proteinase inhibitor I25, cystatin (1);	.	.	.	.	T	0.35158	0.0922	L	0.55213	1.73	0.09310	N	1	D	0.89917	1.0	D	0.77004	0.989	T	0.09335	-1.0679	9	0.87932	D	0	.	4.925	0.13889	0.2874:0.0:0.0:0.7126	.	79	Q5W186	CST9_HUMAN	G	79	ENSP00000366170:E79G	ENSP00000366170:E79G	E	-	2	0	CST9	23534266	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.669000	0.25142	0.469000	0.27268	0.482000	0.46254	GAG		0.532	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1		C	23586266	T	C	23586266	3	2	44	1	0	0	0	0	1	0	0	0	3985	1551	54	4	251	4	CST9	20	23586266	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		23586266	39439254	180	4227										
TP53INP2	58476	hgsc.bcm.edu	37	chr20	33296656	33296656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agtggacggctggctcatcaTtgacctgccgggtgaggcct	15	11	2	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:33296656T>C	ENST00000374810.3	+	3	502	c.113T>C	c.(112-114)aTt>aCt	p.I38T	NCOA6_ENST00000593786.1_Intron|TP53INP2_ENST00000374809.2_Missense_Mutation_p.I38T	NM_021202.1	NP_067025.1	Q8IXH6	T53I2_HUMAN	tumor protein p53 inducible nuclear protein 2	38					autophagic vacuole assembly (GO:0000045)|osteoblast differentiation (GO:0001649)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(1)|urinary_tract(1)	2						TGGCTCATCATTGACCTGCCG	0.662																																																0			20											43	42	42					20																	33296656		2202	4300	6502	32760317	SO:0001583	missense	58476			AL109824	CCDS13240.1	20q11.22	2010-01-05	2004-06-18	2004-06-18	ENSG00000078804	ENSG00000078804			16104	protein-coding gene	gene with protein product	"diabetes and obesity regulated"		"chromosome 20 open reading frame 110"	C20orf110		12477932	Standard	NM_021202		Approved	FLJ21759, FLJ23500, DKFZp434B2411, DKFZp434O0827, dJ1181N3.1, PINH, DOR	uc002xau.1	Q8IXH6	OTTHUMG00000032310	ENST00000374810.3:c.113T>C	20.37:g.33296656T>C	ENSP00000363943:p.Ile38Thr		32760317	A8K8S8|E1P5P6|Q5JX64|Q8IYL5|Q9NU00	Missense_Mutation	SNP	ENST00000374810.3	37	CCDS13240.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.151371	0.78001	.	.	ENSG00000078804	ENST00000374810;ENST00000374809;ENST00000451665;ENST00000414082	T;T;T;T	0.52754	0.65;0.65;1.48;0.65	4.74	4.74	0.60224	.	0.063894	0.64402	D	0.000009	T	0.61590	0.2359	L	0.52573	1.65	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	T	0.65520	-0.6148	10	0.87932	D	0	-7.3787	14.1776	0.65552	0.0:0.0:0.0:1.0	.	38	Q8IXH6	T53I2_HUMAN	T	38	ENSP00000363943:I38T;ENSP00000363942:I38T;ENSP00000395784:I38T;ENSP00000404410:I38T	ENSP00000363942:I38T	I	+	2	0	TP53INP2	32760317	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.082000	0.71318	1.894000	0.54839	0.454000	0.30748	ATT		0.662	TP53INP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078807.2	NM_021202		C	33296656	T	C	33296656	3	2	44	1	0	0	0	0	1	0	0	0	16429	1493	52	4	115	4	TP53INP2	20	33296656	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	9710390	33296656	29728864	181	4228										
PHF20	51230	hgsc.bcm.edu	37	chr20	34459662	34459662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	atccggggctgcaggcttggAgttgaactgcccatcaatgg	14	10	1	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:34459662A>G	ENST00000374012.3	+	9	1322	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	398					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					GCAGGCTTGGAGTTGAACTGC	0.483																																																0			20											122	122	122					20																	34459662		2203	4300	6503	33923076	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1193A>G	20.37:g.34459662A>G	ENSP00000363124:p.Glu398Gly		33923076	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.651858	0.29336	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.46819	1.42;0.86;0.86	5.56	3.29	0.37713	.	0.499842	0.21368	N	0.075696	T	0.23688	0.0573	N	0.08118	0	0.58432	D	0.999994	B;B	0.25667	0.131;0.003	B;B	0.22386	0.039;0.001	T	0.05649	-1.0872	10	0.48119	T	0.1	.	5.1478	0.14994	0.7244:0.1839:0.0916:0.0	.	398;398	Q9BVI0;Q66K49	PHF20_HUMAN;.	G	398	ENSP00000363124:E398G;ENSP00000341900:E398G;ENSP00000363112:E398G	ENSP00000341900:E398G	E	+	2	0	PHF20	33923076	0.956000	0.32656	0.990000	0.47175	0.752000	0.42762	1.482000	0.35486	0.916000	0.36871	0.482000	0.46254	GAG		0.483	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		G	34459662	A	G	34459662	3	3	44	1	0	0	0	0	1	0	0	0	11862	304	11	4	1223	4	PHF20	20	34459662	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10	1163006	34459662	28565858	182	4229										
HNF4A	3172	hgsc.bcm.edu	37	chr20	43034729	43034729	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tcagaaggcaccaacctcaaCgcgcccaacagcctgggtgt	10	15	2	1	rs570058788		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:43034729C>T	ENST00000316099.4	+	2	236	c.147C>T	c.(145-147)aaC>aaT	p.N49N	HNF4A_ENST00000316673.4_Silent_p.N27N|HNF4A_ENST00000609795.1_Silent_p.N27N|HNF4A_ENST00000457232.1_Silent_p.N27N|MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000443598.2_Silent_p.N49N|HNF4A_ENST00000415691.2_Silent_p.N49N	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	49					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CCAACCTCAACGCGCCCAACA	0.627																																					Colon(79;2 1269 8820 14841 52347)											0			20											143	142	142					20																	43034729		2203	4300	6503	42468143	SO:0001819	synonymous_variant	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.147C>T	20.37:g.43034729C>T			42468143	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Silent	SNP	ENST00000316099.4	37	CCDS13330.1																																																																																				0.627	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43034729	C	T	43034729	2	4	44	1	0	0	0	0	0	0	0	1	7274	535	19	1		1	HNF4A	20	43034729	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	8575067	43034729	19990791	183	4230										
GCFC1	94104	hgsc.bcm.edu	37	chr21	34121003	34121003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ctttgccggattcttttgaaAttcgatctaaaaacaacaaa	5	8	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:34121003A>G	ENST00000331923.4	-	11	1919	c.1730T>C	c.(1729-1731)aTt>aCt	p.I577T	PAXBP1_ENST00000290178.4_Missense_Mutation_p.I577T	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	577					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTCTTTTGAAATTCGATCTAA	0.328																																																0			21											40	42	41					21																	34121003		2202	4300	6502	33042874	SO:0001583	missense	0			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1730T>C	21.37:g.34121003A>G	ENSP00000328992:p.Ile577Thr		33042874	D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082603	0.76528	.	.	ENSG00000159086	ENST00000331923;ENST00000290178	T;T	0.37411	1.64;1.2	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.58352	0.2116	M	0.70275	2.135	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.997	D;D;P	0.66084	0.937;0.941;0.879	T	0.61441	-0.7062	10	0.59425	D	0.04	-19.3128	15.5492	0.76133	1.0:0.0:0.0:0.0	.	577;577;86	Q9Y5B6-2;Q9Y5B6;B3KSC0	.;GCFC1_HUMAN;.	T	577	ENSP00000328992:I577T;ENSP00000290178:I577T	ENSP00000290178:I577T	I	-	2	0	GCFC1	33042874	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.962000	0.93254	2.154000	0.67381	0.455000	0.32223	ATT		0.328	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		G	34121003	A	G	34121003	3	3	44	1	0	0	0	0	1	0	0	0	6309	101	4	4	1173	4	GCFC1	21	34121003	Missense_Mutation	SNP	A	TCGA-AG-3885-01A-01W-0899-10		34121003	14008892	184	4231										
CBS	875	hgsc.bcm.edu	37	chr21	44478973	44478973	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tccaccacgggcgcctggtcGaagcccttctcccggaggat	12	16	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:44478973G>A	ENST00000398165.3	-	14	1588	c.1329C>T	c.(1327-1329)ttC>ttT	p.F443F	CBS_ENST00000398158.1_Silent_p.F443F|CBS_ENST00000544202.1_Silent_p.F355F|CBS_ENST00000352178.5_Silent_p.F443F|CBS_ENST00000398168.1_Silent_p.F443F|CBS_ENST00000359624.3_Silent_p.F443F	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	443	CBS. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	GCGCCTGGTCGAAGCCCTTCT	0.662																																																0			21											37	35	36					21																	44478973		2178	4275	6453	43352042	SO:0001819	synonymous_variant	875			L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1329C>T	21.37:g.44478973G>A			43352042	B2R993|D3DSK4|Q99425|Q9BWC5	Silent	SNP	ENST00000398165.3	37	CCDS13693.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.962|9.962	1.222963|1.222963	0.22457|0.22457	.|.	.|.	ENSG00000160200|ENSG00000160200	ENST00000451248|ENST00000458223;ENST00000430013	.|.	.|.	.|.	4.71|4.71	-1.92|-1.92	0.07618|0.07618	.|.	.|.	.|.	.|.	.|.	.|T	.|0.55226	.|0.1907	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.50759	.|-0.8790	.|4	.|.	.|.	.|.	-27.3713|-27.3713	10.1165|10.1165	0.42593|0.42593	0.4423:0.0:0.5577:0.0|0.4423:0.0:0.5577:0.0	.|.	.|.	.|.	.|.	X|L	27|31;97	.|.	.|.	R|S	-|-	1|2	2|0	CBS|CBS	43352042|43352042	0.833000|0.833000	0.29383|0.29383	0.989000|0.989000	0.46669|0.46669	0.882000|0.882000	0.50991|0.50991	-0.118000|-0.118000	0.10692|0.10692	-0.440000|-0.440000	0.07211|0.07211	-0.259000|-0.259000	0.10710|0.10710	CGA|TCG		0.662	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		A	44478973	G	A	44478973	2	1	44	1	0	0	0	0	0	0	0	1	2717	1049	37	1		1	CBS	21	44478973	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	10357970	44478973	3650922	185	4232										
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057593	46057593	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gccagccggattgctgcaccTcctccccctgccagcaggcc	10	20	0	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:46057593T>C	ENST00000380095.1	+	1	321	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	87	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TTGCTGCACCTCCTCCCcctg	0.642																																																0			21											121	115	117					21																	46057593		2203	4300	6503	44882021	SO:0001583	missense	353333			AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"Keratin associated proteins"	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.259T>C	21.37:g.46057593T>C	ENSP00000369438:p.Ser87Pro		44882021		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	t	1.645	-0.515362	0.04200	.	.	ENSG00000221859	ENST00000380095	T	0.01304	5.03	3.33	-0.376	0.12505	.	.	.	.	.	T	0.01189	0.0039	L	0.39326	1.205	0.09310	N	1	B	0.15719	0.014	B	0.12837	0.008	T	0.49234	-0.8961	9	0.14252	T	0.57	.	2.6435	0.04978	0.2295:0.3936:0.0:0.377	.	87	P60014	KR10A_HUMAN	P	87	ENSP00000369438:S87P	ENSP00000369438:S87P	S	+	1	0	KRTAP10-10	44882021	0.000000	0.05858	0.380000	0.26093	0.077000	0.17291	-0.131000	0.10482	0.302000	0.22762	0.383000	0.25322	TCC		0.642	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		C	46057593	T	C	46057593	3	2	44	1	0	0	0	0	1	0	0	0	8527	1551	54	4	261	4	KRTAP10-10	21	46057593	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	1578620	46057593	2072302	186	4233										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47418339	47418339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cgggcaacaggggcgctcccGggataaacgtgagtacgccc	15	13	0	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:47418339G>A	ENST00000361866.3	+	24	1717	c.1603G>A	c.(1603-1605)Ggg>Agg	p.G535R		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	535	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GGGCGCTCCCGGGATAAACGT	0.597																																																0			21											61	60	61					21																	47418339		2203	4300	6503	46242767	SO:0001583	missense	1291			M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1603G>A	21.37:g.47418339G>A	ENSP00000355180:p.Gly535Arg		46242767	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451208	0.63290	.	.	ENSG00000142156	ENST00000361866;ENST00000538397	D	0.99353	-5.77	4.01	4.01	0.46588	.	0.135083	0.49305	D	0.000159	D	0.99674	0.9878	H	0.99169	4.455	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.97174	0.9846	10	0.87932	D	0	-9.0733	13.2368	0.59974	0.0:0.0:1.0:0.0	.	535	P12109	CO6A1_HUMAN	R	535	ENSP00000355180:G535R	ENSP00000355180:G535R	G	+	1	0	COL6A1	46242767	1.000000	0.71417	0.821000	0.32701	0.503000	0.33858	2.817000	0.48034	1.963000	0.57068	0.205000	0.17691	GGG		0.597	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47418339	G	A	47418339	3	1	44	1	0	0	0	0	1	0	0	0	3705	1116	39	1	1697	1	COL6A1	21	47418339	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	1360746	47418339	711556	187	4234										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885564	29885564	+	Silent	SNP	A	A	G													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	aagtctccaacgaaggaggaAgcaaagtcccctgagaaggc					rs202065964|rs371230849		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr22:29885564A>G	ENST00000310624.6	+	4	1968	c.1935A>G	c.(1933-1935)gaA>gaG	p.E645E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CGAAGGAGGAAGCAAAGTCCC	0.562																																																0			22											83	89	87					22																	29885564		2203	4300	6503	28215564	SO:0001819	synonymous_variant	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1935A>G	22.37:g.29885564A>G			28215564	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																				0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		G	29885564	A	G	29885564	2	3	44	1	0	0	0	0	0	0	0	1	10345	69	3	4		4	NEFH	22	29885564	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10		29885564	21419002	188	4235	19	2								
NEFH	4744	hgsc.bcm.edu	37	chr22	29885567	29885567	+	Silent	SNP	A	A	C													0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tctccaacgaaggaggaagcAaagtcccctgagaaggccaa					rs147489453|rs75808076|rs59279731		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr22:29885567A>C	ENST00000310624.6	+	4	1971	c.1938A>C	c.(1936-1938)gcA>gcC	p.A646A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	652	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTG	0.567																																																0			22											78	77	77					22																	29885567		2133	4127	6260	28215567	SO:0001819	synonymous_variant	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1938A>C	22.37:g.29885567A>C			28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																				0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885567	A	C	29885567	2	2	44	1	0	0	0	0	0	0	0	1	10345	117	5	4		4	NEFH	22	29885567	Silent	SNP	A	TCGA-AG-3885-01A-01W-0899-10	3	29885567	21418999	189	4236	19	2								
AMELX	265	hgsc.bcm.edu	37	chrX	11316978	11316978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgtgcaccccatgcagccccTgccgccacagccacctctgc	8	21	1	0			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:11316978T>C	ENST00000380714.3	+	5	523	c.455T>C	c.(454-456)cTg>cCg	p.L152P	ARHGAP6_ENST00000413512.3_Intron|AMELX_ENST00000380712.3_Missense_Mutation_p.L166P|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000380718.1_Intron|AMELX_ENST00000348912.4_Missense_Mutation_p.L136P|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000380736.1_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	152					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						ATGCAGCCCCTGCCGCCACAG	0.662																																																0			X											47	41	43					X																	11316978		2203	4300	6503	11226899	SO:0001583	missense	265				CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"amelogenesis imperfecta 1"	300391	"amelogenin (X chromosome, amelogenesis imperfecta 1)"	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.455T>C	X.37:g.11316978T>C	ENSP00000370090:p.Leu152Pro		11226899	Q96NW6|Q9UCA7	Missense_Mutation	SNP	ENST00000380714.3	37	CCDS14144.1	.	.	.	.	.	.	.	.	.	.	T	10.46	1.357285	0.24598	.	.	ENSG00000125363	ENST00000380714;ENST00000380712;ENST00000348912	D;D;D	0.89123	-2.47;-2.47;-2.47	4.79	3.62	0.41486	.	0.616605	0.14622	N	0.308371	D	0.85396	0.5687	M	0.68952	2.095	0.34886	D	0.745065	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.005;0.003	D	0.84731	0.0745	10	0.51188	T	0.08	-2.7216	5.0054	0.14286	0.0:0.1001:0.1851:0.7148	.	136;152;166	Q99217-2;Q99217;Q99217-3	.;AMELX_HUMAN;.	P	152;166;136	ENSP00000370090:L152P;ENSP00000370088:L166P;ENSP00000335312:L136P	ENSP00000335312:L136P	L	+	2	0	AMELX	11226899	0.973000	0.33851	0.993000	0.49108	0.968000	0.65278	0.883000	0.28200	1.712000	0.51347	0.339000	0.21740	CTG		0.662	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142		C	11316978	T	C	11316978	3	2	44	1	0	0	0	0	1	0	0	0	569	1580	55	4	515	4	AMELX	23	11316978	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10		11316978	143953582	190	4237										
RS1	6247	hgsc.bcm.edu	37	chrX	18674815	18674815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggcacctgcagaccacagagCattgggtcctccttggcaat	11	13	0	2			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:18674815C>T	ENST00000379984.3	-	3	182	c.142G>A	c.(142-144)Gct>Act	p.A48T		NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	48					adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					GACCACAGAGCATTGGGTCCT	0.552																																																0			X											238	185	203					X																	18674815		2203	4300	6503	18584736	SO:0001583	missense	6248			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"retinoschisis (X-linked, juvenile) 1"	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.142G>A	X.37:g.18674815C>T	ENSP00000369320:p.Ala48Thr		18584736	Q0QD39	Missense_Mutation	SNP	ENST00000379984.3	37	CCDS14187.1	.	.	.	.	.	.	.	.	.	.	C	2.347	-0.349822	0.05173	.	.	ENSG00000102104	ENST00000379984	D	0.98221	-4.8	5.15	-5.06	0.02946	.	0.747484	0.13638	N	0.373159	D	0.91513	0.7320	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	D	0.85527	0.1207	10	0.10111	T	0.7	.	7.4925	0.27471	0.1835:0.2027:0.0:0.6138	.	48	O15537	XLRS1_HUMAN	T	48	ENSP00000369320:A48T	ENSP00000369320:A48T	A	-	1	0	RS1	18584736	0.070000	0.21116	0.000000	0.03702	0.004000	0.04260	-0.074000	0.11450	-1.038000	0.03279	-0.853000	0.03031	GCT		0.552	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1			T	18674815	C	T	18674815	3	4	44	1	0	0	0	0	1	0	0	0	13730	710	25	3	548	3	RS1	23	18674815	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	7357837	18674815	136595745	191	4238										
EIF2S3	1968	hgsc.bcm.edu	37	chrX	24082408	24082408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	tgagtacatagtaaagaaaaTtccagtacccccaagagact	7	9	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:24082408T>C	ENST00000253039.4	+	7	981	c.728T>C	c.(727-729)aTt>aCt	p.I243T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	243	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GTAAAGAAAATTCCAGTACCC	0.388																																																0			X											111	116	114					X																	24082408		2203	4297	6500	23992329	SO:0001583	missense	1968			L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"eukaryotic translation initiation factor 2G"	300161	"eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.728T>C	X.37:g.24082408T>C	ENSP00000253039:p.Ile243Thr		23992329	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	37	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.393795	0.62066	.	.	ENSG00000130741	ENST00000253039	T	0.72615	-0.67	5.11	5.11	0.69529	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	D	0.82949	0.5148	H	0.96777	3.88	0.80722	D	1	B	0.24675	0.109	B	0.34418	0.182	D	0.84634	0.0691	10	0.87932	D	0	.	14.2471	0.65995	0.0:0.0:0.0:1.0	.	243	P41091	IF2G_HUMAN	T	243	ENSP00000253039:I243T	ENSP00000253039:I243T	I	+	2	0	EIF2S3	23992329	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.628000	0.83189	1.811000	0.52892	0.486000	0.48141	ATT		0.388	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415		C	24082408	T	C	24082408	3	2	44	1	0	0	0	0	1	0	0	0	5022	1493	52	4	754	4	EIF2S3	23	24082408	Missense_Mutation	SNP	T	TCGA-AG-3885-01A-01W-0899-10	5407593	24082408	131188152	192	4239										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961582	34961582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	agactccggtgtccagtcgcCgcccagagcctcccaagact	10	17	0	3			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:34961582C>T	ENST00000329357.5	+	1	670	c.634C>T	c.(634-636)Cgc>Tgc	p.R212C		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	212	Pro-rich.									breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						GTCCAGTCGCCGCCCAGAGCC	0.652																																																0			X											35	39	37					X																	34961582		2202	4297	6499	34871503	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.634C>T	X.37:g.34961582C>T	ENSP00000328307:p.Arg212Cys		34871503	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	3.551	-0.091646	0.07053	.	.	ENSG00000189132	ENST00000329357	T	0.21543	2.0	0.217	0.217	0.15264	.	.	.	.	.	T	0.10680	0.0261	N	0.17278	0.47	0.22552	N	0.998993	B	0.15473	0.013	B	0.06405	0.002	T	0.28267	-1.0049	9	0.51188	T	0.08	.	3.053	0.06175	0.4809:0.5188:2.0E-4:1.0E-4	.	212	Q8NA70	FA47B_HUMAN	C	212	ENSP00000328307:R212C	ENSP00000328307:R212C	R	+	1	0	FAM47B	34871503	0.075000	0.21258	0.002000	0.10522	0.002000	0.02628	-0.209000	0.09358	0.273000	0.22049	0.277000	0.19347	CGC		0.652	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34961582	C	T	34961582	3	4	44	1	0	0	0	0	1	0	0	0	5589	652	23	1	636	1	FAM47B	23	34961582	Missense_Mutation	SNP	C	TCGA-AG-3885-01A-01W-0899-10	10879174	34961582	120308978	193	4240										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028775	37028775	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	cgcgtatctcatctccgcccGgagcctcctgagactggagt	11	15	2	1			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:37028775G>A	ENST00000358047.3	+	1	2344	c.2292G>A	c.(2290-2292)ccG>ccA	p.P764P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	764										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ATCTCCGCCCGGAGCCTCCTG	0.622																																																0			X											42	42	42					X																	37028775		2202	4300	6502	36938696	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2292G>A	X.37:g.37028775G>A			36938696	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.622	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37028775	G	A	37028775	2	1	44	1	0	0	0	0	0	0	0	1	5590	1103	39	1		1	FAM47C	23	37028775	Silent	SNP	G	TCGA-AG-3885-01A-01W-0899-10	2067193	37028775	118241785	194	4241										
ALG13	79868	hgsc.bcm.edu	37	chrX	110987999	110987999	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ccaccaccaccaccaccaccTcctcctcctcctcctcctcc	0	28	0	0	rs56717389|rs13440710		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:110987999T>A	ENST00000394780.3	+	24	2811	c.2799T>A	c.(2797-2799)ccT>ccA	p.P933P	ALG13_ENST00000251943.4_Intron|ALG13_ENST00000470971.1_3'UTR	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	933	Pro-rich.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)	p.P933P(9)		endometrium(2)|lung(10)|skin(1)	13						caccaccacctcctcctcctc	0.562																																																9	Substitution - coding silent(9)	endometrium(9)	X											10	8	9					X																	110987999		1498	3409	4907	110874655	SO:0001819	synonymous_variant	79868			AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"Tudor domain containing", "OTU domain containing"	30881	protein-coding gene	gene with protein product	"tudor domain containing 13", "N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"	300776	"glycosyltransferase 28 domain containing 1", "chromosome X open reading frame 45", "asparagine-linked glycosylation 13 homolog (S. cerevisiae)"	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2799T>A	X.37:g.110987999T>A			110874655	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Silent	SNP	ENST00000394780.3	37	CCDS55477.1																																																																																				0.562	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466		A	110987999	T	A	110987999	2	1	44	1	0	0	0	0	0	0	0	1	515	1538	54	5		5	ALG13	23	110987999	Silent	SNP	T	TCGA-AG-3885-01A-01W-0899-10	73959224	110987999	44282561	195	4242										
NKRF	55922	hgsc.bcm.edu	37	chrX	118724855	118724855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	ggttcttccagattgtcgccGttaatttttcaataaaatac	6	8	2	1	rs144370117		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:118724855G>A	ENST00000371527.1	-	2	1185	c.533C>T	c.(532-534)aCg>aTg	p.T178M	NKRF_ENST00000304449.5_Missense_Mutation_p.T178M|NKRF_ENST00000542113.1_Missense_Mutation_p.T193M|NKRF_ENST00000487600.1_Intron	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	178	Active repression domain.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						GATTGTCGCCGTTAATTTTTC	0.398																																																0			X						G	MET/THR,MET/THR,MET/THR	1,3834		0,1,1631,571	76	75	75		578,533,533	5.7	1	X	dbSNP_134	75	1,6727		0,1,2427,1872	yes	missense,missense,missense	NKRF	NM_001173487.1,NM_001173488.1,NM_017544.3	81,81,81	0,2,4058,2443	AA,AG,GG,G		0.0149,0.0261,0.0189	possibly-damaging,possibly-damaging,possibly-damaging	193/706,178/691,178/691	118724855	2,10561	2203	4300	6503	118608883	SO:0001583	missense	55922			AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"G patch domain containing"	19374	protein-coding gene	gene with protein product		300440	"NF-kappaB repressing factor"			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.533C>T	X.37:g.118724855G>A	ENSP00000360582:p.Thr178Met		118608883	G3V1N1|Q4VC41|Q9UJ91	Missense_Mutation	SNP	ENST00000371527.1	37	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303557	0.40795	2.61E-4	1.49E-4	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	T;T;T	0.44482	0.92;0.92;0.92	5.7	5.7	0.88788	.	0.242716	0.42053	D	0.000776	T	0.23886	0.0578	N	0.08118	0	0.42964	D	0.994417	P	0.52170	0.951	B	0.35182	0.197	T	0.22521	-1.0214	10	0.66056	D	0.02	-12.8891	17.6846	0.88253	0.0:0.0:1.0:0.0	.	178	O15226	NKRF_HUMAN	M	178;178;193	ENSP00000360582:T178M;ENSP00000304803:T178M;ENSP00000442308:T193M	ENSP00000304803:T178M	T	-	2	0	NKRF	118608883	1.000000	0.71417	0.994000	0.49952	0.912000	0.54170	4.929000	0.63455	2.394000	0.81467	0.600000	0.82982	ACG		0.398	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544		A	118724855	G	A	118724855	3	1	44	1	0	0	0	0	1	0	0	0	10478	1145	40	1	1543	1	NKRF	23	118724855	Missense_Mutation	SNP	G	TCGA-AG-3885-01A-01W-0899-10	7736856	118724855	36545705	196	4243										
BGN	633	hgsc.bcm.edu	37	chrX	152771509	152771509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310880829015544	6	1	0.599240890688259	0	0.647827989933253	0.0090497737556561	0.0920060331825037	0	gtgcccaagggagtgttcagCgggctccggaacatgaactg	15	10	1	1	rs1126499	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:152771509C>T	ENST00000331595.4	+	4	726	c.540C>T	c.(538-540)agC>agT	p.S180S	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	180					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGTGTTCAGCGGGCTCCGGA	0.607													C|||	1266	0.335364	0.0726	0.2853	3775	,	,		11034	0.3016		0.3767	False		,,,				2504	0.2955															0			X						C		628,3207		40,453,95,1139,476	50	46	47		540	-9.4	0.5	X	dbSNP_86	47	3135,3593		508,1207,912,713,960	no	coding-synonymous	BGN	NM_001711.4		548,1660,1007,1852,1436	TT,TC,T,CC,C		46.5963,16.3755,35.6243		180/369	152771509	3763,6800	2203	4300	6503	152424703	SO:0001819	synonymous_variant	633			AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1044	protein-coding gene	gene with protein product	"biglycan proteoglycan"	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.540C>T	X.37:g.152771509C>T			152424703	D3DWU3|P13247	Silent	SNP	ENST00000331595.4	37	CCDS14721.1																																																																																				0.607	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711		T	152771509	C	T	152771509	2	4	44	1	0	0	0	0	0	0	0	1	1419	767	27	1		1	BGN	23	152771509	Silent	SNP	C	TCGA-AG-3885-01A-01W-0899-10	34046654	152771509	2499051	197	4244										
DENND2D	79961	broad.mit.edu	37	chr1	111738540	111738540	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cccattttgctaacccacctCagtgcctgagtcggggatga	10	13	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr1:111738540C>T	ENST00000357640.4	-	6	872	c.643G>A	c.(643-645)Gag>Aag	p.E215K	DENND2D_ENST00000473682.1_5'UTR|DENND2D_ENST00000369752.5_Missense_Mutation_p.E212K	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	215	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.E215K(2)		breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		TAACCCACCTCAGTGCCTGAG	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											143	140	141					1																	111738540		2203	4300	6503	111540063	SO:0001583	missense	79961				CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"DENN/MADD domain containing"	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.643G>A	1.37:g.111738540C>T	ENSP00000350266:p.Glu215Lys		111540063	Q5T5V6|Q9BSU0	Missense_Mutation	SNP	ENST00000357640.4	37	CCDS831.1	.	.	.	.	.	.	.	.	.	.	C	36	5.686917	0.96784	.	.	ENSG00000162777	ENST00000357640;ENST00000369752	T;T	0.12569	2.67;2.67	5.24	5.24	0.73138	DENN (3);	4.374290	0.01156	N	0.006533	T	0.24967	0.0606	L	0.46670	1.46	0.53688	D	0.999977	D;D	0.76494	0.998;0.999	D;D	0.68353	0.928;0.957	T	0.00817	-1.1554	10	0.36615	T	0.2	-23.2792	16.283	0.82707	0.0:1.0:0.0:0.0	.	212;215	Q9H6A0-2;Q9H6A0	.;DEN2D_HUMAN	K	215;212	ENSP00000350266:E215K;ENSP00000358767:E212K	ENSP00000350266:E215K	E	-	1	0	DENND2D	111540063	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.818000	0.86416	2.440000	0.82611	0.561000	0.74099	GAG		0.552	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		T	111738540	C	T	111738540	3	4	45	1	0	0	0	0	1	0	0	0	4442	835	29	3	800	3	DENND2D	1	111738540	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09		111738540	137512081	1	4245										
SYT6	148281	broad.mit.edu	37	chr1	114682272	114682272	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ggctctgtagtttgccgctgCagccgggtgtgacgcatgat	15	10	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr1:114682272C>A	ENST00000610222.1	-	2	623	c.477G>T	c.(475-477)ctG>ctT	p.L159L	SYT6_ENST00000393296.1_Silent_p.L159L|SYT6_ENST00000609117.1_Silent_p.L74L|SYT6_ENST00000369547.1_Silent_p.L74L|SYT6_ENST00000607941.1_Silent_p.L74L			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	159					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.L74L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-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)		TTTGCCGCTGCAGCCGGGTGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	74	81					1																	114682272		2203	4300	6503	114483795	SO:0001819	synonymous_variant	148281				CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.477G>T	1.37:g.114682272C>A			114483795	B1AMB8|B3KPK1	Silent	SNP	ENST00000610222.1	37																																																																																					0.597	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		A	114682272	C	A	114682272	2	1	45	1	0	0	0	0	0	0	0	1	15517	697	25	2		2	SYT6	1	114682272	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	2943732	114682272	134568349	2	4246										
OR2L3	391192	broad.mit.edu	37	chr1	248224090	248224090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cattgttttcattttcctaaTggctctaattggaaacctat	5	8	2	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr1:248224090T>C	ENST00000359959.3	+	1	107	c.107T>C	c.(106-108)aTg>aCg	p.M36T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M36T(1)		cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ATTTTCCTAATGGCTCTAATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											235	234	234					1																	248224090		2203	4297	6500	246290713	SO:0001583	missense	391192			AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.107T>C	1.37:g.248224090T>C	ENSP00000353044:p.Met36Thr		246290713	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.512729	0.00975	.	.	ENSG00000198128	ENST00000359959	T	0.00344	8.02	2.05	0.852	0.18995	.	.	.	.	.	T	0.00144	0.0004	N	0.05574	-0.02	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.04255	-1.0965	9	0.18276	T	0.48	.	5.9817	0.19411	0.0:0.2714:0.0:0.7286	.	36	Q8NG85	OR2L3_HUMAN	T	36	ENSP00000353044:M36T	ENSP00000353044:M36T	M	+	2	0	OR2L3	246290713	0.000000	0.05858	0.030000	0.17652	0.052000	0.14988	0.763000	0.26517	0.067000	0.16545	0.379000	0.24179	ATG		0.388	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		C	248224090	T	C	248224090	3	2	45	1	0	0	0	0	1	0	0	0	11039	1464	51	4	109	4	OR2L3	1	248224090	Missense_Mutation	SNP	T	TCGA-AG-3887-01A-01W-1073-09	133541818	248224090	1026531	3	4247										
PRKD3	23683	broad.mit.edu	37	chr2	37487526	37487526	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	caatcccaggatggtgcaaaTtctgaagagaggttgcaaga	12	7	1	3			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:37487526T>C	ENST00000379066.1	-	15	2648	c.1886A>G	c.(1885-1887)aAt>aGt	p.N629S	PRKD3_ENST00000234179.2_Splice_Site_p.N629S			O94806	KPCD3_HUMAN	protein kinase D3	629	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)	p.N629S(2)		breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				ATGGTGCAAATTCTGAAGAGA	0.383																																					Melanoma(80;621 1355 8613 11814 51767)											2	Substitution - Missense(2)	large_intestine(2)	2											67	64	65					2																	37487526		2203	4300	6503	37341030	SO:0001630	splice_region_variant	23683			AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.1885-1A>G	2.37:g.37487526T>C			37341030	D6W587|Q53TR7|Q8NEL8	Missense_Mutation	SNP	ENST00000379066.1	37	CCDS1789.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.623387	0.28889	.	.	ENSG00000115825	ENST00000379066;ENST00000234179;ENST00000443977	T;T;T	0.63913	-0.07;-0.07;-0.07	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053822	0.64402	D	0.000001	T	0.34366	0.0895	N	0.01267	-0.92	0.80722	D	1	B	0.10296	0.003	B	0.17098	0.017	T	0.27502	-1.0072	10	0.18710	T	0.47	-26.6536	15.4586	0.75336	0.0:0.0:0.0:1.0	.	629	O94806	KPCD3_HUMAN	S	629;629;164	ENSP00000368356:N629S;ENSP00000234179:N629S;ENSP00000398743:N164S	ENSP00000234179:N629S	N	-	2	0	PRKD3	37341030	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.165000	0.64959	2.052000	0.61016	0.528000	0.53228	AAT		0.383	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	Missense_Mutation	C	37487526	T	C	37487526	5	2	45	1	0	0	0	0	0	0	1	0	12554	1507	52	4	806	4	PRKD3	2	37487526	Splice_Site	SNP	T	TCGA-AG-3887-01A-01W-1073-09		37487526	205711847	4	4248										
IL1RN	3557	broad.mit.edu	37	chr2	113890279	113890279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gaacagaaagcaggacaagcGcttcgccttcatccgctcag	10	13	2	1	rs373101669		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:113890279G>A	ENST00000409930.3	+	4	429	c.365G>A	c.(364-366)cGc>cAc	p.R122H	IL1RN_ENST00000409052.1_Missense_Mutation_p.R88H|IL1RN_ENST00000259206.5_Missense_Mutation_p.R125H|IL1RN_ENST00000354115.2_Missense_Mutation_p.R104H|IL1RN_ENST00000361779.3_Missense_Mutation_p.R88H	NM_173842.2	NP_776214.1	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist	122					acute-phase response (GO:0006953)|carboxylic acid metabolic process (GO:0019752)|chronic inflammatory response to antigenic stimulus (GO:0002439)|female pregnancy (GO:0007565)|fever generation (GO:0001660)|immune response (GO:0006955)|insulin secretion (GO:0030073)|lipid metabolic process (GO:0006629)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of membrane potential (GO:0045837)|positive regulation of JUN kinase activity (GO:0043507)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	interleukin-1 receptor antagonist activity (GO:0005152)|interleukin-1 receptor binding (GO:0005149)|interleukin-1 Type I receptor antagonist activity (GO:0045352)|interleukin-1 Type II receptor antagonist activity (GO:0045353)|interleukin-1, Type I receptor binding (GO:0005150)|interleukin-1, Type II receptor binding (GO:0005151)	p.R125H(1)|p.R88H(1)		breast(1)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	10					Rilonacept(DB06372)	CAGGACAAGCGCTTCGCCTTC	0.577									Lichen Sclerosis et Atrophicus, Familial Clustering of																																							2	Substitution - Missense(2)	large_intestine(2)	2						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	90	85	86		311,374,365,263	5.8	1	2		86	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	IL1RN	NM_000577.4,NM_173841.2,NM_173842.2,NM_173843.2	29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	104/160,125/181,122/178,88/144	113890279	1,13005	2203	4300	6503	113606750	SO:0001583	missense	3557	Familial Cancer Database	Lichen Sclerosis, Familial	M55646	CCDS2113.1, CCDS2114.1, CCDS2115.1, CCDS46396.1	2q14.2	2014-09-17			ENSG00000136689	ENSG00000136689		"Interleukins and interleukin receptors", "Endogenous ligands"	6000	protein-coding gene	gene with protein product	"interleukin-1 receptor antagonist protein", "intracellular interleukin-1 receptor antagonist"	147679				1386337, 8432529	Standard	NM_000577		Approved	IL1RA, ICIL-1RA, IL1F3, IRAP, IL-1RN, MGC10430	uc002tjb.3	P18510	OTTHUMG00000131341	ENST00000409930.3:c.365G>A	2.37:g.113890279G>A	ENSP00000387173:p.Arg122His		113606750	A8K4G1|Q14628|Q53SC2|Q7RTZ4|Q96GD6|Q9UPC0	Missense_Mutation	SNP	ENST00000409930.3	37	CCDS46396.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.121714	0.77436	0.0	1.16E-4	ENSG00000136689	ENST00000409052;ENST00000361779;ENST00000259206;ENST00000354115;ENST00000409930	T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04	5.8	5.8	0.92144	.	0.048476	0.85682	D	0.000000	T	0.56834	0.2012	M	0.92833	3.35	0.46011	D	0.998813	D;P;D	0.89917	1.0;0.943;0.983	D;P;P	0.91635	0.999;0.575;0.814	T	0.65932	-0.6048	10	0.72032	D	0.01	-22.6235	15.561	0.76244	0.0:0.0:1.0:0.0	.	122;104;125	P18510;P18510-2;Q53SC2	IL1RA_HUMAN;.;.	H	88;88;125;104;122	ENSP00000387210:R88H;ENSP00000354816:R88H;ENSP00000259206:R125H;ENSP00000329072:R104H;ENSP00000387173:R122H	ENSP00000259206:R125H	R	+	2	0	IL1RN	113606750	1.000000	0.71417	0.998000	0.56505	0.417000	0.31264	5.063000	0.64332	2.755000	0.94549	0.655000	0.94253	CGC		0.577	IL1RN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330802.1	NM_173841		A	113890279	G	A	113890279	3	1	45	1	0	0	0	0	1	0	0	0	7686	1087	38	1	460	1	IL1RN	2	113890279	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	76402753	113890279	129309094	5	4249										
ARHGAP15	55843	broad.mit.edu	37	chr2	144194591	144194591	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tgatataaaagaacagaaacCagagcacagaaaatctttaa	6	6	1	5			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:144194591C>A	ENST00000295095.6	+	8	850	c.683C>A	c.(682-684)cCa>cAa	p.P228Q	AC096558.1_ENST00000549032.1_RNA|AC096558.1_ENST00000550516.1_RNA|RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000442794.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	228					positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)	p.P228Q(1)		endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		GAACAGAAACCAGAGCACAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											72	71	71					2																	144194591		2203	4300	6503	143911061	SO:0001583	missense	55843			AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.683C>A	2.37:g.144194591C>A	ENSP00000295095:p.Pro228Gln		143911061	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	37	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392489	0.42410	.	.	ENSG00000075884	ENST00000295095	T	0.08896	3.04	5.4	5.4	0.78164	.	0.179871	0.49916	D	0.000139	T	0.16896	0.0406	L	0.49350	1.555	0.39274	D	0.964434	D;B	0.61697	0.99;0.032	P;B	0.54664	0.758;0.025	T	0.01045	-1.1470	10	0.36615	T	0.2	.	14.0732	0.64872	0.1507:0.8493:0.0:0.0	.	228;228	B4E0R3;Q53QZ3	.;RHG15_HUMAN	Q	228	ENSP00000295095:P228Q	ENSP00000295095:P228Q	P	+	2	0	ARHGAP15	143911061	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	3.959000	0.56744	2.531000	0.85337	0.650000	0.86243	CCA		0.328	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		A	144194591	C	A	144194591	3	1	45	1	0	0	0	0	1	0	0	0	866	594	21	2	709	2	ARHGAP15	2	144194591	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	30304312	144194591	99004782	6	4250										
FAP	2191	broad.mit.edu	37	chr2	163055367	163055367	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	caagtaacacacttcttgctTggaggatagcttccaatgct	8	10	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:163055367T>A	ENST00000188790.4	-	16	1509	c.1302A>T	c.(1300-1302)ccA>ccT	p.P434P	FAP_ENST00000443424.1_Silent_p.P409P	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha									p.P434P(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						ACTTCTTGCTTGGAGGATAGC	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	2											152	128	136					2																	163055367		2203	4300	6503	162763613	SO:0001819	synonymous_variant	2191			U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1302A>T	2.37:g.163055367T>A			162763613		Silent	SNP	ENST00000188790.4	37	CCDS33311.1																																																																																				0.373	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			A	163055367	T	A	163055367	2	1	45	1	0	0	0	0	0	0	0	1	5692	1799	63	5		5	FAP	2	163055367	Silent	SNP	T	TCGA-AG-3887-01A-01W-1073-09	18860776	163055367	80144006	7	4251										
FIGN	55137	broad.mit.edu	37	chr2	164467524	164467524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gaattcctgaaggcaggtacGctgaaggcggaggcggtgcc	17	9	0	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:164467524G>A	ENST00000333129.3	-	3	1132	c.818C>T	c.(817-819)gCg>gTg	p.A273V	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	273	Pro-rich.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)	p.A273V(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						AGGCAGGTACGCTGAAGGCGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	2											36	40	39					2																	164467524		2007	4162	6169	164175770	SO:0001583	missense	55137			AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.818C>T	2.37:g.164467524G>A	ENSP00000333836:p.Ala273Val		164175770	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	G	11.52	1.662542	0.29515	.	.	ENSG00000182263	ENST00000333129	D	0.93133	-3.17	6.07	5.19	0.71726	.	0.058176	0.64402	D	0.000002	D	0.91808	0.7408	L	0.47716	1.5	0.58432	D	0.999998	D	0.63880	0.993	P	0.44897	0.463	D	0.92091	0.5680	10	0.59425	D	0.04	-9.21	16.7962	0.85602	0.0:0.0:0.87:0.13	.	273	Q5HY92	FIGN_HUMAN	V	273	ENSP00000333836:A273V	ENSP00000333836:A273V	A	-	2	0	FIGN	164175770	1.000000	0.71417	0.929000	0.37066	0.014000	0.08584	7.833000	0.86765	1.555000	0.49500	-0.182000	0.12963	GCG		0.607	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		A	164467524	G	A	164467524	3	1	45	1	0	0	0	0	1	0	0	0	5910	1087	38	1	1465	1	FIGN	2	164467524	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	1412157	164467524	78731849	8	4252										
SCN1A	6323	broad.mit.edu	37	chr2	166898868	166898868	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cctttgggaaggatcttctaGaaagtccatggaaacgtgga	12	7	2	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:166898868G>T	ENST00000303395.4	-	12	2109	c.2110C>A	c.(2110-2112)Cta>Ata	p.L704I	SCN1A_ENST00000409050.1_Missense_Mutation_p.L676I|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.L693I|SCN1A_ENST00000423058.2_Missense_Mutation_p.L704I|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	704					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.L693I(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGATCTTCTAGAAAGTCCATG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											151	144	147					2																	166898868		2203	4300	6503	166607114	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2110C>A	2.37:g.166898868G>T	ENSP00000303540:p.Leu704Ile		166607114	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.284588	0.59867	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75	5.82	5.82	0.92795	Domain of unknown function DUF3451 (1);	0.000000	0.51477	D	0.000085	D	0.94414	0.8203	M	0.74258	2.255	0.49483	D	0.999794	D;D;P	0.69078	0.996;0.997;0.563	D;D;B	0.85130	0.994;0.997;0.417	D	0.92550	0.6049	10	0.27082	T	0.32	.	14.2815	0.66216	0.0706:0.0:0.9294:0.0	.	693;676;704	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	I	704;704;693;676	ENSP00000407030:L704I;ENSP00000303540:L704I;ENSP00000364554:L693I;ENSP00000386312:L676I	ENSP00000303540:L704I	L	-	1	2	SCN1A	166607114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.518000	0.53451	2.745000	0.94114	0.655000	0.94253	CTA		0.348	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166898868	G	T	166898868	3	4	45	1	0	0	0	0	1	0	0	0	13951	933	33	2	3979	2	SCN1A	2	166898868	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	2431344	166898868	76300505	9	4253										
TTN	7273	broad.mit.edu	37	chr2	179419859	179419859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	aacttctgtatattctagagGcaaatcaattacaggaccac	6	9	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr2:179419859G>A	ENST00000591111.1	-	281	83628	c.83404C>T	c.(83404-83406)Cct>Tct	p.P27802S	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P20570S|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P20503S|TTN_ENST00000589042.1_Missense_Mutation_p.P29443S|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P26875S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P20378S|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27802	Ig-like 130.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P20378S(1)|p.P20503S(1)|p.P26873S(1)|p.P20570S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATTCTAGAGGCAAATCAATT	0.368																																																4	Substitution - Missense(4)	large_intestine(4)	2											74	70	72					2																	179419859		1823	4078	5901	179128105	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83404C>T	2.37:g.179419859G>A	ENSP00000465570:p.Pro27802Ser		179128105	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	19.93	3.918860	0.73098	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62364	0.03;0.27;0.23;0.24	5.66	5.66	0.87406	Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.67505	0.2900	N	0.12422	0.21	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.999;0.996	T	0.73563	-0.3943	9	0.87932	D	0	.	20.1041	0.97884	0.0:0.0:1.0:0.0	.	20378;20503;20570;27802	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	26875;20378;20570;20503;20375	ENSP00000343764:P26875S;ENSP00000434586:P20378S;ENSP00000340554:P20570S;ENSP00000352154:P20503S	ENSP00000340554:P20570S	P	-	1	0	TTN	179128105	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.646000	0.74348	2.826000	0.97356	0.655000	0.94253	CCT		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179419859	G	A	179419859	3	1	45	1	0	0	0	0	1	0	0	0	16775	1203	42	3	19780	3	TTN	2	179419859	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	12520991	179419859	63779514	10	4254										
IL17RC	84818	broad.mit.edu	37	chr3	9972097	9972097	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ttggcagagggcagctcgccTtggagagtacttactacaag	13	9	0	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr3:9972097T>A	ENST00000295981.3	+	15	1723	c.1505T>A	c.(1504-1506)cTt>cAt	p.L502H	IL17RC_ENST00000413608.1_Missense_Mutation_p.L431H|IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000403601.3_Missense_Mutation_p.L431H|IL17RC_ENST00000383812.4_Missense_Mutation_p.L416H|IL17RC_ENST00000416074.2_Missense_Mutation_p.L270H|IL17RC_ENST00000455057.1_Missense_Mutation_p.L399H	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	502					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)	p.L502H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GCAGCTCGCCTTGGAGAGTAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											56	53	54					3																	9972097		2203	4300	6503	9947097	SO:0001583	missense	84818			BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1505T>A	3.37:g.9972097T>A	ENSP00000295981:p.Leu502His		9947097	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	De_novo_Start_OutOfFrame	SNP	ENST00000295981.3	37	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675707	0.47781	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36;2.36	5.84	4.65	0.58169	.	0.250149	0.28393	N	0.015520	T	0.34019	0.0883	M	0.63843	1.955	0.28096	N	0.931625	P;D;B;B;D;D;D;P;D;D	0.89917	0.465;0.999;0.335;0.105;1.0;1.0;0.999;0.465;0.999;0.999	B;D;B;B;D;D;P;B;D;D	0.68353	0.148;0.955;0.049;0.071;0.943;0.943;0.903;0.148;0.915;0.957	T	0.13098	-1.0522	10	0.44086	T	0.13	-4.1499	9.0641	0.36453	0.1636:0.0:0.0:0.8364	.	416;270;399;414;431;431;270;416;502;431	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;.;I17RC_HUMAN;.	H	416;502;406;431;270;399;431	ENSP00000373323:L416H;ENSP00000295981:L502H;ENSP00000401128:L406H;ENSP00000384969:L431H;ENSP00000395315:L270H;ENSP00000407894:L399H;ENSP00000396064:L431H	ENSP00000295981:L502H	L	+	2	0	IL17RC	9947097	0.268000	0.24133	0.897000	0.35233	0.308000	0.27856	1.602000	0.36783	1.000000	0.39049	0.459000	0.35465	CTT		0.582	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		A	9972097	T	A	9972097	3	1	45	1	0	0	0	0	1	0	0	0	7662	1609	56	5	1563	5	IL17RC	3	9972097	Missense_Mutation	SNP	T	TCGA-AG-3887-01A-01W-1073-09		9972097	188050333	11	4255										
PIK3CA	5290	broad.mit.edu	37	chr3	178928226	178928226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ttccatctcttaggaaactcCatgcttagagttggagtttg	9	8	1	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr3:178928226C>T	ENST00000263967.3	+	9	1569	c.1412C>T	c.(1411-1413)cCa>cTa	p.P471L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	471	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.P471L(6)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TAGGAAACTCCATGCTTAGAG	0.368		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	6	Substitution - Missense(6)	large_intestine(2)|endometrium(2)|skin(2)	3											99	93	95					3																	178928226		1846	4090	5936	180410920	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1412C>T	3.37:g.178928226C>T	ENSP00000263967:p.Pro471Leu		180410920	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756128	0.89843	.	.	ENSG00000121879	ENST00000263967	T	0.75821	-0.97	5.64	5.64	0.86602	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.107853	0.64402	D	0.000005	D	0.83769	0.5326	M	0.74258	2.255	0.80722	D	1	D	0.56968	0.978	P	0.57620	0.824	T	0.81326	-0.0983	10	0.30854	T	0.27	-14.0418	19.6973	0.96031	0.0:1.0:0.0:0.0	.	471	P42336	PK3CA_HUMAN	L	471	ENSP00000263967:P471L	ENSP00000263967:P471L	P	+	2	0	PIK3CA	180410920	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.466000	0.80914	2.674000	0.91012	0.655000	0.94253	CCA		0.368	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178928226	C	T	178928226	3	4	45	1	0	0	0	0	1	0	0	0	11944	594	21	3	1442	3	PIK3CA	3	178928226	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	168956129	178928226	19094204	12	4256										
RNF168	165918	broad.mit.edu	37	chr3	196199068	196199068	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	agttgtaatgccaataacctGtcctgttcttcttgtttatg	7	8	2	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr3:196199068G>C	ENST00000318037.3	-	6	1932	c.1338C>G	c.(1336-1338)gaC>gaG	p.D446E	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	446					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D446E(1)		NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		CCAATAACCTGTCCTGTTCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											183	178	180					3																	196199068		2203	4300	6503	197683465	SO:0001583	missense	165918			AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.1338C>G	3.37:g.196199068G>C	ENSP00000320898:p.Asp446Glu		197683465	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	37	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912295	0.72983	.	.	ENSG00000163961	ENST00000318037	T	0.59906	0.23	6.08	-0.0015	0.14034	.	0.000000	0.64402	D	0.000002	T	0.72170	0.3427	M	0.80183	2.485	0.37234	D	0.9058	D	0.89917	1.0	D	0.87578	0.998	T	0.75351	-0.3348	10	0.87932	D	0	-29.4718	9.8172	0.40860	0.6423:0.0:0.3577:0.0	.	446	Q8IYW5	RN168_HUMAN	E	446	ENSP00000320898:D446E	ENSP00000320898:D446E	D	-	3	2	RNF168	197683465	0.987000	0.35691	0.968000	0.41197	0.818000	0.46254	0.084000	0.14891	0.131000	0.18576	0.591000	0.81541	GAC		0.408	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		C	196199068	G	C	196199068	3	2	45	1	0	0	0	0	1	0	0	0	13496	1368	48	5	381	5	RNF168	3	196199068	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	17270842	196199068	1823362	13	4257										
SLC4A4	8671	broad.mit.edu	37	chr4	72432767	72432767	+	3'UTR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cgccacacatcatgctgataAaattcctttccttcagtcac	4	14	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr4:72432767A>C	ENST00000264485.5	+	0	3360				SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000340595.3_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.K1049T	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.K1049T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	CATGCTGATAAAATTCCTTTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											146	133	137					4																	72432767		2203	4300	6503	72651631	SO:0001624	3_prime_UTR_variant	8671			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.*3A>C	4.37:g.72432767A>C			72651631	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714513	0.48622	.	.	ENSG00000080493	ENST00000425175	T	0.79454	-1.27	5.6	5.6	0.85130	.	.	.	.	.	T	0.50786	0.1636	N	0.01505	-0.83	0.42146	D	0.991537	B	0.02656	0.0	B	0.04013	0.001	T	0.52801	-0.8527	9	0.59425	D	0.04	.	7.4449	0.27205	0.7832:0.1441:0.0727:0.0	.	1049	A5JJ20	.	T	1049	ENSP00000393557:K1049T	ENSP00000393557:K1049T	K	+	2	0	SLC4A4	72651631	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.021000	0.49651	2.141000	0.66446	0.383000	0.25322	AAA		0.363	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		C	72432767	A	C	72432767	1	2	45	0	1	0	0	0	0	0	0	0	14693	14	1	4		4	SLC4A4	4	72432767	3'UTR	SNP	A	TCGA-AG-3887-01A-01W-1073-09		72432767	118721509	14	4258										
FAT4	79633	broad.mit.edu	37	chr4	126402756	126402757	+	Frame_Shift_Ins	INS	-	-	A													0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcagaatgagaagcgggaatINSatttgttaaggcaaagctta							TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr4:126402756_126402757insA	ENST00000394329.3	+	15	12692_12693	c.12679_12680insA	c.(12679-12681)tatfs	p.Y4227fs	FAT4_ENST00000335110.5_Frame_Shift_Ins_p.Y2468fs	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4227	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y4227fs*1(1)|p.Y4170fs*1(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GAAGCGGGAATATTTGTTAAGG	0.441																																																2	Insertion - Frameshift(2)	large_intestine(2)	4																																								126622207	SO:0001589	frameshift_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12680dupA	4.37:g.126402757_126402757dupA	ENSP00000377862:p.Tyr4227fs		126622206	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Frame_Shift_Ins	INS	ENST00000394329.3	37	CCDS3732.3																																																																																				0.441	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126402757	-	A	126402756	7	5	45	1	0	1	1	0	0	0	0	0	5711	1406	49	0	12737	0	FAT4	4	126402756	Frame_Shift_Ins	INS	-	TCGA-AG-3887-01A-01W-1073-09	53969989	126402756	64751520	15	4259										
DCHS2	54798	broad.mit.edu	37	chr4	155156597	155156597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cttattaaactcaaccattcCggagtggcatccacagggac	8	12	1	0	rs61741036		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr4:155156597C>T	ENST00000357232.4	-	25	7841	c.7842G>A	c.(7840-7842)ccG>ccA	p.P2614P		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2614					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P2614P(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TCAACCATTCCGGAGTGGCAT	0.493													C|||	1	0.000199681	8e-04	0	5008	,	,		19474	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						C		1,4405	2.1+/-5.4	0,1,2202	121	120	120		7842	-11.6	0	4	dbSNP_129	120	0,8600		0,0,4300	no	coding-synonymous	DCHS2	NM_017639.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		2614/2917	155156597	1,13005	2203	4300	6503	155376047	SO:0001819	synonymous_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7842G>A	4.37:g.155156597C>T			155376047	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.493	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155156597	C	T	155156597	2	4	45	1	0	0	0	0	0	0	0	1	4294	639	23	1		1	DCHS2	4	155156597	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	28753841	155156597	35997679	16	4260										
ESM1	11082	broad.mit.edu	37	chr5	54277827	54277827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	accagaatcagtgcttacccGtgagagaaacaaatctgttg	9	9	2	3	rs367904025		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:54277827G>A	ENST00000381405.4	-	2	594	c.449C>T	c.(448-450)aCg>aTg	p.T150M	ESM1_ENST00000381403.4_Intron|ESM1_ENST00000598310.1_Intron	NM_007036.4	NP_008967.1	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1	150					angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of hepatocyte growth factor receptor signaling pathway (GO:1902204)|regulation of cell growth (GO:0001558)|sprouting angiogenesis (GO:0002040)	extracellular region (GO:0005576)	hepatocyte growth factor receptor binding (GO:0005171)|integrin binding (GO:0005178)	p.T150M(1)		breast(1)|kidney(1)|large_intestine(4)|lung(4)	10		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			GTGCTTACCCGTGAGAGAAAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	,MET/THR	0,4406		0,0,2203	110	109	109		,449	5	0.8	5		109	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	ESM1	NM_001135604.1,NM_007036.4	,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,possibly-damaging	,150/185	54277827	1,13005	2203	4300	6503	54313584	SO:0001583	missense	11082			X89426	CCDS3963.1, CCDS47206.1	5q11	2008-02-05			ENSG00000164283	ENSG00000164283			3466	protein-coding gene	gene with protein product		601521				8702785	Standard	NM_001135604		Approved		uc003jpk.3	Q9NQ30	OTTHUMG00000097010	ENST00000381405.4:c.449C>T	5.37:g.54277827G>A	ENSP00000370812:p.Thr150Met		54313584	B2R4G3|Q15330|Q3V4E3|Q96ES3	Missense_Mutation	SNP	ENST00000381405.4	37	CCDS3963.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650943	0.47362	0.0	1.16E-4	ENSG00000164283	ENST00000381405	.	.	.	5.9	5.01	0.66863	.	0.688458	0.14128	N	0.339559	T	0.50956	0.1646	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	P	0.50791	0.65	T	0.54529	-0.8280	9	0.72032	D	0.01	-16.4134	15.229	0.73372	0.0:0.14:0.86:0.0	.	150	Q9NQ30	ESM1_HUMAN	M	150	.	ENSP00000370812:T150M	T	-	2	0	ESM1	54313584	1.000000	0.71417	0.823000	0.32752	0.197000	0.23852	5.422000	0.66453	1.458000	0.47871	0.563000	0.77884	ACG		0.408	ESM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214099.2	NM_007036		A	54277827	G	A	54277827	3	1	45	1	0	0	0	0	1	0	0	0	5265	1145	40	1	113	1	ESM1	5	54277827	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		54277827	126637433	17	4261										
APC	324	broad.mit.edu	37	chr5	112175069	112175069	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctattaaccaagaaacaataCagacttattgtgtagaagat	6	6	0	4			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:112175069C>T	ENST00000457016.1	+	16	4158	c.3778C>T	c.(3778-3780)Cag>Tag	p.Q1260*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1260*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1260*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1260	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1260*(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAATACAGACTTATTG	0.388		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5	GRCh37	CD941589	APC	D							51	53	52					5																	112175069		2202	4300	6502	112202968	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3778C>T	5.37:g.112175069C>T	ENSP00000413133:p.Gln1260*		112202968	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.033442	0.98621	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.053822	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.6155	20.5568	0.99304	0.0:1.0:0.0:0.0	.	.	.	.	X	1260	.	.	Q	+	1	0	APC	112202968	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.861000	0.98227	0.655000	0.94253	CAG		0.388	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175069	C	T	112175069	4	4	45	1	0	0	0	0	0	1	0	0	763	479	17	3	3836	3	APC	5	112175069	Nonsense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	57897242	112175069	68740191	18	4262										
APC	324	broad.mit.edu	37	chr5	112175217	112175218	+	Frame_Shift_Del	DEL	AA	AA	-													0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gcaaatagcagaaataaaagAaaagattggaactaggtcag							TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:112175217_112175218delAA	ENST00000457016.1	+	16	4306_4307	c.3926_3927delAA	c.(3925-3927)gaafs	p.E1309fs	APC_ENST00000257430.4_Frame_Shift_Del_p.E1309fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1309fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1309	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			E -> G (in Ref. 1; AAA60353/AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*4(73)|p.I1311fs*4(2)|p.K1310fs*4(2)|p.?(1)|p.E1309fs*6(1)|p.K1310fs*10(1)|p.K1192fs*3(1)|p.K1308fs*4(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAATAAAAGAAAAGATTGGAA	0.421	E1309fs*4(LS1034_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	82	Deletion - Frameshift(78)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(72)|stomach(5)|thyroid(2)|soft_tissue(2)|skin(1)	5	GRCh37	CD920817|CD995194|CM973705	APC	D|M	rs80338757																																			112203117	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3926_3927delAA	5.37:g.112175219_112175220delAA	ENSP00000413133:p.Glu1309fs		112203116	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.421	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175218	AA	-	112175217	7	5	45	1	0	1	0	1	0	0	0	0	763	246	9	0	3984	0	APC	5	112175217	Frame_Shift_Del	DEL	AA	TCGA-AG-3887-01A-01W-1073-09	148	112175217	68740043	19	4263										
ZNF608	57507	broad.mit.edu	37	chr5	123980114	123980114	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccagttcacaggagtctttcGatcatcatttttcagcttgc	7	11	5	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:123980114G>A	ENST00000306315.5	-	5	4381	c.3946C>T	c.(3946-3948)Cga>Tga	p.R1316*	ZNF608_ENST00000513985.1_5'Flank|ZNF608_ENST00000504926.1_Nonsense_Mutation_p.R889*	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1316							metal ion binding (GO:0046872)	p.R1316*(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		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)		GGAGTCTTTCGATCATCATTT	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											261	245	251					5																	123980114		2203	4300	6503	124008013	SO:0001587	stop_gained	57507			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.3946C>T	5.37:g.123980114G>A	ENSP00000307746:p.Arg1316*		124008013	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Nonsense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	G	47	13.290585	0.99732	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	.	.	.	5.76	4.88	0.63580	.	0.270216	0.37348	N	0.002137	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.5662	17.0898	0.86619	0.0:0.127:0.873:0.0	.	.	.	.	X	889;1316	.	.	R	-	1	2	ZNF608	124008013	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	2.329000	0.43876	1.544000	0.49359	0.643000	0.83706	CGA		0.468	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	123980114	G	A	123980114	4	1	45	1	0	0	0	0	0	1	0	0	18073	1066	37	1	612	1	ZNF608	5	123980114	Nonsense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	11804897	123980114	56935146	20	4264										
PCDHB15	56121	broad.mit.edu	37	chr5	140625822	140625822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctccaccccgatctggcaccGtccagatcctcatcttggtc	7	18	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:140625822G>A	ENST00000231173.3	+	1	676	c.676G>A	c.(676-678)Gtc>Atc	p.V226I		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.V226I(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATCTGGCACCGTCCAGATCCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											51	51	51					5																	140625822		2203	4300	6503	140606006	SO:0001583	missense	56121			AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.676G>A	5.37:g.140625822G>A	ENSP00000231173:p.Val226Ile		140606006	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	A	6.437	0.448677	0.12223	.	.	ENSG00000113248	ENST00000231173	T	0.52983	0.64	4.92	-3.7	0.04437	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.35537	0.0935	L	0.49513	1.565	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.38650	-0.9651	9	0.72032	D	0.01	.	4.4093	0.11425	0.3768:0.0:0.3858:0.2375	.	226	Q9Y5E8	PCDBF_HUMAN	I	226	ENSP00000231173:V226I	ENSP00000231173:V226I	V	+	1	0	PCDHB15	140606006	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.546000	0.00932	-0.776000	0.04578	-0.500000	0.04577	GTC		0.602	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		A	140625822	G	A	140625822	3	1	45	1	0	0	0	0	1	0	0	0	11571	1145	40	1	678	1	PCDHB15	5	140625822	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	16645708	140625822	40289438	21	4265										
CLK4	57396	broad.mit.edu	37	chr5	178030720	178030720	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	attcttcgaaccaggtcaaaCagtttctcatgttcttcatc	5	11	5	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr5:178030720C>A	ENST00000316308.4	-	13	1512	c.1344G>T	c.(1342-1344)ctG>ctT	p.L448L		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	448	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.L448L(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|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)	all cancers(165;0.235)		CCAGGTCAAACAGTTTCTCAT	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	5											89	86	87					5																	178030720		2202	4300	6502	177963326	SO:0001819	synonymous_variant	57396			AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1344G>T	5.37:g.178030720C>A			177963326		Silent	SNP	ENST00000316308.4	37	CCDS4437.1																																																																																				0.313	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			A	178030720	C	A	178030720	2	1	45	1	0	0	0	0	0	0	0	1	3545	465	17	2		2	CLK4	5	178030720	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	37404898	178030720	2884540	22	4266										
KIF13A	63971	broad.mit.edu	37	chr6	17764878	17764878	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcggtggagtctgcatccttCgtctgaatggccagctggtc	13	11	2	1	rs56327112	byFrequency	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr6:17764878C>T	ENST00000259711.6	-	39	4986	c.4881G>A	c.(4879-4881)acG>acA	p.T1627T	KIF13A_ENST00000378816.5_Silent_p.T1592T|KIF13A_ENST00000378826.2_Silent_p.T1592T|KIF13A_ENST00000378843.2_Silent_p.T1579T|KIF13A_ENST00000378814.5_Silent_p.T1579T	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1627					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T1627T(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CTGCATCCTTCGTCTGAATGG	0.517													c|||	6	0.00119808	0.0045	0	5008	,	,		19519	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						C	,,,	14,4098		0,14,2042	78	76	77		4776,4737,4737,4881	-7.2	0	6	dbSNP_129	77	0,8408		0,0,4204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	0,14,6246	TT,TC,CC		0.0,0.3405,0.1118	,,,	1592/1771,1579/1758,1579/1750,1627/1806	17764878	14,12506	2056	4204	6260	17872857	SO:0001819	synonymous_variant	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.4881G>A	6.37:g.17764878C>T			17872857	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																				0.517	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			T	17764878	C	T	17764878	2	4	45	1	0	0	0	0	0	0	0	1	8295	871	31	1		1	KIF13A	6	17764878	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09		17764878	153350189	23	4267										
PNPLA1	285848	broad.mit.edu	37	chr6	36259268	36259268	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gctccatgtgagcctcacccGcttaacggacggggagaatg	13	12	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr6:36259268G>A	ENST00000394571.2	+	2	377	c.377G>A	c.(376-378)cGc>cAc	p.R126H	PNPLA1_ENST00000388715.3_Missense_Mutation_p.R31H|PNPLA1_ENST00000312917.5_Missense_Mutation_p.R31H	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	126	Patatin.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)	p.R31H(1)		breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						AGCCTCACCCGCTTAACGGAC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	61	63					6																	36259268		2203	4300	6503	36367246	SO:0001583	missense	285848				CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"Patatin-like phospholipase domain containing"	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.377G>A	6.37:g.36259268G>A	ENSP00000378072:p.Arg126His		36367246	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882637	0.72410	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.24	4.36	0.52297	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.000000	0.64402	D	0.000012	D	0.82435	0.5036	M	0.71206	2.165	0.43275	D	0.995239	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.84937	0.0863	10	0.87932	D	0	-21.413	11.3522	0.49594	0.0887:0.0:0.9113:0.0	.	126;31	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	H	31;31;126;126	ENSP00000373367:R31H;ENSP00000321116:R31H;ENSP00000391868:R126H;ENSP00000378072:R126H	ENSP00000321116:R31H	R	+	2	0	PNPLA1	36367246	0.999000	0.42202	0.830000	0.32933	0.591000	0.36615	8.356000	0.90085	1.198000	0.43158	0.467000	0.42956	CGC		0.602	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		A	36259268	G	A	36259268	3	1	45	1	0	0	0	0	1	0	0	0	12195	1087	38	1	383	1	PNPLA1	6	36259268	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	18494390	36259268	134855799	24	4268										
SOBP	55084	broad.mit.edu	37	chr6	107954900	107954900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	acattacaccctcccatggaAaataaagcagaaggcaccgg	8	12	0	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr6:107954900A>G	ENST00000317357.5	+	6	1511	c.852A>G	c.(850-852)gaA>gaG	p.E284E		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)									p.E284E(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		CTCCCATGGAAAATAAAGCAG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	6											56	61	60					6																	107954900		1933	4112	6045	108061593	SO:0001819	synonymous_variant	55084			AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.852A>G	6.37:g.107954900A>G			108061593		Silent	SNP	ENST00000317357.5	37	CCDS43488.1																																																																																				0.522	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		G	107954900	A	G	107954900	2	3	45	1	0	0	0	0	0	0	0	1	14949	11	1	4		4	SOBP	6	107954900	Silent	SNP	A	TCGA-AG-3887-01A-01W-1073-09	71695632	107954900	63160167	25	4269										
SYNE1	23345	broad.mit.edu	37	chr6	152708291	152708291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gactcatcctctgtcttttcGtagagctccctggacttcgc	8	14	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr6:152708291G>A	ENST00000367255.5	-	54	9004	c.8403C>T	c.(8401-8403)taC>taT	p.Y2801Y	SYNE1_ENST00000448038.1_Silent_p.Y2808Y|SYNE1_ENST00000341594.5_Silent_p.Y2840Y|SYNE1_ENST00000423061.1_Silent_p.Y2808Y|SYNE1_ENST00000265368.4_Silent_p.Y2801Y	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2801					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.Y2801Y(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTGTCTTTTCGTAGAGCTCCC	0.463										HNSCC(10;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	6											163	147	152					6																	152708291		2203	4300	6503	152749984	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.8403C>T	6.37:g.152708291G>A			152749984	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.463	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152708291	G	A	152708291	2	1	45	1	0	0	0	0	0	0	0	1	15484	1140	40	1		1	SYNE1	6	152708291	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09	44753391	152708291	18406776	26	4270										
MAD1L1	8379	broad.mit.edu	37	chr7	2265091	2265091	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctgctctctccagctccactCgagccctcttgtgactcagc	7	18	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr7:2265091C>G	ENST00000406869.1	-	4	802	c.245G>C	c.(244-246)cGa>cCa	p.R82P	MAD1L1_ENST00000399654.2_Missense_Mutation_p.R82P|MAD1L1_ENST00000402746.1_Intron|MAD1L1_ENST00000265854.7_Missense_Mutation_p.R82P			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	82					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)		p.R82P(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CAGCTCCACTCGAGCCCTCTT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	112	109					7																	2265091		2100	4232	6332	2231617	SO:0001583	missense	8379			U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.245G>C	7.37:g.2265091C>G	ENSP00000385334:p.Arg82Pro		2231617	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.375109	0.82682	.	.	ENSG00000002822	ENST00000399654;ENST00000406869;ENST00000265854;ENST00000429625;ENST00000429779	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	4.96	4.08	0.47627	.	0.000000	0.85682	D	0.000000	T	0.47673	0.1458	M	0.68952	2.095	0.51233	D	0.999911	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.48186	-0.9057	10	0.66056	D	0.02	-9.5157	12.444	0.55641	0.0:0.919:0.0:0.081	.	11;82	C9K086;Q9Y6D9	.;MD1L1_HUMAN	P	82;82;82;11;82	ENSP00000382562:R82P;ENSP00000385334:R82P;ENSP00000265854:R82P;ENSP00000413139:R11P;ENSP00000395457:R82P	ENSP00000265854:R82P	R	-	2	0	MAD1L1	2231617	1.000000	0.71417	0.190000	0.23270	0.998000	0.95712	6.904000	0.75708	1.101000	0.41535	0.650000	0.86243	CGA		0.627	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		G	2265091	C	G	2265091	3	3	45	1	0	0	0	0	1	0	0	0	9177	884	31	5	1975	5	MAD1L1	7	2265091	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09		2265091	156873572	27	4271										
FIS1	51024	broad.mit.edu	37	chr7	100884117	100884117	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ggtccccacctcaccttgagCcggtagttccccacggccag	10	18	1	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr7:100884117C>A	ENST00000223136.4	-	3	329	c.249G>T	c.(247-249)cgG>cgT	p.R83R	FIS1_ENST00000442303.1_Missense_Mutation_p.A60S|CLDN15_ENST00000401528.1_5'Flank|CLDN15_ENST00000308344.5_5'Flank|FIS1_ENST00000474120.1_Missense_Mutation_p.A29S|FIS1_ENST00000482199.1_5'UTR	NM_016068.2	NP_057152.2	Q9Y3D6	FIS1_HUMAN	fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)	83					calcium-mediated signaling using intracellular calcium source (GO:0035584)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|mitochondrion morphogenesis (GO:0070584)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|peroxisome fission (GO:0016559)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|release of cytochrome c from mitochondria (GO:0001836)	integral component of mitochondrial outer membrane (GO:0031307)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|protein complex (GO:0043234)	receptor binding (GO:0005102)	p.R83R(1)		kidney(1)|large_intestine(2)|lung(1)	4	Lung NSC(181;0.168)|all_lung(186;0.215)					TCACCTTGAGCCGGTAGTTCC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	7											92	99	97					7																	100884117		2025	4152	6177	100670837	SO:0001819	synonymous_variant	51024			AF151893	CCDS43626.1	7q22.1	2012-10-01	2006-04-04	2006-01-24	ENSG00000214253	ENSG00000214253			21689	protein-coding gene	gene with protein product	"CGI-135 protein"	609003	"tetratricopeptide repeat domain 11", "fission 1 (mitochondrial outer membrane) homolog (yeast)"	TTC11		14996942, 16010987	Standard	NM_016068		Approved	CGI-135, H_NH0132A01.6, Fis1	uc003uyj.4	Q9Y3D6	OTTHUMG00000157106	ENST00000223136.4:c.249G>T	7.37:g.100884117C>A			100670837	Q9BTP3	Silent	SNP	ENST00000223136.4	37	CCDS43626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.97|11.97	1.796766|1.796766	0.31777|0.31777	.|.	.|.	ENSG00000214253|ENSG00000214253	ENST00000474120;ENST00000442303|ENST00000435848	.|.	.|.	.|.	5.1|5.1	2.08|2.08	0.27032|0.27032	.|.	.|.	.|.	.|.	.|.	T|T	0.63153|0.63153	0.2487|0.2487	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.65331|0.65331	-0.6194|-0.6194	5|5	0.87932|0.87932	D|D	0|0	.|.	7.7333|7.7333	0.28799|0.28799	0.0:0.6968:0.1407:0.1625|0.0:0.6968:0.1407:0.1625	.|.	.|.	.|.	.|.	S|V	29;60|73	.|.	ENSP00000395964:A60S|ENSP00000413500:G73V	A|G	-|-	1|2	0|0	FIS1|FIS1	100670837|100670837	0.963000|0.963000	0.33076|0.33076	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	0.019000|0.019000	0.13444|0.13444	1.136000|1.136000	0.42199|0.42199	0.561000|0.561000	0.74099|0.74099	GCT|GGC		0.627	FIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347449.1	NM_016068		A	100884117	C	A	100884117	2	1	45	1	0	0	0	0	0	0	0	1	5916	726	26	2		2	FIS1	7	100884117	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	98619026	100884117	58254546	28	4272										
C7orf29	113763	broad.mit.edu	37	chr7	150027608	150027608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cacactttcaggagcagagtGtcggggagaggggcgcagcc	17	10	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr7:150027608G>A	ENST00000343855.4	+	1	671	c.115G>A	c.(115-117)Gtc>Atc	p.V39I	LRRC61_ENST00000359623.4_Intron|LRRC61_ENST00000493307.1_Intron|LRRC61_ENST00000323078.7_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	39								p.V39I(1)									GGAGCAGAGTGTCGGGGAGAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	7											97	105	102					7																	150027608		2203	4300	6503	149658541	SO:0001583	missense	113763			BC011406	CCDS5900.1	7q35	2013-05-03	2013-05-03	2013-05-03	ENSG00000188707	ENSG00000188707			21720	protein-coding gene	gene with protein product		615252	"chromosome 7 open reading frame 29"	C7orf29		23533661	Standard	NM_138434		Approved			Q96FA7	OTTHUMG00000158328	ENST00000343855.4:c.115G>A	7.37:g.150027608G>A	ENSP00000343242:p.Val39Ile		149658541		Missense_Mutation	SNP	ENST00000343855.4	37	CCDS5900.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.621910	0.00118	.	.	ENSG00000188707	ENST00000343855	.	.	.	3.93	-1.68	0.08212	.	911.360000	0.00792	N	0.001348	T	0.16300	0.0392	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.11966	-1.0566	9	0.02654	T	1	.	1.3466	0.02165	0.3557:0.1413:0.3596:0.1434	.	39	Q96FA7	CG029_HUMAN	I	39	.	ENSP00000343242:V39I	V	+	1	0	C7orf29	149658541	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.152000	0.16302	-0.308000	0.08792	-1.109000	0.02080	GTC		0.632	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434		A	150027608	G	A	150027608	3	1	45	1	0	0	0	0	1	0	0	0	2391	1377	48	3	117	3	C7orf29	7	150027608	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	49143491	150027608	9111055	29	4273										
SCARA5	286133	broad.mit.edu	37	chr8	27779538	27779539	+	Frame_Shift_Ins	INS	-	-	C													0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tgcaccgcctgcgcctgcagINScccccacagcgcgccctcca							TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr8:27779538_27779539insC	ENST00000354914.3	-	4	950_951	c.465_466insG	c.(463-468)gggctgfs	p.L156fs	SCARA5_ENST00000301906.4_Frame_Shift_Ins_p.L113fs|SCARA5_ENST00000524352.1_Frame_Shift_Ins_p.L156fs|SCARA5_ENST00000380385.2_Intron|SCARA5_ENST00000518030.1_Frame_Shift_Ins_p.L113fs	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	156					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)	p.L156fs*40(1)		central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TGCGCCTGCAGCCCCCACAGCG	0.723																																																1	Insertion - Frameshift(1)	large_intestine(1)	8																																								27835458	SO:0001589	frameshift_variant	286133			AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.466dupG	8.37:g.27779543_27779543dupC	ENSP00000346990:p.Leu156fs		27835457	Q6UXZ1|Q7Z4A1|Q8N4Z7	Frame_Shift_Ins	INS	ENST00000354914.3	37	CCDS6064.1																																																																																				0.723	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		C	27779539	-	C	27779538	7	5	45	1	0	1	1	0	0	0	0	0	13917	962	34	0	1045	0	SCARA5	8	27779538	Frame_Shift_Ins	INS	-	TCGA-AG-3887-01A-01W-1073-09		27779538	118584484	30	4274										
PXDNL	137902	broad.mit.edu	37	chr8	52258474	52258474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gtttcttttgagactcttgcGtcactgctctgaactgtcct	8	11	4	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr8:52258474G>A	ENST00000356297.4	-	20	4035	c.3935C>T	c.(3934-3936)aCg>aTg	p.T1312M	PXDNL_ENST00000543296.1_Intron	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1312					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.T1312M(2)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AGACTCTTGCGTCACTGCTCT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	8											151	140	144					8																	52258474		1965	4158	6123	52421027	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3935C>T	8.37:g.52258474G>A	ENSP00000348645:p.Thr1312Met		52421027	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.06|13.06	2.122934|2.122934	0.37436|0.37436	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000522933|ENST00000356297	.|T	.|0.65364	.|-0.15	3.71|3.71	1.86|1.86	0.25419|0.25419	.|.	.|.	.|.	.|.	.|.	T|T	0.49098|0.49098	0.1537|0.1537	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|D	.|0.63880	.|0.993	.|P	.|0.54346	.|0.749	T|T	0.35076|0.35076	-0.9803|-0.9803	5|9	.|0.45353	.|T	.|0.12	.|.	6.0102|6.0102	0.19571|0.19571	0.2561:0.0:0.7439:0.0|0.2561:0.0:0.7439:0.0	.|.	.|1312	.|A1KZ92	.|PXDNL_HUMAN	C|M	386|1312	.|ENSP00000348645:T1312M	.|ENSP00000348645:T1312M	R|T	-|-	1|2	0|0	PXDNL|PXDNL	52421027|52421027	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	0.876000|0.876000	0.28092|0.28092	0.098000|0.098000	0.17522|0.17522	0.467000|0.467000	0.42956|0.42956	CGC|ACG		0.408	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52258474	G	A	52258474	3	1	45	1	0	0	0	0	1	0	0	0	12885	1145	40	1	472	1	PXDNL	8	52258474	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	24478936	52258474	94105548	31	4275										
LAPTM4B	55353	broad.mit.edu	37	chr8	98863681	98863681	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ggtgctgccaaggagccaccGccaccttacgtgtctgccta	11	15	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr8:98863681G>A	ENST00000521545.2	+	7	894	c.660G>A	c.(658-660)ccG>ccA	p.P220P	LAPTM4B_ENST00000445593.2_Silent_p.P311P			Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta	364					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.P311P(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			AGGAGCCACCGCCACCTTACG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	8											135	107	116					8																	98863681		2203	4300	6503	98932857	SO:0001819	synonymous_variant	55353			AF317417	CCDS6275.1	8q22.1	2008-08-11	2008-08-11		ENSG00000104341	ENSG00000104341			13646	protein-coding gene	gene with protein product		613296					Standard	NM_018407		Approved	LC27	uc003yia.3	Q86VI4	OTTHUMG00000164740	ENST00000521545.2:c.660G>A	8.37:g.98863681G>A			98932857	Q3ZCV5|Q7L909|Q86VH8|Q9H060	Silent	SNP	ENST00000521545.2	37																																																																																					0.517	LAPTM4B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000380016.2			A	98863681	G	A	98863681	2	1	45	1	0	0	0	0	0	0	0	1	8647	1074	38	1		1	LAPTM4B	8	98863681	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09	46605207	98863681	47500341	32	4276										
ANGPT1	284	broad.mit.edu	37	chr8	108509613	108509613	+	IGR	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tttgtgttgtactggtctgtCgtactctcacgacagttgcc	10	10	2	0	rs373049538		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr8:108509613C>A								ANGPT1 (160863 upstream) : RNA5SP275 (387108 downstream)														p.T58T(1)									ACTGGTCTGTCGTACTCTCAC	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	8											228	190	203					8																	108509613		2203	4300	6503	108578789	SO:0001628	intergenic_variant	284																															8.37:g.108509613C>A			108578789		Silent	SNP		37																																																																																				0	0.468									A	108509613	C	A	108509613	1	1	45	0	1	0	0	0	0	0	0	0	610	871	31	2		2	ANGPT1	8	108509613	IGR	SNP	C	TCGA-AG-3887-01A-01W-1073-09	9645932	108509613	37854409	33	4277										
ACO1	48	broad.mit.edu	37	chr9	32407368	32407368	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	attctacattggaatgtcacGcagcacaagaacatagaagt	8	8	2	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr9:32407368G>A	ENST00000309951.6	+	3	345	c.207G>A	c.(205-207)acG>acA	p.T69T	ACO1_ENST00000541043.1_5'UTR|ACO1_ENST00000379923.1_Silent_p.T69T	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	69					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.T69T(1)		breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GGAATGTCACGCAGCACAAGA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	9											139	115	123					9																	32407368		2203	4300	6503	32397368	SO:0001819	synonymous_variant	48			M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.207G>A	9.37:g.32407368G>A			32397368	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																				0.428	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		A	32407368	G	A	32407368	2	1	45	1	0	0	0	0	0	0	0	1	146	1074	38	1		1	ACO1	9	32407368	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09		32407368	108806063	34	4278										
GRHPR	9380	broad.mit.edu	37	chr9	37432009	37432009	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccactgtcattcccaggggcGacgtcgtaaaccaggacgac	11	14	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr9:37432009G>T	ENST00000318158.6	+	8	824	c.739G>T	c.(739-741)Gac>Tac	p.D247Y	GRHPR_ENST00000607784.1_Missense_Mutation_p.D247Y	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	247					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)	p.D247Y(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		TCCCAGGGGCGACGTCGTAAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											161	124	137					9																	37432009		2203	4300	6503	37422009	SO:0001583	missense	9380			AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.739G>T	9.37:g.37432009G>T	ENSP00000313432:p.Asp247Tyr		37422009	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186985	0.38609	.	.	ENSG00000137106	ENST00000318158	T	0.77620	-1.11	5.77	4.88	0.63580	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (2);D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	.	.	.	.	D	0.84338	0.5450	L	0.61036	1.89	0.09310	N	0.99999	D;P	0.64830	0.994;0.763	D;P	0.65323	0.934;0.677	T	0.75255	-0.3382	9	0.66056	D	0.02	.	10.3369	0.43854	0.0712:0.1347:0.794:0.0	.	260;247	Q5M7Z5;Q9UBQ7	.;GRHPR_HUMAN	Y	247	ENSP00000313432:D247Y	ENSP00000313432:D247Y	D	+	1	0	GRHPR	37422009	0.997000	0.39634	0.617000	0.29091	0.016000	0.09150	5.131000	0.64751	1.586000	0.49944	-0.136000	0.14681	GAC		0.557	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		T	37432009	G	T	37432009	3	4	45	1	0	0	0	0	1	0	0	0	6787	1058	37	2	769	2	GRHPR	9	37432009	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	5024641	37432009	103781422	35	4279										
COL13A1	1305	broad.mit.edu	37	chr10	71640268	71640268	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tctccccgcaggggtcccccGgagacgctgggctgtccatc	13	17	1	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr10:71640268G>A	ENST00000398978.3	+	6	937	c.445G>A	c.(445-447)Gga>Aga	p.G149R	COL13A1_ENST00000398966.3_Missense_Mutation_p.G149R|COL13A1_ENST00000398971.3_Missense_Mutation_p.G149R|COL13A1_ENST00000398973.3_Missense_Mutation_p.G149R|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000398972.3_Missense_Mutation_p.G149R|COL13A1_ENST00000354547.3_Missense_Mutation_p.G149R|COL13A1_ENST00000398968.3_Missense_Mutation_p.G149R|COL13A1_ENST00000356340.3_Missense_Mutation_p.G149R|COL13A1_ENST00000398969.3_Intron|COL13A1_ENST00000357811.3_Missense_Mutation_p.G149R|COL13A1_ENST00000398964.3_Intron|COL13A1_ENST00000398974.3_Missense_Mutation_p.G137R|COL13A1_ENST00000520267.1_Intron|COL13A1_ENST00000517713.1_Missense_Mutation_p.G149R|COL13A1_ENST00000522165.1_Missense_Mutation_p.G149R	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1									p.G149R(2)		endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GGGGTCCCCCGGAGACGCTGG	0.622																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	10											33	34	33					10																	71640268		1822	4077	5899	71310274	SO:0001583	missense	1305			AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.445G>A	10.37:g.71640268G>A	ENSP00000381949:p.Gly149Arg		71310274		Missense_Mutation	SNP	ENST00000398978.3	37	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.961267	0.53400	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000517713;ENST00000522165	D;D;D;D;D;D;D;D;D;D;D;D	0.95724	-3.52;-3.69;-3.59;-3.66;-3.79;-3.31;-3.46;-3.42;-3.37;-3.36;-3.21;-3.32	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000003	D	0.97983	0.9336	M	0.88031	2.925	0.46222	D	0.998939	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.999;0.999;0.999;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.98794	1.0737	10	0.87932	D	0	-3.9353	16.1293	0.81414	0.0:0.0:1.0:0.0	.	149;149;149;149;149;149;137;149;149;149;158;149;149;149;149	Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES46;E7ES49;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;G5E987	CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.	R	137;149;149;149;149;149;149;149;149;149;149;149	ENSP00000381946:G137R;ENSP00000381943:G149R;ENSP00000381940:G149R;ENSP00000381938:G149R;ENSP00000348695:G149R;ENSP00000381944:G149R;ENSP00000381945:G149R;ENSP00000381949:G149R;ENSP00000346553:G149R;ENSP00000350463:G149R;ENSP00000430061:G149R;ENSP00000428342:G149R	ENSP00000346553:G149R	G	+	1	0	COL13A1	71310274	1.000000	0.71417	0.998000	0.56505	0.707000	0.40811	4.768000	0.62293	2.559000	0.86315	0.655000	0.94253	GGA		0.622	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		A	71640268	G	A	71640268	3	1	45	1	0	0	0	0	1	0	0	0	3676	1117	39	1	467	1	COL13A1	10	71640268	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		71640268	63894479	36	4280										
PRG3	10394	broad.mit.edu	37	chr11	57146259	57146259	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcatggatagagacaaggttGcctccgtagcatctgctgca	11	10	2	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr11:57146259G>T	ENST00000287143.2	-	4	511	c.402C>A	c.(400-402)ggC>ggA	p.G134G		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.G134G(1)		large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						AGACAAGGTTGCCTCCGTAGC	0.498																																					Melanoma(154;1456 2519 19358 45229)											1	Substitution - coding silent(1)	large_intestine(1)	11											216	207	210					11																	57146259		2201	4296	6497	56902835	SO:0001819	synonymous_variant	10394			AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.402C>A	11.37:g.57146259G>T			56902835	Q5VX23|Q9NXE2	Silent	SNP	ENST00000287143.2	37	CCDS7954.1																																																																																				0.498	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093		T	57146259	G	T	57146259	2	4	45	1	0	0	0	0	0	0	0	1	12514	1306	46	2		2	PRG3	11	57146259	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09		57146259	77860257	37	4281										
PACS1	55690	broad.mit.edu	37	chr11	65983993	65983993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctcaggtgtctgttgcagatCgttctcctgatattgacaat	9	9	3	3			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr11:65983993C>T	ENST00000320580.4	+	6	841	c.808C>T	c.(808-810)Cgt>Tgt	p.R270C		NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	270					protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)	p.R270C(1)	RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						TGTTGCAGATCGTTCTCCTGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											140	128	132					11																	65983993		2201	4295	6496	65740569	SO:0001583	missense	55690			AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115			30032	protein-coding gene	gene with protein product		607492				12855553, 14608369	Standard	NM_018026		Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.808C>T	11.37:g.65983993C>T	ENSP00000316454:p.Arg270Cys		65740569	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Missense_Mutation	SNP	ENST00000320580.4	37	CCDS8129.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324346	0.81580	.	.	ENSG00000175115	ENST00000320580	T	0.19806	2.12	5.32	4.37	0.52481	.	0.053068	0.85682	D	0.000000	T	0.44705	0.1306	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.69824	0.719;0.966	T	0.39901	-0.9591	10	0.72032	D	0.01	-11.3526	15.1718	0.72878	0.0:0.8591:0.1409:0.0	.	270;270	Q6VY07;Q6VY07-2	PACS1_HUMAN;.	C	270	ENSP00000316454:R270C	ENSP00000316454:R270C	R	+	1	0	PACS1	65740569	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.106000	0.77039	2.779000	0.95612	0.491000	0.48974	CGT		0.443	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026		T	65983993	C	T	65983993	3	4	45	1	0	0	0	0	1	0	0	0	11403	884	31	1	830	1	PACS1	11	65983993	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	8837734	65983993	69022523	38	4282										
MCAM	4162	broad.mit.edu	37	chr11	119183069	119183069	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gcgcccactgtgttccttccGggcaggctccagcaccagga	12	16	0	0	rs200709459		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr11:119183069G>A	ENST00000264036.4	-	8	945	c.931C>T	c.(931-933)Cgg>Tgg	p.R311W	MCAM_ENST00000530144.2_5'Flank|MCAM_ENST00000392814.1_Missense_Mutation_p.R260W	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	311	Ig-like C2-type 1.				anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R311W(1)		breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		TGTTCCTTCCGGGCAGGCTCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	81	84					11																	119183069		2199	4295	6494	118688279	SO:0001583	missense	4162			X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.931C>T	11.37:g.119183069G>A	ENSP00000264036:p.Arg311Trp		118688279	O95812|Q59E86|Q6PHR3|Q6ZTR2	Missense_Mutation	SNP	ENST00000264036.4	37	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794640	0.31777	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	T;T	0.12774	2.65;2.65	4.78	0.26	0.15588	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.31702	0.0805	M	0.82923	2.615	0.09310	N	1	D	0.67145	0.996	P	0.58970	0.849	T	0.10291	-1.0636	9	0.72032	D	0.01	-0.4956	9.0336	0.36273	0.0:0.1235:0.3409:0.5356	.	311	P43121	MUC18_HUMAN	W	311;260	ENSP00000264036:R311W;ENSP00000376561:R260W	ENSP00000264036:R311W	R	-	1	2	MCAM	118688279	0.001000	0.12720	0.024000	0.17045	0.153000	0.21895	0.884000	0.28214	0.181000	0.19994	0.561000	0.74099	CGG		0.587	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			A	119183069	G	A	119183069	3	1	45	1	0	0	0	0	1	0	0	0	9398	1115	39	1	1045	1	MCAM	11	119183069	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	53199076	119183069	15823447	39	4283										
OR10G7	390265	broad.mit.edu	37	chr11	123908885	123908885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	aaagaggagtcagcgtggtgTagaaaacggccacaacccca	12	10	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr11:123908885T>C	ENST00000330487.5	-	1	832	c.824A>G	c.(823-825)tAc>tGc	p.Y275C		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y275C(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CAGCGTGGTGTAGAAAACGGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											104	95	98					11																	123908885		2200	4299	6499	123414095	SO:0001583	missense	390265			AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"GPCR / Class A : Olfactory receptors"	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.824A>G	11.37:g.123908885T>C	ENSP00000329689:p.Tyr275Cys		123414095	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.239218	0.22711	.	.	ENSG00000182634	ENST00000330487	T	0.00318	8.12	3.28	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36034	N	0.002828	T	0.00784	0.0026	M	0.91090	3.175	0.35218	D	0.775745	D	0.71674	0.998	D	0.73708	0.981	T	0.54282	-0.8317	10	0.87932	D	0	.	11.7536	0.51862	0.0:0.0:0.0:1.0	.	275	Q8NGN6	O10G7_HUMAN	C	275	ENSP00000329689:Y275C	ENSP00000329689:Y275C	Y	-	2	0	OR10G7	123414095	0.900000	0.30661	0.996000	0.52242	0.063000	0.16089	3.503000	0.53340	1.500000	0.48636	0.455000	0.32223	TAC		0.498	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		C	123908885	T	C	123908885	3	2	45	1	0	0	0	0	1	0	0	0	10933	1638	57	4	115	4	OR10G7	11	123908885	Missense_Mutation	SNP	T	TCGA-AG-3887-01A-01W-1073-09	4725816	123908885	11097631	40	4284										
ROBO3	64221	broad.mit.edu	37	chr11	124740953	124740953	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccccaggaccagatggcagcTcctggagagagcgtggcttt	14	12	0	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr11:124740953T>A	ENST00000397801.1	+	7	1269	c.1077T>A	c.(1075-1077)gcT>gcA	p.A359A	ROBO3_ENST00000538940.1_Silent_p.A337A	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	359	Ig-like C2-type 4.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)		p.A359A(2)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		AGATGGCAGCTCCTGGAGAGA	0.592																																																2	Substitution - coding silent(2)	large_intestine(2)	11											49	54	52					11																	124740953		1966	4139	6105	124246163	SO:0001819	synonymous_variant	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1077T>A	11.37:g.124740953T>A			124246163		Silent	SNP	ENST00000397801.1	37	CCDS44755.1																																																																																				0.592	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		A	124740953	T	A	124740953	2	1	45	1	0	0	0	0	0	0	0	1	13552	1538	54	5		5	ROBO3	11	124740953	Silent	SNP	T	TCGA-AG-3887-01A-01W-1073-09	832068	124740953	10265563	41	4285										
NDUFA9	4704	broad.mit.edu	37	chr12	4771774	4771774	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cgtcggacatctttggaagaGaggatagattccttaattct	10	7	2	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:4771774G>A	ENST00000266544.5	+	6	648	c.628G>A	c.(628-630)Gag>Aag	p.E210K	RP11-500M8.7_ENST00000536588.1_3'UTR	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa	210					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|sodium ion transport (GO:0006814)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)|protein complex binding (GO:0032403)	p.E210K(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						CTTTGGAAGAGAGGATAGATT	0.398																																					Colon(75;996 1244 23946 25294 29232)											1	Substitution - Missense(1)	large_intestine(1)	12											165	157	160					12																	4771774		2203	4300	6503	4642035	SO:0001583	missense	4704			AF050641	CCDS8532.1	12p13.3	2011-09-14	2002-08-29		ENSG00000139180	ENSG00000139180		"Mitochondrial respiratory chain complex / Complex I", "Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	7693	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 22E, member 1", "complex I 39kDa subunit"	603834	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (39kD)"	NDUFS2L		8486360, 19027726	Standard	NM_005002		Approved	SDR22E1, CI-39k	uc001qnc.3	Q16795		ENST00000266544.5:c.628G>A	12.37:g.4771774G>A	ENSP00000266544:p.Glu210Lys		4642035	Q14076|Q2NKX0	Missense_Mutation	SNP	ENST00000266544.5	37	CCDS8532.1	.	.	.	.	.	.	.	.	.	.	G	35	5.420323	0.96111	.	.	ENSG00000139180	ENST00000266544	D	0.93247	-3.19	5.15	5.15	0.70609	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97526	0.9190	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98455	1.0593	10	0.87932	D	0	-1.8039	17.7642	0.88473	0.0:0.0:1.0:0.0	.	210;210	A8K4V2;Q16795	.;NDUA9_HUMAN	K	210	ENSP00000266544:E210K	ENSP00000266544:E210K	E	+	1	0	NDUFA9	4642035	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	9.287000	0.95975	2.530000	0.85305	0.555000	0.69702	GAG		0.398	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398900.2	NM_005002		A	4771774	G	A	4771774	3	1	45	1	0	0	0	0	1	0	0	0	10303	943	33	3	650	3	NDUFA9	12	4771774	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		4771774	129080121	42	4286										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	45	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	20626510	25398284	108453611	43	4287										
PTHLH	5744	broad.mit.edu	37	chr12	28116698	28116698	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gctgatgttcagacacagctCttttgctttgaaagaaaata	8	7	2	4			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:28116698C>G	ENST00000545234.1	-	5	647	c.107G>C	c.(106-108)aGa>aCa	p.R36T	PTHLH_ENST00000535992.1_Missense_Mutation_p.R36T|PTHLH_ENST00000354417.3_Missense_Mutation_p.R36T|PTHLH_ENST00000395872.1_Missense_Mutation_p.R36T|PTHLH_ENST00000539239.1_Missense_Mutation_p.R36T|PTHLH_ENST00000538310.1_Missense_Mutation_p.R36T|PTHLH_ENST00000201015.4_Missense_Mutation_p.R36T|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000395868.3_Missense_Mutation_p.R36T			P12272	PTHR_HUMAN	parathyroid hormone-like hormone	36					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|endochondral ossification (GO:0001958)|endoderm development (GO:0007492)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|lung alveolus development (GO:0048286)|mammary gland bud elongation (GO:0060649)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|nipple sheath formation (GO:0060659)|osteoblast development (GO:0002076)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|protein processing (GO:0016485)|regulation of gene expression (GO:0010468)|skeletal system development (GO:0001501)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)	p.R36T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	10	Lung SC(9;0.184)					AGACACAGCTCTTTTGCTTTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	80	80					12																	28116698		2203	4300	6503	28007965	SO:0001583	missense	5744				CCDS8715.1, CCDS44853.1	12p12.1-p11.2	2014-01-07			ENSG00000087494	ENSG00000087494		"Endogenous ligands"	9607	protein-coding gene	gene with protein product	"osteostatin", "parathyroid hormone-like hormone preproprotein", "parathyroid hormone-related protein preproprotein"	168470				2708388	Standard	NM_002820		Approved	PTHRP, HHM, PLP, PTHR	uc001ril.3	P12272	OTTHUMG00000169221	ENST00000545234.1:c.107G>C	12.37:g.28116698C>G	ENSP00000441765:p.Arg36Thr		28007965	Q15251|Q6FH74	Missense_Mutation	SNP	ENST00000545234.1	37	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568828	0.86439	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963;ENST00000534890	D;D;D;D;D;D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1;-3.1;-3.1;-3.1;-3.1;-3.1	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.93009	0.7775	M	0.66297	2.02	0.52099	D	0.999949	P	0.47484	0.896	P	0.46510	0.519	D	0.93696	0.7011	10	0.87932	D	0	-18.6092	18.7334	0.91744	0.0:1.0:0.0:0.0	.	36	P12272	PTHR_HUMAN	T	36;36;36;36;36;36;36;36;36;44	ENSP00000379213:R36T;ENSP00000441571:R36T;ENSP00000441765:R36T;ENSP00000441890:R36T;ENSP00000346398:R36T;ENSP00000201015:R36T;ENSP00000440613:R36T;ENSP00000379209:R36T;ENSP00000444519:R36T;ENSP00000445157:R44T	ENSP00000201015:R36T	R	-	2	0	PTHLH	28007965	1.000000	0.71417	0.807000	0.32361	0.994000	0.84299	6.248000	0.72418	2.665000	0.90641	0.655000	0.94253	AGA		0.393	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	NM_198965		G	28116698	C	G	28116698	3	3	45	1	0	0	0	0	1	0	0	0	12796	913	32	5	438	5	PTHLH	12	28116698	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	2718414	28116698	105735197	44	4288										
HOXC9	3225	broad.mit.edu	37	chr12	54394194	54394194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cccgtgccctctcagtcgtcCgtggtatatcacccgtacgg	10	16	2	0	rs34136736	byFrequency	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:54394194C>T	ENST00000303450.4	+	1	292	c.222C>T	c.(220-222)tcC>tcT	p.S74S	HOXC-AS1_ENST00000505700.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron|HOXC9_ENST00000504557.1_Intron|HOXC9_ENST00000508190.1_Silent_p.S74S|HOXC-AS1_ENST00000512427.1_RNA	NM_006897.1	NP_008828.1	P31274	HXC9_HUMAN	homeobox C9	74					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.S74S(1)		large_intestine(3)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14						CTCAGTCGTCCGTGGTATATC	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C		1,4405	2.1+/-5.4	0,1,2202	34	33	33		222	1	1	12	dbSNP_126	33	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	HOXC9	NM_006897.1		0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308		74/261	54394194	4,13000	2203	4299	6502	52680461	SO:0001819	synonymous_variant	3225				CCDS8869.1	12q13.13	2011-06-20	2005-12-22			ENSG00000180806		"Homeoboxes / ANTP class : HOXL subclass"	5130	protein-coding gene	gene with protein product		142971	"homeo box C9"	HOX3, HOX3B		1973146	Standard	NM_006897		Approved		uc001seq.3	P31274		ENST00000303450.4:c.222C>T	12.37:g.54394194C>T			52680461	B2RCN7|Q9H1I0	Silent	SNP	ENST00000303450.4	37	CCDS8869.1																																																																																				0.677	HOXC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358958.1			T	54394194	C	T	54394194	2	4	45	1	0	0	0	0	0	0	0	1	7338	639	23	1		1	HOXC9	12	54394194	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	26277496	54394194	79457701	45	4289										
TXNRD1	7296	broad.mit.edu	37	chr12	104645445	104645445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcagtaggtccacatgcacaCgctgtactgaggtaaggctt	11	10	1	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:104645445C>T	ENST00000525566.1	+	2	256	c.232C>T	c.(232-234)Cgc>Tgc	p.R78C	TXNRD1_ENST00000429002.2_Missense_Mutation_p.R78C|TXNRD1_ENST00000526006.1_3'UTR	NM_001093771.2	NP_001087240.1	Q16881	TRXR1_HUMAN	thioredoxin reductase 1	78	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cellular lipid metabolic process (GO:0044255)|mesoderm formation (GO:0001707)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)	p.R78C(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	16					Arsenic trioxide(DB01169)|Flavin adenine dinucleotide(DB03147)	CACATGCACACGCTGTACTGA	0.453																																					Ovarian(139;555 1836 9186 9946 10884)											1	Substitution - Missense(1)	large_intestine(1)	12											91	92	92					12																	104645445		2095	4233	6328	103169575	SO:0001583	missense	7296				CCDS53820.1, CCDS53821.1, CCDS53823.1, CCDS58274.1	12q23-q24.1	2012-03-01							12437	protein-coding gene	gene with protein product		601112				7589432	Standard	NM_001093771		Approved	TXNR, GRIM-12, Trxr1	uc021rcx.2	Q16881		ENST00000525566.1:c.232C>T	12.37:g.104645445C>T	ENSP00000434516:p.Arg78Cys		103169575	B7Z1F4|B7Z3Y8|B7Z904|E9PMY9|F5H780|Q6FI31|Q6VB40|Q6VB41|Q6VB42|Q6VBP2|Q6VBP3|Q6VBP4|Q6VBP5|Q6VBP9|Q6VBQ0|Q6YNQ1|Q76P53|Q7LA96|Q8WVC8|Q99475|Q9UES8|Q9UH79	Missense_Mutation	SNP	ENST00000525566.1	37	CCDS53820.1	.	.	.	.	.	.	.	.	.	.	C	15.52	2.857990	0.51376	.	.	ENSG00000198431	ENST00000525566;ENST00000429002	T;T	0.29655	1.56;1.56	4.85	-1.33	0.09172	Glutaredoxin (2);Thioredoxin-like fold (2);	.	.	.	.	T	0.12561	0.0305	N	0.08118	0	0.09310	N	1	D	0.54397	0.966	B	0.37508	0.252	T	0.21861	-1.0233	9	0.40728	T	0.16	0.0751	9.1985	0.37242	0.0:0.5276:0.0:0.4724	.	78	Q16881	TRXR1_HUMAN	C	78	ENSP00000434516:R78C;ENSP00000412045:R78C	ENSP00000412045:R78C	R	+	1	0	TXNRD1	103169575	0.000000	0.05858	0.000000	0.03702	0.373000	0.29922	0.025000	0.13577	-0.366000	0.08064	0.561000	0.74099	CGC		0.453	TXNRD1-001	KNOWN	basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000389960.1	NM_003330		T	104645445	C	T	104645445	3	4	45	1	0	0	0	0	1	0	0	0	16847	536	19	1	238	1	TXNRD1	12	104645445	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	50251251	104645445	29206450	46	4290										
TMEM132B	114795	broad.mit.edu	37	chr12	126139253	126139253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gaaagtctgcaagaccagatGtaaactcctttcttatgttt	7	8	2	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr12:126139253G>T	ENST00000299308.3	+	9	3242	c.3234G>T	c.(3232-3234)atG>atT	p.M1078I	TMEM132B_ENST00000535886.1_Missense_Mutation_p.M590I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1078						integral component of membrane (GO:0016021)		p.M1078I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		AAGACCAGATGTAAACTCCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											63	58	59					12																	126139253		1865	4084	5949	124705206	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.3234G>T	12.37:g.126139253G>T	ENSP00000299308:p.Met1078Ile		124705206	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138149	0.37728	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.08807	3.83;3.05	5.81	5.81	0.92471	.	0.131674	0.53938	D	0.000055	T	0.09949	0.0244	L	0.34521	1.04	0.43550	D	0.995854	B	0.28933	0.228	B	0.28011	0.085	T	0.17289	-1.0374	10	0.38643	T	0.18	.	20.0838	0.97793	0.0:0.0:1.0:0.0	.	1078	Q14DG7	T132B_HUMAN	I	1078;590	ENSP00000299308:M1078I;ENSP00000440436:M590I	ENSP00000299308:M1078I	M	+	3	0	TMEM132B	124705206	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.845000	0.92153	2.741000	0.93983	0.655000	0.94253	ATG		0.408	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	126139253	G	T	126139253	3	4	45	1	0	0	0	0	1	0	0	0	16085	1377	48	2	3268	2	TMEM132B	12	126139253	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	21493808	126139253	7712642	47	4291										
UGGT2	55757	broad.mit.edu	37	chr13	96553120	96553120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tttaagtacatcttgacagaAcaactggtgagttcgaaaaa	8	6	1	3			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr13:96553120A>G	ENST00000376747.3	-	22	2645	c.2575T>C	c.(2575-2577)Ttc>Ctc	p.F859L		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	859					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.F859L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TCTTGACAGAACAACTGGTGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											128	120	123					13																	96553120		2203	4300	6503	95351121	SO:0001583	missense	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2575T>C	13.37:g.96553120A>G	ENSP00000365938:p.Phe859Leu		95351121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.744124	0.69418	.	.	ENSG00000102595	ENST00000376747	T	0.08193	3.12	5.79	5.79	0.91817	.	0.048765	0.85682	D	0.000000	T	0.11707	0.0285	L	0.60455	1.87	0.80722	D	1	B	0.10296	0.003	B	0.15484	0.013	T	0.07616	-1.0763	10	0.23891	T	0.37	-13.5522	16.1338	0.81465	1.0:0.0:0.0:0.0	.	859	Q9NYU1	UGGG2_HUMAN	L	859	ENSP00000365938:F859L	ENSP00000365938:F859L	F	-	1	0	UGGT2	95351121	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.408000	0.90221	2.216000	0.71823	0.459000	0.35465	TTC		0.358	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		G	96553120	A	G	96553120	3	3	45	1	0	0	0	0	1	0	0	0	16982	43	2	4	2047	4	UGGT2	13	96553120	Missense_Mutation	SNP	A	TCGA-AG-3887-01A-01W-1073-09		96553120	18616758	48	4292										
COL4A1	1282	broad.mit.edu	37	chr13	110845216	110845216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctgtggcccgggaggcccccGatatccgtctatatcacaga	11	14	2	1	rs369960952		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr13:110845216G>A	ENST00000375820.4	-	23	1547	c.1426C>T	c.(1426-1428)Cgg>Tgg	p.R476W	COL4A1_ENST00000543140.1_Missense_Mutation_p.R476W	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	476	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.R476R(1)|p.R470W(1)|p.R476W(1)|p.R470R(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GGAGGCCCCCGATATCCGTCT	0.498													G|||	1	0.000199681	0	0	5008	,	,		17658	0		0	False		,,,				2504	0.001															4	Substitution - Missense(2)|Substitution - coding silent(2)	large_intestine(2)|prostate(2)	13						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	67	69	68		1426	4.9	0.1	13		68	0,8600		0,0,4300	no	missense	COL4A1	NM_001845.4	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	476/1670	110845216	1,13005	2203	4300	6503	109643217	SO:0001583	missense	1282			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1426C>T	13.37:g.110845216G>A	ENSP00000364979:p.Arg476Trp		109643217	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.538106	0.27475	2.27E-4	0.0	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198;ENST00000543140	D;D	0.93859	-3.3;-3.3	4.87	4.87	0.63330	.	0.363174	0.24262	N	0.040075	D	0.95993	0.8695	M	0.91768	3.24	0.29138	N	0.879201	D	0.67145	0.996	P	0.54815	0.761	D	0.93064	0.6477	10	0.66056	D	0.02	.	11.1297	0.48339	0.0854:0.0:0.9146:0.0	.	476	P02462	CO4A1_HUMAN	W	470;476;476;476	ENSP00000364979:R476W;ENSP00000443348:R476W	ENSP00000364973:R470W	R	-	1	2	COL4A1	109643217	1.000000	0.71417	0.060000	0.19600	0.064000	0.16182	4.956000	0.63645	2.400000	0.81607	0.563000	0.77884	CGG		0.498	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			A	110845216	G	A	110845216	3	1	45	1	0	0	0	0	1	0	0	0	3695	1057	37	1	3703	1	COL4A1	13	110845216	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	14292096	110845216	4324662	49	4293										
ARHGAP5	394	broad.mit.edu	37	chr14	32562544	32562544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	agttactgacagccaagcagAtttttttgaaaatgaggcta	9	6	0	4			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr14:32562544A>T	ENST00000345122.3	+	2	2984	c.2669A>T	c.(2668-2670)gAt>gTt	p.D890V	ARHGAP5_ENST00000556611.1_Missense_Mutation_p.D890V|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.D890V|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.D890V	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	890					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.D890V(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGCCAAGCAGATTTTTTTGAA	0.408																																					NSCLC(9;77 350 3443 29227 41353)											1	Substitution - Missense(1)	large_intestine(1)	14											55	53	54					14																	32562544		2203	4298	6501	31632295	SO:0001583	missense	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.2669A>T	14.37:g.32562544A>T	ENSP00000371897:p.Asp890Val		31632295	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.817800	0.50633	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.66	4.52	0.55395	.	0.041485	0.85682	D	0.000000	T	0.54854	0.1884	L	0.46157	1.445	0.80722	D	1	D;D	0.65815	0.995;0.992	D;D	0.69142	0.962;0.916	T	0.56019	-0.8048	10	0.66056	D	0.02	.	11.8736	0.52534	0.9315:0.0:0.0685:0.0	.	890;890	Q13017-2;Q13017	.;RHG05_HUMAN	V	890	ENSP00000452222:D890V;ENSP00000441692:D890V;ENSP00000371897:D890V;ENSP00000393307:D890V	ENSP00000371897:D890V	D	+	2	0	ARHGAP5	31632295	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.456000	0.80751	1.076000	0.40961	0.528000	0.53228	GAT		0.408	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		T	32562544	A	T	32562544	3	4	45	1	0	0	0	0	1	0	0	0	886	333	12	5	2671	5	ARHGAP5	14	32562544	Missense_Mutation	SNP	A	TCGA-AG-3887-01A-01W-1073-09		32562544	74786996	50	4294										
AKAP6	9472	broad.mit.edu	37	chr14	33201708	33201708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	acctgaaaaagacggagctgCttagtaaggttgaagctttg	12	6	0	3			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr14:33201708C>T	ENST00000280979.4	+	10	3219	c.3049C>T	c.(3049-3051)Ctt>Ttt	p.L1017F	AKAP6_ENST00000557272.1_Missense_Mutation_p.L1017F|AKAP6_ENST00000557354.1_Missense_Mutation_p.L1017F	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1017					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.L1017F(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GACGGAGCTGCTTAGTAAGGT	0.388																																					Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Missense(1)	large_intestine(1)	14											131	133	132					14																	33201708		2203	4299	6502	32271459	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3049C>T	14.37:g.33201708C>T	ENSP00000280979:p.Leu1017Phe		32271459	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093622	0.76756	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.23147	3.3;1.92;2.07	5.49	4.61	0.57282	.	0.000000	0.64402	D	0.000017	T	0.37073	0.0990	N	0.24115	0.695	0.48040	D	0.99957	D;D	0.89917	1.0;0.999	D;D	0.85130	0.994;0.997	T	0.28170	-1.0052	10	0.66056	D	0.02	-3.4835	14.3844	0.66934	0.0:0.9284:0.0:0.0716	.	1017;1017	A7E242;Q13023	.;AKAP6_HUMAN	F	1017	ENSP00000280979:L1017F;ENSP00000450531:L1017F;ENSP00000451247:L1017F	ENSP00000280979:L1017F	L	+	1	0	AKAP6	32271459	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.593000	0.61034	1.308000	0.44962	0.585000	0.79938	CTT		0.388	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33201708	C	T	33201708	3	4	45	1	0	0	0	0	1	0	0	0	455	797	28	3	3083	3	AKAP6	14	33201708	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	639164	33201708	74147832	51	4295										
POLE2	5427	broad.mit.edu	37	chr14	50120781	50120781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	agtgatgctttcagcaagtgGtggcctataaaaacaattta	9	6	1	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr14:50120781G>A	ENST00000216367.5	-	15	1237	c.1138C>T	c.(1138-1140)Cca>Tca	p.P380S	POLE2_ENST00000539565.2_Missense_Mutation_p.P354S|POLE2_ENST00000554396.1_Missense_Mutation_p.P380S|POLE2_ENST00000556584.1_5'UTR	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	380					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)	p.P380S(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	TCAGCAAGTGGTGGCCTATAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	72	71					14																	50120781		2203	4300	6503	49190531	SO:0001583	missense	5427			AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.1138C>T	14.37:g.50120781G>A	ENSP00000216367:p.Pro380Ser		49190531	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Missense_Mutation	SNP	ENST00000216367.5	37	CCDS32073.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873276	0.91664	.	.	ENSG00000100479	ENST00000216367;ENST00000539565;ENST00000554396	T;T;T	0.50813	0.73;0.73;0.73	6.16	6.16	0.99307	DNA polymerase alpha/epsilon, subunit B (1);	0.000000	0.85682	D	0.000000	T	0.68595	0.3018	M	0.62154	1.92	0.80722	D	1	D;D;D	0.89917	0.976;1.0;1.0	P;D;D	0.73708	0.883;0.974;0.981	T	0.64896	-0.6299	10	0.51188	T	0.08	-15.3232	20.8598	0.99761	0.0:0.0:1.0:0.0	.	380;354;380	A4FU92;B4DDE6;P56282	.;.;DPOE2_HUMAN	S	380;354;380	ENSP00000216367:P380S;ENSP00000446313:P354S;ENSP00000451621:P380S	ENSP00000216367:P380S	P	-	1	0	POLE2	49190531	1.000000	0.71417	0.997000	0.53966	0.731000	0.41821	9.808000	0.99193	2.937000	0.99478	0.650000	0.86243	CCA		0.299	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692		A	50120781	G	A	50120781	3	1	45	1	0	0	0	0	1	0	0	0	12228	1261	44	3	465	3	POLE2	14	50120781	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	16919073	50120781	57228759	52	4296										
L2HGDH	79944	broad.mit.edu	37	chr14	50734557	50734557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	aaggcaagaactgcattaggCcctagccaaatactgccatc	8	12	0	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr14:50734557C>T	ENST00000267436.4	-	8	1375	c.978G>A	c.(976-978)ggG>ggA	p.G326G	L2HGDH_ENST00000261699.4_Silent_p.G326G|L2HGDH_ENST00000421284.3_Silent_p.G326G			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	326					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)	p.G326G(1)		kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					CTGCATTAGGCCCTAGCCAAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	14											113	101	105					14																	50734557		2203	4300	6503	49804307	SO:0001819	synonymous_variant	79944				CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"2-hydroxyglutarate dehydrogenase"	609584	"chromosome 14 open reading frame 160"	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.978G>A	14.37:g.50734557C>T			49804307	Q9BRR1	Silent	SNP	ENST00000267436.4	37	CCDS9698.1																																																																																				0.398	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884		T	50734557	C	T	50734557	2	4	45	1	0	0	0	0	0	0	0	1	8612	726	26	3		3	L2HGDH	14	50734557	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	613776	50734557	56614983	53	4297										
SGPP1	81537	broad.mit.edu	37	chr14	64153110	64153110	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	agctaaaggtaatgtatctaGagaaggatctaatactagac	9	5	2	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr14:64153110G>C	ENST00000247225.6	-	3	1133	c.1039C>G	c.(1039-1041)Cta>Gta	p.L347V		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	347					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)	p.L347V(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		AATGTATCTAGAGAAGGATCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											86	77	80					14																	64153110		2203	4300	6503	63222863	SO:0001583	missense	81537			AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.1039C>G	14.37:g.64153110G>C	ENSP00000247225:p.Leu347Val		63222863	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	37	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.806504	0.00606	.	.	ENSG00000126821	ENST00000247225	.	.	.	5.99	1.84	0.25277	.	0.327305	0.28815	N	0.014053	T	0.24005	0.0581	L	0.57536	1.79	0.09310	N	0.999997	P	0.41080	0.737	B	0.31946	0.138	T	0.18681	-1.0329	9	0.17369	T	0.5	-19.5421	6.3905	0.21583	0.2634:0.0:0.6206:0.116	.	347	Q9BX95	SGPP1_HUMAN	V	347	.	ENSP00000247225:L347V	L	-	1	2	SGPP1	63222863	0.997000	0.39634	0.120000	0.21714	0.070000	0.16714	2.362000	0.44169	0.075000	0.16796	-0.150000	0.13652	CTA		0.438	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791		C	64153110	G	C	64153110	3	2	45	1	0	0	0	0	1	0	0	0	14256	933	33	5	290	5	SGPP1	14	64153110	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	13418553	64153110	43196430	54	4298										
ATP10A	57194	broad.mit.edu	37	chr15	25961909	25961909	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ctgatccggggacgtgacgaCgactgtgttgcagatggtga	16	8	0	4			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr15:25961909C>A	ENST00000356865.6	-	9	1855	c.1744G>T	c.(1744-1746)Gtc>Ttc	p.V582F		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	582					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V582F(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GACGTGACGACGACTGTGTTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	15											154	136	142					15																	25961909		2203	4300	6503	23513002	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1744G>T	15.37:g.25961909C>A	ENSP00000349325:p.Val582Phe		23513002	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426030	0.83667	.	.	ENSG00000206190	ENST00000356865	T	0.71817	-0.6	5.39	5.39	0.77823	HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.062052	0.64402	D	0.000005	D	0.86464	0.5939	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88386	0.3005	10	0.87932	D	0	-29.2495	19.1608	0.93531	0.0:1.0:0.0:0.0	.	582	O60312	AT10A_HUMAN	F	582	ENSP00000349325:V582F	ENSP00000349325:V582F	V	-	1	0	ATP10A	23513002	0.999000	0.42202	0.371000	0.25978	0.467000	0.32768	3.877000	0.56123	2.521000	0.84997	0.655000	0.94253	GTC		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25961909	C	A	25961909	3	1	45	1	0	0	0	0	1	0	0	0	1117	536	19	2	2807	2	ATP10A	15	25961909	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09		25961909	76569483	55	4299										
HDC	3067	broad.mit.edu	37	chr15	50546857	50546857	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcaaagtggattcactgaccGtgctctgcaggggaaaagga	13	8	3	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr15:50546857G>A	ENST00000267845.3	-	5	848	c.446C>T	c.(445-447)aCg>aTg	p.T149M	HDC_ENST00000543581.1_Missense_Mutation_p.T149M	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.T149M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TTCACTGACCGTGCTCTGCAG	0.468																																					GBM(95;1627 1936 6910 9570)											1	Substitution - Missense(1)	large_intestine(1)	15											72	69	70					15																	50546857		2196	4295	6491	48334149	SO:0001583	missense	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.446C>T	15.37:g.50546857G>A	ENSP00000267845:p.Thr149Met		48334149		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.009858	0.75046	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.40225	1.04;1.04	5.79	4.82	0.62117	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.053861	0.64402	D	0.000001	T	0.75488	0.3856	H	0.95917	3.74	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.83611	0.0134	10	0.87932	D	0	-14.1593	16.3449	0.83120	0.0:0.1318:0.8682:0.0	.	149;149	B7ZM01;P19113	.;DCHS_HUMAN	M	149	ENSP00000267845:T149M;ENSP00000440252:T149M	ENSP00000267845:T149M	T	-	2	0	HDC	48334149	1.000000	0.71417	0.972000	0.41901	0.611000	0.37282	7.658000	0.83755	2.733000	0.93635	0.655000	0.94253	ACG		0.468	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50546857	G	A	50546857	3	1	45	1	0	0	0	0	1	0	0	0	7036	1145	40	1	1574	1	HDC	15	50546857	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	24584948	50546857	51984535	56	4300										
BCL2A1	597	broad.mit.edu	37	chr15	80263104	80263104	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tatgaactccgcaacaaaatAtgaaatctccttataggtat	5	8	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr15:80263104A>G	ENST00000267953.3	-	1	684	c.358T>C	c.(358-360)Tat>Cat	p.Y120H	BCL2A1_ENST00000335661.6_Missense_Mutation_p.Y120H	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	120					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.Y120H(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						GCAACAAAATATGAAATCTCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											117	124	122					15																	80263104		2203	4300	6503	78050159	SO:0001583	missense	597				CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.358T>C	15.37:g.80263104A>G	ENSP00000267953:p.Tyr120His		78050159	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	.	.	.	.	.	.	.	.	.	.	A	4.056	0.008054	0.07912	.	.	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.11169	2.8;2.8	5.48	-1.13	0.09775	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	1.084810	0.06993	N	0.821914	T	0.06462	0.0166	N	0.16602	0.42	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.12837	0.008;0.005	T	0.43032	-0.9416	10	0.33141	T	0.24	-12.9343	5.7601	0.18195	0.5215:0.0:0.3534:0.1251	.	120;120	Q86W13;Q16548	.;B2LA1_HUMAN	H	120	ENSP00000267953:Y120H;ENSP00000335250:Y120H	ENSP00000267953:Y120H	Y	-	1	0	BCL2A1	78050159	0.027000	0.19231	0.000000	0.03702	0.000000	0.00434	0.551000	0.23361	-0.189000	0.10482	-1.151000	0.01829	TAT		0.388	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		G	80263104	A	G	80263104	3	3	45	1	0	0	0	0	1	0	0	0	1367	449	16	4	237	4	BCL2A1	15	80263104	Missense_Mutation	SNP	A	TCGA-AG-3887-01A-01W-1073-09	29716247	80263104	22268288	57	4301										
KIAA1199	57214	broad.mit.edu	37	chr15	81229022	81229022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tgggttttaaaagatgtacaTtcaagcctacaagaccagta	8	7	1	2			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr15:81229022T>C	ENST00000394685.3	+	24	3436	c.3017T>C	c.(3016-3018)aTt>aCt	p.I1006T	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Missense_Mutation_p.I1006T|KIAA1199_ENST00000356249.5_Missense_Mutation_p.I1006T			Q8WUJ3	CEMIP_HUMAN		1006					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.I1006T(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						AAGATGTACATTCAAGCCTAC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	136	134					15																	81229022		2203	4300	6503	79016077	SO:0001583	missense	57214																														ENST00000394685.3:c.3017T>C	15.37:g.81229022T>C	ENSP00000378177:p.Ile1006Thr		79016077	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349844	0.82132	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.72282	-0.64;-0.64;-0.64	5.4	5.4	0.78164	.	0.057734	0.64402	D	0.000001	T	0.76849	0.4045	M	0.72118	2.19	0.48571	D	0.999671	P	0.52463	0.953	P	0.50109	0.631	T	0.79383	-0.1826	10	0.52906	T	0.07	-19.8121	15.4265	0.75055	0.0:0.0:0.0:1.0	.	1006	Q8WUJ3	K1199_HUMAN	T	1006	ENSP00000220244:I1006T;ENSP00000378177:I1006T;ENSP00000348583:I1006T	ENSP00000220244:I1006T	I	+	2	0	KIAA1199	79016077	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.386000	0.79775	2.045000	0.60652	0.383000	0.25322	ATT		0.463	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			C	81229022	T	C	81229022	3	2	45	1	0	0	0	0	1	0	0	0	8234	1493	52	4	3103	4	KIAA1199	15	81229022	Missense_Mutation	SNP	T	TCGA-AG-3887-01A-01W-1073-09	965918	81229022	21302370	58	4302										
SALL1	6299	broad.mit.edu	37	chr16	51174728	51174728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cctctctccggtatgggaacGcaagtggatctgcaaggcac	12	12	2	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr16:51174728G>A	ENST00000251020.4	-	2	1438	c.1405C>T	c.(1405-1407)Cgt>Tgt	p.R469C	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.R372C|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	469					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R469C(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GTATGGGAACGCAAGTGGATC	0.507																																					GBM(103;1352 1446 1855 4775 8890)											1	Substitution - Missense(1)	large_intestine(1)	16	GRCh37	HI971487	SALL1	I							99	93	95					16																	51174728		2198	4300	6498	49732229	SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1405C>T	16.37:g.51174728G>A	ENSP00000251020:p.Arg469Cys		49732229	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831141	0.71258	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.25749	1.78;1.78	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	M	0.83852	2.665	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63967	-0.6517	10	0.87932	D	0	.	18.685	0.91560	0.0:0.0:1.0:0.0	.	469	Q9NSC2	SALL1_HUMAN	C	469;372;433	ENSP00000251020:R469C;ENSP00000407914:R372C	ENSP00000251020:R469C	R	-	1	0	SALL1	49732229	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.864000	0.99589	2.386000	0.81285	0.563000	0.77884	CGT		0.507	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51174728	G	A	51174728	3	1	45	1	0	0	0	0	1	0	0	0	13847	1087	38	1	2577	1	SALL1	16	51174728	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		51174728	39180025	59	4303										
CES1	1066	broad.mit.edu	37	chr16	55857578	55857578	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cccaccatcagcccccctccGtggatccacaccatcacctg	5	22	2	0	rs373389314		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr16:55857578G>A	ENST00000361503.4	-	4	550	c.420C>T	c.(418-420)caC>caT	p.H140H	CES1_ENST00000422046.2_Silent_p.H140H|CES1_ENST00000566555.1_5'UTR|CES1_ENST00000360526.3_Silent_p.H141H			P23141	EST1_HUMAN	carboxylesterase 1	140					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.H141H(1)							all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GCCCCCCTCCGTGGATCCACA	0.562																																					NSCLC(162;1801 2756 42904 52896)											1	Substitution - coding silent(1)	large_intestine(1)	16						G	,,	2,4390		0,2,2194	64	58	60		420,423,420	-7.7	0.7	16		60	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	,,	0,2,6492	AA,AG,GG		0.0,0.0455,0.0154	,,	140/568,141/569,140/567	55857578	2,12986	2196	4298	6494	54415079	SO:0001819	synonymous_variant	1066			BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.420C>T	16.37:g.55857578G>A			54415079	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																				0.562	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		A	55857578	G	A	55857578	2	1	45	1	0	0	0	0	0	0	0	1	3275	1136	40	1		1	CES1	16	55857578	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09	4682850	55857578	34497175	60	4304										
TRPV1	7442	broad.mit.edu	37	chr17	3494318	3494318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cttcaggctgtccgtttgccGcgcgatctccaggagcaggg	14	13	2	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr17:3494318G>A	ENST00000571088.1	-	4	757	c.544C>T	c.(544-546)Cgg>Tgg	p.R182W	TRPV1_ENST00000399759.3_Missense_Mutation_p.R182W|TRPV1_ENST00000399756.4_Missense_Mutation_p.R182W|TRPV1_ENST00000576351.1_Missense_Mutation_p.R182W|TRPV1_ENST00000425167.2_Missense_Mutation_p.R182W|TRPV1_ENST00000310522.5_Missense_Mutation_p.R182W|TRPV1_ENST00000174621.6_Missense_Mutation_p.R180W|SHPK_ENST00000572705.1_Missense_Mutation_p.R182W	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	182					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)	p.R182W(2)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCCGTTTGCCGCGCGATCTCC	0.622																																					Melanoma(38;962 1762 15789)											2	Substitution - Missense(2)	large_intestine(2)	17											65	67	67					17																	3494318		2132	4226	6358	3441067	SO:0001583	missense	7442			AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.544C>T	17.37:g.3494318G>A	ENSP00000461007:p.Arg182Trp		3441067	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.034963	0.54896	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	T;T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61;-0.61	5.19	1.95	0.26073	Ankyrin repeat-containing domain (2);	0.228496	0.44285	D	0.000472	T	0.73481	0.3592	L	0.59436	1.845	0.28444	N	0.916665	D;D;D;D	0.76494	0.991;0.999;0.999;0.998	B;P;P;B	0.57776	0.356;0.505;0.827;0.404	T	0.65985	-0.6035	10	0.87932	D	0	-30.8259	7.4197	0.27065	0.0:0.2441:0.3757:0.3802	.	182;180;182;182	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	W	182;182;180;182;182	ENSP00000382661:R182W;ENSP00000382659:R182W;ENSP00000174621:R180W;ENSP00000409627:R182W;ENSP00000311692:R182W	ENSP00000174621:R180W	R	-	1	2	TRPV1	3441067	0.986000	0.35501	0.998000	0.56505	0.471000	0.32888	2.311000	0.43717	1.321000	0.45227	-0.152000	0.13540	CGG		0.622	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		A	3494318	G	A	3494318	3	1	45	1	0	0	0	0	1	0	0	0	16635	1086	38	1	1700	1	TRPV1	17	3494318	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		3494318	77700892	61	4305										
VTN	7448	broad.mit.edu	37	chr17	26694440	26694440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccagtactgagcgatggagcGtgggtagggagggtccacag	18	8	0	1	rs201545006		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr17:26694440G>A	ENST00000226218.4	-	8	2005	c.1387C>T	c.(1387-1389)Cgc>Tgc	p.R463C	TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_Intron|CTB-96E2.3_ENST00000591482.1_RNA|CTB-96E2.2_ENST00000555059.2_Intron|VTN_ENST00000536498.1_Intron|VTN_ENST00000431468.1_5'Flank	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	463					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.R463C(1)		kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GCGATGGAGCGTGGGTAGGGA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	96	102					17																	26694440		2203	4300	6503	23718567	SO:0001583	missense	7448			BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"Endogenous ligands"	12724	protein-coding gene	gene with protein product	"serum spreading factor", "somatomedin B", "complement S-protein"	193190	"vitronectin (serum spreading factor, somatomedin B, complement S-protein)"			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.1387C>T	17.37:g.26694440G>A	ENSP00000226218:p.Arg463Cys		23718567	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796665	0.70567	.	.	ENSG00000255604	ENST00000226218	T	0.03242	4.0	5.45	5.45	0.79879	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.27027	0.0662	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.06373	-1.0830	10	0.87932	D	0	-29.6817	19.4714	0.94965	0.0:0.0:1.0:0.0	.	463	P04004	VTNC_HUMAN	C	463	ENSP00000226218:R463C	ENSP00000226218:R463C	R	-	1	0	AC002094.1	23718567	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	4.607000	0.61133	2.837000	0.97791	0.591000	0.81541	CGC		0.617	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638		A	26694440	G	A	26694440	3	1	45	1	0	0	0	0	1	0	0	0	17277	1145	40	1	53	1	VTN	17	26694440	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	23200122	26694440	54500770	62	4306										
SMAD4	4089	broad.mit.edu	37	chr18	48604788	48604788	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccgggccctccagctcctagAcgaagtacttcataccatgc	8	16	1	1	rs377767385		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr18:48604788A>T	ENST00000342988.3	+	12	2148	c.1610A>T	c.(1609-1611)gAc>gTc	p.D537V	SMAD4_ENST00000588745.1_Missense_Mutation_p.D441V|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.D537V	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	537	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.D537G(1)|p.L536fs*11(1)|p.L536fs*14(1)|p.D537V(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CAGCTCCTAGACGAAGTACTT	0.483																																																42	Whole gene deletion(36)|Substitution - Missense(2)|Deletion - Frameshift(2)|Unknown(2)	pancreas(26)|large_intestine(6)|lung(3)|breast(3)|stomach(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											79	81	81					18																	48604788		2203	4300	6503	46858786	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1610A>T	18.37:g.48604788A>T	ENSP00000341551:p.Asp537Val		46858786	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703094	0.68501	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98090	-4.71;-4.71	6.07	6.07	0.98685	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (1);	0.000000	0.85682	D	0.000000	D	0.99045	0.9673	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99509	1.0955	10	0.87932	D	0	.	15.6232	0.76824	1.0:0.0:0.0:0.0	.	537	Q13485	SMAD4_HUMAN	V	537	ENSP00000341551:D537V;ENSP00000381452:D537V	ENSP00000341551:D537V	D	+	2	0	SMAD4	46858786	1.000000	0.71417	0.989000	0.46669	0.955000	0.61496	9.118000	0.94355	2.326000	0.78906	0.533000	0.62120	GAC		0.483	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48604788	A	T	48604788	3	4	45	1	0	0	0	0	1	0	0	0	14797	275	10	5	1652	5	SMAD4	18	48604788	Missense_Mutation	SNP	A	TCGA-AG-3887-01A-01W-1073-09		48604788	29472460	63	4307										
ELL	8178	broad.mit.edu	37	chr19	18576618	18576618	+	Frame_Shift_Del	DEL	C	C	-													0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gcgcctcacctggagacataCtgctggatgcagtcgaagct							TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:18576618delC	ENST00000262809.4	-	3	365	c.294delG	c.(292-294)cagfs	p.Q98fs	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	98					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)	p.Q98fs*99(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		TGGAGACATACTGCTGGATGC	0.662			T	MLL	AL																																		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	1	Deletion - Frameshift(1)	large_intestine(1)	19											38	41	40					19																	18576618		2203	4300	6503	18437618	SO:0001589	frameshift_variant	8178			U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23114	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 68"	600284	"chromosome 19 open reading frame 17"	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.294delG	19.37:g.18576618delC	ENSP00000262809:p.Gln98fs		18437618		Frame_Shift_Del	DEL	ENST00000262809.4	37	CCDS12380.1																																																																																				0.662	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		-	18576618	C	-	18576618	7	5	45	1	0	1	0	1	0	0	0	0	5075	564	20	0	1611	0	ELL	19	18576618	Frame_Shift_Del	DEL	C	TCGA-AG-3887-01A-01W-1073-09		18576618	40552365	64	4308										
CILP2	148113	broad.mit.edu	37	chr19	19655854	19655854	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cactcccggccaccgtgggcGtcacccagccctacctggac	10	20	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:19655854G>A	ENST00000291495.5	+	8	2585	c.2500G>A	c.(2500-2502)Gtc>Atc	p.V834I	CILP2_ENST00000586018.1_Missense_Mutation_p.V840I	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	834						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.V834I(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CACCGTGGGCGTCACCCAGCC	0.711																																																1	Substitution - Missense(1)	large_intestine(1)	19											15	15	15					19																	19655854		2083	4088	6171	19516854	SO:0001583	missense	148113			AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2500G>A	19.37:g.19655854G>A	ENSP00000291495:p.Val834Ile		19516854	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366199	0.82463	.	.	ENSG00000160161	ENST00000291495	T	0.10763	2.84	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	L	0.53249	1.67	0.52501	D	0.99995	D;D	0.71674	0.996;0.998	P;P	0.58520	0.762;0.84	T	0.00241	-1.1886	10	0.48119	T	0.1	-41.2155	16.2965	0.82776	0.0:0.0:1.0:0.0	.	834;834	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	I	834	ENSP00000291495:V834I	ENSP00000291495:V834I	V	+	1	0	CILP2	19516854	1.000000	0.71417	0.827000	0.32855	0.850000	0.48378	9.533000	0.98059	2.446000	0.82766	0.555000	0.69702	GTC		0.711	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19655854	G	A	19655854	3	1	45	1	0	0	0	0	1	0	0	0	3436	1145	40	1	2530	1	CILP2	19	19655854	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	1079236	19655854	39473129	65	4309										
CHST8	64377	broad.mit.edu	37	chr19	34180193	34180193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cctgcgacctggaacaatgcGgctggcctgcatgttctctt	11	13	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:34180193G>A	ENST00000262622.4	+	2	784	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	CHST8_ENST00000604556.1_3'UTR|CHST8_ENST00000438847.3_Missense_Mutation_p.R9Q|CHST8_ENST00000434302.1_Missense_Mutation_p.R9Q	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	9					carbohydrate biosynthetic process (GO:0016051)|central nervous system development (GO:0007417)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.R9Q(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(5)	27	Esophageal squamous(110;0.162)					GGAACAATGCGGCTGGCCTGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											98	90	93					19																	34180193		2203	4300	6503	38872033	SO:0001583	missense	64377			AB047801	CCDS12433.1	19q13.1	2008-02-05				ENSG00000124302		"Sulfotransferases, membrane-bound"	15993	protein-coding gene	gene with protein product		610190				10988300, 11001942	Standard	NM_001127895		Approved	GALNAC-4-ST1	uc002nut.4	Q9H2A9		ENST00000262622.4:c.26G>A	19.37:g.34180193G>A	ENSP00000262622:p.Arg9Gln		38872033	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	37	CCDS12433.1	.	.	.	.	.	.	.	.	.	.	G	33	5.196322	0.94960	.	.	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.80393	-1.37;-1.37;-1.37	5.39	5.39	0.77823	.	0.000000	0.41500	D	0.000865	T	0.81945	0.4930	L	0.27053	0.805	0.37588	D	0.920068	D	0.76494	0.999	P	0.61275	0.886	T	0.81200	-0.1041	10	0.25106	T	0.35	-23.9943	18.1353	0.89617	0.0:0.0:1.0:0.0	.	9	Q9H2A9	CHST8_HUMAN	Q	9	ENSP00000392604:R9Q;ENSP00000393879:R9Q;ENSP00000262622:R9Q	ENSP00000262622:R9Q	R	+	2	0	CHST8	38872033	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.967000	0.49216	2.507000	0.84556	0.591000	0.81541	CGG		0.642	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467		A	34180193	G	A	34180193	3	1	45	1	0	0	0	0	1	0	0	0	3416	1116	39	1	28	1	CHST8	19	34180193	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09	14524339	34180193	24948790	66	4310										
GPI	2821	broad.mit.edu	37	chr19	34857731	34857731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cgcccgggagcggatgttcaAtggtgagaagatcaactaca	13	9	2	2	rs370578920		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:34857731A>G	ENST00000356487.5	+	3	498	c.257A>G	c.(256-258)aAt>aGt	p.N86S	GPI_ENST00000586425.1_Missense_Mutation_p.N86S|GPI_ENST00000415930.3_Missense_Mutation_p.N125S	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	86					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)	p.N86S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					CGGATGTTCAATGGTGAGAAG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19						A	SER/ASN,SER/ASN	0,4406		0,0,2203	81	81	81		257,374	-5.9	0.1	19		81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPI	NM_000175.3,NM_001184722.1	46,46	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	86/559,125/570	34857731	1,13005	2203	4300	6503	39549571	SO:0001583	missense	2821			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"glucose phosphate isomerase"			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.257A>G	19.37:g.34857731A>G	ENSP00000348877:p.Asn86Ser		39549571	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Missense_Mutation	SNP	ENST00000356487.5	37	CCDS12437.1	.	.	.	.	.	.	.	.	.	.	A	4.310	0.056813	0.08339	0.0	1.16E-4	ENSG00000105220	ENST00000415930;ENST00000356487;ENST00000392234	D;D	0.93133	-3.17;-3.17	5.54	-5.86	0.02304	.	0.834933	0.11656	N	0.542343	T	0.75034	0.3795	N	0.00395	-1.55	0.09310	N	1	B;B;B;B;B	0.23806	0.0;0.0;0.0;0.091;0.0	B;B;B;B;B	0.36959	0.001;0.003;0.001;0.237;0.0	T	0.70204	-0.4936	10	0.02654	T	1	-12.9609	11.855	0.52431	0.1382:0.3116:0.5502:0.0	.	86;125;69;407;86	B4DE36;B4DG39;B4DVJ0;Q59F85;P06744	.;.;.;.;G6PI_HUMAN	S	125;86;407	ENSP00000405573:N125S;ENSP00000348877:N86S	ENSP00000348877:N86S	N	+	2	0	GPI	39549571	0.000000	0.05858	0.149000	0.22428	0.953000	0.61014	-0.583000	0.05807	-1.389000	0.02090	0.459000	0.35465	AAT		0.602	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3			G	34857731	A	G	34857731	3	3	45	1	0	0	0	0	1	0	0	0	6631	101	4	4	388	4	GPI	19	34857731	Missense_Mutation	SNP	A	TCGA-AG-3887-01A-01W-1073-09	677538	34857731	24271252	67	4311										
RYR1	6261	broad.mit.edu	37	chr19	38989869	38989869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	cctggacttcctgcgctttgCtgtcttcgtcaacggtgagg	12	12	2	1			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:38989869C>A	ENST00000359596.3	+	43	7013	c.7013C>A	c.(7012-7014)gCt>gAt	p.A2338D	RYR1_ENST00000360985.3_Missense_Mutation_p.A2338D|RYR1_ENST00000355481.4_Missense_Mutation_p.A2338D			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2338	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.A2338D(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGCGCTTTGCTGTCTTCGTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											97	72	80					19																	38989869		2203	4300	6503	43681709	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7013C>A	19.37:g.38989869C>A	ENSP00000352608:p.Ala2338Asp		43681709	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512601	0.44660	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.95238	-3.65;-3.65;-3.65	3.69	3.69	0.42338	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000003	D	0.95884	0.8660	L	0.59436	1.845	0.50171	D	0.999852	P;D	0.65815	0.944;0.995	P;D	0.63703	0.714;0.917	D	0.96469	0.9347	10	0.87932	D	0	.	15.1881	0.73020	0.0:1.0:0.0:0.0	.	2338;2338	P21817-2;P21817	.;RYR1_HUMAN	D	2338	ENSP00000352608:A2338D;ENSP00000347667:A2338D;ENSP00000354254:A2338D	ENSP00000347667:A2338D	A	+	2	0	RYR1	43681709	1.000000	0.71417	0.985000	0.45067	0.308000	0.27856	7.651000	0.83577	1.890000	0.54733	0.313000	0.20887	GCT		0.612	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38989869	C	A	38989869	3	1	45	1	0	0	0	0	1	0	0	0	13805	797	28	2	7183	2	RYR1	19	38989869	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	4132138	38989869	20139114	68	4312										
SAE1	10055	broad.mit.edu	37	chr19	47656157	47656157	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	atttctttctttctgcaggtGtgtctgacttgctgctccag	9	10	4	1	rs569028764	byFrequency	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr19:47656157G>T	ENST00000270225.7	+	4	455	c.387G>T	c.(385-387)gtG>gtT	p.V129V	SAE1_ENST00000598840.1_Intron|SAE1_ENST00000540850.1_Intron|SAE1_ENST00000413379.3_Silent_p.V129V|SAE1_ENST00000392776.3_Silent_p.V129V	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	129					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)	p.V129V(1)		endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TTCTGCAGGTGTGTCTGACTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	19											134	128	130					19																	47656157		2203	4300	6503	52347997	SO:0001819	synonymous_variant	10055			BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"Ubiquitin-like modifier activating enzymes"	30660	protein-coding gene	gene with protein product	"activator Of sumo 1"	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.387G>T	19.37:g.47656157G>T			52347997	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Silent	SNP	ENST00000270225.7	37	CCDS12696.1																																																																																				0.408	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500		T	47656157	G	T	47656157	2	4	45	1	0	0	0	0	0	0	0	1	13842	1364	48	2		2	SAE1	19	47656157	Silent	SNP	G	TCGA-AG-3887-01A-01W-1073-09	8666288	47656157	11472826	69	4313										
PAX1	5075	broad.mit.edu	37	chr20	21687619	21687619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ccccggggtcccgggcacggCgggccacgtcagcatcccgc	15	19	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr20:21687619C>T	ENST00000398485.2	+	2	884	c.830C>T	c.(829-831)gCg>gTg	p.A277V	PAX1_ENST00000444366.2_Missense_Mutation_p.A253V|PAX1_ENST00000460221.1_3'UTR	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	277					bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A183V(1)		autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						CCGGGCACGGCGGGCCACGTC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	20											19	22	21					20																	21687619		2194	4288	6482	21635619	SO:0001583	missense	5075				CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"Paired boxes"	8615	protein-coding gene	gene with protein product		167411	"paired box gene 1"			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.830C>T	20.37:g.21687619C>T	ENSP00000381499:p.Ala277Val		21635619	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	37	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	C	17.69	3.450913	0.63290	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.98381	-4.39;-4.9	5.11	5.11	0.69529	.	0.428000	0.27406	N	0.019511	D	0.97523	0.9189	L	0.43152	1.355	0.40725	D	0.982694	P;B;D	0.67145	0.589;0.123;0.996	B;B;P	0.52909	0.065;0.009;0.713	D	0.97461	1.0034	10	0.33940	T	0.23	.	18.1665	0.89729	0.0:1.0:0.0:0.0	.	253;183;277	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	V	277;253	ENSP00000381499:A277V;ENSP00000410355:A253V	ENSP00000381499:A277V	A	+	2	0	PAX1	21635619	0.991000	0.36638	0.449000	0.26957	0.992000	0.81027	3.037000	0.49775	2.381000	0.81170	0.561000	0.74099	GCG		0.667	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			T	21687619	C	T	21687619	3	4	45	1	0	0	0	0	1	0	0	0	11509	768	27	1	836	1	PAX1	20	21687619	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09		21687619	41337901	70	4314										
JPH2	57158	broad.mit.edu	37	chr20	42788287	42788287	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gcaatctcggccttctggcgCgcgatagcagcggcgcgctg	15	14	2	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr20:42788287C>T	ENST00000372980.3	-	2	2012	c.1140G>A	c.(1138-1140)gcG>gcA	p.A380A		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	380	Ala-rich.				calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.A380A(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CCTTCTGGCGCGCGATAGCAG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	20											25	23	24					20																	42788287		2203	4296	6499	42221701	SO:0001819	synonymous_variant	57158			AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1140G>A	20.37:g.42788287C>T			42221701	E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	CCDS13325.1																																																																																				0.667	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			T	42788287	C	T	42788287	2	4	45	1	0	0	0	0	0	0	0	1	7982	755	27	1		1	JPH2	20	42788287	Silent	SNP	C	TCGA-AG-3887-01A-01W-1073-09	21100668	42788287	20237233	71	4315										
RBX1	9978	broad.mit.edu	37	chr22	41363831	41363831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	tcacttccactgcatctctcGctggctcaaaacacgacagg	7	15	3	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chr22:41363831G>A	ENST00000216225.8	+	4	297	c.257G>A	c.(256-258)cGc>cAc	p.R86H	XPNPEP3_ENST00000544094.1_3'UTR	NM_014248.3	NP_055063.1	P62877	RBX1_HUMAN	ring-box 1, E3 ubiquitin protein ligase	86					cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|Notch signaling pathway (GO:0007219)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein neddylation (GO:0045116)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|Cul5-RING ubiquitin ligase complex (GO:0031466)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)|VCB complex (GO:0030891)	NEDD8 ligase activity (GO:0019788)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R86H(1)		large_intestine(1)|lung(3)|skin(1)	5						TGCATCTCTCGCTGGCTCAAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	22											99	96	97					22																	41363831		2203	4300	6503	39693777	SO:0001583	missense	9978			AF140598	CCDS14009.1	22q13.2	2010-09-17	2010-09-17		ENSG00000100387	ENSG00000100387		"RING-type (C3HC4) zinc fingers"	9928	protein-coding gene	gene with protein product	"regulator of cullins 1"	603814	"ring-box 1"			10213691, 10230407	Standard	NM_014248		Approved	ROC1, RNF75, BA554C12.1	uc003azk.3	P62877	OTTHUMG00000151298	ENST00000216225.8:c.257G>A	22.37:g.41363831G>A	ENSP00000216225:p.Arg86His		39693777	B2RDY1|Q8N6Z8|Q9D1S2|Q9WUK9|Q9Y254	Missense_Mutation	SNP	ENST00000216225.8	37	CCDS14009.1	.	.	.	.	.	.	.	.	.	.	G	35	5.529633	0.96446	.	.	ENSG00000100387	ENST00000216225	.	.	.	5.79	5.79	0.91817	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.77274	0.4106	M	0.78637	2.42	0.80722	D	1	D	0.53885	0.963	P	0.56648	0.803	T	0.79342	-0.1843	9	0.72032	D	0.01	.	18.7997	0.92011	0.0:0.0:1.0:0.0	.	86	P62877	RBX1_HUMAN	H	86	.	ENSP00000216225:R86H	R	+	2	0	RBX1	39693777	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.282000	0.95840	2.739000	0.93911	0.462000	0.41574	CGC		0.438	RBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322149.1	NM_014248		A	41363831	G	A	41363831	3	1	45	1	0	0	0	0	1	0	0	0	13202	1087	38	1	271	1	RBX1	22	41363831	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		41363831	9940735	72	4316										
FRMPD4	9758	broad.mit.edu	37	chrX	12734767	12734767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gagcttccaggccgcggaggGgatcgaggaacccctcttgc	15	13	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chrX:12734767G>A	ENST00000380682.1	+	15	2695	c.2189G>A	c.(2188-2190)gGg>gAg	p.G730E		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	730					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.G720E(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GCCGCGGAGGGGATCGAGGAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	110	109					X																	12734767		2203	4300	6503	12644688	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2189G>A	X.37:g.12734767G>A	ENSP00000370057:p.Gly730Glu		12644688	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113894	0.77210	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.25912	1.77	5.71	5.71	0.89125	.	0.050249	0.85682	D	0.000000	T	0.51601	0.1684	M	0.72118	2.19	0.46725	D	0.999171	D;D	0.76494	0.999;0.999	D;D	0.65684	0.937;0.937	T	0.53982	-0.8361	10	0.87932	D	0	-27.4928	18.8648	0.92287	0.0:0.0:1.0:0.0	.	722;730	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	E	730;721;719	ENSP00000370057:G730E	ENSP00000304583:G719E	G	+	2	0	FRMPD4	12644688	1.000000	0.71417	0.596000	0.28811	0.653000	0.38743	9.360000	0.97119	2.402000	0.81655	0.600000	0.82982	GGG		0.557	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		A	12734767	G	A	12734767	3	1	45	1	0	0	0	0	1	0	0	0	6078	1232	43	3	2247	3	FRMPD4	23	12734767	Missense_Mutation	SNP	G	TCGA-AG-3887-01A-01W-1073-09		12734767	142535793	73	4317										
IL1RAPL2	26280	broad.mit.edu	37	chrX	105011533	105011533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	ttattgtaacctgcctctgaCgctactcaacggacagctac	7	13	2	1	rs367966545		TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chrX:105011533C>T	ENST00000372582.1	+	11	2696	c.1940C>T	c.(1939-1941)aCg>aTg	p.T647M	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.T647M	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	647					central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.T647M(2)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTGCCTCTGACGCTACTCAAC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	X											131	131	131					X																	105011533		2203	4300	6503	104898189	SO:0001583	missense	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1940C>T	X.37:g.105011533C>T	ENSP00000361663:p.Thr647Met		104898189	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803705	0.50315	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.07216	3.5;3.5;3.21	5.83	4.96	0.65561	.	0.155567	0.45867	D	0.000330	T	0.12518	0.0304	M	0.71581	2.175	0.54753	D	0.999987	P	0.42337	0.776	B	0.36885	0.235	T	0.01578	-1.1320	10	0.87932	D	0	.	14.3304	0.66553	0.1491:0.8509:0.0:0.0	.	647	Q9NP60	IRPL2_HUMAN	M	647;647;252	ENSP00000361663:T647M;ENSP00000344976:T647M;ENSP00000445576:T252M	ENSP00000344976:T647M	T	+	2	0	IL1RAPL2	104898189	0.998000	0.40836	0.779000	0.31741	0.899000	0.52679	3.749000	0.55150	1.185000	0.42971	0.600000	0.82982	ACG		0.468	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	105011533	C	T	105011533	3	4	45	1	0	0	0	0	1	0	0	0	7683	536	19	1	1978	1	IL1RAPL2	23	105011533	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	92276766	105011533	50259027	74	4318										
SLC6A8	6535	broad.mit.edu	37	chrX	152958817	152958817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	accgcttcaacaacaactgcTacaagtaagcaccgccgccc	6	17	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chrX:152958817T>C	ENST00000253122.5	+	6	1488	c.1012T>C	c.(1012-1014)Tac>Cac	p.Y338H	SLC6A8_ENST00000430077.2_Missense_Mutation_p.Y223H|SLC6A8_ENST00000485324.1_3'UTR	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	338					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)	p.Y338H(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	CAACAACTGCTACAAGTAAGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	X											51	52	52					X																	152958817		2203	4300	6503	152612011	SO:0001583	missense	6535				CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.1012T>C	X.37:g.152958817T>C	ENSP00000253122:p.Tyr338His		152612011	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	37	CCDS14726.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	24.5|24.5	4.542141|4.542141	0.85917|0.85917	.|.	.|.	ENSG00000130821|ENSG00000130821	ENST00000413787|ENST00000253122;ENST00000430077;ENST00000328897	T|T;T	0.78003|0.76448	-1.14|-1.02;-1.02	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.000000	.|0.64402	.|U	.|0.000003	D|D	0.84192|0.84192	0.5418|0.5418	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	.|D;P	.|0.71674	.|0.998;0.932	.|D;P	.|0.66084	.|0.941;0.761	D|D	0.85746|0.85746	0.1340|0.1340	7|10	0.87932|0.72032	D|D	0|0.01	.|.	12.6996|12.6996	0.57024|0.57024	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|357;338	.|Q59EV7;P48029	.|.;SC6A8_HUMAN	P|H	53|338;223;344	ENSP00000400463:L53P|ENSP00000253122:Y338H;ENSP00000403041:Y223H	ENSP00000400463:L53P|ENSP00000253122:Y338H	L|Y	+|+	2|1	0|0	SLC6A8|SLC6A8	152612011|152612011	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.710000|7.710000	0.84655|0.84655	1.843000|1.843000	0.53566|0.53566	0.430000|0.430000	0.28490|0.28490	CTA|TAC		0.637	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			C	152958817	T	C	152958817	3	2	45	1	0	0	0	0	1	0	0	0	14727	1522	53	4	1034	4	SLC6A8	23	152958817	Missense_Mutation	SNP	T	TCGA-AG-3887-01A-01W-1073-09	47947284	152958817	2311743	75	4319										
PLXNA3	55558	broad.mit.edu	37	chrX	153694773	153694773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.671023965141612	3.77450980392157	0.368244858919177	1	1	0	gcccggcgtccgggggcacaCggcttaccatctcaggcagc	14	16	1	0			TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3887-01A-01W-1073-09	TCGA-AG-3887-10A-01W-1073-09	g.chrX:153694773C>T	ENST00000369682.3	+	16	3029	c.2854C>T	c.(2854-2856)Cgg>Tgg	p.R952W		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	952	IPT/TIG 2.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)	p.R952W(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGGGGGCACACGGCTTACCAT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	X											63	74	70					X																	153694773		2202	4300	6502	153347967	SO:0001583	missense	55558			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.2854C>T	X.37:g.153694773C>T	ENSP00000358696:p.Arg952Trp		153347967	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	2.627	-0.287332	0.05605	.	.	ENSG00000130827	ENST00000369682	T	0.77358	-1.09	4.98	2.1	0.27182	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.186098	0.43579	D	0.000544	T	0.64571	0.2610	N	0.25485	0.75	0.21290	N	0.999736	B	0.06786	0.001	B	0.08055	0.003	T	0.51340	-0.8718	10	0.38643	T	0.18	.	12.6135	0.56563	0.5647:0.4353:0.0:0.0	.	952	P51805	PLXA3_HUMAN	W	952	ENSP00000358696:R952W	ENSP00000358696:R952W	R	+	1	2	PLXNA3	153347967	0.000000	0.05858	0.607000	0.28956	0.160000	0.22226	-0.238000	0.08977	0.006000	0.14734	0.591000	0.81541	CGG		0.677	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153694773	C	T	153694773	3	4	45	1	0	0	0	0	1	0	0	0	12152	527	19	1	2912	1	PLXNA3	23	153694773	Missense_Mutation	SNP	C	TCGA-AG-3887-01A-01W-1073-09	735956	153694773	1575787	76	4320										
CASZ1	54897	broad.mit.edu	37	chr1	10714552	10714552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtcttcggtggctcggaagcGctggaagccgtcgttaatga	15	9	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:10714552G>A	ENST00000377022.3	-	10	2079	c.1762C>T	c.(1762-1764)Cgc>Tgc	p.R588C	CASZ1_ENST00000344008.5_Missense_Mutation_p.R588C|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	588					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R588C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	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)		GCTCGGAAGCGCTGGAAGCCG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											185	163	170					1																	10714552		2203	4300	6503	10637139	SO:0001583	missense	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.1762C>T	1.37:g.10714552G>A	ENSP00000366221:p.Arg588Cys		10637139	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.797369	0.90538	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.97	4.97	0.65823	.	0.095697	0.64402	D	0.000001	T	0.75852	0.3906	L	0.52011	1.625	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.78347	-0.2239	9	0.87932	D	0	-35.0999	18.6257	0.91336	0.0:0.0:1.0:0.0	.	612;588;588	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	C	588	.	ENSP00000339445:R588C	R	-	1	0	CASZ1	10637139	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.485000	0.60279	2.478000	0.83669	0.561000	0.74099	CGC		0.587	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10714552	G	A	10714552	3	1	46	1	0	0	0	0	1	0	0	0	2691	1087	38	1	3569	1	CASZ1	1	10714552	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		10714552	238536069	1	4321										
CYP4Z1	199974	broad.mit.edu	37	chr1	47534369	47534369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtgctgttcccttgtgggttGgaccctttacgatgttcttc	11	10	1	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:47534369G>A	ENST00000334194.3	+	2	256	c.253G>A	c.(253-255)Gga>Aga	p.G85R		NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	85						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.G85R(1)		cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						CTTGTGGGTTGGACCCTTTAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											201	175	184					1																	47534369		2203	4300	6503	47306956	SO:0001583	missense	199974			AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"Cytochrome P450s"	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.253G>A	1.37:g.47534369G>A	ENSP00000334246:p.Gly85Arg		47306956	Q5VVE4	Missense_Mutation	SNP	ENST00000334194.3	37	CCDS545.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.050461	0.75960	.	.	ENSG00000186160	ENST00000334194	T	0.73789	-0.78	2.83	2.83	0.33086	.	0.000000	0.64402	U	0.000018	D	0.82323	0.5012	M	0.85462	2.755	0.32184	N	0.579984	P	0.51537	0.946	P	0.56514	0.8	D	0.85362	0.1108	10	0.72032	D	0.01	.	9.2757	0.37698	0.0:0.0:1.0:0.0	.	85	Q86W10	CP4Z1_HUMAN	R	85	ENSP00000334246:G85R	ENSP00000334246:G85R	G	+	1	0	CYP4Z1	47306956	1.000000	0.71417	0.737000	0.30932	0.669000	0.39330	3.993000	0.56987	1.581000	0.49865	0.461000	0.40582	GGA		0.443	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		A	47534369	G	A	47534369	3	1	46	1	0	0	0	0	1	0	0	0	4200	1349	47	3	259	3	CYP4Z1	1	47534369	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	36819817	47534369	201716252	2	4322										
STIL	6491	broad.mit.edu	37	chr1	47767996	47767996	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	agcaagtcggatggtcttctCagtcaccacaagctttggat	10	10	3	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:47767996C>G	ENST00000360380.3	-	5	538	c.175G>C	c.(175-177)Gag>Cag	p.E59Q	STIL_ENST00000371877.3_Missense_Mutation_p.E59Q|STIL_ENST00000396221.2_Missense_Mutation_p.E59Q|STIL_ENST00000337817.5_Missense_Mutation_p.E59Q|STIL_ENST00000243182.6_Missense_Mutation_p.E59Q	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	59					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.E59Q(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				ATGGTCTTCTCAGTCACCACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	103	103					1																	47767996		2203	4300	6503	47540583	SO:0001583	missense	6491			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.175G>C	1.37:g.47767996C>G	ENSP00000353544:p.Glu59Gln		47540583	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.229064	0.58777	.	.	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475;ENST00000413565	T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.42	3.55	0.40652	.	0.150226	0.64402	D	0.000017	T	0.66684	0.2814	M	0.78637	2.42	0.36138	D	0.846586	P;P;P;P;P	0.47762	0.713;0.9;0.713;0.9;0.9	P;P;P;P;P	0.53549	0.729;0.729;0.729;0.729;0.729	T	0.77175	-0.2684	10	0.72032	D	0.01	-12.7646	14.9953	0.71428	0.0:0.9247:0.0:0.0753	.	59;59;59;59;59	E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468	.;.;.;.;STIL_HUMAN	Q	59;59;59;59;59;59;63	ENSP00000353544:E59Q;ENSP00000337367:E59Q;ENSP00000360944:E59Q;ENSP00000379523:E59Q;ENSP00000243182:E59Q;ENSP00000411664:E59Q;ENSP00000412019:E63Q	ENSP00000243182:E59Q	E	-	1	0	STIL	47540583	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	3.461000	0.53035	0.657000	0.30906	-1.360000	0.01215	GAG		0.368	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		G	47767996	C	G	47767996	3	3	46	1	0	0	0	0	1	0	0	0	15321	835	29	5	3747	5	STIL	1	47767996	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	233627	47767996	201482625	3	4323										
SEMA6C	10500	broad.mit.edu	37	chr1	151107280	151107280	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gacccatcacttacccaccaGatcccctgatatccacacag	4	18	1	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:151107280G>T	ENST00000341697.3	-	16	3343	c.1652C>A	c.(1651-1653)tCt>tAt	p.S551Y	SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	551					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.S551Y(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			TTACCCACCAGATCCCCTGAT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											136	122	127					1																	151107280		2203	4300	6503	149373904	SO:0001583	missense	10500			AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1652C>A	1.37:g.151107280G>T	ENSP00000344148:p.Ser551Tyr		149373904	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.338373	0.24253	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.83	3.87	0.44632	.	1.169550	0.06419	N	0.722037	T	0.08179	0.0204	N	0.02539	-0.55	0.20873	N	0.999835	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.12837	0.008;0.0;0.001;0.0	T	0.20273	-1.0280	10	0.22109	T	0.4	.	10.4114	0.44296	0.0:0.0:0.8063:0.1937	.	551;511;551;551	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	Y	551;511;551;551	ENSP00000357910:S551Y;ENSP00000357908:S511Y;ENSP00000357909:S551Y;ENSP00000344148:S551Y	ENSP00000344148:S551Y	S	-	2	0	SEMA6C	149373904	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	2.637000	0.46553	2.529000	0.85273	0.561000	0.74099	TCT		0.532	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151107280	G	T	151107280	3	4	46	1	0	0	0	0	1	0	0	0	14078	942	33	2	1256	2	SEMA6C	1	151107280	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	103339284	151107280	98143341	4	4324										
NUP210L	91181	broad.mit.edu	37	chr1	154091160	154091160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	accatacctgtactttataaCgatataacattcccatagga	4	10	0	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:154091160C>T	ENST00000368559.3	-	11	1522	c.1451G>A	c.(1450-1452)cGt>cAt	p.R484H	NUP210L_ENST00000271854.3_Missense_Mutation_p.R484H	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	484					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)		p.R484H(1)		NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TACTTTATAACGATATAACAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											146	148	148					1																	154091160		1833	4084	5917	152357784	SO:0001583	missense	91181			AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.1451G>A	1.37:g.154091160C>T	ENSP00000357547:p.Arg484His		152357784	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	8.497	0.863426	0.17250	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.05649	3.41;3.41	5.0	1.03	0.20045	Invasin/intimin cell-adhesion (1);	0.463681	0.20461	N	0.091896	T	0.01730	0.0055	L	0.34521	1.04	0.26762	N	0.969976	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.43278	-0.9401	10	0.51188	T	0.08	-3.2393	10.2869	0.43573	0.0:0.6837:0.0:0.3163	.	484;484	E7EP56;Q5VU65	.;P210L_HUMAN	H	484	ENSP00000357547:R484H;ENSP00000271854:R484H	ENSP00000271854:R484H	R	-	2	0	NUP210L	152357784	0.007000	0.16637	0.921000	0.36526	0.526000	0.34562	-0.278000	0.08490	-0.056000	0.13221	-1.346000	0.01242	CGT		0.328	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		T	154091160	C	T	154091160	3	4	46	1	0	0	0	0	1	0	0	0	10792	536	19	1	4335	1	NUP210L	1	154091160	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	2983880	154091160	95159461	5	4325										
ASH1L	55870	broad.mit.edu	37	chr1	155327391	155327391	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ttcacccttttcttcagcttGtgcttagactttctcttctc	4	13	5	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:155327391G>T	ENST00000368346.3	-	14	7599	c.6960C>A	c.(6958-6960)caC>caA	p.H2320Q	RNU6-106P_ENST00000384405.1_RNA|ASH1L_ENST00000392403.3_Missense_Mutation_p.H2315Q			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2320					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.H2315Q(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTTCAGCTTGTGCTTAGACT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											231	206	214					1																	155327391		2203	4300	6503	153594015	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.6960C>A	1.37:g.155327391G>T	ENSP00000357330:p.His2320Gln		153594015	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	g	23.2	4.387082	0.82902	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88431	-2.38;-2.38	4.79	4.79	0.61399	Bromodomain (1);	0.000000	0.85682	D	0.000000	D	0.90123	0.6914	L	0.35854	1.095	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.78314	0.979;0.991	D	0.90409	0.4408	10	0.49607	T	0.09	.	17.6191	0.88076	0.0:0.0:1.0:0.0	.	2320;2315	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	Q	2320;2315	ENSP00000357330:H2320Q;ENSP00000376204:H2315Q	ENSP00000357330:H2320Q	H	-	3	2	ASH1L	153594015	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.411000	0.80078	2.482000	0.83794	0.573000	0.79308	CAC		0.443	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155327391	G	T	155327391	3	4	46	1	0	0	0	0	1	0	0	0	1042	1368	48	2	2009	2	ASH1L	1	155327391	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	1236231	155327391	93923230	6	4326										
CD1E	913	broad.mit.edu	37	chr1	158326577	158326577	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tgtctttctcatgggagccaAcactcaggacaccaagaatt	8	11	3	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:158326577A>C	ENST00000368167.3	+	6	1297	c.1058A>C	c.(1057-1059)aAc>aCc	p.N353T	CD1E_ENST00000452291.2_Missense_Mutation_p.N164T|CD1E_ENST00000444681.2_Missense_Mutation_p.N254T|CD1E_ENST00000368166.3_Missense_Mutation_p.N152T|CD1E_ENST00000368165.3_Missense_Mutation_p.N263T|CD1E_ENST00000368157.1_Missense_Mutation_p.N97T|CD1E_ENST00000368156.1_Missense_Mutation_p.N251T|CD1E_ENST00000368163.3_Missense_Mutation_p.N286T|CD1E_ENST00000368155.3_Missense_Mutation_p.N196T|CD1E_ENST00000368154.1_Missense_Mutation_p.N109T|CD1E_ENST00000368161.3_3'UTR|CD1E_ENST00000368160.3_Missense_Mutation_p.N341T|CD1E_ENST00000368164.3_3'UTR	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	353					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)	p.N353T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					ATGGGAGCCAACACTCAGGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	104	105					1																	158326577		1908	4123	6031	156593201	SO:0001583	missense	913			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.1058A>C	1.37:g.158326577A>C	ENSP00000357149:p.Asn353Thr		156593201	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.319976	0.41096	.	.	ENSG00000158488	ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368163;ENST00000368157;ENST00000368160;ENST00000368156;ENST00000368155;ENST00000368154	T;T;T;T;T;T;T;T;T;T;T	0.56611	5.0;4.46;3.14;3.13;3.41;2.71;0.45;4.61;3.4;2.91;0.47	4.88	-0.124	0.13523	.	1.844580	0.02634	N	0.104653	T	0.47002	0.1422	L	0.54323	1.7	0.09310	N	1	B;D;B;P;P;B;P;D;P;B	0.67145	0.418;0.96;0.218;0.617;0.617;0.1;0.688;0.996;0.902;0.218	B;P;B;B;B;B;B;P;P;B	0.59056	0.053;0.57;0.085;0.121;0.121;0.024;0.115;0.851;0.52;0.085	T	0.28073	-1.0055	10	0.72032	D	0.01	0.0149	7.1281	0.25484	0.552:0.0:0.448:0.0	.	254;263;196;152;341;353;164;109;251;286	E7EP01;P15812-5;P15812-7;P15812-9;P15812-2;P15812;P15812-8;P15812-11;P15812-6;P15812-4	.;.;.;.;.;CD1E_HUMAN;.;.;.;.	T	254;353;164;263;152;286;97;341;251;196;109	ENSP00000402906:N254T;ENSP00000357149:N353T;ENSP00000416228:N164T;ENSP00000357147:N263T;ENSP00000357148:N152T;ENSP00000357145:N286T;ENSP00000357139:N97T;ENSP00000357142:N341T;ENSP00000357138:N251T;ENSP00000357137:N196T;ENSP00000357136:N109T	ENSP00000357136:N109T	N	+	2	0	CD1E	156593201	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.389000	0.20751	0.054000	0.16065	0.533000	0.62120	AAC		0.428	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		C	158326577	A	C	158326577	3	2	46	1	0	0	0	0	1	0	0	0	2984	43	2	4	1080	4	CD1E	1	158326577	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	2999186	158326577	90924044	7	4327										
OR10Z1	128368	broad.mit.edu	37	chr1	158576428	158576428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cctcttcctttccttcctatCcttctctgagacctgctaca	3	17	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:158576428C>T	ENST00000361284.1	+	1	200	c.200C>T	c.(199-201)tCc>tTc	p.S67F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S67F(1)		endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TCCTTCCTATCCTTCTCTGAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											249	244	246					1																	158576428		2203	4300	6503	156843052	SO:0001583	missense	128368			AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.200C>T	1.37:g.158576428C>T	ENSP00000354707:p.Ser67Phe		156843052	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.641731	0.29157	.	.	ENSG00000198967	ENST00000361284	T	0.12361	2.69	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.184684	0.26800	N	0.022426	T	0.42381	0.1200	H	0.95402	3.665	0.19300	N	0.999971	D	0.76494	0.999	D	0.70716	0.97	T	0.52026	-0.8630	10	0.87932	D	0	.	18.0328	0.89290	0.0:1.0:0.0:0.0	.	67	Q8NGY1	O10Z1_HUMAN	F	67	ENSP00000354707:S67F	ENSP00000354707:S67F	S	+	2	0	OR10Z1	156843052	0.064000	0.20934	0.281000	0.24762	0.012000	0.07955	2.453000	0.44970	2.783000	0.95769	0.655000	0.94253	TCC		0.532	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576428	C	T	158576428	3	4	46	1	0	0	0	0	1	0	0	0	10954	855	30	3	202	3	OR10Z1	1	158576428	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	249851	158576428	90674193	8	4328										
SMG7	9887	broad.mit.edu	37	chr1	183515228	183515228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ccccataaaactgtttgagcCgtcattgcaacctcctgtaa	6	13	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:183515228C>T	ENST00000347615.2	+	17	2617	c.2498C>T	c.(2497-2499)cCg>cTg	p.P833L	SMG7_ENST00000456731.2_Missense_Mutation_p.P745L|SMG7_ENST00000367537.3_Missense_Mutation_p.P816L|SMG7_ENST00000515829.2_Missense_Mutation_p.P787L|SMG7_ENST00000508461.1_Missense_Mutation_p.P791L|SMG7_ENST00000507469.1_Missense_Mutation_p.P787L	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	833	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.P833L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CTGTTTGAGCCGTCATTGCAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	85	83					1																	183515228		2203	4300	6503	181781851	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2498C>T	1.37:g.183515228C>T	ENSP00000340766:p.Pro833Leu		181781851	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633866	0.47049	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.62	4.65	0.58169	.	0.301659	0.34245	N	0.004135	T	0.22205	0.0535	N	0.08118	0	0.53688	D	0.99997	B;B;B;B;B;B	0.27700	0.186;0.185;0.186;0.133;0.186;0.185	B;B;B;B;B;B	0.19666	0.01;0.012;0.01;0.026;0.017;0.019	T	0.07065	-1.0792	10	0.37606	T	0.19	-10.9844	11.8691	0.52511	0.3411:0.6589:0.0:0.0	.	791;816;745;787;833;787	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	L	745;816;791;745;833;787;787	ENSP00000407629:P745L;ENSP00000356507:P816L;ENSP00000426915:P791L;ENSP00000388390:P745L;ENSP00000340766:P833L;ENSP00000425133:P787L;ENSP00000421358:P787L	ENSP00000340766:P833L	P	+	2	0	SMG7	181781851	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.732000	0.68563	2.633000	0.89246	0.655000	0.94253	CCG		0.468	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		T	183515228	C	T	183515228	3	4	46	1	0	0	0	0	1	0	0	0	14835	652	23	1	2564	1	SMG7	1	183515228	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	24938800	183515228	65735393	9	4329										
LGR6	59352	broad.mit.edu	37	chr1	202287420	202287420	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtgctgctgctcactctggcCgcagtgcagtgcagcgtctc	13	14	3	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:202287420C>T	ENST00000367278.3	+	18	2078	c.1989C>T	c.(1987-1989)gcC>gcT	p.A663A	LGR6_ENST00000439764.2_Silent_p.A524A|LGR6_ENST00000255432.7_Silent_p.A611A	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	663					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)	p.A663A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TCACTCTGGCCGCAGTGCAGT	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	1											20	18	19					1																	202287420		2203	4300	6503	200554043	SO:0001819	synonymous_variant	59352			AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1989C>T	1.37:g.202287420C>T			200554043	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																				0.682	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		T	202287420	C	T	202287420	2	4	46	1	0	0	0	0	0	0	0	1	8781	639	23	1		1	LGR6	1	202287420	Silent	SNP	C	TCGA-AG-3890-01A-01W-1073-09	18772192	202287420	46963201	10	4330										
LYST	1130	broad.mit.edu	37	chr1	235920623	235920623	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gctggtgatgggtggttaacGaggaccaaaagtgtatctgc	15	6	1	1	rs201154390		TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:235920623G>A	ENST00000389794.3	-	24	7191	c.7017C>T	c.(7015-7017)ctC>ctT	p.L2339L	LYST_ENST00000389793.2_Silent_p.L2339L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2339					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.L2339L(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GGTGGTTAACGAGGACCAAAA	0.338													G|||	1	0.000199681	0	0	5008	,	,		16644	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											107	98	101					1																	235920623		2203	4300	6503	233987246	SO:0001819	synonymous_variant	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.7017C>T	1.37:g.235920623G>A			233987246	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																				0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235920623	G	A	235920623	2	1	46	1	0	0	0	0	0	0	0	1	9158	1045	37	1		1	LYST	1	235920623	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09	33633203	235920623	13329998	11	4331										
CHML	1122	broad.mit.edu	37	chr1	241798077	241798077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	aatgttgaaggttgggagttAgttttttagtttttaagtat	11	0	0	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr1:241798077A>T	ENST00000366553.1	-	1	1155	c.992T>A	c.(991-993)cTa>cAa	p.L331Q	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000331838.5_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	331					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.L331Q(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GTTGGGAGTTAGTTTTTTAGT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	132	132					1																	241798077		2203	4299	6502	239864700	SO:0001583	missense	1122			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.992T>A	1.37:g.241798077A>T	ENSP00000355511:p.Leu331Gln		239864700	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.664530	0.67700	.	.	ENSG00000203668	ENST00000366553	D	0.90261	-2.64	4.96	4.96	0.65561	.	0.156037	0.41194	U	0.000923	D	0.94932	0.8361	.	.	.	0.58432	D	0.999991	D	0.89917	1.0	D	0.87578	0.998	D	0.95361	0.8455	9	0.87932	D	0	-9.28	12.937	0.58320	1.0:0.0:0.0:0.0	.	331	P26374	RAE2_HUMAN	Q	331	ENSP00000355511:L331Q	ENSP00000355511:L331Q	L	-	2	0	CHML	239864700	0.995000	0.38212	0.995000	0.50966	0.991000	0.79684	8.014000	0.88676	2.222000	0.72286	0.533000	0.62120	CTA		0.333	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		T	241798077	A	T	241798077	3	4	46	1	0	0	0	0	1	0	0	0	3357	420	15	5	982	5	CHML	1	241798077	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	5877454	241798077	7452544	12	4332										
PPP1CB	5500	broad.mit.edu	37	chr2	28999821	28999821	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tcagccagcctattcttttgGaattggaagcaccgctgaaa	9	10	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:28999821G>A	ENST00000395366.2	+	2	429	c.157G>A	c.(157-159)Gaa>Aaa	p.E53K	PPP1CB_ENST00000296122.6_Missense_Mutation_p.E53K|PPP1CB_ENST00000358506.2_Missense_Mutation_p.E53K	NM_002709.2	NP_002700.1	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta isozyme	53					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|G2/M transition of mitotic cell cycle (GO:0000086)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|myosin phosphatase activity (GO:0017018)|myosin-light-chain-phosphatase activity (GO:0050115)|phosphatase activity (GO:0016791)|protein kinase binding (GO:0019901)	p.E53K(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					TATTCTTTTGGAATTGGAAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	140	139					2																	28999821		2203	4300	6503	28853325	SO:0001583	missense	5500				CCDS33169.1	2p23	2013-01-18	2010-03-05		ENSG00000213639	ENSG00000213639	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9282	protein-coding gene	gene with protein product		600590	"protein phosphatase 1, catalytic subunit, beta isoform"			8312365	Standard	NM_002709		Approved	PP1B, PP-1B, PP1beta	uc002rmg.3	P62140	OTTHUMG00000152011	ENST00000395366.2:c.157G>A	2.37:g.28999821G>A	ENSP00000378769:p.Glu53Lys		28853325	B2R5V4|D6W565|P37140|Q5U087|Q6FG45	Missense_Mutation	SNP	ENST00000395366.2	37	CCDS33169.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.963271	0.92791	.	.	ENSG00000213639	ENST00000455580;ENST00000420282;ENST00000441461;ENST00000358506;ENST00000296122;ENST00000395366	T;T;T;T;T;T	0.46451	3.38;0.88;0.87;3.38;3.38;3.38	5.36	5.36	0.76844	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.55146	0.1902	M	0.92833	3.35	0.80722	D	1	P;B	0.35507	0.506;0.018	B;B	0.29440	0.102;0.02	T	0.67593	-0.5631	10	0.72032	D	0.01	-18.8464	19.4592	0.94910	0.0:0.0:1.0:0.0	.	25;53	B4E163;P62140	.;PP1B_HUMAN	K	25;53;53;53;53;53	ENSP00000390715:E25K;ENSP00000398839:E53K;ENSP00000414918:E53K;ENSP00000351298:E53K;ENSP00000296122:E53K;ENSP00000378769:E53K	ENSP00000296122:E53K	E	+	1	0	PPP1CB	28853325	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.813000	0.99286	2.656000	0.90262	0.655000	0.94253	GAA		0.408	PPP1CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324841.1			A	28999821	G	A	28999821	3	1	46	1	0	0	0	0	1	0	0	0	12384	1175	41	3	163	3	PPP1CB	2	28999821	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		28999821	214199552	13	4333										
MERTK	10461	broad.mit.edu	37	chr2	112686937	112686937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tgccttcaaacacacagttgGacacataatactttctgaac	5	11	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:112686937G>T	ENST00000295408.4	+	2	559	c.302G>T	c.(301-303)gGa>gTa	p.G101V	MERTK_ENST00000409780.1_Intron|RN7SL297P_ENST00000483161.2_RNA|MERTK_ENST00000421804.2_Missense_Mutation_p.G101V			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	101	Ig-like C2-type 1.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G101V(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						CACACAGTTGGACACATAATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	97	100					2																	112686937		2203	4300	6503	112403408	SO:0001583	missense	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.302G>T	2.37:g.112686937G>T	ENSP00000295408:p.Gly101Val		112403408	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524408	0.44969	.	.	ENSG00000153208	ENST00000295408;ENST00000421804	T;T	0.66638	-0.22;-0.22	4.13	4.13	0.48395	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.000000	0.33477	U	0.004872	T	0.74268	0.3694	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.69480	-0.5134	10	0.08179	T	0.78	-17.8289	13.7598	0.62959	0.0:0.0:1.0:0.0	.	101	Q12866	MERTK_HUMAN	V	101	ENSP00000295408:G101V;ENSP00000389152:G101V	ENSP00000295408:G101V	G	+	2	0	MERTK	112403408	1.000000	0.71417	0.992000	0.48379	0.255000	0.26057	4.853000	0.62911	2.277000	0.76020	0.557000	0.71058	GGA		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			T	112686937	G	T	112686937	3	4	46	1	0	0	0	0	1	0	0	0	9509	1174	41	2	308	2	MERTK	2	112686937	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	83687116	112686937	130512436	14	4334										
MBD5	55777	broad.mit.edu	37	chr2	149247655	149247655	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cccaatactgttaccaccaaGaaactgtccaggggataaaa	7	11	0	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:149247655G>T	ENST00000407073.1	+	12	4752	c.3755G>T	c.(3754-3756)aGa>aTa	p.R1252I	MBD5_ENST00000404807.1_Missense_Mutation_p.R1485I	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1252					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R1252I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		TTACCACCAAGAAACTGTCCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											68	69	68					2																	149247655		2203	4300	6503	148964125	SO:0001583	missense	55777			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3755G>T	2.37:g.149247655G>T	ENSP00000386049:p.Arg1252Ile		148964125	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845499	0.32606	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.50813	0.73;0.77	6.11	4.32	0.51571	.	0.163883	0.44097	D	0.000498	T	0.45155	0.1328	N	0.24115	0.695	0.48288	D	0.99962	D;D	0.60160	0.987;0.987	P;P	0.52217	0.693;0.693	T	0.47898	-0.9081	10	0.87932	D	0	-8.0632	13.2067	0.59800	0.129:0.0:0.871:0.0	.	1485;1252	E9PHH0;Q9P267	.;MBD5_HUMAN	I	1252;1485	ENSP00000386049:R1252I;ENSP00000384672:R1485I	ENSP00000384672:R1485I	R	+	2	0	MBD5	148964125	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.811000	0.75221	0.922000	0.37019	0.655000	0.94253	AGA		0.423	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			T	149247655	G	T	149247655	3	4	46	1	0	0	0	0	1	0	0	0	9377	942	33	2	3781	2	MBD5	2	149247655	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	36560718	149247655	93951718	15	4335										
OBFC2A	64859	broad.mit.edu	37	chr2	192543403	192543403	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	aagcccggactgaaaaacttAaatgtcgtctttattgtcct	7	9	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:192543403A>G	ENST00000425611.2	+	1	146	c.63A>G	c.(61-63)ttA>ttG	p.L21L	NABP1_ENST00000410026.2_Intron|NABP1_ENST00000409510.1_Intron	NM_001031716.2	NP_001026886.1	Q96AH0	SOSB2_HUMAN	nucleic acid binding protein 1	21					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SOSS complex (GO:0070876)	RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L21L(1)									TGAAAAACTTAAATGTCGTCT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	2											42	50	47					2																	192543403		2203	4300	6503	192251648	SO:0001819	synonymous_variant	64859			BC017114	CCDS33352.1, CCDS58745.1	2q32.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000173559	ENSG00000173559			26232	protein-coding gene	gene with protein product	"single-stranded DNA-binding protein 2", "sensor of single-strand DNA complex subunit B2"	612103	"oligonucleotide/oligosaccharide-binding fold containing 2A"	OBFC2A			Standard	NM_001031716		Approved	FLJ22833, DKFZp667M1322, FLJ13624, MGC111163, SSB2, hSSB2, SOSS-B2	uc002usx.3	Q96AH0	OTTHUMG00000132720	ENST00000425611.2:c.63A>G	2.37:g.192543403A>G			192251648	Q658Y8|Q9H5X6	Silent	SNP	ENST00000425611.2	37	CCDS33352.1																																																																																				0.557	NABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256060.1	NM_022837		G	192543403	A	G	192543403	2	3	46	1	0	0	0	0	0	0	0	1	10839	359	13	4		4	OBFC2A	2	192543403	Silent	SNP	A	TCGA-AG-3890-01A-01W-1073-09	43295748	192543403	50655970	16	4336										
EPHA4	2043	broad.mit.edu	37	chr2	222294696	222294696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	acctggagctctccgtccctGtcctcttcaagctgttgggg	11	14	3	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:222294696G>A	ENST00000281821.2	-	15	2713	c.2672C>T	c.(2671-2673)aCa>aTa	p.T891I	EPHA4_ENST00000409854.1_Missense_Mutation_p.T891I|EPHA4_ENST00000409938.1_Missense_Mutation_p.T891I|EPHA4_ENST00000392071.4_Missense_Mutation_p.T840I	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	891					adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)	p.T891I(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CTCCGTCCCTGTCCTCTTCAA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	2											198	195	196					2																	222294696		2203	4300	6503	222002940	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2672C>T	2.37:g.222294696G>A	ENSP00000281821:p.Thr891Ile		222002940	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202211	0.38905	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.61742	0.08;0.08;0.08;0.08	5.93	5.93	0.95920	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40743	0.1129	N	0.21545	0.675	0.80722	D	1	P	0.40398	0.716	B	0.27887	0.084	T	0.31251	-0.9950	10	0.18276	T	0.48	.	20.3539	0.98825	0.0:0.0:1.0:0.0	.	891	P54764	EPHA4_HUMAN	I	891;891;891;840	ENSP00000281821:T891I;ENSP00000386276:T891I;ENSP00000386829:T891I;ENSP00000375923:T840I	ENSP00000281821:T891I	T	-	2	0	EPHA4	222002940	1.000000	0.71417	0.991000	0.47740	0.948000	0.59901	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	ACA		0.493	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			A	222294696	G	A	222294696	3	1	46	1	0	0	0	0	1	0	0	0	5182	1377	48	3	300	3	EPHA4	2	222294696	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	29751293	222294696	20904677	17	4337										
ANKMY1	51281	broad.mit.edu	37	chr2	241463532	241463532	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	acgtcctcaagcccgctttcCacatggccaaggctgccctt	8	17	1	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr2:241463532C>G	ENST00000272972.3	-	7	1549	c.1335G>C	c.(1333-1335)gtG>gtC	p.V445V	ANKMY1_ENST00000391987.1_Silent_p.V445V|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000373320.4_Silent_p.V215V|ANKMY1_ENST00000373318.2_Silent_p.V304V|ANKMY1_ENST00000401804.1_Silent_p.V534V|ANKMY1_ENST00000361678.4_Silent_p.V304V|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000403283.1_Silent_p.V383V|ANKMY1_ENST00000536462.1_Silent_p.V257V|ANKMY1_ENST00000405002.1_Silent_p.V215V|ANKMY1_ENST00000405523.3_Silent_p.V304V	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	445							metal ion binding (GO:0046872)	p.V445V(1)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		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)		GCCCGCTTTCCACATGGCCAA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	2											97	86	89					2																	241463532		2203	4300	6503	241112205	SO:0001819	synonymous_variant	51281			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1335G>C	2.37:g.241463532C>G			241112205	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Silent	SNP	ENST00000272972.3	37	CCDS2536.1																																																																																				0.597	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		G	241463532	C	G	241463532	2	3	46	1	0	0	0	0	0	0	0	1	634	581	21	5		5	ANKMY1	2	241463532	Silent	SNP	C	TCGA-AG-3890-01A-01W-1073-09	19168836	241463532	1735841	18	4338										
STAC	6769	broad.mit.edu	37	chr3	36484923	36484923	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gagcaaaagtgctgacaactTcttccagcgaaccaacagcg	9	12	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr3:36484923T>G	ENST00000273183.3	+	2	479	c.179T>G	c.(178-180)tTc>tGc	p.F60C	STAC_ENST00000457375.2_Missense_Mutation_p.F60C|STAC_ENST00000476388.1_3'UTR	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	60					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)	p.F60C(1)		endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						GCTGACAACTTCTTCCAGCGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	72	78					3																	36484923		2203	4300	6503	36459927	SO:0001583	missense	6769			D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.179T>G	3.37:g.36484923T>G	ENSP00000273183:p.Phe60Cys		36459927	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	37	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238697	0.79800	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000434649	T;T;T	0.78707	-1.2;-0.88;-0.99	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.85470	0.5704	L	0.59436	1.845	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.95	D	0.86999	0.2115	10	0.72032	D	0.01	.	14.71	0.69222	0.0:0.0:0.0:1.0	.	60;60	E9PEA7;Q99469	.;STAC_HUMAN	C	60;60;49	ENSP00000273183:F60C;ENSP00000393713:F60C;ENSP00000398403:F49C	ENSP00000273183:F60C	F	+	2	0	STAC	36459927	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.956000	0.87863	2.011000	0.59026	0.528000	0.53228	TTC		0.502	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		G	36484923	T	G	36484923	3	3	46	1	0	0	0	0	1	0	0	0	15278	1783	62	4	185	4	STAC	3	36484923	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09		36484923	161537507	19	4339										
PCYT1A	5130	broad.mit.edu	37	chr3	195997294	195997294	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	atctccacttaccactgcacAgcgctgcactttggaaggaa	8	13	1	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr3:195997294A>C	ENST00000292823.2	-	3	281	c.109T>G	c.(109-111)Tgt>Ggt	p.C37G	PCYT1A_ENST00000491544.1_5'UTR|RP11-447L10.1_ENST00000431391.1_3'UTR|PCYT1A_ENST00000419333.1_Missense_Mutation_p.C37G|PCYT1A_ENST00000431016.1_Missense_Mutation_p.C37G	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	37					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)	p.C37G(1)		cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	ACCACTGCACAGCGCTGCACT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	3											299	291	294					3																	195997294		2203	4300	6503	197481691	SO:0001583	missense	5130			L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.109T>G	3.37:g.195997294A>C	ENSP00000292823:p.Cys37Gly		197481691	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	37	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.608744	0.28623	.	.	ENSG00000161217	ENST00000441879;ENST00000419333;ENST00000292823;ENST00000431016;ENST00000411591;ENST00000412869;ENST00000443555	.	.	.	6.03	0.689	0.18033	.	0.333481	0.41001	D	0.000961	T	0.29850	0.0746	L	0.34521	1.04	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.05354	-1.0890	9	0.16896	T	0.51	-30.1607	1.2377	0.01956	0.5384:0.1532:0.1614:0.1471	.	37	P49585	PCY1A_HUMAN	G	37	.	ENSP00000292823:C37G	C	-	1	0	PCYT1A	197481691	0.996000	0.38824	0.985000	0.45067	0.975000	0.68041	1.013000	0.29937	0.487000	0.27698	0.533000	0.62120	TGT		0.483	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		C	195997294	A	C	195997294	3	2	46	1	0	0	0	0	1	0	0	0	11641	188	7	4	1026	4	PCYT1A	3	195997294	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	159512371	195997294	2025136	20	4340										
TADA2B	93624	broad.mit.edu	37	chr4	7056151	7056151	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cacgtggacatgtacgtgcgGaagctgaaagagagacagcg	15	8	0	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr4:7056151G>A	ENST00000310074.7	+	2	822	c.633G>A	c.(631-633)cgG>cgA	p.R211R	TADA2B_ENST00000512388.1_Silent_p.R136R|TADA2B_ENST00000515646.1_Silent_p.R119R	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	211					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R211R(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						TGTACGTGCGGAAGCTGAAAG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	4											83	89	87					4																	7056151		2033	4199	6232	7107052	SO:0001819	synonymous_variant	93624			AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011			30781	protein-coding gene	gene with protein product		608790				12972612, 18936164	Standard	NM_152293		Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.633G>A	4.37:g.7056151G>A			7107052	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Silent	SNP	ENST00000310074.7	37	CCDS47007.1																																																																																				0.577	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293		A	7056151	G	A	7056151	2	1	46	1	0	0	0	0	0	0	0	1	15550	1161	41	3		3	TADA2B	4	7056151	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09		7056151	184098125	21	4341										
CENPE	1062	broad.mit.edu	37	chr4	104067001	104067001	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cctactttagctacaatttcTtttatgttttctttgagctg	5	8	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr4:104067001T>C	ENST00000265148.3	-	30	4487	c.4398A>G	c.(4396-4398)aaA>aaG	p.K1466K	CENPE_ENST00000380026.3_Silent_p.K1441K	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1466					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.K1466K(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTACAATTTCTTTTATGTTTT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											82	86	85					4																	104067001		2202	4299	6501	104286450	SO:0001819	synonymous_variant	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4398A>G	4.37:g.104067001T>C			104286450	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																				0.318	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104067001	T	C	104067001	2	2	46	1	0	0	0	0	0	0	0	1	3236	1606	56	4		4	CENPE	4	104067001	Silent	SNP	T	TCGA-AG-3890-01A-01W-1073-09	97010850	104067001	87087275	22	4342										
TET2	54790	broad.mit.edu	37	chr4	106156671	106156671	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	atttttggtagcagtggagaGctacaggacaactgccagca	12	8	0	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr4:106156671G>A	ENST00000540549.1	+	3	2432	c.1572G>A	c.(1570-1572)gaG>gaA	p.E524E	TET2_ENST00000394764.1_Silent_p.E524E|TET2_ENST00000305737.2_Silent_p.E524E|TET2_ENST00000413648.2_Silent_p.E524E|TET2_ENST00000513237.1_Silent_p.E545E|TET2_ENST00000380013.4_Silent_p.E524E|TET2_ENST00000545826.1_Silent_p.E524E			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	524					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.E524E(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GCAGTGGAGAGCTACAGGACA	0.473			"Mis N, F"		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - coding silent(1)	large_intestine(1)	4											71	67	69					4																	106156671		2203	4300	6503	106376120	SO:0001819	synonymous_variant	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.1572G>A	4.37:g.106156671G>A			106376120	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																				0.473	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106156671	G	A	106156671	2	1	46	1	0	0	0	0	0	0	0	1	15809	962	34	3		3	TET2	4	106156671	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09	2089670	106156671	84997605	23	4343										
NDST3	9348	broad.mit.edu	37	chr4	118975946	118975946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tgccatctccttcttatcagGgaagaggctgacattgtcct	9	11	3	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr4:118975946G>T	ENST00000296499.5	+	2	1284	c.881G>T	c.(880-882)gGg>gTg	p.G294V	NDST3_ENST00000433996.2_Missense_Mutation_p.G294V	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	294	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.G294V(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						TTCTTATCAGGGAAGAGGCTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											157	146	150					4																	118975946		2203	4299	6502	119195394	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.881G>T	4.37:g.118975946G>T	ENSP00000296499:p.Gly294Val		119195394	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.576757	0.45902	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.47177	1.19;0.85	5.23	5.23	0.72850	.	0.210967	0.49916	D	0.000128	T	0.71324	0.3326	M	0.79926	2.475	0.80722	D	1	D;D;D	0.76494	0.999;0.957;0.979	D;P;P	0.71184	0.972;0.905;0.79	T	0.76038	-0.3105	10	0.87932	D	0	.	18.795	0.91990	0.0:0.0:1.0:0.0	.	294;294;294	B4DI67;O95803;O95803-2	.;NDST3_HUMAN;.	V	294	ENSP00000296499:G294V;ENSP00000396625:G294V	ENSP00000296499:G294V	G	+	2	0	NDST3	119195394	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.334000	0.65923	2.424000	0.82194	0.655000	0.94253	GGG		0.413	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		T	118975946	G	T	118975946	3	4	46	1	0	0	0	0	1	0	0	0	10288	1232	43	2	883	2	NDST3	4	118975946	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	12819275	118975946	72178330	24	4344										
SFRS12IP1	285672	broad.mit.edu	37	chr5	64023970	64023970	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tcaatttgattttttctttgCttttttctttcttcttttcc	2	8	5	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr5:64023970C>G	ENST00000513458.4	-	4	409	c.242G>C	c.(241-243)aGc>aCc	p.S81T		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	81	Lys-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S81T(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						tttttctttgcttttttcttt	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	5																																								64059726	SO:0001583	missense	285672			AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"p18 splicing regulatory protein"		"SFRS12-interacting protein 1"	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.242G>C	5.37:g.64023970C>G	ENSP00000427401:p.Ser81Thr		64059726	Q32NC8	Missense_Mutation	SNP	ENST00000513458.4	37	CCDS34171.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.773941	0.31411	.	.	ENSG00000153006	ENST00000513458	.	.	.	3.52	2.64	0.31445	.	0.791346	0.12361	N	0.475606	T	0.40145	0.1105	L	0.54323	1.7	0.29924	N	0.822514	P	0.43392	0.805	P	0.45506	0.483	T	0.25502	-1.0130	9	0.20046	T	0.44	-4.3379	8.3881	0.32512	0.2334:0.7666:0.0:0.0	.	81	Q8N9Q2	SR1IP_HUMAN	T	81	.	ENSP00000427401:S81T	S	-	2	0	SREK1IP1	64059726	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	-0.012000	0.12699	1.054000	0.40438	-0.152000	0.13540	AGC		0.274	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		G	64023970	C	G	64023970	3	3	46	1	0	0	0	0	1	0	0	0	14205	797	28	5	233	5	SFRS12IP1	5	64023970	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09		64023970	116891290	25	4345										
APC	324	broad.mit.edu	37	chr5	112174093	112174093	+	Frame_Shift_Del	DEL	T	T	-													0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gcccatacacattcaaacacTtacaatttcactaagtcgga							TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr5:112174093delT	ENST00000457016.1	+	16	3182	c.2802delT	c.(2800-2802)actfs	p.T934fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.T934fs|APC_ENST00000508376.2_Frame_Shift_Del_p.T934fs			P25054	APC_HUMAN	adenomatous polyposis coli	934	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Y935fs*5(1)|p.Y935fs*20(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATTCAAACACTTACAATTTCA	0.363		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Unknown(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	large_intestine(2)|skin(1)	5	GRCh37	CD041147|CD971993	APC	D							70	71	71					5																	112174093		2202	4300	6502	112201992	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2802delT	5.37:g.112174093delT	ENSP00000413133:p.Thr934fs		112201992	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.363	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112174093	T	-	112174093	7	5	46	1	0	1	0	1	0	0	0	0	763	1596	56	0	2860	0	APC	5	112174093	Frame_Shift_Del	DEL	T	TCGA-AG-3890-01A-01W-1073-09	48150123	112174093	68741167	26	4346										
ZNF474	133923	broad.mit.edu	37	chr5	121488577	121488577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gccgaatctttacctcagacCgcctcctggtacaccagaga	8	15	2	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr5:121488577C>T	ENST00000296600.4	+	2	1275	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	298							metal ion binding (GO:0046872)	p.R298C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		TACCTCAGACCGCCTCCTGGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											74	67	69					5																	121488577		2203	4300	6503	121516476	SO:0001583	missense	133923			AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.892C>T	5.37:g.121488577C>T	ENSP00000296600:p.Arg298Cys		121516476	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	2.728	-0.265168	0.05754	.	.	ENSG00000164185	ENST00000296600	T	0.58652	0.32	5.43	0.555	0.17247	.	0.128918	0.33309	U	0.005046	T	0.49474	0.1559	M	0.75615	2.305	0.09310	N	1	B	0.18166	0.026	B	0.19148	0.024	T	0.49380	-0.8946	10	0.66056	D	0.02	-7.0257	2.6977	0.05139	0.1282:0.5301:0.1243:0.2174	.	298	Q6S9Z5	ZN474_HUMAN	C	298	ENSP00000296600:R298C	ENSP00000296600:R298C	R	+	1	0	ZNF474	121516476	0.008000	0.16893	0.000000	0.03702	0.027000	0.11550	0.586000	0.23894	-0.200000	0.10300	-0.736000	0.03550	CGC		0.473	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121488577	C	T	121488577	3	4	46	1	0	0	0	0	1	0	0	0	17971	652	23	1	894	1	ZNF474	5	121488577	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	9314484	121488577	59426683	27	4347										
HMMR	3161	broad.mit.edu	37	chr5	162909781	162909781	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tggcaactgagagctcaaatCaagaatatgtaaggtatata	9	5	2	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr5:162909781C>G	ENST00000358715.3	+	13	1552	c.1516C>G	c.(1516-1518)Caa>Gaa	p.Q506E	HMMR_ENST00000353866.3_Missense_Mutation_p.Q491E|HMMR_ENST00000393915.4_Missense_Mutation_p.Q507E|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000432118.2_Missense_Mutation_p.Q420E			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	506					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)	p.Q506E(1)		cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	GAGCTCAAATCAAGAATATGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	73	73					5																	162909781		2203	4300	6503	162842359	SO:0001583	missense	3161			U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1516C>G	5.37:g.162909781C>G	ENSP00000351554:p.Gln506Glu		162842359	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	C	5.461	0.270129	0.10349	.	.	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.08807	3.05;3.05;3.05;3.05;3.05	5.43	3.52	0.40303	.	0.212390	0.47852	N	0.000209	T	0.04998	0.0134	N	0.19112	0.55	0.26795	N	0.969329	B;B;B;B	0.19200	0.023;0.034;0.029;0.029	B;B;B;B	0.18871	0.022;0.023;0.017;0.017	T	0.37596	-0.9699	10	0.02654	T	1	-6.4027	12.9493	0.58389	0.0:0.4758:0.5242:0.0	.	420;507;491;506	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	E	392;491;507;483;420;506	ENSP00000400527:Q392E;ENSP00000185942:Q491E;ENSP00000377492:Q507E;ENSP00000402673:Q420E;ENSP00000351554:Q506E	ENSP00000185942:Q491E	Q	+	1	0	HMMR	162842359	0.992000	0.36948	0.938000	0.37757	0.771000	0.43674	1.054000	0.30455	1.405000	0.46838	0.650000	0.86243	CAA		0.403	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		G	162909781	C	G	162909781	3	3	46	1	0	0	0	0	1	0	0	0	7263	827	29	5	1569	5	HMMR	5	162909781	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	41421204	162909781	18005479	28	4348										
CDYL	9425	broad.mit.edu	37	chr6	4937855	4937856	+	Missense_Mutation	DNP	GG	GG	TT													0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gctgccgatgacagcaagctGgtactgctcagcgccgttgg							TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:4937855_4937856GG>TT	ENST00000328908.5	+	6	1298_1299	c.1167_1168GG>TT	c.(1165-1170)ctGGta>ctTTta	p.V390L	CDYL_ENST00000343762.5_Missense_Mutation_p.V204L|CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Missense_Mutation_p.V336L|CDYL_ENST00000449732.2_Missense_Mutation_p.V204L			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	390					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.L389>?(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		ACAGCAAGCTGGTACTGCTCAG	0.455																																																1	Complex(1)	large_intestine(1)	6																																								4882855	SO:0001583	missense	9425			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	Exception_encountered	6.37:g.4937855_4937856delinsTT	ENSP00000330512:p.Val390Leu		4882854	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	DNP	ENST00000328908.5	37																																																																																					0.455	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		TT	4937856	GG	TT	4937855	3	4	46	1	0	0	0	0	1	0	0	0	3191	1335	47	2	1019	2	CDYL	6	4937855	Missense_Mutation	DNP	GG	TCGA-AG-3890-01A-01W-1073-09		4937855	166177212	29	4349										
C6orf138	442213	broad.mit.edu	37	chr6	47847354	47847354	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ccaggtattctgcagaagggAtcttacagcaaaagatgctg	11	8	2	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:47847354A>G	ENST00000339488.4	-	3	1259	c.1226T>C	c.(1225-1227)aTc>aCc	p.I409T		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	409						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)	p.I409T(1)									TGCAGAAGGGATCTTACAGCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	90	93					6																	47847354		2203	4300	6503	47955313	SO:0001583	missense	442213				CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1226T>C	6.37:g.47847354A>G	ENSP00000341914:p.Ile409Thr		47955313	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993295	0.35131	.	.	ENSG00000244694	ENST00000339488	D	0.92149	-2.98	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.83959	0.5367	L	0.51422	1.61	0.80722	D	1	B	0.27013	0.166	B	0.32090	0.14	T	0.81737	-0.0796	10	0.12766	T	0.61	.	14.738	0.69430	1.0:0.0:0.0:0.0	.	409	Q6ZW05	CF138_HUMAN	T	409	ENSP00000341914:I409T	ENSP00000341914:I409T	I	-	2	0	C6orf138	47955313	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	1.895000	0.54865	0.528000	0.53228	ATC		0.488	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		G	47847354	A	G	47847354	3	3	46	1	0	0	0	0	1	0	0	0	2338	333	12	4	1318	4	C6orf138	6	47847354	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	42909499	47847354	123267713	30	4350										
ZNF451	26036	broad.mit.edu	37	chr6	57012559	57012559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	atttcataatggacacagatAtttttatgagatggatgagg	10	3	1	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:57012559A>G	ENST00000370706.4	+	10	1920	c.1676A>G	c.(1675-1677)tAt>tGt	p.Y559C	ZNF451_ENST00000491832.2_Missense_Mutation_p.Y559C|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.Y559C|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Y559C(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GGACACAGATATTTTTATGAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											162	164	163					6																	57012559		2203	4300	6503	57120518	SO:0001583	missense	26036			AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1676A>G	6.37:g.57012559A>G	ENSP00000359740:p.Tyr559Cys		57120518	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	37	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957640	0.53400	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.09911	2.93;2.93;2.93	5.41	2.83	0.33086	Zinc finger, C2H2 (1);	0.125791	0.56097	D	0.000037	T	0.15696	0.0378	M	0.68593	2.085	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.998	D;P;D;P	0.65323	0.934;0.86;0.929;0.86	T	0.00972	-1.1495	10	0.54805	T	0.06	-21.823	10.3868	0.44145	0.7396:0.0:0.0:0.2604	.	559;559;559;559	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	C	559	ENSP00000359740:Y559C;ENSP00000350083:Y559C;ENSP00000421645:Y559C	ENSP00000350083:Y559C	Y	+	2	0	ZNF451	57120518	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.743000	0.55104	0.860000	0.35481	0.528000	0.53228	TAT		0.358	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		G	57012559	A	G	57012559	3	3	46	1	0	0	0	0	1	0	0	0	17961	449	16	4	1714	4	ZNF451	6	57012559	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	9165205	57012559	114102508	31	4351										
COL12A1	1303	broad.mit.edu	37	chr6	75812378	75812378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	aggaccctgggggcctggagGacctatgtctccacgaggac	15	12	1	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:75812378G>A	ENST00000322507.8	-	56	8659	c.8350C>T	c.(8350-8352)Cct>Tct	p.P2784S	COL12A1_ENST00000511023.1_5'Flank|COL12A1_ENST00000483888.2_Missense_Mutation_p.P2784S|COL12A1_ENST00000345356.6_Missense_Mutation_p.P1620S|COL12A1_ENST00000416123.2_Missense_Mutation_p.P2708S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2784	Collagen-like 1.|Triple-helical region (COL2) with 1 imperfection.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.P2784S(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GGGCCTGGAGGACCTATGTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											52	52	52					6																	75812378		1832	4088	5920	75869098	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8350C>T	6.37:g.75812378G>A	ENSP00000325146:p.Pro2784Ser		75869098	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281378	0.80692	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05	5.29	5.29	0.74685	.	0.154579	0.43747	D	0.000534	D	0.97888	0.9306	L	0.45744	1.44	0.51233	D	0.999912	D;D	0.58970	0.984;0.958	P;P	0.59595	0.839;0.86	D	0.97365	0.9972	10	0.21014	T	0.42	.	17.1248	0.86711	0.0:0.0:1.0:0.0	.	1620;2784	Q99715-2;Q99715	.;COCA1_HUMAN	S	2784;422;2708;1620;2708;2784	ENSP00000325146:P2784S;ENSP00000399812:P422S;ENSP00000305147:P1620S;ENSP00000412864:P2708S;ENSP00000421216:P2784S	ENSP00000325146:P2784S	P	-	1	0	COL12A1	75869098	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.543000	0.67225	2.466000	0.83321	0.591000	0.81541	CCT		0.502	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75812378	G	A	75812378	3	1	46	1	0	0	0	0	1	0	0	0	3675	1174	41	3	885	3	COL12A1	6	75812378	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	18799819	75812378	95302689	32	4352										
OLIG3	167826	broad.mit.edu	37	chr6	137815030	137815030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tcaggtcgtgcatccgcttgCgttcgcgtccgttgatcttc	11	13	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:137815030C>T	ENST00000367734.2	-	1	501	c.278G>A	c.(277-279)cGc>cAc	p.R93H		NM_175747.2	NP_786923.1	Q7RTU3	OLIG3_HUMAN	oligodendrocyte transcription factor 3	93	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron migration (GO:0097476)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.R93H(1)		endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	11	Breast(32;0.165)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447)		CATCCGCTTGCGTTCGCGTCC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											132	99	110					6																	137815030		2203	4300	6503	137856723	SO:0001583	missense	167826			AK096362	CCDS5186.1	6q23.3	2013-05-21			ENSG00000177468	ENSG00000177468		"Basic helix-loop-helix proteins"	18003	protein-coding gene	gene with protein product		609323					Standard	NM_175747		Approved	Bhlhb7, bHLHe20	uc003qhp.1	Q7RTU3	OTTHUMG00000015657	ENST00000367734.2:c.278G>A	6.37:g.137815030C>T	ENSP00000356708:p.Arg93His		137856723	Q8N8Q0	Missense_Mutation	SNP	ENST00000367734.2	37	CCDS5186.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631274	0.87660	.	.	ENSG00000177468	ENST00000367734	D	0.94000	-3.33	5.44	5.44	0.79542	Helix-loop-helix DNA-binding (5);	0.142257	0.47455	D	0.000240	D	0.97888	0.9306	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.98951	1.0794	10	0.87932	D	0	-1.9	19.2352	0.93856	0.0:1.0:0.0:0.0	.	93	Q7RTU3	OLIG3_HUMAN	H	93	ENSP00000356708:R93H	ENSP00000356708:R93H	R	-	2	0	OLIG3	137856723	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	7.814000	0.86154	2.534000	0.85438	0.591000	0.81541	CGC		0.612	OLIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042405.1	NM_175747		T	137815030	C	T	137815030	3	4	46	1	0	0	0	0	1	0	0	0	10893	768	27	1	544	1	OLIG3	6	137815030	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	62002652	137815030	33300037	33	4353										
PLEKHG1	57480	broad.mit.edu	37	chr6	151153151	151153151	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cctgacctggggatggaggcCacagataagacaaaaagcag	13	9	0	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr6:151153151C>A	ENST00000358517.2	+	15	3115	c.2904C>A	c.(2902-2904)gcC>gcA	p.A968A	PLEKHG1_ENST00000367328.1_Silent_p.A968A			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	968							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A968A(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GGATGGAGGCCACAGATAAGA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	6											125	138	134					6																	151153151		2203	4300	6503	151194844	SO:0001819	synonymous_variant	57480			AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2904C>A	6.37:g.151153151C>A			151194844	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																				0.493	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			A	151153151	C	A	151153151	2	1	46	1	0	0	0	0	0	0	0	1	12099	581	21	2		2	PLEKHG1	6	151153151	Silent	SNP	C	TCGA-AG-3890-01A-01W-1073-09	13338121	151153151	19961916	34	4354										
FERD3L	222894	broad.mit.edu	37	chr7	19184892	19184892	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ggagaccccgggtgcgaagtCgcagaggagagggcgtctcg	19	10	1	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr7:19184892C>T	ENST00000275461.3	-	1	152	c.94G>A	c.(94-96)Gac>Aac	p.D32N	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	32					cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D32N(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						GGTGCGAAGTCGCAGAGGAGA	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	7											37	35	36					7																	19184892		2200	4300	6500	19151417	SO:0001583	missense	222894			AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"Basic helix-loop-helix proteins"	16660	protein-coding gene	gene with protein product			"Fer3-like (Drosophila)"			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.94G>A	7.37:g.19184892C>T	ENSP00000275461:p.Asp32Asn		19151417	Q495K0	Missense_Mutation	SNP	ENST00000275461.3	37	CCDS5368.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004556	0.54254	.	.	ENSG00000146618	ENST00000275461	D	0.96619	-4.07	5.39	5.39	0.77823	.	0.263805	0.27206	N	0.020429	D	0.90892	0.7138	N	0.24115	0.695	0.19300	N	0.999974	P	0.45078	0.85	B	0.30401	0.115	T	0.83170	-0.0094	10	0.22109	T	0.4	-7.8919	19.1723	0.93583	0.0:1.0:0.0:0.0	.	32	Q96RJ6	FER3L_HUMAN	N	32	ENSP00000275461:D32N	ENSP00000275461:D32N	D	-	1	0	FERD3L	19151417	1.000000	0.71417	0.979000	0.43373	0.865000	0.49528	3.764000	0.55264	2.533000	0.85409	0.650000	0.86243	GAC		0.662	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			T	19184892	C	T	19184892	3	4	46	1	0	0	0	0	1	0	0	0	5835	884	31	1	410	1	FERD3L	7	19184892	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09		19184892	139953771	35	4355										
GPNMB	10457	broad.mit.edu	37	chr7	23300196	23300196	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	catgatcctagccacttcctCaattattctaccattaacta	2	13	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr7:23300196C>G	ENST00000381990.2	+	6	983	c.822C>G	c.(820-822)ctC>ctG	p.L274L	GPNMB_ENST00000539136.1_Silent_p.L175L|GPNMB_ENST00000453162.2_Silent_p.L216L|GPNMB_ENST00000258733.4_Silent_p.L274L	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	274	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)	p.L274L(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GCCACTTCCTCAATTATTCTA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	7											176	167	170					7																	23300196		2203	4300	6503	23266721	SO:0001819	synonymous_variant	10457			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.822C>G	7.37:g.23300196C>G			23266721	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																				0.418	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		G	23300196	C	G	23300196	2	3	46	1	0	0	0	0	0	0	0	1	6640	813	29	5		5	GPNMB	7	23300196	Silent	SNP	C	TCGA-AG-3890-01A-01W-1073-09	4115304	23300196	135838467	36	4356										
ZNF138	7697	broad.mit.edu	37	chr7	64292071	64292071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	atgtaaaagtcatgcataaaTtttcaaattcaaatagacac	4	6	3	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr7:64292071T>C	ENST00000359735.3	+	4	627	c.280T>C	c.(280-282)Ttt>Ctt	p.F94L	ZNF138_ENST00000397136.2_Missense_Mutation_p.F94L|ZNF138_ENST00000440598.1_3'UTR|ZNF138_ENST00000440155.2_Missense_Mutation_p.F125L|ZNF138_ENST00000437743.1_Missense_Mutation_p.F119L|ZNF138_ENST00000430838.2_3'UTR|ZNF138_ENST00000307355.7_Missense_Mutation_p.F151L|ZNF138_ENST00000494380.1_3'UTR	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138	94					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F94L(1)		kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				CATGCATAAATTTTCAAATTC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	7											38	40	40					7																	64292071		2200	4287	6487	63929506	SO:0001583	missense	7697			U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"Zinc fingers, C2H2-type", "-"	12922	protein-coding gene	gene with protein product		604080	"zinc finger protein 138 (clone pHZ-32)"				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.280T>C	7.37:g.64292071T>C	ENSP00000352770:p.Phe94Leu		63929506	B4DFX2|B4DP87|E9PHI7|E9PHK7	Missense_Mutation	SNP	ENST00000359735.3	37		.	.	.	.	.	.	.	.	.	.	.	3.855	-0.031152	0.07543	.	.	ENSG00000197008	ENST00000307355;ENST00000359735;ENST00000440155;ENST00000437743;ENST00000397136	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	0.149	-0.298	0.12814	.	.	.	.	.	T	0.23649	0.0572	L	0.33137	0.985	0.18873	N	0.999981	B;B;B	0.20368	0.02;0.044;0.02	B;B;B	0.23716	0.026;0.048;0.016	T	0.22871	-1.0204	9	0.44086	T	0.13	.	3.3639	0.07197	0.3528:0.0:0.0:0.6472	.	125;119;94	E9PHI7;E7EWC5;P52744	.;.;ZN138_HUMAN	L	151;94;125;119;94	ENSP00000303533:F151L;ENSP00000352770:F94L;ENSP00000407262:F125L;ENSP00000399528:F119L;ENSP00000380325:F94L	ENSP00000303533:F151L	F	+	1	0	ZNF138	63929506	0.006000	0.16342	0.006000	0.13384	0.006000	0.05464	-0.366000	0.07563	-1.212000	0.02620	-1.240000	0.01540	TTT		0.299	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524		C	64292071	T	C	64292071	3	2	46	1	0	0	0	0	1	0	0	0	17766	1493	52	4	606	4	ZNF138	7	64292071	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09	40991875	64292071	94846592	37	4357										
LZTS1	11178	broad.mit.edu	37	chr8	20107448	20107448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ccacacgagccgctcatgctGgaagcccgaggacatctggt	12	14	2	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr8:20107448G>T	ENST00000381569.1	-	4	1933	c.1576C>A	c.(1576-1578)Cag>Aag	p.Q526K	LZTS1_ENST00000265801.6_Missense_Mutation_p.Q526K|LZTS1_ENST00000522290.1_Intron			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	526					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q526K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CGCTCATGCTGGAAGCCCGAG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	87	86					8																	20107448		2203	4300	6503	20151728	SO:0001583	missense	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1576C>A	8.37:g.20107448G>T	ENSP00000370981:p.Gln526Lys		20151728	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	g	15.28	2.786117	0.49997	.	.	ENSG00000061337	ENST00000381569;ENST00000265801	T;T	0.41758	0.99;0.99	5.17	5.17	0.71159	.	0.194055	0.45867	D	0.000325	T	0.40743	0.1129	L	0.40543	1.245	0.53005	D	0.999964	P	0.34837	0.472	B	0.37780	0.258	T	0.34675	-0.9819	10	0.51188	T	0.08	-39.5888	17.2477	0.87032	0.0:0.0:1.0:0.0	.	526	Q9Y250	LZTS1_HUMAN	K	526	ENSP00000370981:Q526K;ENSP00000265801:Q526K	ENSP00000265801:Q526K	Q	-	1	0	LZTS1	20151728	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.534000	0.53568	2.419000	0.82065	0.556000	0.70494	CAG		0.647	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		T	20107448	G	T	20107448	3	4	46	1	0	0	0	0	1	0	0	0	9168	1357	47	2	218	2	LZTS1	8	20107448	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		20107448	126256574	38	4358										
PREX2	80243	broad.mit.edu	37	chr8	69017454	69017454	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ttgatcttcacagtgtaagcAgcacatttccagtacctgtg	8	10	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr8:69017454A>C	ENST00000288368.4	+	24	2992				PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2						adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.S933R(1)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CAGTGTAAGCAGCACATTTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											224	189	201					8																	69017454		2203	4300	6503	69180008	SO:0001627	intron_variant	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2716-2890A>C	8.37:g.69017454A>C			69180008	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	4.607	0.112895	0.08831	.	.	ENSG00000046889	ENST00000354677	.	.	.	2.58	0.0884	0.14455	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22941	-1.0202	7	0.49607	T	0.09	.	2.0465	0.03561	0.5862:0.0:0.1535:0.2603	.	933	Q70Z35-3	.	R	933	.	ENSP00000346707:S933R	S	+	1	0	PREX2	69180008	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.177000	0.09796	0.014000	0.14944	0.455000	0.32223	AGC		0.468	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69017454	A	C	69017454	1	2	46	0	1	0	0	0	0	0	0	0	12511	188	7	4		4	PREX2	8	69017454	Intron	SNP	A	TCGA-AG-3890-01A-01W-1073-09	48910006	69017454	77346568	39	4359										
KCNB2	9312	broad.mit.edu	37	chr8	73480007	73480007	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cccgggcttaaacaggaagaCttcaaggtcgacactttccc	9	13	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr8:73480007C>A	ENST00000523207.1	+	2	626	c.38C>A	c.(37-39)aCt>aAt	p.T13N		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	13					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.T13N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	AACAGGAAGACTTCAAGGTCG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	8											88	88	88					8																	73480007		2203	4300	6503	73642561	SO:0001583	missense	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.38C>A	8.37:g.73480007C>A	ENSP00000430846:p.Thr13Asn		73642561	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159962	0.57368	.	.	ENSG00000182674	ENST00000523207	D	0.96685	-4.09	6.11	6.11	0.99139	.	.	.	.	.	D	0.89777	0.6813	N	0.03608	-0.345	0.46167	D	0.998907	B	0.32302	0.363	B	0.25140	0.058	D	0.87090	0.2172	9	0.23302	T	0.38	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	13	Q92953	KCNB2_HUMAN	N	13	ENSP00000430846:T13N	ENSP00000430846:T13N	T	+	2	0	KCNB2	73642561	0.973000	0.33851	0.992000	0.48379	0.988000	0.76386	2.670000	0.46833	2.906000	0.99361	0.655000	0.94253	ACT		0.502	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73480007	C	A	73480007	3	1	46	1	0	0	0	0	1	0	0	0	8034	565	20	2	40	2	KCNB2	8	73480007	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	4462553	73480007	72884015	40	4360										
TSPYL5	85453	broad.mit.edu	37	chr8	98288946	98288946	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	aaaggtagaactgcaagggaTtgggccacaattcttcgttg	12	7	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr8:98288946T>A	ENST00000322128.3	-	1	1230	c.1127A>T	c.(1126-1128)aAt>aTt	p.N376I		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	376					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)		p.N376I(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CTGCAAGGGATTGGGCCACAA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	8											180	192	188					8																	98288946		2203	4300	6503	98358122	SO:0001583	missense	85453			AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.1127A>T	8.37:g.98288946T>A	ENSP00000322802:p.Asn376Ile		98358122	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	.	.	.	.	.	.	.	.	.	.	T	18.81	3.702663	0.68501	.	.	ENSG00000180543	ENST00000322128	T	0.36157	1.27	4.3	4.3	0.51218	.	0.000000	0.35096	N	0.003457	T	0.63307	0.2500	M	0.90595	3.13	0.58432	D	0.99999	D	0.65815	0.995	D	0.74674	0.984	T	0.69997	-0.4993	10	0.87932	D	0	-8.8307	10.1347	0.42699	0.0:0.0:0.0:1.0	.	376	Q86VY4	TSYL5_HUMAN	I	376	ENSP00000322802:N376I	ENSP00000322802:N376I	N	-	2	0	TSPYL5	98358122	0.999000	0.42202	0.993000	0.49108	0.996000	0.88848	2.861000	0.48380	2.174000	0.68829	0.460000	0.39030	AAT		0.458	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		A	98288946	T	A	98288946	3	1	46	1	0	0	0	0	1	0	0	0	16702	1493	52	5	130	5	TSPYL5	8	98288946	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09	24808939	98288946	48075076	41	4361										
ADCY8	114	broad.mit.edu	37	chr8	131916237	131916237	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ttaccatggccctcttccacGttatagtcaccgttgagaca	7	13	2	1	rs75415615	byFrequency	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr8:131916237G>A	ENST00000286355.5	-	7	3784	c.1692C>T	c.(1690-1692)aaC>aaT	p.N564N	ADCY8_ENST00000377928.3_Silent_p.N564N	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	564					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.N564N(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CCTCTTCCACGTTATAGTCAC	0.463										HNSCC(32;0.087)			G|||	12	0.00239617	0.0083	0	5008	,	,		21546	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	8						G		19,4387	26.2+/-53.5	0,19,2184	194	184	187		1692	-4.3	1	8	dbSNP_131	187	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADCY8	NM_001115.2		0,20,6483	AA,AG,GG		0.0116,0.4312,0.1538		564/1252	131916237	20,12986	2203	4300	6503	131985419	SO:0001819	synonymous_variant	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1692C>T	8.37:g.131916237G>A			131985419		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																				0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131916237	G	A	131916237	2	1	46	1	0	0	0	0	0	0	0	1	300	1136	40	1		1	ADCY8	8	131916237	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09	33627291	131916237	14447785	42	4362										
PLIN2	123	broad.mit.edu	37	chr9	19126236	19126236	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ggatactggtcctttgtactGagataggctgaggacatgag	14	6	0	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr9:19126236G>C	ENST00000276914.2	-	3	281	c.102C>G	c.(100-102)ctC>ctG	p.L34L	PLIN2_ENST00000380465.3_Silent_p.L34L|PLIN2_ENST00000380464.3_Silent_p.L34L|PLIN2_ENST00000411567.1_Silent_p.L34L	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	34					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L34L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						CCTTTGTACTGAGATAGGCTG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	9											172	130	144					9																	19126236		2203	4300	6503	19116236	SO:0001819	synonymous_variant	123			X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.102C>G	9.37:g.19126236G>C			19116236	Q9BSC3	Silent	SNP	ENST00000276914.2	37	CCDS6490.1																																																																																				0.537	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		C	19126236	G	C	19126236	2	2	46	1	0	0	0	0	0	0	0	1	12121	1277	45	5		5	PLIN2	9	19126236	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09		19126236	122087195	43	4363										
MCM10	55388	broad.mit.edu	37	chr10	13251284	13251284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	taccaagaggagaagaacatGctaaatttctgaacagcctt	8	8	1	4			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr10:13251284G>A	ENST00000484800.2	+	20	2705	c.2602G>A	c.(2602-2604)Gct>Act	p.A868T	MCM10_ENST00000378714.3_Missense_Mutation_p.A867T|MCM10_ENST00000378694.1_3'UTR			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	868					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.A868T(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGAAGAACATGCTAAATTTCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											100	96	98					10																	13251284		2203	4300	6503	13291290	SO:0001583	missense	55388			AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2602G>A	10.37:g.13251284G>A	ENSP00000418268:p.Ala868Thr		13291290	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.339179	0.60963	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800	T;T	0.15139	2.45;2.45	5.38	4.46	0.54185	Replication factor Mcm10 (1);	0.439235	0.26328	N	0.025011	T	0.26810	0.0656	L	0.51422	1.61	0.26993	N	0.965101	P;P	0.49358	0.905;0.923	P;P	0.51135	0.529;0.66	T	0.03662	-1.1015	10	0.38643	T	0.18	-12.4486	16.3696	0.83350	0.0:0.1852:0.8148:0.0	.	867;868	Q7L590-2;Q7L590	.;MCM10_HUMAN	T	867;868;868	ENSP00000367986:A867T;ENSP00000418268:A868T	ENSP00000354945:A868T	A	+	1	0	MCM10	13291290	0.999000	0.42202	0.996000	0.52242	0.965000	0.64279	1.947000	0.40293	2.512000	0.84698	0.561000	0.74099	GCT		0.398	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		A	13251284	G	A	13251284	3	1	46	1	0	0	0	0	1	0	0	0	9415	1319	46	3	2676	3	MCM10	10	13251284	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		13251284	122283463	44	4364										
PCDH15	65217	broad.mit.edu	37	chr10	55582386	55582386	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	acacaaggccttgaaggagaAagttccaaggaacactcagc	10	10	1	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr10:55582386A>G	ENST00000320301.6	-	33	5494	c.5100T>C	c.(5098-5100)ctT>ctC	p.L1700L	PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395433.1_Silent_p.L1677L|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000437009.1_Silent_p.L1631L|PCDH15_ENST00000361849.3_Silent_p.L1702L|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395432.2_Silent_p.L1660L|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395430.1_Silent_p.L1697L|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1700					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.L1700L(1)|p.L1707L(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTGAAGGAGAAAGTTCCAAGG	0.383										HNSCC(58;0.16)																																						2	Substitution - coding silent(2)	large_intestine(2)	10											106	105	105					10																	55582386		2203	4300	6503	55252392	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.5100T>C	10.37:g.55582386A>G			55252392	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55582386	A	G	55582386	2	3	46	1	0	0	0	0	0	0	0	1	11542	1	1	4		4	PCDH15	10	55582386	Silent	SNP	A	TCGA-AG-3890-01A-01W-1073-09	42331102	55582386	79952361	45	4365										
C10orf119	79892	broad.mit.edu	37	chr10	121596417	121596417	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	actcatcataccgggaggagTgacctcccctccgaagtaat	9	13	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr10:121596417T>C	ENST00000360003.3	-	13	1708	c.1539A>G	c.(1537-1539)tcA>tcG	p.S513S	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Silent_p.S511S	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	513					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.S513S(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CCGGGAGGAGTGACCTCCCCT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											100	92	95					10																	121596417		2203	4300	6503	121586407	SO:0001819	synonymous_variant	79892			BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.1539A>G	10.37:g.121596417T>C			121586407	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																				0.413	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		C	121596417	T	C	121596417	2	2	46	1	0	0	0	0	0	0	0	1	1592	1683	59	4		4	C10orf119	10	121596417	Silent	SNP	T	TCGA-AG-3890-01A-01W-1073-09	66014031	121596417	13938330	46	4366										
OR10A3	26496	broad.mit.edu	37	chr11	7960215	7960215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gctatagatgagcggattgaGcagaggggtaagcaacgtgt	16	5	0	4			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr11:7960215G>T	ENST00000360759.3	-	1	926	c.853C>A	c.(853-855)Ctc>Atc	p.L285I		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	285					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L285I(1)		endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGCGGATTGAGCAGAGGGGTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											177	163	168					11																	7960215		2201	4296	6497	7916791	SO:0001583	missense	26496			BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.853C>A	11.37:g.7960215G>T	ENSP00000353988:p.Leu285Ile		7916791	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	37	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.549641	0.27652	.	.	ENSG00000170683	ENST00000360759	T	0.44083	0.93	4.65	1.77	0.24775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32028	U	0.006697	T	0.51822	0.1697	L	0.47716	1.5	0.24611	N	0.993723	D	0.71674	0.998	D	0.83275	0.996	T	0.37934	-0.9684	10	0.59425	D	0.04	.	8.5403	0.33388	0.2542:0.0:0.7458:0.0	.	285	P58181	O10A3_HUMAN	I	285	ENSP00000353988:L285I	ENSP00000353988:L285I	L	-	1	0	OR10A3	7916791	0.109000	0.22037	1.000000	0.80357	0.005000	0.04900	-0.218000	0.09240	0.305000	0.22832	-0.225000	0.12378	CTC		0.413	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		T	7960215	G	T	7960215	3	4	46	1	0	0	0	0	1	0	0	0	10922	971	34	2	94	2	OR10A3	11	7960215	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		7960215	127046301	47	4367										
GTF2H1	2965	broad.mit.edu	37	chr11	18357325	18357325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gaaaattagtccagaaggaaAagctaaaattcagcttcagc	8	7	2	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr11:18357325A>C	ENST00000265963.4	+	3	339	c.179A>C	c.(178-180)aAa>aCa	p.K60T	GTF2H1_ENST00000534641.1_Intron|GTF2H1_ENST00000531757.1_3'UTR|GTF2H1_ENST00000453096.2_Missense_Mutation_p.K60T|GTF2H1_ENST00000524753.4_5'Flank	NM_005316.3	NP_005307.1	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1, 62kDa	60					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.K60T(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						CCAGAAGGAAAAGCTAAAATT	0.423								Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	11											97	87	91					11																	18357325		2199	4293	6492	18313901	SO:0001583	missense	2965				CCDS7838.1	11p15.1-p14	2012-11-05	2002-08-29		ENSG00000110768	ENSG00000110768		"General transcription factors", "General transcription factor IIH complex subunits"	4655	protein-coding gene	gene with protein product		189972	"general transcription factor IIH, polypeptide 1 (62kD subunit)"			1529339, 8162052	Standard	NM_005316		Approved	BTF2, P62, TFIIH	uc001moh.2	P32780	OTTHUMG00000167690	ENST00000265963.4:c.179A>C	11.37:g.18357325A>C	ENSP00000265963:p.Lys60Thr		18313901	B3KXE0|D3DQY2|Q6I9Y7|Q9H5K5|Q9NQD9	Missense_Mutation	SNP	ENST00000265963.4	37	CCDS7838.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.874110	0.91664	.	.	ENSG00000110768	ENST00000453096;ENST00000525831;ENST00000265963	T;T	0.29142	1.58;1.58	5.75	5.75	0.90469	TFIIH p62 subunit, N-terminal (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.57946	0.2088	M	0.78456	2.415	0.80722	D	1	P	0.45715	0.865	D	0.69142	0.962	T	0.57159	-0.7859	10	0.44086	T	0.13	-10.1612	16.0671	0.80891	1.0:0.0:0.0:0.0	.	60	P32780	TF2H1_HUMAN	T	60	ENSP00000393638:K60T;ENSP00000265963:K60T	ENSP00000265963:K60T	K	+	2	0	GTF2H1	18313901	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.679000	0.91220	2.192000	0.70111	0.460000	0.39030	AAA		0.423	GTF2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395627.2	NM_005316		C	18357325	A	C	18357325	3	2	46	1	0	0	0	0	1	0	0	0	6881	14	1	4	185	4	GTF2H1	11	18357325	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09	10397110	18357325	116649191	48	4368										
RDX	5962	broad.mit.edu	37	chr11	110104081	110104081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	agcttcagcattattctcatCgtgttcatcatgttcgtttt	6	9	4	0	rs34471100		TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr11:110104081C>T	ENST00000343115.4	-	13	1787	c.1468G>A	c.(1468-1470)Gat>Aat	p.D490N	RDX_ENST00000528900.1_Missense_Mutation_p.D143N|RDX_ENST00000530301.1_Intron|RDX_ENST00000544551.1_Missense_Mutation_p.D354N|RDX_ENST00000528498.1_Missense_Mutation_p.D490N|RDX_ENST00000405097.1_Missense_Mutation_p.D490N	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	490	Glu-rich.		D -> N (in dbSNP:rs34471100).		actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)	p.D490N(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		TTATTCTCATCGTGTTCATCA	0.443													C|||	1	0.000199681	8e-04	0	5008	,	,		18238	0		0	False		,,,				2504	0				Esophageal Squamous(55;25 1062 11040 28755 44273)											1	Substitution - Missense(1)	large_intestine(1)	11						C	ASN/ASP	10,4392	16.8+/-37.8	0,10,2191	236	216	223		1468	5.1	1	11	dbSNP_126	223	2,8594	2.2+/-6.3	0,2,4296	yes	missense	RDX	NM_002906.3	23	0,12,6487	TT,TC,CC		0.0233,0.2272,0.0923	benign	490/584	110104081	12,12986	2201	4298	6499	109609291	SO:0001583	missense	5962			BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.1468G>A	11.37:g.110104081C>T	ENSP00000342830:p.Asp490Asn		109609291	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	37	CCDS8343.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	16.96	3.265990	0.59540	0.002272	2.33E-4	ENSG00000137710	ENST00000528498;ENST00000405097;ENST00000528900;ENST00000343115;ENST00000544551;ENST00000530085	D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	6.01	5.09	0.68999	Ezrin/radixin/moesin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80507	0.4636	M	0.80847	2.515	0.58432	D	0.999998	B;P;B;B	0.40834	0.174;0.73;0.208;0.144	B;B;B;B	0.35688	0.067;0.208;0.11;0.028	T	0.77608	-0.2524	10	0.21014	T	0.42	.	11.7841	0.52032	0.0:0.8655:0.0:0.1345	rs34471100	354;490;490;143	F5H1A7;A7YIJ8;P35241;A7YIK3	.;.;RADI_HUMAN;.	N	490;490;143;490;354;160	ENSP00000432112:D490N;ENSP00000384136:D490N;ENSP00000433580:D143N;ENSP00000342830:D490N;ENSP00000445826:D354N;ENSP00000434788:D160N	ENSP00000342830:D490N	D	-	1	0	RDX	109609291	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.638000	0.61353	2.861000	0.98227	0.650000	0.86243	GAT		0.443	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		T	110104081	C	T	110104081	3	4	46	1	0	0	0	0	1	0	0	0	13235	884	31	1	291	1	RDX	11	110104081	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	91746756	110104081	24902435	49	4369										
ZW10	9183	broad.mit.edu	37	chr11	113614651	113614651	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtccaatgtattttcaggctCtaaattcatcacttcgtggt	7	9	4	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr11:113614651C>T	ENST00000200135.3	-	10	1528	c.1384G>A	c.(1384-1386)Gag>Aag	p.E462K		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	462					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)	p.E462K(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TTTTCAGGCTCTAAATTCATC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											227	200	209					11																	113614651		2201	4296	6497	113119861	SO:0001583	missense	9183			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1384G>A	11.37:g.113614651C>T	ENSP00000200135:p.Glu462Lys		113119861	A1A528	Missense_Mutation	SNP	ENST00000200135.3	37	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086649	0.55861	.	.	ENSG00000086827	ENST00000200135	T	0.47528	0.84	5.57	3.67	0.42095	.	0.048140	0.85682	D	0.000000	T	0.42630	0.1211	M	0.70595	2.14	0.58432	D	0.999999	B	0.09022	0.002	B	0.22386	0.039	T	0.24261	-1.0165	10	0.07813	T	0.8	-8.5333	10.0266	0.42074	0.0:0.7855:0.1387:0.0757	.	462	O43264	ZW10_HUMAN	K	462	ENSP00000200135:E462K	ENSP00000200135:E462K	E	-	1	0	ZW10	113119861	1.000000	0.71417	0.950000	0.38849	0.694000	0.40290	2.183000	0.42565	0.686000	0.31488	-0.384000	0.06662	GAG		0.403	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		T	113614651	C	T	113614651	3	4	46	1	0	0	0	0	1	0	0	0	18286	922	32	3	983	3	ZW10	11	113614651	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	3510570	113614651	21391865	50	4370										
ZNF705A	440077	broad.mit.edu	37	chr12	8329645	8329645	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gaatgtaatgattcgggagaAgattgcactcacagttccac	10	8	1	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr12:8329645A>C	ENST00000359286.4	+	5	458	c.369A>C	c.(367-369)gaA>gaC	p.E123D		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E123D(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		ATTCGGGAGAAGATTGCACTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											93	94	94					12																	8329645		2202	4291	6493	8220912	SO:0001583	missense	440077			AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"Zinc fingers, C2H2-type", "-"	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.369A>C	12.37:g.8329645A>C	ENSP00000352233:p.Glu123Asp		8220912		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	.	.	.	.	.	.	.	.	.	.	.	12.66	2.004177	0.35320	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.01629	4.72;4.72	1.35	-1.66	0.08265	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01387	0.0045	L	0.41236	1.265	0.19945	N	0.99994	B	0.32409	0.37	B	0.17098	0.017	T	0.44651	-0.9314	9	0.87932	D	0	.	2.1135	0.03708	0.3249:0.0:0.1856:0.4895	.	123	Q6ZN79	Z705A_HUMAN	D	123	ENSP00000379816:E123D;ENSP00000352233:E123D	ENSP00000352233:E123D	E	+	3	2	ZNF705A	8220912	0.252000	0.23972	0.002000	0.10522	0.081000	0.17604	0.039000	0.13884	-0.450000	0.07107	0.329000	0.21502	GAA		0.383	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328		C	8329645	A	C	8329645	3	2	46	1	0	0	0	0	1	0	0	0	18147	69	3	4	387	4	ZNF705A	12	8329645	Missense_Mutation	SNP	A	TCGA-AG-3890-01A-01W-1073-09		8329645	125522250	51	4371										
GPR19	2842	broad.mit.edu	37	chr12	12814647	12814647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tctccaaatatattttatgaCcttttggtaaaataaaatta	3	5	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr12:12814647C>T	ENST00000540510.1	-	2	928	c.736G>A	c.(736-738)Gtc>Atc	p.V246I	GPR19_ENST00000332427.2_Missense_Mutation_p.V246I			P46093	GPR4_HUMAN	G protein-coupled receptor 19	204					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V246I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		TATTTTATGACCTTTTGGTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											38	42	40					12																	12814647		2203	4300	6503	12705914	SO:0001583	missense	2842				CCDS8652.1	12p12.3	2014-01-30				ENSG00000183150		"GPCR / Class A : Orphans"	4473	protein-coding gene	gene with protein product		602927					Standard	NM_006143		Approved		uc001raq.2	Q15760		ENST00000540510.1:c.736G>A	12.37:g.12814647C>T	ENSP00000441832:p.Val246Ile		12705914	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000540510.1	37	CCDS8652.1	.	.	.	.	.	.	.	.	.	.	C	5.822	0.335880	0.11013	.	.	ENSG00000183150	ENST00000540510;ENST00000332427	T;T	0.23147	1.92;1.92	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.14442	0.0349	N	0.13168	0.305	0.48135	D	0.99959	B	0.20550	0.046	B	0.26310	0.068	T	0.04870	-1.0921	10	0.02654	T	1	-29.8564	13.5819	0.61907	0.0:0.9249:0.0:0.0751	.	246	Q15760	GPR19_HUMAN	I	246	ENSP00000441832:V246I;ENSP00000333744:V246I	ENSP00000333744:V246I	V	-	1	0	GPR19	12705914	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.048000	0.57390	2.642000	0.89623	0.655000	0.94253	GTC		0.433	GPR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400662.1	NM_006143		T	12814647	C	T	12814647	3	4	46	1	0	0	0	0	1	0	0	0	6699	507	18	3	515	3	GPR19	12	12814647	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	4485002	12814647	121037248	52	4372										
SLCO1A2	6579	broad.mit.edu	37	chr12	21422638	21422638	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cacttcctcaaaagaattaaGatgattaaggctggaacaaa	7	7	1	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr12:21422638G>C	ENST00000307378.6	-	16	2577	c.1857C>G	c.(1855-1857)atC>atG	p.I619M	SLCO1A2_ENST00000537524.1_Missense_Mutation_p.I487M|SLCO1A2_ENST00000452078.1_Missense_Mutation_p.I619M|SLCO1A2_ENST00000458504.1_Missense_Mutation_p.I487M	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	619					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)	p.I619M(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	AAAGAATTAAGATGATTAAGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											95	94	95					12																	21422638		2203	4300	6503	21313905	SO:0001583	missense	6579				CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"Solute carriers"	10956	protein-coding gene	gene with protein product		602883	"solute carrier family 21 (organic anion transporter), member 3"	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.1857C>G	12.37:g.21422638G>C	ENSP00000305974:p.Ile619Met		21313905	Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	37	CCDS8686.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.247497	0.39697	.	.	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000458504;ENST00000537524	T;T;T;T	0.45276	1.13;1.13;0.9;0.9	4.76	-0.796	0.10912	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.533866	0.19347	N	0.116501	T	0.36552	0.0971	M	0.64404	1.975	0.09310	N	1	B	0.22211	0.066	B	0.26614	0.071	T	0.37267	-0.9713	10	0.56958	D	0.05	.	8.0539	0.30593	0.5406:0.0:0.4594:0.0	.	619	P46721	SO1A2_HUMAN	M	619;619;487;487	ENSP00000305974:I619M;ENSP00000393973:I619M;ENSP00000394854:I487M;ENSP00000439401:I487M	ENSP00000305974:I619M	I	-	3	3	SLCO1A2	21313905	0.215000	0.23574	0.002000	0.10522	0.005000	0.04900	0.183000	0.16919	-0.074000	0.12820	-0.251000	0.11542	ATC		0.363	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		C	21422638	G	C	21422638	3	2	46	1	0	0	0	0	1	0	0	0	14759	932	33	5	159	5	SLCO1A2	12	21422638	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	8607991	21422638	112429257	53	4373										
CNTN1	1272	broad.mit.edu	37	chr12	41333214	41333214	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtggaagggtgataattgaaTgcaaacctaaagctgcaccg	12	7	0	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr12:41333214T>A	ENST00000551295.2	+	12	1423	c.1306T>A	c.(1306-1308)Tgc>Agc	p.C436S	CNTN1_ENST00000347616.1_Missense_Mutation_p.C436S|CNTN1_ENST00000547702.1_Missense_Mutation_p.C436S|CNTN1_ENST00000547849.1_Missense_Mutation_p.C436S|CNTN1_ENST00000348761.2_Missense_Mutation_p.C425S|CNTN1_ENST00000360099.3_Missense_Mutation_p.C436S	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	436	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.C436S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GATAATTGAATGCAAACCTAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											96	93	94					12																	41333214		2203	4300	6503	39619481	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1306T>A	12.37:g.41333214T>A	ENSP00000447006:p.Cys436Ser		39619481	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.334383	0.81801	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37	4.83	4.83	0.62350	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81959	0.4933	H	0.97659	4.05	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.88677	0.3199	10	0.87932	D	0	.	15.1084	0.72336	0.0:0.0:0.0:1.0	.	436;425;436	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	S	436;436;436;436;436;425	ENSP00000448004:C436S;ENSP00000447006:C436S;ENSP00000448653:C436S;ENSP00000325660:C436S;ENSP00000353213:C436S;ENSP00000261160:C425S	ENSP00000325660:C436S	C	+	1	0	CNTN1	39619481	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.456000	0.80751	2.112000	0.64535	0.459000	0.35465	TGC		0.393	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41333214	T	A	41333214	3	1	46	1	0	0	0	0	1	0	0	0	3646	1464	51	5	1348	5	CNTN1	12	41333214	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09	19910576	41333214	92518681	54	4374										
DIAPH3	81624	broad.mit.edu	37	chr13	60435600	60435600	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	aattcagtatatcagggtacTtctcttcacatatttctacc	4	10	5	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr13:60435600T>A	ENST00000400324.4	-	22	2898	c.2678A>T	c.(2677-2679)aAg>aTg	p.K893M	DIAPH3_ENST00000267215.4_Missense_Mutation_p.K893M|DIAPH3_ENST00000400320.1_Missense_Mutation_p.K847M|DIAPH3_ENST00000377908.2_Missense_Mutation_p.K882M|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400330.1_Missense_Mutation_p.K893M|DIAPH3_ENST00000400319.1_Missense_Mutation_p.K823M	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	893	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K893M(1)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ATCAGGGTACTTCTCTTCACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	13											146	135	138					13																	60435600		1831	4081	5912	59333601	SO:0001583	missense	81624			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2678A>T	13.37:g.60435600T>A	ENSP00000383178:p.Lys893Met		59333601	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.750895	0.69533	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;2.03	5.38	5.38	0.77491	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.163603	0.53938	D	0.000041	T	0.79610	0.4475	M	0.85542	2.76	0.36914	D	0.891026	D;D;D	0.62365	0.991;0.96;0.975	P;P;P	0.61722	0.893;0.844;0.807	D	0.85185	0.1006	10	0.87932	D	0	.	8.7342	0.34519	0.0:0.1481:0.0:0.8519	.	630;630;893	Q9NSV4-2;Q9NSV4-1;Q9NSV4	.;.;DIAP3_HUMAN	M	893;893;882;847;823;882;823;847;893;630;893	ENSP00000383178:K893M;ENSP00000383184:K893M;ENSP00000367141:K882M;ENSP00000383173:K823M;ENSP00000383174:K847M;ENSP00000267215:K893M	ENSP00000267214:K630M	K	-	2	0	DIAPH3	59333601	0.992000	0.36948	0.999000	0.59377	0.980000	0.70556	2.462000	0.45049	2.051000	0.60960	0.459000	0.35465	AAG		0.363	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60435600	T	A	60435600	3	1	46	1	0	0	0	0	1	0	0	0	4531	1609	56	5	951	5	DIAPH3	13	60435600	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09		60435600	54734278	55	4375										
DIS3	22894	broad.mit.edu	37	chr13	73335921	73335921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtcagccccaatagccacagCcaaaagccgatgaacaatga	8	13	1	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr13:73335921C>T	ENST00000377767.4	-	18	2474	c.2374G>A	c.(2374-2376)Gct>Act	p.A792T	DIS3_ENST00000377780.4_Missense_Mutation_p.A762T|DIS3_ENST00000545453.1_Missense_Mutation_p.A630T	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	792					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)	p.A792T(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		ATAGCCACAGCCAAAAGCCGA	0.363										Multiple Myeloma(4;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	13											91	87	89					13																	73335921		2203	4300	6503	72233922	SO:0001583	missense	22894			AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.2374G>A	13.37:g.73335921C>T	ENSP00000366997:p.Ala792Thr		72233922	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	C	36	5.690863	0.96793	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.35236	1.32;1.32;1.32	5.96	5.96	0.96718	Ribonuclease II/R (2);	0.187742	0.56097	N	0.000026	T	0.56804	0.2010	L	0.53249	1.67	0.80722	D	1	D;P	0.60160	0.987;0.951	D;P	0.65233	0.933;0.895	T	0.49960	-0.8883	10	0.48119	T	0.1	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	762;792	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	T	792;762;630	ENSP00000366997:A792T;ENSP00000367011:A762T;ENSP00000440058:A630T	ENSP00000366997:A792T	A	-	1	0	DIS3	72233922	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.582000	0.82546	2.832000	0.97577	0.655000	0.94253	GCT		0.363	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		T	73335921	C	T	73335921	3	4	46	1	0	0	0	0	1	0	0	0	4546	739	26	3	518	3	DIS3	13	73335921	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	12900321	73335921	41833957	56	4376										
FARP1	10160	broad.mit.edu	37	chr13	99020390	99020390	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gggccaaagcacgttgttgtTaagtttgtggtgaaattctt	12	5	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr13:99020390T>G	ENST00000319562.6	+	5	604	c.339T>G	c.(337-339)gtT>gtG	p.V113V	FARP1_ENST00000376586.2_Silent_p.V113V|FARP1_ENST00000595437.1_Silent_p.V113V	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	113	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V113V(2)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ACGTTGTTGTTAAGTTTGTGG	0.358																																																2	Substitution - coding silent(2)	large_intestine(2)	13											100	91	94					13																	99020390		2203	4300	6503	97818391	SO:0001819	synonymous_variant	10160			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.339T>G	13.37:g.99020390T>G			97818391	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1																																																																																				0.358	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		G	99020390	T	G	99020390	2	3	46	1	0	0	0	0	0	0	0	1	5695	1741	61	4		4	FARP1	13	99020390	Silent	SNP	T	TCGA-AG-3890-01A-01W-1073-09	25684469	99020390	16149488	57	4377										
C15orf55	256646	broad.mit.edu	37	chr15	34648027	34648027	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ccacagggaactccgggaccCttgggtgtggagaggagagg	18	9	0	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr15:34648027C>G	ENST00000333756.4	+	7	1889	c.1734C>G	c.(1732-1734)ccC>ccG	p.P578P	NUTM1_ENST00000438749.3_Silent_p.P596P|NUTM1_ENST00000537011.1_Silent_p.P606P	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	578						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P578P(1)									CTCCGGGACCCTTGGGTGTGG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	15											30	33	32					15																	34648027		2200	4297	6497	32435319	SO:0001819	synonymous_variant	256646			AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.1734C>G	15.37:g.34648027C>G			32435319	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Silent	SNP	ENST00000333756.4	37	CCDS32190.1																																																																																				0.607	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		G	34648027	C	G	34648027	2	3	46	1	0	0	0	0	0	0	0	1	1807	668	24	5		5	C15orf55	15	34648027	Silent	SNP	C	TCGA-AG-3890-01A-01W-1073-09		34648027	67883365	58	4378										
LCMT1	51451	broad.mit.edu	37	chr16	25143723	25143723	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtgcctcccctcccccctagGatattttgctcgagtccatg	8	16	0	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr16:25143723G>T	ENST00000399069.3	+	3	361	c.206G>T	c.(205-207)gGa>gTa	p.G69V	LCMT1_ENST00000380966.4_Splice_Site_p.G69V	NM_016309.2	NP_057393.2	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1	69					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|negative regulation of protein complex assembly (GO:0031333)|protein methylation (GO:0006479)|regulation of apoptotic process (GO:0042981)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	cytosol (GO:0005829)	protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.G69V(1)							GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	TCCCCCCTAGGATATTTTGCT	0.483																																					Colon(200;565 2072 24396 47922 50898)											1	Substitution - Missense(1)	large_intestine(1)	16											107	102	103					16																	25143723		1949	4144	6093	25051224	SO:0001630	splice_region_variant	51451			AF037601	CCDS45445.1, CCDS45446.1	16p12.1	2014-08-01			ENSG00000205629	ENSG00000205629			17557	protein-coding gene	gene with protein product	"protein phosphatase methyltransferase 1"	610286				10810093	Standard	XM_005255354		Approved	CGI-68, PPMT1	uc002dnx.1	Q9UIC8	OTTHUMG00000177182	ENST00000399069.3:c.206-1G>T	16.37:g.25143723G>T			25051224	A6NL89|A8K770|Q53FC5|Q96CI5|Q9H6I9|Q9NTG4|Q9Y378	Missense_Mutation	SNP	ENST00000399069.3	37	CCDS45445.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.043432	0.55003	.	.	ENSG00000205629	ENST00000399069;ENST00000380966;ENST00000380962	T;T	0.25912	1.77;1.77	5.51	5.51	0.81932	.	0.060518	0.64402	D	0.000003	T	0.66479	0.2793	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	T	0.78635	-0.2127	9	.	.	.	.	16.9326	0.86195	0.0:0.0:1.0:0.0	.	69;69	Q9UIC8-3;Q9UIC8	.;LCMT1_HUMAN	V	69;69;86	ENSP00000382021:G69V;ENSP00000370353:G69V	.	G	+	2	0	LCMT1	25051224	1.000000	0.71417	0.998000	0.56505	0.796000	0.44982	8.729000	0.91490	2.591000	0.87537	0.655000	0.94253	GGA		0.483	LCMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435747.4	NM_016309	Missense_Mutation	T	25143723	G	T	25143723	5	4	46	1	0	0	0	0	0	0	1	0	8700	1188	41	2	216	2	LCMT1	16	25143723	Splice_Site	SNP	G	TCGA-AG-3890-01A-01W-1073-09		25143723	65211030	59	4379										
KIFC3	3801	broad.mit.edu	37	chr16	57803780	57803780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tctggcaaaggcctcctcaaTggcccggttcttgtcctctt	9	14	4	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr16:57803780T>C	ENST00000379655.4	-	8	1284	c.1027A>G	c.(1027-1029)Att>Gtt	p.I343V	KIFC3_ENST00000539578.1_Missense_Mutation_p.I285V|KIFC3_ENST00000566975.1_5'Flank|KIFC3_ENST00000543930.1_Missense_Mutation_p.I204V|KIFC3_ENST00000445690.2_Missense_Mutation_p.I343V|KIFC3_ENST00000421376.2_Missense_Mutation_p.I204V|KIFC3_ENST00000541240.1_Missense_Mutation_p.I365V|KIFC3_ENST00000562903.1_Missense_Mutation_p.I204V|KIFC3_ENST00000465878.2_Missense_Mutation_p.I204V|KIFC3_ENST00000540079.2_Missense_Mutation_p.I241V	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	343					ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I343V(1)		breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				GCCTCCTCAATGGCCCGGTTC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	16											68	56	60					16																	57803780		2198	4300	6498	56361281	SO:0001583	missense	3801			BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1027A>G	16.37:g.57803780T>C	ENSP00000368976:p.Ile343Val		56361281	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222488	0.39300	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.73897	-0.74;-0.71;-0.7;-0.71;-0.7;-0.79;-0.69	5.74	5.74	0.90152	.	0.053662	0.85682	D	0.000000	T	0.63379	0.2506	L	0.31420	0.93	0.40370	D	0.979335	P;P;P;B;B;P;B	0.44578	0.651;0.754;0.64;0.082;0.058;0.838;0.188	B;P;B;B;B;B;B	0.45119	0.194;0.47;0.097;0.155;0.034;0.279;0.1	T	0.60875	-0.7176	10	0.13470	T	0.59	.	9.3862	0.38345	0.0:0.0799:0.0:0.9201	.	365;285;204;241;48;343;204	B7Z484;F5H4I9;B7Z896;F5H3M2;B7Z3I6;Q9BVG8;A8K6S2	.;.;.;.;.;KIFC3_HUMAN;.	V	343;343;204;365;241;204;285	ENSP00000368976:I343V;ENSP00000401696:I343V;ENSP00000396399:I204V;ENSP00000442008:I365V;ENSP00000438805:I241V;ENSP00000444012:I204V;ENSP00000444884:I285V	ENSP00000368976:I343V	I	-	1	0	KIFC3	56361281	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	2.897000	0.48664	2.198000	0.70561	0.533000	0.62120	ATT		0.627	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		C	57803780	T	C	57803780	3	2	46	1	0	0	0	0	1	0	0	0	8335	1464	51	4	1531	4	KIFC3	16	57803780	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09	32660057	57803780	32550973	60	4380										
TP53	7157	broad.mit.edu	37	chr17	7574023	7574024	+	Frame_Shift_Ins	INS	-	-	T													0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gaacatctcgaagcgctcacINSgcccacggatctgcagcaac					rs375444154		TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr17:7574023_7574024insT	ENST00000269305.4	-	10	1192_1193	c.1003_1004insA	c.(1003-1005)cgtfs	p.R335fs	TP53_ENST00000445888.2_Frame_Shift_Ins_p.R335fs|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000359597.4_Intron|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_3'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	335	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> G (in a sporadic cancer; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.R335fs*2(2)|p.R335fs*10(2)|p.R335L(1)|p.?(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAAGCGCTCACGCCCACGGATC	0.525		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	15	Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(5)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|upper_aerodigestive_tract(1)|stomach(1)	17																																								7514749	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1003_1004insA	17.37:g.7574023_7574024insT	ENSP00000269305:p.Arg335fs		7514748	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.525	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7574024	-	T	7574023	7	5	46	1	0	1	1	0	0	0	0	0	16421	536	19	0	185	0	TP53	17	7574023	Frame_Shift_Ins	INS	-	TCGA-AG-3890-01A-01W-1073-09		7574023	73621187	61	4381										
SHMT1	6470	broad.mit.edu	37	chr17	18233941	18233941	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	agcccttccaccatctgtgcCtttggaacggagatccacaa	8	14	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr17:18233941C>A	ENST00000316694.3	-	10	1233	c.1099G>T	c.(1099-1101)Ggc>Tgc	p.G367C	SHMT1_ENST00000539052.1_Missense_Mutation_p.G229C|SHMT1_ENST00000354098.3_Missense_Mutation_p.G328C|SHMT1_ENST00000352886.6_Missense_Mutation_p.G287C	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	367					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.G367C(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	CCATCTGTGCCTTTGGAACGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	17											118	101	107					17																	18233941		2203	4300	6503	18174666	SO:0001583	missense	6470				CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"cytoplasmic serine hydroxymethyltransferase", "14 kDa protein"	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.1099G>T	17.37:g.18233941C>A	ENSP00000318868:p.Gly367Cys		18174666	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	37	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.655381	0.88056	.	.	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098;ENST00000395685	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.52	5.52	0.82312	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.092522	0.85682	D	0.000000	T	0.74023	0.3662	H	0.98559	4.265	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.988	T	0.83146	-0.0106	10	0.87932	D	0	-27.3016	13.0665	0.59036	0.0:0.9261:0.0:0.0739	.	367;328;367	A8MYA6;P34896-2;P34896	.;.;GLYC_HUMAN	C	367;142;287;229;328;367	ENSP00000318868:G367C;ENSP00000345881:G287C;ENSP00000440089:G229C;ENSP00000318805:G328C	ENSP00000318868:G367C	G	-	1	0	SHMT1	18174666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.026000	0.70873	2.761000	0.94854	0.655000	0.94253	GGC		0.478	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		A	18233941	C	A	18233941	3	1	46	1	0	0	0	0	1	0	0	0	14322	681	24	2	364	2	SHMT1	17	18233941	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	10659918	18233941	62961269	62	4382										
ZNF830	91603	broad.mit.edu	37	chr17	33289465	33289465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tttccgaagccatagttgccGaagaggatgaggagggacgg	16	7	0	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr17:33289465G>A	ENST00000361952.3	+	1	917	c.880G>A	c.(880-882)Gaa>Aaa	p.E294K	CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000421975.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	294					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.E294K(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				CATAGTTGCCGAAGAGGATGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	89	94					17																	33289465		2203	4300	6503	30313578	SO:0001583	missense	91603			AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.880G>A	17.37:g.33289465G>A	ENSP00000354518:p.Glu294Lys		30313578	Q96F60|Q96GZ5|Q9BU38	Missense_Mutation	SNP	ENST00000361952.3	37	CCDS32618.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285509	0.95517	.	.	ENSG00000198783	ENST00000361952	T	0.20881	2.04	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.48370	0.1496	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.40194	-0.9576	10	0.66056	D	0.02	-17.3466	16.1635	0.81734	0.0:0.0:1.0:0.0	.	294	Q96NB3	ZN830_HUMAN	K	294	ENSP00000354518:E294K	ENSP00000354518:E294K	E	+	1	0	ZNF830	30313578	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	8.332000	0.90024	2.894000	0.99253	0.655000	0.94253	GAA		0.507	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		A	33289465	G	A	33289465	3	1	46	1	0	0	0	0	1	0	0	0	18223	1059	37	1	882	1	ZNF830	17	33289465	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	15055524	33289465	47905745	63	4383										
ASXL3	80816	broad.mit.edu	37	chr18	31323783	31323783	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	catggatgataagcagttacTaatatcaagcagcagtgcta	9	7	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr18:31323783T>A	ENST00000269197.5	+	12	3971	c.3971T>A	c.(3970-3972)cTa>cAa	p.L1324Q		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1324	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L1324Q(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAGCAGTTACTAATATCAAGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	18											174	174	174					18																	31323783		2018	4200	6218	29577781	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3971T>A	18.37:g.31323783T>A	ENSP00000269197:p.Leu1324Gln		29577781	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.456157	0.43634	.	.	ENSG00000141431	ENST00000269197	T	0.15952	2.38	5.92	2.27	0.28462	.	.	.	.	.	T	0.11110	0.0271	N	0.24115	0.695	0.19945	N	0.999942	P	0.46395	0.877	B	0.41860	0.368	T	0.15954	-1.0419	9	0.38643	T	0.18	.	6.3032	0.21125	0.0:0.5264:0.0:0.4736	.	1324	Q9C0F0	ASXL3_HUMAN	Q	1324	ENSP00000269197:L1324Q	ENSP00000269197:L1324Q	L	+	2	0	ASXL3	29577781	0.928000	0.31464	0.010000	0.14722	0.939000	0.58152	1.558000	0.36309	0.493000	0.27837	0.533000	0.62120	CTA		0.453	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31323783	T	A	31323783	3	1	46	1	0	0	0	0	1	0	0	0	1069	1522	53	5	4017	5	ASXL3	18	31323783	Missense_Mutation	SNP	T	TCGA-AG-3890-01A-01W-1073-09		31323783	46753465	64	4384										
SMAD2	4087	broad.mit.edu	37	chr18	45374929	45374929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	agaacctctctgaatttgatGggtctgtaaagccatctaca	8	9	3	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr18:45374929G>A	ENST00000402690.2	-	8	1308	c.914C>T	c.(913-915)cCa>cTa	p.P305L	SMAD2_ENST00000356825.4_Missense_Mutation_p.P275L|SMAD2_ENST00000586040.1_Missense_Mutation_p.P275L|SMAD2_ENST00000262160.6_Missense_Mutation_p.P305L|SMAD2_ENST00000591214.1_Missense_Mutation_p.P275L	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	305	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.P305L(1)|p.P305Q(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						TGAATTTGATGGGTCTGTAAA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	18											126	114	118					18																	45374929		2203	4300	6503	43628927	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.914C>T	18.37:g.45374929G>A	ENSP00000384449:p.Pro305Leu		43628927		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	G	33	5.235112	0.95207	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.97114	-4.25;-4.25;-4.25	5.81	5.81	0.92471	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98264	0.9425	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.958;1.0	D	0.99010	1.0814	10	0.87932	D	0	.	20.0912	0.97820	0.0:0.0:1.0:0.0	.	275;275;305	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	L	305;275;305	ENSP00000262160:P305L;ENSP00000349282:P275L;ENSP00000384449:P305L	ENSP00000262160:P305L	P	-	2	0	SMAD2	43628927	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.869000	0.99810	2.746000	0.94184	0.591000	0.81541	CCA		0.403	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		A	45374929	G	A	45374929	3	1	46	1	0	0	0	0	1	0	0	0	14795	1348	47	3	505	3	SMAD2	18	45374929	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	14051146	45374929	32702319	65	4385										
MUC16	94025	broad.mit.edu	37	chr19	9085910	9085910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ggtccatacaattgttggtgGggtgatgggagaatgtgtca	16	4	1	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr19:9085910G>T	ENST00000397910.4	-	1	6108	c.5905C>A	c.(5905-5907)Cca>Aca	p.P1969T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1969	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.P1969T(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTGTTGGTGGGGTGATGGGA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	19											205	202	203					19																	9085910		2071	4228	6299	8946910	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5905C>A	19.37:g.9085910G>T	ENSP00000381008:p.Pro1969Thr		8946910	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.101	-0.405953	0.04832	.	.	ENSG00000181143	ENST00000397910	T	0.03181	4.02	0.235	0.235	0.15431	.	.	.	.	.	T	0.05364	0.0142	N	0.08118	0	.	.	.	D	0.69078	0.997	D	0.68483	0.958	T	0.41822	-0.9487	7	0.87932	D	0	.	.	.	.	.	1969	B5ME49	.	T	1969	ENSP00000381008:P1969T	ENSP00000381008:P1969T	P	-	1	0	MUC16	8946910	0.000000	0.05858	0.270000	0.24601	0.275000	0.26752	-0.552000	0.06020	0.308000	0.22923	0.313000	0.20887	CCA		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9085910	G	T	9085910	3	4	46	1	0	0	0	0	1	0	0	0	10003	1232	43	2	37954	2	MUC16	19	9085910	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		9085910	50043073	66	4386										
LYPD3	27076	broad.mit.edu	37	chr19	43965647	43965647	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	cggtcctggtggccagcggcGcctccagtcaacctgggctc	14	16	1	0	rs202091507	byFrequency	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr19:43965647G>A	ENST00000244333.3	-	5	985	c.897C>T	c.(895-897)ggC>ggT	p.G299G		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	299					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.G299G(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				GGCCAGCGGCGCCTCCAGTCA	0.622													G|||	2	0.000399361	0	0	5008	,	,		15926	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											64	67	66					19																	43965647		2203	4300	6503	48657487	SO:0001819	synonymous_variant	27076			AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.897C>T	19.37:g.43965647G>A			48657487	Q9UJ74	Silent	SNP	ENST00000244333.3	37	CCDS12620.1																																																																																				0.622	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		A	43965647	G	A	43965647	2	1	46	1	0	0	0	0	0	0	0	1	9141	1074	38	1		1	LYPD3	19	43965647	Silent	SNP	G	TCGA-AG-3890-01A-01W-1073-09	34879737	43965647	15163336	67	4387										
KIR2DL1	3811	broad.mit.edu	37	chr19	55295142	55295142	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tacacacagttgaatcactgCgttttcacacagagaaaaat	6	9	2	2			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr19:55295142C>T	ENST00000538269.1	+	2	61				KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL3_ENST00000434419.2_Silent_p.C308C|KIR2DL1_ENST00000291633.7_Silent_p.C334C|KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL1_ENST00000336077.6_Silent_p.C308C			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.C308C(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGAATCACTGCGTTTTCACAC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	19											12	13	12					19																	55295142		1997	4021	6018	59986954	SO:0001627	intron_variant	3802			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-33847C>T	19.37:g.55295142C>T			59986954	O43473|Q14946|Q16541	Silent	SNP	ENST00000538269.1	37																																																																																					0.493	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		T	55295142	C	T	55295142	1	4	46	0	1	0	0	0	0	0	0	0	8337	776	27	1		1	KIR2DL1	19	55295142	Intron	SNP	C	TCGA-AG-3890-01A-01W-1073-09	11329495	55295142	3833841	68	4388										
NLRP7	199713	broad.mit.edu	37	chr19	55452928	55452928	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gaatttctgccagtttcttgCcatcagcctcttccacctca	5	15	5	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr19:55452928C>A	ENST00000590030.1	-	1	192	c.152G>T	c.(151-153)gGc>gTc	p.G51V	NLRP7_ENST00000448121.2_Missense_Mutation_p.G51V|NLRP7_ENST00000446217.1_Missense_Mutation_p.G79V|NLRP7_ENST00000588756.1_Missense_Mutation_p.G51V|NLRP7_ENST00000340844.2_Missense_Mutation_p.G51V|NLRP7_ENST00000328092.5_Missense_Mutation_p.G51V|NLRP7_ENST00000592784.1_Missense_Mutation_p.G51V			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	51	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)	p.G51V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CAGTTTCTTGCCATCAGCCTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											114	108	110					19																	55452928		2203	4300	6503	60144740	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.152G>T	19.37:g.55452928C>A	ENSP00000465520:p.Gly51Val		60144740	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389209	0.25118	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	1.53	1.53	0.23141	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.54271	0.1848	L	0.42686	1.345	0.09310	N	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.34601	-0.9822	9	0.35671	T	0.21	.	6.5079	0.22206	0.0:1.0:0.0:0.0	.	79;51;51;51	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	V	51;51;51;79;51	ENSP00000329568:G51V;ENSP00000409137:G51V;ENSP00000339491:G51V;ENSP00000414273:G79V	ENSP00000329568:G51V	G	-	2	0	NLRP7	60144740	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	0.352000	0.20113	1.144000	0.42321	0.313000	0.20887	GGC		0.448	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55452928	C	A	55452928	3	1	46	1	0	0	0	0	1	0	0	0	10513	739	26	2	3001	2	NLRP7	19	55452928	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	157786	55452928	3676055	69	4389										
ZFP28	140612	broad.mit.edu	37	chr19	57051017	57051017	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tgccttccagggacactgctCttccccaggagagaaacaag	10	13	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr19:57051017C>G	ENST00000301318.3	+	2	303	c.232C>G	c.(232-234)Ctt>Gtt	p.L78V	ZFP28_ENST00000591844.1_Missense_Mutation_p.L78V|ZFP28_ENST00000594386.1_3'UTR|AC005498.3_ENST00000593218.1_lincRNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	78					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L78V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GGACACTGCTCTTCCCCAGGA	0.512																																					Ovarian(124;554 1662 19430 21141 52494)											1	Substitution - Missense(1)	large_intestine(1)	19											118	116	117					19																	57051017		2203	4300	6503	61742829	SO:0001583	missense	140612				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.232C>G	19.37:g.57051017C>G	ENSP00000301318:p.Leu78Val		61742829	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	0.617	-0.822630	0.02755	.	.	ENSG00000196867	ENST00000301318	T	0.06608	3.28	3.58	0.0223	0.14133	.	1.143450	0.06877	N	0.801790	T	0.03053	0.0090	N	0.14661	0.345	0.09310	N	1	B;P	0.43750	0.075;0.816	B;B	0.36534	0.027;0.227	T	0.38222	-0.9671	10	0.17369	T	0.5	.	3.8535	0.08965	0.0:0.544:0.2031:0.253	.	78;78	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	V	78	ENSP00000301318:L78V	ENSP00000301318:L78V	L	+	1	0	ZFP28	61742829	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.342000	0.07801	-0.022000	0.13986	0.462000	0.41574	CTT		0.512	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		G	57051017	C	G	57051017	3	3	46	1	0	0	0	0	1	0	0	0	17681	913	32	5	238	5	ZFP28	19	57051017	Missense_Mutation	SNP	C	TCGA-AG-3890-01A-01W-1073-09	1598089	57051017	2077966	70	4390										
PDYN	5173	broad.mit.edu	37	chr20	1961312	1961312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ccctcatcagctcagactctGctccctccctaaacccgtca	4	20	5	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr20:1961312G>A	ENST00000217305.2	-	4	647	c.422C>T	c.(421-423)gCa>gTa	p.A141V	PDYN_ENST00000540134.1_Missense_Mutation_p.A141V|PDYN_ENST00000539905.1_Missense_Mutation_p.A141V|RP4-684O24.5_ENST00000446562.1_RNA	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	141					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.A141V(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCAGACTCTGCTCCCTCCCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	20											116	109	111					20																	1961312		2203	4300	6503	1909312	SO:0001583	missense	5173				CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.422C>T	20.37:g.1961312G>A	ENSP00000217305:p.Ala141Val		1909312	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416517	0.25552	.	.	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	T;T;T	0.81247	-1.47;-1.47;-1.47	4.71	-3.95	0.04118	.	1.069720	0.07158	N	0.850281	T	0.57989	0.2091	N	0.17082	0.46	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.34900	-0.9810	10	0.30078	T	0.28	8.4254	0.1935	0.00137	0.3113:0.2496:0.2033:0.2357	.	141	P01213	PDYN_HUMAN	V	141	ENSP00000440185:A141V;ENSP00000442259:A141V;ENSP00000217305:A141V	ENSP00000217305:A141V	A	-	2	0	PDYN	1909312	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.225000	0.09151	-1.008000	0.03404	0.491000	0.48974	GCA		0.547	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			A	1961312	G	A	1961312	3	1	46	1	0	0	0	0	1	0	0	0	11730	1319	46	3	346	3	PDYN	20	1961312	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		1961312	61064208	71	4391										
PTGIS	5740	broad.mit.edu	37	chr20	48156158	48156158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gagcagccggtcgagctggcGaaaggtgtggaagacatcag	17	8	1	1			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chr20:48156158G>A	ENST00000244043.4	-	5	651	c.622C>T	c.(622-624)Cgc>Tgc	p.R208C	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	208					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)	p.R208C(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	TCGAGCTGGCGAAAGGTGTGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	20											49	49	49					20																	48156158		2203	4300	6503	47589565	SO:0001583	missense	5740				CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"Cytochrome P450s"	9603	protein-coding gene	gene with protein product	"cytochrome P450, family 8, subfamily A, polypeptide 1"	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.622C>T	20.37:g.48156158G>A	ENSP00000244043:p.Arg208Cys		47589565	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	37	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.917911	0.73098	.	.	ENSG00000124212	ENST00000244043	T	0.68479	-0.33	4.85	4.85	0.62838	.	0.216019	0.37095	N	0.002243	T	0.79131	0.4394	M	0.75615	2.305	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.78054	-0.2354	10	0.37606	T	0.19	-13.5886	11.4291	0.50029	0.0893:0.0:0.9107:0.0	.	208	Q16647	PTGIS_HUMAN	C	208	ENSP00000244043:R208C	ENSP00000244043:R208C	R	-	1	0	PTGIS	47589565	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.518000	0.35877	2.416000	0.81992	0.561000	0.74099	CGC		0.642	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2			A	48156158	G	A	48156158	3	1	46	1	0	0	0	0	1	0	0	0	12787	1058	37	1	904	1	PTGIS	20	48156158	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	46194846	48156158	14869362	72	4392										
CXorf59	286464	broad.mit.edu	37	chrX	36091288	36091288	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tgcctgaaaatttgcacttgGatgaaagtgaaacatcagag	10	6	1	4			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chrX:36091288G>A	ENST00000313548.4	+	4	409	c.223G>A	c.(223-225)Gat>Aat	p.D75N		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	75						integral component of membrane (GO:0016021)		p.D75N(1)									TTTGCACTTGGATGAAAGTGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	63	65					X																	36091288		2202	4300	6502	36001209	SO:0001583	missense	286464			AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.223G>A	X.37:g.36091288G>A	ENSP00000324767:p.Asp75Asn		36001209		Missense_Mutation	SNP	ENST00000313548.4	37	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	G	7.741	0.701356	0.15172	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	4.74	0.511	0.16989	.	1.299200	0.05535	N	0.564651	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.22941	-1.0202	9	0.17369	T	0.5	-0.1147	5.2102	0.15312	0.3206:0.1677:0.5116:0.0	.	75	Q8N9S7	CX059_HUMAN	N	75	.	ENSP00000324767:D75N	D	+	1	0	CXorf59	36001209	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.212000	0.02994	0.007000	0.14760	-0.344000	0.07964	GAT		0.353	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		A	36091288	G	A	36091288	3	1	46	1	0	0	0	0	1	0	0	0	4121	1174	41	3	233	3	CXorf59	23	36091288	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09		36091288	119179272	73	4393										
NGFRAP1	27018	broad.mit.edu	37	chrX	102632732	102632732	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ctaatcaccatgaccatcatGatgaattttgccttatgcct	5	11	2	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chrX:102632732G>A	ENST00000372645.3	+	3	640	c.313G>A	c.(313-315)Gat>Aat	p.D105N	NGFRAP1_ENST00000372635.1_Missense_Mutation_p.D105N|NGFRAP1_ENST00000372634.1_Missense_Mutation_p.D95N|NGFRAP1_ENST00000299872.7_Missense_Mutation_p.D105N|NGFRAP1_ENST00000361298.4_Missense_Mutation_p.D95N			Q00994	BEX3_HUMAN	nerve growth factor receptor (TNFRSF16) associated protein 1	105	Interaction with 14-3-3 epsilon. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|metal ion binding (GO:0046872)	p.D105N(1)		NS(2)|endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						TGACCATCATGATGAATTTTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	X											87	85	85					X																	102632732		2203	4300	6503	102519388	SO:0001583	missense	27018			AF187064	CCDS14508.1, CCDS14509.1	Xq22.2	2014-03-21			ENSG00000166681	ENSG00000166681			13388	protein-coding gene	gene with protein product	"brain expressed, X-linked 3"	300361				10764727, 16221301, 2171551	Standard	NM_206915		Approved	BEX3, HGR74, Bex, NADE, DXS6984E	uc004ekj.1	Q00994	OTTHUMG00000022099	ENST00000372645.3:c.313G>A	X.37:g.102632732G>A	ENSP00000361728:p.Asp105Asn		102519388	B2RD17|D3DXA3|Q5JQT4|Q5JQT5	Missense_Mutation	SNP	ENST00000372645.3	37	CCDS14508.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252081	0.59212	.	.	ENSG00000166681	ENST00000361298;ENST00000372645;ENST00000372635;ENST00000372634;ENST00000299872	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	4.1	3.0	0.34707	.	0.000000	0.46145	D	0.000317	T	0.13243	0.0321	M	0.79258	2.445	0.26892	N	0.967306	B	0.06786	0.001	B	0.04013	0.001	T	0.18935	-1.0321	10	0.66056	D	0.02	-8.5894	5.4021	0.16301	0.2072:0.0:0.7928:0.0	.	105	Q00994	BEX3_HUMAN	N	95;105;105;95;105	ENSP00000354843:D95N;ENSP00000361728:D105N;ENSP00000361718:D105N;ENSP00000361717:D95N;ENSP00000299872:D105N	ENSP00000299872:D105N	D	+	1	0	NGFRAP1	102519388	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.055000	0.41345	0.807000	0.34208	0.600000	0.82982	GAT		0.413	NGFRAP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057709.1	NM_014380		A	102632732	G	A	102632732	3	1	46	1	0	0	0	0	1	0	0	0	10428	1290	45	3	315	3	NGFRAP1	23	102632732	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	66541444	102632732	52637828	74	4394										
DDX26B	203522	broad.mit.edu	37	chrX	134713964	134713964	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	tctccgtagatgaccaaaaaGacccagtagcatctactttg	7	11	2	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chrX:134713964G>C	ENST00000370752.4	+	15	2594	c.2260G>C	c.(2260-2262)Gac>Cac	p.D754H	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	754								p.D754H(1)		large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					TGACCAAAAAGACCCAGTAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											86	75	79					X																	134713964		2203	4300	6503	134541630	SO:0001583	missense	203522			AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"DEAD-boxes"	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.2260G>C	X.37:g.134713964G>C	ENSP00000359788:p.Asp754His		134541630	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Missense_Mutation	SNP	ENST00000370752.4	37	CCDS35401.1	.	.	.	.	.	.	.	.	.	.	G	2.709	-0.269306	0.05716	.	.	ENSG00000165359	ENST00000370752	T	0.30714	1.52	5.26	3.29	0.37713	.	1.433790	0.04600	N	0.398413	T	0.24353	0.0590	N	0.19112	0.55	0.09310	N	1	B;B	0.29162	0.235;0.023	B;B	0.32022	0.139;0.066	T	0.32798	-0.9893	10	0.45353	T	0.12	1.6869	7.3224	0.26536	0.1031:0.3334:0.5635:0.0	.	754;754	B9EIK3;Q5JSJ4	.;DX26B_HUMAN	H	754	ENSP00000359788:D754H	ENSP00000359788:D754H	D	+	1	0	DDX26B	134541630	0.619000	0.27059	0.001000	0.08648	0.014000	0.08584	1.070000	0.30653	0.401000	0.25424	0.422000	0.28245	GAC		0.408	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540		C	134713964	G	C	134713964	3	2	46	1	0	0	0	0	1	0	0	0	4359	942	33	5	2318	5	DDX26B	23	134713964	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	32081232	134713964	20556596	75	4395										
MCF2	4168	broad.mit.edu	37	chrX	138708819	138708819	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	gtcaccacttatttgccgatGacattctagtcttgaactga	7	10	3	3			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chrX:138708819G>A	ENST00000370576.4	-	5	744	c.535C>T	c.(535-537)Cat>Tat	p.H179Y	MCF2_ENST00000370578.4_Missense_Mutation_p.H324Y|MCF2_ENST00000536274.1_Missense_Mutation_p.H140Y|MCF2_ENST00000338585.6_Missense_Mutation_p.H179Y|MCF2_ENST00000414978.1_Missense_Mutation_p.H239Y|MCF2_ENST00000519895.1_Missense_Mutation_p.H239Y|MCF2_ENST00000370573.4_Missense_Mutation_p.H179Y|MCF2_ENST00000520602.1_Missense_Mutation_p.H239Y	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	179					apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.H239Y(1)|p.H179Y(1)		NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					ATTTGCCGATGACATTCTAGT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	X											166	154	158					X																	138708819		2203	4300	6503	138536485	SO:0001583	missense	4168				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.535C>T	X.37:g.138708819G>A	ENSP00000359608:p.His179Tyr		138536485	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	g	11.96	1.795996	0.31777	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	4.98	0.958	0.19619	.	1.768580	0.02618	N	0.102868	T	0.33673	0.0871	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B;P;B	0.36874	0.002;0.13;0.001;0.001;0.004;0.001;0.572;0.002	B;B;B;B;B;B;B;B	0.40506	0.001;0.079;0.002;0.001;0.002;0.002;0.331;0.001	T	0.12116	-1.0560	10	0.11794	T	0.64	.	3.8763	0.09058	0.0857:0.1361:0.4944:0.2838	.	239;324;140;179;179;324;179;179	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	Y	239;179;140;324;239;239;179;179	ENSP00000427745:H239Y;ENSP00000359608:H179Y;ENSP00000438155:H140Y;ENSP00000359610:H324Y;ENSP00000397055:H239Y;ENSP00000430276:H239Y;ENSP00000359605:H179Y;ENSP00000342204:H179Y	ENSP00000342204:H179Y	H	-	1	0	MCF2	138536485	0.007000	0.16637	0.000000	0.03702	0.187000	0.23431	1.599000	0.36751	0.070000	0.16634	0.597000	0.82753	CAT		0.338	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		A	138708819	G	A	138708819	3	1	46	1	0	0	0	0	1	0	0	0	9408	1290	45	3	2406	3	MCF2	23	138708819	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	3994855	138708819	16561741	76	4396										
L1CAM	3897	broad.mit.edu	37	chrX	153136382	153136382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.12987012987013	10	1	1.56314363143631	4.48622222222222	0.620215053763441	0.213756898640463	0.66867542651632	0	ggttgccgttctggcccatcGtcacccgctcgtcctgcttg	11	16	2	0			TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3890-01A-01W-1073-09	TCGA-AG-3890-10A-01W-1073-09	g.chrX:153136382G>A	ENST00000370060.1	-	7	746	c.557C>T	c.(556-558)aCg>aTg	p.T186M	L1CAM_ENST00000543994.1_Missense_Mutation_p.T188M|L1CAM_ENST00000361981.3_Missense_Mutation_p.T181M|L1CAM_ENST00000538883.1_Missense_Mutation_p.T188M|L1CAM_ENST00000370057.3_Missense_Mutation_p.T186M|L1CAM_ENST00000370055.1_Missense_Mutation_p.T181M|L1CAM_ENST00000361699.4_Missense_Mutation_p.T186M	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	186	Ig-like C2-type 2.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.T186M(2)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGCCCATCGTCACCCGCTC	0.607																																																2	Substitution - Missense(2)	large_intestine(2)	X											227	156	180					X																	153136382		2203	4300	6503	152789576	SO:0001583	missense	3897			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.557C>T	X.37:g.153136382G>A	ENSP00000359077:p.Thr186Met		152789576	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.233009	0.39498	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000540065;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	4.57	4.57	0.56435	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.211607	0.32703	N	0.005742	T	0.74884	0.3775	L	0.52011	1.625	0.29094	N	0.881934	P;P;P	0.40230	0.66;0.66;0.708	B;B;B	0.41917	0.254;0.254;0.37	T	0.72587	-0.4248	10	0.37606	T	0.19	.	15.4841	0.75551	0.0:0.0:1.0:0.0	.	181;186;186	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	M	186;188;186;188;181;56;181;186	ENSP00000359077:T186M;ENSP00000438430:T188M;ENSP00000359074:T186M;ENSP00000439645:T188M;ENSP00000354712:T181M;ENSP00000359072:T181M;ENSP00000355380:T186M	ENSP00000355380:T186M	T	-	2	0	L1CAM	152789576	0.038000	0.19896	0.814000	0.32528	0.715000	0.41141	1.932000	0.40143	2.253000	0.74438	0.436000	0.28706	ACG		0.607	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153136382	G	A	153136382	3	1	46	1	0	0	0	0	1	0	0	0	8610	1145	40	1	3308	1	L1CAM	23	153136382	Missense_Mutation	SNP	G	TCGA-AG-3890-01A-01W-1073-09	14427563	153136382	2134178	77	4397										
CDK11A	728642	broad.mit.edu	37	chr1	1635294	1635294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgatctgatcgatttccGaattcccggggaacagaggc	12	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:1635294G>A	ENST00000378633.1	-	17	1968	c.1889C>T	c.(1888-1890)tCg>tTg	p.S630L	CDK11A_ENST00000358779.5_Missense_Mutation_p.S617L|CDK11A_ENST00000495016.1_5'Flank|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000378638.2_Missense_Mutation_p.S593L|CDK11A_ENST00000404249.3_Missense_Mutation_p.S627L|CDK11A_ENST00000357760.2_Missense_Mutation_p.S626L|CDK11A_ENST00000356200.3_Missense_Mutation_p.S593L			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	630	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S626L(1)|p.S642L(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						ATCGATTTCCGAATTCCCGGG	0.587																																					Pancreas(186;965 2119 30274 40311 50569)											2	Substitution - Missense(2)	large_intestine(2)	1											77	81	80					1																	1635294		1993	4169	6162	1625154	SO:0001583	missense	728642			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"Cyclin-dependent kinases"	1730	protein-coding gene	gene with protein product		116951	"cell division cycle 2-like 2", "cell division cycle 2-like 2 (PITSLRE proteins)"	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1889C>T	1.37:g.1635294G>A	ENSP00000367900:p.Ser630Leu		1625154	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Missense_Mutation	SNP	ENST00000378633.1	37		.	.	.	.	.	.	.	.	.	.	-	11.12	1.545817	0.27652	.	.	ENSG00000008128	ENST00000356200;ENST00000404249;ENST00000357760;ENST00000358779;ENST00000378633;ENST00000378638;ENST00000378630	T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73	2.37	2.37	0.29283	.	0.000000	0.85682	D	0.000000	T	0.69351	0.3101	M	0.90019	3.08	0.80722	D	1	D;D;P	0.67145	0.996;0.996;0.886	D;D;P	0.64687	0.928;0.928;0.574	T	0.76777	-0.2834	10	0.87932	D	0	.	11.6771	0.51436	0.0:0.0:1.0:0.0	.	627;617;244	Q9UQ88-2;Q9UQ88-4;Q9UQ88-5	.;.;.	L	593;627;626;617;630;593;593	ENSP00000348529:S593L;ENSP00000384442:S627L;ENSP00000350403:S626L;ENSP00000351629:S617L;ENSP00000367900:S630L;ENSP00000367905:S593L	ENSP00000348529:S593L	S	-	2	0	CDK11A	1625154	1.000000	0.71417	0.029000	0.17559	0.002000	0.02628	4.625000	0.61262	1.345000	0.45676	0.486000	0.48141	TCG		0.587	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		A	1635294	G	A	1635294	3	1	47	1	0	0	0	0	1	0	0	0	3132	1059	37	1	478	1	CDK11A	1	1635294	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09		1635294	247615327	1	4398										
PRDM16	63976	broad.mit.edu	37	chr1	3328634	3328634	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacggggacgggctcggacCtggacagcgacgtggacagc	17	13	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:3328634C>A	ENST00000270722.5	+	9	1922	c.1873C>A	c.(1873-1875)Ctg>Atg	p.L625M	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378398.3_Missense_Mutation_p.L626M|PRDM16_ENST00000378391.2_Missense_Mutation_p.L625M|PRDM16_ENST00000442529.2_Missense_Mutation_p.L625M|PRDM16_ENST00000511072.1_Missense_Mutation_p.L626M|PRDM16_ENST00000441472.2_Missense_Mutation_p.L625M|PRDM16_ENST00000514189.1_Missense_Mutation_p.L626M			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	625					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.L625M(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GGGCTCGGACCTGGACAGCGA	0.682			T	EVI1	"MDS, AML"																																		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	1	Substitution - Missense(1)	large_intestine(1)	1											65	76	72					1																	3328634		2165	4251	6416	3318494	SO:0001583	missense	63976			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1873C>A	1.37:g.3328634C>A	ENSP00000270722:p.Leu625Met		3318494	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015191	0.35511	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.10192	2.95;2.95;2.96;2.97;2.95;2.97;2.96;2.9;2.91	5.1	4.18	0.49190	.	0.000000	0.39909	N	0.001240	T	0.30230	0.0758	M	0.75264	2.295	0.45594	D	0.99853	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.988;0.999;0.977;0.997	T	0.02098	-1.1214	10	0.72032	D	0.01	.	9.7764	0.40621	0.0:0.8417:0.0:0.1583	.	625;625;625;625	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	M	626;626;625;625;625;626;625;441;441;434	ENSP00000426975:L626M;ENSP00000367651:L626M;ENSP00000407968:L625M;ENSP00000405253:L625M;ENSP00000367643:L625M;ENSP00000421400:L626M;ENSP00000270722:L625M;ENSP00000422504:L441M;ENSP00000425796:L434M	ENSP00000270722:L625M	L	+	1	2	PRDM16	3318494	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.980000	0.56895	1.145000	0.42336	0.609000	0.83330	CTG		0.682	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3328634	C	A	3328634	3	1	47	1	0	0	0	0	1	0	0	0	12491	680	24	2	1907	2	PRDM16	1	3328634	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1693340	3328634	245921987	2	4399										
PER3	8863	broad.mit.edu	37	chr1	7886608	7886608	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcccctttgacctcggaaGaatttaaacacgtggggctc	10	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:7886608G>T	ENST00000361923.2	+	16	2177	c.2002G>T	c.(2002-2004)Gaa>Taa	p.E668*	PER3_ENST00000377532.3_Nonsense_Mutation_p.E676*|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	668	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.E668*(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GACCTCGGAAGAATTTAAACA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											61	58	59					1																	7886608		2203	4300	6503	7809195	SO:0001587	stop_gained	8863			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2002G>T	1.37:g.7886608G>T	ENSP00000355031:p.Glu668*		7809195	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Nonsense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	39	7.875677	0.98537	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	.	.	.	4.62	3.7	0.42460	.	0.251086	0.37669	N	0.001993	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	14.0932	0.65004	0.0:0.1509:0.849:0.0	.	.	.	.	X	676;668	.	ENSP00000355031:E668X	E	+	1	0	PER3	7809195	0.997000	0.39634	0.001000	0.08648	0.005000	0.04900	5.719000	0.68462	1.153000	0.42468	0.655000	0.94253	GAA		0.483	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7886608	G	T	7886608	4	4	47	1	0	0	0	0	0	1	0	0	11762	943	33	2	2064	2	PER3	1	7886608	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4557974	7886608	241364013	3	4400										
PER3	8863	broad.mit.edu	37	chr1	7889901	7889901	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttactttctagcagtgtgTtacaggcaacaatggcagtg	10	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:7889901T>G	ENST00000361923.2	+	18	3042	c.2867T>G	c.(2866-2868)gTt>gGt	p.V956G	PER3_ENST00000377532.3_Missense_Mutation_p.V965G|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	956					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.V956G(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TAGCAGTGTGTTACAGGCAAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	93	95					1																	7889901		2203	4300	6503	7812488	SO:0001583	missense	8863			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2867T>G	1.37:g.7889901T>G	ENSP00000355031:p.Val956Gly		7812488	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	2.786	-0.252443	0.05829	.	.	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.10960	2.89;2.82	3.58	1.01	0.19927	.	2.570310	0.01499	N	0.017409	T	0.16041	0.0386	L	0.50333	1.59	0.09310	N	1	D;D;D;D	0.57571	0.965;0.965;0.98;0.965	B;B;P;P	0.51806	0.396;0.396;0.68;0.481	T	0.16928	-1.0386	10	0.22706	T	0.39	.	2.5655	0.04782	0.2311:0.1299:0.0:0.639	.	956;965;965;956	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	G	965;956;167	ENSP00000366755:V965G;ENSP00000355031:V956G	ENSP00000355031:V956G	V	+	2	0	PER3	7812488	0.001000	0.12720	0.006000	0.13384	0.174000	0.22865	0.124000	0.15728	0.574000	0.29417	0.383000	0.25322	GTT		0.468	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		G	7889901	T	G	7889901	3	3	47	1	0	0	0	0	1	0	0	0	11762	1725	60	4	2937	4	PER3	1	7889901	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3293	7889901	241360720	4	4401										
NMNAT1	64802	broad.mit.edu	37	chr1	10042655	10042655	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtaccagatcttgtccaaGaatacattgaaaagcataat	7	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:10042655G>T	ENST00000377205.1	+	5	880	c.736G>T	c.(736-738)Gaa>Taa	p.E246*	RP11-807G9.2_ENST00000413148.1_RNA	NM_022787.3	NP_073624.2	Q9HAN9	NMNA1_HUMAN	nicotinamide nucleotide adenylyltransferase 1	246					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)	p.E246*(1)		large_intestine(2)|lung(2)|stomach(1)	5		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)		TCTTGTCCAAGAATACATTGA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											55	55	55					1																	10042655		2203	4300	6503	9965242	SO:0001587	stop_gained	64802			AF312734	CCDS108.1, CCDS72698.1	1p36.22	2014-01-28	2003-04-30	2003-05-02	ENSG00000173614	ENSG00000173614	2.7.7.1		17877	protein-coding gene	gene with protein product		608700	"nicotinamide nucleotide adenylyltransferase", "Leber congenital amaurosis 9", "Leber's congenital amaurosis 9"	LCA9		11248244, 11027696, 22842227	Standard	XR_244792		Approved	NMNAT, PNAT1	uc001aqp.3	Q9HAN9	OTTHUMG00000001799	ENST00000377205.1:c.736G>T	1.37:g.10042655G>T	ENSP00000366410:p.Glu246*		9965242	B1AN63|Q8TAE9|Q9H247|Q9H6B6	Nonsense_Mutation	SNP	ENST00000377205.1	37	CCDS108.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124050	0.77436	.	.	ENSG00000173614	ENST00000377205	.	.	.	5.01	4.03	0.46877	.	0.409347	0.26598	N	0.023499	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	2.5164	15.9812	0.80111	0.0:0.1345:0.8655:0.0	.	.	.	.	X	246	.	ENSP00000366410:E246X	E	+	1	0	NMNAT1	9965242	0.984000	0.35163	0.368000	0.25939	0.472000	0.32918	3.073000	0.50057	2.476000	0.83614	0.462000	0.41574	GAA		0.473	NMNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005029.1			T	10042655	G	T	10042655	4	4	47	1	0	0	0	0	0	1	0	0	10529	943	33	2	750	2	NMNAT1	1	10042655	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2152754	10042655	239207966	5	4402										
MTOR	2475	broad.mit.edu	37	chr1	11169362	11169362	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaccagtgagcttatctcGaaccctgttaataatctgga	7	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:11169362G>A	ENST00000361445.4	-	56	7589	c.7513C>T	c.(7513-7515)Cga>Tga	p.R2505*	MTOR_ENST00000376838.1_Nonsense_Mutation_p.R710*	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2505	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R2505*(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	AGCTTATCTCGAACCCTGTTA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											178	156	164					1																	11169362		2203	4300	6503	11091949	SO:0001587	stop_gained	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7513C>T	1.37:g.11169362G>A	ENSP00000354558:p.Arg2505*		11091949	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Nonsense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	47	13.841599	0.99766	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	.	.	.	5.82	5.82	0.92795	.	0.072185	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0628	17.2469	0.87030	0.0:0.0:1.0:0.0	.	.	.	.	X	2505;710;161	.	ENSP00000354558:R2505X	R	-	1	2	MTOR	11091949	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.866000	0.63005	2.755000	0.94549	0.591000	0.81541	CGA		0.418	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		A	11169362	G	A	11169362	4	1	47	1	0	0	0	0	0	1	0	0	9984	1066	37	1	148	1	MTOR	1	11169362	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1126707	11169362	238081259	6	4403										
FBXO6	26270	broad.mit.edu	37	chr1	11728882	11728882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcatgaccctctggaaacGcaagtgcctgcgagagggct	12	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:11728882G>A	ENST00000376753.4	+	2	302	c.167G>A	c.(166-168)cGc>cAc	p.R56H		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	56	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)	p.R56H(1)		breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTGGAAACGCAAGTGCCTG	0.622																																					NSCLC(54;506 1562 46490 51389)											1	Substitution - Missense(1)	large_intestine(1)	1											57	61	60					1																	11728882		2203	4300	6503	11651469	SO:0001583	missense	26270			AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"F-boxes /  "other""	13585	protein-coding gene	gene with protein product		605647	"F-box only protein 6"			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.167G>A	1.37:g.11728882G>A	ENSP00000365944:p.Arg56His		11651469	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.608|9.608	1.130396|1.130396	0.21041|0.21041	.|.	.|.	ENSG00000116663|ENSG00000116663	ENST00000449067|ENST00000376753	.|T	.|0.51071	.|0.72	5.15|5.15	3.25|3.25	0.37280|0.37280	.|F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	.|0.268407	.|0.38663	.|N	.|0.001617	T|T	0.37348|0.37348	0.1000|0.1000	L|L	0.52573|0.52573	1.65|1.65	0.35826|0.35826	D|D	0.82497|0.82497	.|P	.|0.34997	.|0.479	.|B	.|0.34779	.|0.189	T|T	0.43475|0.43475	-0.9389|-0.9389	5|10	.|0.49607	.|T	.|0.09	-10.2122|-10.2122	5.1074|5.1074	0.14790|0.14790	0.0797:0.1454:0.6246:0.1504|0.0797:0.1454:0.6246:0.1504	.|.	.|56	.|Q9NRD1	.|FBX6_HUMAN	T|H	44|56	.|ENSP00000365944:R56H	.|ENSP00000365944:R56H	A|R	+|+	1|2	0|0	FBXO6|FBXO6	11651469|11651469	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.057000|0.057000	0.15508|0.15508	2.966000|2.966000	0.49208|0.49208	0.669000|0.669000	0.31146|0.31146	-0.188000|-0.188000	0.12872|0.12872	GCA|CGC		0.622	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438		A	11728882	G	A	11728882	3	1	47	1	0	0	0	0	1	0	0	0	5778	1087	38	1	169	1	FBXO6	1	11728882	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	559520	11728882	237521739	7	4404										
PRDM2	7799	broad.mit.edu	37	chr1	14107602	14107602	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatctttcaaacaggaggaAttagagaatgaaggtctgaa	10	4	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:14107602A>C	ENST00000235372.7	+	8	4168	c.3312A>C	c.(3310-3312)gaA>gaC	p.E1104D	PRDM2_ENST00000311066.5_Missense_Mutation_p.E1104D|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.E903D|PRDM2_ENST00000413440.1_Missense_Mutation_p.E903D|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000505823.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1104					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E1104D(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	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)		AACAGGAGGAATTAGAGAATG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	84	83					1																	14107602		2203	4300	6503	13980189	SO:0001583	missense	7799			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.3312A>C	1.37:g.14107602A>C	ENSP00000235372:p.Glu1104Asp		13980189	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	A	6.816	0.519611	0.13005	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01629	4.83;4.72;4.73;4.73	5.97	-7.09	0.01553	.	0.372870	0.30771	N	0.008915	T	0.01320	0.0043	L	0.32530	0.975	0.20563	N	0.99989	B;B;B	0.26744	0.158;0.001;0.002	B;B;B	0.19946	0.027;0.003;0.006	T	0.42224	-0.9464	10	0.31617	T	0.26	.	12.5019	0.55960	0.2199:0.2087:0.5713:0.0	.	962;1104;1104	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	D	1104;1104;1104;903;903	ENSP00000235372:E1104D;ENSP00000312352:E1104D;ENSP00000411103:E903D;ENSP00000341621:E903D	ENSP00000235372:E1104D	E	+	3	2	PRDM2	13980189	0.001000	0.12720	0.006000	0.13384	0.682000	0.39822	-0.048000	0.11944	-0.780000	0.04553	0.533000	0.62120	GAA		0.453	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		C	14107602	A	C	14107602	3	2	47	1	0	0	0	0	1	0	0	0	12492	98	4	4	3338	4	PRDM2	1	14107602	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2378720	14107602	235143019	8	4405										
AGMAT	79814	broad.mit.edu	37	chr1	15909865	15909865	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcccaagcatcactgattCttcccggatgcggcgaggtc	11	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:15909865C>A	ENST00000375826.3	-	2	440	c.298G>T	c.(298-300)Gaa>Taa	p.E100*	RP4-680D5.2_ENST00000428945.1_RNA|DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	100					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)	p.E100*(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		ATCACTGATTCTTCCCGGATG	0.532																																					NSCLC(126;1678 1780 25805 43508 49531)											1	Substitution - Nonsense(1)	large_intestine(1)	1											57	52	54					1																	15909865		2203	4300	6503	15782452	SO:0001587	stop_gained	79814			AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.298G>T	1.37:g.15909865C>A	ENSP00000364986:p.Glu100*		15782452	Q5TDH1|Q9H5J3	Nonsense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	C	36	5.951880	0.97139	.	.	ENSG00000116771	ENST00000375826	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-21.3377	17.7407	0.88406	0.0:1.0:0.0:0.0	.	.	.	.	X	100	.	ENSP00000364986:E100X	E	-	1	0	AGMAT	15782452	1.000000	0.71417	0.851000	0.33527	0.638000	0.38207	6.995000	0.76257	2.527000	0.85204	0.558000	0.71614	GAA		0.532	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		A	15909865	C	A	15909865	4	1	47	1	0	0	0	0	0	1	0	0	385	922	32	2	784	2	AGMAT	1	15909865	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1802263	15909865	233340756	9	4406										
PADI1	29943	broad.mit.edu	37	chr1	17567231	17567231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcttcctgaaaaacttctaCgcggaagccttcttcccaga	6	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:17567231C>T	ENST00000375471.4	+	15	1826	c.1734C>T	c.(1732-1734)taC>taT	p.Y578Y	PADI1_ENST00000460293.1_3'UTR|PADI1_ENST00000413717.2_Intron|PADI1_ENST00000537499.1_Silent_p.Y135Y|PADI1_ENST00000536552.1_Silent_p.Y49Y	NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	578					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.Y578Y(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		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)	AAAACTTCTACGCGGAAGCCT	0.587																																					Esophageal Squamous(80;414 1257 4580 27746 50832)											1	Substitution - coding silent(1)	large_intestine(1)	1											106	103	104					1																	17567231		2203	4300	6503	17439818	SO:0001819	synonymous_variant	29943			AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.1734C>T	1.37:g.17567231C>T			17439818	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	37	CCDS178.1																																																																																				0.587	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		T	17567231	C	T	17567231	2	4	47	1	0	0	0	0	0	0	0	1	11408	547	19	1		1	PADI1	1	17567231	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1657366	17567231	231683390	10	4407										
KDM1A	23028	broad.mit.edu	37	chr1	23357125	23357125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagtgagcctgaagaaccatCgggtgagttgtagtatccaa	12	7	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:23357125C>T	ENST00000356634.3	+	2	664	c.515C>T	c.(514-516)tCg>tTg	p.S172L	KDM1A_ENST00000400181.4_Missense_Mutation_p.S172L|KDM1A_ENST00000542151.1_Missense_Mutation_p.S172L|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	172					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S172L(1)		breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						GAAGAACCATCGGGTGAGTTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	114	111					1																	23357125		2203	4300	6503	23229712	SO:0001583	missense	23028			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.515C>T	1.37:g.23357125C>T	ENSP00000349049:p.Ser172Leu		23229712	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	37	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560729	0.65538	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	T;T;T	0.34275	1.37;1.37;1.37	5.62	5.62	0.85841	Homeodomain-like (1);	0.083257	0.49916	D	0.000129	T	0.44180	0.1281	N	0.19112	0.55	0.58432	D	0.999998	D;P	0.69078	0.997;0.65	D;B	0.69479	0.964;0.021	T	0.42899	-0.9424	10	0.66056	D	0.02	-16.8776	14.2687	0.66138	0.0:0.8513:0.1487:0.0	.	172;172	O60341-2;O60341	.;KDM1A_HUMAN	L	172	ENSP00000349049:S172L;ENSP00000383042:S172L;ENSP00000439072:S172L	ENSP00000349049:S172L	S	+	2	0	KDM1A	23229712	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.988000	0.70579	2.648000	0.89879	0.484000	0.47621	TCG		0.398	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		T	23357125	C	T	23357125	3	4	47	1	0	0	0	0	1	0	0	0	8143	893	31	1	521	1	KDM1A	1	23357125	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5789894	23357125	225893496	11	4408										
MAN1C1	57134	broad.mit.edu	37	chr1	26013007	26013007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgtccactaacaaaagatgGctacgagggtaacatgttcg	10	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:26013007G>A	ENST00000374332.4	+	2	947	c.617G>A	c.(616-618)gGc>gAc	p.G206D	MAN1C1_ENST00000473891.1_3'UTR|MAN1C1_ENST00000263979.3_Missense_Mutation_p.G26D	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	206					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.G206D(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		ACAAAAGATGGCTACGAGGGT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											145	136	139					1																	26013007		2203	4300	6503	25885594	SO:0001583	missense	57134			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.617G>A	1.37:g.26013007G>A	ENSP00000363452:p.Gly206Asp		25885594	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688199	0.68271	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979	T;T	0.73789	-0.78;-0.78	5.3	5.3	0.74995	.	0.122272	0.53938	D	0.000042	D	0.89220	0.6653	M	0.93898	3.47	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.91472	0.5197	10	0.72032	D	0.01	.	14.8058	0.69956	0.0:0.0:1.0:0.0	.	206	Q9NR34	MA1C1_HUMAN	D	206;26;26	ENSP00000363452:G206D;ENSP00000263979:G26D	ENSP00000263979:G26D	G	+	2	0	MAN1C1	25885594	1.000000	0.71417	0.999000	0.59377	0.515000	0.34225	7.203000	0.77864	2.632000	0.89209	0.563000	0.77884	GGC		0.478	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		A	26013007	G	A	26013007	3	1	47	1	0	0	0	0	1	0	0	0	9243	1203	42	3	623	3	MAN1C1	1	26013007	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2655882	26013007	223237614	12	4409										
PAFAH2	5051	broad.mit.edu	37	chr1	26315944	26315944	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggccagcccttacccaccGccaggttgaacagcaagccc	9	18	0	1	rs200838441		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:26315944G>A	ENST00000374282.3	-	3	418	c.239C>T	c.(238-240)gCg>gTg	p.A80V	PAFAH2_ENST00000493892.1_Intron|PAFAH2_ENST00000374284.1_Missense_Mutation_p.A80V	NM_000437.3	NP_000428.2	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2, 40kDa	80					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|phospholipid binding (GO:0005543)	p.A80V(1)		NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	9		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		CTTACCCACCGCCAGGTTGAA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	VAL/ALA	0,4406		0,0,2203	61	63	62		239	0.7	0.1	1		62	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PAFAH2	NM_000437.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	80/393	26315944	1,13005	2203	4300	6503	26188531	SO:0001583	missense	5051			D87845	CCDS270.1	1p34.3	2008-09-19	2002-08-29		ENSG00000158006	ENSG00000158006			8579	protein-coding gene	gene with protein product		602344	"platelet-activating factor acetylhydrolase 2 (40kD)"			8955149, 9494101	Standard	NM_000437		Approved	HSD-PLA2	uc001bld.4	Q99487	OTTHUMG00000007437	ENST00000374282.3:c.239C>T	1.37:g.26315944G>A	ENSP00000363400:p.Ala80Val		26188531	D3DPK1|O15458|Q5SY02	Missense_Mutation	SNP	ENST00000374282.3	37	CCDS270.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.254884	0.22965	0.0	1.16E-4	ENSG00000158006	ENST00000374282;ENST00000374284;ENST00000439092;ENST00000441420	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.89	0.738	0.18319	.	0.407397	0.23676	N	0.045661	T	0.18718	0.0449	N	0.12569	0.235	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.18681	-1.0329	10	0.17369	T	0.5	-0.6346	5.3729	0.16150	0.2843:0.2609:0.4549:0.0	.	80	Q99487	PAFA2_HUMAN	V	80	ENSP00000363400:A80V;ENSP00000363402:A80V;ENSP00000408313:A80V;ENSP00000411011:A80V	ENSP00000363400:A80V	A	-	2	0	PAFAH2	26188531	0.739000	0.28196	0.075000	0.20258	0.803000	0.45373	0.966000	0.29331	-0.094000	0.12374	0.563000	0.77884	GCG		0.582	PAFAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019544.1	NM_000437		A	26315944	G	A	26315944	3	1	47	1	0	0	0	0	1	0	0	0	11418	1087	38	1	975	1	PAFAH2	1	26315944	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	302937	26315944	222934677	13	4410										
DHDDS	79947	broad.mit.edu	37	chr1	26786594	26786594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atacattttggaacctcttcGaggccatcctgcagttccag	8	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:26786594G>A	ENST00000236342.7	+	8	817	c.724G>A	c.(724-726)Gag>Aag	p.E242K	DHDDS_ENST00000526219.1_Missense_Mutation_p.E203K|DHDDS_ENST00000360009.2_Missense_Mutation_p.E242K|RP3-476K8.3_ENST00000423060.1_RNA|DHDDS_ENST00000525682.2_Missense_Mutation_p.E208K			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	242					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)	p.E242K(1)		breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-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;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		GAACCTCTTCGAGGCCATCCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	133	138					1																	26786594		2203	4300	6503	26659181	SO:0001583	missense	79947			AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682			20603	protein-coding gene	gene with protein product		608172				12591616	Standard	NM_024887		Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000236342.7:c.724G>A	1.37:g.26786594G>A	ENSP00000236342:p.Glu242Lys		26659181	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	Missense_Mutation	SNP	ENST00000236342.7	37	CCDS282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.687|9.687	1.150813|1.150813	0.21371|0.21371	.|.	.|.	ENSG00000117682|ENSG00000117682	ENST00000374192;ENST00000525682;ENST00000236342;ENST00000526219;ENST00000360009;ENST00000430232|ENST00000416052	T;T;T;T;T|.	0.54071|.	0.59;0.59;0.59;0.59;0.59|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55049|0.55049	0.1896|0.1896	N|N	0.21194|0.21194	0.64|0.64	0.80722|0.80722	D|D	1|1	B;D;B;B|.	0.54397|.	0.134;0.966;0.011;0.009|.	B;P;B;B|.	0.48770|.	0.019;0.589;0.019;0.011|.	T|T	0.48681|0.48681	-0.9014|-0.9014	10|5	0.13108|.	T|.	0.6|.	-10.5716|-10.5716	18.564|18.564	0.91111|0.91111	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	208;203;242;242|.	B7Z4B9;Q86SQ9-3;Q86SQ9;Q86SQ9-2|.	.;.;DHDDS_HUMAN;.|.	K|Q	138;208;242;203;242;203|118	ENSP00000434984:E208K;ENSP00000236342:E242K;ENSP00000434219:E203K;ENSP00000353104:E242K;ENSP00000397584:E203K|.	ENSP00000236342:E242K|.	E|R	+|+	1|2	0|0	DHDDS|DHDDS	26659181|26659181	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.387000|0.387000	0.30353|0.30353	7.750000|7.750000	0.85110|0.85110	2.699000|2.699000	0.92147|0.92147	0.561000|0.561000	0.74099|0.74099	GAG|CGA		0.493	DHDDS-011	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392504.1	NM_024887		A	26786594	G	A	26786594	3	1	47	1	0	0	0	0	1	0	0	0	4489	1059	37	1	750	1	DHDDS	1	26786594	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	470650	26786594	222464027	14	4411										
ARID1A	8289	broad.mit.edu	37	chr1	27106354	27106354	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtgtgtccaataccattCgaagcctgtcatttgtgcca	8	11	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:27106354C>T	ENST00000324856.7	+	20	6336	c.5965C>T	c.(5965-5967)Cga>Tga	p.R1989*	ARID1A_ENST00000540690.1_Nonsense_Mutation_p.R317*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.R1606*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.R1772*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1989					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R1989*(8)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		CAATACCATTCGAAGCCTGTC	0.552			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	8	Substitution - Nonsense(8)	ovary(2)|large_intestine(2)|endometrium(2)|pancreas(2)	1											116	98	104					1																	27106354		2203	4300	6503	26978941	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5965C>T	1.37:g.27106354C>T	ENSP00000320485:p.Arg1989*		26978941	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.391795|10.391795	0.99396|0.99396	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690|ENST00000430799	.|.	.|.	.|.	5.0|5.0	5.0|5.0	0.66597|0.66597	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.65091	.|0.2658	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.62291	.|-0.6885	.|4	0.02654|.	T|.	1|.	-1.0676|-1.0676	13.6179|13.6179	0.62120|0.62120	0.1916:0.8084:0.0:0.0|0.1916:0.8084:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1989;1772;1606;317|885	.|.	ENSP00000320485:R1989X|.	R|S	+|+	1|2	2|0	ARID1A|ARID1A	26978941|26978941	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	4.555000|4.555000	0.60767|0.60767	2.760000|2.760000	0.94817|0.94817	0.478000|0.478000	0.44815|0.44815	CGA|TCG		0.552	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27106354	C	T	27106354	4	4	47	1	0	0	0	0	0	1	0	0	913	876	31	1	6043	1	ARID1A	1	27106354	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	319760	27106354	222144267	15	4412										
PIGV	55650	broad.mit.edu	37	chr1	27120648	27120648	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatcaccatgcagaagccttCtctcctcctcgcctggcccc	7	19	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:27120648C>T	ENST00000374145.1	+	3	805	c.123C>T	c.(121-123)ttC>ttT	p.F41F	PIGV_ENST00000449950.2_Missense_Mutation_p.S12F|PIGV_ENST00000078527.4_Silent_p.F41F	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	41					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.F41F(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		CAGAAGCCTTCTCTCCTCCTC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											100	94	96					1																	27120648		2203	4300	6503	26993235	SO:0001819	synonymous_variant	55650			AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.123C>T	1.37:g.27120648C>T			26993235	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Missense_Mutation	SNP	ENST00000374145.1	37	CCDS287.1	.	.	.	.	.	.	.	.	.	.	c	17.07	3.296021	0.60086	.	.	ENSG00000060642	ENST00000449950	.	.	.	5.43	-0.373	0.12516	.	.	.	.	.	T	0.38348	0.1037	.	.	.	0.38673	D	0.952358	B	0.13145	0.007	B	0.12156	0.007	T	0.12889	-1.0530	6	.	.	.	-17.6056	9.0328	0.36269	0.0:0.5705:0.0:0.4295	.	12	B4DWP9	.	F	12	.	.	S	+	2	0	PIGV	26993235	0.992000	0.36948	0.099000	0.21106	0.977000	0.68977	1.207000	0.32333	-0.365000	0.08076	0.558000	0.71614	TCT		0.507	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		T	27120648	C	T	27120648	2	4	47	1	0	0	0	0	0	0	0	1	11932	912	32	3		3	PIGV	1	27120648	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	14294	27120648	222129973	16	4413										
C1orf38	9473	broad.mit.edu	37	chr1	28206484	28206484	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacaggatccagccctgaaaGacctcgtcctcacctgcccc	7	18	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:28206484G>T	ENST00000373921.3	+	3	569	c.565G>T	c.(565-567)Gac>Tac	p.D189Y	THEMIS2_ENST00000328928.7_Missense_Mutation_p.D189Y|THEMIS2_ENST00000373925.1_Missense_Mutation_p.D189Y|THEMIS2_ENST00000373927.3_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	189	CABIT 1.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.D189Y(1)									AGCCCTGAAAGACCTCGTCCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	47	50					1																	28206484		2203	4300	6503	28079071	SO:0001583	missense	9473			AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"induced by contact to basement membrane 1"		"chromosome 1 open reading frame 38"	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.565G>T	1.37:g.28206484G>T	ENSP00000363031:p.Asp189Tyr		28079071	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.474|6.474	0.455663|0.455663	0.12283|0.12283	.|.	.|.	ENSG00000130775|ENSG00000130775	ENST00000373925;ENST00000328928;ENST00000373921|ENST00000456990	T;T;T|T	0.14391|0.14640	2.51;2.51;2.51|2.49	4.81|4.81	1.85|1.85	0.25348|0.25348	.|.	0.525318|.	0.21616|.	N|.	0.071702|.	T|T	0.16041|0.16041	0.0386|0.0386	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	N|N	1|1	P;P;D|.	0.55172|.	0.904;0.922;0.97|.	P;P;P|.	0.50537|.	0.582;0.642;0.643|.	T|T	0.19647|0.19647	-1.0299|-1.0299	10|7	0.56958|0.59425	D|D	0.05|0.04	-15.853|-15.853	4.9792|4.9792	0.14157|0.14157	0.2523:0.1584:0.5892:0.0|0.2523:0.1584:0.5892:0.0	.|.	189;189;189|.	Q5TEJ8-5;Q5TEJ8;Q5TEJ8-2|.	.;THMS2_HUMAN;.|.	Y|N	189|81	ENSP00000363035:D189Y;ENSP00000329862:D189Y;ENSP00000363031:D189Y|ENSP00000398049:K81N	ENSP00000329862:D189Y|ENSP00000398049:K81N	D|K	+|+	1|3	0|2	C1orf38|C1orf38	28079071|28079071	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.020000|0.020000	0.10135|0.10135	0.966000|0.966000	0.29331|0.29331	0.549000|0.549000	0.28973|0.28973	0.561000|0.561000	0.74099|0.74099	GAC|AAG		0.612	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848		T	28206484	G	T	28206484	3	4	47	1	0	0	0	0	1	0	0	0	2045	942	33	2	575	2	C1orf38	1	28206484	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1085836	28206484	221044137	17	4414										
CSMD2	114784	broad.mit.edu	37	chr1	34208949	34208949	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaactcgagacgggccacgTggccactgcttgtgatggag	16	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:34208949T>C	ENST00000373381.4	-	14	2281	c.2105A>G	c.(2104-2106)cAc>cGc	p.H702R		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	662	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.H662R(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ACGGGCCACGTGGCCACTGCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	52	54					1																	34208949		2203	4300	6503	33981536	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2105A>G	1.37:g.34208949T>C	ENSP00000362479:p.His702Arg		33981536	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	T	24.5	4.536780	0.85812	.	.	ENSG00000121904	ENST00000373381	T	0.33216	1.42	5.69	5.69	0.88448	CUB (5);	0.000000	0.85682	D	0.000000	T	0.42854	0.1221	L	0.28344	0.845	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	T	0.28713	-1.0035	10	0.44086	T	0.13	.	15.4289	0.75077	0.0:0.0:0.0:1.0	.	662;702	Q7Z408;E7EUA6	CSMD2_HUMAN;.	R	702	ENSP00000362479:H702R	ENSP00000241312:H662R	H	-	2	0	CSMD2	33981536	1.000000	0.71417	0.999000	0.59377	0.863000	0.49368	7.948000	0.87774	2.291000	0.77112	0.533000	0.62120	CAC		0.597	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		C	34208949	T	C	34208949	3	2	47	1	0	0	0	0	1	0	0	0	3951	1696	59	4	8702	4	CSMD2	1	34208949	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	6002465	34208949	215041672	18	4415										
GRIK3	2899	broad.mit.edu	37	chr1	37346416	37346416	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctccagggcattgcagatGgactggacggcattggtgca	14	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:37346416G>T	ENST00000373091.3	-	3	385	c.369C>A	c.(367-369)tcC>tcA	p.S123S	GRIK3_ENST00000373093.4_Silent_p.S123S	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	123					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.S123S(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATTGCAGATGGACTGGACGG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	1											155	141	146					1																	37346416		2203	4300	6503	37119003	SO:0001819	synonymous_variant	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.369C>A	1.37:g.37346416G>T			37119003	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																				0.622	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37346416	G	T	37346416	2	4	47	1	0	0	0	0	0	0	0	1	6796	1335	47	2		2	GRIK3	1	37346416	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3137467	37346416	211904205	19	4416										
MACF1	23499	broad.mit.edu	37	chr1	39759288	39759288	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagccaagagaaattacttCtctgtgagtctagcacagta	8	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:39759288C>A	ENST00000372915.3	+	17	2253	c.2166C>A	c.(2164-2166)ttC>ttA	p.F722L	MACF1_ENST00000564288.1_Missense_Mutation_p.F717L|MACF1_ENST00000361689.2_Missense_Mutation_p.F722L|MACF1_ENST00000539005.1_Missense_Mutation_p.F722L|MACF1_ENST00000317713.7_Missense_Mutation_p.F722L|MACF1_ENST00000545844.1_Missense_Mutation_p.F722L|MACF1_ENST00000567887.1_Missense_Mutation_p.F754L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	722					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.F722L(2)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			GAAATTACTTCTCTGTGAGTC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	1											122	109	114					1																	39759288		2203	4300	6503	39531875	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.2166C>A	1.37:g.39759288C>A	ENSP00000362006:p.Phe722Leu		39531875	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	16.81	3.226364	0.58668	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	T;T;T;T;T;T;T	0.65916	-0.18;-0.11;-0.18;-0.18;-0.18;-0.18;-0.18	5.63	4.72	0.59763	.	.	.	.	.	T	0.63034	0.2477	L	0.59436	1.845	0.80722	D	1	B;P	0.41313	0.046;0.745	B;P	0.47376	0.037;0.545	T	0.58912	-0.7552	9	0.20519	T	0.43	.	11.0104	0.47659	0.0:0.8578:0.0:0.1422	.	722;687	F8W8Q1;Q9UPN3-3	.;.	L	722;722;722;722;722;680;871;882	ENSP00000439537:F722L;ENSP00000362006:F722L;ENSP00000354573:F722L;ENSP00000313438:F722L;ENSP00000444364:F722L;ENSP00000435070:F680L;ENSP00000437059:F871L	ENSP00000313438:F722L	F	+	3	2	MACF1	39531875	0.993000	0.37304	1.000000	0.80357	0.984000	0.73092	0.798000	0.27014	1.533000	0.49186	-0.140000	0.14226	TTC		0.468	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39759288	C	A	39759288	3	1	47	1	0	0	0	0	1	0	0	0	9174	912	32	2	2232	2	MACF1	1	39759288	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2412872	39759288	209491333	20	4417										
MACF1	23499	broad.mit.edu	37	chr1	39789938	39789938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggctgggtgtctaccctagCgaggaatacacaaggaaaag	14	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:39789938C>T	ENST00000372915.3	+	33	4412	c.4325C>T	c.(4324-4326)gCg>gTg	p.A1442V	MACF1_ENST00000564288.1_Missense_Mutation_p.A1437V|MACF1_ENST00000361689.2_Missense_Mutation_p.A1442V|MACF1_ENST00000539005.1_Missense_Mutation_p.A1442V|MACF1_ENST00000317713.7_Missense_Mutation_p.A1442V|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Missense_Mutation_p.A1442V|MACF1_ENST00000567887.1_Missense_Mutation_p.A1474V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1442					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.A1442V(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			TCTACCCTAGCGAGGAATACA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	92	96					1																	39789938		2203	4300	6503	39562525	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.4325C>T	1.37:g.39789938C>T	ENSP00000362006:p.Ala1442Val		39562525	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	10.42	1.346566	0.24426	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262	T;T;T;T;T;T	0.63580	-0.02;0.05;-0.02;-0.05;0.13;2.01	6.16	5.25	0.73442	.	.	.	.	.	T	0.53077	0.1774	L	0.47716	1.5	0.58432	D	0.999997	B;B;P	0.34546	0.427;0.099;0.456	B;B;B	0.32393	0.145;0.019;0.103	T	0.56679	-0.7939	9	0.59425	D	0.04	.	10.0224	0.42051	0.1695:0.7596:0.0:0.0708	.	1442;1442;1407	F8W8Q1;Q9UPN3-2;Q9UPN3-3	.;.;.	V	1442;1442;1442;1442;1442;1591	ENSP00000439537:A1442V;ENSP00000362006:A1442V;ENSP00000354573:A1442V;ENSP00000313438:A1442V;ENSP00000444364:A1442V;ENSP00000437059:A1591V	ENSP00000313438:A1442V	A	+	2	0	MACF1	39562525	0.576000	0.26700	0.300000	0.25030	0.080000	0.17528	1.021000	0.30040	1.617000	0.50277	0.650000	0.86243	GCG		0.403	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39789938	C	T	39789938	3	4	47	1	0	0	0	0	1	0	0	0	9174	768	27	1	4455	1	MACF1	1	39789938	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	30650	39789938	209460683	21	4418										
MACF1	23499	broad.mit.edu	37	chr1	39792959	39792959	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacaaggcttaccatgacctTtgtgatggttctgcaaatca	8	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:39792959T>C	ENST00000372915.3	+	35	4650	c.4563T>C	c.(4561-4563)ctT>ctC	p.L1521L	MACF1_ENST00000564288.1_Silent_p.L1516L|MACF1_ENST00000361689.2_Silent_p.L1521L|MACF1_ENST00000539005.1_Silent_p.L1521L|MACF1_ENST00000317713.7_Silent_p.L1521L|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Silent_p.L1521L|MACF1_ENST00000567887.1_Silent_p.L1553L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1521					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.L1521L(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACCATGACCTTTGTGATGGTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	1											83	78	80					1																	39792959		2203	4300	6503	39565546	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.4563T>C	1.37:g.39792959T>C			39565546	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																					0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39792959	T	C	39792959	2	2	47	1	0	0	0	0	0	0	0	1	9174	1828	64	4		4	MACF1	1	39792959	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3021	39792959	209457662	22	4419										
MACF1	23499	broad.mit.edu	37	chr1	39801074	39801074	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgaagaaataagagaaaaTcaaggggaagtgattttgga	12	2	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:39801074T>G	ENST00000372915.3	+	36	8916	c.8829T>G	c.(8827-8829)aaT>aaG	p.N2943K	MACF1_ENST00000564288.1_Missense_Mutation_p.N2938K|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000289893.4_Missense_Mutation_p.N1378K|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Missense_Mutation_p.N2975K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	2943					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.N1378K(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			TAAGAGAAAATCAAGGGGAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	53	52					1																	39801074		2203	4300	6503	39573661	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.8829T>G	1.37:g.39801074T>G	ENSP00000362006:p.Asn2943Lys		39573661	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	T	8.293	0.818093	0.16607	.	.	ENSG00000127603	ENST00000372915;ENST00000289893	T;T	0.62788	0.0;1.1	5.09	0.476	0.16779	.	1.437400	0.04470	N	0.375800	T	0.42131	0.1189	N	0.14661	0.345	0.09310	N	1	B	0.20164	0.042	B	0.22753	0.041	T	0.20075	-1.0286	10	0.28530	T	0.3	.	2.9765	0.05939	0.1951:0.3325:0.0:0.4723	.	2943	Q9UPN3	MACF1_HUMAN	K	2943;1378	ENSP00000362006:N2943K;ENSP00000289893:N1378K	ENSP00000289893:N1378K	N	+	3	2	MACF1	39573661	0.020000	0.18652	0.217000	0.23759	0.939000	0.58152	0.224000	0.17738	0.051000	0.15978	0.383000	0.25322	AAT		0.378	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39801074	T	G	39801074	3	3	47	1	0	0	0	0	1	0	0	0	9174	1432	50	4	8905	4	MACF1	1	39801074	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	8115	39801074	209449547	23	4420										
MACF1	23499	broad.mit.edu	37	chr1	39816667	39816667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaggaagcagtgacctccGccttacagcaggagactgaa	13	10	0	3	rs367562249		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:39816667G>A	ENST00000372915.3	+	42	11278	c.11191G>A	c.(11191-11193)Gcc>Acc	p.A3731T	MACF1_ENST00000564288.1_Missense_Mutation_p.A3726T|MACF1_ENST00000361689.2_Missense_Mutation_p.A1664T|MACF1_ENST00000539005.1_Missense_Mutation_p.A1664T|MACF1_ENST00000317713.7_Missense_Mutation_p.A1664T|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000289893.4_Missense_Mutation_p.A2166T|MACF1_ENST00000545844.1_Missense_Mutation_p.A1664T|MACF1_ENST00000567887.1_Missense_Mutation_p.A3763T			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3731					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.A2166T(1)|p.A1664T(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			AGTGACCTCCGCCTTACAGCA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	1						G	THR/ALA,THR/ALA	1,4405		0,1,2202	59	59	59		4990,6496	6.1	1	1		59	0,8600		0,0,4300	no	missense,missense	MACF1	NM_012090.4,NM_033044.3	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1664/5431,2166/5939	39816667	1,13005	2203	4300	6503	39589254	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11191G>A	1.37:g.39816667G>A	ENSP00000362006:p.Ala3731Thr		39589254	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.39|17.39	3.376626|3.376626	0.61735|0.61735	2.27E-4|2.27E-4	0.0|0.0	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893|ENST00000372925	T;T;T;T;T;D;T|.	0.88896|.	-0.13;-0.11;-0.13;-0.16;0.01;-2.44;1.0|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.000000|.	0.64402|.	D|.	0.000011|.	T|T	0.79015|0.79015	0.4375|0.4375	M|M	0.77313|0.77313	2.365|2.365	0.80722|0.80722	D|D	1|1	B;P;P;P|.	0.50819|.	0.152;0.939;0.854;0.879|.	B;P;B;B|.	0.44946|.	0.153;0.465;0.292;0.334|.	T|T	0.76961|0.76961	-0.2765|-0.2765	10|5	0.62326|.	D|.	0.03|.	.|.	20.2194|20.2194	0.98323|0.98323	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3731;1664;1664;1629|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	T|H	1664;3731;1664;1664;1664;1813;2166|797	ENSP00000439537:A1664T;ENSP00000362006:A3731T;ENSP00000354573:A1664T;ENSP00000313438:A1664T;ENSP00000444364:A1664T;ENSP00000437059:A1813T;ENSP00000289893:A2166T|.	ENSP00000289893:A2166T|.	A|R	+|+	1|2	0|0	MACF1|MACF1	39589254|39589254	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.897000|0.897000	0.52465|0.52465	6.266000|6.266000	0.72540|0.72540	2.879000|2.879000	0.98667|0.98667	0.650000|0.650000	0.86243|0.86243	GCC|CGC		0.458	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39816667	G	A	39816667	3	1	47	1	0	0	0	0	1	0	0	0	9174	1087	38	1	11291	1	MACF1	1	39816667	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	15593	39816667	209433954	24	4421										
RLF	6018	broad.mit.edu	37	chr1	40704701	40704701	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggaaatacattcagattatGaaattcattgtgatcttaat	7	4	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:40704701G>T	ENST00000372771.4	+	8	4354	c.4327G>T	c.(4327-4329)Gaa>Taa	p.E1443*		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1443					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1443*(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TTCAGATTATGAAATTCATTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											55	56	56					1																	40704701		2203	4299	6502	40477288	SO:0001587	stop_gained	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.4327G>T	1.37:g.40704701G>T	ENSP00000361857:p.Glu1443*		40477288	Q14CQ1|Q9NU60	Nonsense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	40	8.222633	0.98714	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	.	.	.	6.17	6.17	0.99709	.	0.119316	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-19.8782	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	1443;1136	.	ENSP00000361857:E1443X	E	+	1	0	RLF	40477288	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.682000	0.68182	2.941000	0.99782	0.655000	0.94253	GAA		0.363	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		T	40704701	G	T	40704701	4	4	47	1	0	0	0	0	0	1	0	0	13426	1291	45	2	4357	2	RLF	1	40704701	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	888034	40704701	208545920	25	4422										
RLF	6018	broad.mit.edu	37	chr1	40705211	40705211	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagatccctgtataaagaaaGaagaaaatagaagctgtgaa	9	5	0	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:40705211G>A	ENST00000372771.4	+	8	4864	c.4837G>A	c.(4837-4839)Gaa>Aaa	p.E1613K		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1613					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1613K(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TATAAAGAAAGAAGAAAATAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	48	47					1																	40705211		2203	4300	6503	40477798	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.4837G>A	1.37:g.40705211G>A	ENSP00000361857:p.Glu1613Lys		40477798	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	6.656	0.489534	0.12641	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.13657	2.57	5.93	5.02	0.67125	.	0.472650	0.25205	N	0.032359	T	0.10637	0.0260	L	0.36672	1.1	0.32075	N	0.593928	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.06679	-1.0813	10	0.36615	T	0.2	-12.6865	6.95	0.24540	0.1918:0.1348:0.6734:0.0	.	1306;1613	F5H2M5;Q13129	.;RLF_HUMAN	K	1613;1306	ENSP00000361857:E1613K	ENSP00000361857:E1613K	E	+	1	0	RLF	40477798	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.913000	0.63341	1.521000	0.48983	0.655000	0.94253	GAA		0.443	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40705211	G	A	40705211	3	1	47	1	0	0	0	0	1	0	0	0	13426	943	33	3	4867	3	RLF	1	40705211	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	510	40705211	208545410	26	4423										
TMCO2	127391	broad.mit.edu	37	chr1	40717159	40717159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaacctagaagggataatcGttgctcaaaaacctgccacg	9	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:40717159G>A	ENST00000372766.3	+	2	535	c.442G>A	c.(442-444)Gtt>Att	p.V148I	TMCO2_ENST00000468258.1_3'UTR	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	transmembrane and coiled-coil domains 2	148						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.V148I(1)		kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6	Lung NSC(20;4.38e-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;6.3e-18)			AGGGATAATCGTTGCTCAAAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	71	70					1																	40717159		2203	4300	6503	40489746	SO:0001583	missense	127391			AL050341	CCDS30684.1	1p34.2	2014-02-12			ENSG00000188800	ENSG00000188800			23312	protein-coding gene	gene with protein product							Standard	NM_001008740		Approved	dJ39G22.2	uc001cfe.2	Q7Z6W1	OTTHUMG00000005764	ENST00000372766.3:c.442G>A	1.37:g.40717159G>A	ENSP00000361852:p.Val148Ile		40489746		Missense_Mutation	SNP	ENST00000372766.3	37	CCDS30684.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.177217	0.00312	.	.	ENSG00000188800	ENST00000372766	.	.	.	5.11	-2.89	0.05665	.	0.626644	0.14841	N	0.295266	T	0.09686	0.0238	N	0.02539	-0.55	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.31752	-0.9932	9	0.02654	T	1	-1.1451	6.3636	0.21443	0.4141:0.151:0.4349:0.0	.	148	Q7Z6W1	TMCO2_HUMAN	I	148	.	ENSP00000361852:V148I	V	+	1	0	TMCO2	40489746	0.997000	0.39634	0.730000	0.30809	0.036000	0.12997	0.409000	0.21082	-0.753000	0.04721	-1.899000	0.00529	GTT		0.443	TMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015769.1	NM_001008740		A	40717159	G	A	40717159	3	1	47	1	0	0	0	0	1	0	0	0	16035	1145	40	1	448	1	TMCO2	1	40717159	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	11948	40717159	208533462	27	4424										
KCNQ4	9132	broad.mit.edu	37	chr1	41300696	41300696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagacactgcgaccgtacgaCgtgaaggacgtcattgagca	13	10	1	3	rs542936837		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:41300696C>T	ENST00000347132.5	+	12	1753	c.1671C>T	c.(1669-1671)gaC>gaT	p.D557D	KCNQ4_ENST00000509682.2_Silent_p.D503D|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	557	A-domain (Tetramerization).				inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.D557D(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	GACCGTACGACGTGAAGGACG	0.587													C|||	1	0.000199681	0	0	5008	,	,		19977	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											128	114	119					1																	41300696		2203	4300	6503	41073283	SO:0001819	synonymous_variant	9132			AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1671C>T	1.37:g.41300696C>T			41073283	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	.	.	.	.	.	.	.	.	.	.	C	9.365	1.068929	0.20147	.	.	ENSG00000117013	ENST00000443478	.	.	.	5.12	1.45	0.22620	.	.	.	.	.	T	0.52354	0.1729	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42085	-0.9472	4	.	.	.	-29.3638	5.9979	0.19505	0.0:0.3712:0.0:0.6288	.	.	.	.	C	418	.	.	R	+	1	0	KCNQ4	41073283	0.504000	0.26123	1.000000	0.80357	0.994000	0.84299	-0.251000	0.08818	0.565000	0.29255	0.551000	0.68910	CGT		0.587	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700		T	41300696	C	T	41300696	2	4	47	1	0	0	0	0	0	0	0	1	8106	535	19	1		1	KCNQ4	1	41300696	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	583537	41300696	207949925	28	4425										
ZMYND12	84217	broad.mit.edu	37	chr1	42902188	42902188	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagtcctaatgtcctctgtTccaaatgcacaactggcaaa	7	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:42902188T>G	ENST00000372565.3	-	5	890	c.621A>C	c.(619-621)ggA>ggC	p.G207G	ZMYND12_ENST00000433602.2_Silent_p.G97G|ZMYND12_ENST00000475426.1_5'Flank	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	207						intracellular (GO:0005622)	metal ion binding (GO:0046872)	p.G207G(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGTCCTCTGTTCCAAATGCAC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	1											95	91	92					1																	42902188		2203	4300	6503	42674775	SO:0001819	synonymous_variant	84217			AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"Zinc fingers, MYND-type"	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.621A>C	1.37:g.42902188T>G			42674775	Q5VUS6|Q8TC87|Q96M51	Silent	SNP	ENST00000372565.3	37	CCDS467.1																																																																																				0.398	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257		G	42902188	T	G	42902188	2	3	47	1	0	0	0	0	0	0	0	1	17746	1770	62	4		4	ZMYND12	1	42902188	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1601492	42902188	206348433	29	4426										
SLC6A9	6536	broad.mit.edu	37	chr1	44476409	44476409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgggtacctcccccgttgCgatagcagaggtatgggaag	14	10	0	1	rs200036856		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:44476409C>T	ENST00000360584.2	-	3	586	c.395G>A	c.(394-396)cGc>cAc	p.R132H	SLC6A9_ENST00000357730.2_Missense_Mutation_p.R78H|SLC6A9_ENST00000475075.2_Intron|SLC6A9_ENST00000537678.1_Intron|SLC6A9_ENST00000372307.3_5'UTR|SLC6A9_ENST00000492434.2_Intron|SLC6A9_ENST00000372306.3_Missense_Mutation_p.R59H|SLC6A9_ENST00000372310.3_Missense_Mutation_p.R59H	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	132					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R132H(1)|p.R59H(1)		endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	TCCCCCGTTGCGATAGCAGAG	0.647																																																2	Substitution - Missense(2)	large_intestine(2)	1											127	104	112					1																	44476409		2203	4300	6503	44248996	SO:0001583	missense	6536			S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.395G>A	1.37:g.44476409C>T	ENSP00000353791:p.Arg132His		44248996	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Missense_Mutation	SNP	ENST00000360584.2	37	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142728	0.77888	.	.	ENSG00000196517	ENST00000372306;ENST00000372310;ENST00000360584;ENST00000357730;ENST00000528803;ENST00000466926	T;T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93;-0.93	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.85146	0.5630	M	0.65498	2.005	0.80722	D	1	P;P;P;D	0.89917	0.94;0.926;0.926;1.0	P;B;B;D	0.87578	0.583;0.305;0.305;0.998	D	0.86389	0.1734	10	0.72032	D	0.01	.	17.3604	0.87348	0.0:1.0:0.0:0.0	.	59;59;78;132	B7Z8W5;P48067-2;P48067-3;P48067	.;.;.;SC6A9_HUMAN	H	59;59;132;78;78;113	ENSP00000361380:R59H;ENSP00000361384:R59H;ENSP00000353791:R132H;ENSP00000350362:R78H;ENSP00000435652:R78H;ENSP00000433241:R113H	ENSP00000350362:R78H	R	-	2	0	SLC6A9	44248996	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.664000	0.37439	2.623000	0.88846	0.591000	0.81541	CGC		0.647	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		T	44476409	C	T	44476409	3	4	47	1	0	0	0	0	1	0	0	0	14728	768	27	1	1773	1	SLC6A9	1	44476409	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1574221	44476409	204774212	30	4427										
KIF2C	11004	broad.mit.edu	37	chr1	45213068	45213068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgcagattgattttgatGatgtggctgcaataaaccca	9	8	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:45213068G>T	ENST00000372224.4	+	3	291	c.178G>T	c.(178-180)Gat>Tat	p.D60Y	KIF2C_ENST00000493027.1_3'UTR|KIF2C_ENST00000372218.4_Missense_Mutation_p.D60Y|KIF2C_ENST00000372217.1_Missense_Mutation_p.D6Y|KIF2C_ENST00000372222.3_5'UTR	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	60	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)	p.D60Y(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					TGATTTTGATGATGTGGCTGC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	118	119					1																	45213068		2203	4300	6503	44985655	SO:0001583	missense	11004			U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.178G>T	1.37:g.45213068G>T	ENSP00000361298:p.Asp60Tyr		44985655	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.418030	0.83449	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000455186;ENST00000372217	T;T;T;T;T	0.77229	1.13;-0.89;-0.73;0.9;-1.08	6.07	6.07	0.98685	.	0.051734	0.85682	D	0.000000	D	0.85115	0.5623	L	0.44542	1.39	0.80722	D	1	D;D;D	0.89917	0.958;1.0;0.979	P;D;P	0.91635	0.629;0.999;0.76	D	0.84937	0.0863	10	0.62326	D	0.03	.	18.8245	0.92111	0.0:0.0:1.0:0.0	.	60;6;60	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	Y	60;60;60;51;6	ENSP00000410346:D60Y;ENSP00000361298:D60Y;ENSP00000361292:D60Y;ENSP00000395050:D51Y;ENSP00000361291:D6Y	ENSP00000361291:D6Y	D	+	1	0	KIF2C	44985655	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.999000	0.70665	2.884000	0.98904	0.655000	0.94253	GAT		0.368	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845		T	45213068	G	T	45213068	3	4	47	1	0	0	0	0	1	0	0	0	8320	1290	45	2	188	2	KIF2C	1	45213068	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	736659	45213068	204037553	31	4428										
IPP	3652	broad.mit.edu	37	chr1	46180131	46180131	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgatgcccccaattacataAattaaacctggaagtggaat	7	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:46180131A>C	ENST00000396478.3	-	8	1419	c.1317T>G	c.(1315-1317)atT>atG	p.I439M	IPP_ENST00000495072.1_5'Flank	NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	439						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.I439M(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					CAATTACATAAATTAAACCTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											43	39	41					1																	46180131		2203	4300	6503	45952719	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1317T>G	1.37:g.46180131A>C	ENSP00000379739:p.Ile439Met		45952719	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.922514	0.52653	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	D;D	0.85171	-1.95;-1.95	4.92	2.11	0.27256	Galactose oxidase, beta-propeller (1);	0.047715	0.85682	D	0.000000	D	0.88782	0.6530	M	0.69823	2.125	0.53688	D	0.999978	P;D	0.64830	0.639;0.994	P;D	0.65233	0.524;0.933	D	0.87035	0.2137	10	0.66056	D	0.02	.	7.2896	0.26358	0.7837:0.0:0.0838:0.1324	.	439;439	Q9Y573;A2A6V3	IPP_HUMAN;.	M	439	ENSP00000353024:I439M;ENSP00000379739:I439M	ENSP00000353024:I439M	I	-	3	3	IPP	45952719	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.706000	0.25690	0.665000	0.31066	0.454000	0.30748	ATT		0.373	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		C	46180131	A	C	46180131	3	2	47	1	0	0	0	0	1	0	0	0	7821	10	1	4	547	4	IPP	1	46180131	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	967063	46180131	203070490	32	4429										
IPP	3652	broad.mit.edu	37	chr1	46206618	46206618	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggaggtaataaagggaatcGaattgggtctagcacttcca	12	6	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:46206618G>A	ENST00000396478.3	-	3	781	c.679C>T	c.(679-681)Cga>Tga	p.R227*		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	227						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.R227*(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					AAAGGGAATCGAATTGGGTCT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											170	168	168					1																	46206618		2203	4300	6503	45979205	SO:0001587	stop_gained	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.679C>T	1.37:g.46206618G>A	ENSP00000379739:p.Arg227*		45979205	A2A6V4|D3DQ11|Q8N5C3	Nonsense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	G	35	5.597542	0.96602	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	.	.	.	5.17	4.2	0.49525	.	0.249248	0.41194	D	0.000931	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3396	0.66617	0.0:0.0:0.7561:0.2439	.	.	.	.	X	227	.	ENSP00000353024:R227X	R	-	1	2	IPP	45979205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.208000	0.65203	2.577000	0.86979	0.643000	0.83706	CGA		0.353	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		A	46206618	G	A	46206618	4	1	47	1	0	0	0	0	0	1	0	0	7821	1066	37	1	1205	1	IPP	1	46206618	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	26487	46206618	203044003	33	4430										
CYP4Z1	199974	broad.mit.edu	37	chr1	47583600	47583600	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgtgtttgcaaaaaaagtTtgctaattttaagtcctttc	6	6	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:47583600T>G	ENST00000334194.3	+	12	1515	c.1512T>G	c.(1510-1512)gtT>gtG	p.V504V	CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4Z1_ENST00000471598.1_3'UTR	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	504						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.V504V(1)		cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						CAAAAAAAGTTTGCTAATTTT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											50	45	47					1																	47583600		2203	4300	6503	47356187	SO:0001819	synonymous_variant	199974			AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"Cytochrome P450s"	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1512T>G	1.37:g.47583600T>G			47356187	Q5VVE4	Silent	SNP	ENST00000334194.3	37	CCDS545.1																																																																																				0.373	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		G	47583600	T	G	47583600	2	3	47	1	0	0	0	0	0	0	0	1	4200	1828	64	4		4	CYP4Z1	1	47583600	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1376982	47583600	201667021	34	4431										
EPS15	2060	broad.mit.edu	37	chr1	51934222	51934222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgggcacatgccacaagacGcaaagcaacaaagaattcct	8	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:51934222G>A	ENST00000371733.3	-	5	328	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	EPS15_ENST00000371730.2_Missense_Mutation_p.R78C	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	78	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.R78C(1)|p.0?(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GCCACAAGACGCAAAGCAACA	0.368			T	MLL	ALL																																		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|central_nervous_system(1)	1											65	62	63					1																	51934222		2203	4300	6503	51706810	SO:0001583	missense	2060			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.232C>T	1.37:g.51934222G>A	ENSP00000360798:p.Arg78Cys		51706810	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.715128	0.68844	.	.	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000371727	T;T	0.39056	1.1;1.1	4.76	2.74	0.32292	EPS15 homology (EH) (2);EF-hand-like domain (1);	.	.	.	.	T	0.49932	0.1586	M	0.86805	2.84	0.80722	D	1	B;D	0.60160	0.019;0.987	B;P	0.45610	0.008;0.487	T	0.60791	-0.7193	9	0.87932	D	0	.	9.1397	0.36897	0.0836:0.0:0.7701:0.1462	.	78;78	B1AUU8;P42566	.;EPS15_HUMAN	C	78	ENSP00000360795:R78C;ENSP00000360798:R78C	ENSP00000360792:R78C	R	-	1	0	EPS15	51706810	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.500000	0.53318	1.356000	0.45884	0.650000	0.86243	CGT		0.368	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		A	51934222	G	A	51934222	3	1	47	1	0	0	0	0	1	0	0	0	5205	1087	38	1	2640	1	EPS15	1	51934222	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4350622	51934222	197316399	35	4432										
ZFYVE9	9372	broad.mit.edu	37	chr1	52704080	52704080	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaggagagcaccactgaaGaatccctccggtctggttta	11	11	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:52704080G>T	ENST00000371591.1	+	3	1122	c.991G>T	c.(991-993)Gaa>Taa	p.E331*	ZFYVE9_ENST00000287727.3_Nonsense_Mutation_p.E331*|ZFYVE9_ENST00000357206.2_Nonsense_Mutation_p.E331*	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	331					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)	p.E331*(1)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						CACCACTGAAGAATCCCTCCG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											89	87	87					1																	52704080		2203	4300	6503	52476668	SO:0001587	stop_gained	9372			AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.991G>T	1.37:g.52704080G>T	ENSP00000360647:p.Glu331*		52476668	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Nonsense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647439	0.87958	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	.	.	.	4.75	3.84	0.44239	.	0.464350	0.19156	N	0.121333	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	7.207	0.25913	0.0952:0.2275:0.6773:0.0	.	.	.	.	X	331	.	ENSP00000287727:E331X	E	+	1	0	ZFYVE9	52476668	0.998000	0.40836	0.985000	0.45067	0.925000	0.55904	2.176000	0.42500	1.228000	0.43614	0.563000	0.77884	GAA		0.483	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		T	52704080	G	T	52704080	4	4	47	1	0	0	0	0	0	1	0	0	17710	943	33	2	997	2	ZFYVE9	1	52704080	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	769858	52704080	196546541	36	4433										
C8A	731	broad.mit.edu	37	chr1	57373668	57373668	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggctgtggaagacattatttCtcgggtgcgaggtggcagtt	16	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:57373668C>A	ENST00000361249.3	+	9	1358	c.1262C>A	c.(1261-1263)tCt>tAt	p.S421Y		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	421	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)		p.S421Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GACATTATTTCTCGGGTGCGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											129	122	124					1																	57373668		2203	4300	6503	57146256	SO:0001583	missense	731			M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1262C>A	1.37:g.57373668C>A	ENSP00000354458:p.Ser421Tyr		57146256	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.638448	0.67130	.	.	ENSG00000157131	ENST00000361249	D	0.84516	-1.86	6.03	5.13	0.70059	Membrane attack complex component/perforin (MACPF) domain (3);	0.537705	0.21967	N	0.066520	D	0.92341	0.7570	M	0.89414	3.03	0.32397	N	0.552456	D	0.67145	0.996	D	0.66196	0.942	D	0.94156	0.7410	10	0.66056	D	0.02	-3.8118	11.4633	0.50223	0.0:0.8578:0.0:0.1422	.	421	P07357	CO8A_HUMAN	Y	421	ENSP00000354458:S421Y	ENSP00000354458:S421Y	S	+	2	0	C8A	57146256	0.030000	0.19436	0.960000	0.40013	0.920000	0.55202	1.629000	0.37071	1.568000	0.49683	0.557000	0.71058	TCT		0.507	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		A	57373668	C	A	57373668	3	1	47	1	0	0	0	0	1	0	0	0	2422	913	32	2	1296	2	C8A	1	57373668	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4669588	57373668	191876953	37	4434										
DAB1	1600	broad.mit.edu	37	chr1	57535047	57535047	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatacctgataaatgttttCttccgtttcgggatcacgga	8	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:57535047C>A	ENST00000371231.1	-	7	683	c.649G>T	c.(649-651)Gaa>Taa	p.E217*	DAB1_ENST00000371234.4_Nonsense_Mutation_p.E217*|DAB1_ENST00000420954.2_Intron|DAB1_ENST00000414851.2_Intron|DAB1_ENST00000371236.2_Nonsense_Mutation_p.E217*|DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000439789.2_Intron			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	217					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.E217*(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						TAAATGTTTTCTTCCGTTTCG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											161	146	151					1																	57535047		2203	4300	6503	57307635	SO:0001587	stop_gained	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.649G>T	1.37:g.57535047C>A	ENSP00000360275:p.Glu217*		57307635	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Nonsense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	C	43	10.273817	0.99373	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000371231	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-19.3361	17.8246	0.88661	0.0:1.0:0.0:0.0	.	.	.	.	X	217	.	ENSP00000360275:E217X	E	-	1	0	DAB1	57307635	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.320000	0.79064	2.882000	0.98803	0.655000	0.94253	GAA		0.418	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		A	57535047	C	A	57535047	4	1	47	1	0	0	0	0	0	1	0	0	4223	922	32	2	1046	2	DAB1	1	57535047	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	161379	57535047	191715574	38	4435										
NFIA	4774	broad.mit.edu	37	chr1	61553986	61553986	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgaattgctaagtgaaaaaCcagaggtcaagcagaagtgg	12	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:61553986C>A	ENST00000403491.3	+	2	677	c.193C>A	c.(193-195)Cca>Aca	p.P65T	NFIA_ENST00000371191.1_Missense_Mutation_p.P88T|NFIA_ENST00000407417.3_Missense_Mutation_p.P57T|NFIA_ENST00000371189.4_Missense_Mutation_p.P110T|NFIA_ENST00000479364.1_Intron|NFIA_ENST00000371185.2_Missense_Mutation_p.P65T|NFIA_ENST00000485903.2_Missense_Mutation_p.P65T|NFIA_ENST00000371184.2_Missense_Mutation_p.P65T|NFIA_ENST00000371187.3_Missense_Mutation_p.P65T	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	65					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P65T(1)	NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						AAGTGAAAAACCAGAGGTCAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	91	89					1																	61553986		2203	4300	6503	61326574	SO:0001583	missense	4774			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.193C>A	1.37:g.61553986C>A	ENSP00000384523:p.Pro65Thr		61326574	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Missense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326627	0.60743	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371185;ENST00000371184;ENST00000371187	T;T;T;T;T;T;T;T	0.46451	0.9;0.9;0.87;0.9;0.93;0.93;0.96;0.89	6.07	5.15	0.70609	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.34308	0.0893	N	0.20685	0.6	0.58432	D	0.999997	B;P;P;P	0.38504	0.001;0.634;0.634;0.504	B;B;B;B	0.39562	0.004;0.16;0.16;0.303	T	0.28586	-1.0039	10	0.72032	D	0.01	-8.6901	16.809	0.85713	0.13:0.87:0.0:0.0	.	110;88;65;65	F8W8W3;B1AKN8;Q12857;Q12857-2	.;.;NFIA_HUMAN;.	T	88;57;110;65;65;65;65;65	ENSP00000360233:P88T;ENSP00000384680:P57T;ENSP00000360231:P110T;ENSP00000384523:P65T;ENSP00000419785:P65T;ENSP00000360227:P65T;ENSP00000360226:P65T;ENSP00000360229:P65T	ENSP00000360226:P65T	P	+	1	0	NFIA	61326574	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.833000	0.55790	1.570000	0.49709	0.650000	0.86243	CCA		0.433	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595		A	61553986	C	A	61553986	3	1	47	1	0	0	0	0	1	0	0	0	10401	507	18	2	345	2	NFIA	1	61553986	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4018939	61553986	187696635	39	4436										
ATG4C	84938	broad.mit.edu	37	chr1	63329799	63329799	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaaagaaacaattaaaaaGatttagcacggaagagtttg	9	3	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:63329799G>T	ENST00000317868.4	+	11	1553	c.1346G>T	c.(1345-1347)aGa>aTa	p.R449I	ATG4C_ENST00000371120.3_Missense_Mutation_p.R449I	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	449					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.R449T(2)|p.R449I(2)	ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						CAATTAAAAAGATTTAGCACG	0.313																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	1											52	56	55					1																	63329799		2198	4292	6490	63102387	SO:0001583	missense	84938			AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog C (S. cerevisiae)", "ATG4 autophagy related 4 homolog C (S. cerevisiae)"	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.1346G>T	1.37:g.63329799G>T	ENSP00000322159:p.Arg449Ile		63102387	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.827168	0.71143	.	.	ENSG00000125703	ENST00000317868;ENST00000371120	.	.	.	5.22	4.29	0.51040	.	0.106741	0.64402	D	0.000009	T	0.64382	0.2593	M	0.71581	2.175	0.52501	D	0.999959	P	0.51147	0.942	P	0.55260	0.772	T	0.67181	-0.5735	9	0.44086	T	0.13	-23.8665	14.8806	0.70531	0.0:0.0:0.8552:0.1448	.	449	Q96DT6	ATG4C_HUMAN	I	449	.	ENSP00000322159:R449I	R	+	2	0	ATG4C	63102387	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	5.109000	0.64615	1.148000	0.42385	0.585000	0.79938	AGA		0.313	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		T	63329799	G	T	63329799	3	4	47	1	0	0	0	0	1	0	0	0	1099	942	33	2	1384	2	ATG4C	1	63329799	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1775813	63329799	185920822	40	4437										
PGM1	5236	broad.mit.edu	37	chr1	64120081	64120081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagtgccggggccaccattCggctgtacatcgatagctat	13	11	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:64120081C>T	ENST00000371084.3	+	10	1756	c.1543C>T	c.(1543-1545)Cgg>Tgg	p.R515W	PGM1_ENST00000371083.4_Missense_Mutation_p.R533W|RN7SL130P_ENST00000489463.2_RNA|PGM1_ENST00000483707.1_3'UTR|PGM1_ENST00000540265.1_Missense_Mutation_p.R318W	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	515					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)	p.R515W(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						GGCCACCATTCGGCTGTACAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	89	90					1																	64120081		2203	4300	6503	63892669	SO:0001583	missense	5236			BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1543C>T	1.37:g.64120081C>T	ENSP00000360125:p.Arg515Trp		63892669	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.200808	0.38905	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.63913	-0.07;-0.07;-0.07	5.45	3.56	0.40772	Alpha-D-phosphohexomutase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	H	0.97340	3.985	0.30534	N	0.767131	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77755	-0.2469	10	0.87932	D	0	-28.3353	8.4318	0.32761	0.2754:0.6545:0.0:0.07	.	533;515	P36871-2;P36871	.;PGM1_HUMAN	W	491;515;318;533	ENSP00000360125:R515W;ENSP00000443449:R318W;ENSP00000360124:R533W	ENSP00000360124:R533W	R	+	1	2	PGM1	63892669	0.971000	0.33674	0.008000	0.14137	0.038000	0.13279	2.091000	0.41691	0.768000	0.33290	-0.251000	0.11542	CGG		0.537	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		T	64120081	C	T	64120081	3	4	47	1	0	0	0	0	1	0	0	0	11828	875	31	1	1885	1	PGM1	1	64120081	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	790282	64120081	185130540	41	4438										
ROR1	4919	broad.mit.edu	37	chr1	64643731	64643731	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccatcatgtatggcaaattCtcttctgattcagatatctg	7	9	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:64643731C>A	ENST00000371079.1	+	9	2382	c.2007C>A	c.(2005-2007)ttC>ttA	p.F669L	ROR1_ENST00000545203.1_Missense_Mutation_p.F120L	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	669	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.F669L(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						ATGGCAAATTCTCTTCTGATT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	80	81					1																	64643731		2203	4300	6503	64416319	SO:0001583	missense	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.2007C>A	1.37:g.64643731C>A	ENSP00000360120:p.Phe669Leu		64416319	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749579	0.69533	.	.	ENSG00000185483	ENST00000371079;ENST00000544776;ENST00000545203	T;T	0.61510	0.1;0.1	5.98	5.08	0.68730	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45361	D	0.000366	T	0.67439	0.2893	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	T	0.73483	-0.3968	10	0.87932	D	0	.	15.2072	0.73190	0.0:0.9327:0.0:0.0673	.	669	Q01973	ROR1_HUMAN	L	669;672;120	ENSP00000360120:F669L;ENSP00000441637:F120L	ENSP00000360120:F669L	F	+	3	2	ROR1	64416319	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	2.660000	0.46749	1.551000	0.49450	0.591000	0.81541	TTC		0.453	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		A	64643731	C	A	64643731	3	1	47	1	0	0	0	0	1	0	0	0	13563	912	32	2	2049	2	ROR1	1	64643731	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	523650	64643731	184606890	42	4439										
CACHD1	57685	broad.mit.edu	37	chr1	65095040	65095040	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttccttacacctctagttCttgcagacaacctgaaatcc	4	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:65095040C>A	ENST00000371073.2	+	5	520	c.520C>A	c.(520-522)Ctt>Att	p.L174I	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.L123I			Q5VU97	CAHD1_HUMAN	cache domain containing 1	174					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.L123I(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ACCTCTAGTTCTTGCAGACAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											142	129	133					1																	65095040		1886	4123	6009	64867628	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.520C>A	1.37:g.65095040C>A	ENSP00000360113:p.Leu174Ile		64867628	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	C	18.00	3.525345	0.64747	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.24350	1.86;1.86	5.75	5.75	0.90469	VWA N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	N	0.08118	0	0.80722	D	1	D	0.57257	0.979	D	0.74023	0.982	T	0.35001	-0.9806	10	0.48119	T	0.1	-15.1127	19.9598	0.97242	0.0:1.0:0.0:0.0	.	174	Q5VU97	CAHD1_HUMAN	I	174;123	ENSP00000360113:L174I;ENSP00000290039:L123I	ENSP00000290039:L123I	L	+	1	0	CACHD1	64867628	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.438000	0.59961	2.716000	0.92895	0.655000	0.94253	CTT		0.418	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		A	65095040	C	A	65095040	3	1	47	1	0	0	0	0	1	0	0	0	2543	913	32	2	385	2	CACHD1	1	65095040	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	451309	65095040	184155581	43	4440										
CACHD1	57685	broad.mit.edu	37	chr1	65130183	65130183	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttcctttgtttcccagttCtctgtcagaaatgaagtaat	6	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:65130183C>A	ENST00000371073.2	+	15	2097	c.2097C>A	c.(2095-2097)ttC>ttA	p.F699L	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.F648L			Q5VU97	CAHD1_HUMAN	cache domain containing 1	699					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.F648L(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TTTCCCAGTTCTCTGTCAGAA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	90	93					1																	65130183		2203	4300	6503	64902771	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2097C>A	1.37:g.65130183C>A	ENSP00000360113:p.Phe699Leu		64902771	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	C	15.20	2.763915	0.49574	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.21031	2.03;2.04	6.17	6.17	0.99709	.	0.088408	0.85682	D	0.000000	T	0.04407	0.0121	N	0.03608	-0.345	0.48762	D	0.999707	B	0.14012	0.009	B	0.11329	0.006	T	0.38023	-0.9680	10	0.23891	T	0.37	-31.8356	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	699	Q5VU97	CAHD1_HUMAN	L	699;648	ENSP00000360113:F699L;ENSP00000290039:F648L	ENSP00000290039:F648L	F	+	3	2	CACHD1	64902771	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.801000	0.27055	2.941000	0.99782	0.655000	0.94253	TTC		0.458	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		A	65130183	C	A	65130183	3	1	47	1	0	0	0	0	1	0	0	0	2543	912	32	2	2002	2	CACHD1	1	65130183	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	35143	65130183	184120438	44	4441										
LEPR	3953	broad.mit.edu	37	chr1	66102431	66102431	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataatgataaaaagtctatCtattatttaggggtcacctc	6	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:66102431C>A	ENST00000349533.6	+	20	3416	c.3231C>A	c.(3229-3231)atC>atA	p.I1077I	LEPR_ENST00000406510.3_Silent_p.I144I	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.I1077I(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AAAAGTCTATCTATTATTTAG	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	1											64	72	69					1																	66102431		2203	4300	6503	65875019	SO:0001819	synonymous_variant	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3231C>A	1.37:g.66102431C>A			65875019	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																				0.398	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		A	66102431	C	A	66102431	2	1	47	1	0	0	0	0	0	0	0	1	8750	903	32	2		2	LEPR	1	66102431	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	972248	66102431	183148190	45	4442										
IL23R	149233	broad.mit.edu	37	chr1	67724183	67724183	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatagtgaacttatgaataAtaattccagtgagcaggtcc	8	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:67724183A>G	ENST00000347310.5	+	11	1433	c.1262A>G	c.(1261-1263)aAt>aGt	p.N421S	IL23R_ENST00000371002.1_3'UTR|IL23R_ENST00000395227.1_Missense_Mutation_p.N166S|IL23R_ENST00000473881.1_3'UTR	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	421					defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)		p.N421S(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						CTTATGAATAATAATTCCAGT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	110	104					1																	67724183		2201	4299	6500	67496771	SO:0001583	missense	149233			AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.1262A>G	1.37:g.67724183A>G	ENSP00000321345:p.Asn421Ser		67496771	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	37	CCDS637.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.587|9.587	1.125022|1.125022	0.20959|0.20959	.|.	.|.	ENSG00000162594|ENSG00000162594	ENST00000425614|ENST00000347310;ENST00000431791;ENST00000441823;ENST00000395227	.|T;T	.|0.32023	.|1.47;1.55	6.07|6.07	-2.47|-2.47	0.06442|0.06442	.|.	.|0.750787	.|0.13621	.|N	.|0.374417	T|T	0.06690|0.06690	0.0171|0.0171	L|L	0.41236|0.41236	1.265|1.265	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B	.|0.13145	.|0.001;0.001;0.002;0.001;0.001;0.001;0.007	.|B;B;B;B;B;B;B	.|0.10450	.|0.004;0.005;0.004;0.004;0.004;0.004;0.005	T|T	0.41448|0.41448	-0.9508|-0.9508	5|10	.|0.17832	.|T	.|0.49	.|.	6.9958|6.9958	0.24782|0.24782	0.4389:0.1344:0.4266:0.0|0.4389:0.1344:0.4266:0.0	.|.	.|167;245;56;179;19;166;421	.|Q5VWK5-2;B6HY71;Q5VWK5-5;E9PHX4;Q5VWK5-7;Q5VWK5-6;Q5VWK5	.|.;.;.;.;.;.;IL23R_HUMAN	V|S	183|421;250;179;166	.|ENSP00000321345:N421S;ENSP00000378652:N166S	.|ENSP00000321345:N421S	I|N	+|+	1|2	0|0	IL23R|IL23R	67496771|67496771	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.641000|0.641000	0.38312|0.38312	0.187000|0.187000	0.16998|0.16998	-0.381000|-0.381000	0.07882|0.07882	0.533000|0.533000	0.62120|0.62120	ATA|AAT		0.328	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701		G	67724183	A	G	67724183	3	3	47	1	0	0	0	0	1	0	0	0	7697	101	4	4	1300	4	IL23R	1	67724183	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1621752	67724183	181526438	46	4443										
IL12RB2	3595	broad.mit.edu	37	chr1	67792444	67792444	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaacagcctcaaaatttaTcctgcatacagaagggagaa	8	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:67792444T>C	ENST00000262345.1	+	4	1031	c.391T>C	c.(391-393)Tcc>Ccc	p.S131P	IL12RB2_ENST00000371000.1_Missense_Mutation_p.S131P|IL12RB2_ENST00000544434.1_Missense_Mutation_p.S131P|IL12RB2_ENST00000541374.1_Missense_Mutation_p.S131P	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	131	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.S131P(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TCAAAATTTATCCTGCATACA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	86	86					1																	67792444		2203	4300	6503	67565032	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.391T>C	1.37:g.67792444T>C	ENSP00000262345:p.Ser131Pro		67565032	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890873	0.33348	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.89	3.49	0.39957	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.323797	0.38548	N	0.001649	T	0.31702	0.0805	M	0.85197	2.74	0.24486	N	0.994326	D;D;D;D	0.89917	0.996;1.0;0.998;0.997	D;D;D;D	0.74674	0.914;0.984;0.929;0.952	T	0.25152	-1.0140	10	0.87932	D	0	-15.3746	8.5028	0.33168	0.3108:0.0:0.0:0.6892	.	131;131;131;131	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	P	131	ENSP00000262345:S131P;ENSP00000360039:S131P;ENSP00000445276:S131P;ENSP00000442443:S131P	ENSP00000262345:S131P	S	+	1	0	IL12RB2	67565032	0.992000	0.36948	0.024000	0.17045	0.122000	0.20287	1.784000	0.38674	0.438000	0.26450	0.460000	0.39030	TCC		0.423	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67792444	T	C	67792444	3	2	47	1	0	0	0	0	1	0	0	0	7648	1435	50	4	401	4	IL12RB2	1	67792444	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	68261	67792444	181458177	47	4444										
LRRC7	57554	broad.mit.edu	37	chr1	70504011	70504011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtaatcctctcttaagttCgaaatctagaagcacatctt	5	10	3	1	rs372385321		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:70504011C>T	ENST00000035383.5	+	19	2420	c.2390C>T	c.(2389-2391)tCg>tTg	p.S797L	LRRC7_ENST00000310961.5_Missense_Mutation_p.S802L|LRRC7_ENST00000415775.2_Missense_Mutation_p.S81L	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	797						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.S797L(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CTCTTAAGTTCGAAATCTAGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	140	121	127		2390	5.5	0.1	1		127	0,8600		0,0,4300	no	missense	LRRC7	NM_020794.2	145	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	797/1538	70504011	2,13004	2203	4300	6503	70276599	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2390C>T	1.37:g.70504011C>T	ENSP00000035383:p.Ser797Leu		70276599	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.124180	0.56613	4.54E-4	0.0	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.49432	0.78;0.87;1.95	5.53	5.53	0.82687	.	0.122413	0.56097	D	0.000027	T	0.29850	0.0746	L	0.40543	1.245	0.50813	D	0.999899	P;P;P	0.45240	0.579;0.854;0.772	B;B;B	0.37144	0.104;0.242;0.122	T	0.29458	-1.0011	10	0.66056	D	0.02	.	18.4553	0.90718	0.0:1.0:0.0:0.0	.	81;797;797	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	L	802;797;81;620	ENSP00000309245:S802L;ENSP00000035383:S797L;ENSP00000394867:S81L	ENSP00000035383:S797L	S	+	2	0	LRRC7	70276599	1.000000	0.71417	0.085000	0.20634	0.889000	0.51656	7.434000	0.80377	2.614000	0.88457	0.467000	0.42956	TCG		0.488	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70504011	C	T	70504011	3	4	47	1	0	0	0	0	1	0	0	0	9049	893	31	1	2464	1	LRRC7	1	70504011	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2711567	70504011	178746610	48	4445										
LRRIQ3	127255	broad.mit.edu	37	chr1	74507110	74507110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttttcttttagaaacagaGcttttctctctctagctttt	4	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:74507110G>T	ENST00000395089.1	-	6	1504	c.1505C>A	c.(1504-1506)gCt>gAt	p.A502D	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.A502D			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	502								p.A502D(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						TAGAAACAGAGCTTTTCTCTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	105	106					1																	74507110		1796	4069	5865	74279698	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1505C>A	1.37:g.74507110G>T	ENSP00000378524:p.Ala502Asp		74279698	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	G	4.236	0.042801	0.08196	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.08634	3.07;3.07	5.86	-2.45	0.06481	.	1.942970	0.02466	N	0.087099	T	0.01489	0.0048	L	0.29908	0.895	0.09310	N	1	P	0.34462	0.454	B	0.30251	0.113	T	0.37709	-0.9694	10	0.34782	T	0.22	.	1.529	0.02531	0.278:0.2344:0.3676:0.12	.	502	A6PVS8	LRIQ3_HUMAN	D	502	ENSP00000378524:A502D;ENSP00000346414:A502D	ENSP00000346414:A502D	A	-	2	0	LRRIQ3	74279698	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.077000	0.11394	-0.628000	0.05582	-0.145000	0.13849	GCT		0.328	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		T	74507110	G	T	74507110	3	4	47	1	0	0	0	0	1	0	0	0	9059	971	34	2	377	2	LRRIQ3	1	74507110	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4003099	74507110	174743511	49	4446										
LRRIQ3	127255	broad.mit.edu	37	chr1	74575237	74575237	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttgtggaaaaacacaggGctgaatataaggggagggga	15	3	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:74575237G>A	ENST00000395089.1	-	4	707	c.708C>T	c.(706-708)agC>agT	p.S236S	LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000370909.2_Splice_Site_p.S128S|LRRIQ3_ENST00000354431.4_Splice_Site_p.S236S			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	236	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.							p.S236S(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						AAAACACAGGGCTGAATATAA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	1											101	86	90					1																	74575237		1785	4051	5836	74347825	SO:0001630	splice_region_variant	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.708-1C>T	1.37:g.74575237G>A			74347825	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																				0.313	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	Silent	A	74575237	G	A	74575237	5	1	47	1	0	0	0	0	0	0	1	0	9059	1217	42	3	1182	3	LRRIQ3	1	74575237	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	68127	74575237	174675384	50	4447										
LRRIQ3	127255	broad.mit.edu	37	chr1	74648456	74648456	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagataatacacatatattCtttaactttgcaaacccatt	3	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:74648456C>A	ENST00000395089.1	-	2	338	c.339G>T	c.(337-339)aaG>aaT	p.K113N	LRRIQ3_ENST00000370911.3_Missense_Mutation_p.K113N|LRRIQ3_ENST00000370909.2_Intron|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.K113N			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	113								p.K113N(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CACATATATTCTTTAACTTTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	74	75					1																	74648456		2203	4299	6502	74421044	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.339G>T	1.37:g.74648456C>A	ENSP00000378524:p.Lys113Asn		74421044	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.066138	0.55539	.	.	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000388972;ENST00000370911	T;T;T	0.09911	2.93;2.93;2.93	5.65	3.71	0.42584	.	0.158626	0.42420	D	0.000702	T	0.09774	0.0240	L	0.44542	1.39	0.31549	N	0.658984	D	0.64830	0.994	P	0.60286	0.872	T	0.05194	-1.0900	10	0.44086	T	0.13	.	10.5169	0.44896	0.0:0.8318:0.0:0.1682	.	113	A6PVS8	LRIQ3_HUMAN	N	113	ENSP00000378524:K113N;ENSP00000346414:K113N;ENSP00000359948:K113N	ENSP00000346414:K113N	K	-	3	2	LRRIQ3	74421044	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	1.621000	0.36986	0.666000	0.31087	-0.355000	0.07637	AAG		0.333	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		A	74648456	C	A	74648456	3	1	47	1	0	0	0	0	1	0	0	0	9059	912	32	2	1559	2	LRRIQ3	1	74648456	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	73219	74648456	174602165	51	4448										
TNNI3K	100526835	broad.mit.edu	37	chr1	74716360	74716360	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catttttctctttaaggcaaGaaatcacatattcgaactct	4	9	3	1	rs200196531		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:74716360G>T	ENST00000370899.3	+	6	580	c.543G>T	c.(541-543)aaG>aaT	p.K181N	TNNI3K_ENST00000326637.3_Missense_Mutation_p.K80N|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.K181N|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.K194N|TNNI3K_ENST00000370891.2_Missense_Mutation_p.K181N	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.K80N(1)									TTTAAGGCAAGAAATCACATA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	107	111					1																	74716360		2203	4300	6503	74488948	SO:0001583	missense	51086					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.543G>T	1.37:g.74716360G>T	ENSP00000359936:p.Lys181Asn		74488948		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	G	0.101	-1.151986	0.01700	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45	5.65	0.25	0.15535	Ankyrin repeat-containing domain (3);	0.281067	0.38272	N	0.001745	T	0.00998	0.0033	N	0.01576	-0.805	0.21147	N	0.999776	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43475	-0.9389	10	0.07030	T	0.85	.	5.5077	0.16864	0.0:0.4501:0.2491:0.3009	.	80;181;181;181	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	N	181;181;181;181;80	ENSP00000359936:K181N;ENSP00000359932:K181N;ENSP00000450895:K181N;ENSP00000359928:K181N;ENSP00000322251:K80N	ENSP00000322251:K80N	K	+	3	2	RP11-653A5.2;AC093158.1	74488948	0.999000	0.42202	0.997000	0.53966	0.486000	0.33341	0.593000	0.23999	0.007000	0.14760	-0.197000	0.12766	AAG		0.393	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74716360	G	T	74716360	3	4	47	1	0	0	0	0	1	0	0	0	16368	933	33	2	609	2	TNNI3K	1	74716360	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	67904	74716360	174534261	52	4449										
C1orf173	127254	broad.mit.edu	37	chr1	75038471	75038471	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggctggttcctctcccccaaGaattgcctcttcagaaccgt	8	15	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:75038471G>T	ENST00000326665.5	-	14	3141	c.2923C>A	c.(2923-2925)Ctt>Att	p.L975I	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		975	Glu-rich.							p.L975I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TCTCCCCCAAGAATTGCCTCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											128	118	121					1																	75038471		2203	4300	6503	74811059	SO:0001583	missense	127254																														ENST00000326665.5:c.2923C>A	1.37:g.75038471G>T	ENSP00000322609:p.Leu975Ile		74811059	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	g	13.40	2.225270	0.39300	.	.	ENSG00000178965	ENST00000326665	T	0.18174	2.23	4.65	-0.235	0.13071	.	.	.	.	.	T	0.04182	0.0116	L	0.40543	1.245	0.09310	N	1	P	0.46784	0.884	B	0.43658	0.426	T	0.23154	-1.0196	9	0.32370	T	0.25	0.2926	0.2928	0.00261	0.3139:0.229:0.2654:0.1916	.	975	Q5RHP9	CA173_HUMAN	I	975	ENSP00000322609:L975I	ENSP00000322609:L975I	L	-	1	0	C1orf173	74811059	0.000000	0.05858	0.000000	0.03702	0.439000	0.31926	-1.235000	0.02928	0.064000	0.16427	-0.358000	0.07595	CTT		0.522	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75038471	G	T	75038471	3	4	47	1	0	0	0	0	1	0	0	0	2020	942	33	2	1673	2	C1orf173	1	75038471	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	322111	75038471	174212150	53	4450										
C1orf173	127254	broad.mit.edu	37	chr1	75072551	75072551	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttcctagatttcggcaaaGacggttttttgtcaaggccc	9	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:75072551G>T	ENST00000326665.5	-	10	1441	c.1223C>A	c.(1222-1224)tCt>tAt	p.S408Y	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.S211Y	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		408								p.S408Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TTTCGGCAAAGACGGTTTTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	109	110					1																	75072551		2203	4299	6502	74845139	SO:0001583	missense	127254																														ENST00000326665.5:c.1223C>A	1.37:g.75072551G>T	ENSP00000322609:p.Ser408Tyr		74845139	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305044	0.60305	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.20463	2.53;2.07	5.14	3.23	0.37069	.	.	.	.	.	T	0.13415	0.0325	L	0.29908	0.895	0.33140	D	0.544193	P;D	0.53462	0.867;0.96	P;P	0.51918	0.509;0.684	T	0.02942	-1.1091	9	0.87932	D	0	-1.1162	11.9797	0.53113	0.1516:0.0:0.8484:0.0	.	211;408	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	Y	408;211	ENSP00000322609:S408Y;ENSP00000398581:S211Y	ENSP00000322609:S408Y	S	-	2	0	C1orf173	74845139	0.979000	0.34478	0.002000	0.10522	0.009000	0.06853	1.801000	0.38843	1.294000	0.44707	0.650000	0.86243	TCT		0.418	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75072551	G	T	75072551	3	4	47	1	0	0	0	0	1	0	0	0	2020	942	33	2	3389	2	C1orf173	1	75072551	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	34080	75072551	174178070	54	4451										
ACADM	34	broad.mit.edu	37	chr1	76198353	76198353	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccgaacagcagaaagaatTtcaagctactgctcgtaaat	7	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:76198353T>G	ENST00000370841.4	+	3	580	c.143T>G	c.(142-144)tTt>tGt	p.F48C	ACADM_ENST00000370834.5_Missense_Mutation_p.F48C|ACADM_ENST00000541113.1_Missense_Mutation_p.F12C|ACADM_ENST00000420607.2_Missense_Mutation_p.F52C|ACADM_ENST00000543667.1_5'UTR	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	48					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)	p.F48C(2)		breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	CAGAAAGAATTTCAAGCTACT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	1											97	110	105					1																	76198353		2202	4300	6502	75970941	SO:0001583	missense	34			M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.143T>G	1.37:g.76198353T>G	ENSP00000359878:p.Phe48Cys		75970941	Q5T4U4|Q9NYF1	De_novo_Start_OutOfFrame	SNP	ENST00000370841.4	37	CCDS668.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.650581	0.87958	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000420607	D;D;D;D	0.99760	-6.66;-6.66;-6.66;-6.66	5.77	5.77	0.91146	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.93328	3.405	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.998;0.997;0.998;0.998	D;D;D;D;D	0.74674	0.936;0.984;0.957;0.949;0.97	D	0.96633	0.9468	10	0.87932	D	0	.	15.757	0.78043	0.0:0.0:0.0:1.0	.	12;48;48;52;48	B7Z9I1;E9PJM9;Q5T4U5;P11310-2;P11310	.;.;.;.;ACADM_HUMAN	C	48;48;12;52	ENSP00000359878:F48C;ENSP00000359871:F48C;ENSP00000442324:F12C;ENSP00000409612:F52C	ENSP00000359871:F48C	F	+	2	0	ACADM	75970941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.517000	0.81783	2.196000	0.70406	0.528000	0.53228	TTT		0.353	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			G	76198353	T	G	76198353	3	3	47	1	0	0	0	0	1	0	0	0	113	1841	64	4	165	4	ACADM	1	76198353	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1125802	76198353	173052268	55	4452										
MSH4	4438	broad.mit.edu	37	chr1	76354993	76354993	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctaaacagatttttacaaGaattagtactgatgatgata	7	4	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:76354993G>A	ENST00000263187.3	+	16	2269	c.2165G>A	c.(2164-2166)aGa>aAa	p.R722K		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	722					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)	p.R722K(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						ATTTTTACAAGAATTAGTACT	0.264								Mismatch excision repair (MMR)																																								1	Substitution - Missense(1)	large_intestine(1)	1											51	56	54					1																	76354993		2195	4267	6462	76127581	SO:0001583	missense	4438			U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.2165G>A	1.37:g.76354993G>A	ENSP00000263187:p.Arg722Lys		76127581	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.945437	0.92593	.	.	ENSG00000057468	ENST00000263187	D	0.92446	-3.04	5.31	5.31	0.75309	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96920	0.8994	M	0.93638	3.44	0.51482	D	0.99992	D	0.56746	0.977	D	0.66084	0.941	D	0.97685	1.0175	10	0.87932	D	0	-19.4647	18.9808	0.92755	0.0:0.0:1.0:0.0	.	722	O15457	MSH4_HUMAN	K	722	ENSP00000263187:R722K	ENSP00000263187:R722K	R	+	2	0	MSH4	76127581	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	9.471000	0.97696	2.495000	0.84180	0.650000	0.86243	AGA		0.264	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		A	76354993	G	A	76354993	3	1	47	1	0	0	0	0	1	0	0	0	9902	942	33	3	2227	3	MSH4	1	76354993	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	156640	76354993	172895628	56	4453										
USP33	23032	broad.mit.edu	37	chr1	78194258	78194258	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagattcacaagactgaaaaTctacatccgactggctcttg	7	10	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:78194258T>G	ENST00000370793.1	-	11	1296	c.950A>C	c.(949-951)gAt>gCt	p.D317A	USP33_ENST00000370794.3_Missense_Mutation_p.D286A|USP33_ENST00000370792.3_Missense_Mutation_p.D317A|USP33_ENST00000357428.1_Missense_Mutation_p.D317A	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	317	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.D317A(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						AGACTGAAAATCTACATCCGA	0.373																																					Melanoma(152;72 1870 11110 26780 42647)											1	Substitution - Missense(1)	large_intestine(1)	1											189	160	170					1																	78194258		2203	4300	6503	77966846	SO:0001583	missense	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.950A>C	1.37:g.78194258T>G	ENSP00000359829:p.Asp317Ala		77966846	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476471	0.44044	.	.	ENSG00000077254	ENST00000370794;ENST00000370793;ENST00000357428;ENST00000370792	T;T;T;T	0.09723	2.96;2.95;2.95;2.95	5.3	5.3	0.74995	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.288882	0.26272	N	0.025328	T	0.04907	0.0132	L	0.44542	1.39	0.58432	D	0.999991	B;B;B	0.29341	0.078;0.234;0.242	B;B;B	0.39935	0.037;0.287;0.314	T	0.13872	-1.0493	10	0.07990	T	0.79	.	10.3329	0.43833	0.0:0.0838:0.0:0.9162	.	317;286;317	Q8TEY7-3;Q8TEY7-2;Q8TEY7	.;.;UBP33_HUMAN	A	286;317;317;317	ENSP00000359830:D286A;ENSP00000359829:D317A;ENSP00000350009:D317A;ENSP00000359828:D317A	ENSP00000350009:D317A	D	-	2	0	USP33	77966846	1.000000	0.71417	1.000000	0.80357	0.641000	0.38312	4.572000	0.60886	2.146000	0.66826	0.482000	0.46254	GAT		0.373	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		G	78194258	T	G	78194258	3	3	47	1	0	0	0	0	1	0	0	0	17104	1435	50	4	1950	4	USP33	1	78194258	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1839265	78194258	171056363	57	4454										
PTGFR	5737	broad.mit.edu	37	chr1	78959224	78959224	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatttgttggagcccatttCtggtaagagcctgaagtttt	11	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:78959224C>A	ENST00000370757.3	+	2	1033	c.796C>A	c.(796-798)Ctg>Atg	p.L266M	PTGFR_ENST00000370758.1_Missense_Mutation_p.L266M|PTGFR_ENST00000370756.3_Missense_Mutation_p.L266M	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	266					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)	p.L266M(2)		breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	GAGCCCATTTCTGGTAAGAGC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	1											36	34	35					1																	78959224		2203	4299	6502	78731812	SO:0001583	missense	5737			AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.796C>A	1.37:g.78959224C>A	ENSP00000359793:p.Leu266Met		78731812	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422338	0.62622	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.38240	1.15;1.15;1.15	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.50154	0.1599	L	0.53249	1.67	0.33664	D	0.610109	D;D	0.89917	0.983;1.0	D;D	0.91635	0.93;0.999	T	0.43163	-0.9408	10	0.46703	T	0.11	-8.9354	20.2246	0.98337	0.0:1.0:0.0:0.0	.	266;266	P43088;P43088-2	PF2R_HUMAN;.	M	266	ENSP00000359794:L266M;ENSP00000359793:L266M;ENSP00000359792:L266M	ENSP00000359792:L266M	L	+	1	2	PTGFR	78731812	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.642000	0.61383	2.861000	0.98227	0.655000	0.94253	CTG		0.413	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		A	78959224	C	A	78959224	3	1	47	1	0	0	0	0	1	0	0	0	12784	912	32	2	798	2	PTGFR	1	78959224	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	764966	78959224	170291397	58	4455										
RPF1	80135	broad.mit.edu	37	chr1	84961647	84961647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgggtcattcaattggacGtatgtttgcatctctctttc	9	9	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:84961647G>A	ENST00000370654.5	+	7	797	c.782G>A	c.(781-783)cGt>cAt	p.R261H	GNG5_ENST00000487806.1_5'Flank	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	261	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.R261H(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						TCAATTGGACGTATGTTTGCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	103	106					1																	84961647		2203	4300	6503	84734235	SO:0001583	missense	80135			AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"RNA processing factor 1", "ribosome production factor 1"		"brix domain containing 5"	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.782G>A	1.37:g.84961647G>A	ENSP00000359688:p.Arg261His		84734235	Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	37	CCDS695.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.572450	0.86542	.	.	ENSG00000117133	ENST00000370654	T	0.23552	1.9	5.96	3.01	0.34805	Brix domain (3);Anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.35885	0.0947	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.26326	-1.0106	10	0.87932	D	0	-3.0259	8.8235	0.35041	0.128:0.0:0.7492:0.1227	.	261	Q9H9Y2	RPF1_HUMAN	H	261	ENSP00000359688:R261H	ENSP00000359688:R261H	R	+	2	0	RPF1	84734235	1.000000	0.71417	0.960000	0.40013	0.986000	0.74619	7.606000	0.82863	0.871000	0.35750	0.655000	0.94253	CGT		0.388	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		A	84961647	G	A	84961647	3	1	47	1	0	0	0	0	1	0	0	0	13583	1145	40	1	808	1	RPF1	1	84961647	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6002423	84961647	164288974	59	4456										
MCOLN3	55283	broad.mit.edu	37	chr1	85488044	85488044	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacacgagcatggtagaagTcccaagaagtatgctacaga	10	10	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:85488044T>G	ENST00000370589.2	-	10	1187	c.1135A>C	c.(1135-1137)Act>Cct	p.T379P	MCOLN3_ENST00000474447.1_5'UTR|MCOLN3_ENST00000341115.4_Missense_Mutation_p.T323P|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	379					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T379P(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATGGTAGAAGTCCCAAGAAGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	82	83					1																	85488044		2203	4300	6503	85260632	SO:0001583	missense	55283			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1135A>C	1.37:g.85488044T>G	ENSP00000359621:p.Thr379Pro		85260632	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.672028	0.88348	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.70282	-0.47;-0.47	5.73	5.73	0.89815	Polycystin cation channel, PKD1/PKD2 (1);	0.181563	0.64402	D	0.000016	T	0.81669	0.4871	M	0.84511	2.7	0.52099	D	0.999949	D;D	0.60160	0.984;0.987	P;D	0.65140	0.879;0.932	D	0.83894	0.0286	10	0.51188	T	0.08	-1.9227	16.0087	0.80380	0.0:0.0:0.0:1.0	.	323;379	Q8TDD5-2;Q8TDD5	.;MCLN3_HUMAN	P	379;379;323;323	ENSP00000359621:T379P;ENSP00000342698:T323P	ENSP00000304843:T379P	T	-	1	0	MCOLN3	85260632	1.000000	0.71417	0.712000	0.30502	0.860000	0.49131	5.913000	0.69957	2.174000	0.68829	0.528000	0.53228	ACT		0.388	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85488044	T	G	85488044	3	3	47	1	0	0	0	0	1	0	0	0	9427	1667	58	4	542	4	MCOLN3	1	85488044	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	526397	85488044	163762577	60	4457										
WDR63	126820	broad.mit.edu	37	chr1	85547091	85547091	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttccacccagtcaaaaaaaTtgtccaggtaagcacaatat	5	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:85547091T>G	ENST00000294664.6	+	4	458	c.278T>G	c.(277-279)aTt>aGt	p.I93S	WDR63_ENST00000326813.8_Missense_Mutation_p.I93S|WDR63_ENST00000370596.1_Missense_Mutation_p.I93S	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	93								p.I93S(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		GTCAAAAAAATTGTCCAGGTA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											80	82	81					1																	85547091		2202	4300	6502	85319679	SO:0001583	missense	126820				CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.278T>G	1.37:g.85547091T>G	ENSP00000294664:p.Ile93Ser		85319679	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	CCDS702.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.496423	0.64186	.	.	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664;ENST00000528899	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.84	5.84	0.93424	.	0.637659	0.17010	N	0.190543	T	0.34600	0.0903	L	0.52364	1.645	0.45378	D	0.998366	B;B	0.25351	0.045;0.124	B;B	0.24155	0.032;0.051	T	0.14980	-1.0453	10	0.27785	T	0.31	-17.3174	16.2224	0.82265	0.0:0.0:0.0:1.0	.	93;93	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	S	93;93;93;80	ENSP00000359628:I93S;ENSP00000317463:I93S;ENSP00000294664:I93S;ENSP00000435102:I80S	ENSP00000294664:I93S	I	+	2	0	WDR63	85319679	0.991000	0.36638	0.020000	0.16555	0.875000	0.50365	4.619000	0.61218	2.236000	0.73375	0.528000	0.53228	ATT		0.383	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		G	85547091	T	G	85547091	3	3	47	1	0	0	0	0	1	0	0	0	17354	1493	52	4	288	4	WDR63	1	85547091	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	59047	85547091	163703530	61	4458										
ZNHIT6	54680	broad.mit.edu	37	chr1	86171989	86171989	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgtatgcagttttatctcGaactccattacatgtcagtt	6	8	2	0	rs374783757		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:86171989G>A	ENST00000370574.3	-	3	905	c.772C>T	c.(772-774)Cga>Tga	p.R258*	ZNHIT6_ENST00000431532.2_Nonsense_Mutation_p.R219*			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	258					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.R258*(3)		autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						GTTTTATCTCGAACTCCATTA	0.368																																																3	Substitution - Nonsense(3)	large_intestine(3)	1						G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	125	114	118		655,772	3.5	1	1		118	0,8600		0,0,4300	no	stop-gained,stop-gained	ZNHIT6	NM_001170670.1,NM_017953.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	219/432,258/471	86171989	1,13005	2203	4300	6503	85944577	SO:0001587	stop_gained	54680			AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.772C>T	1.37:g.86171989G>A	ENSP00000359606:p.Arg258*		85944577	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Nonsense_Mutation	SNP	ENST00000370574.3	37	CCDS707.1	.	.	.	.	.	.	.	.	.	.	G	38	6.752255	0.97813	2.27E-4	0.0	ENSG00000117174	ENST00000431532;ENST00000370574	.	.	.	5.43	3.49	0.39957	.	0.212842	0.37348	N	0.002123	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.1369	10.4817	0.44698	0.0:0.1126:0.569:0.3183	.	.	.	.	X	219;258	.	ENSP00000359606:R258X	R	-	1	2	ZNHIT6	85944577	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.807000	0.47955	0.729000	0.32403	0.650000	0.86243	CGA		0.368	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		A	86171989	G	A	86171989	4	1	47	1	0	0	0	0	0	1	0	0	18248	1066	37	1	672	1	ZNHIT6	1	86171989	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	624898	86171989	163078632	62	4459										
COL24A1	255631	broad.mit.edu	37	chr1	86590892	86590892	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcatcatgttgtgtgataTtgtcagacatgtttaggaga	10	4	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:86590892T>G	ENST00000370571.2	-	3	1493	c.1127A>C	c.(1126-1128)aAt>aCt	p.N376T	COL24A1_ENST00000436319.1_Missense_Mutation_p.N376T	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	376					extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.N376T(1)		NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTGTGTGATATTGTCAGACAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											156	139	144					1																	86590892		1919	4126	6045	86363480	SO:0001583	missense	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1127A>C	1.37:g.86590892T>G	ENSP00000359603:p.Asn376Thr		86363480	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.539178	0.00942	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	T;T	0.18016	2.24;2.24	5.45	-0.0268	0.13929	.	0.000000	0.42420	D	0.000712	T	0.02455	0.0075	L	0.27053	0.805	0.09310	N	1	B;B	0.16396	0.017;0.001	B;B	0.12156	0.007;0.002	T	0.41627	-0.9498	10	0.31617	T	0.26	.	1.816	0.03100	0.3317:0.0711:0.2304:0.3669	.	376;376	F8WDM8;Q17RW2	.;COOA1_HUMAN	T	376	ENSP00000359603:N376T;ENSP00000392531:N376T	ENSP00000359603:N376T	N	-	2	0	COL24A1	86363480	0.010000	0.17322	0.001000	0.08648	0.041000	0.13682	0.719000	0.25881	0.031000	0.15407	-0.460000	0.05396	AAT		0.368	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		G	86590892	T	G	86590892	3	3	47	1	0	0	0	0	1	0	0	0	3689	1493	52	4	4249	4	COL24A1	1	86590892	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	418903	86590892	162659729	63	4460										
ODF2L	57489	broad.mit.edu	37	chr1	86820227	86820227	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcataccttttgtcttccttCttctaaagcagcttccagtt	5	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:86820227C>A	ENST00000359242.3	-	16	2034	c.1753G>T	c.(1753-1755)Gaa>Taa	p.E585*	ODF2L_ENST00000370567.1_Nonsense_Mutation_p.E556*|ODF2L_ENST00000524695.1_5'Flank|ODF2L_ENST00000317336.7_Nonsense_Mutation_p.E585*|ODF2L_ENST00000294678.2_Nonsense_Mutation_p.E569*|ODF2L_ENST00000370566.3_Nonsense_Mutation_p.E503*|ODF2L_ENST00000394731.1_Nonsense_Mutation_p.E425*	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	585						centrosome (GO:0005813)		p.E556*(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TGTCTTCCTTCTTCTAAAGCA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											150	148	149					1																	86820227		2203	4300	6503	86592815	SO:0001587	stop_gained	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1753G>T	1.37:g.86820227C>A	ENSP00000359600:p.Glu585*		86592815	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Nonsense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.165600|8.165600	0.98686|0.98686	.|.	.|.	ENSG00000122417|ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000462648;ENST00000294678|ENST00000459999	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.192035|.	0.48767|.	D|.	0.000174|.	.|T	.|0.75496	.|0.3857	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72265	.|-0.4344	.|3	0.59425|.	D|.	0.04|.	-16.8375|-16.8375	19.545|19.545	0.95291|0.95291	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	533;503;585;432;585;556;425;92;569|351	.|.	ENSP00000294678:E569X|.	E|K	-|-	1|3	0|2	ODF2L|ODF2L	86592815|86592815	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.555000|0.555000	0.35460|0.35460	5.996000|5.996000	0.70639|0.70639	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.353	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86820227	C	A	86820227	4	1	47	1	0	0	0	0	0	1	0	0	10859	922	32	2	302	2	ODF2L	1	86820227	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	229335	86820227	162430394	64	4461										
CLCA1	1179	broad.mit.edu	37	chr1	86939207	86939207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatggaagacaaaggctgaCtatgtgagaccaaaacttga	10	7	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:86939207C>T	ENST00000234701.3	+	3	621	c.270C>T	c.(268-270)gaC>gaT	p.D90D	CLCA1_ENST00000394711.1_Silent_p.D90D			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	90	Metalloprotease domain. {ECO:0000269|PubMed:23112050}.				calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)	p.D90D(1)		NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CAAAGGCTGACTATGTGAGAC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											60	61	61					1																	86939207		2203	4300	6503	86711795	SO:0001819	synonymous_variant	1179				CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.270C>T	1.37:g.86939207C>T			86711795	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																				0.348	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		T	86939207	C	T	86939207	2	4	47	1	0	0	0	0	0	0	0	1	3463	564	20	3		3	CLCA1	1	86939207	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	118980	86939207	162311414	65	4462										
CLCA1	1179	broad.mit.edu	37	chr1	86960066	86960066	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccaattctcagggccagtgTcacagccctgattgaatcag	9	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:86960066T>G	ENST00000234701.3	+	12	2228	c.1877T>G	c.(1876-1878)gTc>gGc	p.V626G	CLCA1_ENST00000394711.1_Missense_Mutation_p.V626G			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	626					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)	p.V626G(1)		NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AGGGCCAGTGTCACAGCCCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	64	65					1																	86960066		2203	4300	6503	86732654	SO:0001583	missense	1179				CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1877T>G	1.37:g.86960066T>G	ENSP00000234701:p.Val626Gly		86732654	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	37	CCDS709.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.9|22.9	4.349961|4.349961	0.82132|0.82132	.|.	.|.	ENSG00000016490|ENSG00000016490	ENST00000539889|ENST00000234701;ENST00000394711	.|T;T	.|0.52754	.|0.65;0.65	5.93|5.93	5.93|5.93	0.95920|0.95920	.|Domain of unknown function DUF1973 (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.71082|0.71082	0.3298|0.3298	M|M	0.90977|0.90977	3.165|3.165	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.79032|0.79032	-0.1969|-0.1969	6|10	0.72032|0.87932	D|D	0.01|0	-22.2277|-22.2277	16.0381|16.0381	0.80645|0.80645	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|626;389	.|A8K7I4;B4DUZ6	.|CLCA1_HUMAN;.	W|G	324|626	.|ENSP00000234701:V626G;ENSP00000378200:V626G	ENSP00000443173:C324W|ENSP00000234701:V626G	C|V	+|+	3|2	2|0	CLCA1|CLCA1	86732654|86732654	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.964000|0.964000	0.63967|0.63967	6.039000|6.039000	0.70972|0.70972	2.263000|2.263000	0.75096|0.75096	0.533000|0.533000	0.62120|0.62120	TGT|GTC		0.443	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		G	86960066	T	G	86960066	3	3	47	1	0	0	0	0	1	0	0	0	3463	1667	58	4	1919	4	CLCA1	1	86960066	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	20859	86960066	162290555	66	4463										
GBP7	388646	broad.mit.edu	37	chr1	89598059	89598059	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgactcaaatatctctttaaAtccttcagtaagcagttctt	4	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:89598059A>C	ENST00000294671.2	-	11	1828	c.1690T>G	c.(1690-1692)Ttt>Gtt	p.F564V		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	564						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F564V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		ATCTCTTTAAATCCTTCAGTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	78	78					1																	89598059		2203	4300	6503	89370647	SO:0001583	missense	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1690T>G	1.37:g.89598059A>C	ENSP00000294671:p.Phe564Val		89370647		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.306046	0.60305	.	.	ENSG00000213512	ENST00000294671	T	0.02837	4.14	4.18	4.18	0.49190	Guanylate-binding protein, C-terminal (3);	0.622631	0.15965	N	0.236078	T	0.10680	0.0261	H	0.94808	3.585	0.27159	N	0.961205	D	0.55800	0.973	D	0.64410	0.925	T	0.12889	-1.0530	10	0.66056	D	0.02	.	9.564	0.39387	1.0:0.0:0.0:0.0	.	564	Q8N8V2	GBP7_HUMAN	V	564	ENSP00000294671:F564V	ENSP00000294671:F564V	F	-	1	0	GBP7	89370647	0.387000	0.25188	0.122000	0.21767	0.007000	0.05969	1.377000	0.34317	1.746000	0.51805	0.460000	0.39030	TTT		0.338	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		C	89598059	A	C	89598059	3	2	47	1	0	0	0	0	1	0	0	0	6299	101	4	4	230	4	GBP7	1	89598059	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2637993	89598059	159652562	67	4464										
HFM1	164045	broad.mit.edu	37	chr1	91781472	91781472	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttagtttgtagctgttcaaAatttcttaatataacagtca	5	5	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:91781472A>C	ENST00000370425.3	-	28	3138	c.3040T>G	c.(3040-3042)Ttt>Gtt	p.F1014V	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.F693V|HFM1_ENST00000294696.5_Missense_Mutation_p.F246V	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1014	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.F1014V(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGCTGTTCAAAATTTCTTAAT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	70	70					1																	91781472		2200	4298	6498	91554060	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3040T>G	1.37:g.91781472A>C	ENSP00000359454:p.Phe1014Val		91554060	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.31|11.31	1.602222|1.602222	0.28534|0.28534	.|.	.|.	ENSG00000162669|ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421|ENST00000430465	T;T;T|.	0.59906|.	0.23;0.23;0.23|.	5.25|5.25	5.25|5.25	0.73442|0.73442	Sec63 domain (2);|.	0.238496|.	0.38720|.	N|.	0.001588|.	T|T	0.61413|0.61413	0.2345|0.2345	L|L	0.59436|0.59436	1.845|1.845	0.41952|0.41952	D|D	0.990665|0.990665	P;D;P|.	0.55172|.	0.868;0.97;0.889|.	B;P;P|.	0.54965|.	0.4;0.765;0.534|.	T|T	0.62310|0.62310	-0.6881|-0.6881	10|5	0.25106|.	T|.	0.35|.	.|.	15.1412|15.1412	0.72612|0.72612	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	693;225;1014|.	A6NGI5;B1B0B5;A2PYH4|.	.;.;HFM1_HUMAN|.	V|M	1014;246;693;698|225	ENSP00000359454:F1014V;ENSP00000294696:F246V;ENSP00000359453:F693V|.	ENSP00000294696:F246V|.	F|I	-|-	1|3	0|3	HFM1|HFM1	91554060|91554060	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.458000|0.458000	0.32498|0.32498	5.737000|5.737000	0.68606|0.68606	1.992000|1.992000	0.58205|0.58205	0.377000|0.377000	0.23210|0.23210	TTT|ATT		0.303	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91781472	A	C	91781472	3	2	47	1	0	0	0	0	1	0	0	0	7104	14	1	4	1315	4	HFM1	1	91781472	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2183413	91781472	157469149	68	4465										
HFM1	164045	broad.mit.edu	37	chr1	91818705	91818705	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagcagcaccatcttttaaGatatctgtaatagaaatata	5	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:91818705G>T	ENST00000370425.3	-	15	1832	c.1734C>A	c.(1732-1734)atC>atA	p.I578I	HFM1_ENST00000462405.1_5'Flank|HFM1_ENST00000370424.3_Silent_p.I257I|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	578	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.I578I(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CATCTTTTAAGATATCTGTAA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	1											84	77	79					1																	91818705		1809	4071	5880	91591293	SO:0001819	synonymous_variant	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1734C>A	1.37:g.91818705G>T			91591293	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2																																																																																				0.318	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		T	91818705	G	T	91818705	2	4	47	1	0	0	0	0	0	0	0	1	7104	932	33	2		2	HFM1	1	91818705	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	37233	91818705	157431916	69	4466										
BRDT	676	broad.mit.edu	37	chr1	92430235	92430235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttaaatacaattaagaagCgcttggagaataaatattat	6	3	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:92430235C>T	ENST00000362005.3	+	4	662	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	BRDT_ENST00000402388.1_Missense_Mutation_p.R82C|BRDT_ENST00000394530.3_Intron|BRDT_ENST00000370389.2_Missense_Mutation_p.R9C|BRDT_ENST00000399546.2_Missense_Mutation_p.R82C	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	82	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)	p.R82C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AATTAAGAAGCGCTTGGAGAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	1											27	29	28					1																	92430235		2182	4274	6456	92202823	SO:0001583	missense	676			AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.244C>T	1.37:g.92430235C>T	ENSP00000354568:p.Arg82Cys		92202823	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.851446	0.71719	.	.	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000423434;ENST00000440509;ENST00000427104;ENST00000448194;ENST00000426141;ENST00000450792;ENST00000548992;ENST00000552654;ENST00000402388	T;T;T;T;T;T;T;T;T;T;T;T	0.51325	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93;0.71;1.93;1.93;1.93	5.67	5.67	0.87782	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000003	T	0.72961	0.3526	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80358	-0.1416	10	0.87932	D	0	-7.13	14.295	0.66304	0.1488:0.8512:0.0:0.0	.	82;82	B7Z890;Q58F21	.;BRDT_HUMAN	C	82;9;82;82;82;82;82;82;82;82;82;9;82	ENSP00000354568:R82C;ENSP00000359416:R9C;ENSP00000387822:R82C;ENSP00000396351:R82C;ENSP00000416714:R82C;ENSP00000400002:R82C;ENSP00000410587:R82C;ENSP00000404969:R82C;ENSP00000414349:R82C;ENSP00000447394:R82C;ENSP00000446599:R9C;ENSP00000384051:R82C	ENSP00000354568:R82C	R	+	1	0	BRDT	92202823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.151000	0.42263	2.690000	0.91761	0.650000	0.86243	CGC		0.274	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		T	92430235	C	T	92430235	3	4	47	1	0	0	0	0	1	0	0	0	1511	768	27	1	250	1	BRDT	1	92430235	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	611530	92430235	156820386	70	4467										
EPHX4	253152	broad.mit.edu	37	chr1	92508385	92508385	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttttttcctgcaggtattCttggcgttaccaactgagag	9	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:92508385C>A	ENST00000370383.4	+	3	421	c.323C>A	c.(322-324)tCt>tAt	p.S108Y	EPHX4_ENST00000480758.1_3'UTR	NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	108						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.S108Y(1)		central_nervous_system(1)|large_intestine(3)|lung(8)	12						TGCAGGTATTCTTGGCGTTAC	0.323																																					GBM(140;473 1857 5172 22066 49719)											1	Substitution - Missense(1)	large_intestine(1)	1											84	86	85					1																	92508385		2203	4300	6503	92280973	SO:0001583	missense	253152			AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"Abhydrolase domain containing"	23758	protein-coding gene	gene with protein product			"abhydrolase domain containing 7"	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.323C>A	1.37:g.92508385C>A	ENSP00000359410:p.Ser108Tyr		92280973	Q8NCC6	Missense_Mutation	SNP	ENST00000370383.4	37	CCDS736.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.821208	0.90873	.	.	ENSG00000172031	ENST00000370383	T	0.04275	3.66	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.09465	-1.0673	10	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	108	Q8IUS5	EPHX4_HUMAN	Y	108	ENSP00000359410:S108Y	ENSP00000359410:S108Y	S	+	2	0	EPHX4	92280973	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.901000	0.75693	2.854000	0.98071	0.655000	0.94253	TCT		0.323	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567		A	92508385	C	A	92508385	3	1	47	1	0	0	0	0	1	0	0	0	5195	913	32	2	333	2	EPHX4	1	92508385	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	78150	92508385	156742236	71	4468										
ALG14	199857	broad.mit.edu	37	chr1	95530462	95530462	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagctcgatctagttcaaaaGaatttattttattggcactc	6	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:95530462G>T	ENST00000370205.5	-	2	294	c.248C>A	c.(247-249)tCt>tAt	p.S83Y	RP11-313A24.1_ENST00000451611.1_RNA|ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	83					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.S83Y(1)		endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		TAGTTCAAAAGAATTTATTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											141	140	140					1																	95530462		2203	4299	6502	95303050	SO:0001583	missense	199857				CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"asparagine-linked glycosylation 14 homolog (yeast)", "asparagine-linked glycosylation 14 homolog (S. cerevisiae)"			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.248C>A	1.37:g.95530462G>T	ENSP00000359224:p.Ser83Tyr		95303050	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	.	.	.	.	.	.	.	.	.	.	g	5.227	0.227305	0.09916	.	.	ENSG00000172339	ENST00000370205	T	0.77358	-1.09	5.82	2.42	0.29668	.	0.444819	0.24185	N	0.040779	T	0.49966	0.1588	L	0.49126	1.545	0.09310	N	1	B	0.29805	0.257	B	0.28553	0.091	T	0.46748	-0.9169	10	0.56958	D	0.05	-0.4015	4.6321	0.12507	0.1345:0.1359:0.5908:0.1389	.	83	Q96F25	ALG14_HUMAN	Y	83	ENSP00000359224:S83Y	ENSP00000359224:S83Y	S	-	2	0	ALG14	95303050	0.940000	0.31905	0.571000	0.28486	0.074000	0.17049	2.247000	0.43151	0.763000	0.33175	-0.215000	0.12644	TCT		0.378	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		T	95530462	G	T	95530462	3	4	47	1	0	0	0	0	1	0	0	0	516	942	33	2	414	2	ALG14	1	95530462	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3022077	95530462	153720159	72	4469										
DPYD	1806	broad.mit.edu	37	chr1	97564144	97564144	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaatcttgttttctgctatGattttcttgcgctgttccag	7	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:97564144G>T	ENST00000370192.3	-	21	2767	c.2667C>A	c.(2665-2667)atC>atA	p.I889I	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	889					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.I889I(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TTTCTGCTATGATTTTCTTGC	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											121	121	121					1																	97564144		2203	4300	6503	97336732	SO:0001819	synonymous_variant	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2667C>A	1.37:g.97564144G>T			97336732	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Silent	SNP	ENST00000370192.3	37	CCDS30777.1																																																																																				0.373	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	97564144	G	T	97564144	2	4	47	1	0	0	0	0	0	0	0	1	4756	1280	45	2		2	DPYD	1	97564144	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2033682	97564144	151686477	73	4470										
LPPR4	9890	broad.mit.edu	37	chr1	99771647	99771647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaataagaatgaaagtcGaaagttgtccttgcaagtta	10	4	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:99771647G>A	ENST00000370185.3	+	7	1870	c.1373G>A	c.(1372-1374)cGa>cAa	p.R458Q	LPPR4_ENST00000457765.1_Missense_Mutation_p.R400Q|LPPR4_ENST00000370184.1_Missense_Mutation_p.R300Q	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		458					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.R458Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		AATGAAAGTCGAAAGTTGTCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	70	71					1																	99771647		2203	4300	6503	99544235	SO:0001583	missense	9890																														ENST00000370185.3:c.1373G>A	1.37:g.99771647G>A	ENSP00000359204:p.Arg458Gln		99544235	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.858871	0.51376	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	T;T;T	0.30448	2.08;1.97;1.53	5.5	5.5	0.81552	.	0.107611	0.64402	D	0.000005	T	0.29556	0.0737	L	0.58810	1.83	0.58432	D	0.999991	D;D	0.57899	0.981;0.964	P;B	0.47044	0.535;0.248	T	0.02282	-1.1183	9	.	.	.	-18.2466	19.3904	0.94578	0.0:0.0:1.0:0.0	.	400;458	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	Q	458;400;458;300	ENSP00000359204:R458Q;ENSP00000394913:R400Q;ENSP00000359203:R300Q	.	R	+	2	0	RP4-788L13.1	99544235	1.000000	0.71417	0.290000	0.24890	0.837000	0.47467	5.975000	0.70475	2.575000	0.86900	0.650000	0.86243	CGA		0.493	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			A	99771647	G	A	99771647	3	1	47	1	0	0	0	0	1	0	0	0	8956	1058	37	1	1399	1	LPPR4	1	99771647	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2207503	99771647	149478974	74	4471										
CDC14A	8556	broad.mit.edu	37	chr1	100819343	100819343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatattttgctactttaagGaatagaccaaaaagcacagt	6	6	0	1	rs532210944		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:100819343G>T	ENST00000336454.3	+	2	430	c.75G>T	c.(73-75)agG>agT	p.R25S	CDC14A_ENST00000544534.1_Missense_Mutation_p.R25S|CDC14A_ENST00000370125.2_Missense_Mutation_p.R25S|CDC14A_ENST00000361544.6_Missense_Mutation_p.R25S|CDC14A_ENST00000370124.3_Missense_Mutation_p.R25S|CDC14A_ENST00000542213.1_5'UTR	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	25	A.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R25S(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		CTACTTTAAGGAATAGACCAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	108	114					1																	100819343		2203	4300	6503	100591931	SO:0001583	missense	8556			AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.75G>T	1.37:g.100819343G>T	ENSP00000336739:p.Arg25Ser		100591931	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	37	CCDS769.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992695	0.35131	.	.	ENSG00000079335	ENST00000455467;ENST00000370125;ENST00000361544;ENST00000370124;ENST00000336454;ENST00000544534	T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.32971	0.0847	L	0.50847	1.595	0.80722	D	1	B;B;B;P;B	0.45672	0.249;0.09;0.249;0.864;0.054	B;B;B;P;B	0.44696	0.131;0.085;0.131;0.458;0.039	T	0.10451	-1.0629	10	0.41790	T	0.15	-13.8031	16.9976	0.86372	0.0:0.0:1.0:0.0	.	25;25;25;25;25	A6MA65;Q9UNH5-3;Q9UNH5;Q9UNH5-2;Q52LH9	.;.;CC14A_HUMAN;.;.	S	26;25;25;25;25;25	ENSP00000388501:R26S;ENSP00000359143:R25S;ENSP00000354916:R25S;ENSP00000359142:R25S;ENSP00000336739:R25S;ENSP00000442543:R25S	ENSP00000336739:R25S	R	+	3	2	CDC14A	100591931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.954000	0.40362	2.399000	0.81585	0.555000	0.69702	AGG		0.348	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		T	100819343	G	T	100819343	3	4	47	1	0	0	0	0	1	0	0	0	3062	1165	41	2	81	2	CDC14A	1	100819343	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1047696	100819343	148431278	75	4472										
CDC14A	8556	broad.mit.edu	37	chr1	100949997	100949997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaacacaaaacatggaacGatttggagaggtaagttttc	9	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:100949997G>A	ENST00000336454.3	+	11	1482	c.1127G>A	c.(1126-1128)cGa>cAa	p.R376Q	CDC14A_ENST00000544534.1_Missense_Mutation_p.R376Q|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000361544.6_Missense_Mutation_p.R376Q|CDC14A_ENST00000370124.3_Missense_Mutation_p.R376Q|CDC14A_ENST00000542213.1_Missense_Mutation_p.R318Q	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	376					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R376Q(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AACATGGAACGATTTGGAGAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	80	79					1																	100949997		2203	4300	6503	100722585	SO:0001583	missense	8556			AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.1127G>A	1.37:g.100949997G>A	ENSP00000336739:p.Arg376Gln		100722585	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	37	CCDS769.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.376372	0.42105	.	.	ENSG00000079335	ENST00000542213;ENST00000361544;ENST00000370124;ENST00000336454;ENST00000544534	T;T;T;T;T	0.10192	2.9;2.91;2.93;3.1;2.91	5.65	4.74	0.60224	.	0.102203	0.64402	D	0.000003	T	0.03651	0.0104	L	0.54323	1.7	0.40055	D	0.975824	P;B;B;B;B	0.37276	0.589;0.107;0.223;0.122;0.018	B;B;B;B;B	0.25987	0.065;0.018;0.017;0.041;0.003	T	0.37820	-0.9689	10	0.19590	T	0.45	-12.5582	11.6993	0.51560	0.0832:0.0:0.9168:0.0	.	318;376;376;376;376	F5H7B3;A6MA65;Q9UNH5;Q9UNH5-2;Q52LH9	.;.;CC14A_HUMAN;.;.	Q	318;376;376;376;376	ENSP00000442640:R318Q;ENSP00000354916:R376Q;ENSP00000359142:R376Q;ENSP00000336739:R376Q;ENSP00000442543:R376Q	ENSP00000336739:R376Q	R	+	2	0	CDC14A	100722585	0.999000	0.42202	0.968000	0.41197	0.618000	0.37518	1.806000	0.38892	1.384000	0.46424	0.555000	0.69702	CGA		0.343	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		A	100949997	G	A	100949997	3	1	47	1	0	0	0	0	1	0	0	0	3062	1058	37	1	1169	1	CDC14A	1	100949997	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	130654	100949997	148300624	76	4473										
VCAM1	7412	broad.mit.edu	37	chr1	101200232	101200232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatggcgcctataccatccGaaaggcccagttgaaggatg	12	10	0	2	rs200879051		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:101200232G>A	ENST00000294728.2	+	8	2068	c.1967G>A	c.(1966-1968)cGa>cAa	p.R656Q	VCAM1_ENST00000370115.1_Missense_Mutation_p.R457Q|VCAM1_ENST00000347652.2_Missense_Mutation_p.R564Q|VCAM1_ENST00000370119.4_Missense_Mutation_p.R594Q	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	656	Ig-like C2-type 7.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)	p.R656Q(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TATACCATCCGAAAGGCCCAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	96	95					1																	101200232		2203	4300	6503	100972820	SO:0001583	missense	7412			M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1967G>A	1.37:g.101200232G>A	ENSP00000294728:p.Arg656Gln		100972820	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	G	6.384	0.439050	0.12104	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.77	-3.22	0.05125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.857483	0.11060	N	0.604085	T	0.15262	0.0368	L	0.28649	0.875	0.09310	N	1	B;B;B	0.19200	0.002;0.0;0.034	B;B;B	0.14578	0.001;0.001;0.011	T	0.16100	-1.0414	10	0.12430	T	0.62	-0.0142	0.7736	0.01028	0.386:0.1774:0.2446:0.192	.	594;564;656	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	Q	594;564;656;457	ENSP00000359137:R594Q;ENSP00000304611:R564Q;ENSP00000294728:R656Q;ENSP00000359133:R457Q	ENSP00000294728:R656Q	R	+	2	0	VCAM1	100972820	0.000000	0.05858	0.262000	0.24481	0.187000	0.23431	-1.234000	0.02931	-0.386000	0.07821	-0.122000	0.15005	CGA		0.393	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		A	101200232	G	A	101200232	3	1	47	1	0	0	0	0	1	0	0	0	17177	1058	37	1	1997	1	VCAM1	1	101200232	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	250235	101200232	148050389	77	4474										
S1PR1	1901	broad.mit.edu	37	chr1	101705030	101705030	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttccgcctcttcctgctaAtcagcgcctgctgggtcatc	8	16	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:101705030A>G	ENST00000305352.6	+	2	865	c.490A>G	c.(490-492)Atc>Gtc	p.I164V	RP4-575N6.4_ENST00000432195.1_RNA|S1PR1_ENST00000475821.1_3'UTR	NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	164					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.I164V(1)		NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						CTTCCTGCTAATCAGCGCCTG	0.567											OREG0013620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											103	96	98					1																	101705030		2203	4300	6503	101477618	SO:0001583	missense	1901			M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate", "CD molecules"	3165	protein-coding gene	gene with protein product		601974	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.490A>G	1.37:g.101705030A>G	ENSP00000305416:p.Ile164Val	1360	101477618	D3DT66|Q9BYY4|Q9NYN8	Missense_Mutation	SNP	ENST00000305352.6	37	CCDS777.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.480655	0.63849	.	.	ENSG00000170989	ENST00000305352;ENST00000424264	T	0.74421	-0.84	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.048325	0.85682	D	0.000000	T	0.81427	0.4820	M	0.78223	2.4	0.80722	D	1	P	0.45212	0.853	P	0.58266	0.836	D	0.83705	0.0184	10	0.59425	D	0.04	.	15.5483	0.76126	1.0:0.0:0.0:0.0	.	164	P21453	S1PR1_HUMAN	V	164	ENSP00000305416:I164V	ENSP00000305416:I164V	I	+	1	0	S1PR1	101477618	1.000000	0.71417	0.951000	0.38953	0.733000	0.41908	9.227000	0.95236	2.064000	0.61679	0.374000	0.22700	ATC		0.567	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400		G	101705030	A	G	101705030	3	3	47	1	0	0	0	0	1	0	0	0	13830	101	4	4	492	4	S1PR1	1	101705030	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	504798	101705030	147545591	78	4475										
COL11A1	1301	broad.mit.edu	37	chr1	103352503	103352503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatttcttccattccatccGagtaatcaagaatattatca	3	9	3	1	rs143531636	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:103352503G>A	ENST00000370096.3	-	63	5030	c.4718C>T	c.(4717-4719)tCg>tTg	p.S1573L	COL11A1_ENST00000353414.4_Missense_Mutation_p.S1534L|COL11A1_ENST00000512756.1_Missense_Mutation_p.S1457L|COL11A1_ENST00000358392.2_Missense_Mutation_p.S1585L	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1573					cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.S1585L(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		CATTCCATCCGAGTAATCAAG	0.408													G|||	2	0.000399361	0	0.0029	5008	,	,		17113	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	LEU/SER,LEU/SER,LEU/SER,LEU/SER	1,4405		0,1,2202	202	188	193		4370,4754,4718,4601	4.6	0.8	1	dbSNP_134	193	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	COL11A1	NM_080630.3,NM_080629.2,NM_001854.3,NM_001190709.1	145,145,145,145	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign,benign,benign	1457/1691,1585/1819,1573/1807,1534/1768	103352503	2,13004	2203	4300	6503	103125091	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4718C>T	1.37:g.103352503G>A	ENSP00000359114:p.Ser1573Leu		103125091	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	14.75	2.629512	0.46944	2.27E-4	1.16E-4	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.88741	-2.36;-2.37;-2.37;-2.42	5.53	4.61	0.57282	.	0.357495	0.29602	N	0.011699	T	0.79358	0.4432	L	0.50333	1.59	0.38231	D	0.941034	B;B;B;B;B	0.26975	0.043;0.072;0.165;0.103;0.021	B;B;B;B;B	0.22152	0.012;0.026;0.038;0.017;0.016	T	0.76881	-0.2795	10	0.35671	T	0.21	.	15.7266	0.77766	0.0:0.0:0.8621:0.1379	.	1457;1534;1585;1573;793	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	L	1573;1585;1534;793;1457	ENSP00000359114:S1573L;ENSP00000351163:S1585L;ENSP00000302551:S1534L;ENSP00000426533:S1457L	ENSP00000302551:S1534L	S	-	2	0	COL11A1	103125091	0.997000	0.39634	0.802000	0.32245	0.871000	0.50021	4.258000	0.58822	1.325000	0.45301	0.313000	0.20887	TCG		0.408	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103352503	G	A	103352503	3	1	47	1	0	0	0	0	1	0	0	0	3673	1059	37	1	722	1	COL11A1	1	103352503	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1647473	103352503	145898118	79	4476										
AMY2B	280	broad.mit.edu	37	chr1	104116508	104116508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattttggacaaactgcataAtctaaacagtaactggttcc	6	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:104116508A>C	ENST00000361355.4	+	6	1308	c.692A>C	c.(691-693)aAt>aCt	p.N231T	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	231					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)	p.N231T(1)		breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		AAACTGCATAATCTAAACAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											173	172	172					1																	104116508		2203	4297	6500	103918031	SO:0001583	missense	280			M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"amylase, alpha 2B; pancreatic"	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.692A>C	1.37:g.104116508A>C	ENSP00000354610:p.Asn231Thr		103918031	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180866	0.38511	.	.	ENSG00000240038	ENST00000361355	D	0.98264	-4.83	4.47	4.47	0.54385	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.109676	0.64402	D	0.000011	D	0.96046	0.8712	M	0.74467	2.265	0.58432	D	0.999999	B	0.13145	0.007	B	0.13407	0.009	D	0.95562	0.8630	10	0.56958	D	0.05	.	13.7962	0.63173	1.0:0.0:0.0:0.0	.	231	P19961	AMY2B_HUMAN	T	231	ENSP00000354610:N231T	ENSP00000354610:N231T	N	+	2	0	AMY2B	103918031	1.000000	0.71417	0.996000	0.52242	0.337000	0.28794	6.148000	0.71788	1.662000	0.50781	0.451000	0.29950	AAT		0.373	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		C	104116508	A	C	104116508	3	2	47	1	0	0	0	0	1	0	0	0	595	101	4	4	706	4	AMY2B	1	104116508	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	764005	104116508	145134113	80	4477										
SORT1	6272	broad.mit.edu	37	chr1	109910090	109910090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggtacatggaaggtagtcAagactagaatgacctggaga	14	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:109910090A>G	ENST00000256637.6	-	3	438	c.380T>C	c.(379-381)tTg>tCg	p.L127S	SORT1_ENST00000482236.1_5'UTR|SORT1_ENST00000538502.1_5'UTR	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	127					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)	p.L127S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		GAAGGTAGTCAAGACTAGAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											166	164	165					1																	109910090		2203	4300	6503	109711613	SO:0001583	missense	6272			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.380T>C	1.37:g.109910090A>G	ENSP00000256637:p.Leu127Ser		109711613	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.012068	0.75046	.	.	ENSG00000134243	ENST00000256637	T	0.47528	0.84	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.61887	0.2383	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69003	-0.5260	10	0.87932	D	0	-10.2568	11.7338	0.51752	1.0:0.0:0.0:0.0	.	127	Q99523	SORT_HUMAN	S	127	ENSP00000256637:L127S	ENSP00000256637:L127S	L	-	2	0	SORT1	109711613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.127000	0.71642	2.029000	0.59856	0.477000	0.44152	TTG		0.378	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959		G	109910090	A	G	109910090	3	3	47	1	0	0	0	0	1	0	0	0	14972	131	5	4	2187	4	SORT1	1	109910090	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	5793582	109910090	139340531	81	4478										
RBM15	64783	broad.mit.edu	37	chr1	110883615	110883615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtagactttgccgacaccGaacatcgttaccagcagcag	10	12	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:110883615G>A	ENST00000369784.3	+	1	2488	c.1588G>A	c.(1588-1590)Gaa>Aaa	p.E530K	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.E530K|RBM15_ENST00000487146.2_Missense_Mutation_p.E530K	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	530					negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E530K(1)		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)		TGCCGACACCGAACATCGTTA	0.562			T	MKL1	acute megakaryocytic leukemia																																		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	1	Substitution - Missense(1)	large_intestine(1)	1											83	82	82					1																	110883615		2203	4300	6503	110685138	SO:0001583	missense	64783			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1588G>A	1.37:g.110883615G>A	ENSP00000358799:p.Glu530Lys		110685138	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061210	0.76187	.	.	ENSG00000162775	ENST00000369784	T	0.22336	1.96	4.44	4.44	0.53790	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.44483	D	0.000444	T	0.18841	0.0452	L	0.57536	1.79	0.80722	D	1	P;D	0.63046	0.88;0.992	B;P	0.45577	0.13;0.486	T	0.03807	-1.1002	10	0.59425	D	0.04	-10.7667	17.2705	0.87101	0.0:0.0:1.0:0.0	.	530;530	Q96T37-3;Q96T37	.;RBM15_HUMAN	K	530	ENSP00000358799:E530K	ENSP00000358799:E530K	E	+	1	0	RBM15	110685138	1.000000	0.71417	0.989000	0.46669	0.754000	0.42855	9.263000	0.95617	2.306000	0.77630	0.655000	0.94253	GAA		0.562	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		A	110883615	G	A	110883615	3	1	47	1	0	0	0	0	1	0	0	0	13153	1059	37	1	1590	1	RBM15	1	110883615	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	973525	110883615	138367006	82	4479										
KCNA3	3738	broad.mit.edu	37	chr1	111216003	111216003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagttggaaacaatcacggGaactggcaatgcgatggtca	13	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:111216003G>A	ENST00000369769.2	-	1	1652	c.1429C>T	c.(1429-1431)Ccc>Tcc	p.P477S		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	477					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)	p.P477S(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	ACAATCACGGGAACTGGCAAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	76	82					1																	111216003		2203	4300	6503	111017526	SO:0001583	missense	3738			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1429C>T	1.37:g.111216003G>A	ENSP00000358784:p.Pro477Ser		111017526	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	37	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002086	0.74932	.	.	ENSG00000177272	ENST00000369769	D	0.98419	-4.92	5.91	5.91	0.95273	Ion transport (1);	0.000000	0.85682	U	0.000000	D	0.98855	0.9613	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99872	1.1098	10	0.87932	D	0	.	20.2896	0.98541	0.0:0.0:1.0:0.0	.	477	P22001	KCNA3_HUMAN	S	477	ENSP00000358784:P477S	ENSP00000358784:P477S	P	-	1	0	KCNA3	111017526	1.000000	0.71417	0.486000	0.27416	0.889000	0.51656	9.864000	0.99589	2.794000	0.96219	0.655000	0.94253	CCC		0.537	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		A	111216003	G	A	111216003	3	1	47	1	0	0	0	0	1	0	0	0	8025	1174	41	3	302	3	KCNA3	1	111216003	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	332388	111216003	138034618	83	4480										
SYT6	148281	broad.mit.edu	37	chr1	114680549	114680549	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccccatccaccgacttctgCttgtagagctcaggcttgat	8	14	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:114680549C>A	ENST00000610222.1	-	3	785	c.639G>T	c.(637-639)aaG>aaT	p.K213N	SYT6_ENST00000393296.1_Missense_Mutation_p.K213N|SYT6_ENST00000607941.1_Missense_Mutation_p.K128N|SYT6_ENST00000369547.1_Missense_Mutation_p.K128N|SYT6_ENST00000609117.1_Missense_Mutation_p.K128N			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	213					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.K128N(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-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)		CCGACTTCTGCTTGTAGAGCT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	94	98					1																	114680549		2203	4300	6503	114482072	SO:0001583	missense	148281				CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.639G>T	1.37:g.114680549C>A	ENSP00000476396:p.Lys213Asn		114482072	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	37		.	.	.	.	.	.	.	.	.	.	C	17.82	3.482473	0.63962	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.60672	0.19;0.17;0.19;0.17	5.56	4.65	0.58169	.	0.051709	0.85682	D	0.000000	T	0.62417	0.2426	M	0.81802	2.56	0.54753	D	0.999984	D	0.54772	0.968	P	0.58660	0.843	T	0.69491	-0.5131	10	0.87932	D	0	.	8.7587	0.34661	0.0:0.7219:0.0:0.2781	.	213	Q5T7P8	SYT6_HUMAN	N	128;213;128;213	ENSP00000358560:K128N;ENSP00000376974:K213N;ENSP00000358559:K128N;ENSP00000358558:K213N	ENSP00000358558:K213N	K	-	3	2	SYT6	114482072	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.945000	0.29056	1.346000	0.45694	0.655000	0.94253	AAG		0.562	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		A	114680549	C	A	114680549	3	1	47	1	0	0	0	0	1	0	0	0	15517	796	28	2	913	2	SYT6	1	114680549	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3464546	114680549	134570072	84	4481										
AMPD1	270	broad.mit.edu	37	chr1	115218606	115218606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaaaatgtggaaggaaattCttggaacggaacacatcact	9	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:115218606C>A	ENST00000520113.2	-	11	1521	c.1506G>T	c.(1504-1506)aaG>aaT	p.K502N	AMPD1_ENST00000369538.3_Missense_Mutation_p.K498N|AMPD1_ENST00000353928.6_Missense_Mutation_p.K469N			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	502					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.K469N(2)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	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)	GAAGGAAATTCTTGGAACGGA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	1											97	103	101					1																	115218606		2203	4300	6503	115020129	SO:0001583	missense	270			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1506G>T	1.37:g.115218606C>A	ENSP00000430075:p.Lys502Asn		115020129	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651461	0.67472	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95853	-3.83;-3.83;-3.83	5.58	5.58	0.84498	Adenosine/AMP deaminase (1);	0.084621	0.85682	D	0.000000	D	0.93615	0.7961	N	0.25031	0.7	0.80722	D	1	P;D	0.60575	0.916;0.988	P;P	0.62298	0.697;0.9	D	0.91430	0.5165	10	0.15499	T	0.54	-22.8731	19.5788	0.95458	0.0:1.0:0.0:0.0	.	498;469	Q5TF02;P23109	.;AMPD1_HUMAN	N	502;498;469	ENSP00000430075:K502N;ENSP00000358551:K498N;ENSP00000316520:K469N	ENSP00000316520:K469N	K	-	3	2	AMPD1	115020129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.362000	0.52314	2.626000	0.88956	0.561000	0.74099	AAG		0.438	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			A	115218606	C	A	115218606	3	1	47	1	0	0	0	0	1	0	0	0	585	912	32	2	860	2	AMPD1	1	115218606	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	538057	115218606	134032015	85	4482										
NRAS	4893	broad.mit.edu	37	chr1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatggcactgtactcttctTgtccagctgtatccagtatg	8	11	3	0	rs11554290	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	1016	Substitution - Missense(1016)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	1											180	156	164					1																	115256529		2203	4300	6503	115058052	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg		115058052	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		C	115256529	T	C	115256529	3	2	47	1	0	0	0	0	1	0	0	0	10671	1812	63	4	399	4	NRAS	1	115256529	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	37923	115256529	133994092	86	4483										
TSHB	7252	broad.mit.edu	37	chr1	115576730	115576730	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctatttttcctatcctgttgCtttaagctgtaagtgtggca	8	8	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:115576730C>A	ENST00000369517.1	+	2	299	c.299C>A	c.(298-300)gCt>gAt	p.A100D	TSHB_ENST00000256592.1_Missense_Mutation_p.A100D			P01222	TSHB_HUMAN	thyroid stimulating hormone, beta	100					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|G-protein coupled receptor signaling pathway (GO:0007186)|peptide hormone processing (GO:0016486)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to vitamin A (GO:0033189)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.A100D(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7	Lung SC(450;0.211)	all_cancers(81;3.22e-07)|all_epithelial(167;1.4e-06)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TATCCTGTTGCTTTAAGCTGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											212	199	204					1																	115576730		2203	4300	6503	115378253	SO:0001583	missense	7252			BC069298	CCDS880.1	1p13	2013-02-28			ENSG00000134200	ENSG00000134200		"Endogenous ligands"	12372	protein-coding gene	gene with protein product		188540				2457586, 3243440	Standard	NM_000549		Approved		uc001efs.2	P01222	OTTHUMG00000011881	ENST00000369517.1:c.299C>A	1.37:g.115576730C>A	ENSP00000358530:p.Ala100Asp		115378253	B1AKP0|Q16163	Missense_Mutation	SNP	ENST00000369517.1	37	CCDS880.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451193	0.84209	.	.	ENSG00000134200	ENST00000256592;ENST00000369517	T;T	0.71817	-0.6;-0.6	6.03	6.03	0.97812	Cystine knot (1);Gonadotropin, beta subunit, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.89639	0.6773	H	0.96748	3.875	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91938	0.5560	10	0.87932	D	0	-18.226	20.1519	0.98089	0.0:1.0:0.0:0.0	.	100	P01222	TSHB_HUMAN	D	100	ENSP00000256592:A100D;ENSP00000358530:A100D	ENSP00000256592:A100D	A	+	2	0	TSHB	115378253	1.000000	0.71417	0.992000	0.48379	0.980000	0.70556	6.300000	0.72776	2.861000	0.98227	0.655000	0.94253	GCT		0.428	TSHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032833.2	NM_000549		A	115576730	C	A	115576730	3	1	47	1	0	0	0	0	1	0	0	0	16661	797	28	2	305	2	TSHB	1	115576730	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	320201	115576730	133673891	87	4484										
CASQ2	845	broad.mit.edu	37	chr1	116275543	116275543	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctttgtcaaaggtggcaaaGaatttgatgtaaggctggaa	12	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:116275543G>T	ENST00000261448.5	-	5	824	c.585C>A	c.(583-585)ttC>ttA	p.F195L	CASQ2_ENST00000456138.2_Missense_Mutation_p.F124L|CASQ2_ENST00000488931.1_5'UTR	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	195					cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.F195L(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		AGGTGGCAAAGAATTTGATGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	116	117					1																	116275543		2203	4300	6503	116077066	SO:0001583	missense	845			BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"Protein disulfide isomerases"	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.585C>A	1.37:g.116275543G>T	ENSP00000261448:p.Phe195Leu		116077066	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.259235	0.80246	.	.	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	D;D	0.90444	-2.67;-2.67	5.68	0.36	0.16097	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.93314	0.7869	M	0.87456	2.885	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.92596	0.6087	10	0.72032	D	0.01	-18.207	9.9025	0.41355	0.301:0.0:0.699:0.0	.	124;195	B4DIB0;O14958	.;CASQ2_HUMAN	L	195;124;195	ENSP00000261448:F195L;ENSP00000403858:F124L	ENSP00000261448:F195L	F	-	3	2	CASQ2	116077066	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.521000	0.35910	0.170000	0.19704	-0.312000	0.09012	TTC		0.383	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232		T	116275543	G	T	116275543	3	4	47	1	0	0	0	0	1	0	0	0	2687	933	33	2	642	2	CASQ2	1	116275543	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	698813	116275543	132975078	88	4485										
CD101	9398	broad.mit.edu	37	chr1	117560087	117560087	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagatttcagttactgtaaAgtctctgggtaagtgtcaaa	10	5	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:117560087A>C	ENST00000256652.4	+	5	1662	c.1604A>C	c.(1603-1605)aAg>aCg	p.K535T	CD101_ENST00000369470.1_Missense_Mutation_p.K535T	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	535					cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.K535T(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTTACTGTAAAGTCTCTGGGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	67	66					1																	117560087		2203	4300	6503	117361610	SO:0001583	missense	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1604A>C	1.37:g.117560087A>C	ENSP00000256652:p.Lys535Thr		117361610	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	A	2.124	-0.400647	0.04865	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03301	3.98;3.98	4.76	2.46	0.29980	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.617765	0.16059	N	0.231590	T	0.01189	0.0039	L	0.42245	1.32	0.09310	N	1	P	0.46395	0.877	P	0.45829	0.494	T	0.29274	-1.0017	10	0.07030	T	0.85	-12.6877	6.2262	0.20710	0.8005:0.0:0.1995:0.0	.	535	Q93033	IGSF2_HUMAN	T	535	ENSP00000256652:K535T;ENSP00000358482:K535T	ENSP00000256652:K535T	K	+	2	0	CD101	117361610	0.000000	0.05858	0.054000	0.19295	0.887000	0.51463	-0.119000	0.10676	0.422000	0.26005	0.533000	0.62120	AAG		0.468	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		C	117560087	A	C	117560087	3	2	47	1	0	0	0	0	1	0	0	0	2968	72	3	4	1622	4	CD101	1	117560087	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1284544	117560087	131690534	89	4486										
CD101	9398	broad.mit.edu	37	chr1	117564584	117564584	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaagaagtcaggactaacaGaattgaaactcaagcccaca	7	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:117564584G>T	ENST00000256652.4	+	7	2465	c.2407G>T	c.(2407-2409)Gaa>Taa	p.E803*	CD101_ENST00000369470.1_Nonsense_Mutation_p.E803*	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	803					cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.E803*(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGGACTAACAGAATTGAAACT	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											84	86	85					1																	117564584		2203	4300	6503	117366107	SO:0001587	stop_gained	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.2407G>T	1.37:g.117564584G>T	ENSP00000256652:p.Glu803*		117366107	Q15856	Nonsense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	38	6.921675	0.97936	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	.	.	.	5.3	3.41	0.39046	.	0.422554	0.22485	N	0.059441	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-14.4059	7.3697	0.26794	0.0893:0.1679:0.7428:0.0	.	.	.	.	X	803	.	ENSP00000256652:E803X	E	+	1	0	CD101	117366107	0.851000	0.29673	0.348000	0.25681	0.971000	0.66376	1.997000	0.40786	0.794000	0.33899	0.650000	0.86243	GAA		0.483	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117564584	G	T	117564584	4	4	47	1	0	0	0	0	0	1	0	0	2968	943	33	2	2433	2	CD101	1	117564584	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4497	117564584	131686037	90	4487										
TBX15	6913	broad.mit.edu	37	chr1	119466177	119466177	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtcactgctgaagtctttgCgaatcacatgaactcgaggc	11	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:119466177C>T	ENST00000369429.3	-	5	752	c.743G>A	c.(742-744)cGc>cAc	p.R248H	TBX15_ENST00000207157.3_Missense_Mutation_p.R142H			Q96SF7	TBX15_HUMAN	T-box 15	248					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R142H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		GAAGTCTTTGCGAATCACATG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											173	166	168					1																	119466177		2203	4300	6503	119267700	SO:0001583	missense	6913			AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"T-boxes"	11594	protein-coding gene	gene with protein product		604127	"T-box 14"	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.743G>A	1.37:g.119466177C>T	ENSP00000358437:p.Arg248His		119267700	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		.	.	.	.	.	.	.	.	.	.	C	34	5.329657	0.95733	.	.	ENSG00000092607	ENST00000344218;ENST00000207157;ENST00000369429	T;T	0.81163	-1.46;-1.46	5.78	5.78	0.91487	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.89546	0.6746	M	0.82630	2.6	0.80722	D	1	D	0.76494	0.999	D	0.69142	0.962	D	0.89748	0.3938	10	0.66056	D	0.02	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	248	Q96SF7	TBX15_HUMAN	H	12;142;248	ENSP00000207157:R142H;ENSP00000358437:R248H	ENSP00000207157:R142H	R	-	2	0	TBX15	119267700	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.763000	0.68818	2.730000	0.93505	0.655000	0.94253	CGC		0.453	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		T	119466177	C	T	119466177	3	4	47	1	0	0	0	0	1	0	0	0	15691	768	27	1	1081	1	TBX15	1	119466177	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1901593	119466177	129784444	91	4488										
NOTCH2	4853	broad.mit.edu	37	chr1	120462975	120462975	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctgtgtccatggccgtcGatcaatggggtcatcttctt	11	11	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:120462975G>A	ENST00000256646.2	-	30	5575	c.5356C>T	c.(5356-5358)Cga>Tga	p.R1786*	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1786					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.R1786*(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATGGCCGTCGATCAATGGGG	0.532			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Nonsense(1)	large_intestine(1)	1											174	136	149					1																	120462975		2203	4300	6503	120264498	SO:0001587	stop_gained	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5356C>T	1.37:g.120462975G>A	ENSP00000256646:p.Arg1786*		120264498	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	45	11.948779	0.99620	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.82	4.83	0.62350	.	0.000000	0.31734	U	0.007146	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	15.0168	0.71591	0.0:0.0:0.7776:0.2224	.	.	.	.	X	1786	.	ENSP00000256646:R1786X	R	-	1	2	NOTCH2	120264498	0.974000	0.33945	0.943000	0.38184	0.797000	0.45037	1.959000	0.40412	2.761000	0.94854	0.655000	0.94253	CGA		0.532	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120462975	G	A	120462975	4	1	47	1	0	0	0	0	0	1	0	0	10579	1066	37	1	2079	1	NOTCH2	1	120462975	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	996798	120462975	128787646	92	4489										
LIX1L	128077	broad.mit.edu	37	chr1	145487368	145487368	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcccgtggtgctgacttaaaGaatggggctctagtggttta	13	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:145487368G>T	ENST00000369308.3	+	2	431	c.357G>T	c.(355-357)aaG>aaT	p.K119N	RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000437207.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	119								p.K119N(1)		large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGACTTAAAGAATGGGGCTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											178	166	170					1																	145487368		2203	4300	6503	144198725	SO:0001583	missense	128077			AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.357G>T	1.37:g.145487368G>T	ENSP00000358314:p.Lys119Asn		144198725	Q6AI36	Missense_Mutation	SNP	ENST00000369308.3	37	CCDS915.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.816645	0.70912	.	.	ENSG00000152022	ENST00000369308;ENST00000449167	.	.	.	5.23	4.32	0.51571	.	0.107968	0.64402	D	0.000013	T	0.43787	0.1263	L	0.52573	1.65	0.48830	D	0.99971	P	0.48694	0.914	P	0.45913	0.497	T	0.50338	-0.8840	9	0.59425	D	0.04	-35.7989	11.5576	0.50757	0.0856:0.0:0.9144:0.0	.	119	Q8IVB5	LIX1L_HUMAN	N	119;66	.	ENSP00000358314:K119N	K	+	3	2	LIX1L	144198725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.010000	0.29898	1.443000	0.47586	0.655000	0.94253	AAG		0.493	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		T	145487368	G	T	145487368	3	4	47	1	0	0	0	0	1	0	0	0	8856	933	33	2	363	2	LIX1L	1	145487368	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	25024393	145487368	103763253	93	4490										
ARNT	405	broad.mit.edu	37	chr1	150789891	150789891	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctggtaccatgtccaattcTgtttgctgttgctgctgcct	9	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:150789891T>G	ENST00000358595.5	-	16	1724	c.1524A>C	c.(1522-1524)acA>acC	p.T508T	ARNT_ENST00000515192.1_Silent_p.T494T|ARNT_ENST00000505755.1_Silent_p.T493T|ARNT_ENST00000354396.2_Silent_p.T508T	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	508					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.T508T(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGTCCAATTCTGTTTGCTGTT	0.393			T	ETV6	AML																																		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	1	Substitution - coding silent(1)	large_intestine(1)	1											160	135	143					1																	150789891		2203	4300	6503	149056515	SO:0001819	synonymous_variant	405			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1524A>C	1.37:g.150789891T>G			149056515	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Silent	SNP	ENST00000358595.5	37	CCDS970.1																																																																																				0.393	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			G	150789891	T	G	150789891	2	3	47	1	0	0	0	0	0	0	0	1	966	1567	55	4		4	ARNT	1	150789891	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	5302523	150789891	98460730	94	4491										
SETDB1	9869	broad.mit.edu	37	chr1	150915098	150915098	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgacctgatagtcagcatgCgaattctgggcaagaagaga	13	7	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:150915098C>T	ENST00000271640.5	+	6	797	c.607C>T	c.(607-609)Cga>Tga	p.R203*	SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368963.1_Nonsense_Mutation_p.R203*|SETDB1_ENST00000368962.2_Nonsense_Mutation_p.R203*|SETDB1_ENST00000368969.4_Nonsense_Mutation_p.R203*	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	203					bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R203*(1)		NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGTCAGCATGCGAATTCTGGG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											120	114	116					1																	150915098		2203	4300	6503	149181722	SO:0001587	stop_gained	9869			D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.607C>T	1.37:g.150915098C>T	ENSP00000271640:p.Arg203*		149181722	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Nonsense_Mutation	SNP	ENST00000271640.5	37	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800633	0.90538	.	.	ENSG00000143379	ENST00000271640;ENST00000368962;ENST00000534805;ENST00000368969;ENST00000368963;ENST00000498193	.	.	.	5.98	3.91	0.45181	.	0.262921	0.40554	N	0.001077	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.133	0.86730	0.279:0.721:0.0:0.0	.	.	.	.	X	203	.	ENSP00000271640:R203X	R	+	1	2	SETDB1	149181722	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.225000	0.51246	1.501000	0.48654	0.563000	0.77884	CGA		0.438	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			T	150915098	C	T	150915098	4	4	47	1	0	0	0	0	0	1	0	0	14175	760	27	1	625	1	SETDB1	1	150915098	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	125207	150915098	98335523	95	4492										
POGZ	23126	broad.mit.edu	37	chr1	151384199	151384199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtatcctcatggatcatccGaaaatggacatctacctcag	8	11	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:151384199G>A	ENST00000271715.2	-	12	2142	c.1828C>T	c.(1828-1830)Cgg>Tgg	p.R610W	POGZ_ENST00000531094.1_Missense_Mutation_p.R548W|POGZ_ENST00000409503.1_Missense_Mutation_p.R601W|POGZ_ENST00000368863.2_Missense_Mutation_p.R515W|POGZ_ENST00000392723.1_Missense_Mutation_p.R557W|POGZ_ENST00000540984.1_5'UTR|POGZ_ENST00000491586.1_Missense_Mutation_p.R566W|POGZ_ENST00000361398.3_Missense_Mutation_p.R557W	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	610					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R610W(1)|p.R566W(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGGATCATCCGAAAATGGACA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	1											111	95	101					1																	151384199		2203	4300	6503	149650823	SO:0001583	missense	23126			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.1828C>T	1.37:g.151384199G>A	ENSP00000271715:p.Arg610Trp		149650823	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993121	0.74703	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586	T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;4.92	5.01	4.07	0.47477	Zinc finger, C2H2-like (1);	0.000000	0.46145	D	0.000316	T	0.57592	0.2064	M	0.90922	3.16	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.99;0.929;0.997;0.995;0.992;0.99	T	0.68284	-0.5449	10	0.87932	D	0	-18.8	11.486	0.50354	0.0:0.0:0.6743:0.3257	.	548;601;515;566;557;610	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	W	557;610;557;515;601;548;566	ENSP00000376484:R557W;ENSP00000271715:R610W;ENSP00000354467:R557W;ENSP00000357856:R515W;ENSP00000386836:R601W;ENSP00000431259:R548W;ENSP00000418408:R566W	ENSP00000271715:R610W	R	-	1	2	POGZ	149650823	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.521000	0.53472	1.293000	0.44690	0.563000	0.77884	CGG		0.458	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151384199	G	A	151384199	3	1	47	1	0	0	0	0	1	0	0	0	12217	1057	37	1	2436	1	POGZ	1	151384199	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	469101	151384199	97866422	96	4493										
TCHHL1	126637	broad.mit.edu	37	chr1	152057846	152057846	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacttgaccaggggactgaaGaattgtgctctttcttggct	12	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152057846G>T	ENST00000368806.1	-	3	2376	c.2312C>A	c.(2311-2313)tCt>tAt	p.S771Y		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	771							calcium ion binding (GO:0005509)	p.S771Y(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			GGGGACTGAAGAATTGTGCTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											156	147	150					1																	152057846		2203	4300	6503	150324470	SO:0001583	missense	126637				CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.2312C>A	1.37:g.152057846G>T	ENSP00000357796:p.Ser771Tyr		150324470	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	13.39	2.221810	0.39300	.	.	ENSG00000182898	ENST00000368806	T	0.32515	1.45	4.56	2.69	0.31865	.	1.537360	0.04338	N	0.353562	T	0.19685	0.0473	L	0.34521	1.04	0.09310	N	1	D	0.56968	0.978	P	0.54460	0.753	T	0.18053	-1.0349	10	0.62326	D	0.03	3.7172	6.5563	0.22462	0.1007:0.1819:0.7174:0.0	.	771	Q5QJ38	TCHL1_HUMAN	Y	771	ENSP00000357796:S771Y	ENSP00000357796:S771Y	S	-	2	0	TCHHL1	150324470	0.597000	0.26874	0.070000	0.20053	0.002000	0.02628	0.796000	0.26986	0.370000	0.24538	-0.121000	0.15023	TCT		0.493	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		T	152057846	G	T	152057846	3	4	47	1	0	0	0	0	1	0	0	0	15740	942	33	2	406	2	TCHHL1	1	152057846	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	673647	152057846	97192775	97	4494										
TCHHL1	126637	broad.mit.edu	37	chr1	152059970	152059970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactgatgatgccattactgTcaatattcagaagatttgaa	7	6	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152059970T>C	ENST00000368806.1	-	3	252	c.188A>G	c.(187-189)gAc>gGc	p.D63G		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	63	EF-hand.						calcium ion binding (GO:0005509)	p.D63G(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			GCCATTACTGTCAATATTCAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	59	60					1																	152059970		2203	4300	6503	150326594	SO:0001583	missense	126637				CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.188A>G	1.37:g.152059970T>C	ENSP00000357796:p.Asp63Gly		150326594	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	6.788	0.514342	0.12944	.	.	ENSG00000182898	ENST00000368806	T	0.17854	2.25	5.3	4.17	0.49024	EF-hand-like domain (1);	0.376138	0.19302	N	0.117610	T	0.03871	0.0109	L	0.34521	1.04	0.09310	N	1	P	0.38711	0.643	B	0.33454	0.164	T	0.28839	-1.0031	10	0.42905	T	0.14	-5.6773	6.4109	0.21690	0.0:0.123:0.0:0.877	.	63	Q5QJ38	TCHL1_HUMAN	G	63	ENSP00000357796:D63G	ENSP00000357796:D63G	D	-	2	0	TCHHL1	150326594	0.014000	0.17966	0.697000	0.30258	0.038000	0.13279	1.572000	0.36461	0.851000	0.35264	0.372000	0.22366	GAC		0.348	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		C	152059970	T	C	152059970	3	2	47	1	0	0	0	0	1	0	0	0	15740	1667	58	4	2530	4	TCHHL1	1	152059970	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2124	152059970	97190651	98	4495										
TCHH	7062	broad.mit.edu	37	chr1	152081399	152081399	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctgttcctcttcacggaAttttctgtcacgctcttggc	8	13	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152081399A>T	ENST00000368804.1	-	2	4293	c.4294T>A	c.(4294-4296)Ttc>Atc	p.F1432I		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1432	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.F1432I(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTTCACGGAATTTTCTGTCA	0.597											OREG0031687	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																																				1	Substitution - Missense(1)	large_intestine(1)	1											90	90	90					1																	152081399		1895	4108	6003	150348023	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4294T>A	1.37:g.152081399A>T	ENSP00000357794:p.Phe1432Ile	1745	150348023	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	a	9.135	1.012475	0.19277	.	.	ENSG00000159450	ENST00000368804	T	0.05717	3.4	3.32	-1.57	0.08506	.	.	.	.	.	T	0.01523	0.0049	L	0.58101	1.795	0.09310	N	1	P	0.39551	0.678	B	0.30646	0.118	T	0.44651	-0.9314	9	0.27785	T	0.31	.	4.5094	0.11903	0.3353:0.0:0.4756:0.1891	.	1432	Q07283	TRHY_HUMAN	I	1432	ENSP00000357794:F1432I	ENSP00000357794:F1432I	F	-	1	0	TCHH	150348023	0.003000	0.15002	0.022000	0.16811	0.013000	0.08279	0.019000	0.13444	-0.188000	0.10499	-0.467000	0.05162	TTC		0.597	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152081399	A	T	152081399	3	4	47	1	0	0	0	0	1	0	0	0	15739	101	4	5	1541	5	TCHH	1	152081399	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	21429	152081399	97169222	99	4496										
RPTN	126638	broad.mit.edu	37	chr1	152128411	152128411	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtctgaccatagtgagaActctgatcttgtgtgtctgg	11	8	5	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152128411A>G	ENST00000316073.3	-	3	1228	c.1164T>C	c.(1162-1164)agT>agC	p.S388S		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	388	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S388S(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CATAGTGAGAACTCTGATCTT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											793	684	717					1																	152128411		1568	3582	5150	150395035	SO:0001819	synonymous_variant	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1164T>C	1.37:g.152128411A>G			150395035	B7ZBZ3	Silent	SNP	ENST00000316073.3	37	CCDS41397.1																																																																																				0.488	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		G	152128411	A	G	152128411	2	3	47	1	0	0	0	0	0	0	0	1	13701	40	2	4		4	RPTN	1	152128411	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	47012	152128411	97122210	100	4497										
LCE3B	353143	broad.mit.edu	37	chr1	152586484	152586484	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctgcaggtcccaccgatgCcggcgccagagctccaactc	11	17	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152586484C>T	ENST00000335633.1	+	1	198	c.198C>T	c.(196-198)tgC>tgT	p.C66C		NM_178433.1	NP_848520.1	Q5TA77	LCE3B_HUMAN	late cornified envelope 3B	66	Cys-rich.				keratinization (GO:0031424)			p.C66C(1)		large_intestine(1)|lung(2)|prostate(1)	4	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0313)|Kidney(5;0.0367)		CCCACCGATGCCGGCGCCAGA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	1											58	55	56					1																	152586484		1820	2703	4523	150853108	SO:0001819	synonymous_variant	353143				CCDS1016.1	1q21.3	2008-02-05			ENSG00000187238	ENSG00000187238		"Late cornified envelopes"	29462	protein-coding gene	gene with protein product		612614				11698679	Standard	NM_178433		Approved	LEP14	uc010pds.2	Q5TA77	OTTHUMG00000012395	ENST00000335633.1:c.198C>T	1.37:g.152586484C>T			150853108		Silent	SNP	ENST00000335633.1	37	CCDS1016.1																																																																																				0.642	LCE3B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034515.2	NM_178433		T	152586484	C	T	152586484	2	4	47	1	0	0	0	0	0	0	0	1	8692	747	26	3		3	LCE3B	1	152586484	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	458073	152586484	96664137	101	4498										
LCE1B	353132	broad.mit.edu	37	chr1	152785204	152785204	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacagaccccagagctctggCtgctgcagccagccctccgg	11	18	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:152785204C>T	ENST00000360090.3	+	1	758	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	94	Gly-rich.				keratinization (GO:0031424)			p.G94G(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAGCTCTGGCTGCTGCAGCC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	1											28	35	32					1																	152785204		2199	4296	6495	151051828	SO:0001819	synonymous_variant	353132			BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"Late cornified envelopes"	16611	protein-coding gene	gene with protein product		612604	"small proline rich-like (epidermal differentiation complex) 2A"	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.282C>T	1.37:g.152785204C>T			151051828	A4IF40	Silent	SNP	ENST00000360090.3	37	CCDS1027.1																																																																																				0.657	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349		T	152785204	C	T	152785204	2	4	47	1	0	0	0	0	0	0	0	1	8682	784	28	3		3	LCE1B	1	152785204	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	198720	152785204	96465417	102	4499										
CRTC2	200186	broad.mit.edu	37	chr1	153925092	153925092	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatgcttgtcatctagcaaGttctcctcaatagcaggtac	7	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:153925092G>A	ENST00000368633.1	-	8	784	c.657C>T	c.(655-657)aaC>aaT	p.N219N	CRTC2_ENST00000368630.3_Intron|CRTC2_ENST00000476883.1_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	219					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.N219N(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	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)			CATCTAGCAAGTTCTCCTCAA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											242	239	240					1																	153925092		2203	4300	6503	152191716	SO:0001819	synonymous_variant	200186			AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.657C>T	1.37:g.153925092G>A			152191716	Q6UUV8|Q7Z3X7|Q8N332	Silent	SNP	ENST00000368633.1	37	CCDS30875.1																																																																																				0.517	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153925092	G	A	153925092	2	1	47	1	0	0	0	0	0	0	0	1	3906	1020	36	3		3	CRTC2	1	153925092	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1139888	153925092	95325529	103	4500										
SLC39A1	27173	broad.mit.edu	37	chr1	153934789	153934789	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccaaaaagacgccccccgcGaaacagcttactaggctcag	9	15	1	1	rs570195454	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:153934789G>A	ENST00000368623.3	-	2	984	c.225C>T	c.(223-225)ttC>ttT	p.F75F	SLC39A1_ENST00000537590.1_Intron|SLC39A1_ENST00000461071.1_5'UTR|SLC39A1_ENST00000356205.4_Silent_p.F75F|SLC39A1_ENST00000368621.1_Silent_p.F75F|SLC39A1_ENST00000310483.6_Silent_p.F75F			Q9NY26	S39A1_HUMAN	solute carrier family 39 (zinc transporter), member 1	75					cation transport (GO:0006812)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic cation transmembrane transporter activity (GO:0022890)|zinc ion transmembrane transporter activity (GO:0005385)	p.F75F(1)		kidney(2)|large_intestine(2)|lung(7)|urinary_tract(1)	12	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)	Colorectal(1306;0.019)		CGCCCCCCGCGAAACAGCTTA	0.612													G|||	2	0.000399361	0	0	5008	,	,		17771	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	1											91	98	95					1																	153934789		2203	4300	6503	152201413	SO:0001819	synonymous_variant	27173			BC007886	CCDS1055.1, CCDS72920.1	1q21	2013-05-22		2002-02-15	ENSG00000143570	ENSG00000143570		"Solute carriers"	12876	protein-coding gene	gene with protein product		604740	"zinc/iron regulated transporter-like"	ZIRTL		10610721, 10681536	Standard	NM_014437		Approved	ZIP1	uc031ppi.1	Q9NY26	OTTHUMG00000037158	ENST00000368623.3:c.225C>T	1.37:g.153934789G>A			152201413	B4DDY7|Q5T4K1|Q8N2H7|Q9BTV0|Q9UBI7|Q9Y2Z7|Q9Y380	Silent	SNP	ENST00000368623.3	37	CCDS1055.1																																																																																				0.612	SLC39A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090284.1	NM_014437		A	153934789	G	A	153934789	2	1	47	1	0	0	0	0	0	0	0	1	14649	1049	37	1		1	SLC39A1	1	153934789	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	9697	153934789	95315832	104	4501										
TPM3	7170	broad.mit.edu	37	chr1	154143175	154143175	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcttcctcatatttatcttCtttttgagagtactgtaaga	5	7	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:154143175C>A	ENST00000368530.2	-	7	847	c.655G>T	c.(655-657)Gaa>Taa	p.E219*	TPM3_ENST00000302206.5_Nonsense_Mutation_p.E92*|TPM3_ENST00000323144.7_Nonsense_Mutation_p.E182*|TPM3_ENST00000341485.5_Nonsense_Mutation_p.E166*|TPM3_ENST00000330188.9_Nonsense_Mutation_p.E182*|TPM3_ENST00000469717.1_5'UTR|TPM3_ENST00000271850.7_Nonsense_Mutation_p.E219*|TPM3_ENST00000368531.2_Nonsense_Mutation_p.E182*|TPM3_ENST00000341372.3_Nonsense_Mutation_p.E157*|TPM3_ENST00000328159.4_Nonsense_Mutation_p.E182*|TPM3_ENST00000368533.3_Nonsense_Mutation_p.E182*	NM_152263.2	NP_689476.2	P06753	TPM3_HUMAN	tropomyosin 3	219					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)		p.E219*(1)|p.E182*(1)	TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					TATTTATCTTCTTTTTGAGAG	0.343			T	"NTRK1, ALK, ROS1"	"papillary thyroid, ALCL, NSCLC"																																		Dom	yes		1	1q22-q23	7170	tropomyosin 3		"E, L"	2	Substitution - Nonsense(2)	large_intestine(2)	1											101	106	104					1																	154143175		2203	4300	6503	152409799	SO:0001587	stop_gained	7170			BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549		"Tropomyosins"	12012	protein-coding gene	gene with protein product		191030		NEM1		1829807	Standard	NM_153649		Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368530.2:c.655G>T	1.37:g.154143175C>A	ENSP00000357516:p.Glu219*		152409799	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	Nonsense_Mutation	SNP	ENST00000368530.2	37	CCDS41403.1	.	.	.	.	.	.	.	.	.	.	C	37	5.986133	0.97173	.	.	ENSG00000143549	ENST00000368533;ENST00000341485;ENST00000330188;ENST00000341372;ENST00000328159;ENST00000271850;ENST00000302206;ENST00000368531;ENST00000323144;ENST00000368530	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.1804	18.9228	0.92532	0.0:1.0:0.0:0.0	.	.	.	.	X	182;166;182;158;182;219;92;182;182;219	.	ENSP00000271850:E219X	E	-	1	0	TPM3	152409799	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.543000	0.85770	0.563000	0.77884	GAA		0.343	TPM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087271.2	NM_152263		A	154143175	C	A	154143175	4	1	47	1	0	0	0	0	0	1	0	0	16447	922	32	2	389	2	TPM3	1	154143175	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	208386	154143175	95107446	105	4502										
ASH1L	55870	broad.mit.edu	37	chr1	155449689	155449689	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagtttctttctctttaaaGtcttcattttatttattttg	3	6	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:155449689G>T	ENST00000368346.3	-	3	3611	c.2972C>A	c.(2971-2973)aCt>aAt	p.T991N	ASH1L_ENST00000392403.3_Missense_Mutation_p.T991N			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	991					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.T991N(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTCTTTAAAGTCTTCATTTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	50	49					1																	155449689		2200	4297	6497	153716313	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2972C>A	1.37:g.155449689G>T	ENSP00000357330:p.Thr991Asn		153716313	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	G	15.38	2.816830	0.50633	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.90004	-2.6;-2.6	5.31	5.31	0.75309	.	0.057120	0.64402	D	0.000001	D	0.88489	0.6450	L	0.27053	0.805	0.80722	D	1	D;D	0.58268	0.97;0.982	P;P	0.60345	0.749;0.873	D	0.90057	0.4153	10	0.87932	D	0	.	18.7713	0.91893	0.0:0.0:1.0:0.0	.	991;991	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	N	991	ENSP00000357330:T991N;ENSP00000376204:T991N	ENSP00000357330:T991N	T	-	2	0	ASH1L	153716313	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.041000	0.64196	2.768000	0.95171	0.650000	0.86243	ACT		0.308	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155449689	G	T	155449689	3	4	47	1	0	0	0	0	1	0	0	0	1042	1029	36	2	6026	2	ASH1L	1	155449689	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1306514	155449689	93800932	106	4503										
ASH1L	55870	broad.mit.edu	37	chr1	155450063	155450063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaatttctggctgtaaaatTgggggttcttgttcttcctt	9	7	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:155450063T>C	ENST00000368346.3	-	3	3237	c.2598A>G	c.(2596-2598)ccA>ccG	p.P866P	ASH1L_ENST00000392403.3_Silent_p.P866P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	866					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.P866P(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GCTGTAAAATTGGGGGTTCTT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	1											126	135	132					1																	155450063		2203	4300	6503	153716687	SO:0001819	synonymous_variant	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2598A>G	1.37:g.155450063T>C			153716687	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																					0.428	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155450063	T	C	155450063	2	2	47	1	0	0	0	0	0	0	0	1	1042	1799	63	4		4	ASH1L	1	155450063	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	374	155450063	93800558	107	4504										
YY1AP1	55249	broad.mit.edu	37	chr1	155630672	155630672	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctagcaccatcagccatgtgCcgcagttcttcctggatgga	10	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:155630672C>T	ENST00000295566.4	-	11	1190	c.1167G>A	c.(1165-1167)cgG>cgA	p.R389R	YY1AP1_ENST00000407221.1_Silent_p.R312R|YY1AP1_ENST00000535662.1_Silent_p.R189R|YY1AP1_ENST00000359205.5_Silent_p.R332R|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000368339.5_Silent_p.R481R|YY1AP1_ENST00000368330.2_Silent_p.R343R|YY1AP1_ENST00000355499.4_Silent_p.R343R|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000311573.5_Silent_p.R312R|YY1AP1_ENST00000405763.3_3'UTR|YY1AP1_ENST00000404643.1_Silent_p.R323R|YY1AP1_ENST00000347088.5_Silent_p.R343R|YY1AP1_ENST00000361831.5_Silent_p.R332R|YY1AP1_ENST00000368340.5_Silent_p.R461R	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	389					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R389R(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CAGCCATGTGCCGCAGTTCTT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											95	91	92					1																	155630672		2203	4298	6501	153897296	SO:0001819	synonymous_variant	55249			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1167G>A	1.37:g.155630672C>T			153897296	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Silent	SNP	ENST00000295566.4	37	CCDS1115.1																																																																																				0.458	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155630672	C	T	155630672	2	4	47	1	0	0	0	0	0	0	0	1	17548	726	26	3		3	YY1AP1	1	155630672	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	180609	155630672	93619949	108	4505										
RIT1	6016	broad.mit.edu	37	chr1	155870317	155870317	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcccgtacaagggcatggaaAacatcatcaatatagtagcg	9	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:155870317A>C	ENST00000368323.3	-	6	726	c.522T>G	c.(520-522)gtT>gtG	p.V174V	RIT1_ENST00000368322.3_Silent_p.V191V|RIT1_ENST00000539040.1_Silent_p.V138V	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	174					GTP catabolic process (GO:0006184)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)	p.V174V(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			GGGCATGGAAAACATCATCAA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	1											219	215	216					1																	155870317		2203	4300	6503	154136941	SO:0001819	synonymous_variant	6016			AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622			10023	protein-coding gene	gene with protein product	"Ric-like, expressed in many tissues", "GTP-binding protein Roc1"	609591	"Ric (Drosophila)-like, expressed in many tissues"	RIT		8824319, 8918462	Standard	NM_006912		Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.522T>G	1.37:g.155870317A>C			154136941	B4DQE8|O00646|O00720|Q5VY89|Q5VY90	Silent	SNP	ENST00000368323.3	37	CCDS1123.1																																																																																				0.453	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	NM_006912		C	155870317	A	C	155870317	2	2	47	1	0	0	0	0	0	0	0	1	13423	1	1	4		4	RIT1	1	155870317	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	239645	155870317	93380304	109	4506										
ARHGEF11	9826	broad.mit.edu	37	chr1	156912567	156912567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagatgatgaagaaggcccGtttatctgtgtgaggaaagg	15	5	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:156912567G>A	ENST00000361409.2	-	32	3863	c.3121C>T	c.(3121-3123)Cgg>Tgg	p.R1041W	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R1081W|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.R457W|ARHGEF11_ENST00000487682.1_5'UTR	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1041	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1081W(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAGAAGGCCCGTTTATCTGTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											167	135	146					1																	156912567		2203	4300	6503	155179191	SO:0001583	missense	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3121C>T	1.37:g.156912567G>A	ENSP00000354644:p.Arg1041Trp		155179191	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961511	0.74016	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.66099	-0.19;-0.19;-0.19	4.9	3.92	0.45320	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.48767	D	0.000161	T	0.72835	0.3510	M	0.74467	2.265	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.991;0.994	T	0.76119	-0.3076	10	0.87932	D	0	-21.5293	13.6341	0.62213	0.0:0.0:0.7664:0.2336	.	457;1041;1081	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	W	1081;1041;457	ENSP00000357177:R1081W;ENSP00000354644:R1041W;ENSP00000313470:R457W	ENSP00000313470:R457W	R	-	1	2	ARHGEF11	155179191	0.127000	0.22367	1.000000	0.80357	0.983000	0.72400	1.545000	0.36169	2.547000	0.85894	0.655000	0.94253	CGG		0.532	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156912567	G	A	156912567	3	1	47	1	0	0	0	0	1	0	0	0	896	1144	40	1	1483	1	ARHGEF11	1	156912567	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1042250	156912567	92338054	110	4507										
FCRL5	83416	broad.mit.edu	37	chr1	157494229	157494229	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggtgacatcttcatgataAaaccagtacaggattgggga	12	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:157494229A>C	ENST00000361835.3	-	10	2236	c.2079T>G	c.(2077-2079)ttT>ttG	p.F693L	FCRL5_ENST00000368191.3_Missense_Mutation_p.F608L|FCRL5_ENST00000461387.1_5'Flank|FCRL5_ENST00000368190.3_Missense_Mutation_p.F693L|FCRL5_ENST00000356953.4_Missense_Mutation_p.F693L	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	693	Ig-like C2-type 7.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.F693L(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CTTCATGATAAAACCAGTACA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	65	63					1																	157494229		2203	4300	6503	155760853	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2079T>G	1.37:g.157494229A>C	ENSP00000354691:p.Phe693Leu		155760853	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.293663	0.40594	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191	T;T;T;T	0.02395	4.31;4.31;4.31;4.31	4.69	2.36	0.29203	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08670	0.0215	M	0.91249	3.19	0.80722	D	1	D;P;D;D	0.89917	0.985;0.845;1.0;1.0	D;P;D;D	0.85130	0.971;0.901;0.994;0.997	T	0.01283	-1.1396	9	0.51188	T	0.08	.	6.4685	0.21995	0.8041:0.0:0.1959:0.0	.	608;693;693;693	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9	.;.;.;FCRL5_HUMAN	L	693;693;693;608	ENSP00000354691:F693L;ENSP00000349434:F693L;ENSP00000357173:F693L;ENSP00000357174:F608L	ENSP00000349434:F693L	F	-	3	2	FCRL5	155760853	0.987000	0.35691	0.538000	0.28064	0.005000	0.04900	1.306000	0.33505	0.390000	0.25115	-0.389000	0.06534	TTT		0.572	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		C	157494229	A	C	157494229	3	2	47	1	0	0	0	0	1	0	0	0	5817	11	1	4	886	4	FCRL5	1	157494229	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	581662	157494229	91756392	111	4508										
FCRL2	79368	broad.mit.edu	37	chr1	157716535	157716535	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctccaagtgttatgatttCttcacagaagagtagatgac	8	8	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:157716535C>A	ENST00000361516.3	-	12	1566	c.1518G>T	c.(1516-1518)aaG>aaT	p.K506N	FCRL2_ENST00000392274.3_3'UTR|FCRL2_ENST00000368181.4_Missense_Mutation_p.K200N	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	506					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.K506N(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GTTATGATTTCTTCACAGAAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	101	103					1																	157716535		2203	4300	6503	155983159	SO:0001583	missense	79368			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1518G>T	1.37:g.157716535C>A	ENSP00000355157:p.Lys506Asn		155983159	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032756	0.54790	.	.	ENSG00000132704	ENST00000292389;ENST00000361516;ENST00000368181	T;T	0.35421	1.31;2.96	3.44	0.276	0.15663	.	1.167990	0.06649	U	0.762374	T	0.38692	0.1050	M	0.76170	2.325	0.09310	N	1	P;D;D	0.76494	0.886;0.999;0.969	B;D;P	0.73708	0.29;0.981;0.725	T	0.09574	-1.0668	10	0.72032	D	0.01	.	3.7434	0.08539	0.0:0.5503:0.2046:0.2451	.	200;506;253	Q96LA5-5;Q96LA5;Q96LA5-2	.;FCRL2_HUMAN;.	N	200;506;200	ENSP00000355157:K506N;ENSP00000357163:K200N	ENSP00000292389:K200N	K	-	3	2	FCRL2	155983159	0.003000	0.15002	0.001000	0.08648	0.553000	0.35397	0.010000	0.13242	-0.049000	0.13379	0.650000	0.86243	AAG		0.403	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		A	157716535	C	A	157716535	3	1	47	1	0	0	0	0	1	0	0	0	5814	912	32	2	12	2	FCRL2	1	157716535	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	222306	157716535	91534086	112	4509										
OR10T2	128360	broad.mit.edu	37	chr1	158369175	158369175	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaagaaagatgacaaaaaGcagcagctggagctccccca	11	10	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:158369175G>A	ENST00000334438.1	-	1	81	c.82C>T	c.(82-84)Ctt>Ttt	p.L28F		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L28F(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					ATGACAAAAAGCAGCAGCTGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											37	41	40					1																	158369175		2203	4300	6503	156635799	SO:0001583	missense	128360			AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"GPCR / Class A : Olfactory receptors"	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.82C>T	1.37:g.158369175G>A	ENSP00000334115:p.Leu28Phe		156635799	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.506459	0.26949	.	.	ENSG00000186306	ENST00000334438	T	0.17213	2.29	4.64	4.64	0.57946	.	0.000000	0.34223	U	0.004156	T	0.11495	0.0280	L	0.46885	1.475	0.09310	N	1	P	0.46621	0.881	P	0.44518	0.452	T	0.02411	-1.1163	10	0.54805	T	0.06	.	16.4258	0.83814	0.0:0.0:1.0:0.0	.	28	Q8NGX3	O10T2_HUMAN	F	28	ENSP00000334115:L28F	ENSP00000334115:L28F	L	-	1	0	OR10T2	156635799	0.645000	0.27286	0.144000	0.22314	0.903000	0.53119	1.543000	0.36147	2.390000	0.81377	0.585000	0.79938	CTT		0.488	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		A	158369175	G	A	158369175	3	1	47	1	0	0	0	0	1	0	0	0	10950	971	34	3	864	3	OR10T2	1	158369175	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	652640	158369175	90881446	113	4510										
OR6Y1	391112	broad.mit.edu	37	chr1	158517133	158517133	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagtgtcatggaatagaagaGaattacgacggtcaggtggg	15	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:158517133G>T	ENST00000302617.3	-	1	762	c.763C>A	c.(763-765)Ctc>Atc	p.L255I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L255I(1)		NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					GAATAGAAGAGAATTACGACG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											186	179	181					1																	158517133		2203	4300	6503	156783757	SO:0001583	missense	391112			BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.763C>A	1.37:g.158517133G>T	ENSP00000304807:p.Leu255Ile		156783757	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	G	1.166	-0.642480	0.03531	.	.	ENSG00000197532	ENST00000302617	T	0.00256	8.42	5.34	3.38	0.38709	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37669	N	0.001985	T	0.00039	0.0001	N	0.10782	0.045	0.09310	N	0.999998	B	0.33299	0.407	B	0.36092	0.217	T	0.17167	-1.0378	10	0.02654	T	1	.	3.8315	0.08876	0.079:0.1443:0.4784:0.2983	.	255	Q8NGX8	OR6Y1_HUMAN	I	255	ENSP00000304807:L255I	ENSP00000304807:L255I	L	-	1	0	OR6Y1	156783757	0.001000	0.12720	0.875000	0.34327	0.965000	0.64279	-0.108000	0.10857	1.465000	0.48006	0.655000	0.94253	CTC		0.498	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517133	G	T	158517133	3	4	47	1	0	0	0	0	1	0	0	0	11244	942	33	2	216	2	OR6Y1	1	158517133	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	147958	158517133	90733488	114	4511										
OR10Z1	128368	broad.mit.edu	37	chr1	158576287	158576287	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcctgggcttctccagttCtggggagttgcagctccttc	11	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:158576287C>A	ENST00000361284.1	+	1	59	c.59C>A	c.(58-60)tCt>tAt	p.S20Y		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S20Y(1)		endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TTCTCCAGTTCTGGGGAGTTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											151	150	150					1																	158576287		2203	4300	6503	156842911	SO:0001583	missense	128368			AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.59C>A	1.37:g.158576287C>A	ENSP00000354707:p.Ser20Tyr		156842911	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	C	5.210	0.224287	0.09863	.	.	ENSG00000198967	ENST00000361284	T	0.01106	5.33	5.25	2.78	0.32641	.	0.357235	0.20609	N	0.089015	T	0.00210	0.0006	N	0.13168	0.305	0.23859	N	0.996649	B	0.02656	0.0	B	0.06405	0.002	T	0.44003	-0.9356	10	0.02654	T	1	.	3.1824	0.06589	0.1662:0.2466:0.0:0.5872	.	20	Q8NGY1	O10Z1_HUMAN	Y	20	ENSP00000354707:S20Y	ENSP00000354707:S20Y	S	+	2	0	OR10Z1	156842911	0.000000	0.05858	0.989000	0.46669	0.201000	0.24016	-0.028000	0.12350	0.435000	0.26365	-0.290000	0.09829	TCT		0.478	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		A	158576287	C	A	158576287	3	1	47	1	0	0	0	0	1	0	0	0	10954	913	32	2	61	2	OR10Z1	1	158576287	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	59154	158576287	90674334	115	4512										
MNDA	4332	broad.mit.edu	37	chr1	158811964	158811964	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggtgaatgaatacaagaaAattcttttgctgaaaggatt	9	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:158811964A>C	ENST00000368141.4	+	2	282	c.21A>C	c.(19-21)aaA>aaC	p.K7N	MNDA_ENST00000491210.1_3'UTR	NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	7	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K7N(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AATACAAGAAAATTCTTTTGC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	60	60					1																	158811964		2203	4300	6503	157078588	SO:0001583	missense	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.21A>C	1.37:g.158811964A>C	ENSP00000357123:p.Lys7Asn		157078588		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	A	6.599	0.478923	0.12581	.	.	ENSG00000163563	ENST00000368141	T	0.48836	0.8	3.51	2.37	0.29283	Pyrin (2);	.	.	.	.	T	0.20740	0.0499	L	0.36672	1.1	0.09310	N	1	P	0.38582	0.638	P	0.47015	0.534	T	0.21211	-1.0252	9	0.14656	T	0.56	-6.3766	5.4693	0.16660	0.8674:0.0:0.1326:0.0	.	7	P41218	MNDA_HUMAN	N	7	ENSP00000357123:K7N	ENSP00000357123:K7N	K	+	3	2	MNDA	157078588	0.001000	0.12720	0.038000	0.18304	0.017000	0.09413	0.425000	0.21346	0.522000	0.28464	0.455000	0.32223	AAA		0.308	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		C	158811964	A	C	158811964	3	2	47	1	0	0	0	0	1	0	0	0	9706	11	1	4	23	4	MNDA	1	158811964	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	235677	158811964	90438657	116	4513										
IGSF9	57549	broad.mit.edu	37	chr1	159897155	159897155	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacagcagagtggcctgttCggggtgggggactggctgtc	18	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:159897155C>T	ENST00000368094.1	-	21	3717	c.3520G>A	c.(3520-3522)Gaa>Aaa	p.E1174K	IGSF9_ENST00000493195.1_5'UTR|TAGLN2_ENST00000478033.1_5'Flank|TAGLN2_ENST00000320307.4_5'Flank|TAGLN2_ENST00000368097.4_5'Flank|IGSF9_ENST00000361509.3_Missense_Mutation_p.E1158K	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	1174					dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.E1158K(1)		central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GTGGCCTGTTCGGGGTGGGGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	57	56					1																	159897155		2150	4222	6372	158163779	SO:0001583	missense	57549			AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.3520G>A	1.37:g.159897155C>T	ENSP00000357073:p.Glu1174Lys		158163779		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495498	0.85069	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.67865	-0.29;-0.21	5.41	5.41	0.78517	.	0.000000	0.42548	D	0.000699	T	0.48696	0.1514	L	0.29908	0.895	0.34872	D	0.743689	P;D	0.61697	0.911;0.99	P;P	0.47470	0.459;0.548	T	0.51872	-0.8650	9	.	.	.	-9.3123	14.6989	0.69142	0.0:1.0:0.0:0.0	.	1174;712	Q9P2J2;C9JI81	TUTLA_HUMAN;.	K	1158;1174;712	ENSP00000355049:E1158K;ENSP00000357073:E1174K	.	E	-	1	0	IGSF9	158163779	0.991000	0.36638	0.978000	0.43139	0.740000	0.42216	3.215000	0.51169	2.536000	0.85505	0.563000	0.77884	GAA		0.602	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159897155	C	T	159897155	3	4	47	1	0	0	0	0	1	0	0	0	7626	893	31	1	23	1	IGSF9	1	159897155	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1085191	159897155	89353466	117	4514										
PEX19	5824	broad.mit.edu	37	chr1	160249980	160249980	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acgctgtgctgctcctgataTttttcaaactgctctggagg	10	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:160249980T>G	ENST00000368072.5	-	6	672	c.651A>C	c.(649-651)aaA>aaC	p.K217N	PEX19_ENST00000440949.3_Missense_Mutation_p.K127N|PEX19_ENST00000532508.1_5'UTR|DCAF8_ENST00000608310.1_Missense_Mutation_p.K70N|DCAF8_ENST00000556710.1_Missense_Mutation_p.K70N	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	217					chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)	p.K217N(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCTCCTGATATTTTTCAAACT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											172	169	170					1																	160249980		2203	4300	6503	158516604	SO:0001583	missense	5824			Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"housekeeping gene, 33kD"	600279	"peroxisomal farnesylated protein"	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.651A>C	1.37:g.160249980T>G	ENSP00000357051:p.Lys217Asn		158516604	D3DVE7|Q5QNY4|Q8NI97	Missense_Mutation	SNP	ENST00000368072.5	37	CCDS1201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.21|18.21	3.574580|3.574580	0.65878|0.65878	.|.	.|.	ENSG00000162735|ENSG00000132716;ENSG00000258465;ENSG00000258465;ENSG00000162735;ENSG00000162735;ENSG00000162735;ENSG00000162735	ENST00000495624|ENST00000555195;ENST00000556710;ENST00000485079;ENST00000368072;ENST00000429425;ENST00000440949;ENST00000392220	.|T;T	.|0.65732	.|-0.17;-0.17	5.66|5.66	0.715|0.715	0.18186|0.18186	.|.	.|0.107805	.|0.56097	.|D	.|0.000023	T|T	0.25865|0.25865	0.0630|0.0630	N|N	0.16478|0.16478	0.41|0.41	0.44462|0.44462	D|D	0.997394|0.997394	.|P;P	.|0.45011	.|0.648;0.848	.|B;B	.|0.40506	.|0.331;0.234	T|T	0.05209|0.05209	-1.0899|-1.0899	5|10	.|0.44086	.|T	.|0.13	-18.9395|-18.9395	9.3068|9.3068	0.37881|0.37881	0.0:0.3953:0.0:0.6047|0.0:0.3953:0.0:0.6047	.|.	.|70;217	.|G3V3G9;P40855	.|.;PEX19_HUMAN	L|N	55|70;70;87;217;197;127;197	.|ENSP00000451989:K70N;ENSP00000451235:K70N	.|ENSP00000357051:K217N	I|K	-|-	1|3	0|2	PEX19|RP11-574F21.3;PEX19;DCAF8	158516604|158516604	0.986000|0.986000	0.35501|0.35501	0.997000|0.997000	0.53966|0.53966	0.949000|0.949000	0.60115|0.60115	0.082000|0.082000	0.14847|0.14847	0.122000|0.122000	0.18314|0.18314	-0.360000|-0.360000	0.07572|0.07572	ATA|AAA		0.443	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857		G	160249980	T	G	160249980	3	3	47	1	0	0	0	0	1	0	0	0	11775	1490	52	4	260	4	PEX19	1	160249980	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	352825	160249980	89000641	118	4515										
FCGR3A	2214	broad.mit.edu	37	chr1	161518237	161518237	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacttctagctgcaccgggTcactgagggtggagaggttt	16	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:161518237T>C	ENST00000436743.1	-	4	447	c.293A>G	c.(292-294)gAc>gGc	p.D98G	FCGR3A_ENST00000540048.1_Missense_Mutation_p.D98G|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000443193.1_Missense_Mutation_p.D133G|FCGR3A_ENST00000367969.3_Missense_Mutation_p.D134G	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	98	Ig-like C2-type 1.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D134G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTGCACCGGGTCACTGAGGGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	124	125					1																	161518237		2203	4297	6500	159784861	SO:0001583	missense	2214			BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.293A>G	1.37:g.161518237T>C	ENSP00000416607:p.Asp98Gly		159784861	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.944848|4.944848	0.92593|0.92593	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336|ENST00000426740	T;T;T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63;2.63;2.63|.	4.43|4.43	4.43|4.43	0.53597|0.53597	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.56097|.	D|.	0.000036|.	T|T	0.72653|0.72653	0.3487|0.3487	M|M	0.90252|0.90252	3.1|3.1	0.37457|0.37457	D|D	0.915074|0.915074	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;0.999;0.996|.	T|T	0.78783|0.78783	-0.2069|-0.2069	10|5	0.87932|.	D|.	0|.	.|.	10.2704|10.2704	0.43479|0.43479	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	98;133;98|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	G|A	134;133;98;98;98;97|115	ENSP00000356946:D134G;ENSP00000392047:D133G;ENSP00000416607:D98G;ENSP00000356944:D98G;ENSP00000444971:D98G;ENSP00000396567:D97G|.	ENSP00000356944:D98G|.	D|T	-|-	2|1	0|0	FCGR3A|FCGR3A	159784861|159784861	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.798000|0.798000	0.45092|0.45092	3.351000|3.351000	0.52232|0.52232	1.989000|1.989000	0.58080|0.58080	0.482000|0.482000	0.46254|0.46254	GAC|ACC		0.512	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569		C	161518237	T	C	161518237	3	2	47	1	0	0	0	0	1	0	0	0	5803	1667	58	4	483	4	FCGR3A	1	161518237	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1268257	161518237	87732384	119	4516										
NOS1AP	9722	broad.mit.edu	37	chr1	162337008	162337008	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccttaggtaggcgcgactgCttggtgaagctggagtgctt	15	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:162337008C>T	ENST00000361897.5	+	10	1674	c.1272C>T	c.(1270-1272)tgC>tgT	p.C424C	NOS1AP_ENST00000454693.1_3'UTR|RP11-565P22.6_ENST00000431696.1_Intron|NOS1AP_ENST00000530878.1_Silent_p.C419C|NOS1AP_ENST00000493151.1_Silent_p.C129C	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	424					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)	p.C424C(2)|p.C129C(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			GGCGCGACTGCTTGGTGAAGC	0.682																																																3	Substitution - coding silent(3)	large_intestine(3)	1											50	56	54					1																	162337008		2203	4300	6503	160603632	SO:0001819	synonymous_variant	9722			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1272C>T	1.37:g.162337008C>T			160603632	B7ZLF5|O43564|Q3T551|Q5VU95	Silent	SNP	ENST00000361897.5	37	CCDS1237.1																																																																																				0.682	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		T	162337008	C	T	162337008	2	4	47	1	0	0	0	0	0	0	0	1	10573	805	28	3		3	NOS1AP	1	162337008	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	818771	162337008	86913613	120	4517										
C1orf226	400793	broad.mit.edu	37	chr1	162353067	162353067	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaccacccaggacatgcTgatttcatcacagcctgtcc	8	14	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:162353067T>C	ENST00000458626.2	+	2	585	c.413T>C	c.(412-414)cTg>cCg	p.L138P	C1orf226_ENST00000426197.2_Missense_Mutation_p.L181P	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	138								p.L181P(2)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						CAGGACATGCTGATTTCATCA	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	1											47	52	50					1																	162353067		1972	4159	6131	160619691	SO:0001583	missense	400793			AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.413T>C	1.37:g.162353067T>C	ENSP00000437071:p.Leu138Pro		160619691	B4DF31	Missense_Mutation	SNP	ENST00000458626.2	37	CCDS53422.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.154259	0.78114	.	.	ENSG00000239887	ENST00000420220;ENST00000426197;ENST00000458626	.	.	.	4.58	4.58	0.56647	.	1.669100	0.04032	N	0.301610	T	0.48589	0.1508	L	0.27053	0.805	.	.	.	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.987	T	0.38286	-0.9668	8	0.87932	D	0	-11.6005	13.23	0.59938	0.0:0.0:0.0:1.0	.	181;138	A1L170-2;A1L170	.;CA226_HUMAN	P	138;181;138	.	ENSP00000398035:L138P	L	+	2	0	C1orf226	160619691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.828000	0.75308	2.052000	0.61016	0.533000	0.62120	CTG		0.592	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		C	162353067	T	C	162353067	3	2	47	1	0	0	0	0	1	0	0	0	2038	1580	55	4	552	4	C1orf226	1	162353067	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	16059	162353067	86897554	121	4518										
DDR2	4921	broad.mit.edu	37	chr1	162731039	162731039	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgctaaaggtgtgaagatCtttaaggaggtacagtgcta	12	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:162731039C>A	ENST00000367922.3	+	10	1332	c.894C>A	c.(892-894)atC>atA	p.I298I	DDR2_ENST00000367921.3_Silent_p.I298I	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	298					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.I298I(1)		central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	GTGTGAAGATCTTTAAGGAGG	0.507																																					NSCLC(161;314 2006 8283 19651 23192)											1	Substitution - coding silent(1)	large_intestine(1)	1											172	125	141					1																	162731039		2203	4300	6503	160997663	SO:0001819	synonymous_variant	4921			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.894C>A	1.37:g.162731039C>A			160997663	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																				0.507	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		A	162731039	C	A	162731039	2	1	47	1	0	0	0	0	0	0	0	1	4343	903	32	2		2	DDR2	1	162731039	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	377972	162731039	86519582	122	4519										
DDR2	4921	broad.mit.edu	37	chr1	162745566	162745566	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaatacatggagaatggaGatctcaatcagtttctttcc	8	8	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:162745566G>T	ENST00000367922.3	+	16	2419	c.1981G>T	c.(1981-1983)Gat>Tat	p.D661Y	DDR2_ENST00000367921.3_Missense_Mutation_p.D661Y|RN7SL861P_ENST00000473793.2_RNA	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	661	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D661Y(1)		central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	GGAGAATGGAGATCTCAATCA	0.483																																					NSCLC(161;314 2006 8283 19651 23192)											1	Substitution - Missense(1)	large_intestine(1)	1											146	139	142					1																	162745566		2203	4300	6503	161012190	SO:0001583	missense	4921			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.1981G>T	1.37:g.162745566G>T	ENSP00000356899:p.Asp661Tyr		161012190	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	37	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.690490	0.88735	.	.	ENSG00000162733	ENST00000367922;ENST00000367921	D;D	0.90900	-2.75;-2.75	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97002	0.9021	H	0.96576	3.845	0.44587	D	0.997551	D	0.89917	1.0	D	0.97110	1.0	D	0.98152	1.0442	9	0.87932	D	0	.	17.6743	0.88226	0.0:0.0:1.0:0.0	.	661	Q16832	DDR2_HUMAN	Y	661	ENSP00000356899:D661Y;ENSP00000356898:D661Y	ENSP00000356898:D661Y	D	+	1	0	DDR2	161012190	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.671000	0.98627	2.555000	0.86185	0.655000	0.94253	GAT		0.483	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		T	162745566	G	T	162745566	3	4	47	1	0	0	0	0	1	0	0	0	4343	942	33	2	2031	2	DDR2	1	162745566	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	14527	162745566	86505055	123	4520										
ALDH9A1	223	broad.mit.edu	37	chr1	165649907	165649907	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaaagggagaaggtttaaaGaccatggcattacctgcata	11	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:165649907G>T	ENST00000354775.4	-	5	910	c.606C>A	c.(604-606)gtC>gtA	p.V202V	ALDH9A1_ENST00000461664.1_5'UTR|ALDH9A1_ENST00000538148.1_Silent_p.V108V	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	178					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)	p.V178V(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					AAGGTTTAAAGACCATGGCAT	0.443																																					Ovarian(179;1583 2014 18106 33801 42447)											1	Substitution - coding silent(1)	large_intestine(1)	1											93	94	94					1																	165649907		2203	4300	6503	163916531	SO:0001819	synonymous_variant	223			U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"Aldehyde dehydrogenases"	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.606C>A	1.37:g.165649907G>T			163916531	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																				0.443	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1			T	165649907	G	T	165649907	2	4	47	1	0	0	0	0	0	0	0	1	506	929	33	2		2	ALDH9A1	1	165649907	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2904341	165649907	83600714	124	4521										
POU2F1	5451	broad.mit.edu	37	chr1	167368480	167368480	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgatcagctcaatatggaaAaagaggtgattcgtgtttgg	12	5	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:167368480A>C	ENST00000541643.3	+	13	1420	c.1258A>C	c.(1258-1260)Aaa>Caa	p.K420Q	POU2F1_ENST00000367862.5_Missense_Mutation_p.K432Q|POU2F1_ENST00000367866.2_Missense_Mutation_p.K443Q|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000429375.2_Missense_Mutation_p.K380Q|POU2F1_ENST00000420254.3_Missense_Mutation_p.K420Q			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	420					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K420Q(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						CAATATGGAAAAAGAGGTGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	122	124					1																	167368480		2203	4300	6503	165635104	SO:0001583	missense	5451			BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"Homeoboxes / POU class"	9212	protein-coding gene	gene with protein product		164175	"POU domain class 2, transcription factor 1"	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.1258A>C	1.37:g.167368480A>C	ENSP00000441285:p.Lys420Gln		165635104	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	37		.	.	.	.	.	.	.	.	.	.	A	21.7	4.184691	0.78677	.	.	ENSG00000143190	ENST00000367866;ENST00000429375;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	D;D;D;D;D;D;D	0.96334	-3.98;-3.98;-3.98;-3.98;-3.98;-3.98;-3.98	6.04	6.04	0.98038	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97763	0.9266	M	0.77616	2.38	0.80722	D	1	D;D;D;D;D	0.71674	0.995;0.998;0.994;0.994;0.995	D;D;D;D;D	0.75020	0.983;0.985;0.971;0.971;0.983	D	0.98693	1.0697	10	0.87932	D	0	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	380;420;432;418;420	B4E029;P14859-4;P14859-2;P14859-3;P14859	.;.;.;.;PO2F1_HUMAN	Q	443;380;418;420;420;432;328	ENSP00000356840:K443Q;ENSP00000401217:K380Q;ENSP00000356839:K418Q;ENSP00000414660:K420Q;ENSP00000441285:K420Q;ENSP00000356836:K432Q;ENSP00000415993:K328Q	ENSP00000356836:K432Q	K	+	1	0	POU2F1	165635104	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.317000	0.78254	0.459000	0.35465	AAA		0.433	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		C	167368480	A	C	167368480	3	2	47	1	0	0	0	0	1	0	0	0	12302	15	1	4	1300	4	POU2F1	1	167368480	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1718573	167368480	81882141	125	4522										
RCSD1	92241	broad.mit.edu	37	chr1	167659335	167659335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaattcaaggtcaagagctCgcctctgattgagaagcttc	9	9	3	3	rs186993523	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:167659335C>T	ENST00000367854.3	+	4	579	c.248C>T	c.(247-249)tCg>tTg	p.S83L	RCSD1_ENST00000537350.1_Missense_Mutation_p.S53L	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	83					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)	p.S83L(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					GTCAAGAGCTCGCCTCTGATT	0.423													C|||	4	0.000798722	0	0.0043	5008	,	,		21815	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											142	129	133					1																	167659335		2203	4300	6503	165925959	SO:0001583	missense	92241			BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.248C>T	1.37:g.167659335C>T	ENSP00000356828:p.Ser83Leu		165925959	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	37	CCDS1263.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	32	5.132397	0.94473	.	.	ENSG00000198771	ENST00000367854;ENST00000537350	T;T	0.71817	-0.6;-0.39	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000001	D	0.82806	0.5117	M	0.76838	2.35	0.42190	D	0.991721	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	T	0.81406	-0.0947	9	0.45353	T	0.12	-12.0066	19.9564	0.97221	0.0:1.0:0.0:0.0	.	53;83	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	L	83;53	ENSP00000356828:S83L;ENSP00000439409:S53L	ENSP00000356828:S83L	S	+	2	0	RCSD1	165925959	0.998000	0.40836	0.971000	0.41717	0.998000	0.95712	4.981000	0.63819	2.708000	0.92522	0.650000	0.86243	TCG		0.423	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		T	167659335	C	T	167659335	3	4	47	1	0	0	0	0	1	0	0	0	13222	893	31	1	262	1	RCSD1	1	167659335	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	290855	167659335	81591286	126	4523										
ADCY10	55811	broad.mit.edu	37	chr1	167805745	167805745	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgttaaaacgtggtcaaaGaaattcaagatcttttctct	6	6	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:167805745G>T	ENST00000367851.4	-	23	3295	c.3111C>A	c.(3109-3111)ttC>ttA	p.F1037L	ADCY10_ENST00000545172.1_Missense_Mutation_p.F884L|ADCY10_ENST00000367848.1_Missense_Mutation_p.F945L	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1037					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.F1037L(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CGTGGTCAAAGAAATTCAAGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	85	85					1																	167805745		2203	4300	6503	166072369	SO:0001583	missense	55811			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.3111C>A	1.37:g.167805745G>T	ENSP00000356825:p.Phe1037Leu		166072369	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	G	7.812	0.715882	0.15306	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.31510	1.49;1.5;1.5	5.08	1.97	0.26223	.	0.335593	0.26546	N	0.023769	T	0.08582	0.0213	L	0.46741	1.465	0.32240	N	0.572908	B;B	0.18461	0.028;0.016	B;B	0.16722	0.016;0.007	T	0.15636	-1.0430	9	0.23302	T	0.38	-22.1817	4.2926	0.10886	0.1881:0.0:0.6323:0.1797	.	945;1037	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	L	884;1037;945	ENSP00000441992:F884L;ENSP00000356825:F1037L;ENSP00000356822:F945L	ENSP00000356822:F945L	F	-	3	2	ADCY10	166072369	1.000000	0.71417	0.991000	0.47740	0.249000	0.25844	0.745000	0.26259	0.819000	0.34492	0.655000	0.94253	TTC		0.323	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167805745	G	T	167805745	3	4	47	1	0	0	0	0	1	0	0	0	293	933	33	2	1765	2	ADCY10	1	167805745	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	146410	167805745	81444876	127	4524										
ADCY10	55811	broad.mit.edu	37	chr1	167865926	167865926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggggtggttttaagaagtTaacctaaataaaagcaaatg	12	3	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:167865926T>C	ENST00000367851.4	-	7	830	c.646A>G	c.(646-648)Aac>Gac	p.N216D	ADCY10_ENST00000545172.1_Missense_Mutation_p.N63D|ADCY10_ENST00000367848.1_Missense_Mutation_p.N124D	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	216					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.N216D(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						TTTAAGAAGTTAACCTAAATA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	94	90					1																	167865926		2203	4300	6503	166132550	SO:0001583	missense	55811			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.646A>G	1.37:g.167865926T>C	ENSP00000356825:p.Asn216Asp		166132550	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.754296	0.49362	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.31247	1.55;1.5;1.51	5.32	5.32	0.75619	.	0.700897	0.14079	N	0.342837	T	0.05777	0.0151	N	0.08118	0	0.25130	N	0.990575	P;P;P	0.43231	0.763;0.763;0.801	B;B;B	0.36608	0.229;0.163;0.192	T	0.06643	-1.0815	9	0.11485	T	0.65	-8.8882	11.961	0.53009	0.0:0.0:0.0:1.0	.	63;124;216	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	D	63;216;124	ENSP00000441992:N63D;ENSP00000356825:N216D;ENSP00000356822:N124D	ENSP00000356822:N124D	N	-	1	0	ADCY10	166132550	0.996000	0.38824	0.998000	0.56505	0.814000	0.46013	2.351000	0.44071	2.133000	0.65898	0.528000	0.53228	AAC		0.323	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		C	167865926	T	C	167865926	3	2	47	1	0	0	0	0	1	0	0	0	293	1754	61	4	4294	4	ADCY10	1	167865926	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	60181	167865926	81384695	128	4525										
GPR161	23432	broad.mit.edu	37	chr1	168054942	168054942	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaataagttgattttggcttCggcctcaatggctttggcca	10	8	1	1	rs199866265		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:168054942C>T	ENST00000367838.1	-	8	1730	c.1417G>A	c.(1417-1419)Gaa>Aaa	p.E473K	GPR161_ENST00000546300.1_Missense_Mutation_p.E359K|GPR161_ENST00000367836.1_Missense_Mutation_p.E341K|GPR161_ENST00000539777.1_Missense_Mutation_p.E395K|GPR161_ENST00000537209.1_Missense_Mutation_p.E493K|GPR161_ENST00000361697.2_Missense_Mutation_p.E473K|GPR161_ENST00000367835.1_Missense_Mutation_p.E473K|GPR161_ENST00000271357.5_Missense_Mutation_p.E473K	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	473					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)	p.E473K(1)		breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					ATTTTGGCTTCGGCCTCAATG	0.567													c|||	1	0.000199681	0	0	5008	,	,		20610	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											70	71	71					1																	168054942		2203	4300	6503	166321566	SO:0001583	missense	23432			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1417G>A	1.37:g.168054942C>T	ENSP00000356812:p.Glu473Lys		166321566	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	25.7	4.666890	0.88251	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;D;T;T;T;T;T	0.82255	-0.12;-0.12;-1.59;-0.12;-1.13;-1.11;-0.04;-0.12	5.94	5.94	0.96194	.	0.048446	0.85682	D	0.000000	T	0.58538	0.2129	N	0.08118	0	0.28328	N	0.921907	P;P;P;P;P	0.48230	0.846;0.76;0.907;0.76;0.555	B;B;B;B;B	0.34138	0.131;0.038;0.176;0.062;0.038	T	0.72057	-0.4405	9	0.72032	D	0.01	-16.2524	19.9728	0.97289	0.0:1.0:0.0:0.0	.	493;359;395;493;473	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8	.;.;.;.;GP161_HUMAN	K	473;473;341;473;359;395;493;473	ENSP00000356812:E473K;ENSP00000271357:E473K;ENSP00000356810:E341K;ENSP00000356809:E473K;ENSP00000444348:E359K;ENSP00000437576:E395K;ENSP00000441039:E493K;ENSP00000355194:E473K	ENSP00000271357:E473K	E	-	1	0	GPR161	166321566	1.000000	0.71417	0.985000	0.45067	0.996000	0.88848	7.343000	0.79319	2.816000	0.96949	0.645000	0.84053	GAA		0.567	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		T	168054942	C	T	168054942	3	4	47	1	0	0	0	0	1	0	0	0	6685	893	31	1	176	1	GPR161	1	168054942	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	189016	168054942	81195679	129	4526										
BLZF1	8548	broad.mit.edu	37	chr1	169347745	169347745	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caatacagtgtgatgtatggCgaagtaaattccttgcaagc	10	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169347745C>T	ENST00000367808.3	+	4	1069	c.646C>T	c.(646-648)Cga>Tga	p.R216*	BLZF1_ENST00000329281.2_Nonsense_Mutation_p.R216*			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	216					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)	p.R216*(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					TGATGTATGGCGAAGTAAATT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	1											95	97	97					1																	169347745		2203	4300	6503	167614369	SO:0001587	stop_gained	8548			U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.646C>T	1.37:g.169347745C>T	ENSP00000356782:p.Arg216*		167614369	O15298|Q5T531|Q5T533|Q9GZX4	Nonsense_Mutation	SNP	ENST00000367808.3	37	CCDS1278.1	.	.	.	.	.	.	.	.	.	.	C	37	6.062399	0.97246	.	.	ENSG00000117475	ENST00000367808;ENST00000329281;ENST00000426663	.	.	.	6.17	4.25	0.50352	.	0.055634	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7065	15.4433	0.75204	0.3705:0.6295:0.0:0.0	.	.	.	.	X	216	.	ENSP00000327541:R216X	R	+	1	2	BLZF1	167614369	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.079000	0.50104	0.864000	0.35578	0.655000	0.94253	CGA		0.363	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666		T	169347745	C	T	169347745	4	4	47	1	0	0	0	0	0	1	0	0	1454	760	27	1	656	1	BLZF1	1	169347745	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1292803	169347745	79902876	130	4527										
F5	2153	broad.mit.edu	37	chr1	169511880	169511880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaattgagaactgagttCttgccaatgaggtgtctcag	12	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169511880C>A	ENST00000367797.3	-	13	2649	c.2448G>T	c.(2446-2448)aaG>aaT	p.K816N	F5_ENST00000367796.3_Missense_Mutation_p.K821N	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	816	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.K816N(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GAACTGAGTTCTTGCCAATGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											170	167	168					1																	169511880		2203	4300	6503	167778504	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.2448G>T	1.37:g.169511880C>A	ENSP00000356771:p.Lys816Asn		167778504	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.308931	0.23821	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.24151	1.87;1.87	5.8	2.39	0.29439	.	0.837341	0.11450	N	0.562895	T	0.08313	0.0207	L	0.46157	1.445	0.22112	N	0.999352	B	0.15473	0.013	B	0.14023	0.01	T	0.19844	-1.0293	9	0.30854	T	0.27	-5.2164	6.2873	0.21041	0.1369:0.6472:0.1334:0.0825	.	816	P12259	FA5_HUMAN	N	816;821	ENSP00000356771:K816N;ENSP00000356770:K821N	ENSP00000356770:K821N	K	-	3	2	F5	167778504	0.004000	0.15560	0.060000	0.19600	0.021000	0.10359	0.803000	0.27083	0.764000	0.33197	-0.515000	0.04445	AAG		0.483	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169511880	C	A	169511880	3	1	47	1	0	0	0	0	1	0	0	0	5361	912	32	2	4278	2	F5	1	169511880	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	164135	169511880	79738741	131	4528										
F5	2153	broad.mit.edu	37	chr1	169526090	169526090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccagctgatgtggtcatggGcacaaactgttatatctgag	12	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169526090G>A	ENST00000367797.3	-	6	947	c.746C>T	c.(745-747)gCc>gTc	p.A249V	F5_ENST00000546081.1_Missense_Mutation_p.A112V|F5_ENST00000367796.3_Missense_Mutation_p.A249V	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	249	F5/8 type A 1.|Plastocyanin-like 2.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.A249V(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTGGTCATGGGCACAAACTGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM950384	F5	M							64	56	58					1																	169526090		2203	4300	6503	167792714	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.746C>T	1.37:g.169526090G>A	ENSP00000356771:p.Ala249Val		167792714	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200414	0.79015	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99709	-6.48;-6.48;-6.48	6.07	6.07	0.98685	Cupredoxin (2);	0.196194	0.52532	D	0.000069	D	0.99089	0.9687	L	0.41027	1.25	0.31244	N	0.6948529999999999	D	0.69078	0.997	P	0.61874	0.895	D	0.99906	1.1181	9	0.11485	T	0.65	-23.1495	15.7416	0.77901	0.0667:0.0:0.9333:0.0	.	249	P12259	FA5_HUMAN	V	249;249;112	ENSP00000356771:A249V;ENSP00000356770:A249V;ENSP00000439664:A112V	ENSP00000356770:A249V	A	-	2	0	F5	167792714	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	7.594000	0.82698	2.890000	0.99128	0.650000	0.86243	GCC		0.463	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169526090	G	A	169526090	3	1	47	1	0	0	0	0	1	0	0	0	5361	1203	42	3	6008	3	F5	1	169526090	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	14210	169526090	79724531	132	4529										
F5	2153	broad.mit.edu	37	chr1	169551753	169551753	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaaaggaagttacagaaaGattcaaactggaaataaaat	7	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169551753G>T	ENST00000367797.3	-	2	367	c.166C>A	c.(166-168)Ctt>Att	p.L56I	F5_ENST00000546081.1_Intron|F5_ENST00000367796.3_Missense_Mutation_p.L56I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	56	F5/8 type A 1.|Plastocyanin-like 1.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.L56I(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTTACAGAAAGATTCAAACTG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	1											25	26	25					1																	169551753		2160	4242	6402	167818377	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.166C>A	1.37:g.169551753G>T	ENSP00000356771:p.Leu56Ile		167818377	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	G	8.977	0.974460	0.18736	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98958	-5.27;-5.27	5.68	-6.99	0.01605	Cupredoxin (2);	1.139280	0.06300	N	0.700645	D	0.87229	0.6125	N	0.14661	0.345	0.09310	N	0.999995	B	0.21520	0.057	B	0.16722	0.016	D	0.85483	0.1180	10	0.37606	T	0.19	0.0812	1.4194	0.02309	0.2612:0.1005:0.1781:0.4602	.	56	P12259	FA5_HUMAN	I	56	ENSP00000356771:L56I;ENSP00000356770:L56I	ENSP00000356770:L56I	L	-	1	0	F5	167818377	0.000000	0.05858	0.103000	0.21229	0.698000	0.40448	-1.054000	0.03496	-1.271000	0.02430	-0.172000	0.13284	CTT		0.279	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		T	169551753	G	T	169551753	3	4	47	1	0	0	0	0	1	0	0	0	5361	942	33	2	6604	2	F5	1	169551753	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	25663	169551753	79698868	133	4530										
SELP	6403	broad.mit.edu	37	chr1	169586354	169586354	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcttgatgtatatctccacGcagtcctcgttgttcctttt	6	12	2	1	rs374152128		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169586354G>A	ENST00000263686.6	-	3	430	c.393C>T	c.(391-393)tgC>tgT	p.C131C	SELP_ENST00000367788.2_Silent_p.C131C|SELP_ENST00000458599.2_Silent_p.C131C|SELP_ENST00000367791.2_Silent_p.C131C|SELP_ENST00000367786.2_Silent_p.C131C|SELP_ENST00000367793.2_Silent_p.C131C|SELP_ENST00000367792.2_Silent_p.C131C|SELP_ENST00000367794.2_Silent_p.C131C	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	131	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)	p.C131C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	ATATCTCCACGCAGTCCTCGT	0.483													G|||	1	0.000199681	0	0	5008	,	,		17112	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	255	233	240		393	-8.3	0.9	1		240	0,8600		0,0,4300	no	coding-synonymous	SELP	NM_003005.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		131/831	169586354	1,13005	2203	4300	6503	167852978	SO:0001819	synonymous_variant	6403			BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"CD molecules"	10721	protein-coding gene	gene with protein product		173610	"selectin P (granule membrane protein 140kD, antigen CD62)"	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.393C>T	1.37:g.169586354G>A			167852978	Q5R344|Q8IVD1	Silent	SNP	ENST00000263686.6	37	CCDS1282.1	.	.	.	.	.	.	.	.	.	.	G	9.885	1.202544	0.22121	2.27E-4	0.0	ENSG00000174175	ENST00000446728	.	.	.	5.79	-8.26	0.01021	.	.	.	.	.	T	0.50446	0.1616	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67409	-0.5678	4	.	.	.	-19.8016	17.3003	0.87181	0.8117:0.0:0.1883:0.0	.	.	.	.	C	131	.	.	R	-	1	0	SELP	167852978	0.000000	0.05858	0.887000	0.34795	0.867000	0.49689	-1.695000	0.01913	-1.454000	0.01926	-0.251000	0.11542	CGT		0.483	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005		A	169586354	G	A	169586354	2	1	47	1	0	0	0	0	0	0	0	1	14056	1079	38	1		1	SELP	1	169586354	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	34601	169586354	79664267	134	4531										
SELE	6401	broad.mit.edu	37	chr1	169702735	169702735	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acccaaagtgagagctgagaGaaactgtgaagcaatcatga	11	7	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:169702735G>T	ENST00000333360.7	-	2	158	c.19C>A	c.(19-21)Ctc>Atc	p.L7I	SELE_ENST00000367779.4_Missense_Mutation_p.L7I|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367777.1_Missense_Mutation_p.L7I|SELE_ENST00000367780.4_Missense_Mutation_p.L7I|SELE_ENST00000367781.4_Missense_Mutation_p.L7I|SELE_ENST00000367782.4_Missense_Mutation_p.L7I|SELE_ENST00000367775.1_Missense_Mutation_p.L7I|SELE_ENST00000367774.1_Missense_Mutation_p.L7I|SELE_ENST00000367776.1_Missense_Mutation_p.L7I	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	7					actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.L7I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	AGAGCTGAGAGAAACTGTGAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											150	156	154					1																	169702735		2203	4300	6503	167969359	SO:0001583	missense	6401			M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.19C>A	1.37:g.169702735G>T	ENSP00000331736:p.Leu7Ile		167969359	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860376	0.32884	.	.	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.23147	1.97;1.92;2.1;1.92;1.97;1.92;2.1;1.97;1.92	4.84	1.88	0.25563	.	0.254981	0.20850	N	0.084551	T	0.13927	0.0337	M	0.75447	2.3	0.09310	N	1	D	0.58268	0.982	P	0.48598	0.583	T	0.08146	-1.0736	10	0.22109	T	0.4	-11.1635	4.3965	0.11365	0.1995:0.1885:0.612:0.0	.	7	P16581	LYAM2_HUMAN	I	7	ENSP00000356755:L7I;ENSP00000356756:L7I;ENSP00000356754:L7I;ENSP00000356753:L7I;ENSP00000331736:L7I;ENSP00000356751:L7I;ENSP00000356749:L7I;ENSP00000356750:L7I;ENSP00000356748:L7I	ENSP00000331736:L7I	L	-	1	0	SELE	167969359	0.702000	0.27816	0.036000	0.18154	0.021000	0.10359	0.773000	0.26661	0.692000	0.31613	-0.214000	0.12660	CTC		0.393	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		T	169702735	G	T	169702735	3	4	47	1	0	0	0	0	1	0	0	0	14050	942	33	2	1861	2	SELE	1	169702735	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	116381	169702735	79547886	135	4532										
C1orf129	80133	broad.mit.edu	37	chr1	170940963	170940963	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttcccatgaagatccctcGattgtaaaacaagcatcatt	6	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:170940963G>A	ENST00000367758.3	+	8	654	c.555G>A	c.(553-555)tcG>tcA	p.S185S	MROH9_ENST00000367759.4_Silent_p.S185S	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	185								p.S185S(1)									AAGATCCCTCGATTGTAAAAC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											308	276	286					1																	170940963		1954	4142	6096	169207587	SO:0001819	synonymous_variant	80133			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.555G>A	1.37:g.170940963G>A			169207587	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																				0.438	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		A	170940963	G	A	170940963	2	1	47	1	0	0	0	0	0	0	0	1	2002	1045	37	1		1	C1orf129	1	170940963	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1238228	170940963	78309658	136	4533										
BAT2L2	23215	broad.mit.edu	37	chr1	171509871	171509871	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaaccagaagcagagaaatTtccttcaacagaaactgcaa	6	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:171509871T>G	ENST00000338920.4	+	16	3497	c.3260T>G	c.(3259-3261)tTt>tGt	p.F1087C	PRRC2C_ENST00000392078.3_Missense_Mutation_p.F1089C|PRRC2C_ENST00000367742.3_Missense_Mutation_p.F1089C|PRRC2C_ENST00000426496.2_Missense_Mutation_p.F1087C	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1087					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.F1089C(1)									GCAGAGAAATTTCCTTCAACA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	100	98					1																	171509871		2203	4300	6503	169776495	SO:0001583	missense	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.3260T>G	1.37:g.171509871T>G	ENSP00000343629:p.Phe1087Cys		169776495	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.518808	0.00967	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.01887	4.58;4.58;4.58;4.58	5.6	-8.56	0.00904	.	2.619140	0.01480	N	0.016651	T	0.00608	0.0020	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40869	-0.9540	10	0.37606	T	0.19	.	12.0033	0.53243	0.0:0.3325:0.4814:0.1861	.	1087	Q9Y520-4	.	C	1089;1088;1087;1089;1087;844	ENSP00000375928:F1089C;ENSP00000410219:F1087C;ENSP00000356716:F1089C;ENSP00000343629:F1087C	ENSP00000343629:F1087C	F	+	2	0	PRRC2C	169776495	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.940000	0.03929	-1.340000	0.02227	-0.321000	0.08615	TTT		0.488	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171509871	T	G	171509871	3	3	47	1	0	0	0	0	1	0	0	0	1322	1841	64	4	3318	4	BAT2L2	1	171509871	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	568908	171509871	77740750	137	4534										
DNM3	26052	broad.mit.edu	37	chr1	172001594	172001594	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccttatggatgaaggaacGgatgccagggatgttctaga	14	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:172001594G>A	ENST00000355305.5	+	5	799	c.642G>A	c.(640-642)acG>acA	p.T214T	DNM3_ENST00000520906.1_Silent_p.T214T|DNM3_ENST00000358155.4_Silent_p.T214T|DNM3_ENST00000367733.2_Silent_p.T214T|DNM3_ENST00000367731.1_Silent_p.T214T			Q9UQ16	DYN3_HUMAN	dynamin 3	214	Dynamin-type G.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.T214T(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ATGAAGGAACGGATGCCAGGG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											179	172	174					1																	172001594		1886	4123	6009	170268217	SO:0001819	synonymous_variant	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.642G>A	1.37:g.172001594G>A			170268217	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Silent	SNP	ENST00000355305.5	37																																																																																					0.373	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		A	172001594	G	A	172001594	2	1	47	1	0	0	0	0	0	0	0	1	4684	1103	39	1		1	DNM3	1	172001594	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	491723	172001594	77249027	138	4535										
C1orf9	51430	broad.mit.edu	37	chr1	172544672	172544672	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttagatatccaacaaataAgtggattaagctgggtactt	8	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:172544672A>C	ENST00000263688.3	+	11	1391	c.1172A>C	c.(1171-1173)aAg>aCg	p.K391T	SUCO_ENST00000610051.1_Missense_Mutation_p.K354T|SUCO_ENST00000608151.1_Missense_Mutation_p.K550T|SUCO_ENST00000367723.4_Missense_Mutation_p.K549T	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	391	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.K550T(1)|p.K391T(1)									CCAACAAATAAGTGGATTAAG	0.274																																																2	Substitution - Missense(2)	large_intestine(2)	1											82	83	83					1																	172544672		2203	4296	6499	170811295	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1172A>C	1.37:g.172544672A>C	ENSP00000263688:p.Lys391Thr		170811295	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054720	0.75960	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	T;T	0.45276	0.9;0.9	5.49	5.49	0.81192	Galactose-binding domain-like (1);Sad1/UNC-like, C-terminal (2);	0.043012	0.85682	D	0.000000	T	0.40448	0.1117	N	0.20574	0.59	0.80722	D	1	D;P;D;D	0.89917	0.998;0.949;1.0;1.0	D;P;D;D	0.91635	0.975;0.875;0.998;0.999	T	0.48736	-0.9009	10	0.62326	D	0.03	-20.7321	14.7072	0.69200	1.0:0.0:0.0:0.0	.	354;391;550;391	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	T	550;391	ENSP00000356696:K550T;ENSP00000263688:K391T	ENSP00000263688:K391T	K	+	2	0	C1orf9	170811295	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	9.235000	0.95353	2.216000	0.71823	0.377000	0.23210	AAG		0.274	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		C	172544672	A	C	172544672	3	2	47	1	0	0	0	0	1	0	0	0	2073	72	3	4	1214	4	C1orf9	1	172544672	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	543078	172544672	76705949	139	4536										
C1orf9	51430	broad.mit.edu	37	chr1	172579070	172579070	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agccctttacgaaccagagaGatttttctaatatgggagaa	9	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:172579070G>T	ENST00000263688.3	+	24	3655	c.3436G>T	c.(3436-3438)Gat>Tat	p.D1146Y	SUCO_ENST00000610051.1_Missense_Mutation_p.D775Y|SUCO_ENST00000608151.1_Missense_Mutation_p.D1298Y|SUCO_ENST00000367723.4_Missense_Mutation_p.D1297Y	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1146					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.D1298Y(1)|p.D1146Y(1)									GAACCAGAGAGATTTTTCTAA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	1											97	100	99					1																	172579070		2203	4300	6503	170845693	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3436G>T	1.37:g.172579070G>T	ENSP00000263688:p.Asp1146Tyr		170845693	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149341	0.57151	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.56	5.56	0.83823	.	0.277492	0.36002	N	0.002853	T	0.73659	0.3615	M	0.65975	2.015	0.49213	D	0.999764	D;D;D	0.76494	0.996;0.999;0.999	D;D;D	0.70227	0.953;0.968;0.968	T	0.75252	-0.3383	9	0.62326	D	0.03	-19.0758	18.0863	0.89458	0.0:0.0:1.0:0.0	.	775;1298;1146	B4DYM4;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	Y	1298;1146	.	ENSP00000263688:D1146Y	D	+	1	0	C1orf9	170845693	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.583000	0.60964	2.617000	0.88574	0.650000	0.86243	GAT		0.388	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172579070	G	T	172579070	3	4	47	1	0	0	0	0	1	0	0	0	2073	942	33	2	3530	2	C1orf9	1	172579070	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	34398	172579070	76671551	140	4537										
SLC9A11	284525	broad.mit.edu	37	chr1	173476170	173476170	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaacatcacacagttctgaAaccttaagtcctataataaa	4	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:173476170A>C	ENST00000367714.3	-	25	3472	c.3050T>G	c.(3049-3051)tTt>tGt	p.F1017C	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1017					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.F1017C(1)									ACAGTTCTGAAACCTTAAGTC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	90	87					1																	173476170		2202	4298	6500	171742793	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.3050T>G	1.37:g.173476170A>C	ENSP00000356687:p.Phe1017Cys		171742793	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.829741	0.32329	.	.	ENSG00000162753	ENST00000367714	T	0.04360	3.64	5.75	3.32	0.38043	.	0.222920	0.31847	N	0.006966	T	0.06416	0.0165	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.65573	0.936	T	0.12016	-1.0564	10	0.66056	D	0.02	-29.4508	3.9755	0.09472	0.6732:0.0:0.0994:0.2274	.	1017	Q5TAH2	S9A11_HUMAN	C	1017	ENSP00000356687:F1017C	ENSP00000356687:F1017C	F	-	2	0	SLC9A11	171742793	1.000000	0.71417	0.941000	0.38009	0.082000	0.17680	2.462000	0.45049	1.004000	0.39156	0.460000	0.39030	TTT		0.289	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		C	173476170	A	C	173476170	3	2	47	1	0	0	0	0	1	0	0	0	14748	14	1	4	340	4	SLC9A11	1	173476170	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	897100	173476170	75774451	141	4538										
SLC9A11	284525	broad.mit.edu	37	chr1	173542451	173542451	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgttcatatacagatgaaaAaattcttaagaacctaggat	6	5	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:173542451A>C	ENST00000367714.3	-	9	1338	c.916T>G	c.(916-918)Ttt>Gtt	p.F306V	RP3-436N22.3_ENST00000431459.1_RNA|SLC9C2_ENST00000536496.1_Missense_Mutation_p.F204V|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	306					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.F306V(1)									ACAGATGAAAAAATTCTTAAG	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	1											32	34	34					1																	173542451		2200	4290	6490	171809074	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.916T>G	1.37:g.173542451A>C	ENSP00000356687:p.Phe306Val		171809074	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	7.534	0.659234	0.14645	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.05081	3.5;3.5	5.17	0.036	0.14190	Cation/H+ exchanger (1);	0.493944	0.18879	N	0.128611	T	0.01489	0.0048	L	0.44542	1.39	0.09310	N	1	P	0.34462	0.454	B	0.34931	0.192	T	0.46857	-0.9161	10	0.23891	T	0.37	-12.8049	3.7965	0.08741	0.565:0.0:0.2775:0.1575	.	306	Q5TAH2	S9A11_HUMAN	V	306;204	ENSP00000356687:F306V;ENSP00000445437:F204V	ENSP00000356687:F306V	F	-	1	0	SLC9A11	171809074	0.253000	0.23982	0.356000	0.25785	0.073000	0.16967	0.701000	0.25616	0.322000	0.23283	0.533000	0.62120	TTT		0.264	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		C	173542451	A	C	173542451	3	2	47	1	0	0	0	0	1	0	0	0	14748	14	1	4	2538	4	SLC9A11	1	173542451	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	66281	173542451	75708170	142	4539										
PAPPA2	60676	broad.mit.edu	37	chr1	176526002	176526002	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccattttcacaaccctgaacGaacccaaaccagagacccaa	4	16	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:176526002G>T	ENST00000367662.3	+	2	1708	c.544G>T	c.(544-546)Gaa>Taa	p.E182*	PAPPA2_ENST00000367661.3_Nonsense_Mutation_p.E182*	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	182					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E182K(2)|p.E182*(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						AACCCTGAACGAACCCAAACC	0.587																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	lung(2)|large_intestine(1)	1											99	103	102					1																	176526002		2009	4178	6187	174792625	SO:0001587	stop_gained	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.544G>T	1.37:g.176526002G>T	ENSP00000356634:p.Glu182*		174792625	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Nonsense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	45	11.646732	0.99586	.	.	ENSG00000116183	ENST00000367662;ENST00000367661	.	.	.	4.26	2.33	0.28932	.	1.250560	0.06075	U	0.660727	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	6.461	0.21956	0.2067:0.0:0.7933:0.0	.	.	.	.	X	182	.	ENSP00000356633:E182X	E	+	1	0	PAPPA2	174792625	0.002000	0.14202	0.013000	0.15412	0.023000	0.10783	0.911000	0.28584	1.936000	0.56123	0.561000	0.74099	GAA		0.587	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176526002	G	T	176526002	4	4	47	1	0	0	0	0	0	1	0	0	11464	1059	37	2	546	2	PAPPA2	1	176526002	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2983551	176526002	72724619	143	4540										
ASTN1	460	broad.mit.edu	37	chr1	176845724	176845724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggggtcttcacgatcacgtCgcttggcctggagcgccgtc	14	13	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:176845724C>T	ENST00000367654.3	-	21	3647	c.3436G>A	c.(3436-3438)Gac>Aac	p.D1146N	ASTN1_ENST00000361833.2_Missense_Mutation_p.D1138N|ASTN1_ENST00000424564.2_Missense_Mutation_p.D1138N|ASTN1_ENST00000367657.3_Missense_Mutation_p.D1138N	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1146					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.D1138N(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						ACGATCACGTCGCTTGGCCTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	104	115					1																	176845724		2203	4300	6503	175112347	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3436G>A	1.37:g.176845724C>T	ENSP00000356626:p.Asp1146Asn		175112347	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	C	11.82	1.753772	0.31046	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.19	5.19	0.71726	.	0.102547	0.64402	D	0.000003	T	0.20577	0.0495	N	0.14661	0.345	0.44918	D	0.99793	P;P	0.42871	0.792;0.792	B;B	0.25759	0.063;0.063	T	0.08371	-1.0725	10	0.27082	T	0.32	-22.4939	13.9878	0.64345	0.0:0.8481:0.1518:0.0	.	1138;1138	O14525-2;B1AJS1	.;.	N	1138;1138;1146;1138;1138	ENSP00000356629:D1138N;ENSP00000354536:D1138N;ENSP00000356626:D1146N;ENSP00000395041:D1138N	ENSP00000354536:D1138N	D	-	1	0	ASTN1	175112347	1.000000	0.71417	0.219000	0.23793	0.221000	0.24807	5.384000	0.66225	2.400000	0.81607	0.655000	0.94253	GAC		0.582	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176845724	C	T	176845724	3	4	47	1	0	0	0	0	1	0	0	0	1065	884	31	1	488	1	ASTN1	1	176845724	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	319722	176845724	72404897	144	4541										
C1orf49	84066	broad.mit.edu	37	chr1	178485789	178485789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggattttgataaacttcacGaatttgtggaaattatgaag	9	3	1	2	rs200491990		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:178485789G>A	ENST00000319416.2	+	5	368	c.256G>A	c.(256-258)Gaa>Aaa	p.E86K	TEX35_ENST00000367641.3_Missense_Mutation_p.E86K|TEX35_ENST00000367639.1_Missense_Mutation_p.E94K|TEX35_ENST00000258298.2_Missense_Mutation_p.E10K|TEX35_ENST00000367642.3_Intron|TEX35_ENST00000367643.3_Missense_Mutation_p.E86K	NM_032126.4	NP_115502.2			testis expressed 35									p.E86K(1)									TAAACTTCACGAATTTGTGGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	100	105					1																	178485789		2203	4300	6503	176752412	SO:0001583	missense	84066			AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.256G>A	1.37:g.178485789G>A	ENSP00000323795:p.Glu86Lys		176752412		Missense_Mutation	SNP	ENST00000319416.2	37	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155503	0.78114	.	.	ENSG00000240021	ENST00000319416;ENST00000258298;ENST00000367643;ENST00000367641;ENST00000367639	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.12	4.19	0.49359	.	0.145433	0.32161	N	0.006499	T	0.27900	0.0687	L	0.50333	1.59	0.32634	N	0.521625	P;P;D	0.56287	0.874;0.95;0.975	B;B;P	0.47827	0.296;0.404;0.558	T	0.38265	-0.9669	10	0.56958	D	0.05	-22.7736	8.8704	0.35311	0.0998:0.0:0.9002:0.0	.	94;86;86	Q5T0J7-2;Q5T0J7-3;Q5T0J7	.;.;CA049_HUMAN	K	86;10;86;86;94	ENSP00000323795:E86K;ENSP00000258298:E10K;ENSP00000356615:E86K;ENSP00000356613:E86K;ENSP00000356611:E94K	ENSP00000258298:E10K	E	+	1	0	C1orf49	176752412	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	2.748000	0.47483	2.542000	0.85734	0.655000	0.94253	GAA		0.433	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126		A	178485789	G	A	178485789	3	1	47	1	0	0	0	0	1	0	0	0	2047	1059	37	1	298	1	C1orf49	1	178485789	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1640065	178485789	70764832	145	4542										
ACBD6	84320	broad.mit.edu	37	chr1	180382535	180382535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattcacatccacatttttcGatttgatggctttggttata	6	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:180382535G>A	ENST00000367595.3	-	5	1226	c.539C>T	c.(538-540)tCg>tTg	p.S180L	ACBD6_ENST00000475338.2_5'Flank	NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	180						cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)	p.S180L(1)	ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						CACATTTTTCGATTTGATGGC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											276	259	265					1																	180382535		2202	4299	6501	178649158	SO:0001583	missense	84320			BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847			"Ankyrin repeat domain containing"	23339	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 6"			18268358	Standard	NM_032360		Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.539C>T	1.37:g.180382535G>A	ENSP00000356567:p.Ser180Leu		178649158		Missense_Mutation	SNP	ENST00000367595.3	37	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638602	0.47153	.	.	ENSG00000135847	ENST00000367595	T	0.73047	-0.71	5.63	2.68	0.31781	Ankyrin repeat-containing domain (4);	0.190000	0.47852	N	0.000208	T	0.61236	0.2331	L	0.49640	1.575	0.48395	D	0.999647	B	0.13594	0.008	B	0.10450	0.005	T	0.56353	-0.7993	10	0.62326	D	0.03	-1.6421	7.5969	0.28054	0.1468:0.1347:0.7185:0.0	.	180	Q9BR61	ACBD6_HUMAN	L	180	ENSP00000356567:S180L	ENSP00000356567:S180L	S	-	2	0	ACBD6	178649158	1.000000	0.71417	0.688000	0.30117	0.857000	0.48899	4.113000	0.57851	0.380000	0.24823	-0.157000	0.13467	TCG		0.343	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	NM_032360		A	180382535	G	A	180382535	3	1	47	1	0	0	0	0	1	0	0	0	126	1059	37	1	325	1	ACBD6	1	180382535	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1896746	180382535	68868086	146	4543										
CACNA1E	777	broad.mit.edu	37	chr1	181705499	181705499	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggagaagaagaagcagaaGaaggagaagcgtgagacagg	18	3	0	7			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:181705499G>T	ENST00000367573.2	+	22	3351	c.3351G>T	c.(3349-3351)aaG>aaT	p.K1117N	CACNA1E_ENST00000357570.5_Missense_Mutation_p.K1068N|CACNA1E_ENST00000367570.1_Missense_Mutation_p.K1117N|CACNA1E_ENST00000526775.1_Missense_Mutation_p.K1098N|CACNA1E_ENST00000358338.5_Missense_Mutation_p.K1049N|CACNA1E_ENST00000360108.3_Missense_Mutation_p.K1098N|CACNA1E_ENST00000367567.4_Missense_Mutation_p.K724N	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1117					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.K1117N(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						agaagcagaagaaggagaagC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	123	114					1																	181705499		2175	4254	6429	179972122	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3351G>T	1.37:g.181705499G>T	ENSP00000356545:p.Lys1117Asn		179972122	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302985	0.23736	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.04	2.16	0.27623	.	0.785086	0.12692	N	0.447143	T	0.15652	0.0377	N	0.03608	-0.345	0.47698	D	0.999493	P;B;P	0.42518	0.589;0.227;0.782	B;B;B	0.37888	0.173;0.079;0.26	T	0.03354	-1.1045	10	0.51188	T	0.08	.	7.3446	0.26656	0.437:0.0:0.563:0.0	.	1098;1117;1117	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	N	1117;1098;1068;1049;724;1098;1117	ENSP00000356542:K1117N;ENSP00000434814:K1098N;ENSP00000350183:K1068N;ENSP00000351101:K1049N;ENSP00000356539:K724N;ENSP00000353222:K1098N;ENSP00000356545:K1117N	ENSP00000350183:K1068N	K	+	3	2	CACNA1E	179972122	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.253000	0.43205	0.176000	0.19873	0.555000	0.69702	AAG		0.542	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181705499	G	T	181705499	3	4	47	1	0	0	0	0	1	0	0	0	2548	933	33	2	3437	2	CACNA1E	1	181705499	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1322964	181705499	67545122	147	4544										
CACNA1E	777	broad.mit.edu	37	chr1	181745240	181745240	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccccttgcccttcagatgCtcaacctgtttgtggccgtc	8	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:181745240C>A	ENST00000367573.2	+	38	5143	c.5143C>A	c.(5143-5145)Ctc>Atc	p.L1715I	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L1666I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L1715I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L1696I|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L1647I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L1696I|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L1322I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1715					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.L1715I(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCTTCAGATGCTCAACCTGTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											230	229	229					1																	181745240		2002	4181	6183	180011863	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5143C>A	1.37:g.181745240C>A	ENSP00000356545:p.Leu1715Ile		180011863	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.018641	0.93404	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98717	-5.09;-5.09;-5.09;-5.09;-5.09;-5.09;-5.09	5.83	4.89	0.63831	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98979	0.9652	M	0.76574	2.34	0.80722	D	1	P;D;D	0.89917	0.91;1.0;0.998	P;D;D	0.91635	0.906;0.999;0.99	D	0.99761	1.1021	10	0.87932	D	0	.	15.6974	0.77512	0.138:0.862:0.0:0.0	.	1696;1715;1715	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	I	1715;1696;1666;1647;1322;1696;1715	ENSP00000356542:L1715I;ENSP00000434814:L1696I;ENSP00000350183:L1666I;ENSP00000351101:L1647I;ENSP00000356539:L1322I;ENSP00000353222:L1696I;ENSP00000356545:L1715I	ENSP00000350183:L1666I	L	+	1	0	CACNA1E	180011863	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.881000	0.56152	1.414000	0.47017	0.655000	0.94253	CTC		0.547	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181745240	C	A	181745240	3	1	47	1	0	0	0	0	1	0	0	0	2548	797	28	2	5293	2	CACNA1E	1	181745240	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	39741	181745240	67505381	148	4545										
GLUL	2752	broad.mit.edu	37	chr1	182353584	182353584	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcgccggtttcattgagaaGacacgtgcggatgagggctt	14	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:182353584G>T	ENST00000331872.6	-	7	1618	c.1078C>A	c.(1078-1080)Ctt>Att	p.L360I	GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000417584.2_Missense_Mutation_p.L360I|GLUL_ENST00000311223.5_Missense_Mutation_p.L360I|GLUL_ENST00000339526.4_Missense_Mutation_p.L360I	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	360					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.L360I(1)		endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	TCATTGAGAAGACACGTGCGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	41	42					1																	182353584		2203	4300	6503	180620207	SO:0001583	missense	2752			AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.1078C>A	1.37:g.182353584G>T	ENSP00000356537:p.Leu360Ile		180620207	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	37	CCDS1344.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032306	0.35893	.	.	ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	5.34	5.34	0.76211	Glutamine synthetase/guanido kinase, catalytic domain (1);	0.065655	0.64402	D	0.000008	T	0.79358	0.4432	N	0.21508	0.67	0.51482	D	0.999924	B	0.02656	0.0	B	0.13407	0.009	T	0.71961	-0.4434	10	0.07030	T	0.85	-21.2157	12.6607	0.56811	0.0:0.0:0.8345:0.1655	.	360	P15104	GLNA_HUMAN	I	360	ENSP00000356537:L360I;ENSP00000307900:L360I;ENSP00000398320:L360I;ENSP00000344958:L360I	ENSP00000307900:L360I	L	-	1	0	GLUL	180620207	1.000000	0.71417	0.992000	0.48379	0.996000	0.88848	2.381000	0.44336	2.488000	0.83962	0.563000	0.77884	CTT		0.537	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		T	182353584	G	T	182353584	3	4	47	1	0	0	0	0	1	0	0	0	6498	942	33	2	47	2	GLUL	1	182353584	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	608344	182353584	66897037	149	4546										
RNASEL	6041	broad.mit.edu	37	chr1	182545493	182545493	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcctcttttttcataaaacTtattcatttttttcataaca	1	8	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:182545493T>G	ENST00000367559.3	-	6	2190	c.1937A>C	c.(1936-1938)aAg>aCg	p.K646T	RNASEL_ENST00000444138.1_Missense_Mutation_p.K646T	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	646	KEN. {ECO:0000255|PROSITE- ProRule:PRU00725}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.K646T(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						TTCATAAAACTTATTCATTTT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	48	47					1																	182545493		2201	4293	6494	180812116	SO:0001583	missense	6041			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"Ankyrin repeat domain containing"	10050	protein-coding gene	gene with protein product		180435	"prostate cancer 1"	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1937A>C	1.37:g.182545493T>G	ENSP00000356530:p.Lys646Thr		180812116	Q5W0L2|Q6AI46	Missense_Mutation	SNP	ENST00000367559.3	37	CCDS1347.1	.	.	.	.	.	.	.	.	.	.	T	3.826	-0.036742	0.07497	.	.	ENSG00000135828	ENST00000367559;ENST00000444138	T;T	0.34859	1.34;1.34	5.23	-10.5	0.00291	KEN domain, ribonuclease activator (2);	3.637770	0.00718	N	0.000860	T	0.21387	0.0515	L	0.47716	1.5	0.09310	N	0.999999	B	0.23185	0.081	B	0.22152	0.038	T	0.18871	-1.0323	10	0.13853	T	0.58	1.1321	1.6409	0.02752	0.1875:0.197:0.3733:0.2423	.	646	Q05823	RN5A_HUMAN	T	646	ENSP00000356530:K646T;ENSP00000411147:K646T	ENSP00000356530:K646T	K	-	2	0	RNASEL	180812116	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.538000	0.00219	-1.938000	0.01046	-2.254000	0.00282	AAG		0.294	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133		G	182545493	T	G	182545493	3	3	47	1	0	0	0	0	1	0	0	0	13453	1609	56	4	296	4	RNASEL	1	182545493	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	191909	182545493	66705128	150	4547										
C1orf14	81626	broad.mit.edu	37	chr1	182908473	182908473	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttatatttctccaaagttTttttaaaacgttgtgcgata	5	5	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:182908473T>G	ENST00000367547.3	-	5	1150	c.914A>C	c.(913-915)aAa>aCa	p.K305T	SHCBP1L_ENST00000423786.1_Missense_Mutation_p.K186T|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	377								p.K305T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CTCCAAAGTTTTTTTAAAACG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	66	66					1																	182908473		2203	4300	6503	181175096	SO:0001583	missense	81626			AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.914A>C	1.37:g.182908473T>G	ENSP00000356518:p.Lys305Thr		181175096	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.258903	0.59321	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.45276	0.9;0.91	4.97	4.97	0.65823	.	0.000000	0.64402	D	0.000013	T	0.49592	0.1566	L	0.51422	1.61	0.34995	D	0.7554	D;D;D	0.65815	0.991;0.976;0.995	P;P;P	0.60345	0.749;0.784;0.873	T	0.60915	-0.7168	10	0.40728	T	0.16	-20.2148	7.4714	0.27351	0.0:0.0977:0.0:0.9023	.	377;186;305	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	T	305;374;186	ENSP00000356518:K305T;ENSP00000397308:K186T	ENSP00000287709:K374T	K	-	2	0	SHCBP1L	181175096	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.606000	0.36826	1.873000	0.54277	0.460000	0.39030	AAA		0.343	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		G	182908473	T	G	182908473	3	3	47	1	0	0	0	0	1	0	0	0	2006	1841	64	4	1071	4	C1orf14	1	182908473	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	362980	182908473	66342148	151	4548										
APOBEC4	403314	broad.mit.edu	37	chr1	183617370	183617370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattggactcaaaacaacccGcggccataagctggccaggc	10	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:183617370G>A	ENST00000308641.4	-	2	818	c.547C>T	c.(547-549)Cgg>Tgg	p.R183W	RGL1_ENST00000536277.1_Intron|RGL1_ENST00000304685.4_Intron|APOBEC4_ENST00000481562.1_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	183					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.R183W(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						AAAACAACCCGCGGCCATAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	50	49					1																	183617370		2203	4300	6503	181883993	SO:0001583	missense	403314			BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"Apolipoprotein B mRNA editing enzymes"	32152	protein-coding gene	gene with protein product		609908	"chromosome 1 open reading frame 169"	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.547C>T	1.37:g.183617370G>A	ENSP00000310622:p.Arg183Trp		181883993	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383112	0.25031	.	.	ENSG00000173627	ENST00000308641	T	0.65549	-0.16	5.0	4.06	0.47325	.	0.778256	0.11474	N	0.560389	T	0.59514	0.2199	N	0.24115	0.695	0.21897	N	0.999481	D	0.56035	0.974	P	0.51266	0.664	T	0.52472	-0.8571	10	0.49607	T	0.09	-17.8513	13.9545	0.64140	0.0:0.0:0.8316:0.1684	.	183	Q8WW27	ABEC4_HUMAN	W	183	ENSP00000310622:R183W	ENSP00000310622:R183W	R	-	1	2	APOBEC4	181883993	0.004000	0.15560	0.487000	0.27428	0.420000	0.31355	1.033000	0.30191	1.023000	0.39654	0.655000	0.94253	CGG		0.468	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454		A	183617370	G	A	183617370	3	1	47	1	0	0	0	0	1	0	0	0	796	1086	38	1	560	1	APOBEC4	1	183617370	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	708897	183617370	65633251	152	4549										
GLT25D2	23127	broad.mit.edu	37	chr1	183938423	183938423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcttgcctgctggagaagGcaaagacaatgatgtcatca	11	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:183938423G>A	ENST00000361927.4	-	5	1183	c.812C>T	c.(811-813)gCc>gTc	p.A271V	COLGALT2_ENST00000546159.1_Missense_Mutation_p.A271V	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	271					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.A271V(1)									GCTGGAGAAGGCAAAGACAAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											104	92	96					1																	183938423		2203	4300	6503	182205046	SO:0001583	missense	23127			AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.812C>T	1.37:g.183938423G>A	ENSP00000354960:p.Ala271Val		182205046	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	37	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	35	5.555316	0.96514	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.22743	1.94;1.94	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.75484	0.986;0.976	T	0.65059	-0.6260	10	0.51188	T	0.08	.	19.2702	0.94006	0.0:0.0:1.0:0.0	.	271;271	F5H3T5;Q8IYK4	.;GT252_HUMAN	V	271	ENSP00000439112:A271V;ENSP00000354960:A271V	ENSP00000354960:A271V	A	-	2	0	GLT25D2	182205046	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.438000	0.97539	2.557000	0.86248	0.591000	0.81541	GCC		0.473	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		A	183938423	G	A	183938423	3	1	47	1	0	0	0	0	1	0	0	0	6487	1203	42	3	1100	3	GLT25D2	1	183938423	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	321053	183938423	65312198	153	4550										
HMCN1	83872	broad.mit.edu	37	chr1	186082064	186082064	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcaggaaagactacaagaGaatttattctcactgtaaat	7	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186082064G>A	ENST00000271588.4	+	72	11339	c.11110G>A	c.(11110-11112)Gaa>Aaa	p.E3704K	HMCN1_ENST00000367492.2_Missense_Mutation_p.E3704K	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3704	Ig-like C2-type 35.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.E3704K(1)|p.E3704*(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GACTACAAGAGAATTTATTCT	0.373																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(2)	1											98	95	96					1																	186082064		2203	4300	6503	184348687	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11110G>A	1.37:g.186082064G>A	ENSP00000271588:p.Glu3704Lys		184348687	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480875	0.63849	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.65732	-0.17;-0.17	4.91	4.91	0.64330	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.251924	0.46758	D	0.000278	T	0.43100	0.1232	N	0.10874	0.06	0.46028	D	0.998824	P	0.41131	0.739	B	0.39706	0.307	T	0.42172	-0.9467	10	0.07482	T	0.82	.	18.4556	0.90720	0.0:0.0:1.0:0.0	.	3704	Q96RW7	HMCN1_HUMAN	K	3704	ENSP00000271588:E3704K;ENSP00000356462:E3704K	ENSP00000271588:E3704K	E	+	1	0	HMCN1	184348687	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.371000	0.52379	2.416000	0.81992	0.655000	0.94253	GAA		0.373	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186082064	G	A	186082064	3	1	47	1	0	0	0	0	1	0	0	0	7241	943	33	3	11396	3	HMCN1	1	186082064	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2143641	186082064	63168557	154	4551										
HMCN1	83872	broad.mit.edu	37	chr1	186097227	186097227	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagctggaggattctggcttCtatacctgtgttgctaacaa	10	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186097227C>A	ENST00000271588.4	+	83	12937	c.12708C>A	c.(12706-12708)ttC>ttA	p.F4236L	HMCN1_ENST00000367492.2_Missense_Mutation_p.F4236L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4236	Ig-like C2-type 41.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.F4236L(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATTCTGGCTTCTATACCTGTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	84	86					1																	186097227		2203	4300	6503	184363850	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12708C>A	1.37:g.186097227C>A	ENSP00000271588:p.Phe4236Leu		184363850	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	1.473	-0.559310	0.03967	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.65916	-0.18;-0.18	5.46	4.53	0.55603	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.713834	0.14690	N	0.304215	T	0.35307	0.0927	N	0.03084	-0.415	0.27698	N	0.945899	B	0.12630	0.006	B	0.10450	0.005	T	0.18178	-1.0345	10	0.28530	T	0.3	.	6.822	0.23862	0.0:0.6919:0.1556:0.1525	.	4236	Q96RW7	HMCN1_HUMAN	L	4236	ENSP00000271588:F4236L;ENSP00000356462:F4236L	ENSP00000271588:F4236L	F	+	3	2	HMCN1	184363850	0.135000	0.22499	0.876000	0.34364	0.030000	0.12068	0.156000	0.16382	1.257000	0.44085	0.655000	0.94253	TTC		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186097227	C	A	186097227	3	1	47	1	0	0	0	0	1	0	0	0	7241	912	32	2	13038	2	HMCN1	1	186097227	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15163	186097227	63153394	155	4552										
HMCN1	83872	broad.mit.edu	37	chr1	186099771	186099771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaaagggagtggatattgAaattagccacagaatccggc	12	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186099771A>G	ENST00000271588.4	+	85	13401	c.13172A>G	c.(13171-13173)gAa>gGa	p.E4391G	HMCN1_ENST00000367492.2_Missense_Mutation_p.E4391G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4391	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.E4391G(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTGGATATTGAAATTAGCCAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	102	102					1																	186099771		2203	4300	6503	184366394	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13172A>G	1.37:g.186099771A>G	ENSP00000271588:p.Glu4391Gly		184366394	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399293	0.42512	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68181	-0.31;-0.31	5.48	4.34	0.51931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.393600	0.31404	N	0.007717	T	0.68559	0.3014	L	0.28054	0.825	0.29532	N	0.852716	D	0.69078	0.997	D	0.81914	0.995	T	0.63466	-0.6631	10	0.23891	T	0.37	.	11.661	0.51347	0.7174:0.2826:0.0:0.0	.	4391	Q96RW7	HMCN1_HUMAN	G	4391	ENSP00000271588:E4391G;ENSP00000356462:E4391G	ENSP00000271588:E4391G	E	+	2	0	HMCN1	184366394	1.000000	0.71417	0.807000	0.32361	0.719000	0.41307	2.818000	0.48041	0.993000	0.38866	0.482000	0.46254	GAA		0.498	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186099771	A	G	186099771	3	3	47	1	0	0	0	0	1	0	0	0	7241	246	9	4	13510	4	HMCN1	1	186099771	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2544	186099771	63150850	156	4553										
HMCN1	83872	broad.mit.edu	37	chr1	186106960	186106960	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtagctggtcggaatggagtCtttgggaagaatgcacaagg	16	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186106960C>A	ENST00000271588.4	+	89	14009	c.13780C>A	c.(13780-13782)Ctt>Att	p.L4594I	HMCN1_ENST00000367492.2_Missense_Mutation_p.L4594I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4594	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.L4594I(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGAATGGAGTCTTTGGGAAGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											178	174	176					1																	186106960		2203	4300	6503	184373583	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13780C>A	1.37:g.186106960C>A	ENSP00000271588:p.Leu4594Ile		184373583	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	6.758	0.508631	0.12883	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.53640	0.61;0.61	5.65	1.47	0.22746	.	0.932937	0.09248	N	0.828265	T	0.29652	0.0740	N	0.21508	0.67	0.09310	N	1	B	0.20164	0.042	B	0.18561	0.022	T	0.21895	-1.0232	10	0.27785	T	0.31	.	4.9026	0.13782	0.1391:0.4673:0.0:0.3936	.	4594	Q96RW7	HMCN1_HUMAN	I	4594	ENSP00000271588:L4594I;ENSP00000356462:L4594I	ENSP00000271588:L4594I	L	+	1	0	HMCN1	184373583	0.000000	0.05858	0.445000	0.26908	0.659000	0.38960	-0.174000	0.09839	0.643000	0.30638	0.555000	0.69702	CTT		0.488	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186106960	C	A	186106960	3	1	47	1	0	0	0	0	1	0	0	0	7241	913	32	2	14134	2	HMCN1	1	186106960	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7189	186106960	63143661	157	4554										
PRG4	10216	broad.mit.edu	37	chr1	186277699	186277699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctacaacagaaaaaactaccGaatccaaaataacagctaca	3	11	0	1	rs371574559		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186277699G>A	ENST00000445192.2	+	7	2893	c.2848G>A	c.(2848-2850)Gaa>Aaa	p.E950K	PRG4_ENST00000367483.4_Missense_Mutation_p.E909K|PRG4_ENST00000367484.3_Missense_Mutation_p.E479K|PRG4_ENST00000367486.3_Missense_Mutation_p.E907K|PRG4_ENST00000367485.4_Missense_Mutation_p.E857K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	950					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.E950K(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AAAAACTACCGAATCCAAAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											213	229	224					1																	186277699		2203	4300	6503	184544322	SO:0001583	missense	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2848G>A	1.37:g.186277699G>A	ENSP00000399679:p.Glu950Lys		184544322	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	G	8.644	0.896756	0.17686	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.05139	3.5;3.64;3.6;3.49;3.62	3.53	1.32	0.21799	.	1.704460	0.03895	N	0.279406	T	0.02304	0.0071	N	0.04880	-0.145	0.09310	N	1	B;B;B;B	0.34181	0.44;0.216;0.138;0.216	B;B;B;B	0.19148	0.024;0.024;0.01;0.024	T	0.31779	-0.9931	10	0.06891	T	0.86	-1.5784	3.1847	0.06597	0.3739:0.0:0.4375:0.1886	.	816;857;950;909	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	K	907;479;816;909;857;950	ENSP00000356456:E907K;ENSP00000356454:E479K;ENSP00000356453:E909K;ENSP00000356455:E857K;ENSP00000399679:E950K	ENSP00000356452:E816K	E	+	1	0	PRG4	184544322	0.003000	0.15002	0.002000	0.10522	0.044000	0.14063	1.009000	0.29886	0.581000	0.29539	0.430000	0.28490	GAA		0.383	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186277699	G	A	186277699	3	1	47	1	0	0	0	0	1	0	0	0	12515	1059	37	1	2870	1	PRG4	1	186277699	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	170739	186277699	62972922	158	4555										
C1orf27	54953	broad.mit.edu	37	chr1	186360864	186360864	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggccaaggaaatagaaaatGgtgtttatttgattaatgga	12	2	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186360864G>T	ENST00000287859.6	+	8	777	c.652G>T	c.(652-654)Ggt>Tgt	p.G218C	C1orf27_ENST00000432021.3_Missense_Mutation_p.G218C|C1orf27_ENST00000367470.3_Missense_Mutation_p.G218C|C1orf27_ENST00000419367.3_Missense_Mutation_p.G186C	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	218						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.G218C(2)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						AATAGAAAATGGTGTTTATTT	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	1											92	93	93					1																	186360864		1844	4086	5930	184627487	SO:0001583	missense	54953			BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.652G>T	1.37:g.186360864G>T	ENSP00000287859:p.Gly218Cys		184627487	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604356	0.46423	.	.	ENSG00000157181	ENST00000367470;ENST00000419367;ENST00000432021;ENST00000287859	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.32	3.37	0.38596	.	0.310331	0.34067	N	0.004296	T	0.55641	0.1933	M	0.68952	2.095	0.31298	N	0.688654	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.983;0.989;0.989	T	0.59568	-0.7430	10	0.62326	D	0.03	-21.9996	5.0815	0.14659	0.2477:0.0:0.6089:0.1434	.	186;218;218	E9PFR7;Q5SWX8-2;Q5SWX8	.;.;ODR4_HUMAN	C	218;186;218;218	ENSP00000356440:G218C;ENSP00000395084:G186C;ENSP00000402029:G218C;ENSP00000287859:G218C	ENSP00000287859:G218C	G	+	1	0	C1orf27	184627487	0.998000	0.40836	0.998000	0.56505	0.955000	0.61496	1.728000	0.38105	0.559000	0.29153	-0.355000	0.07637	GGT		0.323	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		T	186360864	G	T	186360864	3	4	47	1	0	0	0	0	1	0	0	0	2042	1348	47	2	678	2	C1orf27	1	186360864	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	83165	186360864	62889757	159	4556										
PLA2G4A	5321	broad.mit.edu	37	chr1	186863263	186863263	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgccaattatgtcatggatGaaactctagggacagcaaca	9	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186863263G>T	ENST00000367466.3	+	5	450	c.298G>T	c.(298-300)Gaa>Taa	p.E100*	PLA2G4A_ENST00000442353.2_Nonsense_Mutation_p.E100*|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	100	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.E100*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TGTCATGGATGAAACTCTAGG	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											153	150	151					1																	186863263		2203	4298	6501	185129886	SO:0001587	stop_gained	5321			M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.298G>T	1.37:g.186863263G>T	ENSP00000356436:p.Glu100*		185129886	B1AKG4|Q29R80	Nonsense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	38	6.906244	0.97924	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-24.2273	18.8654	0.92290	0.0:0.0:1.0:0.0	.	.	.	.	X	100	.	ENSP00000356436:E100X	E	+	1	0	PLA2G4A	185129886	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.091000	0.94151	2.686000	0.91538	0.650000	0.86243	GAA		0.328	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186863263	G	T	186863263	4	4	47	1	0	0	0	0	0	1	0	0	12032	1291	45	2	312	2	PLA2G4A	1	186863263	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	502399	186863263	62387358	160	4557										
PLA2G4A	5321	broad.mit.edu	37	chr1	186901976	186901976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgtgatgaaggcattatacGaatcaggaattctggattgt	12	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:186901976G>A	ENST00000367466.3	+	8	792	c.640G>A	c.(640-642)Gaa>Aaa	p.E214K	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.E154K|PLA2G4A_ENST00000466600.1_Intron	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	214	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.E214K(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	GGCATTATACGAATCAGGAAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											217	214	215					1																	186901976		2203	4300	6503	185168599	SO:0001583	missense	5321			M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.640G>A	1.37:g.186901976G>A	ENSP00000356436:p.Glu214Lys		185168599	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907126	0.52333	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.06218	3.33;3.33	6.16	6.16	0.99307	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.11836	0.0288	L	0.39085	1.19	0.58432	D	0.999998	D;D	0.63046	0.986;0.992	P;P	0.52066	0.616;0.689	T	0.19128	-1.0315	10	0.18710	T	0.47	-27.724	19.4236	0.94732	0.0:0.0:1.0:0.0	.	154;214	E7EU42;P47712	.;PA24A_HUMAN	K	214;154	ENSP00000356436:E214K;ENSP00000406892:E154K	ENSP00000356436:E214K	E	+	1	0	PLA2G4A	185168599	1.000000	0.71417	0.976000	0.42696	0.699000	0.40488	7.568000	0.82369	2.937000	0.99478	0.650000	0.86243	GAA		0.423	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		A	186901976	G	A	186901976	3	1	47	1	0	0	0	0	1	0	0	0	12032	1059	37	1	666	1	PLA2G4A	1	186901976	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	38713	186901976	62348645	161	4558										
RGS21	431704	broad.mit.edu	37	chr1	192335140	192335140	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgaggctcagaaattaatCtattgtctcatggccaagga	10	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:192335140C>A	ENST00000417209.2	+	5	519	c.345C>A	c.(343-345)atC>atA	p.I115I		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	115	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.I115I(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						AGAAATTAATCTATTGTCTCA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	91	92					1																	192335140		1829	4077	5906	190601763	SO:0001819	synonymous_variant	431704			AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"Regulators of G-protein signaling"	26839	protein-coding gene	gene with protein product		612407	"regulator of G-protein signalling 21"			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.345C>A	1.37:g.192335140C>A			190601763		Silent	SNP	ENST00000417209.2	37	CCDS41448.1																																																																																				0.368	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2			A	192335140	C	A	192335140	2	1	47	1	0	0	0	0	0	0	0	1	13341	903	32	2		2	RGS21	1	192335140	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5433164	192335140	56915481	162	4559										
RGS2	5997	broad.mit.edu	37	chr1	192780151	192780151	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttttttaaagtcggaattCtgtgaagaaaatattgaatt	8	3	1	3	rs149228054		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:192780151C>A	ENST00000235382.5	+	4	346	c.315C>A	c.(313-315)ttC>ttA	p.F105L		NM_002923.3	NP_002914.1	P41220	RGS2_HUMAN	regulator of G-protein signaling 2	105	Necessary to inhibit protein synthesis.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				brown fat cell differentiation (GO:0050873)|cell cycle (GO:0007049)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phospholipase activity (GO:0010519)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of microtubule polymerization (GO:0031116)|regulation of adrenergic receptor signaling pathway (GO:0071877)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of translation (GO:0006417)|relaxation of cardiac muscle (GO:0055119)|relaxation of vascular smooth muscle (GO:0060087)|spermatogenesis (GO:0007283)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.F105L(1)		large_intestine(3)|lung(1)|urinary_tract(1)	5						AGTCGGAATTCTGTGAAGAAA	0.408																																					Pancreas(71;51 2183 4981)											1	Substitution - Missense(1)	large_intestine(1)	1						C	LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	105	112	109		315	1.6	1	1	dbSNP_134	109	0,8600		0,0,4300	no	missense	RGS2	NM_002923.3	22	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	possibly-damaging	105/212	192780151	1,13005	2203	4300	6503	191046774	SO:0001583	missense	5997			L13463	CCDS1377.1	1q31	2014-06-19	2014-06-19		ENSG00000116741	ENSG00000116741		"Regulators of G-protein signaling", "Endogenous ligands"	9998	protein-coding gene	gene with protein product		600861	"regulator of G-protein signalling 2, 24kD", "regulator of G-protein signalling 2, 24kDa", "regulator of G-protein signaling 2, 24kDa"	G0S8		8179820	Standard	NM_002923		Approved		uc001gsl.3	P41220	OTTHUMG00000035600	ENST00000235382.5:c.315C>A	1.37:g.192780151C>A	ENSP00000235382:p.Phe105Leu		191046774	Q6I9U5	Missense_Mutation	SNP	ENST00000235382.5	37	CCDS1377.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042846	0.75732	2.27E-4	0.0	ENSG00000116741	ENST00000235382	T	0.02050	4.48	5.0	1.61	0.23674	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.046316	0.85682	D	0.000000	T	0.11410	0.0278	M	0.86805	2.84	0.52501	D	0.999959	D	0.71674	0.998	D	0.66351	0.943	T	0.00939	-1.1507	10	0.87932	D	0	.	10.3025	0.43661	0.0:0.7321:0.0:0.2679	.	105	P41220	RGS2_HUMAN	L	105	ENSP00000235382:F105L	ENSP00000235382:F105L	F	+	3	2	RGS2	191046774	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.743000	0.47442	0.519000	0.28406	0.563000	0.77884	TTC		0.408	RGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086396.1	NM_002923		A	192780151	C	A	192780151	3	1	47	1	0	0	0	0	1	0	0	0	13339	912	32	2	329	2	RGS2	1	192780151	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	445011	192780151	56470470	163	4560										
TROVE2	6738	broad.mit.edu	37	chr1	193045078	193045078	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggctgtagagaaagtgaagCgcacaagagatgagctagaa	14	5	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:193045078C>T	ENST00000367446.3	+	3	919	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	TROVE2_ENST00000367441.1_Missense_Mutation_p.R237C|TROVE2_ENST00000367445.3_Missense_Mutation_p.R237C|TROVE2_ENST00000367443.1_Missense_Mutation_p.R237C|TROVE2_ENST00000367444.3_Missense_Mutation_p.R237C|TROVE2_ENST00000416058.2_5'UTR|TROVE2_ENST00000400968.2_Missense_Mutation_p.R237C|TROVE2_ENST00000432079.1_5'UTR|TROVE2_ENST00000460715.2_Intron	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	237	RNA-binding. {ECO:0000250}.|TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)	p.R237C(1)		biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						GAAAGTGAAGCGCACAAGAGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	78	78					1																	193045078		1831	4087	5918	191311701	SO:0001583	missense	6738			BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.709C>T	1.37:g.193045078C>T	ENSP00000356416:p.Arg237Cys		191311701	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	37	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.176527	0.78564	.	.	ENSG00000116747	ENST00000400968;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43;2.43	6.04	6.04	0.98038	TROVE (2);	0.139692	0.64402	D	0.000004	T	0.21962	0.0529	L	0.34521	1.04	0.80722	D	1	D;B;P;D	0.58970	0.984;0.052;0.951;0.98	P;B;B;B	0.46585	0.521;0.012;0.387;0.206	T	0.00171	-1.1959	10	0.56958	D	0.05	-8.4961	20.6437	0.99549	0.0:1.0:0.0:0.0	.	237;237;237;237	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	C	237	ENSP00000383752:R237C;ENSP00000356416:R237C;ENSP00000356413:R237C;ENSP00000356415:R237C;ENSP00000356414:R237C;ENSP00000356411:R237C	ENSP00000356411:R237C	R	+	1	0	TROVE2	191311701	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.331000	0.79192	2.890000	0.99128	0.650000	0.86243	CGC		0.348	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		T	193045078	C	T	193045078	3	4	47	1	0	0	0	0	1	0	0	0	16616	768	27	1	715	1	TROVE2	1	193045078	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	264927	193045078	56205543	164	4561										
CDC73	79577	broad.mit.edu	37	chr1	193104712	193104712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcagaagcaaagaaaccacGaattgaggtaaagaaactgt	10	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:193104712G>A	ENST00000367435.3	+	5	600	c.416G>A	c.(415-417)cGa>cAa	p.R139Q	MIR1278_ENST00000408753.1_RNA	NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	139					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.R139Q(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						AAGAAACCACGAATTGAGGTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	49	49					1																	193104712		2203	4299	6502	191371335	SO:0001583	missense	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.416G>A	1.37:g.193104712G>A	ENSP00000356405:p.Arg139Gln		191371335	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289609	0.80914	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.87412	-2.25	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.88966	0.6581	M	0.79805	2.47	0.80722	D	1	B	0.24721	0.11	B	0.22753	0.041	D	0.85781	0.1361	10	0.56958	D	0.05	-7.7983	20.1688	0.98156	0.0:0.0:1.0:0.0	.	139	Q6P1J9	CDC73_HUMAN	Q	139	ENSP00000356405:R139Q	ENSP00000356405:R139Q	R	+	2	0	CDC73	191371335	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.281000	0.95811	2.766000	0.95052	0.603000	0.83216	CGA		0.313	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		A	193104712	G	A	193104712	3	1	47	1	0	0	0	0	1	0	0	0	3091	1058	37	1	434	1	CDC73	1	193104712	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	59634	193104712	56145909	165	4562										
KCNT2	343450	broad.mit.edu	37	chr1	196295850	196295850	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttaaaatatacttacgggTtatccaatagcagtactatg	6	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:196295850T>C	ENST00000294725.9	-	19	3188	c.2273A>G	c.(2272-2274)aAc>aGc	p.N758S	KCNT2_ENST00000367433.5_Missense_Mutation_p.N758S|KCNT2_ENST00000498426.1_Intron|KCNT2_ENST00000609185.1_Missense_Mutation_p.N708S|KCNT2_ENST00000367431.4_Missense_Mutation_p.N708S|KCNT2_ENST00000451324.2_Missense_Mutation_p.N369S			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	758					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.N758S(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TACTTACGGGTTATCCAATAG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	54	54					1																	196295850		2202	4294	6496	194562473	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2273A>G	1.37:g.196295850T>C	ENSP00000294725:p.Asn758Ser		194562473	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192094	0.38707	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000451324;ENST00000294725	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000003	T	0.67163	0.2864	L	0.52266	1.64	0.40020	D	0.975393	B;B;B;B;B	0.18741	0.007;0.013;0.03;0.03;0.007	B;B;B;B;B	0.20577	0.009;0.02;0.03;0.03;0.009	T	0.63093	-0.6714	10	0.08179	T	0.78	.	15.4964	0.75653	0.0:0.0:0.0:1.0	.	758;740;758;708;758	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	S	758;708;369;758	ENSP00000356403:N758S;ENSP00000356401:N708S;ENSP00000405474:N369S;ENSP00000294725:N758S	ENSP00000294725:N758S	N	-	2	0	KCNT2	194562473	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.219000	0.72231	2.107000	0.64212	0.528000	0.53228	AAC		0.294	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196295850	T	C	196295850	3	2	47	1	0	0	0	0	1	0	0	0	8113	1725	60	4	1174	4	KCNT2	1	196295850	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3191138	196295850	52954771	166	4563										
ZBTB41	360023	broad.mit.edu	37	chr1	197157452	197157452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttcttgatgctttaaccGagcaaaccgtgatttaaaat	6	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:197157452G>A	ENST00000367405.4	-	4	1584	c.1516C>T	c.(1516-1518)Cgg>Tgg	p.R506W	ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R506W(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						TGCTTTAACCGAGCAAACCGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	88	87					1																	197157452		2203	4300	6503	195424075	SO:0001583	missense	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.1516C>T	1.37:g.197157452G>A	ENSP00000356375:p.Arg506Trp		195424075	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Missense_Mutation	SNP	ENST00000367405.4	37	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836447	0.71373	.	.	ENSG00000177888	ENST00000367405	T	0.28454	1.61	5.48	4.52	0.55395	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37261	U	0.002164	T	0.44498	0.1296	L	0.41710	1.295	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.11792	-1.0573	10	0.38643	T	0.18	.	13.3035	0.60338	0.0:0.0:0.7248:0.2752	.	506	Q5SVQ8	ZBT41_HUMAN	W	506	ENSP00000356375:R506W	ENSP00000356375:R506W	R	-	1	2	ZBTB41	195424075	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.814000	0.48010	2.734000	0.93682	0.563000	0.77884	CGG		0.368	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		A	197157452	G	A	197157452	3	1	47	1	0	0	0	0	1	0	0	0	17582	1057	37	1	1241	1	ZBTB41	1	197157452	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	861602	197157452	52093169	167	4564										
PTPRC	5788	broad.mit.edu	37	chr1	198685892	198685892	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatacgaaatatgttttatCattacatgcctacatcattg	4	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:198685892C>A	ENST00000367376.2	+	13	1538	c.1367C>A	c.(1366-1368)tCa>tAa	p.S456*	PTPRC_ENST00000352140.3_Nonsense_Mutation_p.S408*|PTPRC_ENST00000348564.6_Nonsense_Mutation_p.S297*|PTPRC_ENST00000594404.1_Nonsense_Mutation_p.S295*|PTPRC_ENST00000442510.2_Nonsense_Mutation_p.S458*	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	456	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S456*(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						TATGTTTTATCATTACATGCC	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											73	75	74					1																	198685892		2202	4300	6502	196952515	SO:0001587	stop_gained	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1367C>A	1.37:g.198685892C>A	ENSP00000356346:p.Ser456*		196952515	A8K7W6|Q16614|Q9H0Y6	Nonsense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	18.35	3.604449	0.66445	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	.	.	.	4.43	1.45	0.22620	.	0.760161	0.11248	N	0.583985	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.165	0.15081	0.3651:0.5379:0.0:0.097	.	.	.	.	X	458;392;408;408;342;456;390;295	.	ENSP00000306782:S295X	S	+	2	0	PTPRC	196952515	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.203000	0.09438	0.345000	0.23873	0.650000	0.86243	TCA		0.308	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198685892	C	A	198685892	4	1	47	1	0	0	0	0	0	1	0	0	12834	838	29	2	1424	2	PTPRC	1	198685892	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1528440	198685892	50564729	168	4565										
PTPRC	5788	broad.mit.edu	37	chr1	198711085	198711085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcctgaggatcctcacttgCtcctcaaactgagaaggaga	10	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:198711085C>T	ENST00000367376.2	+	24	2656	c.2485C>T	c.(2485-2487)Ctc>Ttc	p.L829F	PTPRC_ENST00000352140.3_Missense_Mutation_p.L781F|PTPRC_ENST00000348564.6_Missense_Mutation_p.L670F|PTPRC_ENST00000594404.1_Missense_Mutation_p.L668F|PTPRC_ENST00000442510.2_Missense_Mutation_p.L831F	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	829	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L829F(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						TCCTCACTTGCTCCTCAAACT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	58	59					1																	198711085		2203	4300	6503	196977708	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2485C>T	1.37:g.198711085C>T	ENSP00000356346:p.Leu829Phe		196977708	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	29.5	5.010877	0.93346	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	T	0.12569	2.67	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.43579	D	0.000547	T	0.33904	0.0879	L	0.46614	1.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.00112	-1.2044	10	0.35671	T	0.21	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	670;781;829	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	F	831;781;829;668	ENSP00000193532:L781F	ENSP00000306782:L668F	L	+	1	0	PTPRC	196977708	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	7.736000	0.84948	2.884000	0.98904	0.655000	0.94253	CTC		0.453	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198711085	C	T	198711085	3	4	47	1	0	0	0	0	1	0	0	0	12834	797	28	3	2586	3	PTPRC	1	198711085	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	25193	198711085	50539536	169	4566										
KIF14	9928	broad.mit.edu	37	chr1	200583505	200583505	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcacaaaatcttggaattaTtcctggttcttcactaaatc	4	9	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:200583505T>G	ENST00000367350.4	-	4	1834	c.1396A>C	c.(1396-1398)Ata>Cta	p.I466L		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	466	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.I466L(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						CTTGGAATTATTCCTGGTTCT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	73	71					1																	200583505		2203	4300	6503	198850128	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.1396A>C	1.37:g.200583505T>G	ENSP00000356319:p.Ile466Leu		198850128	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	T	18.93	3.727311	0.69074	.	.	ENSG00000118193	ENST00000367350	T	0.72282	-0.64	5.72	5.72	0.89469	Kinesin, motor domain (4);	0.050576	0.85682	D	0.000000	T	0.65322	0.2680	N	0.17248	0.465	0.48632	D	0.99968	P	0.40032	0.699	P	0.47786	0.557	T	0.65565	-0.6137	10	0.33940	T	0.23	.	15.9899	0.80197	0.0:0.0:0.0:1.0	.	466	Q15058	KIF14_HUMAN	L	466	ENSP00000356319:I466L	ENSP00000356319:I466L	I	-	1	0	KIF14	198850128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.281000	0.58965	2.181000	0.69327	0.528000	0.53228	ATA		0.323	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		G	200583505	T	G	200583505	3	3	47	1	0	0	0	0	1	0	0	0	8297	1493	52	4	3658	4	KIF14	1	200583505	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1872420	200583505	48667116	170	4567										
IPO9	55705	broad.mit.edu	37	chr1	201839937	201839937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatctagaccagattcttcGtgccatcctcagtaagatgc	8	11	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:201839937G>A	ENST00000361565.4	+	18	2429	c.2360G>A	c.(2359-2361)cGt>cAt	p.R787H		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	787					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)	p.R787H(1)		cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						CAGATTCTTCGTGCCATCCTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											54	54	54					1																	201839937		2203	4300	6503	200106560	SO:0001583	missense	55705			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.2360G>A	1.37:g.201839937G>A	ENSP00000354742:p.Arg787His		200106560	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	G	35	5.444906	0.96187	.	.	ENSG00000198700	ENST00000361565	T	0.66460	-0.21	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77287	0.4108	L	0.51914	1.62	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.76228	-0.3036	10	0.45353	T	0.12	-5.8686	17.091	0.86622	0.0:0.0:1.0:0.0	.	787	Q96P70	IPO9_HUMAN	H	787	ENSP00000354742:R787H	ENSP00000354742:R787H	R	+	2	0	IPO9	200106560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.363000	0.97131	2.629000	0.89072	0.591000	0.81541	CGT		0.567	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		A	201839937	G	A	201839937	3	1	47	1	0	0	0	0	1	0	0	0	7820	1145	40	1	2430	1	IPO9	1	201839937	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1256432	201839937	47410684	171	4568										
ELF3	1999	broad.mit.edu	37	chr1	201983066	201983066	+	Frame_Shift_Del	DEL	C	C	-													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgaaggcgtcttcaagttCctgcgctccgaggctgtggc							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:201983066delC	ENST00000359651.3	+	7	4107	c.915delC	c.(913-915)ttcfs	p.F305fs	ELF3_ENST00000367283.3_Frame_Shift_Del_p.F305fs|ELF3_ENST00000367284.5_Frame_Shift_Del_p.F305fs|RP11-510N19.5_ENST00000504773.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.L306fs*19(2)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						TCTTCAAGTTCCTGCGCTCCG	0.592																																																2	Deletion - Frameshift(2)	large_intestine(2)	1											91	74	80					1																	201983066		2203	4300	6503	200249689	SO:0001589	frameshift_variant	1999			AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.915delC	1.37:g.201983066delC	ENSP00000352673:p.Phe305fs		200249689		Frame_Shift_Del	DEL	ENST00000359651.3	37	CCDS1419.1																																																																																				0.592	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		-	201983066	C	-	201983066	7	5	47	1	0	1	0	1	0	0	0	0	5068	854	30	0	941	0	ELF3	1	201983066	Frame_Shift_Del	DEL	C	TCGA-AG-3892-01A-01W-1073-09	143129	201983066	47267555	172	4569										
PPP1R12B	4660	broad.mit.edu	37	chr1	202399862	202399862	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttttctccatttccagcttCgaagtgaaaaggagacacgg	10	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:202399862C>T	ENST00000608999.1	+	7	1078	c.925C>T	c.(925-927)Cga>Tga	p.R309*	PPP1R12B_ENST00000336894.4_Nonsense_Mutation_p.R309*|PPP1R12B_ENST00000480184.1_Nonsense_Mutation_p.R309*|PPP1R12B_ENST00000356764.2_Nonsense_Mutation_p.R309*	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	309					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)	p.R309*(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			TTTCCAGCTTCGAAGTGAAAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											95	89	91					1																	202399862		2203	4300	6503	200666485	SO:0001587	stop_gained	4660			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.925C>T	1.37:g.202399862C>T	ENSP00000476755:p.Arg309*		200666485	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Nonsense_Mutation	SNP	ENST00000608999.1	37	CCDS1426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.898840|6.898840	0.97920|0.97920	.|.	.|.	ENSG00000077157|ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000480184;ENST00000356764|ENST00000466968	.|.	.|.	.|.	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.138507|.	0.33127|.	N|.	0.005245|.	.|T	.|0.76241	.|0.3960	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74328	.|-0.3701	.|4	0.02654|.	T|.	1|.	.|.	19.5746|19.5746	0.95436|0.95436	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	309|104	.|.	ENSP00000337897:R309X|.	R|S	+|+	1|2	2|0	PPP1R12B|PPP1R12B	200666485|200666485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.109000|5.109000	0.64615|0.64615	2.638000|2.638000	0.89438|0.89438	0.655000|0.655000	0.94253|0.94253	CGA|TCG		0.378	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		T	202399862	C	T	202399862	4	4	47	1	0	0	0	0	0	1	0	0	12389	876	31	1	951	1	PPP1R12B	1	202399862	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	416796	202399862	46850759	173	4570										
MYBPH	4608	broad.mit.edu	37	chr1	203144471	203144471	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacctccctctctgcagagCtccagcacatagccctggag	8	17	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:203144471C>T	ENST00000255416.4	-	2	381	c.324G>A	c.(322-324)gaG>gaA	p.E108E		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	108	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.E108E(1)		endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		CTCTGCAGAGCTCCAGCACAT	0.622																																					NSCLC(32;174 1025 14462 23899 42933)											1	Substitution - coding silent(1)	large_intestine(1)	1											103	120	114					1																	203144471		2203	4300	6503	201411094	SO:0001819	synonymous_variant	4608			BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7552	protein-coding gene	gene with protein product		160795	"myosin-binding protein H"			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.324G>A	1.37:g.203144471C>T			201411094	Q16886|Q86YC5	Silent	SNP	ENST00000255416.4	37	CCDS30975.1																																																																																				0.622	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997		T	203144471	C	T	203144471	2	4	47	1	0	0	0	0	0	0	0	1	10044	796	28	3		3	MYBPH	1	203144471	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	744609	203144471	46106150	174	4571										
SLC41A1	254428	broad.mit.edu	37	chr1	205779240	205779240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagcagccacggtcccaaaGcctgccaggaggaatggaaa	12	13	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:205779240G>A	ENST00000367137.3	-	2	1344	c.330C>T	c.(328-330)ggC>ggT	p.G110G		NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	110					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.G110G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CGGTCCCAAAGCCTGCCAGGA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	1											105	99	101					1																	205779240		2203	4300	6503	204045863	SO:0001819	synonymous_variant	254428			AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"Solute carriers"	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.330C>T	1.37:g.205779240G>A			204045863	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																				0.612	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1			A	205779240	G	A	205779240	2	1	47	1	0	0	0	0	0	0	0	1	14666	958	34	3		3	SLC41A1	1	205779240	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2634769	205779240	43471381	175	4572										
C4BPA	722	broad.mit.edu	37	chr1	207318054	207318054	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacaatccactttggataaaGaactataatttttctcaaaa	4	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:207318054G>T	ENST00000367070.3	+	12	1980	c.1786G>T	c.(1786-1788)Gaa>Taa	p.E596*		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	596					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.E596*(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TTTGGATAAAGAACTATAATT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											32	33	33					1																	207318054		2203	4300	6503	205384677	SO:0001587	stop_gained	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1786G>T	1.37:g.207318054G>T	ENSP00000356037:p.Glu596*		205384677	Q5VVQ8	Nonsense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.616746	0.66672	.	.	ENSG00000123838	ENST00000367070	.	.	.	3.63	-3.43	0.04810	.	3.415640	0.01700	N	0.027133	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	5.2496	0.15515	0.0:0.2886:0.1951:0.5164	.	.	.	.	X	596	.	ENSP00000356037:E596X	E	+	1	0	C4BPA	205384677	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.676000	0.01946	-0.711000	0.04995	-0.181000	0.13052	GAA		0.403	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207318054	G	T	207318054	4	4	47	1	0	0	0	0	0	1	0	0	2255	943	33	2	1828	2	C4BPA	1	207318054	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1538814	207318054	41932567	176	4573										
CR2	1380	broad.mit.edu	37	chr1	207648424	207648424	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatgggtacaagctcaataAaacacattctgcatattccc	5	11	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:207648424A>C	ENST00000367058.3	+	13	2591	c.2402A>C	c.(2401-2403)aAa>aCa	p.K801T	CR2_ENST00000367057.3_Missense_Mutation_p.K860T|CR2_ENST00000458541.2_Missense_Mutation_p.K774T|CR2_ENST00000367059.3_Missense_Mutation_p.K801T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	801	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.K860T(1)		NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						AAGCTCAATAAAACACATTCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											166	149	155					1																	207648424		2203	4300	6503	205715047	SO:0001583	missense	1380			M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2402A>C	1.37:g.207648424A>C	ENSP00000356025:p.Lys801Thr		205715047	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	8.841	0.942236	0.18281	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	4.7	2.44	0.29823	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.50582	0.1624	N	0.17379	0.485	0.09310	N	1	P;B;D	0.54772	0.908;0.09;0.968	P;B;P	0.53401	0.725;0.045;0.653	T	0.30995	-0.9959	9	0.24483	T	0.36	.	5.2973	0.15758	0.7769:0.0:0.2231:0.0	.	801;801;860	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	T	801;860;801;774	ENSP00000356025:K801T;ENSP00000356024:K860T;ENSP00000356026:K801T;ENSP00000404222:K774T	ENSP00000356024:K860T	K	+	2	0	CR2	205715047	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	0.408000	0.21065	0.918000	0.36919	0.533000	0.62120	AAA		0.468	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		C	207648424	A	C	207648424	3	2	47	1	0	0	0	0	1	0	0	0	3848	14	1	4	2633	4	CR2	1	207648424	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	330370	207648424	41602197	177	4574										
CR1	1378	broad.mit.edu	37	chr1	207753946	207753946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggggcaaaggtgtcctttgTctgtgatgaagggtaagtgt	16	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:207753946T>C	ENST00000367049.4	+	31	5204	c.5204T>C	c.(5203-5205)gTc>gCc	p.V1735A	CR1_ENST00000400960.2_Missense_Mutation_p.V1285A|CR1_ENST00000367053.1_Missense_Mutation_p.V1285A|CR1_ENST00000367052.1_Missense_Mutation_p.V1285A|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.V1285A|RP11-78B10.2_ENST00000597497.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1285	Sushi 27. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.V1290A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GTGTCCTTTGTCTGTGATGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											206	192	197					1																	207753946		1885	4118	6003	205820569	SO:0001583	missense	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.5204T>C	1.37:g.207753946T>C	ENSP00000356016:p.Val1735Ala		205820569	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	T	9.055	0.993068	0.19043	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.89	2.52	0.30459	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.61198	0.2328	L	0.46885	1.475	0.09310	N	1	D;P;D	0.56521	0.976;0.747;0.972	P;P;P	0.61800	0.894;0.558;0.838	T	0.50767	-0.8789	9	0.09338	T	0.73	.	3.5037	0.07683	0.1972:0.1045:0.0:0.6982	.	1285;1285;1735	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	A	1285;1285;1285;1285;835;1735	ENSP00000356019:V1285A;ENSP00000356018:V1285A;ENSP00000356020:V1285A;ENSP00000383744:V1285A;ENSP00000436139:V835A;ENSP00000356016:V1735A	ENSP00000356016:V1735A	V	+	2	0	CR1	205820569	0.003000	0.15002	0.021000	0.16686	0.518000	0.34316	0.334000	0.19787	0.679000	0.31345	0.533000	0.62120	GTC		0.478	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		C	207753946	T	C	207753946	3	2	47	1	0	0	0	0	1	0	0	0	3846	1667	58	4	5326	4	CR1	1	207753946	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	105522	207753946	41496675	178	4575										
INTS7	25896	broad.mit.edu	37	chr1	212193518	212193518	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgaatcacagaaaaaattCtcttcacaaattcatccaca	2	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:212193518C>A	ENST00000366994.3	-	3	421	c.317G>T	c.(316-318)aGa>aTa	p.R106I	INTS7_ENST00000440600.2_Intron|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.R106I|INTS7_ENST00000366992.3_Missense_Mutation_p.R106I	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	106					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)		p.R106I(1)		NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		AGAAAAAATTCTCTTCACAAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	77	77					1																	212193518		2203	4297	6500	210260141	SO:0001583	missense	25896			AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.317G>T	1.37:g.212193518C>A	ENSP00000355961:p.Arg106Ile		210260141	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066573	0.93898	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992	T;T;T	0.30981	1.51;1.51;1.51	5.21	5.21	0.72293	Armadillo-like helical (1);Armadillo-type fold (1);	0.046080	0.85682	D	0.000000	T	0.59959	0.2232	M	0.80183	2.485	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.78314	0.991;0.991;0.991	T	0.64390	-0.6419	10	0.59425	D	0.04	-23.1031	18.7919	0.91976	0.0:1.0:0.0:0.0	.	106;106;106	Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;INT7_HUMAN	I	106	ENSP00000355961:R106I;ENSP00000355960:R106I;ENSP00000355959:R106I	ENSP00000355959:R106I	R	-	2	0	INTS7	210260141	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.474000	0.81024	2.431000	0.82371	0.650000	0.86243	AGA		0.333	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		A	212193518	C	A	212193518	3	1	47	1	0	0	0	0	1	0	0	0	7804	913	32	2	2643	2	INTS7	1	212193518	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4439572	212193518	37057103	179	4576										
ANGEL2	90806	broad.mit.edu	37	chr1	213178624	213178624	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcaggcagcatatggaatTttgggctgtaagagtaaaac	14	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:213178624T>G	ENST00000366962.3	-	5	1039	c.885A>C	c.(883-885)aaA>aaC	p.K295N	ANGEL2_ENST00000535388.1_Missense_Mutation_p.K126N|ANGEL2_ENST00000360506.2_Missense_Mutation_p.K126N|ANGEL2_ENST00000544555.1_Missense_Mutation_p.K126N|ANGEL2_ENST00000540642.1_Missense_Mutation_p.K169N	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	295								p.K295N(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CATATGGAATTTTGGGCTGTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	89	91					1																	213178624		2203	4300	6503	211245247	SO:0001583	missense	90806			AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.885A>C	1.37:g.213178624T>G	ENSP00000355929:p.Lys295Asn		211245247	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Missense_Mutation	SNP	ENST00000366962.3	37	CCDS1512.1	.	.	.	.	.	.	.	.	.	.	T	5.407	0.260242	0.10239	.	.	ENSG00000174606	ENST00000366962;ENST00000360506;ENST00000544555;ENST00000540642;ENST00000535388	T;D;D;T;D	0.95205	1.64;-3.64;-3.64;1.26;-3.64	5.61	0.662	0.17880	Endonuclease/exonuclease/phosphatase (2);	0.338093	0.37304	N	0.002144	D	0.90844	0.7124	L	0.54323	1.7	0.09310	N	0.999997	B;B	0.13594	0.002;0.008	B;B	0.20577	0.006;0.03	T	0.80865	-0.1191	10	0.38643	T	0.18	-11.6016	9.8459	0.41026	0.0:0.3498:0.0:0.6502	.	169;295	F5H476;Q5VTE6	.;ANGE2_HUMAN	N	295;126;126;169;126	ENSP00000355929:K295N;ENSP00000353696:K126N;ENSP00000443193:K126N;ENSP00000446124:K169N;ENSP00000438141:K126N	ENSP00000353696:K126N	K	-	3	2	ANGEL2	211245247	0.139000	0.22563	0.024000	0.17045	0.301000	0.27625	0.661000	0.25023	-0.134000	0.11516	-0.297000	0.09499	AAA		0.433	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		G	213178624	T	G	213178624	3	3	47	1	0	0	0	0	1	0	0	0	609	1838	64	4	769	4	ANGEL2	1	213178624	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	985106	213178624	36071997	180	4577										
CENPF	1063	broad.mit.edu	37	chr1	214814805	214814805	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catatgaggatcttagtcaaAaatacaaagcagcacaggaa	8	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:214814805A>C	ENST00000366955.3	+	12	3292	c.3124A>C	c.(3124-3126)Aaa>Caa	p.K1042Q		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.K1042Q(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TCTTAGTCAAAAATACAAAGC	0.323																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											47	53	51					1																	214814805		2203	4299	6502	212881428	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3124A>C	1.37:g.214814805A>C	ENSP00000355922:p.Lys1042Gln		212881428	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946984	0.34377	.	.	ENSG00000117724	ENST00000366955	T	0.03951	3.75	4.86	3.7	0.42460	.	0.576602	0.14479	N	0.317056	T	0.03520	0.0101	.	.	.	0.21740	N	0.999562	P	0.43412	0.806	B	0.35413	0.202	T	0.43925	-0.9361	9	0.35671	T	0.21	.	6.9839	0.24718	0.7731:0.1476:0.0793:0.0	.	1042	P49454	CENPF_HUMAN	Q	1042	ENSP00000355922:K1042Q	ENSP00000355922:K1042Q	K	+	1	0	CENPF	212881428	0.986000	0.35501	0.242000	0.24170	0.749000	0.42624	2.670000	0.46833	0.767000	0.33267	0.496000	0.49642	AAA		0.323	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214814805	A	C	214814805	3	2	47	1	0	0	0	0	1	0	0	0	3237	15	1	4	3166	4	CENPF	1	214814805	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1636181	214814805	34435816	181	4578										
CENPF	1063	broad.mit.edu	37	chr1	214826270	214826270	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttttaaagtctagtaaaGaagagctcaataattcattg	6	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:214826270G>T	ENST00000366955.3	+	16	8428	c.8260G>T	c.(8260-8262)Gaa>Taa	p.E2754*	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2850	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E2754*(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GTCTAGTAAAGAAGAGCTCAA	0.343																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Nonsense(1)	large_intestine(1)	1											92	96	95					1																	214826270		2203	4299	6502	212892893	SO:0001587	stop_gained	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8260G>T	1.37:g.214826270G>T	ENSP00000355922:p.Glu2754*		212892893	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	50	16.707560	0.99870	.	.	ENSG00000117724	ENST00000366955;ENST00000391896	.	.	.	3.93	3.93	0.45458	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	14.955	0.71107	0.0:0.0:1.0:0.0	.	.	.	.	X	2754;153	.	ENSP00000355922:E2754X	E	+	1	0	CENPF	212892893	1.000000	0.71417	0.995000	0.50966	0.958000	0.62258	3.084000	0.50143	1.748000	0.51833	0.511000	0.50034	GAA		0.343	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214826270	G	T	214826270	4	4	47	1	0	0	0	0	0	1	0	0	3237	943	33	2	8318	2	CENPF	1	214826270	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	11465	214826270	34424351	182	4579										
CENPF	1063	broad.mit.edu	37	chr1	214830366	214830366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaaccaaggaggcagatgAatacttggataagtactgtt	10	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:214830366A>G	ENST00000366955.3	+	18	8744	c.8576A>G	c.(8575-8577)gAa>gGa	p.E2859G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2955	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E2859G(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAGGCAGATGAATACTTGGAT	0.388																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											110	107	108					1																	214830366		2203	4300	6503	212896989	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8576A>G	1.37:g.214830366A>G	ENSP00000355922:p.Glu2859Gly		212896989	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924871	0.52759	.	.	ENSG00000117724	ENST00000366955	T	0.06371	3.31	5.37	4.24	0.50183	.	0.239140	0.21520	N	0.073238	T	0.08537	0.0212	M	0.66939	2.045	0.25743	N	0.985138	B	0.25521	0.128	B	0.23275	0.045	T	0.20405	-1.0276	10	0.54805	T	0.06	.	7.1443	0.25575	0.798:0.0:0.0714:0.1307	.	2955	P49454	CENPF_HUMAN	G	2859	ENSP00000355922:E2859G	ENSP00000355922:E2859G	E	+	2	0	CENPF	212896989	1.000000	0.71417	0.065000	0.19835	0.527000	0.34593	5.519000	0.67074	0.983000	0.38602	0.533000	0.62120	GAA		0.388	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214830366	A	G	214830366	3	3	47	1	0	0	0	0	1	0	0	0	3237	246	9	4	8642	4	CENPF	1	214830366	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4096	214830366	34420255	183	4580										
CENPF	1063	broad.mit.edu	37	chr1	214830463	214830463	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggcccatctgtgttcacaGcaatctaaacaagattcccg	8	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:214830463G>A	ENST00000366955.3	+	18	8841	c.8673G>A	c.(8671-8673)caG>caA	p.Q2891Q		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2987	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.Q2891Q(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TGTGTTCACAGCAATCTAAAC	0.428																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - coding silent(1)	large_intestine(1)	1											198	187	191					1																	214830463		2203	4300	6503	212897086	SO:0001819	synonymous_variant	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8673G>A	1.37:g.214830463G>A			212897086	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.428	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		A	214830463	G	A	214830463	2	1	47	1	0	0	0	0	0	0	0	1	3237	962	34	3		3	CENPF	1	214830463	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	97	214830463	34420158	184	4581										
KCTD3	51133	broad.mit.edu	37	chr1	215751367	215751367	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaggcttctcttatgtgaaGaattggagcgttcctcttgt	11	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:215751367G>T	ENST00000259154.4	+	6	634	c.340G>T	c.(340-342)Gaa>Taa	p.E114*		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	114					protein homooligomerization (GO:0051260)			p.E114*(2)		breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		CTTATGTGAAGAATTGGAGCG	0.343																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											183	181	182					1																	215751367		2203	4300	6503	213817990	SO:0001587	stop_gained	51133			AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"potassium channel tetramerisation domain containing 3"			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.340G>T	1.37:g.215751367G>T	ENSP00000259154:p.Glu114*		213817990	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Nonsense_Mutation	SNP	ENST00000259154.4	37	CCDS1515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.492127|5.492127	0.96339|0.96339	.|.	.|.	ENSG00000136636|ENSG00000136636	ENST00000259154;ENST00000366945|ENST00000448333	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80025	.|0.4548	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77710	.|-0.2486	.|3	0.51188|.	T|.	0.08|.	-34.8986|-34.8986	20.0591|20.0591	0.97667|0.97667	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	114|86	.|.	ENSP00000259154:E114X|.	E|R	+|+	1|2	0|0	KCTD3|KCTD3	213817990|213817990	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.995000|0.995000	0.86356|0.86356	9.404000|9.404000	0.97306|0.97306	2.739000|2.739000	0.93911|0.93911	0.491000|0.491000	0.48974|0.48974	GAA|AGA		0.343	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		T	215751367	G	T	215751367	4	4	47	1	0	0	0	0	0	1	0	0	8131	943	33	2	362	2	KCTD3	1	215751367	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	920904	215751367	33499254	185	4582										
USH2A	7399	broad.mit.edu	37	chr1	215802328	215802328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacatgcactccggttgctgCggatactcacaggtgtccca	10	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:215802328C>T	ENST00000307340.3	-	71	15733	c.15347G>A	c.(15346-15348)cGc>cAc	p.R5116H	USH2A_ENST00000366943.2_Missense_Mutation_p.R5140H|SNORD116_ENST00000365628.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5116					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.R5116H(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCGGTTGCTGCGGATACTCAC	0.522										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											122	123	123					1																	215802328		2203	4300	6503	213868951	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15347G>A	1.37:g.215802328C>T	ENSP00000305941:p.Arg5116His		213868951	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.419734	0.25552	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.15372	2.43;2.53	5.67	4.76	0.60689	.	0.185589	0.25680	U	0.029004	T	0.16938	0.0407	M	0.65975	2.015	0.30239	N	0.795189	B	0.26445	0.149	B	0.15052	0.012	T	0.11567	-1.0582	10	0.19147	T	0.46	.	9.8145	0.40844	0.0:0.7872:0.0:0.2128	.	5116	O75445	USH2A_HUMAN	H	5116;5140	ENSP00000305941:R5116H;ENSP00000355910:R5140H	ENSP00000305941:R5116H	R	-	2	0	USH2A	213868951	0.122000	0.22280	0.903000	0.35520	0.085000	0.17905	0.532000	0.23067	1.399000	0.46721	-0.218000	0.12543	CGC		0.522	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215802328	C	T	215802328	3	4	47	1	0	0	0	0	1	0	0	0	17076	768	27	1	269	1	USH2A	1	215802328	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	50961	215802328	33448293	186	4583										
USH2A	7399	broad.mit.edu	37	chr1	216219799	216219799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctatgtagttctcctcactgCctgaatagatcagcctccca	6	14	3	2	rs111033268		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:216219799C>T	ENST00000307340.3	-	32	6685	c.6299G>A	c.(6298-6300)gGc>gAc	p.G2100D	USH2A_ENST00000366943.2_Missense_Mutation_p.G2100D	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2100	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.G2100D(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTCCTCACTGCCTGAATAGAT	0.403										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											112	94	100					1																	216219799		2203	4300	6503	214286422	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6299G>A	1.37:g.216219799C>T	ENSP00000305941:p.Gly2100Asp		214286422	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071836	0.76301	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.57907	0.37;0.37	5.42	4.5	0.54988	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.45361	D	0.000368	T	0.68915	0.3053	M	0.71581	2.175	0.53005	D	0.999963	D	0.89917	1.0	D	0.91635	0.999	T	0.67518	-0.5650	10	0.29301	T	0.29	.	13.2939	0.60286	0.0:0.9236:0.0:0.0764	.	2100	O75445	USH2A_HUMAN	D	2100	ENSP00000305941:G2100D;ENSP00000355910:G2100D	ENSP00000305941:G2100D	G	-	2	0	USH2A	214286422	0.979000	0.34478	0.802000	0.32245	0.089000	0.18198	2.824000	0.48088	1.420000	0.47138	0.650000	0.86243	GGC		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216219799	C	T	216219799	3	4	47	1	0	0	0	0	1	0	0	0	17076	739	26	3	9473	3	USH2A	1	216219799	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	417471	216219799	33030822	187	4584										
USH2A	7399	broad.mit.edu	37	chr1	216420166	216420166	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttgttacacagcagagagCcatttattgtcccagtctta	7	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:216420166C>A	ENST00000307340.3	-	13	2956	c.2570G>T	c.(2569-2571)gGc>gTc	p.G857V	USH2A_ENST00000366943.2_Missense_Mutation_p.G857V|USH2A_ENST00000366942.3_Missense_Mutation_p.G857V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	857	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.G857V(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAGCAGAGAGCCATTTATTGT	0.428										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											223	205	211					1																	216420166		2203	4300	6503	214486789	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2570G>T	1.37:g.216420166C>A	ENSP00000305941:p.Gly857Val		214486789	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.430170	0.62844	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.54866	0.55;0.55;0.55	6.03	2.97	0.34412	EGF-like, laminin (3);	0.163834	0.28549	N	0.014955	T	0.63426	0.2510	M	0.67397	2.05	0.80722	D	1	P;D	0.62365	0.551;0.991	P;P	0.62740	0.617;0.906	T	0.64106	-0.6485	10	0.51188	T	0.08	.	8.5741	0.33587	0.0:0.6321:0.2423:0.1256	.	857;857	O75445-2;O75445	.;USH2A_HUMAN	V	857	ENSP00000305941:G857V;ENSP00000355910:G857V;ENSP00000355909:G857V	ENSP00000305941:G857V	G	-	2	0	USH2A	214486789	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.755000	0.38379	1.518000	0.48934	0.655000	0.94253	GGC		0.428	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216420166	C	A	216420166	3	1	47	1	0	0	0	0	1	0	0	0	17076	739	26	2	13292	2	USH2A	1	216420166	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	200367	216420166	32830455	188	4585										
ESRRG	2104	broad.mit.edu	37	chr1	216692548	216692548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaattcttctttttccagctTcatgctcttgtatttcttta	3	9	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:216692548T>C	ENST00000408911.3	-	6	1231	c.1078A>G	c.(1078-1080)Aag>Gag	p.K360E	ESRRG_ENST00000463665.1_Missense_Mutation_p.K298E|ESRRG_ENST00000366940.2_Missense_Mutation_p.K337E|ESRRG_ENST00000366938.2_Missense_Mutation_p.K337E|ESRRG_ENST00000366937.1_Missense_Mutation_p.K372E|ESRRG_ENST00000493748.1_Missense_Mutation_p.K337E|ESRRG_ENST00000361395.2_Missense_Mutation_p.K337E|ESRRG_ENST00000361525.3_Missense_Mutation_p.K337E|ESRRG_ENST00000359162.2_Missense_Mutation_p.K337E|ESRRG_ENST00000360012.3_Missense_Mutation_p.K337E|ESRRG_ENST00000487276.1_Missense_Mutation_p.K337E|ESRRG_ENST00000493603.1_Missense_Mutation_p.K337E|ESRRG_ENST00000391890.3_Missense_Mutation_p.K344E	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	360					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.K360E(1)		endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	TTTTCCAGCTTCATGCTCTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	116	118					1																	216692548		2203	4300	6503	214759171	SO:0001583	missense	2104			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.1078A>G	1.37:g.216692548T>C	ENSP00000386171:p.Lys360Glu		214759171	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.251757	0.59212	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;T;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;0.72;-4.05;-4.05;-4.05	6.06	6.06	0.98353	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.95108	0.8415	L	0.56340	1.77	0.80722	D	1	B;P;P	0.37441	0.215;0.541;0.595	B;B;B	0.38225	0.199;0.175;0.268	D	0.95121	0.8246	10	0.72032	D	0.01	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	298;372;360	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	E	337;337;372;360;337;337;337;337;337;344;298;337;337;337;337	ENSP00000355225:K337E;ENSP00000355907:K337E;ENSP00000355904:K372E;ENSP00000386171:K360E;ENSP00000352077:K337E;ENSP00000354584:K337E;ENSP00000355905:K337E;ENSP00000353108:K337E;ENSP00000419594:K337E;ENSP00000375761:K344E;ENSP00000418629:K298E;ENSP00000419155:K337E;ENSP00000417374:K337E;ENSP00000419514:K337E	ENSP00000346386:K337E	K	-	1	0	ESRRG	214759171	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.013000	0.88655	2.324000	0.78689	0.533000	0.62120	AAG		0.368	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		C	216692548	T	C	216692548	3	2	47	1	0	0	0	0	1	0	0	0	5275	1792	62	4	306	4	ESRRG	1	216692548	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	272382	216692548	32558073	189	4586										
MIA3	375056	broad.mit.edu	37	chr1	222835663	222835663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcccctaccagggtactcGatgaaggcaaggtaaatgca	10	11	0	1	rs202243744		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:222835663G>A	ENST00000344922.5	+	26	5276	c.5251G>A	c.(5251-5253)Gat>Aat	p.D1751N	MIA3_ENST00000344441.6_Missense_Mutation_p.D1751N|MIA3_ENST00000340535.7_Missense_Mutation_p.D629N|MIA3_ENST00000344507.1_Intron|RP11-378J18.8_ENST00000608771.1_RNA	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1751	Pro-rich.				chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.D1751N(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		CAGGGTACTCGATGAAGGCAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											157	152	153					1																	222835663		1895	4109	6004	220902286	SO:0001583	missense	375056				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.5251G>A	1.37:g.222835663G>A	ENSP00000340900:p.Asp1751Asn		220902286	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.165651|4.165651	0.78339|0.78339	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471|ENST00000450260	T;T;T|.	0.38722|.	1.12;1.12;2.93|.	5.77|5.77	4.86|4.86	0.63082|0.63082	.|.	.|.	.|.	.|.	.|.	T|T	0.57198|0.57198	0.2037|0.2037	M|M	0.68952|0.68952	2.095|2.095	0.27391|0.27391	N|N	0.955129|0.955129	D;D|.	0.76494|.	0.999;0.998|.	P;P|.	0.62089|.	0.898;0.84|.	T|T	0.52888|0.52888	-0.8515|-0.8515	9|5	0.37606|.	T|.	0.19|.	.|.	13.0772|13.0772	0.59093|0.59093	0.0752:0.0:0.9248:0.0|0.0752:0.0:0.9248:0.0	.|.	629;1751|.	Q5JRA6-4;Q5JRA6|.	.;MIA3_HUMAN|.	N|Q	1751;1751;1692;629;629|35	ENSP00000340900:D1751N;ENSP00000340587:D1751N;ENSP00000345866:D629N|.	ENSP00000284471:D629N|.	D|R	+|+	1|2	0|0	MIA3|MIA3	220902286|220902286	1.000000|1.000000	0.71417|0.71417	0.030000|0.030000	0.17652|0.17652	0.042000|0.042000	0.13812|0.13812	4.284000|4.284000	0.58983|0.58983	1.586000|1.586000	0.49944|0.49944	0.650000|0.650000	0.86243|0.86243	GAT|CGA		0.428	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		A	222835663	G	A	222835663	3	1	47	1	0	0	0	0	1	0	0	0	9595	1058	37	1	5353	1	MIA3	1	222835663	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6143115	222835663	26414958	190	4587										
CAPN2	824	broad.mit.edu	37	chr1	223931893	223931893	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaaaccagagcttccaggaAaactatgcagggatctttca	8	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:223931893A>C	ENST00000295006.5	+	3	708	c.399A>C	c.(397-399)gaA>gaC	p.E133D	CAPN2_ENST00000433674.2_Missense_Mutation_p.E55D	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	133	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.E133D(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		GCTTCCAGGAAAACTATGCAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											101	107	105					1																	223931893		2203	4300	6503	221998516	SO:0001583	missense	824			J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.399A>C	1.37:g.223931893A>C	ENSP00000295006:p.Glu133Asp		221998516	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	A	9.957	1.221875	0.22457	.	.	ENSG00000162909	ENST00000433674;ENST00000434648;ENST00000295006;ENST00000366869	D;D;D	0.88975	-2.45;-2.45;-2.45	5.15	-10.3	0.00346	Peptidase C2, calpain, catalytic domain (3);	0.324044	0.35525	N	0.003157	T	0.66867	0.2833	N	0.12961	0.28	0.28770	N	0.900406	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.55829	-0.8079	10	0.25751	T	0.34	.	3.0752	0.06243	0.4964:0.1948:0.1696:0.1392	.	55;133	B7ZA96;P17655	.;CAN2_HUMAN	D	55;55;133;162	ENSP00000413158:E55D;ENSP00000399949:E55D;ENSP00000295006:E133D	ENSP00000295006:E133D	E	+	3	2	CAPN2	221998516	0.000000	0.05858	0.565000	0.28409	0.930000	0.56654	-3.484000	0.00455	-2.152000	0.00794	-0.605000	0.04089	GAA		0.537	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		C	223931893	A	C	223931893	3	2	47	1	0	0	0	0	1	0	0	0	2633	11	1	4	416	4	CAPN2	1	223931893	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1096230	223931893	25318728	191	4588										
DEGS1	8560	broad.mit.edu	37	chr1	224377714	224377714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctctcttttatgcctttcGacctctgttcatcaacccca	4	16	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:224377714G>A	ENST00000323699.4	+	2	684	c.518G>A	c.(517-519)cGa>cAa	p.R173Q	DEGS1_ENST00000391877.3_Missense_Mutation_p.R173Q|DEGS1_ENST00000465848.1_3'UTR	NM_003676.3	NP_003667.1	O15121	DEGS1_HUMAN	delta(4)-desaturase, sphingolipid 1	173					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.R173Q(1)		breast(1)|kidney(3)|large_intestine(2)|lung(4)	10	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		TATGCCTTTCGACCTCTGTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											199	200	200					1																	224377714		2203	4300	6503	222444337	SO:0001583	missense	8560			AF002668	CCDS1540.1	1q42.11	2013-09-02	2011-12-09	2004-12-14	ENSG00000143753	ENSG00000143753		"Fatty acid desaturases"	13709	protein-coding gene	gene with protein product	"sphingolipid delta(4)-desaturase 1", "dihydroceramide desaturase 1"	615843	"degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)"			9188692, 20105137	Standard	NM_003676		Approved	MLD, Des-1, DES1, FADS7, DEGS-1	uc001hoj.3	O15121	OTTHUMG00000037496	ENST00000323699.4:c.518G>A	1.37:g.224377714G>A	ENSP00000316476:p.Arg173Gln		222444337		Missense_Mutation	SNP	ENST00000323699.4	37	CCDS1540.1	.	.	.	.	.	.	.	.	.	.	G	35	5.549275	0.96488	.	.	ENSG00000143753	ENST00000415210;ENST00000323699;ENST00000391877	T;T;T	0.18174	2.23;2.23;2.23	5.91	5.91	0.95273	Fatty acid desaturase, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.60379	0.2264	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.73269	-0.4036	10	0.72032	D	0.01	.	20.303	0.98618	0.0:0.0:1.0:0.0	.	173;152	O15121;E7EMA0	DEGS1_HUMAN;.	Q	152;173;173	ENSP00000400545:R152Q;ENSP00000316476:R173Q;ENSP00000375749:R173Q	ENSP00000316476:R173Q	R	+	2	0	DEGS1	222444337	1.000000	0.71417	0.842000	0.33263	0.934000	0.57294	9.869000	0.99810	2.806000	0.96561	0.549000	0.68633	CGA		0.388	DEGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091285.2			A	224377714	G	A	224377714	3	1	47	1	0	0	0	0	1	0	0	0	4433	1058	37	1	524	1	DEGS1	1	224377714	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	445821	224377714	24872907	192	4589										
PRSS38	339501	broad.mit.edu	37	chr1	228033805	228033805	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatggatatgtgataacataGaaatcacgcccactcctgct	7	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:228033805G>T	ENST00000366757.3	+	5	901	c.877G>T	c.(877-879)Gaa>Taa	p.E293*		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	293	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.E293*(1)|p.E293K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						TGATAACATAGAAATCACGCC	0.552																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	upper_aerodigestive_tract(1)|large_intestine(1)	1											83	80	81					1																	228033805		2203	4300	6503	226100428	SO:0001587	stop_gained	339501				CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.877G>T	1.37:g.228033805G>T	ENSP00000355719:p.Glu293*		226100428	Q7RTY6	Nonsense_Mutation	SNP	ENST00000366757.3	37	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	G	9.045	0.990652	0.18966	.	.	ENSG00000185888	ENST00000366757	.	.	.	4.21	-8.41	0.00961	.	1.225170	0.06384	N	0.715805	.	.	.	.	.	.	0.54753	D	0.999989	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	2.4559	0.04529	0.4743:0.2235:0.189:0.1132	.	.	.	.	X	293	.	ENSP00000355719:E293X	E	+	1	0	PRSS38	226100428	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.163000	0.03138	-1.741000	0.01344	-0.471000	0.05019	GAA		0.552	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228033805	G	T	228033805	4	4	47	1	0	0	0	0	0	1	0	0	12661	943	33	2	895	2	PRSS38	1	228033805	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3656091	228033805	21216816	193	4590										
WNT3A	89780	broad.mit.edu	37	chr1	228238550	228238550	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggatggtgtctcgggagttCgccgacgcccgggagaaccg	18	11	1	1	rs141170201		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:228238550C>T	ENST00000284523.1	+	3	585	c.507C>T	c.(505-507)ttC>ttT	p.F169F	WNT3A_ENST00000366753.2_Silent_p.F169F	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	169					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)	p.F169F(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				CTCGGGAGTTCGCCGACGCCC	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		2,4404	6.2+/-15.9	0,2,2201	83	79	80		507	-1.7	0.7	1	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	WNT3A	NM_033131.3		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		169/353	228238550	2,13004	2203	4300	6503	226305173	SO:0001819	synonymous_variant	89780			AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.507C>T	1.37:g.228238550C>T			226305173	Q3SY79|Q3SY80|Q969P2	Silent	SNP	ENST00000284523.1	37	CCDS1564.1																																																																																				0.672	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		T	228238550	C	T	228238550	2	4	47	1	0	0	0	0	0	0	0	1	17429	883	31	1		1	WNT3A	1	228238550	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	204745	228238550	21012071	194	4591										
OBSCN	84033	broad.mit.edu	37	chr1	228437822	228437822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagctccagctcgaaagttcGaatggaggctgtgggctgca	15	9	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:228437822G>A	ENST00000422127.1	+	14	4234	c.4190G>A	c.(4189-4191)cGa>cAa	p.R1397Q	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.R1489Q|OBSCN_ENST00000284548.11_Missense_Mutation_p.R1397Q|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1397	Ig-like 14.			R -> C (in Ref. 1; CAC85746). {ECO:0000305}.|RM -> HV (in Ref. 1; CAC85749). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.R1397Q(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCGAAAGTTCGAATGGAGGCT	0.672																																																2	Substitution - Missense(2)	large_intestine(2)	1											72	80	77					1																	228437822		2092	4200	6292	226504445	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.4190G>A	1.37:g.228437822G>A	ENSP00000409493:p.Arg1397Gln		226504445	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	7.490	0.650547	0.14516	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.66995	-0.24;-0.24	5.2	-3.32	0.04973	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.423322	0.22467	N	0.059665	T	0.46171	0.1379	L	0.31371	0.925	0.19300	N	0.999975	P;D	0.60160	0.594;0.987	B;P	0.48063	0.195;0.565	T	0.57723	-0.7762	10	0.02654	T	1	.	7.3491	0.26680	0.6013:0.0:0.2851:0.1136	.	1397;1397	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Q	1397	ENSP00000284548:R1397Q;ENSP00000409493:R1397Q	ENSP00000284548:R1397Q	R	+	2	0	OBSCN	226504445	0.000000	0.05858	0.021000	0.16686	0.002000	0.02628	-0.104000	0.10923	-0.496000	0.06650	-0.140000	0.14226	CGA		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228437822	G	A	228437822	3	1	47	1	0	0	0	0	1	0	0	0	10843	1058	37	1	4240	1	OBSCN	1	228437822	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	199272	228437822	20812799	195	4592										
OBSCN	84033	broad.mit.edu	37	chr1	228482673	228482673	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgcagattcatggcctgtCtgtggcagacactggggagt	15	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:228482673C>T	ENST00000422127.1	+	43	11632	c.11588C>T	c.(11587-11589)tCt>tTt	p.S3863F	RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Missense_Mutation_p.S982F|OBSCN_ENST00000366707.4_Missense_Mutation_p.S982F|OBSCN_ENST00000284548.11_Missense_Mutation_p.S3863F|OBSCN_ENST00000570156.2_Missense_Mutation_p.S4292F|OBSCN_ENST00000359599.6_Missense_Mutation_p.S2710F	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3863	Ig-like 39.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.S4146F(1)|p.S3917F(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATGGCCTGTCTGTGGCAGAC	0.607																																																2	Substitution - Missense(2)	large_intestine(2)	1											134	138	136					1																	228482673		2136	4230	6366	226549296	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11588C>T	1.37:g.228482673C>T	ENSP00000409493:p.Ser3863Phe		226549296	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223818	0.39300	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.01	-4.01	0.04045	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.533070	0.03576	N	0.229437	T	0.65291	0.2677	N	0.24115	0.695	0.09310	N	1	D;D	0.64830	0.994;0.993	P;P	0.61658	0.892;0.782	T	0.59852	-0.7376	10	0.56958	D	0.05	.	6.9802	0.24698	0.509:0.2855:0.0:0.2054	.	3863;3863	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	F	3863;3863;982;982;2710	ENSP00000284548:S3863F;ENSP00000409493:S3863F;ENSP00000355668:S982F;ENSP00000355670:S982F;ENSP00000352613:S2710F	ENSP00000284548:S3863F	S	+	2	0	OBSCN	226549296	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.041000	0.03542	-0.490000	0.06707	0.563000	0.77884	TCT		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228482673	C	T	228482673	3	4	47	1	0	0	0	0	1	0	0	0	10843	913	32	3	11754	3	OBSCN	1	228482673	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	44851	228482673	20767948	196	4593										
NUP133	55746	broad.mit.edu	37	chr1	229641805	229641805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttcagccaatgttagggCttccatgactttaacaggaa	8	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:229641805C>T	ENST00000261396.3	-	2	374	c.283G>A	c.(283-285)Gcc>Acc	p.A95T	RP4-613A2.1_ENST00000417605.1_RNA|NUP133_ENST00000537506.1_Missense_Mutation_p.A79T|NUP133_ENST00000366678.3_Missense_Mutation_p.A95T	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	95					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.A95T(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				AATGTTAGGGCTTCCATGACT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											157	146	150					1																	229641805		2203	4300	6503	227708428	SO:0001583	missense	55746				CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.283G>A	1.37:g.229641805C>T	ENSP00000261396:p.Ala95Thr		227708428	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466495	0.84425	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506;ENST00000366678	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.48205	0.1487	M	0.77616	2.38	0.80722	D	1	D	0.56968	0.978	P	0.52159	0.691	T	0.49960	-0.8883	10	0.40728	T	0.16	-6.3985	16.8472	0.85984	0.0:1.0:0.0:0.0	.	95	Q8WUM0	NU133_HUMAN	T	95;95;95;79;95	ENSP00000261396:A95T;ENSP00000355640:A95T;ENSP00000443496:A79T;ENSP00000355639:A95T	ENSP00000261396:A95T	A	-	1	0	NUP133	227708428	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	6.664000	0.74437	2.391000	0.81399	0.555000	0.69702	GCC		0.398	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229641805	C	T	229641805	3	4	47	1	0	0	0	0	1	0	0	0	10785	797	28	3	3287	3	NUP133	1	229641805	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1159132	229641805	19608816	197	4594										
KIAA1383	54627	broad.mit.edu	37	chr1	232940913	232940913	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgataaaaccattacccaAaaaactcactgtcttttacc	3	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:232940913A>C	ENST00000418460.1	+	1	271	c.144A>C	c.(142-144)caA>caC	p.Q48H		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	0					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)	p.Q48H(2)									CCATTACCCAAAAAACTCACT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	1											202	202	202					1																	232940913		1872	4099	5971	231007536	SO:0001583	missense	54627			AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.144A>C	1.37:g.232940913A>C	ENSP00000403208:p.Gln48His		231007536	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.396159	0.42512	.	.	ENSG00000212916	ENST00000418460	.	.	.	3.3	-0.445	0.12242	.	.	.	.	.	T	0.27559	0.0677	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.36720	-0.9736	5	0.87932	D	0	.	0.4358	0.00478	0.3444:0.2965:0.1736:0.1855	.	.	.	.	H	48	.	ENSP00000403208:Q48H	Q	+	3	2	KIAA1383	231007536	0.013000	0.17824	0.000000	0.03702	0.357000	0.29423	2.218000	0.42889	-0.084000	0.12595	0.260000	0.18958	CAA		0.378	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		C	232940913	A	C	232940913	3	2	47	1	0	0	0	0	1	0	0	0	8249	11	1	4	146	4	KIAA1383	1	232940913	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3299108	232940913	16309708	198	4595										
PCNXL2	80003	broad.mit.edu	37	chr1	233393897	233393897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggaagttggactcatttgGcatttgtccttccttagcct	9	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:233393897G>A	ENST00000258229.9	-	5	1945	c.1711C>T	c.(1711-1713)Cca>Tca	p.P571S	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	571						integral component of membrane (GO:0016021)		p.P571S(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GACTCATTTGGCATTTGTCCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	122	124					1																	233393897		1913	4131	6044	231460520	SO:0001583	missense	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.1711C>T	1.37:g.233393897G>A	ENSP00000258229:p.Pro571Ser		231460520	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.441818	0.83993	.	.	ENSG00000135749	ENST00000258229	T	0.08896	3.04	5.7	5.7	0.88788	.	.	.	.	.	T	0.17450	0.0419	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.13980	-1.0489	9	0.16420	T	0.52	.	19.8253	0.96616	0.0:0.0:1.0:0.0	.	571	A6NKB5	PCX2_HUMAN	S	571	ENSP00000258229:P571S	ENSP00000258229:P571S	P	-	1	0	PCNXL2	231460520	1.000000	0.71417	0.957000	0.39632	0.708000	0.40852	5.901000	0.69861	2.682000	0.91365	0.655000	0.94253	CCA		0.413	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233393897	G	A	233393897	3	1	47	1	0	0	0	0	1	0	0	0	11623	1203	42	3	4822	3	PCNXL2	1	233393897	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	452984	233393897	15856724	199	4596										
LYST	1130	broad.mit.edu	37	chr1	235955020	235955020	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaccatcaaaactgctatCtggtaaaattaatgatttgt	6	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:235955020C>A	ENST00000389794.3	-	12	4696	c.4522G>T	c.(4522-4524)Gat>Tat	p.D1508Y	LYST_ENST00000389793.2_Missense_Mutation_p.D1508Y|LYST_ENST00000536965.1_Intron			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1508					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.D1508Y(2)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AAACTGCTATCTGGTAAAATT	0.338																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											155	153	154					1																	235955020		2203	4300	6503	234021643	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4522G>T	1.37:g.235955020C>A	ENSP00000374444:p.Asp1508Tyr		234021643	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.391208	0.25118	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.65178	-0.14;-0.14	5.76	3.91	0.45181	.	1.053090	0.07222	N	0.861116	T	0.73837	0.3638	L	0.59436	1.845	0.45676	D	0.998599	P;D	0.62365	0.946;0.991	P;P	0.58077	0.77;0.832	T	0.64106	-0.6485	10	0.87932	D	0	.	12.4236	0.55534	0.0:0.8648:0.0:0.1352	.	1508;1508	Q99698-3;Q99698	.;LYST_HUMAN	Y	1508	ENSP00000374444:D1508Y;ENSP00000374443:D1508Y	ENSP00000374443:D1508Y	D	-	1	0	LYST	234021643	0.200000	0.23398	0.008000	0.14137	0.007000	0.05969	3.347000	0.52200	0.909000	0.36697	-0.142000	0.14014	GAT		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235955020	C	A	235955020	3	1	47	1	0	0	0	0	1	0	0	0	9158	913	32	2	7051	2	LYST	1	235955020	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2561123	235955020	13295601	200	4597										
HEATR1	55127	broad.mit.edu	37	chr1	236755321	236755321	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcctccacttgtagaaagaGaaacaaactgatggaaaagc	8	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:236755321G>T	ENST00000366582.3	-	11	1508	c.1394C>A	c.(1393-1395)tCt>tAt	p.S465Y	HEATR1_ENST00000366581.2_Missense_Mutation_p.S465Y	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	465					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.S465Y(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGTAGAAAGAGAAACAAACTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	119	119					1																	236755321		2203	4300	6503	234821944	SO:0001583	missense	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1394C>A	1.37:g.236755321G>T	ENSP00000355541:p.Ser465Tyr		234821944	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978774	0.53720	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.66815	-0.23;3.24	5.27	5.27	0.74061	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81987	0.4939	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83467	0.0057	10	0.72032	D	0.01	.	19.2485	0.93913	0.0:0.0:1.0:0.0	.	465	Q9H583	HEAT1_HUMAN	Y	465	ENSP00000355541:S465Y;ENSP00000355540:S465Y	ENSP00000355540:S465Y	S	-	2	0	HEATR1	234821944	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	7.629000	0.83207	2.612000	0.88384	0.650000	0.86243	TCT		0.383	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236755321	G	T	236755321	3	4	47	1	0	0	0	0	1	0	0	0	7048	942	33	2	5180	2	HEATR1	1	236755321	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	800301	236755321	12495300	201	4598										
RYR2	6262	broad.mit.edu	37	chr1	237863701	237863701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaattacaccacagtggccCtgctgccaatgctgtcttca	7	14	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:237863701C>T	ENST00000366574.2	+	65	9618	c.9301C>T	c.(9301-9303)Ctg>Ttg	p.L3101L	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.L3085L|RYR2_ENST00000360064.6_Silent_p.L3099L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3101					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.L3099L(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CACAGTGGCCCTGCTGCCAAT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	1											38	38	38					1																	237863701		1895	4120	6015	235930324	SO:0001819	synonymous_variant	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.9301C>T	1.37:g.237863701C>T			235930324	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.423	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237863701	C	T	237863701	2	4	47	1	0	0	0	0	0	0	0	1	13806	680	24	3		3	RYR2	1	237863701	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1108380	237863701	11386920	202	4599										
FMN2	56776	broad.mit.edu	37	chr1	240286540	240286540	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcctccagaagaagcagaGaagttttgctcccggatcat	12	10	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:240286540G>A	ENST00000319653.9	+	2	1907	c.1677G>A	c.(1675-1677)gaG>gaA	p.E559E		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	559					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.E702E(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AAGAAGCAGAGAAGTTTTGCT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											136	121	126					1																	240286540		2203	4300	6503	238353163	SO:0001819	synonymous_variant	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1677G>A	1.37:g.240286540G>A			238353163	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.522	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240286540	G	A	240286540	2	1	47	1	0	0	0	0	0	0	0	1	5969	933	33	3		3	FMN2	1	240286540	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2422839	240286540	8964081	203	4600										
KMO	8564	broad.mit.edu	37	chr1	241713007	241713007	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggctaccttcacacgtggaaGaagcattaacttagcccttt	8	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:241713007G>T	ENST00000366559.4	+	3	466	c.155G>T	c.(154-156)aGa>aTa	p.R52I	KMO_ENST00000366557.4_Missense_Mutation_p.R52I|KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366558.3_Missense_Mutation_p.R52I	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)									p.R52I(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			ACACGTGGAAGAAGCATTAAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											175	154	161					1																	241713007		2203	4300	6503	239779630	SO:0001583	missense	8564			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.155G>T	1.37:g.241713007G>T	ENSP00000355517:p.Arg52Ile		239779630		Missense_Mutation	SNP	ENST00000366559.4	37	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764121	0.89932	.	.	ENSG00000117009	ENST00000366559;ENST00000366558;ENST00000366557	T;T;T	0.51817	0.69;0.69;0.69	5.37	5.37	0.77165	Monooxygenase, FAD-binding (1);	0.000000	0.85682	D	0.000000	T	0.75817	0.3901	M	0.93594	3.435	0.80722	D	1	D;D;D	0.76494	0.999;0.996;0.999	D;D;D	0.74348	0.983;0.972;0.97	T	0.82139	-0.0605	10	0.87932	D	0	.	14.9668	0.71201	0.0:0.0:1.0:0.0	.	52;52;52	O15229;A8K693;O15229-2	KMO_HUMAN;.;.	I	52	ENSP00000355517:R52I;ENSP00000355516:R52I;ENSP00000355515:R52I	ENSP00000355515:R52I	R	+	2	0	KMO	239779630	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.994000	0.76251	2.677000	0.91161	0.655000	0.94253	AGA		0.423	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679		T	241713007	G	T	241713007	3	4	47	1	0	0	0	0	1	0	0	0	8445	942	33	2	165	2	KMO	1	241713007	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1426467	241713007	7537614	204	4601										
WDR64	128025	broad.mit.edu	37	chr1	241850792	241850792	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagctacataatgactgggTtatgaaaattagatatattt	8	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:241850792T>C	ENST00000366552.2	+	7	1046	c.839T>C	c.(838-840)gTt>gCt	p.V280A	WDR64_ENST00000437684.2_Missense_Mutation_p.V280A	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	280								p.V280A(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			AATGACTGGGTTATGAAAATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	97	96					1																	241850792		2203	4299	6502	239917415	SO:0001583	missense	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.839T>C	1.37:g.241850792T>C	ENSP00000355510:p.Val280Ala		239917415	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	T	17.42	3.384240	0.61845	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.63913	1.0;-0.07;4.58	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000030	T	0.69967	0.3170	L	0.57536	1.79	0.34554	D	0.71166	.	.	.	.	.	.	T	0.80607	-0.1307	8	0.72032	D	0.01	-29.8402	13.9042	0.63823	0.0:0.0:0.0:1.0	.	.	.	.	A	280;280;51	ENSP00000355510:V280A;ENSP00000402446:V280A;ENSP00000406656:V51A	ENSP00000355510:V280A	V	+	2	0	WDR64	239917415	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	5.032000	0.64140	2.097000	0.63578	0.533000	0.62120	GTT		0.353	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		C	241850792	T	C	241850792	3	2	47	1	0	0	0	0	1	0	0	0	17355	1725	60	4	865	4	WDR64	1	241850792	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	137785	241850792	7399829	205	4602										
C1orf101	257044	broad.mit.edu	37	chr1	244735752	244735752	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacaacaagagcattcatttTcttaagtacatctggtcaaa	5	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:244735752T>G	ENST00000366534.4	+	11	1682	c.1628T>G	c.(1627-1629)tTc>tGc	p.F543C	C1orf101_ENST00000366533.4_Missense_Mutation_p.F543C|C1orf101_ENST00000473875.1_3'UTR|C1orf101_ENST00000366531.3_Missense_Mutation_p.F392C	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	543						CatSper complex (GO:0036128)		p.F543C(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			GCATTCATTTTCTTAAGTACA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											103	96	99					1																	244735752		2203	4300	6503	242802375	SO:0001583	missense	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.1628T>G	1.37:g.244735752T>G	ENSP00000355492:p.Phe543Cys		242802375	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	37	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	T	9.174	1.021851	0.19433	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042;ENST00000366531	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.19	-10.4	0.00318	.	3.119150	0.00757	N	0.001117	T	0.13286	0.0322	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.09022	0.0;0.001;0.002;0.001	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.17715	-1.0360	10	0.54805	T	0.06	.	0.8801	0.01232	0.1948:0.2779:0.3046:0.2227	.	463;543;543;392	B1AQM6;Q5SY80;Q5SY80-2;B4DZR4	.;CA101_HUMAN;.;.	C	543;543;543;463;392	ENSP00000355492:F543C;ENSP00000355491:F543C;ENSP00000395796:F463C;ENSP00000355489:F392C	ENSP00000355489:F392C	F	+	2	0	C1orf101	242802375	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.079000	0.03410	-1.634000	0.01537	0.528000	0.53228	TTC		0.323	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		G	244735752	T	G	244735752	3	3	47	1	0	0	0	0	1	0	0	0	1982	1783	62	4	1670	4	C1orf101	1	244735752	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2884960	244735752	4514869	206	4603										
VN1R5	317705	broad.mit.edu	37	chr1	247419954	247419954	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctacccccagtgaaacgggGccagtcttctgtttgtcata	10	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:247419954G>A								RP11-488L18.8 (14829 upstream) : Y_RNA (38182 downstream)																							GTGAAACGGGGCCAGTCTTCT	0.468																																																0			1											256	242	247					1																	247419954		1923	4139	6062	245486577	SO:0001628	intergenic_variant	317705																															1.37:g.247419954G>A			245486577		Missense_Mutation	SNP		37																																																																																				0	0.468									A	247419954	G	A	247419954	1	1	47	0	1	0	0	0	0	0	0	0	17221	1203	42	3		3	VN1R5	1	247419954	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2684202	247419954	1830667	207	4604										
NLRP3	114548	broad.mit.edu	37	chr1	247611728	247611728	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtctgaaatgtatttcaaTtatgagacaaaaagtgcgtt	8	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:247611728T>G	ENST00000336119.3	+	9	3779	c.3033T>G	c.(3031-3033)aaT>aaG	p.N1011K	NLRP3_ENST00000391828.3_Missense_Mutation_p.N1011K|NLRP3_ENST00000366497.2_Missense_Mutation_p.N954K|NLRP3_ENST00000391827.2_Missense_Mutation_p.N954K|NLRP3_ENST00000348069.2_Missense_Mutation_p.N897K|NLRP3_ENST00000366496.2_Missense_Mutation_p.N954K	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	1011					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.N1011K(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TGTATTTCAATTATGAGACAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	102	100					1																	247611728		2203	4300	6503	245678351	SO:0001583	missense	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.3033T>G	1.37:g.247611728T>G	ENSP00000337383:p.Asn1011Lys		245678351	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550089	0.45383	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64	4.36	-0.448	0.12230	.	0.000000	0.45867	D	0.000325	T	0.37073	0.0990	L	0.60455	1.87	0.26033	N	0.981718	P;P;B;B;P	0.40066	0.57;0.701;0.2;0.05;0.615	B;B;B;B;B	0.39185	0.196;0.293;0.047;0.022;0.155	T	0.25398	-1.0133	10	0.26408	T	0.33	.	7.2261	0.26016	0.0:0.4719:0.0:0.5281	.	991;954;897;954;1011	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	K	1011;954;1011;897;954;954	ENSP00000375704:N1011K;ENSP00000355453:N954K;ENSP00000337383:N1011K;ENSP00000294752:N897K;ENSP00000355452:N954K;ENSP00000375703:N954K	ENSP00000337383:N1011K	N	+	3	2	NLRP3	245678351	0.963000	0.33076	0.551000	0.28230	0.964000	0.63967	0.032000	0.13732	-0.086000	0.12550	0.443000	0.29094	AAT		0.428	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		G	247611728	T	G	247611728	3	3	47	1	0	0	0	0	1	0	0	0	10509	1490	52	4	3067	4	NLRP3	1	247611728	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	191774	247611728	1638893	208	4605										
TRIM58	25893	broad.mit.edu	37	chr1	248023999	248023999	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggccaacgtggggaaaaaGactgtcatttggaaggtaag	15	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:248023999G>T	ENST00000366481.3	+	2	549	c.501G>T	c.(499-501)aaG>aaT	p.K167N		NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	167						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.K167N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	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)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TGGGGAAAAAGACTGTCATTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	106	106					1																	248023999		2203	4300	6503	246090622	SO:0001583	missense	25893			AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.501G>T	1.37:g.248023999G>T	ENSP00000355437:p.Lys167Asn		246090622	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	37	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.253814	0.22965	.	.	ENSG00000162722	ENST00000366481	T	0.06294	3.32	4.02	0.881	0.19166	.	0.233460	0.29853	N	0.011038	T	0.09202	0.0227	M	0.63428	1.95	0.09310	N	1	P	0.42483	0.781	P	0.44732	0.459	T	0.10823	-1.0613	10	0.87932	D	0	.	6.6317	0.22861	0.2905:0.0:0.7095:0.0	.	167	Q8NG06	TRI58_HUMAN	N	167	ENSP00000355437:K167N	ENSP00000355437:K167N	K	+	3	2	TRIM58	246090622	0.956000	0.32656	0.113000	0.21522	0.012000	0.07955	0.603000	0.24149	0.360000	0.24265	0.655000	0.94253	AAG		0.478	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		T	248023999	G	T	248023999	3	4	47	1	0	0	0	0	1	0	0	0	16571	933	33	2	507	2	TRIM58	1	248023999	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	412271	248023999	1226622	209	4606										
OR2T33	391195	broad.mit.edu	37	chr1	248436194	248436194	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattttgctggtgttttatgTttacacacgtccccagccac	7	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:248436194T>C	ENST00000318021.2	-	1	944	c.923A>G	c.(922-924)aAc>aGc	p.N308S		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N308S(1)		NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GTGTTTTATGTTTACACACGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											154	155	154					1																	248436194		2203	4300	6503	246502817	SO:0001583	missense	391195				CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.923A>G	1.37:g.248436194T>C	ENSP00000324687:p.Asn308Ser		246502817	B2RNN0	Missense_Mutation	SNP	ENST00000318021.2	37	CCDS31109.1	.	.	.	.	.	.	.	.	.	.	-	0.007	-1.941305	0.00479	.	.	ENSG00000177212	ENST00000318021	T	0.35789	1.29	1.54	0.185	0.15096	.	1.741500	0.04297	U	0.346628	T	0.15609	0.0376	N	0.08118	0	0.09310	N	1	B	0.18013	0.025	B	0.16289	0.015	T	0.18461	-1.0336	10	0.02654	T	1	.	4.5755	0.12232	0.2863:0.0:0.0:0.7137	.	308	Q8NG76	O2T33_HUMAN	S	308	ENSP00000324687:N308S	ENSP00000324687:N308S	N	-	2	0	OR2T33	246502817	0.000000	0.05858	0.001000	0.08648	0.153000	0.21895	-0.178000	0.09782	0.032000	0.15435	0.147000	0.16070	AAC		0.403	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		C	248436194	T	C	248436194	3	2	47	1	0	0	0	0	1	0	0	0	11055	1725	60	4	42	4	OR2T33	1	248436194	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	412195	248436194	814427	210	4607										
OR2T33	391195	broad.mit.edu	37	chr1	248436682	248436682	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgcacccaggagccaacaCgacatggtcatcctcaggca	10	15	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:248436682C>T	ENST00000318021.2	-	1	456	c.435G>A	c.(433-435)tcG>tcA	p.S145S		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S145S(2)		NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GGAGCCAACACGACATGGTCA	0.572																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	1											146	138	141					1																	248436682		2203	4300	6503	246503305	SO:0001819	synonymous_variant	391195				CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.435G>A	1.37:g.248436682C>T			246503305	B2RNN0	Silent	SNP	ENST00000318021.2	37	CCDS31109.1																																																																																				0.572	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		T	248436682	C	T	248436682	2	4	47	1	0	0	0	0	0	0	0	1	11055	523	19	1		1	OR2T33	1	248436682	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	488	248436682	813939	211	4608										
OR2T4	127074	broad.mit.edu	37	chr1	248525879	248525879	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataaggatgtcatgggggctCtgaagaaaatgttaacagtg	13	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:248525879C>A	ENST00000366475.1	+	1	997	c.997C>A	c.(997-999)Ctg>Atg	p.L333M		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	333						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L333M(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATGGGGGCTCTGAAGAAAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											107	113	111					1																	248525879		2203	4300	6503	246592502	SO:0001583	missense	127074			BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.997C>A	1.37:g.248525879C>A	ENSP00000355431:p.Leu333Met		246592502	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	6.877	0.531173	0.13127	.	.	ENSG00000196944	ENST00000366475	T	0.46451	0.87	3.0	-1.77	0.07982	.	0.402618	0.17996	N	0.155046	T	0.22085	0.0532	N	0.21545	0.675	0.09310	N	1	B	0.32829	0.386	B	0.35770	0.21	T	0.10200	-1.0640	10	0.39692	T	0.17	.	2.287	0.04129	0.1343:0.4113:0.2651:0.1892	.	333	Q8NH00	OR2T4_HUMAN	M	333	ENSP00000355431:L333M	ENSP00000355431:L333M	L	+	1	2	OR2T4	246592502	0.000000	0.05858	0.681000	0.30009	0.961000	0.63080	-0.761000	0.04751	0.024000	0.15214	-0.291000	0.09656	CTG		0.408	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248525879	C	A	248525879	3	1	47	1	0	0	0	0	1	0	0	0	11058	912	32	2	999	2	OR2T4	1	248525879	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	89197	248525879	724742	212	4609										
OR2T1	26696	broad.mit.edu	37	chr1	248570399	248570399	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaagggtgtcaggaggtgtCttttgacagtcgactccttc	12	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr1:248570399C>A	ENST00000366474.1	+	1	1104	c.1104C>A	c.(1102-1104)gtC>gtA	p.V368V		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	368						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V368V(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAGGAGGTGTCTTTTGACAGT	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	1											109	118	115					1																	248570399		2203	4300	6503	246637022	SO:0001819	synonymous_variant	26696			U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"GPCR / Class A : Olfactory receptors"	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.1104C>A	1.37:g.248570399C>A			246637022	Q6IEZ9	Silent	SNP	ENST00000366474.1	37	CCDS31115.1																																																																																				0.507	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			A	248570399	C	A	248570399	2	1	47	1	0	0	0	0	0	0	0	1	11047	900	32	2		2	OR2T1	1	248570399	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	44520	248570399	680222	213	4610										
KIDINS220	57498	broad.mit.edu	37	chr2	8925953	8925953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgggaattcaggagcgagTccagcacttgccaccatgta	11	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:8925953T>C	ENST00000256707.3	-	17	2328	c.2147A>G	c.(2146-2148)gAc>gGc	p.D716G	KIDINS220_ENST00000418530.1_Missense_Mutation_p.D674G|KIDINS220_ENST00000473731.1_Missense_Mutation_p.D716G|KIDINS220_ENST00000319688.5_Missense_Mutation_p.D717G|KIDINS220_ENST00000427284.1_Missense_Mutation_p.D716G	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	716	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.D716G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CAGGAGCGAGTCCAGCACTTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											127	121	123					2																	8925953		2007	4191	6198	8843404	SO:0001583	missense	57498			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2147A>G	2.37:g.8925953T>C	ENSP00000256707:p.Asp716Gly		8843404	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.264246	0.39995	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.66815	0.9;-0.23;-0.2;-0.13;-0.2;-0.16;-0.14	5.55	5.55	0.83447	KAP P-loop (1);	0.096049	0.64402	D	0.000001	T	0.58779	0.2146	L	0.39397	1.21	0.58432	D	0.999993	P;B;B;B	0.48162	0.906;0.005;0.153;0.108	B;B;B;B	0.42738	0.396;0.006;0.236;0.347	T	0.56829	-0.7914	10	0.22109	T	0.4	.	14.2614	0.66088	0.0:0.0:0.0:1.0	.	717;717;674;716	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	G	463;400;716;716;674;716;717;717	ENSP00000420364:D463G;ENSP00000256707:D716G;ENSP00000411849:D716G;ENSP00000414923:D674G;ENSP00000418974:D716G;ENSP00000419964:D717G;ENSP00000319947:D717G	ENSP00000256707:D716G	D	-	2	0	KIDINS220	8843404	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.851000	0.62896	2.097000	0.63578	0.533000	0.62120	GAC		0.448	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		C	8925953	T	C	8925953	3	2	47	1	0	0	0	0	1	0	0	0	8292	1667	58	4	3224	4	KIDINS220	2	8925953	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09		8925953	234273420	214	4611										
KIDINS220	57498	broad.mit.edu	37	chr2	8958876	8958876	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaattaattccttcactatTtccagattgccttgttcggc	5	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:8958876T>C	ENST00000256707.3	-	3	337	c.156A>G	c.(154-156)gaA>gaG	p.E52E	KIDINS220_ENST00000418530.1_Silent_p.E10E|KIDINS220_ENST00000473731.1_Silent_p.E52E|KIDINS220_ENST00000319688.5_Silent_p.E52E|KIDINS220_ENST00000427284.1_Silent_p.E52E	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	52					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.E52E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCTTCACTATTTCCAGATTGC	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	2											125	121	122					2																	8958876		1829	4089	5918	8876327	SO:0001819	synonymous_variant	57498			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.156A>G	2.37:g.8958876T>C			8876327	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Silent	SNP	ENST00000256707.3	37	CCDS42650.1																																																																																				0.338	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		C	8958876	T	C	8958876	2	2	47	1	0	0	0	0	0	0	0	1	8292	1838	64	4		4	KIDINS220	2	8958876	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	32923	8958876	234240497	215	4612										
MBOAT2	129642	broad.mit.edu	37	chr2	9098719	9098719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcttgaatgtagataagttCgaaaccaaatggctgctagc	10	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:9098719C>T	ENST00000305997.3	-	2	326	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	43					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R43Q(2)	MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TAGATAAGTTCGAAACCAAAT	0.358																																					Ovarian(194;1699 3813 22401)											2	Substitution - Missense(2)	large_intestine(2)	2											70	71	71					2																	9098719		2203	4300	6503	9016170	SO:0001583	missense	129642			BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.128G>A	2.37:g.9098719C>T	ENSP00000302177:p.Arg43Gln		9016170	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041664	0.93685	.	.	ENSG00000143797	ENST00000305997	T	0.12465	2.68	6.03	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.55774	-0.8088	10	0.72032	D	0.01	-4.7565	17.4628	0.87624	0.0:0.8759:0.1241:0.0	.	43;43	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	Q	43	ENSP00000302177:R43Q	ENSP00000302177:R43Q	R	-	2	0	MBOAT2	9016170	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.409000	0.80053	1.547000	0.49401	0.655000	0.94253	CGA		0.358	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		T	9098719	C	T	9098719	3	4	47	1	0	0	0	0	1	0	0	0	9387	884	31	1	1482	1	MBOAT2	2	9098719	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	139843	9098719	234100654	216	4613										
ODC1	4953	broad.mit.edu	37	chr2	10580869	10580869	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctacacattaatactagccGaagcacaggctgctctgtgg	9	11	2	0	rs141788096		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:10580869G>A	ENST00000234111.4	-	12	1877	c.1367C>T	c.(1366-1368)tCg>tTg	p.S456L	ODC1_ENST00000405333.1_Missense_Mutation_p.S456L	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	456					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)	p.S456L(1)		NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	AATACTAGCCGAAGCACAGGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	LEU/SER	0,4406		0,0,2203	91	86	88		1367	5.9	0.1	2	dbSNP_134	88	3,8597	3.0+/-9.4	0,3,4297	no	missense	ODC1	NM_002539.1	145	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	456/462	10580869	3,13003	2203	4300	6503	10498320	SO:0001583	missense	4953				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1367C>T	2.37:g.10580869G>A	ENSP00000234111:p.Ser456Leu		10498320	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	37	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.680686	0.68042	0.0	3.49E-4	ENSG00000115758	ENST00000234111;ENST00000405333	T;T	0.47528	0.84;0.84	5.88	5.88	0.94601	.	0.317504	0.36374	N	0.002632	T	0.48926	0.1527	L	0.54323	1.7	0.44603	D	0.997573	B	0.06786	0.001	B	0.04013	0.001	T	0.36720	-0.9736	10	0.51188	T	0.08	.	20.2314	0.98350	0.0:0.0:1.0:0.0	.	456	P11926	DCOR_HUMAN	L	456	ENSP00000234111:S456L;ENSP00000385333:S456L	ENSP00000234111:S456L	S	-	2	0	ODC1	10498320	1.000000	0.71417	0.126000	0.21872	0.925000	0.55904	7.138000	0.77305	2.789000	0.95967	0.591000	0.81541	TCG		0.502	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			A	10580869	G	A	10580869	3	1	47	1	0	0	0	0	1	0	0	0	10856	1059	37	1	22	1	ODC1	2	10580869	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1482150	10580869	232618504	217	4614										
KCNF1	3754	broad.mit.edu	37	chr2	11053646	11053646	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagtccttctggtgggccaTcatcaccatgaccaccgtcg	9	16	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:11053646T>C	ENST00000295082.1	+	1	1584	c.1094T>C	c.(1093-1095)aTc>aCc	p.I365T		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	365					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.I365T(1)		NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		TGGTGGGCCATCATCACCATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2											122	96	105					2																	11053646		2203	4300	6503	10971097	SO:0001583	missense	3754			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1094T>C	2.37:g.11053646T>C	ENSP00000295082:p.Ile365Thr		10971097	O43527|Q585L3	Missense_Mutation	SNP	ENST00000295082.1	37	CCDS1676.1	.	.	.	.	.	.	.	.	.	.	t	9.097	1.003262	0.19121	.	.	ENSG00000162975	ENST00000295082	D	0.98512	-4.97	5.32	5.32	0.75619	Ion transport (1);	0.058433	0.64402	D	0.000001	D	0.97266	0.9106	L	0.49778	1.585	0.80722	D	1	P	0.48089	0.905	P	0.50314	0.637	D	0.96687	0.9508	10	0.14656	T	0.56	.	15.5838	0.76465	0.0:0.0:0.0:1.0	.	365	Q9H3M0	KCNF1_HUMAN	T	365	ENSP00000295082:I365T	ENSP00000295082:I365T	I	+	2	0	KCNF1	10971097	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.134000	0.65973	0.529000	0.55759	ATC		0.587	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		C	11053646	T	C	11053646	3	2	47	1	0	0	0	0	1	0	0	0	8047	1435	50	4	1096	4	KCNF1	2	11053646	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	472777	11053646	232145727	218	4615										
GREB1	9687	broad.mit.edu	37	chr2	11772086	11772086	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccaaccaccggccgtcacGaacatgggctctttaatctg	8	15	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:11772086G>A	ENST00000381486.2	+	27	4963	c.4663G>A	c.(4663-4665)Gaa>Aaa	p.E1555K	GREB1_ENST00000234142.5_Missense_Mutation_p.E1555K|GREB1_ENST00000396123.1_Missense_Mutation_p.E553K	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1555						integral component of membrane (GO:0016021)		p.E1555K(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CGGCCGTCACGAACATGGGCT	0.448																																					Ovarian(39;850 945 2785 23371 33093)											1	Substitution - Missense(1)	large_intestine(1)	2											99	96	97					2																	11772086		1931	4132	6063	11689537	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4663G>A	2.37:g.11772086G>A	ENSP00000370896:p.Glu1555Lys		11689537	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401534	0.83120	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.54675	0.56;0.56;0.56	5.48	4.6	0.57074	.	0.095779	0.64402	D	0.000001	T	0.71099	0.3300	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.75150	-0.3419	10	0.72032	D	0.01	-26.1706	14.1031	0.65070	0.0727:0.0:0.9273:0.0	.	1555	Q4ZG55	GREB1_HUMAN	K	1555;1555;553	ENSP00000370896:E1555K;ENSP00000234142:E1555K;ENSP00000379429:E553K	ENSP00000234142:E1555K	E	+	1	0	GREB1	11689537	1.000000	0.71417	0.656000	0.29637	0.525000	0.34531	9.343000	0.97047	1.317000	0.45149	0.557000	0.71058	GAA		0.448	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11772086	G	A	11772086	3	1	47	1	0	0	0	0	1	0	0	0	6781	1059	37	1	4873	1	GREB1	2	11772086	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	718440	11772086	231427287	219	4616										
LPIN1	23175	broad.mit.edu	37	chr2	11959625	11959625	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacagagaagtgattgaaaaGaagccagaaaagtttaaagt	10	3	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:11959625G>T	ENST00000256720.2	+	18	2403	c.2310G>T	c.(2308-2310)aaG>aaT	p.K770N	LPIN1_ENST00000449576.2_Missense_Mutation_p.K855N|LPIN1_ENST00000396099.1_Missense_Mutation_p.K812N|LPIN1_ENST00000425416.2_Missense_Mutation_p.K776N|LPIN1_ENST00000396097.1_Missense_Mutation_p.K500N|LPIN1_ENST00000404113.2_Missense_Mutation_p.K271N	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	770	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.K770N(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TGATTGAAAAGAAGCCAGAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	125	123					2																	11959625		2203	4300	6503	11877076	SO:0001583	missense	23175			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2310G>T	2.37:g.11959625G>T	ENSP00000256720:p.Lys770Asn		11877076	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748603	0.69533	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	5.32	5.32	0.75619	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.153040	0.56097	D	0.000025	D	0.88198	0.6372	M	0.79258	2.445	0.80722	D	1	D;D;P	0.71674	0.998;0.998;0.503	D;D;P	0.77557	0.99;0.979;0.803	D	0.88787	0.3275	10	0.87932	D	0	-39.0765	10.0931	0.42458	0.1539:0.0:0.8461:0.0	.	271;855;770	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	N	855;812;776;770;500;271	ENSP00000397908:K855N;ENSP00000379406:K812N;ENSP00000401522:K776N;ENSP00000256720:K770N;ENSP00000379404:K500N;ENSP00000386120:K271N	ENSP00000256720:K770N	K	+	3	2	LPIN1	11877076	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.175000	0.50855	2.654000	0.90174	0.655000	0.94253	AAG		0.388	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		T	11959625	G	T	11959625	3	4	47	1	0	0	0	0	1	0	0	0	8947	933	33	2	2376	2	LPIN1	2	11959625	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	187539	11959625	231239748	220	4617										
LPIN1	23175	broad.mit.edu	37	chr2	11960605	11960605	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accgtcaaccctaaaggagaGctggtacaggaacatgcaaa	10	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:11960605G>A	ENST00000256720.2	+	19	2571	c.2478G>A	c.(2476-2478)gaG>gaA	p.E826E	LPIN1_ENST00000449576.2_Silent_p.E911E|LPIN1_ENST00000396099.1_Silent_p.E868E|LPIN1_ENST00000425416.2_Silent_p.E832E|LPIN1_ENST00000396097.1_Silent_p.E556E|LPIN1_ENST00000404113.2_Silent_p.E327E	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	826	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.E826E(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		CTAAAGGAGAGCTGGTACAGG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											126	115	119					2																	11960605		2203	4300	6503	11878056	SO:0001819	synonymous_variant	23175			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2478G>A	2.37:g.11960605G>A			11878056	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																				0.358	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		A	11960605	G	A	11960605	2	1	47	1	0	0	0	0	0	0	0	1	8947	962	34	3		3	LPIN1	2	11960605	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	980	11960605	231238768	221	4618										
TRIB2	28951	broad.mit.edu	37	chr2	12880840	12880840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attttagcgtctcgaattcaGcatatggtgctaaggaagtg	11	6	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:12880840G>A	ENST00000155926.4	+	3	2371	c.952G>A	c.(952-954)Gca>Aca	p.A318T	TRIB2_ENST00000381465.2_Missense_Mutation_p.A182T	NM_021643.3	NP_067675.1			tribbles pseudokinase 2									p.A318T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTCGAATTCAGCATATGGTGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	74	75					2																	12880840		2203	4300	6503	12798291	SO:0001583	missense	28951			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000155926.4:c.952G>A	2.37:g.12880840G>A	ENSP00000155926:p.Ala318Thr		12798291		Missense_Mutation	SNP	ENST00000155926.4	37	CCDS1683.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.771572	0.31320	.	.	ENSG00000071575	ENST00000155926;ENST00000381465	T;T	0.47528	0.88;0.84	5.94	5.94	0.96194	Protein kinase-like domain (1);	0.045930	0.85682	D	0.000000	T	0.30727	0.0774	N	0.08118	0	0.80722	D	1	B	0.18863	0.031	B	0.18263	0.021	T	0.13980	-1.0489	10	0.14656	T	0.56	-11.4536	19.354	0.94404	0.0:0.0:1.0:0.0	.	318	Q92519	TRIB2_HUMAN	T	318;182	ENSP00000155926:A318T;ENSP00000370874:A182T	ENSP00000155926:A318T	A	+	1	0	TRIB2	12798291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.348000	0.59379	2.820000	0.97059	0.650000	0.86243	GCA		0.522	TRIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207114.2	NM_021643		A	12880840	G	A	12880840	3	1	47	1	0	0	0	0	1	0	0	0	16523	971	34	3	962	3	TRIB2	2	12880840	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	920235	12880840	230318533	222	4619										
NBAS	51594	broad.mit.edu	37	chr2	15557667	15557667	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctacactattcatcagtaatCttagtttttcaatgtctttc	3	9	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:15557667C>A	ENST00000281513.5	-	24	2772	c.2747G>T	c.(2746-2748)aGa>aTa	p.R916I	NBAS_ENST00000441750.1_Intron	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	916					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R916I(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CATCAGTAATCTTAGTTTTTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	65	67					2																	15557667		2203	4300	6503	15475118	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.2747G>T	2.37:g.15557667C>A	ENSP00000281513:p.Arg916Ile		15475118	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.01|15.01	2.706269|2.706269	0.48412|0.48412	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000429842|ENST00000281513	.|T	.|0.18174	.|2.23	5.72|5.72	5.72|5.72	0.89469|0.89469	.|Secretory pathway Sec39 (1);	.|0.254644	.|0.43416	.|D	.|0.000574	T|T	0.18964|0.18964	0.0455|0.0455	L|L	0.56769|0.56769	1.78|1.78	0.58432|0.58432	D|D	0.999996|0.999996	.|P	.|0.40875	.|0.731	.|B	.|0.36186	.|0.219	T|T	0.01212|0.01212	-1.1417|-1.1417	5|10	.|0.87932	.|D	.|0	.|.	13.1141|13.1141	0.59289|0.59289	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	.|916	.|A2RRP1	.|NBAS_HUMAN	N|I	13|916	.|ENSP00000281513:R916I	.|ENSP00000281513:R916I	K|R	-|-	3|2	2|0	NBAS|NBAS	15475118|15475118	1.000000|1.000000	0.71417|0.71417	0.913000|0.913000	0.36048|0.36048	0.859000|0.859000	0.49053|0.49053	2.399000|2.399000	0.44495|0.44495	2.715000|2.715000	0.92844|0.92844	0.585000|0.585000	0.79938|0.79938	AAG|AGA		0.323	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15557667	C	A	15557667	3	1	47	1	0	0	0	0	1	0	0	0	10216	913	32	2	4484	2	NBAS	2	15557667	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2676827	15557667	227641706	223	4620										
RAD51AP2	729475	broad.mit.edu	37	chr2	17696942	17696942	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctttctgtgaaaatcctttGaattagctatctccctttct	4	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:17696942G>T	ENST00000399080.2	-	1	2764	c.2741C>A	c.(2740-2742)tCa>tAa	p.S914*		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	914								p.S914*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AAAATCCTTTGAATTAGCTAT	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											41	41	41					2																	17696942		1799	4061	5860	17560423	SO:0001587	stop_gained	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.2741C>A	2.37:g.17696942G>T	ENSP00000382030:p.Ser914*		17560423		Nonsense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	G	36	5.749977	0.96890	.	.	ENSG00000214842	ENST00000399080	.	.	.	5.62	2.71	0.32032	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.3586	5.395	0.16265	0.25:0.0:0.6005:0.1495	.	.	.	.	X	914	.	ENSP00000382030:S914X	S	-	2	0	RAD51AP2	17560423	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	1.641000	0.37197	0.774000	0.33427	-0.345000	0.07892	TCA		0.299	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		T	17696942	G	T	17696942	4	4	47	1	0	0	0	0	0	1	0	0	13024	1294	45	2	750	2	RAD51AP2	2	17696942	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2139275	17696942	225502431	224	4621										
SMC6	79677	broad.mit.edu	37	chr2	17902299	17902299	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attcaattgtttttcaatttCattgacctaagaaagaaatt	4	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:17902299C>A	ENST00000448223.2	-	11	1122	c.853G>T	c.(853-855)Gaa>Taa	p.E285*	SMC6_ENST00000381272.4_Nonsense_Mutation_p.E311*|SMC6_ENST00000351948.4_Nonsense_Mutation_p.E285*|SMC6_ENST00000402989.1_Nonsense_Mutation_p.E285*	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	285					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.E285*(1)		NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTTCAATTTCATTGACCTAA	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											77	79	78					2																	17902299		2203	4297	6500	17765780	SO:0001587	stop_gained	79677			AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.853G>T	2.37:g.17902299C>A	ENSP00000404092:p.Glu285*		17765780	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Nonsense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	C	39	7.896399	0.98548	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	.	.	.	5.97	5.97	0.96955	.	0.044218	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	20.0338	0.97549	0.0:1.0:0.0:0.0	.	.	.	.	X	285;285;311;285;311	.	ENSP00000323439:E285X	E	-	1	0	SMC6	17765780	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.237000	0.72345	2.836000	0.97738	0.655000	0.94253	GAA		0.308	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17902299	C	A	17902299	4	1	47	1	0	0	0	0	0	1	0	0	14824	835	29	2	2494	2	SMC6	2	17902299	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	205357	17902299	225297074	225	4622										
GEN1	348654	broad.mit.edu	37	chr2	17962312	17962312	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actttttctcatgatttaaaAtcagaagttgaatcagagct	6	6	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:17962312A>C	ENST00000381254.2	+	14	2047	c.1833A>C	c.(1831-1833)aaA>aaC	p.K611N	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Missense_Mutation_p.K611N	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	611					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K611N(1)		breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ATGATTTAAAATCAGAAGTTG	0.383								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	2											51	53	53					2																	17962312		2190	4298	6488	17825793	SO:0001583	missense	348654			AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"Holliday junction resolvase"	612449	"Gen endonuclease homolog 1 (Drosophila)"			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1833A>C	2.37:g.17962312A>C	ENSP00000370653:p.Lys611Asn		17825793	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338733	0.24253	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000536097	T;T	0.28666	1.6;1.6	5.29	-0.118	0.13547	.	0.707310	0.12193	N	0.491003	T	0.25195	0.0612	M	0.65975	2.015	0.09310	N	1	P	0.41313	0.745	B	0.38106	0.265	T	0.15235	-1.0444	10	0.22109	T	0.4	-4.8602	4.6439	0.12563	0.5259:0.0:0.3332:0.141	.	611	Q17RS7	GEN_HUMAN	N	611;611;248	ENSP00000318977:K611N;ENSP00000370653:K611N	ENSP00000318977:K611N	K	+	3	2	GEN1	17825793	0.785000	0.28726	0.132000	0.22025	0.443000	0.32047	0.290000	0.18975	0.106000	0.17784	0.533000	0.62120	AAA		0.383	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		C	17962312	A	C	17962312	3	2	47	1	0	0	0	0	1	0	0	0	6355	98	4	4	1883	4	GEN1	2	17962312	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	60013	17962312	225237061	226	4623										
APOB	338	broad.mit.edu	37	chr2	21229937	21229937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaacacatagccgaatgccGacatctctatggtgaatgga	11	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:21229937G>A	ENST00000233242.1	-	26	9930	c.9803C>T	c.(9802-9804)tCg>tTg	p.S3268L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3268					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.S3268L(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGAATGCCGACATCTCTAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	72	75					2																	21229937		2203	4300	6503	21083442	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9803C>T	2.37:g.21229937G>A	ENSP00000233242:p.Ser3268Leu		21083442	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.471930	0.01044	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.34859	1.34	4.6	-5.1	0.02911	.	1.803930	0.03240	N	0.180300	T	0.11580	0.0282	N	0.01493	-0.835	0.58432	D	0.999999	B	0.12013	0.005	B	0.12837	0.008	T	0.52147	-0.8614	10	0.02654	T	1	.	9.016	0.36170	0.1341:0.2821:0.5838:0.0	.	3268	P04114	APOB_HUMAN	L	3268	ENSP00000233242:S3268L	ENSP00000233242:S3268L	S	-	2	0	APOB	21083442	0.687000	0.27671	0.001000	0.08648	0.507000	0.33981	1.058000	0.30504	-0.889000	0.03950	-0.471000	0.05019	TCG		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21229937	G	A	21229937	3	1	47	1	0	0	0	0	1	0	0	0	785	1059	37	1	3904	1	APOB	2	21229937	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3267625	21229937	221969436	227	4624										
ASXL2	55252	broad.mit.edu	37	chr2	25978930	25978930	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgggctgctgaagtgaaGaattcattgttaagggctga	13	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:25978930G>T	ENST00000435504.4	-	10	1286	c.993C>A	c.(991-993)ttC>ttA	p.F331L	ASXL2_ENST00000272341.4_Missense_Mutation_p.F71L|ASXL2_ENST00000404843.1_Missense_Mutation_p.F71L|ASXL2_ENST00000336112.4_Missense_Mutation_p.F303L			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	331					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)	p.F71L(1)|p.F331L(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGAAGTGAAGAATTCATTGT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	2											130	127	128					2																	25978930		1886	4114	6000	25832434	SO:0001583	missense	55252					2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.993C>A	2.37:g.25978930G>T	ENSP00000391447:p.Phe331Leu		25832434	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		.	.	.	.	.	.	.	.	.	.	G	22.7	4.326747	0.81690	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.52754	0.65;0.65;1.08;1.08	6.08	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.996	T	0.71915	-0.4448	10	0.87932	D	0	-15.3561	15.0129	0.71562	0.0804:0.0:0.9196:0.0	.	71;331	Q76L83-2;Q76L83	.;ASXL2_HUMAN	L	331;303;71;71	ENSP00000391447:F331L;ENSP00000337250:F303L;ENSP00000383920:F71L;ENSP00000272341:F71L	ENSP00000272341:F71L	F	-	3	2	ASXL2	25832434	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.678000	0.61641	2.894000	0.99253	0.655000	0.94253	TTC		0.453	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		T	25978930	G	T	25978930	3	4	47	1	0	0	0	0	1	0	0	0	1068	933	33	2	3330	2	ASXL2	2	25978930	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4748993	25978930	217220443	228	4625										
KIF3C	3797	broad.mit.edu	37	chr2	26204606	26204606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggcatcatacacggcgtCaaaggtgaaggtcttgggca	14	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:26204606C>A	ENST00000264712.3	-	1	760	c.181G>T	c.(181-183)Gac>Tac	p.D61Y	KIF3C_ENST00000405914.1_Missense_Mutation_p.D61Y	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	61	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.D61Y(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TACACGGCGTCAAAGGTGAAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	87	85					2																	26204606		2203	4300	6503	26058110	SO:0001583	missense	3797				CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"Kinesins"	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.181G>T	2.37:g.26204606C>A	ENSP00000264712:p.Asp61Tyr		26058110	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	37	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014176	0.75161	.	.	ENSG00000084731	ENST00000264712;ENST00000405914	D;D	0.83163	-1.69;-1.69	5.45	5.45	0.79879	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.95909	0.8668	H	0.99890	4.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.98076	1.0401	10	0.87932	D	0	.	16.7781	0.85557	0.0:1.0:0.0:0.0	.	61;61	B7ZM25;O14782	.;KIF3C_HUMAN	Y	61	ENSP00000264712:D61Y;ENSP00000385030:D61Y	ENSP00000264712:D61Y	D	-	1	0	KIF3C	26058110	1.000000	0.71417	0.997000	0.53966	0.874000	0.50279	7.757000	0.85209	2.557000	0.86248	0.563000	0.77884	GAC		0.622	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			A	26204606	C	A	26204606	3	1	47	1	0	0	0	0	1	0	0	0	8323	826	29	2	2232	2	KIF3C	2	26204606	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	225676	26204606	216994767	229	4626										
HADHA	3030	broad.mit.edu	37	chr2	26417502	26417502	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggtagtatagaagccaggTccatcctgccaaggaagaga	12	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:26417502T>C	ENST00000380649.3	-	16	1755	c.1626A>G	c.(1624-1626)ggA>ggG	p.G542G		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	542					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)	p.G542G(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAAGCCAGGTCCATCCTGCC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	2											77	65	69					2																	26417502		2203	4300	6503	26271006	SO:0001819	synonymous_variant	3030			D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1626A>G	2.37:g.26417502T>C			26271006	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	37	CCDS1721.1																																																																																				0.517	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26417502	T	C	26417502	2	2	47	1	0	0	0	0	0	0	0	1	6964	1654	58	4		4	HADHA	2	26417502	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	212896	26417502	216781871	230	4627										
HADHB	3032	broad.mit.edu	37	chr2	26486264	26486264	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagctgtccagaccaaaacGaagaagacgttagccaaacc	8	11	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:26486264G>A	ENST00000317799.5	+	4	230	c.126G>A	c.(124-126)acG>acA	p.T42T	HADHB_ENST00000405867.3_Silent_p.T42T|HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000545822.1_Silent_p.T20T|HADHB_ENST00000537713.1_Silent_p.T42T	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	42					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)	p.T42T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGACCAAAACGAAGAAGACGT	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	2											138	126	130					2																	26486264		2203	4300	6503	26339768	SO:0001819	synonymous_variant	3032				CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.126G>A	2.37:g.26486264G>A			26339768	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																				0.328	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		A	26486264	G	A	26486264	2	1	47	1	0	0	0	0	0	0	0	1	6965	1045	37	1		1	HADHB	2	26486264	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	68762	26486264	216713109	231	4628										
C2orf39	92749	broad.mit.edu	37	chr2	26676379	26676379	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccccaatgatgtcctcaaGattctggaggccttcgtcat	8	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:26676379G>T	ENST00000288710.2	+	14	1955	c.1881G>T	c.(1879-1881)aaG>aaT	p.K627N		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	627					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.K627N(1)									ATGTCCTCAAGATTCTGGAGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2											59	61	60					2																	26676379		2203	4300	6503	26529883	SO:0001583	missense	92749			AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1881G>T	2.37:g.26676379G>T	ENSP00000288710:p.Lys627Asn		26529883	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039761	0.75732	.	.	ENSG00000157856	ENST00000288710	T	0.17054	2.3	5.03	5.03	0.67393	.	0.366835	0.31721	N	0.007178	T	0.30727	0.0774	M	0.63428	1.95	0.33207	D	0.552889	P	0.49862	0.929	P	0.54856	0.762	T	0.41716	-0.9493	10	0.56958	D	0.05	-46.4855	11.7612	0.51903	0.0862:0.0:0.9138:0.0	.	627	Q96MC2	CC164_HUMAN	N	627	ENSP00000288710:K627N	ENSP00000288710:K627N	K	+	3	2	CCDC164	26529883	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	2.819000	0.48049	2.506000	0.84524	0.609000	0.83330	AAG		0.602	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		T	26676379	G	T	26676379	3	4	47	1	0	0	0	0	1	0	0	0	2170	933	33	2	1935	2	C2orf39	2	26676379	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	190115	26676379	216522994	232	4629										
OTOF	9381	broad.mit.edu	37	chr2	26684962	26684962	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcacccaccccctcacgaaGatgtcactggacttctcccc	5	20	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:26684962G>T	ENST00000272371.2	-	42	5406	c.5280C>A	c.(5278-5280)atC>atA	p.I1760I	OTOF_ENST00000339598.3_Silent_p.I993I|OTOF_ENST00000402415.3_Silent_p.I1070I|OTOF_ENST00000403946.3_Silent_p.I1760I|OTOF_ENST00000338581.6_Silent_p.I993I	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1760					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.I1760I(1)|p.I993I(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTCACGAAGATGTCACTGG	0.627																																					GBM(102;732 1451 20652 24062 31372)											2	Substitution - coding silent(2)	large_intestine(2)	2											175	158	164					2																	26684962		2203	4300	6503	26538466	SO:0001819	synonymous_variant	9381			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.5280C>A	2.37:g.26684962G>T			26538466	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																				0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			T	26684962	G	T	26684962	2	4	47	1	0	0	0	0	0	0	0	1	11334	932	33	2		2	OTOF	2	26684962	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	8583	26684962	216514411	233	4630										
AGBL5	60509	broad.mit.edu	37	chr2	27276386	27276386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcatggccccctttgtgcGcacactgcccacccggccac	11	19	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:27276386G>A	ENST00000360131.4	+	3	491	c.332G>A	c.(331-333)cGc>cAc	p.R111H	RP11-503P10.1_ENST00000607407.1_RNA|AGBL5_ENST00000323064.8_Missense_Mutation_p.R111H	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	111					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.R111H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTTTGTGCGCACACTGCCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	79	80					2																	27276386		2203	4300	6503	27129890	SO:0001583	missense	60509			BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.332G>A	2.37:g.27276386G>A	ENSP00000353249:p.Arg111His		27129890	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	37	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492901	0.84962	.	.	ENSG00000084693	ENST00000453161;ENST00000323064;ENST00000360131	T;T	0.15834	2.41;2.39	5.67	5.67	0.87782	.	0.044130	0.85682	D	0.000000	T	0.34890	0.0913	M	0.62016	1.91	0.52099	D	0.999946	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.98;0.984;0.984	T	0.02596	-1.1136	10	0.18276	T	0.48	-4.9759	12.6154	0.56573	0.0795:0.0:0.9205:0.0	.	111;111;111	Q8NDL9;Q8NDL9-3;Q8NDL9-2	CBPC5_HUMAN;.;.	H	111	ENSP00000323681:R111H;ENSP00000353249:R111H	ENSP00000323681:R111H	R	+	2	0	AGBL5	27129890	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.070000	0.64376	2.666000	0.90696	0.561000	0.74099	CGC		0.537	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		A	27276386	G	A	27276386	3	1	47	1	0	0	0	0	1	0	0	0	378	1087	38	1	338	1	AGBL5	2	27276386	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	591424	27276386	215922987	234	4631										
C2orf53	339779	broad.mit.edu	37	chr2	27360551	27360552	+	Missense_Mutation	DNP	AC	AC	CA													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcggtgccccagctggaccAccagggcctgggccagggcc							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	AC	AC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:27360551_27360552AC>CA	ENST00000335524.3	-	3	1171_1172	c.646_647GT>TG	c.(646-648)GTg>TGg	p.V216W		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		216								p.V216>?(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGCTGGACCACCAGGGCCTGG	0.668																																																1	Complex(1)	large_intestine(1)	2																																								27214056	SO:0001583	missense	339779																														ENST00000335524.3:c.646_647delinsCA	2.37:g.27360551_27360552delinsCA	ENSP00000335017:p.Val216Trp		27214055	Q86UE2	Missense_Mutation	DNP	ENST00000335524.3	37	CCDS1739.1																																																																																				0.668	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			CA	27360552	AC	CA	27360551	3	2	47	1	0	0	0	0	1	0	0	0	2180	159	6	4	595	4	C2orf53	2	27360551	Missense_Mutation	DNP	AC	TCGA-AG-3892-01A-01W-1073-09	84165	27360551	215838822	235	4632										
C2orf53	339779	broad.mit.edu	37	chr2	27360721	27360721	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaggtgggctggggcctggGgaagtgagtgtggagctatg	22	4	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:27360721G>A	ENST00000335524.3	-	3	1002	c.477C>T	c.(475-477)tcC>tcT	p.S159S		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		159	Pro-rich.							p.S159S(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGGCCTGGGGAAGTGAGTG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	2											52	53	52					2																	27360721		2203	4300	6503	27214225	SO:0001819	synonymous_variant	339779																														ENST00000335524.3:c.477C>T	2.37:g.27360721G>A			27214225	Q86UE2	Silent	SNP	ENST00000335524.3	37	CCDS1739.1																																																																																				0.617	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			A	27360721	G	A	27360721	2	1	47	1	0	0	0	0	0	0	0	1	2180	1219	43	3		3	C2orf53	2	27360721	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	170	27360721	215838652	236	4633										
CLIP4	79745	broad.mit.edu	37	chr2	29383296	29383296	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggtaggacagagactgggCaccattaggttctttgggac	15	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:29383296C>A	ENST00000320081.5	+	12	1752	c.1497C>A	c.(1495-1497)ggC>ggA	p.G499G	CLIP4_ENST00000404424.1_Silent_p.G499G|CLIP4_ENST00000401605.1_Silent_p.G499G|CLIP4_ENST00000401617.2_Silent_p.G392G	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	499								p.G499G(1)		endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					AGAGACTGGGCACCATTAGGT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	2											123	115	117					2																	29383296		2203	4300	6503	29236800	SO:0001819	synonymous_variant	79745			AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1497C>A	2.37:g.29383296C>A			29236800	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	37	CCDS1770.1																																																																																				0.428	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		A	29383296	C	A	29383296	2	1	47	1	0	0	0	0	0	0	0	1	3541	697	25	2		2	CLIP4	2	29383296	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2022575	29383296	213816077	237	4634										
MEMO1	51072	broad.mit.edu	37	chr2	32117097	32117097	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaagaaaccacaaagagatTactaggatccgctagatatt	8	7	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32117097T>G	ENST00000295065.5	-	6	853	c.544A>C	c.(544-546)Aat>Cat	p.N182H	MEMO1_ENST00000426310.2_Missense_Mutation_p.N159H|MEMO1_ENST00000404530.1_Missense_Mutation_p.N182H|MEMO1_ENST00000379383.3_Missense_Mutation_p.N185H|DPY30_ENST00000446765.1_5'UTR|MEMO1_ENST00000490459.1_Intron	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	182					regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.N182H(1)		NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					ACAAAGAGATTACTAGGATCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	121	118					2																	32117097		2203	4300	6503	31970601	SO:0001583	missense	51072			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.544A>C	2.37:g.32117097T>G	ENSP00000295065:p.Asn182His		31970601	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Missense_Mutation	SNP	ENST00000295065.5	37	CCDS1776.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161636	0.78226	.	.	ENSG00000162959	ENST00000295065;ENST00000379383;ENST00000404530;ENST00000426310	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.81592	0.4855	M	0.92367	3.3	0.80722	D	1	B;P	0.47545	0.285;0.897	B;P	0.51170	0.404;0.661	D	0.86353	0.1712	9	0.87932	D	0	-17.738	15.6821	0.77376	0.0:0.0:0.0:1.0	.	159;182	Q9Y316-2;Q9Y316	.;MEMO1_HUMAN	H	182;185;182;159	.	ENSP00000295065:N182H	N	-	1	0	MEMO1	31970601	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.905000	0.87416	2.179000	0.69175	0.482000	0.46254	AAT		0.368	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955		G	32117097	T	G	32117097	3	3	47	1	0	0	0	0	1	0	0	0	9501	1754	61	4	365	4	MEMO1	2	32117097	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2733801	32117097	211082276	238	4635										
NLRC4	58484	broad.mit.edu	37	chr2	32449564	32449564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcagttactagtttaaaaGcacctgtaataacactgaga	7	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32449564G>A	ENST00000404025.2	-	10	3541	c.3053C>T	c.(3052-3054)gCt>gTt	p.A1018V	NLRC4_ENST00000402280.1_Missense_Mutation_p.A1018V|NLRC4_ENST00000342905.6_Missense_Mutation_p.A353V|NLRC4_ENST00000360906.5_Missense_Mutation_p.A1018V			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	1018					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.A1018V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAGTTTAAAAGCACCTGTAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											93	92	92					2																	32449564		2203	4300	6503	32303068	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.3053C>T	2.37:g.32449564G>A	ENSP00000385090:p.Ala1018Val		32303068	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844491	0.32606	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.56103	0.48;0.48;1.34;0.48	4.57	-2.49	0.06403	.	0.442525	0.16785	N	0.199634	T	0.29620	0.0739	N	0.24115	0.695	0.27400	N	0.954885	B;B	0.18461	0.026;0.028	B;B	0.11329	0.006;0.004	T	0.09662	-1.0664	9	0.59425	D	0.04	-0.4734	3.6605	0.08237	0.0892:0.1326:0.2405:0.5376	.	353;1018	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	V	1018;1018;353;1018	ENSP00000354159:A1018V;ENSP00000385428:A1018V;ENSP00000339666:A353V;ENSP00000385090:A1018V	ENSP00000339666:A353V	A	-	2	0	NLRC4	32303068	0.003000	0.15002	0.108000	0.21378	0.686000	0.39977	-1.349000	0.02627	-0.104000	0.12154	-0.157000	0.13467	GCT		0.363	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		A	32449564	G	A	32449564	3	1	47	1	0	0	0	0	1	0	0	0	10500	971	34	3	25	3	NLRC4	2	32449564	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	332467	32449564	210749809	239	4636										
NLRC4	58484	broad.mit.edu	37	chr2	32475010	32475010	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccctgctgggaatgtaggtTtctggggcctcttccatgtg	14	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32475010T>A	ENST00000404025.2	-	5	2411	c.1923A>T	c.(1921-1923)gaA>gaT	p.E641D	NLRC4_ENST00000402280.1_Missense_Mutation_p.E641D|NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000360906.5_Missense_Mutation_p.E641D			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	641					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.E641D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GAATGTAGGTTTCTGGGGCCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	150	146					2																	32475010		2203	4300	6503	32328514	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1923A>T	2.37:g.32475010T>A	ENSP00000385090:p.Glu641Asp		32328514	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	T	2.877	-0.232602	0.05983	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.51574	0.7;0.7;0.7	3.58	-0.812	0.10853	.	0.913477	0.08946	N	0.870812	T	0.22166	0.0534	N	0.08118	0	0.29476	N	0.856711	B	0.10296	0.003	B	0.08055	0.003	T	0.34527	-0.9825	9	0.13853	T	0.58	.	6.1991	0.20565	0.0:0.1032:0.4332:0.4636	.	641	Q9NPP4	NLRC4_HUMAN	D	641	ENSP00000354159:E641D;ENSP00000385428:E641D;ENSP00000385090:E641D	ENSP00000354159:E641D	E	-	3	2	NLRC4	32328514	0.523000	0.26274	0.332000	0.25469	0.689000	0.40095	0.072000	0.14617	0.094000	0.17404	-0.451000	0.05528	GAA		0.493	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		A	32475010	T	A	32475010	3	1	47	1	0	0	0	0	1	0	0	0	10500	1838	64	5	1175	5	NLRC4	2	32475010	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	25446	32475010	210724363	240	4637										
NLRC4	58484	broad.mit.edu	37	chr2	32475156	32475156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagaagtcaaataagtaatCggggatgttccctgagttga	11	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32475156C>T	ENST00000404025.2	-	5	2265	c.1777G>A	c.(1777-1779)Gat>Aat	p.D593N	NLRC4_ENST00000402280.1_Missense_Mutation_p.D593N|NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000360906.5_Missense_Mutation_p.D593N			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	593					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.D593N(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					AATAAGTAATCGGGGATGTTC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	2											96	99	98					2																	32475156		2203	4300	6503	32328660	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1777G>A	2.37:g.32475156C>T	ENSP00000385090:p.Asp593Asn		32328660	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	C	7.846	0.722865	0.15439	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.54675	0.56;0.56;0.56	3.0	3.0	0.34707	.	0.296248	0.23720	N	0.045226	T	0.41971	0.1182	L	0.27053	0.805	0.31540	N	0.660023	D	0.65815	0.995	P	0.51777	0.679	T	0.50013	-0.8877	9	0.37606	T	0.19	.	3.8079	0.08785	0.2435:0.6285:0.0:0.128	.	593	Q9NPP4	NLRC4_HUMAN	N	593	ENSP00000354159:D593N;ENSP00000385428:D593N;ENSP00000385090:D593N	ENSP00000354159:D593N	D	-	1	0	NLRC4	32328660	0.707000	0.27866	0.980000	0.43619	0.691000	0.40173	1.097000	0.30988	2.007000	0.58848	0.543000	0.68304	GAT		0.398	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		T	32475156	C	T	32475156	3	4	47	1	0	0	0	0	1	0	0	0	10500	884	31	1	1321	1	NLRC4	2	32475156	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	146	32475156	210724217	241	4638										
NLRC4	58484	broad.mit.edu	37	chr2	32475708	32475708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggacacatcctgcagttCgaaatcaaacttgtgggaga	11	9	1	1	rs144123569		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32475708C>T	ENST00000404025.2	-	5	1713	c.1225G>A	c.(1225-1227)Gaa>Aaa	p.E409K	NLRC4_ENST00000402280.1_Missense_Mutation_p.E409K|NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000360906.5_Missense_Mutation_p.E409K			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	409	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.|Winged-helix domain (WHD). {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.E409K(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TCCTGCAGTTCGAAATCAAAC	0.473													C|||	1	0.000199681	8e-04	0	5008	,	,		22313	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											55	57	57					2																	32475708		2203	4300	6503	32329212	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1225G>A	2.37:g.32475708C>T	ENSP00000385090:p.Glu409Lys		32329212	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.006	-2.077324	0.00375	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.10860	2.83;2.83;2.83	2.97	-1.66	0.08265	.	1.102920	0.07138	N	0.846839	T	0.09069	0.0224	L	0.44542	1.39	0.23192	N	0.998144	B	0.09022	0.002	B	0.04013	0.001	T	0.40156	-0.9578	9	0.27082	T	0.32	.	6.1007	0.20045	0.0:0.3531:0.3734:0.2735	.	409	Q9NPP4	NLRC4_HUMAN	K	409	ENSP00000354159:E409K;ENSP00000385428:E409K;ENSP00000385090:E409K	ENSP00000354159:E409K	E	-	1	0	NLRC4	32329212	0.030000	0.19436	0.003000	0.11579	0.006000	0.05464	-0.681000	0.05191	-0.970000	0.03569	-2.441000	0.00211	GAA		0.473	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		T	32475708	C	T	32475708	3	4	47	1	0	0	0	0	1	0	0	0	10500	893	31	1	1873	1	NLRC4	2	32475708	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	552	32475708	210723665	242	4639										
BIRC6	57448	broad.mit.edu	37	chr2	32702499	32702499	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccgttctaatttagacacaGaagttacaacagcaaaagaa	6	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32702499G>T	ENST00000421745.2	+	35	7050	c.6916G>T	c.(6916-6918)Gaa>Taa	p.E2306*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2306					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.E2278*(1)|p.E2306*(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTTAGACACAGAAGTTACAAC	0.383																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Nonsense(2)	large_intestine(2)	2											146	137	140					2																	32702499		2203	4300	6503	32556003	SO:0001587	stop_gained	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6916G>T	2.37:g.32702499G>T	ENSP00000393596:p.Glu2306*		32556003	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	49	15.258168	0.99828	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.8	5.8	0.92144	.	0.068128	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	20.0716	0.97726	0.0:0.0:1.0:0.0	.	.	.	.	X	2306	.	ENSP00000393596:E2306X	E	+	1	0	BIRC6	32556003	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	9.727000	0.98787	2.741000	0.93983	0.585000	0.79938	GAA		0.383	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32702499	G	T	32702499	4	4	47	1	0	0	0	0	0	1	0	0	1439	943	33	2	7054	2	BIRC6	2	32702499	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	226791	32702499	210496874	243	4640										
BIRC6	57448	broad.mit.edu	37	chr2	32733313	32733313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccttccatctgaagatcagGtatccaaaacaaggtatgtt	7	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32733313G>A	ENST00000421745.2	+	51	10101	c.9967G>A	c.(9967-9969)Gta>Ata	p.V3323I		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3323					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.V3323I(1)|p.V3295I(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGAAGATCAGGTATCCAAAAC	0.343																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Missense(2)	large_intestine(2)	2											39	35	36					2																	32733313		2203	4300	6503	32586817	SO:0001583	missense	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9967G>A	2.37:g.32733313G>A	ENSP00000393596:p.Val3323Ile		32586817	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673126	0.67928	.	.	ENSG00000115760	ENST00000421745	T	0.75050	-0.9	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.82692	0.5092	L	0.47716	1.5	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	T	0.80540	-0.1337	10	0.39692	T	0.17	.	19.7818	0.96418	0.0:0.0:1.0:0.0	.	3323	Q9NR09	BIRC6_HUMAN	I	3323	ENSP00000393596:V3323I	ENSP00000393596:V3323I	V	+	1	0	BIRC6	32586817	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.375000	0.97178	2.736000	0.93811	0.655000	0.94253	GTA		0.343	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32733313	G	A	32733313	3	1	47	1	0	0	0	0	1	0	0	0	1439	1261	44	3	10169	3	BIRC6	2	32733313	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	30814	32733313	210466060	244	4641										
BIRC6	57448	broad.mit.edu	37	chr2	32819112	32819112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgcagccaccaccagtttgCggcaagcaaatcagggtaca	10	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:32819112C>T	ENST00000421745.2	+	67	13620	c.13486C>T	c.(13486-13488)Cgg>Tgg	p.R4496W		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4496					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.R4496W(1)|p.R4468W(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CACCAGTTTGCGGCAAGCAAA	0.398																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Missense(2)	large_intestine(2)	2											73	72	72					2																	32819112		2203	4300	6503	32672616	SO:0001583	missense	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13486C>T	2.37:g.32819112C>T	ENSP00000393596:p.Arg4496Trp		32672616	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579847	0.46006	.	.	ENSG00000115760	ENST00000421745	T	0.75050	-0.9	5.51	2.58	0.30949	.	0.060703	0.64402	D	0.000004	T	0.64305	0.2586	L	0.43152	1.355	0.58432	D	0.999999	B	0.10296	0.003	B	0.04013	0.001	T	0.61158	-0.7119	10	0.66056	D	0.02	.	9.3902	0.38367	0.2564:0.6761:0.0:0.0675	.	4496	Q9NR09	BIRC6_HUMAN	W	4496	ENSP00000393596:R4496W	ENSP00000393596:R4496W	R	+	1	2	BIRC6	32672616	0.957000	0.32711	0.994000	0.49952	0.886000	0.51366	1.466000	0.35310	0.659000	0.30945	0.650000	0.86243	CGG		0.398	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32819112	C	T	32819112	3	4	47	1	0	0	0	0	1	0	0	0	1439	759	27	1	13752	1	BIRC6	2	32819112	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	85799	32819112	210380261	245	4642										
CRIM1	51232	broad.mit.edu	37	chr2	36623787	36623787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gactgatgaccaactgcttgGttttaaaccatgcaatgaaa	8	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:36623787G>A	ENST00000280527.2	+	2	729	c.362G>A	c.(361-363)gGt>gAt	p.G121D		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	121					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G121D(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				CAACTGCTTGGTTTTAAACCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	102	103					2																	36623787		2203	4300	6503	36477291	SO:0001583	missense	51232			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.362G>A	2.37:g.36623787G>A	ENSP00000280527:p.Gly121Asp		36477291	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.558290	0.86231	.	.	ENSG00000150938	ENST00000280527	T	0.04406	3.63	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.19446	0.0467	L	0.59436	1.845	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.00118	-1.2034	10	0.59425	D	0.04	-12.3171	17.8252	0.88662	0.0:0.0:1.0:0.0	.	121	Q9NZV1	CRIM1_HUMAN	D	121	ENSP00000280527:G121D	ENSP00000280527:G121D	G	+	2	0	CRIM1	36477291	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.398000	0.73244	2.447000	0.82792	0.585000	0.79938	GGT		0.398	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		A	36623787	G	A	36623787	3	1	47	1	0	0	0	0	1	0	0	0	3879	1261	44	3	368	3	CRIM1	2	36623787	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3804675	36623787	206575586	246	4643										
STRN	6801	broad.mit.edu	37	chr2	37085086	37085086	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctgctgaacaggacaacaAacgctgatgtgctgcactat	9	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:37085086A>C	ENST00000263918.4	-	14	1758	c.1750T>G	c.(1750-1752)Ttg>Gtg	p.L584V	STRN_ENST00000379213.2_Missense_Mutation_p.L535V	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	584					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.L584V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				CAGGACAACAAACGCTGATGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	59	60					2																	37085086		2203	4300	6503	36938590	SO:0001583	missense	6801			AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"WD repeat domain containing"	11424	protein-coding gene	gene with protein product		614765	"striatin, calmodulin-binding protein"			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.1750T>G	2.37:g.37085086A>C	ENSP00000263918:p.Leu584Val		36938590	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	37	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.999670	0.74818	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.67698	-0.28;-0.28	5.27	1.58	0.23477	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73916	0.3648	L	0.58969	1.84	0.58432	D	0.999999	D;D	0.71674	0.994;0.998	D;D	0.73380	0.977;0.98	T	0.69457	-0.5140	10	0.45353	T	0.12	-7.4433	8.898	0.35476	0.7848:0.0:0.2152:0.0	.	535;584	O43815-2;O43815	.;STRN_HUMAN	V	584;559;535	ENSP00000263918:L584V;ENSP00000368513:L535V	ENSP00000263918:L584V	L	-	1	2	STRN	36938590	1.000000	0.71417	0.950000	0.38849	0.996000	0.88848	2.387000	0.44389	0.039000	0.15632	0.397000	0.26171	TTG		0.428	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			C	37085086	A	C	37085086	3	2	47	1	0	0	0	0	1	0	0	0	15368	11	1	4	612	4	STRN	2	37085086	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	461299	37085086	206114287	247	4644										
MAP4K3	8491	broad.mit.edu	37	chr2	39487900	39487900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacattctaagtggacatgGtataggaaaatctatgtgct	9	5	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:39487900G>A	ENST00000263881.3	-	29	2479	c.2155C>T	c.(2155-2157)Cca>Tca	p.P719S	MAP4K3_ENST00000536018.1_Missense_Mutation_p.P272S|MAP4K3_ENST00000341681.5_Missense_Mutation_p.P698S|MAP4K3_ENST00000437545.1_Missense_Mutation_p.P635S	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	719	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.P719S(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				AGTGGACATGGTATAGGAAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	68	68					2																	39487900		2203	4300	6503	39341404	SO:0001583	missense	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.2155C>T	2.37:g.39487900G>A	ENSP00000263881:p.Pro719Ser		39341404	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.458655	0.84317	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000542094;ENST00000536018	T;T;T;T	0.76060	-0.99;-0.81;-0.96;1.96	4.98	4.98	0.66077	Citron-like (3);	0.000000	0.85682	D	0.000000	D	0.86965	0.6060	M	0.80508	2.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.87509	0.2438	10	0.51188	T	0.08	.	18.4448	0.90680	0.0:0.0:1.0:0.0	.	698;719	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	S	719;635;698;15;272	ENSP00000263881:P719S;ENSP00000416958:P635S;ENSP00000345434:P698S;ENSP00000440580:P272S	ENSP00000263881:P719S	P	-	1	0	MAP4K3	39341404	1.000000	0.71417	0.533000	0.28001	0.818000	0.46254	7.599000	0.82757	2.580000	0.87095	0.655000	0.94253	CCA		0.348	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		A	39487900	G	A	39487900	3	1	47	1	0	0	0	0	1	0	0	0	9291	1261	44	3	553	3	MAP4K3	2	39487900	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2402814	39487900	203711473	248	4645										
THADA	63892	broad.mit.edu	37	chr2	43804227	43804227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccccactccgacccatgCttccgttctgccagtccaac	5	21	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:43804227C>T	ENST00000405006.4	-	10	1322	c.971G>A	c.(970-972)aGc>aAc	p.S324N	THADA_ENST00000402360.2_Missense_Mutation_p.S324N|THADA_ENST00000403856.1_Missense_Mutation_p.S324N|THADA_ENST00000404790.1_Missense_Mutation_p.S324N|THADA_ENST00000415080.2_Missense_Mutation_p.S34N|THADA_ENST00000405975.2_Missense_Mutation_p.S324N|THADA_ENST00000330266.7_Missense_Mutation_p.S34N	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	324								p.S324N(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CCGACCCATGCTTCCGTTCTG	0.498											OREG0014580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											62	65	64					2																	43804227		1972	4168	6140	43657731	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.971G>A	2.37:g.43804227C>T	ENSP00000385995:p.Ser324Asn	919	43657731	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.484341	0.26598	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.32272	1.51;2.88;2.73;2.88;1.48;1.47;1.46	5.55	3.72	0.42706	.	0.564634	0.20212	N	0.096864	T	0.26882	0.0658	L	0.50333	1.59	0.25754	N	0.985023	B;B;B;B;B	0.18310	0.027;0.003;0.004;0.001;0.002	B;B;B;B;B	0.15484	0.013;0.004;0.009;0.002;0.002	T	0.07158	-1.0787	10	0.35671	T	0.21	0.2511	10.9571	0.47364	0.0:0.8228:0.0:0.1772	.	324;324;324;34;324	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	N	34;324;324;34;324;324;324;324	ENSP00000331105:S34N;ENSP00000386088:S324N;ENSP00000416048:S34N;ENSP00000385995:S324N;ENSP00000385441:S324N;ENSP00000384266:S324N;ENSP00000385469:S324N	ENSP00000331105:S34N	S	-	2	0	THADA	43657731	0.013000	0.17824	0.999000	0.59377	0.434000	0.31775	0.039000	0.13884	2.614000	0.88457	0.561000	0.74099	AGC		0.498	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		T	43804227	C	T	43804227	3	4	47	1	0	0	0	0	1	0	0	0	15879	797	28	3	5006	3	THADA	2	43804227	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4316327	43804227	199395146	249	4646										
PLEKHH2	130271	broad.mit.edu	37	chr2	43927278	43927278	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaaaaatttcaatcccagaGactcgattattcatcttcat	3	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:43927278G>T	ENST00000282406.4	+	8	1291	c.1181G>T	c.(1180-1182)aGa>aTa	p.R394I		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	394					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)	p.R394I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAATCCCAGAGACTCGATTAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	63	63					2																	43927278		2203	4300	6503	43780782	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.1181G>T	2.37:g.43927278G>T	ENSP00000282406:p.Arg394Ile		43780782	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138481	0.37728	.	.	ENSG00000152527	ENST00000282406	T	0.73789	-0.78	5.59	4.68	0.58851	.	0.410721	0.26844	N	0.022201	T	0.74129	0.3676	L	0.50333	1.59	0.41104	D	0.985693	P;D	0.53151	0.627;0.958	B;P	0.51135	0.064;0.66	T	0.75342	-0.3351	10	0.52906	T	0.07	-6.5183	10.2154	0.43166	0.0709:0.0:0.7926:0.1366	.	394;394	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	I	394	ENSP00000282406:R394I	ENSP00000282406:R394I	R	+	2	0	PLEKHH2	43780782	0.992000	0.36948	1.000000	0.80357	0.836000	0.47400	2.398000	0.44486	2.635000	0.89317	0.563000	0.77884	AGA		0.393	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43927278	G	T	43927278	3	4	47	1	0	0	0	0	1	0	0	0	12108	942	33	2	1207	2	PLEKHH2	2	43927278	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	123051	43927278	199272095	250	4647										
DYNC2LI1	51626	broad.mit.edu	37	chr2	44023043	44023043	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagcaggatcatgaattaatTgacccatttccggtacctct	7	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:44023043T>G	ENST00000260605.8	+	7	622	c.522T>G	c.(520-522)atT>atG	p.I174M	DYNC2LI1_ENST00000443170.3_Missense_Mutation_p.I48M|DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.I175M|DYNC2LI1_ENST00000489222.2_3'UTR	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	174					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)	p.I174M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ATGAATTAATTGACCCATTTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	127	129					2																	44023043		2203	4300	6503	43876547	SO:0001583	missense	51626				CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"Cytoplasmic dyneins"	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.522T>G	2.37:g.44023043T>G	ENSP00000260605:p.Ile174Met		43876547	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.77|13.77	2.335835|2.335835	0.41398|0.41398	.|.	.|.	ENSG00000138036|ENSG00000138036	ENST00000260605;ENST00000443170|ENST00000378587	T;T|.	0.36340|.	1.26;1.26|.	5.24|5.24	1.56|1.56	0.23342|0.23342	.|.	0.191757|.	0.53938|.	D|.	0.000056|.	T|T	0.55146|0.55146	0.1902|0.1902	L|L	0.56769|0.56769	1.78|1.78	0.39861|0.39861	D|D	0.973381|0.973381	B;B;B|.	0.25772|.	0.11;0.134;0.11|.	B;B;B|.	0.37198|.	0.157;0.243;0.157|.	T|T	0.50808|0.50808	-0.8784|-0.8784	10|5	0.44086|.	T|.	0.13|.	-10.597|-10.597	4.5294|4.5294	0.11997|0.11997	0.1319:0.22:0.0:0.648|0.1319:0.22:0.0:0.648	.|.	175;174;174|.	Q8TCX1-2;Q8TCX1;Q8TCX1-3|.	.;DC2L1_HUMAN;.|.	M|W	174;48|158	ENSP00000260605:I174M;ENSP00000388941:I48M|.	ENSP00000260605:I174M|.	I|L	+|+	3|2	3|0	DYNC2LI1|DYNC2LI1	43876547|43876547	1.000000|1.000000	0.71417|0.71417	0.956000|0.956000	0.39512|0.39512	0.990000|0.990000	0.78478|0.78478	0.920000|0.920000	0.28705|0.28705	0.475000|0.475000	0.27415|0.27415	0.482000|0.482000	0.46254|0.46254	ATT|TTG		0.348	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008		G	44023043	T	G	44023043	3	3	47	1	0	0	0	0	1	0	0	0	4858	1800	63	4	647	4	DYNC2LI1	2	44023043	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	95765	44023043	199176330	251	4648										
DYNC2LI1	51626	broad.mit.edu	37	chr2	44023914	44023914	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacttcgatttgttgcacatTattatggagcatcattaatg	7	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:44023914T>C	ENST00000260605.8	+	8	734	c.634T>C	c.(634-636)Tat>Cat	p.Y212H	DYNC2LI1_ENST00000443170.3_Missense_Mutation_p.Y86H|DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.Y213H|DYNC2LI1_ENST00000489222.2_3'UTR	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	212					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)	p.Y212H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGTTGCACATTATTATGGAGC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											163	150	154					2																	44023914		2203	4300	6503	43877418	SO:0001583	missense	51626				CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"Cytoplasmic dyneins"	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.634T>C	2.37:g.44023914T>C	ENSP00000260605:p.Tyr212His		43877418	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.598764	0.28445	.	.	ENSG00000138036	ENST00000260605;ENST00000443170	T;T	0.27104	1.69;1.69	5.02	3.88	0.44766	.	0.449069	0.26586	N	0.023545	T	0.16685	0.0401	L	0.27053	0.805	0.36912	D	0.890977	B;B;B	0.24043	0.096;0.058;0.096	B;B;B	0.25405	0.035;0.016;0.06	T	0.12682	-1.0538	10	0.17369	T	0.5	-7.718	10.3174	0.43745	0.0:0.0766:0.0:0.9234	.	213;212;212	Q8TCX1-2;Q8TCX1;Q8TCX1-3	.;DC2L1_HUMAN;.	H	212;86	ENSP00000260605:Y212H;ENSP00000388941:Y86H	ENSP00000260605:Y212H	Y	+	1	0	DYNC2LI1	43877418	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.915000	0.63355	0.946000	0.37632	0.528000	0.53228	TAT		0.348	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008		C	44023914	T	C	44023914	3	2	47	1	0	0	0	0	1	0	0	0	4858	1754	61	4	763	4	DYNC2LI1	2	44023914	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	871	44023914	199175459	252	4649										
LRPPRC	10128	broad.mit.edu	37	chr2	44174888	44174888	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actttttgaaagtctaaattCttactctcaaccaacaagtg	4	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:44174888C>A	ENST00000260665.7	-	19	2004	c.1947G>T	c.(1945-1947)aaG>aaT	p.K649N		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	649					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.K649N(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGTCTAAATTCTTACTCTCAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	65	64					2																	44174888		2202	4290	6492	44028392	SO:0001583	missense	10128			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1947G>T	2.37:g.44174888C>A	ENSP00000260665:p.Lys649Asn		44028392	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	C	7.815	0.716526	0.15306	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	T	0.57752	0.38	5.6	5.6	0.85130	.	1.127620	0.06416	N	0.721456	T	0.33089	0.0851	N	0.14661	0.345	0.80722	D	1	P;B	0.36282	0.546;0.002	B;B	0.26094	0.066;0.002	T	0.08166	-1.0735	10	0.24483	T	0.36	-11.2136	9.0238	0.36215	0.0:0.8754:0.0:0.1246	.	549;649	F5H4J6;P42704	.;LPPRC_HUMAN	N	549;649	ENSP00000260665:K649N	ENSP00000260665:K649N	K	-	3	2	LRPPRC	44028392	0.228000	0.23718	1.000000	0.80357	0.130000	0.20726	1.632000	0.37102	2.806000	0.96561	0.655000	0.94253	AAG		0.299	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		A	44174888	C	A	44174888	3	1	47	1	0	0	0	0	1	0	0	0	8994	912	32	2	2317	2	LRPPRC	2	44174888	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	150974	44174888	199024485	253	4650										
MCFD2	90411	broad.mit.edu	37	chr2	47132679	47132679	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcatctctcaaaacaccatCtattatgttaatcagttcat	2	10	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:47132679C>A	ENST00000409105.1	-	5	543	c.364G>T	c.(364-366)Gat>Tat	p.D122Y	MCFD2_ENST00000409973.1_Missense_Mutation_p.D122Y|MCFD2_ENST00000444761.2_Missense_Mutation_p.D103Y|MCFD2_ENST00000409800.1_Missense_Mutation_p.D70Y|MCFD2_ENST00000409913.1_Missense_Mutation_p.D70Y|MCFD2_ENST00000409218.1_Missense_Mutation_p.D122Y|MCFD2_ENST00000493804.1_5'UTR|MCFD2_ENST00000409147.1_Missense_Mutation_p.D70Y|MCFD2_ENST00000319466.4_Missense_Mutation_p.D122Y|MCFD2_ENST00000409207.1_Missense_Mutation_p.D122Y|AC016722.4_ENST00000429761.1_RNA	NM_001171506.2	NP_001164977.1	Q8NI22	MCFD2_HUMAN	multiple coagulation factor deficiency 2	122	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)	p.D122Y(1)		central_nervous_system(1)|large_intestine(1)|lung(2)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Antihemophilic Factor(DB00025)	AAAACACCATCTATTATGTTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											253	193	213					2																	47132679		2203	4300	6503	46986183	SO:0001583	missense	90411			AF475284	CCDS33192.1, CCDS54354.1, CCDS54355.1	2p21	2014-09-17			ENSG00000180398	ENSG00000180398		"EF-hand domain containing"	18451	protein-coding gene	gene with protein product		607788				12717434, 2463956	Standard	NM_139279		Approved	F5F8D, LMAN1IP, SDNSF	uc021vha.1	Q8NI22	OTTHUMG00000153100	ENST00000409105.1:c.364G>T	2.37:g.47132679C>A	ENSP00000386651:p.Asp122Tyr		46986183	A8K7W2|D6W5A9|E9PD95|Q53SS3|Q68D61|Q8N3M5	Missense_Mutation	SNP	ENST00000409105.1	37	CCDS33192.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801050	0.90538	.	.	ENSG00000180398	ENST00000444761;ENST00000409105;ENST00000409913;ENST00000319466;ENST00000409800;ENST00000409207;ENST00000409973;ENST00000409147;ENST00000409218;ENST00000412438	D;D;D;D;D;D;D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73;-3.73;-3.73;-3.73;-3.73;-3.73;-3.73	5.52	5.52	0.82312	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.98485	0.9495	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99113	1.0847	10	0.87932	D	0	-15.337	19.2223	0.93803	0.0:1.0:0.0:0.0	.	103;122	E9PD95;Q8NI22	.;MCFD2_HUMAN	Y	103;122;70;122;70;122;122;70;122;122	ENSP00000394647:D103Y;ENSP00000386651:D122Y;ENSP00000386941:D70Y;ENSP00000317271:D122Y;ENSP00000387202:D70Y;ENSP00000386386:D122Y;ENSP00000386279:D122Y;ENSP00000387082:D70Y;ENSP00000386261:D122Y;ENSP00000402717:D122Y	ENSP00000317271:D122Y	D	-	1	0	MCFD2	46986183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.273000	0.78527	2.873000	0.98535	0.563000	0.77884	GAT		0.378	MCFD2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329518.1	NM_139279		A	47132679	C	A	47132679	3	1	47	1	0	0	0	0	1	0	0	0	9411	913	32	2	80	2	MCFD2	2	47132679	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2957791	47132679	196066694	254	4651										
MSH2	4436	broad.mit.edu	37	chr2	47657038	47657038	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accgactctatcagggtataAatcaactacctaatgttata	5	9	3	0	rs63751644		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:47657038A>C	ENST00000233146.2	+	7	1457	c.1234A>C	c.(1234-1236)Aat>Cat	p.N412H	MSH2_ENST00000406134.1_Missense_Mutation_p.N412H|MSH2_ENST00000543555.1_Missense_Mutation_p.N346H	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	412					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)|p.N412H(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCAGGGTATAAATCAACTACC	0.353			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	5	Whole gene deletion(2)|Unknown(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)	2											74	68	70					2																	47657038		2203	4300	6503	47510542	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1234A>C	2.37:g.47657038A>C	ENSP00000233146:p.Asn412His		47510542	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	9.793|9.793	1.178533|1.178533	0.21787|0.21787	.|.	.|.	ENSG00000095002|ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000422810;ENST00000413880|ENST00000448533	D;D;D|.	0.90385|.	-2.66;-2.66;-2.66|.	5.45|5.45	5.45|5.45	0.79879|0.79879	DNA mismatch repair protein MutS, core (3);|.	0.229818|.	0.51477|.	D|.	0.000083|.	T|.	0.76807|.	0.4039|.	M|M	0.80183|0.80183	2.485|2.485	0.50467|0.50467	D|D	0.999874|0.999874	B;B;B|.	0.14805|.	0.004;0.011;0.002|.	B;B;B|.	0.15052|.	0.006;0.01;0.012|.	T|.	0.78526|.	-0.2170|.	10|.	0.44086|.	T|.	0.13|.	-11.4304|-11.4304	15.5058|15.5058	0.75739|0.75739	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	346;412;412|.	B4E2Z2;E9PHA6;P43246|.	.;.;MSH2_HUMAN|.	H|Y	412;346;412;412;412;412;62;198|411	ENSP00000233146:N412H;ENSP00000442697:N346H;ENSP00000384199:N412H|.	ENSP00000233146:N412H|.	N|X	+|+	1|3	0|2	MSH2|MSH2	47510542|47510542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.212000|4.212000	0.58514|0.58514	2.078000|2.078000	0.62432|0.62432	0.529000|0.529000	0.55759|0.55759	AAT|TAA		0.353	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			C	47657038	A	C	47657038	3	2	47	1	0	0	0	0	1	0	0	0	9900	14	1	4	1260	4	MSH2	2	47657038	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	524359	47657038	195542335	255	4652										
MSH6	2956	broad.mit.edu	37	chr2	48033753	48033753	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggacatagaaaagcaagaGaatttgagaagatgaatcag	12	3	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:48033753G>T	ENST00000234420.5	+	9	4116	c.3964G>T	c.(3964-3966)Gaa>Taa	p.E1322*	MSH6_ENST00000538136.1_Nonsense_Mutation_p.E1020*|MSH6_ENST00000540021.1_Nonsense_Mutation_p.E1192*|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	1322					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)|p.E1322*(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAAAGCAAGAGAATTTGAGAA	0.343			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	4	Substitution - Nonsense(2)|Whole gene deletion(2)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)	2											49	51	50					2																	48033753		2203	4300	6503	47887257	SO:0001587	stop_gained	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.3964G>T	2.37:g.48033753G>T	ENSP00000234420:p.Glu1322*		47887257	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Nonsense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	G	46	12.222035	0.99648	.	.	ENSG00000116062	ENST00000234420;ENST00000543270;ENST00000540021;ENST00000538136	.	.	.	6.03	5.12	0.69794	.	0.044936	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-22.7694	17.4293	0.87535	0.0:0.1238:0.8762:0.0	.	.	.	.	X	1322;286;1192;1020	.	ENSP00000234420:E1322X	E	+	1	0	MSH6	47887257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.956000	0.87863	2.861000	0.98227	0.655000	0.94253	GAA		0.343	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		T	48033753	G	T	48033753	4	4	47	1	0	0	0	0	0	1	0	0	9904	943	33	2	3998	2	MSH6	2	48033753	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	376715	48033753	195165620	256	4653										
FBXO11	80204	broad.mit.edu	37	chr2	48036302	48036302	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatttctaagttacctgtaGaaatcatgcatgggatagct	8	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:48036302G>T	ENST00000403359.3	-	21	2622	c.2550C>A	c.(2548-2550)ttC>ttA	p.F850L	MSH6_ENST00000234420.5_3'UTR|FBXO11_ENST00000402508.1_Missense_Mutation_p.F766L|FBXO11_ENST00000316377.4_Missense_Mutation_p.F766L|FBXO11_ENST00000434523.2_Missense_Mutation_p.F274L|FBXO11_ENST00000405808.1_Missense_Mutation_p.F4L	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	850					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)|p.F766L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTTACCTGTAGAAATCATGCA	0.338			"Mis, F, D"		DLBCL																																		Rec	yes		2	2p16.3	80204	F-box protein 11		L	3	Whole gene deletion(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	2											100	104	103					2																	48036302		2202	4297	6499	47889806	SO:0001583	missense	80204			AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.2550C>A	2.37:g.48036302G>T	ENSP00000384823:p.Phe850Leu		47889806	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.157988	0.78114	.	.	ENSG00000138081	ENST00000405808;ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523	T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49	4.95	4.07	0.47477	.	0.000000	0.85682	D	0.000000	T	0.74152	0.3679	N	0.12663	0.25	0.80722	D	1	B	0.29862	0.259	B	0.43386	0.418	T	0.76271	-0.3020	10	0.66056	D	0.02	-3.4524	13.5865	0.61933	0.075:0.0:0.925:0.0	.	274	B3KUR1	.	L	4;766;850;766;274	ENSP00000385127:F4L;ENSP00000385398:F766L;ENSP00000384823:F850L;ENSP00000323822:F766L;ENSP00000397359:F274L	ENSP00000323822:F766L	F	-	3	2	FBXO11	47889806	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.582000	0.53921	1.438000	0.47492	0.561000	0.74099	TTC		0.338	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		T	48036302	G	T	48036302	3	4	47	1	0	0	0	0	1	0	0	0	5746	933	33	2	245	2	FBXO11	2	48036302	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2549	48036302	195163071	257	4654										
FOXN2	3344	broad.mit.edu	37	chr2	48573767	48573767	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttgcctgtcaaagaaatTtatagctggattctggacca	9	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:48573767T>G	ENST00000340553.3	+	3	675	c.414T>G	c.(412-414)atT>atG	p.I138M		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	138					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I138M(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			TCAAAGAAATTTATAGCTGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	121	117					2																	48573767		2203	4299	6502	48427271	SO:0001583	missense	3344				CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.414T>G	2.37:g.48573767T>G	ENSP00000343633:p.Ile138Met		48427271	Q15769|Q6P4Q2	Missense_Mutation	SNP	ENST00000340553.3	37	CCDS1838.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092426	0.55968	.	.	ENSG00000170802	ENST00000413569;ENST00000304367;ENST00000340553	D;D	0.97731	-4.51;-4.51	5.28	4.09	0.47781	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	H	0.97682	4.055	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98866	1.0764	10	0.87932	D	0	.	5.1258	0.14884	0.1435:0.1346:0.0:0.7219	.	138	P32314	FOXN2_HUMAN	M	138;47;138	ENSP00000388486:I138M;ENSP00000343633:I138M	ENSP00000305685:I47M	I	+	3	3	FOXN2	48427271	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.214000	0.32419	2.212000	0.71576	0.482000	0.46254	ATT		0.378	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		G	48573767	T	G	48573767	3	3	47	1	0	0	0	0	1	0	0	0	6039	1829	64	4	416	4	FOXN2	2	48573767	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	537465	48573767	194625606	258	4655										
STON1	11037	broad.mit.edu	37	chr2	48808452	48808452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctaaataagtgttcactcaActatatctgtgagaagcttg	7	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:48808452A>G	ENST00000406226.1	+	3	875	c.680A>G	c.(679-681)aAc>aGc	p.N227S	STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.N227S|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.N227S|STON1_ENST00000404752.1_Missense_Mutation_p.N227S|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.N227S|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.N227S|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.N227S|STON1_ENST00000309835.3_Missense_Mutation_p.N227S	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	227					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.N227S(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGTTCACTCAACTATATCTGT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2											83	77	79					2																	48808452		2203	4300	6503	48661956	SO:0001583	missense	286749			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.680A>G	2.37:g.48808452A>G	ENSP00000384615:p.Asn227Ser		48661956	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	A	0.357	-0.941320	0.02322	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.13;3.13;3.13;3.13;3.28	5.24	-0.139	0.13460	.	0.477909	0.26590	N	0.023527	T	0.02970	0.0088	N	0.04297	-0.235	0.20563	N	0.999885	B;B;B	0.22746	0.074;0.002;0.004	B;B;B	0.21708	0.036;0.001;0.005	T	0.46190	-0.9209	10	0.02654	T	1	.	11.1576	0.48497	0.4713:0.0:0.5287:0.0	.	227;227;227	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	S	227	ENSP00000385273:N227S;ENSP00000384615:N227S;ENSP00000310969:N227S;ENSP00000385499:N227S;ENSP00000385701:N227S;ENSP00000378236:N227S;ENSP00000311493:N227S;ENSP00000378234:N227S	ENSP00000310969:N227S	N	+	2	0	STON1-GTF2A1L;STON1	48661956	0.912000	0.30974	0.980000	0.43619	0.783000	0.44284	0.033000	0.13754	-0.091000	0.12440	0.533000	0.62120	AAC		0.413	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		G	48808452	A	G	48808452	3	3	47	1	0	0	0	0	1	0	0	0	15355	43	2	4	682	4	STON1	2	48808452	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	234685	48808452	194390921	259	4656										
STON1	11037	broad.mit.edu	37	chr2	48809174	48809174	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgagttgccgaagcgagatGaatcctattatgagaaggac	12	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:48809174G>T	ENST00000406226.1	+	3	1597	c.1402G>T	c.(1402-1404)Gaa>Taa	p.E468*	STON1-GTF2A1L_ENST00000402114.2_Nonsense_Mutation_p.E468*|STON1-GTF2A1L_ENST00000405008.1_Nonsense_Mutation_p.E468*|STON1_ENST00000404752.1_Nonsense_Mutation_p.E468*|STON1-GTF2A1L_ENST00000394754.1_Nonsense_Mutation_p.E468*|STON1-GTF2A1L_ENST00000309827.2_Nonsense_Mutation_p.E468*|STON1-GTF2A1L_ENST00000394751.3_Nonsense_Mutation_p.E468*|STON1_ENST00000309835.3_Nonsense_Mutation_p.E468*	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	468	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.E468*(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAAGCGAGATGAATCCTATTA	0.368																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											116	122	120					2																	48809174		2203	4300	6503	48662678	SO:0001587	stop_gained	286749			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1402G>T	2.37:g.48809174G>T	ENSP00000384615:p.Glu468*		48662678	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Nonsense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	G	35	5.447235	0.96205	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	.	.	.	5.3	5.3	0.74995	.	0.554178	0.21819	N	0.068646	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.4615	0.55734	0.0757:0.0:0.9243:0.0	.	.	.	.	X	468	.	ENSP00000310969:E468X	E	+	1	0	STON1-GTF2A1L;STON1	48662678	1.000000	0.71417	0.926000	0.36857	0.204000	0.24138	2.781000	0.47750	2.769000	0.95229	0.655000	0.94253	GAA		0.368	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		T	48809174	G	T	48809174	4	4	47	1	0	0	0	0	0	1	0	0	15355	1291	45	2	1404	2	STON1	2	48809174	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	722	48809174	194390199	260	4657										
MTIF2	4528	broad.mit.edu	37	chr2	55471182	55471182	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacctcagattctacttcaaGaatttcttctcctgcagaag	5	12	5	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:55471182G>T	ENST00000263629.4	-	11	1609	c.1294C>A	c.(1294-1296)Ctt>Att	p.L432I	MTIF2_ENST00000394600.3_Missense_Mutation_p.L432I|MTIF2_ENST00000403721.1_Missense_Mutation_p.L432I	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	432					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.L432I(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TCTACTTCAAGAATTTCTTCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											62	59	60					2																	55471182		2203	4300	6503	55324686	SO:0001583	missense	4528			L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1294C>A	2.37:g.55471182G>T	ENSP00000263629:p.Leu432Ile		55324686	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	G	17.84	3.488129	0.64074	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000535023	T;T;T	0.60672	0.17;0.17;0.17	5.88	4.99	0.66335	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.58892	0.2154	N	0.20807	0.61	0.80722	D	1	B	0.15719	0.014	P	0.45138	0.471	T	0.59621	-0.7420	10	0.41790	T	0.15	-8.4488	16.22	0.82254	0.0:0.0:0.8659:0.1341	.	432	P46199	IF2M_HUMAN	I	432	ENSP00000384481:L432I;ENSP00000263629:L432I;ENSP00000378099:L432I	ENSP00000263629:L432I	L	-	1	0	MTIF2	55324686	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.534000	0.73833	1.445000	0.47624	0.650000	0.86243	CTT		0.343	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		T	55471182	G	T	55471182	3	4	47	1	0	0	0	0	1	0	0	0	9964	942	33	2	913	2	MTIF2	2	55471182	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6662008	55471182	187728191	261	4658										
CCDC88A	55704	broad.mit.edu	37	chr2	55571636	55571636	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctaataaaacttgattGtcttcttttaattcctataa	3	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:55571636G>A	ENST00000436346.1	-	11	1897	c.1056C>T	c.(1054-1056)gaC>gaT	p.D352D	CCDC88A_ENST00000263630.8_Silent_p.D352D|AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000413716.2_Silent_p.D352D|CCDC88A_ENST00000336838.6_Silent_p.D352D	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	352					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.D352D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						AAACTTGATTGTCTTCTTTTA	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	2											92	94	93					2																	55571636		2202	4297	6499	55425140	SO:0001819	synonymous_variant	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1056C>T	2.37:g.55571636G>A			55425140	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	37																																																																																					0.279	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		A	55571636	G	A	55571636	2	1	47	1	0	0	0	0	0	0	0	1	2869	1368	48	3		3	CCDC88A	2	55571636	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	100454	55571636	187627737	262	4659										
XPO1	7514	broad.mit.edu	37	chr2	61719472	61719472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatttaccatgcatgaattCgaacagcttgttaactacag	7	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:61719472C>T	ENST00000401558.2	-	15	2438	c.1711G>A	c.(1711-1713)Gaa>Aaa	p.E571K	XPO1_ENST00000406957.1_Missense_Mutation_p.E571K|XPO1_ENST00000404992.2_Missense_Mutation_p.E571K	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	571	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)	p.E571K(5)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			TGCATGAATTCGAACAGCTTG	0.313			Mis		CLL																																	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	5	Substitution - Missense(5)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|prostate(1)|endometrium(1)	2											66	63	64					2																	61719472		2203	4300	6503	61572976	SO:0001583	missense	7514			Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.1711G>A	2.37:g.61719472C>T	ENSP00000384863:p.Glu571Lys		61572976	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	C	36	5.629400	0.96671	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.66099	-0.19;-0.19;-0.19	5.63	5.63	0.86233	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85856	0.5794	H	0.94734	3.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88632	0.3170	10	0.66056	D	0.02	-19.4383	20.0572	0.97657	0.0:1.0:0.0:0.0	.	218;571	B3KWD0;O14980	.;XPO1_HUMAN	K	571	ENSP00000384863:E571K;ENSP00000385942:E571K;ENSP00000385559:E571K	ENSP00000384863:E571K	E	-	1	0	XPO1	61572976	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	7.722000	0.84778	2.826000	0.97356	0.655000	0.94253	GAA		0.313	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		T	61719472	C	T	61719472	3	4	47	1	0	0	0	0	1	0	0	0	17485	893	31	1	1548	1	XPO1	2	61719472	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6147836	61719472	181479901	263	4660										
AFTPH	54812	broad.mit.edu	37	chr2	64779347	64779347	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggaaaggatacaattagaaGaaatagaatgtgcagtttta	10	2	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:64779347G>T	ENST00000422803.1	+	2	1053	c.739G>T	c.(739-741)Gaa>Taa	p.E247*	AFTPH_ENST00000238855.7_Nonsense_Mutation_p.E247*|AFTPH_ENST00000238856.4_Nonsense_Mutation_p.E247*|AFTPH_ENST00000409933.1_Nonsense_Mutation_p.E247*|AFTPH_ENST00000409183.1_5'Flank			Q6ULP2	AFTIN_HUMAN	aftiphilin	247					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)	p.E247*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						ACAATTAGAAGAAATAGAATG	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											46	49	48					2																	64779347		2203	4299	6502	64632851	SO:0001587	stop_gained	54812			AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.739G>T	2.37:g.64779347G>T	ENSP00000397726:p.Glu247*		64632851	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Nonsense_Mutation	SNP	ENST00000422803.1	37		.	.	.	.	.	.	.	.	.	.	G	38	7.095496	0.98059	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933	.	.	.	5.78	5.78	0.91487	.	0.158539	0.44902	D	0.000406	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-8.7126	20.3754	0.98918	0.0:0.0:1.0:0.0	.	.	.	.	X	247	.	ENSP00000238855:E247X	E	+	1	0	AFTPH	64632851	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	5.161000	0.64935	2.894000	0.99253	0.591000	0.81541	GAA		0.343	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		T	64779347	G	T	64779347	4	4	47	1	0	0	0	0	0	1	0	0	364	943	33	2	741	2	AFTPH	2	64779347	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3059875	64779347	178420026	264	4661										
MEIS1	4211	broad.mit.edu	37	chr2	66664875	66664875	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttgtcatgcagtacgacGatctaccccattacgggggc	11	11	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:66664875G>A	ENST00000272369.9	+	2	476	c.19G>A	c.(19-21)Gat>Aat	p.D7N	MEIS1_ENST00000488550.1_Missense_Mutation_p.D7N|MEIS1-AS2_ENST00000439433.1_RNA|MEIS1-AS1_ENST00000454595.1_RNA|MEIS1_ENST00000495021.2_5'Flank|MEIS1_ENST00000398506.2_Missense_Mutation_p.D5N|MEIS1_ENST00000560281.2_Missense_Mutation_p.D7N|MEIS1_ENST00000444274.2_5'Flank|MEIS1_ENST00000407092.2_Missense_Mutation_p.D7N	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	7					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	p.D7N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						GCAGTACGACGATCTACCCCA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	45	45					2																	66664875		2000	4180	6180	66518379	SO:0001583	missense	4211				CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"Homeoboxes / TALE class"	7000	protein-coding gene	gene with protein product		601739	"Meis1 (mouse) homolog", "Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.19G>A	2.37:g.66664875G>A	ENSP00000272369:p.Asp7Asn		66518379	A8MV50	Missense_Mutation	SNP	ENST00000272369.9	37	CCDS46309.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738665	0.89573	.	.	ENSG00000143995	ENST00000272369;ENST00000407092;ENST00000398506	T;T;T	0.28895	1.59;1.59;1.59	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	L	0.38175	1.15	0.80722	D	1	P;B;P	0.48350	0.909;0.332;0.909	P;B;P	0.47941	0.562;0.096;0.562	T	0.10590	-1.0623	10	0.72032	D	0.01	.	19.3962	0.94608	0.0:0.0:1.0:0.0	.	5;7;7	O00470-2;O00470;F8W8U3	.;MEIS1_HUMAN;.	N	7;7;5	ENSP00000272369:D7N;ENSP00000384461:D7N;ENSP00000381518:D5N	ENSP00000272369:D7N	D	+	1	0	MEIS1	66518379	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.149000	0.94659	2.746000	0.94184	0.655000	0.94253	GAT		0.567	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398		A	66664875	G	A	66664875	3	1	47	1	0	0	0	0	1	0	0	0	9497	1058	37	1	25	1	MEIS1	2	66664875	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1885528	66664875	176534498	265	4662										
ETAA1	54465	broad.mit.edu	37	chr2	67631445	67631445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaaatcagtctattaaagCccctgttaatactgatcttt	4	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:67631445C>T	ENST00000272342.5	+	5	1761	c.1631C>T	c.(1630-1632)gCc>gTc	p.A544V	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	544						cytoplasm (GO:0005737)		p.A544V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TCTATTAAAGCCCCTGTTAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	51	50					2																	67631445		2203	4298	6501	67484949	SO:0001583	missense	54465			AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1631C>T	2.37:g.67631445C>T	ENSP00000272342:p.Ala544Val		67484949	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.557056	0.00136	.	.	ENSG00000143971	ENST00000272342	T	0.15372	2.43	5.61	1.11	0.20524	.	0.795302	0.11594	N	0.548409	T	0.06050	0.0157	N	0.12569	0.235	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.40590	-0.9555	10	0.02654	T	1	-25.2659	1.4896	0.02454	0.1423:0.3766:0.1402:0.341	.	544	Q9NY74	ETAA1_HUMAN	V	544	ENSP00000272342:A544V	ENSP00000272342:A544V	A	+	2	0	ETAA1	67484949	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-0.418000	0.07080	0.293000	0.22520	0.655000	0.94253	GCC		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		T	67631445	C	T	67631445	3	4	47	1	0	0	0	0	1	0	0	0	5280	739	26	3	1649	3	ETAA1	2	67631445	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	966570	67631445	175567928	266	4663										
PLEK	5341	broad.mit.edu	37	chr2	68607958	68607958	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggatatcaagaaggccattaAatgcattgaaggaggccaga	12	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:68607958A>C	ENST00000234313.7	+	3	481	c.302A>C	c.(301-303)aAa>aCa	p.K101T		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	101	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.K101T(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		AAGGCCATTAAATGCATTGAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	135	136					2																	68607958		2203	4300	6503	68461462	SO:0001583	missense	5341			X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.302A>C	2.37:g.68607958A>C	ENSP00000234313:p.Lys101Thr		68461462	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.236414	0.39498	.	.	ENSG00000115956	ENST00000234313	T	0.76968	-1.06	5.8	4.65	0.58169	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.132017	0.64402	D	0.000003	T	0.43433	0.1247	N	0.00554	-1.385	0.40159	D	0.977043	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.004	T	0.30297	-0.9983	10	0.21014	T	0.42	.	7.6739	0.28473	0.789:0.1404:0.0706:0.0	.	119;101	Q59GZ2;P08567	.;PLEK_HUMAN	T	101	ENSP00000234313:K101T	ENSP00000234313:K101T	K	+	2	0	PLEK	68461462	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.724000	0.54962	1.026000	0.39733	0.533000	0.62120	AAA		0.473	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		C	68607958	A	C	68607958	3	2	47	1	0	0	0	0	1	0	0	0	12084	14	1	4	312	4	PLEK	2	68607958	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	976513	68607958	174591415	267	4664										
PROKR1	10887	broad.mit.edu	37	chr2	68882498	68882498	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcactacctcactgccttCtacatcgtcgagtgcatcgc	7	15	2	0	rs377223485		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:68882498C>A	ENST00000303786.3	+	3	1392	c.972C>A	c.(970-972)ttC>ttA	p.F324L	PROKR1_ENST00000394342.2_Missense_Mutation_p.F324L			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	324					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.F324L(1)		endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TCACTGCCTTCTACATCGTCG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											189	135	153					2																	68882498		2203	4300	6503	68736002	SO:0001583	missense	10887			AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"GPCR / Class A : Prokineticin receptors"	4524	protein-coding gene	gene with protein product		607122	"G protein-coupled receptor 73"	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.972C>A	2.37:g.68882498C>A	ENSP00000303775:p.Phe324Leu		68736002	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624569	0.66901	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.71222	-0.55;-0.55	4.68	0.859	0.19036	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.77068	0.4076	M	0.66506	2.035	0.53688	D	0.999975	D	0.56287	0.975	P	0.62184	0.899	T	0.75286	-0.3371	10	0.72032	D	0.01	.	8.6291	0.33908	0.0:0.6621:0.0:0.3379	.	324	Q8TCW9	PKR1_HUMAN	L	324	ENSP00000303775:F324L;ENSP00000377874:F324L	ENSP00000303775:F324L	F	+	3	2	PROKR1	68736002	1.000000	0.71417	0.983000	0.44433	0.946000	0.59487	1.004000	0.29822	0.142000	0.18901	0.655000	0.94253	TTC		0.532	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			A	68882498	C	A	68882498	3	1	47	1	0	0	0	0	1	0	0	0	12586	912	32	2	978	2	PROKR1	2	68882498	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	274540	68882498	174316875	268	4665										
C2orf42	54980	broad.mit.edu	37	chr2	70409104	70409104	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgggactttagtcctcagaGaatttggttccatttttcag	9	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:70409104G>T	ENST00000264434.2	-	3	393	c.14C>A	c.(13-15)tCt>tAt	p.S5Y	C2orf42_ENST00000470096.1_5'UTR|C2orf42_ENST00000420306.1_Missense_Mutation_p.S5Y	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	5								p.S5Y(1)		endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						AGTCCTCAGAGAATTTGGTTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											24	24	24					2																	70409104		2203	4300	6503	70262608	SO:0001583	missense	54980			AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.14C>A	2.37:g.70409104G>T	ENSP00000264434:p.Ser5Tyr		70262608	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	g	19.68	3.873446	0.72180	.	.	ENSG00000115998	ENST00000264434;ENST00000420306;ENST00000447804;ENST00000417865;ENST00000419381;ENST00000457952;ENST00000428010;ENST00000425268;ENST00000428751;ENST00000417203	T;T	0.49720	0.77;0.77	5.07	5.07	0.68467	.	0.268041	0.38720	N	0.001598	T	0.55000	0.1893	L	0.44542	1.39	0.41131	D	0.985888	D	0.54207	0.965	P	0.53649	0.731	T	0.59129	-0.7512	10	0.87932	D	0	-5.8203	17.2597	0.87066	0.0:0.0:1.0:0.0	.	5	Q9NWW7	CB042_HUMAN	Y	5	ENSP00000264434:S5Y;ENSP00000404515:S5Y	ENSP00000264434:S5Y	S	-	2	0	C2orf42	70262608	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.370000	0.73114	2.637000	0.89404	0.574000	0.79327	TCT		0.413	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		T	70409104	G	T	70409104	3	4	47	1	0	0	0	0	1	0	0	0	2172	942	33	2	1742	2	C2orf42	2	70409104	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1526606	70409104	172790269	269	4666										
ZNF638	27332	broad.mit.edu	37	chr2	71592753	71592753	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctaggaggacattctattCgttgtaaatcaaagaatctt	7	6	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:71592753C>T	ENST00000409544.1	+	6	2542	c.1912C>T	c.(1912-1914)Cgt>Tgt	p.R638C	ZNF638_ENST00000377802.2_Missense_Mutation_p.R638C|ZNF638_ENST00000264447.4_Missense_Mutation_p.R638C|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000355812.3_Missense_Mutation_p.R638C	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	638					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R638C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						ACATTCTATTCGTTGTAAATC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	70	71					2																	71592753		2203	4300	6503	71446261	SO:0001583	missense	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1912C>T	2.37:g.71592753C>T	ENSP00000386433:p.Arg638Cys		71446261	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.282526	0.59867	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000394137;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.73258	-0.14;-0.73;0.43;-0.13;1.44;1.44	5.17	5.17	0.71159	.	0.177641	0.35585	N	0.003101	T	0.72550	0.3474	L	0.29908	0.895	0.41880	D	0.990317	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.998;0.999;0.999	P;P;P;P;P;P	0.59703	0.732;0.862;0.809;0.731;0.791;0.809	T	0.74657	-0.3592	10	0.56958	D	0.05	-4.3213	14.0291	0.64604	0.0:1.0:0.0:0.0	.	638;744;638;638;638;638	A8K583;F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;.;ZN638_HUMAN;.	C	638;744;217;638;638;638;638	ENSP00000386669:R638C;ENSP00000438189:R744C;ENSP00000348066:R638C;ENSP00000367033:R638C;ENSP00000264447:R638C;ENSP00000386433:R638C	ENSP00000264447:R638C	R	+	1	0	ZNF638	71446261	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.256000	0.51492	2.691000	0.91804	0.563000	0.77884	CGT		0.363	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71592753	C	T	71592753	3	4	47	1	0	0	0	0	1	0	0	0	18094	884	31	1	1930	1	ZNF638	2	71592753	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1183649	71592753	171606620	270	4667										
EMX1	2016	broad.mit.edu	37	chr2	73161063	73161063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggccaatggggaggacatcGatgtcacctccaatgactag	12	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:73161063G>A	ENST00000258106.6	+	3	1231	c.853G>A	c.(853-855)Gat>Aat	p.D285N	EMX1_ENST00000394111.5_3'UTR	NM_004097.2	NP_004088.2	Q04741	EMX1_HUMAN	empty spiracles homeobox 1	252					brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|in utero embryonic development (GO:0001701)|neuron projection extension (GO:1990138)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.D285N(1)		cervix(1)|large_intestine(2)|lung(3)	6						GGAGGACATCGATGTCACCTC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	70	67					2																	73161063		2132	4240	6372	73014571	SO:0001583	missense	2016			X68879	CCDS1921.2	2p13.2	2011-06-20	2007-02-15		ENSG00000135638	ENSG00000135638		"Homeoboxes / ANTP class : NKL subclass"	3340	protein-coding gene	gene with protein product		600034	"empty spiracles homolog 1 (Drosophila)"			7959790	Standard	XM_005264203		Approved		uc002sin.1	Q04741	OTTHUMG00000129778	ENST00000258106.6:c.853G>A	2.37:g.73161063G>A	ENSP00000258106:p.Asp285Asn		73014571	Q0D2P0|Q53T30|Q86XB0	Missense_Mutation	SNP	ENST00000258106.6	37	CCDS1921.2	.	.	.	.	.	.	.	.	.	.	G	33	5.199590	0.94997	.	.	ENSG00000135638	ENST00000258106	D	0.94417	-3.42	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.96870	0.8978	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.96958	0.9699	10	0.59425	D	0.04	-15.1927	16.7907	0.85589	0.0:0.0:1.0:0.0	.	252	Q04741	EMX1_HUMAN	N	285	ENSP00000258106:D285N	ENSP00000258106:D285N	D	+	1	0	EMX1	73014571	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.657000	0.98554	2.639000	0.89480	0.491000	0.48974	GAT		0.622	EMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251994.3			A	73161063	G	A	73161063	3	1	47	1	0	0	0	0	1	0	0	0	5120	1058	37	1	863	1	EMX1	2	73161063	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1568310	73161063	170038310	271	4668										
ALMS1	7840	broad.mit.edu	37	chr2	73717163	73717163	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcttttgtgccacctaaaGaagtggattttcattcttca	7	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:73717163G>T	ENST00000264448.6	+	10	8185	c.8074G>T	c.(8074-8076)Gaa>Taa	p.E2692*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.E2650*|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2692					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E2692*(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GCCACCTAAAGAAGTGGATTT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											167	156	160					2																	73717163		1865	4097	5962	73570671	SO:0001587	stop_gained	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8074G>T	2.37:g.73717163G>T	ENSP00000264448:p.Glu2692*		73570671	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	38	6.737623	0.97801	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	.	.	.	4.1	3.22	0.36961	.	0.279917	0.25906	N	0.027528	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	10.9785	0.47480	0.0983:0.0:0.9017:0.0	.	.	.	.	X	2650;2692	.	ENSP00000264448:E2692X	E	+	1	0	ALMS1	73570671	1.000000	0.71417	0.990000	0.47175	0.921000	0.55340	2.601000	0.46249	0.691000	0.31592	-1.151000	0.01829	GAA		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73717163	G	T	73717163	4	4	47	1	0	0	0	0	0	1	0	0	535	943	33	2	8112	2	ALMS1	2	73717163	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	556100	73717163	169482210	272	4669										
RTKN	6242	broad.mit.edu	37	chr2	74656988	74656988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggggagcaagatgggactgCtccctgaacccccagcactg	13	13	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:74656988C>T	ENST00000233330.6	-	6	889	c.572G>A	c.(571-573)aGc>aAc	p.S191N	RTKN_ENST00000305557.5_Missense_Mutation_p.S228N|RTKN_ENST00000272430.5_Missense_Mutation_p.S241N|RTKN_ENST00000484453.1_5'Flank	NM_001015056.1	NP_001015056.1			rhotekin									p.S228N(1)|p.S241N(1)		endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						GATGGGACTGCTCCCTGAACC	0.637																																																2	Substitution - Missense(2)	large_intestine(2)	2											42	42	42					2																	74656988		2203	4300	6503	74510496	SO:0001583	missense	6242			AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.572G>A	2.37:g.74656988C>T	ENSP00000233330:p.Ser191Asn		74510496		Missense_Mutation	SNP	ENST00000233330.6	37	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.890881	0.33348	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.32023	1.47;1.48;1.48	4.77	2.89	0.33648	.	0.489958	0.25186	N	0.032495	T	0.14527	0.0351	N	0.11427	0.14	0.32663	N	0.517824	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.002	T	0.13953	-1.0490	10	0.23302	T	0.38	.	8.7383	0.34541	0.0:0.8037:0.0:0.1963	.	241;228	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	N	228;241;191	ENSP00000305298:S228N;ENSP00000272430:S241N;ENSP00000233330:S191N	ENSP00000233330:S191N	S	-	2	0	RTKN	74510496	1.000000	0.71417	0.980000	0.43619	0.929000	0.56500	2.490000	0.45294	1.206000	0.43276	0.561000	0.74099	AGC		0.637	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		T	74656988	C	T	74656988	3	4	47	1	0	0	0	0	1	0	0	0	13759	797	28	3	997	3	RTKN	2	74656988	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	939825	74656988	168542385	273	4670										
DQX1	165545	broad.mit.edu	37	chr2	74746692	74746692	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcctctaaccttgagaaaGtatcctgacaccagtgcttt	6	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:74746692G>T	ENST00000404568.3	-	10	2016	c.1797C>A	c.(1795-1797)taC>taA	p.Y599*	DQX1_ENST00000393951.2_Nonsense_Mutation_p.Y599*	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	599						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.Y481*(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CCTTGAGAAAGTATCCTGACA	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											127	131	130					2																	74746692		2203	4300	6503	74600200	SO:0001587	stop_gained	165545			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1797C>A	2.37:g.74746692G>T	ENSP00000384621:p.Tyr599*		74600200	Q6B017|Q8NAM8	Nonsense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	37	6.306376	0.97458	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	.	.	.	5.55	4.66	0.58398	.	0.182364	0.37219	N	0.002181	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-23.0667	13.3494	0.60593	0.0:0.0:0.8409:0.1591	.	.	.	.	X	599	.	ENSP00000377523:Y599X	Y	-	3	2	DQX1	74600200	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.308000	0.59129	1.294000	0.44707	0.561000	0.74099	TAC		0.478	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74746692	G	T	74746692	4	4	47	1	0	0	0	0	0	1	0	0	4762	1024	36	2	368	2	DQX1	2	74746692	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	89704	74746692	168452681	274	4671										
SEMA4F	10505	broad.mit.edu	37	chr2	74883717	74883717	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacatacaattactctgttCtccttgtggatcctgcctcc	5	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:74883717C>A	ENST00000357877.2	+	2	351	c.202C>A	c.(202-204)Ctc>Atc	p.L68I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.L68I	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	68	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.L68I(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TTACTCTGTTCTCCTTGTGGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											134	120	125					2																	74883717		2203	4300	6503	74737225	SO:0001583	missense	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.202C>A	2.37:g.74883717C>A	ENSP00000350547:p.Leu68Ile		74737225	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.355738	0.82243	.	.	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	4.9	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.351137	0.26193	N	0.025799	T	0.34337	0.0894	M	0.73753	2.245	0.24729	N	0.993109	P;P;D;D	0.67145	0.905;0.811;0.996;0.992	B;B;D;D	0.75484	0.427;0.386;0.986;0.954	T	0.14337	-1.0476	10	0.23302	T	0.38	.	13.5155	0.61539	0.0:1.0:0.0:0.0	.	68;68;68;68	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	I	68	ENSP00000350547:L68I;ENSP00000342675:L68I;ENSP00000407698:L68I;ENSP00000409141:L68I	ENSP00000342675:L68I	L	+	1	0	SEMA4F	74737225	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.347000	0.52200	2.568000	0.86640	0.650000	0.86243	CTC		0.562	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74883717	C	A	74883717	3	1	47	1	0	0	0	0	1	0	0	0	14072	913	32	2	208	2	SEMA4F	2	74883717	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	137025	74883717	168315656	275	4672										
CTNNA2	1496	broad.mit.edu	37	chr2	80085150	80085150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcttccaggtgagacgatgCggatcgcctcctccgagttt	12	12	1	1	rs574924497		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:80085150C>T	ENST00000402739.4	+	3	315	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W	CTNNA2_ENST00000541047.1_Missense_Mutation_p.R104W|CTNNA2_ENST00000496558.1_Missense_Mutation_p.R104W|CTNNA2_ENST00000540488.1_Missense_Mutation_p.R104W|CTNNA2_ENST00000361291.4_Missense_Mutation_p.R138W|CTNNA2_ENST00000466387.1_Missense_Mutation_p.R104W	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	104					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.R104W(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						TGAGACGATGCGGATCGCCTC	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	2											93	90	91					2																	80085150		2051	4187	6238	79938658	SO:0001583	missense	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.310C>T	2.37:g.80085150C>T	ENSP00000384638:p.Arg104Trp		79938658	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	C	18.60	3.658494	0.67586	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.67	3.69	0.42338	.	0.065224	0.64402	D	0.000013	T	0.50871	0.1641	L	0.47716	1.5	0.53005	D	0.999969	D;D;D	0.76494	0.999;0.997;0.998	D;P;P	0.66979	0.948;0.764;0.877	T	0.46789	-0.9166	10	0.44086	T	0.13	.	15.1718	0.72878	0.447:0.553:0.0:0.0	.	104;104;104	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	W	104;104;104;138;104;104;104	ENSP00000418191:R104W;ENSP00000419295:R104W;ENSP00000387073:R104W;ENSP00000355398:R138W;ENSP00000384638:R104W;ENSP00000444675:R104W;ENSP00000441705:R104W	ENSP00000355398:R138W	R	+	1	2	CTNNA2	79938658	1.000000	0.71417	0.998000	0.56505	0.714000	0.41099	1.304000	0.33482	0.693000	0.31634	-0.181000	0.13052	CGG		0.562	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80085150	C	T	80085150	3	4	47	1	0	0	0	0	1	0	0	0	4019	759	27	1	320	1	CTNNA2	2	80085150	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5201433	80085150	163114223	276	4673										
DNAH6	1768	broad.mit.edu	37	chr2	84804497	84804497	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgatactaggcttctaagaGaaaaattaattccatcacct	5	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:84804497G>T	ENST00000237449.6	+	12	2049	c.2041G>T	c.(2041-2043)Gaa>Taa	p.E681*	DNAH6_ENST00000389394.3_Nonsense_Mutation_p.E681*|DNAH6_ENST00000398278.2_Nonsense_Mutation_p.E681*			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	681	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E681*(1)|p.E260*(1)		NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GCTTCTAAGAGAAAAATTAAT	0.348																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											61	56	58					2																	84804497		2203	4300	6503	84658008	SO:0001587	stop_gained	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2041G>T	2.37:g.84804497G>T	ENSP00000237449:p.Glu681*		84658008	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Nonsense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	35	5.476767	0.96291	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	.	.	.	5.48	3.58	0.41010	.	0.116109	0.38663	N	0.001611	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	9.898	0.41331	0.0783:0.1416:0.7801:0.0	.	.	.	.	X	681	.	ENSP00000237449:E681X	E	+	1	0	DNAH6	84658008	1.000000	0.71417	0.980000	0.43619	0.474000	0.32979	2.659000	0.46741	2.584000	0.87258	0.561000	0.74099	GAA		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84804497	G	T	84804497	4	4	47	1	0	0	0	0	0	1	0	0	4616	943	33	2	2087	2	DNAH6	2	84804497	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4719347	84804497	158394876	277	4674										
IMMT	10989	broad.mit.edu	37	chr2	86406562	86406562	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaaaactcttaccgatttCtttggcaatggaacattata	5	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:86406562C>A	ENST00000410111.3	-	3	690	c.303G>T	c.(301-303)aaG>aaT	p.K101N	IMMT_ENST00000449247.2_Missense_Mutation_p.K101N|IMMT_ENST00000254636.5_Missense_Mutation_p.K14N|IMMT_ENST00000442664.2_Missense_Mutation_p.K101N|IMMT_ENST00000409051.2_Missense_Mutation_p.K101N	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	101					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.K101N(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTACCGATTTCTTTGGCAATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											43	41	41					2																	86406562		1826	4090	5916	86260073	SO:0001583	missense	10989			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.303G>T	2.37:g.86406562C>A	ENSP00000387262:p.Lys101Asn		86260073	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214724	0.39102	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	T;T;T;T;T	0.55413	0.52;1.07;1.18;1.18;1.12	4.97	4.09	0.47781	.	0.222920	0.46145	D	0.000313	T	0.64080	0.2566	L	0.43152	1.355	0.80722	D	1	P;D;P;D;D;P;P;P;P	0.89917	0.481;1.0;0.537;1.0;1.0;0.635;0.481;0.635;0.537	B;D;P;D;D;B;B;B;P	0.97110	0.347;0.999;0.479;0.999;1.0;0.347;0.347;0.347;0.479	T	0.65315	-0.6198	10	0.56958	D	0.05	-16.9329	13.3115	0.60382	0.0:0.9231:0.0:0.0769	.	101;101;101;101;101;101;101;101;101	F5GZ32;B9A067;B4DKR1;Q05DN3;B4E2B5;F8W9I1;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;.;.;IMMT_HUMAN	N	14;101;101;101;101;101;101;101;101	ENSP00000254636:K14N;ENSP00000396899:K101N;ENSP00000387262:K101N;ENSP00000407788:K101N;ENSP00000387227:K101N	ENSP00000254636:K14N	K	-	3	2	IMMT	86260073	1.000000	0.71417	0.999000	0.59377	0.072000	0.16883	3.609000	0.54117	1.090000	0.41315	-0.140000	0.14226	AAG		0.343	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86406562	C	A	86406562	3	1	47	1	0	0	0	0	1	0	0	0	7739	912	32	2	2025	2	IMMT	2	86406562	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1602065	86406562	156792811	278	4675										
ZNF514	84874	broad.mit.edu	37	chr2	95815475	95815475	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttttctccagtatgagttCtttgatgtttaataagggat	9	5	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:95815475C>A	ENST00000295208.2	-	5	1217	c.755G>T	c.(754-756)aGa>aTa	p.R252I	MRPS5_ENST00000475040.1_5'Flank|ZNF514_ENST00000411425.1_Missense_Mutation_p.R252I	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R252I(1)		large_intestine(4)|lung(6)|urinary_tract(1)	11						AGTATGAGTTCTTTGATGTTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											107	114	112					2																	95815475		2203	4300	6503	95179202	SO:0001583	missense	84874			AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.755G>T	2.37:g.95815475C>A	ENSP00000295208:p.Arg252Ile		95179202	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	37	CCDS2011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.92|18.92	3.726635|3.726635	0.69074|0.69074	.|.	.|.	ENSG00000144026|ENSG00000144026	ENST00000542127|ENST00000295208;ENST00000411425	.|T;T	.|0.02446	.|4.29;4.29	3.18|3.18	3.18|3.18	0.36537|0.36537	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.08935	.|0.0221	L|L	0.53561|0.53561	1.675|1.675	0.46203|0.46203	D|D	0.998921|0.998921	.|D;P	.|0.63046	.|0.992;0.544	.|P;B	.|0.60789	.|0.879;0.125	.|T	.|0.16070	.|-1.0415	.|9	.|0.44086	.|T	.|0.13	.|.	12.6059|12.6059	0.56523|0.56523	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|252;71	.|Q96K75;Q658L7	.|ZN514_HUMAN;.	.|I	-1|252	.|ENSP00000295208:R252I;ENSP00000405509:R252I	.|ENSP00000295208:R252I	.|R	-|-	.|2	.|0	ZNF514|ZNF514	95179202|95179202	0.000000|0.000000	0.05858|0.05858	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	0.782000|0.782000	0.26788|0.26788	2.065000|2.065000	0.61736|0.61736	0.655000|0.655000	0.94253|0.94253	.|AGA		0.453	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		A	95815475	C	A	95815475	3	1	47	1	0	0	0	0	1	0	0	0	17998	913	32	2	451	2	ZNF514	2	95815475	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9408913	95815475	147383898	279	4676										
ANKRD36B	57730	broad.mit.edu	37	chr2	98164053	98164053	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggctatattcaaaagagaatCtttctcgtctcttgtagcct	7	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:98164053C>A	ENST00000443455.1	-	0	1635							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		AAAAGAGAATCTTTCTCGTCT	0.294																																																0			2																																								97530485			57730			AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98164053C>A			97530485	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																					0.294	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		A	98164053	C	A	98164053	1	1	47	0	1	0	0	0	0	0	0	0	666	913	32	2		2	ANKRD36B	2	98164053	RNA	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2348578	98164053	145035320	280	4677										
TMEM131	23505	broad.mit.edu	37	chr2	98431766	98431766	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagatggcttttttgccttCgatgctgaaaggaagcataa	11	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:98431766C>T	ENST00000186436.5	-	13	1416	c.1188G>A	c.(1186-1188)tcG>tcA	p.S396S	TMEM131_ENST00000425805.2_Missense_Mutation_p.R311Q	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	396						integral component of membrane (GO:0016021)		p.S283S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TTTTTGCCTTCGATGCTGAAA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	2											81	75	77					2																	98431766		1788	4056	5844	97798198	SO:0001819	synonymous_variant	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.1188G>A	2.37:g.98431766C>T			97798198		Silent	SNP	ENST00000186436.5	37	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.519965	0.44866	.	.	ENSG00000075568	ENST00000425805	.	.	.	5.86	0.658	0.17855	.	.	.	.	.	T	0.39384	0.1076	.	.	.	0.09310	N	0.99999	.	.	.	.	.	.	T	0.36986	-0.9725	5	0.87932	D	0	11.8046	6.0132	0.19588	0.0:0.1953:0.1382:0.6665	.	.	.	.	Q	311	.	ENSP00000401670:R311Q	R	-	2	0	TMEM131	97798198	1.000000	0.71417	0.998000	0.56505	0.751000	0.42716	1.341000	0.33907	-0.038000	0.13624	-0.247000	0.11927	CGA		0.284	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		T	98431766	C	T	98431766	2	4	47	1	0	0	0	0	0	0	0	1	16083	871	31	1		1	TMEM131	2	98431766	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	267713	98431766	144767607	281	4678										
LIPT1	51601	broad.mit.edu	37	chr2	99778719	99778719	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tataaaactggctcggagaaGaagtggaggaggaacagtct	14	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:99778719G>T	ENST00000393473.2	+	3	523	c.299G>T	c.(298-300)aGa>aTa	p.R100I	LIPT1_ENST00000340066.1_Missense_Mutation_p.R100I|LIPT1_ENST00000393474.3_Missense_Mutation_p.R100I|LIPT1_ENST00000393477.3_Missense_Mutation_p.R100I|MRPL30_ENST00000410042.1_Intron|LIPT1_ENST00000393471.2_Missense_Mutation_p.R100I	NM_001204830.1|NM_015929.3	NP_001191759.1|NP_057013.1	Q9Y234	LIPT_HUMAN	lipoyltransferase 1	100	BPL/LPL catalytic. {ECO:0000255|PROSITE- ProRule:PRU01067}.				cellular protein modification process (GO:0006464)|lipid metabolic process (GO:0006629)|protein lipoylation (GO:0009249)	mitochondrion (GO:0005739)	transferase activity, transferring acyl groups (GO:0016746)	p.R100I(1)		large_intestine(6)|lung(1)	7					Lipoic Acid(DB00166)	GCTCGGAGAAGAAGTGGAGGA	0.358																																					GBM(84;665 1268 21657 25485 30647)											1	Substitution - Missense(1)	large_intestine(1)	2											61	58	59					2																	99778719		2203	4300	6503	99145151	SO:0001583	missense	51601			AB017566	CCDS2039.1	2q11.2	2010-11-25			ENSG00000144182	ENSG00000144182	2.3.1.181		29569	protein-coding gene	gene with protein product		610284				10103005	Standard	NM_145197		Approved	MGC12290, MGC13378	uc002szq.4	Q9Y234	OTTHUMG00000130640	ENST00000393473.2:c.299G>T	2.37:g.99778719G>T	ENSP00000377115:p.Arg100Ile		99145151	Q4ZFZ1	Missense_Mutation	SNP	ENST00000393473.2	37	CCDS2039.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144768	0.57044	.	.	ENSG00000144182	ENST00000393473;ENST00000393477;ENST00000393474;ENST00000340066;ENST00000393471;ENST00000449211;ENST00000434566;ENST00000415142	D;D;D;D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29	4.91	-0.655	0.11439	Biotin/lipoate A/B protein ligase (1);	0.293151	0.36374	N	0.002628	D	0.85831	0.5788	L	0.38692	1.165	0.80722	D	1	P	0.47545	0.897	B	0.42827	0.399	T	0.77579	-0.2535	10	0.21540	T	0.41	-15.922	4.6603	0.12639	0.3548:0.0:0.5062:0.139	.	100	Q9Y234	LIPT_HUMAN	I	100	ENSP00000377115:R100I;ENSP00000377118:R100I;ENSP00000377116:R100I;ENSP00000342071:R100I;ENSP00000377114:R100I;ENSP00000387387:R100I;ENSP00000393591:R100I;ENSP00000398168:R100I	ENSP00000342071:R100I	R	+	2	0	LIPT1	99145151	1.000000	0.71417	0.814000	0.32528	0.994000	0.84299	2.743000	0.47442	-0.332000	0.08489	-0.150000	0.13652	AGA		0.358	LIPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253128.1	NM_015929		T	99778719	G	T	99778719	3	4	47	1	0	0	0	0	1	0	0	0	8853	942	33	2	301	2	LIPT1	2	99778719	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1346953	99778719	143420654	282	4679										
REV1	51455	broad.mit.edu	37	chr2	100065819	100065819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttccacaatccattctggtCgaattactttttcccccttt	3	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:100065819C>T	ENST00000258428.3	-	4	557	c.329G>A	c.(328-330)cGa>cAa	p.R110Q	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.R110Q	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	110	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.R110Q(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCATTCTGGTCGAATTACTTT	0.244								Direct reversal of damage																																								1	Substitution - Missense(1)	large_intestine(1)	2											78	81	80					2																	100065819		2203	4300	6503	99432251	SO:0001583	missense	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.329G>A	2.37:g.100065819C>T	ENSP00000258428:p.Arg110Gln		99432251	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.243362	0.79912	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.79247	-1.25;-1.25	6.06	6.06	0.98353	BRCT (4);	0.054701	0.64402	D	0.000001	D	0.86151	0.5864	L	0.58669	1.825	0.51012	D	0.999903	D;P;P	0.76494	0.999;0.844;0.635	D;B;B	0.64042	0.921;0.326;0.353	D	0.84632	0.0690	10	0.49607	T	0.09	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	89;110;110	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	Q	110	ENSP00000377091:R110Q;ENSP00000258428:R110Q	ENSP00000258428:R110Q	R	-	2	0	REV1	99432251	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	5.695000	0.68279	2.880000	0.98712	0.650000	0.86243	CGA		0.244	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		T	100065819	C	T	100065819	3	4	47	1	0	0	0	0	1	0	0	0	13276	884	31	1	3506	1	REV1	2	100065819	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	287100	100065819	143133554	283	4680										
LONRF2	164832	broad.mit.edu	37	chr2	100911973	100911973	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaatatcgaaatattaattCttcggccagaacagttatgt	6	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:100911973C>A	ENST00000393437.3	-	8	2158	c.1519G>T	c.(1519-1521)Gaa>Taa	p.E507*	LONRF2_ENST00000409647.1_Nonsense_Mutation_p.E264*	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	507							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.E507*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						AATATTAATTCTTCGGCCAGA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											108	105	106					2																	100911973		2203	4300	6503	100278405	SO:0001587	stop_gained	164832			AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"RING-type (C3HC4) zinc fingers"	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1519G>T	2.37:g.100911973C>A	ENSP00000377086:p.Glu507*		100278405	B9A006|Q6ZSR4	Nonsense_Mutation	SNP	ENST00000393437.3	37	CCDS2046.2	.	.	.	.	.	.	.	.	.	.	C	42	9.806971	0.99268	.	.	ENSG00000170500	ENST00000393437;ENST00000409647	.	.	.	4.25	4.25	0.50352	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-10.2635	17.0183	0.86425	0.0:1.0:0.0:0.0	.	.	.	.	X	507;264	.	ENSP00000377086:E507X	E	-	1	0	LONRF2	100278405	1.000000	0.71417	0.331000	0.25455	0.686000	0.39977	2.404000	0.44539	2.054000	0.61138	0.655000	0.94253	GAA		0.338	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		A	100911973	C	A	100911973	4	1	47	1	0	0	0	0	0	1	0	0	8924	922	32	2	765	2	LONRF2	2	100911973	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	846154	100911973	142287400	284	4681										
MAP4K4	9448	broad.mit.edu	37	chr2	102440450	102440450	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaatactctcatcacagaAacattgcaacatattatggt	5	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:102440450A>C	ENST00000347699.4	+	4	241	c.241A>C	c.(241-243)Aac>Cac	p.N81H	MAP4K4_ENST00000350198.4_Missense_Mutation_p.N81H|MAP4K4_ENST00000456652.1_Missense_Mutation_p.N81H|MAP4K4_ENST00000324219.4_Missense_Mutation_p.N81H|MAP4K4_ENST00000350878.4_Missense_Mutation_p.N61H|MAP4K4_ENST00000413150.2_Missense_Mutation_p.N81H|MAP4K4_ENST00000302217.5_Missense_Mutation_p.N81H|MAP4K4_ENST00000425019.1_Missense_Mutation_p.N81H	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	81	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.N81H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCATCACAGAAACATTGCAAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											79	78	79					2																	102440450		1871	4102	5973	101806882	SO:0001583	missense	9448			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.241A>C	2.37:g.102440450A>C	ENSP00000314363:p.Asn81His		101806882	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959258	0.74016	.	.	ENSG00000071054	ENST00000427603;ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T;T;T;T	0.33438	2.87;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;2.24	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	M	0.80508	2.5	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;0.999;0.999;0.999;0.998;0.998	T	0.64744	-0.6335	10	0.87932	D	0	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	61;81;81;81;81;81;81;81;81	B7Z388;B7Z3V5;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;M4K4_HUMAN;.;.;.;.	H	81;81;81;81;81;81;81;81;43;61	ENSP00000403016:N81H;ENSP00000392830:N81H;ENSP00000313644:N81H;ENSP00000281111:N81H;ENSP00000303600:N81H;ENSP00000389752:N81H;ENSP00000387370:N81H;ENSP00000314363:N81H;ENSP00000409720:N43H;ENSP00000343658:N61H	ENSP00000303600:N81H	N	+	1	0	MAP4K4	101806882	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.287000	0.95975	2.220000	0.72140	0.533000	0.62120	AAC		0.378	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		C	102440450	A	C	102440450	3	2	47	1	0	0	0	0	1	0	0	0	9292	14	1	4	255	4	MAP4K4	2	102440450	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1528477	102440450	140758923	285	4682										
IL1R2	7850	broad.mit.edu	37	chr2	102625050	102625050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggagcaatgttgcgcttgTacgtgttggtaatgggagtt	15	5	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:102625050T>C	ENST00000332549.3	+	2	242	c.13T>C	c.(13-15)Tac>Cac	p.Y5H	IL1R2_ENST00000393414.2_Missense_Mutation_p.Y5H|IL1R2_ENST00000441002.1_Missense_Mutation_p.Y5H	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	5					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.Y5H(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						GTTGCGCTTGTACGTGTTGGT	0.532																																					Pancreas(106;189 1628 2302 5133 12295)											1	Substitution - Missense(1)	large_intestine(1)	2											263	231	242					2																	102625050		2203	4300	6503	101991482	SO:0001583	missense	7850			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.13T>C	2.37:g.102625050T>C	ENSP00000330959:p.Tyr5His		101991482	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.856911	0.32791	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000457817;ENST00000441002	T;T;T;T	0.34472	2.09;2.09;1.36;2.13	4.74	3.59	0.41128	.	1.336870	0.04711	N	0.417578	T	0.28167	0.0695	N	0.24115	0.695	0.09310	N	1	P	0.50943	0.94	P	0.44732	0.459	T	0.12553	-1.0543	10	0.16420	T	0.52	.	6.6385	0.22897	0.0:0.1128:0.0:0.8872	.	5	P27930	IL1R2_HUMAN	H	5	ENSP00000330959:Y5H;ENSP00000377066:Y5H;ENSP00000408415:Y5H;ENSP00000414611:Y5H	ENSP00000330959:Y5H	Y	+	1	0	IL1R2	101991482	0.001000	0.12720	0.004000	0.12327	0.023000	0.10783	0.735000	0.26115	0.788000	0.33755	0.379000	0.24179	TAC		0.532	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		C	102625050	T	C	102625050	3	2	47	1	0	0	0	0	1	0	0	0	7680	1638	57	4	15	4	IL1R2	2	102625050	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	184600	102625050	140574323	286	4683										
IL18R1	8809	broad.mit.edu	37	chr2	102984390	102984390	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gattgaaacaaccaccaaaaGctggtacaaaagcagtggat	9	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:102984390G>A	ENST00000409599.1	+	4	520	c.164G>A	c.(163-165)aGc>aAc	p.S55N	IL18R1_ENST00000233957.1_Missense_Mutation_p.S55N|IL18R1_ENST00000334376.3_Missense_Mutation_p.S55N			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	55	Ig-like C2-type 1.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.S55N(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						ACCACCAAAAGCTGGTACAAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											140	131	134					2																	102984390		2203	4300	6503	102350822	SO:0001583	missense	8809			U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.164G>A	2.37:g.102984390G>A	ENSP00000387211:p.Ser55Asn		102350822	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	G	9.149	1.015808	0.19355	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957;ENST00000334376	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.23	0.373	0.16178	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.728116	0.13439	N	0.387857	T	0.16257	0.0391	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.25169	0.002;0.119;0.002	B;B;B	0.23716	0.001;0.048;0.001	T	0.29701	-1.0003	10	0.14656	T	0.56	.	7.0978	0.25319	0.7265:0.0:0.2735:0.0	.	55;55;55	B7ZKV7;Q86YL8;Q13478	.;.;IL18R_HUMAN	N	55	ENSP00000386663:S55N;ENSP00000387211:S55N;ENSP00000233957:S55N;ENSP00000334030:S55N	ENSP00000233957:S55N	S	+	2	0	IL18R1	102350822	0.000000	0.05858	0.061000	0.19648	0.005000	0.04900	0.291000	0.18994	0.201000	0.20466	0.563000	0.77884	AGC		0.448	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		A	102984390	G	A	102984390	3	1	47	1	0	0	0	0	1	0	0	0	7668	971	34	3	170	3	IL18R1	2	102984390	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	359340	102984390	140214983	287	4684										
IL18RAP	8807	broad.mit.edu	37	chr2	103068556	103068556	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggattcacgtggaaccagcTcagaattacctctaggattt	10	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:103068556T>A	ENST00000264260.2	+	12	2304	c.1715T>A	c.(1714-1716)cTc>cAc	p.L572H	IL18RAP_ENST00000409369.1_Missense_Mutation_p.L430H	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	572					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L572H(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						TGGAACCAGCTCAGAATTACC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	143	139					2																	103068556		2203	4300	6503	102434988	SO:0001583	missense	8807			AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1715T>A	2.37:g.103068556T>A	ENSP00000264260:p.Leu572His		102434988	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	37	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.673083	0.67928	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.02916	4.13;4.11	5.8	4.65	0.58169	.	1.232420	0.05702	N	0.594231	T	0.08714	0.0216	L	0.29908	0.895	0.09310	N	1	D	0.76494	0.999	D	0.63488	0.915	T	0.46857	-0.9161	10	0.87932	D	0	.	9.5178	0.39115	0.0:0.0788:0.0:0.9212	.	572	O95256	I18RA_HUMAN	H	572;430	ENSP00000264260:L572H;ENSP00000387201:L430H	ENSP00000264260:L572H	L	+	2	0	IL18RAP	102434988	0.001000	0.12720	0.020000	0.16555	0.202000	0.24057	1.047000	0.30367	1.034000	0.39945	0.528000	0.53228	CTC		0.488	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		A	103068556	T	A	103068556	3	1	47	1	0	0	0	0	1	0	0	0	7669	1551	54	5	1753	5	IL18RAP	2	103068556	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	84166	103068556	140130817	288	4685										
SLC9A4	389015	broad.mit.edu	37	chr2	103141542	103141542	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgagaagcaggctaaagaGattctgatccgccgccagaa	12	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:103141542G>T	ENST00000295269.4	+	10	2335	c.1878G>T	c.(1876-1878)gaG>gaT	p.E626D		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	626					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.E626D(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AGGCTAAAGAGATTCTGATCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	2											166	175	172					2																	103141542		2203	4300	6503	102507974	SO:0001583	missense	389015				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1878G>T	2.37:g.103141542G>T	ENSP00000295269:p.Glu626Asp		102507974	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497278	0.44455	.	.	ENSG00000180251	ENST00000295269	T	0.55760	0.5	5.84	3.8	0.43715	.	0.168817	0.52532	D	0.000068	T	0.49355	0.1552	M	0.79475	2.455	0.33131	D	0.543043	B	0.12013	0.005	B	0.16289	0.015	T	0.60378	-0.7275	10	0.72032	D	0.01	.	5.0028	0.14273	0.3799:0.0:0.6201:0.0	.	626	Q6AI14	SL9A4_HUMAN	D	626	ENSP00000295269:E626D	ENSP00000295269:E626D	E	+	3	2	SLC9A4	102507974	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	3.245000	0.51407	1.467000	0.48044	0.643000	0.83706	GAG		0.512	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		T	103141542	G	T	103141542	3	4	47	1	0	0	0	0	1	0	0	0	14753	933	33	2	1916	2	SLC9A4	2	103141542	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	72986	103141542	140057831	289	4686										
C2orf49	79074	broad.mit.edu	37	chr2	105959411	105959411	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagagaatggagataatgatCgactgaagcctcccccgcag	11	11	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:105959411C>T	ENST00000258457.2	+	3	602	c.373C>T	c.(373-375)Cga>Tga	p.R125*	C2orf49_ENST00000437250.2_Nonsense_Mutation_p.R163*|C2orf49_ENST00000410049.1_Nonsense_Mutation_p.R125*			Q9BVC5	ASHWN_HUMAN	chromosome 2 open reading frame 49	125					embryonic morphogenesis (GO:0048598)	tRNA-splicing ligase complex (GO:0072669)		p.R125*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6						AGATAATGATCGACTGAAGCC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											106	106	106					2																	105959411		2203	4300	6503	105325843	SO:0001587	stop_gained	79074			BC001310	CCDS2068.1, CCDS74550.1	2q12.2	2009-04-22			ENSG00000135974	ENSG00000135974			28772	protein-coding gene	gene with protein product	"ashwin"					12477932	Standard	NM_001286537		Approved	MGC5509, asw	uc002tcs.1	Q9BVC5	OTTHUMG00000130808	ENST00000258457.2:c.373C>T	2.37:g.105959411C>T	ENSP00000258457:p.Arg125*		105325843	B3KXN3|B4E2G9	Nonsense_Mutation	SNP	ENST00000258457.2	37	CCDS2068.1	.	.	.	.	.	.	.	.	.	.	C	38	6.729144	0.97796	.	.	ENSG00000135974	ENST00000258457;ENST00000437250;ENST00000410049	.	.	.	5.73	5.73	0.89815	.	0.053156	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.365	16.166	0.81757	0.0:0.8668:0.1332:0.0	.	.	.	.	X	125;163;125	.	ENSP00000258457:R125X	R	+	1	2	C2orf49	105325843	0.990000	0.36364	0.189000	0.23252	0.998000	0.95712	1.923000	0.40055	2.688000	0.91661	0.650000	0.86243	CGA		0.398	C2orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253353.2	NM_024093		T	105959411	C	T	105959411	4	4	47	1	0	0	0	0	0	1	0	0	2177	876	31	1	383	1	C2orf49	2	105959411	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2817869	105959411	137239962	290	4687										
RANBP2	5903	broad.mit.edu	37	chr2	109352028	109352028	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtgaagatggatggaataAactttttgacttgattcagt	11	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:109352028A>C	ENST00000283195.6	+	5	572	c.446A>C	c.(445-447)aAa>aCa	p.K149T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	149					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K149T(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GGATGGAATAAACTTTTTGAC	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	2											11	12	12					2																	109352028		1104	2154	3258	108718460	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.446A>C	2.37:g.109352028A>C	ENSP00000283195:p.Lys149Thr		108718460	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	17.27	3.347967	0.61183	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.39056	1.1	4.98	4.98	0.66077	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.35038	0.0918	L	0.40543	1.245	0.29870	N	0.826914	P	0.38922	0.651	B	0.35859	0.212	T	0.23868	-1.0176	9	0.27785	T	0.31	-27.5235	14.9618	0.71161	1.0:0.0:0.0:0.0	.	149	P49792	RBP2_HUMAN	T	149	ENSP00000283195:K149T	ENSP00000283195:K149T	K	+	2	0	RANBP2	108718460	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.786000	0.55431	2.012000	0.59069	0.454000	0.30748	AAA		0.368	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109352028	A	C	109352028	3	2	47	1	0	0	0	0	1	0	0	0	13065	14	1	4	464	4	RANBP2	2	109352028	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3392617	109352028	133847345	291	4688										
ANAPC1	64682	broad.mit.edu	37	chr2	112638397	112638397	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcctttcttcatagaagttCgacatgggttccaaatatca	7	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:112638397C>T	ENST00000341068.3	-	2	778	c.6G>A	c.(4-6)tcG>tcA	p.S2S	ANAPC1_ENST00000489177.1_5'UTR	NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	2					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.S2S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						CATAGAAGTTCGACATGGGTT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	2											55	54	54					2																	112638397		2203	4300	6503	112354868	SO:0001819	synonymous_variant	64682			AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.6G>A	2.37:g.112638397C>T			112354868	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	37	CCDS2093.1																																																																																				0.388	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		T	112638397	C	T	112638397	2	4	47	1	0	0	0	0	0	0	0	1	598	871	31	1		1	ANAPC1	2	112638397	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3286369	112638397	130560976	292	4689										
TTL	150465	broad.mit.edu	37	chr2	113251897	113251897	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcgcctcttataacagaaaGaaagaggatggagagggcaa	12	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:113251897G>T	ENST00000233336.6	+	3	605	c.414G>T	c.(412-414)aaG>aaT	p.K138N		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	138	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)	p.K138N(1)		breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		ATAACAGAAAGAAAGAGGATG	0.468			T	ETV6	ALL																																		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	1	Substitution - Missense(1)	large_intestine(1)	2											60	60	60					2																	113251897		2203	4300	6503	112968368	SO:0001583	missense	150465				CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.414G>T	2.37:g.113251897G>T	ENSP00000233336:p.Lys138Asn		112968368	Q585T3|Q7Z302|Q8N426	Missense_Mutation	SNP	ENST00000233336.6	37	CCDS2096.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619641	0.46736	.	.	ENSG00000114999	ENST00000233336	T	0.05855	3.38	5.56	5.56	0.83823	.	0.148158	0.64402	D	0.000010	T	0.08537	0.0212	L	0.36672	1.1	0.52501	D	0.999951	B	0.27316	0.175	B	0.33392	0.163	T	0.38478	-0.9659	10	0.19147	T	0.46	.	18.6492	0.91423	0.0:0.0:1.0:0.0	.	138	Q8NG68	TTL_HUMAN	N	138	ENSP00000233336:K138N	ENSP00000233336:K138N	K	+	3	2	TTL	112968368	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	0.837000	0.27558	2.779000	0.95612	0.561000	0.74099	AAG		0.468	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		T	113251897	G	T	113251897	3	4	47	1	0	0	0	0	1	0	0	0	16761	933	33	2	424	2	TTL	2	113251897	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	613500	113251897	129947476	293	4690										
CKAP2L	150468	broad.mit.edu	37	chr2	113514069	113514069	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgttcttgactactggtttCtttgatgactgaactttact	7	7	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:113514069C>A	ENST00000302450.6	-	4	957	c.879G>T	c.(877-879)aaG>aaT	p.K293N	CKAP2L_ENST00000481732.1_5'Flank|CKAP2L_ENST00000541405.1_Missense_Mutation_p.K128N	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	293						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.K293N(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						CTACTGGTTTCTTTGATGACT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											94	98	96					2																	113514069		2203	4300	6503	113230540	SO:0001583	missense	150468			AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.879G>T	2.37:g.113514069C>A	ENSP00000305204:p.Lys293Asn		113230540	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509865	0.27036	.	.	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.15256	2.44;3.11	4.69	1.93	0.25924	.	0.424342	0.23454	N	0.048004	T	0.22820	0.0551	M	0.68317	2.08	0.09310	N	1	P	0.48016	0.904	P	0.49887	0.625	T	0.05599	-1.0875	10	0.34782	T	0.22	-6.8178	6.6415	0.22911	0.0:0.7084:0.0:0.2916	.	293	Q8IYA6	CKP2L_HUMAN	N	128;293	ENSP00000438763:K128N;ENSP00000305204:K293N	ENSP00000305204:K293N	K	-	3	2	CKAP2L	113230540	0.346000	0.24844	0.010000	0.14722	0.117000	0.20001	0.044000	0.13992	0.456000	0.26937	0.585000	0.79938	AAG		0.398	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		A	113514069	C	A	113514069	3	1	47	1	0	0	0	0	1	0	0	0	3449	912	32	2	1382	2	CKAP2L	2	113514069	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	262172	113514069	129685304	294	4691										
DPP10	57628	broad.mit.edu	37	chr2	116572543	116572543	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaggttcagtagaagtaaaGgaccaaataacagctgtgaa	10	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:116572543G>T	ENST00000410059.1	+	20	2355	c.1875G>T	c.(1873-1875)aaG>aaT	p.K625N	DPP10_ENST00000310323.8_Missense_Mutation_p.K618N|DPP10_ENST00000393147.2_Missense_Mutation_p.K629N|DPP10_ENST00000409163.1_Missense_Mutation_p.K575N	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	625						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.K625N(1)|p.K618N(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TAGAAGTAAAGGACCAAATAA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	2											103	108	107					2																	116572543		2203	4300	6503	116289013	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1875G>T	2.37:g.116572543G>T	ENSP00000386565:p.Lys625Asn		116289013	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729583	0.69074	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.16	4.28	0.50868	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.111045	0.64402	D	0.000009	T	0.37433	0.1003	L	0.31578	0.945	0.46096	D	0.998864	D;D;D;D	0.65815	0.987;0.973;0.995;0.99	P;P;P;P	0.62813	0.802;0.674;0.907;0.875	T	0.19712	-1.0297	10	0.72032	D	0.01	-26.8542	9.1594	0.37012	0.1636:0.0:0.8364:0.0	.	618;629;621;625	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	N	625;575;629;618;575	ENSP00000386565:K625N;ENSP00000387038:K575N;ENSP00000376855:K629N;ENSP00000309066:K618N	ENSP00000309066:K618N	K	+	3	2	DPP10	116289013	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.468000	0.45102	1.416000	0.47057	0.655000	0.94253	AAG		0.363	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116572543	G	T	116572543	3	4	47	1	0	0	0	0	1	0	0	0	4738	991	35	2	2124	2	DPP10	2	116572543	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3058474	116572543	126626830	295	4692										
PTPN4	5775	broad.mit.edu	37	chr2	120702749	120702749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaaattcattattcacattCgcaacaagatctagaaagtc	4	10	3	2	rs370792318		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:120702749C>T	ENST00000263708.2	+	16	2219	c.1448C>T	c.(1447-1449)tCg>tTg	p.S483L	PTPN4_ENST00000544261.1_Missense_Mutation_p.S116L	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	483					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.S483L(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	TATTCACATTCGCAACAAGAT	0.368													C|||	1	0.000199681	8e-04	0	5008	,	,		14522	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	81	83	82		1448	5.2	1	2		82	0,8600		0,0,4300	no	missense	PTPN4	NM_002830.2	145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	483/927	120702749	1,13005	2203	4300	6503	120419219	SO:0001583	missense	5775				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1448C>T	2.37:g.120702749C>T	ENSP00000263708:p.Ser483Leu		120419219	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614869	0.87359	2.27E-4	0.0	ENSG00000088179	ENST00000263708;ENST00000544261;ENST00000431283	T;T;T	0.72615	-0.67;2.89;0.88	5.2	5.2	0.72013	.	0.054263	0.85682	D	0.000000	T	0.77384	0.4122	L	0.34521	1.04	0.53688	D	0.999971	D	0.69078	0.997	D	0.70227	0.968	T	0.75408	-0.3328	10	0.34782	T	0.22	.	19.1079	0.93303	0.0:1.0:0.0:0.0	.	483	P29074	PTN4_HUMAN	L	483;116;109	ENSP00000263708:S483L;ENSP00000445841:S116L;ENSP00000387457:S109L	ENSP00000263708:S483L	S	+	2	0	PTPN4	120419219	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	4.944000	0.63561	2.566000	0.86566	0.655000	0.94253	TCG		0.368	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			T	120702749	C	T	120702749	3	4	47	1	0	0	0	0	1	0	0	0	12827	893	31	1	1506	1	PTPN4	2	120702749	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4130206	120702749	122496624	296	4693										
CNTNAP5	129684	broad.mit.edu	37	chr2	125521351	125521351	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagaagccgcttggagaatTggtcccttgcgttgctatgg	13	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:125521351T>C	ENST00000431078.1	+	15	2698	c.2334T>C	c.(2332-2334)atT>atC	p.I778I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	778	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.I778I(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTTGGAGAATTGGTCCCTTGC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	2											80	77	78					2																	125521351		1882	4106	5988	125237821	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2334T>C	2.37:g.125521351T>C			125237821	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.433	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			C	125521351	T	C	125521351	2	2	47	1	0	0	0	0	0	0	0	1	3656	1800	63	4		4	CNTNAP5	2	125521351	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	4818602	125521351	117678022	297	4694										
UGGT1	56886	broad.mit.edu	37	chr2	128903499	128903499	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaccatcacaatgcataaAatcctggagaccaccacctt	5	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:128903499A>C	ENST00000259253.6	+	18	2021	c.1974A>C	c.(1972-1974)aaA>aaC	p.K658N	UGGT1_ENST00000375990.3_Missense_Mutation_p.K634N	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	658					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.K658N(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CAATGCATAAAATCCTGGAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	112	114					2																	128903499		2203	4300	6503	128619969	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1974A>C	2.37:g.128903499A>C	ENSP00000259253:p.Lys658Asn		128619969	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.700364	0.48307	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.31510	1.49;1.49	5.76	0.431	0.16523	.	0.000000	0.85682	D	0.000000	T	0.31327	0.0793	M	0.71581	2.175	0.58432	D	0.999993	B;B	0.30709	0.291;0.041	B;B	0.36845	0.234;0.039	T	0.05273	-1.0895	10	0.24483	T	0.36	.	9.0077	0.36122	0.6676:0.0:0.3324:0.0	.	634;658	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	N	634;658	ENSP00000365158:K634N;ENSP00000259253:K658N	ENSP00000259253:K658N	K	+	3	2	UGGT1	128619969	1.000000	0.71417	0.997000	0.53966	0.901000	0.52897	1.749000	0.38319	-0.148000	0.11234	-0.334000	0.08254	AAA		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		C	128903499	A	C	128903499	3	2	47	1	0	0	0	0	1	0	0	0	16981	11	1	4	2044	4	UGGT1	2	128903499	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3382148	128903499	114295874	298	4695										
GPR148	344561	broad.mit.edu	37	chr2	131487602	131487602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccaggtaccaccacattgActctgggactcacacatggc	9	14	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:131487602A>G	ENST00000309926.4	+	1	960	c.878A>G	c.(877-879)gAc>gGc	p.D293G		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D293G(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CACCACATTGACTCTGGGACT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											161	123	136					2																	131487602		2203	4300	6503	131204072	SO:0001583	missense	344561			AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.878A>G	2.37:g.131487602A>G	ENSP00000308908:p.Asp293Gly		131204072	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	0.010	-1.779696	0.00634	.	.	ENSG00000173302	ENST00000309926	T	0.07444	3.19	3.37	-3.57	0.04612	GPCR, rhodopsin-like superfamily (1);	1.567220	0.04826	N	0.437922	T	0.03220	0.0094	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.21014	T	0.42	2.1425	5.0114	0.14315	0.4217:0.1514:0.4269:0.0	.	293	Q8TDV2	GP148_HUMAN	G	293	ENSP00000308908:D293G	ENSP00000308908:D293G	D	+	2	0	GPR148	131204072	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-0.030000	0.12308	-0.706000	0.05028	-0.624000	0.04008	GAC		0.572	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		G	131487602	A	G	131487602	3	3	47	1	0	0	0	0	1	0	0	0	6673	275	10	4	880	4	GPR148	2	131487602	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2584103	131487602	111711771	299	4696										
CCNT2	905	broad.mit.edu	37	chr2	135710270	135710270	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaataggttgaagaagattCgaaactggagggtaagagaa	13	3	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:135710270C>T	ENST00000264157.5	+	8	793	c.763C>T	c.(763-765)Cga>Tga	p.R255*	CCNT2_ENST00000295238.6_Nonsense_Mutation_p.R255*|CCNT2_ENST00000537343.1_Nonsense_Mutation_p.R80*	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	255					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R255*(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		GAAGAAGATTCGAAACTGGAG	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											76	83	81					2																	135710270		2203	4300	6503	135426740	SO:0001587	stop_gained	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.763C>T	2.37:g.135710270C>T	ENSP00000264157:p.Arg255*		135426740	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Nonsense_Mutation	SNP	ENST00000264157.5	37	CCDS2174.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.5|24.5	4.541663|4.541663	0.85917|0.85917	.|.	.|.	ENSG00000082258|ENSG00000082258	ENST00000446247;ENST00000537343;ENST00000295238;ENST00000264157|ENST00000452521;ENST00000438691	.|.	.|.	.|.	5.7|5.7	4.83|4.83	0.62350|0.62350	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.50905	.|0.1643	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.61530	.|-0.7044	.|3	0.02654|.	T|.	1|.	.|.	8.2114|8.2114	0.31486|0.31486	0.1299:0.7325:0.0:0.1376|0.1299:0.7325:0.0:0.1376	.|.	.|.	.|.	.|.	X|L	96;80;255;255|77;45	.|.	ENSP00000264157:R255X|.	R|S	+|+	1|2	2|0	CCNT2|CCNT2	135426740|135426740	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.781000|0.781000	0.44180|0.44180	2.246000|2.246000	0.43142|0.43142	1.415000|1.415000	0.47037|0.47037	-0.142000|-0.142000	0.14014|0.14014	CGA|TCG		0.303	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		T	135710270	C	T	135710270	4	4	47	1	0	0	0	0	0	1	0	0	2941	876	31	1	793	1	CCNT2	2	135710270	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4222668	135710270	107489103	300	4697										
YSK4	80122	broad.mit.edu	37	chr2	135743788	135743788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctagatcattagttaaaattCggctggcatttactttacta	6	7	1	1	rs140658941	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:135743788C>T	ENST00000375845.3	-	7	2684	c.2654G>A	c.(2653-2655)cGa>cAa	p.R885Q	MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.R902Q|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.R772Q	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	885							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R885Q(1)|p.R237L(1)|p.R885L(1)|p.R237Q(1)									AGTTAAAATTCGGCTGGCATT	0.378													C|||	4	0.000798722	0.0023	0	5008	,	,		20491	0.001		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	2						C	,GLN/ARG	12,4394	19.1+/-41.9	0,12,2191	83	85	85		,2654	1.1	0	2	dbSNP_134	85	0,8600		0,0,4300	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,43	0,12,6491	TT,TC,CC		0.0,0.2724,0.0923	,benign	,885/1329	135743788	12,12994	2203	4300	6503	135460258	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2654G>A	2.37:g.135743788C>T	ENSP00000365005:p.Arg885Gln		135460258	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.001	-3.063502	0.00037	0.002724	0.0	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.69175	-0.19;-0.21;2.12;-0.38	4.86	1.1	0.20463	.	0.480060	0.17580	N	0.169151	T	0.32133	0.0819	N	0.03154	-0.405	0.09310	N	0.999996	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.04013	0.001;0.0;0.0	T	0.29792	-1.0000	10	0.02654	T	1	.	6.1132	0.20112	0.0:0.0958:0.163:0.7412	.	772;902;885	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	Q	885;772;902;275	ENSP00000365005:R885Q;ENSP00000351140:R772Q;ENSP00000376647:R902Q;ENSP00000392827:R275Q	ENSP00000351140:R772Q	R	-	2	0	YSK4	135460258	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.267000	0.08619	0.034000	0.15491	-1.280000	0.01385	CGA		0.378	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		T	135743788	C	T	135743788	3	4	47	1	0	0	0	0	1	0	0	0	17535	884	31	1	1348	1	YSK4	2	135743788	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	33518	135743788	107455585	301	4698										
LCT	3938	broad.mit.edu	37	chr2	136566201	136566201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattgccgtggaaggccacGaagggtcctcctcctcagcc	11	15	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:136566201G>A	ENST00000264162.2	-	8	3726	c.3716C>T	c.(3715-3717)tCg>tTg	p.S1239L	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1239	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.S1239L(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGAAGGCCACGAAGGGTCCTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											154	128	137					2																	136566201		2203	4300	6503	136282671	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.3716C>T	2.37:g.136566201G>A	ENSP00000264162:p.Ser1239Leu		136282671	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	G	9.951	1.220130	0.22373	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.53640	0.61	5.76	5.76	0.90799	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.452247	0.25795	N	0.028256	T	0.49474	0.1559	L	0.38953	1.18	0.09310	N	1	P	0.44627	0.839	P	0.49477	0.612	T	0.49113	-0.8973	10	0.59425	D	0.04	-10.0745	14.7612	0.69607	0.0:0.0:0.8556:0.1444	.	1239	P09848	LPH_HUMAN	L	1239;671	ENSP00000264162:S1239L	ENSP00000264162:S1239L	S	-	2	0	LCT	136282671	0.974000	0.33945	0.099000	0.21106	0.261000	0.26267	3.875000	0.56108	2.706000	0.92434	0.563000	0.77884	TCG		0.562	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136566201	G	A	136566201	3	1	47	1	0	0	0	0	1	0	0	0	8715	1059	37	1	2107	1	LCT	2	136566201	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	822413	136566201	106633172	302	4699										
THSD7B	80731	broad.mit.edu	37	chr2	138030124	138030124	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatgccacagtaaaacagtCtcgatacagaatcatcatcc	5	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:138030124C>A	ENST00000409968.1	+	11	2466	c.2288C>A	c.(2287-2289)tCt>tAt	p.S763Y	THSD7B_ENST00000413152.2_Missense_Mutation_p.S732Y|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Missense_Mutation_p.S763Y			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	763	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.S763Y(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		GTAAAACAGTCTCGATACAGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	100	102					2																	138030124		1910	4119	6029	137746594	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2288C>A	2.37:g.138030124C>A	ENSP00000387145:p.Ser763Tyr		137746594		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	19.02	3.744917	0.69418	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.18657	2.2;2.2;2.2	5.72	5.72	0.89469	.	0.108658	0.64402	D	0.000004	T	0.47948	0.1473	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.966	T	0.32719	-0.9896	10	0.48119	T	0.1	.	18.6606	0.91470	0.0:1.0:0.0:0.0	.	763;732	Q9C0I4;C9JKN6	THS7B_HUMAN;.	Y	763;763;732	ENSP00000387145:S763Y;ENSP00000272643:S763Y;ENSP00000413841:S732Y	ENSP00000272643:S763Y	S	+	2	0	THSD7B	137746594	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.132000	0.64758	2.689000	0.91719	0.655000	0.94253	TCT		0.393	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		A	138030124	C	A	138030124	3	1	47	1	0	0	0	0	1	0	0	0	15919	913	32	2	2233	2	THSD7B	2	138030124	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1463923	138030124	105169249	303	4700										
LRP1B	53353	broad.mit.edu	37	chr2	141081485	141081485	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctagttgtttataacgatgaGatatcaaaacaccttttgtt	6	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:141081485G>T	ENST00000389484.3	-	81	13462	c.12491C>A	c.(12490-12492)tCt>tAt	p.S4164Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4164					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S4164Y(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ATAACGATGAGATATCAAAAC	0.259										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											52	59	57					2																	141081485		2203	4287	6490	140797955	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12491C>A	2.37:g.141081485G>T	ENSP00000374135:p.Ser4164Tyr		140797955	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.444|8.444	0.851607|0.851607	0.17034|0.17034	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000437977|ENST00000389484;ENST00000544579	.|D	.|0.90955	.|-2.76	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	.|0.158983	.|0.43260	.|D	.|0.000599	T|T	0.71854|0.71854	0.3389|0.3389	N|N	0.01267|0.01267	-0.92|-0.92	0.38111|0.38111	D|D	0.937574|0.937574	.|B	.|0.09022	.|0.002	.|B	.|0.08055	.|0.003	T|T	0.71163|0.71163	-0.4673|-0.4673	5|10	.|0.02654	.|T	.|1	.|.	13.2385|13.2385	0.59983|0.59983	0.0829:0.0:0.9171:0.0|0.0829:0.0:0.9171:0.0	.|.	.|4164	.|Q9NZR2	.|LRP1B_HUMAN	I|Y	396|4164;4102	.|ENSP00000374135:S4164Y	.|ENSP00000374135:S4164Y	L|S	-|-	1|2	0|0	LRP1B|LRP1B	140797955|140797955	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	3.359000|3.359000	0.52292|0.52292	2.679000|2.679000	0.91253|0.91253	0.655000|0.655000	0.94253|0.94253	CTC|TCT		0.259	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141081485	G	T	141081485	3	4	47	1	0	0	0	0	1	0	0	0	8984	942	33	2	1352	2	LRP1B	2	141081485	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3051361	141081485	102117888	304	4701										
LRP1B	53353	broad.mit.edu	37	chr2	141283813	141283813	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaatatcttactgcagttCttttcatctgaagcatctgc	7	9	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:141283813C>A	ENST00000389484.3	-	48	8840	c.7869G>T	c.(7867-7869)aaG>aaT	p.K2623N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2623	LDL-receptor class A 13. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.K2623N(2)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		TACTGCAGTTCTTTTCATCTG	0.433										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											2	Substitution - Missense(2)	large_intestine(2)	2											162	137	146					2																	141283813		2203	4300	6503	141000283	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7869G>T	2.37:g.141283813C>A	ENSP00000374135:p.Lys2623Asn		141000283	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138103	0.56936	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95821	-3.82	5.08	4.1	0.47936	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94318	0.8174	L	0.31294	0.92	0.39350	D	0.965736	D	0.67145	0.996	D	0.64321	0.924	D	0.91831	0.5475	10	0.17832	T	0.49	.	10.9158	0.47135	0.0:0.8374:0.0:0.1626	.	2623	Q9NZR2	LRP1B_HUMAN	N	2623;2561	ENSP00000374135:K2623N	ENSP00000374135:K2623N	K	-	3	2	LRP1B	141000283	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.411000	0.34702	1.331000	0.45412	0.650000	0.86243	AAG		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141283813	C	A	141283813	3	1	47	1	0	0	0	0	1	0	0	0	8984	912	32	2	6106	2	LRP1B	2	141283813	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	202328	141283813	101915560	305	4702										
LRP1B	53353	broad.mit.edu	37	chr2	141747132	141747132	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgattggattcatcttcattGctcccacagtcattagctcc	6	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:141747132G>A	ENST00000389484.3	-	17	3710	c.2739C>T	c.(2737-2739)agC>agT	p.S913S	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	913	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S913S(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CATCTTCATTGCTCCCACAGT	0.398										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - coding silent(1)	large_intestine(1)	2											136	128	131					2																	141747132		2203	4300	6503	141463602	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2739C>T	2.37:g.141747132G>A			141463602	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141747132	G	A	141747132	2	1	47	1	0	0	0	0	0	0	0	1	8984	1310	46	3		3	LRP1B	2	141747132	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	463319	141747132	101452241	306	4703										
LYPD6B	130576	broad.mit.edu	37	chr2	150071119	150071119	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaattacccaccaatcacacTaatgcagtgtttgccgtaat	6	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:150071119T>G	ENST00000409029.1	+	7	649	c.447T>G	c.(445-447)acT>acG	p.T149T	LYPD6B_ENST00000280115.7_Silent_p.T173T|LYPD6B_ENST00000498249.1_3'UTR|LYPD6B_ENST00000409642.3_Silent_p.T173T|LYPD6B_ENST00000409876.1_Silent_p.T149T			Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	149	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.T173T(1)		endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11						CCAATCACACTAATGCAGTGT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	2											160	159	160					2																	150071119		2043	4185	6228	149779365	SO:0001819	synonymous_variant	130576				CCDS46423.1	2q23.2	2012-07-20			ENSG00000150556	ENSG00000150556			27018	protein-coding gene	gene with protein product	"cancer/testis antigen 116"					18360792	Standard	NM_177964		Approved	CT116, LYPD7	uc002twv.1	Q8NI32	OTTHUMG00000153743	ENST00000409029.1:c.447T>G	2.37:g.150071119T>G			149779365	D3DP90|Q53TK0|Q7Z747|Q8IXK7	Silent	SNP	ENST00000409029.1	37																																																																																					0.468	LYPD6B-003	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000332299.2	NM_177964		G	150071119	T	G	150071119	2	3	47	1	0	0	0	0	0	0	0	1	9145	1509	53	4		4	LYPD6B	2	150071119	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	8323987	150071119	93128254	307	4704										
TNFAIP6	7130	broad.mit.edu	37	chr2	152236016	152236016	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacttctactggaaataaaaActttttagctggaagattta	6	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:152236016A>C	ENST00000243347.3	+	6	878	c.803A>C	c.(802-804)aAc>aCc	p.N268T		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	268					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)	p.N268T(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	GGAAATAAAAACTTTTTAGCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	63	60					2																	152236016		2203	4300	6503	151944262	SO:0001583	missense	7130				CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.803A>C	2.37:g.152236016A>C	ENSP00000243347:p.Asn268Thr		151944262	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.369420	0.42003	.	.	ENSG00000123610	ENST00000243347	T	0.18810	2.19	5.56	4.41	0.53225	.	0.331135	0.33023	N	0.005370	T	0.13030	0.0316	N	0.24115	0.695	0.26760	N	0.970023	B	0.20052	0.041	B	0.16289	0.015	T	0.22695	-1.0209	10	0.21014	T	0.42	.	9.8449	0.41021	0.9211:0.0:0.0789:0.0	.	268	P98066	TSG6_HUMAN	T	268	ENSP00000243347:N268T	ENSP00000243347:N268T	N	+	2	0	TNFAIP6	151944262	1.000000	0.71417	0.995000	0.50966	0.972000	0.66771	1.942000	0.40243	0.934000	0.37316	0.533000	0.62120	AAC		0.333	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		C	152236016	A	C	152236016	3	2	47	1	0	0	0	0	1	0	0	0	16314	43	2	4	825	4	TNFAIP6	2	152236016	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2164897	152236016	90963357	308	4705										
RIF1	55183	broad.mit.edu	37	chr2	152321475	152321475	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatgattcattaattgtttCtgaaaccaaatcaaaagaaa	4	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:152321475C>T	ENST00000243326.5	+	29	5924	c.5441C>T	c.(5440-5442)tCt>tTt	p.S1814F	RIF1_ENST00000430328.2_Missense_Mutation_p.S1814F|RIF1_ENST00000453091.2_Missense_Mutation_p.S1814F|RIF1_ENST00000428287.2_Missense_Mutation_p.S1814F|RIF1_ENST00000444746.2_Missense_Mutation_p.S1814F			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.S1814F(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTAATTGTTTCTGAAACCAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	66	64					2																	152321475		2199	4297	6496	152029721	SO:0001583	missense	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.5441C>T	2.37:g.152321475C>T	ENSP00000243326:p.Ser1814Phe		152029721	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507527	0.27036	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5	5.68	3.88	0.44766	.	0.601697	0.17717	N	0.164366	T	0.12987	0.0315	L	0.34521	1.04	0.28830	N	0.897173	P;P	0.49090	0.868;0.919	B;B	0.43701	0.246;0.428	T	0.03957	-1.0989	10	0.66056	D	0.02	-3.4012	11.1325	0.48356	0.0:0.8475:0.0:0.1525	.	1814;1814	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	F	1814	ENSP00000390181:S1814F;ENSP00000414615:S1814F;ENSP00000415691:S1814F;ENSP00000243326:S1814F;ENSP00000416123:S1814F	ENSP00000243326:S1814F	S	+	2	0	RIF1	152029721	0.003000	0.15002	0.111000	0.21465	0.020000	0.10135	1.048000	0.30379	1.397000	0.46682	0.650000	0.86243	TCT		0.308	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152321475	C	T	152321475	3	4	47	1	0	0	0	0	1	0	0	0	13396	913	32	3	5555	3	RIF1	2	152321475	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	85459	152321475	90877898	309	4706										
NEB	4703	broad.mit.edu	37	chr2	152393738	152393738	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaagccaagtcaagtcttCtttatattttacctgggaga	7	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:152393738C>A	ENST00000172853.10	-	113	16159	c.16012G>T	c.(16012-16014)Gaa>Taa	p.E5338*	NEB_ENST00000604864.1_Nonsense_Mutation_p.E7039*|NEB_ENST00000397345.3_Nonsense_Mutation_p.E7039*|NEB_ENST00000427231.2_Nonsense_Mutation_p.E7039*|NEB_ENST00000603639.1_Nonsense_Mutation_p.E7039*|NEB_ENST00000409198.1_Nonsense_Mutation_p.E5338*			P20929	NEBU_HUMAN	nebulin	5338					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E5338*(1)|p.E7039*(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTCAAGTCTTCTTTATATTTT	0.383																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											64	60	61					2																	152393738		1827	4083	5910	152101984	SO:0001587	stop_gained	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16012G>T	2.37:g.152393738C>A	ENSP00000172853:p.Glu5338*		152101984	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Nonsense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	57	28.172618	0.99973	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000420924	.	.	.	6.07	3.23	0.37069	.	0.135993	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.5888	0.56432	0.124:0.6376:0.2384:0.0	.	.	.	.	X	5338;7039;7039;1387;1769;5338;127	.	ENSP00000172853:E5338X	E	-	1	0	NEB	152101984	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.798000	0.55522	0.417000	0.25871	0.650000	0.86243	GAA		0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152393738	C	A	152393738	4	1	47	1	0	0	0	0	0	1	0	0	10333	922	32	2	4739	2	NEB	2	152393738	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	72263	152393738	90805635	310	4707										
NEB	4703	broad.mit.edu	37	chr2	152522908	152522908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttctcgtaggcctccttaTatttgcactatttgaaaaca	5	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:152522908T>C	ENST00000172853.10	-	41	4874	c.4727A>G	c.(4726-4728)tAt>tGt	p.Y1576C	NEB_ENST00000604864.1_Missense_Mutation_p.Y1576C|NEB_ENST00000397345.3_Missense_Mutation_p.Y1576C|NEB_ENST00000427231.2_Missense_Mutation_p.Y1576C|NEB_ENST00000603639.1_Missense_Mutation_p.Y1576C|NEB_ENST00000409198.1_Missense_Mutation_p.Y1576C			P20929	NEBU_HUMAN	nebulin	1576					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.Y1576C(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GGCCTCCTTATATTTGCACTA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	2											100	87	91					2																	152522908		1848	4090	5938	152231154	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4727A>G	2.37:g.152522908T>C	ENSP00000172853:p.Tyr1576Cys		152231154	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	21.5	4.160884	0.78226	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	D;D;D;D	0.99958	-9.03;-9.03;-9.03;-9.03	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.99957	0.9982	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95530	0.8602	10	0.87932	D	0	.	16.0711	0.80936	0.0:0.0:0.0:1.0	.	1576	P20929	NEBU_HUMAN	C	1576	ENSP00000386259:Y1576C;ENSP00000380505:Y1576C;ENSP00000416578:Y1576C;ENSP00000172853:Y1576C	ENSP00000172853:Y1576C	Y	-	2	0	NEB	152231154	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.040000	0.89188	2.197000	0.70478	0.482000	0.46254	TAT		0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152522908	T	C	152522908	3	2	47	1	0	0	0	0	1	0	0	0	10333	1406	49	4	21527	4	NEB	2	152522908	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	129170	152522908	90676465	311	4708										
FMNL2	114793	broad.mit.edu	37	chr2	153484972	153484972	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgatgcagtttagtaaaatCgagaggctcatgcagaagat	11	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:153484972C>T	ENST00000475377.2	+	5	650	c.450C>T	c.(448-450)atC>atT	p.I150I	FMNL2_ENST00000288670.9_Silent_p.I775I			Q96PY5	FMNL2_HUMAN	formin-like 2	775	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.I775I(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TTAGTAAAATCGAGAGGCTCA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	2											132	137	135					2																	153484972		2089	4232	6321	153193218	SO:0001819	synonymous_variant	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000475377.2:c.450C>T	2.37:g.153484972C>T			153193218	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000475377.2	37																																																																																					0.483	FMNL2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333583.3	NM_052905		T	153484972	C	T	153484972	2	4	47	1	0	0	0	0	0	0	0	1	5971	874	31	1		1	FMNL2	2	153484972	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	962064	153484972	89714401	312	4709										
UPP2	151531	broad.mit.edu	37	chr2	158978037	158978037	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagtactgaactggacaaaGaactgtctgaagaactgttc	10	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:158978037G>T	ENST00000005756.4	+	5	765	c.571G>T	c.(571-573)Gaa>Taa	p.E191*	UPP2_ENST00000605860.1_Nonsense_Mutation_p.E248*|UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Nonsense_Mutation_p.E248*	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	191					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)	p.E191*(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	ACTGGACAAAGAACTGTCTGA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											181	177	178					2																	158978037		2203	4299	6502	158686283	SO:0001587	stop_gained	151531			AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.571G>T	2.37:g.158978037G>T	ENSP00000005756:p.Glu191*		158686283	B3KV87	Nonsense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.947026	0.73672	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	.	.	.	5.62	3.81	0.43845	.	0.419090	0.27946	N	0.017205	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	15.1982	0.73112	0.0:0.2675:0.7325:0.0	.	.	.	.	X	248;191	.	ENSP00000005756:E191X	E	+	1	0	UPP2	158686283	1.000000	0.71417	0.993000	0.49108	0.014000	0.08584	4.795000	0.62489	0.726000	0.32339	-0.264000	0.10439	GAA		0.413	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		T	158978037	G	T	158978037	4	4	47	1	0	0	0	0	0	1	0	0	17053	943	33	2	768	2	UPP2	2	158978037	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5493065	158978037	84221336	313	4710										
TANC1	85461	broad.mit.edu	37	chr2	160005721	160005721	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgacaaggctgggatttTtactgggagaagggatccca	14	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:160005721T>G	ENST00000263635.6	+	6	670	c.433T>G	c.(433-435)Tta>Gta	p.L145V	TANC1_ENST00000454300.1_Intron	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	145					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)		p.L145V(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GCTGGGATTTTTACTGGGAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											129	124	125					2																	160005721		1882	4103	5985	159713967	SO:0001583	missense	85461			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.433T>G	2.37:g.160005721T>G	ENSP00000263635:p.Leu145Val		159713967	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.115743	0.77323	.	.	ENSG00000115183	ENST00000263635	T	0.54675	0.56	5.83	4.64	0.57946	.	0.000000	0.64402	D	0.000004	T	0.69360	0.3102	M	0.75264	2.295	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.87578	0.991;0.998	T	0.71094	-0.4692	10	0.87932	D	0	.	9.3196	0.37955	0.0:0.1398:0.0:0.8602	.	144;145	B9EK39;Q9C0D5	.;TANC1_HUMAN	V	145	ENSP00000263635:L145V	ENSP00000263635:L145V	L	+	1	2	TANC1	159713967	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.196000	0.42686	0.986000	0.38683	0.533000	0.62120	TTA		0.458	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			G	160005721	T	G	160005721	3	3	47	1	0	0	0	0	1	0	0	0	15583	1838	64	4	447	4	TANC1	2	160005721	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1027684	160005721	83193652	314	4711										
TANK	10010	broad.mit.edu	37	chr2	162091890	162091890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctaatcaagacagtgactCggtggtactaagtggcacag	11	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:162091890C>T	ENST00000392749.2	+	8	1378	c.1139C>T	c.(1138-1140)tCg>tTg	p.S380L	TANK_ENST00000405852.1_Missense_Mutation_p.R406W|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000402568.1_3'UTR|TANK_ENST00000259075.2_Missense_Mutation_p.S380L|TANK_ENST00000406287.1_3'UTR|AC009299.2_ENST00000445372.1_RNA	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	380					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.S380L(3)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						GACAGTGACTCGGTGGTACTA	0.418																																																3	Substitution - Missense(3)	large_intestine(2)|kidney(1)	2											172	164	167					2																	162091890		2203	4300	6503	161800136	SO:0001583	missense	10010			U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.1139C>T	2.37:g.162091890C>T	ENSP00000376505:p.Ser380Leu		161800136	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.058|5.058	0.196409|0.196409	0.09599|0.09599	.|.	.|.	ENSG00000136560|ENSG00000136560	ENST00000405852|ENST00000259075;ENST00000392749;ENST00000439442	T|T;T;T	0.35605|0.19806	1.3|2.12;2.12;2.18	5.63|5.63	4.38|4.38	0.52667|0.52667	.|.	.|0.153629	.|0.42294	.|N	.|0.000723	T|T	0.05777|0.05777	0.0151|0.0151	N|N	0.00960|0.00960	-1.095|-1.095	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.26985|0.26985	-1.0087|-1.0087	7|10	0.51188|0.02654	T|T	0.08|1	-4.8203|-4.8203	10.3619|10.3619	0.43998|0.43998	0.0:0.0855:0.0:0.9145|0.0:0.0855:0.0:0.9145	.|.	.|380	.|Q92844	.|TANK_HUMAN	W|L	406|380;380;153	ENSP00000385487:R406W|ENSP00000259075:S380L;ENSP00000376505:S380L;ENSP00000387439:S153L	ENSP00000385487:R406W|ENSP00000259075:S380L	R|S	+|+	1|2	2|0	TANK|TANK	161800136|161800136	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.864000|0.864000	0.49448|0.49448	2.765000|2.765000	0.47621|0.47621	0.845000|0.845000	0.35118|0.35118	-0.218000|-0.218000	0.12543|0.12543	CGG|TCG		0.418	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		T	162091890	C	T	162091890	3	4	47	1	0	0	0	0	1	0	0	0	15585	893	31	1	1198	1	TANK	2	162091890	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2086169	162091890	81107483	315	4712										
PSMD14	10213	broad.mit.edu	37	chr2	162247659	162247659	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattattactccattactatTaactatcggaaaaatgaact	3	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:162247659T>G	ENST00000409682.3	+	9	1319	c.615T>G	c.(613-615)atT>atG	p.I205M		NM_005805.5	NP_005796.1	O00487	PSDE_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	205					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K63-linked deubiquitination (GO:0070536)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, lid subcomplex (GO:0008541)	endopeptidase activator activity (GO:0061133)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|proteasome binding (GO:0070628)|ubiquitin thiolesterase activity (GO:0004221)	p.I205M(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	12						CCATTACTATTAACTATCGGA	0.244																																																1	Substitution - Missense(1)	large_intestine(1)	2											17	16	17					2																	162247659		1747	3973	5720	161955905	SO:0001583	missense	10213			U86782	CCDS46437.1	2q14.3	2008-05-22			ENSG00000115233	ENSG00000115233		"Proteasome (prosome, macropain) subunits"	16889	protein-coding gene	gene with protein product		607173				9374539	Standard	NM_005805		Approved	POH1, pad1, Rpn11	uc002ubu.3	O00487	OTTHUMG00000153882	ENST00000409682.3:c.615T>G	2.37:g.162247659T>G	ENSP00000386541:p.Ile205Met		161955905	B3KNW2|O00176	Missense_Mutation	SNP	ENST00000409682.3	37	CCDS46437.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.210341	0.79240	.	.	ENSG00000115233	ENST00000409682	.	.	.	5.2	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.79423	0.4443	M	0.94101	3.495	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.80810	-0.1216	9	0.87932	D	0	.	3.1413	0.06456	0.0:0.3864:0.0:0.6136	.	205	O00487	PSDE_HUMAN	M	205	.	ENSP00000386541:I205M	I	+	3	3	PSMD14	161955905	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.118000	0.71583	1.966000	0.57179	0.383000	0.25322	ATT		0.244	PSMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332833.1	NM_005805		G	162247659	T	G	162247659	3	3	47	1	0	0	0	0	1	0	0	0	12731	1742	61	4	641	4	PSMD14	2	162247659	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	155769	162247659	80951714	316	4713										
GCG	2641	broad.mit.edu	37	chr2	163000624	163000624	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttcatctcatcagagaaaGaaccatcagcatgtctgcgg	9	10	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:163000624G>T	ENST00000418842.2	-	5	703	c.449C>A	c.(448-450)tCt>tAt	p.S150Y	GCG_ENST00000375497.3_Missense_Mutation_p.S150Y	NM_002054.4	NP_002045.1	P01275	GLUC_HUMAN	glucagon	150					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|protein kinase A signaling (GO:0010737)|regulation of insulin secretion (GO:0050796)|response to starvation (GO:0042594)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|secretory granule lumen (GO:0034774)	glucagon receptor binding (GO:0031769)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)	p.S150Y(2)		breast(1)|central_nervous_system(1)|large_intestine(3)|lung(9)	14						ATCAGAGAAAGAACCATCAGC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	2											116	111	112					2																	163000624		1897	4126	6023	162708870	SO:0001583	missense	2641				CCDS46439.1	2q36-q37	2013-02-26			ENSG00000115263	ENSG00000115263		"Endogenous ligands"	4191	protein-coding gene	gene with protein product	"glicentin-related polypeptide", "glucagon-like peptide 1", "glucagon-like peptide 2", "preproglucagon"	138030				2753890, 3725587	Standard	NM_002054		Approved	GLP1, GLP2, GRPP	uc002ucc.4	P01275	OTTHUMG00000153892	ENST00000418842.2:c.449C>A	2.37:g.163000624G>T	ENSP00000387662:p.Ser150Tyr		162708870	A6NN65|Q53TP6	Missense_Mutation	SNP	ENST00000418842.2	37	CCDS46439.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113149	0.77210	.	.	ENSG00000115263	ENST00000418842;ENST00000375497	T;T	0.32272	1.46;1.46	5.75	5.75	0.90469	Glucagon/GIP/secretin/VIP (3);	0.172267	0.38492	N	0.001680	T	0.51500	0.1678	L	0.57536	1.79	0.44295	D	0.997168	D	0.76494	0.999	D	0.74348	0.983	T	0.50474	-0.8824	10	0.87932	D	0	-21.6438	14.5254	0.67884	0.0:0.1462:0.8538:0.0	.	150	P01275	GLUC_HUMAN	Y	150	ENSP00000387662:S150Y;ENSP00000364647:S150Y	ENSP00000364647:S150Y	S	-	2	0	GCG	162708870	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.514000	0.53422	2.717000	0.92951	0.650000	0.86243	TCT		0.393	GCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332860.1	NM_002054		T	163000624	G	T	163000624	3	4	47	1	0	0	0	0	1	0	0	0	6310	942	33	2	101	2	GCG	2	163000624	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	752965	163000624	80198749	317	4714										
COBLL1	22837	broad.mit.edu	37	chr2	165551796	165551796	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtctataaagtgggtaattCtttaggtaagaagcagtgga	12	3	2	1	rs377161034		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:165551796C>A	ENST00000392717.2	-	13	2338	c.2334G>T	c.(2332-2334)aaG>aaT	p.K778N	COBLL1_ENST00000375458.2_Missense_Mutation_p.K702N|COBLL1_ENST00000342193.4_Missense_Mutation_p.K740N|COBLL1_ENST00000194871.6_Missense_Mutation_p.K807N|COBLL1_ENST00000409184.3_Missense_Mutation_p.K740N			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	778						extracellular vesicular exosome (GO:0070062)		p.K740N(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GTGGGTAATTCTTTAGGTAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	ASN/LYS	0,4406		0,0,2203	167	170	169		2220	4.2	1	2		169	1,8599	1.2+/-3.3	0,1,4299	no	missense	COBLL1	NM_014900.3	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	740/1167	165551796	1,13005	2203	4300	6503	165260042	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2334G>T	2.37:g.165551796C>A	ENSP00000376478:p.Lys778Asn		165260042	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	C	18.16	3.563045	0.65538	0.0	1.16E-4	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.03	4.23	0.50019	.	0.233173	0.37955	N	0.001865	T	0.59918	0.2229	L	0.58101	1.795	0.33416	D	0.579252	D;D;D	0.63880	0.969;0.969;0.993	P;P;P	0.58331	0.711;0.711;0.837	T	0.70189	-0.4940	9	0.48119	T	0.1	-10.5989	8.1049	0.30879	0.0:0.7102:0.0:0.2898	.	778;807;740	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	N	702;740;740;778;807	.	ENSP00000194871:K807N	K	-	3	2	COBLL1	165260042	0.157000	0.22836	0.987000	0.45799	0.948000	0.59901	0.201000	0.17276	1.553000	0.49476	0.557000	0.71058	AAG		0.363	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165551796	C	A	165551796	3	1	47	1	0	0	0	0	1	0	0	0	3660	912	32	2	1292	2	COBLL1	2	165551796	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2551172	165551796	77647577	318	4715										
SLC38A11	151258	broad.mit.edu	37	chr2	165765237	165765237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcactgttacaacaatgtgGaaaaccgatgaaagattccc	7	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:165765237G>T	ENST00000409149.3	-	10	1131	c.840C>A	c.(838-840)ttC>ttA	p.F280L	SLC38A11_ENST00000303735.4_Missense_Mutation_p.F258L|SLC38A11_ENST00000409662.1_Missense_Mutation_p.F280L|SLC38A11_ENST00000409058.1_Missense_Mutation_p.F311L|SLC38A11_ENST00000493887.1_5'Flank	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	280					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.F258L(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						CAACAATGTGGAAAACCGATG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	79	82					2																	165765237		2203	4300	6503	165473483	SO:0001583	missense	151258				CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"Solute carriers"	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.840C>A	2.37:g.165765237G>T	ENSP00000386272:p.Phe280Leu		165473483	B4DF99|Q8N887	Missense_Mutation	SNP	ENST00000409149.3	37	CCDS56142.1	.	.	.	.	.	.	.	.	.	.	G	4.962	0.178758	0.09443	.	.	ENSG00000169507	ENST00000303735;ENST00000409149;ENST00000409058;ENST00000409662;ENST00000424914	T;T;T;T;T	0.01918	4.56;4.56;4.56;4.56;4.56	5.73	3.94	0.45596	.	0.362296	0.36740	N	0.002440	T	0.01489	0.0048	N	0.05078	-0.115	0.37107	D	0.900157	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.55296	-0.8163	10	0.39692	T	0.17	-4.3928	10.1509	0.42794	0.1573:0.0:0.8427:0.0	.	280;258	Q08AI6;Q08AI6-2	S38AB_HUMAN;.	L	258;280;311;280;101	ENSP00000306178:F258L;ENSP00000386272:F280L;ENSP00000387345:F311L;ENSP00000386774:F280L;ENSP00000401448:F101L	ENSP00000306178:F258L	F	-	3	2	SLC38A11	165473483	1.000000	0.71417	0.805000	0.32314	0.285000	0.27093	4.290000	0.59019	0.894000	0.36317	0.555000	0.69702	TTC		0.408	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512		T	165765237	G	T	165765237	3	4	47	1	0	0	0	0	1	0	0	0	14640	1165	41	2	388	2	SLC38A11	2	165765237	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	213441	165765237	77434136	319	4716										
SCN3A	6328	broad.mit.edu	37	chr2	165947005	165947005	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttgtaataggctcataagaGactttggaggggtttgatgc	14	4	1	2	rs141161490	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:165947005G>T	ENST00000360093.3	-	28	6149	c.5658C>A	c.(5656-5658)gtC>gtA	p.V1886V	SCN3A_ENST00000283254.7_Silent_p.V1886V|SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000409101.3_Silent_p.V1837V|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000540861.1_Silent_p.V369V	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1886					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V1886V(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCTCATAAGAGACTTTGGAGG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	2											72	67	68					2																	165947005		2203	4300	6503	165655251	SO:0001819	synonymous_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.5658C>A	2.37:g.165947005G>T			165655251	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																					0.418	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		T	165947005	G	T	165947005	2	4	47	1	0	0	0	0	0	0	0	1	13955	929	33	2		2	SCN3A	2	165947005	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	181768	165947005	77252368	320	4717										
SCN1A	6323	broad.mit.edu	37	chr2	166897933	166897933	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagattaagaatatgttggaAaatttataccaacagggtgg	10	4	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:166897933A>C	ENST00000303395.4	-	13	2222	c.2223T>G	c.(2221-2223)ttT>ttG	p.F741L	SCN1A_ENST00000409050.1_Missense_Mutation_p.F713L|SCN1A_ENST00000375405.3_Missense_Mutation_p.F730L|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.F741L			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	741					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.F730L(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATATGTTGGAAAATTTATACC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	96	92					2																	166897933		2203	4300	6503	166606179	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2223T>G	2.37:g.166897933A>C	ENSP00000303540:p.Phe741Leu		166606179	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.444401	0.83993	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96334	-3.98;-3.98;-3.96;-3.96	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000003	D	0.97676	0.9238	M	0.73753	2.245	0.58432	D	0.999999	D;D;B	0.67145	0.996;0.993;0.33	D;D;B	0.73380	0.98;0.956;0.084	D	0.97312	0.9938	10	0.32370	T	0.25	.	15.9597	0.79918	1.0:0.0:0.0:0.0	.	730;713;741	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	L	741;741;730;713	ENSP00000407030:F741L;ENSP00000303540:F741L;ENSP00000364554:F730L;ENSP00000386312:F713L	ENSP00000303540:F741L	F	-	3	2	SCN1A	166606179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.477000	0.81069	2.226000	0.72624	0.482000	0.46254	TTT		0.368	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		C	166897933	A	C	166897933	3	2	47	1	0	0	0	0	1	0	0	0	13951	11	1	4	3862	4	SCN1A	2	166897933	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	950928	166897933	76301440	321	4718										
SCN1A	6323	broad.mit.edu	37	chr2	166904194	166904194	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtcgaaacaaggacaaaaaAgcccaactgaaggtatcaaa	8	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:166904194A>C	ENST00000303395.4	-	8	1112	c.1113T>G	c.(1111-1113)gcT>gcG	p.A371A	SCN1A_ENST00000409050.1_Silent_p.A371A|SCN1A_ENST00000375405.3_Silent_p.A371A|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Silent_p.A371A			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	371					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.A371A(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGACAAAAAAGCCCAACTGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	2											114	116	116					2																	166904194		2203	4300	6503	166612440	SO:0001819	synonymous_variant	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1113T>G	2.37:g.166904194A>C			166612440	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																				0.403	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		C	166904194	A	C	166904194	2	2	47	1	0	0	0	0	0	0	0	1	13951	59	3	4		4	SCN1A	2	166904194	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6261	166904194	76295179	322	4719										
SCN9A	6335	broad.mit.edu	37	chr2	167159616	167159616	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttacttctaaagtcttcttcActctctagggtattcattat	4	9	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:167159616A>G	ENST00000409435.1	-	6	884	c.885T>C	c.(883-885)agT>agC	p.S295S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000375387.4_Silent_p.S296S|SCN9A_ENST00000409672.1_Silent_p.S295S|SCN9A_ENST00000303354.6_Silent_p.S296S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	295					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.S295S(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGTCTTCTTCACTCTCTAGGG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	2											88	82	84					2																	167159616		1955	4206	6161	166867862	SO:0001819	synonymous_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.885T>C	2.37:g.167159616A>G			166867862	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																				0.308	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		G	167159616	A	G	167159616	2	3	47	1	0	0	0	0	0	0	0	1	13962	156	6	4		4	SCN9A	2	167159616	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	255422	167159616	76039757	323	4720										
SCN7A	6332	broad.mit.edu	37	chr2	167298178	167298178	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacaacaacaggaccaagtCtttcagggccacccatgagt	9	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:167298178C>A	ENST00000409855.1	-	14	2011	c.1885G>T	c.(1885-1887)Gac>Tac	p.D629Y		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	629					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.D629Y(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AGGACCAAGTCTTTCAGGGCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	120	118					2																	167298178		2159	4289	6448	167006424	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1885G>T	2.37:g.167298178C>A	ENSP00000386796:p.Asp629Tyr		167006424		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223122	0.58668	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.98455	-4.94;-4.94	4.78	-0.183	0.13284	Ion transport (1);	0.549826	0.17125	N	0.186065	D	0.95287	0.8471	N	0.10837	0.055	0.30118	N	0.805916	D	0.57257	0.979	P	0.58331	0.837	D	0.91176	0.4972	10	0.87932	D	0	.	3.8609	0.08996	0.1647:0.4416:0.0:0.3937	.	629	Q01118	SCN7A_HUMAN	Y	629	ENSP00000386796:D629Y;ENSP00000413699:D629Y	ENSP00000259060:D629Y	D	-	1	0	SCN7A	167006424	1.000000	0.71417	0.024000	0.17045	0.013000	0.08279	4.072000	0.57563	-0.064000	0.13043	0.585000	0.79938	GAC		0.388	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167298178	C	A	167298178	3	1	47	1	0	0	0	0	1	0	0	0	13960	913	32	2	3211	2	SCN7A	2	167298178	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	138562	167298178	75901195	324	4721										
SCN7A	6332	broad.mit.edu	37	chr2	167322035	167322035	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttccaaataataaaagtttTctgtttctgaaaaacaggca	5	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:167322035T>G	ENST00000409855.1	-	8	1004	c.878A>C	c.(877-879)gAa>gCa	p.E293A		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	293					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E293A(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	ATAAAAGTTTTCTGTTTCTGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											31	29	29					2																	167322035		1810	4075	5885	167030281	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.878A>C	2.37:g.167322035T>G	ENSP00000386796:p.Glu293Ala		167030281		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	8.824	0.938167	0.18206	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98164	-4.12;-4.15;-4.76	5.33	2.9	0.33743	Ion transport (1);	0.721055	0.12829	N	0.435778	D	0.94971	0.8373	L	0.51914	1.62	0.22982	N	0.998477	B	0.13145	0.007	B	0.14578	0.011	D	0.86696	0.1926	10	0.25751	T	0.34	.	1.1398	0.01762	0.1675:0.1339:0.1746:0.524	.	293	Q01118	SCN7A_HUMAN	A	293	ENSP00000386796:E293A;ENSP00000413699:E293A;ENSP00000403846:E293A	ENSP00000259060:E293A	E	-	2	0	SCN7A	167030281	0.013000	0.17824	0.684000	0.30055	0.727000	0.41649	0.066000	0.14489	0.930000	0.37217	0.477000	0.44152	GAA		0.343	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			G	167322035	T	G	167322035	3	3	47	1	0	0	0	0	1	0	0	0	13960	1783	62	4	4242	4	SCN7A	2	167322035	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	23857	167322035	75877338	325	4722										
XIRP2	129446	broad.mit.edu	37	chr2	168096388	168096388	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaattcatagcagccaggtTggcacttcaagaagcagcca	10	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168096388T>C	ENST00000409728.1	+	7	1070	c.981T>C	c.(979-981)gtT>gtC	p.V327V	XIRP2_ENST00000420519.1_Silent_p.V327V|XIRP2_ENST00000409195.1_Silent_p.V294V|XIRP2_ENST00000409605.1_Silent_p.V72V|XIRP2_ENST00000295237.9_Silent_p.V294V|XIRP2_ENST00000409756.2_Silent_p.V294V|XIRP2_ENST00000409273.1_Silent_p.V72V|XIRP2_ENST00000409043.1_Silent_p.V294V	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	119					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.V294V(7)|p.V327V(7)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GCAGCCAGGTTGGCACTTCAA	0.368																																																14	Substitution - coding silent(14)	kidney(12)|large_intestine(2)	2											84	85	85					2																	168096388		1865	4110	5975	167804634	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.981T>C	2.37:g.168096388T>C			167804634	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409728.1	37	CCDS56143.1																																																																																				0.368	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		C	168096388	T	C	168096388	2	2	47	1	0	0	0	0	0	0	0	1	17470	1799	63	4		4	XIRP2	2	168096388	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	774353	168096388	75102985	326	4723										
XIRP2	129446	broad.mit.edu	37	chr2	168101105	168101105	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaacctcttgattcaattaAatattttagtgatgtggaag	7	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168101105A>C	ENST00000409195.1	+	9	3292	c.3203A>C	c.(3202-3204)aAa>aCa	p.K1068T	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.K1068T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.K846T|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	893					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.K1068T(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GATTCAATTAAATATTTTAGT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											30	28	29					2																	168101105		1804	4068	5872	167809351	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3203A>C	2.37:g.168101105A>C	ENSP00000386840:p.Lys1068Thr		167809351	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.409754	0.62399	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03441	3.93;3.93;3.93	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.17831	0.0428	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.00052	-1.2189	10	0.59425	D	0.04	-32.4183	15.6264	0.76863	1.0:0.0:0.0:0.0	.	893;893;846	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	T	1068;1068;846	ENSP00000386840:K1068T;ENSP00000295237:K1068T;ENSP00000387255:K846T	ENSP00000295237:K1068T	K	+	2	0	XIRP2	167809351	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.962000	0.93254	2.333000	0.79357	0.533000	0.62120	AAA		0.328	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168101105	A	C	168101105	3	2	47	1	0	0	0	0	1	0	0	0	17470	14	1	4	3233	4	XIRP2	2	168101105	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4717	168101105	75098268	327	4724										
XIRP2	129446	broad.mit.edu	37	chr2	168103002	168103002	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcttcatgaaaatgatggTgacacaattgagcgtgaaga	10	6	2	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168103002T>C	ENST00000409195.1	+	9	5189	c.5100T>C	c.(5098-5100)ggT>ggC	p.G1700G	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.G1700G|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Silent_p.G1478G|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1525					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.G1700G(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAATGATGGTGACACAATTG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	2											125	121	122					2																	168103002		1887	4105	5992	167811248	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5100T>C	2.37:g.168103002T>C			167811248	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																				0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168103002	T	C	168103002	2	2	47	1	0	0	0	0	0	0	0	1	17470	1683	59	4		4	XIRP2	2	168103002	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1897	168103002	75096371	328	4725										
XIRP2	129446	broad.mit.edu	37	chr2	168115186	168115186	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaataagaataataataaCaattatgtagcagtctcata	5	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168115186C>T	ENST00000409728.1	+	11	2318	c.2229C>T	c.(2227-2229)aaC>aaT	p.N743N	XIRP2_ENST00000420519.1_Silent_p.N743N|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409605.1_Silent_p.N488N|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Silent_p.N710N|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409043.1_Silent_p.N710N	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1261					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.N743N(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATAATAATAACAATTATGTAG	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	2											30	29	29					2																	168115186		1805	4054	5859	167823432	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2229C>T	2.37:g.168115186C>T			167823432	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409728.1	37	CCDS56143.1																																																																																				0.323	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		T	168115186	C	T	168115186	2	4	47	1	0	0	0	0	0	0	0	1	17470	477	17	3		3	XIRP2	2	168115186	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	12184	168115186	75084187	329	4726										
XIRP2	129446	broad.mit.edu	37	chr2	168115682	168115682	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgcttggatttaagggaaTttggaaaggatgttaaacct	11	4	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168115682T>G	ENST00000409728.1	+	11	2814	c.2725T>G	c.(2725-2727)Ttt>Gtt	p.F909V	XIRP2_ENST00000420519.1_Missense_Mutation_p.F909V|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409605.1_Missense_Mutation_p.F654V|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.F876V|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409043.1_Missense_Mutation_p.F876V	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.F909V(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTTAAGGGAATTTGGAAAGGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	73	75					2																	168115682		1846	4088	5934	167823928	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2725T>G	2.37:g.168115682T>G	ENSP00000386619:p.Phe909Val		167823928	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	T	6.431	0.447719	0.12223	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.78126	-1.13;-1.14;-1.13;-1.14;-1.15	5.78	1.57	0.23409	.	.	.	.	.	T	0.62756	0.2454	.	.	.	0.22975	N	0.99848	B;B	0.28933	0.228;0.228	B;B	0.26969	0.052;0.075	T	0.53136	-0.8481	8	0.49607	T	0.09	.	3.8307	0.08873	0.1564:0.3011:0.0:0.5425	.	876;909	A4UGR9-4;A4UGR9-6	.;.	V	876;909;876;909;654	ENSP00000386454:F876V;ENSP00000386619:F909V;ENSP00000386724:F876V;ENSP00000415541:F909V;ENSP00000386981:F654V	ENSP00000386454:F876V	F	+	1	0	XIRP2	167823928	0.269000	0.24143	0.877000	0.34402	0.305000	0.27757	-0.327000	0.07955	0.283000	0.22279	0.454000	0.30748	TTT		0.343	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		G	168115682	T	G	168115682	3	3	47	1	0	0	0	0	1	0	0	0	17470	1493	52	4	12043	4	XIRP2	2	168115682	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	496	168115682	75083691	330	4727										
XIRP2	129446	broad.mit.edu	37	chr2	168115752	168115752	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caataatgaaaacacaggttTtgatgctctgagccatgaat	8	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:168115752T>G	ENST00000409728.1	+	11	2884	c.2795T>G	c.(2794-2796)tTt>tGt	p.F932C	XIRP2_ENST00000420519.1_Missense_Mutation_p.F932C|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409605.1_Missense_Mutation_p.F677C|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.F899C|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409043.1_Missense_Mutation_p.F899C	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.F932C(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACACAGGTTTTGATGCTCTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	85	88					2																	168115752		1901	4133	6034	167823998	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2795T>G	2.37:g.168115752T>G	ENSP00000386619:p.Phe932Cys		167823998	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.764532	0.31228	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.78364	-1.16;-1.17;-1.16;-1.17;-1.17	5.91	0.493	0.16878	.	.	.	.	.	T	0.64983	0.2648	.	.	.	0.09310	N	1	B;B	0.17667	0.006;0.023	B;B	0.14578	0.004;0.011	T	0.55438	-0.8141	8	0.87932	D	0	.	5.1221	0.14865	0.0:0.1658:0.2828:0.5514	.	899;932	A4UGR9-4;A4UGR9-6	.;.	C	899;932;899;932;677	ENSP00000386454:F899C;ENSP00000386619:F932C;ENSP00000386724:F899C;ENSP00000415541:F932C;ENSP00000386981:F677C	ENSP00000386454:F899C	F	+	2	0	XIRP2	167823998	0.006000	0.16342	0.001000	0.08648	0.012000	0.07955	0.611000	0.24268	-0.130000	0.11599	-0.417000	0.06048	TTT		0.423	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		G	168115752	T	G	168115752	3	3	47	1	0	0	0	0	1	0	0	0	17470	1841	64	4	12113	4	XIRP2	2	168115752	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	70	168115752	75083621	331	4728										
LRP2	4036	broad.mit.edu	37	chr2	169985579	169985579	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttagattttcgtttgaagaGattccattttgtcacctaaa	6	6	1	3	rs267598995		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:169985579G>T	ENST00000263816.3	-	78	14029	c.13744C>A	c.(13744-13746)Ctc>Atc	p.L4582I		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4582					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.L4582I(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CGTTTGAAGAGATTCCATTTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	130	126					2																	169985579		2203	4300	6503	169693825	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.13744C>A	2.37:g.169985579G>T	ENSP00000263816:p.Leu4582Ile		169693825	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	8.505	0.865118	0.17250	.	.	ENSG00000081479	ENST00000263816	D	0.89810	-2.57	5.75	3.38	0.38709	.	0.266746	0.44285	N	0.000475	T	0.67363	0.2885	N	0.03608	-0.345	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.58418	-0.7640	10	0.05351	T	0.99	.	4.4325	0.11535	0.4654:0.0:0.2186:0.316	.	4582	P98164	LRP2_HUMAN	I	4582	ENSP00000263816:L4582I	ENSP00000263816:L4582I	L	-	1	0	LRP2	169693825	1.000000	0.71417	0.995000	0.50966	0.844000	0.47949	3.964000	0.56780	0.440000	0.26502	-0.474000	0.04947	CTC		0.303	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	169985579	G	T	169985579	3	4	47	1	0	0	0	0	1	0	0	0	8985	942	33	2	231	2	LRP2	2	169985579	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1869827	169985579	73213794	332	4729										
LRP2	4036	broad.mit.edu	37	chr2	170072805	170072805	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtagagtttctgctcttcGatgtcaagagtgacacactc	9	10	3	3	rs137904820		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:170072805G>A	ENST00000263816.3	-	35	6069	c.5784C>T	c.(5782-5784)atC>atT	p.I1928I		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1928					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.I1928I(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TCTGCTCTTCGATGTCAAGAG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	2											144	128	133					2																	170072805		2203	4300	6503	169781051	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5784C>T	2.37:g.170072805G>A			169781051	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.498	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170072805	G	A	170072805	2	1	47	1	0	0	0	0	0	0	0	1	8985	1048	37	1		1	LRP2	2	170072805	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	87226	170072805	73126568	333	4730										
LRP2	4036	broad.mit.edu	37	chr2	170127576	170127576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaggtgaacgggatcccacGaatagcaacttgggatgaaa	12	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:170127576G>A	ENST00000263816.3	-	16	2443	c.2158C>T	c.(2158-2160)Cgt>Tgt	p.R720C	LRP2_ENST00000443831.1_Intron	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	720					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R720C(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGGATCCCACGAATAGCAACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	72	77					2																	170127576		2203	4300	6503	169835822	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2158C>T	2.37:g.170127576G>A	ENSP00000263816:p.Arg720Cys		169835822	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057719	0.76074	.	.	ENSG00000081479	ENST00000263816	D	0.91996	-2.95	5.77	5.77	0.91146	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97268	0.9909	10	0.87932	D	0	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	720	P98164	LRP2_HUMAN	C	720	ENSP00000263816:R720C	ENSP00000263816:R720C	R	-	1	0	LRP2	169835822	1.000000	0.71417	1.000000	0.80357	0.386000	0.30323	4.853000	0.62911	2.885000	0.99019	0.655000	0.94253	CGT		0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170127576	G	A	170127576	3	1	47	1	0	0	0	0	1	0	0	0	8985	1058	37	1	12065	1	LRP2	2	170127576	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	54771	170127576	73071797	334	4731										
FASTKD1	79675	broad.mit.edu	37	chr2	170402845	170402845	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttatgtaattaatatcatcCatgaaatgctgtaaagtagc	6	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:170402845C>A	ENST00000453153.2	-	8	1930	c.1584G>T	c.(1582-1584)atG>atT	p.M528I	FASTKD1_ENST00000453929.2_Missense_Mutation_p.M528I	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	528					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.M528I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						TAATATCATCCATGAAATGCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	70	70					2																	170402845		2203	4300	6503	170111091	SO:0001583	missense	79675			AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1584G>T	2.37:g.170402845C>A	ENSP00000400513:p.Met528Ile		170111091	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.110009	0.00353	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.15487	2.43;2.42	4.78	2.91	0.33838	.	0.691151	0.16261	N	0.222260	T	0.09379	0.0231	L	0.39085	1.19	0.23855	N	0.996655	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.39418	-0.9615	10	0.06891	T	0.86	-1.0669	2.5965	0.04855	0.1522:0.5271:0.1481:0.1726	.	528;528	Q53R41-2;Q53R41	.;FAKD1_HUMAN	I	528	ENSP00000400513:M528I;ENSP00000403229:M528I	ENSP00000400513:M528I	M	-	3	0	FASTKD1	170111091	0.988000	0.35896	0.020000	0.16555	0.006000	0.05464	0.131000	0.15870	0.698000	0.31739	0.655000	0.94253	ATG		0.368	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170402845	C	A	170402845	3	1	47	1	0	0	0	0	1	0	0	0	5704	594	21	2	991	2	FASTKD1	2	170402845	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	275269	170402845	72796528	335	4732										
PHOSPHO2	493911	broad.mit.edu	37	chr2	170557689	170557689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgaaatgaaaagagcagtgAcatcattgcctttcactcca	7	9	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:170557689A>G	ENST00000359744.3	+	4	596	c.208A>G	c.(208-210)Aca>Gca	p.T70A	KLHL23_ENST00000272797.4_Intron|KLHL23_ENST00000602521.1_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	70							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)	p.T70A(1)		breast(1)|large_intestine(1)|lung(6)|skin(2)	10						AAGAGCAGTGACATCATTGCC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											111	111	111					2																	170557689		2203	4300	6503	170265935	SO:0001583	missense	493911			BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.208A>G	2.37:g.170557689A>G	ENSP00000352782:p.Thr70Ala		170265935	B2RC30|D3DPC7	Missense_Mutation	SNP	ENST00000359744.3	37	CCDS33319.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415545	0.25552	.	.	ENSG00000144362	ENST00000359744;ENST00000438710	T;T	0.42131	0.98;0.98	5.24	2.8	0.32819	HAD-like domain (1);	0.398571	0.25078	U	0.033308	T	0.28333	0.0700	L	0.39020	1.185	0.26799	N	0.969233	B	0.14438	0.01	B	0.16722	0.016	T	0.22243	-1.0222	10	0.15499	T	0.54	.	8.0184	0.30395	0.792:0.1367:0.0714:0.0	.	70	Q8TCD6	PHOP2_HUMAN	A	70	ENSP00000352782:T70A;ENSP00000411844:T70A	ENSP00000352782:T70A	T	+	1	0	PHOSPHO2	170265935	1.000000	0.71417	0.576000	0.28549	0.994000	0.84299	4.391000	0.59652	0.373000	0.24621	0.533000	0.62120	ACA		0.348	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489		G	170557689	A	G	170557689	3	3	47	1	0	0	0	0	1	0	0	0	11888	275	10	4	210	4	PHOSPHO2	2	170557689	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	154844	170557689	72641684	336	4733										
PDK1	5163	broad.mit.edu	37	chr2	173429762	173429762	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcatcgaaaacacattggaAgcataaatccaaactgcaat	5	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:173429762A>C	ENST00000282077.3	+	5	834	c.652A>C	c.(652-654)Agc>Cgc	p.S218R	PDK1_ENST00000392571.2_Missense_Mutation_p.S238R|PDK1_ENST00000410055.1_Missense_Mutation_p.S218R|PDK1_ENST00000544863.1_Missense_Mutation_p.S63R|PDK1_ENST00000543905.1_Missense_Mutation_p.S142R			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	218	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.S218R(1)		central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			ACACATTGGAAGCATAAATCC	0.308									Autosomal Dominant Polycystic Kidney Disease																																							1	Substitution - Missense(1)	large_intestine(1)	2											150	136	141					2																	173429762		2203	4299	6502	173138008	SO:0001583	missense	5163	Familial Cancer Database	ADPKD	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"pyruvate dehydrogenase kinase, isoenzyme 1"			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.652A>C	2.37:g.173429762A>C	ENSP00000282077:p.Ser218Arg		173138008	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Missense_Mutation	SNP	ENST00000282077.3	37	CCDS2250.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.383838	0.82792	.	.	ENSG00000152256	ENST00000443353;ENST00000543905;ENST00000544863;ENST00000282077;ENST00000392571;ENST00000410055;ENST00000416991;ENST00000439519	T;T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49;1.49	5.94	5.94	0.96194	ATPase-like, ATP-binding domain (1);Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (2);	0.077153	0.85682	D	0.000000	T	0.53981	0.1830	M	0.90198	3.095	0.80722	D	1	P;P	0.48834	0.916;0.607	P;P	0.52109	0.69;0.61	T	0.58775	-0.7577	10	0.25106	T	0.35	-17.8348	16.3939	0.83550	1.0:0.0:0.0:0.0	.	218;238	Q15118;E9PD65	PDK1_HUMAN;.	R	142;142;63;218;238;218;136;142	ENSP00000399558:S142R;ENSP00000438567:S142R;ENSP00000437502:S63R;ENSP00000282077:S218R;ENSP00000376352:S238R;ENSP00000386985:S218R;ENSP00000399160:S136R;ENSP00000388366:S142R	ENSP00000282077:S218R	S	+	1	0	PDK1	173138008	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.114000	0.71560	2.276000	0.75962	0.455000	0.32223	AGC		0.308	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610		C	173429762	A	C	173429762	3	2	47	1	0	0	0	0	1	0	0	0	11706	72	3	4	670	4	PDK1	2	173429762	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2872073	173429762	69769611	337	4734										
EVX2	344191	broad.mit.edu	37	chr2	176948315	176948315	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgcccttggcggggagttCtcccagagcgctgtgcaggg	16	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:176948315C>A	ENST00000308618.4	-	1	326	c.190G>T	c.(190-192)Gaa>Taa	p.E64*		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	64					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.E64*(1)		kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		GCGGGGAGTTCTCCCAGAGCG	0.632																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											41	48	45					2																	176948315		2203	4300	6503	176656561	SO:0001587	stop_gained	344191				CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"Homeoboxes / ANTP class : HOXL subclass"	3507	protein-coding gene	gene with protein product		142991	"eve, even-skipped homeobox homolog 2 (Drosophila)"			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.190G>T	2.37:g.176948315C>A	ENSP00000312385:p.Glu64*		176656561		Nonsense_Mutation	SNP	ENST00000308618.4	37	CCDS33333.1	.	.	.	.	.	.	.	.	.	.	C	37	6.509922	0.97624	.	.	ENSG00000174279	ENST00000308618	.	.	.	5.84	5.84	0.93424	.	0.153691	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-25.7969	20.1278	0.97990	0.0:1.0:0.0:0.0	.	.	.	.	X	64	.	ENSP00000312385:E64X	E	-	1	0	EVX2	176656561	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.270000	0.78493	2.768000	0.95171	0.561000	0.74099	GAA		0.632	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1			A	176948315	C	A	176948315	4	1	47	1	0	0	0	0	0	1	0	0	5308	922	32	2	1250	2	EVX2	2	176948315	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3518553	176948315	66251058	338	4735										
OSBPL6	114880	broad.mit.edu	37	chr2	179238714	179238714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttctgagttctttgatgCccaagaggtgctcctctctg	10	10	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179238714C>T	ENST00000190611.4	+	15	1869	c.1493C>T	c.(1492-1494)gCc>gTc	p.A498V	OSBPL6_ENST00000409045.3_Missense_Mutation_p.A467V|OSBPL6_ENST00000359685.3_Missense_Mutation_p.A462V|OSBPL6_ENST00000392505.2_Missense_Mutation_p.A523V|OSBPL6_ENST00000409631.1_Missense_Mutation_p.A462V|OSBPL6_ENST00000357080.4_Missense_Mutation_p.A431V|OSBPL6_ENST00000315022.2_Missense_Mutation_p.A502V	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	498					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.A498V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TTCTTTGATGCCCAAGAGGTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	130	135					2																	179238714		2203	4300	6503	178946960	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1493C>T	2.37:g.179238714C>T	ENSP00000190611:p.Ala498Val		178946960	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.736496	0.96865	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.28069	2.0;1.94;1.63;2.02;1.94;1.94;2.0	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.61689	0.2367	M	0.80183	2.485	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;0.996;0.999;0.997;0.998	D;D;D;D;D;D	0.97110	1.0;0.997;0.99;0.997;0.985;0.994	T	0.63919	-0.6528	10	0.87932	D	0	-14.3978	20.2182	0.98305	0.0:1.0:0.0:0.0	.	467;502;462;523;498;431	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	V	523;462;431;467;498;462;502	ENSP00000376293:A523V;ENSP00000352713:A462V;ENSP00000349591:A431V;ENSP00000387248:A467V;ENSP00000190611:A498V;ENSP00000386885:A462V;ENSP00000318723:A502V	ENSP00000190611:A498V	A	+	2	0	OSBPL6	178946960	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.747000	0.85070	2.785000	0.95823	0.655000	0.94253	GCC		0.483	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		T	179238714	C	T	179238714	3	4	47	1	0	0	0	0	1	0	0	0	11312	739	26	3	1665	3	OSBPL6	2	179238714	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2290399	179238714	63960659	339	4736										
FKBP7	65977	broad.mit.edu	37	chr2	179343206	179343206	+	5'Flank	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaacaatgaatctgaataaGaaatgcatggtttttggcat	8	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179343206G>T	ENST00000234453.5	+	0	0				FKBP7_ENST00000464248.1_5'UTR|FKBP7_ENST00000424785.2_Missense_Mutation_p.F7L|FKBP7_ENST00000434643.2_Missense_Mutation_p.F7L	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)	p.F7L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			ATCTGAATAAGAAATGCATGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	141	134					2																	179343206		2203	4299	6502	179051452	SO:0001631	upstream_gene_variant	51661			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446		2.37:g.179343206G>T	Exception_encountered		179051452	Q4ZG69|Q86TQ1|Q9NXT3	Missense_Mutation	SNP	ENST00000234453.5	37	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781655	0.31502	.	.	ENSG00000079150	ENST00000424785;ENST00000350591;ENST00000434643	T;T	0.40225	1.04;1.05	5.46	-0.242	0.13039	.	1.643580	0.02938	N	0.140084	T	0.30759	0.0775	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.0	T	0.12967	-1.0527	10	0.21014	T	0.42	-22.9079	7.3479	0.26674	0.2254:0.3327:0.4419:0.0	.	7;7;7	B4DRE2;Q9Y680-3;Q9Y680-2	.;.;.	L	7	ENSP00000413152:F7L;ENSP00000415486:F7L	ENSP00000233092:F7L	F	-	3	2	FKBP7	179051452	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	0.124000	0.15728	0.006000	0.14734	-0.305000	0.09177	TTC		0.507	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		T	179343206	G	T	179343206	1	4	47	0	1	0	0	0	0	0	0	0	5932	933	33	2		2	FKBP7	2	179343206	5'Flank	SNP	G	TCGA-AG-3892-01A-01W-1073-09	104492	179343206	63856167	340	4737										
TTN	7273	broad.mit.edu	37	chr2	179398806	179398806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatttcgtatttctcactgTtctccagctgtcggacgcca	8	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179398806T>C	ENST00000591111.1	-	308	97837	c.97613A>G	c.(97612-97614)aAc>aGc	p.N32538S	TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N34179S|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N25306S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N31611S|TTN_ENST00000460472.2_Missense_Mutation_p.N25114S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N25239S|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32538	Ig-like 143.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.N31609S(1)|p.N25306S(1)|p.N25114S(1)|p.N25239S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCTCACTGTTCTCCAGCTG	0.413																																																4	Substitution - Missense(4)	large_intestine(4)	2											117	113	114					2																	179398806		1956	4149	6105	179107052	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97613A>G	2.37:g.179398806T>C	ENSP00000465570:p.Asn32538Ser		179107052	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.29	1.893212	0.33442	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.39	5.39	0.77823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46756	0.1409	N	0.17345	0.48	0.29734	N	0.837655	B;B;B;B	0.17465	0.022;0.022;0.022;0.022	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.48352	-0.9043	9	0.87932	D	0	.	9.7721	0.40595	0.0:0.0818:0.0:0.9182	.	25114;25239;25306;32538	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	31611;25114;25306;25239;25111	ENSP00000343764:N31611S;ENSP00000434586:N25114S;ENSP00000340554:N25306S;ENSP00000352154:N25239S	ENSP00000340554:N25306S	N	-	2	0	TTN	179107052	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.171000	0.31896	2.175000	0.68902	0.397000	0.26171	AAC		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179398806	T	C	179398806	3	2	47	1	0	0	0	0	1	0	0	0	16775	1725	60	4	5463	4	TTN	2	179398806	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	55600	179398806	63800567	341	4738										
TTN	7273	broad.mit.edu	37	chr2	179425410	179425410	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttctacgatgtaatagtcGatatctgcaccaccatcttc	5	11	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179425410G>A	ENST00000591111.1	-	276	80750	c.80526C>T	c.(80524-80526)atC>atT	p.I26842I	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.I28483I|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Silent_p.I19610I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.I25915I|TTN_ENST00000460472.2_Silent_p.I19418I|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.I19543I			Q8WZ42	TITIN_HUMAN	titin	26842	Fibronectin type-III 95. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.I19543I(1)|p.I25913I(1)|p.I19418I(1)|p.I19610I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTAATAGTCGATATCTGCAC	0.458																																																4	Substitution - coding silent(4)	large_intestine(4)	2											59	58	59					2																	179425410		1958	4154	6112	179133656	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.80526C>T	2.37:g.179425410G>A			179133656	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179425410	G	A	179425410	2	1	47	1	0	0	0	0	0	0	0	1	16775	1048	37	1		1	TTN	2	179425410	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	26604	179425410	63773963	342	4739										
TTN	7273	broad.mit.edu	37	chr2	179427743	179427743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgccttttcccatttaacttCgggttctggtcgacctttga	8	11	1	1	rs72648217		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179427743C>T	ENST00000591111.1	-	276	78417	c.78193G>A	c.(78193-78195)Gaa>Aaa	p.E26065K	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E27706K|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E18833K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E25138K|TTN_ENST00000460472.2_Missense_Mutation_p.E18641K|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E18766K			Q8WZ42	TITIN_HUMAN	titin	26065	Ig-like 126.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E18833K(1)|p.E25136K(1)|p.E18766K(1)|p.E18641K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTTAACTTCGGGTTCTGGT	0.438													C|||	1	0.000199681	0	0	5008	,	,		22967	0		0	False		,,,				2504	0.001															4	Substitution - Missense(4)	large_intestine(4)	2											127	126	127					2																	179427743		1932	4122	6054	179135989	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78193G>A	2.37:g.179427743C>T	ENSP00000465570:p.Glu26065Lys		179135989	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.79	2.937124	0.52972	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	6.04	5.15	0.70609	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57725	0.2073	L	0.37466	1.105	0.49389	D	0.999783	B;B;B;B	0.33841	0.428;0.428;0.428;0.287	B;B;B;B	0.29942	0.109;0.109;0.109;0.076	T	0.61584	-0.7033	9	0.87932	D	0	.	15.7069	0.77592	0.0:0.934:0.0:0.066	.	18641;18766;18833;26065	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	25138;18641;18833;18766;18639	ENSP00000343764:E25138K;ENSP00000434586:E18641K;ENSP00000340554:E18833K;ENSP00000352154:E18766K	ENSP00000340554:E18833K	E	-	1	0	TTN	179135989	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.919000	0.63383	1.540000	0.49301	0.561000	0.74099	GAA		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179427743	C	T	179427743	3	4	47	1	0	0	0	0	1	0	0	0	16775	893	31	1	25011	1	TTN	2	179427743	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2333	179427743	63771630	343	4740										
TTN	7273	broad.mit.edu	37	chr2	179432957	179432957	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctttgtccatatctgttttCggcaaatattctaaattggt	7	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179432957C>T	ENST00000591111.1	-	276	73203	c.72979G>A	c.(72979-72981)Gaa>Aaa	p.E24327K	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E25968K|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E17095K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E23400K|TTN_ENST00000460472.2_Missense_Mutation_p.E16903K|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E17028K			Q8WZ42	TITIN_HUMAN	titin	24327	Fibronectin type-III 76. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E23398K(1)|p.E17028K(1)|p.E17095K(1)|p.E16903K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATCTGTTTTCGGCAAATATT	0.423																																																4	Substitution - Missense(4)	large_intestine(4)	2											147	143	144					2																	179432957		1862	4102	5964	179141203	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72979G>A	2.37:g.179432957C>T	ENSP00000465570:p.Glu24327Lys		179141203	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.20	3.057281	0.55325	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	6.03	6.03	0.97812	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.75824	0.3902	M	0.79258	2.445	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.76623	-0.2891	9	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	16903;17028;17095;24327	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	23400;16903;17095;17028;16901	ENSP00000343764:E23400K;ENSP00000434586:E16903K;ENSP00000340554:E17095K;ENSP00000352154:E17028K	ENSP00000340554:E17095K	E	-	1	0	TTN	179141203	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.041000	0.70988	2.854000	0.98071	0.655000	0.94253	GAA		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179432957	C	T	179432957	3	4	47	1	0	0	0	0	1	0	0	0	16775	893	31	1	30225	1	TTN	2	179432957	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5214	179432957	63766416	344	4741										
TTN	7273	broad.mit.edu	37	chr2	179434246	179434246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccatttaacttctggtgtaGgacgaccttttataggaaca	8	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179434246G>A	ENST00000591111.1	-	276	71914	c.71690C>T	c.(71689-71691)cCt>cTt	p.P23897L	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P25538L|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P16665L|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P22970L|TTN_ENST00000460472.2_Missense_Mutation_p.P16473L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P16598L			Q8WZ42	TITIN_HUMAN	titin	23897	Ig-like 120.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P16598L(1)|p.P16665L(1)|p.P22968L(1)|p.P16473L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGGTGTAGGACGACCTTT	0.403																																																4	Substitution - Missense(4)	large_intestine(4)	2											97	84	88					2																	179434246		1887	4126	6013	179142492	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71690C>T	2.37:g.179434246G>A	ENSP00000465570:p.Pro23897Leu		179142492	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	19.23	3.786793	0.70337	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91774	0.7398	H	0.97340	3.985	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.94317	0.7550	9	0.87932	D	0	.	19.4973	0.95079	0.0:0.0:1.0:0.0	.	16473;16598;16665;23897	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	22970;16473;16665;16598;16471	ENSP00000343764:P22970L;ENSP00000434586:P16473L;ENSP00000340554:P16665L;ENSP00000352154:P16598L	ENSP00000340554:P16665L	P	-	2	0	TTN	179142492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.608000	0.88229	0.655000	0.94253	CCT		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179434246	G	A	179434246	3	1	47	1	0	0	0	0	1	0	0	0	16775	1000	35	3	31514	3	TTN	2	179434246	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1289	179434246	63765127	345	4742										
TTN	7273	broad.mit.edu	37	chr2	179436439	179436439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagttggaggccctggtttgTcaagaacgataacattaagg	12	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179436439T>C	ENST00000591111.1	-	276	69721	c.69497A>G	c.(69496-69498)gAc>gGc	p.D23166G	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D24807G|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D15934G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D22239G|TTN_ENST00000460472.2_Missense_Mutation_p.D15742G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D15867G			Q8WZ42	TITIN_HUMAN	titin	23166					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D22237G(1)|p.D15742G(1)|p.D15867G(1)|p.D15934G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTGGTTTGTCAAGAACGAT	0.448																																																4	Substitution - Missense(4)	large_intestine(4)	2											100	95	97					2																	179436439		1915	4110	6025	179144685	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69497A>G	2.37:g.179436439T>C	ENSP00000465570:p.Asp23166Gly		179144685	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.83	2.355523	0.41700	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.93	5.93	0.95920	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.62134	0.2403	M	0.65677	2.01	0.80722	D	1	P;P;P;P	0.52316	0.952;0.952;0.952;0.952	P;P;P;P	0.49477	0.612;0.612;0.612;0.612	T	0.67059	-0.5766	9	0.87932	D	0	.	16.3709	0.83357	0.0:0.0:0.0:1.0	.	15742;15867;15934;23166	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	22239;15742;15934;15867;15740	ENSP00000343764:D22239G;ENSP00000434586:D15742G;ENSP00000340554:D15934G;ENSP00000352154:D15867G	ENSP00000340554:D15934G	D	-	2	0	TTN	179144685	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.261000	0.74972	0.528000	0.53228	GAC		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179436439	T	C	179436439	3	2	47	1	0	0	0	0	1	0	0	0	16775	1667	58	4	33707	4	TTN	2	179436439	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2193	179436439	63762934	346	4743										
TTN	7273	broad.mit.edu	37	chr2	179596918	179596918	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcagtagactccacaaaaGacattctgtgtttgctgctc	8	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179596918G>T	ENST00000591111.1	-	55	16051	c.15827C>A	c.(15826-15828)tCt>tAt	p.S5276Y	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S5593Y|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.S4349Y|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12094	Ig-like 33.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S4349Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCCACAAAAGACATTCTGTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											174	170	171					2																	179596918		1936	4143	6079	179305163	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.15827C>A	2.37:g.179596918G>T	ENSP00000465570:p.Ser5276Tyr		179305163	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.64	1.699459	0.30142	.	.	ENSG00000155657	ENST00000342992	T	0.68765	-0.35	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.82240	0.4994	M	0.75264	2.295	0.80722	D	1	D	0.67145	0.996	D	0.64877	0.93	T	0.82281	-0.0535	9	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	5276	Q8WZ42	TITIN_HUMAN	Y	4349	ENSP00000343764:S4349Y	ENSP00000343764:S4349Y	S	-	2	0	TTN	179305163	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.602000	0.61098	2.941000	0.99782	0.655000	0.94253	TCT		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179596918	G	T	179596918	3	4	47	1	0	0	0	0	1	0	0	0	16775	942	33	2	87975	2	TTN	2	179596918	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	160479	179596918	63602455	347	4744										
TTN	7273	broad.mit.edu	37	chr2	179604701	179604701	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccaccttttcaatatttCttagccactcagagaaaaga	4	12	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:179604701C>A	ENST00000591111.1	-	46	12532	c.12308G>T	c.(12307-12309)aGa>aTa	p.R4103I	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R4420I|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R4249I|TTN_ENST00000342992.6_Intron|TTN_ENST00000460472.2_Missense_Mutation_p.R4057I|TTN_ENST00000359218.5_Missense_Mutation_p.R4182I|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R4249I(1)|p.R4182I(1)|p.R4057I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCAATATTTCTTAGCCACTC	0.473																																																3	Substitution - Missense(3)	large_intestine(3)	2											93	95	94					2																	179604701		1951	4130	6081	179312946	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12308G>T	2.37:g.179604701C>A	ENSP00000465570:p.Arg4103Ile		179312946	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	8.389	0.839256	0.16891	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.62105	0.11;0.06;0.05	5.56	4.68	0.58851	.	.	.	.	.	T	0.47266	0.1436	L	0.29908	0.895	0.31719	N	0.638484	B;B;B	0.21381	0.055;0.055;0.055	B;B;B	0.18263	0.021;0.021;0.021	T	0.53865	-0.8378	9	0.87932	D	0	.	5.5304	0.16980	0.0:0.6117:0.1594:0.2289	.	4057;4182;4249	D3DPF9;E7EQE6;E7ET18	.;.;.	I	4057;4249;4182;4057	ENSP00000434586:R4057I;ENSP00000340554:R4249I;ENSP00000352154:R4182I	ENSP00000340554:R4249I	R	-	2	0	TTN	179312946	0.338000	0.24775	1.000000	0.80357	0.489000	0.33432	1.718000	0.38001	1.365000	0.46057	-0.150000	0.13652	AGA		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179604701	C	A	179604701	3	1	47	1	0	0	0	0	1	0	0	0	16775	913	32	2	91530	2	TTN	2	179604701	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7783	179604701	63594672	348	4745										
ITGA4	3676	broad.mit.edu	37	chr2	182358103	182358103	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgcaaggtgctatttataTttacaatggccgtgcagatg	10	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:182358103T>G	ENST00000397033.2	+	11	1635	c.1205T>G	c.(1204-1206)aTt>aGt	p.I402S		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	402					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.I402S(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GCTATTTATATTTACAATGGC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	106	109					2																	182358103		1859	4102	5961	182066348	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1205T>G	2.37:g.182358103T>G	ENSP00000380227:p.Ile402Ser		182066348	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.473128	0.84640	.	.	ENSG00000115232	ENST00000425522;ENST00000397033;ENST00000233573	T;T	0.62105	0.05;0.05	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.86331	0.5907	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90928	0.4788	10	0.87932	D	0	.	16.2005	0.82071	0.0:0.0:0.0:1.0	.	402	P13612	ITA4_HUMAN	S	402	ENSP00000380227:I402S;ENSP00000233573:I402S	ENSP00000233573:I402S	I	+	2	0	ITGA4	182066348	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.929000	0.75852	2.227000	0.72691	0.528000	0.53228	ATT		0.348	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			G	182358103	T	G	182358103	3	3	47	1	0	0	0	0	1	0	0	0	7899	1493	52	4	1247	4	ITGA4	2	182358103	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2753402	182358103	60841270	349	4746										
ITGA4	3676	broad.mit.edu	37	chr2	182394329	182394329	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaaataatggtaccaaattCttttagcccccaaactgata	6	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:182394329C>A	ENST00000397033.2	+	23	2922	c.2492C>A	c.(2491-2493)tCt>tAt	p.S831Y		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	831					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.S831Y(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GTACCAAATTCTTTTAGCCCC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	2											101	98	99					2																	182394329		1829	4087	5916	182102574	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2492C>A	2.37:g.182394329C>A	ENSP00000380227:p.Ser831Tyr		182102574	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891237	0.72524	.	.	ENSG00000115232	ENST00000397033	T	0.48201	0.82	5.74	4.84	0.62591	Integrin alpha-2 (1);	0.328980	0.36268	N	0.002684	T	0.57242	0.2040	L	0.51422	1.61	0.40031	D	0.975533	D	0.57257	0.979	P	0.55222	0.771	T	0.63014	-0.6731	10	0.72032	D	0.01	.	15.6347	0.76944	0.1385:0.8615:0.0:0.0	.	831	P13612	ITA4_HUMAN	Y	831	ENSP00000380227:S831Y	ENSP00000380227:S831Y	S	+	2	0	ITGA4	182102574	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	3.964000	0.56780	1.375000	0.46248	0.557000	0.71058	TCT		0.313	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182394329	C	A	182394329	3	1	47	1	0	0	0	0	1	0	0	0	7899	913	32	2	2582	2	ITGA4	2	182394329	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36226	182394329	60805044	350	4747										
DNAJC10	54431	broad.mit.edu	37	chr2	183627513	183627513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaactgttaaattttatttCtacgaaagagcaaaggtatg	7	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:183627513C>A	ENST00000264065.7	+	22	2665	c.2250C>A	c.(2248-2250)ttC>ttA	p.F750L		NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	750	Thioredoxin 4. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)	p.F750L(1)		breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AATTTTATTTCTACGAAAGAG	0.403																																					Pancreas(56;860 1183 25669 35822 48585)											1	Substitution - Missense(1)	large_intestine(1)	2											115	113	114					2																	183627513		2203	4300	6503	183335758	SO:0001583	missense	54431				CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"Heat shock proteins / DNAJ (HSP40)", "Protein disulfide isomerases"	24637	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 19"	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.2250C>A	2.37:g.183627513C>A	ENSP00000264065:p.Phe750Leu		183335758	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Missense_Mutation	SNP	ENST00000264065.7	37	CCDS33345.1	.	.	.	.	.	.	.	.	.	.	C	4.049	0.006813	0.07866	.	.	ENSG00000077232	ENST00000264065;ENST00000392392	T	0.38240	1.15	5.94	-0.341	0.12639	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.651748	0.15485	N	0.259849	T	0.12561	0.0305	N	0.03608	-0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.25710	-1.0124	10	0.09590	T	0.72	.	7.2848	0.26333	0.0:0.4883:0.3212:0.1905	.	704;750	Q8IXB1-2;Q8IXB1	.;DJC10_HUMAN	L	750;704	ENSP00000264065:F750L	ENSP00000264065:F750L	F	+	3	2	DNAJC10	183335758	0.900000	0.30661	0.001000	0.08648	0.368000	0.29767	0.132000	0.15891	-0.368000	0.08040	0.563000	0.77884	TTC		0.403	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981		A	183627513	C	A	183627513	3	1	47	1	0	0	0	0	1	0	0	0	4640	912	32	2	2328	2	DNAJC10	2	183627513	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1233184	183627513	59571860	351	4748										
ZC3H15	55854	broad.mit.edu	37	chr2	187370221	187370221	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taccaaaatcactctagaatCttttcttgcctggaagaaaa	5	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:187370221C>A	ENST00000337859.6	+	7	988	c.761C>A	c.(760-762)tCt>tAt	p.S254Y	AC018867.2_ENST00000595956.1_5'Flank|ZC3H15_ENST00000544130.1_Missense_Mutation_p.S49Y	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	254	Required for interaction with DRG1. {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S254Y(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			ACTCTAGAATCTTTTCTTGCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	80	80					2																	187370221		1834	4087	5921	187078466	SO:0001583	missense	55854				CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"Zinc fingers, CCCH-type domain containing"	29528	protein-coding gene	gene with protein product	"likely ortholog of mouse immediate early response, erythropoietin 4"					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.761C>A	2.37:g.187370221C>A	ENSP00000338788:p.Ser254Tyr		187078466	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	37	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.624194	0.87560	.	.	ENSG00000065548	ENST00000337859;ENST00000544130;ENST00000536434	T	0.33654	1.4	6.17	6.17	0.99709	.	0.145747	0.64402	D	0.000006	T	0.52386	0.1731	M	0.83603	2.65	0.53005	D	0.999969	D	0.56521	0.976	P	0.48030	0.564	T	0.59434	-0.7455	10	0.87932	D	0	-11.0559	17.262	0.87072	0.0:0.8668:0.1332:0.0	.	254	Q8WU90	ZC3HF_HUMAN	Y	254;49;254	ENSP00000338788:S254Y	ENSP00000338788:S254Y	S	+	2	0	ZC3H15	187078466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.750000	0.68712	2.941000	0.99782	0.655000	0.94253	TCT		0.368	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		A	187370221	C	A	187370221	3	1	47	1	0	0	0	0	1	0	0	0	17606	913	32	2	787	2	ZC3H15	2	187370221	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3742708	187370221	55829152	352	4749										
ZC3H15	55854	broad.mit.edu	37	chr2	187370494	187370494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcgtgaagtgtttgaatttCgtcctgaactggtcaatgat	11	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:187370494C>T	ENST00000337859.6	+	8	1119	c.892C>T	c.(892-894)Cgt>Tgt	p.R298C	ZC3H15_ENST00000544130.1_Missense_Mutation_p.R93C	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	298					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R298C(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			GTTTGAATTTCGTCCTGAACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											141	132	135					2																	187370494		1984	4163	6147	187078739	SO:0001583	missense	55854				CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"Zinc fingers, CCCH-type domain containing"	29528	protein-coding gene	gene with protein product	"likely ortholog of mouse immediate early response, erythropoietin 4"					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.892C>T	2.37:g.187370494C>T	ENSP00000338788:p.Arg298Cys		187078739	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	37	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513987	0.64522	.	.	ENSG00000065548	ENST00000337859;ENST00000544130;ENST00000536434	T	0.32988	1.43	6.17	5.29	0.74685	.	0.209823	0.51477	D	0.000088	T	0.32346	0.0826	L	0.55990	1.75	0.80722	D	1	B	0.18610	0.029	B	0.10450	0.005	T	0.05305	-1.0893	10	0.54805	T	0.06	-0.5749	15.9972	0.80260	0.0:0.935:0.0:0.065	.	298	Q8WU90	ZC3HF_HUMAN	C	298;93;298	ENSP00000338788:R298C	ENSP00000338788:R298C	R	+	1	0	ZC3H15	187078739	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.781000	0.55394	2.941000	0.99782	0.655000	0.94253	CGT		0.418	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		T	187370494	C	T	187370494	3	4	47	1	0	0	0	0	1	0	0	0	17606	884	31	1	922	1	ZC3H15	2	187370494	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	273	187370494	55828879	353	4750										
ZSWIM2	151112	broad.mit.edu	37	chr2	187693200	187693200	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaattatctaatttgatagaGcatagattatctattgttgt	7	3	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:187693200G>T	ENST00000295131.2	-	9	1452	c.1413C>A	c.(1411-1413)tgC>tgA	p.C471*		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	471					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C471*(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATTTGATAGAGCATAGATTAT	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											42	49	47					2																	187693200		2200	4298	6498	187401445	SO:0001587	stop_gained	151112			AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1413C>A	2.37:g.187693200G>T	ENSP00000295131:p.Cys471*		187401445	B3KXV6|Q53SI3|Q57ZY3	Nonsense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335014	0.41398	.	.	ENSG00000163012	ENST00000295131	.	.	.	5.6	2.55	0.30701	.	1.204280	0.05816	N	0.614780	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.4896	8.2208	0.31541	0.0855:0.2903:0.6241:0.0	.	.	.	.	X	471	.	ENSP00000295131:C471X	C	-	3	2	ZSWIM2	187401445	0.000000	0.05858	0.053000	0.19242	0.228000	0.25075	-0.104000	0.10923	0.214000	0.20742	0.591000	0.81541	TGC		0.299	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		T	187693200	G	T	187693200	4	4	47	1	0	0	0	0	0	1	0	0	18280	963	34	2	492	2	ZSWIM2	2	187693200	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	322706	187693200	55506173	354	4751										
TFPI	7035	broad.mit.edu	37	chr2	188368393	188368393	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctgtgataattgtgtgttCttcatcttcctcagaatcag	7	9	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:188368393C>A	ENST00000233156.3	-	2	397	c.103G>T	c.(103-105)Gaa>Taa	p.E35*	AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000339091.4_Nonsense_Mutation_p.E35*|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000409676.1_Nonsense_Mutation_p.E35*|TFPI_ENST00000392365.1_Nonsense_Mutation_p.E35*	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	35					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E35*(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	ATTGTGTGTTCTTCATCTTCC	0.348																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											114	119	117					2																	188368393		2203	4300	6503	188076638	SO:0001587	stop_gained	7035				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.103G>T	2.37:g.188368393C>A	ENSP00000233156:p.Glu35*		188076638	O95103|Q53TS4	Nonsense_Mutation	SNP	ENST00000233156.3	37	CCDS2294.1	.	.	.	.	.	.	.	.	.	.	C	37	6.146342	0.97324	.	.	ENSG00000003436	ENST00000392365;ENST00000233156;ENST00000426055;ENST00000435414;ENST00000409676;ENST00000339091;ENST00000437725;ENST00000421427;ENST00000453013;ENST00000417013;ENST00000420747	.	.	.	5.31	4.42	0.53409	.	0.286853	0.27411	N	0.019490	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	11.727	0.51714	0.0:0.8225:0.1775:0.0	.	.	.	.	X	35	.	ENSP00000233156:E35X	E	-	1	0	TFPI	188076638	0.349000	0.24870	0.360000	0.25837	0.467000	0.32768	1.190000	0.32126	1.442000	0.47568	0.655000	0.94253	GAA		0.348	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		A	188368393	C	A	188368393	4	1	47	1	0	0	0	0	0	1	0	0	15847	922	32	2	971	2	TFPI	2	188368393	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	675193	188368393	54830980	355	4752										
GULP1	51454	broad.mit.edu	37	chr2	189452663	189452663	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccagatattcaatcaaaatTagatgagatgcaggtgacta	8	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:189452663T>G	ENST00000409580.1	+	12	1544	c.830T>G	c.(829-831)tTa>tGa	p.L277*	GULP1_ENST00000409830.1_Nonsense_Mutation_p.L277*|GULP1_ENST00000359135.3_Nonsense_Mutation_p.L277*|GULP1_ENST00000409843.1_Nonsense_Mutation_p.L277*|GULP1_ENST00000409609.1_Nonsense_Mutation_p.L277*|GULP1_ENST00000409805.1_Nonsense_Mutation_p.L174*			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	277					apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)	p.L277*(1)		endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CAATCAAAATTAGATGAGATG	0.373																																					Pancreas(178;563 2065 20199 42378 52815)											1	Substitution - Nonsense(1)	large_intestine(1)	2											78	78	78					2																	189452663		2203	4300	6503	189160908	SO:0001587	stop_gained	51454			AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.830T>G	2.37:g.189452663T>G	ENSP00000386289:p.Leu277*		189160908	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Nonsense_Mutation	SNP	ENST00000409580.1	37	CCDS2295.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.6|25.6	4.658325|4.658325	0.88154|0.88154	.|.	.|.	ENSG00000144366|ENSG00000144366	ENST00000409843;ENST00000409830;ENST00000409805;ENST00000359135;ENST00000409580;ENST00000409609|ENST00000451191;ENST00000433052	.|.	.|.	.|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.182079|.	0.38326|.	N|.	0.001735|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	-7.0442|-7.0442	15.2228|15.2228	0.73327|0.73327	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|E	277;277;174;277;277;277|102;162	.|.	ENSP00000352047:L277X|.	L|X	+|+	2|1	0|0	GULP1|GULP1	189160908|189160908	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.698000|7.698000	0.84413|0.84413	2.198000|2.198000	0.70561|0.70561	0.482000|0.482000	0.46254|0.46254	TTA|TAG		0.373	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		G	189452663	T	G	189452663	4	3	47	1	0	0	0	0	0	1	0	0	6922	1764	61	4	864	4	GULP1	2	189452663	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1084270	189452663	53746710	356	4753										
COL3A1	1281	broad.mit.edu	37	chr2	189854843	189854843	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaatcaggtagacccggaCgacctggagagcgaggattg	16	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:189854843C>T	ENST00000304636.3	+	9	882	c.712C>T	c.(712-714)Cga>Tga	p.R238*	COL3A1_ENST00000317840.5_Nonsense_Mutation_p.R238*	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	238	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.R238*(1)		NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TAGACCCGGACGACCTGGAGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											71	73	72					2																	189854843		2203	4300	6503	189563088	SO:0001587	stop_gained	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.712C>T	2.37:g.189854843C>T	ENSP00000304408:p.Arg238*		189563088	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Nonsense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	C	37	6.349121	0.97494	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	.	.	.	5.68	2.7	0.31948	.	0.000000	0.42420	D	0.000707	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	15.3924	0.74755	0.6901:0.3099:0.0:0.0	.	.	.	.	X	238	.	ENSP00000304408:R238X	R	+	1	2	COL3A1	189563088	0.432000	0.25554	0.966000	0.40874	0.935000	0.57460	1.056000	0.30480	0.328000	0.23435	0.591000	0.81541	CGA		0.383	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189854843	C	T	189854843	4	4	47	1	0	0	0	0	0	1	0	0	3694	528	19	1	746	1	COL3A1	2	189854843	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	402180	189854843	53344530	357	4754										
MYO1B	4430	broad.mit.edu	37	chr2	192234334	192234334	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttttcatggttggtaaatCgaatcaatgaaagcattaag	9	4	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:192234334C>T	ENST00000392318.3	+	12	1346	c.1099C>T	c.(1099-1101)Cga>Tga	p.R367*	RNU6-1045P_ENST00000516321.1_RNA|MYO1B_ENST00000339514.4_Nonsense_Mutation_p.R367*|MYO1B_ENST00000392316.1_Nonsense_Mutation_p.R367*|MYO1B_ENST00000304164.4_Nonsense_Mutation_p.R367*	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	367	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R367*(2)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GTTGGTAAATCGAATCAATGA	0.318																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											73	73	73					2																	192234334		2203	4300	6503	191942579	SO:0001587	stop_gained	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.1099C>T	2.37:g.192234334C>T	ENSP00000376132:p.Arg367*		191942579	O43794|Q7Z6L5	Nonsense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	37	6.255787	0.97417	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2594	0.54642	0.2139:0.7861:0.0:0.0	.	.	.	.	X	367	.	ENSP00000306382:R367X	R	+	1	2	MYO1B	191942579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.934000	0.48956	2.565000	0.86533	0.655000	0.94253	CGA		0.318	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		T	192234334	C	T	192234334	4	4	47	1	0	0	0	0	0	1	0	0	10099	876	31	1	1141	1	MYO1B	2	192234334	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2379491	192234334	50965039	358	4755										
SDPR	8436	broad.mit.edu	37	chr2	192701020	192701020	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcatggctttctccctctcGgactttcttccgcccgaaag	8	15	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:192701020G>A	ENST00000304141.4	-	2	1236	c.907C>T	c.(907-909)Cga>Tga	p.R303*		NM_004657.5	NP_004648.1			serum deprivation response									p.R303*(1)		NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			TCTCCCTCTCGGACTTTCTTC	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											100	109	106					2																	192701020		2203	4300	6503	192409265	SO:0001587	stop_gained	8436			AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.907C>T	2.37:g.192701020G>A	ENSP00000305675:p.Arg303*		192409265		Nonsense_Mutation	SNP	ENST00000304141.4	37	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	G	36	5.612045	0.96637	.	.	ENSG00000168497	ENST00000304141	.	.	.	5.01	4.12	0.48240	.	0.389998	0.26586	N	0.023550	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.8234	14.7254	0.69341	0.0:0.0:0.8542:0.1458	.	.	.	.	X	303	.	ENSP00000305675:R303X	R	-	1	2	SDPR	192409265	0.991000	0.36638	0.999000	0.59377	0.080000	0.17528	3.592000	0.53993	1.317000	0.45149	0.563000	0.77884	CGA		0.488	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		A	192701020	G	A	192701020	4	1	47	1	0	0	0	0	0	1	0	0	14007	1124	39	1	374	1	SDPR	2	192701020	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	466686	192701020	50498353	359	4756										
DNAH7	56171	broad.mit.edu	37	chr2	196605508	196605508	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accacaggcactgtatcataAagaattttgggatgcgattc	9	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:196605508A>C	ENST00000312428.6	-	64	11950	c.11850T>G	c.(11848-11850)ctT>ctG	p.L3950L	DNAH7_ENST00000484183.1_5'UTR|DNAH7_ENST00000409063.1_Silent_p.L433L	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3950					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.L3950L(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTGTATCATAAAGAATTTTGG	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	2											94	89	91					2																	196605508		1787	4066	5853	196313753	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11850T>G	2.37:g.196605508A>C			196313753	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	8.775	0.926948	0.18056	.	.	ENSG00000118997	ENST00000438565	.	.	.	4.83	-2.41	0.06562	.	.	.	.	.	T	0.58708	0.2141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61720	-0.7005	5	0.87932	D	0	.	6.4786	0.22049	0.4817:0.3683:0.15:0.0	.	.	.	.	C	51	.	ENSP00000409732:F51C	F	-	2	0	DNAH7	196313753	0.984000	0.35163	0.997000	0.53966	0.978000	0.69477	0.122000	0.15687	-0.149000	0.11215	-0.263000	0.10527	TTT		0.284	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196605508	A	C	196605508	2	2	47	1	0	0	0	0	0	0	0	1	4617	1	1	4		4	DNAH7	2	196605508	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3904488	196605508	46593865	360	4757										
DNAH7	56171	broad.mit.edu	37	chr2	196636561	196636561	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcccaagatgtcactagcGacctcattcactacttcatc	5	14	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:196636561G>A	ENST00000312428.6	-	61	11356	c.11256C>T	c.(11254-11256)gtC>gtT	p.V3752V	DNAH7_ENST00000409063.1_Silent_p.V235V	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3752					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.V3752V(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TGTCACTAGCGACCTCATTCA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	2											246	221	229					2																	196636561		1985	4159	6144	196344806	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11256C>T	2.37:g.196636561G>A			196344806	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.428	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196636561	G	A	196636561	2	1	47	1	0	0	0	0	0	0	0	1	4617	1045	37	1		1	DNAH7	2	196636561	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	31053	196636561	46562812	361	4758										
HECW2	57520	broad.mit.edu	37	chr2	197080630	197080630	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccccatttctccacacagaaTcttcttgggccgttactccc	5	17	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:197080630T>G	ENST00000260983.3	-	28	4748	c.4566A>C	c.(4564-4566)agA>agC	p.R1522S	HECW2_ENST00000409111.1_Missense_Mutation_p.R1166S|snoU13_ENST00000459047.1_RNA	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1522	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1522S(1)		biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						CCACACAGAATCTTCTTGGGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	81	82					2																	197080630		2203	4300	6503	196788875	SO:0001583	missense	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4566A>C	2.37:g.197080630T>G	ENSP00000260983:p.Arg1522Ser		196788875	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.687426	0.68157	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.57595	0.39;0.39	5.35	-0.906	0.10524	HECT (4);	0.000000	0.85682	D	0.000000	T	0.61426	0.2346	L	0.58583	1.82	0.58432	D	0.999992	D	0.69078	0.997	D	0.80764	0.994	T	0.58702	-0.7590	10	0.66056	D	0.02	.	7.923	0.29857	0.0:0.392:0.1145:0.4936	.	1522	Q9P2P5	HECW2_HUMAN	S	1166;1522	ENSP00000386775:R1166S;ENSP00000260983:R1522S	ENSP00000260983:R1522S	R	-	3	2	HECW2	196788875	0.111000	0.22076	0.993000	0.49108	0.994000	0.84299	-0.650000	0.05378	-0.292000	0.08999	-0.250000	0.11733	AGA		0.413	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		G	197080630	T	G	197080630	3	3	47	1	0	0	0	0	1	0	0	0	7064	1432	50	4	160	4	HECW2	2	197080630	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	444069	197080630	46118743	362	4759										
GTF3C3	9330	broad.mit.edu	37	chr2	197645342	197645342	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcaacttcactgtgatatCtattggcacgccatcaggta	7	11	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:197645342C>A	ENST00000263956.3	-	9	1248	c.1159G>T	c.(1159-1161)Gat>Tat	p.D387Y	GTF3C3_ENST00000409364.3_Missense_Mutation_p.D387Y	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	387					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.D387Y(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ACTGTGATATCTATTGGCACG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											161	136	145					2																	197645342		2203	4300	6503	197353587	SO:0001583	missense	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1159G>T	2.37:g.197645342C>A	ENSP00000263956:p.Asp387Tyr		197353587	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234456	0.79800	.	.	ENSG00000119041	ENST00000263956;ENST00000448087;ENST00000409364	T;T	0.60672	0.43;0.17	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.76730	0.4028	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	T	0.78091	-0.2339	10	0.87932	D	0	-29.7859	19.3887	0.94570	0.0:1.0:0.0:0.0	.	387;387	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	Y	387;72;387	ENSP00000263956:D387Y;ENSP00000386465:D387Y	ENSP00000263956:D387Y	D	-	1	0	GTF3C3	197353587	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	6.726000	0.74758	2.826000	0.97356	0.655000	0.94253	GAT		0.398	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			A	197645342	C	A	197645342	3	1	47	1	0	0	0	0	1	0	0	0	6895	913	32	2	1541	2	GTF3C3	2	197645342	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	564712	197645342	45554031	363	4760										
SF3B1	23451	broad.mit.edu	37	chr2	198272801	198272801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcaatttctctttcccacCgccaagcctgaagctgttca	5	15	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:198272801C>T	ENST00000335508.6	-	9	1251	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	387	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.R387Q(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TCTTTCCCACCGCCAAGCCTG	0.363			Mis		myelodysplastic syndrome																																		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	1	Substitution - Missense(1)	large_intestine(1)	2											77	74	75					2																	198272801		2203	4300	6503	197981046	SO:0001583	missense	23451			AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1160G>A	2.37:g.198272801C>T	ENSP00000335321:p.Arg387Gln		197981046	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834903	0.91036	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.69	5.69	0.88448	Splicing factor 3B subunit 1 (1);	0.000000	0.85682	D	0.000000	T	0.66297	0.2775	M	0.81239	2.535	0.80722	D	1	P	0.42039	0.769	B	0.36186	0.219	T	0.72394	-0.4307	9	0.54805	T	0.06	.	19.8199	0.96589	0.0:1.0:0.0:0.0	.	387	O75533	SF3B1_HUMAN	Q	387	.	ENSP00000335321:R387Q	R	-	2	0	SF3B1	197981046	1.000000	0.71417	0.976000	0.42696	0.974000	0.67602	7.683000	0.84093	2.677000	0.91161	0.655000	0.94253	CGG		0.363	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198272801	C	T	198272801	3	4	47	1	0	0	0	0	1	0	0	0	14186	652	23	1	2822	1	SF3B1	2	198272801	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	627459	198272801	44926572	364	4761										
MARS2	92935	broad.mit.edu	37	chr2	198571048	198571048	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtggccggccacctctcatAtcataggtaaggacattctc	10	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:198571048A>C	ENST00000282276.6	+	1	962	c.919A>C	c.(919-921)Atc>Ctc	p.I307L	AC011997.1_ENST00000409845.1_Intron	NM_138395.3	NP_612404.1	Q96GW9	SYMM_HUMAN	methionyl-tRNA synthetase 2, mitochondrial	307					cell death (GO:0008219)|gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)	p.I307L(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	22					L-Methionine(DB00134)	CACCTCTCATATCATAGGTAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											83	87	86					2																	198571048		2203	4300	6503	198279293	SO:0001583	missense	92935			BC009115	CCDS33358.1	2q33.1	2014-01-30	2007-02-26		ENSG00000247626	ENSG00000247626	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	25133	protein-coding gene	gene with protein product	"methionine tRNA ligase 2, mitochondrial"	609728				15274629	Standard	NM_138395		Approved	mtMetRS, SPAX3	uc002uuq.3	Q96GW9	OTTHUMG00000154487	ENST00000282276.6:c.919A>C	2.37:g.198571048A>C	ENSP00000282276:p.Ile307Leu		198279293	A0AVC3|Q76E79|Q8IW62|Q8N7N4	Missense_Mutation	SNP	ENST00000282276.6	37	CCDS33358.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.691691	0.30052	.	.	ENSG00000247626	ENST00000282276;ENST00000499940	T	0.42900	0.96	5.26	1.66	0.24008	Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.293824	0.35936	N	0.002898	T	0.17662	0.0424	N	0.11341	0.13	0.35933	D	0.832633	B	0.24186	0.099	B	0.31869	0.137	T	0.26224	-1.0109	10	0.02654	T	1	-12.303	4.0374	0.09735	0.5463:0.1773:0.2763:0.0	.	307	Q96GW9	SYMM_HUMAN	L	307;234	ENSP00000282276:I307L	ENSP00000282276:I307L	I	+	1	0	MARS2	198279293	0.027000	0.19231	0.984000	0.44739	0.997000	0.91878	0.248000	0.18198	0.340000	0.23745	0.533000	0.62120	ATC		0.522	MARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335477.1	NM_138395		C	198571048	A	C	198571048	3	2	47	1	0	0	0	0	1	0	0	0	9347	449	16	4	921	4	MARS2	2	198571048	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	298247	198571048	44628325	365	4762										
PLCL1	5334	broad.mit.edu	37	chr2	198950155	198950155	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttaattataataagaagttCttatcaagaatctatccaag	5	5	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:198950155C>A	ENST00000428675.1	+	2	2312	c.1914C>A	c.(1912-1914)ttC>ttA	p.F638L	PLCL1_ENST00000437704.2_Missense_Mutation_p.F540L	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	638	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.F540L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	ATAAGAAGTTCTTATCAAGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											36	39	38					2																	198950155		2202	4300	6502	198658400	SO:0001583	missense	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1914C>A	2.37:g.198950155C>A	ENSP00000402861:p.Phe638Leu		198658400	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	C	13.33	2.203532	0.38905	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.51574	0.7;0.7	5.36	3.58	0.41010	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.64402	D	0.000001	T	0.54464	0.1860	M	0.79926	2.475	0.44595	D	0.997568	P;P	0.51933	0.949;0.949	P;P	0.50537	0.643;0.643	T	0.55186	-0.8180	9	.	.	.	.	6.1788	0.20459	0.0:0.6114:0.0:0.3886	.	638;564	Q15111;B4DYZ4	PLCL1_HUMAN;.	L	638;540	ENSP00000402861:F638L;ENSP00000414138:F540L	.	F	+	3	2	PLCL1	198658400	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.177000	0.31969	0.838000	0.34948	0.561000	0.74099	TTC		0.378	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198950155	C	A	198950155	3	1	47	1	0	0	0	0	1	0	0	0	12070	912	32	2	1920	2	PLCL1	2	198950155	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	379107	198950155	44249218	366	4763										
C2orf69	205327	broad.mit.edu	37	chr2	200790404	200790404	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacttatccagaagtcttgaAagaatttgcacaaacaggaa	7	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:200790404A>C	ENST00000319974.5	+	2	1136	c.953A>C	c.(952-954)aAa>aCa	p.K318T	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	318						extracellular region (GO:0005576)		p.K318T(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						GAAGTCTTGAAAGAATTTGCA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	104	106					2																	200790404		1886	4113	5999	200498649	SO:0001583	missense	205327				CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"hypothetical protein FLJ38973"					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.953A>C	2.37:g.200790404A>C	ENSP00000312770:p.Lys318Thr		200498649	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	37	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124774	0.56613	.	.	ENSG00000178074	ENST00000319974	.	.	.	5.63	4.49	0.54785	.	0.278401	0.41500	D	0.000873	T	0.63070	0.2480	L	0.53249	1.67	0.39030	D	0.959916	D	0.54772	0.968	P	0.55303	0.773	T	0.67795	-0.5578	9	0.59425	D	0.04	-8.7272	10.2873	0.43575	0.9233:0.0:0.0767:0.0	.	318	Q8N8R5	CB069_HUMAN	T	318	.	ENSP00000312770:K318T	K	+	2	0	C2orf69	200498649	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.246000	0.51414	2.130000	0.65690	0.533000	0.62120	AAA		0.378	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689		C	200790404	A	C	200790404	3	2	47	1	0	0	0	0	1	0	0	0	2194	14	1	4	959	4	C2orf69	2	200790404	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1840249	200790404	42408969	367	4764										
SGOL2	151246	broad.mit.edu	37	chr2	201434543	201434543	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggaagtgttatttcttaaaGaaaataatcaaaatgtatat	6	3	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:201434543G>T	ENST00000357799.4	+	6	729	c.631G>T	c.(631-633)Gaa>Taa	p.E211*	SGOL2_ENST00000409203.3_Nonsense_Mutation_p.E211*	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	211					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.E211*(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						ATTTCTTAAAGAAAATAATCA	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											97	97	97					2																	201434543		1806	4064	5870	201142788	SO:0001587	stop_gained	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.631G>T	2.37:g.201434543G>T	ENSP00000350447:p.Glu211*		201142788	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Nonsense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018160	0.35606	.	.	ENSG00000163535	ENST00000357799;ENST00000409203	.	.	.	5.31	4.35	0.52113	.	0.089608	0.49305	D	0.000159	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-25.8304	8.0144	0.30372	0.1107:0.0:0.8893:0.0	.	.	.	.	X	211	.	ENSP00000350447:E211X	E	+	1	0	SGOL2	201142788	0.995000	0.38212	1.000000	0.80357	0.250000	0.25880	1.890000	0.39728	2.747000	0.94245	0.585000	0.79938	GAA		0.299	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		T	201434543	G	T	201434543	4	4	47	1	0	0	0	0	0	1	0	0	14254	943	33	2	649	2	SGOL2	2	201434543	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	644139	201434543	41764830	368	4765										
INO80D	54891	broad.mit.edu	37	chr2	206869647	206869647	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgttgtgtggggagaggtGatatggtcactgtagggaga	19	2	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:206869647G>T	ENST00000403263.1	-	11	2933	c.2529C>A	c.(2527-2529)atC>atA	p.I843I	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	843					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.I843I(1)|p.I738I(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						GGGGAGAGGTGATATGGTCAC	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	2											224	210	215					2																	206869647		2135	4250	6385	206577892	SO:0001819	synonymous_variant	54891				CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"INO80 complex subunits"	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.2529C>A	2.37:g.206869647G>T			206577892	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																				0.512	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		T	206869647	G	T	206869647	2	4	47	1	0	0	0	0	0	0	0	1	7770	1280	45	2		2	INO80D	2	206869647	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5435104	206869647	36329726	369	4766										
DYTN	391475	broad.mit.edu	37	chr2	207564577	207564577	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggctcagattggacccaaGacaggaatttttcttctttg	10	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:207564577G>T	ENST00000452335.2	-	7	709	c.593C>A	c.(592-594)tCt>tAt	p.S198Y	DYTN_ENST00000477734.1_5'UTR|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	198						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.S198Y(2)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		TTGGACCCAAGACAGGAATTT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	2											78	81	80					2																	207564577		1905	4136	6041	207272822	SO:0001583	missense	391475			ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.593C>A	2.37:g.207564577G>T	ENSP00000396593:p.Ser198Tyr		207272822		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.824085	0.50739	.	.	ENSG00000232125	ENST00000452335	T	0.73575	-0.76	5.89	3.07	0.35406	EF-hand domain, type 2 (1);	.	.	.	.	T	0.79592	0.4472	L	0.42245	1.32	0.09310	N	1	D	0.89917	1.0	D	0.76071	0.987	T	0.66952	-0.5793	9	0.59425	D	0.04	-2.8466	9.4343	0.38628	0.0744:0.307:0.6186:0.0	.	198	A2CJ06	DYTN_HUMAN	Y	198	ENSP00000396593:S198Y	ENSP00000396593:S198Y	S	-	2	0	DYTN	207272822	0.950000	0.32346	0.038000	0.18304	0.693000	0.40251	1.894000	0.39768	0.795000	0.33922	0.561000	0.74099	TCT		0.483	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			T	207564577	G	T	207564577	3	4	47	1	0	0	0	0	1	0	0	0	4872	942	33	2	1167	2	DYTN	2	207564577	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	694930	207564577	35634796	370	4767										
PIKFYVE	200576	broad.mit.edu	37	chr2	209153536	209153536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctgggaaatctcctgctcGaaataggtaaactgacaaat	9	8	1	1	rs187383957	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:209153536G>A	ENST00000264380.4	+	7	1063	c.905G>A	c.(904-906)cGa>cAa	p.R302Q	PIKFYVE_ENST00000308862.6_Missense_Mutation_p.R216Q|PIKFYVE_ENST00000392202.3_Missense_Mutation_p.R205Q|PIKFYVE_ENST00000407449.1_Missense_Mutation_p.R302Q	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	302					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R302Q(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TCTCCTGCTCGAAATAGGTAA	0.363													G|||	5	0.000998403	0	0.0072	5008	,	,		18877	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											83	83	83					2																	209153536		2203	4300	6503	208861781	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.905G>A	2.37:g.209153536G>A	ENSP00000264380:p.Arg302Gln		208861781	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	36	5.747155	0.96882	.	.	ENSG00000115020	ENST00000392202;ENST00000264380;ENST00000407449;ENST00000308862;ENST00000452564	T;T;T	0.68181	1.47;-0.31;1.6	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000005	T	0.71634	0.3363	N	0.24115	0.695	0.58432	D	0.999991	D;D;D;D;D	0.76494	0.999;0.999;0.998;0.994;0.997	D;D;D;P;D	0.75484	0.978;0.978;0.986;0.885;0.964	T	0.63449	-0.6635	10	0.12766	T	0.61	-10.4276	20.6208	0.99490	0.0:0.0:1.0:0.0	.	302;302;216;302;205	Q9Y2I7;E9PDH4;Q9Y2I7-3;Q08AR7;Q9Y2I7-2	FYV1_HUMAN;.;.;.;.	Q	205;302;302;216;302	ENSP00000264380:R302Q;ENSP00000384356:R302Q;ENSP00000405736:R302Q	ENSP00000264380:R302Q	R	+	2	0	PIKFYVE	208861781	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.164000	0.89661	2.882000	0.98803	0.655000	0.94253	CGA		0.363	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		A	209153536	G	A	209153536	3	1	47	1	0	0	0	0	1	0	0	0	11955	1058	37	1	927	1	PIKFYVE	2	209153536	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1588959	209153536	34045837	371	4768										
PIKFYVE	200576	broad.mit.edu	37	chr2	209179025	209179025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atattgtacttagaatccttAtttaatcgccgagtagagga	8	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:209179025A>C	ENST00000264380.4	+	14	1862	c.1704A>C	c.(1702-1704)ttA>ttC	p.L568F		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	568					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.L568F(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TAGAATCCTTATTTAATCGCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	75	72					2																	209179025		2203	4300	6503	208887270	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.1704A>C	2.37:g.209179025A>C	ENSP00000264380:p.Leu568Phe		208887270	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.747745	0.69533	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.35421	1.31;1.54	5.6	1.76	0.24704	.	0.000000	0.64402	D	0.000016	T	0.35364	0.0929	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.19128	-1.0315	10	0.19590	T	0.45	-10.8717	4.9937	0.14228	0.6335:0.145:0.2215:0.0	.	568;512	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	F	568;144;512	ENSP00000264380:L568F;ENSP00000405736:L512F	ENSP00000264380:L568F	L	+	3	2	PIKFYVE	208887270	0.998000	0.40836	1.000000	0.80357	0.977000	0.68977	0.581000	0.23819	0.418000	0.25898	0.528000	0.53228	TTA		0.373	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		C	209179025	A	C	209179025	3	2	47	1	0	0	0	0	1	0	0	0	11955	446	16	4	1765	4	PIKFYVE	2	209179025	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	25489	209179025	34020348	372	4769										
MAP2	4133	broad.mit.edu	37	chr2	210558312	210558312	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatgaagaaataggcataaTtcagacctccacagagcaca	8	9	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:210558312T>G	ENST00000360351.4	+	7	1924	c.1418T>G	c.(1417-1419)aTt>aGt	p.I473S	MAP2_ENST00000447185.1_Missense_Mutation_p.I469S|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	473					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.I473S(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	ATAGGCATAATTCAGACCTCC	0.438																																					Pancreas(27;423 979 28787 29963)											1	Substitution - Missense(1)	large_intestine(1)	2											56	58	57					2																	210558312		2203	4299	6502	210266557	SO:0001583	missense	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1418T>G	2.37:g.210558312T>G	ENSP00000353508:p.Ile473Ser		210266557	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	T	5.342	0.248431	0.10130	.	.	ENSG00000078018	ENST00000360351;ENST00000445941;ENST00000447185	T;T;T	0.25579	1.79;1.79;1.79	6.16	2.29	0.28610	MAP2/Tau projection (1);	0.738078	0.12909	N	0.429081	T	0.19927	0.0479	L	0.51422	1.61	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.12837	0.004;0.008	T	0.34179	-0.9839	10	0.66056	D	0.02	-0.3192	1.3829	0.02234	0.127:0.2427:0.1476:0.4828	.	469;473	P11137-3;P11137	.;MAP2_HUMAN	S	473;555;469	ENSP00000353508:I473S;ENSP00000409969:I555S;ENSP00000392164:I469S	ENSP00000353508:I473S	I	+	2	0	MAP2	210266557	0.001000	0.12720	0.062000	0.19696	0.780000	0.44128	0.256000	0.18351	0.479000	0.27511	0.528000	0.53228	ATT		0.438	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210558312	T	G	210558312	3	3	47	1	0	0	0	0	1	0	0	0	9265	1493	52	4	1432	4	MAP2	2	210558312	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1379287	210558312	32641061	373	4770										
MAP2	4133	broad.mit.edu	37	chr2	210558484	210558484	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccatctgcattaattgaaaaGagctcaattcaggaactttt	6	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:210558484G>T	ENST00000360351.4	+	7	2096	c.1590G>T	c.(1588-1590)aaG>aaT	p.K530N	MAP2_ENST00000447185.1_Missense_Mutation_p.K526N|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	530					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.K530N(3)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TAATTGAAAAGAGCTCAATTC	0.408																																					Pancreas(27;423 979 28787 29963)											3	Substitution - Missense(3)	large_intestine(2)|breast(1)	2											88	88	88					2																	210558484		2203	4300	6503	210266729	SO:0001583	missense	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1590G>T	2.37:g.210558484G>T	ENSP00000353508:p.Lys530Asn		210266729	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	G	9.829	1.187961	0.21954	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.22539	1.95;1.95	6.16	4.32	0.51571	MAP2/Tau projection (1);	0.175469	0.40302	N	0.001127	T	0.30759	0.0775	L	0.56769	1.78	0.21841	N	0.999519	P;P	0.51147	0.928;0.942	P;P	0.52386	0.572;0.697	T	0.11991	-1.0565	10	0.87932	D	0	-15.9978	8.8039	0.34925	0.2349:0.0:0.7651:0.0	.	526;530	P11137-3;P11137	.;MAP2_HUMAN	N	530;526	ENSP00000353508:K530N;ENSP00000392164:K526N	ENSP00000353508:K530N	K	+	3	2	MAP2	210266729	0.991000	0.36638	0.942000	0.38095	0.044000	0.14063	1.626000	0.37039	0.877000	0.35895	-0.143000	0.13931	AAG		0.408	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210558484	G	T	210558484	3	4	47	1	0	0	0	0	1	0	0	0	9265	933	33	2	1604	2	MAP2	2	210558484	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	172	210558484	32640889	374	4771										
MAP2	4133	broad.mit.edu	37	chr2	210574836	210574836	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgccgagtgagaagaaggTcgccatcatacgtactcctc	12	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:210574836T>C	ENST00000360351.4	+	12	5437	c.4931T>C	c.(4930-4932)gTc>gCc	p.V1644A	MAP2_ENST00000447185.1_Missense_Mutation_p.V1640A|MAP2_ENST00000361559.4_Missense_Mutation_p.V288A|MAP2_ENST00000475600.1_3'UTR|MAP2_ENST00000199940.6_Missense_Mutation_p.V345A|MAP2_ENST00000392194.1_Missense_Mutation_p.V288A	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1644					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.V1644A(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	GAGAAGAAGGTCGCCATCATA	0.537																																					Pancreas(27;423 979 28787 29963)											1	Substitution - Missense(1)	large_intestine(1)	2											114	100	105					2																	210574836		2203	4300	6503	210283081	SO:0001583	missense	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4931T>C	2.37:g.210574836T>C	ENSP00000353508:p.Val1644Ala		210283081	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	T	19.29	3.798636	0.70567	.	.	ENSG00000078018	ENST00000199940;ENST00000360351;ENST00000361559;ENST00000392194;ENST00000447185	T;T;T;T;T	0.25912	1.77;2.94;2.03;2.03;2.94	5.76	4.61	0.57282	.	0.119010	0.37437	N	0.002081	T	0.36026	0.0952	L	0.32530	0.975	0.80722	D	1	D;B;D;D;B	0.76494	0.999;0.037;0.969;0.999;0.201	D;B;D;D;B	0.79784	0.993;0.024;0.93;0.991;0.161	T	0.04065	-1.0980	10	0.23891	T	0.37	-14.4679	11.5968	0.50979	0.0:0.0695:0.0:0.9305	.	1640;288;289;1644;345	P11137-3;P11137-2;Q59FX9;P11137;Q8IUX2	.;.;.;MAP2_HUMAN;.	A	345;1644;288;288;1640	ENSP00000199940:V345A;ENSP00000353508:V1644A;ENSP00000355290:V288A;ENSP00000376032:V288A;ENSP00000392164:V1640A	ENSP00000199940:V345A	V	+	2	0	MAP2	210283081	1.000000	0.71417	0.580000	0.28601	0.644000	0.38419	7.997000	0.88414	1.019000	0.39547	-0.326000	0.08463	GTC		0.537	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		C	210574836	T	C	210574836	3	2	47	1	0	0	0	0	1	0	0	0	9265	1667	58	4	5140	4	MAP2	2	210574836	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	16352	210574836	32624537	375	4772										
CPS1	1373	broad.mit.edu	37	chr2	211469886	211469886	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgacaggttggaaagaaataGaatatgaagtggttcgagat	13	2	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:211469886G>T	ENST00000233072.5	+	17	2093	c.1897G>T	c.(1897-1899)Gaa>Taa	p.E633*	CPS1_ENST00000451903.2_Nonsense_Mutation_p.E182*|CPS1_ENST00000430249.2_Nonsense_Mutation_p.E639*	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	633	ATP-grasp 1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.E633*(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GAAAGAAATAGAATATGAAGT	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											150	137	142					2																	211469886		2203	4300	6503	211178131	SO:0001587	stop_gained	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1897G>T	2.37:g.211469886G>T	ENSP00000233072:p.Glu633*		211178131	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Nonsense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	40	8.222242	0.98712	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-38.6238	19.8155	0.96566	0.0:0.0:1.0:0.0	.	.	.	.	X	639;641;633;182	.	ENSP00000233072:E633X	E	+	1	0	CPS1	211178131	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.682000	0.91365	0.650000	0.86243	GAA		0.393	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211469886	G	T	211469886	4	4	47	1	0	0	0	0	0	1	0	0	3829	943	33	2	1985	2	CPS1	2	211469886	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	895050	211469886	31729487	376	4773										
CPS1	1373	broad.mit.edu	37	chr2	211473151	211473151	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttccagaaattaagaacgtCgtatccgggaagacatcagc	9	10	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:211473151C>T	ENST00000233072.5	+	19	2455	c.2259C>T	c.(2257-2259)gtC>gtT	p.V753V	CPS1_ENST00000451903.2_Silent_p.V302V|CPS1_ENST00000430249.2_Silent_p.V759V	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	753					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.V753V(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTAAGAACGTCGTATCCGGGA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											122	118	119					2																	211473151		2203	4300	6503	211181396	SO:0001819	synonymous_variant	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2259C>T	2.37:g.211473151C>T			211181396	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1																																																																																				0.423	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211473151	C	T	211473151	2	4	47	1	0	0	0	0	0	0	0	1	3829	871	31	1		1	CPS1	2	211473151	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3265	211473151	31726222	377	4774										
SPAG16	79582	broad.mit.edu	37	chr2	214204890	214204890	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tactatttttttttcagcaaAgctagagaagatttgctgaa	7	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:214204890A>C	ENST00000331683.5	+	6	635	c.540A>C	c.(538-540)aaA>aaC	p.K180N	SPAG16_ENST00000374309.3_Missense_Mutation_p.K86N|SPAG16_ENST00000447990.1_Missense_Mutation_p.K180N|SPAG16_ENST00000413312.1_Missense_Mutation_p.K149N|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000272898.7_Missense_Mutation_p.K180N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	180					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.K180N(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		TTTTCAGCAAAGCTAGAGAAG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											26	28	28					2																	214204890		2201	4293	6494	213913135	SO:0001583	missense	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.540A>C	2.37:g.214204890A>C	ENSP00000332592:p.Lys180Asn		213913135	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.349607	0.61183	.	.	ENSG00000144451	ENST00000331683;ENST00000413312;ENST00000272898;ENST00000447990;ENST00000374309	T;T	0.59772	0.28;0.24	5.96	-1.4	0.08968	.	0.175781	0.49916	D	0.000122	T	0.63355	0.2504	L	0.48174	1.505	0.34925	D	0.748781	D;D;D;B;D	0.76494	0.999;0.999;0.999;0.011;0.999	D;D;D;B;D	0.80764	0.994;0.974;0.918;0.02;0.994	T	0.67413	-0.5677	10	0.46703	T	0.11	.	10.4628	0.44590	0.7252:0.0:0.2748:0.0	.	86;31;149;120;180	B4DYB5;Q8N0X2-2;Q8N0X2-3;Q4G1A2;Q8N0X2	.;.;.;.;SPG16_HUMAN	N	180;149;180;180;86	ENSP00000332592:K180N;ENSP00000363428:K86N	ENSP00000272898:K180N	K	+	3	2	SPAG16	213913135	0.998000	0.40836	0.995000	0.50966	0.850000	0.48378	0.256000	0.18351	-0.142000	0.11354	-0.408000	0.06270	AAA		0.294	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		C	214204890	A	C	214204890	3	2	47	1	0	0	0	0	1	0	0	0	15017	69	3	4	578	4	SPAG16	2	214204890	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2731739	214204890	28994483	378	4775										
BARD1	580	broad.mit.edu	37	chr2	215646178	215646178	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaccacattttaattgaattCttcttgtttcctgcatcatt	3	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:215646178C>A	ENST00000260947.4	-	4	554	c.420G>T	c.(418-420)aaG>aaT	p.K140N	BARD1_ENST00000449967.2_5'UTR|BARD1_ENST00000471787.1_5'UTR	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	140					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K140N(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TAATTGAATTCTTCTTGTTTC	0.318									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	2											83	86	85					2																	215646178		2203	4299	6502	215354423	SO:0001583	missense	580	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.420G>T	2.37:g.215646178C>A	ENSP00000260947:p.Lys140Asn		215354423	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842534	0.71488	.	.	ENSG00000138376	ENST00000260947	T	0.80123	-1.34	6.05	3.31	0.37934	.	0.099817	0.64402	D	0.000002	D	0.87002	0.6069	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85560	0.1227	10	0.66056	D	0.02	-21.7587	9.2399	0.37489	0.0:0.733:0.0:0.267	.	140	Q99728	BARD1_HUMAN	N	140	ENSP00000260947:K140N	ENSP00000260947:K140N	K	-	3	2	BARD1	215354423	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.883000	0.39658	0.450000	0.26774	0.650000	0.86243	AAG		0.318	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		A	215646178	C	A	215646178	3	1	47	1	0	0	0	0	1	0	0	0	1313	912	32	2	1945	2	BARD1	2	215646178	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1441288	215646178	27553195	379	4776										
ABCA12	26154	broad.mit.edu	37	chr2	215876210	215876210	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcaatttgctctttagttAatttataagtcaaaaaatcc	4	6	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:215876210A>C	ENST00000272895.7	-	17	2504	c.2285T>G	c.(2284-2286)tTa>tGa	p.L762*	ABCA12_ENST00000389661.4_Nonsense_Mutation_p.L444*	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	762					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.L762*(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		CTCTTTAGTTAATTTATAAGT	0.348																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Nonsense(1)	large_intestine(1)	2											63	70	68					2																	215876210		2203	4300	6503	215584455	SO:0001587	stop_gained	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2285T>G	2.37:g.215876210A>C	ENSP00000272895:p.Leu762*		215584455	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Nonsense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	37	6.282761	0.97440	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	.	.	.	5.16	5.16	0.70880	.	0.283615	0.25022	N	0.033749	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	8.7143	0.34401	0.8308:0.0:0.0:0.1692	.	.	.	.	X	762;444	.	ENSP00000272895:L762X	L	-	2	0	ABCA12	215584455	0.972000	0.33761	1.000000	0.80357	0.559000	0.35586	1.505000	0.35736	2.073000	0.62155	0.533000	0.62120	TTA		0.348	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215876210	A	C	215876210	4	2	47	1	0	0	0	0	0	1	0	0	30	372	13	4	5650	4	ABCA12	2	215876210	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	230032	215876210	27323163	380	4777										
ABCA12	26154	broad.mit.edu	37	chr2	215890473	215890473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaaaagattttttaaatCgtattgtggactgcaggagt	11	3	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:215890473C>T	ENST00000272895.7	-	11	1430	c.1211G>A	c.(1210-1212)cGa>cAa	p.R404Q	AC072062.3_ENST00000602182.1_RNA|AC072062.3_ENST00000595058.1_RNA|AC072062.3_ENST00000437897.3_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.R86Q|AC072062.3_ENST00000419251.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	404					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.R404Q(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TTTTTTAAATCGTATTGTGGA	0.343																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											75	78	77					2																	215890473		2203	4300	6503	215598718	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1211G>A	2.37:g.215890473C>T	ENSP00000272895:p.Arg404Gln		215598718	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.534966	0.27475	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.58060	0.36;0.36	5.96	-3.84	0.04256	.	0.931591	0.09010	N	0.861665	T	0.24851	0.0603	N	0.08118	0	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.27739	-1.0065	10	0.11794	T	0.64	.	7.9349	0.29925	0.0:0.2817:0.1183:0.6	.	404;86	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	Q	404;86	ENSP00000272895:R404Q;ENSP00000374312:R86Q	ENSP00000272895:R404Q	R	-	2	0	ABCA12	215598718	0.002000	0.14202	0.045000	0.18777	0.748000	0.42578	-1.304000	0.02741	-0.784000	0.04528	0.655000	0.94253	CGA		0.343	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215890473	C	T	215890473	3	4	47	1	0	0	0	0	1	0	0	0	30	884	31	1	6748	1	ABCA12	2	215890473	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	14263	215890473	27308900	381	4778										
FN1	2335	broad.mit.edu	37	chr2	216259432	216259432	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggttgtggtaattctataAccagtaatgtctggagaaaa	12	4	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:216259432A>G	ENST00000359671.1	-	24	3880	c.3615T>C	c.(3613-3615)ggT>ggC	p.G1205G	FN1_ENST00000346544.3_Silent_p.G1205G|FN1_ENST00000336916.4_Silent_p.G1205G|FN1_ENST00000323926.6_Silent_p.G1205G|FN1_ENST00000357009.2_Silent_p.G1205G|FN1_ENST00000345488.5_Silent_p.G1205G|FN1_ENST00000357867.4_Silent_p.G1205G|FN1_ENST00000421182.1_Silent_p.G1205G|FN1_ENST00000446046.1_Silent_p.G1205G|FN1_ENST00000443816.1_Silent_p.G1205G|FN1_ENST00000356005.4_Silent_p.G1205G|FN1_ENST00000354785.4_Silent_p.G1205G|FN1_ENST00000432072.2_Silent_p.G1205G			P02751	FINC_HUMAN	fibronectin 1	1205	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.G1205G(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	TAATTCTATAACCAGTAATGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											81	89	87					2																	216259432		2203	4300	6503	215967677	SO:0001819	synonymous_variant	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3615T>C	2.37:g.216259432A>G			215967677	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																					0.443	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216259432	A	G	216259432	2	3	47	1	0	0	0	0	0	0	0	1	5981	30	2	4		4	FN1	2	216259432	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	368959	216259432	26939941	382	4779										
XRCC5	7520	broad.mit.edu	37	chr2	216992289	216992289	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agagagttaaaaagacttggAcagttgtggatgcaaaaacc	11	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:216992289A>C	ENST00000392133.3	+	10	1290	c.829A>C	c.(829-831)Aca>Cca	p.T277P	XRCC5_ENST00000392132.2_Missense_Mutation_p.T277P			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	277	Ku.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.T277P(1)		endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		AAAGACTTGGACAGTTGTGGA	0.308								Non-homologous end-joining																																								1	Substitution - Missense(1)	large_intestine(1)	2											91	97	95					2																	216992289		2203	4300	6503	216700534	SO:0001583	missense	7520			AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.829A>C	2.37:g.216992289A>C	ENSP00000375978:p.Thr277Pro		216700534	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	37	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760362	0.49468	.	.	ENSG00000079246	ENST00000392133;ENST00000392132	T;T	0.31510	1.49;1.49	6.17	1.11	0.20524	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);DNA helicase, ATP-dependent, Ku type (1);	0.656463	0.16245	N	0.222959	T	0.29355	0.0731	M	0.72118	2.19	0.41367	D	0.987462	B	0.32283	0.362	B	0.35073	0.195	T	0.03795	-1.1003	10	0.29301	T	0.29	.	5.6055	0.17377	0.5247:0.0:0.3464:0.129	.	277	P13010	XRCC5_HUMAN	P	277	ENSP00000375978:T277P;ENSP00000375977:T277P	ENSP00000375977:T277P	T	+	1	0	XRCC5	216700534	0.746000	0.28272	0.986000	0.45419	0.896000	0.52359	1.603000	0.36794	-0.037000	0.13646	-0.250000	0.11733	ACA		0.308	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		C	216992289	A	C	216992289	3	2	47	1	0	0	0	0	1	0	0	0	17496	275	10	4	859	4	XRCC5	2	216992289	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	732857	216992289	26207084	383	4780										
SPEG	10290	broad.mit.edu	37	chr2	220329280	220329280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtttctacacttgcaaagCggtcaatgagtatggtgctc	11	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:220329280C>T	ENST00000312358.7	+	9	2963	c.2831C>T	c.(2830-2832)gCg>gTg	p.A944V	SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396689.2_Missense_Mutation_p.A95V|SPEG_ENST00000396698.1_Missense_Mutation_p.A840V|SPEG_ENST00000396695.2_Missense_Mutation_p.A152V|SPEG_ENST00000396688.1_Missense_Mutation_p.A95V|SPEG_ENST00000396686.1_Missense_Mutation_p.A95V	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	944	Ig-like 3.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A944V(2)		breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACTTGCAAAGCGGTCAATGAG	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	2											90	100	97					2																	220329280		2167	4277	6444	220037524	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2831C>T	2.37:g.220329280C>T	ENSP00000311684:p.Ala944Val		220037524	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587831	0.66105	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698;ENST00000396695;ENST00000396688;ENST00000396686;ENST00000396689	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41823	D	0.000815	D	0.83954	0.5366	M	0.80616	2.505	0.39815	D	0.972754	D;D;D	0.69078	0.997;0.988;0.997	P;P;D	0.68039	0.766;0.654;0.955	D	0.86029	0.1512	10	0.52906	T	0.07	.	16.7035	0.85365	0.0:1.0:0.0:0.0	.	944;152;840	Q15772;Q15772-3;B9ZVR7	SPEG_HUMAN;.;.	V	944;944;840;152;95;95;95	ENSP00000311684:A944V;ENSP00000379926:A840V;ENSP00000379923:A152V;ENSP00000379919:A95V;ENSP00000379917:A95V;ENSP00000379920:A95V	ENSP00000265327:A944V	A	+	2	0	SPEG	220037524	1.000000	0.71417	0.799000	0.32177	0.005000	0.04900	5.326000	0.65875	2.484000	0.83849	0.561000	0.74099	GCG		0.632	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220329280	C	T	220329280	3	4	47	1	0	0	0	0	1	0	0	0	15075	768	27	1	2865	1	SPEG	2	220329280	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3336991	220329280	22870093	384	4781										
SCG2	7857	broad.mit.edu	37	chr2	224463935	224463935	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagctgcttcagccccagaGatgaggaaaattaaagggat	12	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:224463935G>A	ENST00000305409.2	-	2	298	c.66C>T	c.(64-66)atC>atT	p.I22I		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0			L -> R (in MEN1; no effect on histone methylation; almost no effect on JUND- binding; no repression of JUND transactivation). {ECO:0000269|PubMed:14992727, ECO:0000269|PubMed:9103196, ECO:0000269|PubMed:9989505}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.I22I(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		CAGCCCCAGAGATGAGGAAAA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											64	69	68					2																	224463935		2203	4299	6502	224172179	SO:0001819	synonymous_variant	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.66C>T	2.37:g.224463935G>A			224172179	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	37	CCDS2457.1																																																																																				0.423	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224463935	G	A	224463935	2	1	47	1	0	0	0	0	0	0	0	1	13928	932	33	3		3	SCG2	2	224463935	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4134655	224463935	18735438	385	4782										
KIAA1486	57624	broad.mit.edu	37	chr2	226273726	226273726	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaatgcgtcagatattgctCgagagaatgatcgcttgaga	12	6	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:226273726C>T	ENST00000272907.6	+	2	543	c.130C>T	c.(130-132)Cga>Tga	p.R44*	NYAP2_ENST00000409269.2_Nonsense_Mutation_p.R44*	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	44					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.R44*(1)|p.R44R(1)									AGATATTGCTCGAGAGAATGA	0.408																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	2											104	94	97					2																	226273726		1881	4110	5991	225981970	SO:0001587	stop_gained	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.130C>T	2.37:g.226273726C>T	ENSP00000272907:p.Arg44*		225981970	A2RRN4|Q96NL2	Nonsense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	37	6.010483	0.97200	.	.	ENSG00000144460	ENST00000272907;ENST00000409269	.	.	.	5.92	4.08	0.47627	.	0.000000	0.52532	D	0.000079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9567	13.9926	0.64376	0.3984:0.6015:0.0:0.0	.	.	.	.	X	44	.	ENSP00000272907:R44X	R	+	1	2	KIAA1486	225981970	1.000000	0.71417	0.986000	0.45419	0.770000	0.43624	2.515000	0.45512	0.798000	0.33994	-0.321000	0.08615	CGA		0.408	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226273726	C	T	226273726	4	4	47	1	0	0	0	0	0	1	0	0	8258	876	31	1	132	1	KIAA1486	2	226273726	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1809791	226273726	16925647	386	4783										
WDR69	164781	broad.mit.edu	37	chr2	228783526	228783526	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattttcagtgctgccacaaGaaaatgcattgccaaactgg	8	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:228783526G>T	ENST00000309931.2	+	11	1087	c.1004G>T	c.(1003-1005)aGa>aTa	p.R335I	DAW1_ENST00000373666.2_3'UTR|DAW1_ENST00000545118.1_Missense_Mutation_p.R320I	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	335						cilium (GO:0005929)		p.R335K(1)|p.R335I(1)									GCTGCCACAAGAAAATGCATT	0.353																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	2											75	74	74					2																	228783526		2203	4300	6503	228491770	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.1004G>T	2.37:g.228783526G>T	ENSP00000311899:p.Arg335Ile		228491770	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.397789	0.25205	.	.	ENSG00000123977	ENST00000309931;ENST00000545118	T;T	0.60920	0.15;0.15	5.32	3.49	0.39957	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.492489	0.23541	N	0.047071	T	0.51160	0.1658	L	0.57536	1.79	0.48452	D	0.99965	B	0.12630	0.006	B	0.19666	0.026	T	0.53408	-0.8443	10	0.56958	D	0.05	.	8.2805	0.31898	0.2449:0.0:0.7551:0.0	.	335	Q8N136	WDR69_HUMAN	I	335;320	ENSP00000311899:R335I;ENSP00000437887:R320I	ENSP00000311899:R335I	R	+	2	0	WDR69	228491770	1.000000	0.71417	0.973000	0.42090	0.975000	0.68041	1.852000	0.39348	1.372000	0.46190	0.650000	0.86243	AGA		0.353	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		T	228783526	G	T	228783526	3	4	47	1	0	0	0	0	1	0	0	0	17359	942	33	2	1046	2	WDR69	2	228783526	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2509800	228783526	14415847	387	4784										
TRIP12	9320	broad.mit.edu	37	chr2	230693939	230693939	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaattgttctatggaaaaGctgtgacatccgaggaccaa	9	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:230693939G>A	ENST00000283943.5	-	7	1454	c.1276C>T	c.(1276-1278)Ctt>Ttt	p.L426F	TRIP12_ENST00000389045.3_Missense_Mutation_p.L129F|TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389044.4_Missense_Mutation_p.L474F	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	426					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.L426F(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CTATGGAAAAGCTGTGACATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	73	74					2																	230693939		2203	4300	6503	230402183	SO:0001583	missense	9320			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1276C>T	2.37:g.230693939G>A	ENSP00000283943:p.Leu426Phe		230402183	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.832619	0.71258	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.54866	0.58;1.04;0.55	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.66684	0.2814	L	0.45137	1.4	0.80722	D	1	D;D;D;D	0.69078	0.995;0.995;0.995;0.997	D;D;D;P	0.70487	0.969;0.969;0.969;0.878	T	0.66901	-0.5806	10	0.52906	T	0.07	.	19.0849	0.93200	0.0:0.0:1.0:0.0	.	432;129;474;426	D4HL82;Q14CF1;Q14CA3;Q14669	.;.;.;TRIPC_HUMAN	F	426;129;474	ENSP00000283943:L426F;ENSP00000373697:L129F;ENSP00000373696:L474F	ENSP00000283943:L426F	L	-	1	0	TRIP12	230402183	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	9.233000	0.95337	2.520000	0.84964	0.557000	0.71058	CTT		0.418	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230693939	G	A	230693939	3	1	47	1	0	0	0	0	1	0	0	0	16596	971	34	3	4842	3	TRIP12	2	230693939	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1910413	230693939	12505434	388	4785										
GIGYF2	26058	broad.mit.edu	37	chr2	233704626	233704626	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagtcccaggccacgctgtCgttggctgaaatccaaaaac	9	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:233704626C>A	ENST00000409547.1	+	25	3145	c.2834C>A	c.(2833-2835)tCg>tAg	p.S945*	GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.S967*|GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.S967*|GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.S945*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.S966*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.S939*|GIGYF2_ENST00000452341.2_Nonsense_Mutation_p.S776*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	945	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.S945*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GCCACGCTGTCGTTGGCTGAA	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											80	75	77					2																	233704626		2203	4300	6503	233412870	SO:0001587	stop_gained	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2834C>A	2.37:g.233704626C>A	ENSP00000386537:p.Ser945*		233412870	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	43	10.407416	0.99399	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000452341	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5485	19.1613	0.93533	0.0:1.0:0.0:0.0	.	.	.	.	X	967;945;967;945;939;966;776	.	ENSP00000362664:S945X	S	+	2	0	GIGYF2	233412870	1.000000	0.71417	0.972000	0.41901	0.682000	0.39822	7.277000	0.78572	2.517000	0.84864	0.650000	0.86243	TCG		0.458	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233704626	C	A	233704626	4	1	47	1	0	0	0	0	0	1	0	0	6398	893	31	2	2986	2	GIGYF2	2	233704626	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3010687	233704626	9494747	389	4786										
DGKD	8527	broad.mit.edu	37	chr2	234343074	234343074	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgtgctgataacagaaaaGaaatggaagattggattgca	12	3	0	4	rs199985859		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:234343074G>T	ENST00000264057.2	+	4	409	c.397G>T	c.(397-399)Gaa>Taa	p.E133*	DGKD_ENST00000409813.3_Nonsense_Mutation_p.E89*	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	133	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.E133*(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TAACAGAAAAGAAATGGAAGA	0.418													G|||	1	0.000199681	0	0	5008	,	,		19971	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	2											161	161	161					2																	234343074		2203	4300	6503	234007813	SO:0001587	stop_gained	8527			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.397G>T	2.37:g.234343074G>T	ENSP00000264057:p.Glu133*		234007813	Q14158|Q6PK55|Q8NG53	Nonsense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.491856	0.96339	.	.	ENSG00000077044	ENST00000264057;ENST00000427930;ENST00000447484;ENST00000409813	.	.	.	4.89	4.89	0.63831	.	0.165514	0.39274	N	0.001403	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.6329	0.91366	0.0:0.0:1.0:0.0	.	.	.	.	X	133;69;103;89	.	ENSP00000264057:E133X	E	+	1	0	DGKD	234007813	1.000000	0.71417	0.868000	0.34077	0.997000	0.91878	9.108000	0.94275	2.717000	0.92951	0.563000	0.77884	GAA		0.418	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234343074	G	T	234343074	4	4	47	1	0	0	0	0	0	1	0	0	4478	943	33	2	435	2	DGKD	2	234343074	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	638448	234343074	8856299	390	4787										
UGT1A8	54658	broad.mit.edu	37	chr2	234526697	234526697	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttctgagttcatccaatgGtttttttaacttattttttt	4	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:234526697G>T	ENST00000373450.4	+	1	407	c.344G>T	c.(343-345)gGt>gTt	p.G115V		NM_019076.4	NP_061949.3	P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	121					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)	p.G115V(1)		breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	TCATCCAATGGTTTTTTTAAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	123	121					2																	234526697		2203	4300	6503	234191436	SO:0001583	missense	54576			M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000373450.4:c.344G>T	2.37:g.234526697G>T	ENSP00000362549:p.Gly115Val		234191436	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000373450.4	37	CCDS33402.1	.	.	.	.	.	.	.	.	.	.	G	6.663	0.490776	0.12702	.	.	ENSG00000242366	ENST00000373450	T	0.59224	0.28	3.83	-6.32	0.01995	.	.	.	.	.	T	0.24236	0.0587	N	0.01751	-0.74	0.09310	N	0.999999	B;B	0.11235	0.004;0.004	B;B	0.14023	0.01;0.01	T	0.20706	-1.0267	9	0.33940	T	0.23	.	7.2633	0.26216	0.1935:0.2819:0.5246:0.0	.	115;115	Q5DSZ6;Q9HAW9	.;UD18_HUMAN	V	115	ENSP00000362549:G115V	ENSP00000362549:G115V	G	+	2	0	UGT1A8	234191436	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-3.077000	0.00615	-1.186000	0.02713	0.400000	0.26472	GGT		0.373	UGT1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130994.1			T	234526697	G	T	234526697	3	4	47	1	0	0	0	0	1	0	0	0	16991	1261	44	2	346	2	UGT1A8	2	234526697	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	183623	234526697	8672676	391	4788										
COL6A3	1293	broad.mit.edu	37	chr2	238296762	238296762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggaagtcgagaatgactgCgaaattgacacttccggtgt	12	7	0	3	rs141609058		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:238296762C>T	ENST00000295550.4	-	4	1227	c.775G>A	c.(775-777)Gca>Aca	p.A259T	COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000346358.4_Missense_Mutation_p.A259T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A53T|COL6A3_ENST00000392004.3_Missense_Mutation_p.A53T|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000353578.4_Missense_Mutation_p.A53T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	259	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A259T(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		AGAATGACTGCGAAATTGACA	0.423													C|||	1	0.000199681	8e-04	0	5008	,	,		20312	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	,,THR/ALA,THR/ALA,THR/ALA	18,4388	25.3+/-52.1	0,18,2185	59	60	59		,,157,157,775	1	1	2	dbSNP_134	59	0,8600		0,0,4300	yes	intron,intron,missense,missense,missense	COL6A3	NM_057164.4,NM_057166.4,NM_057167.3,NM_057165.4,NM_004369.3	,,58,58,58	0,18,6485	TT,TC,CC		0.0,0.4085,0.1384	,,benign,benign,benign	,,53/2972,53/1238,259/3178	238296762	18,12988	2203	4300	6503	237961501	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.775G>A	2.37:g.238296762C>T	ENSP00000295550:p.Ala259Thr		237961501	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.665547	0.29604	0.004085	0.0	ENSG00000163359	ENST00000295550;ENST00000353578;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000433762	D;D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67;-1.67	5.43	0.971	0.19698	von Willebrand factor, type A (3);	1.007410	0.07997	N	0.988076	T	0.67031	0.2850	L	0.38175	1.15	0.09310	N	0.999999	B;B;P;B	0.35894	0.004;0.033;0.526;0.009	B;B;B;B	0.28849	0.003;0.013;0.095;0.003	T	0.52510	-0.8566	10	0.14252	T	0.57	.	1.9296	0.03324	0.2056:0.3994:0.2339:0.1611	.	259;53;53;259	E9PCV6;E9PGQ9;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	259;53;53;259;53;259	ENSP00000295550:A259T;ENSP00000315873:A53T;ENSP00000386844:A53T;ENSP00000295546:A259T;ENSP00000375861:A53T;ENSP00000389539:A259T	ENSP00000295550:A259T	A	-	1	0	COL6A3	237961501	0.935000	0.31712	0.999000	0.59377	0.998000	0.95712	0.487000	0.22356	0.164000	0.19529	0.650000	0.86243	GCA		0.423	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238296762	C	T	238296762	3	4	47	1	0	0	0	0	1	0	0	0	3707	768	27	1	8969	1	COL6A3	2	238296762	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3770065	238296762	4902611	392	4789										
RBM44	375316	broad.mit.edu	37	chr2	238725832	238725832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtcaagatactaacacagaGagtactcagtttcagtcaag	8	8	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr2:238725832G>T	ENST00000409864.1	+	3	527	c.273G>T	c.(271-273)gaG>gaT	p.E91D	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.E91D			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	90						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.E91D(2)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		CTAACACAGAGAGTACTCAGT	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	2											60	60	60					2																	238725832		1837	4074	5911	238390571	SO:0001583	missense	375316			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.273G>T	2.37:g.238725832G>T	ENSP00000386727:p.Glu91Asp		238390571	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	G	9.281	1.048137	0.19827	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.28895	1.59;1.59	5.62	-1.06	0.10002	.	1.073890	0.07176	N	0.853264	T	0.20129	0.0484	L	0.32530	0.975	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.30119	-0.9989	10	0.25106	T	0.35	-0.5191	5.7717	0.18257	0.2461:0.3644:0.3895:0.0	.	90	Q6ZP01	RBM44_HUMAN	D	91	ENSP00000321179:E91D;ENSP00000386727:E91D	ENSP00000321179:E91D	E	+	3	2	RBM44	238390571	0.000000	0.05858	0.000000	0.03702	0.799000	0.45148	-0.214000	0.09292	0.060000	0.16281	0.563000	0.77884	GAG		0.328	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		T	238725832	G	T	238725832	3	4	47	1	0	0	0	0	1	0	0	0	13175	933	33	2	279	2	RBM44	2	238725832	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	429070	238725832	4473541	393	4790										
CHL1	10752	broad.mit.edu	37	chr3	431154	431154	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgactctctattctggagaaGactgtaagtgatgcacctaa	9	8	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:431154G>T	ENST00000256509.2	+	20	3109	c.2467G>T	c.(2467-2469)Gac>Tac	p.D823Y	CHL1_ENST00000397491.2_Missense_Mutation_p.D807Y	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.D823Y(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		TTCTGGAGAAGACTGTAAGTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											73	65	68					3																	431154		2203	4300	6503	406154	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2467G>T	3.37:g.431154G>T	ENSP00000256509:p.Asp823Tyr		406154	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.259613|4.259613	0.80246|0.80246	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000256509;ENST00000397491|ENST00000445697	T;T|.	0.57107|.	0.42;0.42|.	5.4|5.4	5.4|5.4	0.78164|0.78164	Fibronectin, type III (2);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85961|0.85961	0.5819|0.5819	M|M	0.91038|0.91038	3.17|3.17	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.993;0.997;1.0|.	D|D	0.88703|0.88703	0.3217|0.3217	10|5	0.87932|.	D|.	0|.	.|.	19.1737|19.1737	0.93594|0.93594	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	807;807;823|.	B3KX75;O00533;O00533-2|.	.;CHL1_HUMAN;.|.	Y|N	823;807|9	ENSP00000256509:D823Y;ENSP00000380628:D807Y|.	ENSP00000256509:D823Y|.	D|K	+|+	1|3	0|2	CHL1|CHL1	406154|406154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.112000|9.112000	0.94314|0.94314	2.524000|2.524000	0.85096|0.85096	0.591000|0.591000	0.81541|0.81541	GAC|AAG		0.428	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	431154	G	T	431154	3	4	47	1	0	0	0	0	1	0	0	0	3355	942	33	2	2537	2	CHL1	3	431154	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09		431154	197591276	394	4791										
IL5RA	3568	broad.mit.edu	37	chr3	3118234	3118234	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattttacagataagcgagaGaattaacaagatgaagcaga	9	5	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:3118234G>T	ENST00000446632.2	-	10	1646	c.1072C>A	c.(1072-1074)Ctc>Atc	p.L358I	IL5RA_ENST00000256452.3_Missense_Mutation_p.L358I|IL5RA_ENST00000418488.2_Missense_Mutation_p.L263I|IL5RA_ENST00000445864.2_Missense_Mutation_p.L149I|IL5RA_ENST00000438560.1_Missense_Mutation_p.L358I	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	358					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)	p.L358I(1)		cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		ATAAGCGAGAGAATTAACAAG	0.408																																					GBM(169;430 2801 24955 28528)											1	Substitution - Missense(1)	large_intestine(1)	3											113	95	101					3																	3118234		2203	4300	6503	3093234	SO:0001583	missense	3568			M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.1072C>A	3.37:g.3118234G>T	ENSP00000412209:p.Leu358Ile		3093234	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	7.127	0.579175	0.13686	.	.	ENSG00000091181	ENST00000446632;ENST00000353055;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864	D;D;D;T;T	0.95980	-3.87;-3.87;-3.87;1.27;1.52	4.83	-0.332	0.12675	.	0.852591	0.10341	N	0.686278	D	0.89357	0.6692	L	0.33245	0.995	0.09310	N	1	B;B;B;B;B	0.28933	0.139;0.031;0.218;0.139;0.228	B;B;B;B;B	0.28011	0.027;0.006;0.085;0.039;0.051	T	0.79032	-0.1969	10	0.28530	T	0.3	-3.2155	3.9956	0.09556	0.4656:0.1919:0.3425:0.0	.	358;358;149;263;59	B4E2G0;Q01344;B3IU77;E7ERY4;Q14632	.;IL5RA_HUMAN;.;.;.	I	358;69;358;358;263;149	ENSP00000412209:L358I;ENSP00000390753:L358I;ENSP00000256452:L358I;ENSP00000388858:L263I;ENSP00000402598:L149I	ENSP00000256452:L358I	L	-	1	0	IL5RA	3093234	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.809000	0.04510	-0.003000	0.14444	-1.224000	0.01588	CTC		0.408	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			T	3118234	G	T	3118234	3	4	47	1	0	0	0	0	1	0	0	0	7721	942	33	2	202	2	IL5RA	3	3118234	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2687080	3118234	194904196	395	4792										
LRRN1	57633	broad.mit.edu	37	chr3	3887326	3887326	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catccaccgcttggctttccGaagtgtccctgctctggaaa	9	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:3887326G>A	ENST00000319331.3	+	2	1762	c.1001G>A	c.(1000-1002)cGa>cAa	p.R334Q	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	334						integral component of membrane (GO:0016021)		p.R334Q(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TTGGCTTTCCGAAGTGTCCCT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											60	57	58					3																	3887326		2203	4300	6503	3862326	SO:0001583	missense	57633			AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.1001G>A	3.37:g.3887326G>A	ENSP00000314901:p.Arg334Gln		3862326	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Missense_Mutation	SNP	ENST00000319331.3	37	CCDS33685.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030586	0.54790	.	.	ENSG00000175928	ENST00000319331	T	0.56103	0.48	5.59	5.59	0.84812	.	0.054378	0.64402	D	0.000003	T	0.39860	0.1094	L	0.38649	1.16	0.50813	D	0.999894	P	0.37176	0.586	B	0.18561	0.022	T	0.27468	-1.0073	10	0.23302	T	0.38	.	19.5917	0.95518	0.0:0.0:1.0:0.0	.	334	Q6UXK5	LRRN1_HUMAN	Q	334	ENSP00000314901:R334Q	ENSP00000314901:R334Q	R	+	2	0	LRRN1	3862326	1.000000	0.71417	0.659000	0.29680	0.995000	0.86356	5.716000	0.68437	2.614000	0.88457	0.650000	0.86243	CGA		0.488	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		A	3887326	G	A	3887326	3	1	47	1	0	0	0	0	1	0	0	0	9063	1058	37	1	1003	1	LRRN1	3	3887326	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	769092	3887326	194135104	396	4793										
ITPR1	3708	broad.mit.edu	37	chr3	4722294	4722294	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctcctgtgtatatttaagCgagagtttgatgaaagcaat	10	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:4722294C>T	ENST00000443694.2	+	22	2980	c.2980C>T	c.(2980-2982)Cga>Tga	p.R994*	ITPR1_ENST00000423119.2_Nonsense_Mutation_p.R1000*|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Nonsense_Mutation_p.R1009*|ITPR1_ENST00000302640.8_Nonsense_Mutation_p.R994*|ITPR1_ENST00000357086.4_Nonsense_Mutation_p.R1000*|ITPR1_ENST00000456211.2_Nonsense_Mutation_p.R985*			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1009					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.R985*(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TATATTTAAGCGAGAGTTTGA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											110	107	108					3																	4722294		1874	4092	5966	4697294	SO:0001587	stop_gained	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.2980C>T	3.37:g.4722294C>T	ENSP00000401671:p.Arg994*		4697294	E7EPX7|E9PDE9|Q14660|Q99897	Nonsense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	41	8.817682	0.98964	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.	.	.	4.62	3.74	0.42951	.	0.449318	0.22299	N	0.061883	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	12.1324	0.53950	0.3112:0.6888:0.0:0.0	.	.	.	.	X	1009;994;1009;1000;1000;985;994	.	ENSP00000306253:R994X	R	+	1	2	ITPR1	4697294	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.841000	0.27613	1.141000	0.42275	0.491000	0.48974	CGA		0.398	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4722294	C	T	4722294	4	4	47	1	0	0	0	0	0	1	0	0	7941	760	27	1	3115	1	ITPR1	3	4722294	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	834968	4722294	193300136	397	4794										
ITPR1	3708	broad.mit.edu	37	chr3	4732962	4732962	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgtccagtatataaagttCttacagacaattgtcaaggc	7	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:4732962C>A	ENST00000443694.2	+	29	3918	c.3918C>A	c.(3916-3918)ttC>ttA	p.F1306L	ITPR1_ENST00000423119.2_Missense_Mutation_p.F1312L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.F1321L|ITPR1_ENST00000302640.8_Missense_Mutation_p.F1306L|ITPR1_ENST00000357086.4_Missense_Mutation_p.F1312L|ITPR1_ENST00000456211.2_Missense_Mutation_p.F1297L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1321					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.F1297L(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ATATAAAGTTCTTACAGACAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											74	74	74					3																	4732962		1867	4121	5988	4707962	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3918C>A	3.37:g.4732962C>A	ENSP00000401671:p.Phe1306Leu		4707962	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292492	0.59976	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	T;T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08;-0.08	5.24	3.44	0.39384	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	T	0.71854	0.3389	L	0.61218	1.895	0.80722	D	1	B;D	0.89917	0.372;1.0	B;D	0.91635	0.302;0.999	T	0.67405	-0.5679	10	0.33141	T	0.24	.	8.3322	0.32193	0.0:0.7581:0.0:0.2419	.	1321;1312	Q14643;G5E9P1	ITPR1_HUMAN;.	L	1321;1306;1321;1312;1312;1297;1306	ENSP00000306253:F1306L;ENSP00000346595:F1321L;ENSP00000405934:F1312L;ENSP00000349597:F1312L;ENSP00000397885:F1297L;ENSP00000401671:F1306L	ENSP00000306253:F1306L	F	+	3	2	ITPR1	4707962	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	2.671000	0.46842	0.578000	0.29487	0.655000	0.94253	TTC		0.398	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4732962	C	A	4732962	3	1	47	1	0	0	0	0	1	0	0	0	7941	912	32	2	4081	2	ITPR1	3	4732962	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	10668	4732962	193289468	398	4795										
FANCD2	2177	broad.mit.edu	37	chr3	10076388	10076388	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctccttaagataatagaaGaatttgttagtggcctggag	10	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:10076388G>T	ENST00000419585.1	+	5	444	c.283G>T	c.(283-285)Gaa>Taa	p.E95*	FANCD2_ENST00000383806.1_Nonsense_Mutation_p.E95*|FANCD2_ENST00000287647.3_Nonsense_Mutation_p.E95*|FANCD2_ENST00000383807.1_Nonsense_Mutation_p.E95*|FANCD2_ENST00000431693.1_Nonsense_Mutation_p.E95*|RNU6-670P_ENST00000364312.1_RNA			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	95	Interaction with FANCE.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.E95*(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GATAATAGAAGAATTTGTTAG	0.353			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	1	Substitution - Nonsense(1)	large_intestine(1)	3											39	34	36					3																	10076388		2199	4292	6491	10051388	SO:0001587	stop_gained	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.283G>T	3.37:g.10076388G>T	ENSP00000398754:p.Glu95*		10051388	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Nonsense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	G	38	6.698964	0.97772	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585;ENST00000431693	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	17.849	0.88739	0.0:0.0:1.0:0.0	.	.	.	.	X	95	.	ENSP00000287647:E95X	E	+	1	0	FANCD2	10051388	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.572000	0.67411	2.812000	0.96745	0.557000	0.71058	GAA		0.353	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			T	10076388	G	T	10076388	4	4	47	1	0	0	0	0	0	1	0	0	5684	943	33	2	297	2	FANCD2	3	10076388	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5343426	10076388	187946042	399	4796										
ATP2B2	491	broad.mit.edu	37	chr3	10442759	10442759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccgtcggcagggaggaggTcacctggcaagaggaagggc	20	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:10442759T>C	ENST00000352432.4	-	4	728	c.659A>G	c.(658-660)gAc>gGc	p.D220G	ATP2B2_ENST00000360273.2_Missense_Mutation_p.D220G|ATP2B2_ENST00000343816.4_Missense_Mutation_p.D220G|ATP2B2_ENST00000397077.1_Missense_Mutation_p.D220G|ATP2B2_ENST00000383800.4_Missense_Mutation_p.D220G			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	220					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.D220G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AGGGAGGAGGTCACCTGGCAA	0.567																																					Ovarian(125;1619 1709 15675 19819 38835)											1	Substitution - Missense(1)	large_intestine(1)	3											68	65	66					3																	10442759		2203	4300	6503	10417759	SO:0001583	missense	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.659A>G	3.37:g.10442759T>C	ENSP00000324172:p.Asp220Gly		10417759	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.509739	0.85282	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	5.6	5.6	0.85130	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.96855	0.8973	M	0.92026	3.265	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.996	D	0.97746	1.0211	10	0.87932	D	0	-43.6108	15.7913	0.78367	0.0:0.0:0.0:1.0	.	220;232;220	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	G	220;220;220;220;220;186;107;220	ENSP00000324172:D220G;ENSP00000373311:D220G;ENSP00000380267:D220G;ENSP00000353414:D220G;ENSP00000344677:D220G;ENSP00000414854:D107G	ENSP00000342954:D220G	D	-	2	0	ATP2B2	10417759	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	8.018000	0.88722	2.124000	0.65301	0.528000	0.53228	GAC		0.567	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		C	10442759	T	C	10442759	3	2	47	1	0	0	0	0	1	0	0	0	1141	1667	58	4	3148	4	ATP2B2	3	10442759	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	366371	10442759	187579671	400	4797										
TSEN2	80746	broad.mit.edu	37	chr3	12574176	12574176	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaggaggtgattctgagtCgatgggtttcttcacgagag	15	5	3	3	rs376815626		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:12574176C>T	ENST00000284995.6	+	12	1741	c.1354C>T	c.(1354-1356)Cga>Tga	p.R452*	TSEN2_ENST00000402228.3_Nonsense_Mutation_p.R452*|TSEN2_ENST00000314571.7_Nonsense_Mutation_p.R426*|TSEN2_ENST00000415684.1_Nonsense_Mutation_p.R426*|TSEN2_ENST00000454502.2_Nonsense_Mutation_p.R393*|TSEN2_ENST00000383797.5_Nonsense_Mutation_p.R435*|C3orf83_ENST00000567514.1_Intron|TSEN2_ENST00000475595.1_3'UTR	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	452					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)	p.R452*(1)		central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						GATTCTGAGTCGATGGGTTTC	0.378													C|||	1	0.000199681	0	0	5008	,	,		19005	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	3						C	stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	186	175	179		1354,1276,1177,1354	5.2	0.9	3		179	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained,stop-gained	TSEN2	NM_001145392.1,NM_001145393.1,NM_001145394.1,NM_025265.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	452/466,426/440,393/407,452/466	12574176	1,13005	2203	4300	6503	12549176	SO:0001587	stop_gained	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"tRNA splicing endonuclease subunits"	28422	protein-coding gene	gene with protein product		608753	"tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)", "tRNA splicing endonuclease 2 homolog (S. cerevisiae)"			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.1354C>T	3.37:g.12574176C>T	ENSP00000284995:p.Arg452*		12549176	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Nonsense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	C	39	7.807817	0.98501	0.0	1.16E-4	ENSG00000154743	ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000537959;ENST00000415684	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4867	15.369	0.74548	0.0:1.0:0.0:0.0	.	.	.	.	X	426;393;435;452;452;425;426	.	ENSP00000284995:R452X	R	+	1	2	TSEN2	12549176	0.998000	0.40836	0.903000	0.35520	0.965000	0.64279	3.059000	0.49947	2.395000	0.81488	0.455000	0.32223	CGA		0.378	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265		T	12574176	C	T	12574176	4	4	47	1	0	0	0	0	0	1	0	0	16652	876	31	1	1435	1	TSEN2	3	12574176	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2131417	12574176	185448254	401	4798										
METTL6	131965	broad.mit.edu	37	chr3	15455639	15455639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcatacagtccgtagtcacGaaacaagacacttttgcctg	7	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:15455639G>A	ENST00000443029.1	-	5	802	c.562C>T	c.(562-564)Cgt>Tgt	p.R188C	METTL6_ENST00000450816.2_Missense_Mutation_p.R143C|METTL6_ENST00000383790.3_Missense_Mutation_p.R188C			Q8TCB7	METL6_HUMAN	methyltransferase like 6	188							methyltransferase activity (GO:0008168)	p.R188C(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						CCGTAGTCACGAAACAAGACA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											107	97	100					3																	15455639		1860	4105	5965	15430643	SO:0001583	missense	131965			AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.562C>T	3.37:g.15455639G>A	ENSP00000407613:p.Arg188Cys		15430643	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	37	CCDS43056.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.954289|3.954289	0.73902|0.73902	.|.	.|.	ENSG00000206562|ENSG00000206562	ENST00000383790;ENST00000450816|ENST00000458728	T;T|.	0.13778|.	3.77;2.56|.	5.63|5.63	4.7|4.7	0.59300|0.59300	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87087|0.87087	0.6090|0.6090	H|H	0.97440|0.97440	4.005|4.005	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	D|D	0.90077|0.90077	0.4167|0.4167	10|5	0.87932|.	D|.	0|.	-11.7617|-11.7617	12.0981|12.0981	0.53767|0.53767	0.0:0.0:0.6869:0.3131|0.0:0.0:0.6869:0.3131	.|.	143;188|.	B4DDX3;Q8TCB7|.	.;METL6_HUMAN|.	C|L	188;143|56	ENSP00000373300:R188C;ENSP00000410726:R143C|.	ENSP00000373300:R188C|.	R|S	-|-	1|2	0|0	METTL6|METTL6	15430643|15430643	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.650000|0.650000	0.38633|0.38633	3.212000|3.212000	0.51145|0.51145	2.803000|2.803000	0.96430|0.96430	0.585000|0.585000	0.79938|0.79938	CGT|TCG		0.383	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		A	15455639	G	A	15455639	3	1	47	1	0	0	0	0	1	0	0	0	9534	1058	37	1	300	1	METTL6	3	15455639	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2881463	15455639	182566791	402	4799										
TBC1D5	9779	broad.mit.edu	37	chr3	17415983	17415983	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctgaccatcatgctcaaAagttgaaaaccaaggttcag	7	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:17415983A>C	ENST00000253692.7	-	12	2466	c.802T>G	c.(802-804)Ttt>Gtt	p.F268V	TBC1D5_ENST00000429383.4_Missense_Mutation_p.F268V|TBC1D5_ENST00000429924.2_Missense_Mutation_p.F220V|TBC1D5_ENST00000446818.2_Missense_Mutation_p.F268V|TBC1D5_ENST00000414318.2_Intron	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	268	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)	p.F268V(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						TCATGCTCAAAAGTTGAAAAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											64	64	64					3																	17415983		2202	4295	6497	17390987	SO:0001583	missense	9779			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.802T>G	3.37:g.17415983A>C	ENSP00000253692:p.Phe268Val		17390987	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	37	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.107229	0.37145	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	5.44	5.44	0.79542	Rab-GAP/TBC domain (4);	0.046386	0.85682	D	0.000000	T	0.28267	0.0698	M	0.77406	2.37	0.80722	D	1	B;B;B	0.30146	0.039;0.014;0.27	B;B;B	0.38755	0.103;0.063;0.281	T	0.06250	-1.0837	10	0.17369	T	0.5	-21.1655	15.804	0.78477	1.0:0.0:0.0:0.0	.	220;268;268	C9J3F6;C9JP52;Q92609	.;.;TBCD5_HUMAN	V	268;268;268;220	ENSP00000253692:F268V;ENSP00000398127:F268V;ENSP00000402935:F268V;ENSP00000411925:F220V	ENSP00000253692:F268V	F	-	1	0	TBC1D5	17390987	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.767000	0.91732	2.193000	0.70182	0.533000	0.62120	TTT		0.313	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		C	17415983	A	C	17415983	3	2	47	1	0	0	0	0	1	0	0	0	15662	14	1	4	1699	4	TBC1D5	3	17415983	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1960344	17415983	180606447	403	4800										
EFHB	151651	broad.mit.edu	37	chr3	19924151	19924151	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcttcaccataattagttCtgtcactgatgcgacgaatt	6	10	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:19924151C>A	ENST00000295824.9	-	12	2380	c.2219G>T	c.(2218-2220)aGa>aTa	p.R740I	EFHB_ENST00000344838.4_Missense_Mutation_p.R610I	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	740							calcium ion binding (GO:0005509)	p.R740I(1)		breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						ATAATTAGTTCTGTCACTGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	78	84					3																	19924151		2203	4300	6503	19899155	SO:0001583	missense	151651			AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2219G>T	3.37:g.19924151C>A	ENSP00000295824:p.Arg740Ile		19899155	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	C	14.73	2.623486	0.46840	.	.	ENSG00000163576	ENST00000295824;ENST00000344838	T;T	0.24723	1.84;1.85	5.55	3.7	0.42460	.	0.270585	0.35124	N	0.003425	T	0.20780	0.0500	L	0.56769	1.78	0.45439	D	0.99841	P;B	0.45078	0.85;0.346	B;B	0.40285	0.325;0.052	T	0.06058	-1.0848	9	.	.	.	-11.2614	2.3557	0.04295	0.1411:0.5176:0.1291:0.2121	.	610;740	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	I	740;610	ENSP00000295824:R740I;ENSP00000342263:R610I	.	R	-	2	0	EFHB	19899155	0.828000	0.29307	0.930000	0.37139	0.780000	0.44128	0.163000	0.16520	0.763000	0.33175	0.655000	0.94253	AGA		0.433	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		A	19924151	C	A	19924151	3	1	47	1	0	0	0	0	1	0	0	0	4956	913	32	2	290	2	EFHB	3	19924151	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2508168	19924151	178098279	404	4801										
ZNF385D	79750	broad.mit.edu	37	chr3	21465509	21465509	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaggactgtatttaggtttCgggggcttcccagcagctct	12	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:21465509C>T	ENST00000281523.2	-	7	1418	c.900G>A	c.(898-900)ccG>ccA	p.P300P		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	300						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.P300P(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						ATTTAGGTTTCGGGGGCTTCC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	3											173	171	171					3																	21465509		2203	4300	6503	21440513	SO:0001819	synonymous_variant	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.900G>A	3.37:g.21465509C>T			21440513		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																				0.408	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		T	21465509	C	T	21465509	2	4	47	1	0	0	0	0	0	0	0	1	17917	871	31	1		1	ZNF385D	3	21465509	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1541358	21465509	176556921	405	4802										
ZNF385D	79750	broad.mit.edu	37	chr3	21606079	21606079	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacttacatcagaattaaatCtcaactggcaaatgttgcat	5	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:21606079C>A	ENST00000281523.2	-	3	781	c.263G>T	c.(262-264)aGa>aTa	p.R88I	ZNF385D-AS1_ENST00000412369.1_RNA|ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	88						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R88I(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						AGAATTAAATCTCAACTGGCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	130	130					3																	21606079		2203	4300	6503	21581083	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.263G>T	3.37:g.21606079C>A	ENSP00000281523:p.Arg88Ile		21581083		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.479053	0.63849	.	.	ENSG00000151789	ENST00000281523	T	0.22743	1.94	5.73	5.73	0.89815	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.045544	0.85682	D	0.000000	T	0.39172	0.1068	M	0.71581	2.175	0.58432	D	0.999996	D	0.56746	0.977	P	0.56612	0.802	T	0.10291	-1.0636	10	0.54805	T	0.06	-0.2164	13.1477	0.59472	0.0:0.9271:0.0:0.0728	.	88	Q9H6B1	Z385D_HUMAN	I	88	ENSP00000281523:R88I	ENSP00000281523:R88I	R	-	2	0	ZNF385D	21581083	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.716000	0.92895	0.561000	0.74099	AGA		0.343	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21606079	C	A	21606079	3	1	47	1	0	0	0	0	1	0	0	0	17917	913	32	2	948	2	ZNF385D	3	21606079	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	140570	21606079	176416351	406	4803										
NR1D2	9975	broad.mit.edu	37	chr3	24009435	24009435	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctaaactctatgtttgaAtttagtgagaagctaaatgc	8	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:24009435A>C	ENST00000312521.4	+	7	1783	c.1464A>C	c.(1462-1464)gaA>gaC	p.E488D	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	488	Interaction with ZNHIT1.|Ligand-binding.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E488D(1)		NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						CTATGTTTGAATTTAGTGAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											161	153	156					3																	24009435		2203	4300	6503	23984439	SO:0001583	missense	9975			BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.1464A>C	3.37:g.24009435A>C	ENSP00000310006:p.Glu488Asp		23984439	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	37	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	A	4.430	0.079510	0.08533	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.96522	-4.04	5.94	1.03	0.20045	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.238676	0.48767	N	0.000163	D	0.88855	0.6550	N	0.13198	0.31	0.52501	D	0.99995	B	0.14805	0.011	B	0.16722	0.016	T	0.76838	-0.2811	10	0.10111	T	0.7	.	9.6072	0.39641	0.6206:0.0:0.3794:0.0	.	488	Q14995	NR1D2_HUMAN	D	488	ENSP00000310006:E488D	ENSP00000310006:E488D	E	+	3	2	NR1D2	23984439	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	1.203000	0.32284	-0.050000	0.13356	-0.250000	0.11733	GAA		0.398	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			C	24009435	A	C	24009435	3	2	47	1	0	0	0	0	1	0	0	0	10647	98	4	4	1490	4	NR1D2	3	24009435	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2403356	24009435	174012995	407	4804										
RARB	5915	broad.mit.edu	37	chr3	25502692	25502692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctattatagcaattgaaAcacagagcaccagctctgag	7	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:25502692A>G	ENST00000404969.1	+	2	187	c.187A>G	c.(187-189)Aca>Gca	p.T63A	RARB_ENST00000437042.2_5'UTR|RARB_ENST00000458646.1_5'UTR|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000330688.4_Missense_Mutation_p.T56A			P10826	RARB_HUMAN	retinoic acid receptor, beta	63	Modulating.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.T63A(1)|p.T56A(1)		breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	AGCAATTGAAACACAGAGCAC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	3											84	91	88					3																	25502692		2203	4300	6503	25477696	SO:0001583	missense	5915			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"Nuclear hormone receptors"	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.187A>G	3.37:g.25502692A>G	ENSP00000385865:p.Thr63Ala		25477696	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	A	15.86	2.957808	0.53400	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000330688	D;D;D	0.92348	-2.8;-3.02;-3.01	5.71	5.71	0.89125	.	0.369764	0.29355	N	0.012390	D	0.93223	0.7841	L	0.43923	1.385	0.80722	D	1	P;B	0.46706	0.883;0.005	P;B	0.56278	0.795;0.012	D	0.93367	0.6732	10	0.52906	T	0.07	.	16.0288	0.80560	1.0:0.0:0.0:0.0	.	63;56	P10826;F1D8S6	RARB_HUMAN;.	A	63;63;63;56	ENSP00000373282:T63A;ENSP00000385865:T63A;ENSP00000332296:T56A	ENSP00000332296:T56A	T	+	1	0	RARB	25477696	1.000000	0.71417	0.993000	0.49108	0.522000	0.34438	9.339000	0.96797	2.199000	0.70637	0.524000	0.50904	ACA		0.453	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		G	25502692	A	G	25502692	3	3	47	1	0	0	0	0	1	0	0	0	13090	43	2	4	172	4	RARB	3	25502692	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1493257	25502692	172519738	408	4805										
RARB	5915	broad.mit.edu	37	chr3	25611288	25611288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagaaaaagaaggagacttCgaagcaagaatgcacagaga	11	6	0	5	rs372148180		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:25611288C>T	ENST00000404969.1	+	4	509	c.509C>T	c.(508-510)tCg>tTg	p.S170L	RARB_ENST00000437042.2_Missense_Mutation_p.S51L|RARB_ENST00000458646.1_Missense_Mutation_p.S51L|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000330688.4_Missense_Mutation_p.S163L			P10826	RARB_HUMAN	retinoic acid receptor, beta	170	Hinge.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S163L(1)|p.S170L(1)		breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	AAGGAGACTTCGAAGCAAGAA	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	3						C	LEU/SER,LEU/SER	2,4404	4.2+/-10.8	0,2,2201	114	111	112		488,152	4.6	1	3		112	0,8600		0,0,4300	no	missense,missense	RARB	NM_000965.3,NM_016152.3	145,145	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign	163/449,51/337	25611288	2,13004	2203	4300	6503	25586292	SO:0001583	missense	5915			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"Nuclear hormone receptors"	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.509C>T	3.37:g.25611288C>T	ENSP00000385865:p.Ser170Leu		25586292	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	C	12.43	1.936212	0.34189	4.54E-4	0.0	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000437042;ENST00000330688;ENST00000458646	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	4.57	4.57	0.56435	Nuclear hormone receptor, ligand-binding (2);	0.520692	0.21026	N	0.081434	T	0.19565	0.0470	N	0.08118	0	0.36590	D	0.87405	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.001	T	0.12578	-1.0542	10	0.28530	T	0.3	.	12.3826	0.55315	0.0:0.9179:0.0:0.0821	.	170;163	P10826;F1D8S6	RARB_HUMAN;.	L	170;170;170;51;163;51	ENSP00000373282:S170L;ENSP00000385865:S170L;ENSP00000398840:S51L;ENSP00000332296:S163L;ENSP00000391391:S51L	ENSP00000332296:S163L	S	+	2	0	RARB	25586292	0.927000	0.31430	0.996000	0.52242	0.988000	0.76386	3.052000	0.49893	2.530000	0.85305	0.561000	0.74099	TCG		0.502	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		T	25611288	C	T	25611288	3	4	47	1	0	0	0	0	1	0	0	0	13090	893	31	1	502	1	RARB	3	25611288	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	108596	25611288	172411142	409	4806										
OXSM	54995	broad.mit.edu	37	chr3	25832704	25832704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaactcacctggtttgggatCgtcttatcggaggagagagt	14	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:25832704C>T	ENST00000280701.3	+	2	292	c.193C>T	c.(193-195)Cgt>Tgt	p.R65C	OXSM_ENST00000449808.1_3'UTR|NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Missense_Mutation_p.R65C	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	65					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)	p.R65C(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GGTTTGGGATCGTCTTATCGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											170	156	160					3																	25832704		2203	4300	6503	25807708	SO:0001583	missense	54995			BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.193C>T	3.37:g.25832704C>T	ENSP00000280701:p.Arg65Cys		25807708		Missense_Mutation	SNP	ENST00000280701.3	37	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.584185	0.46110	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	5.14	4.25	0.50352	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.049932	0.85682	D	0.000000	T	0.80116	0.4564	M	0.88105	2.93	0.80722	D	1	B;D	0.76494	0.313;0.999	B;D	0.70716	0.042;0.97	T	0.83194	-0.0082	9	0.72032	D	0.01	-6.9519	11.391	0.49815	0.1418:0.7216:0.1366:0.0	.	65;65	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	C	65	.	ENSP00000280701:R65C	R	+	1	0	OXSM	25807708	1.000000	0.71417	0.934000	0.37439	0.325000	0.28411	3.822000	0.55708	1.352000	0.45808	0.561000	0.74099	CGT		0.463	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		T	25832704	C	T	25832704	3	4	47	1	0	0	0	0	1	0	0	0	11366	884	31	1	195	1	OXSM	3	25832704	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	221416	25832704	172189726	410	4807										
SLC4A7	9497	broad.mit.edu	37	chr3	27498146	27498146	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataattaggtacatacaggtAacttcttctccagacgaaat	6	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:27498146A>C	ENST00000295736.5	-	1	99	c.29T>G	c.(28-30)tTa>tGa	p.L10*	SLC4A7_ENST00000388777.4_Intron|SLC4A7_ENST00000455077.1_Intron|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000446700.1_Intron|SLC4A7_ENST00000445684.1_Intron|SLC4A7_ENST00000437179.1_Intron|SLC4A7_ENST00000454389.1_Intron|SLC4A7_ENST00000428386.1_Nonsense_Mutation_p.L10*|SLC4A7_ENST00000440156.1_Intron|SLC4A7_ENST00000425128.2_Intron	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	10					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.L10*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ACATACAGGTAACTTCTTCTC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											133	132	132					3																	27498146		2202	4300	6502	27473150	SO:0001587	stop_gained	9497			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.29T>G	3.37:g.27498146A>C	ENSP00000295736:p.Leu10*		27473150	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Nonsense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	A	35	5.498060	0.96355	.	.	ENSG00000033867	ENST00000295736;ENST00000428386;ENST00000428179	.	.	.	5.11	0.94	0.19513	.	2.131160	0.02111	N	0.054791	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.3623	0.04310	0.604:0.1539:0.093:0.1491	.	.	.	.	X	10	.	ENSP00000295736:L10X	L	-	2	0	SLC4A7	27473150	0.348000	0.24861	0.955000	0.39395	0.997000	0.91878	1.275000	0.33144	0.327000	0.23409	0.482000	0.46254	TTA		0.353	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		C	27498146	A	C	27498146	4	2	47	1	0	0	0	0	0	1	0	0	14695	372	13	4	3715	4	SLC4A7	3	27498146	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1665442	27498146	170524284	411	4808										
STT3B	201595	broad.mit.edu	37	chr3	31621349	31621349	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccttattcattggattttaAatacattgaacataactgtt	5	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:31621349A>C	ENST00000295770.2	+	3	681	c.472A>C	c.(472-474)Aat>Cat	p.N158H	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	158					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.N158H(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TTGGATTTTAAATACATTGAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	87	88					3																	31621349		2203	4300	6503	31596353	SO:0001583	missense	201595			AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.472A>C	3.37:g.31621349A>C	ENSP00000295770:p.Asn158His		31596353	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.244508	0.22796	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.35008	0.0917	N	0.04245	-0.25	0.80722	D	1	B	0.12013	0.005	B	0.21360	0.034	T	0.31336	-0.9947	9	0.07813	T	0.8	-17.8789	16.3945	0.83586	1.0:0.0:0.0:0.0	.	158	Q8TCJ2	STT3B_HUMAN	H	158	.	ENSP00000295770:N158H	N	+	1	0	STT3B	31596353	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.339000	0.96797	2.265000	0.75225	0.482000	0.46254	AAT		0.343	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		C	31621349	A	C	31621349	3	2	47	1	0	0	0	0	1	0	0	0	15373	14	1	4	482	4	STT3B	3	31621349	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4123203	31621349	166401081	412	4809										
CCR4	1233	broad.mit.edu	37	chr3	32995914	32995914	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctctgccaatactgtgggCtcctccaaatttactctgct	7	13	2	0	rs371348585		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:32995914C>A	ENST00000330953.5	+	2	1168	c.1000C>A	c.(1000-1002)Ctc>Atc	p.L334I		NM_005508.4	NP_005499.1	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	334					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuron migration (GO:0001764)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of positive chemotaxis (GO:0050927)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)|tolerance induction (GO:0002507)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.L334I(1)		NS(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)|stomach(1)	16						ATACTGTGGGCTCCTCCAAAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											52	53	53					3																	32995914		2201	4300	6501	32970918	SO:0001583	missense	1233			X85740	CCDS2656.1	3p24-p21.3	2012-08-08			ENSG00000183813	ENSG00000183813		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1605	protein-coding gene	gene with protein product		604836				7642634, 8884276	Standard	NM_005508		Approved	CC-CKR-4, CMKBR4, CKR4, k5-5, ChemR13, CD194	uc003cfg.1	P51679	OTTHUMG00000130752	ENST00000330953.5:c.1000C>A	3.37:g.32995914C>A	ENSP00000332659:p.Leu334Ile		32970918	Q9ULY6|Q9ULY7	Missense_Mutation	SNP	ENST00000330953.5	37	CCDS2656.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.663038	0.00107	.	.	ENSG00000183813	ENST00000330953	T	0.66995	-0.24	5.43	-7.01	0.01594	.	1.382940	0.05222	N	0.508774	T	0.40145	0.1105	N	0.26042	0.785	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41592	-0.9500	10	0.05833	T	0.94	.	2.3773	0.04345	0.2288:0.3119:0.0753:0.384	.	334	P51679	CCR4_HUMAN	I	334	ENSP00000332659:L334I	ENSP00000332659:L334I	L	+	1	0	CCR4	32970918	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	-1.678000	0.01942	-2.069000	0.00882	-1.119000	0.02030	CTC		0.463	CCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253252.2			A	32995914	C	A	32995914	3	1	47	1	0	0	0	0	1	0	0	0	2949	797	28	2	1002	2	CCR4	3	32995914	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1374565	32995914	165026516	413	4810										
ARPP21	10777	broad.mit.edu	37	chr3	35730866	35730866	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttctgattaacacattaaaGaataattccaggtaaattat	4	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:35730866G>T	ENST00000187397.4	+	7	930	c.474G>T	c.(472-474)aaG>aaT	p.K158N	ARPP21_ENST00000337271.5_Missense_Mutation_p.K158N|ARPP21_ENST00000417925.1_Missense_Mutation_p.K158N|ARPP21_ENST00000458225.1_Missense_Mutation_p.K158N|ARPP21_ENST00000444190.1_Missense_Mutation_p.K158N	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	158					cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.K158N(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						ACACATTAAAGAATAATTCCA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											60	62	61					3																	35730866		2203	4298	6501	35705870	SO:0001583	missense	10777			AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.474G>T	3.37:g.35730866G>T	ENSP00000187397:p.Lys158Asn		35705870	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.378335	0.82682	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	5.86	5.86	0.93980	Single-stranded nucleic acid binding R3H (1);	0.094495	0.64402	D	0.000001	T	0.56108	0.1963	M	0.64997	1.995	0.45541	D	0.998497	B;B;B	0.26845	0.161;0.024;0.161	B;B;B	0.38056	0.264;0.135;0.264	T	0.48433	-0.9036	10	0.33141	T	0.24	-24.5717	20.5632	0.99335	0.0:0.0:1.0:0.0	.	158;158;158	Q9UBL0-3;Q9UBL0;Q9UBL0-4	.;ARP21_HUMAN;.	N	158	ENSP00000414351:K158N;ENSP00000337792:K158N;ENSP00000405276:K158N;ENSP00000187397:K158N;ENSP00000412326:K158N	ENSP00000187397:K158N	K	+	3	2	ARPP21	35705870	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.043000	0.57354	2.937000	0.99478	0.650000	0.86243	AAG		0.338	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		T	35730866	G	T	35730866	3	4	47	1	0	0	0	0	1	0	0	0	979	933	33	2	505	2	ARPP21	3	35730866	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2734952	35730866	162291564	414	4811										
ARPP21	10777	broad.mit.edu	37	chr3	35780946	35780946	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcagcccagctatgtaatCgcctctacaggccagcagct	9	15	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:35780946C>T	ENST00000187397.4	+	17	2238	c.1782C>T	c.(1780-1782)atC>atT	p.I594I	ARPP21_ENST00000337271.5_Silent_p.I575I|ARPP21_ENST00000417925.1_Silent_p.I595I|ARPP21_ENST00000458225.1_Silent_p.I595I|ARPP21_ENST00000444190.1_Silent_p.I575I	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	594	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.I594I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						GCTATGTAATCGCCTCTACAG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	3											58	59	58					3																	35780946		2203	4300	6503	35755950	SO:0001819	synonymous_variant	10777			AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1782C>T	3.37:g.35780946C>T			35755950	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Silent	SNP	ENST00000187397.4	37	CCDS2661.1																																																																																				0.627	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		T	35780946	C	T	35780946	2	4	47	1	0	0	0	0	0	0	0	1	979	874	31	1		1	ARPP21	3	35780946	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	50080	35780946	162241484	415	4812										
LRRFIP2	9209	broad.mit.edu	37	chr3	37132966	37132966	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggccctgatacctttagttCtttaagcccctgcatgtatc	8	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:37132966C>A	ENST00000336686.4	-	18	1179	c.1099G>T	c.(1099-1101)Gaa>Taa	p.E367*	Y_RNA_ENST00000383918.1_RNA|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421276.2_Nonsense_Mutation_p.E135*|LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000421307.1_Nonsense_Mutation_p.E367*|LRRFIP2_ENST00000440230.1_Nonsense_Mutation_p.E135*			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	367	DVL3-binding.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.E367*(1)|p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						ACCTTTAGTTCTTTAAGCCCC	0.448																																																2	Substitution - Nonsense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	3											212	180	191					3																	37132966		2203	4300	6503	37107970	SO:0001587	stop_gained	9209			AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1099G>T	3.37:g.37132966C>A	ENSP00000338727:p.Glu367*		37107970	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Nonsense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	C	39	7.852254	0.98525	.	.	ENSG00000093167	ENST00000421307;ENST00000336686;ENST00000421276;ENST00000440230;ENST00000416425	.	.	.	5.94	5.07	0.68467	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-15.0523	15.0966	0.72238	0.0:0.9324:0.0:0.0676	.	.	.	.	X	367;367;135;135;135	.	ENSP00000338727:E367X	E	-	1	0	LRRFIP2	37107970	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.464000	0.80887	1.527000	0.49086	0.563000	0.77884	GAA		0.448	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37132966	C	A	37132966	4	1	47	1	0	0	0	0	0	1	0	0	9057	922	32	2	1110	2	LRRFIP2	3	37132966	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1352020	37132966	160889464	416	4813										
EXOG	9941	broad.mit.edu	37	chr3	38565470	38565470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagaagctcagtatctaccGaaccactggcgctaggggcc	12	13	2	1	rs368056983		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:38565470G>A	ENST00000287675.5	+	6	820	c.724G>A	c.(724-726)Gaa>Aaa	p.E242K	EXOG_ENST00000358249.2_Intron|EXOG_ENST00000422077.2_Missense_Mutation_p.E192K	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	242					DNA catabolic process, endonucleolytic (GO:0000737)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.E242K(1)		central_nervous_system(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	17						AGTATCTACCGAACCACTGGC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	68	71	70		574,724	5.5	0.5	3		70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EXOG	NM_001145464.1,NM_005107.3	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	192/319,242/369	38565470	1,13005	2203	4300	6503	38540474	SO:0001583	missense	9941			AB020523	CCDS2680.1, CCDS46795.1	3p21.3	2010-05-07	2009-01-08	2009-01-08	ENSG00000157036	ENSG00000157036	3.1.30.-		3347	protein-coding gene	gene with protein product		604051	"endonuclease G-like 1", "endonuclease G-like 2"	ENDOGL1, ENDOGL2		10231028, 18187503	Standard	NM_005107		Approved	ENGL-a, ENGL, ENGL-b	uc003cih.2	Q9Y2C4	OTTHUMG00000131295	ENST00000287675.5:c.724G>A	3.37:g.38565470G>A	ENSP00000287675:p.Glu242Lys		38540474	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Missense_Mutation	SNP	ENST00000287675.5	37	CCDS2680.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.110575	0.56398	0.0	1.16E-4	ENSG00000157036	ENST00000287675;ENST00000422077	T;T	0.43688	0.94;0.95	5.54	5.54	0.83059	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.125559	0.52532	D	0.000067	T	0.25457	0.0619	N	0.17838	0.53	0.80722	D	1	P;P	0.45634	0.698;0.863	B;B	0.36335	0.065;0.222	T	0.04650	-1.0936	10	0.15952	T	0.53	-27.0099	15.1902	0.73038	0.0:0.1402:0.8598:0.0	.	192;242	Q9Y2C4-4;Q9Y2C4	.;EXOG_HUMAN	K	242;192	ENSP00000287675:E242K;ENSP00000404305:E192K	ENSP00000287675:E242K	E	+	1	0	EXOG	38540474	1.000000	0.71417	0.492000	0.27490	0.916000	0.54674	5.454000	0.66651	2.884000	0.98904	0.655000	0.94253	GAA		0.517	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107		A	38565470	G	A	38565470	3	1	47	1	0	0	0	0	1	0	0	0	5325	1059	37	1	746	1	EXOG	3	38565470	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1432504	38565470	159456960	417	4814										
SCN11A	11280	broad.mit.edu	37	chr3	38888876	38888876	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttacatgattcttttgatCgcagcatggggctgagcagg	13	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:38888876C>T	ENST00000302328.3	-	26	4883	c.4685G>A	c.(4684-4686)cGa>cAa	p.R1562Q	SCN11A_ENST00000450244.1_Missense_Mutation_p.R1562Q|SCN11A_ENST00000456224.3_Missense_Mutation_p.R1524Q	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1562					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R1562Q(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCTTTTGATCGCAGCATGGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	96	97					3																	38888876		2203	4300	6503	38863880	SO:0001583	missense	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4685G>A	3.37:g.38888876C>T	ENSP00000307599:p.Arg1562Gln		38863880	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	c	13.16	2.154906	0.38021	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224	D;D;D	0.97430	-4.38;-4.38;-4.38	5.3	-2.15	0.07102	Ion transport (1);	2.067950	0.02264	N	0.067819	D	0.92802	0.7711	N	0.21282	0.65	0.09310	N	1	B	0.16603	0.018	B	0.06405	0.002	D	0.85206	0.1018	10	0.62326	D	0.03	.	6.1028	0.20057	0.1412:0.4819:0.0:0.3769	.	1562	Q9UI33	SCNBA_HUMAN	Q	1562;1562;1524	ENSP00000307599:R1562Q;ENSP00000400945:R1562Q;ENSP00000416757:R1524Q	ENSP00000307599:R1562Q	R	-	2	0	SCN11A	38863880	0.000000	0.05858	0.000000	0.03702	0.805000	0.45488	-0.551000	0.06027	-0.245000	0.09625	0.441000	0.28932	CGA		0.453	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38888876	C	T	38888876	3	4	47	1	0	0	0	0	1	0	0	0	13950	884	31	1	694	1	SCN11A	3	38888876	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	323406	38888876	159133554	418	4815										
GORASP1	64689	broad.mit.edu	37	chr3	39139727	39139727	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgtcacagcccagggtgTtattctgtggtagagatctg	12	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:39139727T>G	ENST00000319283.3	-	9	2144	c.1323A>C	c.(1321-1323)taA>taC	p.*441Y	GORASP1_ENST00000479927.1_Nonstop_Mutation_p.*346Y|GORASP1_ENST00000422110.2_Nonstop_Mutation_p.*286Y|GORASP1_ENST00000476334.1_5'Flank	NM_031899.2	NP_114105.1	Q9BQQ3	GORS1_HUMAN	golgi reassembly stacking protein 1, 65kDa	0					Golgi organization (GO:0007030)|mitotic cell cycle (GO:0000278)|negative regulation of dendrite morphogenesis (GO:0050774)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)		p.*441Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(1)|ovary(3)|urinary_tract(1)	14				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		GCCCAGGGTGTTATTCTGTGG	0.587																																																1	Nonstop extension(1)	large_intestine(1)	3											76	67	70					3																	39139727		2203	4300	6503	39114731	SO:0001578	stop_lost	64689			AJ409349	CCDS2681.1, CCDS63596.1, CCDS63597.1	3p22-p21.33	2008-04-23	2002-08-29	2002-05-24	ENSG00000114745	ENSG00000114745			16769	protein-coding gene	gene with protein product		606867	"golgi phosphoprotein 5"	GOLPH5			Standard	NM_001278789		Approved	GRASP65, P65, FLJ23443	uc003ciw.1	Q9BQQ3	OTTHUMG00000131292	ENST00000319283.3:c.1323A>C	3.37:g.39139727T>G			39114731	B3KWC8|Q3SYG7|Q8N272|Q96H42	Nonstop_Mutation	SNP	ENST00000319283.3	37	CCDS2681.1	.	.	.	.	.	.	.	.	.	.	T	8.592	0.884731	0.17540	.	.	ENSG00000114745	ENST00000319283;ENST00000422110;ENST00000479927	.	.	.	4.65	3.48	0.39840	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9392	0.24483	0.0:0.1044:0.0:0.8956	.	.	.	.	Y	441;286;346	.	.	X	-	3	2	GORASP1	39114731	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.143000	0.16115	0.909000	0.36697	0.533000	0.62120	TAA		0.587	GORASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254060.1			G	39139727	T	G	39139727	4	3	47	1	0	0	0	0	0	0	0	0	6595	1732	60	4	3	4	GORASP1	3	39139727	Nonstop_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	250851	39139727	158882703	419	4816										
CSRNP1	64651	broad.mit.edu	37	chr3	39185747	39185747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagctcccgcttctcctcccGatcgatccttcgcacacctg	6	20	1	0	rs200194534		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:39185747G>A	ENST00000273153.5	-	4	838	c.661C>T	c.(661-663)Cgg>Tgg	p.R221W	CSRNP1_ENST00000514182.1_Missense_Mutation_p.R221W	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	221					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R221W(1)		central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						TTCTCCTCCCGATCGATCCTT	0.632													G|||	1	0.000199681	0	0	5008	,	,		20689	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											82	76	78					3																	39185747		2203	4300	6503	39160751	SO:0001583	missense	64651			AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.661C>T	3.37:g.39185747G>A	ENSP00000273153:p.Arg221Trp		39160751	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	CCDS2682.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.35	3.603914	0.66445	.	.	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.15372	2.43;2.43	5.14	5.14	0.70334	.	0.130824	0.50627	D	0.000111	T	0.38799	0.1054	M	0.68952	2.095	0.41250	D	0.986705	D	0.89917	1.0	D	0.87578	0.998	T	0.13308	-1.0514	10	0.66056	D	0.02	-24.1529	12.2316	0.54490	0.0:0.0:0.7138:0.2862	.	221	Q96S65	CSRN1_HUMAN	W	221	ENSP00000273153:R221W;ENSP00000422532:R221W	ENSP00000273153:R221W	R	-	1	2	CSRNP1	39160751	0.027000	0.19231	0.761000	0.31378	0.896000	0.52359	0.899000	0.28417	2.563000	0.86464	0.561000	0.74099	CGG		0.632	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		A	39185747	G	A	39185747	3	1	47	1	0	0	0	0	1	0	0	0	3969	1057	37	1	1116	1	CSRNP1	3	39185747	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	46020	39185747	158836683	420	4817										
MYRIP	25924	broad.mit.edu	37	chr3	40231682	40231682	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccgcaggctcttcccgaGaagttgggcaccaggccaga	12	15	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:40231682G>A	ENST00000302541.6	+	10	1735	c.1393G>A	c.(1393-1395)Gaa>Aaa	p.E465K	MYRIP_ENST00000444716.1_Missense_Mutation_p.E465K|MYRIP_ENST00000539167.1_Missense_Mutation_p.E278K|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000396217.3_Missense_Mutation_p.E376K|MYRIP_ENST00000425621.1_Missense_Mutation_p.E465K	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	465	Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)	p.E465K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		CTCTTCCCGAGAAGTTGGGCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	63	62					3																	40231682		2203	4300	6503	40206686	SO:0001583	missense	25924			AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1393G>A	3.37:g.40231682G>A	ENSP00000301972:p.Glu465Lys		40206686	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245025	0.59103	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	5.78	5.78	0.91487	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.342788	0.31199	N	0.008068	T	0.42720	0.1215	L	0.48642	1.525	0.42041	D	0.991079	D;P;P	0.58268	0.982;0.925;0.939	P;P;P	0.62560	0.904;0.54;0.67	T	0.04203	-1.0969	9	.	.	.	.	17.5052	0.87743	0.0:0.0:1.0:0.0	.	376;465;465	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	K	465;465;465;376;278	ENSP00000398665:E465K;ENSP00000301972:E465K;ENSP00000389323:E465K;ENSP00000379519:E376K;ENSP00000438297:E278K	.	E	+	1	0	MYRIP	40206686	1.000000	0.71417	0.994000	0.49952	0.314000	0.28054	2.752000	0.47516	2.745000	0.94114	0.655000	0.94253	GAA		0.617	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		A	40231682	G	A	40231682	3	1	47	1	0	0	0	0	1	0	0	0	10130	943	33	3	1427	3	MYRIP	3	40231682	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1045935	40231682	157790748	421	4818										
ZNF620	253639	broad.mit.edu	37	chr3	40557900	40557900	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agccttgattcagcatcagaGaatccacactggagaaaagc	9	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:40557900G>T	ENST00000314529.6	+	5	964	c.815G>T	c.(814-816)aGa>aTa	p.R272I	ZNF620_ENST00000418905.1_Missense_Mutation_p.R158I	NM_175888.3	NP_787084.1	Q6ZNG0	ZN620_HUMAN	zinc finger protein 620	272					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R272I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(1)|urinary_tract(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CAGCATCAGAGAATCCACACT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											62	65	64					3																	40557900		2203	4300	6503	40532904	SO:0001583	missense	253639			AK093599	CCDS33740.1, CCDS58825.1	3p21.33	2013-01-08			ENSG00000177842	ENSG00000177842		"Zinc fingers, C2H2-type", "-"	28742	protein-coding gene	gene with protein product						12477932	Standard	NM_175888		Approved	MGC50836	uc003ckk.4	Q6ZNG0	OTTHUMG00000156044	ENST00000314529.6:c.815G>T	3.37:g.40557900G>T	ENSP00000322265:p.Arg272Ile		40532904	Q8N223	Missense_Mutation	SNP	ENST00000314529.6	37	CCDS33740.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.344961	0.41498	.	.	ENSG00000177842	ENST00000314529;ENST00000418905	T;T	0.24908	1.83;1.83	2.83	1.94	0.25998	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35653	0.0939	L	0.47016	1.485	0.48087	D	0.999589	D	0.89917	1.0	D	0.75484	0.986	T	0.08493	-1.0719	8	.	.	.	.	4.9854	0.14187	0.2888:0.0:0.7112:0.0	.	272	Q6ZNG0	ZN620_HUMAN	I	272;158	ENSP00000322265:R272I;ENSP00000391472:R158I	.	R	+	2	0	ZNF620	40532904	0.000000	0.05858	0.805000	0.32314	0.521000	0.34408	-0.608000	0.05641	0.533000	0.28675	0.591000	0.81541	AGA		0.453	ZNF620-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342824.1	XM_171060		T	40557900	G	T	40557900	3	4	47	1	0	0	0	0	1	0	0	0	18083	942	33	2	829	2	ZNF620	3	40557900	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	326218	40557900	157464530	422	4819										
CTNNB1	1499	broad.mit.edu	37	chr3	41275649	41275649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggctactgttggattgattcGaaatcttgccctttgtcccg	10	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:41275649G>A	ENST00000349496.5	+	10	1824	c.1544G>A	c.(1543-1545)cGa>cAa	p.R515Q	CTNNB1_ENST00000453024.1_Missense_Mutation_p.R508Q|CTNNB1_ENST00000405570.1_Missense_Mutation_p.R515Q|CTNNB1_ENST00000396183.3_Missense_Mutation_p.R515Q|CTNNB1_ENST00000396185.3_Missense_Mutation_p.R515Q	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	515					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R515Q(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGATTGATTCGAAATCTTGCC	0.438		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	3											152	134	140					3																	41275649		2203	4300	6503	41250653	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1544G>A	3.37:g.41275649G>A	ENSP00000344456:p.Arg515Gln		41250653	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	35	5.543244	0.96474	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.053363	0.85682	D	0.000000	D	0.85225	0.5648	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.69479	0.865;0.964	D	0.87095	0.2175	10	0.48119	T	0.1	-12.54	20.1865	0.98220	0.0:0.0:1.0:0.0	.	443;515	B4DSW9;P35222	.;CTNB1_HUMAN	Q	515;515;515;508;515	ENSP00000385604:R515Q;ENSP00000379486:R515Q;ENSP00000344456:R515Q;ENSP00000411226:R508Q;ENSP00000379488:R515Q	ENSP00000344456:R515Q	R	+	2	0	CTNNB1	41250653	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.775000	0.95449	0.655000	0.94253	CGA		0.438	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41275649	G	A	41275649	3	1	47	1	0	0	0	0	1	0	0	0	4022	1058	37	1	1578	1	CTNNB1	3	41275649	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	717749	41275649	156746781	423	4820										
ULK4	54986	broad.mit.edu	37	chr3	41977373	41977373	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatcaggtcaattccaaattCtctcacaacatcttctggga	5	11	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:41977373C>A	ENST00000301831.4	-	4	760	c.298G>T	c.(298-300)Gaa>Taa	p.E100*	ULK4_ENST00000420927.1_Nonsense_Mutation_p.E100*	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E100*(2)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ATTCCAAATTCTCTCACAACA	0.373																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											133	128	129					3																	41977373		1884	4112	5996	41952377	SO:0001587	stop_gained	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.298G>T	3.37:g.41977373C>A	ENSP00000301831:p.Glu100*		41952377	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Nonsense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	c	38	6.917765	0.97932	.	.	ENSG00000168038	ENST00000301831;ENST00000420927	.	.	.	5.86	3.13	0.36017	.	0.611892	0.19061	N	0.123762	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	8.3118	0.32075	0.0:0.7258:0.131:0.1431	.	.	.	.	X	100	.	ENSP00000301831:E100X	E	-	1	0	ULK4	41952377	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.716000	0.47219	0.840000	0.34995	-0.121000	0.15023	GAA		0.373	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		A	41977373	C	A	41977373	4	1	47	1	0	0	0	0	0	1	0	0	17018	922	32	2	3665	2	ULK4	3	41977373	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	701724	41977373	156045057	424	4821										
CCDC13	152206	broad.mit.edu	37	chr3	42787435	42787435	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgctctgcaaaacaagaaTttgttgagcccgacccctcc	7	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:42787435T>G	ENST00000310232.6	-	7	888	c.805A>C	c.(805-807)Att>Ctt	p.I269L	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	269								p.I269L(1)		endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						AAAACAAGAATTTGTTGAGCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											79	77	78					3																	42787435		2203	4300	6503	42762439	SO:0001583	missense	152206			AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.805A>C	3.37:g.42787435T>G	ENSP00000309836:p.Ile269Leu		42762439		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953788	0.92660	.	.	ENSG00000244607	ENST00000310232	T	0.60672	0.17	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.77003	0.4067	M	0.85630	2.765	0.51767	D	0.999935	D	0.67145	0.996	D	0.77557	0.99	T	0.78802	-0.2061	10	0.40728	T	0.16	.	13.8423	0.63446	0.0:0.0:0.0:1.0	.	269	Q8IYE1	CCD13_HUMAN	L	269	ENSP00000309836:I269L	ENSP00000309836:I269L	I	-	1	0	CCDC13	42762439	1.000000	0.71417	0.865000	0.33974	0.988000	0.76386	6.712000	0.74681	1.922000	0.55676	0.533000	0.62120	ATT		0.517	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		G	42787435	T	G	42787435	3	3	47	1	0	0	0	0	1	0	0	0	2771	1493	52	4	1382	4	CCDC13	3	42787435	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	810062	42787435	155234995	425	4822										
CCBP2	1238	broad.mit.edu	37	chr3	42906744	42906744	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccagggccgggctttaaaAatagctgcagccttggtggt	15	9	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:42906744A>C	ENST00000422265.1	+	3	925	c.750A>C	c.(748-750)aaA>aaC	p.K250N	CYP8B1_ENST00000437102.1_Intron|KRBOX1_ENST00000426937.1_Intron|ACKR2_ENST00000442925.1_Missense_Mutation_p.K250N|ACKR2_ENST00000273145.2_Missense_Mutation_p.K250N|RP11-141M3.5_ENST00000471537.1_RNA	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	250					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.K250N(1)									GGGCTTTAAAAATAGCTGCAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											132	125	127					3																	42906744		2203	4300	6503	42881748	SO:0001583	missense	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.750A>C	3.37:g.42906744A>C	ENSP00000416996:p.Lys250Asn		42881748	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	A	6.421	0.445814	0.12164	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.45276	0.9;0.9;0.9	4.49	2.59	0.31030	GPCR, rhodopsin-like superfamily (1);	0.451712	0.17818	N	0.160971	T	0.40619	0.1124	L	0.48362	1.52	0.09310	N	0.999999	P	0.43542	0.81	P	0.47528	0.549	T	0.15065	-1.0450	9	.	.	.	.	8.0429	0.30532	0.2074:0.0:0.7926:0.0	.	250	O00590	CCBP2_HUMAN	N	250	ENSP00000396150:K250N;ENSP00000416996:K250N;ENSP00000273145:K250N	.	K	+	3	2	CCBP2	42881748	0.000000	0.05858	0.009000	0.14445	0.116000	0.19942	-0.009000	0.12765	0.448000	0.26722	0.460000	0.39030	AAA		0.522	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		C	42906744	A	C	42906744	3	2	47	1	0	0	0	0	1	0	0	0	2740	11	1	4	752	4	CCBP2	3	42906744	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	119309	42906744	155115686	426	4823										
C3orf23	285343	broad.mit.edu	37	chr3	44434423	44434423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacttagaaaagaactagatCgtttaaaagatgaactgtct	7	6	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:44434423C>T	ENST00000342649.4	+	6	1076	c.649C>T	c.(649-651)Cgt>Tgt	p.R217C	TCAIM_ENST00000417237.1_Missense_Mutation_p.R217C	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	217						mitochondrion (GO:0005739)		p.R217C(1)									AGAACTAGATCGTTTAAAAGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											101	103	103					3																	44434423		2203	4296	6499	44409427	SO:0001583	missense	285343				CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.649C>T	3.37:g.44434423C>T	ENSP00000341539:p.Arg217Cys		44409427	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	37	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.417801	0.83449	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.48836	0.8;0.8	5.78	5.78	0.91487	.	0.048877	0.85682	D	0.000000	T	0.70011	0.3175	M	0.71581	2.175	0.58432	D	0.999998	D	0.89917	1.0	D	0.72982	0.979	T	0.71520	-0.4568	10	0.87932	D	0	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	217	Q8N3R3	CC023_HUMAN	C	217	ENSP00000402581:R217C;ENSP00000341539:R217C	ENSP00000341539:R217C	R	+	1	0	C3orf23	44409427	1.000000	0.71417	0.974000	0.42286	0.997000	0.91878	4.711000	0.61881	2.730000	0.93505	0.655000	0.94253	CGT		0.323	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		T	44434423	C	T	44434423	3	4	47	1	0	0	0	0	1	0	0	0	2222	884	31	1	719	1	C3orf23	3	44434423	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1527679	44434423	153588007	427	4824										
TGM4	7047	broad.mit.edu	37	chr3	44943320	44943320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcatcccagcacgcagtgtgAcaggcttcgattcagctcac	10	14	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:44943320A>G	ENST00000296125.4	+	8	936	c.868A>G	c.(868-870)Aca>Gca	p.T290A	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	290					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T290A(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	ACGCAGTGTGACAGGCTTCGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	3											122	105	111					3																	44943320		2203	4300	6503	44918324	SO:0001583	missense	7047			BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.868A>G	3.37:g.44943320A>G	ENSP00000296125:p.Thr290Ala		44918324	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.330009	0.60743	.	.	ENSG00000163810	ENST00000296125	T	0.55760	0.5	3.03	0.347	0.16022	Transglutaminase-like (2);	0.145259	0.28021	U	0.016914	T	0.65396	0.2687	M	0.79475	2.455	0.35361	D	0.788216	D	0.89917	1.0	D	0.83275	0.996	T	0.67538	-0.5645	10	0.72032	D	0.01	.	4.7019	0.12830	0.7319:0.0:0.101:0.1671	.	290	P49221	TGM4_HUMAN	A	290	ENSP00000296125:T290A	ENSP00000296125:T290A	T	+	1	0	TGM4	44918324	1.000000	0.71417	0.000000	0.03702	0.007000	0.05969	3.807000	0.55591	-0.055000	0.13244	0.460000	0.39030	ACA		0.562	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		G	44943320	A	G	44943320	3	3	47	1	0	0	0	0	1	0	0	0	15871	275	10	4	898	4	TGM4	3	44943320	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	508897	44943320	153079110	428	4825										
CDCP1	64866	broad.mit.edu	37	chr3	45153825	45153825	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaactgcagctctaaaccGatgctcttatgagctttgac	8	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:45153825G>A	ENST00000296129.1	-	3	539	c.405C>T	c.(403-405)atC>atT	p.I135I	CDCP1_ENST00000425231.2_Silent_p.I135I|CDCP1_ENST00000490471.1_5'Flank	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	135						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I135I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		GCTCTAAACCGATGCTCTTAT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	3											161	167	165					3																	45153825		2203	4300	6503	45128829	SO:0001819	synonymous_variant	64866			AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.405C>T	3.37:g.45153825G>A			45128829	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Silent	SNP	ENST00000296129.1	37	CCDS2727.1																																																																																				0.552	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		A	45153825	G	A	45153825	2	1	47	1	0	0	0	0	0	0	0	1	3099	1048	37	1		1	CDCP1	3	45153825	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	210505	45153825	152868605	429	4826										
CCR9	10803	broad.mit.edu	37	chr3	45942318	45942318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagagccctattcctaacaTggctgatgactatggctctg	10	11	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:45942318T>C	ENST00000357632.2	+	3	218	c.38T>C	c.(37-39)aTg>aCg	p.M13T	CCR9_ENST00000355983.2_Start_Codon_SNP_p.M1T|LZTFL1_ENST00000536047.1_Intron|LZTFL1_ENST00000539217.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Start_Codon_SNP_p.M1T|CCR9_ENST00000422395.1_Missense_Mutation_p.W42R	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	13					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.M13T(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		ATTCCTAACATGGCTGATGAC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											110	101	104					3																	45942318		2203	4300	6503	45917322	SO:0001583	missense	10803			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.38T>C	3.37:g.45942318T>C	ENSP00000350256:p.Met13Thr		45917322	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	37	CCDS2732.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.33|10.33	1.319633|1.319633	0.23994|0.23994	.|.	.|.	ENSG00000173585|ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983|ENST00000422395	T;T;T|.	0.67865|.	-0.28;-0.29;-0.29|.	4.42|4.42	0.794|0.794	0.18638|0.18638	.|.	2.782670|.	0.02033|.	N|.	0.048728|.	T|T	0.24005|0.24005	0.0581|0.0581	N|N	0.05124|0.05124	-0.11|-0.11	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.11941|0.11941	-1.0567|-1.0567	10|6	0.66056|0.87932	D|D	0.02|0	.|.	1.0127|1.0127	0.01501|0.01501	0.1552:0.179:0.1606:0.5053|0.1552:0.179:0.1606:0.5053	.|.	13|.	P51686|.	CCR9_HUMAN|.	T|R	13;1;1|42	ENSP00000350256:M13T;ENSP00000379292:M1T;ENSP00000348260:M1T|.	ENSP00000348260:M1T|ENSP00000393267:W42R	M|W	+|+	2|1	0|0	CCR9|CCR9	45917322|45917322	0.000000|0.000000	0.05858|0.05858	0.019000|0.019000	0.16419|0.16419	0.381000|0.381000	0.30169|0.30169	-1.232000|-1.232000	0.02936|0.02936	0.291000|0.291000	0.22468|0.22468	0.460000|0.460000	0.39030|0.39030	ATG|TGG		0.448	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			C	45942318	T	C	45942318	3	2	47	1	0	0	0	0	1	0	0	0	2954	1464	51	4	44	4	CCR9	3	45942318	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	788493	45942318	152080112	430	4827										
PRSS42	339906	broad.mit.edu	37	chr3	46874626	46874626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggacaaaagctctttggaCtgagaccaccacacttgtgt	10	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:46874626C>A	ENST00000429665.1	-	3	441	c.442G>T	c.(442-444)Gtc>Ttc	p.V148F	PRSS42_ENST00000447340.1_Missense_Mutation_p.V44F	NM_182702.1	NP_874361.1	Q7Z5A4	PRS42_HUMAN	protease, serine, 42	148	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				germ cell development (GO:0007281)|spermatogenesis (GO:0007283)	anchored component of plasma membrane (GO:0046658)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.V148F(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	8						GCTCTTTGGACTGAGACCACC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	131	131					3																	46874626		1973	4151	6124	46849630	SO:0001583	missense	339906				CCDS46816.1	3p21.31	2010-05-07			ENSG00000178055	ENSG00000178055		"Serine peptidases / Serine peptidases"	30716	protein-coding gene	gene with protein product	"testis serine protease 2"					12838346	Standard	NM_182702		Approved	TESSP2	uc011bap.2	Q7Z5A4	OTTHUMG00000156496	ENST00000429665.1:c.442G>T	3.37:g.46874626C>A	ENSP00000401701:p.Val148Phe		46849630		Missense_Mutation	SNP	ENST00000429665.1	37	CCDS46816.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.661254	0.47572	.	.	ENSG00000178055	ENST00000447340;ENST00000429665	D;T	0.95307	-3.67;1.03	4.43	-1.1	0.09872	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.524486	0.14471	N	0.317574	D	0.96731	0.8933	M	0.89095	3.005	0.09310	N	1	D;D	0.76494	0.999;0.984	D;D	0.87578	0.998;0.919	D	0.91333	0.5091	10	0.72032	D	0.01	.	8.0057	0.30323	0.0:0.3581:0.0:0.6419	.	148;44	Q7Z5A4;C9JX34	PRS42_HUMAN;.	F	44;148	ENSP00000401581:V44F;ENSP00000401701:V148F	ENSP00000401701:V148F	V	-	1	0	PRSS42	46849630	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.143000	0.16115	-0.485000	0.06754	0.505000	0.49811	GTC		0.453	PRSS42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344347.1	NM_182702		A	46874626	C	A	46874626	3	1	47	1	0	0	0	0	1	0	0	0	12662	565	20	2	450	2	PRSS42	3	46874626	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	932308	46874626	151147804	431	4828										
SETD2	29072	broad.mit.edu	37	chr3	47162849	47162849	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcagaatagtgtctataacTttgactgctccgagaagaac	9	8	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:47162849T>G	ENST00000409792.3	-	3	3319	c.3277A>C	c.(3277-3279)Agt>Cgt	p.S1093R		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1093					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.S1093R(1)|p.S590R(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTCTATAACTTTGACTGCTC	0.413			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Missense(2)	large_intestine(2)	3											115	113	114					3																	47162849		2203	4300	6503	47137853	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3277A>C	3.37:g.47162849T>G	ENSP00000386759:p.Ser1093Arg		47137853	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	9.909	1.209045	0.22205	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	D;T	0.89050	-2.46;1.39	5.31	4.15	0.48705	.	0.202758	0.35495	N	0.003176	T	0.78013	0.4217	N	0.14661	0.345	0.18873	N	0.999984	B;B	0.30068	0.267;0.144	B;B	0.27608	0.081;0.022	T	0.71839	-0.4471	10	0.72032	D	0.01	.	9.0914	0.36612	0.0:0.1252:0.0:0.8748	.	1093;1093	F2Z317;Q9BYW2	.;SETD2_HUMAN	R	1093;1093;1093;1049	ENSP00000386759:S1093R;ENSP00000416401:S1049R	ENSP00000386759:S1093R	S	-	1	0	SETD2	47137853	0.954000	0.32549	0.952000	0.39060	0.917000	0.54804	1.682000	0.37628	2.236000	0.73375	0.533000	0.62120	AGT		0.413	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47162849	T	G	47162849	3	3	47	1	0	0	0	0	1	0	0	0	14168	1609	56	4	4493	4	SETD2	3	47162849	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	288223	47162849	150859581	432	4829										
IMPDH2	25915	broad.mit.edu	37	chr3	49062377	49062377	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttgtccatggcatcgagaGaacccataccgcgatatttc	9	12	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:49062377G>T	ENST00000326925.6	+	0	2012				IMPDH2_ENST00000326739.4_Missense_Mutation_p.S416Y|DALRD3_ENST00000496568.1_5'Flank	NM_199069.1	NP_951032.1	Q9BU61	NDUF3_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 3						mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)		p.S416Y(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	8						GGCATCGAGAGAACCCATACC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	84	86					3																	49062377		2203	4300	6503	49037381	SO:0001628	intergenic_variant	3615				CCDS2784.1, CCDS2785.1	3p21.31	2012-10-12	2012-05-08	2009-03-18	ENSG00000178057	ENSG00000178057		"Mitochondrial respiratory chain complex assembly factors"	29918	protein-coding gene	gene with protein product		612911	"chromosome 3 open reading frame 60", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3"	C3orf60		12653254, 9349717	Standard	NM_199069		Approved	MGC10527, DKFZP564J0123, E3-3, 2P1	uc003cvq.3	Q9BU61	OTTHUMG00000156773		3.37:g.49062377G>T			49037381		Missense_Mutation	SNP	ENST00000326925.6	37	CCDS2784.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.670619|4.670619	0.88348|0.88348	.|.	.|.	ENSG00000178035|ENSG00000178035	ENST00000429182|ENST00000326739	.|D	.|0.89810	.|-2.57	5.33|5.33	5.33|5.33	0.75918|0.75918	.|Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97244|0.97244	0.9099|0.9099	H|H	0.99312|0.99312	4.51|4.51	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	D|D	0.99107|0.99107	1.0845|1.0845	5|10	.|0.87932	.|D	.|0	-13.3086|-13.3086	19.0076|19.0076	0.92857|0.92857	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|416	.|P12268	.|IMDH2_HUMAN	L|Y	371|416	.|ENSP00000321584:S416Y	.|ENSP00000321584:S416Y	F|S	-|-	3|2	2|0	IMPDH2|IMPDH2	49037381|49037381	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.990000|0.990000	0.78478|0.78478	9.321000|9.321000	0.96353|0.96353	2.489000|2.489000	0.83994|0.83994	0.655000|0.655000	0.94253|0.94253	TTC|TCT		0.537	NDUFAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345683.2	NM_199069		T	49062377	G	T	49062377	1	4	47	0	1	0	0	0	0	0	0	0	7748	942	33	2		2	IMPDH2	3	49062377	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1899528	49062377	148960053	433	4830										
LAMB2	3913	broad.mit.edu	37	chr3	49166482	49166482	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgtcctcagcctcccaaaTtaggtggtccaggaagggcc	13	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:49166482T>G	ENST00000418109.1	-	14	1866	c.1702A>C	c.(1702-1704)Att>Ctt	p.I568L	LAMB2_ENST00000305544.4_Missense_Mutation_p.I568L	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	568	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.I568L(1)		NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCCTCCCAAATTAGGTGGTCC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											57	57	57					3																	49166482		2203	4300	6503	49141486	SO:0001583	missense	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1702A>C	3.37:g.49166482T>G	ENSP00000388325:p.Ile568Leu		49141486	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.554711	0.27739	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.33654	1.4;1.4	5.27	4.11	0.48088	Laminin IV (1);	0.333222	0.31020	N	0.008405	T	0.18299	0.0439	N	0.11201	0.11	0.21950	N	0.999457	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	10	0.15066	T	0.55	.	10.6011	0.45367	0.0:0.0762:0.0:0.9238	.	568	P55268	LAMB2_HUMAN	L	568	ENSP00000388325:I568L;ENSP00000307156:I568L	ENSP00000307156:I568L	I	-	1	0	LAMB2	49141486	0.999000	0.42202	0.945000	0.38365	0.995000	0.86356	2.144000	0.42197	0.847000	0.35167	0.533000	0.62120	ATT		0.617	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		G	49166482	T	G	49166482	3	3	47	1	0	0	0	0	1	0	0	0	8633	1493	52	4	3774	4	LAMB2	3	49166482	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	104105	49166482	148855948	434	4831										
RHOA	387	broad.mit.edu	37	chr3	49397763	49397763	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaacactccatgtacccaAaagcgccaatcctgtttgcc	6	15	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:49397763A>C	ENST00000418115.1	-	5	845	c.461T>G	c.(460-462)tTt>tGt	p.F154C	RHOA_ENST00000422781.1_3'UTR|GPX1_ENST00000419349.1_5'Flank|RHOA_ENST00000454011.2_3'UTR|GPX1_ENST00000496791.1_5'Flank|GPX1_ENST00000419783.1_5'Flank	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	154					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)	p.F154C(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CATGTACCCAAAAGCGCCAAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											330	273	292					3																	49397763		2203	4300	6503	49372767	SO:0001583	missense	387			BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"ras homolog gene family, member A"	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.461T>G	3.37:g.49397763A>C	ENSP00000400175:p.Phe154Cys		49372767	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.786506	0.70337	.	.	ENSG00000067560	ENST00000418115	T	0.76968	-1.06	6.03	6.03	0.97812	Small GTP-binding protein domain (1);	0.110550	0.64402	D	0.000006	T	0.72708	0.3494	N	0.04959	-0.14	0.80722	D	1	P	0.38642	0.641	P	0.55112	0.769	T	0.77122	-0.2704	10	0.66056	D	0.02	.	10.6084	0.45408	0.8566:0.0:0.0:0.1434	.	154	P61586	RHOA_HUMAN	C	154	ENSP00000400175:F154C	ENSP00000400175:F154C	F	-	2	0	RHOA	49372767	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.307000	0.78920	2.308000	0.77769	0.533000	0.62120	TTT		0.438	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664		C	49397763	A	C	49397763	3	2	47	1	0	0	0	0	1	0	0	0	13368	14	1	4	124	4	RHOA	3	49397763	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	231281	49397763	148624667	435	4832										
RBM5	10181	broad.mit.edu	37	chr3	50151431	50151431	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agagtttgaataagcagaaaGaaaactttaaaaatagcttt	7	3	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:50151431G>T	ENST00000347869.3	+	19	1841	c.1666G>T	c.(1666-1668)Gaa>Taa	p.E556*	RP11-493K19.3_ENST00000437204.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	556	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E556*(1)		breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TAAGCAGAAAGAAAACTTTAA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											55	57	57					3																	50151431		2203	4300	6503	50126435	SO:0001587	stop_gained	10181			U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1666G>T	3.37:g.50151431G>T	ENSP00000343054:p.Glu556*		50126435	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Nonsense_Mutation	SNP	ENST00000347869.3	37	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	G	40	8.154709	0.98680	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-19.2486	19.3898	0.94576	0.0:0.0:1.0:0.0	.	.	.	.	X	556;555;246	.	ENSP00000343054:E556X	E	+	1	0	RBM5	50126435	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.579000	0.87056	0.555000	0.69702	GAA		0.398	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		T	50151431	G	T	50151431	4	4	47	1	0	0	0	0	0	1	0	0	13180	943	33	2	1736	2	RBM5	3	50151431	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	753668	50151431	147870999	436	4833										
DOCK3	1795	broad.mit.edu	37	chr3	51127777	51127777	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggaagataccgatgtcttCttttccttatatgacatgag	10	7	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:51127777C>A	ENST00000266037.9	+	9	731	c.708C>A	c.(706-708)ttC>ttA	p.F236L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	236					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.F236L(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CCGATGTCTTCTTTTCCTTAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											75	71	72					3																	51127777		1931	4146	6077	51102817	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.708C>A	3.37:g.51127777C>A	ENSP00000266037:p.Phe236Leu		51102817	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946395	0.53079	.	.	ENSG00000088538	ENST00000266037	T	0.04603	3.59	5.33	3.5	0.40072	.	0.000000	0.85682	D	0.000000	T	0.05410	0.0143	L	0.28776	0.89	0.47778	D	0.999513	P	0.46784	0.884	P	0.47162	0.54	T	0.53739	-0.8396	10	0.14252	T	0.57	.	11.0644	0.47966	0.0:0.7823:0.0:0.2177	.	236	Q8IZD9	DOCK3_HUMAN	L	236	ENSP00000266037:F236L	ENSP00000266037:F236L	F	+	3	2	DOCK3	51102817	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.058000	0.49939	1.372000	0.46190	0.467000	0.42956	TTC		0.458	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51127777	C	A	51127777	3	1	47	1	0	0	0	0	1	0	0	0	4699	912	32	2	742	2	DOCK3	3	51127777	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	976346	51127777	146894653	437	4834										
DOCK3	1795	broad.mit.edu	37	chr3	51251554	51251554	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgcttttgtttttgcaggTcttatcatttctctgcagct	7	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:51251554T>C	ENST00000266037.9	+	14	1151	c.1128T>C	c.(1126-1128)ggT>ggC	p.G376G		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	376					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.G376G(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TTTTTGCAGGTCTTATCATTT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	3											103	97	99					3																	51251554		1862	4121	5983	51226594	SO:0001630	splice_region_variant	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1127-1T>C	3.37:g.51251554T>C			51226594	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																				0.368	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	Silent	C	51251554	T	C	51251554	5	2	47	1	0	0	0	0	0	0	1	0	4699	1681	58	4	1182	4	DOCK3	3	51251554	Splice_Site	SNP	T	TCGA-AG-3892-01A-01W-1073-09	123777	51251554	146770876	438	4835										
DOCK3	1795	broad.mit.edu	37	chr3	51315156	51315156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggaggcggtaagagggcagCggtgcccgcagtgcacagcc	18	11	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:51315156C>T	ENST00000266037.9	+	26	2817	c.2794C>T	c.(2794-2796)Cgg>Tgg	p.R932W		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	932					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R932W(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AAGAGGGCAGCGGTGCCCGCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											39	42	41					3																	51315156		2049	4180	6229	51290196	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2794C>T	3.37:g.51315156C>T	ENSP00000266037:p.Arg932Trp		51290196	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106712	0.94292	.	.	ENSG00000088538	ENST00000266037	T	0.67345	-0.26	5.25	5.25	0.73442	.	0.050697	0.85682	D	0.000000	T	0.60051	0.2239	L	0.51422	1.61	0.80722	D	1	P	0.50617	0.937	B	0.34991	0.193	T	0.69472	-0.5136	10	0.72032	D	0.01	.	19.2367	0.93864	0.0:1.0:0.0:0.0	.	932	Q8IZD9	DOCK3_HUMAN	W	932	ENSP00000266037:R932W	ENSP00000266037:R932W	R	+	1	2	DOCK3	51290196	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.976000	0.63785	2.637000	0.89404	0.585000	0.79938	CGG		0.557	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51315156	C	T	51315156	3	4	47	1	0	0	0	0	1	0	0	0	4699	759	27	1	2896	1	DOCK3	3	51315156	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	63602	51315156	146707274	439	4836										
ITIH3	3699	broad.mit.edu	37	chr3	52840981	52840981	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgactccaagaccagaaaGacttactttggaaaactggg	9	10	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:52840981G>T	ENST00000449956.2	+	19	2127	c.2121G>T	c.(2119-2121)aaG>aaT	p.K707N	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	707					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.K707N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		AGACCAGAAAGACTTACTTTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											31	34	33					3																	52840981		2042	4195	6237	52816021	SO:0001583	missense	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.2121G>T	3.37:g.52840981G>T	ENSP00000415769:p.Lys707Asn		52816021	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	G	1.598	-0.527343	0.04141	.	.	ENSG00000162267	ENST00000273291;ENST00000449956	T	0.11712	2.75	5.41	1.47	0.22746	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.369436	0.29900	N	0.010905	T	0.04003	0.0112	N	0.12611	0.24	0.28404	N	0.918501	B	0.02656	0.0	B	0.06405	0.002	T	0.36962	-0.9726	10	0.15952	T	0.53	-15.0518	1.2283	0.01938	0.2624:0.1501:0.4335:0.1541	.	707	Q06033	ITIH3_HUMAN	N	702;707	ENSP00000415769:K707N	ENSP00000273291:K702N	K	+	3	2	ITIH3	52816021	0.999000	0.42202	0.356000	0.25785	0.910000	0.53928	0.306000	0.19279	-0.009000	0.14296	0.555000	0.69702	AAG		0.572	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52840981	G	T	52840981	3	4	47	1	0	0	0	0	1	0	0	0	7926	933	33	2	2195	2	ITIH3	3	52840981	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1525825	52840981	145181449	440	4837										
LRTM1	57408	broad.mit.edu	37	chr3	54958657	54958657	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgactgacctttatagacaAatttctccagccagagttta	6	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:54958657A>C	ENST00000273286.5	-	2	755	c.593T>G	c.(592-594)tTt>tGt	p.F198C	CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.F122C|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000415676.2_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	198	LRRCT.					integral component of membrane (GO:0016021)		p.F198C(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		TTTATAGACAAATTTCTCCAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											76	81	80					3																	54958657		2203	4300	6503	54933697	SO:0001583	missense	57408			AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.593T>G	3.37:g.54958657A>C	ENSP00000273286:p.Phe198Cys		54933697	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	37	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	A	18.49	3.635366	0.67130	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90261	4.25;-2.64	5.82	5.82	0.92795	Cysteine-rich flanking region, C-terminal (1);	0.051462	0.85682	D	0.000000	D	0.95573	0.8561	M	0.85542	2.76	0.58432	D	0.999994	D	0.89917	1.0	D	0.73380	0.98	D	0.95662	0.8716	10	0.52906	T	0.07	.	16.1729	0.81831	1.0:0.0:0.0:0.0	.	198	Q9HBL6	LRTM1_HUMAN	C	198;122	ENSP00000273286:F198C;ENSP00000419772:F122C	ENSP00000273286:F198C	F	-	2	0	LRTM1	54933697	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	6.444000	0.73452	2.214000	0.71695	0.533000	0.62120	TTT		0.453	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		C	54958657	A	C	54958657	3	2	47	1	0	0	0	0	1	0	0	0	9073	14	1	4	452	4	LRTM1	3	54958657	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2117676	54958657	143063773	441	4838										
CCDC66	285331	broad.mit.edu	37	chr3	56601013	56601013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accagctgatatattcagtaCtctgggggaaagggaatgtg	13	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:56601013C>A	ENST00000394672.3	+	6	816	c.746C>A	c.(745-747)aCt>aAt	p.T249N	CCDC66_ENST00000436465.2_Missense_Mutation_p.T249N|CCDC66_ENST00000442522.2_3'UTR|CCDC66_ENST00000538560.1_Missense_Mutation_p.T249N|CCDC66_ENST00000326595.7_Missense_Mutation_p.T215N	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	249					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)			p.T132N(1)		breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		ATATTCAGTACTCTGGGGGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											120	127	125					3																	56601013		2203	4300	6503	56576053	SO:0001583	missense	285331			AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.746C>A	3.37:g.56601013C>A	ENSP00000378167:p.Thr249Asn		56576053	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.403169	0.83230	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465;ENST00000538560	D;D;D;D;D	0.99607	-6.27;-6.27;-6.27;-6.27;-6.27	5.51	5.51	0.81932	.	0.146935	0.44285	D	0.000474	D	0.99554	0.9840	M	0.76328	2.33	0.47621	D	0.999473	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98472	1.0601	10	0.62326	D	0.03	-3.125	17.595	0.88009	0.0:1.0:0.0:0.0	.	249;249	A2RUB6;A2RUB6-2	CCD66_HUMAN;.	N	249;249;215;249;249	ENSP00000401451:T249N;ENSP00000378167:T249N;ENSP00000326050:T215N;ENSP00000404320:T249N;ENSP00000444919:T249N	ENSP00000326050:T215N	T	+	2	0	CCDC66	56576053	0.995000	0.38212	1.000000	0.80357	0.990000	0.78478	2.569000	0.45973	2.591000	0.87537	0.655000	0.94253	ACT		0.358	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		A	56601013	C	A	56601013	3	1	47	1	0	0	0	0	1	0	0	0	2844	565	20	2	768	2	CCDC66	3	56601013	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1642356	56601013	141421417	442	4839										
C3orf14	57415	broad.mit.edu	37	chr3	62319060	62319060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattcaaaatgaggcacagcGataacttcttcacatgctat	6	10	3	1	rs368325890		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:62319060G>A	ENST00000494481.1	+	6	697	c.383G>A	c.(382-384)cGa>cAa	p.R128Q	C3orf14_ENST00000542214.1_Missense_Mutation_p.R128Q|PTPRG-AS1_ENST00000490916.1_RNA|C3orf14_ENST00000232519.5_Missense_Mutation_p.R128Q|PTPRG-AS1_ENST00000495542.1_RNA|C3orf14_ENST00000462069.1_Missense_Mutation_p.R128Q			Q9HBI5	CC014_HUMAN	chromosome 3 open reading frame 14	128								p.R128Q(1)		central_nervous_system(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00023)|KIRC - Kidney renal clear cell carcinoma(15;0.00877)|Kidney(15;0.0101)		GAGGCACAGCGATAACTTCTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	75	74	74		383	-4.4	0	3		74	0,8600		0,0,4300	no	missense	C3orf14	NM_020685.3	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	128/129	62319060	1,13005	2203	4300	6503	62294100	SO:0001583	missense	57415			AF236158	CCDS2896.1	3p14.2	2011-11-29			ENSG00000114405	ENSG00000114405			25024	protein-coding gene	gene with protein product						12477932	Standard	XM_005265338		Approved	HT021	uc003dlg.3	Q9HBI5	OTTHUMG00000158704	ENST00000494481.1:c.383G>A	3.37:g.62319060G>A	ENSP00000418086:p.Arg128Gln		62294100	B2R9U0	Missense_Mutation	SNP	ENST00000494481.1	37	CCDS2896.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.619081	0.28801	2.27E-4	0.0	ENSG00000114405	ENST00000462069;ENST00000232519;ENST00000494481;ENST00000542214	.	.	.	5.81	-4.4	0.03600	.	3.917030	0.01003	N	0.003710	T	0.09024	0.0223	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14896	-1.0456	9	0.08381	T	0.77	-10.9396	1.603	0.02678	0.4556:0.1058:0.2085:0.2302	.	128	Q9HBI5	CC014_HUMAN	Q	128	.	ENSP00000232519:R128Q	R	+	2	0	C3orf14	62294100	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.358000	0.07641	-1.006000	0.03412	-0.157000	0.13467	CGA		0.338	C3orf14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351807.1	NM_020685		A	62319060	G	A	62319060	3	1	47	1	0	0	0	0	1	0	0	0	2214	1058	37	1	397	1	C3orf14	3	62319060	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5718047	62319060	135703370	443	4840										
EPHA3	2042	broad.mit.edu	37	chr3	89448568	89448568	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atacgtattccaaatccgagCccgaacagccgctggatatg	9	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:89448568C>T	ENST00000336596.2	+	7	1757	c.1532C>T	c.(1531-1533)gCc>gTc	p.A511V	EPHA3_ENST00000494014.1_Missense_Mutation_p.A511V|EPHA3_ENST00000452448.2_Missense_Mutation_p.A511V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	511	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.A511V(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CAAATCCGAGCCCGAACAGCC	0.463										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	large_intestine(1)	3											93	90	91					3																	89448568		2203	4300	6503	89531258	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1532C>T	3.37:g.89448568C>T	ENSP00000337451:p.Ala511Val		89531258	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	32	5.189396	0.94923	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.76060	-0.99;-0.99;-0.99	5.53	5.53	0.82687	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89653	0.6777	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.996;1.0	D	0.91259	0.5035	9	.	.	.	.	19.4691	0.94956	0.0:1.0:0.0:0.0	.	511;511	P29320;P29320-2	EPHA3_HUMAN;.	V	511	ENSP00000337451:A511V;ENSP00000399926:A511V;ENSP00000419190:A511V	.	A	+	2	0	EPHA3	89531258	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	7.818000	0.86416	2.607000	0.88179	0.563000	0.77884	GCC		0.463	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89448568	C	T	89448568	3	4	47	1	0	0	0	0	1	0	0	0	5181	739	26	3	1558	3	EPHA3	3	89448568	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	27129508	89448568	108573862	444	4841										
STX19	415117	broad.mit.edu	37	chr3	93733429	93733429	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaatgaaaagatcccttaAatcctttatttggttctcca	5	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:93733429A>C	ENST00000315099.2	-	2	941	c.685T>G	c.(685-687)Tta>Gta	p.L229V	ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000486562.1_Intron|ARL13B_ENST00000535334.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000303097.7_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	229	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)		p.L229V(1)		kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						AGATCCCTTAAATCCTTTATT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	66	66					3																	93733429		2202	4299	6501	95216119	SO:0001583	missense	415117			AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.685T>G	3.37:g.93733429A>C	ENSP00000320679:p.Leu229Val		95216119		Missense_Mutation	SNP	ENST00000315099.2	37	CCDS33793.1	.	.	.	.	.	.	.	.	.	.	A	4.109	0.018389	0.07959	.	.	ENSG00000178750	ENST00000315099	T	0.38722	1.12	4.71	2.32	0.28847	t-SNARE (1);Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.000000	0.64402	D	0.000002	T	0.32071	0.0817	M	0.64404	1.975	0.46061	D	0.998844	P	0.42785	0.79	B	0.35931	0.214	T	0.05500	-1.0881	10	0.38643	T	0.18	.	5.5712	0.17198	0.626:0.1364:0.2376:0.0	.	229	Q8N4C7	STX19_HUMAN	V	229	ENSP00000320679:L229V	ENSP00000320679:L229V	L	-	1	2	STX19	95216119	0.175000	0.23083	0.986000	0.45419	0.987000	0.75469	0.278000	0.18753	0.396000	0.25283	0.529000	0.55759	TTA		0.323	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850		C	93733429	A	C	93733429	3	2	47	1	0	0	0	0	1	0	0	0	15381	11	1	4	203	4	STX19	3	93733429	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4284861	93733429	104289001	445	4842										
OR5K3	403277	broad.mit.edu	37	chr3	98110133	98110133	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggcaggatcaattcaaatCtttactatagtcttagtttc	6	7	4	0	rs369365160		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:98110133C>A	ENST00000383695.1	+	1	624	c.624C>A	c.(622-624)atC>atA	p.I208I	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I208I(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						CAATTCAAATCTTTACTATAG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	3											100	99	99					3																	98110133		2203	4300	6503	99592823	SO:0001819	synonymous_variant	403277				CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"GPCR / Class A : Olfactory receptors"	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.624C>A	3.37:g.98110133C>A			99592823		Silent	SNP	ENST00000383695.1	37	CCDS33803.1																																																																																				0.308	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			A	98110133	C	A	98110133	2	1	47	1	0	0	0	0	0	0	0	1	11199	903	32	2		2	OR5K3	3	98110133	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4376704	98110133	99912297	446	4843										
C3orf26	84319	broad.mit.edu	37	chr3	99895198	99895198	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatttgagccccttaaaatTtctggtttttgactggaact	7	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:99895198T>G	ENST00000421999.2	+	9	841	c.695T>G	c.(694-696)tTt>tGt	p.F232C	CMSS1_ENST00000489081.1_Missense_Mutation_p.F214C	NM_032359.3	NP_115735.2	Q9BQ75	CMS1_HUMAN	cms1 ribosomal small subunit homolog (yeast)	232							poly(A) RNA binding (GO:0044822)	p.F232C(1)									CCCTTAAAATTTCTGGTTTTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											86	89	88					3																	99895198		2203	4300	6503	101377888	SO:0001583	missense	84319				CCDS2935.1, CCDS54618.1	3q12.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000184220	ENSG00000184220			28666	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 26"	C3orf26		12477932	Standard	NM_032359		Approved	MGC4308	uc003dtl.3	Q9BQ75	OTTHUMG00000159054	ENST00000421999.2:c.695T>G	3.37:g.99895198T>G	ENSP00000410396:p.Phe232Cys		101377888	A8K5S7|B4DUM1|E9PHS3	Missense_Mutation	SNP	ENST00000421999.2	37	CCDS2935.1	.	.	.	.	.	.	.	.	.	.	T	7.630	0.678613	0.14841	.	.	ENSG00000184220	ENST00000421999;ENST00000489081;ENST00000478909	T;T;T	0.31510	1.49;1.49;1.49	4.84	3.5	0.40072	DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.106709	0.64402	D	0.000003	T	0.23210	0.0561	L	0.45581	1.43	0.38089	D	0.936895	B	0.11235	0.004	B	0.13407	0.009	T	0.09640	-1.0665	9	.	.	.	.	7.3444	0.26656	0.379:0.0:0.0:0.621	.	232	Q9BQ75	CC026_HUMAN	C	232;214;188	ENSP00000410396:F232C;ENSP00000419161:F214C;ENSP00000417293:F188C	.	F	+	2	0	C3orf26	101377888	1.000000	0.71417	1.000000	0.80357	0.128000	0.20619	4.199000	0.58426	1.923000	0.55706	0.482000	0.46254	TTT		0.388	CMSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353060.1	NM_032359		G	99895198	T	G	99895198	3	3	47	1	0	0	0	0	1	0	0	0	2224	1841	64	4	743	4	C3orf26	3	99895198	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1785065	99895198	98127232	447	4844										
NIT2	56954	broad.mit.edu	37	chr3	100064474	100064474	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggaaaaattacatttcaaGaatctaaaacattgagtccg	6	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:100064474G>A	ENST00000394140.4	+	5	473	c.382G>A	c.(382-384)Gaa>Aaa	p.E128K		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	128	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)	p.E128K(1)|p.E128*(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						TACATTTCAAGAATCTAAAAC	0.388																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(2)	3											115	108	110					3																	100064474		2203	4300	6503	101547164	SO:0001583	missense	56954			AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.382G>A	3.37:g.100064474G>A	ENSP00000377696:p.Glu128Lys		101547164	B2R9A3|D3DN47|Q8WUF0	Missense_Mutation	SNP	ENST00000394140.4	37	CCDS33806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.481036|5.481036	0.96307|0.96307	.|.	.|.	ENSG00000114021|ENSG00000114021	ENST00000394140|ENST00000497785	D|.	0.92348|.	-3.02|.	5.56|5.56	5.56|5.56	0.83823|0.83823	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.92163|0.92163	0.7515|0.7515	H|H	0.99764|0.99764	4.76|4.76	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	D|D	0.95325|0.95325	0.8424|0.8424	10|5	0.87932|.	D|.	0|.	-16.4056|-16.4056	19.4938|19.4938	0.95064|0.95064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	128|.	Q9NQR4|.	NIT2_HUMAN|.	K|K	128|221	ENSP00000377696:E128K|.	ENSP00000377696:E128K|.	E|R	+|+	1|2	0|0	NIT2|NIT2	101547164|101547164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	8.802000|8.802000	0.91910|0.91910	2.777000|2.777000	0.95525|0.95525	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.388	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202		A	100064474	G	A	100064474	3	1	47	1	0	0	0	0	1	0	0	0	10465	943	33	3	400	3	NIT2	3	100064474	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	169276	100064474	97957956	448	4845										
IMPG2	50939	broad.mit.edu	37	chr3	100963582	100963582	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagtgaatgaacttgaaggCaatgaatcaatagaaagaaa	10	3	1	7			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:100963582C>T	ENST00000193391.7	-	13	1780	c.1593G>A	c.(1591-1593)ttG>ttA	p.L531L		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	531					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.L531L(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	AACTTGAAGGCAATGAATCAA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	3											85	79	81					3																	100963582		2203	4300	6503	102446272	SO:0001819	synonymous_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1593G>A	3.37:g.100963582C>T			102446272	A8MWT5|Q9UKD4|Q9UKK5	Silent	SNP	ENST00000193391.7	37	CCDS2940.1																																																																																				0.343	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			T	100963582	C	T	100963582	2	4	47	1	0	0	0	0	0	0	0	1	7750	709	25	3		3	IMPG2	3	100963582	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	899108	100963582	97058848	449	4846										
SENP7	57337	broad.mit.edu	37	chr3	101046585	101046585	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctgtttaggaactttaggGcatagatccaccatgtttgt	9	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:101046585G>A	ENST00000394095.2	-	23	2993	c.2940C>T	c.(2938-2940)tgC>tgT	p.C980C	SENP7_ENST00000358203.3_Silent_p.C816C|SENP7_ENST00000394085.3_Silent_p.C168C|SENP7_ENST00000314261.7_Silent_p.C914C|SENP7_ENST00000394094.2_Silent_p.C915C|SENP7_ENST00000394091.1_Silent_p.C816C|SENP7_ENST00000348610.3_Silent_p.C947C	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	980	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.C914C(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GAACTTTAGGGCATAGATCCA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	3											216	191	199					3																	101046585		2203	4300	6503	102529275	SO:0001819	synonymous_variant	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2940C>T	3.37:g.101046585G>A			102529275	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																				0.343	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101046585	G	A	101046585	2	1	47	1	0	0	0	0	0	0	0	1	14088	1195	42	3		3	SENP7	3	101046585	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	83003	101046585	96975845	450	4847										
RG9MTD1	54931	broad.mit.edu	37	chr3	101283714	101283714	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttacccttcataggaagaGaaataacttaacaattttgc	5	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:101283714G>T	ENST00000309922.6	+	2	243	c.89G>T	c.(88-90)aGa>aTa	p.R30I		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	30					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.R30I(1)									CATAGGAAGAGAAATAACTTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											149	139	142					3																	101283714		1819	4077	5896	102766404	SO:0001583	missense	54931			AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.89G>T	3.37:g.101283714G>T	ENSP00000312356:p.Arg30Ile		102766404	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	37	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	G	9.809	1.182646	0.21870	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.26518	2.34;1.73	6.04	1.18	0.20946	.	0.900493	0.09677	N	0.770352	T	0.13329	0.0323	N	0.19112	0.55	0.09310	N	0.999997	P	0.37864	0.61	B	0.31191	0.125	T	0.17167	-1.0378	10	0.66056	D	0.02	-22.1533	4.9798	0.14158	0.3278:0.2615:0.4107:0.0	.	30	Q7L0Y3	MRRP1_HUMAN	I	30	ENSP00000312356:R30I;ENSP00000419389:R30I	ENSP00000312356:R30I	R	+	2	0	RG9MTD1	102766404	0.998000	0.40836	0.095000	0.20976	0.488000	0.33401	0.701000	0.25616	-0.058000	0.13177	0.563000	0.77884	AGA		0.388	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		T	101283714	G	T	101283714	3	4	47	1	0	0	0	0	1	0	0	0	13308	942	33	2	91	2	RG9MTD1	3	101283714	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	237129	101283714	96738716	451	4848										
MORC1	27136	broad.mit.edu	37	chr3	108818291	108818291	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcgtaaaaagaataaagtCttttccaattctcatggacc	5	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:108818291C>A	ENST00000483760.1	-	6	380	c.337G>T	c.(337-339)Gac>Tac	p.D113Y	MORC1_ENST00000232603.5_Missense_Mutation_p.D113Y|MORC1-AS1_ENST00000480826.1_RNA					MORC family CW-type zinc finger 1									p.D113Y(2)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						AGAATAAAGTCTTTTCCAATT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	3											106	105	106					3																	108818291		2201	4299	6500	110300981	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.337G>T	3.37:g.108818291C>A	ENSP00000417282:p.Asp113Tyr		110300981		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	C	20.5	4.007224	0.75046	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.73152	-0.72;-0.72	4.91	4.91	0.64330	ATPase-like, ATP-binding domain (3);	0.000000	0.52532	D	0.000076	D	0.86686	0.5992	M	0.90019	3.08	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89003	0.3423	10	0.72032	D	0.01	-20.2305	15.9856	0.80151	0.0:1.0:0.0:0.0	.	113;113	E7ERX1;Q86VD1	.;MORC1_HUMAN	Y	113	ENSP00000232603:D113Y;ENSP00000417282:D113Y	ENSP00000232603:D113Y	D	-	1	0	MORC1	110300981	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	6.641000	0.74324	2.712000	0.92718	0.650000	0.86243	GAC		0.348	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108818291	C	A	108818291	3	1	47	1	0	0	0	0	1	0	0	0	9731	913	32	2	2709	2	MORC1	3	108818291	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7534577	108818291	89204139	452	4849										
DPPA2	151871	broad.mit.edu	37	chr3	109023367	109023367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattatcttctatgcctgggGatgggaaaatgcaggcaggt	13	6	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:109023367G>A	ENST00000478945.1	-	7	1055	c.809C>T	c.(808-810)tCc>tTc	p.S270F		NM_138815.3	NP_620170.3	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	270					lung-associated mesenchyme development (GO:0060484)|positive regulation of stem cell proliferation (GO:2000648)|regulation of histone methylation (GO:0031060)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|nucleic acid binding (GO:0003676)	p.S270F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TATGCCTGGGGATGGGAAAAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											75	71	72					3																	109023367		2203	4300	6503	110506057	SO:0001583	missense	151871			AY283672	CCDS2956.1	3q13.13	2010-05-04			ENSG00000163530	ENSG00000163530			19197	protein-coding gene	gene with protein product	"cancer/testis antigen 100"	614445				15583978	Standard	NM_138815		Approved	PESCRG1, CT100	uc003dxo.3	Q7Z7J5	OTTHUMG00000159227	ENST00000478945.1:c.809C>T	3.37:g.109023367G>A	ENSP00000417710:p.Ser270Phe		110506057	Q8WVF0	Missense_Mutation	SNP	ENST00000478945.1	37	CCDS2956.1	.	.	.	.	.	.	.	.	.	.	G	4.460	0.085120	0.08583	.	.	ENSG00000163530	ENST00000478945	T	0.34072	1.38	5.2	2.34	0.29019	.	1.048650	0.07482	N	0.904142	T	0.30135	0.0755	L	0.36672	1.1	0.09310	N	1	B	0.18863	0.031	B	0.23419	0.046	T	0.35968	-0.9767	10	0.87932	D	0	3.0E-4	5.9715	0.19355	0.0893:0.0:0.5646:0.346	.	270	Q7Z7J5	DPPA2_HUMAN	F	270	ENSP00000417710:S270F	ENSP00000417710:S270F	S	-	2	0	DPPA2	110506057	0.047000	0.20315	0.000000	0.03702	0.156000	0.22039	0.636000	0.24644	0.302000	0.22762	0.555000	0.69702	TCC		0.478	DPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353938.1	NM_138815		A	109023367	G	A	109023367	3	1	47	1	0	0	0	0	1	0	0	0	4745	1174	41	3	95	3	DPPA2	3	109023367	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	205076	109023367	88999063	453	4850										
PLCXD2	257068	broad.mit.edu	37	chr3	111427208	111427208	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtggaaagtttgacgctgcGaactctgtgggagaagaact	14	6	1	3	rs201796337		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:111427208G>A	ENST00000477665.1	+	2	923	c.599G>A	c.(598-600)cGa>cAa	p.R200Q	PLCXD2_ENST00000393934.3_Missense_Mutation_p.R200Q	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	200	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)	p.R200Q(1)		endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						TTGACGCTGCGAACTCTGTGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	58	58	58		599,599	-6.8	0	3		58	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	PLCXD2	NM_001185106.1,NM_153268.3	43,43	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	200/306,200/305	111427208	2,13004	2203	4300	6503	112909898	SO:0001583	missense	257068			AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.599G>A	3.37:g.111427208G>A	ENSP00000420686:p.Arg200Gln		112909898	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	37	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	G	0.104	-1.148449	0.01714	0.0	2.33E-4	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.73	-6.77	0.01727	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.17959	0.0431	N	0.02765	-0.5	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33189	-0.9878	8	0.19147	T	0.46	-0.5606	16.6553	0.85226	0.3462:0.0:0.6538:0.0	.	200;200	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	Q	200	.	ENSP00000377511:R200Q	R	+	2	0	PLCXD2	112909898	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.039000	0.12124	-1.233000	0.02551	-0.150000	0.13652	CGA		0.512	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111427208	G	A	111427208	3	1	47	1	0	0	0	0	1	0	0	0	12073	1058	37	1	605	1	PLCXD2	3	111427208	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2403841	111427208	86595222	454	4851										
TMPRSS7	344805	broad.mit.edu	37	chr3	111793181	111793181	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacttttaagtgtggcaatGatatttgctttaggaaacaa	9	4	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:111793181G>T	ENST00000452346.2	+	14	1708	c.1705G>T	c.(1705-1707)Gat>Tat	p.D569Y	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.D443Y			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	569	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D298Y(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GTGTGGCAATGATATTTGCTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											179	168	171					3																	111793181		1918	4119	6037	113275871	SO:0001583	missense	344805			BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1705G>T	3.37:g.111793181G>T	ENSP00000398236:p.Asp569Tyr		113275871	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	37		.	.	.	.	.	.	.	.	.	.	G	18.30	3.594516	0.66219	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	D;D	0.95342	-3.68;-3.68	6.17	3.44	0.39384	.	0.297427	0.37483	N	0.002080	D	0.90549	0.7038	N	0.17474	0.49	0.40973	D	0.984717	P;P	0.48589	0.912;0.892	P;B	0.51487	0.671;0.413	D	0.89334	0.3649	10	0.66056	D	0.02	.	6.9549	0.24565	0.319:0.0:0.681:0.0	.	569;443	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	Y	569;557;543;443	ENSP00000398236:D569Y;ENSP00000411645:D443Y	ENSP00000411645:D443Y	D	+	1	0	TMPRSS7	113275871	1.000000	0.71417	0.997000	0.53966	0.936000	0.57629	3.547000	0.53663	0.944000	0.37579	0.655000	0.94253	GAT		0.373	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111793181	G	T	111793181	3	4	47	1	0	0	0	0	1	0	0	0	16291	1290	45	2	1369	2	TMPRSS7	3	111793181	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	365973	111793181	86229249	455	4852										
CD200R1	131450	broad.mit.edu	37	chr3	112666716	112666716	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acattacctaaagcatgattCtccttgctagtttgcagcat	6	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:112666716C>T	ENST00000308611.3	-	2	387	c.123G>A	c.(121-123)gaG>gaA	p.E41E	CD200R1_ENST00000440122.2_Silent_p.E41E|CD200R1_ENST00000490004.1_Intron|CD200R1_ENST00000471858.1_Intron|CD200R1_ENST00000295863.4_Intron	NM_138806.3	NP_620161.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	22					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.E41E(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						AAGCATGATTCTCCTTGCTAG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	3											122	115	118					3																	112666716		2203	4300	6503	114149406	SO:0001819	synonymous_variant	131450			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000308611.3:c.123G>A	3.37:g.112666716C>T			114149406	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000308611.3	37	CCDS2969.1																																																																																				0.378	CD200R1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354466.1	NM_138806		T	112666716	C	T	112666716	2	4	47	1	0	0	0	0	0	0	0	1	2987	912	32	3		3	CD200R1	3	112666716	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	873535	112666716	85355714	456	4853										
GTPBP8	29083	broad.mit.edu	37	chr3	112715818	112715818	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgccatagaaatgtgtgaaGaatttgcattaccttatgtg	9	5	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:112715818G>T	ENST00000383678.2	+	4	728	c.646G>T	c.(646-648)Gaa>Taa	p.E216*	GTPBP8_ENST00000383677.3_Nonsense_Mutation_p.E183*|GTPBP8_ENST00000467752.1_Nonsense_Mutation_p.E105*|GTPBP8_ENST00000473129.1_Nonsense_Mutation_p.E66*	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	216	EngB-type G.				barrier septum assembly (GO:0000917)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.E216*(1)		kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	6						AATGTGTGAAGAATTTGCATT	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											143	147	146					3																	112715818		2202	4299	6501	114198508	SO:0001587	stop_gained	29083			BC037163	CCDS33820.1, CCDS33821.1	3q13.2	2008-02-05			ENSG00000163607	ENSG00000163607			25007	protein-coding gene	gene with protein product							Standard	NM_014170		Approved	HSPC135	uc003dzn.3	Q8N3Z3	OTTHUMG00000159268	ENST00000383678.2:c.646G>T	3.37:g.112715818G>T	ENSP00000373176:p.Glu216*		114198508	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Nonsense_Mutation	SNP	ENST00000383678.2	37	CCDS33820.1	.	.	.	.	.	.	.	.	.	.	G	37	5.986490	0.97173	.	.	ENSG00000163607	ENST00000383678;ENST00000383677;ENST00000305485;ENST00000467752;ENST00000473129	.	.	.	5.73	5.73	0.89815	.	0.173338	0.49916	D	0.000122	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-17.649	18.6782	0.91537	0.0:0.0:1.0:0.0	.	.	.	.	X	216;183;239;105;66	.	ENSP00000303802:E239X	E	+	1	0	GTPBP8	114198508	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.065000	0.76727	2.710000	0.92621	0.561000	0.74099	GAA		0.333	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		T	112715818	G	T	112715818	4	4	47	1	0	0	0	0	0	1	0	0	6905	943	33	2	660	2	GTPBP8	3	112715818	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	49102	112715818	85306612	457	4854										
ZBTB20	26137	broad.mit.edu	37	chr3	114070651	114070651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgctgctcgttgagggtctCgagcacggaattgctgaagt	15	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:114070651C>T	ENST00000474710.1	-	4	452	c.274G>A	c.(274-276)Gag>Aag	p.E92K	ZBTB20_ENST00000462705.1_Missense_Mutation_p.E19K|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000481632.1_Missense_Mutation_p.E19K|ZBTB20_ENST00000471418.1_Missense_Mutation_p.E19K|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000357258.3_Missense_Mutation_p.E19K|ZBTB20_ENST00000393785.2_Missense_Mutation_p.E19K|ZBTB20_ENST00000464560.1_Missense_Mutation_p.E19K	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	92						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.E19K(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		TTGAGGGTCTCGAGCACGGAA	0.592																																					NSCLC(69;748 1344 9802 11203 30933)											1	Substitution - Missense(1)	large_intestine(1)	3											66	69	68					3																	114070651		2203	4299	6502	115553341	SO:0001583	missense	26137			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.274G>A	3.37:g.114070651C>T	ENSP00000419153:p.Glu92Lys		115553341	Q63HP6|Q8N6R5|Q9Y410	Missense_Mutation	SNP	ENST00000474710.1	37	CCDS54626.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472330	0.84533	.	.	ENSG00000181722	ENST00000462705;ENST00000393785;ENST00000481632;ENST00000471418;ENST00000474710;ENST00000357258;ENST00000464560;ENST00000470311	T;T;T;T;T;T;T;T	0.70631	1.99;1.99;1.99;1.99;1.99;1.99;1.99;-0.5	6.1	6.1	0.99115	BTB/POZ fold (2);	0.051855	0.85682	D	0.000000	T	0.57330	0.2046	N	0.17564	0.495	0.58432	D	0.999997	D	0.53462	0.96	B	0.36989	0.238	T	0.65948	-0.6044	10	0.87932	D	0	.	20.7146	0.99709	0.0:1.0:0.0:0.0	.	92	Q9HC78	ZBT20_HUMAN	K	19;19;19;19;92;19;19;19	ENSP00000420324:E19K;ENSP00000377375:E19K;ENSP00000418092:E19K;ENSP00000419902:E19K;ENSP00000419153:E92K;ENSP00000349803:E19K;ENSP00000417307:E19K;ENSP00000420684:E19K	ENSP00000349803:E19K	E	-	1	0	ZBTB20	115553341	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.920000	0.70017	2.902000	0.99343	0.650000	0.86243	GAG		0.592	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		T	114070651	C	T	114070651	3	4	47	1	0	0	0	0	1	0	0	0	17568	893	31	1	1959	1	ZBTB20	3	114070651	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1354833	114070651	83951779	458	4855										
ARHGAP31	57514	broad.mit.edu	37	chr3	119120696	119120696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaccaagggaaatttcaatcGaacagttaccaccggtggat	9	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:119120696G>A	ENST00000264245.4	+	10	1629	c.1097G>A	c.(1096-1098)cGa>cAa	p.R366Q		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	366					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.R366Q(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AATTTCAATCGAACAGTTACC	0.512																																					Pancreas(7;176 297 5394 51128 51241)											1	Substitution - Missense(1)	large_intestine(1)	3											29	32	31					3																	119120696		1923	4132	6055	120603386	SO:0001583	missense	57514				CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.1097G>A	3.37:g.119120696G>A	ENSP00000264245:p.Arg366Gln		120603386	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.288097	0.80803	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.09255	3.0	5.48	5.48	0.80851	.	0.212247	0.32785	N	0.005649	T	0.17023	0.0409	M	0.64997	1.995	0.40145	D	0.97688	D	0.53745	0.962	B	0.42319	0.383	T	0.01188	-1.1424	10	0.87932	D	0	.	18.5258	0.90971	0.0:0.0:1.0:0.0	.	366	Q2M1Z3	RHG31_HUMAN	Q	366	ENSP00000264245:R366Q	ENSP00000264245:R366Q	R	+	2	0	ARHGAP31	120603386	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.895000	0.48648	2.850000	0.98022	0.655000	0.94253	CGA		0.512	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119120696	G	A	119120696	3	1	47	1	0	0	0	0	1	0	0	0	880	1058	37	1	1135	1	ARHGAP31	3	119120696	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5050045	119120696	78901734	459	4856										
ARHGAP31	57514	broad.mit.edu	37	chr3	119133024	119133024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggcctgcacccagacctcGccagcctggctcctctggaa	11	17	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:119133024G>A	ENST00000264245.4	+	12	2780	c.2248G>A	c.(2248-2250)Gcc>Acc	p.A750T		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	750	Pro-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.A750T(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CCCAGACCTCGCCAGCCTGGC	0.592																																					Pancreas(7;176 297 5394 51128 51241)											1	Substitution - Missense(1)	large_intestine(1)	3											52	57	56					3																	119133024		1996	4160	6156	120615714	SO:0001583	missense	57514				CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2248G>A	3.37:g.119133024G>A	ENSP00000264245:p.Ala750Thr		120615714	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.532782	0.27387	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07114	3.22	5.3	-5.06	0.02946	.	0.742689	0.12728	N	0.444136	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.40421	-0.9564	10	0.23891	T	0.37	.	4.654	0.12608	0.338:0.1019:0.4663:0.0939	.	750	Q2M1Z3	RHG31_HUMAN	T	750	ENSP00000264245:A750T	ENSP00000264245:A750T	A	+	1	0	ARHGAP31	120615714	0.000000	0.05858	0.000000	0.03702	0.268000	0.26511	-0.651000	0.05372	-0.899000	0.03901	-0.137000	0.14449	GCC		0.592	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119133024	G	A	119133024	3	1	47	1	0	0	0	0	1	0	0	0	880	1087	38	1	2294	1	ARHGAP31	3	119133024	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	12328	119133024	78889406	460	4857										
GPR156	165829	broad.mit.edu	37	chr3	119886062	119886062	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccggtggcagcggcagaaGaactcatctgagctgctgga	16	10	2	3	rs368406321		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:119886062G>T	ENST00000464295.1	-	10	2707	c.2262C>A	c.(2260-2262)ttC>ttA	p.F754L	GPR156_ENST00000461057.1_Missense_Mutation_p.F750L|GPR156_ENST00000315843.3_Missense_Mutation_p.F754L			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	754						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)	p.F754L(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		AGCGGCAGAAGAACTCATCTG	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	3											78	88	85					3																	119886062		2203	4300	6503	121368752	SO:0001583	missense	165829			AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2262C>A	3.37:g.119886062G>T	ENSP00000417261:p.Phe754Leu		121368752	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	37	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	G	9.521	1.108331	0.20714	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.22945	1.93;1.93;1.93	4.97	3.03	0.35002	.	0.662303	0.15293	N	0.270073	T	0.11367	0.0277	N	0.08118	0	0.29944	N	0.820789	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.18840	-1.0324	9	.	.	.	-9.4612	7.6332	0.28251	0.0:0.2571:0.4193:0.3235	.	750;754	E9PFZ4;Q8NFN8	.;GP156_HUMAN	L	754;754;750	ENSP00000417261:F754L;ENSP00000324553:F754L;ENSP00000418758:F750L	.	F	-	3	2	GPR156	121368752	0.642000	0.27260	1.000000	0.80357	0.987000	0.75469	0.664000	0.25068	1.459000	0.47892	0.561000	0.74099	TTC		0.562	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		T	119886062	G	T	119886062	3	4	47	1	0	0	0	0	1	0	0	0	6681	933	33	2	186	2	GPR156	3	119886062	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	753038	119886062	78136368	461	4858										
RABL3	285282	broad.mit.edu	37	chr3	120424908	120424908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagagcttccaatgaccaacGacgcaagttttgggaggact	12	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:120424908G>A	ENST00000273375.3	-	4	351	c.322C>T	c.(322-324)Cgt>Tgt	p.R108C	RABL3_ENST00000483733.1_Missense_Mutation_p.R108C|RABL3_ENST00000491398.1_5'UTR	NM_173825.3	NP_776186.2	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3	108	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)	p.R108G(1)|p.R108C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)	17				GBM - Glioblastoma multiforme(114;0.151)		AATGACCAACGACGCAAGTTT	0.383																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	3											114	115	114					3																	120424908		2203	4300	6503	121907598	SO:0001583	missense	285282			BC020832	CCDS3001.1	3q13.33	2008-02-05			ENSG00000144840	ENSG00000144840			18072	protein-coding gene	gene with protein product						12477932	Standard	NM_173825		Approved	MGC23920	uc003edx.3	Q5HYI8	OTTHUMG00000159668	ENST00000273375.3:c.322C>T	3.37:g.120424908G>A	ENSP00000273375:p.Arg108Cys		121907598	Q8WUD3	Missense_Mutation	SNP	ENST00000273375.3	37	CCDS3001.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802850	0.90623	.	.	ENSG00000144840	ENST00000273375;ENST00000483733	T;T	0.77620	-1.11;-1.11	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.85287	0.5662	L	0.46819	1.47	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85142	0.0981	10	0.52906	T	0.07	-6.8433	18.6251	0.91334	0.0:0.0:1.0:0.0	.	108	Q5HYI8	RABL3_HUMAN	C	108	ENSP00000273375:R108C;ENSP00000419986:R108C	ENSP00000273375:R108C	R	-	1	0	RABL3	121907598	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.405000	0.80007	2.647000	0.89833	0.655000	0.94253	CGT		0.383	RABL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356776.1	NM_173825		A	120424908	G	A	120424908	3	1	47	1	0	0	0	0	1	0	0	0	13009	1058	37	1	408	1	RABL3	3	120424908	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	538846	120424908	77597522	462	4859										
POLQ	10721	broad.mit.edu	37	chr3	121230747	121230747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcttacctccagaatagctCgtatcatgctgccagttact	6	13	2	1	rs375451342		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:121230747C>T	ENST00000264233.5	-	10	1726	c.1598G>A	c.(1597-1599)cGa>cAa	p.R533Q		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	533	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.R668Q(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAGAATAGCTCGTATCATGCT	0.368								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - Missense(1)	large_intestine(1)	3						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	110	107	108		1598	5.3	1	3		108	0,8600		0,0,4300	no	missense	POLQ	NM_199420.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	533/2591	121230747	1,13005	2203	4300	6503	122713437	SO:0001583	missense	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1598G>A	3.37:g.121230747C>T	ENSP00000264233:p.Arg533Gln		122713437	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	36	5.598116	0.96614	2.27E-4	0.0	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.43294	0.95	5.32	5.32	0.75619	Helicase, C-terminal (1);	0.066760	0.56097	D	0.000029	T	0.61223	0.2330	M	0.93328	3.405	0.58432	D	0.999998	P	0.50819	0.939	B	0.44133	0.442	T	0.75611	-0.3258	10	0.72032	D	0.01	.	18.9823	0.92760	0.0:1.0:0.0:0.0	.	533	O75417	DPOLQ_HUMAN	Q	156;533;669	ENSP00000264233:R533Q	ENSP00000264233:R533Q	R	-	2	0	POLQ	122713437	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.149000	0.77396	2.458000	0.83093	0.455000	0.32223	CGA		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121230747	C	T	121230747	3	4	47	1	0	0	0	0	1	0	0	0	12239	884	31	1	6258	1	POLQ	3	121230747	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	805839	121230747	76791683	463	4860										
POLQ	10721	broad.mit.edu	37	chr3	121251840	121251840	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacatatattgatttaccttCacttgtagcatgggctcaaa	6	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:121251840C>A	ENST00000264233.5	-	6	1085	c.957G>T	c.(955-957)gtG>gtT	p.V319V	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	319					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.V452V(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GATTTACCTTCACTTGTAGCA	0.348								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - coding silent(1)	large_intestine(1)	3											62	67	65					3																	121251840		2203	4300	6503	122734530	SO:0001819	synonymous_variant	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.957G>T	3.37:g.121251840C>A			122734530	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																				0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121251840	C	A	121251840	2	1	47	1	0	0	0	0	0	0	0	1	12239	813	29	2		2	POLQ	3	121251840	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	21093	121251840	76770590	464	4861										
FBXO40	51725	broad.mit.edu	37	chr3	121340649	121340649	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agacccccagtgaggagtgtTtggacacagccctggccctg	13	13	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:121340649T>C	ENST00000338040.4	+	3	787	c.373T>C	c.(373-375)Ttg>Ctg	p.L125L		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	125					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L125L(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		TGAGGAGTGTTTGGACACAGC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	3											53	57	56					3																	121340649		2203	4300	6503	122823339	SO:0001819	synonymous_variant	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.373T>C	3.37:g.121340649T>C			122823339	B2RAX7|Q32M70|Q9ULM5	Silent	SNP	ENST00000338040.4	37	CCDS33835.1																																																																																				0.522	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		C	121340649	T	C	121340649	2	2	47	1	0	0	0	0	0	0	0	1	5768	1838	64	4		4	FBXO40	3	121340649	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	88809	121340649	76681781	465	4862										
GOLGB1	2804	broad.mit.edu	37	chr3	121416427	121416427	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtcaaattcatgctgaagTtcttccttacttatttgtcc	6	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:121416427T>C	ENST00000340645.5	-	13	3053	c.2928A>G	c.(2926-2928)gaA>gaG	p.E976E	GOLGB1_ENST00000393667.3_Silent_p.E981E	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	976					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.E976E(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CATGCTGAAGTTCTTCCTTAC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3											82	85	84					3																	121416427		2203	4300	6503	122899117	SO:0001819	synonymous_variant	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2928A>G	3.37:g.121416427T>C			122899117	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	1.550	-0.539364	0.04053	.	.	ENSG00000173230	ENST00000489400	.	.	.	5.35	7.93E-4	0.14043	.	.	.	.	.	T	0.50326	0.1609	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34378	-0.9831	4	.	.	.	.	5.1281	0.14896	0.0:0.3601:0.1587:0.4812	.	.	.	.	S	847	.	.	N	-	2	0	GOLGB1	122899117	0.000000	0.05858	0.993000	0.49108	0.719000	0.41307	-0.715000	0.04997	-0.123000	0.11745	0.533000	0.62120	AAC		0.388	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121416427	T	C	121416427	2	2	47	1	0	0	0	0	0	0	0	1	6585	1722	60	4		4	GOLGB1	3	121416427	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	75778	121416427	76606003	466	4863										
CSTA	1475	broad.mit.edu	37	chr3	122056405	122056405	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttctttaggttaaaccacaGcttgaagaaaaaacaaatga	6	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:122056405G>A	ENST00000264474.3	+	2	127	c.78G>A	c.(76-78)caG>caA	p.Q26Q	CSTA_ENST00000479204.1_Silent_p.Q26Q	NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	26					keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.Q26Q(1)		large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		TTAAACCACAGCTTGAAGAAA	0.353																																					Pancreas(26;157 1503 12440)											1	Substitution - coding silent(1)	large_intestine(1)	3											82	84	84					3																	122056405		2203	4300	6503	123539095	SO:0001819	synonymous_variant	1475				CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.78G>A	3.37:g.122056405G>A			123539095	Q6IB90	Silent	SNP	ENST00000264474.3	37	CCDS3011.1																																																																																				0.353	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213		A	122056405	G	A	122056405	2	1	47	1	0	0	0	0	0	0	0	1	3987	962	34	3		3	CSTA	3	122056405	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	639978	122056405	75966025	467	4864										
PARP9	83666	broad.mit.edu	37	chr3	122271311	122271311	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagtacatggtatatatatTtacagaacaagttaaatcct	5	6	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:122271311T>G	ENST00000360356.2	-	5	1393	c.1166A>C	c.(1165-1167)aAa>aCa	p.K389T	PARP9_ENST00000471785.1_Missense_Mutation_p.K354T|PARP9_ENST00000492382.1_Intron|PARP9_ENST00000462315.1_Missense_Mutation_p.K354T|PARP9_ENST00000477522.2_Missense_Mutation_p.K354T	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	389	Macro 2. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.K389T(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		GTATATATATTTACAGAACAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											83	83	83					3																	122271311		2203	4300	6503	123754001	SO:0001583	missense	83666			AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.1166A>C	3.37:g.122271311T>G	ENSP00000353512:p.Lys389Thr		123754001	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	T	5.007	0.186903	0.09547	.	.	ENSG00000138496	ENST00000360356;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	4.3	-3.51	0.04696	Appr-1-p processing (3);	1.351180	0.04897	N	0.450527	T	0.27063	0.0663	M	0.65498	2.005	0.09310	N	1	B;B;B	0.30511	0.282;0.175;0.041	B;B;B	0.30316	0.114;0.112;0.032	T	0.31806	-0.9930	10	0.56958	D	0.05	.	1.0782	0.01637	0.1505:0.294:0.1551:0.4004	.	354;389;354	E9PFM7;Q8IXQ6;Q8IXQ6-2	.;PARP9_HUMAN;.	T	389;354;354;312;354	ENSP00000353512:K389T;ENSP00000419506:K354T;ENSP00000419001:K354T;ENSP00000418894:K354T	ENSP00000353512:K389T	K	-	2	0	PARP9	123754001	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.372000	0.07504	-0.709000	0.05008	-1.832000	0.00591	AAA		0.358	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		G	122271311	T	G	122271311	3	3	47	1	0	0	0	0	1	0	0	0	11497	1841	64	4	1479	4	PARP9	3	122271311	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	214906	122271311	75751119	468	4865										
SEMA5B	54437	broad.mit.edu	37	chr3	122634448	122634448	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccatgggccgaagcccccAtcccgtgtcacattccgcac	9	18	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:122634448A>C	ENST00000357599.3	-	14	2213	c.1827T>G	c.(1825-1827)gaT>gaG	p.D609E	SEMA5B_ENST00000195173.4_Missense_Mutation_p.D609E|SEMA5B_ENST00000451055.2_Missense_Mutation_p.D663E	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	609					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.D609E(1)|p.D663E(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CGAAGCCCCCATCCCGTGTCA	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	3											60	59	59					3																	122634448		2203	4300	6503	124117138	SO:0001583	missense	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1827T>G	3.37:g.122634448A>C	ENSP00000350215:p.Asp609Glu		124117138	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.396791	0.62177	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	4.88	0.989	0.19802	.	0.205916	0.51477	D	0.000089	T	0.36717	0.0977	M	0.81614	2.55	0.45172	D	0.998189	D;D;D	0.58268	0.982;0.969;0.969	P;P;P	0.56127	0.792;0.701;0.701	T	0.25537	-1.0129	10	0.87932	D	0	.	8.8731	0.35327	0.7715:0.0:0.2285:0.0	.	551;609;609	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	E	609;609;551;663;609	ENSP00000350215:D609E;ENSP00000195173:D609E;ENSP00000389588:D663E;ENSP00000377208:D609E	ENSP00000195173:D609E	D	-	3	2	SEMA5B	124117138	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	1.306000	0.33505	0.317000	0.23160	-0.441000	0.05720	GAT		0.572	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		C	122634448	A	C	122634448	3	2	47	1	0	0	0	0	1	0	0	0	14075	214	8	4	1668	4	SEMA5B	3	122634448	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	363137	122634448	75387982	469	4866										
ADCY5	111	broad.mit.edu	37	chr3	123036874	123036874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggggatactcactggggcaCgatggtgatctggacaaagc	15	9	2	1	rs147630334	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:123036874C>T	ENST00000462833.1	-	11	3559	c.2347G>A	c.(2347-2349)Gtg>Atg	p.V783M	ADCY5_ENST00000309879.5_Missense_Mutation_p.V433M|ADCY5_ENST00000491190.1_Missense_Mutation_p.V416M	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	783					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.V783M(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		CACTGGGGCACGATGGTGATC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	135	113	121		1297,2347	2.2	1	3	dbSNP_134	121	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	ADCY5	NM_001199642.1,NM_183357.2	21,21	0,12,6491	TT,TC,CC		0.1279,0.0227,0.0923	benign,benign	433/912,783/1262	123036874	12,12994	2203	4300	6503	124519564	SO:0001583	missense	111			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.2347G>A	3.37:g.123036874C>T	ENSP00000419361:p.Val783Met		124519564	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.29	2.193992	0.38707	2.27E-4	0.001279	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.24	2.18	0.27775	.	0.088050	0.45867	D	0.000336	T	0.21347	0.0514	N	0.13235	0.315	0.49130	D	0.999757	B;B	0.18610	0.015;0.029	B;B	0.12156	0.007;0.007	T	0.04191	-1.0970	10	0.32370	T	0.25	.	5.9246	0.19101	0.1375:0.6166:0.0:0.2458	.	783;416	O95622;B3KWA8	ADCY5_HUMAN;.	M	783;416;433;342	ENSP00000419361:V783M;ENSP00000418537:V416M;ENSP00000308685:V433M;ENSP00000420082:V342M	ENSP00000308685:V433M	V	-	1	0	ADCY5	124519564	0.051000	0.20477	0.986000	0.45419	0.995000	0.86356	0.475000	0.22164	0.737000	0.32582	0.491000	0.48974	GTG		0.577	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		T	123036874	C	T	123036874	3	4	47	1	0	0	0	0	1	0	0	0	297	536	19	1	1482	1	ADCY5	3	123036874	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	402426	123036874	74985556	470	4867										
MYLK	4638	broad.mit.edu	37	chr3	123376014	123376014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtgagttcagactcctggCttggctcactggttccatac	10	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:123376014C>T	ENST00000475616.1	-	21	4246	c.4247G>A	c.(4246-4248)aGc>aAc	p.S1416N	MYLK_ENST00000360304.3_Missense_Mutation_p.S1416N|MYLK_ENST00000359169.1_Missense_Mutation_p.S1416N|MYLK_ENST00000354792.5_Missense_Mutation_p.S216N|MYLK_ENST00000346322.5_Missense_Mutation_p.S1347N|MYLK_ENST00000360772.3_Missense_Mutation_p.S1416N			Q15746	MYLK_HUMAN	myosin light chain kinase	1416	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.S1416N(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		AGACTCCTGGCTTGGCTCACT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											170	155	160					3																	123376014		2203	4300	6503	124858704	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.4247G>A	3.37:g.123376014C>T	ENSP00000418335:p.Ser1416Asn		124858704	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	34	5.405960	0.96051	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616;ENST00000508240	T;T;T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54;-0.54;-0.54	5.25	5.25	0.73442	Fibronectin, type III (3);Immunoglobulin-like fold (1);	.	.	.	.	D	0.90335	0.6976	H	0.97491	4.015	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.997;0.999;0.997;0.999	D	0.93438	0.6791	9	0.72032	D	0.01	.	19.1913	0.93667	0.0:1.0:0.0:0.0	.	1416;1347;1416;1347;1416	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	N	1416;1416;1416;1347;216;1416;216	ENSP00000354004:S1416N;ENSP00000353452:S1416N;ENSP00000352088:S1416N;ENSP00000320622:S1347N;ENSP00000346846:S216N;ENSP00000418335:S1416N;ENSP00000422984:S216N	ENSP00000320622:S1347N	S	-	2	0	MYLK	124858704	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.744000	0.85034	2.624000	0.88883	0.561000	0.74099	AGC		0.507	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		T	123376014	C	T	123376014	3	4	47	1	0	0	0	0	1	0	0	0	10086	797	28	3	1541	3	MYLK	3	123376014	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	339140	123376014	74646416	471	4868										
KALRN	8997	broad.mit.edu	37	chr3	124193561	124193561	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caactgcctgaggatgtgggAcactgctttgttacctgggt	13	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:124193561A>G	ENST00000240874.3	+	26	4234	c.4077A>G	c.(4075-4077)ggA>ggG	p.G1359G	KALRN_ENST00000360013.3_Silent_p.G1359G|KALRN_ENST00000460856.1_Silent_p.G1350G	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1359	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G1359G(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGGATGTGGGACACTGCTTTG	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	3											184	171	175					3																	124193561		2203	4300	6503	125676251	SO:0001819	synonymous_variant	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4077A>G	3.37:g.124193561A>G			125676251	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	A	9.511	1.105860	0.20632	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.61714	0.2369	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60611	-0.7229	4	.	.	.	.	10.3924	0.44181	0.8534:0.0:0.0:0.1466	.	.	.	.	G	1328	.	.	D	+	2	0	KALRN	125676251	0.986000	0.35501	1.000000	0.80357	0.999000	0.98932	0.245000	0.18142	2.311000	0.77944	0.533000	0.62120	GAC		0.512	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		G	124193561	A	G	124193561	2	3	47	1	0	0	0	0	0	0	0	1	7996	262	10	4		4	KALRN	3	124193561	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	817547	124193561	73828869	472	4869										
UMPS	7372	broad.mit.edu	37	chr3	124457045	124457045	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgatatttgaagaccggaAgtttgcagatataggaaaca	10	5	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:124457045A>C	ENST00000232607.2	+	3	1047	c.941A>C	c.(940-942)aAg>aCg	p.K314T	UMPS_ENST00000538242.1_Missense_Mutation_p.K136T|UMPS_ENST00000498715.1_3'UTR|UMPS_ENST00000536109.1_Missense_Mutation_p.K222T|UMPS_ENST00000413078.2_Missense_Mutation_p.K136T	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	314	OMPdecase.				'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)	p.K314T(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	GAAGACCGGAAGTTTGCAGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											60	63	62					3																	124457045		2190	4298	6488	125939735	SO:0001583	missense	7372				CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.941A>C	3.37:g.124457045A>C	ENSP00000232607:p.Lys314Thr		125939735	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	Missense_Mutation	SNP	ENST00000232607.2	37	CCDS3029.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326248	0.81580	.	.	ENSG00000114491	ENST00000232607;ENST00000536109;ENST00000538242;ENST00000413078	D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69	5.43	5.43	0.79202	Orotidine 5&apos (2);Aldolase-type TIM barrel (1);-phosphate decarboxylase domain (2);Ribulose-phosphate binding barrel (1);	0.052951	0.64402	D	0.000001	D	0.98058	0.9360	M	0.91196	3.185	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99029	1.0820	10	0.87932	D	0	-20.7979	14.2022	0.65712	1.0:0.0:0.0:0.0	.	136;136;314	B5LY72;B5LY70;P11172	.;.;UMPS_HUMAN	T	314;222;136;136	ENSP00000232607:K314T;ENSP00000443577:K222T;ENSP00000444988:K136T;ENSP00000397965:K136T	ENSP00000232607:K314T	K	+	2	0	UMPS	125939735	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.170000	0.89673	2.279000	0.76181	0.533000	0.62120	AAG		0.353	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373		C	124457045	A	C	124457045	3	2	47	1	0	0	0	0	1	0	0	0	17021	72	3	4	951	4	UMPS	3	124457045	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	263484	124457045	73565385	473	4870										
HEG1	57493	broad.mit.edu	37	chr3	124689614	124689614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggccgggtagagtccgtttCgttcaagttctggattcctt	12	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:124689614C>T	ENST00000311127.4	-	17	4095	c.4028G>A	c.(4027-4029)cGa>cAa	p.R1343Q		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	1343					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.R1343Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						GAGTCCGTTTCGTTCAAGTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											111	107	108					3																	124689614		1882	4103	5985	126172304	SO:0001583	missense	57493			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.4028G>A	3.37:g.124689614C>T	ENSP00000311502:p.Arg1343Gln		126172304	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005748	0.93287	.	.	ENSG00000173706	ENST00000311127;ENST00000487661	D;T	0.91407	-2.84;0.69	5.28	4.39	0.52855	.	0.000000	0.33290	U	0.005067	D	0.90041	0.6890	N	0.14661	0.345	0.52099	D	0.999941	D	0.89917	1.0	D	0.72982	0.979	D	0.91270	0.5043	10	0.87932	D	0	.	13.6488	0.62299	0.0:0.9253:0.0:0.0747	.	1343	Q9ULI3	HEG1_HUMAN	Q	1343;227	ENSP00000311502:R1343Q;ENSP00000417648:R227Q	ENSP00000311502:R1343Q	R	-	2	0	HEG1	126172304	0.998000	0.40836	0.997000	0.53966	0.988000	0.76386	3.642000	0.54367	2.644000	0.89710	0.655000	0.94253	CGA		0.438	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124689614	C	T	124689614	3	4	47	1	0	0	0	0	1	0	0	0	7065	884	31	1	121	1	HEG1	3	124689614	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	232569	124689614	73332816	474	4871										
CHST13	166012	broad.mit.edu	37	chr3	126255175	126255175	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaagagaagccccctgcaGaagctctatgacctggatca	11	11	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:126255175G>T	ENST00000319340.2	+	2	209	c.159G>T	c.(157-159)caG>caT	p.Q53H		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	53					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.Q53H(1)		central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		GCCCCCTGCAGAAGCTCTATG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											111	110	110					3																	126255175		2203	4300	6503	127737865	SO:0001583	missense	166012			AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"Sulfotransferases, membrane-bound"	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.159G>T	3.37:g.126255175G>T	ENSP00000317404:p.Gln53His		127737865	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	37	CCDS3039.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.547805	0.27652	.	.	ENSG00000180767	ENST00000319340;ENST00000383575	T	0.69175	-0.38	3.18	2.3	0.28687	.	0.491092	0.19463	U	0.113646	T	0.71771	0.3379	L	0.47190	1.495	0.46061	D	0.998842	D	0.89917	1.0	D	0.91635	0.999	T	0.70260	-0.4921	10	0.66056	D	0.02	-10.9697	6.172	0.20422	0.1402:0.0:0.8598:0.0	.	53	Q8NET6	CHSTD_HUMAN	H	53	ENSP00000317404:Q53H	ENSP00000317404:Q53H	Q	+	3	2	CHST13	127737865	0.962000	0.33011	0.513000	0.27749	0.224000	0.24922	1.530000	0.36007	0.896000	0.36366	0.467000	0.42956	CAG		0.592	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		T	126255175	G	T	126255175	3	4	47	1	0	0	0	0	1	0	0	0	3407	933	33	2	165	2	CHST13	3	126255175	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1565561	126255175	71767255	475	4872										
TRH	7200	broad.mit.edu	37	chr3	129695691	129695691	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcaccctggccgacgagaaGatgaggcttcatggtcagtc	13	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:129695691G>T	ENST00000302649.3	+	3	888	c.361G>T	c.(361-363)Gat>Tat	p.D121Y	TRH_ENST00000507066.1_Missense_Mutation_p.D117Y	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	121					adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)	p.D121Y(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						CCGACGAGAAGATGAGGCTTC	0.612																																					Esophageal Squamous(60;321 1330 17401 41911)											1	Substitution - Missense(1)	large_intestine(1)	3											67	60	62					3																	129695691		2203	4300	6503	131178381	SO:0001583	missense	7200				CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"Endogenous ligands"	12298	protein-coding gene	gene with protein product	"prothyroliberin"	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.361G>T	3.37:g.129695691G>T	ENSP00000303452:p.Asp121Tyr		131178381	B2R8R1|Q2TB83	Missense_Mutation	SNP	ENST00000302649.3	37	CCDS3066.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654999	0.29425	.	.	ENSG00000170893	ENST00000302649;ENST00000507066	T;T	0.48836	0.8;0.8	4.55	3.67	0.42095	.	0.634788	0.16959	N	0.192567	T	0.63920	0.2552	M	0.77820	2.39	0.23920	N	0.996465	D	0.61697	0.99	P	0.62649	0.905	T	0.55147	-0.8186	10	0.87932	D	0	-3.5786	8.8684	0.35300	0.1067:0.0:0.8933:0.0	.	121	P20396	TRH_HUMAN	Y	121;117	ENSP00000303452:D121Y;ENSP00000426522:D117Y	ENSP00000303452:D121Y	D	+	1	0	TRH	131178381	0.659000	0.27411	0.015000	0.15790	0.146000	0.21551	2.655000	0.46707	1.038000	0.40049	0.591000	0.81541	GAT		0.612	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117		T	129695691	G	T	129695691	3	4	47	1	0	0	0	0	1	0	0	0	16518	942	33	2	367	2	TRH	3	129695691	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3440516	129695691	68326739	476	4873										
ASTE1	28990	broad.mit.edu	37	chr3	130735120	130735120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtgcccagccgtgtctgcGccttcactctttggaactct	9	14	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:130735120G>A	ENST00000264992.3	-	5	2018	c.1577C>T	c.(1576-1578)gCg>gTg	p.A526V	ATP2C1_ENST00000328560.8_3'UTR|ASTE1_ENST00000514044.1_Missense_Mutation_p.A526V|ATP2C1_ENST00000393221.4_3'UTR|ATP2C1_ENST00000513801.1_3'UTR|ATP2C1_ENST00000504381.1_3'UTR|ATP2C1_ENST00000507488.2_3'UTR|ATP2C1_ENST00000533801.2_3'UTR|ATP2C1_ENST00000359644.3_3'UTR|ATP2C1_ENST00000422190.2_3'UTR	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	526					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.A526V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						CCGTGTCTGCGCCTTCACTCT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											185	163	170					3																	130735120		2203	4300	6503	132217810	SO:0001583	missense	28990			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1577C>T	3.37:g.130735120G>A	ENSP00000264992:p.Ala526Val		132217810	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	8.689	0.907077	0.17833	.	.	ENSG00000034533	ENST00000514044;ENST00000264992	.	.	.	5.47	-1.57	0.08506	.	0.664644	0.15775	N	0.245257	T	0.21387	0.0515	L	0.28274	0.84	0.09310	N	1	B;B	0.11235	0.0;0.004	B;B	0.06405	0.0;0.002	T	0.34179	-0.9839	9	0.06365	T	0.9	-4.7575	8.0875	0.30782	0.0989:0.0645:0.6047:0.2319	.	526;526	D6RG30;Q2TB18	.;ASTE1_HUMAN	V	526	.	ENSP00000264992:A526V	A	-	2	0	ASTE1	132217810	0.165000	0.22948	0.087000	0.20705	0.004000	0.04260	0.317000	0.19487	-0.867000	0.04063	-2.560000	0.00174	GCG		0.488	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		A	130735120	G	A	130735120	3	1	47	1	0	0	0	0	1	0	0	0	1063	1087	38	1	470	1	ASTE1	3	130735120	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1039429	130735120	67287310	477	4874										
DNAJC13	23317	broad.mit.edu	37	chr3	132209753	132209753	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttgaagacaaaaggacaaGatatttttcagagaagtata	8	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:132209753G>T	ENST00000260818.6	+	32	3729	c.3481G>T	c.(3481-3483)Gat>Tat	p.D1161Y		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1161					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.D1161Y(1)|p.D544Y(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AAAAGGACAAGATATTTTTCA	0.294																																																2	Substitution - Missense(2)	large_intestine(2)	3											24	26	25					3																	132209753		2194	4293	6487	133692443	SO:0001583	missense	23317			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.3481G>T	3.37:g.132209753G>T	ENSP00000260818:p.Asp1161Tyr		133692443	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354292	0.82243	.	.	ENSG00000138246	ENST00000260818	T	0.19938	2.11	5.33	5.33	0.75918	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.45438	0.1342	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.41662	-0.9496	10	0.72032	D	0.01	.	19.0448	0.93015	0.0:0.0:1.0:0.0	.	1161	O75165	DJC13_HUMAN	Y	1161	ENSP00000260818:D1161Y	ENSP00000260818:D1161Y	D	+	1	0	DNAJC13	133692443	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.495000	0.84180	0.591000	0.81541	GAT		0.294	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132209753	G	T	132209753	3	4	47	1	0	0	0	0	1	0	0	0	4643	942	33	2	3603	2	DNAJC13	3	132209753	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1474633	132209753	65812677	478	4875										
TF	7018	broad.mit.edu	37	chr3	133476640	133476640	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggcaaagacaaatcaaaaGaattccaactattcagctct	5	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:133476640G>T	ENST00000402696.3	+	8	1383	c.898G>T	c.(898-900)Gaa>Taa	p.E300*	TF_ENST00000264998.3_Nonsense_Mutation_p.E173*	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	300	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.E300*(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	CAAATCAAAAGAATTCCAACT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											82	84	83					3																	133476640		2203	4300	6503	134959330	SO:0001587	stop_gained	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.898G>T	3.37:g.133476640G>T	ENSP00000385834:p.Glu300*		134959330	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Nonsense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	.	.	.	.	.	.	.	.	.	.	G	39	7.705858	0.98444	.	.	ENSG00000091513	ENST00000402696;ENST00000264998	.	.	.	4.91	2.86	0.33363	.	1.011170	0.07887	N	0.970523	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-1.4879	8.6818	0.34214	0.0954:0.2016:0.703:0.0	.	.	.	.	X	300;173	.	ENSP00000264998:E173X	E	+	1	0	TF	134959330	0.000000	0.05858	0.002000	0.10522	0.549000	0.35272	0.001000	0.13038	1.320000	0.45209	0.561000	0.74099	GAA		0.438	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133476640	G	T	133476640	4	4	47	1	0	0	0	0	0	1	0	0	15824	943	33	2	928	2	TF	3	133476640	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1266887	133476640	64545790	479	4876										
EPHB1	2047	broad.mit.edu	37	chr3	134898789	134898789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttgccaaggagattgatgTatcttttgtgaaaattgaag	11	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:134898789T>C	ENST00000398015.3	+	10	2217	c.1847T>C	c.(1846-1848)gTa>gCa	p.V616A	EPHB1_ENST00000493838.1_Missense_Mutation_p.V177A	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	616					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.V616A(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GAGATTGATGTATCTTTTGTG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	3											155	149	151					3																	134898789		1956	4168	6124	136381479	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1847T>C	3.37:g.134898789T>C	ENSP00000381097:p.Val616Ala		136381479	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	6.218	0.408331	0.11754	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.08370	3.1;3.1	5.83	5.83	0.93111	Protein kinase-like domain (1);	0.140958	0.46145	D	0.000316	T	0.04952	0.0133	N	0.15975	0.35	0.80722	D	1	B	0.32188	0.359	B	0.28553	0.091	T	0.16867	-1.0388	10	0.02654	T	1	.	16.1997	0.82060	0.0:0.0:0.0:1.0	.	616	P54762	EPHB1_HUMAN	A	616;177	ENSP00000381097:V616A;ENSP00000419574:V177A	ENSP00000381097:V616A	V	+	2	0	EPHB1	136381479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.240000	0.73641	0.528000	0.53228	GTA		0.488	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		C	134898789	T	C	134898789	3	2	47	1	0	0	0	0	1	0	0	0	5187	1638	57	4	1885	4	EPHB1	3	134898789	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1422149	134898789	63123641	480	4877										
STAG1	10274	broad.mit.edu	37	chr3	136221553	136221553	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctcggcttcatattgtcTctgggtattatcctgatgaa	8	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:136221553T>G	ENST00000383202.2	-	8	1001	c.745A>C	c.(745-747)Aga>Cga	p.R249R	STAG1_ENST00000236698.5_Silent_p.R249R|STAG1_ENST00000434713.2_Silent_p.R23R	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	249					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R249R(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TCATATTGTCTCTGGGTATTA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	3											128	120	123					3																	136221553		2203	4300	6503	137704243	SO:0001819	synonymous_variant	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.745A>C	3.37:g.136221553T>G			137704243	O00539|Q6P275	Silent	SNP	ENST00000383202.2	37	CCDS3090.1																																																																																				0.383	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136221553	T	G	136221553	2	3	47	1	0	0	0	0	0	0	0	1	15281	1559	54	4		4	STAG1	3	136221553	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1322764	136221553	61800877	481	4878										
A4GNT	51146	broad.mit.edu	37	chr3	137843320	137843320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcccacacttcatagtagCgcctccactctcgataggag	7	14	2	0	rs570351376		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:137843320C>T	ENST00000236709.3	-	3	1010	c.809G>A	c.(808-810)cGc>cAc	p.R270H		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	270					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)	p.R270H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						TTCATAGTAGCGCCTCCACTC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											92	89	90					3																	137843320		2203	4300	6503	139326010	SO:0001583	missense	51146			AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.809G>A	3.37:g.137843320C>T	ENSP00000236709:p.Arg270His		139326010	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	ENST00000236709.3	37	CCDS3097.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605401	0.66445	.	.	ENSG00000118017	ENST00000236709	D	0.82711	-1.64	5.39	2.31	0.28768	Alpha 1,4-glycosyltransferase domain (1);	0.403521	0.22739	N	0.056237	D	0.88179	0.6367	M	0.81239	2.535	0.18873	N	0.999985	D	0.89917	1.0	D	0.68621	0.959	T	0.77043	-0.2734	10	0.45353	T	0.12	-7.9379	6.5038	0.22184	0.2362:0.6206:0.0:0.1432	.	270	Q9UNA3	A4GCT_HUMAN	H	270	ENSP00000236709:R270H	ENSP00000236709:R270H	R	-	2	0	A4GNT	139326010	0.408000	0.25360	0.998000	0.56505	0.978000	0.69477	0.171000	0.16685	1.253000	0.44018	0.563000	0.77884	CGC		0.498	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161		T	137843320	C	T	137843320	3	4	47	1	0	0	0	0	1	0	0	0	7	768	27	1	217	1	A4GNT	3	137843320	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1621767	137843320	60179110	482	4879										
PIK3CB	5291	broad.mit.edu	37	chr3	138433373	138433373	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagttttcgttgatttcttCgtttttactttatccaaaac	4	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:138433373C>T	ENST00000477593.1	-	8	1312	c.1239G>A	c.(1237-1239)acG>acA	p.T413T	PIK3CB_ENST00000544716.1_5'Flank|PIK3CB_ENST00000289153.2_Silent_p.T413T			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	413	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.T413T(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	TTGATTTCTTCGTTTTTACTT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	3											157	147	151					3																	138433373		2203	4300	6503	139916063	SO:0001819	synonymous_variant	5291				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.1239G>A	3.37:g.138433373C>T			139916063	D3DNF0|Q24JU2	Silent	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	C	9.475	1.096752	0.20552	.	.	ENSG00000051382	ENST00000493568	.	.	.	5.46	-5.19	0.02832	.	.	.	.	.	T	0.38268	0.1034	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40794	-0.9544	4	.	.	.	-12.2416	2.4988	0.04628	0.2374:0.1714:0.0912:0.5001	.	.	.	.	Q	62	.	.	R	-	2	0	PIK3CB	139916063	0.001000	0.12720	0.952000	0.39060	0.995000	0.86356	-1.420000	0.02457	-0.687000	0.05162	-0.143000	0.13931	CGA		0.318	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			T	138433373	C	T	138433373	2	4	47	1	0	0	0	0	0	0	0	1	11945	871	31	1		1	PIK3CB	3	138433373	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	590053	138433373	59589057	483	4880										
GK5	256356	broad.mit.edu	37	chr3	141934529	141934529	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaatttgaggataaagattTtctacctattaaggaaaaga	7	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:141934529T>G	ENST00000392993.2	-	2	304	c.153A>C	c.(151-153)gaA>gaC	p.E51D	GK5_ENST00000466685.3_5'UTR|GK5_ENST00000544571.1_Missense_Mutation_p.E51D	NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	51					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)	p.E51D(1)		kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						GATAAAGATTTTCTACCTATT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	3											36	37	37					3																	141934529		2198	4289	6487	143417219	SO:0001583	missense	256356			BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"Glycerol kinases"	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.153A>C	3.37:g.141934529T>G	ENSP00000418001:p.Glu51Asp		143417219	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	37	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138921	0.56936	.	.	ENSG00000175066	ENST00000392993;ENST00000544571	T;T	0.58210	0.35;0.35	5.42	3.05	0.35203	Carbohydrate kinase, FGGY, N-terminal (1);	0.443819	0.24172	N	0.040891	T	0.45478	0.1344	L	0.52364	1.645	0.43536	D	0.995824	B	0.15930	0.015	B	0.21546	0.035	T	0.32851	-0.9891	10	0.51188	T	0.08	-12.8003	8.9788	0.35953	0.0:0.1539:0.0:0.8461	.	51	Q6ZS86	GLPK5_HUMAN	D	51	ENSP00000418001:E51D;ENSP00000440860:E51D	ENSP00000418001:E51D	E	-	3	2	GK5	143417219	0.985000	0.35326	0.990000	0.47175	0.845000	0.48019	1.268000	0.33062	0.374000	0.24650	0.477000	0.44152	GAA		0.318	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		G	141934529	T	G	141934529	3	3	47	1	0	0	0	0	1	0	0	0	6442	1838	64	4	1496	4	GK5	3	141934529	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3501156	141934529	56087901	484	4881										
XRN1	54464	broad.mit.edu	37	chr3	142030480	142030480	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcagtttcaacttgaaaaGaagatgcaggttgagcaatc	11	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:142030480G>T	ENST00000264951.4	-	42	5111	c.4994C>A	c.(4993-4995)tCt>tAt	p.S1665Y	XRN1_ENST00000392981.2_Missense_Mutation_p.S1653Y	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1665					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.S1665Y(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AACTTGAAAAGAAGATGCAGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											134	140	138					3																	142030480		2203	4300	6503	143513170	SO:0001583	missense	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4994C>A	3.37:g.142030480G>T	ENSP00000264951:p.Ser1665Tyr		143513170	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	g	18.65	3.670517	0.67814	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.39787	1.06;1.07	5.65	5.65	0.86999	.	0.502596	0.21503	N	0.073482	T	0.45196	0.1330	L	0.29908	0.895	0.80722	D	1	D;D	0.56521	0.976;0.96	P;B	0.50617	0.646;0.443	T	0.44406	-0.9330	10	0.87932	D	0	-6.4562	17.9095	0.88929	0.0:0.0:1.0:0.0	.	1653;1665	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	Y	1665;1653	ENSP00000264951:S1665Y;ENSP00000376707:S1653Y	ENSP00000264951:S1665Y	S	-	2	0	XRN1	143513170	1.000000	0.71417	0.700000	0.30305	0.808000	0.45660	3.906000	0.56340	2.666000	0.90696	0.651000	0.88453	TCT		0.423	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142030480	G	T	142030480	3	4	47	1	0	0	0	0	1	0	0	0	17499	942	33	2	130	2	XRN1	3	142030480	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	95951	142030480	55991950	485	4882										
ATR	545	broad.mit.edu	37	chr3	142268985	142268985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaacttacagtaagaaaacGattaagatcaggaaagtcga	9	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:142268985G>A	ENST00000350721.4	-	14	3086	c.2965C>T	c.(2965-2967)Cgt>Tgt	p.R989C	ATR_ENST00000383101.3_Missense_Mutation_p.R925C	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	989					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R989C(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GTAAGAAAACGATTAAGATCA	0.358								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	3											101	92	95					3																	142268985		2203	4300	6503	143751675	SO:0001583	missense	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2965C>T	3.37:g.142268985G>A	ENSP00000343741:p.Arg989Cys		143751675	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082204	0.94050	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.64991	-0.13;-0.13	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.055191	0.64402	D	0.000001	T	0.62060	0.2397	L	0.27053	0.805	0.80722	D	1	D	0.67145	0.996	P	0.50791	0.65	T	0.65994	-0.6033	10	0.62326	D	0.03	-11.8232	19.529	0.95219	0.0:0.0:1.0:0.0	.	989	Q13535	ATR_HUMAN	C	989;925	ENSP00000343741:R989C;ENSP00000372581:R925C	ENSP00000343741:R989C	R	-	1	0	ATR	143751675	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.750000	0.98875	2.604000	0.88044	0.585000	0.79938	CGT		0.358	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142268985	G	A	142268985	3	1	47	1	0	0	0	0	1	0	0	0	1205	1058	37	1	5105	1	ATR	3	142268985	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	238505	142268985	55753445	486	4883										
SR140	23350	broad.mit.edu	37	chr3	142733211	142733211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaatgagtacagctaagcGaactttaagtaaaaaggaac	8	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:142733211G>A	ENST00000473835.2	+	4	371	c.281G>A	c.(280-282)cGa>cAa	p.R94Q	U2SURP_ENST00000397933.2_5'UTR|U2SURP_ENST00000493598.2_Missense_Mutation_p.R94Q	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	94					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R94Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ACAGCTAAGCGAACTTTAAGT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	3											53	49	51					3																	142733211		1811	4074	5885	144215901	SO:0001583	missense	23350			BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.281G>A	3.37:g.142733211G>A	ENSP00000418563:p.Arg94Gln		144215901	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	36	5.670812	0.96754	.	.	ENSG00000163714	ENST00000473835;ENST00000493782;ENST00000319822;ENST00000493598;ENST00000465175	T;T	0.11495	2.77;2.79	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.35038	0.0918	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;P	0.64776	0.929;0.913;0.806	T	0.01961	-1.1239	10	0.48119	T	0.1	-8.5639	19.7727	0.96373	0.0:0.0:1.0:0.0	.	94;94;94	B4DK81;O15042-2;O15042	.;.;SR140_HUMAN	Q	94;94;94;94;64	ENSP00000418563:R94Q;ENSP00000422011:R94Q	ENSP00000322376:R94Q	R	+	2	0	U2SURP	144215901	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.301000	0.96167	2.758000	0.94735	0.563000	0.77884	CGA		0.294	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		A	142733211	G	A	142733211	3	1	47	1	0	0	0	0	1	0	0	0	15170	1058	37	1	295	1	SR140	3	142733211	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	464226	142733211	55289219	487	4884										
PLSCR4	57088	broad.mit.edu	37	chr3	145917794	145917794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctgagttgtttttaatatCatatctattattagtttcaa	5	4	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:145917794C>A	ENST00000354952.2	-	6	670	c.430G>T	c.(430-432)Gat>Tat	p.D144Y	PLSCR4_ENST00000383083.2_Intron|PLSCR4_ENST00000433593.2_Intron|PLSCR4_ENST00000493382.1_Missense_Mutation_p.D144Y|PLSCR4_ENST00000446574.2_Missense_Mutation_p.D144Y	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	144					cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)	p.D144Y(2)		kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						TTTTTAATATCATATCTATTA	0.353																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3											53	55	54					3																	145917794		2203	4300	6503	147400484	SO:0001583	missense	57088			AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.430G>T	3.37:g.145917794C>A	ENSP00000347038:p.Asp144Tyr		147400484	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378744	0.82682	.	.	ENSG00000114698	ENST00000354952;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000476202	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.94;1.94	4.87	4.87	0.63330	.	0.089923	0.48767	D	0.000178	T	0.49115	0.1538	L	0.50333	1.59	0.80722	D	1	D	0.67145	0.996	D	0.64877	0.93	T	0.49283	-0.8956	10	0.87932	D	0	.	17.3112	0.87211	0.0:1.0:0.0:0.0	.	144	Q9NRQ2	PLS4_HUMAN	Y	144	ENSP00000347038:D144Y;ENSP00000399315:D144Y;ENSP00000419040:D144Y;ENSP00000417896:D144Y;ENSP00000418173:D144Y	ENSP00000347038:D144Y	D	-	1	0	PLSCR4	147400484	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	4.549000	0.60726	2.683000	0.91414	0.655000	0.94253	GAT		0.353	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		A	145917794	C	A	145917794	3	1	47	1	0	0	0	0	1	0	0	0	12143	826	29	2	575	2	PLSCR4	3	145917794	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3184583	145917794	52104636	488	4885										
PLSCR4	57088	broad.mit.edu	37	chr3	145918846	145918846	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaggctcaaaatgctgaaGaacatgtatgttgtccaact	9	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:145918846G>T	ENST00000354952.2	-	5	613	c.373C>A	c.(373-375)Ctt>Att	p.L125I	PLSCR4_ENST00000383083.2_Intron|PLSCR4_ENST00000433593.2_Intron|PLSCR4_ENST00000493382.1_Missense_Mutation_p.L125I|PLSCR4_ENST00000446574.2_Missense_Mutation_p.L125I	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	125					cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)	p.L125I(1)		kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						AAATGCTGAAGAACATGTATG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	85	84					3																	145918846		2203	4295	6498	147401536	SO:0001583	missense	57088			AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.373C>A	3.37:g.145918846G>T	ENSP00000347038:p.Leu125Ile		147401536	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269079	0.40095	.	.	ENSG00000114698	ENST00000354952;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000476202;ENST00000481701	T;T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95;1.95	5.25	4.38	0.52667	.	0.359219	0.23702	N	0.045404	T	0.13756	0.0333	N	0.16478	0.41	0.80722	D	1	B	0.22080	0.064	B	0.20767	0.031	T	0.05716	-1.0868	10	0.49607	T	0.09	.	11.1862	0.48657	0.0856:0.0:0.9144:0.0	.	125	Q9NRQ2	PLS4_HUMAN	I	125	ENSP00000347038:L125I;ENSP00000399315:L125I;ENSP00000419040:L125I;ENSP00000417896:L125I;ENSP00000418173:L125I;ENSP00000418419:L125I	ENSP00000347038:L125I	L	-	1	0	PLSCR4	147401536	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.512000	0.53407	1.451000	0.47736	-0.140000	0.14226	CTT		0.318	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		T	145918846	G	T	145918846	3	4	47	1	0	0	0	0	1	0	0	0	12143	942	33	2	636	2	PLSCR4	3	145918846	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1052	145918846	52103584	489	4886										
HPS3	84343	broad.mit.edu	37	chr3	148889925	148889925	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaactagaactgaaggatttCatgaatgttctcccagaaga	9	7	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:148889925C>A	ENST00000296051.2	+	17	3071	c.2931C>A	c.(2929-2931)ttC>ttA	p.F977L	HPS3_ENST00000460120.1_Missense_Mutation_p.F812L	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	977					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.F977L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGAAGGATTTCATGAATGTTC	0.338									Hermansky-Pudlak syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	3											118	114	115					3																	148889925		2202	4300	6502	150372615	SO:0001583	missense	84343	Familial Cancer Database	HPS, HPS1-8	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2931C>A	3.37:g.148889925C>A	ENSP00000296051:p.Phe977Leu		150372615	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775529	0.70107	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.61274	0.14;0.12	5.94	3.21	0.36854	.	0.000000	0.85682	D	0.000000	T	0.70552	0.3237	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69778	-0.5053	10	0.87932	D	0	-27.2798	9.1469	0.36939	0.0:0.7254:0.0:0.2746	.	812;977	G5E9V4;Q969F9	.;HPS3_HUMAN	L	977;812	ENSP00000296051:F977L;ENSP00000418230:F812L	ENSP00000296051:F977L	F	+	3	2	HPS3	150372615	0.978000	0.34361	0.972000	0.41901	0.986000	0.74619	1.308000	0.33528	0.418000	0.25898	0.557000	0.71058	TTC		0.338	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		A	148889925	C	A	148889925	3	1	47	1	0	0	0	0	1	0	0	0	7361	825	29	2	2997	2	HPS3	3	148889925	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2971079	148889925	49132505	490	4887										
CP	1356	broad.mit.edu	37	chr3	148927157	148927157	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcaatatgtttttctttttCtttatctagagaatctggag	7	5	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:148927157C>A	ENST00000264613.6	-	4	884	c.622G>T	c.(622-624)Gaa>Taa	p.E208*		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	208	F5/8 type A 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.E208*(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TTTTCTTTTTCTTTATCTAGA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											52	52	52					3																	148927157		2203	4299	6502	150409847	SO:0001587	stop_gained	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.622G>T	3.37:g.148927157C>A	ENSP00000264613:p.Glu208*		150409847	Q14063|Q2PP18|Q9UKS4	Nonsense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	39	7.308805	0.98203	.	.	ENSG00000047457	ENST00000264613	.	.	.	5.48	5.48	0.80851	.	0.352875	0.31472	N	0.007589	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-25.6999	12.9942	0.58638	0.0:0.9258:0.0:0.0742	.	.	.	.	X	208	.	ENSP00000264613:E208X	E	-	1	0	CP	150409847	0.983000	0.35010	0.975000	0.42487	0.662000	0.39071	3.336000	0.52113	2.703000	0.92315	0.650000	0.86243	GAA		0.303	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148927157	C	A	148927157	4	1	47	1	0	0	0	0	0	1	0	0	3793	922	32	2	2639	2	CP	3	148927157	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	37232	148927157	49095273	491	4888										
GPR87	53836	broad.mit.edu	37	chr3	151012745	151012745	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctgcatcatggactattcGaaatggaaatgtcagcgtca	9	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151012745G>A	ENST00000260843.4	-	3	753	c.289C>T	c.(289-291)Cga>Tga	p.R97*	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	97					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.R97*(1)		endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGGACTATTCGAAATGGAAAT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											137	137	137					3																	151012745		2203	4300	6503	152495435	SO:0001587	stop_gained	53836			AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"GPCR / Class A : Orphans"	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.289C>T	3.37:g.151012745G>A	ENSP00000260843:p.Arg97*		152495435	Q5KU35|Q96JZ8|Q9BXC2	Nonsense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	G	36	5.860041	0.97036	.	.	ENSG00000138271	ENST00000260843	.	.	.	5.31	2.19	0.27852	.	0.072417	0.49916	D	0.000138	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-4.6222	13.7861	0.63110	0.0:0.0:0.3072:0.6928	.	.	.	.	X	97	.	ENSP00000260843:R97X	R	-	1	2	GPR87	152495435	0.745000	0.28261	0.870000	0.34147	0.821000	0.46438	2.793000	0.47845	0.654000	0.30846	-0.181000	0.13052	CGA		0.373	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			A	151012745	G	A	151012745	4	1	47	1	0	0	0	0	0	1	0	0	6736	1066	37	1	791	1	GPR87	3	151012745	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2085588	151012745	47009685	492	4889										
IGSF10	285313	broad.mit.edu	37	chr3	151156065	151156065	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattgttgaaaagggtatatCtcctagtcctgtggccactg	10	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151156065C>A	ENST00000282466.3	-	6	6283	c.6284G>T	c.(6283-6285)aGa>aTa	p.R2095I	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2095	Ig-like C2-type 7.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.R2095I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AAGGGTATATCTCCTAGTCCT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											150	146	147					3																	151156065		2203	4300	6503	152638755	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6284G>T	3.37:g.151156065C>A	ENSP00000282466:p.Arg2095Ile		152638755	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.123657	0.56613	.	.	ENSG00000152580	ENST00000282466	T	0.40756	1.02	5.79	5.79	0.91817	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000147	T	0.73140	0.3549	M	0.89658	3.05	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;1.0	T	0.77300	-0.2639	10	0.62326	D	0.03	.	20.0375	0.97569	0.0:1.0:0.0:0.0	.	2095;122	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	I	2095	ENSP00000282466:R2095I	ENSP00000282466:R2095I	R	-	2	0	IGSF10	152638755	0.915000	0.31059	0.039000	0.18376	0.069000	0.16628	3.087000	0.50167	2.739000	0.93911	0.655000	0.94253	AGA		0.473	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151156065	C	A	151156065	3	1	47	1	0	0	0	0	1	0	0	0	7618	913	32	2	1591	2	IGSF10	3	151156065	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	143320	151156065	46866365	493	4890										
IGSF10	285313	broad.mit.edu	37	chr3	151156327	151156327	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtagacaccactgtctttttCtgttactgatccaataaaca	5	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151156327C>A	ENST00000282466.3	-	6	6021	c.6022G>T	c.(6022-6024)Gaa>Taa	p.E2008*	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2008	Ig-like C2-type 6.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.E2008*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CTGTCTTTTTCTGTTACTGAT	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											123	117	119					3																	151156327		2203	4300	6503	152639017	SO:0001587	stop_gained	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6022G>T	3.37:g.151156327C>A	ENSP00000282466:p.Glu2008*		152639017	Q86YJ9|Q8N772|Q8NA84	Nonsense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	47	13.583937	0.99751	.	.	ENSG00000152580	ENST00000282466	.	.	.	5.52	5.52	0.82312	.	0.148628	0.30704	N	0.009060	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	19.4344	0.94785	0.0:1.0:0.0:0.0	.	.	.	.	X	2008	.	ENSP00000282466:E2008X	E	-	1	0	IGSF10	152639017	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	7.440000	0.80464	2.589000	0.87451	0.655000	0.94253	GAA		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151156327	C	A	151156327	4	1	47	1	0	0	0	0	0	1	0	0	7618	922	32	2	1853	2	IGSF10	3	151156327	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	262	151156327	46866103	494	4891										
IGSF10	285313	broad.mit.edu	37	chr3	151163870	151163870	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgagtctttgcttataataCtaggaagcatagggttaagg	11	4	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151163870C>A	ENST00000282466.3	-	4	3898	c.3899G>T	c.(3898-3900)aGt>aTt	p.S1300I		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1300					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.S1300I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCTTATAATACTAGGAAGCAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											253	235	241					3																	151163870		2203	4300	6503	152646560	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.3899G>T	3.37:g.151163870C>A	ENSP00000282466:p.Ser1300Ile		152646560	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	9.430	1.085337	0.20390	.	.	ENSG00000152580	ENST00000282466	T	0.69685	-0.42	4.51	1.65	0.23941	.	0.745647	0.11787	N	0.529610	T	0.56963	0.2021	L	0.32530	0.975	0.09310	N	1	B	0.30021	0.265	B	0.36608	0.229	T	0.51036	-0.8756	10	0.49607	T	0.09	.	8.5502	0.33447	0.0:0.6435:0.0:0.3565	.	1300	Q6WRI0	IGS10_HUMAN	I	1300	ENSP00000282466:S1300I	ENSP00000282466:S1300I	S	-	2	0	IGSF10	152646560	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.398000	0.07259	0.123000	0.18342	-1.094000	0.02160	AGT		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151163870	C	A	151163870	3	1	47	1	0	0	0	0	1	0	0	0	7618	565	20	2	4032	2	IGSF10	3	151163870	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7543	151163870	46858560	495	4892										
IGSF10	285313	broad.mit.edu	37	chr3	151166618	151166618	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctttctagtatcagaggaGaatcactgtacaaagccaaa	7	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151166618G>A	ENST00000282466.3	-	4	1150	c.1151C>T	c.(1150-1152)tCt>tTt	p.S384F		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	384					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.S384F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TATCAGAGGAGAATCACTGTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											82	77	79					3																	151166618		2203	4300	6503	152649308	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.1151C>T	3.37:g.151166618G>A	ENSP00000282466:p.Ser384Phe		152649308	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.668189	0.67814	.	.	ENSG00000152580	ENST00000282466	T	0.72725	-0.68	5.22	5.22	0.72569	.	0.142496	0.32533	N	0.005976	T	0.64260	0.2582	L	0.50333	1.59	0.42812	D	0.993963	P	0.37441	0.595	B	0.31016	0.123	T	0.64728	-0.6339	10	0.29301	T	0.29	.	18.7742	0.91904	0.0:0.0:1.0:0.0	.	384	Q6WRI0	IGS10_HUMAN	F	384	ENSP00000282466:S384F	ENSP00000282466:S384F	S	-	2	0	IGSF10	152649308	1.000000	0.71417	0.984000	0.44739	0.715000	0.41141	6.404000	0.73268	2.447000	0.82792	0.650000	0.86243	TCT		0.398	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151166618	G	A	151166618	3	1	47	1	0	0	0	0	1	0	0	0	7618	942	33	3	6780	3	IGSF10	3	151166618	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2748	151166618	46855812	496	4893										
SUCNR1	56670	broad.mit.edu	37	chr3	151598976	151598976	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagattgctctcttcctaaaGcagaggaataggcaggttgc	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:151598976G>T	ENST00000362032.5	+	3	750	c.645G>T	c.(643-645)aaG>aaT	p.K215N	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	215						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.K215N(1)		endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	TCTTCCTAAAGCAGAGGAATA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											164	153	157					3																	151598976		2203	4300	6503	153081666	SO:0001583	missense	56670			AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.645G>T	3.37:g.151598976G>T	ENSP00000355156:p.Lys215Asn		153081666	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	37	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902963	0.52227	.	.	ENSG00000198829	ENST00000362032	T	0.39056	1.1	5.46	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.249450	0.35646	U	0.003077	T	0.52693	0.1750	L	0.56199	1.76	0.28579	N	0.910254	D	0.71674	0.998	D	0.69824	0.966	T	0.43130	-0.9410	10	0.40728	T	0.16	.	7.7585	0.28938	0.364:0.0:0.636:0.0	.	215	Q9BXA5	SUCR1_HUMAN	N	215	ENSP00000355156:K215N	ENSP00000355156:K215N	K	+	3	2	SUCNR1	153081666	0.281000	0.24258	0.954000	0.39281	0.749000	0.42624	0.503000	0.22610	1.381000	0.46364	0.650000	0.86243	AAG		0.423	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151598976	G	T	151598976	3	4	47	1	0	0	0	0	1	0	0	0	15405	962	34	2	651	2	SUCNR1	3	151598976	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	432358	151598976	46423454	497	4894										
MME	4311	broad.mit.edu	37	chr3	154859897	154859897	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaccaaacttaagcccattCttaccaaatattctgccagg	4	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:154859897C>A	ENST00000460393.1	+	11	1195	c.1075C>A	c.(1075-1077)Ctt>Att	p.L359I	MME_ENST00000492661.1_Missense_Mutation_p.L359I|MME_ENST00000360490.2_Missense_Mutation_p.L359I|MME_ENST00000462745.1_Missense_Mutation_p.L359I|MME_ENST00000493237.1_Missense_Mutation_p.L359I	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	359					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.L359I(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TAAGCCCATTCTTACCAAATA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											170	173	172					3																	154859897		2203	4300	6503	156342591	SO:0001583	missense	4311				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1075C>A	3.37:g.154859897C>A	ENSP00000418525:p.Leu359Ile		156342591	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582832	0.28268	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	6.02	6.02	0.97574	Peptidase M13 (1);	0.069412	0.56097	D	0.000021	T	0.75347	0.3837	L	0.28458	0.855	0.80722	D	1	B	0.23316	0.083	B	0.41894	0.369	T	0.65001	-0.6274	10	0.05436	T	0.98	-22.1291	20.5269	0.99230	0.0:1.0:0.0:0.0	.	359	P08473	NEP_HUMAN	I	359	ENSP00000420389:L359I;ENSP00000418525:L359I;ENSP00000419653:L359I;ENSP00000417079:L359I;ENSP00000353679:L359I	ENSP00000353679:L359I	L	+	1	0	MME	156342591	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.321000	0.43805	2.859000	0.98148	0.591000	0.81541	CTT		0.368	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154859897	C	A	154859897	3	1	47	1	0	0	0	0	1	0	0	0	9675	913	32	2	1113	2	MME	3	154859897	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3260921	154859897	43162533	498	4895										
CCNL1	57018	broad.mit.edu	37	chr3	156867317	156867317	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgttgtctatcctcaggttCttttttgactgtcttcacat	6	10	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:156867317C>A	ENST00000295926.3	-	9	1208	c.1090G>T	c.(1090-1092)Gaa>Taa	p.E364*	CCNL1_ENST00000479052.1_5'Flank|CCNL1_ENST00000461804.1_Nonsense_Mutation_p.E364*	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	364					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)		p.E364*(1)		NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TCCTCAGGTTCTTTTTTGACT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											149	140	143					3																	156867317		2203	4300	6503	158350011	SO:0001587	stop_gained	57018			AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.1090G>T	3.37:g.156867317C>A	ENSP00000295926:p.Glu364*		158350011	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Nonsense_Mutation	SNP	ENST00000295926.3	37	CCDS3178.1	.	.	.	.	.	.	.	.	.	.	C	38	7.234485	0.98154	.	.	ENSG00000163660	ENST00000461804;ENST00000295926	.	.	.	5.68	5.68	0.88126	.	0.093640	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-18.288	19.8158	0.96568	0.0:1.0:0.0:0.0	.	.	.	.	X	364	.	ENSP00000295926:E364X	E	-	1	0	CCNL1	158350011	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	7.139000	0.77314	2.680000	0.91292	0.655000	0.94253	GAA		0.358	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307		A	156867317	C	A	156867317	4	1	47	1	0	0	0	0	0	1	0	0	2937	922	32	2	502	2	CCNL1	3	156867317	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2007420	156867317	41155113	499	4896										
MFSD1	64747	broad.mit.edu	37	chr3	158527032	158527032	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagctggtttaaaggcaaaGaattaaacctggtgtttgga	12	4	0	2	rs367562194		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:158527032G>T	ENST00000264266.8	+	6	567	c.505G>T	c.(505-507)Gaa>Taa	p.E169*	MFSD1_ENST00000415822.2_Nonsense_Mutation_p.E218*|MFSD1_ENST00000392813.4_Nonsense_Mutation_p.E179*			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	169					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.E169*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TAAAGGCAAAGAATTAAACCT	0.358																																					Pancreas(62;1186 1654 36636 37908)											1	Substitution - Nonsense(1)	large_intestine(1)	3						G	stop/GLU,stop/GLU	0,4406		0,0,2203	109	111	111		535,652	4.7	1	3		111	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	MFSD1	NM_001167903.1,NM_022736.2	,	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	,	179/476,218/515	158527032	1,13005	2203	4300	6503	160009726	SO:0001587	stop_gained	64747			BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.505G>T	3.37:g.158527032G>T	ENSP00000264266:p.Glu169*		160009726	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Nonsense_Mutation	SNP	ENST00000264266.8	37		.	.	.	.	.	.	.	.	.	.	G	37	6.401265	0.97537	0.0	1.16E-4	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000474670;ENST00000477743	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-17.3382	17.627	0.88096	0.0:0.0:1.0:0.0	.	.	.	.	X	218;179;169;142;3	.	ENSP00000264266:E169X	E	+	1	0	MFSD1	160009726	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.293000	0.96082	2.308000	0.77769	0.462000	0.41574	GAA		0.358	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		T	158527032	G	T	158527032	4	4	47	1	0	0	0	0	0	1	0	0	9557	943	33	2	674	2	MFSD1	3	158527032	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1659715	158527032	39495398	500	4897										
IQCJ	654502	broad.mit.edu	37	chr3	158970581	158970581	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcaatctacagcccttggAatcaaaggtgaaaatgtaag	8	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:158970581A>G	ENST00000451172.1	+	3	245	c.140A>G	c.(139-141)gAa>gGa	p.E47G	IQCJ_ENST00000481796.1_Intron|IQCJ_ENST00000482126.1_Intron|IQCJ-SCHIP1_ENST00000485419.1_Missense_Mutation_p.E47G|IQCJ_ENST00000397832.2_Missense_Mutation_p.E47G|IQCJ-SCHIP1_ENST00000476809.1_Intron|IQCJ-SCHIP1_ENST00000467442.1_Intron	NM_001042705.2	NP_001036170.1	Q1A5X6	IQCJ_HUMAN	IQ motif containing J	47	IQ.							p.E47G(2)		cervix(1)|endometrium(2)|large_intestine(2)|lung(10)	15			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CAGCCCTTGGAATCAAAGGTG	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	3											83	79	81					3																	158970581		1828	4083	5911	160453275	SO:0001583	missense	29970			DQ309553, DQ309554	CCDS46946.1, CCDS46947.1, CCDS56290.1	3q25.32	2011-03-24			ENSG00000214216	ENSG00000214216			32406	protein-coding gene	gene with protein product		611622				17045569	Standard	NM_001042705		Approved			Q1A5X6	OTTHUMG00000166440	ENST00000451172.1:c.140A>G	3.37:g.158970581A>G	ENSP00000402153:p.Glu47Gly		160453275	B7ZMM2|B9EH97|Q1A5X5	Missense_Mutation	SNP	ENST00000451172.1	37	CCDS46946.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.461370	0.84317	.	.	ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000214216;ENSG00000214216	ENST00000471575;ENST00000485419;ENST00000483486;ENST00000488898;ENST00000397832;ENST00000451172	T	0.46451	0.87	5.66	5.66	0.87406	.	0.371727	0.23463	U	0.047901	T	0.53238	0.1784	L	0.29908	0.895	0.80722	D	1	D;D;D	0.76494	0.999;0.992;0.979	D;P;P	0.78314	0.991;0.856;0.666	T	0.56938	-0.7896	10	0.87932	D	0	.	14.8842	0.70555	1.0:0.0:0.0:0.0	.	47;47;47	Q9P0W5-5;Q1A5X6;Q1A5X6-2	.;IQCJ_HUMAN;.	G	47;47;47;18;47;47	ENSP00000420182:E47G	ENSP00000380932:E47G	E	+	2	0	IQCJ-SCHIP1;IQCJ	160453275	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.930000	0.70104	2.153000	0.67306	0.460000	0.39030	GAA		0.343	IQCJ-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352395.1	NM_001042705.1		G	158970581	A	G	158970581	3	3	47	1	0	0	0	0	1	0	0	0	7833	246	9	4	150	4	IQCJ	3	158970581	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	443549	158970581	39051849	501	4898										
IFT80	57560	broad.mit.edu	37	chr3	160073831	160073831	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacacaagcgtaaagtatgAaacgatccaacagcaaataa	6	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:160073831A>C	ENST00000326448.7	-	8	1179	c.747T>G	c.(745-747)ttT>ttG	p.F249L	IFT80_ENST00000496589.1_Missense_Mutation_p.F112L|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.F420L|IFT80_ENST00000483465.1_Missense_Mutation_p.F112L	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	249					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)		p.F249L(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GTAAAGTATGAAACGATCCAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											141	128	132					3																	160073831		2203	4300	6503	161556525	SO:0001583	missense	57560			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.747T>G	3.37:g.160073831A>C	ENSP00000312778:p.Phe249Leu		161556525	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.543501	0.65198	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589;ENST00000465537	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.28	4.11	0.48088	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.089503	0.43747	U	0.000523	T	0.48314	0.1493	L	0.57536	1.79	0.58432	D	0.999999	B	0.19200	0.034	B	0.19666	0.026	T	0.31724	-0.9933	10	0.11794	T	0.64	.	8.7677	0.34713	0.8324:0.0:0.1676:0.0	.	249	Q9P2H3	IFT80_HUMAN	L	249;112;112;112	ENSP00000312778:F249L;ENSP00000418196:F112L;ENSP00000420646:F112L;ENSP00000418602:F112L	ENSP00000312778:F249L	F	-	3	2	IFT80	161556525	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	1.837000	0.39201	0.847000	0.35167	0.482000	0.46254	TTT		0.433	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		C	160073831	A	C	160073831	3	2	47	1	0	0	0	0	1	0	0	0	7585	243	9	4	1638	4	IFT80	3	160073831	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1103250	160073831	37948599	502	4899										
ZBBX	79740	broad.mit.edu	37	chr3	167016185	167016185	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtatcaaaaataaagaatCtctcaagtccttgatattgt	5	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:167016185C>A	ENST00000392766.2	-	18	2127	c.1787G>T	c.(1786-1788)aGa>aTa	p.R596I	ZBBX_ENST00000307529.5_Missense_Mutation_p.R596I|ZBBX_ENST00000392764.1_Missense_Mutation_p.R567I|ZBBX_ENST00000455345.2_Missense_Mutation_p.R596I|ZBBX_ENST00000392767.2_Missense_Mutation_p.R596I	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	596						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R596I(4)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AATAAAGAATCTCTCAAGTCC	0.303																																																4	Substitution - Missense(4)	large_intestine(4)	3											132	134	134					3																	167016185		1828	4070	5898	168498879	SO:0001583	missense	79740			AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1787G>T	3.37:g.167016185C>A	ENSP00000376519:p.Arg596Ile		168498879	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	C	17.69	3.451207	0.63290	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.12569	2.84;2.84;2.86;2.86;2.67	4.9	-0.367	0.12541	.	0.319140	0.32548	N	0.005959	T	0.11024	0.0269	L	0.50333	1.59	0.33545	D	0.595343	B;B	0.26809	0.16;0.099	B;B	0.29598	0.104;0.027	T	0.07139	-1.0788	10	0.66056	D	0.02	-3.4584	4.1053	0.10033	0.1591:0.4484:0.0:0.3924	.	596;596	A8MT70-2;A8MT70	.;ZBBX_HUMAN	I	596;596;596;596;567	ENSP00000376519:R596I;ENSP00000376520:R596I;ENSP00000390232:R596I;ENSP00000305065:R596I;ENSP00000376517:R567I	ENSP00000305065:R596I	R	-	2	0	ZBBX	168498879	0.903000	0.30736	0.959000	0.39883	0.981000	0.71138	-0.088000	0.11198	-0.055000	0.13244	0.591000	0.81541	AGA		0.303	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		A	167016185	C	A	167016185	3	1	47	1	0	0	0	0	1	0	0	0	17556	913	32	2	631	2	ZBBX	3	167016185	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6942354	167016185	31006245	503	4900										
SERPINI1	5274	broad.mit.edu	37	chr3	167543043	167543043	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaccaatacaggtacaattCtattcatgggacgagtcatg	9	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:167543043C>A	ENST00000295777.5	+	9	1596	c.1165C>A	c.(1165-1167)Cta>Ata	p.L389I	SERPINI1_ENST00000446050.2_Missense_Mutation_p.L389I|SERPINI1_ENST00000488374.1_3'UTR	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	389					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L389I(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(7)|skin(2)	20						AGGTACAATTCTATTCATGGG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	118	117					3																	167543043		2203	4300	6503	169025737	SO:0001583	missense	5274			Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"Serine (or cysteine) peptidase inhibitors"	8943	protein-coding gene	gene with protein product		602445	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.1165C>A	3.37:g.167543043C>A	ENSP00000295777:p.Leu389Ile		169025737	A8K217|D3DNP1|Q6AHZ4	Missense_Mutation	SNP	ENST00000295777.5	37	CCDS3203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.30|12.30	1.895135|1.895135	0.33442|0.33442	.|.	.|.	ENSG00000163536|ENSG00000163536	ENST00000446050;ENST00000295777;ENST00000466979|ENST00000466865	D;D|.	0.90955|.	-2.76;-2.76|.	5.71|5.71	3.54|3.54	0.40534|0.40534	Serpin domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64713|0.64713	0.2623|0.2623	M|M	0.82193|0.82193	2.58|2.58	0.54753|0.54753	D|D	0.999989|0.999989	B|.	0.20164|.	0.042|.	B|.	0.35278|.	0.199|.	T|T	0.65940|0.65940	-0.6046|-0.6046	10|5	0.56958|.	D|.	0.05|.	.|.	2.2255|2.2255	0.03983|0.03983	0.2346:0.3206:0.0:0.4448|0.2346:0.3206:0.0:0.4448	.|.	389|.	Q99574|.	NEUS_HUMAN|.	I|Y	389;389;137|97	ENSP00000397373:L389I;ENSP00000295777:L389I|.	ENSP00000295777:L389I|.	L|S	+|+	1|2	2|0	SERPINI1|SERPINI1	169025737|169025737	0.995000|0.995000	0.38212|0.38212	0.842000|0.842000	0.33263|0.33263	0.644000|0.644000	0.38419|0.38419	0.363000|0.363000	0.20301|0.20301	1.279000|1.279000	0.44446|0.44446	0.591000|0.591000	0.81541|0.81541	CTA|TCT		0.308	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1			A	167543043	C	A	167543043	3	1	47	1	0	0	0	0	1	0	0	0	14155	912	32	2	1195	2	SERPINI1	3	167543043	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	526858	167543043	30479387	504	4901										
SLC2A2	6514	broad.mit.edu	37	chr3	170715808	170715808	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaaaagactttcctttggTttctggaactttaaaaaatg	6	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:170715808T>C	ENST00000314251.3	-	11	1538	c.1459A>G	c.(1459-1461)Acc>Gcc	p.T487A	RNU1-70P_ENST00000362618.1_RNA|SLC2A2_ENST00000382808.4_Missense_Mutation_p.T368A	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	487					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.T487A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TTTCCTTTGGTTTCTGGAACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											54	58	56					3																	170715808		2202	4300	6502	172198502	SO:0001583	missense	6514			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1459A>G	3.37:g.170715808T>C	ENSP00000323568:p.Thr487Ala		172198502	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.996590	0.93167	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	T;T	0.80994	-1.44;-1.44	6.17	6.17	0.99709	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.93684	0.7982	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95647	0.8703	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	487	P11168	GTR2_HUMAN	A	487;368	ENSP00000323568:T487A;ENSP00000372258:T368A	ENSP00000323568:T487A	T	-	1	0	SLC2A2	172198502	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.484000	0.81180	2.371000	0.80710	0.533000	0.62120	ACC		0.433	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		C	170715808	T	C	170715808	3	2	47	1	0	0	0	0	1	0	0	0	14581	1725	60	4	119	4	SLC2A2	3	170715808	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3172765	170715808	27306622	505	4902										
SLC2A2	6514	broad.mit.edu	37	chr3	170723155	170723155	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggtagctggaattggtgaaGagctgaattatagagacttt	13	4	0	4	rs200467142		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:170723155G>T	ENST00000314251.3	-	7	961	c.882C>A	c.(880-882)ctC>ctA	p.L294L	SLC2A2_ENST00000382808.4_Silent_p.L175L	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	294					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.L294L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	AATTGGTGAAGAGCTGAATTA	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		17043	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											219	194	202					3																	170723155		2203	4300	6503	172205849	SO:0001819	synonymous_variant	6514			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.882C>A	3.37:g.170723155G>T			172205849	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																				0.413	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		T	170723155	G	T	170723155	2	4	47	1	0	0	0	0	0	0	0	1	14581	929	33	2		2	SLC2A2	3	170723155	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7347	170723155	27299275	506	4903										
SLC2A2	6514	broad.mit.edu	37	chr3	170723873	170723873	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacagatcataattgcccaAgataaattcaagaccaataa	4	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:170723873A>C	ENST00000314251.3	-	6	713	c.634T>G	c.(634-636)Ttg>Gtg	p.L212V	SLC2A2_ENST00000382808.4_Missense_Mutation_p.L93V	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	212					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.L212V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAATTGCCCAAGATAAATTCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	83	86					3																	170723873		2203	4299	6502	172206567	SO:0001583	missense	6514			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.634T>G	3.37:g.170723873A>C	ENSP00000323568:p.Leu212Val		172206567	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.215868	0.39102	.	.	ENSG00000163581	ENST00000314251;ENST00000382808;ENST00000461867	T;T;T	0.74632	-0.86;-0.86;-0.86	5.62	1.73	0.24493	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.062053	0.64402	D	0.000004	D	0.85847	0.5792	M	0.88310	2.945	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	D	0.85560	0.1227	10	0.87932	D	0	.	10.8028	0.46497	0.2897:0.0:0.7103:0.0	.	212	P11168	GTR2_HUMAN	V	212;93;39	ENSP00000323568:L212V;ENSP00000372258:L93V;ENSP00000418888:L39V	ENSP00000323568:L212V	L	-	1	2	SLC2A2	172206567	1.000000	0.71417	0.913000	0.36048	0.156000	0.22039	2.305000	0.43664	0.108000	0.17862	-0.874000	0.02982	TTG		0.403	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		C	170723873	A	C	170723873	3	2	47	1	0	0	0	0	1	0	0	0	14581	69	3	4	964	4	SLC2A2	3	170723873	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	718	170723873	27298557	507	4904										
TNIK	23043	broad.mit.edu	37	chr3	170912393	170912393	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttcttgatcaggtcggtgAcagagccagcaccacaaaac	10	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:170912393A>G	ENST00000436636.2	-	5	682	c.338T>C	c.(337-339)gTc>gCc	p.V113A	TNIK_ENST00000470834.1_Missense_Mutation_p.V113A|TNIK_ENST00000538048.1_Missense_Mutation_p.V113A|TNIK_ENST00000341852.6_Missense_Mutation_p.V113A|TNIK_ENST00000488470.1_Missense_Mutation_p.V113A|TNIK_ENST00000284483.8_Missense_Mutation_p.V113A|TNIK_ENST00000369326.5_Missense_Mutation_p.V113A|TNIK_ENST00000475336.1_Missense_Mutation_p.V113A|TNIK_ENST00000460047.1_Missense_Mutation_p.V113A|TNIK_ENST00000357327.5_Missense_Mutation_p.V113A	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	113	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.V113A(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CAGGTCGGTGACAGAGCCAGC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	3											177	179	178					3																	170912393		1989	4156	6145	172395087	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.338T>C	3.37:g.170912393A>G	ENSP00000399511:p.Val113Ala		172395087	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.959316	0.92726	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834;ENST00000468757	T;T;T;T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;2.48	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	L	0.42686	1.345	0.80722	D	1	P;D;D;D;D;D;D;D	0.69078	0.693;0.98;0.997;0.994;0.98;0.98;0.997;0.984	P;D;D;D;D;D;D;D	0.76575	0.607;0.98;0.985;0.964;0.98;0.98;0.985;0.988	T	0.35919	-0.9769	10	0.87932	D	0	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	113;113;113;113;113;113;113;113	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	A	113;113;113;113;113;113;113;113;113;113;87	ENSP00000399511:V113A;ENSP00000358332:V113A;ENSP00000443278:V113A;ENSP00000345352:V113A;ENSP00000284483:V113A;ENSP00000418156:V113A;ENSP00000349880:V113A;ENSP00000418916:V113A;ENSP00000418378:V113A;ENSP00000419990:V113A;ENSP00000417338:V87A	ENSP00000284483:V113A	V	-	2	0	TNIK	172395087	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.307000	0.96226	2.326000	0.78906	0.533000	0.62120	GTC		0.453	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		G	170912393	A	G	170912393	3	3	47	1	0	0	0	0	1	0	0	0	16352	275	10	4	3860	4	TNIK	3	170912393	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	188520	170912393	27110037	508	4905										
PIK3CA	5290	broad.mit.edu	37	chr3	178947900	178947900	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtaacatcatggtgaaagaCgatggacaagtaatggtttt	11	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:178947900C>T	ENST00000263967.3	+	19	2932	c.2775C>T	c.(2773-2775)gaC>gaT	p.D925D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	925	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D925D(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGGTGAAAGACGATGGACAAG	0.343		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	2	Substitution - coding silent(2)	large_intestine(2)	3											159	146	150					3																	178947900		1888	4116	6004	180430594	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2775C>T	3.37:g.178947900C>T			180430594	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.343	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178947900	C	T	178947900	2	4	47	1	0	0	0	0	0	0	0	1	11944	535	19	1		1	PIK3CA	3	178947900	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	8035507	178947900	19074530	509	4906										
MCF2L2	23101	broad.mit.edu	37	chr3	182947467	182947467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatatacctgttgtgaaattCgtaaagttctctaatattcc	5	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:182947467C>T	ENST00000328913.3	-	17	2329	c.2032G>A	c.(2032-2034)Gaa>Aaa	p.E678K	MCF2L2_ENST00000473233.1_Missense_Mutation_p.E678K|MCF2L2_ENST00000447025.2_Missense_Mutation_p.E678K	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	678	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E678K(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TTGTGAAATTCGTAAAGTTCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	97	95					3																	182947467		2203	4300	6503	184430161	SO:0001583	missense	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2032G>A	3.37:g.182947467C>T	ENSP00000328118:p.Glu678Lys		184430161	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.643942	0.67244	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025	T;T;T	0.62788	0.0;0.0;0.0	5.06	5.06	0.68205	Dbl homology (DH) domain (5);	0.136757	0.48767	D	0.000177	T	0.69169	0.3081	L	0.41356	1.27	0.80722	D	1	D;D	0.76494	0.99;0.999	D;D	0.63703	0.917;0.913	T	0.70528	-0.4847	10	0.52906	T	0.07	.	13.9585	0.64164	0.0:1.0:0.0:0.0	.	678;678	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	K	678	ENSP00000328118:E678K;ENSP00000420070:E678K;ENSP00000388190:E678K	ENSP00000328118:E678K	E	-	1	0	MCF2L2	184430161	0.979000	0.34478	0.989000	0.46669	0.626000	0.37791	2.595000	0.46197	2.350000	0.79820	0.655000	0.94253	GAA		0.328	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		T	182947467	C	T	182947467	3	4	47	1	0	0	0	0	1	0	0	0	9410	893	31	1	1368	1	MCF2L2	3	182947467	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3999567	182947467	15074963	510	4907										
ECE2	9718	broad.mit.edu	37	chr3	184008048	184008048	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacctttcccacagtacgaAatttctgaagattctttctt	4	12	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:184008048A>C	ENST00000402825.3	+	14	1911	c.1911A>C	c.(1909-1911)gaA>gaC	p.E637D	ECE2_ENST00000359140.4_Missense_Mutation_p.E490D|ECE2_ENST00000357474.5_Missense_Mutation_p.E565D|ECE2_ENST00000404464.3_Missense_Mutation_p.E519D|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	637	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.E637D(1)|p.E490D(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CACAGTACGAAATTTCTGAAG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	3											52	49	50					3																	184008048		2203	4300	6503	185490742	SO:0001583	missense	9718			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1911A>C	3.37:g.184008048A>C	ENSP00000384223:p.Glu637Asp		185490742	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	A	3.214	-0.160921	0.06502	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.04	2.59	0.31030	.	0.114059	0.64402	N	0.000020	T	0.72676	0.3490	L	0.55990	1.75	0.50039	D	0.999841	B;B;B;B;B;B;B	0.09022	0.0;0.002;0.0;0.0;0.0;0.002;0.0	B;B;B;B;B;B;B	0.10450	0.002;0.003;0.001;0.003;0.002;0.005;0.001	T	0.60652	-0.7221	10	0.30854	T	0.27	-5.74	1.0888	0.01659	0.5216:0.1659:0.1531:0.1595	.	239;490;508;519;565;490;637	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	D	637;490;519;565;511	ENSP00000384223:E637D;ENSP00000352052:E490D;ENSP00000385846:E519D;ENSP00000350066:E565D;ENSP00000398444:E511D	ENSP00000350066:E565D	E	+	3	2	ECE2	185490742	0.999000	0.42202	0.997000	0.53966	0.207000	0.24258	0.593000	0.23999	0.250000	0.21479	0.368000	0.22195	GAA		0.448	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		C	184008048	A	C	184008048	3	2	47	1	0	0	0	0	1	0	0	0	4901	11	1	4	2529	4	ECE2	3	184008048	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1060581	184008048	14014382	511	4908										
TBCCD1	55171	broad.mit.edu	37	chr3	186276256	186276256	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcaggagactgagatttgtTtctgggactgggccactctt	13	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:186276256T>G	ENST00000424280.1	-	3	921	c.442A>C	c.(442-444)Aac>Cac	p.N148H	TBCCD1_ENST00000338733.5_Missense_Mutation_p.N148H|TBCCD1_ENST00000446782.1_Missense_Mutation_p.N52H	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	148					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)		p.N148H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TGAGATTTGTTTCTGGGACTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											140	139	140					3																	186276256		2203	4300	6503	187758950	SO:0001583	missense	55171			BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.442A>C	3.37:g.186276256T>G	ENSP00000411253:p.Asn148His		187758950	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	37	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	T	8.304	0.820531	0.16678	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782;ENST00000413695;ENST00000430560	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;0.86	5.24	2.77	0.32553	.	1.204470	0.05503	N	0.558802	T	0.53899	0.1825	N	0.16478	0.41	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37197	-0.9716	10	0.27082	T	0.32	-0.9741	6.0677	0.19871	0.0:0.0843:0.348:0.5677	.	52;148	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	H	148;148;52;148;132	ENSP00000411253:N148H;ENSP00000341652:N148H;ENSP00000397091:N52H;ENSP00000391109:N148H;ENSP00000407506:N132H	ENSP00000341652:N148H	N	-	1	0	TBCCD1	187758950	0.807000	0.29009	0.676000	0.29932	0.365000	0.29674	0.567000	0.23608	0.356000	0.24157	0.533000	0.62120	AAC		0.413	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		G	186276256	T	G	186276256	3	3	47	1	0	0	0	0	1	0	0	0	15671	1841	64	4	1251	4	TBCCD1	3	186276256	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2268208	186276256	11746174	512	4909										
ATP13A5	344905	broad.mit.edu	37	chr3	193080376	193080376	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaactttctgaaaccgcttCtccaggtcgttccaaacata	5	14	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:193080376C>A	ENST00000342358.4	-	4	552	c.435G>T	c.(433-435)gaG>gaT	p.E145D		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	145						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.E145D(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GAAACCGCTTCTCCAGGTCGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											168	161	163					3																	193080376		2203	4300	6503	194563070	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.435G>T	3.37:g.193080376C>A	ENSP00000341942:p.Glu145Asp		194563070	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737853	0.49045	.	.	ENSG00000187527	ENST00000342358	T	0.35236	1.32	5.42	4.54	0.55810	.	0.263376	0.32868	N	0.005544	T	0.41236	0.1150	M	0.74546	2.27	0.29213	N	0.874465	P	0.34892	0.474	B	0.38500	0.275	T	0.39663	-0.9603	10	0.30078	T	0.28	-8.6501	12.0311	0.53397	0.0:0.9158:0.0:0.0842	.	145	Q4VNC0	AT135_HUMAN	D	145	ENSP00000341942:E145D	ENSP00000341942:E145D	E	-	3	2	ATP13A5	194563070	0.982000	0.34865	1.000000	0.80357	0.893000	0.52053	0.687000	0.25407	1.424000	0.47217	0.655000	0.94253	GAG		0.438	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193080376	C	A	193080376	3	1	47	1	0	0	0	0	1	0	0	0	1128	912	32	2	3327	2	ATP13A5	3	193080376	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6804120	193080376	4942054	513	4910										
ATP13A4	84239	broad.mit.edu	37	chr3	193159367	193159367	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agacttcatccctgatgttaAtgtaattgtcctacaaagca	6	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:193159367A>G	ENST00000342695.4	-	20	2649	c.2327T>C	c.(2326-2328)aTt>aCt	p.I776T	ATP13A4_ENST00000392443.3_Missense_Mutation_p.I757T	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	776						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.I776T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CCTGATGTTAATGTAATTGTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											134	119	124					3																	193159367		2203	4300	6503	194642061	SO:0001583	missense	84239			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.2327T>C	3.37:g.193159367A>G	ENSP00000339182:p.Ile776Thr		194642061	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	37	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	A	12.38	1.920203	0.33908	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.85861	-1.76;-2.04	5.85	5.85	0.93711	HAD-like domain (1);	0.076942	0.53938	D	0.000056	T	0.81654	0.4868	L	0.51853	1.615	0.80722	D	1	B;B;B	0.30211	0.273;0.002;0.143	B;B;B	0.37198	0.243;0.025;0.243	T	0.75703	-0.3225	10	0.12103	T	0.63	-30.5818	11.7077	0.51607	0.8525:0.1475:0.0:0.0	.	757;776;776	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	T	757;776	ENSP00000376238:I757T;ENSP00000339182:I776T	ENSP00000339182:I776T	I	-	2	0	ATP13A4	194642061	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.303000	0.65738	2.222000	0.72286	0.533000	0.62120	ATT		0.368	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		G	193159367	A	G	193159367	3	3	47	1	0	0	0	0	1	0	0	0	1127	101	4	4	1307	4	ATP13A4	3	193159367	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	78991	193159367	4863063	514	4911										
OPA1	4976	broad.mit.edu	37	chr3	193374898	193374898	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaccctacaagaagaattTtcccgctttatgacagaacc	7	11	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:193374898T>G	ENST00000392438.3	+	21	2277	c.2043T>G	c.(2041-2043)ttT>ttG	p.F681L	OPA1_ENST00000361908.3_Missense_Mutation_p.F718L|OPA1_ENST00000361510.2_Missense_Mutation_p.F736L|OPA1_ENST00000361150.2_Missense_Mutation_p.F682L|OPA1_ENST00000361715.2_Missense_Mutation_p.F700L|OPA1_ENST00000361828.2_Missense_Mutation_p.F699L	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	681					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)	p.F736L(1)		breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		AAGAAGAATTTTCCCGCTTTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											72	77	75					3																	193374898		2203	4300	6503	194857592	SO:0001583	missense	4976			AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2043T>G	3.37:g.193374898T>G	ENSP00000376233:p.Phe681Leu		194857592	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.445482	0.63178	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150	D;D;D;D;D;D	0.96716	-3.72;-3.72;-3.64;-3.65;-3.75;-4.1	5.78	4.64	0.57946	.	0.044369	0.85682	D	0.000000	D	0.96691	0.8920	M	0.65975	2.015	0.80722	D	1	P;D;P;P;B;D;D;D	0.69078	0.937;0.997;0.937;0.937;0.412;0.977;0.982;0.988	P;D;P;P;B;P;D;P	0.70716	0.62;0.97;0.62;0.751;0.134;0.751;0.952;0.751	D	0.94574	0.7773	10	0.20519	T	0.43	-21.2669	7.8724	0.29573	0.0:0.1529:0.0:0.8471	.	645;681;663;682;699;718;700;736	E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.;OPA1_HUMAN;.;.;.;.;.;.	L	718;681;736;700;699;682	ENSP00000354681:F718L;ENSP00000376233:F681L;ENSP00000355324:F736L;ENSP00000355311:F700L;ENSP00000354429:F699L;ENSP00000354781:F682L	ENSP00000354781:F682L	F	+	3	2	OPA1	194857592	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.863000	0.48396	2.197000	0.70478	0.533000	0.62120	TTT		0.333	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		G	193374898	T	G	193374898	3	3	47	1	0	0	0	0	1	0	0	0	10902	1838	64	4	2298	4	OPA1	3	193374898	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	215531	193374898	4647532	515	4912										
GP5	2814	broad.mit.edu	37	chr3	194118502	194118502	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatccaacaacttcaggttCtccagattcgtgaagagact	7	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:194118502C>T	ENST00000401815.1	-	1	581	c.510G>A	c.(508-510)gaG>gaA	p.E170E	GP5_ENST00000323007.3_Silent_p.E170E			P40197	GPV_HUMAN	glycoprotein V (platelet)	170					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.E170E(2)		breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		ACTTCAGGTTCTCCAGATTCG	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	3											71	74	73					3																	194118502		2203	4300	6503	195599791	SO:0001819	synonymous_variant	2814			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"CD molecules"	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.510G>A	3.37:g.194118502C>T			195599791	D1MER9	Silent	SNP	ENST00000401815.1	37	CCDS3307.1																																																																																				0.502	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488		T	194118502	C	T	194118502	2	4	47	1	0	0	0	0	0	0	0	1	6603	912	32	3		3	GP5	3	194118502	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	743604	194118502	3903928	516	4913										
TFRC	7037	broad.mit.edu	37	chr3	195798938	195798938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgctgagtttaaattcacGaaattgattttcaacataca	5	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr3:195798938G>A	ENST00000360110.4	-	5	689	c.520C>T	c.(520-522)Cgt>Tgt	p.R174C	TFRC_ENST00000392396.3_Missense_Mutation_p.R174C|RNU7-18P_ENST00000516365.1_RNA|TFRC_ENST00000420415.1_Missense_Mutation_p.R93C|TFRC_ENST00000535031.1_5'UTR|TFRC_ENST00000540528.1_3'UTR	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	174					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)	p.R174C(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	TTAAATTCACGAAATTGATTT	0.358			T	BCL6	NHL																																		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	1	Substitution - Missense(1)	large_intestine(1)	3											74	73	73					3																	195798938		2203	4300	6503	197283335	SO:0001583	missense	7037			X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"CD molecules"	11763	protein-coding gene	gene with protein product		190010	"transferrin receptor (p90, CD71)"				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.520C>T	3.37:g.195798938G>A	ENSP00000353224:p.Arg174Cys		197283335	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	37	CCDS3312.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.570086	0.28003	.	.	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396	T;T;T	0.44083	0.93;0.93;0.93	5.5	0.686	0.18015	.	1.119740	0.06522	N	0.739921	T	0.51856	0.1699	M	0.79805	2.47	0.09310	N	0.999999	D	0.67145	0.996	P	0.45577	0.486	T	0.53788	-0.8389	10	0.66056	D	0.02	-0.0054	12.2853	0.54789	0.0:0.0:0.3267:0.6733	.	174	P02786	TFR1_HUMAN	C	174;93;174	ENSP00000353224:R174C;ENSP00000390133:R93C;ENSP00000376197:R174C	ENSP00000353224:R174C	R	-	1	0	TFRC	197283335	0.034000	0.19679	0.005000	0.12908	0.140000	0.21249	0.885000	0.28227	0.309000	0.22966	-0.293000	0.09583	CGT		0.358	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			A	195798938	G	A	195798938	3	1	47	1	0	0	0	0	1	0	0	0	15851	1058	37	1	1822	1	TFRC	3	195798938	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1680436	195798938	2223492	517	4914										
ZNF721	170960	broad.mit.edu	37	chr4	436610	436610	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctctccagtatgaattCtcctatgtacataaaggatt	6	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:436610C>A	ENST00000338977.5	-	2	1658	c.1610G>T	c.(1609-1611)aGa>aTa	p.R537I	ZNF721_ENST00000511833.2_Missense_Mutation_p.R549I|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R319I(1)|p.R549I(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGTATGAATTCTCCTATGTAC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											89	97	94					4																	436610		2111	4259	6370	426610	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1610G>T	4.37:g.436610C>A	ENSP00000340524:p.Arg537Ile		426610	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	15.60	2.882652	0.51908	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.02446	4.29;4.29	1.28	1.28	0.21552	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09024	0.0223	L	0.53780	1.695	0.33086	D	0.537277	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.76071	0.987;0.987;0.978	T	0.17961	-1.0352	9	0.45353	T	0.12	.	8.0662	0.30661	0.0:1.0:0.0:0.0	.	537;549;549	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	I	537;549	ENSP00000340524:R537I;ENSP00000428878:R549I	ENSP00000340524:R537I	R	-	2	0	ZNF721	426610	0.000000	0.05858	0.041000	0.18516	0.796000	0.44982	-0.682000	0.05185	0.672000	0.31204	0.184000	0.17185	AGA		0.403	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	436610	C	A	436610	3	1	47	1	0	0	0	0	1	0	0	0	18161	913	32	2	1129	2	ZNF721	4	436610	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09		436610	190717666	518	4915										
NOP14	8602	broad.mit.edu	37	chr4	2959399	2959399	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgttgctgttgtattctccGaagcgtttatctctgaatac	8	8	2	1	rs375247657		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:2959399G>A	ENST00000314262.6	-	2	312	c.264C>T	c.(262-264)ttC>ttT	p.F88F	NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000416614.2_Silent_p.F88F|NOP14_ENST00000398071.4_Silent_p.F88F|NOP14_ENST00000502735.1_Silent_p.F88F	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	88					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.F88F(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						TGTATTCTCCGAAGCGTTTAT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G		0,4406		0,0,2203	206	190	196		264	-3.3	0.9	4		196	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NOP14	NM_003703.1		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		88/858	2959399	2,13004	2203	4300	6503	2929197	SO:0001819	synonymous_variant	8602			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.264C>T	4.37:g.2959399G>A			2929197	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Silent	SNP	ENST00000314262.6	37	CCDS33945.1																																																																																				0.418	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		A	2959399	G	A	2959399	2	1	47	1	0	0	0	0	0	0	0	1	10567	1049	37	1		1	NOP14	4	2959399	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2522789	2959399	188194877	519	4916										
LYAR	55646	broad.mit.edu	37	chr4	4270335	4270335	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaatagttcccttccagttGaatttacctacaatataaat	3	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:4270335G>T	ENST00000343470.4	-	9	1167	c.927C>A	c.(925-927)ttC>ttA	p.F309L	LYAR_ENST00000452476.1_Missense_Mutation_p.F309L	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	309	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F309L(1)		endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCTTCCAGTTGAATTTACCTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	112	114					4																	4270335		2203	4298	6501	4321236	SO:0001583	missense	55646			AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.927C>A	4.37:g.4270335G>T	ENSP00000345917:p.Phe309Leu		4321236	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	37	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.202734	0.79127	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	T;T	0.37752	1.18;1.18	5.61	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.60327	0.2260	M	0.85041	2.73	0.53688	D	0.999979	D	0.76494	0.999	D	0.80764	0.994	T	0.62613	-0.6817	10	0.44086	T	0.13	-20.9978	9.7641	0.40550	0.1644:0.0:0.8356:0.0	.	309	Q9NX58	LYAR_HUMAN	L	309	ENSP00000345917:F309L;ENSP00000397367:F309L	ENSP00000345917:F309L	F	-	3	2	LYAR	4321236	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.761000	0.55242	1.293000	0.44690	0.561000	0.74099	TTC		0.343	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		T	4270335	G	T	4270335	3	4	47	1	0	0	0	0	1	0	0	0	9133	1281	45	2	220	2	LYAR	4	4270335	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1310936	4270335	186883941	520	4917										
CRMP1	1400	broad.mit.edu	37	chr4	5830234	5830234	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttattcctgattttgacGcgctggtacaggtgctccgg	11	11	0	2	rs143852988		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:5830234G>A	ENST00000397890.2	-	12	1657	c.1443C>T	c.(1441-1443)cgC>cgT	p.R481R	EVC_ENST00000382674.2_Intron|CRMP1_ENST00000512574.1_Silent_p.R479R|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.R595R	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	481					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.R595R(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TGATTTTGACGCGCTGGTACA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	4											94	79	84					4																	5830234		2203	4300	6503	5881135	SO:0001819	synonymous_variant	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1443C>T	4.37:g.5830234G>A			5881135	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																				0.592	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5830234	G	A	5830234	2	1	47	1	0	0	0	0	0	0	0	1	3896	1074	38	1		1	CRMP1	4	5830234	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1559899	5830234	185324042	521	4918										
ACOX3	8310	broad.mit.edu	37	chr4	8398776	8398776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagctttaggttaaggatgGccaggctcacgatggagacc	13	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:8398776G>A	ENST00000356406.5	-	9	1021	c.944C>T	c.(943-945)gCc>gTc	p.A315V	ACOX3_ENST00000413009.2_Missense_Mutation_p.A315V|ACOX3_ENST00000503233.1_Missense_Mutation_p.A315V	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	315					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)	p.A315V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GTTAAGGATGGCCAGGCTCAC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	65	66					4																	8398776		2203	4300	6503	8449676	SO:0001583	missense	8310			Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.944C>T	4.37:g.8398776G>A	ENSP00000348775:p.Ala315Val		8449676	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.426987	0.43122	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.72505	-0.66;-0.66;-0.66	5.0	3.2	0.36748	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.423339	0.25909	N	0.027501	T	0.78953	0.4365	M	0.75615	2.305	0.26895	N	0.967243	P;P;P	0.51791	0.849;0.948;0.924	P;P;P	0.55260	0.461;0.662;0.772	T	0.72763	-0.4195	10	0.49607	T	0.09	-20.0563	13.9779	0.64284	0.0:0.2905:0.7095:0.0	.	315;315;315	B2R856;O15254-2;O15254	.;.;ACOX3_HUMAN	V	315	ENSP00000413994:A315V;ENSP00000348775:A315V;ENSP00000421625:A315V	ENSP00000348775:A315V	A	-	2	0	ACOX3	8449676	0.998000	0.40836	0.001000	0.08648	0.001000	0.01503	2.783000	0.47766	0.456000	0.26937	0.609000	0.83330	GCC		0.602	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8398776	G	A	8398776	3	1	47	1	0	0	0	0	1	0	0	0	160	1203	42	3	1198	3	ACOX3	4	8398776	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2568542	8398776	182755500	522	4919										
ACOX3	8310	broad.mit.edu	37	chr4	8401376	8401376	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaccttgtggaacatggcGaaactgtggggaagcagcag	15	8	0	1	rs372351617		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:8401376G>A	ENST00000356406.5	-	8	857	c.780C>T	c.(778-780)ttC>ttT	p.F260F	ACOX3_ENST00000413009.2_Silent_p.F260F|ACOX3_ENST00000503233.1_Silent_p.F260F	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	260					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)	p.F260F(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GGAACATGGCGAAACTGTGGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G	,	0,4406		0,0,2203	68	66	67		780,780	-1.6	0.4	4		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ACOX3	NM_001101667.1,NM_003501.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	260/625,260/701	8401376	1,13005	2203	4300	6503	8452276	SO:0001819	synonymous_variant	8310			Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.780C>T	4.37:g.8401376G>A			8452276	Q96AJ8	Silent	SNP	ENST00000356406.5	37	CCDS3401.1																																																																																				0.577	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8401376	G	A	8401376	2	1	47	1	0	0	0	0	0	0	0	1	160	1049	37	1		1	ACOX3	4	8401376	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2600	8401376	182752900	523	4920										
SLC2A9	56606	broad.mit.edu	37	chr4	9836601	9836601	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccgctgagattgctggaaGaactcaccagtcaagatgaa	12	9	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:9836601G>T	ENST00000264784.3	-	11	1376	c.1323C>A	c.(1321-1323)ttC>ttA	p.F441L	SLC2A9_ENST00000309065.3_Missense_Mutation_p.F412L|SLC2A9_ENST00000506583.1_Missense_Mutation_p.F412L	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	441					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)	p.F412L(1)|p.F441L(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	ATTGCTGGAAGAACTCACCAG	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	4											86	77	80					4																	9836601		2203	4300	6503	9445699	SO:0001583	missense	56606			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"Solute carriers"	13446	protein-coding gene	gene with protein product	"urate voltage-driven efflux transporter 1"	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.1323C>A	4.37:g.9836601G>T	ENSP00000264784:p.Phe441Leu		9445699	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	G	0.113	-1.136239	0.01742	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.71103	-0.54;-0.54;-0.54	5.39	0.87	0.19102	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.239855	0.43260	N	0.000581	T	0.30039	0.0752	N	0.01742	-0.745	0.33970	D	0.64676	B;B	0.02656	0.0;0.0	B;B	0.11329	0.003;0.006	T	0.30504	-0.9976	10	0.02654	T	1	.	0.8892	0.01250	0.1545:0.1905:0.2693:0.3857	.	412;441	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	L	412;441;412	ENSP00000422209:F412L;ENSP00000264784:F441L;ENSP00000311383:F412L	ENSP00000264784:F441L	F	-	3	2	SLC2A9	9445699	0.907000	0.30839	0.998000	0.56505	0.064000	0.16182	-0.038000	0.12144	0.213000	0.20722	0.585000	0.79938	TTC		0.527	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			T	9836601	G	T	9836601	3	4	47	1	0	0	0	0	1	0	0	0	14589	933	33	2	307	2	SLC2A9	4	9836601	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1435225	9836601	181317675	524	4921										
BOD1L	259282	broad.mit.edu	37	chr4	13571645	13571645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggtcaggattatcgcttcGcttttttcacaggggcttcc	11	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:13571645G>A	ENST00000040738.5	-	26	9281	c.9146C>T	c.(9145-9147)gCg>gTg	p.A3049V		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	3049						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A3049V(1)									TTATCGCTTCGCTTTTTTCAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	4											150	127	135					4																	13571645		2203	4300	6503	13180743	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.9146C>T	4.37:g.13571645G>A	ENSP00000040738:p.Ala3049Val		13180743	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.24|14.24	2.476506|2.476506	0.44044|0.44044	.|.	.|.	ENSG00000038219|ENSG00000038219	ENST00000040738|ENST00000507943	T|.	0.16743|.	2.32|.	4.85|4.85	4.01|4.01	0.46588|0.46588	.|.	0.000000|.	0.53938|.	D|.	0.000052|.	T|.	0.49270|.	0.1547|.	L|L	0.36672|0.36672	1.1|1.1	0.35827|0.35827	D|D	0.825057|0.825057	P|.	0.48230|.	0.907|.	B|.	0.29176|.	0.099|.	T|.	0.55471|.	-0.8136|.	10|.	0.87932|.	D|.	0|.	-6.4719|-6.4719	11.5893|11.5893	0.50938|0.50938	0.0841:0.0:0.9159:0.0|0.0841:0.0:0.9159:0.0	.|.	3049|.	Q8NFC6|.	BOD1L_HUMAN|.	V|X	3049|205	ENSP00000040738:A3049V|.	ENSP00000040738:A3049V|.	A|R	-|-	2|1	0|2	BOD1L|BOD1L	13180743|13180743	0.961000|0.961000	0.32948|0.32948	0.780000|0.780000	0.31762|0.31762	0.924000|0.924000	0.55760|0.55760	4.388000|4.388000	0.59633|0.59633	1.158000|1.158000	0.42547|0.42547	0.655000|0.655000	0.94253|0.94253	GCG|CGA		0.552	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13571645	G	A	13571645	3	1	47	1	0	0	0	0	1	0	0	0	1484	1087	38	1	13	1	BOD1L	4	13571645	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3735044	13571645	177582631	525	4922										
SLIT2	9353	broad.mit.edu	37	chr4	20543194	20543194	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaaccatacttcctgaaaGaaatacccatccaggatgtg	6	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:20543194G>T	ENST00000504154.1	+	20	2347	c.2095G>T	c.(2095-2097)Gaa>Taa	p.E699*	SLIT2_ENST00000503837.1_Nonsense_Mutation_p.E695*|SLIT2_ENST00000273739.5_Nonsense_Mutation_p.E703*|SLIT2_ENST00000503823.1_Nonsense_Mutation_p.E691*	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	699	LRRCT 3.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.E699*(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CTTCCTGAAAGAAATACCCAT	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											108	100	103					4																	20543194		2203	4300	6503	20152292	SO:0001587	stop_gained	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.2095G>T	4.37:g.20543194G>T	ENSP00000422591:p.Glu699*		20152292	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Nonsense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	G	44	10.982806	0.99499	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.2896	0.98541	0.0:0.0:1.0:0.0	.	.	.	.	X	691;699;703;695;695	.	ENSP00000273739:E703X	E	+	1	0	SLIT2	20152292	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.471000	0.97696	2.794000	0.96219	0.655000	0.94253	GAA		0.423	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20543194	G	T	20543194	4	4	47	1	0	0	0	0	0	1	0	0	14777	943	33	2	2173	2	SLIT2	4	20543194	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6971549	20543194	170611082	526	4923										
SLIT2	9353	broad.mit.edu	37	chr4	20620554	20620554	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcggcggaaatactctttCgaatgcactgacggctcctc	10	12	1	1	rs370110126		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:20620554C>T	ENST00000504154.1	+	37	4764	c.4512C>T	c.(4510-4512)ttC>ttT	p.F1504F	SLIT2_ENST00000503837.1_Silent_p.F1500F|SLIT2_ENST00000273739.5_Silent_p.F1517F|SLIT2_ENST00000503823.1_Silent_p.F1496F	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1504	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039, ECO:0000305}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.F1504F(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AATACTCTTTCGAATGCACTG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	4						C		1,4405	2.1+/-5.4	0,1,2202	121	103	109		4512	-0.6	0.7	4		109	0,8600		0,0,4300	no	coding-synonymous	SLIT2	NM_004787.1		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1504/1530	20620554	1,13005	2203	4300	6503	20229652	SO:0001819	synonymous_variant	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.4512C>T	4.37:g.20620554C>T			20229652	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																				0.567	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20620554	C	T	20620554	2	4	47	1	0	0	0	0	0	0	0	1	14777	883	31	1		1	SLIT2	4	20620554	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	77360	20620554	170533722	527	4924										
PI4K2B	55300	broad.mit.edu	37	chr4	25253965	25253965	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actattggtacttcagagatGaatgcattcttggatgaccc	9	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:25253965G>T	ENST00000264864.6	+	2	480	c.291G>T	c.(289-291)atG>atT	p.M97I	PI4K2B_ENST00000512921.1_Start_Codon_SNP_p.M1I	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	97					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.M97I(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				CTTCAGAGATGAATGCATTCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	115	116					4																	25253965		2203	4300	6503	24863063	SO:0001583	missense	55300			AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.291G>T	4.37:g.25253965G>T	ENSP00000264864:p.Met97Ile		24863063	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	37	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496240	0.26861	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	T	0.40756	1.02	5.09	4.24	0.50183	.	0.509214	0.24328	N	0.039487	T	0.30262	0.0759	L	0.41236	1.265	0.25215	N	0.989948	B	0.02656	0.0	B	0.06405	0.002	T	0.16630	-1.0396	10	0.22109	T	0.4	-0.0066	7.8425	0.29406	0.0833:0.0:0.7565:0.1603	.	97	Q8TCG2	P4K2B_HUMAN	I	1;97;66	ENSP00000264864:M97I	ENSP00000264864:M97I	M	+	3	0	PI4K2B	24863063	1.000000	0.71417	0.293000	0.24932	0.660000	0.38997	3.602000	0.54066	1.112000	0.41740	0.467000	0.42956	ATG		0.393	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		T	25253965	G	T	25253965	3	4	47	1	0	0	0	0	1	0	0	0	11903	1290	45	2	297	2	PI4K2B	4	25253965	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4633411	25253965	165900311	528	4925										
RBPJ	3516	broad.mit.edu	37	chr4	26407808	26407808	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttttagggaagctatgcGaaattatttaaaagagcgag	11	3	0	1	rs141690523		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:26407808G>A	ENST00000361572.6	+	3	304	c.110G>A	c.(109-111)cGa>cAa	p.R37Q	RBPJ_ENST00000355476.3_Missense_Mutation_p.R23Q|RBPJ_ENST00000504907.1_Missense_Mutation_p.R23Q|RBPJ_ENST00000342295.1_Missense_Mutation_p.R37Q|RBPJ_ENST00000348160.4_Missense_Mutation_p.R24Q|RBPJ_ENST00000345843.3_Missense_Mutation_p.R22Q|RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000342320.4_Missense_Mutation_p.R23Q|RBPJ_ENST00000507561.1_Missense_Mutation_p.R2Q			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	37					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R23Q(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				GAAGCTATGCGAAATTATTTA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	89	98	95		110,71,65,68	5.4	1	4	dbSNP_134	95	2,8592	2.2+/-6.3	0,2,4295	no	missense,missense,missense,missense	RBPJ	NM_005349.2,NM_015874.3,NM_203283.1,NM_203284.1	43,43,43,43	0,3,6497	AA,AG,GG		0.0233,0.0227,0.0231	benign,benign,benign,benign	37/501,24/488,22/486,23/487	26407808	3,12997	2203	4297	6500	26016906	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.110G>A	4.37:g.26407808G>A	ENSP00000354528:p.Arg37Gln		26016906	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.983686	0.74474	2.27E-4	2.33E-4	ENSG00000168214	ENST00000512351;ENST00000510778;ENST00000506956;ENST00000512671;ENST00000345843;ENST00000342295;ENST00000361572;ENST00000514807;ENST00000348160;ENST00000509158;ENST00000355476;ENST00000505958;ENST00000507561;ENST00000514730;ENST00000507574;ENST00000514675;ENST00000515573;ENST00000511546;ENST00000504907;ENST00000342320;ENST00000504938	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.4	5.4	0.78164	LAG1, DNA binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.74749	0.3757	L	0.52573	1.65	0.80722	D	1	P;P;B;P;B;B	0.48089	0.905;0.905;0.349;0.48;0.332;0.349	B;B;B;B;B;B	0.21708	0.036;0.036;0.005;0.012;0.012;0.008	T	0.79550	-0.1757	10	0.48119	T	0.1	-8.6297	18.7556	0.91832	0.0:0.0:1.0:0.0	.	37;23;24;23;22;37	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	Q	23;60;23;37;22;37;37;23;24;23;23;23;2;23;2;23;2;23;23;23;2	ENSP00000424789:R23Q;ENSP00000427170:R60Q;ENSP00000425750:R23Q;ENSP00000423644:R37Q;ENSP00000305815:R22Q;ENSP00000345206:R37Q;ENSP00000354528:R37Q;ENSP00000424989:R23Q;ENSP00000339699:R24Q;ENSP00000424804:R23Q;ENSP00000347659:R23Q;ENSP00000423907:R2Q;ENSP00000425061:R23Q;ENSP00000422617:R2Q;ENSP00000423575:R23Q;ENSP00000423406:R2Q;ENSP00000422838:R23Q;ENSP00000423703:R23Q;ENSP00000340124:R23Q;ENSP00000424459:R2Q	ENSP00000345206:R37Q	R	+	2	0	RBPJ	26016906	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.858000	0.92256	2.517000	0.84864	0.591000	0.81541	CGA		0.323	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		A	26407808	G	A	26407808	3	1	47	1	0	0	0	0	1	0	0	0	13198	1058	37	1	183	1	RBPJ	4	26407808	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1153843	26407808	164746468	529	4926										
RBPJ	3516	broad.mit.edu	37	chr4	26431557	26431557	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaccaaataaagagatgaTaaatgatggcgcttcctgga	10	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:26431557T>C	ENST00000361572.6	+	9	1159	c.965T>C	c.(964-966)aTa>aCa	p.I322T	RBPJ_ENST00000355476.3_Missense_Mutation_p.I308T|RBPJ_ENST00000504907.1_Missense_Mutation_p.I308T|RBPJ_ENST00000342295.1_Missense_Mutation_p.I322T|RBPJ_ENST00000348160.4_Missense_Mutation_p.I309T|RBPJ_ENST00000345843.3_Missense_Mutation_p.I307T|RBPJ_ENST00000342320.4_Missense_Mutation_p.I308T|RBPJ_ENST00000507561.1_Missense_Mutation_p.I287T			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	322					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I308T(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				AAAGAGATGATAAATGATGGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											61	58	59					4																	26431557		2203	4300	6503	26040655	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.965T>C	4.37:g.26431557T>C	ENSP00000354528:p.Ile322Thr		26040655	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.172625	0.78452	.	.	ENSG00000168214	ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000504907;ENST00000342320	T;T;T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32	5.61	5.61	0.85477	Beta-trefoil (2);	0.046487	0.85682	D	0.000000	T	0.57548	0.2061	M	0.70595	2.14	0.80722	D	1	P;D;D;D;D;D	0.63046	0.647;0.992;0.975;0.968;0.968;0.986	P;P;P;P;P;P	0.62089	0.605;0.898;0.856;0.775;0.775;0.856	T	0.61787	-0.6991	10	0.72032	D	0.01	-18.9194	15.8004	0.78450	0.0:0.0:0.0:1.0	.	322;308;309;308;307;322	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	T	307;322;322;309;308;287;308;308	ENSP00000305815:I307T;ENSP00000345206:I322T;ENSP00000354528:I322T;ENSP00000339699:I309T;ENSP00000347659:I308T;ENSP00000423907:I287T;ENSP00000423703:I308T;ENSP00000340124:I308T	ENSP00000345206:I322T	I	+	2	0	RBPJ	26040655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.597000	0.82733	2.143000	0.66587	0.528000	0.53228	ATA		0.383	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		C	26431557	T	C	26431557	3	2	47	1	0	0	0	0	1	0	0	0	13198	1406	49	4	1062	4	RBPJ	4	26431557	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	23749	26431557	164722719	530	4927										
ARAP2	116984	broad.mit.edu	37	chr4	36126551	36126551	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaagagaacgtataaatgCtccatattttttaattcttt	6	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:36126551C>A	ENST00000303965.4	-	22	4168	c.3679G>T	c.(3679-3681)Gca>Tca	p.A1227S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1227	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.A1227S(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						CGTATAAATGCTCCATATTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											167	168	168					4																	36126551		2203	4300	6503	35802946	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.3679G>T	4.37:g.36126551C>A	ENSP00000302895:p.Ala1227Ser		35802946	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	C	9.486	1.099510	0.20552	.	.	ENSG00000047365	ENST00000303965	T	0.18174	2.23	5.24	3.08	0.35506	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.260577	0.38381	N	0.001707	T	0.09598	0.0236	N	0.19112	0.55	0.28791	N	0.89929	B	0.20459	0.045	B	0.18871	0.023	T	0.24083	-1.0170	10	0.18276	T	0.48	.	8.9932	0.36037	0.0:0.6707:0.0:0.3293	.	1227	Q8WZ64	ARAP2_HUMAN	S	1227	ENSP00000302895:A1227S	ENSP00000302895:A1227S	A	-	1	0	ARAP2	35802946	0.072000	0.21174	0.942000	0.38095	0.986000	0.74619	0.324000	0.19610	1.149000	0.42402	0.585000	0.79938	GCA		0.363	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36126551	C	A	36126551	3	1	47	1	0	0	0	0	1	0	0	0	839	797	28	2	1483	2	ARAP2	4	36126551	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9694994	36126551	155027725	531	4928										
ARAP2	116984	broad.mit.edu	37	chr4	36179496	36179496	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttccacttaacacagtaaAaatttttgccttatagcctc	4	10	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:36179496A>C	ENST00000303965.4	-	9	2299	c.1810T>G	c.(1810-1812)Ttt>Gtt	p.F604V		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	604	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.F604V(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AACACAGTAAAAATTTTTGCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											146	144	145					4																	36179496		2203	4300	6503	35855891	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.1810T>G	4.37:g.36179496A>C	ENSP00000302895:p.Phe604Val		35855891	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.617679	0.87359	.	.	ENSG00000047365	ENST00000303965	T	0.31769	1.48	5.33	5.33	0.75918	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.239442	0.35151	N	0.003419	T	0.48021	0.1477	L	0.46157	1.445	0.36170	D	0.848715	D;D	0.61697	0.988;0.99	D;P	0.67231	0.95;0.828	T	0.59354	-0.7470	10	0.87932	D	0	.	14.9671	0.71201	1.0:0.0:0.0:0.0	.	534;604	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	V	604	ENSP00000302895:F604V	ENSP00000302895:F604V	F	-	1	0	ARAP2	35855891	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.293000	0.72731	2.023000	0.59567	0.397000	0.26171	TTT		0.373	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		C	36179496	A	C	36179496	3	2	47	1	0	0	0	0	1	0	0	0	839	14	1	4	3404	4	ARAP2	4	36179496	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	52945	36179496	154974780	532	4929										
ARAP2	116984	broad.mit.edu	37	chr4	36189182	36189182	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaggggaattattcctttCgaatacatctcctgtattgg	9	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:36189182C>T	ENST00000303965.4	-	8	2058	c.1569G>A	c.(1567-1569)tcG>tcA	p.S523S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	523	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.S523S(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTATTCCTTTCGAATACATCT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											76	77	77					4																	36189182		2203	4293	6496	35865577	SO:0001819	synonymous_variant	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.1569G>A	4.37:g.36189182C>T			35865577	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																				0.318	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		T	36189182	C	T	36189182	2	4	47	1	0	0	0	0	0	0	0	1	839	871	31	1		1	ARAP2	4	36189182	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9686	36189182	154965094	533	4930										
ARAP2	116984	broad.mit.edu	37	chr4	36214095	36214095	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccctgggtcaaaaattcattCtttatagatcgcttctatta	5	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:36214095C>A	ENST00000303965.4	-	5	1545	c.1056G>T	c.(1054-1056)aaG>aaT	p.K352N		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	352					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.K352N(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAAATTCATTCTTTATAGATC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	101	102					4																	36214095		2203	4299	6502	35890490	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.1056G>T	4.37:g.36214095C>A	ENSP00000302895:p.Lys352Asn		35890490	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.069728	0.36470	.	.	ENSG00000047365	ENST00000303965	T	0.10005	2.92	5.64	3.0	0.34707	.	0.533626	0.19756	N	0.106764	T	0.12944	0.0314	L	0.56769	1.78	0.34321	D	0.686619	P;P	0.41313	0.745;0.664	B;B	0.41236	0.351;0.102	T	0.14531	-1.0469	10	0.72032	D	0.01	.	8.1359	0.31054	0.0:0.7469:0.0:0.2531	.	282;352	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	N	352	ENSP00000302895:K352N	ENSP00000302895:K352N	K	-	3	2	ARAP2	35890490	0.446000	0.25665	0.989000	0.46669	0.663000	0.39108	0.081000	0.14823	0.412000	0.25729	0.655000	0.94253	AAG		0.343	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36214095	C	A	36214095	3	1	47	1	0	0	0	0	1	0	0	0	839	912	32	2	4174	2	ARAP2	4	36214095	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	24913	36214095	154940181	534	4931										
TLR10	81793	broad.mit.edu	37	chr4	38775286	38775286	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcacccacagagaatcatgTtcactgtatgaaataaatgc	6	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:38775286T>C	ENST00000308973.4	-	4	2531	c.1926A>G	c.(1924-1926)gaA>gaG	p.E642E	TLR10_ENST00000506111.1_Silent_p.E642E|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Silent_p.E642E|TLR10_ENST00000508334.1_Silent_p.E642E	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	642	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.E642E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GAGAATCATGTTCACTGTATG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	4											117	112	113					4																	38775286		2203	4300	6503	38451681	SO:0001819	synonymous_variant	81793			AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.1926A>G	4.37:g.38775286T>C			38451681	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																				0.413	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			C	38775286	T	C	38775286	2	2	47	1	0	0	0	0	0	0	0	1	15989	1722	60	4		4	TLR10	4	38775286	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2561191	38775286	152378990	535	4932										
UGDH	7358	broad.mit.edu	37	chr4	39523018	39523018	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacgcattgattcttgattCattgacatcaacaaccgtta	5	11	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:39523018C>A	ENST00000316423.6	-	2	457	c.115G>T	c.(115-117)Gaa>Taa	p.E39*	UGDH_ENST00000506179.1_Nonsense_Mutation_p.E39*|UGDH_ENST00000507089.1_Intron|UGDH_ENST00000501493.2_Nonsense_Mutation_p.E39*|UGDH_ENST00000515398.1_Intron	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	39					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)	p.E39*(1)		breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						ATTCTTGATTCATTGACATCA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											159	141	147					4																	39523018		2203	4300	6503	39199413	SO:0001587	stop_gained	7358			AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.115G>T	4.37:g.39523018C>A	ENSP00000319501:p.Glu39*		39199413	B3KUU2|B4DN25|O60589	Nonsense_Mutation	SNP	ENST00000316423.6	37	CCDS3455.1	.	.	.	.	.	.	.	.	.	.	C	35	5.583511	0.96578	.	.	ENSG00000109814	ENST00000316423;ENST00000501493;ENST00000506179;ENST00000515021;ENST00000514106;ENST00000509391;ENST00000505698;ENST00000510490	.	.	.	6.07	6.07	0.98685	.	0.044677	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-6.7851	19.6475	0.95784	0.0:1.0:0.0:0.0	.	.	.	.	X	39;39;39;52;39;39;39;39	.	ENSP00000319501:E39X	E	-	1	0	UGDH	39199413	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.704000	0.68347	2.885000	0.99019	0.655000	0.94253	GAA		0.378	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		A	39523018	C	A	39523018	4	1	47	1	0	0	0	0	0	1	0	0	16980	835	29	2	1413	2	UGDH	4	39523018	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	747732	39523018	151631258	536	4933										
SHISA3	152573	broad.mit.edu	37	chr4	42403167	42403167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccaatccgcttctcactccGcagctatcagacagagaccc	7	17	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:42403167G>A	ENST00000319234.4	+	2	634	c.416G>A	c.(415-417)cGc>cAc	p.R139H		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	139					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.R139H(1)		endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						TTCTCACTCCGCAGCTATCAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	4											178	191	186					4																	42403167		2203	4300	6503	42097924	SO:0001583	missense	152573			BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"Shisa homologs"	25159	protein-coding gene	gene with protein product			"shisa homolog 3 (Xenopus laevis)"				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.416G>A	4.37:g.42403167G>A	ENSP00000326445:p.Arg139His		42097924	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	37	CCDS33979.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679757	0.88542	.	.	ENSG00000178343	ENST00000319234	T	0.43688	0.94	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.60157	0.2247	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.56438	-0.7979	10	0.41790	T	0.15	-27.3746	18.4196	0.90586	0.0:0.0:1.0:0.0	.	139	A0PJX4	SHSA3_HUMAN	H	139	ENSP00000326445:R139H	ENSP00000326445:R139H	R	+	2	0	SHISA3	42097924	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	6.984000	0.76186	2.692000	0.91855	0.655000	0.94253	CGC		0.592	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		A	42403167	G	A	42403167	3	1	47	1	0	0	0	0	1	0	0	0	14318	1087	38	1	422	1	SHISA3	4	42403167	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2880149	42403167	148751109	537	4934										
ATP10D	57205	broad.mit.edu	37	chr4	47514781	47514781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggagcctatgtgaacaatcGaatacgaacaacaaagtaca	8	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:47514781G>A	ENST00000273859.3	+	2	493	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	ATP10D_ENST00000504445.1_Missense_Mutation_p.R75Q	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	75					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R75Q(1)		NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						GTGAACAATCGAATACGAACA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	86	85					4																	47514781		2203	4300	6503	47209538	SO:0001583	missense	57205			AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.224G>A	4.37:g.47514781G>A	ENSP00000273859:p.Arg75Gln		47209538	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.133702	0.37630	.	.	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.78816	-1.21;-1.21	5.31	4.47	0.54385	.	0.440980	0.21433	N	0.074608	T	0.71195	0.3311	L	0.53617	1.68	0.26358	N	0.977091	B;B	0.25850	0.136;0.07	B;B	0.22152	0.038;0.014	T	0.64542	-0.6383	10	0.51188	T	0.08	-6.5077	9.6885	0.40114	0.177:0.0:0.823:0.0	.	75;75	Q9P241;Q6PEW3	AT10D_HUMAN;.	Q	75	ENSP00000273859:R75Q;ENSP00000420909:R75Q	ENSP00000273859:R75Q	R	+	2	0	ATP10D	47209538	0.665000	0.27466	1.000000	0.80357	0.333000	0.28666	1.727000	0.38095	1.364000	0.46038	0.557000	0.71058	CGA		0.398	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		A	47514781	G	A	47514781	3	1	47	1	0	0	0	0	1	0	0	0	1119	1058	37	1	226	1	ATP10D	4	47514781	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5111614	47514781	143639495	538	4935										
CNGA1	1259	broad.mit.edu	37	chr4	47938520	47938520	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caataagcggtttcagaaatTtctcaaccttggttaatctt	6	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:47938520T>G	ENST00000514170.1	-	11	2310	c.1991A>C	c.(1990-1992)aAa>aCa	p.K664T	CNGA1_ENST00000358519.4_Missense_Mutation_p.K664T|CNGA1_ENST00000420489.2_Missense_Mutation_p.K664T|CNGA1_ENST00000402813.3_Missense_Mutation_p.K733T|CNGA1_ENST00000544810.1_Missense_Mutation_p.K664T			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	664					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.K664T(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TTTCAGAAATTTCTCAACCTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	89	90					4																	47938520		1847	4104	5951	47633277	SO:0001583	missense	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.1991A>C	4.37:g.47938520T>G	ENSP00000426862:p.Lys664Thr		47633277	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	T	3.916	-0.019092	0.07634	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	D;D;D;D;D	0.96940	-4.08;-4.18;-4.18;-4.18;-4.18	4.25	-2.99	0.05497	.	0.436518	0.27176	N	0.020574	D	0.88698	0.6507	L	0.31420	0.93	0.38282	D	0.942469	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.73786	-0.3873	10	0.11182	T	0.66	.	5.8046	0.18432	0.0:0.3116:0.132:0.5564	.	664;664	Q4W5E3;P29973	.;CNGA1_HUMAN	T	733;664;664;664;664	ENSP00000384264:K733T;ENSP00000426862:K664T;ENSP00000443401:K664T;ENSP00000351320:K664T;ENSP00000389881:K664T	ENSP00000351320:K664T	K	-	2	0	CNGA1	47633277	0.991000	0.36638	0.543000	0.28128	0.973000	0.67179	0.536000	0.23129	-0.621000	0.05633	-0.415000	0.06103	AAA		0.463	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		G	47938520	T	G	47938520	3	3	47	1	0	0	0	0	1	0	0	0	3602	1841	64	4	85	4	CNGA1	4	47938520	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	423739	47938520	143215756	539	4936										
CNGA1	1259	broad.mit.edu	37	chr4	47942804	47942804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgttcgtacaaacatatCgattaaatagactatgtctg	6	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:47942804C>T	ENST00000514170.1	-	10	959	c.640G>A	c.(640-642)Gat>Aat	p.D214N	CNGA1_ENST00000358519.4_Missense_Mutation_p.D214N|CNGA1_ENST00000420489.2_Missense_Mutation_p.D214N|CNGA1_ENST00000402813.3_Missense_Mutation_p.D283N|CNGA1_ENST00000544810.1_Missense_Mutation_p.D214N			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	214					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.D214N(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						ACAAACATATCGATTAAATAG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	4											75	71	72					4																	47942804		1824	4077	5901	47637561	SO:0001583	missense	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.640G>A	4.37:g.47942804C>T	ENSP00000426862:p.Asp214Asn		47637561	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.758377	0.69763	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	D;D;D;D;D	0.98120	-4.73;-4.73;-4.73;-4.73;-4.73	5.53	5.53	0.82687	Ion transport (1);	0.049448	0.85682	D	0.000000	D	0.99296	0.9754	H	0.97587	4.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98708	1.0703	10	0.87932	D	0	.	19.4468	0.94851	0.0:1.0:0.0:0.0	.	214;214	Q4W5E3;P29973	.;CNGA1_HUMAN	N	283;214;214;214;214	ENSP00000384264:D283N;ENSP00000426862:D214N;ENSP00000443401:D214N;ENSP00000351320:D214N;ENSP00000389881:D214N	ENSP00000351320:D214N	D	-	1	0	CNGA1	47637561	1.000000	0.71417	0.904000	0.35570	0.003000	0.03518	7.487000	0.81328	2.594000	0.87642	0.655000	0.94253	GAT		0.289	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		T	47942804	C	T	47942804	3	4	47	1	0	0	0	0	1	0	0	0	3602	884	31	1	1440	1	CNGA1	4	47942804	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4284	47942804	143211472	540	4937										
TEC	7006	broad.mit.edu	37	chr4	48147493	48147493	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcccgaatagctttgattgcGactttgtactgggctcgcca	10	11	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:48147493G>A	ENST00000381501.3	-	13	1342	c.1185C>T	c.(1183-1185)gtC>gtT	p.V395V	TEC_ENST00000511471.2_5'UTR	NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	395	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.V395V(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						CTTTGATTGCGACTTTGTACT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											165	141	149					4																	48147493		2203	4300	6503	47842250	SO:0001819	synonymous_variant	7006			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1185C>T	4.37:g.48147493G>A			47842250	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																				0.448	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			A	48147493	G	A	48147493	2	1	47	1	0	0	0	0	0	0	0	1	15781	1045	37	1		1	TEC	4	48147493	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	204689	48147493	143006783	541	4938										
TEC	7006	broad.mit.edu	37	chr4	48172308	48172308	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacatccgggtgctaatttTtcagtttgtctacaacactg	7	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:48172308T>G	ENST00000381501.3	-	5	568	c.411A>C	c.(409-411)gaA>gaC	p.E137D		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	137					B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.E137D(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						GTGCTAATTTTTCAGTTTGTC	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	4											63	68	66					4																	48172308		2200	4294	6494	47867065	SO:0001583	missense	7006			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.411A>C	4.37:g.48172308T>G	ENSP00000370912:p.Glu137Asp		47867065	B7ZKZ6|Q3MIS5	Missense_Mutation	SNP	ENST00000381501.3	37	CCDS3481.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.964859	0.34659	.	.	ENSG00000135605	ENST00000381501	D	0.93366	-3.21	5.5	5.5	0.81552	Pleckstrin homology-type (1);Zinc finger, Btk motif (4);	0.054446	0.64402	D	0.000001	D	0.87826	0.6275	N	0.26042	0.785	0.45046	D	0.99806	B	0.18166	0.026	B	0.16289	0.015	D	0.83733	0.0199	10	0.13853	T	0.58	.	15.6057	0.76668	0.0:0.0:0.0:1.0	.	137	P42680	TEC_HUMAN	D	137	ENSP00000370912:E137D	ENSP00000370912:E137D	E	-	3	2	TEC	47867065	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.700000	0.37815	2.082000	0.62665	0.477000	0.44152	GAA		0.284	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			G	48172308	T	G	48172308	3	3	47	1	0	0	0	0	1	0	0	0	15781	1838	64	4	1540	4	TEC	4	48172308	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	24815	48172308	142981968	542	4939										
USP46	64854	broad.mit.edu	37	chr4	53464862	53464862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatagtgatataatgcccacGattaggaccactggaaaaga	9	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:53464862G>A	ENST00000441222.3	-	8	1115	c.931C>T	c.(931-933)Cgt>Tgt	p.R311C	USP46_ENST00000451218.2_Missense_Mutation_p.R284C|USP46_ENST00000508499.1_Missense_Mutation_p.R304C	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	311	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R311C(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			TAATGCCCACGATTAGGACCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	64	67					4																	53464862		1834	4094	5928	53159619	SO:0001583	missense	64854			AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"Ubiquitin-specific peptidases"	20075	protein-coding gene	gene with protein product		612849	"ubiquitin specific protease 46"			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.931C>T	4.37:g.53464862G>A	ENSP00000407818:p.Arg311Cys		53159619	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Missense_Mutation	SNP	ENST00000441222.3	37	CCDS47053.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626413	0.46840	.	.	ENSG00000109189	ENST00000441222;ENST00000451218;ENST00000508499	T;T;T	0.31769	1.48;1.48;1.48	5.06	5.06	0.68205	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.56097	D	0.000022	T	0.28566	0.0707	L	0.37466	1.105	0.80722	D	1	P;B;P;P	0.44986	0.615;0.33;0.847;0.816	B;B;B;B	0.40940	0.17;0.139;0.344;0.233	T	0.03112	-1.1071	10	0.39692	T	0.17	-8.2084	17.7896	0.88548	0.0:0.0:1.0:0.0	.	195;299;311;304	P62068-2;P62068-4;P62068;P62068-3	.;.;UBP46_HUMAN;.	C	311;284;304	ENSP00000407818:R311C;ENSP00000390102:R284C;ENSP00000423244:R304C	ENSP00000407818:R311C	R	-	1	0	USP46	53159619	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	5.156000	0.64905	2.524000	0.85096	0.655000	0.94253	CGT		0.358	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832		A	53464862	G	A	53464862	3	1	47	1	0	0	0	0	1	0	0	0	17117	1058	37	1	177	1	USP46	4	53464862	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5292554	53464862	137689414	543	4940										
PDGFRA	5156	broad.mit.edu	37	chr4	55127320	55127320	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atccttccaaatgaaaatgaAaaggttgtgcagctgaattc	8	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:55127320A>G	ENST00000257290.5	+	3	439	c.108A>G	c.(106-108)gaA>gaG	p.E36E	PDGFRA_ENST00000508170.1_Silent_p.E36E|FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	36	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.E36E(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	ATGAAAATGAAAAGGTTGTGC	0.478			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - coding silent(1)	large_intestine(1)	4											111	114	113					4																	55127320		2203	4300	6503	54822077	SO:0001819	synonymous_variant	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.108A>G	4.37:g.55127320A>G			54822077	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																				0.478	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		G	55127320	A	G	55127320	2	3	47	1	0	0	0	0	0	0	0	1	11692	11	1	4		4	PDGFRA	4	55127320	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1662458	55127320	136026956	544	4941										
PDGFRA	5156	broad.mit.edu	37	chr4	55144560	55144560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcatcacagagtattgcttCtatggagatttggtcaacta	8	7	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:55144560C>A	ENST00000257290.5	+	15	2365	c.2034C>A	c.(2032-2034)ttC>ttA	p.F678L	FIP1L1_ENST00000507166.1_Missense_Mutation_p.F438L	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	678	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.F678L(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	AGTATTGCTTCTATGGAGATT	0.433			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - Missense(1)	large_intestine(1)	4											104	104	104					4																	55144560		2203	4300	6503	54839317	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2034C>A	4.37:g.55144560C>A	ENSP00000257290:p.Phe678Leu		54839317	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.239320	0.39598	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.88818	-2.43;-2.43	6.06	5.22	0.72569	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.33650	U	0.004696	D	0.83385	0.5243	N	0.04880	-0.145	0.80722	D	1	B;D	0.54397	0.285;0.966	B;P	0.55577	0.236;0.779	D	0.83734	0.0200	10	0.39692	T	0.17	.	9.7694	0.40580	0.0:0.8063:0.0:0.1937	.	678;678	P16234-3;P16234	.;PGFRA_HUMAN	L	438;678	ENSP00000423325:F438L;ENSP00000257290:F678L	ENSP00000423325:F438L	F	+	3	2	FIP1L1;PDGFRA	54839317	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.094000	0.50227	1.576000	0.49790	0.655000	0.94253	TTC		0.433	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55144560	C	A	55144560	3	1	47	1	0	0	0	0	1	0	0	0	11692	912	32	2	2088	2	PDGFRA	4	55144560	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	17240	55144560	136009716	545	4942										
REST	5978	broad.mit.edu	37	chr4	57777356	57777356	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcagagttcacagtgctaaGaaattttttgtggaagagag	11	4	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:57777356G>T	ENST00000309042.7	+	2	866	c.552G>T	c.(550-552)aaG>aaT	p.K184N		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	184					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K184N(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					ACAGTGCTAAGAAATTTTTTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											79	80	79					4																	57777356		2203	4300	6503	57472113	SO:0001583	missense	5978			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.552G>T	4.37:g.57777356G>T	ENSP00000311816:p.Lys184Asn		57472113	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.525118	0.44969	.	.	ENSG00000084093	ENST00000456010;ENST00000309042;ENST00000358605	T	0.09538	2.97	6.02	4.13	0.48395	Zinc finger, C2H2 (1);	0.079841	0.51477	D	0.000086	T	0.09730	0.0239	L	0.41824	1.3	0.53688	D	0.999979	B;P	0.51057	0.406;0.941	B;B	0.39027	0.081;0.288	T	0.08493	-1.0719	10	0.56958	D	0.05	-23.9963	12.396	0.55384	0.0684:0.0:0.8047:0.1269	.	184;184	Q13127-2;Q13127	.;REST_HUMAN	N	184	ENSP00000311816:K184N	ENSP00000311816:K184N	K	+	3	2	REST	57472113	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	2.375000	0.44283	1.562000	0.49601	0.655000	0.94253	AAG		0.478	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		T	57777356	G	T	57777356	3	4	47	1	0	0	0	0	1	0	0	0	13271	933	33	2	554	2	REST	4	57777356	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2632796	57777356	133376920	546	4943										
LPHN3	23284	broad.mit.edu	37	chr4	62679560	62679560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggacaagtttcatacatttCtccgccaattcaccttgact	5	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:62679560C>A	ENST00000514591.1	+	8	1558	c.1229C>A	c.(1228-1230)tCt>tAt	p.S410Y	LPHN3_ENST00000507625.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000509896.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000514996.1_Missense_Mutation_p.S410Y|LPHN3_ENST00000508946.1_Missense_Mutation_p.S410Y|LPHN3_ENST00000508693.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000512091.2_Missense_Mutation_p.S410Y|LPHN3_ENST00000511324.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000504896.1_Missense_Mutation_p.S410Y|LPHN3_ENST00000506700.1_Missense_Mutation_p.S410Y|LPHN3_ENST00000514157.1_Missense_Mutation_p.S410Y|LPHN3_ENST00000507164.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000506720.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000506746.1_Missense_Mutation_p.S478Y|LPHN3_ENST00000545650.1_Missense_Mutation_p.S410Y			Q9HAR2	LPHN3_HUMAN	latrophilin 3	410					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.S410Y(3)|p.S410F(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						tcatacatttctccgccaatt	0.363																																																6	Substitution - Missense(6)	large_intestine(3)|lung(3)	4											127	118	121					4																	62679560		1934	4142	6076	62362155	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1229C>A	4.37:g.62679560C>A	ENSP00000422533:p.Ser410Tyr		62362155	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.177586	0.38413	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.71341	-0.52;-0.53;-0.56;-0.56;-0.52;-0.53;-0.56;-0.55;-0.55;-0.53;-0.53;-0.53;-0.56;-0.56;-0.53	3.67	3.67	0.42095	.	0.651853	0.15757	N	0.246156	T	0.55609	0.1931	N	0.19112	0.55	0.25694	N	0.985659	B;B	0.13145	0.004;0.007	B;B	0.16722	0.004;0.016	T	0.52675	-0.8544	10	0.59425	D	0.04	.	11.1945	0.48704	0.0:1.0:0.0:0.0	.	410;410	E9PE04;Q9HAR2-2	.;.	Y	410;410;478;478;410;410;410;410;410;478;478;478;410;410;410;478;478;410	ENSP00000423388:S410Y;ENSP00000422533:S410Y;ENSP00000423787:S478Y;ENSP00000425033:S478Y;ENSP00000424120:S410Y;ENSP00000439831:S410Y;ENSP00000421476:S478Y;ENSP00000424030:S478Y;ENSP00000421372:S478Y;ENSP00000425201:S410Y;ENSP00000423434:S410Y;ENSP00000421627:S410Y;ENSP00000420931:S478Y;ENSP00000425884:S478Y;ENSP00000424258:S410Y	ENSP00000280009:S410Y	S	+	2	0	LPHN3	62362155	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.846000	0.48262	2.343000	0.79666	0.563000	0.77884	TCT		0.363	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62679560	C	A	62679560	3	1	47	1	0	0	0	0	1	0	0	0	8946	913	32	2	1251	2	LPHN3	4	62679560	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4902204	62679560	128474716	547	4944										
LPHN3	23284	broad.mit.edu	37	chr4	62903502	62903502	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattgctgtagtggcaaaagTacagagagttccattggttc	11	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:62903502T>C	ENST00000514591.1	+	23	3770	c.3441T>C	c.(3439-3441)agT>agC	p.S1147S	LPHN3_ENST00000507625.1_Silent_p.S1206S|LPHN3_ENST00000509896.1_Silent_p.S1215S|LPHN3_ENST00000514996.1_Silent_p.S1138S|LPHN3_ENST00000508946.1_Silent_p.S1147S|LPHN3_ENST00000508693.1_Silent_p.S1215S|LPHN3_ENST00000512091.2_Silent_p.S1147S|LPHN3_ENST00000511324.1_Silent_p.S1206S|LPHN3_ENST00000504896.1_Silent_p.S1147S|LPHN3_ENST00000506700.1_Silent_p.S1138S|LPHN3_ENST00000514157.1_Silent_p.S1138S|LPHN3_ENST00000507164.1_Silent_p.S1206S|LPHN3_ENST00000506720.1_Silent_p.S1215S|LPHN3_ENST00000506746.1_Silent_p.S1206S|LPHN3_ENST00000545650.1_Silent_p.S1147S			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1125					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.S1147S(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GTGGCAAAAGTACAGAGAGTT	0.413																																																3	Substitution - coding silent(3)	large_intestine(3)	4											144	146	145					4																	62903502		1964	4177	6141	62586097	SO:0001819	synonymous_variant	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3441T>C	4.37:g.62903502T>C			62586097	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251248	0.22880	.	.	ENSG00000150471	ENST00000502815	.	.	.	5.33	4.16	0.48862	.	.	.	.	.	T	0.55337	0.1914	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51553	-0.8691	4	.	.	.	.	5.9598	0.19293	0.1455:0.0785:0.0:0.776	.	.	.	.	H	596	.	.	Y	+	1	0	LPHN3	62586097	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.608000	0.36847	0.981000	0.38548	0.528000	0.53228	TAC		0.413	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			C	62903502	T	C	62903502	2	2	47	1	0	0	0	0	0	0	0	1	8946	1635	57	4		4	LPHN3	4	62903502	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	223942	62903502	128250774	548	4945										
EPHA5	2044	broad.mit.edu	37	chr4	66280129	66280129	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagtaatagttgtctctttAgatttgataatcgtgtagct	9	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:66280129A>C	ENST00000273854.3	-	7	2160	c.1560T>G	c.(1558-1560)tcT>tcG	p.S520S	EPHA5_ENST00000354839.4_Silent_p.S520S|EPHA5_ENST00000432638.2_Silent_p.S356S|EPHA5_ENST00000511294.1_Silent_p.S520S	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	520	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.S520S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						TTGTCTCTTTAGATTTGATAA	0.398										TSP Lung(17;0.13)																																						1	Substitution - coding silent(1)	large_intestine(1)	4											176	142	153					4																	66280129		2203	4300	6503	65962724	SO:0001819	synonymous_variant	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1560T>G	4.37:g.66280129A>C			65962724	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																				0.398	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		C	66280129	A	C	66280129	2	2	47	1	0	0	0	0	0	0	0	1	5183	407	15	4		4	EPHA5	4	66280129	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3376627	66280129	124874147	549	4946										
TMPRSS11F	389208	broad.mit.edu	37	chr4	68930434	68930434	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggatccaaatcctgtgacGaacacacttgttttaggtgg	10	8	0	1	rs144406616		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:68930434G>A	ENST00000356291.2	-	8	1043	c.984C>T	c.(982-984)ttC>ttT	p.F328F	UBA6-AS1_ENST00000499180.2_RNA|RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	328	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.F328F(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						ATCCTGTGACGAACACACTTG	0.393													G|||	1	0.000199681	0	0	5008	,	,		17449	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						G		1,4405	2.1+/-5.4	0,1,2202	72	72	72		984	0.6	1	4	dbSNP_134	72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TMPRSS11F	NM_207407.2		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		328/439	68930434	3,13003	2203	4300	6503	68613029	SO:0001819	synonymous_variant	389208			AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.984C>T	4.37:g.68930434G>A			68613029	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																				0.393	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68930434	G	A	68930434	2	1	47	1	0	0	0	0	0	0	0	1	16282	1049	37	1		1	TMPRSS11F	4	68930434	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2650305	68930434	122223842	550	4947										
TMPRSS11F	389208	broad.mit.edu	37	chr4	68930597	68930597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaataattttcctcacatttCgtttcactgcgggtggtgtt	9	8	2	0	rs377605520		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:68930597C>T	ENST00000356291.2	-	8	880	c.821G>A	c.(820-822)cGa>cAa	p.R274Q	UBA6-AS1_ENST00000499180.2_RNA|RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	274	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.R274Q(3)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						CCTCACATTTCGTTTCACTGC	0.343																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	4						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	77	71	73		821	4.9	0.9	4		73	0,8600		0,0,4300	no	missense	TMPRSS11F	NM_207407.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	274/439	68930597	1,13005	2203	4300	6503	68613192	SO:0001583	missense	389208			AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.821G>A	4.37:g.68930597C>T	ENSP00000348639:p.Arg274Gln		68613192	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082564	0.36758	2.27E-4	0.0	ENSG00000198092	ENST00000356291	D	0.93547	-3.24	5.71	4.86	0.63082	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.48286	D	0.000187	D	0.89114	0.6623	M	0.68728	2.09	0.32928	D	0.516753	D	0.55385	0.971	B	0.32211	0.142	D	0.92248	0.5806	10	0.52906	T	0.07	.	11.1263	0.48320	0.0:0.9129:0.0:0.0871	.	274	Q6ZWK6	TM11F_HUMAN	Q	274	ENSP00000348639:R274Q	ENSP00000348639:R274Q	R	-	2	0	TMPRSS11F	68613192	0.001000	0.12720	0.940000	0.37924	0.227000	0.25037	1.314000	0.33597	2.709000	0.92574	0.655000	0.94253	CGA		0.343	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		T	68930597	C	T	68930597	3	4	47	1	0	0	0	0	1	0	0	0	16282	884	31	1	507	1	TMPRSS11F	4	68930597	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	163	68930597	122223679	551	4948										
TMPRSS11B	132724	broad.mit.edu	37	chr4	69094579	69094579	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataatcttcaaaaagtcttCttgaagtatcactggaaatg	6	6	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:69094579C>A	ENST00000332644.5	-	9	1131	c.970G>T	c.(970-972)Gaa>Taa	p.E324*		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	324	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.E324*(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						AAAAAGTCTTCTTGAAGTATC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											102	93	96					4																	69094579		2203	4300	6503	68777174	SO:0001587	stop_gained	132724			BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"Serine peptidases / Transmembrane"	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.970G>T	4.37:g.69094579C>A	ENSP00000330475:p.Glu324*		68777174	A8K4D9	Nonsense_Mutation	SNP	ENST00000332644.5	37	CCDS3521.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.154379	0.57259	.	.	ENSG00000185873	ENST00000332644	.	.	.	4.47	-4.0	0.04057	.	1.012140	0.07945	N	0.979984	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.1461	0.86767	0.0:0.7337:0.1607:0.1056	.	.	.	.	X	324	.	ENSP00000330475:E324X	E	-	1	0	TMPRSS11B	68777174	0.060000	0.20803	0.331000	0.25455	0.402000	0.30811	-0.276000	0.08514	-1.095000	0.03050	-0.955000	0.02649	GAA		0.353	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		A	69094579	C	A	69094579	4	1	47	1	0	0	0	0	0	1	0	0	16279	922	32	2	288	2	TMPRSS11B	4	69094579	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	163982	69094579	122059697	552	4949										
UGT2B15	7367	broad.mit.edu	37	chr4	69431384	69431384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attcaaaatcccaataggttCgaatgagccacatttcagct	6	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:69431384C>T	ENST00000317746.2	-	2	821	c.779G>A	c.(778-780)cGa>cAa	p.R260Q		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	260					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.R260Q(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	CCAATAGGTTCGAATGAGCCA	0.403																																					Melanoma(18;649 833 28984 37818 38500)											1	Substitution - Missense(1)	large_intestine(1)	4											69	70	69					4																	69431384		2084	3885	5969	69113979	SO:0001583	missense	7367			U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"UDP glucuronosyltransferases"	12547	protein-coding gene	gene with protein product		601903	"UDP glycosyltransferase 2 family, polypeptide B17"			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.779G>A	4.37:g.69431384C>T	ENSP00000320401:p.Arg260Gln		69113979		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	18.56	3.649698	0.67358	.	.	ENSG00000197888	ENST00000317746	T	0.62105	0.05	2.49	2.49	0.30216	.	0.000000	0.64402	U	0.000004	T	0.68732	0.3033	M	0.73753	2.245	0.26977	N	0.965445	.	.	.	.	.	.	T	0.63475	-0.6629	8	0.59425	D	0.04	.	10.7333	0.46109	0.0:1.0:0.0:0.0	.	.	.	.	Q	260	ENSP00000320401:R260Q	ENSP00000320401:R260Q	R	-	2	0	UGT2B17	69113979	1.000000	0.71417	0.552000	0.28243	0.908000	0.53690	5.137000	0.64789	1.424000	0.47217	0.400000	0.26472	CGA		0.403	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		T	69431384	C	T	69431384	3	4	47	1	0	0	0	0	1	0	0	0	16998	884	31	1	833	1	UGT2B15	4	69431384	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	336805	69431384	121722892	553	4950										
UGT2B7	7364	broad.mit.edu	37	chr4	69962614	69962614	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggtgacataactagaaagTtctgtaaagatgtagtttca	9	4	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:69962614T>C	ENST00000508661.1	+	1	403	c.376T>C	c.(376-378)Ttc>Ctc	p.F126L	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.F126L			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	126					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.F126L(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AACTAGAAAGTTCTGTAAAGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	4											53	54	53					4																	69962614		2188	4297	6485	69997203	SO:0001583	missense	7364			BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.376T>C	4.37:g.69962614T>C	ENSP00000427659:p.Phe126Leu		69997203	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	T	0.007	-1.987645	0.00443	.	.	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.60299	0.2;0.2	2.2	-4.4	0.03600	.	1.178490	0.06381	N	0.715244	T	0.21718	0.0523	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.10965	-1.0607	9	.	.	.	.	4.4424	0.11580	0.1605:0.5068:0.0:0.3327	.	126;126	E9PBP8;P16662	.;UD2B7_HUMAN	L	126	ENSP00000304811:F126L;ENSP00000427659:F126L	.	F	+	1	0	UGT2B7	69997203	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.312000	0.08113	-1.663000	0.01481	-0.991000	0.02546	TTC		0.313	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		C	69962614	T	C	69962614	3	2	47	1	0	0	0	0	1	0	0	0	17002	1725	60	4	378	4	UGT2B7	4	69962614	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	531230	69962614	121191662	554	4951										
UGT2A1	10941	broad.mit.edu	37	chr4	70512732	70512732	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggtaggagatgaaatttcTtattctgtcagtgaaagaca	11	4	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:70512732T>G	ENST00000503640.1	-	1	686	c.631A>C	c.(631-633)Aga>Cga	p.R211R	UGT2A1_ENST00000286604.4_Silent_p.R211R|UGT2A1_ENST00000514019.1_Silent_p.R211R|UGT2A1_ENST00000512704.1_Silent_p.R211R	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	211					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.R211R(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						ATGAAATTTCTTATTCTGTCA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	4											83	76	78					4																	70512732		2203	4299	6502	70547321	SO:0001819	synonymous_variant	10941			AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.631A>C	4.37:g.70512732T>G			70547321	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Silent	SNP	ENST00000503640.1	37	CCDS3529.1																																																																																				0.383	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		G	70512732	T	G	70512732	2	3	47	1	0	0	0	0	0	0	0	1	16993	1617	56	4		4	UGT2A1	4	70512732	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	550118	70512732	120641544	555	4952										
ENAM	10117	broad.mit.edu	37	chr4	71508597	71508597	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatatgccagtcccaaattTtaattctgttgatcaacatg	5	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:71508597T>G	ENST00000396073.3	+	9	1735	c.1454T>G	c.(1453-1455)tTt>tGt	p.F485C	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	485					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.F485C(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			GTCCCAAATTTTAATTCTGTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											38	39	39					4																	71508597		2200	4299	6499	71727461	SO:0001583	missense	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1454T>G	4.37:g.71508597T>G	ENSP00000379383:p.Phe485Cys		71727461	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	T	14.84	2.656981	0.47467	.	.	ENSG00000132464	ENST00000396073	T	0.37584	1.19	5.93	4.77	0.60923	.	0.105878	0.43260	D	0.000590	T	0.57888	0.2084	M	0.83953	2.67	0.33429	D	0.580905	D	0.89917	1.0	D	0.73708	0.981	T	0.70483	-0.4859	10	0.52906	T	0.07	-8.2758	7.9595	0.30062	0.0:0.0884:0.0:0.9116	.	485	Q9NRM1	ENAM_HUMAN	C	485	ENSP00000379383:F485C	ENSP00000379383:F485C	F	+	2	0	ENAM	71727461	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	2.750000	0.47500	2.281000	0.76405	0.533000	0.62120	TTT		0.388	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		G	71508597	T	G	71508597	3	3	47	1	0	0	0	0	1	0	0	0	5125	1841	64	4	1484	4	ENAM	4	71508597	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	995865	71508597	119645679	556	4953										
ADAMTS3	9508	broad.mit.edu	37	chr4	73414530	73414530	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgcagaaagagtatgggagaGatagcgtccttctagatttg	13	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:73414530G>T	ENST00000286657.4	-	3	205	c.169C>A	c.(169-171)Ctc>Atc	p.L57I	ADAMTS3_ENST00000505193.1_5'UTR	NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	57					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L57I(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTATGGGAGAGATAGCGTCCT	0.443																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Missense(1)	large_intestine(1)	4											86	81	82					4																	73414530		2203	4300	6503	73633394	SO:0001583	missense	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.169C>A	4.37:g.73414530G>T	ENSP00000286657:p.Leu57Ile		73633394	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.546409	0.45383	.	.	ENSG00000156140	ENST00000286657	T	0.06933	3.24	5.74	4.88	0.63580	Peptidase M12B, propeptide (1);	0.100936	0.40064	N	0.001182	T	0.07548	0.0190	L	0.31804	0.96	0.35372	D	0.789101	B	0.24368	0.102	B	0.32289	0.143	T	0.31530	-0.9940	10	0.23302	T	0.38	.	9.3379	0.38062	0.0:0.2527:0.4998:0.2475	.	57	O15072	ATS3_HUMAN	I	57	ENSP00000286657:L57I	ENSP00000286657:L57I	L	-	1	0	ADAMTS3	73633394	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.548000	0.45794	1.518000	0.48934	0.643000	0.83706	CTC		0.443	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73414530	G	T	73414530	3	4	47	1	0	0	0	0	1	0	0	0	267	942	33	2	3528	2	ADAMTS3	4	73414530	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1905933	73414530	117739746	557	4954										
ALB	213	broad.mit.edu	37	chr4	74279174	74279174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatctgtgaaaatcaagattCgatctccagtaaactgaagg	8	7	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:74279174C>T	ENST00000503124.1	+	6	638	c.431C>T	c.(430-432)tCg>tTg	p.S144L	ALB_ENST00000295897.4_Missense_Mutation_p.S294L|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Missense_Mutation_p.S179L|ALB_ENST00000415165.2_Missense_Mutation_p.S102L|ALB_ENST00000509063.1_Missense_Mutation_p.S294L			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.S294L(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AATCAAGATTCGATCTCCAGT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	4											97	94	95					4																	74279174		2203	4300	6503	74498038	SO:0001583	missense	213			V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.431C>T	4.37:g.74279174C>T	ENSP00000421027:p.Ser144Leu		74498038	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	C	10.05	1.244651	0.22796	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51	6.02	3.25	0.37280	Serum albumin-like (1);Serum albumin, N-terminal (3);	1.305960	0.05191	N	0.503146	T	0.65698	0.2716	L	0.60455	1.87	0.09310	N	1	P;B;B;B;B	0.52842	0.956;0.324;0.324;0.449;0.449	B;B;B;B;B	0.40009	0.316;0.027;0.042;0.053;0.027	T	0.54549	-0.8277	10	0.72032	D	0.01	-0.6139	4.5748	0.12228	0.3999:0.3998:0.1293:0.071	.	179;102;144;294;294	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768	.;.;.;.;ALBU_HUMAN	L	294;102;144;294;179;303	ENSP00000295897:S294L;ENSP00000401820:S102L;ENSP00000421027:S144L;ENSP00000422784:S294L;ENSP00000384695:S179L	ENSP00000295897:S294L	S	+	2	0	ALB	74498038	0.000000	0.05858	0.000000	0.03702	0.474000	0.32979	-0.062000	0.11674	0.370000	0.24538	0.650000	0.86243	TCG		0.423	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74279174	C	T	74279174	3	4	47	1	0	0	0	0	1	0	0	0	486	893	31	1	911	1	ALB	4	74279174	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	864644	74279174	116875102	558	4955										
ALB	213	broad.mit.edu	37	chr4	74285353	74285353	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggagacctgctttgccgaGgaggtactacagttctcttc	11	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:74285353G>T	ENST00000503124.1	+	11	1539	c.1332G>T	c.(1330-1332)gaG>gaT	p.E444D	ALB_ENST00000295897.4_Missense_Mutation_p.E594D|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Missense_Mutation_p.E479D|ALB_ENST00000415165.2_Missense_Mutation_p.E402D|ALB_ENST00000509063.1_Missense_Mutation_p.E594D			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.E594D(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTTTGCCGAGGAGGTACTAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											143	142	142					4																	74285353		2203	4300	6503	74504217	SO:0001583	missense	213			V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1332G>T	4.37:g.74285353G>T	ENSP00000421027:p.Glu444Asp		74504217	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.81|13.81	2.347435|2.347435	0.41599|0.41599	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T;T|.	0.59224|.	0.28;0.28;0.28;0.28;0.28|.	6.06|6.06	-1.2|-1.2	0.09554|0.09554	Serum albumin, conserved site (1);Serum albumin-like (1);Serum albumin, N-terminal (2);|.	0.983616|.	0.08341|.	N|.	0.960885|.	T|.	0.45836|.	0.1362|.	M|M	0.73598|0.73598	2.24|2.24	0.22446|0.22446	N|N	0.999093|0.999093	B;B;B;B;B|.	0.21381|.	0.055;0.005;0.052;0.003;0.011|.	B;B;B;B;B|.	0.22152|.	0.006;0.002;0.038;0.01;0.013|.	T|.	0.44922|.	-0.9296|.	10|.	0.51188|.	T|.	0.08|.	-0.1134|-0.1134	5.9234|5.9234	0.19094|0.19094	0.6413:0.0:0.2009:0.1578|0.6413:0.0:0.2009:0.1578	.|.	479;402;444;594;594|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	D|X	594;402;381;444;594;479;603|439	ENSP00000295897:E594D;ENSP00000401820:E402D;ENSP00000421027:E444D;ENSP00000422784:E594D;ENSP00000384695:E479D|.	ENSP00000295897:E594D|.	E|G	+|+	3|1	2|0	ALB|ALB	74504217|74504217	0.084000|0.084000	0.21492|0.21492	0.057000|0.057000	0.19452|0.19452	0.243000|0.243000	0.25628|0.25628	0.253000|0.253000	0.18296|0.18296	-0.130000|-0.130000	0.11599|0.11599	0.655000|0.655000	0.94253|0.94253	GAG|GGA		0.418	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74285353	G	T	74285353	3	4	47	1	0	0	0	0	1	0	0	0	486	991	35	2	1832	2	ALB	4	74285353	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6179	74285353	116868923	559	4956										
ART3	419	broad.mit.edu	37	chr4	77003569	77003569	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttgataaagaaagtgaaaGaattactttaatacctctga	6	5	2	5	rs550091630		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:77003569G>T	ENST00000355810.4	+	3	781	c.662G>T	c.(661-663)aGa>aTa	p.R221I	ART3_ENST00000341029.5_Missense_Mutation_p.R221I|ART3_ENST00000513494.1_3'UTR|ART3_ENST00000349321.3_Missense_Mutation_p.R221I	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	221					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R221I(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAAAGTGAAAGAATTACTTTA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	62	62					4																	77003569		2203	4300	6503	77222593	SO:0001583	missense	419			X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.662G>T	4.37:g.77003569G>T	ENSP00000348064:p.Arg221Ile		77222593	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.136190	0.37728	.	.	ENSG00000156219	ENST00000341029;ENST00000355810;ENST00000349321	T;T;T	0.09073	3.02;3.02;3.02	6.04	1.91	0.25777	.	0.796466	0.12165	N	0.493615	T	0.17662	0.0424	M	0.76170	2.325	0.09310	N	1	P;D;P;P;P	0.53151	0.863;0.958;0.889;0.865;0.889	B;P;P;B;B	0.51657	0.355;0.676;0.457;0.307;0.359	T	0.09207	-1.0685	9	.	.	.	-11.3866	8.0494	0.30568	0.4892:0.0:0.5108:0.0	.	191;221;221;221;221	D6RBN3;B4DHX3;Q13508;Q13508-3;Q13508-2	.;.;NAR3_HUMAN;.;.	I	221	ENSP00000343843:R221I;ENSP00000348064:R221I;ENSP00000304313:R221I	.	R	+	2	0	ART3	77222593	0.000000	0.05858	0.045000	0.18777	0.905000	0.53344	0.090000	0.15025	0.021000	0.15133	0.563000	0.77884	AGA		0.403	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179		T	77003569	G	T	77003569	3	4	47	1	0	0	0	0	1	0	0	0	999	942	33	2	668	2	ART3	4	77003569	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2718216	77003569	114150707	560	4957										
CCDC158	339965	broad.mit.edu	37	chr4	77247111	77247111	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaggagtgagtgcactggaGacttcttaggagaagaattg	14	4	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:77247111G>A	ENST00000388914.3	-	22	3208	c.3056C>T	c.(3055-3057)tCt>tTt	p.S1019F		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1019	Ser-rich.							p.S1019F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						GTGCACTGGAGACTTCTTAGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											162	158	159					4																	77247111		1857	4099	5956	77466135	SO:0001583	missense	339965			BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.3056C>T	4.37:g.77247111G>A	ENSP00000373566:p.Ser1019Phe		77466135	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.653663	0.67472	.	.	ENSG00000163749	ENST00000388914;ENST00000318586	T	0.47177	0.85	4.96	4.96	0.65561	.	0.468805	0.18561	N	0.137628	T	0.47544	0.1451	N	0.24115	0.695	0.80722	D	1	P	0.49559	0.925	P	0.53809	0.735	T	0.45963	-0.9225	10	0.59425	D	0.04	.	13.9054	0.63831	0.0:0.0:1.0:0.0	.	1019	Q5M9N0	CD158_HUMAN	F	1019;439	ENSP00000373566:S1019F	ENSP00000316815:S439F	S	-	2	0	CCDC158	77466135	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	4.235000	0.58666	2.753000	0.94483	0.555000	0.69702	TCT		0.358	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		A	77247111	G	A	77247111	3	1	47	1	0	0	0	0	1	0	0	0	2796	942	33	3	297	3	CCDC158	4	77247111	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	243542	77247111	113907165	561	4958										
CNOT6L	246175	broad.mit.edu	37	chr4	78663367	78663367	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagacatgattttggcacgtGactttggagaaaaaaatcca	9	7	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:78663367G>T	ENST00000504123.1	-	8	930	c.800C>A	c.(799-801)tCa>tAa	p.S267*	CNOT6L_ENST00000264903.4_Nonsense_Mutation_p.S267*|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	267	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						TTTGGCACGTGACTTTGGAGA	0.393																																																0			4											80	71	74					4																	78663367		1904	4131	6035	78882391	SO:0001587	stop_gained	246175			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.800C>A	4.37:g.78663367G>T	ENSP00000424896:p.Ser267*		78882391	Q9UF92	Nonsense_Mutation	SNP	ENST00000504123.1	37		.	.	.	.	.	.	.	.	.	.	G	26.3	4.727138	0.89390	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000505983	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.5357	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	267;267;274;42	.	ENSP00000264903:S267X	S	-	2	0	CNOT6L	78882391	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	TCA		0.393	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			T	78663367	G	T	78663367	4	4	47	1	0	0	0	0	0	1	0	0	3629	1294	45	2	887	2	CNOT6L	4	78663367	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1416256	78663367	112490909	562	4959										
C4orf22	255119	broad.mit.edu	37	chr4	81866076	81866076	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaaaagagacagaaaaattCttaatgtggacccaaaggta	8	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:81866076C>A	ENST00000358105.3	+	5	638	c.589C>A	c.(589-591)Ctt>Att	p.L197I	C4orf22_ENST00000508675.1_Missense_Mutation_p.L214I	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	197								p.L197I(1)		NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						CAGAAAAATTCTTAATGTGGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	75	73					4																	81866076		2203	4297	6500	82085100	SO:0001583	missense	255119			BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.589C>A	4.37:g.81866076C>A	ENSP00000350818:p.Leu197Ile		82085100	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	37	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	C	1.754	-0.488569	0.04352	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.20598	2.06;2.06	5.57	3.66	0.41972	.	0.083419	0.45361	D	0.000370	T	0.08268	0.0206	N	0.05383	-0.06	0.34134	D	0.665559	B;B	0.18013	0.025;0.001	B;B	0.24006	0.05;0.008	T	0.23332	-1.0191	10	0.02654	T	1	.	8.0694	0.30680	0.208:0.704:0.0:0.088	.	214;197	E7EQ13;Q6V702	.;CD022_HUMAN	I	197;214	ENSP00000350818:L197I;ENSP00000425786:L214I	ENSP00000350818:L197I	L	+	1	0	C4orf22	82085100	0.997000	0.39634	1.000000	0.80357	0.989000	0.77384	0.775000	0.26689	2.618000	0.88619	0.655000	0.94253	CTT		0.333	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		A	81866076	C	A	81866076	3	1	47	1	0	0	0	0	1	0	0	0	2261	913	32	2	607	2	C4orf22	4	81866076	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3202709	81866076	109288200	563	4960										
BMP3	651	broad.mit.edu	37	chr4	81967605	81967605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacagagaaaggggcctcatCggaagagccagacgctccaa	12	11	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:81967605C>T	ENST00000282701.2	+	2	1350	c.1030C>T	c.(1030-1032)Cgg>Tgg	p.R344W		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	344					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)	p.R344W(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						GGGGCCTCATCGGAAGAGCCA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	4											45	46	46					4																	81967605		2203	4300	6503	82186629	SO:0001583	missense	651			M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.1030C>T	4.37:g.81967605C>T	ENSP00000282701:p.Arg344Trp		82186629	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	C	9.241	1.038312	0.19669	.	.	ENSG00000152785	ENST00000282701	T	0.74737	-0.87	5.16	3.28	0.37604	.	0.211174	0.50627	D	0.000103	T	0.53981	0.1830	N	0.08118	0	0.09310	N	0.999994	B	0.28291	0.206	B	0.13407	0.009	T	0.54807	-0.8238	10	0.66056	D	0.02	.	14.8548	0.70329	0.0:0.7271:0.2729:0.0	.	344	P12645	BMP3_HUMAN	W	344	ENSP00000282701:R344W	ENSP00000282701:R344W	R	+	1	2	BMP3	82186629	0.997000	0.39634	0.381000	0.26106	0.009000	0.06853	3.559000	0.53756	1.287000	0.44583	-0.175000	0.13238	CGG		0.493	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			T	81967605	C	T	81967605	3	4	47	1	0	0	0	0	1	0	0	0	1462	875	31	1	1036	1	BMP3	4	81967605	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	101529	81967605	109186671	564	4961										
THAP9	79725	broad.mit.edu	37	chr4	83827671	83827671	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaagacttatctccgtaaaGaactacaggatgatcaagaa	7	7	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:83827671G>T	ENST00000302236.5	+	3	522	c.471G>T	c.(469-471)aaG>aaT	p.K157N		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	157					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.K157N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				TCTCCGTAAAGAACTACAGGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											80	76	77					4																	83827671		2203	4300	6503	84046695	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.471G>T	4.37:g.83827671G>T	ENSP00000305533:p.Lys157Asn		84046695	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.778381	0.31502	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.39406	1.08	3.87	2.59	0.31030	.	0.924711	0.09070	N	0.853090	T	0.28234	0.0697	L	0.38175	1.15	0.27290	N	0.957861	B	0.30482	0.281	B	0.22152	0.038	T	0.19321	-1.0309	10	0.22109	T	0.4	-6.4201	5.9756	0.19377	0.8806:0.0:0.1194:0.0	.	157	Q9H5L6	THAP9_HUMAN	N	157	ENSP00000305533:K157N	ENSP00000305533:K157N	K	+	3	2	THAP9	84046695	0.922000	0.31269	0.839000	0.33178	0.946000	0.59487	1.372000	0.34261	0.834000	0.34852	-0.423000	0.05987	AAG		0.383	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		T	83827671	G	T	83827671	3	4	47	1	0	0	0	0	1	0	0	0	15890	933	33	2	481	2	THAP9	4	83827671	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1860066	83827671	107326605	565	4962										
AGPAT9	84803	broad.mit.edu	37	chr4	84502803	84502803	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtctgacgtgttttatttCtccaagaagggattggaagc	11	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:84502803C>A	ENST00000395226.2	+	4	515	c.297C>A	c.(295-297)ttC>ttA	p.F99L	AGPAT9_ENST00000264409.4_Missense_Mutation_p.F99L	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	99					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.F99L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				TGTTTTATTTCTCCAAGAAGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											181	179	180					4																	84502803		2203	4300	6503	84721827	SO:0001583	missense	84803			AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.297C>A	4.37:g.84502803C>A	ENSP00000378651:p.Phe99Leu		84721827	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	37	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454991	0.84209	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.50001	0.76;0.76	5.66	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.71581	2.175	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	T	0.62267	-0.6890	10	0.33141	T	0.24	-22.2884	10.6518	0.45653	0.0:0.8542:0.0:0.1458	.	99	Q53EU6	GPAT3_HUMAN	L	99	ENSP00000378651:F99L;ENSP00000264409:F99L	ENSP00000264409:F99L	F	+	3	2	AGPAT9	84721827	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.051000	0.71072	1.414000	0.47017	0.644000	0.83932	TTC		0.438	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		A	84502803	C	A	84502803	3	1	47	1	0	0	0	0	1	0	0	0	392	912	32	2	307	2	AGPAT9	4	84502803	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	675132	84502803	106651473	566	4963										
CDS1	1040	broad.mit.edu	37	chr4	85538804	85538804	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgatctaccatggtttagaAcactaagttggtaagtaagc	9	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:85538804A>C	ENST00000295887.5	+	4	853	c.430A>C	c.(430-432)Aca>Cca	p.T144P		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.T144P(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		ATGGTTTAGAACACTAAGTTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	113	114					4																	85538804		2203	4298	6501	85757828	SO:0001583	missense	1040			U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.430A>C	4.37:g.85538804A>C	ENSP00000295887:p.Thr144Pro		85757828	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	37	CCDS3608.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.908301	0.72868	.	.	ENSG00000163624	ENST00000295887	T	0.45276	0.9	5.69	5.69	0.88448	.	0.046220	0.85682	D	0.000000	T	0.62527	0.2435	M	0.82056	2.57	0.58432	D	0.999995	D	0.61697	0.99	D	0.64410	0.925	T	0.64719	-0.6341	10	0.42905	T	0.14	-15.5171	11.7116	0.51628	0.8603:0.0:0.0:0.1397	.	144	Q92903	CDS1_HUMAN	P	144	ENSP00000295887:T144P	ENSP00000295887:T144P	T	+	1	0	CDS1	85757828	1.000000	0.71417	0.996000	0.52242	0.815000	0.46073	5.115000	0.64655	2.167000	0.68274	0.533000	0.62120	ACA		0.348	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			C	85538804	A	C	85538804	3	2	47	1	0	0	0	0	1	0	0	0	3183	43	2	4	444	4	CDS1	4	85538804	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1036001	85538804	105615472	567	4964										
CDS1	1040	broad.mit.edu	37	chr4	85555012	85555012	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgttgggctattaacagttCgcatggactcatgtcacttt	9	8	2	0	rs375840719		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:85555012C>T	ENST00000295887.5	+	7	1065	c.642C>T	c.(640-642)ttC>ttT	p.F214F		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.F214F(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		ATTAACAGTTCGCATGGACTC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	4						C		1,4405	2.1+/-5.4	0,1,2202	145	123	131		642	5.1	1	4		131	0,8600		0,0,4300	no	coding-synonymous	CDS1	NM_001263.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		214/462	85555012	1,13005	2203	4300	6503	85774036	SO:0001819	synonymous_variant	1040			U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.642C>T	4.37:g.85555012C>T			85774036	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	37	CCDS3608.1																																																																																				0.393	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			T	85555012	C	T	85555012	2	4	47	1	0	0	0	0	0	0	0	1	3183	883	31	1		1	CDS1	4	85555012	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	16208	85555012	105599264	568	4965										
MAPK10	5602	broad.mit.edu	37	chr4	87023118	87023118	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtacagcaggtaagacattcGctcatggtctaattccatct	8	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:87023118G>A	ENST00000359221.3	-	7	1019	c.493C>T	c.(493-495)Cga>Tga	p.R165*	MAPK10_ENST00000449047.2_Nonsense_Mutation_p.R20*|MAPK10_ENST00000395157.3_Nonsense_Mutation_p.R20*|MAPK10_ENST00000395166.1_Nonsense_Mutation_p.R127*|MAPK10_ENST00000395160.3_Nonsense_Mutation_p.R20*|MAPK10_ENST00000513839.1_5'UTR|MAPK10_ENST00000395161.2_Nonsense_Mutation_p.R165*|MAPK10_ENST00000361569.2_Nonsense_Mutation_p.R165*|MAPK10_ENST00000395169.3_Nonsense_Mutation_p.R127*			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)	p.R165*(1)|p.R20*(1)		breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		TAAGACATTCGCTCATGGTCT	0.408																																																2	Substitution - Nonsense(2)	large_intestine(2)	4											271	251	257					4																	87023118		2203	4300	6503	87242142	SO:0001587	stop_gained	5602			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.493C>T	4.37:g.87023118G>A	ENSP00000352157:p.Arg165*		87242142	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Nonsense_Mutation	SNP	ENST00000359221.3	37	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.151358|8.151358	0.98678|0.98678	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000515400|ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161	.|.	.|.	.|.	5.94|5.94	4.05|4.05	0.47172|0.47172	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.35364|.	0.0929|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.24012|.	-1.0172|.	3|.	.|0.02654	.|T	.|1	-1.9218|-1.9218	15.34|15.34	0.74287|0.74287	0.0:0.0:0.7738:0.2262|0.0:0.0:0.7738:0.2262	.|.	.|.	.|.	.|.	V|X	77|127;165;20;165;127;20;20;165	.|.	.|ENSP00000352157:R165X	A|R	-|-	2|1	0|2	MAPK10|MAPK10	87242142|87242142	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.958000|5.958000	0.70330|0.70330	2.824000|2.824000	0.97209|0.97209	0.650000|0.650000	0.86243|0.86243	GCG|CGA		0.408	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			A	87023118	G	A	87023118	4	1	47	1	0	0	0	0	0	1	0	0	9302	1095	38	1	938	1	MAPK10	4	87023118	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1468106	87023118	104131158	569	4966										
AFF1	4299	broad.mit.edu	37	chr4	88052956	88052956	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcctatagattcataatgtCattaaaatccttctcagatg	4	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:88052956C>A	ENST00000307808.6	+	17	3512	c.3092C>A	c.(3091-3093)tCa>tAa	p.S1031*	AFF1_ENST00000544085.1_Nonsense_Mutation_p.S669*|AFF1_ENST00000395146.4_Nonsense_Mutation_p.S1038*	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1031					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S1038*(1)		breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTCATAATGTCATTAAAATCC	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											103	99	100					4																	88052956		2202	4300	6502	88271980	SO:0001587	stop_gained	4299			L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3092C>A	4.37:g.88052956C>A	ENSP00000305689:p.Ser1031*		88271980	B4DTU1|E9PBM3	Nonsense_Mutation	SNP	ENST00000307808.6	37	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	C	39	7.630674	0.98399	.	.	ENSG00000172493	ENST00000395146;ENST00000307808;ENST00000544085	.	.	.	5.64	5.64	0.86602	.	0.426786	0.22313	N	0.061714	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-15.4231	14.191	0.65637	0.1496:0.8504:0.0:0.0	.	.	.	.	X	1038;1031;669	.	ENSP00000305689:S1031X	S	+	2	0	AFF1	88271980	0.996000	0.38824	0.996000	0.52242	0.112000	0.19704	1.774000	0.38573	2.653000	0.90120	0.655000	0.94253	TCA		0.303	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		A	88052956	C	A	88052956	4	1	47	1	0	0	0	0	0	1	0	0	356	838	29	2	3200	2	AFF1	4	88052956	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1029838	88052956	103101320	570	4967										
ABCG2	9429	broad.mit.edu	37	chr4	89018725	89018725	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accatcataagggtaaacatCataacgaagaaggcatctgc	8	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:89018725C>A	ENST00000237612.3	-	13	2072	c.1527G>T	c.(1525-1527)atG>atT	p.M509I	ABCG2_ENST00000515655.1_Missense_Mutation_p.M509I	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	509	ABC transmembrane type-2.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.M509I(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GGGTAAACATCATAACGAAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											123	110	115					4																	89018725		2203	4300	6503	89237749	SO:0001583	missense	9429			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.1527G>T	4.37:g.89018725C>A	ENSP00000237612:p.Met509Ile		89237749	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145727	0.57044	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.71698	-0.59;-0.59	5.5	5.5	0.81552	ABC-2 type transporter (1);	0.205916	0.64402	D	0.000011	T	0.79470	0.4451	L	0.58428	1.81	0.50467	D	0.999877	P;P;P	0.51933	0.766;0.949;0.891	B;P;P	0.56163	0.312;0.793;0.643	T	0.79722	-0.1684	10	0.52906	T	0.07	-27.1498	19.0075	0.92857	0.0:1.0:0.0:0.0	.	509;509;509	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	I	509	ENSP00000426917:M509I;ENSP00000237612:M509I	ENSP00000237612:M509I	M	-	3	0	ABCG2	89237749	1.000000	0.71417	1.000000	0.80357	0.241000	0.25554	4.939000	0.63526	2.584000	0.87258	0.557000	0.71058	ATG		0.458	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		A	89018725	C	A	89018725	3	1	47	1	0	0	0	0	1	0	0	0	69	826	29	2	456	2	ABCG2	4	89018725	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	965769	89018725	102135551	571	4968										
ABCG2	9429	broad.mit.edu	37	chr4	89022393	89022393	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctactcacatgaagagcttCttctctaccacaaagagttc	5	13	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:89022393C>A	ENST00000237612.3	-	11	1901	c.1356G>T	c.(1354-1356)aaG>aaT	p.K452N	ABCG2_ENST00000515655.1_Missense_Mutation_p.K452N	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	452	ABC transmembrane type-2.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.K452N(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	TGAAGAGCTTCTTCTCTACCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	77	84					4																	89022393		2203	4300	6503	89241417	SO:0001583	missense	9429			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.1356G>T	4.37:g.89022393C>A	ENSP00000237612:p.Lys452Asn		89241417	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.103158	0.56183	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.71579	-0.58;-0.58	5.76	3.81	0.43845	ABC-2 type transporter (1);	0.041854	0.85682	D	0.000000	T	0.69287	0.3094	M	0.64997	1.995	0.45035	D	0.998054	P;P;B	0.41524	0.753;0.567;0.314	B;B;B	0.42163	0.288;0.248;0.378	T	0.69367	-0.5164	10	0.52906	T	0.07	-17.3661	12.4218	0.55524	0.0:0.8463:0.0:0.1537	.	452;452;452	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	N	452	ENSP00000426917:K452N;ENSP00000237612:K452N	ENSP00000237612:K452N	K	-	3	2	ABCG2	89241417	0.989000	0.36119	1.000000	0.80357	0.993000	0.82548	0.245000	0.18142	0.716000	0.32124	0.650000	0.86243	AAG		0.517	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		A	89022393	C	A	89022393	3	1	47	1	0	0	0	0	1	0	0	0	69	912	32	2	635	2	ABCG2	4	89022393	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3668	89022393	102131883	572	4969										
HERC6	55008	broad.mit.edu	37	chr4	89329708	89329708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacgacttccattgatgtggActtagaaatggcaagagata	10	6	0	3	rs571683231		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:89329708A>G	ENST00000264346.7	+	11	1366	c.1307A>G	c.(1306-1308)gAc>gGc	p.D436G	HERC6_ENST00000380265.5_Missense_Mutation_p.D436G	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	436					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.D436G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		ATTGATGTGGACTTAGAAATG	0.338													A|||	1	0.000199681	0	0.0014	5008	,	,		19240	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											79	70	73					4																	89329708		1843	4097	5940	89548731	SO:0001583	missense	55008			AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1307A>G	4.37:g.89329708A>G	ENSP00000264346:p.Asp436Gly		89548731	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.721379	0.48728	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.57273	0.41;0.72	4.63	0.507	0.16967	.	0.163537	0.40728	N	0.001022	T	0.60274	0.2256	M	0.73962	2.25	0.31111	N	0.709984	P;P	0.51351	0.944;0.908	P;P	0.53146	0.719;0.527	T	0.65734	-0.6096	10	0.72032	D	0.01	.	10.0251	0.42066	0.5422:0.4578:0.0:0.0	.	436;436	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	G	436	ENSP00000369617:D436G;ENSP00000264346:D436G	ENSP00000264346:D436G	D	+	2	0	HERC6	89548731	1.000000	0.71417	0.368000	0.25939	0.782000	0.44232	2.837000	0.48191	0.023000	0.15187	0.397000	0.26171	GAC		0.338	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			G	89329708	A	G	89329708	3	3	47	1	0	0	0	0	1	0	0	0	7083	275	10	4	1146	4	HERC6	4	89329708	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	307315	89329708	101824568	573	4970										
HERC3	8916	broad.mit.edu	37	chr4	89599224	89599224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgttcgcaggaacaaccttgTtggagatgccctaagagagc	12	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:89599224T>C	ENST00000402738.1	+	19	2374	c.2135T>C	c.(2134-2136)gTt>gCt	p.V712A	HERC3_ENST00000543130.1_Missense_Mutation_p.V156A|HERC3_ENST00000264345.3_Missense_Mutation_p.V712A	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	712					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.V712A(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		AACAACCTTGTTGGAGATGCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	106	106					4																	89599224		2203	4300	6503	89818247	SO:0001583	missense	8916			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.2135T>C	4.37:g.89599224T>C	ENSP00000385684:p.Val712Ala		89818247	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797257	0.90538	.	.	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130;ENST00000512194	T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3	5.35	5.35	0.76521	HECT (1);	0.000000	0.85682	D	0.000000	D	0.88078	0.6340	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88902	0.3353	10	0.62326	D	0.03	.	15.5138	0.75806	0.0:0.0:0.0:1.0	.	712	Q15034	HERC3_HUMAN	A	712;712;156;105	ENSP00000385684:V712A;ENSP00000264345:V712A;ENSP00000441703:V156A;ENSP00000421021:V105A	ENSP00000264345:V712A	V	+	2	0	HERC3	89818247	1.000000	0.71417	0.935000	0.37517	0.985000	0.73830	7.482000	0.81143	2.250000	0.74265	0.454000	0.30748	GTT		0.478	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		C	89599224	T	C	89599224	3	2	47	1	0	0	0	0	1	0	0	0	7080	1725	60	4	2201	4	HERC3	4	89599224	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	269516	89599224	101555052	574	4971										
FAM13A	10144	broad.mit.edu	37	chr4	89859247	89859247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagttgcttacttttactaTgataagcctagccaggtttt	7	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:89859247T>C	ENST00000264344.5	-	5	958	c.751A>G	c.(751-753)Ata>Gta	p.I251V	FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_Missense_Mutation_p.I42V|FAM13A_ENST00000509094.1_Missense_Mutation_p.I251V	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	251					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.I251V(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						ACTTTTACTATGATAAGCCTA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	4											88	87	87					4																	89859247		2203	4300	6503	90078270	SO:0001583	missense	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.751A>G	4.37:g.89859247T>C	ENSP00000264344:p.Ile251Val		90078270	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	T	10.12	1.264242	0.23136	.	.	ENSG00000138640	ENST00000264344;ENST00000511976;ENST00000509094	T;T;T	0.28895	2.32;1.59;2.14	4.03	-3.3	0.05003	.	0.945041	0.08860	N	0.883125	T	0.14313	0.0346	N	0.22421	0.69	0.27636	N	0.947864	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.28038	-1.0056	10	0.30078	T	0.28	.	0.5676	0.00690	0.3724:0.1636:0.1266:0.3374	.	42;251	E9PGM7;O94988	.;FA13A_HUMAN	V	251;42;251	ENSP00000264344:I251V;ENSP00000421914:I42V;ENSP00000426517:I251V	ENSP00000264344:I251V	I	-	1	0	FAM13A	90078270	0.044000	0.20184	0.285000	0.24819	0.994000	0.84299	-0.945000	0.03909	-0.574000	0.05990	0.528000	0.53228	ATA		0.284	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			C	89859247	T	C	89859247	3	2	47	1	0	0	0	0	1	0	0	0	5468	1464	51	4	2433	4	FAM13A	4	89859247	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	260023	89859247	101295029	575	4972										
FAM190A	401145	broad.mit.edu	37	chr4	91229870	91229870	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagagcactcaactaacaaGaatgtctttataaattgtct	5	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:91229870G>T	ENST00000509176.1	+	2	723	c.435G>T	c.(433-435)aaG>aaT	p.K145N	CCSER1_ENST00000432775.2_Missense_Mutation_p.K145N|CCSER1_ENST00000333691.8_Missense_Mutation_p.K145N	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	145								p.K145N(1)									CAACTAACAAGAATGTCTTTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											52	51	51					4																	91229870		1826	4082	5908	91448893	SO:0001583	missense	401145				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.435G>T	4.37:g.91229870G>T	ENSP00000425040:p.Lys145Asn		91448893	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.017786	0.54576	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.53206	1.15;0.63;1.15	5.18	5.18	0.71444	.	0.057621	0.64402	D	0.000003	T	0.55970	0.1954	L	0.33485	1.01	0.34045	D	0.655447	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.71870	0.943;0.975;0.964	T	0.66638	-0.5873	10	0.87932	D	0	-23.6471	12.6532	0.56774	0.1194:0.0:0.8806:0.0	.	145;145;145	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	N	145	ENSP00000425040:K145N;ENSP00000389283:K145N;ENSP00000329482:K145N	ENSP00000329482:K145N	K	+	3	2	FAM190A	91448893	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.047000	0.49854	2.793000	0.96121	0.655000	0.94253	AAG		0.378	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	91229870	G	T	91229870	3	4	47	1	0	0	0	0	1	0	0	0	5537	933	33	2	437	2	FAM190A	4	91229870	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1370623	91229870	99924406	576	4973										
SMARCAD1	56916	broad.mit.edu	37	chr4	95199798	95199798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttaccccccaagaaagatcGaattgagttgtgtgcaatgt	10	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:95199798G>A	ENST00000354268.4	+	18	2283	c.2210G>A	c.(2209-2211)cGa>cAa	p.R737Q	SMARCAD1_ENST00000509418.1_Missense_Mutation_p.R307Q|SMARCAD1_ENST00000457823.2_Missense_Mutation_p.R737Q			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	737					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.R737Q(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AAGAAAGATCGAATTGAGTTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	97	95					4																	95199798		2198	4300	6498	95418821	SO:0001583	missense	56916			AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2210G>A	4.37:g.95199798G>A	ENSP00000346217:p.Arg737Gln		95418821	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	G	3.763	-0.049167	0.07407	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	5.55	-9.99	0.00435	SNF2-related (1);	1.372300	0.05135	N	0.493304	T	0.79930	0.4531	N	0.05078	-0.115	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.65685	-0.6108	10	0.23302	T	0.38	1.7678	14.3145	0.66440	0.2865:0.0:0.6031:0.1104	.	737;737	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	Q	737;737;737;307	ENSP00000351947:R737Q;ENSP00000415576:R737Q;ENSP00000346217:R737Q;ENSP00000423286:R307Q	ENSP00000346217:R737Q	R	+	2	0	SMARCAD1	95418821	0.000000	0.05858	0.005000	0.12908	0.129000	0.20672	0.145000	0.16157	-1.752000	0.01325	-1.223000	0.01593	CGA		0.338	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		A	95199798	G	A	95199798	3	1	47	1	0	0	0	0	1	0	0	0	14809	1058	37	1	2276	1	SMARCAD1	4	95199798	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3969928	95199798	95954478	577	4974										
BMPR1B	658	broad.mit.edu	37	chr4	96069973	96069973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgcctccagaagtgttggAcgagagcttgaacagaaatc	11	8	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:96069973A>G	ENST00000515059.1	+	11	1434	c.1151A>G	c.(1150-1152)gAc>gGc	p.D384G	BMPR1B_ENST00000394931.1_Missense_Mutation_p.D384G|BMPR1B_ENST00000440890.2_Missense_Mutation_p.D414G|BMPR1B_ENST00000264568.4_Missense_Mutation_p.D384G	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	384	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.D384G(2)		breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		GAAGTGTTGGACGAGAGCTTG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	4											187	162	171					4																	96069973		2203	4300	6503	96288996	SO:0001583	missense	658			D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.1151A>G	4.37:g.96069973A>G	ENSP00000426617:p.Asp384Gly		96288996	B2R953|B4DSV1|P78366	Missense_Mutation	SNP	ENST00000515059.1	37	CCDS3642.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.939887	0.73557	.	.	ENSG00000138696	ENST00000515059;ENST00000512312;ENST00000509540;ENST00000440890;ENST00000264568;ENST00000394931	T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050345	0.85682	D	0.000000	T	0.62502	0.2433	N	0.20357	0.565	0.80722	D	1	D	0.55605	0.972	P	0.55615	0.78	T	0.67998	-0.5525	10	0.87932	D	0	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	384	O00238	BMR1B_HUMAN	G	384;384;384;414;384;384	ENSP00000426617:D384G;ENSP00000425444:D384G;ENSP00000421671:D384G;ENSP00000401907:D414G;ENSP00000264568:D384G;ENSP00000378389:D384G	ENSP00000264568:D384G	D	+	2	0	BMPR1B	96288996	1.000000	0.71417	0.984000	0.44739	0.996000	0.88848	9.139000	0.94554	2.371000	0.80710	0.533000	0.62120	GAC		0.428	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		G	96069973	A	G	96069973	3	3	47	1	0	0	0	0	1	0	0	0	1471	275	10	4	1181	4	BMPR1B	4	96069973	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	870175	96069973	95084303	578	4975										
UNC5C	8633	broad.mit.edu	37	chr4	96106245	96106245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagagggaatgggcgatatCgtgaattgacaggcgcaggt	16	7	0	3	rs139502011	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:96106245C>T	ENST00000453304.1	-	13	2587	c.2239G>A	c.(2239-2241)Gat>Aat	p.D747N		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	747					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)	p.D747N(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TGGGCGATATCGTGAATTGAC	0.463													C|||	3	0.000599042	0	0	5008	,	,		16094	0		0.002	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	4						C	ASN/ASP	0,4406		0,0,2203	120	121	120		2239	5.9	0.3	4	dbSNP_134	120	11,8589	8.4+/-32.0	0,11,4289	yes	missense	UNC5C	NM_003728.3	23	0,11,6492	TT,TC,CC		0.1279,0.0,0.0846	benign	747/932	96106245	11,12995	2203	4300	6503	96325268	SO:0001583	missense	8633			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.2239G>A	4.37:g.96106245C>T	ENSP00000406022:p.Asp747Asn		96325268	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	35	5.543036	0.96474	0.0	0.001279	ENSG00000182168	ENST00000453304;ENST00000331502	T	0.53857	0.6	5.87	5.87	0.94306	.	0.048289	0.85682	D	0.000000	T	0.76990	0.4065	M	0.85859	2.78	0.80722	D	1	D;D	0.65815	0.971;0.995	P;D	0.69142	0.539;0.962	T	0.79356	-0.1837	10	0.87932	D	0	.	20.2788	0.98501	0.0:1.0:0.0:0.0	.	747;747	A8K385;O95185	.;UNC5C_HUMAN	N	747;706	ENSP00000406022:D747N	ENSP00000328673:D706N	D	-	1	0	UNC5C	96325268	1.000000	0.71417	0.293000	0.24932	0.802000	0.45316	7.745000	0.85046	2.788000	0.95919	0.650000	0.86243	GAT		0.463	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96106245	C	T	96106245	3	4	47	1	0	0	0	0	1	0	0	0	17033	884	31	1	572	1	UNC5C	4	96106245	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36272	96106245	95048031	579	4976										
PDHA2	5161	broad.mit.edu	37	chr4	96762095	96762095	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgtgttcgtgaggcaacaaAatttgcagctaactactgta	10	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:96762095A>C	ENST00000295266.4	+	1	857	c.794A>C	c.(793-795)aAa>aCa	p.K265T		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	265					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.K265T(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		GAGGCAACAAAATTTGCAGCT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											144	144	144					4																	96762095		2203	4300	6503	96981118	SO:0001583	missense	5161				CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.794A>C	4.37:g.96762095A>C	ENSP00000295266:p.Lys265Thr		96981118	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	37	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.788899	0.49997	.	.	ENSG00000163114	ENST00000295266	D	0.97256	-4.31	4.91	1.22	0.21188	Dehydrogenase, E1 component (1);	0.156795	0.56097	D	0.000033	D	0.96119	0.8735	L	0.58428	1.81	0.40830	D	0.983583	P	0.50528	0.936	P	0.52710	0.707	D	0.93975	0.7253	10	0.72032	D	0.01	-12.2262	7.567	0.27885	0.7642:0.0:0.2358:0.0	.	265	P29803	ODPAT_HUMAN	T	265	ENSP00000295266:K265T	ENSP00000295266:K265T	K	+	2	0	PDHA2	96981118	0.997000	0.39634	0.034000	0.17996	0.567000	0.35839	2.709000	0.47160	0.135000	0.18707	0.383000	0.25322	AAA		0.483	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			C	96762095	A	C	96762095	3	2	47	1	0	0	0	0	1	0	0	0	11696	14	1	4	796	4	PDHA2	4	96762095	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	655850	96762095	94392181	580	4977										
C4orf37	285555	broad.mit.edu	37	chr4	99055575	99055575	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcaatggtaaaagtactttCtctggcagtcaaagaaagaa	10	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:99055575C>A	ENST00000295268.3	-	2	234	c.145G>T	c.(145-147)Gaa>Taa	p.E49*		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	49								p.E49*(1)									AAAGTACTTTCTCTGGCAGTC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											96	98	97					4																	99055575		2203	4299	6502	99274598	SO:0001587	stop_gained	285555			BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.145G>T	4.37:g.99055575C>A	ENSP00000295268:p.Glu49*		99274598		Nonsense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417323	0.83449	.	.	ENSG00000163116	ENST00000295268	.	.	.	5.38	2.66	0.31614	.	0.516613	0.19035	N	0.124446	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-1.3708	6.3034	0.21125	0.0:0.6783:0.1514:0.1704	.	.	.	.	X	49	.	ENSP00000295268:E49X	E	-	1	0	C4orf37	99274598	0.297000	0.24408	0.322000	0.25334	0.385000	0.30292	0.080000	0.14802	0.311000	0.23014	-0.182000	0.12963	GAA		0.358	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		A	99055575	C	A	99055575	4	1	47	1	0	0	0	0	0	1	0	0	2273	922	32	2	1274	2	C4orf37	4	99055575	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2293480	99055575	92098701	581	4978										
RAP1GDS1	5910	broad.mit.edu	37	chr4	99264294	99264294	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgtatctcttttagatacGgaaacaagtgaaaaaatcca	6	6	1	2	rs376264971		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:99264294G>A	ENST00000408927.3	+	3	230	c.117G>A	c.(115-117)acG>acA	p.T39T	RAP1GDS1_ENST00000339360.5_Silent_p.T40T|RAP1GDS1_ENST00000453712.2_Silent_p.T40T|RAP1GDS1_ENST00000408900.3_Silent_p.T39T|RAP1GDS1_ENST00000512857.1_3'UTR|RAP1GDS1_ENST00000264572.7_Silent_p.T40T|RAP1GDS1_ENST00000380158.4_Silent_p.T40T	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	39					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)	p.T40T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		TTTTAGATACGGAAACAAGTG	0.363			T	NUP98	T-ALL																																		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	1	Substitution - coding silent(1)	large_intestine(1)	4						G	,,,,,	2,3660		0,2,1829	65	65	65		120,117,120,117,120,120	0	0.2	4		65	0,8156		0,0,4078	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAP1GDS1	NM_001100426.1,NM_001100427.1,NM_001100428.1,NM_001100429.1,NM_001100430.1,NM_021159.4	,,,,,	0,2,5907	AA,AG,GG		0.0,0.0546,0.0169	,,,,,	40/609,39/608,40/560,39/559,40/517,40/608	99264294	2,11816	1831	4078	5909	99483317	SO:0001819	synonymous_variant	5910				CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.117G>A	4.37:g.99264294G>A			99483317	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Silent	SNP	ENST00000408927.3	37	CCDS43253.1																																																																																				0.363	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		A	99264294	G	A	99264294	2	1	47	1	0	0	0	0	0	0	0	1	13076	1103	39	1		1	RAP1GDS1	4	99264294	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	208719	99264294	91889982	582	4979										
ADH6	130	broad.mit.edu	37	chr4	100126162	100126162	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaattagtggatctagattCaacttctctgccatataatc	6	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:100126162C>A	ENST00000237653.7	-	8	1407	c.1023G>T	c.(1021-1023)ttG>ttT	p.L341F	RP11-696N14.1_ENST00000506454.1_RNA|ADH6_ENST00000394899.2_Missense_Mutation_p.L341F|ADH6_ENST00000407820.2_Missense_Mutation_p.L132F|RP11-696N14.1_ENST00000506160.1_RNA|ADH6_ENST00000394897.1_Nonstop_Mutation_p.*296L|RP11-696N14.1_ENST00000500358.2_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	341					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)	p.L341F(1)		breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	GATCTAGATTCAACTTCTCTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											153	145	148					4																	100126162		2203	4300	6503	100345185	SO:0001583	missense	130			AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"Alcohol dehydrogenases"	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.1023G>T	4.37:g.100126162C>A	ENSP00000237653:p.Leu341Phe		100345185	B3KS45|Q58F53	Nonstop_Mutation	SNP	ENST00000237653.7	37	CCDS3647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.061|4.061	0.009088|0.009088	0.07912|0.07912	.|.	.|.	ENSG00000172955|ENSG00000172955	ENST00000394899;ENST00000407820;ENST00000237653|ENST00000394897	T;T;T|.	0.06933|.	3.24;3.24;3.24|.	3.79|3.79	2.56|2.56	0.30785|0.30785	.|.	0.612730|.	0.17063|.	N|.	0.188484|.	T|.	0.31167|.	0.0788|.	N|N	0.17838|0.17838	0.53|0.53	0.34967|0.34967	D|D	0.752763|0.752763	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|.	0.30090|.	-0.9990|.	10|.	0.05525|.	T|.	0.97|.	-7.079|-7.079	5.5377|5.5377	0.17021|0.17021	0.6917:0.1588:0.1496:0.0|0.6917:0.1588:0.1496:0.0	.|.	218;341;341|.	B4DPD8;P28332;P28332-2|.	.;ADH6_HUMAN;.|.	F|L	341;132;341|296	ENSP00000378359:L341F;ENSP00000384997:L132F;ENSP00000237653:L341F|.	ENSP00000237653:L341F|.	L|X	-|-	3|2	2|2	ADH6|ADH6	100345185|100345185	0.058000|0.058000	0.20735|0.20735	0.044000|0.044000	0.18714|0.18714	0.010000|0.010000	0.07245|0.07245	0.596000|0.596000	0.24044|0.24044	0.423000|0.423000	0.26033|0.26033	-0.433000|-0.433000	0.05886|0.05886	TTG|TGA		0.358	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672		A	100126162	C	A	100126162	3	1	47	1	0	0	0	0	1	0	0	0	312	825	29	2	116	2	ADH6	4	100126162	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	861868	100126162	91028114	583	4980										
ADH1B	125	broad.mit.edu	37	chr4	100240005	100240005	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctcaatggaaaagggtttCtttacctcccatagcacagc	7	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:100240005C>A	ENST00000305046.8	-	2	124	c.57G>T	c.(55-57)aaG>aaT	p.K19N	ADH1B_ENST00000394887.3_5'UTR|ADH1B_ENST00000504498.1_5'UTR			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	19					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)	p.K19N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	AAAAGGGTTTCTTTACCTCCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	97	98					4																	100240005		2203	4300	6503	100459028	SO:0001583	missense	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.57G>T	4.37:g.100240005C>A	ENSP00000306606:p.Lys19Asn		100459028	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Missense_Mutation	SNP	ENST00000305046.8	37	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.350700	0.01256	.	.	ENSG00000196616	ENST00000305046;ENST00000412614	T	0.03212	4.01	3.6	-7.2	0.01495	GroES-like (1);	0.891818	0.09641	N	0.774981	T	0.01387	0.0045	N	0.04162	-0.26	0.30357	N	0.784221	B	0.02656	0.0	B	0.06405	0.002	T	0.47032	-0.9148	10	0.14656	T	0.56	0.8647	5.9678	0.19334	0.2808:0.1862:0.4657:0.0673	.	19	P00325	ADH1B_HUMAN	N	19	ENSP00000306606:K19N	ENSP00000306606:K19N	K	-	3	2	ADH1B	100459028	0.000000	0.05858	0.006000	0.13384	0.895000	0.52256	-4.881000	0.00174	-2.316000	0.00645	-0.321000	0.08615	AAG		0.373	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		A	100240005	C	A	100240005	3	1	47	1	0	0	0	0	1	0	0	0	308	912	32	2	1102	2	ADH1B	4	100240005	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	113843	100240005	90914271	584	4981										
BANK1	55024	broad.mit.edu	37	chr4	102946432	102946432	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagatggagctgaggcaaatGaaatggaaggggaaggaaaa	16	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:102946432G>T	ENST00000322953.4	+	9	1634	c.1360G>T	c.(1360-1362)Gaa>Taa	p.E454*	BANK1_ENST00000444316.2_Nonsense_Mutation_p.E424*|RP11-498M5.2_ENST00000505091.1_RNA|BANK1_ENST00000428908.1_Nonsense_Mutation_p.E321*|BANK1_ENST00000508653.1_Nonsense_Mutation_p.E321*|BANK1_ENST00000504592.1_Nonsense_Mutation_p.E439*|BANK1_ENST00000510950.1_3'UTR	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	454					B cell activation (GO:0042113)			p.E454*(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TGAGGCAAATGAAATGGAAGG	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											219	202	208					4																	102946432		2203	4300	6503	103165455	SO:0001587	stop_gained	55024			AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1360G>T	4.37:g.102946432G>T	ENSP00000320509:p.Glu454*		103165455	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Nonsense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.234366	0.79800	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	.	.	.	4.59	1.88	0.25563	.	1.616790	0.03775	N	0.260344	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	5.6275	0.17490	0.2497:0.1423:0.6079:0.0	.	.	.	.	X	439;454;321;321;424	.	ENSP00000320509:E454X	E	+	1	0	BANK1	103165455	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.078000	0.11375	0.132000	0.18615	-0.444000	0.05651	GAA		0.463	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		T	102946432	G	T	102946432	4	4	47	1	0	0	0	0	0	1	0	0	1310	1291	45	2	1394	2	BANK1	4	102946432	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2706427	102946432	88207844	585	4982										
NHEDC1	150159	broad.mit.edu	37	chr4	103911024	103911024	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgtctccttttttgtctgTggttttatttcttctgtatc	6	7	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:103911024T>G	ENST00000296422.7	-	3	285	c.144A>C	c.(142-144)ccA>ccC	p.P48P	SLC9B1_ENST00000394789.3_Silent_p.P48P	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	48					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.P48P(1)									TTTTTGTCTGTGGTTTTATTT	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	4											181	161	168					4																	103911024		2201	4294	6495	104130473	SO:0001819	synonymous_variant	150159			AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.144A>C	4.37:g.103911024T>G			104130473	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Silent	SNP	ENST00000296422.7	37	CCDS34041.1																																																																																				0.299	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		G	103911024	T	G	103911024	2	3	47	1	0	0	0	0	0	0	0	1	10431	1683	59	4		4	NHEDC1	4	103911024	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	964592	103911024	87243252	586	4983										
CENPE	1062	broad.mit.edu	37	chr4	104068611	104068611	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctctttccttggttagagAttttatctcttcctgacttt	6	9	2	2	rs548664264		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:104068611A>C	ENST00000265148.3	-	29	4125	c.4036T>G	c.(4036-4038)Tct>Gct	p.S1346A	CENPE_ENST00000380026.3_Missense_Mutation_p.S1321A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1346					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.S1346A(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTGGTTAGAGATTTTATCTCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											148	141	143					4																	104068611		2203	4299	6502	104288060	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4036T>G	4.37:g.104068611A>C	ENSP00000265148:p.Ser1346Ala		104288060	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	A	8.219	0.802080	0.16397	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.73258	-0.73;-0.73	5.03	3.76	0.43208	.	.	.	.	.	T	0.59662	0.2210	M	0.61703	1.905	0.18873	N	0.999981	P;B	0.41673	0.759;0.024	B;B	0.37692	0.256;0.003	T	0.54255	-0.8321	9	0.05620	T	0.96	.	8.1957	0.31396	0.7971:0.2029:0.0:0.0	.	1321;1346	Q02224-3;Q02224	.;CENPE_HUMAN	A	1346;1346;1321	ENSP00000265148:S1346A;ENSP00000369365:S1321A	ENSP00000265148:S1346A	S	-	1	0	CENPE	104288060	0.000000	0.05858	0.990000	0.47175	0.962000	0.63368	-0.103000	0.10940	1.884000	0.54569	0.482000	0.46254	TCT		0.368	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104068611	A	C	104068611	3	2	47	1	0	0	0	0	1	0	0	0	3236	333	12	4	4153	4	CENPE	4	104068611	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	157587	104068611	87085665	587	4984										
TET2	54790	broad.mit.edu	37	chr4	106155525	106155525	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcagtcaaccaaatgtctcCgatttgagtgataagaaaga	9	7	2	4	rs540228872		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:106155525C>T	ENST00000540549.1	+	3	1286	c.426C>T	c.(424-426)tcC>tcT	p.S142S	TET2_ENST00000394764.1_Silent_p.S142S|TET2_ENST00000413648.2_Silent_p.S142S|TET2_ENST00000305737.2_Silent_p.S142S|TET2_ENST00000380013.4_Silent_p.S142S|TET2_ENST00000545826.1_Silent_p.S142S|TET2_ENST00000513237.1_Silent_p.S163S			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	142					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.S142S(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CAAATGTCTCCGATTTGAGTG	0.398			"Mis N, F"		MDS								C|||	1	0.000199681	0	0	5008	,	,		20817	0		0	False		,,,				2504	0.001						Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - coding silent(1)	large_intestine(1)	4											53	54	54					4																	106155525		2203	4300	6503	106374974	SO:0001819	synonymous_variant	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.426C>T	4.37:g.106155525C>T			106374974	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																				0.398	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106155525	C	T	106155525	2	4	47	1	0	0	0	0	0	0	0	1	15809	639	23	1		1	TET2	4	106155525	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2086914	106155525	84998751	588	4985										
PPA2	27068	broad.mit.edu	37	chr4	106345476	106345476	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataacttctccacaagaaaGaatctttaaagaaaaaagaa	4	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:106345476G>T	ENST00000341695.5	-	7	562	c.532C>A	c.(532-534)Ctt>Att	p.L178I	PPA2_ENST00000348706.5_Missense_Mutation_p.L149I|PPA2_ENST00000380004.2_Missense_Mutation_p.L160I|PPA2_ENST00000432483.2_Missense_Mutation_p.L76I|PPA2_ENST00000354147.3_Intron|PPA2_ENST00000310267.7_Missense_Mutation_p.L99I|PPA2_ENST00000357415.4_Missense_Mutation_p.L193I|PPA2_ENST00000509426.1_5'UTR	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	178					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)	p.L178I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		CCACAAGAAAGAATCTTTAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	55	54					4																	106345476		2203	4299	6502	106564925	SO:0001583	missense	27068				CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.532C>A	4.37:g.106345476G>T	ENSP00000343885:p.Leu178Ile		106564925	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.76|10.76	1.440208|1.440208	0.25900|0.25900	.|.	.|.	ENSG00000138777|ENSG00000138777	ENST00000508518|ENST00000341695;ENST00000348706;ENST00000432483;ENST00000357415;ENST00000380004;ENST00000510015;ENST00000310267;ENST00000504028	.|T;T;T;T;T;T;T;T	.|0.46451	.|0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.38|5.38	2.3|2.3	0.28687|0.28687	.|.	.|0.404148	.|0.30134	.|N	.|0.010337	T|T	0.32436|0.32436	0.0829|0.0829	L|L	0.56199|0.56199	1.76|1.76	0.23607|0.23607	N|N	0.997307|0.997307	.|B;B;B;B;B	.|0.31790	.|0.082;0.34;0.024;0.1;0.068	.|B;B;B;B;B	.|0.29862	.|0.065;0.108;0.022;0.038;0.063	T|T	0.15378|0.15378	-1.0439|-1.0439	5|10	.|0.22109	.|T	.|0.4	-29.8429|-29.8429	8.007|8.007	0.30332|0.30332	0.3876:0.0:0.6124:0.0|0.3876:0.0:0.6124:0.0	.|.	.|99;76;149;160;178	.|B4DFH3;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.|.;.;.;.;IPYR2_HUMAN	L|I	156|178;149;76;193;160;105;99;173	.|ENSP00000343885:L178I;ENSP00000313061:L149I;ENSP00000389957:L76I;ENSP00000349996:L193I;ENSP00000369340:L160I;ENSP00000423363:L105I;ENSP00000311150:L99I;ENSP00000421177:L173I	.|ENSP00000311150:L99I	F|L	-|-	3|1	2|0	PPA2|PPA2	106564925|106564925	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.548000|0.548000	0.35241|0.35241	1.547000|1.547000	0.36190|0.36190	0.211000|0.211000	0.20683|0.20683	-0.136000|-0.136000	0.14681|0.14681	TTC|CTT		0.313	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869		T	106345476	G	T	106345476	3	4	47	1	0	0	0	0	1	0	0	0	12318	942	33	2	496	2	PPA2	4	106345476	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	189951	106345476	84808800	589	4986										
CFI	3426	broad.mit.edu	37	chr4	110682704	110682704	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtataacaaaccacatcagcGaaatcctggtaacccatagt	6	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:110682704G>A	ENST00000394634.2	-	4	834	c.627C>T	c.(625-627)ttC>ttT	p.F209F	CFI_ENST00000394635.3_Silent_p.F209F|CFI_ENST00000512148.1_Silent_p.F209F	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	209	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.F209F(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		CCACATCAGCGAAATCCTGGT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	4											158	147	151					4																	110682704		2203	4300	6503	110902153	SO:0001819	synonymous_variant	3426			J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"Complement system"	5394	protein-coding gene	gene with protein product	"Konglutinogen-activating factor", "C3b-inactivator"	217030	"I factor (complement)"	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.627C>T	4.37:g.110682704G>A			110902153	O60442	Silent	SNP	ENST00000394634.2	37	CCDS34049.1																																																																																				0.393	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		A	110682704	G	A	110682704	2	1	47	1	0	0	0	0	0	0	0	1	3295	1049	37	1		1	CFI	4	110682704	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4337228	110682704	80471572	590	4987										
ALPK1	80216	broad.mit.edu	37	chr4	113352015	113352015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttatgttcccgagagtttcGagtgcaggttggataaactt	11	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:113352015G>A	ENST00000458497.1	+	11	1591	c.1312G>A	c.(1312-1314)Gag>Aag	p.E438K	ALPK1_ENST00000177648.9_Missense_Mutation_p.E438K|ALPK1_ENST00000504176.2_Missense_Mutation_p.E360K	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	438							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E438K(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CGAGAGTTTCGAGTGCAGGTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											103	102	103					4																	113352015		2203	4300	6503	113571464	SO:0001583	missense	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.1312G>A	4.37:g.113352015G>A	ENSP00000398048:p.Glu438Lys		113571464	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	g	0.013	-1.618513	0.00828	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.36699	1.24;1.24;1.24	5.72	-1.59	0.08453	.	0.455087	0.24321	N	0.039556	T	0.04634	0.0126	N	0.00116	-2.08	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34950	-0.9808	10	0.02654	T	1	-3.2445	2.7251	0.05211	0.4051:0.3539:0.1273:0.1137	.	360;360;438	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	K	438;438;360	ENSP00000398048:E438K;ENSP00000177648:E438K;ENSP00000426044:E360K	ENSP00000177648:E438K	E	+	1	0	ALPK1	113571464	0.000000	0.05858	0.005000	0.12908	0.110000	0.19582	0.347000	0.20014	-0.471000	0.06891	-0.285000	0.09966	GAG		0.413	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113352015	G	A	113352015	3	1	47	1	0	0	0	0	1	0	0	0	544	1059	37	1	1346	1	ALPK1	4	113352015	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2669311	113352015	77802261	591	4988										
LARP7	51574	broad.mit.edu	37	chr4	113568042	113568042	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtataccacattataagtcTactggagatccaaagggatt	8	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:113568042T>G	ENST00000344442.5	+	5	761	c.483T>G	c.(481-483)tcT>tcG	p.S161S	MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|MIR302B_ENST00000362188.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302C_ENST00000362232.1_RNA|MIR367_ENST00000362299.1_RNA|LARP7_ENST00000509061.1_Silent_p.S168S|MIR302A_ENST00000385192.1_RNA|LARP7_ENST00000324052.6_Silent_p.S161S	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	161	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S161S(1)		endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		ATTATAAGTCTACTGGAGATC	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	4											91	93	92					4																	113568042		1813	4083	5896	113787491	SO:0001819	synonymous_variant	51574			AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.483T>G	4.37:g.113568042T>G			113787491	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Silent	SNP	ENST00000344442.5	37	CCDS3701.2																																																																																				0.333	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		G	113568042	T	G	113568042	2	3	47	1	0	0	0	0	0	0	0	1	8655	1509	53	4		4	LARP7	4	113568042	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	216027	113568042	77586234	592	4989										
ANK2	287	broad.mit.edu	37	chr4	114232525	114232525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggatggtatgaattacctgcGatacagcttggagggaggac	15	6	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:114232525G>A	ENST00000357077.4	+	24	2716	c.2663G>A	c.(2662-2664)cGa>cAa	p.R888Q	ANK2_ENST00000506722.1_Missense_Mutation_p.R867Q|ANK2_ENST00000264366.6_Missense_Mutation_p.R888Q|ANK2_ENST00000509550.1_Missense_Mutation_p.R97Q|ANK2_ENST00000394537.3_Missense_Mutation_p.R888Q	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	888					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R888Q(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AATTACCTGCGATACAGCTTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											148	123	131					4																	114232525		2203	4300	6503	114451974	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2663G>A	4.37:g.114232525G>A	ENSP00000349588:p.Arg888Gln		114451974	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.078230	0.55753	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	T;T;T;T;T;T;T;T	0.77098	-0.2;-0.09;-0.28;-0.19;-0.31;-0.31;-0.38;-1.07	5.15	5.15	0.70609	.	0.000000	0.47852	D	0.000213	T	0.73481	0.3592	M	0.61703	1.905	0.80722	D	1	B;P;P;P;P;P	0.45902	0.414;0.868;0.599;0.868;0.844;0.681	B;B;B;B;B;B	0.36134	0.016;0.155;0.194;0.218;0.114;0.116	T	0.73827	-0.3860	10	0.23891	T	0.37	.	19.0034	0.92842	0.0:0.0:1.0:0.0	.	97;888;888;888;867;867	E9PCH6;Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	.;ANK2_HUMAN;.;.;.;.	Q	867;834;867;903;888;888;888;867;97	ENSP00000423799:R867Q;ENSP00000421011:R834Q;ENSP00000421067:R867Q;ENSP00000424722:R903Q;ENSP00000378044:R888Q;ENSP00000349588:R888Q;ENSP00000264366:R888Q;ENSP00000426944:R97Q	ENSP00000264366:R888Q	R	+	2	0	ANK2	114451974	1.000000	0.71417	0.956000	0.39512	0.997000	0.91878	9.299000	0.96137	2.547000	0.85894	0.655000	0.94253	CGA		0.428	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114232525	G	A	114232525	3	1	47	1	0	0	0	0	1	0	0	0	621	1058	37	1	2782	1	ANK2	4	114232525	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	664483	114232525	76921751	593	4990										
ANK2	287	broad.mit.edu	37	chr4	114238867	114238867	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgccaacctaccagccttCgatccttcagttccgacagg	7	17	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:114238867C>T	ENST00000357077.4	+	25	2751	c.2698C>T	c.(2698-2700)Cga>Tga	p.R900*	ANK2_ENST00000506722.1_Nonsense_Mutation_p.R879*|ANK2_ENST00000264366.6_Nonsense_Mutation_p.R900*|ANK2_ENST00000509550.1_Nonsense_Mutation_p.R109*|ANK2_ENST00000394537.3_Nonsense_Mutation_p.R900*	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	900					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R900*(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TACCAGCCTTCGATCCTTCAG	0.537																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											157	127	137					4																	114238867		2203	4300	6503	114458316	SO:0001587	stop_gained	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2698C>T	4.37:g.114238867C>T	ENSP00000349588:p.Arg900*		114458316	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Nonsense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	43	10.355041	0.99390	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	.	.	.	6.06	6.06	0.98353	.	0.000000	0.47093	D	0.000241	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	X	879;846;879;915;900;900;900;879;109	.	ENSP00000264366:R900X	R	+	1	2	ANK2	114458316	1.000000	0.71417	0.981000	0.43875	0.998000	0.95712	4.732000	0.62029	2.880000	0.98712	0.650000	0.86243	CGA		0.537	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114238867	C	T	114238867	4	4	47	1	0	0	0	0	0	1	0	0	621	876	31	1	2821	1	ANK2	4	114238867	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6342	114238867	76915409	594	4991										
ANK2	287	broad.mit.edu	37	chr4	114275856	114275856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacaagagaaaggtaaagttCgggtagaaaaagaaaagggg	14	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:114275856C>T	ENST00000357077.4	+	38	6135	c.6082C>T	c.(6082-6084)Cgg>Tgg	p.R2028W	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.R1995W|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2028					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R2028W(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AGGTAAAGTTCGGGTAGAAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											40	47	45					4																	114275856		2201	4298	6499	114495305	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6082C>T	4.37:g.114275856C>T	ENSP00000349588:p.Arg2028Trp		114495305	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397761	0.42512	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.68765	-0.34;-0.35	5.53	4.67	0.58626	.	0.129029	0.35013	N	0.003515	T	0.72120	0.3421	L	0.60455	1.87	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.56700	0.642;0.804	T	0.72154	-0.4376	9	.	.	.	.	11.0813	0.48062	0.129:0.8023:0.0:0.0687	.	1995;2028	Q01484;Q01484-4	ANK2_HUMAN;.	W	2028;1995	ENSP00000349588:R2028W;ENSP00000264366:R1995W	.	R	+	1	2	ANK2	114495305	0.053000	0.20554	0.073000	0.20177	0.268000	0.26511	1.651000	0.37302	1.407000	0.46875	0.563000	0.77884	CGG		0.463	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114275856	C	T	114275856	3	4	47	1	0	0	0	0	1	0	0	0	621	875	31	1	6297	1	ANK2	4	114275856	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36989	114275856	76878420	595	4992										
NDST3	9348	broad.mit.edu	37	chr4	118975587	118975587	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgagaagagtgtacagagCtttcagttaaaaggtttccc	11	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:118975587C>A	ENST00000296499.5	+	2	925	c.522C>A	c.(520-522)agC>agA	p.S174R	NDST3_ENST00000433996.2_Missense_Mutation_p.S174R	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	174	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.S174R(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						GTGTACAGAGCTTTCAGTTAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	68	68					4																	118975587		2203	4299	6502	119195035	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.522C>A	4.37:g.118975587C>A	ENSP00000296499:p.Ser174Arg		119195035	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940751	0.34283	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.46063	1.22;0.88	5.3	1.64	0.23874	.	0.271009	0.45361	D	0.000373	T	0.38321	0.1036	L	0.46157	1.445	0.35525	D	0.801768	B;B;P	0.49090	0.425;0.425;0.919	B;P;B	0.48227	0.31;0.571;0.414	T	0.42932	-0.9422	10	0.30854	T	0.27	.	8.5133	0.33231	0.0:0.5453:0.0:0.4547	.	174;174;174	B4DI67;O95803;O95803-2	.;NDST3_HUMAN;.	R	174	ENSP00000296499:S174R;ENSP00000396625:S174R	ENSP00000296499:S174R	S	+	3	2	NDST3	119195035	0.009000	0.17119	0.999000	0.59377	0.975000	0.68041	0.253000	0.18296	0.232000	0.21100	0.655000	0.94253	AGC		0.363	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		A	118975587	C	A	118975587	3	1	47	1	0	0	0	0	1	0	0	0	10288	796	28	2	524	2	NDST3	4	118975587	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4699731	118975587	72178689	596	4993										
METTL14	57721	broad.mit.edu	37	chr4	119615606	119615606	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaggtttagctgacagatTtgaagaatatcctaaactga	8	7	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:119615606T>G	ENST00000388822.5	+	6	595	c.428T>G	c.(427-429)tTt>tGt	p.F143C	METTL14_ENST00000506780.1_Missense_Mutation_p.F105C			Q9HCE5	MET14_HUMAN	methyltransferase like 14	143					mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)	p.F143C(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						GCTGACAGATTTGAAGAATAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											93	96	95					4																	119615606		2203	4300	6503	119835054	SO:0001583	missense	57721			AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.428T>G	4.37:g.119615606T>G	ENSP00000373474:p.Phe143Cys		119835054	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	37	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	N	21.4	4.140347	0.77775	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.77003	0.4067	M	0.64080	1.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	T	0.78692	-0.2105	9	0.59425	D	0.04	-1.7863	15.7609	0.78080	0.0:0.0:0.0:1.0	.	105;143	D6RBL4;Q9HCE5	.;MTL14_HUMAN	C	143;105	.	ENSP00000373474:F143C	F	+	2	0	METTL14	119835054	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.331000	0.79192	2.132000	0.65825	0.377000	0.23210	TTT		0.343	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		G	119615606	T	G	119615606	3	3	47	1	0	0	0	0	1	0	0	0	9528	1841	64	4	450	4	METTL14	4	119615606	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	640019	119615606	71538670	597	4994										
C4orf31	79625	broad.mit.edu	37	chr4	121957422	121957422	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctataagaaggtaactaAcagaactttctagttttcac	5	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:121957422A>G	ENST00000379692.4	-	4	2230	c.1704T>C	c.(1702-1704)tgT>tgC	p.C568C	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	568					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.C568C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						AAGGTAACTAACAGAACTTTC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	4											98	109	105					4																	121957422		2203	4300	6503	122176872	SO:0001819	synonymous_variant	79625			BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 31"	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.1704T>C	4.37:g.121957422A>G			122176872	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																				0.388	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574		G	121957422	A	G	121957422	2	3	47	1	0	0	0	0	0	0	0	1	2267	41	2	4		4	C4orf31	4	121957422	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2341816	121957422	69196854	598	4995										
TNIP3	79931	broad.mit.edu	37	chr4	122068308	122068308	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atccgatcgttcctttttgaAgtcttcttcgtatatttgca	6	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:122068308A>C	ENST00000509841.1	-	10	940	c.862T>G	c.(862-864)Ttc>Gtc	p.F288V	TNIP3_ENST00000511909.1_5'UTR|TNIP3_ENST00000507879.1_Missense_Mutation_p.F281V|TNIP3_ENST00000057513.3_Missense_Mutation_p.F211V|TNIP3_ENST00000454328.1_Missense_Mutation_p.F211V	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3									p.F211V(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						TCCTTTTTGAAGTCTTCTTCG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											177	173	174					4																	122068308		2203	4300	6503	122287758	SO:0001583	missense	79931			AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.862T>G	4.37:g.122068308A>C	ENSP00000426613:p.Phe288Val		122287758		Missense_Mutation	SNP	ENST00000509841.1	37	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202252	0.79127	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	D	0.98406	0.9470	M	0.84326	2.69	0.36819	D	0.886293	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.99968	1.1908	10	0.87932	D	0	-10.7028	15.4209	0.75009	1.0:0.0:0.0:0.0	.	281;211	B4DVF5;Q96KP6	.;TNIP3_HUMAN	V	211;211;281;288	ENSP00000057513:F211V;ENSP00000411817:F211V;ENSP00000427106:F281V;ENSP00000426613:F288V	ENSP00000057513:F211V	F	-	1	0	TNIP3	122287758	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.275000	0.72594	2.053000	0.61076	0.460000	0.39030	TTC		0.363	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		C	122068308	A	C	122068308	3	2	47	1	0	0	0	0	1	0	0	0	16355	72	3	4	366	4	TNIP3	4	122068308	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	110886	122068308	69085968	599	4996										
KIAA1109	84162	broad.mit.edu	37	chr4	123122189	123122189	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcaatgccagctacccccGaatatggaacatgccgcaga	8	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:123122189G>A	ENST00000264501.4	+	15	1779	c.1406G>A	c.(1405-1407)cGa>cAa	p.R469Q	KIAA1109_ENST00000388738.3_Missense_Mutation_p.R469Q|KIAA1109_ENST00000455637.1_Missense_Mutation_p.R469Q|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	469					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R469Q(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGCTACCCCCGAATATGGAAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	85	87					4																	123122189		1904	4133	6037	123341639	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1406G>A	4.37:g.123122189G>A	ENSP00000264501:p.Arg469Gln		123341639	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	33	5.213652	0.95069	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	D;D;D	0.93953	-3.32;-3.32;-3.32	5.93	5.93	0.95920	.	0.177349	0.35495	U	0.003167	D	0.94994	0.8380	L	0.47716	1.5	0.45733	D	0.998639	D	0.89917	1.0	P	0.59546	0.859	D	0.94362	0.7588	10	0.51188	T	0.08	.	20.3465	0.98790	0.0:0.0:1.0:0.0	.	469	Q2LD37	K1109_HUMAN	Q	469	ENSP00000264501:R469Q;ENSP00000373390:R469Q;ENSP00000389925:R469Q	ENSP00000264501:R469Q	R	+	2	0	KIAA1109	123341639	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	7.749000	0.85096	2.798000	0.96311	0.655000	0.94253	CGA		0.378	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123122189	G	A	123122189	3	1	47	1	0	0	0	0	1	0	0	0	8229	1058	37	1	1456	1	KIAA1109	4	123122189	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1053881	123122189	68032087	600	4997										
KIAA1109	84162	broad.mit.edu	37	chr4	123283194	123283194	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttattttagattaatttCttggactggaagaaagattg	8	2	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:123283194C>A	ENST00000264501.4	+	86	15183	c.14810C>A	c.(14809-14811)tCt>tAt	p.S4937Y	KIAA1109_ENST00000388738.3_Missense_Mutation_p.S4937Y			Q2LD37	K1109_HUMAN	KIAA1109	4937					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S4937Y(2)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGATTAATTTCTTGGACTGGA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	4											70	69	69					4																	123283194		1799	4069	5868	123502644	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14810C>A	4.37:g.123283194C>A	ENSP00000264501:p.Ser4937Tyr		123502644	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.035433|4.035433	0.75617|0.75617	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	.|T;T;T	.|0.52526	.|0.66;0.66;0.66	5.12|5.12	5.12|5.12	0.69794|0.69794	.|Fragile site-associated protein, C-terminal (1);	.|0.055003	.|0.85682	.|D	.|0.000000	T|T	0.70202|0.70202	0.3197|0.3197	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|D;D	.|0.69078	.|0.994;0.997	.|D;D	.|0.83275	.|0.967;0.996	T|T	0.74074|0.74074	-0.3782|-0.3782	5|10	.|0.72032	.|D	.|0.01	.|.	18.5514|18.5514	0.91066|0.91066	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|4936;4937	.|Q2LD37-4;Q2LD37	.|.;K1109_HUMAN	I|Y	1313|4937;4937;1606;538	.|ENSP00000264501:S4937Y;ENSP00000373390:S4937Y;ENSP00000410874:S1606Y	.|ENSP00000264501:S4937Y	L|S	+|+	1|2	0|0	KIAA1109|KIAA1109	123502644|123502644	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	7.673000|7.673000	0.83973|0.83973	2.407000|2.407000	0.81776|0.81776	0.591000|0.591000	0.81541|0.81541	CTT|TCT		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123283194	C	A	123283194	3	1	47	1	0	0	0	0	1	0	0	0	8229	913	32	2	15144	2	KIAA1109	4	123283194	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	161005	123283194	67871082	601	4998										
ADAD1	132612	broad.mit.edu	37	chr4	123317451	123317451	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatttcacagatcgttaaaGaaagatttaatcaactaatt	5	5	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:123317451G>T	ENST00000296513.2	+	7	828	c.643G>T	c.(643-645)Gaa>Taa	p.E215*	ADAD1_ENST00000388724.2_Nonsense_Mutation_p.E215*|ADAD1_ENST00000492454.1_3'UTR|ADAD1_ENST00000388725.2_Nonsense_Mutation_p.E197*	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	215					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.E215*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GATCGTTAAAGAAAGATTTAA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											59	66	63					4																	123317451		2201	4290	6491	123536901	SO:0001587	stop_gained	132612			AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.643G>T	4.37:g.123317451G>T	ENSP00000296513:p.Glu215*		123536901	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Nonsense_Mutation	SNP	ENST00000296513.2	37	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	G	32	5.171155	0.94807	.	.	ENSG00000164113	ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	.	.	.	6.05	6.05	0.98169	.	0.335080	0.34484	N	0.003933	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-16.7019	19.3801	0.94529	0.0:0.0:1.0:0.0	.	.	.	.	X	215;215;215;197	.	ENSP00000296513:E215X	E	+	1	0	ADAD1	123536901	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.948000	0.49066	2.880000	0.98712	0.655000	0.94253	GAA		0.323	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		T	123317451	G	T	123317451	4	4	47	1	0	0	0	0	0	1	0	0	231	943	33	2	661	2	ADAD1	4	123317451	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	34257	123317451	67836825	602	4999										
ANKRD50	57182	broad.mit.edu	37	chr4	125592877	125592877	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctctttctaaggcttgtcGaactatgcatgatgtgcgat	9	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:125592877G>A	ENST00000504087.1	-	4	2592	c.1555C>T	c.(1555-1557)Cga>Tga	p.R519*	ANKRD50_ENST00000515641.1_Nonsense_Mutation_p.R340*	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	519								p.R519*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						AAGGCTTGTCGAACTATGCAT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											116	111	113					4																	125592877		2203	4300	6503	125812327	SO:0001587	stop_gained	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1555C>T	4.37:g.125592877G>A	ENSP00000425658:p.Arg519*		125812327	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Nonsense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	G	46	12.320697	0.99657	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	.	.	.	4.74	3.88	0.44766	.	0.079809	0.49305	D	0.000148	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	13.4277	0.61035	0.0:0.0:0.618:0.3819	.	.	.	.	X	519;340	.	ENSP00000425658:R519X	R	-	1	2	ANKRD50	125812327	1.000000	0.71417	0.996000	0.52242	0.932000	0.56968	3.909000	0.56363	1.183000	0.42943	0.555000	0.69702	CGA		0.418	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		A	125592877	G	A	125592877	4	1	47	1	0	0	0	0	0	1	0	0	677	1066	37	1	2738	1	ANKRD50	4	125592877	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2275426	125592877	65561399	603	5000										
FAT4	79633	broad.mit.edu	37	chr4	126389779	126389779	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttatgtcaaatttgccacGattaaaagtcatgccttatt	5	7	2	0	rs368157923		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:126389779G>A	ENST00000394329.3	+	11	12025	c.12012G>A	c.(12010-12012)acG>acA	p.T4004T	FAT4_ENST00000335110.5_Silent_p.T2267T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4004	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T4004T(1)|p.T3969T(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AATTTGCCACGATTAAAAGTC	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	4						G		0,4406		0,0,2203	75	74	74		12012	-6.9	0.8	4		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAT4	NM_024582.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		4004/4982	126389779	1,13005	2203	4300	6503	126609229	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12012G>A	4.37:g.126389779G>A			126609229	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126389779	G	A	126389779	2	1	47	1	0	0	0	0	0	0	0	1	5711	1045	37	1		1	FAT4	4	126389779	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	796902	126389779	64764497	604	5001										
FAT4	79633	broad.mit.edu	37	chr4	126412823	126412823	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatgtagatgtttttaaagAtttggcatctcttccagaaa	7	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:126412823A>C	ENST00000394329.3	+	17	14859	c.14846A>C	c.(14845-14847)gAt>gCt	p.D4949A	FAT4_ENST00000335110.5_Missense_Mutation_p.D3190A	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4949					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D4949A(1)|p.D4892A(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GTTTTTAAAGATTTGGCATCT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	4											50	51	51					4																	126412823		2203	4300	6503	126632273	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.14846A>C	4.37:g.126412823A>C	ENSP00000377862:p.Asp4949Ala		126632273	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	14.70	2.612573	0.46631	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	D;D	0.88431	-2.13;-2.38	4.98	4.98	0.66077	.	0.000000	0.35378	U	0.003259	D	0.93749	0.8002	M	0.75777	2.31	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.998	D	0.94442	0.7659	10	0.87932	D	0	.	13.8827	0.63691	1.0:0.0:0.0:0.0	.	3190;4949;4948	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	A	4949;3190	ENSP00000377862:D4949A;ENSP00000335169:D3190A	ENSP00000335169:D3190A	D	+	2	0	FAT4	126632273	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.145000	0.94634	1.877000	0.54381	0.397000	0.26171	GAT		0.473	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126412823	A	C	126412823	3	2	47	1	0	0	0	0	1	0	0	0	5711	333	12	4	14912	4	FAT4	4	126412823	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	23044	126412823	64741453	605	5002										
HSPA4L	22824	broad.mit.edu	37	chr4	128719816	128719816	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgttagccaagcttaaagaGacttcagaaaatgctttgaa	8	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:128719816G>T	ENST00000296464.4	+	4	792	c.381G>T	c.(379-381)gaG>gaT	p.E127D	HSPA4L_ENST00000439123.2_Missense_Mutation_p.E158D|HSPA4L_ENST00000508776.1_Missense_Mutation_p.E127D|HSPA4L_ENST00000505726.1_Missense_Mutation_p.E101D	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	127					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.E127D(1)		central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AGCTTAAAGAGACTTCAGAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											142	142	142					4																	128719816		2203	4300	6503	128939266	SO:0001583	missense	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.381G>T	4.37:g.128719816G>T	ENSP00000296464:p.Glu127Asp		128939266	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945888	0.53079	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000505726	T;T;T;T	0.01092	5.35;5.35;5.35;5.35	4.59	2.88	0.33553	.	0.124348	0.53938	D	0.000058	T	0.02848	0.0085	L	0.35793	1.09	0.41159	D	0.986088	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.64546	-0.6382	10	0.30078	T	0.28	.	8.2931	0.31969	0.2408:0.0:0.7592:0.0	.	101;127	E9PDE8;O95757	.;HS74L_HUMAN	D	127;158;127;101	ENSP00000422482:E127D;ENSP00000393926:E158D;ENSP00000296464:E127D;ENSP00000425645:E101D	ENSP00000296464:E127D	E	+	3	2	HSPA4L	128939266	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.828000	0.48120	0.583000	0.29574	-0.145000	0.13849	GAG		0.363	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		T	128719816	G	T	128719816	3	4	47	1	0	0	0	0	1	0	0	0	7434	933	33	2	395	2	HSPA4L	4	128719816	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2306993	128719816	62434460	606	5003										
SCLT1	132320	broad.mit.edu	37	chr4	129857970	129857970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caattgaacttcaaatccacGttcctttattgaaaattcat	3	9	2	2	rs201434760		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:129857970G>A	ENST00000281142.5	-	18	2172	c.1669C>T	c.(1669-1671)Cgt>Tgt	p.R557C	SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000503215.1_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	557					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)	p.R557C(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TCAAATCCACGTTCCTTTATT	0.343													G|||	1	0.000199681	0	0	5008	,	,		18048	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	4											83	74	77					4																	129857970		2203	4300	6503	130077420	SO:0001583	missense	132320			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1669C>T	4.37:g.129857970G>A	ENSP00000281142:p.Arg557Cys		130077420	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	12.51	1.960191	0.34565	.	.	ENSG00000151466	ENST00000281142	T	0.51325	0.71	4.85	4.85	0.62838	.	0.363123	0.32819	N	0.005617	T	0.29684	0.0741	N	0.14661	0.345	0.80722	D	1	P	0.49447	0.924	B	0.36885	0.235	T	0.10636	-1.0621	9	.	.	.	-1.6181	17.9433	0.89031	0.0:0.0:1.0:0.0	.	557	Q96NL6	SCLT1_HUMAN	C	557	ENSP00000281142:R557C	.	R	-	1	0	SCLT1	130077420	1.000000	0.71417	0.948000	0.38648	0.043000	0.13939	6.060000	0.71141	2.403000	0.81681	0.591000	0.81541	CGT		0.343	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		A	129857970	G	A	129857970	3	1	47	1	0	0	0	0	1	0	0	0	13943	1145	40	1	413	1	SCLT1	4	129857970	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1138154	129857970	61296306	607	5004										
SCLT1	132320	broad.mit.edu	37	chr4	129913325	129913325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcatttttgaaaatacctaAgtttttttcggagttgttcg	7	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:129913325A>C	ENST00000281142.5	-	9	1186	c.683T>G	c.(682-684)cTt>cGt	p.L228R	SCLT1_ENST00000434680.1_Missense_Mutation_p.L228R|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000503215.1_Missense_Mutation_p.L205R	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	228					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)	p.L228R(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						AAAATACCTAAGTTTTTTTCG	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	4											58	55	56					4																	129913325		2200	4292	6492	130132775	SO:0001583	missense	132320			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.683T>G	4.37:g.129913325A>C	ENSP00000281142:p.Leu228Arg		130132775	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.746150	0.49151	.	.	ENSG00000151466	ENST00000281142;ENST00000434680;ENST00000503215	T;T;T	0.09817	2.94;2.94;2.94	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.27489	0.0675	M	0.68952	2.095	0.52501	D	0.999951	D;D	0.76494	0.999;0.999	D;D	0.72075	0.976;0.938	T	0.00931	-1.1510	9	.	.	.	.	9.7744	0.40609	0.8457:0.0:0.0:0.1543	.	228;228	Q96NL6-2;Q96NL6	.;SCLT1_HUMAN	R	228;228;205	ENSP00000281142:L228R;ENSP00000401539:L228R;ENSP00000424029:L205R	.	L	-	2	0	SCLT1	130132775	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	2.980000	0.49321	1.976000	0.57569	0.528000	0.53228	CTT		0.318	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		C	129913325	A	C	129913325	3	2	47	1	0	0	0	0	1	0	0	0	13943	72	3	4	1435	4	SCLT1	4	129913325	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	55355	129913325	61240951	608	5005										
PCDH10	57575	broad.mit.edu	37	chr4	134084132	134084132	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttctgttttctgcttacagGtatggatctcttctccaatt	6	9	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:134084132G>A	ENST00000264360.5	+	4	3624	c.2798G>A	c.(2797-2799)gGt>gAt	p.G933D		NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	933					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G933D(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		CTGCTTACAGGTATGGATCTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											144	121	128					4																	134084132		2203	4300	6503	134303582	SO:0001630	splice_region_variant	57575			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.2798-1G>A	4.37:g.134084132G>A			134303582	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.508795	0.44660	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.55760	0.5	4.94	4.94	0.65067	.	0.187789	0.25964	N	0.027167	T	0.44685	0.1305	N	0.05351	-0.065	0.58432	D	0.999997	D	0.57899	0.981	P	0.52109	0.69	T	0.40813	-0.9543	9	.	.	.	.	18.3153	0.90218	0.0:0.0:1.0:0.0	.	933	Q9P2E7	PCD10_HUMAN	D	933	ENSP00000264360:G933D	.	G	+	2	0	PCDH10	134303582	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	7.309000	0.78937	2.717000	0.92951	0.650000	0.86243	GGT		0.463	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	Missense_Mutation	A	134084132	G	A	134084132	5	1	47	1	0	0	0	0	0	0	1	0	11538	1275	44	3	2872	3	PCDH10	4	134084132	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4170807	134084132	57070144	609	5006										
PCDH18	54510	broad.mit.edu	37	chr4	138449934	138449934	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaacttggtcttggctgaTattgcccctggtgaagcatt	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:138449934T>C	ENST00000344876.4	-	2	2914	c.2528A>G	c.(2527-2529)tAt>tGt	p.Y843C	PCDH18_ENST00000510305.1_Missense_Mutation_p.Y54C|PCDH18_ENST00000511115.1_Missense_Mutation_p.Y23C|PCDH18_ENST00000507846.1_Missense_Mutation_p.Y622C|PCDH18_ENST00000412923.2_Missense_Mutation_p.Y842C	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	843					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y843C(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TCTTGGCTGATATTGCCCCTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											130	141	138					4																	138449934		2203	4300	6503	138669384	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2528A>G	4.37:g.138449934T>C	ENSP00000355082:p.Tyr843Cys		138669384	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.667949	0.88348	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305;ENST00000511115	T;T;T;T;T	0.55413	0.65;0.63;0.52;1.29;1.21	5.03	5.03	0.67393	.	0.000000	0.39475	N	0.001357	T	0.68165	0.2971	L	0.57536	1.79	0.80722	D	1	D;D;B;D	0.89917	1.0;0.999;0.161;0.998	D;P;B;P	0.81914	0.995;0.894;0.052;0.818	T	0.69371	-0.5163	10	0.49607	T	0.09	.	14.9405	0.70989	0.0:0.0:0.0:1.0	.	23;622;842;843	B4DLR6;D6RIG4;Q9HCL0-2;Q9HCL0	.;.;.;PCD18_HUMAN	C	843;842;622;54;23	ENSP00000355082:Y843C;ENSP00000390688:Y842C;ENSP00000425903:Y622C;ENSP00000424269:Y54C;ENSP00000425647:Y23C	ENSP00000355082:Y843C	Y	-	2	0	PCDH18	138669384	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.819000	0.86621	2.108000	0.64289	0.533000	0.62120	TAT		0.408	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		C	138449934	T	C	138449934	3	2	47	1	0	0	0	0	1	0	0	0	11544	1406	49	4	891	4	PCDH18	4	138449934	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	4365802	138449934	52704342	610	5007										
PCDH18	54510	broad.mit.edu	37	chr4	138452983	138452983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtcaattgtagcccctatgCtgatttccccattatcctcg	7	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:138452983C>A	ENST00000344876.4	-	1	646	c.260G>T	c.(259-261)aGc>aTc	p.S87I	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.S87I	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	87	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S87I(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					AGCCCCTATGCTGATTTCCCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											171	168	169					4																	138452983		2203	4300	6503	138672433	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.260G>T	4.37:g.138452983C>A	ENSP00000355082:p.Ser87Ile		138672433	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.611708	0.28712	.	.	ENSG00000189184	ENST00000344876;ENST00000412923	T;T	0.26518	1.73;1.73	5.96	5.07	0.68467	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.51477	U	0.000085	T	0.44456	0.1294	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.986;0.999	T	0.13019	-1.0525	10	0.13853	T	0.58	.	12.4034	0.55426	0.1318:0.7411:0.1272:0.0	.	87;87	Q9HCL0-2;Q9HCL0	.;PCD18_HUMAN	I	87	ENSP00000355082:S87I;ENSP00000390688:S87I	ENSP00000355082:S87I	S	-	2	0	PCDH18	138672433	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	4.797000	0.62503	2.831000	0.97527	0.650000	0.86243	AGC		0.433	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138452983	C	A	138452983	3	1	47	1	0	0	0	0	1	0	0	0	11544	797	28	2	3163	2	PCDH18	4	138452983	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3049	138452983	52701293	611	5008										
SMARCA5	8467	broad.mit.edu	37	chr4	144447611	144447611	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgataggagataaagaacaaAgagtaagtttctagtatttc	9	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:144447611A>C	ENST00000283131.3	+	6	1261	c.799A>C	c.(799-801)Aga>Cga	p.R267R		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	267	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R267R(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					TAAAGAACAAAGAGTAAGTTT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	4											74	79	77					4																	144447611		2203	4300	6503	144667061	SO:0001819	synonymous_variant	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.799A>C	4.37:g.144447611A>C			144667061		Silent	SNP	ENST00000283131.3	37	CCDS3761.1																																																																																				0.358	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			C	144447611	A	C	144447611	2	2	47	1	0	0	0	0	0	0	0	1	14808	64	3	4		4	SMARCA5	4	144447611	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	5994628	144447611	46706665	612	5009										
GYPE	2996	broad.mit.edu	37	chr4	144797948	144797948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaagatgatcattccaacaAcaacaagcatcacctcaaaa	3	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:144797948A>G	ENST00000358615.4	-	3	248	c.197T>C	c.(196-198)gTt>gCt	p.V66A	GYPE_ENST00000437468.2_Missense_Mutation_p.V66A	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	66						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V66A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					CATTCCAACAACAACAAGCAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											123	117	119					4																	144797948		2002	4206	6208	145017398	SO:0001583	missense	2996				CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"Blood group antigens"	4705	protein-coding gene	gene with protein product		138590	"glycophorin E"				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.197T>C	4.37:g.144797948A>G	ENSP00000351430:p.Val66Ala		145017398	D3DNZ5	Missense_Mutation	SNP	ENST00000358615.4	37	CCDS47138.1	.	.	.	.	.	.	.	.	.	.	A	10.06	1.247999	0.22880	.	.	ENSG00000197465	ENST00000358615;ENST00000437468	T;T	0.04654	3.58;3.58	1.8	1.8	0.24995	.	.	.	.	.	T	0.03053	0.0090	.	.	.	0.09310	N	1	P	0.39424	0.673	B	0.26614	0.071	T	0.43015	-0.9417	8	0.87932	D	0	.	5.6804	0.17771	1.0:0.0:0.0:0.0	.	66	P15421	GLPE_HUMAN	A	66	ENSP00000351430:V66A;ENSP00000400698:V66A	ENSP00000351430:V66A	V	-	2	0	GYPE	145017398	0.023000	0.18921	0.001000	0.08648	0.001000	0.01503	3.545000	0.53648	1.084000	0.41184	0.163000	0.16589	GTT		0.373	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364780.1	NM_002102		G	144797948	A	G	144797948	3	3	47	1	0	0	0	0	1	0	0	0	6932	43	2	4	43	4	GYPE	4	144797948	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	350337	144797948	46356328	613	5010										
PRMT10	90826	broad.mit.edu	37	chr4	148559835	148559835	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtatccaacctaatctcttCatcaaggtacatatgatacc	4	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:148559835C>A	ENST00000322396.6	-	12	2628	c.2386G>T	c.(2386-2388)Gaa>Taa	p.E796*	PRMT10_ENST00000541232.1_Nonsense_Mutation_p.E683*|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		796	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)	p.E796*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						CTAATCTCTTCATCAAGGTAC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											87	79	82					4																	148559835		2203	4300	6503	148779285	SO:0001587	stop_gained	90826																														ENST00000322396.6:c.2386G>T	4.37:g.148559835C>A	ENSP00000314396:p.Glu796*		148779285	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Nonsense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	C	40	7.932973	0.98568	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	.	.	.	5.66	5.66	0.87406	.	0.452281	0.27072	N	0.021061	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-39.5649	19.7417	0.96234	0.0:1.0:0.0:0.0	.	.	.	.	X	796;683	.	ENSP00000314396:E796X	E	-	1	0	PRMT10	148779285	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.553000	0.53713	2.665000	0.90641	0.650000	0.86243	GAA		0.378	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			A	148559835	C	A	148559835	4	1	47	1	0	0	0	0	0	1	0	0	12570	835	29	2	155	2	PRMT10	4	148559835	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3761887	148559835	42594441	614	5011										
LRBA	987	broad.mit.edu	37	chr4	151773687	151773687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaagaattagaggaaatagCcacagcttctattatgtcag	8	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:151773687C>T	ENST00000357115.3	-	23	3418	c.3175G>A	c.(3175-3177)Gct>Act	p.A1059T	LRBA_ENST00000510413.1_Missense_Mutation_p.A1059T|LRBA_ENST00000535741.1_Missense_Mutation_p.A1059T|LRBA_ENST00000507224.1_Missense_Mutation_p.A1059T	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1059						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.A1059T(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GAGGAAATAGCCACAGCTTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	88	89					4																	151773687		2203	4300	6503	151993137	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3175G>A	4.37:g.151773687C>T	ENSP00000349629:p.Ala1059Thr		151993137	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.270291	0.00257	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.54479	0.98;1.14;0.99;0.57	5.25	2.83	0.33086	.	2.433590	0.01553	N	0.019774	T	0.26122	0.0637	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.33394	-0.9870	10	0.09843	T	0.71	.	7.3616	0.26750	0.0:0.3651:0.0:0.6349	.	1059;1059	P50851;P50851-2	LRBA_HUMAN;.	T	1059	ENSP00000446299:A1059T;ENSP00000421552:A1059T;ENSP00000349629:A1059T;ENSP00000422180:A1059T	ENSP00000349629:A1059T	A	-	1	0	LRBA	151993137	0.005000	0.15991	0.024000	0.17045	0.083000	0.17756	0.596000	0.24044	0.191000	0.20236	-0.254000	0.11334	GCT		0.383	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151773687	C	T	151773687	3	4	47	1	0	0	0	0	1	0	0	0	8960	739	26	3	5560	3	LRBA	4	151773687	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3213852	151773687	39380589	615	5012										
FBXW7	55294	broad.mit.edu	37	chr4	153332915	153332915	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctcagagagcctccagttCgtcgtcttttgctgcccaca	8	15	2	1	rs200698994		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:153332915C>T	ENST00000281708.4	-	2	1270	c.41G>A	c.(40-42)cGa>cAa	p.R14Q	FBXW7_ENST00000603841.1_Missense_Mutation_p.R14Q|FBXW7_ENST00000604872.1_Missense_Mutation_p.R14Q|FBXW7_ENST00000603548.1_Missense_Mutation_p.R14Q	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	14					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R14Q(4)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GCCTCCAGTTCGTCGTCTTTT	0.483			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	4	Substitution - Missense(4)	large_intestine(4)	4						C	GLN/ARG	0,4406		0,0,2203	87	76	80		41	5.7	1	4		80	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FBXW7	NM_033632.2	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	14/708	153332915	2,13004	2203	4300	6503	153552365	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.41G>A	4.37:g.153332915C>T	ENSP00000281708:p.Arg14Gln		153552365	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396739	0.42512	0.0	2.33E-4	ENSG00000109670	ENST00000281708	T	0.62105	0.05	5.67	5.67	0.87782	.	0.000000	0.53938	D	0.000060	T	0.53658	0.1810	N	0.24115	0.695	0.80722	D	1	D;B	0.55800	0.973;0.029	B;B	0.43950	0.437;0.002	T	0.51529	-0.8694	10	0.28530	T	0.3	-4.8228	19.7677	0.96349	0.0:1.0:0.0:0.0	.	14;14	G0Z2K0;Q969H0	.;FBXW7_HUMAN	Q	14	ENSP00000281708:R14Q	ENSP00000281708:R14Q	R	-	2	0	FBXW7	153552365	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.507000	0.66999	2.668000	0.90789	0.650000	0.86243	CGA		0.483	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153332915	C	T	153332915	3	4	47	1	0	0	0	0	1	0	0	0	5788	884	31	1	2542	1	FBXW7	4	153332915	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1559228	153332915	37821361	616	5013										
TMEM154	201799	broad.mit.edu	37	chr4	153573888	153573888	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaaagtaagaggaccaataAaatcaatgggattaacacca	7	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:153573888A>C	ENST00000304385.3	-	2	487	c.256T>G	c.(256-258)Tta>Gta	p.L86V	TMEM154_ENST00000504064.1_Missense_Mutation_p.L86V	NM_152680.2	NP_689893.1	Q6P9G4	TM154_HUMAN	transmembrane protein 154	86						integral component of membrane (GO:0016021)		p.L86V(1)		kidney(2)|large_intestine(1)	3	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				AGGACCAATAAAATCAATGGG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	4											105	106	105					4																	153573888		2203	4300	6503	153793338	SO:0001583	missense	201799			AK056590	CCDS3779.1	4q31.3	2008-02-05			ENSG00000170006	ENSG00000170006			26489	protein-coding gene	gene with protein product						12477932	Standard	NM_152680		Approved	FLJ32028	uc003imw.2	Q6P9G4	OTTHUMG00000161463	ENST00000304385.3:c.256T>G	4.37:g.153573888A>C	ENSP00000302144:p.Leu86Val		153793338	Q8WUT7|Q96MQ8	Missense_Mutation	SNP	ENST00000304385.3	37	CCDS3779.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.403424	0.42613	.	.	ENSG00000170006	ENST00000304385;ENST00000504064	T;T	0.38560	1.13;1.13	6.01	2.33	0.28932	.	0.749683	0.11718	N	0.536181	T	0.42086	0.1187	L	0.44542	1.39	0.09310	N	1	D	0.61697	0.99	P	0.55011	0.766	T	0.18461	-1.0336	10	0.25106	T	0.35	-14.7236	4.3458	0.11133	0.6445:0.1808:0.1747:0.0	.	86	Q6P9G4	TM154_HUMAN	V	86	ENSP00000302144:L86V;ENSP00000422156:L86V	ENSP00000302144:L86V	L	-	1	2	TMEM154	153793338	0.006000	0.16342	0.001000	0.08648	0.364000	0.29643	1.087000	0.30865	0.522000	0.28464	0.524000	0.50904	TTA		0.313	TMEM154-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365024.1	NM_152680		C	153573888	A	C	153573888	3	2	47	1	0	0	0	0	1	0	0	0	16110	11	1	4	319	4	TMEM154	4	153573888	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	240973	153573888	37580388	617	5014										
KIAA0922	23240	broad.mit.edu	37	chr4	154533547	154533547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaacaggacatacctttcGtagaggtctgtatttttttt	8	6	1	2	rs150625995	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:154533547G>A	ENST00000409663.3	+	26	3611	c.3559G>A	c.(3559-3561)Gta>Ata	p.V1187I	KIAA0922_ENST00000440693.1_Missense_Mutation_p.V1104I|KIAA0922_ENST00000409959.3_Missense_Mutation_p.V1188I	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1187						integral component of membrane (GO:0016021)		p.V1040I(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CATACCTTTCGTAGAGGTCTG	0.323													G|||	2	0.000399361	0	0	5008	,	,		18818	0.001		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	55	57	56		3562,3559	-0.8	0	4	dbSNP_134	56	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	29,29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	1188/1611,1187/1610	154533547	1,13003	2203	4299	6502	154752997	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3559G>A	4.37:g.154533547G>A	ENSP00000386574:p.Val1187Ile		154752997	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.112	-1.136766	0.01742	0.0	1.16E-4	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.19394	2.43;2.15;2.43;2.15	5.62	-0.759	0.11045	.	0.988438	0.08244	N	0.975733	T	0.07503	0.0189	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.26120	0.142;0.004;0.002	B;B;B	0.21151	0.033;0.001;0.001	T	0.37337	-0.9710	10	0.15952	T	0.53	0.1039	2.5519	0.04750	0.2147:0.3377:0.3315:0.1161	.	1104;1188;1187	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	I	1187;1104;1188;965	ENSP00000386574:V1187I;ENSP00000409663:V1104I;ENSP00000386787:V1188I;ENSP00000240487:V965I	ENSP00000240487:V965I	V	+	1	0	KIAA0922	154752997	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	-0.426000	0.07008	-0.190000	0.10465	-0.252000	0.11476	GTA		0.323	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154533547	G	A	154533547	3	1	47	1	0	0	0	0	1	0	0	0	8222	1145	40	1	3664	1	KIAA0922	4	154533547	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	959659	154533547	36620729	618	5015										
KIAA0922	23240	broad.mit.edu	37	chr4	154557596	154557596	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacatggaaaaccaagcggtCgtgtgcaaggaatactaccc	10	11	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:154557596C>T	ENST00000409663.3	+	35	4750	c.4698C>T	c.(4696-4698)gtC>gtT	p.V1566V	KIAA0922_ENST00000440693.1_Silent_p.V1483V|KIAA0922_ENST00000409959.3_Silent_p.V1567V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1566						integral component of membrane (GO:0016021)		p.V1419V(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				ACCAAGCGGTCGTGTGCAAGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	4											101	99	100					4																	154557596		2203	4300	6503	154777046	SO:0001819	synonymous_variant	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.4698C>T	4.37:g.154557596C>T			154777046	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																				0.507	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		T	154557596	C	T	154557596	2	4	47	1	0	0	0	0	0	0	0	1	8222	871	31	1		1	KIAA0922	4	154557596	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	24049	154557596	36596680	619	5016										
TLR2	7097	broad.mit.edu	37	chr4	154624559	154624559	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccttcactaagattcaaaGaaaagattttgctggactta	6	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:154624559G>T	ENST00000260010.6	+	1	1908	c.500G>T	c.(499-501)aGa>aTa	p.R167I		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	167					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)	p.R167I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	AAGATTCAAAGAAAAGATTTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											77	80	79					4																	154624559		2203	4300	6503	154844009	SO:0001583	missense	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.500G>T	4.37:g.154624559G>T	ENSP00000260010:p.Arg167Ile		154844009	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.756972	0.31137	.	.	ENSG00000137462	ENST00000260010	D	0.90069	-2.61	5.51	1.05	0.20165	.	0.735756	0.12961	N	0.424983	T	0.80899	0.4712	L	0.27053	0.805	0.40553	D	0.981135	B	0.18741	0.03	B	0.12156	0.007	T	0.71115	-0.4686	10	0.72032	D	0.01	.	8.9942	0.36041	0.5616:0.0:0.4384:0.0	.	167	O60603	TLR2_HUMAN	I	167	ENSP00000260010:R167I	ENSP00000260010:R167I	R	+	2	0	TLR2	154844009	0.978000	0.34361	0.502000	0.27614	0.966000	0.64601	2.426000	0.44731	0.007000	0.14760	0.655000	0.94253	AGA		0.373	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			T	154624559	G	T	154624559	3	4	47	1	0	0	0	0	1	0	0	0	15990	942	33	2	502	2	TLR2	4	154624559	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	66963	154624559	36529717	620	5017										
DCHS2	54798	broad.mit.edu	37	chr4	155219346	155219346	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaacacatcaaaagggttCtgttccaaaactggatcatt	7	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:155219346C>A	ENST00000357232.4	-	18	4754	c.4755G>T	c.(4753-4755)caG>caT	p.Q1585H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1585	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q1585H(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAAAAGGGTTCTGTTCCAAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											103	102	102					4																	155219346		2203	4300	6503	155438796	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4755G>T	4.37:g.155219346C>A	ENSP00000349768:p.Gln1585His		155438796	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723223	0.48728	.	.	ENSG00000197410	ENST00000357232	T	0.62105	0.05	5.66	3.93	0.45458	Cadherin (2);Cadherin-like (1);	0.170574	0.40818	N	0.001002	T	0.73999	0.3659	M	0.79926	2.475	0.80722	D	1	D	0.65815	0.995	P	0.57371	0.819	T	0.73633	-0.3921	10	0.49607	T	0.09	.	11.2418	0.48974	0.0:0.7364:0.0:0.2636	.	1585	Q6V1P9	PCD23_HUMAN	H	1585	ENSP00000349768:Q1585H	ENSP00000349768:Q1585H	Q	-	3	2	DCHS2	155438796	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	1.237000	0.32695	0.434000	0.26340	-0.813000	0.03139	CAG		0.463	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155219346	C	A	155219346	3	1	47	1	0	0	0	0	1	0	0	0	4294	912	32	2	4027	2	DCHS2	4	155219346	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	594787	155219346	35934930	621	5018										
RBM46	166863	broad.mit.edu	37	chr4	155720248	155720248	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagctaaaccagtaaataaaGaaaacacttggagacagcat	7	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:155720248G>T	ENST00000281722.3	+	4	1169	c.934G>T	c.(934-936)Gaa>Taa	p.E312*	RBM46_ENST00000510397.1_Nonsense_Mutation_p.E312*|RBM46_ENST00000514866.1_Nonsense_Mutation_p.E312*	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	312							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.E312*(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				AGTAAATAAAGAAAACACTTG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											74	74	74					4																	155720248		2203	4300	6503	155939698	SO:0001587	stop_gained	166863			BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.934G>T	4.37:g.155720248G>T	ENSP00000281722:p.Glu312*		155939698	B3KWU8|B4DZ27	Nonsense_Mutation	SNP	ENST00000281722.3	37	CCDS3790.1	.	.	.	.	.	.	.	.	.	.	G	38	6.652934	0.97734	.	.	ENSG00000151962	ENST00000514866;ENST00000281722;ENST00000510397	.	.	.	6.17	6.17	0.99709	.	0.152061	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.0662	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	312	.	ENSP00000281722:E312X	E	+	1	0	RBM46	155939698	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.369000	0.59511	2.941000	0.99782	0.655000	0.94253	GAA		0.388	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		T	155720248	G	T	155720248	4	4	47	1	0	0	0	0	0	1	0	0	13177	943	33	2	944	2	RBM46	4	155720248	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	500902	155720248	35434028	622	5019										
GUCY1B3	2983	broad.mit.edu	37	chr4	156716587	156716587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatcctttctcacatcaataCtgtttttgtattgagaagca	6	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:156716587C>T	ENST00000264424.8	+	7	903	c.821C>T	c.(820-822)aCt>aTt	p.T274I	GUCY1B3_ENST00000505154.1_Missense_Mutation_p.T206I|GUCY1B3_ENST00000507146.1_Missense_Mutation_p.T206I|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.T274I|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.T206I|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.T296I|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.T254I	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	274					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.T274I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		CACATCAATACTGTTTTTGTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											133	121	125					4																	156716587		1833	4093	5926	156936037	SO:0001583	missense	2983			AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.821C>T	4.37:g.156716587C>T	ENSP00000264424:p.Thr274Ile		156936037	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	37	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.539277	0.65085	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	5.77	5.77	0.91146	Haem NO binding associated (1);	0.045090	0.85682	D	0.000000	D	0.92727	0.7688	M	0.73962	2.25	0.80722	D	1	D;P;P;P;P	0.61697	0.99;0.885;0.599;0.919;0.813	P;P;B;P;P	0.53760	0.677;0.734;0.444;0.548;0.528	D	0.91965	0.5582	10	0.48119	T	0.1	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	254;296;206;274;274	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	I	206;296;254;206;274;274;206	ENSP00000427226:T206I;ENSP00000426786:T296I;ENSP00000426319:T254I;ENSP00000422313:T206I;ENSP00000264424:T274I;ENSP00000420842:T274I;ENSP00000425065:T206I	ENSP00000264424:T274I	T	+	2	0	GUCY1B3	156936037	1.000000	0.71417	0.607000	0.28956	0.226000	0.24999	7.283000	0.78640	2.885000	0.99019	0.655000	0.94253	ACT		0.373	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			T	156716587	C	T	156716587	3	4	47	1	0	0	0	0	1	0	0	0	6916	565	20	3	847	3	GUCY1B3	4	156716587	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	996339	156716587	34437689	623	5020										
GRIA2	2891	broad.mit.edu	37	chr4	158256990	158256990	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggccagggatgcagacacGaaaatttggaatgggatggt	17	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:158256990G>A	ENST00000264426.9	+	10	1713	c.1434G>A	c.(1432-1434)acG>acA	p.T478T	GRIA2_ENST00000449365.1_Silent_p.T431T|GRIA2_ENST00000507898.1_Silent_p.T431T|GRIA2_ENST00000296526.7_Silent_p.T478T|GRIA2_ENST00000393815.2_Silent_p.T431T	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	478					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.T478T(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ATGCAGACACGAAAATTTGGA	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	4											185	165	172					4																	158256990		2203	4300	6503	158476440	SO:0001819	synonymous_variant	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1434G>A	4.37:g.158256990G>A			158476440	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	37	CCDS43274.1																																																																																				0.423	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158256990	G	A	158256990	2	1	47	1	0	0	0	0	0	0	0	1	6789	1045	37	1		1	GRIA2	4	158256990	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1540403	158256990	32897286	624	5021										
GRIA2	2891	broad.mit.edu	37	chr4	158284078	158284078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcaagggccgaggcgaaacGaatgaaggtggcaaagaatg	16	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:158284078G>A	ENST00000264426.9	+	15	2813	c.2534G>A	c.(2533-2535)cGa>cAa	p.R845Q	AC079233.1_ENST00000578227.1_RNA|GRIA2_ENST00000449365.1_Missense_Mutation_p.R798Q|GRIA2_ENST00000507898.1_Missense_Mutation_p.R798Q|GRIA2_ENST00000296526.7_Missense_Mutation_p.R845Q|GRIA2_ENST00000393815.2_Missense_Mutation_p.R798Q	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	845					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R845Q(4)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAGGCGAAACGAATGAAGGTG	0.448																																																4	Substitution - Missense(4)	large_intestine(4)	4											151	135	140					4																	158284078		2203	4300	6503	158503528	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2534G>A	4.37:g.158284078G>A	ENSP00000264426:p.Arg845Gln		158503528	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567681	0.65651	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.15139	2.45;2.45;2.49;2.5;2.45	6.08	6.08	0.98989	.	0.069737	0.64402	D	0.000015	T	0.33177	0.0854	M	0.80982	2.52	0.80722	D	1	D;D;P	0.61697	0.99;0.97;0.76	P;P;B	0.45660	0.478;0.489;0.091	T	0.16394	-1.0404	10	0.66056	D	0.02	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	845;845;798	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	Q	798;798;845;845;798	ENSP00000426845:R798Q;ENSP00000377403:R798Q;ENSP00000296526:R845Q;ENSP00000264426:R845Q;ENSP00000389837:R798Q	ENSP00000264426:R845Q	R	+	2	0	GRIA2	158503528	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.004000	0.88535	2.894000	0.99253	0.591000	0.81541	CGA		0.448	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158284078	G	A	158284078	3	1	47	1	0	0	0	0	1	0	0	0	6789	1058	37	1	2711	1	GRIA2	4	158284078	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	27088	158284078	32870198	625	5022										
TMEM144	55314	broad.mit.edu	37	chr4	159133887	159133887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtagctatccttttgtttgGctcaaattttgtgccactta	7	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:159133887G>A	ENST00000296529.6	+	3	588	c.68G>A	c.(67-69)gGc>gAc	p.G23D	TMEM144_ENST00000509278.1_Missense_Mutation_p.G23D|TMEM144_ENST00000514558.1_Missense_Mutation_p.G23D	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	23						integral component of membrane (GO:0016021)		p.G23D(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CTTTTGTTTGGCTCAAATTTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											176	153	161					4																	159133887		2203	4300	6503	159353337	SO:0001583	missense	55314			AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.68G>A	4.37:g.159133887G>A	ENSP00000296529:p.Gly23Asp		159353337	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	37	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.705903	0.89018	.	.	ENSG00000164124	ENST00000505049;ENST00000505189;ENST00000508243;ENST00000296529;ENST00000512481;ENST00000504569;ENST00000509278;ENST00000514558;ENST00000503200;ENST00000502698;ENST00000514971	T;T;T;T;T;T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.87521	0.6198	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89683	0.3892	10	0.87932	D	0	-9.5555	18.3118	0.90203	0.0:0.0:1.0:0.0	.	23	Q7Z5S9	TM144_HUMAN	D	23	ENSP00000425266:G23D;ENSP00000421289:G23D;ENSP00000422297:G23D;ENSP00000296529:G23D;ENSP00000424659:G23D;ENSP00000422082:G23D;ENSP00000425815:G23D;ENSP00000426211:G23D;ENSP00000420990:G23D;ENSP00000425907:G23D;ENSP00000422899:G23D	ENSP00000296529:G23D	G	+	2	0	TMEM144	159353337	1.000000	0.71417	0.978000	0.43139	0.977000	0.68977	7.367000	0.79558	2.619000	0.88677	0.655000	0.94253	GGC		0.323	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		A	159133887	G	A	159133887	3	1	47	1	0	0	0	0	1	0	0	0	16097	1203	42	3	70	3	TMEM144	4	159133887	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	849809	159133887	32020389	626	5023										
PPID	5481	broad.mit.edu	37	chr4	159640400	159640400	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccacctgtcccattctgatTtgagaagtctccaccctgaa	6	14	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:159640400T>G	ENST00000307720.3	-	3	372	c.265A>C	c.(265-267)Aat>Cat	p.N89H		NM_005038.2	NP_005029.1	Q08752	PPID_HUMAN	peptidylprolyl isomerase D	89	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				apoptotic process (GO:0006915)|cellular response to UV-A (GO:0071492)|chaperone-mediated protein folding (GO:0061077)|lipid particle organization (GO:0034389)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|protein transport (GO:0015031)|viral release from host cell (GO:0019076)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|estrogen receptor binding (GO:0030331)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|transcription factor binding (GO:0008134)	p.N89H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)		CCATTCTGATTTGAGAAGTCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											85	86	86					4																	159640400		2203	4300	6503	159859850	SO:0001583	missense	5481				CCDS3801.1	4q31.3	2013-01-10	2008-10-24		ENSG00000171497	ENSG00000171497		"Tetratricopeptide (TTC) repeat domain containing"	9257	protein-coding gene	gene with protein product	"cyclophilin 40"	601753	"peptidylprolyl isomerase D (cyclophilin D)"			8509368	Standard	NM_005038		Approved	CYP-40	uc003iqc.3	Q08752	OTTHUMG00000161927	ENST00000307720.3:c.265A>C	4.37:g.159640400T>G	ENSP00000303754:p.Asn89His		159859850	B2R9V2	Missense_Mutation	SNP	ENST00000307720.3	37	CCDS3801.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.710318	0.48517	.	.	ENSG00000171497	ENST00000307720	T	0.22743	1.94	4.83	4.83	0.62350	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.000000	0.46442	D	0.000297	T	0.15696	0.0378	L	0.27053	0.805	0.80722	D	1	P	0.35628	0.513	B	0.32211	0.142	T	0.05321	-1.0892	10	0.41790	T	0.15	-28.3767	15.1104	0.72351	0.0:0.0:0.0:1.0	.	89	Q08752	PPID_HUMAN	H	89	ENSP00000303754:N89H	ENSP00000303754:N89H	N	-	1	0	PPID	159859850	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.897000	0.69831	2.113000	0.64589	0.459000	0.35465	AAT		0.333	PPID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366436.1	NM_005038		G	159640400	T	G	159640400	3	3	47	1	0	0	0	0	1	0	0	0	12355	1841	64	4	879	4	PPID	4	159640400	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	506513	159640400	31513876	627	5024										
FNIP2	57600	broad.mit.edu	37	chr4	159816947	159816947	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacaggagatgtaccttaaaAgtaaaatgctatctgaatat	7	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:159816947A>C	ENST00000264433.6	+	16	3271	c.3196A>C	c.(3196-3198)Agt>Cgt	p.S1066R	C4orf45_ENST00000434826.2_Intron|C4orf45_ENST00000508011.1_Intron|FNIP2_ENST00000379346.3_Missense_Mutation_p.S1089R	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1066					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S392R(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		GTACCTTAAAAGTAAAATGCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											144	143	143					4																	159816947		1911	4134	6045	160036397	SO:0001583	missense	57600			AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.3196A>C	4.37:g.159816947A>C	ENSP00000264433:p.Ser1066Arg		160036397	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099199	0.76983	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.51817	0.69;0.69	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77629	-0.2516	9	.	.	.	.	15.5709	0.76337	1.0:0.0:0.0:0.0	.	1066	Q9P278	FNIP2_HUMAN	R	1066;1089	ENSP00000264433:S1066R;ENSP00000368651:S1089R	.	S	+	1	0	FNIP2	160036397	1.000000	0.71417	0.140000	0.22221	0.513000	0.34164	9.281000	0.95811	2.099000	0.63709	0.482000	0.46254	AGT		0.438	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		C	159816947	A	C	159816947	3	2	47	1	0	0	0	0	1	0	0	0	5995	72	3	4	3258	4	FNIP2	4	159816947	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	176547	159816947	31337329	628	5025										
RAPGEF2	9693	broad.mit.edu	37	chr4	160264339	160264339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggatctcaccttccttcacGaaggtaaacataaggcagag	9	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:160264339G>A	ENST00000264431.4	+	15	3063	c.2644G>A	c.(2644-2646)Gaa>Aaa	p.E882K		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	882	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.E870K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CTTCCTTCACGAAGGTAAACA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	106	110					4																	160264339		1863	4102	5965	160483789	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2644G>A	4.37:g.160264339G>A	ENSP00000264431:p.Glu882Lys		160483789	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824567	0.90955	.	.	ENSG00000109756	ENST00000264431	T	0.38560	1.13	5.82	5.82	0.92795	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.88640	2.97	0.80722	D	1	D	0.71674	0.998	D	0.70227	0.968	T	0.71935	-0.4442	10	0.40728	T	0.16	.	20.0926	0.97825	0.0:0.0:1.0:0.0	.	882	Q9Y4G8	RPGF2_HUMAN	K	882	ENSP00000264431:E882K	ENSP00000264431:E882K	E	+	1	0	RAPGEF2	160483789	1.000000	0.71417	0.996000	0.52242	0.723000	0.41478	9.836000	0.99456	2.745000	0.94114	0.561000	0.74099	GAA		0.383	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		A	160264339	G	A	160264339	3	1	47	1	0	0	0	0	1	0	0	0	13081	1059	37	1	2702	1	RAPGEF2	4	160264339	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	447392	160264339	30889937	629	5026										
PALLD	23022	broad.mit.edu	37	chr4	169846212	169846212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggattgtgtcctgtactgCcaggctggacgtttacagtg	14	8	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:169846212C>T	ENST00000505667.1	+	20	3514	c.3341C>T	c.(3340-3342)gCc>gTc	p.A1114V	CBR4_ENST00000509108.1_Intron|PALLD_ENST00000507735.1_Missense_Mutation_p.A610V|PALLD_ENST00000335742.7_Missense_Mutation_p.A939V|PALLD_ENST00000512127.1_Missense_Mutation_p.A715V|PALLD_ENST00000261509.6_Missense_Mutation_p.A1097V			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1321					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)	p.A939V(1)|p.A1097V(1)		breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TCCTGTACTGCCAGGCTGGAC	0.443									Pancreatic Cancer, Familial Clustering of																												Esophageal Squamous(109;1482 1532 18347 40239 51172)											2	Substitution - Missense(2)	large_intestine(2)	4											132	125	128					4																	169846212		2203	4300	6503	170082787	SO:0001583	missense	23022	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.3341C>T	4.37:g.169846212C>T	ENSP00000425556:p.Ala1114Val		170082787	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	C	32	5.128543	0.94473	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000507735	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	5.6	5.6	0.85130	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.31897	U	0.006890	T	0.79347	0.4430	L	0.56280	1.765	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.998;0.999	T	0.75772	-0.3200	10	0.33940	T	0.23	.	19.6074	0.95586	0.0:1.0:0.0:0.0	.	1114;1321;715;1097	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	V	1097;939;1114;715;610	ENSP00000261509:A1097V;ENSP00000336735:A939V;ENSP00000425556:A1114V;ENSP00000426947:A715V;ENSP00000424016:A610V	ENSP00000261509:A1097V	A	+	2	0	PALLD	170082787	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	7.818000	0.86416	2.627000	0.88993	0.650000	0.86243	GCC		0.443	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		T	169846212	C	T	169846212	3	4	47	1	0	0	0	0	1	0	0	0	11438	739	26	3	3922	3	PALLD	4	169846212	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9581873	169846212	21308064	630	5027										
NEK1	4750	broad.mit.edu	37	chr4	170511900	170511900	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatttaatgtctcgatgaaGaatttttctatcatgtacat	6	5	3	3	rs56850122		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:170511900G>T	ENST00000439128.2	-	5	1013	c.373C>A	c.(373-375)Ctt>Att	p.L125I	NEK1_ENST00000510533.1_Missense_Mutation_p.L125I|NEK1_ENST00000511633.1_Missense_Mutation_p.L125I|NEK1_ENST00000512193.1_Missense_Mutation_p.L125I|NEK1_ENST00000507142.1_Missense_Mutation_p.L125I	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	125	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.L125I(2)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TCTCGATGAAGAATTTTTCTA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	4											88	81	83					4																	170511900		1823	4076	5899	170748475	SO:0001583	missense	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.373C>A	4.37:g.170511900G>T	ENSP00000408020:p.Leu125Ile		170748475	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.467462	0.84533	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000118	T	0.24431	0.0592	N	0.05467	-0.045	0.54753	D	0.999986	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.997;0.999;0.998;0.999;0.998;0.999	T	0.10941	-1.0608	10	0.62326	D	0.03	.	10.2101	0.43136	0.1253:0.0:0.8747:0.0	.	125;125;125;125;125;125	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	I	125	ENSP00000408020:L125I;ENSP00000423332:L125I;ENSP00000427653:L125I;ENSP00000424757:L125I;ENSP00000424938:L125I	ENSP00000408020:L125I	L	-	1	0	NEK1	170748475	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.728000	0.62000	2.540000	0.85666	0.591000	0.81541	CTT		0.358	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			T	170511900	G	T	170511900	3	4	47	1	0	0	0	0	1	0	0	0	10352	942	33	2	3523	2	NEK1	4	170511900	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	665688	170511900	20642376	631	5028										
GALNTL6	442117	broad.mit.edu	37	chr4	173873287	173873287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctccacgggggacatctctGcccagaaggagctgcgcaag	13	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:173873287G>A	ENST00000506823.1	+	10	1906	c.1249G>A	c.(1249-1251)Gcc>Acc	p.A417T	GALNTL6_ENST00000508122.1_Missense_Mutation_p.A400T	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	417					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A417T(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						GGACATCTCTGCCCAGAAGGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	4											57	60	59					4																	173873287		2203	4300	6503	174109862	SO:0001583	missense	442117				CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.1249G>A	4.37:g.173873287G>A	ENSP00000423313:p.Ala417Thr		174109862	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	37	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	g	13.98	2.399795	0.42512	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	T;T	0.68624	-0.34;-0.34	5.36	5.36	0.76844	.	0.076311	0.56097	D	0.000036	T	0.61299	0.2336	L	0.49699	1.58	0.58432	D	0.999995	B	0.12630	0.006	B	0.12156	0.007	T	0.57010	-0.7884	10	0.39692	T	0.17	.	14.3136	0.66432	0.0:0.0:0.8516:0.1484	.	417	Q49A17	GLTL6_HUMAN	T	417;400	ENSP00000423313:A417T;ENSP00000423827:A400T	ENSP00000423313:A417T	A	+	1	0	GALNTL6	174109862	1.000000	0.71417	0.975000	0.42487	0.823000	0.46562	4.596000	0.61055	2.668000	0.90789	0.478000	0.44815	GCC		0.572	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		A	173873287	G	A	173873287	3	1	47	1	0	0	0	0	1	0	0	0	6245	1319	46	3	1283	3	GALNTL6	4	173873287	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3361387	173873287	17280989	632	5029										
SCRG1	11341	broad.mit.edu	37	chr4	174312452	174312452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actccttccggaaggttgtgAcagttgtgatcttttagtat	10	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:174312452A>G	ENST00000296506.3	-	2	596	c.114T>C	c.(112-114)tgT>tgC	p.C38C		NM_007281.2	NP_009212.1	O75711	SCRG1_HUMAN	stimulator of chondrogenesis 1	38					nervous system development (GO:0007399)	extracellular space (GO:0005615)		p.C38C(1)		large_intestine(1)|lung(4)|skin(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.15e-17)|Epithelial(43;4.33e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.62e-09)|STAD - Stomach adenocarcinoma(60;0.00278)|GBM - Glioblastoma multiforme(59;0.00659)|LUSC - Lung squamous cell carcinoma(193;0.0919)		GAAGGTTGTGACAGTTGTGAT	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	4											233	208	216					4																	174312452		2203	4300	6503	174549027	SO:0001819	synonymous_variant	11341			AJ224677	CCDS3818.1	4q34.1	2009-07-09				ENSG00000164106			17036	protein-coding gene	gene with protein product	"scrapie responsive gene 1"	603163				9660755, 9516475	Standard	NM_007281		Approved	SCRG-1	uc003ite.3	O75711		ENST00000296506.3:c.114T>C	4.37:g.174312452A>G			174549027		Silent	SNP	ENST00000296506.3	37	CCDS3818.1																																																																																				0.453	SCRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364304.2	NM_007281		G	174312452	A	G	174312452	2	3	47	1	0	0	0	0	0	0	0	1	13973	273	10	4		4	SCRG1	4	174312452	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	439165	174312452	16841824	633	5030										
GLRA3	8001	broad.mit.edu	37	chr4	175564972	175564972	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgaatatcctcatgcctaaGaattttatagataacccagt	5	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:175564972G>T	ENST00000274093.3	-	10	1862	c.1360C>A	c.(1360-1362)Ctt>Att	p.L454I	GLRA3_ENST00000340217.5_Missense_Mutation_p.L439I	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	454					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.L454I(2)		endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		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)|Ivermectin(DB00602)|Lindane(DB00431)	TCATGCCTAAGAATTTTATAG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											87	96	93					4																	175564972		2203	4300	6503	175801547	SO:0001583	missense	8001			AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"Ligand-gated ion channels / Glycine receptors"	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.1360C>A	4.37:g.175564972G>T	ENSP00000274093:p.Leu454Ile		175801547	D3DP44|O75816|Q5D0E3	Missense_Mutation	SNP	ENST00000274093.3	37	CCDS3822.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167603	0.38315	.	.	ENSG00000145451	ENST00000274093;ENST00000340217	D;D	0.84370	-1.84;-1.84	5.87	5.87	0.94306	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.057478	0.64402	D	0.000001	T	0.71409	0.3336	N	0.20574	0.59	0.54753	D	0.999987	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.007	T	0.63932	-0.6525	10	0.02654	T	1	.	11.9178	0.52776	0.0:0.1225:0.7357:0.1418	.	439;454	O75311-2;O75311	.;GLRA3_HUMAN	I	454;439	ENSP00000274093:L454I;ENSP00000345284:L439I	ENSP00000274093:L454I	L	-	1	0	GLRA3	175801547	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.777000	0.55364	2.779000	0.95612	0.591000	0.81541	CTT		0.403	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1			T	175564972	G	T	175564972	3	4	47	1	0	0	0	0	1	0	0	0	6476	942	33	2	38	2	GLRA3	4	175564972	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1252520	175564972	15589304	634	5031										
GPM6A	2823	broad.mit.edu	37	chr4	176572986	176572986	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatccaatatccacttaccAaactgacgaaggtccaagca	6	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:176572986A>T	ENST00000280187.7	-	5	585	c.540T>A	c.(538-540)ttT>ttA	p.F180L	GPM6A_ENST00000515090.1_Splice_Site_p.F173L|GPM6A_ENST00000393658.2_Splice_Site_p.F180L|GPM6A_ENST00000506894.1_Splice_Site_p.F169L	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	180					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)	p.F180L(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TCCACTTACCAAACTGACGAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											133	128	130					4																	176572986		2203	4300	6503	176809980	SO:0001630	splice_region_variant	2823				CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.541+1T>A	4.37:g.176572986A>T			176809980	B7Z642|E9PHI5|Q92602	Missense_Mutation	SNP	ENST00000280187.7	37	CCDS3824.1	.	.	.	.	.	.	.	.	.	.	A	17.77	3.471607	0.63737	.	.	ENSG00000150625	ENST00000280187;ENST00000393658;ENST00000506894;ENST00000515090;ENST00000503397;ENST00000512610;ENST00000502754	D;D;D;D;D;D;D	0.99282	-5.68;-5.68;-5.68;-5.68;-5.68;-5.68;-5.68	5.62	0.497	0.16902	.	0.145170	0.64402	D	0.000004	D	0.97396	0.9148	L	0.48642	1.525	0.52099	D	0.999949	B;B;B	0.27286	0.174;0.055;0.055	B;B;B	0.29942	0.109;0.109;0.06	D	0.93530	0.6869	10	0.54805	T	0.06	-24.4279	9.593	0.39557	0.742:0.0:0.258:0.0	.	173;169;180	B7Z642;E9PHI5;P51674	.;.;GPM6A_HUMAN	L	180;180;169;173;172;117;117	ENSP00000280187:F180L;ENSP00000377268:F180L;ENSP00000421578:F169L;ENSP00000423984:F173L;ENSP00000422959:F172L;ENSP00000426984:F117L;ENSP00000426821:F117L	ENSP00000280187:F180L	F	-	3	2	GPM6A	176809980	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.174000	0.42482	-0.047000	0.13423	0.528000	0.53228	TTT		0.413	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1		Missense_Mutation	T	176572986	A	T	176572986	5	4	47	1	0	0	0	0	0	0	1	0	6635	144	5	5	312	5	GPM6A	4	176572986	Splice_Site	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1008014	176572986	14581290	635	5032										
VEGFC	7424	broad.mit.edu	37	chr4	177609008	177609008	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgaggaaaacataaaatcttCctgagccaggcatctgcaga	9	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:177609008C>A	ENST00000280193.2	-	5	1193	c.778G>T	c.(778-780)Gaa>Taa	p.E260*	VEGFC_ENST00000507638.1_5'Flank|RP11-313E19.2_ENST00000504017.1_RNA|RP11-313E19.2_ENST00000509194.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	260					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.E260*(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		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)		ATAAAATCTTCCTGAGCCAGG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											115	109	110					4																	177609008		1910	4130	6040	177846002	SO:0001587	stop_gained	7424			BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.778G>T	4.37:g.177609008C>A	ENSP00000280193:p.Glu260*		177846002	B2R9Q8	Nonsense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	C	38	6.876038	0.97904	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.57	4.73	0.59995	.	0.599099	0.18508	N	0.139147	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-5.7306	16.8792	0.86059	0.0:0.1301:0.8699:0.0	.	.	.	.	X	260	.	ENSP00000280193:E260X	E	-	1	0	VEGFC	177846002	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	4.280000	0.58959	1.487000	0.48415	-0.153000	0.13522	GAA		0.433	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		A	177609008	C	A	177609008	4	1	47	1	0	0	0	0	0	1	0	0	17192	864	30	2	496	2	VEGFC	4	177609008	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1036022	177609008	13545268	636	5033										
ODZ3	55714	broad.mit.edu	37	chr4	183602991	183602991	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtatagaccctgggtgttCtaatcatggtgtgtgtatcc	11	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183602991C>A	ENST00000511685.1	+	11	1982	c.1859C>A	c.(1858-1860)tCt>tAt	p.S620Y	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.S620Y			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	620	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S620Y(1)									CCTGGGTGTTCTAATCATGGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											70	65	66					4																	183602991		1921	4119	6040	183839985	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1859C>A	4.37:g.183602991C>A	ENSP00000424226:p.Ser620Tyr		183839985	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308308	0.81247	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.08102	3.13;3.13	5.5	5.5	0.81552	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.23611	0.0571	M	0.89968	3.075	0.80722	D	1	B	0.25235	0.121	B	0.31290	0.127	T	0.07083	-1.0791	9	0.87932	D	0	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	620	Q9P273	TEN3_HUMAN	Y	620	ENSP00000424226:S620Y;ENSP00000385276:S620Y	ENSP00000385276:S620Y	S	+	2	0	ODZ3	183839985	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	TCT		0.418	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183602991	C	A	183602991	3	1	47	1	0	0	0	0	1	0	0	0	10867	913	32	2	1897	2	ODZ3	4	183602991	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5993983	183602991	7551285	637	5034										
ODZ3	55714	broad.mit.edu	37	chr4	183675616	183675616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctggataataatgtagttTtacagatcactgaaaatcgt	7	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183675616T>C	ENST00000511685.1	+	22	4219	c.4096T>C	c.(4096-4098)Tta>Cta	p.L1366L	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Silent_p.L1366L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1366					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.L1366L(1)									TAATGTAGTTTTACAGATCAC	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	4											53	50	51					4																	183675616		1952	4150	6102	183912610	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4096T>C	4.37:g.183675616T>C			183912610	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.468	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			C	183675616	T	C	183675616	2	2	47	1	0	0	0	0	0	0	0	1	10867	1838	64	4		4	ODZ3	4	183675616	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	72625	183675616	7478660	638	5035										
ODZ3	55714	broad.mit.edu	37	chr4	183713642	183713642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcttctacaaacagctttCttgggtacaagtcggagggt	11	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183713642C>A	ENST00000511685.1	+	26	5940	c.5817C>A	c.(5815-5817)ttC>ttA	p.F1939L	TENM3_ENST00000406950.2_Missense_Mutation_p.F1939L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1939					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.F1939L(1)									AAACAGCTTTCTTGGGTACAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	59	59					4																	183713642		1902	4111	6013	183950636	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5817C>A	4.37:g.183713642C>A	ENSP00000424226:p.Phe1939Leu		183950636	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049480	0.36181	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86164	-2.08;-2.08	4.74	4.74	0.60224	.	.	.	.	.	T	0.78654	0.4317	N	0.25647	0.755	0.44789	D	0.997794	B	0.13594	0.008	B	0.12156	0.007	T	0.72093	-0.4394	9	0.27082	T	0.32	.	11.7197	0.51675	0.0:0.9189:0.0:0.081	.	1939	Q9P273	TEN3_HUMAN	L	1939	ENSP00000424226:F1939L;ENSP00000385276:F1939L	ENSP00000385276:F1939L	F	+	3	2	ODZ3	183950636	1.000000	0.71417	0.921000	0.36526	0.769000	0.43574	4.587000	0.60991	2.608000	0.88229	0.591000	0.81541	TTC		0.448	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183713642	C	A	183713642	3	1	47	1	0	0	0	0	1	0	0	0	10867	912	32	2	5915	2	ODZ3	4	183713642	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	38026	183713642	7440634	639	5036			1	6		4	4	1071	N	G_C	6.785059e-05
ODZ3	55714	broad.mit.edu	37	chr4	183713936	183713936	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagggtgtgatcaatgaaacGccactgcctattgatctgta	10	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183713936G>A	ENST00000511685.1	+	26	6234	c.6111G>A	c.(6109-6111)acG>acA	p.T2037T	TENM3_ENST00000406950.2_Silent_p.T2037T			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2037					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T2037T(2)									TCAATGAAACGCCACTGCCTA	0.383																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	4											115	115	115					4																	183713936		1975	4169	6144	183950930	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.6111G>A	4.37:g.183713936G>A			183950930	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.383	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183713936	G	A	183713936	2	1	47	1	0	0	0	0	0	0	0	1	10867	1074	38	1		1	ODZ3	4	183713936	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	294	183713936	7440340	640	5037			1	6		4	4	1071	N	G_C	6.785059e-05
ODZ3	55714	broad.mit.edu	37	chr4	183714059	183714059	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagctgtaatgacctatacGaagcactttgatgctcatgg	9	9	1	2	rs61746883		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183714059G>A	ENST00000511685.1	+	26	6357	c.6234G>A	c.(6232-6234)acG>acA	p.T2078T	TENM3_ENST00000406950.2_Silent_p.T2078T			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2078					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T2078T(1)									TGACCTATACGAAGCACTTTG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G		1,3721		0,1,1860	45	44	44		6234	-9.6	0.6	4	dbSNP_129	44	1,8197		0,1,4098	no	coding-synonymous	ODZ3	NM_001080477.1		0,2,5958	AA,AG,GG		0.0122,0.0269,0.0168		2078/2700	183714059	2,11918	1861	4099	5960	183951053	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.6234G>A	4.37:g.183714059G>A			183951053	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.378	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183714059	G	A	183714059	2	1	47	1	0	0	0	0	0	0	0	1	10867	1045	37	1		1	ODZ3	4	183714059	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	123	183714059	7440217	641	5038			1	6		4	4	1071	N	G_C	6.785059e-05
ODZ3	55714	broad.mit.edu	37	chr4	183714712	183714712	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggatgaattctatattgcatCggataacacagggacaccac	9	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:183714712C>T	ENST00000511685.1	+	26	7010	c.6887C>T	c.(6886-6888)tCg>tTg	p.S2296L	TENM3_ENST00000406950.2_Missense_Mutation_p.S2296L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2296					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S2296L(1)									TATATTGCATCGGATAACACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	72	72					4																	183714712		1917	4141	6058	183951706	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.6887C>T	4.37:g.183714712C>T	ENSP00000424226:p.Ser2296Leu		183951706	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635210	0.47049	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86164	-2.08;-2.08	5.02	5.02	0.67125	.	.	.	.	.	D	0.84070	0.5391	L	0.43152	1.355	0.49483	D	0.999796	B	0.23185	0.081	B	0.12837	0.008	T	0.81417	-0.0942	9	0.66056	D	0.02	.	18.553	0.91072	0.0:1.0:0.0:0.0	.	2296	Q9P273	TEN3_HUMAN	L	2296	ENSP00000424226:S2296L;ENSP00000385276:S2296L	ENSP00000385276:S2296L	S	+	2	0	ODZ3	183951706	1.000000	0.71417	0.070000	0.20053	0.463000	0.32649	5.964000	0.70379	2.603000	0.88011	0.655000	0.94253	TCG		0.413	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183714712	C	T	183714712	3	4	47	1	0	0	0	0	1	0	0	0	10867	893	31	1	6985	1	ODZ3	4	183714712	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	653	183714712	7439564	642	5039			1	6		4	4	1071	N	G_C	6.785059e-05
MLF1IP	201973	broad.mit.edu	37	chr4	185616539	185616539	+	IGR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttaaataacagagctggaAggctggatgaatcatactgt	10	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr4:185616539A>C	ENST00000314970.6	+	0	2289				MLF1IP_ENST00000281453.5_Missense_Mutation_p.L387R|MLF1IP_ENST00000506535.1_5'Flank	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)						mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)	p.L387R(1)									CAGAGCTGGAAGGCTGGATGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	116	113					4																	185616539		2203	4300	6503	185853533	SO:0001628	intergenic_variant	79682			AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495		4.37:g.185616539A>C			185853533	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983159	0.74474	.	.	ENSG00000151725	ENST00000281453	T	0.35236	1.32	6.02	6.02	0.97574	.	0.112774	0.40144	N	0.001179	T	0.61299	0.2336	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65038	-0.6265	10	0.87932	D	0	-16.7233	15.1131	0.72375	1.0:0.0:0.0:0.0	.	387	Q71F23	CENPU_HUMAN	R	387	ENSP00000281453:L387R	ENSP00000281453:L387R	L	-	2	0	MLF1IP	185853533	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.710000	0.68392	2.304000	0.77564	0.528000	0.53228	CTT		0.378	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		C	185616539	A	C	185616539	1	2	47	0	1	0	0	0	0	0	0	0	9645	72	3	4		4	MLF1IP	4	185616539	IGR	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1901827	185616539	5537737	643	5040										
PLEKHG4B	153478	broad.mit.edu	37	chr5	155502	155502	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgtgaagaagccatcattTtcctacagaattcattctgc	6	10	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:155502T>G	ENST00000283426.6	+	7	1134	c.1084T>G	c.(1084-1086)Ttc>Gtc	p.F362V		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	362							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F362V(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGCCATCATTTTCCTACAGAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											97	94	95					5																	155502		2203	4300	6503	208502	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1084T>G	5.37:g.155502T>G	ENSP00000283426:p.Phe362Val		208502		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	11.32	1.604578	0.28623	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.28666	1.6;3.06	3.65	3.65	0.41850	.	.	.	.	.	T	0.36026	0.0952	M	0.71581	2.175	0.26784	N	0.969539	P	0.48764	0.915	P	0.47528	0.549	T	0.14144	-1.0483	9	0.18710	T	0.47	.	8.7019	0.34332	0.0:0.0:0.0:1.0	.	362	Q96PX9	PKH4B_HUMAN	V	362;276	ENSP00000283426:F362V;ENSP00000422493:F276V	ENSP00000283426:F362V	F	+	1	0	PLEKHG4B	208502	0.981000	0.34729	0.040000	0.18447	0.010000	0.07245	2.035000	0.41155	1.291000	0.44653	0.383000	0.25322	TTC		0.453	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		G	155502	T	G	155502	3	3	47	1	0	0	0	0	1	0	0	0	12103	1841	64	4	1110	4	PLEKHG4B	5	155502	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09		155502	180759758	644	5041										
PLEKHG4B	153478	broad.mit.edu	37	chr5	173017	173017	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgttcctctgcaggtgaaTttgaaggaacaggggcagct	14	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:173017T>G	ENST00000283426.6	+	15	3038	c.2988T>G	c.(2986-2988)aaT>aaG	p.N996K		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	996	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N996K(1)|p.N187K(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TGCAGGTGAATTTGAAGGAAC	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	5											93	91	91					5																	173017		2203	4300	6503	226017	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2988T>G	5.37:g.173017T>G	ENSP00000283426:p.Asn996Lys		226017		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.816423	0.32145	.	.	ENSG00000153404	ENST00000283426	T	0.12147	2.71	3.1	-2.94	0.05581	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	.	.	.	.	T	0.38054	0.1026	M	0.92691	3.335	0.31836	N	0.624053	D	0.76494	0.999	D	0.68765	0.96	T	0.41592	-0.9500	9	0.48119	T	0.1	.	8.439	0.32803	0.0:0.5305:0.0:0.4695	.	996	Q96PX9	PKH4B_HUMAN	K	996	ENSP00000283426:N996K	ENSP00000283426:N996K	N	+	3	2	PLEKHG4B	226017	0.947000	0.32204	0.400000	0.26346	0.208000	0.24298	0.143000	0.16115	-0.724000	0.04908	0.383000	0.25322	AAT		0.502	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		G	173017	T	G	173017	3	3	47	1	0	0	0	0	1	0	0	0	12103	1490	52	4	3046	4	PLEKHG4B	5	173017	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	17515	173017	180742243	645	5042										
FASTKD3	79072	broad.mit.edu	37	chr5	7866830	7866830	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggatggcattcattaagtGaacatgaatgaagaagtttc	10	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:7866830G>T	ENST00000264669.5	-	2	1503	c.1367C>A	c.(1366-1368)tCa>tAa	p.S456*	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	456					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.S456L(1)|p.S456*(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TTCATTAAGTGAACATGAATG	0.368																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	5											63	64	64					5																	7866830		2203	4300	6503	7919830	SO:0001587	stop_gained	79072			AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1367C>A	5.37:g.7866830G>T	ENSP00000264669:p.Ser456*		7919830	Q9BVD3	Nonsense_Mutation	SNP	ENST00000264669.5	37	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.805369	0.90623	.	.	ENSG00000124279	ENST00000264669	.	.	.	4.95	4.05	0.47172	.	0.424965	0.24813	N	0.035388	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-6.8164	7.5157	0.27600	0.2839:0.0:0.7161:0.0	.	.	.	.	X	456	.	ENSP00000264669:S456X	S	-	2	0	FASTKD3	7919830	0.995000	0.38212	0.183000	0.23137	0.428000	0.31595	2.314000	0.43743	1.226000	0.43582	0.655000	0.94253	TCA		0.368	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		T	7866830	G	T	7866830	4	4	47	1	0	0	0	0	0	1	0	0	5706	1294	45	2	645	2	FASTKD3	5	7866830	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7693813	7866830	173048430	646	5043										
MTRR	4552	broad.mit.edu	37	chr5	7878150	7878150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacaagaggagataagtggCgcactcccggtggcatcacc	14	11	1	2	rs139333376	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:7878150C>T	ENST00000264668.2	+	5	606	c.576C>T	c.(574-576)ggC>ggT	p.G192G	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Silent_p.G165G|MTRR_ENST00000502509.1_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	192					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)	p.G192G(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AGATAAGTGGCGCACTCCCGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C	,	2,4404	4.2+/-10.8	0,2,2201	61	59	60		495,576	-7.5	0	5	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	165/699,192/726	7878150	2,13004	2203	4300	6503	7931150	SO:0001819	synonymous_variant	4552			AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.576C>T	5.37:g.7878150C>T			7931150	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	C	5.699	0.313586	0.10789	4.54E-4	0.0	ENSG00000124275	ENST00000514220	.	.	.	5.91	-7.48	0.01360	.	.	.	.	.	T	0.19366	0.0465	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33059	-0.9883	4	.	.	.	-4.6769	5.8633	0.18760	0.2316:0.516:0.1298:0.1225	.	.	.	.	C	94	.	.	R	+	1	0	MTRR	7931150	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.316000	0.01123	-0.813000	0.04357	-0.266000	0.10368	CGC		0.507	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7878150	C	T	7878150	2	4	47	1	0	0	0	0	0	0	0	1	9991	755	27	1		1	MTRR	5	7878150	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	11320	7878150	173037110	647	5044										
TAS2R1	50834	broad.mit.edu	37	chr5	9629596	9629596	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagataagcaatggcactgaGaactcagcaacaaaagagaa	9	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:9629596G>T	ENST00000382492.2	-	1	867	c.549C>A	c.(547-549)ttC>ttA	p.F183L	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	183					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.F183L(2)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						ATGGCACTGAGAACTCAGCAA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	5											73	81	78					5																	9629596		2203	4300	6503	9682596	SO:0001583	missense	50834			AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.549C>A	5.37:g.9629596G>T	ENSP00000371932:p.Phe183Leu		9682596	Q646G8	Missense_Mutation	SNP	ENST00000382492.2	37	CCDS3876.1	.	.	.	.	.	.	.	.	.	.	G	5.914	0.352768	0.11182	.	.	ENSG00000169777	ENST00000382492	T	0.44083	0.93	5.65	-5.4	0.02656	.	1.119980	0.06863	N	0.799468	T	0.13072	0.0317	N	0.02345	-0.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19549	-1.0302	9	.	.	.	.	3.2968	0.06969	0.2645:0.3706:0.2702:0.0947	.	183	Q9NYW7	TA2R1_HUMAN	L	183	ENSP00000371932:F183L	.	F	-	3	2	TAS2R1	9682596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.527000	0.00946	-0.651000	0.05415	0.655000	0.94253	TTC		0.433	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			T	9629596	G	T	9629596	3	4	47	1	0	0	0	0	1	0	0	0	15604	933	33	2	354	2	TAS2R1	5	9629596	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1751446	9629596	171285664	648	5045										
DNAH5	1767	broad.mit.edu	37	chr5	13885136	13885136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaggaatgaatacgtttgCgaatggcctctagtgtattc	12	6	1	2	rs200704983		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:13885136C>T	ENST00000265104.4	-	19	3049	c.2945G>A	c.(2944-2946)cGc>cAc	p.R982H	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	982	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R982H(2)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AATACGTTTGCGAATGGCCTC	0.443									Kartagener syndrome				C|||	1	0.000199681	0	0	5008	,	,		16035	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	5											126	118	121					5																	13885136		2203	4300	6503	13938136	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2945G>A	5.37:g.13885136C>T	ENSP00000265104:p.Arg982His		13938136	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	22.0	4.237217	0.79800	.	.	ENSG00000039139	ENST00000265104	T	0.25579	1.79	5.73	5.73	0.89815	.	0.056303	0.64402	D	0.000001	T	0.35885	0.0947	M	0.78049	2.395	0.80722	D	1	B	0.30179	0.271	B	0.26310	0.068	T	0.21109	-1.0255	10	0.59425	D	0.04	.	19.9025	0.96993	0.0:1.0:0.0:0.0	.	982	Q8TE73	DYH5_HUMAN	H	982	ENSP00000265104:R982H	ENSP00000265104:R982H	R	-	2	0	DNAH5	13938136	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.251000	0.78297	2.722000	0.93159	0.655000	0.94253	CGC		0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13885136	C	T	13885136	3	4	47	1	0	0	0	0	1	0	0	0	4615	768	27	1	11173	1	DNAH5	5	13885136	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4255540	13885136	167030124	649	5046										
CDH12	1010	broad.mit.edu	37	chr5	21760696	21760696	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacgaactgtaaaatttggtTtgatagcagcctcaggtgat	10	7	1	2	rs533294662		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:21760696T>G	ENST00000382254.1	-	13	2690	c.1604A>C	c.(1603-1605)aAa>aCa	p.K535T	CDH12_ENST00000521384.1_5'UTR|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000522262.1_Missense_Mutation_p.K495T|CDH12_ENST00000504376.2_Missense_Mutation_p.K535T	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	535	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K535T(1)|p.K535I(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						AAAATTTGGTTTGATAGCAGC	0.388										HNSCC(59;0.17)																																						2	Substitution - Missense(2)	large_intestine(1)|lung(1)	5											133	140	138					5																	21760696		2203	4300	6503	21796453	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.1604A>C	5.37:g.21760696T>G	ENSP00000371689:p.Lys535Thr		21796453	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.003908	0.54254	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.52754	0.65;0.65;0.65	5.19	4.03	0.46877	Cadherin (4);Cadherin-like (1);	0.090340	0.85682	D	0.000000	T	0.28764	0.0713	N	0.20574	0.59	0.47341	D	0.999399	B;P	0.37914	0.005;0.611	B;B	0.29077	0.021;0.098	T	0.11591	-1.0581	10	0.62326	D	0.03	.	10.8601	0.46821	0.0:0.074:0.0:0.926	.	495;535	B7Z2U6;P55289	.;CAD12_HUMAN	T	535;535;495	ENSP00000423577:K535T;ENSP00000371689:K535T;ENSP00000428786:K495T	ENSP00000371689:K535T	K	-	2	0	CDH12	21796453	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	2.555000	0.45854	0.928000	0.37168	0.528000	0.53228	AAA		0.388	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		G	21760696	T	G	21760696	3	3	47	1	0	0	0	0	1	0	0	0	3104	1841	64	4	792	4	CDH12	5	21760696	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	7875560	21760696	159154564	650	5047										
PRDM9	56979	broad.mit.edu	37	chr5	23523417	23523417	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagatcaccaaggggagaaaCtgctatgagtatgtggatgg	14	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:23523417C>A	ENST00000296682.3	+	9	1082	c.900C>A	c.(898-900)aaC>aaA	p.N300K		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	300	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.N300K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AGGGGAGAAACTGCTATGAGT	0.428										HNSCC(3;0.000094)																																						1	Substitution - Missense(1)	large_intestine(1)	5											133	128	130					5																	23523417		2203	4300	6503	23559174	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.900C>A	5.37:g.23523417C>A	ENSP00000296682:p.Asn300Lys		23559174	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	c	12.15	1.850489	0.32699	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.72282	-0.64	3.72	2.83	0.33086	SET domain (2);	0.379291	0.19289	N	0.117958	T	0.51415	0.1673	L	0.31526	0.94	0.35004	D	0.756246	B	0.30584	0.286	B	0.19148	0.024	T	0.55360	-0.8153	10	0.31617	T	0.26	-29.9332	7.7661	0.28980	0.0:0.8715:0.0:0.1285	.	300	Q9NQV7	PRDM9_HUMAN	K	300;94	ENSP00000296682:N300K	ENSP00000253473:N94K	N	+	3	2	PRDM9	23559174	0.845000	0.29573	1.000000	0.80357	0.991000	0.79684	0.484000	0.22308	0.831000	0.34780	0.592000	0.82586	AAC		0.428	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23523417	C	A	23523417	3	1	47	1	0	0	0	0	1	0	0	0	12497	564	20	2	930	2	PRDM9	5	23523417	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1762721	23523417	157391843	651	5048										
PRDM9	56979	broad.mit.edu	37	chr5	23524503	23524503	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggccttccagtaccacagGcagatcttctatagaacctg	9	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:23524503G>A	ENST00000296682.3	+	10	1193	c.1011G>A	c.(1009-1011)agG>agA	p.R337R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	337	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R337R(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AGTACCACAGGCAGATCTTCT	0.547										HNSCC(3;0.000094)																																						1	Substitution - coding silent(1)	large_intestine(1)	5											67	69	68					5																	23524503		1895	4105	6000	23560260	SO:0001819	synonymous_variant	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1011G>A	5.37:g.23524503G>A			23560260	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																				0.547	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23524503	G	A	23524503	2	1	47	1	0	0	0	0	0	0	0	1	12497	1194	42	3		3	PRDM9	5	23524503	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1086	23524503	157390757	652	5049										
PRDM9	56979	broad.mit.edu	37	chr5	23526584	23526584	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaaagaaaggtccaaactcTtgaataaaaggacatggcag	9	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:23526584T>G	ENST00000296682.3	+	11	1569	c.1387T>G	c.(1387-1389)Ttg>Gtg	p.L463V		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	463					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.L463V(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GTCCAAACTCTTGAATAAAAG	0.463										HNSCC(3;0.000094)																																						1	Substitution - Missense(1)	large_intestine(1)	5											39	41	40					5																	23526584		2200	4297	6497	23562341	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1387T>G	5.37:g.23526584T>G	ENSP00000296682:p.Leu463Val		23562341	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	T	5.701	0.313898	0.10789	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.08896	3.04	2.43	-4.86	0.03132	.	1.488970	0.04762	N	0.426383	T	0.06872	0.0175	L	0.47716	1.5	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.34079	-0.9843	10	0.23891	T	0.37	4.8536	4.111	0.10058	0.4161:0.0:0.2964:0.2875	.	463	Q9NQV7	PRDM9_HUMAN	V	463;257	ENSP00000296682:L463V	ENSP00000253473:L257V	L	+	1	2	PRDM9	23562341	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.360000	0.20250	-1.799000	0.01248	-0.626000	0.03995	TTG		0.463	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		G	23526584	T	G	23526584	3	3	47	1	0	0	0	0	1	0	0	0	12497	1606	56	4	1425	4	PRDM9	5	23526584	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2081	23526584	157388676	653	5050										
CDH9	1007	broad.mit.edu	37	chr5	26890660	26890660	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acggtccatatcagtatgccGatcaacagagtacctggcag	10	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:26890660G>A	ENST00000231021.4	-	8	1439	c.1267C>T	c.(1267-1269)Cgg>Tgg	p.R423W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	423	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R423W(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCAGTATGCCGATCAACAGAG	0.383																																					Melanoma(8;187 585 15745 40864 52829)											1	Substitution - Missense(1)	large_intestine(1)	5											82	84	83					5																	26890660		2203	4300	6503	26926417	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1267C>T	5.37:g.26890660G>A	ENSP00000231021:p.Arg423Trp		26926417	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239870	0.79912	.	.	ENSG00000113100	ENST00000231021	T	0.53423	0.62	5.09	5.09	0.68999	Cadherin (4);Cadherin-like (1);	0.066379	0.64402	D	0.000007	T	0.53174	0.1780	M	0.79693	2.465	0.80722	D	1	B;B	0.25772	0.061;0.134	B;B	0.27380	0.025;0.079	T	0.53258	-0.8464	9	.	.	.	.	17.0519	0.86521	0.0:0.0:1.0:0.0	.	16;423	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	423	ENSP00000231021:R423W	.	R	-	1	2	CDH9	26926417	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.591000	0.67536	2.385000	0.81259	0.453000	0.30009	CGG		0.383	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26890660	G	A	26890660	3	1	47	1	0	0	0	0	1	0	0	0	3123	1057	37	1	1122	1	CDH9	5	26890660	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3364076	26890660	154024600	654	5051										
CDH9	1007	broad.mit.edu	37	chr5	26915805	26915805	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattttggctcattgtcattGatatcatgtattttaatgat	6	4	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:26915805G>T	ENST00000231021.4	-	3	628	c.456C>A	c.(454-456)atC>atA	p.I152I		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	152	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I152I(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CATTGTCATTGATATCATGTA	0.373																																					Melanoma(8;187 585 15745 40864 52829)											1	Substitution - coding silent(1)	large_intestine(1)	5											97	96	96					5																	26915805		2203	4300	6503	26951562	SO:0001819	synonymous_variant	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.456C>A	5.37:g.26915805G>T			26951562	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																				0.373	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26915805	G	T	26915805	2	4	47	1	0	0	0	0	0	0	0	1	3123	1280	45	2		2	CDH9	5	26915805	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	25145	26915805	153999455	655	5052										
RNASEN	29102	broad.mit.edu	37	chr5	31486628	31486628	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctcttcaatgaaatgaatCgtgtagtctatgttgaatct	7	6	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:31486628C>T	ENST00000511367.2	-	13	2128	c.1884G>A	c.(1882-1884)acG>acA	p.T628T	DROSHA_ENST00000442743.1_Silent_p.T591T|DROSHA_ENST00000513349.1_Silent_p.T591T|DROSHA_ENST00000344624.3_Silent_p.T628T	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	628	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.T628T(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TGAAATGAATCGTGTAGTCTA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	5											129	131	131					5																	31486628		1940	4150	6090	31522385	SO:0001819	synonymous_variant	29102			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.1884G>A	5.37:g.31486628C>T			31522385	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1																																																																																				0.378	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		T	31486628	C	T	31486628	2	4	47	1	0	0	0	0	0	0	0	1	13454	871	31	1		1	RNASEN	5	31486628	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4570823	31486628	149428632	656	5053										
PDZD2	23037	broad.mit.edu	37	chr5	32091233	32091233	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acccagttcagccagtgataCgggtgaagctgcccaggatc	12	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:32091233C>T	ENST00000438447.1	+	20	8067	c.7679C>T	c.(7678-7680)aCg>aTg	p.T2560M	PDZD2_ENST00000282493.3_Missense_Mutation_p.T2560M			O15018	PDZD2_HUMAN	PDZ domain containing 2	2560					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.T2560M(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCAGTGATACGGGTGAAGCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											48	51	50					5																	32091233		2203	4300	6503	32126990	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.7679C>T	5.37:g.32091233C>T	ENSP00000402033:p.Thr2560Met		32126990	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	8.499	0.863829	0.17250	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06849	3.25;3.25	4.76	-9.51	0.00581	.	3.139240	0.00932	N	0.002734	T	0.02418	0.0074	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39663	-0.9603	10	0.33940	T	0.23	.	2.0967	0.03669	0.3407:0.3739:0.1338:0.1516	.	2560	O15018	PDZD2_HUMAN	M	2560;2361;2560	ENSP00000402033:T2560M;ENSP00000282493:T2560M	ENSP00000282493:T2560M	T	+	2	0	PDZD2	32126990	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.245000	0.08890	-2.337000	0.00628	-1.434000	0.01081	ACG		0.502	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32091233	C	T	32091233	3	4	47	1	0	0	0	0	1	0	0	0	11732	536	19	1	7753	1	PDZD2	5	32091233	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	604605	32091233	148824027	657	5054										
MTMR12	54545	broad.mit.edu	37	chr5	32233914	32233914	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttccgttggcctttgtccaGttttggcttttccacataaa	7	10	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:32233914G>T	ENST00000382142.3	-	15	1809	c.1639C>A	c.(1639-1641)Ctg>Atg	p.L547M	MTMR12_ENST00000510216.1_5'UTR|RNU6-1079P_ENST00000362861.1_RNA|MTMR12_ENST00000264934.5_Intron|MTMR12_ENST00000280285.5_Intron	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	547	Interaction with MTM1.|Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)	p.L547M(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CCTTTGTCCAGTTTTGGCTTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											219	182	194					5																	32233914		2203	4300	6503	32269671	SO:0001583	missense	54545			AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	18191	protein-coding gene	gene with protein product		606501	"phosphatidylinositol-3-phosphate associated protein"	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.1639C>A	5.37:g.32233914G>T	ENSP00000371577:p.Leu547Met		32269671	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.764182	0.49574	.	.	ENSG00000150712	ENST00000382142	D	0.94497	-3.44	5.77	3.01	0.34805	Myotubularin phosphatase domain (1);	4.564580	0.00357	N	0.000028	D	0.91835	0.7416	L	0.44542	1.39	0.80722	D	1	B	0.34103	0.437	B	0.31495	0.131	T	0.78280	-0.2265	10	0.34782	T	0.22	.	8.8409	0.35142	0.135:0.125:0.74:0.0	.	547	Q9C0I1	MTMRC_HUMAN	M	547	ENSP00000371577:L547M	ENSP00000371577:L547M	L	-	1	2	MTMR12	32269671	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.256000	0.51492	0.778000	0.33520	0.655000	0.94253	CTG		0.483	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061		T	32233914	G	T	32233914	3	4	47	1	0	0	0	0	1	0	0	0	9971	1020	36	2	612	2	MTMR12	5	32233914	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	142681	32233914	148681346	658	5055										
ZFR	51663	broad.mit.edu	37	chr5	32395407	32395407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcaaatctggatttacttTtttctattaatataaataag	4	4	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:32395407T>G	ENST00000265069.8	-	11	1939	c.1837A>C	c.(1837-1839)Aaa>Caa	p.K613Q	MIR579_ENST00000385221.1_RNA	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	613					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K613Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GGATTTACTTTTTTCTATTAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											50	47	48					5																	32395407		2202	4300	6502	32431164	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1837A>C	5.37:g.32395407T>G	ENSP00000265069:p.Lys613Gln		32431164	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.144302	0.77888	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.43294	0.95	5.96	5.96	0.96718	Zinc finger, U1-type (1);	0.087907	0.85682	D	0.000000	T	0.68320	0.2988	M	0.82823	2.61	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.73338	-0.4014	10	0.87932	D	0	.	16.4277	0.83824	0.0:0.0:0.0:1.0	.	613	Q96KR1	ZFR_HUMAN	Q	613;591	ENSP00000265069:K613Q	ENSP00000265069:K613Q	K	-	1	0	ZFR	32431164	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.841000	0.86834	2.279000	0.76181	0.533000	0.62120	AAA		0.318	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			G	32395407	T	G	32395407	3	3	47	1	0	0	0	0	1	0	0	0	17698	1850	64	4	1427	4	ZFR	5	32395407	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	161493	32395407	148519853	659	5056										
TARS	6897	broad.mit.edu	37	chr5	33457480	33457480	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagttccaagaggaagctaAaaaccgagatcataggaaaa	10	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:33457480A>C	ENST00000265112.3	+	9	1267	c.956A>C	c.(955-957)aAa>aCa	p.K319T	TARS_ENST00000541634.1_Missense_Mutation_p.K215T|TARS_ENST00000414361.2_Missense_Mutation_p.K198T|TARS_ENST00000455217.2_Missense_Mutation_p.K352T|TARS_ENST00000502553.1_Missense_Mutation_p.K319T	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	319					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)	p.K319T(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	GAGGAAGCTAAAAACCGAGAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											113	118	117					5																	33457480		2203	4300	6503	33493237	SO:0001583	missense	6897			AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.956A>C	5.37:g.33457480A>C	ENSP00000265112:p.Lys319Thr		33493237	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Missense_Mutation	SNP	ENST00000265112.3	37	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.510702	0.64522	.	.	ENSG00000113407	ENST00000502553;ENST00000265112;ENST00000541634;ENST00000455217;ENST00000414361	T;T;T	0.50277	0.76;0.76;0.75	5.7	5.7	0.88788	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.000000	0.85682	D	0.000000	T	0.58836	0.2150	M	0.78223	2.4	0.80722	D	1	B;P;P;P	0.45672	0.172;0.864;0.855;0.864	B;P;P;P	0.47299	0.091;0.52;0.543;0.52	T	0.63400	-0.6646	10	0.51188	T	0.08	-0.2451	16.0011	0.80292	1.0:0.0:0.0:0.0	.	198;352;215;319	E7ERI3;B4DEG8;G3XAN9;P26639	.;.;.;SYTC_HUMAN	T	319;319;215;352;198	ENSP00000424387:K319T;ENSP00000265112:K319T;ENSP00000387710:K352T	ENSP00000265112:K319T	K	+	2	0	TARS	33493237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.812000	0.55628	2.183000	0.69458	0.529000	0.55759	AAA		0.393	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		C	33457480	A	C	33457480	3	2	47	1	0	0	0	0	1	0	0	0	15598	14	1	4	990	4	TARS	5	33457480	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1062073	33457480	147457780	660	5057										
ADAMTS12	81792	broad.mit.edu	37	chr5	33549454	33549454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtccacgcactgaatctcgCgtatcttgaagcccccactg	8	15	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:33549454C>T	ENST00000504830.1	-	21	4495	c.4160G>A	c.(4159-4161)cGc>cAc	p.R1387H	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.R1302H	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1387	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R1387H(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CTGAATCTCGCGTATCTTGAA	0.557										HNSCC(64;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	5											86	96	92					5																	33549454		2203	4300	6503	33585211	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4160G>A	5.37:g.33549454C>T	ENSP00000422554:p.Arg1387His		33585211	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812782	0.90707	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.78707	-1.2;-1.2	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.91713	0.7380	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	D	0.94149	0.7404	10	0.87932	D	0	.	15.5546	0.76184	0.0:1.0:0.0:0.0	.	1302;1387	P58397-3;P58397	.;ATS12_HUMAN	H	1387;1302	ENSP00000422554:R1387H;ENSP00000344847:R1302H	ENSP00000344847:R1302H	R	-	2	0	ADAMTS12	33585211	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	5.549000	0.67261	2.398000	0.81561	0.650000	0.86243	CGC		0.557	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33549454	C	T	33549454	3	4	47	1	0	0	0	0	1	0	0	0	257	768	27	1	640	1	ADAMTS12	5	33549454	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	91974	33549454	147365806	661	5058										
ADAMTS12	81792	broad.mit.edu	37	chr5	33577232	33577232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggcacatgtgacactgcGaatccgcactccaccaccac	7	17	0	1	rs375366015		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:33577232G>A	ENST00000504830.1	-	19	3234	c.2899C>T	c.(2899-2901)Cgc>Tgc	p.R967C	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.R882C|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	967	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R967C(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GTGACACTGCGAATCCGCACT	0.502										HNSCC(64;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	5						G	CYS/ARG	0,4406		0,0,2203	98	94	95		2899	5.3	1	5		95	2,8598	2.2+/-6.3	0,2,4298	no	missense	ADAMTS12	NM_030955.2	180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	967/1595	33577232	2,13004	2203	4300	6503	33612989	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2899C>T	5.37:g.33577232G>A	ENSP00000422554:p.Arg967Cys		33612989	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700125	0.88924	0.0	2.33E-4	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.80909	-1.43;-1.43	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.94650	0.8275	H	0.99169	4.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.96677	0.9501	10	0.87932	D	0	.	19.111	0.93317	0.0:0.0:1.0:0.0	.	882;967	P58397-3;P58397	.;ATS12_HUMAN	C	967;882	ENSP00000422554:R967C;ENSP00000344847:R882C	ENSP00000344847:R882C	R	-	1	0	ADAMTS12	33612989	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.861000	0.69553	2.756000	0.94617	0.655000	0.94253	CGC		0.502	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33577232	G	A	33577232	3	1	47	1	0	0	0	0	1	0	0	0	257	1058	37	1	1909	1	ADAMTS12	5	33577232	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	27778	33577232	147338028	662	5059										
SPEF2	79925	broad.mit.edu	37	chr5	35759770	35759770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacaacaagagatttactcGaatccctttggtccaactgg	9	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:35759770G>A	ENST00000356031.3	+	25	3723	c.3569G>A	c.(3568-3570)cGa>cAa	p.R1190Q	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.R1185Q	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1190					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)		p.R1190Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGATTTACTCGAATCCCTTTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											116	113	114					5																	35759770		1840	4081	5921	35795527	SO:0001583	missense	79925			AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.3569G>A	5.37:g.35759770G>A	ENSP00000348314:p.Arg1190Gln		35795527	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	g	15.14	2.745693	0.49151	.	.	ENSG00000152582	ENST00000356031;ENST00000440995	T;T	0.32988	1.43;1.43	5.45	4.59	0.56863	.	0.270973	0.36555	N	0.002531	T	0.54303	0.1850	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.55617	-0.8113	10	0.41790	T	0.15	.	13.7356	0.62815	0.0755:0.0:0.9245:0.0	.	1185;1190	Q9C093-2;Q9C093	.;SPEF2_HUMAN	Q	1190;1185	ENSP00000348314:R1190Q;ENSP00000412125:R1185Q	ENSP00000348314:R1190Q	R	+	2	0	SPEF2	35795527	0.945000	0.32115	0.073000	0.20177	0.143000	0.21401	3.605000	0.54088	1.452000	0.47756	-0.119000	0.15052	CGA		0.393	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35759770	G	A	35759770	3	1	47	1	0	0	0	0	1	0	0	0	15074	1058	37	1	3688	1	SPEF2	5	35759770	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2182538	35759770	145155490	663	5060										
SKP2	6502	broad.mit.edu	37	chr5	36168445	36168445	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtacagcacatggacctatcGaactcagttatagaagtgtc	9	9	1	1	rs137857862		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:36168445G>A	ENST00000274255.6	+	5	763	c.567G>A	c.(565-567)tcG>tcA	p.S189S	SKP2_ENST00000546211.1_Intron|SKP2_ENST00000274254.5_Silent_p.S189S|SKP2_ENST00000508514.1_Intron	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	189					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)	p.S189S(1)		breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGGACCTATCGAACTCAGTTA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G	,	0,4406		0,0,2203	253	260	257		567,567	-9.6	0.3	5	dbSNP_134	257	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SKP2	NM_005983.3,NM_032637.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	189/425,189/411	36168445	2,13004	2203	4300	6503	36204202	SO:0001819	synonymous_variant	6502			U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"F-boxes / Leucine-rich repeats"	10901	protein-coding gene	gene with protein product		601436	"S-phase kinase-associated protein 2 (p45)"			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.567G>A	5.37:g.36168445G>A			36204202	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Silent	SNP	ENST00000274255.6	37	CCDS3916.1																																																																																				0.502	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983		A	36168445	G	A	36168445	2	1	47	1	0	0	0	0	0	0	0	1	14399	1045	37	1		1	SKP2	5	36168445	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	408675	36168445	144746815	664	5061										
NIPBL	25836	broad.mit.edu	37	chr5	36985162	36985162	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcagaatctaaaccaaatgAaaaccgattggtggagacaa	9	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:36985162A>C	ENST00000282516.8	+	10	2379	c.1880A>C	c.(1879-1881)gAa>gCa	p.E627A	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.E627A	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	627					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.E627A(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			AAACCAAATGAAAACCGATTG	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	5											65	68	67					5																	36985162		2197	4298	6495	37020919	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1880A>C	5.37:g.36985162A>C	ENSP00000282516:p.Glu627Ala		37020919	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415554	0.25552	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94723	-3.5;-3.5	5.98	5.98	0.97165	.	0.053505	0.85682	D	0.000000	D	0.90525	0.7031	N	0.24115	0.695	0.41168	D	0.986144	P;P	0.37955	0.478;0.612	B;B	0.37692	0.079;0.256	D	0.90882	0.4754	10	0.48119	T	0.1	.	16.4781	0.84144	1.0:0.0:0.0:0.0	.	627;627	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	A	627	ENSP00000282516:E627A;ENSP00000406266:E627A	ENSP00000282516:E627A	E	+	2	0	NIPBL	37020919	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	3.829000	0.55760	2.288000	0.76882	0.528000	0.53228	GAA		0.348	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	36985162	A	C	36985162	3	2	47	1	0	0	0	0	1	0	0	0	10459	246	9	4	1914	4	NIPBL	5	36985162	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	816717	36985162	143930098	665	5062										
C5orf42	65250	broad.mit.edu	37	chr5	37183288	37183288	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattcttattgacttcattCgaaggatattgtaaaaaagg	7	5	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:37183288C>T	ENST00000508244.1	-	25	5088	c.4995G>A	c.(4993-4995)tcG>tcA	p.S1665S	C5orf42_ENST00000274258.7_Silent_p.S546S|C5orf42_ENST00000425232.2_Silent_p.S1665S			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1665						integral component of membrane (GO:0016021)		p.S546S(1)|p.S1665S(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGACTTCATTCGAAGGATATT	0.318																																																2	Substitution - coding silent(2)	large_intestine(2)	5											76	73	74					5																	37183288		2203	4300	6503	37219045	SO:0001819	synonymous_variant	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.4995G>A	5.37:g.37183288C>T			37219045	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																				0.318	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37183288	C	T	37183288	2	4	47	1	0	0	0	0	0	0	0	1	2307	871	31	1		1	C5orf42	5	37183288	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	198126	37183288	143731972	666	5063										
LIFR	3977	broad.mit.edu	37	chr5	38482264	38482264	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgatcgagtttccagaacCtcaacattatttggggtaca	9	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:38482264C>T	ENST00000263409.4	-	20	2889	c.2727G>A	c.(2725-2727)gaG>gaA	p.E909E	LIFR_ENST00000453190.2_Silent_p.E909E	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	909					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.E909E(2)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TTTCCAGAACCTCAACATTAT	0.373			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	2	Substitution - coding silent(2)	large_intestine(2)	5											62	64	63					5																	38482264		2203	4300	6503	38518021	SO:0001819	synonymous_variant	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2727G>A	5.37:g.38482264C>T			38518021	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																				0.373	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38482264	C	T	38482264	2	4	47	1	0	0	0	0	0	0	0	1	8803	680	24	3		3	LIFR	5	38482264	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1298976	38482264	142432996	667	5064										
FYB	2533	broad.mit.edu	37	chr5	39135054	39135054	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcttgaagctcagttcattCtttcctcctttgacatcaca	5	12	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:39135054C>A	ENST00000351578.6	-	8	1768	c.1578G>T	c.(1576-1578)aaG>aaT	p.K526N	FYB_ENST00000515010.1_Missense_Mutation_p.K526N|FYB_ENST00000512982.1_Missense_Mutation_p.K526N|FYB_ENST00000540520.1_Missense_Mutation_p.K536N|FYB_ENST00000505428.1_Missense_Mutation_p.K526N	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	526	SH3.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)	p.K526N(2)		endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TCAGTTCATTCTTTCCTCCTT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	5											195	176	182					5																	39135054		1866	4122	5988	39170811	SO:0001583	missense	2533			U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1578G>T	5.37:g.39135054C>A	ENSP00000316460:p.Lys526Asn		39170811	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844237	0.71488	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.09538	2.97;2.97;2.97;2.97;2.97	5.67	4.8	0.61643	Src homology-3 domain (2);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	M	0.69823	2.125	0.44789	D	0.99779	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.02144	-1.1206	10	0.72032	D	0.01	-18.2515	10.682	0.45819	0.0:0.8544:0.0:0.1456	.	536;526	B4DLN2;O15117	.;FYB_HUMAN	N	526;526;526;526;536;526	ENSP00000316460:K526N;ENSP00000426346:K526N;ENSP00000425845:K526N;ENSP00000427114:K526N;ENSP00000442840:K536N	ENSP00000316460:K526N	K	-	3	2	FYB	39170811	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.656000	0.37355	1.371000	0.46172	0.655000	0.94253	AAG		0.418	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		A	39135054	C	A	39135054	3	1	47	1	0	0	0	0	1	0	0	0	6143	912	32	2	959	2	FYB	5	39135054	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	652790	39135054	141780206	668	5065										
C9	735	broad.mit.edu	37	chr5	39311474	39311474	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctttcacatgcagaaacatTttttcctgtgttgtagagca	7	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:39311474T>G	ENST00000263408.4	-	7	971	c.876A>C	c.(874-876)aaA>aaC	p.K292N		NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	292	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)		p.K292N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			GCAGAAACATTTTTTCCTGTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	78	80					5																	39311474		2203	4299	6502	39347231	SO:0001583	missense	735				CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"Complement system"	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.876A>C	5.37:g.39311474T>G	ENSP00000263408:p.Lys292Asn		39347231		Missense_Mutation	SNP	ENST00000263408.4	37	CCDS3929.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.123049	0.37436	.	.	ENSG00000113600	ENST00000263408	D	0.84146	-1.81	5.48	3.14	0.36123	Membrane attack complex component/perforin (MACPF) domain (2);	0.245700	0.41396	D	0.000884	D	0.89986	0.6874	M	0.76838	2.35	0.47123	D	0.999327	D	0.76494	0.999	D	0.77557	0.99	D	0.87301	0.2305	10	0.30854	T	0.27	-43.5786	8.5747	0.33592	0.0:0.1613:0.0:0.8387	.	292	P02748	CO9_HUMAN	N	292	ENSP00000263408:K292N	ENSP00000263408:K292N	K	-	3	2	C9	39347231	0.658000	0.27402	0.557000	0.28306	0.048000	0.14542	0.937000	0.28951	0.929000	0.37192	0.460000	0.39030	AAA		0.333	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3			G	39311474	T	G	39311474	3	3	47	1	0	0	0	0	1	0	0	0	2449	1838	64	4	823	4	C9	5	39311474	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	176420	39311474	141603786	669	5066										
C7	730	broad.mit.edu	37	chr5	40936571	40936571	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataaacctcctcctaacataGaacttactggaaatgggtaa	6	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:40936571G>T	ENST00000313164.9	+	5	771	c.412G>T	c.(412-414)Gaa>Taa	p.E138*		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	138	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.E138*(1)					Ovarian(839;0.0112)				TCCTAACATAGAACTTACTGG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											83	80	81					5																	40936571		1923	4143	6066	40972328	SO:0001587	stop_gained	730			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.412G>T	5.37:g.40936571G>T	ENSP00000322061:p.Glu138*		40972328	Q6P3T5|Q92489	Nonsense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	G	39	7.881835	0.98542	.	.	ENSG00000112936	ENST00000313164;ENST00000440677;ENST00000515157	.	.	.	5.02	5.02	0.67125	.	0.102645	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-31.9172	18.483	0.90819	0.0:0.0:1.0:0.0	.	.	.	.	X	138	.	ENSP00000322061:E138X	E	+	1	0	C7	40972328	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.975000	0.76128	2.779000	0.95612	0.491000	0.48974	GAA		0.408	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			T	40936571	G	T	40936571	4	4	47	1	0	0	0	0	0	1	0	0	2381	943	33	2	430	2	C7	5	40936571	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1625097	40936571	139978689	670	5067										
C6	729	broad.mit.edu	37	chr5	41176584	41176584	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaagaaagttacctgagttCtttagttcctcactgctaaa	7	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:41176584C>A	ENST00000263413.3	-	8	1425	c.1161G>T	c.(1159-1161)aaG>aaT	p.K387N	C6_ENST00000475349.1_5'UTR|C6_ENST00000337836.5_Missense_Mutation_p.K387N	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	387	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.K387N(1)		central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TACCTGAGTTCTTTAGTTCCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	67	68					5																	41176584		2203	4300	6503	41212341	SO:0001583	missense	729			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1161G>T	5.37:g.41176584C>A	ENSP00000263413:p.Lys387Asn		41212341		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.561718	0.27915	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.85339	-1.97;-1.97	5.21	4.34	0.51931	Membrane attack complex component/perforin (MACPF) domain (3);	0.643479	0.16795	N	0.199203	D	0.82884	0.5134	L	0.45581	1.43	0.41765	D	0.989731	B	0.28820	0.224	B	0.39503	0.301	T	0.80193	-0.1484	10	0.46703	T	0.11	-8.1545	8.6354	0.33945	0.0:0.7718:0.0:0.2282	.	387	P13671	CO6_HUMAN	N	387	ENSP00000338861:K387N;ENSP00000263413:K387N	ENSP00000263413:K387N	K	-	3	2	C6	41212341	0.933000	0.31639	0.934000	0.37439	0.630000	0.37929	0.098000	0.15189	1.427000	0.47276	0.591000	0.81541	AAG		0.398	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41176584	C	A	41176584	3	1	47	1	0	0	0	0	1	0	0	0	2321	912	32	2	1687	2	C6	5	41176584	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	240013	41176584	139738676	671	5068										
HCN1	348980	broad.mit.edu	37	chr5	45303768	45303768	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaatgacaccagcaacaccGtgttgaatgaaatacatttt	7	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:45303768G>A	ENST00000303230.4	-	6	1608	c.1551C>T	c.(1549-1551)caC>caT	p.H517H		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	517					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.H517H(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						CAGCAACACCGTGTTGAATGA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	5											105	102	103					5																	45303768		2203	4300	6503	45339525	SO:0001819	synonymous_variant	348980			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1551C>T	5.37:g.45303768G>A			45339525		Silent	SNP	ENST00000303230.4	37	CCDS3952.1																																																																																				0.388	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45303768	G	A	45303768	2	1	47	1	0	0	0	0	0	0	0	1	7017	1136	40	1		1	HCN1	5	45303768	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4127184	45303768	135611492	672	5069										
IL6ST	3572	broad.mit.edu	37	chr5	55237006	55237006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccatgccaactgtttcaaaTctttctacttgtccctcagt	4	13	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:55237006T>G	ENST00000381298.2	-	17	2973	c.2661A>C	c.(2659-2661)agA>agC	p.R887S	CTD-2031P19.5_ENST00000576302.1_RNA|IL6ST_ENST00000502326.3_Missense_Mutation_p.R887S|IL6ST_ENST00000381294.3_Missense_Mutation_p.R826S|IL6ST_ENST00000336909.5_Missense_Mutation_p.R887S|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_3'UTR	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	887					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)	p.R887S(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTGTTTCAAATCTTTCTACTT	0.458			O		hepatocellular ca																																		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	1	Substitution - Missense(1)	large_intestine(1)	5											115	102	106					5																	55237006		2203	4300	6503	55272763	SO:0001583	missense	3572			M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.2661A>C	5.37:g.55237006T>G	ENSP00000370698:p.Arg887Ser		55272763	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	T	5.525	0.281865	0.10458	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.38560	1.39;1.39;1.13	5.73	-1.47	0.08772	.	0.853808	0.11173	N	0.591825	T	0.23965	0.0580	L	0.48362	1.52	0.09310	N	0.999999	B;P;B	0.36616	0.046;0.561;0.046	B;B;B	0.24394	0.012;0.053;0.012	T	0.15694	-1.0428	10	0.45353	T	0.12	.	1.9154	0.03296	0.1373:0.2587:0.1106:0.4934	.	887;826;887	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	S	887;887;826	ENSP00000370698:R887S;ENSP00000338799:R887S;ENSP00000370694:R826S	ENSP00000338799:R887S	R	-	3	2	IL6ST	55272763	0.000000	0.05858	0.401000	0.26359	0.032000	0.12392	-0.449000	0.06812	0.100000	0.17581	-0.379000	0.06801	AGA		0.458	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		G	55237006	T	G	55237006	3	3	47	1	0	0	0	0	1	0	0	0	7724	1432	50	4	99	4	IL6ST	5	55237006	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	9933238	55237006	125678254	673	5070										
ANKRD55	79722	broad.mit.edu	37	chr5	55407329	55407329	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcttttctggtaagagatAttttgaattgtctgaggttt	9	3	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:55407329A>G	ENST00000341048.4	-	10	1397	c.1246T>C	c.(1246-1248)Tat>Cat	p.Y416H	ANKRD55_ENST00000434982.2_Missense_Mutation_p.Y128H|ANKRD55_ENST00000504958.2_Missense_Mutation_p.Y373H|ANKRD55_ENST00000505970.2_5'Flank	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	416								p.Y416H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				GGTAAGAGATATTTTGAATTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											123	125	124					5																	55407329		2203	4300	6503	55443086	SO:0001583	missense	79722			AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"Ankyrin repeat domain containing"	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.1246T>C	5.37:g.55407329A>G	ENSP00000342295:p.Tyr416His		55443086	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	37	CCDS34161.1	.	.	.	.	.	.	.	.	.	.	.	13.81	2.348399	0.41599	.	.	ENSG00000164512	ENST00000507283;ENST00000341048;ENST00000504958;ENST00000434982	T;T;T	0.54675	0.9;0.56;0.99	5.59	4.43	0.53597	.	0.160108	0.42682	N	0.000669	T	0.40546	0.1121	L	0.32530	0.975	0.38854	D	0.956337	B;P	0.42409	0.355;0.779	B;B	0.37480	0.057;0.251	T	0.43702	-0.9375	10	0.59425	D	0.04	.	11.7264	0.51712	0.9307:0.0:0.0693:0.0	.	416;415	B3KVT8;Q3KP44	.;ANR55_HUMAN	H	416;416;373;128	ENSP00000342295:Y416H;ENSP00000424230:Y373H;ENSP00000429421:Y128H	ENSP00000342295:Y416H	Y	-	1	0	ANKRD55	55443086	1.000000	0.71417	0.998000	0.56505	0.751000	0.42716	5.405000	0.66351	1.069000	0.40788	0.529000	0.55759	TAT		0.483	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669		G	55407329	A	G	55407329	3	3	47	1	0	0	0	0	1	0	0	0	681	449	16	4	610	4	ANKRD55	5	55407329	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	170323	55407329	125507931	674	5071										
HTR1A	3350	broad.mit.edu	37	chr5	63256907	63256907	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcggaatatgcgcccatagaGaaccagcatgagcagcagcg	12	11	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:63256907G>T	ENST00000323865.3	-	1	873	c.640C>A	c.(640-642)Ctc>Atc	p.L214I	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	214					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.L214I(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CGCCCATAGAGAACCAGCATG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											99	111	107					5																	63256907		2203	4300	6503	63292663	SO:0001583	missense	3350			AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.640C>A	5.37:g.63256907G>T	ENSP00000316244:p.Leu214Ile		63292663	Q6LAE7	Missense_Mutation	SNP	ENST00000323865.3	37	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336824	0.60963	.	.	ENSG00000178394	ENST00000323865	T	0.39787	1.06	5.7	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.52725	0.1752	L	0.56340	1.77	0.80722	D	1	D	0.58970	0.984	P	0.57152	0.814	T	0.49173	-0.8967	10	0.44086	T	0.13	.	14.0781	0.64903	0.0732:0.0:0.9268:0.0	.	214	P08908	5HT1A_HUMAN	I	214	ENSP00000316244:L214I	ENSP00000316244:L214I	L	-	1	0	HTR1A	63292663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.831000	0.62752	2.692000	0.91855	0.655000	0.94253	CTC		0.582	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		T	63256907	G	T	63256907	3	4	47	1	0	0	0	0	1	0	0	0	7457	942	33	2	631	2	HTR1A	5	63256907	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7849578	63256907	117658353	675	5072										
SFRS12IP1	285672	broad.mit.edu	37	chr5	64036933	64036933	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttcttcattctcttcatcGctatcttcactacttgtact	3	12	6	0	rs542515899		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:64036933G>A	ENST00000513458.4	-	3	323	c.156C>T	c.(154-156)agC>agT	p.S52S	SREK1IP1_ENST00000506252.1_5'Flank	NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	52					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S52S(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						TCTCTTCATCGCTATCTTCAC	0.363													G|||	1	0.000199681	8e-04	0	5008	,	,		17963	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											96	89	91					5																	64036933		2203	4299	6502	64072689	SO:0001819	synonymous_variant	285672			AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"p18 splicing regulatory protein"		"SFRS12-interacting protein 1"	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.156C>T	5.37:g.64036933G>A			64072689	Q32NC8	Silent	SNP	ENST00000513458.4	37	CCDS34171.1																																																																																				0.363	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		A	64036933	G	A	64036933	2	1	47	1	0	0	0	0	0	0	0	1	14205	1078	38	1		1	SFRS12IP1	5	64036933	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	780026	64036933	116878327	676	5073										
ERBB2IP	55914	broad.mit.edu	37	chr5	65346632	65346632	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatacaaaggaaacagattCtttatcagatgaagttacac	7	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:65346632C>A	ENST00000284037.5	+	20	2314	c.1925C>A	c.(1924-1926)tCt>tAt	p.S642Y	ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S638Y|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S642Y|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S642Y	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	642					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)	p.S642C(1)|p.S642Y(1)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GAAACAGATTCTTTATCAGAT	0.318																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	5											86	88	87					5																	65346632		2202	4300	6502	65382388	SO:0001583	missense	55914				CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.1925C>A	5.37:g.65346632C>A	ENSP00000284037:p.Ser642Tyr		65382388	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467678	0.84533	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.08546	3.08;3.08;3.08;3.08;3.08;3.08;3.08;3.08;3.08	5.66	5.66	0.87406	.	0.052784	0.85682	D	0.000000	T	0.21103	0.0508	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;1.0;0.999	D;D;D;D;D;D;D	0.91635	0.999;0.998;0.998;0.996;0.996;0.991;0.997	T	0.00724	-1.1593	10	0.51188	T	0.08	.	19.7415	0.96232	0.0:1.0:0.0:0.0	.	642;642;642;638;642;642;642	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	Y	642;642;642;642;642;642;638;642;642	ENSP00000284037:S642Y;ENSP00000370330:S642Y;ENSP00000370326:S642Y;ENSP00000370323:S642Y;ENSP00000370322:S642Y;ENSP00000370325:S642Y;ENSP00000422766:S638Y;ENSP00000426632:S642Y;ENSP00000422015:S642Y	ENSP00000284037:S642Y	S	+	2	0	ERBB2IP	65382388	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	7.463000	0.80869	2.668000	0.90789	0.561000	0.74099	TCT		0.318	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65346632	C	A	65346632	3	1	47	1	0	0	0	0	1	0	0	0	5220	913	32	2	1995	2	ERBB2IP	5	65346632	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1309699	65346632	115568628	677	5074										
PIK3R1	5295	broad.mit.edu	37	chr5	67588951	67588951	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagaagtgaatgaaaaacttCgagatacagcagacgggacc	11	7	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:67588951C>T	ENST00000521381.1	+	9	1658	c.1042C>T	c.(1042-1044)Cga>Tga	p.R348*	PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.R48*|PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.R78*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.R348*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.R348*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.R348*|PIK3R1_ENST00000523872.1_5'UTR	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	348	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R348*(7)|p.R48*(1)|p.R78*(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TGAAAAACTTCGAGATACAGC	0.353			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	11	Substitution - Nonsense(9)|Whole gene deletion(1)|Unknown(1)	large_intestine(5)|endometrium(5)|lung(1)	5											84	86	85					5																	67588951		2203	4300	6503	67624707	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1042C>T	5.37:g.67588951C>T	ENSP00000428056:p.Arg348*		67624707	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	37	6.145650	0.97324	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000522084;ENST00000320694;ENST00000336483;ENST00000519025	.	.	.	5.02	5.02	0.67125	.	0.118259	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.6425	18.8724	0.92320	0.0:1.0:0.0:0.0	.	.	.	.	X	348;348;348;348;78;78;48;78;21	.	ENSP00000274335:R348X	R	+	1	2	PIK3R1	67624707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.939000	0.48995	2.770000	0.95276	0.484000	0.47621	CGA		0.353	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67588951	C	T	67588951	4	4	47	1	0	0	0	0	0	1	0	0	11949	876	31	1	1202	1	PIK3R1	5	67588951	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2242319	67588951	113326309	678	5075										
PIK3R1	5295	broad.mit.edu	37	chr5	67589168	67589168	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattaatcaaaatatttcatCgagatgggaaatatggcttc	7	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:67589168C>T	ENST00000521381.1	+	10	1772	c.1156C>T	c.(1156-1158)Cga>Tga	p.R386*	PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.R86*|PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.R116*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.R386*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.R386*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.R386*|PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.R23*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	386	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R386*(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AATATTTCATCGAGATGGGAA	0.303			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	3	Substitution - Nonsense(1)|Whole gene deletion(1)|Unknown(1)	large_intestine(2)|lung(1)	5											54	61	59					5																	67589168		2199	4295	6494	67624924	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1156C>T	5.37:g.67589168C>T	ENSP00000428056:p.Arg386*		67624924	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	36	5.931983	0.97116	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7661	19.0433	0.93010	0.0:1.0:0.0:0.0	.	.	.	.	X	386;386;386;386;116;86;23;116;59;23	.	ENSP00000274335:R386X	R	+	1	2	PIK3R1	67624924	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.889000	0.69766	2.797000	0.96272	0.555000	0.69702	CGA		0.303	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67589168	C	T	67589168	4	4	47	1	0	0	0	0	0	1	0	0	11949	876	31	1	1320	1	PIK3R1	5	67589168	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	217	67589168	113326092	679	5076										
MAP1B	4131	broad.mit.edu	37	chr5	71490563	71490563	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaatggtcaagaagtagatCtcccgatttcctacttaact	6	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71490563C>A	ENST00000296755.7	+	5	1679	c.1381C>A	c.(1381-1383)Ctc>Atc	p.L461I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	461					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.L461I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AGAAGTAGATCTCCCGATTTC	0.453																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											99	100	100					5																	71490563		2203	4300	6503	71526319	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.1381C>A	5.37:g.71490563C>A	ENSP00000296755:p.Leu461Ile		71526319	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.076552	0.00375	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	T;T;T	0.03330	3.97;3.97;3.97	5.63	4.47	0.54385	.	0.097447	0.44688	N	0.000430	T	0.01800	0.0057	N	0.04355	-0.22	0.29394	N	0.862395	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40384	-0.9566	10	0.02654	T	1	-10.9902	11.8713	0.52520	0.6777:0.3223:0.0:0.0	.	335;461	A2BDK6;P46821	.;MAP1B_HUMAN	I	461;478;335	ENSP00000296755:L461I;ENSP00000423444:L478I;ENSP00000423416:L335I	ENSP00000296755:L461I	L	+	1	0	MAP1B	71526319	1.000000	0.71417	0.999000	0.59377	0.629000	0.37895	2.320000	0.43797	0.939000	0.37446	-0.309000	0.09137	CTC		0.453	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71490563	C	A	71490563	3	1	47	1	0	0	0	0	1	0	0	0	9258	913	32	2	1399	2	MAP1B	5	71490563	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3901395	71490563	109424697	680	5077			2	7		6	6	3741	N	G_C	8.595788e-06
MAP1B	4131	broad.mit.edu	37	chr5	71491402	71491402	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagctccctaaagacgcaaaGaaatcatctactcctctgtc	5	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71491402G>T	ENST00000296755.7	+	5	2518	c.2220G>T	c.(2218-2220)aaG>aaT	p.K740N		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	740	Lys-rich (highly basic, contains many KKEE and KKEI/V repeats).				axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.K740N(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AAGACGCAAAGAAATCATCTA	0.393																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											61	65	64					5																	71491402		2203	4300	6503	71527158	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2220G>T	5.37:g.71491402G>T	ENSP00000296755:p.Lys740Asn		71527158	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	5.677	0.309582	0.10733	.	.	ENSG00000131711	ENST00000296755	T	0.23348	1.91	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000002	T	0.40171	0.1106	L	0.40543	1.245	0.48762	D	0.999704	D;D	0.69078	0.997;0.997	P;P	0.60789	0.879;0.879	T	0.02173	-1.1201	10	0.27785	T	0.31	-20.9645	19.2913	0.94100	0.0:0.0:1.0:0.0	.	614;740	A2BDK6;P46821	.;MAP1B_HUMAN	N	740	ENSP00000296755:K740N	ENSP00000296755:K740N	K	+	3	2	MAP1B	71527158	1.000000	0.71417	0.989000	0.46669	0.046000	0.14306	6.489000	0.73641	2.644000	0.89710	0.655000	0.94253	AAG		0.393	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71491402	G	T	71491402	3	4	47	1	0	0	0	0	1	0	0	0	9258	933	33	2	2238	2	MAP1B	5	71491402	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	839	71491402	109423858	681	5078			2	7		6	6	3741	N	G_C	8.595788e-06
MAP1B	4131	broad.mit.edu	37	chr5	71492742	71492742	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacaccgctcaacggattttCtgaaggatcaaaaacagatg	8	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71492742C>A	ENST00000296755.7	+	5	3858	c.3560C>A	c.(3559-3561)tCt>tAt	p.S1187Y		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1187					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.S1187Y(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AACGGATTTTCTGAAGGATCA	0.418																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											73	67	69					5																	71492742		2203	4300	6503	71528498	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3560C>A	5.37:g.71492742C>A	ENSP00000296755:p.Ser1187Tyr		71528498	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.285165	0.23478	.	.	ENSG00000131711	ENST00000296755	T	0.03772	3.81	5.26	5.26	0.73747	.	0.000000	0.56097	D	0.000025	T	0.12305	0.0299	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.64042	0.921;0.921	T	0.04537	-1.0944	10	0.52906	T	0.07	-14.7141	19.0668	0.93114	0.0:1.0:0.0:0.0	.	1061;1187	A2BDK6;P46821	.;MAP1B_HUMAN	Y	1187	ENSP00000296755:S1187Y	ENSP00000296755:S1187Y	S	+	2	0	MAP1B	71528498	0.981000	0.34729	0.347000	0.25668	0.028000	0.11728	2.606000	0.46291	2.743000	0.94032	0.655000	0.94253	TCT		0.418	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71492742	C	A	71492742	3	1	47	1	0	0	0	0	1	0	0	0	9258	913	32	2	3578	2	MAP1B	5	71492742	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1340	71492742	109422518	682	5079			2	7		6	6	3741	N	G_C	8.595788e-06
MAP1B	4131	broad.mit.edu	37	chr5	71493290	71493290	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaattcagtgatgccaaaGatgagaatgaaagggcttca	11	5	2	5	rs148650535		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71493290G>T	ENST00000296755.7	+	5	4406	c.4108G>T	c.(4108-4110)Gat>Tat	p.D1370Y		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1370					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.D1370Y(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		TGATGCCAAAGATGAGAATGA	0.468																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											78	80	79					5																	71493290		2203	4300	6503	71529046	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4108G>T	5.37:g.71493290G>T	ENSP00000296755:p.Asp1370Tyr		71529046	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.220804	0.39201	.	.	ENSG00000131711	ENST00000296755	T	0.03607	3.87	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000004	T	0.04588	0.0125	N	0.24115	0.695	0.54753	D	0.999987	B;B	0.32829	0.386;0.386	B;B	0.31495	0.131;0.131	T	0.49409	-0.8943	10	0.87932	D	0	-22.9965	19.877	0.96880	0.0:0.0:1.0:0.0	.	1244;1370	A2BDK6;P46821	.;MAP1B_HUMAN	Y	1370	ENSP00000296755:D1370Y	ENSP00000296755:D1370Y	D	+	1	0	MAP1B	71529046	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	7.539000	0.82063	2.709000	0.92574	0.561000	0.74099	GAT		0.468	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71493290	G	T	71493290	3	4	47	1	0	0	0	0	1	0	0	0	9258	942	33	2	4126	2	MAP1B	5	71493290	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	548	71493290	109421970	683	5080			2	7		6	6	3741	N	G_C	8.595788e-06
MAP1B	4131	broad.mit.edu	37	chr5	71494136	71494136	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtctattgaatttggccaaGaatctcctgagcaatccctt	7	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71494136G>T	ENST00000296755.7	+	5	5252	c.4954G>T	c.(4954-4956)Gaa>Taa	p.E1652*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1652					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E1652*(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		ATTTGGCCAAGAATCTCCTGA	0.478																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Nonsense(1)	large_intestine(1)	5											114	118	117					5																	71494136		2203	4300	6503	71529892	SO:0001587	stop_gained	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4954G>T	5.37:g.71494136G>T	ENSP00000296755:p.Glu1652*		71529892	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	46	12.256563	0.99651	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-20.9815	18.7095	0.91651	0.0:0.0:1.0:0.0	.	.	.	.	X	1652	.	ENSP00000296755:E1652X	E	+	1	0	MAP1B	71529892	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.476000	0.97823	2.435000	0.82474	0.313000	0.20887	GAA		0.478	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71494136	G	T	71494136	4	4	47	1	0	0	0	0	0	1	0	0	9258	943	33	2	4972	2	MAP1B	5	71494136	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	846	71494136	109421124	684	5081			2	7		6	6	3741	N	G_C	8.595788e-06
MAP1B	4131	broad.mit.edu	37	chr5	71494303	71494303	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cataagataccacctatggaGgagccgtcctacacccaaga	8	13	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71494303G>T	ENST00000296755.7	+	5	5419	c.5121G>T	c.(5119-5121)gaG>gaT	p.E1707D		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1707					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E1707D(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		CACCTATGGAGGAGCCGTCCT	0.498																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											104	102	103					5																	71494303		2203	4300	6503	71530059	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5121G>T	5.37:g.71494303G>T	ENSP00000296755:p.Glu1707Asp		71530059	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	8.944	0.966637	0.18659	.	.	ENSG00000131711	ENST00000296755	T	0.03358	3.96	4.47	2.65	0.31530	.	0.098474	0.44285	D	0.000467	T	0.01800	0.0057	N	0.08118	0	0.36726	D	0.881429	B;B	0.14012	0.009;0.009	B;B	0.14578	0.005;0.011	T	0.48456	-0.9034	10	0.51188	T	0.08	-23.4023	1.6475	0.02764	0.2567:0.1411:0.4577:0.1445	.	1581;1707	A2BDK6;P46821	.;MAP1B_HUMAN	D	1707	ENSP00000296755:E1707D	ENSP00000296755:E1707D	E	+	3	2	MAP1B	71530059	0.974000	0.33945	0.997000	0.53966	0.900000	0.52787	0.073000	0.14640	0.607000	0.29982	0.448000	0.29417	GAG		0.498	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71494303	G	T	71494303	3	4	47	1	0	0	0	0	1	0	0	0	9258	991	35	2	5139	2	MAP1B	5	71494303	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	167	71494303	109420957	685	5082			2	7		6	6	3741	N	G_C	8.595788e-06
ZNF366	167465	broad.mit.edu	37	chr5	71756658	71756658	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttctgcttggtctcctcGctctcctggggctcggcttt	10	15	3	0	rs371586695		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:71756658G>A	ENST00000318442.5	-	2	1156	c.666C>T	c.(664-666)agC>agT	p.S222S		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	222					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.S222S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGGTCTCCTCGCTCTCCTGGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G		0,4406		0,0,2203	88	87	88		666	-0.5	1	5		88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF366	NM_152625.1		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		222/745	71756658	2,13004	2203	4300	6503	71792414	SO:0001819	synonymous_variant	167465			AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.666C>T	5.37:g.71756658G>A			71792414	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																				0.662	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			A	71756658	G	A	71756658	2	1	47	1	0	0	0	0	0	0	0	1	17909	1078	38	1		1	ZNF366	5	71756658	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	262355	71756658	109158602	686	5083										
FAM169A	26049	broad.mit.edu	37	chr5	74137451	74137451	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgtaatcttcagcagaattTtccaattcctcatggctgca	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:74137451T>G	ENST00000389156.4	-	2	141	c.51A>C	c.(49-51)gaA>gaC	p.E17D	FAM169A_ENST00000380515.3_Missense_Mutation_p.E17D|FAM169A_ENST00000510496.1_Missense_Mutation_p.E17D	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	17						membrane (GO:0016020)|nucleus (GO:0005634)		p.E17D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						CAGCAGAATTTTCCAATTCCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	95	98					5																	74137451		1845	4099	5944	74173207	SO:0001583	missense	26049				CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.51A>C	5.37:g.74137451T>G	ENSP00000373808:p.Glu17Asp		74173207	A8K1T9|Q6MZT0|Q9H989	Missense_Mutation	SNP	ENST00000389156.4	37	CCDS43330.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.068348	0.76301	.	.	ENSG00000198780	ENST00000389156;ENST00000510496;ENST00000380515;ENST00000513277;ENST00000514200;ENST00000506954	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.61	3.16	0.36331	.	0.075820	0.49916	N	0.000127	T	0.52468	0.1736	L	0.59436	1.845	0.47341	D	0.999398	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.50898	-0.8773	10	0.56958	D	0.05	-12.3526	3.0262	0.06091	0.1763:0.2831:0.0:0.5406	.	17;17	D6RB01;Q9Y6X4	.;F169A_HUMAN	D	17	ENSP00000373808:E17D;ENSP00000424578:E17D;ENSP00000369886:E17D;ENSP00000423631:E17D;ENSP00000423883:E17D;ENSP00000421451:E17D	ENSP00000369886:E17D	E	-	3	2	FAM169A	74173207	1.000000	0.71417	0.988000	0.46212	0.966000	0.64601	2.070000	0.41491	0.385000	0.24970	0.477000	0.44152	GAA		0.398	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2			G	74137451	T	G	74137451	3	3	47	1	0	0	0	0	1	0	0	0	5503	1838	64	4	2009	4	FAM169A	5	74137451	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2380793	74137451	106777809	687	5084										
POLK	51426	broad.mit.edu	37	chr5	74892497	74892497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaaactttaaaatgttctCgtgttcacatgtttctgcta	6	7	3	1	rs535351080		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:74892497C>T	ENST00000241436.4	+	13	2151	c.1979C>T	c.(1978-1980)tCg>tTg	p.S660L	POLK_ENST00000380481.3_Missense_Mutation_p.S570L|POLK_ENST00000508526.1_Missense_Mutation_p.S462L|POLK_ENST00000352007.5_Missense_Mutation_p.S462L|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000504026.1_Intron|CTC-366B18.2_ENST00000511329.1_RNA	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	660					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.S660L(2)		endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		AAAATGTTCTCGTGTTCACAT	0.373								DNA polymerases (catalytic subunits)																																								2	Substitution - Missense(2)	large_intestine(2)	5											85	83	84					5																	74892497		2203	4300	6503	74928253	SO:0001583	missense	51426			AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1979C>T	5.37:g.74892497C>T	ENSP00000241436:p.Ser660Leu		74928253	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444338	0.25987	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000508526;ENST00000380481	T;T;T;T	0.56444	1.23;0.46;0.46;1.23	4.96	1.94	0.25998	.	1.603320	0.03736	N	0.254187	T	0.47210	0.1433	L	0.54323	1.7	0.09310	N	1	B;B	0.17465	0.022;0.008	B;B	0.09377	0.004;0.002	T	0.20571	-1.0271	10	0.40728	T	0.16	0.0361	3.9565	0.09391	0.1575:0.5803:0.1639:0.0984	.	462;660	Q9UBT6-3;Q9UBT6	.;POLK_HUMAN	L	660;462;462;570	ENSP00000241436:S660L;ENSP00000342256:S462L;ENSP00000426853:S462L;ENSP00000369848:S570L	ENSP00000241436:S660L	S	+	2	0	POLK	74928253	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.371000	0.20450	0.146000	0.19002	0.655000	0.94253	TCG		0.373	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		T	74892497	C	T	74892497	3	4	47	1	0	0	0	0	1	0	0	0	12235	893	31	1	2025	1	POLK	5	74892497	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	755046	74892497	106022763	688	5085										
F2RL2	2151	broad.mit.edu	37	chr5	75914392	75914392	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaggggaactcttcaaaaGaatttgggggagctccacga	12	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:75914392G>T	ENST00000296641.4	-	2	343	c.140C>A	c.(139-141)tCt>tAt	p.S47Y	IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.S25Y|IQGAP2_ENST00000396234.3_Intron|IQGAP2_ENST00000379730.3_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	47					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)	p.S47Y(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		CTCTTCAAAAGAATTTGGGGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	97	93					5																	75914392		2201	4299	6500	75950148	SO:0001583	missense	2151			U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"GPCR / Class A : Protease activated receptors"	3539	protein-coding gene	gene with protein product	"proteinase-activated receptor-3"	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.140C>A	5.37:g.75914392G>T	ENSP00000296641:p.Ser47Tyr		75950148	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	G	2.303	-0.359793	0.05138	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.65364	-0.15;-0.14	4.65	1.68	0.24146	.	1.155620	0.06477	U	0.732184	T	0.51244	0.1663	L	0.48642	1.525	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.49062	-0.8978	10	0.72032	D	0.01	-4.6145	1.5319	0.02537	0.1749:0.1169:0.3703:0.3379	.	47	O00254	PAR3_HUMAN	Y	47;25	ENSP00000296641:S47Y;ENSP00000426703:S25Y	ENSP00000296641:S47Y	S	-	2	0	F2RL2	75950148	0.000000	0.05858	0.427000	0.26684	0.090000	0.18270	-0.367000	0.07553	0.966000	0.38159	0.563000	0.77884	TCT		0.423	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			T	75914392	G	T	75914392	3	4	47	1	0	0	0	0	1	0	0	0	5358	942	33	2	988	2	F2RL2	5	75914392	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1021895	75914392	105000868	689	5086										
AP3B1	8546	broad.mit.edu	37	chr5	77334942	77334942	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggatattttctatctttcGatcagtagtgttattcagtg	9	5	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:77334942G>A	ENST00000255194.6	-	23	2909	c.2734C>T	c.(2734-2736)Cga>Tga	p.R912*	AP3B1_ENST00000523204.1_5'UTR|AP3B1_ENST00000519295.1_Nonsense_Mutation_p.R863*	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	912					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)	p.R912*(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TCTATCTTTCGATCAGTAGTG	0.323									Hermansky-Pudlak syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	5											135	127	130					5																	77334942		2203	4300	6503	77370698	SO:0001587	stop_gained	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2734C>T	5.37:g.77334942G>A	ENSP00000255194:p.Arg912*		77370698	E5RJ68|O00580|Q7Z393|Q9HD66	Nonsense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	G	43	10.160365	0.99350	.	.	ENSG00000132842	ENST00000255194;ENST00000519295	.	.	.	5.76	2.99	0.34606	.	1.001980	0.08043	N	0.995504	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	2.6331	5.9188	0.19070	0.0649:0.1203:0.5657:0.2491	.	.	.	.	X	912;863	.	ENSP00000255194:R912X	R	-	1	2	AP3B1	77370698	0.994000	0.37717	0.260000	0.24451	0.982000	0.71751	2.183000	0.42565	0.343000	0.23821	0.591000	0.81541	CGA		0.323	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			A	77334942	G	A	77334942	4	1	47	1	0	0	0	0	0	1	0	0	744	1066	37	1	570	1	AP3B1	5	77334942	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1420550	77334942	103580318	690	5087										
DMGDH	29958	broad.mit.edu	37	chr5	78322359	78322359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatgatagcgtcatacagcGccacagaatcttctcttctg	7	12	5	2	rs369589026		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:78322359G>A	ENST00000255189.3	-	13	2106	c.2078C>T	c.(2077-2079)gCg>gTg	p.A693V	DMGDH_ENST00000540686.1_Missense_Mutation_p.A313V|DMGDH_ENST00000380311.4_Missense_Mutation_p.A492V	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	693					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)	p.A693V(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		GTCATACAGCGCCACAGAATC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	VAL/ALA	0,4406		0,0,2203	93	85	88		2078	2.8	0	5		88	1,8599	1.2+/-3.3	0,1,4299	no	missense	DMGDH	NM_013391.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	693/867	78322359	1,13005	2203	4300	6503	78358115	SO:0001583	missense	29958			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2078C>T	5.37:g.78322359G>A	ENSP00000255189:p.Ala693Val		78358115	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	G	4.132	0.022725	0.08006	0.0	1.16E-4	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.52	2.8	0.32819	Glycine cleavage T-protein, N-terminal (1);	0.502011	0.23716	N	0.045280	T	0.71384	0.3333	M	0.79693	2.465	0.09310	N	1	P;P;B;B	0.43542	0.81;0.777;0.137;0.072	B;B;B;B	0.32342	0.126;0.144;0.04;0.067	T	0.62263	-0.6891	10	0.29301	T	0.29	.	10.3035	0.43667	0.2119:0.0:0.7881:0.0	.	313;492;543;693	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	V	693;532;492;313;543	ENSP00000255189:A693V;ENSP00000430972:A532V;ENSP00000369667:A492V;ENSP00000439478:A313V	ENSP00000255189:A693V	A	-	2	0	DMGDH	78358115	0.811000	0.29063	0.001000	0.08648	0.031000	0.12232	4.061000	0.57485	0.722000	0.32252	-0.224000	0.12420	GCG		0.498	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		A	78322359	G	A	78322359	3	1	47	1	0	0	0	0	1	0	0	0	4592	1087	38	1	538	1	DMGDH	5	78322359	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	987417	78322359	102592901	691	5088										
CMYA5	202333	broad.mit.edu	37	chr5	79027472	79027472	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcatttccaccgtatgcaAcccaggaagcagagaaaaga	8	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79027472A>C	ENST00000446378.2	+	2	2915	c.2884A>C	c.(2884-2886)Acc>Ccc	p.T962P		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	962					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.T962P(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ACCGTATGCAACCCAGGAAGC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	5											91	85	87					5																	79027472		1883	4130	6013	79063228	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.2884A>C	5.37:g.79027472A>C	ENSP00000394770:p.Thr962Pro		79063228	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	4.680	0.126345	0.08931	.	.	ENSG00000164309	ENST00000446378	T	0.49720	0.77	5.87	1.79	0.24919	.	0.962520	0.08563	N	0.927225	T	0.54303	0.1850	M	0.76574	2.34	0.09310	N	1	D	0.67145	0.996	P	0.50708	0.648	T	0.41305	-0.9516	10	0.48119	T	0.1	.	6.1022	0.20053	0.6734:0.1478:0.1788:0.0	.	962	Q8N3K9	CMYA5_HUMAN	P	962	ENSP00000394770:T962P	ENSP00000394770:T962P	T	+	1	0	CMYA5	79063228	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.670000	0.25157	0.476000	0.27440	0.533000	0.62120	ACC		0.398	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79027472	A	C	79027472	3	2	47	1	0	0	0	0	1	0	0	0	3596	43	2	4	2890	4	CMYA5	5	79027472	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	705113	79027472	101887788	692	5089										
CMYA5	202333	broad.mit.edu	37	chr5	79028825	79028825	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcagatgaacattcagttCttgcagaagaagacaaggtg	11	7	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79028825C>A	ENST00000446378.2	+	2	4268	c.4237C>A	c.(4237-4239)Ctt>Att	p.L1413I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1413					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.L1413I(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ACATTCAGTTCTTGCAGAAGA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	5											33	33	33					5																	79028825		1888	4101	5989	79064581	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.4237C>A	5.37:g.79028825C>A	ENSP00000394770:p.Leu1413Ile		79064581	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	5.692	0.312319	0.10789	.	.	ENSG00000164309	ENST00000446378	T	0.06933	3.24	6.08	1.23	0.21249	.	0.726321	0.11256	N	0.583138	T	0.06325	0.0163	L	0.29908	0.895	0.09310	N	1	P	0.39282	0.666	B	0.37508	0.252	T	0.33214	-0.9877	10	0.72032	D	0.01	.	5.2689	0.15615	0.0:0.5563:0.1371:0.3066	.	1413	Q8N3K9	CMYA5_HUMAN	I	1413	ENSP00000394770:L1413I	ENSP00000394770:L1413I	L	+	1	0	CMYA5	79064581	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	0.043000	0.13971	-0.057000	0.13199	0.650000	0.86243	CTT		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79028825	C	A	79028825	3	1	47	1	0	0	0	0	1	0	0	0	3596	913	32	2	4243	2	CMYA5	5	79028825	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1353	79028825	101886435	693	5090										
CMYA5	202333	broad.mit.edu	37	chr5	79029830	79029830	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcagccatttactttttctTtaaaaggattatcagaggag	7	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79029830T>G	ENST00000446378.2	+	2	5273	c.5242T>G	c.(5242-5244)Tta>Gta	p.L1748V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1748					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.L1748V(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TACTTTTTCTTTAAAAGGATT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	5											49	48	48					5																	79029830		1826	4077	5903	79065586	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.5242T>G	5.37:g.79029830T>G	ENSP00000394770:p.Leu1748Val		79065586	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.261836	0.39995	.	.	ENSG00000164309	ENST00000446378	T	0.49139	0.79	3.64	3.64	0.41730	.	.	.	.	.	T	0.32376	0.0827	N	0.22421	0.69	0.26503	N	0.974743	P	0.46784	0.884	B	0.43123	0.409	T	0.04593	-1.0940	9	0.15499	T	0.54	.	8.7081	0.34367	0.0:0.0:0.0:1.0	.	1748	Q8N3K9	CMYA5_HUMAN	V	1748	ENSP00000394770:L1748V	ENSP00000394770:L1748V	L	+	1	2	CMYA5	79065586	0.661000	0.27430	0.907000	0.35723	0.378000	0.30076	0.223000	0.17719	1.304000	0.44892	0.460000	0.39030	TTA		0.438	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79029830	T	G	79029830	3	3	47	1	0	0	0	0	1	0	0	0	3596	1838	64	4	5248	4	CMYA5	5	79029830	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1005	79029830	101885430	694	5091										
CMYA5	202333	broad.mit.edu	37	chr5	79031062	79031062	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacaaaatccacctacacaAccaaaggtggctaagccgga	7	13	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79031062A>G	ENST00000446378.2	+	2	6505	c.6474A>G	c.(6472-6474)caA>caG	p.Q2158Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2158					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.Q2158Q(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CACCTACACAACCAAAGGTGG	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	5											75	72	73					5																	79031062		1875	4107	5982	79066818	SO:0001819	synonymous_variant	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6474A>G	5.37:g.79031062A>G			79066818	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																				0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79031062	A	G	79031062	2	3	47	1	0	0	0	0	0	0	0	1	3596	40	2	4		4	CMYA5	5	79031062	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1232	79031062	101884198	695	5092										
CMYA5	202333	broad.mit.edu	37	chr5	79031216	79031216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacacagccaagtccatccGtagaaaaagcagtgactgtg	9	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79031216G>A	ENST00000446378.2	+	2	6659	c.6628G>A	c.(6628-6630)Gta>Ata	p.V2210I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2210					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.V2210I(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAGTCCATCCGTAGAAAAAGC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	5											114	111	112					5																	79031216		1883	4101	5984	79066972	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6628G>A	5.37:g.79031216G>A	ENSP00000394770:p.Val2210Ile		79066972	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409480	0.25378	.	.	ENSG00000164309	ENST00000446378	T	0.19394	2.15	6.16	4.38	0.52667	.	0.939574	0.08847	N	0.885044	T	0.20861	0.0502	L	0.60455	1.87	0.09310	N	1	B	0.33379	0.41	B	0.19666	0.026	T	0.17776	-1.0358	10	0.56958	D	0.05	.	8.9359	0.35700	0.0785:0.1482:0.7733:0.0	.	2210	Q8N3K9	CMYA5_HUMAN	I	2210	ENSP00000394770:V2210I	ENSP00000394770:V2210I	V	+	1	0	CMYA5	79066972	0.103000	0.21917	0.068000	0.19968	0.587000	0.36485	0.718000	0.25866	0.918000	0.36919	0.650000	0.86243	GTA		0.398	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79031216	G	A	79031216	3	1	47	1	0	0	0	0	1	0	0	0	3596	1145	40	1	6634	1	CMYA5	5	79031216	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	154	79031216	101884044	696	5093										
CMYA5	202333	broad.mit.edu	37	chr5	79034299	79034299	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgatggaacaggaatataTtttgagaagtacatactcaa	9	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79034299T>G	ENST00000446378.2	+	2	9742	c.9711T>G	c.(9709-9711)taT>taG	p.Y3237*		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3237					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.Y3237*(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CAGGAATATATTTTGAGAAGT	0.418																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											61	59	60					5																	79034299		1894	4121	6015	79070055	SO:0001587	stop_gained	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9711T>G	5.37:g.79034299T>G	ENSP00000394770:p.Tyr3237*		79070055	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Nonsense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	51	18.454740	0.99905	.	.	ENSG00000164309	ENST00000446378	.	.	.	5.67	4.48	0.54585	.	0.295611	0.24638	N	0.036821	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8456	0.52383	0.0:0.0694:0.0:0.9306	.	.	.	.	X	3237	.	ENSP00000394770:Y3237X	Y	+	3	2	CMYA5	79070055	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.509000	0.45459	0.932000	0.37266	0.533000	0.62120	TAT		0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79034299	T	G	79034299	4	3	47	1	0	0	0	0	0	1	0	0	3596	1500	52	4	9717	4	CMYA5	5	79034299	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3083	79034299	101880961	697	5094										
SPZ1	84654	broad.mit.edu	37	chr5	79616659	79616659	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgcacaagtttttgcaagaGatttggtaaatcgtttagaa	9	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79616659G>T	ENST00000296739.4	+	1	870	c.625G>T	c.(625-627)Gat>Tat	p.D209Y		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	209	Basic motif. {ECO:0000255}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D209Y(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TTTTGCAAGAGATTTGGTAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											63	58	59					5																	79616659		1820	4070	5890	79652415	SO:0001583	missense	84654				CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.625G>T	5.37:g.79616659G>T	ENSP00000369611:p.Asp209Tyr		79652415	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.778255	0.49786	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.58797	0.31;1.29	4.45	1.49	0.22878	.	1.016950	0.07865	N	0.966985	T	0.64702	0.2622	L	0.47190	1.495	0.09310	N	1	D	0.58268	0.982	P	0.60012	0.867	T	0.51857	-0.8652	10	0.52906	T	0.07	-10.6905	8.2206	0.31539	0.0894:0.3624:0.5482:0.0	.	209	Q9BXG8	SPZ1_HUMAN	Y	209	ENSP00000426530:D209Y;ENSP00000369611:D209Y	ENSP00000369611:D209Y	D	+	1	0	SPZ1	79652415	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	0.366000	0.20365	0.285000	0.22329	0.563000	0.77884	GAT		0.353	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		T	79616659	G	T	79616659	3	4	47	1	0	0	0	0	1	0	0	0	15166	942	33	2	627	2	SPZ1	5	79616659	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	582360	79616659	101298601	698	5095										
DHFR	1719	broad.mit.edu	37	chr5	79945224	79945224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttacttgagttctctgctgaGaactaaattaattctaccct	5	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:79945224G>T	ENST00000439211.2	-	3	719	c.226C>A	c.(226-228)Ctc>Atc	p.L76I	DHFR_ENST00000511032.1_Missense_Mutation_p.L76I|DHFR_ENST00000504396.1_Missense_Mutation_p.L24I|DHFR_ENST00000513048.1_5'UTR|DHFR_ENST00000505337.1_Missense_Mutation_p.L76I	NM_000791.3	NP_000782.1	P00374	DYR_HUMAN	dihydrofolate reductase	76	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.				folic acid metabolic process (GO:0046655)|G1/S transition of mitotic cell cycle (GO:0000082)|glycine biosynthetic process (GO:0006545)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to methotrexate (GO:0031427)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	dihydrofolate reductase activity (GO:0004146)|drug binding (GO:0008144)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)	p.L76I(1)		kidney(1)|large_intestine(1)	2		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.69e-46)|Epithelial(54;7.49e-41)|all cancers(79;1.54e-35)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Proguanil(DB01131)|Pyrimethamine(DB00205)|Trimethoprim(DB00440)|Trimetrexate(DB01157)	TCTCTGCTGAGAACTAAATTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	56	56					5																	79945224		2107	4260	6367	79980980	SO:0001583	missense	1719				CCDS47240.1	5q11.2-q13.2	2012-10-02			ENSG00000228716	ENSG00000228716	1.5.1.3		2861	protein-coding gene	gene with protein product		126060					Standard	XM_005248455		Approved		uc003kgy.1	P00374	OTTHUMG00000162529	ENST00000439211.2:c.226C>A	5.37:g.79945224G>T	ENSP00000396308:p.Leu76Ile		79980980	B4DDD2|Q14130|Q6IRW8	Missense_Mutation	SNP	ENST00000439211.2	37	CCDS47240.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.886745	0.72410	.	.	ENSG00000228716	ENST00000439211;ENST00000505337;ENST00000511032;ENST00000504396	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.41	5.41	0.78517	Dihydrofolate reductase domain (2);Dihydrofolate reductase-like domain (2);	.	.	.	.	D	0.83732	0.5318	L	0.56199	1.76	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.79784	0.993;0.993;0.993	T	0.82898	-0.0229	8	.	.	.	-8.0414	11.4602	0.50206	0.0839:0.0:0.9161:0.0	.	76;76;76	B4DM58;P00374;B0YJ76	.;DYR_HUMAN;.	I	76;76;76;24	ENSP00000396308:L76I;ENSP00000426474:L76I;ENSP00000422732:L76I;ENSP00000421334:L24I	.	L	-	1	0	DHFR	79980980	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.827000	0.75303	2.524000	0.85096	0.557000	0.71058	CTC		0.328	DHFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369450.1	NM_000791		T	79945224	G	T	79945224	3	4	47	1	0	0	0	0	1	0	0	0	4492	942	33	2	353	2	DHFR	5	79945224	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	328565	79945224	100970036	699	5096										
RASGRF2	5924	broad.mit.edu	37	chr5	80409437	80409437	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaatccccacgtctgtgtcGcaaattctcttccccgccac	5	18	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:80409437G>A	ENST00000265080.4	+	15	2235	c.2168G>A	c.(2167-2169)cGc>cAc	p.R723H	CTD-2193P3.2_ENST00000508993.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	723	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R723H(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CGTCTGTGTCGCAAATTCTCT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											92	94	93					5																	80409437		2203	4300	6503	80445193	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2168G>A	5.37:g.80409437G>A	ENSP00000265080:p.Arg723His		80445193	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.912205	0.92178	.	.	ENSG00000113319	ENST00000265080	T	0.78003	-1.14	5.31	5.31	0.75309	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.200700	0.53938	D	0.000052	D	0.87838	0.6278	M	0.77103	2.36	0.58432	D	0.999999	D	0.76494	0.999	D	0.64687	0.928	D	0.89117	0.3500	10	0.72032	D	0.01	.	18.6673	0.91495	0.0:0.0:1.0:0.0	.	723	O14827	RGRF2_HUMAN	H	723	ENSP00000265080:R723H	ENSP00000265080:R723H	R	+	2	0	RASGRF2	80445193	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	9.430000	0.97488	2.498000	0.84270	0.650000	0.86243	CGC		0.473	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		A	80409437	G	A	80409437	3	1	47	1	0	0	0	0	1	0	0	0	13110	1087	38	1	2226	1	RASGRF2	5	80409437	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	464213	80409437	100505823	700	5097										
RASGRF2	5924	broad.mit.edu	37	chr5	80515554	80515554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacatcatcagagagatacGccagttccagcagacttcct	7	13	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:80515554G>A	ENST00000265080.4	+	26	3645	c.3578G>A	c.(3577-3579)cGc>cAc	p.R1193H	CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000511495.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	1193	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1193H(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		AGAGAGATACGCCAGTTCCAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											82	82	82					5																	80515554		2203	4300	6503	80551310	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.3578G>A	5.37:g.80515554G>A	ENSP00000265080:p.Arg1193His		80551310	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	G	34	5.380955	0.95945	.	.	ENSG00000113319	ENST00000265080	T	0.31769	1.48	5.68	5.68	0.88126	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.52597	0.1744	M	0.76170	2.325	0.80722	D	1	D	0.76494	0.999	P	0.55508	0.777	T	0.55592	-0.8117	10	0.72032	D	0.01	.	19.7831	0.96426	0.0:0.0:1.0:0.0	.	1193	O14827	RGRF2_HUMAN	H	1193	ENSP00000265080:R1193H	ENSP00000265080:R1193H	R	+	2	0	RASGRF2	80551310	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.687000	0.91594	0.561000	0.74099	CGC		0.343	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		A	80515554	G	A	80515554	3	1	47	1	0	0	0	0	1	0	0	0	13110	1087	38	1	3680	1	RASGRF2	5	80515554	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	106117	80515554	100399706	701	5098										
ZCCHC9	84240	broad.mit.edu	37	chr5	80600765	80600765	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacataaaaagaacaaaaaGaaaaaagagtacttaaatga	5	3	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:80600765G>T	ENST00000254037.2	+	1	3344	c.189G>T	c.(187-189)aaG>aaT	p.K63N	ZCCHC9_ENST00000438268.2_Missense_Mutation_p.K63N|ZCCHC9_ENST00000407610.3_Missense_Mutation_p.K63N|ZCCHC9_ENST00000506458.1_Intron|ZCCHC9_ENST00000380199.5_Missense_Mutation_p.K63N			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	63	Poly-Lys.				negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K63N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		AGAACAAAAAGAAAAAAGAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	70	70					5																	80600765		2203	4300	6503	80636521	SO:0001583	missense	84240			BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"Zinc fingers, CCHC domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25424	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 41"					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.189G>T	5.37:g.80600765G>T	ENSP00000254037:p.Lys63Asn		80636521	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260596	0.80246	.	.	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.18	5.18	0.71444	.	0.148065	0.56097	D	0.000021	T	0.61837	0.2379	M	0.65498	2.005	0.54753	D	0.999986	D	0.63880	0.993	P	0.53954	0.738	T	0.66404	-0.5932	10	0.72032	D	0.01	-14.7519	18.6578	0.91460	0.0:0.0:1.0:0.0	.	63	Q8N567	ZCHC9_HUMAN	N	63	ENSP00000254037:K63N;ENSP00000385047:K63N;ENSP00000369546:K63N;ENSP00000412637:K63N	ENSP00000254037:K63N	K	+	3	2	ZCCHC9	80636521	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.803000	0.62546	2.544000	0.85801	0.655000	0.94253	AAG		0.373	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		T	80600765	G	T	80600765	3	4	47	1	0	0	0	0	1	0	0	0	17634	933	33	2	191	2	ZCCHC9	5	80600765	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	85211	80600765	100314495	702	5099										
VCAN	1462	broad.mit.edu	37	chr5	82816219	82816219	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagagatgagaacagatacTtatacagatgaaatacaaga	8	6	0	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:82816219T>G	ENST00000265077.3	+	7	2659	c.2094T>G	c.(2092-2094)acT>acG	p.T698T	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Silent_p.T650T|VCAN_ENST00000342785.4_Silent_p.T698T|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	698	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.T698T(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	GAACAGATACTTATACAGATG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	5											53	55	54					5																	82816219		2188	4294	6482	82851975	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2094T>G	5.37:g.82816219T>G			82851975	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.353	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82816219	T	G	82816219	2	3	47	1	0	0	0	0	0	0	0	1	17178	1596	56	4		4	VCAN	5	82816219	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2215454	82816219	98099041	703	5100										
VCAN	1462	broad.mit.edu	37	chr5	82816938	82816938	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacctctctaagccagtatCtactgttccccaatttgcac	6	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:82816938C>A	ENST00000265077.3	+	7	3378	c.2813C>A	c.(2812-2814)tCt>tAt	p.S938Y	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.S890Y|VCAN_ENST00000342785.4_Missense_Mutation_p.S938Y|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	938	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.S938Y(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AAGCCAGTATCTACTGTTCCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	5											133	123	127					5																	82816938		2203	4300	6503	82852694	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2813C>A	5.37:g.82816938C>A	ENSP00000265077:p.Ser938Tyr		82852694	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	9.286	1.049301	0.19827	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.23950	1.88;1.88;1.88	5.77	4.68	0.58851	.	0.332151	0.25820	N	0.028098	T	0.36054	0.0953	L	0.57536	1.79	0.25771	N	0.984831	D;P	0.59767	0.986;0.904	P;B	0.54100	0.742;0.36	T	0.19976	-1.0289	10	0.54805	T	0.06	.	9.3833	0.38327	0.0:0.871:0.0:0.129	.	938;938	P13611-3;P13611	.;CSPG2_HUMAN	Y	938;938;890	ENSP00000265077:S938Y;ENSP00000342768:S938Y;ENSP00000425959:S890Y	ENSP00000265077:S938Y	S	+	2	0	VCAN	82852694	0.162000	0.22906	0.066000	0.19879	0.132000	0.20833	2.839000	0.48207	1.094000	0.41399	0.655000	0.94253	TCT		0.438	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82816938	C	A	82816938	3	1	47	1	0	0	0	0	1	0	0	0	17178	913	32	2	2835	2	VCAN	5	82816938	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	719	82816938	98098322	704	5101										
VCAN	1462	broad.mit.edu	37	chr5	82817254	82817254	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaaagaacagactgcagaGaaaccagttcctgctctcag	10	10	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:82817254G>A	ENST00000265077.3	+	7	3694	c.3129G>A	c.(3127-3129)gaG>gaA	p.E1043E	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Silent_p.E995E|VCAN_ENST00000342785.4_Silent_p.E1043E|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1043	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.E1043E(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AGACTGCAGAGAAACCAGTTC	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	5											47	45	45					5																	82817254		2203	4300	6503	82853010	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.3129G>A	5.37:g.82817254G>A			82853010	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82817254	G	A	82817254	2	1	47	1	0	0	0	0	0	0	0	1	17178	933	33	3		3	VCAN	5	82817254	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	316	82817254	98098006	705	5102										
VCAN	1462	broad.mit.edu	37	chr5	82836565	82836565	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatactatcatagatattgaTcatactaaacctgtgtatga	5	6	2	3	rs75771891	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:82836565T>A	ENST00000265077.3	+	8	8308	c.7743T>A	c.(7741-7743)gaT>gaA	p.D2581E	VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.D1594E	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2581	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.D2581E(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	TAGATATTGATCATACTAAAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											66	68	67					5																	82836565		2203	4300	6503	82872321	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7743T>A	5.37:g.82836565T>A	ENSP00000265077:p.Asp2581Glu		82872321	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487666	0.64074	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.58940	0.3;0.3	6.04	2.48	0.30137	.	0.000000	0.64402	D	0.000004	T	0.67316	0.2880	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.63950	-0.6521	10	0.45353	T	0.12	.	8.1049	0.30879	0.0:0.2229:0.0:0.7771	.	1594;2581	P13611-2;P13611	.;CSPG2_HUMAN	E	2581;1594	ENSP00000265077:D2581E;ENSP00000340062:D1594E	ENSP00000265077:D2581E	D	+	3	2	VCAN	82872321	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	1.300000	0.33436	0.547000	0.28938	-0.371000	0.07208	GAT		0.343	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82836565	T	A	82836565	3	1	47	1	0	0	0	0	1	0	0	0	17178	1432	50	5	7769	5	VCAN	5	82836565	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	19311	82836565	98078695	706	5103										
MEF2C	4208	broad.mit.edu	37	chr5	88018519	88018519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaatgggggagtggaattCgttccggtgatcctctcggt	14	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:88018519C>T	ENST00000437473.2	-	11	1741	c.1324G>A	c.(1324-1326)Gaa>Aaa	p.E442K	MEF2C_ENST00000539796.1_Missense_Mutation_p.E386K|MEF2C_ENST00000504921.2_Missense_Mutation_p.E442K|MEF2C_ENST00000510942.1_Missense_Mutation_p.E434K|MEF2C_ENST00000424173.2_Missense_Mutation_p.E432K|CTC-467M3.1_ENST00000510274.1_RNA|MEF2C_ENST00000340208.5_Missense_Mutation_p.E452K|MEF2C_ENST00000506554.1_3'UTR|MEF2C_ENST00000514028.1_Missense_Mutation_p.E442K|MEF2C_ENST00000514015.1_Missense_Mutation_p.E410K|MEF2C_ENST00000508569.1_Missense_Mutation_p.E402K	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C	442					apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E442K(2)|p.E432K(1)		breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		GAGTGGAATTCGTTCCGGTGA	0.582										HNSCC(66;0.2)																																						3	Substitution - Missense(3)	large_intestine(2)|lung(1)	5											151	158	156					5																	88018519		2024	4180	6204	88054275	SO:0001583	missense	4208			AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.1324G>A	5.37:g.88018519C>T	ENSP00000396219:p.Glu442Lys		88054275	C9JMZ0|D7F7N5|F8W7V7	Missense_Mutation	SNP	ENST00000437473.2	37	CCDS47245.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.257651	0.59321	.	.	ENSG00000081189	ENST00000340208;ENST00000424173;ENST00000504921;ENST00000514028;ENST00000437473;ENST00000510942;ENST00000508569;ENST00000514015;ENST00000539796	T;T;T;T;T;T;T;T;T	0.64618	0.23;0.22;0.25;0.23;0.23;0.23;-0.11;-0.11;0.65	5.47	5.47	0.80525	.	0.140035	0.64402	D	0.000004	T	0.52533	0.1740	N	0.22421	0.69	0.58432	D	0.999993	B;P;P;B	0.39551	0.164;0.678;0.589;0.093	B;B;B;B	0.37601	0.03;0.254;0.054;0.04	T	0.59380	-0.7465	10	0.72032	D	0.01	-1.9866	19.3051	0.94158	0.0:1.0:0.0:0.0	.	432;452;442;434	C9JMZ0;F8W7V7;Q06413;Q06413-2	.;.;MEF2C_HUMAN;.	K	452;432;442;442;442;434;402;410;386	ENSP00000340874:E452K;ENSP00000389610:E432K;ENSP00000421925:E442K;ENSP00000426665:E442K;ENSP00000396219:E442K;ENSP00000422390:E434K;ENSP00000423597:E402K;ENSP00000424606:E410K;ENSP00000441153:E386K	ENSP00000340874:E452K	E	-	1	0	MEF2C	88054275	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.723000	0.93209	0.655000	0.94253	GAA		0.582	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		T	88018519	C	T	88018519	3	4	47	1	0	0	0	0	1	0	0	0	9487	893	31	1	101	1	MEF2C	5	88018519	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5181954	88018519	92896741	707	5104										
GPR98	84059	broad.mit.edu	37	chr5	89938788	89938788	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attctatggaaacacgggagTactagaatttaaacctggag	10	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:89938788T>C	ENST00000405460.2	+	13	2579	c.2483T>C	c.(2482-2484)gTa>gCa	p.V828A		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	828	Calx-beta 6. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.V828A(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AACACGGGAGTACTAGAATTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	127	129					5																	89938788		1836	4084	5920	89974544	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.2483T>C	5.37:g.89938788T>C	ENSP00000384582:p.Val828Ala		89974544	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360402	0.61403	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.28069	1.63	5.16	5.16	0.70880	Na-Ca exchanger/integrin-beta4 (1);	0.159061	0.53938	D	0.000044	T	0.26484	0.0647	L	0.27053	0.805	0.80722	D	1	P	0.52316	0.952	B	0.43445	0.42	T	0.05649	-1.0872	10	0.66056	D	0.02	.	14.9991	0.71459	0.0:0.0:0.0:1.0	.	828	Q8WXG9	GPR98_HUMAN	A	828	ENSP00000384582:V828A	ENSP00000296619:V828A	V	+	2	0	GPR98	89974544	0.998000	0.40836	0.234000	0.24042	0.870000	0.49936	7.413000	0.80104	1.945000	0.56424	0.482000	0.46254	GTA		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89938788	T	C	89938788	3	2	47	1	0	0	0	0	1	0	0	0	6742	1638	57	4	2533	4	GPR98	5	89938788	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1920269	89938788	90976472	708	5105										
GPR98	84059	broad.mit.edu	37	chr5	90087050	90087050	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagatgtggctgttgggcttCgaatatcatcggatcataaa	12	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:90087050C>T	ENST00000405460.2	+	70	14500	c.14404C>T	c.(14404-14406)Cga>Tga	p.R4802*	GPR98_ENST00000425867.2_Nonsense_Mutation_p.R463*	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4802					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R4802*(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGTTGGGCTTCGAATATCATC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											52	50	50					5																	90087050		1989	4166	6155	90122806	SO:0001587	stop_gained	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.14404C>T	5.37:g.90087050C>T	ENSP00000384582:p.Arg4802*		90122806	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	55	24.910598	0.99962	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	.	.	.	5.9	5.02	0.67125	.	0.565396	0.19055	N	0.123938	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9875	0.80174	0.0:0.8652:0.1348:0.0	.	.	.	.	X	4802;4802;463	.	ENSP00000296619:R4802X	R	+	1	2	GPR98	90122806	0.056000	0.20664	0.011000	0.14972	0.640000	0.38277	1.045000	0.30341	1.468000	0.48064	0.655000	0.94253	CGA		0.463	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90087050	C	T	90087050	4	4	47	1	0	0	0	0	0	1	0	0	6742	876	31	1	14682	1	GPR98	5	90087050	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	148262	90087050	90828210	709	5106										
GPR98	84059	broad.mit.edu	37	chr5	90136422	90136422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagtgctgaaacaattggtCgtaccatcatatctccagct	9	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:90136422C>T	ENST00000405460.2	+	78	16735	c.16639C>T	c.(16639-16641)Cgt>Tgt	p.R5547C	GPR98_ENST00000425867.2_Missense_Mutation_p.R1208C	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5547					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R5547C(2)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AACAATTGGTCGTACCATCAT	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	5											74	73	74					5																	90136422		1905	4125	6030	90172178	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.16639C>T	5.37:g.90136422C>T	ENSP00000384582:p.Arg5547Cys		90172178	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801004	0.50315	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.31769	1.48;1.49	6.16	6.16	0.99307	.	0.094899	0.85682	D	0.000000	T	0.54398	0.1856	L	0.60455	1.87	0.51012	D	0.999903	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.70016	0.928;0.759;0.967	T	0.35151	-0.9800	9	.	.	.	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	1208;5547;1208	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	C	5547;5547;1208	ENSP00000384582:R5547C;ENSP00000392618:R1208C	.	R	+	1	0	GPR98	90172178	0.878000	0.30173	0.313000	0.25210	0.087000	0.18053	3.318000	0.51975	2.937000	0.99478	0.650000	0.86243	CGT		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90136422	C	T	90136422	3	4	47	1	0	0	0	0	1	0	0	0	6742	884	31	1	16949	1	GPR98	5	90136422	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	49372	90136422	90778838	710	5107										
C5orf36	285600	broad.mit.edu	37	chr5	93856010	93856010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgcttgttttaaccacacGaacagcattttctctgaact	5	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:93856010G>A	ENST00000329378.7	-	5	1162	c.913C>T	c.(913-915)Cgt>Tgt	p.R305C	KIAA0825_ENST00000427991.2_Missense_Mutation_p.R305C|KIAA0825_ENST00000513200.3_Missense_Mutation_p.R305C|KIAA0825_ENST00000312498.7_Missense_Mutation_p.R305C	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	305								p.R305C(4)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTAACCACACGAACAGCATTT	0.358																																																4	Substitution - Missense(4)	large_intestine(2)|skin(2)	5											60	59	60					5																	93856010		2203	4299	6502	93881766	SO:0001583	missense	285600			BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.913C>T	5.37:g.93856010G>A	ENSP00000331385:p.Arg305Cys		93881766	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	37	CCDS4070.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441820	0.43326	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;D;D	0.86030	0.88;0.88;-2.06;-2.06	4.81	3.02	0.34903	.	1.917730	0.01683	N	0.026294	D	0.87245	0.6129	L	0.36672	1.1	0.09310	N	1	B;D	0.71674	0.007;0.998	B;P	0.56700	0.003;0.804	T	0.71517	-0.4569	10	0.59425	D	0.04	.	8.5601	0.33505	0.0813:0.1533:0.7654:0.0	.	305;305	Q8IV33;Q8IV33-2	K0825_HUMAN;.	C	305	ENSP00000424618:R305C;ENSP00000400288:R305C;ENSP00000312205:R305C;ENSP00000331385:R305C	ENSP00000312205:R305C	R	-	1	0	KIAA0825	93881766	0.579000	0.26725	0.358000	0.25811	0.757000	0.42996	2.851000	0.48302	0.626000	0.30322	-0.515000	0.04445	CGT		0.358	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		A	93856010	G	A	93856010	3	1	47	1	0	0	0	0	1	0	0	0	2301	1058	37	1	2987	1	C5orf36	5	93856010	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3719588	93856010	87059250	711	5108										
MCTP1	79772	broad.mit.edu	37	chr5	94204080	94204080	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggggtgaatcccaatcaaaGcaactattaacgtagtatgc	10	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:94204080G>A	ENST00000515393.1	-	17	2393	c.2394C>T	c.(2392-2394)tgC>tgT	p.C798C	MCTP1_ENST00000505078.1_Silent_p.C314C|MCTP1_ENST00000429576.2_Silent_p.C531C|MCTP1_ENST00000505208.1_Silent_p.C577C|MCTP1_ENST00000312216.8_Silent_p.C577C	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	798					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.C798C(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CCCAATCAAAGCAACTATTAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	5											81	71	74					5																	94204080		2203	4300	6503	94229836	SO:0001819	synonymous_variant	79772				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2394C>T	5.37:g.94204080G>A			94229836	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	37	CCDS34203.1																																																																																				0.358	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94204080	G	A	94204080	2	1	47	1	0	0	0	0	0	0	0	1	9430	963	34	3		3	MCTP1	5	94204080	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	348070	94204080	86711180	712	5109										
ELL2	22936	broad.mit.edu	37	chr5	95236709	95236709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctatttcactgtatccagGccagtctctttgaagctctt	7	11	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:95236709G>A	ENST00000237853.4	-	6	1166	c.817C>T	c.(817-819)Cct>Tct	p.P273S	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	273					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.P273S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CTGTATCCAGGCCAGTCTCTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											84	89	87					5																	95236709		2203	4299	6502	95262465	SO:0001583	missense	22936			U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.817C>T	5.37:g.95236709G>A	ENSP00000237853:p.Pro273Ser		95262465	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.614620	0.87359	.	.	ENSG00000118985	ENST00000237853;ENST00000513343	T;T	0.37411	1.2;1.2	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.65831	0.2729	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70454	-0.4867	10	0.87932	D	0	-11.9205	19.0238	0.92925	0.0:0.0:1.0:0.0	.	273	O00472	ELL2_HUMAN	S	273;91	ENSP00000237853:P273S;ENSP00000423915:P91S	ENSP00000237853:P273S	P	-	1	0	ELL2	95262465	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.476000	0.97823	2.580000	0.87095	0.561000	0.74099	CCT		0.348	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		A	95236709	G	A	95236709	3	1	47	1	0	0	0	0	1	0	0	0	5076	1203	42	3	1133	3	ELL2	5	95236709	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1032629	95236709	85678551	713	5110										
ST8SIA4	7903	broad.mit.edu	37	chr5	100231434	100231434	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gattgaagagccagcctttcGaatgattttatcagagctat	9	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:100231434G>A	ENST00000231461.5	-	2	479	c.169C>T	c.(169-171)Cga>Tga	p.R57*	ST8SIA4_ENST00000451528.2_Nonsense_Mutation_p.R57*	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	57					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.R57*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		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)		CCAGCCTTTCGAATGATTTTA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											112	109	110					5																	100231434		2203	4299	6502	100259333	SO:0001587	stop_gained	7903			L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.169C>T	5.37:g.100231434G>A	ENSP00000231461:p.Arg57*		100259333	A8KA07|G3V104|Q8N1F4|Q92693	Nonsense_Mutation	SNP	ENST00000231461.5	37	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	G	37	6.260157	0.97421	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	.	.	.	5.96	5.96	0.96718	.	0.083749	0.50627	D	0.000120	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	19.3963	0.94608	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000231461:R57X	R	-	1	2	ST8SIA4	100259333	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.235000	0.51328	2.814000	0.96858	0.655000	0.94253	CGA		0.373	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		A	100231434	G	A	100231434	4	1	47	1	0	0	0	0	0	1	0	0	15273	1066	37	1	930	1	ST8SIA4	5	100231434	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4994725	100231434	80683826	714	5111										
SLCO6A1	133482	broad.mit.edu	37	chr5	101834231	101834231	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtagaaaatcatgaagcaGcgaatgttattgcaacactc	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:101834231G>A	ENST00000506729.1	-	1	489	c.318C>T	c.(316-318)cgC>cgT	p.R106R	SLCO6A1_ENST00000379810.1_Silent_p.R106R|SLCO6A1_ENST00000513675.1_Silent_p.R106R|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000389019.3_Silent_p.R106R|SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379807.3_Silent_p.R106R			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	106	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R106R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TCATGAAGCAGCGAATGTTAT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	5											84	83	84					5																	101834231		2203	4300	6503	101862130	SO:0001819	synonymous_variant	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.318C>T	5.37:g.101834231G>A			101862130	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																				0.552	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101834231	G	A	101834231	2	1	47	1	0	0	0	0	0	0	0	1	14769	958	34	3		3	SLCO6A1	5	101834231	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1602797	101834231	79081029	715	5112										
MAN2A1	4124	broad.mit.edu	37	chr5	109200797	109200797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagaaaagggtttgattgtCggttctctagcaaaggcaca	11	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:109200797C>T	ENST00000261483.4	+	21	4284	c.3232C>T	c.(3232-3234)Cgg>Tgg	p.R1078W	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1078					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.R1078W(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GTTTGATTGTCGGTTCTCTAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											161	142	149					5																	109200797		2202	4300	6502	109228696	SO:0001583	missense	4124				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3232C>T	5.37:g.109200797C>T	ENSP00000261483:p.Arg1078Trp		109228696	Q16767	Missense_Mutation	SNP	ENST00000261483.4	37	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.438601	0.25900	.	.	ENSG00000112893	ENST00000261483	D	0.83755	-1.76	5.53	3.43	0.39272	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.343569	0.31685	N	0.007235	D	0.87857	0.6283	M	0.76328	2.33	0.33610	D	0.603421	D	0.69078	0.997	P	0.58970	0.849	D	0.91232	0.5015	9	.	.	.	-1.7191	12.4132	0.55480	0.6043:0.3957:0.0:0.0	.	1078	Q16706	MA2A1_HUMAN	W	1078	ENSP00000261483:R1078W	.	R	+	1	2	MAN2A1	109228696	1.000000	0.71417	0.777000	0.31699	0.037000	0.13140	2.031000	0.41117	1.417000	0.47077	-0.284000	0.09977	CGG		0.458	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			T	109200797	C	T	109200797	3	4	47	1	0	0	0	0	1	0	0	0	9244	875	31	1	3314	1	MAN2A1	5	109200797	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7366566	109200797	71714463	716	5113										
EPB41L4A	64097	broad.mit.edu	37	chr5	111504758	111504758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcgatactggcggtaacttCgtggcgaatgagaatgcctg	14	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:111504758C>T	ENST00000261486.5	-	21	2060	c.1784G>A	c.(1783-1785)cGa>cAa	p.R595Q	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	595				RS -> KL (in Ref. 3; BAB17229). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.R595Q(1)|p.R222Q(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GCGGTAACTTCGTGGCGAATG	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	5											133	139	137					5																	111504758		2098	4221	6319	111532657	SO:0001583	missense	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1784G>A	5.37:g.111504758C>T	ENSP00000261486:p.Arg595Gln		111532657	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.748368	0.89663	.	.	ENSG00000129595	ENST00000261486	D	0.84146	-1.81	5.86	5.86	0.93980	.	0.073620	0.52532	D	0.000076	D	0.88485	0.6449	L	0.29908	0.895	0.39264	D	0.96426	D;D	0.89917	0.995;1.0	P;D	0.83275	0.559;0.996	D	0.87468	0.2412	10	0.34782	T	0.22	.	18.9573	0.92664	0.0:1.0:0.0:0.0	.	595;222	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	Q	595	ENSP00000261486:R595Q	ENSP00000261486:R595Q	R	-	2	0	EPB41L4A	111532657	0.999000	0.42202	0.130000	0.21974	0.773000	0.43773	5.813000	0.69201	2.777000	0.95525	0.591000	0.81541	CGA		0.498	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			T	111504758	C	T	111504758	3	4	47	1	0	0	0	0	1	0	0	0	5168	884	31	1	288	1	EPB41L4A	5	111504758	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2303961	111504758	69410502	717	5114										
EPB41L4A	64097	broad.mit.edu	37	chr5	111576502	111576502	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaaaaaagaatgaggtttcGttacactaagagagaaagag	10	4	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:111576502G>A	ENST00000261486.5	-	10	1077	c.801C>T	c.(799-801)aaC>aaT	p.N267N	RP11-526F3.1_ENST00000504004.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	267	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.N267N(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ATGAGGTTTCGTTACACTAAG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	5											57	54	55					5																	111576502		1812	4088	5900	111604401	SO:0001819	synonymous_variant	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.801C>T	5.37:g.111576502G>A			111604401	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																				0.368	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111576502	G	A	111576502	2	1	47	1	0	0	0	0	0	0	0	1	5168	1136	40	1		1	EPB41L4A	5	111576502	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	71744	111576502	69338758	718	5115										
EPB41L4A	64097	broad.mit.edu	37	chr5	111754704	111754704	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggagcaaaacttcgcagtaAaattcttccggaacagcgca	9	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:111754704A>C	ENST00000261486.5	-	1	309	c.33T>G	c.(31-33)ttT>ttG	p.F11L	EPB41L4A-AS2_ENST00000600409.1_5'Flank	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	11	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.F11L(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CTTCGCAGTAAAATTCTTCCG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	84	80					5																	111754704		1980	4181	6161	111782603	SO:0001583	missense	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.33T>G	5.37:g.111754704A>C	ENSP00000261486:p.Phe11Leu		111782603	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.313769	0.40996	.	.	ENSG00000129595	ENST00000261486	T	0.75260	-0.92	5.1	1.38	0.22167	Band 4.1 domain (1);FERM domain (1);	0.062767	0.64402	D	0.000006	T	0.69851	0.3157	L	0.31926	0.97	0.36997	D	0.895082	P	0.52842	0.956	P	0.62184	0.899	T	0.68142	-0.5487	10	0.02654	T	1	.	9.3474	0.38118	0.6287:0.0:0.3713:0.0	.	11	Q9HCS5	E41LA_HUMAN	L	11	ENSP00000261486:F11L	ENSP00000261486:F11L	F	-	3	2	EPB41L4A	111782603	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.309000	0.33539	0.010000	0.14839	-0.385000	0.06624	TTT		0.607	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			C	111754704	A	C	111754704	3	2	47	1	0	0	0	0	1	0	0	0	5168	11	1	4	2119	4	EPB41L4A	5	111754704	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	178202	111754704	69160556	719	5116										
APC	324	broad.mit.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	47	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	419927	112174631	68740629	720	5117										
APC	324	broad.mit.edu	37	chr5	112174774	112174774	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaagagagaccaacaaaTtatagcataaaatataatga	7	4	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:112174774T>G	ENST00000457016.1	+	16	3863	c.3483T>G	c.(3481-3483)aaT>aaG	p.N1161K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.N1161K|APC_ENST00000257430.4_Missense_Mutation_p.N1161K			P25054	APC_HUMAN	adenomatous polyposis coli	1161	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.N1161K(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GACCAACAAATTATAGCATAA	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											58	61	60					5																	112174774		2202	4300	6502	112202673	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3483T>G	5.37:g.112174774T>G	ENSP00000413133:p.Asn1161Lys		112202673	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	9.447	1.089477	0.20390	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86	5.76	3.38	0.38709	.	0.136255	0.50627	D	0.000117	T	0.77955	0.4208	N	0.12182	0.205	0.34142	D	0.666501	B;B	0.10296	0.003;0.002	B;B	0.12156	0.007;0.007	T	0.68872	-0.5294	9	.	.	.	-21.7039	5.8988	0.18955	0.0:0.1439:0.1394:0.7167	.	1163;1161	Q4LE70;P25054	.;APC_HUMAN	K	1161	ENSP00000413133:N1161K;ENSP00000257430:N1161K;ENSP00000427089:N1161K;ENSP00000423828:N1161K	.	N	+	3	2	APC	112202673	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.094000	0.30951	0.463000	0.27118	0.533000	0.62120	AAT		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174774	T	G	112174774	3	3	47	1	0	0	0	0	1	0	0	0	763	1490	52	4	3541	4	APC	5	112174774	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	143	112174774	68740486	721	5118										
DCP2	167227	broad.mit.edu	37	chr5	112336790	112336790	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttgtttccaggtctttgaaGaaactggttttgatatcaaa	9	5	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:112336790G>T	ENST00000389063.2	+	5	640	c.442G>T	c.(442-444)Gaa>Taa	p.E148*	DCP2_ENST00000515408.1_Nonsense_Mutation_p.E148*|DCP2_ENST00000543319.1_5'UTR	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	148	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)	p.E148*(1)		endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		GGTCTTTGAAGAAACTGGTTT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											44	47	46					5																	112336790		2200	4297	6497	112364689	SO:0001587	stop_gained	167227			AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"Nudix motif containing"	24452	protein-coding gene	gene with protein product	"nudix (nucleoside diphosphate linked moiety X)-type motif 20", "M(7)GpppN-mRNA hydrolase"	609844	"DCP2 decapping enzyme homolog (S. cerevisiae)"			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.442G>T	5.37:g.112336790G>T	ENSP00000373715:p.Glu148*		112364689	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Nonsense_Mutation	SNP	ENST00000389063.2	37	CCDS34210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.230232|5.230232	0.95207|0.95207	.|.	.|.	ENSG00000172795|ENSG00000172795	ENST00000515408;ENST00000389063|ENST00000513585	.|.	.|.	.|.	5.63|5.63	4.77|4.77	0.60923|0.60923	.|.	0.043096|.	0.85682|.	D|.	0.000000|.	.|T	.|0.70570	.|0.3239	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70252	.|-0.4923	.|4	0.87932|.	D|.	0|.	-20.4308|-20.4308	14.8369|14.8369	0.70190|0.70190	0.0691:0.0:0.9309:0.0|0.0691:0.0:0.9309:0.0	.|.	.|.	.|.	.|.	X|I	148|129	.|.	ENSP00000373715:E148X|.	E|R	+|+	1|2	0|0	DCP2|DCP2	112364689|112364689	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.938000|0.938000	0.57974|0.57974	9.352000|9.352000	0.97076|0.97076	1.526000|1.526000	0.49068|0.49068	0.643000|0.643000	0.83706|0.83706	GAA|AGA		0.323	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624		T	112336790	G	T	112336790	4	4	47	1	0	0	0	0	0	1	0	0	4306	943	33	2	460	2	DCP2	5	112336790	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	162016	112336790	68578470	722	5119										
MCC	4163	broad.mit.edu	37	chr5	112399855	112399855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtgatgttttcatcccccGactggtctcctatgtggcag	11	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:112399855G>A	ENST00000302475.4	-	12	2032	c.1469C>T	c.(1468-1470)tCg>tTg	p.S490L	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Missense_Mutation_p.S427L|MCC_ENST00000408903.3_Missense_Mutation_p.S680L	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	490			S -> L (in a colorectal cancer sample). {ECO:0000269|PubMed:1651563}.		negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.S680L(1)|p.S490L(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TTCATCCCCCGACTGGTCTCC	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	5											77	73	74					5																	112399855		2202	4300	6502	112427754	SO:0001583	missense	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1469C>T	5.37:g.112399855G>A	ENSP00000305617:p.Ser490Leu		112427754	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137082	0.77775	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.36520	2.41;2.42;1.25	5.64	5.64	0.86602	.	0.427064	0.23779	N	0.044645	T	0.24275	0.0588	N	0.08118	0	0.47308	D	0.999384	B;B;B	0.22604	0.012;0.072;0.043	B;B;B	0.22386	0.007;0.039;0.012	T	0.06215	-1.0839	10	0.28530	T	0.3	-5.272	19.6921	0.96007	0.0:0.0:1.0:0.0	.	490;680;490	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	L	490;427;680	ENSP00000305617:S490L;ENSP00000421615:S427L;ENSP00000386227:S680L	ENSP00000305617:S490L	S	-	2	0	MCC	112427754	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.671000	0.61590	2.633000	0.89246	0.563000	0.77884	TCG		0.532	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		A	112399855	G	A	112399855	3	1	47	1	0	0	0	0	1	0	0	0	9403	1059	37	1	1044	1	MCC	5	112399855	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	63065	112399855	68515405	723	5120										
CCDC112	153733	broad.mit.edu	37	chr5	114611749	114611749	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcaatttcttccatcatttCtctgagcttctcaacaactg	3	12	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:114611749C>A	ENST00000512261.1	-	6	636	c.220G>T	c.(220-222)Gaa>Taa	p.E74*	CCDC112_ENST00000379611.5_Nonsense_Mutation_p.E157*|CCDC112_ENST00000506442.1_Nonsense_Mutation_p.E74*|CCDC112_ENST00000395557.4_Nonsense_Mutation_p.E74*|CCDC112_ENST00000503027.1_5'UTR			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112	74								p.E157*(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		TCCATCATTTCTCTGAGCTTC	0.284																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											72	77	75					5																	114611749		2199	4292	6491	114639648	SO:0001587	stop_gained	153733			BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.220G>T	5.37:g.114611749C>A	ENSP00000423712:p.Glu74*		114639648	Q6A334	Nonsense_Mutation	SNP	ENST00000512261.1	37	CCDS4117.1	.	.	.	.	.	.	.	.	.	.	C	40	8.094487	0.98651	.	.	ENSG00000164221	ENST00000379611;ENST00000512261;ENST00000506442;ENST00000395557	.	.	.	5.58	4.71	0.59529	.	0.203196	0.50627	D	0.000114	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-23.1116	13.8721	0.63626	0.0:0.9267:0.0:0.0733	.	.	.	.	X	157;74;74;74	.	ENSP00000368931:E157X	E	-	1	0	CCDC112	114639648	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.894000	0.63206	2.618000	0.88619	0.460000	0.39030	GAA		0.284	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370999.1	NM_152549		A	114611749	C	A	114611749	4	1	47	1	0	0	0	0	0	1	0	0	2755	922	32	2	1144	2	CCDC112	5	114611749	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2211894	114611749	66303511	724	5121										
CDO1	1036	broad.mit.edu	37	chr5	115146889	115146889	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcacactggttttccctcaaGactctttcagacttcttgac	6	13	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:115146889G>T	ENST00000250535.4	-	3	928	c.372C>A	c.(370-372)gtC>gtA	p.V124V	CDO1_ENST00000502631.1_5'UTR	NM_001801.2	NP_001792.2	Q16878	CDO1_HUMAN	cysteine dioxygenase type 1	124					cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|inflammatory response (GO:0006954)|L-cysteine catabolic process (GO:0019448)|lactation (GO:0007595)|oxidation-reduction process (GO:0055114)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|sulfur amino acid biosynthetic process (GO:0000097)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)	cytosol (GO:0005829)	cysteine dioxygenase activity (GO:0017172)|ferrous iron binding (GO:0008198)	p.V124V(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|skin(5)	11		all_cancers(142;0.0046)|all_epithelial(76;0.000161)|Prostate(80;0.0132)|Ovarian(225;0.0776)		OV - Ovarian serous cystadenocarcinoma(64;7.8e-08)|Epithelial(69;7.32e-07)|all cancers(49;3.24e-05)	L-Cysteine(DB00151)	TTTCCCTCAAGACTCTTTCAG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	5											257	248	251					5																	115146889		2202	4300	6502	115174788	SO:0001819	synonymous_variant	1036				CCDS4121.1	5q23.2	2013-06-11	2013-06-11		ENSG00000129596	ENSG00000129596	1.13.11.20		1795	protein-coding gene	gene with protein product		603943	"cysteine dioxygenase, type I"			7524679	Standard	NM_001801		Approved		uc003krg.3	Q16878	OTTHUMG00000128891	ENST00000250535.4:c.372C>A	5.37:g.115146889G>T			115174788	B2RAK4|P78513|Q6FHZ8|Q8TB64	Silent	SNP	ENST00000250535.4	37	CCDS4121.1																																																																																				0.408	CDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250853.2	NM_001801		T	115146889	G	T	115146889	2	4	47	1	0	0	0	0	0	0	0	1	3175	929	33	2		2	CDO1	5	115146889	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	535140	115146889	65768371	725	5122										
DMXL1	1657	broad.mit.edu	37	chr5	118433743	118433743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gattacagataatcccaggaGctaaacatggaaatattcaa	7	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:118433743G>A	ENST00000311085.8	+	2	237	c.157G>A	c.(157-159)Gct>Act	p.A53T	DMXL1_ENST00000539542.1_Missense_Mutation_p.A53T	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	53								p.A53T(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AATCCCAGGAGCTAAACATGG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	5											130	133	132					5																	118433743		2202	4300	6502	118461642	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.157G>A	5.37:g.118433743G>A	ENSP00000309690:p.Ala53Thr		118461642		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.912226	0.92178	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.11277	2.83;2.79;2.83	5.98	5.11	0.69529	WD40 repeat-like-containing domain (1);	0.053356	0.85682	D	0.000000	T	0.15565	0.0375	M	0.66939	2.045	0.45415	D	0.998392	B;B	0.34200	0.441;0.314	B;B	0.33620	0.167;0.065	T	0.01436	-1.1355	10	0.46703	T	0.11	-12.7096	14.73	0.69374	0.0699:0.0:0.9301:0.0	.	53;53	F5H269;Q9Y485	.;DMXL1_HUMAN	T	53	ENSP00000427692:A53T;ENSP00000309690:A53T;ENSP00000439479:A53T	ENSP00000309690:A53T	A	+	1	0	DMXL1	118461642	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.612000	0.74187	1.542000	0.49330	0.585000	0.79938	GCT		0.313	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118433743	G	A	118433743	3	1	47	1	0	0	0	0	1	0	0	0	4605	971	34	3	163	3	DMXL1	5	118433743	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3286854	118433743	62481517	726	5123										
DMXL1	1657	broad.mit.edu	37	chr5	118506692	118506692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttgaaaaagaggtgatagCtcttcagaggacttgtgact	12	6	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:118506692C>T	ENST00000311085.8	+	24	6286	c.6206C>T	c.(6205-6207)gCt>gTt	p.A2069V	DMXL1_ENST00000539542.1_Missense_Mutation_p.A2069V	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2069								p.A2069V(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GAGGTGATAGCTCTTCAGAGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											90	89	89					5																	118506692		2202	4300	6502	118534591	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.6206C>T	5.37:g.118506692C>T	ENSP00000309690:p.Ala2069Val		118534591		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466477	0.84425	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.78481	-1.18;-1.18	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.86184	0.5872	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.977	D	0.85861	0.1410	10	0.51188	T	0.08	-16.3169	19.3932	0.94594	0.0:1.0:0.0:0.0	.	2069;2069	F5H269;Q9Y485	.;DMXL1_HUMAN	V	2069	ENSP00000309690:A2069V;ENSP00000439479:A2069V	ENSP00000309690:A2069V	A	+	2	0	DMXL1	118534591	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.413000	0.80104	2.577000	0.86979	0.557000	0.71058	GCT		0.388	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118506692	C	T	118506692	3	4	47	1	0	0	0	0	1	0	0	0	4605	797	28	3	6300	3	DMXL1	5	118506692	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	72949	118506692	62408568	727	5124										
SRFBP1	153443	broad.mit.edu	37	chr5	121356324	121356324	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggacacgaaagaaggaaagTagttgtcattcttcagttaa	10	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:121356324T>G	ENST00000339397.4	+	6	966	c.894T>G	c.(892-894)agT>agG	p.S298R	SRFBP1_ENST00000504881.1_3'UTR	NM_152546.2	NP_689759.2			serum response factor binding protein 1									p.S298R(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AGAAGGAAAGTAGTTGTCATT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											97	86	89					5																	121356324		1867	4102	5969	121384223	SO:0001583	missense	153443			AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.894T>G	5.37:g.121356324T>G	ENSP00000341324:p.Ser298Arg		121384223		Missense_Mutation	SNP	ENST00000339397.4	37	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.903080	0.33628	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.57	2.01	0.26516	.	0.735512	0.14391	N	0.322506	T	0.31670	0.0804	M	0.61703	1.905	0.09310	N	0.999998	P	0.49961	0.93	B	0.39068	0.289	T	0.15407	-1.0438	9	0.40728	T	0.16	-4.1337	9.4774	0.38880	0.0:0.1976:0.0:0.8024	.	298	Q8NEF9	SRFB1_HUMAN	R	298	.	ENSP00000341324:S298R	S	+	3	2	SRFBP1	121384223	0.000000	0.05858	0.652000	0.29579	0.763000	0.43281	0.008000	0.13197	0.946000	0.37632	0.460000	0.39030	AGT		0.383	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		G	121356324	T	G	121356324	3	3	47	1	0	0	0	0	1	0	0	0	15183	1635	57	4	916	4	SRFBP1	5	121356324	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2849632	121356324	59558936	728	5125										
MEGF10	84466	broad.mit.edu	37	chr5	126676306	126676306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcctggattttatgaaagCggggaaatgtgtgtccgtaa	13	5	0	1	rs77203884	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:126676306C>T	ENST00000274473.6	+	5	570	c.303C>T	c.(301-303)agC>agT	p.S101S	MEGF10_ENST00000508365.1_Silent_p.S101S|MEGF10_ENST00000503335.2_Silent_p.S101S|MEGF10_ENST00000418761.2_Silent_p.S101S	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	101	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.S101S(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		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)		TTTATGAAAGCGGGGAAATGT	0.458													c|||	14	0.00279553	0.0098	0.0014	5008	,	,		18687	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						T		40,4366	42.3+/-75.8	0,40,2163	189	175	180		303	0.9	0.9	5	dbSNP_133	180	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MEGF10	NM_032446.2		0,41,6462	TT,TC,CC		0.0116,0.9079,0.3152		101/1141	126676306	41,12965	2203	4300	6503	126704205	SO:0001819	synonymous_variant	84466			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.303C>T	5.37:g.126676306C>T			126704205	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																				0.458	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126676306	C	T	126676306	2	4	47	1	0	0	0	0	0	0	0	1	9490	767	27	1		1	MEGF10	5	126676306	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5319982	126676306	54238954	729	5126										
CTXN3	613212	broad.mit.edu	37	chr5	126993442	126993442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctggagaaagggcagttcGaccatgcccttgcttaggag	14	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:126993442G>A	ENST00000379445.3	+	3	780	c.229G>A	c.(229-231)Gac>Aac	p.D77N	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Missense_Mutation_p.D77N	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	77						integral component of membrane (GO:0016021)		p.D77N(1)		endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		AGGGCAGTTCGACCATGCCCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											71	66	68					5																	126993442		2203	4300	6503	127021341	SO:0001583	missense	613212			AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.229G>A	5.37:g.126993442G>A	ENSP00000368758:p.Asp77Asn		127021341	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.981674	0.93044	.	.	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.37752	1.18;1.18	4.52	4.52	0.55395	.	0.154868	0.64402	D	0.000020	T	0.61324	0.2338	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.66476	-0.5914	9	0.87932	D	0	-34.2799	18.1587	0.89702	0.0:0.0:1.0:0.0	.	77	Q4LDR2	CTXN3_HUMAN	N	77	ENSP00000368758:D77N;ENSP00000378732:D77N	ENSP00000368758:D77N	D	+	1	0	CTXN3	127021341	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	9.042000	0.93793	2.793000	0.96121	0.655000	0.94253	GAC		0.502	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841		A	126993442	G	A	126993442	3	1	47	1	0	0	0	0	1	0	0	0	4056	1058	37	1	231	1	CTXN3	5	126993442	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	317136	126993442	53921818	730	5127										
SLC27A6	28965	broad.mit.edu	37	chr5	128326055	128326055	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccacttgtgtgttaaagaaGaaattttcagcaagccagtt	9	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:128326055G>T	ENST00000262462.4	+	4	1877	c.867G>T	c.(865-867)aaG>aaT	p.K289N	SLC27A6_ENST00000506176.1_Missense_Mutation_p.K289N|SLC27A6_ENST00000395266.1_Missense_Mutation_p.K289N			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	289					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.K289N(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		TGTTAAAGAAGAAATTTTCAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											145	139	141					5																	128326055		2203	4300	6503	128353954	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.867G>T	5.37:g.128326055G>T	ENSP00000262462:p.Lys289Asn		128353954	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.618939	0.46736	.	.	ENSG00000113396	ENST00000508645;ENST00000262462;ENST00000395266;ENST00000506176	T;T;T;T	0.48201	2.89;0.82;0.82;0.82	4.59	3.72	0.42706	AMP-dependent synthetase/ligase (1);	0.093924	0.64402	D	0.000001	T	0.50905	0.1643	M	0.77486	2.375	0.58432	D	0.999996	B	0.27997	0.197	B	0.33295	0.161	T	0.52480	-0.8570	9	.	.	.	-16.4753	13.4713	0.61283	0.0765:0.0:0.9235:0.0	.	289	Q9Y2P4	S27A6_HUMAN	N	108;289;289;289	ENSP00000421759:K108N;ENSP00000262462:K289N;ENSP00000378684:K289N;ENSP00000421024:K289N	.	K	+	3	2	SLC27A6	128353954	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.406000	0.44557	1.529000	0.49120	0.650000	0.86243	AAG		0.358	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		T	128326055	G	T	128326055	3	4	47	1	0	0	0	0	1	0	0	0	14567	933	33	2	881	2	SLC27A6	5	128326055	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1332613	128326055	52589205	731	5128										
SLC27A6	28965	broad.mit.edu	37	chr5	128351581	128351581	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acattttcttctaacagagaGaaggagaaaaggatcataag	9	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:128351581G>A	ENST00000262462.4	+	5	1983	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K	SLC27A6_ENST00000506176.1_Missense_Mutation_p.E325K|SLC27A6_ENST00000395266.1_Missense_Mutation_p.E325K			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	325					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.E325K(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		CTAACAGAGAGAAGGAGAAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											92	95	94					5																	128351581		2203	4300	6503	128379480	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.973G>A	5.37:g.128351581G>A	ENSP00000262462:p.Glu325Lys		128379480	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740225	0.49045	.	.	ENSG00000113396	ENST00000508645;ENST00000262462;ENST00000395266;ENST00000506176	T;T;T;T	0.50001	2.89;0.76;0.76;0.76	3.92	3.92	0.45320	AMP-dependent synthetase/ligase (1);	0.325480	0.35040	N	0.003484	T	0.47173	0.1431	L	0.55834	1.745	0.49798	D	0.999822	B	0.24721	0.11	B	0.32022	0.139	T	0.43196	-0.9406	9	.	.	.	-0.0975	17.3065	0.87196	0.0:0.0:1.0:0.0	.	325	Q9Y2P4	S27A6_HUMAN	K	144;325;325;325	ENSP00000421759:E144K;ENSP00000262462:E325K;ENSP00000378684:E325K;ENSP00000421024:E325K	.	E	+	1	0	SLC27A6	128379480	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	7.002000	0.76304	2.499000	0.84300	0.461000	0.40582	GAA		0.308	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		A	128351581	G	A	128351581	3	1	47	1	0	0	0	0	1	0	0	0	14567	943	33	3	991	3	SLC27A6	5	128351581	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	25526	128351581	52563679	732	5129										
IL5	3567	broad.mit.edu	37	chr5	131877812	131877812	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgtgcctattccctgaaaGatttcttcagtgcacagttg	9	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:131877812G>A	ENST00000231454.1	-	3	244	c.201C>T	c.(199-201)atC>atT	p.I67I		NM_000879.2	NP_000870.1	P05113	IL5_HUMAN	interleukin 5	67					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of eosinophil differentiation (GO:0045645)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of podosome assembly (GO:0071803)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-5 receptor binding (GO:0005137)	p.I67I(1)		endometrium(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Pranlukast(DB01411)	TTCCCTGAAAGATTTCTTCAG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	5											86	83	84					5																	131877812		2203	4300	6503	131905711	SO:0001819	synonymous_variant	3567			X04688	CCDS4156.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000113525	ENSG00000113525		"Interleukins and interleukin receptors"	6016	protein-coding gene	gene with protein product	"interleukin-5", "T-cell replacing factor", "B cell differentiation factor I", "eosinophil differentiation factor", "colony-stimulating factor, eosinophil"	147850	"interleukin 5 (colony-stimulating factor, eosinophil)"			3498940	Standard	NM_000879		Approved	IL-5, EDF, TRF	uc003kxe.1	P05113	OTTHUMG00000059496	ENST00000231454.1:c.201C>T	5.37:g.131877812G>A			131905711	Q13840	Silent	SNP	ENST00000231454.1	37	CCDS4156.1																																																																																				0.373	IL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132339.1	NM_000879		A	131877812	G	A	131877812	2	1	47	1	0	0	0	0	0	0	0	1	7720	932	33	3		3	IL5	5	131877812	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3526231	131877812	49037448	733	5130										
RAD50	10111	broad.mit.edu	37	chr5	131911585	131911585	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaaaagcaaaaagacagaAtttaaaactctggaaggagt	9	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:131911585A>C	ENST00000265335.6	+	3	717	c.330A>C	c.(328-330)gaA>gaC	p.E110D	RAD50_ENST00000378823.3_5'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	110					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.E110D(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAAAGACAGAATTTAAAACTC	0.358								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	5											82	80	80					5																	131911585		2203	4300	6503	131939484	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.330A>C	5.37:g.131911585A>C	ENSP00000265335:p.Glu110Asp		131939484	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.940456	0.52972	.	.	ENSG00000113522	ENST00000416135;ENST00000265335;ENST00000453394	T;T;T	0.23950	1.88;3.33;3.33	5.76	3.36	0.38483	.	0.152463	0.64402	D	0.000014	T	0.29355	0.0731	L	0.48877	1.53	0.80722	D	1	P	0.45634	0.863	P	0.49953	0.627	T	0.01375	-1.1371	10	0.30078	T	0.28	-23.4732	9.465	0.38806	0.8563:0.0:0.1437:0.0	.	110	Q92878	RAD50_HUMAN	D	11;110;110	ENSP00000389515:E11D;ENSP00000265335:E110D;ENSP00000400049:E110D	ENSP00000265335:E110D	E	+	3	2	RAD50	131939484	0.957000	0.32711	1.000000	0.80357	0.994000	0.84299	0.206000	0.17375	0.445000	0.26639	0.459000	0.35465	GAA		0.358	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		C	131911585	A	C	131911585	3	2	47	1	0	0	0	0	1	0	0	0	13021	98	4	4	340	4	RAD50	5	131911585	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	33773	131911585	49003675	734	5131										
RAD50	10111	broad.mit.edu	37	chr5	131923370	131923370	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gataatagtgaactggaagaGaaaatggaaaaggtttgtgg	14	1	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:131923370G>T	ENST00000265335.6	+	6	1260	c.873G>T	c.(871-873)gaG>gaT	p.E291D	RAD50_ENST00000378823.3_Missense_Mutation_p.E152D|RAD50_ENST00000487596.1_3'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	291					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.E152D(1)|p.E291D(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AACTGGAAGAGAAAATGGAAA	0.323								Homologous recombination																																								2	Substitution - Missense(2)	large_intestine(2)	5											70	74	73					5																	131923370		2203	4298	6501	131951269	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.873G>T	5.37:g.131923370G>T	ENSP00000265335:p.Glu291Asp		131951269	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.215413	0.39102	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.07327	3.5;3.2;3.2	5.77	5.77	0.91146	.	0.265562	0.43579	D	0.000549	T	0.08358	0.0208	L	0.32530	0.975	0.41700	D	0.989396	B	0.14805	0.011	B	0.19666	0.026	T	0.28522	-1.0041	10	0.11794	T	0.64	-4.3721	17.1336	0.86733	0.0:0.0:1.0:0.0	.	291	Q92878	RAD50_HUMAN	D	152;291;291	ENSP00000368100:E152D;ENSP00000265335:E291D;ENSP00000400049:E291D	ENSP00000265335:E291D	E	+	3	2	RAD50	131951269	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.487000	0.60293	2.709000	0.92574	0.655000	0.94253	GAG		0.323	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131923370	G	T	131923370	3	4	47	1	0	0	0	0	1	0	0	0	13021	933	33	2	895	2	RAD50	5	131923370	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	11785	131923370	48991890	735	5132										
GDF9	2661	broad.mit.edu	37	chr5	132197607	132197607	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acactcattttggggaagaaGaaattgtctgaagtattcac	9	6	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:132197607G>T	ENST00000378673.2	-	3	1905	c.1039C>A	c.(1039-1041)Ctt>Att	p.L347I	GDF9_ENST00000296875.2_Missense_Mutation_p.L347I|GDF9_ENST00000464378.1_5'Flank			O60383	GDF9_HUMAN	growth differentiation factor 9	347					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)	p.L347I(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGGGGAAGAAGAAATTGTCTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	5											69	70	70					5																	132197607		2203	4300	6503	132225506	SO:0001583	missense	2661				CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"Endogenous ligands"	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.1039C>A	5.37:g.132197607G>T	ENSP00000367942:p.Leu347Ile		132225506	Q4VAW5	Missense_Mutation	SNP	ENST00000378673.2	37	CCDS4162.1	.	.	.	.	.	.	.	.	.	.	G	9.473	1.096164	0.20552	.	.	ENSG00000164404	ENST00000378673;ENST00000296875	T;T	0.81163	-1.46;-1.46	6.13	2.4	0.29515	Transforming growth factor-beta, C-terminal (1);	0.504141	0.21565	N	0.072516	T	0.78464	0.4287	M	0.85373	2.75	0.26428	N	0.975985	D	0.54207	0.965	B	0.43658	0.426	T	0.68168	-0.5480	10	0.26408	T	0.33	.	4.3303	0.11060	0.1184:0.2467:0.5201:0.1148	.	347	O60383	GDF9_HUMAN	I	347	ENSP00000367942:L347I;ENSP00000296875:L347I	ENSP00000296875:L347I	L	-	1	0	GDF9	132225506	0.053000	0.20554	0.371000	0.25978	0.207000	0.24258	0.543000	0.23237	0.170000	0.19704	-0.139000	0.14373	CTT		0.488	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260		T	132197607	G	T	132197607	3	4	47	1	0	0	0	0	1	0	0	0	6339	942	33	2	329	2	GDF9	5	132197607	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	274237	132197607	48717653	736	5133										
HSPA4	3308	broad.mit.edu	37	chr5	132424110	132424110	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatagagttaaagaaagaaGatatttatgcagtggagata	10	1	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:132424110G>A	ENST00000304858.2	+	9	1289	c.1000G>A	c.(1000-1002)Gat>Aat	p.D334N	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	334					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.D334N(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAAGAAAGAAGATATTTATGC	0.308																																					Colon(114;1299 1588 6063 12302 48757)											1	Substitution - Missense(1)	large_intestine(1)	5											50	47	48					5																	132424110		2203	4300	6503	132452009	SO:0001583	missense	3308			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1000G>A	5.37:g.132424110G>A	ENSP00000302961:p.Asp334Asn		132452009	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759406	0.89932	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.01145	5.27	6.02	4.23	0.50019	.	0.042199	0.85682	D	0.000000	T	0.03263	0.0095	M	0.82716	2.605	0.80722	D	1	B	0.23442	0.085	B	0.34093	0.175	T	0.19844	-1.0293	10	0.49607	T	0.09	-20.1391	11.9268	0.52825	0.0653:0.1228:0.8119:0.0	.	334	P34932	HSP74_HUMAN	N	334	ENSP00000302961:D334N	ENSP00000302961:D334N	D	+	1	0	HSPA4	132452009	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.476000	0.97823	0.868000	0.35678	-0.181000	0.13052	GAT		0.308	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		A	132424110	G	A	132424110	3	1	47	1	0	0	0	0	1	0	0	0	7433	942	33	3	1034	3	HSPA4	5	132424110	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	226503	132424110	48491150	737	5134										
FSTL4	23105	broad.mit.edu	37	chr5	132648367	132648367	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaggccatgtagaactcgcGgagggtcagggagctgtcac	16	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:132648367G>T	ENST00000265342.7	-	6	955	c.706C>A	c.(706-708)Cgc>Agc	p.R236S		NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	236						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R236S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAGAACTCGCGGAGGGTCAGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											146	126	133					5																	132648367		2203	4300	6503	132676266	SO:0001583	missense	23105			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.706C>A	5.37:g.132648367G>T	ENSP00000265342:p.Arg236Ser		132676266	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	G	7.092	0.572438	0.13623	.	.	ENSG00000053108	ENST00000265342	T	0.58940	0.3	5.67	3.83	0.44106	EF-hand-like domain (1);	0.787684	0.12634	N	0.451950	T	0.38295	0.1035	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.17098	0.017	T	0.18429	-1.0337	10	0.23891	T	0.37	-6.9576	13.7267	0.62763	0.0:0.3057:0.6943:0.0	.	236	Q6MZW2	FSTL4_HUMAN	S	236	ENSP00000265342:R236S	ENSP00000265342:R236S	R	-	1	0	FSTL4	132676266	0.952000	0.32445	0.042000	0.18584	0.422000	0.31414	6.106000	0.71511	0.693000	0.31634	0.655000	0.94253	CGC		0.527	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		T	132648367	G	T	132648367	3	4	47	1	0	0	0	0	1	0	0	0	6098	1116	39	2	1866	2	FSTL4	5	132648367	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	224257	132648367	48266893	738	5135										
PKD2L2	27039	broad.mit.edu	37	chr5	137257338	137257338	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaaagatttgcacaatttCgaattgttcttggagatttt	7	5	1	2	rs201700977		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:137257338C>T	ENST00000508883.1	+	9	1368	c.1342C>T	c.(1342-1344)Cga>Tga	p.R448*	PKD2L2_ENST00000508638.1_Intron|PKD2L2_ENST00000350250.4_Nonsense_Mutation_p.R414*|PKD2L2_ENST00000290431.5_Nonsense_Mutation_p.R448*|PKD2L2_ENST00000502810.1_Nonsense_Mutation_p.R426*			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	448					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.R448*(1)		breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGCACAATTTCGAATTGTTCT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	5						C	stop/ARG	0,3592		0,0,1796	123	111	114		1342	5.9	1	5		114	2,8142		0,2,4070	yes	stop-gained	PKD2L2	NM_014386.2		0,2,5866	TT,TC,CC		0.0246,0.0,0.017		448/614	137257338	2,11734	1796	4072	5868	137285237	SO:0001587	stop_gained	27039			AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.1342C>T	5.37:g.137257338C>T	ENSP00000424725:p.Arg448*		137285237	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Nonsense_Mutation	SNP	ENST00000508883.1	37		.	.	.	.	.	.	.	.	.	.	C	37	6.213939	0.97380	0.0	2.46E-4	ENSG00000078795	ENST00000350250;ENST00000502810;ENST00000508883;ENST00000290431	.	.	.	5.89	5.89	0.94794	.	0.000000	0.53938	D	0.000043	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7685	19.8512	0.96741	0.0:1.0:0.0:0.0	.	.	.	.	X	414;426;448;448	.	ENSP00000290431:R448X	R	+	1	2	PKD2L2	137285237	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.215000	0.65241	2.797000	0.96272	0.563000	0.77884	CGA		0.323	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		T	137257338	C	T	137257338	4	4	47	1	0	0	0	0	0	1	0	0	11999	876	31	1	1376	1	PKD2L2	5	137257338	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4608971	137257338	43657922	739	5136										
FAM13B	51306	broad.mit.edu	37	chr5	137281985	137281985	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctttctcttctaccaaatGatctttggtcattttctgga	6	9	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:137281985G>T	ENST00000033079.3	-	18	2561	c.2110C>A	c.(2110-2112)Cat>Aat	p.H704N	FAM13B_ENST00000425075.2_Intron|FAM13B_ENST00000420893.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	704					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.H704N(1)		endometrium(4)|kidney(2)|lung(5)	11						TCTACCAAATGATCTTTGGTC	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	5											52	59	57					5																	137281985		2200	4290	6490	137309884	SO:0001583	missense	51306			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2110C>A	5.37:g.137281985G>T	ENSP00000033079:p.His704Asn		137309884	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432798	0.43224	.	.	ENSG00000031003	ENST00000033079	T	0.08193	3.12	5.71	4.83	0.62350	.	0.230194	0.44483	D	0.000442	T	0.07503	0.0189	L	0.34521	1.04	0.80722	D	1	B	0.15473	0.013	B	0.11329	0.006	T	0.14420	-1.0473	10	0.59425	D	0.04	-7.1086	8.97	0.35901	0.0686:0.0:0.6683:0.2631	.	704	Q9NYF5	FA13B_HUMAN	N	704	ENSP00000033079:H704N	ENSP00000033079:H704N	H	-	1	0	FAM13B	137309884	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.978000	0.70501	1.395000	0.46643	0.467000	0.42956	CAT		0.294	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			T	137281985	G	T	137281985	3	4	47	1	0	0	0	0	1	0	0	0	5469	1290	45	2	661	2	FAM13B	5	137281985	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	24647	137281985	43633275	740	5137										
BRD8	10902	broad.mit.edu	37	chr5	137488269	137488269	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacaagcagttcactaggttCtctctccgggctgctttcct	8	13	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:137488269C>A	ENST00000254900.5	-	21	3129	c.2758G>T	c.(2758-2760)Gaa>Taa	p.E920*		NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	920					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.E920*(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCACTAGGTTCTCTCTCCGGG	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											212	214	213					5																	137488269		2203	4300	6503	137516168	SO:0001587	stop_gained	10902			AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.2758G>T	5.37:g.137488269C>A	ENSP00000254900:p.Glu920*		137516168	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Nonsense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	C	44	11.046822	0.99507	.	.	ENSG00000112983	ENST00000254900;ENST00000427976	.	.	.	5.39	5.39	0.77823	.	0.000000	0.43919	D	0.000506	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	0.3052	16.0138	0.80422	0.0:1.0:0.0:0.0	.	.	.	.	X	920;26	.	ENSP00000254900:E920X	E	-	1	0	BRD8	137516168	0.961000	0.32948	1.000000	0.80357	0.923000	0.55619	2.918000	0.48829	2.795000	0.96236	0.655000	0.94253	GAA		0.547	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		A	137488269	C	A	137488269	4	1	47	1	0	0	0	0	0	1	0	0	1509	922	32	2	977	2	BRD8	5	137488269	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	206284	137488269	43426991	741	5138										
ETF1	2107	broad.mit.edu	37	chr5	137847186	137847186	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attaatttcttctcttgaatGaatttcacgttggagaggac	8	6	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:137847186G>T	ENST00000360541.5	-	7	1061	c.840C>A	c.(838-840)ttC>ttA	p.F280L	ETF1_ENST00000503014.1_Missense_Mutation_p.F266L|ETF1_ENST00000499810.2_Missense_Mutation_p.F247L	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	280					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)	p.F280L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TCTCTTGAATGAATTTCACGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	80	81					5																	137847186		2202	4299	6501	137875085	SO:0001583	missense	2107			AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.840C>A	5.37:g.137847186G>T	ENSP00000353741:p.Phe280Leu		137875085	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Missense_Mutation	SNP	ENST00000360541.5	37	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700897	0.48307	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014	.	.	.	5.74	2.05	0.26809	eRF1 domain 3 (1);	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	L	0.59436	1.845	0.80722	D	1	B;B;B	0.25169	0.119;0.002;0.031	B;B;B	0.23275	0.045;0.007;0.04	T	0.27297	-1.0078	9	0.24483	T	0.36	-5.8356	8.8681	0.35298	0.3526:0.0:0.6474:0.0	.	266;247;280	B7Z7P8;Q96CG1;P62495	.;.;ERF1_HUMAN	L	247;280;266	.	ENSP00000353741:F280L	F	-	3	2	ETF1	137875085	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	2.899000	0.48679	0.100000	0.17581	-0.140000	0.14226	TTC		0.348	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		T	137847186	G	T	137847186	3	4	47	1	0	0	0	0	1	0	0	0	5281	1281	45	2	493	2	ETF1	5	137847186	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	358917	137847186	43068074	742	5139										
ETF1	2107	broad.mit.edu	37	chr5	137848478	137848478	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaacatatcagattgacttAgttcagttttaaagtcagcg	7	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:137848478A>C	ENST00000360541.5	-	6	928	c.707T>G	c.(706-708)cTa>cGa	p.L236R	ETF1_ENST00000503014.1_Missense_Mutation_p.L222R|ETF1_ENST00000499810.2_Missense_Mutation_p.L203R	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	236					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)	p.L236R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGATTGACTTAGTTCAGTTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	71	71					5																	137848478		2203	4300	6503	137876377	SO:0001583	missense	2107			AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.707T>G	5.37:g.137848478A>C	ENSP00000353741:p.Leu236Arg		137876377	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Missense_Mutation	SNP	ENST00000360541.5	37	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612050	0.87258	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014	T;T;T	0.56444	0.46;0.46;0.46	5.48	5.48	0.80851	eRF1 domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.83714	0.5314	H	0.98918	4.37	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.991;0.995;0.997	D	0.90457	0.4443	10	0.87932	D	0	-0.2475	15.2674	0.73672	1.0:0.0:0.0:0.0	.	222;203;236	B7Z7P8;Q96CG1;P62495	.;.;ERF1_HUMAN	R	203;236;222	ENSP00000421288:L203R;ENSP00000353741:L236R;ENSP00000422203:L222R	ENSP00000353741:L236R	L	-	2	0	ETF1	137876377	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.225000	0.95219	2.081000	0.62600	0.533000	0.62120	CTA		0.428	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		C	137848478	A	C	137848478	3	2	47	1	0	0	0	0	1	0	0	0	5281	420	15	4	630	4	ETF1	5	137848478	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1292	137848478	43066782	743	5140										
LRRTM2	26045	broad.mit.edu	37	chr5	138210120	138210120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgagagtcgcagtagaagaGcagcttctcgcagcggcatt	13	10	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:138210120G>A	ENST00000274711.6	-	2	508	c.130C>T	c.(130-132)Ctc>Ttc	p.L44F	CTNNA1_ENST00000520400.1_Intron|LRRTM2_ENST00000518785.1_Intron|LRRTM2_ENST00000521094.2_Intron|LRRTM2_ENST00000523537.1_Intron|CTNNA1_ENST00000540387.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000518825.1_Intron|CTNNA1_ENST00000355078.5_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	44	LRRNT.				long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.L44F(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CAGTAGAAGAGCAGCTTCTCG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	41	41					5																	138210120		2003	4157	6160	138238019	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.130C>T	5.37:g.138210120G>A	ENSP00000274711:p.Leu44Phe		138238019	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.440801	0.25900	.	.	ENSG00000146006	ENST00000274711	T	0.04502	3.61	5.14	5.14	0.70334	Leucine-rich repeat-containing N-terminal (1);	0.085592	0.51477	D	0.000093	T	0.02888	0.0086	N	0.14661	0.345	0.47819	D	0.999522	B	0.24721	0.11	B	0.20577	0.03	T	0.42783	-0.9431	10	0.07030	T	0.85	.	11.82	0.52232	0.0805:0.0:0.9195:0.0	.	44	O43300	LRRT2_HUMAN	F	44	ENSP00000274711:L44F	ENSP00000274711:L44F	L	-	1	0	LRRTM2	138238019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.491000	0.73649	2.675000	0.91044	0.655000	0.94253	CTC		0.552	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			A	138210120	G	A	138210120	3	1	47	1	0	0	0	0	1	0	0	0	9069	971	34	3	1424	3	LRRTM2	5	138210120	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	361642	138210120	42705140	744	5141										
DNAJC18	202052	broad.mit.edu	37	chr5	138760743	138760743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtctgtgtcctctcatgtCggtgccgtcgacggtaatag	13	10	2	0	rs201230885		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:138760743C>T	ENST00000302060.5	-	5	700	c.620G>A	c.(619-621)cGa>cAa	p.R207Q		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	207						integral component of membrane (GO:0016021)		p.R207Q(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCTCTCATGTCGGTGCCGTCG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											269	245	253					5																	138760743		2203	4300	6503	138788642	SO:0001583	missense	202052			AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.620G>A	5.37:g.138760743C>T	ENSP00000302843:p.Arg207Gln		138788642		Missense_Mutation	SNP	ENST00000302060.5	37	CCDS4214.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946856	0.73672	.	.	ENSG00000170464	ENST00000302060;ENST00000508445	T;T	0.58940	0.3;0.86	5.72	5.72	0.89469	.	0.062425	0.64402	D	0.000005	T	0.67382	0.2887	L	0.52266	1.64	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.61686	-0.7012	10	0.22706	T	0.39	0.0921	11.8524	0.52419	0.0:0.9196:0.0:0.0804	.	207	Q9H819	DJC18_HUMAN	Q	207;40	ENSP00000302843:R207Q;ENSP00000426338:R40Q	ENSP00000302843:R207Q	R	-	2	0	DNAJC18	138788642	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	2.812000	0.47994	2.699000	0.92147	0.563000	0.77884	CGA		0.458	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		T	138760743	C	T	138760743	3	4	47	1	0	0	0	0	1	0	0	0	4648	884	31	1	472	1	DNAJC18	5	138760743	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	550623	138760743	42154517	745	5142										
NRG2	9542	broad.mit.edu	37	chr5	139245195	139245195	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaaacatctctgtccgaaGaatccatttggacatctgga	7	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:139245195G>T	ENST00000361474.1	-	5	1352	c.1128C>A	c.(1126-1128)ttC>ttA	p.F376L	NRG2_ENST00000541337.1_Intron|NRG2_ENST00000340391.3_Missense_Mutation_p.F173L|NRG2_ENST00000545385.1_Intron|NRG2_ENST00000394770.1_Missense_Mutation_p.F376L|NRG2_ENST00000289422.7_Missense_Mutation_p.F376L|NRG2_ENST00000289409.4_Intron|NRG2_ENST00000358522.3_Intron	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	376	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.F376L(1)|p.F284L(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGTCCGAAGAATCCATTTG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	5											86	82	84					5																	139245195		2203	4300	6503	139225379	SO:0001583	missense	9542				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1128C>A	5.37:g.139245195G>T	ENSP00000354910:p.Phe376Leu		139225379		Missense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.667984	0.67814	.	.	ENSG00000158458	ENST00000289422;ENST00000361474;ENST00000446269;ENST00000394770;ENST00000340391;ENST00000544729;ENST00000378238	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.93	5.93	0.95920	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.242522	0.36444	N	0.002597	T	0.47040	0.1424	M	0.89163	3.01	0.58432	D	0.999991	B;B	0.32188	0.245;0.359	B;B	0.33620	0.08;0.167	T	0.53436	-0.8439	10	0.87932	D	0	-19.2332	18.5214	0.90954	0.0:0.0:1.0:0.0	.	376;376	O14511;O14511-3	NRG2_HUMAN;.	L	376;376;376;376;173;284;376	ENSP00000289422:F376L;ENSP00000354910:F376L;ENSP00000378251:F376L;ENSP00000342660:F173L;ENSP00000367483:F376L	ENSP00000289422:F376L	F	-	3	2	NRG2	139225379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.576000	0.90770	2.814000	0.96858	0.655000	0.94253	TTC		0.433	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		T	139245195	G	T	139245195	3	4	47	1	0	0	0	0	1	0	0	0	10679	933	33	2	1539	2	NRG2	5	139245195	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	484452	139245195	41670065	746	5143										
ANKHD1	54882	broad.mit.edu	37	chr5	139838784	139838784	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccagacagaagaaactcaaGaaactgctcttactttggct	7	11	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:139838784G>T	ENST00000360839.2	+	9	1670	c.1516G>T	c.(1516-1518)Gaa>Taa	p.E506*	ANKHD1_ENST00000394723.3_Nonsense_Mutation_p.E506*|ANKHD1_ENST00000297183.6_Nonsense_Mutation_p.E506*|ANKHD1-EIF4EBP3_ENST00000532219.1_Nonsense_Mutation_p.E506*|ANKHD1_ENST00000394722.3_Nonsense_Mutation_p.E495*	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	506						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.E506*(2)		breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAACTCAAGAAACTGCTCT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											74	75	75					5																	139838784		2203	4300	6503	139818968	SO:0001587	stop_gained	404734			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1516G>T	5.37:g.139838784G>T	ENSP00000354085:p.Glu506*		139818968	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Nonsense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	G	40	8.504266	0.98841	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.4165	0.94703	0.0:0.0:1.0:0.0	.	.	.	.	X	506;520;506;506;21;506;506;495;506	.	ENSP00000432016:E506X	E	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139818968	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.612000	0.98347	2.604000	0.88044	0.555000	0.69702	GAA		0.363	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139838784	G	T	139838784	4	4	47	1	0	0	0	0	0	1	0	0	628	943	33	2	1550	2	ANKHD1	5	139838784	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	593589	139838784	41076476	747	5144										
ANKHD1	54882	broad.mit.edu	37	chr5	139866564	139866564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgccacgtgtgccaacgcatAcacttgccatggttgtacct	9	13	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:139866564A>G	ENST00000360839.2	+	14	2318	c.2164A>G	c.(2164-2166)Aca>Gca	p.T722A	ANKHD1_ENST00000297183.6_Missense_Mutation_p.T722A|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.T722A	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	722						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.T722A(2)		breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCAACGCATACACTTGCCAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	5											87	80	83					5																	139866564		2203	4300	6503	139846748	SO:0001583	missense	404734			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.2164A>G	5.37:g.139866564A>G	ENSP00000354085:p.Thr722Ala		139846748	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	5.573	0.290619	0.10567	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000412116;ENST00000532219	T;T;T;T;T	0.65364	0.09;0.05;0.07;-0.15;0.05	5.03	3.89	0.44902	Ankyrin repeat-containing domain (1);	0.131318	0.51477	D	0.000092	T	0.30792	0.0776	N	0.04203	-0.255	0.43141	D	0.994899	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.28332	-1.0047	10	0.02654	T	1	.	7.8085	0.29217	0.8205:0.0:0.1795:0.0	.	722;722;722	Q8IWZ3-4;Q8IWZ2;Q8IWZ3	.;.;ANKH1_HUMAN	A	722;755;722;722;256;741;128;722	ENSP00000354085:T722A;ENSP00000297183:T722A;ENSP00000394489:T741A;ENSP00000405602:T128A;ENSP00000432016:T722A	ENSP00000432016:T722A	T	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139846748	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.848000	0.62874	1.882000	0.54519	0.459000	0.35465	ACA		0.413	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139866564	A	G	139866564	3	3	47	1	0	0	0	0	1	0	0	0	628	391	14	4	2324	4	ANKHD1	5	139866564	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	27780	139866564	41048696	748	5145										
PCDHA2	56146	broad.mit.edu	37	chr5	140176233	140176233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctggacgagaacgacaacGcgccggcactgttggcgcct	14	13	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140176233G>A	ENST00000526136.1	+	1	1684	c.1684G>A	c.(1684-1686)Gcg>Acg	p.A562T	PCDHA2_ENST00000378132.1_Missense_Mutation_p.A562T|PCDHA2_ENST00000520672.2_Missense_Mutation_p.A562T|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	562	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A562T(4)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACGACAACGCGCCGGCACT	0.697																																																4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	5											86	84	85					5																	140176233		2203	4298	6501	140156417	SO:0001583	missense	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1684G>A	5.37:g.140176233G>A	ENSP00000431748:p.Ala562Thr		140156417	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	g	19.52	3.842971	0.71488	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.43294	0.95;0.95;0.95	4.05	3.1	0.35709	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.39475	U	0.001345	T	0.52661	0.1748	M	0.65975	2.015	0.32499	N	0.539106	D;P;D	0.60160	0.965;0.609;0.987	P;B;P	0.54140	0.743;0.082;0.743	T	0.67133	-0.5747	10	0.54805	T	0.06	.	13.8621	0.63566	0.0:0.1536:0.8464:0.0	.	562;562;562	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	T	562	ENSP00000430584:A562T;ENSP00000367372:A562T;ENSP00000431748:A562T	ENSP00000367372:A562T	A	+	1	0	PCDHA2	140156417	0.887000	0.30362	0.998000	0.56505	0.724000	0.41520	1.626000	0.37039	1.989000	0.58080	0.644000	0.83932	GCG		0.697	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140176233	G	A	140176233	3	1	47	1	0	0	0	0	1	0	0	0	11555	1087	38	1	1686	1	PCDHA2	5	140176233	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	309669	140176233	40739027	749	5146										
PCDHA3	56145	broad.mit.edu	37	chr5	140183257	140183257	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actcctctggaaatacattaAtagttaagtatgaattatgt	6	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140183257A>C	ENST00000522353.2	+	1	2394				PCDHA3_ENST00000532566.2_Splice_Site_p.*825Y|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3						cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.*825Y(1)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATACATTAATAGTTAAGTA	0.294																																																1	Nonstop extension(1)	large_intestine(1)	5											22	27	25					5																	140183257		2143	4283	6426	140163441	SO:0001627	intron_variant	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.2394+81A>C	5.37:g.140183257A>C			140163441	O75286	Nonstop_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	13.05	2.122194	0.37436	.	.	ENSG00000255408	ENST00000532566	.	.	.	3.88	2.59	0.31030	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3436	0.11122	0.7198:0.0:0.104:0.1761	.	.	.	.	Y	825	.	.	X	+	3	2	PCDHA3	140163441	0.000000	0.05858	0.014000	0.15608	0.132000	0.20833	0.713000	0.25794	1.528000	0.49103	0.433000	0.28618	TAA		0.294	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		C	140183257	A	C	140183257	1	2	47	0	1	0	0	0	0	0	0	0	11556	116	4	4		4	PCDHA3	5	140183257	Intron	SNP	A	TCGA-AG-3892-01A-01W-1073-09	7024	140183257	40732003	750	5147										
PCDHA12	56137	broad.mit.edu	37	chr5	140255868	140255868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaatgcttccgatccagacGaaggacttaatggagaaatt	9	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140255868G>A	ENST00000398631.2	+	1	811	c.811G>A	c.(811-813)Gaa>Aaa	p.E271K	PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	271	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E271K(2)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATCCAGACGAAGGACTTAA	0.388																																					Pancreas(113;759 1672 13322 24104 50104)											2	Substitution - Missense(2)	large_intestine(2)	5											108	111	110					5																	140255868		1866	4099	5965	140236052	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.811G>A	5.37:g.140255868G>A	ENSP00000381628:p.Glu271Lys		140236052	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631655	0.67015	.	.	ENSG00000251664	ENST00000398631	T	0.52295	0.67	5.07	3.26	0.37387	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.67599	0.2910	M	0.90650	3.135	0.28968	N	0.88941	P;P	0.47191	0.867;0.891	P;P	0.55011	0.52;0.766	T	0.65307	-0.6200	9	0.72032	D	0.01	.	11.1018	0.48179	0.1546:0.0:0.8454:0.0	.	271;271	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	K	271	ENSP00000381628:E271K	ENSP00000381628:E271K	E	+	1	0	PCDHA12	140236052	0.959000	0.32827	0.673000	0.29887	0.775000	0.43874	2.839000	0.48207	1.134000	0.42165	0.591000	0.81541	GAA		0.388	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140255868	G	A	140255868	3	1	47	1	0	0	0	0	1	0	0	0	11553	1059	37	1	813	1	PCDHA12	5	140255868	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	72611	140255868	40659392	751	5148										
PCDHB3	56132	broad.mit.edu	37	chr5	140481307	140481307	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaaacagccctattcctgaGaactcgggagagactgtact	10	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140481307G>T	ENST00000231130.2	+	1	1074	c.1074G>T	c.(1072-1074)gaG>gaT	p.E358D	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	358	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E358D(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTATTCCTGAGAACTCGGGAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	84	85					5																	140481307		2203	4300	6503	140461491	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1074G>T	5.37:g.140481307G>T	ENSP00000231130:p.Glu358Asp		140461491	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835209	0.50951	.	.	ENSG00000113205	ENST00000231130	T	0.75367	-0.93	4.93	1.91	0.25777	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.92001	0.7466	H	0.99935	4.985	0.33467	D	0.585708	D	0.89917	1.0	D	0.91635	0.999	D	0.92750	0.6215	9	0.87932	D	0	.	10.4207	0.44348	0.3118:0.0:0.6882:0.0	.	358	Q9Y5E6	PCDB3_HUMAN	D	358	ENSP00000231130:E358D	ENSP00000231130:E358D	E	+	3	2	PCDHB3	140461491	0.000000	0.05858	0.997000	0.53966	0.637000	0.38172	-1.126000	0.03254	0.495000	0.27882	0.655000	0.94253	GAG		0.483	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140481307	G	T	140481307	3	4	47	1	0	0	0	0	1	0	0	0	11574	933	33	2	1076	2	PCDHB3	5	140481307	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	225439	140481307	40433953	752	5149										
PCDHB3	56132	broad.mit.edu	37	chr5	140482476	140482476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccgggaccctgtcccagaGctaccagtacgaggtgtgtc	12	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140482476G>A	ENST00000231130.2	+	1	2243	c.2243G>A	c.(2242-2244)aGc>aAc	p.S748N	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	748					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S748N(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTCCCAGAGCTACCAGTAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											30	32	31					5																	140482476		2153	4249	6402	140462660	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.2243G>A	5.37:g.140482476G>A	ENSP00000231130:p.Ser748Asn		140462660	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	5.112	0.206291	0.09704	.	.	ENSG00000113205	ENST00000231130	T	0.13657	2.57	4.33	4.33	0.51752	.	.	.	.	.	T	0.13927	0.0337	L	0.52905	1.665	0.22968	N	0.998494	B	0.19200	0.034	B	0.20384	0.029	T	0.10314	-1.0635	9	0.42905	T	0.14	.	6.5759	0.22567	0.1003:0.1845:0.7152:0.0	.	748	Q9Y5E6	PCDB3_HUMAN	N	748	ENSP00000231130:S748N	ENSP00000231130:S748N	S	+	2	0	PCDHB3	140462660	0.000000	0.05858	1.000000	0.80357	0.080000	0.17528	-0.350000	0.07721	2.099000	0.63709	0.491000	0.48974	AGC		0.627	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		A	140482476	G	A	140482476	3	1	47	1	0	0	0	0	1	0	0	0	11574	971	34	3	2245	3	PCDHB3	5	140482476	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1169	140482476	40432784	753	5150										
PCDHB7	56129	broad.mit.edu	37	chr5	140553866	140553866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagagactcgggcaccaacGcccaggtcatctactccctg	9	16	2	1	rs200942040	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140553866G>A	ENST00000231137.3	+	1	1624	c.1450G>A	c.(1450-1452)Gcc>Acc	p.A484T		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A484T(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGCACCAACGCCCAGGTCAT	0.642													G|||	4	0.000798722	0	0	5008	,	,		16191	0.004		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	5											103	101	102					5																	140553866		2203	4300	6503	140534050	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1450G>A	5.37:g.140553866G>A	ENSP00000231137:p.Ala484Thr		140534050	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	g	18.01	3.526939	0.64860	.	.	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.52295	0.67	4.34	4.34	0.51931	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.69780	0.3149	M	0.93197	3.39	0.43043	D	0.994631	D	0.76494	0.999	D	0.71656	0.974	T	0.82914	-0.0221	9	0.87932	D	0	.	16.8701	0.86038	0.0:0.0:1.0:0.0	.	484	Q9Y5E2	PCDB7_HUMAN	T	484;267	ENSP00000231137:A484T	ENSP00000231137:A484T	A	+	1	0	PCDHB7	140534050	0.996000	0.38824	1.000000	0.80357	0.133000	0.20885	6.176000	0.71955	2.112000	0.64535	0.552000	0.68991	GCC		0.642	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140553866	G	A	140553866	3	1	47	1	0	0	0	0	1	0	0	0	11578	1087	38	1	1452	1	PCDHB7	5	140553866	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	71390	140553866	40361394	754	5151										
PCDHB8	56128	broad.mit.edu	37	chr5	140558318	140558318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtctacattgaagttgtcGatgtcaatgataatgcccct	9	8	2	2	rs146359786		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140558318G>A	ENST00000239444.2	+	1	948	c.703G>A	c.(703-705)Gat>Aat	p.D235N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	235	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D235N(2)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAAGTTGTCGATGTCAATGA	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	5						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	184	230	214		703	4.2	0	5	dbSNP_134	214	0,8566		0,0,4283	no	missense	PCDHB8	NM_019120.3	23	0,1,6485	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	235/802	140558318	1,12971	2203	4283	6486	140538502	SO:0001583	missense	56128			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.703G>A	5.37:g.140558318G>A	ENSP00000239444:p.Asp235Asn		140538502	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	g	14.96	2.691508	0.48097	2.27E-4	0.0	ENSG00000120322	ENST00000239444	T	0.74209	-0.82	4.25	4.25	0.50352	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.89136	0.6629	M	0.92459	3.31	0.47584	D	0.999465	D	0.89917	1.0	D	0.97110	1.0	D	0.92309	0.5856	9	0.87932	D	0	.	16.2711	0.82622	0.0:0.0:1.0:0.0	.	235	Q9UN66	PCDB8_HUMAN	N	235	ENSP00000239444:D235N	ENSP00000239444:D235N	D	+	1	0	PCDHB8	140538502	1.000000	0.71417	0.042000	0.18584	0.003000	0.03518	9.809000	0.99208	1.911000	0.55334	0.585000	0.79938	GAT		0.512	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		A	140558318	G	A	140558318	3	1	47	1	0	0	0	0	1	0	0	0	11579	1058	37	1	705	1	PCDHB8	5	140558318	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4452	140558318	40356942	755	5152										
PCDHGA2	56113	broad.mit.edu	37	chr5	140719984	140719984	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcccatgaccccgacagcaaCgacaatgctcatgtaactta	7	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:140719984C>T	ENST00000394576.2	+	1	1446	c.1446C>T	c.(1444-1446)aaC>aaT	p.N482N	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	482	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N482N(2)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGACAGCAACGACAATGCTC	0.537																																																2	Substitution - coding silent(2)	large_intestine(2)	5											98	102	100					5																	140719984		2203	4300	6503	140700168	SO:0001819	synonymous_variant	56113			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1446C>T	5.37:g.140719984C>T			140700168	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																				0.537	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		T	140719984	C	T	140719984	2	4	47	1	0	0	0	0	0	0	0	1	11585	535	19	1		1	PCDHGA2	5	140719984	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	161666	140719984	40195276	756	5153										
FCHSD1	89848	broad.mit.edu	37	chr5	141024217	141024217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtccgggaagttgagatatCgctcagggacaaagcctacc	13	10	1	1	rs558644593		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:141024217C>T	ENST00000435817.2	-	16	1615	c.1565G>A	c.(1564-1566)cGa>cAa	p.R522Q	FCHSD1_ENST00000522783.1_Missense_Mutation_p.R448Q|FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522126.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	522	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.							p.R522Q(1)	FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTGAGATATCGCTCAGGGAC	0.552													C|||	1	0.000199681	8e-04	0	5008	,	,		15956	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											71	75	74					5																	141024217		1998	4169	6167	141004401	SO:0001583	missense	89848			AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.1565G>A	5.37:g.141024217C>T	ENSP00000399259:p.Arg522Gln		141004401	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.535704	0.64972	.	.	ENSG00000197948	ENST00000435817;ENST00000522783;ENST00000518499	T;T;T	0.13420	2.59;2.59;2.59	5.56	4.69	0.59074	Src homology-3 domain (3);	0.310909	0.23930	N	0.043153	T	0.13713	0.0332	N	0.20845	0.615	0.80722	D	1	D;P	0.65815	0.995;0.821	P;B	0.51170	0.661;0.266	T	0.03157	-1.1066	10	0.59425	D	0.04	-18.5861	9.4746	0.38864	0.0:0.7953:0.0:0.2047	.	202;522	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	Q	522;448;205	ENSP00000399259:R522Q;ENSP00000428677:R448Q;ENSP00000430448:R205Q	ENSP00000399259:R522Q	R	-	2	0	FCHSD1	141004401	0.897000	0.30589	0.997000	0.53966	0.972000	0.66771	1.482000	0.35486	1.362000	0.46000	0.551000	0.68910	CGA		0.552	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		T	141024217	C	T	141024217	3	4	47	1	0	0	0	0	1	0	0	0	5808	884	31	1	527	1	FCHSD1	5	141024217	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	304233	141024217	39891043	757	5154										
NDFIP1	80762	broad.mit.edu	37	chr5	141515304	141515304	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttcatttaggatgaggatTttgtgggtcgggatgatttt	13	2	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:141515304T>G	ENST00000253814.4	+	4	762	c.292T>G	c.(292-294)Ttt>Gtt	p.F98V		NM_030571.3	NP_085048.1	Q9BT67	NFIP1_HUMAN	Nedd4 family interacting protein 1	98					cellular iron ion homeostasis (GO:0006879)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of protein transport (GO:0051224)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transporter activity (GO:0032410)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein ubiquitination (GO:0031398)|regulation of isotype switching to IgG isotypes (GO:0048302)|regulation of lymphocyte differentiation (GO:0045619)|regulation of myeloid leukocyte differentiation (GO:0002761)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cell cortex (GO:0005938)|endosome (GO:0005768)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)	p.F98V(1)		large_intestine(3)|lung(1)|ovary(1)	5		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGATGAGGATTTTGTGGGTCG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	5											178	168	171					5																	141515304		2203	4300	6503	141495488	SO:0001583	missense	80762			BC004317	CCDS4273.1	5q31.3	2008-02-05			ENSG00000131507	ENSG00000131507			17592	protein-coding gene	gene with protein product		612050				11042109, 11748237	Standard	NM_030571		Approved	N4WBP5, MGC10924	uc003lmi.4	Q9BT67	OTTHUMG00000129659	ENST00000253814.4:c.292T>G	5.37:g.141515304T>G	ENSP00000253814:p.Phe98Val		141495488	B2RDB8|D3DQF0|Q658T8|Q8N2E3|Q8N2F9	Missense_Mutation	SNP	ENST00000253814.4	37	CCDS4273.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189155	0.78789	.	.	ENSG00000131507	ENST00000253814	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.57621	0.2066	L	0.52759	1.655	0.80722	D	1	D	0.53619	0.961	P	0.48270	0.572	T	0.54070	-0.8348	9	0.18276	T	0.48	-1.0569	15.3691	0.74548	0.0:0.0:0.0:1.0	.	98	Q9BT67	NFIP1_HUMAN	V	98	.	ENSP00000253814:F98V	F	+	1	0	NDFIP1	141495488	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.654000	0.83653	2.122000	0.65172	0.397000	0.26171	TTT		0.333	NDFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251859.2	NM_030571		G	141515304	T	G	141515304	3	3	47	1	0	0	0	0	1	0	0	0	10276	1841	64	4	306	4	NDFIP1	5	141515304	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	491087	141515304	39399956	758	5155										
TCERG1	10915	broad.mit.edu	37	chr5	145838593	145838593	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgcaggctcaggcccaggcGcaggctcaggcccaggcaca	15	16	2	0	rs140816235	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:145838593G>A	ENST00000296702.5	+	4	623	c.585G>A	c.(583-585)gcG>gcA	p.A195A	TCERG1_ENST00000394421.2_Silent_p.A195A	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	195	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.A195A(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			aggcccaggcgcaggctcagg	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G	,	1,4403		0,1,2201	29	31	30		585,585	-6.7	0.9	5	dbSNP_134	30	5,8593	3.7+/-12.6	0,5,4294	no	coding-synonymous,coding-synonymous	TCERG1	NM_001040006.1,NM_006706.3	,	0,6,6495	AA,AG,GG		0.0582,0.0227,0.0461	,	195/1078,195/1099	145838593	6,12996	2202	4299	6501	145818786	SO:0001819	synonymous_variant	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.585G>A	5.37:g.145838593G>A			145818786	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																				0.667	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		A	145838593	G	A	145838593	2	1	47	1	0	0	0	0	0	0	0	1	15724	1074	38	1		1	TCERG1	5	145838593	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4323289	145838593	35076667	759	5156										
PPP2R2B	5521	broad.mit.edu	37	chr5	145980011	145980011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctgttgcttggatcttccGgctcttcaaaaactgcagaa	8	10	4	1	rs148423117		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:145980011G>A	ENST00000394413.3	-	7	1373	c.803C>T	c.(802-804)cCg>cTg	p.P268L	PPP2R2B_ENST00000508545.2_Missense_Mutation_p.P257L|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.P268L|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.P268L|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.P274L|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.P271L|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.P326L|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.P257L|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.P268L|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.P334L|CTB-99A3.1_ENST00000512730.1_RNA			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	268					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.P271L(3)|p.P326L(2)|p.P268L(1)|p.P257L(1)		endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGATCTTCCGGCTCTTCAAA	0.413																																																7	Substitution - Missense(7)	kidney(4)|large_intestine(3)	5						G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	56	56	56		803,803,803,803,812,743,770	5.8	1	5	dbSNP_134	56	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	PPP2R2B	NM_001127381.1,NM_004576.2,NM_181674.2,NM_181675.2,NM_181676.2,NM_181677.2,NM_181678.2	98,98,98,98,98,98,98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	268/444,268/444,268/444,268/444,271/447,248/424,257/433	145980011	1,13005	2203	4300	6503	145960204	SO:0001583	missense	5521			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9305	protein-coding gene	gene with protein product	"PP2A subunit B isoform beta"	604325	"spinocerebellar ataxia 12", "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.803C>T	5.37:g.145980011G>A	ENSP00000377935:p.Pro268Leu		145960204	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928122	0.73327	2.27E-4	0.0	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	M	0.79475	2.455	0.80722	D	1	P;P;P;P;P;P	0.43750	0.816;0.816;0.816;0.664;0.705;0.816	B;B;B;B;B;B	0.34590	0.13;0.186;0.134;0.13;0.035;0.186	T	0.43637	-0.9379	10	0.51188	T	0.08	-22.597	20.0467	0.97609	0.0:0.0:1.0:0.0	.	326;274;257;334;271;268	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	L	268;257;334;268;268;268;257;271;274;326	ENSP00000377935:P268L;ENSP00000431320:P257L;ENSP00000377936:P334L;ENSP00000377933:P268L;ENSP00000349283:P268L;ENSP00000398779:P268L;ENSP00000377932:P257L;ENSP00000336591:P271L;ENSP00000421396:P274L;ENSP00000377931:P326L	ENSP00000336591:P271L	P	-	2	0	AC011357.1	145960204	1.000000	0.71417	0.977000	0.42913	0.992000	0.81027	9.869000	0.99810	2.749000	0.94314	0.655000	0.94253	CCG		0.413	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678		A	145980011	G	A	145980011	3	1	47	1	0	0	0	0	1	0	0	0	12419	1116	39	1	540	1	PPP2R2B	5	145980011	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	141418	145980011	34935249	760	5157										
SPINK5	11005	broad.mit.edu	37	chr5	147493943	147493943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggagacatgcgatgaatttCggagacttttgcaaaatgga	12	5	0	3	rs376918928		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:147493943C>T	ENST00000256084.7	+	21	1948	c.1906C>T	c.(1906-1908)Cgg>Tgg	p.R636W	SPINK5_ENST00000398454.1_Missense_Mutation_p.R636W|SPINK5_ENST00000359874.3_Missense_Mutation_p.R636W	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	636	Kazal-like 10. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R636W(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATGAATTTCGGAGACTTTT	0.408													C|||	1	0.000199681	8e-04	0	5008	,	,		17527	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	5						C	TRP/ARG,TRP/ARG,TRP/ARG	0,3656		0,0,1828	61	58	59		1906,1906,1906	3.6	1	5		59	2,8176		0,2,4087	no	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	101,101,101	0,2,5915	TT,TC,CC		0.0245,0.0,0.0169	probably-damaging,probably-damaging,probably-damaging	636/1095,636/917,636/1065	147493943	2,11832	1828	4089	5917	147474136	SO:0001583	missense	11005			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1906C>T	5.37:g.147493943C>T	ENSP00000256084:p.Arg636Trp		147474136	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.684151	0.47991	0.0	2.45E-4	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.07444	3.19;3.19;3.19;3.19	5.42	3.58	0.41010	Proteinase inhibitor I1, Kazal (1);	0.406582	0.20305	N	0.094945	T	0.25644	0.0624	M	0.73430	2.235	0.23848	N	0.996672	P;D;D;D	0.89917	0.826;1.0;1.0;1.0	B;D;D;D	0.72338	0.327;0.977;0.95;0.977	T	0.03706	-1.1011	10	0.44086	T	0.13	-3.814	11.1562	0.48489	0.3354:0.6646:0.0:0.0	.	617;636;636;636	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	W	636;636;617;636	ENSP00000381472:R636W;ENSP00000352936:R636W;ENSP00000421519:R617W;ENSP00000256084:R636W	ENSP00000256084:R636W	R	+	1	2	SPINK5	147474136	0.998000	0.40836	0.998000	0.56505	0.669000	0.39330	0.764000	0.26532	0.724000	0.32296	-0.181000	0.13052	CGG		0.408	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147493943	C	T	147493943	3	4	47	1	0	0	0	0	1	0	0	0	15101	875	31	1	1988	1	SPINK5	5	147493943	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1513932	147493943	33421317	761	5158										
SPINK5	11005	broad.mit.edu	37	chr5	147503468	147503468	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagagaaaataaccctgttCgaggcccatatggcaagatg	10	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:147503468C>T	ENST00000256084.7	+	27	2653	c.2611C>T	c.(2611-2613)Cga>Tga	p.R871*	SPINK5_ENST00000398454.1_Nonsense_Mutation_p.R871*|SPINK5_ENST00000359874.3_Nonsense_Mutation_p.R871*	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	871	Kazal-like 13. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R871*(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAACCCTGTTCGAGGCCCATA	0.388																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											109	108	108					5																	147503468		1885	4122	6007	147483661	SO:0001587	stop_gained	11005			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2611C>T	5.37:g.147503468C>T	ENSP00000256084:p.Arg871*		147483661	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Nonsense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398593	0.83120	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	.	.	.	4.36	3.48	0.39840	.	0.000000	0.39475	N	0.001359	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-6.1463	9.7341	0.40377	0.206:0.794:0.0:0.0	.	.	.	.	X	871;871;852;871	.	ENSP00000256084:R871X	R	+	1	2	SPINK5	147483661	0.221000	0.23642	1.000000	0.80357	0.244000	0.25665	1.667000	0.37471	1.417000	0.47077	0.585000	0.79938	CGA		0.388	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147503468	C	T	147503468	4	4	47	1	0	0	0	0	0	1	0	0	15101	876	31	1	2717	1	SPINK5	5	147503468	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9525	147503468	33411792	762	5159										
FBXO38	81545	broad.mit.edu	37	chr5	147790243	147790243	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccctaaccaaagatggtgtCttttctgccctaaagatggc	8	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:147790243C>A	ENST00000340253.5	+	9	1176	c.1008C>A	c.(1006-1008)gtC>gtA	p.V336V	FBXO38_ENST00000513826.1_Silent_p.V336V|FBXO38_ENST00000394370.3_Silent_p.V336V|FBXO38_ENST00000296701.6_Silent_p.V336V			Q6PIJ6	FBX38_HUMAN	F-box protein 38	336					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V336V(1)	ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGATGGTGTCTTTTCTGCCC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	5											172	169	170					5																	147790243		2203	4300	6503	147770436	SO:0001819	synonymous_variant	81545			BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.1008C>A	5.37:g.147790243C>A			147770436	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Silent	SNP	ENST00000340253.5	37																																																																																					0.393	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		A	147790243	C	A	147790243	2	1	47	1	0	0	0	0	0	0	0	1	5765	900	32	2		2	FBXO38	5	147790243	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	286775	147790243	33125017	763	5160										
PDE6A	5145	broad.mit.edu	37	chr5	149324027	149324027	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catttctctgtctgtaaattCtcctgaaagtcccgcaggag	8	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:149324027C>A	ENST00000255266.5	-	1	329	c.210G>T	c.(208-210)gaG>gaT	p.E70D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	70					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.E70D(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TCTGTAAATTCTCCTGAAAGT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											71	71	71					5																	149324027		2203	4300	6503	149304220	SO:0001583	missense	5145				CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.210G>T	5.37:g.149324027C>A	ENSP00000255266:p.Glu70Asp		149304220	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.384781	0.25031	.	.	ENSG00000132915	ENST00000255266	T	0.69561	-0.41	5.47	-0.983	0.10263	.	1.092800	0.06873	N	0.801119	T	0.50429	0.1615	L	0.39633	1.23	0.35569	D	0.805298	B	0.14805	0.011	B	0.17979	0.02	T	0.46965	-0.9153	10	0.08179	T	0.78	.	5.7177	0.17970	0.0:0.328:0.3747:0.2973	.	70	P16499	PDE6A_HUMAN	D	70	ENSP00000255266:E70D	ENSP00000255266:E70D	E	-	3	2	PDE6A	149304220	0.859000	0.29813	0.835000	0.33067	0.838000	0.47535	0.079000	0.14782	-0.196000	0.10366	0.561000	0.74099	GAG		0.532	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149324027	C	A	149324027	3	1	47	1	0	0	0	0	1	0	0	0	11676	912	32	2	2460	2	PDE6A	5	149324027	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1533784	149324027	31591233	764	5161										
SLC26A2	1836	broad.mit.edu	37	chr5	149360114	149360114	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggttcttttgccaaccaaaGaactcaatgaacacttcaaa	5	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:149360114G>T	ENST00000286298.4	+	3	1226	c.958G>T	c.(958-960)Gaa>Taa	p.E320*		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	320					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.E320*(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GCCAACCAAAGAACTCAATGA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											121	113	116					5																	149360114		2203	4300	6503	149340307	SO:0001587	stop_gained	1836			U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.958G>T	5.37:g.149360114G>T	ENSP00000286298:p.Glu320*		149340307	A8K2U3|B2R6J1|Q6N051	Nonsense_Mutation	SNP	ENST00000286298.4	37	CCDS4300.1	.	.	.	.	.	.	.	.	.	.	G	39	7.589697	0.98378	.	.	ENSG00000155850	ENST00000286298	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	19.4109	0.94671	0.0:0.0:1.0:0.0	.	.	.	.	X	320	.	ENSP00000286298:E320X	E	+	1	0	SLC26A2	149340307	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.972000	0.88022	2.579000	0.87056	0.585000	0.79938	GAA		0.403	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		T	149360114	G	T	149360114	4	4	47	1	0	0	0	0	0	1	0	0	14554	943	33	2	964	2	SLC26A2	5	149360114	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	36087	149360114	31555146	765	5162										
SLC26A2	1836	broad.mit.edu	37	chr5	149361012	149361012	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggaagaaggcagcaaagaGaaagatcaaagaaaaagtag	12	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:149361012G>T	ENST00000286298.4	+	3	2124	c.1856G>T	c.(1855-1857)aGa>aTa	p.R619I		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	619	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.			R -> G (in Ref. 6; CAE45819). {ECO:0000305}.	3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.R619I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GCAGCAAAGAGAAAGATCAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	80	79					5																	149361012		2203	4300	6503	149341205	SO:0001583	missense	1836			U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.1856G>T	5.37:g.149361012G>T	ENSP00000286298:p.Arg619Ile		149341205	A8K2U3|B2R6J1|Q6N051	Missense_Mutation	SNP	ENST00000286298.4	37	CCDS4300.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713439	0.48517	.	.	ENSG00000155850	ENST00000286298	D	0.94232	-3.38	6.07	3.27	0.37495	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.244690	0.49305	D	0.000148	D	0.92922	0.7748	M	0.64997	1.995	0.43798	D	0.996343	P	0.45240	0.854	P	0.50314	0.637	D	0.91045	0.4874	10	0.49607	T	0.09	.	8.5329	0.33346	0.0619:0.1131:0.7075:0.1174	.	619	P50443	S26A2_HUMAN	I	619	ENSP00000286298:R619I	ENSP00000286298:R619I	R	+	2	0	SLC26A2	149341205	0.408000	0.25360	0.997000	0.53966	0.726000	0.41606	0.291000	0.18994	0.868000	0.35678	0.655000	0.94253	AGA		0.388	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		T	149361012	G	T	149361012	3	4	47	1	0	0	0	0	1	0	0	0	14554	942	33	2	1862	2	SLC26A2	5	149361012	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	898	149361012	31554248	766	5163										
ZNF300	91975	broad.mit.edu	37	chr5	150275179	150275179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctctcctgtatgaattCgctggtgtcccggaaggtgg	13	9	1	1	rs147702441	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:150275179C>T	ENST00000274599.5	-	6	2042	c.1622G>A	c.(1621-1623)cGa>cAa	p.R541Q	ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000394226.2_Missense_Mutation_p.R541Q|ZNF300_ENST00000446148.2_Missense_Mutation_p.R557Q|ZNF300_ENST00000418587.2_Missense_Mutation_p.R505Q	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	541					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R541Q(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTATGAATTCGCTGGTGTCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	57	59	58		1670,1514,1622	2.7	1	5	dbSNP_134	58	8,8590	7.1+/-27.0	0,8,4291	no	missense,missense,missense	ZNF300	NM_001172831.1,NM_001172832.1,NM_052860.2	43,43,43	0,9,6493	TT,TC,CC		0.093,0.0227,0.0692	probably-damaging,probably-damaging,probably-damaging	557/621,505/569,541/605	150275179	9,12995	2203	4299	6502	150255372	SO:0001583	missense	91975			AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"Zinc fingers, C2H2-type", "-"	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.1622G>A	5.37:g.150275179C>T	ENSP00000274599:p.Arg541Gln		150255372	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Missense_Mutation	SNP	ENST00000274599.5	37	CCDS4311.2	.	.	.	.	.	.	.	.	.	.	C	13.78	2.338011	0.41398	2.27E-4	9.3E-4	ENSG00000145908	ENST00000446148;ENST00000274599;ENST00000418587;ENST00000394226	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	3.58	2.7	0.31948	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23249	0.0562	L	0.48260	1.515	0.22171	N	0.999311	D	0.63880	0.993	P	0.44860	0.462	T	0.12630	-1.0540	9	0.62326	D	0.03	.	5.6611	0.17670	0.0:0.7535:0.0:0.2465	.	541	Q96RE9	ZN300_HUMAN	Q	557;541;505;541	ENSP00000397178:R557Q;ENSP00000274599:R541Q;ENSP00000392593:R505Q;ENSP00000377773:R541Q	ENSP00000274599:R541Q	R	-	2	0	ZNF300	150255372	0.000000	0.05858	1.000000	0.80357	0.954000	0.61252	-0.365000	0.07573	0.861000	0.35504	0.591000	0.81541	CGA		0.433	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860		T	150275179	C	T	150275179	3	4	47	1	0	0	0	0	1	0	0	0	17870	884	31	1	196	1	ZNF300	5	150275179	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	914167	150275179	30640081	767	5164										
NMUR2	56923	broad.mit.edu	37	chr5	151771789	151771789	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaagctttgatagtttgttCttgacatctgttcactagag	10	6	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:151771789C>A	ENST00000255262.3	-	4	1376	c.1211G>T	c.(1210-1212)aGa>aTa	p.R404I		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	404					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.R404I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			ATAGTTTGTTCTTGACATCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											153	161	158					5																	151771789		2203	4300	6503	151751982	SO:0001583	missense	56923			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.1211G>T	5.37:g.151771789C>A	ENSP00000255262:p.Arg404Ile		151751982	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	8.994	0.978508	0.18812	.	.	ENSG00000132911	ENST00000255262	T	0.71461	-0.57	3.71	-1.45	0.08828	.	4.715920	0.00166	N	0.000007	T	0.58779	0.2146	L	0.36672	1.1	0.09310	N	1	B	0.18610	0.029	B	0.06405	0.002	T	0.32161	-0.9917	10	0.35671	T	0.21	0.215	4.9622	0.14072	0.1381:0.5123:0.0:0.3496	.	404	Q9GZQ4	NMUR2_HUMAN	I	404	ENSP00000255262:R404I	ENSP00000255262:R404I	R	-	2	0	NMUR2	151751982	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.667000	0.05274	-0.343000	0.08351	-0.444000	0.05651	AGA		0.443	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		A	151771789	C	A	151771789	3	1	47	1	0	0	0	0	1	0	0	0	10538	913	32	2	40	2	NMUR2	5	151771789	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1496610	151771789	29143471	768	5165										
LARP1	23367	broad.mit.edu	37	chr5	154193632	154193632	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatggacaagccagcactcGaacacacagactttgggaaa	9	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:154193632G>A	ENST00000336314.4	+	19	3060	c.3036G>A	c.(3034-3036)tcG>tcA	p.S1012S		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	1089					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.S1089S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GCCAGCACTCGAACACACAGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	5											39	40	40					5																	154193632		2203	4300	6503	154173825	SO:0001819	synonymous_variant	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.3036G>A	5.37:g.154193632G>A			154173825	O94836|Q8N4M2|Q8NB73|Q9UFD7	Silent	SNP	ENST00000336314.4	37	CCDS4328.1																																																																																				0.607	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		A	154193632	G	A	154193632	2	1	47	1	0	0	0	0	0	0	0	1	8650	1045	37	1		1	LARP1	5	154193632	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2421843	154193632	26721628	769	5166										
HAVCR2	84868	broad.mit.edu	37	chr5	156533771	156533771	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacacatctcctttgcggaaAtccccatttagccagtatct	6	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:156533771A>C	ENST00000307851.4	-	2	991	c.261T>G	c.(259-261)gaT>gaG	p.D87E	HAVCR2_ENST00000522593.1_Missense_Mutation_p.D87E|HAVCR2_ENST00000517358.1_5'UTR|CTB-120L21.1_ENST00000517708.1_RNA	NM_032782.4	NP_116171.3	Q8TDQ0	HAVR2_HUMAN	hepatitis A virus cellular receptor 2	87	Ig-like V-type.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D87E(1)		cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTTGCGGAAATCCCCATTTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											158	145	150					5																	156533771		2203	4300	6503	156466349	SO:0001583	missense	84868			AK027334	CCDS4333.1	5q34	2014-01-14			ENSG00000135077	ENSG00000135077		"Immunoglobulin superfamily / V-set domain containing"	18437	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 3"	606652				11823861	Standard	NM_032782		Approved	Tim-3, TIM3, FLJ14428, TIMD3	uc003lwk.2	Q8TDQ0	OTTHUMG00000130249	ENST00000307851.4:c.261T>G	5.37:g.156533771A>C	ENSP00000312002:p.Asp87Glu		156466349	B2RAY2|Q8WW60|Q96K94	Missense_Mutation	SNP	ENST00000307851.4	37	CCDS4333.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193967	0.38707	.	.	ENSG00000135077	ENST00000307851;ENST00000522593	T;T	0.66995	-0.24;-0.24	5.48	0.274	0.15654	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.927270	0.01858	N	0.036419	T	0.64594	0.2612	M	0.69823	2.125	0.09310	N	1	B;B	0.26577	0.153;0.03	B;B	0.21151	0.033;0.019	T	0.41142	-0.9525	10	0.49607	T	0.09	2.7796	5.3533	0.16047	0.556:0.1413:0.3027:0.0	.	87;87	Q8TDQ0-2;Q8TDQ0	.;HAVR2_HUMAN	E	87	ENSP00000312002:D87E;ENSP00000430873:D87E	ENSP00000312002:D87E	D	-	3	2	HAVCR2	156466349	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.997000	0.29731	-0.103000	0.12175	0.533000	0.62120	GAT		0.483	HAVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252574.2			C	156533771	A	C	156533771	3	2	47	1	0	0	0	0	1	0	0	0	6995	98	4	4	668	4	HAVCR2	5	156533771	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2340139	156533771	24381489	770	5167										
EBF1	1879	broad.mit.edu	37	chr5	158140131	158140131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtacagggcctcggcaatgtCggccgctctcttcagaatga	12	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:158140131C>T	ENST00000313708.6	-	13	1498	c.1216G>A	c.(1216-1218)Gac>Aac	p.D406N	EBF1_ENST00000517373.1_Missense_Mutation_p.D398N|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.D375N	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	406					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D406N(1)	HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCGGCAATGTCGGCCGCTCTC	0.527			T	HMGA2	lipoma																																		Dom	yes		5	5q34	1879	early B-cell factor 1		M	1	Substitution - Missense(1)	large_intestine(1)	5											87	73	78					5																	158140131		2203	4300	6503	158072709	SO:0001583	missense	1879			AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1216G>A	5.37:g.158140131C>T	ENSP00000322898:p.Asp406Asn		158072709	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	37	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	35	5.463074	0.96257	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.48201	0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.71213	0.3313	M	0.81942	2.565	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.997;0.999	P;D;P;P	0.64877	0.612;0.93;0.686;0.89	T	0.72450	-0.4290	10	0.59425	D	0.04	-9.1318	20.2985	0.98592	0.0:1.0:0.0:0.0	.	406;393;406;375	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	N	406;406;375;398	ENSP00000322898:D406N;ENSP00000370029:D375N;ENSP00000428020:D398N	ENSP00000322898:D406N	D	-	1	0	EBF1	158072709	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.818000	0.86416	2.793000	0.96121	0.655000	0.94253	GAC		0.527	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		T	158140131	C	T	158140131	3	4	47	1	0	0	0	0	1	0	0	0	4891	884	31	1	575	1	EBF1	5	158140131	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1606360	158140131	22775129	771	5168										
SLU7	10569	broad.mit.edu	37	chr5	159835031	159835031	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctctctcattgctctagtTtttggatcatagtaggcaga	8	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:159835031T>G	ENST00000297151.4	-	9	1251	c.864A>C	c.(862-864)aaA>aaC	p.K288N		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	288					alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)	p.K288N(1)		endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGCTCTAGTTTTTGGATCAT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	5											152	162	158					5																	159835031		2203	4300	6503	159767609	SO:0001583	missense	10569			AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.864A>C	5.37:g.159835031T>G	ENSP00000297151:p.Lys288Asn		159767609	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	37	CCDS4352.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.231726	0.79688	.	.	ENSG00000164609	ENST00000297151	T	0.65916	-0.18	6.16	5.02	0.67125	Pre-mRNA splicing Prp18-interacting factor (1);	0.041485	0.85682	D	0.000000	T	0.81427	0.4820	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84831	0.0802	10	0.87932	D	0	-10.07	11.8233	0.52252	0.0:0.0674:0.0:0.9326	.	288	O95391	SLU7_HUMAN	N	288	ENSP00000297151:K288N	ENSP00000297151:K288N	K	-	3	2	SLU7	159767609	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.070000	0.50033	2.367000	0.80283	0.528000	0.53228	AAA		0.303	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425		G	159835031	T	G	159835031	3	3	47	1	0	0	0	0	1	0	0	0	14792	1838	64	4	928	4	SLU7	5	159835031	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1694900	159835031	21080229	772	5169										
SLU7	10569	broad.mit.edu	37	chr5	159835664	159835664	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatatgtattaccatctgaGaatttggttcctcttctccc	5	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:159835664G>T	ENST00000297151.4	-	7	1067	c.680C>A	c.(679-681)tCt>tAt	p.S227Y		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	227					alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)	p.S227Y(1)		endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TACCATCTGAGAATTTGGTTC	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	5											64	67	66					5																	159835664		2203	4295	6498	159768242	SO:0001583	missense	10569			AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.680C>A	5.37:g.159835664G>T	ENSP00000297151:p.Ser227Tyr		159768242	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	37	CCDS4352.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.499499	0.44455	.	.	ENSG00000164609	ENST00000297151	T	0.45276	0.9	6.16	6.16	0.99307	Pre-mRNA splicing Prp18-interacting factor (1);	0.058746	0.64402	D	0.000001	T	0.40619	0.1124	L	0.52573	1.65	0.49582	D	0.999803	B	0.10296	0.003	B	0.09377	0.004	T	0.13683	-1.0500	10	0.59425	D	0.04	-23.6165	14.9398	0.70983	0.0675:0.0:0.9325:0.0	.	227	O95391	SLU7_HUMAN	Y	227	ENSP00000297151:S227Y	ENSP00000297151:S227Y	S	-	2	0	SLU7	159768242	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	5.310000	0.65780	2.937000	0.99478	0.650000	0.86243	TCT		0.294	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425		T	159835664	G	T	159835664	3	4	47	1	0	0	0	0	1	0	0	0	14792	942	33	2	1120	2	SLU7	5	159835664	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	633	159835664	21079596	773	5170										
ATP10B	23120	broad.mit.edu	37	chr5	160113098	160113098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcttacctttcataaattCgaatgttggagcagtttatt	6	6	2	0	rs201710345		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:160113098C>T	ENST00000327245.5	-	6	1304	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	ATP10B_ENST00000518411.1_5'Flank|CTC-529G1.1_ENST00000524198.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	153					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R153Q(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	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)			TTCATAAATTCGAATGTTGGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG	0,3746		0,0,1873	88	82	84		458	-5.6	0	5		84	2,8214		0,2,4106	no	missense	ATP10B	NM_025153.2	43	0,2,5979	TT,TC,CC		0.0243,0.0,0.0167	benign	153/1462	160113098	2,11960	1873	4108	5981	160045676	SO:0001583	missense	23120			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.458G>A	5.37:g.160113098C>T	ENSP00000313600:p.Arg153Gln		160045676	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	C	6.919	0.539295	0.13250	0.0	2.43E-4	ENSG00000118322	ENST00000327245	T	0.72167	-0.63	5.24	-5.61	0.02489	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	1.032440	0.07663	N	0.934141	T	0.46425	0.1392	N	0.04655	-0.195	0.09310	N	1	B;B;B	0.16396	0.017;0.011;0.003	B;B;B	0.14023	0.01;0.009;0.002	T	0.36792	-0.9733	9	.	.	.	.	17.0574	0.86537	0.0:0.8307:0.0:0.1693	.	197;153;153	B4DHG1;O94823-2;O94823	.;.;AT10B_HUMAN	Q	153	ENSP00000313600:R153Q	.	R	-	2	0	ATP10B	160045676	0.001000	0.12720	0.001000	0.08648	0.643000	0.38383	-0.085000	0.11250	-1.212000	0.02620	-0.136000	0.14681	CGA		0.423	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160113098	C	T	160113098	3	4	47	1	0	0	0	0	1	0	0	0	1118	884	31	1	4011	1	ATP10B	5	160113098	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	277434	160113098	20802162	774	5171										
HMMR	3161	broad.mit.edu	37	chr5	162896761	162896761	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactaagggaaaaaacatctCtctctgcaaataatgctaca	5	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:162896761C>A	ENST00000358715.3	+	5	421	c.385C>A	c.(385-387)Ctc>Atc	p.L129I	HMMR_ENST00000353866.3_Missense_Mutation_p.L114I|HMMR_ENST00000393915.4_Missense_Mutation_p.L130I|HMMR_ENST00000432118.2_Missense_Mutation_p.L43I			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	129					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)	p.L129I(1)		cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AAAAACATCTCTCTCTGCAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											121	109	113					5																	162896761		2203	4300	6503	162829339	SO:0001583	missense	3161			U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.385C>A	5.37:g.162896761C>A	ENSP00000351554:p.Leu129Ile		162829339	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071587	0.76301	.	.	ENSG00000072571	ENST00000416990;ENST00000520345;ENST00000522094;ENST00000353866;ENST00000434157;ENST00000393915;ENST00000432118;ENST00000358715	T;T;T;T;T	0.81247	1.19;-1.47;-1.47;1.51;-1.47	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.89420	0.6710	M	0.74258	2.255	0.44702	D	0.997691	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.997;0.997	D	0.89980	0.4100	10	0.52906	T	0.07	-0.9364	16.9456	0.86229	0.1289:0.8711:0.0:0.0	.	43;130;114;129	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	I	15;15;15;114;114;130;43;129	ENSP00000400527:L15I;ENSP00000185942:L114I;ENSP00000377492:L130I;ENSP00000402673:L43I;ENSP00000351554:L129I	ENSP00000185942:L114I	L	+	1	0	HMMR	162829339	1.000000	0.71417	0.933000	0.37362	0.676000	0.39594	5.623000	0.67757	1.602000	0.50124	0.655000	0.94253	CTC		0.408	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		A	162896761	C	A	162896761	3	1	47	1	0	0	0	0	1	0	0	0	7263	913	32	2	406	2	HMMR	5	162896761	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2783663	162896761	18018499	775	5172										
ODZ2	57451	broad.mit.edu	37	chr5	167626074	167626074	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctccccactgtccaccttCtttagtgctgcccctgggca	7	18	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:167626074C>A	ENST00000518659.1	+	16	3156	c.3117C>A	c.(3115-3117)ttC>ttA	p.F1039L	TENM2_ENST00000545108.1_Missense_Mutation_p.F1039L|TENM2_ENST00000519204.1_Missense_Mutation_p.F918L|TENM2_ENST00000403607.2_Missense_Mutation_p.F863L|TENM2_ENST00000520394.1_Missense_Mutation_p.F807L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1039					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.F872L(1)|p.F1039L(1)									TGTCCACCTTCTTTAGTGCTG	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	5											64	66	66					5																	167626074		2048	4193	6241	167558652	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3117C>A	5.37:g.167626074C>A	ENSP00000429430:p.Phe1039Leu		167558652	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	16.58	3.163281	0.57476	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89875	-2.11;-2.09;-2.21;-2.55;-2.58	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.93864	0.8037	M	0.84433	2.695	0.46542	D	0.999095	B;B;D	0.58268	0.149;0.023;0.982	B;B;D	0.68943	0.109;0.034;0.961	D	0.92565	0.6061	10	0.29301	T	0.29	.	12.555	0.56248	0.0:0.9236:0.0:0.0764	.	1039;1039;807	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	1039;1039;918;807;863	ENSP00000429430:F1039L;ENSP00000438635:F1039L;ENSP00000428964:F918L;ENSP00000427874:F807L;ENSP00000384905:F863L	ENSP00000384905:F863L	F	+	3	2	ODZ2	167558652	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.825000	0.62708	2.545000	0.85829	0.563000	0.77884	TTC		0.577	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167626074	C	A	167626074	3	1	47	1	0	0	0	0	1	0	0	0	10866	912	32	2	3152	2	ODZ2	5	167626074	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4729313	167626074	13289186	776	5173										
DOCK2	1794	broad.mit.edu	37	chr5	169122842	169122842	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacctcaacagggataaaatTtacttgatttgtcaaatagt	7	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169122842T>G	ENST00000256935.8	+	10	959	c.879T>G	c.(877-879)atT>atG	p.I293M		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	293					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.I293M(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGATAAAATTTACTTGATTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	100	98					5																	169122842		2203	4300	6503	169055420	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.879T>G	5.37:g.169122842T>G	ENSP00000256935:p.Ile293Met		169055420	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.267185	0.40095	.	.	ENSG00000134516	ENST00000256935	T	0.18338	2.22	5.98	0.521	0.17046	.	0.046530	0.85682	D	0.000000	T	0.13927	0.0337	L	0.50333	1.59	0.80722	D	1	B	0.31485	0.325	B	0.28385	0.089	T	0.06427	-1.0827	10	0.44086	T	0.13	.	9.3421	0.38087	0.0:0.3183:0.0:0.6817	.	293	Q92608	DOCK2_HUMAN	M	293	ENSP00000256935:I293M	ENSP00000256935:I293M	I	+	3	3	DOCK2	169055420	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	1.033000	0.30191	-0.130000	0.11599	0.528000	0.53228	ATT		0.458	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169122842	T	G	169122842	3	3	47	1	0	0	0	0	1	0	0	0	4698	1829	64	4	917	4	DOCK2	5	169122842	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1496768	169122842	11792418	777	5174										
DOCK2	1794	broad.mit.edu	37	chr5	169504787	169504787	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagacagatgtccatcatctCtctggcttccatgaattctg	7	12	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169504787C>A	ENST00000256935.8	+	48	5020	c.4940C>A	c.(4939-4941)tCt>tAt	p.S1647Y	DOCK2_ENST00000540750.1_Missense_Mutation_p.S708Y|DOCK2_ENST00000520908.1_Missense_Mutation_p.S1139Y|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1647					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.S1647Y(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCATCATCTCTCTGGCTTCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	117	123					5																	169504787		2203	4300	6503	169437365	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4940C>A	5.37:g.169504787C>A	ENSP00000256935:p.Ser1647Tyr		169437365	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.722170	0.68959	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.11169	3.53;3.15;2.8	5.08	5.08	0.68730	.	0.070590	0.64402	D	0.000013	T	0.16214	0.0390	L	0.34521	1.04	0.48696	D	0.999693	P;D;P	0.54397	0.845;0.966;0.681	B;P;B	0.50440	0.185;0.641;0.185	T	0.00766	-1.1575	10	0.72032	D	0.01	.	17.3229	0.87241	0.0:1.0:0.0:0.0	.	1139;203;1647	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	Y	1647;1139;708	ENSP00000256935:S1647Y;ENSP00000429283:S1139Y;ENSP00000438827:S708Y	ENSP00000256935:S1647Y	S	+	2	0	DOCK2	169437365	1.000000	0.71417	0.987000	0.45799	0.963000	0.63663	6.785000	0.75089	2.387000	0.81309	0.558000	0.71614	TCT		0.597	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169504787	C	A	169504787	3	1	47	1	0	0	0	0	1	0	0	0	4698	913	32	2	5130	2	DOCK2	5	169504787	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	381945	169504787	11410473	778	5175										
FOXI1	2299	broad.mit.edu	37	chr5	169533233	169533233	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgccccaggcctatggagTgcagaggccgctgctgccca	13	16	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169533233T>G	ENST00000306268.6	+	1	333	c.272T>G	c.(271-273)gTg>gGg	p.V91G	FOXI1_ENST00000449804.2_Missense_Mutation_p.V91G			Q12951	FOXI1_HUMAN	forkhead box I1	91	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.V91G(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCCTATGGAGTGCAGAGGCCG	0.706									Pendred syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											8	7	7					5																	169533233		2178	4248	6426	169465811	SO:0001583	missense	2299	Familial Cancer Database	Goiter-Deafness syndrome	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.272T>G	5.37:g.169533233T>G	ENSP00000304286:p.Val91Gly		169465811	Q14518|Q66SR7|Q8N6L8	Missense_Mutation	SNP	ENST00000306268.6	37	CCDS4372.1	.	.	.	.	.	.	.	.	.	.	T	2.607	-0.291728	0.05568	.	.	ENSG00000168269	ENST00000306268;ENST00000449804	D;D	0.94457	-3.32;-3.43	5.15	3.99	0.46301	.	0.192211	0.51477	D	0.000085	D	0.88481	0.6448	L	0.31664	0.95	0.45962	D	0.998784	B;B	0.26547	0.152;0.094	B;B	0.24006	0.05;0.037	T	0.81718	-0.0805	10	0.15499	T	0.54	.	10.642	0.45598	0.0:0.0752:0.0:0.9248	.	91;91	Q12951-2;Q12951	.;FOXI1_HUMAN	G	91	ENSP00000304286:V91G;ENSP00000415483:V91G	ENSP00000304286:V91G	V	+	2	0	FOXI1	169465811	1.000000	0.71417	0.461000	0.27105	0.030000	0.12068	4.031000	0.57267	0.815000	0.34398	0.533000	0.62120	GTG		0.706	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		G	169533233	T	G	169533233	3	3	47	1	0	0	0	0	1	0	0	0	6028	1696	59	4	274	4	FOXI1	5	169533233	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	28446	169533233	11382027	779	5176										
FOXI1	2299	broad.mit.edu	37	chr5	169535099	169535099	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccaactgtgagaaaatgttCgacaatggaaatttccgcag	9	9	0	1	rs532647880		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169535099C>T	ENST00000306268.6	+	2	682	c.621C>T	c.(619-621)ttC>ttT	p.F207F	FOXI1_ENST00000449804.2_Intron			Q12951	FOXI1_HUMAN	forkhead box I1	207					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.F207F(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGAAAATGTTCGACAATGGAA	0.468									Pendred syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	5											73	71	72					5																	169535099		2203	4300	6503	169467677	SO:0001819	synonymous_variant	2299	Familial Cancer Database	Goiter-Deafness syndrome	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.621C>T	5.37:g.169535099C>T			169467677	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	37	CCDS4372.1																																																																																				0.468	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		T	169535099	C	T	169535099	2	4	47	1	0	0	0	0	0	0	0	1	6028	883	31	1		1	FOXI1	5	169535099	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1866	169535099	11380161	780	5177										
C5orf58	133874	broad.mit.edu	37	chr5	169661157	169661157	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaatgagagaaattgcagaAattctccctgctcaggaaaa	9	7	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169661157A>C	ENST00000521850.1	+	1	1707	c.18A>C	c.(16-18)gaA>gaC	p.E6D	C5orf58_ENST00000517575.1_Intron|C5orf58_ENST00000593851.1_Missense_Mutation_p.E6D			C9J3I9	CE058_HUMAN	chromosome 5 open reading frame 58	6								p.E6D(1)		large_intestine(1)|lung(4)|urinary_tract(1)	6						AAATTGCAGAAATTCTCCCTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											117	113	115					5																	169661157		1861	4106	5967	169593735	SO:0001583	missense	133874			BC030767	CCDS47338.1	5q35.1	2009-09-30			ENSG00000234511	ENSG00000234511			37272	protein-coding gene	gene with protein product							Standard	NM_001102609		Approved		uc010jjn.3	C9J3I9	OTTHUMG00000163122	ENST00000521850.1:c.18A>C	5.37:g.169661157A>C	ENSP00000428956:p.Glu6Asp		169593735		Missense_Mutation	SNP	ENST00000521850.1	37	CCDS47338.1	.	.	.	.	.	.	.	.	.	.	A	9.398	1.077205	0.20227	.	.	ENSG00000234511	ENST00000521850	.	.	.	3.87	-6.59	0.01830	.	.	.	.	.	T	0.23649	0.0572	N	0.14661	0.345	0.09310	N	1	B	0.22604	0.072	B	0.24701	0.055	T	0.38045	-0.9679	8	0.87932	D	0	.	10.4055	0.44254	0.2353:0.6761:0.0886:0.0	.	6	C9J3I9	CE058_HUMAN	D	6	.	ENSP00000428956:E6D	E	+	3	2	C5orf58	169593735	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.985000	0.03751	-1.176000	0.02747	0.533000	0.62120	GAA		0.403	C5orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371739.1	NM_001102609		C	169661157	A	C	169661157	3	2	47	1	0	0	0	0	1	0	0	0	2319	11	1	4	20	4	C5orf58	5	169661157	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	126058	169661157	11254103	781	5178										
LCP2	3937	broad.mit.edu	37	chr5	169689852	169689852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcaacagtcttaccttcccGctggaatcgagggctgcaag	11	12	1	0	rs369378243		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:169689852G>A	ENST00000046794.5	-	12	1427	c.812C>T	c.(811-813)gCg>gTg	p.A271V	LCP2_ENST00000521416.1_Missense_Mutation_p.A66V	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	271					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)		p.A271V(2)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	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)		TTACCTTCCCGCTGGAATCGA	0.433													G|||	1	0.000199681	0	0	5008	,	,		21173	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	5						G	VAL/ALA	0,3940		0,0,1970	131	129	130		812	-3.8	0	5		130	1,8321		0,1,4160	no	missense	LCP2	NM_005565.3	64	0,1,6130	AA,AG,GG		0.012,0.0,0.0082	benign	271/534	169689852	1,12261	1970	4161	6131	169622430	SO:0001583	missense	3937				CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.812C>T	5.37:g.169689852G>A	ENSP00000046794:p.Ala271Val		169622430	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	G	7.714	0.695785	0.15106	0.0	1.2E-4	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.47528	0.88;0.84	5.4	-3.84	0.04256	.	1.768460	0.02589	N	0.099729	T	0.32164	0.0820	L	0.36672	1.1	0.09310	N	1	B;B;B	0.15141	0.012;0.006;0.003	B;B;B	0.10450	0.005;0.001;0.003	T	0.05162	-1.0902	9	.	.	.	-0.271	1.8643	0.03195	0.295:0.3744:0.2038:0.1268	.	66;271;271	E7ESF6;A8KA25;Q13094	.;.;LCP2_HUMAN	V	271;66;38	ENSP00000046794:A271V;ENSP00000428871:A66V	.	A	-	2	0	LCP2	169622430	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.042000	0.13949	-0.786000	0.04516	-0.176000	0.13171	GCG		0.433	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		A	169689852	G	A	169689852	3	1	47	1	0	0	0	0	1	0	0	0	8714	1087	38	1	829	1	LCP2	5	169689852	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	28695	169689852	11225408	782	5179										
GABRP	2568	broad.mit.edu	37	chr5	170238981	170238981	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacaacaaaggaagtagaaGaagtcagtattactaatatc	9	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:170238981G>T	ENST00000518525.1	+	11	1506	c.1042G>T	c.(1042-1044)Gaa>Taa	p.E348*	GABRP_ENST00000519385.1_Missense_Mutation_p.R285I|GABRP_ENST00000265294.4_Nonsense_Mutation_p.E348*			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	348					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.E348*(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGAAGTAGAAGAAGTCAGTAT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											113	106	109					5																	170238981		2203	4300	6503	170171559	SO:0001587	stop_gained	2568			U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4089	protein-coding gene	gene with protein product	"GABA(A) receptor, pi"	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1042G>T	5.37:g.170238981G>T	ENSP00000430100:p.Glu348*		170171559	A8KA36|D3DQL2|Q32MJ1	Nonsense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.581168|6.581168	0.97680|0.97680	.|.	.|.	ENSG00000094755|ENSG00000094755	ENST00000518525;ENST00000265294|ENST00000539175;ENST00000519385	.|T	.|0.74106	.|-0.81	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.113271|.	0.64402|.	D|.	0.000017|.	.|T	.|0.72550	.|0.3474	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|P	.|0.50943	.|0.94	.|B	.|0.41571	.|0.36	.|T	.|0.77451	.|-0.2583	.|8	0.02654|0.87932	T|D	1|0	.|.	17.6875|17.6875	0.88260|0.88260	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|285	.|E7EWG0	.|.	X|I	348|183;285	.|ENSP00000430727:R285I	ENSP00000265294:E348X|ENSP00000430727:R285I	E|R	+|+	1|2	0|0	GABRP|GABRP	170171559|170171559	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	6.743000|6.743000	0.74848|0.74848	2.709000|2.709000	0.92574|0.92574	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.373	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		T	170238981	G	T	170238981	4	4	47	1	0	0	0	0	0	1	0	0	6193	943	33	2	1076	2	GABRP	5	170238981	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	549129	170238981	10676279	783	5180										
FBXW11	23291	broad.mit.edu	37	chr5	171303406	171303406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgatgtcggtcgcagaagcCatgtcccacacagcaatgga	12	11	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:171303406C>T	ENST00000265094.5	-	8	1178	c.1041G>A	c.(1039-1041)atG>atA	p.M347I	FBXW11_ENST00000296933.6_Missense_Mutation_p.M334I|FBXW11_ENST00000393802.2_Missense_Mutation_p.M313I|FBXW11_ENST00000425623.2_Missense_Mutation_p.M315I|FBXW11_ENST00000522891.1_5'UTR	NM_012300.2	NP_036432.2	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11	347					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.M347I(1)|p.M334I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	21	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCGCAGAAGCCATGTCCCACA	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	5											137	91	107					5																	171303406		2203	4300	6503	171236011	SO:0001583	missense	23291			AB014596	CCDS34289.1, CCDS47340.1, CCDS47341.1	5q35.1	2013-01-09	2007-02-08	2004-06-16	ENSG00000072803	ENSG00000072803		"F-boxes / WD-40 domains", "WD repeat domain containing"	13607	protein-coding gene	gene with protein product		605651	"F-box and WD-40 domain protein 1B", "F-box and WD-40 domain protein 11"	FBXW1B		10531035, 10694485	Standard	NM_033644		Approved	KIAA0696, Fbw1b, BTRCP2, BTRC2, Hos, Fbw11	uc003mbm.1	Q9UKB1	OTTHUMG00000163267	ENST00000265094.5:c.1041G>A	5.37:g.171303406C>T	ENSP00000265094:p.Met347Ile		171236011	B2RC98|Q9P2S8|Q9P2S9|Q9Y4C6	Missense_Mutation	SNP	ENST00000265094.5	37	CCDS34289.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.717891	0.68844	.	.	ENSG00000072803	ENST00000296933;ENST00000265094;ENST00000393802;ENST00000425623	T;T;T;T	0.31510	1.49;2.4;1.49;1.49	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.24236	0.0587	N	0.02765	-0.5	0.80722	D	1	B;P;D;P	0.53312	0.234;0.934;0.959;0.772	B;P;P;B	0.51415	0.051;0.669;0.608;0.216	T	0.30880	-0.9963	10	0.34782	T	0.22	-22.2761	18.9884	0.92782	0.0:1.0:0.0:0.0	.	315;313;347;334	B4DH70;Q9UKB1-2;Q9UKB1;Q9UKB1-3	.;.;FBW1B_HUMAN;.	I	334;347;313;315	ENSP00000296933:M334I;ENSP00000265094:M347I;ENSP00000377391:M313I;ENSP00000444929:M315I	ENSP00000265094:M347I	M	-	3	0	FBXW11	171236011	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.911000	0.69939	2.648000	0.89879	0.650000	0.86243	ATG		0.532	FBXW11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372382.1	NM_012300		T	171303406	C	T	171303406	3	4	47	1	0	0	0	0	1	0	0	0	5783	594	21	3	607	3	FBXW11	5	171303406	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1064425	171303406	9611854	784	5181										
STK10	6793	broad.mit.edu	37	chr5	171533668	171533668	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagggtccgacttggcgatCtttagcaggacccgcatggg	16	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:171533668C>A	ENST00000176763.5	-	6	1087	c.744G>T	c.(742-744)aaG>aaT	p.K248N		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	248	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.K248N(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACTTGGCGATCTTTAGCAGGA	0.652											OREG0017039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	5											117	106	110					5																	171533668		2203	4300	6503	171466273	SO:0001583	missense	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.744G>T	5.37:g.171533668C>A	ENSP00000176763:p.Lys248Asn	1893	171466273	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.153232	0.38021	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.26223	1.75	4.86	1.06	0.20224	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28034	0.0691	N	0.17922	0.545	0.58432	D	0.999999	D	0.64830	0.994	D	0.73708	0.981	T	0.07195	-1.0785	10	0.72032	D	0.01	.	5.3626	0.16095	0.1402:0.6248:0.0:0.2349	.	248	O94804	STK10_HUMAN	N	248	ENSP00000176763:K248N	ENSP00000176763:K248N	K	-	3	2	STK10	171466273	0.741000	0.28217	0.997000	0.53966	0.004000	0.04260	0.345000	0.19979	0.007000	0.14760	-0.895000	0.02911	AAG		0.652	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171533668	C	A	171533668	3	1	47	1	0	0	0	0	1	0	0	0	15325	912	32	2	2218	2	STK10	5	171533668	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	230262	171533668	9381592	785	5182										
NSD1	64324	broad.mit.edu	37	chr5	176562826	176562826	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacacagaaaaataagcaaaGaaatgaagtggacggcagca	10	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:176562826G>T	ENST00000439151.2	+	2	767	c.722G>T	c.(721-723)aGa>aTa	p.R241I	NSD1_ENST00000361032.4_Missense_Mutation_p.R241I|NSD1_ENST00000511258.1_Intron|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000354179.4_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	241					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R241I(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	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)		AATAAGCAAAGAAATGAAGTG	0.438			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Substitution - Missense(2)	large_intestine(2)	5											84	82	82					5																	176562826		2203	4300	6503	176495432	SO:0001583	missense	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.722G>T	5.37:g.176562826G>T	ENSP00000395929:p.Arg241Ile		176495432	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187807	0.57909	.	.	ENSG00000165671	ENST00000439151;ENST00000361032	D;D	0.94687	-3.25;-3.49	4.74	4.74	0.60224	.	0.000000	0.48767	D	0.000171	D	0.94098	0.8108	N	0.19112	0.55	0.80722	D	1	D;D;D	0.69078	0.997;0.995;0.997	D;D;D	0.80764	0.994;0.986;0.991	D	0.94581	0.7779	10	0.72032	D	0.01	.	13.1063	0.59249	0.0:0.0:1.0:0.0	.	241;241;241	Q96L73-3;Q96L73;Q6PJ64	.;NSD1_HUMAN;.	I	241	ENSP00000395929:R241I;ENSP00000354310:R241I	ENSP00000354310:R241I	R	+	2	0	NSD1	176495432	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.069000	0.50026	2.459000	0.83118	0.655000	0.94253	AGA		0.438	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176562826	G	T	176562826	3	4	47	1	0	0	0	0	1	0	0	0	10700	942	33	2	724	2	NSD1	5	176562826	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5029158	176562826	4352434	786	5183										
FAM193B	54540	broad.mit.edu	37	chr5	176963530	176963531	+	Frame_Shift_Ins	INS	-	-	G													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgacatggccctggagtgtINSggggggcagtggcagcagca					rs543681398		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:176963530_176963531insG	ENST00000514747.1	-	4	952_953	c.904_905insC	c.(904-906)cacfs	p.H302fs	FAM193B_ENST00000329540.5_5'UTR|FAM193B_ENST00000508298.1_Intron|FAM193B_ENST00000443375.2_Frame_Shift_Ins_p.H189fs	NM_001190946.1	NP_001177875.1	Q96PV7	F193B_HUMAN	family with sequence similarity 193, member B	302	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.H189fs*55(1)		kidney(1)|large_intestine(3)	4						CCCTGGAGTGTGGGGGGCAGTG	0.673																																																1	Insertion - Frameshift(1)	large_intestine(1)	5																																								176896137	SO:0001589	frameshift_variant	54540				CCDS54954.1	5q35	2010-02-17			ENSG00000146067	ENSG00000146067			25524	protein-coding gene	gene with protein product		615813				11572484	Standard	NR_024019		Approved	KIAA1931, FLJ10404	uc003mhu.3	Q96PV7	OTTHUMG00000163396	ENST00000514747.1:c.905dupC	5.37:g.176963536_176963536dupG	ENSP00000422131:p.His302fs		176896136	E9PET5|Q9NW00	Frame_Shift_Ins	INS	ENST00000514747.1	37	CCDS54954.1																																																																																				0.673	FAM193B-003	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373121.1	NM_019057		G	176963531	-	G	176963530	7	5	47	1	0	1	1	0	0	0	0	0	5541	1696	59	0	1827	0	FAM193B	5	176963530	Frame_Shift_Ins	INS	-	TCGA-AG-3892-01A-01W-1073-09	400704	176963530	3951730	787	5184										
ZNF354B	117608	broad.mit.edu	37	chr5	178309840	178309840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatcctgcatatatgaagaGaaattaaagaaacagcagga	9	5	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:178309840G>T	ENST00000322434.3	+	5	613	c.387G>T	c.(385-387)gaG>gaT	p.E129D	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	129					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E129D(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TATATGAAGAGAAATTAAAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											39	41	40					5																	178309840		2170	4291	6461	178242446	SO:0001583	missense	117608			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.387G>T	5.37:g.178309840G>T	ENSP00000327143:p.Glu129Asp		178242446	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.815310	0.00073	.	.	ENSG00000178338	ENST00000322434;ENST00000520377	T;T	0.05786	3.39;6.21	3.53	-1.58	0.08479	.	.	.	.	.	T	0.02533	0.0077	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46498	-0.9187	9	0.02654	T	1	.	5.5479	0.17073	0.0:0.2362:0.4711:0.2927	.	129	Q96LW1	Z354B_HUMAN	D	129	ENSP00000327143:E129D;ENSP00000429827:E129D	ENSP00000327143:E129D	E	+	3	2	ZNF354B	178242446	0.000000	0.05858	0.005000	0.12908	0.161000	0.22273	-1.393000	0.02521	-0.193000	0.10415	-0.311000	0.09066	GAG		0.328	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		T	178309840	G	T	178309840	3	4	47	1	0	0	0	0	1	0	0	0	17904	933	33	2	401	2	ZNF354B	5	178309840	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1346310	178309840	2605420	788	5185										
ZFP2	80108	broad.mit.edu	37	chr5	178358763	178358763	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcccttactgtacatcaaaGaattcatactggagagaaac	6	10	2	2	rs376749929		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:178358763G>T	ENST00000361362.2	+	5	979	c.449G>T	c.(448-450)aGa>aTa	p.R150I	ZFP2_ENST00000520301.1_Missense_Mutation_p.R150I|ZFP2_ENST00000503510.2_Missense_Mutation_p.R150I|ZFP2_ENST00000523286.1_Missense_Mutation_p.R150I	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R150I(2)		NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		GTACATCAAAGAATTCATACT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	5						G	ILE/ARG	0,4406		0,0,2203	52	55	54		449	3.8	1	5		54	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZFP2	NM_030613.2	97	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	150/462	178358763	1,13005	2203	4300	6503	178291369	SO:0001583	missense	80108			AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.449G>T	5.37:g.178358763G>T	ENSP00000354453:p.Arg150Ile		178291369	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	g	15.72	2.915461	0.52546	0.0	1.16E-4	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.71	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35151	N	0.003406	T	0.50922	0.1644	M	0.80332	2.49	0.47183	D	0.99934	D	0.89917	1.0	D	0.85130	0.997	T	0.54964	-0.8214	10	0.56958	D	0.05	-15.0571	12.0605	0.53561	0.0:0.0:0.8266:0.1734	.	150	Q6ZN57	ZFP2_HUMAN	I	150	ENSP00000354453:R150I;ENSP00000430980:R150I;ENSP00000430531:R150I;ENSP00000438114:R150I	ENSP00000354453:R150I	R	+	2	0	ZFP2	178291369	0.080000	0.21391	1.000000	0.80357	0.837000	0.47467	2.428000	0.44749	1.176000	0.42840	0.591000	0.81541	AGA		0.413	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		T	178358763	G	T	178358763	3	4	47	1	0	0	0	0	1	0	0	0	17680	942	33	2	451	2	ZFP2	5	178358763	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	48923	178358763	2556497	789	5186										
MAML1	9794	broad.mit.edu	37	chr5	179200942	179200942	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacaccttgggtccatccaaCtccagctgtcctcgagtgtt	8	14	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:179200942C>A	ENST00000292599.3	+	5	2378	c.2115C>A	c.(2113-2115)aaC>aaA	p.N705K	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)									p.N705K(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTCCATCCAACTCCAGCTGTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											130	130	130					5																	179200942		2203	4300	6503	179133548	SO:0001583	missense	9794			D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2115C>A	5.37:g.179200942C>A	ENSP00000292599:p.Asn705Lys		179133548		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.678457	0.29783	.	.	ENSG00000161021	ENST00000292599	T	0.46063	0.88	5.1	2.32	0.28847	.	0.726025	0.13623	N	0.374307	T	0.26557	0.0649	L	0.47716	1.5	0.09310	N	1	P	0.44627	0.839	B	0.30646	0.118	T	0.12915	-1.0529	10	0.09843	T	0.71	-5.4108	10.6052	0.45390	0.0:0.7859:0.0:0.2141	.	705	Q92585	MAML1_HUMAN	K	705	ENSP00000292599:N705K	ENSP00000292599:N705K	N	+	3	2	MAML1	179133548	0.864000	0.29904	0.004000	0.12327	0.932000	0.56968	1.230000	0.32612	0.174000	0.19809	0.462000	0.41574	AAC		0.587	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179200942	C	A	179200942	3	1	47	1	0	0	0	0	1	0	0	0	9235	564	20	2	2133	2	MAML1	5	179200942	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	842179	179200942	1714318	790	5187										
MAPK9	5601	broad.mit.edu	37	chr5	179663384	179663384	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtttgctatttctaacctaTcatcgacagccttcaagggg	9	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr5:179663384T>G	ENST00000452135.2	-	12	1573	c.1275A>C	c.(1273-1275)tgA>tgC	p.*425C	MAPK9_ENST00000393360.3_3'UTR|MAPK9_ENST00000347470.4_Nonstop_Mutation_p.*340C|MAPK9_ENST00000343111.6_3'UTR|MAPK9_ENST00000455781.1_Nonstop_Mutation_p.*425C			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	0					cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)	p.*425C(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCTAACCTATCATCGACAGC	0.493																																																1	Nonstop extension(1)	large_intestine(1)	5											94	79	84					5																	179663384		2203	4300	6503	179595990	SO:0001578	stop_lost	5601			U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.1275A>C	5.37:g.179663384T>G	ENSP00000394560:p.*425Trpext*1		179595990	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Nonstop_Mutation	SNP	ENST00000452135.2	37	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	T	18.50	3.637625	0.67130	.	.	ENSG00000050748	ENST00000452135;ENST00000455781;ENST00000347470	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1024	0.81184	0.0:0.0:0.0:1.0	.	.	.	.	C	425;425;340	.	.	X	-	3	0	MAPK9	179595990	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	6.151000	0.71806	2.200000	0.70718	0.459000	0.35465	TGA		0.493	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			G	179663384	T	G	179663384	4	3	47	1	0	0	0	0	0	0	0	0	9317	1448	50	4	3	4	MAPK9	5	179663384	Nonstop_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	462442	179663384	1251876	791	5188										
TUBB2A	7280	broad.mit.edu	37	chr6	3154140	3154140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcctcgaactccccttgtTcgtcggccgtggcgtcctgg	11	17	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:3154140T>C	ENST00000333628.3	-	4	1357	c.1295A>G	c.(1294-1296)gAa>gGa	p.E432G	RP1-40E16.11_ENST00000447644.1_RNA|TUBB2A_ENST00000489942.1_5'Flank	NM_001069.2	NP_001060.1	Q13885	TBB2A_HUMAN	tubulin, beta 2A class IIa	432					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.E432G(1)		endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				CTCCCCTTGTTCGTCGGCCGT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	94	101					6																	3154140		2203	4300	6503	3099139	SO:0001583	missense	7280			AY159127	CCDS4484.1	6p25.2	2012-10-02	2011-10-10	2005-11-03	ENSG00000137267	ENSG00000137267		"Tubulins"	12412	protein-coding gene	gene with protein product	"class IIa beta-tubulin"	615101	"tubulin, beta polypeptide", "tubulin, beta 2", "tubulin, beta 2A"	TUBB, TUBB2		14574404	Standard	NM_001069		Approved	dJ40E16.7	uc003mvc.3	Q13885	OTTHUMG00000014135	ENST00000333628.3:c.1295A>G	6.37:g.3154140T>C	ENSP00000369703:p.Glu432Gly		3099139	Q6FGZ8|Q8IWR2	Missense_Mutation	SNP	ENST00000333628.3	37	CCDS4484.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.086275	0.36855	.	.	ENSG00000137267	ENST00000333628;ENST00000392362	T	0.74209	-0.82	4.96	4.96	0.65561	.	0.000000	0.49305	U	0.000146	T	0.65954	0.2741	L	0.56124	1.755	0.58432	D	0.999999	P;P;P	0.47762	0.495;0.495;0.9	B;B;P	0.44772	0.178;0.178;0.46	T	0.73538	-0.3951	10	0.87932	D	0	.	14.9189	0.70818	0.0:0.0:0.0:1.0	.	432;432;432	B2R6L0;Q13885;Q8N6N5	.;TBB2A_HUMAN;.	G	432;342	ENSP00000369703:E432G	ENSP00000369703:E432G	E	-	2	0	TUBB2A	3099139	1.000000	0.71417	0.712000	0.30502	0.883000	0.51084	7.880000	0.87243	1.996000	0.58369	0.454000	0.30748	GAA		0.567	TUBB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039662.1	NM_001069		C	3154140	T	C	3154140	3	2	47	1	0	0	0	0	1	0	0	0	16794	1783	62	4	46	4	TUBB2A	6	3154140	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09		3154140	167960927	792	5189										
SIRT5	23408	broad.mit.edu	37	chr6	13588578	13588578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaggtatggcagattttcGaaagttttttgcaaaagcaa	9	4	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:13588578G>A	ENST00000606117.1	+	4	427	c.131G>A	c.(130-132)cGa>cAa	p.R44Q	SIRT5_ENST00000397350.2_Intron|SIRT5_ENST00000379262.4_Missense_Mutation_p.R44Q|SIRT5_ENST00000359782.3_Missense_Mutation_p.R44Q	NM_012241.4	NP_036373.1			sirtuin 5									p.R44Q(2)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			GCAGATTTTCGAAAGTTTTTT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	6											102	96	98					6																	13588578		2203	4300	6503	13696557	SO:0001583	missense	23408			AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5", "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000606117.1:c.131G>A	6.37:g.13588578G>A	ENSP00000476228:p.Arg44Gln		13696557		Missense_Mutation	SNP	ENST00000606117.1	37	CCDS4526.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.106034	0.77096	.	.	ENSG00000124523	ENST00000359782;ENST00000379262;ENST00000379250	T;T;T	0.41758	0.99;0.99;0.99	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.39835	0.1093	L	0.43646	1.37	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.997	P;P;P	0.55222	0.771;0.733;0.705	T	0.10965	-1.0607	10	0.33141	T	0.24	-19.5395	17.7879	0.88543	0.0:0.0:1.0:0.0	.	44;44;44	F5H5Z9;Q9NXA8;Q9NXA8-2	.;SIRT5_HUMAN;.	Q	44	ENSP00000352830:R44Q;ENSP00000368564:R44Q;ENSP00000368552:R44Q	ENSP00000352830:R44Q	R	+	2	0	SIRT5	13696557	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	7.466000	0.80914	2.287000	0.76781	0.585000	0.79938	CGA		0.403	SIRT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039908.2			A	13588578	G	A	13588578	3	1	47	1	0	0	0	0	1	0	0	0	14378	1058	37	1	137	1	SIRT5	6	13588578	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	10434438	13588578	157526489	793	5190										
HIST1H2BB	3018	broad.mit.edu	37	chr6	26043588	26043588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccccaggcagcagcaggcGcacagccgtctgaatctccc	10	18	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:26043588G>A	ENST00000357905.2	-	1	297	c.298C>T	c.(298-300)Cgc>Tgc	p.R100C	HIST1H3C_ENST00000540144.1_5'Flank	NM_021062.2	NP_066406.1	P33778	H2B1B_HUMAN	histone cluster 1, H2bb	100					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R100C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						AGCAGCAGGCGCACAGCCGTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6											55	55	55					6																	26043588		2203	4300	6503	26151567	SO:0001583	missense	3018			AF531285	CCDS4575.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196226			"Histones / Replication-dependent"	4751	protein-coding gene	gene with protein product		602803	"H2B histone family, member F", "histone 1, H2bb"	H2BFF		8227173, 12408966	Standard	NM_021062		Approved	H2B/f	uc003nfu.3	P33778	OTTHUMG00000014421	ENST00000357905.2:c.298C>T	6.37:g.26043588G>A	ENSP00000350580:p.Arg100Cys		26151567	Q4KN36	Missense_Mutation	SNP	ENST00000357905.2	37	CCDS4575.1	.	.	.	.	.	.	.	.	.	.	g	12.49	1.954225	0.34471	.	.	ENSG00000196226	ENST00000357905	T	0.52754	0.65	5.08	4.19	0.49359	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000016	T	0.27697	0.0681	L	0.49571	1.57	0.52501	D	0.999955	B	0.09022	0.002	B	0.04013	0.001	T	0.14392	-1.0474	10	0.46703	T	0.11	.	14.0611	0.64800	0.0:0.0:0.8479:0.1521	.	100	P33778	H2B1B_HUMAN	C	100	ENSP00000350580:R100C	ENSP00000350580:R100C	R	-	1	0	HIST1H2BB	26151567	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.743000	0.62110	1.206000	0.43276	0.467000	0.42956	CGC		0.562	HIST1H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040083.1	NM_021062		A	26043588	G	A	26043588	3	1	47	1	0	0	0	0	1	0	0	0	7162	1087	38	1	86	1	HIST1H2BB	6	26043588	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	12455010	26043588	145071479	794	5191										
HFE	3077	broad.mit.edu	37	chr6	26091204	26091204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtcgccgtgtggagccccGaactccatgggtttccagta	13	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:26091204G>A	ENST00000357618.5	+	2	334	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	HFE_ENST00000349999.4_Intron|HFE_ENST00000309234.6_Missense_Mutation_p.R71Q|HFE_ENST00000353147.5_Intron|HFE_ENST00000470149.1_Missense_Mutation_p.R71Q|HFE_ENST00000352392.4_Intron|HFE_ENST00000488199.1_Intron|HFE_ENST00000336625.8_Missense_Mutation_p.R71Q|HFE_ENST00000397022.3_Missense_Mutation_p.R48Q|HFE_ENST00000461397.1_Missense_Mutation_p.R71Q|HFE_ENST00000317896.7_Missense_Mutation_p.R71Q	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	71	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)	p.R71Q(1)		endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTGGAGCCCCGAACTCCATGG	0.507									Hemochromatosis																																							1	Substitution - Missense(1)	large_intestine(1)	6											103	100	101					6																	26091204		2203	4300	6503	26199183	SO:0001583	missense	3077	Familial Cancer Database			CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.212G>A	6.37:g.26091204G>A	ENSP00000417404:p.Arg71Gln		26199183	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.978645	0.74360	.	.	ENSG00000010704	ENST00000397022;ENST00000317896;ENST00000535098;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000309234	D;T;D;D;T;D;D	0.90324	-2.65;5.61;-2.65;-2.65;5.61;-2.65;-2.65	5.3	2.57	0.30868	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.427116	0.19838	N	0.104922	D	0.89230	0.6656	M	0.86097	2.795	0.09310	N	1	D;P;P;D;D;D	0.67145	0.996;0.795;0.795;0.995;0.985;0.996	P;B;B;P;B;P	0.52823	0.71;0.117;0.117;0.587;0.319;0.71	T	0.83330	-0.0013	10	0.87932	D	0	.	7.258	0.26187	0.271:0.0:0.729:0.0	.	71;71;71;71;48;71	Q6B0J5;Q30201-7;Q30201-10;Q30201-3;Q30201-5;Q30201	.;.;.;.;.;HFE_HUMAN	Q	48;71;71;71;71;71;71;71	ENSP00000380217:R48Q;ENSP00000313776:R71Q;ENSP00000417404:R71Q;ENSP00000419725:R71Q;ENSP00000337819:R71Q;ENSP00000420802:R71Q;ENSP00000311698:R71Q	ENSP00000311698:R71Q	R	+	2	0	HFE	26199183	0.072000	0.21174	0.001000	0.08648	0.297000	0.27493	2.992000	0.49417	0.383000	0.24910	0.655000	0.94253	CGA		0.507	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1			A	26091204	G	A	26091204	3	1	47	1	0	0	0	0	1	0	0	0	7102	1058	37	1	218	1	HFE	6	26091204	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	47616	26091204	145023863	795	5192										
BTN3A2	11118	broad.mit.edu	37	chr6	26370789	26370789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcctgcatcatcagaaatTccctcctcggcctggaaaag	7	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:26370789T>C	ENST00000356386.2	+	5	861	c.673T>C	c.(673-675)Tcc>Ccc	p.S225P	BTN3A2_ENST00000527422.1_Missense_Mutation_p.S225P|BTN3A2_ENST00000396948.1_Missense_Mutation_p.S225P|BTN3A2_ENST00000396934.3_Missense_Mutation_p.S202P|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000377708.2_Missense_Mutation_p.S225P|BTN3A2_ENST00000508906.2_Missense_Mutation_p.S183P	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	225					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.S225P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						CATCAGAAATTCCCTCCTCGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											121	118	119					6																	26370789		2203	4300	6503	26478768	SO:0001583	missense	11118			U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.673T>C	6.37:g.26370789T>C	ENSP00000348751:p.Ser225Pro		26478768	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	.	.	.	.	.	.	.	.	.	.	t	0.777	-0.763812	0.02996	.	.	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.75477	-0.94;3.32;3.32;3.32;3.32;3.32;3.32	2.31	-1.44	0.08856	Immunoglobulin-like fold (1);	.	.	.	.	T	0.21145	0.0509	N	0.03209	-0.39	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.12156	0.007;0.003	T	0.15206	-1.0445	9	0.30854	T	0.27	.	2.1537	0.03807	0.2439:0.3601:0.0:0.396	.	202;225	F8W6E0;P78410	.;BT3A2_HUMAN	P	183;225;225;225;202;225;225;183	ENSP00000435952:S183P;ENSP00000432138:S225P;ENSP00000348751:S225P;ENSP00000380140:S202P;ENSP00000366937:S225P;ENSP00000380152:S225P;ENSP00000442687:S183P	ENSP00000348751:S225P	S	+	1	0	BTN3A2	26478768	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-1.978000	0.01494	-0.391000	0.07763	0.333000	0.21579	TCC		0.542	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			C	26370789	T	C	26370789	3	2	47	1	0	0	0	0	1	0	0	0	1566	1783	62	4	683	4	BTN3A2	6	26370789	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	279585	26370789	144744278	796	5193										
ZSCAN16	80345	broad.mit.edu	37	chr6	28093467	28093467	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accaaggagcagattttagaCctgctggtgctagaacagtt	11	8	0	3	rs557759664		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:28093467C>T	ENST00000340487.4	+	2	395	c.246C>T	c.(244-246)gaC>gaT	p.D82D	ZSCAN16-AS1_ENST00000600652.1_RNA|ZSCAN16-AS1_ENST00000602810.1_RNA	NM_025231.1	NP_079507.1	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16	82	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D82D(1)		large_intestine(5)|liver(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						AGATTTTAGACCTGCTGGTGC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	6											115	104	107					6																	28093467		2203	4300	6503	28201446	SO:0001819	synonymous_variant	80345			AK025844	CCDS4644.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000196812	ENSG00000196812		"-", "Zinc fingers, C2H2-type"	20813	protein-coding gene	gene with protein product			"zinc finger protein 392", "zinc finger protein 435"	ZNF392, ZNF435			Standard	NM_025231		Approved	FLJ22191, dJ265C24.3	uc003nkm.3	Q9H4T2	OTTHUMG00000014509	ENST00000340487.4:c.246C>T	6.37:g.28093467C>T			28201446	Q9H6K2	Silent	SNP	ENST00000340487.4	37	CCDS4644.1																																																																																				0.562	ZSCAN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040177.1	NM_025231		T	28093467	C	T	28093467	2	4	47	1	0	0	0	0	0	0	0	1	18268	506	18	3		3	ZSCAN16	6	28093467	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1722678	28093467	143021600	797	5194										
ZKSCAN4	387032	broad.mit.edu	37	chr6	28213576	28213576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacattcatggcaataatgtCgcctactccctatggcattt	6	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:28213576C>T	ENST00000377294.2	-	5	1199	c.956G>A	c.(955-957)cGa>cAa	p.R319Q	ZKSCAN4_ENST00000423974.2_Missense_Mutation_p.R164Q	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	319					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R319Q(2)		endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GCAATAATGTCGCCTACTCCC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	6											120	102	108					6																	28213576		2203	4300	6503	28321555	SO:0001583	missense	387032			AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"Zinc fingers, C2H2-type", "-", "-", "-"	13854	protein-coding gene	gene with protein product		611643	"zinc finger protein 307", "zinc finger protein 427"	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.956G>A	6.37:g.28213576C>T	ENSP00000366509:p.Arg319Gln		28321555	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	.	.	.	.	.	.	.	.	.	.	C	1.930	-0.446281	0.04604	.	.	ENSG00000187626	ENST00000377294;ENST00000423974;ENST00000449813;ENST00000356796	T;T	0.07444	3.19;3.19	5.1	1.65	0.23941	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01061	0.0035	L	0.28649	0.875	0.09310	N	1	P	0.36438	0.553	B	0.20955	0.032	T	0.43829	-0.9367	9	0.11794	T	0.64	.	3.0723	0.06235	0.1947:0.3433:0.0:0.462	.	319	Q969J2	ZKSC4_HUMAN	Q	319;164;25;195	ENSP00000366509:R319Q;ENSP00000401978:R164Q	ENSP00000349249:R195Q	R	-	2	0	ZKSCAN4	28321555	0.000000	0.05858	0.049000	0.19019	0.006000	0.05464	-0.770000	0.04705	0.587000	0.29643	0.655000	0.94253	CGA		0.463	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		T	28213576	C	T	28213576	3	4	47	1	0	0	0	0	1	0	0	0	17728	884	31	1	685	1	ZKSCAN4	6	28213576	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	120109	28213576	142901491	798	5195										
GPX6	257202	broad.mit.edu	37	chr6	28472181	28472181	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcgggccccaccagaaatTtctcaaagttccagcggata	8	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:28472181T>G	ENST00000474923.1	-	4	497	c.454A>C	c.(454-456)Aat>Cat	p.N152H	GPX6_ENST00000483058.1_5'Flank|GPX6_ENST00000361902.1_Missense_Mutation_p.K185T			P59796	GPX6_HUMAN	glutathione peroxidase 6 (olfactory)	0					response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)	p.K185T(1)		NS(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Glutathione(DB00143)	CACCAGAAATTTCTCAAAGTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	75	75					6																	28472181		1923	4154	6077	28580160	SO:0001583	missense	257202				CCDS43432.1	6p22.1	2012-03-01			ENSG00000198704	ENSG00000198704	1.11.1.9		4558	protein-coding gene	gene with protein product		607913	"glutathione peroxidase pseudogene 3"	GPXP3			Standard	NM_182701		Approved		uc021yrx.1	P59796	OTTHUMG00000044828	ENST00000474923.1:c.454A>C	6.37:g.28472181T>G	ENSP00000417364:p.Asn152His		28580160	Q4PJ17	Missense_Mutation	SNP	ENST00000474923.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.81|18.81	3.702095|3.702095	0.68501|0.68501	.|.	.|.	ENSG00000198704|ENSG00000198704	ENST00000361902|ENST00000474923	T|T	0.04049|0.12672	3.72|2.66	4.31|4.31	4.31|4.31	0.51392|0.51392	Thioredoxin-like fold (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.34716|0.34716	0.0907|0.0907	H|H	0.98487|0.98487	4.245|4.245	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.59268|0.59268	-0.7486|-0.7486	10|7	0.87932|0.11794	D|T	0|0.64	.|.	12.0768|12.0768	0.53649|0.53649	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	185|.	P59796|.	GPX6_HUMAN|.	T|H	185|152	ENSP00000354581:K185T|ENSP00000417364:N152H	ENSP00000354581:K185T|ENSP00000417364:N152H	K|N	-|-	2|1	0|0	GPX6|GPX6	28580160|28580160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.554000|0.554000	0.35429|0.35429	6.635000|6.635000	0.74295|0.74295	2.148000|2.148000	0.66965|0.66965	0.482000|0.482000	0.46254|0.46254	AAA|AAT		0.532	GPX6-002	PUTATIVE	basic|exp_conf|seleno	protein_coding	protein_coding	OTTHUMT00000356246.5			G	28472181	T	G	28472181	3	3	47	1	0	0	0	0	1	0	0	0	6765	1841	64	4	115	4	GPX6	6	28472181	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	258605	28472181	142642886	799	5196										
OR12D2	26529	broad.mit.edu	37	chr6	29365148	29365148	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacattatcacttatctcttCttcaagacccgttcttgtag	4	11	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:29365148C>A	ENST00000383555.2	+	1	733	c.672C>A	c.(670-672)ttC>ttA	p.F224L	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F224L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTTATCTCTTCTTCAAGACCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											193	193	193					6																	29365148		1511	2709	4220	29473127	SO:0001583	missense	26529				CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"GPCR / Class A : Olfactory receptors"	8178	protein-coding gene	gene with protein product			"olfactory receptor, family 12, subfamily D, member 2"				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.672C>A	6.37:g.29365148C>A	ENSP00000373047:p.Phe224Leu		29473127	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-2.010583	0.00422	.	.	ENSG00000168787	ENST00000383555	T	0.33438	1.41	3.94	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.423728	0.22573	N	0.058318	T	0.03178	0.0093	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.41928	-0.9481	10	0.12103	T	0.63	.	4.5799	0.12253	0.0:0.6109:0.1943:0.1948	.	224	P58182	O12D2_HUMAN	L	224	ENSP00000373047:F224L	ENSP00000373047:F224L	F	+	3	2	OR12D2	29473127	0.732000	0.28121	0.008000	0.14137	0.033000	0.12548	2.857000	0.48349	2.019000	0.59389	0.205000	0.17691	TTC		0.443	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2			A	29365148	C	A	29365148	3	1	47	1	0	0	0	0	1	0	0	0	10962	912	32	2	674	2	OR12D2	6	29365148	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	892967	29365148	141749919	800	5197										
ZFP57	346171	broad.mit.edu	37	chr6	29643209	29643209	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggacaaactctctccactgTtcctcttcttgctcaagctt	5	14	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:29643209T>G	ENST00000488757.1	-	3	456	c.306A>C	c.(304-306)gaA>gaC	p.E102D	ZFP57_ENST00000376883.1_Missense_Mutation_p.E82D|ZFP57_ENST00000376881.3_Missense_Mutation_p.E82D	NM_001109809.2	NP_001103279.2	Q9NU63	ZFP57_HUMAN	ZFP57 zinc finger protein	69					DNA methylation involved in embryo development (GO:0043045)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system development (GO:0007422)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	nuclear heterochromatin (GO:0005720)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E82D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5)	44						CTCTCCACTGTTCCTCTTCTT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6											275	256	262					6																	29643209		1944	4150	6094	29751188	SO:0001583	missense	346171			AL050328	CCDS43436.1, CCDS43436.2	6p22.1	2013-01-08	2012-11-27	2005-07-20	ENSG00000204644	ENSG00000204644		"Zinc fingers, C2H2-type", "-"	18791	protein-coding gene	gene with protein product		612192	"chromosome 6 open reading frame 40", "zinc finger protein 57 homolog (mouse)"	C6orf40			Standard	NM_001109809		Approved	ZNF698, bA145L22, bA145L22.2	uc011dlw.2	Q9NU63	OTTHUMG00000031158	ENST00000488757.1:c.306A>C	6.37:g.29643209T>G	ENSP00000418259:p.Glu102Asp		29751188	B0S894|B0V254|B2RXJ7|Q5SSB1	Missense_Mutation	SNP	ENST00000488757.1	37	CCDS43436.2	.	.	.	.	.	.	.	.	.	.	T	5.971	0.363128	0.11296	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	T;T;T	0.07114	3.22;3.47;3.47	3.7	-3.24	0.05094	.	2.317820	0.02029	N	0.048387	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B;B	0.22146	0.065;0.039	B;B	0.18871	0.023;0.015	T	0.44081	-0.9351	10	0.26408	T	0.33	0.0133	5.1253	0.14880	0.0:0.4265:0.1803:0.3932	.	102;82	Q9NU63-3;Q9NU63-2	.;.	D	102;82;82	ENSP00000418259:E102D;ENSP00000366078:E82D;ENSP00000366080:E82D	ENSP00000366078:E82D	E	-	3	2	ZFP57	29751188	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.121000	0.01322	-0.621000	0.05633	-0.912000	0.02778	GAA		0.493	ZFP57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355773.1	XM_294093		G	29643209	T	G	29643209	3	3	47	1	0	0	0	0	1	0	0	0	17690	1722	60	4	1312	4	ZFP57	6	29643209	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	278061	29643209	141471858	801	5198										
HLA-G	3135	broad.mit.edu	37	chr6	29796474	29796474	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcggacactgcggctcagatCtccaagcgcaagtgtgaggc	14	12	2	2	rs199952088		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:29796474C>T	ENST00000360323.6	+	3	522	c.498C>T	c.(496-498)atC>atT	p.I166I	HLA-G_ENST00000376828.2_Silent_p.I171I|HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.I166I			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	166	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I166I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CGGCTCAGATCTCCAAGCGCA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	6											99	83	89					6																	29796474		1511	2709	4220	29904453	SO:0001819	synonymous_variant	3135				CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.498C>T	6.37:g.29796474C>T			29904453		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																				0.607	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29796474	C	T	29796474	2	4	47	1	0	0	0	0	0	0	0	1	7233	903	32	3		3	HLA-G	6	29796474	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	153265	29796474	141318593	802	5199										
C6orf136	221545	broad.mit.edu	37	chr6	30618798	30618798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctcttccttcagtcccacGactacagtctgtattccttg	6	14	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:30618798G>A	ENST00000376473.5	+	3	661	c.502G>A	c.(502-504)Gac>Aac	p.D168N	C6orf136_ENST00000376471.4_Missense_Mutation_p.D34N|C6orf136_ENST00000293604.6_Missense_Mutation_p.D349N|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000528347.2_Missense_Mutation_p.D25N	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136	168						mitochondrion (GO:0005739)		p.D25N(1)		endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						TCAGTCCCACGACTACAGTCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	107	111					6																	30618798		2203	4300	6503	30726777	SO:0001583	missense	221545			BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.502G>A	6.37:g.30618798G>A	ENSP00000365656:p.Asp168Asn		30726777	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Missense_Mutation	SNP	ENST00000376473.5	37	CCDS43443.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643220	0.87859	.	.	ENSG00000204564	ENST00000293604;ENST00000376473;ENST00000376471;ENST00000446773;ENST00000528347	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	L	0.38838	1.175	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.75484	0.976;0.986;0.944	T	0.55095	-0.8194	9	0.31617	T	0.26	-23.0502	16.6565	0.85230	0.0:0.0:1.0:0.0	.	34;349;168	A9R9P9;F8VX15;Q5SQH8	.;.;CF136_HUMAN	N	349;168;34;286;25	.	ENSP00000293604:D349N	D	+	1	0	C6orf136	30726777	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.422000	0.59854	2.665000	0.90641	0.561000	0.74099	GAC		0.433	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029		A	30618798	G	A	30618798	3	1	47	1	0	0	0	0	1	0	0	0	2337	1058	37	1	1055	1	C6orf136	6	30618798	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	822324	30618798	140496269	803	5200										
MSH5	4439	broad.mit.edu	37	chr6	31728482	31728482	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcaggtaggcttgatcacaTtcatggccctggtaggcagc	12	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:31728482T>G	ENST00000375755.3	+	20	2114	c.1828T>G	c.(1828-1830)Ttc>Gtc	p.F610V	MSH5_ENST00000534153.4_Missense_Mutation_p.F627V|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.F627V|SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000431848.2_Missense_Mutation_p.F309V|SAPCD1_ENST00000425424.1_5'Flank|MSH5_ENST00000375742.3_Missense_Mutation_p.F627V|MSH5_ENST00000375703.3_Missense_Mutation_p.F610V|MSH5_ENST00000375740.3_Missense_Mutation_p.F627V|MSH5_ENST00000375750.3_Missense_Mutation_p.F610V|MSH5_ENST00000395853.1_Missense_Mutation_p.F284V	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	610					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)	p.F627V(1)|p.F610V(1)		breast(1)|ovary(2)|skin(2)	5						CTTGATCACATTCATGGCCCT	0.552								Direct reversal of damage;Mismatch excision repair (MMR)																																								2	Substitution - Missense(2)	large_intestine(2)	6											130	123	125					6																	31728482		1511	2709	4220	31836461	SO:0001583	missense	4439			AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"mutS (E. coli) homolog 5", "mutS homolog 5 (E. coli)"			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1828T>G	6.37:g.31728482T>G	ENSP00000364908:p.Phe610Val		31836461	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	CCDS4720.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824128	0.90873	.	.	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000383401;ENST00000375750;ENST00000534153;ENST00000375703;ENST00000375740;ENST00000431848;ENST00000395853	D;D;D;D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76	5.93	5.93	0.95920	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.80560	0.4646	N	0.17723	0.515	0.47659	D	0.999485	D;D;D;P;D	0.89917	1.0;1.0;0.988;0.562;1.0	D;D;D;B;D	0.79784	0.993;0.992;0.914;0.444;0.988	D	0.83933	0.0307	9	0.46703	T	0.11	-13.3522	14.3464	0.66668	0.0:0.0:0.0:1.0	.	295;627;610;610;627	Q59EC5;O43196-4;O43196;O43196-2;O43196-3	.;.;MSH5_HUMAN;.;.	V	610;627;142;610;627;610;627;309;284	ENSP00000364908:F610V;ENSP00000364894:F627V;ENSP00000364903:F610V;ENSP00000431693:F627V;ENSP00000364855:F610V;ENSP00000364892:F627V;ENSP00000416784:F309V;ENSP00000379194:F284V	ENSP00000364855:F610V	F	+	1	0	MSH5	31836461	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.470000	0.66756	2.281000	0.76405	0.533000	0.62120	TTC		0.552	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			G	31728482	T	G	31728482	3	3	47	1	0	0	0	0	1	0	0	0	9903	1493	52	4	1953	4	MSH5	6	31728482	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1109684	31728482	139386585	804	5201										
RDBP	7936	broad.mit.edu	37	chr6	31922848	31922848	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctaacctctcatacagaGatttcctctggggacgtctg	8	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:31922848G>T	ENST00000375429.3	-	6	618	c.392C>A	c.(391-393)tCt>tAt	p.S131Y	NELFE_ENST00000444811.2_Missense_Mutation_p.S131Y|NELFE_ENST00000375425.5_Missense_Mutation_p.S138Y|MIR1236_ENST00000408340.1_RNA	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	131					gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.S131Y(1)									CTCATACAGAGATTTCCTCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											90	95	93					6																	31922848		1511	2709	4220	32030827	SO:0001583	missense	7936			M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"RNA binding motif (RRM) containing"	13974	protein-coding gene	gene with protein product		154040	"RD RNA-binding protein", "RD RNA binding protein"	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.392C>A	6.37:g.31922848G>T	ENSP00000364578:p.Ser131Tyr		32030827	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Missense_Mutation	SNP	ENST00000375429.3	37	CCDS4730.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.312594	0.81358	.	.	ENSG00000204356	ENST00000375429;ENST00000375425;ENST00000444811;ENST00000441998;ENST00000454913;ENST00000436289;ENST00000426722	T;T;T;T;T;T	0.45668	1.48;1.48;1.47;0.89;1.48;0.89	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.42539	0.1207	N	0.14661	0.345	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.998;0.995	D;D;D;D	0.83275	0.986;0.996;0.994;0.986	T	0.52540	-0.8562	10	0.87932	D	0	-6.126	18.8028	0.92025	0.0:0.0:1.0:0.0	.	131;131;131;131	B4DUN1;A2ABK1;E9PCL7;P18615	.;.;.;NELFE_HUMAN	Y	131;138;131;131;131;131;131	ENSP00000364578:S131Y;ENSP00000364574:S138Y;ENSP00000388400:S131Y;ENSP00000397914:S131Y;ENSP00000409389:S131Y;ENSP00000414029:S131Y	ENSP00000364574:S138Y	S	-	2	0	RDBP	32030827	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.238000	0.72350	2.746000	0.94184	0.655000	0.94253	TCT		0.458	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			T	31922848	G	T	31922848	3	4	47	1	0	0	0	0	1	0	0	0	13225	942	33	2	774	2	RDBP	6	31922848	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	194366	31922848	139192219	805	5202										
TNXB	7148	broad.mit.edu	37	chr6	32046999	32046999	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaagagtcgaagctgccctGggggacggtccagaagaggc	17	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:32046999G>C	ENST00000375244.3	-	11	4387	c.4186C>G	c.(4186-4188)Cag>Gag	p.Q1396E	RNA5SP206_ENST00000516703.1_RNA|TNXB_ENST00000375247.2_Missense_Mutation_p.Q1396E			P22105	TENX_HUMAN	tenascin XB	1483	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.Q1483E(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AAGCTGCCCTGGGGGACGGTC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	130	126					6																	32046999		1260	2540	3800	32154977	SO:0001583	missense	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4186C>G	6.37:g.32046999G>C	ENSP00000364393:p.Gln1396Glu		32154977	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	G	6.210	0.406901	0.11754	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56444	0.46;0.46	5.52	3.59	0.41128	.	0.411501	0.17832	N	0.160505	T	0.09335	0.0230	N	0.10685	0.025	0.19575	N	0.999968	B	0.02656	0.0	B	0.10450	0.005	T	0.32455	-0.9906	10	0.02654	T	1	.	8.8844	0.35394	0.0:0.3045:0.5384:0.1571	.	1396	P22105-3	.	E	1396	ENSP00000364393:Q1396E;ENSP00000364396:Q1396E	ENSP00000364393:Q1396E	Q	-	1	0	TNXB	32154977	0.591000	0.26824	1.000000	0.80357	0.526000	0.34562	0.547000	0.23299	1.452000	0.47756	0.591000	0.81541	CAG		0.682	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		C	32046999	G	C	32046999	3	2	47	1	0	0	0	0	1	0	0	0	16385	1357	47	5	10663	5	TNXB	6	32046999	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	124151	32046999	139068068	806	5203										
HLA-DQA2	3118	broad.mit.edu	37	chr6	32713006	32713006	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctggccagtacacccatgaAtttgatggagacgaggagtt	12	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:32713006A>C	ENST00000374940.3	+	2	255	c.153A>C	c.(151-153)gaA>gaC	p.E51D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	51	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)	p.E51D(1)		endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	ACACCCATGAATTTGATGGAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	6											196	191	193					6																	32713006		1511	2709	4220	32820984	SO:0001583	missense	3118				CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.153A>C	6.37:g.32713006A>C	ENSP00000364076:p.Glu51Asp		32820984	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	11.19	1.566193	0.27915	.	.	ENSG00000237541	ENST00000374940	T	0.00840	5.63	3.2	0.808	0.18719	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.134780	0.49305	U	0.000143	T	0.00906	0.0030	M	0.65320	2	0.25005	N	0.991444	D	0.55800	0.973	P	0.62740	0.906	T	0.53429	-0.8440	10	0.25106	T	0.35	.	4.4486	0.11609	0.69:0.0:0.31:0.0	.	51	P01906	DQA2_HUMAN	D	51	ENSP00000364076:E51D	ENSP00000364076:E51D	E	+	3	2	HLA-DQA2	32820984	0.977000	0.34250	0.993000	0.49108	0.064000	0.16182	-0.066000	0.11598	0.425000	0.26087	0.321000	0.21382	GAA		0.498	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		C	32713006	A	C	32713006	3	2	47	1	0	0	0	0	1	0	0	0	7226	98	4	4	159	4	HLA-DQA2	6	32713006	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	666007	32713006	138402061	807	5204										
PSMB8	5696	broad.mit.edu	37	chr6	32808741	32808741	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgccaccaccaccattattGattggcttcccggtactggt	8	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:32808741G>T	ENST00000374882.3	-	6	876	c.826C>A	c.(826-828)Caa>Aaa	p.Q276K	PSMB8_ENST00000374881.2_Missense_Mutation_p.Q272K|TAP2_ENST00000452392.2_5'Flank|PSMB8_ENST00000395339.3_Missense_Mutation_p.Q252K|TAP2_ENST00000374897.2_5'Flank|TAP2_ENST00000374899.4_5'Flank	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	276					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.Q276K(1)|p.Q272K(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	CACCATTATTGATTGGCTTCC	0.522																																					NSCLC(48;53 1172 10859 13624 22883)											2	Substitution - Missense(2)	large_intestine(2)	6											139	115	123					6																	32808741		2203	4300	6503	32916719	SO:0001583	missense	5696				CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"Proteasome (prosome, macropain) subunits"	9545	protein-coding gene	gene with protein product		177046	"proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)", "large multifunctional peptidase 7"	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.826C>A	6.37:g.32808741G>T	ENSP00000364016:p.Gln276Lys		32916719	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Missense_Mutation	SNP	ENST00000374882.3	37	CCDS4757.1	.	.	.	.	.	.	.	.	.	.	G	7.116	0.576962	0.13686	.	.	ENSG00000204264	ENST00000395339;ENST00000374882;ENST00000374881	T;T;T	0.37058	1.22;1.8;1.79	4.77	1.68	0.24146	.	0.789526	0.12303	N	0.480944	T	0.04137	0.0115	N	0.03253	-0.375	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.14023	0.01;0.002	T	0.46331	-0.9199	10	0.10111	T	0.7	.	7.2973	0.26401	0.0:0.3841:0.4405:0.1754	.	272;276	P28062-2;P28062	.;PSB8_HUMAN	K	252;276;272	ENSP00000378748:Q252K;ENSP00000364016:Q276K;ENSP00000364015:Q272K	ENSP00000364015:Q272K	Q	-	1	0	PSMB8	32916719	0.003000	0.15002	0.005000	0.12908	0.021000	0.10359	0.722000	0.25925	0.550000	0.28991	0.643000	0.83706	CAA		0.522	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919		T	32808741	G	T	32808741	3	4	47	1	0	0	0	0	1	0	0	0	12717	1299	45	2	8	2	PSMB8	6	32808741	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	95735	32808741	138306326	808	5205										
HLA-DMB	3109	broad.mit.edu	37	chr6	32906579	32906579	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtgctgtgagaggacattCgccaagctattcagcacccc	11	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:32906579C>T	ENST00000418107.2	-	2	481	c.219G>A	c.(217-219)gcG>gcA	p.A73A	AL645941.1_ENST00000390777.1_RNA|XXbac-BPG181M17.5_ENST00000429234.1_Silent_p.A105A|HLA-DMB_ENST00000416244.2_Silent_p.A73A	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	73	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|MHC class II protein complex assembly (GO:0002399)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001190)|positive regulation of T cell proliferation (GO:0042102)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)	p.A73A(2)		breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						AGAGGACATTCGCCAAGCTAT	0.527																																																2	Substitution - coding silent(2)	large_intestine(2)	6											124	124	124					6																	32906579		1511	2709	4220	33014557	SO:0001819	synonymous_variant	3109				CCDS4760.1	6p21.3	2014-05-16			ENSG00000242574	ENSG00000242574		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4935	protein-coding gene	gene with protein product		142856				1922365	Standard	NM_002118		Approved	D6S221E, RING7	uc003ocl.2	P28068	OTTHUMG00000031176	ENST00000418107.2:c.219G>A	6.37:g.32906579C>T			33014557	O77936|Q13012|Q29751|Q58ZE2|Q5SNZ8|Q5STC4|Q9XRX2	Silent	SNP	ENST00000418107.2	37	CCDS4760.1																																																																																				0.527	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	NM_002118		T	32906579	C	T	32906579	2	4	47	1	0	0	0	0	0	0	0	1	7220	871	31	1		1	HLA-DMB	6	32906579	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	97838	32906579	138208488	809	5206										
HLA-DPB1	3115	broad.mit.edu	37	chr6	33048480	33048480	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccagggacggcaggaatgCtacgcgtttaatgggacaca	13	9	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33048480C>A	ENST00000418931.2	+	2	248	c.132C>A	c.(130-132)tgC>tgA	p.C44*	HLA-DPB1_ENST00000535465.1_Nonsense_Mutation_p.C44*|HLA-DPA1_ENST00000419277.1_5'UTR|HLA-DPB1_ENST00000471184.1_3'UTR	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	44	Beta-1.		C -> G (in allele DPB1*26:02).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.C44*(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGCAGGAATGCTACGCGTTTA	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											59	61	60					6																	33048480		1511	2709	4220	33156458	SO:0001587	stop_gained	3115				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.132C>A	6.37:g.33048480C>A	ENSP00000408146:p.Cys44*		33156458	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Nonsense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.246643|5.246643	0.95305|0.95305	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	.|.	.|.	.|.	3.93|3.93	3.93|3.93	0.45458|0.45458	.|.	.|0.054564	.|0.85682	.|D	.|0.000000	T|.	0.06508|.	0.0167|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.21415|.	-1.0246|.	3|.	.|0.02654	.|T	.|1	.|.	7.625|7.625	0.28208|0.28208	0.0:0.8834:0.0:0.1166|0.0:0.8834:0.0:0.1166	.|.	.|.	.|.	.|.	D|X	11|44;44;44;21	.|.	.|ENSP00000389210:C44X	A|C	+|+	2|3	0|2	HLA-DPB1|HLA-DPB1	33156458|33156458	0.629000|0.629000	0.27146|0.27146	0.804000|0.804000	0.32291|0.32291	0.209000|0.209000	0.24338|0.24338	0.404000|0.404000	0.20999|0.20999	2.200000|2.200000	0.70718|0.70718	0.579000|0.579000	0.79373|0.79373	GCT|TGC		0.592	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		A	33048480	C	A	33048480	4	1	47	1	0	0	0	0	0	1	0	0	7224	805	28	2	138	2	HLA-DPB1	6	33048480	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	141901	33048480	138066587	810	5207										
COL11A2	1302	broad.mit.edu	37	chr6	33143404	33143404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccagtcggtccagtgcgtcCctttggcccctcaggaccat	10	16	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33143404C>T	ENST00000374708.4	-	28	2323	c.2065G>A	c.(2065-2067)Gga>Aga	p.G689R	COL11A2_ENST00000341947.2_Missense_Mutation_p.G775R|COL11A2_ENST00000361917.1_Missense_Mutation_p.G668R|COL11A2_ENST00000395197.1_Missense_Mutation_p.G715R|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Missense_Mutation_p.G728R|COL11A2_ENST00000374714.1_Missense_Mutation_p.G749R|COL11A2_ENST00000374712.1_Missense_Mutation_p.G694R|COL11A2_ENST00000357486.1_Missense_Mutation_p.G754R	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	775	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.G775R(1)		biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCAGTGCGTCCCTTTGGCCCC	0.652																																					Melanoma(1;90 116 3946 5341 17093)											1	Substitution - Missense(1)	large_intestine(1)	6											109	94	100					6																	33143404		1509	2709	4218	33251382	SO:0001583	missense	1302			U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.2065G>A	6.37:g.33143404C>T	ENSP00000363840:p.Gly689Arg		33251382	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696668	0.88830	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29;-6.29;-6.29;-6.29;-6.29	4.3	4.3	0.51218	.	0.065961	0.64402	D	0.000014	D	0.99822	0.9921	H	0.98525	4.255	0.80722	D	1	D;D;D	0.89917	1.0;0.985;1.0	D;D;D	0.97110	1.0;0.99;1.0	D	0.96723	0.9534	10	0.87932	D	0	.	14.6683	0.68924	0.0:1.0:0.0:0.0	.	668;689;775	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	R	689;775;754;749;728;715;694;668	ENSP00000363840:G689R;ENSP00000339915:G775R;ENSP00000350079:G754R;ENSP00000363846:G749R;ENSP00000363845:G728R;ENSP00000378623:G715R;ENSP00000363844:G694R;ENSP00000355123:G668R	ENSP00000339915:G775R	G	-	1	0	COL11A2	33251382	0.999000	0.42202	1.000000	0.80357	0.978000	0.69477	5.454000	0.66651	2.421000	0.82119	0.478000	0.44815	GGA		0.652	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33143404	C	T	33143404	3	4	47	1	0	0	0	0	1	0	0	0	3674	632	22	3	3035	3	COL11A2	6	33143404	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	94924	33143404	137971663	811	5208										
RXRB	6257	broad.mit.edu	37	chr6	33165653	33165653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccggcaagagtatgtaaggtCtttgcggatggtgcgtttga	15	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33165653C>A	ENST00000374680.3	-	4	917	c.706G>T	c.(706-708)Gac>Tac	p.D236Y	SLC39A7_ENST00000374675.3_5'Flank|RXRB_ENST00000544186.1_Missense_Mutation_p.D46Y|RXRB_ENST00000413614.2_Missense_Mutation_p.D140Y|RNY4P10_ENST00000365571.1_RNA|SLC39A7_ENST00000374677.3_5'Flank|RXRB_ENST00000374685.4_Missense_Mutation_p.D236Y	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	236					cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.D236Y(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	TATGTAAGGTCTTTGCGGATG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	70	76					6																	33165653		1511	2709	4220	33273631	SO:0001583	missense	6257			M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.706G>T	6.37:g.33165653C>A	ENSP00000363812:p.Asp236Tyr		33273631	P28703|Q59G65|Q5JP92|Q5STQ1	Missense_Mutation	SNP	ENST00000374680.3	37	CCDS4768.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148776	0.78001	.	.	ENSG00000204231	ENST00000374685;ENST00000374680;ENST00000544186;ENST00000413614	D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06	4.3	4.3	0.51218	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.103245	0.64402	D	0.000004	D	0.96864	0.8976	L	0.53561	1.675	0.80722	D	1	D;D;P;B;D;D;D;D	0.89917	1.0;1.0;0.887;0.414;0.96;1.0;1.0;1.0	D;D;P;B;P;D;D;D	0.91635	0.999;0.999;0.733;0.365;0.887;0.999;0.999;0.999	D	0.97171	0.9844	10	0.62326	D	0.03	.	14.662	0.68879	0.0:1.0:0.0:0.0	.	140;236;119;46;236;236;276;236	B7Z3E4;B7Z6J2;B7Z6X3;E9PK95;Q5STQ1;Q5STP9;Q59G65;P28702	.;.;.;.;.;.;.;RXRB_HUMAN	Y	236;236;46;140	ENSP00000363817:D236Y;ENSP00000363812:D236Y;ENSP00000439222:D46Y;ENSP00000415561:D140Y	ENSP00000363812:D236Y	D	-	1	0	RXRB	33273631	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	4.785000	0.62418	2.393000	0.81446	0.448000	0.29417	GAC		0.547	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		A	33165653	C	A	33165653	3	1	47	1	0	0	0	0	1	0	0	0	13801	913	32	2	923	2	RXRB	6	33165653	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	22249	33165653	137949414	812	5209										
RPS18	6222	broad.mit.edu	37	chr6	33244217	33244217	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccactggccgccgtggccgcAccgtgggtgtgtccaagaag	15	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33244217A>G	ENST00000439602.2	+	6	543	c.433A>G	c.(433-435)Acc>Gcc	p.T145A	RPS18_ENST00000474973.1_Missense_Mutation_p.T75A|B3GALT4_ENST00000451237.1_5'Flank|RPS18_ENST00000476222.1_3'UTR			P62269	RS18_HUMAN	ribosomal protein S18	145					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribosome (GO:0005840)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.T145A(1)		kidney(2)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	9						CCGTGGCCGCACCGTGGGTGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											46	46	46					6																	33244217		2203	4294	6497	33352195	SO:0001583	missense	6222			X69150	CCDS4771.1	6p21.3	2011-04-05			ENSG00000231500	ENSG00000231500		"S ribosomal proteins"	10401	protein-coding gene	gene with protein product		180473		D6S218E		8441687, 9582194	Standard	NM_022551		Approved	KE3, KE-3, HKE3, S18	uc003odp.1	P62269	OTTHUMG00000031053	ENST00000439602.2:c.433A>G	6.37:g.33244217A>G	ENSP00000393241:p.Thr145Ala		33352195	P25232|Q5SUJ3|Q6IPF8	Missense_Mutation	SNP	ENST00000439602.2	37	CCDS4771.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.583338	0.65992	.	.	ENSG00000231500	ENST00000439602;ENST00000474973	.	.	.	4.48	4.48	0.54585	Ribosomal protein S13-like, H2TH (1);	0.126503	0.53938	D	0.000056	T	0.47728	0.1461	M	0.72894	2.215	0.54753	D	0.999989	B	0.15141	0.012	B	0.24006	0.05	T	0.57791	-0.7750	9	0.59425	D	0.04	.	10.1487	0.42780	1.0:0.0:0.0:0.0	.	145	P62269	RS18_HUMAN	A	145;75	.	ENSP00000393241:T145A	T	+	1	0	RPS18	33352195	1.000000	0.71417	0.871000	0.34182	0.991000	0.79684	7.771000	0.85420	1.904000	0.55121	0.386000	0.25728	ACC		0.488	RPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076059.2			G	33244217	A	G	33244217	3	3	47	1	0	0	0	0	1	0	0	0	13665	159	6	4	455	4	RPS18	6	33244217	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	78564	33244217	137870850	813	5210										
TAPBP	6892	broad.mit.edu	37	chr6	33272205	33272205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaagtgcccagagaggctgAcagagccatcggaatggtgg	16	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33272205A>G	ENST00000489157.1	-	4	1030	c.818T>C	c.(817-819)gTc>gCc	p.V273A	TAPBP_ENST00000475304.1_Missense_Mutation_p.V378A|TAPBP_ENST00000426633.2_Missense_Mutation_p.V360A|TAPBP_ENST00000456592.2_Missense_Mutation_p.V360A|TAPBP_ENST00000434618.2_Missense_Mutation_p.V360A			O15533	TPSN_HUMAN	TAP binding protein (tapasin)	360					amide transport (GO:0042886)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|peptide antigen stabilization (GO:0050823)|peptide transport (GO:0015833)|protein complex assembly (GO:0006461)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|MHC class I peptide loading complex (GO:0042824)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)|peptide antigen-transporting ATPase activity (GO:0015433)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)|unfolded protein binding (GO:0051082)	p.V360A(1)		endometrium(2)|large_intestine(5)|lung(8)|ovary(3)	18						AGAGAGGCTGACAGAGCCATC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	6											31	33	32					6																	33272205		2202	4297	6499	33380183	SO:0001583	missense	6892			Y13582	CCDS34426.1, CCDS34427.1, CCDS34428.1, CCDS34427.2, CCDS34428.2	6p21.3	2014-09-17			ENSG00000231925	ENSG00000231925		"Immunoglobulin superfamily / C1-set domain containing"	11566	protein-coding gene	gene with protein product		601962				9238042	Standard	NM_003190		Approved	TAPA	uc003odz.3	O15533	OTTHUMG00000031090	ENST00000489157.1:c.818T>C	6.37:g.33272205A>G	ENSP00000419659:p.Val273Ala		33380183	A2AB91|A2ABC0|B0V003|B0V0A6|B2ZUA4|E9PGM2|O15210|O15272|Q5STJ8|Q5STK6|Q5STQ5|Q5STQ6|Q66K65|Q96KK7|Q9HAN8|Q9UEE0|Q9UEE4|Q9UIZ6|Q9Y6K2	Missense_Mutation	SNP	ENST00000489157.1	37	CCDS34427.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300539	0.81136	.	.	ENSG00000231925	ENST00000434618;ENST00000475304;ENST00000489157;ENST00000426633;ENST00000456592;ENST00000449540	T;T;T;T;T	0.02812	4.15;4.15;4.15;4.15;4.15	5.51	5.51	0.81932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.376195	0.26514	N	0.023953	T	0.04998	0.0134	M	0.63428	1.95	0.32373	N	0.55557	P;P;P;P;P	0.50819	0.939;0.936;0.822;0.846;0.915	P;P;B;P;P	0.57204	0.558;0.815;0.325;0.477;0.686	T	0.03706	-1.1011	10	0.72032	D	0.01	-16.4586	12.0049	0.53252	1.0:0.0:0.0:0.0	.	360;273;378;360;360	G5E9H8;E9PGM2;A2AB90;O15533-3;O15533	.;.;.;.;TPSN_HUMAN	A	360;378;273;360;360;360	ENSP00000395701:V360A;ENSP00000417949:V378A;ENSP00000419659:V273A;ENSP00000404833:V360A;ENSP00000387803:V360A	ENSP00000404833:V360A	V	-	2	0	TAPBP	33380183	0.575000	0.26692	0.997000	0.53966	0.810000	0.45777	2.108000	0.41854	2.100000	0.63781	0.408000	0.27601	GTC		0.682	TAPBP-006	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276425.2			G	33272205	A	G	33272205	3	3	47	1	0	0	0	0	1	0	0	0	15591	275	10	4	463	4	TAPBP	6	33272205	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	27988	33272205	137842862	814	5211										
KIFC1	3833	broad.mit.edu	37	chr6	33374422	33374422	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctacctgctgcagaactcTctgggtggtagtgctaagat	11	10	1	2	rs371316441		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:33374422T>C	ENST00000428849.2	+	9	2331	c.1881T>C	c.(1879-1881)tcT>tcC	p.S627S		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	627	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)	p.S627S(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						TGCAGAACTCTCTGGGTGGTA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	6						T		2,4404	4.2+/-10.8	0,2,2201	141	131	135		1881	0.1	1	6		135	0,8600		0,0,4300	no	coding-synonymous	KIFC1	NM_002263.3		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		627/674	33374422	2,13004	2203	4300	6503	33482400	SO:0001819	synonymous_variant	3833			D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"Kinesins"	6389	protein-coding gene	gene with protein product		603763	"kinesin-like 2"	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1881T>C	6.37:g.33374422T>C			33482400	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Silent	SNP	ENST00000428849.2	37	CCDS34430.1																																																																																				0.527	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263		C	33374422	T	C	33374422	2	2	47	1	0	0	0	0	0	0	0	1	8333	1538	54	4		4	KIFC1	6	33374422	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	102217	33374422	137740645	815	5212										
PPARD	5467	broad.mit.edu	37	chr6	35393738	35393738	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccccaagctgctgcagaagaTggctgacctgcggcaactgg	13	13	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:35393738T>C	ENST00000311565.4	+	9	1557	c.1208T>C	c.(1207-1209)aTg>aCg	p.M403T	PPARD_ENST00000418635.2_Missense_Mutation_p.M305T|PPARD_ENST00000360694.3_Missense_Mutation_p.M403T|PPARD_ENST00000448077.2_Missense_Mutation_p.M364T|PPARD_ENST00000540939.1_Missense_Mutation_p.M300T	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	403	Ligand-binding.				adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.M403T(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	CTGCAGAAGATGGCTGACCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											103	91	95					6																	35393738		2203	4300	6503	35501716	SO:0001583	missense	5467			L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"Nuclear hormone receptors"	9235	protein-coding gene	gene with protein product		600409	"peroxisome proliferative activated receptor, delta"			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.1208T>C	6.37:g.35393738T>C	ENSP00000310928:p.Met403Thr		35501716	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Missense_Mutation	SNP	ENST00000311565.4	37	CCDS4803.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.516319	0.85495	.	.	ENSG00000112033	ENST00000448077;ENST00000360694;ENST00000418635;ENST00000311565;ENST00000540939	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	5.05	5.05	0.67936	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.080011	0.85682	D	0.000000	T	0.76543	0.4002	M	0.80616	2.505	0.80722	D	1	P;D;D	0.61080	0.907;0.989;0.989	P;P;P	0.55577	0.628;0.718;0.779	T	0.81714	-0.0807	10	0.87932	D	0	.	14.8191	0.70059	0.0:0.0:0.0:1.0	.	305;364;403	E9PE18;B7Z3W1;Q03181	.;.;PPARD_HUMAN	T	364;403;305;403;300	ENSP00000414372:M364T;ENSP00000353916:M403T;ENSP00000413314:M305T;ENSP00000310928:M403T;ENSP00000443759:M300T	ENSP00000310928:M403T	M	+	2	0	PPARD	35501716	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.004000	0.88535	1.898000	0.54952	0.459000	0.35465	ATG		0.607	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238		C	35393738	T	C	35393738	3	2	47	1	0	0	0	0	1	0	0	0	12329	1464	51	4	1255	4	PPARD	6	35393738	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2019316	35393738	135721329	816	5213										
PI16	221476	broad.mit.edu	37	chr6	36929308	36929308	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgttgaggagaccaacatcGaattactggtgtgcaactat	11	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:36929308G>A	ENST00000373674.3	+	3	803	c.475G>A	c.(475-477)Gaa>Aaa	p.E159K		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	159	SCP.				negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)	p.E159K(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GACCAACATCGAATTACTGGT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											142	127	132					6																	36929308		2203	4300	6503	37037286	SO:0001583	missense	221476				CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"microseminoprotein, beta-binding protein"		"protease inhibitor 16"				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.475G>A	6.37:g.36929308G>A	ENSP00000362778:p.Glu159Lys		37037286	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.063577	0.36373	.	.	ENSG00000164530	ENST00000536757;ENST00000373674;ENST00000539035	T	0.07908	3.15	5.08	2.3	0.28687	CAP domain (3);	0.788386	0.11936	N	0.515210	T	0.00967	0.0032	N	0.03177	-0.4	0.09310	N	1	B;B	0.30889	0.043;0.299	B;B	0.21546	0.002;0.035	T	0.47249	-0.9132	10	0.33141	T	0.24	.	6.5358	0.22352	0.0:0.5538:0.2881:0.1581	.	159;159	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	K	159;159;11	ENSP00000362778:E159K	ENSP00000362778:E159K	E	+	1	0	PI16	37037286	0.241000	0.23857	0.027000	0.17364	0.877000	0.50540	0.506000	0.22658	0.310000	0.22990	-0.270000	0.10280	GAA		0.582	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370		A	36929308	G	A	36929308	3	1	47	1	0	0	0	0	1	0	0	0	11900	1059	37	1	485	1	PI16	6	36929308	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1535570	36929308	134185759	817	5214										
DNAH8	1769	broad.mit.edu	37	chr6	38810668	38810668	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccactccttaaacataagGatgatattgaggtacataag	7	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:38810668G>T	ENST00000359357.3	+	33	4437	c.4183G>T	c.(4183-4185)Gat>Tat	p.D1395Y	DNAH8_ENST00000441566.1_Missense_Mutation_p.D1395Y|DNAH8_ENST00000449981.2_Missense_Mutation_p.D1612Y			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1395					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D1395Y(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TAAACATAAGGATGATATTGA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	6											102	95	97					6																	38810668		2203	4300	6503	38918646	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4183G>T	6.37:g.38810668G>T	ENSP00000352312:p.Asp1395Tyr		38918646	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	19.65	3.868069	0.72065	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.63096	-0.02;-0.02;-0.02	5.12	5.12	0.69794	Dynein heavy chain, domain-2 (1);	0.105656	0.64402	D	0.000006	T	0.74512	0.3726	M	0.83603	2.65	0.53005	D	0.999964	P	0.50443	0.935	P	0.56788	0.806	T	0.78807	-0.2059	10	0.72032	D	0.01	.	18.9269	0.92549	0.0:0.0:1.0:0.0	.	1395	Q96JB1	DYH8_HUMAN	Y	1600;1600;1395;1395	ENSP00000333363:D1600Y;ENSP00000352312:D1395Y;ENSP00000402294:D1395Y	ENSP00000333363:D1600Y	D	+	1	0	DNAH8	38918646	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.957000	0.87870	2.532000	0.85374	0.557000	0.71058	GAT		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38810668	G	T	38810668	3	4	47	1	0	0	0	0	1	0	0	0	4618	1174	41	2	4305	2	DNAH8	6	38810668	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1881360	38810668	132304399	818	5215										
DNAH8	1769	broad.mit.edu	37	chr6	38889244	38889244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcaagctgagctggataaaGtacaggcaaaatttgatgca	11	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:38889244G>T	ENST00000359357.3	+	69	10227	c.9973G>T	c.(9973-9975)Gta>Tta	p.V3325L	RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000441566.1_Missense_Mutation_p.V3289L|DNAH8_ENST00000449981.2_Missense_Mutation_p.V3542L|RP1-207H1.3_ENST00000418399.1_RNA			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3325	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V3325L(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCTGGATAAAGTACAGGCAAA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	6											73	69	71					6																	38889244		2203	4300	6503	38997222	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.9973G>T	6.37:g.38889244G>T	ENSP00000352312:p.Val3325Leu		38997222	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	28.4	4.921094	0.92249	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.66099	-0.19;-0.19;-0.19	5.47	5.47	0.80525	Dynein heavy chain, coiled coil stalk (1);	0.067309	0.64402	D	0.000016	T	0.56761	0.2007	L	0.35854	1.095	0.80722	D	1	D	0.65815	0.995	D	0.65987	0.94	T	0.53443	-0.8438	10	0.02654	T	1	.	19.6762	0.95934	0.0:0.0:1.0:0.0	.	3325	Q96JB1	DYH8_HUMAN	L	3530;3530;3325;3289	ENSP00000333363:V3530L;ENSP00000352312:V3325L;ENSP00000402294:V3289L	ENSP00000333363:V3530L	V	+	1	0	DNAH8	38997222	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.813000	0.99286	2.729000	0.93468	0.591000	0.81541	GTA		0.448	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38889244	G	T	38889244	3	4	47	1	0	0	0	0	1	0	0	0	4618	1029	36	2	10239	2	DNAH8	6	38889244	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	78576	38889244	132225823	819	5216										
DNAH8	1769	broad.mit.edu	37	chr6	38919247	38919247	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatgcttcctgtccatgggAtctgaccccaccaatcaaat	6	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:38919247A>G	ENST00000359357.3	+	80	12005	c.11751A>G	c.(11749-11751)ggA>ggG	p.G3917G	RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000441566.1_Silent_p.G3881G|DNAH8_ENST00000449981.2_Silent_p.G4134G			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3917	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G3917G(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGTCCATGGGATCTGACCCCA	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	6											202	212	209					6																	38919247		2203	4300	6503	39027225	SO:0001819	synonymous_variant	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11751A>G	6.37:g.38919247A>G			39027225	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																					0.423	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38919247	A	G	38919247	2	3	47	1	0	0	0	0	0	0	0	1	4618	320	12	4		4	DNAH8	6	38919247	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	30003	38919247	132195820	820	5217										
GLP1R	2740	broad.mit.edu	37	chr6	39053697	39053697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaaggtccagctggaatttCggaagagctgggagcgctgg	18	7	0	1	rs199796313		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:39053697C>T	ENST00000373256.4	+	13	1283	c.1240C>T	c.(1240-1242)Cgg>Tgg	p.R414W		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	414					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.R414W(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	GCTGGAATTTCGGAAGAGCTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	6											140	143	142					6																	39053697		2203	4300	6503	39161675	SO:0001583	missense	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.1240C>T	6.37:g.39053697C>T	ENSP00000362353:p.Arg414Trp		39161675	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102348	0.56183	.	.	ENSG00000112164	ENST00000373256	T	0.66460	-0.21	6.17	5.31	0.75309	.	0.000000	0.64402	D	0.000009	T	0.62159	0.2405	M	0.87381	2.88	0.50171	D	0.999851	B	0.16166	0.016	B	0.15870	0.014	T	0.67201	-0.5730	10	0.62326	D	0.03	.	15.8154	0.78595	0.0:0.9352:0.0:0.0648	.	414	P43220	GLP1R_HUMAN	W	414	ENSP00000362353:R414W	ENSP00000362353:R414W	R	+	1	2	GLP1R	39161675	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.456000	0.60081	1.633000	0.50488	-0.137000	0.14449	CGG		0.547	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			T	39053697	C	T	39053697	3	4	47	1	0	0	0	0	1	0	0	0	6472	875	31	1	1290	1	GLP1R	6	39053697	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	134450	39053697	132061370	821	5218										
KCNK16	83795	broad.mit.edu	37	chr6	39284137	39284137	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcccagtgggaggatcagcGccagccacgccaggcccagg	16	15	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:39284137G>A	ENST00000373229.5	-	5	756	c.743C>T	c.(742-744)gCg>gTg	p.A248V	KCNK16_ENST00000437525.2_Missense_Mutation_p.A248V|KCNK16_ENST00000425054.2_Intron|KCNK17_ENST00000453413.2_5'Flank|KCNK16_ENST00000507712.1_Intron|KCNK16_ENST00000373227.4_Intron|KCNK17_ENST00000373231.4_5'Flank	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	248					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A248V(1)		large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						GAGGATCAGCGCCAGCCACGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6											29	31	31					6																	39284137		2203	4300	6503	39392115	SO:0001583	missense	83795			AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.743C>T	6.37:g.39284137G>A	ENSP00000362326:p.Ala248Val		39392115	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	37	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293479	0.80914	.	.	ENSG00000095981	ENST00000373229;ENST00000437525	T;T	0.32023	1.47;1.47	5.11	4.23	0.50019	Ion transport 2 (1);	0.954854	0.08598	N	0.921933	T	0.46946	0.1419	M	0.76574	2.34	0.37793	D	0.927439	D;D	0.76494	0.999;0.999	D;D	0.67103	0.949;0.949	T	0.42464	-0.9450	10	0.72032	D	0.01	.	14.8222	0.70082	0.0:0.0:0.8546:0.1454	.	248;248	B5TJL9;Q96T55	.;KCNKG_HUMAN	V	248	ENSP00000362326:A248V;ENSP00000415375:A248V	ENSP00000362326:A248V	A	-	2	0	KCNK16	39392115	0.981000	0.34729	0.858000	0.33744	0.994000	0.84299	5.454000	0.66651	1.255000	0.44051	0.462000	0.41574	GCG		0.642	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		A	39284137	G	A	39284137	3	1	47	1	0	0	0	0	1	0	0	0	8084	1087	38	1	579	1	KCNK16	6	39284137	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	230440	39284137	131830930	822	5219										
XPO5	57510	broad.mit.edu	37	chr6	43516063	43516063	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctcctctaggaacaccttCtgacgctcgtagttcttaaa	7	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:43516063C>T	ENST00000265351.7	-	18	2205	c.1995G>A	c.(1993-1995)caG>caA	p.Q665Q	XPO5_ENST00000424378.2_5'Flank	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	665					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.Q665Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			GGAACACCTTCTGACGCTCGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	6											153	150	151					6																	43516063		1934	4148	6082	43624041	SO:0001819	synonymous_variant	57510			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1995G>A	6.37:g.43516063C>T			43624041	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																				0.493	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		T	43516063	C	T	43516063	2	4	47	1	0	0	0	0	0	0	0	1	17487	912	32	3		3	XPO5	6	43516063	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4231926	43516063	127599004	823	5220										
CAPN11	11131	broad.mit.edu	37	chr6	44148342	44148342	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccggcccccaggaaaaggtCtctgaggatgacatggacca	12	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:44148342C>A	ENST00000398776.1	+	16	1727	c.1689C>A	c.(1687-1689)gtC>gtA	p.V563V	CAPN11_ENST00000542245.1_Silent_p.V563V	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	563	Linker.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)	p.V563V(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AGGAAAAGGTCTCTGAGGATG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											41	43	43					6																	44148342		1884	4113	5997	44256320	SO:0001819	synonymous_variant	11131			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1689C>A	6.37:g.44148342C>A			44256320	B2RA64|Q5T3G1|Q8N4R5	Silent	SNP	ENST00000398776.1	37	CCDS47436.1																																																																																				0.582	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			A	44148342	C	A	44148342	2	1	47	1	0	0	0	0	0	0	0	1	2630	900	32	2		2	CAPN11	6	44148342	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	632279	44148342	126966725	824	5221										
CYP39A1	51302	broad.mit.edu	37	chr6	46620169	46620169	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttgctttctctataaattCtagaggggctttcccaaact	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:46620169C>A	ENST00000275016.2	-	1	354	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	SLC25A27_ENST00000411689.2_5'Flank|SLC25A27_ENST00000371347.5_5'Flank|SLC25A27_ENST00000452689.2_5'Flank	NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	51					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)	p.E51*(1)	EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						TCTATAAATTCTAGAGGGGCT	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											177	204	195					6																	46620169		2203	4300	6503	46728128	SO:0001587	stop_gained	51302			AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.151G>T	6.37:g.46620169C>A	ENSP00000275016:p.Glu51*		46728128	Q5VTT0|Q96FW5	Nonsense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	C	38	7.230604	0.98150	.	.	ENSG00000146233	ENST00000275016	.	.	.	5.39	4.5	0.54988	.	0.151300	0.44097	D	0.000491	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-22.2833	9.473	0.38853	0.0:0.7742:0.1467:0.0792	.	.	.	.	X	51	.	ENSP00000275016:E51X	E	-	1	0	CYP39A1	46728128	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	1.652000	0.37313	1.372000	0.46190	0.655000	0.94253	GAA		0.448	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			A	46620169	C	A	46620169	4	1	47	1	0	0	0	0	0	1	0	0	4183	922	32	2	1306	2	CYP39A1	6	46620169	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2471827	46620169	124494898	825	5222										
TDRD6	221400	broad.mit.edu	37	chr6	46656967	46656967	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttgctgcctgaatattttCgaatgccggtggtgacctac	10	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:46656967C>T	ENST00000316081.6	+	1	1102	c.1102C>T	c.(1102-1104)Cga>Tga	p.R368*	RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Nonsense_Mutation_p.R368*|RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	368	Tudor 2. {ECO:0000255|PROSITE- ProRule:PRU00211}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)		p.R368*(1)		NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TGAATATTTTCGAATGCCGGT	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											134	119	124					6																	46656967		2203	4300	6503	46764926	SO:0001587	stop_gained	221400			AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.1102C>T	6.37:g.46656967C>T	ENSP00000346065:p.Arg368*		46764926	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Nonsense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	C	35	5.516299	0.96402	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	.	.	.	5.65	5.65	0.86999	.	0.255981	0.36932	N	0.002340	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8198	19.5221	0.95189	0.0:1.0:0.0:0.0	.	.	.	.	X	368	.	ENSP00000346065:R368X	R	+	1	2	TDRD6	46764926	0.995000	0.38212	0.709000	0.30452	0.825000	0.46686	3.360000	0.52299	2.941000	0.99782	0.655000	0.94253	CGA		0.547	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		T	46656967	C	T	46656967	4	4	47	1	0	0	0	0	0	1	0	0	15773	876	31	1	1104	1	TDRD6	6	46656967	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36798	46656967	124458100	826	5223										
GPR110	266977	broad.mit.edu	37	chr6	46988506	46988506	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgactcaaaaccttgaattCtttcatatgcttttttaagc	4	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:46988506C>A	ENST00000371253.2	-	7	787	c.572G>T	c.(571-573)aGa>aTa	p.R191I	GPR110_ENST00000371243.2_Missense_Mutation_p.R191I|GPR110_ENST00000283297.5_5'Flank|GPR110_ENST00000449332.2_5'UTR	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	191	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R191I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						ACCTTGAATTCTTTCATATGC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											91	86	88					6																	46988506		2203	4300	6503	47096465	SO:0001583	missense	266977			AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.572G>T	6.37:g.46988506C>A	ENSP00000360299:p.Arg191Ile		47096465	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085394	0.36758	.	.	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000371243	T;T	0.35236	1.32;1.32	5.12	1.22	0.21188	SEA (1);	0.681363	0.13437	N	0.388007	T	0.11410	0.0278	L	0.35487	1.065	0.09310	N	1	P;P	0.48503	0.911;0.728	P;B	0.44811	0.461;0.403	T	0.08638	-1.0712	10	0.39692	T	0.17	0.1548	4.0256	0.09685	0.1623:0.5673:0.0:0.2704	.	191;191	Q5T601-2;Q5T601	.;GP110_HUMAN	I	191	ENSP00000360299:R191I;ENSP00000360289:R191I	ENSP00000360289:R191I	R	-	2	0	GPR110	47096465	0.010000	0.17322	0.009000	0.14445	0.729000	0.41735	0.216000	0.17585	-0.079000	0.12707	-0.150000	0.13652	AGA		0.388	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46988506	C	A	46988506	3	1	47	1	0	0	0	0	1	0	0	0	6647	913	32	2	2246	2	GPR110	6	46988506	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	331539	46988506	124126561	827	5224										
PGK2	5232	broad.mit.edu	37	chr6	49753713	49753713	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaagctctagactggcaccGcctccagtgctgacatggct	11	13	1	3	rs199596449		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:49753713G>A	ENST00000304801.3	-	1	1340	c.1188C>T	c.(1186-1188)ggC>ggT	p.G396G		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	396				G -> R (in Ref. 1; CAA28872). {ECO:0000305}.	glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)	p.G396G(2)		autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					GACTGGCACCGCCTCCAGTGC	0.483													G|||	1	0.000199681	0	0	5008	,	,		19987	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	6						G		0,4406		0,0,2203	104	101	102		1188	-8.4	0.7	6		102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PGK2	NM_138733.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		396/418	49753713	2,13004	2203	4300	6503	49861672	SO:0001819	synonymous_variant	5232			K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.1188C>T	6.37:g.49753713G>A			49861672	B2R6Y8|Q9H107	Silent	SNP	ENST00000304801.3	37	CCDS4930.1																																																																																				0.483	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			A	49753713	G	A	49753713	2	1	47	1	0	0	0	0	0	0	0	1	11822	1074	38	1		1	PGK2	6	49753713	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2765207	49753713	121361354	828	5225										
PGK2	5232	broad.mit.edu	37	chr6	49754855	49754855	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcatgatgactcgcttccCtctaacatccagtttgtcta	5	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:49754855C>A	ENST00000304801.3	-	1	198	c.46G>T	c.(46-48)Ggg>Tgg	p.G16W		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	16					glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)	p.G16W(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					ACTCGCTTCCCTCTAACATCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											155	143	147					6																	49754855		2203	4300	6503	49862814	SO:0001583	missense	5232			K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.46G>T	6.37:g.49754855C>A	ENSP00000305995:p.Gly16Trp		49862814	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	37	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871374	0.72065	.	.	ENSG00000170950	ENST00000304801	D	0.93659	-3.26	4.9	4.9	0.64082	Phosphoglycerate kinase, N-terminal (1);	0.107770	0.64402	D	0.000007	D	0.98264	0.9425	H	0.99347	4.525	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.99305	1.0902	10	0.87932	D	0	-3.1132	16.3743	0.83379	0.0:1.0:0.0:0.0	.	16	P07205	PGK2_HUMAN	W	16	ENSP00000305995:G16W	ENSP00000305995:G16W	G	-	1	0	PGK2	49862814	1.000000	0.71417	0.963000	0.40424	0.980000	0.70556	5.167000	0.64972	2.645000	0.89757	0.650000	0.86243	GGG		0.408	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			A	49754855	C	A	49754855	3	1	47	1	0	0	0	0	1	0	0	0	11822	681	24	2	1211	2	PGK2	6	49754855	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1142	49754855	121360212	829	5226										
TFAP2D	83741	broad.mit.edu	37	chr6	50686805	50686805	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtttcttttattaagggCtctgtggaggcccagtgtgg	13	7	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:50686805C>T	ENST00000008391.3	+	3	768	c.540C>T	c.(538-540)ggC>ggT	p.G180G	TFAP2D_ENST00000492804.1_3'UTR	NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.G180G(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					TTATTAAGGGCTCTGTGGAGG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	6											108	104	105					6																	50686805		2203	4300	6503	50794764	SO:0001819	synonymous_variant	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.540C>T	6.37:g.50686805C>T			50794764		Silent	SNP	ENST00000008391.3	37	CCDS4933.1																																																																																				0.403	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50686805	C	T	50686805	2	4	47	1	0	0	0	0	0	0	0	1	15829	784	28	3		3	TFAP2D	6	50686805	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	931950	50686805	120428262	830	5227										
GSTA5	221357	broad.mit.edu	37	chr6	52698975	52698975	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagtagcgattttttattttCtctttgaccaaggcagtctt	7	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:52698975C>A	ENST00000370989.2	-	4	407	c.378G>T	c.(376-378)gaG>gaT	p.E126D	GSTA5_ENST00000284562.2_Missense_Mutation_p.E126D|GSTA5_ENST00000475052.1_5'UTR			Q7RTV2	GSTA5_HUMAN	glutathione S-transferase alpha 5	126	GST C-terminal.				glutathione metabolic process (GO:0006749)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)	p.E126D(1)		endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Lung NSC(77;0.0912)				Glutathione(DB00143)	TTTTTATTTTCTCTTTGACCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											270	261	264					6																	52698975		2203	4300	6503	52806934	SO:0001583	missense	221357			BK000212	CCDS4946.1	6p12.2	2012-06-21	2008-11-26		ENSG00000182793	ENSG00000182793	2.5.1.18	"Glutathione S-transferases / Soluble"	19662	protein-coding gene	gene with protein product		607605	"glutathione S-transferase A5"			12042665	Standard	NM_153699		Approved		uc003pba.1	Q7RTV2	OTTHUMG00000014857	ENST00000370989.2:c.378G>T	6.37:g.52698975C>A	ENSP00000360028:p.Glu126Asp		52806934	Q5SZC2	Missense_Mutation	SNP	ENST00000370989.2	37	CCDS4946.1	.	.	.	.	.	.	.	.	.	.	C	1.535	-0.543333	0.04053	.	.	ENSG00000182793	ENST00000370989;ENST00000284562	T;T	0.02050	4.48;4.48	2.58	-5.17	0.02849	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.798663	0.11638	N	0.544103	T	0.00328	0.0010	N	0.16098	0.37	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44667	-0.9313	10	0.16420	T	0.52	.	2.3079	0.04179	0.1408:0.2412:0.4177:0.2003	.	126	Q7RTV2	GSTA5_HUMAN	D	126	ENSP00000360028:E126D;ENSP00000284562:E126D	ENSP00000284562:E126D	E	-	3	2	GSTA5	52806934	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-1.385000	0.02540	-1.793000	0.01258	0.184000	0.17185	GAG		0.388	GSTA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040917.1	NM_153699		A	52698975	C	A	52698975	3	1	47	1	0	0	0	0	1	0	0	0	6855	912	32	2	302	2	GSTA5	6	52698975	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2012170	52698975	118416092	831	5228										
COL21A1	81578	broad.mit.edu	37	chr6	55923979	55923979	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacctgggggaccaggaggAccttgttctccaggataccc	12	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:55923979A>G	ENST00000244728.5	-	29	3067	c.2670T>C	c.(2668-2670)ggT>ggC	p.G890G	COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000535941.1_Silent_p.G890G|COL21A1_ENST00000370808.2_Silent_p.G256G|COL21A1_ENST00000370819.1_Silent_p.G887G	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	890	Collagen-like 7.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G890G(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			GACCAGGAGGACCTTGTTCTC	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	6											74	79	78					6																	55923979		1859	4094	5953	56031938	SO:0001819	synonymous_variant	81578			AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2670T>C	6.37:g.55923979A>G			56031938	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1																																																																																				0.423	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			G	55923979	A	G	55923979	2	3	47	1	0	0	0	0	0	0	0	1	3686	262	10	4		4	COL21A1	6	55923979	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3225004	55923979	115191088	832	5229										
DST	667	broad.mit.edu	37	chr6	56420154	56420154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagacaaacctgctttctgtTcaacatccttaaatgatttt	4	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:56420154T>C	ENST00000361203.3	-	56	14499	c.14492A>G	c.(14491-14493)gAa>gGa	p.E4831G	DST_ENST00000312431.6_3'UTR|DST_ENST00000370754.5_Missense_Mutation_p.E5011G|DST_ENST00000446842.2_Missense_Mutation_p.E4507G|DST_ENST00000370788.2_Missense_Mutation_p.E2745G|DST_ENST00000244364.6_Missense_Mutation_p.E2419G|DST_ENST00000370769.4_Missense_Mutation_p.E4833G|DST_ENST00000421834.2_Missense_Mutation_p.E2745G			Q03001	DYST_HUMAN	dystonin	4831					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.E4833G(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGCTTTCTGTTCAACATCCTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											93	93	93					6																	56420154		1857	4103	5960	56528113	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.14492A>G	6.37:g.56420154T>C	ENSP00000354508:p.Glu4831Gly		56528113	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	T	18.71	3.681540	0.68042	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.96	5.96	0.96718	.	0.000000	0.56097	D	0.000033	T	0.52158	0.1717	M	0.74881	2.28	0.27291	N	0.957838	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.995;0.989	D;D;D;P;D	0.85130	0.99;0.99;0.997;0.862;0.948	T	0.51276	-0.8726	9	0.35671	T	0.21	.	16.4311	0.83844	0.0:0.0:0.0:1.0	.	2745;4833;5011;4831;2419	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	G	2419;5011;4833;2745;4507;2745;4831	ENSP00000244364:E2419G;ENSP00000359790:E5011G;ENSP00000359805:E4833G;ENSP00000400883:E2745G;ENSP00000393645:E4507G;ENSP00000359824:E2745G;ENSP00000354508:E4831G	ENSP00000244364:E2419G	E	-	2	0	DST	56528113	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.013000	0.88655	2.277000	0.76020	0.528000	0.53228	GAA		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56420154	T	C	56420154	3	2	47	1	0	0	0	0	1	0	0	0	4794	1783	62	4	8435	4	DST	6	56420154	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	496175	56420154	114694913	833	5230										
FAM135A	57579	broad.mit.edu	37	chr6	71185209	71185209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaagaggttgttttaaatgAtgttatgatcttcaaagtaa	9	2	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:71185209A>G	ENST00000418814.2	+	6	868	c.254A>G	c.(253-255)gAt>gGt	p.D85G	FAM135A_ENST00000505769.1_Missense_Mutation_p.D85G|FAM135A_ENST00000505868.1_Missense_Mutation_p.D85G|FAM135A_ENST00000457062.2_Missense_Mutation_p.D42G|FAM135A_ENST00000361499.3_Missense_Mutation_p.D85G|FAM135A_ENST00000370479.3_Missense_Mutation_p.D42G	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	85								p.D42G(1)		breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						GTTTTAAATGATGTTATGATC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	6											42	45	44					6																	71185209		2194	4274	6468	71241930	SO:0001583	missense	57579			AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.254A>G	6.37:g.71185209A>G	ENSP00000410768:p.Asp85Gly		71241930	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.473754	0.84640	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000515323;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T;T	0.79141	-1.24;1.64;-1.24;-1.24;1.64;-1.24;-1.24	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.86096	0.5851	M	0.81942	2.565	0.50813	D	0.999893	D;D;D;D	0.89917	0.999;0.998;1.0;1.0	D;D;D;D	0.79108	0.979;0.992;0.989;0.989	D	0.88309	0.2955	10	0.72032	D	0.01	.	15.5385	0.76021	1.0:0.0:0.0:0.0	.	85;85;85;42	D6RC17;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	G	85;42;85;85;42;85;85	ENSP00000410768:D85G;ENSP00000359510:D42G;ENSP00000423785:D85G;ENSP00000422406:D85G;ENSP00000409201:D42G;ENSP00000354913:D85G;ENSP00000423307:D85G	ENSP00000194672:D85G	D	+	2	0	FAM135A	71241930	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.141000	0.66446	0.455000	0.32223	GAT		0.279	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71185209	A	G	71185209	3	3	47	1	0	0	0	0	1	0	0	0	5464	333	12	4	264	4	FAM135A	6	71185209	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	14765055	71185209	99929858	834	5231										
EEF1A1	1915	broad.mit.edu	37	chr6	74227884	74227884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taccagaacggcgatcaatcTtttccttcagctcagcaaac	6	13	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:74227884T>G	ENST00000316292.9	-	6	2124	c.1133A>C	c.(1132-1134)aAg>aCg	p.K378T	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.K378T|EEF1A1_ENST00000331523.2_Missense_Mutation_p.K378T	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	378					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)	p.K378T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GCGATCAATCTTTTCCTTCAG	0.483											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Missense(1)	large_intestine(1)	6											15	17	16					6																	74227884		2112	4236	6348	74284605	SO:0001583	missense	1915			BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1133A>C	6.37:g.74227884T>G	ENSP00000339063:p.Lys378Thr	1151	74284605	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.064723	0.76187	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.49720	0.77;0.77;0.77	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.77003	0.4067	H	0.98996	4.395	0.80722	D	1	D;D;D	0.69078	0.991;0.991;0.997	D;D;D	0.68483	0.934;0.934;0.958	D	0.86981	0.2104	10	0.87932	D	0	.	14.7177	0.69284	0.0:0.0:0.0:1.0	.	378;378;378	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	T	378;376;378;378;357	ENSP00000339063:K378T;ENSP00000339053:K378T;ENSP00000330054:K378T	ENSP00000339053:K378T	K	-	2	0	EEF1A1	74284605	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.654000	0.83653	1.929000	0.55896	0.454000	0.30748	AAG		0.483	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		G	74227884	T	G	74227884	3	3	47	1	0	0	0	0	1	0	0	0	4934	1609	56	4	263	4	EEF1A1	6	74227884	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3042675	74227884	96887183	835	5232										
COL12A1	1303	broad.mit.edu	37	chr6	75825621	75825621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttctgtcaggttgtatgCttcaagcattttaaaacctt	6	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:75825621C>T	ENST00000322507.8	-	49	7885	c.7576G>A	c.(7576-7578)Gca>Aca	p.A2526T	COL12A1_ENST00000483888.2_Missense_Mutation_p.A2526T|COL12A1_ENST00000416123.2_Missense_Mutation_p.A2526T|COL12A1_ENST00000345356.6_Missense_Mutation_p.A1362T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2526	Laminin G-like.|Nonhelical region (NC3).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.A2526T(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						AGGTTGTATGCTTCAAGCATT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											81	77	78					6																	75825621		1854	4093	5947	75882341	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.7576G>A	6.37:g.75825621C>T	ENSP00000325146:p.Ala2526Thr		75882341	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925775	0.52759	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888;ENST00000493109	T;T;T;T;T;T	0.02280	4.36;4.36;4.36;4.36;4.36;4.36	4.84	3.97	0.46021	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.059521	0.64402	D	0.000005	T	0.03520	0.0101	L	0.58810	1.83	0.37078	D	0.898857	D;D	0.61080	0.989;0.965	P;P	0.59595	0.86;0.543	T	0.40850	-0.9541	10	0.56958	D	0.05	.	10.9759	0.47465	0.1535:0.7155:0.131:0.0	.	1362;2526	Q99715-2;Q99715	.;COCA1_HUMAN	T	2526;164;2526;1362;2526;2526;80	ENSP00000325146:A2526T;ENSP00000399812:A164T;ENSP00000305147:A1362T;ENSP00000412864:A2526T;ENSP00000421216:A2526T;ENSP00000423423:A80T	ENSP00000325146:A2526T	A	-	1	0	COL12A1	75882341	1.000000	0.71417	0.991000	0.47740	0.121000	0.20230	3.853000	0.55941	1.012000	0.39366	0.655000	0.94253	GCA		0.343	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75825621	C	T	75825621	3	4	47	1	0	0	0	0	1	0	0	0	3675	797	28	3	1687	3	COL12A1	6	75825621	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1597737	75825621	95289446	836	5233										
LCA5	167691	broad.mit.edu	37	chr6	80197018	80197018	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccatcaaattagcttttttCtcttttcttgtaattaaatc	2	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:80197018C>A	ENST00000392959.1	-	9	2408	c.1797G>T	c.(1795-1797)gaG>gaT	p.E599D	LCA5_ENST00000369846.4_Missense_Mutation_p.E599D	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	599					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)	p.E599D(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TAGCTTTTTTCTCTTTTCTTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											96	97	97					6																	80197018		2203	4300	6503	80253737	SO:0001583	missense	167691				CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1797G>T	6.37:g.80197018C>A	ENSP00000376686:p.Glu599Asp		80253737	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016911	0.54576	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.38401	1.14;1.14	5.55	2.58	0.30949	.	0.119371	0.56097	D	0.000036	T	0.26159	0.0638	L	0.31664	0.95	0.32290	N	0.566438	D	0.89917	1.0	D	0.85130	0.997	T	0.19321	-1.0309	10	0.87932	D	0	-8.9685	4.3864	0.11319	0.146:0.5006:0.0:0.3534	.	599	Q86VQ0	LCA5_HUMAN	D	599	ENSP00000358861:E599D;ENSP00000376686:E599D	ENSP00000358861:E599D	E	-	3	2	LCA5	80253737	1.000000	0.71417	0.999000	0.59377	0.910000	0.53928	0.577000	0.23758	0.217000	0.20800	0.585000	0.79938	GAG		0.358	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80197018	C	A	80197018	3	1	47	1	0	0	0	0	1	0	0	0	8678	912	32	2	300	2	LCA5	6	80197018	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4371397	80197018	90918049	837	5234										
LCA5	167691	broad.mit.edu	37	chr6	80203459	80203459	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtactcagttcaaggtttttCgatagctcctatatgtataa	7	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:80203459C>T	ENST00000392959.1	-	5	1340	c.729G>A	c.(727-729)tcG>tcA	p.S243S	LCA5_ENST00000467898.3_Silent_p.S243S|LCA5_ENST00000369846.4_Silent_p.S243S	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	243					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)	p.S243S(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		CAAGGTTTTTCGATAGCTCCT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	6											90	82	85					6																	80203459		2203	4300	6503	80260178	SO:0001819	synonymous_variant	167691				CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.729G>A	6.37:g.80203459C>T			80260178	E1P542|Q9BWX7	Silent	SNP	ENST00000392959.1	37	CCDS4990.1																																																																																				0.343	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		T	80203459	C	T	80203459	2	4	47	1	0	0	0	0	0	0	0	1	8678	871	31	1		1	LCA5	6	80203459	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6441	80203459	90911608	838	5235										
LCA5	167691	broad.mit.edu	37	chr6	80222980	80222980	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactctgctgaaactagtttCtttgccaaatcatctcgttc	5	11	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:80222980C>A	ENST00000392959.1	-	4	1280	c.669G>T	c.(667-669)aaG>aaT	p.K223N	LCA5_ENST00000467898.3_Missense_Mutation_p.K223N|LCA5_ENST00000369846.4_Missense_Mutation_p.K223N	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	223					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)	p.K223N(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		AAACTAGTTTCTTTGCCAAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											144	139	140					6																	80222980		2203	4300	6503	80279699	SO:0001583	missense	167691				CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.669G>T	6.37:g.80222980C>A	ENSP00000376686:p.Lys223Asn		80279699	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822341	0.71028	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.77620	-1.11;-1.11	6.07	6.07	0.98685	.	0.131898	0.51477	D	0.000088	D	0.82751	0.5105	M	0.63843	1.955	0.43330	D	0.995368	D;D	0.76494	0.963;0.999	P;D	0.71656	0.798;0.974	D	0.84027	0.0357	10	0.72032	D	0.01	-19.572	12.8913	0.58073	0.0:0.9266:0.0:0.0734	.	223;223	B4DRL2;Q86VQ0	.;LCA5_HUMAN	N	223	ENSP00000358861:K223N;ENSP00000376686:K223N	ENSP00000358861:K223N	K	-	3	2	LCA5	80279699	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.558000	0.45879	2.885000	0.99019	0.655000	0.94253	AAG		0.353	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80222980	C	A	80222980	3	1	47	1	0	0	0	0	1	0	0	0	8678	912	32	2	1448	2	LCA5	6	80222980	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	19521	80222980	90892087	839	5236										
ELOVL4	6785	broad.mit.edu	37	chr6	80629172	80629172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggtatcgtttccaccaaaGatatttctgaatccatgggc	8	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:80629172G>T	ENST00000369816.4	-	5	934	c.634C>A	c.(634-636)Ctt>Att	p.L212I		NM_022726.3	NP_073563.1	Q9GZR5	ELOV4_HUMAN	ELOVL fatty acid elongase 4	212					cellular lipid metabolic process (GO:0044255)|detection of visible light (GO:0009584)|fatty acid biosynthetic process (GO:0006633)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)	G-protein coupled photoreceptor activity (GO:0008020)|transferase activity (GO:0016740)	p.L212I(1)		central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)	TTCCACCAAAGATATTTCTGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	93	95					6																	80629172		2203	4299	6502	80685891	SO:0001583	missense	6785			AF277094	CCDS4992.1	6q14	2013-01-08	2011-05-25		ENSG00000118402	ENSG00000118402			14415	protein-coding gene	gene with protein product	"cancer/testis antigen 118"	605512	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"	STGD2, STGD3		11138005	Standard	NM_022726		Approved	CT118	uc003pja.4	Q9GZR5	OTTHUMG00000015087	ENST00000369816.4:c.634C>A	6.37:g.80629172G>T	ENSP00000358831:p.Leu212Ile		80685891	B2R6B5|Q5TCS2|Q86YJ1|Q9H139	Missense_Mutation	SNP	ENST00000369816.4	37	CCDS4992.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.338728	0.60963	.	.	ENSG00000118402	ENST00000369816	T	0.21361	2.01	5.81	3.71	0.42584	.	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	M	0.63169	1.94	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	T	0.03887	-1.0995	10	0.54805	T	0.06	-19.8465	10.065	0.42297	0.2356:0.0:0.7644:0.0	.	212	Q9GZR5	ELOV4_HUMAN	I	212	ENSP00000358831:L212I	ENSP00000358831:L212I	L	-	1	0	ELOVL4	80685891	1.000000	0.71417	0.996000	0.52242	0.476000	0.33039	4.154000	0.58125	1.474000	0.48178	0.650000	0.86243	CTT		0.338	ELOVL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041315.1			T	80629172	G	T	80629172	3	4	47	1	0	0	0	0	1	0	0	0	5089	942	33	2	318	2	ELOVL4	6	80629172	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	406192	80629172	90485895	840	5237										
IBTK	25998	broad.mit.edu	37	chr6	82921222	82921222	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctaccaagtctagcacaaaGaacacatttatgacaaggaa	6	10	1	2	rs527414843		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:82921222G>T	ENST00000306270.7	-	14	2908	c.2359C>A	c.(2359-2361)Ctt>Att	p.L787I	IBTK_ENST00000503631.1_Missense_Mutation_p.L586I|RNU6-130P_ENST00000411112.1_RNA|IBTK_ENST00000510291.1_Missense_Mutation_p.L787I	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	787	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.L787I(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CTAGCACAAAGAACACATTTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	81	82					6																	82921222		2203	4300	6503	82977941	SO:0001583	missense	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2359C>A	6.37:g.82921222G>T	ENSP00000305721:p.Leu787Ile		82977941	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882665	0.72410	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	D;D;D	0.89343	-2.5;-2.5;-2.5	6.08	6.08	0.98989	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.90705	3.14	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.999	D	0.94312	0.7546	10	0.48119	T	0.1	-18.763	20.6721	0.99693	0.0:0.0:1.0:0.0	.	586;787;787;787	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	I	787;586;787	ENSP00000305721:L787I;ENSP00000422762:L586I;ENSP00000426405:L787I	ENSP00000305721:L787I	L	-	1	0	IBTK	82977941	1.000000	0.71417	1.000000	0.80357	0.258000	0.26162	7.578000	0.82498	2.894000	0.99253	0.591000	0.81541	CTT		0.338	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		T	82921222	G	T	82921222	3	4	47	1	0	0	0	0	1	0	0	0	7497	942	33	2	1766	2	IBTK	6	82921222	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2292050	82921222	88193845	841	5238										
CYB5R4	51167	broad.mit.edu	37	chr6	84644378	84644378	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actcatgatacgaggcttttCtgtttgatgctgccaccaag	9	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:84644378C>A	ENST00000369681.5	+	11	1019	c.879C>A	c.(877-879)ttC>ttA	p.F293L	CYB5R4_ENST00000479164.1_3'UTR	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	293	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)	p.F293L(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		CGAGGCTTTTCTGTTTGATGC	0.393																																					Esophageal Squamous(86;1289 1332 25971 40349 52675)											1	Substitution - Missense(1)	large_intestine(1)	6											128	124	126					6																	84644378		2203	4300	6503	84701097	SO:0001583	missense	51167			AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"NADPH cytochrome B5 oxidoreductase"	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.879C>A	6.37:g.84644378C>A	ENSP00000358695:p.Phe293Leu		84701097	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	C	18.31	3.594843	0.66219	.	.	ENSG00000065615	ENST00000369681	D	0.93659	-3.26	5.76	5.76	0.90799	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);Oxidoreductase, FAD-binding domain (1);	0.134564	0.64402	N	0.000001	D	0.85805	0.5782	L	0.44542	1.39	0.80722	D	1	B	0.12013	0.005	B	0.26517	0.07	T	0.80379	-0.1407	10	0.22109	T	0.4	.	12.8691	0.57955	0.0:0.925:0.0:0.075	.	293	Q7L1T6	NB5R4_HUMAN	L	293	ENSP00000358695:F293L	ENSP00000358695:F293L	F	+	3	2	CYB5R4	84701097	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	2.601000	0.46249	2.727000	0.93392	0.650000	0.86243	TTC		0.393	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230		A	84644378	C	A	84644378	3	1	47	1	0	0	0	0	1	0	0	0	4135	912	32	2	921	2	CYB5R4	6	84644378	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1723156	84644378	86470689	842	5239										
SYNCRIP	10492	broad.mit.edu	37	chr6	86324652	86324652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggttgtacccatcagctttgCgctttcctcctacatttcca	6	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:86324652C>T	ENST00000369622.3	-	11	2194	c.1694G>A	c.(1693-1695)cGc>cAc	p.R565H	SYNCRIP_ENST00000355238.6_Intron|RP11-321N4.5_ENST00000503906.1_Intron	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	565					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R565H(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		ATCAGCTTTGCGCTTTCCTCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	6											153	151	152					6																	86324652		2203	4300	6503	86381371	SO:0001583	missense	10492			AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.1694G>A	6.37:g.86324652C>T	ENSP00000358635:p.Arg565His		86381371	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	37	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.157159	0.57259	.	.	ENSG00000135316	ENST00000369622	T	0.32023	1.47	5.19	5.19	0.71726	.	0.407810	0.29198	N	0.012859	T	0.49406	0.1555	M	0.72118	2.19	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.74674	0.964;0.984	T	0.53063	-0.8491	10	0.66056	D	0.02	.	18.7087	0.91648	0.0:1.0:0.0:0.0	.	565;530	O60506;O60506-2	HNRPQ_HUMAN;.	H	565	ENSP00000358635:R565H	ENSP00000358635:R565H	R	-	2	0	SYNCRIP	86381371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.817000	0.86213	2.419000	0.82065	0.563000	0.77884	CGC		0.602	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		T	86324652	C	T	86324652	3	4	47	1	0	0	0	0	1	0	0	0	15483	768	27	1	227	1	SYNCRIP	6	86324652	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1680274	86324652	84790415	843	5240										
ZNF292	23036	broad.mit.edu	37	chr6	87966154	87966154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttcaatccagtgaagtagCtgtgtccattaaggtgtctc	9	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:87966154C>T	ENST00000369577.3	+	8	2850	c.2807C>T	c.(2806-2808)gCt>gTt	p.A936V	ZNF292_ENST00000339907.4_Missense_Mutation_p.A931V	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	936						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A791V(1)|p.A936V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AGTGAAGTAGCTGTGTCCATT	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	6											78	74	76					6																	87966154		1907	4125	6032	88022873	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.2807C>T	6.37:g.87966154C>T	ENSP00000358590:p.Ala936Val		88022873	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	C	8.621	0.891490	0.17613	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07216	3.21;3.22	5.77	4.87	0.63330	.	0.594677	0.18507	N	0.139176	T	0.02119	0.0066	N	0.19112	0.55	0.32791	N	0.501197	B	0.09022	0.002	B	0.06405	0.002	T	0.44772	-0.9306	10	0.25751	T	0.34	.	10.4682	0.44620	0.1346:0.796:0.0:0.0694	.	936	O60281	ZN292_HUMAN	V	936;931	ENSP00000358590:A936V;ENSP00000342847:A931V	ENSP00000342847:A931V	A	+	2	0	ZNF292	88022873	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.312000	0.33574	2.729000	0.93468	0.591000	0.81541	GCT		0.463	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		T	87966154	C	T	87966154	3	4	47	1	0	0	0	0	1	0	0	0	17865	797	28	3	2837	3	ZNF292	6	87966154	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1641502	87966154	83148913	844	5241										
C6orf165	154313	broad.mit.edu	37	chr6	88123615	88123615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgatatgaattatacgaatCgaggtaatgtatactaccta	7	6	0	1	rs370690253		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:88123615C>T	ENST00000507897.1	+	4	363	c.280C>T	c.(280-282)Cga>Tga	p.R94*	C6ORF165_ENST00000369562.4_Nonsense_Mutation_p.R94*			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	94								p.R94*(2)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		TTATACGAATCGAGGTAATGT	0.313																																																2	Substitution - Nonsense(2)	large_intestine(2)	6						C	stop/ARG	0,4404		0,0,2202	69	66	67		280	3.5	1	6		67	1,8591	1.2+/-3.3	0,1,4295	no	stop-gained	C6orf165	NM_001031743.2		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		94/623	88123615	1,12995	2202	4296	6498	88180334	SO:0001587	stop_gained	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.280C>T	6.37:g.88123615C>T	ENSP00000426769:p.Arg94*		88180334	A8K969|E1P507|Q8N9U4	Nonsense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149032	0.57151	0.0	1.16E-4	ENSG00000213204	ENST00000369562;ENST00000480123	.	.	.	5.32	3.5	0.40072	.	0.068726	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2298	0.59936	0.584:0.416:0.0:0.0	.	.	.	.	X	94	.	ENSP00000358575:R94X	R	+	1	2	C6orf165	88180334	0.975000	0.34042	1.000000	0.80357	0.097000	0.18754	0.878000	0.28126	0.580000	0.29522	0.484000	0.47621	CGA		0.313	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88123615	C	T	88123615	4	4	47	1	0	0	0	0	0	1	0	0	2347	876	31	1	290	1	C6orf165	6	88123615	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	157461	88123615	82991452	845	5242										
C6orf165	154313	broad.mit.edu	37	chr6	88125438	88125438	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacatcaccgggtcctagaGtctagattaggctctgttac	10	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:88125438G>T	ENST00000507897.1	+	5	401	c.318G>T	c.(316-318)gaG>gaT	p.E106D	C6ORF165_ENST00000369562.4_Missense_Mutation_p.E106D			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	106								p.E106D(2)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GGGTCCTAGAGTCTAGATTAG	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	6											81	84	83					6																	88125438		2203	4300	6503	88182157	SO:0001583	missense	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.318G>T	6.37:g.88125438G>T	ENSP00000426769:p.Glu106Asp		88182157	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.729790	0.30684	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.21543	2.0;2.0	5.6	1.11	0.20524	.	0.112746	0.56097	D	0.000021	T	0.06872	0.0175	L	0.45581	1.43	0.34387	D	0.693736	B;B	0.13145	0.007;0.002	B;B	0.16722	0.016;0.003	T	0.09079	-1.0691	10	0.48119	T	0.1	.	6.4681	0.21993	0.3276:0.1292:0.5432:0.0	.	106;106	Q8IYR0;E1P509	CF165_HUMAN;.	D	106	ENSP00000358575:E106D;ENSP00000422494:E106D	ENSP00000358575:E106D	E	+	3	2	C6orf165	88182157	1.000000	0.71417	0.982000	0.44146	0.736000	0.42039	1.565000	0.36386	0.286000	0.22352	-0.234000	0.12200	GAG		0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88125438	G	T	88125438	3	4	47	1	0	0	0	0	1	0	0	0	2347	1020	36	2	332	2	C6orf165	6	88125438	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1823	88125438	82989629	846	5243										
RARS2	57038	broad.mit.edu	37	chr6	88240639	88240639	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttttatcatctgctgcttCtttattaacttgtacataaa	3	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:88240639C>T	ENST00000369536.5	-	9	679	c.634G>A	c.(634-636)Gaa>Aaa	p.E212K		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	212					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.E212K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		TCTGCTGCTTCTTTATTAACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											137	134	135					6																	88240639		2203	4300	6503	88297358	SO:0001583	missense	57038			AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.634G>A	6.37:g.88240639C>T	ENSP00000358549:p.Glu212Lys		88297358	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.433853	0.83776	.	.	ENSG00000146282	ENST00000369536	T	0.62364	0.03	6.02	6.02	0.97574	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.134574	0.64402	D	0.000003	T	0.53045	0.1772	L	0.41632	1.29	0.50039	D	0.999848	B	0.25235	0.121	B	0.35971	0.215	T	0.54016	-0.8356	10	0.66056	D	0.02	.	20.1358	0.98028	0.0:1.0:0.0:0.0	.	212	Q5T160	SYRM_HUMAN	K	212	ENSP00000358549:E212K	ENSP00000358549:E212K	E	-	1	0	RARS2	88297358	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.365000	0.73090	2.865000	0.98341	0.655000	0.94253	GAA		0.368	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88240639	C	T	88240639	3	4	47	1	0	0	0	0	1	0	0	0	13096	922	32	3	1150	3	RARS2	6	88240639	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	115201	88240639	82874428	847	5244										
AKIRIN2	55122	broad.mit.edu	37	chr6	88391445	88391445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgtcttctcttctgcattCgtttatactcttgttttatg	5	8	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:88391445C>T	ENST00000257787.5	-	2	796	c.272G>A	c.(271-273)cGa>cAa	p.R91Q		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	91					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)	p.R91Q(1)		large_intestine(4)	4						CTTCTGCATTCGTTTATACTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											154	124	134					6																	88391445		2203	4300	6503	88448164	SO:0001583	missense	55122			BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"chromosome 6 open reading frame 166"	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.272G>A	6.37:g.88391445C>T	ENSP00000257787:p.Arg91Gln		88448164	Q9BQB1	Missense_Mutation	SNP	ENST00000257787.5	37	CCDS5013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.837082	0.97009	.	.	ENSG00000135334	ENST00000257787	T	0.49432	0.78	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	M	0.89840	3.065	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.76911	-0.2784	10	0.72032	D	0.01	-4.4041	20.6593	0.99626	0.0:1.0:0.0:0.0	.	91	Q53H80	AKIR2_HUMAN	Q	91	ENSP00000257787:R91Q	ENSP00000257787:R91Q	R	-	2	0	AKIRIN2	88448164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.885000	0.99019	0.655000	0.94253	CGA		0.348	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064		T	88391445	C	T	88391445	3	4	47	1	0	0	0	0	1	0	0	0	462	884	31	1	355	1	AKIRIN2	6	88391445	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	150806	88391445	82723622	848	5245										
RNGTT	8732	broad.mit.edu	37	chr6	89650880	89650880	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcttggtcctaacattgtCttcagaggtaagaatcttcc	7	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:89650880C>T	ENST00000369485.4	-	2	270	c.84G>A	c.(82-84)aaG>aaA	p.K28K	RNGTT_ENST00000538899.1_Intron|RNGTT_ENST00000265607.6_Silent_p.K28K|RNGTT_ENST00000369475.3_Silent_p.K28K	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	28	TPase.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)	p.K28K(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CTAACATTGTCTTCAGAGGTA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	6											159	156	157					6																	89650880		2203	4300	6503	89707599	SO:0001819	synonymous_variant	8732			AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.84G>A	6.37:g.89650880C>T			89707599	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Silent	SNP	ENST00000369485.4	37	CCDS5017.1																																																																																				0.328	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			T	89650880	C	T	89650880	2	4	47	1	0	0	0	0	0	0	0	1	13540	912	32	3		3	RNGTT	6	89650880	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1259435	89650880	81464187	849	5246										
PNRC1	10957	broad.mit.edu	37	chr6	89793717	89793717	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accgagaacattaaaaattcGcatttgaagaaatcagcatt	6	7	1	3	rs147195455		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:89793717G>A	ENST00000336032.3	+	2	903	c.786G>A	c.(784-786)tcG>tcA	p.S262S	PNRC1_ENST00000354922.3_Silent_p.S77S|PNRC1_ENST00000369472.1_Silent_p.S77S	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.S262S(1)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		TTAAAAATTCGCATTTGAAGA	0.358										Multiple Myeloma(7;0.094)																																						1	Substitution - coding silent(1)	large_intestine(1)	6						G		1,4405	2.1+/-5.4	0,1,2202	61	68	66		786	1.8	0.2	6	dbSNP_134	66	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PNRC1	NM_006813.2		0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308		262/328	89793717	4,13002	2203	4300	6503	89850436	SO:0001819	synonymous_variant	10957			U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.786G>A	6.37:g.89793717G>A			89850436	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	37	CCDS5018.1																																																																																				0.358	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		A	89793717	G	A	89793717	2	1	47	1	0	0	0	0	0	0	0	1	12205	1074	38	1		1	PNRC1	6	89793717	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	142837	89793717	81321350	850	5247										
RRAGD	58528	broad.mit.edu	37	chr6	90088946	90088946	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatattatttacttactgaGataaagatgttcagcaaatt	6	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:90088946G>T	ENST00000369415.4	-	4	1032	c.756C>A	c.(754-756)atC>atA	p.I252I	RRAGD_ENST00000492783.1_5'UTR|RRAGD_ENST00000359203.3_Silent_p.I101I	NM_021244.4	NP_067067.1			Ras-related GTP binding D									p.I252I(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(2)	15		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)		TACTTACTGAGATAAAGATGT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	6											71	74	73					6																	90088946		2202	4300	6502	90145665	SO:0001819	synonymous_variant	58528			AF272036	CCDS5022.1	6q15-q16	2008-02-05			ENSG00000025039	ENSG00000025039			19903	protein-coding gene	gene with protein product		608268				11073942	Standard	NM_021244		Approved	DKFZP761H171, bA11D8.2.1	uc003pnd.4	Q9NQL2	OTTHUMG00000015200	ENST00000369415.4:c.756C>A	6.37:g.90088946G>T			90145665		Silent	SNP	ENST00000369415.4	37	CCDS5022.1																																																																																				0.318	RRAGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041484.1	NM_021244		T	90088946	G	T	90088946	2	4	47	1	0	0	0	0	0	0	0	1	13712	932	33	2		2	RRAGD	6	90088946	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	295229	90088946	81026121	851	5248										
CASP8AP2	9994	broad.mit.edu	37	chr6	90576717	90576717	+	RNA	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcatgacattaaaaaaaaTtttaacatctgctttgataa	4	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:90576717T>A	ENST00000551025.1	+	0	5145									caspase 8 associated protein 2									p.N1236K(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TTAAAAAAAATTTTAACATCT	0.333																																					Colon(187;1656 2025 17045 31481 39901)											1	Substitution - Missense(1)	large_intestine(1)	6											21	22	22					6																	90576717		1796	4073	5869	90633438			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90576717T>A			90633438		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.333	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90576717	T	A	90576717	1	1	47	0	1	0	0	0	0	0	0	0	2684	1490	52	5		5	CASP8AP2	6	90576717	RNA	SNP	T	TCGA-AG-3892-01A-01W-1073-09	487771	90576717	80538350	852	5249										
EPHA7	2045	broad.mit.edu	37	chr6	94120442	94120442	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaataatggaccagcacttCttgtagtacactttgacaga	7	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:94120442C>A	ENST00000369303.4	-	3	793	c.609G>T	c.(607-609)aaG>aaT	p.K203N	EPHA7_ENST00000369297.1_Missense_Mutation_p.K203N	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	203	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.K203N(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ACCAGCACTTCTTGTAGTACA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	84	83					6																	94120442		2203	4300	6503	94177163	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.609G>T	6.37:g.94120442C>A	ENSP00000358309:p.Lys203Asn		94177163	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095423	0.76870	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.10960	2.82;2.82	5.66	5.66	0.87406	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.33990	0.0882	M	0.85197	2.74	0.58432	D	0.999997	D;D;D;D	0.89917	0.989;0.999;0.999;1.0	D;D;D;D	0.83275	0.978;0.949;0.993;0.996	T	0.16335	-1.0406	10	0.87932	D	0	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	203;203;203;203	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	N	203	ENSP00000358309:K203N;ENSP00000358303:K203N	ENSP00000358303:K203N	K	-	3	2	EPHA7	94177163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.984000	0.70548	2.826000	0.97356	0.655000	0.94253	AAG		0.433	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	94120442	C	A	94120442	3	1	47	1	0	0	0	0	1	0	0	0	5185	912	32	2	2447	2	EPHA7	6	94120442	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3543725	94120442	76994625	853	5250										
KIAA0776	23376	broad.mit.edu	37	chr6	96973207	96973207	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgattcatattgaaaataGaattggtgacattattaaat	6	4	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:96973207G>T	ENST00000369278.4	+	4	353	c.287G>T	c.(286-288)aGa>aTa	p.R96I		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	96	Required for E3 UFM1-protein ligase activity.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.R96I(1)									ATTGAAAATAGAATTGGTGAC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	109	103					6																	96973207		2202	4284	6486	97079928	SO:0001583	missense	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.287G>T	6.37:g.96973207G>T	ENSP00000358283:p.Arg96Ile		97079928	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737677	0.89573	.	.	ENSG00000014123	ENST00000369278	T	0.44881	0.91	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.51669	0.1688	L	0.61036	1.89	0.80722	D	1	D	0.67145	0.996	D	0.69142	0.962	T	0.33317	-0.9873	10	0.20046	T	0.44	-21.883	18.6914	0.91585	0.0:0.0:1.0:0.0	.	96	O94874	UFL1_HUMAN	I	96	ENSP00000358283:R96I	ENSP00000358283:R96I	R	+	2	0	KIAA0776	97079928	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.230000	0.78097	2.663000	0.90544	0.650000	0.86243	AGA		0.274	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		T	96973207	G	T	96973207	3	4	47	1	0	0	0	0	1	0	0	0	8214	942	33	2	301	2	KIAA0776	6	96973207	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2852765	96973207	74141860	854	5251										
USP45	85015	broad.mit.edu	37	chr6	99891446	99891446	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgaagaaacttacctgatGaaatcttttcaggtggagaa	9	6	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:99891446G>T	ENST00000327681.6	-	15	2600	c.2068C>A	c.(2068-2070)Cat>Aat	p.H690N	USP45_ENST00000369233.2_Missense_Mutation_p.H642N|USP45_ENST00000539675.1_5'UTR|USP45_ENST00000500704.2_Missense_Mutation_p.H690N|USP45_ENST00000392738.2_Missense_Mutation_p.H370N	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	690	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.H690N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTACCTGATGAAATCTTTTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											52	52	52					6																	99891446		2203	4300	6503	99998167	SO:0001583	missense	85015			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.2068C>A	6.37:g.99891446G>T	ENSP00000333376:p.His690Asn		99998167	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.512754	0.64522	.	.	ENSG00000123552	ENST00000392738;ENST00000500704;ENST00000327681;ENST00000369233	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	5.69	4.82	0.62117	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.173945	0.51477	D	0.000097	T	0.26340	0.0643	L	0.42632	1.34	0.80722	D	1	D;D	0.63046	0.992;0.985	D;P	0.63703	0.917;0.795	T	0.03112	-1.1071	10	0.46703	T	0.11	.	10.7149	0.46006	0.1452:0.0:0.8548:0.0	.	690;370	Q70EL2;Q70EL2-3	UBP45_HUMAN;.	N	370;690;690;642	ENSP00000376495:H370N;ENSP00000424372:H690N;ENSP00000333376:H690N;ENSP00000358236:H642N	ENSP00000333376:H690N	H	-	1	0	USP45	99998167	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	6.444000	0.73452	1.413000	0.46997	0.563000	0.77884	CAT		0.343	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		T	99891446	G	T	99891446	3	4	47	1	0	0	0	0	1	0	0	0	17116	1290	45	2	392	2	USP45	6	99891446	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2918239	99891446	71223621	855	5252										
GRIK2	2898	broad.mit.edu	37	chr6	101847237	101847237	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttactgtggattggataTtctcaaggaaccacacatgt	9	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:101847237T>G	ENST00000421544.1	+	1	574	c.84T>G	c.(82-84)taT>taG	p.Y28*	GRIK2_ENST00000369138.1_Nonsense_Mutation_p.Y28*|GRIK2_ENST00000358361.3_Nonsense_Mutation_p.Y28*|GRIK2_ENST00000318991.6_Nonsense_Mutation_p.Y28*|GRIK2_ENST00000413795.1_Nonsense_Mutation_p.Y28*|GRIK2_ENST00000369137.3_Nonsense_Mutation_p.Y28*	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	28					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.Y28*(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGATTGGATATTCTCAAGGAA	0.468																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											167	153	158					6																	101847237		2203	4300	6503	101953958	SO:0001587	stop_gained	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.84T>G	6.37:g.101847237T>G	ENSP00000397026:p.Tyr28*		101953958	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Nonsense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	T	43	9.890063	0.99289	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289	.	.	.	5.32	4.17	0.49024	.	0.083622	0.48286	D	0.000193	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.97	0.47434	0.0:0.0727:0.0:0.9273	.	.	.	.	X	28	.	ENSP00000313276:Y28X	Y	+	3	2	GRIK2	101953958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.422000	0.52749	1.050000	0.40346	0.533000	0.62120	TAT		0.468	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	101847237	T	G	101847237	4	3	47	1	0	0	0	0	0	1	0	0	6795	1500	52	4	86	4	GRIK2	6	101847237	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1955791	101847237	69267830	856	5253										
GRIK2	2898	broad.mit.edu	37	chr6	102503400	102503400	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggcttggtgctttcagtttTtgtggcagtgggagaatttt	14	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:102503400T>G	ENST00000421544.1	+	15	2997	c.2507T>G	c.(2506-2508)tTt>tGt	p.F836C	GRIK2_ENST00000369138.1_Missense_Mutation_p.F836C|GRIK2_ENST00000369134.4_Missense_Mutation_p.F787C|GRIK2_ENST00000318991.6_Missense_Mutation_p.F836C|GRIK2_ENST00000413795.1_Missense_Mutation_p.F836C|GRIK2_ENST00000369137.3_Missense_Mutation_p.F760C	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	836					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.F836C(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CTTTCAGTTTTTGTGGCAGTG	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	6											94	107	102					6																	102503400		2203	4300	6503	102610093	SO:0001583	missense	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2507T>G	6.37:g.102503400T>G	ENSP00000397026:p.Phe836Cys		102610093	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.249142	0.80024	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.13538	2.68;2.63;2.58;2.89;2.63;2.68	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.21674	0.0522	L	0.52759	1.655	0.58432	D	0.999996	D;D;D	0.65815	0.995;0.992;0.995	D;P;D	0.63703	0.917;0.765;0.917	T	0.00800	-1.1561	10	0.87932	D	0	.	15.9826	0.80125	0.0:0.0:0.0:1.0	.	836;836;836	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	C	836;836;836;760;836;787;611	ENSP00000397026:F836C;ENSP00000405596:F836C;ENSP00000358134:F836C;ENSP00000358133:F760C;ENSP00000313276:F836C;ENSP00000358130:F787C	ENSP00000313276:F836C	F	+	2	0	GRIK2	102610093	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.040000	0.89188	2.176000	0.68965	0.477000	0.44152	TTT		0.408	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102503400	T	G	102503400	3	3	47	1	0	0	0	0	1	0	0	0	6795	1841	64	4	2565	4	GRIK2	6	102503400	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	656163	102503400	68611667	857	5254										
GRIK2	2898	broad.mit.edu	37	chr6	102516368	102516368	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacgacagaaggttgccaggTaaagaaaccatggcataaag	11	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:102516368T>C	ENST00000421544.1	+	16	3199	c.2709T>C	c.(2707-2709)ggT>ggC	p.G903G	GRIK2_ENST00000369138.1_3'UTR|GRIK2_ENST00000369134.4_Silent_p.G854G|GRIK2_ENST00000413795.1_3'UTR|GRIK2_ENST00000369137.3_Silent_p.G827G	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	903					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.G903G(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGTTGCCAGGTAAAGAAACCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	6											79	71	73					6																	102516368		2203	4300	6503	102623061	SO:0001819	synonymous_variant	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2709T>C	6.37:g.102516368T>C			102623061	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																				0.433	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			C	102516368	T	C	102516368	2	2	47	1	0	0	0	0	0	0	0	1	6795	1625	57	4		4	GRIK2	6	102516368	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	12968	102516368	68598699	858	5255										
BVES	11149	broad.mit.edu	37	chr6	105564596	105564596	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttatcatttaaggtgggatCattcaatgagtagagcttat	9	4	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:105564596C>A	ENST00000314641.5	-	6	1012	c.796G>T	c.(796-798)Gat>Tat	p.D266Y	BVES_ENST00000336775.5_Missense_Mutation_p.D266Y|BVES_ENST00000446408.2_Missense_Mutation_p.D266Y	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	266					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)	p.D266Y(1)		NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				AAGGTGGGATCATTCAATGAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	68	69					6																	105564596		2202	4296	6498	105671289	SO:0001583	missense	11149			AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.796G>T	6.37:g.105564596C>A	ENSP00000313172:p.Asp266Tyr		105671289	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	37	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600182	0.87055	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.37752	1.18;1.18;1.18	5.55	5.55	0.83447	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.55800	0.1943	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.57929	-0.7726	10	0.87932	D	0	-33.8687	19.8623	0.96787	0.0:1.0:0.0:0.0	.	266	Q8NE79	POPD1_HUMAN	Y	266	ENSP00000313172:D266Y;ENSP00000337259:D266Y;ENSP00000397310:D266Y	ENSP00000313172:D266Y	D	-	1	0	BVES	105671289	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.776000	0.85560	2.769000	0.95229	0.650000	0.86243	GAT		0.279	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		A	105564596	C	A	105564596	3	1	47	1	0	0	0	0	1	0	0	0	1578	826	29	2	298	2	BVES	6	105564596	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3048228	105564596	65550471	859	5256										
BVES	11149	broad.mit.edu	37	chr6	105581444	105581444	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaatgggctggactctgtAtaattcattttgaaaattcc	7	8	3	1	rs144286946	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:105581444A>C	ENST00000314641.5	-	2	225	c.9T>G	c.(7-9)taT>taG	p.Y3*	BVES-AS1_ENST00000580511.1_RNA|BVES_ENST00000336775.5_Nonsense_Mutation_p.Y3*|BVES_ENST00000446408.2_Nonsense_Mutation_p.Y3*	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	3					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)	p.Y3*(1)		NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TGGACTCTGTATAATTCATTT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											97	100	99					6																	105581444		2203	4300	6503	105688137	SO:0001587	stop_gained	11149			AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.9T>G	6.37:g.105581444A>C	ENSP00000313172:p.Tyr3*		105688137	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Nonsense_Mutation	SNP	ENST00000314641.5	37	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.866546	0.91511	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	.	.	.	5.42	0.386	0.16254	.	1.574940	0.03092	N	0.159911	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.213	2.853	0.05563	0.4389:0.115:0.3335:0.1127	.	.	.	.	X	3	.	ENSP00000313172:Y3X	Y	-	3	2	BVES	105688137	0.029000	0.19370	0.983000	0.44433	0.867000	0.49689	-0.186000	0.09670	0.070000	0.16634	-0.371000	0.07208	TAT		0.323	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		C	105581444	A	C	105581444	4	2	47	1	0	0	0	0	0	1	0	0	1578	456	16	4	1101	4	BVES	6	105581444	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	16848	105581444	65533623	860	5257										
BEND3	57673	broad.mit.edu	37	chr6	107419781	107419781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatcagccgcctcctcttcaCgccggggacagagtctagca	11	15	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:107419781C>T	ENST00000369042.1	-	3	404	c.214G>A	c.(214-216)Gtg>Atg	p.V72M	BEND3_ENST00000429433.2_Missense_Mutation_p.V72M			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	72								p.V72M(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						CTCCTCTTCACGCCGGGGACA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											53	50	51					6																	107419781		2203	4300	6503	107526474	SO:0001583	missense	57673			AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.214G>A	6.37:g.107419781C>T	ENSP00000358038:p.Val72Met		107526474	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	37	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370054	0.61624	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	5.86	5.86	0.93980	.	0.294692	0.27331	N	0.019849	T	0.26231	0.0640	N	0.24115	0.695	0.34887	D	0.745184	P	0.35174	0.488	B	0.28465	0.09	T	0.32268	-0.9913	9	0.59425	D	0.04	-6.5316	16.9016	0.86115	0.0:1.0:0.0:0.0	.	72	Q5T5X7	BEND3_HUMAN	M	72	.	ENSP00000358038:V72M	V	-	1	0	BEND3	107526474	1.000000	0.71417	0.948000	0.38648	0.798000	0.45092	4.470000	0.60175	2.771000	0.95319	0.650000	0.86243	GTG		0.582	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		T	107419781	C	T	107419781	3	4	47	1	0	0	0	0	1	0	0	0	1400	536	19	1	2280	1	BEND3	6	107419781	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1838337	107419781	63695286	861	5258										
SCML4	256380	broad.mit.edu	37	chr6	108042026	108042026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcggggaccaccagcggtgGcagcaggaccacccccaagg	15	15	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:108042026G>A	ENST00000369020.3	-	6	1099	c.854C>T	c.(853-855)gCc>gTc	p.A285V	SCML4_ENST00000369021.3_Missense_Mutation_p.A256V|SCML4_ENST00000369022.2_Missense_Mutation_p.A227V|SCML4_ENST00000479803.1_5'UTR|SCML4_ENST00000369025.2_Missense_Mutation_p.A43V	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A256V(1)		endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		ACCAGCGGTGGCAGCAGGACC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											44	52	49					6																	108042026		2203	4300	6503	108148719	SO:0001583	missense	256380				CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.854C>T	6.37:g.108042026G>A	ENSP00000358016:p.Ala285Val		108148719	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	G	7.885	0.731165	0.15507	.	.	ENSG00000146285	ENST00000369022;ENST00000369025;ENST00000369020;ENST00000369021	T;T;T	0.48522	0.86;0.86;0.81	5.19	4.32	0.51571	.	0.379656	0.27139	N	0.020750	T	0.14056	0.0340	N	0.08118	0	0.09310	N	1	B;B;B	0.29988	0.008;0.0;0.264	B;B;B	0.28011	0.016;0.002;0.085	T	0.13980	-1.0489	10	0.37606	T	0.19	.	16.0137	0.80422	0.0:0.1344:0.8656:0.0	.	285;285;256	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	V	227;43;285;256	ENSP00000358018:A227V;ENSP00000358016:A285V;ENSP00000358017:A256V	ENSP00000358016:A285V	A	-	2	0	SCML4	108148719	0.820000	0.29190	0.002000	0.10522	0.016000	0.09150	3.093000	0.50217	1.409000	0.46915	0.650000	0.86243	GCC		0.647	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		A	108042026	G	A	108042026	3	1	47	1	0	0	0	0	1	0	0	0	13948	1203	42	3	402	3	SCML4	6	108042026	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	622245	108042026	63073041	862	5259										
NR2E1	7101	broad.mit.edu	37	chr6	108502797	108502797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagtttccggaatgctgccGccattgcagcccttcaagat	10	12	1	1	rs200730208		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:108502797G>A	ENST00000368986.4	+	8	1645	c.937G>A	c.(937-939)Gcc>Acc	p.A313T	NR2E1_ENST00000368983.3_Missense_Mutation_p.A350T	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	313	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.A313T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		GAATGCTGCCGCCATTGCAGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											132	121	124					6																	108502797		2203	4300	6503	108609490	SO:0001583	missense	7101			Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.937G>A	6.37:g.108502797G>A	ENSP00000357982:p.Ala313Thr		108609490	Q6ZMP8	Missense_Mutation	SNP	ENST00000368986.4	37	CCDS5063.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970708	0.53614	.	.	ENSG00000112333	ENST00000368986;ENST00000368983	D;D	0.96885	-4.16;-4.16	5.97	5.97	0.96955	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.87771	0.6261	N	0.17379	0.485	0.80722	D	1	P	0.45634	0.863	B	0.32393	0.145	D	0.88241	0.2910	10	0.25751	T	0.34	.	20.4062	0.99009	0.0:0.0:1.0:0.0	.	313	Q9Y466	NR2E1_HUMAN	T	313;350	ENSP00000357982:A313T;ENSP00000357979:A350T	ENSP00000357979:A350T	A	+	1	0	NR2E1	108609490	1.000000	0.71417	0.972000	0.41901	0.787000	0.44495	9.404000	0.97306	2.831000	0.97527	0.655000	0.94253	GCC		0.458	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108502797	G	A	108502797	3	1	47	1	0	0	0	0	1	0	0	0	10656	1087	38	1	967	1	NR2E1	6	108502797	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	460771	108502797	62612270	863	5260										
CDC40	51362	broad.mit.edu	37	chr6	110533452	110533452	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcttcccaaaaaacaaattCatgtgtggtctggacacaca	6	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:110533452C>A	ENST00000368932.1	+	8	945	c.844C>A	c.(844-846)Cat>Aat	p.H282N	CDC40_ENST00000307731.1_Missense_Mutation_p.H282N|CDC40_ENST00000368930.1_Missense_Mutation_p.H282N			O60508	PRP17_HUMAN	cell division cycle 40	282					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.H282N(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		AAAACAAATTCATGTGTGGTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	106	109					6																	110533452		2203	4300	6503	110640145	SO:0001583	missense	51362			AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.844C>A	6.37:g.110533452C>A	ENSP00000357928:p.His282Asn		110640145	B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	37	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974266	0.92919	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.043715	0.85682	D	0.000000	T	0.67211	0.2869	L	0.46947	1.48	0.80722	D	1	D	0.67145	0.996	D	0.74674	0.984	T	0.67304	-0.5704	10	0.62326	D	0.03	-18.6193	20.1295	0.97995	0.0:1.0:0.0:0.0	.	282	O60508	PRP17_HUMAN	N	282	ENSP00000357928:H282N;ENSP00000357929:H282N;ENSP00000357926:H282N;ENSP00000304370:H282N	ENSP00000304370:H282N	H	+	1	0	CDC40	110640145	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.398000	0.79919	2.758000	0.94735	0.591000	0.81541	CAT		0.398	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		A	110533452	C	A	110533452	3	1	47	1	0	0	0	0	1	0	0	0	3076	826	29	2	870	2	CDC40	6	110533452	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2030655	110533452	60581615	864	5261										
SLC22A16	85413	broad.mit.edu	37	chr6	110763633	110763633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtggggctattactaacagGaccttgtaggtccagtgata	12	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:110763633G>A	ENST00000368919.3	-	4	1063	c.997C>T	c.(997-999)Cct>Tct	p.P333S	SLC22A16_ENST00000439654.1_Missense_Mutation_p.P333S|SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000330550.4_Missense_Mutation_p.P299S|RN7SL617P_ENST00000485298.2_RNA	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	333					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)	p.P333S(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	TTACTAACAGGACCTTGTAGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	108	109					6																	110763633		2203	4300	6503	110870326	SO:0001583	missense	85413				CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.997C>T	6.37:g.110763633G>A	ENSP00000357915:p.Pro333Ser		110870326	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	G	4.550	0.102180	0.08731	.	.	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	4.78	-2.61	0.06171	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.683660	0.02710	N	0.112756	T	0.19685	0.0473	N	0.11064	0.09	0.09310	N	1	B;B	0.18461	0.028;0.023	B;B	0.22152	0.038;0.014	T	0.06625	-1.0816	10	0.10377	T	0.69	.	1.1907	0.01864	0.2314:0.1057:0.3484:0.3145	.	333;299	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	S	333;250;299;333;163;290	ENSP00000357915:P333S;ENSP00000395642:P250S;ENSP00000328583:P299S;ENSP00000408799:P333S;ENSP00000409306:P163S;ENSP00000416310:P290S	ENSP00000328583:P299S	P	-	1	0	SLC22A16	110870326	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.267000	0.18552	-0.144000	0.11314	0.655000	0.94253	CCT		0.413	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		A	110763633	G	A	110763633	3	1	47	1	0	0	0	0	1	0	0	0	14484	1174	41	3	756	3	SLC22A16	6	110763633	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	230181	110763633	60351434	865	5262										
RFPL4B	442247	broad.mit.edu	37	chr6	112671544	112671544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccgtgtgggaattttcctgGatgctgacttagaagaaatc	12	7	0	3	rs148347745		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:112671544G>T	ENST00000441065.2	+	3	946	c.634G>T	c.(634-636)Gat>Tat	p.D212Y	RP11-506B6.6_ENST00000585611.1_RNA|RP11-506B6.6_ENST00000590673.1_RNA|RP11-506B6.6_ENST00000587816.1_RNA	NM_001013734.2	NP_001013756.2	Q6ZWI9	RFPLB_HUMAN	ret finger protein-like 4B	212	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.D212Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	14		all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209)		all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244)		AATTTTCCTGGATGCTGACTT	0.453													G|||	1	0.000199681	8e-04	0	5008	,	,		20614	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	TYR/ASP	3,4403	6.2+/-15.9	0,3,2200	70	66	67		634	3.6	0	6	dbSNP_134	67	0,8600		0,0,4300	no	missense	RFPL4B	NM_001013734.2	160	0,3,6500	TT,TG,GG		0.0,0.0681,0.0231	probably-damaging	212/264	112671544	3,13003	2203	4300	6503	112778237	SO:0001583	missense	442247			AK122906	CCDS34515.1	6q21	2007-04-24			ENSG00000251258	ENSG00000251258		"RING-type (C3HC4) zinc fingers"	33264	protein-coding gene	gene with protein product							Standard	NM_001013734		Approved	RNF211	uc003pvx.1	Q6ZWI9	OTTHUMG00000015390	ENST00000441065.2:c.634G>T	6.37:g.112671544G>T	ENSP00000423391:p.Asp212Tyr		112778237	A2RU91	Missense_Mutation	SNP	ENST00000441065.2	37	CCDS34515.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222226	0.79464	6.81E-4	0.0	ENSG00000251258	ENST00000441065	D	0.81499	-1.5	4.48	3.59	0.41128	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.36002	N	0.002847	D	0.90789	0.7108	H	0.96576	3.845	0.31926	N	0.612869	D	0.89917	1.0	D	0.87578	0.998	D	0.90421	0.4417	10	0.87932	D	0	.	12.7351	0.57218	0.0:0.1669:0.8331:0.0	.	212	Q6ZWI9	RFPLB_HUMAN	Y	212	ENSP00000423391:D212Y	ENSP00000423391:D212Y	D	+	1	0	RFPL4B	112778237	1.000000	0.71417	0.006000	0.13384	0.609000	0.37215	5.263000	0.65507	1.453000	0.47775	0.655000	0.94253	GAT		0.453	RFPL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041885.2	NM_001013734		T	112671544	G	T	112671544	3	4	47	1	0	0	0	0	1	0	0	0	13293	1174	41	2	636	2	RFPL4B	6	112671544	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1907911	112671544	58443523	866	5263										
FRK	2444	broad.mit.edu	37	chr6	116289807	116289807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgtagtggctcacaaattCgttcagtgttgaaaagattc	11	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:116289807C>T	ENST00000606080.1	-	3	1008	c.562G>A	c.(562-564)Gaa>Aaa	p.E188K	FRK_ENST00000538210.1_Missense_Mutation_p.E46K	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	188	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.E188K(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	CTCACAAATTCGTTCAGTGTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											164	154	157					6																	116289807		2203	4300	6503	116396500	SO:0001583	missense	2444			U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.562G>A	6.37:g.116289807C>T	ENSP00000476145:p.Glu188Lys		116396500	B4DY49|Q13128|Q9NTR5	Missense_Mutation	SNP	ENST00000606080.1	37	CCDS5103.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398374	0.25205	.	.	ENSG00000111816	ENST00000368626;ENST00000538210	T;T	0.30182	1.54;1.54	5.88	4.01	0.46588	SH2 motif (5);	0.186083	0.36101	N	0.002793	T	0.16428	0.0395	M	0.75884	2.315	0.49798	D	0.999821	B	0.27229	0.172	B	0.17433	0.018	T	0.07654	-1.0761	10	0.48119	T	0.1	.	7.1687	0.25706	0.1384:0.7162:0.0:0.1453	.	188	P42685	FRK_HUMAN	K	188;46	ENSP00000357615:E188K;ENSP00000443075:E46K	ENSP00000357615:E188K	E	-	1	0	FRK	116396500	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	1.662000	0.37418	1.504000	0.48704	-0.218000	0.12543	GAA		0.403	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		T	116289807	C	T	116289807	3	4	47	1	0	0	0	0	1	0	0	0	6067	893	31	1	979	1	FRK	6	116289807	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3618263	116289807	54825260	867	5264										
RFX6	222546	broad.mit.edu	37	chr6	117240431	117240431	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttgtatcttctctgaaacGacaaacatctttcttacatc	3	10	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:117240431G>A	ENST00000332958.2	+	11	1170	c.1154G>A	c.(1153-1155)cGa>cAa	p.R385Q		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	385					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)	p.R385Q(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						TCTCTGAAACGACAAACATCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											107	105	105					6																	117240431		2203	4300	6503	117347124	SO:0001583	missense	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1154G>A	6.37:g.117240431G>A	ENSP00000332208:p.Arg385Gln		117347124	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	G	36	5.765789	0.96914	.	.	ENSG00000185002	ENST00000332958	T	0.75704	-0.96	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.87022	0.6074	M	0.84082	2.675	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.87083	0.2167	10	0.87932	D	0	-14.9338	20.6721	0.99693	0.0:0.0:1.0:0.0	.	385	Q8HWS3	RFX6_HUMAN	Q	385	ENSP00000332208:R385Q	ENSP00000332208:R385Q	R	+	2	0	RFX6	117347124	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.295000	0.96095	2.894000	0.99253	0.591000	0.81541	CGA		0.388	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117240431	G	A	117240431	3	1	47	1	0	0	0	0	1	0	0	0	13304	1058	37	1	1196	1	RFX6	6	117240431	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	950624	117240431	53874636	868	5265										
RFX6	222546	broad.mit.edu	37	chr6	117245835	117245835	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccatccataaacaaggttCttttcatttgattcgaatgc	5	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:117245835C>A	ENST00000332958.2	+	15	1575	c.1559C>A	c.(1558-1560)tCt>tAt	p.S520Y		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	520					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)	p.S520Y(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AAACAAGGTTCTTTTCATTTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											131	127	128					6																	117245835		2203	4300	6503	117352528	SO:0001583	missense	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1559C>A	6.37:g.117245835C>A	ENSP00000332208:p.Ser520Tyr		117352528	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416899	0.83449	.	.	ENSG00000185002	ENST00000332958	T	0.64803	-0.12	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.79969	0.4538	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.82684	-0.0335	10	0.87932	D	0	-18.9274	19.3617	0.94442	0.0:1.0:0.0:0.0	.	520	Q8HWS3	RFX6_HUMAN	Y	520	ENSP00000332208:S520Y	ENSP00000332208:S520Y	S	+	2	0	RFX6	117352528	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.398000	0.79919	2.646000	0.89796	0.655000	0.94253	TCT		0.393	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117245835	C	A	117245835	3	1	47	1	0	0	0	0	1	0	0	0	13304	913	32	2	1617	2	RFX6	6	117245835	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5404	117245835	53869232	869	5266										
MCM9	254394	broad.mit.edu	37	chr6	119245025	119245025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctacacctggttggagacGaagacaagcctgagaggcaa	12	10	1	3	rs182397736	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:119245025G>A	ENST00000316316.6	-	3	858	c.572C>T	c.(571-573)tCg>tTg	p.S191L	MCM9_ENST00000316068.3_Missense_Mutation_p.S191L	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	191					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.S191L(2)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		GGTTGGAGACGAAGACAAGCC	0.423													G|||	3	0.000599042	0	0.0043	5008	,	,		20280	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	6											90	87	88					6																	119245025		2203	4300	6503	119286724	SO:0001583	missense	254394			BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.572C>T	6.37:g.119245025G>A	ENSP00000314505:p.Ser191Leu		119286724	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	4	0.0018315018315018315	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	G	18.93	3.727891	0.69074	.	.	ENSG00000111877	ENST00000316316;ENST00000316068	T;T	0.06142	3.74;3.34	5.55	5.55	0.83447	.	.	.	.	.	T	0.02610	0.0079	L	0.52126	1.63	0.50632	D	0.999884	B	0.26708	0.157	B	0.19391	0.025	T	0.37291	-0.9712	9	0.13108	T	0.6	.	12.0593	0.53555	0.0789:0.0:0.9211:0.0	.	191	Q9NXL9-2	.	L	191	ENSP00000314505:S191L;ENSP00000312870:S191L	ENSP00000312870:S191L	S	-	2	0	MCM9	119286724	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.821000	0.69257	2.607000	0.88179	0.563000	0.77884	TCG		0.423	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255		A	119245025	G	A	119245025	3	1	47	1	0	0	0	0	1	0	0	0	9424	1059	37	1	623	1	MCM9	6	119245025	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1999190	119245025	51870042	870	5267										
FAM184A	79632	broad.mit.edu	37	chr6	119301498	119301498	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaagctgtatctccagattCtgtttcagcaaggaaatcta	8	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:119301498C>A	ENST00000338891.7	-	10	2549	c.2106G>T	c.(2104-2106)caG>caT	p.Q702H	FAM184A_ENST00000368475.4_Missense_Mutation_p.Q582H|FAM184A_ENST00000352896.5_Missense_Mutation_p.Q582H|FAM184A_ENST00000521531.1_Missense_Mutation_p.Q702H|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	702						extracellular space (GO:0005615)		p.Q702H(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TCTCCAGATTCTGTTTCAGCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	58	58					6																	119301498		1859	4115	5974	119343197	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2106G>T	6.37:g.119301498C>A	ENSP00000342604:p.Gln702His		119343197	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.895953	0.72639	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	6.17	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.42832	0.1220	M	0.64997	1.995	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.83275	0.994;0.979;0.996	T	0.45011	-0.9290	10	0.87932	D	0	-8.371	9.3135	0.37919	0.0:0.7502:0.121:0.1288	.	702;582;702	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	H	702;582;582;702	ENSP00000342604:Q702H;ENSP00000326608:Q582H;ENSP00000357460:Q582H;ENSP00000430442:Q702H	ENSP00000342604:Q702H	Q	-	3	2	FAM184A	119343197	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.849000	0.39318	0.944000	0.37579	0.655000	0.94253	CAG		0.438	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119301498	C	A	119301498	3	1	47	1	0	0	0	0	1	0	0	0	5527	912	32	2	1352	2	FAM184A	6	119301498	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	56473	119301498	51813569	871	5268										
FAM184A	79632	broad.mit.edu	37	chr6	119332524	119332524	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtacttcctttaggttttCtagctcttgttgaagctgat	8	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:119332524C>A	ENST00000338891.7	-	6	2046	c.1603G>T	c.(1603-1605)Gaa>Taa	p.E535*	FAM184A_ENST00000368475.4_Nonsense_Mutation_p.E415*|FAM184A_ENST00000352896.5_Nonsense_Mutation_p.E415*|FAM184A_ENST00000521531.1_Nonsense_Mutation_p.E535*|FAM184A_ENST00000522284.1_Nonsense_Mutation_p.E415*|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	535						extracellular space (GO:0005615)		p.E535*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TTTAGGTTTTCTAGCTCTTGT	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											135	127	129					6																	119332524		1811	4069	5880	119374223	SO:0001587	stop_gained	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1603G>T	6.37:g.119332524C>A	ENSP00000342604:p.Glu535*		119374223	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Nonsense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.35|14.35	2.509561|2.509561	0.44660|0.44660	.|.	.|.	ENSG00000111879|ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284|ENST00000448815	.|.	.|.	.|.	5.1|5.1	4.23|4.23	0.50019|0.50019	.|.	0.104089|.	0.64402|.	D|.	0.000004|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.34782|.	T|.	0.22|.	-15.6655|-15.6655	13.4189|13.4189	0.60985|0.60985	0.0:0.9246:0.0:0.0754|0.0:0.9246:0.0:0.0754	.|.	.|.	.|.	.|.	X|Y	535;415;415;535;415|120	.|.	ENSP00000342604:E535X|.	E|X	-|-	1|3	0|2	FAM184A|FAM184A	119374223|119374223	1.000000|1.000000	0.71417|0.71417	0.948000|0.948000	0.38648|0.38648	0.563000|0.563000	0.35712|0.35712	6.173000|6.173000	0.71937|0.71937	1.375000|1.375000	0.46248|0.46248	0.484000|0.484000	0.47621|0.47621	GAA|TAG		0.299	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119332524	C	A	119332524	4	1	47	1	0	0	0	0	0	1	0	0	5527	922	32	2	1871	2	FAM184A	6	119332524	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	31026	119332524	51782543	872	5269										
FAM184A	79632	broad.mit.edu	37	chr6	119345888	119345888	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttctcttgtttcagcaaGaatttgttgaatttcttctt	5	6	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:119345888G>T	ENST00000338891.7	-	2	693	c.250C>A	c.(250-252)Ctt>Att	p.L84I	FAM184A_ENST00000368475.4_5'UTR|FAM184A_ENST00000352896.5_5'UTR|FAM184A_ENST00000521531.1_Missense_Mutation_p.L84I|FAM184A_ENST00000522284.1_5'UTR|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	84						extracellular space (GO:0005615)		p.L84I(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GTTTCAGCAAGAATTTGTTGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	63	65					6																	119345888		1821	4083	5904	119387587	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.250C>A	6.37:g.119345888G>T	ENSP00000342604:p.Leu84Ile		119387587	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.402508	0.42613	.	.	ENSG00000111879	ENST00000338891;ENST00000521531	T;T	0.30182	1.54;1.54	5.82	4.95	0.65309	.	0.070737	0.64402	D	0.000020	T	0.14787	0.0357	L	0.56769	1.78	0.80722	D	1	B	0.13145	0.007	B	0.17722	0.019	T	0.05146	-1.0903	10	0.24483	T	0.36	-7.598	10.5271	0.44954	0.0687:0.0:0.7981:0.1333	.	84	Q8NB25	F184A_HUMAN	I	84	ENSP00000342604:L84I;ENSP00000430442:L84I	ENSP00000342604:L84I	L	-	1	0	FAM184A	119387587	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.172000	0.42463	1.478000	0.48253	0.655000	0.94253	CTT		0.323	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119345888	G	T	119345888	3	4	47	1	0	0	0	0	1	0	0	0	5527	942	33	2	3240	2	FAM184A	6	119345888	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	13364	119345888	51769179	873	5270										
C6orf170	221322	broad.mit.edu	37	chr6	121577398	121577398	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttcatcgagaagttttttCgaaaactgggcaattatatg	8	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:121577398C>T	ENST00000398212.2	-	16	1816	c.1767G>A	c.(1765-1767)tcG>tcA	p.S589S	TBC1D32_ENST00000275159.6_Silent_p.S589S	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	589					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.S589S(1)									GAAGTTTTTTCGAAAACTGGG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	6											45	40	42					6																	121577398		1803	4080	5883	121619097	SO:0001819	synonymous_variant	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1767G>A	6.37:g.121577398C>T			121619097	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																				0.338	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121577398	C	T	121577398	2	4	47	1	0	0	0	0	0	0	0	1	2350	871	31	1		1	C6orf170	6	121577398	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2231510	121577398	49537669	874	5271										
C6orf170	221322	broad.mit.edu	37	chr6	121600356	121600356	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgccaaaataccagctatAtgaattaaagctgtctcaga	6	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:121600356A>G	ENST00000398212.2	-	15	1693	c.1644T>C	c.(1642-1644)caT>caC	p.H548H	TBC1D32_ENST00000275159.6_Silent_p.H548H	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	548					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.H548H(1)									TACCAGCTATATGAATTAAAG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	6											64	63	63					6																	121600356		1810	4080	5890	121642055	SO:0001819	synonymous_variant	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1644T>C	6.37:g.121600356A>G			121642055	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																				0.338	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121600356	A	G	121600356	2	3	47	1	0	0	0	0	0	0	0	1	2350	446	16	4		4	C6orf170	6	121600356	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	22958	121600356	49514711	875	5272										
FABP7	2173	broad.mit.edu	37	chr6	123104893	123104893	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtgatgtggttgctgttcGccactatgagaaggcataaa	13	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:123104893G>A	ENST00000368444.3	+	4	700	c.380G>A	c.(379-381)cGc>cAc	p.R127H		NM_001446.3	NP_001437.1	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	127	Fatty acid binding.				cell proliferation in forebrain (GO:0021846)|epithelial cell proliferation (GO:0050673)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|prepulse inhibition (GO:0060134)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.R127H(1)		kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|Dihomo-gamma-linolenic acid(DB00154)|Icosapent(DB00159)	GTTGCTGTTCGCCACTATGAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											167	159	162					6																	123104893		2203	4300	6503	123146592	SO:0001583	missense	2173			D88648	CCDS5127.1	6q22-q23	2013-03-01			ENSG00000164434	ENSG00000164434		"Fatty acid binding protein family"	3562	protein-coding gene	gene with protein product	"brain lipid binding protein"	602965				9375786	Standard	NM_001446		Approved	B-FABP, BLBP	uc003pzf.3	O15540	OTTHUMG00000015489	ENST00000368444.3:c.380G>A	6.37:g.123104893G>A	ENSP00000357429:p.Arg127His		123146592	B2R4L1|O14951|Q6IAU7|Q9H047	Missense_Mutation	SNP	ENST00000368444.3	37	CCDS5127.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262460	0.95368	.	.	ENSG00000164434	ENST00000368444	T	0.60171	0.21	5.4	5.4	0.78164	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.78336	0.4267	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82010	-0.0669	9	0.87932	D	0	.	19.5193	0.95179	0.0:0.0:1.0:0.0	.	127	O15540	FABP7_HUMAN	H	127	ENSP00000357429:R127H	ENSP00000357429:R127H	R	+	2	0	FABP7	123146592	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.357000	0.79456	2.689000	0.91719	0.462000	0.41574	CGC		0.403	FABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042037.1	NM_001446		A	123104893	G	A	123104893	3	1	47	1	0	0	0	0	1	0	0	0	5378	1087	38	1	394	1	FABP7	6	123104893	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1504537	123104893	48010174	876	5273										
LAMA2	3908	broad.mit.edu	37	chr6	129794399	129794399	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagatactaatcaggaggaGaatatagcaacttcgtcttc	8	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:129794399G>A	ENST00000421865.2	+	52	7390	c.7341G>A	c.(7339-7341)gaG>gaA	p.E2447E		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2447	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.E2447E(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATCAGGAGGAGAATATAGCAA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	6											71	70	70					6																	129794399		2203	4300	6503	129836092	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7341G>A	6.37:g.129794399G>A			129836092	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.348	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129794399	G	A	129794399	2	1	47	1	0	0	0	0	0	0	0	1	8628	933	33	3		3	LAMA2	6	129794399	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6689506	129794399	41320668	877	5274										
L3MBTL3	84456	broad.mit.edu	37	chr6	130389489	130389489	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctagggtataaagaagaaGaattcaattggcagacctat	9	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:130389489G>T	ENST00000529410.1	+	14	1494	c.1015G>T	c.(1015-1017)Gaa>Taa	p.E339*	L3MBTL3_ENST00000526019.1_Nonsense_Mutation_p.E314*|L3MBTL3_ENST00000533560.1_Nonsense_Mutation_p.E314*|L3MBTL3_ENST00000368136.2_Nonsense_Mutation_p.E339*|L3MBTL3_ENST00000368139.2_Nonsense_Mutation_p.E314*|L3MBTL3_ENST00000361794.2_Nonsense_Mutation_p.E339*			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	339					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.E339*(1)		cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		TAAAGAAGAAGAATTCAATTG	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											106	107	107					6																	130389489		2203	4297	6500	130431182	SO:0001587	stop_gained	84456			AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1015G>T	6.37:g.130389489G>T	ENSP00000431962:p.Glu339*		130431182	Q4VXE1|Q5VUM9|Q6P9B5	Nonsense_Mutation	SNP	ENST00000529410.1	37	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	G	37	6.464700	0.97590	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	19.7959	0.96481	0.0:0.0:1.0:0.0	.	.	.	.	X	339;314;339;314;314;339	.	ENSP00000354526:E339X	E	+	1	0	L3MBTL3	130431182	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	9.729000	0.98795	2.687000	0.91594	0.557000	0.71058	GAA		0.328	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		T	130389489	G	T	130389489	4	4	47	1	0	0	0	0	0	1	0	0	8615	943	33	2	1053	2	L3MBTL3	6	130389489	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	595090	130389489	40725578	878	5275										
ENPP1	5167	broad.mit.edu	37	chr6	132207858	132207858	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggactgataacagcgagagCtgtgtggtaagtagcttttg	14	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:132207858C>T	ENST00000360971.2	+	24	2621	c.2601C>T	c.(2599-2601)agC>agT	p.S867S		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	867	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)	p.S815S(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	ACAGCGAGAGCTGTGTGGTAA	0.388																																					Colon(104;336 1535 5856 11019 33782)											1	Substitution - coding silent(1)	large_intestine(1)	6											112	103	106					6																	132207858		2203	4300	6503	132249551	SO:0001819	synonymous_variant	5167			M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2601C>T	6.37:g.132207858C>T			132249551	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Silent	SNP	ENST00000360971.2	37	CCDS5150.2																																																																																				0.388	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			T	132207858	C	T	132207858	2	4	47	1	0	0	0	0	0	0	0	1	5142	796	28	3		3	ENPP1	6	132207858	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1818369	132207858	38907209	879	5276										
STX7	8417	broad.mit.edu	37	chr6	132793477	132793477	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaatgtacttatctgtttCtttggcaagctggttagtat	8	5	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:132793477C>A	ENST00000367941.2	-	4	306	c.193G>T	c.(193-195)Gaa>Taa	p.E65*	STX7_ENST00000448348.3_5'UTR|STX7_ENST00000367937.4_Nonsense_Mutation_p.E65*	NM_003569.2	NP_003560.2	O15400	STX7_HUMAN	syntaxin 7	65					intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.E65*(2)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(1)|lung(5)	19	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)		TTATCTGTTTCTTTGGCAAGC	0.393																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											175	151	159					6																	132793477		2203	4300	6503	132835170	SO:0001587	stop_gained	8417			U77942	CCDS5153.1	6q23.1	2008-02-05			ENSG00000079950	ENSG00000079950			11442	protein-coding gene	gene with protein product		603217				9358037	Standard	NM_003569		Approved		uc003qdg.2	O15400	OTTHUMG00000015577	ENST00000367941.2:c.193G>T	6.37:g.132793477C>A	ENSP00000356918:p.Glu65*		132835170	E1P579|Q5SZW2|Q96ES9	Nonsense_Mutation	SNP	ENST00000367941.2	37	CCDS5153.1	.	.	.	.	.	.	.	.	.	.	C	37	6.634603	0.97722	.	.	ENSG00000079950	ENST00000367941;ENST00000448348;ENST00000309255;ENST00000367937	.	.	.	6.17	6.17	0.99709	.	0.089154	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-16.2361	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	65	.	ENSP00000309600:E65X	E	-	1	0	STX7	132835170	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.001000	0.76297	2.941000	0.99782	0.655000	0.94253	GAA		0.393	STX7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042252.2			A	132793477	C	A	132793477	4	1	47	1	0	0	0	0	0	1	0	0	15389	922	32	2	620	2	STX7	6	132793477	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	585619	132793477	38321590	880	5277										
TAAR5	9038	broad.mit.edu	37	chr6	132909837	132909837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggtacaaatcaacagtgCgtgtctgcggtgagaagacc	12	9	2	2	rs145127866	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:132909837C>T	ENST00000258034.2	-	1	1040	c.989G>A	c.(988-990)cGc>cAc	p.R330H		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	330			R -> C (in dbSNP:rs35839363).		G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)	p.R330H(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		ATCAACAGTGCGTGTCTGCGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	HIS/ARG	0,4406	2.1+/-5.4	0,0,2203	92	85	87		989	2.6	0.1	6	dbSNP_134	87	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TAAR5	NM_003967.2	29	0,8,6495	TT,TC,CC		0.093,0.0,0.0615	benign	330/338	132909837	8,12998	2203	4300	6503	132951530	SO:0001583	missense	9038			AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"GPCR / Class A : Trace amine associated receptors"	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.989G>A	6.37:g.132909837C>T	ENSP00000258034:p.Arg330His		132951530	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Missense_Mutation	SNP	ENST00000258034.2	37	CCDS5156.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	4.009	-0.001075	0.07819	0.0	9.3E-4	ENSG00000135569	ENST00000258034	T	0.70869	-0.52	5.34	2.59	0.31030	.	0.610822	0.14696	N	0.303863	T	0.26810	0.0656	N	0.17474	0.49	0.09310	N	1	P	0.36495	0.556	B	0.30179	0.112	T	0.04915	-1.0918	10	0.42905	T	0.14	-1.3902	5.4498	0.16556	0.0733:0.2735:0.5219:0.1313	.	330	O14804	TAAR5_HUMAN	H	330	ENSP00000258034:R330H	ENSP00000258034:R330H	R	-	2	0	TAAR5	132951530	0.000000	0.05858	0.137000	0.22149	0.119000	0.20118	0.025000	0.13577	0.377000	0.24735	-0.344000	0.07964	CGC		0.493	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967		T	132909837	C	T	132909837	3	4	47	1	0	0	0	0	1	0	0	0	15530	768	27	1	28	1	TAAR5	6	132909837	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	116360	132909837	38205230	881	5278										
SGK1	6446	broad.mit.edu	37	chr6	134638589	134638589	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggaatccattcatgtcttTgtttaccattttccaccgtg	7	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:134638589T>C	ENST00000367858.5	-	1	607	c.10A>G	c.(10-12)Aaa>Gaa	p.K4E	SGK1_ENST00000524929.1_Missense_Mutation_p.K4E	NM_001143676.1	NP_001137148.1	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	0	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.K4E(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCATGTCTTTGTTTACCATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											180	163	168					6																	134638589		1568	3582	5150	134680282	SO:0001583	missense	6446			AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000367858.5:c.10A>G	6.37:g.134638589T>C	ENSP00000356832:p.Lys4Glu		134680282	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000367858.5	37	CCDS47476.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.213976	0.79352	.	.	ENSG00000118515	ENST00000367858;ENST00000524929;ENST00000533224	T	0.75367	-0.93	5.26	5.26	0.73747	.	0.000000	0.34245	N	0.004135	D	0.82403	0.5029	.	.	.	0.35345	D	0.78679	D;B	0.69078	0.997;0.062	D;B	0.69654	0.965;0.031	D	0.86440	0.1766	9	0.87932	D	0	.	15.1662	0.72828	0.0:0.0:0.0:1.0	.	4;4	Q7Z3I4;O00141-2	.;.	E	4	ENSP00000356832:K4E	ENSP00000356832:K4E	K	-	1	0	SGK1	134680282	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.826000	0.55738	1.995000	0.58328	0.482000	0.46254	AAA		0.438	SGK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042304.2			C	134638589	T	C	134638589	3	2	47	1	0	0	0	0	1	0	0	0	14244	1821	63	4	1992	4	SGK1	6	134638589	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1728752	134638589	36476478	882	5279										
AHI1	54806	broad.mit.edu	37	chr6	135679300	135679300	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatctacctgatggttacaAggctttctttctatgctgat	8	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:135679300A>C	ENST00000367800.4	-	22	3351	c.3135T>G	c.(3133-3135)ccT>ccG	p.P1045P	AHI1_ENST00000457866.2_Silent_p.P1045P|AHI1_ENST00000417892.2_Silent_p.P399P	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1045					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)		p.P1045P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		GATGGTTACAAGGCTTTCTTT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	6											301	296	297					6																	135679300		1867	4103	5970	135720993	SO:0001819	synonymous_variant	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3135T>G	6.37:g.135679300A>C			135720993	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Silent	SNP	ENST00000367800.4	37	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	A	8.018	0.758985	0.15846	.	.	ENSG00000135541	ENST00000367799	.	.	.	5.4	1.38	0.22167	.	.	.	.	.	T	0.36386	0.0965	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	-8.9277	5.261	0.15573	0.6518:0.0:0.0745:0.2738	.	.	.	.	R	545	.	.	L	-	2	0	AHI1	135720993	0.991000	0.36638	0.984000	0.44739	0.792000	0.44763	1.656000	0.37355	0.424000	0.26061	0.455000	0.32223	CTT		0.343	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135679300	A	C	135679300	2	2	47	1	0	0	0	0	0	0	0	1	413	59	3	4		4	AHI1	6	135679300	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1040711	135679300	35435767	883	5280										
MAP7	9053	broad.mit.edu	37	chr6	136693712	136693712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agagttttggtcgatccatcGaatttctagagtgtgcagct	11	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:136693712G>A	ENST00000354570.3	-	8	1213	c.803C>T	c.(802-804)tCg>tTg	p.S268L	MAP7_ENST00000544465.1_Missense_Mutation_p.S253L|MAP7_ENST00000438100.2_Missense_Mutation_p.S253L|MAP7_ENST00000432797.2_Missense_Mutation_p.S122L|MAP7_ENST00000454590.1_Missense_Mutation_p.S290L	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	268					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.S268L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		TCGATCCATCGAATTTCTAGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											206	180	189					6																	136693712		2203	4300	6503	136735405	SO:0001583	missense	9053			X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.803C>T	6.37:g.136693712G>A	ENSP00000346581:p.Ser268Leu		136735405	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	37	CCDS5178.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.270146	0.23221	.	.	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100;ENST00000432797;ENST00000345567	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	5.67	3.83	0.44106	.	0.763445	0.11544	N	0.553417	T	0.01523	0.0049	N	0.05351	-0.065	0.23082	N	0.998324	B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.0;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0;0.001;0.001;0.0	T	0.47222	-0.9134	10	0.27785	T	0.31	-0.12	11.0815	0.48062	0.1542:0.0:0.8458:0.0	.	253;290;253;290;290;174;231;268	B7Z290;B7ZB64;F5H1E2;E9PCP3;B7Z400;F8W783;Q14244-2;Q14244	.;.;.;.;.;.;.;MAP7_HUMAN	L	268;290;253;253;122;174	ENSP00000346581:S268L;ENSP00000414712:S290L;ENSP00000445737:S253L;ENSP00000400790:S253L;ENSP00000414879:S122L	ENSP00000344217:S174L	S	-	2	0	MAP7	136735405	1.000000	0.71417	0.881000	0.34555	0.983000	0.72400	2.910000	0.48766	1.336000	0.45506	0.591000	0.81541	TCG		0.512	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		A	136693712	G	A	136693712	3	1	47	1	0	0	0	0	1	0	0	0	9296	1059	37	1	1490	1	MAP7	6	136693712	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1014412	136693712	34421355	884	5281										
ECT2L	345930	broad.mit.edu	37	chr6	139206654	139206654	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttttagtgcagagaaatGataccagcattccgaacttt	7	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:139206654G>T	ENST00000423192.1	+	16	2201	c.2040G>T	c.(2038-2040)atG>atT	p.M680I	ECT2L_ENST00000367682.2_Missense_Mutation_p.M680I|ECT2L_ENST00000541398.1_Intron			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	680	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.M680I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						GCAGAGAAATGATACCAGCAT	0.443			"N, Splice, Mis"		ETP ALL																																		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	1	Substitution - Missense(1)	large_intestine(1)	6											105	99	101					6																	139206654		1915	4125	6040	139248347	SO:0001583	missense	345930				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.2040G>T	6.37:g.139206654G>T	ENSP00000387388:p.Met680Ile		139248347	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	G	8.898	0.955764	0.18507	.	.	ENSG00000203734	ENST00000423192;ENST00000367682	T;T	0.29142	1.58;1.58	5.3	2.59	0.31030	Dbl homology (DH) domain (5);	0.325021	0.18440	U	0.141162	T	0.08044	0.0201	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30060	-0.9991	10	0.49607	T	0.09	2.5451	4.779	0.13192	0.2594:0.1573:0.5833:0.0	.	680	Q008S8	ECT2L_HUMAN	I	680	ENSP00000387388:M680I;ENSP00000356655:M680I	ENSP00000356655:M680I	M	+	3	0	ECT2L	139248347	0.000000	0.05858	0.002000	0.10522	0.966000	0.64601	0.400000	0.20932	0.259000	0.21709	-0.136000	0.14681	ATG		0.443	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139206654	G	T	139206654	3	4	47	1	0	0	0	0	1	0	0	0	4913	1290	45	2	2098	2	ECT2L	6	139206654	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2512942	139206654	31908413	885	5282										
HIVEP2	3097	broad.mit.edu	37	chr6	143093232	143093232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacctggatgttgtgttgccGaactagcctgggctgtgtgt	14	8	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:143093232G>A	ENST00000367604.1	-	4	3283	c.2644C>T	c.(2644-2646)Cgg>Tgg	p.R882W	HIVEP2_ENST00000367603.2_Missense_Mutation_p.R882W|HIVEP2_ENST00000012134.2_Missense_Mutation_p.R882W			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	882					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R882W(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TTGTGTTGCCGAACTAGCCTG	0.562																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - Missense(1)	large_intestine(1)	6											77	83	81					6																	143093232		2073	4223	6296	143134925	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.2644C>T	6.37:g.143093232G>A	ENSP00000356576:p.Arg882Trp		143134925	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658183	0.88154	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.53423	0.62;0.62;0.62	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.69717	0.3142	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74717	-0.3571	10	0.87932	D	0	-28.358	19.3961	0.94607	0.0:0.0:1.0:0.0	.	882	P31629	ZEP2_HUMAN	W	882	ENSP00000356576:R882W;ENSP00000356575:R882W;ENSP00000012134:R882W	ENSP00000012134:R882W	R	-	1	2	HIVEP2	143134925	1.000000	0.71417	0.995000	0.50966	0.837000	0.47467	7.941000	0.87700	2.598000	0.87819	0.591000	0.81541	CGG		0.562	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			A	143093232	G	A	143093232	3	1	47	1	0	0	0	0	1	0	0	0	7208	1057	37	1	4720	1	HIVEP2	6	143093232	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3886578	143093232	28021835	886	5283										
PEX3	8504	broad.mit.edu	37	chr6	143800288	143800288	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctagacaatatggctgagttCtttcgacctactgaacagga	9	9	1	3	rs35288644		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:143800288C>A	ENST00000367591.4	+	10	957	c.894C>A	c.(892-894)ttC>ttA	p.F298L		NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	298					peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.F298L(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		TGGCTGAGTTCTTTCGACCTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	94	95					6																	143800288		2203	4300	6503	143841981	SO:0001583	missense	8504			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.894C>A	6.37:g.143800288C>A	ENSP00000356563:p.Phe298Leu		143841981	Q6FGP5	Missense_Mutation	SNP	ENST00000367591.4	37	CCDS5199.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691031	0.68271	.	.	ENSG00000034693	ENST00000367591	T	0.41065	1.01	5.65	2.89	0.33648	.	0.000000	0.85682	D	0.000000	T	0.33556	0.0867	L	0.56769	1.78	0.58432	D	0.999997	D	0.61080	0.989	P	0.57620	0.824	T	0.20706	-1.0267	10	0.12766	T	0.61	-16.4617	10.2766	0.43515	0.0:0.6705:0.0:0.3295	.	298	P56589	PEX3_HUMAN	L	298	ENSP00000356563:F298L	ENSP00000356563:F298L	F	+	3	2	PEX3	143841981	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.635000	0.24629	0.863000	0.35553	0.650000	0.86243	TTC		0.333	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1			A	143800288	C	A	143800288	3	1	47	1	0	0	0	0	1	0	0	0	11778	912	32	2	932	2	PEX3	6	143800288	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	707056	143800288	27314779	887	5284										
LTV1	84946	broad.mit.edu	37	chr6	144184235	144184235	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatttcagcccaaacaaattCgaatatcttctaaaacagga	4	9	3	0	rs201919461		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:144184235C>T	ENST00000367576.5	+	10	1263	c.1129C>T	c.(1129-1131)Cga>Tga	p.R377*	ZC2HC1B_ENST00000539295.1_5'Flank|ZC2HC1B_ENST00000237275.6_5'Flank	NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	377						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R377*(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		CAAACAAATTCGAATATCTTC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	6						C	stop/ARG	0,4406		0,0,2203	77	81	80		1129	4.7	0.8	6		80	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	LTV1	NM_032860.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		377/476	144184235	1,13005	2203	4300	6503	144225928	SO:0001587	stop_gained	84946			BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 93", "LTV1 homolog (S. cerevisiae)"	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.1129C>T	6.37:g.144184235C>T	ENSP00000356548:p.Arg377*		144225928	Q96JX8	Nonsense_Mutation	SNP	ENST00000367576.5	37	CCDS5201.1	.	.	.	.	.	.	.	.	.	.	C	37	5.980441	0.97168	0.0	1.16E-4	ENSG00000135521	ENST00000367576	.	.	.	5.61	4.72	0.59763	.	0.645091	0.16450	N	0.213887	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.512	13.6837	0.62502	0.3376:0.6624:0.0:0.0	.	.	.	.	X	377	.	ENSP00000356548:R377X	R	+	1	2	LTV1	144225928	0.755000	0.28372	0.787000	0.31911	0.834000	0.47266	1.738000	0.38207	1.329000	0.45376	0.585000	0.79938	CGA		0.328	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860		T	144184235	C	T	144184235	4	4	47	1	0	0	0	0	0	1	0	0	9110	876	31	1	1167	1	LTV1	6	144184235	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	383947	144184235	26930832	888	5285										
UTRN	7402	broad.mit.edu	37	chr6	144843176	144843176	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggaattagatcatcacttCttcctacagattatctggtt	6	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:144843176C>T	ENST00000367545.3	+	39	5602	c.5602C>T	c.(5602-5604)Ctt>Ttt	p.L1868F		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1868					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L1868F(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATCATCACTTCTTCCTACAGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											130	139	136					6																	144843176		2203	4300	6503	144884869	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.5602C>T	6.37:g.144843176C>T	ENSP00000356515:p.Leu1868Phe		144884869	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869191	0.32977	.	.	ENSG00000152818	ENST00000367545	T	0.60299	0.2	5.7	5.7	0.88788	.	0.000000	0.47852	D	0.000201	T	0.28101	0.0693	L	0.44542	1.39	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.09640	-1.0665	10	0.09590	T	0.72	.	10.8695	0.46875	0.0:0.8859:0.0:0.1141	.	1868	P46939	UTRO_HUMAN	F	1868	ENSP00000356515:L1868F	ENSP00000356515:L1868F	L	+	1	0	UTRN	144884869	0.748000	0.28294	0.828000	0.32881	0.470000	0.32858	1.974000	0.40559	2.696000	0.92011	0.561000	0.74099	CTT		0.313	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144843176	C	T	144843176	3	4	47	1	0	0	0	0	1	0	0	0	17143	913	32	3	5756	3	UTRN	6	144843176	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	658941	144843176	26271891	889	5286										
SASH1	23328	broad.mit.edu	37	chr6	148846459	148846459	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttggaggatttgacttgacGaatcgctctctgcacgttgg	12	8	1	2	rs373832720		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:148846459G>A	ENST00000367467.3	+	11	1717	c.1242G>A	c.(1240-1242)acG>acA	p.T414T	AL033378.1_ENST00000411390.2_RNA	NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	414					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.T414T(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TTGACTTGACGAATCGCTCTC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G		1,4405	2.1+/-5.4	0,1,2202	216	199	205		1242	-11.3	0	6		205	0,8600		0,0,4300	no	coding-synonymous	SASH1	NM_015278.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		414/1248	148846459	1,13005	2203	4300	6503	148888152	SO:0001819	synonymous_variant	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1242G>A	6.37:g.148846459G>A			148888152	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																				0.458	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148846459	G	A	148846459	2	1	47	1	0	0	0	0	0	0	0	1	13885	1045	37	1		1	SASH1	6	148846459	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4003283	148846459	22268608	890	5287										
SYNE1	23345	broad.mit.edu	37	chr6	152737784	152737784	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggtattgggctttggaaaGaatgccatccagactgacgg	13	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:152737784G>T	ENST00000367255.5	-	41	6389	c.5788C>A	c.(5788-5790)Ctt>Att	p.L1930I	SYNE1_ENST00000423061.1_Missense_Mutation_p.L1937I|SYNE1_ENST00000448038.1_Missense_Mutation_p.L1937I|SYNE1_ENST00000341594.5_Missense_Mutation_p.L1967I|SYNE1_ENST00000265368.4_Missense_Mutation_p.L1930I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1930					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L1930I(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCTTTGGAAAGAATGCCATCC	0.458										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											105	102	103					6																	152737784		2203	4300	6503	152779477	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5788C>A	6.37:g.152737784G>T	ENSP00000356224:p.Leu1930Ile		152779477	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481588	0.63849	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	6.17	6.17	0.99709	.	0.000000	0.56097	D	0.000032	T	0.56848	0.2013	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.998;0.98	D;D;D;P	0.80764	0.994;0.939;0.939;0.736	T	0.48163	-0.9059	10	0.40728	T	0.16	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1913;1930;1930;1937	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	I	1930;1937;1930;1937;1967	ENSP00000356224:L1930I;ENSP00000396024:L1937I;ENSP00000265368:L1930I;ENSP00000390975:L1937I;ENSP00000341887:L1967I	ENSP00000265368:L1930I	L	-	1	0	SYNE1	152779477	1.000000	0.71417	0.132000	0.22025	0.563000	0.35712	7.954000	0.87848	2.941000	0.99782	0.655000	0.94253	CTT		0.458	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152737784	G	T	152737784	3	4	47	1	0	0	0	0	1	0	0	0	15484	942	33	2	21102	2	SYNE1	6	152737784	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3891325	152737784	18377283	891	5288										
RGS17	26575	broad.mit.edu	37	chr6	153332811	153332811	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtgcattaaagtatatatCtgaagttgggcatcttcata	8	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:153332811C>T	ENST00000367225.2	-	4	555	c.531G>A	c.(529-531)caG>caA	p.Q177Q	RGS17_ENST00000206262.1_Silent_p.Q177Q			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	177	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.Q177Q(1)|p.Q177H(1)		cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		AAGTATATATCTGAAGTTGGG	0.353																																					Esophageal Squamous(78;500 1236 6775 24364 49058)											2	Substitution - Missense(1)|Substitution - coding silent(1)	cervix(1)|large_intestine(1)	6											60	60	60					6																	153332811		2203	4300	6503	153374504	SO:0001819	synonymous_variant	26575			AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"Regulators of G-protein signaling"	14088	protein-coding gene	gene with protein product		607191	"regulator of G-protein signalling 17"			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.531G>A	6.37:g.153332811C>T			153374504	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	37	CCDS5244.1																																																																																				0.353	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2			T	153332811	C	T	153332811	2	4	47	1	0	0	0	0	0	0	0	1	13336	912	32	3		3	RGS17	6	153332811	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	595027	153332811	17782256	892	5289										
TAGAP	117289	broad.mit.edu	37	chr6	159457181	159457181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgcgcctccagcatcctcGccctcatgctccccaccgtc	7	21	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:159457181G>A	ENST00000367066.3	-	10	2205	c.1874C>T	c.(1873-1875)gCg>gTg	p.A625V	RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.A447V|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	625					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.A625V(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CAGCATCCTCGCCCTCATGCT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	67	68					6																	159457181		2203	4300	6503	159377169	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1874C>T	6.37:g.159457181G>A	ENSP00000356033:p.Ala625Val		159377169	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169119	0.57584	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	T;T	0.18810	2.19;2.44	5.68	4.73	0.59995	.	0.471562	0.20715	N	0.087006	T	0.08802	0.0218	M	0.67953	2.075	0.22446	N	0.999093	P	0.39352	0.669	B	0.24269	0.052	T	0.09185	-1.0686	10	0.48119	T	0.1	-24.029	10.4658	0.44607	0.0791:0.0:0.7568:0.164	.	625	Q8N103	TAGAP_HUMAN	V	625;447	ENSP00000356033:A625V;ENSP00000322650:A447V	ENSP00000322650:A447V	A	-	2	0	TAGAP	159377169	0.001000	0.12720	0.303000	0.25071	0.056000	0.15407	0.629000	0.24538	2.676000	0.91093	0.563000	0.77884	GCG		0.647	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159457181	G	A	159457181	3	1	47	1	0	0	0	0	1	0	0	0	15576	1087	38	1	325	1	TAGAP	6	159457181	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6124370	159457181	11657886	893	5290										
WTAP	9589	broad.mit.edu	37	chr6	160160025	160160025	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaattctctttataggttCgattgagtgaaacagacttc	8	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:160160025C>T	ENST00000358372.4	+	3	1791	c.34C>T	c.(34-36)Cga>Tga	p.R12*	WTAP_ENST00000337387.4_Nonsense_Mutation_p.R12*|SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	12					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)		p.R12*(2)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		TTTATAGGTTCGATTGAGTGA	0.308																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											76	78	78					6																	160160025		2201	4294	6495	160080015	SO:0001587	stop_gained	9589			AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.34C>T	6.37:g.160160025C>T	ENSP00000351141:p.Arg12*		160080015	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Nonsense_Mutation	SNP	ENST00000358372.4	37	CCDS5266.1	.	.	.	.	.	.	.	.	.	.	C	51	17.860599	0.99894	.	.	ENSG00000146457	ENST00000358372;ENST00000337387	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.5038	17.4453	0.87577	0.0:1.0:0.0:0.0	.	.	.	.	X	12	.	ENSP00000336911:R12X	R	+	1	2	WTAP	160080015	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.194000	0.65125	2.612000	0.88384	0.591000	0.81541	CGA		0.308	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857		T	160160025	C	T	160160025	4	4	47	1	0	0	0	0	0	1	0	0	17449	876	31	1	40	1	WTAP	6	160160025	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	702844	160160025	10955042	894	5291										
TCP1	6950	broad.mit.edu	37	chr6	160200077	160200077	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaataaaaggaacatcagaTcaatcattaagggctccaga	7	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:160200077T>G	ENST00000321394.7	-	12	1951	c.1671A>C	c.(1669-1671)tgA>tgC	p.*557C	ACAT2_ENST00000541436.1_3'UTR|SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000544255.1_Nonstop_Mutation_p.*333C|TCP1_ENST00000420894.2_3'UTR|TCP1_ENST00000392168.2_Nonstop_Mutation_p.*402C|ACAT2_ENST00000367048.4_3'UTR|ACAT2_ENST00000472052.1_3'UTR	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	0					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.*557C(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		GAACATCAGATCAATCATTAA	0.313																																																1	Nonstop extension(1)	large_intestine(1)	6											54	55	55					6																	160200077		2203	4299	6502	160120067	SO:0001578	stop_lost	6950			X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"Heat Shock Proteins / Chaperonins"	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.1671A>C	6.37:g.160200077T>G	ENSP00000317334:p.*557Trpext*18		160120067	E1P5B2|Q15556|Q5TCM3	Nonstop_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.210089	0.58343	.	.	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000392168	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9941	0.80228	0.0:0.0:0.0:1.0	.	.	.	.	C	557;333;402	.	.	X	-	3	0	TCP1	160120067	0.998000	0.40836	0.993000	0.49108	0.464000	0.32679	3.047000	0.49854	2.190000	0.69967	0.454000	0.30748	TGA		0.313	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		G	160200077	T	G	160200077	4	3	47	1	0	0	0	0	0	0	0	0	15748	1448	50	4	3	4	TCP1	6	160200077	Nonstop_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	40052	160200077	10914990	895	5292										
MAS1	4142	broad.mit.edu	37	chr6	160328349	160328349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggctacaacacgggcctctAtctgctgacggccattagtg	11	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:160328349A>G	ENST00000252660.4	+	1	376	c.362A>G	c.(361-363)tAt>tGt	p.Y121C		NM_002377.2	NP_002368.1	P04201	MAS_HUMAN	MAS1 proto-oncogene, G protein-coupled receptor	121					activation of NF-kappaB-inducing kinase activity (GO:0007250)|anatomical structure morphogenesis (GO:0009653)|cell proliferation (GO:0008283)|cellular response to peptide hormone stimulus (GO:0071375)|G-protein coupled receptor signaling pathway (GO:0007186)|hippocampus development (GO:0021766)|male gonad development (GO:0008584)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|protein kinase C signaling (GO:0070528)|regulation of inflammatory response (GO:0050727)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin receptor activity (GO:0001595)|angiotensin type II receptor activity (GO:0004945)|G-protein coupled receptor activity (GO:0004930)|peptide binding (GO:0042277)|peptide hormone binding (GO:0017046)	p.Y121C(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		ACGGGCCTCTATCTGCTGACG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	130	133					6																	160328349		2203	4300	6503	160248339	SO:0001583	missense	4142			M13150	CCDS5272.1	6q24-q27	2014-06-26	2014-06-26		ENSG00000130368	ENSG00000130368		"GPCR / Class A : Orphans"	6899	protein-coding gene	gene with protein product		165180	"MAS1 oncogene"				Standard	NM_002377		Approved		uc003qsz.3	P04201	OTTHUMG00000015944	ENST00000252660.4:c.362A>G	6.37:g.160328349A>G	ENSP00000252660:p.Tyr121Cys		160248339	E1P5B3|Q2TBC9|Q6FG47	Missense_Mutation	SNP	ENST00000252660.4	37	CCDS5272.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997183	0.54147	.	.	ENSG00000130368	ENST00000252660	T	0.37752	1.18	5.65	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.130465	0.34906	N	0.003590	T	0.25005	0.0607	L	0.28608	0.87	0.41145	D	0.98598	D	0.59357	0.985	P	0.58454	0.839	T	0.06092	-1.0846	10	0.38643	T	0.18	.	7.9945	0.30261	0.8432:0.0:0.1568:0.0	.	121	P04201	MAS_HUMAN	C	121	ENSP00000252660:Y121C	ENSP00000252660:Y121C	Y	+	2	0	MAS1	160248339	0.986000	0.35501	0.804000	0.32291	0.991000	0.79684	2.758000	0.47565	0.979000	0.38497	0.533000	0.62120	TAT		0.488	MAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042930.2	NM_002377		G	160328349	A	G	160328349	3	3	47	1	0	0	0	0	1	0	0	0	9350	449	16	4	364	4	MAS1	6	160328349	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	128272	160328349	10786718	896	5293										
IGF2R	3482	broad.mit.edu	37	chr6	160468929	160468929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccacgctggagcagtacGacctctccaggtgaggcaga	12	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:160468929G>A	ENST00000356956.1	+	17	2483	c.2335G>A	c.(2335-2337)Gac>Aac	p.D779N		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	779					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.D779N(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GGAGCAGTACGACCTCTCCAG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	6											88	73	78					6																	160468929		2203	4300	6503	160388919	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2335G>A	6.37:g.160468929G>A	ENSP00000349437:p.Asp779Asn		160388919	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.065174	0.76187	.	.	ENSG00000197081	ENST00000356956	T	0.15017	2.46	5.14	5.14	0.70334	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.40791	0.1131	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.41124	-0.9526	10	0.49607	T	0.09	-7.7925	18.6253	0.91334	0.0:0.0:1.0:0.0	.	779	P11717	MPRI_HUMAN	N	779	ENSP00000349437:D779N	ENSP00000349437:D779N	D	+	1	0	IGF2R	160388919	1.000000	0.71417	0.907000	0.35723	0.179000	0.23085	9.455000	0.97625	2.407000	0.81776	0.561000	0.74099	GAC		0.577	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		A	160468929	G	A	160468929	3	1	47	1	0	0	0	0	1	0	0	0	7597	1058	37	1	2401	1	IGF2R	6	160468929	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	140580	160468929	10646138	897	5294										
MAP3K4	4216	broad.mit.edu	37	chr6	161527593	161527593	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagctatccagaagtcagtcCgattgtttgaagaaaagagg	11	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:161527593C>T	ENST00000392142.4	+	20	4052	c.3904C>T	c.(3904-3906)Cga>Tga	p.R1302*	MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.R1298*|MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.R1252*|MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.R1248*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1302					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.R1301*(1)|p.R1302*(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GAAGTCAGTCCGATTGTTTGA	0.403																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											117	108	111					6																	161527593		2203	4300	6503	161447583	SO:0001587	stop_gained	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3904C>T	6.37:g.161527593C>T	ENSP00000375986:p.Arg1302*		161447583	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	43	10.499508	0.99416	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	4.95	4.95	0.65309	.	0.177320	0.38058	N	0.001826	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.7574	13.2058	0.59795	0.1592:0.8408:0.0:0.0	.	.	.	.	X	1252;1302;1252;1298;1248	.	ENSP00000297332:R1248X	R	+	1	2	MAP3K4	161447583	0.968000	0.33430	0.991000	0.47740	0.950000	0.60333	3.853000	0.55941	2.271000	0.75665	0.650000	0.86243	CGA		0.403	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161527593	C	T	161527593	4	4	47	1	0	0	0	0	0	1	0	0	9282	644	23	1	3982	1	MAP3K4	6	161527593	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1058664	161527593	9587474	898	5295										
PARK2	5071	broad.mit.edu	37	chr6	162475138	162475138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttactgcactagtcccaggGcagtgtggggattggcattc	13	10	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:162475138G>A	ENST00000366898.1	-	5	705	c.603C>T	c.(601-603)tgC>tgT	p.C201C	PARK2_ENST00000338468.3_Silent_p.C10C|PARK2_ENST00000366892.1_Silent_p.C201C|PARK2_ENST00000366896.1_Intron|PARK2_ENST00000366897.1_Intron|PARK2_ENST00000366894.1_Silent_p.C10C	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	201					adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)	p.C201C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TAGTCCCAGGGCAGTGTGGGG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	6											143	126	132					6																	162475138		2203	4300	6503	162395128	SO:0001819	synonymous_variant	5071				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.603C>T	6.37:g.162475138G>A			162395128	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Silent	SNP	ENST00000366898.1	37	CCDS5281.1																																																																																				0.408	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			A	162475138	G	A	162475138	2	1	47	1	0	0	0	0	0	0	0	1	11480	1195	42	3		3	PARK2	6	162475138	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	947545	162475138	8639929	899	5296										
C6orf118	168090	broad.mit.edu	37	chr6	165723058	165723058	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaggccacttacattcaggCtcccgctcctccgccatcgc	7	20	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:165723058C>T	ENST00000230301.8	-	1	38	c.18G>A	c.(16-18)gaG>gaA	p.E6E	C6orf118_ENST00000543069.1_5'Flank	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	6								p.E6E(1)		breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		TACATTCAGGCTCCCGCTCCT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	6											81	74	77					6																	165723058		2203	4300	6503	165643048	SO:0001819	synonymous_variant	168090				CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.18G>A	6.37:g.165723058C>T			165643048	Q8TC11	Silent	SNP	ENST00000230301.8	37	CCDS5288.1																																																																																				0.547	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		T	165723058	C	T	165723058	2	4	47	1	0	0	0	0	0	0	0	1	2329	796	28	3		3	C6orf118	6	165723058	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3247920	165723058	5392009	900	5297										
KIF25	3834	broad.mit.edu	37	chr6	168440763	168440763	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggctgtcggcagcgcctcGaaactgatggagctcgttca	14	11	1	1	rs146483835		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr6:168440763G>A	ENST00000443060.2	+	7	904	c.513G>A	c.(511-513)tcG>tcA	p.S171S	KIF25_ENST00000351261.3_Silent_p.S171S|KIF25_ENST00000354419.2_Silent_p.S171S			Q9UIL4	KIF25_HUMAN	kinesin family member 25	171	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S171S(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCAGCGCCTCGAAACTGATGG	0.607													G|||	1	0.000199681	0	0	5008	,	,		18640	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	3,4403	6.2+/-15.9	0,3,2200	93	87	89		513,513	-7.6	0	6	dbSNP_134	89	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIF25	NM_005355.3,NM_030615.2	,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,	171/333,171/385	168440763	3,13003	2203	4300	6503	168183612	SO:0001819	synonymous_variant	3834			AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"Kinesins"	6390	protein-coding gene	gene with protein product		603815	"kinesin-like 3"	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.513G>A	6.37:g.168440763G>A			168183612	O94775|Q5SZU9	Silent	SNP	ENST00000443060.2	37	CCDS5305.1																																																																																				0.607	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			A	168440763	G	A	168440763	2	1	47	1	0	0	0	0	0	0	0	1	8314	1045	37	1		1	KIF25	6	168440763	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2717705	168440763	2674304	901	5298										
ICA1	3382	broad.mit.edu	37	chr7	8167696	8167696	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaaggaggaagcattgaaGatctcactcaacagcagcag	10	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:8167696G>T	ENST00000402384.3	-	13	1403	c.1137C>A	c.(1135-1137)atC>atA	p.I379I	ICA1_ENST00000406470.2_Silent_p.I379I|ICA1_ENST00000422063.2_Silent_p.I408I|ICA1_ENST00000401396.1_Silent_p.I367I|ICA1_ENST00000265577.7_Silent_p.I378I|ICA1_ENST00000396675.3_Silent_p.I379I			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	379					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)		p.I379I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		AAGCATTGAAGATCTCACTCA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	7											147	141	143					7																	8167696		2203	4300	6503	8134221	SO:0001819	synonymous_variant	3382				CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"islet cell autoantigen 1 (69kD)"			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.1137C>A	7.37:g.8167696G>T			8134221	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Silent	SNP	ENST00000402384.3	37	CCDS34602.1																																																																																				0.552	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968		T	8167696	G	T	8167696	2	4	47	1	0	0	0	0	0	0	0	1	7498	932	33	2		2	ICA1	7	8167696	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09		8167696	150970967	902	5299										
NXPH1	30010	broad.mit.edu	37	chr7	8791030	8791030	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatcatggcaatgggacattTagtgtttatttcaggcataa	10	5	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:8791030T>C	ENST00000405863.1	+	3	1358	c.447T>C	c.(445-447)ttT>ttC	p.F149F	NXPH1_ENST00000602349.1_Silent_p.F32F|NXPH1_ENST00000497400.1_3'UTR	NM_152745.2	NP_689958.1	P58417	NXPH1_HUMAN	neurexophilin 1	149	III.					extracellular region (GO:0005576)		p.F149F(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|ovary(1)	17		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		ATGGGACATTTAGTGTTTATT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	7											87	86	86					7																	8791030		1884	4120	6004	8757555	SO:0001819	synonymous_variant	30010			AB047362	CCDS47540.1	7p22	2003-03-20			ENSG00000122584	ENSG00000122584			20693	protein-coding gene	gene with protein product		604639				9570794	Standard	NM_152745		Approved		uc003srv.3	P58417	OTTHUMG00000151941	ENST00000405863.1:c.447T>C	7.37:g.8791030T>C			8757555	Q8NB31	Silent	SNP	ENST00000405863.1	37	CCDS47540.1																																																																																				0.403	NXPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324591.1	NM_152745		C	8791030	T	C	8791030	2	2	47	1	0	0	0	0	0	0	0	1	10821	1751	61	4		4	NXPH1	7	8791030	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	623334	8791030	150347633	903	5300										
TMEM195	392636	broad.mit.edu	37	chr7	15405188	15405188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggcttcaggtgaccaaatCggtacagcattaagaacatc	10	9	1	2	rs181773805	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:15405188C>T	ENST00000342526.3	-	12	1383	c.1214G>A	c.(1213-1215)cGa>cAa	p.R405Q		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	405					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.R405Q(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						GTGACCAAATCGGTACAGCAT	0.408													C|||	6	0.00119808	0	0	5008	,	,		15754	0		0.001	False		,,,				2504	0.0051															1	Substitution - Missense(1)	large_intestine(1)	7						C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	118	106	110		1214	2	0	7		110	1,8599	1.2+/-3.3	0,1,4299	no	missense	AGMO	NM_001004320.1	43	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	possibly-damaging	405/446	15405188	3,13003	2203	4300	6503	15371713	SO:0001583	missense	392636				CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"Fatty acid hydroxylase domain containing"	33784	protein-coding gene	gene with protein product		613738	"transmembrane protein 195"	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.1214G>A	7.37:g.15405188C>T	ENSP00000341662:p.Arg405Gln		15371713	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.273	1.046102	0.19748	4.54E-4	1.16E-4	ENSG00000187546	ENST00000342526;ENST00000418075	T	0.29917	1.55	5.78	2.01	0.26516	.	0.254889	0.36854	N	0.002363	T	0.23611	0.0571	L	0.56769	1.78	0.09310	N	1	B	0.29909	0.261	B	0.15870	0.014	T	0.13495	-1.0507	10	0.28530	T	0.3	-28.6374	8.2944	0.31976	0.0:0.5672:0.0:0.4328	.	405	Q6ZNB7	ALKMO_HUMAN	Q	405;47	ENSP00000341662:R405Q	ENSP00000341662:R405Q	R	-	2	0	AGMO	15371713	0.009000	0.17119	0.031000	0.17742	0.026000	0.11368	-0.136000	0.10405	0.095000	0.17434	0.655000	0.94253	CGA		0.408	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320		T	15405188	C	T	15405188	3	4	47	1	0	0	0	0	1	0	0	0	16156	884	31	1	131	1	TMEM195	7	15405188	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6614158	15405188	143733475	904	5301										
MACC1	346389	broad.mit.edu	37	chr7	20201469	20201469	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcctgaccgaaaatgttttCtttcagtgattagcattttt	6	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:20201469C>A	ENST00000400331.5	-	4	325	c.17G>T	c.(16-18)aGa>aTa	p.R6I	MACC1_ENST00000589011.1_Missense_Mutation_p.R6I|MACC1_ENST00000332878.4_Missense_Mutation_p.R6I|MACC1_ENST00000471019.1_5'Flank	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	6					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R6I(1)		endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						AAAATGTTTTCTTTCAGTGAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	7											116	114	115					7																	20201469		2202	4300	6502	20167994	SO:0001583	missense	346389				CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.17G>T	7.37:g.20201469C>A	ENSP00000383185:p.Arg6Ile		20167994	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	C	9.657	1.143205	0.21205	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.10763	2.84;2.84	5.51	-6.36	0.01969	.	0.855181	0.10253	N	0.696980	T	0.07638	0.0192	L	0.51422	1.61	0.18873	N	0.999987	B	0.11235	0.004	B	0.08055	0.003	T	0.37731	-0.9693	10	0.62326	D	0.03	-0.4765	2.6997	0.05145	0.1478:0.1734:0.1947:0.4841	.	6	Q6ZN28	MACC1_HUMAN	I	6	ENSP00000383185:R6I;ENSP00000328410:R6I	ENSP00000328410:R6I	R	-	2	0	MACC1	20167994	0.000000	0.05858	0.002000	0.10522	0.121000	0.20230	-0.463000	0.06696	-1.339000	0.02230	-0.211000	0.12701	AGA		0.333	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20201469	C	A	20201469	3	1	47	1	0	0	0	0	1	0	0	0	9173	913	32	2	2557	2	MACC1	7	20201469	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4796281	20201469	138937194	905	5302										
SP4	6671	broad.mit.edu	37	chr7	21469929	21469929	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtcagcttcagcctaatggAatgcagaatgcacaggatca	10	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:21469929A>G	ENST00000222584.3	+	3	1364	c.1146A>G	c.(1144-1146)ggA>ggG	p.G382G		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	382					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.G382G(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						AGCCTAATGGAATGCAGAATG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	7											90	85	86					7																	21469929		2203	4300	6503	21436454	SO:0001819	synonymous_variant	6671				CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1146A>G	7.37:g.21469929A>G			21436454	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																				0.478	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		G	21469929	A	G	21469929	2	3	47	1	0	0	0	0	0	0	0	1	15003	233	9	4		4	SP4	7	21469929	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1268460	21469929	137668734	906	5303										
DNAH11	8701	broad.mit.edu	37	chr7	21818585	21818585	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttgctttaggtgggagatCtaaaagccagacttgcctct	10	8	2	2	rs201171938		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:21818585C>A	ENST00000409508.3	+	57	9377	c.9346C>A	c.(9346-9348)Cta>Ata	p.L3116I	DNAH11_ENST00000328843.6_Missense_Mutation_p.L3123I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3123	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L3123I(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GGTGGGAGATCTAAAAGCCAG	0.458									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											85	82	83					7																	21818585		1913	4126	6039	21785110	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.9346C>A	7.37:g.21818585C>A	ENSP00000475939:p.Leu3116Ile		21785110	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	20.1	3.940964	0.73557	.	.	ENSG00000105877	ENST00000328843	T	0.80824	-1.42	6.03	5.15	0.70609	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.30695	U	0.009069	D	0.89876	0.6842	.	.	.	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.91337	0.5094	9	0.87932	D	0	.	15.5309	0.75960	0.0:0.934:0.0:0.066	.	3123	Q96DT5	DYH11_HUMAN	I	3123	ENSP00000330671:L3123I	ENSP00000330671:L3123I	L	+	1	2	DNAH11	21785110	1.000000	0.71417	0.991000	0.47740	0.933000	0.57130	3.691000	0.54720	1.564000	0.49628	-0.137000	0.14449	CTA		0.458	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21818585	C	A	21818585	3	1	47	1	0	0	0	0	1	0	0	0	4610	912	32	2	9594	2	DNAH11	7	21818585	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	348656	21818585	137320078	907	5304										
DNAH11	8701	broad.mit.edu	37	chr7	21934518	21934518	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagggggaattggcattatCtcctgctgtggaagcccagc	13	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:21934518C>T	ENST00000409508.3	+	79	12981	c.12950C>T	c.(12949-12951)tCt>tTt	p.S4317F	DNAH11_ENST00000328843.6_Missense_Mutation_p.S4324F	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4324					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S4324F(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTGGCATTATCTCCTGCTGTG	0.458									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											130	118	122					7																	21934518		1924	4140	6064	21901043	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.12950C>T	7.37:g.21934518C>T	ENSP00000475939:p.Ser4317Phe		21901043	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	16.52	3.146625	0.57044	.	.	ENSG00000105877	ENST00000328843	T	0.10573	2.86	5.62	4.74	0.60224	Dynein heavy chain (1);	0.217682	0.49916	D	0.000140	T	0.29850	0.0746	.	.	.	0.58432	D	0.999991	D	0.69078	0.997	D	0.65233	0.933	T	0.03212	-1.1060	9	0.87932	D	0	.	11.8648	0.52486	0.0:0.8092:0.1233:0.0676	.	4324	Q96DT5	DYH11_HUMAN	F	4324	ENSP00000330671:S4324F	ENSP00000330671:S4324F	S	+	2	0	DNAH11	21901043	0.999000	0.42202	0.626000	0.29213	0.363000	0.29612	4.934000	0.63491	1.373000	0.46208	0.563000	0.77884	TCT		0.458	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21934518	C	T	21934518	3	4	47	1	0	0	0	0	1	0	0	0	4610	913	32	3	13286	3	DNAH11	7	21934518	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	115933	21934518	137204145	908	5305										
STK31	56164	broad.mit.edu	37	chr7	23871798	23871798	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtagcttgatatgttataGaagttcaatgactgctgaac	9	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:23871798G>C	ENST00000355870.3	+	24	2992	c.2873G>C	c.(2872-2874)aGa>aCa	p.R958T	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.R935T|STK31_ENST00000354639.3_Missense_Mutation_p.R935T|STK31_ENST00000433467.2_Missense_Mutation_p.R935T	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	958	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)	p.R958T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATATGTTATAGAAGTTCAATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											119	116	117					7																	23871798		2203	4300	6503	23838323	SO:0001583	missense	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.2873G>C	7.37:g.23871798G>C	ENSP00000348132:p.Arg958Thr		23838323	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797173	0.31777	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.73681	-0.77;1.24;-0.77;-0.77	4.87	2.0	0.26442	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095518	0.45867	D	0.000323	T	0.61999	0.2392	N	0.13098	0.295	0.22366	N	0.999165	D;D;D	0.57257	0.979;0.979;0.979	P;P;P	0.52343	0.696;0.696;0.696	T	0.55003	-0.8208	10	0.59425	D	0.04	-3.6663	4.6919	0.12785	0.267:0.1591:0.5739:0.0	.	935;958;958	B4DZ06;A4D159;Q9BXU1	.;.;STK31_HUMAN	T	958;935;935;935	ENSP00000348132:R958T;ENSP00000411852:R935T;ENSP00000346660:R935T;ENSP00000406146:R935T	ENSP00000346660:R935T	R	+	2	0	STK31	23838323	1.000000	0.71417	0.196000	0.23383	0.250000	0.25880	3.139000	0.50577	0.177000	0.19895	0.491000	0.48974	AGA		0.363	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		C	23871798	G	C	23871798	3	2	47	1	0	0	0	0	1	0	0	0	15335	942	33	5	2967	5	STK31	7	23871798	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1937280	23871798	135266865	909	5306										
MPP6	51678	broad.mit.edu	37	chr7	24690152	24690152	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctggtaattgcccgaatcCtccatgggggaatgatagat	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:24690152C>T	ENST00000222644.5	+	5	722	c.472C>T	c.(472-474)Ctc>Ttc	p.L158F	MPP6_ENST00000409761.1_Missense_Mutation_p.L46F|MPP6_ENST00000396475.2_Missense_Mutation_p.L158F			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.L158F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						TGCCCGAATCCTCCATGGGGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											87	91	89					7																	24690152		2203	4300	6503	24656677	SO:0001583	missense	51678			AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.472C>T	7.37:g.24690152C>T	ENSP00000222644:p.Leu158Phe		24656677	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	37	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103079	0.76983	.	.	ENSG00000105926	ENST00000432190;ENST00000222644;ENST00000409761;ENST00000396475;ENST00000430180	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	6.06	6.06	0.98353	PDZ/DHR/GLGF (4);	0.000000	0.51477	D	0.000099	T	0.56702	0.2003	M	0.69463	2.115	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.55218	-0.8175	10	0.87932	D	0	.	18.8014	0.92018	0.0:1.0:0.0:0.0	.	158	Q9NZW5	MPP6_HUMAN	F	158;158;46;158;158	ENSP00000395859:L158F;ENSP00000222644:L158F;ENSP00000386262:L46F;ENSP00000379737:L158F;ENSP00000391020:L158F	ENSP00000222644:L158F	L	+	1	0	MPP6	24656677	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.488000	0.53229	2.882000	0.98803	0.655000	0.94253	CTC		0.358	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			T	24690152	C	T	24690152	3	4	47	1	0	0	0	0	1	0	0	0	9768	681	24	3	486	3	MPP6	7	24690152	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	818354	24690152	134448511	910	5307										
GGCT	79017	broad.mit.edu	37	chr7	30540294	30540294	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgccaaagtcaagcttaaAatcctacaaaggaaatcaaa	5	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:30540294A>C	ENST00000275428.4	-	2	279	c.145T>G	c.(145-147)Ttt>Gtt	p.F49V	GGCT_ENST00000598361.1_De_novo_Start_OutOfFrame|GGCT_ENST00000409436.1_Missense_Mutation_p.F49V|GGCT_ENST00000409390.1_Missense_Mutation_p.F49V|GGCT_ENST00000005374.6_Missense_Mutation_p.F49V|GGCT_ENST00000409144.1_Intron	NM_024051.3	NP_076956.1	O75223	GGCT_HUMAN	gamma-glutamylcyclotransferase	49					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|release of cytochrome c from mitochondria (GO:0001836)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	gamma-glutamylcyclotransferase activity (GO:0003839)|protein homodimerization activity (GO:0042803)	p.F49V(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8						TCAAGCTTAAAATCCTACAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	69	71					7																	30540294		2203	4300	6503	30506819	SO:0001583	missense	79017			BC019243	CCDS5428.1, CCDS56474.1, CCDS56475.1, CCDS56476.1	7p15-p14	2010-04-23	2010-04-23	2008-08-04	ENSG00000006625	ENSG00000006625	2.3.2.4		21705	protein-coding gene	gene with protein product		137170	"chromosome 7 open reading frame 24"	C7orf24, GCTG		17932939, 18515354	Standard	NM_024051		Approved	MGC3077, CRF21, Ggc	uc003tba.3	O75223	OTTHUMG00000128593	ENST00000275428.4:c.145T>G	7.37:g.30540294A>C	ENSP00000275428:p.Phe49Val		30506819	B2RDN0|B8ZZN4|B8ZZR8|Q9BS37	Missense_Mutation	SNP	ENST00000275428.4	37	CCDS5428.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.490757	0.84962	.	.	ENSG00000006625	ENST00000275428;ENST00000005374;ENST00000409390;ENST00000409436	.	.	.	6.16	6.16	0.99307	Butirosin biosynthesis, BtrG-like (1);AIG2-like (1);	0.214361	0.50627	D	0.000120	T	0.73783	0.3631	M	0.83118	2.625	0.80722	D	1	P;P	0.43352	0.804;0.785	B;P	0.47981	0.311;0.563	T	0.77838	-0.2439	9	0.72032	D	0.01	-6.6107	15.9872	0.80168	1.0:0.0:0.0:0.0	.	49;49	O75223-2;O75223	.;GGCT_HUMAN	V	49	.	ENSP00000005374:F49V	F	-	1	0	GGCT	30506819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.410000	0.90225	2.367000	0.80283	0.528000	0.53228	TTT		0.388	GGCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250447.2	NM_024051		C	30540294	A	C	30540294	3	2	47	1	0	0	0	0	1	0	0	0	6375	14	1	4	433	4	GGCT	7	30540294	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	5850142	30540294	128598369	911	5308										
INMT	11185	broad.mit.edu	37	chr7	30795039	30795039	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccctctctctctctgcagcGgccgatgggaggagaaggag	14	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:30795039G>A	ENST00000013222.5	+	3	380	c.364G>A	c.(364-366)Ggc>Agc	p.G122S	INMT_ENST00000409539.1_Splice_Site_p.G121S|INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Intron	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	122					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)	p.G122S(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						TCTCTGCAGCGGCCGATGGGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	7											15	15	15					7																	30795039		2202	4297	6499	30761564	SO:0001630	splice_region_variant	11185				CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.363-1G>A	7.37:g.30795039G>A			30761564	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	.	.	.	.	.	.	.	.	.	.	G	2.871	-0.234028	0.05983	.	.	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03094	4.05;4.05	3.05	-3.96	0.04106	.	1.289490	0.05278	N	0.518766	T	0.01421	0.0046	N	0.01515	-0.825	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49214	-0.8963	10	0.09338	T	0.73	-3.918	9.4879	0.38942	0.7654:0.0:0.2346:0.0	.	121;122	B8ZZ69;O95050	.;INMT_HUMAN	S	122;121	ENSP00000013222:G122S;ENSP00000386961:G121S	ENSP00000013222:G122S	G	+	1	0	INMT	30761564	0.000000	0.05858	0.000000	0.03702	0.229000	0.25112	-0.024000	0.12435	-1.054000	0.03214	-0.367000	0.07326	GGC		0.627	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	Missense_Mutation	A	30795039	G	A	30795039	5	1	47	1	0	0	0	0	0	0	1	0	7766	1130	39	1	374	1	INMT	7	30795039	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	254745	30795039	128343624	912	5309										
CCDC129	223075	broad.mit.edu	37	chr7	31682353	31682353	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggaggtagaaagccaagaGatcagagccacagcttagta	12	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:31682353G>T	ENST00000407970.3	+	11	1407	c.1369G>T	c.(1369-1371)Gat>Tat	p.D457Y	CCDC129_ENST00000451887.2_Missense_Mutation_p.D483Y|CCDC129_ENST00000319386.3_Missense_Mutation_p.D309Y|CCDC129_ENST00000409210.1_Missense_Mutation_p.D365Y	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	457								p.D309Y(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAAGCCAAGAGATCAGAGCCA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											74	69	71					7																	31682353		2203	4300	6503	31648878	SO:0001583	missense	223075			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1369G>T	7.37:g.31682353G>T	ENSP00000384416:p.Asp457Tyr		31648878	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620239	0.46736	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.25250	1.9;2.06;2.06;1.81	5.85	1.68	0.24146	.	0.667388	0.13877	N	0.356624	T	0.37183	0.0994	L	0.59436	1.845	0.09310	N	1	D;D;D;D	0.71674	0.995;0.987;0.987;0.998	P;P;P;P	0.62560	0.834;0.875;0.875;0.904	T	0.08806	-1.0704	10	0.54805	T	0.06	-3.3093	5.0335	0.14423	0.1687:0.0:0.5974:0.2339	.	483;467;457;309	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	Y	309;457;483;467;365	ENSP00000313062:D309Y;ENSP00000384416:D457Y;ENSP00000395835:D483Y;ENSP00000387214:D365Y	ENSP00000313062:D309Y	D	+	1	0	CCDC129	31648878	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.272000	0.18644	0.828000	0.34709	0.585000	0.79938	GAT		0.512	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31682353	G	T	31682353	3	4	47	1	0	0	0	0	1	0	0	0	2770	942	33	2	1407	2	CCDC129	7	31682353	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	887314	31682353	127456310	913	5310										
CCDC129	223075	broad.mit.edu	37	chr7	31683325	31683325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgggccccagcccctcaccAaatccgtctctctagactca	6	18	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:31683325A>G	ENST00000407970.3	+	11	2379	c.2341A>G	c.(2341-2343)Aaa>Gaa	p.K781E	CCDC129_ENST00000451887.2_Missense_Mutation_p.K807E|CCDC129_ENST00000319386.3_Missense_Mutation_p.K633E|CCDC129_ENST00000409210.1_Missense_Mutation_p.K689E	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	781								p.K633E(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						GCCCCTCACCAAATCCGTCTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											93	79	84					7																	31683325		2203	4300	6503	31649850	SO:0001583	missense	223075			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2341A>G	7.37:g.31683325A>G	ENSP00000384416:p.Lys781Glu		31649850	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919764	0.73098	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.62	4.42	0.53409	.	0.468479	0.19053	N	0.124000	T	0.49609	0.1567	M	0.69823	2.125	0.25235	N	0.989792	D;D;D;D	0.61697	0.972;0.99;0.99;0.988	P;P;P;P	0.55011	0.673;0.766;0.766;0.761	T	0.45818	-0.9235	10	0.72032	D	0.01	-18.3016	10.2568	0.43403	0.8223:0.1777:0.0:0.0	.	807;791;781;633	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	E	633;781;807;791;689	ENSP00000313062:K633E;ENSP00000384416:K781E;ENSP00000395835:K807E;ENSP00000387214:K689E	ENSP00000313062:K633E	K	+	1	0	CCDC129	31649850	1.000000	0.71417	0.997000	0.53966	0.869000	0.49853	2.959000	0.49153	2.141000	0.66446	0.533000	0.62120	AAA		0.512	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		G	31683325	A	G	31683325	3	3	47	1	0	0	0	0	1	0	0	0	2770	131	5	4	2379	4	CCDC129	7	31683325	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	972	31683325	127455338	914	5311										
HERPUD2	64224	broad.mit.edu	37	chr7	35678031	35678031	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgggctaaacgcgggataCactgggaatccaggtggagc	16	8	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:35678031C>A	ENST00000396081.1	-	5	1350	c.546G>T	c.(544-546)gtG>gtT	p.V182V	HERPUD2_ENST00000426180.1_5'UTR|HERPUD2_ENST00000311350.3_Silent_p.V182V	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	182					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.V182V(1)		kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						ACGCGGGATACACTGGGAATC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	7											78	73	75					7																	35678031		2203	4300	6503	35644556	SO:0001819	synonymous_variant	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.546G>T	7.37:g.35678031C>A			35644556	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	37	CCDS5446.1																																																																																				0.403	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		A	35678031	C	A	35678031	2	1	47	1	0	0	0	0	0	0	0	1	7085	465	17	2		2	HERPUD2	7	35678031	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3994706	35678031	123460632	915	5312										
TXNDC3	51314	broad.mit.edu	37	chr7	37916591	37916591	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcattacttcgaccaaatCtctttcatgaaaggaaaggt	8	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:37916591C>A	ENST00000199447.4	+	12	1348	c.976C>A	c.(976-978)Ctc>Atc	p.L326I	NME8_ENST00000440017.1_Missense_Mutation_p.L326I|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	326	NDK 2.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)	p.L326I(1)									TCGACCAAATCTCTTTCATGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	7											47	47	47					7																	37916591		2203	4300	6503	37883116	SO:0001583	missense	51314			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.976C>A	7.37:g.37916591C>A	ENSP00000199447:p.Leu326Ile		37883116	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	C	5.702	0.314031	0.10789	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.54479	0.57;0.57	3.67	1.4	0.22301	.	0.632758	0.13350	N	0.394517	T	0.33118	0.0852	L	0.27053	0.805	0.09310	N	1	B	0.25048	0.117	B	0.33392	0.163	T	0.34179	-0.9839	10	0.02654	T	1	-1.7303	5.7761	0.18279	0.3354:0.4745:0.1901:0.0	.	326	Q8N427	TXND3_HUMAN	I	326	ENSP00000199447:L326I;ENSP00000397063:L326I	ENSP00000199447:L326I	L	+	1	0	TXNDC3	37883116	0.011000	0.17503	0.029000	0.17559	0.951000	0.60555	0.226000	0.17776	0.306000	0.22856	0.591000	0.81541	CTC		0.308	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		A	37916591	C	A	37916591	3	1	47	1	0	0	0	0	1	0	0	0	16838	913	32	2	1014	2	TXNDC3	7	37916591	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2238560	37916591	121222072	916	5313										
SFRP4	6424	broad.mit.edu	37	chr7	37951817	37951817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatgagcgggacttgagttCgagggatgggtgatgaggac	18	4	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:37951817C>T	ENST00000436072.2	-	4	1072	c.695G>A	c.(694-696)cGa>cAa	p.R232Q	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	232	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R232Q(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GACTTGAGTTCGAGGGATGGG	0.478																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	7											237	215	222					7																	37951817		2203	4300	6503	37918342	SO:0001583	missense	6424			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.695G>A	7.37:g.37951817C>T	ENSP00000410715:p.Arg232Gln		37918342	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Missense_Mutation	SNP	ENST00000436072.2	37	CCDS5453.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.465911	0.84425	.	.	ENSG00000106483	ENST00000436072;ENST00000446575;ENST00000447200	T;T	0.22336	1.96;1.96	5.9	5.02	0.67125	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.295141	0.33834	N	0.004504	T	0.18087	0.0434	L	0.28400	0.85	0.29939	N	0.821191	B	0.33940	0.433	B	0.34722	0.188	T	0.07751	-1.0756	10	0.51188	T	0.08	.	13.8802	0.63678	0.0:0.9257:0.0:0.0743	.	232	Q6FHJ7	SFRP4_HUMAN	Q	232;229;98	ENSP00000410715:R232Q;ENSP00000402262:R98Q	ENSP00000410715:R232Q	R	-	2	0	SFRP4	37918342	0.918000	0.31147	0.999000	0.59377	0.997000	0.91878	1.773000	0.38563	1.483000	0.48342	0.650000	0.86243	CGA		0.478	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		T	37951817	C	T	37951817	3	4	47	1	0	0	0	0	1	0	0	0	14200	884	31	1	357	1	SFRP4	7	37951817	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	35226	37951817	121186846	917	5314										
CDK13	8621	broad.mit.edu	37	chr7	40133980	40133980	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcagcatcagccccaggatGaccccaaaagagaaggtggg	12	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:40133980G>T	ENST00000181839.4	+	14	4545	c.3940G>T	c.(3940-3942)Gac>Tac	p.D1314Y	CDK13_ENST00000340829.5_Missense_Mutation_p.D1254Y	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1314					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.D1314Y(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						GCCCCAGGATGACCCCAAAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											121	118	119					7																	40133980		2203	4300	6503	40100505	SO:0001583	missense	8621			M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.3940G>T	7.37:g.40133980G>T	ENSP00000181839:p.Asp1314Tyr		40100505	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	37	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983267	0.53827	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.46451	0.87;0.87	5.3	5.3	0.74995	.	.	.	.	.	T	0.47728	0.1461	L	0.40543	1.245	0.42490	D	0.992894	D;D	0.60160	0.987;0.978	P;P	0.55303	0.773;0.598	T	0.35400	-0.9790	8	.	.	.	-1.9966	14.456	0.67416	0.0:0.0:1.0:0.0	.	1254;1314	Q14004-2;Q14004	.;CDK13_HUMAN	Y	1314;1254	ENSP00000181839:D1314Y;ENSP00000340557:D1254Y	.	D	+	1	0	CDK13	40100505	1.000000	0.71417	0.829000	0.32907	0.982000	0.71751	5.851000	0.69481	2.487000	0.83934	0.655000	0.94253	GAC		0.498	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		T	40133980	G	T	40133980	3	4	47	1	0	0	0	0	1	0	0	0	3135	1290	45	2	3994	2	CDK13	7	40133980	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2182163	40133980	119004683	918	5315										
C7orf11	136647	broad.mit.edu	37	chr7	40172806	40172806	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttccaactcattagacattCttttttctctaacacgccct	2	13	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:40172806C>A	ENST00000306984.6	-	2	483	c.392G>T	c.(391-393)aGa>aTa	p.R131I	C7orf10_ENST00000401647.2_5'Flank|C7orf10_ENST00000309930.5_5'Flank|C7orf10_ENST00000540834.1_5'Flank|C7orf10_ENST00000335693.4_5'Flank	NM_138701.3	NP_619646.1	Q8TAP9	MPLKI_HUMAN	M-phase specific PLK1 interacting protein	131					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)		p.R131I(1)									ATTAGACATTCTTTTTTCTCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											122	127	125					7																	40172806		2203	4300	6503	40139331	SO:0001583	missense	136647			AX048113	CCDS5463.1	7p14	2014-09-17	2012-03-01	2012-03-01	ENSG00000168303	ENSG00000168303			16002	protein-coding gene	gene with protein product	tricothiodystrophy, non-photosensitive 1	609188	"chromosome 7 open reading frame 11"	C7orf11		11829489	Standard	NM_138701		Approved	ORF20, TTDN1	uc003thl.4	Q8TAP9	OTTHUMG00000128797	ENST00000306984.6:c.392G>T	7.37:g.40172806C>A	ENSP00000304553:p.Arg131Ile		40139331		Missense_Mutation	SNP	ENST00000306984.6	37	CCDS5463.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238670	0.79800	.	.	ENSG00000168303	ENST00000306984	T	0.78707	-1.2	5.55	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	L	0.51422	1.61	0.80722	D	1	P	0.48016	0.904	B	0.43082	0.407	T	0.79926	-0.1597	10	0.87932	D	0	-4.2495	16.5729	0.84629	0.0:0.8696:0.1304:0.0	.	131	Q8TAP9	TTDN1_HUMAN	I	131	ENSP00000304553:R131I	ENSP00000304553:R131I	R	-	2	0	C7orf11	40139331	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.841000	0.69409	1.556000	0.49512	0.591000	0.81541	AGA		0.363	MPLKIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250729.3	NM_138701		A	40172806	C	A	40172806	3	1	47	1	0	0	0	0	1	0	0	0	2383	913	32	2	151	2	C7orf11	7	40172806	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	38826	40172806	118965857	919	5316										
INHBA	3624	broad.mit.edu	37	chr7	41730112	41730112	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcactgccttccttggaaatCtcgaagtgcagcgtcttcct	8	13	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:41730112C>A	ENST00000242208.4	-	3	663	c.417G>T	c.(415-417)gaG>gaT	p.E139D	INHBA_ENST00000442711.1_Missense_Mutation_p.E139D|INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	139					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.E139D(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCTTGGAAATCTCGAAGTGCA	0.488										TSP Lung(11;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	7											51	47	49					7																	41730112		2203	4300	6503	41696637	SO:0001583	missense	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.417G>T	7.37:g.41730112C>A	ENSP00000242208:p.Glu139Asp		41696637	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.429073	0.43122	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.60171	0.21;0.21	6.06	4.24	0.50183	Transforming growth factor-beta, N-terminal (1);	0.163250	0.53938	D	0.000050	T	0.39384	0.1076	N	0.24115	0.695	0.44214	D	0.997043	B	0.12013	0.005	B	0.16289	0.015	T	0.12967	-1.0527	10	0.20046	T	0.44	-29.3423	9.0661	0.36465	0.0:0.7238:0.0:0.2762	.	139	P08476	INHBA_HUMAN	D	139	ENSP00000242208:E139D;ENSP00000397197:E139D	ENSP00000242208:E139D	E	-	3	2	INHBA	41696637	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.323000	0.33701	0.875000	0.35847	0.655000	0.94253	GAG		0.488	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			A	41730112	C	A	41730112	3	1	47	1	0	0	0	0	1	0	0	0	7762	912	32	2	867	2	INHBA	7	41730112	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1557306	41730112	117408551	920	5317										
GLI3	2737	broad.mit.edu	37	chr7	42004342	42004342	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcccacggtttggtcataGaactgaccagagtaattctg	10	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:42004342G>T	ENST00000395925.3	-	15	4413	c.4329C>A	c.(4327-4329)ttC>ttA	p.F1443L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1443					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F1443L(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TTTGGTCATAGAACTGACCAG	0.512									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							1	Substitution - Missense(1)	large_intestine(1)	7											62	63	63					7																	42004342		2203	4300	6503	41970867	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4329C>A	7.37:g.42004342G>T	ENSP00000379258:p.Phe1443Leu		41970867	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	6.227	0.410087	0.11812	.	.	ENSG00000106571	ENST00000395925	T	0.12361	2.69	5.62	2.59	0.31030	.	0.399652	0.30501	N	0.009499	T	0.06600	0.0169	N	0.25890	0.77	0.80722	D	1	B	0.10296	0.003	B	0.04013	0.001	T	0.23833	-1.0177	10	0.06757	T	0.87	.	4.1413	0.10194	0.1427:0.2173:0.5315:0.1085	.	1443	P10071	GLI3_HUMAN	L	1443	ENSP00000379258:F1443L	ENSP00000379258:F1443L	F	-	3	2	GLI3	41970867	0.855000	0.29742	0.999000	0.59377	0.994000	0.84299	1.434000	0.34958	0.696000	0.31696	0.655000	0.94253	TTC		0.512	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42004342	G	T	42004342	3	4	47	1	0	0	0	0	1	0	0	0	6459	933	33	2	417	2	GLI3	7	42004342	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	274230	42004342	117134321	921	5318										
GLI3	2737	broad.mit.edu	37	chr7	42007393	42007393	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccatgattggggtttcatcGatggcactgaggtctcctat	11	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:42007393G>A	ENST00000395925.3	-	14	2316	c.2232C>T	c.(2230-2232)atC>atT	p.I744I	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	744					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I744I(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GGGTTTCATCGATGGCACTGA	0.542									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							1	Substitution - coding silent(1)	large_intestine(1)	7											215	196	203					7																	42007393		2203	4300	6503	41973918	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2232C>T	7.37:g.42007393G>A			41973918	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.542	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42007393	G	A	42007393	2	1	47	1	0	0	0	0	0	0	0	1	6459	1048	37	1		1	GLI3	7	42007393	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3051	42007393	117131270	922	5319										
HECW1	23072	broad.mit.edu	37	chr7	43532709	43532709	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgacaagattgtggcatttCttcgccagccaaacattttt	7	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:43532709C>A	ENST00000395891.2	+	19	3972	c.3367C>A	c.(3367-3369)Ctt>Att	p.L1123I	HECW1_ENST00000453890.1_Missense_Mutation_p.L1089I	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1123					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L1102I(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TGTGGCATTTCTTCGCCAGCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	7											76	72	73					7																	43532709		1931	4149	6080	43499234	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3367C>A	7.37:g.43532709C>A	ENSP00000379228:p.Leu1123Ile		43499234	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588957	0.86851	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	D;D	0.84873	-1.91;-1.91	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.91643	0.7359	M	0.66297	2.02	0.80722	D	1	D;D	0.71674	0.998;0.974	D;P	0.80764	0.994;0.78	D	0.91724	0.5391	10	0.54805	T	0.06	.	18.624	0.91331	0.0:1.0:0.0:0.0	.	1089;1123	B4DH42;Q76N89	.;HECW1_HUMAN	I	1123;1089;1123	ENSP00000379228:L1123I;ENSP00000407774:L1089I	ENSP00000265522:L1123I	L	+	1	0	HECW1	43499234	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.608000	0.61141	2.499000	0.84300	0.655000	0.94253	CTT		0.468	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43532709	C	A	43532709	3	1	47	1	0	0	0	0	1	0	0	0	7063	913	32	2	3433	2	HECW1	7	43532709	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1525316	43532709	115605954	923	5320										
PKD1L1	168507	broad.mit.edu	37	chr7	47835736	47835736	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttggggtaaagtcatgaGaaaacctctcagctaggaaa	10	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:47835736G>A	ENST00000289672.2	-	55	8256	c.8206C>T	c.(8206-8208)Ctc>Ttc	p.L2736F	C7orf69_ENST00000418326.2_Intron|C7orf69_ENST00000258776.4_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2736					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.L2736F(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AAAGTCATGAGAAAACCTCTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	7											49	52	51					7																	47835736		2203	4298	6501	47802261	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.8206C>T	7.37:g.47835736G>A	ENSP00000289672:p.Leu2736Phe		47802261	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	0.066	-1.212487	0.01555	.	.	ENSG00000158683	ENST00000289672	T	0.33216	1.42	5.46	0.563	0.17296	.	2.633870	0.01691	N	0.026669	T	0.19248	0.0462	N	0.11560	0.145	0.09310	N	0.999998	B	0.22080	0.064	B	0.21151	0.033	T	0.20605	-1.0270	10	0.33940	T	0.23	-6.5686	7.8577	0.29491	0.4575:0.0:0.5425:0.0	.	2736	Q8TDX9	PK1L1_HUMAN	F	2736	ENSP00000289672:L2736F	ENSP00000289672:L2736F	L	-	1	0	PKD1L1	47802261	0.044000	0.20184	0.001000	0.08648	0.084000	0.17831	-0.053000	0.11846	-0.188000	0.10499	0.655000	0.94253	CTC		0.328	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47835736	G	A	47835736	3	1	47	1	0	0	0	0	1	0	0	0	11995	942	33	3	355	3	PKD1L1	7	47835736	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4303027	47835736	111302927	924	5321										
SUN3	256979	broad.mit.edu	37	chr7	48068523	48068523	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcagcccttcttgcctttgTttttccactcatgatcccct	6	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:48068523T>C	ENST00000297325.4	-	1	172	c.13A>G	c.(13-15)Aca>Gca	p.T5A	SUN3_ENST00000453192.2_5'UTR|SUN3_ENST00000395572.2_Missense_Mutation_p.T5A|SUN3_ENST00000412142.1_5'UTR	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	5						integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)		p.T5A(1)|p.T5S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTTGCCTTTGTTTTTCCACTC	0.433																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7											121	114	117					7																	48068523		2203	4300	6503	48035048	SO:0001583	missense	256979			AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.13A>G	7.37:g.48068523T>C	ENSP00000297325:p.Thr5Ala		48035048	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	37	CCDS34636.1	.	.	.	.	.	.	.	.	.	.	T	3.477	-0.106785	0.06924	.	.	ENSG00000164744	ENST00000297325;ENST00000395572	T;T	0.21543	2.0;2.0	4.05	-1.79	0.07932	.	1.288690	0.05484	N	0.555320	T	0.09949	0.0244	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.36553	-0.9743	10	0.15066	T	0.55	-10.0057	8.0055	0.30323	0.0:0.3117:0.1936:0.4948	.	5	Q8TAQ9	SUN3_HUMAN	A	5	ENSP00000297325:T5A;ENSP00000378939:T5A	ENSP00000297325:T5A	T	-	1	0	SUN3	48035048	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.443000	0.06862	-0.724000	0.04908	-1.937000	0.00501	ACA		0.433	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		C	48068523	T	C	48068523	3	2	47	1	0	0	0	0	1	0	0	0	15432	1725	60	4	1100	4	SUN3	7	48068523	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	232787	48068523	111070140	925	5322										
ABCA13	154664	broad.mit.edu	37	chr7	48315144	48315144	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatcatagaaaaacttaaaAatgtcaactttacaaaagtt	3	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:48315144A>C	ENST00000435803.1	+	17	5905	c.5881A>C	c.(5881-5883)Aat>Cat	p.N1961H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1961					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.N1906H(1)|p.N1961H(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAAACTTAAAAATGTCAACTT	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	7											51	49	50					7																	48315144		1814	4072	5886	48285690	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5881A>C	7.37:g.48315144A>C	ENSP00000411096:p.Asn1961His		48285690	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.904135	0.33628	.	.	ENSG00000179869	ENST00000435803	T	0.16324	2.35	5.49	-1.34	0.09143	.	1.364740	0.04922	N	0.455152	T	0.21387	0.0515	L	0.60455	1.87	0.09310	N	1	P	0.51933	0.949	P	0.49752	0.621	T	0.17319	-1.0373	9	.	.	.	.	1.0324	0.01541	0.3851:0.2611:0.2191:0.1346	.	1961	Q86UQ4	ABCAD_HUMAN	H	1961	ENSP00000411096:N1961H	.	N	+	1	0	ABCA13	48285690	0.043000	0.20138	0.002000	0.10522	0.888000	0.51559	0.545000	0.23268	-0.213000	0.10094	0.477000	0.44152	AAT		0.333	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48315144	A	C	48315144	3	2	47	1	0	0	0	0	1	0	0	0	31	14	1	4	5776	4	ABCA13	7	48315144	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	246621	48315144	110823519	926	5323										
FIGNL1	63979	broad.mit.edu	37	chr7	50513125	50513125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcagcagtttgtaaactgcGaataggaccaagagaagcct	11	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:50513125G>A	ENST00000419119.1	-	2	3414	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	FIGNL1_ENST00000433017.1_Missense_Mutation_p.R621C|FIGNL1_ENST00000395556.2_Missense_Mutation_p.R621C|FIGNL1_ENST00000356889.4_Missense_Mutation_p.R621C			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	621					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)	p.R621C(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				TGTAAACTGCGAATAGGACCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											93	87	89					7																	50513125		2203	4300	6503	50480619	SO:0001583	missense	63979			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1861C>T	7.37:g.50513125G>A	ENSP00000410811:p.Arg621Cys		50480619	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.819937	0.90873	.	.	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.98090	-4.71;-4.71;-4.71;-4.71	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.99399	0.9788	H	0.98769	4.325	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98370	1.0553	10	0.87932	D	0	-6.7561	19.8676	0.96824	0.0:0.0:1.0:0.0	.	621	Q6PIW4	FIGL1_HUMAN	C	621	ENSP00000349356:R621C;ENSP00000378924:R621C;ENSP00000399997:R621C;ENSP00000410811:R621C	ENSP00000349356:R621C	R	-	1	0	FIGNL1	50480619	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGC		0.438	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		A	50513125	G	A	50513125	3	1	47	1	0	0	0	0	1	0	0	0	5911	1058	37	1	167	1	FIGNL1	7	50513125	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2197981	50513125	108625538	927	5324										
CCT6A	908	broad.mit.edu	37	chr7	56130750	56130750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggttgatgagatcatgcGagctggaatgtcttctctga	12	7	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:56130750G>A	ENST00000275603.4	+	14	1787	c.1568G>A	c.(1567-1569)cGa>cAa	p.R523Q	SUMF2_ENST00000437307.2_5'Flank|CCT6A_ENST00000540286.1_Missense_Mutation_p.R492Q|CCT6A_ENST00000335503.3_Missense_Mutation_p.R478Q|SUMF2_ENST00000413756.1_5'Flank|SUMF2_ENST00000434526.2_5'Flank|SNORA15_ENST00000384439.1_RNA|SUMF2_ENST00000275607.9_5'Flank|SUMF2_ENST00000342190.6_5'Flank|CCT6A_ENST00000462133.1_3'UTR|SUMF2_ENST00000395436.2_5'Flank|SUMF2_ENST00000395435.2_5'Flank	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	523					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.R523Q(1)		breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAGATCATGCGAGCTGGAATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	7											148	134	139					7																	56130750		2203	4300	6503	56098244	SO:0001583	missense	908			M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"Heat Shock Proteins / Chaperonins"	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.1568G>A	7.37:g.56130750G>A	ENSP00000275603:p.Arg523Gln		56098244	A6NCD2|Q3KP28|Q75LP4|Q96S46	Missense_Mutation	SNP	ENST00000275603.4	37	CCDS5523.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.584228	0.86748	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	T;T;T	0.78595	-1.19;-1.19;-1.19	4.73	4.73	0.59995	.	0.060198	0.64402	N	0.000005	T	0.80105	0.4562	M	0.66378	2.025	0.80722	D	1	D;B;P	0.56035	0.974;0.382;0.929	P;P;P	0.47118	0.538;0.473;0.538	T	0.82301	-0.0525	10	0.48119	T	0.1	-5.6829	16.7024	0.85357	0.0:0.0:1.0:0.0	.	492;478;523	B4DPJ8;A6NCD2;P40227	.;.;TCPZ_HUMAN	Q	523;478;492;381	ENSP00000275603:R523Q;ENSP00000352019:R478Q;ENSP00000438488:R492Q	ENSP00000275603:R523Q	R	+	2	0	CCT6A	56098244	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	9.191000	0.94940	2.180000	0.69256	0.313000	0.20887	CGA		0.428	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762		A	56130750	G	A	56130750	3	1	47	1	0	0	0	0	1	0	0	0	2963	1058	37	1	1622	1	CCT6A	7	56130750	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5617625	56130750	103007913	928	5325										
ZNF479	90827	broad.mit.edu	37	chr7	57188594	57188594	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatttccagtatatcttgtTttatctctattggaatttga	5	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:57188594T>G	ENST00000331162.4	-	5	798	c.528A>C	c.(526-528)aaA>aaC	p.K176N		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	176					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K176N(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			TATATCTTGTTTTATCTCTAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	7											53	50	51					7																	57188594		1885	4123	6008	57192536	SO:0001583	missense	90827			AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.528A>C	7.37:g.57188594T>G	ENSP00000333776:p.Lys176Asn		57192536		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	t	1.105	-0.660045	0.03454	.	.	ENSG00000185177	ENST00000331162	T	0.29142	1.58	0.946	-1.89	0.07689	.	.	.	.	.	T	0.23727	0.0574	L	0.60067	1.865	0.09310	N	1	B	0.15141	0.012	B	0.11329	0.006	T	0.24368	-1.0162	9	0.46703	T	0.11	.	1.8771	0.03220	0.4335:0.2786:0.0:0.2879	.	176	Q96JC4	ZN479_HUMAN	N	176	ENSP00000333776:K176N	ENSP00000333776:K176N	K	-	3	2	ZNF479	57192536	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.458000	0.02372	-2.055000	0.00899	-2.146000	0.00336	AAA		0.294	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		G	57188594	T	G	57188594	3	3	47	1	0	0	0	0	1	0	0	0	17972	1838	64	4	1050	4	ZNF479	7	57188594	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1057844	57188594	101950069	929	5326										
ZNF107	51427	broad.mit.edu	37	chr7	64167008	64167008	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacttcaaatgtaaagaatGtagcaaatcattttgcgtgc	7	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:64167008G>T	ENST00000395391.1	+	4	1701	c.326G>T	c.(325-327)tGt>tTt	p.C109F	ZNF107_ENST00000344930.3_Missense_Mutation_p.C109F|ZNF107_ENST00000423627.1_Missense_Mutation_p.C109F			Q9UII5	ZN107_HUMAN	zinc finger protein 107	109					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C109F(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TGTAAAGAATGTAGCAAATCA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	7											32	31	31					7																	64167008		2201	4300	6501	63804443	SO:0001583	missense	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.326G>T	7.37:g.64167008G>T	ENSP00000378789:p.Cys109Phe		63804443		Missense_Mutation	SNP	ENST00000395391.1	37	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	14.21	2.467433	0.43839	.	.	ENSG00000196247	ENST00000541526;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T	0.59364	0.27;0.27;0.27	0.916	0.916	0.19373	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.68384	0.2995	M	0.93241	3.395	0.39686	D	0.970976	P	0.39250	0.665	P	0.45428	0.48	T	0.69495	-0.5130	8	.	.	.	.	7.1683	0.25704	0.0:0.0:1.0:0.0	.	109	Q9UII5	ZN107_HUMAN	F	109	ENSP00000343443:C109F;ENSP00000400037:C109F;ENSP00000378789:C109F	.	C	+	2	0	ZNF107	63804443	1.000000	0.71417	0.154000	0.22540	0.153000	0.21895	3.372000	0.52387	0.300000	0.22699	0.305000	0.20034	TGT		0.303	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		T	64167008	G	T	64167008	3	4	47	1	0	0	0	0	1	0	0	0	17754	1377	48	2	332	2	ZNF107	7	64167008	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6978414	64167008	94971655	930	5327										
ZNF92	168374	broad.mit.edu	37	chr7	64864193	64864193	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacccttactaaacataaaaGaattcatacgggagaaaaac	5	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:64864193G>T	ENST00000328747.7	+	4	1365	c.1166G>T	c.(1165-1167)aGa>aTa	p.R389I	ZNF92_ENST00000357512.2_Missense_Mutation_p.R357I|ZNF92_ENST00000450302.2_Missense_Mutation_p.R320I|ZNF92_ENST00000431504.1_Missense_Mutation_p.R313I	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	389					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R389I(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				AAACATAAAAGAATTCATACG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											36	41	39					7																	64864193		2196	4294	6490	64501628	SO:0001583	missense	168374			M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.1166G>T	7.37:g.64864193G>T	ENSP00000332595:p.Arg389Ile		64501628	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	37	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	G	4.401	0.074165	0.08485	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	0.418	-0.581	0.11713	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03827	0.0108	M	0.69823	2.125	0.43242	D	0.995156	B;B	0.11235	0.001;0.004	B;B	0.12837	0.002;0.008	T	0.29274	-1.0017	9	0.42905	T	0.14	.	4.6192	0.12442	0.3005:0.0:0.6995:0.0	.	357;389	Q03936-3;Q03936	.;ZNF92_HUMAN	I	389;313;357;320	ENSP00000332595:R389I;ENSP00000400495:R313I;ENSP00000350113:R357I;ENSP00000396126:R320I	ENSP00000332595:R389I	R	+	2	0	ZNF92	64501628	0.000000	0.05858	0.220000	0.23810	0.211000	0.24417	-0.064000	0.11636	-0.396000	0.07703	-0.384000	0.06662	AGA		0.363	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		T	64864193	G	T	64864193	3	4	47	1	0	0	0	0	1	0	0	0	18240	942	33	2	1180	2	ZNF92	7	64864193	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	697185	64864193	94274470	931	5328										
RABGEF1	27342	broad.mit.edu	37	chr7	66273978	66273978	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agacctctcccaggaagcaaGaagctgagagttggtctcct	11	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:66273978G>T	ENST00000284957.5	+	9	1260	c.1183G>T	c.(1183-1185)Gaa>Taa	p.E395*	RABGEF1_ENST00000437078.2_Nonsense_Mutation_p.E409*|KCTD7_ENST00000451741.2_Nonsense_Mutation_p.E395*|RABGEF1_ENST00000484547.2_3'UTR|KCTD7_ENST00000380828.2_Nonsense_Mutation_p.E435*|RABGEF1_ENST00000450873.2_Nonsense_Mutation_p.E395*|RABGEF1_ENST00000439720.2_Nonsense_Mutation_p.E408*|GTF2IRD1P1_ENST00000457166.1_RNA|KCTD7_ENST00000510829.2_Nonsense_Mutation_p.E395*			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	612					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)	p.E395*(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						CAGGAAGCAAGAAGCTGAGAG	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											92	86	88					7																	66273978		2203	4300	6503	65911413	SO:0001587	stop_gained	27342			AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.1183G>T	7.37:g.66273978G>T	ENSP00000284957:p.Glu395*		65911413	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Nonsense_Mutation	SNP	ENST00000284957.5	37	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	G	37	6.199947	0.97371	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	.	.	.	5.83	5.83	0.93111	.	0.268542	0.43260	D	0.000590	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-18.7009	19.551	0.95319	0.0:0.0:1.0:0.0	.	.	.	.	X	479;435;395;395;311;395;395;408;409	.	ENSP00000370207:E479X	E	+	1	0	RABGEF1;KCTD7	65911413	1.000000	0.71417	0.985000	0.45067	0.987000	0.75469	5.095000	0.64529	2.937000	0.99478	0.650000	0.86243	GAA		0.458	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504		T	66273978	G	T	66273978	4	4	47	1	0	0	0	0	0	1	0	0	13003	943	33	2	1213	2	RABGEF1	7	66273978	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1409785	66273978	92864685	932	5329										
AUTS2	26053	broad.mit.edu	37	chr7	70231120	70231120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcaagacatcttgcgacagGaactgaacactcgttttttg	9	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:70231120G>A	ENST00000342771.4	+	9	1810	c.1489G>A	c.(1489-1491)Gaa>Aaa	p.E497K	AUTS2_ENST00000406775.2_Missense_Mutation_p.E497K	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	497								p.E497K(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTTGCGACAGGAACTGAACAC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	7											141	137	138					7																	70231120		2203	4300	6503	69869056	SO:0001583	missense	26053			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1489G>A	7.37:g.70231120G>A	ENSP00000344087:p.Glu497Lys		69869056	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	35	5.552512	0.96501	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.54279	0.58;0.58	5.77	5.77	0.91146	.	0.093567	0.64402	D	0.000001	T	0.71492	0.3346	M	0.64404	1.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.986	T	0.68307	-0.5443	9	.	.	.	-14.5446	19.9983	0.97395	0.0:0.0:1.0:0.0	.	497;497	Q8WXX7-2;Q8WXX7	.;AUTS2_HUMAN	K	497	ENSP00000385263:E497K;ENSP00000344087:E497K	.	E	+	1	0	AUTS2	69869056	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.159000	0.94728	2.724000	0.93272	0.561000	0.74099	GAA		0.577	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	70231120	G	A	70231120	3	1	47	1	0	0	0	0	1	0	0	0	1226	1175	41	3	1668	3	AUTS2	7	70231120	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3957142	70231120	88907543	933	5330										
BCL7B	9275	broad.mit.edu	37	chr7	72957958	72957958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcgggctgctgaactgttcGattttgacttttctttctag	9	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:72957958G>A	ENST00000223368.2	-	3	608	c.185C>T	c.(184-186)tCg>tTg	p.S62L	BCL7B_ENST00000411832.1_Missense_Mutation_p.S62L|BCL7B_ENST00000482231.1_5'UTR	NM_001707.3	NP_001698.2	Q9BQE9	BCL7B_HUMAN	B-cell CLL/lymphoma 7B	62							actin binding (GO:0003779)	p.S62L(2)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	9		Lung NSC(55;0.0659)|all_lung(88;0.152)				TGAACTGTTCGATTTTGACTT	0.468																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	7											158	158	158					7																	72957958		2203	4300	6503	72595894	SO:0001583	missense	9275			X89985	CCDS5550.1, CCDS56489.1, CCDS75613.1	7q11.23	2008-07-18			ENSG00000106635	ENSG00000106635			1005	protein-coding gene	gene with protein product		605846				8605326, 9806765	Standard	NM_001707		Approved		uc003tyf.2	Q9BQE9	OTTHUMG00000023412	ENST00000223368.2:c.185C>T	7.37:g.72957958G>A	ENSP00000223368:p.Ser62Leu		72595894	A8K226|C9JWD3|D3DXF0|O43769|Q13845|Q6ZW75	Missense_Mutation	SNP	ENST00000223368.2	37	CCDS5550.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.205956	0.58234	.	.	ENSG00000106635	ENST00000223368;ENST00000411832	T	0.45276	0.9	5.38	5.38	0.77491	.	0.293955	0.30979	N	0.008493	T	0.48295	0.1492	L	0.27053	0.805	0.32609	N	0.524901	D;D	0.76494	0.999;0.96	D;B	0.72625	0.978;0.238	T	0.52946	-0.8507	10	0.33141	T	0.24	.	12.2259	0.54459	0.0:0.1707:0.8293:0.0	.	62;62	C9JWD3;Q9BQE9	.;BCL7B_HUMAN	L	62	ENSP00000223368:S62L	ENSP00000223368:S62L	S	-	2	0	BCL7B	72595894	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.812000	0.55628	2.793000	0.96121	0.655000	0.94253	TCG		0.468	BCL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252194.1	NM_001707		A	72957958	G	A	72957958	3	1	47	1	0	0	0	0	1	0	0	0	1380	1059	37	1	439	1	BCL7B	7	72957958	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2726838	72957958	86180705	934	5331										
CCDC146	57639	broad.mit.edu	37	chr7	76891505	76891505	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actaccatgatgaactttctCgtaagcaaagagagaaagaa	8	7	1	5	rs148455218		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:76891505C>T	ENST00000285871.4	+	9	1181	c.1054C>T	c.(1054-1056)Cgt>Tgt	p.R352C	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Missense_Mutation_p.R98C	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	352								p.R352C(1)|p.R352S(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TGAACTTTCTCGTAAGCAAAG	0.403																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						C	CYS/ARG	0,4406		0,0,2203	100	100	100		1054	5.8	1	7	dbSNP_134	100	3,8597	3.0+/-9.4	0,3,4297	no	missense	CCDC146	NM_020879.2	180	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	352/956	76891505	3,13003	2203	4300	6503	76729441	SO:0001583	missense	57639			BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1054C>T	7.37:g.76891505C>T	ENSP00000285871:p.Arg352Cys		76729441	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372813	0.61624	0.0	3.49E-4	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.42131	0.98;0.98	5.78	5.78	0.91487	.	0.380168	0.29501	N	0.011975	T	0.44095	0.1277	L	0.58101	1.795	0.58432	D	0.999996	B;B	0.26876	0.162;0.104	B;B	0.19946	0.023;0.027	T	0.36114	-0.9761	10	0.66056	D	0.02	-1.5862	18.7832	0.91942	0.0:1.0:0.0:0.0	.	98;352	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	C	352;98	ENSP00000285871:R352C;ENSP00000413885:R98C	ENSP00000285871:R352C	R	+	1	0	AC007000.1	76729441	0.971000	0.33674	0.999000	0.59377	0.992000	0.81027	1.796000	0.38794	2.744000	0.94065	0.563000	0.77884	CGT		0.403	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		T	76891505	C	T	76891505	3	4	47	1	0	0	0	0	1	0	0	0	2786	884	31	1	1084	1	CCDC146	7	76891505	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3933547	76891505	82247158	935	5332										
PTPN12	5782	broad.mit.edu	37	chr7	77200461	77200461	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacagccactggagaaaaaGaagaaaatgttaaaaagaac	8	7	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:77200461G>T	ENST00000248594.6	+	2	438	c.166G>T	c.(166-168)Gaa>Taa	p.E56*	PTPN12_ENST00000415482.2_5'UTR|PTPN12_ENST00000435495.2_5'UTR	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	56	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)	p.E56*(1)		breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TGGAGAAAAAGAAGAAAATGT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											48	49	49					7																	77200461		2201	4295	6496	77038397	SO:0001587	stop_gained	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.166G>T	7.37:g.77200461G>T	ENSP00000248594:p.Glu56*		77038397	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Nonsense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.683503|5.683503	0.96774|0.96774	.|.	.|.	ENSG00000127947|ENSG00000127947	ENST00000248594|ENST00000522115	.|.	.|.	.|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.71728	.|0.3374	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67499	.|-0.5655	.|5	0.66056|0.29301	D|T	0.02|0.29	.|.	18.9405|18.9405	0.92604|0.92604	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	56|18	.|.	ENSP00000248594:E56X|ENSP00000430726:K18N	E|K	+|+	1|3	0|2	PTPN12|PTPN12	77038397|77038397	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.306000|3.306000	0.51881|0.51881	2.546000|2.546000	0.85860|0.85860	0.460000|0.460000	0.39030|0.39030	GAA|AAG		0.308	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			T	77200461	G	T	77200461	4	4	47	1	0	0	0	0	0	1	0	0	12816	943	33	2	172	2	PTPN12	7	77200461	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	308956	77200461	81938202	936	5333										
MAGI2	9863	broad.mit.edu	37	chr7	77998481	77998481	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttagagacttactcaacataAtaagtgccataaatgggatc	7	7	1	1	rs374543762		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:77998481A>C	ENST00000354212.4	-	7	1348	c.1095T>G	c.(1093-1095)taT>taG	p.Y365*	MAGI2_ENST00000522391.1_Nonsense_Mutation_p.Y365*|MAGI2_ENST00000419488.1_Nonsense_Mutation_p.Y365*|MAGI2_ENST00000536571.1_Nonsense_Mutation_p.Y197*|MAGI2_ENST00000535697.1_Nonsense_Mutation_p.Y202*	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	365	Interaction with DDN.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.Y365*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				ACTCAACATAATAAGTGCCAT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											68	69	68					7																	77998481		2201	4299	6500	77836417	SO:0001587	stop_gained	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1095T>G	7.37:g.77998481A>C	ENSP00000346151:p.Tyr365*		77836417	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Nonsense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	42	9.491633	0.99186	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	.	.	.	5.86	-0.549	0.11829	.	0.000000	0.33650	U	0.004697	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7639	0.40548	0.6514:0.0:0.3486:0.0	.	.	.	.	X	365;365;365;365;197;202	.	ENSP00000346151:Y365X	Y	-	3	2	MAGI2	77836417	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	1.925000	0.40074	-0.309000	0.08779	0.482000	0.46254	TAT		0.308	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	77998481	A	C	77998481	4	2	47	1	0	0	0	0	0	1	0	0	9221	108	4	4	3336	4	MAGI2	7	77998481	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	798020	77998481	81140182	937	5334										
CACNA2D1	781	broad.mit.edu	37	chr7	81593665	81593665	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggatcaatctctccaaaaAatcttccaatctggtgaaga	7	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:81593665A>C	ENST00000356253.5	-	33	2876	c.2621T>G	c.(2620-2622)tTt>tGt	p.F874C	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.F862C|CACNA2D1_ENST00000535308.1_Missense_Mutation_p.F74C			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	874					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.F862C(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTCTCCAAAAAATCTTCCAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											48	48	48					7																	81593665		2203	4300	6503	81431601	SO:0001583	missense	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2621T>G	7.37:g.81593665A>C	ENSP00000348589:p.Phe874Cys		81431601	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	A	21.9	4.217731	0.79352	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	D;D;D	0.82167	-1.58;-1.58;-1.58	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.91523	0.7323	M	0.82517	2.595	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.92799	0.6255	10	0.87932	D	0	-23.1057	15.7082	0.77602	1.0:0.0:0.0:0.0	.	74;862	B7Z658;P54289-2	.;.	C	862;881;874;74	ENSP00000349320:F862C;ENSP00000348589:F874C;ENSP00000443124:F74C	ENSP00000284088:F881C	F	-	2	0	CACNA2D1	81431601	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.478000	0.90428	2.167000	0.68274	0.528000	0.53228	TTT		0.353	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81593665	A	C	81593665	3	2	47	1	0	0	0	0	1	0	0	0	2554	14	1	4	718	4	CACNA2D1	7	81593665	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3595184	81593665	77544998	938	5335										
CACNA2D1	781	broad.mit.edu	37	chr7	81637059	81637059	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccggaagagttccagtaatgAcaagtcccagttcctaaaaa	8	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:81637059A>C	ENST00000356253.5	-	16	1631	c.1376T>G	c.(1375-1377)gTc>gGc	p.V459G	MIR1255B1_ENST00000439234.1_RNA|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.V459G|CACNA2D1_ENST00000464354.1_5'UTR|MIR1255B1_ENST00000454066.1_RNA			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	459	Cache.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.V459G(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TCCAGTAATGACAAGTCCCAG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	7											46	45	45					7																	81637059		2203	4298	6501	81474995	SO:0001583	missense	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1376T>G	7.37:g.81637059A>C	ENSP00000348589:p.Val459Gly		81474995	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	A	24.7	4.560506	0.86335	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.09445	2.98;2.98	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.37461	0.1004	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.29822	-0.9999	10	0.87932	D	0	-16.494	15.4403	0.75178	1.0:0.0:0.0:0.0	.	459	P54289-2	.	G	459	ENSP00000349320:V459G;ENSP00000348589:V459G	ENSP00000284088:V459G	V	-	2	0	CACNA2D1	81474995	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.866000	0.92307	2.122000	0.65172	0.477000	0.44152	GTC		0.308	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81637059	A	C	81637059	3	2	47	1	0	0	0	0	1	0	0	0	2554	275	10	4	1995	4	CACNA2D1	7	81637059	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	43394	81637059	77501604	939	5336										
PCLO	27445	broad.mit.edu	37	chr7	82435023	82435023	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcctcggaataggaaataGattagtctcccctgcagtgc	9	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:82435023G>T	ENST00000333891.9	-	21	15251	c.14914C>A	c.(14914-14916)Cta>Ata	p.L4972I		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.L4972I(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATAGGAAATAGATTAGTCTCC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	7											61	64	63					7																	82435023		2015	4188	6203	82272959	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14914C>A	7.37:g.82435023G>T	ENSP00000334319:p.Leu4972Ile		82272959		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.064580	0.36470	.	.	ENSG00000186472	ENST00000333891	T	0.15256	2.44	5.69	5.69	0.88448	.	.	.	.	.	T	0.16811	0.0404	N	0.08118	0	0.80722	D	1	D	0.57571	0.98	P	0.52514	0.701	T	0.06789	-1.0807	9	0.87932	D	0	.	15.4168	0.74977	0.0:0.0:0.8603:0.1397	.	4972	Q9Y6V0-5	.	I	4972	ENSP00000334319:L4972I	ENSP00000334319:L4972I	L	-	1	2	PCLO	82272959	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.044000	0.41241	2.668000	0.90789	0.557000	0.71058	CTA		0.478	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82435023	G	T	82435023	3	4	47	1	0	0	0	0	1	0	0	0	11614	933	33	2	534	2	PCLO	7	82435023	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	797964	82435023	76703640	940	5337										
PCLO	27445	broad.mit.edu	37	chr7	82581432	82581432	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctccttccaaatggtaatTtataaaccacatcacagcac	4	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:82581432T>G	ENST00000333891.9	-	5	9174	c.8837A>C	c.(8836-8838)aAa>aCa	p.K2946T	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.K2946T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.K2946T(2)|p.K2877T(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AAATGGTAATTTATAAACCAC	0.428																																																3	Substitution - Missense(3)	large_intestine(3)	7											101	100	101					7																	82581432		1913	4133	6046	82419368	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8837A>C	7.37:g.82581432T>G	ENSP00000334319:p.Lys2946Thr		82419368		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	9.043	0.990210	0.18966	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.29142	1.62;1.58	5.67	3.27	0.37495	.	.	.	.	.	T	0.21631	0.0521	L	0.34521	1.04	0.80722	D	1	B;B	0.18166	0.015;0.026	B;B	0.18561	0.022;0.022	T	0.05599	-1.0875	9	0.87932	D	0	.	5.9274	0.19120	0.0:0.141:0.14:0.719	.	2946;2946	Q9Y6V0-5;Q9Y6V0-6	.;.	T	2877;2946;2946	ENSP00000334319:K2946T;ENSP00000388393:K2946T	ENSP00000334319:K2946T	K	-	2	0	PCLO	82419368	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.859000	0.48364	0.403000	0.25479	0.455000	0.32223	AAA		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82581432	T	G	82581432	3	3	47	1	0	0	0	0	1	0	0	0	11614	1841	64	4	6692	4	PCLO	7	82581432	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	146409	82581432	76557231	941	5338										
PCLO	27445	broad.mit.edu	37	chr7	82585490	82585490	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttccctttgtttcttccttCttctggctctcagtactgct	5	13	4	0	rs185258926	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:82585490C>T	ENST00000333891.9	-	5	5116	c.4779G>A	c.(4777-4779)aaG>aaA	p.K1593K	PCLO_ENST00000423517.2_Silent_p.K1593K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.K1593K(2)|p.K1524K(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTCTTCCTTCTTCTGGCTCT	0.423													C|||	2	0.000399361	0.0015	0	5008	,	,		22317	0		0	False		,,,				2504	0															3	Substitution - coding silent(3)	large_intestine(3)	7						C	,	5,3931		0,5,1963	210	201	204		4779,4779	2.4	0.8	7		204	0,8300		0,0,4150	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	0,5,6113	TT,TC,CC		0.0,0.127,0.0409	,	1593/4936,1593/5143	82585490	5,12231	1968	4150	6118	82423426	SO:0001819	synonymous_variant	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4779G>A	7.37:g.82585490C>T			82423426		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.423	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82585490	C	T	82585490	2	4	47	1	0	0	0	0	0	0	0	1	11614	912	32	3		3	PCLO	7	82585490	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4058	82585490	76553173	942	5339										
SEMA3D	223117	broad.mit.edu	37	chr7	84628806	84628806	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggtctctgtgatgtcttcGatttcgtttcttcttcattt	7	9	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:84628806G>A	ENST00000284136.6	-	17	2327	c.2284C>T	c.(2284-2286)Cga>Tga	p.R762*	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	762	Arg/Lys-rich (basic).				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R762*(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TGATGTCTTCGATTTCGTTTC	0.453																																					Ovarian(63;442 1191 17318 29975 31528)											1	Substitution - Nonsense(1)	large_intestine(1)	7											178	144	156					7																	84628806		2203	4300	6503	84466742	SO:0001587	stop_gained	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2284C>T	7.37:g.84628806G>A	ENSP00000284136:p.Arg762*		84466742	A6NK46|Q6UW77|Q8NCQ1	Nonsense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.197154	0.58126	.	.	ENSG00000153993	ENST00000284136	.	.	.	5.93	1.9	0.25705	.	0.117189	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.2036	0.89847	0.0:0.0:0.383:0.617	.	.	.	.	X	762	.	ENSP00000284136:R762X	R	-	1	2	SEMA3D	84466742	0.993000	0.37304	0.381000	0.26106	0.247000	0.25773	1.104000	0.31074	-0.140000	0.11394	-0.808000	0.03180	CGA		0.453	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		A	84628806	G	A	84628806	4	1	47	1	0	0	0	0	0	1	0	0	14064	1066	37	1	53	1	SEMA3D	7	84628806	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2043316	84628806	74509857	943	5340										
SEMA3D	223117	broad.mit.edu	37	chr7	84727134	84727134	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tactgaccttcttaaaatttTtgtttaagtcaaccagactg	5	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:84727134T>G	ENST00000284136.6	-	2	342	c.299A>C	c.(298-300)aAa>aCa	p.K100T	SEMA3D_ENST00000444867.1_Missense_Mutation_p.K100T	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	100	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.K100T(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CTTAAAATTTTTGTTTAAGTC	0.353																																					Ovarian(63;442 1191 17318 29975 31528)											1	Substitution - Missense(1)	large_intestine(1)	7											80	84	83					7																	84727134		2203	4297	6500	84565070	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.299A>C	7.37:g.84727134T>G	ENSP00000284136:p.Lys100Thr		84565070	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.131708	0.37630	.	.	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.11385	2.78;2.78	5.56	3.06	0.35304	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.227922	0.51477	N	0.000097	T	0.10895	0.0266	L	0.50847	1.595	0.52501	D	0.999953	B;B	0.13145	0.003;0.007	B;B	0.15052	0.007;0.012	T	0.06481	-1.0824	10	0.62326	D	0.03	.	8.6339	0.33936	0.0:0.0679:0.1299:0.8022	.	100;100	C9JYT6;O95025	.;SEM3D_HUMAN	T	100	ENSP00000284136:K100T;ENSP00000401366:K100T	ENSP00000284136:K100T	K	-	2	0	SEMA3D	84565070	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.168000	0.42424	0.428000	0.26173	0.482000	0.46254	AAA		0.353	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84727134	T	G	84727134	3	3	47	1	0	0	0	0	1	0	0	0	14064	1841	64	4	2098	4	SEMA3D	7	84727134	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	98328	84727134	74411529	944	5341										
ABCB4	5244	broad.mit.edu	37	chr7	87041325	87041325	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atactaaaagtaattccataGatgtgtgccttctgcacaga	7	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:87041325G>T	ENST00000265723.4	-	23	2919	c.2808C>A	c.(2806-2808)atC>atA	p.I936I	ABCB4_ENST00000545634.1_Silent_p.I936I|ABCB4_ENST00000453593.1_Intron|ABCB4_ENST00000358400.3_Intron|ABCB4_ENST00000359206.3_Silent_p.I936I	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	936	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.I936I(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TAATTCCATAGATGTGTGCCT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	7											70	67	68					7																	87041325		2203	4300	6503	86879261	SO:0001819	synonymous_variant	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2808C>A	7.37:g.87041325G>T			86879261	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																				0.403	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87041325	G	T	87041325	2	4	47	1	0	0	0	0	0	0	0	1	43	932	33	2		2	ABCB4	7	87041325	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2314191	87041325	72097338	945	5342										
ABCB4	5244	broad.mit.edu	37	chr7	87073085	87073085	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaaaaactgtcaattttaGgattctaaataaaacaaaat	4	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:87073085G>T	ENST00000265723.4	-	11	1235	c.1124C>A	c.(1123-1125)cCt>cAt	p.P375H	ABCB4_ENST00000545634.1_Missense_Mutation_p.P375H|ABCB4_ENST00000453593.1_Missense_Mutation_p.P375H|ABCB4_ENST00000358400.3_Missense_Mutation_p.P375H|ABCB4_ENST00000359206.3_Missense_Mutation_p.P375H	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	375					cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.P375H(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	GTCAATTTTAGGATTCTAAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	100	102					7																	87073085		2203	4300	6503	86911021	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1124C>A	7.37:g.87073085G>T	ENSP00000265723:p.Pro375His		86911021	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.076836	0.76415	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;-1.34	5.47	4.57	0.56435	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.91650	0.7361	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;1.0;1.0	D	0.93551	0.6886	10	0.87932	D	0	-9.4423	16.0631	0.80853	0.0:0.1345:0.8655:0.0	.	375;375;375	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	H	375	ENSP00000352135:P375H;ENSP00000351172:P375H;ENSP00000265723:P375H;ENSP00000392983:P375H;ENSP00000437465:P375H	ENSP00000265723:P375H	P	-	2	0	ABCB4	86911021	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.729000	0.74775	1.258000	0.44101	0.591000	0.81541	CCT		0.348	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87073085	G	T	87073085	3	4	47	1	0	0	0	0	1	0	0	0	43	1000	35	2	2808	2	ABCB4	7	87073085	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	31760	87073085	72065578	946	5343										
ABCB1	5243	broad.mit.edu	37	chr7	87179202	87179202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gataaagtcataggcattggCttccttgacagctttctcaa	8	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:87179202C>T	ENST00000265724.3	-	14	1936	c.1519G>A	c.(1519-1521)Gcc>Acc	p.A507T	ABCB1_ENST00000543898.1_Missense_Mutation_p.A443T	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	507	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.A507T(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TAGGCATTGGCTTCCTTGACA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											253	240	244					7																	87179202		2203	4300	6503	87017138	SO:0001583	missense	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1519G>A	7.37:g.87179202C>T	ENSP00000265724:p.Ala507Thr		87017138	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906661	0.92107	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.92752	-3.1;-3.1	6.02	6.02	0.97574	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.052920	0.85682	D	0.000000	D	0.95909	0.8668	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.97110	0.985;1.0	D	0.95560	0.8628	10	0.87932	D	0	-19.9521	20.547	0.99278	0.0:1.0:0.0:0.0	.	443;507	B5AK60;P08183	.;MDR1_HUMAN	T	288;507;443	ENSP00000265724:A507T;ENSP00000444095:A443T	ENSP00000265724:A507T	A	-	1	0	ABCB1	87017138	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.944000	0.63561	2.850000	0.98022	0.650000	0.86243	GCC		0.438	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		T	87179202	C	T	87179202	3	4	47	1	0	0	0	0	1	0	0	0	40	797	28	3	2387	3	ABCB1	7	87179202	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	106117	87179202	71959461	947	5344										
RUNDC3B	154661	broad.mit.edu	37	chr7	87445561	87445561	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatggaaaacaagacacattAaatgtaatgagtgaaggtaa	10	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:87445561A>C	ENST00000338056.3	+	11	1671	c.1260A>C	c.(1258-1260)ttA>ttC	p.L420F	RUNDC3B_ENST00000394654.3_Missense_Mutation_p.L403F|RUNDC3B_ENST00000493037.1_Missense_Mutation_p.L354F	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	420								p.L420F(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					AAGACACATTAAATGTAATGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											76	70	72					7																	87445561		2203	4300	6503	87283497	SO:0001583	missense	154661				CCDS5609.1, CCDS47635.1, CCDS47636.1	7q21.12	2009-01-14			ENSG00000105784	ENSG00000105784			30286	protein-coding gene	gene with protein product						12645870	Standard	NM_138290		Approved	RPIP9, RPIB9	uc003ujb.3	Q96NL0	OTTHUMG00000131035	ENST00000338056.3:c.1260A>C	7.37:g.87445561A>C	ENSP00000337732:p.Leu420Phe		87283497	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Missense_Mutation	SNP	ENST00000338056.3	37	CCDS5609.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.097266	0.37048	.	.	ENSG00000105784	ENST00000338056;ENST00000493037;ENST00000394654	T;T;T	0.47177	0.85;0.85;0.85	5.26	2.92	0.33932	.	0.338062	0.31784	N	0.007066	T	0.40119	0.1104	N	0.22421	0.69	0.29057	N	0.884132	B;B;B;D;B	0.57571	0.001;0.001;0.0;0.98;0.003	B;B;B;P;B	0.54174	0.001;0.001;0.001;0.744;0.004	T	0.27905	-1.0060	10	0.49607	T	0.09	-2.7361	5.0208	0.14360	0.7302:0.0:0.1296:0.1401	.	403;403;276;354;420	E9PBR4;B4DFD0;Q96NL0-2;Q96NL0-4;Q96NL0	.;.;.;.;RUN3B_HUMAN	F	420;354;403	ENSP00000337732:L420F;ENSP00000420394:L354F;ENSP00000378149:L403F	ENSP00000337732:L420F	L	+	3	2	RUNDC3B	87283497	1.000000	0.71417	0.997000	0.53966	0.939000	0.58152	0.708000	0.25719	0.426000	0.26116	0.528000	0.53228	TTA		0.358	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290		C	87445561	A	C	87445561	3	2	47	1	0	0	0	0	1	0	0	0	13782	359	13	4	1302	4	RUNDC3B	7	87445561	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	266359	87445561	71693102	948	5345										
ZNF804B	219578	broad.mit.edu	37	chr7	88847567	88847567	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtatcacaaacaccaggaGtttgacaatcatattaattc	5	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:88847567G>A	ENST00000333190.4	+	2	816	c.207G>A	c.(205-207)gaG>gaA	p.E69E		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	69							metal ion binding (GO:0046872)	p.E69E(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AACACCAGGAGTTTGACAATC	0.383										HNSCC(36;0.09)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											94	91	92					7																	88847567		2203	4300	6503	88685503	SO:0001819	synonymous_variant	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.207G>A	7.37:g.88847567G>A			88685503	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																				0.383	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88847567	G	A	88847567	2	1	47	1	0	0	0	0	0	0	0	1	18210	1020	36	3		3	ZNF804B	7	88847567	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1402006	88847567	70291096	949	5346										
AKAP9	10142	broad.mit.edu	37	chr7	91603230	91603230	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctgaatctacaataatgaGaactctacatagtggagaaa	7	7	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:91603230G>T	ENST00000359028.2	+	3	515	c.290G>T	c.(289-291)aGa>aTa	p.R97I	AKAP9_ENST00000358100.2_Missense_Mutation_p.R97I|AKAP9_ENST00000356239.3_Missense_Mutation_p.R85I|AKAP9_ENST00000394564.1_Missense_Mutation_p.R85I			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	97					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.R85I(1)|p.R97I(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACAATAATGAGAACTCTACAT	0.353			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - Missense(2)	large_intestine(2)	7											68	65	66					7																	91603230		2203	4300	6503	91441166	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.290G>T	7.37:g.91603230G>T	ENSP00000351922:p.Arg97Ile		91441166	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	G	4.396	0.073205	0.08485	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.66638	2.55;2.55;2.55;-0.22;-0.22	3.75	0.829	0.18847	.	.	.	.	.	T	0.72550	0.3474	L	0.55481	1.735	0.24980	N	0.991601	D;D;D;B	0.76494	0.999;0.997;0.989;0.4	D;D;P;B	0.70016	0.967;0.952;0.893;0.082	T	0.59579	-0.7428	9	0.72032	D	0.01	.	5.2503	0.15519	0.1881:0.1684:0.6434:0.0	.	85;85;97;85	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	I	85;97;97;97;97;85;54	ENSP00000348573:R85I;ENSP00000351922:R97I;ENSP00000350813:R97I;ENSP00000378065:R85I;ENSP00000391704:R54I	ENSP00000348573:R85I	R	+	2	0	AKAP9	91441166	0.978000	0.34361	0.001000	0.08648	0.006000	0.05464	1.756000	0.38390	0.037000	0.15575	-0.154000	0.13518	AGA		0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		T	91603230	G	T	91603230	3	4	47	1	0	0	0	0	1	0	0	0	459	942	33	2	260	2	AKAP9	7	91603230	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2755663	91603230	67535433	950	5347										
AKAP9	10142	broad.mit.edu	37	chr7	91726945	91726945	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagaactagaaattgggttCttcaacagaaaatagaagga	9	4	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:91726945C>A	ENST00000359028.2	+	42	10681	c.10456C>A	c.(10456-10458)Ctt>Att	p.L3486I	AKAP9_ENST00000358100.2_Missense_Mutation_p.L3432I|AKAP9_ENST00000356239.3_Missense_Mutation_p.L3482I			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3486					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.L3486I(2)|p.L3482I(2)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAATTGGGTTCTTCAACAGAA	0.353			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	4	Substitution - Missense(4)	large_intestine(4)	7											80	81	81					7																	91726945		2203	4300	6503	91564881	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10456C>A	7.37:g.91726945C>A	ENSP00000351922:p.Leu3486Ile		91564881	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	C	11.70	1.715644	0.30413	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.04654	3.68;3.68;3.69;3.58	5.32	4.43	0.53597	.	0.000000	0.37577	N	0.002028	T	0.10637	0.0260	M	0.75447	2.3	0.30182	N	0.80032	D;B;B;P;P	0.53885	0.963;0.087;0.404;0.539;0.539	P;B;B;B;B	0.48454	0.578;0.063;0.082;0.17;0.17	T	0.04855	-1.0922	10	0.59425	D	0.04	.	8.4654	0.32953	0.1541:0.7682:0.0:0.0777	.	757;3486;3486;3482;3474	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	I	3482;3486;3432;3486;1328	ENSP00000348573:L3482I;ENSP00000351922:L3486I;ENSP00000350813:L3432I;ENSP00000378042:L1328I	ENSP00000348573:L3482I	L	+	1	0	AKAP9	91564881	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	1.693000	0.37742	1.349000	0.45751	0.585000	0.79938	CTT		0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91726945	C	A	91726945	3	1	47	1	0	0	0	0	1	0	0	0	459	913	32	2	10610	2	AKAP9	7	91726945	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	123715	91726945	67411718	951	5348										
SAMD9	54809	broad.mit.edu	37	chr7	92730826	92730826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcagctcgaccttgtaaacGaagcaaaagttcttggactt	8	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:92730826G>A	ENST00000379958.2	-	3	4854	c.4585C>T	c.(4585-4587)Cgt>Tgt	p.R1529C		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1529						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.R1529C(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CCTTGTAAACGAAGCAAAAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	81	81					7																	92730826		2203	4300	6503	92568762	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.4585C>T	7.37:g.92730826G>A	ENSP00000369292:p.Arg1529Cys		92568762	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288674	0.59976	.	.	ENSG00000205413	ENST00000379958	T	0.30981	1.51	4.34	4.34	0.51931	.	0.083461	0.45606	U	0.000348	T	0.45276	0.1334	L	0.41824	1.3	0.40117	D	0.976551	D	0.89917	1.0	D	0.65987	0.94	T	0.48068	-0.9067	10	0.72032	D	0.01	.	15.8966	0.79338	0.0:0.0:1.0:0.0	.	1529	Q5K651	SAMD9_HUMAN	C	1529	ENSP00000369292:R1529C	ENSP00000369292:R1529C	R	-	1	0	SAMD9	92568762	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	1.597000	0.36729	2.420000	0.82092	0.609000	0.83330	CGT		0.368	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92730826	G	A	92730826	3	1	47	1	0	0	0	0	1	0	0	0	13863	1058	37	1	188	1	SAMD9	7	92730826	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1003881	92730826	66407837	952	5349										
SAMD9	54809	broad.mit.edu	37	chr7	92733272	92733272	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttgaatcattgcttcaagTctttcatatttatccctttt	3	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:92733272T>C	ENST00000379958.2	-	3	2408	c.2139A>G	c.(2137-2139)agA>agG	p.R713R		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	713						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.R713R(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTGCTTCAAGTCTTTCATATT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											179	177	178					7																	92733272		2203	4300	6503	92571208	SO:0001819	synonymous_variant	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2139A>G	7.37:g.92733272T>C			92571208	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																				0.388	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92733272	T	C	92733272	2	2	47	1	0	0	0	0	0	0	0	1	13863	1664	58	4		4	SAMD9	7	92733272	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2446	92733272	66405391	953	5350										
SAMD9L	219285	broad.mit.edu	37	chr7	92761627	92761627	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttttggataattcattttCtttgtggaaaaagggagtga	10	2	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:92761627C>A	ENST00000318238.4	-	5	4874	c.3658G>T	c.(3658-3660)Gaa>Taa	p.E1220*	SAMD9L_ENST00000411955.1_Nonsense_Mutation_p.E1220*|SAMD9L_ENST00000437805.1_Nonsense_Mutation_p.E1220*	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1220					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.E1220*(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			AATTCATTTTCTTTGTGGAAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											94	88	90					7																	92761627		2203	4299	6502	92599563	SO:0001587	stop_gained	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.3658G>T	7.37:g.92761627C>A	ENSP00000326247:p.Glu1220*		92599563	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Nonsense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	C	48	14.733070	0.99808	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	.	.	.	4.77	2.95	0.34219	.	0.428747	0.22262	N	0.062393	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-4.6343	6.2489	0.20835	0.0:0.5497:0.291:0.1593	.	.	.	.	X	1220	.	ENSP00000326247:E1220X	E	-	1	0	SAMD9L	92599563	0.000000	0.05858	0.505000	0.27651	0.547000	0.35210	-0.559000	0.05971	0.720000	0.32209	0.467000	0.42956	GAA		0.368	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92761627	C	A	92761627	4	1	47	1	0	0	0	0	0	1	0	0	13864	922	32	2	1100	2	SAMD9L	7	92761627	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	28355	92761627	66377036	954	5351										
CALCR	799	broad.mit.edu	37	chr7	93090148	93090148	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaccgggtcccttcgcacGagctctccattgggtactac	9	15	1	0	rs147794595	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:93090148G>A	ENST00000394441.1	-	7	948	c.633C>T	c.(631-633)ctC>ctT	p.L211L	CALCR_ENST00000421592.1_Silent_p.L227L|CALCR_ENST00000360249.4_Silent_p.L227L|CALCR_ENST00000426151.1_Silent_p.L211L|CALCR_ENST00000359558.2_Silent_p.L245L	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	245					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.L245L(1)|p.L211L(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CCCTTCGCACGAGCTCTCCAT	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	7						G	,,	5,4401	9.9+/-24.2	0,5,2198	126	123	124		735,633,633	-6.9	0	7	dbSNP_134	124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	,,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,,	245/509,211/475,211/475	93090148	5,13001	2203	4300	6503	92928084	SO:0001819	synonymous_variant	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.633C>T	7.37:g.93090148G>A			92928084	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	37	CCDS5631.1																																																																																				0.388	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		A	93090148	G	A	93090148	2	1	47	1	0	0	0	0	0	0	0	1	2585	1045	37	1		1	CALCR	7	93090148	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	328521	93090148	66048515	955	5352										
TFPI2	7980	broad.mit.edu	37	chr7	93518432	93518432	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggtgacacccaccggaaaaGaatttttcacatgtcatgga	9	10	2	2	rs150637497		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:93518432G>T	ENST00000222543.5	-	3	687	c.375C>A	c.(373-375)ttC>ttA	p.F125L	GNGT1_ENST00000455502.1_Intron|TFPI2_ENST00000545378.1_Intron|AC002076.10_ENST00000435257.1_RNA	NM_001271003.1|NM_001271004.1|NM_006528.3	NP_001257932.1|NP_001257933.1|NP_006519.1	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	125	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F125L(1)		endometrium(1)|large_intestine(5)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			CACCGGAAAAGAATTTTTCAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	81	91	87		375	0.6	0	7	dbSNP_134	87	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TFPI2	NM_006528.2	22	0,2,6501	TT,TG,GG		0.0116,0.0227,0.0154	benign	125/236	93518432	2,13004	2203	4300	6503	93356368	SO:0001583	missense	7980			L27624	CCDS5632.1	7q	2008-07-18			ENSG00000105825	ENSG00000105825			11761	protein-coding gene	gene with protein product		600033				7896752, 8945635	Standard	NM_006528		Approved	PP5, TFPI-2, REF1	uc003umy.2	P48307	OTTHUMG00000022963	ENST00000222543.5:c.375C>A	7.37:g.93518432G>T	ENSP00000222543:p.Phe125Leu		93356368	Q66ME8|Q8NAK6|Q9UC86	Missense_Mutation	SNP	ENST00000222543.5	37	CCDS5632.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.837747	0.32513	2.27E-4	1.16E-4	ENSG00000105825	ENST00000222543;ENST00000451238	T;T	0.68765	-0.35;-0.35	5.25	0.641	0.17759	Proteinase inhibitor I2, Kunitz metazoa (5);	0.210131	0.51477	N	0.000100	T	0.71160	0.3307	M	0.93420	3.415	0.09310	N	1	B;B	0.18166	0.026;0.026	B;B	0.22152	0.038;0.022	T	0.65249	-0.6214	10	0.44086	T	0.13	.	9.9807	0.41811	0.5133:0.0:0.4867:0.0	.	114;125	Q8NAK6;P48307	.;TFPI2_HUMAN	L	125;46	ENSP00000222543:F125L;ENSP00000416370:F46L	ENSP00000222543:F125L	F	-	3	2	TFPI2	93356368	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.189000	0.09629	0.139000	0.18822	0.467000	0.42956	TTC		0.443	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254720.2	NM_006528		T	93518432	G	T	93518432	3	4	47	1	0	0	0	0	1	0	0	0	15848	933	33	2	344	2	TFPI2	7	93518432	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	428284	93518432	65620231	956	5353										
TRRAP	8295	broad.mit.edu	37	chr7	98495485	98495485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgtgaggacagtgagactcGaacagtaagtgtttcgctga	14	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:98495485G>A	ENST00000359863.4	+	8	838	c.629G>A	c.(628-630)cGa>cAa	p.R210Q	TRRAP_ENST00000355540.3_Missense_Mutation_p.R210Q|TRRAP_ENST00000446306.3_Missense_Mutation_p.R210Q	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	210					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R210Q(2)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGTGAGACTCGAACAGTAAGT	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	7											165	151	156					7																	98495485		2203	4300	6503	98333421	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.629G>A	7.37:g.98495485G>A	ENSP00000352925:p.Arg210Gln		98333421	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.363547	0.61513	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.02472	4.28;4.28	5.58	5.58	0.84498	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.02929	0.0087	N	0.00554	-1.385	0.80722	D	1	D;D	0.69078	0.997;0.994	D;P	0.66847	0.947;0.885	T	0.73411	-0.3991	10	0.11794	T	0.64	.	19.5633	0.95382	0.0:0.0:1.0:0.0	.	210;210	Q9Y4A5-2;Q9Y4A5	.;TRRAP_HUMAN	Q	210	ENSP00000352925:R210Q;ENSP00000347733:R210Q	ENSP00000347733:R210Q	R	+	2	0	TRRAP	98333421	1.000000	0.71417	0.911000	0.35937	0.930000	0.56654	9.765000	0.98953	2.650000	0.89964	0.591000	0.81541	CGA		0.463	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98495485	G	A	98495485	3	1	47	1	0	0	0	0	1	0	0	0	16641	1058	37	1	655	1	TRRAP	7	98495485	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4977053	98495485	60643178	957	5354										
GJC3	349149	broad.mit.edu	37	chr7	99526508	99526508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccaccactgggaggctatCggttgctttcttgtgtcttc	10	11	2	0	rs191464858		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:99526508C>T	ENST00000312891.2	-	1	735	c.736G>A	c.(736-738)Gat>Aat	p.D246N	RP4-604G5.1_ENST00000456499.1_RNA	NM_181538.2	NP_853516.1	Q8NFK1	CXG3_HUMAN	gap junction protein, gamma 3, 30.2kDa	246					cell communication (GO:0007154)|myelination (GO:0042552)|sensory perception of sound (GO:0007605)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)		p.D246N(2)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	9	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GGGAGGCTATCGGTTGCTTTC	0.478													C|||	1	0.000199681	0	0	5008	,	,		19703	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	7											133	130	131					7																	99526508		2203	4300	6503	99364444	SO:0001583	missense	349149			AF503615	CCDS34697.1	7q22.1	2008-09-04	2007-11-06	2007-11-06	ENSG00000176402	ENSG00000176402		"Ion channels / Gap junction proteins (connexins)"	17495	protein-coding gene	gene with protein product	"connexin 30.2"	611925	"gap junction protein, epsilon 1, 29kDa"	GJE1			Standard	NM_181538		Approved	CX30.2	uc011kjd.2	Q8NFK1	OTTHUMG00000156649	ENST00000312891.2:c.736G>A	7.37:g.99526508C>T	ENSP00000325775:p.Asp246Asn		99364444	A4D296|Q86XI9	Missense_Mutation	SNP	ENST00000312891.2	37	CCDS34697.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	4.624	0.116041	0.08831	.	.	ENSG00000176402	ENST00000312891	D	0.97941	-4.62	3.75	0.763	0.18459	.	2.765090	0.01548	N	0.019552	D	0.92205	0.7528	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.04013	0.001	D	0.87471	0.2414	10	0.17369	T	0.5	.	5.4255	0.16423	0.0:0.5913:0.0:0.4087	.	246	Q8NFK1	CXG3_HUMAN	N	246	ENSP00000325775:D246N	ENSP00000325775:D246N	D	-	1	0	GJC3	99364444	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.166000	0.09954	0.143000	0.18926	0.655000	0.94253	GAT		0.478	GJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345052.1	NM_181538		T	99526508	C	T	99526508	3	4	47	1	0	0	0	0	1	0	0	0	6436	884	31	1	111	1	GJC3	7	99526508	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1031023	99526508	59612155	958	5355										
COPS6	10980	broad.mit.edu	37	chr7	99688890	99688890	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctgatagcacagcacagcGccatcaagatgctgcacagc	9	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:99688890G>A	ENST00000303904.3	+	8	716	c.679G>A	c.(679-681)Gcc>Acc	p.A227T	COPS6_ENST00000418625.1_Missense_Mutation_p.A226T|MIR93_ENST00000385024.1_RNA|MIR106B_ENST00000385301.1_RNA|MIR25_ENST00000384816.1_RNA	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	227	Interaction with Vpr.				cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.A227T(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ACAGCACAGCGCCATCAAGAT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											207	193	197					7																	99688890		2203	4300	6503	99526826	SO:0001583	missense	10980			BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"COP9 subunit 6 (MOV34 homolog, 34 kD)"	614729	"COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.679G>A	7.37:g.99688890G>A	ENSP00000304102:p.Ala227Thr		99526826	A4D2A3|O15387	Missense_Mutation	SNP	ENST00000303904.3	37	CCDS5682.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.471304	0.84533	.	.	ENSG00000168090	ENST00000303904;ENST00000418625	T;T	0.56611	0.45;0.45	5.06	4.19	0.49359	.	0.057914	0.64402	N	0.000002	T	0.77811	0.4186	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82528	-0.0412	10	0.66056	D	0.02	-9.2235	11.0489	0.47876	0.0891:0.0:0.9109:0.0	.	227	Q7L5N1	CSN6_HUMAN	T	227;226	ENSP00000304102:A227T;ENSP00000400617:A226T	ENSP00000304102:A227T	A	+	1	0	COPS6	99526826	1.000000	0.71417	0.912000	0.35992	0.890000	0.51754	8.430000	0.90283	1.361000	0.45981	0.655000	0.94253	GCC		0.582	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833		A	99688890	G	A	99688890	3	1	47	1	0	0	0	0	1	0	0	0	3743	1087	38	1	709	1	COPS6	7	99688890	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	162382	99688890	59449773	959	5356										
SRRT	51593	broad.mit.edu	37	chr7	100484691	100484691	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggacaagctcctcctttaCctgcgcatcgtgcattcctt	7	14	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:100484691C>T	ENST00000347433.4	+	15	2003	c.1845C>T	c.(1843-1845)taC>taT	p.Y615Y	SRRT_ENST00000457580.2_Silent_p.Y615Y|SRRT_ENST00000432932.1_Silent_p.Y614Y|SRRT_ENST00000388793.4_Silent_p.Y614Y			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	615					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.Y615Y(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TCCTCCTTTACCTGCGCATCG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	7											167	159	162					7																	100484691		2203	4300	6503	100322627	SO:0001819	synonymous_variant	51593				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.1845C>T	7.37:g.100484691C>T			100322627	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Silent	SNP	ENST00000347433.4	37	CCDS34709.1																																																																																				0.602	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		T	100484691	C	T	100484691	2	4	47	1	0	0	0	0	0	0	0	1	15211	518	18	3		3	SRRT	7	100484691	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	795801	100484691	58653972	960	5357										
LRRC17	10234	broad.mit.edu	37	chr7	102584740	102584740	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgactatggcgtattagaaGacttgtattttttgaaactc	8	5	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:102584740G>T	ENST00000339431.4	+	4	1307	c.1012G>T	c.(1012-1014)Gac>Tac	p.D338Y	FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379308.3_Intron|LRRC17_ENST00000485478.1_3'UTR|LRRC17_ENST00000249377.4_3'UTR|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	338					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)		p.D338Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						CGTATTAGAAGACTTGTATTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											122	125	124					7																	102584740		2203	4299	6502	102371976	SO:0001583	missense	10234			U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.1012G>T	7.37:g.102584740G>T	ENSP00000344242:p.Asp338Tyr		102371976	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154375	0.78114	.	.	ENSG00000128606	ENST00000339431	T	0.58797	0.31	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000009	T	0.64702	0.2622	L	0.28694	0.88	0.80722	D	1	D	0.71674	0.998	D	0.65573	0.936	T	0.63391	-0.6648	10	0.44086	T	0.13	-37.2838	16.293	0.82759	0.0:0.1321:0.8679:0.0	.	338	Q8N6Y2	LRC17_HUMAN	Y	338	ENSP00000344242:D338Y	ENSP00000344242:D338Y	D	+	1	0	LRRC17	102371976	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.925000	0.87563	2.746000	0.94184	0.655000	0.94253	GAC		0.368	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		T	102584740	G	T	102584740	3	4	47	1	0	0	0	0	1	0	0	0	9002	942	33	2	1040	2	LRRC17	7	102584740	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2100049	102584740	56553923	961	5358										
DNAJC2	27000	broad.mit.edu	37	chr7	102957318	102957318	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacagattcacagctttaatTagtaattgtagatcatcttc	5	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:102957318T>C	ENST00000379263.3	-	13	1636	c.1386A>G	c.(1384-1386)ctA>ctG	p.L462L	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Silent_p.L409L	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	462	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)	p.L420L(1)|p.L409L(1)		endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						CAGCTTTAATTAGTAATTGTA	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	7											149	138	141					7																	102957318		1846	4085	5931	102744554	SO:0001819	synonymous_variant	27000			X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1386A>G	7.37:g.102957318T>C			102744554	A4VCI0|Q9BVX1	Silent	SNP	ENST00000379263.3	37	CCDS43628.1																																																																																				0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			C	102957318	T	C	102957318	2	2	47	1	0	0	0	0	0	0	0	1	4650	1741	61	4		4	DNAJC2	7	102957318	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	372578	102957318	56181345	962	5359										
DNAJC2	27000	broad.mit.edu	37	chr7	102967024	102967024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacactggggtaaacacttCgaagaaattatcctttgctt	7	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:102967024C>T	ENST00000379263.3	-	5	788	c.538G>A	c.(538-540)Gaa>Aaa	p.E180K	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Missense_Mutation_p.E180K	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	180	ZRF1-UBD.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)	p.E180K(2)		endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GTAAACACTTCGAAGAAATTA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	7											103	98	99					7																	102967024		1853	4094	5947	102754260	SO:0001583	missense	27000			X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.538G>A	7.37:g.102967024C>T	ENSP00000368565:p.Glu180Lys		102754260	A4VCI0|Q9BVX1	Missense_Mutation	SNP	ENST00000379263.3	37	CCDS43628.1	.	.	.	.	.	.	.	.	.	.	c	14.14	2.445250	0.43429	.	.	ENSG00000105821	ENST00000249270;ENST00000379263;ENST00000537811;ENST00000454277	.	.	.	5.55	3.74	0.42951	.	0.303254	0.40469	N	0.001091	T	0.28300	0.0699	N	0.11341	0.13	0.80722	D	1	B;B	0.17465	0.022;0.0	B;B	0.12156	0.007;0.001	T	0.09250	-1.0683	9	0.06625	T	0.88	-22.3275	11.3252	0.49444	0.0:0.8006:0.1309:0.0685	.	180;180	Q99543-2;Q99543	.;DNJC2_HUMAN	K	180;180;180;106	.	ENSP00000249270:E180K	E	-	1	0	DNAJC2	102754260	0.993000	0.37304	0.972000	0.41901	0.975000	0.68041	2.817000	0.48034	0.889000	0.36185	-0.185000	0.12909	GAA		0.378	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			T	102967024	C	T	102967024	3	4	47	1	0	0	0	0	1	0	0	0	4650	893	31	1	1379	1	DNAJC2	7	102967024	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9706	102967024	56171639	963	5360										
RELN	5649	broad.mit.edu	37	chr7	103159849	103159849	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgacagaatattccaagaGaacaccttggttacggttgt	9	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:103159849G>T	ENST00000428762.1	-	49	7942	c.7783C>A	c.(7783-7785)Ctc>Atc	p.L2595I	RELN_ENST00000424685.2_Missense_Mutation_p.L2595I|RELN_ENST00000343529.5_Missense_Mutation_p.L2595I	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2595					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.L2595I(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TATTCCAAGAGAACACCTTGG	0.413																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											163	133	143					7																	103159849		2203	4300	6503	102947085	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7783C>A	7.37:g.103159849G>T	ENSP00000392423:p.Leu2595Ile		102947085	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	31	5.092888	0.94149	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.25250	1.81;1.81;1.81	5.87	5.87	0.94306	Neuraminidase (3);	0.000000	0.85682	D	0.000000	T	0.50411	0.1614	L	0.60455	1.87	0.58432	D	0.999999	D;B	0.61080	0.989;0.036	D;B	0.70716	0.97;0.435	T	0.43245	-0.9403	10	0.72032	D	0.01	.	20.2191	0.98319	0.0:0.0:1.0:0.0	.	2595;2595	P78509-2;P78509	.;RELN_HUMAN	I	2595;2595;2595;112;2595	ENSP00000392423:L2595I;ENSP00000345694:L2595I;ENSP00000388446:L2595I	ENSP00000345694:L2595I	L	-	1	0	RELN	102947085	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.595000	0.82710	2.780000	0.95670	0.655000	0.94253	CTC		0.413	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103159849	G	T	103159849	3	4	47	1	0	0	0	0	1	0	0	0	13257	942	33	2	2667	2	RELN	7	103159849	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	192825	103159849	55978814	964	5361										
NAMPT	10135	broad.mit.edu	37	chr7	105908954	105908954	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagcctggaacaggatctttCgttccataatattttttaat	6	7	1	0	rs61740998		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:105908954C>T	ENST00000222553.3	-	6	1006	c.699G>A	c.(697-699)acG>acA	p.T233T	NAMPT_ENST00000484527.1_5'Flank|NAMPT_ENST00000354289.4_Silent_p.T233T	NM_005746.2	NP_005737.1	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	233					cell-cell signaling (GO:0007267)|circadian regulation of gene expression (GO:0032922)|NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|nicotinamide metabolic process (GO:0006769)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|nicotinamide phosphoribosyltransferase activity (GO:0047280)|nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)	p.T233T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						CAGGATCTTTCGTTCCATAAT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	7											46	49	48					7																	105908954		2203	4300	6503	105696190	SO:0001819	synonymous_variant	10135			U02020	CCDS5737.1	7q22.3	2012-10-02	2008-03-27	2008-03-27	ENSG00000105835	ENSG00000105835			30092	protein-coding gene	gene with protein product	"visfatin"	608764	"pre-B-cell colony enhancing factor 1"	PBEF1		8289818	Standard	NM_005746		Approved	PBEF	uc003vdq.3	P43490	OTTHUMG00000140388	ENST00000222553.3:c.699G>A	7.37:g.105908954C>T			105696190	A4D0Q9|A4D0R0|Q3KQV0|Q8WW95	Silent	SNP	ENST00000222553.3	37	CCDS5737.1																																																																																				0.358	NAMPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277146.1	NM_182790		T	105908954	C	T	105908954	2	4	47	1	0	0	0	0	0	0	0	1	10179	871	31	1		1	NAMPT	7	105908954	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2749105	105908954	53229709	965	5362										
PRKAR2B	5577	broad.mit.edu	37	chr7	106710753	106710753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataaaccgattcacaaggcGtgcctcaggtaagtctgatt	9	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:106710753G>A	ENST00000265717.4	+	2	594	c.335G>A	c.(334-336)cGt>cAt	p.R112H	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	112	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.R112H(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TTCACAAGGCGTGCCTCAGGT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	7											86	89	88					7																	106710753		2203	4297	6500	106497989	SO:0001583	missense	5577				CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.335G>A	7.37:g.106710753G>A	ENSP00000265717:p.Arg112His		106497989	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	37	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879358	0.51801	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.87412	-2.25	4.05	4.05	0.47172	.	0.051579	0.64402	D	0.000003	D	0.82986	0.5156	M	0.78049	2.395	0.44373	D	0.997277	P	0.49696	0.927	B	0.31191	0.125	D	0.86525	0.1818	10	0.87932	D	0	-26.9415	11.91	0.52733	0.0:0.0:1.0:0.0	.	112	P31323	KAP3_HUMAN	H	112;112;99	ENSP00000265717:R112H	ENSP00000265717:R112H	R	+	2	0	PRKAR2B	106497989	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.590000	0.61013	2.250000	0.74265	0.655000	0.94253	CGT		0.303	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			A	106710753	G	A	106710753	3	1	47	1	0	0	0	0	1	0	0	0	12540	1145	40	1	341	1	PRKAR2B	7	106710753	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	801799	106710753	52427910	966	5363										
SLC26A4	5172	broad.mit.edu	37	chr7	107315540	107315540	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaaaaactacaatggagttCtctctattatctatgtaagt	5	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:107315540C>A	ENST00000265715.3	+	6	975	c.751C>A	c.(751-753)Ctc>Atc	p.L251I		NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	251					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.L251I(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						CAATGGAGTTCTCTCTATTAT	0.453									Pendred syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											162	161	161					7																	107315540		2203	4300	6503	107102776	SO:0001583	missense	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.751C>A	7.37:g.107315540C>A	ENSP00000265715:p.Leu251Ile		107102776	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566987	0.86439	.	.	ENSG00000091137	ENST00000265715	D	0.92805	-3.11	5.59	5.59	0.84812	Sulphate transporter (1);	0.074268	0.56097	D	0.000037	D	0.94188	0.8135	L	0.52823	1.66	0.80722	D	1	D	0.55605	0.972	P	0.60609	0.877	D	0.91857	0.5496	10	0.22706	T	0.39	.	19.5865	0.95492	0.0:1.0:0.0:0.0	.	251	O43511	S26A4_HUMAN	I	251	ENSP00000265715:L251I	ENSP00000265715:L251I	L	+	1	0	SLC26A4	107102776	0.997000	0.39634	1.000000	0.80357	0.971000	0.66376	3.438000	0.52871	2.638000	0.89438	0.650000	0.86243	CTC		0.453	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		A	107315540	C	A	107315540	3	1	47	1	0	0	0	0	1	0	0	0	14556	913	32	2	769	2	SLC26A4	7	107315540	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	604787	107315540	51823123	967	5364										
DOCK4	9732	broad.mit.edu	37	chr7	111540490	111540490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatttatccacaggaatggGaagtttcagcagttcagacc	10	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:111540490G>A	ENST00000437633.1	-	15	1676	c.1420C>T	c.(1420-1422)Ccc>Tcc	p.P474S	DOCK4_ENST00000428084.1_Missense_Mutation_p.P474S|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	474	DHR-1.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.P462S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ACAGGAATGGGAAGTTTCAGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	91	92					7																	111540490		1966	4154	6120	111327726	SO:0001583	missense	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1420C>T	7.37:g.111540490G>A	ENSP00000404179:p.Pro474Ser		111327726	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169606	0.57584	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.12672	2.66;2.66	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.14743	0.0356	N	0.25031	0.7	0.80722	D	1	B;B;B	0.32968	0.213;0.392;0.392	B;B;B	0.41174	0.262;0.349;0.262	T	0.08953	-1.0697	10	0.09843	T	0.71	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	474;474;474	Q149N2;Q149N5;Q8N1I0	.;.;DOCK4_HUMAN	S	462;474;474;462;473	ENSP00000410746:P474S;ENSP00000404179:P474S	ENSP00000345432:P462S	P	-	1	0	DOCK4	111327726	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	6.518000	0.73764	2.873000	0.98535	0.563000	0.77884	CCC		0.502	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111540490	G	A	111540490	3	1	47	1	0	0	0	0	1	0	0	0	4700	1174	41	3	4632	3	DOCK4	7	111540490	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4224950	111540490	47598173	968	5365										
TMEM168	64418	broad.mit.edu	37	chr7	112424286	112424286	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagtttggaatagctaagaAagatttcattctcagatcaa	7	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:112424286A>C	ENST00000312814.6	-	2	1155	c.595T>G	c.(595-597)Ttc>Gtc	p.F199V	TMEM168_ENST00000454074.1_Missense_Mutation_p.F199V	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	199						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.F199V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						ATAGCTAAGAAAGATTTCATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											41	43	42					7																	112424286		2203	4300	6503	112211522	SO:0001583	missense	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.595T>G	7.37:g.112424286A>C	ENSP00000323068:p.Phe199Val		112211522	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.822256	0.50739	.	.	ENSG00000146802	ENST00000312814;ENST00000454074	.	.	.	6.06	6.06	0.98353	.	0.090444	0.85682	D	0.000000	T	0.49236	0.1545	L	0.44542	1.39	0.80722	D	1	B	0.33807	0.426	B	0.29077	0.098	T	0.44159	-0.9346	9	0.23891	T	0.37	-20.4302	16.6245	0.84952	1.0:0.0:0.0:0.0	.	199	Q9H0V1	TM168_HUMAN	V	199	.	ENSP00000323068:F199V	F	-	1	0	TMEM168	112211522	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.475000	0.53136	2.323000	0.78572	0.528000	0.53228	TTC		0.358	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		C	112424286	A	C	112424286	3	2	47	1	0	0	0	0	1	0	0	0	16122	14	1	4	1514	4	TMEM168	7	112424286	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	883796	112424286	46714377	969	5366										
PPP1R3A	5506	broad.mit.edu	37	chr7	113519740	113519740	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttagctcctccttcatgTtttttattaaggtttcctgc	5	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:113519740T>G	ENST00000284601.3	-	4	1475	c.1407A>C	c.(1405-1407)aaA>aaC	p.K469N		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	469					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.K469N(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						CTCCTTCATGTTTTTTATTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											55	55	55					7																	113519740		2203	4297	6500	113306976	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1407A>C	7.37:g.113519740T>G	ENSP00000284601:p.Lys469Asn		113306976	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.449724	0.26074	.	.	ENSG00000154415	ENST00000284601;ENST00000449795	T;T	0.37235	2.26;1.21	5.52	-3.9	0.04181	.	0.704761	0.13681	N	0.370152	T	0.20455	0.0492	L	0.42245	1.32	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21348	-1.0248	10	0.21540	T	0.41	-2.6918	2.6967	0.05137	0.115:0.2748:0.1:0.5102	.	469	Q16821	PPR3A_HUMAN	N	469;148	ENSP00000284601:K469N;ENSP00000401278:K148N	ENSP00000284601:K469N	K	-	3	2	PPP1R3A	113306976	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.052000	0.11865	-0.901000	0.03891	-1.450000	0.01041	AAA		0.398	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		G	113519740	T	G	113519740	3	3	47	1	0	0	0	0	1	0	0	0	12405	1722	60	4	1965	4	PPP1R3A	7	113519740	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1095454	113519740	45618923	970	5367										
PPP1R3A	5506	broad.mit.edu	37	chr7	113522155	113522155	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttacatcttttacatttCgattactggcttccaaatct	4	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:113522155C>T	ENST00000284601.3	-	3	973	c.905G>A	c.(904-906)cGa>cAa	p.R302Q		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	302					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.R302Q(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTTTACATTTCGATTACTGGC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											192	160	171					7																	113522155		2203	4300	6503	113309391	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.905G>A	7.37:g.113522155C>T	ENSP00000284601:p.Arg302Gln		113309391	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.388949	0.01185	.	.	ENSG00000154415	ENST00000284601	T	0.13307	2.6	5.92	3.51	0.40186	.	0.301944	0.28641	N	0.014635	T	0.02193	0.0068	N	0.00104	-2.125	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43718	-0.9374	10	0.02654	T	1	-2.2676	9.2721	0.37677	0.0:0.0642:0.123:0.8128	.	302	Q16821	PPR3A_HUMAN	Q	302	ENSP00000284601:R302Q	ENSP00000284601:R302Q	R	-	2	0	PPP1R3A	113309391	0.997000	0.39634	0.412000	0.26496	0.974000	0.67602	1.506000	0.35747	0.460000	0.27045	-0.415000	0.06103	CGA		0.338	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113522155	C	T	113522155	3	4	47	1	0	0	0	0	1	0	0	0	12405	884	31	1	2471	1	PPP1R3A	7	113522155	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2415	113522155	45616508	971	5368										
MDFIC	29969	broad.mit.edu	37	chr7	114619680	114619680	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaatggaattcaccacgggGccaaacacggatccgcagat	11	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:114619680G>A	ENST00000393486.1	+	4	927	c.337G>A	c.(337-339)Gcc>Acc	p.A113T	MDFIC_ENST00000257724.3_Missense_Mutation_p.A222T	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing									p.A222T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						TCACCACGGGGCCAAACACGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											92	90	90					7																	114619680		2203	4300	6503	114406916	SO:0001583	missense	29969			AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.337G>A	7.37:g.114619680G>A	ENSP00000377126:p.Ala113Thr		114406916		Missense_Mutation	SNP	ENST00000393486.1	37	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.768681	0.69878	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	5.11	0.69529	.	0.518379	0.19372	N	0.115871	T	0.58864	0.2152	L	0.50919	1.6	0.80722	D	1	B	0.15930	0.015	B	0.15052	0.012	T	0.56757	-0.7926	9	0.59425	D	0.04	1.5523	15.0715	0.72040	0.0678:0.0:0.9322:0.0	.	113	Q9P1T7	MDFIC_HUMAN	T	222;113;99;58	.	ENSP00000257724:A222T	A	+	1	0	MDFIC	114406916	1.000000	0.71417	0.968000	0.41197	0.848000	0.48234	3.757000	0.55212	1.538000	0.49270	0.591000	0.81541	GCC		0.463	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072		A	114619680	G	A	114619680	3	1	47	1	0	0	0	0	1	0	0	0	9435	1203	42	3	720	3	MDFIC	7	114619680	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1097525	114619680	44518983	972	5369										
MET	4233	broad.mit.edu	37	chr7	116339776	116339776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccagatcatccattgcattCgatatcagtgagaaggctaa	8	10	2	2	rs367722737		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:116339776C>T	ENST00000318493.6	+	2	825	c.638C>T	c.(637-639)tCg>tTg	p.S213L	MET_ENST00000436117.2_Missense_Mutation_p.S213L|MET_ENST00000397752.3_Missense_Mutation_p.S213L			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S213L(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CCATTGCATTCGATATCAGTG	0.403			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	1	Substitution - Missense(1)	large_intestine(1)	7						C	LEU/SER,LEU/SER	0,3788		0,0,1894	160	157	158		638,638	6.2	1	7		158	1,8231		0,1,4115	no	missense,missense	MET	NM_000245.2,NM_001127500.1	145,145	0,1,6009	TT,TC,CC		0.0121,0.0,0.0083	probably-damaging,probably-damaging	213/1391,213/1409	116339776	1,12019	1894	4116	6010	116127012	SO:0001583	missense	4233	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.638C>T	7.37:g.116339776C>T	ENSP00000317272:p.Ser213Leu		116127012	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497776	0.64186	0.0	1.21E-4	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.14640	2.49;2.49;2.49	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.056791	0.64402	D	0.000001	T	0.42607	0.1210	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;0.998;0.999;0.999;0.999;0.999;1.0;0.997;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.976;0.975;1.0;0.962;0.975;0.975;0.975;0.975;0.999;0.942;0.975;0.999;0.999	T	0.09662	-1.0664	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	213;213;213;213;213;213;213;213;213;213;213;213;213	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	L	213	ENSP00000380860:S213L;ENSP00000317272:S213L;ENSP00000410980:S213L	ENSP00000317272:S213L	S	+	2	0	MET	116127012	1.000000	0.71417	0.973000	0.42090	0.367000	0.29736	7.210000	0.77924	2.941000	0.99782	0.655000	0.94253	TCG		0.403	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116339776	C	T	116339776	3	4	47	1	0	0	0	0	1	0	0	0	9515	893	31	1	640	1	MET	7	116339776	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1720096	116339776	42798887	973	5370										
CTTNBP2	83992	broad.mit.edu	37	chr7	117359688	117359688	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgatagatcattctctaaaGacctaacacaaagttcagaa	6	8	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:117359688G>T	ENST00000160373.3	-	21	4605	c.4514C>A	c.(4513-4515)tCt>tAt	p.S1505Y		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1505					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.S1505Y(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ATTCTCTAAAGACCTAACACA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											100	93	95					7																	117359688		2203	4300	6503	117146924	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4514C>A	7.37:g.117359688G>T	ENSP00000160373:p.Ser1505Tyr		117146924	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.618381	0.46736	.	.	ENSG00000077063	ENST00000160373	T	0.67171	-0.25	5.24	4.36	0.52297	.	0.473985	0.22785	N	0.055674	T	0.67277	0.2876	M	0.80183	2.485	0.29416	N	0.860866	P	0.35208	0.49	B	0.30029	0.11	T	0.69844	-0.5035	10	0.87932	D	0	-3.8474	14.6927	0.69098	0.0:0.1633:0.8367:0.0	.	1505	Q8WZ74	CTTB2_HUMAN	Y	1505	ENSP00000160373:S1505Y	ENSP00000160373:S1505Y	S	-	2	0	CTTNBP2	117146924	1.000000	0.71417	0.861000	0.33841	0.960000	0.62799	5.049000	0.64244	1.324000	0.45282	0.563000	0.77884	TCT		0.408	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117359688	G	T	117359688	3	4	47	1	0	0	0	0	1	0	0	0	4051	942	33	2	489	2	CTTNBP2	7	117359688	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1019912	117359688	41778975	974	5371										
C7orf58	79974	broad.mit.edu	37	chr7	120767207	120767207	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaggaccaaaatacagaaGaattccttttaaatgacact	6	7	0	4	rs202229385		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:120767207G>T	ENST00000310396.5	+	10	1665	c.1198G>T	c.(1198-1200)Gaa>Taa	p.E400*	CPED1_ENST00000450913.2_Nonsense_Mutation_p.E400*|CPED1_ENST00000423795.1_Nonsense_Mutation_p.E180*	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	400						endoplasmic reticulum (GO:0005783)		p.E400*(1)									AAATACAGAAGAATTCCTTTT	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											87	93	91					7																	120767207		2198	4291	6489	120554443	SO:0001587	stop_gained	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.1198G>T	7.37:g.120767207G>T	ENSP00000309772:p.Glu400*		120554443	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Nonsense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120807	0.94385	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	.	.	.	4.33	1.4	0.22301	.	0.519378	0.20018	N	0.100962	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	7.1038	0.25353	0.2963:0.0:0.7037:0.0	.	.	.	.	X	400;400;400;180;180	.	ENSP00000309772:E400X	E	+	1	0	C7orf58	120554443	1.000000	0.71417	0.979000	0.43373	0.751000	0.42716	0.969000	0.29370	0.367000	0.24454	0.467000	0.42956	GAA		0.289	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120767207	G	T	120767207	4	4	47	1	0	0	0	0	0	1	0	0	2411	943	33	2	1232	2	C7orf58	7	120767207	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3407519	120767207	38371456	975	5372										
HYAL4	23553	broad.mit.edu	37	chr7	123508524	123508524	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgataaaatataatttaaGactaaatttgaaaatgtttc	4	2	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:123508524G>T	ENST00000223026.4	+	3	835	c.197G>T	c.(196-198)aGa>aTa	p.R66I	HYAL4_ENST00000476325.1_Missense_Mutation_p.R66I	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	66					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.R66I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						TATAATTTAAGACTAAATTTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											39	43	42					7																	123508524		2202	4299	6501	123295760	SO:0001583	missense	23553			AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.197G>T	7.37:g.123508524G>T	ENSP00000223026:p.Arg66Ile		123295760	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1	.	.	.	.	.	.	.	.	.	.	G	9.587	1.125070	0.20959	.	.	ENSG00000106302	ENST00000223026;ENST00000476325	T;T	0.29917	1.55;1.55	5.19	-2.26	0.06867	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.760794	0.12554	N	0.458819	T	0.14743	0.0356	L	0.27053	0.805	0.09310	N	1	B;B	0.18013	0.006;0.025	B;B	0.22152	0.014;0.038	T	0.25047	-1.0143	9	.	.	.	-6.6542	1.1735	0.01830	0.3063:0.2784:0.2703:0.145	.	66;66	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	I	66	ENSP00000223026:R66I;ENSP00000417186:R66I	.	R	+	2	0	HYAL4	123295760	0.000000	0.05858	0.000000	0.03702	0.900000	0.52787	-0.880000	0.04183	-0.277000	0.09193	0.655000	0.94253	AGA		0.378	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		T	123508524	G	T	123508524	3	4	47	1	0	0	0	0	1	0	0	0	7487	942	33	2	199	2	HYAL4	7	123508524	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2741317	123508524	35630139	976	5373										
SPAM1	6677	broad.mit.edu	37	chr7	123593734	123593734	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccatgttgcttgactctgaAtttcagagcacctcctgtta	7	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:123593734A>C	ENST00000439500.1	+	4	723	c.110A>C	c.(109-111)aAt>aCt	p.N37T	SPAM1_ENST00000460182.1_Missense_Mutation_p.N37T|SPAM1_ENST00000340011.5_Missense_Mutation_p.N37T|SPAM1_ENST00000402183.2_Missense_Mutation_p.N37T|SPAM1_ENST00000223028.7_Missense_Mutation_p.N37T	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	37					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)	p.N37T(2)		breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TTGACTCTGAATTTCAGAGCA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	7											77	71	73					7																	123593734		2203	4300	6503	123380970	SO:0001583	missense	6677			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.110A>C	7.37:g.123593734A>C	ENSP00000402123:p.Asn37Thr		123380970	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	A	11.04	1.522358	0.27211	.	.	ENSG00000106304	ENST00000402183;ENST00000413927;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T;T	0.41400	2.57;1.0;2.57;2.57;2.57;2.57	6.02	4.82	0.62117	.	1.441520	0.03853	N	0.272659	T	0.28962	0.0719	N	0.08118	0	0.09310	N	1	B;B	0.24132	0.098;0.098	B;B	0.15484	0.013;0.013	T	0.11227	-1.0596	10	0.23891	T	0.37	-20.075	13.9514	0.64118	0.8656:0.1344:0.0:0.0	.	37;37	Q8TC30;P38567	.;HYALP_HUMAN	T	37	ENSP00000386028:N37T;ENSP00000391491:N37T;ENSP00000417934:N37T;ENSP00000345849:N37T;ENSP00000402123:N37T;ENSP00000223028:N37T	ENSP00000223028:N37T	N	+	2	0	SPAM1	123380970	0.026000	0.19158	0.003000	0.11579	0.130000	0.20726	3.082000	0.50128	2.299000	0.77371	0.528000	0.53228	AAT		0.403	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			C	123593734	A	C	123593734	3	2	47	1	0	0	0	0	1	0	0	0	15025	101	4	4	112	4	SPAM1	7	123593734	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	85210	123593734	35544929	977	5374										
GCC1	79571	broad.mit.edu	37	chr7	127224531	127224531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcactctgctcttgggcccGatcatgctgctgcgtgataa	11	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:127224531G>A	ENST00000321407.2	-	1	1130	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	236					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.R236W(1)		breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TCTTGGGCCCGATCATGCTGC	0.597											OREG0003809	type=REGULATORY REGION|Gene=GCC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Missense(1)	large_intestine(1)	7											80	76	77					7																	127224531		2203	4300	6503	127011767	SO:0001583	missense	79571			AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.706C>T	7.37:g.127224531G>A	ENSP00000318821:p.Arg236Trp	1555	127011767	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	37	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325192	0.60634	.	.	ENSG00000179562	ENST00000321407	T	0.55234	0.53	5.27	0.919	0.19392	.	0.106801	0.64402	D	0.000016	T	0.67998	0.2953	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.71279	-0.4640	10	0.66056	D	0.02	-32.1056	13.6083	0.62061	0.0:0.0:0.462:0.538	.	236	Q96CN9	GCC1_HUMAN	W	236	ENSP00000318821:R236W	ENSP00000318821:R236W	R	-	1	2	GCC1	127011767	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.788000	0.26872	0.315000	0.23110	-0.182000	0.12963	CGG		0.597	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		A	127224531	G	A	127224531	3	1	47	1	0	0	0	0	1	0	0	0	6305	1057	37	1	1629	1	GCC1	7	127224531	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3630797	127224531	31914132	978	5375										
GCC1	79571	broad.mit.edu	37	chr7	127224767	127224767	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtcttcagctggtgcagtCttttgtccacctccccacct	8	15	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:127224767C>A	ENST00000321407.2	-	1	894	c.470G>T	c.(469-471)aGa>aTa	p.R157I	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	157					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.R157I(1)		breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CTGGTGCAGTCTTTTGTCCAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											115	114	114					7																	127224767		2203	4300	6503	127012003	SO:0001583	missense	79571			AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.470G>T	7.37:g.127224767C>A	ENSP00000318821:p.Arg157Ile		127012003	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	37	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259138	0.80246	.	.	ENSG00000179562	ENST00000321407	T	0.13089	2.62	5.96	5.96	0.96718	.	0.114641	0.53938	D	0.000044	T	0.30603	0.0770	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.00397	-1.1765	10	0.49607	T	0.09	-12.3947	11.2654	0.49108	0.0:0.9177:0.0:0.0823	.	157	Q96CN9	GCC1_HUMAN	I	157	ENSP00000318821:R157I	ENSP00000318821:R157I	R	-	2	0	GCC1	127012003	0.981000	0.34729	0.977000	0.42913	0.998000	0.95712	3.589000	0.53972	2.844000	0.97970	0.650000	0.86243	AGA		0.552	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		A	127224767	C	A	127224767	3	1	47	1	0	0	0	0	1	0	0	0	6305	913	32	2	1865	2	GCC1	7	127224767	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	236	127224767	31913896	979	5376										
PLXNA4	91584	broad.mit.edu	37	chr7	131888126	131888126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgaagtgcccattccacAcgactgtcaactccacgggc	9	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:131888126A>G	ENST00000359827.3	-	11	3313	c.2351T>C	c.(2350-2352)gTg>gCg	p.V784A	PLXNA4_ENST00000321063.4_Missense_Mutation_p.V784A			Q9HCM2	PLXA4_HUMAN	plexin A4	784					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.V784A(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCCATTCCACACGACTGTCAA	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	7											118	116	117					7																	131888126		1955	4140	6095	131538666	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2351T>C	7.37:g.131888126A>G	ENSP00000352882:p.Val784Ala		131538666	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499304	0.64298	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.66460	-0.21;-0.21	4.76	4.76	0.60689	.	0.063440	0.64402	D	0.000006	T	0.67664	0.2917	M	0.83312	2.635	0.49582	D	0.9998	B	0.23442	0.085	B	0.18871	0.023	T	0.65915	-0.6052	10	0.23302	T	0.38	.	14.6154	0.68544	1.0:0.0:0.0:0.0	.	784	Q9HCM2	PLXA4_HUMAN	A	784	ENSP00000323194:V784A;ENSP00000352882:V784A	ENSP00000323194:V784A	V	-	2	0	PLXNA4	131538666	1.000000	0.71417	0.998000	0.56505	0.634000	0.38068	9.287000	0.95975	1.916000	0.55485	0.459000	0.35465	GTG		0.557	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		G	131888126	A	G	131888126	3	3	47	1	0	0	0	0	1	0	0	0	12153	159	6	4	3421	4	PLXNA4	7	131888126	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4663359	131888126	27250537	980	5377										
PLXNA4	91584	broad.mit.edu	37	chr7	132192727	132192727	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaaaaccatagacatagtaGatatcaaagtcagggatgat	8	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:132192727G>T	ENST00000359827.3	-	2	1688	c.726C>A	c.(724-726)atC>atA	p.I242I	PLXNA4_ENST00000423507.2_Silent_p.I242I|PLXNA4_ENST00000378539.5_Silent_p.I242I|PLXNA4_ENST00000321063.4_Silent_p.I242I			Q9HCM2	PLXA4_HUMAN	plexin A4	242	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.I242I(3)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						AGACATAGTAGATATCAAAGT	0.498																																																3	Substitution - coding silent(3)	large_intestine(3)	7											97	90	92					7																	132192727		2203	4300	6503	131843267	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.726C>A	7.37:g.132192727G>T			131843267	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.498	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	132192727	G	T	132192727	2	4	47	1	0	0	0	0	0	0	0	1	12153	932	33	2		2	PLXNA4	7	132192727	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	304601	132192727	26945936	981	5378										
CALD1	800	broad.mit.edu	37	chr7	134644857	134644857	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccactgcagcaggcacaccaAataaggtgagcatctgattt	9	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:134644857A>C	ENST00000361675.2	+	12	2423	c.2194A>C	c.(2194-2196)Aat>Cat	p.N732H	CALD1_ENST00000466704.1_3'UTR|CALD1_ENST00000424922.1_Missense_Mutation_p.N471H|CALD1_ENST00000495522.1_Missense_Mutation_p.N496H|CALD1_ENST00000361388.2_Missense_Mutation_p.N503H|CALD1_ENST00000543443.1_Missense_Mutation_p.N482H|CALD1_ENST00000422748.1_Missense_Mutation_p.N502H|CALD1_ENST00000361901.2_Missense_Mutation_p.N477H|CALD1_ENST00000393118.2_Missense_Mutation_p.N497H|CALD1_ENST00000417172.1_Missense_Mutation_p.N477H			Q05682	CALD1_HUMAN	caldesmon 1	732					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)	p.N732H(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						AGGCACACCAAATAAGGTGAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											117	100	106					7																	134644857		2203	4300	6503	134295397	SO:0001583	missense	800			M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.2194A>C	7.37:g.134644857A>C	ENSP00000354826:p.Asn732His		134295397	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.524426	0.44969	.	.	ENSG00000122786	ENST00000417172;ENST00000361388;ENST00000422748;ENST00000432646;ENST00000361675;ENST00000361901;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.74	5.74	0.90152	.	0.000000	0.56097	D	0.000036	T	0.74268	0.3694	M	0.80982	2.52	0.44579	D	0.997542	D;D;D;D;D;D;D;D;D;D	0.89917	0.997;0.996;0.997;0.997;0.996;0.996;0.999;0.996;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.991;0.985;0.991;0.991;0.978;0.978;0.985;0.985;0.996;0.999	T	0.77233	-0.2663	10	0.56958	D	0.05	-27.9772	16.0292	0.80564	1.0:0.0:0.0:0.0	.	426;482;502;496;471;497;477;503;732;477	B4DPW5;F5H1Z9;A8K0X1;E7EX44;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682;Q9NYG1	.;.;.;.;.;.;.;.;CALD1_HUMAN;.	H	477;503;502;110;732;477;497;471;496;482	ENSP00000398826:N477H;ENSP00000355000:N503H;ENSP00000395710:N502H;ENSP00000354826:N732H;ENSP00000354513:N477H;ENSP00000376826:N497H;ENSP00000393621:N471H;ENSP00000419673:N496H;ENSP00000445641:N482H	ENSP00000355000:N503H	N	+	1	0	CALD1	134295397	1.000000	0.71417	0.894000	0.35097	0.017000	0.09413	5.161000	0.64935	2.187000	0.69744	0.533000	0.62120	AAT		0.418	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		C	134644857	A	C	134644857	3	2	47	1	0	0	0	0	1	0	0	0	2587	14	1	4	2289	4	CALD1	7	134644857	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2452130	134644857	24493806	982	5379										
DGKI	9162	broad.mit.edu	37	chr7	137080385	137080385	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatgctcctgcatccaccaGaagctggcacacagcccggt	10	15	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:137080385G>T	ENST00000288490.5	-	33	3040	c.3040C>A	c.(3040-3042)Ctg>Atg	p.L1014M	DGKI_ENST00000453654.2_Missense_Mutation_p.L683M|DGKI_ENST00000446122.1_Missense_Mutation_p.L996M|DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000424189.2_Missense_Mutation_p.L1027M	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	1014					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.L1014M(1)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GCATCCACCAGAAGCTGGCAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	7											77	67	71					7																	137080385		2203	4300	6503	136730925	SO:0001583	missense	9162			AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.3040C>A	7.37:g.137080385G>T	ENSP00000288490:p.Leu1014Met		136730925	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.634513	0.67130	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.73575	-0.76;-0.76;-0.76	5.35	3.52	0.40303	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000002	D	0.89350	0.6690	H	0.96777	3.88	0.47905	D	0.999543	D;D	0.89917	0.998;1.0	D;D	0.83275	0.983;0.996	D	0.90760	0.4664	10	0.87932	D	0	.	9.8701	0.41168	0.2169:0.0:0.7831:0.0	.	683;1014	E9PFX6;O75912	.;DGKI_HUMAN	M	683;931;1017;1014;996	ENSP00000392161:L683M;ENSP00000288490:L1014M;ENSP00000399131:L996M	ENSP00000288490:L1014M	L	-	1	2	DGKI	136730925	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.207000	0.42788	1.379000	0.46325	0.650000	0.86243	CTG		0.562	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137080385	G	T	137080385	3	4	47	1	0	0	0	0	1	0	0	0	4482	933	33	2	165	2	DGKI	7	137080385	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2435528	137080385	22058278	983	5380										
WEE2	494551	broad.mit.edu	37	chr7	141418873	141418873	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttattaaaatactttagaGatgtgttttacgagaaacca	6	4	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:141418873G>T	ENST00000397541.2	+	4	993	c.587G>T	c.(586-588)aGa>aTa	p.R196I	WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000484172.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	196					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.R196I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					ATACTTTAGAGATGTGTTTTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	78	79					7																	141418873		1791	4062	5853	141065342	SO:0001630	splice_region_variant	494551			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.586-1G>T	7.37:g.141418873G>T			141065342		Missense_Mutation	SNP	ENST00000397541.2	37	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154122	0.78114	.	.	ENSG00000214102	ENST00000397541	T	0.26660	1.72	5.52	2.22	0.28083	Protein kinase-like domain (1);	0.000000	0.85682	U	0.000000	T	0.47210	0.1433	M	0.80746	2.51	0.80722	D	1	D	0.56287	0.975	P	0.62491	0.903	T	0.46456	-0.9190	10	0.87932	D	0	.	11.0835	0.48074	0.1837:0.0:0.8163:0.0	.	196	P0C1S8	WEE2_HUMAN	I	196	ENSP00000380675:R196I	ENSP00000380675:R196I	R	+	2	0	WEE2	141065342	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	4.449000	0.60034	0.132000	0.18615	0.561000	0.74099	AGA		0.338	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558	Missense_Mutation	T	141418873	G	T	141418873	5	4	47	1	0	0	0	0	0	0	1	0	17385	956	33	2	601	2	WEE2	7	141418873	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4338488	141418873	17719790	984	5381										
OR9A4	130075	broad.mit.edu	37	chr7	141618768	141618768	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcctttttgctatattcttCtttttctacttggtgacatt	4	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:141618768C>A	ENST00000548136.1	+	1	152	c.93C>A	c.(91-93)ttC>ttA	p.F31L	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F31L(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					CTATATTCTTCTTTTTCTACT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											209	219	216					7																	141618768		2197	4297	6494	141265237	SO:0001583	missense	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.93C>A	7.37:g.141618768C>A	ENSP00000448789:p.Phe31Leu		141265237	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	37	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.717146	0.00093	.	.	ENSG00000258083	ENST00000548136	T	0.00287	8.29	3.81	-1.49	0.08718	.	.	.	.	.	T	0.00073	0.0002	N	0.01188	-0.97	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13282	-1.0515	9	0.11794	T	0.64	-14.4428	0.1291	0.00072	0.2773:0.27:0.168:0.2848	.	31	Q8NGU2	OR9A4_HUMAN	L	31	ENSP00000448789:F31L	ENSP00000386148:F31L	F	+	3	2	OR9A4	141265237	0.000000	0.05858	0.033000	0.17914	0.070000	0.16714	-1.508000	0.02266	-0.479000	0.06813	-0.183000	0.12914	TTC		0.403	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		A	141618768	C	A	141618768	3	1	47	1	0	0	0	0	1	0	0	0	11280	912	32	2	95	2	OR9A4	7	141618768	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	199895	141618768	17519895	985	5382										
OR9A4	130075	broad.mit.edu	37	chr7	141619232	141619232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaccgagggcaattgctcaAactatcctgcaataatactc	7	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:141619232A>C	ENST00000548136.1	+	1	616	c.557A>C	c.(556-558)aAa>aCa	p.K186T	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K186T(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					CAATTGCTCAAACTATCCTGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											163	162	163					7																	141619232		2063	4246	6309	141265701	SO:0001583	missense	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.557A>C	7.37:g.141619232A>C	ENSP00000448789:p.Lys186Thr		141265701	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	37	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	.	12.12	1.841537	0.32513	.	.	ENSG00000258083	ENST00000548136	T	0.00267	8.38	3.8	0.19	0.15125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00271	0.0008	M	0.84326	2.69	0.29884	N	0.825785	B	0.25206	0.12	B	0.32211	0.142	T	0.05354	-1.0890	9	0.72032	D	0.01	-3.4582	6.929	0.24432	0.677:0.0:0.323:0.0	.	186	Q8NGU2	OR9A4_HUMAN	T	186	ENSP00000448789:K186T	ENSP00000386148:K186T	K	+	2	0	OR9A4	141265701	0.000000	0.05858	0.382000	0.26119	0.386000	0.30323	1.132000	0.31418	0.181000	0.19994	0.533000	0.62120	AAA		0.383	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		C	141619232	A	C	141619232	3	2	47	1	0	0	0	0	1	0	0	0	11280	14	1	4	559	4	OR9A4	7	141619232	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	464	141619232	17519431	986	5383										
TAS2R39	259285	broad.mit.edu	37	chr7	142880937	142880937	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgtgaagattgccaatttCtcctacccccttttcctcaa	4	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:142880937C>A	ENST00000446620.1	+	1	426	c.426C>A	c.(424-426)ttC>ttA	p.F142L		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	142					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.F142L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					TTGCCAATTTCTCCTACCCCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	87	89					7																	142880937		1881	4096	5977	142591059	SO:0001583	missense	259285			AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.426C>A	7.37:g.142880937C>A	ENSP00000405095:p.Phe142Leu		142591059	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	37	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403736	0.62288	.	.	ENSG00000236398	ENST00000446620	T	0.00976	5.48	4.86	3.03	0.35002	.	.	.	.	.	T	0.02304	0.0071	M	0.72894	2.215	0.24371	N	0.994833	P	0.39883	0.693	P	0.45946	0.498	T	0.33445	-0.9868	9	0.72032	D	0.01	.	7.7302	0.28783	0.0:0.7065:0.0:0.2935	.	142	P59534	T2R39_HUMAN	L	142	ENSP00000405095:F142L	ENSP00000405095:F142L	F	+	3	2	TAS2R39	142591059	0.013000	0.17824	0.366000	0.25914	0.993000	0.82548	-0.000000	0.12993	0.742000	0.32697	0.650000	0.86243	TTC		0.393	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		A	142880937	C	A	142880937	3	1	47	1	0	0	0	0	1	0	0	0	15615	912	32	2	428	2	TAS2R39	7	142880937	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1261705	142880937	16257726	987	5384										
OR6B1	135946	broad.mit.edu	37	chr7	143701517	143701517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagccatgggctctgcttccGcctcgctcttggttcctggg	13	14	2	0	rs373139746		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:143701517G>A	ENST00000408922.2	+	1	496	c.428G>A	c.(427-429)cGc>cAc	p.R143H		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	143			R -> C (in dbSNP:rs7787378).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R143L(1)|p.R143H(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					CTCTGCTTCCGCCTCGCTCTT	0.562																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						G	HIS/ARG	1,4287		0,1,2143	80	82	82		428	0.3	0.2	7		82	0,8558		0,0,4279	no	missense	OR6B1	NM_001005281.1	29	0,1,6422	AA,AG,GG		0.0,0.0233,0.0078	benign	143/312	143701517	1,12845	2144	4279	6423	143332450	SO:0001583	missense	135946				CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"GPCR / Class A : Olfactory receptors"	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.428G>A	7.37:g.143701517G>A	ENSP00000386151:p.Arg143His		143332450	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	.	.	.	.	.	.	.	.	.	.	G	5.206	0.223507	0.09863	2.33E-4	0.0	ENSG00000221813	ENST00000408922	T	0.00130	8.69	5.26	0.292	0.15737	GPCR, rhodopsin-like superfamily (1);	0.415982	0.17515	N	0.171466	T	0.00109	0.0003	L	0.39633	1.23	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.13710	-1.0499	10	0.15066	T	0.55	.	4.9549	0.14035	0.3181:0.0:0.5455:0.1364	.	143	O95007	OR6B1_HUMAN	H	143	ENSP00000386151:R143H	ENSP00000386151:R143H	R	+	2	0	OR6B1	143332450	0.000000	0.05858	0.157000	0.22605	0.142000	0.21351	-0.483000	0.06536	-0.124000	0.11724	0.655000	0.94253	CGC		0.562	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1			A	143701517	G	A	143701517	3	1	47	1	0	0	0	0	1	0	0	0	11218	1087	38	1	430	1	OR6B1	7	143701517	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	820580	143701517	15437146	988	5385										
OR2A5	393046	broad.mit.edu	37	chr7	143747556	143747556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggatttccactcagcctaaGgattcagatgctcctctctg	9	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:143747556G>T	ENST00000408906.2	+	1	96	c.62G>T	c.(61-63)aGg>aTg	p.R21M		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R21M(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CTCAGCCTAAGGATTCAGATG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	7											99	108	105					7																	143747556		2170	4288	6458	143378489	SO:0001583	missense	393046			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.62G>T	7.37:g.143747556G>T	ENSP00000386208:p.Arg21Met		143378489	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	G	2.737	-0.263094	0.05754	.	.	ENSG00000221836	ENST00000408906	T	0.00441	7.41	5.06	-5.29	0.02747	.	.	.	.	.	T	0.00328	0.0010	L	0.39898	1.24	0.09310	N	1	B	0.14012	0.009	B	0.14023	0.01	T	0.30475	-0.9977	9	0.62326	D	0.03	.	12.9787	0.58552	0.4141:0.0:0.5859:0.0	.	21	Q96R48	OR2A5_HUMAN	M	21	ENSP00000386208:R21M	ENSP00000386208:R21M	R	+	2	0	OR2A5	143378489	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.271000	0.01166	-1.080000	0.03109	-0.300000	0.09419	AGG		0.522	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			T	143747556	G	T	143747556	3	4	47	1	0	0	0	0	1	0	0	0	11012	1000	35	2	64	2	OR2A5	7	143747556	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	46039	143747556	15391107	989	5386										
OR2A14	135941	broad.mit.edu	37	chr7	143827015	143827015	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgccatcctgaggagcagcaGaaagttctttccctgtttta	9	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:143827015G>T	ENST00000408899.2	+	1	865	c.810G>T	c.(808-810)caG>caT	p.Q270H		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q270H(1)		large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					AGGAGCAGCAGAAAGTTCTTT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											127	134	132					7																	143827015		1958	4157	6115	143457948	SO:0001583	missense	135941				CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"GPCR / Class A : Olfactory receptors"	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.810G>T	7.37:g.143827015G>T	ENSP00000386137:p.Gln270His		143457948	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	37	CCDS43672.1	.	.	.	.	.	.	.	.	.	.	G	6.613	0.481575	0.12581	.	.	ENSG00000221938	ENST00000408899	T	0.00130	8.69	4.18	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.285780	0.18915	U	0.127625	T	0.00073	0.0002	N	0.14661	0.345	0.28911	N	0.892719	B	0.15141	0.012	B	0.24394	0.053	T	0.14615	-1.0466	10	0.59425	D	0.04	-3.9469	3.4177	0.07381	0.2224:0.0:0.5774:0.2002	.	270	Q96R47	O2A14_HUMAN	H	270	ENSP00000386137:Q270H	ENSP00000386137:Q270H	Q	+	3	2	OR2A14	143457948	0.002000	0.14202	1.000000	0.80357	0.089000	0.18198	0.240000	0.18042	0.481000	0.27557	0.561000	0.74099	CAG		0.552	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1			T	143827015	G	T	143827015	3	4	47	1	0	0	0	0	1	0	0	0	11007	933	33	2	812	2	OR2A14	7	143827015	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	79459	143827015	15311648	990	5387										
OR2A7	401427	broad.mit.edu	37	chr7	143955912	143955912	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaacagcaggagatatttCttctgctccttggggttccc	10	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:143955912C>A	ENST00000493325.1	-	1	903	c.810G>T	c.(808-810)aaG>aaT	p.K270N	OR2A1-AS1_ENST00000478806.1_RNA|RP4-545C24.1_ENST00000460955.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000498397.1_RNA|ARHGEF35_ENST00000543357.1_Intron|OR2A1-AS1_ENST00000487102.1_RNA	NM_001005328.1	NP_001005328.1	Q96R45	OR2A7_HUMAN	olfactory receptor, family 2, subfamily A, member 7	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K270N(2)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	6	Melanoma(164;0.14)					GGAGATATTTCTTCTGCTCCT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	7											64	71	69					7																	143955912		2203	4297	6500	143586845	SO:0001583	missense	401427				CCDS55177.1	7q35	2013-09-20			ENSG00000243896	ENSG00000243896		"GPCR / Class A : Olfactory receptors"	8234	protein-coding gene	gene with protein product							Standard	NM_001005328		Approved	HSDJ0798C17	uc011kuc.2	Q96R45	OTTHUMG00000158002	ENST00000493325.1:c.810G>T	7.37:g.143955912C>A	ENSP00000420502:p.Lys270Asn		143586845	B2RN57|Q6IFP4	Missense_Mutation	SNP	ENST00000493325.1	37	CCDS55177.1	.	.	.	.	.	.	.	.	.	.	c	8.144	0.785933	0.16189	.	.	ENSG00000243896	ENST00000493325	T	0.00063	8.78	3.17	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.02960	-0.455	0.26338	N	0.977417	B	0.20887	0.049	B	0.25759	0.063	T	0.02059	-1.1221	9	0.38643	T	0.18	.	6.3274	0.21251	0.0:0.861:0.0:0.139	.	270	Q96R45	OR2A7_HUMAN	N	270	ENSP00000420502:K270N	ENSP00000420502:K270N	K	-	3	2	OR2A7	143586845	0.002000	0.14202	1.000000	0.80357	0.886000	0.51366	0.004000	0.13106	0.893000	0.36288	0.508000	0.49915	AAG		0.453	OR2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349979.1			A	143955912	C	A	143955912	3	1	47	1	0	0	0	0	1	0	0	0	11013	912	32	2	125	2	OR2A7	7	143955912	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	128897	143955912	15182751	991	5388										
C7orf33	202865	broad.mit.edu	37	chr7	148311180	148311180	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgggggatggaatttattgCtcctgtatcagctcccacca	10	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:148311180C>A	ENST00000307003.2	+	2	612	c.251C>A	c.(250-252)gCt>gAt	p.A84D		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	84								p.A84D(1)		central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GAATTTATTGCTCCTGTATCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	87	88					7																	148311180		2203	4300	6503	147942113	SO:0001583	missense	202865			BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.251C>A	7.37:g.148311180C>A	ENSP00000304071:p.Ala84Asp		147942113		Missense_Mutation	SNP	ENST00000307003.2	37	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	C	0.993	-0.693422	0.03303	.	.	ENSG00000170279	ENST00000307003	.	.	.	1.06	-1.35	0.09114	.	.	.	.	.	T	0.19248	0.0462	N	0.19112	0.55	0.09310	N	1	D	0.58268	0.982	P	0.47102	0.537	T	0.10636	-1.0621	8	0.59425	D	0.04	.	2.3778	0.04346	0.0:0.4116:0.3295:0.259	.	84	Q8WU49	CG033_HUMAN	D	84	.	ENSP00000304071:A84D	A	+	2	0	C7orf33	147942113	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.943000	0.01539	-0.529000	0.06358	0.448000	0.29417	GCT		0.488	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304		A	148311180	C	A	148311180	3	1	47	1	0	0	0	0	1	0	0	0	2394	797	28	2	257	2	C7orf33	7	148311180	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4355268	148311180	10827483	992	5389										
GIMAP4	55303	broad.mit.edu	37	chr7	150269396	150269396	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagctcatggaaggaaacaGaacttgtcgtagttgacaca	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:150269396G>T	ENST00000255945.2	+	3	413	c.238G>T	c.(238-240)Gaa>Taa	p.E80*	GIMAP4_ENST00000461940.1_Nonsense_Mutation_p.E94*|GIMAP4_ENST00000494750.1_3'UTR	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	80	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)	p.E80*(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAAGGAAACAGAACTTGTCGT	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											116	98	104					7																	150269396		2203	4300	6503	149900329	SO:0001587	stop_gained	55303			AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"GTPases, IMAP"	21872	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 1"	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.238G>T	7.37:g.150269396G>T	ENSP00000255945:p.Glu80*		149900329		Nonsense_Mutation	SNP	ENST00000255945.2	37	CCDS5904.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.687531	0.68157	.	.	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000479232	.	.	.	4.61	4.61	0.57282	.	0.833888	0.11080	N	0.601927	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	12.8024	0.57594	0.0:0.0:1.0:0.0	.	.	.	.	X	80;94;94	.	ENSP00000255945:E80X	E	+	1	0	GIMAP4	149900329	0.000000	0.05858	0.098000	0.21074	0.047000	0.14425	0.131000	0.15870	2.416000	0.81992	0.655000	0.94253	GAA		0.488	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326		T	150269396	G	T	150269396	4	4	47	1	0	0	0	0	0	1	0	0	6401	943	33	2	244	2	GIMAP4	7	150269396	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1958216	150269396	8869267	993	5390										
KCNH2	3757	broad.mit.edu	37	chr7	150648020	150648020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcctcaccgcgttcatgtCgatgccgttggtgtaggacc	13	12	2	0	rs199852343		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:150648020C>T	ENST00000262186.5	-	8	2535	c.2134G>A	c.(2134-2136)Gac>Aac	p.D712N	KCNH2_ENST00000430723.3_Missense_Mutation_p.D712N|KCNH2_ENST00000392968.2_Missense_Mutation_p.D616N|KCNH2_ENST00000330883.4_Missense_Mutation_p.D372N	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	712					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)	p.D712N(1)		NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCGTTCATGTCGATGCCGTTG	0.637																																					GBM(137;110 1844 13671 20123 45161)											1	Substitution - Missense(1)	large_intestine(1)	7											85	69	75					7																	150648020		2203	4300	6503	150278953	SO:0001583	missense	3757			U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.2134G>A	7.37:g.150648020C>T	ENSP00000262186:p.Asp712Asn		150278953	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	19.63	3.863415	0.71949	.	.	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186;ENST00000430723	D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17	4.36	4.36	0.52297	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.98115	0.9378	M	0.87971	2.92	0.50313	D	0.999869	D;D;D;D;D	0.89917	0.98;1.0;0.992;0.99;0.987	P;D;P;P;P	0.81914	0.535;0.995;0.809;0.885;0.842	D	0.99084	1.0838	10	0.87932	D	0	.	14.7478	0.69501	0.0:1.0:0.0:0.0	.	616;712;372;712;372	C4PFH9;G5E9I0;Q708S9;Q12809;Q12809-2	.;.;.;KCNH2_HUMAN;.	N	372;616;712;712	ENSP00000328531:D372N;ENSP00000376695:D616N;ENSP00000262186:D712N;ENSP00000387657:D712N	ENSP00000262186:D712N	D	-	1	0	KCNH2	150278953	1.000000	0.71417	1.000000	0.80357	0.181000	0.23173	7.733000	0.84916	2.126000	0.65437	0.313000	0.20887	GAC		0.637	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		T	150648020	C	T	150648020	3	4	47	1	0	0	0	0	1	0	0	0	8053	884	31	1	1646	1	KCNH2	7	150648020	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	378624	150648020	8490643	994	5391										
SMARCD3	6604	broad.mit.edu	37	chr7	150939642	150939642	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatcctcagcatcaggcttCgcagggttaaaagtgttgga	12	8	2	0	rs200087546		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:150939642C>T	ENST00000262188.8	-	5	914	c.504G>A	c.(502-504)gcG>gcA	p.A168A	SMARCD3_ENST00000477169.1_5'UTR|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000356800.2_Silent_p.A155A|SMARCD3_ENST00000392811.2_Silent_p.A155A	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	168					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.A155A(3)|p.A168A(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATCAGGCTTCGCAGGGTTAA	0.577													C|||	1	0.000199681	0	0	5008	,	,		19639	0		0	False		,,,				2504	0.001															4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	7											111	119	116					7																	150939642		2203	4300	6503	150570575	SO:0001819	synonymous_variant	6604			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60C", "Swp73-like protein", "SWI/SNF complex 60 kDa subunit C", "60kDa BRG-1/Brm associated factor subunit c"	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.504G>A	7.37:g.150939642C>T			150570575	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Silent	SNP	ENST00000262188.8	37	CCDS34780.1																																																																																				0.577	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		T	150939642	C	T	150939642	2	4	47	1	0	0	0	0	0	0	0	1	14816	871	31	1		1	SMARCD3	7	150939642	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	291622	150939642	8199021	995	5392										
GALNTL5	168391	broad.mit.edu	37	chr7	151716736	151716736	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatattttcatttaggagcaGttttttcttcgaaagcctgg	8	6	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:151716736G>T	ENST00000392800.2	+	9	1436	c.1182G>T	c.(1180-1182)caG>caT	p.Q394H	GALNTL5_ENST00000431418.2_Missense_Mutation_p.Q394H	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	394					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.Q394H(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		TTTAGGAGCAGTTTTTTCTTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											85	86	86					7																	151716736		2203	4300	6503	151347669	SO:0001583	missense	168391			AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.1182G>T	7.37:g.151716736G>T	ENSP00000376548:p.Gln394His		151347669	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	G	4.974	0.180831	0.09443	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.68624	-0.34;-0.34	4.77	-0.584	0.11702	.	0.827620	0.10442	N	0.674228	T	0.45677	0.1354	N	0.25201	0.72	0.23943	N	0.996397	B;P	0.50617	0.085;0.937	B;P	0.46026	0.022;0.501	T	0.35847	-0.9772	10	0.14656	T	0.56	.	0.6826	0.00877	0.1945:0.1646:0.327:0.3139	.	145;394	A8MZD3;Q7Z4T8	.;GLTL5_HUMAN	H	394	ENSP00000392582:Q394H;ENSP00000376548:Q394H	ENSP00000376548:Q394H	Q	+	3	2	GALNTL5	151347669	0.997000	0.39634	0.134000	0.22075	0.035000	0.12851	0.148000	0.16224	0.192000	0.20272	-0.266000	0.10368	CAG		0.378	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		T	151716736	G	T	151716736	3	4	47	1	0	0	0	0	1	0	0	0	6244	1020	36	2	1212	2	GALNTL5	7	151716736	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	777094	151716736	7421927	996	5393										
CNPY1	285888	broad.mit.edu	37	chr7	155301689	155301689	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagcgaatctcttgaaagttCtctccttcgtcacagggtct	9	11	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr7:155301689C>A	ENST00000321736.5	-	2	206	c.44G>T	c.(43-45)aGa>aTa	p.R15I	CNPY1_ENST00000406197.1_Missense_Mutation_p.R15I|AC008060.5_ENST00000415333.1_RNA	NM_001103176.1	NP_001096646.1	Q3B7I2	CNPY1_HUMAN	canopy FGF signaling regulator 1	15								p.R15I(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		CTTGAAAGTTCTCTCCTTCGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	77	78					7																	155301689		1820	4082	5902	154994450	SO:0001583	missense	285888				CCDS43684.1	7q36.3	2014-02-12	2013-07-23		ENSG00000146910	ENSG00000146910			27786	protein-coding gene	gene with protein product		612493	"canopy 1 homolog (zebrafish)"			16488878	Standard	NM_001103176		Approved		uc003wmc.1	Q3B7I2	OTTHUMG00000151353	ENST00000321736.5:c.44G>T	7.37:g.155301689C>A	ENSP00000317439:p.Arg15Ile		154994450	A6NGX3	Missense_Mutation	SNP	ENST00000321736.5	37	CCDS43684.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.215182	0.39102	.	.	ENSG00000146910	ENST00000406197;ENST00000321736	T;T	0.38722	1.12;1.12	5.0	1.73	0.24493	.	0.186249	0.45606	D	0.000347	T	0.32102	0.0818	.	.	.	0.09310	N	0.999999	P	0.37573	0.6	B	0.36608	0.229	T	0.19257	-1.0311	9	0.87932	D	0	-9.4838	8.2792	0.31889	0.0:0.2929:0.0:0.7071	.	15	Q3B7I2	CNPY1_HUMAN	I	15	ENSP00000384514:R15I;ENSP00000317439:R15I	ENSP00000317439:R15I	R	-	2	0	CNPY1	154994450	0.239000	0.23836	0.008000	0.14137	0.957000	0.61999	0.375000	0.20518	0.291000	0.22468	0.557000	0.71058	AGA		0.418	CNPY1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322335.1	XM_001129537		A	155301689	C	A	155301689	3	1	47	1	0	0	0	0	1	0	0	0	3633	913	32	2	246	2	CNPY1	7	155301689	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3584953	155301689	3836974	997	5394										
C8orf42	157695	broad.mit.edu	37	chr8	444561	444561	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctttgttaaacagtgaagTcacttctttccaacctcgga	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:444561T>C	ENST00000324079.6	-	2	385	c.145A>G	c.(145-147)Act>Gct	p.T49A	TDRP_ENST00000524229.1_5'UTR|TDRP_ENST00000427263.2_Missense_Mutation_p.T49A|TDRP_ENST00000523656.1_Missense_Mutation_p.T49A			Q86YL5	TDRP_HUMAN	testis development related protein	49					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T49A(1)									AACAGTGAAGTCACTTCTTTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											150	133	139					8																	444561		1889	4120	6009	434561	SO:0001583	missense	157695			AY194292	CCDS47759.1, CCDS59090.1	8p23.3	2013-06-03	2013-06-03	2013-06-03	ENSG00000180190	ENSG00000180190			26951	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 42"	C8orf42		20170638	Standard	NM_175075		Approved	INM01, TDRP1, TDRP2		Q86YL5	OTTHUMG00000163593	ENST00000324079.6:c.145A>G	8.37:g.444561T>C	ENSP00000315111:p.Thr49Ala		434561	B6VF03|B9EG53	Missense_Mutation	SNP	ENST00000324079.6	37	CCDS47759.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.026393	0.75390	.	.	ENSG00000180190	ENST00000324079;ENST00000523656;ENST00000427263	.	.	.	5.92	4.76	0.60689	.	0.101705	0.64402	N	0.000002	T	0.47563	0.1452	L	0.61218	1.895	0.42202	D	0.991779	P;B	0.45474	0.859;0.336	B;B	0.38458	0.274;0.078	T	0.52298	-0.8594	9	0.66056	D	0.02	-16.477	10.0969	0.42480	0.0:0.0792:0.0:0.9208	.	49;49	B6VF03;Q86YL5	.;CH042_HUMAN	A	49	.	ENSP00000315111:T49A	T	-	1	0	C8orf42	434561	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	4.801000	0.62532	1.063000	0.40649	0.528000	0.53228	ACT		0.373	TDRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374442.1	NM_175075		C	444561	T	C	444561	3	2	47	1	0	0	0	0	1	0	0	0	2434	1667	58	4	420	4	C8orf42	8	444561	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09		444561	145919461	998	5395										
CSMD1	64478	broad.mit.edu	37	chr8	3047450	3047450	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacccacacagctggggatCgtgtcgttccactgtgccaa	10	14	1	0	rs117013822	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:3047450C>T	ENST00000520002.1	-	35	5940	c.5385G>A	c.(5383-5385)acG>acA	p.T1795T	CSMD1_ENST00000602723.1_Silent_p.T1795T|CSMD1_ENST00000542608.1_Silent_p.T1794T|CSMD1_ENST00000539096.1_Silent_p.T1794T|CSMD1_ENST00000602557.1_Silent_p.T1795T|CSMD1_ENST00000537824.1_Silent_p.T1794T|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000400186.3_Silent_p.T1795T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1795	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.T1794T(1)|p.T1523T(1)		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)		AGCTGGGGATCGTGTCGTTCC	0.597													C|||	21	0.00419329	0	0	5008	,	,		5345	0.0188		0	False		,,,				2504	0.002															2	Substitution - coding silent(2)	large_intestine(2)	8											33	37	35					8																	3047450		2016	4164	6180	3034857	SO:0001819	synonymous_variant	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5385G>A	8.37:g.3047450C>T			3034857	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		12	0.005494505494505495	0	0.0	0	0.0	12	0.02097902097902098	0	0.0	C	0.270	-0.993252	0.02145	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.2	-10.4	0.00318	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49143	-0.8970	4	.	.	.	.	3.1536	0.06497	0.1277:0.3037:0.3196:0.2491	.	.	.	.	N	1275	.	.	D	-	1	0	CSMD1	3034857	0.001000	0.12720	0.002000	0.10522	0.147000	0.21601	-1.964000	0.01512	-3.843000	0.00100	-1.056000	0.02311	GAT		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3047450	C	T	3047450	2	4	47	1	0	0	0	0	0	0	0	1	3950	871	31	1		1	CSMD1	8	3047450	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2602889	3047450	143316572	999	5396										
CSMD1	64478	broad.mit.edu	37	chr8	3265610	3265610	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaggctcaacatcaaaatCattaaagattaggtgaattc	7	7	3	3	rs267601901		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:3265610C>A	ENST00000520002.1	-	15	2440	c.1885G>T	c.(1885-1887)Gat>Tat	p.D629Y	CSMD1_ENST00000602723.1_Missense_Mutation_p.D629Y|CSMD1_ENST00000542608.1_Missense_Mutation_p.D628Y|CSMD1_ENST00000539096.1_Missense_Mutation_p.D628Y|CSMD1_ENST00000602557.1_Missense_Mutation_p.D629Y|CSMD1_ENST00000537824.1_Missense_Mutation_p.D628Y|CSMD1_ENST00000400186.3_Missense_Mutation_p.D629Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	629	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.D628Y(1)|p.D357Y(1)		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)		ACATCAAAATCATTAAAGATT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	8											79	71	73					8																	3265610		1894	4105	5999	3253017	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1885G>T	8.37:g.3265610C>A	ENSP00000430733:p.Asp629Tyr		3253017	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.449877|4.449877	0.84101|0.84101	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.19806|.	2.12;2.12;2.12;2.12;2.12|.	5.23|5.23	5.23|5.23	0.72850|0.72850	CUB (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77877|.	0.4196|.	M|M	0.79011|0.79011	2.435|2.435	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|.	0.78437|.	-0.2204|.	10|.	0.48119|.	T|.	0.1|.	.|.	18.7996|18.7996	0.92010|0.92010	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	629;629|.	E5RIG2;Q96PZ7|.	.;CSMD1_HUMAN|.	Y|L	629;629;491;628;628;628|108	ENSP00000383047:D629Y;ENSP00000430733:D629Y;ENSP00000441462:D628Y;ENSP00000446243:D628Y;ENSP00000441675:D628Y|.	ENSP00000320445:D491Y|.	D|X	-|-	1|2	0|2	CSMD1|CSMD1	3253017|3253017	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.867000|0.867000	0.49689|0.49689	7.619000|7.619000	0.83057|0.83057	2.437000|2.437000	0.82529|0.82529	0.467000|0.467000	0.42956|0.42956	GAT|TGA		0.418	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3265610	C	A	3265610	3	1	47	1	0	0	0	0	1	0	0	0	3950	826	29	2	9040	2	CSMD1	8	3265610	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	218160	3265610	143098412	1000	5397										
AGPAT5	55326	broad.mit.edu	37	chr8	6614699	6614699	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cataggatgcttatagaattTtatgagtcaccagatccaga	8	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:6614699T>G	ENST00000285518.6	+	8	1197	c.885T>G	c.(883-885)ttT>ttG	p.F295L	AGPAT5_ENST00000530716.1_3'UTR	NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	295					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.F295L(1)	AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TTATAGAATTTTATGAGTCAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											35	36	36					8																	6614699		2202	4300	6502	6602107	SO:0001583	missense	55326			AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.885T>G	8.37:g.6614699T>G	ENSP00000285518:p.Phe295Leu		6602107	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	37	CCDS34796.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.5|22.5	4.303045|4.303045	0.81136|0.81136	.|.	.|.	ENSG00000155189|ENSG00000155189	ENST00000518327|ENST00000285518	T|T	0.67171|0.65178	-0.25|-0.14	6.04|6.04	-0.291|-0.291	0.12843|0.12843	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.74405|0.74405	0.3712|0.3712	M|M	0.92169|0.92169	3.28|3.28	0.80722|0.80722	D|D	1|1	.|D	.|0.55800	.|0.973	.|P	.|0.53549	.|0.729	T|T	0.75676|0.75676	-0.3235|-0.3235	8|10	0.87932|0.52906	D|T	0|0.07	-15.0245|-15.0245	9.61|9.61	0.39657|0.39657	0.0:0.4793:0.0:0.5207|0.0:0.4793:0.0:0.5207	.|.	.|295	.|Q9NUQ2	.|PLCE_HUMAN	C|L	112|295	ENSP00000430751:F112C|ENSP00000285518:F295L	ENSP00000430751:F112C|ENSP00000285518:F295L	F|F	+|+	2|3	0|2	AGPAT5|AGPAT5	6602107|6602107	0.990000|0.990000	0.36364|0.36364	0.994000|0.994000	0.49952|0.49952	0.988000|0.988000	0.76386|0.76386	0.270000|0.270000	0.18607|0.18607	-0.119000|-0.119000	0.11830|0.11830	-0.366000|-0.366000	0.07423|0.07423	TTT|TTT		0.313	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		G	6614699	T	G	6614699	3	3	47	1	0	0	0	0	1	0	0	0	390	1838	64	4	915	4	AGPAT5	8	6614699	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3349089	6614699	139749323	1001	5398										
SPAG11B	10407	broad.mit.edu	37	chr8	7320331	7320331	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggggctctttccctgagttCtccgagagcctcagtggctg	13	12	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:7320331C>A	ENST00000297498.2	-	2	278	c.112G>T	c.(112-114)Gaa>Taa	p.E38*	SPAG11B_ENST00000359758.5_Nonsense_Mutation_p.E38*|SPAG11B_ENST00000361111.2_Nonsense_Mutation_p.E38*|SPAG11B_ENST00000317900.5_Nonsense_Mutation_p.E38*|SPAG11B_ENST00000398462.2_Nonsense_Mutation_p.E38*	NM_016512.3	NP_057596.1	Q08648	SG11B_HUMAN	sperm associated antigen 11B	38					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.E38*(2)		large_intestine(2)|lung(3)|urinary_tract(1)	6				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		TCCCTGAGTTCTCCGAGAGCC	0.592																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											13	18	16					8																	7320331		2069	4095	6164	7307741	SO:0001587	stop_gained	10407			AF168616	CCDS5964.1, CCDS5965.1, CCDS5966.1, CCDS5967.1, CCDS47774.1	8p23.1	2014-02-21	2007-03-15	2007-03-15	ENSG00000164871	ENSG00000164871			14534	protein-coding gene	gene with protein product	"epididymal protein 2B"	606560				8167223, 1693137	Standard	NM_058200		Approved	HE2, EP2, EP2C, EP2D, EDDM2B	uc003wrl.3	Q08648	OTTHUMG00000129219	ENST00000297498.2:c.112G>T	8.37:g.7320331C>A	ENSP00000297498:p.Glu38*		7307741	E9PFH0|Q546A0|Q6ZYB2|Q9H4P8|Q9H4P9|Q9H4Q0|Q9H4Q1|Q9H4Q2|Q9NRT3|Q9NRV4|Q9NRV5|Q9NRV6|Q9NRV7|Q9NRV8	Nonsense_Mutation	SNP	ENST00000297498.2	37	CCDS5966.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.317226	0.60524	.	.	ENSG00000164871	ENST00000528943;ENST00000359758;ENST00000361111;ENST00000297498;ENST00000398462;ENST00000317900	.	.	.	2.59	-1.71	0.08133	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	2.6534	0.05005	0.229:0.3355:0.0:0.4355	.	.	.	.	X	21;38;38;38;38;38	.	ENSP00000297498:E38X	E	-	1	0	SPAG11B	7307741	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.119000	0.10676	-0.461000	0.06993	-0.384000	0.06662	GAA		0.592	SPAG11B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251390.2	NM_058202, NM_058200, NM_058201, NM_016512, NM_058203, NM_058206, NM_058207		A	7320331	C	A	7320331	4	1	47	1	0	0	0	0	0	1	0	0	15016	922	32	2	607	2	SPAG11B	8	7320331	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	705632	7320331	139043691	1002	5399										
PPP1R3B	79660	broad.mit.edu	37	chr8	8998613	8998613	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccctgtctgaaccggcataAgtgtccttcacgtactgaca	8	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:8998613A>C	ENST00000310455.3	-	2	699	c.549T>G	c.(547-549)acT>acG	p.T183T	PPP1R3B_ENST00000519699.1_Silent_p.T183T|RP11-10A14.3_ENST00000522057.1_RNA|RP11-10A14.3_ENST00000520017.1_RNA	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B	183	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase regulator activity (GO:0019888)	p.T183T(1)		endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	12				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		AACCGGCATAAGTGTCCTTCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	8											220	185	196					8																	8998613		2203	4300	6503	9036023	SO:0001819	synonymous_variant	79660			AK024067	CCDS5973.1	8p23.1	2012-04-17	2011-10-04		ENSG00000173281	ENSG00000173281		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14942	protein-coding gene	gene with protein product	"PP1 subunit R4", "hepatic glycogen-targeting subunit, G(L)"	610541	"protein phosphatase 1, regulatory (inhibitor) subunit 3B"			11948623, 17555403	Standard	NM_024607		Approved	GL, FLJ14005, PPP1R4	uc003wsn.4	Q86XI6	OTTHUMG00000129329	ENST00000310455.3:c.549T>G	8.37:g.8998613A>C			9036023	B3KTV3|Q9H812	Silent	SNP	ENST00000310455.3	37	CCDS5973.1																																																																																				0.473	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	NM_024607		C	8998613	A	C	8998613	2	2	47	1	0	0	0	0	0	0	0	1	12406	59	3	4		4	PPP1R3B	8	8998613	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1678282	8998613	137365409	1003	5400										
PRSS55	203074	broad.mit.edu	37	chr8	10387032	10387032	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accagaatgtggtgacagatCtattttcgagggaagaactc	11	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:10387032C>A	ENST00000328655.3	+	2	210	c.170C>A	c.(169-171)tCt>tAt	p.S57Y	PRSS55_ENST00000522210.1_Missense_Mutation_p.S57Y|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	57						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.S57Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GGTGACAGATCTATTTTCGAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	8											130	132	132					8																	10387032		2203	4300	6503	10424442	SO:0001583	missense	203074			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.170C>A	8.37:g.10387032C>A	ENSP00000333003:p.Ser57Tyr		10424442	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.053838	0.36277	.	.	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.89196	-2.48;-2.45	3.96	3.96	0.45880	Peptidase cysteine/serine, trypsin-like (1);	.	.	.	.	D	0.83271	0.5218	L	0.36672	1.1	0.28930	N	0.891633	B	0.24651	0.108	B	0.09377	0.004	T	0.78826	-0.2051	9	0.87932	D	0	.	11.797	0.52106	0.0:1.0:0.0:0.0	.	57	Q6UWB4	PRS55_HUMAN	Y	57	ENSP00000333003:S57Y;ENSP00000430459:S57Y	ENSP00000333003:S57Y	S	+	2	0	PRSS55	10424442	0.929000	0.31497	0.911000	0.35937	0.002000	0.02628	1.994000	0.40757	2.480000	0.83734	0.491000	0.48974	TCT		0.527	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10387032	C	A	10387032	3	1	47	1	0	0	0	0	1	0	0	0	12668	913	32	2	176	2	PRSS55	8	10387032	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1388419	10387032	135976990	1004	5401										
DEFB136	613210	broad.mit.edu	37	chr8	11831560	11831560	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcctggcggacacccgaaGaaacatacggctttctggct	10	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:11831560G>T	ENST00000382209.2	-	2	122	c.123C>A	c.(121-123)ttC>ttA	p.F41L		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	41					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.F41L(1)		endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		GACACCCGAAGAAACATACGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											170	175	174					8																	11831560		2001	4178	6179	11868969	SO:0001583	missense	613210			DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"Defensins, beta"	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.123C>A	8.37:g.11831560G>T	ENSP00000371644:p.Phe41Leu		11868969	Q4QY36	Missense_Mutation	SNP	ENST00000382209.2	37	CCDS43709.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107744	0.37242	.	.	ENSG00000205884	ENST00000382209	T	0.15017	2.46	4.06	2.28	0.28536	.	0.261006	0.27891	N	0.017435	T	0.30634	0.0771	.	.	.	0.28338	N	0.921492	D	0.60160	0.987	P	0.61477	0.889	T	0.06303	-1.0834	9	0.87932	D	0	-0.686	6.4987	0.22155	0.219:0.0:0.781:0.0	.	41	Q30KP8	DB136_HUMAN	L	41	ENSP00000371644:F41L	ENSP00000371644:F41L	F	-	3	2	DEFB136	11868969	0.975000	0.34042	0.957000	0.39632	0.007000	0.05969	0.553000	0.23391	0.682000	0.31407	-0.266000	0.10368	TTC		0.468	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018		T	11831560	G	T	11831560	3	4	47	1	0	0	0	0	1	0	0	0	4431	933	33	2	115	2	DEFB136	8	11831560	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1444528	11831560	134532462	1005	5402										
DLC1	10395	broad.mit.edu	37	chr8	12957491	12957491	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaccacgttgttaaatgtTgactgattgaaaggatcgaa	9	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:12957491T>G	ENST00000276297.4	-	9	2764	c.2355A>C	c.(2353-2355)tcA>tcC	p.S785S	DLC1_ENST00000512044.2_Silent_p.S382S|DLC1_ENST00000358919.2_Silent_p.S348S|DLC1_ENST00000520226.1_Silent_p.S274S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	785	Focal adhesion-targeting (FAT).				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.S785S(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGTTAAATGTTGACTGATTGA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	8											89	82	84					8																	12957491		2203	4300	6503	13001862	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2355A>C	8.37:g.12957491T>G			13001862	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.547	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		G	12957491	T	G	12957491	2	3	47	1	0	0	0	0	0	0	0	1	4561	1799	63	4		4	DLC1	8	12957491	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1125931	12957491	133406531	1006	5403										
DLC1	10395	broad.mit.edu	37	chr8	13356684	13356684	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttgttttgatgttgtgaAaaaccactcttctccaggcc	7	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:13356684A>G	ENST00000276297.4	-	2	1306	c.897T>C	c.(895-897)ttT>ttC	p.F299F	DLC1_ENST00000511869.1_Silent_p.F299F|DLC1_ENST00000316609.5_Silent_p.F299F	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	299					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.F299F(2)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GATGTTGTGAAAAACCACTCT	0.463																																																2	Substitution - coding silent(2)	large_intestine(2)	8											195	182	186					8																	13356684		2203	4300	6503	13401055	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.897T>C	8.37:g.13356684A>G			13401055	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.463	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		G	13356684	A	G	13356684	2	3	47	1	0	0	0	0	0	0	0	1	4561	11	1	4		4	DLC1	8	13356684	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	399193	13356684	133007338	1007	5404										
DLC1	10395	broad.mit.edu	37	chr8	13357316	13357316	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcttcaccttcatggctgtCattttcgtccacatcctttg	5	13	4	0	rs150090193		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:13357316C>A	ENST00000276297.4	-	2	674	c.265G>T	c.(265-267)Gac>Tac	p.D89Y	DLC1_ENST00000511869.1_Missense_Mutation_p.D89Y|DLC1_ENST00000316609.5_Missense_Mutation_p.D89Y	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	89					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.D89Y(5)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TCATGGCTGTCATTTTCGTCC	0.443																																																5	Substitution - Missense(5)	lung(3)|large_intestine(2)	8											221	221	221					8																	13357316		2203	4300	6503	13401687	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.265G>T	8.37:g.13357316C>A	ENSP00000276297:p.Asp89Tyr		13401687	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342451	0.41498	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.32988	1.43;1.43;1.43	5.55	2.53	0.30540	.	0.302054	0.23900	N	0.043455	T	0.44705	0.1306	L	0.54323	1.7	0.35272	D	0.780576	B;D;D	0.89917	0.33;1.0;0.998	B;D;P	0.76575	0.091;0.988;0.87	T	0.54899	-0.8224	10	0.87932	D	0	.	7.0376	0.25002	0.1305:0.6749:0.1259:0.0686	.	89;89;89	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	Y	89	ENSP00000276297:D89Y;ENSP00000321034:D89Y;ENSP00000425878:D89Y	ENSP00000276297:D89Y	D	-	1	0	DLC1	13401687	1.000000	0.71417	0.714000	0.30535	0.303000	0.27691	2.066000	0.41452	0.787000	0.33731	0.655000	0.94253	GAC		0.443	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	13357316	C	A	13357316	3	1	47	1	0	0	0	0	1	0	0	0	4561	826	29	2	4474	2	DLC1	8	13357316	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	632	13357316	133006706	1008	5405										
SGCZ	137868	broad.mit.edu	37	chr8	14095188	14095188	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtaagaccagcggactatCctgggaaacatgtataaaat	9	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:14095188C>T	ENST00000382080.1	-	4	1052	c.337G>A	c.(337-339)Gat>Aat	p.D113N	SGCZ_ENST00000421524.2_Splice_Site_p.D66N	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	100					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)		p.D113N(1)		NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		AGCGGACTATCCTGGGAAACA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	8											200	195	196					8																	14095188		2203	4300	6503	14139559	SO:0001630	splice_region_variant	137868			AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.337-1G>A	8.37:g.14095188C>T			14139559	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	37	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	c	17.15	3.316790	0.60524	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.96427	-4.01;-4.01	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.94870	0.8342	L	0.57536	1.79	0.32434	N	0.547571	B;B	0.19331	0.035;0.028	B;B	0.23275	0.045;0.018	D	0.92783	0.6242	10	0.23891	T	0.37	.	18.6034	0.91257	0.0:1.0:0.0:0.0	.	66;113	Q08AT0;Q96LD1-2	.;.	N	113;66	ENSP00000371512:D113N;ENSP00000405224:D66N	ENSP00000371512:D113N	D	-	1	0	SGCZ	14139559	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.935000	0.75886	2.712000	0.92718	0.591000	0.81541	GAT		0.343	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167	Missense_Mutation	T	14095188	C	T	14095188	5	4	47	1	0	0	0	0	0	0	1	0	14241	869	30	3	621	3	SGCZ	8	14095188	Splice_Site	SNP	C	TCGA-AG-3892-01A-01W-1073-09	737872	14095188	132268834	1009	5406										
SGCZ	137868	broad.mit.edu	37	chr8	14412352	14412352	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacctctttcgccatccataAattcccactgggtaaagttg	6	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:14412352A>C	ENST00000382080.1	-	2	838	c.123T>G	c.(121-123)atT>atG	p.I41M	SGCZ_ENST00000421524.2_Missense_Mutation_p.I28M	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	28					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)		p.I41M(2)		NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		GCCATCCATAAATTCCCACTG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	8											234	224	227					8																	14412352		2203	4300	6503	14456723	SO:0001583	missense	137868			AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.123T>G	8.37:g.14412352A>C	ENSP00000371512:p.Ile41Met		14456723	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	37	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	A	15.55	2.866071	0.51588	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.95518	-3.73;-3.73	5.39	4.22	0.49857	.	0.051250	0.85682	D	0.000000	D	0.95834	0.8644	M	0.76170	2.325	0.47374	D	0.999403	P;P	0.50943	0.94;0.926	P;B	0.51742	0.678;0.41	D	0.94917	0.8070	10	0.59425	D	0.04	.	10.9874	0.47530	0.8527:0.0:0.0:0.1473	.	28;41	Q08AT0;Q96LD1-2	.;.	M	41;28	ENSP00000371512:I41M;ENSP00000405224:I28M	ENSP00000371512:I41M	I	-	3	3	SGCZ	14456723	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.627000	0.37050	0.971000	0.38288	0.528000	0.53228	ATT		0.383	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		C	14412352	A	C	14412352	3	2	47	1	0	0	0	0	1	0	0	0	14241	10	1	4	843	4	SGCZ	8	14412352	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	317164	14412352	131951670	1010	5407										
TUSC3	7991	broad.mit.edu	37	chr8	15508236	15508236	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaatatcaaatactggcGaactcctggcgctattcatc	8	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:15508236G>A	ENST00000503731.1	+	3	487	c.339G>A	c.(337-339)gcG>gcA	p.A113A	TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000382020.4_Silent_p.A113A|TUSC3_ENST00000506802.1_Silent_p.A113A|TUSC3_ENST00000509380.1_Silent_p.A113A	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	113	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)	p.A113A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		AAATACTGGCGAACTCCTGGC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	8											228	220	223					8																	15508236		2203	4300	6503	15552607	SO:0001819	synonymous_variant	7991			AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.339G>A	8.37:g.15508236G>A			15552607	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Silent	SNP	ENST00000503731.1	37	CCDS5994.1																																																																																				0.388	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		A	15508236	G	A	15508236	2	1	47	1	0	0	0	0	0	0	0	1	16818	1045	37	1		1	TUSC3	8	15508236	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1095884	15508236	130855786	1011	5408										
MTUS1	57509	broad.mit.edu	37	chr8	17510728	17510728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcttgctcttcttttttgTtcttctgatttcaatttttc	3	9	6	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:17510728T>C	ENST00000262102.6	-	12	3575	c.3351A>G	c.(3349-3351)gaA>gaG	p.E1117E	MTUS1_ENST00000400046.1_Silent_p.E189E|MTUS1_ENST00000381869.3_Silent_p.E1063E|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000297488.6_Silent_p.E283E|MTUS1_ENST00000381861.3_Silent_p.E364E|MTUS1_ENST00000519263.1_Silent_p.E1063E|MTUS1_ENST00000544260.1_Silent_p.E262E	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1117					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E1117E(1)|p.E364E(1)|p.E283E(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCTTTTTTGTTCTTCTGATT	0.308																																																3	Substitution - coding silent(3)	large_intestine(3)	8											189	174	178					8																	17510728		1818	4082	5900	17555008	SO:0001819	synonymous_variant	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.3351A>G	8.37:g.17510728T>C			17555008	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																				0.308	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17510728	T	C	17510728	2	2	47	1	0	0	0	0	0	0	0	1	9995	1722	60	4		4	MTUS1	8	17510728	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2002492	17510728	128853294	1012	5409										
FGL1	2267	broad.mit.edu	37	chr8	17726445	17726445	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttcatctccaactttgaAattcttatattgtgcataac	3	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:17726445A>C	ENST00000398056.2	-	8	1386	c.571T>G	c.(571-573)Ttc>Gtc	p.F191V	FGL1_ENST00000398054.1_Missense_Mutation_p.F191V|FGL1_ENST00000381841.2_Missense_Mutation_p.F191V|FGL1_ENST00000381840.2_Missense_Mutation_p.F191V|FGL1_ENST00000522444.1_Missense_Mutation_p.F191V|FGL1_ENST00000518650.1_Missense_Mutation_p.F191V|FGL1_ENST00000427924.1_Missense_Mutation_p.F191V			Q08830	FGL1_HUMAN	fibrinogen-like 1	191	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)		p.F191V(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		CCAACTTTGAAATTCTTATAT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	8											53	58	57					8																	17726445		2203	4290	6493	17770725	SO:0001583	missense	2267			D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"Fibrinogen C domain containing"	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.571T>G	8.37:g.17726445A>C	ENSP00000381133:p.Phe191Val		17770725	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Missense_Mutation	SNP	ENST00000398056.2	37	CCDS6004.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215608	0.79352	.	.	ENSG00000104760	ENST00000221204;ENST00000398056;ENST00000521427;ENST00000522444;ENST00000381841;ENST00000427924;ENST00000398054;ENST00000381840;ENST00000518650	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	4.77	4.77	0.60923	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.76898	0.4052	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.996	D;D;D	0.91635	0.981;0.999;0.953	T	0.82246	-0.0552	10	0.62326	D	0.03	.	14.6056	0.68475	1.0:0.0:0.0:0.0	.	161;191;191	E7ERS0;Q8NG32;Q08830	.;.;FGL1_HUMAN	V	191;191;161;191;191;191;191;191;191	ENSP00000381133:F191V;ENSP00000429757:F191V;ENSP00000371263:F191V;ENSP00000401952:F191V;ENSP00000381131:F191V;ENSP00000371262:F191V;ENSP00000428430:F191V	ENSP00000221204:F191V	F	-	1	0	FGL1	17770725	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.743000	0.91592	1.924000	0.55735	0.377000	0.23210	TTC		0.284	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467		C	17726445	A	C	17726445	3	2	47	1	0	0	0	0	1	0	0	0	5891	14	1	4	379	4	FGL1	8	17726445	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	215717	17726445	128637577	1013	5410										
PCM1	5108	broad.mit.edu	37	chr8	17829985	17829985	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtaaccgcaaaaatcaattAgatacaaacggaagaagacg	8	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:17829985A>C	ENST00000519253.1	+	23	3983	c.3732A>C	c.(3730-3732)ttA>ttC	p.L1244F	PCM1_ENST00000524226.1_Missense_Mutation_p.L1245F|PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000325083.8_Missense_Mutation_p.L1244F			Q15154	PCM1_HUMAN	pericentriolar material 1	1244					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.L1244F(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		AAAATCAATTAGATACAAACG	0.368			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Missense(1)	large_intestine(1)	8											96	91	92					8																	17829985		1846	4091	5937	17874265	SO:0001583	missense	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3732A>C	8.37:g.17829985A>C	ENSP00000431099:p.Leu1244Phe		17874265	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	A	2.323	-0.355247	0.05138	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.49720	0.77;0.77;0.77	4.97	0.923	0.19413	.	1.123680	0.06519	N	0.739336	T	0.27663	0.0680	N	0.22421	0.69	0.29286	N	0.869724	B;P;B;P	0.36909	0.004;0.573;0.006;0.573	B;B;B;B	0.33521	0.009;0.165;0.006;0.165	T	0.22556	-1.0213	10	0.23302	T	0.38	0.0288	2.1767	0.03864	0.591:0.1085:0.1512:0.1494	.	106;1244;1245;1244	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	F	1244;1244;1245	ENSP00000327077:L1244F;ENSP00000431099:L1244F;ENSP00000430521:L1245F	ENSP00000327077:L1244F	L	+	3	2	PCM1	17874265	0.147000	0.22687	0.082000	0.20525	0.066000	0.16364	0.351000	0.20096	0.057000	0.16193	0.402000	0.26972	TTA		0.368	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		C	17829985	A	C	17829985	3	2	47	1	0	0	0	0	1	0	0	0	11615	417	15	4	3814	4	PCM1	8	17829985	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	103540	17829985	128534037	1014	5411										
PIWIL2	55124	broad.mit.edu	37	chr8	22172598	22172598	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcggagtgtggcccagaaGattttacttcagattaactg	10	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:22172598G>T	ENST00000454009.2	+	18	2657	c.2148G>T	c.(2146-2148)aaG>aaT	p.K716N	PIWIL2_ENST00000521356.1_Missense_Mutation_p.K716N|PIWIL2_ENST00000356766.6_Missense_Mutation_p.K716N	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	716	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.K716N(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		TGGCCCAGAAGATTTTACTTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	8											142	137	139					8																	22172598		2203	4300	6503	22228543	SO:0001583	missense	55124			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.2148G>T	8.37:g.22172598G>T	ENSP00000406956:p.Lys716Asn		22228543	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.649040	0.67358	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.19105	2.17;2.17;2.17	5.75	2.1	0.27182	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.30510	0.0767	L	0.41961	1.31	0.58432	D	0.999996	D;D	0.69078	0.972;0.997	D;D	0.70016	0.912;0.967	T	0.02238	-1.1190	10	0.21014	T	0.42	-2.5778	9.0205	0.36198	0.7847:0.0:0.2153:0.0	.	716;716	E7ECA4;Q8TC59	.;PIWL2_HUMAN	N	716	ENSP00000349208:K716N;ENSP00000428267:K716N;ENSP00000406956:K716N	ENSP00000349208:K716N	K	+	3	2	PIWIL2	22228543	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.129000	0.31381	0.190000	0.20209	-0.247000	0.11927	AAG		0.488	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			T	22172598	G	T	22172598	3	4	47	1	0	0	0	0	1	0	0	0	11989	933	33	2	2214	2	PIWIL2	8	22172598	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4342613	22172598	124191424	1015	5412										
ADAM28	10863	broad.mit.edu	37	chr8	24187506	24187506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatacctttaggaccacagCgataatcttcttagagttgc	7	10	3	1	rs149927944		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:24187506C>T	ENST00000265769.4	+	11	1091	c.981C>T	c.(979-981)agC>agT	p.S327S	RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000437154.2_Silent_p.S327S|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000540823.1_Silent_p.S94S|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000518516.1_3'UTR|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_Silent_p.S74S	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	327	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S327S(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		AGGACCACAGCGATAATCTTC	0.393													T|||	1	0.000199681	8e-04	0	5008	,	,		20473	0		0	False		,,,				2504	0				NSCLC(193;488 2149 22258 34798 40734)											1	Substitution - coding silent(1)	large_intestine(1)	8						T	,	4,4402	825.7+/-416.5	0,4,2199	139	130	133		981,981	3.5	0.3	8	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,	327/776,327/541	24187506	4,13002	2203	4300	6503	24243451	SO:0001819	synonymous_variant	10863			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.981C>T	8.37:g.24187506C>T			24243451	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																				0.393	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		T	24187506	C	T	24187506	2	4	47	1	0	0	0	0	0	0	0	1	246	767	27	1		1	ADAM28	8	24187506	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2014908	24187506	122176516	1016	5413										
NEFL	4747	broad.mit.edu	37	chr8	24810436	24810436	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcacctccttcttcttcttCttttgcttcttcagactctt	2	14	8	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:24810436C>A	ENST00000221169.5	-	0	2114							P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)	p.E507*(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		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)		tcttcttcttcttttgcttct	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											139	133	135					8																	24810436		1857	4088	5945	24866353			4747				CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24810436C>A			24866353	B9ZVN2|Q16154|Q8IU72	Nonsense_Mutation	SNP	ENST00000221169.5	37																																																																																					0.423	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24810436	C	A	24810436	1	1	47	0	1	0	0	0	0	0	0	0	10346	922	32	2		2	NEFL	8	24810436	RNA	SNP	C	TCGA-AG-3892-01A-01W-1073-09	622930	24810436	121553586	1017	5414										
EBF2	64641	broad.mit.edu	37	chr8	25718853	25718853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgtggtgtgccataaagaGcttccactagatctgcagct	11	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:25718853G>A	ENST00000520164.1	-	12	1673	c.1136C>T	c.(1135-1137)gCt>gTt	p.A379V	EBF2_ENST00000408929.3_Missense_Mutation_p.A231V|EBF2_ENST00000535548.1_Missense_Mutation_p.A110V	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	379					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A379V(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GCCATAAAGAGCTTCCACTAG	0.403																																					Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)											2	Substitution - Missense(2)	large_intestine(2)	8											162	157	159					8																	25718853		1904	4121	6025	25774770	SO:0001583	missense	64641			AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1136C>T	8.37:g.25718853G>A	ENSP00000430241:p.Ala379Val		25774770	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.841340	0.32513	.	.	ENSG00000221818	ENST00000520164;ENST00000408929;ENST00000535548	T;T;T	0.41758	0.99;0.99;0.99	5.5	5.5	0.81552	Helix-loop-helix DNA-binding (1);	0.048156	0.85682	D	0.000000	T	0.44286	0.1286	M	0.83953	2.67	0.58432	D	0.999999	P	0.45768	0.866	B	0.26969	0.075	T	0.61436	-0.7063	10	0.66056	D	0.02	.	19.3942	0.94598	0.0:0.0:1.0:0.0	.	379	Q9HAK2	COE2_HUMAN	V	379;231;110	ENSP00000430241:A379V;ENSP00000386178:A231V;ENSP00000437909:A110V	ENSP00000386178:A231V	A	-	2	0	EBF2	25774770	1.000000	0.71417	0.992000	0.48379	0.040000	0.13550	7.884000	0.87274	2.587000	0.87381	0.655000	0.94253	GCT		0.403	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		A	25718853	G	A	25718853	3	1	47	1	0	0	0	0	1	0	0	0	4892	971	34	3	611	3	EBF2	8	25718853	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	908417	25718853	120645169	1018	5415										
TEX15	56154	broad.mit.edu	37	chr8	30701275	30701275	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaactcacagaatgcattAtattttaatcttccttggaa	5	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:30701275A>C	ENST00000256246.2	-	1	5333	c.5259T>G	c.(5257-5259)taT>taG	p.Y1753*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1753					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.Y1753*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGAATGCATTATATTTTAATC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											70	67	68					8																	30701275		2203	4300	6503	30820817	SO:0001587	stop_gained	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5259T>G	8.37:g.30701275A>C	ENSP00000256246:p.Tyr1753*		30820817		Nonsense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	A	44	10.584125	0.99432	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.69	-2.47	0.06442	.	0.127324	0.36303	N	0.002664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.3638	0.60671	0.3445:0.0:0.6555:0.0	.	.	.	.	X	1753	.	ENSP00000256246:Y1753X	Y	-	3	2	TEX15	30820817	0.901000	0.30685	0.984000	0.44739	0.975000	0.68041	-0.027000	0.12371	-0.370000	0.08016	-0.274000	0.10170	TAT		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30701275	A	C	30701275	4	2	47	1	0	0	0	0	0	1	0	0	15818	456	16	4	3126	4	TEX15	8	30701275	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4982422	30701275	115662747	1019	5416										
TEX15	56154	broad.mit.edu	37	chr8	30704165	30704165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatctttcaatgcaagggagTcagctgtcgggctgaatcct	11	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:30704165T>C	ENST00000256246.2	-	1	2443	c.2369A>G	c.(2368-2370)gAc>gGc	p.D790G	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	790					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.D790G(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGCAAGGGAGTCAGCTGTCGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											48	50	49					8																	30704165		2202	4299	6501	30823707	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2369A>G	8.37:g.30704165T>C	ENSP00000256246:p.Asp790Gly		30823707		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.334022	0.41297	.	.	ENSG00000133863	ENST00000256246	T	0.12465	2.68	5.93	4.78	0.61160	.	0.429133	0.21581	N	0.072244	T	0.10508	0.0257	N	0.14661	0.345	0.09310	N	1	B	0.34329	0.449	B	0.39840	0.311	T	0.18871	-1.0323	10	0.87932	D	0	.	8.8186	0.35011	0.0:0.0846:0.0:0.9154	.	790	Q9BXT5	TEX15_HUMAN	G	790	ENSP00000256246:D790G	ENSP00000256246:D790G	D	-	2	0	TEX15	30823707	0.042000	0.20092	0.001000	0.08648	0.001000	0.01503	2.631000	0.46502	1.068000	0.40764	-0.256000	0.11100	GAC		0.353	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30704165	T	C	30704165	3	2	47	1	0	0	0	0	1	0	0	0	15818	1667	58	4	6016	4	TEX15	8	30704165	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2890	30704165	115659857	1020	5417										
PURG	29942	broad.mit.edu	37	chr8	30889502	30889502	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttattgtccactctgaaaGaagtcccctctgggagttca	8	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:30889502G>T	ENST00000475541.1	-	1	1729	c.797C>A	c.(796-798)tCt>tAt	p.S266Y	WRN_ENST00000298139.5_5'Flank|PURG_ENST00000339382.2_Missense_Mutation_p.S266Y	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	266						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.S266Y(2)		endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		CACTCTGAAAGAAGTCCCCTC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	8											78	71	73					8																	30889502		2203	4300	6503	31009044	SO:0001583	missense	29942			AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.797C>A	8.37:g.30889502G>T	ENSP00000418721:p.Ser266Tyr		31009044	Q8TE64	Missense_Mutation	SNP	ENST00000475541.1	37	CCDS6081.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.504627	0.64410	.	.	ENSG00000172733	ENST00000339382;ENST00000475541	T;T	0.33438	1.41;1.41	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.49338	0.1551	M	0.65320	2	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.83275	0.996;0.971	T	0.43940	-0.9360	10	0.02654	T	1	-4.8319	18.4618	0.90741	0.0:0.0:1.0:0.0	.	266;266	Q9UJV8;Q9UJV8-2	PURG_HUMAN;.	Y	266	ENSP00000345168:S266Y;ENSP00000418721:S266Y	ENSP00000345168:S266Y	S	-	2	0	PURG	31009044	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.438000	0.82558	0.655000	0.94253	TCT		0.453	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1	NM_013357		T	30889502	G	T	30889502	3	4	47	1	0	0	0	0	1	0	0	0	12866	942	33	2	359	2	PURG	8	30889502	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	185337	30889502	115474520	1021	5418										
NRG1	3084	broad.mit.edu	37	chr8	32600207	32600207	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcaggtgcccaaatgagtTtactggtgatcgctgccaaa	10	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:32600207T>G	ENST00000405005.3	+	7	700				NRG1_ENST00000356819.4_Missense_Mutation_p.F216C|NRG1_ENST00000519301.1_Missense_Mutation_p.F161C|NRG1_ENST00000520407.1_Missense_Mutation_p.F397C|NRG1_ENST00000341377.5_Missense_Mutation_p.L239V|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.F271C|NRG1_ENST00000287842.3_Missense_Mutation_p.F216C|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000539990.1_Missense_Mutation_p.F62C|NRG1_ENST00000523079.1_Missense_Mutation_p.F216C|NRG1_ENST00000287845.5_Missense_Mutation_p.F182C			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.F216C(1)|p.F397C(1)|p.F271C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CCAAATGAGTTTACTGGTGAT	0.438																																																3	Substitution - Missense(3)	large_intestine(3)	8											188	168	175					8																	32600207		2203	4300	6503	32719749	SO:0001627	intron_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.700+614T>G	8.37:g.32600207T>G			32719749	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.91|19.91	3.914831|3.914831	0.72983|0.72983	.|.	.|.	ENSG00000157168|ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000520407;ENST00000523534;ENST00000523079;ENST00000356819;ENST00000287845;ENST00000287842;ENST00000520502;ENST00000518084;ENST00000519240;ENST00000539990|ENST00000341377;ENST00000523041	D;D;D;D;D;D;D;D;T;T;T;D|T	0.93953|0.78481	-3.32;-3.32;-3.32;-3.32;-3.32;-3.32;-3.32;-3.32;1.49;0.43;1.49;-3.32|-1.18	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|.	.|.	.|.	.|.	D|D	0.89220|0.89220	0.6653|0.6653	M|M	0.85373|0.85373	2.75|2.75	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D;D|D	0.89917|0.67145	0.998;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0|0.996	D;D;D;D;D;P;D;D;D;D;D|D	0.85130|0.72625	0.995;0.993;0.987;0.971;0.993;0.905;0.997;0.987;0.987;0.969;0.995|0.978	D|D	0.90732|0.90732	0.4643|0.4643	9|9	0.87932|0.87932	D|D	0|0	.|.	16.5582|16.5582	0.84512|0.84512	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	62;216;182;216;215;181;271;216;216;216;397|239	B7Z1E3;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;B0FWZ3;Q02297-10;Q02297-7;Q02297-6;Q02297-8;Q02297-9|Q02297-4	.;.;.;.;.;.;.;.;.;.;.|.	C|V	178;161;397;284;216;216;182;216;271;62;62;62|239;188	ENSP00000430053:F178C;ENSP00000429582:F161C;ENSP00000434640:F397C;ENSP00000429067:F284C;ENSP00000430120:F216C;ENSP00000349275:F216C;ENSP00000287845:F182C;ENSP00000287842:F216C;ENSP00000433289:F271C;ENSP00000428546:F62C;ENSP00000428411:F62C;ENSP00000439276:F62C|ENSP00000340497:L239V	ENSP00000287842:F216C|ENSP00000340497:L239V	F|L	+|+	2|1	0|2	NRG1|NRG1	32719749|32719749	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.015000|8.015000	0.88690|0.88690	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	TTT|TTA		0.438	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			G	32600207	T	G	32600207	1	3	47	0	1	0	0	0	0	0	0	0	10678	1841	64	4		4	NRG1	8	32600207	Intron	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1710705	32600207	113763815	1022	5419										
NRG1	3084	broad.mit.edu	37	chr8	32620765	32620765	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatagctgagctaaggagaaAcaaggcacacagatccaaat	9	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:32620765A>G	ENST00000405005.3	+	12	1268				NRG1_ENST00000356819.4_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000521670.1_Missense_Mutation_p.N433S|NRG1_ENST00000539990.1_Intron|RP11-1002K11.1_ENST00000607314.1_lincRNA|NRG1_ENST00000287845.5_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.N433S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CTAAGGAGAAACAAGGCACAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											178	161	167					8																	32620765		2203	4300	6503	32740307	SO:0001627	intron_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.1269-501A>G	8.37:g.32620765A>G			32740307	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.567764	0.28003	.	.	ENSG00000157168	ENST00000521670	T	0.70399	-0.48	4.34	4.34	0.51931	.	.	.	.	.	T	0.64789	0.2630	N	0.08118	0	0.80722	D	1	P;B;B	0.51057	0.941;0.178;0.273	P;B;B	0.60415	0.874;0.074;0.115	T	0.69281	-0.5186	9	0.62326	D	0.03	.	10.2028	0.43094	1.0:0.0:0.0:0.0	.	279;429;433	B7Z1D7;B0FYA9;Q02297-3	.;.;.	S	433	ENSP00000428828:N433S	ENSP00000428828:N433S	N	+	2	0	NRG1	32740307	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.336000	0.43938	2.182000	0.69389	0.528000	0.53228	AAC		0.388	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			G	32620765	A	G	32620765	1	3	47	0	1	0	0	0	0	0	0	0	10678	43	2	4		4	NRG1	8	32620765	Intron	SNP	A	TCGA-AG-3892-01A-01W-1073-09	20558	32620765	113743257	1023	5420										
FUT10	84750	broad.mit.edu	37	chr8	33310894	33310894	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaattcccattttcttttCctgttgaaggtcaatccttc	4	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:33310894C>T	ENST00000327671.5	-	3	847	c.216G>A	c.(214-216)agG>agA	p.R72R	FUT10_ENST00000518672.1_Silent_p.R44R|FUT10_ENST00000524021.1_Silent_p.R44R|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_5'UTR	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	72					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.R72R(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		ATTTTCTTTTCCTGTTGAAGG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	8											110	104	106					8																	33310894		2203	4300	6503	33430436	SO:0001819	synonymous_variant	84750			AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.216G>A	8.37:g.33310894C>T			33430436	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																				0.448	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		T	33310894	C	T	33310894	2	4	47	1	0	0	0	0	0	0	0	1	6121	854	30	3		3	FUT10	8	33310894	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	690129	33310894	113053128	1024	5421										
KCNU1	157855	broad.mit.edu	37	chr8	36662779	36662779	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatttggttttcaatgctttCtttagtttctattttggatt	7	4	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:36662779C>A	ENST00000399881.3	+	4	481	c.444C>A	c.(442-444)ttC>ttA	p.F148L		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	148					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.F148L(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TCAATGCTTTCTTTAGTTTCT	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	8											187	165	172					8																	36662779		1850	4087	5937	36781937	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.444C>A	8.37:g.36662779C>A	ENSP00000382770:p.Phe148Leu		36781937		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.619650	0.87460	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	T;T	0.44482	0.92;0.92	5.46	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000007	T	0.48077	0.1480	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51725	-0.8669	10	0.87932	D	0	-0.5318	12.5765	0.56367	0.0:0.9187:0.0:0.0813	.	148	A8MYU2	KCNU1_HUMAN	L	148	ENSP00000429951:F148L;ENSP00000382770:F148L	ENSP00000382770:F148L	F	+	3	2	KCNU1	36781937	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	4.837000	0.62796	2.572000	0.86782	0.655000	0.94253	TTC		0.383	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36662779	C	A	36662779	3	1	47	1	0	0	0	0	1	0	0	0	8114	912	32	2	458	2	KCNU1	8	36662779	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3351885	36662779	109701243	1025	5422										
IDO1	3620	broad.mit.edu	37	chr8	39776378	39776378	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttactgccaactctccaaGaaactggaactgcctcctat	5	15	1	1	rs12545878		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:39776378G>T	ENST00000518237.1	+	4	987	c.348G>T	c.(346-348)aaG>aaT	p.K116N	RP11-44K6.4_ENST00000522970.1_RNA|IDO1_ENST00000522495.1_Missense_Mutation_p.K116N|RP11-44K6.3_ENST00000517623.1_RNA	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	116					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)	p.K116N(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	AACTCTCCAAGAAACTGGAAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											107	104	105					8																	39776378		1862	4098	5960	39895535	SO:0001583	missense	3620			M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.348G>T	8.37:g.39776378G>T	ENSP00000430950:p.Lys116Asn		39895535	Q540B4	Missense_Mutation	SNP	ENST00000518237.1	37	CCDS47847.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.544463	0.27563	.	.	ENSG00000131203	ENST00000519154;ENST00000522495;ENST00000518237	T;T;T	0.44881	0.91;0.91;0.91	5.85	4.94	0.65067	.	0.614821	0.16388	N	0.216562	T	0.31071	0.0785	N	0.21142	0.635	0.33089	D	0.537676	P	0.34934	0.476	B	0.38954	0.286	T	0.41484	-0.9506	9	.	.	.	-15.5224	9.5655	0.39396	0.1022:0.0:0.8978:0.0	.	116	P14902	I23O1_HUMAN	N	116	ENSP00000428716:K116N;ENSP00000430505:K116N;ENSP00000430950:K116N	.	K	+	3	2	IDO1	39895535	0.000000	0.05858	0.999000	0.59377	0.444000	0.32077	0.304000	0.19228	1.394000	0.46624	0.557000	0.71058	AAG		0.353	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		T	39776378	G	T	39776378	3	4	47	1	0	0	0	0	1	0	0	0	7522	933	33	2	362	2	IDO1	8	39776378	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3113599	39776378	106587644	1026	5423										
ZMAT4	79698	broad.mit.edu	37	chr8	40554844	40554844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgccttgataatgggaatcgGccaccaccgctgaagtgaat	11	10	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:40554844G>A	ENST00000297737.6	-	4	415	c.269C>T	c.(268-270)gCc>gTc	p.A90V	ZMAT4_ENST00000315769.7_Missense_Mutation_p.A90V	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	90						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A90V(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ATGGGAATCGGCCACCACCGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											151	136	141					8																	40554844		2203	4300	6503	40674001	SO:0001583	missense	79698			AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.269C>T	8.37:g.40554844G>A	ENSP00000297737:p.Ala90Val		40674001	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	37	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	G	36	5.608570	0.96626	.	.	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.23348	1.91;1.91;1.91	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	M	0.82630	2.6	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.59573	-0.7429	10	0.87932	D	0	-18.2353	19.8676	0.96824	0.0:0.0:1.0:0.0	.	90;90	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	V	90	ENSP00000319785:A90V;ENSP00000297737:A90V;ENSP00000428423:A90V	ENSP00000297737:A90V	A	-	2	0	ZMAT4	40674001	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	9.258000	0.95555	2.941000	0.99782	0.655000	0.94253	GCC		0.498	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40554844	G	A	40554844	3	1	47	1	0	0	0	0	1	0	0	0	17733	1203	42	3	436	3	ZMAT4	8	40554844	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	778466	40554844	105809178	1027	5424										
ANK1	286	broad.mit.edu	37	chr8	41547811	41547811	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggtgtcctcgtacttcatCgccttgcgcagaaacgacag	11	12	1	1	rs199719745		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:41547811C>T	ENST00000347528.4	-	33	4121	c.4038G>A	c.(4036-4038)gcG>gcA	p.A1346A	ANK1_ENST00000396945.1_Silent_p.A1346A|ANK1_ENST00000265709.8_Silent_p.A1387A|ANK1_ENST00000379758.2_Silent_p.A1346A|ANK1_ENST00000289734.7_Silent_p.A1346A|ANK1_ENST00000352337.4_Silent_p.A1346A|ANK1_ENST00000396942.1_Silent_p.A1346A	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1346	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.A1346A(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	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)			CGTACTTCATCGCCTTGCGCA	0.597													C|||	1	0.000199681	8e-04	0	5008	,	,		19026	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											138	114	122					8																	41547811		2203	4300	6503	41666968	SO:0001819	synonymous_variant	286			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4038G>A	8.37:g.41547811C>T			41666968	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.02	1.235699	0.22626	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.08	-6.44	0.01920	.	.	.	.	.	T	0.53546	0.1803	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57306	-0.7834	4	.	.	.	.	11.7964	0.52102	0.0:0.2077:0.554:0.2383	.	.	.	.	N	668	.	.	D	-	1	0	ANK1	41666968	0.822000	0.29219	0.516000	0.27786	0.952000	0.60782	-0.145000	0.10265	-1.867000	0.01144	-0.302000	0.09304	GAT		0.597	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41547811	C	T	41547811	2	4	47	1	0	0	0	0	0	0	0	1	620	871	31	1		1	ANK1	8	41547811	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	992967	41547811	104816211	1028	5425										
AP3M2	10947	broad.mit.edu	37	chr8	42015607	42015607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagcctcctaccatccttcGaacggttgtcaacaccatca	5	15	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:42015607G>A	ENST00000518421.1	+	4	713	c.422G>A	c.(421-423)cGa>cAa	p.R141Q	AP3M2_ENST00000174653.3_Missense_Mutation_p.R141Q|AP3M2_ENST00000517922.1_Missense_Mutation_p.R141Q|AP3M2_ENST00000520685.1_Intron|AP3M2_ENST00000396926.3_Missense_Mutation_p.R141Q	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	141					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)		p.R141Q(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	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)			ACCATCCTTCGAACGGTTGTC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											111	103	106					8																	42015607		2203	4300	6503	42134764	SO:0001583	missense	10947			D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.422G>A	8.37:g.42015607G>A	ENSP00000428787:p.Arg141Gln		42134764	B2RCR0|D3DSY2|Q7Z472	Missense_Mutation	SNP	ENST00000518421.1	37	CCDS6125.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535738	0.85812	.	.	ENSG00000070718	ENST00000518421;ENST00000174653;ENST00000396926;ENST00000521280;ENST00000517922;ENST00000517499	T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-0.99;-1.01	4.79	4.79	0.61399	Longin-like (1);	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	L	0.52126	1.63	0.80722	D	1	B;P	0.48294	0.403;0.908	B;B	0.36378	0.042;0.223	T	0.76208	-0.3043	10	0.46703	T	0.11	-10.2754	18.2325	0.89938	0.0:0.0:1.0:0.0	.	141;141	E7ER80;P53677	.;AP3M2_HUMAN	Q	141;141;141;26;141;50	ENSP00000428787:R141Q;ENSP00000174653:R141Q;ENSP00000380132:R141Q;ENSP00000430616:R26Q;ENSP00000429435:R141Q	ENSP00000174653:R141Q	R	+	2	0	AP3M2	42134764	1.000000	0.71417	0.906000	0.35671	0.970000	0.65996	9.330000	0.96422	2.363000	0.80096	0.650000	0.86243	CGA		0.468	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			A	42015607	G	A	42015607	3	1	47	1	0	0	0	0	1	0	0	0	748	1058	37	1	428	1	AP3M2	8	42015607	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	467796	42015607	104348415	1029	5426										
CHRNB3	1142	broad.mit.edu	37	chr8	42586936	42586936	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacgtcacgtttttcccgttCgaccgacagaactgctccat	8	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:42586936C>T	ENST00000289957.2	+	5	614	c.486C>T	c.(484-486)ttC>ttT	p.F162F		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	162					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)	p.F162F(1)		endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	TTTTCCCGTTCGACCGACAGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	8											67	52	57					8																	42586936		2203	4300	6503	42706093	SO:0001819	synonymous_variant	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.486C>T	8.37:g.42586936C>T			42706093	Q15827	Silent	SNP	ENST00000289957.2	37	CCDS6134.1																																																																																				0.478	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			T	42586936	C	T	42586936	2	4	47	1	0	0	0	0	0	0	0	1	3398	883	31	1		1	CHRNB3	8	42586936	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	571329	42586936	103777086	1030	5427										
CHRNA6	8973	broad.mit.edu	37	chr8	42611452	42611452	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaccagtgggaccaccagaGatgtggatgggatggtttct	14	9	1	1	rs371233399		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:42611452G>T	ENST00000276410.2	-	5	1245	c.890C>A	c.(889-891)tCt>tAt	p.S297Y	CHRNA6_ENST00000530869.1_5'Flank|CHRNA6_ENST00000534622.1_Missense_Mutation_p.S282Y	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	297					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.S297Y(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	GACCACCAGAGATGTGGATGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	TYR/SER,TYR/SER	0,4406		0,0,2203	95	81	86		845,890	6	0.5	8		86	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CHRNA6	NM_001199279.1,NM_004198.3	144,144	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	282/480,297/495	42611452	1,13005	2203	4300	6503	42730609	SO:0001583	missense	8973			U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.890C>A	8.37:g.42611452G>T	ENSP00000276410:p.Ser297Tyr		42730609	B2R8V4|B4DQH1	Missense_Mutation	SNP	ENST00000276410.2	37	CCDS6135.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.925946	0.73327	0.0	1.16E-4	ENSG00000147434	ENST00000276410;ENST00000534622	D;D	0.93488	-3.23;-3.23	5.97	5.97	0.96955	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.98432	0.9478	H	0.98996	4.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98994	1.0809	10	0.87932	D	0	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	282;297	B4DQH1;Q15825	.;ACHA6_HUMAN	Y	297;282	ENSP00000276410:S297Y;ENSP00000433871:S282Y	ENSP00000276410:S297Y	S	-	2	0	CHRNA6	42730609	1.000000	0.71417	0.549000	0.28204	0.521000	0.34408	9.776000	0.99001	2.828000	0.97474	0.655000	0.94253	TCT		0.483	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			T	42611452	G	T	42611452	3	4	47	1	0	0	0	0	1	0	0	0	3393	942	33	2	602	2	CHRNA6	8	42611452	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	24516	42611452	103752570	1031	5428										
SNAI2	6591	broad.mit.edu	37	chr8	49832658	49832658	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttatgtttggccagcccaGaaaaagttgaataggtctta	10	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:49832658G>A	ENST00000396822.1	-	3	779	c.422C>T	c.(421-423)tCt>tTt	p.S141F	SNAI2_ENST00000020945.1_Missense_Mutation_p.S141F			O43623	SNAI2_HUMAN	snail family zinc finger 2	141					canonical Wnt signaling pathway (GO:0060070)|cartilage morphogenesis (GO:0060536)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to ionizing radiation (GO:0071479)|desmosome disassembly (GO:0035921)|embryo development (GO:0009790)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|epithelium development (GO:0060429)|negative regulation of anoikis (GO:2000811)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter (GO:1900387)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|negative regulation of vitamin D receptor signaling pathway (GO:0070563)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone acetylation (GO:0035066)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of chemokine production (GO:0032642)|regulation of osteoblast differentiation (GO:0045667)|regulation of tight junction assembly (GO:2000810)|sensory perception of sound (GO:0007605)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.S141F(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)	18		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				GGCCAGCCCAGAAAAAGTTGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											102	103	103					8																	49832658		2203	4300	6503	49995211	SO:0001583	missense	6591			U97060	CCDS6146.1	8q11.21	2013-05-23	2013-05-23	2002-02-28	ENSG00000019549	ENSG00000019549		"Snail homologs", "Zinc fingers, C2H2-type"	11094	protein-coding gene	gene with protein product		602150	"slug homolog, zinc finger protein (chicken)", "snail homolog 2 (Drosophila)"	SLUG		9337409, 9721220	Standard	NM_003068		Approved	SLUGH1, SNAIL2	uc003xqp.3	O43623	OTTHUMG00000149912	ENST00000396822.1:c.422C>T	8.37:g.49832658G>A	ENSP00000380034:p.Ser141Phe		49995211	B2R6P6|Q53FC1	Missense_Mutation	SNP	ENST00000396822.1	37	CCDS6146.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075577	0.76415	.	.	ENSG00000019549	ENST00000020945;ENST00000396822	T;T	0.32023	1.47;1.47	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	L	0.53780	1.695	0.80722	D	1	P	0.52463	0.953	P	0.56865	0.808	T	0.48103	-0.9064	10	0.87932	D	0	-14.4802	19.1193	0.93355	0.0:0.0:1.0:0.0	.	141	O43623	SNAI2_HUMAN	F	141	ENSP00000020945:S141F;ENSP00000380034:S141F	ENSP00000020945:S141F	S	-	2	0	SNAI2	49995211	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	7.475000	0.81041	2.516000	0.84829	0.561000	0.74099	TCT		0.453	SNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313873.2	NM_003068		A	49832658	G	A	49832658	3	1	47	1	0	0	0	0	1	0	0	0	14864	942	33	3	392	3	SNAI2	8	49832658	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7221206	49832658	96531364	1032	5429										
MTFR1	9650	broad.mit.edu	37	chr8	66619478	66619478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatgaacagtgtaaaacttCggtcagtgaagaggtgagga	14	4	1	5	rs200858272		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:66619478C>T	ENST00000262146.4	+	6	877	c.751C>T	c.(751-753)Cgg>Tgg	p.R251W	MTFR1_ENST00000517944.1_3'UTR|MTFR1_ENST00000458689.2_Missense_Mutation_p.R218W	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	251	Necessary and sufficient to promote mitochondrial fission. {ECO:0000250}.				aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)		p.R251W(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			TGTAAAACTTCGGTCAGTGAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											87	84	85					8																	66619478		2203	4300	6503	66782032	SO:0001583	missense	9650				CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"likely ortholog of chicken chondrocyte protein with a poly proline region"					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.751C>T	8.37:g.66619478C>T	ENSP00000262146:p.Arg251Trp		66782032	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Missense_Mutation	SNP	ENST00000262146.4	37	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.1|27.1	4.804627|4.804627	0.90623|0.90623	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518609;ENST00000262146;ENST00000458689;ENST00000521247|ENST00000527155	T;T;T|.	0.56275|.	0.47;0.47;0.47|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85470|0.85470	0.5704|0.5704	M|M	0.90705|0.90705	3.14|3.14	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.999;1.0;0.999;1.0|.	D|D	0.87972|0.87972	0.2737|0.2737	10|5	0.87932|.	D|.	0|.	0.0167|0.0167	19.1023|19.1023	0.93279|0.93279	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	251;235;218;251|.	B4E3G8;E5RJS5;E7EP84;Q15390|.	.;.;.;MTFR1_HUMAN|.	W|L	235;251;218;67|64	ENSP00000262146:R251W;ENSP00000391502:R218W;ENSP00000429253:R67W|.	ENSP00000262146:R251W|.	R|S	+|+	1|2	2|0	MTFR1|MTFR1	66782032|66782032	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	6.694000|6.694000	0.74587|0.74587	2.504000|2.504000	0.84457|0.84457	0.563000|0.563000	0.77884|0.77884	CGG|TCG		0.373	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637		T	66619478	C	T	66619478	3	4	47	1	0	0	0	0	1	0	0	0	9955	875	31	1	769	1	MTFR1	8	66619478	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	16786820	66619478	79744544	1033	5430										
DNAJC5B	85479	broad.mit.edu	37	chr8	66963834	66963834	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggactctgtcaacaacaggaGaagctctatacgaaattctt	8	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:66963834G>T	ENST00000276570.5	+	3	339	c.52G>T	c.(52-54)Gaa>Taa	p.E18*	DNAJC5B_ENST00000519330.1_3'UTR	NM_033105.4	NP_149096.2	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 beta	18						membrane (GO:0016020)		p.E18*(1)		endometrium(3)|large_intestine(6)|liver(1)|lung(6)|prostate(1)|skin(3)	20		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			AACAACAGGAGAAGCTCTATA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											137	127	131					8																	66963834		2203	4300	6503	67126388	SO:0001587	stop_gained	85479			AF368276	CCDS6183.1	8q13.1	2012-10-02			ENSG00000147570	ENSG00000147570		"Heat shock proteins / DNAJ (HSP40)"	24138	protein-coding gene	gene with protein product		613945				12477932	Standard	NM_033105		Approved	MGC26226, CSP-beta	uc003xvs.1	Q9UF47	OTTHUMG00000164470	ENST00000276570.5:c.52G>T	8.37:g.66963834G>T	ENSP00000276570:p.Glu18*		67126388	Q969Y8	Nonsense_Mutation	SNP	ENST00000276570.5	37	CCDS6183.1	.	.	.	.	.	.	.	.	.	.	G	39	7.292490	0.98192	.	.	ENSG00000147570	ENST00000276570;ENST00000522619	.	.	.	5.88	5.01	0.66863	.	0.060237	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	13.0001	0.58670	0.0754:0.0:0.9246:0.0	.	.	.	.	X	18	.	ENSP00000276570:E18X	E	+	1	0	DNAJC5B	67126388	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.644000	0.54381	1.501000	0.48654	0.563000	0.77884	GAA		0.398	DNAJC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378915.1	NM_033105		T	66963834	G	T	66963834	4	4	47	1	0	0	0	0	0	1	0	0	4662	943	33	2	54	2	DNAJC5B	8	66963834	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	344356	66963834	79400188	1034	5431										
TRIM55	84675	broad.mit.edu	37	chr8	67062668	67062668	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtcaacctcaatagagaaGaaaagataatacgtgaaatt	7	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:67062668G>T	ENST00000315962.4	+	7	1325	c.952G>T	c.(952-954)Gaa>Taa	p.E318*	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000353317.5_Nonsense_Mutation_p.E318*|TRIM55_ENST00000276573.7_Nonsense_Mutation_p.E318*	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	318	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.E318*(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CAATAGAGAAGAAAAGATAAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											100	96	98					8																	67062668		2203	4300	6503	67225222	SO:0001587	stop_gained	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.952G>T	8.37:g.67062668G>T	ENSP00000323913:p.Glu318*		67225222	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Nonsense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	G	38	6.872739	0.97901	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	.	.	.	5.84	5.84	0.93424	.	0.199732	0.52532	D	0.000067	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	20.1535	0.98095	0.0:0.0:1.0:0.0	.	.	.	.	X	318	.	ENSP00000276573:E318X	E	+	1	0	TRIM55	67225222	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.365000	0.44196	2.764000	0.94973	0.650000	0.86243	GAA		0.408	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		T	67062668	G	T	67062668	4	4	47	1	0	0	0	0	0	1	0	0	16569	943	33	2	978	2	TRIM55	8	67062668	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	98834	67062668	79301354	1035	5432										
ARFGEF1	10565	broad.mit.edu	37	chr8	68178266	68178266	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcccttgttctattatttCtttttgttgctttaggacct	5	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:68178266C>A	ENST00000262215.3	-	14	2487	c.2098G>T	c.(2098-2100)Gaa>Taa	p.E700*	ARFGEF1_ENST00000520381.1_Nonsense_Mutation_p.E154*	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	700					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.E700*(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCTATTATTTCTTTTTGTTGC	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											128	118	121					8																	68178266		2203	4300	6503	68340820	SO:0001587	stop_gained	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.2098G>T	8.37:g.68178266C>A	ENSP00000262215:p.Glu700*		68340820	Q9NV46|Q9UFV2|Q9UNL0	Nonsense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	44	11.046626	0.99507	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	19.3684	0.94473	0.0:1.0:0.0:0.0	.	.	.	.	X	154;700	.	ENSP00000262215:E700X	E	-	1	0	ARFGEF1	68340820	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.743000	0.85020	2.591000	0.87537	0.585000	0.79938	GAA		0.408	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68178266	C	A	68178266	4	1	47	1	0	0	0	0	0	1	0	0	852	922	32	2	3555	2	ARFGEF1	8	68178266	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1115598	68178266	78185756	1036	5433										
CPA6	57094	broad.mit.edu	37	chr8	68334861	68334861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatccagtgtcacgtagttCgaaagcaaatgcataaggta	9	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:68334861C>T	ENST00000297770.4	-	11	1407	c.1192G>A	c.(1192-1194)Gaa>Aaa	p.E398K	CPA6_ENST00000297769.4_Missense_Mutation_p.E154K	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	398						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.E398K(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TCACGTAGTTCGAAAGCAAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											130	130	130					8																	68334861		2203	4300	6503	68497415	SO:0001583	missense	57094			AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.1192G>A	8.37:g.68334861C>T	ENSP00000297770:p.Glu398Lys		68497415	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.151144	0.78001	.	.	ENSG00000165078	ENST00000297769;ENST00000297770	T;T	0.59364	0.27;0.27	5.86	4.99	0.66335	Peptidase M14, carboxypeptidase A (2);	0.049117	0.85682	N	0.000000	T	0.75539	0.3863	M	0.75150	2.29	0.33097	D	0.538687	P;D	0.89917	0.842;1.0	B;D	0.97110	0.214;1.0	D	0.84068	0.0378	10	0.72032	D	0.01	.	14.9884	0.71365	0.0:0.9318:0.0:0.0682	.	154;398	Q8N4T0-3;Q8N4T0	.;CBPA6_HUMAN	K	154;398	ENSP00000297769:E154K;ENSP00000297770:E398K	ENSP00000297769:E154K	E	-	1	0	CPA6	68497415	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.464000	0.80887	1.486000	0.48398	0.591000	0.81541	GAA		0.383	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		T	68334861	C	T	68334861	3	4	47	1	0	0	0	0	1	0	0	0	3800	893	31	1	125	1	CPA6	8	68334861	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	156595	68334861	78029161	1037	5434										
NCOA2	10499	broad.mit.edu	37	chr8	71056898	71056898	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgctactgttccctaaatTtccttggtttcctatcatcc	5	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:71056898T>G	ENST00000452400.2	-	13	2972	c.2791A>C	c.(2791-2793)Aat>Cat	p.N931H	NCOA2_ENST00000267974.4_Intron	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	931					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)	p.N931H(1)	PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TTCCCTAAATTTCCTTGGTTT	0.408			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	1	Substitution - Missense(1)	large_intestine(1)	8											171	151	158					8																	71056898		1886	4124	6010	71219452	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2791A>C	8.37:g.71056898T>G	ENSP00000399968:p.Asn931His		71219452	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757600	0.49468	.	.	ENSG00000140396	ENST00000452400	T	0.01725	4.67	5.48	5.48	0.80851	.	0.245147	0.48767	D	0.000176	T	0.01870	0.0059	L	0.29908	0.895	0.80722	D	1	P	0.44877	0.845	B	0.37601	0.254	T	0.63773	-0.6561	10	0.66056	D	0.02	.	11.6735	0.51417	0.0:0.0706:0.0:0.9294	.	931	Q15596	NCOA2_HUMAN	H	931	ENSP00000399968:N931H	ENSP00000399968:N931H	N	-	1	0	NCOA2	71219452	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.232000	0.32636	2.307000	0.77673	0.528000	0.53228	AAT		0.408	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			G	71056898	T	G	71056898	3	3	47	1	0	0	0	0	1	0	0	0	10260	1841	64	4	1647	4	NCOA2	8	71056898	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2722037	71056898	75307124	1038	5435										
ZFHX4	79776	broad.mit.edu	37	chr8	77616716	77616716	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaatctaacaggggagatCgtttaccagcctgatgggtc	12	8	1	2	rs187480056	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:77616716C>T	ENST00000521891.2	+	2	841	c.393C>T	c.(391-393)atC>atT	p.I131I	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Silent_p.I131I|ZFHX4_ENST00000518282.1_Silent_p.I131I|ZFHX4_ENST00000050961.6_Silent_p.I131I	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.I131I(2)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAGGGGAGATCGTTTACCAGC	0.493										HNSCC(33;0.089)			C|||	5	0.000998403	0	0	5008	,	,		21089	0		0	False		,,,				2504	0.0051															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	8						C		0,3894		0,0,1947	110	108	109		393	-3.7	1	8		109	2,8314		0,2,4156	no	coding-synonymous	ZFHX4	NM_024721.4		0,2,6103	TT,TC,CC		0.0241,0.0,0.0164		131/3617	77616716	2,12208	1947	4158	6105	77779271	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.393C>T	8.37:g.77616716C>T			77779271	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.493	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77616716	C	T	77616716	2	4	47	1	0	0	0	0	0	0	0	1	17674	874	31	1		1	ZFHX4	8	77616716	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6559818	77616716	68747306	1039	5436										
ZFHX4	79776	broad.mit.edu	37	chr8	77768012	77768012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcttgctttagtgactaccGaactccaaccatgcaagaat	8	11	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:77768012G>A	ENST00000521891.2	+	10	9303	c.8855G>A	c.(8854-8856)cGa>cAa	p.R2952Q	ZFHX4_ENST00000455469.2_Missense_Mutation_p.R2907Q|ZFHX4_ENST00000518282.1_Missense_Mutation_p.R2926Q|ZFHX4_ENST00000050961.6_Missense_Mutation_p.R2907Q	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2907					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R2936Q(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGTGACTACCGAACTCCAACC	0.448										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											63	62	62					8																	77768012		1977	4155	6132	77930567	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8855G>A	8.37:g.77768012G>A	ENSP00000430497:p.Arg2952Gln		77930567	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514880	0.64634	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.96365	-3.99;-3.99;-3.99;-3.99	5.19	5.19	0.71726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.37530	U	0.002043	D	0.96719	0.8929	L	0.29908	0.895	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.79784	0.993;0.988;0.982	D	0.97551	1.0092	10	0.72032	D	0.01	.	18.8924	0.92410	0.0:0.0:1.0:0.0	.	2907;2907;2952	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	Q	2952;2936;2907;2907;2926	ENSP00000430497:R2952Q;ENSP00000399605:R2907Q;ENSP00000050961:R2907Q;ENSP00000430848:R2926Q	ENSP00000050961:R2907Q	R	+	2	0	ZFHX4	77930567	1.000000	0.71417	0.994000	0.49952	0.726000	0.41606	9.591000	0.98241	2.696000	0.92011	0.655000	0.94253	CGA		0.448	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77768012	G	A	77768012	3	1	47	1	0	0	0	0	1	0	0	0	17674	1058	37	1	8889	1	ZFHX4	8	77768012	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	151296	77768012	68596010	1040	5437										
SLC7A13	157724	broad.mit.edu	37	chr8	87242174	87242174	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tactcagcaaggagcagagcTtggccagcaactacccctga	10	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:87242174T>G	ENST00000297524.3	-	1	436	c.333A>C	c.(331-333)caA>caC	p.Q111H	SLC7A13_ENST00000419776.2_Missense_Mutation_p.Q111H|SLC7A13_ENST00000520624.1_Intron	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	111						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)	p.Q111H(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						GGAGCAGAGCTTGGCCAGCAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8											65	63	64					8																	87242174		2203	4300	6503	87311290	SO:0001583	missense	157724			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.333A>C	8.37:g.87242174T>G	ENSP00000297524:p.Gln111His		87311290	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	T	0.794	-0.757804	0.03019	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.89681	-2.55;-2.55	4.33	0.223	0.15292	Amino acid permease domain (1);	0.384600	0.22159	N	0.063802	D	0.83335	0.5232	L	0.52759	1.655	0.09310	N	1	B;P	0.43826	0.355;0.818	B;B	0.43508	0.144;0.422	T	0.75297	-0.3367	10	0.66056	D	0.02	.	3.8081	0.08786	0.1566:0.1973:0.0:0.6461	.	111;111	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	H	111	ENSP00000297524:Q111H;ENSP00000410982:Q111H	ENSP00000297524:Q111H	Q	-	3	2	SLC7A13	87311290	1.000000	0.71417	0.013000	0.15412	0.063000	0.16089	1.154000	0.31688	-0.042000	0.13535	0.421000	0.28195	CAA		0.483	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		G	87242174	T	G	87242174	3	3	47	1	0	0	0	0	1	0	0	0	14732	1606	56	4	1095	4	SLC7A13	8	87242174	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	9474162	87242174	59121848	1041	5438										
DCAF4L2	138009	broad.mit.edu	37	chr8	88885814	88885814	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagtgaggcccagcacataGaattcaccttccgattaggg	10	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:88885814G>T	ENST00000319675.3	-	1	482	c.386C>A	c.(385-387)tCt>tAt	p.S129Y		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	129								p.S129Y(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CCAGCACATAGAATTCACCTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	108	110					8																	88885814		2203	4300	6503	88954930	SO:0001583	missense	138009			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.386C>A	8.37:g.88885814G>T	ENSP00000316496:p.Ser129Tyr		88954930		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602655	0.46423	.	.	ENSG00000176566	ENST00000319675	T	0.73152	-0.72	1.39	1.39	0.22231	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.199369	0.56097	D	0.000036	T	0.75027	0.3794	M	0.68952	2.095	0.36901	D	0.890417	D	0.60160	0.987	D	0.63033	0.91	T	0.75733	-0.3214	10	0.72032	D	0.01	.	3.7503	0.08563	0.2516:0.0:0.7484:0.0	.	129	Q8NA75	DC4L2_HUMAN	Y	129	ENSP00000316496:S129Y	ENSP00000316496:S129Y	S	-	2	0	DCAF4L2	88954930	1.000000	0.71417	0.031000	0.17742	0.020000	0.10135	3.073000	0.50057	0.750000	0.32877	0.467000	0.42956	TCT		0.572	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		T	88885814	G	T	88885814	3	4	47	1	0	0	0	0	1	0	0	0	4278	942	33	2	805	2	DCAF4L2	8	88885814	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1643640	88885814	57478208	1042	5439										
TMEM64	169200	broad.mit.edu	37	chr8	91638050	91638050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattcaattccacttgagctCgatgaactacataaaacatg	5	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:91638050C>T	ENST00000458549.2	-	3	1169	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	TMEM64_ENST00000519519.1_Missense_Mutation_p.R70Q|TMEM64_ENST00000418210.2_Missense_Mutation_p.R279Q	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	331					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.R137Q(1)		endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			CACTTGAGCTCGATGAACTAC	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	73	75					8																	91638050		2203	4300	6503	91707226	SO:0001583	missense	169200			AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.992G>A	8.37:g.91638050C>T	ENSP00000414786:p.Arg331Gln		91707226	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Missense_Mutation	SNP	ENST00000458549.2	37	CCDS34920.2	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584777	0.86748	.	.	ENSG00000180694	ENST00000458549;ENST00000418210;ENST00000422900;ENST00000519519	.	.	.	5.78	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.66396	0.2785	M	0.73598	2.24	0.80722	D	1	D;P;D	0.61697	0.99;0.933;0.983	P;B;P	0.50825	0.651;0.344;0.548	T	0.68819	-0.5308	9	0.40728	T	0.16	.	14.6796	0.69006	0.0:0.9304:0.0:0.0695	.	279;70;331	F5GXM4;Q6YI46-2;Q6YI46	.;.;TMM64_HUMAN	Q	331;279;148;70	.	ENSP00000411951:R279Q	R	-	2	0	TMEM64	91707226	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.625000	0.83145	1.454000	0.47793	0.655000	0.94253	CGA		0.303	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495		T	91638050	C	T	91638050	3	4	47	1	0	0	0	0	1	0	0	0	16232	884	31	1	154	1	TMEM64	8	91638050	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2752236	91638050	54725972	1043	5440										
TMEM55A	55529	broad.mit.edu	37	chr8	92008946	92008946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatatgcacagcagcgtcttCgtggaagtgcactacccact	9	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:92008946C>T	ENST00000285419.3	-	6	880	c.566G>A	c.(565-567)cGa>cAa	p.R189Q		NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	189						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.R189Q(2)		breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			GCAGCGTCTTCGTGGAAGTGC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	8											69	61	64					8																	92008946		2203	4300	6503	92078122	SO:0001583	missense	55529			BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.566G>A	8.37:g.92008946C>T	ENSP00000285419:p.Arg189Gln		92078122	B2R9H4|Q68CU2	Missense_Mutation	SNP	ENST00000285419.3	37	CCDS6252.1	.	.	.	.	.	.	.	.	.	.	C	36	5.896146	0.97081	.	.	ENSG00000155099	ENST00000285419;ENST00000520014	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.76321	0.3971	L	0.50333	1.59	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.75639	-0.3248	9	0.62326	D	0.03	-21.4811	20.4008	0.98991	0.0:1.0:0.0:0.0	.	189	Q8N4L2	TM55A_HUMAN	Q	189;195	.	ENSP00000285419:R189Q	R	-	2	0	TMEM55A	92078122	1.000000	0.71417	0.969000	0.41365	0.995000	0.86356	7.487000	0.81328	2.826000	0.97356	0.655000	0.94253	CGA		0.358	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376778.1	NM_018710		T	92008946	C	T	92008946	3	4	47	1	0	0	0	0	1	0	0	0	16220	884	31	1	215	1	TMEM55A	8	92008946	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	370896	92008946	54355076	1044	5441										
RUNX1T1	862	broad.mit.edu	37	chr8	92998376	92998376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcaactgggtctgggttgaCgggactctgctgcctagagt	15	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:92998376C>T	ENST00000523629.1	-	9	1709	c.1255G>A	c.(1255-1257)Gtc>Atc	p.V419I	RUNX1T1_ENST00000396218.1_Missense_Mutation_p.V392I|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.V382I|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.V430I|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.V419I|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.V392I|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.V382I|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.V382I	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	419					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V419I(1)|p.V382I(1)|p.V430I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TCTGGGTTGACGGGACTCTGC	0.453																																																3	Substitution - Missense(3)	large_intestine(3)	8											108	116	113					8																	92998376		2203	4300	6503	93067552	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1255G>A	8.37:g.92998376C>T	ENSP00000428543:p.Val419Ile		93067552	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998890	0.54147	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.30182	1.55;1.55;1.55;1.55;1.55;1.55;1.54;1.55	5.67	4.76	0.60689	.	0.226064	0.45606	N	0.000357	T	0.16428	0.0395	N	0.08118	0	0.50813	D	0.999899	B;B;B	0.31519	0.327;0.318;0.301	B;B;B	0.25987	0.048;0.048;0.065	T	0.06625	-1.0816	10	0.37606	T	0.19	-11.7341	13.7947	0.63164	0.0:0.9239:0.0:0.0761	.	430;419;392	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	I	419;392;419;382;382;382;430;392	ENSP00000428543:V419I;ENSP00000379520:V392I;ENSP00000265814:V419I;ENSP00000353504:V382I;ENSP00000390137:V382I;ENSP00000428742:V382I;ENSP00000402257:V430I;ENSP00000430728:V392I	ENSP00000265814:V419I	V	-	1	0	RUNX1T1	93067552	1.000000	0.71417	0.884000	0.34674	0.976000	0.68499	5.571000	0.67404	1.334000	0.45468	0.655000	0.94253	GTC		0.453	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	92998376	C	T	92998376	3	4	47	1	0	0	0	0	1	0	0	0	13784	536	19	1	575	1	RUNX1T1	8	92998376	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	989430	92998376	53365646	1045	5442										
RBM12B	389677	broad.mit.edu	37	chr8	94748488	94748488	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatggcacgtcttgcatcttCatctgttgcaaaaataataa	6	8	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:94748488C>A	ENST00000399300.2	-	3	364	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	RBM12B_ENST00000517700.1_Nonsense_Mutation_p.E51*|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	51							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E51*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			CTTGCATCTTCATCTGTTGCA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											122	116	118					8																	94748488		1814	4094	5908	94817664	SO:0001587	stop_gained	389677				CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.151G>T	8.37:g.94748488C>A	ENSP00000382239:p.Glu51*		94817664	A8MYB5	Nonsense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354026	0.82243	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560;ENST00000521947	.	.	.	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-26.0498	19.4609	0.94916	0.0:1.0:0.0:0.0	.	.	.	.	X	51	.	ENSP00000382239:E51X	E	-	1	0	RBM12B	94817664	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.763000	0.68818	2.688000	0.91661	0.655000	0.94253	GAA		0.418	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		A	94748488	C	A	94748488	4	1	47	1	0	0	0	0	0	1	0	0	13151	835	29	2	2858	2	RBM12B	8	94748488	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1750112	94748488	51615534	1046	5443										
PTDSS1	9791	broad.mit.edu	37	chr8	97332520	97332520	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgcataaaatttggacaaGatctcttctctaagacccaa	5	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:97332520G>A	ENST00000517309.1	+	10	1446	c.1120G>A	c.(1120-1122)Gat>Aat	p.D374N	PTDSS1_ENST00000522072.1_Missense_Mutation_p.D171N|PTDSS1_ENST00000455950.2_Missense_Mutation_p.D228N	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	374					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.D374N(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	ATTTGGACAAGATCTCTTCTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	8											269	251	257					8																	97332520		2203	4300	6503	97401696	SO:0001583	missense	9791			D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.1120G>A	8.37:g.97332520G>A	ENSP00000430548:p.Asp374Asn		97401696	E5RFC5|Q9BUQ5	Missense_Mutation	SNP	ENST00000517309.1	37	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137978	0.77775	.	.	ENSG00000156471	ENST00000517309;ENST00000455950;ENST00000522072	T;T;T	0.44482	0.97;0.95;0.92	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.43743	0.1261	L	0.50333	1.59	0.80722	D	1	B	0.29766	0.256	B	0.38296	0.27	T	0.22487	-1.0215	10	0.19590	T	0.45	-17.7802	16.1835	0.81929	0.0:0.0:1.0:0.0	.	374	P48651	PTSS1_HUMAN	N	374;228;171	ENSP00000430548:D374N;ENSP00000401248:D228N;ENSP00000430928:D171N	ENSP00000401248:D228N	D	+	1	0	PTDSS1	97401696	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.491000	0.90468	2.553000	0.86117	0.585000	0.79938	GAT		0.393	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2			A	97332520	G	A	97332520	3	1	47	1	0	0	0	0	1	0	0	0	12770	942	33	3	1158	3	PTDSS1	8	97332520	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2584032	97332520	49031502	1047	5444										
PGCP	10404	broad.mit.edu	37	chr8	97797217	97797217	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagaatggcatctctaagaGgacttttgaagaaataaaag	9	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:97797217G>T	ENST00000220763.5	+	2	302	c.92G>T	c.(91-93)aGg>aTg	p.R31M		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	31					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)	p.R31M(1)									ATCTCTAAGAGGACTTTTGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											93	95	94					8																	97797217		2203	4300	6503	97866393	SO:0001583	missense	10404			AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.92G>T	8.37:g.97797217G>T	ENSP00000220763:p.Arg31Met		97866393	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	37	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794088	0.31777	.	.	ENSG00000104324	ENST00000220763;ENST00000519900;ENST00000517742;ENST00000519484;ENST00000521142	T;T	0.48201	0.82;0.83	5.28	0.103	0.14526	.	0.838495	0.10774	N	0.635674	T	0.35624	0.0938	L	0.44542	1.39	0.09310	N	1	P;P	0.48640	0.913;0.845	B;B	0.40741	0.339;0.174	T	0.22556	-1.0213	10	0.51188	T	0.08	-5.5887	6.1142	0.20117	0.3871:0.1363:0.4766:0.0	.	31;31	B5MDX4;Q9Y646	.;PGCP_HUMAN	M	31	ENSP00000220763:R31M;ENSP00000429146:R31M	ENSP00000220763:R31M	R	+	2	0	AC010859.1	97866393	0.000000	0.05858	0.237000	0.24090	0.818000	0.46254	0.057000	0.14279	0.449000	0.26747	0.563000	0.77884	AGG		0.383	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		T	97797217	G	T	97797217	3	4	47	1	0	0	0	0	1	0	0	0	11817	1000	35	2	94	2	PGCP	8	97797217	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	464697	97797217	48566805	1048	5445										
PGCP	10404	broad.mit.edu	37	chr8	97797528	97797528	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataagatagccatcctgggtCttggcagcagcattgggact	12	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:97797528C>A	ENST00000220763.5	+	2	613	c.403C>A	c.(403-405)Ctt>Att	p.L135I		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	135					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)	p.L135I(1)									CATCCTGGGTCTTGGCAGCAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	8											64	68	67					8																	97797528		2203	4300	6503	97866704	SO:0001583	missense	10404			AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.403C>A	8.37:g.97797528C>A	ENSP00000220763:p.Leu135Ile		97866704	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	37	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278051	0.59758	.	.	ENSG00000104324	ENST00000220763;ENST00000517742;ENST00000519484	T;T	0.72615	0.34;-0.67	5.35	4.46	0.54185	.	0.000000	0.64402	D	0.000001	D	0.84543	0.5495	M	0.85542	2.76	0.44798	D	0.9978	D;D	0.89917	0.99;1.0	D;D	0.91635	0.968;0.999	D	0.86253	0.1650	10	0.62326	D	0.03	-12.4642	13.784	0.63099	0.0:0.9259:0.0:0.0741	.	135;135	B5MDX4;Q9Y646	.;PGCP_HUMAN	I	135	ENSP00000220763:L135I;ENSP00000429146:L135I	ENSP00000220763:L135I	L	+	1	0	AC010859.1	97866704	0.963000	0.33076	0.952000	0.39060	0.113000	0.19764	2.198000	0.42705	2.667000	0.90743	0.655000	0.94253	CTT		0.438	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		A	97797528	C	A	97797528	3	1	47	1	0	0	0	0	1	0	0	0	11817	913	32	2	405	2	PGCP	8	97797528	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	311	97797528	48566494	1049	5446										
MATN2	4147	broad.mit.edu	37	chr8	99019810	99019810	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagggacacgtgctccgcagCgatgggaagacgtgtgcaag	17	9	0	1	rs370974462		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:99019810C>T	ENST00000520016.1	+	9	1678	c.1554C>T	c.(1552-1554)agC>agT	p.S518S	MATN2_ENST00000254898.5_Silent_p.S518S|MATN2_ENST00000524308.1_Silent_p.S477S|MATN2_ENST00000522025.2_Silent_p.S234S|MATN2_ENST00000521689.1_Silent_p.S518S			O00339	MATN2_HUMAN	matrilin 2	518	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S518S(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGCTCCGCAGCGATGGGAAGA	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	8						C	,	1,4299		0,1,2149	138	134	136		1554,1554	-3.1	1	8		136	4,8502		0,4,4249	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	0,5,6398	TT,TC,CC		0.047,0.0233,0.039	,	518/957,518/938	99019810	5,12801	2150	4253	6403	99088986	SO:0001819	synonymous_variant	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1554C>T	8.37:g.99019810C>T			99088986	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	8.475	0.858472	0.17178	2.33E-4	4.7E-4	ENSG00000132561	ENST00000518154	.	.	.	5.65	-3.14	0.05250	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.0497	7.1079	0.25374	0.0:0.488:0.1411:0.3709	.	.	.	.	X	301	.	.	R	+	1	2	MATN2	99088986	0.001000	0.12720	0.956000	0.39512	0.778000	0.44026	-1.459000	0.02370	-0.828000	0.04273	-0.768000	0.03414	CGA		0.557	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99019810	C	T	99019810	2	4	47	1	0	0	0	0	0	0	0	1	9364	767	27	1		1	MATN2	8	99019810	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1222282	99019810	47344212	1050	5447										
POP1	10940	broad.mit.edu	37	chr8	99153060	99153060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgacagttggggatcctcGaataaatttgccccaaaaga	9	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:99153060G>A	ENST00000401707.2	+	11	1619	c.1538G>A	c.(1537-1539)cGa>cAa	p.R513Q	POP1_ENST00000349693.3_Missense_Mutation_p.R513Q	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	513					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)	p.R513Q(1)		autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GGGGATCCTCGAATAAATTTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	85	84					8																	99153060		2203	4300	6503	99222236	SO:0001583	missense	10940			D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1538G>A	8.37:g.99153060G>A	ENSP00000385787:p.Arg513Gln		99222236	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527654	0.85706	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.74947	-0.89;-0.89	5.7	5.7	0.88788	.	0.069249	0.56097	D	0.000025	T	0.76659	0.4018	M	0.84326	2.69	0.80722	D	1	D	0.56968	0.978	B	0.39152	0.292	T	0.82520	-0.0416	10	0.66056	D	0.02	-13.9927	18.0753	0.89425	0.0:0.0:1.0:0.0	.	513	Q99575	POP1_HUMAN	Q	513	ENSP00000385787:R513Q;ENSP00000339529:R513Q	ENSP00000339529:R513Q	R	+	2	0	POP1	99222236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.200000	0.95010	2.705000	0.92388	0.650000	0.86243	CGA		0.408	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99153060	G	A	99153060	3	1	47	1	0	0	0	0	1	0	0	0	12282	1058	37	1	1576	1	POP1	8	99153060	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	133250	99153060	47210962	1051	5448										
POP1	10940	broad.mit.edu	37	chr8	99168622	99168622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccatgttgctgccacagggaGtcacctctgcgttctcaggt	11	13	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:99168622G>A	ENST00000401707.2	+	15	2483	c.2402G>A	c.(2401-2403)aGt>aAt	p.S801N	POP1_ENST00000349693.3_Missense_Mutation_p.S801N	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	801					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)	p.S801N(1)		autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GCCACAGGGAGTCACCTCTGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	113	113					8																	99168622		2203	4300	6503	99237798	SO:0001583	missense	10940			D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.2402G>A	8.37:g.99168622G>A	ENSP00000385787:p.Ser801Asn		99237798	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433653	0.25813	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.37752	1.18;1.18	5.56	1.74	0.24563	.	1.491850	0.03536	N	0.223257	T	0.36635	0.0974	M	0.69823	2.125	0.09310	N	1	B	0.28128	0.201	B	0.27608	0.081	T	0.14699	-1.0463	10	0.17832	T	0.49	-5.3991	4.904	0.13789	0.322:0.1454:0.5326:0.0	.	801	Q99575	POP1_HUMAN	N	801	ENSP00000385787:S801N;ENSP00000339529:S801N	ENSP00000339529:S801N	S	+	2	0	POP1	99237798	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.554000	0.23407	0.035000	0.15519	-0.218000	0.12543	AGT		0.488	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99168622	G	A	99168622	3	1	47	1	0	0	0	0	1	0	0	0	12282	1029	36	3	2456	3	POP1	8	99168622	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	15562	99168622	47195400	1052	5449										
KCNS2	3788	broad.mit.edu	37	chr8	99440435	99440435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacttcgaccgcaaccctgaGctcttcccctacgtgctgca	7	17	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:99440435G>T	ENST00000287042.4	+	2	578	c.228G>T	c.(226-228)gaG>gaT	p.E76D	KCNS2_ENST00000521839.1_Missense_Mutation_p.E76D	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	76					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.E76D(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			GCAACCCTGAGCTCTTCCCCT	0.587																																					Pancreas(138;844 2489 9202 24627)											1	Substitution - Missense(1)	large_intestine(1)	8											133	103	113					8																	99440435		2203	4300	6503	99509611	SO:0001583	missense	3788			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.228G>T	8.37:g.99440435G>T	ENSP00000287042:p.Glu76Asp		99509611	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	g	11.64	1.698409	0.30142	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	T;T	0.76578	-1.03;-1.03	5.4	2.61	0.31194	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.366030	0.27936	N	0.017253	T	0.54303	0.1850	N	0.11698	0.16	0.26512	N	0.974578	B	0.22414	0.069	B	0.19391	0.025	T	0.36016	-0.9765	10	0.21540	T	0.41	.	5.8836	0.18868	0.2669:0.138:0.5951:0.0	.	76	Q9ULS6	KCNS2_HUMAN	D	76	ENSP00000287042:E76D;ENSP00000430712:E76D	ENSP00000287042:E76D	E	+	3	2	KCNS2	99509611	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	0.364000	0.20325	1.281000	0.44480	0.558000	0.71614	GAG		0.587	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		T	99440435	G	T	99440435	3	4	47	1	0	0	0	0	1	0	0	0	8110	962	34	2	230	2	KCNS2	8	99440435	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	271813	99440435	46923587	1053	5450										
SNX31	169166	broad.mit.edu	37	chr8	101608977	101608977	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcattattgccaacagaaaGaacagctccagagcctgatt	7	11	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:101608977G>T	ENST00000311812.2	-	10	1018	c.868C>A	c.(868-870)Ctt>Att	p.L290I	SNX31_ENST00000519521.1_5'Flank|SNX31_ENST00000428383.2_Missense_Mutation_p.L191I	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	290					protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)	p.L290I(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			CCAACAGAAAGAACAGCTCCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	8											136	136	136					8																	101608977		2203	4300	6503	101678153	SO:0001583	missense	169166				CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"Sorting nexins"	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.868C>A	8.37:g.101608977G>T	ENSP00000312368:p.Leu290Ile		101678153	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.916301	0.00503	.	.	ENSG00000174226	ENST00000311812;ENST00000428383	T;T	0.22539	2.3;1.95	4.54	0.367	0.16140	.	0.619023	0.13666	N	0.371250	T	0.11879	0.0289	L	0.41573	1.285	0.09310	N	1	B;B	0.20671	0.047;0.007	B;B	0.19946	0.027;0.007	T	0.35699	-0.9778	10	0.09843	T	0.71	-1.9517	2.4047	0.04410	0.0956:0.3418:0.2317:0.331	.	191;290	Q8N9S9-2;Q8N9S9	.;SNX31_HUMAN	I	290;191	ENSP00000312368:L290I;ENSP00000405024:L191I	ENSP00000312368:L290I	L	-	1	0	SNX31	101678153	0.176000	0.23096	0.002000	0.10522	0.060000	0.15804	0.599000	0.24089	0.170000	0.19704	0.557000	0.71058	CTT		0.547	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628		T	101608977	G	T	101608977	3	4	47	1	0	0	0	0	1	0	0	0	14938	942	33	2	474	2	SNX31	8	101608977	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2168542	101608977	44755045	1054	5451										
ODF1	4956	broad.mit.edu	37	chr8	103564262	103564262	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagccatagaagatgagaagCgagagcttgccaagtaaaat	12	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:103564262C>T	ENST00000285402.3	+	1	463	c.307C>T	c.(307-309)Cga>Tga	p.R103*		NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	103					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.R103*(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			AGATGAGAAGCGAGAGCTTGC	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											84	80	81					8																	103564262		2203	4300	6503	103633438	SO:0001587	stop_gained	4956			M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.307C>T	8.37:g.103564262C>T	ENSP00000285402:p.Arg103*		103633438	Q3SX72	Nonsense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	.	.	.	.	.	.	.	.	.	.	C	37	6.467073	0.97590	.	.	ENSG00000155087	ENST00000285402	.	.	.	5.56	3.14	0.36123	.	0.125800	0.36409	N	0.002607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.1263	10.104	0.42521	0.6068:0.3932:0.0:0.0	.	.	.	.	X	103	.	ENSP00000285402:R103X	R	+	1	2	ODF1	103633438	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.332000	0.33805	0.364000	0.24374	-0.274000	0.10170	CGA		0.363	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			T	103564262	C	T	103564262	4	4	47	1	0	0	0	0	0	1	0	0	10857	760	27	1	309	1	ODF1	8	103564262	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1955285	103564262	42799760	1055	5452										
TRHR	7201	broad.mit.edu	37	chr8	110100517	110100517	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgtttcaacagcacagtatCttcaaggaagcaggtaagca	9	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:110100517C>T	ENST00000518632.1	+	2	1127	c.776C>T	c.(775-777)tCt>tTt	p.S259F	TRHR_ENST00000311762.2_Missense_Mutation_p.S259F			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	259					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)	p.S259F(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			AGCACAGTATCTTCAAGGAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	8											31	31	31					8																	110100517		2202	4295	6497	110169693	SO:0001583	missense	7201				CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.776C>T	8.37:g.110100517C>T	ENSP00000430711:p.Ser259Phe		110169693	Q2M339	Missense_Mutation	SNP	ENST00000518632.1	37	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.787406	0.31593	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	T;T	0.39056	1.1;1.1	5.88	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.262093	0.43747	D	0.000521	T	0.50803	0.1637	M	0.84511	2.7	0.26921	N	0.966687	B	0.21606	0.058	B	0.24394	0.053	T	0.52946	-0.8507	10	0.66056	D	0.02	-7.9521	14.6214	0.68588	0.0:0.7232:0.2768:0.0	.	259	P34981	TRFR_HUMAN	F	259	ENSP00000430711:S259F;ENSP00000309818:S259F	ENSP00000309818:S259F	S	+	2	0	TRHR	110169693	1.000000	0.71417	0.781000	0.31783	0.989000	0.77384	7.481000	0.81124	1.476000	0.48215	0.655000	0.94253	TCT		0.378	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			T	110100517	C	T	110100517	3	4	47	1	0	0	0	0	1	0	0	0	16520	913	32	3	778	3	TRHR	8	110100517	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6536255	110100517	36263505	1056	5453										
CSMD3	114788	broad.mit.edu	37	chr8	113649183	113649183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcccaaagttgaacccgattCgactaccatattgaggaatg	8	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:113649183C>T	ENST00000297405.5	-	22	3822	c.3578G>A	c.(3577-3579)cGa>cAa	p.R1193Q	CSMD3_ENST00000352409.3_Missense_Mutation_p.R1193Q|CSMD3_ENST00000343508.3_Missense_Mutation_p.R1153Q|CSMD3_ENST00000455883.2_Missense_Mutation_p.R1089Q	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1193	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1193Q(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAACCCGATTCGACTACCATA	0.458										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											204	175	185					8																	113649183		2203	4300	6503	113718359	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3578G>A	8.37:g.113649183C>T	ENSP00000297405:p.Arg1193Gln		113718359	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	34	5.341868	0.95783	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84	5.56	5.56	0.83823	Complement control module (2);Sushi/SCR/CCP (3);	0.222920	0.27206	N	0.020439	T	0.50922	0.1644	M	0.67953	2.075	0.40049	D	0.975756	D;D;D	0.89917	0.967;0.973;1.0	P;P;D	0.87578	0.783;0.764;0.998	T	0.36648	-0.9739	10	0.28530	T	0.3	.	19.5386	0.95266	0.0:1.0:0.0:0.0	.	1089;1193;1153	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Q	1153;1193;533;1089;1193	ENSP00000345799:R1153Q;ENSP00000297405:R1193Q;ENSP00000341558:R533Q;ENSP00000412263:R1089Q;ENSP00000343124:R1193Q	ENSP00000297405:R1193Q	R	-	2	0	CSMD3	113718359	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.913000	0.63341	2.610000	0.88304	0.650000	0.86243	CGA		0.458	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113649183	C	T	113649183	3	4	47	1	0	0	0	0	1	0	0	0	3952	884	31	1	7745	1	CSMD3	8	113649183	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3548666	113649183	32714839	1057	5454										
TAF2	6873	broad.mit.edu	37	chr8	120814213	120814213	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcagcatctactgtaaattCtaatttccatgtacacaatt	4	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:120814213C>A	ENST00000378164.2	-	6	911	c.613G>T	c.(613-615)Gaa>Taa	p.E205*		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	205					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.E205*(2)		NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ACTGTAAATTCTAATTTCCAT	0.338																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											86	78	81					8																	120814213		2203	4300	6503	120883394	SO:0001587	stop_gained	6873			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.613G>T	8.37:g.120814213C>A	ENSP00000367406:p.Glu205*		120883394	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Nonsense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	C	40	8.485828	0.98832	.	.	ENSG00000064313	ENST00000378164	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-20.17	20.2576	0.98430	0.0:1.0:0.0:0.0	.	.	.	.	X	205	.	ENSP00000367406:E205X	E	-	1	0	TAF2	120883394	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.776000	0.85560	2.783000	0.95769	0.655000	0.94253	GAA		0.338	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		A	120814213	C	A	120814213	4	1	47	1	0	0	0	0	0	1	0	0	15563	922	32	2	3070	2	TAF2	8	120814213	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7165030	120814213	25549809	1058	5455										
COL14A1	7373	broad.mit.edu	37	chr8	121215985	121215985	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgaatgagctgcaggagatCgcctctgaaccagacagcac	12	11	1	5	rs369585103		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:121215985C>A	ENST00000297848.3	+	9	1185	c.915C>A	c.(913-915)atC>atA	p.I305I	COL14A1_ENST00000247781.3_Silent_p.I210I|COL14A1_ENST00000537875.1_Silent_p.I305I|COL14A1_ENST00000309791.4_Silent_p.I305I|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.I305I(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TGCAGGAGATCGCCTCTGAAC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	8											139	119	126					8																	121215985		2203	4300	6503	121285166	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.915C>A	8.37:g.121215985C>A			121285166		Silent	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	9.207	1.029978	0.19512	.	.	ENSG00000187955	ENST00000523142	.	.	.	5.09	-0.335	0.12662	.	.	.	.	.	T	0.50497	0.1619	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38243	-0.9670	4	.	.	.	.	5.1785	0.15148	0.134:0.4381:0.0:0.4279	.	.	.	.	S	62	.	.	R	+	1	0	COL14A1	121285166	0.206000	0.23470	0.998000	0.56505	0.853000	0.48598	-0.428000	0.06991	0.032000	0.15435	0.561000	0.74099	CGC		0.498	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121215985	C	A	121215985	2	1	47	1	0	0	0	0	0	0	0	1	3677	874	31	2		2	COL14A1	8	121215985	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	401772	121215985	25148037	1059	5456										
COL14A1	7373	broad.mit.edu	37	chr8	121344960	121344960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagcatgggaccgcaaggcGccctgggaccacctgtgagt	15	12	0	1	rs370064596		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:121344960G>A	ENST00000297848.3	+	42	5041	c.4771G>A	c.(4771-4773)Gcc>Acc	p.A1591T	COL14A1_ENST00000247781.3_Missense_Mutation_p.A1496T|COL14A1_ENST00000309791.4_Missense_Mutation_p.A1591T	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.A1591T(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			ACCGCAAGGCGCCCTGGGACC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	97	88	91		4771	4.6	1	8		91	0,8600		0,0,4300	no	missense	COL14A1	NM_021110.1	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1591/1797	121344960	1,13005	2203	4300	6503	121414141	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4771G>A	8.37:g.121344960G>A	ENSP00000297848:p.Ala1591Thr		121414141		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022215	0.35701	2.27E-4	0.0	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	D;D;D	0.94376	-3.41;-3.41;-3.41	5.52	4.59	0.56863	.	0.322526	0.36167	N	0.002741	D	0.88987	0.6587	L	0.42632	1.34	0.80722	D	1	B	0.10296	0.003	B	0.13407	0.009	T	0.83170	-0.0094	10	0.16896	T	0.51	.	12.072	0.53622	0.0:0.0:0.7867:0.2133	.	1591	Q05707	COEA1_HUMAN	T	1591;1591;1496	ENSP00000311809:A1591T;ENSP00000297848:A1591T;ENSP00000247781:A1496T	ENSP00000247781:A1496T	A	+	1	0	COL14A1	121414141	0.998000	0.40836	0.993000	0.49108	0.321000	0.28281	3.176000	0.50863	1.153000	0.42468	0.561000	0.74099	GCC		0.507	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121344960	G	A	121344960	3	1	47	1	0	0	0	0	1	0	0	0	3677	1087	38	1	4933	1	COL14A1	8	121344960	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	128975	121344960	25019062	1060	5457										
MRPL13	28998	broad.mit.edu	37	chr8	121437583	121437583	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgaagctgagcagctgttActtgtctaaatccacctggg	12	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:121437583A>C	ENST00000306185.3	-	4	560	c.269T>G	c.(268-270)gTa>gGa	p.V90G		NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13	90					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.V90G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			AGCAGCTGTTACTTGTCTAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	8											110	117	115					8																	121437583		2203	4300	6503	121506764	SO:0001583	missense	28998			AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.269T>G	8.37:g.121437583A>C	ENSP00000306548:p.Val90Gly		121506764	B2R4R8|Q9UI04	Missense_Mutation	SNP	ENST00000306185.3	37	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414198	0.42817	.	.	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	5.26	4.08	0.47627	Ribosomal protein L13 domain (2);	0.000000	0.85682	D	0.000000	T	0.76969	0.4062	M	0.87617	2.895	0.80722	D	1	P	0.35077	0.483	P	0.46237	0.508	T	0.76796	-0.2827	9	0.48119	T	0.1	-2.9629	11.6099	0.51053	0.8504:0.1496:0.0:0.0	.	90	Q9BYD1	RM13_HUMAN	G	90;66	.	ENSP00000306548:V90G	V	-	2	0	MRPL13	121506764	1.000000	0.71417	0.992000	0.48379	0.911000	0.54048	7.673000	0.83973	0.910000	0.36722	0.377000	0.23210	GTA		0.363	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078		C	121437583	A	C	121437583	3	2	47	1	0	0	0	0	1	0	0	0	9808	391	14	4	283	4	MRPL13	8	121437583	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	92623	121437583	24926439	1061	5458										
ANXA13	312	broad.mit.edu	37	chr8	124693578	124693578	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atacttctcttggaactttgCtttgatcccctgaaggtcca	7	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:124693578C>A	ENST00000419625.1	-	11	925	c.853G>T	c.(853-855)Gca>Tca	p.A285S	ANXA13_ENST00000262219.6_Missense_Mutation_p.A326S	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	285					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)	p.A326S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TGGAACTTTGCTTTGATCCCC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	8											170	178	175					8																	124693578		2203	4300	6503	124762759	SO:0001583	missense	312			Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.853G>T	8.37:g.124693578C>A	ENSP00000390809:p.Ala285Ser		124762759	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	37	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.227658	0.39399	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	T;T	0.03386	3.95;3.95	5.81	4.94	0.65067	Annexin repeat, conserved site (1);	0.185294	0.56097	D	0.000026	T	0.03434	0.0099	N	0.20530	0.585	0.30084	N	0.808957	P;P	0.38395	0.533;0.629	B;B	0.39706	0.197;0.307	T	0.34428	-0.9829	10	0.23891	T	0.37	.	11.8686	0.52507	0.0:0.9182:0.0:0.0818	.	285;326	P27216;P27216-2	ANX13_HUMAN;.	S	326;285	ENSP00000262219:A326S;ENSP00000390809:A285S	ENSP00000262219:A326S	A	-	1	0	ANXA13	124762759	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.523000	0.53488	1.452000	0.47756	0.655000	0.94253	GCA		0.463	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		A	124693578	C	A	124693578	3	1	47	1	0	0	0	0	1	0	0	0	717	797	28	2	101	2	ANXA13	8	124693578	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3255995	124693578	21670444	1062	5459										
FER1L6	654463	broad.mit.edu	37	chr8	125033865	125033865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgttgatgaaatgattcacGaagcccaaaactttgtggaa	9	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:125033865G>A	ENST00000522917.1	+	17	2295	c.2089G>A	c.(2089-2091)Gaa>Aaa	p.E697K	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.E697K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	697						integral component of membrane (GO:0016021)		p.E697K(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AATGATTCACGAAGCCCAAAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	8											102	100	101					8																	125033865		1899	4112	6011	125103046	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2089G>A	8.37:g.125033865G>A	ENSP00000428280:p.Glu697Lys		125103046		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	0.838	-0.743016	0.03088	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.81659	-1.52;-1.52	5.77	1.82	0.25136	.	0.715706	0.12788	U	0.439079	T	0.68016	0.2955	L	0.43152	1.355	0.24052	N	0.996044	B	0.14805	0.011	B	0.09377	0.004	T	0.48536	-0.9027	10	0.09084	T	0.74	.	7.1995	0.25873	0.2025:0.1235:0.6741:0.0	.	697	Q2WGJ9	FR1L6_HUMAN	K	697	ENSP00000428280:E697K;ENSP00000381982:E697K	ENSP00000381982:E697K	E	+	1	0	FER1L6	125103046	0.598000	0.26882	0.055000	0.19348	0.389000	0.30415	1.001000	0.29783	0.055000	0.16094	0.591000	0.81541	GAA		0.418	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125033865	G	A	125033865	3	1	47	1	0	0	0	0	1	0	0	0	5834	1059	37	1	2151	1	FER1L6	8	125033865	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	340287	125033865	21330157	1063	5460										
FER1L6	654463	broad.mit.edu	37	chr8	125113491	125113491	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accaagagggagaacatcttCtctttagagaagatggagtg	12	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:125113491C>A	ENST00000522917.1	+	38	5243	c.5037C>A	c.(5035-5037)ttC>ttA	p.F1679L	FER1L6_ENST00000399018.1_Missense_Mutation_p.F1679L|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1679	C2 6. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)		p.F1679L(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGAACATCTTCTCTTTAGAGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											99	96	97					8																	125113491		2039	4238	6277	125182672	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.5037C>A	8.37:g.125113491C>A	ENSP00000428280:p.Phe1679Leu		125182672		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635554	0.47049	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.86097	-2.07;-2.07	5.71	-3.93	0.04143	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.059114	0.64402	U	0.000002	D	0.87018	0.6073	L	0.52206	1.635	0.46149	D	0.998894	D	0.76494	0.999	D	0.75020	0.985	D	0.84225	0.0463	10	0.54805	T	0.06	-14.0459	12.4329	0.55583	0.0:0.3587:0.0:0.6413	.	1679	Q2WGJ9	FR1L6_HUMAN	L	1679	ENSP00000428280:F1679L;ENSP00000381982:F1679L	ENSP00000381982:F1679L	F	+	3	2	FER1L6	125182672	0.961000	0.32948	0.665000	0.29768	0.056000	0.15407	0.095000	0.15127	-1.038000	0.03279	-0.253000	0.11424	TTC		0.498	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125113491	C	A	125113491	3	1	47	1	0	0	0	0	1	0	0	0	5834	912	32	2	5183	2	FER1L6	8	125113491	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	79626	125113491	21250531	1064	5461										
TATDN1	83940	broad.mit.edu	37	chr8	125507733	125507733	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtctcaatcattaattttTcactaggaattgacttcaaa	4	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:125507733T>G	ENST00000276692.6	-	10	681	c.644A>C	c.(643-645)gAa>gCa	p.E215A	TATDN1_ENST00000519548.1_Missense_Mutation_p.E168A|TATDN1_ENST00000517678.1_Missense_Mutation_p.E161A|TATDN1_ENST00000521546.1_5'Flank	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1	215					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.E215A(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CATTAATTTTTCACTAGGAAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	8											39	40	39					8																	125507733		2200	4287	6487	125576914	SO:0001583	missense	83940			AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068	ENST00000276692.6:c.644A>C	8.37:g.125507733T>G	ENSP00000276692:p.Glu215Ala		125576914	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602266	0.66445	.	.	ENSG00000147687	ENST00000276692;ENST00000519548;ENST00000522810;ENST00000517678	.	.	.	5.58	5.58	0.84498	Deoxyribonuclease, TatD-related, conserved site (1);	0.102547	0.64402	D	0.000003	T	0.71970	0.3403	M	0.85373	2.75	0.58432	D	0.99999	P;B	0.38745	0.645;0.225	B;B	0.43194	0.411;0.347	T	0.76937	-0.2774	9	0.66056	D	0.02	-23.3835	15.76	0.78073	0.0:0.0:0.0:1.0	.	251;215	E5RG17;Q6P1N9	.;TATD1_HUMAN	A	215;168;251;161	.	ENSP00000276692:E215A	E	-	2	0	TATDN1	125576914	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.437000	0.80417	2.125000	0.65367	0.528000	0.53228	GAA		0.294	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		G	125507733	T	G	125507733	3	3	47	1	0	0	0	0	1	0	0	0	15630	1783	62	4	261	4	TATDN1	8	125507733	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	394242	125507733	20856289	1065	5462										
TATDN1	83940	broad.mit.edu	37	chr8	125520867	125520867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaattcagcatgtgagtttCgacaatgaagaaacattggt	9	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:125520867C>T	ENST00000276692.6	-	7	489	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	TATDN1_ENST00000605953.1_Missense_Mutation_p.R151Q|TATDN1_ENST00000519548.1_Missense_Mutation_p.R104Q|TATDN1_ENST00000517678.1_Missense_Mutation_p.R97Q|TATDN1_ENST00000521546.1_5'UTR	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1	151					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.R151Q(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATGTGAGTTTCGACAATGAAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	8											53	50	51					8																	125520867		2203	4295	6498	125590048	SO:0001583	missense	83940			AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068	ENST00000276692.6:c.452G>A	8.37:g.125520867C>T	ENSP00000276692:p.Arg151Gln		125590048	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	C	35	5.575121	0.96553	.	.	ENSG00000147687	ENST00000276692;ENST00000519548;ENST00000522810;ENST00000517678;ENST00000523888;ENST00000523152	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.91462	0.7305	H	0.98802	4.335	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94444	0.7661	9	0.87932	D	0	-12.2863	19.8917	0.96932	0.0:1.0:0.0:0.0	.	151;151	E5RG17;Q6P1N9	.;TATD1_HUMAN	Q	151;104;151;97;104;91	.	ENSP00000276692:R151Q	R	-	2	0	TATDN1	125590048	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.085000	0.76875	2.705000	0.92388	0.591000	0.81541	CGA		0.279	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		T	125520867	C	T	125520867	3	4	47	1	0	0	0	0	1	0	0	0	15630	884	31	1	465	1	TATDN1	8	125520867	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	13134	125520867	20843155	1066	5463										
ASAP1	50807	broad.mit.edu	37	chr8	131073086	131073086	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtttgggaggtaagtctgaGagttggggtttgggtggcag	21	2	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:131073086G>T	ENST00000518721.1	-	28	3158	c.2931C>A	c.(2929-2931)ctC>ctA	p.L977L	ASAP1_ENST00000357668.1_Silent_p.L977L	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	977	Pro-rich.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.L977L(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						GTAAGTCTGAGAGTTGGGGTT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	8											89	97	94					8																	131073086		2203	4300	6503	131142268	SO:0001819	synonymous_variant	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2931C>A	8.37:g.131073086G>T			131142268	B2RNV3	Silent	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	G	8.474	0.858170	0.17178	.	.	ENSG00000153317	ENST00000524124;ENST00000519483	T;T	0.10860	3.07;2.83	5.62	4.75	0.60458	.	0.952676	0.08712	N	0.904787	T	0.09949	0.0244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19679	-1.0298	7	0.14656	T	0.56	.	7.4152	0.27040	0.0927:0.1843:0.723:0.0	.	.	.	.	I	798;334	ENSP00000429391:L798I;ENSP00000429829:L334I	ENSP00000429829:L334I	L	-	1	0	ASAP1	131142268	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.381000	0.20619	1.357000	0.45904	0.561000	0.74099	CTC		0.582	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		T	131073086	G	T	131073086	2	4	47	1	0	0	0	0	0	0	0	1	1011	929	33	2		2	ASAP1	8	131073086	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5552219	131073086	15290936	1067	5464										
LRRC6	23639	broad.mit.edu	37	chr8	133673745	133673745	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attttgaagatagagaatttTtaaatcccggcaccatttat	6	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:133673745T>G	ENST00000519595.1	-	2	237	c.139A>C	c.(139-141)Aaa>Caa	p.K47Q	LRRC6_ENST00000520446.1_5'UTR|LRRC6_ENST00000518642.1_Missense_Mutation_p.K47Q|LRRC6_ENST00000250173.1_Missense_Mutation_p.K47Q			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	47					cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)		p.K47Q(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			TAGAGAATTTTTAAATCCCGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											44	46	45					8																	133673745		2203	4300	6503	133742927	SO:0001583	missense	23639			U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"leucine rich testes protein"	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.139A>C	8.37:g.133673745T>G	ENSP00000429791:p.Lys47Gln		133742927	Q13648|Q4G183	Missense_Mutation	SNP	ENST00000519595.1	37		.	.	.	.	.	.	.	.	.	.	T	19.97	3.925617	0.73213	.	.	ENSG00000129295	ENST00000519595;ENST00000518642;ENST00000250173;ENST00000395414	T;T;T	0.54479	0.57;0.57;0.57	6.02	6.02	0.97574	.	0.127518	0.64402	D	0.000001	T	0.68641	0.3023	L	0.58101	1.795	0.54753	D	0.999987	D	0.65815	0.995	D	0.68353	0.957	T	0.69495	-0.5130	10	0.54805	T	0.06	-43.2293	15.7743	0.78198	0.0:0.0:0.0:1.0	.	47	Q86X45	LRRC6_HUMAN	Q	47	ENSP00000429791:K47Q;ENSP00000428610:K47Q;ENSP00000250173:K47Q	ENSP00000250173:K47Q	K	-	1	0	LRRC6	133742927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.785000	0.68998	2.321000	0.78463	0.529000	0.55759	AAA		0.353	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472		G	133673745	T	G	133673745	3	3	47	1	0	0	0	0	1	0	0	0	9045	1850	64	4	1305	4	LRRC6	8	133673745	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2600659	133673745	12690277	1068	5465										
FAM135B	51059	broad.mit.edu	37	chr8	139163587	139163587	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctccttgggcacagatgagAaagggagacaggtggcagtg	16	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:139163587A>C	ENST00000395297.1	-	13	3301	c.3131T>G	c.(3130-3132)tTc>tGc	p.F1044C		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1044								p.F1044C(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CACAGATGAGAAAGGGAGACA	0.532										HNSCC(54;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	8											65	64	64					8																	139163587		2203	4300	6503	139232769	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3131T>G	8.37:g.139163587A>C	ENSP00000378710:p.Phe1044Cys		139232769	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	A	21.6	4.170168	0.78452	.	.	ENSG00000147724	ENST00000395297	T	0.23950	1.88	5.32	5.32	0.75619	.	0.056910	0.64402	D	0.000001	T	0.52533	0.1740	M	0.77103	2.36	0.51012	D	0.999906	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.921	T	0.58142	-0.7688	10	0.87932	D	0	-25.1287	14.4636	0.67467	1.0:0.0:0.0:0.0	.	1044;1044;1044	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	C	1044	ENSP00000378710:F1044C	ENSP00000276737:F1044C	F	-	2	0	FAM135B	139232769	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.962000	0.93254	2.020000	0.59435	0.528000	0.53228	TTC		0.532	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139163587	A	C	139163587	3	2	47	1	0	0	0	0	1	0	0	0	5465	246	9	4	1121	4	FAM135B	8	139163587	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	5489842	139163587	7200435	1069	5466										
FLJ43860	389690	broad.mit.edu	37	chr8	142481240	142481240	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgtctgggtcctggcacaGcatccccagtatgcccacca	9	17	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:142481240G>A	ENST00000430863.1	-	0	2001					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5									p.L641L(1)									TCCTGGCACAGCATCCCCAGT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	8											118	124	122					8																	142481240		2036	4189	6225	142550422			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142481240G>A			142550422		Silent	SNP	ENST00000430863.1	37																																																																																					0.542	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		A	142481240	G	A	142481240	1	1	47	0	1	0	0	0	0	0	0	0	5949	962	34	3		3	FLJ43860	8	142481240	RNA	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3317653	142481240	3882782	1070	5467										
CYP11B1	1584	broad.mit.edu	37	chr8	143958608	143958608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcacttctggattcagccgCaatcggttgaagcgccattc	10	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:143958608C>A	ENST00000292427.4	-	3	458	c.426G>T	c.(424-426)ttG>ttT	p.L142F	CYP11B1_ENST00000377675.3_Missense_Mutation_p.L213F|CYP11B1_ENST00000517471.1_Missense_Mutation_p.L142F	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	142					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.L142F(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	GATTCAGCCGCAATCGGTTGA	0.612									Familial Hyperaldosteronism type I																																							1	Substitution - Missense(1)	large_intestine(1)	8											60	48	52					8																	143958608		2203	4300	6503	143955610	SO:0001583	missense	1584	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.426G>T	8.37:g.143958608C>A	ENSP00000292427:p.Leu142Phe		143955610	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	15.11	2.737336	0.49045	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.68479	-0.33;2.7;-0.33	3.74	2.85	0.33270	.	1.123640	0.06894	N	0.804778	T	0.80325	0.4602	M	0.85462	2.755	0.09310	N	1	D;D;D	0.89917	0.999;0.996;1.0	D;D;D	0.79108	0.992;0.985;0.987	T	0.63730	-0.6571	10	0.10111	T	0.7	.	7.8241	0.29305	0.0:0.8749:0.0:0.1251	.	213;142;142	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	F	142;142;213	ENSP00000292427:L142F;ENSP00000428043:L142F;ENSP00000366903:L213F	ENSP00000292427:L142F	L	-	3	2	CYP11B1	143955610	0.008000	0.16893	0.006000	0.13384	0.299000	0.27559	0.417000	0.21214	0.855000	0.35359	-0.266000	0.10368	TTG		0.612	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			A	143958608	C	A	143958608	3	1	47	1	0	0	0	0	1	0	0	0	4151	709	25	2	1113	2	CYP11B1	8	143958608	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1477368	143958608	2405414	1071	5468										
C8orf31	286122	broad.mit.edu	37	chr8	144124639	144124639	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccaccgcattgcagaggtCtcccttgcagcaagagatct	10	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:144124639C>A	ENST00000395172.1	+	3	498	c.146C>A	c.(145-147)tCt>tAt	p.S49Y	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	49								p.S49Y(1)		breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TTGCAGAGGTCTCCCTTGCAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	8											40	43	42					8																	144124639		2203	4300	6503	144196014	SO:0001583	missense	286122				CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.146C>A	8.37:g.144124639C>A	ENSP00000378601:p.Ser49Tyr		144196014	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	37	CCDS6395.1	.	.	.	.	.	.	.	.	.	.	c	11.37	1.618702	0.28801	.	.	ENSG00000177335	ENST00000395172	T	0.55413	0.52	2.38	2.38	0.29361	.	.	.	.	.	T	0.49474	0.1559	N	0.08118	0	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.35450	-0.9788	9	0.87932	D	0	.	8.5538	0.33469	0.0:1.0:0.0:0.0	.	49	Q8N9H6	CH031_HUMAN	Y	49	ENSP00000378601:S49Y	ENSP00000378601:S49Y	S	+	2	0	C8orf31	144196014	0.006000	0.16342	0.007000	0.13788	0.057000	0.15508	0.915000	0.28638	1.680000	0.50976	0.435000	0.28638	TCT		0.617	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687		A	144124639	C	A	144124639	3	1	47	1	0	0	0	0	1	0	0	0	2426	913	32	2	152	2	C8orf31	8	144124639	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	166031	144124639	2239383	1072	5469										
ZNF7	7553	broad.mit.edu	37	chr8	146067469	146067469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcctcatccaccatcagaGaatccacacaggagagaggc	9	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:146067469G>T	ENST00000528372.1	+	5	1217	c.977G>T	c.(976-978)aGa>aTa	p.R326I	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.R230I|ZNF7_ENST00000325241.6_Missense_Mutation_p.R326I|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000446747.2_Missense_Mutation_p.R337I			P17097	ZNF7_HUMAN	zinc finger protein 7	326					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R326I(2)		endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		CACCATCAGAGAATCCACACA	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	8											62	61	61					8																	146067469		2203	4300	6503	146038273	SO:0001583	missense	7553			AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.977G>T	8.37:g.146067469G>T	ENSP00000432724:p.Arg326Ile		146038273	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	37	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932678	0.52866	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	5.04	5.04	0.67666	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000146	T	0.50854	0.1640	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.976;0.976	T	0.52931	-0.8509	9	.	.	.	-27.6824	10.8322	0.46667	0.0875:0.0:0.9125:0.0	.	337;326	B4DT08;P17097	.;ZNF7_HUMAN	I	326;337;230;326	ENSP00000320627:R326I;ENSP00000393260:R337I;ENSP00000439424:R230I;ENSP00000432724:R326I	.	R	+	2	0	ZNF7	146038273	0.000000	0.05858	0.991000	0.47740	0.325000	0.28411	0.003000	0.13083	2.629000	0.89072	0.555000	0.69702	AGA		0.517	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		T	146067469	G	T	146067469	3	4	47	1	0	0	0	0	1	0	0	0	18141	942	33	2	991	2	ZNF7	8	146067469	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1942830	146067469	296553	1073	5470										
ZNF7	7553	broad.mit.edu	37	chr8	146068068	146068068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataaaggagagaagccctacGaatgcctccaatgcggaaaa	10	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr8:146068068G>A	ENST00000528372.1	+	5	1816	c.1576G>A	c.(1576-1578)Gaa>Aaa	p.E526K	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.E430K|ZNF7_ENST00000325241.6_Missense_Mutation_p.E526K|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000446747.2_Missense_Mutation_p.E537K			P17097	ZNF7_HUMAN	zinc finger protein 7	526					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E526K(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		GAAGCCCTACGAATGCCTCCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	88	86					8																	146068068		2203	4300	6503	146038872	SO:0001583	missense	7553			AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1576G>A	8.37:g.146068068G>A	ENSP00000432724:p.Glu526Lys		146038872	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	37	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708122	0.48412	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	4.75	1.88	0.25563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.143577	0.32444	N	0.006095	T	0.06096	0.0158	N	0.01464	-0.85	0.09310	N	0.999999	B;B	0.17465	0.022;0.022	B;B	0.15484	0.013;0.013	T	0.39781	-0.9597	9	.	.	.	-16.5637	7.3618	0.26750	0.4283:0.0:0.5717:0.0	.	537;526	B4DT08;P17097	.;ZNF7_HUMAN	K	526;537;430;526	ENSP00000320627:E526K;ENSP00000393260:E537K;ENSP00000439424:E430K;ENSP00000432724:E526K	.	E	+	1	0	ZNF7	146038872	0.000000	0.05858	0.284000	0.24805	0.891000	0.51852	-0.128000	0.10531	0.593000	0.29745	0.655000	0.94253	GAA		0.443	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		A	146068068	G	A	146068068	3	1	47	1	0	0	0	0	1	0	0	0	18141	1059	37	1	1590	1	ZNF7	8	146068068	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	599	146068068	295954	1074	5471										
C9orf68	55064	broad.mit.edu	37	chr9	4617927	4617927	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgcttgccactgacctttCtctgagaaggggctgatcca	12	11	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:4617927C>A	ENST00000454239.2	-	10	1236	c.991G>T	c.(991-993)Gaa>Taa	p.E331*	SPATA6L_ENST00000381890.5_Intron|SPATA6L_ENST00000475086.1_Nonsense_Mutation_p.E273*|SPATA6L_ENST00000381895.5_Nonsense_Mutation_p.E208*			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	331								p.E331*(1)									ACTGACCTTTCTCTGAGAAGG	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											80	81	81					9																	4617927		1932	4137	6069	4607927	SO:0001587	stop_gained	55064			AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 68"	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.991G>T	9.37:g.4617927C>A	ENSP00000404277:p.Glu331*		4607927	B4DIY4|Q5JVJ5|Q8IY90	Nonsense_Mutation	SNP	ENST00000454239.2	37		.	.	.	.	.	.	.	.	.	.	C	41	9.005029	0.99033	.	.	ENSG00000106686	ENST00000454239;ENST00000475086;ENST00000381895	.	.	.	4.89	4.89	0.63831	.	0.514389	0.17833	N	0.160470	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	13.7445	0.62868	0.0:1.0:0.0:0.0	.	.	.	.	X	331;273;208	.	ENSP00000371319:E208X	E	-	1	0	C9orf68	4607927	0.821000	0.29204	0.977000	0.42913	0.143000	0.21401	0.420000	0.21263	2.699000	0.92147	0.563000	0.77884	GAA		0.522	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985		A	4617927	C	A	4617927	4	1	47	1	0	0	0	0	0	1	0	0	2497	922	32	2	199	2	C9orf68	9	4617927	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09		4617927	136595504	1075	5472										
C9orf68	55064	broad.mit.edu	37	chr9	4618898	4618898	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaggctgtcaagagaagaaGctagaagaaagaggaacagg	14	5	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:4618898G>A	ENST00000454239.2	-	9	1018	c.773C>T	c.(772-774)gCt>gTt	p.A258V	SPATA6L_ENST00000381890.5_Intron|SPATA6L_ENST00000475086.1_Splice_Site_p.A200V|SPATA6L_ENST00000381895.5_Splice_Site_p.A135V			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	258								p.A258V(1)									AAGAGAAGAAGCTAGAAGAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	9											77	70	72					9																	4618898		1827	4089	5916	4608898	SO:0001630	splice_region_variant	55064			AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 68"	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.773-1C>T	9.37:g.4618898G>A			4608898	B4DIY4|Q5JVJ5|Q8IY90	Missense_Mutation	SNP	ENST00000454239.2	37		.	.	.	.	.	.	.	.	.	.	G	15.00	2.702103	0.48307	.	.	ENSG00000106686	ENST00000454239;ENST00000475086;ENST00000381895	T;T;T	0.35048	1.83;1.79;1.33	5.6	4.71	0.59529	.	0.105921	0.42682	N	0.000676	T	0.30541	0.0768	L	0.54323	1.7	0.42596	D	0.993261	P;P;B	0.43973	0.521;0.823;0.028	B;B;B	0.39738	0.204;0.308;0.027	T	0.07966	-1.0745	10	0.15499	T	0.54	.	10.381	0.44113	0.0872:0.0:0.9128:0.0	.	200;135;258	B4DIY4;E7ENB5;Q8N4H0	.;.;CI068_HUMAN	V	258;200;135	ENSP00000404277:A258V;ENSP00000417063:A200V;ENSP00000371319:A135V	ENSP00000371319:A135V	A	-	2	0	C9orf68	4608898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.105000	0.41825	1.627000	0.50400	0.644000	0.83932	GCT		0.313	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985	Missense_Mutation	A	4618898	G	A	4618898	5	1	47	1	0	0	0	0	0	0	1	0	2497	985	34	3	421	3	C9orf68	9	4618898	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	971	4618898	136594533	1076	5473										
INSL6	11172	broad.mit.edu	37	chr9	5185387	5185387	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtatgggctgtaggcttcGaccttctccgaggcctgtgc	14	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:5185387G>A	ENST00000381641.3	-	1	281	c.216C>T	c.(214-216)gtC>gtT	p.V72V		NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	72					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.V72V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		TGTAGGCTTCGACCTTCTCCG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	9											113	116	115					9																	5185387		2203	4300	6503	5175387	SO:0001819	synonymous_variant	11172			AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"relaxin/insulin-like factor 1"	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.216C>T	9.37:g.5185387G>A			5175387	A0AVS0|Q9NS16	Silent	SNP	ENST00000381641.3	37	CCDS6458.1																																																																																				0.542	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179		A	5185387	G	A	5185387	2	1	47	1	0	0	0	0	0	0	0	1	7791	1045	37	1		1	INSL6	9	5185387	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	566489	5185387	136028044	1077	5474										
IL33	90865	broad.mit.edu	37	chr9	6256123	6256123	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attaaagtagactcttctgaGaatttgtgtactgaaaatat	7	4	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:6256123G>T	ENST00000381434.3	+	7	781	c.768G>T	c.(766-768)gaG>gaT	p.E256D	IL33_ENST00000456383.2_Missense_Mutation_p.E214D|IL33_ENST00000417746.2_Missense_Mutation_p.E130D	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	256					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)	p.E256D(1)		breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		ACTCTTCTGAGAATTTGTGTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	9											115	116	116					9																	6256123		2203	4300	6503	6246123	SO:0001583	missense	90865			AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"Interleukins and interleukin receptors"	16028	protein-coding gene	gene with protein product	"DVS27-related protein", "nuclear factor for high endothelial venules", "interleukin-1 family, member 11"	608678	"chromosome 9 open reading frame 26 (NF-HEV)"	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.768G>T	9.37:g.6256123G>T	ENSP00000370842:p.Glu256Asp		6246123	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	G	9.742	1.165187	0.21538	.	.	ENSG00000137033	ENST00000417746;ENST00000456383;ENST00000381434	T;T;T	0.48522	0.81;0.81;0.81	5.13	-3.94	0.04130	.	1.202640	0.06055	N	0.657347	T	0.22820	0.0551	N	0.14661	0.345	0.09310	N	1	B;B;B	0.22211	0.012;0.066;0.066	B;B;B	0.18871	0.013;0.023;0.023	T	0.10382	-1.0632	10	0.23302	T	0.38	-0.5391	1.5195	0.02512	0.3127:0.3202:0.2445:0.1226	.	130;214;256	B4DJ35;B4E1Q9;O95760	.;.;IL33_HUMAN	D	130;214;256	ENSP00000394039:E130D;ENSP00000414238:E214D;ENSP00000370842:E256D	ENSP00000370842:E256D	E	+	3	2	IL33	6246123	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-0.086000	0.11233	-0.865000	0.04073	0.655000	0.94253	GAG		0.388	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439		T	6256123	G	T	6256123	3	4	47	1	0	0	0	0	1	0	0	0	7714	933	33	2	794	2	IL33	9	6256123	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1070736	6256123	134957308	1078	5475										
TPD52L3	89882	broad.mit.edu	37	chr9	6330998	6330998	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgatcttcaataaatacacGttaaatcaaggaaggaatta	6	5	3	1	rs192550349		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:6330998G>A	ENST00000344545.5	+	0	2572				TPD52L3_ENST00000314556.3_Silent_p.T130T	NM_033516.5	NP_277051	Q96J77	TPD55_HUMAN	tumor protein D52-like 3									p.T130T(2)		large_intestine(1)|lung(9)|skin(1)	11		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0198)|Lung(218;0.1)		ATAAATACACGTTAAATCAAG	0.313													G|||	1	0.000199681	0	0	5008	,	,		20283	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	9											102	101	101					9																	6330998		2202	4298	6500	6320998	SO:0001628	intergenic_variant	89882			AY032877	CCDS34984.1, CCDS34985.1, CCDS34986.1	9p24.1	2008-02-05			ENSG00000170777	ENSG00000170777			23382	protein-coding gene	gene with protein product							Standard	NM_033516		Approved	NYD-SP25	uc003zjw.3	Q96J77	OTTHUMG00000019518		9.37:g.6330998G>A			6320998	Q5TCR3|Q5TCR4|Q5TCR5|Q8N4P5|Q8WWF7|Q96M09	Silent	SNP	ENST00000344545.5	37	CCDS34986.1																																																																																				0.313	TPD52L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051658.1	NM_033516		A	6330998	G	A	6330998	1	1	47	0	1	0	0	0	0	0	0	0	16440	1132	40	1		1	TPD52L3	9	6330998	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	74875	6330998	134882433	1079	5476										
MPDZ	8777	broad.mit.edu	37	chr9	13125380	13125380	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catctttgctgtcttcagaaGgctaataaactggcagggtg	11	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:13125380G>T	ENST00000319217.7	-	35	4889	c.4642C>A	c.(4642-4644)Ctt>Att	p.L1548I	MPDZ_ENST00000546205.1_Missense_Mutation_p.L1562I|MPDZ_ENST00000541718.1_Missense_Mutation_p.L1548I|MPDZ_ENST00000381015.4_Missense_Mutation_p.L1548I|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000381022.2_Missense_Mutation_p.L1548I|MPDZ_ENST00000536827.1_Missense_Mutation_p.L1515I|MPDZ_ENST00000447879.1_Missense_Mutation_p.L1515I|MPDZ_ENST00000538841.1_Missense_Mutation_p.L407I	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1548	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.L1548I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		GTCTTCAGAAGGCTAATAAAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											88	86	87					9																	13125380		1897	4115	6012	13115380	SO:0001583	missense	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4642C>A	9.37:g.13125380G>T	ENSP00000320006:p.Leu1548Ile		13115380	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	G	13.02	2.112270	0.37242	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.83	5.83	0.93111	PDZ/DHR/GLGF (4);	0.000000	0.42172	D	0.000742	T	0.57301	0.2044	L	0.42245	1.32	0.80722	D	1	D;P;P;D;D;D;D	0.89917	1.0;0.875;0.877;1.0;0.999;0.996;0.975	D;P;P;D;D;D;D	0.75484	0.985;0.683;0.705;0.986;0.983;0.928;0.925	T	0.46048	-0.9219	10	0.11794	T	0.64	.	14.2892	0.66265	0.0707:0.0:0.9293:0.0	.	1515;407;253;1515;1428;1548;1548	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970	.;.;.;.;.;.;MPDZ_HUMAN	I	1548;1548;1548;117;484;407;1515;1515;1548;1428;1562	ENSP00000320006:L1548I;ENSP00000439807:L1548I;ENSP00000370410:L1548I;ENSP00000415964:L117I;ENSP00000444230:L484I;ENSP00000444717:L407I;ENSP00000444151:L1515I;ENSP00000415208:L1515I;ENSP00000370403:L1548I;ENSP00000446358:L1562I	ENSP00000320006:L1548I	L	-	1	0	MPDZ	13115380	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	4.296000	0.59055	2.761000	0.94854	0.650000	0.86243	CTT		0.418	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		T	13125380	G	T	13125380	3	4	47	1	0	0	0	0	1	0	0	0	9752	1000	35	2	1531	2	MPDZ	9	13125380	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6794382	13125380	128088051	1080	5477										
MPDZ	8777	broad.mit.edu	37	chr9	13247771	13247771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgcagcttggtttgcaagcGctctgctgcatgcagggccc	13	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:13247771G>A	ENST00000319217.7	-	3	293	c.46C>T	c.(46-48)Cgc>Tgc	p.R16C	MPDZ_ENST00000546205.1_Missense_Mutation_p.R16C|MPDZ_ENST00000541718.1_Missense_Mutation_p.R16C|MPDZ_ENST00000381015.4_Missense_Mutation_p.R16C|MPDZ_ENST00000381022.2_Missense_Mutation_p.R16C|MPDZ_ENST00000536827.1_Missense_Mutation_p.R16C|MPDZ_ENST00000447879.1_Missense_Mutation_p.R16C	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	16	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.R16C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		GTTTGCAAGCGCTCTGCTGCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	9											250	238	242					9																	13247771		1917	4135	6052	13237771	SO:0001583	missense	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.46C>T	9.37:g.13247771G>A	ENSP00000320006:p.Arg16Cys		13237771	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	G	18.70	3.680113	0.68042	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.20463	2.11;2.07;2.07;2.08;2.11;2.11;2.11	5.68	5.68	0.88126	.	0.000000	0.45867	D	0.000339	T	0.44808	0.1311	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.33445	-0.9868	10	0.87932	D	0	.	13.6986	0.62595	0.0:0.0:0.8459:0.1541	.	16;16;16	B7ZMI4;O75970-3;O75970-2	.;.;.	C	16	ENSP00000320006:R16C;ENSP00000439807:R16C;ENSP00000370410:R16C;ENSP00000444151:R16C;ENSP00000415208:R16C;ENSP00000370403:R16C;ENSP00000446358:R16C	ENSP00000320006:R16C	R	-	1	0	MPDZ	13237771	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.975000	0.70475	2.690000	0.91761	0.491000	0.48974	CGC		0.488	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13247771	G	A	13247771	3	1	47	1	0	0	0	0	1	0	0	0	9752	1087	38	1	6255	1	MPDZ	9	13247771	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	122391	13247771	127965660	1081	5478										
FREM1	158326	broad.mit.edu	37	chr9	14842347	14842347	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccctggcttcttcatgatctCcccagcctgtggaggctttg	10	14	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:14842347C>T	ENST00000380880.3	-	9	2488	c.1705G>A	c.(1705-1707)Gag>Aag	p.E569K	FREM1_ENST00000422223.2_Missense_Mutation_p.E569K|FREM1_ENST00000380881.4_Missense_Mutation_p.E570K			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	569					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.E570K(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTCATGATCTCCCCAGCCTGT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	9											112	110	111					9																	14842347		1950	4134	6084	14832347	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1705G>A	9.37:g.14842347C>T	ENSP00000370262:p.Glu569Lys		14832347	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.051403	0.75960	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.48522	0.81;0.81;0.81	5.93	5.04	0.67666	.	0.151090	0.64402	D	0.000020	T	0.70596	0.3242	M	0.86420	2.815	0.51767	D	0.999938	D	0.61080	0.989	P	0.61070	0.883	T	0.76069	-0.3094	10	0.48119	T	0.1	-21.9832	17.391	0.87431	0.0:0.8754:0.1246:0.0	.	569	Q5H8C1	FREM1_HUMAN	K	570;569;569	ENSP00000370263:E570K;ENSP00000412940:E569K;ENSP00000370262:E569K	ENSP00000370257:E572K	E	-	1	0	FREM1	14832347	1.000000	0.71417	0.997000	0.53966	0.603000	0.37013	4.652000	0.61454	1.541000	0.49316	-0.127000	0.14921	GAG		0.483	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14842347	C	T	14842347	3	4	47	1	0	0	0	0	1	0	0	0	6063	864	30	3	5000	3	FREM1	9	14842347	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1594576	14842347	126371084	1082	5479										
FREM1	158326	broad.mit.edu	37	chr9	14857648	14857648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagatgctgataacgaaggCccatcagcaggaactcctca	9	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:14857648C>T	ENST00000380880.3	-	5	1514	c.731G>A	c.(730-732)gGc>gAc	p.G244D	FREM1_ENST00000422223.2_Missense_Mutation_p.G244D|FREM1_ENST00000380881.4_Missense_Mutation_p.G244D			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	244					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.G244D(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATAACGAAGGCCCATCAGCAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											167	163	164					9																	14857648		1905	4128	6033	14847648	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.731G>A	9.37:g.14857648C>T	ENSP00000370262:p.Gly244Asp		14847648	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.385615	0.82792	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.15952	2.38;2.39;2.39	6.17	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.40398	0.1115	M	0.69358	2.11	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.08289	-1.0729	10	0.87932	D	0	-19.2211	15.01	0.71542	0.0:0.9327:0.0:0.0673	.	244	Q5H8C1	FREM1_HUMAN	D	244	ENSP00000370263:G244D;ENSP00000412940:G244D;ENSP00000370262:G244D	ENSP00000370257:G244D	G	-	2	0	FREM1	14847648	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	4.514000	0.60482	2.941000	0.99782	0.655000	0.94253	GGC		0.473	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14857648	C	T	14857648	3	4	47	1	0	0	0	0	1	0	0	0	6063	739	26	3	5990	3	FREM1	9	14857648	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15301	14857648	126355783	1083	5480										
HAUS6	54801	broad.mit.edu	37	chr9	19058679	19058679	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaggctaaacattccaaatCttgcttgcaaattactttct	5	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:19058679C>A	ENST00000380502.3	-	16	2553	c.2086G>T	c.(2086-2088)Gat>Tat	p.D696Y	HAUS6_ENST00000380496.1_Missense_Mutation_p.D560Y	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	696					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.D696Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CATTCCAAATCTTGCTTGCAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											49	51	50					9																	19058679		2201	4277	6478	19048679	SO:0001583	missense	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.2086G>T	9.37:g.19058679C>A	ENSP00000369871:p.Asp696Tyr		19048679	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.902484	0.52227	.	.	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.27104	1.69;1.7	5.04	3.16	0.36331	.	0.628614	0.16355	N	0.218008	T	0.40522	0.1120	M	0.62723	1.935	0.30276	N	0.791819	D;D;D	0.71674	0.998;0.983;0.998	P;P;P	0.60415	0.874;0.847;0.874	T	0.36939	-0.9727	10	0.72032	D	0.01	-4.8349	8.727	0.34476	0.0:0.7542:0.0:0.2458	.	661;560;696	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	Y	696;560	ENSP00000369871:D696Y;ENSP00000369865:D560Y	ENSP00000369865:D560Y	D	-	1	0	HAUS6	19048679	0.481000	0.25941	0.995000	0.50966	0.916000	0.54674	0.741000	0.26202	1.240000	0.43803	0.453000	0.30009	GAT		0.433	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		A	19058679	C	A	19058679	3	1	47	1	0	0	0	0	1	0	0	0	6991	913	32	2	789	2	HAUS6	9	19058679	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4201031	19058679	122154752	1084	5481										
KIAA1797	54914	broad.mit.edu	37	chr9	20740295	20740295	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaatgcaagctcttaaggaAggacaaggtggggaaaagaa	13	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:20740295A>C	ENST00000380249.1	+	7	712	c.348A>C	c.(346-348)gaA>gaC	p.E116D	FOCAD_ENST00000338382.6_Missense_Mutation_p.E116D	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	116						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.E116D(1)									CTCTTAAGGAAGGACAAGGTG	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	86	85					9																	20740295		2203	4299	6502	20730295	SO:0001583	missense	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.348A>C	9.37:g.20740295A>C	ENSP00000369599:p.Glu116Asp		20730295	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235492	0.39498	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.23147	1.92;1.92	5.55	5.55	0.83447	Domain of unknown function DUF3730 (1);	0.261285	0.37669	N	0.001998	T	0.17577	0.0422	N	0.24115	0.695	0.27148	N	0.961483	P	0.47191	0.891	P	0.45753	0.492	T	0.09552	-1.0669	10	0.14252	T	0.57	-4.7294	7.1599	0.25659	0.8682:0.0:0.1318:0.0	.	116	Q5VW36	K1797_HUMAN	D	116	ENSP00000369599:E116D;ENSP00000344307:E116D	ENSP00000344307:E116D	E	+	3	2	KIAA1797	20730295	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.138000	0.50570	2.107000	0.64212	0.459000	0.35465	GAA		0.274	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		C	20740295	A	C	20740295	3	2	47	1	0	0	0	0	1	0	0	0	8279	69	3	4	362	4	KIAA1797	9	20740295	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1681616	20740295	120473136	1085	5482										
IFNA10	3446	broad.mit.edu	37	chr9	21206947	21206947	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtctgtccttcaggcaggaGaaaggagagattcttcccat	11	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:21206947G>T	ENST00000357374.2	-	1	195	c.150C>A	c.(148-150)ttC>ttA	p.F50L		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	50					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.F50L(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TCAGGCAGGAGAAAGGAGAGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	9											110	116	114					9																	21206947		2203	4299	6502	21196947	SO:0001583	missense	3446				CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"Interferons"	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.150C>A	9.37:g.21206947G>T	ENSP00000369566:p.Phe50Leu		21196947	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	.	.	.	.	.	.	.	.	.	.	-	7.996	0.754353	0.15778	.	.	ENSG00000186803	ENST00000357374	T	0.04706	3.57	3.65	-0.277	0.12898	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.417150	0.04304	N	0.347745	T	0.04952	0.0133	L	0.37697	1.125	0.09310	N	1	B	0.06786	0.001	B	0.17098	0.017	T	0.46541	-0.9184	10	0.15952	T	0.53	.	7.6685	0.28445	0.107:0.377:0.516:0.0	.	50	P01566	IFN10_HUMAN	L	50	ENSP00000369566:F50L	ENSP00000369566:F50L	F	-	3	2	IFNA10	21196947	0.000000	0.05858	0.002000	0.10522	0.614000	0.37383	0.260000	0.18424	0.141000	0.18875	0.499000	0.49734	TTC		0.512	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171		T	21206947	G	T	21206947	3	4	47	1	0	0	0	0	1	0	0	0	7553	933	33	2	423	2	IFNA10	9	21206947	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	466652	21206947	120006484	1086	5483										
KLHL9	55958	broad.mit.edu	37	chr9	21333625	21333625	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acattctactgtggccagttCaccagctgcactgcgcccac	8	16	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:21333625C>A	ENST00000359039.4	-	1	1754	c.1234G>T	c.(1234-1236)Gaa>Taa	p.E412*	KLHL9_ENST00000537938.1_Nonsense_Mutation_p.E344*			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	412					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)		p.E412*(1)		endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		GTGGCCAGTTCACCAGCTGCA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											114	104	107					9																	21333625		2203	4300	6503	21323625	SO:0001587	stop_gained	55958			AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.1234G>T	9.37:g.21333625C>A	ENSP00000351933:p.Glu412*		21323625	Q8TCQ2	Nonsense_Mutation	SNP	ENST00000359039.4	37	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	C	37	6.225254	0.97390	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	15.4894	0.75593	0.0:1.0:0.0:0.0	.	.	.	.	X	412;344	.	ENSP00000351933:E412X	E	-	1	0	KLHL9	21323625	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.005000	0.70716	2.323000	0.78572	0.655000	0.94253	GAA		0.453	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		A	21333625	C	A	21333625	4	1	47	1	0	0	0	0	0	1	0	0	8417	835	29	2	623	2	KLHL9	9	21333625	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	126678	21333625	119879806	1087	5484										
PLAA	9373	broad.mit.edu	37	chr9	26935019	26935019	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattatactcaccagtatttTtgtggccttttagaatataa	5	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:26935019T>G	ENST00000397292.3	-	2	752	c.335A>C	c.(334-336)aAa>aCa	p.K112T	PLAA_ENST00000520884.1_Missense_Mutation_p.K112T	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	112					inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)	p.K55T(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		ACCAGTATTTTTGTGGCCTTT	0.333																																					Melanoma(175;2670 2735 14091 35526)											1	Substitution - Missense(1)	large_intestine(1)	9											88	91	90					9																	26935019		2203	4300	6503	26925019	SO:0001583	missense	9373			AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.335A>C	9.37:g.26935019T>G	ENSP00000380460:p.Lys112Thr		26925019	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Missense_Mutation	SNP	ENST00000397292.3	37	CCDS35000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.815|8.815	0.936087|0.936087	0.18206|0.18206	.|.	.|.	ENSG00000137055|ENSG00000137055	ENST00000397292;ENST00000520884|ENST00000523212	T;T|.	0.55052|.	0.54;0.54|.	5.32|5.32	5.32|5.32	0.75619|0.75619	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.044564|.	0.85682|.	D|.	0.000000|.	T|T	0.21761|0.21761	0.0524|0.0524	N|N	0.01352|0.01352	-0.895|-0.895	0.58432|0.58432	D|D	0.999997|0.999997	B;B|.	0.14805|.	0.011;0.001|.	B;B|.	0.19666|.	0.026;0.004|.	T|T	0.23904|0.23904	-1.0175|-1.0175	10|5	0.06494|.	T|.	0.89|.	-16.3051|-16.3051	12.4451|12.4451	0.55647|0.55647	0.0:0.0:0.1395:0.8605|0.0:0.0:0.1395:0.8605	.|.	112;112|.	E5RIM3;Q9Y263|.	.;PLAP_HUMAN|.	T|H	112|88	ENSP00000380460:K112T;ENSP00000429372:K112T|.	ENSP00000380460:K112T|.	K|Q	-|-	2|3	0|2	PLAA|PLAA	26925019|26925019	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	5.918000|5.918000	0.69996|0.69996	1.995000|1.995000	0.58328|0.58328	0.482000|0.482000	0.46254|0.46254	AAA|CAA		0.333	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		G	26935019	T	G	26935019	3	3	47	1	0	0	0	0	1	0	0	0	12042	1841	64	4	2104	4	PLAA	9	26935019	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	5601394	26935019	114278412	1088	5485										
TEK	7010	broad.mit.edu	37	chr9	27206730	27206730	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggcaattttggccaagttCttaaggcgcgcatcaagaag	12	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:27206730C>A	ENST00000380036.4	+	15	2957	c.2515C>A	c.(2515-2517)Ctt>Att	p.L839I	TEK_ENST00000406359.4_Missense_Mutation_p.L796I|TEK_ENST00000519097.1_Missense_Mutation_p.L691I	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	839	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L839I(1)		breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TGGCCAAGTTCTTAAGGCGCG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											83	75	78					9																	27206730		2203	4300	6503	27196730	SO:0001583	missense	7010			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2515C>A	9.37:g.27206730C>A	ENSP00000369375:p.Leu839Ile		27196730	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.602351	0.28534	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.69561	-0.41;-0.41;-0.41	5.9	5.0	0.66597	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40728	N	0.001023	T	0.64789	0.2630	N	0.16567	0.415	0.44424	D	0.997343	B;P;B;D	0.69078	0.003;0.557;0.017;0.997	B;P;B;D	0.91635	0.037;0.576;0.089;0.999	T	0.59979	-0.7352	10	0.09338	T	0.73	.	11.6247	0.51138	0.1251:0.8095:0.0:0.0654	.	691;872;796;839	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	I	691;839;796	ENSP00000430686:L691I;ENSP00000369375:L839I;ENSP00000383977:L796I	ENSP00000369375:L839I	L	+	1	0	TEK	27196730	0.976000	0.34144	0.809000	0.32408	0.990000	0.78478	2.071000	0.41500	1.500000	0.48636	0.637000	0.83480	CTT		0.453	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			A	27206730	C	A	27206730	3	1	47	1	0	0	0	0	1	0	0	0	15790	913	32	2	2573	2	TEK	9	27206730	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	271711	27206730	114006701	1089	5486										
LINGO2	158038	broad.mit.edu	37	chr9	27950531	27950531	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctgggatggcgatcaatcGccttctgtgacagctaacag	11	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:27950531G>A	ENST00000379992.2	-	6	588	c.139C>T	c.(139-141)Cga>Tga	p.R47*	LINGO2_ENST00000308675.3_Nonsense_Mutation_p.R47*	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	47	LRRNT.					integral component of membrane (GO:0016021)		p.R47*(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		GCGATCAATCGCCTTCTGTGA	0.493																																																2	Substitution - Nonsense(2)	large_intestine(2)	9											129	127	128					9																	27950531		2203	4300	6503	27940531	SO:0001587	stop_gained	158038			AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.139C>T	9.37:g.27950531G>A	ENSP00000369328:p.Arg47*		27940531	A8K4K7|B2RPM5|Q6ZMD0	Nonsense_Mutation	SNP	ENST00000379992.2	37	CCDS6524.1	.	.	.	.	.	.	.	.	.	.	G	36	5.710938	0.96821	.	.	ENSG00000174482	ENST00000379992;ENST00000308675	.	.	.	5.74	1.46	0.22682	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8426	0.78861	0.0:0.0:0.5204:0.4796	.	.	.	.	X	47	.	.	R	-	1	2	LINGO2	27940531	1.000000	0.71417	0.172000	0.22920	0.962000	0.63368	4.589000	0.61006	0.396000	0.25283	0.561000	0.74099	CGA		0.493	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		A	27950531	G	A	27950531	4	1	47	1	0	0	0	0	0	1	0	0	8839	1095	38	1	1685	1	LINGO2	9	27950531	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	743801	27950531	113262900	1090	5487										
TOPORS	10210	broad.mit.edu	37	chr9	32542526	32542526	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaccttgatctgcttgtgCtttcactacttagagacaga	9	9	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:32542526C>T	ENST00000360538.2	-	3	2113	c.1997G>A	c.(1996-1998)aGc>aAc	p.S666N	TOPORS_ENST00000379858.1_Missense_Mutation_p.S601N	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	666	Arg-rich.|Interaction with TOP1.|Interaction with p53/TP53.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S666N(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TCTGCTTGTGCTTTCACTACT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											280	262	268					9																	32542526		2203	4300	6503	32532526	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1997G>A	9.37:g.32542526C>T	ENSP00000353735:p.Ser666Asn		32532526	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	8.815	0.936113	0.18206	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.23552	1.9;2.01	6.16	5.26	0.73747	.	0.000000	0.64402	D	0.000009	T	0.22205	0.0535	L	0.29908	0.895	0.31274	N	0.691363	B	0.26195	0.144	B	0.21708	0.036	T	0.11421	-1.0588	10	0.54805	T	0.06	-10.9893	16.5364	0.84373	0.0:0.869:0.131:0.0	.	666	Q9NS56	TOPRS_HUMAN	N	666;601	ENSP00000353735:S666N;ENSP00000369187:S601N	ENSP00000353735:S666N	S	-	2	0	TOPORS	32532526	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	5.348000	0.66004	1.604000	0.50143	-0.182000	0.12963	AGC		0.398	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32542526	C	T	32542526	3	4	47	1	0	0	0	0	1	0	0	0	16410	797	28	3	1144	3	TOPORS	9	32542526	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4591995	32542526	108670905	1091	5488										
TAF1L	138474	broad.mit.edu	37	chr9	32631919	32631919	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgaatgaatttctcatctTttgtagtccgtatgcgcaca	7	8	2	2	rs556381126		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:32631919T>G	ENST00000242310.4	-	1	3748	c.3659A>C	c.(3658-3660)aAa>aCa	p.K1220T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1220					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.K1220T(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTTCTCATCTTTTGTAGTCCG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											143	133	136					9																	32631919		2203	4300	6503	32621919	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3659A>C	9.37:g.32631919T>G	ENSP00000418379:p.Lys1220Thr		32621919	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.929461	0.34096	.	.	ENSG00000122728	ENST00000242310	T	0.62941	-0.01	0.479	0.479	0.16796	.	0.088024	0.85682	D	0.000000	T	0.54759	0.1878	M	0.68952	2.095	0.52501	D	0.999959	B	0.25809	0.135	B	0.31390	0.129	T	0.49826	-0.8898	10	0.46703	T	0.11	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1220	Q8IZX4	TAF1L_HUMAN	T	1220	ENSP00000418379:K1220T	ENSP00000418379:K1220T	K	-	2	0	TAF1L	32621919	1.000000	0.71417	0.981000	0.43875	0.333000	0.28666	5.066000	0.64351	0.426000	0.26116	0.164000	0.16699	AAA		0.448	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32631919	T	G	32631919	3	3	47	1	0	0	0	0	1	0	0	0	15562	1841	64	4	1825	4	TAF1L	9	32631919	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	89393	32631919	108581512	1092	5489										
ARID3C	138715	broad.mit.edu	37	chr9	34627855	34627855	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcttcttcagcatcttcctCttcctcagccccaacattcc	2	18	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:34627855C>A	ENST00000378909.2	-	1	249	c.157G>T	c.(157-159)Gag>Tag	p.E53*		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	53	Glu-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E53*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		gcatcttcctcttcctcAGCC	0.692																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											24	20	21					9																	34627855		2190	4278	6468	34617855	SO:0001587	stop_gained	138715				CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.157G>T	9.37:g.34627855C>A	ENSP00000368189:p.Glu53*		34617855		Nonsense_Mutation	SNP	ENST00000378909.2	37	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	c	35	5.547224	0.96488	.	.	ENSG00000205143	ENST00000378909	.	.	.	5.15	5.15	0.70609	.	1.023330	0.07809	N	0.957793	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-12.1614	15.4913	0.75607	0.0:1.0:0.0:0.0	.	.	.	.	X	53	.	ENSP00000368189:E53X	E	-	1	0	ARID3C	34617855	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	4.842000	0.62831	2.675000	0.91044	0.486000	0.48141	GAG		0.692	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		A	34627855	C	A	34627855	4	1	47	1	0	0	0	0	0	1	0	0	918	922	32	2	1108	2	ARID3C	9	34627855	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1995936	34627855	106585576	1093	5490										
C9orf131	138724	broad.mit.edu	37	chr9	35045410	35045410	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaaactctaaggttctggtCtcaggcaagagaaaggacaa	10	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:35045410C>A	ENST00000312292.5	+	2	2831	c.2784C>A	c.(2782-2784)gtC>gtA	p.V928V	C9orf131_ENST00000354479.5_Silent_p.V855V|C9orf131_ENST00000421362.2_Silent_p.V880V|FLJ00273_ENST00000595331.1_5'Flank	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	928								p.V928V(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			AGGTTCTGGTCTCAGGCAAGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	9											133	135	135					9																	35045410		2203	4300	6503	35035410	SO:0001819	synonymous_variant	138724			BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.2784C>A	9.37:g.35045410C>A			35035410	A6NLE6|E9PB26|Q86XC6|Q9UF74	Silent	SNP	ENST00000312292.5	37	CCDS6572.2																																																																																				0.532	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		A	35045410	C	A	35045410	2	1	47	1	0	0	0	0	0	0	0	1	2463	900	32	2		2	C9orf131	9	35045410	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	417555	35045410	106168021	1094	5491										
RUSC2	9853	broad.mit.edu	37	chr9	35555271	35555271	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgctgctcaagtctcagtCccagctccctcaggggaacc	9	17	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:35555271C>T	ENST00000455600.1	+	3	2798	c.2229C>T	c.(2227-2229)gtC>gtT	p.V743V		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	743						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)	p.V743V(1)		NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			AAGTCTCAGTCCCAGCTCCCT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	9											29	33	32					9																	35555271		2203	4300	6503	35545271	SO:0001819	synonymous_variant	9853			AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.2229C>T	9.37:g.35555271C>T			35545271	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	37	CCDS35008.1																																																																																				0.672	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		T	35555271	C	T	35555271	2	4	47	1	0	0	0	0	0	0	0	1	13788	842	30	3		3	RUSC2	9	35555271	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	509861	35555271	105658160	1095	5492										
CD72	971	broad.mit.edu	37	chr9	35610743	35610743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttacattttgagctttgagCataagtcctaaaaagtagta	8	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:35610743C>T	ENST00000396757.1	-	9	1122	c.958G>A	c.(958-960)Gct>Act	p.A320T	CD72_ENST00000259633.4_Missense_Mutation_p.A320T|CD72_ENST00000490239.1_5'UTR|MIR4667_ENST00000578933.1_RNA			P21854	CD72_HUMAN	CD72 molecule	320	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor binding (GO:0005102)|transmembrane signaling receptor activity (GO:0004888)	p.A320T(1)		large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GAGCTTTGAGCATAAGTCCTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	101	108					9																	35610743		2203	4300	6503	35600743	SO:0001583	missense	971				CCDS6581.1	9p	2008-07-21	2006-03-28		ENSG00000137101	ENSG00000137101		"CD molecules"	1696	protein-coding gene	gene with protein product		107272	"CD72 antigen"			2044654, 1711157	Standard	NM_001782		Approved	LYB2, CD72b	uc003zxb.2	P21854	OTTHUMG00000019870	ENST00000396757.1:c.958G>A	9.37:g.35610743C>T	ENSP00000379980:p.Ala320Thr		35600743		Missense_Mutation	SNP	ENST00000396757.1	37	CCDS6581.1	.	.	.	.	.	.	.	.	.	.	C	3.618	-0.078245	0.07184	.	.	ENSG00000137101	ENST00000396757;ENST00000396759;ENST00000259633	T;T	0.18016	2.24;2.24	4.08	-8.17	0.01057	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	4.335170	0.00763	N	0.001159	T	0.07324	0.0185	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.16289	0.015	T	0.25882	-1.0119	10	0.20519	T	0.43	22.1415	1.2381	0.01957	0.1369:0.2975:0.2062:0.3594	.	320	P21854	CD72_HUMAN	T	320	ENSP00000379980:A320T;ENSP00000259633:A320T	ENSP00000259633:A320T	A	-	1	0	CD72	35600743	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.620000	0.00207	-2.636000	0.00432	-0.742000	0.03525	GCT		0.433	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	NM_001782		T	35610743	C	T	35610743	3	4	47	1	0	0	0	0	1	0	0	0	3040	710	25	3	125	3	CD72	9	35610743	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	55472	35610743	105602688	1096	5493										
TLN1	7094	broad.mit.edu	37	chr9	35699390	35699390	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctggatgagctcagtgacGgaaccagccacacgctttga	12	12	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:35699390G>A	ENST00000314888.9	-	51	7190	c.6837C>T	c.(6835-6837)tcC>tcT	p.S2279S	TLN1_ENST00000540444.1_Silent_p.S2167S	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2279					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.S2279S(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCAGTGACGGAACCAGCCA	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	9											150	118	129					9																	35699390		2203	4300	6503	35689390	SO:0001819	synonymous_variant	7094			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6837C>T	9.37:g.35699390G>A			35689390	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																				0.567	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35699390	G	A	35699390	2	1	47	1	0	0	0	0	0	0	0	1	15986	1103	39	1		1	TLN1	9	35699390	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	88647	35699390	105514041	1097	5494										
RECK	8434	broad.mit.edu	37	chr9	36121662	36121662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatcctgatcattcccgtcGatcactatccaaaagctctg	6	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:36121662G>A	ENST00000377966.3	+	20	3237	c.2671G>A	c.(2671-2673)Gat>Aat	p.D891N		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	891					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D891N(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CATTCCCGTCGATCACTATCC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											205	175	185					9																	36121662		2203	4300	6503	36111662	SO:0001583	missense	8434			E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.2671G>A	9.37:g.36121662G>A	ENSP00000367202:p.Asp891Asn		36111662	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969586	0.74246	.	.	ENSG00000122707	ENST00000377966	T	0.42131	0.98	5.66	5.66	0.87406	.	0.054173	0.64402	D	0.000001	T	0.36880	0.0983	L	0.38531	1.155	0.58432	D	0.999999	D;D	0.58970	0.984;0.984	B;B	0.43251	0.413;0.413	T	0.06716	-1.0811	10	0.25106	T	0.35	-21.2466	17.2407	0.87013	0.0:0.0:1.0:0.0	.	891;891	A8K9D8;O95980	.;RECK_HUMAN	N	891	ENSP00000367202:D891N	ENSP00000367202:D891N	D	+	1	0	RECK	36111662	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.587000	0.98229	2.658000	0.90341	0.655000	0.94253	GAT		0.453	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			A	36121662	G	A	36121662	3	1	47	1	0	0	0	0	1	0	0	0	13237	1058	37	1	2749	1	RECK	9	36121662	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	422272	36121662	105091769	1098	5495										
FRMPD1	22844	broad.mit.edu	37	chr9	37707475	37707475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagaccctcatccctgtgcGacacacagtaaagatagaca	7	13	2	3	rs139830645	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:37707475G>A	ENST00000539465.1	+	3	757	c.164G>A	c.(163-165)cGa>cAa	p.R55Q	FRMPD1_ENST00000377765.3_Missense_Mutation_p.R55Q|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	55						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.R55Q(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		ATCCCTGTGCGACACACAGTA	0.507													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		18968	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						G	GLN/ARG	77,4329	67.0+/-104.6	0,77,2126	112	113	113		164	2.5	1	9	dbSNP_134	113	0,8600		0,0,4300	yes	missense	FRMPD1	NM_014907.2	43	0,77,6426	AA,AG,GG		0.0,1.7476,0.592	benign	55/1579	37707475	77,12929	2203	4300	6503	37697475	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.164G>A	9.37:g.37707475G>A	ENSP00000444411:p.Arg55Gln		37697475	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	17.28	3.348352	0.61183	0.017476	0.0	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000359927	T;T;T	0.38722	1.12;1.12;1.66	5.97	2.51	0.30379	PDZ/DHR/GLGF (1);	0.298611	0.33438	N	0.004916	T	0.12689	0.0308	N	0.22421	0.69	0.80722	D	1	B	0.16802	0.019	B	0.08055	0.003	T	0.04650	-1.0936	10	0.49607	T	0.09	-4.6826	5.2918	0.15731	0.6086:0.0:0.3914:0.0	.	55	Q5SYB0	FRPD1_HUMAN	Q	55	ENSP00000366995:R55Q;ENSP00000444411:R55Q;ENSP00000439868:R55Q	ENSP00000439868:R55Q	R	+	2	0	FRMPD1	37697475	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	1.301000	0.33447	0.711000	0.32018	0.655000	0.94253	CGA		0.507	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37707475	G	A	37707475	3	1	47	1	0	0	0	0	1	0	0	0	6076	1058	37	1	170	1	FRMPD1	9	37707475	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1585813	37707475	103505956	1099	5496										
FRMPD1	22844	broad.mit.edu	37	chr9	37733737	37733737	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctattaagcaacttatttCtgctgcccagctacgtttaa	5	11	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:37733737C>A	ENST00000539465.1	+	12	1726	c.1133C>A	c.(1132-1134)tCt>tAt	p.S378Y	FRMPD1_ENST00000377765.3_Missense_Mutation_p.S378Y|FRMPD1_ENST00000536622.1_Missense_Mutation_p.S200Y|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000541302.1_Missense_Mutation_p.S247Y			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	378	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.S378Y(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CAACTTATTTCTGCTGCCCAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											138	139	139					9																	37733737		2203	4300	6503	37723737	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1133C>A	9.37:g.37733737C>A	ENSP00000444411:p.Ser378Tyr		37723737	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376052	0.82682	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55	5.16	5.16	0.70880	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.124913	0.56097	D	0.000032	D	0.87688	0.6240	M	0.65498	2.005	0.80722	D	1	P;P	0.48589	0.912;0.879	P;P	0.54210	0.745;0.635	D	0.89181	0.3544	10	0.87932	D	0	-14.7429	16.1394	0.81513	0.0:1.0:0.0:0.0	.	247;378	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	Y	378;378;200;247	ENSP00000366995:S378Y;ENSP00000444411:S378Y;ENSP00000437762:S200Y;ENSP00000444804:S247Y	ENSP00000366995:S378Y	S	+	2	0	FRMPD1	37723737	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.373000	0.52394	2.400000	0.81607	0.609000	0.83330	TCT		0.343	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37733737	C	A	37733737	3	1	47	1	0	0	0	0	1	0	0	0	6076	913	32	2	1175	2	FRMPD1	9	37733737	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	26262	37733737	103479694	1100	5497										
DCAF10	79269	broad.mit.edu	37	chr9	37860057	37860057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatctcaggagtttcaccacGaaatagtcttgaagtcgtaa	8	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:37860057G>A	ENST00000377724.3	+	6	1543	c.1178G>A	c.(1177-1179)cGa>cAa	p.R393Q	DCAF10_ENST00000242323.7_Missense_Mutation_p.R356Q|DCAF10_ENST00000483167.1_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	393					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.R393Q(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						GTTTCACCACGAAATAGTCTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											111	99	103					9																	37860057		2203	4300	6503	37850057	SO:0001583	missense	79269			BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	23686	protein-coding gene	gene with protein product			"WD repeat domain 32"	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1178G>A	9.37:g.37860057G>A	ENSP00000366953:p.Arg393Gln		37850057	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Missense_Mutation	SNP	ENST00000377724.3	37	CCDS6613.2	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524282	0.85600	.	.	ENSG00000122741	ENST00000377724;ENST00000242323	T;T	0.73469	-0.59;-0.75	5.81	5.81	0.92471	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	L	0.54323	1.7	0.58432	D	0.999997	D;D	0.89917	0.997;1.0	D;D	0.79108	0.947;0.992	T	0.75955	-0.3135	10	0.13108	T	0.6	.	17.5687	0.87928	0.0:0.0:1.0:0.0	.	356;393	Q5QP82-2;Q5QP82	.;DCA10_HUMAN	Q	393;356	ENSP00000366953:R393Q;ENSP00000242323:R356Q	ENSP00000242323:R356Q	R	+	2	0	DCAF10	37850057	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.110000	0.94302	2.759000	0.94783	0.591000	0.81541	CGA		0.438	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345		A	37860057	G	A	37860057	3	1	47	1	0	0	0	0	1	0	0	0	4267	1058	37	1	1200	1	DCAF10	9	37860057	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	126320	37860057	103353374	1101	5498										
ZNF658	26149	broad.mit.edu	37	chr9	40774221	40774221	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acattcattatgttcaccaaAtttatctccagcttgtgttt	4	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:40774221A>C	ENST00000602553.1	-	5	1348	c.1054T>G	c.(1054-1056)Ttt>Gtt	p.F352V	ZNF658_ENST00000377626.3_Missense_Mutation_p.F352V|ZNF658_ENST00000441795.1_Missense_Mutation_p.F350V			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	352					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F352V(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGTTCACCAAATTTATCTCCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											86	91	89					9																	40774221		2202	4280	6482	40764221	SO:0001583	missense	26149			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1054T>G	9.37:g.40774221A>C	ENSP00000473484:p.Phe352Val		40764221	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	a	8.557	0.876798	0.17395	.	.	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.14391	2.51;2.51	1.81	-3.62	0.04543	.	.	.	.	.	T	0.05868	0.0153	N	0.12182	0.205	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.11329	0.006;0.001	T	0.34650	-0.9820	9	0.66056	D	0.02	.	1.5643	0.02601	0.2194:0.1835:0.4152:0.1819	.	352;352	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	V	350;352	ENSP00000408462:F350V;ENSP00000366853:F352V	ENSP00000366853:F352V	F	-	1	0	ZNF658	40764221	0.000000	0.05858	0.000000	0.03702	0.232000	0.25224	0.149000	0.16243	-1.348000	0.02205	0.315000	0.21342	TTT		0.358	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		C	40774221	A	C	40774221	3	2	47	1	0	0	0	0	1	0	0	0	18108	101	4	4	2129	4	ZNF658	9	40774221	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2914164	40774221	100439210	1102	5499										
PGM5	5239	broad.mit.edu	37	chr9	71006474	71006474	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggaccttatgtgagaaaagTtctgtgtgatgagctggggg	17	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:71006474T>G	ENST00000396396.1	+	5	951	c.722T>G	c.(721-723)gTt>gGt	p.V241G	PGM5_ENST00000604870.2_3'UTR|PGM5_ENST00000396392.1_Missense_Mutation_p.V241G	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	241					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)	p.V241G(1)		endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						GTGAGAAAAGTTCTGTGTGAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											6	6	6					9																	71006474		1910	3993	5903	70196294	SO:0001583	missense	5239			L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"phosphoglucomutase-related protein"	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.722T>G	9.37:g.71006474T>G	ENSP00000379678:p.Val241Gly		70196294	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Missense_Mutation	SNP	ENST00000396396.1	37	CCDS6622.2	.	.	.	.	.	.	.	.	.	.	.	15.68	2.904505	0.52333	.	.	ENSG00000154330	ENST00000396396;ENST00000396392;ENST00000377314;ENST00000431583	T;T;T	0.68479	-0.33;-0.33;-0.33	4.92	4.92	0.64577	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (1);Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (1);	0.114545	0.56097	D	0.000022	T	0.69691	0.3139	M	0.83774	2.66	0.80722	D	1	B	0.02656	0.0	B	0.12837	0.008	T	0.71027	-0.4711	10	0.87932	D	0	.	13.5311	0.61623	0.0:0.0:0.0:1.0	.	241	Q15124	PGM5_HUMAN	G	241;241;192;158	ENSP00000379678:V241G;ENSP00000379674:V241G;ENSP00000394864:V158G	ENSP00000366531:V192G	V	+	2	0	PGM5	70196294	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.935000	0.87658	1.844000	0.53588	0.454000	0.30748	GTT		0.438	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965		G	71006474	T	G	71006474	3	3	47	1	0	0	0	0	1	0	0	0	11832	1725	60	4	740	4	PGM5	9	71006474	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	30232253	71006474	70206957	1103	5500										
FAM189A2	9413	broad.mit.edu	37	chr9	71992598	71992598	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccctgatgattttgtgccGcctgtgcctcccccttccta	8	16	0	2	rs562098000		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:71992598G>A	ENST00000257515.8	+	6	852	c.432G>A	c.(430-432)ccG>ccA	p.P144P	FAM189A2_ENST00000455972.1_Silent_p.P144P|FAM189A2_ENST00000303068.7_5'UTR	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2	144						integral component of membrane (GO:0016021)		p.P144P(1)		endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						ATTTTGTGCCGCCTGTGCCTC	0.532													G|||	1	0.000199681	0	0	5008	,	,		19018	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9											132	112	118					9																	71992598		2203	4300	6503	71182418	SO:0001819	synonymous_variant	9413			L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"chromosome 9 open reading frame 61"	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.432G>A	9.37:g.71992598G>A			71182418	Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Silent	SNP	ENST00000257515.8	37	CCDS6629.1																																																																																				0.532	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816		A	71992598	G	A	71992598	2	1	47	1	0	0	0	0	0	0	0	1	5532	1074	38	1		1	FAM189A2	9	71992598	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	986124	71992598	69220833	1104	5501										
TRPM3	80036	broad.mit.edu	37	chr9	73168150	73168150	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggccatgatggccggcacGatccaagctcctgtcttgca	11	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:73168150G>A	ENST00000377111.2	-	22	3507	c.3264C>T	c.(3262-3264)atC>atT	p.I1088I	TRPM3_ENST00000357533.2_Silent_p.I1092I|TRPM3_ENST00000396285.1_Silent_p.I947I|TRPM3_ENST00000360823.2_Silent_p.I950I|TRPM3_ENST00000377110.3_Silent_p.I1088I|TRPM3_ENST00000377106.1_Silent_p.I960I|TRPM3_ENST00000423814.3_Silent_p.I1115I|TRPM3_ENST00000396292.4_Silent_p.I960I|TRPM3_ENST00000408909.2_Silent_p.I947I|TRPM3_ENST00000377105.1_Silent_p.I947I|TRPM3_ENST00000358082.3_Silent_p.I950I|TRPM3_ENST00000396280.5_Silent_p.I937I	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1113					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.I960I(1)|p.I1092I(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGGCCGGCACGATCCAAGCTC	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	9											85	66	72					9																	73168150		2203	4300	6503	72357970	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.3264C>T	9.37:g.73168150G>A			72357970	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	G	8.535	0.871945	0.17322	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.81	-5.03	0.02973	.	.	.	.	.	T	0.65196	0.2668	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66941	-0.5796	4	.	.	.	-13.48	16.0966	0.81129	0.7022:0.0:0.2978:0.0	.	.	.	.	C	937	.	.	R	-	1	0	TRPM3	72357970	0.056000	0.20664	0.968000	0.41197	0.948000	0.59901	-0.565000	0.05929	-0.788000	0.04504	-0.768000	0.03414	CGT		0.532	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73168150	G	A	73168150	2	1	47	1	0	0	0	0	0	0	0	1	16627	1048	37	1		1	TRPM3	9	73168150	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1175552	73168150	68045281	1105	5502										
TMEM2	23670	broad.mit.edu	37	chr9	74315640	74315640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgcacaggctcatattcttCgattttggataatgagccat	8	8	2	1	rs548434215	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:74315640C>T	ENST00000377044.4	-	19	3834	c.3295G>A	c.(3295-3297)Gaa>Aaa	p.E1099K	TMEM2_ENST00000377066.5_Missense_Mutation_p.E1036K|TMEM2_ENST00000396272.3_Missense_Mutation_p.E92K	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1099					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.E1099K(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		TCATATTCTTCGATTTTGGAT	0.428													C|||	2	0.000399361	0	0	5008	,	,		18903	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											120	110	113					9																	74315640		2203	4300	6503	73505460	SO:0001583	missense	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3295G>A	9.37:g.74315640C>T	ENSP00000366243:p.Glu1099Lys		73505460	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288438	0.80803	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272;ENST00000377055	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	6.17	6.17	0.99709	.	0.186658	0.56097	D	0.000021	T	0.54382	0.1855	M	0.66297	2.02	0.53005	D	0.999961	P;P	0.49635	0.773;0.926	B;P	0.45310	0.223;0.476	T	0.46317	-0.9200	10	0.22706	T	0.39	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1099;1036	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	K	1099;1036;92;128	ENSP00000366243:E1099K;ENSP00000366266:E1036K;ENSP00000379569:E92K;ENSP00000366254:E128K	ENSP00000366243:E1099K	E	-	1	0	TMEM2	73505460	0.462000	0.25791	0.868000	0.34077	0.945000	0.59286	3.255000	0.51484	2.941000	0.99782	0.655000	0.94253	GAA		0.428	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		T	74315640	C	T	74315640	3	4	47	1	0	0	0	0	1	0	0	0	16160	893	31	1	880	1	TMEM2	9	74315640	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1147490	74315640	66897791	1106	5503										
PRUNE2	158471	broad.mit.edu	37	chr9	79461537	79461537	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggaactcaacgttggcatcGctctgctcaaccggattaat	9	12	3	0	rs553816550		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:79461537G>A	ENST00000376718.3	-	4	525	c.402C>T	c.(400-402)agC>agT	p.S134S	PRUNE2_ENST00000376713.3_Silent_p.S134S|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	134					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.S134S(2)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CGTTGGCATCGCTCTGCTCAA	0.483													G|||	1	0.000199681	0	0	5008	,	,		18176	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	9											115	112	113					9																	79461537		2203	4300	6503	78651357	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.402C>T	9.37:g.79461537G>A			78651357	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1																																																																																				0.483	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79461537	G	A	79461537	2	1	47	1	0	0	0	0	0	0	0	1	12675	1078	38	1		1	PRUNE2	9	79461537	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5145897	79461537	61751894	1107	5504										
VPS13A	23230	broad.mit.edu	37	chr9	79888237	79888237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaacatcacagatttcacaGaaaataattcctctcttgga	6	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:79888237G>T	ENST00000360280.3	+	24	2729	c.2469G>T	c.(2467-2469)caG>caT	p.Q823H	VPS13A_ENST00000376636.3_Missense_Mutation_p.Q823H|VPS13A_ENST00000376634.4_Missense_Mutation_p.Q823H|VPS13A_ENST00000357409.5_Missense_Mutation_p.Q823H	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	823					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.Q823H(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AGATTTCACAGAAAATAATTC	0.284																																																2	Substitution - Missense(2)	large_intestine(2)	9											59	64	62					9																	79888237		2202	4294	6496	79078057	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2469G>T	9.37:g.79888237G>T	ENSP00000353422:p.Gln823His		79078057	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996775	0.35226	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.48201	0.98;0.82;0.89;0.98	5.43	4.34	0.51931	.	1.175070	0.06376	N	0.714394	T	0.59582	0.2204	L	0.54323	1.7	0.80722	D	1	D;P;D;D	0.62365	0.964;0.956;0.991;0.974	P;P;P;P	0.57502	0.75;0.674;0.822;0.758	T	0.51434	-0.8706	10	0.45353	T	0.12	.	9.9643	0.41715	0.1077:0.0:0.8923:0.0	.	823;823;823;823	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	H	823	ENSP00000365821:Q823H;ENSP00000365823:Q823H;ENSP00000353422:Q823H;ENSP00000349985:Q823H	ENSP00000349985:Q823H	Q	+	3	2	VPS13A	79078057	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	2.399000	0.44495	2.544000	0.85801	0.563000	0.77884	CAG		0.284	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79888237	G	T	79888237	3	4	47	1	0	0	0	0	1	0	0	0	17229	933	33	2	2563	2	VPS13A	9	79888237	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	426700	79888237	61325194	1108	5505										
FLJ46321	389763	broad.mit.edu	37	chr9	84609498	84609498	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcatatcatatgaagaacaAgaaagttcctgggaaaaggg	11	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:84609498A>C	ENST00000344803.2	+	4	4160	c.4113A>C	c.(4111-4113)caA>caC	p.Q1371H		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1371					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.Q1371H(2)									ATGAAGAACAAGAAAGTTCCT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	9											28	25	26					9																	84609498		1840	4085	5925	83799318	SO:0001583	missense	389763				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4113A>C	9.37:g.84609498A>C	ENSP00000341988:p.Gln1371His		83799318		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758121	0.31137	.	.	ENSG00000214929	ENST00000344803	T	0.08720	3.06	3.13	-0.695	0.11291	.	.	.	.	.	T	0.04770	0.0129	N	0.14661	0.345	0.09310	N	1	P	0.50943	0.94	B	0.44224	0.444	T	0.31251	-0.9950	9	0.66056	D	0.02	-8.3498	2.2062	0.03936	0.5051:0.0:0.2691:0.2258	.	1371	Q6ZQQ2	F75D1_HUMAN	H	1371	ENSP00000341988:Q1371H	ENSP00000341988:Q1371H	Q	+	3	2	FAM75D1	83799318	0.007000	0.16637	0.001000	0.08648	0.003000	0.03518	0.306000	0.19279	-0.133000	0.11537	0.533000	0.62120	CAA		0.418	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84609498	A	C	84609498	3	2	47	1	0	0	0	0	1	0	0	0	5951	69	3	4	4127	4	FLJ46321	9	84609498	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4721261	84609498	56603933	1109	5506										
RASEF	158158	broad.mit.edu	37	chr9	85605307	85605307	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccattttcccaaactttaccGagcaaggtgcagaacagcct	7	13	0	1	rs189903199		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:85605307G>A	ENST00000376447.3	-	16	2376	c.2116C>T	c.(2116-2118)Cga>Tga	p.R706*		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	706					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.R706*(2)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						AAACTTTACCGAGCAAGGTGC	0.383													G|||	1	0.000199681	0	0	5008	,	,		18270	0.001		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(1)|kidney(1)	9											131	117	121					9																	85605307		2203	4300	6503	84795127	SO:0001630	splice_region_variant	158158			AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.2117+1C>T	9.37:g.85605307G>A			84795127	A6NC29|Q96N04	Nonsense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	39	7.357333	0.98235	.	.	ENSG00000165105	ENST00000376447	.	.	.	5.73	2.73	0.32206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.6287	0.39765	0.0668:0.0:0.6822:0.251	.	.	.	.	X	706	.	ENSP00000365630:R706X	R	-	1	2	RASEF	84795127	1.000000	0.71417	0.968000	0.41197	0.349000	0.29174	3.426000	0.52778	0.738000	0.32606	0.655000	0.94253	CGA		0.383	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573	Nonsense_Mutation	A	85605307	G	A	85605307	5	1	47	1	0	0	0	0	0	0	1	0	13105	1072	37	1	114	1	RASEF	9	85605307	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	995809	85605307	55608124	1110	5507										
KIF27	55582	broad.mit.edu	37	chr9	86506359	86506359	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtcactgacaggttaagttTtgttagttcttcactcagtt	8	7	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:86506359T>G	ENST00000297814.2	-	6	1803	c.1660A>C	c.(1660-1662)Aaa>Caa	p.K554Q	KIF27_ENST00000334204.2_Missense_Mutation_p.K554Q|KIF27_ENST00000413982.1_Missense_Mutation_p.K554Q|KIF27_ENST00000376347.1_5'Flank	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	554					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K554Q(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						AGGTTAAGTTTTGTTAGTTCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	82	85					9																	86506359		2203	4298	6501	85696179	SO:0001583	missense	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1660A>C	9.37:g.86506359T>G	ENSP00000297814:p.Lys554Gln		85696179	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.471595	0.63737	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.58358	0.34;0.34;0.34	5.07	5.07	0.68467	.	0.197462	0.34386	N	0.004005	T	0.53674	0.1811	L	0.51422	1.61	0.25545	N	0.98714	P;P;D	0.59767	0.952;0.921;0.986	P;P;P	0.51701	0.677;0.52;0.593	T	0.49698	-0.8912	10	0.33141	T	0.24	.	9.9448	0.41602	0.0:0.0803:0.0:0.9197	.	554;554;554	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	Q	554	ENSP00000297814:K554Q;ENSP00000401688:K554Q;ENSP00000333928:K554Q	ENSP00000297814:K554Q	K	-	1	0	KIF27	85696179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.151000	0.42263	2.134000	0.65973	0.528000	0.53228	AAA		0.358	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		G	86506359	T	G	86506359	3	3	47	1	0	0	0	0	1	0	0	0	8317	1850	64	4	2597	4	KIF27	9	86506359	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	901052	86506359	54707072	1111	5508										
KIF27	55582	broad.mit.edu	37	chr9	86518334	86518334	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggctttgcaaagcttctcGaagcaatttaatctcaaatt	6	9	2	0	rs371692315		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:86518334G>A	ENST00000297814.2	-	4	1242	c.1099C>T	c.(1099-1101)Cga>Tga	p.R367*	KIF27_ENST00000334204.2_Nonsense_Mutation_p.R367*|KIF27_ENST00000413982.1_Nonsense_Mutation_p.R367*	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	367					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R367*(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						AAAGCTTCTCGAAGCAATTTA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	9						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	123	127	126		1099	4.7	1	9		126	0,8600		0,0,4300	no	stop-gained	KIF27	NM_017576.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		367/1402	86518334	1,13005	2203	4300	6503	85708154	SO:0001587	stop_gained	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1099C>T	9.37:g.86518334G>A	ENSP00000297814:p.Arg367*		85708154	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Nonsense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	G	37	6.448000	0.97577	2.27E-4	0.0	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	.	.	.	5.56	4.65	0.58169	.	0.000000	0.47093	D	0.000258	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	13.3835	0.60783	0.0:0.0:0.7137:0.2863	.	.	.	.	X	367	.	ENSP00000297814:R367X	R	-	1	2	KIF27	85708154	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.091000	0.41691	1.317000	0.45149	0.655000	0.94253	CGA		0.443	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86518334	G	A	86518334	4	1	47	1	0	0	0	0	0	1	0	0	8317	1066	37	1	3166	1	KIF27	9	86518334	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	11975	86518334	54695097	1112	5509										
SLC28A3	64078	broad.mit.edu	37	chr9	86917179	86917179	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agacagcatctcatcaattcGatgttcgtatttggccatca	7	10	3	1	rs542312574		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:86917179G>A	ENST00000376238.4	-	5	509	c.460C>T	c.(460-462)Cga>Tga	p.R154*	SLC28A3_ENST00000537648.1_Nonsense_Mutation_p.R85*	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	154					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)	p.R154*(1)		endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	TCATCAATTCGATGTTCGTAT	0.453																																					Ovarian(106;425 1539 34835 42413 43572)											1	Substitution - Nonsense(1)	large_intestine(1)	9											121	110	114					9																	86917179		2203	4300	6503	86106999	SO:0001587	stop_gained	64078			AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.460C>T	9.37:g.86917179G>A	ENSP00000365413:p.Arg154*		86106999	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Nonsense_Mutation	SNP	ENST00000376238.4	37	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653356	0.47362	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	.	.	.	5.33	5.33	0.75918	.	0.745599	0.12769	N	0.440684	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-0.8791	11.3464	0.49563	0.0:0.0:0.719:0.281	.	.	.	.	X	154;85	.	ENSP00000365413:R154X	R	-	1	2	SLC28A3	86106999	0.237000	0.23815	0.008000	0.14137	0.007000	0.05969	3.297000	0.51810	2.775000	0.95449	0.655000	0.94253	CGA		0.453	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		A	86917179	G	A	86917179	4	1	47	1	0	0	0	0	0	1	0	0	14570	1066	37	1	1671	1	SLC28A3	9	86917179	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	398845	86917179	54296252	1113	5510										
NTRK2	4915	broad.mit.edu	37	chr9	87339179	87339179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggctccttaaggataactaAcatttcatccgatgacagtg	9	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:87339179A>G	ENST00000323115.4	+	7	1114	c.761A>G	c.(760-762)aAc>aGc	p.N254S	NTRK2_ENST00000277120.3_Missense_Mutation_p.N254S|NTRK2_ENST00000304053.6_Missense_Mutation_p.N254S|NTRK2_ENST00000395882.1_Missense_Mutation_p.N254S|NTRK2_ENST00000376213.1_Missense_Mutation_p.N254S|NTRK2_ENST00000359847.3_Missense_Mutation_p.N254S|NTRK2_ENST00000376208.1_Missense_Mutation_p.N254S|NTRK2_ENST00000376214.1_Missense_Mutation_p.N254S|NTRK2_ENST00000395866.2_Missense_Mutation_p.N98S			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	254	Ig-like C2-type 1.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)	p.N254S(3)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	AGGATAACTAACATTTCATCC	0.398										TSP Lung(25;0.17)																																						3	Substitution - Missense(3)	large_intestine(3)	9											162	153	156					9																	87339179		2203	4300	6503	86528999	SO:0001583	missense	4915			AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.761A>G	9.37:g.87339179A>G	ENSP00000314586:p.Asn254Ser		86528999	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	37	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.173949	0.78452	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.28	4.14	0.48551	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.098626	0.64402	D	0.000002	T	0.50888	0.1642	L	0.52364	1.645	0.49915	D	0.999833	D;D;D;D;P;P;D;D	0.59357	0.985;0.968;0.968;0.974;0.955;0.944;0.98;0.968	P;P;P;D;P;P;P;P	0.65140	0.814;0.854;0.889;0.932;0.829;0.737;0.834;0.889	T	0.38950	-0.9637	10	0.18276	T	0.48	.	10.7625	0.46272	0.9252:0.0:0.0748:0.0	.	98;254;254;254;254;254;300;254	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	S	254;254;254;254;254;254;254;254;98	ENSP00000365387:N254S;ENSP00000365386:N254S;ENSP00000379221:N254S;ENSP00000365381:N254S;ENSP00000306167:N254S;ENSP00000277120:N254S;ENSP00000314586:N254S;ENSP00000352906:N254S;ENSP00000379207:N98S	ENSP00000277120:N254S	N	+	2	0	NTRK2	86528999	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.986000	0.70563	2.126000	0.65437	0.383000	0.25322	AAC		0.398	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87339179	A	G	87339179	3	3	47	1	0	0	0	0	1	0	0	0	10738	43	2	4	787	4	NTRK2	9	87339179	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	422000	87339179	53874252	1114	5511										
DAPK1	1612	broad.mit.edu	37	chr9	90261452	90261452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttgctcattaaaagaggctCgagaatcgatgtccaggata	11	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:90261452C>T	ENST00000408954.3	+	13	1543	c.1208C>T	c.(1207-1209)tCg>tTg	p.S403L	DAPK1_ENST00000469640.2_Missense_Mutation_p.S403L|DAPK1_ENST00000358077.5_Missense_Mutation_p.S403L|DAPK1_ENST00000491893.1_Missense_Mutation_p.S403L|DAPK1_ENST00000472284.1_Missense_Mutation_p.S403L	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	403					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S403L(2)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						AAAAGAGGCTCGAGAATCGAT	0.358									Chronic Lymphocytic Leukemia, Familial Clustering of																																							2	Substitution - Missense(2)	large_intestine(2)	9											91	85	87					9																	90261452		1846	4080	5926	89451272	SO:0001583	missense	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.1208C>T	9.37:g.90261452C>T	ENSP00000386135:p.Ser403Leu		89451272	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441798	0.63067	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4	5.02	4.13	0.48395	Ankyrin repeat-containing domain (4);	0.165128	0.25461	N	0.030519	T	0.12305	0.0299	N	0.21508	0.67	0.41307	D	0.987089	P;B;B	0.49307	0.922;0.0;0.0	B;B;B	0.39185	0.293;0.002;0.001	T	0.06427	-1.0827	10	0.72032	D	0.01	.	13.814	0.63281	0.0:0.9263:0.0:0.0737	.	403;403;403	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	L	403	ENSP00000350785:S403L;ENSP00000417076:S403L;ENSP00000418885:S403L;ENSP00000386135:S403L;ENSP00000419026:S403L	ENSP00000350785:S403L	S	+	2	0	DAPK1	89451272	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.894000	0.75655	1.490000	0.48466	0.655000	0.94253	TCG		0.358	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		T	90261452	C	T	90261452	3	4	47	1	0	0	0	0	1	0	0	0	4241	893	31	1	1254	1	DAPK1	9	90261452	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2922273	90261452	50951979	1115	5512										
NOL8	55035	broad.mit.edu	37	chr9	95069207	95069207	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgatcctctgtttgtagaaTtgcttaagttgatttgcaaa	8	6	1	3	rs371775904		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:95069207T>G	ENST00000535387.1	-	9	2671	c.2672A>C	c.(2671-2673)aAt>aCt	p.N891T	NOL8_ENST00000545558.1_Missense_Mutation_p.N929T|NOL8_ENST00000358855.4_Missense_Mutation_p.N861T|NOL8_ENST00000542053.1_Missense_Mutation_p.N861T|NOL8_ENST00000442668.2_Missense_Mutation_p.N929T					nucleolar protein 8									p.N929T(1)|p.N931T(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						GTTTGTAGAATTGCTTAAGTT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	9											179	175	176					9																	95069207		1836	4097	5933	94109028	SO:0001583	missense	55035			AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2672A>C	9.37:g.95069207T>G	ENSP00000441300:p.Asn891Thr		94109028		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	T	9.722	1.160058	0.21454	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33	5.77	-3.81	0.04294	.	0.779066	0.12678	N	0.448226	T	0.27169	0.0666	L	0.38838	1.175	0.09310	N	0.999997	P;P	0.41978	0.767;0.666	B;B	0.44044	0.439;0.252	T	0.20974	-1.0259	10	0.07813	T	0.8	-8.4161	14.2432	0.65971	0.0:0.5462:0.0:0.4538	.	861;929	Q76FK4-2;Q76FK4	.;NOL8_HUMAN	T	929;893;861;929;891;861;929	ENSP00000401177:N929T;ENSP00000351723:N861T;ENSP00000441140:N929T;ENSP00000441300:N891T;ENSP00000440709:N861T;ENSP00000414112:N929T	ENSP00000351723:N861T	N	-	2	0	NOL8	94109028	0.000000	0.05858	0.005000	0.12908	0.970000	0.65996	-1.662000	0.01970	-0.889000	0.03950	-0.334000	0.08254	AAT		0.348	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		G	95069207	T	G	95069207	3	3	47	1	0	0	0	0	1	0	0	0	10558	1493	52	4	745	4	NOL8	9	95069207	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	4807755	95069207	46144224	1116	5513										
OGN	4969	broad.mit.edu	37	chr9	95148531	95148531	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtaaattaagaggcacggaTtccagggcattatggtccaa	12	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:95148531T>G	ENST00000262551.4	-	6	1098	c.678A>C	c.(676-678)gaA>gaC	p.E226D	OGN_ENST00000375561.5_Missense_Mutation_p.E226D|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	226					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)		p.E226D(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						GAGGCACGGATTCCAGGGCAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	9											197	189	192					9																	95148531		2203	4300	6503	94188352	SO:0001583	missense	4969			AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.678A>C	9.37:g.95148531T>G	ENSP00000262551:p.Glu226Asp		94188352	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	37	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	T	5.993	0.367071	0.11352	.	.	ENSG00000106809	ENST00000262551;ENST00000375561	D;D	0.83992	-1.79;-1.79	5.29	0.437	0.16555	.	0.045275	0.85682	D	0.000000	T	0.59142	0.2172	N	0.12422	0.21	0.44454	D	0.997381	B;B	0.20052	0.034;0.041	B;B	0.19391	0.02;0.025	T	0.44667	-0.9313	10	0.06625	T	0.88	.	5.1728	0.15120	0.1256:0.2736:0.0:0.6008	.	284;226	B4DI63;P20774	.;MIME_HUMAN	D	226	ENSP00000262551:E226D;ENSP00000364711:E226D	ENSP00000262551:E226D	E	-	3	2	OGN	94188352	0.989000	0.36119	1.000000	0.80357	0.969000	0.65631	0.127000	0.15790	0.170000	0.19704	0.533000	0.62120	GAA		0.368	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		G	95148531	T	G	95148531	3	3	47	1	0	0	0	0	1	0	0	0	10877	1490	52	4	226	4	OGN	9	95148531	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	79324	95148531	46064900	1117	5514										
C9orf102	375748	broad.mit.edu	37	chr9	98660163	98660163	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggctgcagttttgcataaAaagggaactcgtgaggatat	12	6	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:98660163A>C	ENST00000288985.7	+	3	842	c.537A>C	c.(535-537)aaA>aaC	p.K179N	ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	179	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)	p.K179N(1)									TTTTGCATAAAAAGGGAACTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	114	111					9																	98660163		2203	4298	6501	97699984	SO:0001583	missense	375748			BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"chromosome 9 open reading frame 102", "excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.537A>C	9.37:g.98660163A>C	ENSP00000288985:p.Lys179Asn		97699984	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.183769	0.57800	.	.	ENSG00000182150	ENST00000288985	D	0.93189	-3.18	4.83	2.51	0.30379	DEAD-like helicase (2);SNF2-related (1);	0.201870	0.31859	N	0.006945	D	0.94032	0.8088	L	0.50919	1.6	0.80722	D	1	D	0.67145	0.996	D	0.72338	0.977	D	0.91588	0.5284	10	0.46703	T	0.11	-11.1855	8.2548	0.31748	0.6906:0.0:0.3094:0.0	.	179	Q5T890	RAD26_HUMAN	N	179	ENSP00000288985:K179N	ENSP00000288985:K179N	K	+	3	2	C9orf102	97699984	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.559000	0.45888	0.362000	0.24319	0.459000	0.35465	AAA		0.343	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895		C	98660163	A	C	98660163	3	2	47	1	0	0	0	0	1	0	0	0	2451	11	1	4	547	4	C9orf102	9	98660163	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3511632	98660163	42553268	1118	5515										
ZNF782	158431	broad.mit.edu	37	chr9	99580476	99580476	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttctccccagtgtgagttCtctgatgccctctgagattt	9	12	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:99580476C>A	ENST00000481138.1	-	6	2490	c.1829G>T	c.(1828-1830)aGa>aTa	p.R610I	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.R478I	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	610					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R610I(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				AGTGTGAGTTCTCTGATGCCC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											126	121	123					9																	99580476		2203	4300	6503	98620297	SO:0001583	missense	158431			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.1829G>T	9.37:g.99580476C>A	ENSP00000419397:p.Arg610Ile		98620297	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	17.09|17.09	3.301194|3.301194	0.60195|0.60195	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338	.|T;T	.|0.02446	.|4.29;4.29	3.06|3.06	2.15|2.15	0.27550|0.27550	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.36628	.|N	.|0.002489	T|T	0.08846|0.08846	0.0219|0.0219	L|L	0.60067|0.60067	1.865|1.865	0.37450|0.37450	D|D	0.914787|0.914787	.|D	.|0.61080	.|0.989	.|D	.|0.65233	.|0.933	T|T	0.09400|0.09400	-1.0676|-1.0676	5|10	.|0.59425	.|D	.|0.04	.|.	8.5101|8.5101	0.33213|0.33213	0.0:0.8787:0.0:0.1213|0.0:0.8787:0.0:0.1213	.|.	.|610	.|Q6ZMW2	.|ZN782_HUMAN	D|I	598|610;478	.|ENSP00000419397:R610I;ENSP00000440624:R478I	.|ENSP00000419397:R610I	E|R	-|-	3|2	2|0	ZNF782|ZNF782	98620297|98620297	0.000000|0.000000	0.05858|0.05858	0.999000|0.999000	0.59377|0.59377	0.993000|0.993000	0.82548|0.82548	-0.093000|-0.093000	0.11111|0.11111	0.848000|0.848000	0.35191|0.35191	0.655000|0.655000	0.94253|0.94253	GAG|AGA		0.453	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		A	99580476	C	A	99580476	3	1	47	1	0	0	0	0	1	0	0	0	18194	913	32	2	274	2	ZNF782	9	99580476	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	920313	99580476	41632955	1119	5516										
ZNF782	158431	broad.mit.edu	37	chr9	99581812	99581812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccatttgtcacaaacattacGctcatgagccttttcttttg	5	11	3	1	rs137898408		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:99581812G>A	ENST00000481138.1	-	6	1154	c.493C>T	c.(493-495)Cgt>Tgt	p.R165C	ZNF782_ENST00000466833.1_5'UTR|ZNF782_ENST00000535338.1_Missense_Mutation_p.R33C	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	165			R -> H (in dbSNP:rs4645656).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R165C(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				CAAACATTACGCTCATGAGCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	CYS/ARG	0,4406		0,0,2203	83	85	84		493	-2.7	0	9	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF782	NM_001001662.1	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	165/700	99581812	1,13005	2203	4300	6503	98621633	SO:0001583	missense	158431			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.493C>T	9.37:g.99581812G>A	ENSP00000419397:p.Arg165Cys		98621633	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.542|6.542	0.468270|0.468270	0.12461|0.12461	0.0|0.0	1.16E-4|1.16E-4	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338;ENST00000478850	.|T;T;T	.|0.05855	.|3.55;3.38;6.32	3.38|3.38	-2.74|-2.74	0.05932|0.05932	.|.	.|.	.|.	.|.	.|.	T|T	0.01523|0.01523	0.0049|0.0049	N|N	0.00621|0.00621	-1.32|-1.32	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.47355|0.47355	-0.9124|-0.9124	5|9	.|0.17369	.|T	.|0.5	.|.	4.5855|4.5855	0.12280|0.12280	0.452:0.3186:0.2294:0.0|0.452:0.3186:0.2294:0.0	.|.	.|165	.|Q6ZMW2	.|ZN782_HUMAN	V|C	153|165;33;165	.|ENSP00000419397:R165C;ENSP00000440624:R33C;ENSP00000417577:R165C	.|ENSP00000417577:R165C	A|R	-|-	2|1	0|0	ZNF782|ZNF782	98621633|98621633	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.111000|0.111000	0.19643|0.19643	0.481000|0.481000	0.22260|0.22260	-0.574000|-0.574000	0.05990|0.05990	-0.893000|-0.893000	0.02921|0.02921	GCG|CGT		0.433	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		A	99581812	G	A	99581812	3	1	47	1	0	0	0	0	1	0	0	0	18194	1087	38	1	1610	1	ZNF782	9	99581812	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1336	99581812	41631619	1120	5517										
FAM22G	441457	broad.mit.edu	37	chr9	99700232	99700232	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagatccacagatggatttCttggccctaagccaggagct	10	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:99700232C>A	ENST00000372322.3	+	6	1410	c.1389C>A	c.(1387-1389)ttC>ttA	p.F463L	NUTM2G_ENST00000354649.3_Missense_Mutation_p.F463L|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	463								p.F463L(1)									AGATGGATTTCTTGGCCCTAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	57	56					9																	99700232		1840	4065	5905	98740053	SO:0001583	missense	441457				CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"family with sequence similarity 22, member G"	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1389C>A	9.37:g.99700232C>A	ENSP00000361397:p.Phe463Leu		98740053	A6NNI5|Q5VZR3	Missense_Mutation	SNP	ENST00000372322.3	37	CCDS55329.1	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.205705	0.00292	.	.	ENSG00000188152	ENST00000354649;ENST00000372322;ENST00000417159;ENST00000375230	T;T	0.19532	2.14;2.94	1.01	0.0242	0.14140	.	1.630770	0.03760	N	0.258047	T	0.10078	0.0247	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.20538	-1.0272	10	0.02654	T	1	.	4.4592	0.11657	0.3741:0.6259:0.0:0.0	.	463	Q5VZR2-2	.	L	463;463;312;344	ENSP00000346670:F463L;ENSP00000361397:F463L	ENSP00000346670:F463L	F	+	3	2	FAM22G	98740053	0.000000	0.05858	0.001000	0.08648	0.099000	0.18886	-0.325000	0.07976	0.025000	0.15241	-0.431000	0.05894	TTC		0.577	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741		A	99700232	C	A	99700232	3	1	47	1	0	0	0	0	1	0	0	0	5562	912	32	2	1411	2	FAM22G	9	99700232	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	118420	99700232	41513199	1121	5518										
HEMGN	55363	broad.mit.edu	37	chr9	100692500	100692500	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatatttcaggtgaatattCttcaagctgggatgtttctt	9	5	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:100692500C>A	ENST00000259456.3	-	4	1320	c.1177G>T	c.(1177-1179)Gaa>Taa	p.E393*		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	393					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.E393*(1)		NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				GGTGAATATTCTTCAAGCTGG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											185	196	192					9																	100692500		2203	4300	6503	99732321	SO:0001587	stop_gained	55363			AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.1177G>T	9.37:g.100692500C>A	ENSP00000259456:p.Glu393*		99732321	Q6XAR3|Q86XY5|Q9NPC0	Nonsense_Mutation	SNP	ENST00000259456.3	37	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	C	18.40	3.616364	0.66672	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.32	0.26	0.15588	.	0.896444	0.09033	U	0.858535	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-0.379	2.8593	0.05582	0.2005:0.4701:0.0:0.3294	.	.	.	.	X	393	.	ENSP00000259456:E393X	E	-	1	0	HEMGN	99732321	0.000000	0.05858	0.011000	0.14972	0.112000	0.19704	-0.138000	0.10374	0.175000	0.19841	0.655000	0.94253	GAA		0.393	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		A	100692500	C	A	100692500	4	1	47	1	0	0	0	0	0	1	0	0	7071	922	32	2	285	2	HEMGN	9	100692500	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	992268	100692500	40520931	1122	5519										
HEMGN	55363	broad.mit.edu	37	chr9	100693100	100693100	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcttcaggttccttcatgtCttggcatattttggaagaat	9	7	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:100693100C>T	ENST00000259456.3	-	4	720	c.577G>A	c.(577-579)Gac>Aac	p.D193N		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	193					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.D193N(1)		NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TCCTTCATGTCTTGGCATATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											274	273	273					9																	100693100		2203	4300	6503	99732921	SO:0001583	missense	55363			AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.577G>A	9.37:g.100693100C>T	ENSP00000259456:p.Asp193Asn		99732921	Q6XAR3|Q86XY5|Q9NPC0	Missense_Mutation	SNP	ENST00000259456.3	37	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774186	0.49786	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.52	4.52	0.55395	.	0.702006	0.14018	N	0.347002	T	0.50240	0.1604	L	0.56769	1.78	0.09310	N	1	D	0.61697	0.99	P	0.54174	0.744	T	0.38802	-0.9644	9	0.20046	T	0.44	-4.7744	13.183	0.59666	0.0:1.0:0.0:0.0	.	193	Q9BXL5	HEMGN_HUMAN	N	193	.	ENSP00000259456:D193N	D	-	1	0	HEMGN	99732921	0.045000	0.20229	0.142000	0.22268	0.035000	0.12851	2.395000	0.44459	2.260000	0.74910	0.650000	0.86243	GAC		0.378	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		T	100693100	C	T	100693100	3	4	47	1	0	0	0	0	1	0	0	0	7071	913	32	3	885	3	HEMGN	9	100693100	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	600	100693100	40520331	1123	5520										
COL15A1	1306	broad.mit.edu	37	chr9	101832135	101832135	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggctaattgtcctatgtatCgaaaacagtttcatgacaga	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:101832135C>T	ENST00000375001.3	+	42	4557	c.4134C>T	c.(4132-4134)atC>atT	p.I1378I		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1378	Nonhelical region 10 (NC10).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.I1378I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TCCTATGTATCGAAAACAGTT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	9											89	79	82					9																	101832135		2203	4300	6503	100871956	SO:0001819	synonymous_variant	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.4134C>T	9.37:g.101832135C>T			100871956	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.448	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101832135	C	T	101832135	2	4	47	1	0	0	0	0	0	0	0	1	3678	874	31	1		1	COL15A1	9	101832135	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1139035	101832135	39381296	1124	5521										
TGFBR1	7046	broad.mit.edu	37	chr9	101910029	101910029	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttgtttgtgaacagaagtTaaggccaaatatcccaaaca	8	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:101910029T>G	ENST00000374994.4	+	8	1466	c.1349T>G	c.(1348-1350)tTa>tGa	p.L450*	RNA5SP290_ENST00000517133.1_RNA|TGFBR1_ENST00000374990.2_Nonsense_Mutation_p.L373*|TGFBR1_ENST00000552516.1_Nonsense_Mutation_p.L454*|TGFBR1_ENST00000550253.1_Nonsense_Mutation_p.L381*	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	450	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.L450*(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				GAACAGAAGTTAAGGCCAAAT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											105	104	104					9																	101910029		2203	4300	6503	100949850	SO:0001587	stop_gained	7046				CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.1349T>G	9.37:g.101910029T>G	ENSP00000364133:p.Leu450*		100949850	Q6IR47|Q706C0|Q706C1	Nonsense_Mutation	SNP	ENST00000374994.4	37	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	T	38	6.696129	0.97768	.	.	ENSG00000106799	ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000550253	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3665	0.74526	0.0:0.0:0.0:1.0	.	.	.	.	X	450;412;373;454;381	.	ENSP00000364129:L373X	L	+	2	0	TGFBR1	100949850	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.139000	0.71728	2.258000	0.74832	0.533000	0.62120	TTA		0.358	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			G	101910029	T	G	101910029	4	3	47	1	0	0	0	0	0	1	0	0	15860	1764	61	4	1379	4	TGFBR1	9	101910029	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	77894	101910029	39303402	1125	5522										
TMEFF1	8577	broad.mit.edu	37	chr9	103261135	103261135	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagaagatggagatggtttGaaatgtgcatgccaatttca	11	4	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:103261135G>T	ENST00000374879.4	+	2	717	c.285G>T	c.(283-285)ttG>ttT	p.L95F	MSANTD3-TMEFF1_ENST00000502978.1_Nonsense_Mutation_p.E59*|TMEFF1_ENST00000334943.6_Missense_Mutation_p.L56F	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	95	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L95F(1)		NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				GAGATGGTTTGAAATGTGCAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	9											128	125	126					9																	103261135		2203	4300	6503	102300956	SO:0001583	missense	8577			U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.285G>T	9.37:g.103261135G>T	ENSP00000364013:p.Leu95Phe		102300956	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	37	CCDS6750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.330008|4.330008	0.81690|0.81690	.|.	.|.	ENSG00000251349|ENSG00000241697	ENST00000502978|ENST00000334943;ENST00000374879	.|T;T	.|0.75589	.|-0.95;-0.95	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Epidermal growth factor-like, type 3 (1);	.|0.151191	.|0.44285	.|D	.|0.000464	.|T	.|0.75752	.|0.3892	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|P;P	.|0.45011	.|0.848;0.739	.|P;B	.|0.50352	.|0.638;0.407	.|T	.|0.68697	.|-0.5340	.|10	.|0.09843	.|T	.|0.71	-34.8311|-34.8311	17.7937|17.7937	0.88562|0.88562	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|95;56	.|Q8IYR6;Q8IYR6-2	.|TEFF1_HUMAN;.	X|F	59|56;95	.|ENSP00000334447:L56F;ENSP00000364013:L95F	.|ENSP00000334447:L56F	E|L	+|+	1|3	0|2	C9orf30-TMEFF1|TMEFF1	102300956|102300956	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.158000|5.158000	0.64917|0.64917	2.878000|2.878000	0.98634|0.98634	0.650000|0.650000	0.86243|0.86243	GAA|TTG		0.328	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		T	103261135	G	T	103261135	3	4	47	1	0	0	0	0	1	0	0	0	16052	1281	45	2	291	2	TMEFF1	9	103261135	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1351106	103261135	37952296	1126	5523										
SMC2	10592	broad.mit.edu	37	chr9	106864280	106864280	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtaccaaaaagtaatgagaGaaatagaacatttgagtcgt	9	4	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:106864280G>T	ENST00000286398.7	+	8	964	c.676G>T	c.(676-678)Gaa>Taa	p.E226*	SMC2_ENST00000374793.3_Nonsense_Mutation_p.E226*|SMC2_ENST00000374787.3_Nonsense_Mutation_p.E226*|SMC2_ENST00000303219.8_Nonsense_Mutation_p.E226*	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	226					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.E226*(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						AGTAATGAGAGAAATAGAACA	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											87	97	94					9																	106864280		2198	4298	6496	105904101	SO:0001587	stop_gained	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.676G>T	9.37:g.106864280G>T	ENSP00000286398:p.Glu226*		105904101	Q6IEE0|Q9P1P2	Nonsense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	G	40	7.975024	0.98591	.	.	ENSG00000136824	ENST00000286398;ENST00000440179;ENST00000374793;ENST00000303219;ENST00000536893;ENST00000374787	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-26.9392	19.1404	0.93444	0.0:0.0:1.0:0.0	.	.	.	.	X	226;81;226;226;226;226	.	ENSP00000286398:E226X	E	+	1	0	SMC2	105904101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.785000	0.85724	2.937000	0.99478	0.650000	0.86243	GAA		0.299	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106864280	G	T	106864280	4	4	47	1	0	0	0	0	0	1	0	0	14820	943	33	2	702	2	SMC2	9	106864280	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3603145	106864280	34349151	1127	5524										
OR13F1	138805	broad.mit.edu	37	chr9	107267243	107267243	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatcagctcagtggaaggtCgaagtaaagccttttcaacg	11	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:107267243C>T	ENST00000334726.2	+	1	789	c.700C>T	c.(700-702)Cga>Tga	p.R234*		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R234*(1)		endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AGTGGAAGGTCGAAGTAAAGC	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											206	186	193					9																	107267243		2203	4300	6503	106307064	SO:0001587	stop_gained	138805				CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"GPCR / Class A : Olfactory receptors"	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.700C>T	9.37:g.107267243C>T	ENSP00000334452:p.Arg234*		106307064	Q6IF50	Nonsense_Mutation	SNP	ENST00000334726.2	37	CCDS35087.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.957569	0.34565	.	.	ENSG00000186881	ENST00000334726	.	.	.	4.3	1.24	0.21308	.	0.340853	0.20123	N	0.098743	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8154	0.23826	0.3234:0.5879:0.0:0.0887	.	.	.	.	X	234	.	ENSP00000334452:R234X	R	+	1	2	OR13F1	106307064	0.000000	0.05858	0.022000	0.16811	0.149000	0.21700	-2.350000	0.01092	0.273000	0.22049	0.655000	0.94253	CGA		0.488	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1			T	107267243	C	T	107267243	4	4	47	1	0	0	0	0	0	1	0	0	10972	876	31	1	702	1	OR13F1	9	107267243	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	402963	107267243	33946188	1128	5525										
LPAR1	1902	broad.mit.edu	37	chr9	113704123	113704123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtgtcaatgaggccctgaCgaaggagccatgtgctaaca	13	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:113704123C>T	ENST00000374431.3	-	4	754	c.371G>A	c.(370-372)cGt>cAt	p.R124H	LPAR1_ENST00000374430.2_Missense_Mutation_p.R124H|LPAR1_ENST00000358883.4_Missense_Mutation_p.R124H|LPAR1_ENST00000541779.1_Missense_Mutation_p.R125H|LPAR1_ENST00000538760.1_Missense_Mutation_p.R125H	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	124					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.R124H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						GAGGCCCTGACGAAGGAGCCA	0.527																																					NSCLC(115;661 2323 9836 34256)											1	Substitution - Missense(1)	large_intestine(1)	9											140	137	138					9																	113704123		2203	4300	6503	112743944	SO:0001583	missense	1902			U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3166	protein-coding gene	gene with protein product		602282	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.371G>A	9.37:g.113704123C>T	ENSP00000363553:p.Arg124His		112743944	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	37	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373723	0.82573	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760;ENST00000441240	T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22	5.53	4.64	0.57946	GPCR, rhodopsin-like superfamily (1);	0.050017	0.85682	N	0.000000	T	0.65386	0.2686	M	0.91249	3.19	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.66602	0.945;0.945;0.945	T	0.74414	-0.3673	10	0.87932	D	0	.	13.4093	0.60933	0.0:0.9247:0.0:0.0753	.	125;125;124	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	H	124;125;124;124;106;125;124	ENSP00000363553:R124H;ENSP00000445697:R125H;ENSP00000363552:R124H;ENSP00000351755:R124H;ENSP00000440201:R125H;ENSP00000401810:R124H	ENSP00000351755:R124H	R	-	2	0	LPAR1	112743944	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.786000	0.85741	1.357000	0.45904	0.655000	0.94253	CGT		0.527	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159		T	113704123	C	T	113704123	3	4	47	1	0	0	0	0	1	0	0	0	8933	536	19	1	731	1	LPAR1	9	113704123	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6436880	113704123	27509308	1129	5526										
OR2K2	26248	broad.mit.edu	37	chr9	114089768	114089768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accatagggacccaatcagaGatgttcgtgtgtttgatgca	11	8	1	2	rs545492183		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:114089768G>T	ENST00000374428.1	-	1	1032	c.1033C>A	c.(1033-1035)Ctc>Atc	p.L345I	OR2K2_ENST00000302681.1_Missense_Mutation_p.L316I			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	345						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L316F(1)|p.L345I(1)|p.L316I(1)|p.L345F(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						CCCAATCAGAGATGTTCGTGT	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	9											102	87	92					9																	114089768		2203	4300	6503	113129589	SO:0001583	missense	26248			X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"GPCR / Class A : Olfactory receptors"	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.1033C>A	9.37:g.114089768G>T	ENSP00000363550:p.Leu345Ile		113129589	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		.	.	.	.	.	.	.	.	.	.	G	5.683	0.310504	0.10733	.	.	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.10382	2.88;2.96	4.84	-2.75	0.05914	.	.	.	.	.	T	0.04137	0.0115	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39542	-0.9609	9	0.62326	D	0.03	.	0.993	0.01461	0.3298:0.2714:0.2604:0.1385	.	345	Q8NGT1	OR2K2_HUMAN	I	316;345	ENSP00000305055:L316I;ENSP00000363550:L345I	ENSP00000305055:L316I	L	-	1	0	OR2K2	113129589	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.654000	0.05354	-0.410000	0.07542	-0.176000	0.13171	CTC		0.408	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		T	114089768	G	T	114089768	3	4	47	1	0	0	0	0	1	0	0	0	11036	942	33	2	7	2	OR2K2	9	114089768	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	385645	114089768	27123663	1130	5527										
DNAJC25	548645	broad.mit.edu	37	chr9	114409504	114409504	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtggatgttagagtagtgAttttggtcagcgtgtgtgct	16	3	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:114409504A>C	ENST00000313525.3	+	2	510	c.454A>C	c.(454-456)Att>Ctt	p.I152L	DNAJC25-GNG10_ENST00000374294.3_Intron|DNAJC25_ENST00000556107.1_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	152						integral component of membrane (GO:0016021)		p.I152L(1)		kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						TAGAGTAGTGATTTTGGTCAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											359	362	361					9																	114409504		2121	4243	6364	113449325	SO:0001583	missense	548645				CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.454A>C	9.37:g.114409504A>C	ENSP00000320650:p.Ile152Leu		113449325	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	37	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.318150	0.40996	.	.	ENSG00000059769	ENST00000313525	T	0.41758	0.99	5.04	3.91	0.45181	.	0.048016	0.85682	D	0.000000	T	0.32941	0.0846	L	0.48260	1.515	0.80722	D	1	P	0.38788	0.647	B	0.35470	0.203	T	0.04915	-1.0918	10	0.32370	T	0.25	-13.0338	10.3061	0.43680	0.9226:0.0:0.0774:0.0	.	152	Q9H1X3	DJC25_HUMAN	L	152	ENSP00000320650:I152L	ENSP00000320650:I152L	I	+	1	0	DNAJC25	113449325	1.000000	0.71417	0.931000	0.37212	0.908000	0.53690	3.533000	0.53561	0.775000	0.33450	0.460000	0.39030	ATT		0.413	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		C	114409504	A	C	114409504	3	2	47	1	0	0	0	0	1	0	0	0	4654	333	12	4	460	4	DNAJC25	9	114409504	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	319736	114409504	26803927	1131	5528										
C9orf80	58493	broad.mit.edu	37	chr9	115451826	115451826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgcaaagctgccttctgtTgggctgcaatatgctgctgc	11	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:115451826T>C	ENST00000374242.4	-	4	505	c.200A>G	c.(199-201)cAa>cGa	p.Q67R	INIP_ENST00000374236.1_Missense_Mutation_p.Q37R|INIP_ENST00000374234.1_Intron|INIP_ENST00000497712.2_5'UTR|INIP_ENST00000374238.1_Intron	NM_021218.1	NP_067041.1	Q9NRY2	SOSSC_HUMAN	INTS3 and NABP interacting protein	67					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)		p.Q67R(1)									TGCCTTCTGTTGGGCTGCAAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	106	111					9																	115451826		2203	4300	6503	114491647	SO:0001583	missense	58493			AF161411	CCDS6785.1	9q32	2012-06-19	2012-06-19	2012-06-19	ENSG00000148153	ENSG00000148153			24994	protein-coding gene	gene with protein product	"hSSB-interacting protein 1", "sensor of single-strand DNA complex subunit C", "minute INTS3/hSSB-associated element"	613273	"chromosome 9 open reading frame 80"	C9orf80		11042152	Standard	NM_021218		Approved	HSPC043, hSSBIP1, SOSS-C, MISE	uc004bgg.3	Q9NRY2	OTTHUMG00000020509	ENST00000374242.4:c.200A>G	9.37:g.115451826T>C	ENSP00000363360:p.Gln67Arg		114491647	Q5VWJ7|Q96E04|Q9P090	Missense_Mutation	SNP	ENST00000374242.4	37	CCDS6785.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.729093	0.89390	.	.	ENSG00000148153	ENST00000374242;ENST00000374236	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.73853	0.3640	M	0.65975	2.015	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.69423	-0.5149	9	0.09084	T	0.74	-16.9616	16.0461	0.80722	0.0:0.0:0.0:1.0	.	67	Q9NRY2	SOSSC_HUMAN	R	67;37	.	ENSP00000363353:Q37R	Q	-	2	0	C9orf80	114491647	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	6.767000	0.74975	2.326000	0.78906	0.472000	0.43445	CAA		0.478	INIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053692.2	NM_021218		C	115451826	T	C	115451826	3	2	47	1	0	0	0	0	1	0	0	0	2504	1812	63	4	122	4	C9orf80	9	115451826	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1042322	115451826	25761605	1132	5529										
RGS3	5998	broad.mit.edu	37	chr9	116224127	116224127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctctacagtggtccctggcGaagttgtgaagaggtgacta	14	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:116224127G>A	ENST00000374140.2	+	3	430	c.221G>A	c.(220-222)cGa>cAa	p.R74Q	RGS3_ENST00000350696.5_Missense_Mutation_p.R74Q|RGS3_ENST00000317613.6_5'Flank	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	74					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R74Q(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGTCCCTGGCGAAGTTGTGAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	9											119	120	119					9																	116224127		2023	4181	6204	115263948	SO:0001583	missense	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.221G>A	9.37:g.116224127G>A	ENSP00000363255:p.Arg74Gln		115263948	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	A	0.033	-1.324115	0.01309	.	.	ENSG00000138835	ENST00000374140;ENST00000350696	T;T	0.45668	0.89;0.89	3.28	0.894	0.19242	.	1.796160	0.03688	N	0.246668	T	0.20129	0.0484	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19910	-1.0291	10	0.02654	T	1	.	5.828	0.18564	0.6162:0.0:0.3838:0.0	.	74	P49796	RGS3_HUMAN	Q	74	ENSP00000363255:R74Q;ENSP00000259406:R74Q	ENSP00000259406:R74Q	R	+	2	0	RGS3	115263948	0.001000	0.12720	0.004000	0.12327	0.022000	0.10575	0.155000	0.16362	-0.091000	0.12440	-0.516000	0.04426	CGA		0.532	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		A	116224127	G	A	116224127	3	1	47	1	0	0	0	0	1	0	0	0	13343	1058	37	1	227	1	RGS3	9	116224127	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	772301	116224127	24989304	1133	5530										
TNC	3371	broad.mit.edu	37	chr9	117819606	117819606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaatcaataatttcaatggTaaaggtctcgaagatcccat	8	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:117819606T>C	ENST00000350763.4	-	15	4816	c.4405A>G	c.(4405-4407)Acc>Gcc	p.T1469A	TNC_ENST00000345230.3_Intron|TNC_ENST00000423613.2_Intron|TNC_ENST00000535648.1_Missense_Mutation_p.T1105A|TNC_ENST00000537320.1_Intron|TNC_ENST00000346706.3_Intron|TNC_ENST00000481475.1_5'Flank|TNC_ENST00000341037.4_Missense_Mutation_p.T1378A|TNC_ENST00000340094.3_Missense_Mutation_p.T1105A|TNC_ENST00000542877.1_Missense_Mutation_p.T1105A	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1469	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.T1469A(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ATTTCAATGGTAAAGGTCTCG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											154	165	161					9																	117819606		2203	4300	6503	116859427	SO:0001583	missense	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.4405A>G	9.37:g.117819606T>C	ENSP00000265131:p.Thr1469Ala		116859427	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.73|15.73	2.918772|2.918772	0.52546|0.52546	.|.	.|.	ENSG00000041982|ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000350763;ENST00000341037;ENST00000542877|ENST00000544972	T;T;T;T;T|.	0.57273|.	0.41;0.41;0.41;0.41;0.41|.	5.81|5.81	5.81|5.81	0.92471|0.92471	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.148640|.	0.52532|.	D|.	0.000066|.	T|T	0.64724|0.64724	0.2624|0.2624	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	D|.	0.54964|.	0.969|.	D|.	0.64410|.	0.925|.	T|T	0.64529|0.64529	-0.6386|-0.6386	10|5	0.16420|.	T|.	0.52|.	.|.	10.4863|10.4863	0.44724|0.44724	0.0:0.0724:0.0:0.9276|0.0:0.0724:0.0:0.9276	.|.	1469|.	P24821|.	TENA_HUMAN|.	A|C	1105;1105;1469;1378;1105|122	ENSP00000344400:T1105A;ENSP00000438152:T1105A;ENSP00000265131:T1469A;ENSP00000339553:T1378A;ENSP00000442242:T1105A|.	ENSP00000344400:T1105A|.	T|Y	-|-	1|2	0|0	TNC|TNC	116859427|116859427	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.834000|1.834000	0.39171|0.39171	2.212000|2.212000	0.71576|0.71576	0.460000|0.460000	0.39030|0.39030	ACC|TAC		0.438	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		C	117819606	T	C	117819606	3	2	47	1	0	0	0	0	1	0	0	0	16309	1638	57	4	2256	4	TNC	9	117819606	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1595479	117819606	23393825	1134	5531										
TNC	3371	broad.mit.edu	37	chr9	117840469	117840469	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtgacatctttcacctcGatctggctgggggcatccaa	10	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:117840469G>T	ENST00000350763.4	-	7	2838	c.2427C>A	c.(2425-2427)atC>atA	p.I809I	TNC_ENST00000345230.3_Silent_p.I809I|TNC_ENST00000423613.2_Silent_p.I809I|TNC_ENST00000535648.1_Silent_p.I809I|TNC_ENST00000537320.1_Silent_p.I809I|TNC_ENST00000346706.3_Silent_p.I809I|TNC_ENST00000341037.4_Silent_p.I809I|TNC_ENST00000340094.3_Silent_p.I809I|TNC_ENST00000542877.1_Silent_p.I809I	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	809	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.I809I(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CTTTCACCTCGATCTGGCTGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	9											109	106	107					9																	117840469		2203	4300	6503	116880290	SO:0001819	synonymous_variant	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2427C>A	9.37:g.117840469G>T			116880290	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.547	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117840469	G	T	117840469	2	4	47	1	0	0	0	0	0	0	0	1	16309	1048	37	2		2	TNC	9	117840469	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	20863	117840469	23372962	1135	5532										
DBC1	1620	broad.mit.edu	37	chr9	122011325	122011325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtggtaggtctcctgccaaGcaggcggatgctcctttgaa	13	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:122011325G>A	ENST00000265922.3	-	3	783	c.322C>T	c.(322-324)Ctt>Ttt	p.L108F	BRINP1_ENST00000373964.2_Missense_Mutation_p.L108F	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	108	MACPF.				cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.L108F(1)									CTCCTGCCAAGCAGGCGGATG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											127	99	108					9																	122011325		2203	4300	6503	121051146	SO:0001583	missense	1620			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.322C>T	9.37:g.122011325G>A	ENSP00000265922:p.Leu108Phe		121051146	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685907	0.88639	.	.	ENSG00000078725	ENST00000373969;ENST00000265922;ENST00000373964	D;D	0.91011	-2.77;-2.77	5.66	5.66	0.87406	Membrane attack complex component/perforin (MACPF) domain (2);	0.061993	0.64402	D	0.000003	D	0.94886	0.8347	M	0.64404	1.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.994;0.996	D	0.94751	0.7927	10	0.87932	D	0	-13.8673	20.1076	0.97898	0.0:0.0:1.0:0.0	.	108;108	O60477-2;O60477	.;DBC1_HUMAN	F	108	ENSP00000265922:L108F;ENSP00000363075:L108F	ENSP00000265922:L108F	L	-	1	0	DBC1	121051146	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.976000	0.88070	2.823000	0.97156	0.650000	0.86243	CTT		0.562	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	122011325	G	A	122011325	3	1	47	1	0	0	0	0	1	0	0	0	4253	971	34	3	1987	3	DBC1	9	122011325	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4170856	122011325	19202106	1136	5533										
FBXW2	26190	broad.mit.edu	37	chr9	123550147	123550147	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatggtcctccagttgcttCattctcaaaatagccttcaa	5	12	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:123550147C>A	ENST00000608872.1	-	3	577	c.390G>T	c.(388-390)atG>atT	p.M130I	FBXW2_ENST00000340778.5_Missense_Mutation_p.M130I	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	130					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)	p.M130I(1)		ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						CCAGTTGCTTCATTCTCAAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	99	101					9																	123550147		1907	4115	6022	122589968	SO:0001583	missense	26190			AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.390G>T	9.37:g.123550147C>A	ENSP00000476369:p.Met130Ile		122589968	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	37	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166367	0.57476	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833;ENST00000453291	T;T;T	0.80033	0.33;-1.33;0.62	5.7	5.7	0.88788	F-box domain, Skp2-like (1);	0.073186	0.85682	D	0.000000	T	0.75376	0.3841	N	0.24115	0.695	0.80722	D	1	B;P;P	0.35872	0.015;0.525;0.525	B;B;B	0.42214	0.004;0.38;0.38	T	0.73956	-0.3819	10	0.35671	T	0.21	-4.0876	17.3282	0.87255	0.0:1.0:0.0:0.0	.	130;130;130	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	I	130;130;130;1	ENSP00000363036:M130I;ENSP00000341161:M130I;ENSP00000398662:M1I	ENSP00000341161:M130I	M	-	3	0	FBXW2	122589968	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.629000	0.83207	2.692000	0.91855	0.655000	0.94253	ATG		0.428	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			A	123550147	C	A	123550147	3	1	47	1	0	0	0	0	1	0	0	0	5785	826	29	2	998	2	FBXW2	9	123550147	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1538822	123550147	17663284	1137	5534										
OR1J2	26740	broad.mit.edu	37	chr9	125273880	125273880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcccgactgtaagcagttCtattgacaaggatgtcattg	9	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:125273880C>A	ENST00000335302.5	+	1	800	c.800C>A	c.(799-801)tCt>tAt	p.S267Y		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	267						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S267Y(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						GTAAGCAGTTCTATTGACAAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											209	187	194					9																	125273880		2203	4300	6503	124313701	SO:0001583	missense	26740				CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.800C>A	9.37:g.125273880C>A	ENSP00000335575:p.Ser267Tyr		124313701	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043336	0.55003	.	.	ENSG00000197233	ENST00000335302	T	0.00277	8.34	5.14	-2.25	0.06888	GPCR, rhodopsin-like superfamily (1);	0.388195	0.18524	U	0.138666	T	0.00412	0.0013	M	0.89478	3.035	0.09310	N	1	P	0.38167	0.621	P	0.48921	0.595	T	0.40021	-0.9585	10	0.87932	D	0	.	3.5296	0.07771	0.1162:0.5262:0.1143:0.2433	.	267	Q8NGS2	OR1J2_HUMAN	Y	267	ENSP00000335575:S267Y	ENSP00000335575:S267Y	S	+	2	0	OR1J2	124313701	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.688000	0.05150	-0.210000	0.10140	0.632000	0.83419	TCT		0.473	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			A	125273880	C	A	125273880	3	1	47	1	0	0	0	0	1	0	0	0	10991	913	32	2	802	2	OR1J2	9	125273880	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1723733	125273880	15939551	1138	5535										
OR1L8	138881	broad.mit.edu	37	chr9	125330488	125330488	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcataggagatggtcttcTtttctgacaggaagttcatc	10	8	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:125330488T>G	ENST00000304865.2	-	1	350	c.269A>C	c.(268-270)aAg>aCg	p.K90T		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K90T(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GATGGTCTTCTTTTCTGACAG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	9											76	78	78					9																	125330488		2203	4300	6503	124370309	SO:0001583	missense	138881				CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"GPCR / Class A : Olfactory receptors"	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.269A>C	9.37:g.125330488T>G	ENSP00000306607:p.Lys90Thr		124370309	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	.	.	.	.	.	.	.	.	.	.	T	2.155	-0.393617	0.04899	.	.	ENSG00000171496	ENST00000304865	T	0.01998	4.51	4.39	2.04	0.26737	GPCR, rhodopsin-like superfamily (1);	0.341890	0.20664	U	0.087968	T	0.01222	0.0040	N	0.05078	-0.115	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.49409	-0.8943	10	0.22706	T	0.39	-0.0934	7.0489	0.25061	0.0:0.2598:0.0:0.7402	.	90	Q8NGR8	OR1L8_HUMAN	T	90	ENSP00000306607:K90T	ENSP00000306607:K90T	K	-	2	0	OR1L8	124370309	0.000000	0.05858	0.127000	0.21898	0.920000	0.55202	-1.117000	0.03283	0.351000	0.24027	0.369000	0.22263	AAG		0.463	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1			G	125330488	T	G	125330488	3	3	47	1	0	0	0	0	1	0	0	0	10998	1609	56	4	664	4	OR1L8	9	125330488	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	56608	125330488	15882943	1139	5536										
OR5C1	392391	broad.mit.edu	37	chr9	125551745	125551745	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctgccgctcccggaagatCaatagcttcttctgcgatat	8	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:125551745C>A	ENST00000373680.2	+	1	596	c.534C>A	c.(532-534)atC>atA	p.I178I		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I178I(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						CCCGGAAGATCAATAGCTTCT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	9											86	78	81					9																	125551745		2203	4300	6503	124591566	SO:0001819	synonymous_variant	392391			AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"GPCR / Class A : Olfactory receptors"	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.534C>A	9.37:g.125551745C>A			124591566	B2RN54|B9EGT0|Q96RC4	Silent	SNP	ENST00000373680.2	37	CCDS35131.1																																																																																				0.572	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			A	125551745	C	A	125551745	2	1	47	1	0	0	0	0	0	0	0	1	11184	816	29	2		2	OR5C1	9	125551745	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	221257	125551745	15661686	1140	5537										
OR1K1	392392	broad.mit.edu	37	chr9	125562897	125562897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtatatcctgctcatggctCgcttgtccttctgtgcttcc	8	13	2	0	rs143974581		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:125562897C>T	ENST00000277309.2	+	1	528	c.496C>T	c.(496-498)Cgc>Tgc	p.R166C		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R166C(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						GCTCATGGCTCGCTTGTCCTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	CYS/ARG	0,4406		0,0,2203	161	98	120		496	1.1	0	9	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR1K1	NM_080859.1	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	166/317	125562897	1,13005	2203	4300	6503	124602718	SO:0001583	missense	392392			AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.496C>T	9.37:g.125562897C>T	ENSP00000277309:p.Arg166Cys		124602718	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	37	CCDS35132.1	.	.	.	.	.	.	.	.	.	.	C	8.518	0.868011	0.17250	0.0	1.16E-4	ENSG00000165204	ENST00000277309	T	0.00188	8.59	3.99	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	U	0.001306	T	0.00241	0.0007	M	0.81497	2.545	0.09310	N	1	P	0.43231	0.801	B	0.42798	0.398	T	0.43572	-0.9383	10	0.87932	D	0	.	4.1422	0.10198	0.317:0.5009:0.0:0.1821	.	166	Q8NGR3	OR1K1_HUMAN	C	166	ENSP00000277309:R166C	ENSP00000277309:R166C	R	+	1	0	OR1K1	124602718	0.000000	0.05858	0.019000	0.16419	0.009000	0.06853	-0.182000	0.09726	0.023000	0.15187	-0.244000	0.11960	CGC		0.597	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			T	125562897	C	T	125562897	3	4	47	1	0	0	0	0	1	0	0	0	10993	884	31	1	498	1	OR1K1	9	125562897	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	11152	125562897	15650534	1141	5538										
GAPVD1	26130	broad.mit.edu	37	chr9	128099642	128099642	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgttttaactccagctgaAatggaggcattcaagcaaag	9	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:128099642A>G	ENST00000495955.1	+	17	2939	c.2649A>G	c.(2647-2649)gaA>gaG	p.E883E	GAPVD1_ENST00000470056.1_Silent_p.E883E|GAPVD1_ENST00000394104.2_Silent_p.E883E|GAPVD1_ENST00000312123.9_Silent_p.E862E|GAPVD1_ENST00000394105.2_Silent_p.E910E|GAPVD1_ENST00000297933.6_Silent_p.E883E|GAPVD1_ENST00000265956.4_Silent_p.E857E|GAPVD1_ENST00000394083.2_Silent_p.E862E			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	883					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.E910E(1)		central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						ctccagctgaaatggaggcat	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	9											90	87	88					9																	128099642		2203	4300	6503	127139463	SO:0001819	synonymous_variant	26130				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2649A>G	9.37:g.128099642A>G			127139463	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.527|7.527	0.657915|0.657915	0.14645|0.14645	.|.	.|.	ENSG00000165219|ENSG00000165219	ENST00000431329|ENST00000436712	.|.	.|.	.|.	6.17|6.17	-0.792|-0.792	0.10925|0.10925	.|.	.|.	.|.	.|.	.|.	T|T	0.42381|0.42381	0.1200|0.1200	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.26677|0.26677	-1.0096|-1.0096	4|4	.|.	.|.	.|.	.|.	2.577|2.577	0.04808|0.04808	0.2959:0.1086:0.4074:0.1881|0.2959:0.1086:0.4074:0.1881	.|.	.|.	.|.	.|.	R|D	720|720	.|.	.|.	K|N	+|+	2|1	0|0	GAPVD1|GAPVD1	127139463|127139463	0.639000|0.639000	0.27234|0.27234	0.981000|0.981000	0.43875|0.43875	0.980000|0.980000	0.70556|0.70556	0.187000|0.187000	0.16998|0.16998	-0.032000|-0.032000	0.13758|0.13758	0.533000|0.533000	0.62120|0.62120	AAA|AAT		0.507	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			G	128099642	A	G	128099642	2	3	47	1	0	0	0	0	0	0	0	1	6259	11	1	4		4	GAPVD1	9	128099642	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2536745	128099642	13113789	1142	5539										
C9orf117	286207	broad.mit.edu	37	chr9	130474995	130474995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccctcaccaacagatgcaccGcgatgaagaggacagtgacg	11	13	1	4	rs551402620		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:130474995G>A	ENST00000373295.2	+	7	1185	c.1145G>A	c.(1144-1146)cGc>cAc	p.R382H	C9orf117_ENST00000373293.5_Missense_Mutation_p.R31H|C9orf117_ENST00000464092.1_3'UTR	NM_001012502.2	NP_001012520.2	Q5JU67	CI117_HUMAN	chromosome 9 open reading frame 117	382								p.R382H(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						CAGATGCACCGCGATGAAGAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	85	83					9																	130474995		2187	4277	6464	129514816	SO:0001583	missense	286207			AK094948	CCDS43878.1	9q34.11	2012-04-02			ENSG00000160401	ENSG00000160401			27843	protein-coding gene	gene with protein product							Standard	NM_001012502		Approved		uc004brn.1	Q5JU67	OTTHUMG00000020709	ENST00000373295.2:c.1145G>A	9.37:g.130474995G>A	ENSP00000362392:p.Arg382His		129514816	A5D8T9	Missense_Mutation	SNP	ENST00000373295.2	37	CCDS43878.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.895054	0.33442	.	.	ENSG00000160401	ENST00000373295;ENST00000373293	T	0.43294	0.95	5.26	4.36	0.52297	.	0.713313	0.13225	N	0.404073	T	0.19927	0.0479	N	0.08118	0	0.09310	N	1	P	0.36768	0.569	B	0.14023	0.01	T	0.04481	-1.0948	10	0.42905	T	0.14	1.2929	12.1211	0.53891	0.0:0.8268:0.1732:0.0	.	382	Q5JU67	CI117_HUMAN	H	382;31	ENSP00000362392:R382H	ENSP00000362391:R31H	R	+	2	0	C9orf117	129514816	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.623000	0.24447	1.219000	0.43474	-0.375000	0.07067	CGC		0.592	C9orf117-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054215.2	NM_001012502		A	130474995	G	A	130474995	3	1	47	1	0	0	0	0	1	0	0	0	2457	1087	38	1	1171	1	C9orf117	9	130474995	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2375353	130474995	10738436	1143	5540										
DNM1	1759	broad.mit.edu	37	chr9	130984838	130984838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggggagcccgcattaaccGaatcttccacgagcgcttcc	11	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:130984838G>A	ENST00000372923.3	+	8	1183	c.1091G>A	c.(1090-1092)cGa>cAa	p.R364Q	DNM1_ENST00000475805.1_Missense_Mutation_p.R364Q|DNM1_ENST00000341179.7_Missense_Mutation_p.R364Q|DNM1_ENST00000393594.3_Missense_Mutation_p.R364Q|DNM1_ENST00000486160.1_Missense_Mutation_p.R364Q	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	364					endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.R364Q(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						CGCATTAACCGAATCTTCCAC	0.587																																					GBM(113;146 1575 2722 28670 29921)											2	Substitution - Missense(2)	large_intestine(2)	9											88	89	88					9																	130984838		2203	4300	6503	130024659	SO:0001583	missense	1759			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1091G>A	9.37:g.130984838G>A	ENSP00000362014:p.Arg364Gln		130024659	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.850856	0.91277	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160	T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7	5.88	5.88	0.94601	Dynamin central domain (1);	0.000000	0.85682	D	0.000000	D	0.85775	0.5775	M	0.82132	2.575	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.927;0.994	D	0.85845	0.1400	10	0.59425	D	0.04	-24.5224	20.221	0.98325	0.0:0.0:1.0:0.0	.	364;364;364	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	Q	364;364;364;359;364;364	ENSP00000419225:R364Q;ENSP00000345680:R364Q;ENSP00000362014:R364Q;ENSP00000377219:R364Q;ENSP00000420045:R364Q	ENSP00000345680:R364Q	R	+	2	0	DNM1	130024659	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	9.869000	0.99810	2.792000	0.96026	0.555000	0.69702	CGA		0.587	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		A	130984838	G	A	130984838	3	1	47	1	0	0	0	0	1	0	0	0	4681	1058	37	1	1121	1	DNM1	9	130984838	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	509843	130984838	10228593	1144	5541										
GOLGA2	2801	broad.mit.edu	37	chr9	131036225	131036225	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctcctgtaggaacaccaggGctattcctctgctgatattc	9	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:131036225G>A	ENST00000421699.2	-	2	123	c.111C>T	c.(109-111)agC>agT	p.S37S	SWI5_ENST00000418976.1_5'Flank|SWI5_ENST00000419867.2_5'Flank|GOLGA2_ENST00000490628.1_Silent_p.S37S|SWI5_ENST00000320188.5_5'Flank|SWI5_ENST00000495313.1_5'Flank|GOLGA2_ENST00000609374.1_Silent_p.S25S|SWI5_ENST00000608796.1_5'Flank	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	37					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.S25S(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						GAACACCAGGGCTATTCCTCT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	9											166	182	177					9																	131036225		2203	4300	6503	130076046	SO:0001819	synonymous_variant	2801			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.111C>T	9.37:g.131036225G>A			130076046	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	CCDS6896.2																																																																																				0.418	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		A	131036225	G	A	131036225	2	1	47	1	0	0	0	0	0	0	0	1	6572	1194	42	3		3	GOLGA2	9	131036225	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	51387	131036225	10177206	1145	5542										
ODF2	4957	broad.mit.edu	37	chr9	131262356	131262356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctcgttaggcggaccgccGctaccagagccggctgcaag	13	15	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:131262356G>A	ENST00000434106.3	+	21	2675	c.2312G>A	c.(2311-2313)cGc>cAc	p.R771H	ODF2_ENST00000604420.1_Missense_Mutation_p.R771H|ODF2_ENST00000444119.2_Missense_Mutation_p.R747H|ODF2_ENST00000393527.3_Missense_Mutation_p.R747H|ODF2_ENST00000372807.5_Missense_Mutation_p.R766H|ODF2_ENST00000351030.3_Missense_Mutation_p.R766H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	771					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.R747H(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GCGGACCGCCGCTACCAGAGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											95	86	89					9																	131262356		2203	4300	6503	130302177	SO:0001583	missense	4957			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2312G>A	9.37:g.131262356G>A	ENSP00000403453:p.Arg771His		130302177	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	G	34	5.329563	0.95733	.	.	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.27104	1.71;1.7;1.69	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.45478	0.1344	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.986;0.995;0.995	T	0.11446	-1.0587	10	0.26408	T	0.33	-4.358	18.0467	0.89335	0.0:0.0:1.0:0.0	.	766;116;771;747	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	H	766;771;747	ENSP00000342581:R766H;ENSP00000361882:R771H;ENSP00000307781:R747H	ENSP00000307781:R747H	R	+	2	0	ODF2	130302177	1.000000	0.71417	0.996000	0.52242	0.845000	0.48019	7.427000	0.80284	2.504000	0.84457	0.561000	0.74099	CGC		0.542	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			A	131262356	G	A	131262356	3	1	47	1	0	0	0	0	1	0	0	0	10858	1087	38	1	2508	1	ODF2	9	131262356	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	226131	131262356	9951075	1146	5543										
PKN3	29941	broad.mit.edu	37	chr9	131482765	131482765	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacctgcgctactttgagggCgagttcacagggctgccgcc	14	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:131482765C>T	ENST00000291906.4	+	22	2943	c.2550C>T	c.(2548-2550)ggC>ggT	p.G850G	ZDHHC12_ENST00000467312.1_5'Flank	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	850	AGC-kinase C-terminal.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)	p.G850G(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						ACTTTGAGGGCGAGTTCACAG	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	9											66	70	68					9																	131482765		2203	4300	6503	130522586	SO:0001819	synonymous_variant	29941			AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.2550C>T	9.37:g.131482765C>T			130522586	Q9UM03	Silent	SNP	ENST00000291906.4	37	CCDS6908.1																																																																																				0.677	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		T	131482765	C	T	131482765	2	4	47	1	0	0	0	0	0	0	0	1	12012	755	27	1		1	PKN3	9	131482765	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	220409	131482765	9730666	1147	5544										
NUP188	23511	broad.mit.edu	37	chr9	131767990	131767990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccactcccacctttgactccGaagtggccccctccttcggg	8	19	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:131767990G>A	ENST00000372577.2	+	41	4825	c.4804G>A	c.(4804-4806)Gaa>Aaa	p.E1602K	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1602					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.E1602K(1)		breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CTTTGACTCCGAAGTGGCCCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	9											247	234	238					9																	131767990		2203	4300	6503	130807811	SO:0001583	missense	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4804G>A	9.37:g.131767990G>A	ENSP00000361658:p.Glu1602Lys		130807811	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076507	0.76415	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.35605	1.3	5.32	5.32	0.75619	.	0.047041	0.85682	D	0.000000	T	0.26702	0.0653	N	0.24115	0.695	0.51233	D	0.99991	B	0.31519	0.327	B	0.16722	0.016	T	0.08868	-1.0701	10	0.66056	D	0.02	-28.1702	18.0037	0.89203	0.0:0.0:1.0:0.0	.	1602	Q5SRE5	NU188_HUMAN	K	1491;1602	ENSP00000361658:E1602K	ENSP00000349125:E1491K	E	+	1	0	NUP188	130807811	1.000000	0.71417	0.944000	0.38274	0.868000	0.49771	9.148000	0.94652	2.482000	0.83794	0.561000	0.74099	GAA		0.552	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			A	131767990	G	A	131767990	3	1	47	1	0	0	0	0	1	0	0	0	10789	1059	37	1	4966	1	NUP188	9	131767990	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	285225	131767990	9445441	1148	5545										
SETX	23064	broad.mit.edu	37	chr9	135221704	135221704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatttcaagaagaggaactCgaagcttattttcaaagtct	8	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:135221704C>T	ENST00000224140.5	-	4	514	c.332G>A	c.(331-333)cGa>cAa	p.R111Q	SETX_ENST00000372169.2_Missense_Mutation_p.R111Q|SETX_ENST00000393220.1_Missense_Mutation_p.R111Q	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	111					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.R111Q(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AAGAGGAACTCGAAGCTTATT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	9											136	130	132					9																	135221704		2203	4300	6503	134211525	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.332G>A	9.37:g.135221704C>T	ENSP00000224140:p.Arg111Gln		134211525	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677170	0.88445	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.88124	-2.26;-2.34;-1.96	5.43	5.43	0.79202	.	0.199292	0.33631	N	0.004704	D	0.90024	0.6885	L	0.29908	0.895	0.30719	N	0.748423	D	0.89917	1.0	D	0.80764	0.994	D	0.88674	0.3197	10	0.72032	D	0.01	.	18.2287	0.89927	0.0:1.0:0.0:0.0	.	111	Q7Z333	SETX_HUMAN	Q	111	ENSP00000224140:R111Q;ENSP00000361242:R111Q;ENSP00000376913:R111Q	ENSP00000224140:R111Q	R	-	2	0	SETX	134211525	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	4.216000	0.58540	2.561000	0.86390	0.557000	0.71058	CGA		0.348	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		T	135221704	C	T	135221704	3	4	47	1	0	0	0	0	1	0	0	0	14178	884	31	1	7793	1	SETX	9	135221704	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3453714	135221704	5991727	1149	5546										
TTF1	7270	broad.mit.edu	37	chr9	135251433	135251433	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcataataaaagatgtctcGaaatgggaaaacttgcttgg	9	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:135251433G>A	ENST00000334270.2	-	11	2626	c.2587C>T	c.(2587-2589)Cga>Tga	p.R863*	TTF1_ENST00000461970.1_5'UTR	NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	863					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R863*(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		AAGATGTCTCGAAATGGGAAA	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											141	135	137					9																	135251433		2203	4300	6503	134241254	SO:0001587	stop_gained	7270			BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.2587C>T	9.37:g.135251433G>A	ENSP00000333920:p.Arg863*		134241254	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Nonsense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	g	24.6	4.547002	0.86022	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	.	.	.	4.97	-8.47	0.00939	.	2.240520	0.02869	N	0.131248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	21.1647	0.99947	0.0:0.0:0.8276:0.1724	.	.	.	.	X	863	.	ENSP00000245588:R863X	R	-	1	2	TTF1	134241254	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.008000	0.12788	-1.734000	0.01355	-0.471000	0.05019	CGA		0.438	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		A	135251433	G	A	135251433	4	1	47	1	0	0	0	0	0	1	0	0	16758	1066	37	1	134	1	TTF1	9	135251433	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	29729	135251433	5961998	1150	5547										
C9orf96	169436	broad.mit.edu	37	chr9	136259426	136259426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttaccaacagacccctttCgtaagtcctggatggcccct	7	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:136259426C>T	ENST00000371957.3	+	8	699	c.592C>T	c.(592-594)Cgt>Tgt	p.R198C	C9orf96_ENST00000371955.1_5'UTR	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		198	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.R198C(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AGACCCCTTTCGTAAGTCCTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	9											214	181	192					9																	136259426		2203	4300	6503	135249247	SO:0001583	missense	169436																														ENST00000371957.3:c.592C>T	9.37:g.136259426C>T	ENSP00000361025:p.Arg198Cys		135249247	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	.	.	.	.	.	.	.	.	.	.	C	8.645	0.896782	0.17686	.	.	ENSG00000198870	ENST00000371957	T	0.65178	-0.14	4.63	1.62	0.23740	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.203520	0.05947	N	0.638099	T	0.45657	0.1353	N	0.21508	0.67	0.09310	N	0.999998	B	0.11235	0.004	B	0.01281	0.0	T	0.29852	-0.9998	10	0.37606	T	0.19	-2.6209	4.354	0.11169	0.1767:0.6235:0.0:0.1998	.	198	Q8NE28	SGK71_HUMAN	C	198	ENSP00000361025:R198C	ENSP00000361025:R198C	R	+	1	0	C9orf96	135249247	0.000000	0.05858	0.003000	0.11579	0.037000	0.13140	0.342000	0.19926	0.366000	0.24427	0.456000	0.33151	CGT		0.567	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1			T	136259426	C	T	136259426	3	4	47	1	0	0	0	0	1	0	0	0	2514	884	31	1	622	1	C9orf96	9	136259426	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1007993	136259426	4954005	1151	5548										
OLFM1	10439	broad.mit.edu	37	chr9	138011470	138011470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccacccctggtcgggcacgGggcaggtggtctacaacggt	15	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:138011470G>A	ENST00000371793.3	+	6	1155	c.904G>A	c.(904-906)Ggg>Agg	p.G302R	OLFM1_ENST00000371796.3_Missense_Mutation_p.G275R|OLFM1_ENST00000252854.4_Missense_Mutation_p.G284R	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	302	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)	p.G284R(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		GTCGGGCACGGGGCAGGTGGT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	9											97	89	92					9																	138011470		2203	4300	6503	137151291	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.904G>A	9.37:g.138011470G>A	ENSP00000360858:p.Gly302Arg		137151291	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	G	23.7	4.450523	0.84101	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793;ENST00000539877	D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.02	5.07	5.07	0.68467	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	D	0.97632	0.9224	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.81914	0.995;0.98	D	0.98789	1.0735	10	0.87932	D	0	.	18.4324	0.90630	0.0:0.0:1.0:0.0	.	302;284	Q99784;Q6IMJ8	NOE1_HUMAN;.	R	284;275;302;199	ENSP00000252854:G284R;ENSP00000360861:G275R;ENSP00000360858:G302R;ENSP00000443806:G199R	ENSP00000252854:G284R	G	+	1	0	OLFM1	137151291	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	9.571000	0.98176	2.357000	0.79964	0.561000	0.74099	GGG		0.532	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		A	138011470	G	A	138011470	3	1	47	1	0	0	0	0	1	0	0	0	10883	1232	43	3	882	3	OLFM1	9	138011470	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1752044	138011470	3201961	1152	5549										
GLT6D1	360203	broad.mit.edu	37	chr9	138516033	138516033	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgtcatgaataactccgttCagatattctttgatgaagtc	7	7	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:138516033C>A	ENST00000371763.1	-	5	994	c.741G>T	c.(739-741)ctG>ctT	p.L247L		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	247					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)	p.L247L(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TAACTCCGTTCAGATATTCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	9											142	140	141					9																	138516033		1844	4098	5942	137655854	SO:0001819	synonymous_variant	360203			AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"Glycosyltransferase family 6 domain containing"	23671	protein-coding gene	gene with protein product		613699	"galactosyltransferase family 6 domain containing 1"	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.741G>T	9.37:g.138516033C>A			137655854		Silent	SNP	ENST00000371763.1	37	CCDS43900.1																																																																																				0.383	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		A	138516033	C	A	138516033	2	1	47	1	0	0	0	0	0	0	0	1	6488	813	29	2		2	GLT6D1	9	138516033	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	504563	138516033	2697398	1153	5550										
SNAPC4	6621	broad.mit.edu	37	chr9	139283037	139283037	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggcactggaaggcgctgcGgctggtcttcccaggcccaa	14	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:139283037G>A	ENST00000298532.2	-	10	1350	c.982C>T	c.(982-984)Cgc>Tgc	p.R328C		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa									p.R328C(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AAGGCGCTGCGGCTGGTCTTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	84	88					9																	139283037		2203	4300	6503	138402858	SO:0001583	missense	6621			AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.982C>T	9.37:g.139283037G>A	ENSP00000298532:p.Arg328Cys		138402858		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.693317	0.48202	.	.	ENSG00000165684	ENST00000298532	T	0.29917	1.55	4.94	4.94	0.65067	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.70971	0.3285	H	0.99238	4.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81640	-0.0841	10	0.87932	D	0	-29.0022	11.1255	0.48315	0.0:0.0:0.7027:0.2973	.	328	Q5SXM2	SNPC4_HUMAN	C	328	ENSP00000298532:R328C	ENSP00000298532:R328C	R	-	1	0	SNAPC4	138402858	0.998000	0.40836	0.936000	0.37596	0.329000	0.28539	2.595000	0.46197	2.292000	0.77174	0.511000	0.50034	CGC		0.587	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		A	139283037	G	A	139283037	3	1	47	1	0	0	0	0	1	0	0	0	14874	1116	39	1	3479	1	SNAPC4	9	139283037	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	767004	139283037	1930394	1154	5551										
CACNA1B	774	broad.mit.edu	37	chr9	140991019	140991019	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcctaggtcctcaccacttGgatgagttcatccgggtctg	10	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr9:140991019G>T	ENST00000371372.1	+	37	5323	c.5178G>T	c.(5176-5178)ttG>ttT	p.L1726F	CACNA1B_ENST00000371357.1_Missense_Mutation_p.L1725F|CACNA1B_ENST00000277549.5_Missense_Mutation_p.L920F|CACNA1B_ENST00000371363.1_Missense_Mutation_p.L1724F|CACNA1B_ENST00000371365.2_Missense_Mutation_p.L90F|CACNA1B_ENST00000277551.2_Missense_Mutation_p.L1726F|CACNA1B_ENST00000371355.4_Missense_Mutation_p.L1727F	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1726	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.L1726F(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CTCACCACTTGGATGAGTTCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	9											115	114	114					9																	140991019		2114	4259	6373	140110840	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.5178G>T	9.37:g.140991019G>T	ENSP00000360423:p.Leu1726Phe		140110840	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.28|16.28	3.078602|3.078602	0.55753|0.55753	.|.	.|.	ENSG00000148408|ENSG00000148408	ENST00000413253|ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355;ENST00000371365	.|D;D;D;D;D;D;D	.|0.98028	.|-4.39;-4.4;-4.67;-4.38;-4.37;-4.38;-4.51	4.44|4.44	1.53|1.53	0.23141|0.23141	.|.	.|0.000000	.|0.64402	.|D	.|0.000007	.|D	.|0.98021	.|0.9348	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.996	.|D	.|0.95493	.|0.8571	.|10	.|0.87932	.|D	.|0	.|.	1.84|1.84	0.03147|0.03147	0.1573:0.1355:0.4314:0.2757|0.1573:0.1355:0.4314:0.2757	.|.	.|1725;1724	.|B1AQK7;B1AQK6	.|.;.	X|F	91|1726;1726;920;1724;1725;1727;90	.|ENSP00000360423:L1726F;ENSP00000277551:L1726F;ENSP00000277549:L920F;ENSP00000360414:L1724F;ENSP00000360408:L1725F;ENSP00000360406:L1727F;ENSP00000360416:L90F	.|ENSP00000277549:L920F	G|L	+|+	1|3	0|2	CACNA1B|CACNA1B	140110840|140110840	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.973000|0.973000	0.67179|0.67179	0.587000|0.587000	0.23909|0.23909	0.098000|0.098000	0.17522|0.17522	-0.262000|-0.262000	0.10625|0.10625	GGA|TTG		0.547	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140991019	G	T	140991019	3	4	47	1	0	0	0	0	1	0	0	0	2545	1339	47	2	5320	2	CACNA1B	9	140991019	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1707982	140991019	222412	1155	5552										
DIP2C	22982	broad.mit.edu	37	chr10	461734	461734	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataattcttcaaagtcatcGacaaagaattctcgtaaagg	6	7	4	1	rs140437755		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:461734G>A	ENST00000280886.6	-	7	921	c.834C>T	c.(832-834)gtC>gtT	p.V278V	DIP2C_ENST00000381496.3_Silent_p.V171V	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	278						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.V278V(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CAAAGTCATCGACAAAGAATT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	10						G		0,4406		0,0,2203	161	155	157		834	-5.3	1	10	dbSNP_134	157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DIP2C	NM_014974.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		278/1557	461734	1,13005	2203	4300	6503	451734	SO:0001819	synonymous_variant	22982			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.834C>T	10.37:g.461734G>A			451734	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																				0.418	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	461734	G	A	461734	2	1	47	1	0	0	0	0	0	0	0	1	4540	1045	37	1		1	DIP2C	10	461734	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09		461734	135073013	1156	5553										
AKR1C2	1646	broad.mit.edu	37	chr10	5043729	5043729	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaagtgtagaatatgtcttCtctcttcacactgccatctg	7	10	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:5043729C>A	ENST00000380753.4	-	2	416	c.229G>T	c.(229-231)Gaa>Taa	p.E77*	AKR1C2_ENST00000407674.1_Nonsense_Mutation_p.E77*|AKR1C2_ENST00000455190.1_Nonsense_Mutation_p.E77*|AKR1C2_ENST00000421196.3_Nonsense_Mutation_p.E77*	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	77					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.E77*(2)		breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	AATATGTCTTCTCTCTTCACA	0.448																																																2	Substitution - Nonsense(2)	large_intestine(2)	10											142	118	126					10																	5043729		2203	4297	6500	5033729	SO:0001587	stop_gained	1646			L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"Aldo-keto reductases"	385	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"	600450	"aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)", "testicular 17,20-desmolase deficiency"	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.229G>T	10.37:g.5043729C>A	ENSP00000370129:p.Glu77*		5033729	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Nonsense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.462356	0.63513	.	.	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	.	.	.	2.35	1.43	0.22495	.	0.103283	0.39544	N	0.001339	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.8629	0.24077	0.0:0.8443:0.0:0.1557	.	.	.	.	X	77	.	ENSP00000370129:E77X	E	-	1	0	AKR1C2	5033729	1.000000	0.71417	0.994000	0.49952	0.312000	0.27988	2.103000	0.41806	0.527000	0.28560	0.205000	0.17691	GAA		0.448	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		A	5043729	C	A	5043729	4	1	47	1	0	0	0	0	0	1	0	0	470	922	32	2	829	2	AKR1C2	10	5043729	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4581995	5043729	130491018	1157	5554										
AKR1C3	8644	broad.mit.edu	37	chr10	5149674	5149674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgctagccaccctaattaTccatattcagatgaatatta	4	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:5149674T>C	ENST00000380554.3	+	9	1603	c.951T>C	c.(949-951)taT>taC	p.Y317Y	AKR1C3_ENST00000605149.1_Silent_p.Y294Y|AKR1C3_ENST00000439082.2_Silent_p.Y198Y	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	317					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.Y317Y(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	ACCCTAATTATCCATATTCAG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											94	89	90					10																	5149674		2203	4300	6503	5139674	SO:0001819	synonymous_variant	8644			L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.951T>C	10.37:g.5149674T>C			5139674	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	37	CCDS7063.1																																																																																				0.413	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		C	5149674	T	C	5149674	2	2	47	1	0	0	0	0	0	0	0	1	471	1442	50	4		4	AKR1C3	10	5149674	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	105945	5149674	130385073	1158	5555										
AKR1C4	1109	broad.mit.edu	37	chr10	5260709	5260709	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accatcctgattatccatttTcagatgaatattagcataga	5	8	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:5260709T>G	ENST00000380448.1	+	11	1211	c.958T>G	c.(958-960)Tca>Gca	p.S320A	AKR1C4_ENST00000263126.1_Missense_Mutation_p.S320A			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	320					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.S320A(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						TTATCCATTTTCAGATGAATA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											143	120	128					10																	5260709		2203	4300	6503	5250709	SO:0001583	missense	1109			M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"Aldo-keto reductases"	387	protein-coding gene	gene with protein product	"chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"	600451	"aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.958T>G	10.37:g.5260709T>G	ENSP00000369814:p.Ser320Ala		5250709	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	T	6.032	0.374325	0.11409	.	.	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.25085	1.82;1.82	2.83	-5.67	0.02444	NADP-dependent oxidoreductase domain (2);	2.924460	0.01494	N	0.017234	T	0.13798	0.0334	L	0.33189	0.99	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14420	-1.0473	10	0.14252	T	0.57	.	0.4419	0.00487	0.31:0.1189:0.2068:0.3643	.	320	P17516	AK1C4_HUMAN	A	320	ENSP00000369814:S320A;ENSP00000263126:S320A	ENSP00000263126:S320A	S	+	1	0	AKR1C4	5250709	0.001000	0.12720	0.002000	0.10522	0.065000	0.16274	-0.714000	0.05002	-0.585000	0.05905	0.260000	0.18958	TCA		0.408	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818		G	5260709	T	G	5260709	3	3	47	1	0	0	0	0	1	0	0	0	472	1783	62	4	992	4	AKR1C4	10	5260709	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	111035	5260709	130274038	1159	5556										
ITIH2	3698	broad.mit.edu	37	chr10	7786819	7786819	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggataaagagatgtccttttCtgttttacttcatcgtgttt	8	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:7786819C>A	ENST00000358415.4	+	19	2640	c.2474C>A	c.(2473-2475)tCt>tAt	p.S825Y	ITIH2_ENST00000379587.4_Missense_Mutation_p.S814Y	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	825					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S825Y(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						ATGTCCTTTTCTGTTTTACTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											152	141	145					10																	7786819		2203	4300	6503	7826825	SO:0001583	missense	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.2474C>A	10.37:g.7786819C>A	ENSP00000351190:p.Ser825Tyr		7826825	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.655116	0.67472	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.11930	2.73;2.73	5.79	5.79	0.91817	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.235571	0.40469	N	0.001083	T	0.27349	0.0671	M	0.76838	2.35	0.29132	N	0.879586	P	0.52316	0.952	P	0.54815	0.761	T	0.28554	-1.0040	10	0.37606	T	0.19	-8.3691	7.5955	0.28046	0.0:0.8047:0.0:0.1953	.	825	P19823	ITIH2_HUMAN	Y	825;814	ENSP00000351190:S825Y;ENSP00000368906:S814Y	ENSP00000351190:S825Y	S	+	2	0	ITIH2	7826825	1.000000	0.71417	0.989000	0.46669	0.831000	0.47069	2.906000	0.48735	2.737000	0.93849	0.591000	0.81541	TCT		0.428	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		A	7786819	C	A	7786819	3	1	47	1	0	0	0	0	1	0	0	0	7925	913	32	2	2548	2	ITIH2	10	7786819	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2526110	7786819	127747928	1160	5557										
UPF2	26019	broad.mit.edu	37	chr10	12077252	12077252	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatcatcttccagtctcttCttcttgtcttcaggggcctt	6	12	7	0	rs113169760		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:12077252C>A	ENST00000356352.2	-	1	644	c.171G>T	c.(169-171)aaG>aaT	p.K57N	UPF2_ENST00000397053.2_Missense_Mutation_p.K57N|UPF2_ENST00000357604.5_Missense_Mutation_p.K57N|UPF2_ENST00000460569.1_5'UTR			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	57	Glu/Lys-rich.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.K57N(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				CCAGTCTCTTCTTCTTGTCTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											230	208	215					10																	12077252		2203	4300	6503	12117258	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.171G>T	10.37:g.12077252C>A	ENSP00000348708:p.Lys57Asn		12117258	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605160	0.66445	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.15372	2.43;2.43;2.43	5.78	4.88	0.63580	.	0.062614	0.64402	D	0.000008	T	0.16385	0.0394	L	0.34521	1.04	0.40752	D	0.982925	P	0.37781	0.608	B	0.37943	0.261	T	0.03684	-1.1013	10	0.72032	D	0.01	.	14.905	0.70711	0.0:0.9315:0.0:0.0685	.	57	Q9HAU5	RENT2_HUMAN	N	57	ENSP00000348708:K57N;ENSP00000350221:K57N;ENSP00000380244:K57N	ENSP00000348708:K57N	K	-	3	2	UPF2	12117258	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.370000	0.52372	1.589000	0.49982	0.591000	0.81541	AAG		0.453	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			A	12077252	C	A	12077252	3	1	47	1	0	0	0	0	1	0	0	0	17044	912	32	2	3731	2	UPF2	10	12077252	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4290433	12077252	123457495	1161	5558										
PHYH	5264	broad.mit.edu	37	chr10	13336521	13336521	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggagcatattcggatttCgaaatggtcacatctctcat	8	9	3	0	rs115198308	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:13336521C>T	ENST00000263038.4	-	4	379	c.321G>A	c.(319-321)tcG>tcA	p.S107S	PHYH_ENST00000396920.3_Silent_p.S88S|PHYH_ENST00000396913.2_Silent_p.S7S	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	107					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)	p.S107S(2)		NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	ATTCGGATTTCGAAATGGTCA	0.403													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		20846	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	10						C	,	44,4362	46.7+/-81.2	0,44,2159	157	132	140		21,321	-2.5	0	10	dbSNP_132	140	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	PHYH	NM_001037537.1,NM_006214.3	,	0,47,6456	TT,TC,CC		0.0349,0.9986,0.3614	,	7/239,107/339	13336521	47,12959	2203	4300	6503	13376527	SO:0001819	synonymous_variant	5264				CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"Refsum disease", "phytanoyl-CoA dioxygenase"	602026	"phytanoyl-CoA hydroxylase (Refsum disease)", "phytanoyl-CoA hydroxylase"			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.321G>A	10.37:g.13336521C>T			13376527	A8MTS8|B1ALH5	Silent	SNP	ENST00000263038.4	37	CCDS7097.1																																																																																				0.403	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			T	13336521	C	T	13336521	2	4	47	1	0	0	0	0	0	0	0	1	11895	871	31	1		1	PHYH	10	13336521	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1259269	13336521	122198226	1162	5559										
PRPF18	8559	broad.mit.edu	37	chr10	13656058	13656058	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcaataacggatattattaAattcatgttgcagagagaat	7	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:13656058A>C	ENST00000378572.3	+	8	924	c.764A>C	c.(763-765)aAa>aCa	p.K255T		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	255					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)	p.K255T(1)		central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GATATTATTAAATTCATGTTG	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	10											54	57	56					10																	13656058		2203	4290	6493	13696064	SO:0001583	missense	8559			U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.764A>C	10.37:g.13656058A>C	ENSP00000367835:p.Lys255Thr		13696064	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796792	0.90453	.	.	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000378544	.	.	.	5.51	5.51	0.81932	Prp18 (3);	0.000000	0.85682	D	0.000000	T	0.71417	0.3337	L	0.60904	1.88	0.80722	D	1	P	0.44281	0.831	P	0.53035	0.716	T	0.74680	-0.3584	9	0.87932	D	0	-30.4584	15.6147	0.76756	1.0:0.0:0.0:0.0	.	255	Q99633	PRP18_HUMAN	T	255;249;249	.	ENSP00000367805:K249T	K	+	2	0	PRPF18	13696064	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.316000	0.96319	2.104000	0.64026	0.477000	0.44152	AAA		0.284	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			C	13656058	A	C	13656058	3	2	47	1	0	0	0	0	1	0	0	0	12597	14	1	4	794	4	PRPF18	10	13656058	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	319537	13656058	121878689	1163	5560										
DCLRE1C	64421	broad.mit.edu	37	chr10	14996006	14996006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catctgcccctcgaaagaacTcatagcgccgccgatcccag	8	17	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:14996006T>G	ENST00000378278.2	-	1	41	c.4A>C	c.(4-6)Agt>Cgt	p.S2R	DCLRE1C_ENST00000378246.2_5'UTR|DCLRE1C_ENST00000378254.1_5'UTR|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.S2R|DCLRE1C_ENST00000396817.2_5'UTR|DCLRE1C_ENST00000378258.1_5'UTR|DCLRE1C_ENST00000357717.2_5'UTR|DCLRE1C_ENST00000453695.2_5'UTR|DCLRE1C_ENST00000378255.1_5'UTR|DCLRE1C_ENST00000378249.1_5'UTR			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	2					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.S2R(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						TCGAAAGAACTCATAGCGCCG	0.642								Non-homologous end-joining																																								1	Substitution - Missense(1)	large_intestine(1)	10											47	52	51					10																	14996006		2203	4300	6503	15036012	SO:0001583	missense	64421			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.4A>C	10.37:g.14996006T>G	ENSP00000367527:p.Ser2Arg		15036012	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	T	32	5.163607	0.94727	.	.	ENSG00000152457	ENST00000378289;ENST00000378278	D;D	0.85013	-1.56;-1.93	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.91385	0.7282	M	0.69185	2.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.92281	0.5833	10	0.87932	D	0	.	15.6303	0.76904	0.0:0.0:0.0:1.0	.	2;2	Q96SD1-4;Q96SD1	.;DCR1C_HUMAN	R	2	ENSP00000367538:S2R;ENSP00000367527:S2R	ENSP00000367527:S2R	S	-	1	0	DCLRE1C	15036012	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	6.998000	0.76277	2.234000	0.73211	0.459000	0.35465	AGT		0.642	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		G	14996006	T	G	14996006	3	3	47	1	0	0	0	0	1	0	0	0	4302	1551	54	4	2130	4	DCLRE1C	10	14996006	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1339948	14996006	120538741	1164	5561										
ITGA8	8516	broad.mit.edu	37	chr10	15726040	15726040	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactcggcataggcgctgaaGttctgaattgctacatagca	10	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:15726040G>T	ENST00000378076.3	-	4	884	c.531C>A	c.(529-531)aaC>aaA	p.N177K		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	177					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.N177K(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						AGGCGCTGAAGTTCTGAATTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											108	107	107					10																	15726040		2203	4300	6503	15766046	SO:0001583	missense	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.531C>A	10.37:g.15726040G>T	ENSP00000367316:p.Asn177Lys		15766046	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961110	0.74016	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.54675	0.56	6.03	-1.73	0.08081	.	0.000000	0.85682	D	0.000000	T	0.65186	0.2667	M	0.69358	2.11	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.66408	-0.5931	10	0.59425	D	0.04	.	12.1049	0.53807	0.4607:0.0:0.5393:0.0	.	177;177	F5H818;P53708	.;ITA8_HUMAN	K	177	ENSP00000367316:N177K	ENSP00000367316:N177K	N	-	3	2	ITGA8	15766046	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	1.098000	0.31000	-0.080000	0.12685	-0.302000	0.09304	AAC		0.453	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		T	15726040	G	T	15726040	3	4	47	1	0	0	0	0	1	0	0	0	7903	1020	36	2	2768	2	ITGA8	10	15726040	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	730034	15726040	119808707	1165	5562										
VIM	7431	broad.mit.edu	37	chr10	17277192	17277192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtccctggaacgccagatgCgtgaaatggaagagaacttt	12	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:17277192C>T	ENST00000224237.5	+	6	1178	c.1033C>T	c.(1033-1035)Cgt>Tgt	p.R345C	VIM_ENST00000544301.1_Missense_Mutation_p.R345C|RP11-124N14.3_ENST00000456355.1_RNA			P08670	VIME_HUMAN	vimentin	345	Coil 2.|Rod.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.R345C(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACGCCAGATGCGTGAAATGGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	10											101	89	93					10																	17277192		2203	4300	6503	17317198	SO:0001583	missense	7431			M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1033C>T	10.37:g.17277192C>T	ENSP00000224237:p.Arg345Cys		17317198	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	37	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.658455	0.88154	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533	D;D	0.89810	-2.57;-2.57	5.91	5.91	0.95273	Filament (1);	0.000000	0.47455	D	0.000221	D	0.95175	0.8436	M	0.83692	2.655	0.80722	D	1	P;P;D;P	0.89917	0.726;0.68;1.0;0.726	P;B;D;P	0.76575	0.528;0.393;0.988;0.528	D	0.95036	0.8174	10	0.87932	D	0	.	20.2904	0.98542	0.0:1.0:0.0:0.0	.	345;332;345;345	Q53HU8;F5H288;B0YJC4;P08670	.;.;.;VIME_HUMAN	C	345;345;332	ENSP00000446007:R345C;ENSP00000224237:R345C	ENSP00000224237:R345C	R	+	1	0	VIM	17317198	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.930000	0.63462	2.788000	0.95919	0.643000	0.83706	CGT		0.478	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		T	17277192	C	T	17277192	3	4	47	1	0	0	0	0	1	0	0	0	17206	768	27	1	1055	1	VIM	10	17277192	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1551152	17277192	118257555	1166	5563										
DNAJC1	64215	broad.mit.edu	37	chr10	22217461	22217461	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcgttcatcatcctttaaAacttcataaatggccaccaa	3	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:22217461A>C	ENST00000376980.3	-	3	635	c.345T>G	c.(343-345)gtT>gtG	p.V115V	DNAJC1_ENST00000376946.1_Intron	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	115	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.V115V(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				CATCCTTTAAAACTTCATAAA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	10											97	99	99					10																	22217461		2203	4299	6502	22257467	SO:0001819	synonymous_variant	64215			AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.345T>G	10.37:g.22217461A>C			22257467	B0YIZ8|Q5VX89|Q9H6B8	Silent	SNP	ENST00000376980.3	37	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	A	5.250	0.231545	0.09969	.	.	ENSG00000136770	ENST00000447548	.	.	.	5.33	4.18	0.49190	.	.	.	.	.	T	0.58018	0.2093	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53920	-0.8370	4	.	.	.	-7.162	7.6671	0.28437	0.7144:0.1461:0.0:0.1395	.	.	.	.	V	104	.	.	F	-	1	0	DNAJC1	22257467	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.972000	0.40540	0.954000	0.37851	-0.313000	0.08912	TTT		0.313	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		C	22217461	A	C	22217461	2	2	47	1	0	0	0	0	0	0	0	1	4639	1	1	4		4	DNAJC1	10	22217461	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4940269	22217461	113317286	1167	5564										
GPR158	57512	broad.mit.edu	37	chr10	25701216	25701216	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catatttcaggaagtacaaaAgatgtgtcagaagaagccta	9	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:25701216A>T	ENST00000376351.3	+	4	1508	c.1149A>T	c.(1147-1149)aaA>aaT	p.K383N		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	383					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.K383N(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GAAGTACAAAAGATGTGTCAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											187	178	181					10																	25701216		2203	4300	6503	25741222	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1149A>T	10.37:g.25701216A>T	ENSP00000365529:p.Lys383Asn		25741222	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.299720	0.23650	.	.	ENSG00000151025	ENST00000376351	T	0.60171	0.21	5.44	-1.16	0.09678	.	0.230975	0.35495	N	0.003178	T	0.36331	0.0963	L	0.29908	0.895	0.30964	N	0.723273	B	0.20887	0.049	B	0.25759	0.063	T	0.16305	-1.0407	10	0.22706	T	0.39	.	5.0973	0.14740	0.3305:0.1047:0.4621:0.1026	.	383	Q5T848	GP158_HUMAN	N	383	ENSP00000365529:K383N	ENSP00000365529:K383N	K	+	3	2	GPR158	25741222	0.733000	0.28132	0.881000	0.34555	0.776000	0.43924	0.107000	0.15375	-0.263000	0.09378	-0.248000	0.11899	AAA		0.458	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25701216	A	T	25701216	3	4	47	1	0	0	0	0	1	0	0	0	6683	69	3	5	1163	5	GPR158	10	25701216	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3483755	25701216	109833531	1168	5565										
WAC	51322	broad.mit.edu	37	chr10	28884882	28884882	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtctgatcaccagccaaaGaaatcatttgatgctaatgg	8	9	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:28884882G>T	ENST00000354911.4	+	7	992	c.831G>T	c.(829-831)aaG>aaT	p.K277N	WAC_ENST00000375664.4_Missense_Mutation_p.K232N|WAC_ENST00000375646.1_Intron|WAC_ENST00000347934.4_Intron|WAC_ENST00000428935.1_Missense_Mutation_p.K232N	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	277					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)	p.K277N(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						ACCAGCCAAAGAAATCATTTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											133	122	126					10																	28884882		2203	4300	6503	28924888	SO:0001583	missense	51322			AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.831G>T	10.37:g.28884882G>T	ENSP00000346986:p.Lys277Asn		28924888	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	37	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013367	0.54468	.	.	ENSG00000095787	ENST00000375664;ENST00000354911;ENST00000428935;ENST00000424454;ENST00000538000;ENST00000414108	T;T;T;T	0.51817	1.86;1.86;1.41;0.69	5.28	5.28	0.74379	.	0.236011	0.42821	D	0.000644	T	0.59770	0.2218	L	0.36672	1.1	0.58432	D	0.999995	D;D	0.61080	0.989;0.981	D;D	0.72625	0.978;0.95	T	0.54403	-0.8299	10	0.29301	T	0.29	-0.9824	18.895	0.92420	0.0:0.0:1.0:0.0	.	232;277	Q9BTA9-2;Q9BTA9	.;WAC_HUMAN	N	232;277;232;232;232;232	ENSP00000364816:K232N;ENSP00000346986:K277N;ENSP00000399706:K232N;ENSP00000415645:K232N	ENSP00000346986:K277N	K	+	3	2	WAC	28924888	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.565000	0.67365	2.464000	0.83262	0.455000	0.32223	AAG		0.448	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		T	28884882	G	T	28884882	3	4	47	1	0	0	0	0	1	0	0	0	17287	933	33	2	857	2	WAC	10	28884882	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3183666	28884882	106649865	1169	5566										
CCDC7	79741	broad.mit.edu	37	chr10	32740795	32740795	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attccatcgagtaagacaaaGaacttactaccagaagatga	7	8	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:32740795G>T	ENST00000362006.5	+	2	768	c.225G>T	c.(223-225)aaG>aaT	p.K75N	CCDC7_ENST00000537047.1_Missense_Mutation_p.K75N|CCDC7_ENST00000545067.1_Missense_Mutation_p.K75N|CCDC7_ENST00000539197.1_Missense_Mutation_p.K75N|CCDC7_ENST00000535327.1_Missense_Mutation_p.K75N|CCDC7_ENST00000277657.6_Missense_Mutation_p.K75N	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	75								p.K75N(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				GTAAGACAAAGAACTTACTAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	61	63					10																	32740795		2203	4300	6503	32780801	SO:0001583	missense	221016			BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 68"	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.225G>T	10.37:g.32740795G>T	ENSP00000355078:p.Lys75Asn		32780801	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	G	6.776	0.512077	0.12944	.	.	ENSG00000216937	ENST00000324147;ENST00000277657;ENST00000362006;ENST00000545067;ENST00000539197;ENST00000537047;ENST00000535327	T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8	5.44	-1.33	0.09172	.	.	.	.	.	T	0.29976	0.0750	L	0.34521	1.04	0.09310	N	1	B;B	0.27882	0.019;0.192	B;B	0.23018	0.015;0.043	T	0.20840	-1.0263	9	0.56958	D	0.05	-35.2717	3.8645	0.09010	0.2368:0.0:0.3555:0.4077	.	75;75	A6YT98;Q96M83	.;CCDC7_HUMAN	N	75	ENSP00000277657:K75N;ENSP00000355078:K75N;ENSP00000439930:K75N;ENSP00000441041:K75N;ENSP00000440632:K75N;ENSP00000442531:K75N	ENSP00000277657:K75N	K	+	3	2	CCDC7	32780801	0.065000	0.20965	0.002000	0.10522	0.028000	0.11728	0.038000	0.13862	-0.211000	0.10124	-0.136000	0.14681	AAG		0.393	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		T	32740795	G	T	32740795	3	4	47	1	0	0	0	0	1	0	0	0	2848	933	33	2	227	2	CCDC7	10	32740795	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3855913	32740795	102793952	1170	5567										
ZNF248	57209	broad.mit.edu	37	chr10	38121585	38121585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctcctatctgagatctcTtatttgtaaaaaatgctgcc	5	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:38121585T>G	ENST00000395867.3	-	6	1248	c.698A>C	c.(697-699)aAg>aCg	p.K233T	ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Missense_Mutation_p.K233T|ZNF248_ENST00000494133.1_Intron|AL135791.1_ENST00000583461.1_RNA	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K233T(1)		NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						CTGAGATCTCTTATTTGTAAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	10											59	58	59					10																	38121585		2203	4299	6502	38161591	SO:0001583	missense	57209			AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.698A>C	10.37:g.38121585T>G	ENSP00000379208:p.Lys233Thr		38161591	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.497001	0.26861	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.15372	2.43;2.43	4.65	4.65	0.58169	.	0.286881	0.25094	N	0.033183	T	0.11239	0.0274	N	0.17474	0.49	0.24688	N	0.993324	B	0.31125	0.309	B	0.27608	0.081	T	0.20174	-1.0283	10	0.87932	D	0	.	12.3245	0.55003	0.0:0.0:0.0:1.0	.	233	Q8NDW4	ZN248_HUMAN	T	233	ENSP00000379208:K233T;ENSP00000349882:K233T	ENSP00000349882:K233T	K	-	2	0	ZNF248	38161591	0.005000	0.15991	0.989000	0.46669	0.795000	0.44927	-0.037000	0.12164	2.082000	0.62665	0.460000	0.39030	AAG		0.358	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		G	38121585	T	G	38121585	3	3	47	1	0	0	0	0	1	0	0	0	17832	1609	56	4	1045	4	ZNF248	10	38121585	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	5380790	38121585	97413162	1171	5568										
ZNF33A	7581	broad.mit.edu	37	chr10	38343562	38343562	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaaaaaagtctgatgaattTaatgcctgtgggaaattgtt	11	3	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:38343562T>G	ENST00000458705.2	+	5	665	c.507T>G	c.(505-507)ttT>ttG	p.F169L	ZNF33A_ENST00000307441.9_Missense_Mutation_p.F169L|ZNF33A_ENST00000432900.2_Missense_Mutation_p.F176L|ZNF33A_ENST00000374618.3_Missense_Mutation_p.F170L|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F169L(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CTGATGAATTTAATGCCTGTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	10											63	64	63					10																	38343562		2203	4299	6502	38383568	SO:0001583	missense	7581			D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.507T>G	10.37:g.38343562T>G	ENSP00000387713:p.Phe169Leu		38383568	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	T	10.45	1.354513	0.24512	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	2.26	2.26	0.28386	.	0.444320	0.16836	N	0.197543	T	0.17023	0.0409	N	0.14661	0.345	0.19775	N	0.999951	B;B;B	0.15141	0.004;0.001;0.012	B;B;B	0.11329	0.006;0.003;0.006	T	0.17501	-1.0367	10	0.52906	T	0.07	.	8.0427	0.30532	0.0:0.0:0.0:1.0	.	176;169;170	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	L	170;176;169;169	ENSP00000363747:F170L;ENSP00000402467:F176L;ENSP00000387713:F169L;ENSP00000304268:F169L	ENSP00000304268:F169L	F	+	3	2	ZNF33A	38383568	0.003000	0.15002	0.998000	0.56505	0.514000	0.34195	0.885000	0.28227	1.021000	0.39600	0.377000	0.23210	TTT		0.318	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		G	38343562	T	G	38343562	3	3	47	1	0	0	0	0	1	0	0	0	17893	1751	61	4	524	4	ZNF33A	10	38343562	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	221977	38343562	97191185	1172	5569										
ZNF33A	7581	broad.mit.edu	37	chr10	38344089	38344089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagaagtcacatctcactcGacatcagagggtgcacacag	11	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:38344089G>A	ENST00000458705.2	+	5	1192	c.1034G>A	c.(1033-1035)cGa>cAa	p.R345Q	ZNF33A_ENST00000307441.9_Missense_Mutation_p.R345Q|ZNF33A_ENST00000432900.2_Missense_Mutation_p.R352Q|ZNF33A_ENST00000374618.3_Missense_Mutation_p.R346Q|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	345					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R345Q(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CATCTCACTCGACATCAGAGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											121	112	115					10																	38344089		2203	4300	6503	38384095	SO:0001583	missense	7581			D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1034G>A	10.37:g.38344089G>A	ENSP00000387713:p.Arg345Gln		38384095	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	G	1.478	-0.557926	0.03967	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.26223	3.21;1.75;3.21;3.21	2.05	0.898	0.19264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.389279	0.15551	N	0.256394	T	0.08358	0.0208	N	0.13235	0.315	0.09310	N	1	P;P;P	0.48089	0.905;0.703;0.7	B;B;B	0.28638	0.075;0.092;0.076	T	0.28004	-1.0057	10	0.13108	T	0.6	.	7.9186	0.29833	0.0:0.2575:0.7425:0.0	.	352;345;346	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	Q	346;352;345;345	ENSP00000363747:R346Q;ENSP00000402467:R352Q;ENSP00000387713:R345Q;ENSP00000304268:R345Q	ENSP00000304268:R345Q	R	+	2	0	ZNF33A	38384095	0.000000	0.05858	0.972000	0.41901	0.815000	0.46073	-1.771000	0.01789	1.117000	0.41842	0.460000	0.39030	CGA		0.403	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		A	38344089	G	A	38344089	3	1	47	1	0	0	0	0	1	0	0	0	17893	1058	37	1	1051	1	ZNF33A	10	38344089	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	527	38344089	97190658	1173	5570										
ZNF33B	7582	broad.mit.edu	37	chr10	43088932	43088932	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttatctcctatgtgagttCtctgatgctgtgtaagatgt	10	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:43088932C>A	ENST00000359467.3	-	5	1580	c.1466G>T	c.(1465-1467)aGa>aTa	p.R489I	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	489					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R489I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						TATGTGAGTTCTCTGATGCTG	0.403																																					Melanoma(137;1247 1767 16772 25727 43810)											1	Substitution - Missense(1)	large_intestine(1)	10											98	92	94					10																	43088932		2203	4299	6502	42408938	SO:0001583	missense	7582			X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1466G>T	10.37:g.43088932C>A	ENSP00000352444:p.Arg489Ile		42408938	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.453187	0.26161	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.24908	1.83	2.58	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.240647	0.21572	N	0.072393	T	0.19127	0.0459	L	0.53671	1.685	0.36585	D	0.873766	B	0.26876	0.162	B	0.21708	0.036	T	0.11717	-1.0576	10	0.49607	T	0.09	.	3.204	0.06659	0.2641:0.5903:0.0:0.1456	.	489	Q06732	ZN33B_HUMAN	I	489;455	ENSP00000352444:R489I	ENSP00000352444:R489I	R	-	2	0	ZNF33B	42408938	0.000000	0.05858	0.997000	0.53966	0.760000	0.43138	-0.204000	0.09425	0.639000	0.30564	0.416000	0.27883	AGA		0.403	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		A	43088932	C	A	43088932	3	1	47	1	0	0	0	0	1	0	0	0	17894	913	32	2	874	2	ZNF33B	10	43088932	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4744843	43088932	92445815	1174	5571										
BMS1	9790	broad.mit.edu	37	chr10	43288429	43288429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggagattttgccgtgagtgAcatcagtttcctcccagacc	10	11	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:43288429A>G	ENST00000374518.5	+	8	989	c.926A>G	c.(925-927)gAc>gGc	p.D309G		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	309					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.D309G(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GCCGTGAGTGACATCAGTTTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											129	130	130					10																	43288429		2203	4300	6503	42608435	SO:0001583	missense	9790			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.926A>G	10.37:g.43288429A>G	ENSP00000363642:p.Asp309Gly		42608435	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	a	16.05	3.014052	0.54468	.	.	ENSG00000165733	ENST00000374518	T	0.44083	0.93	5.51	5.51	0.81932	AARP2CN (2);	0.044609	0.85682	D	0.000000	T	0.58538	0.2129	L	0.54908	1.71	0.58432	D	0.999995	D	0.59357	0.985	D	0.65010	0.931	T	0.58999	-0.7536	10	0.51188	T	0.08	.	15.7626	0.78096	1.0:0.0:0.0:0.0	.	309	Q14692	BMS1_HUMAN	G	309	ENSP00000363642:D309G	ENSP00000363642:D309G	D	+	2	0	BMS1	42608435	1.000000	0.71417	0.956000	0.39512	0.754000	0.42855	8.743000	0.91592	2.129000	0.65627	0.467000	0.42956	GAC		0.473	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		G	43288429	A	G	43288429	3	3	47	1	0	0	0	0	1	0	0	0	1473	275	10	4	952	4	BMS1	10	43288429	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	199497	43288429	92246318	1175	5572										
HNRNPF	3185	broad.mit.edu	37	chr10	43882996	43882996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggagtcctcgaagccgcaCgaagccatcgttggcgctgt	14	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:43882996C>T	ENST00000544000.1	-	4	744	c.337G>A	c.(337-339)Gtg>Atg	p.V113M	HNRNPF_ENST00000356053.3_Missense_Mutation_p.V113M|HNRNPF_ENST00000498176.1_5'Flank|HNRNPF_ENST00000337970.3_Missense_Mutation_p.V113M|HNRNPF_ENST00000443950.2_Missense_Mutation_p.V113M|HNRNPF_ENST00000357065.4_Missense_Mutation_p.V113M	NM_001098207.1	NP_001091677.1	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F	113	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.V113M(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|urinary_tract(1)	19						CGAAGCCGCACGAAGCCATCG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	10											138	113	121					10																	43882996		2203	4300	6503	43203002	SO:0001583	missense	3185				CCDS7204.1	10q11.21	2013-02-12		2008-04-18	ENSG00000169813	ENSG00000169813		"RNA binding motif (RRM) containing"	5039	protein-coding gene	gene with protein product		601037		HNRPF		7499401	Standard	NM_001098208		Approved		uc001jas.2	P52597	OTTHUMG00000018029	ENST00000544000.1:c.337G>A	10.37:g.43882996C>T	ENSP00000438061:p.Val113Met		43203002	B3KM84|Q5T0N2|Q96AU2	Missense_Mutation	SNP	ENST00000544000.1	37	CCDS7204.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.368863	0.42003	.	.	ENSG00000169813	ENST00000544000;ENST00000443950;ENST00000356053;ENST00000357065;ENST00000337970;ENST00000540544	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	4.04	3.14	0.36123	RNA recognition motif domain (2);	0.059234	0.64402	D	0.000003	T	0.70561	0.3238	H	0.97874	4.095	0.58432	D	0.999997	D	0.76494	0.999	D	0.75484	0.986	T	0.78602	-0.2140	10	0.87932	D	0	-27.1198	10.0601	0.42270	0.0:0.8991:0.0:0.1009	.	113	P52597	HNRPF_HUMAN	M	113;113;113;113;113;36	ENSP00000438061:V113M;ENSP00000400433:V113M;ENSP00000348345:V113M;ENSP00000349573:V113M;ENSP00000338477:V113M	ENSP00000338477:V113M	V	-	1	0	HNRNPF	43203002	1.000000	0.71417	0.994000	0.49952	0.772000	0.43724	4.234000	0.58658	1.293000	0.44690	-0.136000	0.14681	GTG		0.517	HNRNPF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047705.2			T	43882996	C	T	43882996	3	4	47	1	0	0	0	0	1	0	0	0	7286	536	19	1	914	1	HNRNPF	10	43882996	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	594567	43882996	91651751	1176	5573										
MAPK8	5599	broad.mit.edu	37	chr10	49618104	49618104	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggagctcatggatgcaaatCtttgccaagtgattcagatg	11	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:49618104C>A	ENST00000374189.1	+	5	524	c.343C>A	c.(343-345)Ctt>Att	p.L115I	MAPK8_ENST00000360332.3_Missense_Mutation_p.L115I|MAPK8_ENST00000395611.3_Missense_Mutation_p.L115I|MAPK8_ENST00000374182.3_Missense_Mutation_p.L115I|MAPK8_ENST00000374174.1_Missense_Mutation_p.L115I			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.L115I(1)|p.L115F(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		GGATGCAAATCTTTGCCAAGT	0.383																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	10											177	163	168					10																	49618104		2203	4300	6503	49288110	SO:0001583	missense	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.343C>A	10.37:g.49618104C>A	ENSP00000363304:p.Leu115Ile		49288110	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.716924	0.89205	.	.	ENSG00000107643	ENST00000432379;ENST00000429041;ENST00000374189;ENST00000426557;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000374174;ENST00000395611	D;D;D;D;D;D;D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14;-3.14;-3.14;-3.14;-3.14;-3.14;-3.14	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	M	0.92026	3.265	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.999	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	D	0.97583	1.0112	10	0.87932	D	0	.	19.547	0.95302	0.0:1.0:0.0:0.0	.	115;115;115;115;115	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	I	115;32;115;115;115;115;115;115;115;115	ENSP00000387936:L115I;ENSP00000393223:L32I;ENSP00000363304:L115I;ENSP00000397729:L115I;ENSP00000363297:L115I;ENSP00000363294:L115I;ENSP00000353483:L115I;ENSP00000363291:L115I;ENSP00000363289:L115I;ENSP00000378974:L115I	ENSP00000353483:L115I	L	+	1	0	MAPK8	49288110	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.927000	0.63440	2.695000	0.91970	0.650000	0.86243	CTT		0.383	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			A	49618104	C	A	49618104	3	1	47	1	0	0	0	0	1	0	0	0	9313	913	32	2	357	2	MAPK8	10	49618104	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5735108	49618104	85916643	1177	5574										
CHAT	1103	broad.mit.edu	37	chr10	50859978	50859978	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tataagtttgacaactatggGaaaacattcattaagaagca	7	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:50859978G>A	ENST00000337653.2	+	11	1713	c.1560G>A	c.(1558-1560)ggG>ggA	p.G520G	CHAT_ENST00000395559.2_Silent_p.G402G|CHAT_ENST00000339797.1_Silent_p.G402G|CHAT_ENST00000455728.2_Silent_p.G402G|CHAT_ENST00000395562.2_Silent_p.G438G|CHAT_ENST00000351556.3_Silent_p.G402G	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	520	Coenzyme A binding.				adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.G520G(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	ACAACTATGGGAAAACATTCA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											68	64	65					10																	50859978		2203	4300	6503	50529984	SO:0001819	synonymous_variant	1103			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1560G>A	10.37:g.50859978G>A			50529984	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	37	CCDS7232.1																																																																																				0.413	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50859978	G	A	50859978	2	1	47	1	0	0	0	0	0	0	0	1	3319	1161	41	3		3	CHAT	10	50859978	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1241874	50859978	84674769	1178	5575										
PRKG1	5592	broad.mit.edu	37	chr10	53564439	53564439	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcataccgagtatatggaAtttttaaaaaggtaggatgc	10	4	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:53564439A>C	ENST00000401604.2	+	4	836	c.642A>C	c.(640-642)gaA>gaC	p.E214D	PRKG1_ENST00000373985.1_Missense_Mutation_p.E202D|PRKG1_ENST00000373980.4_Missense_Mutation_p.E229D			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	214	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.E229D(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AGTATATGGAATTTTTAAAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	79	82					10																	53564439		2203	4300	6503	53234445	SO:0001583	missense	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.642A>C	10.37:g.53564439A>C	ENSP00000384200:p.Glu214Asp		53234445	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	6.260	0.416108	0.11870	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.29	0.147	0.14838	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.058843	0.64402	D	0.000003	T	0.09512	0.0234	N	0.01874	-0.695	0.39931	D	0.974285	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23084	-1.0198	10	0.13108	T	0.6	-21.7804	8.9779	0.35946	0.5754:0.0:0.4246:0.0	.	229;214	Q13976-2;Q13976	.;KGP1_HUMAN	D	214;202;229;87	ENSP00000384200:E214D;ENSP00000363097:E202D;ENSP00000363092:E229D;ENSP00000363087:E87D	ENSP00000363087:E87D	E	+	3	2	PRKG1	53234445	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.798000	0.38814	0.069000	0.16605	0.402000	0.26972	GAA		0.383	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	53564439	A	C	53564439	3	2	47	1	0	0	0	0	1	0	0	0	12556	98	4	4	971	4	PRKG1	10	53564439	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2704461	53564439	81970308	1179	5576										
PCDH15	65217	broad.mit.edu	37	chr10	55582852	55582852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgggtctacaaaatctgttCtctgtgaaatgtctgaattt	8	6	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:55582852C>A	ENST00000320301.6	-	33	5028	c.4634G>T	c.(4633-4635)aGa>aTa	p.R1545I	PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.R1547I|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.R1522I|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.R1476I|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.R1505I|PCDH15_ENST00000395430.1_Missense_Mutation_p.R1542I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1545					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.R1552I(2)|p.R1545I(2)|p.R1552K(1)|p.R1545K(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAAATCTGTTCTCTGTGAAAT	0.393										HNSCC(58;0.16)																																						6	Substitution - Missense(6)	large_intestine(4)|upper_aerodigestive_tract(2)	10											86	93	90					10																	55582852		2203	4297	6500	55252858	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4634G>T	10.37:g.55582852C>A	ENSP00000322604:p.Arg1545Ile		55252858	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	5.722	0.317719	0.10845	.	.	ENSG00000150275	ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T	0.59906	0.28;0.26;0.3;0.27;0.26;0.23	5.91	0.533	0.17121	.	.	.	.	.	T	0.60534	0.2276	M	0.65498	2.005	0.39324	D	0.965307	P;B;B;B;B;P;P;B	0.49090	0.919;0.04;0.047;0.04;0.399;0.7;0.859;0.022	P;B;B;B;B;B;P;B	0.49708	0.62;0.018;0.04;0.018;0.071;0.288;0.62;0.018	T	0.60850	-0.7181	9	0.48119	T	0.1	.	10.663	0.45712	0.0:0.5206:0.0:0.4794	.	1522;1545;1547;1552;1476;1505;1542;1545	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;Q96QU1	.;.;.;.;.;.;.;PCD15_HUMAN	I	1505;1547;1522;1545;1542;1552;1476	ENSP00000378820:R1505I;ENSP00000354950:R1547I;ENSP00000378821:R1522I;ENSP00000322604:R1545I;ENSP00000378818:R1542I;ENSP00000412628:R1476I	ENSP00000322604:R1545I	R	-	2	0	PCDH15	55252858	0.939000	0.31865	0.008000	0.14137	0.030000	0.12068	1.257000	0.32932	-0.147000	0.11254	-0.157000	0.13467	AGA		0.393	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55582852	C	A	55582852	3	1	47	1	0	0	0	0	1	0	0	0	11542	913	32	2	2843	2	PCDH15	10	55582852	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2018413	55582852	79951895	1180	5577										
ANK3	288	broad.mit.edu	37	chr10	61834043	61834043	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggttccaattccataaaaGtaggtgaaggtttaggtgac	11	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:61834043G>T	ENST00000280772.2	-	37	6787	c.6596C>A	c.(6595-6597)aCt>aAt	p.T2199N	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2199					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.T2199N(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTCCATAAAAGTAGGTGAAGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											123	123	123					10																	61834043		2203	4300	6503	61504049	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.6596C>A	10.37:g.61834043G>T	ENSP00000280772:p.Thr2199Asn		61504049	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	6.538	0.467546	0.12402	.	.	ENSG00000151150	ENST00000280772	T	0.63255	-0.03	6.05	6.05	0.98169	.	0.546643	0.15276	N	0.270975	T	0.55000	0.1893	N	0.22421	0.69	0.41184	D	0.986254	B	0.27068	0.167	B	0.26310	0.068	T	0.52019	-0.8631	10	0.56958	D	0.05	.	20.6032	0.99464	0.0:0.0:1.0:0.0	.	2199	Q12955	ANK3_HUMAN	N	2199	ENSP00000280772:T2199N	ENSP00000280772:T2199N	T	-	2	0	ANK3	61504049	0.512000	0.26186	0.009000	0.14445	0.982000	0.71751	3.816000	0.55658	2.875000	0.98604	0.643000	0.83706	ACT		0.448	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61834043	G	T	61834043	3	4	47	1	0	0	0	0	1	0	0	0	622	1029	36	2	6878	2	ANK3	10	61834043	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6251191	61834043	73700704	1181	5578										
ARID5B	84159	broad.mit.edu	37	chr10	63817044	63817044	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaagaaaggaaaacgccgAtagaacgaataccctattta	8	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:63817044A>G	ENST00000279873.7	+	6	1425	c.1015A>G	c.(1015-1017)Ata>Gta	p.I339V	ARID5B_ENST00000309334.5_Missense_Mutation_p.I96V	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	339	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)	p.I339V(1)		NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					GAAAACGCCGATAGAACGAAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											104	112	109					10																	63817044		2203	4300	6503	63487050	SO:0001583	missense	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1015A>G	10.37:g.63817044A>G	ENSP00000279873:p.Ile339Val		63487050	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	37	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.283872	0.80803	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.64085	-0.08;-0.08	5.96	5.96	0.96718	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	M	0.62209	1.925	0.80722	D	1	P;P	0.50943	0.94;0.761	P;P	0.61003	0.882;0.822	T	0.75408	-0.3328	10	0.49607	T	0.09	-16.4409	16.4484	0.83959	1.0:0.0:0.0:0.0	.	96;339	Q14865-2;Q14865	.;ARI5B_HUMAN	V	339;96	ENSP00000279873:I339V;ENSP00000308862:I96V	ENSP00000279873:I339V	I	+	1	0	ARID5B	63487050	1.000000	0.71417	0.979000	0.43373	0.998000	0.95712	8.962000	0.93254	2.285000	0.76669	0.533000	0.62120	ATA		0.368	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63817044	A	G	63817044	3	3	47	1	0	0	0	0	1	0	0	0	922	333	12	4	1037	4	ARID5B	10	63817044	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1983001	63817044	71717703	1182	5579										
TET1	80312	broad.mit.edu	37	chr10	70333934	70333934	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttactgcaagaacagaaaGaacagccatcagatctgtaa	7	9	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:70333934G>T	ENST00000373644.4	+	2	2048	c.1839G>T	c.(1837-1839)aaG>aaT	p.K613N		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	613	Sufficient for binding to genomic CpG islands.				chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.K613N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AGAACAGAAAGAACAGCCATC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											81	86	84					10																	70333934		2203	4300	6503	70003940	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1839G>T	10.37:g.70333934G>T	ENSP00000362748:p.Lys613Asn		70003940	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973686	0.53720	.	.	ENSG00000138336	ENST00000373644	T	0.09911	2.93	5.27	2.0	0.26442	Zinc finger, CXXC-type (2);	0.169907	0.36665	N	0.002474	T	0.24160	0.0585	M	0.66939	2.045	0.27877	N	0.939828	D	0.89917	1.0	D	0.85130	0.997	T	0.02683	-1.1124	10	0.72032	D	0.01	.	4.9337	0.13930	0.5335:0.0:0.4665:0.0	.	613	Q8NFU7	TET1_HUMAN	N	613	ENSP00000362748:K613N	ENSP00000362748:K613N	K	+	3	2	TET1	70003940	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.212000	0.32394	0.613000	0.30089	0.467000	0.42956	AAG		0.458	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70333934	G	T	70333934	3	4	47	1	0	0	0	0	1	0	0	0	15808	933	33	2	1841	2	TET1	10	70333934	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6516890	70333934	65200813	1183	5580										
TET1	80312	broad.mit.edu	37	chr10	70451194	70451194	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atattggtggggtggccatcGcacctgctcacggctcggtt	14	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:70451194G>A	ENST00000373644.4	+	12	6243	c.6034G>A	c.(6034-6036)Gca>Aca	p.A2012T		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	2012					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.A2012T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GGTGGCCATCGCACCTGCTCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	123	126					10																	70451194		2203	4300	6503	70121200	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.6034G>A	10.37:g.70451194G>A	ENSP00000362748:p.Ala2012Thr		70121200	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.496312	0.85069	.	.	ENSG00000138336	ENST00000373644	T	0.14766	2.48	5.6	5.6	0.85130	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	0.299915	0.36134	N	0.002768	T	0.39332	0.1074	M	0.78049	2.395	0.42665	D	0.993495	D	0.89917	1.0	D	0.91635	0.999	T	0.15350	-1.0440	10	0.87932	D	0	.	14.7863	0.69806	0.0:0.0:0.8557:0.1443	.	2012	Q8NFU7	TET1_HUMAN	T	2012	ENSP00000362748:A2012T	ENSP00000362748:A2012T	A	+	1	0	TET1	70121200	1.000000	0.71417	0.668000	0.29813	0.657000	0.38888	7.406000	0.80017	2.806000	0.96561	0.655000	0.94253	GCA		0.552	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70451194	G	A	70451194	3	1	47	1	0	0	0	0	1	0	0	0	15808	1087	38	1	6076	1	TET1	10	70451194	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	117260	70451194	65083553	1184	5581										
KIAA1274	27143	broad.mit.edu	37	chr10	72294540	72294540	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgagttgcatgacctgaaaGaagtggtcttggaaaaccag	12	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:72294540G>T	ENST00000263563.6	+	10	1436	c.1168G>T	c.(1168-1170)Gaa>Taa	p.E390*		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	390						cytosol (GO:0005829)		p.E390*(1)									TGACCTGAAAGAAGTGGTCTT	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											72	67	69					10																	72294540		2203	4300	6503	71964546	SO:0001587	stop_gained	27143			AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.1168G>T	10.37:g.72294540G>T	ENSP00000263563:p.Glu390*		71964546	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Nonsense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	G	38	7.235509	0.98154	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	.	.	.	5.34	4.44	0.53790	.	0.099226	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-5.3082	13.7744	0.63044	0.0747:0.0:0.9253:0.0	.	.	.	.	X	390	.	ENSP00000263563:E390X	E	+	1	0	KIAA1274	71964546	1.000000	0.71417	0.394000	0.26270	0.449000	0.32228	6.118000	0.71583	1.385000	0.46445	0.563000	0.77884	GAA		0.577	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72294540	G	T	72294540	4	4	47	1	0	0	0	0	0	1	0	0	8241	943	33	2	1202	2	KIAA1274	10	72294540	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1843346	72294540	63240207	1185	5582										
CDH23	64072	broad.mit.edu	37	chr10	73326600	73326600	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccagcccccctcccaattCttcgccattgacagcgcccg	6	20	1	1	rs371933124		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:73326600C>A	ENST00000224721.6	+	6	551	c.546C>A	c.(544-546)ttC>ttA	p.F182L	CDH23_ENST00000461841.3_Missense_Mutation_p.F222L|CDH23_ENST00000398809.4_Missense_Mutation_p.F177L|CDH23_ENST00000299366.7_Missense_Mutation_p.F222L|CDH23_ENST00000398842.3_Missense_Mutation_p.F177L	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	177	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.F177L(2)|p.F182L(2)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCTCCCAATTCTTCGCCATTG	0.617																																																4	Substitution - Missense(4)	large_intestine(4)	10											48	51	50					10																	73326600		2031	4183	6214	72996606	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.546C>A	10.37:g.73326600C>A	ENSP00000224721:p.Phe182Leu		72996606	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	13.13	2.144130	0.37825	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.01665	4.7;4.7	5.43	3.2	0.36748	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.02156	0.0067	N	0.04090	-0.28	0.80722	D	1	B;D;B;D	0.69078	0.419;0.997;0.029;0.997	B;D;B;D	0.78314	0.168;0.91;0.01;0.991	T	0.68735	-0.5330	10	0.11485	T	0.65	.	7.956	0.30042	0.1397:0.716:0.0:0.1443	.	177;177;177;177	A5D6V9;Q9H251;Q9H251-5;E7ESV7	.;CAD23_HUMAN;.;.	L	182;177;177;177;177;182;182;118	ENSP00000381789:F177L;ENSP00000381822:F177L	ENSP00000224721:F182L	F	+	3	2	CDH23	72996606	1.000000	0.71417	0.998000	0.56505	0.944000	0.59088	1.909000	0.39917	1.277000	0.44412	0.561000	0.74099	TTC		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73326600	C	A	73326600	3	1	47	1	0	0	0	0	1	0	0	0	3114	912	32	2	553	2	CDH23	10	73326600	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1032060	73326600	62208147	1186	5583										
CDH23	64072	broad.mit.edu	37	chr10	73461952	73461952	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagctgatgcgcaaaatcgtCgtctctgttactgactgtat	10	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:73461952C>T	ENST00000224721.6	+	22	2591	c.2586C>T	c.(2584-2586)gtC>gtT	p.V862V	CDH23_ENST00000299366.7_Silent_p.V902V	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	857	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.V862V(2)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCAAAATCGTCGTCTCTGTTA	0.652																																																2	Substitution - coding silent(2)	large_intestine(2)	10											118	137	130					10																	73461952		2125	4202	6327	73131958	SO:0001819	synonymous_variant	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2586C>T	10.37:g.73461952C>T			73131958	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																					0.652	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73461952	C	T	73461952	2	4	47	1	0	0	0	0	0	0	0	1	3114	871	31	1		1	CDH23	10	73461952	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	135352	73461952	62072795	1187	5584										
CDH23	64072	broad.mit.edu	37	chr10	73560498	73560498	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgtagccagcaaccgtcgcGaaaattcagtgcaggtgagg	13	9	1	1	rs41281336	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:73560498G>A	ENST00000224721.6	+	52	7488	c.7483G>A	c.(7483-7485)Gaa>Aaa	p.E2495K	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.E250K	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2490	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.E2495K(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CAACCGTCGCGAAAATTCAGT	0.562													G|||	3	0.000599042	8e-04	0	5008	,	,		18715	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						G	LYS/GLU,LYS/GLU,LYS/GLU	1,3991		0,1,1995	51	55	54		748,748,7468	5.5	1	10	dbSNP_127	54	4,8296		0,4,4146	yes	missense,missense,missense	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	56,56,56	0,5,6141	AA,AG,GG		0.0482,0.0251,0.0407	probably-damaging,probably-damaging,probably-damaging	250/1115,250/1080,2490/3355	73560498	5,12287	1996	4150	6146	73230504	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7483G>A	10.37:g.73560498G>A	ENSP00000224721:p.Glu2495Lys		73230504	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	3	0.005244755244755245	2	0.002638522427440633	G	35	5.422533	0.96111	2.51E-4	4.82E-4	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.53857	0.6	5.5	5.5	0.81552	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53546	0.1803	L	0.33624	1.015	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.80764	0.994;0.895	T	0.50154	-0.8861	10	0.11794	T	0.64	.	19.3982	0.94617	0.0:0.0:1.0:0.0	rs41281336	2490;2490	E9PEX1;Q9H251	.;CAD23_HUMAN	K	2495;2490;2493;250	ENSP00000381768:E250K	ENSP00000224721:E2495K	E	+	1	0	CDH23	73230504	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	9.199000	0.95003	2.584000	0.87258	0.585000	0.79938	GAA		0.562	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73560498	G	A	73560498	3	1	47	1	0	0	0	0	1	0	0	0	3114	1059	37	1	8019	1	CDH23	10	73560498	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	98546	73560498	61974249	1188	5585										
OIT3	170392	broad.mit.edu	37	chr10	74684270	74684270	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctctgcccaccctcaagcTtcgtgactccctctactttg	6	17	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:74684270T>G	ENST00000334011.5	+	7	1453	c.1235T>G	c.(1234-1236)cTt>cGt	p.L412R		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	412	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L412R(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					ACCCTCAAGCTTCGTGACTCC	0.542																																					Colon(7;19 345 13446 17537)											1	Substitution - Missense(1)	large_intestine(1)	10											131	120	124					10																	74684270		2203	4300	6503	74354276	SO:0001583	missense	170392				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1235T>G	10.37:g.74684270T>G	ENSP00000333900:p.Leu412Arg		74354276	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.322532	0.81580	.	.	ENSG00000138315	ENST00000334011	D	0.86030	-2.06	5.26	5.26	0.73747	Zona pellucida sperm-binding protein (3);	0.000000	0.50627	D	0.000116	D	0.92087	0.7492	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93146	0.6545	10	0.87932	D	0	-16.1712	15.1596	0.72771	0.0:0.0:0.0:1.0	.	412	Q8WWZ8	OIT3_HUMAN	R	412	ENSP00000333900:L412R	ENSP00000333900:L412R	L	+	2	0	OIT3	74354276	1.000000	0.71417	0.918000	0.36340	0.962000	0.63368	7.739000	0.84976	1.989000	0.58080	0.460000	0.39030	CTT		0.542	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		G	74684270	T	G	74684270	3	3	47	1	0	0	0	0	1	0	0	0	10880	1609	56	4	1261	4	OIT3	10	74684270	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1123772	74684270	60850477	1189	5586										
P4HA1	5033	broad.mit.edu	37	chr10	74831898	74831898	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacaaatccttctggatcttTtgtcgctgtactagttagcc	7	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:74831898T>G	ENST00000307116.2	-	4	330	c.214A>C	c.(214-216)Aaa>Caa	p.K72Q	RP11-344N10.2_ENST00000431293.2_RNA|P4HA1_ENST00000412021.2_Missense_Mutation_p.K72Q|P4HA1_ENST00000440381.1_Missense_Mutation_p.K72Q|P4HA1_ENST00000394890.2_Missense_Mutation_p.K72Q|P4HA1_ENST00000373008.2_Missense_Mutation_p.K72Q|P4HA1_ENST00000263556.3_Missense_Mutation_p.K72Q			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	72					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.K72Q(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TCTGGATCTTTTGTCGCTGTA	0.358																																					Colon(147;367 2405 2662 52127)											2	Substitution - Missense(2)	large_intestine(2)	10											150	148	148					10																	74831898		2203	4300	6503	74501904	SO:0001583	missense	5033				CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.214A>C	10.37:g.74831898T>G	ENSP00000307318:p.Lys72Gln		74501904	C9JL12|Q15082|Q15083|Q5VSQ5	Missense_Mutation	SNP	ENST00000307116.2	37		.	.	.	.	.	.	.	.	.	.	T	12.67	2.007306	0.35415	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	T;T;T;T;T;T	0.44482	0.93;0.92;0.93;0.93;0.92;0.93	5.21	2.87	0.33458	Prolyl 4-hydroxylase alpha-subunit, N-terminal (1);	0.147775	0.64402	D	0.000010	T	0.23289	0.0563	N	0.13098	0.295	0.43593	D	0.995941	B;B;B	0.19583	0.018;0.016;0.037	B;B;B	0.21360	0.021;0.034;0.034	T	0.04386	-1.0955	10	0.21540	T	0.41	-14.3861	9.3069	0.37881	0.0:0.1459:0.0:0.8541	.	72;72;72	C9JL12;Q5VSQ6;P13674	.;.;P4HA1_HUMAN	Q	72	ENSP00000307318:K72Q;ENSP00000362099:K72Q;ENSP00000411688:K72Q;ENSP00000378353:K72Q;ENSP00000263556:K72Q;ENSP00000414464:K72Q	ENSP00000263556:K72Q	K	-	1	0	P4HA1	74501904	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	4.104000	0.57790	0.446000	0.26666	0.402000	0.26972	AAA		0.358	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		G	74831898	T	G	74831898	3	3	47	1	0	0	0	0	1	0	0	0	11387	1850	64	4	1513	4	P4HA1	10	74831898	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	147628	74831898	60702849	1190	5587										
NUDT13	25961	broad.mit.edu	37	chr10	74881983	74881983	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggatgcacaaagaatagaaGattctgtgctgattggatgc	12	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:74881983G>A	ENST00000357321.4	+	4	392	c.274G>A	c.(274-276)Gat>Aat	p.D92N	NUDT13_ENST00000537969.1_5'UTR|RP11-152N13.16_ENST00000608444.1_RNA|NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000372997.3_Missense_Mutation_p.D92N|NUDT13_ENST00000349051.5_Missense_Mutation_p.D92N|NUDT13_ENST00000488223.1_3'UTR	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13									p.D92N(1)		large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					AAGAATAGAAGATTCTGTGCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											177	167	171					10																	74881983		2203	4300	6503	74551989	SO:0001583	missense	25961			AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.274G>A	10.37:g.74881983G>A	ENSP00000349874:p.Asp92Asn		74551989		Missense_Mutation	SNP	ENST00000357321.4	37	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551129	0.86127	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.28666	1.6;1.6;1.6	6.08	4.12	0.48240	NADH pyrophosphatase-like, N-terminal (1);	0.296331	0.41712	D	0.000825	T	0.38081	0.1027	L	0.60455	1.87	0.80722	D	1	D;D;B	0.55172	0.96;0.97;0.163	P;P;B	0.53401	0.648;0.725;0.122	T	0.17501	-1.0367	10	0.49607	T	0.09	.	7.238	0.26079	0.0771:0.1352:0.6644:0.1233	.	92;92;92	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	N	92	ENSP00000349874:D92N;ENSP00000335326:D92N;ENSP00000362088:D92N	ENSP00000335326:D92N	D	+	1	0	NUDT13	74551989	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.430000	0.44766	1.578000	0.49821	0.655000	0.94253	GAT		0.433	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		A	74881983	G	A	74881983	3	1	47	1	0	0	0	0	1	0	0	0	10760	942	33	3	284	3	NUDT13	10	74881983	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	50085	74881983	60652764	1191	5588										
ECD	11319	broad.mit.edu	37	chr10	74897827	74897827	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gattggagcctcagaaggttCtctgcaatattaaaggacaa	10	7	2	1	rs34313575	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:74897827C>A	ENST00000372979.4	-	12	1629	c.1423G>T	c.(1423-1425)Gaa>Taa	p.E475*	ECD_ENST00000430082.2_Splice_Site_p.E508*|ECD_ENST00000454759.2_Splice_Site_p.E432*	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	475					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.E475*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TCAGAAGGTTCTCTGCAATAT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											47	46	46					10																	74897827		2203	4300	6503	74567833	SO:0001630	splice_region_variant	11319			BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1422-1G>T	10.37:g.74897827C>A			74567833	C9JX46|E9PAW8	Nonsense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	C	38	6.825452	0.97865	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	.	.	.	5.96	4.11	0.48088	.	0.809523	0.12132	N	0.496645	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-2.7707	10.0653	0.42299	0.0:0.8384:0.0:0.1616	.	.	.	.	X	475;508;432	.	ENSP00000362070:E475X	E	-	1	0	ECD	74567833	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.879000	0.28146	1.511000	0.48818	0.650000	0.86243	GAA		0.313	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Nonsense_Mutation	A	74897827	C	A	74897827	5	1	47	1	0	0	0	0	0	0	1	0	4899	927	32	2	523	2	ECD	10	74897827	Splice_Site	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15844	74897827	60636920	1192	5589										
MYOZ1	58529	broad.mit.edu	37	chr10	75397517	75397517	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaccattgagctgtcagaGaaaacatcagggtggttctc	10	10	4	2	rs139515548		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:75397517G>T	ENST00000359322.4	-	3	601	c.237C>A	c.(235-237)ttC>ttA	p.F79L		NM_021245.3	NP_067068.1			myozenin 1									p.F79L(1)		central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					AGCTGTCAGAGAAAACATCAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	LEU/PHE	0,4406		0,0,2203	137	128	131		237	1.3	1	10	dbSNP_134	131	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYOZ1	NM_021245.2	22	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	possibly-damaging	79/300	75397517	1,13005	2203	4300	6503	75067523	SO:0001583	missense	58529			AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"calsarcin-2"	605603	"myozenin"	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.237C>A	10.37:g.75397517G>T	ENSP00000352272:p.Phe79Leu		75067523		Missense_Mutation	SNP	ENST00000359322.4	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137475	0.77775	0.0	1.16E-4	ENSG00000177791	ENST00000359322	T	0.63417	-0.04	6.17	1.28	0.21552	.	0.000000	0.85682	D	0.000000	T	0.73560	0.3602	M	0.71581	2.175	0.58432	D	0.999997	D	0.76494	0.999	D	0.83275	0.996	T	0.71523	-0.4567	10	0.56958	D	0.05	-13.3648	9.312	0.37910	0.3941:0.0:0.6059:0.0	.	79	Q9NP98	MYOZ1_HUMAN	L	79	ENSP00000352272:F79L	ENSP00000352272:F79L	F	-	3	2	MYOZ1	75067523	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.780000	0.55386	0.192000	0.20272	-0.793000	0.03317	TTC		0.483	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1			T	75397517	G	T	75397517	3	4	47	1	0	0	0	0	1	0	0	0	10125	933	33	2	678	2	MYOZ1	10	75397517	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	499690	75397517	60137230	1193	5590										
MYST4	23522	broad.mit.edu	37	chr10	76788342	76788342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtggccaaaaggaacaaagCgcggtctatctaagtggagg	14	7	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:76788342C>T	ENST00000287239.4	+	18	4249	c.3760C>T	c.(3760-3762)Cgc>Tgc	p.R1254C	KAT6B_ENST00000372711.1_Missense_Mutation_p.R1071C|KAT6B_ENST00000372714.1_Missense_Mutation_p.R962C|KAT6B_ENST00000372724.1_Missense_Mutation_p.R962C|KAT6B_ENST00000372725.1_Missense_Mutation_p.R962C	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1254					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1254C(1)									AGGAACAAAGCGCGGTCTATC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											80	79	80					10																	76788342		2203	4300	6503	76458348	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3760C>T	10.37:g.76788342C>T	ENSP00000287239:p.Arg1254Cys		76458348	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.352834	0.41700	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.84442	-1.79;-1.79;-1.85;-1.79;-1.8	5.22	5.22	0.72569	.	0.280615	0.25596	N	0.029581	D	0.86104	0.5853	L	0.29908	0.895	0.80722	D	1	D;D;D	0.71674	0.998;0.976;0.996	P;P;P	0.56916	0.809;0.644;0.65	D	0.88078	0.2805	10	0.87932	D	0	-1.5229	16.9383	0.86209	0.0:1.0:0.0:0.0	.	1071;962;1254	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	C	962;962;1254;962;1071	ENSP00000361810:R962C;ENSP00000361809:R962C;ENSP00000287239:R1254C;ENSP00000361799:R962C;ENSP00000361796:R1071C	ENSP00000287239:R1254C	R	+	1	0	KAT6B	76458348	1.000000	0.71417	0.963000	0.40424	0.557000	0.35523	6.914000	0.75764	2.437000	0.82529	0.491000	0.48974	CGC		0.443	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		T	76788342	C	T	76788342	3	4	47	1	0	0	0	0	1	0	0	0	10135	768	27	1	3822	1	MYST4	10	76788342	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1390825	76788342	58746405	1194	5591										
KCNMA1	3778	broad.mit.edu	37	chr10	78785210	78785210	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgaagagtgcataccgctttCggcttctgcaaaacgacaag	10	11	1	1	rs372858979		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:78785210C>T	ENST00000286628.8	-	16	1928				KCNMA1_ENST00000372443.1_Intron|KCNMA1_ENST00000404771.3_Intron|KCNMA1_ENST00000354353.5_Intron|KCNMA1_ENST00000404857.1_Intron|KCNMA1_ENST00000286627.5_Intron|KCNMA1_ENST00000406533.3_Intron|KCNMA1_ENST00000372440.1_Intron	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1						blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	ATACCGCTTTCGGCTTCTGCA	0.373													C|||	1	0.000199681	8e-04	0	5008	,	,		10725	0		0	False		,,,				2504	0															0			10						C	GLN/ARG,,,	1,3671		0,1,1835	84	82	82		1934,,,	5.9	1	10		82	0,8162		0,0,4081	no	missense,intron,intron,intron	KCNMA1	NM_001014797.2,NM_001161352.1,NM_001161353.1,NM_002247.3	43,,,	0,1,5916	TT,TC,CC		0.0,0.0272,0.0085	,,,	645/1183,,,	78785210	1,11833	1836	4081	5917	78455216	SO:0001627	intron_variant	3778			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.1928+2370G>A	10.37:g.78785210C>T			78455216	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37																																																																																					0.373	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		T	78785210	C	T	78785210	1	4	47	0	1	0	0	0	0	0	0	0	8094	884	31	1		1	KCNMA1	10	78785210	Intron	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1996868	78785210	56749537	1195	5592										
ANXA11	311	broad.mit.edu	37	chr10	81923335	81923335	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaagtgccctgatgtgtcGcttcgaatggcctcttccag	12	11	1	1	rs574331613		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:81923335G>A	ENST00000438331.1	-	11	1466	c.984C>T	c.(982-984)agC>agT	p.S328S	ANXA11_ENST00000535999.1_Silent_p.S328S|ANXA11_ENST00000360615.4_Silent_p.S328S|ANXA11_ENST00000265447.4_Silent_p.S328S|ANXA11_ENST00000537102.1_Silent_p.S295S|ANXA11_ENST00000422982.3_Silent_p.S328S|ANXA11_ENST00000372231.3_Silent_p.S328S	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	328					cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)	p.S328S(1)		endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			CTGATGTGTCGCTTCGAATGG	0.527													.|||	1	0.000199681	8e-04	0	5008	,	,		17266	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											44	46	46					10																	81923335		2198	4290	6488	81913315	SO:0001819	synonymous_variant	311			L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.984C>T	10.37:g.81923335G>A			81913315	B4DVE7	Silent	SNP	ENST00000438331.1	37	CCDS7364.1																																																																																				0.527	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		A	81923335	G	A	81923335	2	1	47	1	0	0	0	0	0	0	0	1	716	1078	38	1		1	ANXA11	10	81923335	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3138125	81923335	53611412	1196	5593										
PTEN	5728	broad.mit.edu	37	chr10	89624245	89624245	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatgacagccatcatcaaaGagatcgttagcagaaacaaa	7	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:89624245G>T	ENST00000371953.3	+	1	1376	c.19G>T	c.(19-21)Gag>Tag	p.E7*	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	7					activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.E7*(9)|p.A3fs*14(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CATCATCAAAGAGATCGTTAG	0.488		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	60	Whole gene deletion(37)|Unknown(13)|Substitution - Nonsense(9)|Deletion - Frameshift(1)	prostate(14)|central_nervous_system(10)|skin(7)|lung(6)|endometrium(5)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											162	159	160					10																	89624245		2203	4300	6503	89614225	SO:0001587	stop_gained	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.19G>T	10.37:g.89624245G>T	ENSP00000361021:p.Glu7*		89614225	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	49	15.654251	0.99841	.	.	ENSG00000171862	ENST00000371953	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.2094	16.4773	0.84136	0.0:0.0:1.0:0.0	.	.	.	.	X	7	.	.	E	+	1	0	PTEN	89614225	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.961000	0.76042	2.160000	0.67779	0.561000	0.74099	GAG		0.488	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624245	G	T	89624245	4	4	47	1	0	0	0	0	0	1	0	0	12772	943	33	2	21	2	PTEN	10	89624245	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7700910	89624245	45910502	1197	5594										
LIPF	8513	broad.mit.edu	37	chr10	90427393	90427393	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgactgaagatggttataTtcttgaagtcaatagaattc	9	4	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:90427393T>G	ENST00000238983.4	+	3	219	c.173T>G	c.(172-174)aTt>aGt	p.I58S	LIPF_ENST00000355843.2_Missense_Mutation_p.I68S|LIPF_ENST00000608620.1_Missense_Mutation_p.I58S|LIPF_ENST00000394375.3_Missense_Mutation_p.I68S	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	58					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)	p.I58S(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	GATGGTTATATTCTTGAAGTC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	102	96					10																	90427393		2203	4295	6498	90417373	SO:0001583	missense	8513			X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.173T>G	10.37:g.90427393T>G	ENSP00000238983:p.Ile58Ser		90417373	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Missense_Mutation	SNP	ENST00000238983.4	37	CCDS7389.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.405959	0.62288	.	.	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	D;D;T	0.88509	-2.39;-2.39;-0.51	4.64	4.64	0.57946	Partial AB-hydrolase lipase domain (1);	0.000000	0.53938	D	0.000047	D	0.96250	0.8777	H	0.97635	4.045	0.47819	D	0.999522	P;D;D;D;D	0.89917	0.952;1.0;1.0;0.996;1.0	D;D;D;D;D	0.81914	0.958;0.994;0.993;0.977;0.995	D	0.97222	0.9878	10	0.66056	D	0.02	-14.5144	13.1566	0.59520	0.0:0.0:0.0:1.0	.	58;68;68;68;58	Q5VXI8;F5H1P4;B7Z723;Q658L8;P07098	.;.;.;.;LIPG_HUMAN	S	68;58;58	ENSP00000377900:I68S;ENSP00000238983:I58S;ENSP00000348101:I58S	ENSP00000238983:I58S	I	+	2	0	LIPF	90417373	0.989000	0.36119	0.942000	0.38095	0.713000	0.41058	4.767000	0.62286	1.942000	0.56320	0.528000	0.53228	ATT		0.333	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			G	90427393	T	G	90427393	3	3	47	1	0	0	0	0	1	0	0	0	8846	1493	52	4	179	4	LIPF	10	90427393	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	803148	90427393	45107354	1198	5595										
LIPF	8513	broad.mit.edu	37	chr10	90438396	90438396	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggatgcccctcaagaagtTtacaatgacattgtttctat	7	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:90438396T>G	ENST00000238983.4	+	10	1201	c.1155T>G	c.(1153-1155)gtT>gtG	p.V385V	LIPF_ENST00000355843.2_Silent_p.V362V|LIPF_ENST00000608620.1_Silent_p.V352V|LIPF_ENST00000394375.3_Silent_p.V395V	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	385					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)	p.V385V(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	CTCAAGAAGTTTACAATGACA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	10											62	67	65					10																	90438396		2203	4300	6503	90428376	SO:0001819	synonymous_variant	8513			X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.1155T>G	10.37:g.90438396T>G			90428376	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Silent	SNP	ENST00000238983.4	37	CCDS7389.1																																																																																				0.338	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			G	90438396	T	G	90438396	2	3	47	1	0	0	0	0	0	0	0	1	8846	1828	64	4		4	LIPF	10	90438396	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	11003	90438396	45096351	1199	5596										
FAS	355	broad.mit.edu	37	chr10	90767572	90767572	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttccaaatgcagaagatgTagattgtgtgatgaaggaca	11	5	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:90767572T>C	ENST00000355279.2	+	3	312	c.312T>C	c.(310-312)tgT>tgC	p.C104C	FAS_ENST00000355740.2_Silent_p.C104C|FAS_ENST00000357339.2_Silent_p.C104C|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000352159.4_Silent_p.C104C			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C104C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	GCAGAAGATGTAGATTGTGTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											145	136	139					10																	90767572		2203	4300	6503	90757552	SO:0001819	synonymous_variant	355			M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.312T>C	10.37:g.90767572T>C			90757552	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000355279.2	37	CCDS7395.1																																																																																				0.413	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			C	90767572	T	C	90767572	2	2	47	1	0	0	0	0	0	0	0	1	5700	1644	57	4		4	FAS	10	90767572	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	329176	90767572	44767175	1200	5597										
FAS	355	broad.mit.edu	37	chr10	90774124	90774124	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctttgtactcttgcagagAaaattcagactatcatcctc	5	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:90774124A>C	ENST00000355740.2	+	9	1145	c.925A>C	c.(925-927)Aaa>Caa	p.K309Q	RP11-399O19.9_ENST00000562983.1_RNA|FAS_ENST00000357339.2_Missense_Mutation_p.K288Q|FAS_ENST00000352159.4_3'UTR|FAS_ENST00000355279.2_3'UTR	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K309Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	TCTTGCAGAGAAAATTCAGAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											66	69	68					10																	90774124		2203	4299	6502	90764104	SO:0001583	missense	355			M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355740.2:c.925A>C	10.37:g.90774124A>C	ENSP00000347979:p.Lys309Gln		90764104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355740.2	37	CCDS7393.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.678318	0.29783	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000357339	D;D	0.86562	-2.14;-2.14	4.55	2.19	0.27852	Death (3);DEATH-like (2);	0.899723	0.09265	N	0.825966	D	0.87034	0.6077	M	0.70275	2.135	0.09310	N	1	P;D	0.58268	0.955;0.982	B;P	0.47827	0.422;0.558	T	0.76307	-0.3007	10	0.62326	D	0.03	-26.4853	5.6841	0.17792	0.7831:0.0:0.2169:0.0	.	288;309	P25445-6;P25445	.;TNR6_HUMAN	Q	336;309;288	ENSP00000347979:K309Q;ENSP00000349896:K288Q	ENSP00000347979:K309Q	K	+	1	0	FAS	90764104	0.001000	0.12720	0.004000	0.12327	0.071000	0.16799	0.960000	0.29253	0.806000	0.34183	0.528000	0.53228	AAA		0.348	FAS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049274.3			C	90774124	A	C	90774124	3	2	47	1	0	0	0	0	1	0	0	0	5700	247	9	4	959	4	FAS	10	90774124	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6552	90774124	44760623	1201	5598										
KIF20B	9585	broad.mit.edu	37	chr10	91497519	91497519	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatagaaactgctacaagaaGcattacaaataatgtttcac	6	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:91497519G>A	ENST00000371728.3	+	20	2986	c.2921G>A	c.(2920-2922)aGc>aAc	p.S974N	KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Missense_Mutation_p.S974N|KIF20B_ENST00000260753.4_Missense_Mutation_p.S934N|KIF20B_ENST00000416354.1_Missense_Mutation_p.S1004N	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	974					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.S934N(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GCTACAAGAAGCATTACAAAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											61	66	64					10																	91497519		2199	4294	6493	91487499	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.2921G>A	10.37:g.91497519G>A	ENSP00000360793:p.Ser974Asn		91487499	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	G	0.166	-1.076487	0.01903	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.65732	-0.13;-0.12;-0.17;-0.1	5.69	-1.67	0.08238	.	0.605419	0.15605	N	0.253697	T	0.23370	0.0565	N	0.01048	-1.04	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.29488	-1.0010	10	0.14252	T	0.57	-0.2533	6.0368	0.19712	0.364:0.3675:0.2685:0.0	.	974;934	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	N	934;1004;974;974	ENSP00000260753:S934N;ENSP00000411545:S1004N;ENSP00000377830:S974N;ENSP00000360793:S974N	ENSP00000260753:S934N	S	+	2	0	KIF20B	91487499	0.066000	0.20996	0.003000	0.11579	0.971000	0.66376	0.263000	0.18478	-0.281000	0.09141	0.591000	0.81541	AGC		0.313	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		A	91497519	G	A	91497519	3	1	47	1	0	0	0	0	1	0	0	0	8308	971	34	3	2875	3	KIF20B	10	91497519	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	723395	91497519	44037228	1202	5599										
ANKRD1	27063	broad.mit.edu	37	chr10	92677503	92677503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttaccatatcacggaattCgatctgggctccagcttcca	7	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:92677503C>T	ENST00000371697.3	-	5	786	c.538G>A	c.(538-540)Gaa>Aaa	p.E180K		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	180					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)	p.E180K(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				TCACGGAATTCGATCTGGGCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											88	81	83					10																	92677503		2203	4300	6503	92667483	SO:0001583	missense	27063			X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.538G>A	10.37:g.92677503C>T	ENSP00000360762:p.Glu180Lys		92667483	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	37	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	C	32	5.144267	0.94603	.	.	ENSG00000148677	ENST00000371697	T	0.64438	-0.1	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.75162	0.3812	L	0.53671	1.685	0.58432	D	0.999999	D	0.67145	0.996	D	0.63283	0.913	T	0.75536	-0.3283	10	0.59425	D	0.04	.	19.766	0.96342	0.0:1.0:0.0:0.0	.	180	Q15327	ANKR1_HUMAN	K	180	ENSP00000360762:E180K	ENSP00000360762:E180K	E	-	1	0	ANKRD1	92667483	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	6.758000	0.74929	2.743000	0.94032	0.585000	0.79938	GAA		0.418	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		T	92677503	C	T	92677503	3	4	47	1	0	0	0	0	1	0	0	0	637	893	31	1	441	1	ANKRD1	10	92677503	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1179984	92677503	42857244	1203	5600										
HECTD2	143279	broad.mit.edu	37	chr10	93257924	93257924	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcaatgttgaagaagatttCtattcaacatttcaggtact	8	6	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:93257924C>A	ENST00000298068.5	+	16	1834	c.1740C>A	c.(1738-1740)ttC>ttA	p.F580L	HECTD2_ENST00000446394.1_Missense_Mutation_p.F584L|HECTD2_ENST00000536715.1_Missense_Mutation_p.F169L|HECTD2_ENST00000371667.1_Missense_Mutation_p.F230L	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	580	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.F580L(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						AAGAAGATTTCTATTCAACAT	0.299																																					NSCLC(12;376 469 1699 39910 41417)											1	Substitution - Missense(1)	large_intestine(1)	10											78	80	79					10																	93257924		2203	4295	6498	93247904	SO:0001583	missense	143279			AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"HECT domain containing 2"			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.1740C>A	10.37:g.93257924C>A	ENSP00000298068:p.Phe580Leu		93247904	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	37	CCDS7414.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.969676	0.53614	.	.	ENSG00000165338	ENST00000446394;ENST00000298068;ENST00000536715;ENST00000371667	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.47	4.37	0.52481	HECT (4);	0.000000	0.85682	D	0.000000	T	0.26629	0.0651	N	0.11341	0.13	0.48762	D	0.999702	B;B	0.27971	0.196;0.03	B;B	0.38194	0.267;0.05	T	0.10941	-1.0608	10	0.41790	T	0.15	.	6.6339	0.22872	0.0:0.7419:0.0:0.2581	.	584;580	E7ERR3;Q5U5R9	.;HECD2_HUMAN	L	584;580;169;230	ENSP00000401023:F584L;ENSP00000298068:F580L;ENSP00000439687:F169L;ENSP00000360731:F230L	ENSP00000298068:F580L	F	+	3	2	HECTD2	93247904	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.244000	0.32778	2.572000	0.86782	0.555000	0.69702	TTC		0.299	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			A	93257924	C	A	93257924	3	1	47	1	0	0	0	0	1	0	0	0	7061	912	32	2	1826	2	HECTD2	10	93257924	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	580421	93257924	42276823	1204	5601										
BTAF1	9044	broad.mit.edu	37	chr10	93754333	93754333	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggagatagccctgctcaaGaattggtgaattctctgcag	12	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:93754333G>T	ENST00000265990.6	+	23	3549	c.3241G>T	c.(3241-3243)Gaa>Taa	p.E1081*	BTAF1_ENST00000544642.1_5'Flank	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1081					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E1081*(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CCCTGCTCAAGAATTGGTGAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											66	69	68					10																	93754333		2203	4300	6503	93744313	SO:0001587	stop_gained	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.3241G>T	10.37:g.93754333G>T	ENSP00000265990:p.Glu1081*		93744313	B4E0W6|O43578	Nonsense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	G	43	9.886801	0.99288	.	.	ENSG00000095564	ENST00000265990	.	.	.	5.87	5.87	0.94306	.	0.051193	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-22.7345	20.1991	0.98252	0.0:0.0:1.0:0.0	.	.	.	.	X	1081	.	ENSP00000265990:E1081X	E	+	1	0	BTAF1	93744313	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	9.038000	0.93771	2.775000	0.95449	0.650000	0.86243	GAA		0.373	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93754333	G	T	93754333	4	4	47	1	0	0	0	0	0	1	0	0	1539	943	33	2	3331	2	BTAF1	10	93754333	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	496409	93754333	41780414	1205	5602										
IDE	3416	broad.mit.edu	37	chr10	94214254	94214254	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcacaaggggaaacagtgGcagaccacgcttgaattcgg	12	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:94214254G>T	ENST00000265986.6	-	25	3063	c.3007C>A	c.(3007-3009)Cca>Aca	p.P1003T	IDE_ENST00000371581.5_Missense_Mutation_p.P448T|IDE_ENST00000496903.1_5'UTR	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	1003					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.P1003T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	GGAAACAGTGGCAGACCACGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											165	162	163					10																	94214254		2203	4300	6503	94204234	SO:0001583	missense	3416			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.3007C>A	10.37:g.94214254G>T	ENSP00000265986:p.Pro1003Thr		94204234	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742142	0.69418	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.31510	1.52;1.49	5.9	5.9	0.94986	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	L	0.53729	1.69	0.80722	D	1	D;D	0.60160	0.987;0.977	B;P	0.46253	0.426;0.509	T	0.03957	-1.0989	10	0.31617	T	0.26	-10.0283	20.2789	0.98501	0.0:0.0:1.0:0.0	.	1003;448	P14735;B3KSB8	IDE_HUMAN;.	T	1003;448	ENSP00000265986:P1003T;ENSP00000360637:P448T	ENSP00000265986:P1003T	P	-	1	0	IDE	94204234	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.009000	0.93606	2.788000	0.95919	0.650000	0.86243	CCA		0.413	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		T	94214254	G	T	94214254	3	4	47	1	0	0	0	0	1	0	0	0	7514	1203	42	2	56	2	IDE	10	94214254	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	459921	94214254	41320493	1206	5603										
KIF11	3832	broad.mit.edu	37	chr10	94407996	94407996	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccaatgttgtgaggcttcaAgttcagacatcactgagaaa	10	8	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:94407996A>C	ENST00000260731.3	+	19	2665	c.2575A>C	c.(2575-2577)Agt>Cgt	p.S859R		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	859					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)	p.S859R(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGAGGCTTCAAGTTCAGACAT	0.323																																					Colon(47;212 1003 2764 4062 8431)											1	Substitution - Missense(1)	large_intestine(1)	10											67	62	63					10																	94407996		2203	4300	6503	94397976	SO:0001583	missense	3832			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.2575A>C	10.37:g.94407996A>C	ENSP00000260731:p.Ser859Arg		94397976	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	37	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	A	1.772	-0.484138	0.04383	.	.	ENSG00000138160	ENST00000260731	T	0.72835	-0.69	5.67	-3.07	0.05363	.	0.639379	0.15882	N	0.239996	T	0.43166	0.1235	L	0.27053	0.805	0.09310	N	1	B	0.21688	0.059	B	0.18263	0.021	T	0.22173	-1.0224	10	0.15066	T	0.55	.	0.2718	0.00232	0.2883:0.2765:0.1669:0.2683	.	859	P52732	KIF11_HUMAN	R	859	ENSP00000260731:S859R	ENSP00000260731:S859R	S	+	1	0	KIF11	94397976	0.011000	0.17503	0.447000	0.26932	0.103000	0.19146	-1.001000	0.03690	-0.533000	0.06323	-0.331000	0.08364	AGT		0.323	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		C	94407996	A	C	94407996	3	2	47	1	0	0	0	0	1	0	0	0	8293	72	3	4	2649	4	KIF11	10	94407996	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	193742	94407996	41126751	1207	5604										
HHEX	3087	broad.mit.edu	37	chr10	94454506	94454506	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacattgagggcgataaaaGctattttaatgctggatgat	12	4	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:94454506G>T	ENST00000282728.5	+	4	2593	c.794G>T	c.(793-795)aGc>aTc	p.S265I	HHEX_ENST00000472590.2_Missense_Mutation_p.S93I|HHEX_ENST00000492654.2_Missense_Mutation_p.S93I	NM_002729.4	NP_002720.1	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	265					anterior/posterior pattern specification (GO:0009952)|B cell differentiation (GO:0030183)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|DNA conformation change (GO:0071103)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|forebrain morphogenesis (GO:0048853)|gall bladder development (GO:0061010)|hepatic duct development (GO:0061011)|hepatoblast differentiation (GO:0061017)|hepatocyte differentiation (GO:0070365)|in utero embryonic development (GO:0001701)|interkinetic nuclear migration (GO:0022027)|mRNA export from nucleus (GO:0006406)|multicellular organism growth (GO:0035264)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|pancreas development (GO:0031016)|poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|primary lung bud formation (GO:0060431)|primitive streak formation (GO:0090009)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|eukaryotic initiation factor 4E binding (GO:0008190)|protein homodimerization activity (GO:0042803)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S265I(1)		kidney(2)|large_intestine(2)|lung(5)|ovary(1)	10						GGCGATAAAAGCTATTTTAAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	67	67					10																	94454506		2203	4300	6503	94444486	SO:0001583	missense	3087			Z21533	CCDS7423.1	10q23.33	2011-06-20	2007-02-15		ENSG00000152804	ENSG00000152804		"Homeoboxes / ANTP class : NKL subclass"	4901	protein-coding gene	gene with protein product		604420		PRHX		8096636, 8103988	Standard	NM_002729		Approved	HEX, HOX11L-PEN	uc001kid.3	Q03014	OTTHUMG00000018762	ENST00000282728.5:c.794G>T	10.37:g.94454506G>T	ENSP00000282728:p.Ser265Ile		94444486	B1AQ17|Q96CE9	Missense_Mutation	SNP	ENST00000282728.5	37	CCDS7423.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468961	0.63625	.	.	ENSG00000152804	ENST00000282728;ENST00000472590;ENST00000492654	D;D;D	0.90844	-2.74;-1.7;-1.7	5.44	5.44	0.79542	.	0.200515	0.42548	D	0.000691	D	0.85097	0.5619	N	0.14661	0.345	0.26227	N	0.979074	B	0.22480	0.07	B	0.25140	0.058	T	0.77046	-0.2733	10	0.72032	D	0.01	-4.0999	19.4568	0.94895	0.0:0.0:1.0:0.0	.	265	Q03014	HHEX_HUMAN	I	265;93;93	ENSP00000282728:S265I;ENSP00000450017:S93I;ENSP00000447953:S93I	ENSP00000282728:S265I	S	+	2	0	HHEX	94444486	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.448000	0.66612	2.832000	0.97577	0.655000	0.94253	AGC		0.428	HHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049402.2			T	94454506	G	T	94454506	3	4	47	1	0	0	0	0	1	0	0	0	7112	971	34	2	808	2	HHEX	10	94454506	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	46510	94454506	41080241	1208	5605										
CYP2C18	1562	broad.mit.edu	37	chr10	96466604	96466604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcataataaaatagctgaaAattttgcttacattaaaagt	5	4	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:96466604A>C	ENST00000285979.6	+	5	905	c.706A>C	c.(706-708)Aat>Cat	p.N236H	CYP2C19_ENST00000464755.1_3'UTR|CYP2C18_ENST00000339022.5_Intron	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	236					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.N236H(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	AATAGCTGAAAATTTTGCTTA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											50	54	52					10																	96466604		2203	4300	6503	96456594	SO:0001583	missense	1562			M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.706A>C	10.37:g.96466604A>C	ENSP00000285979:p.Asn236His		96456594	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Missense_Mutation	SNP	ENST00000285979.6	37	CCDS7435.1	.	.	.	.	.	.	.	.	.	.	a	9.766	1.171343	0.21621	.	.	ENSG00000108242	ENST00000285979	T	0.69306	-0.39	3.65	3.65	0.41850	.	0.583461	0.16864	U	0.196382	T	0.60856	0.2301	M	0.77486	2.375	0.09310	N	0.99999	P	0.41624	0.757	B	0.35770	0.21	T	0.61327	-0.7085	10	0.56958	D	0.05	.	5.7004	0.17879	0.8774:0.0:0.1226:0.0	.	236	P33260	CP2CI_HUMAN	H	236	ENSP00000285979:N236H	ENSP00000285979:N236H	N	+	1	0	CYP2C18	96456594	0.293000	0.24371	0.018000	0.16275	0.043000	0.13939	3.070000	0.50033	1.652000	0.50683	0.255000	0.18592	AAT		0.308	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		C	96466604	A	C	96466604	3	2	47	1	0	0	0	0	1	0	0	0	4171	14	1	4	724	4	CYP2C18	10	96466604	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2012098	96466604	39068143	1209	5606										
BLNK	29760	broad.mit.edu	37	chr10	97951767	97951767	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atacttcagtctggtggaatCttttgtgttattctgactgt	9	6	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:97951767C>A	ENST00000224337.5	-	17	1474	c.1333G>T	c.(1333-1335)Gat>Tat	p.D445Y	BLNK_ENST00000413476.2_Missense_Mutation_p.D393Y|BLNK_ENST00000371176.2_Missense_Mutation_p.D422Y|BLNK_ENST00000427367.2_Missense_Mutation_p.D410Y	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	445	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.D445Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		CTGGTGGAATCTTTTGTGTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											246	239	241					10																	97951767		2203	4300	6503	97941757	SO:0001583	missense	29760			AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"SH2 domain containing"	14211	protein-coding gene	gene with protein product	"B-cell adapter containing a SH2 domain protein", "B-cell activation", "Src homology [SH2] domain-containing leukocyte protein of 65 kD", "B cell adaptor containing SH2 domain"	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.1333G>T	10.37:g.97951767C>A	ENSP00000224337:p.Asp445Tyr		97941757	O75498|O75499|Q2MD49	Missense_Mutation	SNP	ENST00000224337.5	37	CCDS7446.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.249075|4.249075	0.80024|0.80024	.|.	.|.	ENSG00000095585|ENSG00000095585	ENST00000224337;ENST00000371176;ENST00000427367;ENST00000413476;ENST00000537049;ENST00000393894|ENST00000393889	.|.	.|.	.|.	5.13|5.13	5.13|5.13	0.70059|0.70059	SH2 motif (2);|.	0.050121|.	0.85682|.	D|.	0.000000|.	T|T	0.73171|0.73171	0.3553|0.3553	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;0.998|.	D;D;D;D;D;D|.	0.97110|.	0.999;1.0;0.999;0.999;0.999;0.979|.	T|T	0.75921|0.75921	-0.3147|-0.3147	9|6	0.56958|0.87932	D|D	0.05|0	-26.8354|-26.8354	17.7201|17.7201	0.88349|0.88349	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	370;393;422;288;422;445|.	Q2MD54;Q2MD49;Q8WV28-2;Q2MD59;Q2MD52;Q8WV28|.	.;.;.;.;.;BLNK_HUMAN|.	Y|N	445;422;410;393;288;174|170	.|.	ENSP00000224337:D445Y|ENSP00000377467:K170N	D|K	-|-	1|3	0|2	BLNK|BLNK	97941757|97941757	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.676000|4.676000	0.61627|0.61627	2.567000|2.567000	0.86603|0.86603	0.557000|0.557000	0.71058|0.71058	GAT|AAG		0.363	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314		A	97951767	C	A	97951767	3	1	47	1	0	0	0	0	1	0	0	0	1448	913	32	2	41	2	BLNK	10	97951767	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1485163	97951767	37582980	1210	5607										
DNTT	1791	broad.mit.edu	37	chr10	98084064	98084064	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggggctgaagacttctgaGaagtggttcaggatgggttt	17	4	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:98084064G>T	ENST00000371174.2	+	6	894	c.792G>T	c.(790-792)gaG>gaT	p.E264D	DNTT_ENST00000419175.1_Missense_Mutation_p.E264D			P04053	TDT_HUMAN	DNA nucleotidylexotransferase	264	Mediates interaction with DNTTIP2.				DNA modification (GO:0006304)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA nucleotidylexotransferase activity (GO:0003912)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.E264D(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		AGACTTCTGAGAAGTGGTTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											134	131	132					10																	98084064		2203	4300	6503	98074054	SO:0001583	missense	1791			AB046378	CCDS7447.1	10q23-q24	2013-05-21	2013-05-21		ENSG00000107447	ENSG00000107447	2.7.7.31	"DNA polymerases"	2983	protein-coding gene	gene with protein product	"Terminal deoxynucleotidyltransferase"	187410	"deoxynucleotidyltransferase, terminal"				Standard	NM_004088		Approved	TDT	uc001kmf.3	P04053	OTTHUMG00000018832	ENST00000371174.2:c.792G>T	10.37:g.98084064G>T	ENSP00000360216:p.Glu264Asp		98074054	Q53FH1|Q5W103|Q96E50	Missense_Mutation	SNP	ENST00000371174.2	37	CCDS7447.1	.	.	.	.	.	.	.	.	.	.	G	2.728	-0.264990	0.05754	.	.	ENSG00000107447	ENST00000419175;ENST00000371174	T;T	0.43688	0.94;0.94	4.69	3.72	0.42706	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (2);	0.152645	0.64402	D	0.000019	T	0.16981	0.0408	N	0.05124	-0.11	0.42086	D	0.99127	B;B	0.15141	0.01;0.012	B;B	0.15484	0.008;0.013	T	0.13980	-1.0489	10	0.07482	T	0.82	-5.6016	7.5447	0.27759	0.0:0.178:0.6377:0.1843	.	264;264	P04053-2;P04053	.;TDT_HUMAN	D	264	ENSP00000401169:E264D;ENSP00000360216:E264D	ENSP00000360216:E264D	E	+	3	2	DNTT	98074054	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.429000	0.34903	2.597000	0.87782	0.655000	0.94253	GAG		0.413	DNTT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049607.1	NM_004088		T	98084064	G	T	98084064	3	4	47	1	0	0	0	0	1	0	0	0	4691	933	33	2	814	2	DNTT	10	98084064	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	132297	98084064	37450683	1211	5608										
C10orf12	26148	broad.mit.edu	37	chr10	98744001	98744001	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaagctctgggccaaatttCgagagaatcctgatcaagtg	11	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:98744001C>T	ENST00000286067.2	+	1	2961	c.2854C>T	c.(2854-2856)Cga>Tga	p.R952*		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	952								p.R952*(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GGCCAAATTTCGAGAGAATCC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											87	98	95					10																	98744001		2203	4300	6503	98733991	SO:0001587	stop_gained	26148			BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.2854C>T	10.37:g.98744001C>T	ENSP00000286067:p.Arg952*		98733991	Q9H945|Q9Y457	Nonsense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	C	35	5.561915	0.96527	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	.	.	.	5.71	4.79	0.61399	.	0.340768	0.20894	N	0.083762	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.2512	9.3624	0.38203	0.1451:0.7835:0.0:0.0714	.	.	.	.	X	952;786	.	ENSP00000286067:R952X	R	+	1	2	C10orf12	98733991	0.611000	0.26992	0.999000	0.59377	0.224000	0.24922	1.326000	0.33735	1.393000	0.46605	0.655000	0.94253	CGA		0.463	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		T	98744001	C	T	98744001	4	4	47	1	0	0	0	0	0	1	0	0	1593	876	31	1	2856	1	C10orf12	10	98744001	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	659937	98744001	36790746	1212	5609										
ARHGAP19	84986	broad.mit.edu	37	chr10	99025838	99025838	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaagataatgggctgacctCgaagggaagaatcattgcag	12	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:99025838C>A	ENST00000358531.4	-	2	129	c.101G>T	c.(100-102)cGa>cTa	p.R34L	ARHGAP19_ENST00000355366.5_Missense_Mutation_p.R25L|ARHGAP19-SLIT1_ENST00000316676.8_Missense_Mutation_p.R34L|ARHGAP19_ENST00000371027.1_Missense_Mutation_p.R25L|ARHGAP19-SLIT1_ENST00000453547.2_Missense_Mutation_p.R34L|ARHGAP19-SLIT1_ENST00000358308.3_Missense_Mutation_p.R34L	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	34					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.R34L(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		GGGCTGACCTCGAAGGGAAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											82	81	81					10																	99025838		2203	4300	6503	99015828	SO:0001583	missense	84986			AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"Rho GTPase activating proteins"	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.101G>T	10.37:g.99025838C>A	ENSP00000351333:p.Arg34Leu		99015828	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Missense_Mutation	SNP	ENST00000358531.4	37	CCDS7454.2	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791549	0.50102	.	.	ENSG00000213390	ENST00000453547;ENST00000316676;ENST00000355366;ENST00000358531;ENST00000371027;ENST00000358308	T;T;T;T;T;T	0.10099	2.99;3.02;3.02;3.03;3.02;2.91	5.54	4.64	0.57946	.	0.311451	0.25416	U	0.030827	T	0.08358	0.0208	N	0.19112	0.55	0.32945	D	0.518952	B;B;B	0.24368	0.082;0.049;0.102	B;B;B	0.24541	0.039;0.018;0.054	T	0.06006	-1.0851	10	0.66056	D	0.02	-2.2584	11.489	0.50371	0.0:0.8554:0.0:0.1446	.	34;34;25	Q14CB8-6;Q14CB8;Q14CB8-3	.;RHG19_HUMAN;.	L	34;34;25;34;25;34	ENSP00000414774:R34L;ENSP00000324468:R34L;ENSP00000347526:R25L;ENSP00000351333:R34L;ENSP00000360066:R25L;ENSP00000351058:R34L	ENSP00000324468:R34L	R	-	2	0	ARHGAP19	99015828	0.946000	0.32159	1.000000	0.80357	0.994000	0.84299	0.505000	0.22642	1.326000	0.45319	0.557000	0.71058	CGA		0.398	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900		A	99025838	C	A	99025838	3	1	47	1	0	0	0	0	1	0	0	0	869	884	31	2	1427	2	ARHGAP19	10	99025838	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	281837	99025838	36508909	1213	5610										
HPSE2	60495	broad.mit.edu	37	chr10	100242526	100242526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaagtgtaatggacccacGaacgtagttgtggctgagat	12	6	0	1	rs144545292		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:100242526G>A	ENST00000370552.3	-	11	1539	c.1480C>T	c.(1480-1482)Cgt>Tgt	p.R494C	HPSE2_ENST00000404542.1_Missense_Mutation_p.R382C|HPSE2_ENST00000370549.1_Missense_Mutation_p.R436C|HPSE2_ENST00000370546.1_Missense_Mutation_p.R494C	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	494					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)	p.R494C(2)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		ATGGACCCACGAACGTAGTTG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	10						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	90	80	84		1306,1144,1480,1480	5.3	1	10	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	HPSE2	NM_001166244.1,NM_001166245.1,NM_001166246.1,NM_021828.4	180,180,180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	436/535,382/481,494/549,494/593	100242526	1,13005	2203	4300	6503	100232516	SO:0001583	missense	60495			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1480C>T	10.37:g.100242526G>A	ENSP00000359583:p.Arg494Cys		100232516	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765044	0.69878	0.0	1.16E-4	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.48836	0.8;0.82;1.36;0.83	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.63780	0.2540	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.996;0.989;0.997;0.99	T	0.64723	-0.6340	10	0.66056	D	0.02	-4.6739	14.3001	0.66341	0.0:0.0:0.8515:0.1484	.	382;494;436;494	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	C	494;436;494;382	ENSP00000359583:R494C;ENSP00000359580:R436C;ENSP00000359577:R494C;ENSP00000384384:R382C	ENSP00000359577:R494C	R	-	1	0	HPSE2	100232516	1.000000	0.71417	0.987000	0.45799	0.832000	0.47134	5.457000	0.66672	2.677000	0.91161	0.655000	0.94253	CGT		0.403	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		A	100242526	G	A	100242526	3	1	47	1	0	0	0	0	1	0	0	0	7366	1058	37	1	344	1	HPSE2	10	100242526	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1216688	100242526	35292221	1214	5611										
ABCC2	1244	broad.mit.edu	37	chr10	101591537	101591537	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagcaccgactatccagcatCtcagagggacatgagagttg	11	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:101591537C>A	ENST00000370449.4	+	22	3166	c.3053C>A	c.(3052-3054)tCt>tAt	p.S1018Y		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1018	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.S1018Y(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TATCCAGCATCTCAGAGGGAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											112	109	110					10																	101591537		2203	4300	6503	101581527	SO:0001583	missense	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3053C>A	10.37:g.101591537C>A	ENSP00000359478:p.Ser1018Tyr		101581527	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	C	9.203	1.028977	0.19512	.	.	ENSG00000023839	ENST00000370449	D	0.89617	-2.54	5.64	5.64	0.86602	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.392641	0.30752	N	0.008953	D	0.91613	0.7350	L	0.60845	1.875	0.26995	N	0.965041	D	0.55605	0.972	P	0.56788	0.806	D	0.86687	0.1920	10	0.54805	T	0.06	-13.2759	15.3886	0.74723	0.1479:0.8521:0.0:0.0	.	1018	Q92887	MRP2_HUMAN	Y	1018	ENSP00000359478:S1018Y	ENSP00000359478:S1018Y	S	+	2	0	ABCC2	101581527	0.127000	0.22367	0.995000	0.50966	0.035000	0.12851	1.922000	0.40045	2.661000	0.90470	0.591000	0.81541	TCT		0.473	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101591537	C	A	101591537	3	1	47	1	0	0	0	0	1	0	0	0	53	913	32	2	3139	2	ABCC2	10	101591537	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1349011	101591537	33943210	1215	5612										
PPRC1	23082	broad.mit.edu	37	chr10	103899315	103899315	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtagtgctggagattgtgggGcaggcagccacagctggcga	18	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:103899315G>A	ENST00000278070.2	+	5	1089	c.1050G>A	c.(1048-1050)ggG>ggA	p.G350G	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Silent_p.G350G	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	350					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G350G(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		AGATTGTGGGGCAGGCAGCCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	10											114	114	114					10																	103899315		2203	4300	6503	103889305	SO:0001819	synonymous_variant	23082			AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.1050G>A	10.37:g.103899315G>A			103889305	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Silent	SNP	ENST00000278070.2	37	CCDS7529.1																																																																																				0.597	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103899315	G	A	103899315	2	1	47	1	0	0	0	0	0	0	0	1	12444	1190	42	3		3	PPRC1	10	103899315	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2307778	103899315	31635432	1216	5613										
C10orf79	80217	broad.mit.edu	37	chr10	105903290	105903290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattgtccaactcatccataGctttcattaactgggcaaag	6	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:105903290G>T	ENST00000357060.3	-	32	4167	c.4052C>A	c.(4051-4053)gCt>gAt	p.A1351D	WDR96_ENST00000479392.1_5'Flank|WDR96_ENST00000428666.1_Missense_Mutation_p.A1323D	NM_025145.5	NP_079421.5												p.A1351D(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTCATCCATAGCTTTCATTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											142	133	136					10																	105903290		2203	4300	6503	105893280	SO:0001583	missense	80217																														ENST00000357060.3:c.4052C>A	10.37:g.105903290G>T	ENSP00000349568:p.Ala1351Asp		105893280		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.73|19.73	3.881326|3.881326	0.72294|0.72294	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666|ENST00000457071;ENST00000434629	T;T|.	0.16457|.	2.37;2.34|.	6.02|6.02	5.11|5.11	0.69529|0.69529	.|.	0.153716|.	0.64402|.	D|.	0.000017|.	T|T	0.72938|0.72938	0.3523|0.3523	M|M	0.71581|0.71581	2.175|2.175	0.44295|0.44295	D|D	0.997162|0.997162	P;D|.	0.65815|.	0.948;0.995|.	P;D|.	0.65323|.	0.66;0.934|.	T|T	0.71790|0.71790	-0.4486|-0.4486	10|5	0.26408|.	T|.	0.33|.	.|.	14.3797|14.3797	0.66902|0.66902	0.0709:0.0:0.9291:0.0|0.0709:0.0:0.9291:0.0	.|.	1323;1351|.	G5E9L1;Q8NDM7|.	.;WDR96_HUMAN|.	D|I	1351;1323|200;683	ENSP00000349568:A1351D;ENSP00000400289:A1323D|.	ENSP00000349568:A1351D|.	A|L	-|-	2|1	0|2	WDR96|WDR96	105893280|105893280	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	5.161000|5.161000	0.64935|0.64935	2.857000|2.857000	0.98124|0.98124	0.650000|0.650000	0.86243|0.86243	GCT|CTA		0.433	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	105903290	G	T	105903290	3	4	47	1	0	0	0	0	1	0	0	0	1622	971	34	2	973	2	C10orf79	10	105903290	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2003975	105903290	29631457	1217	5614										
C10orf79	80217	broad.mit.edu	37	chr10	105920835	105920835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcatttaactcctttactTttttctcataatctttgaat	1	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:105920835T>C	ENST00000357060.3	-	27	3615	c.3500A>G	c.(3499-3501)aAa>aGa	p.K1167R	WDR96_ENST00000428666.1_Missense_Mutation_p.K1168R	NM_025145.5	NP_079421.5												p.K1167R(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTCCTTTACTTTTTTCTCATA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											121	112	115					10																	105920835		2203	4300	6503	105910825	SO:0001583	missense	80217																														ENST00000357060.3:c.3500A>G	10.37:g.105920835T>C	ENSP00000349568:p.Lys1167Arg		105910825		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.571609|4.571609	0.86542|0.86542	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000457071;ENST00000434629|ENST00000357060;ENST00000428666	T|T;T	0.53206|0.18960	0.63|2.18;2.2	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.49133|0.49133	0.1539|0.1539	M|M	0.82056|0.82056	2.57|2.57	0.45216|0.45216	D|D	0.998223|0.998223	.|D;D	.|0.76494	.|0.963;0.999	.|D;D	.|0.77557	.|0.909;0.99	T|T	0.48364|0.48364	-0.9042|-0.9042	8|10	0.87932|0.41790	D|T	0|0.15	.|.	15.8596|15.8596	0.79012|0.79012	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1168;1167	.|G5E9L1;Q8NDM7	.|.;WDR96_HUMAN	E|R	16;528|1167;1168	ENSP00000391364:K528E|ENSP00000349568:K1167R;ENSP00000400289:K1168R	ENSP00000391364:K528E|ENSP00000349568:K1167R	K|K	-|-	1|2	0|0	WDR96|WDR96	105910825|105910825	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.638000|4.638000	0.61353|0.61353	2.226000|2.226000	0.72624|0.72624	0.533000|0.533000	0.62120|0.62120	AAG|AAA		0.328	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	105920835	T	C	105920835	3	2	47	1	0	0	0	0	1	0	0	0	1622	1841	64	4	1545	4	C10orf79	10	105920835	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	17545	105920835	29613912	1218	5615										
CCDC147	159686	broad.mit.edu	37	chr10	106118308	106118308	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaaatgcagagattgtagtGaattctgcgaaggtcgccac	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:106118308G>T	ENST00000369704.3	+	2	353	c.219G>T	c.(217-219)gtG>gtT	p.V73V	CCDC147_ENST00000312902.5_5'UTR	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		73						extracellular space (GO:0005615)		p.V73V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGATTGTAGTGAATTCTGCGA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	10											86	74	78					10																	106118308		2203	4300	6503	106108298	SO:0001819	synonymous_variant	159686																														ENST00000369704.3:c.219G>T	10.37:g.106118308G>T			106108298	D3DRA6|Q8NA27	Silent	SNP	ENST00000369704.3	37	CCDS31282.1																																																																																				0.433	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			T	106118308	G	T	106118308	2	4	47	1	0	0	0	0	0	0	0	1	2787	1277	45	2		2	CCDC147	10	106118308	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	197473	106118308	29416439	1219	5616										
SORCS3	22986	broad.mit.edu	37	chr10	106907522	106907522	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatcaagagcagcagaggtCtaatggggaacatcattatt	10	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:106907522C>A	ENST00000369701.3	+	9	1677	c.1450C>A	c.(1450-1452)Cta>Ata	p.L484I		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	484					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.L484I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CAGCAGAGGTCTAATGGGGAA	0.433																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - Missense(1)	large_intestine(1)	10											196	158	171					10																	106907522		2203	4299	6502	106897512	SO:0001583	missense	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1450C>A	10.37:g.106907522C>A	ENSP00000358715:p.Leu484Ile		106897512	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	10.13	1.265410	0.23136	.	.	ENSG00000156395	ENST00000369701	T	0.22134	1.97	5.42	5.42	0.78866	VPS10 (1);	0.227351	0.38326	N	0.001737	T	0.18087	0.0434	L	0.36672	1.1	0.35973	D	0.835441	B	0.20780	0.048	B	0.18871	0.023	T	0.10847	-1.0612	9	.	.	.	.	15.1218	0.72450	0.0:0.859:0.141:0.0	.	484	Q9UPU3	SORC3_HUMAN	I	484	ENSP00000358715:L484I	.	L	+	1	2	SORCS3	106897512	0.190000	0.23276	1.000000	0.80357	0.930000	0.56654	2.070000	0.41491	2.716000	0.92895	0.650000	0.86243	CTA		0.433	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	106907522	C	A	106907522	3	1	47	1	0	0	0	0	1	0	0	0	14969	912	32	2	1484	2	SORCS3	10	106907522	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	789214	106907522	28627225	1220	5617										
SMC3	9126	broad.mit.edu	37	chr10	112343972	112343972	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctacccaggaaagaacggatCtttatgcaaagcagggtcga	11	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:112343972C>A	ENST00000361804.4	+	13	1249	c.1123C>A	c.(1123-1125)Ctt>Att	p.L375I		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	375					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)	p.L375I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AAGAACGGATCTTTATGCAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	106	106					10																	112343972		2203	4300	6503	112333962	SO:0001583	missense	9126			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1123C>A	10.37:g.112343972C>A	ENSP00000354720:p.Leu375Ile		112333962	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	37	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.286171	0.80803	.	.	ENSG00000108055	ENST00000361804	T	0.79454	-1.27	5.76	5.76	0.90799	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	M	0.75264	2.295	0.80722	D	1	D	0.69078	0.997	P	0.62649	0.905	D	0.86473	0.1786	10	0.46703	T	0.11	.	19.973	0.97292	0.0:1.0:0.0:0.0	.	375	Q9UQE7	SMC3_HUMAN	I	375	ENSP00000354720:L375I	ENSP00000354720:L375I	L	+	1	0	SMC3	112333962	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.973000	0.49264	2.725000	0.93324	0.460000	0.39030	CTT		0.368	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		A	112343972	C	A	112343972	3	1	47	1	0	0	0	0	1	0	0	0	14821	913	32	2	1173	2	SMC3	10	112343972	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5436450	112343972	23190775	1221	5618										
NRAP	4892	broad.mit.edu	37	chr10	115406696	115406696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttacgtcactagcgagttCgtgagctttcttggcgttct	10	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:115406696C>T	ENST00000359988.3	-	10	1223	c.979G>A	c.(979-981)Gaa>Aaa	p.E327K	NRAP_ENST00000369358.4_Missense_Mutation_p.E327K|NRAP_ENST00000369360.3_Missense_Mutation_p.E327K|NRAP_ENST00000360478.3_Missense_Mutation_p.E327K	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.E327K(3)|p.E327*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTAGCGAGTTCGTGAGCTTTC	0.527																																																4	Substitution - Missense(3)|Substitution - Nonsense(1)	large_intestine(4)	10											249	194	213					10																	115406696		2203	4300	6503	115396686	SO:0001583	missense	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.979G>A	10.37:g.115406696C>T	ENSP00000353078:p.Glu327Lys		115396686		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413299	0.62511	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.71	3.87	0.44632	.	0.142736	0.64402	D	0.000006	T	0.49779	0.1577	M	0.77313	2.365	0.37841	D	0.929041	P;P;P	0.49862	0.902;0.929;0.812	P;P;B	0.48795	0.544;0.59;0.311	T	0.54925	-0.8220	10	0.19590	T	0.45	.	12.5859	0.56416	0.0:0.8654:0.0:0.1346	.	327;327;327	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	K	327;327;327;327;56;56	ENSP00000358365:E327K;ENSP00000358367:E327K;ENSP00000353078:E327K;ENSP00000353666:E327K	ENSP00000353078:E327K	E	-	1	0	NRAP	115396686	1.000000	0.71417	0.977000	0.42913	0.923000	0.55619	5.461000	0.66699	0.884000	0.36064	0.643000	0.83706	GAA		0.527	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115406696	C	T	115406696	3	4	47	1	0	0	0	0	1	0	0	0	10669	893	31	1	4345	1	NRAP	10	115406696	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3062724	115406696	20128051	1222	5619										
DCLRE1A	9937	broad.mit.edu	37	chr10	115609288	115609288	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggagcaggtgtactagacaAgttttctgtatttaaaattg	10	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:115609288A>C	ENST00000361384.2	-	2	2493	c.1576T>G	c.(1576-1578)Ttg>Gtg	p.L526V	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.L526V	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	526	Nuclear focus formation.				mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)		p.L526V(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		GTACTAGACAAGTTTTCTGTA	0.363								Other identified genes with known or suspected DNA repair function																																								1	Substitution - Missense(1)	large_intestine(1)	10											104	107	106					10																	115609288		2203	4300	6503	115599278	SO:0001583	missense	9937				CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.1576T>G	10.37:g.115609288A>C	ENSP00000355185:p.Leu526Val		115599278	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	37	CCDS7584.1	.	.	.	.	.	.	.	.	.	.	A	9.411	1.080626	0.20309	.	.	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.63096	-0.02;-0.02	5.7	-3.28	0.05033	.	3.154460	0.00481	N	0.000136	T	0.35278	0.0926	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08785	-1.0705	10	0.16896	T	0.51	4.4748	2.0998	0.03677	0.3255:0.3817:0.1697:0.1231	.	526	Q6PJP8	DCR1A_HUMAN	V	526	ENSP00000355185:L526V;ENSP00000358311:L526V	ENSP00000355185:L526V	L	-	1	2	DCLRE1A	115599278	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.110000	0.10824	-0.898000	0.03906	-0.446000	0.05623	TTG		0.363	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		C	115609288	A	C	115609288	3	2	47	1	0	0	0	0	1	0	0	0	4300	69	3	4	1578	4	DCLRE1A	10	115609288	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	202592	115609288	19925459	1223	5620										
GFRA1	2674	broad.mit.edu	37	chr10	117824003	117824003	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcttggaggagcagccattGattttgtggttatgtggctg	15	5	0	1	rs76681527		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:117824003G>T	ENST00000355422.6	-	11	1854	c.1304C>A	c.(1303-1305)tCa>tAa	p.S435*	GFRA1_ENST00000544592.1_Nonsense_Mutation_p.S314*|GFRA1_ENST00000369236.1_Nonsense_Mutation_p.S430*|GFRA1_ENST00000439649.3_Nonsense_Mutation_p.S430*	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	435					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.S430*(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		AGCAGCCATTGATTTTGTGGT	0.453																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - Nonsense(1)	large_intestine(1)	10											178	140	153					10																	117824003		2203	4300	6503	117813993	SO:0001587	stop_gained	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.1304C>A	10.37:g.117824003G>T	ENSP00000347591:p.Ser435*		117813993	A8KA21|O15507|O43912	Nonsense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	G	43	10.125228	0.99342	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	.	.	.	6.06	6.06	0.98353	.	0.205947	0.43110	D	0.000607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7696	18.8014	0.92018	0.0:0.0:1.0:0.0	.	.	.	.	X	435;430;430;314;430	.	ENSP00000347591:S430X	S	-	2	0	GFRA1	117813993	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	6.069000	0.71209	2.882000	0.98803	0.655000	0.94253	TCA		0.453	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		T	117824003	G	T	117824003	4	4	47	1	0	0	0	0	0	1	0	0	6367	1294	45	2	97	2	GFRA1	10	117824003	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2214715	117824003	17710744	1224	5621										
PNLIPRP3	119548	broad.mit.edu	37	chr10	118225646	118225646	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatcctgatgcatttattgCttatccttgtagatcctaca	5	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:118225646C>A	ENST00000369230.3	+	8	1039	c.893C>A	c.(892-894)gCt>gAt	p.A298D		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	298					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.A298D(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GCATTTATTGCTTATCCTTGT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	10											121	116	118					10																	118225646		2201	4299	6500	118215636	SO:0001583	missense	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.893C>A	10.37:g.118225646C>A	ENSP00000358232:p.Ala298Asp		118215636		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.768174	0.31320	.	.	ENSG00000203837	ENST00000369230	D	0.93426	-3.22	4.93	3.0	0.34707	Lipase, N-terminal (1);	0.259771	0.24752	N	0.035900	D	0.96907	0.8990	M	0.93978	3.48	0.23984	N	0.996263	D	0.89917	1.0	D	0.81914	0.995	D	0.90720	0.4634	10	0.87932	D	0	.	9.2461	0.37527	0.0:0.5849:0.3259:0.0892	.	298	Q17RR3	LIPR3_HUMAN	D	298	ENSP00000358232:A298D	ENSP00000358232:A298D	A	+	2	0	PNLIPRP3	118215636	0.981000	0.34729	0.982000	0.44146	0.775000	0.43874	1.942000	0.40243	1.325000	0.45301	0.655000	0.94253	GCT		0.318	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		A	118225646	C	A	118225646	3	1	47	1	0	0	0	0	1	0	0	0	12183	797	28	2	923	2	PNLIPRP3	10	118225646	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	401643	118225646	17309101	1225	5622										
TIAL1	7073	broad.mit.edu	37	chr10	121341983	121341983	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcttacctttcccaaaatTtttctcccattcatagcagc	2	13	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:121341983T>G	ENST00000436547.2	-	3	260	c.216A>C	c.(214-216)aaA>aaC	p.K72N	TIAL1_ENST00000369092.4_5'UTR|TIAL1_ENST00000369093.2_Missense_Mutation_p.K89N	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	72	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K89N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TTCCCAAAATTTTTCTCCCAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	143	139					10																	121341983		2203	4298	6501	121331973	SO:0001583	missense	7073			AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.216A>C	10.37:g.121341983T>G	ENSP00000394902:p.Lys72Asn		121331973	A8K3T0|A8K4L9	Missense_Mutation	SNP	ENST00000436547.2	37	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.134355	0.56828	.	.	ENSG00000151923	ENST00000369093;ENST00000436547;ENST00000412524;ENST00000369086	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	6.02	6.02	0.97574	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.26159	0.0638	N	0.16016	0.355	0.80722	D	1	B;D	0.89917	0.135;1.0	B;D	0.79108	0.204;0.992	T	0.10683	-1.0619	10	0.35671	T	0.21	-21.4618	16.542	0.84395	0.0:0.0:0.0:1.0	.	89;72	A8K4L9;Q01085	.;TIAR_HUMAN	N	89;72;33;33	ENSP00000358089:K89N;ENSP00000394902:K72N;ENSP00000403573:K33N;ENSP00000358082:K33N	ENSP00000358082:K33N	K	-	3	2	TIAL1	121331973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.210000	0.51129	2.304000	0.77564	0.528000	0.53228	AAA		0.363	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		G	121341983	T	G	121341983	3	3	47	1	0	0	0	0	1	0	0	0	15928	1838	64	4	951	4	TIAL1	10	121341983	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3116337	121341983	14192764	1226	5623										
WDR11	55717	broad.mit.edu	37	chr10	122649475	122649475	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtaaaggaaatcaaaaatTaatagcaatgtacaatgatg	8	3	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:122649475T>G	ENST00000263461.6	+	18	2543	c.2297T>G	c.(2296-2298)tTa>tGa	p.L766*	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.L766*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AATCAAAAATTAATAGCAATG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											116	110	112					10																	122649475		2203	4300	6503	122639465	SO:0001587	stop_gained	55717			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2297T>G	10.37:g.122649475T>G	ENSP00000263461:p.Leu766*		122639465	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Nonsense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	t	43	10.101035	0.99337	.	.	ENSG00000120008	ENST00000263461	.	.	.	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0903	15.8895	0.79286	0.0:0.0:0.0:1.0	.	.	.	.	X	766	.	ENSP00000263461:L766X	L	+	2	0	WDR11	122639465	1.000000	0.71417	0.893000	0.35052	0.996000	0.88848	7.508000	0.81686	2.207000	0.71202	0.533000	0.62120	TTA		0.388	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			G	122649475	T	G	122649475	4	3	47	1	0	0	0	0	0	1	0	0	17313	1764	61	4	2367	4	WDR11	10	122649475	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1307492	122649475	12885272	1227	5624										
FGFR2	2263	broad.mit.edu	37	chr10	123310820	123310820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaccttgtagcctccaatgCgatgctcctgcttaaactcc	6	15	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:123310820C>T	ENST00000358487.5	-	5	880	c.608G>A	c.(607-609)cGc>cAc	p.R203H	FGFR2_ENST00000346997.2_Missense_Mutation_p.R203H|FGFR2_ENST00000369061.4_Missense_Mutation_p.R203H|FGFR2_ENST00000369059.1_Missense_Mutation_p.R88H|FGFR2_ENST00000351936.6_Missense_Mutation_p.R203H|FGFR2_ENST00000457416.2_Missense_Mutation_p.R203H|FGFR2_ENST00000369056.1_Missense_Mutation_p.R203H|FGFR2_ENST00000356226.4_Missense_Mutation_p.R88H|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000359354.2_Missense_Mutation_p.R203H|FGFR2_ENST00000369060.4_Missense_Mutation_p.R203H|FGFR2_ENST00000357555.5_Missense_Mutation_p.R114H|FGFR2_ENST00000360144.3_Missense_Mutation_p.R114H	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	203	Ig-like C2-type 2.		R -> C (in breast cancer samples; infiltrating ductal carcinoma; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.R203H(2)|p.R114H(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GCCTCCAATGCGATGCTCCTG	0.448		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	3	Substitution - Missense(3)	large_intestine(3)	10											126	121	123					10																	123310820		2203	4300	6503	123300810	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.608G>A	10.37:g.123310820C>T	ENSP00000351276:p.Arg203His		123300810	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810627	0.90707	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	D;D;D;D;D;D;D;D;D;D;D;D;D;T	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;1.19	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92374	0.7580	M	0.79614	2.46	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;P;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.921;1.0	D;D;D;D;D;D;D;D;D;D;B;D	0.97110	1.0;1.0;0.993;1.0;0.998;0.993;0.982;1.0;0.997;0.997;0.304;0.998	D	0.92996	0.6419	10	0.56958	D	0.05	.	18.0697	0.89402	0.0:1.0:0.0:0.0	.	222;222;88;203;222;203;114;88;203;222;114;203	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	H	114;203;203;203;88;203;88;203;203;203;114;203;203;114;203	ENSP00000350166:R114H;ENSP00000358057:R203H;ENSP00000351276:R203H;ENSP00000348559:R88H;ENSP00000358056:R203H;ENSP00000358055:R88H;ENSP00000263451:R203H;ENSP00000410294:R203H;ENSP00000309878:R203H;ENSP00000353262:R114H;ENSP00000358052:R203H;ENSP00000358054:R203H;ENSP00000337665:R114H;ENSP00000352309:R203H	ENSP00000337665:R114H	R	-	2	0	FGFR2	123300810	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.714000	0.84703	2.255000	0.74692	0.609000	0.83330	CGC		0.448	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123310820	C	T	123310820	3	4	47	1	0	0	0	0	1	0	0	0	5885	768	27	1	2169	1	FGFR2	10	123310820	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	661345	123310820	12223927	1228	5625										
ATE1	11101	broad.mit.edu	37	chr10	123670624	123670624	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttatttatcaatgcaaagTcacccgcaacagcatcatcc	5	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:123670624T>G	ENST00000224652.6	-	5	465	c.380A>C	c.(379-381)gAc>gCc	p.D127A	ATE1_ENST00000540606.1_Missense_Mutation_p.D120A|ATE1_ENST00000369040.3_Missense_Mutation_p.D31A|ATE1_ENST00000543447.1_Missense_Mutation_p.D12A|ATE1_ENST00000535655.1_5'UTR|ATE1_ENST00000369043.3_Missense_Mutation_p.D127A	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	127					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)	p.D127A(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CAATGCAAAGTCACCCGCAAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											116	120	119					10																	123670624		2203	4300	6503	123660614	SO:0001583	missense	11101			AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.380A>C	10.37:g.123670624T>G	ENSP00000224652:p.Asp127Ala		123660614	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.40|14.40	2.523845|2.523845	0.44866|0.44866	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000369043;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447;ENST00000455628|ENST00000423243	.|.	.|.	.|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.377633|.	0.29369|.	N|.	0.012348|.	T|.	0.64560|.	0.2609|.	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	B;P;B;B|.	0.41624|.	0.046;0.757;0.376;0.082|.	B;B;B;B|.	0.39185|.	0.036;0.293;0.164;0.036|.	T|.	0.65364|.	-0.6186|.	9|.	0.33141|.	T|.	0.24|.	-14.9234|-14.9234	8.9282|8.9282	0.35655|0.35655	0.0:0.1257:0.0:0.8743|0.0:0.1257:0.0:0.8743	.|.	120;31;127;127|.	F5GXE4;B4E107;O95260;O95260-2|.	.;.;ATE1_HUMAN;.|.	A|C	127;127;31;120;12;120|123	.|.	ENSP00000224652:D127A|.	D|X	-|-	2|3	0|0	ATE1|ATE1	123660614|123660614	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.865000|0.865000	0.49528|0.49528	1.436000|1.436000	0.34980|0.34980	2.207000|2.207000	0.71202|0.71202	0.460000|0.460000	0.39030|0.39030	GAC|TGA		0.353	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976		G	123670624	T	G	123670624	3	3	47	1	0	0	0	0	1	0	0	0	1079	1667	58	4	1341	4	ATE1	10	123670624	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	359804	123670624	11864123	1229	5626										
CUZD1	50624	broad.mit.edu	37	chr10	124598705	124598705	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgctggaggttccgtcaaaGactttaatgttttcactttc	8	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:124598705G>T	ENST00000368904.1	-	5	1225	c.276C>A	c.(274-276)gtC>gtA	p.V92V	CUZD1_ENST00000545804.1_Silent_p.V92V|CUZD1_ENST00000392790.1_Silent_p.V92V					CUB and zona pellucida-like domains 1									p.V92V(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		TTCCGTCAAAGACTTTAATGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	10											171	158	162					10																	124598705		2203	4300	6503	124588695	SO:0001819	synonymous_variant	50624			AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.276C>A	10.37:g.124598705G>T			124588695		Silent	SNP	ENST00000368904.1	37	CCDS7631.1																																																																																				0.443	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034		T	124598705	G	T	124598705	2	4	47	1	0	0	0	0	0	0	0	1	4072	929	33	2		2	CUZD1	10	124598705	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	928081	124598705	10936042	1230	5627										
CPXM2	119587	broad.mit.edu	37	chr10	125557552	125557552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctcccattatcaaaccaggActgagggtttatgcggatgt	11	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:125557552A>G	ENST00000241305.3	-	6	983	c.829T>C	c.(829-831)Tcc>Ccc	p.S277P	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	277	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S277P(1)|p.S277A(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TCAAACCAGGACTGAGGGTTT	0.537																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	10											125	104	111					10																	125557552		2203	4300	6503	125547542	SO:0001583	missense	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.829T>C	10.37:g.125557552A>G	ENSP00000241305:p.Ser277Pro		125547542	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.207311	0.39003	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	D	0.98455	-4.94	4.46	3.28	0.37604	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.061433	0.64402	D	0.000002	D	0.98764	0.9584	M	0.89163	3.01	0.80722	D	1	D	0.61080	0.989	D	0.71656	0.974	D	0.98894	1.0774	10	0.87932	D	0	-5.8711	9.0236	0.36215	0.7061:0.0:0.0:0.2939	.	277	Q8N436	CPXM2_HUMAN	P	277;110;277	ENSP00000241305:S277P	ENSP00000241305:S277P	S	-	1	0	CPXM2	125547542	0.997000	0.39634	0.918000	0.36340	0.067000	0.16453	3.567000	0.53813	0.700000	0.31782	0.455000	0.32223	TCC		0.537	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		G	125557552	A	G	125557552	3	3	47	1	0	0	0	0	1	0	0	0	3844	275	10	4	1477	4	CPXM2	10	125557552	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	958847	125557552	9977195	1231	5628										
FAM175B	23172	broad.mit.edu	37	chr10	126519950	126519950	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgttgaaaagagtgagcgAgttgttgaatcttgtcaggc	14	4	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:126519950A>G	ENST00000298492.5	+	8	741	c.696A>G	c.(694-696)cgA>cgG	p.R232R		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	232					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)	p.R232R(1)		NS(1)	1						AGAGTGAGCGAGTTGTTGAAT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	10											98	86	90					10																	126519950		2203	4300	6503	126509940	SO:0001819	synonymous_variant	23172			D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"Abraxas brother"	611144	"KIAA0157"	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.696A>G	10.37:g.126519950A>G			126509940	B4DKR2|Q96H11	Silent	SNP	ENST00000298492.5	37	CCDS31308.2																																																																																				0.373	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		G	126519950	A	G	126519950	2	3	47	1	0	0	0	0	0	0	0	1	5514	291	11	4		4	FAM175B	10	126519950	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	962398	126519950	9014797	1232	5629										
FANK1	92565	broad.mit.edu	37	chr10	127668864	127668864	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtggttcaggttctcgattGaagaagaagaccccaaaatg	11	7	2	4	rs146106149	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:127668864G>T	ENST00000368693.1	+	2	252	c.148G>T	c.(148-150)Gaa>Taa	p.E50*	FANK1_ENST00000449042.2_Nonsense_Mutation_p.E44*|FANK1_ENST00000368689.1_Nonsense_Mutation_p.E44*|FANK1_ENST00000368695.1_Nonsense_Mutation_p.E44*			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	50	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E50*(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GTTCTCGATTGAAGAAGAAGA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											112	106	108					10																	127668864		2203	4300	6503	127658854	SO:0001587	stop_gained	92565			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.148G>T	10.37:g.127668864G>T	ENSP00000357682:p.Glu50*		127658854	Q6UXY9|Q6X7T6	Nonsense_Mutation	SNP	ENST00000368693.1	37	CCDS31309.1	.	.	.	.	.	.	.	.	.	.	G	34	5.354475	0.95830	.	.	ENSG00000203780	ENST00000368695;ENST00000368693;ENST00000449042;ENST00000417114;ENST00000445510;ENST00000368691;ENST00000368689;ENST00000368692	.	.	.	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-34.5901	17.1173	0.86692	0.0:0.0:1.0:0.0	.	.	.	.	X	44;50;44;44;44;44;44;50	.	ENSP00000357678:E44X	E	+	1	0	FANK1	127658854	1.000000	0.71417	0.692000	0.30179	0.936000	0.57629	6.054000	0.71096	2.313000	0.78055	0.563000	0.77884	GAA		0.443	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		T	127668864	G	T	127668864	4	4	47	1	0	0	0	0	0	1	0	0	5691	1291	45	2	154	2	FANK1	10	127668864	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1148914	127668864	7865883	1233	5630										
DOCK1	1793	broad.mit.edu	37	chr10	129046280	129046280	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attcatttacagggaaacttCgtggcttgcatgacagctat	9	8	1	1	rs548775401		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr10:129046280C>T	ENST00000280333.6	+	28	2902	c.2793C>T	c.(2791-2793)ttC>ttT	p.F931F	DOCK1_ENST00000484400.1_3'UTR	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	931					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.F931F(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGGGAAACTTCGTGGCTTGCA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	10											80	76	77					10																	129046280		1899	4121	6020	128936270	SO:0001819	synonymous_variant	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2793C>T	10.37:g.129046280C>T			128936270	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																					0.403	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	129046280	C	T	129046280	2	4	47	1	0	0	0	0	0	0	0	1	4695	883	31	1		1	DOCK1	10	129046280	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1377416	129046280	6488467	1234	5631										
MUC5B	727897	broad.mit.edu	37	chr11	1264583	1264584	+	Frame_Shift_Ins	INS	-	-	C													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actcctgggacaactcccatINSccccccagtgctgaccacca							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:1264583_1264584insC	ENST00000529681.1	+	31	6531_6532	c.6473_6474insC	c.(6472-6477)atccccfs	p.IP2158fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Ins_p.IP2161fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2158	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.V2164fs*98(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		acaactcccatccccccagtgc	0.649																																																1	Insertion - Frameshift(1)	large_intestine(1)	11																																								1221160	SO:0001589	frameshift_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.6479dupC	11.37:g.1264589_1264589dupC	ENSP00000436812:p.Ile2158fs		1221159	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Ins	INS	ENST00000529681.1	37	CCDS44515.2																																																																																				0.649	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1264584	-	C	1264583	7	5	47	1	0	1	1	0	0	0	0	0	10009	1435	50	0	6604	0	MUC5B	11	1264583	Frame_Shift_Ins	INS	-	TCGA-AG-3892-01A-01W-1073-09		1264583	133741933	1235	5632										
OR51T1	401665	broad.mit.edu	37	chr11	4903613	4903613	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagttttcttacttccccttCttgtagccataaacactgtg	5	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:4903613C>A	ENST00000322049.1	+	1	484	c.484C>A	c.(484-486)Ctt>Att	p.L162I	OR51T1_ENST00000380378.1_Missense_Mutation_p.L189I|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L189I(1)|p.L162I(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACTTCCCCTTCTTGTAGCCAT	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	11											160	149	153					11																	4903613		2201	4298	6499	4860189	SO:0001583	missense	401665			BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.484C>A	11.37:g.4903613C>A	ENSP00000322679:p.Leu162Ile		4860189	Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	37		.	.	.	.	.	.	.	.	.	.	C	0.007	-2.004519	0.00431	.	.	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.39997	1.05;1.05	4.8	-9.59	0.00556	GPCR, rhodopsin-like superfamily (1);	3.535090	0.00951	N	0.002965	T	0.16811	0.0404	N	0.11651	0.15	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20638	-1.0269	10	0.14656	T	0.56	.	2.2149	0.03957	0.2838:0.3775:0.1378:0.2009	.	162	Q8NGJ9	O51T1_HUMAN	I	189;162	ENSP00000369738:L189I;ENSP00000322679:L162I	ENSP00000322679:L162I	L	+	1	0	OR51T1	4860189	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-4.084000	0.00298	-3.525000	0.00147	-1.213000	0.01624	CTT		0.458	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		A	4903613	C	A	4903613	3	1	47	1	0	0	0	0	1	0	0	0	11137	913	32	2	567	2	OR51T1	11	4903613	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3639030	4903613	130102903	1236	5633										
OR52A5	390054	broad.mit.edu	37	chr11	5153680	5153680	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtggctgccaacatggccaAaaaaatgtacatgggtatat	10	7	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5153680A>C	ENST00000307388.1	-	1	192	c.193T>G	c.(193-195)Ttg>Gtg	p.L65V		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	65					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L65V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		AACATGGCCAAAAAAATGTAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											73	73	73					11																	5153680		2201	4298	6499	5110256	SO:0001583	missense	390054			BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"GPCR / Class A : Olfactory receptors"	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.193T>G	11.37:g.5153680A>C	ENSP00000303469:p.Leu65Val		5110256		Missense_Mutation	SNP	ENST00000307388.1	37	CCDS31373.1	.	.	.	.	.	.	.	.	.	.	A	9.238	1.037668	0.19669	.	.	ENSG00000171944	ENST00000307388	T	0.14022	2.54	5.22	-2.94	0.05581	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32753	N	0.005699	T	0.19087	0.0458	M	0.90252	3.1	0.22675	N	0.998866	P	0.35959	0.53	B	0.36418	0.224	T	0.16867	-1.0388	10	0.87932	D	0	.	8.2264	0.31570	0.3257:0.0:0.5436:0.1306	.	65	Q9H2C5	O52A5_HUMAN	V	65	ENSP00000303469:L65V	ENSP00000303469:L65V	L	-	1	2	OR52A5	5110256	0.000000	0.05858	0.330000	0.25442	0.270000	0.26580	-0.268000	0.08607	-0.403000	0.07622	-0.290000	0.09829	TTG		0.378	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160		C	5153680	A	C	5153680	3	2	47	1	0	0	0	0	1	0	0	0	11141	11	1	4	760	4	OR52A5	11	5153680	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	250067	5153680	129852836	1237	5634										
OR51V1	283111	broad.mit.edu	37	chr11	5221880	5221880	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgagaagaaaggaagaattCgtgctggtgctagggcttac	15	5	0	3	rs550954546		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5221880C>T	ENST00000321255.1	-	1	50	c.51G>A	c.(49-51)acG>acA	p.T17T		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	17					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T17T(1)		endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGAAGAATTCGTGCTGGTGC	0.428													C|||	1	0.000199681	0	0	5008	,	,		20524	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	11											83	81	82					11																	5221880		2201	4298	6499	5178456	SO:0001819	synonymous_variant	283111			BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"GPCR / Class A : Olfactory receptors"	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.51G>A	11.37:g.5221880C>T			5178456		Silent	SNP	ENST00000321255.1	37	CCDS31375.1																																																																																				0.428	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		T	5221880	C	T	5221880	2	4	47	1	0	0	0	0	0	0	0	1	11138	871	31	1		1	OR51V1	11	5221880	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	68200	5221880	129784636	1238	5635										
HBB	3043	broad.mit.edu	37	chr11	5247996	5247996	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatccccaaaggactcaaaGaacctctgggtccaagggta	10	11	2	2	rs36029927|rs281864570|rs35755331|rs281864897|rs281864900|rs80356821	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5247996G>T	ENST00000335295.4	-	2	175	c.126C>A	c.(124-126)ttC>ttA	p.F42L	CoTC_ribozyme_ENST00000408104.1_RNA	NM_000518.4	NP_000509.1	P68871	HBB_HUMAN	hemoglobin, beta	42			F -> Y (in Mequon).|Missing (in Bruxelles). {ECO:0000269|PubMed:2599881}.	F -> L (in Ref. 13; AAR96398). {ECO:0000305}.	bicarbonate transport (GO:0015701)|blood coagulation (GO:0007596)|hydrogen peroxide catabolic process (GO:0042744)|nitric oxide transport (GO:0030185)|oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|platelet aggregation (GO:0070527)|positive regulation of cell death (GO:0010942)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein heterooligomerization (GO:0051291)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|renal absorption (GO:0070293)|response to hydrogen peroxide (GO:0042542)|small molecule metabolic process (GO:0044281)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|hemoglobin binding (GO:0030492)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.F42L(2)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)	15		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Iron Dextran(DB00893)	AGGACTCAAAGAACCTCTGGG	0.517									Sickle Cell Trait																																							2	Substitution - Missense(2)	large_intestine(2)	11	GRCh37	CD920864|CI032768	HBB	D|I	rs34532766						101	99	100					11																	5247996		2201	4298	6499	5204572	SO:0001583	missense	3043	Familial Cancer Database		J00173	CCDS7753.1	11p15.5	2014-05-19			ENSG00000244734	ENSG00000244734			4827	protein-coding gene	gene with protein product		141900				2649166	Standard	NM_000518		Approved	CD113t-C, HBD, beta-globin	uc001mae.1	P68871	OTTHUMG00000066678	ENST00000335295.4:c.126C>A	11.37:g.5247996G>T	ENSP00000333994:p.Phe42Leu		5204572	A4GX73|B2ZUE0|P02023|Q13852|Q14481|Q14510|Q45KT0|Q549N7|Q6FI08|Q6R7N2|Q8IZI1|Q9BX96|Q9UCD6|Q9UCP8|Q9UCP9	Missense_Mutation	SNP	ENST00000335295.4	37	CCDS7753.1	.	.	.	.	.	.	.	.	.	.	g	20.7	4.029800	0.75504	.	.	ENSG00000244734	ENST00000335295;ENST00000380315	D;D	0.91631	-2.88;-2.88	5.1	4.19	0.49359	Globin-like (1);Globin, structural domain (1);	.	.	.	.	D	0.90497	0.7023	L	0.48986	1.54	0.38186	D	0.939757	B	0.27882	0.192	B	0.41619	0.361	D	0.88927	0.3370	9	0.72032	D	0.01	-10.8741	5.8737	0.18816	0.2238:0.0:0.7762:0.0	.	42	P68871	HBB_HUMAN	L	42	ENSP00000333994:F42L;ENSP00000369671:F42L	ENSP00000333994:F42L	F	-	3	2	HBB	5204572	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.277000	0.33167	2.812000	0.96745	0.555000	0.69702	TTC		0.517	HBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142977.2	NM_000518		T	5247996	G	T	5247996	3	4	47	1	0	0	0	0	1	0	0	0	6999	933	33	2	325	2	HBB	11	5247996	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	26116	5247996	129758520	1239	5636										
HBD	3045	broad.mit.edu	37	chr11	5255410	5255410	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatccccaaaggactcaaaGaacctctgggtccaagggta	10	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5255410G>T	ENST00000380299.3	-	2	340	c.126C>A	c.(124-126)ttC>ttA	p.F42L	HBD_ENST00000292901.3_Missense_Mutation_p.F42L	NM_000519.3	NP_000510.1	P02042	HBD_HUMAN	hemoglobin, delta	42					blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.F42L(1)		endometrium(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	16		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;5.69e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGACTCAAAGAACCTCTGGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											106	103	104					11																	5255410		2201	4298	6499	5211986	SO:0001583	missense	3045			AY034468	CCDS31376.1	11p15.5	2012-10-02			ENSG00000223609	ENSG00000223609			4829	protein-coding gene	gene with protein product		142000				2649166	Standard	NM_000519		Approved		uc001maf.1	P02042	OTTHUMG00000066674	ENST00000380299.3:c.126C>A	11.37:g.5255410G>T	ENSP00000369654:p.Phe42Leu		5211986	Q3Y5H3|Q8WXT7	Missense_Mutation	SNP	ENST00000380299.3	37	CCDS31376.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080423	0.76528	.	.	ENSG00000223609	ENST00000292901;ENST00000380299;ENST00000429817	D;D;D	0.91631	-2.88;-2.88;-2.88	4.45	3.53	0.40419	Globin-like (1);Globin, structural domain (1);	0.107759	0.64402	D	0.000003	D	0.87744	0.6254	L	0.41415	1.275	0.35852	D	0.826835	B	0.32604	0.377	B	0.34093	0.175	D	0.90743	0.4651	10	0.72032	D	0.01	-0.071	11.8981	0.52667	0.0918:0.0:0.9082:0.0	.	42	P02042	HBD_HUMAN	L	42	ENSP00000292901:F42L;ENSP00000369654:F42L;ENSP00000393810:F42L	ENSP00000292901:F42L	F	-	3	2	HBD	5211986	1.000000	0.71417	0.918000	0.36340	0.842000	0.47809	2.126000	0.42026	2.463000	0.83235	0.585000	0.79938	TTC		0.517	HBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142970.1	NM_000519		T	5255410	G	T	5255410	3	4	47	1	0	0	0	0	1	0	0	0	7000	933	33	2	325	2	HBD	11	5255410	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7414	5255410	129751106	1240	5637										
OR52H1	390067	broad.mit.edu	37	chr11	5566716	5566716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggtcctggattgtaactgCtcaggttgaaaatgatcatg	12	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5566716C>T	ENST00000322653.4	-	1	63	c.38G>A	c.(37-39)aGc>aAc	p.S13N	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S13N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTGTAACTGCTCAGGTTGAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											94	91	92					11																	5566716		2201	4297	6498	5523292	SO:0001583	missense	390067			AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"GPCR / Class A : Olfactory receptors"	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.38G>A	11.37:g.5566716C>T	ENSP00000326259:p.Ser13Asn		5523292	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.925901	0.34002	.	.	ENSG00000181616	ENST00000322653	T	0.54071	0.59	5.2	3.22	0.36961	.	0.153772	0.46758	D	0.000261	T	0.44582	0.1300	L	0.49571	1.57	0.20764	N	0.99986	P	0.40660	0.726	B	0.39617	0.305	T	0.42899	-0.9424	10	0.66056	D	0.02	.	8.3065	0.32045	0.1614:0.5442:0.2944:0.0	.	13	Q8NGJ2	O52H1_HUMAN	N	13	ENSP00000326259:S13N	ENSP00000326259:S13N	S	-	2	0	OR52H1	5523292	0.001000	0.12720	0.936000	0.37596	0.686000	0.39977	0.432000	0.21461	1.206000	0.43276	-0.127000	0.14921	AGC		0.448	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		T	5566716	C	T	5566716	3	4	47	1	0	0	0	0	1	0	0	0	11150	797	28	3	927	3	OR52H1	11	5566716	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	311306	5566716	129439800	1241	5638										
OR52E6	390078	broad.mit.edu	37	chr11	5862609	5862609	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagtatgagggatgatacgAtgtccacagaagggcaacct	12	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5862609A>C	ENST00000329322.5	-	1	518	c.519T>G	c.(517-519)caT>caG	p.H173Q	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.H177Q	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	173						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H177Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATGATACGATGTCCACAGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											150	140	143					11																	5862609		2201	4296	6497	5819185	SO:0001583	missense	390078			AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"GPCR / Class A : Olfactory receptors"	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.519T>G	11.37:g.5862609A>C	ENSP00000328878:p.His173Gln		5819185	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	.	.	.	.	.	.	.	.	.	.	A	4.325	0.059683	0.08339	.	.	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.36878	1.23;1.23	3.45	-5.92	0.02261	GPCR, rhodopsin-like superfamily (1);	0.207429	0.33309	N	0.005055	T	0.22898	0.0553	L	0.56280	1.765	0.09310	N	1	B	0.31227	0.314	B	0.38327	0.271	T	0.37079	-0.9721	10	0.12766	T	0.61	.	1.9219	0.03309	0.4617:0.1323:0.2722:0.1338	.	173	Q96RD3	O52E6_HUMAN	Q	173;177	ENSP00000328878:H173Q;ENSP00000369279:H177Q	ENSP00000328878:H173Q	H	-	3	2	OR52E6	5819185	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-4.489000	0.00226	-0.952000	0.03649	-0.330000	0.08379	CAT		0.483	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167		C	5862609	A	C	5862609	3	2	47	1	0	0	0	0	1	0	0	0	11148	330	12	4	424	4	OR52E6	11	5862609	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	295893	5862609	129143907	1242	5639										
OR52E4	390081	broad.mit.edu	37	chr11	5906456	5906456	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaaatatttgtacagaaaGaataattctgtattaaagtt	6	2	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:5906456G>T	ENST00000316987.2	+	1	956	c.934G>T	c.(934-936)Gaa>Taa	p.E312*		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E312*(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTACAGAAAGAATAATTCTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											41	38	39					11																	5906456		2003	4178	6181	5863032	SO:0001587	stop_gained	390081			AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.934G>T	11.37:g.5906456G>T	ENSP00000321426:p.Glu312*		5863032	Q6IFG0	Nonsense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801444	0.50315	.	.	ENSG00000180974	ENST00000316987	.	.	.	5.26	2.23	0.28157	.	1.233700	0.06081	N	0.661884	.	.	.	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.2859	0.10855	0.1806:0.0:0.4421:0.3772	.	.	.	.	X	312	.	ENSP00000321426:E312X	E	+	1	0	OR52E4	5863032	0.473000	0.25878	0.342000	0.25602	0.728000	0.41692	0.082000	0.14847	0.289000	0.22422	0.643000	0.83706	GAA		0.363	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		T	5906456	G	T	5906456	4	4	47	1	0	0	0	0	0	1	0	0	11147	943	33	2	936	2	OR52E4	11	5906456	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	43847	5906456	129100060	1243	5640										
ZNF214	7761	broad.mit.edu	37	chr11	7021709	7021709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgtactaactgatgaattCgaagatttgagctctggctg	11	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:7021709C>T	ENST00000278314.4	-	3	1520	c.1205G>A	c.(1204-1206)cGa>cAa	p.R402Q	ZNF214_ENST00000531083.1_5'Flank|ZNF214_ENST00000536068.1_Missense_Mutation_p.R402Q	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R402Q(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		CTGATGAATTCGAAGATTTGA	0.418																																					Ovarian(22;251 657 736 21522 46864)											1	Substitution - Missense(1)	large_intestine(1)	11											85	90	88					11																	7021709		2201	4296	6497	6978285	SO:0001583	missense	7761			AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"Zinc fingers, C2H2-type", "-"	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.1205G>A	11.37:g.7021709C>T	ENSP00000278314:p.Arg402Gln		6978285	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	.	.	.	.	.	.	.	.	.	.	C	8.783	0.928703	0.18131	.	.	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.35973	1.28;1.28	3.75	1.82	0.25136	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.259797	0.20591	N	0.089359	T	0.08670	0.0215	N	0.02169	-0.655	0.23070	N	0.998347	P	0.36465	0.554	B	0.21151	0.033	T	0.31888	-0.9927	10	0.07990	T	0.79	.	6.9138	0.24349	0.0:0.7164:0.1793:0.1042	.	402	Q9UL59	ZN214_HUMAN	Q	402	ENSP00000278314:R402Q;ENSP00000445373:R402Q	ENSP00000278314:R402Q	R	-	2	0	ZNF214	6978285	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.205000	0.09411	0.529000	0.28599	0.655000	0.94253	CGA		0.418	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1			T	7021709	C	T	7021709	3	4	47	1	0	0	0	0	1	0	0	0	17809	884	31	1	619	1	ZNF214	11	7021709	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1115253	7021709	127984807	1244	5641										
SCUBE2	57758	broad.mit.edu	37	chr11	9069061	9069061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagcgtgcggatggctttaCggagccgcttctcggttcgc	15	11	1	1	rs144080898	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:9069061C>T	ENST00000309263.3	-	15	1829	c.1757G>A	c.(1756-1758)cGt>cAt	p.R586H	RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000520467.1_Missense_Mutation_p.R615H|SCUBE2_ENST00000457346.2_Missense_Mutation_p.R615H|SCUBE2_ENST00000450649.2_Missense_Mutation_p.R460H			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	586						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R586H(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GATGGCTTTACGGAGCCGCTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	82	68	73		1379,1844	5.2	1	11	dbSNP_134	73	2,8590	3.0+/-9.4	0,2,4294	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	29,29	0,3,6494	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	460/808,615/972	9069061	3,12991	2201	4296	6497	9025637	SO:0001583	missense	57758			AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.1757G>A	11.37:g.9069061C>T	ENSP00000310658:p.Arg586His		9025637	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.630560	0.87660	2.27E-4	2.33E-4	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;D;D	0.84589	-1.3;-1.41;-1.87;-1.51	5.21	5.21	0.72293	.	0.048843	0.85682	D	0.000000	D	0.91355	0.7273	M	0.68952	2.095	0.80722	D	1	D;D;D	0.76494	0.999;0.996;0.997	D;D;P	0.66196	0.942;0.933;0.818	D	0.91946	0.5567	10	0.72032	D	0.01	.	19.1303	0.93402	0.0:1.0:0.0:0.0	.	460;615;586	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	H	615;586;460;615	ENSP00000390481:R615H;ENSP00000310658:R586H;ENSP00000415187:R460H;ENSP00000429969:R615H	ENSP00000310658:R586H	R	-	2	0	SCUBE2	9025637	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	5.890000	0.69774	2.603000	0.88011	0.655000	0.94253	CGT		0.567	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		T	9069061	C	T	9069061	3	4	47	1	0	0	0	0	1	0	0	0	13982	536	19	1	1274	1	SCUBE2	11	9069061	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2047352	9069061	125937455	1245	5642										
USP47	55031	broad.mit.edu	37	chr11	11969545	11969545	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcagctttcaaacaacatTtagagccctttgttggagtt	9	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:11969545T>G	ENST00000399455.2	+	22	3325	c.3205T>G	c.(3205-3207)Tta>Gta	p.L1069V	USP47_ENST00000539466.1_5'UTR|USP47_ENST00000527733.1_Missense_Mutation_p.L1049V|USP47_ENST00000339865.5_Missense_Mutation_p.L981V	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1069					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)	p.L981V(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		CAAACAACATTTAGAGCCCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											156	146	149					11																	11969545		1839	4081	5920	11926121	SO:0001583	missense	55031			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3205T>G	11.37:g.11969545T>G	ENSP00000382382:p.Leu1069Val		11926121	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	T	18.85	3.711898	0.68730	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455	D;D;D	0.94862	-3.54;-3.54;-3.54	5.46	4.34	0.51931	.	0.000000	0.85682	D	0.000000	D	0.95516	0.8543	L	0.54323	1.7	0.80722	D	1	D;D	0.63880	0.993;0.974	D;D	0.70487	0.967;0.969	D	0.94784	0.7956	10	0.87932	D	0	.	9.1982	0.37242	0.0:0.1493:0.0:0.8507	.	1049;981	E9PM46;Q96K76-2	.;.	V	981;1049;1069	ENSP00000339957:L981V;ENSP00000433146:L1049V;ENSP00000382382:L1069V	ENSP00000339957:L981V	L	+	1	2	USP47	11926121	0.422000	0.25473	0.983000	0.44433	0.981000	0.71138	0.831000	0.27476	0.886000	0.36113	-0.376000	0.06991	TTA		0.393	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		G	11969545	T	G	11969545	3	3	47	1	0	0	0	0	1	0	0	0	17118	1838	64	4	3019	4	USP47	11	11969545	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2900484	11969545	123036971	1246	5643										
PDE3B	5140	broad.mit.edu	37	chr11	14882859	14882859	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaatggcccagcaaaagttCgagacttgcatttgaaatgg	10	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:14882859C>T	ENST00000282096.4	+	14	3186	c.2833C>T	c.(2833-2835)Cga>Tga	p.R945*	PDE3B_ENST00000455098.2_Nonsense_Mutation_p.R894*	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	945	Catalytic. {ECO:0000250}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)	p.R945*(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	AGCAAAAGTTCGAGACTTGCA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											128	124	125					11																	14882859		2200	4294	6494	14839435	SO:0001587	stop_gained	5140			U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2833C>T	11.37:g.14882859C>T	ENSP00000282096:p.Arg945*		14839435	B7ZM37|O00639|Q14408|Q6SEI4	Nonsense_Mutation	SNP	ENST00000282096.4	37	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	C	41	9.010505	0.99035	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	.	.	.	5.32	5.32	0.75619	.	0.193215	0.45361	D	0.000373	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8378	0.63419	0.1912:0.8088:0.0:0.0	.	.	.	.	X	945;894	.	ENSP00000282096:R945X	R	+	1	2	PDE3B	14839435	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.747000	0.55134	2.477000	0.83638	0.591000	0.81541	CGA		0.403	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		T	14882859	C	T	14882859	4	4	47	1	0	0	0	0	0	1	0	0	11669	876	31	1	2887	1	PDE3B	11	14882859	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2913314	14882859	120123657	1247	5644										
SOX6	55553	broad.mit.edu	37	chr11	16071447	16071447	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggctctgctgtcttgggtCgggatgagagattcagaggc	16	8	3	3	rs563514211		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:16071447C>T	ENST00000352083.6	-	11	1366	c.1289G>A	c.(1288-1290)cGa>cAa	p.R430Q	SOX6_ENST00000527619.1_Missense_Mutation_p.R392Q|SOX6_ENST00000316399.6_Missense_Mutation_p.R430Q|SOX6_ENST00000528252.1_Missense_Mutation_p.R389Q|SOX6_ENST00000396356.3_Missense_Mutation_p.R430Q|SOX6_ENST00000528429.1_Missense_Mutation_p.R430Q			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	430					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R430P(1)|p.R430Q(1)|p.R392P(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						TGTCTTGGGTCGGGATGAGAG	0.458													C|||	1	0.000199681	0	0	5008	,	,		16822	0		0	False		,,,				2504	0.001															3	Substitution - Missense(3)	lung(2)|large_intestine(1)	11											207	215	213					11																	16071447		2200	4294	6494	16028023	SO:0001583	missense	55553			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.1289G>A	11.37:g.16071447C>T	ENSP00000339876:p.Arg430Gln		16028023	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	C	33	5.259369	0.95368	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429	D;D;D;D;D;D	0.98105	-4.63;-4.67;-4.63;-4.72;-4.72;-4.67	6.01	6.01	0.97437	.	0.124998	0.56097	D	0.000037	D	0.98169	0.9395	L	0.59436	1.845	0.80722	D	1	D;D;D	0.71674	0.998;0.994;0.991	P;P;P	0.61397	0.888;0.767;0.585	D	0.97842	1.0269	10	0.44086	T	0.13	.	20.5211	0.99222	0.0:1.0:0.0:0.0	.	430;430;392	P35712-3;P35712;P35712-2	.;SOX6_HUMAN;.	Q	430;430;430;389;392;430	ENSP00000324948:R430Q;ENSP00000339876:R430Q;ENSP00000379644:R430Q;ENSP00000432134:R389Q;ENSP00000434455:R392Q;ENSP00000433233:R430Q	ENSP00000324948:R430Q	R	-	2	0	SOX6	16028023	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.440000	0.80464	2.861000	0.98227	0.650000	0.86243	CGA		0.458	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		T	16071447	C	T	16071447	3	4	47	1	0	0	0	0	1	0	0	0	14992	884	31	1	1263	1	SOX6	11	16071447	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1188588	16071447	118935069	1248	5645										
ABCC8	6833	broad.mit.edu	37	chr11	17426076	17426076	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacctggacgccacccggaaGtacttctggatgaagtagca	11	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:17426076G>T	ENST00000389817.3	-	28	3608	c.3540C>A	c.(3538-3540)taC>taA	p.Y1180*	ABCC8_ENST00000302539.4_Nonsense_Mutation_p.Y1181*			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1180	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.Y1180*(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	CCACCCGGAAGTACTTCTGGA	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											97	79	85					11																	17426076		2200	4293	6493	17382652	SO:0001587	stop_gained	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3540C>A	11.37:g.17426076G>T	ENSP00000374467:p.Tyr1180*		17382652	A6NMX8|E3UYX6|O75948|Q16583	Nonsense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.223406|6.223406	0.97390|0.97390	.|.	.|.	ENSG00000006071|ENSG00000006071	ENST00000528374|ENST00000389817;ENST00000302539	.|.	.|.	.|.	5.32|5.32	4.41|4.41	0.53225|0.53225	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.32285|.	0.0824|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35425|.	-0.9789|.	3|.	.|0.02654	.|T	.|1	.|.	12.107|12.107	0.53818|0.53818	0.1433:0.0:0.8567:0.0|0.1433:0.0:0.8567:0.0	.|.	.|.	.|.	.|.	I|X	4|1180;1181	.|.	.|ENSP00000303960:Y1181X	L|Y	-|-	1|3	0|2	ABCC8|ABCC8	17382652|17382652	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.171000|4.171000	0.58236|0.58236	1.233000|1.233000	0.43693|0.43693	0.514000|0.514000	0.50259|0.50259	CTT|TAC		0.562	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		T	17426076	G	T	17426076	4	4	47	1	0	0	0	0	0	1	0	0	58	1024	36	2	1253	2	ABCC8	11	17426076	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1354629	17426076	117580440	1249	5646										
KCNC1	3746	broad.mit.edu	37	chr11	17757864	17757864	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accgacgtggagccctgctgCtggatgacgtaccgccagca	13	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:17757864C>A	ENST00000379472.3	+	1	345	c.315C>A	c.(313-315)tgC>tgA	p.C105*	KCNC1_ENST00000265969.6_Nonsense_Mutation_p.C105*	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	105					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.C105*(1)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	AGCCCTGCTGCTGGATGACGT	0.711																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											34	36	36					11																	17757864		2200	4292	6492	17714440	SO:0001587	stop_gained	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.315C>A	11.37:g.17757864C>A	ENSP00000368785:p.Cys105*		17714440	K4DI87	Nonsense_Mutation	SNP	ENST00000379472.3	37	CCDS7827.1	.	.	.	.	.	.	.	.	.	.	C	37	6.333994	0.97485	.	.	ENSG00000129159	ENST00000265969;ENST00000379472	.	.	.	5.09	3.21	0.36854	.	0.090440	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.6117	0.39668	0.0:0.711:0.0:0.289	.	.	.	.	X	105	.	ENSP00000265969:C105X	C	+	3	2	KCNC1	17714440	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.160000	0.31761	0.544000	0.28883	0.491000	0.48974	TGC		0.711	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		A	17757864	C	A	17757864	4	1	47	1	0	0	0	0	0	1	0	0	8035	805	28	2	317	2	KCNC1	11	17757864	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	331788	17757864	117248652	1250	5647										
MRGPRX4	117196	broad.mit.edu	37	chr11	18195536	18195536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatttacaggatgcacctgAatttggaagtcttatattgt	8	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:18195536A>G	ENST00000314254.3	+	1	1153	c.733A>G	c.(733-735)Aat>Gat	p.N245D	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	245			N -> S (in dbSNP:rs7102322).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N245D(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GATGCACCTGAATTTGGAAGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											131	121	124					11																	18195536		2199	4293	6492	18152112	SO:0001583	missense	117196			AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.733A>G	11.37:g.18195536A>G	ENSP00000314042:p.Asn245Asp		18152112	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	.	.	.	.	.	.	.	.	.	.	A	0.704	-0.789660	0.02884	.	.	ENSG00000179817	ENST00000314254	T	0.72505	-0.66	2.85	-5.7	0.02421	GPCR, rhodopsin-like superfamily (1);	2.904660	0.00848	N	0.001818	T	0.41003	0.1140	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.42241	-0.9463	10	0.34782	T	0.22	.	5.3823	0.16197	0.4452:0.0:0.1245:0.4303	.	245	Q96LA9	MRGX4_HUMAN	D	245	ENSP00000314042:N245D	ENSP00000314042:N245D	N	+	1	0	MRGPRX4	18152112	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.126000	0.01316	-2.647000	0.00426	-2.775000	0.00119	AAT		0.507	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		G	18195536	A	G	18195536	3	3	47	1	0	0	0	0	1	0	0	0	9799	246	9	4	735	4	MRGPRX4	11	18195536	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	437672	18195536	116810980	1251	5648										
LDHA	3939	broad.mit.edu	37	chr11	18421014	18421014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgctcttgttgatgtcatcGaagacaaattgaagggagag	12	5	2	4	rs144856598		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:18421014G>A	ENST00000422447.3	+	3	436	c.163G>A	c.(163-165)Gaa>Aaa	p.E55K	LDHA_ENST00000227157.4_Missense_Mutation_p.E55K|LDHA_ENST00000379412.5_Missense_Mutation_p.E55K|LDHA_ENST00000540430.1_Missense_Mutation_p.E84K|LDHA_ENST00000430553.2_Missense_Mutation_p.E55K|LDHA_ENST00000542179.1_Missense_Mutation_p.E55K|LDHA_ENST00000396222.2_Missense_Mutation_p.E55K	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	55					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)	p.E55K(1)|p.E84K(1)		central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						TGATGTCATCGAAGACAAATT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	11						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4398		0,0,2199	137	125	129		163,250,163,163,163	5	1	11	dbSNP_134	129	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense,missense,missense	LDHA	NM_001135239.1,NM_001165414.1,NM_001165415.1,NM_001165416.1,NM_005566.3	56,56,56,56,56	0,1,6491	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	55/275,84/362,55/275,55/242,55/333	18421014	1,12983	2199	4293	6492	18377590	SO:0001583	missense	3939			X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.163G>A	11.37:g.18421014G>A	ENSP00000395337:p.Glu55Lys		18377590	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566295	0.86439	0.0	1.16E-4	ENSG00000134333	ENST00000422447;ENST00000543445;ENST00000430553;ENST00000396222;ENST00000535451;ENST00000227157;ENST00000478970;ENST00000495052;ENST00000540430;ENST00000379412;ENST00000542179	D;D;D;D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	5.03	5.03	0.67393	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.84969	0.5590	L	0.46819	1.47	0.80722	D	1	B;B;B;B	0.25719	0.002;0.132;0.019;0.004	B;B;B;B	0.29524	0.01;0.103;0.02;0.005	T	0.80792	-0.1224	10	0.33940	T	0.23	-2.5971	18.9079	0.92471	0.0:0.0:1.0:0.0	.	84;55;55;55	B7Z5E3;B4DKQ2;F8W819;P00338	.;.;.;LDHA_HUMAN	K	55;55;55;55;55;55;55;55;84;55;55	ENSP00000395337:E55K;ENSP00000440161:E55K;ENSP00000406172:E55K;ENSP00000379524:E55K;ENSP00000444292:E55K;ENSP00000227157:E55K;ENSP00000441241:E55K;ENSP00000446415:E55K;ENSP00000445175:E84K;ENSP00000368722:E55K;ENSP00000445331:E55K	ENSP00000227157:E55K	E	+	1	0	LDHA	18377590	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	9.490000	0.97952	2.768000	0.95171	0.655000	0.94253	GAA		0.378	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		A	18421014	G	A	18421014	3	1	47	1	0	0	0	0	1	0	0	0	8720	1059	37	1	260	1	LDHA	11	18421014	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	225478	18421014	116585502	1252	5649										
ANO5	203859	broad.mit.edu	37	chr11	22242678	22242678	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaagcaaagattctatcttCttccgagatgggattaggca	9	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:22242678C>T	ENST00000324559.8	+	5	533	c.216C>T	c.(214-216)ttC>ttT	p.F72F		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	72					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)	p.F72F(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATTCTATCTTCTTCCGAGATG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	11											95	92	93					11																	22242678		2203	4300	6503	22199254	SO:0001819	synonymous_variant	203859			AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.216C>T	11.37:g.22242678C>T			22199254		Silent	SNP	ENST00000324559.8	37	CCDS31444.1																																																																																				0.343	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		T	22242678	C	T	22242678	2	4	47	1	0	0	0	0	0	0	0	1	700	912	32	3		3	ANO5	11	22242678	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3821664	22242678	112763838	1253	5650										
ANO3	63982	broad.mit.edu	37	chr11	26621243	26621243	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctgtatcaatttcataatCattatgttgctgaatcttgt	6	6	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:26621243C>A	ENST00000256737.3	+	17	2670	c.1818C>A	c.(1816-1818)atC>atA	p.I606I	ANO3_ENST00000525139.1_Silent_p.I590I|ANO3_ENST00000531568.1_Silent_p.I460I|ANO3_ENST00000537978.1_Silent_p.I590I	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	606					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.I606I(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						ATTTCATAATCATTATGTTGC	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	11											161	143	149					11																	26621243		2203	4299	6502	26577819	SO:0001819	synonymous_variant	63982			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1818C>A	11.37:g.26621243C>A			26577819	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																				0.358	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26621243	C	A	26621243	2	1	47	1	0	0	0	0	0	0	0	1	698	816	29	2		2	ANO3	11	26621243	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4378565	26621243	108385273	1254	5651										
ANO3	63982	broad.mit.edu	37	chr11	26660771	26660771	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcaaatatggaacaacttCatggaactaggatacccgtg	9	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:26660771C>A	ENST00000256737.3	+	21	2976	c.2124C>A	c.(2122-2124)ttC>ttA	p.F708L	ANO3_ENST00000525139.1_Missense_Mutation_p.F692L|ANO3_ENST00000531568.1_Missense_Mutation_p.F562L|ANO3_ENST00000537978.1_Missense_Mutation_p.F692L	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	708					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.F708L(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						GGAACAACTTCATGGAACTAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											159	136	143					11																	26660771		2203	4299	6502	26617347	SO:0001583	missense	63982			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2124C>A	11.37:g.26660771C>A	ENSP00000256737:p.Phe708Leu		26617347	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	37	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.921147	0.52653	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.61627	0.09;0.09;0.09;0.09	5.39	1.41	0.22369	.	0.000000	0.85682	D	0.000000	T	0.50069	0.1594	L	0.31526	0.94	0.80722	D	1	P;P	0.46784	0.884;0.884	P;P	0.49922	0.542;0.626	T	0.34875	-0.9811	10	0.30078	T	0.28	.	10.5846	0.45275	0.0:0.6052:0.0:0.3948	.	610;708	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	L	692;692;708;610;562	ENSP00000440737:F692L;ENSP00000432576:F692L;ENSP00000256737:F708L;ENSP00000432394:F562L	ENSP00000256737:F708L	F	+	3	2	ANO3	26617347	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	0.726000	0.25984	0.263000	0.21812	0.467000	0.42956	TTC		0.408	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26660771	C	A	26660771	3	1	47	1	0	0	0	0	1	0	0	0	698	825	29	2	2206	2	ANO3	11	26660771	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	39528	26660771	108345745	1255	5652										
BBOX1	8424	broad.mit.edu	37	chr11	27147226	27147226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgataaaggccaagtggttCgcatcaacttcaataacgca	8	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:27147226C>T	ENST00000529202.1	+	7	1201	c.862C>T	c.(862-864)Cgc>Tgc	p.R288C	RP11-1L12.3_ENST00000530430.1_RNA|BBOX1_ENST00000528583.1_Missense_Mutation_p.R288C|BBOX1_ENST00000263182.3_Missense_Mutation_p.R288C|BBOX1_ENST00000525090.1_Missense_Mutation_p.R288C|RP11-1L12.3_ENST00000526061.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	288					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)	p.R288C(1)		breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	ccaagtggttcgcatcaactt	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	69	74					11																	27147226		2198	4298	6496	27103802	SO:0001583	missense	8424			AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.862C>T	11.37:g.27147226C>T	ENSP00000435781:p.Arg288Cys		27103802	B2R8L7|D3DQZ1|Q6IBJ2	Missense_Mutation	SNP	ENST00000529202.1	37	CCDS7862.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144372	0.77888	.	.	ENSG00000129151	ENST00000529202;ENST00000263182;ENST00000528583;ENST00000525090	D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74	6.03	6.03	0.97812	.	0.102971	0.64402	D	0.000003	D	0.91489	0.7313	M	0.78285	2.405	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90723	0.4636	10	0.51188	T	0.08	.	19.1304	0.93404	0.0:1.0:0.0:0.0	.	288	O75936	BODG_HUMAN	C	288	ENSP00000435781:R288C;ENSP00000263182:R288C;ENSP00000434918:R288C;ENSP00000433772:R288C	ENSP00000263182:R288C	R	+	1	0	BBOX1	27103802	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.583000	0.60964	2.854000	0.98071	0.655000	0.94253	CGC		0.333	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		T	27147226	C	T	27147226	3	4	47	1	0	0	0	0	1	0	0	0	1335	884	31	1	884	1	BBOX1	11	27147226	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	486455	27147226	107859290	1256	5653										
LGR4	55366	broad.mit.edu	37	chr11	27390235	27390235	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccctctatggaaaaggggaaAacagcctgctactgtagcac	10	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:27390235A>C	ENST00000379214.4	-	18	2478	c.2035T>G	c.(2035-2037)Ttt>Gtt	p.F679V	LGR4_ENST00000389858.4_Missense_Mutation_p.F655V	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	679					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.F679V(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AAAAGGGGAAAACAGCCTGCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											93	84	87					11																	27390235		2202	4299	6501	27346811	SO:0001583	missense	55366			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2035T>G	11.37:g.27390235A>C	ENSP00000368516:p.Phe679Val		27346811	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	A	9.666	1.145308	0.21288	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.71103	-0.54;1.31	5.72	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.306103	0.34223	N	0.004148	T	0.43787	0.1263	N	0.03608	-0.345	0.80722	D	1	B;B	0.20671	0.002;0.047	B;B	0.28465	0.003;0.09	T	0.13656	-1.0501	10	0.39692	T	0.17	.	5.6485	0.17602	0.6638:0.1314:0.2048:0.0	.	655;679	G5E9B3;Q9BXB1	.;LGR4_HUMAN	V	679;655	ENSP00000368516:F679V;ENSP00000374508:F655V	ENSP00000368516:F679V	F	-	1	0	LGR4	27346811	1.000000	0.71417	0.899000	0.35326	0.711000	0.40976	3.237000	0.51344	0.411000	0.25702	0.528000	0.53228	TTT		0.438	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		C	27390235	A	C	27390235	3	2	47	1	0	0	0	0	1	0	0	0	8779	14	1	4	824	4	LGR4	11	27390235	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	243009	27390235	107616281	1257	5654										
KCNA4	3739	broad.mit.edu	37	chr11	30033975	30033975	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagaccgctgtcgcctcctcCtccgactaccccggctgctc	8	21	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:30033975C>A	ENST00000328224.6	-	2	1484	c.251G>T	c.(250-252)aGg>aTg	p.R84M	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	84				RRRRQ -> EEEAT (in Ref. 1; AAA60034). {ECO:0000305}.	potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.R84M(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	TCGCCTCCTCCTCCGACTACC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	11											44	46	45					11																	30033975		2048	4198	6246	29990551	SO:0001583	missense	3739			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.251G>T	11.37:g.30033975C>A	ENSP00000328511:p.Arg84Met		29990551		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.683566	0.29872	.	.	ENSG00000182255	ENST00000328224	D	0.96967	-4.19	4.84	4.84	0.62591	.	8.526260	0.00751	U	0.001060	D	0.93151	0.7819	N	0.19112	0.55	0.39860	D	0.973361	P	0.39964	0.697	B	0.29353	0.101	T	0.79217	-0.1894	10	0.48119	T	0.1	.	17.9672	0.89102	0.0:1.0:0.0:0.0	.	84	P22459	KCNA4_HUMAN	M	84	ENSP00000328511:R84M	ENSP00000328511:R84M	R	-	2	0	KCNA4	29990551	0.507000	0.26146	0.783000	0.31826	0.092000	0.18411	1.521000	0.35910	2.239000	0.73571	0.561000	0.74099	AGG		0.632	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30033975	C	A	30033975	3	1	47	1	0	0	0	0	1	0	0	0	8026	681	24	2	1714	2	KCNA4	11	30033975	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2643740	30033975	104972541	1258	5655										
FSHB	2488	broad.mit.edu	37	chr11	30255342	30255342	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctcctttggtgaaatgaaaGaataaagatcagtggacatt	10	5	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:30255342G>T	ENST00000417547.1	+	3	424	c.385G>T	c.(385-387)Gaa>Taa	p.E129*	FSHB_ENST00000254122.3_Nonsense_Mutation_p.E129*|FSHB_ENST00000533718.1_Nonsense_Mutation_p.E129*	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	129					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)	p.E129*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						TGAAATGAAAGAATAAAGATC	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											46	43	44					11																	30255342		2202	4299	6501	30211918	SO:0001587	stop_gained	2488				CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"Endogenous ligands"	3964	protein-coding gene	gene with protein product	"follitropin, beta chain", "follicle-stimulating hormone beta subunit"	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.385G>T	11.37:g.30255342G>T	ENSP00000416606:p.Glu129*		30211918	A2TF08|A5JVV3|Q14D61	Nonsense_Mutation	SNP	ENST00000417547.1	37	CCDS7868.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641414	0.47153	.	.	ENSG00000131808	ENST00000254122;ENST00000417547;ENST00000533718	.	.	.	5.65	3.7	0.42460	.	0.335594	0.30277	N	0.009987	.	.	.	.	.	.	0.28739	N	0.902051	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	6.484	0.22079	0.074:0.1281:0.6652:0.1328	.	.	.	.	X	129	.	ENSP00000254122:E129X	E	+	1	0	FSHB	30211918	0.789000	0.28775	0.705000	0.30386	0.289000	0.27227	2.724000	0.47285	0.854000	0.35336	-0.345000	0.07892	GAA		0.507	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510		T	30255342	G	T	30255342	4	4	47	1	0	0	0	0	0	1	0	0	6091	943	33	2	391	2	FSHB	11	30255342	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	221367	30255342	104751174	1259	5656										
MPPED2	744	broad.mit.edu	37	chr11	30516889	30516889	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcactgttacctccgaatCttgtaagtaaatactgtttg	6	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:30516889C>T	ENST00000358117.5	-	3	612	c.490G>A	c.(490-492)Gat>Aat	p.D164N	MPPED2_ENST00000448418.2_Missense_Mutation_p.D164N	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	164					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.D164N(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						ACCTCCGAATCTTGTAAGTAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											141	128	132					11																	30516889		2202	4299	6501	30473465	SO:0001583	missense	744			U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"chromosome 11 open reading frame 8"	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.490G>A	11.37:g.30516889C>T	ENSP00000350833:p.Asp164Asn		30473465	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	37	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112515	0.94339	.	.	ENSG00000066382	ENST00000448418;ENST00000358117	T;T	0.43294	0.95;0.95	5.61	5.61	0.85477	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.61899	0.2384	L	0.53561	1.675	0.80722	D	1	D;P	0.89917	1.0;0.903	D;P	0.97110	1.0;0.724	T	0.56189	-0.8020	10	0.36615	T	0.2	-11.8404	19.6426	0.95764	0.0:1.0:0.0:0.0	.	164;164	Q15777;E9PB10	MPPD2_HUMAN;.	N	164	ENSP00000388258:D164N;ENSP00000350833:D164N	ENSP00000350833:D164N	D	-	1	0	MPPED2	30473465	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.650000	0.89964	0.655000	0.94253	GAT		0.413	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584		T	30516889	C	T	30516889	3	4	47	1	0	0	0	0	1	0	0	0	9772	913	32	3	482	3	MPPED2	11	30516889	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	261547	30516889	104489627	1260	5657										
C11orf41	25758	broad.mit.edu	37	chr11	33628362	33628362	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtcatcggcagtcctcaaCggcgaggtaagtgcctggag	15	10	2	0	rs375293606		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:33628362C>T	ENST00000321505.4	+	13	4344	c.4164C>T	c.(4162-4164)aaC>aaT	p.N1388N	KIAA1549L_ENST00000389726.3_Silent_p.N1394N			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1388						integral component of membrane (GO:0016021)		p.N1388N(1)									CAGTCCTCAACGGCGAGGTAA	0.587													C|||	1	0.000199681	0	0.0014	5008	,	,		17845	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		5,4069		0,5,2032	20	22	21		4164	-6.9	0.9	11		21	1,8395		0,1,4197	no	coding-synonymous	C11orf41	NM_012194.2		0,6,6229	TT,TC,CC		0.0119,0.1227,0.0481		1388/1850	33628362	6,12464	2037	4198	6235	33584938	SO:0001819	synonymous_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.4164C>T	11.37:g.33628362C>T			33584938	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	4.733	0.136376	0.09032	0.001227	1.19E-4	ENSG00000110427	ENST00000526400	.	.	.	5.42	-6.9	0.01655	.	.	.	.	.	T	0.59542	0.2201	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63350	-0.6657	4	.	.	.	-17.5858	13.4248	0.61020	0.0:0.486:0.0:0.514	.	.	.	.	M	786	.	.	T	+	2	0	C11orf41	33584938	0.001000	0.12720	0.917000	0.36280	0.325000	0.28411	-2.225000	0.01212	-1.148000	0.02847	-0.263000	0.10527	ACG		0.587	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33628362	C	T	33628362	2	4	47	1	0	0	0	0	0	0	0	1	1644	535	19	1		1	C11orf41	11	33628362	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3111473	33628362	101378154	1261	5658										
ELF5	2001	broad.mit.edu	37	chr11	34502479	34502479	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcaggagatagaagcaggtCtcgtacaaattcccatagat	9	8	2	3	rs143609015		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:34502479C>T	ENST00000312319.2	-	6	770	c.541G>A	c.(541-543)Gac>Aac	p.D181N	ELF5_ENST00000257832.2_Missense_Mutation_p.D171N|ELF5_ENST00000429939.2_Missense_Mutation_p.D76N|ELF5_ENST00000528709.1_5'Flank	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	181					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.D181N(1)		large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				AGAAGCAGGTCTCGTACAAAT	0.358																																					Melanoma(61;202 1660 4348 21594)											1	Substitution - Missense(1)	large_intestine(1)	11											76	76	76					11																	34502479		2202	4298	6500	34459055	SO:0001583	missense	2001			AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.541G>A	11.37:g.34502479C>T	ENSP00000311010:p.Asp181Asn		34459055	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Missense_Mutation	SNP	ENST00000312319.2	37	CCDS7892.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265338	0.95399	.	.	ENSG00000135374	ENST00000257832;ENST00000312319;ENST00000429939	T;T;T	0.14266	2.52;2.52;2.52	5.7	5.7	0.88788	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	M	0.68728	2.09	0.80722	D	1	P;D	0.76494	0.859;0.999	P;D	0.85130	0.842;0.997	T	0.07597	-1.0764	10	0.87932	D	0	.	19.4287	0.94755	0.0:1.0:0.0:0.0	.	76;181	A6XAE6;Q9UKW6	.;ELF5_HUMAN	N	171;181;76	ENSP00000257832:D171N;ENSP00000311010:D181N;ENSP00000407589:D76N	ENSP00000257832:D171N	D	-	1	0	ELF5	34459055	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	4.985000	0.63845	2.701000	0.92244	0.561000	0.74099	GAC		0.358	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381		T	34502479	C	T	34502479	3	4	47	1	0	0	0	0	1	0	0	0	5070	913	32	3	264	3	ELF5	11	34502479	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	874117	34502479	100504037	1262	5659										
TRIM44	54765	broad.mit.edu	37	chr11	35756977	35756977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctgtttgtctttcagggcGatgaggaaggacccaggtaa	13	7	3	1	rs181043254	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:35756977G>A	ENST00000299413.5	+	4	1298	c.991G>A	c.(991-993)Gat>Aat	p.D331N	TRIM44_ENST00000532066.1_3'UTR	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	331						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.D331N(2)		endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				CTTTCAGGGCGATGAGGAAGG	0.413													G|||	4	0.000798722	0	0.0014	5008	,	,		21483	0		0	False		,,,				2504	0.0031															2	Substitution - Missense(2)	large_intestine(2)	11											242	207	219					11																	35756977		2202	4298	6500	35713553	SO:0001583	missense	54765			BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19016	protein-coding gene	gene with protein product		612298	"tripartite motif-containing 44"				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.991G>A	11.37:g.35756977G>A	ENSP00000299413:p.Asp331Asn		35713553	D3DR14|Q96QY2|Q9UGK0	Missense_Mutation	SNP	ENST00000299413.5	37	CCDS31461.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.71	1.720728	0.30503	.	.	ENSG00000166326	ENST00000299413	T	0.31510	1.49	5.56	4.42	0.53409	.	0.000000	0.39274	N	0.001407	T	0.15046	0.0363	N	0.08118	0	0.26488	N	0.974988	D	0.61697	0.99	B	0.44315	0.446	T	0.07501	-1.0769	10	0.25106	T	0.35	-25.2742	7.1628	0.25672	0.1445:0.0:0.8555:0.0	.	331	Q96DX7	TRI44_HUMAN	N	331	ENSP00000299413:D331N	ENSP00000299413:D331N	D	+	1	0	TRIM44	35713553	0.606000	0.26949	0.996000	0.52242	0.992000	0.81027	1.016000	0.29976	2.774000	0.95407	0.650000	0.86243	GAT		0.413	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583		A	35756977	G	A	35756977	3	1	47	1	0	0	0	0	1	0	0	0	16559	1058	37	1	1005	1	TRIM44	11	35756977	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1254498	35756977	99249539	1263	5660										
RAG1	5896	broad.mit.edu	37	chr11	36595001	36595001	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaagctcaaaaggaaaaGaaggattcctttgaggggaa	13	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:36595001G>T	ENST00000299440.5	+	2	259	c.147G>T	c.(145-147)aaG>aaT	p.K49N		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	49	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K49N(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				AAAAGGAAAAGAAGGATTCCT	0.438									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - Missense(1)	large_intestine(1)	11											53	59	57					11																	36595001		2202	4298	6500	36551577	SO:0001583	missense	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.147G>T	11.37:g.36595001G>T	ENSP00000299440:p.Lys49Asn		36551577	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.969489	0.00457	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.71341	-0.56;-0.55	6.14	0.515	0.17013	.	0.397398	0.26556	N	0.023708	T	0.37865	0.1019	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20739	-1.0266	10	0.02654	T	1	.	1.5773	0.02627	0.2031:0.1222:0.403:0.2717	.	49	P15918	RAG1_HUMAN	N	49	ENSP00000434610:K49N;ENSP00000299440:K49N	ENSP00000299440:K49N	K	+	3	2	RAG1	36551577	0.991000	0.36638	0.838000	0.33150	0.181000	0.23173	0.231000	0.17872	0.184000	0.20083	-0.188000	0.12872	AAG		0.438	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36595001	G	T	36595001	3	4	47	1	0	0	0	0	1	0	0	0	13040	933	33	2	149	2	RAG1	11	36595001	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	838024	36595001	98411515	1264	5661										
RAG1	5896	broad.mit.edu	37	chr11	36597747	36597747	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgggcaagtgagggaaatGagtctggtaacaaactgttt	13	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:36597747G>T	ENST00000299440.5	+	2	3005	c.2893G>T	c.(2893-2895)Gag>Tag	p.E965*		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	965					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E965*(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				TGAGGGAAATGAGTCTGGTAA	0.458									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - Nonsense(1)	large_intestine(1)	11											98	104	102					11																	36597747		2202	4298	6500	36554323	SO:0001587	stop_gained	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2893G>T	11.37:g.36597747G>T	ENSP00000299440:p.Glu965*		36554323	E9PPC4|Q8IY72|Q8NER2	Nonsense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	39	7.726346	0.98456	.	.	ENSG00000166349	ENST00000299440	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1028	0.97881	0.0:0.0:1.0:0.0	.	.	.	.	X	965	.	.	E	+	1	0	RAG1	36554323	1.000000	0.71417	0.699000	0.30290	0.984000	0.73092	9.420000	0.97426	2.827000	0.97445	0.644000	0.83932	GAG		0.458	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36597747	G	T	36597747	4	4	47	1	0	0	0	0	0	1	0	0	13040	1291	45	2	2895	2	RAG1	11	36597747	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2746	36597747	98408769	1265	5662										
LRRC4C	57689	broad.mit.edu	37	chr11	40136759	40136759	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccttcagtgacattgaggtCtgcagggggctccacaatca	12	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:40136759C>A	ENST00000278198.2	-	2	3047	c.1084G>T	c.(1084-1086)Gac>Tac	p.D362Y	LRRC4C_ENST00000527150.1_Missense_Mutation_p.D362Y|LRRC4C_ENST00000530763.1_Missense_Mutation_p.D362Y|LRRC4C_ENST00000528697.1_Missense_Mutation_p.D362Y			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	362	Ig-like C2-type.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.D362Y(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACATTGAGGTCTGCAGGGGGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	78	81					11																	40136759		2203	4300	6503	40093335	SO:0001583	missense	57689			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1084G>T	11.37:g.40136759C>A	ENSP00000278198:p.Asp362Tyr		40093335	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158854	0.57368	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.56934	0.2019	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.66351	0.943	T	0.58148	-0.7687	10	0.66056	D	0.02	.	18.9424	0.92610	0.0:1.0:0.0:0.0	.	362	Q9HCJ2	LRC4C_HUMAN	Y	362	ENSP00000278198:D362Y;ENSP00000436976:D362Y;ENSP00000437132:D362Y;ENSP00000434761:D362Y	ENSP00000278198:D362Y	D	-	1	0	LRRC4C	40093335	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.754000	0.85163	2.728000	0.93425	0.650000	0.86243	GAC		0.512	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		A	40136759	C	A	40136759	3	1	47	1	0	0	0	0	1	0	0	0	9037	913	32	2	842	2	LRRC4C	11	40136759	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3539012	40136759	94869757	1266	5663										
ACCSL	390110	broad.mit.edu	37	chr11	44069663	44069663	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccccagagaccacagcatctAtacccagctgttggagataa	8	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:44069663A>G	ENST00000378832.1	+	1	133	c.77A>G	c.(76-78)tAt>tGt	p.Y26C		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	26					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)	p.Y26C(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CACAGCATCTATACCCAGCTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11											48	53	52					11																	44069663		2032	4196	6228	44026239	SO:0001583	missense	390110				CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.77A>G	11.37:g.44069663A>G	ENSP00000368109:p.Tyr26Cys		44026239		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	A	4.406	0.075086	0.08485	.	.	ENSG00000205126	ENST00000378832	T	0.69175	-0.38	3.27	-2.63	0.06133	.	2.160190	0.02287	N	0.069959	T	0.53270	0.1786	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17349	-1.0372	10	0.34782	T	0.22	-0.5717	3.1011	0.06327	0.3103:0.0:0.3352:0.3545	.	26	Q4AC99	1A1L2_HUMAN	C	26	ENSP00000368109:Y26C	ENSP00000368109:Y26C	Y	+	2	0	ACCSL	44026239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.101000	0.10973	-0.534000	0.06315	-0.376000	0.06991	TAT		0.592	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		G	44069663	A	G	44069663	3	3	47	1	0	0	0	0	1	0	0	0	134	449	16	4	79	4	ACCSL	11	44069663	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3932904	44069663	90936853	1267	5664										
CHST1	8534	broad.mit.edu	37	chr11	45671729	45671729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgccagagccggtacgtgtCgcggaaggtctcgctgcgcg	16	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:45671729C>T	ENST00000308064.2	-	4	1415	c.745G>A	c.(745-747)Gac>Aac	p.D249N	RP11-495O11.1_ENST00000525563.1_RNA|CHST1_ENST00000533673.1_5'Flank	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	249					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)	p.D249N(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		CGGTACGTGTCGCGGAAGGTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											63	57	59					11																	45671729		2203	4299	6502	45628305	SO:0001583	missense	8534			U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"Sulfotransferases, membrane-bound"	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.745G>A	11.37:g.45671729C>T	ENSP00000309270:p.Asp249Asn		45628305	D3DQP2	Missense_Mutation	SNP	ENST00000308064.2	37	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491132	0.64074	.	.	ENSG00000175264	ENST00000308064	D	0.81579	-1.51	4.89	4.89	0.63831	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.89079	0.6613	M	0.81239	2.535	0.54753	D	0.999988	D	0.89917	1.0	D	0.71414	0.973	D	0.86997	0.2114	10	0.20046	T	0.44	-15.1298	18.0436	0.89326	0.0:1.0:0.0:0.0	.	249	O43916	CHST1_HUMAN	N	249	ENSP00000309270:D249N	ENSP00000309270:D249N	D	-	1	0	CHST1	45628305	1.000000	0.71417	0.955000	0.39395	0.914000	0.54420	7.810000	0.86072	2.252000	0.74401	0.462000	0.41574	GAC		0.647	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654		T	45671729	C	T	45671729	3	4	47	1	0	0	0	0	1	0	0	0	3403	884	31	1	494	1	CHST1	11	45671729	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1602066	45671729	89334787	1268	5665										
PHF21A	51317	broad.mit.edu	37	chr11	45957274	45957274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccatttaagtaacttctgTttctcttcttcttttgctaa	3	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:45957274T>C	ENST00000418153.2	-	17	1897	c.1698A>G	c.(1696-1698)aaA>aaG	p.K566K	PHF21A_ENST00000323180.6_Silent_p.K520K|PHF21A_ENST00000527753.1_5'Flank|PHF21A_ENST00000257821.4_Silent_p.K567K			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	566	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K520K(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						GTAACTTCTGTTTCTCTTCTT	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	11											213	181	191					11																	45957274		2201	4298	6499	45913850	SO:0001819	synonymous_variant	51317			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1698A>G	11.37:g.45957274T>C			45913850	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	T	8.271	0.813279	0.16537	.	.	ENSG00000135365	ENST00000525676	.	.	.	4.97	1.4	0.22301	.	.	.	.	.	T	0.55162	0.1903	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46317	-0.9200	4	.	.	.	-8.4369	7.8133	0.29243	0.0:0.3204:0.0:0.6796	.	.	.	.	A	11	.	.	T	-	1	0	PHF21A	45913850	0.999000	0.42202	1.000000	0.80357	0.927000	0.56198	0.542000	0.23222	0.340000	0.23745	0.460000	0.39030	ACA		0.328	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		C	45957274	T	C	45957274	2	2	47	1	0	0	0	0	0	0	0	1	11864	1722	60	4		4	PHF21A	11	45957274	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	285545	45957274	89049242	1269	5666										
PHF21A	51317	broad.mit.edu	37	chr11	45958052	45958052	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gataactccttacctgctttGtaggcaatataggaatgaac	8	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:45958052G>A	ENST00000418153.2	-	16	1873	c.1674C>T	c.(1672-1674)taC>taT	p.Y558Y	PHF21A_ENST00000323180.6_Silent_p.Y512Y|PHF21A_ENST00000527753.1_5'Flank|PHF21A_ENST00000257821.4_Silent_p.Y559Y			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	558	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Y512Y(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TACCTGCTTTGTAGGCAATAT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	11											120	118	119					11																	45958052		2202	4299	6501	45914628	SO:0001819	synonymous_variant	51317			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1674C>T	11.37:g.45958052G>A			45914628	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	G	8.640	0.895664	0.17686	.	.	ENSG00000135365	ENST00000525676	.	.	.	5.74	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.8481	8.7232	0.34454	0.3041:0.0:0.6959:0.0	.	.	.	.	X	3	.	.	Q	-	1	0	PHF21A	45914628	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.893000	0.48633	0.793000	0.33875	0.563000	0.77884	CAA		0.343	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		A	45958052	G	A	45958052	2	1	47	1	0	0	0	0	0	0	0	1	11864	1372	48	3		3	PHF21A	11	45958052	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	778	45958052	89048464	1270	5667										
DDB2	1643	broad.mit.edu	37	chr11	47259490	47259490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaggacgatcgacgtgttcGatggaaactcagggaagatg	15	6	1	2	rs375649516		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:47259490G>A	ENST00000256996.4	+	8	1321	c.1126G>A	c.(1126-1128)Gat>Aat	p.D376N	ACP2_ENST00000525230.1_5'Flank|DDB2_ENST00000378601.3_3'UTR|DDB2_ENST00000378603.3_Missense_Mutation_p.D312N|DDB2_ENST00000378600.3_Missense_Mutation_p.D187N	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	376					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.D376N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						CGACGTGTTCGATGGAAACTC	0.483			"Mis, N"			"skin basal cell, skin squamous cell, melanoma"		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	1	Substitution - Missense(1)	large_intestine(1)	11						G	ASN/ASP	0,4402		0,0,2201	116	105	109		1126	6.1	1	11		109	1,8595	1.2+/-3.3	0,1,4297	no	missense	DDB2	NM_000107.2	23	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	376/428	47259490	1,12997	2201	4298	6499	47216066	SO:0001583	missense	1643	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"WD repeat domain containing"	2718	protein-coding gene	gene with protein product	"xeroderma pigmentosum group E protein", "UV-damaged DNA-binding protein 2", "DDB p48 subunit"	600811	"damage-specific DNA binding protein 2 (48kD)"			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.1126G>A	11.37:g.47259490G>A	ENSP00000256996:p.Asp376Asn		47216066	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	ENST00000256996.4	37	CCDS7927.1	.	.	.	.	.	.	.	.	.	.	G	35	5.458313	0.96240	0.0	1.16E-4	ENSG00000134574	ENST00000256996;ENST00000378603;ENST00000378600	T;T;T	0.72394	-0.58;2.2;-0.65	6.08	6.08	0.98989	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84023	0.5381	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;0.99;1.0	D;P;D	0.97110	0.949;0.65;1.0	T	0.81754	-0.0788	10	0.45353	T	0.12	-6.9478	20.6634	0.99662	0.0:0.0:1.0:0.0	.	312;187;376	Q92466-4;Q92466-2;Q92466	.;.;DDB2_HUMAN	N	376;312;187	ENSP00000256996:D376N;ENSP00000367866:D312N;ENSP00000367863:D187N	ENSP00000256996:D376N	D	+	1	0	DDB2	47216066	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.259000	0.95561	2.894000	0.99253	0.655000	0.94253	GAT		0.483	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107		A	47259490	G	A	47259490	3	1	47	1	0	0	0	0	1	0	0	0	4330	1058	37	1	1156	1	DDB2	11	47259490	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1301438	47259490	87747026	1271	5668										
ACP2	53	broad.mit.edu	37	chr11	47267287	47267287	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataggctgccacgagatgttCgggttgaagcgctgcatccc	13	11	0	2	rs371621192		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:47267287C>T	ENST00000256997.3	-	4	512	c.396G>A	c.(394-396)ccG>ccA	p.P132P	ACP2_ENST00000525230.1_5'Flank|ACP2_ENST00000537863.1_5'UTR|ACP2_ENST00000444355.2_Silent_p.P132P|ACP2_ENST00000529444.1_Silent_p.P132P|ACP2_ENST00000527256.1_Silent_p.P100P|ACP2_ENST00000533929.1_Silent_p.P104P|ACP2_ENST00000530453.1_Silent_p.P132P	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	132					dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)	p.P132P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ACGAGATGTTCGGGTTGAAGC	0.587																																					Melanoma(90;262 1440 11488 44828 48531)											1	Substitution - coding silent(1)	large_intestine(1)	11						C	,	0,4402		0,0,2201	106	96	100		396,396	-11.6	0.9	11		100	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	ACP2	NM_001131064.1,NM_001610.2	,	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	,	132/161,132/424	47267287	1,12997	2201	4298	6499	47223863	SO:0001819	synonymous_variant	53			X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.396G>A	11.37:g.47267287C>T			47223863	E9PCI1|Q561W5|Q9BTU7	Silent	SNP	ENST00000256997.3	37	CCDS7928.1																																																																																				0.587	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610		T	47267287	C	T	47267287	2	4	47	1	0	0	0	0	0	0	0	1	163	871	31	1		1	ACP2	11	47267287	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7797	47267287	87739229	1272	5669										
NUP160	23279	broad.mit.edu	37	chr11	47833757	47833757	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagagctgggtaagattcatTcgaatattcaaaggctgagc	11	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:47833757T>G	ENST00000378460.2	-	17	2146	c.2100A>C	c.(2098-2100)cgA>cgC	p.R700R	NUP160_ENST00000528071.1_Silent_p.R586R|NUP160_ENST00000528501.1_3'UTR|NUP160_ENST00000531016.1_5'Flank|NUP160_ENST00000530326.1_Silent_p.R586R	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	700					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.R700R(1)		NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TAAGATTCATTCGAATATTCA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	11											127	119	122					11																	47833757		2201	4298	6499	47790333	SO:0001819	synonymous_variant	23279			D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.2100A>C	11.37:g.47833757T>G			47790333	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																				0.403	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		G	47833757	T	G	47833757	2	3	47	1	0	0	0	0	0	0	0	1	10788	1770	62	4		4	NUP160	11	47833757	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	566470	47833757	87172759	1273	5670										
OR4X1	390113	broad.mit.edu	37	chr11	48285616	48285616	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctacttatcctttgtggaGatctgctactgttctgtcat	8	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:48285616G>T	ENST00000320048.1	+	1	204	c.204G>T	c.(202-204)gaG>gaT	p.E68D		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E68D(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						CCTTTGTGGAGATCTGCTACT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											138	127	131					11																	48285616		2201	4298	6499	48242192	SO:0001583	missense	390113			AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"GPCR / Class A : Olfactory receptors"	14854	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily X, member 1"				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.204G>T	11.37:g.48285616G>T	ENSP00000321506:p.Glu68Asp		48242192	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	G	0.428	-0.904826	0.02453	.	.	ENSG00000176567	ENST00000320048	T	0.00008	9.61	4.29	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.00138	-2.015	0.09310	N	0.999999	D	0.76494	0.999	D	0.83275	0.996	T	0.58098	-0.7696	9	0.02654	T	1	.	4.857	0.13564	0.1136:0.0:0.6755:0.2109	.	68	Q8NH49	OR4X1_HUMAN	D	68	ENSP00000321506:E68D	ENSP00000321506:E68D	E	+	3	2	OR4X1	48242192	0.000000	0.05858	0.998000	0.56505	0.161000	0.22273	-1.634000	0.02020	1.106000	0.41623	0.563000	0.77884	GAG		0.488	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		T	48285616	G	T	48285616	3	4	47	1	0	0	0	0	1	0	0	0	11115	933	33	2	206	2	OR4X1	11	48285616	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	451859	48285616	86720900	1274	5671										
OR4C46	119749	broad.mit.edu	37	chr11	51516025	51516025	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcacggttgtcatcttattCtttgtgccctgcatatttgt	7	9	4	0	rs140563000	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:51516025C>A	ENST00000328188.1	+	1	744	c.744C>A	c.(742-744)ttC>ttA	p.F248L		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F248L(1)		endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCATCTTATTCTTTGTGCCCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	LEU/PHE	0,4402		0,0,2201	125	105	112		744	0.4	0.6	11	dbSNP_134	112	4,8588		0,4,4292	no	missense	OR4C46	NM_001004703.1	22	0,4,6493	AA,AC,CC		0.0466,0.0,0.0308	benign	248/310	51516025	4,12990	2201	4296	6497	51372601	SO:0001583	missense	119749				CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"GPCR / Class A : Olfactory receptors"	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.744C>A	11.37:g.51516025C>A	ENSP00000329056:p.Phe248Leu		51372601		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	5.295	0.239876	0.10023	0.0	4.66E-4	ENSG00000185926	ENST00000328188	T	0.00285	8.3	2.47	0.404	0.16355	GPCR, rhodopsin-like superfamily (1);	0.142736	0.32533	N	0.005977	T	0.00271	0.0008	M	0.79258	2.445	0.23411	N	0.997734	B	0.18610	0.029	B	0.27887	0.084	T	0.45160	-0.9280	10	0.72032	D	0.01	.	5.0307	0.14407	0.0:0.4987:0.0:0.5013	.	248	A6NHA9	O4C46_HUMAN	L	248	ENSP00000329056:F248L	ENSP00000329056:F248L	F	+	3	2	OR4C46	51372601	0.000000	0.05858	0.633000	0.29310	0.078000	0.17371	-1.819000	0.01716	-0.009000	0.14296	0.121000	0.15741	TTC		0.443	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		A	51516025	C	A	51516025	3	1	47	1	0	0	0	0	1	0	0	0	11082	912	32	2	746	2	OR4C46	11	51516025	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3230409	51516025	83490491	1275	5672										
OR4A16	81327	broad.mit.edu	37	chr11	55110920	55110920	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcacccaaattgatgataGacttactctgtgataaaatc	6	8	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:55110920G>T	ENST00000314721.2	+	1	294	c.244G>T	c.(244-246)Gac>Tac	p.D82Y		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D82Y(1)		NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						ATTGATGATAGACTTACTCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											203	183	190					11																	55110920		2201	4296	6497	54867496	SO:0001583	missense	81327			AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.244G>T	11.37:g.55110920G>T	ENSP00000325128:p.Asp82Tyr		54867496	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	g	5.658	0.306019	0.10733	.	.	ENSG00000181961	ENST00000314721	T	0.00922	5.54	2.57	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03178	0.0093	M	0.83953	2.67	0.32279	N	0.567822	B	0.32604	0.377	B	0.43658	0.426	T	0.00179	-1.1950	9	0.87932	D	0	.	10.8399	0.46708	0.0:0.0:1.0:0.0	.	82	Q8NH70	O4A16_HUMAN	Y	82	ENSP00000325128:D82Y	ENSP00000325128:D82Y	D	+	1	0	OR4A16	54867496	0.000000	0.05858	0.181000	0.23098	0.003000	0.03518	0.562000	0.23531	1.445000	0.47624	0.423000	0.28283	GAC		0.458	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		T	55110920	G	T	55110920	3	4	47	1	0	0	0	0	1	0	0	0	11072	942	33	2	246	2	OR4A16	11	55110920	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3594895	55110920	79895596	1276	5673										
OR5F1	338674	broad.mit.edu	37	chr11	55762062	55762062	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgtgtctgctaatcccaataGgacgaactcagtcagtgagg	11	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:55762062G>T	ENST00000278409.1	-	1	39	c.40C>A	c.(40-42)Cta>Ata	p.L14I		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	14					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L14I(1)		endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AATCCCAATAGGACGAACTCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	11											58	60	59					11																	55762062		2201	4296	6497	55518638	SO:0001583	missense	338674			AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.40C>A	11.37:g.55762062G>T	ENSP00000278409:p.Leu14Ile		55518638	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276220	0.59649	.	.	ENSG00000149133	ENST00000278409	T	0.00561	6.59	3.03	2.09	0.27110	.	.	.	.	.	T	0.00754	0.0025	M	0.79011	2.435	0.26698	N	0.971222	P	0.46395	0.877	B	0.38106	0.265	T	0.47182	-0.9137	9	0.87932	D	0	.	8.9992	0.36072	0.1189:0.0:0.8811:0.0	.	14	O95221	OR5F1_HUMAN	I	14	ENSP00000278409:L14I	ENSP00000278409:L14I	L	-	1	2	OR5F1	55518638	0.000000	0.05858	0.411000	0.26484	0.091000	0.18340	-0.235000	0.09016	0.391000	0.25143	0.297000	0.19635	CTA		0.348	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		T	55762062	G	T	55762062	3	4	47	1	0	0	0	0	1	0	0	0	11189	991	35	2	907	2	OR5F1	11	55762062	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	651142	55762062	79244454	1277	5674										
OR8K3	219473	broad.mit.edu	37	chr11	56086721	56086721	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatgtaatatttttgtttaAattttgtacaatatgattcc	4	3	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:56086721A>G	ENST00000312711.1	+	1	939	c.939A>G	c.(937-939)taA>taG	p.*313*		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.*313*(1)		central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TTTTTGTTTAAATTTTGTACA	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	11											23	23	23					11																	56086721		2195	4289	6484	55843297	SO:0001630	splice_region_variant	219473			AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.936+1A>G	11.37:g.56086721A>G			55843297	Q6IFC4	Silent	SNP	ENST00000312711.1	37	CCDS31527.1																																																																																				0.303	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202	Silent	G	56086721	A	G	56086721	5	3	47	1	0	0	0	0	0	0	1	0	11275	29	1	4	941	4	OR8K3	11	56086721	Splice_Site	SNP	A	TCGA-AG-3892-01A-01W-1073-09	324659	56086721	78919795	1278	5675										
OR8K1	390157	broad.mit.edu	37	chr11	56113551	56113551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacacaatcacacggcagtgAccaaggtgactgaatttatt	8	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:56113551A>G	ENST00000279783.2	+	1	131	c.37A>G	c.(37-39)Acc>Gcc	p.T13A		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T13A(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CACGGCAGTGACCAAGGTGAC	0.383										HNSCC(65;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	11											89	85	87					11																	56113551		2201	4296	6497	55870127	SO:0001583	missense	390157			AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.37A>G	11.37:g.56113551A>G	ENSP00000279783:p.Thr13Ala		55870127	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.733899	0.48939	.	.	ENSG00000150261	ENST00000279783	T	0.00711	5.8	4.68	0.87	0.19102	.	1.040270	0.07622	N	0.927195	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	P	0.49783	0.928	B	0.37833	0.259	T	0.52593	-0.8555	10	0.87932	D	0	0.0	5.5231	0.16943	0.4879:0.3456:0.0:0.1665	.	13	Q8NGG5	OR8K1_HUMAN	A	13	ENSP00000279783:T13A	ENSP00000279783:T13A	T	+	1	0	OR8K1	55870127	0.000000	0.05858	0.001000	0.08648	0.594000	0.36715	0.843000	0.27640	-0.121000	0.11787	0.368000	0.22195	ACC		0.383	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		G	56113551	A	G	56113551	3	3	47	1	0	0	0	0	1	0	0	0	11274	275	10	4	39	4	OR8K1	11	56113551	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	26830	56113551	78892965	1279	5676										
OR5M1	390168	broad.mit.edu	37	chr11	56380139	56380139	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggttcagcattgggctcaaAaaagtataaaagactgcagt	11	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:56380139A>C	ENST00000526538.1	-	1	839	c.840T>G	c.(838-840)ttT>ttG	p.F280L		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F280L(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						TTGGGCTCAAAAAAGTATAAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	11											179	174	175					11																	56380139		1827	4092	5919	56136715	SO:0001583	missense	390168			AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"GPCR / Class A : Olfactory receptors"	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.840T>G	11.37:g.56380139A>C	ENSP00000435416:p.Phe280Leu		56136715	Q6IF60|Q96RB6	Missense_Mutation	SNP	ENST00000526538.1	37	CCDS53631.1	.	.	.	.	.	.	.	.	.	.	A	9.412	1.080766	0.20309	.	.	ENSG00000255012	ENST00000526538	T	0.00029	8.91	3.71	1.25	0.21368	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.02225	-0.63	0.09310	N	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.48175	-0.9058	9	0.20046	T	0.44	.	1.5972	0.02666	0.3967:0.3377:0.1013:0.1643	.	280	Q8NGP8	OR5M1_HUMAN	L	280	ENSP00000435416:F280L	ENSP00000435416:F280L	F	-	3	2	OR5M1	56136715	0.000000	0.05858	0.601000	0.28877	0.223000	0.24884	-0.312000	0.08113	0.074000	0.16767	0.232000	0.17820	TTT		0.398	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740		C	56380139	A	C	56380139	3	2	47	1	0	0	0	0	1	0	0	0	11203	11	1	4	111	4	OR5M1	11	56380139	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	266588	56380139	78626377	1280	5677										
SERPING1	710	broad.mit.edu	37	chr11	57367638	57367638	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacccagctcccaacagattCtcctacccagcccactactg	4	19	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:57367638C>A	ENST00000278407.4	+	3	565	c.338C>A	c.(337-339)tCt>tAt	p.S113Y	SERPING1_ENST00000378324.2_Missense_Mutation_p.S61Y|SERPING1_ENST00000340687.6_Missense_Mutation_p.S113Y|SERPING1_ENST00000403558.1_Missense_Mutation_p.S147Y|SERPING1_ENST00000378323.4_Missense_Mutation_p.S118Y	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	113	7 X 4 AA tandem repeats of [QE]-P-T-[TQ].		Missing (in HAE; phenotype consistent with hereditary angioedema type 2). {ECO:0000269|PubMed:12773530}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S113Y(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						ccaacagattctcctacccag	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											229	235	233					11																	57367638		2201	4296	6497	57124214	SO:0001583	missense	710			X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.338C>A	11.37:g.57367638C>A	ENSP00000278407:p.Ser113Tyr		57124214	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	37	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.521803	0.27211	.	.	ENSG00000149131	ENST00000405496;ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558;ENST00000433668	D;D;D;D;D;D	0.90069	-2.61;-1.98;-2.04;-1.98;-1.98;-2.07	4.23	2.23	0.28157	Serpin domain (1);	2.164530	0.02226	N	0.064406	D	0.83514	0.5271	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.32283	0.362;0.362;0.362;0.362	B;B;B;B	0.25291	0.059;0.059;0.059;0.059	T	0.70099	-0.4965	10	0.54805	T	0.06	.	6.2564	0.20876	0.0:0.7385:0.0:0.2615	.	118;147;113;113	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	Y	113;113;113;118;61;147;113	ENSP00000384561:S113Y;ENSP00000278407:S113Y;ENSP00000341861:S113Y;ENSP00000367574:S118Y;ENSP00000367575:S61Y;ENSP00000384420:S147Y	ENSP00000278407:S113Y	S	+	2	0	SERPING1	57124214	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.238000	0.18004	0.280000	0.22209	-0.291000	0.09656	TCT		0.562	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		A	57367638	C	A	57367638	3	1	47	1	0	0	0	0	1	0	0	0	14153	913	32	2	344	2	SERPING1	11	57367638	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	987499	57367638	77638878	1281	5678										
MED19	219541	broad.mit.edu	37	chr11	57472676	57472676	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtagtgtgtgatcagattCgtgctgcctgtcagctctgt	12	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:57472676C>T	ENST00000431606.2	-	2	272	c.243G>A	c.(241-243)acG>acA	p.T81T	MED19_ENST00000337672.2_Silent_p.T81T			A0JLT2	MED19_HUMAN	mediator complex subunit 19	81						mediator complex (GO:0016592)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.T81T(1)		cervix(1)|large_intestine(1)|lung(1)|ovary(2)	5						TGATCAGATTCGTGCTGCCTG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	11											76	76	76					11																	57472676		2201	4296	6497	57229252	SO:0001819	synonymous_variant	219541			AY148462	CCDS7966.1	11q12.1	2008-02-05	2007-07-30		ENSG00000156603	ENSG00000156603			29600	protein-coding gene	gene with protein product		612385	"mediator of RNA polymerase II transcription, subunit 19 homolog (S. cerevisiae)"			9417904	Standard	NM_153450		Approved	LCMR1	uc001nlb.3	A0JLT2	OTTHUMG00000167199	ENST00000431606.2:c.243G>A	11.37:g.57472676C>T			57229252	Q8IV02|Q8IZD1	Silent	SNP	ENST00000431606.2	37																																																																																					0.428	MED19-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000393702.1	NM_153450		T	57472676	C	T	57472676	2	4	47	1	0	0	0	0	0	0	0	1	9467	871	31	1		1	MED19	11	57472676	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	105038	57472676	77533840	1282	5679										
OR5B12	390191	broad.mit.edu	37	chr11	58206881	58206881	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagattcctgtcccataaaaGatggaaactgcagtaaggtg	10	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:58206881G>T	ENST00000302572.2	-	1	765	c.744C>A	c.(742-744)atC>atA	p.I248I		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I248I(1)		large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TCCCATAAAAGATGGAAACTG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	11											79	76	77					11																	58206881		2201	4295	6496	57963457	SO:0001819	synonymous_variant	390191			AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.744C>A	11.37:g.58206881G>T			57963457	B2RNL2|Q6IEV5	Silent	SNP	ENST00000302572.2	37	CCDS31551.1																																																																																				0.433	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		T	58206881	G	T	58206881	2	4	47	1	0	0	0	0	0	0	0	1	11179	932	33	2		2	OR5B12	11	58206881	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	734205	58206881	76799635	1283	5680										
OR5AN1	390195	broad.mit.edu	37	chr11	59132603	59132603	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctatggctatattggcatCtccatcatgaagatcacttc	6	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:59132603C>T	ENST00000313940.2	+	1	719	c.672C>T	c.(670-672)atC>atT	p.I224I		NM_001004729.1	NP_001004729.1	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN, member 1	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I224I(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	21						ATATTGGCATCTCCATCATGA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	11											218	197	204					11																	59132603		2201	4295	6496	58889179	SO:0001819	synonymous_variant	390195			AB065806	CCDS31559.1	11q12.1	2012-08-09			ENSG00000176495	ENSG00000176495		"GPCR / Class A : Olfactory receptors"	15255	protein-coding gene	gene with protein product		615702					Standard	NM_001004729		Approved		uc010rks.2	Q8NGI8	OTTHUMG00000167337	ENST00000313940.2:c.672C>T	11.37:g.59132603C>T			58889179	B9EIS2|Q6IEV4	Silent	SNP	ENST00000313940.2	37	CCDS31559.1																																																																																				0.418	OR5AN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394231.1	NM_001004729		T	59132603	C	T	59132603	2	4	47	1	0	0	0	0	0	0	0	1	11174	903	32	3		3	OR5AN1	11	59132603	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	925722	59132603	75873913	1284	5681										
MS4A2	2206	broad.mit.edu	37	chr11	59861003	59861003	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgccagaaattttttgagaCcaagtgctttatggcttcct	8	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:59861003C>T	ENST00000278888.3	+	5	611	c.509C>T	c.(508-510)aCc>aTc	p.T170I		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	170					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.T170I(1)		endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	TTTTTTGAGACCAAGTGCTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											164	153	157					11																	59861003		2201	4295	6496	59617579	SO:0001583	missense	2206			M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.509C>T	11.37:g.59861003C>T	ENSP00000278888:p.Thr170Ile		59617579	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	37	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	C	8.627	0.892814	0.17613	.	.	ENSG00000149534	ENST00000278888	T	0.02258	4.37	4.33	-4.24	0.03777	.	1.541520	0.03241	N	0.180347	T	0.02380	0.0073	L	0.48642	1.525	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.005	T	0.45934	-0.9227	10	0.37606	T	0.19	1.6323	1.7794	0.03028	0.2525:0.1737:0.0898:0.484	.	100;170	Q14298;Q01362	.;FCERB_HUMAN	I	170	ENSP00000278888:T170I	ENSP00000278888:T170I	T	+	2	0	MS4A2	59617579	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.071000	0.11505	-0.803000	0.04415	-0.781000	0.03364	ACC		0.433	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59861003	C	T	59861003	3	4	47	1	0	0	0	0	1	0	0	0	9890	507	18	3	527	3	MS4A2	11	59861003	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	728400	59861003	75145513	1285	5682										
MS4A7	58475	broad.mit.edu	37	chr11	60157008	60157008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctatcctcattgccttattCggagtactattatccaatat	4	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:60157008C>T	ENST00000300184.3	+	5	681	c.485C>T	c.(484-486)tCg>tTg	p.S162L	MS4A7_ENST00000358246.1_Missense_Mutation_p.S117L|MS4A7_ENST00000530234.2_Intron|MS4A7_ENST00000534016.1_Missense_Mutation_p.S117L|MS4A14_ENST00000531787.1_Intron	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	162						integral component of membrane (GO:0016021)		p.S162L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						TTGCCTTATTCGGAGTACTAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											134	123	127					11																	60157008		2203	4300	6503	59913584	SO:0001583	missense	58475			AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.485C>T	11.37:g.60157008C>T	ENSP00000300184:p.Ser162Leu		59913584	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	C	7.397	0.632037	0.14322	.	.	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530614;ENST00000530027	T;T;T;T;T	0.02323	4.34;4.34;4.34;4.34;4.34	3.69	1.74	0.24563	.	1.738880	0.03964	N	0.290529	T	0.02304	0.0071	N	0.20483	0.58	0.09310	N	0.999995	B;B;B	0.22211	0.066;0.054;0.066	B;B;B	0.23716	0.048;0.019;0.04	T	0.46428	-0.9192	10	0.10111	T	0.7	-6.4453	4.5669	0.12191	0.0:0.6409:0.2294:0.1296	.	117;117;162	E9PIV6;Q9GZW8-2;Q9GZW8	.;.;MS4A7_HUMAN	L	162;117;117;117;98	ENSP00000300184:S162L;ENSP00000350983:S117L;ENSP00000434637:S117L;ENSP00000433861:S117L;ENSP00000434819:S98L	ENSP00000300184:S162L	S	+	2	0	MS4A7	59913584	0.000000	0.05858	0.039000	0.18376	0.712000	0.41017	-0.260000	0.08708	0.506000	0.28125	0.563000	0.77884	TCG		0.433	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1			T	60157008	C	T	60157008	3	4	47	1	0	0	0	0	1	0	0	0	9896	893	31	1	499	1	MS4A7	11	60157008	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	296005	60157008	74849508	1286	5683										
MS4A14	84689	broad.mit.edu	37	chr11	60167907	60167907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caggatacctcacagtaaccGataagaaatcaaaacttctg	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:60167907G>A	ENST00000300187.6	+	3	575	c.298G>A	c.(298-300)Gat>Aat	p.D100N	MS4A14_ENST00000395001.1_5'UTR|MS4A14_ENST00000531783.1_Missense_Mutation_p.D100N|MS4A14_ENST00000395005.2_Intron|MS4A14_ENST00000531787.1_Intron	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	100						integral component of membrane (GO:0016021)		p.D100N(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CACAGTAACCGATAAGAAATC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	11											86	81	83					11																	60167907		2202	4300	6502	59924483	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.298G>A	11.37:g.60167907G>A	ENSP00000300187:p.Asp100Asn		59924483	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	8.208	0.799625	0.16397	.	.	ENSG00000166928	ENST00000300187;ENST00000531783	T;T	0.02236	4.38;4.38	4.9	-9.8	0.00490	.	2.021940	0.02412	N	0.081749	T	0.00845	0.0028	N	0.02802	-0.49	0.09310	N	0.999999	B	0.17465	0.022	B	0.08055	0.003	T	0.47661	-0.9100	10	0.13470	T	0.59	-0.0452	3.1664	0.06538	0.4448:0.2796:0.186:0.0895	.	100	Q96JA4	M4A14_HUMAN	N	100	ENSP00000300187:D100N;ENSP00000433761:D100N	ENSP00000300187:D100N	D	+	1	0	MS4A14	59924483	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.869000	0.04232	-2.006000	0.00958	-1.844000	0.00574	GAT		0.308	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			A	60167907	G	A	60167907	3	1	47	1	0	0	0	0	1	0	0	0	9888	1058	37	1	308	1	MS4A14	11	60167907	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	10899	60167907	74838609	1287	5684										
TUT1	64852	broad.mit.edu	37	chr11	62342608	62342608	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagggaggaaaacctgtaaGaaatgatggagatcagggaa	15	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:62342608G>T	ENST00000476907.1	-	9	3274	c.2583C>A	c.(2581-2583)ttC>ttA	p.F861L	TUT1_ENST00000308436.7_Missense_Mutation_p.F899L|MIR3654_ENST00000496634.2_Intron|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000532986.1_5'Flank|EEF1G_ENST00000378019.3_5'Flank			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	861					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)	p.F861L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AAACCTGTAAGAAATGATGGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											58	60	59					11																	62342608		2202	4299	6501	62099184	SO:0001583	missense	64852			BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.2583C>A	11.37:g.62342608G>T	ENSP00000419607:p.Phe861Leu		62099184	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	37		.	.	.	.	.	.	.	.	.	.	G	22.4	4.288333	0.80803	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	T;T	0.70164	-0.46;-0.41	5.56	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.76955	0.4060	M	0.68952	2.095	0.38911	D	0.95754	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	T	0.76987	-0.2755	10	0.72032	D	0.01	-22.0112	8.409	0.32632	0.2285:0.0:0.7715:0.0	.	861;899	Q9H6E5;F5H0R1	STPAP_HUMAN;.	L	899;861	ENSP00000308000:F899L;ENSP00000419607:F861L	ENSP00000308000:F899L	F	-	3	2	TUT1	62099184	0.997000	0.39634	0.980000	0.43619	0.946000	0.59487	0.962000	0.29280	0.476000	0.27440	0.655000	0.94253	TTC		0.522	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		T	62342608	G	T	62342608	3	4	47	1	0	0	0	0	1	0	0	0	16820	933	33	2	45	2	TUT1	11	62342608	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2174701	62342608	72663908	1288	5685										
RTN3	10313	broad.mit.edu	37	chr11	63488414	63488414	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaagcccatcactatcagaGaaactactagggtagatgct	9	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:63488414G>T	ENST00000377819.5	+	3	2594	c.2440G>T	c.(2440-2442)Gaa>Taa	p.E814*	RTN3_ENST00000540798.1_Nonsense_Mutation_p.E702*|RTN3_ENST00000339997.4_Nonsense_Mutation_p.E795*|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	814					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.E795*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						CACTATCAGAGAAACTACTAG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											69	72	71					11																	63488414		2201	4298	6499	63244990	SO:0001587	stop_gained	10313			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.2440G>T	11.37:g.63488414G>T	ENSP00000367050:p.Glu814*		63244990	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Nonsense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179082	0.94846	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	.	.	.	5.67	2.77	0.32553	.	2.511560	0.01289	N	0.009946	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.6994	8.4419	0.32820	0.2456:0.0:0.7544:0.0	.	.	.	.	X	814;795;702	.	ENSP00000344106:E795X	E	+	1	0	RTN3	63244990	0.530000	0.26330	0.024000	0.17045	0.072000	0.16883	2.509000	0.45459	0.416000	0.25844	0.655000	0.94253	GAA		0.428	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		T	63488414	G	T	63488414	4	4	47	1	0	0	0	0	0	1	0	0	13764	943	33	2	2450	2	RTN3	11	63488414	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1145806	63488414	71518102	1289	5686										
PYGM	5837	broad.mit.edu	37	chr11	64519437	64519437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaggcagttgaggagctgtCgtttatattcgtgaatccgc	14	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:64519437C>T	ENST00000164139.3	-	14	2125	c.1727G>A	c.(1726-1728)cGa>cAa	p.R576Q	PYGM_ENST00000377432.3_Missense_Mutation_p.R488Q|PYGM_ENST00000462303.1_5'UTR	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	576					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)	p.R576Q(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAGGAGCTGTCGTTTATATTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											206	174	185					11																	64519437		2201	4297	6498	64276013	SO:0001583	missense	5837				CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1727G>A	11.37:g.64519437C>T	ENSP00000164139:p.Arg576Gln		64276013	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	36	5.825684	0.96996	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.96041	-3.89;-3.86	5.71	5.71	0.89125	.	0.000000	0.53938	D	0.000045	D	0.98826	0.9604	H	0.99026	4.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99441	1.0938	10	0.87932	D	0	-18.3338	17.3513	0.87324	0.0:1.0:0.0:0.0	.	488;576	A6NDY6;P11217	.;PYGM_HUMAN	Q	488;576;557	ENSP00000366650:R488Q;ENSP00000164139:R576Q	ENSP00000164139:R576Q	R	-	2	0	PYGM	64276013	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.783000	0.85696	2.698000	0.92095	0.561000	0.74099	CGA		0.517	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64519437	C	T	64519437	3	4	47	1	0	0	0	0	1	0	0	0	12899	884	31	1	829	1	PYGM	11	64519437	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1031023	64519437	70487079	1290	5687										
FAU	740	broad.mit.edu	37	chr11	64888220	64888220	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgttgacaaagcgccggttgTactgcatccgccgcttagcc	11	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:64888220T>C	ENST00000279242.2	+	0	0				FAU_ENST00000531743.1_Missense_Mutation_p.Y112C|FAU_ENST00000279259.3_3'UTR|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000529259.1_3'UTR|FAU_ENST00000529639.1_Missense_Mutation_p.Y112C|MRPL49_ENST00000531705.1_5'Flank|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000527548.1_Missense_Mutation_p.Y112C|FAU_ENST00000525297.1_Missense_Mutation_p.Y77C	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)	p.Y112C(1)		endometrium(1)|ovary(1)	2						GCGCCGGTTGTACTGCATCCG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											77	83	81					11																	64888220		2201	4297	6498	64644796	SO:0001631	upstream_gene_variant	2197				CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		11.37:g.64888220T>C	Exception_encountered		64644796	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	37	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554691	0.86231	.	.	ENSG00000149806	ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.73651	0.3614	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.77107	-0.2710	7	0.87932	D	0	.	13.4889	0.61382	0.0:0.0:0.0:1.0	.	.	.	.	C	112;112;77;112	ENSP00000435370:Y112C;ENSP00000431822:Y112C;ENSP00000436110:Y77C;ENSP00000434440:Y112C	ENSP00000436110:Y77C	Y	-	2	0	FAU	64644796	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.862000	0.87013	2.090000	0.63153	0.533000	0.62120	TAC		0.498	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		C	64888220	T	C	64888220	1	2	47	0	1	0	0	0	0	0	0	0	5713	1638	57	4		4	FAU	11	64888220	5'Flank	SNP	T	TCGA-AG-3892-01A-01W-1073-09	368783	64888220	70118296	1291	5688										
ACTN3	89	broad.mit.edu	37	chr11	66319057	66319057	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccacaaaatcgccaacgtTaacaaggccctggacttcat	6	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:66319057T>G	ENST00000502692.1	+	0	566				ACTN3_ENST00000513398.1_RNA	NM_001258371.1	NP_001245300.1	Q08043	ACTN3_HUMAN	actinin, alpha 3 (gene/pseudogene)						focal adhesion assembly (GO:0048041)|muscle filament sliding (GO:0030049)|regulation of apoptotic process (GO:0042981)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.V106V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)	10						TCGCCAACGTTAACAAGGCCC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	11											73	76	75					11																	66319057		2164	4286	6450	66075633			89			M86407		11q13.2	2013-10-02	2012-10-05		ENSG00000248746	ENSG00000248746			165	protein-coding gene	gene with protein product		102574	"actinin, alpha 3"			1339456	Standard	NM_001104		Approved		uc031qbp.1	Q08043	OTTHUMG00000160815		11.37:g.66319057T>G			66075633	A6NP77|Q4KKV2	Silent	SNP	ENST00000502692.1	37																																																																																					0.557	ACTN3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000362465.1	NM_001104		G	66319057	T	G	66319057	1	3	47	0	1	0	0	0	0	0	0	0	206	1741	61	4		4	ACTN3	11	66319057	RNA	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1430837	66319057	68687459	1292	5689										
RBM4	5936	broad.mit.edu	37	chr11	66407509	66407509	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccggtcatcgaatgtgacatCgtgaaagattatgccttcgt	10	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:66407509C>T	ENST00000409406.1	+	1	1104	c.327C>T	c.(325-327)atC>atT	p.I109I	RBM4_ENST00000483858.1_Silent_p.I109I|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000396053.4_Silent_p.I109I|RBM4_ENST00000578778.1_Silent_p.I109I|RBM4_ENST00000506523.2_Silent_p.I109I|RBM4_ENST00000408993.2_Silent_p.I109I|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000532968.1_Silent_p.I109I|RBM4_ENST00000514361.3_Intron|RBM4_ENST00000530235.1_Silent_p.I109I|RBM4_ENST00000310092.7_Silent_p.I109I|RBM4_ENST00000398692.4_Silent_p.I109I|RBM4_ENST00000503028.2_Silent_p.I109I			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	109	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.I109I(1)		endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		AATGTGACATCGTGAAAGATT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	11											142	129	133					11																	66407509		2200	4292	6492	66164085	SO:0001819	synonymous_variant	5936			U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.327C>T	11.37:g.66407509C>T			66164085	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Silent	SNP	ENST00000409406.1	37	CCDS41676.1																																																																																				0.512	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896		T	66407509	C	T	66407509	2	4	47	1	0	0	0	0	0	0	0	1	13171	874	31	1		1	RBM4	11	66407509	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	88452	66407509	68599007	1293	5690										
SAPS3	55291	broad.mit.edu	37	chr11	68326038	68326038	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatttgtttccctaggcaaGaaattatagagcagcttcta	8	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:68326038G>T	ENST00000393800.2	+	8	990	c.736G>T	c.(736-738)Gaa>Taa	p.E246*	PPP6R3_ENST00000265637.4_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000529710.1_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000534534.1_Intron|PPP6R3_ENST00000265636.5_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000393799.2_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000524904.1_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000393801.3_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000527403.2_Nonsense_Mutation_p.E246*|PPP6R3_ENST00000524845.1_Nonsense_Mutation_p.E246*	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	246					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.E246*(2)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CCCTAGGCAAGAAATTATAGA	0.383																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											93	94	94					11																	68326038		2200	4294	6494	68082614	SO:0001587	stop_gained	55291			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.736G>T	11.37:g.68326038G>T	ENSP00000377389:p.Glu246*		68082614	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Nonsense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	G	40	8.142206	0.98675	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403	.	.	.	5.45	5.45	0.79879	.	0.136365	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	19.4735	0.94973	0.0:0.0:1.0:0.0	.	.	.	.	X	246	.	ENSP00000265636:E246X	E	+	1	0	PPP6R3	68082614	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.446000	0.97590	2.836000	0.97738	0.655000	0.94253	GAA		0.383	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		T	68326038	G	T	68326038	4	4	47	1	0	0	0	0	0	1	0	0	13875	943	33	2	758	2	SAPS3	11	68326038	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1918529	68326038	66680478	1294	5691										
IGHMBP2	3508	broad.mit.edu	37	chr11	68685250	68685250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagagagaaaagtaattttcGaaatgaaattaagctgttaa	9	2	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:68685250G>A	ENST00000255078.3	+	7	1070	c.959G>A	c.(958-960)cGa>cAa	p.R320Q		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	320	Leu-rich.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)	p.R320Q(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGTAATTTTCGAAATGAAATT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											86	90	89					11																	68685250		2200	4294	6494	68441826	SO:0001583	missense	3508			L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"Zinc fingers, AN1-type domain containing"	5542	protein-coding gene	gene with protein product	"cardiac transcription factor 1", "zinc finger, AN1-type domain 7"	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.959G>A	11.37:g.68685250G>A	ENSP00000255078:p.Arg320Gln		68441826	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.345677	0.24426	.	.	ENSG00000132740	ENST00000255078	D	0.82433	-1.61	4.81	2.94	0.34122	DEAD-like helicase (1);Helicase/UvrB domain (1);ATPase, AAA+ type, core (1);	1.041280	0.07637	N	0.929734	T	0.69700	0.3140	N	0.19112	0.55	0.09310	N	1	P	0.38582	0.638	B	0.36666	0.23	T	0.56715	-0.7933	10	0.27082	T	0.32	-15.8357	5.8834	0.18868	0.172:0.0:0.6744:0.1536	.	320	P38935	SMBP2_HUMAN	Q	320	ENSP00000255078:R320Q	ENSP00000255078:R320Q	R	+	2	0	IGHMBP2	68441826	0.195000	0.23338	0.001000	0.08648	0.843000	0.47879	1.553000	0.36255	0.455000	0.26910	0.561000	0.74099	CGA		0.383	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		A	68685250	G	A	68685250	3	1	47	1	0	0	0	0	1	0	0	0	7612	1058	37	1	985	1	IGHMBP2	11	68685250	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	359212	68685250	66321266	1295	5692										
MRGPRD	116512	broad.mit.edu	37	chr11	68747870	68747870	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagagggtcaggctggacaGagtcatcactggggttaaga	15	6	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:68747870G>A	ENST00000309106.3	-	1	585	c.586C>T	c.(586-588)Ctg>Ttg	p.L196L		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	196						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L196L(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGGCTGGACAGAGTCATCACT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	11											52	46	48					11																	68747870		2200	4294	6494	68504446	SO:0001819	synonymous_variant	116512			AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"GPCR / Class A : Orphans"	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.586C>T	11.37:g.68747870G>A			68504446	Q8NGK7	Silent	SNP	ENST00000309106.3	37	CCDS31625.1																																																																																				0.597	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923		A	68747870	G	A	68747870	2	1	47	1	0	0	0	0	0	0	0	1	9793	933	33	3		3	MRGPRD	11	68747870	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	62620	68747870	66258646	1296	5693										
OR2AT4	341152	broad.mit.edu	37	chr11	74800230	74800230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagcagtggtagatgtaggCaatgctgttatatgccatct	12	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:74800230C>T	ENST00000305159.3	-	1	569	c.529G>A	c.(529-531)Gcc>Acc	p.A177T		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A177T(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						TAGATGTAGGCAATGCTGTTA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11											96	84	88					11																	74800230		2200	4293	6493	74477878	SO:0001583	missense	341152			BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.529G>A	11.37:g.74800230C>T	ENSP00000304846:p.Ala177Thr		74477878	B9EGZ8	Missense_Mutation	SNP	ENST00000305159.3	37	CCDS31639.1	.	.	.	.	.	.	.	.	.	.	C	3.334	-0.135945	0.06711	.	.	ENSG00000171561	ENST00000305159	T	0.36699	1.24	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.273316	0.19367	U	0.115983	T	0.23688	0.0573	N	0.05383	-0.06	0.09310	N	1	B	0.25904	0.137	B	0.36666	0.23	T	0.26087	-1.0113	10	0.18710	T	0.47	.	12.4856	0.55871	0.0:0.8316:0.1684:0.0	.	177	A6NND4	O2AT4_HUMAN	T	177	ENSP00000304846:A177T	ENSP00000304846:A177T	A	-	1	0	OR2AT4	74477878	0.008000	0.16893	0.084000	0.20598	0.199000	0.23934	1.263000	0.33004	2.617000	0.88574	0.650000	0.86243	GCC		0.572	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		T	74800230	C	T	74800230	3	4	47	1	0	0	0	0	1	0	0	0	11018	710	25	3	436	3	OR2AT4	11	74800230	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6052360	74800230	60206286	1297	5694										
PAK1	5058	broad.mit.edu	37	chr11	77054927	77054927	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaccaggatctcattaataAtcagctctttcttgggctgc	8	10	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:77054927A>C	ENST00000356341.3	-	10	1466	c.935T>G	c.(934-936)aTt>aGt	p.I312S	PAK1_ENST00000525542.1_5'UTR|PAK1_ENST00000528203.1_Missense_Mutation_p.I214S|PAK1_ENST00000278568.4_Missense_Mutation_p.I312S|PAK1_ENST00000530617.1_Missense_Mutation_p.I312S	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	312	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I312S(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					CTCATTAATAATCAGCTCTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											234	201	212					11																	77054927		2200	4292	6492	76732575	SO:0001583	missense	5058			U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.935T>G	11.37:g.77054927A>C	ENSP00000348696:p.Ile312Ser		76732575	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	37	CCDS8250.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.1|25.1	4.598992|4.598992	0.87055|0.87055	.|.	.|.	ENSG00000149269|ENSG00000149269	ENST00000533285|ENST00000356341;ENST00000530617;ENST00000278568;ENST00000528203	.|T;T;T;T	.|0.64803	.|-0.12;-0.12;-0.12;-0.12	5.9|5.9	5.9|5.9	0.94986|0.94986	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76126|0.76126	0.3944|0.3944	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.988;0.994;0.997	.|D;D;D;D	.|0.91635	.|0.999;0.99;0.977;0.984	T|T	0.78201|0.78201	-0.2296|-0.2296	5|10	.|0.87932	.|D	.|0	.|.	16.3322|16.3322	0.83039|0.83039	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|214;312;312;312	.|E9PM17;B3KNX7;Q13153;Q13153-2	.|.;.;PAK1_HUMAN;.	E|S	33|312;312;312;214	.|ENSP00000348696:I312S;ENSP00000433423:I312S;ENSP00000278568:I312S;ENSP00000433211:I214S	.|ENSP00000278568:I312S	D|I	-|-	3|2	2|0	PAK1|PAK1	76732575|76732575	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	8.932000|8.932000	0.92897|0.92897	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	GAT|ATT		0.433	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		C	77054927	A	C	77054927	3	2	47	1	0	0	0	0	1	0	0	0	11430	101	4	4	779	4	PAK1	11	77054927	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2254697	77054927	57951589	1298	5695										
RAB30	27314	broad.mit.edu	37	chr11	82708340	82708340	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacaattttgaacaggaaatCataatcttccatactcattt	3	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:82708340C>A	ENST00000533486.1	-	3	303	c.19G>T	c.(19-21)Gat>Tat	p.D7Y	RAB30_ENST00000532548.1_Missense_Mutation_p.D7Y|RAB30_ENST00000534141.1_Missense_Mutation_p.D7Y|RP11-659G9.3_ENST00000527550.1_RNA|RAB30_ENST00000527633.1_Missense_Mutation_p.D7Y|RAB30_ENST00000260056.2_Missense_Mutation_p.D7Y|RAB30_ENST00000525117.1_Missense_Mutation_p.D7Y	NM_014488.3	NP_055303.2	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family	7					Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cis-Golgi network (GO:0005801)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D7Y(1)		endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						AACAGGAAATCATAATCTTCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	81	84					11																	82708340		2203	4300	6503	82385988	SO:0001583	missense	27314			U57092	CCDS8264.1	11q12-q14	2008-07-21				ENSG00000137502		"RAB, member RAS oncogene"	9770	protein-coding gene	gene with protein product		605693				8863739, 9792283	Standard	NM_014488		Approved		uc001ozu.3	Q15771		ENST00000533486.1:c.19G>T	11.37:g.82708340C>A	ENSP00000435189:p.Asp7Tyr		82385988	Q6FGK1|Q6MZH2|Q96CI8	Missense_Mutation	SNP	ENST00000533486.1	37	CCDS8264.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.303908	0.81136	.	.	ENSG00000137502	ENST00000533486;ENST00000534141;ENST00000260056;ENST00000527633;ENST00000531021;ENST00000534301;ENST00000525117;ENST00000532548;ENST00000526205;ENST00000534103;ENST00000530224;ENST00000533276;ENST00000528379	T;T;T;T;T;T;T;T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.87245	0.6129	M	0.74881	2.28	0.80722	D	1	P;D;D	0.76494	0.922;0.999;0.991	B;P;P	0.54460	0.318;0.753;0.635	D	0.86531	0.1822	9	.	.	.	.	20.0609	0.97674	0.0:1.0:0.0:0.0	.	7;7;7	E9PLM3;Q6MZH2;Q15771	.;.;RAB30_HUMAN	Y	7	ENSP00000435189:D7Y;ENSP00000434974:D7Y;ENSP00000260056:D7Y;ENSP00000435089:D7Y;ENSP00000434953:D7Y;ENSP00000432193:D7Y;ENSP00000433243:D7Y;ENSP00000437235:D7Y;ENSP00000432336:D7Y;ENSP00000435542:D7Y;ENSP00000436282:D7Y;ENSP00000434528:D7Y;ENSP00000434106:D7Y	.	D	-	1	0	RAB30	82385988	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.763000	0.85283	2.755000	0.94549	0.655000	0.94253	GAT		0.483	RAB30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392141.1	NM_014488		A	82708340	C	A	82708340	3	1	47	1	0	0	0	0	1	0	0	0	12956	826	29	2	608	2	RAB30	11	82708340	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5653413	82708340	52298176	1299	5696										
SYTL2	54843	broad.mit.edu	37	chr11	85438946	85438946	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagggggcttaccttgctgAcggtctctagaactgccacc	13	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:85438946A>G	ENST00000528231.1	-	7	1729	c.1452T>C	c.(1450-1452)cgT>cgC	p.R484R	SYTL2_ENST00000525423.1_5'UTR|SYTL2_ENST00000359152.5_Silent_p.R42R|SYTL2_ENST00000524452.1_Silent_p.R484R|SYTL2_ENST00000316356.4_Silent_p.R485R|SYTL2_ENST00000389960.4_Silent_p.R484R|SYTL2_ENST00000527523.1_Silent_p.R436R|SYTL2_ENST00000354566.3_5'Flank	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	484					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.R485R(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TACCTTGCTGACGGTCTCTAG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	11											84	76	79					11																	85438946		2203	4299	6502	85116594	SO:0001819	synonymous_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1452T>C	11.37:g.85438946A>G			85116594	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																				0.453	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		G	85438946	A	G	85438946	2	3	47	1	0	0	0	0	0	0	0	1	15522	262	10	4		4	SYTL2	11	85438946	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2730606	85438946	49567570	1300	5697										
CCDC83	220047	broad.mit.edu	37	chr11	85622351	85622351	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcacaggaaggaagttgaaGaattaaaaaatgctattcat	8	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:85622351G>T	ENST00000342404.3	+	8	916	c.700G>T	c.(700-702)Gaa>Taa	p.E234*	CCDC83_ENST00000376067.1_Nonsense_Mutation_p.E135*|CCDC83_ENST00000529676.2_3'UTR|CCDC83_ENST00000280245.4_Nonsense_Mutation_p.E234*			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	234								p.E234*(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGAAGTTGAAGAATTAAAAAA	0.333																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											100	110	107					11																	85622351		2203	4299	6502	85299999	SO:0001587	stop_gained	220047			AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.700G>T	11.37:g.85622351G>T	ENSP00000344512:p.Glu234*		85299999	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Nonsense_Mutation	SNP	ENST00000342404.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.456155|6.456155	0.97581|0.97581	.|.	.|.	ENSG00000150676|ENSG00000150676	ENST00000280245;ENST00000376067;ENST00000342404|ENST00000526729	.|.	.|.	.|.	5.08|5.08	2.2|2.2	0.27929|0.27929	.|.	0.453670|.	0.22269|.	N|.	0.062282|.	.|T	.|0.42177	.|0.1191	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.48603	.|-0.9021	.|3	.|.	.|.	.|.	-0.4613|-0.4613	7.0839|7.0839	0.25247|0.25247	0.2838:0.0:0.7162:0.0|0.2838:0.0:0.7162:0.0	.|.	.|.	.|.	.|.	X|N	234;135;234|139	.|.	.|.	E|K	+|+	1|3	0|2	CCDC83|CCDC83	85299999|85299999	0.129000|0.129000	0.22400|0.22400	0.536000|0.536000	0.28039|0.28039	0.283000|0.283000	0.27025|0.27025	-0.609000|-0.609000	0.05635|0.05635	0.192000|0.192000	0.20272|0.20272	0.313000|0.313000	0.20887|0.20887	GAA|AAG		0.333	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		T	85622351	G	T	85622351	4	4	47	1	0	0	0	0	0	1	0	0	2863	943	33	2	726	2	CCDC83	11	85622351	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	183405	85622351	49384165	1301	5698										
NOX4	50507	broad.mit.edu	37	chr11	89135544	89135544	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccatacaaatcttcacaaAtttgtgctgggtaaactctg	6	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:89135544A>C	ENST00000263317.4	-	9	1034	c.796T>G	c.(796-798)Ttt>Gtt	p.F266V	NOX4_ENST00000527956.1_Missense_Mutation_p.F242V|NOX4_ENST00000532825.1_Missense_Mutation_p.F242V|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000542487.1_Missense_Mutation_p.F242V|NOX4_ENST00000535633.1_Missense_Mutation_p.F242V|NOX4_ENST00000413594.2_Missense_Mutation_p.F287V|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000527626.1_Missense_Mutation_p.F100V|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000534731.1_Missense_Mutation_p.F266V|NOX4_ENST00000528341.1_Missense_Mutation_p.F241V|NOX4_ENST00000424319.1_Missense_Mutation_p.F242V|NOX4_ENST00000343727.5_Missense_Mutation_p.F242V			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	266	Ferric oxidoreductase.|Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.F266V(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				ATCTTCACAAATTTGTGCTGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											67	72	70					11																	89135544		2201	4299	6500	88775192	SO:0001583	missense	50507			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.796T>G	11.37:g.89135544A>C	ENSP00000263317:p.Phe266Val		88775192	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	A	0.741	-0.776386	0.02951	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.94931	-3.49;-3.49;-3.49;-3.47;-3.41;-3.56;-3.49;-3.49;-3.23;-3.46;-3.52	4.29	1.37	0.22104	.	0.990505	0.08226	N	0.978279	D	0.91932	0.7445	M	0.72894	2.215	0.09310	N	1	B;B;B;B;B	0.10296	0.0;0.0;0.001;0.0;0.003	B;B;B;B;B	0.10450	0.001;0.001;0.001;0.002;0.005	T	0.79458	-0.1795	9	.	.	.	-0.0028	4.0156	0.09642	0.6342:0.0:0.2181:0.1476	.	242;100;241;266;266	E9PMY6;E9PR43;E9PPP2;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	V	242;242;242;266;266;242;242;242;100;241;287	ENSP00000412446:F242V;ENSP00000440172:F242V;ENSP00000344747:F242V;ENSP00000436892:F266V;ENSP00000263317:F266V;ENSP00000434924:F242V;ENSP00000433797:F242V;ENSP00000439373:F242V;ENSP00000436093:F100V;ENSP00000436970:F241V;ENSP00000405705:F287V	.	F	-	1	0	NOX4	88775192	0.469000	0.25846	0.001000	0.08648	0.090000	0.18270	1.756000	0.38390	0.039000	0.15632	0.383000	0.25322	TTT		0.378	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		C	89135544	A	C	89135544	3	2	47	1	0	0	0	0	1	0	0	0	10589	101	4	4	980	4	NOX4	11	89135544	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3513193	89135544	45870972	1302	5699										
FOLH1B	219595	broad.mit.edu	37	chr11	89407302	89407302	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcaagctgggatgcagaaGaatttggtcttcttggttct	12	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:89407302G>T	ENST00000532352.1	+	0	1162							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.E117*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						GGATGCAGAAGAATTTGGTCT	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											44	44	44					11																	89407302		2196	4278	6474	89046950			219595			AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"prostate specific membrane antigen like protein", "Cell growth-inhibiting gene 26 protein", "glutamate carboxypeptidase III"	609020	"folate hydrolase 2"	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89407302G>T			89046950		Nonsense_Mutation	SNP	ENST00000532352.1	37																																																																																					0.318	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696		T	89407302	G	T	89407302	1	4	47	0	1	0	0	0	0	0	0	0	5999	943	33	2		2	FOLH1B	11	89407302	RNA	SNP	G	TCGA-AG-3892-01A-01W-1073-09	271758	89407302	45599214	1303	5700										
FAT3	120114	broad.mit.edu	37	chr11	92616283	92616283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagtggggacggccgcaacGtctaccaggaggtggggccc	18	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:92616283G>A	ENST00000298047.6	+	23	12678	c.12661G>A	c.(12661-12663)Gtc>Atc	p.V4221I	FAT3_ENST00000409404.2_Missense_Mutation_p.V4221I|FAT3_ENST00000533797.1_Missense_Mutation_p.V556I|FAT3_ENST00000525166.1_Missense_Mutation_p.V4071I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4221					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V4221I(2)|p.V796I(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CGGCCGCAACGTCTACCAGGA	0.652										TCGA Ovarian(4;0.039)																																						3	Substitution - Missense(3)	large_intestine(3)	11											57	70	66					11																	92616283		1962	4130	6092	92255931	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12661G>A	11.37:g.92616283G>A	ENSP00000298047:p.Val4221Ile		92255931	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	4.255	0.046344	0.08243	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.84442	-0.79;-0.71;-0.8;-1.85	5.85	-0.337	0.12654	.	.	.	.	.	T	0.51719	0.1691	N	0.00621	-1.32	0.80722	D	1	B;B	0.13594	0.0;0.008	B;B	0.06405	0.0;0.002	T	0.54173	-0.8333	9	0.02654	T	1	.	8.1575	0.31178	0.1457:0.681:0.1734:0.0	.	4221;4221	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	I	4221;4221;4071;556	ENSP00000298047:V4221I;ENSP00000387040:V4221I;ENSP00000432586:V4071I;ENSP00000436399:V556I	ENSP00000298047:V4221I	V	+	1	0	FAT3	92255931	1.000000	0.71417	0.923000	0.36655	0.858000	0.48976	1.301000	0.33447	0.051000	0.15978	-0.175000	0.13238	GTC		0.652	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92616283	G	A	92616283	3	1	47	1	0	0	0	0	1	0	0	0	5710	1145	40	1	12751	1	FAT3	11	92616283	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3208981	92616283	42390233	1304	5701										
CCDC67	159989	broad.mit.edu	37	chr11	93170799	93170799	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaaagaacttgaaaaacttCtaaatacacatattgatgaa	4	6	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:93170799C>A	ENST00000298050.3	+	14	1829	c.1729C>A	c.(1729-1731)Cta>Ata	p.L577I	CCDC67_ENST00000525646.1_Missense_Mutation_p.L319I	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	577					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)		p.L569I(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				TGAAAAACTTCTAAATACACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	74	73					11																	93170799		1801	4078	5879	92810447	SO:0001583	missense	159989			AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1729C>A	11.37:g.93170799C>A	ENSP00000298050:p.Leu577Ile		92810447	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990142	0.74589	.	.	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646;ENST00000529909	T;T;T	0.41065	1.48;1.48;1.01	5.98	4.98	0.66077	.	0.306190	0.22824	N	0.055182	T	0.60715	0.2290	M	0.77313	2.365	0.29568	N	0.850108	D	0.89917	1.0	D	0.85130	0.997	T	0.61178	-0.7115	10	0.62326	D	0.03	.	7.0226	0.24922	0.0:0.8613:0.0:0.1387	.	577	Q05D60	CCD67_HUMAN	I	577;577;319;58	ENSP00000432111:L577I;ENSP00000298050:L577I;ENSP00000435079:L319I	ENSP00000298050:L577I	L	+	1	2	CCDC67	92810447	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.002000	0.49496	2.838000	0.97847	0.655000	0.94253	CTA		0.358	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		A	93170799	C	A	93170799	3	1	47	1	0	0	0	0	1	0	0	0	2845	912	32	2	1779	2	CCDC67	11	93170799	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	554516	93170799	41835717	1305	5702										
C11orf54	28970	broad.mit.edu	37	chr11	93488490	93488490	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggagaaatacagtgagaaaTgtcatgattttcagtgtgca	11	4	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:93488490T>G	ENST00000331239.4	+	6	624	c.445T>G	c.(445-447)Tgt>Ggt	p.C149G	C11orf54_ENST00000540113.1_Missense_Mutation_p.C130G|C11orf54_ENST00000354421.3_Missense_Mutation_p.C149G|C11orf54_ENST00000528099.1_Missense_Mutation_p.C149G|C11orf54_ENST00000528288.1_Missense_Mutation_p.C149G			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	149					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)	p.C149G(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAGTGAGAAATGTCATGATTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	93	95					11																	93488490		2201	4298	6499	93128138	SO:0001583	missense	28970			AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.445T>G	11.37:g.93488490T>G	ENSP00000331209:p.Cys149Gly		93128138	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Missense_Mutation	SNP	ENST00000331239.4	37		.	.	.	.	.	.	.	.	.	.	T	6.188	0.402809	0.11696	.	.	ENSG00000182919	ENST00000528288;ENST00000331239;ENST00000528099;ENST00000354421;ENST00000540113;ENST00000530620;ENST00000524485;ENST00000527363;ENST00000526335;ENST00000533154	.	.	.	5.94	-1.95	0.07548	Domain of unknown function DUF1907 (1);	0.460546	0.26776	N	0.022545	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.002;0.006	B;B	0.22152	0.038;0.012	T	0.19451	-1.0305	9	0.25751	T	0.34	-3.0389	7.3156	0.26499	0.0971:0.296:0.0:0.6068	.	149;149	Q9H0W9;Q9H0W9-3	CK054_HUMAN;.	G	149;149;149;149;130;130;130;149;149;38	.	ENSP00000331209:C149G	C	+	1	0	C11orf54	93128138	0.195000	0.23338	0.006000	0.13384	0.621000	0.37620	0.346000	0.19997	-0.302000	0.08869	-1.345000	0.01243	TGT		0.423	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039		G	93488490	T	G	93488490	3	3	47	1	0	0	0	0	1	0	0	0	1653	1464	51	4	463	4	C11orf54	11	93488490	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	317691	93488490	41518026	1306	5703										
MRE11A	4361	broad.mit.edu	37	chr11	94203791	94203791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatcttcctccctttaataCgcagcaaaccaacatgtctg	4	14	3	0	rs190142346		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:94203791C>T	ENST00000323929.3	-	9	1085	c.863G>A	c.(862-864)cGt>cAt	p.R288H	RP11-685N10.1_ENST00000541092.1_RNA|MRE11A_ENST00000323977.3_Missense_Mutation_p.R288H|MRE11A_ENST00000393241.4_Missense_Mutation_p.R288H|MRE11A_ENST00000407439.3_Missense_Mutation_p.R291H	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	288					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.R288H(1)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				CCCTTTAATACGCAGCAAACC	0.393								Homologous recombination	Ataxia-Telangiectasia-Like Disorder				C|||	1	0.000199681	0	0	5008	,	,		18425	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											97	86	90					11																	94203791		2201	4297	6498	93843439	SO:0001583	missense	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.863G>A	11.37:g.94203791C>T	ENSP00000325863:p.Arg288His		93843439	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.82	2.351224	0.41700	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	5.5	3.65	0.41850	.	0.043634	0.85682	N	0.000000	T	0.72228	0.3434	L	0.28344	0.845	0.80722	D	1	B;B;B	0.11235	0.004;0.002;0.004	B;B;B	0.06405	0.002;0.002;0.001	T	0.65467	-0.6161	10	0.42905	T	0.14	-6.4527	11.2637	0.49097	0.0:0.7963:0.0:0.2037	.	291;288;288	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	H	288;291;288;288	ENSP00000325863:R288H;ENSP00000385614:R291H;ENSP00000326094:R288H;ENSP00000376933:R288H	ENSP00000325863:R288H	R	-	2	0	MRE11A	93843439	0.911000	0.30947	0.695000	0.30226	0.979000	0.70002	1.804000	0.38873	0.808000	0.34231	-0.142000	0.14014	CGT		0.393	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		T	94203791	C	T	94203791	3	4	47	1	0	0	0	0	1	0	0	0	9789	536	19	1	1311	1	MRE11A	11	94203791	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	715301	94203791	40802725	1307	5704										
PIWIL4	143689	broad.mit.edu	37	chr11	94351195	94351195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaccgtgctggtgtaggggAtggtcagctgaaaacactta	14	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:94351195A>G	ENST00000299001.6	+	17	2301	c.2090A>G	c.(2089-2091)gAt>gGt	p.D697G	PIWIL4_ENST00000537419.1_Missense_Mutation_p.D48G|RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	697	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)	p.D697G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGTGTAGGGGATGGTCAGCTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											97	90	92					11																	94351195		2201	4298	6499	93990843	SO:0001583	missense	143689			AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.2090A>G	11.37:g.94351195A>G	ENSP00000299001:p.Asp697Gly		93990843	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533791	0.45073	.	.	ENSG00000134627	ENST00000299001;ENST00000537419	T;T	0.34667	1.35;1.35	5.89	4.74	0.60224	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.165433	0.39687	N	0.001300	T	0.69593	0.3128	H	0.95982	3.75	0.40472	D	0.980351	D	0.69078	0.997	D	0.68765	0.96	T	0.79188	-0.1906	10	0.87932	D	0	-15.2713	12.2573	0.54631	0.8577:0.1423:0.0:0.0	.	697	Q7Z3Z4	PIWL4_HUMAN	G	697;48	ENSP00000299001:D697G;ENSP00000439710:D48G	ENSP00000299001:D697G	D	+	2	0	PIWIL4	93990843	1.000000	0.71417	0.023000	0.16930	0.079000	0.17450	7.613000	0.82986	1.024000	0.39682	0.460000	0.39030	GAT		0.433	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		G	94351195	A	G	94351195	3	3	47	1	0	0	0	0	1	0	0	0	11991	333	12	4	2156	4	PIWIL4	11	94351195	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	147404	94351195	40655321	1308	5705										
ENDOD1	23052	broad.mit.edu	37	chr11	94862121	94862121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaaatccaggatgaagaacGaatggtacaatctcaaaaga	8	8	1	3	rs200901212		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:94862121G>A	ENST00000278505.4	+	2	999	c.881G>A	c.(880-882)cGa>cAa	p.R294Q		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	294						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.R294Q(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				GATGAAGAACGAATGGTACAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	86	87					11																	94862121		1860	4091	5951	94501769	SO:0001583	missense	23052			BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.881G>A	11.37:g.94862121G>A	ENSP00000278505:p.Arg294Gln		94501769	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.530408	0.27387	.	.	ENSG00000149218	ENST00000278505	T	0.33438	1.41	5.9	5.9	0.94986	.	0.209937	0.33346	N	0.005001	T	0.21761	0.0524	L	0.55103	1.725	0.27024	N	0.964405	P	0.49253	0.921	B	0.35859	0.212	T	0.41980	-0.9478	10	0.35671	T	0.21	-16.9912	4.9356	0.13939	0.0805:0.149:0.6159:0.1547	.	294	O94919	ENDD1_HUMAN	Q	294	ENSP00000278505:R294Q	ENSP00000278505:R294Q	R	+	2	0	ENDOD1	94501769	0.996000	0.38824	0.962000	0.40283	0.238000	0.25445	2.963000	0.49184	2.800000	0.96347	0.455000	0.32223	CGA		0.443	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		A	94862121	G	A	94862121	3	1	47	1	0	0	0	0	1	0	0	0	5127	1058	37	1	887	1	ENDOD1	11	94862121	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	510926	94862121	40144395	1309	5706										
MAML2	84441	broad.mit.edu	37	chr11	95712130	95712130	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttaggaattgttccccaaGatttcatcaagattgatgtc	7	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:95712130G>T	ENST00000524717.1	-	5	4737	c.3453C>A	c.(3451-3453)atC>atA	p.I1151I		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1151					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.I1151I(2)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TGTTCCCCAAGATTTCATCAA	0.393			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	2	Substitution - coding silent(2)	large_intestine(2)	11											52	50	51					11																	95712130		1841	4102	5943	95351778	SO:0001819	synonymous_variant	84441			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3453C>A	11.37:g.95712130G>T			95351778	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																				0.393	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95712130	G	T	95712130	2	4	47	1	0	0	0	0	0	0	0	1	9236	932	33	2		2	MAML2	11	95712130	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	850009	95712130	39294386	1310	5707										
CCDC82	79780	broad.mit.edu	37	chr11	96086848	96086848	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcttgaaagtaatccgcaaAattgagatattcttcaagtt	6	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:96086848A>C	ENST00000278520.5	-	9	2025	c.1597T>G	c.(1597-1599)Ttt>Gtt	p.F533V	CCDC82_ENST00000423339.2_Missense_Mutation_p.F533V|CCDC82_ENST00000542662.1_Missense_Mutation_p.F533V			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	533								p.F533V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		TAATCCGCAAAATTGAGATAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	11											112	114	113					11																	96086848		2199	4295	6494	95726496	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.1597T>G	11.37:g.96086848A>C	ENSP00000278520:p.Phe533Val		95726496	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	A	7.120	0.577724	0.13686	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.21543	2.0;2.0;2.0	5.9	-5.35	0.02697	.	2.547520	0.00881	N	0.002136	T	0.10895	0.0266	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.14062	-1.0486	10	0.24483	T	0.36	12.5374	0.5118	0.00597	0.2698:0.1244:0.242:0.3639	.	533	Q8N4S0	CCD82_HUMAN	V	533	ENSP00000278520:F533V;ENSP00000444010:F533V;ENSP00000397156:F533V	ENSP00000278520:F533V	F	-	1	0	CCDC82	95726496	0.000000	0.05858	0.000000	0.03702	0.941000	0.58515	-0.686000	0.05161	-0.839000	0.04212	0.528000	0.53228	TTT		0.313	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		C	96086848	A	C	96086848	3	2	47	1	0	0	0	0	1	0	0	0	2862	14	1	4	41	4	CCDC82	11	96086848	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	374718	96086848	38919668	1311	5708										
CCDC82	79780	broad.mit.edu	37	chr11	96116606	96116606	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcctcctcatcaacttcaTcactgcttgggcaagattcc	5	15	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:96116606T>G	ENST00000278520.5	-	4	1246	c.818A>C	c.(817-819)gAt>gCt	p.D273A	CCDC82_ENST00000423339.2_Missense_Mutation_p.D273A|CCDC82_ENST00000542662.1_Missense_Mutation_p.D273A			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	273								p.D273A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		atcaacttcatcaCTGCTTGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	11											98	90	93					11																	96116606		2197	4294	6491	95756254	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.818A>C	11.37:g.96116606T>G	ENSP00000278520:p.Asp273Ala		95756254	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	T	2.322	-0.355421	0.05138	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.24151	1.87;1.87;1.87	5.77	4.61	0.57282	.	0.869029	0.09753	U	0.760309	T	0.30634	0.0771	L	0.57536	1.79	0.09310	N	1	P;P	0.42296	0.775;0.657	B;B	0.43916	0.436;0.255	T	0.11966	-1.0566	10	0.29301	T	0.29	-6.5547	8.8943	0.35453	0.0:0.0861:0.0:0.9139	.	273;273	Q8N4S0-2;Q8N4S0	.;CCD82_HUMAN	A	273	ENSP00000278520:D273A;ENSP00000444010:D273A;ENSP00000397156:D273A	ENSP00000278520:D273A	D	-	2	0	CCDC82	95756254	0.213000	0.23551	0.036000	0.18154	0.036000	0.12997	0.074000	0.14662	0.964000	0.38108	0.472000	0.43445	GAT		0.338	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		G	96116606	T	G	96116606	3	3	47	1	0	0	0	0	1	0	0	0	2862	1435	50	4	840	4	CCDC82	11	96116606	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	29758	96116606	38889910	1312	5709										
CNTN5	53942	broad.mit.edu	37	chr11	99715657	99715657	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaactgattctgatgaaaaGaaggtagcattgaattgtga	10	5	1	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:99715657G>T	ENST00000524871.1	+	5	641	c.351G>T	c.(349-351)aaG>aaT	p.K117N	CNTN5_ENST00000528682.1_Missense_Mutation_p.K117N|CNTN5_ENST00000527185.1_Missense_Mutation_p.K117N|CNTN5_ENST00000279463.3_Missense_Mutation_p.K117N|CNTN5_ENST00000418526.2_Missense_Mutation_p.K43N	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	117	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.K117N(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		CTGATGAAAAGAAGGTAGCAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											162	148	152					11																	99715657		1849	4094	5943	99220867	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.351G>T	11.37:g.99715657G>T	ENSP00000435637:p.Lys117Asn		99220867	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.340069	0.60963	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	5.33	4.4	0.53042	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.115868	0.64402	N	0.000013	T	0.61060	0.2317	N	0.11756	0.17	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.998;0.999	P;P;P	0.59115	0.767;0.77;0.852	T	0.63247	-0.6680	10	0.44086	T	0.13	.	10.5594	0.45135	0.0747:0.1348:0.7905:0.0	.	117;43;117	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	N	117;117;117;43;117	ENSP00000433575:K117N;ENSP00000436185:K117N;ENSP00000435637:K117N;ENSP00000393229:K43N;ENSP00000279463:K117N	ENSP00000279463:K117N	K	+	3	2	CNTN5	99220867	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.939000	0.48995	1.341000	0.45600	0.650000	0.86243	AAG		0.358	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99715657	G	T	99715657	3	4	47	1	0	0	0	0	1	0	0	0	3650	933	33	2	361	2	CNTN5	11	99715657	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3599051	99715657	35290859	1313	5710										
CNTN5	53942	broad.mit.edu	37	chr11	99715827	99715827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttttcctaagatggcttcGaaatggaacagaaatagatc	8	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:99715827G>A	ENST00000524871.1	+	6	700	c.410G>A	c.(409-411)cGa>cAa	p.R137Q	CNTN5_ENST00000528682.1_Missense_Mutation_p.R137Q|CNTN5_ENST00000527185.1_Missense_Mutation_p.R137Q|CNTN5_ENST00000279463.3_Missense_Mutation_p.R137Q|CNTN5_ENST00000418526.2_Missense_Mutation_p.R63Q	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	137	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.R137Q(1)|p.R137L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		AGATGGCTTCGAAATGGAACA	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	11											97	87	90					11																	99715827		1831	4092	5923	99221037	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.410G>A	11.37:g.99715827G>A	ENSP00000435637:p.Arg137Gln		99221037	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189811	0.78789	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.53	5.53	0.82687	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.210160	0.35151	N	0.003415	T	0.51143	0.1657	L	0.48260	1.515	0.44816	D	0.997825	D;D;D	0.67145	0.984;0.993;0.996	P;P;P	0.55345	0.585;0.449;0.774	T	0.33111	-0.9881	10	0.23891	T	0.37	.	18.4469	0.90688	0.0:0.0:1.0:0.0	.	137;63;137	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	Q	137;137;137;63;137	ENSP00000433575:R137Q;ENSP00000436185:R137Q;ENSP00000435637:R137Q;ENSP00000393229:R63Q;ENSP00000279463:R137Q	ENSP00000279463:R137Q	R	+	2	0	CNTN5	99221037	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.046000	0.76592	2.597000	0.87782	0.650000	0.86243	CGA		0.353	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	99715827	G	A	99715827	3	1	47	1	0	0	0	0	1	0	0	0	3650	1058	37	1	424	1	CNTN5	11	99715827	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	170	99715827	35290689	1314	5711										
MMP13	4322	broad.mit.edu	37	chr11	102815030	102815030	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaatttgctggcatgacgcGaacaatacggttactccaga	11	9	0	2	rs558960918		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:102815030G>A	ENST00000260302.3	-	10	1409	c.1381C>T	c.(1381-1383)Cgc>Tgc	p.R461C		NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	461	Interaction with collagen.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R461C(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	GGCATGACGCGAACAATACGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	11											138	150	146					11																	102815030		2202	4299	6501	102320240	SO:0001583	missense	4322			X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.1381C>T	11.37:g.102815030G>A	ENSP00000260302:p.Arg461Cys		102320240	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234853	0.58886	.	.	ENSG00000137745	ENST00000260302	T	0.02446	4.29	5.99	4.02	0.46733	Hemopexin/matrixin (2);	.	.	.	.	T	0.17280	0.0415	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02087	-1.1216	9	0.87932	D	0	.	15.2217	0.73316	0.0:0.0:0.7371:0.2629	.	461	P45452	MMP13_HUMAN	C	461	ENSP00000260302:R461C	ENSP00000260302:R461C	R	-	1	0	MMP13	102320240	1.000000	0.71417	0.972000	0.41901	0.348000	0.29142	4.323000	0.59221	1.483000	0.48342	0.655000	0.94253	CGC		0.348	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		A	102815030	G	A	102815030	3	1	47	1	0	0	0	0	1	0	0	0	9682	1058	37	1	38	1	MMP13	11	102815030	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3099203	102815030	32191486	1315	5712										
AASDHPPT	60496	broad.mit.edu	37	chr11	105962137	105962137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctccattaaacttggataTaggccaagtttataaagaaa	6	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:105962137T>C	ENST00000278618.4	+	4	848	c.626T>C	c.(625-627)aTa>aCa	p.I209T	RP11-677I18.3_ENST00000532422.1_RNA	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	209					macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)	p.I209T(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		AACTTGGATATAGGCCAAGTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	107	104					11																	105962137		2201	4299	6500	105467347	SO:0001583	missense	60496			AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.626T>C	11.37:g.105962137T>C	ENSP00000278618:p.Ile209Thr		105467347	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.300439	0.23650	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.77	5.77	0.91146	4&apos (2);-phosphopantetheinyl transferase (2);	0.259984	0.45126	D	0.000389	T	0.40979	0.1139	L	0.31065	0.9	0.32876	D	0.509851	B	0.02656	0.0	B	0.06405	0.002	T	0.45614	-0.9249	9	0.13853	T	0.58	.	16.0816	0.81007	0.0:0.0:0.0:1.0	.	209	Q9NRN7	ADPPT_HUMAN	T	144;144;209	.	ENSP00000278618:I209T	I	+	2	0	AASDHPPT	105467347	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	5.066000	0.64351	2.202000	0.70862	0.477000	0.44152	ATA		0.353	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423		C	105962137	T	C	105962137	3	2	47	1	0	0	0	0	1	0	0	0	23	1406	49	4	640	4	AASDHPPT	11	105962137	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3147107	105962137	29044379	1316	5713										
GUCY1A2	2977	broad.mit.edu	37	chr11	106849448	106849448	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttagagatattgtggaaattCttttctgcatccctgtaact	7	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:106849448C>A	ENST00000526355.2	-	3	852	c.384G>T	c.(382-384)aaG>aaT	p.K128N	GUCY1A2_ENST00000282249.2_Missense_Mutation_p.K128N|GUCY1A2_ENST00000347596.2_Missense_Mutation_p.K128N	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	128					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.K128N(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TGTGGAAATTCTTTTCTGCAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	11											111	107	109					11																	106849448		2201	4298	6499	106354658	SO:0001583	missense	2977			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.384G>T	11.37:g.106849448C>A	ENSP00000431245:p.Lys128Asn		106354658	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648857	0.47362	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.87412	-1.92;-2.25;-1.92	5.73	4.82	0.62117	.	0.154543	0.28989	U	0.013491	D	0.83931	0.5361	N	0.22421	0.69	0.41443	D	0.987935	B;B;P	0.47484	0.22;0.372;0.896	B;B;P	0.51550	0.27;0.098;0.673	T	0.82110	-0.0619	10	0.25751	T	0.34	.	13.5827	0.61911	0.0:0.9249:0.0:0.0751	.	128;128;128	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	N	128	ENSP00000431245:K128N;ENSP00000282249:K128N;ENSP00000344874:K128N	ENSP00000282249:K128N	K	-	3	2	GUCY1A2	106354658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.013000	0.49582	1.579000	0.49836	0.655000	0.94253	AAG		0.368	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106849448	C	A	106849448	3	1	47	1	0	0	0	0	1	0	0	0	6914	912	32	2	1838	2	GUCY1A2	11	106849448	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	887311	106849448	28157068	1317	5714										
CWF19L2	143884	broad.mit.edu	37	chr11	107299966	107299966	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttttcatcaccaataaatTtttcattattgctatttttt	1	7	3	0	rs550302523		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:107299966T>G	ENST00000282251.5	-	8	1019	c.992A>C	c.(991-993)aAa>aCa	p.K331T	CWF19L2_ENST00000433523.1_Missense_Mutation_p.K331T	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	331							catalytic activity (GO:0003824)	p.K177T(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		ACCAATAAATTTTTCATTATT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											97	96	97					11																	107299966		2201	4298	6499	106805176	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.992A>C	11.37:g.107299966T>G	ENSP00000282251:p.Lys331Thr		106805176	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	T	2.846	-0.239282	0.05944	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.21031	2.03;2.03	5.16	1.54	0.23209	.	0.625149	0.17760	N	0.162928	T	0.22003	0.0530	M	0.73962	2.25	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18745	-1.0327	10	0.33940	T	0.23	-6.5673	8.0344	0.30484	0.0:0.3268:0.0:0.6732	.	331	Q2TBE0	C19L2_HUMAN	T	331	ENSP00000282251:K331T;ENSP00000387533:K331T	ENSP00000282251:K331T	K	-	2	0	CWF19L2	106805176	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.502000	0.06390	0.366000	0.24427	0.482000	0.46254	AAA		0.323	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		G	107299966	T	G	107299966	3	3	47	1	0	0	0	0	1	0	0	0	4078	1841	64	4	1736	4	CWF19L2	11	107299966	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	450518	107299966	27706550	1318	5715										
ATM	472	broad.mit.edu	37	chr11	108151823	108151823	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatcctgtagccctatctgCgaaaaacaggctttgtttgc	8	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:108151823C>T	ENST00000452508.2	+	25	3693	c.3504C>T	c.(3502-3504)tgC>tgT	p.C1168C	ATM_ENST00000278616.4_Silent_p.C1168C			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1168					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.C1168C(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GCCCTATCTGCGAAAAACAGG	0.363			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - coding silent(1)	large_intestine(1)	11											120	121	121					11																	108151823		2201	4298	6499	107657033	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3504C>T	11.37:g.108151823C>T			107657033	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.363	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108151823	C	T	108151823	2	4	47	1	0	0	0	0	0	0	0	1	1110	776	27	1		1	ATM	11	108151823	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	851857	108151823	26854693	1319	5716										
ATM	472	broad.mit.edu	37	chr11	108202645	108202645	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggatcacccccatcacactTtgtttattatactggcctta	5	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:108202645T>G	ENST00000452508.2	+	53	7858	c.7669T>G	c.(7669-7671)Ttg>Gtg	p.L2557V	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.L2557V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2557	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L2557V(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CCATCACACTTTGTTTATTAT	0.318			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											88	89	89					11																	108202645		2201	4298	6499	107707855	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7669T>G	11.37:g.108202645T>G	ENSP00000388058:p.Leu2557Val		107707855	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.476825	0.63849	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.82167	-1.58;-1.58	5.28	4.15	0.48705	PIK-related kinase (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88381	0.6421	M	0.70595	2.14	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	D	0.87571	0.2478	10	0.72032	D	0.01	.	8.3628	0.32369	0.0:0.152:0.0:0.848	.	2557	Q13315	ATM_HUMAN	V	2557	ENSP00000278616:L2557V;ENSP00000388058:L2557V	ENSP00000278616:L2557V	L	+	1	2	ATM	107707855	1.000000	0.71417	0.992000	0.48379	0.833000	0.47200	2.222000	0.42926	0.859000	0.35456	0.363000	0.22086	TTG		0.318	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108202645	T	G	108202645	3	3	47	1	0	0	0	0	1	0	0	0	1110	1838	64	4	7871	4	ATM	11	108202645	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	50822	108202645	26803871	1320	5717										
EXPH5	23086	broad.mit.edu	37	chr11	108384958	108384958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggagcatttaaactaacacGttggtaaacattctgtgaat	9	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:108384958G>A	ENST00000265843.4	-	6	1386	c.1276C>T	c.(1276-1278)Cgt>Tgt	p.R426C	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.R350C|EXPH5_ENST00000525344.1_Missense_Mutation_p.R419C|EXPH5_ENST00000443411.1_Missense_Mutation_p.R238C	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	426					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.R426C(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AAACTAACACGTTGGTAAACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											147	147	147					11																	108384958		2201	4298	6499	107890168	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1276C>T	11.37:g.108384958G>A	ENSP00000265843:p.Arg426Cys		107890168	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	9.954	1.220915	0.22457	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04360	4.22;4.15;4.0;4.22;4.07;3.64	5.66	2.12	0.27331	.	0.642064	0.15822	N	0.242924	T	0.04679	0.0127	N	0.22421	0.69	0.09310	N	1	D	0.61697	0.99	P	0.47744	0.556	T	0.38607	-0.9653	10	0.62326	D	0.03	-0.7619	5.0948	0.14727	0.0:0.1639:0.1628:0.6733	.	426	Q8NEV8	EXPH5_HUMAN	C	426;350;238;419;270;350;238	ENSP00000265843:R426C;ENSP00000391966:R350C;ENSP00000411390:R238C;ENSP00000432546:R419C;ENSP00000432683:R350C;ENSP00000446434:R238C	ENSP00000265843:R426C	R	-	1	0	EXPH5	107890168	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	0.132000	0.15891	0.116000	0.18110	-0.479000	0.04858	CGT		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		A	108384958	G	A	108384958	3	1	47	1	0	0	0	0	1	0	0	0	5335	1145	40	1	4697	1	EXPH5	11	108384958	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	182313	108384958	26621558	1321	5718										
PPP2R1B	5519	broad.mit.edu	37	chr11	111618731	111618731	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagcttttcatcaaagaatTccacaccctacagatacaga	4	12	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:111618731T>G	ENST00000527614.1	-	11	1411	c.1346A>C	c.(1345-1347)gAa>gCa	p.E449A	PPP2R1B_ENST00000426998.2_Missense_Mutation_p.E385A|PPP2R1B_ENST00000341980.6_Missense_Mutation_p.E404A|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.E322A|PPP2R1B_ENST00000427203.2_Missense_Mutation_p.E288A|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.E449A	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	449					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)		p.E449A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		ATCAAAGAATTCCACACCCTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											110	99	103					11																	111618731		2201	4296	6497	111123941	SO:0001583	missense	5519			AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9303	protein-coding gene	gene with protein product	"PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform"	603113	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.1346A>C	11.37:g.111618731T>G	ENSP00000437193:p.Glu449Ala		111123941	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469856	0.63625	.	.	ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000427203;ENST00000341980;ENST00000393055	T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44	5.73	5.73	0.89815	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35885	0.0947	L	0.53671	1.685	0.80722	D	1	B;P;B;B;B;B	0.35793	0.413;0.521;0.08;0.199;0.08;0.166	B;B;B;B;B;B	0.40410	0.224;0.328;0.123;0.2;0.125;0.124	T	0.15350	-1.0440	10	0.54805	T	0.06	-19.4496	14.2586	0.66070	0.0:0.0:0.0:1.0	.	322;404;288;385;449;449	A8MY67;F8W8G1;B7Z1G3;B4DWW5;P30154;P30154-2	.;.;.;.;2AAB_HUMAN;.	A	449;322;385;449;288;404;322	ENSP00000311344:E449A;ENSP00000410671:E385A;ENSP00000437193:E449A;ENSP00000415759:E288A;ENSP00000343317:E404A;ENSP00000376775:E322A	ENSP00000311344:E449A	E	-	2	0	PPP2R1B	111123941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.387000	0.79785	2.308000	0.77769	0.533000	0.62120	GAA		0.353	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		G	111618731	T	G	111618731	3	3	47	1	0	0	0	0	1	0	0	0	12417	1783	62	4	702	4	PPP2R1B	11	111618731	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3233773	111618731	23387785	1322	5719										
ALG9	79796	broad.mit.edu	37	chr11	111711524	111711524	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagccaatacgggtggcctaAattctgaactgcaagacaca	9	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:111711524A>C	ENST00000531154.1	-	10	986	c.514T>G	c.(514-516)Tta>Gta	p.L172V	ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000398006.2_Missense_Mutation_p.L172V	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	343					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)	p.L575V(1)|p.L172V(1)|p.L576V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		GGGTGGCCTAAATTCTGAACT	0.343																																																3	Substitution - Missense(3)	large_intestine(3)	11											110	107	108					11																	111711524		1831	4084	5915	111216734	SO:0001583	missense	79796				CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	15672	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dol-P-Man dependent alpha-1,2-mannosyltransferase"	606941	"disrupted in bipolar affective disorder 1", "asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)", "asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)", "asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.514T>G	11.37:g.111711524A>C	ENSP00000435517:p.Leu172Val		111216734	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	37	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.156330	0.78114	.	.	ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306	T;T	0.62941	-0.01;-0.01	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.69975	0.3171	L	0.60957	1.885	0.80722	D	1	D;P;D;D	0.76494	0.999;0.685;0.997;0.987	D;B;P;P	0.80764	0.994;0.312;0.906;0.872	T	0.68496	-0.5393	10	0.25106	T	0.35	-12.3809	6.1489	0.20301	0.8019:0.0:0.1981:0.0	.	172;343;576;343	B4DQI3;Q9H6U8-3;B4DYW0;Q9H6U8	.;.;.;ALG9_HUMAN	V	172;172;576	ENSP00000435517:L172V;ENSP00000381090:L172V	ENSP00000381090:L172V	L	-	1	2	ALG9	111216734	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.589000	0.82641	2.222000	0.72286	0.533000	0.62120	TTA		0.343	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		C	111711524	A	C	111711524	3	2	47	1	0	0	0	0	1	0	0	0	524	11	1	4	853	4	ALG9	11	111711524	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	92793	111711524	23294992	1323	5720										
C11orf57	55216	broad.mit.edu	37	chr11	111953428	111953428	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaagggaaacaaccacataAacgcaagaaaaaatccagga	8	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:111953428A>C	ENST00000280352.9	+	6	1247	c.611A>C	c.(610-612)aAa>aCa	p.K204T	C11orf57_ENST00000532163.1_Missense_Mutation_p.K176T|C11orf57_ENST00000420986.2_Missense_Mutation_p.K204T|C11orf57_ENST00000393047.3_Missense_Mutation_p.K205T|TIMM8B_ENST00000507614.1_5'Flank	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	204	Lys-rich.							p.K204T(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		CAACCACATAAACGCAAGAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											106	112	110					11																	111953428		2201	4297	6498	111458638	SO:0001583	missense	55216			BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.611A>C	11.37:g.111953428A>C	ENSP00000339076:p.Lys204Thr		111458638	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Missense_Mutation	SNP	ENST00000280352.9	37	CCDS41715.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.054905	0.55325	.	.	ENSG00000150776	ENST00000420986;ENST00000532163;ENST00000280352;ENST00000393047;ENST00000525785;ENST00000393048	.	.	.	5.5	5.5	0.81552	.	0.252366	0.46442	D	0.000285	T	0.55033	0.1895	N	0.11560	0.145	0.38213	D	0.940521	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66015	-0.6028	9	0.62326	D	0.03	-1.4453	14.9534	0.71091	1.0:0.0:0.0:0.0	.	205;204	Q6ZUT1-2;Q6ZUT1	.;CK057_HUMAN	T	204;176;204;205;176;59	.	ENSP00000339076:K204T	K	+	2	0	C11orf57	111458638	1.000000	0.71417	0.997000	0.53966	0.632000	0.37999	3.521000	0.53472	2.302000	0.77476	0.533000	0.62120	AAA		0.403	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		C	111953428	A	C	111953428	3	2	47	1	0	0	0	0	1	0	0	0	1654	14	1	4	632	4	C11orf57	11	111953428	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	241904	111953428	23053088	1324	5721										
ZW10	9183	broad.mit.edu	37	chr11	113609028	113609028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagaataattctcttcatcGtccatatttgaaaagttcct	5	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:113609028G>A	ENST00000200135.3	-	13	1986	c.1842C>T	c.(1840-1842)gaC>gaT	p.D614D		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	614					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)	p.D614D(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TCTCTTCATCGTCCATATTTG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	11											120	114	116					11																	113609028		2201	4296	6497	113114238	SO:0001819	synonymous_variant	9183			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1842C>T	11.37:g.113609028G>A			113114238	A1A528	Silent	SNP	ENST00000200135.3	37	CCDS8363.1																																																																																				0.408	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		A	113609028	G	A	113609028	2	1	47	1	0	0	0	0	0	0	0	1	18286	1136	40	1		1	ZW10	11	113609028	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1655600	113609028	21397488	1325	5722										
ZBTB16	7704	broad.mit.edu	37	chr11	113934842	113934842	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggatgggggacaaggttgagGaaagaggcaaagaggggcct	20	4	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:113934842G>T	ENST00000335953.4	+	2	1200	c.820G>T	c.(820-822)Gaa>Taa	p.E274*	ZBTB16_ENST00000392996.2_Nonsense_Mutation_p.E274*	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	274					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E274*(1)		central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		CAAGGTTGAGGAAAGAGGCAA	0.627																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											46	40	42					11																	113934842		2201	4296	6497	113440052	SO:0001587	stop_gained	7704			Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.820G>T	11.37:g.113934842G>T	ENSP00000338157:p.Glu274*		113440052	Q8TAL4	Nonsense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	G	37	6.001141	0.97189	.	.	ENSG00000109906	ENST00000335953;ENST00000392996	.	.	.	5.63	5.63	0.86233	.	0.234953	0.43110	D	0.000604	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.1954	19.679	0.95950	0.0:0.0:1.0:0.0	.	.	.	.	X	274	.	ENSP00000338157:E274X	E	+	1	0	ZBTB16	113440052	1.000000	0.71417	0.984000	0.44739	0.665000	0.39181	9.776000	0.99001	2.651000	0.90000	0.655000	0.94253	GAA		0.627	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		T	113934842	G	T	113934842	4	4	47	1	0	0	0	0	0	1	0	0	17565	1175	41	2	822	2	ZBTB16	11	113934842	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	325814	113934842	21071674	1326	5723										
RNF214	257160	broad.mit.edu	37	chr11	117109610	117109610	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccatccagtcactcggtCtcttaaggcagggtgccata	9	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:117109610C>A	ENST00000531452.1	+	3	447	c.401C>A	c.(400-402)tCt>tAt	p.S134Y	RNF214_ENST00000531287.1_Intron|RNF214_ENST00000530849.1_Intron|RNF214_ENST00000300650.4_Missense_Mutation_p.S134Y	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	134							zinc ion binding (GO:0008270)	p.S134Y(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		GTCACTCGGTCTCTTAAGGCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											63	66	65					11																	117109610		1977	4164	6141	116614820	SO:0001583	missense	257160			AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.401C>A	11.37:g.117109610C>A	ENSP00000431643:p.Ser134Tyr		116614820	B2RUW0|B4DTD1	Missense_Mutation	SNP	ENST00000531452.1	37	CCDS41720.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184419	0.78677	.	.	ENSG00000167257	ENST00000534428;ENST00000531452;ENST00000300650	T;T	0.39997	1.05;1.05	5.39	5.39	0.77823	.	0.289185	0.30464	N	0.009572	T	0.51176	0.1659	L	0.44542	1.39	0.33847	D	0.63214	D	0.54207	0.965	P	0.56700	0.804	T	0.64381	-0.6421	10	0.66056	D	0.02	-6.0202	14.6798	0.69009	0.0:1.0:0.0:0.0	.	134	Q8ND24	RN214_HUMAN	Y	134	ENSP00000431643:S134Y;ENSP00000300650:S134Y	ENSP00000300650:S134Y	S	+	2	0	RNF214	116614820	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.233000	0.43027	2.524000	0.85096	0.591000	0.81541	TCT		0.542	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		A	117109610	C	A	117109610	3	1	47	1	0	0	0	0	1	0	0	0	13515	913	32	2	407	2	RNF214	11	117109610	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3174768	117109610	17896906	1327	5724										
RNF214	257160	broad.mit.edu	37	chr11	117110570	117110570	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagatcaagatattgaaaaGaatttggtaagtatttaaac	7	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:117110570G>T	ENST00000531452.1	+	4	718	c.672G>T	c.(670-672)aaG>aaT	p.K224N	RNF214_ENST00000531287.1_Missense_Mutation_p.K69N|RNF214_ENST00000530849.1_Missense_Mutation_p.K69N|RNF214_ENST00000300650.4_Missense_Mutation_p.K224N	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	224							zinc ion binding (GO:0008270)	p.K224N(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		ATATTGAAAAGAATTTGGTAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											65	64	64					11																	117110570		1820	4072	5892	116615780	SO:0001583	missense	257160			AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.672G>T	11.37:g.117110570G>T	ENSP00000431643:p.Lys224Asn		116615780	B2RUW0|B4DTD1	Missense_Mutation	SNP	ENST00000531452.1	37	CCDS41720.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344029	0.24339	.	.	ENSG00000167257	ENST00000531287;ENST00000531452;ENST00000530849;ENST00000300650	T;T;D;T	0.94650	2.57;1.13;-3.48;1.13	5.96	3.1	0.35709	.	0.237004	0.42053	D	0.000769	D	0.94748	0.8305	L	0.57536	1.79	0.34761	D	0.732716	B;D	0.67145	0.403;0.996	B;P	0.61874	0.221;0.895	D	0.94047	0.7314	10	0.27082	T	0.32	-10.3497	9.033	0.36271	0.2819:0.0:0.7181:0.0	.	69;224	B4DTD1;Q8ND24	.;RN214_HUMAN	N	69;224;69;224	ENSP00000435361:K69N;ENSP00000431643:K224N;ENSP00000432903:K69N;ENSP00000300650:K224N	ENSP00000300650:K224N	K	+	3	2	RNF214	116615780	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.862000	0.39448	0.873000	0.35799	-0.142000	0.14014	AAG		0.333	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		T	117110570	G	T	117110570	3	4	47	1	0	0	0	0	1	0	0	0	13515	933	33	2	682	2	RNF214	11	117110570	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	960	117110570	17895946	1328	5725										
DSCAML1	57453	broad.mit.edu	37	chr11	117310593	117310593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactgaattgcaaggcagccGaacatctttcatccaaggtg	9	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:117310593G>A	ENST00000321322.6	-	22	4103	c.4102C>T	c.(4102-4104)Cgg>Tgg	p.R1368W	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R1098W	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1308	Ig-like C2-type 10.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.R1368W(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	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)		CAAGGCAGCCGAACATCTTTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	11											165	144	151					11																	117310593		2201	4296	6497	116815803	SO:0001583	missense	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4102C>T	11.37:g.117310593G>A	ENSP00000315465:p.Arg1368Trp		116815803	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808759	0.70797	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.28666	1.6;1.6	4.89	2.9	0.33743	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51753	0.1693	M	0.72479	2.2	0.58432	D	0.999998	D	0.89917	1.0	D	0.73708	0.981	T	0.56848	-0.7911	9	0.62326	D	0.03	.	12.818	0.57677	0.0:0.0:0.7048:0.2952	.	1308	Q8TD84	DSCL1_HUMAN	W	1098;1368;1075	ENSP00000434335:R1098W;ENSP00000315465:R1368W	ENSP00000315465:R1368W	R	-	1	2	DSCAML1	116815803	0.209000	0.23505	0.999000	0.59377	0.930000	0.56654	1.444000	0.35068	1.272000	0.44329	-0.314000	0.08810	CGG		0.582	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117310593	G	A	117310593	3	1	47	1	0	0	0	0	1	0	0	0	4780	1057	37	1	2287	1	DSCAML1	11	117310593	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	200023	117310593	17695923	1329	5726										
TMPRSS13	84000	broad.mit.edu	37	chr11	117779363	117779363	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggacagccgcatgagggCgatgtcatagtcgtcctcct	12	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:117779363C>T	ENST00000430170.2	-	9	1333	c.1246G>A	c.(1246-1248)Gcc>Acc	p.A416T	TMPRSS13_ENST00000526090.1_Missense_Mutation_p.A416T|TMPRSS13_ENST00000445164.2_Missense_Mutation_p.A416T|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.A381T|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.A416T	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	416	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.A416T(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		CGCATGAGGGCGATGTCATAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	11											34	39	37					11																	117779363		2134	4239	6373	117284573	SO:0001583	missense	84000			AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.1246G>A	11.37:g.117779363C>T	ENSP00000387702:p.Ala416Thr		117284573	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	C	35	5.579165	0.96565	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	T;T;T;T;D	0.92299	-1.12;-1.12;-1.12;-1.12;-3.01	4.98	4.98	0.66077	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000008	D	0.97167	0.9074	M	0.93978	3.48	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.99;1.0;0.987;0.975	D	0.98336	1.0536	10	0.87932	D	0	.	17.8409	0.88715	0.0:1.0:0.0:0.0	.	411;411;411;416	E9PHM4;Q9BYE2-4;Q9BYE2;E9PRA0	.;.;TMPSD_HUMAN;.	T	381;411;416;416;416;416	ENSP00000435813:A381T;ENSP00000434279:A416T;ENSP00000387702:A416T;ENSP00000394114:A416T;ENSP00000436502:A416T	ENSP00000337113:A411T	A	-	1	0	TMPRSS13	117284573	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.397000	0.79903	2.314000	0.78098	0.655000	0.94253	GCC		0.632	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		T	117779363	C	T	117779363	3	4	47	1	0	0	0	0	1	0	0	0	16284	768	27	1	477	1	TMPRSS13	11	117779363	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	468770	117779363	17227153	1330	5727										
IL10RA	3587	broad.mit.edu	37	chr11	117859201	117859201	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtctgaaagtacctgctatGaagtggcgctcctgaggtga	13	8	1	4	rs572945136	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:117859201G>T	ENST00000227752.3	+	2	292	c.172G>T	c.(172-174)Gaa>Taa	p.E58*	IL10RA_ENST00000545409.1_5'UTR|IL10RA_ENST00000541785.1_Nonsense_Mutation_p.E38*|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	58					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.E58*(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		TACCTGCTATGAAGTGGCGCT	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											85	77	79					11																	117859201		2201	4296	6497	117364411	SO:0001587	stop_gained	3587			U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.172G>T	11.37:g.117859201G>T	ENSP00000227752:p.Glu58*		117364411	A8K6I0|B0YJ27	Nonsense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880037	0.72294	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	.	.	.	5.13	5.13	0.70059	.	1.594970	0.03311	N	0.190495	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-12.1501	14.0811	0.64922	0.0:0.0:1.0:0.0	.	.	.	.	X	58;38;38	.	ENSP00000227752:E58X	E	+	1	0	IL10RA	117364411	1.000000	0.71417	1.000000	0.80357	0.075000	0.17131	4.413000	0.59795	2.374000	0.81015	0.555000	0.69702	GAA		0.552	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117859201	G	T	117859201	4	4	47	1	0	0	0	0	0	1	0	0	7641	1291	45	2	178	2	IL10RA	11	117859201	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	79838	117859201	17147315	1331	5728										
SCN2B	6327	broad.mit.edu	37	chr11	118038803	118038803	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcaccccagccttcaccttCcatgaggacctgcagatgga	10	15	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:118038803C>A	ENST00000278947.5	-	3	686	c.445G>T	c.(445-447)Gaa>Taa	p.E149*		NM_004588.4	NP_004579.1	O60939	SCN2B_HUMAN	sodium channel, voltage-gated, type II, beta subunit	149	Ig-like C2-type.				cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|nervous system development (GO:0007399)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	voltage-gated sodium channel complex (GO:0001518)	sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.E149*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	7	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;3.19e-05)|Epithelial(105;0.00117)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CCTTCACCTTCCATGAGGACC	0.617																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											48	38	42					11																	118038803		2200	4296	6496	117544013	SO:0001587	stop_gained	6327			AY358945	CCDS8390.1	11q23.3	2013-09-19	2012-02-28		ENSG00000149575	ENSG00000149575		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	10589	protein-coding gene	gene with protein product		601327	"sodium channel, voltage-gated, type II, beta polypeptide", "sodium channel, voltage-gated, type II, beta"			10198179	Standard	NM_004588		Approved		uc001psf.2	O60939	OTTHUMG00000048248	ENST00000278947.5:c.445G>T	11.37:g.118038803C>A	ENSP00000278947:p.Glu149*		117544013	O75302|Q9UNN3	Nonsense_Mutation	SNP	ENST00000278947.5	37	CCDS8390.1	.	.	.	.	.	.	.	.	.	.	C	32	5.160323	0.94727	.	.	ENSG00000149575	ENST00000278947	.	.	.	4.9	3.94	0.45596	.	0.108034	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	16.3527	0.83220	0.0:0.8567:0.1433:0.0	.	.	.	.	X	149	.	ENSP00000278947:E149X	E	-	1	0	SCN2B	117544013	0.987000	0.35691	0.993000	0.49108	0.507000	0.33981	1.809000	0.38922	2.552000	0.86080	0.655000	0.94253	GAA		0.617	SCN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109748.2	NM_004588		A	118038803	C	A	118038803	4	1	47	1	0	0	0	0	0	1	0	0	13954	864	30	2	210	2	SCN2B	11	118038803	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	179602	118038803	16967713	1332	5729										
MPZL2	10205	broad.mit.edu	37	chr11	118130796	118130796	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctccaccactttatgagctCtttcggcccatcgctttttc	5	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:118130796C>A	ENST00000278937.2	-	4	685	c.557G>T	c.(556-558)aGa>aTa	p.R186I	MPZL2_ENST00000438295.2_Missense_Mutation_p.R186I|MPZL2_ENST00000525647.1_5'Flank	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	186					anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R186I(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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;3.04e-05)		TTTATGAGCTCTTTCGGCCCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											246	248	247					11																	118130796		2200	4296	6496	117636006	SO:0001583	missense	10205			AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"Immunoglobulin superfamily / V-set domain containing"	3496	protein-coding gene	gene with protein product		604873	"epithelial V-like antigen 1"	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.557G>T	11.37:g.118130796C>A	ENSP00000278937:p.Arg186Ile		117636006	A8K2R1	Missense_Mutation	SNP	ENST00000278937.2	37	CCDS8393.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.063175	0.55432	.	.	ENSG00000149573	ENST00000278937;ENST00000438295	D;D	0.97404	-4.37;-4.37	6.07	4.15	0.48705	.	0.864324	0.10690	N	0.645339	D	0.92753	0.7696	N	0.19112	0.55	0.18873	N	0.999989	B	0.33448	0.412	B	0.32289	0.143	D	0.86623	0.1880	10	0.37606	T	0.19	.	10.6437	0.45606	0.0:0.7833:0.0:0.2167	.	186	O60487	MPZL2_HUMAN	I	186	ENSP00000278937:R186I;ENSP00000408362:R186I	ENSP00000278937:R186I	R	-	2	0	MPZL2	117636006	0.003000	0.15002	0.773000	0.31616	0.993000	0.82548	0.400000	0.20932	1.495000	0.48549	0.655000	0.94253	AGA		0.463	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797		A	118130796	C	A	118130796	3	1	47	1	0	0	0	0	1	0	0	0	9780	913	32	2	98	2	MPZL2	11	118130796	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	91993	118130796	16875720	1333	5730										
MLL	4297	broad.mit.edu	37	chr11	118376502	118376502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaaatctagcatcatgtatTttgaaccggcacccctgtta	6	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:118376502T>C	ENST00000389506.5	+	27	9886	c.9886T>C	c.(9886-9888)Ttt>Ctt	p.F3296L	KMT2A_ENST00000354520.4_Missense_Mutation_p.F3258L|KMT2A_ENST00000534358.1_Missense_Mutation_p.F3299L			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3296					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.F3296L(1)									CATCATGTATTTTGAACCGGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											104	103	103					11																	118376502		2200	4295	6495	117881712	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.9886T>C	11.37:g.118376502T>C	ENSP00000374157:p.Phe3296Leu		117881712	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.589515	0.28357	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.78707	-1.19;-1.2;-1.16	5.82	5.82	0.92795	.	0.060171	0.64402	D	0.000001	T	0.62612	0.2442	N	0.19112	0.55	0.52099	D	0.999942	B;B	0.24963	0.115;0.115	B;B	0.15870	0.014;0.014	T	0.60439	-0.7263	10	0.09084	T	0.74	.	16.1809	0.81898	0.0:0.0:0.0:1.0	.	3299;3296	E9PQG7;Q03164	.;MLL1_HUMAN	L	3299;3296;3258;2206	ENSP00000436786:F3299L;ENSP00000374157:F3296L;ENSP00000346516:F3258L	ENSP00000346516:F3258L	F	+	1	0	MLL	117881712	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.691000	0.61738	2.229000	0.72834	0.383000	0.25322	TTT		0.463	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		C	118376502	T	C	118376502	3	2	47	1	0	0	0	0	1	0	0	0	9650	1841	64	4	9992	4	MLL	11	118376502	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	245706	118376502	16630014	1334	5731										
VPS11	55823	broad.mit.edu	37	chr11	118944541	118944541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagaacctatttgagatggCgattaaccttgccaagagcc	10	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:118944541C>T	ENST00000300793.6	+	8	1157	c.1115C>T	c.(1114-1116)gCg>gTg	p.A372V	VPS11_ENST00000527798.1_3'UTR	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	373					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.A372V(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		TTTGAGATGGCGATTAACCTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	90	93					11																	118944541		1901	4122	6023	118449751	SO:0001583	missense	55823			AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"RING-type (C3HC4) zinc fingers"	14583	protein-coding gene	gene with protein product		608549	"vacuolar protein sorting 11 (yeast homolog)"				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.1115C>T	11.37:g.118944541C>T	ENSP00000475301:p.Ala372Val		118449751	Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Missense_Mutation	SNP	ENST00000300793.6	37																																																																																					0.478	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729		T	118944541	C	T	118944541	3	4	47	1	0	0	0	0	1	0	0	0	17228	768	27	1	1143	1	VPS11	11	118944541	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	568039	118944541	16061975	1335	5732										
MCAM	4162	broad.mit.edu	37	chr11	119181151	119181151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaacttcaactacaagttCgctcttacgagacgggggta	9	10	2	1	rs201149343		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:119181151C>T	ENST00000264036.4	-	15	1833	c.1819G>A	c.(1819-1821)Gaa>Aaa	p.E607K	MCAM_ENST00000392814.1_3'UTR	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	607					anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E607K(2)		breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		ACTACAAGTTCGCTCTTACGA	0.592																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	11											108	109	109					11																	119181151		2199	4295	6494	118686361	SO:0001583	missense	4162			X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.1819G>A	11.37:g.119181151C>T	ENSP00000264036:p.Glu607Lys		118686361	O95812|Q59E86|Q6PHR3|Q6ZTR2	Missense_Mutation	SNP	ENST00000264036.4	37	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.598639	0.46318	.	.	ENSG00000076706	ENST00000264036	T	0.57907	0.37	5.28	4.37	0.52481	.	.	.	.	.	T	0.29223	0.0727	N	0.17474	0.49	0.80722	D	1	P	0.40638	0.725	B	0.23716	0.048	T	0.11251	-1.0595	9	0.41790	T	0.15	-13.4298	11.1149	0.48254	0.0:0.846:0.0:0.154	.	607	P43121	MUC18_HUMAN	K	607	ENSP00000264036:E607K	ENSP00000264036:E607K	E	-	1	0	MCAM	118686361	1.000000	0.71417	0.830000	0.32933	0.793000	0.44817	3.841000	0.55850	1.219000	0.43474	0.563000	0.77884	GAA		0.592	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			T	119181151	C	T	119181151	3	4	47	1	0	0	0	0	1	0	0	0	9398	893	31	1	129	1	MCAM	11	119181151	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	236610	119181151	15825365	1336	5733										
USP2	9099	broad.mit.edu	37	chr11	119228214	119228214	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgttttctgaggcaaattCtcttaagtccaggtctctta	9	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:119228214C>A	ENST00000260187.2	-	11	1882	c.1588G>T	c.(1588-1590)Gaa>Taa	p.E530*	USP2_ENST00000525735.1_Nonsense_Mutation_p.E321*|USP2_ENST00000455332.2_Nonsense_Mutation_p.E287*	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	530	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E530*(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GAGGCAAATTCTCTTAAGTCC	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											98	103	101					11																	119228214		2199	4295	6494	118733424	SO:0001587	stop_gained	9099			AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.1588G>T	11.37:g.119228214C>A	ENSP00000260187:p.Glu530*		118733424	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Nonsense_Mutation	SNP	ENST00000260187.2	37	CCDS8422.1	.	.	.	.	.	.	.	.	.	.	C	38	7.148130	0.98096	.	.	ENSG00000036672	ENST00000455332;ENST00000260187;ENST00000392808;ENST00000525735	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-3.7313	18.7244	0.91708	0.0:1.0:0.0:0.0	.	.	.	.	X	287;530;277;321	.	ENSP00000260187:E530X	E	-	1	0	USP2	118733424	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.673000	0.61604	2.678000	0.91216	0.655000	0.94253	GAA		0.522	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		A	119228214	C	A	119228214	4	1	47	1	0	0	0	0	0	1	0	0	17091	922	32	2	241	2	USP2	11	119228214	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	47063	119228214	15778302	1337	5734										
SC5DL	6309	broad.mit.edu	37	chr11	121177986	121177986	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccccaaatcttacagccatTtattaatggctcagctcatc	4	14	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:121177986T>G	ENST00000392789.2	+	5	902	c.665T>G	c.(664-666)tTt>tGt	p.F222C	SC5D_ENST00000264027.4_Missense_Mutation_p.F222C|SC5D_ENST00000534230.1_Intron	NM_001024956.2	NP_001020127.1	O75845	SC5D_HUMAN	sterol-C5-desaturase	222				PQILQPFINGSAHHTDHHMFFDYNYGQYFTLWDRIGGSFKN PSSFEGKGPLSYVKEMTEGKRSSHSGNGCKNEKLFNGEFTK TE -> RMKNYSMESLQRLNRLLPSYS (in Ref. 1; BAA18970). {ECO:0000305}.	cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via lathosterol (GO:0033490)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	C-5 sterol desaturase activity (GO:0000248)|iron ion binding (GO:0005506)|lathosterol oxidase activity (GO:0050046)	p.F222C(1)									TTACAGCCATTTATTAATGGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											162	164	164					11																	121177986		2203	4299	6502	120683196	SO:0001583	missense	6309				CCDS8435.1	11q23.3	2013-03-04	2013-03-04	2013-03-04	ENSG00000109929	ENSG00000109929	1.14.21.6	"Fatty acid hydroxylase domain containing"	10547	protein-coding gene	gene with protein product	"lathosterol oxidase"	602286	"sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like"	SC5DL		8976377	Standard	NM_006918		Approved		uc001pxu.3	O75845	OTTHUMG00000166068	ENST00000392789.2:c.665T>G	11.37:g.121177986T>G	ENSP00000376539:p.Phe222Cys		120683196	O00119|Q6GTM5|Q9UK15	Missense_Mutation	SNP	ENST00000392789.2	37	CCDS8435.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.244282	0.79912	.	.	ENSG00000109929	ENST00000264027;ENST00000392789	D;D	0.84944	-1.92;-1.92	6.02	6.02	0.97574	Fatty acid hydroxylase (1);	0.278521	0.39759	N	0.001267	D	0.92802	0.7711	M	0.86953	2.85	0.38716	D	0.953339	D	0.55385	0.971	D	0.64687	0.928	D	0.94565	0.7766	10	0.72032	D	0.01	-9.8785	15.5272	0.75919	0.0:0.0:0.0:1.0	.	222	O75845	SC5D_HUMAN	C	222	ENSP00000264027:F222C;ENSP00000376539:F222C	ENSP00000264027:F222C	F	+	2	0	SC5DL	120683196	1.000000	0.71417	0.797000	0.32132	0.942000	0.58702	4.240000	0.58701	2.311000	0.77944	0.533000	0.62120	TTT		0.373	SC5D-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387702.1	NM_001024956		G	121177986	T	G	121177986	3	3	47	1	0	0	0	0	1	0	0	0	13903	1841	64	4	679	4	SC5DL	11	121177986	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1949772	121177986	13828530	1338	5735										
CRTAM	56253	broad.mit.edu	37	chr11	122738726	122738726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttctttttttgtagaaaacGaagtttcagaacacacacta	5	7	2	2	rs148256561		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:122738726G>A	ENST00000227348.4	+	9	1017	c.970G>A	c.(970-972)Gaa>Aaa	p.E324K	CRTAM_ENST00000533709.1_Missense_Mutation_p.E125K	NM_019604.2	NP_062550.2			cytotoxic and regulatory T cell molecule									p.E324K(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	19		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		TGTAGAAAACGAAGTTTCAGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	80	71	74		970	4.9	1	11	dbSNP_134	74	1,8597		0,1,4298	no	missense	CRTAM	NM_019604.2	56	0,2,6499	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	324/394	122738726	2,13000	2202	4299	6501	122243936	SO:0001583	missense	56253			AF001622	CCDS8437.1	11q24.1	2013-01-11			ENSG00000109943	ENSG00000109943		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	24313	protein-coding gene	gene with protein product	"class I MHC restricted T cell associated molecule"	612597				10811014, 16300832	Standard	NM_019604		Approved	CD355	uc001pyj.3	O95727	OTTHUMG00000166026	ENST00000227348.4:c.970G>A	11.37:g.122738726G>A	ENSP00000227348:p.Glu324Lys		122243936		Missense_Mutation	SNP	ENST00000227348.4	37	CCDS8437.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.888420	0.72524	2.27E-4	1.16E-4	ENSG00000109943	ENST00000227348;ENST00000533709	T;T	0.66099	-0.19;0.92	4.89	4.89	0.63831	.	0.258920	0.37348	N	0.002135	T	0.73776	0.3630	M	0.68952	2.095	0.58432	D	0.999994	D;D	0.69078	0.997;0.992	P;P	0.58520	0.84;0.665	T	0.77670	-0.2501	10	0.72032	D	0.01	.	15.5745	0.76365	0.0:0.0:1.0:0.0	.	125;324	O95727-2;O95727	.;CRTAM_HUMAN	K	324;125	ENSP00000227348:E324K;ENSP00000433728:E125K	ENSP00000227348:E324K	E	+	1	0	CRTAM	122243936	1.000000	0.71417	0.988000	0.46212	0.492000	0.33523	5.944000	0.70219	2.249000	0.74217	0.563000	0.77884	GAA		0.323	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604		A	122738726	G	A	122738726	3	1	47	1	0	0	0	0	1	0	0	0	3903	1059	37	1	1004	1	CRTAM	11	122738726	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1560740	122738726	12267790	1339	5736										
OR10G9	219870	broad.mit.edu	37	chr11	123893819	123893819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaatcttcctggtggtttacGtgctcactgtgctggggaac	13	9	2	0	rs201447659		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:123893819G>A	ENST00000375024.1	+	1	100	c.100G>A	c.(100-102)Gtg>Atg	p.V34M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V34M(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GGTGGTTTACGTGCTCACTGT	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		20523	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											168	152	158					11																	123893819		2201	4299	6500	123399029	SO:0001583	missense	219870			AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"GPCR / Class A : Olfactory receptors"	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.100G>A	11.37:g.123893819G>A	ENSP00000364164:p.Val34Met		123399029		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274055	0.23221	.	.	ENSG00000236981	ENST00000375024	T	0.03035	4.07	3.33	1.36	0.22044	.	0.946353	0.08678	N	0.909827	T	0.02119	0.0066	N	0.14661	0.345	0.09310	N	1	B	0.26876	0.162	B	0.22880	0.042	T	0.49725	-0.8909	10	0.14656	T	0.56	.	4.1116	0.10062	0.0953:0.1568:0.5867:0.1612	.	34	Q8NGN4	O10G9_HUMAN	M	34	ENSP00000364164:V34M	ENSP00000364164:V34M	V	+	1	0	OR10G9	123399029	0.000000	0.05858	0.009000	0.14445	0.415000	0.31203	-1.724000	0.01865	0.212000	0.20703	0.655000	0.94253	GTG		0.572	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		A	123893819	G	A	123893819	3	1	47	1	0	0	0	0	1	0	0	0	10935	1145	40	1	102	1	OR10G9	11	123893819	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1155093	123893819	11112697	1340	5737										
OR8D2	283160	broad.mit.edu	37	chr11	124189273	124189273	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtgatgtagaacacagaaGacaccttctctttttccata	6	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:124189273G>T	ENST00000357438.2	-	1	911	c.821C>A	c.(820-822)tCt>tAt	p.S274Y		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	274						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S274Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		GAACACAGAAGACACCTTCTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											156	161	159					11																	124189273		2201	4299	6500	123694483	SO:0001583	missense	283160			AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"GPCR / Class A : Olfactory receptors"	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.821C>A	11.37:g.124189273G>T	ENSP00000350022:p.Ser274Tyr		123694483	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	.	.	.	.	.	.	.	.	.	.	g	12.43	1.935034	0.34189	.	.	ENSG00000197263	ENST00000357438	T	0.36878	1.23	3.34	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.45657	0.1353	L	0.48642	1.525	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.14420	-1.0473	10	0.72032	D	0.01	.	4.8806	0.13677	0.4023:0.0:0.5977:0.0	.	274	Q9GZM6	OR8D2_HUMAN	Y	274	ENSP00000350022:S274Y	ENSP00000350022:S274Y	S	-	2	0	OR8D2	123694483	0.000000	0.05858	0.119000	0.21687	0.784000	0.44337	0.119000	0.15626	1.005000	0.39183	0.530000	0.56133	TCT		0.428	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		T	124189273	G	T	124189273	3	4	47	1	0	0	0	0	1	0	0	0	11263	942	33	2	117	2	OR8D2	11	124189273	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	295454	124189273	10817243	1341	5738										
ROBO4	54538	broad.mit.edu	37	chr11	124765468	124765468	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaggcctccaagctctgcGctctgccagccggccagcag	13	16	2	0	rs534292971		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:124765468G>A	ENST00000306534.3	-	6	1406	c.921C>T	c.(919-921)agC>agT	p.S307S	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.S162S	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	307	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.S307S(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CAAGCTCTGCGCTCTGCCAGC	0.657													G|||	1	0.000199681	0	0	5008	,	,		14922	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	11											33	41	38					11																	124765468		2199	4291	6490	124270678	SO:0001819	synonymous_variant	54538			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.921C>T	11.37:g.124765468G>A			124270678	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																				0.657	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124765468	G	A	124765468	2	1	47	1	0	0	0	0	0	0	0	1	13553	1078	38	1		1	ROBO4	11	124765468	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	576195	124765468	10241048	1342	5739										
BARX2	8538	broad.mit.edu	37	chr11	129321108	129321108	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccatccccacatcagaagaGattgaagctgaagagaagat	9	9	1	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:129321108G>A	ENST00000281437.4	+	4	747	c.651G>A	c.(649-651)gaG>gaA	p.E217E	BARX2_ENST00000526127.1_Silent_p.E72E|BARX2_ENST00000531946.1_Silent_p.E95E	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	217					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	p.E217E(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		CATCAGAAGAGATTGAAGCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	11											77	66	70					11																	129321108		2201	4297	6498	128826318	SO:0001819	synonymous_variant	8538			AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"Homeoboxes / ANTP class : NKL subclass"	956	protein-coding gene	gene with protein product		604823	"BarH-like homeobox 2"			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.651G>A	11.37:g.129321108G>A			128826318	O43518|Q6NT51	Silent	SNP	ENST00000281437.4	37	CCDS8481.1																																																																																				0.517	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658		A	129321108	G	A	129321108	2	1	47	1	0	0	0	0	0	0	0	1	1317	933	33	3		3	BARX2	11	129321108	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4555640	129321108	5685408	1343	5740										
TMEM45B	120224	broad.mit.edu	37	chr11	129727340	129727340	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcattgtggccgtcaactatTctcttgtttactggtatgtc	9	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:129727340T>G	ENST00000524567.1	+	5	984	c.703T>G	c.(703-705)Tct>Gct	p.S235A	TMEM45B_ENST00000281441.3_Missense_Mutation_p.S235A			Q96B21	TM45B_HUMAN	transmembrane protein 45B	235						integral component of membrane (GO:0016021)		p.S235A(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		CGTCAACTATTCTCTTGTTTA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											233	177	196					11																	129727340		2201	4297	6498	129232550	SO:0001583	missense	120224			AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.703T>G	11.37:g.129727340T>G	ENSP00000436293:p.Ser235Ala		129232550	A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	37	CCDS8482.1	.	.	.	.	.	.	.	.	.	.	T	0.020	-1.436337	0.01108	.	.	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.42900	0.96;0.96	5.79	0.275	0.15659	.	0.575966	0.20730	N	0.086728	T	0.22975	0.0555	L	0.28400	0.85	0.23070	N	0.99834	B	0.02656	0.0	B	0.06405	0.002	T	0.21211	-1.0252	10	0.12103	T	0.63	-22.4141	6.2093	0.20619	0.3506:0.0:0.2403:0.4091	.	235	Q96B21	TM45B_HUMAN	A	235	ENSP00000281441:S235A;ENSP00000436293:S235A	ENSP00000281441:S235A	S	+	1	0	TMEM45B	129232550	0.001000	0.12720	0.099000	0.21106	0.068000	0.16541	-0.007000	0.12810	0.067000	0.16545	-0.336000	0.08194	TCT		0.488	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		G	129727340	T	G	129727340	3	3	47	1	0	0	0	0	1	0	0	0	16209	1783	62	4	717	4	TMEM45B	11	129727340	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	406232	129727340	5279176	1344	5741										
APLP2	334	broad.mit.edu	37	chr11	129979480	129979480	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaaacaaaagaagaagttCttcagtactgtcaggaggta	10	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:129979480C>A	ENST00000263574.5	+	2	334	c.262C>A	c.(262-264)Ctt>Att	p.L88I	APLP2_ENST00000345598.5_Missense_Mutation_p.L88I|APLP2_ENST00000543137.1_5'UTR|APLP2_ENST00000532456.1_3'UTR|APLP2_ENST00000528499.1_Missense_Mutation_p.L88I|APLP2_ENST00000338167.5_Missense_Mutation_p.L88I|APLP2_ENST00000539648.1_Intron|APLP2_ENST00000278756.7_Missense_Mutation_p.L98I	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	88					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.L88I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	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)		AGAAGAAGTTCTTCAGTACTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											95	87	90					11																	129979480		2201	4297	6498	129484690	SO:0001583	missense	334			L19597	CCDS8486.1, CCDS44773.1, CCDS44774.1, CCDS44775.1, CCDS58196.1	11q24	2008-02-05			ENSG00000084234	ENSG00000084234			598	protein-coding gene	gene with protein product		104776		APPL2		10702673	Standard	NM_001642		Approved	APPH	uc021qsg.1	Q06481	OTTHUMG00000165767	ENST00000263574.5:c.262C>A	11.37:g.129979480C>A	ENSP00000263574:p.Leu88Ile		129484690	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000263574.5	37	CCDS8486.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198147	0.94997	.	.	ENSG00000084234	ENST00000530416;ENST00000533195;ENST00000533713;ENST00000528499;ENST00000263574;ENST00000345598;ENST00000338167;ENST00000278756	D;D;D;D;D	0.97598	-4.45;-2.87;-4.22;-2.92;-2.91	5.93	5.93	0.95920	Amyloidogenic glycoprotein, extracellular (1);Amyloidogenic glycoprotein, heparin-binding (3);	0.000000	0.85682	D	0.000000	D	0.98890	0.9624	M	0.92317	3.295	0.80722	D	1	D;D;D;D;D	0.71674	0.994;0.993;0.998;0.993;0.997	D;D;D;D;D	0.91635	0.999;0.991;0.99;0.991;0.998	D	0.99441	1.0938	10	0.87932	D	0	-18.4285	19.3421	0.94347	0.0:1.0:0.0:0.0	.	88;88;88;88;88	Q06481;Q06481-2;Q06481-5;Q06481-4;Q06481-3	APLP2_HUMAN;.;.;.;.	I	35;113;73;88;88;88;88;98	ENSP00000435914:L88I;ENSP00000263574:L88I;ENSP00000263575:L88I;ENSP00000345444:L88I;ENSP00000278756:L98I	ENSP00000263574:L88I	L	+	1	0	APLP2	129484690	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.774000	0.68906	2.826000	0.97356	0.655000	0.94253	CTT		0.403	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	NM_001642		A	129979480	C	A	129979480	3	1	47	1	0	0	0	0	1	0	0	0	779	913	32	2	268	2	APLP2	11	129979480	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	252140	129979480	5027036	1345	5742										
ZBTB44	29068	broad.mit.edu	37	chr11	130131323	130131323	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaagtaaaattgcagttaGaattattttcttgtccagca	8	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:130131323G>T	ENST00000357899.4	-	2	718	c.446C>A	c.(445-447)tCt>tAt	p.S149Y	ZBTB44_ENST00000525842.1_Missense_Mutation_p.S149Y|ZBTB44_ENST00000530205.1_Missense_Mutation_p.S149Y|ZBTB44_ENST00000397753.1_Missense_Mutation_p.S149Y			Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S149Y(1)		autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		ATTGCAGTTAGAATTATTTTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	55	56					11																	130131323		1866	4114	5980	129636533	SO:0001583	missense	29068			AK024659	CCDS44776.1, CCDS73414.1, CCDS73415.1	11q24.3	2013-01-08	2006-09-19	2006-09-19		ENSG00000196323		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	25001	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 15"	BTBD15		11042152	Standard	NM_014155		Approved	HSPC063, ZNF851	uc001qgb.4	Q8NCP5		ENST00000357899.4:c.446C>A	11.37:g.130131323G>T	ENSP00000350574:p.Ser149Tyr		129636533	Q6IPT8|Q86VJ7|Q86XX5	Missense_Mutation	SNP	ENST00000357899.4	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	14.54|14.54|14.54	2.565573|2.565573|2.565573	0.45694|0.45694|0.45694	.|.|.	.|.|.	ENSG00000196323|ENSG00000196323|ENSG00000196323	ENST00000527478|ENST00000529982|ENST00000525842;ENST00000397753;ENST00000445008;ENST00000357899;ENST00000530205;ENST00000338191	.|.|T;T;T;T;T	.|.|0.53423	.|.|0.62;0.62;0.62;0.62;0.62	5.37|5.37|5.37	5.37|5.37|5.37	0.77165|0.77165|0.77165	.|.|.	.|.|0.225089	.|.|0.44483	.|.|D	.|.|0.000457	T|T|T	0.36331|0.36331|0.36331	0.0963|0.0963|0.0963	N|N|N	0.14661|0.14661|0.14661	0.345|0.345|0.345	0.37770|0.37770|0.37770	D|D|D	0.92664|0.92664|0.92664	.|.|B;B;B;B	.|.|0.31351	.|.|0.32;0.32;0.07;0.32	.|.|B;B;B;B	.|.|0.38056	.|.|0.264;0.176;0.058;0.264	T|T|T	0.47045|0.47045|0.47045	-0.9147|-0.9147|-0.9147	5|5|10	.|.|0.87932	.|.|D	.|.|0	.|.|.	12.4582|12.4582|12.4582	0.55716|0.55716|0.55716	0.0767:0.0:0.9233:0.0|0.0767:0.0:0.9233:0.0|0.0767:0.0:0.9233:0.0	.|.|.	.|.|149;149;149;149	.|.|Q8NCP5-4;Q8NCP5-3;Q8NCP5;Q8NCP5-2	.|.|.;.;ZBT44_HUMAN;.	L|I|Y	145|3|149;149;149;149;149;61	.|.|ENSP00000433457:S149Y;ENSP00000380861:S149Y;ENSP00000408079:S149Y;ENSP00000350574:S149Y;ENSP00000434177:S149Y	.|.|ENSP00000341618:S61Y	F|L|S	-|-|-	3|1|2	2|2|0	ZBTB44|ZBTB44|ZBTB44	129636533|129636533|129636533	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.650000|7.650000|7.650000	0.83521|0.83521|0.83521	2.509000|2.509000|2.509000	0.84616|0.84616|0.84616	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTA|TCT		0.458	ZBTB44-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000386126.1	NM_014155		T	130131323	G	T	130131323	3	4	47	1	0	0	0	0	1	0	0	0	17584	942	33	2	935	2	ZBTB44	11	130131323	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	151843	130131323	4875193	1346	5743										
SNX19	399979	broad.mit.edu	37	chr11	130749590	130749590	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggcatttgttcaccccaagAatttctactacgagatctga	7	11	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:130749590A>C	ENST00000265909.4	-	10	3344	c.2775T>G	c.(2773-2775)atT>atG	p.I925M	SNX19_ENST00000539184.1_Missense_Mutation_p.I368M|SNX19_ENST00000534726.1_Missense_Mutation_p.I165M|SNX19_ENST00000545537.1_Missense_Mutation_p.I165M|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000528555.1_Missense_Mutation_p.I305M|SNX19_ENST00000530356.1_Missense_Mutation_p.I305M|SNX19_ENST00000426933.2_Missense_Mutation_p.I93M	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	925					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.I925M(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TCACCCCAAGAATTTCTACTA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	80	81					11																	130749590		2201	4297	6498	130254800	SO:0001583	missense	399979			D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2775T>G	11.37:g.130749590A>C	ENSP00000265909:p.Ile925Met		130254800	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	A	4.967	0.179556	0.09443	.	.	ENSG00000120451	ENST00000265909;ENST00000534726;ENST00000545537;ENST00000426933;ENST00000528555;ENST00000530356;ENST00000539184	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	6.06	4.14	0.48551	Sorting nexin, C-terminal (1);	0.453272	0.24930	N	0.034479	T	0.20861	0.0502	L	0.42245	1.32	0.41655	D	0.989159	B;P	0.40000	0.029;0.698	B;B	0.35688	0.049;0.208	T	0.04752	-1.0929	10	0.23891	T	0.37	-11.3321	6.0556	0.19809	0.2156:0.1385:0.6459:0.0	.	368;925	F5H5D1;Q92543	.;SNX19_HUMAN	M	925;165;165;93;305;305;368	ENSP00000265909:I925M;ENSP00000433699:I165M;ENSP00000437982:I165M;ENSP00000413345:I93M;ENSP00000435122:I305M;ENSP00000432307:I305M;ENSP00000443480:I368M	ENSP00000265909:I925M	I	-	3	3	SNX19	130254800	1.000000	0.71417	0.972000	0.41901	0.171000	0.22731	1.510000	0.35790	0.828000	0.34709	-0.248000	0.11899	ATT		0.453	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		C	130749590	A	C	130749590	3	2	47	1	0	0	0	0	1	0	0	0	14927	242	9	4	211	4	SNX19	11	130749590	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	618267	130749590	4256926	1347	5744										
GLB1L3	112937	broad.mit.edu	37	chr11	134151327	134151327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaatttgacttctctgggaAcctggacctggagtatgtgg	12	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr11:134151327A>G	ENST00000431683.2	+	4	419	c.419A>G	c.(418-420)aAc>aGc	p.N140S	GLB1L3_ENST00000389887.5_Missense_Mutation_p.N140S	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	140					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)	p.N140S(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		TTCTCTGGGAACCTGGACCTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											229	224	226					11																	134151327		2201	4297	6498	133656537	SO:0001583	missense	112937				CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.419A>G	11.37:g.134151327A>G	ENSP00000396615:p.Asn140Ser		133656537	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.964408	0.53507	.	.	ENSG00000166105	ENST00000389887;ENST00000431683	D;D	0.97959	-4.63;-4.63	4.16	2.99	0.34606	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.96062	0.8717	M	0.71296	2.17	0.25779	N	0.984759	P;B	0.49961	0.93;0.447	P;B	0.45037	0.467;0.439	D	0.89717	0.3916	9	0.15499	T	0.54	.	7.6557	0.28373	0.8032:0.0:0.0:0.1968	.	140;140	Q8NCI6-4;Q8NCI6	.;GLBL3_HUMAN	S	140	ENSP00000374537:N140S;ENSP00000396615:N140S	ENSP00000374537:N140S	N	+	2	0	GLB1L3	133656537	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	5.810000	0.69179	0.714000	0.32081	0.459000	0.35465	AAC		0.512	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		G	134151327	A	G	134151327	3	3	47	1	0	0	0	0	1	0	0	0	6450	43	2	4	433	4	GLB1L3	11	134151327	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	3401737	134151327	855189	1348	5745										
WNK1	65125	broad.mit.edu	37	chr12	936297	936297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttcagtttcttcatactcGaactccacctatcattcacc	2	15	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:936297G>A	ENST00000315939.6	+	3	1665	c.1022G>A	c.(1021-1023)cGa>cAa	p.R341Q	WNK1_ENST00000537687.1_Missense_Mutation_p.R341Q|WNK1_ENST00000535572.1_Missense_Mutation_p.R341Q|WNK1_ENST00000530271.2_Missense_Mutation_p.R341Q|WNK1_ENST00000447667.2_Missense_Mutation_p.R341Q	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	341	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.R341Q(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CTTCATACTCGAACTCCACCT	0.443																																					Colon(19;451 567 6672 12618 28860)											1	Substitution - Missense(1)	large_intestine(1)	12											175	169	171					12																	936297		2203	4300	6503	806558	SO:0001583	missense	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1022G>A	12.37:g.936297G>A	ENSP00000313059:p.Arg341Gln		806558	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	37	5.990134	0.97179	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.54	5.54	0.83059	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49305	D	0.000151	T	0.72028	0.3410	L	0.31371	0.925	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.999;0.999	T	0.74945	-0.3491	10	0.87932	D	0	-9.5701	19.4859	0.95028	0.0:0.0:1.0:0.0	.	341;341;341	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	Q	341	ENSP00000441972:R341Q;ENSP00000313059:R341Q;ENSP00000444465:R341Q;ENSP00000392542:R341Q;ENSP00000433548:R341Q	ENSP00000313059:R341Q	R	+	2	0	WNK1	806558	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.617000	0.88574	0.591000	0.81541	CGA		0.443	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	936297	G	A	936297	3	1	47	1	0	0	0	0	1	0	0	0	17417	1058	37	1	1032	1	WNK1	12	936297	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09		936297	132915598	1349	5746										
RAD52	5893	broad.mit.edu	37	chr12	1023246	1023246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaccacaccatcccctgcatCgggagtcacagcccactttt	7	17	1	0	rs184776294		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:1023246C>T	ENST00000358495.3	-	11	1147	c.1009G>A	c.(1009-1011)Gat>Aat	p.D337N	RAD52_ENST00000539046.1_Missense_Mutation_p.D260N|RAD52_ENST00000430095.2_Missense_Mutation_p.D337N|RAD52_ENST00000535376.1_5'UTR	NM_134424.2	NP_602296.2	P43351	RAD52_HUMAN	RAD52 homolog (S. cerevisiae)	337					DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)	p.D337N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			TCCCCTGCATCGGGAGTCACA	0.502								Homologous recombination					C|||	1	0.000199681	0	0	5008	,	,		18661	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											95	89	91					12																	1023246		1929	4135	6064	893507	SO:0001583	missense	5893				CCDS8507.2	12p13-p12.2	2008-08-05	2001-11-28		ENSG00000002016	ENSG00000002016			9824	protein-coding gene	gene with protein product		600392	"RAD52 (S. cerevisiae) homolog"			7774919, 18313388	Standard	XM_005253721		Approved		uc001qis.1	P43351	OTTHUMG00000090361	ENST00000358495.3:c.1009G>A	12.37:g.1023246C>T	ENSP00000351284:p.Asp337Asn		893507	Q13205|Q9Y5T7|Q9Y5T8|Q9Y5T9	Missense_Mutation	SNP	ENST00000358495.3	37	CCDS8507.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	17.13	3.310127	0.60414	.	.	ENSG00000002016	ENST00000358495;ENST00000430095;ENST00000539046	T;T;T	0.37915	1.59;1.59;1.17	4.87	2.75	0.32379	.	0.321794	0.36444	N	0.002593	T	0.46034	0.1372	M	0.70275	2.135	0.09310	N	0.999991	D	0.71674	0.998	P	0.56216	0.794	T	0.30297	-0.9983	10	0.46703	T	0.11	-7.3799	6.3712	0.21483	0.0:0.6502:0.0:0.3498	.	337	P43351	RAD52_HUMAN	N	337;337;260	ENSP00000351284:D337N;ENSP00000387901:D337N;ENSP00000445245:D260N	ENSP00000351284:D337N	D	-	1	0	RAD52	893507	0.373000	0.25073	0.010000	0.14722	0.007000	0.05969	1.018000	0.30002	0.582000	0.29556	0.561000	0.74099	GAT		0.502	RAD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206733.2	NM_134424		T	1023246	C	T	1023246	3	4	47	1	0	0	0	0	1	0	0	0	13028	884	31	1	255	1	RAD52	12	1023246	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	86949	1023246	132828649	1350	5747										
AKAP3	10566	broad.mit.edu	37	chr12	4737263	4737263	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcaggcctttcctgccctcGaaacctctttctctcccgag	6	17	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:4737263G>A	ENST00000545990.2	-	5	1329	c.805C>T	c.(805-807)Cga>Tga	p.R269*	AKAP3_ENST00000228850.1_Nonsense_Mutation_p.R269*|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	269					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.R269*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TCCTGCCCTCGAAACCTCTTT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											85	79	81					12																	4737263		2203	4300	6503	4607524	SO:0001587	stop_gained	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.805C>T	12.37:g.4737263G>A	ENSP00000440994:p.Arg269*		4607524	O75945|Q86X01|Q9UM61	Nonsense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	32	5.114376	0.94339	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	.	.	.	4.98	-0.261	0.12963	.	0.521329	0.17868	N	0.159295	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3144	1.2545	0.01989	0.2632:0.0947:0.3415:0.3006	.	.	.	.	X	269	.	ENSP00000228850:R269X	R	-	1	2	AKAP3	4607524	0.000000	0.05858	0.000000	0.03702	0.342000	0.28953	0.160000	0.16462	0.125000	0.18397	0.655000	0.94253	CGA		0.438	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4737263	G	A	4737263	4	1	47	1	0	0	0	0	0	1	0	0	452	1066	37	1	1764	1	AKAP3	12	4737263	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3714017	4737263	129114632	1351	5748										
VWF	7450	broad.mit.edu	37	chr12	6105339	6105339	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgccagtcagcttgaaattCtgcccatcaaaggtcacgat	8	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:6105339C>T	ENST00000261405.5	-	35	6146	c.5892G>A	c.(5890-5892)caG>caA	p.Q1964Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1964	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.Q1964Q(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCTTGAAATTCTGCCCATCAA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											51	45	47					12																	6105339		2203	4300	6503	5975600	SO:0001819	synonymous_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.5892G>A	12.37:g.6105339C>T			5975600	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.532	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6105339	C	T	6105339	2	4	47	1	0	0	0	0	0	0	0	1	17286	912	32	3		3	VWF	12	6105339	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1368076	6105339	127746556	1352	5749										
VWF	7450	broad.mit.edu	37	chr12	6122676	6122676	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttgtggaggaaggaattgCccaaggtgaccatggtaggg	17	5	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:6122676C>T	ENST00000261405.5	-	32	5845	c.5591G>A	c.(5590-5592)gGc>gAc	p.G1864D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1864	VWFA 3; main binding site for collagens type I and III. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.G1864D(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAAGGAATTGCCCAAGGTGAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	12											96	98	98					12																	6122676		2203	4300	6503	5992937	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.5591G>A	12.37:g.6122676C>T	ENSP00000261405:p.Gly1864Asp		5992937	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	3.538	-0.094243	0.07053	.	.	ENSG00000110799	ENST00000261405	T	0.78003	-1.14	5.21	0.213	0.15244	von Willebrand factor, type A (1);	0.819332	0.10551	N	0.661457	T	0.61489	0.2351	L	0.28649	0.875	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.41052	-0.9530	10	0.12430	T	0.62	.	8.274	0.31862	0.0:0.4917:0.0:0.5083	.	1864	P04275	VWF_HUMAN	D	1864	ENSP00000261405:G1864D	ENSP00000261405:G1864D	G	-	2	0	VWF	5992937	0.019000	0.18553	0.006000	0.13384	0.890000	0.51754	0.194000	0.17135	0.132000	0.18615	0.650000	0.86243	GGC		0.488	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6122676	C	T	6122676	3	4	47	1	0	0	0	0	1	0	0	0	17286	739	26	3	2934	3	VWF	12	6122676	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	17337	6122676	127729219	1353	5750										
LTBR	4055	broad.mit.edu	37	chr12	6499319	6499319	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggaagctgggagcctccGaaggcccatccatacttccc	11	15	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:6499319G>A	ENST00000228918.4	+	9	1169	c.843G>A	c.(841-843)ccG>ccA	p.P281P	LTBR_ENST00000541102.1_Silent_p.P138P|LTBR_ENST00000539925.1_Silent_p.P262P	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	281					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.P281P(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						GGGAGCCTCCGAAGGCCCATC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	12											109	109	109					12																	6499319		2203	4300	6503	6369580	SO:0001819	synonymous_variant	4055			L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"Tumor necrosis factor receptor superfamily"	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.843G>A	12.37:g.6499319G>A			6369580	B7Z1D2|D3DUR2|F5GXE7	Silent	SNP	ENST00000228918.4	37	CCDS8544.1																																																																																				0.562	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			A	6499319	G	A	6499319	2	1	47	1	0	0	0	0	0	0	0	1	9106	1045	37	1		1	LTBR	12	6499319	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	376643	6499319	127352576	1354	5751										
NCAPD2	9918	broad.mit.edu	37	chr12	6626808	6626808	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgcagaaggagacccagaAattacaagagatgagggccc	12	9	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:6626808A>C	ENST00000315579.5	+	12	2166	c.1367A>C	c.(1366-1368)aAa>aCa	p.K456T	NCAPD2_ENST00000545962.1_Missense_Mutation_p.K411T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	456	Interactions with SMC2 and SMC4.				mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)	p.K456T(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						GAGACCCAGAAATTACAAGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											83	85	85					12																	6626808		2203	4300	6503	6497069	SO:0001583	missense	9918			D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.1367A>C	12.37:g.6626808A>C	ENSP00000325017:p.Lys456Thr		6497069	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.905909	0.92107	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.08634	3.07;3.07;3.07	5.49	5.49	0.81192	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.22898	0.0553	L	0.47190	1.495	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.999;0.953;0.999	T	0.00380	-1.1776	10	0.46703	T	0.11	-17.931	15.2855	0.73826	1.0:0.0:0.0:0.0	.	411;417;456	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	T	456;328;411;328	ENSP00000325017:K456T;ENSP00000371895:K328T;ENSP00000444417:K411T	ENSP00000325017:K456T	K	+	2	0	NCAPD2	6497069	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.240000	0.89813	2.090000	0.63153	0.459000	0.35465	AAA		0.473	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		C	6626808	A	C	6626808	3	2	47	1	0	0	0	0	1	0	0	0	10236	14	1	4	1409	4	NCAPD2	12	6626808	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	127489	6626808	127225087	1355	5752										
CHD4	1108	broad.mit.edu	37	chr12	6707237	6707237	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattcttccgctgatagtttCggaacatcacctgacagtgc	8	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:6707237C>T	ENST00000357008.2	-	12	1878	c.1715G>A	c.(1714-1716)cGa>cAa	p.R572Q	CHD4_ENST00000544484.1_Missense_Mutation_p.R569Q|CHD4_ENST00000309577.6_Missense_Mutation_p.R572Q|CHD4_ENST00000544040.1_Missense_Mutation_p.R565Q	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	572	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R572Q(2)		central_nervous_system(2)	2						CTGATAGTTTCGGAACATCAC	0.463																																					Colon(32;586 792 4568 16848 45314)											2	Substitution - Missense(2)	large_intestine(2)	12											131	132	132					12																	6707237		2203	4300	6503	6577498	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.1715G>A	12.37:g.6707237C>T	ENSP00000349508:p.Arg572Gln		6577498	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	31	5.085702	0.94100	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	4.21	4.21	0.49690	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.000000	0.85682	D	0.000000	D	0.86197	0.5875	M	0.88450	2.955	0.80722	D	1	D;D;D	0.76494	0.999;0.996;0.998	D;D;D	0.79784	0.993;0.953;0.979	D	0.89481	0.3750	10	0.72032	D	0.01	0.2404	16.7682	0.85529	0.0:1.0:0.0:0.0	.	572;572;565	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	Q	569;565;572;572;546	ENSP00000440392:R569Q;ENSP00000440542:R565Q;ENSP00000312419:R572Q;ENSP00000349508:R572Q	ENSP00000312419:R572Q	R	-	2	0	CHD4	6577498	1.000000	0.71417	0.994000	0.49952	0.908000	0.53690	7.625000	0.83145	2.176000	0.68965	0.467000	0.42956	CGA		0.463	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		T	6707237	C	T	6707237	3	4	47	1	0	0	0	0	1	0	0	0	3333	884	31	1	4139	1	CHD4	12	6707237	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	80429	6707237	127144658	1356	5753										
C1S	716	broad.mit.edu	37	chr12	7177456	7177456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggaagtcccagaaggacGaaccaattttgataatgaca	10	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:7177456G>A	ENST00000406697.1	+	15	2196	c.1568G>A	c.(1567-1569)cGa>cAa	p.R523Q	C1S_ENST00000495061.1_3'UTR|C1S_ENST00000360817.5_Missense_Mutation_p.R523Q|C1S_ENST00000328916.3_Missense_Mutation_p.R523Q|C1S_ENST00000402681.3_Missense_Mutation_p.R356Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	523	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)	p.R523Q(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	CCAGAAGGACGAACCAATTTT	0.527																																					GBM(156;750 1943 12971 24779 31015)											1	Substitution - Missense(1)	large_intestine(1)	12											61	60	61					12																	7177456		2203	4300	6503	7047717	SO:0001583	missense	716				CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1568G>A	12.37:g.7177456G>A	ENSP00000385035:p.Arg523Gln		7047717	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.382949	0.42207	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02	5.16	5.16	0.70880	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.36519	N	0.002555	T	0.57562	0.2062	N	0.12920	0.275	0.09310	N	1	B	0.29805	0.257	B	0.23150	0.044	T	0.41875	-0.9484	10	0.12766	T	0.61	.	12.198	0.54309	0.0774:0.0:0.9226:0.0	.	523	P09871	C1S_HUMAN	Q	523;523;523;517;356	ENSP00000385035:R523Q;ENSP00000328173:R523Q;ENSP00000354057:R523Q;ENSP00000384171:R356Q	ENSP00000328173:R523Q	R	+	2	0	C1S	7047717	0.026000	0.19158	0.050000	0.19076	0.041000	0.13682	-0.031000	0.12287	2.676000	0.91093	0.561000	0.74099	CGA		0.527	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		A	7177456	G	A	7177456	3	1	47	1	0	0	0	0	1	0	0	0	1980	1058	37	1	1610	1	C1S	12	7177456	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	470219	7177456	126674439	1357	5754										
CD163	9332	broad.mit.edu	37	chr12	7637787	7637787	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgtgtcaggtccttttggaCactgaacattgtccacccac	9	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:7637787C>A	ENST00000359156.4	-	11	2886	c.2684G>T	c.(2683-2685)tGt>tTt	p.C895F	CD163_ENST00000539632.1_5'UTR|CD163_ENST00000396620.3_Missense_Mutation_p.C928F|CD163_ENST00000541972.1_Missense_Mutation_p.C883F|CD163_ENST00000432237.2_Missense_Mutation_p.C895F	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	895	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.C895F(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	TCCTTTTGGACACTGAACATT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	114	115					12																	7637787		2203	4300	6503	7529054	SO:0001583	missense	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.2684G>T	12.37:g.7637787C>A	ENSP00000352071:p.Cys895Phe		7529054	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.305432	0.40795	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.54	5.54	0.83059	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.49916	D	0.000133	D	0.90051	0.6893	H	0.97415	4	0.48975	D	0.999736	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.991;0.999	D	0.93052	0.6466	10	0.87932	D	0	.	17.3432	0.87303	0.0:1.0:0.0:0.0	.	928;895;895	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	F	895;883;928;895	ENSP00000352071:C895F;ENSP00000444071:C883F;ENSP00000379863:C928F;ENSP00000403885:C895F	ENSP00000352071:C895F	C	-	2	0	CD163	7529054	1.000000	0.71417	0.975000	0.42487	0.009000	0.06853	6.475000	0.73582	2.776000	0.95493	0.650000	0.86243	TGT		0.552	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7637787	C	A	7637787	3	1	47	1	0	0	0	0	1	0	0	0	2973	478	17	2	810	2	CD163	12	7637787	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	460331	7637787	126214108	1358	5755										
CLEC4A	50856	broad.mit.edu	37	chr12	8278246	8278246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatatttttcctgctattgGcaatctcattctttattgct	5	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:8278246G>A	ENST00000229332.5	+	2	419	c.172G>A	c.(172-174)Gca>Aca	p.A58T	CLEC4A_ENST00000345999.3_Intron|CLEC4A_ENST00000352620.3_Missense_Mutation_p.A58T|CLEC4A_ENST00000360500.3_Intron	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	58					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.A58T(1)		cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		CCTGCTATTGGCAATCTCATT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											199	160	174					12																	8278246		2203	4300	6503	8169513	SO:0001583	missense	50856			AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"C-type lectin domain containing"	13257	protein-coding gene	gene with protein product		605306	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.172G>A	12.37:g.8278246G>A	ENSP00000229332:p.Ala58Thr		8169513	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	CCDS8590.1	.	.	.	.	.	.	.	.	.	.	G	8.005	0.756259	0.15846	.	.	ENSG00000111729	ENST00000229332;ENST00000352620;ENST00000546339	T;T;T	0.58210	5.34;2.29;0.35	3.89	-0.0773	0.13719	.	.	.	.	.	T	0.31009	0.0783	L	0.33485	1.01	0.19945	N	0.99994	B;B	0.29805	0.016;0.257	B;B	0.26614	0.018;0.071	T	0.25117	-1.0141	9	0.05620	T	0.96	.	6.4161	0.21717	0.4457:0.0:0.5543:0.0	.	58;58	Q9UMR7-2;Q9UMR7	.;CLC4A_HUMAN	T	58;58;47	ENSP00000229332:A58T;ENSP00000247243:A58T;ENSP00000443082:A47T	ENSP00000229332:A58T	A	+	1	0	CLEC4A	8169513	0.023000	0.18921	0.189000	0.23252	0.706000	0.40770	-0.027000	0.12371	-0.016000	0.14127	0.655000	0.94253	GCA		0.413	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450		A	8278246	G	A	8278246	3	1	47	1	0	0	0	0	1	0	0	0	3518	1203	42	3	178	3	CLEC4A	12	8278246	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	640459	8278246	125573649	1359	5756										
FAM90A1	55138	broad.mit.edu	37	chr12	8374495	8374495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggacgcttggtgggacacGaacacagggaccctcagact	14	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:8374495G>A	ENST00000538603.1	-	7	1876	c.1318C>T	c.(1318-1320)Cgt>Tgt	p.R440C	FAM90A1_ENST00000307435.6_Missense_Mutation_p.R440C|RP11-266K4.1_ENST00000542600.1_RNA	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	440							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R440C(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		GGTGGGACACGAACACAGGGA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											36	48	43					12																	8374495		1701	3195	4896	8265762	SO:0001583	missense	55138			AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1318C>T	12.37:g.8374495G>A	ENSP00000445418:p.Arg440Cys		8265762	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	5.039	0.192941	0.09599	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.15372	2.43;2.43	1.06	-0.159	0.13379	.	.	.	.	.	T	0.06142	0.0159	N	0.02802	-0.49	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.33085	-0.9882	9	0.54805	T	0.06	0.1514	3.8781	0.09066	0.0:0.0:0.5819:0.4181	.	440	Q86YD7	F90A1_HUMAN	C	440	ENSP00000307798:R440C;ENSP00000445418:R440C	ENSP00000307798:R440C	R	-	1	0	FAM90A1	8265762	0.002000	0.14202	0.000000	0.03702	0.009000	0.06853	-0.631000	0.05496	-0.054000	0.13266	0.205000	0.17691	CGT		0.602	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		A	8374495	G	A	8374495	3	1	47	1	0	0	0	0	1	0	0	0	5669	1058	37	1	80	1	FAM90A1	12	8374495	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	96249	8374495	125477400	1360	5757										
AICDA	57379	broad.mit.edu	37	chr12	8757906	8757906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcacagaagtagaggcgcGcggtgaagatcctcagactg	13	11	2	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:8757906G>A	ENST00000229335.6	-	3	435	c.332C>T	c.(331-333)gCg>gTg	p.A111V	AICDA_ENST00000537228.1_Missense_Mutation_p.A111V	NM_020661.2	NP_065712.1	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	111	Required for interaction with RNF126. {ECO:0000269|PubMed:23277564}.				B cell differentiation (GO:0030183)|cellular response to lipopolysaccharide (GO:0071222)|DNA demethylation (GO:0080111)|isotype switching (GO:0045190)|mRNA processing (GO:0006397)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|somatic diversification of immunoglobulins (GO:0016445)|somatic hypermutation of immunoglobulin genes (GO:0016446)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A111V(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)	16	Lung SC(5;0.184)					GTAGAGGCGCGCGGTGAAGAT	0.637																																					GBM(62;896 1067 5527 26594 30137)											1	Substitution - Missense(1)	large_intestine(1)	12	GRCh37	CM064963	AICDA	M							31	34	33					12																	8757906		1987	4158	6145	8649173	SO:0001583	missense	57379			AB040430	CCDS41747.1	12p13	2014-09-17			ENSG00000111732	ENSG00000111732		"Apolipoprotein B mRNA editing enzymes"	13203	protein-coding gene	gene with protein product		605257					Standard	NM_020661		Approved	HIGM2, CDA2, ARP2, AID	uc001qur.2	Q9GZX7	OTTHUMG00000168676	ENST00000229335.6:c.332C>T	12.37:g.8757906G>A	ENSP00000229335:p.Ala111Val		8649173	Q6QJ81|Q8NFC1	Missense_Mutation	SNP	ENST00000229335.6	37	CCDS41747.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.712088|5.712088	0.96830|0.96830	.|.	.|.	ENSG00000111732|ENSG00000111732	ENST00000229335;ENST00000537228|ENST00000543081;ENST00000545512	T;T|.	0.67171|.	-0.25;-0.25|.	5.45|5.45	5.45|5.45	0.79879|0.79879	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);|.	0.049216|.	0.85682|.	D|.	0.000000|.	T|T	0.77605|0.77605	0.4155|0.4155	M|M	0.79258|0.79258	2.445|2.445	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.61080|.	0.989;0.989;0.989|.	P;P;P|.	0.56751|.	0.751;0.805;0.805|.	T|T	0.78026|0.78026	-0.2365|-0.2365	10|5	0.87932|.	D|.	0|.	-18.2239|-18.2239	17.8461|17.8461	0.88730|0.88730	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	111;111;111|.	Q9GZX7;Q6QJ80;Q6QJ81|.	AICDA_HUMAN;.;.|.	V|C	111|110	ENSP00000229335:A111V;ENSP00000445691:A111V|.	ENSP00000229335:A111V|.	A|R	-|-	2|1	0|0	AICDA|AICDA	8649173|8649173	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.186000|9.186000	0.94906|0.94906	2.554000|2.554000	0.86153|0.86153	0.561000|0.561000	0.74099|0.74099	GCG|CGC		0.637	AICDA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400575.1	NM_020661		A	8757906	G	A	8757906	3	1	47	1	0	0	0	0	1	0	0	0	422	1087	38	1	276	1	AICDA	12	8757906	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	383411	8757906	125093989	1361	5758										
CD69	969	broad.mit.edu	37	chr12	9908983	9908983	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacttggaaggacccttcatGacgtgttgagaaatggggac	13	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:9908983G>T	ENST00000228434.3	-	2	177	c.97C>A	c.(97-99)Cat>Aat	p.H33N	CD69_ENST00000536709.1_Missense_Mutation_p.H33N	NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	33					cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.H33N(1)		endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						GACCCTTCATGACGTGTTGAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											161	140	147					12																	9908983		2203	4300	6503	9800250	SO:0001583	missense	969			Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"C-type lectin domain containing", "CD molecules"	1694	protein-coding gene	gene with protein product		107273	"CD69 antigen (p60, early T-cell activation antigen)"			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.97C>A	12.37:g.9908983G>T	ENSP00000228434:p.His33Asn		9800250		Missense_Mutation	SNP	ENST00000228434.3	37	CCDS8604.1	.	.	.	.	.	.	.	.	.	.	G	8.775	0.926945	0.18056	.	.	ENSG00000110848	ENST00000228434;ENST00000536709	T;T	0.01560	5.1;4.77	4.43	3.53	0.40419	.	0.948337	0.08779	N	0.895082	T	0.02929	0.0087	L	0.50333	1.59	0.09310	N	1	B;B	0.26708	0.157;0.079	B;B	0.34301	0.179;0.032	T	0.41233	-0.9520	9	.	.	.	-1.698	7.6019	0.28081	0.1129:0.0:0.8871:0.0	.	33;33	B4E0H7;Q07108	.;CD69_HUMAN	N	33	ENSP00000228434:H33N;ENSP00000442597:H33N	.	H	-	1	0	CD69	9800250	0.005000	0.15991	0.053000	0.19242	0.004000	0.04260	1.556000	0.36288	2.462000	0.83206	0.655000	0.94253	CAT		0.438	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1			T	9908983	G	T	9908983	3	4	47	1	0	0	0	0	1	0	0	0	3037	1290	45	2	518	2	CD69	12	9908983	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1151077	9908983	123942912	1362	5759										
OLR1	4973	broad.mit.edu	37	chr12	10324613	10324613	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctagtacctttagctttttTtccatttgacttctcatcag	4	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:10324613T>A	ENST00000309539.3	-	1	124	c.64A>T	c.(64-66)Aaa>Taa	p.K22*	TMEM52B_ENST00000381923.2_Intron|TMEM52B_ENST00000545924.1_Intron|OLR1_ENST00000545927.1_Nonsense_Mutation_p.K22*|OLR1_ENST00000432556.2_Nonsense_Mutation_p.K22*|OLR1_ENST00000544577.1_Nonsense_Mutation_p.K22*	NM_002543.3	NP_002534.1	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like) receptor 1	22					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell death (GO:0008219)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|lipoprotein metabolic process (GO:0042157)|proteolysis (GO:0006508)|response to hydrogen peroxide (GO:0042542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|low-density lipoprotein receptor activity (GO:0005041)	p.K22*(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TTAGCTTTTTTTCCATTTGAC	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											171	143	152					12																	10324613		2203	4300	6503	10215880	SO:0001587	stop_gained	4973			D89050	CCDS8618.1, CCDS53745.1, CCDS53746.1	12p13.1-p12.3	2011-08-30	2006-12-07		ENSG00000173391	ENSG00000173391		"C-type lectin domain containing"	8133	protein-coding gene	gene with protein product		602601	"oxidised low density lipoprotein (lectin-like) receptor 1"			9763655	Standard	NM_002543		Approved	LOX-1, SCARE1, CLEC8A	uc001qxo.1	P78380	OTTHUMG00000168527	ENST00000309539.3:c.64A>T	12.37:g.10324613T>A	ENSP00000309124:p.Lys22*		10215880	A8K7V9|B4DI48|G3V1I4|Q2PP00|Q7Z484	Nonsense_Mutation	SNP	ENST00000309539.3	37	CCDS8618.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848496	0.71603	.	.	ENSG00000173391	ENST00000309539;ENST00000544577;ENST00000545927;ENST00000432556	.	.	.	4.09	-1.7	0.08159	.	0.694331	0.13175	N	0.407952	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.515	0.16902	0.0:0.1648:0.1756:0.6596	.	.	.	.	X	22	.	ENSP00000309124:K22X	K	-	1	0	OLR1	10215880	0.000000	0.05858	0.003000	0.11579	0.928000	0.56348	-0.974000	0.03794	-0.324000	0.08589	0.477000	0.44152	AAA		0.403	OLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400091.1	NM_002543		A	10324613	T	A	10324613	4	1	47	1	0	0	0	0	0	1	0	0	10894	1850	64	5	781	5	OLR1	12	10324613	Nonsense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	415630	10324613	123527282	1363	5760										
TAS2R10	50839	broad.mit.edu	37	chr12	10978130	10978130	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgcacagtaaaacatgataTttctatggccatgcctataa	6	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:10978130T>G	ENST00000240619.2	-	1	827	c.739A>C	c.(739-741)Ata>Cta	p.I247L		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	247					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.I247V(1)|p.I247L(1)		breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						AAACATGATATTTCTATGGCC	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											104	102	103					12																	10978130		2203	4300	6503	10869397	SO:0001583	missense	50839			AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.739A>C	12.37:g.10978130T>G	ENSP00000240619:p.Ile247Leu		10869397	Q3MIM9|Q6NTD9	Missense_Mutation	SNP	ENST00000240619.2	37	CCDS8634.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.438524	0.25900	.	.	ENSG00000121318	ENST00000240619	T	0.00753	5.74	4.04	-2.67	0.06059	.	0.640097	0.12626	N	0.452612	T	0.01189	0.0039	M	0.81942	2.565	0.09310	N	1	B	0.18741	0.03	B	0.29663	0.105	T	0.41627	-0.9498	10	0.30078	T	0.28	.	3.1554	0.06503	0.4674:0.2365:0.0:0.2961	.	247	Q9NYW0	T2R10_HUMAN	L	247	ENSP00000240619:I247L	ENSP00000240619:I247L	I	-	1	0	TAS2R10	10869397	0.000000	0.05858	0.007000	0.13788	0.064000	0.16182	-5.237000	0.00138	-0.573000	0.05998	0.477000	0.44152	ATA		0.378	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			G	10978130	T	G	10978130	3	3	47	1	0	0	0	0	1	0	0	0	15605	1493	52	4	188	4	TAS2R10	12	10978130	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	653517	10978130	122873765	1364	5761										
LRP6	4040	broad.mit.edu	37	chr12	12317235	12317235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatatcagtccaataaattCggttgtctgtcacatcaaaa	5	8	4	0	rs376188127		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:12317235C>T	ENST00000261349.4	-	9	2100	c.2024G>A	c.(2023-2025)cGa>cAa	p.R675Q	LRP6_ENST00000543091.1_Missense_Mutation_p.R675Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	675	Beta-propeller 3.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R675Q(3)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CCAATAAATTCGGTTGTCTGT	0.358																																																3	Substitution - Missense(3)	large_intestine(3)	12						C	GLN/ARG	1,4403	2.1+/-5.4	0,1,2201	85	87	86		2024	5.4	1	12		86	0,8600		0,0,4300	no	missense	LRP6	NM_002336.2	43	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	675/1614	12317235	1,13003	2202	4300	6502	12208502	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.2024G>A	12.37:g.12317235C>T	ENSP00000261349:p.Arg675Gln		12208502	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132673	0.94517	2.27E-4	0.0	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96802	-4.13;-4.13	5.41	5.41	0.78517	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.50627	U	0.000115	D	0.97785	0.9273	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.941	D	0.96857	0.9629	10	0.31617	T	0.26	.	19.571	0.95419	0.0:1.0:0.0:0.0	.	675;675	F5H7J9;O75581	.;LRP6_HUMAN	Q	675	ENSP00000261349:R675Q;ENSP00000442472:R675Q	ENSP00000261349:R675Q	R	-	2	0	LRP6	12208502	1.000000	0.71417	0.966000	0.40874	0.987000	0.75469	6.013000	0.70776	2.709000	0.92574	0.655000	0.94253	CGA		0.358	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12317235	C	T	12317235	3	4	47	1	0	0	0	0	1	0	0	0	8991	884	31	1	2877	1	LRP6	12	12317235	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1339105	12317235	121534660	1365	5762										
CDKN1B	1027	broad.mit.edu	37	chr12	12871797	12871797	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagagccaacagaacagaaGaaaatgtttcagacggttcc	9	8	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:12871797G>T	ENST00000228872.4	+	2	1230	c.514G>T	c.(514-516)Gaa>Taa	p.E172*	CDKN1B_ENST00000396340.1_Intron|CDKN1B_ENST00000477087.1_3'UTR	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	172					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)	p.E172*(1)		breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CAGAACAGAAGAAAATGTTTC	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	12	GRCh37	CM023042	CDKN1B	M							82	94	90					12																	12871797		2203	4300	6503	12763064	SO:0001587	stop_gained	1027			AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.514G>T	12.37:g.12871797G>T	ENSP00000228872:p.Glu172*		12763064	Q16307|Q5U0H2|Q9BUS6	Nonsense_Mutation	SNP	ENST00000228872.4	37	CCDS8653.1	.	.	.	.	.	.	.	.	.	.	G	44	11.050420	0.99508	.	.	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000442489	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	16.7715	0.85538	0.0:0.0:1.0:0.0	.	.	.	.	X	172;121;78	.	ENSP00000228872:E172X	E	+	1	0	CDKN1B	12763064	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.218000	0.72224	2.384000	0.81235	0.655000	0.94253	GAA		0.438	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		T	12871797	G	T	12871797	4	4	47	1	0	0	0	0	0	1	0	0	3165	943	33	2	520	2	CDKN1B	12	12871797	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	554562	12871797	120980098	1366	5763										
GUCY2C	2984	broad.mit.edu	37	chr12	14778806	14778806	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatagctgtagacgtcggaTcaaggtatccatatagcttt	9	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:14778806T>G	ENST00000261170.3	-	21	2429	c.2293A>C	c.(2293-2295)Atc>Ctc	p.I765L		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	765					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)	p.I765L(1)		breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	AGACGTCGGATCAAGGTATCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											146	134	138					12																	14778806		2203	4300	6503	14670073	SO:0001583	missense	2984				CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2293A>C	12.37:g.14778806T>G	ENSP00000261170:p.Ile765Leu		14670073	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	37	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	T	13.82	2.351032	0.41599	.	.	ENSG00000070019	ENST00000261170	T	0.61392	0.11	5.31	5.31	0.75309	Protein kinase-like domain (1);	0.045766	0.85682	D	0.000000	T	0.41903	0.1179	N	0.25825	0.765	0.80722	D	1	P	0.36990	0.577	B	0.37091	0.241	T	0.39800	-0.9596	10	0.02654	T	1	.	15.5703	0.76330	0.0:0.0:0.0:1.0	.	765	P25092	GUC2C_HUMAN	L	765	ENSP00000261170:I765L	ENSP00000261170:I765L	I	-	1	0	GUCY2C	14670073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.943000	0.87716	2.138000	0.66242	0.460000	0.39030	ATC		0.388	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			G	14778806	T	G	14778806	3	3	47	1	0	0	0	0	1	0	0	0	6917	1435	50	4	956	4	GUCY2C	12	14778806	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1907009	14778806	119073089	1367	5764										
ART4	420	broad.mit.edu	37	chr12	14993959	14993959	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgccacatcctaaaataattCttctgggcttctatgtcttt	5	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:14993959C>A	ENST00000228936.4	-	2	654	c.273G>T	c.(271-273)aaG>aaT	p.K91N	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	91					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)	p.K91N(1)		large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						TAAAATAATTCTTCTGGGCTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											121	118	119					12																	14993959		2203	4300	6503	14885226	SO:0001583	missense	420			X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"CD molecules", "Blood group antigens"	726	protein-coding gene	gene with protein product		110600	"Dombrock blood group", "ADP-ribosyltransferase 4 (DO blood group)", "ADP-ribosyltransferase 4"	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.273G>T	12.37:g.14993959C>A	ENSP00000228936:p.Lys91Asn		14885226	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	37	CCDS8668.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315457	0.23908	.	.	ENSG00000111339	ENST00000228936;ENST00000420600	T;T	0.09538	2.97;2.97	4.35	-1.91	0.07641	.	0.792671	0.12321	N	0.479297	T	0.22704	0.0548	M	0.74881	2.28	0.09310	N	1	D;D	0.60575	0.988;0.988	P;P	0.60886	0.88;0.88	T	0.07366	-1.0776	10	0.87932	D	0	-11.297	5.9255	0.19110	0.0:0.4653:0.1287:0.406	.	91;91	A8K6J7;Q93070	.;NAR4_HUMAN	N	91;74	ENSP00000228936:K91N;ENSP00000405689:K74N	ENSP00000228936:K91N	K	-	3	2	ART4	14885226	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.940000	0.03929	-0.372000	0.07992	0.563000	0.77884	AAG		0.423	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071		A	14993959	C	A	14993959	3	1	47	1	0	0	0	0	1	0	0	0	1000	912	32	2	679	2	ART4	12	14993959	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	215153	14993959	118857936	1368	5765										
GYS2	2998	broad.mit.edu	37	chr12	21733292	21733292	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttacctggcagccatgcttaTtcattgcgtccactgctctt	7	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:21733292T>A	ENST00000261195.2	-	2	541	c.287A>T	c.(286-288)aAt>aTt	p.N96I		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	96					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.N96I(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GCCATGCTTATTCATTGCGTC	0.398																																					Colon(149;9 1820 3690 10544 50424)											1	Substitution - Missense(1)	large_intestine(1)	12											205	185	192					12																	21733292		2203	4300	6503	21624559	SO:0001583	missense	2998				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.287A>T	12.37:g.21733292T>A	ENSP00000261195:p.Asn96Ile		21624559	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.847413	0.32606	.	.	ENSG00000111713	ENST00000261195	T	0.64438	-0.1	5.16	4.01	0.46588	.	0.230543	0.42682	D	0.000674	T	0.48095	0.1481	L	0.29908	0.895	0.26533	N	0.974223	B	0.06786	0.001	B	0.15484	0.013	T	0.46693	-0.9173	10	0.66056	D	0.02	-30.4523	8.8592	0.35247	0.0:0.1511:0.0:0.8489	.	96	P54840	GYS2_HUMAN	I	96	ENSP00000261195:N96I	ENSP00000261195:N96I	N	-	2	0	GYS2	21624559	0.927000	0.31430	0.991000	0.47740	0.917000	0.54804	1.512000	0.35812	0.981000	0.38548	0.460000	0.39030	AAT		0.398	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		A	21733292	T	A	21733292	3	1	47	1	0	0	0	0	1	0	0	0	6934	1493	52	5	1884	5	GYS2	12	21733292	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	6739333	21733292	112118603	1369	5766										
CASC1	55259	broad.mit.edu	37	chr12	25276189	25276189	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttcatctctcgttcacatTttatggcttcagattcttcc	4	12	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:25276189T>G	ENST00000320267.9	-	9	1097	c.1016A>C	c.(1015-1017)aAa>aCa	p.K339T	CASC1_ENST00000545133.1_Missense_Mutation_p.K280T|CASC1_ENST00000395990.2_Missense_Mutation_p.K299T|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000537577.1_Missense_Mutation_p.K227T|CASC1_ENST00000395987.3_Missense_Mutation_p.K345T|CASC1_ENST00000354189.5_Missense_Mutation_p.K403T	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	339								p.K345T(1)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	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)			TCGTTCACATTTTATGGCTTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											82	74	76					12																	25276189		2201	4297	6498	25167456	SO:0001583	missense	55259			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.1016A>C	12.37:g.25276189T>G	ENSP00000313141:p.Lys339Thr		25167456	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.761|9.761	1.170051|1.170051	0.21621|0.21621	.|.	.|.	ENSG00000118307|ENSG00000118307	ENST00000556006|ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000395992;ENST00000545133;ENST00000389246	.|T;T;T;T;T	.|0.49432	.|0.78;1.39;1.39;0.8;0.8	3.66|3.66	2.51|2.51	0.30379|0.30379	.|Casc1 domain (1);	0.458477|0.458477	0.21625|0.21625	N|N	0.071562|0.071562	T|T	0.47414|0.47414	0.1444|0.1444	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	.|P;P;D;P;P	.|0.56521	.|0.763;0.873;0.976;0.801;0.763	.|P;P;P;B;B	.|0.54140	.|0.463;0.544;0.743;0.355;0.242	T|T	0.25572|0.25572	-1.0128|-1.0128	6|10	.|0.31617	.|T	.|0.26	-19.4064|-19.4064	5.7558|5.7558	0.18172|0.18172	0.0:0.1216:0.0:0.8784|0.0:0.1216:0.0:0.8784	.|.	.|227;280;403;339;345	.|F5H555;F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9	.|.;.;.;CASC1_HUMAN;.	N|T	175|403;345;339;299;227;345;280;149	.|ENSP00000346126:K403T;ENSP00000379310:K345T;ENSP00000313141:K339T;ENSP00000379313:K299T;ENSP00000437373:K280T	.|ENSP00000313141:K339T	K|K	-|-	3|2	2|0	CASC1|CASC1	25167456|25167456	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.076000|0.076000	0.17211|0.17211	0.779000|0.779000	0.26746|0.26746	0.770000|0.770000	0.33336|0.33336	0.528000|0.528000	0.53228|0.53228	AAA|AAA		0.323	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		G	25276189	T	G	25276189	3	3	47	1	0	0	0	0	1	0	0	0	2666	1841	64	4	1162	4	CASC1	12	25276189	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3542897	25276189	108575706	1370	5767										
KRAS	3845	broad.mit.edu	37	chr12	25378706	25378706	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaactcttttaatttgttCtctgggaaagaaaaaaaagt	6	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:25378706C>A	ENST00000256078.4	-	4	355	c.292G>T	c.(292-294)Gaa>Taa	p.E98*	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Splice_Site_p.E98*|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	98					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.E98*(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TTAATTTGTTCTCTGGGAAAG	0.338		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	1	Substitution - Nonsense(1)	large_intestine(1)	12											67	68	68					12																	25378706		2202	4299	6501	25269973	SO:0001630	splice_region_variant	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.291-1G>T	12.37:g.25378706C>A			25269973	A8K8Z5|B0LPF9|P01118|Q96D10	Nonsense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	34	5.365235	0.95877	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1236	0.93374	0.0:1.0:0.0:0.0	.	.	.	.	X	98	.	ENSP00000256078:E98X	E	-	1	0	KRAS	25269973	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.763000	0.85283	2.833000	0.97629	0.585000	0.79938	GAA		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	Nonsense_Mutation	A	25378706	C	A	25378706	5	1	47	1	0	0	0	0	0	0	1	0	8459	927	32	2	406	2	KRAS	12	25378706	Splice_Site	SNP	C	TCGA-AG-3892-01A-01W-1073-09	102517	25378706	108473189	1371	5768										
RASSF8	11228	broad.mit.edu	37	chr12	26208285	26208285	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccggtgcaccatggaactTaaagtatgggtggatggagt	16	6	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:26208285T>C	ENST00000405154.2	+	2	208	c.9T>C	c.(7-9)ctT>ctC	p.L3L	RASSF8_ENST00000541490.1_Silent_p.L3L|RASSF8_ENST00000282884.9_Silent_p.L3L|RASSF8_ENST00000381352.3_Silent_p.L3L|RASSF8_ENST00000542865.1_Silent_p.L3L	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	3	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)			p.L3L(1)		cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					CCATGGAACTTAAAGTATGGG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	12											190	156	167					12																	26208285		2203	4300	6503	26099552	SO:0001819	synonymous_variant	11228			U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"chromosome 12 open reading frame 2"	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.9T>C	12.37:g.26208285T>C			26099552	A8K1Z0|O95647|Q5SCI2|Q76KB6	Silent	SNP	ENST00000405154.2	37	CCDS53765.1																																																																																				0.502	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211		C	26208285	T	C	26208285	2	2	47	1	0	0	0	0	0	0	0	1	13129	1741	61	4		4	RASSF8	12	26208285	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	829579	26208285	107643610	1372	5769										
ITPR2	3709	broad.mit.edu	37	chr12	26811002	26811002	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cataaatttacagatgagttCttgagttacagggatagcag	10	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:26811002C>A	ENST00000381340.3	-	17	2364	c.1948G>T	c.(1948-1950)Gaa>Taa	p.E650*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	650					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.E650*(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CAGATGAGTTCTTGAGTTACA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											105	98	100					12																	26811002		1856	4099	5955	26702269	SO:0001587	stop_gained	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1948G>T	12.37:g.26811002C>A	ENSP00000370744:p.Glu650*		26702269	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	44	11.020178	0.99503	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	18.071	0.89407	0.0:1.0:0.0:0.0	.	.	.	.	X	650	.	ENSP00000370744:E650X	E	-	1	0	ITPR2	26702269	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.638000	0.83328	2.495000	0.84180	0.655000	0.94253	GAA		0.343	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26811002	C	A	26811002	4	1	47	1	0	0	0	0	0	1	0	0	7942	922	32	2	6321	2	ITPR2	12	26811002	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	602717	26811002	107040893	1373	5770										
TMTC1	83857	broad.mit.edu	37	chr12	29908642	29908642	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaactgtaaaatgacttacGacttgtcttgcttgttggaa	8	6	1	1	rs143546206		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:29908642G>A	ENST00000539277.1	-	4	789	c.731C>T	c.(730-732)tCg>tTg	p.S244L	TMTC1_ENST00000256062.5_Splice_Site_p.S136L|TMTC1_ENST00000551659.1_Splice_Site_p.S244L|TMTC1_ENST00000552618.1_Splice_Site_p.S244L|TMTC1_ENST00000381224.2_Splice_Site_p.S136L	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	244						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.S136L(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AATGACTTACGACTTGTCTTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	LEU/SER,LEU/SER	0,4406		0,0,2203	92	83	86		731,407	1.2	0.9	12	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	TMTC1	NM_001193451.1,NM_175861.3	145,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	244/883,136/775	29908642	1,13005	2203	4300	6503	29799909	SO:0001630	splice_region_variant	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.731+1C>T	12.37:g.29908642G>A			29799909	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	G	8.136	0.784167	0.16189	0.0	1.16E-4	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.67345	-0.26;-0.04;-0.26;-0.12;1.55	5.28	1.17	0.20885	.	0.995128	0.08157	N	0.989167	T	0.34600	0.0903	N	0.02539	-0.55	0.25516	N	0.987412	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.25745	-1.0123	9	.	.	.	-0.3302	3.6345	0.08143	0.3721:0.1867:0.4411:0.0	.	136;244	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	L	136;244;244;244;136	ENSP00000256062:S136L;ENSP00000448112:S244L;ENSP00000449043:S244L;ENSP00000442046:S244L;ENSP00000370622:S136L	.	S	-	2	0	TMTC1	29799909	0.693000	0.27728	0.924000	0.36721	0.903000	0.53119	0.239000	0.18023	0.699000	0.31761	0.655000	0.94253	TCG		0.388	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	Missense_Mutation	A	29908642	G	A	29908642	5	1	47	1	0	0	0	0	0	0	1	0	16299	1072	37	1	1977	1	TMTC1	12	29908642	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3097640	29908642	103943253	1374	5771										
DENND5B	160518	broad.mit.edu	37	chr12	31540716	31540716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatccactgtgggagcaggcGatccctacagacccaaacag	10	13	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:31540716G>A	ENST00000389082.5	-	21	3910	c.3646C>T	c.(3646-3648)Cgc>Tgc	p.R1216C	DENND5B_ENST00000536562.1_Missense_Mutation_p.R1251C|DENND5B_ENST00000306833.6_Missense_Mutation_p.R1251C	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1216	RUN 2. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1216C(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GGGAGCAGGCGATCCCTACAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											74	69	70					12																	31540716		2032	4185	6217	31431983	SO:0001583	missense	160518			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.3646C>T	12.37:g.31540716G>A	ENSP00000373734:p.Arg1216Cys		31431983	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135511	0.94517	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562	T;T;T	0.32023	1.47;1.47;1.47	5.29	5.29	0.74685	RUN (3);	0.304535	0.31821	N	0.007005	T	0.45216	0.1331	L	0.40543	1.245	0.58432	D	0.999999	D;D	0.69078	0.994;0.997	P;P	0.58820	0.846;0.761	T	0.37641	-0.9697	10	0.87932	D	0	-19.5091	19.1165	0.93343	0.0:0.0:1.0:0.0	.	1216;1251	Q6ZUT9;G3V1S3	DEN5B_HUMAN;.	C	1216;1251;1251	ENSP00000373734:R1216C;ENSP00000306482:R1251C;ENSP00000444889:R1251C	ENSP00000306482:R1251C	R	-	1	0	DENND5B	31431983	1.000000	0.71417	0.941000	0.38009	0.992000	0.81027	7.502000	0.81614	2.761000	0.94854	0.655000	0.94253	CGC		0.527	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31540716	G	A	31540716	3	1	47	1	0	0	0	0	1	0	0	0	4448	1058	37	1	182	1	DENND5B	12	31540716	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1632074	31540716	102311179	1375	5772										
DNM1L	10059	broad.mit.edu	37	chr12	32866233	32866233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcctaattccattatcctcGctgtcactgctgctaataca	4	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:32866233G>A	ENST00000549701.1	+	6	621	c.547G>A	c.(547-549)Gct>Act	p.A183T	DNM1L_ENST00000381000.4_Missense_Mutation_p.A196T|DNM1L_ENST00000547312.1_Missense_Mutation_p.A183T|DNM1L_ENST00000553257.1_Missense_Mutation_p.A196T|DNM1L_ENST00000452533.2_Missense_Mutation_p.A183T|DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000414834.2_Intron|DNM1L_ENST00000358214.5_Missense_Mutation_p.A196T|DNM1L_ENST00000266481.6_Missense_Mutation_p.A183T			O00429	DNM1L_HUMAN	dynamin 1-like	183	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.A183T(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CATTATCCTCGCTGTCACTGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											126	120	122					12																	32866233		2203	4300	6503	32757500	SO:0001583	missense	10059			AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.547G>A	12.37:g.32866233G>A	ENSP00000450399:p.Ala183Thr		32757500	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Missense_Mutation	SNP	ENST00000549701.1	37	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	G	36	5.597992	0.96602	.	.	ENSG00000087470	ENST00000452533;ENST00000411996;ENST00000266479;ENST00000553257;ENST00000549701;ENST00000358214;ENST00000266481;ENST00000551476;ENST00000550154;ENST00000547312;ENST00000381000;ENST00000548750	D;D;D;D;D;D;D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8;-3.8;-3.8;-3.8;-3.8;-3.8;-3.3	5.21	5.21	0.72293	Dynamin, GTPase domain (2);	0.000000	0.85682	D	0.000000	D	0.98257	0.9423	M	0.91818	3.245	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.993;0.995;0.986;0.989;0.996	D	0.99349	1.0914	10	0.87932	D	0	.	18.764	0.91865	0.0:0.0:1.0:0.0	.	236;236;249;236;183	D3DUW6;D3DUW5;F8W8D1;D3DUW7;O00429	.;.;.;.;DNM1L_HUMAN	T	183;249;183;196;183;196;183;166;159;183;196;154	ENSP00000415131:A183T;ENSP00000449089:A196T;ENSP00000450399:A183T;ENSP00000350948:A196T;ENSP00000266481:A183T;ENSP00000447845:A166T;ENSP00000447013:A159T;ENSP00000448610:A183T;ENSP00000370388:A196T;ENSP00000447788:A154T	ENSP00000266479:A183T	A	+	1	0	DNM1L	32757500	1.000000	0.71417	0.964000	0.40570	0.983000	0.72400	7.727000	0.84838	2.442000	0.82660	0.585000	0.79938	GCT		0.393	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062		A	32866233	G	A	32866233	3	1	47	1	0	0	0	0	1	0	0	0	4682	1087	38	1	569	1	DNM1L	12	32866233	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1325517	32866233	100985662	1376	5773										
SYT10	341359	broad.mit.edu	37	chr12	33532815	33532815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggttttcgatgataggccagCatttcattccagtggtctcg	11	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:33532815C>T	ENST00000228567.3	-	6	1748	c.1452G>A	c.(1450-1452)atG>atA	p.M484I	SYT10_ENST00000535526.1_Missense_Mutation_p.M303I	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	484					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.M484I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GATAGGCCAGCATTTCATTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											250	208	222					12																	33532815		2203	4300	6503	33424082	SO:0001583	missense	341359			AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.1452G>A	12.37:g.33532815C>T	ENSP00000228567:p.Met484Ile		33424082	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208988	0.79240	.	.	ENSG00000110975	ENST00000228567;ENST00000535526	T;T	0.72051	-0.62;-0.62	4.3	4.3	0.51218	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.50627	U	0.000120	T	0.75236	0.3822	M	0.74467	2.265	0.80722	D	1	P	0.40250	0.709	B	0.43990	0.438	T	0.78398	-0.2219	10	0.49607	T	0.09	.	17.0422	0.86492	0.0:1.0:0.0:0.0	.	484	Q6XYQ8	SYT10_HUMAN	I	484;303	ENSP00000228567:M484I;ENSP00000438691:M303I	ENSP00000228567:M484I	M	-	3	0	SYT10	33424082	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.329000	0.79170	2.679000	0.91253	0.650000	0.86243	ATG		0.468	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		T	33532815	C	T	33532815	3	4	47	1	0	0	0	0	1	0	0	0	15505	710	25	3	127	3	SYT10	12	33532815	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	666582	33532815	100319080	1377	5774										
KIF21A	55605	broad.mit.edu	37	chr12	39726135	39726135	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attagccacatttttatctcCctctccattctccttgacta	2	14	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:39726135C>T	ENST00000361418.5	-	21	2947	c.2932G>A	c.(2932-2934)Gga>Aga	p.G978R	KIF21A_ENST00000541463.2_Missense_Mutation_p.G942R|KIF21A_ENST00000544797.2_Missense_Mutation_p.G965R|KIF21A_ENST00000395670.3_Missense_Mutation_p.G978R|KIF21A_ENST00000361961.3_Missense_Mutation_p.G965R			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	978					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G965R(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TTTTTATCTCCCTCTCCATTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											227	208	214					12																	39726135		2203	4300	6503	38012402	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2932G>A	12.37:g.39726135C>T	ENSP00000354878:p.Gly978Arg		38012402	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787823	0.49997	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T;T	0.69040	-0.37;-0.33;0.42;-0.37;-0.28;-0.34	5.67	4.59	0.56863	.	0.296088	0.23951	N	0.042949	T	0.61324	0.2338	L	0.43152	1.355	0.34136	D	0.665783	P;P;B;B;B	0.42203	0.573;0.773;0.136;0.145;0.404	B;B;B;B;B	0.43274	0.219;0.414;0.091;0.146;0.268	T	0.66650	-0.5870	10	0.20046	T	0.44	.	15.5118	0.75789	0.0:0.9228:0.0:0.0772	.	965;942;978;965;978	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3	.;.;KI21A_HUMAN;.;.	R	965;978;978;32;26;965;978;942	ENSP00000354851:G965R;ENSP00000379029:G978R;ENSP00000448792:G26R;ENSP00000445606:G965R;ENSP00000354878:G978R;ENSP00000438075:G942R	ENSP00000344501:G978R	G	-	1	0	KIF21A	38012402	0.895000	0.30542	1.000000	0.80357	0.984000	0.73092	3.187000	0.50950	2.663000	0.90544	0.557000	0.71058	GGA		0.383	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		T	39726135	C	T	39726135	3	4	47	1	0	0	0	0	1	0	0	0	8309	632	22	3	2164	3	KIF21A	12	39726135	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6193320	39726135	94125760	1378	5775										
ABCD2	225	broad.mit.edu	37	chr12	39997797	39997797	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataattccgtgatccacatCaataacttttcctgtaatta	3	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:39997797C>A	ENST00000308666.3	-	5	1552	c.1417G>T	c.(1417-1419)Gat>Tat	p.D473Y		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	473					fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.D473Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TGATCCACATCAATAACTTTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	89	89					12																	39997797		2203	4300	6503	38284064	SO:0001583	missense	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1417G>T	12.37:g.39997797C>A	ENSP00000310688:p.Asp473Tyr		38284064	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.974305	0.34848	.	.	ENSG00000173208	ENST00000308666	D	0.94966	-3.57	5.08	5.08	0.68730	.	0.124068	0.52532	D	0.000065	D	0.90369	0.6986	L	0.31065	0.9	0.51482	D	0.999922	B	0.24533	0.105	B	0.19391	0.025	D	0.86846	0.2020	9	.	.	.	-14.2665	18.4742	0.90786	0.0:1.0:0.0:0.0	.	473	Q9UBJ2	ABCD2_HUMAN	Y	473	ENSP00000310688:D473Y	.	D	-	1	0	ABCD2	38284064	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.373000	0.59537	2.376000	0.81061	0.563000	0.77884	GAT		0.318	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		A	39997797	C	A	39997797	3	1	47	1	0	0	0	0	1	0	0	0	61	826	29	2	829	2	ABCD2	12	39997797	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	271662	39997797	93854098	1379	5776										
CNTN1	1272	broad.mit.edu	37	chr12	41327666	41327666	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaggataaacatcaagcaaGaatttatgttcaaggtagat	8	4	2	2	rs148624625	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:41327666G>T	ENST00000551295.2	+	9	1088	c.971G>T	c.(970-972)aGa>aTa	p.R324I	CNTN1_ENST00000348761.2_Missense_Mutation_p.R313I|CNTN1_ENST00000360099.3_Missense_Mutation_p.R324I|CNTN1_ENST00000347616.1_Missense_Mutation_p.R324I|CNTN1_ENST00000547849.1_Missense_Mutation_p.R324I|CNTN1_ENST00000547702.1_Missense_Mutation_p.R324I	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	324	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R324I(1)|p.R324K(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CATCAAGCAAGAATTTATGTT	0.308																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	12											65	67	66					12																	41327666		2203	4299	6502	39613933	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.971G>T	12.37:g.41327666G>T	ENSP00000447006:p.Arg324Ile		39613933	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920659	0.33908	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.11	3.2	0.36748	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.483471	0.23706	N	0.045375	T	0.64182	0.2575	M	0.68317	2.08	0.50171	D	0.999851	B;P;P	0.43431	0.293;0.769;0.807	B;B;P	0.45428	0.071;0.349;0.48	T	0.57883	-0.7734	10	0.24483	T	0.36	.	7.7108	0.28677	0.3409:0.0:0.6591:0.0	.	324;313;324	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	I	324;324;324;324;324;313	ENSP00000448004:R324I;ENSP00000447006:R324I;ENSP00000448653:R324I;ENSP00000325660:R324I;ENSP00000353213:R324I;ENSP00000261160:R313I	ENSP00000325660:R324I	R	+	2	0	CNTN1	39613933	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.410000	0.34691	0.619000	0.30197	0.561000	0.74099	AGA		0.308	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41327666	G	T	41327666	3	4	47	1	0	0	0	0	1	0	0	0	3646	942	33	2	1001	2	CNTN1	12	41327666	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1329869	41327666	92524229	1380	5777										
CNTN1	1272	broad.mit.edu	37	chr12	41337967	41337967	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atattcactaccagaggaatTttatggtatgtgttttaagt	8	4	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:41337967T>G	ENST00000551295.2	+	14	1795	c.1678T>G	c.(1678-1680)Ttt>Gtt	p.F560V	CNTN1_ENST00000348761.2_Missense_Mutation_p.F549V|CNTN1_ENST00000360099.3_Missense_Mutation_p.F560V|CNTN1_ENST00000347616.1_Missense_Mutation_p.F560V|CNTN1_ENST00000547849.1_Missense_Mutation_p.F560V|CNTN1_ENST00000547702.1_Missense_Mutation_p.F560V	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	560	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.F560V(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CCAGAGGAATTTTATGGTATG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	71	73					12																	41337967		2203	4299	6502	39624234	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1678T>G	12.37:g.41337967T>G	ENSP00000447006:p.Phe560Val		39624234	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	7.468	0.646011	0.14451	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72	5.0	5.0	0.66597	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.428353	0.26948	N	0.021699	T	0.09423	0.0232	N	0.03000	-0.44	0.29200	N	0.875302	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.14699	-1.0463	10	0.21540	T	0.41	.	6.2236	0.20695	0.1491:0.0:0.1783:0.6726	.	560;549;560	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	V	560;560;560;560;560;549	ENSP00000448004:F560V;ENSP00000447006:F560V;ENSP00000448653:F560V;ENSP00000325660:F560V;ENSP00000353213:F560V;ENSP00000261160:F549V	ENSP00000325660:F560V	F	+	1	0	CNTN1	39624234	0.878000	0.30173	0.999000	0.59377	0.977000	0.68977	1.436000	0.34980	2.239000	0.73571	0.496000	0.49642	TTT		0.348	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41337967	T	G	41337967	3	3	47	1	0	0	0	0	1	0	0	0	3646	1841	64	4	1728	4	CNTN1	12	41337967	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	10301	41337967	92513928	1381	5778										
ADAMTS20	80070	broad.mit.edu	37	chr12	43825186	43825186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgtatgaagttcacatggActcagagattcaggtttggt	11	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:43825186A>G	ENST00000389420.3	-	22	3209	c.3210T>C	c.(3208-3210)agT>agC	p.S1070S	ADAMTS20_ENST00000553158.1_Silent_p.S1070S|ADAMTS20_ENST00000395541.2_Silent_p.S224S	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1070	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S1070S(1)|p.C1070C(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		GTTCACATGGACTCAGAGATT	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	12											148	130	136					12																	43825186		2203	4300	6503	42111453	SO:0001819	synonymous_variant	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3210T>C	12.37:g.43825186A>G			42111453	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																				0.418	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43825186	A	G	43825186	2	3	47	1	0	0	0	0	0	0	0	1	266	272	10	4		4	ADAMTS20	12	43825186	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2487219	43825186	90026709	1382	5779										
ADAMTS20	80070	broad.mit.edu	37	chr12	43833725	43833725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaataagttctttctcttgtCgattagtactattaattctt	4	6	3	0	rs142203536		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:43833725C>T	ENST00000389420.3	-	17	2437	c.2438G>A	c.(2437-2439)cGa>cAa	p.R813Q	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.R813Q|ADAMTS20_ENST00000395541.2_5'Flank	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	813	Spacer.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R813Q(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		TTTCTCTTGTCGATTAGTACT	0.299													C|||	1	0.000199681	8e-04	0	5008	,	,		16115	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						C	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	94	87	89		2438	5.4	0.9	12	dbSNP_134	89	0,8594		0,0,4297	no	missense	ADAMTS20	NM_025003.3	43	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	813/1911	43833725	1,12995	2201	4297	6498	42119992	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2438G>A	12.37:g.43833725C>T	ENSP00000374071:p.Arg813Gln		42119992	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357829	0.82243	2.27E-4	0.0	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.51574	0.7;0.7	5.44	5.44	0.79542	ADAM-TS Spacer 1 (1);	0.000000	0.44688	D	0.000423	T	0.65059	0.2655	M	0.70275	2.135	0.80722	D	1	D	0.76494	0.999	D	0.67548	0.952	T	0.59139	-0.7510	10	0.28530	T	0.3	.	15.3321	0.74223	0.0:0.9302:0.0:0.0698	.	813	P59510	ATS20_HUMAN	Q	813	ENSP00000374071:R813Q;ENSP00000448341:R813Q	ENSP00000374068:R813Q	R	-	2	0	ADAMTS20	42119992	0.998000	0.40836	0.944000	0.38274	0.951000	0.60555	3.749000	0.55150	2.937000	0.99478	0.650000	0.86243	CGA		0.299	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43833725	C	T	43833725	3	4	47	1	0	0	0	0	1	0	0	0	266	884	31	1	3385	1	ADAMTS20	12	43833725	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	8539	43833725	90018170	1383	5780										
PUS7L	83448	broad.mit.edu	37	chr12	44148553	44148553	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctctggtttttgtcaaggaTtctgcctattgagaattcag	9	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:44148553T>G	ENST00000416848.2	-	2	984	c.496A>C	c.(496-498)Atc>Ctc	p.I166L	PUS7L_ENST00000344862.5_Missense_Mutation_p.I166L|PUS7L_ENST00000553166.1_Missense_Mutation_p.I166L|PUS7L_ENST00000551923.1_Missense_Mutation_p.I166L|PUS7L_ENST00000431332.3_Intron	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	166					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.I166L(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TTGTCAAGGATTCTGCCTATT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											111	110	110					12																	44148553		2203	4300	6503	42434820	SO:0001583	missense	83448			BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.496A>C	12.37:g.44148553T>G	ENSP00000415899:p.Ile166Leu		42434820	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222270	0.39300	.	.	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166	T;T;T;T	0.24151	1.96;1.96;1.96;1.87	5.26	4.08	0.47627	Pseudouridine synthase, catalytic domain (1);	0.220196	0.46758	D	0.000280	T	0.21267	0.0512	M	0.63428	1.95	0.22719	N	0.998813	P	0.35844	0.524	B	0.28849	0.095	T	0.23833	-1.0177	10	0.48119	T	0.1	-4.7458	5.9722	0.19359	0.2547:0.0709:0.0:0.6744	.	166	Q9H0K6	PUS7L_HUMAN	L	166	ENSP00000415899:I166L;ENSP00000343081:I166L;ENSP00000447706:I166L;ENSP00000446865:I166L	ENSP00000343081:I166L	I	-	1	0	PUS7L	42434820	0.585000	0.26774	0.703000	0.30354	0.969000	0.65631	0.643000	0.24750	1.051000	0.40369	0.482000	0.46254	ATC		0.368	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		G	44148553	T	G	44148553	3	3	47	1	0	0	0	0	1	0	0	0	12871	1493	52	4	1641	4	PUS7L	12	44148553	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	314828	44148553	89703342	1384	5781										
SLC38A4	55089	broad.mit.edu	37	chr12	47162096	47162096	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcaaggtttacttaccccGaccttttggggtgacctaaa	9	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:47162096G>A	ENST00000447411.1	-	15	1745	c.1539C>T	c.(1537-1539)gtC>gtT	p.V513V	SLC38A4_ENST00000266579.4_Silent_p.V513V	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	513					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)	p.V513V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					TACTTACCCCGACCTTTTGGG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	12											37	40	39					12																	47162096		2203	4300	6503	45448363	SO:0001819	synonymous_variant	55089			AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.1539C>T	12.37:g.47162096G>A			45448363	A8K553	Silent	SNP	ENST00000447411.1	37	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198183	0.22037	.	.	ENSG00000139209	ENST00000550670	.	.	.	5.63	-2.35	0.06684	.	.	.	.	.	T	0.51907	0.1702	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47471	-0.9115	4	.	.	.	-5.0462	7.9952	0.30265	0.6227:0.1157:0.2616:0.0	.	.	.	.	L	39	.	.	S	-	2	0	SLC38A4	45448363	0.298000	0.24417	0.692000	0.30179	0.985000	0.73830	-0.294000	0.08309	-0.282000	0.09128	0.655000	0.94253	TCG		0.353	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			A	47162096	G	A	47162096	2	1	47	1	0	0	0	0	0	0	0	1	14643	1045	37	1		1	SLC38A4	12	47162096	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3013543	47162096	86689799	1385	5782										
C12orf54	121273	broad.mit.edu	37	chr12	48888618	48888618	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attccttgatgaccccaaagTtgagaagattgcagttcagc	9	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:48888618T>G	ENST00000548364.1	+	7	337	c.280T>G	c.(280-282)Ttg>Gtg	p.L94V	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Missense_Mutation_p.L94V			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	94								p.L94V(1)		endometrium(1)|large_intestine(4)	5						GACCCCAAAGTTGAGAAGATT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											140	137	138					12																	48888618		2203	4300	6503	47174885	SO:0001583	missense	121273			BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.280T>G	12.37:g.48888618T>G	ENSP00000447109:p.Leu94Val		47174885	Q6X4S9|Q8N5S2	Missense_Mutation	SNP	ENST00000548364.1	37	CCDS8764.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.661047	0.47572	.	.	ENSG00000177627	ENST00000314014;ENST00000548364	T;T	0.50813	0.73;0.73	4.88	0.751	0.18392	.	0.702601	0.11763	N	0.531934	T	0.29716	0.0742	N	0.24115	0.695	0.09310	N	1	B	0.30851	0.297	B	0.30179	0.112	T	0.20773	-1.0265	10	0.54805	T	0.06	-0.0561	5.5026	0.16836	0.1688:0.0:0.3498:0.4814	.	94	Q6X4T0	CL054_HUMAN	V	94	ENSP00000316898:L94V;ENSP00000447109:L94V	ENSP00000316898:L94V	L	+	1	2	C12orf54	47174885	0.011000	0.17503	0.000000	0.03702	0.590000	0.36582	0.830000	0.27462	0.379000	0.24794	0.529000	0.55759	TTG		0.478	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319		G	48888618	T	G	48888618	3	3	47	1	0	0	0	0	1	0	0	0	1703	1722	60	4	306	4	C12orf54	12	48888618	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1726522	48888618	84963277	1386	5783										
C12orf41	54934	broad.mit.edu	37	chr12	49048753	49048753	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactgggtcttcagcaatttCtttgactaaatgatcttcaa	6	9	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:49048753C>A	ENST00000420613.2	-	9	1365	c.1318G>T	c.(1318-1320)Gaa>Taa	p.E440*	KANSL2_ENST00000550347.1_Nonsense_Mutation_p.E623*|KANSL2_ENST00000548701.1_5'UTR|KANSL2_ENST00000553086.1_Nonsense_Mutation_p.E406*|SNORA2A_ENST00000383885.1_RNA|SNORA34_ENST00000408564.2_RNA	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	440					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)		p.E440*(2)									TCAGCAATTTCTTTGACTAAA	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											77	78	78					12																	49048753		1905	4119	6024	47335020	SO:0001587	stop_gained	54934			AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.1318G>T	12.37:g.49048753C>A	ENSP00000415436:p.Glu440*		47335020	Q8N3B5|Q96CV0|Q9NX51	Nonsense_Mutation	SNP	ENST00000420613.2	37	CCDS44869.1	.	.	.	.	.	.	.	.	.	.	C	37	6.369893	0.97511	.	.	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000547087;ENST00000553086	.	.	.	5.72	5.72	0.89469	.	0.283030	0.39341	N	0.001397	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-4.7574	10.8237	0.46620	0.0:0.9141:0.0:0.0859	.	.	.	.	X	623;440;154;406	.	ENSP00000415436:E440X	E	-	1	0	C12orf41	47335020	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.393000	0.59665	2.704000	0.92352	0.557000	0.71058	GAA		0.453	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		A	49048753	C	A	49048753	4	1	47	1	0	0	0	0	0	1	0	0	1691	922	32	2	168	2	C12orf41	12	49048753	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	160135	49048753	84803142	1387	5784										
KRT83	3889	broad.mit.edu	37	chr12	52710781	52710781	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaaccacggaggtgtctgaGatgtgggattggagaatgcg	16	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:52710781G>A	ENST00000293670.3	-	5	839	c.777C>T	c.(775-777)atC>atT	p.I259I		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	259	Linker 12.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.I259I(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGTGTCTGAGATGTGGGATT	0.532																																					GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)											1	Substitution - coding silent(1)	large_intestine(1)	12											141	124	130					12																	52710781		2203	4300	6503	50997048	SO:0001819	synonymous_variant	3889			X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.777C>T	12.37:g.52710781G>A			50997048	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																				0.532	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		A	52710781	G	A	52710781	2	1	47	1	0	0	0	0	0	0	0	1	8518	932	33	3		3	KRT83	12	52710781	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3662028	52710781	81141114	1388	5785										
KRT5	3852	broad.mit.edu	37	chr12	52909583	52909583	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgttcaaagctacttacaGatgttgactggtccaactcc	7	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:52909583G>T	ENST00000252242.4	-	8	1863	c.1473C>A	c.(1471-1473)atC>atA	p.I491I		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	491	Tail.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.I491I(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTACTTACAGATGTTGACTG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	12											165	148	154					12																	52909583		2203	4300	6503	51195850	SO:0001630	splice_region_variant	3852				CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1474+1C>A	12.37:g.52909583G>T			51195850	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363126	0.41902	.	.	ENSG00000186081	ENST00000548409	.	.	.	5.81	3.01	0.34805	.	.	.	.	.	T	0.58850	0.2151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53995	-0.8359	4	.	.	.	.	9.3282	0.38005	0.2242:0.0:0.7758:0.0	.	.	.	.	M	199	.	.	L	-	1	2	KRT5	51195850	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.540000	0.36115	0.811000	0.34303	0.655000	0.94253	CTG		0.388	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		Silent	T	52909583	G	T	52909583	5	4	47	1	0	0	0	0	0	0	1	0	8500	956	33	2	307	2	KRT5	12	52909583	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	198802	52909583	80942312	1389	5786										
TARBP2	8620	broad.mit.edu	37	chr12	53898568	53898568	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccgcaaagaattcaccatGacctgtcgagtggagcgttt	10	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:53898568G>T	ENST00000267017.3	-	0	592				TARBP2_ENST00000266987.2_Missense_Mutation_p.M194I|TARBP2_ENST00000456234.2_Missense_Mutation_p.M173I|TARBP2_ENST00000552857.1_Missense_Mutation_p.M103I|TARBP2_ENST00000394357.2_Missense_Mutation_p.M173I	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)	p.M194I(1)		haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						AATTCACCATGACCTGTCGAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	80	80					12																	53898568		2203	4300	6503	52184835	SO:0001628	intergenic_variant	6895			AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		12.37:g.53898568G>T			52184835	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.630246	0.28978	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000552857;ENST00000394357;ENST00000550407	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	4.9	4.9	0.64082	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	N	0.00746	-1.225	0.80722	D	1	D;B	0.59357	0.985;0.229	D;B	0.72338	0.977;0.348	T	0.66991	-0.5783	10	0.11182	T	0.66	0.0049	17.3565	0.87337	0.0:0.0:1.0:0.0	.	194;194	A8K3X2;Q15633	.;TRBP2_HUMAN	I	194;173;103;173;95	ENSP00000266987:M194I;ENSP00000416077:M173I;ENSP00000449537:M103I;ENSP00000377885:M173I	ENSP00000266987:M194I	M	+	3	0	TARBP2	52184835	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.377000	0.79668	2.717000	0.92951	0.491000	0.48974	ATG		0.582	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		T	53898568	G	T	53898568	1	4	47	0	1	0	0	0	0	0	0	0	15595	1290	45	2		2	TARBP2	12	53898568	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	988985	53898568	79953327	1390	5787										
ITGA7	3679	broad.mit.edu	37	chr12	56088241	56088241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttacgtggccaacagcagCtctacctccagttccgtggt	10	14	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:56088241C>T	ENST00000555728.1	-	18	2503	c.2475G>A	c.(2473-2475)gaG>gaA	p.E825E	ITGA7_ENST00000394229.2_Silent_p.E781E|ITGA7_ENST00000452168.2_Silent_p.E688E|ITGA7_ENST00000257879.6_Silent_p.E781E|ITGA7_ENST00000553804.1_Silent_p.E785E|ITGA7_ENST00000394230.2_Silent_p.E785E|ITGA7_ENST00000347027.6_Silent_p.E775E|ITGA7_ENST00000257880.7_Silent_p.E825E			Q13683	ITA7_HUMAN	integrin, alpha 7	825					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.E781E(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCAACAGCAGCTCTACCTCCA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	12											72	64	67					12																	56088241		2203	4300	6503	54374508	SO:0001819	synonymous_variant	3679				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2475G>A	12.37:g.56088241C>T			54374508	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																					0.587	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		T	56088241	C	T	56088241	2	4	47	1	0	0	0	0	0	0	0	1	7902	796	28	3		3	ITGA7	12	56088241	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2189673	56088241	77763654	1391	5788										
CNPY2	10330	broad.mit.edu	37	chr12	56704794	56704794	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtcagcctctcgggaaaaGaattcaatgagttcatcctc	8	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:56704794G>T	ENST00000273308.4	-	5	993	c.453C>A	c.(451-453)ttC>ttA	p.F151L	CNPY2_ENST00000551720.1_5'Flank|RP11-977G19.12_ENST00000546789.1_RNA|RP11-977G19.10_ENST00000549318.1_Missense_Mutation_p.F151L|RP11-977G19.11_ENST00000549860.1_RNA|RP11-977G19.11_ENST00000549565.1_RNA	NM_014255.5	NP_055070.1	Q9Y2B0	CNPY2_HUMAN	canopy FGF signaling regulator 2	151	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				negative regulation of gene expression (GO:0010629)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of low-density lipoprotein particle clearance (GO:0010988)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)		p.F151L(1)		large_intestine(2)|lung(2)	4						CTCGGGAAAAGAATTCAATGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											123	118	120					12																	56704794		2203	4300	6503	54991061	SO:0001583	missense	10330			AB015631	CCDS8914.1	12q15	2013-07-23	2013-07-23	2007-10-22		ENSG00000257727			13529	protein-coding gene	gene with protein product		605861	"transmembrane protein 4", "canopy 2 homolog (zebrafish)"	TMEM4		10072769, 15905959	Standard	NM_001190991		Approved	HP10390, ZSIG9, Cnpy2	uc001sku.2	Q9Y2B0	OTTHUMG00000170330	ENST00000273308.4:c.453C>A	12.37:g.56704794G>T	ENSP00000273308:p.Phe151Leu		54991061	B2R7B9|Q9UHE9	Missense_Mutation	SNP	ENST00000273308.4	37	CCDS8914.1	.	.	.	.	.	.	.	.	.	.	G	9.211	1.030939	0.19590	.	.	ENSG00000144785;ENSG00000257727;ENSG00000257727;ENSG00000257727	ENST00000549318;ENST00000273308;ENST00000551475;ENST00000551286	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.29	4.4	0.53042	Saposin B (1);	0.000000	0.85682	D	0.000000	T	0.15522	0.0374	N	0.05414	-0.055	0.80722	D	1	B	0.15141	0.012	B	0.17098	0.017	T	0.10405	-1.0631	10	0.02654	T	1	-12.6409	9.2619	0.37616	0.1664:0.0:0.8336:0.0	.	151	Q9Y2B0	CNPY2_HUMAN	L	151;151;151;99	ENSP00000446743:F151L;ENSP00000273308:F151L;ENSP00000448809:F151L;ENSP00000446784:F99L	ENSP00000273308:F151L	F	-	3	2	RP11-977G19.10;CNPY2	54991061	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.197000	0.51028	1.379000	0.46325	0.561000	0.74099	TTC		0.478	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255		T	56704794	G	T	56704794	3	4	47	1	0	0	0	0	1	0	0	0	3634	933	33	2	103	2	CNPY2	12	56704794	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	616553	56704794	77147101	1392	5789										
HSD17B6	8630	broad.mit.edu	37	chr12	57181005	57181005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgacatcggtgcatccgcGaactcgatattcagctggct	10	12	2	1	rs557368967		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:57181005G>A	ENST00000554643.1	+	6	1182	c.833G>A	c.(832-834)cGa>cAa	p.R278Q	HSD17B6_ENST00000555805.1_Missense_Mutation_p.R278Q|HSD17B6_ENST00000322165.1_Missense_Mutation_p.R278Q|HSD17B6_ENST00000555159.1_Missense_Mutation_p.R278Q|HSD17B6_ENST00000554150.1_Missense_Mutation_p.R278Q			O14756	H17B6_HUMAN	hydroxysteroid (17-beta) dehydrogenase 6	278					androgen biosynthetic process (GO:0006702)|androgen catabolic process (GO:0006710)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|intracellular (GO:0005622)|membrane (GO:0016020)	catalytic activity (GO:0003824)|electron carrier activity (GO:0009055)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|oxidoreductase activity (GO:0016491)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.R278Q(1)		endometrium(1)|large_intestine(2)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10					Succinic acid(DB00139)	GTGCATCCGCGAACTCGATAT	0.443													G|||	1	0.000199681	8e-04	0	5008	,	,		19076	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											139	115	123					12																	57181005		2203	4300	6503	55467272	SO:0001583	missense	8630			AF016509	CCDS8925.1	12q13.3	2012-12-07	2012-12-07		ENSG00000025423	ENSG00000025423	1.1.1.62, 1.1.1.63, 1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	23316	protein-coding gene	gene with protein product	"oxidative 3-alpha-hydroxysteroid-dehydrogenase", "3(alpha->beta)-hydroxysteroid epimerasel", "retinol dehydrogenase", "oxidoreductase", "NAD+ -dependent 3 alpha-hydroxysteroid dehydrogenase", "3-hydroxysteroid epimerase", "short chain dehydrogenase/reductase family 9C, member 6"	606623	"hydroxysteroid (17-beta) dehydrogenase 6", "hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse)"			11165032, 19027726	Standard	XM_005269207		Approved	HSE, RODH, SDR9C6	uc001smg.1	O14756	OTTHUMG00000170854	ENST00000554643.1:c.833G>A	12.37:g.57181005G>A	ENSP00000451406:p.Arg278Gln		55467272	O43275	Missense_Mutation	SNP	ENST00000554643.1	37	CCDS8925.1	.	.	.	.	.	.	.	.	.	.	g	19.90	3.912611	0.72983	.	.	ENSG00000025423	ENST00000555159;ENST00000555805;ENST00000554643;ENST00000554150;ENST00000322165	D;D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.85;-2.85	4.97	4.08	0.47627	NAD(P)-binding domain (1);	0.121470	0.38381	N	0.001704	D	0.89487	0.6729	M	0.79475	2.455	0.30192	N	0.799429	P	0.46395	0.877	B	0.40534	0.332	D	0.87197	0.2238	10	0.45353	T	0.12	.	12.1803	0.54208	0.0844:0.0:0.9156:0.0	.	278	O14756	H17B6_HUMAN	Q	278	ENSP00000450698:R278Q;ENSP00000451753:R278Q;ENSP00000451406:R278Q;ENSP00000452273:R278Q;ENSP00000318631:R278Q	ENSP00000318631:R278Q	R	+	2	0	HSD17B6	55467272	0.961000	0.32948	0.048000	0.18961	0.239000	0.25481	4.830000	0.62745	1.312000	0.45043	0.651000	0.88453	CGA		0.443	HSD17B6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410714.1	NM_003725		A	57181005	G	A	57181005	3	1	47	1	0	0	0	0	1	0	0	0	7408	1058	37	1	847	1	HSD17B6	12	57181005	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	476211	57181005	76670890	1393	5790										
LRP1	4035	broad.mit.edu	37	chr12	57592421	57592421	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgcgaggactacattgaatTtgccagcctggatggctcca	11	12	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:57592421T>G	ENST00000243077.3	+	60	10110	c.9644T>G	c.(9643-9645)tTt>tGt	p.F3215C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3215					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.F3215C(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TACATTGAATTTGCCAGCCTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12											57	43	48					12																	57592421		2203	4300	6503	55878688	SO:0001583	missense	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.9644T>G	12.37:g.57592421T>G	ENSP00000243077:p.Phe3215Cys		55878688	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.278429	0.59758	.	.	ENSG00000123384	ENST00000243077	D	0.95788	-3.81	4.39	4.39	0.52855	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000001	D	0.95862	0.8653	L	0.40543	1.245	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95060	0.8195	10	0.38643	T	0.18	.	13.0175	0.58766	0.0:0.0:0.0:1.0	.	3215	Q07954	LRP1_HUMAN	C	3215	ENSP00000243077:F3215C	ENSP00000243077:F3215C	F	+	2	0	LRP1	55878688	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.089000	0.71384	1.971000	0.57363	0.459000	0.35465	TTT		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57592421	T	G	57592421	3	3	47	1	0	0	0	0	1	0	0	0	8980	1841	64	4	9882	4	LRP1	12	57592421	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	411416	57592421	76259474	1394	5791										
MARS	4141	broad.mit.edu	37	chr12	57908826	57908826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccctggaagcggattaaagGcagtgaggctgacaggtagg	17	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:57908826G>A	ENST00000262027.5	+	17	2323	c.2189G>A	c.(2188-2190)gGc>gAc	p.G730D	MARS_ENST00000315473.5_Missense_Mutation_p.G496D|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	730					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)	p.G730D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	CGGATTAAAGGCAGTGAGGCT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	12											70	66	67					12																	57908826		2203	4300	6503	56195093	SO:0001583	missense	4141			X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2189G>A	12.37:g.57908826G>A	ENSP00000262027:p.Gly730Asp		56195093	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	37	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025879	0.75390	.	.	ENSG00000166986	ENST00000262027;ENST00000315473	T;T	0.38401	1.14;1.14	5.32	4.42	0.53409	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.054686	0.64402	D	0.000001	T	0.59609	0.2206	M	0.83953	2.67	0.80722	D	1	P;D	0.69078	0.923;0.997	P;D	0.67382	0.613;0.951	T	0.63211	-0.6688	10	0.54805	T	0.06	-17.0655	12.6964	0.57005	0.0819:0.0:0.9181:0.0	.	496;730	A6NC17;P56192	.;SYMC_HUMAN	D	730;496	ENSP00000262027:G730D;ENSP00000314653:G496D	ENSP00000262027:G730D	G	+	2	0	MARS	56195093	1.000000	0.71417	0.966000	0.40874	0.976000	0.68499	5.582000	0.67477	2.650000	0.89964	0.591000	0.81541	GGC		0.512	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		A	57908826	G	A	57908826	3	1	47	1	0	0	0	0	1	0	0	0	9346	1203	42	3	2255	3	MARS	12	57908826	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	316405	57908826	75943069	1395	5792										
SLC16A7	9194	broad.mit.edu	37	chr12	60168780	60168780	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacttgggaaaaagttaataAgtatttagatttctcccttt	6	5	1	1	rs567459331		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:60168780A>C	ENST00000261187.4	+	4	868	c.704A>C	c.(703-705)aAg>aCg	p.K235T	SLC16A7_ENST00000547379.1_Missense_Mutation_p.K235T|SLC16A7_ENST00000552024.1_Missense_Mutation_p.K235T|SLC16A7_ENST00000552432.1_Missense_Mutation_p.K235T|SLC16A7_ENST00000543448.1_Missense_Mutation_p.K136T	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	235					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.K235T(1)		endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	AAAGTTAATAAGTATTTAGAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											45	46	45					12																	60168780		2203	4300	6503	58455047	SO:0001583	missense	9194			AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"Solute carriers"	10928	protein-coding gene	gene with protein product		603654	"solute carrier family 16 (monocarboxylic acid transporters), member 7"			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.704A>C	12.37:g.60168780A>C	ENSP00000261187:p.Lys235Thr		58455047	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296459	0.23650	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448;ENST00000548444	D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.76	-0.848	0.10727	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.348273	0.35291	N	0.003306	T	0.73434	0.3586	M	0.79805	2.47	0.29240	N	0.872701	B	0.14805	0.011	B	0.17979	0.02	T	0.60556	-0.7240	9	.	.	.	.	2.1308	0.03749	0.5647:0.1207:0.1986:0.116	.	235	O60669	MOT2_HUMAN	T	235;235;235;235;235;136;120	ENSP00000449547:K235T;ENSP00000448071:K235T;ENSP00000448742:K235T;ENSP00000446722:K235T;ENSP00000261187:K235T;ENSP00000443731:K136T;ENSP00000447814:K120T	.	K	+	2	0	SLC16A7	58455047	0.982000	0.34865	0.000000	0.03702	0.631000	0.37964	3.057000	0.49931	-0.074000	0.12820	-0.336000	0.08194	AAG		0.323	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		C	60168780	A	C	60168780	3	2	47	1	0	0	0	0	1	0	0	0	14450	72	3	4	714	4	SLC16A7	12	60168780	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2259954	60168780	73683115	1396	5793										
SLC16A7	9194	broad.mit.edu	37	chr12	60169185	60169185	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacctcgtgggtgcaccaaGattttccagtgccgtcggac	13	12	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:60169185G>T	ENST00000261187.4	+	4	1273	c.1109G>T	c.(1108-1110)aGa>aTa	p.R370I	SLC16A7_ENST00000547379.1_Missense_Mutation_p.R370I|SLC16A7_ENST00000552024.1_Missense_Mutation_p.R370I|SLC16A7_ENST00000552432.1_Missense_Mutation_p.R370I|SLC16A7_ENST00000543448.1_Missense_Mutation_p.R271I	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	370					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.R370I(1)		endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	GGTGCACCAAGATTTTCCAGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	12											123	112	116					12																	60169185		2203	4300	6503	58455452	SO:0001583	missense	9194			AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"Solute carriers"	10928	protein-coding gene	gene with protein product		603654	"solute carrier family 16 (monocarboxylic acid transporters), member 7"			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.1109G>T	12.37:g.60169185G>T	ENSP00000261187:p.Arg370Ile		58455452	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353548	0.61293	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448	T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66	5.77	4.89	0.63831	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.043123	0.85682	D	0.000000	T	0.75539	0.3863	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82546	-0.0403	9	.	.	.	.	14.9998	0.71462	0.0683:0.0:0.9317:0.0	.	370	O60669	MOT2_HUMAN	I	370;370;370;370;370;271	ENSP00000449547:R370I;ENSP00000448071:R370I;ENSP00000448742:R370I;ENSP00000446722:R370I;ENSP00000261187:R370I;ENSP00000443731:R271I	.	R	+	2	0	SLC16A7	58455452	1.000000	0.71417	0.949000	0.38748	0.058000	0.15608	7.965000	0.87945	1.578000	0.49821	0.655000	0.94253	AGA		0.458	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		T	60169185	G	T	60169185	3	4	47	1	0	0	0	0	1	0	0	0	14450	942	33	2	1119	2	SLC16A7	12	60169185	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	405	60169185	73682710	1397	5794										
GRIP1	23426	broad.mit.edu	37	chr12	66786260	66786260	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggctagaaatagggaacttCttggggctcgatgctgactg	14	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:66786260C>A	ENST00000398016.3	-	18	2204	c.2136G>T	c.(2134-2136)aaG>aaT	p.K712N	GRIP1_ENST00000542021.1_5'Flank|GRIP1_ENST00000359742.4_Missense_Mutation_p.K764N|GRIP1_ENST00000286445.7_Missense_Mutation_p.K764N	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.K712N(1)		NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TAGGGAACTTCTTGGGGCTCG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											114	112	112					12																	66786260		1920	4139	6059	65072527	SO:0001583	missense	23426			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2136G>T	12.37:g.66786260C>A	ENSP00000381098:p.Lys712Asn		65072527	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.84|13.84	2.358321|2.358321	0.41801|0.41801	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000538164	T;T;T;T;T;T|.	0.20332|.	2.08;2.09;2.09;2.08;2.17;2.17|.	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	0.173853|.	0.43416|.	D|.	0.000580|.	T|T	0.71668|0.71668	0.3367|0.3367	L|L	0.56769|0.56769	1.78|1.78	0.50632|0.50632	D|D	0.999887|0.999887	B;P;B;B|.	0.36683|.	0.001;0.565;0.356;0.016|.	B;B;B;B|.	0.32211|.	0.007;0.142;0.138;0.022|.	T|T	0.69632|0.69632	-0.5093|-0.5093	9|5	.|.	.|.	.|.	-17.7282|-17.7282	18.2146|18.2146	0.89881|0.89881	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	712;764;712;764|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.	.;GRIP1_HUMAN;.;.|.	N|I	712;764;764;712;656;604|579	ENSP00000381098:K712N;ENSP00000352780:K764N;ENSP00000286445:K764N;ENSP00000446047:K712N;ENSP00000446024:K656N;ENSP00000446011:K604N|.	.|.	K|R	-|-	3|2	2|0	GRIP1|GRIP1	65072527|65072527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	4.239000|4.239000	0.58694|0.58694	2.622000|2.622000	0.88805|0.88805	0.462000|0.462000	0.41574|0.41574	AAG|AGA		0.468	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66786260	C	A	66786260	3	1	47	1	0	0	0	0	1	0	0	0	6808	912	32	2	1122	2	GRIP1	12	66786260	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6617075	66786260	67065635	1398	5795										
MDM1	56890	broad.mit.edu	37	chr12	68716947	68716947	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagataaacccttgaaatttCttttgtattcagtttcatgg	7	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:68716947C>A	ENST00000303145.7	-	5	793	c.707G>T	c.(706-708)aGa>aTa	p.R236I	MDM1_ENST00000411698.2_Missense_Mutation_p.R191I|MDM1_ENST00000545724.1_5'Flank|MDM1_ENST00000540418.1_5'UTR	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	236					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)		p.R236I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		CTTGAAATTTCTTTTGTATTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	12											121	120	121					12																	68716947		2203	4300	6503	67003214	SO:0001583	missense	56890			AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.707G>T	12.37:g.68716947C>A	ENSP00000302537:p.Arg236Ile		67003214	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.837764	0.71373	.	.	ENSG00000111554	ENST00000303145;ENST00000411698;ENST00000541686	T;T;T	0.26518	1.73;1.73;1.73	4.65	3.73	0.42828	.	0.114641	0.53938	D	0.000042	T	0.50497	0.1619	M	0.76002	2.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	T	0.54390	-0.8301	9	.	.	.	-6.2412	15.32	0.74115	0.0:0.8589:0.1411:0.0	.	191;236	E7EPQ3;Q8TC05	.;MDM1_HUMAN	I	236;191;231	ENSP00000302537:R236I;ENSP00000391006:R191I;ENSP00000446000:R231I	.	R	-	2	0	MDM1	67003214	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.800000	0.47900	1.243000	0.43853	0.491000	0.48974	AGA		0.318	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68716947	C	A	68716947	3	1	47	1	0	0	0	0	1	0	0	0	9442	913	32	2	1477	2	MDM1	12	68716947	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1930687	68716947	65134948	1399	5796										
NUP107	57122	broad.mit.edu	37	chr12	69125453	69125453	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagaaagataatggtgaatTtagtcatcatgacctggccc	9	7	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:69125453T>G	ENST00000229179.4	+	22	2284	c.1952T>G	c.(1951-1953)tTt>tGt	p.F651C	NUP107_ENST00000378905.2_Intron|NUP107_ENST00000539906.1_Missense_Mutation_p.F622C	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	651					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)	p.F651C(1)	NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AATGGTGAATTTAGTCATCAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	66	66					12																	69125453		2203	4300	6503	67411720	SO:0001583	missense	57122			AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1952T>G	12.37:g.69125453T>G	ENSP00000229179:p.Phe651Cys		67411720	B4DZ67|Q6PJE1	Missense_Mutation	SNP	ENST00000229179.4	37	CCDS8985.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.845943	0.71603	.	.	ENSG00000111581	ENST00000229179;ENST00000539906	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	N	0.14661	0.345	0.80722	D	1	P;P	0.49961	0.93;0.93	P;P	0.45913	0.497;0.497	T	0.30060	-0.9991	8	.	.	.	-20.7043	16.0725	0.80946	0.0:0.0:0.0:1.0	.	622;651	B4DZ67;P57740	.;NU107_HUMAN	C	651;622	.	.	F	+	2	0	NUP107	67411720	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.770000	0.74990	2.263000	0.75096	0.528000	0.53228	TTT		0.358	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		G	69125453	T	G	69125453	3	3	47	1	0	0	0	0	1	0	0	0	10784	1841	64	4	2038	4	NUP107	12	69125453	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	408506	69125453	64726442	1400	5797										
NUP107	57122	broad.mit.edu	37	chr12	69126508	69126508	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaaggcaatgcaattatgaGaaaattcttgggtatagtat	9	4	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:69126508G>A	ENST00000229179.4	+	23	2422	c.2090G>A	c.(2089-2091)aGa>aAa	p.R697K	NUP107_ENST00000378905.2_Missense_Mutation_p.R458K|NUP107_ENST00000401003.3_3'UTR|NUP107_ENST00000539906.1_Missense_Mutation_p.R668K	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	697					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)	p.R697K(1)	NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			GCAATTATGAGAAAATTCTTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											65	75	72					12																	69126508		2203	4300	6503	67412775	SO:0001583	missense	57122			AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.2090G>A	12.37:g.69126508G>A	ENSP00000229179:p.Arg697Lys		67412775	B4DZ67|Q6PJE1	Missense_Mutation	SNP	ENST00000229179.4	37	CCDS8985.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.131819	0.77662	.	.	ENSG00000111581	ENST00000229179;ENST00000378905;ENST00000539906	.	.	.	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.82019	0.4946	M	0.86268	2.805	0.34607	D	0.717187	D;D;D	0.89917	1.0;0.987;1.0	D;D;D	0.91635	0.999;0.991;0.999	D	0.86957	0.2089	8	.	.	.	-20.6351	19.3514	0.94389	0.0:0.0:1.0:0.0	.	668;458;697	B4DZ67;Q6PJE1;P57740	.;.;NU107_HUMAN	K	697;458;668	.	.	R	+	2	0	NUP107	67412775	1.000000	0.71417	1.000000	0.80357	0.215000	0.24574	8.814000	0.91968	2.746000	0.94184	0.563000	0.77884	AGA		0.428	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		A	69126508	G	A	69126508	3	1	47	1	0	0	0	0	1	0	0	0	10784	942	33	3	2180	3	NUP107	12	69126508	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1055	69126508	64725387	1401	5798										
BEST3	144453	broad.mit.edu	37	chr12	70048845	70048845	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttctgtgtcaattaaaaGagctggctgagagctcatgg	12	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:70048845G>T	ENST00000330891.5	-	10	2075	c.1849C>A	c.(1849-1851)Ctt>Att	p.L617I	BEST3_ENST00000331471.4_Intron|BEST3_ENST00000553096.1_Missense_Mutation_p.L511I|BEST3_ENST00000488961.1_Missense_Mutation_p.L404I	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	617					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.L617I(1)		cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			TCAATTAAAAGAGCTGGCTGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	81	82					12																	70048845		1887	4111	5998	68335112	SO:0001583	missense	144453			AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.1849C>A	12.37:g.70048845G>T	ENSP00000332413:p.Leu617Ile		68335112	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271964	0.59649	.	.	ENSG00000127325	ENST00000488961;ENST00000330891;ENST00000553096	D;D;D	0.98012	-4.36;-4.66;-4.64	5.53	5.53	0.82687	.	0.534882	0.17561	N	0.169807	D	0.96374	0.8817	L	0.34521	1.04	0.80722	D	1	P;P	0.50819	0.487;0.939	B;P	0.48952	0.146;0.596	D	0.95550	0.8620	10	0.33940	T	0.23	-7.2764	17.2224	0.86961	0.0:0.0:1.0:0.0	.	617;404	Q8N1M1;B5MDI8	BEST3_HUMAN;.	I	404;617;511	ENSP00000433213:L404I;ENSP00000332413:L617I;ENSP00000449548:L511I	ENSP00000332413:L617I	L	-	1	0	BEST3	68335112	0.349000	0.24870	0.023000	0.16930	0.192000	0.23643	3.181000	0.50903	2.593000	0.87608	0.563000	0.77884	CTT		0.478	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		T	70048845	G	T	70048845	3	4	47	1	0	0	0	0	1	0	0	0	1407	942	33	2	161	2	BEST3	12	70048845	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	922337	70048845	63803050	1402	5799										
BEST3	144453	broad.mit.edu	37	chr12	70091460	70091460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttattgctgtataaagaacaGcaaaaacaataaattccctg	5	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:70091460G>A	ENST00000330891.5	-	2	345	c.119C>T	c.(118-120)gCt>gTt	p.A40V	BEST3_ENST00000533674.1_Intron|BEST3_ENST00000266661.4_Intron|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000551160.1_Intron|BEST3_ENST00000331471.4_Missense_Mutation_p.A40V|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000553096.1_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	40					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.A40V(1)		cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			ATAAAGAACAGCAAAAACAAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	92	93					12																	70091460		1847	4094	5941	68377727	SO:0001583	missense	144453			AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.119C>T	12.37:g.70091460G>A	ENSP00000332413:p.Ala40Val		68377727	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654338	0.47467	.	.	ENSG00000127325	ENST00000331471;ENST00000330891;ENST00000548658	D;D;D	0.98419	-4.92;-4.92;-4.92	5.84	5.84	0.93424	.	0.224693	0.46145	D	0.000311	D	0.91918	0.7441	N	0.00308	-1.67	0.80722	D	1	B;B	0.25105	0.118;0.0	B;B	0.29353	0.101;0.002	D	0.87807	0.2629	10	0.42905	T	0.14	-18.8603	20.1535	0.98095	0.0:0.0:1.0:0.0	.	40;40	Q8N1M1;Q8N1M1-1	BEST3_HUMAN;.	V	40	ENSP00000329064:A40V;ENSP00000332413:A40V;ENSP00000446575:A40V	ENSP00000332413:A40V	A	-	2	0	BEST3	68377727	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.874000	0.48483	2.764000	0.94973	0.650000	0.86243	GCT		0.343	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		A	70091460	G	A	70091460	3	1	47	1	0	0	0	0	1	0	0	0	1407	971	34	3	1923	3	BEST3	12	70091460	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	42615	70091460	63760435	1403	5800										
PTPRR	5801	broad.mit.edu	37	chr12	71148079	71148079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctgcccttgtaaaacattTttctttaaaagcaaaacaga	5	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:71148079T>G	ENST00000283228.2	-	5	1082	c.630A>C	c.(628-630)aaA>aaC	p.K210N	PTPRR_ENST00000440835.2_5'UTR|PTPRR_ENST00000378778.1_Missense_Mutation_p.K4N|PTPRR_ENST00000342084.4_Missense_Mutation_p.K98N|PTPRR_ENST00000549308.1_5'UTR	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	210					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.K210N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		GTAAAACATTTTTCTTTAAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	79	79					12																	71148079		2203	4298	6501	69434346	SO:0001583	missense	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.630A>C	12.37:g.71148079T>G	ENSP00000283228:p.Lys210Asn		69434346	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420326	0.62622	.	.	ENSG00000153233	ENST00000283228;ENST00000378778;ENST00000342084	T;T;T	0.35421	1.31;1.31;1.31	5.86	4.67	0.58626	.	0.259223	0.26680	U	0.023045	T	0.38692	0.1050	L	0.47716	1.5	0.49051	D	0.999749	D;P;P;P	0.53619	0.961;0.592;0.787;0.682	P;B;P;B	0.47206	0.541;0.322;0.526;0.172	T	0.33879	-0.9851	10	0.72032	D	0.01	-24.8944	13.2648	0.60127	0.0:0.0:0.1318:0.8682	.	59;98;4;210	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	N	210;4;98	ENSP00000283228:K210N;ENSP00000368054:K4N;ENSP00000339605:K98N	ENSP00000283228:K210N	K	-	3	2	PTPRR	69434346	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.902000	0.48703	2.237000	0.73441	0.523000	0.50628	AAA		0.348	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		G	71148079	T	G	71148079	3	3	47	1	0	0	0	0	1	0	0	0	12847	1838	64	4	1383	4	PTPRR	12	71148079	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1056619	71148079	62703816	1404	5801										
NAV3	89795	broad.mit.edu	37	chr12	78400534	78400534	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccccgcagcctcccagttcaGgacctagtgatggtgggaag	13	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:78400534G>T	ENST00000397909.2	+	8	1389	c.1216G>T	c.(1216-1218)Gga>Tga	p.G406*	NAV3_ENST00000536525.2_Nonsense_Mutation_p.G406*|NAV3_ENST00000228327.6_Nonsense_Mutation_p.G406*|NAV3_ENST00000266692.7_Nonsense_Mutation_p.G406*			Q8IVL0	NAV3_HUMAN	neuron navigator 3	406						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.G406*(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TCCCAGTTCAGGACCTAGTGA	0.493										HNSCC(70;0.22)																																						1	Substitution - Nonsense(1)	large_intestine(1)	12											110	110	110					12																	78400534		1969	4147	6116	76924665	SO:0001587	stop_gained	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1216G>T	12.37:g.78400534G>T	ENSP00000381007:p.Gly406*		76924665	Q8NFW7|Q9Y2E7	Nonsense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.056933|7.056933	0.98032|0.98032	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000550503	.|.	.|.	.|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.196462|.	0.23991|.	U|.	0.042576|.	.|T	.|0.74635	.|0.3742	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72388	.|-0.4309	.|4	0.08381|.	T|.	0.77|.	-15.3704|-15.3704	18.1163|18.1163	0.89556|0.89556	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|M	406|229	.|.	ENSP00000228327:G406X|.	G|R	+|+	1|2	0|0	NAV3|NAV3	76924665|76924665	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.897000|0.897000	0.52465|0.52465	3.945000|3.945000	0.56637|0.56637	2.715000|2.715000	0.92844|0.92844	0.655000|0.655000	0.94253|0.94253	GGA|AGG		0.493	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78400534	G	T	78400534	4	4	47	1	0	0	0	0	0	1	0	0	10215	1001	35	2	1246	2	NAV3	12	78400534	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7252455	78400534	55451361	1405	5802										
NAV3	89795	broad.mit.edu	37	chr12	78582464	78582464	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgctagctactgtataggaGacttaattagatcccataac	7	8	0	2	rs376780536		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:78582464G>A	ENST00000397909.2	+	33	6135	c.5962G>A	c.(5962-5964)Gac>Aac	p.D1988N	NAV3_ENST00000552300.1_Intron|NAV3_ENST00000536525.2_Missense_Mutation_p.D1966N|NAV3_ENST00000228327.6_Missense_Mutation_p.D1966N|NAV3_ENST00000266692.7_Missense_Mutation_p.D1789N			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1988						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.D1966N(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTGTATAGGAGACTTAATTAG	0.393										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/ASP	0,3838		0,0,1919	121	117	118		5896	5.1	1	12		118	1,8273		0,1,4136	no	missense	NAV3	NM_014903.4	23	0,1,6055	AA,AG,GG		0.0121,0.0,0.0083	probably-damaging	1966/2364	78582464	1,12111	1919	4137	6056	77106595	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5962G>A	12.37:g.78582464G>A	ENSP00000381007:p.Asp1988Asn		77106595	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.154355|5.154355	0.94686|0.94686	0.0|0.0	1.21E-4|1.21E-4	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.29142|.	1.66;1.67;1.66;1.58;2.43|.	5.95|5.95	5.06|5.06	0.68205|0.68205	.|.	0.000000|.	0.41294|.	U|.	0.000904|.	T|T	0.67353|0.67353	0.2884|0.2884	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;B;D;B|.	0.71674|.	0.998;0.001;0.991;0.006|.	D;B;P;B|.	0.67900|.	0.954;0.008;0.787;0.011|.	T|T	0.65315|0.65315	-0.6198|-0.6198	10|5	0.49607|.	T|.	0.09|.	-7.0815|-7.0815	15.2307|15.2307	0.73386|0.73386	0.0669:0.0:0.9331:0.0|0.0669:0.0:0.9331:0.0	.|.	1966;1789;1988;1966|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	N|K	1966;1988;1966;1789;580;588|860	ENSP00000446132:D1966N;ENSP00000381007:D1988N;ENSP00000228327:D1966N;ENSP00000266692:D1789N;ENSP00000448303:D588N|.	ENSP00000228327:D1966N|.	D|R	+|+	1|2	0|0	NAV3|NAV3	77106595|77106595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.786000|9.786000	0.99046|0.99046	1.539000|1.539000	0.49286|0.49286	0.655000|0.655000	0.94253|0.94253	GAC|AGA		0.393	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78582464	G	A	78582464	3	1	47	1	0	0	0	0	1	0	0	0	10215	942	33	3	6022	3	NAV3	12	78582464	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	181930	78582464	55269431	1406	5803										
NAV3	89795	broad.mit.edu	37	chr12	78591070	78591070	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctggctgaacagtgcagtgCtgataataatggagtggagc	14	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:78591070C>A	ENST00000397909.2	+	35	6508	c.6335C>A	c.(6334-6336)gCt>gAt	p.A2112D	NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000536525.2_Missense_Mutation_p.A2090D|NAV3_ENST00000228327.6_Missense_Mutation_p.A2090D|NAV3_ENST00000266692.7_Missense_Mutation_p.A1913D			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2112						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.A2090D(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CAGTGCAGTGCTGATAATAAT	0.348										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											126	114	118					12																	78591070		1847	4094	5941	77115201	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6335C>A	12.37:g.78591070C>A	ENSP00000381007:p.Ala2112Asp		77115201	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.20|16.20	3.055216|3.055216	0.55325|0.55325	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.29655|.	1.67;1.66;1.67;1.56;2.45|.	5.35|5.35	5.35|5.35	0.76521|0.76521	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);|.	0.000000|.	0.39834|.	U|.	0.001245|.	T|.	0.68449|.	0.3002|.	L|L	0.43701|0.43701	1.375|1.375	0.80722|0.80722	D|D	1|1	P;P;D;P|.	0.55172|.	0.949;0.557;0.97;0.902|.	P;B;P;P|.	0.56563|.	0.542;0.234;0.801;0.52|.	T|.	0.63681|.	-0.6582|.	10|.	0.52906|.	T|.	0.07|.	-19.0918|-19.0918	19.4322|19.4322	0.94775|0.94775	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2090;1913;2112;2090|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	D|X	2090;2112;2090;1913;704;712|984	ENSP00000446132:A2090D;ENSP00000381007:A2112D;ENSP00000228327:A2090D;ENSP00000266692:A1913D;ENSP00000448303:A712D|.	ENSP00000228327:A2090D|.	A|C	+|+	2|3	0|2	NAV3|NAV3	77115201|77115201	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.793000|0.793000	0.44817|0.44817	4.827000|4.827000	0.62723|0.62723	2.649000|2.649000	0.89929|0.89929	0.655000|0.655000	0.94253|0.94253	GCT|TGC		0.348	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78591070	C	A	78591070	3	1	47	1	0	0	0	0	1	0	0	0	10215	797	28	2	6403	2	NAV3	12	78591070	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	8606	78591070	55260825	1407	5804										
PPFIA2	8499	broad.mit.edu	37	chr12	81839465	81839465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcttagtgatctttcatgtCgtgacacaaggcactccaaa	7	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:81839465C>T	ENST00000549396.1	-	6	600	c.440G>A	c.(439-441)cGa>cAa	p.R147Q	PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R73Q|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R147Q|PPFIA2_ENST00000550359.2_5'UTR|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R129Q|PPFIA2_ENST00000550584.2_Missense_Mutation_p.R147Q|PPFIA2_ENST00000407050.4_Missense_Mutation_p.R73Q|RP11-315E17.1_ENST00000550272.1_RNA|PPFIA2_ENST00000552948.1_Missense_Mutation_p.R147Q|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R129Q	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	147	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.R147Q(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TCTTTCATGTCGTGACACAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	89	92					12																	81839465		1881	4113	5994	80363596	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.440G>A	12.37:g.81839465C>T	ENSP00000450337:p.Arg147Gln		80363596	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	C	37	6.001707	0.97189	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000551442	T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.58004	0.2092	N	0.19112	0.55	0.80722	D	1	D;D	0.71674	0.998;0.994	D;D	0.75484	0.986;0.921	T	0.61922	-0.6963	10	0.87932	D	0	-10.6387	20.3736	0.98901	0.0:1.0:0.0:0.0	.	47;147	B7Z4H8;O75334	.;LIPA2_HUMAN	Q	147;129;73;158;129;147;73;147;129	ENSP00000450337:R147Q;ENSP00000450298:R129Q;ENSP00000385093:R73Q;ENSP00000327416:R129Q;ENSP00000449338:R147Q;ENSP00000388373:R73Q;ENSP00000447868:R147Q;ENSP00000449469:R129Q	ENSP00000327416:R129Q	R	-	2	0	PPFIA2	80363596	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	CGA		0.393	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81839465	C	T	81839465	3	4	47	1	0	0	0	0	1	0	0	0	12341	884	31	1	3441	1	PPFIA2	12	81839465	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3248395	81839465	52012430	1408	5805										
SLC6A15	55117	broad.mit.edu	37	chr12	85285752	85285752	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcagatccttcttcaacatCtgtatctttctcttcctggc	4	13	6	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:85285752C>A	ENST00000266682.5	-	2	689	c.148G>T	c.(148-150)Gat>Tat	p.D50Y	SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.D50Y	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	50					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.D50Y(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TCTTCAACATCTGTATCTTTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											215	195	202					12																	85285752		2203	4300	6503	83809883	SO:0001583	missense	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.148G>T	12.37:g.85285752C>A	ENSP00000266682:p.Asp50Tyr		83809883	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708288	0.68615	.	.	ENSG00000072041	ENST00000266682;ENST00000450363;ENST00000549540	T;T;T	0.74002	-0.8;-0.48;0.81	5.53	4.64	0.57946	.	0.411674	0.30714	N	0.009036	T	0.80363	0.4609	M	0.72479	2.2	0.58432	D	0.999996	P;P	0.51351	0.944;0.938	P;P	0.50617	0.492;0.646	T	0.82904	-0.0226	10	0.59425	D	0.04	.	16.1592	0.81686	0.1344:0.8656:0.0:0.0	.	50;50	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	Y	50	ENSP00000266682:D50Y;ENSP00000390706:D50Y;ENSP00000448308:D50Y	ENSP00000266682:D50Y	D	-	1	0	SLC6A15	83809883	1.000000	0.71417	0.241000	0.24154	0.716000	0.41182	5.933000	0.70130	1.450000	0.47717	0.655000	0.94253	GAT		0.403	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		A	85285752	C	A	85285752	3	1	47	1	0	0	0	0	1	0	0	0	14715	913	32	2	2202	2	SLC6A15	12	85285752	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3446287	85285752	48566143	1409	5806										
LRRIQ1	84125	broad.mit.edu	37	chr12	85492678	85492678	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaatcttgttttactaagaGaattgcacttggatgataac	8	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:85492678G>T	ENST00000393217.2	+	13	3176	c.3115G>T	c.(3115-3117)Gaa>Taa	p.E1039*		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1039								p.E1039*(3)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTTACTAAGAGAATTGCACTT	0.294																																																3	Substitution - Nonsense(3)	large_intestine(3)	12											82	85	84					12																	85492678		2202	4294	6496	84016809	SO:0001587	stop_gained	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3115G>T	12.37:g.85492678G>T	ENSP00000376910:p.Glu1039*		84016809	Q567P4|Q9BS17|Q9HA36	Nonsense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	G	40	8.443873	0.98813	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	.	.	.	5.4	5.4	0.78164	.	0.056303	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.9326	0.70929	0.0:0.0:0.848:0.152	.	.	.	.	X	1039;1014;1039	.	ENSP00000256007:E1039X	E	+	1	0	LRRIQ1	84016809	1.000000	0.71417	0.998000	0.56505	0.796000	0.44982	2.903000	0.48711	2.521000	0.84997	0.585000	0.79938	GAA		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85492678	G	T	85492678	4	4	47	1	0	0	0	0	0	1	0	0	9058	943	33	2	3161	2	LRRIQ1	12	85492678	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	206926	85492678	48359217	1410	5807										
MGAT4C	25834	broad.mit.edu	37	chr12	86377441	86377441	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcccttataagttgtttgTctccttcctaaataccaaga	4	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:86377441T>G	ENST00000604798.1	-	7	1359	c.155A>C	c.(154-156)gAc>gCc	p.D52A	MGAT4C_ENST00000548651.1_Missense_Mutation_p.D52A|MGAT4C_ENST00000393205.2_Missense_Mutation_p.D81A|MGAT4C_ENST00000552808.2_Missense_Mutation_p.D52A|MGAT4C_ENST00000552435.2_Missense_Mutation_p.D52A|MGAT4C_ENST00000549405.2_Missense_Mutation_p.D52A|MGAT4C_ENST00000332156.1_Missense_Mutation_p.D52A			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	52					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.D52A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AAGTTGTTTGTCTCCTTCCTA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	106	105					12																	86377441		2203	4300	6503	84901572	SO:0001583	missense	25834				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.155A>C	12.37:g.86377441T>G	ENSP00000474896:p.Asp52Ala		84901572	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453868	0.63290	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225;ENST00000552435	T;T;T;T;T;T	0.44083	1.51;1.48;1.51;1.51;1.51;0.93	5.44	5.44	0.79542	.	0.067176	0.64402	D	0.000011	T	0.34308	0.0893	L	0.44542	1.39	0.44024	D	0.996745	P;P	0.37914	0.505;0.611	B;B	0.35182	0.158;0.197	T	0.10590	-1.0623	10	0.13853	T	0.58	-8.4345	15.502	0.75705	0.0:0.0:0.0:1.0	.	81;52	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	A	52;81;52;52;52;52;52;52	ENSP00000331664:D52A;ENSP00000376900:D81A;ENSP00000449022:D52A;ENSP00000446647:D52A;ENSP00000447253:D52A;ENSP00000449172:D52A	ENSP00000331664:D52A	D	-	2	0	MGAT4C	84901572	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.665000	0.83852	2.071000	0.62044	0.460000	0.39030	GAC		0.308	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		G	86377441	T	G	86377441	3	3	47	1	0	0	0	0	1	0	0	0	9577	1667	58	4	1289	4	MGAT4C	12	86377441	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	884763	86377441	47474454	1411	5808										
C12orf50	160419	broad.mit.edu	37	chr12	88381687	88381687	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtagcatttaatacatgcgTtgtaggtactagtcgggtag	12	5	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:88381687T>C	ENST00000298699.2	-	9	937	c.757A>G	c.(757-759)Acg>Gcg	p.T253A	C12orf50_ENST00000550553.1_Intron	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	253								p.T253A(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						AATACATGCGTTGTAGGTACT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											158	141	147					12																	88381687		2203	4300	6503	86905818	SO:0001583	missense	160419			AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.757A>G	12.37:g.88381687T>C	ENSP00000298699:p.Thr253Ala		86905818	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	37	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858959	0.32884	.	.	ENSG00000165805	ENST00000298699	T	0.32988	1.43	5.76	2.12	0.27331	.	0.684740	0.14380	N	0.323164	T	0.28928	0.0718	M	0.65975	2.015	0.58432	D	0.999996	B	0.06786	0.001	B	0.09377	0.004	T	0.04115	-1.0976	10	0.32370	T	0.25	.	7.3786	0.26843	0.0:0.2509:0.0:0.7491	.	253	Q8NA57	CL050_HUMAN	A	253	ENSP00000298699:T253A	ENSP00000298699:T253A	T	-	1	0	C12orf50	86905818	0.163000	0.22920	0.763000	0.31416	0.823000	0.46562	-0.108000	0.10857	0.123000	0.18342	-0.263000	0.10527	ACG		0.358	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589		C	88381687	T	C	88381687	3	2	47	1	0	0	0	0	1	0	0	0	1699	1725	60	4	507	4	C12orf50	12	88381687	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2004246	88381687	45470208	1412	5809										
DUSP6	1848	broad.mit.edu	37	chr12	89744373	89744373	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattagtctcacctatgaaaGaaatggcctcagggaaaaac	8	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:89744373G>T	ENST00000279488.7	-	2	2061	c.830C>A	c.(829-831)tCt>tAt	p.S277Y	DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547140.1_5'UTR|DUSP6_ENST00000547291.1_Missense_Mutation_p.S152Y	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	277	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.S277Y(1)		large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						ACCTATGAAAGAAATGGCCTC	0.418																																					Colon(132;3456 5224)											1	Substitution - Missense(1)	large_intestine(1)	12											87	97	94					12																	89744373		2203	4300	6503	88268504	SO:0001583	missense	1848			BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.830C>A	12.37:g.89744373G>T	ENSP00000279488:p.Ser277Tyr		88268504	O75109|Q53Y75|Q9BSH6	Missense_Mutation	SNP	ENST00000279488.7	37	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056798	0.76074	.	.	ENSG00000139318	ENST00000279488;ENST00000547291	T;T	0.61040	0.14;0.14	5.86	4.97	0.65823	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.198644	0.56097	D	0.000039	T	0.63558	0.2521	M	0.73319	2.225	0.58432	D	0.999998	B	0.33739	0.422	B	0.38921	0.285	T	0.67345	-0.5694	10	0.72032	D	0.01	.	17.0901	0.86619	0.0:0.1268:0.8732:0.0	.	277	Q16828	DUS6_HUMAN	Y	277;152	ENSP00000279488:S277Y;ENSP00000449838:S152Y	ENSP00000279488:S277Y	S	-	2	0	DUSP6	88268504	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.758000	0.68776	1.462000	0.47948	0.655000	0.94253	TCT		0.418	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		T	89744373	G	T	89744373	3	4	47	1	0	0	0	0	1	0	0	0	4840	942	33	2	323	2	DUSP6	12	89744373	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1362686	89744373	44107522	1413	5810										
POC1B	282809	broad.mit.edu	37	chr12	89860596	89860596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgtggtgttcttgggtagAtatcaagaagatgtggtggt	16	2	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:89860596A>G	ENST00000313546.3	-	9	1111	c.983T>C	c.(982-984)aTc>aCc	p.I328T	POC1B_ENST00000378528.2_Missense_Mutation_p.S115P|POC1B_ENST00000393179.4_Missense_Mutation_p.I198T|POC1B_ENST00000549504.1_Missense_Mutation_p.S79P|POC1B_ENST00000549035.1_Missense_Mutation_p.I286T|POC1B_ENST00000541909.1_Missense_Mutation_p.I198T	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	328					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)		p.I328T(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						TCTTGGGTAGATATCAAGAAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											228	213	218					12																	89860596		2203	4300	6503	88384727	SO:0001583	missense	282809			AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"WD repeat domain containing"	30836	protein-coding gene	gene with protein product		614784	"WD repeat domain 51B", "POC1 centriolar protein homolog B (Chlamydomonas)"	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.983T>C	12.37:g.89860596A>G	ENSP00000323302:p.Ile328Thr		88384727	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	37	CCDS31869.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.60|17.60	3.430019|3.430019	0.62844|0.62844	.|.	.|.	ENSG00000139323|ENSG00000139323	ENST00000393179;ENST00000313546;ENST00000549035;ENST00000541909|ENST00000378528;ENST00000549504	T;T;T;T|T	0.61859|0.76578	0.29;0.07;0.28;0.47|-1.03	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.096735|.	0.64402|.	D|.	0.000001|.	T|T	0.81735|0.81735	0.4885|0.4885	L|L	0.55990|0.55990	1.75|1.75	0.27113|0.27113	N|N	0.962323|0.962323	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	T|T	0.77539|0.77539	-0.2550|-0.2550	10|7	0.33940|0.87932	T|D	0.23|0	.|.	15.1292|15.1292	0.72507|0.72507	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	328|.	Q8TC44|.	POC1B_HUMAN|.	T|P	198;328;286;198|115;79	ENSP00000376877:I198T;ENSP00000323302:I328T;ENSP00000447916:I286T;ENSP00000440301:I198T|ENSP00000367789:S115P	ENSP00000323302:I328T|ENSP00000367789:S115P	I|S	-|-	2|1	0|0	POC1B|POC1B	88384727|88384727	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.901000|0.901000	0.52897|0.52897	8.159000|8.159000	0.89651|0.89651	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	ATC|TCT		0.343	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240		G	89860596	A	G	89860596	3	3	47	1	0	0	0	0	1	0	0	0	12207	333	12	4	469	4	POC1B	12	89860596	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	116223	89860596	43991299	1414	5811										
C12orf12	196477	broad.mit.edu	37	chr12	91347616	91347616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcgacctcttcttcctcctCgctcgcctcctttgcatcac	4	19	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:91347616C>T	ENST00000358859.2	-	1	1337	c.904G>A	c.(904-906)Gag>Aag	p.E302K	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	302	Glu-rich.							p.E302K(1)									tcttcctcctcGCTCGCCTCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											208	185	193					12																	91347616		2203	4300	6503	89871747	SO:0001583	missense	196477			BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.904G>A	12.37:g.91347616C>T	ENSP00000351727:p.Glu302Lys		89871747	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	37	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	C	7.737	0.700562	0.15106	.	.	ENSG00000197651	ENST00000358859	T	0.25749	1.78	4.28	1.15	0.20763	.	.	.	.	.	T	0.16171	0.0389	N	0.14661	0.345	0.09310	N	1	D	0.56287	0.975	B	0.43155	0.41	T	0.14868	-1.0457	9	0.39692	T	0.17	2.9967	11.5622	0.50782	0.0:0.4506:0.5494:0.0	.	302	Q8TC90	CL012_HUMAN	K	302	ENSP00000351727:E302K	ENSP00000351727:E302K	E	-	1	0	C12orf12	89871747	0.935000	0.31712	0.015000	0.15790	0.053000	0.15095	1.879000	0.39618	0.041000	0.15688	0.460000	0.39030	GAG		0.537	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		T	91347616	C	T	91347616	3	4	47	1	0	0	0	0	1	0	0	0	1680	893	31	1	320	1	C12orf12	12	91347616	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1487020	91347616	42504279	1415	5812										
DCN	1634	broad.mit.edu	37	chr12	91539867	91539867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccgagttgaatggcagagcGcacgtagacacatctgaagg	13	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:91539867G>A	ENST00000052754.5	-	8	1549	c.1048C>T	c.(1048-1050)Cgc>Tgc	p.R350C	DCN_ENST00000552962.1_Missense_Mutation_p.R350C|DCN_ENST00000547568.2_Missense_Mutation_p.R203C|DCN_ENST00000441303.2_Missense_Mutation_p.R163C|DCN_ENST00000228329.5_Missense_Mutation_p.R241C|DCN_ENST00000420120.2_Missense_Mutation_p.R241C|DCN_ENST00000393155.1_Missense_Mutation_p.R350C|DCN_ENST00000425043.1_Missense_Mutation_p.R203C|DCN_ENST00000303320.3_Missense_Mutation_p.R163C	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	350					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)	p.R350C(1)		central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						ATGGCAGAGCGCACGTAGACA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											115	113	114					12																	91539867		2203	4300	6503	90063998	SO:0001583	missense	1634			AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.1048C>T	12.37:g.91539867G>A	ENSP00000052754:p.Arg350Cys		90063998	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Missense_Mutation	SNP	ENST00000052754.5	37	CCDS9039.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	31|31	5.099193|5.099193	0.94197|0.94197	.|.	.|.	ENSG00000011465|ENSG00000011465	ENST00000548218|ENST00000052754;ENST00000228329;ENST00000303320;ENST00000393155;ENST00000425043;ENST00000552962;ENST00000420120;ENST00000441303;ENST00000547568	.|T;T;T;T;T;T;T;T;T	.|0.79454	.|0.26;-0.0;-1.27;0.26;0.22;0.26;-0.0;-1.27;0.22	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89245|0.89245	0.6660|0.6660	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.999;1.0;1.0;1.0	.|P;D;D;D	.|0.83275	.|0.727;0.996;0.909;0.913	D|D	0.90008|0.90008	0.4119|0.4119	5|10	.|0.87932	.|D	.|0	.|.	19.6547|19.6547	0.95831|0.95831	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|350;163;203;241	.|P07585;P07585-4;P07585-3;P07585-2	.|PGS2_HUMAN;.;.;.	V|C	40|350;241;163;350;203;350;241;163;203	.|ENSP00000052754:R350C;ENSP00000228329:R241C;ENSP00000302031:R163C;ENSP00000376862:R350C;ENSP00000401021:R203C;ENSP00000447654:R350C;ENSP00000413723:R241C;ENSP00000399815:R163C;ENSP00000447674:R203C	.|ENSP00000052754:R350C	A|R	-|-	2|1	0|0	DCN|DCN	90063998|90063998	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.875000|7.875000	0.87205|0.87205	2.661000|2.661000	0.90470|0.90470	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.408	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		A	91539867	G	A	91539867	3	1	47	1	0	0	0	0	1	0	0	0	4303	1087	38	1	35	1	DCN	12	91539867	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	192251	91539867	42312028	1416	5813										
FGD6	55785	broad.mit.edu	37	chr12	95488438	95488438	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctattgccctggaaatcGcttctagccattcatccctt	5	14	3	0	rs377183623		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:95488438G>A	ENST00000343958.4	-	15	3753	c.3530C>T	c.(3529-3531)gCg>gTg	p.A1177V	FGD6_ENST00000546711.1_Missense_Mutation_p.A1177V|FGD6_ENST00000549499.1_Missense_Mutation_p.A1177V	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1177	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.A1177V(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CCTGGAAATCGCTTCTAGCCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	VAL/ALA	0,4406		0,0,2203	151	147	148		3530	5.2	0.9	12		148	1,8599	1.2+/-3.3	0,1,4299	no	missense	FGD6	NM_018351.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1177/1431	95488438	1,13005	2203	4300	6503	94012569	SO:0001583	missense	55785			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3530C>T	12.37:g.95488438G>A	ENSP00000344446:p.Ala1177Val		94012569	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.386941	0.61956	0.0	1.16E-4	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000551521;ENST00000549499	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	6.04	5.15	0.70609	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.48767	D	0.000171	D	0.85860	0.5795	L	0.42245	1.32	0.58432	D	0.999999	P;D	0.89917	0.938;1.0	P;D	0.97110	0.653;1.0	D	0.85902	0.1435	10	0.45353	T	0.12	-14.1217	15.5249	0.75894	0.0661:0.0:0.9339:0.0	.	1177;1177	Q6ZV73-2;Q6ZV73	.;FGD6_HUMAN	V	1177;1177;173;1177	ENSP00000344446:A1177V;ENSP00000450342:A1177V;ENSP00000450240:A173V;ENSP00000449005:A1177V	ENSP00000344446:A1177V	A	-	2	0	FGD6	94012569	1.000000	0.71417	0.946000	0.38457	0.993000	0.82548	9.139000	0.94554	1.568000	0.49683	0.561000	0.74099	GCG		0.388	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		A	95488438	G	A	95488438	3	1	47	1	0	0	0	0	1	0	0	0	5856	1087	38	1	790	1	FGD6	12	95488438	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3948571	95488438	38363457	1417	5814										
MYBPC1	4604	broad.mit.edu	37	chr12	102060533	102060533	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctcaaaggtacatcagcaAaacagtctgatgaaaatggg	9	7	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:102060533A>C	ENST00000550270.1	+	21	2293	c.2293A>C	c.(2293-2295)Aaa>Caa	p.K765Q	MYBPC1_ENST00000452455.2_Missense_Mutation_p.K765Q|MYBPC1_ENST00000441232.1_Missense_Mutation_p.K765Q|MYBPC1_ENST00000545503.2_Intron|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000360610.2_Missense_Mutation_p.K765Q|MYBPC1_ENST00000541119.1_Intron|MYBPC1_ENST00000536007.1_Intron|MYBPC1_ENST00000549145.1_Missense_Mutation_p.K778Q|MYBPC1_ENST00000547509.1_Intron|MYBPC1_ENST00000361466.2_Intron|MYBPC1_ENST00000551300.1_Intron|MYBPC1_ENST00000547405.1_Intron|MYBPC1_ENST00000553190.1_Intron|MYBPC1_ENST00000392934.3_Intron|MYBPC1_ENST00000361685.2_Intron			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	765	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.K765Q(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						TACATCAGCAAAACAGTCTGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											135	142	140					12																	102060533		2203	4300	6503	100584664	SO:0001583	missense	4604				CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.2293A>C	12.37:g.102060533A>C	ENSP00000449702:p.Lys765Gln		100584664	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.698087	0.48307	.	.	ENSG00000196091	ENST00000452455;ENST00000441232;ENST00000360610;ENST00000549145;ENST00000550270	T;T;T;T;T	0.60299	0.21;0.2;0.21;0.21;0.21	5.48	5.48	0.80851	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.37625	0.1010	N	0.14661	0.345	0.18873	N	0.999987	P;P	0.35793	0.521;0.521	B;B	0.35182	0.197;0.197	T	0.16837	-1.0389	9	0.34782	T	0.22	.	6.3807	0.21533	0.8721:0.0:0.1279:0.0	.	765;765	E7EWS6;Q00872	.;MYPC1_HUMAN	Q	765;765;765;778;765	ENSP00000400908:K765Q;ENSP00000388989:K765Q;ENSP00000353822:K765Q;ENSP00000447660:K778Q;ENSP00000449702:K765Q	ENSP00000353822:K765Q	K	+	1	0	MYBPC1	100584664	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.968000	0.56809	2.307000	0.77673	0.528000	0.53228	AAA		0.368	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			C	102060533	A	C	102060533	3	2	47	1	0	0	0	0	1	0	0	0	10041	15	1	4	2458	4	MYBPC1	12	102060533	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6572095	102060533	31791362	1418	5815										
STAB2	55576	broad.mit.edu	37	chr12	104049075	104049075	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggtacagcaagttcagatCtttgttagaggtaagcactt	10	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:104049075C>A	ENST00000388887.2	+	14	1802	c.1598C>A	c.(1597-1599)tCt>tAt	p.S533Y	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.S533Y(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AAGTTCAGATCTTTGTTAGAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	114	114					12																	104049075		2203	4300	6503	102573205	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1598C>A	12.37:g.104049075C>A	ENSP00000373539:p.Ser533Tyr		102573205		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558702	0.65538	.	.	ENSG00000136011	ENST00000388887	D	0.92249	-3.0	5.71	5.71	0.89125	FAS1 domain (4);	0.277143	0.36815	N	0.002392	D	0.95497	0.8537	M	0.80982	2.52	0.42295	D	0.99215	D	0.71674	0.998	D	0.66979	0.948	D	0.95631	0.8689	10	0.72032	D	0.01	.	12.7882	0.57518	0.0:0.9246:0.0:0.0754	.	533	Q8WWQ8	STAB2_HUMAN	Y	533	ENSP00000373539:S533Y	ENSP00000373539:S533Y	S	+	2	0	STAB2	102573205	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	3.386000	0.52492	2.704000	0.92352	0.561000	0.74099	TCT		0.299	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104049075	C	A	104049075	3	1	47	1	0	0	0	0	1	0	0	0	15277	913	32	2	1652	2	STAB2	12	104049075	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1988542	104049075	29802820	1419	5816										
STAB2	55576	broad.mit.edu	37	chr12	104054536	104054536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatacagttcaacaccaccGacaatgtaagtgaaaactca	5	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:104054536G>A	ENST00000388887.2	+	17	2068	c.1864G>A	c.(1864-1866)Gac>Aac	p.D622N	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.D622N(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CAACACCACCGACAATGTAAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											193	156	169					12																	104054536		2203	4300	6503	102578666	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1864G>A	12.37:g.104054536G>A	ENSP00000373539:p.Asp622Asn		102578666		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	9.875	1.199988	0.22121	.	.	ENSG00000136011	ENST00000388887	D	0.90261	-2.64	5.63	-6.76	0.01732	FAS1 domain (5);	2.263330	0.01515	N	0.018111	D	0.85089	0.5617	L	0.43152	1.355	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.70303	-0.4909	10	0.20046	T	0.44	.	11.1632	0.48528	0.7241:0.0846:0.1913:0.0	.	622	Q8WWQ8	STAB2_HUMAN	N	622	ENSP00000373539:D622N	ENSP00000373539:D622N	D	+	1	0	STAB2	102578666	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.218000	0.09240	-1.172000	0.02762	-0.140000	0.14226	GAC		0.453	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104054536	G	A	104054536	3	1	47	1	0	0	0	0	1	0	0	0	15277	1058	37	1	1930	1	STAB2	12	104054536	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5461	104054536	29797359	1420	5817										
POLR3B	55703	broad.mit.edu	37	chr12	106857272	106857272	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagctacaaaggagcaacaGactcatatattgaaaaagtg	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:106857272G>A	ENST00000228347.4	+	23	2809	c.2587G>A	c.(2587-2589)Gac>Aac	p.D863N	POLR3B_ENST00000539066.1_Missense_Mutation_p.D805N	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	863					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.D863N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						AGGAGCAACAGACTCATATAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	12											68	67	67					12																	106857272		2203	4300	6503	105381402	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.2587G>A	12.37:g.106857272G>A	ENSP00000228347:p.Asp863Asn		105381402	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808245	0.50421	.	.	ENSG00000013503	ENST00000228347;ENST00000539066	T;T	0.71934	-0.61;-0.61	5.73	5.73	0.89815	RNA polymerase Rpb2, OB-fold (1);DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.040742	0.85682	D	0.000000	T	0.58552	0.2130	N	0.12887	0.27	0.80722	D	1	B	0.15719	0.014	B	0.22152	0.038	T	0.52381	-0.8583	10	0.40728	T	0.16	-29.9656	19.8984	0.96975	0.0:0.0:1.0:0.0	.	863	Q9NW08	RPC2_HUMAN	N	863;805	ENSP00000228347:D863N;ENSP00000445721:D805N	ENSP00000228347:D863N	D	+	1	0	POLR3B	105381402	1.000000	0.71417	0.953000	0.39169	0.109000	0.19521	9.827000	0.99397	2.712000	0.92718	0.555000	0.69702	GAC		0.378	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		A	106857272	G	A	106857272	3	1	47	1	0	0	0	0	1	0	0	0	12260	942	33	3	2677	3	POLR3B	12	106857272	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2802736	106857272	26994623	1421	5818										
BTBD11	121551	broad.mit.edu	37	chr12	107914293	107914293	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctaccagacagcctgaatCttcacagagacccacagcgg	9	15	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:107914293C>A	ENST00000280758.5	+	2	1693	c.1165C>A	c.(1165-1167)Ctt>Att	p.L389I	BTBD11_ENST00000490090.2_Missense_Mutation_p.L389I|BTBD11_ENST00000420571.2_Missense_Mutation_p.L389I	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	389						integral component of membrane (GO:0016021)		p.L389I(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CAGCCTGAATCTTCACAGAGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											122	114	117					12																	107914293		2203	4300	6503	106438423	SO:0001583	missense	121551			AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.1165C>A	12.37:g.107914293C>A	ENSP00000280758:p.Leu389Ile		106438423	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.189857	0.57909	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000415943	T;T;T;T	0.53423	1.26;1.31;1.3;0.62	4.1	4.1	0.47936	Histone-fold (2);	0.078670	0.47852	D	0.000210	T	0.50701	0.1631	L	0.42245	1.32	0.80722	D	1	D;P;D	0.54207	0.965;0.849;0.962	P;B;B	0.53360	0.724;0.396;0.438	T	0.40646	-0.9552	10	0.14656	T	0.56	.	17.2433	0.87021	0.0:1.0:0.0:0.0	.	389;389;389	A6QL63-2;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	I	389;389;389;23	ENSP00000280758:L389I;ENSP00000413889:L389I;ENSP00000447319:L389I;ENSP00000407416:L23I	ENSP00000280758:L389I	L	+	1	0	BTBD11	106438423	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	7.335000	0.79234	2.229000	0.72834	0.655000	0.94253	CTT		0.537	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	107914293	C	A	107914293	3	1	47	1	0	0	0	0	1	0	0	0	1542	913	32	2	1171	2	BTBD11	12	107914293	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1057021	107914293	25937602	1422	5819										
WSCD2	9671	broad.mit.edu	37	chr12	108604021	108604021	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcgagcgaggcagcgtgtgCggcggcgccaaccgcctctc	17	15	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:108604021C>T	ENST00000332082.4	+	5	1439	c.621C>T	c.(619-621)tgC>tgT	p.C207C	WSCD2_ENST00000549903.1_Silent_p.C207C|WSCD2_ENST00000261400.3_Silent_p.C207C|WSCD2_ENST00000547525.1_Silent_p.C207C			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	207	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)		p.C207C(2)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						GCAGCGTGTGCGGCGGCGCCA	0.682																																																2	Substitution - coding silent(2)	large_intestine(2)	12											15	21	19					12																	108604021		2198	4280	6478	107128151	SO:0001819	synonymous_variant	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.621C>T	12.37:g.108604021C>T			107128151	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	37	CCDS41828.1																																																																																				0.682	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108604021	C	T	108604021	2	4	47	1	0	0	0	0	0	0	0	1	17447	776	27	1		1	WSCD2	12	108604021	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	689728	108604021	25247874	1423	5820										
WSCD2	9671	broad.mit.edu	37	chr12	108618546	108618546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgttccggggctgcttccGcaggcccgacaacctttccc	11	16	0	0	rs139768498	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:108618546G>A	ENST00000332082.4	+	6	1531	c.713G>A	c.(712-714)cGc>cAc	p.R238H	WSCD2_ENST00000549903.1_Missense_Mutation_p.R238H|WSCD2_ENST00000261400.3_Missense_Mutation_p.R238H|WSCD2_ENST00000547525.1_Missense_Mutation_p.R238H			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	238	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)		p.R238H(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						GGCTGCTTCCGCAGGCCCGAC	0.532													G|||	7	0.00139776	0.0053	0	5008	,	,		21813	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	HIS/ARG	4,3828		0,4,1912	68	72	71		713	2.4	1	12	dbSNP_134	71	1,8271		0,1,4135	yes	missense	WSCD2	NM_014653.2	29	0,5,6047	AA,AG,GG		0.0121,0.1044,0.0413	benign	238/566	108618546	5,12099	1916	4136	6052	107142676	SO:0001583	missense	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.713G>A	12.37:g.108618546G>A	ENSP00000331933:p.Arg238His		107142676	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	13.59	2.282653	0.40394	0.001044	1.21E-4	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000551638;ENST00000332082;ENST00000549903	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	5.39	2.4	0.29515	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.150693	0.64402	N	0.000015	T	0.34513	0.0900	L	0.41961	1.31	0.51482	D	0.999928	B	0.11235	0.004	B	0.14578	0.011	T	0.35126	-0.9801	10	0.54805	T	0.06	-36.3526	10.5165	0.44892	0.2469:0.0:0.7531:0.0	.	238	Q2TBF2	WSCD2_HUMAN	H	238;238;85;238;238	ENSP00000448047:R238H;ENSP00000261400:R238H;ENSP00000446744:R85H;ENSP00000331933:R238H;ENSP00000447272:R238H	ENSP00000261400:R238H	R	+	2	0	WSCD2	107142676	0.790000	0.28787	0.993000	0.49108	0.632000	0.37999	0.856000	0.27818	0.847000	0.35167	0.655000	0.94253	CGC		0.532	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		A	108618546	G	A	108618546	3	1	47	1	0	0	0	0	1	0	0	0	17447	1087	38	1	727	1	WSCD2	12	108618546	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	14525	108618546	25233349	1424	5821										
FOXN4	121643	broad.mit.edu	37	chr12	109723184	109723184	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catctcctcctccatcttgtCgatgcgggccaggttcagag	10	14	3	1	rs373055287		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:109723184C>T	ENST00000299162.5	-	8	930	c.826G>A	c.(826-828)Gac>Aac	p.D276N	FOXN4_ENST00000355216.1_Missense_Mutation_p.D96N	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	276					amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D276N(1)|p.D96N(1)		large_intestine(5)|lung(9)|ovary(2)	16						TCCATCTTGTCGATGCGGGCC	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	12						C	ASN/ASP	0,4406		0,0,2203	82	65	71		826	3.8	1	12		71	1,8599	1.2+/-3.3	0,1,4299	no	missense	FOXN4	NM_213596.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	276/518	109723184	1,13005	2203	4300	6503	108207567	SO:0001583	missense	121643			AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"Forkhead boxes"	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.826G>A	12.37:g.109723184C>T	ENSP00000299162:p.Asp276Asn		108207567	Q6ZMR4|Q96NZ0	Missense_Mutation	SNP	ENST00000299162.5	37	CCDS9126.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.28|15.28	2.785985|2.785985	0.49997|0.49997	0.0|0.0	1.16E-4|1.16E-4	ENSG00000139445|ENSG00000139445	ENST00000355216;ENST00000299162|ENST00000266856	D;D|.	0.95412|.	-3.7;-3.7|.	4.71|4.71	3.81|3.81	0.43845|0.43845	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59945|0.59945	0.2231|0.2231	L|L	0.43598|0.43598	1.365|1.365	0.80722|0.80722	D|D	1|1	P;P|.	0.52692|.	0.955;0.955|.	P;P|.	0.51079|.	0.658;0.557|.	T|T	0.63207|0.63207	-0.6689|-0.6689	10|6	0.14252|0.87932	T|D	0.57|0	-10.5193|-10.5193	12.1006|12.1006	0.53780|0.53780	0.0:0.916:0.0:0.084|0.0:0.916:0.0:0.084	.|.	276;276|.	A6H901;Q96NZ1|.	.;FOXN4_HUMAN|.	N|Q	96;276|234	ENSP00000347354:D96N;ENSP00000299162:D276N|.	ENSP00000299162:D276N|ENSP00000266856:R234Q	D|R	-|-	1|2	0|0	FOXN4|FOXN4	108207567|108207567	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.891000|0.891000	0.51852|0.51852	7.783000|7.783000	0.85696|0.85696	1.109000|1.109000	0.41680|0.41680	0.555000|0.555000	0.69702|0.69702	GAC|CGA		0.612	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735		T	109723184	C	T	109723184	3	4	47	1	0	0	0	0	1	0	0	0	6041	884	31	1	739	1	FOXN4	12	109723184	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1104638	109723184	24128711	1425	5822										
ATP2A2	488	broad.mit.edu	37	chr12	110778764	110778764	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccacaagtctaaaatcgtaGaatttcttcagtcttttgat	5	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:110778764G>T	ENST00000539276.2	+	14	2171	c.2062G>T	c.(2062-2064)Gaa>Taa	p.E688*	ATP2A2_ENST00000395494.2_Nonsense_Mutation_p.E661*|ATP2A2_ENST00000308664.6_Nonsense_Mutation_p.E688*			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	688					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)	p.E688*(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TAAAATCGTAGAATTTCTTCA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											45	47	46					12																	110778764		2203	4300	6503	109263147	SO:0001587	stop_gained	488				CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2062G>T	12.37:g.110778764G>T	ENSP00000440045:p.Glu688*		109263147	A6NDN7|B4DF05|P16614|Q86VJ2	Nonsense_Mutation	SNP	ENST00000539276.2	37	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.601956|6.601956	0.97697|0.97697	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000308664;ENST00000395494;ENST00000539276|ENST00000548169	.|.	.|.	.|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80037	.|0.4550	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77705	.|-0.2488	.|3	0.25106|.	T|.	0.35|.	.|.	20.0784|20.0784	0.97758|0.97758	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	688;661;688|578	.|.	ENSP00000311186:E688X|.	E|R	+|+	1|2	0|0	ATP2A2|ATP2A2	109263147|109263147	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.989000|0.989000	0.77384|0.77384	9.869000|9.869000	0.99810|0.99810	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.483	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		T	110778764	G	T	110778764	4	4	47	1	0	0	0	0	0	1	0	0	1138	943	33	2	2116	2	ATP2A2	12	110778764	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1055580	110778764	23073131	1426	5823										
MYL2	4633	broad.mit.edu	37	chr12	111353562	111353562	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatcgttcttgtcaatgaaGccatccctgttctggtccat	8	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:111353562G>A	ENST00000228841.8	-	3	173	c.126C>T	c.(124-126)ggC>ggT	p.G42G	MYL2_ENST00000548438.1_Intron	NM_000432.3	NP_000423.2	P10916	MLRV_HUMAN	myosin, light chain 2, regulatory, cardiac, slow	42	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cardiac muscle contraction (GO:0060048)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle cell fate specification (GO:0042694)|muscle fiber development (GO:0048747)|muscle filament sliding (GO:0030049)|negative regulation of cell growth (GO:0030308)|post-embryonic development (GO:0009791)|regulation of striated muscle contraction (GO:0006942)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|myofibril (GO:0030016)|myosin complex (GO:0016459)|sarcomere (GO:0030017)	actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)	p.G42G(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)	12						TGTCAATGAAGCCATCCCTGT	0.527																																					GBM(14;268 426 18829 21617 25540)											1	Substitution - coding silent(1)	large_intestine(1)	12											241	206	218					12																	111353562		2203	4300	6503	109837945	SO:0001819	synonymous_variant	4633				CCDS31901.1	12q24.11	2014-09-17	2006-09-29		ENSG00000111245	ENSG00000111245		"Myosins / Light chain", "EF-hand domain containing"	7583	protein-coding gene	gene with protein product	"cardiac ventricular myosin light chain 2"	160781	"myosin, light polypeptide 2, regulatory, cardiac, slow"			1386340	Standard	NM_000432		Approved	CMH10	uc001try.4	P10916	OTTHUMG00000169535	ENST00000228841.8:c.126C>T	12.37:g.111353562G>A			109837945	Q16123	Silent	SNP	ENST00000228841.8	37	CCDS31901.1																																																																																				0.527	MYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404677.2	NM_000432		A	111353562	G	A	111353562	2	1	47	1	0	0	0	0	0	0	0	1	10077	958	34	3		3	MYL2	12	111353562	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	574798	111353562	22498333	1427	5824										
RPL6	6128	broad.mit.edu	37	chr12	112843793	112843793	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggttgaagtggcaatgacaAatttctggtgtgttcttcgt	12	5	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:112843793A>C	ENST00000424576.2	-	6	763	c.578T>G	c.(577-579)tTt>tGt	p.F193C	RPL6_ENST00000202773.9_Missense_Mutation_p.F193C	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	193				LNRVPLRRTHQKFVIATSTKIDISN -> SIEFLYEEHTRN LSLPLQPKSISAI (in Ref. 5; AAB30819). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.F193C(2)		cervix(1)|large_intestine(6)|lung(3)	10						GGCAATGACAAATTTCTGGTG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	12											48	50	49					12																	112843793		2203	4298	6501	111328176	SO:0001583	missense	6128			X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"L ribosomal proteins"	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.578T>G	12.37:g.112843793A>C	ENSP00000403172:p.Phe193Cys		111328176	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.167826	0.57476	.	.	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.35048	1.33;1.33	5.05	5.05	0.67936	Translation protein SH3-like, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.47930	0.1472	M	0.85630	2.765	0.58432	D	0.999997	B	0.19200	0.034	B	0.27262	0.078	T	0.53542	-0.8424	10	0.87932	D	0	.	14.8254	0.70107	1.0:0.0:0.0:0.0	.	193	Q02878	RL6_HUMAN	C	193;193;133	ENSP00000202773:F193C;ENSP00000403172:F193C	ENSP00000202773:F193C	F	-	2	0	RPL6	111328176	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.604000	0.90877	1.906000	0.55180	0.482000	0.46254	TTT		0.413	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1			C	112843793	A	C	112843793	3	2	47	1	0	0	0	0	1	0	0	0	13635	14	1	4	296	4	RPL6	12	112843793	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1490231	112843793	21008102	1428	5825										
PLBD2	196463	broad.mit.edu	37	chr12	113821939	113821939	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaccaccattggcaacaaGaacccagccctgtggaagta	10	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:113821939G>T	ENST00000280800.3	+	7	1018	c.987G>T	c.(985-987)aaG>aaT	p.K329N	PLBD2_ENST00000545182.2_Missense_Mutation_p.K329N	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	329					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.K329N(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TTGGCAACAAGAACCCAGCCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	12											69	61	64					12																	113821939		2203	4300	6503	112306322	SO:0001583	missense	196463			BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"PLB homolog 2 (Dictyostelium)", "mannose-6-phosphate protein associated protein p76"					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.987G>T	12.37:g.113821939G>T	ENSP00000280800:p.Lys329Asn		112306322	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	37	CCDS9168.1	.	.	.	.	.	.	.	.	.	.	G	8.895	0.954941	0.18431	.	.	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.17528	2.27;2.27	4.84	3.95	0.45737	.	0.722612	0.13003	N	0.421508	T	0.08223	0.0205	N	0.10972	0.075	0.27211	N	0.959906	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.36187	-0.9758	10	0.18276	T	0.48	-12.2249	6.4492	0.21894	0.0:0.4813:0.3019:0.2169	.	329;329	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	N	329	ENSP00000443463:K329N;ENSP00000280800:K329N	ENSP00000280800:K329N	K	+	3	2	PLBD2	112306322	0.997000	0.39634	0.998000	0.56505	0.956000	0.61745	1.160000	0.31761	1.020000	0.39573	0.305000	0.20034	AAG		0.622	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542		T	113821939	G	T	113821939	3	4	47	1	0	0	0	0	1	0	0	0	12057	933	33	2	1013	2	PLBD2	12	113821939	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	978146	113821939	20029956	1429	5826										
RBM19	9904	broad.mit.edu	37	chr12	114397111	114397111	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccggcttgctcttccctttCgagggctcagcatccaggcc	11	16	2	0	rs573482794	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:114397111C>T	ENST00000545145.2	-	5	555	c.477G>A	c.(475-477)tcG>tcA	p.S159S	RBM19_ENST00000261741.5_Silent_p.S159S|RBM19_ENST00000392561.3_Silent_p.S159S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	159					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S159S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCTTCCCTTTCGAGGGCTCAG	0.597													C|||	2	0.000399361	8e-04	0	5008	,	,		16881	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	12											120	101	108					12																	114397111		2203	4300	6503	112881494	SO:0001819	synonymous_variant	9904			AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.477G>A	12.37:g.114397111C>T			112881494	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																				0.597	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114397111	C	T	114397111	2	4	47	1	0	0	0	0	0	0	0	1	13158	871	31	1		1	RBM19	12	114397111	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	575172	114397111	19454784	1430	5827										
MED13L	23389	broad.mit.edu	37	chr12	116675341	116675341	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accagaatatccataactctTtgcaatctggtttgacatca	5	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:116675341T>G	ENST00000281928.3	-	2	448	c.242A>C	c.(241-243)aAa>aCa	p.K81T	MED13L_ENST00000551197.1_5'UTR	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	81						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.K81T(1)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CCATAACTCTTTGCAATCTGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											152	137	142					12																	116675341		2203	4300	6503	115159724	SO:0001583	missense	23389			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.242A>C	12.37:g.116675341T>G	ENSP00000281928:p.Lys81Thr		115159724	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.666385	0.67814	.	.	ENSG00000123066	ENST00000281928;ENST00000548743	T;T	0.81247	-1.47;-1.47	5.57	4.44	0.53790	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.64402	D	0.000002	D	0.85177	0.5637	L	0.58510	1.815	0.45161	D	0.998172	D	0.63046	0.992	D	0.63283	0.913	D	0.86364	0.1719	10	0.87932	D	0	.	10.9116	0.47112	0.0:0.0734:0.0:0.9266	.	81	Q71F56	MD13L_HUMAN	T	81;71	ENSP00000281928:K81T;ENSP00000448553:K71T	ENSP00000281928:K81T	K	-	2	0	MED13L	115159724	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.101000	0.64566	2.123000	0.65237	0.459000	0.35465	AAA		0.423	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			G	116675341	T	G	116675341	3	3	47	1	0	0	0	0	1	0	0	0	9461	1841	64	4	6510	4	MED13L	12	116675341	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2278230	116675341	17176554	1431	5828										
FBXO21	23014	broad.mit.edu	37	chr12	117610305	117610305	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttggcaccaccttaataaGaagtgacttgggaagttgac	10	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:117610305G>T	ENST00000330622.5	-	7	983	c.984C>A	c.(982-984)ttC>ttA	p.F328L	FBXO21_ENST00000549689.1_5'Flank|FBXO21_ENST00000427718.2_Missense_Mutation_p.F328L			O94952	FBX21_HUMAN	F-box protein 21	328					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)	p.F328L(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|pancreas(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	29	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		ACCTTAATAAGAAGTGACTTG	0.502																																					GBM(168;452 2038 13535 17701 43680)											1	Substitution - Missense(1)	large_intestine(1)	12											117	105	109					12																	117610305		2203	4300	6503	116094688	SO:0001583	missense	23014			AB020682	CCDS9184.1, CCDS44989.1	12q24.23	2004-06-15	2004-06-15					"F-boxes /  "other""	13592	protein-coding gene	gene with protein product		609095	"F-box only protein 21"			10048485, 10531035	Standard	NM_033624		Approved	FBX21, KIAA0875	uc001twk.3	O94952	OTTHUMG00000169495	ENST00000330622.5:c.984C>A	12.37:g.117610305G>T	ENSP00000328187:p.Phe328Leu		116094688	B3KMF0|Q5BJG0|Q9H087	Missense_Mutation	SNP	ENST00000330622.5	37	CCDS9184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.9|26.9	4.786137|4.786137	0.90282|0.90282	.|.	.|.	ENSG00000135108|ENSG00000135108	ENST00000427718;ENST00000257563;ENST00000535590;ENST00000330622|ENST00000550180	T;T|.	0.57752|.	0.39;0.38|.	5.45|5.45	4.55|4.55	0.56014|0.56014	F-box domain, Skp2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62865|0.62865	0.2463|0.2463	L|L	0.53729|0.53729	1.69|1.69	0.53005|0.53005	D|D	0.999967|0.999967	D;D;D|.	0.76494|.	0.999;0.979;0.993|.	D;D;P|.	0.85130|.	0.997;0.982;0.876|.	T|T	0.60047|0.60047	-0.7339|-0.7339	10|5	0.37606|.	T|.	0.19|.	-12.0798|-12.0798	12.7378|12.7378	0.57234|0.57234	0.1341:0.0:0.8659:0.0|0.1341:0.0:0.8659:0.0	.|.	244;328;328|.	Q8IUQ5;O94952;O94952-1|.	.;FBX21_HUMAN;.|.	L|I	328;244;244;328|272	ENSP00000414468:F328L;ENSP00000328187:F328L|.	ENSP00000257563:F244L|.	F|L	-|-	3|1	2|0	FBXO21|FBXO21	116094688|116094688	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.897000|0.897000	0.52465|0.52465	3.845000|3.845000	0.55880|0.55880	2.579000|2.579000	0.87056|0.87056	0.655000|0.655000	0.94253|0.94253	TTC|CTT		0.502	FBXO21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404409.1	NM_033624		T	117610305	G	T	117610305	3	4	47	1	0	0	0	0	1	0	0	0	5752	933	33	2	926	2	FBXO21	12	117610305	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	934964	117610305	16241590	1432	5829										
KSR2	283455	broad.mit.edu	37	chr12	118405898	118405898	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacctccagggtccggatttCtttttgtgtgaggtcgttgg	13	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:118405898C>A	ENST00000339824.5	-	1	890	c.163G>T	c.(163-165)Gaa>Taa	p.E55*	KSR2_ENST00000425217.1_Nonsense_Mutation_p.E26*			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	55					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.E87*(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTCCGGATTTCTTTTTGTGTG	0.458																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											216	188	197					12																	118405898		1568	3582	5150	116890281	SO:0001587	stop_gained	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.163G>T	12.37:g.118405898C>A	ENSP00000339952:p.Glu55*		116890281	A0PJT2|Q3B828|Q8N775	Nonsense_Mutation	SNP	ENST00000339824.5	37		.	.	.	.	.	.	.	.	.	.	C	39	7.471112	0.98306	.	.	ENSG00000171435	ENST00000425217;ENST00000339824	.	.	.	4.74	4.74	0.60224	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	15.2228	0.73327	0.0:1.0:0.0:0.0	.	.	.	.	X	26;55	.	ENSP00000339952:E55X	E	-	1	0	KSR2	116890281	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.802000	0.75175	2.158000	0.67659	0.491000	0.48974	GAA		0.458	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		A	118405898	C	A	118405898	4	1	47	1	0	0	0	0	0	1	0	0	8604	922	32	2	2769	2	KSR2	12	118405898	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	795593	118405898	15445997	1433	5830										
VSIG10	54621	broad.mit.edu	37	chr12	118511730	118511730	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggtaggccccagacacctgGcatgtaagcgtcacattgcc	12	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:118511730G>A	ENST00000359236.5	-	5	1269	c.993C>T	c.(991-993)tgC>tgT	p.C331C		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	331	Ig-like C2-type 4.					integral component of membrane (GO:0016021)		p.C331C(1)		endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CAGACACCTGGCATGTAAGCG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	12											50	51	51					12																	118511730		1944	4150	6094	116996113	SO:0001819	synonymous_variant	54621				CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.993C>T	12.37:g.118511730G>A			116996113	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																				0.562	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		A	118511730	G	A	118511730	2	1	47	1	0	0	0	0	0	0	0	1	17263	1195	42	3		3	VSIG10	12	118511730	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	105832	118511730	15340165	1434	5831										
CIT	11113	broad.mit.edu	37	chr12	120159173	120159173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcttcagtagatcagcccGatctagagcttcttgcagtc	9	11	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:120159173G>A	ENST00000261833.7	-	28	3599	c.3547C>T	c.(3547-3549)Cgg>Tgg	p.R1183W	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.R1225W	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1183	Interaction with Rho/Rac.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R1226W(1)|p.R1183W(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		AGATCAGCCCGATCTAGAGCT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	12											157	138	144					12																	120159173		2203	4300	6503	118643556	SO:0001583	missense	11113			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3547C>T	12.37:g.120159173G>A	ENSP00000261833:p.Arg1183Trp		118643556	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745423	0.89663	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.65364	-0.11;-0.15	5.91	5.01	0.66863	.	0.070538	0.64402	D	0.000014	T	0.61048	0.2316	L	0.34521	1.04	0.51233	D	0.999913	D;D;D	0.76494	0.999;0.999;0.997	P;P;P	0.50490	0.642;0.642;0.627	T	0.66139	-0.5998	10	0.87932	D	0	.	14.7712	0.69679	0.0:0.0:0.7369:0.2631	.	1225;1183;716	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	W	1225;1183	ENSP00000376306:R1225W;ENSP00000261833:R1183W	ENSP00000261833:R1183W	R	-	1	2	CIT	118643556	1.000000	0.71417	0.959000	0.39883	0.997000	0.91878	5.662000	0.68032	1.474000	0.48178	0.655000	0.94253	CGG		0.473	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		A	120159173	G	A	120159173	3	1	47	1	0	0	0	0	1	0	0	0	3444	1057	37	1	2616	1	CIT	12	120159173	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1647443	120159173	13692722	1435	5832										
CLIP1	6249	broad.mit.edu	37	chr12	122825734	122825734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attctgcaaattttctatttCgtgttggtaatctagtctca	6	7	4	0	rs201352592		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:122825734C>T	ENST00000540338.1	-	10	2058	c.2017G>A	c.(2017-2019)Gaa>Aaa	p.E673K	CLIP1_ENST00000358808.2_Missense_Mutation_p.E662K|CLIP1_ENST00000537178.1_Missense_Mutation_p.E627K|CLIP1_ENST00000545889.1_Missense_Mutation_p.E363K|CLIP1_ENST00000361654.4_Missense_Mutation_p.E627K|CLIP1_ENST00000302528.7_Missense_Mutation_p.E662K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	673					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.E662K(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TTTTCTATTTCGTGTTGGTAA	0.388													C|||	1	0.000199681	8e-04	0	5008	,	,		20755	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						C	LYS/GLU,LYS/GLU	3,4403	4.2+/-10.8	0,3,2200	138	142	141		1984,1879	4.6	0.9	12		141	0,8600		0,0,4300	no	missense,missense	CLIP1	NM_002956.2,NM_198240.1	56,56	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging,probably-damaging	662/1428,627/1393	122825734	3,13003	2203	4300	6503	121391687	SO:0001583	missense	6249				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.2017G>A	12.37:g.122825734C>T	ENSP00000439093:p.Glu673Lys		121391687	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	27.6	4.848676	0.91277	6.81E-4	0.0	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.63744	2.53;0.62;0.62;0.51;0.56;-0.06	5.5	4.61	0.57282	.	0.105274	0.64402	N	0.000003	T	0.75273	0.3827	M	0.71036	2.16	0.58432	D	0.999999	P;D;D;D	0.71674	0.681;0.997;0.997;0.998	B;D;D;P	0.64042	0.071;0.921;0.921;0.906	T	0.76011	-0.3115	10	0.40728	T	0.16	-14.727	14.5804	0.68284	0.0:0.9298:0.0:0.0702	.	363;627;662;673	F5H0N7;P30622-2;P30622-1;P30622	.;.;.;CLIP1_HUMAN	K	363;662;662;507;627;673;596	ENSP00000438743:E363K;ENSP00000303585:E662K;ENSP00000351665:E662K;ENSP00000445531:E627K;ENSP00000439093:E673K;ENSP00000437786:E596K	ENSP00000303585:E662K	E	-	1	0	CLIP1	121391687	1.000000	0.71417	0.909000	0.35828	0.985000	0.73830	7.445000	0.80570	1.459000	0.47892	0.655000	0.94253	GAA		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122825734	C	T	122825734	3	4	47	1	0	0	0	0	1	0	0	0	3538	893	31	1	2363	1	CLIP1	12	122825734	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2666561	122825734	11026161	1436	5833										
ZCCHC8	55596	broad.mit.edu	37	chr12	122966147	122966147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtgggtaccctagctggcGcatccgatagataaaaggtg	14	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:122966147G>A	ENST00000336229.4	-	10	1070	c.940C>T	c.(940-942)Cgc>Tgc	p.R314C	ZCCHC8_ENST00000543897.1_Missense_Mutation_p.R76C|ZCCHC8_ENST00000536306.1_Missense_Mutation_p.R76C	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	314					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R314C(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		CCTAGCTGGCGCATCCGATAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											92	91	91					12																	122966147		1835	4091	5926	121532100	SO:0001583	missense	55596			BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.940C>T	12.37:g.122966147G>A	ENSP00000337313:p.Arg314Cys		121532100	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	G	23.5	4.424067	0.83667	.	.	ENSG00000033030	ENST00000536306;ENST00000543897;ENST00000336229;ENST00000544054;ENST00000536663	T;T;T	0.70282	-0.47;-0.47;0.08	5.47	4.54	0.55810	PSP, proline-rich (2);	0.000000	0.85682	D	0.000000	D	0.85652	0.5746	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88226	0.2900	10	0.87932	D	0	-13.2062	15.6143	0.76753	0.0:0.0:0.8619:0.1381	.	314	Q6NZY4	ZCHC8_HUMAN	C	76;76;314;76;76	ENSP00000441423:R76C;ENSP00000438993:R76C;ENSP00000337313:R314C	ENSP00000337313:R314C	R	-	1	0	ZCCHC8	121532100	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.411000	0.59781	2.573000	0.86826	0.455000	0.32223	CGC		0.428	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		A	122966147	G	A	122966147	3	1	47	1	0	0	0	0	1	0	0	0	17633	1087	38	1	1203	1	ZCCHC8	12	122966147	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	140413	122966147	10885748	1437	5834										
SBNO1	55206	broad.mit.edu	37	chr12	123810863	123810863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctgcagcttgctgaaaccGctctctggcgatgacccact	9	14	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:123810863G>A	ENST00000602398.1	-	14	1838	c.1711C>T	c.(1711-1713)Cgg>Tgg	p.R571W	SBNO1_ENST00000420886.2_Missense_Mutation_p.R571W|SBNO1_ENST00000602750.1_Missense_Mutation_p.R570W|SBNO1_ENST00000267176.4_Missense_Mutation_p.R570W			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	571					regulation of transcription, DNA-templated (GO:0006355)			p.R570W(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TGCTGAAACCGCTCTCTGGCG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											135	123	127					12																	123810863		2203	4300	6503	122376816	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1711C>T	12.37:g.123810863G>A	ENSP00000473665:p.Arg571Trp		122376816	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057300	0.76074	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	T;T	0.32753	1.44;1.44	6.07	2.88	0.33553	.	0.118377	0.53938	D	0.000046	T	0.29321	0.0730	L	0.29908	0.895	0.49051	D	0.999741	D;P;P	0.57899	0.981;0.917;0.956	B;P;P	0.48227	0.368;0.571;0.502	T	0.09684	-1.0663	10	0.66056	D	0.02	-17.4488	13.7466	0.62879	0.0:0.0:0.3215:0.6785	.	571;570;569	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	W	571;570;570	ENSP00000387361:R571W;ENSP00000267176:R570W	ENSP00000267176:R570W	R	-	1	2	SBNO1	122376816	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	1.591000	0.36665	0.823000	0.34589	0.655000	0.94253	CGG		0.398	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123810863	G	A	123810863	3	1	47	1	0	0	0	0	1	0	0	0	13899	1086	38	1	2546	1	SBNO1	12	123810863	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	844716	123810863	10041032	1438	5835										
DNAH10	196385	broad.mit.edu	37	chr12	124416236	124416236	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atattggccaagtggccaaaGaaatagaaaacaagatgccc	9	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:124416236G>T	ENST00000409039.3	+	74	12641	c.12616G>T	c.(12616-12618)Gaa>Taa	p.E4206*	DNAH10OS_ENST00000514254.2_Intron|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4206					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E2798*(1)|p.E4206*(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGTGGCCAAAGAAATAGAAAA	0.512																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											62	64	63					12																	124416236		1899	4117	6016	122982189	SO:0001587	stop_gained	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.12616G>T	12.37:g.124416236G>T	ENSP00000386770:p.Glu4206*		122982189	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Nonsense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	55	23.501352	0.99955	.	.	ENSG00000197653	ENST00000409039	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9279	0.92552	0.0:0.0:1.0:0.0	.	.	.	.	X	4206	.	ENSP00000386770:E4206X	E	+	1	0	DNAH10	122982189	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.869000	0.99810	2.563000	0.86464	0.655000	0.94253	GAA		0.512	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124416236	G	T	124416236	4	4	47	1	0	0	0	0	0	1	0	0	4609	943	33	2	12910	2	DNAH10	12	124416236	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	605373	124416236	9435659	1439	5836										
BRI3BP	140707	broad.mit.edu	37	chr12	125509608	125509608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccgcgcgctcctgctggtcGgcgtcgtcctcctggcctac	12	19	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:125509608G>A	ENST00000341446.8	+	3	479	c.388G>A	c.(388-390)Ggc>Agc	p.G130S		NM_080626.5	NP_542193.3			BRI3 binding protein									p.G130S(1)		large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		CCTGCTGGTCGGCGTCGTCCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	12											69	64	66					12																	125509608		2203	4300	6503	124075561	SO:0001583	missense	140707			AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.388G>A	12.37:g.125509608G>A	ENSP00000340761:p.Gly130Ser		124075561		Missense_Mutation	SNP	ENST00000341446.8	37	CCDS9262.1	.	.	.	.	.	.	.	.	.	.	g	31	5.086987	0.94100	.	.	ENSG00000184992	ENST00000341446	.	.	.	5.37	5.37	0.77165	.	0.095910	0.64402	D	0.000001	T	0.71804	0.3383	L	0.48642	1.525	0.58432	D	0.999992	D	0.71674	0.998	P	0.60236	0.871	T	0.70156	-0.4949	9	0.39692	T	0.17	-7.6551	19.1126	0.93323	0.0:0.0:1.0:0.0	.	130	Q8WY22	BRI3B_HUMAN	S	130	.	ENSP00000340761:G130S	G	+	1	0	BRI3BP	124075561	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	9.284000	0.95882	2.495000	0.84180	0.556000	0.70494	GGC		0.637	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		A	125509608	G	A	125509608	3	1	47	1	0	0	0	0	1	0	0	0	1516	1116	39	1	398	1	BRI3BP	12	125509608	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1093372	125509608	8342287	1440	5837										
RIMBP2	23504	broad.mit.edu	37	chr12	130890752	130890752	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcatcaatttcaccaaaaaCtgtaataatatctcctgtgc	3	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:130890752C>A	ENST00000261655.4	-	17	3125	c.2962G>T	c.(2962-2964)Gtt>Ttt	p.V988F		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	988	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.V988F(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCACCAAAAACTGTAATAATA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	12											56	59	58					12																	130890752		2203	4299	6502	129456705	SO:0001583	missense	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2962G>T	12.37:g.130890752C>A	ENSP00000261655:p.Val988Phe		129456705	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110403	0.77210	.	.	ENSG00000060709	ENST00000261655;ENST00000536632	T;T	0.59906	0.23;0.23	5.26	5.26	0.73747	Src homology-3 domain (3);Variant SH3 (1);	0.000000	0.64402	D	0.000001	D	0.82518	0.5054	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86701	0.1929	10	0.87932	D	0	-13.8408	19.2114	0.93757	0.0:1.0:0.0:0.0	.	988	O15034	RIMB2_HUMAN	F	988;125	ENSP00000261655:V988F;ENSP00000439030:V125F	ENSP00000261655:V988F	V	-	1	0	RIMBP2	129456705	1.000000	0.71417	0.406000	0.26421	0.949000	0.60115	5.979000	0.70508	2.616000	0.88540	0.563000	0.77884	GTT		0.259	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130890752	C	A	130890752	3	1	47	1	0	0	0	0	1	0	0	0	13400	565	20	2	208	2	RIMBP2	12	130890752	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5381144	130890752	2961143	1441	5838										
POLE	5426	broad.mit.edu	37	chr12	133249847	133249847	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcgacagcatctgacacaGaatacgtggccagagtctga	12	10	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:133249847G>A	ENST00000320574.5	-	14	1419	c.1376C>T	c.(1375-1377)tCt>tTt	p.S459F	POLE_ENST00000535270.1_Missense_Mutation_p.S432F	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	459			S -> F (found in a colorectal sample; somatic mutation). {ECO:0000269|PubMed:23263490}.		base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.S459F(2)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	ATCTGACACAGAATACGTGGC	0.527								DNA polymerases (catalytic subunits)																																								2	Substitution - Missense(2)	large_intestine(2)	12											185	156	166					12																	133249847		2203	4300	6503	131759920	SO:0001583	missense	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.1376C>T	12.37:g.133249847G>A	ENSP00000322570:p.Ser459Phe		131759920	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145562	0.57044	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577;ENST00000535934	T;T;T;T	0.44083	4.77;4.77;4.77;0.93	5.37	4.47	0.54385	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.74007	0.3660	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82255	-0.0548	10	0.87932	D	0	.	13.4599	0.61221	0.0755:0.0:0.9245:0.0	.	432;459	F5H1D6;Q07864	.;DPOE1_HUMAN	F	459;470;432;239;394;77	ENSP00000322570:S459F;ENSP00000406383:S470F;ENSP00000445753:S432F;ENSP00000442519:S239F	ENSP00000322570:S459F	S	-	2	0	POLE	131759920	1.000000	0.71417	0.176000	0.23000	0.185000	0.23345	7.962000	0.87912	2.524000	0.85096	0.313000	0.20887	TCT		0.527	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133249847	G	A	133249847	3	1	47	1	0	0	0	0	1	0	0	0	12227	942	33	3	5628	3	POLE	12	133249847	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2359095	133249847	602048	1442	5839										
ZNF140	7699	broad.mit.edu	37	chr12	133683196	133683196	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaacccctatgaatatgaaAattcatttaattaccactca	2	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr12:133683196A>C	ENST00000355557.2	+	5	2616	c.1333A>C	c.(1333-1335)Aat>Cat	p.N445H	ZNF140_ENST00000544426.1_Missense_Mutation_p.N342H|ZNF140_ENST00000440550.2_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N445H(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TGAATATGAAAATTCATTTAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	61	60					12																	133683196		2200	4292	6492	132193269	SO:0001583	missense	7699			U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1333A>C	12.37:g.133683196A>C	ENSP00000347755:p.Asn445His		132193269	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	37	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.785911	0.49997	.	.	ENSG00000196387	ENST00000355557;ENST00000544426	T;T	0.60548	0.18;0.18	3.47	3.47	0.39725	.	0.204155	0.24368	N	0.039127	T	0.48095	0.1481	L	0.28608	0.87	0.80722	D	1	P	0.42039	0.769	B	0.42882	0.401	T	0.55711	-0.8098	10	0.87932	D	0	.	11.8975	0.52663	1.0:0.0:0.0:0.0	.	445	P52738	ZN140_HUMAN	H	445;342	ENSP00000347755:N445H;ENSP00000445411:N342H	ENSP00000347755:N445H	N	+	1	0	ZNF140	132193269	0.032000	0.19561	1.000000	0.80357	0.989000	0.77384	2.111000	0.41883	1.819000	0.53055	0.460000	0.39030	AAT		0.348	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		C	133683196	A	C	133683196	3	2	47	1	0	0	0	0	1	0	0	0	17768	14	1	4	1347	4	ZNF140	12	133683196	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	433349	133683196	168699	1443	5840										
ZMYM2	7750	broad.mit.edu	37	chr13	20656206	20656206	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atatttattgatcctggataCcaaacatttgagcaagaatt	6	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:20656206C>T	ENST00000382874.2	+	23	3694	c.3504C>T	c.(3502-3504)taC>taT	p.Y1168Y	ZMYM2_ENST00000382869.3_Silent_p.Y1168Y|ZMYM2_ENST00000494061.2_3'UTR|ZMYM2_ENST00000382871.2_Silent_p.Y1168Y	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1168					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.Y1168Y(1)		large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		ATCCTGGATACCAAACATTTG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	13											56	52	53					13																	20656206		1809	4077	5886	19554206	SO:0001819	synonymous_variant	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3504C>T	13.37:g.20656206C>T			19554206	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	37	CCDS45016.1																																																																																				0.338	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		T	20656206	C	T	20656206	2	4	47	1	0	0	0	0	0	0	0	1	17739	518	18	3		3	ZMYM2	13	20656206	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09		20656206	94513672	1444	5841										
ZMYM2	7750	broad.mit.edu	37	chr13	20657133	20657133	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaaaacaaagcgtgtcttCgataccaagtgtcttccttg	9	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:20657133C>T	ENST00000382874.2	+	24	3971	c.3781C>T	c.(3781-3783)Cga>Tga	p.R1261*	ZMYM2_ENST00000382869.3_Nonsense_Mutation_p.R1261*|ZMYM2_ENST00000494061.2_3'UTR|ZMYM2_ENST00000382871.2_Nonsense_Mutation_p.R1261*	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.R1261*(1)		large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		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)		AGCGTGTCTTCGATACCAAGT	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											69	64	65					13																	20657133		1851	4099	5950	19555133	SO:0001587	stop_gained	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3781C>T	13.37:g.20657133C>T	ENSP00000372327:p.Arg1261*		19555133	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Nonsense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	C	43	10.432931	0.99404	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382870	.	.	.	5.0	4.15	0.48705	.	0.212247	0.43747	D	0.000531	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.4688	13.4861	0.61366	0.2844:0.7156:0.0:0.0	.	.	.	.	X	1261;1261;1259;1259;639	.	ENSP00000372322:R1261X	R	+	1	2	ZMYM2	19555133	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.776000	0.47709	1.209000	0.43321	0.484000	0.47621	CGA		0.338	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		T	20657133	C	T	20657133	4	4	47	1	0	0	0	0	0	1	0	0	17739	876	31	1	3863	1	ZMYM2	13	20657133	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	927	20657133	94512745	1445	5842										
PARP4	143	broad.mit.edu	37	chr13	25072367	25072368	+	Splice_Site	DNP	CC	CC	AA													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggcctccctccattcccaCctggaaaacaggatgtgctt							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:25072367_25072368CC>AA	ENST00000381989.3	-	6	583	c.478_478GG>TT	c.(478-480)GGgt>TTggt	p.G160L		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	160					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.?(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCCATTCCCACCTGGAAAACAG	0.46																																																1	Unknown(1)	large_intestine(1)	13																																								23970368	SO:0001630	splice_region_variant	143			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.478_478delinsAA	13.37:g.25072367_25072368delinsAA			23970367	O75903|Q14682|Q5QNZ9|Q9H1M6	Splice_Site	DNP	ENST00000381989.3	37	CCDS9307.1																																																																																				0.46	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	Missense_Mutation	AA	25072368	CC	AA	25072367	5	1	47	1	0	0	0	0	0	0	1	0	11494	521	18	2	4812	2	PARP4	13	25072367	Splice_Site	DNP	CC	TCGA-AG-3892-01A-01W-1073-09	4415234	25072367	90097511	1446	5843										
ATP12A	479	broad.mit.edu	37	chr13	25280568	25280568	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcccggacatccccccagcaGaagctgatcattgtggaggg	13	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:25280568G>T	ENST00000381946.3	+	15	2303	c.2136G>T	c.(2134-2136)caG>caT	p.Q712H	RNY1P7_ENST00000384743.1_RNA|ATP12A_ENST00000218548.6_Missense_Mutation_p.Q718H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	712					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.Q712H(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CCCCCCAGCAGAAGCTGATCA	0.562																																					Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - Missense(1)	large_intestine(1)	13											97	75	83					13																	25280568		2203	4300	6503	24178568	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2136G>T	13.37:g.25280568G>T	ENSP00000371372:p.Gln712His		24178568	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544556	0.65198	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.96232	-3.95;-3.95	5.79	3.0	0.34707	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.64402	D	0.000001	D	0.95968	0.8687	L	0.37630	1.12	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94717	0.7897	10	0.87932	D	0	.	7.8015	0.29176	0.3528:0.0:0.6472:0.0	.	718;712	P54707-2;P54707	.;AT12A_HUMAN	H	718;712	ENSP00000218548:Q718H;ENSP00000371372:Q712H	ENSP00000218548:Q718H	Q	+	3	2	ATP12A	24178568	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.214000	0.42853	0.723000	0.32274	0.563000	0.77884	CAG		0.562	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25280568	G	T	25280568	3	4	47	1	0	0	0	0	1	0	0	0	1123	933	33	2	2212	2	ATP12A	13	25280568	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	208201	25280568	89889310	1447	5844										
RNF17	56163	broad.mit.edu	37	chr13	25367460	25367460	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccctgatgtgataattgaaGaaattattgaagacaacgtg	10	5	0	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:25367460G>T	ENST00000255324.5	+	10	1268	c.1216G>T	c.(1216-1218)Gaa>Taa	p.E406*	RNF17_ENST00000381921.1_Nonsense_Mutation_p.E406*|RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000255325.6_Nonsense_Mutation_p.E406*	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	406					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E406*(2)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GATAATTGAAGAAATTATTGA	0.393																																																2	Substitution - Nonsense(2)	large_intestine(2)	13											124	122	122					13																	25367460		2203	4300	6503	24265460	SO:0001587	stop_gained	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1216G>T	13.37:g.25367460G>T	ENSP00000255324:p.Glu406*		24265460	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Nonsense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	37	6.037815	0.97226	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325;ENST00000255326	.	.	.	5.29	5.29	0.74685	.	0.099000	0.44902	D	0.000414	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	15.9521	0.79846	0.0:0.0:1.0:0.0	.	.	.	.	X	406;406;265;407;406	.	ENSP00000255324:E406X	E	+	1	0	RNF17	24265460	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.890000	0.69774	2.755000	0.94549	0.650000	0.86243	GAA		0.393	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25367460	G	T	25367460	4	4	47	1	0	0	0	0	0	1	0	0	13498	943	33	2	1254	2	RNF17	13	25367460	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	86892	25367460	89802418	1448	5845										
RNF17	56163	broad.mit.edu	37	chr13	25416221	25416221	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttagttgagcttttcgattCtcttggtgctcctgaaatga	9	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:25416221C>A	ENST00000255324.5	+	19	2577	c.2525C>A	c.(2524-2526)tCt>tAt	p.S842Y	RNF17_ENST00000381921.1_Missense_Mutation_p.S842Y|RNF17_ENST00000339524.3_5'Flank	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	842					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S842Y(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		CTTTTCGATTCTCTTGGTGCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											158	150	153					13																	25416221		2203	4300	6503	24314221	SO:0001583	missense	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2525C>A	13.37:g.25416221C>A	ENSP00000255324:p.Ser842Tyr		24314221	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554032	0.27739	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.32023	1.47;1.47;1.47	5.29	4.39	0.52855	Staphylococcal nuclease (SNase-like) (1);	0.445478	0.22567	N	0.058400	T	0.24890	0.0604	L	0.29908	0.895	0.39868	D	0.973469	P;P;P	0.52170	0.926;0.587;0.951	P;B;P	0.45829	0.459;0.412;0.494	T	0.05582	-1.0876	10	0.62326	D	0.03	-8.1665	7.4939	0.27477	0.0:0.742:0.1626:0.0954	.	842;842;842	B7Z7S1;Q9BXT8-5;Q9BXT8	.;.;RNF17_HUMAN	Y	842;842;701;166	ENSP00000255324:S842Y;ENSP00000371346:S842Y;ENSP00000388892:S166Y	ENSP00000255324:S842Y	S	+	2	0	RNF17	24314221	0.034000	0.19679	0.689000	0.30133	0.103000	0.19146	0.168000	0.16622	1.257000	0.44085	0.585000	0.79938	TCT		0.338	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		A	25416221	C	A	25416221	3	1	47	1	0	0	0	0	1	0	0	0	13498	913	32	2	2599	2	RNF17	13	25416221	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	48761	25416221	89753657	1449	5846										
ATP8A2	51761	broad.mit.edu	37	chr13	26106445	26106445	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacaatgcagttaacaaaaaGaaaacaataggtaagatccc	7	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:26106445G>T	ENST00000381655.2	+	5	598	c.456G>T	c.(454-456)aaG>aaT	p.K152N	ATP8A2_ENST00000255283.8_Missense_Mutation_p.K112N	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	112					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.K152N(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TTAACAAAAAGAAAACAATAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	13											93	82	86					13																	26106445		1817	4074	5891	25004445	SO:0001583	missense	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.456G>T	13.37:g.26106445G>T	ENSP00000371070:p.Lys152Asn		25004445	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520532	0.85495	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000381648	T;T	0.76709	-1.04;-1.04	5.73	5.73	0.89815	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.048444	0.85682	D	0.000000	D	0.86577	0.5966	M	0.62723	1.935	0.58432	D	0.999998	D;D;D	0.65815	0.985;0.995;0.985	P;D;P	0.66979	0.889;0.948;0.889	D	0.85520	0.1203	10	0.46703	T	0.11	.	19.492	0.95054	0.0:0.0:1.0:0.0	.	112;112;112	B7Z880;Q9NTI2-3;Q9NTI2	.;.;AT8A2_HUMAN	N	152;112;112	ENSP00000371070:K152N;ENSP00000255283:K112N	ENSP00000255283:K112N	K	+	3	2	ATP8A2	25004445	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.347000	0.73004	2.702000	0.92279	0.643000	0.83706	AAG		0.323	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		T	26106445	G	T	26106445	3	4	47	1	0	0	0	0	1	0	0	0	1194	933	33	2	474	2	ATP8A2	13	26106445	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	690224	26106445	89063433	1450	5847										
ATP8A2	51761	broad.mit.edu	37	chr13	26402264	26402264	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctctttcagctttggttCgcctttgttaatggattttc	7	9	2	0	rs201549197		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:26402264C>T	ENST00000381655.2	+	28	2830	c.2688C>T	c.(2686-2688)ttC>ttT	p.F896F	ATP8A2_ENST00000491840.1_3'UTR|ATP8A2_ENST00000255283.8_Intron	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	856					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.F896F(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AGCTTTGGTTCGCCTTTGTTA	0.403													C|||	1	0.000199681	0	0	5008	,	,		19955	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13						C		0,3716		0,0,1858	267	239	248		2688	3.2	1	13		248	1,8205		0,1,4102	no	coding-synonymous	ATP8A2	NM_016529.4		0,1,5960	TT,TC,CC		0.0122,0.0,0.0084		896/1189	26402264	1,11921	1858	4103	5961	25300264	SO:0001819	synonymous_variant	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2688C>T	13.37:g.26402264C>T			25300264	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1																																																																																				0.403	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		T	26402264	C	T	26402264	2	4	47	1	0	0	0	0	0	0	0	1	1194	883	31	1		1	ATP8A2	13	26402264	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	295819	26402264	88767614	1451	5848										
GTF3A	219402	broad.mit.edu	37	chr13	28009314	28009314	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtacatgatcctgacaagaaGaaaatgaagctcaaagtaag	9	6	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:28009314G>T	ENST00000381116.1	-	0	1104				GTF3A_ENST00000381140.4_Missense_Mutation_p.K306N|GTF3A_ENST00000470606.1_3'UTR|MTIF3_ENST00000461838.1_5'Flank			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3						formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		CTGACAAGAAGAAAATGAAGC	0.343																																																0			13											125	110	115					13																	28009314		1568	3582	5150	26907314	SO:0001628	intergenic_variant	2971			BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633		13.37:g.28009314G>T			26907314	Q05BL8|Q5W0V0|Q86X68	Missense_Mutation	SNP	ENST00000381116.1	37	CCDS9322.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617744	0.46736	.	.	ENSG00000122034	ENST00000381140;ENST00000439403	T;T	0.10005	2.92;3.06	4.94	3.17	0.36434	Zinc finger, C2H2 (1);	0.172827	0.64402	D	0.000008	T	0.14917	0.0360	L	0.61218	1.895	0.40900	D	0.984145	P;P	0.44877	0.835;0.845	P;B	0.45232	0.474;0.368	T	0.17930	-1.0353	9	0.66056	D	0.02	-10.5848	8.9276	0.35650	0.2748:0.0:0.7252:0.0	.	281;306	Q92664-2;Q92664	.;TF3A_HUMAN	N	306;119	ENSP00000370532:K306N;ENSP00000393050:K119N	ENSP00000370532:K306N	K	+	3	2	GTF3A	26907314	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	1.759000	0.38420	1.225000	0.43566	0.650000	0.86243	AAG		0.343	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044300.1	NM_152912		T	28009314	G	T	28009314	1	4	47	0	1	0	0	0	0	0	0	0	6892	933	33	2		2	GTF3A	13	28009314	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1607050	28009314	87160564	1452	5849										
KATNAL1	84056	broad.mit.edu	37	chr13	30784544	30784544	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggatctaattcgacctcacGaaggttgatcttcagaagct	9	9	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:30784544G>A	ENST00000380615.3	-	10	1350	c.1183C>T	c.(1183-1185)Cgt>Tgt	p.R395C	KATNAL1_ENST00000380617.3_Missense_Mutation_p.R395C	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1									p.R395C(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		TCGACCTCACGAAGGTTGATC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											168	158	161					13																	30784544		2203	4300	6503	29682544	SO:0001583	missense	84056			AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"ATPases / AAA-type"	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.1183C>T	13.37:g.30784544G>A	ENSP00000369989:p.Arg395Cys		29682544		Missense_Mutation	SNP	ENST00000380615.3	37	CCDS31956.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935294	0.52866	.	.	ENSG00000102781	ENST00000380615;ENST00000380617	D;D	0.95205	-3.64;-3.64	5.77	4.9	0.64082	.	0.106600	0.64402	D	0.000012	D	0.95027	0.8390	M	0.92077	3.27	0.80722	D	1	B	0.33238	0.403	B	0.23852	0.049	D	0.94308	0.7543	10	0.72032	D	0.01	-19.013	15.8114	0.78568	0.0:0.0:0.8629:0.137	.	395	Q9BW62	KATL1_HUMAN	C	395	ENSP00000369989:R395C;ENSP00000369991:R395C	ENSP00000369989:R395C	R	-	1	0	KATNAL1	29682544	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	6.107000	0.71517	1.367000	0.46095	0.655000	0.94253	CGT		0.373	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		A	30784544	G	A	30784544	3	1	47	1	0	0	0	0	1	0	0	0	8006	1058	37	1	297	1	KATNAL1	13	30784544	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2775230	30784544	84385334	1453	5850										
FRY	10129	broad.mit.edu	37	chr13	32705849	32705849	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatttatggcggagctaaaaGaattacggcacaaagagcag	11	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:32705849G>T	ENST00000380250.3	+	8	1253	c.757G>T	c.(757-759)Gaa>Taa	p.E253*		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	253						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E253*(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GGAGCTAAAAGAATTACGGCA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											110	102	104					13																	32705849		1828	4085	5913	31603849	SO:0001587	stop_gained	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.757G>T	13.37:g.32705849G>T	ENSP00000369600:p.Glu253*		31603849	Q9Y3N6	Nonsense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	43	10.522614	0.99421	.	.	ENSG00000073910	ENST00000380250;ENST00000267067	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.877	0.96880	0.0:0.0:1.0:0.0	.	.	.	.	X	253;181	.	ENSP00000267067:E181X	E	+	1	0	FRY	31603849	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.696000	0.92011	0.650000	0.86243	GAA		0.383	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32705849	G	T	32705849	4	4	47	1	0	0	0	0	0	1	0	0	6082	943	33	2	787	2	FRY	13	32705849	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1921305	32705849	82464029	1454	5851										
FRY	10129	broad.mit.edu	37	chr13	32826038	32826038	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaacaaaagagaagttggtAcatgtcctttctctgtgtgg	11	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:32826038A>G	ENST00000380250.3	+	50	7690	c.7194A>G	c.(7192-7194)gtA>gtG	p.V2398V		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2398						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V2398V(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AGAAGTTGGTACATGTCCTTT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	13											218	206	210					13																	32826038		1864	4106	5970	31724038	SO:0001819	synonymous_variant	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.7194A>G	13.37:g.32826038A>G			31724038	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																				0.393	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		G	32826038	A	G	32826038	2	3	47	1	0	0	0	0	0	0	0	1	6082	378	14	4		4	FRY	13	32826038	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	120189	32826038	82343840	1455	5852										
BRCA2	675	broad.mit.edu	37	chr13	32906578	32906578	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtagaacaaaaaatctacaAaaagtaagaactagcaagac	6	6	1	3	rs276174927		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:32906578A>C	ENST00000380152.3	+	10	1196	c.963A>C	c.(961-963)caA>caC	p.Q321H	BRCA2_ENST00000544455.1_Missense_Mutation_p.Q321H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	321					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.Q321H(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAAATCTACAAAAAGTAAGAA	0.289			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											49	55	53					13																	32906578		2203	4296	6499	31804578	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.963A>C	13.37:g.32906578A>C	ENSP00000369497:p.Gln321His		31804578	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	5.773	0.327017	0.10900	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00966	5.49;5.49	5.07	-0.0936	0.13648	.	0.761042	0.11606	N	0.547278	T	0.00998	0.0033	L	0.46157	1.445	0.09310	N	1	B;P	0.51351	0.221;0.944	B;B	0.39027	0.07;0.288	T	0.51180	-0.8738	10	0.66056	D	0.02	.	4.9252	0.13889	0.4228:0.1786:0.3986:0.0	.	321;321	P51587;A1YBP1	BRCA2_HUMAN;.	H	321;321;319	ENSP00000369497:Q321H;ENSP00000439902:Q321H	ENSP00000369497:Q321H	Q	+	3	2	BRCA2	31804578	0.899000	0.30636	0.000000	0.03702	0.003000	0.03518	0.279000	0.18771	-0.136000	0.11475	-0.256000	0.11100	CAA		0.289	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32906578	A	C	32906578	3	2	47	1	0	0	0	0	1	0	0	0	1502	11	1	4	997	4	BRCA2	13	32906578	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	80540	32906578	82263300	1456	5853										
BRCA2	90634	broad.mit.edu	37	chr13	32972801	32972801	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agattatctcagactgaaacGacgttgtactacatctctga	7	9	2	4	rs80358397		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:32972801G>A	ENST00000380130.2	-	0	3046				BRCA2_ENST00000544455.1_Missense_Mutation_p.R3384Q|BRCA2_ENST00000380152.3_Missense_Mutation_p.R3384Q	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1									p.R3384Q(2)		large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		AGACTGAAACGACGTTGTACT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	13											73	72	72					13																	32972801		2203	4300	6503	31870801	SO:0001628	intergenic_variant	675			U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		13.37:g.32972801G>A			31870801	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653510	0.47362	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00745	5.75;5.75	5.6	2.92	0.33932	.	0.946366	0.08847	N	0.884960	T	0.00906	0.0030	L	0.60455	1.87	0.09310	N	1	P	0.49961	0.93	B	0.30943	0.122	T	0.53982	-0.8361	10	0.40728	T	0.16	.	7.8806	0.29621	0.2644:0.0:0.7356:0.0	.	3384	P51587	BRCA2_HUMAN	Q	3384	ENSP00000369497:R3384Q;ENSP00000439902:R3384Q	ENSP00000369497:R3384Q	R	+	2	0	BRCA2	31870801	0.002000	0.14202	0.003000	0.11579	0.009000	0.06853	1.144000	0.31565	0.736000	0.32559	0.655000	0.94253	CGA		0.398	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818		A	32972801	G	A	32972801	1	1	47	0	1	0	0	0	0	0	0	0	1502	1058	37	1		1	BRCA2	13	32972801	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	66223	32972801	82197077	1457	5854										
N4BP2L1	90634	broad.mit.edu	37	chr13	32978388	32978388	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttccagcctgaaaagattCttttgttcggtctgaaatac	7	8	2	3	rs372468111		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:32978388C>A	ENST00000380133.2	-	4	524				N4BP2L1_ENST00000530622.2_Intron|N4BP2L1_ENST00000459716.1_Intron|N4BP2L1_ENST00000380130.2_Intron|N4BP2L1_ENST00000380139.4_Missense_Mutation_p.K139N			Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1									p.K139N(1)		large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		TGAAAAGATTCTTTTGTTCGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	13											86	85	85					13																	32978388		2203	4300	6503	31876388	SO:0001627	intron_variant	90634			U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697	ENST00000380133.2:c.473+69G>T	13.37:g.32978388C>A			31876388	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380133.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427931	0.62733	.	.	ENSG00000139597	ENST00000380139	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	T	0.52885	0.1762	.	.	.	0.80722	D	1	P	0.39940	0.696	B	0.43838	0.433	T	0.51687	-0.8674	7	0.39692	T	0.17	.	8.8985	0.35479	0.0:0.8673:0.0:0.1327	.	139	Q5TBK1-2	.	N	139	.	ENSP00000369484:K139N	K	-	3	2	N4BP2L1	31876388	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.017000	0.29989	2.639000	0.89480	0.655000	0.94253	AAG		0.348	N4BP2L1-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044412.2	NM_052818		A	32978388	C	A	32978388	1	1	47	0	1	0	0	0	0	0	0	0	10141	912	32	2		2	N4BP2L1	13	32978388	Intron	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5587	32978388	82191490	1458	5855										
N4BP2L2	10443	broad.mit.edu	37	chr13	33018029	33018029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatccagtcacaaaatctccGacttcattttgtagaccatc	4	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:33018029G>A	ENST00000504114.1	-	6	691	c.600C>T	c.(598-600)gtC>gtT	p.V200V	N4BP2L2_ENST00000446957.2_Intron|N4BP2L2_ENST00000357505.6_Silent_p.V200V|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000399396.3_Silent_p.V215V			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.V215V(1)		kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		CAAAATCTCCGACTTCATTTT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											63	56	58					13																	33018029		1815	4072	5887	31916029	SO:0001819	synonymous_variant	10443			U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.600C>T	13.37:g.33018029G>A			31916029	A3KME8	Silent	SNP	ENST00000504114.1	37																																																																																					0.373	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887		A	33018029	G	A	33018029	2	1	47	1	0	0	0	0	0	0	0	1	10142	1045	37	1		1	N4BP2L2	13	33018029	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	39641	33018029	82151849	1459	5856										
N4BP2L2	10443	broad.mit.edu	37	chr13	33110502	33110502	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctttattactaagatctttCttttcttcatcaggttttaa	4	7	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:33110502C>A	ENST00000267068.3	-	2	827	c.663G>T	c.(661-663)aaG>aaT	p.K221N	N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.K221N|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000399396.3_Intron	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	221					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.K221N(1)		kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TAAGATCTTTCTTTTCTTCAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13											88	85	86					13																	33110502		2203	4299	6502	32008502	SO:0001583	missense	10443			U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.663G>T	13.37:g.33110502C>A	ENSP00000267068:p.Lys221Asn		32008502	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	C	9.541	1.113314	0.20795	.	.	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.45668	0.89;0.89;0.89	5.58	1.64	0.23874	.	.	.	.	.	T	0.30230	0.0758	L	0.47716	1.5	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.11329	0.006;0.006	T	0.33214	-0.9877	9	0.46703	T	0.11	-6.1708	1.1969	0.01877	0.3817:0.2913:0.1001:0.2269	.	221;221	D6R968;Q92802	.;N42L2_HUMAN	N	221	ENSP00000394239:K221N;ENSP00000423362:K221N;ENSP00000267068:K221N	ENSP00000267068:K221N	K	-	3	2	N4BP2L2	32008502	0.000000	0.05858	0.000000	0.03702	0.884000	0.51177	-0.533000	0.06157	-0.008000	0.14320	0.563000	0.77884	AAG		0.353	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		A	33110502	C	A	33110502	3	1	47	1	0	0	0	0	1	0	0	0	10142	912	32	2	2969	2	N4BP2L2	13	33110502	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	92473	33110502	82059376	1460	5857										
NBEA	26960	broad.mit.edu	37	chr13	35747658	35747658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaaagacagagagacagggGaaataaatcttcccatggaa	11	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:35747658G>A	ENST00000400445.3	+	27	5015	c.4481G>A	c.(4480-4482)gGa>gAa	p.G1494E	NBEA_ENST00000379939.2_Missense_Mutation_p.G1491E|NBEA_ENST00000310336.4_Missense_Mutation_p.G1494E|NBEA_ENST00000540320.1_Missense_Mutation_p.G1494E	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1494					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.G1494E(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AGAGACAGGGGAAATAAATCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	75	75					13																	35747658		1842	4094	5936	34645658	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4481G>A	13.37:g.35747658G>A	ENSP00000383295:p.Gly1494Glu		34645658	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829621	0.50845	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.71	4.79	0.61399	.	0.269071	0.36815	N	0.002396	T	0.35566	0.0936	L	0.42245	1.32	0.80722	D	1	P;B	0.35433	0.501;0.228	B;B	0.25140	0.058;0.045	T	0.16041	-1.0416	10	0.30078	T	0.28	.	13.3848	0.60789	0.0:0.0:0.7635:0.2365	.	1494;1491	Q8NFP9;Q5T321	NBEA_HUMAN;.	E	1494;1494;1491;1494;153	ENSP00000440951:G1494E;ENSP00000383295:G1494E;ENSP00000369271:G1491E;ENSP00000308534:G1494E	ENSP00000308534:G1494E	G	+	2	0	NBEA	34645658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.398000	0.52579	2.699000	0.92147	0.650000	0.86243	GGA		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35747658	G	A	35747658	3	1	47	1	0	0	0	0	1	0	0	0	10217	1174	41	3	4587	3	NBEA	13	35747658	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2637156	35747658	79422220	1461	5858										
SPG20	23111	broad.mit.edu	37	chr13	36903630	36903630	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggatttggaattcattttCttcttctgctctgttccagt	8	8	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:36903630C>A	ENST00000451493.1	-	4	1250	c.1033G>T	c.(1033-1035)Gaa>Taa	p.E345*	SPG20_ENST00000438666.2_Nonsense_Mutation_p.E345*|SPG20_ENST00000494062.2_Nonsense_Mutation_p.E345*|SPG20_ENST00000355182.4_Nonsense_Mutation_p.E345*|SPG20_ENST00000495510.1_5'UTR	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	345					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)	p.E345*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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)		AATTCATTTTCTTCTTCTGCT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											160	151	154					13																	36903630		2203	4300	6503	35801630	SO:0001587	stop_gained	23111			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1033G>T	13.37:g.36903630C>A	ENSP00000414147:p.Glu345*		35801630	O60349|Q86Y67|Q9H1T2|Q9H1T3	Nonsense_Mutation	SNP	ENST00000451493.1	37	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	C	38	7.249640	0.98164	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	.	.	.	5.36	5.36	0.76844	.	0.767593	0.12595	N	0.455266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-31.1429	14.5523	0.68075	0.0:1.0:0.0:0.0	.	.	.	.	X	345	.	ENSP00000347314:E345X	E	-	1	0	SPG20	35801630	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.976000	0.40579	2.504000	0.84457	0.585000	0.79938	GAA		0.408	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			A	36903630	C	A	36903630	4	1	47	1	0	0	0	0	0	1	0	0	15081	922	32	2	991	2	SPG20	13	36903630	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1155972	36903630	78266248	1462	5859										
SMAD9	4093	broad.mit.edu	37	chr13	37453773	37453773	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccagcctagcagtctcttCactgcggggctggtgaagga	13	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:37453773C>T	ENST00000399275.2	-	1	193	c.54G>A	c.(52-54)gtG>gtA	p.V18V	SMAD9_ENST00000483941.1_5'UTR|SMAD9_ENST00000350148.5_Silent_p.V18V|SMAD9_ENST00000379826.4_Silent_p.V18V			O15198	SMAD9_HUMAN	SMAD family member 9	18	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)	p.V18V(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		GCAGTCTCTTCACTGCGGGGC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	13											57	62	60					13																	37453773		2203	4300	6503	36351773	SO:0001819	synonymous_variant	4093				CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.54G>A	13.37:g.37453773C>T			36351773	A2A2Y6|O14989|Q5TBA1	Silent	SNP	ENST00000399275.2	37	CCDS45032.1																																																																																				0.572	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		T	37453773	C	T	37453773	2	4	47	1	0	0	0	0	0	0	0	1	14801	813	29	3		3	SMAD9	13	37453773	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	550143	37453773	77716105	1463	5860										
TRPC4	7223	broad.mit.edu	37	chr13	38225390	38225390	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaagagtaatactaacatgCtgtgttcttacccctattgt	6	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:38225390C>T	ENST00000379705.3	-	8	2937				TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000379681.3_Silent_p.Q697Q|TRPC4_ENST00000358477.2_Intron|TRPC4_ENST00000355779.2_Intron|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000447043.1_Intron			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.Q697Q(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TACTAACATGCTGTGTTCTTA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	13											113	110	111					13																	38225390		2203	4300	6503	37123390	SO:0001627	intron_variant	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2079+11G>A	13.37:g.38225390C>T			37123390	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																				0.338	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38225390	C	T	38225390	1	4	47	0	1	0	0	0	0	0	0	0	16620	796	28	3		3	TRPC4	13	38225390	Intron	SNP	C	TCGA-AG-3892-01A-01W-1073-09	771617	38225390	76944488	1464	5861										
TRPC4	7223	broad.mit.edu	37	chr13	38225470	38225470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagtgtgtccagatccattTgatcaggtaccagagagact	10	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:38225470T>C	ENST00000379705.3	-	8	2868	c.2011A>G	c.(2011-2013)Aaa>Gaa	p.K671E	TRPC4_ENST00000379679.1_Missense_Mutation_p.K498E|TRPC4_ENST00000338947.5_Missense_Mutation_p.K498E|TRPC4_ENST00000379681.3_Missense_Mutation_p.K671E|TRPC4_ENST00000358477.2_Missense_Mutation_p.K671E|TRPC4_ENST00000355779.2_Missense_Mutation_p.K671E|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000447043.1_Missense_Mutation_p.K671E			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	671	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.K671E(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CAGATCCATTTGATCAGGTAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	13											132	128	130					13																	38225470		2203	4300	6503	37123470	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2011A>G	13.37:g.38225470T>C	ENSP00000369027:p.Lys671Glu		37123470	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.362867	0.41902	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000447043	T;T;T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	5.8	5.8	0.92144	.	0.283048	0.44902	D	0.000414	T	0.77046	0.4073	L	0.46157	1.445	0.22213	N	0.999283	B;B;B;B;B	0.19200	0.001;0.034;0.008;0.004;0.005	B;B;B;B;B	0.19666	0.009;0.025;0.026;0.009;0.004	T	0.67929	-0.5543	10	0.49607	T	0.09	-37.5651	16.1484	0.81586	0.0:0.0:0.0:1.0	.	671;671;498;671;671	Q9UBN4-3;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	E	671;671;498;498;671;671;671	ENSP00000369027:K671E;ENSP00000369003:K671E;ENSP00000342580:K498E;ENSP00000369001:K498E;ENSP00000348025:K671E;ENSP00000351264:K671E;ENSP00000414316:K671E	ENSP00000342580:K498E	K	-	1	0	TRPC4	37123470	0.973000	0.33851	1.000000	0.80357	0.978000	0.69477	2.489000	0.45285	2.226000	0.72624	0.459000	0.35465	AAA		0.423	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38225470	T	C	38225470	3	2	47	1	0	0	0	0	1	0	0	0	16620	1821	63	4	953	4	TRPC4	13	38225470	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	80	38225470	76944408	1465	5862										
TRPC4	7223	broad.mit.edu	37	chr13	38357363	38357363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccttttccacagcattcaaGtaggctttttctgatggcga	8	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:38357363G>A	ENST00000379705.3	-	2	965	c.108C>T	c.(106-108)taC>taT	p.Y36Y	TRPC4_ENST00000379679.1_Silent_p.Y36Y|TRPC4_ENST00000338947.5_Silent_p.Y36Y|TRPC4_ENST00000379681.3_Silent_p.Y36Y|TRPC4_ENST00000358477.2_Silent_p.Y36Y|TRPC4_ENST00000355779.2_Silent_p.Y36Y|TRPC4_ENST00000426868.2_Silent_p.Y36Y|TRPC4_ENST00000379673.2_Silent_p.Y36Y|TRPC4_ENST00000447043.1_Silent_p.Y36Y			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	36					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.Y36Y(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CAGCATTCAAGTAGGCTTTTT	0.378																																																2	Substitution - coding silent(2)	large_intestine(2)	13											170	166	167					13																	38357363		2203	4300	6503	37255363	SO:0001819	synonymous_variant	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.108C>T	13.37:g.38357363G>A			37255363	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																				0.378	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		A	38357363	G	A	38357363	2	1	47	1	0	0	0	0	0	0	0	1	16620	1024	36	3		3	TRPC4	13	38357363	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	131893	38357363	76812515	1466	5863										
FREM2	341640	broad.mit.edu	37	chr13	39262299	39262299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgccacacagccgccagtcGctcaccaaacagggactgga	10	16	1	0	rs201675703		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:39262299G>A	ENST00000280481.7	+	1	1034	c.818G>A	c.(817-819)cGc>cAc	p.R273H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	273					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R273H(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GCCGCCAGTCGCTCACCAAAC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	13											57	60	59					13																	39262299		2202	4299	6501	38160299	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.818G>A	13.37:g.39262299G>A	ENSP00000280481:p.Arg273His		38160299	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	9.263	1.043599	0.19748	.	.	ENSG00000150893	ENST00000280481	T	0.19250	2.16	5.81	0.771	0.18504	.	0.408176	0.27917	N	0.017334	T	0.13670	0.0331	L	0.46157	1.445	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.16070	-1.0415	10	0.39692	T	0.17	.	1.7756	0.03021	0.2427:0.1058:0.4352:0.2164	.	273	Q5SZK8	FREM2_HUMAN	H	273	ENSP00000280481:R273H	ENSP00000280481:R273H	R	+	2	0	FREM2	38160299	0.000000	0.05858	0.008000	0.14137	0.981000	0.71138	0.521000	0.22893	0.349000	0.23975	0.655000	0.94253	CGC		0.622	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39262299	G	A	39262299	3	1	47	1	0	0	0	0	1	0	0	0	6064	1087	38	1	820	1	FREM2	13	39262299	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	904936	39262299	75907579	1467	5864										
STOML3	161003	broad.mit.edu	37	chr13	39544392	39544392	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtgtccctaagacatttCtcagagtggtttgagccagc	10	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:39544392C>A	ENST00000379631.4	-	5	790	c.446G>T	c.(445-447)aGa>aTa	p.R149I	STOML3_ENST00000423210.1_Missense_Mutation_p.R140I	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	149					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.R149I(1)		breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		TAAGACATTTCTCAGAGTGGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	13											152	138	142					13																	39544392		2203	4300	6503	38442392	SO:0001583	missense	161003			BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.446G>T	13.37:g.39544392C>A	ENSP00000368952:p.Arg149Ile		38442392	B4E285|Q5JS35	Missense_Mutation	SNP	ENST00000379631.4	37	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	C	33	5.249973	0.95305	.	.	ENSG00000133115	ENST00000379631;ENST00000423210	D;D	0.97976	-4.64;-4.64	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.99402	0.9789	H	0.99600	4.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.98143	1.0437	10	0.87932	D	0	-16.6063	17.6563	0.88179	0.0:1.0:0.0:0.0	.	140;149	B4E285;Q8TAV4	.;STML3_HUMAN	I	149;140	ENSP00000368952:R149I;ENSP00000401989:R140I	ENSP00000368952:R149I	R	-	2	0	STOML3	38442392	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.514000	0.81750	2.513000	0.84729	0.563000	0.77884	AGA		0.453	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			A	39544392	C	A	39544392	3	1	47	1	0	0	0	0	1	0	0	0	15354	913	32	2	441	2	STOML3	13	39544392	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	282093	39544392	75625486	1468	5865										
MTRF1	9617	broad.mit.edu	37	chr13	41797460	41797460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgggtgaaattatatgtccGaattcgctctgactgggctc	11	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:41797460G>A	ENST00000379480.4	-	9	1256	c.1156C>T	c.(1156-1158)Cgg>Tgg	p.R386W	MTRF1_ENST00000430347.2_Missense_Mutation_p.R399W|MTRF1_ENST00000379477.1_Missense_Mutation_p.R386W	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	386					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)	p.R386W(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		TTATATGTCCGAATTCGCTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											261	239	247					13																	41797460		2203	4300	6503	40695460	SO:0001583	missense	9617			AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"mitochontrial peptide chain release factor 1"	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.1156C>T	13.37:g.41797460G>A	ENSP00000368793:p.Arg386Trp		40695460	B4DG01|Q5T6Y5|Q8IUQ6	Missense_Mutation	SNP	ENST00000379480.4	37	CCDS9378.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280943	0.80692	.	.	ENSG00000120662	ENST00000379480;ENST00000379477;ENST00000430347	T;T;T	0.46819	0.86;0.86;0.86	4.95	4.95	0.65309	Peptide chain release factor class I/class II (1);	0.187569	0.47455	D	0.000229	T	0.80460	0.4627	H	0.97962	4.115	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.72338	0.977;0.916	D	0.88025	0.2771	10	0.87932	D	0	-7.5541	17.1093	0.86671	0.0:0.0:1.0:0.0	.	399;386	B4DG01;O75570	.;RF1M_HUMAN	W	386;386;399	ENSP00000368793:R386W;ENSP00000368790:R386W;ENSP00000400031:R399W	ENSP00000368790:R386W	R	-	1	2	MTRF1	40695460	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.685000	0.68204	2.560000	0.86352	0.655000	0.94253	CGG		0.373	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294		A	41797460	G	A	41797460	3	1	47	1	0	0	0	0	1	0	0	0	9989	1057	37	1	189	1	MTRF1	13	41797460	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2253068	41797460	73372418	1469	5866										
KIAA0564	23078	broad.mit.edu	37	chr13	42524079	42524079	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatatttcttactgtagttCtgtggcacaagttctggatt	8	6	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:42524079C>T	ENST00000379310.3	-	2	302	c.234G>A	c.(232-234)caG>caA	p.Q78Q	VWA8_ENST00000281496.6_Silent_p.Q78Q	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	78						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.Q78Q(2)									TACTGTAGTTCTGTGGCACAA	0.249																																																2	Substitution - coding silent(2)	large_intestine(2)	13											22	22	22					13																	42524079		2193	4292	6485	41422079	SO:0001819	synonymous_variant	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.234G>A	13.37:g.42524079C>T			41422079	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	37	CCDS41881.1																																																																																				0.249	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42524079	C	T	42524079	2	4	47	1	0	0	0	0	0	0	0	1	8206	912	32	3		3	KIAA0564	13	42524079	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	726619	42524079	72645799	1470	5867										
DGKH	160851	broad.mit.edu	37	chr13	42734235	42734235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacatgtggcagtgttctccGtctacaggattggaaatgcc	11	9	2	0	rs370149879		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:42734235G>A	ENST00000337343.4	+	7	839	c.818G>A	c.(817-819)cGt>cAt	p.R273H	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.R137H|DGKH_ENST00000379274.2_Missense_Mutation_p.R137H|DGKH_ENST00000540693.1_Missense_Mutation_p.R273H|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000261491.5_Missense_Mutation_p.R273H	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	273					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R273H(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		AGTGTTCTCCGTCTACAGGAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	203	163	177		818,410,410,818,818	6	1	13		177	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	273/1165,137/1101,137/1085,273/1165,273/1221	42734235	1,13005	2203	4300	6503	41632235	SO:0001583	missense	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.818G>A	13.37:g.42734235G>A	ENSP00000337572:p.Arg273His		41632235	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461375	0.84317	2.27E-4	0.0	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15	5.97	5.97	0.96955	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.053696	0.85682	D	0.000000	D	0.97340	0.9130	M	0.87180	2.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.995	D;D;D	0.87578	0.998;0.997;0.931	D	0.97337	0.9954	10	0.87932	D	0	.	20.4135	0.99023	0.0:0.0:1.0:0.0	.	137;273;273	Q86XP1-3;Q86XP1-2;Q86XP1	.;.;DGKH_HUMAN	H	273;273;273;137;137	ENSP00000440823:R273H;ENSP00000337572:R273H;ENSP00000261491:R273H;ENSP00000368576:R137H;ENSP00000445114:R137H	ENSP00000261491:R273H	R	+	2	0	DGKH	41632235	1.000000	0.71417	0.968000	0.41197	0.640000	0.38277	7.586000	0.82596	2.835000	0.97688	0.591000	0.81541	CGT		0.483	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42734235	G	A	42734235	3	1	47	1	0	0	0	0	1	0	0	0	4481	1145	40	1	844	1	DGKH	13	42734235	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	210156	42734235	72435643	1471	5868										
ZC3H13	23091	broad.mit.edu	37	chr13	46559497	46559497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtcatttctaatttcacttCgagactcatttctggactca	6	10	6	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:46559497C>T	ENST00000242848.4	-	10	2003	c.1655G>A	c.(1654-1656)cGa>cAa	p.R552Q	ZC3H13_ENST00000282007.3_Missense_Mutation_p.R552Q			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	552	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R552Q(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		AATTTCACTTCGAGACTCATT	0.423																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Missense(1)	large_intestine(1)	13											96	98	97					13																	46559497		2203	4300	6503	45457498	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1655G>A	13.37:g.46559497C>T	ENSP00000242848:p.Arg552Gln		45457498	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	C	17.64	3.440050	0.63067	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	T;T	0.44881	1.91;0.91	5.73	5.73	0.89815	.	0.000000	0.49916	D	0.000136	T	0.55784	0.1942	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.43147	-0.9409	10	0.28530	T	0.3	.	20.2602	0.98440	0.0:1.0:0.0:0.0	.	552;552	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	Q	552;552;368	ENSP00000242848:R552Q;ENSP00000282007:R552Q	ENSP00000242848:R552Q	R	-	2	0	ZC3H13	45457498	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.497000	0.66924	2.861000	0.98227	0.655000	0.94253	CGA		0.423	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46559497	C	T	46559497	3	4	47	1	0	0	0	0	1	0	0	0	17604	884	31	1	3071	1	ZC3H13	13	46559497	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3825262	46559497	68610381	1472	5869										
LCP1	3936	broad.mit.edu	37	chr13	46708363	46708363	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctggccaccaccaatttCttcgaggatattcagtgtat	7	11	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:46708363C>A	ENST00000398576.2	-	17	1913	c.1525G>T	c.(1525-1527)Gaa>Taa	p.E509*	LCP1_ENST00000323076.2_Nonsense_Mutation_p.E509*|LCP1_ENST00000435666.2_Nonsense_Mutation_p.E78*			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	509	Actin-binding 2.				actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)	p.E509*(1)		breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|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;5.39e-05)		CCACCAATTTCTTCGAGGATA	0.353			T	BCL6	NHL																																		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	1	Substitution - Nonsense(1)	large_intestine(1)	13											105	91	96					13																	46708363		2203	4300	6503	45606364	SO:0001587	stop_gained	3936			M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"EF-hand domain containing"	6528	protein-coding gene	gene with protein product	"plastin 2"	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1525G>T	13.37:g.46708363C>A	ENSP00000381581:p.Glu509*		45606364	B2R613|B4DUA0|Q5TBN4	Nonsense_Mutation	SNP	ENST00000398576.2	37	CCDS9403.1	.	.	.	.	.	.	.	.	.	.	C	37	6.402342	0.97537	.	.	ENSG00000136167	ENST00000323076;ENST00000398576;ENST00000435666	.	.	.	5.72	5.72	0.89469	.	0.290426	0.41823	D	0.000806	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-2.1472	18.8847	0.92372	0.0:1.0:0.0:0.0	.	.	.	.	X	509;509;78	.	ENSP00000315757:E509X	E	-	1	0	LCP1	45606364	1.000000	0.71417	0.994000	0.49952	0.025000	0.11179	7.776000	0.85560	2.717000	0.92951	0.655000	0.94253	GAA		0.353	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298		A	46708363	C	A	46708363	4	1	47	1	0	0	0	0	0	1	0	0	8713	922	32	2	370	2	LCP1	13	46708363	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	148866	46708363	68461515	1473	5870										
LCP1	3936	broad.mit.edu	37	chr13	46721099	46721099	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttgtgcagggcagggtatCtgttaaagaggttggcaata	15	4	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:46721099C>A	ENST00000398576.2	-	13	1506	c.1118G>T	c.(1117-1119)aGa>aTa	p.R373I	LCP1_ENST00000323076.2_Missense_Mutation_p.R373I			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	373	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)	p.R373I(1)		breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|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;5.39e-05)		GGCAGGGTATCTGTTAAAGAG	0.522			T	BCL6	NHL																																		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	1	Substitution - Missense(1)	large_intestine(1)	13											105	101	102					13																	46721099		2203	4300	6503	45619100	SO:0001583	missense	3936			M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"EF-hand domain containing"	6528	protein-coding gene	gene with protein product	"plastin 2"	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1118G>T	13.37:g.46721099C>A	ENSP00000381581:p.Arg373Ile		45619100	B2R613|B4DUA0|Q5TBN4	Missense_Mutation	SNP	ENST00000398576.2	37	CCDS9403.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861067	0.51482	.	.	ENSG00000136167	ENST00000323076;ENST00000398576	D;D	0.95238	-3.65;-3.65	5.32	3.2	0.36748	Calponin homology domain (4);	0.178528	0.64402	D	0.000016	D	0.89473	0.6725	N	0.24115	0.695	0.80722	D	1	B	0.33318	0.408	B	0.39840	0.311	D	0.84438	0.0581	10	0.49607	T	0.09	-6.9065	7.1109	0.25390	0.0:0.5187:0.0:0.4813	.	373	P13796	PLSL_HUMAN	I	373	ENSP00000315757:R373I;ENSP00000381581:R373I	ENSP00000315757:R373I	R	-	2	0	LCP1	45619100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.150000	0.42254	0.444000	0.26612	0.555000	0.69702	AGA		0.522	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298		A	46721099	C	A	46721099	3	1	47	1	0	0	0	0	1	0	0	0	8713	913	32	2	793	2	LCP1	13	46721099	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	12736	46721099	68448779	1474	5871										
C13orf18	80183	broad.mit.edu	37	chr13	46933739	46933739	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attcatactggattcaaagtCttttcggacacactcttcat	5	10	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:46933739C>A	ENST00000429979.1	-	9	1751	c.1147G>T	c.(1147-1149)Gac>Tac	p.D383Y	KIAA0226L_ENST00000378797.2_Missense_Mutation_p.D383Y|KIAA0226L_ENST00000378787.3_Missense_Mutation_p.D383Y|KIAA0226L_ENST00000378781.3_3'UTR|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.D248Y|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.D316Y|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.D226Y|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.D226Y|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.D383Y	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	383								p.D383Y(1)		NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GATTCAAAGTCTTTTCGGACA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	13											65	62	63					13																	46933739		2203	4297	6500	45831740	SO:0001583	missense	80183			AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 18"	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1147G>T	13.37:g.46933739C>A	ENSP00000396935:p.Asp383Tyr		45831740	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	C	13.45	2.242211	0.39598	.	.	ENSG00000102445	ENST00000429979;ENST00000378797;ENST00000378784;ENST00000389908;ENST00000378787;ENST00000409879;ENST00000322896;ENST00000534925	T;T;T;T;T;T	0.52295	0.7;0.67;0.71;0.7;0.67;0.75	5.19	2.43	0.29744	.	0.510831	0.19159	N	0.121252	T	0.60090	0.2242	M	0.66939	2.045	0.80722	D	1	P;D;D;P;P;D	0.89917	0.94;0.963;0.998;0.911;0.946;1.0	P;P;P;P;P;D	0.69479	0.643;0.707;0.87;0.594;0.77;0.964	T	0.55860	-0.8074	10	0.52906	T	0.07	-3.8937	7.0269	0.24944	0.0:0.6086:0.241:0.1503	.	226;226;383;248;316;383	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3;Q9H714-4	.;.;K226L_HUMAN;.;.;.	Y	383;383;316;383;383;226;226;248	ENSP00000396935:D383Y;ENSP00000368074:D383Y;ENSP00000368061:D316Y;ENSP00000374558:D383Y;ENSP00000368064:D383Y;ENSP00000437501:D248Y	ENSP00000315633:D226Y	D	-	1	0	KIAA0226L	45831740	1.000000	0.71417	0.885000	0.34714	0.507000	0.33981	2.029000	0.41098	0.251000	0.21505	-0.208000	0.12717	GAC		0.318	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		A	46933739	C	A	46933739	3	1	47	1	0	0	0	0	1	0	0	0	1724	913	32	2	869	2	C13orf18	13	46933739	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	212640	46933739	68236139	1475	5872										
CYSLTR2	57105	broad.mit.edu	37	chr13	49281794	49281794	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaaagtgggtttatgcaaaGacagactgcataaagctttg	12	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:49281794G>T	ENST00000282018.3	+	1	844	c.841G>T	c.(841-843)Gac>Tac	p.D281Y		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	281					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)	p.D281Y(1)		endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	TTTATGCAAAGACAGACTGCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	13											168	146	154					13																	49281794		2203	4300	6503	48179795	SO:0001583	missense	57105			AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.841G>T	13.37:g.49281794G>T	ENSP00000282018:p.Asp281Tyr		48179795	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.468684	0.26335	.	.	ENSG00000152207	ENST00000282018	T	0.21361	2.01	5.51	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	0.763785	0.11700	N	0.538015	T	0.30759	0.0775	L	0.43152	1.355	0.09310	N	0.999999	D	0.57257	0.979	P	0.55222	0.771	T	0.08411	-1.0723	10	0.62326	D	0.03	.	10.503	0.44817	0.1549:0.0:0.8451:0.0	.	281	Q9NS75	CLTR2_HUMAN	Y	281	ENSP00000282018:D281Y	ENSP00000282018:D281Y	D	+	1	0	CYSLTR2	48179795	0.000000	0.05858	0.013000	0.15412	0.012000	0.07955	0.445000	0.21677	1.337000	0.45525	0.655000	0.94253	GAC		0.463	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			T	49281794	G	T	49281794	3	4	47	1	0	0	0	0	1	0	0	0	4208	942	33	2	843	2	CYSLTR2	13	49281794	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2348055	49281794	65888084	1476	5873										
CDADC1	81602	broad.mit.edu	37	chr13	49854747	49854747	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgcaggcataaaacaaatCtatgcaggagatgtagatgt	12	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:49854747C>A	ENST00000251108.6	+	8	1436	c.1323C>A	c.(1321-1323)atC>atA	p.I441I	CDADC1_ENST00000444959.1_Silent_p.I243I	NM_001193478.1|NM_030911.3	NP_001180407.1|NP_112173.1	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	441							hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)	p.I441I(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	16		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		TAAAACAAATCTATGCAGGAG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	13											114	109	111					13																	49854747		2203	4300	6503	48752748	SO:0001819	synonymous_variant	81602			AY027525	CCDS9415.1	13q14.11	2008-02-05			ENSG00000102543	ENSG00000102543			20299	protein-coding gene	gene with protein product							Standard	NM_001193478		Approved	NYD-SP15	uc001vcu.3	Q9BWV3	OTTHUMG00000016913	ENST00000251108.6:c.1323C>A	13.37:g.49854747C>A			48752748	Q49A08|Q4G119|Q5TAW9|Q7Z764|Q9NT36	Silent	SNP	ENST00000251108.6	37	CCDS9415.1																																																																																				0.383	CDADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044902.2	NM_030911		A	49854747	C	A	49854747	2	1	47	1	0	0	0	0	0	0	0	1	3059	903	32	2		2	CDADC1	13	49854747	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	572953	49854747	65315131	1477	5874										
CAB39L	81617	broad.mit.edu	37	chr13	49933954	49933954	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgttgttaaatatctgggtCacatctttttttccctgtta	6	7	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:49933954C>T	ENST00000355854.4	-	4	788	c.291G>A	c.(289-291)gtG>gtA	p.V97V	CAB39L_ENST00000347776.5_Silent_p.V97V|CAB39L_ENST00000410043.1_Silent_p.V97V|CAB39L_ENST00000409308.1_Silent_p.V97V	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	97					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)		p.V97V(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		ATATCTGGGTCACATCTTTTT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	13											115	108	111					13																	49933954		2203	4300	6503	48831955	SO:0001819	synonymous_variant	81617			AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.291G>A	13.37:g.49933954C>T			48831955	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Silent	SNP	ENST00000355854.4	37	CCDS9416.2																																																																																				0.333	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925		T	49933954	C	T	49933954	2	4	47	1	0	0	0	0	0	0	0	1	2532	813	29	3		3	CAB39L	13	49933954	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	79207	49933954	65235924	1478	5875										
NEK5	341676	broad.mit.edu	37	chr13	52693533	52693533	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacttctttctttgaagcttCtttttcttgtatgggcatct	6	9	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:52693533C>A	ENST00000355568.4	-	4	275	c.136G>T	c.(136-138)Gaa>Taa	p.E46*		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.E103*(1)|p.E46*(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		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)		TTTGAAGCTTCTTTTTCTTGT	0.323																																																2	Substitution - Nonsense(2)	large_intestine(2)	13											76	77	77					13																	52693533		2200	4299	6499	51591534	SO:0001587	stop_gained	341676			BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)-related kinase 5"			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.136G>T	13.37:g.52693533C>A	ENSP00000347767:p.Glu46*		51591534	Q5TAP5	Nonsense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	C	33	5.193387	0.94960	.	.	ENSG00000197168	ENST00000355568	.	.	.	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	19.0074	0.92857	0.0:1.0:0.0:0.0	.	.	.	.	X	46	.	ENSP00000347767:E46X	E	-	1	0	NEK5	51591534	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.266000	0.51569	2.474000	0.83562	0.655000	0.94253	GAA		0.323	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		A	52693533	C	A	52693533	4	1	47	1	0	0	0	0	0	1	0	0	10358	922	32	2	2066	2	NEK5	13	52693533	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2759579	52693533	62476345	1479	5876										
THSD1	55901	broad.mit.edu	37	chr13	52951827	52951827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgggggacggtccccgacGagctctgtggggctctgttc	16	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:52951827G>A	ENST00000258613.4	-	5	2456	c.2278C>T	c.(2278-2280)Cgt>Tgt	p.R760C	THSD1_ENST00000349258.4_Missense_Mutation_p.R707C|THSD1_ENST00000544466.1_Missense_Mutation_p.R381C	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	760					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.R760C(1)		breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		GGTCCCCGACGAGCTCTGTGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	13											118	124	122					13																	52951827		2203	4300	6503	51849828	SO:0001583	missense	55901			AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.2278C>T	13.37:g.52951827G>A	ENSP00000258613:p.Arg760Cys		51849828	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	37	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700720	0.48307	.	.	ENSG00000136114	ENST00000349258;ENST00000544466;ENST00000258613	T;T;T	0.39229	1.8;1.09;1.98	5.38	3.37	0.38596	.	0.324118	0.31542	N	0.007473	T	0.41488	0.1161	L	0.50333	1.59	0.30119	N	0.805889	D;D	0.71674	0.998;0.997	P;P	0.50049	0.629;0.614	T	0.46965	-0.9153	10	0.87932	D	0	-13.5217	6.3987	0.21626	0.0936:0.0:0.5714:0.335	.	707;760	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	C	707;381;760	ENSP00000340650:R707C;ENSP00000438512:R381C;ENSP00000258613:R760C	ENSP00000258613:R760C	R	-	1	0	THSD1	51849828	0.994000	0.37717	0.785000	0.31869	0.480000	0.33159	4.637000	0.61346	1.410000	0.46936	0.502000	0.49764	CGT		0.547	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			A	52951827	G	A	52951827	3	1	47	1	0	0	0	0	1	0	0	0	15916	1058	37	1	284	1	THSD1	13	52951827	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	258294	52951827	62218051	1480	5877										
RNF219	79596	broad.mit.edu	37	chr13	79190225	79190225	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatccagtgacttaaaaccGttattacaagggctcttgct	7	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:79190225G>A	ENST00000282003.6	-	6	1729	c.1671C>T	c.(1669-1671)aaC>aaT	p.N557N	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	557	Ser-rich.						zinc ion binding (GO:0008270)	p.N557N(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		ACTTAAAACCGTTATTACAAG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	13											142	143	143					13																	79190225		2203	4300	6503	78088226	SO:0001819	synonymous_variant	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1671C>T	13.37:g.79190225G>A			78088226	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Silent	SNP	ENST00000282003.6	37	CCDS31997.1																																																																																				0.413	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79190225	G	A	79190225	2	1	47	1	0	0	0	0	0	0	0	1	13519	1136	40	1		1	RNF219	13	79190225	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	26238398	79190225	35979653	1481	5878										
RNF219	79596	broad.mit.edu	37	chr13	79191193	79191193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccagggctttcttgaggcGattggtttcacgctcatact	10	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:79191193G>A	ENST00000282003.6	-	6	761	c.703C>T	c.(703-705)Cgc>Tgc	p.R235C	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	235							zinc ion binding (GO:0008270)	p.R235C(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		TTCTTGAGGCGATTGGTTTCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											107	102	103					13																	79191193		2203	4300	6503	78089194	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.703C>T	13.37:g.79191193G>A	ENSP00000282003:p.Arg235Cys		78089194	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533362	0.64972	.	.	ENSG00000152193	ENST00000282003	.	.	.	6.17	6.17	0.99709	.	0.121708	0.56097	D	0.000037	T	0.64405	0.2595	M	0.61703	1.905	0.54753	D	0.999989	D	0.65815	0.995	P	0.49387	0.609	T	0.67503	-0.5654	9	0.87932	D	0	-10.8595	15.581	0.76439	0.0:0.0:0.8623:0.1377	.	235	Q5W0B1	RN219_HUMAN	C	235	.	ENSP00000282003:R235C	R	-	1	0	RNF219	78089194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.085000	0.76875	2.941000	0.99782	0.655000	0.94253	CGC		0.383	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79191193	G	A	79191193	3	1	47	1	0	0	0	0	1	0	0	0	13519	1058	37	1	1481	1	RNF219	13	79191193	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	968	79191193	35978685	1482	5879										
DCT	1638	broad.mit.edu	37	chr13	95118826	95118826	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctacctggagatctctttCcagacacaacaaatggtacc	6	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:95118826C>T	ENST00000377028.5	-	3	1095	c.682G>A	c.(682-684)Gaa>Aaa	p.E228K	DCT_ENST00000446125.1_Missense_Mutation_p.E228K|AL139318.1_ENST00000390768.1_RNA|DCT_ENST00000490854.1_5'UTR	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	228					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)	p.E228K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		AGATCTCTTTCCAGACACAAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13											66	66	66					13																	95118826		2203	4300	6503	93916827	SO:0001583	missense	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.682G>A	13.37:g.95118826C>T	ENSP00000366227:p.Glu228Lys		93916827	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	C	35	5.492439	0.96339	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.99825	-6.97;-6.97	5.7	5.7	0.88788	Tyrosinase (3);Uncharacterised domain, di-copper centre (2);	0.043611	0.85682	D	0.000000	D	0.99896	0.9950	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96538	0.9398	10	0.87932	D	0	-20.5965	19.8418	0.96692	0.0:1.0:0.0:0.0	.	228;228	Q09GT4;P40126	.;TYRP2_HUMAN	K	228	ENSP00000366227:E228K;ENSP00000392762:E228K	ENSP00000366227:E228K	E	-	1	0	DCT	93916827	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.802000	0.85969	2.685000	0.91497	0.561000	0.74099	GAA		0.378	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			T	95118826	C	T	95118826	3	4	47	1	0	0	0	0	1	0	0	0	4310	864	30	3	1008	3	DCT	13	95118826	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15927633	95118826	20051052	1483	5880										
DZIP1	22873	broad.mit.edu	37	chr13	96246324	96246324	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attttgttgttatttaatttCtgttcattttcccttcctga	4	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:96246324C>T	ENST00000376829.2	-	16	2405	c.1554G>A	c.(1552-1554)caG>caA	p.Q518Q	DZIP1_ENST00000361396.2_Silent_p.Q499Q|DZIP1_ENST00000347108.3_Silent_p.Q518Q|DZIP1_ENST00000361156.3_Silent_p.Q499Q	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	518					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.Q499Q(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TATTTAATTTCTGTTCATTTT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	13											130	108	115					13																	96246324		2203	4300	6503	95044325	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1554G>A	13.37:g.96246324C>T			95044325	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.333	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		T	96246324	C	T	96246324	2	4	47	1	0	0	0	0	0	0	0	1	4874	912	32	3		3	DZIP1	13	96246324	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1127498	96246324	18923554	1484	5881										
TM9SF2	9375	broad.mit.edu	37	chr13	100172322	100172322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaagcatcagaaggaaagcGcccatctgaaaatcttggtc	9	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:100172322G>A	ENST00000376387.4	+	3	462	c.272G>A	c.(271-273)cGc>cAc	p.R91H	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	91					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.R91H(2)		endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					GAAGGAAAGCGCCCATCTGAA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	13											81	80	80					13																	100172322		2203	4300	6503	98970323	SO:0001583	missense	9375			U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.272G>A	13.37:g.100172322G>A	ENSP00000365567:p.Arg91His		98970323	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	37	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874852	0.51695	.	.	ENSG00000125304	ENST00000376387	T	0.41400	1.0	5.75	5.75	0.90469	.	0.095027	0.64402	D	0.000001	T	0.33059	0.0850	N	0.21097	0.63	0.53005	D	0.999963	B;B	0.31655	0.223;0.334	B;B	0.29663	0.038;0.105	T	0.05435	-1.0885	10	0.29301	T	0.29	-1.8324	19.9911	0.97363	0.0:0.0:1.0:0.0	.	91;91	E9PHW5;Q99805	.;TM9S2_HUMAN	H	91	ENSP00000365567:R91H	ENSP00000365567:R91H	R	+	2	0	TM9SF2	98970323	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.083000	0.89515	2.734000	0.93682	0.585000	0.79938	CGC		0.343	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			A	100172322	G	A	100172322	3	1	47	1	0	0	0	0	1	0	0	0	16017	1087	38	1	282	1	TM9SF2	13	100172322	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3925998	100172322	14997556	1485	5882										
CLYBL	171425	broad.mit.edu	37	chr13	100515340	100515340	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgcaatgggtttgctcaaTtttaaggtaaggaagccata	10	6	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:100515340T>G	ENST00000376360.1	+	4	561	c.534T>G	c.(532-534)aaT>aaG	p.N178K	CLYBL_ENST00000376354.1_Intron|CLYBL_ENST00000376355.3_Intron|CLYBL_ENST00000444838.2_Intron|CLYBL_ENST00000339105.4_Missense_Mutation_p.N178K			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	178						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)	p.N178K(1)		NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GTTTGCTCAATTTTAAGGTAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	13											66	67	67					13																	100515340		2203	4300	6503	99313341	SO:0001583	missense	171425			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.534T>G	13.37:g.100515340T>G	ENSP00000365538:p.Asn178Lys		99313341	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402915	0.83230	.	.	ENSG00000125246	ENST00000376360;ENST00000339105;ENST00000416504	T;T;T	0.46451	0.87;0.87;0.87	5.42	5.42	0.78866	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.041017	0.85682	D	0.000000	T	0.61110	0.2321	M	0.85859	2.78	0.80722	D	1	D	0.56968	0.978	P	0.57846	0.828	T	0.66775	-0.5838	10	0.59425	D	0.04	-14.0302	10.1731	0.42922	0.0:0.0748:0.0:0.9252	.	178	Q8N0X4	CLYBL_HUMAN	K	178;178;95	ENSP00000365538:N178K;ENSP00000342991:N178K;ENSP00000403408:N95K	ENSP00000342991:N178K	N	+	3	2	CLYBL	99313341	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.635000	0.61332	2.180000	0.69256	0.460000	0.39030	AAT		0.308	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1			G	100515340	T	G	100515340	3	3	47	1	0	0	0	0	1	0	0	0	3579	1490	52	4	548	4	CLYBL	13	100515340	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	343018	100515340	14654538	1486	5883										
NALCN	259232	broad.mit.edu	37	chr13	102030979	102030979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atccatcaaaaacacaccagCgatctttcacataggaacta	4	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:102030979C>T	ENST00000251127.6	-	4	398	c.317G>A	c.(316-318)cGc>cAc	p.R106H	NALCN_ENST00000376200.5_Missense_Mutation_p.R106H|NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Missense_Mutation_p.R106H	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	106					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.R106H(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AACACACCAGCGATCTTTCAC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	13											97	101	99					13																	102030979		2203	4299	6502	100828980	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.317G>A	13.37:g.102030979C>T	ENSP00000251127:p.Arg106His		100828980	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895864	0.52121	.	.	ENSG00000102452	ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582	D;D;D	0.98455	-4.94;-4.94;-4.94	5.57	5.57	0.84162	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95658	0.8588	L	0.27053	0.805	0.80722	D	1	P;B	0.40931	0.733;0.391	B;B	0.38020	0.263;0.189	D	0.95039	0.8176	10	0.30854	T	0.27	.	19.5302	0.95226	0.0:1.0:0.0:0.0	.	106;106	F2Z323;Q8IZF0	.;NALCN_HUMAN	H	106	ENSP00000251127:R106H;ENSP00000365367:R106H;ENSP00000365373:R106H	ENSP00000251127:R106H	R	-	2	0	NALCN	100828980	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.351000	0.79395	2.633000	0.89246	0.591000	0.81541	CGC		0.323	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	102030979	C	T	102030979	3	4	47	1	0	0	0	0	1	0	0	0	10178	768	27	1	5063	1	NALCN	13	102030979	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1515639	102030979	13138899	1487	5884										
ERCC5	2073	broad.mit.edu	37	chr13	103510633	103510633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatctttacaggaagagttCtttcataatcctcaagcgat	6	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:103510633C>A	ENST00000355739.4	+	6	1960	c.537C>A	c.(535-537)ttC>ttA	p.F179L	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.L605I|ERCC5_ENST00000535557.1_Missense_Mutation_p.F179L	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	179					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)	p.F179L(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					AGGAAGAGTTCTTTCATAATC	0.338			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	1	Substitution - Missense(1)	large_intestine(1)	13											82	83	82					13																	103510633		2203	4300	6503	102308634	SO:0001583	missense	2073	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.537C>A	13.37:g.103510633C>A	ENSP00000347978:p.Phe179Leu		102308634	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874165	0.33069	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557;ENST00000375955	T;T	0.19806	2.12;2.12	5.31	4.45	0.53987	.	0.189959	0.47093	D	0.000242	T	0.11836	0.0288	L	0.35723	1.085	0.38723	D	0.953491	B;P;P	0.43826	0.087;0.818;0.671	B;B;B	0.37650	0.057;0.255;0.134	T	0.17319	-1.0373	10	0.11182	T	0.66	-11.3097	4.2693	0.10778	0.2102:0.5767:0.1312:0.0819	.	179;179;604	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	L	604;179;179;11	ENSP00000347978:F179L;ENSP00000442117:F179L	ENSP00000347978:F179L	F	+	3	2	ERCC5	102308634	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	0.515000	0.22801	1.199000	0.43173	0.655000	0.94253	TTC		0.338	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103510633	C	A	103510633	3	1	47	1	0	0	0	0	1	0	0	0	5229	912	32	2	559	2	ERCC5	13	103510633	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1479654	103510633	11659245	1488	5885										
ARGLU1	55082	broad.mit.edu	37	chr13	107196474	107196474	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctttcctcatgaatctttCtttgttcttcaacaattctc	2	12	6	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:107196474C>A	ENST00000400198.3	-	4	936	c.692G>T	c.(691-693)aGa>aTa	p.R231I	ARGLU1_ENST00000375926.1_Missense_Mutation_p.R100I|ARGLU1_ENST00000472226.1_5'UTR	NM_018011.3	NP_060481.3	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	231	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R231I(1)		large_intestine(1)|lung(5)|pancreas(1)	7	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					ATGAATCTTTCTTTGTTCTTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											130	117	121					13																	107196474		1813	4068	5881	105994475	SO:0001583	missense	55082			BC071587	CCDS41906.1	13q33.3	2011-10-03	2007-11-28		ENSG00000134884	ENSG00000134884			25482	protein-coding gene	gene with protein product		614046				21454576	Standard	NM_018011		Approved	FLJ10154	uc001vqk.4	Q9NWB6	OTTHUMG00000017321	ENST00000400198.3:c.692G>T	13.37:g.107196474C>A	ENSP00000383059:p.Arg231Ile		105994475	B4E0Y3|Q5T257|Q6IQ34	Missense_Mutation	SNP	ENST00000400198.3	37	CCDS41906.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319921	0.81469	.	.	ENSG00000134884	ENST00000400198;ENST00000375926	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.82930	0.5144	M	0.79475	2.455	0.80722	D	1	D	0.64830	0.994	D	0.71870	0.975	D	0.84226	0.0464	9	0.87932	D	0	-3.044	19.8476	0.96716	0.0:1.0:0.0:0.0	.	231	Q9NWB6	ARGL1_HUMAN	I	231;100	.	ENSP00000365092:R100I	R	-	2	0	ARGLU1	105994475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.372000	0.79612	2.704000	0.92352	0.650000	0.86243	AGA		0.338	ARGLU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045727.1	NM_018011		A	107196474	C	A	107196474	3	1	47	1	0	0	0	0	1	0	0	0	860	913	32	2	133	2	ARGLU1	13	107196474	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3685841	107196474	7973404	1489	5886										
CARKD	79587	broad.mit.edu	37	chr13	111290841	111290841	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccgacatgatcgccgaggTgggggccgccttcagcaagc	14	14	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:111290841T>G	ENST00000257347.4	-	0	1879				CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000458711.2_Missense_Mutation_p.V206G|CARKD_ENST00000309957.2_Silent_p.G382G|CARKD_ENST00000424185.2_Missense_Mutation_p.V227G	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)						cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)	p.G382G(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	ATCGCCGAGGTGGGGGCCGCC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	13											38	42	41					13																	111290841		2203	4300	6503	110088842	SO:0001628	intergenic_variant	55739			BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	25695	protein-coding gene	gene with protein product	"cysteine tRNA ligase 2, mitochondrial (putative)"	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347		13.37:g.111290841T>G			110088842	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.670286	0.67814	.	.	ENSG00000213995	ENST00000458711;ENST00000424185	T;T	0.24723	1.84;1.84	5.4	5.4	0.78164	Uncharacterised domain, carbohydrate kinase-related (1);	.	.	.	.	T	0.48857	0.1523	.	.	.	0.80722	D	1	D;D;D	0.62365	0.991;0.984;0.958	P;P;D	0.65573	0.834;0.891;0.936	T	0.46992	-0.9151	7	.	.	.	-0.0192	15.423	0.75028	0.0:0.0:0.0:1.0	.	206;227;337	B4DQR1;Q8IW45-4;Q8IW45	.;.;CARKD_HUMAN	G	206;227	ENSP00000412789:V206G;ENSP00000413191:V227G	.	V	+	2	0	CARKD	110088842	1.000000	0.71417	0.004000	0.12327	0.479000	0.33129	7.555000	0.82223	2.039000	0.60335	0.459000	0.35465	GTG		0.617	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537		G	111290841	T	G	111290841	1	3	47	0	1	0	0	0	0	0	0	0	2660	1683	59	4		4	CARKD	13	111290841	IGR	SNP	T	TCGA-AG-3892-01A-01W-1073-09	4094367	111290841	3879037	1490	5887										
TUBGCP3	10426	broad.mit.edu	37	chr13	113143948	113143948	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcacatttttggtatagattCtttaaattctccaatcctct	4	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:113143948C>A	ENST00000261965.3	-	21	2698	c.2512G>T	c.(2512-2514)Gaa>Taa	p.E838*		NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	838					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E838*(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	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)					GGTATAGATTCTTTAAATTCT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											270	239	250					13																	113143948		2203	4300	6503	112191949	SO:0001587	stop_gained	10426			AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.2512G>T	13.37:g.113143948C>A	ENSP00000261965:p.Glu838*		112191949	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Nonsense_Mutation	SNP	ENST00000261965.3	37	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	40	8.046176	0.98627	.	.	ENSG00000126216	ENST00000261965	.	.	.	5.25	5.25	0.73442	.	0.257370	0.45606	D	0.000350	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-18.7016	18.9187	0.92516	0.0:1.0:0.0:0.0	.	.	.	.	X	838	.	ENSP00000261965:E838X	E	-	1	0	TUBGCP3	112191949	1.000000	0.71417	0.117000	0.21633	0.084000	0.17831	6.912000	0.75753	2.469000	0.83416	0.549000	0.68633	GAA		0.438	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		A	113143948	C	A	113143948	4	1	47	1	0	0	0	0	0	1	0	0	16807	922	32	2	219	2	TUBGCP3	13	113143948	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1853107	113143948	2025930	1491	5888										
ATP11A	23250	broad.mit.edu	37	chr13	113536359	113536359	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcacagctgccctaggtcccGtgtgggaatgctcgtgtgat	13	11	1	1	rs563595559		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:113536359G>A	ENST00000487903.1	+	0	3735				ATP11A_ENST00000375645.3_3'UTR|ATP11A_ENST00000375630.2_Missense_Mutation_p.R1186H			P98196	AT11A_HUMAN	ATPase, class VI, type 11A						phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1186H(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	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_lung(25;0.134)|all_epithelial(44;0.141)				CCTAGGTCCCGTGTGGGAATG	0.637													G|||	1	0.000199681	0	0.0014	5008	,	,		19402	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13											198	179	185					13																	113536359		2203	4300	6503	112584360	SO:0001624	3_prime_UTR_variant	23250			AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.*242G>A	13.37:g.113536359G>A			112584360	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	9.430	1.085345	0.20390	.	.	ENSG00000068650	ENST00000375630;ENST00000419631	T;T	0.43688	0.94;1.93	3.43	0.613	0.17597	.	.	.	.	.	T	0.18882	0.0453	N	0.08118	0	0.09310	N	1	B	0.28055	0.199	B	0.19666	0.026	T	0.14227	-1.0480	9	0.42905	T	0.14	.	4.871	0.13633	0.1869:0.0:0.6472:0.1659	.	1186	E9PEJ6	.	H	1186;178	ENSP00000364781:R1186H;ENSP00000410824:R178H	ENSP00000364781:R1186H	R	+	2	0	ATP11A	112584360	0.490000	0.26012	0.000000	0.03702	0.000000	0.00434	1.776000	0.38594	-0.171000	0.10797	-1.734000	0.00692	CGT		0.637	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		A	113536359	G	A	113536359	1	1	47	0	1	0	0	0	0	0	0	0	1120	1145	40	1		1	ATP11A	13	113536359	3'UTR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	392411	113536359	1633519	1492	5889										
CDC16	8881	broad.mit.edu	37	chr13	115007715	115007715	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctactgttttgaagcgttCgatcttttaacatcacatca	6	9	4	1	rs145297166	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr13:115007715C>T	ENST00000356221.3	+	6	609	c.501C>T	c.(499-501)ttC>ttT	p.F167F	MIR548AR_ENST00000582191.1_RNA|CDC16_ENST00000375312.3_Silent_p.F73F|CDC16_ENST00000252457.5_Silent_p.F166F|CDC16_ENST00000360383.3_Silent_p.F167F|CDC16_ENST00000375310.1_Silent_p.F73F|CDC16_ENST00000375308.1_Silent_p.F73F|CDC16_ENST00000252458.6_Silent_p.F73F			Q13042	CDC16_HUMAN	cell division cycle 16	167					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)		p.F166F(1)		endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TTGAAGCGTTCGATCTTTTAA	0.373													c|||	2	0.000399361	8e-04	0	5008	,	,		19028	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13						T	,	1,4405	826.1+/-416.6	0,1,2202	127	125	126		501,501	2	1	13	dbSNP_134	126	2,8598	819.1+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	167/621,167/621	115007715	3,13003	2203	4300	6503	114025817	SO:0001819	synonymous_variant	8881			U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.501C>T	13.37:g.115007715C>T			114025817	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																				0.373	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115007715	C	T	115007715	2	4	47	1	0	0	0	0	0	0	0	1	3064	883	31	1		1	CDC16	13	115007715	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1471356	115007715	162163	1493	5890										
OR4M1	441670	broad.mit.edu	37	chr14	20248760	20248760	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggagaggaagataatttcCtttggtggatgcattgcaca	13	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:20248760C>A	ENST00000315957.4	+	1	360	c.279C>A	c.(277-279)tcC>tcA	p.S93S		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S93S(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		AGATAATTTCCTTTGGTGGAT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	14											252	273	266					14																	20248760		2203	4300	6503	19318600	SO:0001819	synonymous_variant	441670				CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"GPCR / Class A : Olfactory receptors"	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.279C>A	14.37:g.20248760C>A			19318600	B9EH18|Q6IFA3	Silent	SNP	ENST00000315957.4	37	CCDS32021.1																																																																																				0.448	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			A	20248760	C	A	20248760	2	1	47	1	0	0	0	0	0	0	0	1	11106	668	24	2		2	OR4M1	14	20248760	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09		20248760	87100780	1494	5891										
OR4K2	390431	broad.mit.edu	37	chr14	20344641	20344641	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctttcaatcattgatatgtCtcttgcttctttcgccaccc	4	13	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:20344641C>A	ENST00000298642.2	+	1	251	c.215C>A	c.(214-216)tCt>tAt	p.S72Y		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	72						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S72Y(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATTGATATGTCTCTTGCTTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											327	313	318					14																	20344641		2203	4300	6503	19414481	SO:0001583	missense	390431				CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.215C>A	14.37:g.20344641C>A	ENSP00000298642:p.Ser72Tyr		19414481	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	37	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	11.95	1.790684	0.31685	.	.	ENSG00000165762	ENST00000298642	T	0.00428	7.44	5.27	5.27	0.74061	GPCR, rhodopsin-like superfamily (1);	0.143255	0.32640	N	0.005821	T	0.00356	0.0011	L	0.38531	1.155	0.28118	N	0.930715	B	0.29301	0.241	B	0.31390	0.129	T	0.50725	-0.8794	10	0.52906	T	0.07	.	12.012	0.53293	0.0:0.8262:0.1738:0.0	.	72	Q8NGD2	OR4K2_HUMAN	Y	72	ENSP00000298642:S72Y	ENSP00000298642:S72Y	S	+	2	0	OR4K2	19414481	0.015000	0.18098	1.000000	0.80357	0.988000	0.76386	1.920000	0.40025	2.740000	0.93945	0.563000	0.77884	TCT		0.423	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			A	20344641	C	A	20344641	3	1	47	1	0	0	0	0	1	0	0	0	11103	913	32	2	217	2	OR4K2	14	20344641	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	95881	20344641	87004899	1495	5892										
CHD8	57680	broad.mit.edu	37	chr14	21869225	21869225	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaggtgtgtcaattaccaaAttattctatgaagagaacag	8	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:21869225A>C	ENST00000557364.1	-	22	4442	c.4179T>G	c.(4177-4179)aaT>aaG	p.N1393K	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Missense_Mutation_p.N1393K|CHD8_ENST00000430710.3_Missense_Mutation_p.N1114K			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1393					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.N1393K(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CAATTACCAAATTATTCTATG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											93	88	89					14																	21869225		1885	4122	6007	20939065	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.4179T>G	14.37:g.21869225A>C	ENSP00000451601:p.Asn1393Lys		20939065	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.606|3.606	-0.080582|-0.080582	0.07141|0.07141	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000555935|ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	.|D;D;D	.|0.83419	.|-1.72;-1.72;-1.72	5.04|5.04	1.13|1.13	0.20643|0.20643	.|.	.|0.056851	.|0.64402	.|D	.|0.000001	T|T	0.70228|0.70228	0.3200|0.3200	L|L	0.33485|0.33485	1.01|1.01	0.34349|0.34349	D|D	0.689659|0.689659	.|B;B	.|0.18610	.|0.006;0.029	.|B;B	.|0.22386	.|0.008;0.039	T|T	0.61461|0.61461	-0.7058|-0.7058	5|10	.|0.20046	.|T	.|0.44	-18.0977|-18.0977	8.2184|8.2184	0.31526|0.31526	0.4226:0.0:0.5774:0.0|0.4226:0.0:0.5774:0.0	.|.	.|1393;1114	.|Q9HCK8;Q9HCK8-2	.|CHD8_HUMAN;.	V|K	619|1114;1393;1113;1393	.|ENSP00000406288:N1114K;ENSP00000382863:N1393K;ENSP00000451601:N1393K	.|ENSP00000262707:N1113K	F|N	-|-	1|3	0|2	CHD8|CHD8	20939065|20939065	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.907000|0.907000	0.53573|0.53573	0.918000|0.918000	0.28678|0.28678	0.032000|0.032000	0.15435|0.15435	-0.242000|-0.242000	0.12053|0.12053	TTT|AAT		0.378	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		C	21869225	A	C	21869225	3	2	47	1	0	0	0	0	1	0	0	0	3337	98	4	4	3634	4	CHD8	14	21869225	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1524584	21869225	85480315	1496	5893										
MYH7	4625	broad.mit.edu	37	chr14	23898176	23898176	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caactcacatcgaagatctcGaagccagcgatgtccaggac	9	13	2	1	rs45508293	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:23898176G>A	ENST00000355349.3	-	14	1557	c.1395C>T	c.(1393-1395)ttC>ttT	p.F465F		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	465	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.F465F(2)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGAAGATCTCGAAGCCAGCGA	0.542													g|||	3	0.000599042	0.0023	0	5008	,	,		23008	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	14						G		9,4397	15.5+/-35.6	0,9,2194	88	77	81		1395	-7.4	0.7	14	dbSNP_127	81	0,8600		0,0,4300	no	coding-synonymous	MYH7	NM_000257.2		0,9,6494	AA,AG,GG		0.0,0.2043,0.0692		465/1936	23898176	9,12997	2203	4300	6503	22968016	SO:0001819	synonymous_variant	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1395C>T	14.37:g.23898176G>A			22968016	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																				0.542	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23898176	G	A	23898176	2	1	47	1	0	0	0	0	0	0	0	1	10069	1049	37	1		1	MYH7	14	23898176	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2028951	23898176	83451364	1497	5894										
MYH7	4625	broad.mit.edu	37	chr14	23899802	23899802	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctcctcagcgtcatcaatGgaggccacggtggtctctcc	11	14	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:23899802G>T	ENST00000355349.3	-	11	1128	c.966C>A	c.(964-966)tcC>tcA	p.S322S		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	322	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.S322S(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGTCATCAATGGAGGCCACGG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	14											111	82	92					14																	23899802		2203	4300	6503	22969642	SO:0001819	synonymous_variant	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.966C>A	14.37:g.23899802G>T			22969642	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																				0.552	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23899802	G	T	23899802	2	4	47	1	0	0	0	0	0	0	0	1	10069	1335	47	2		2	MYH7	14	23899802	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1626	23899802	83449738	1498	5895										
DHRS2	10202	broad.mit.edu	37	chr14	24108510	24108510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggggaggggctgagtgtggCgggcattgtgtgccacgtgg	23	6	0	1	rs562246921		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:24108510C>T	ENST00000250383.6	+	3	739	c.263C>T	c.(262-264)gCg>gTg	p.A88V	DHRS2_ENST00000553896.1_3'UTR|DHRS2_ENST00000344777.7_Missense_Mutation_p.A88V	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	88					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)	p.A88V(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		CTGAGTGTGGCGGGCATTGTG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	14											31	35	33					14																	24108510		2201	4299	6500	23178350	SO:0001583	missense	10202				CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18349	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 1"	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.263C>T	14.37:g.24108510C>T	ENSP00000250383:p.Ala88Val		23178350	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	.	.	.	.	.	.	.	.	.	.	.	4.104	0.017412	0.07959	.	.	ENSG00000100867	ENST00000432832;ENST00000250383;ENST00000344777	T;T;T	0.20738	2.05;2.05;2.05	4.96	-3.33	0.04958	NAD(P)-binding domain (1);	0.656003	0.15984	N	0.235171	T	0.06600	0.0169	N	0.05012	-0.13	0.09310	N	1	B;B;B;B	0.21905	0.022;0.008;0.062;0.021	B;B;B;B	0.20184	0.028;0.015;0.014;0.007	T	0.34129	-0.9841	10	0.16896	T	0.51	.	4.0306	0.09708	0.3414:0.2723:0.0:0.3863	.	66;88;88;66	Q13268;C9JZP6;D3DS54;Q13268-2	DHRS2_HUMAN;.;.;.	V	88	ENSP00000401213:A88V;ENSP00000250383:A88V;ENSP00000344674:A88V	ENSP00000250383:A88V	A	+	2	0	DHRS2	23178350	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.893000	0.04127	-0.492000	0.06687	0.491000	0.48974	GCG		0.687	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		T	24108510	C	T	24108510	3	4	47	1	0	0	0	0	1	0	0	0	4501	768	27	1	269	1	DHRS2	14	24108510	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	208708	24108510	83241030	1499	5896										
DHRS4L1	90668	broad.mit.edu	37	chr14	24520093	24520093	+	5'Flank	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagaggattctcttggcatCgtgtctttcctgtgctctga	10	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:24520093C>T	ENST00000342740.5	+	0	0				RP11-468E2.9_ENST00000558293.1_RNA|LRRC16B_ENST00000334420.7_5'Flank	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B							cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CTCTTGGCATCGTGTCTTTCC	0.582																																																0			14											76	75	76					14																	24520093		2203	4300	6503	23589933	SO:0001631	upstream_gene_variant	728635			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23			14.37:g.24520093C>T	Exception_encountered		23589933	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																				0.582	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24520093	C	T	24520093	1	4	47	0	1	0	0	0	0	0	0	0	4504	874	31	1		1	DHRS4L1	14	24520093	5'Flank	SNP	C	TCGA-AG-3892-01A-01W-1073-09	411583	24520093	82829447	1500	5897										
TM9SF1	10548	broad.mit.edu	37	chr14	24662353	24662353	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatgggtccagagtcctatCttgtggctgtgtggcaggaa	14	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:24662353C>A	ENST00000261789.4	-	3	826	c.468G>T	c.(466-468)aaG>aaT	p.K156N	TM9SF1_ENST00000528669.1_Missense_Mutation_p.K156N|TM9SF1_ENST00000524835.1_Missense_Mutation_p.K69N|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000530611.1_Missense_Mutation_p.K365N|TM9SF1_ENST00000396854.4_Missense_Mutation_p.K156N|TM9SF1_ENST00000556387.1_Missense_Mutation_p.K365N	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	156					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.K156N(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AGAGTCCTATCTTGTGGCTGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14											97	94	95					14																	24662353		2203	4300	6503	23732193	SO:0001583	missense	10548			U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.468G>T	14.37:g.24662353C>A	ENSP00000261789:p.Lys156Asn		23732193	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413229	0.62511	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	4.99	4.11	0.48088	.	0.053116	0.64402	D	0.000001	T	0.53286	0.1787	M	0.61387	1.9	0.58432	D	0.999995	P;P;B	0.51240	0.943;0.599;0.425	P;P;B	0.53722	0.733;0.574;0.221	T	0.54437	-0.8294	10	0.52906	T	0.07	-11.5412	7.2156	0.25957	0.0:0.8078:0.0:0.1922	.	156;156;156	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	N	156;156;365;69;156;156;69;156;156;156;365	ENSP00000261789:K156N;ENSP00000432997:K156N;ENSP00000451949:K365N;ENSP00000434387:K69N;ENSP00000380063:K156N;ENSP00000431447:K156N;ENSP00000437127:K69N;ENSP00000435857:K156N;ENSP00000432435:K156N;ENSP00000433792:K156N;ENSP00000433967:K365N	ENSP00000433967:K365N	K	-	3	2	TM9SF1;RP11-468E2.1	23732193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.558000	0.45879	1.327000	0.45338	0.655000	0.94253	AAG		0.488	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		A	24662353	C	A	24662353	3	1	47	1	0	0	0	0	1	0	0	0	16016	912	32	2	1411	2	TM9SF1	14	24662353	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	142260	24662353	82687187	1501	5898										
CHMP4A	29082	broad.mit.edu	37	chr14	24680977	24680977	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttcttgatcagtatcttCtctgtctccttcagtttctg	6	10	7	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:24680977C>T	ENST00000609024.1	-	2	138	c.90G>A	c.(88-90)gaG>gaA	p.E30E	AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000542700.2_5'UTR|MDP1_ENST00000532557.1_5'Flank|CHMP4A_ENST00000347519.6_Silent_p.E73E|TM9SF1_ENST00000530611.1_Silent_p.E30E|NEDD8-MDP1_ENST00000604306.1_5'Flank|TM9SF1_ENST00000556387.1_Silent_p.E30E|CHMP4A_ENST00000530996.1_5'UTR			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	30	Interaction with phosphoinosides.|Intramolecular interaction with C- terminus. {ECO:0000250}.				endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)	p.E73E(1)		NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		TCAGTATCTTCTCTGTCTCCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	14											209	186	194					14																	24680977		2203	4300	6503	23750817	SO:0001819	synonymous_variant	29082			AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"Charged multivesicular body proteins"	20274	protein-coding gene	gene with protein product		610051	"chromosome 14 open reading frame 123", "chromatin modifying protein 4A"	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.90G>A	14.37:g.24680977C>T			23750817	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Silent	SNP	ENST00000609024.1	37		.	.	.	.	.	.	.	.	.	.	C	12.74	2.027611	0.35797	.	.	ENSG00000254505	ENST00000548308	.	.	.	5.39	1.44	0.22558	.	0.000000	0.39759	N	0.001277	T	0.56920	0.2018	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49753	-0.8906	5	.	.	.	-17.9599	8.7429	0.34569	0.0:0.6628:0.0:0.3372	.	.	.	.	K	50	.	.	E	-	1	0	AL096870.1	23750817	0.986000	0.35501	0.949000	0.38748	0.968000	0.65278	1.143000	0.31553	0.254000	0.21573	-0.291000	0.09656	GAA		0.443	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169		T	24680977	C	T	24680977	2	4	47	1	0	0	0	0	0	0	0	1	3362	912	32	3		3	CHMP4A	14	24680977	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	18624	24680977	82668563	1502	5899										
NEDD8	4738	broad.mit.edu	37	chr14	24687414	24687414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctccacacgctccttgattCgctccacctttagagagaca	6	16	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:24687414C>T	ENST00000250495.5	-	3	260	c.74G>A	c.(73-75)cGa>cAa	p.R25Q	AL136419.6_ENST00000565988.1_RNA|NEDD8-MDP1_ENST00000534348.1_Missense_Mutation_p.R25Q|MDP1_ENST00000396833.2_5'Flank|MDP1_ENST00000288087.7_5'Flank|MDP1_ENST00000532557.1_5'Flank|NEDD8_ENST00000524927.1_Missense_Mutation_p.R25Q|NEDD8-MDP1_ENST00000604306.1_5'UTR	NM_006156.2	NP_006147.1	Q15843	NEDD8_HUMAN	neural precursor cell expressed, developmentally down-regulated 8	25					anatomical structure morphogenesis (GO:0009653)|cellular protein modification process (GO:0006464)|protein localization (GO:0008104)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to organic cyclic compound (GO:0014070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.R25Q(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5				GBM - Glioblastoma multiforme(265;0.0186)		CTCCTTGATTCGCTCCACCTT	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	14											118	103	108					14																	24687414		2203	4300	6503	23757254	SO:0001583	missense	4738			D23662	CCDS9621.1	14q11.2	2008-08-13			ENSG00000129559	ENSG00000129559			7732	protein-coding gene	gene with protein product		603171				9353319	Standard	NM_006156		Approved	Nedd-8		Q15843	OTTHUMG00000029325	ENST00000250495.5:c.74G>A	14.37:g.24687414C>T	ENSP00000250495:p.Arg25Gln		23757254	Q3SXN8|Q6LES6	Missense_Mutation	SNP	ENST00000250495.5	37	CCDS9621.1	.	.	.	.	.	.	.	.	.	.	C	32	5.179410	0.94846	.	.	ENSG00000255526;ENSG00000129559;ENSG00000129559	ENST00000534348;ENST00000250495;ENST00000524927	T;T;T	0.71222	-0.55;-0.55;-0.55	5.15	5.15	0.70609	Ubiquitin supergroup (1);Ubiquitin (2);	0.068063	0.56097	N	0.000028	T	0.57330	0.2046	N	0.16862	0.45	0.80722	D	1	D	0.55605	0.972	B	0.40410	0.328	T	0.67106	-0.5754	10	0.87932	D	0	-5.2715	17.5536	0.87884	0.0:1.0:0.0:0.0	.	25	Q15843	NEDD8_HUMAN	Q	25	ENSP00000431482:R25Q;ENSP00000250495:R25Q;ENSP00000448192:R25Q	ENSP00000250495:R25Q	R	-	2	0	NEDD8-MDP1;NEDD8	23757254	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.780000	0.62382	2.675000	0.91044	0.655000	0.94253	CGA		0.517	NEDD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073146.2	NM_006156		T	24687414	C	T	24687414	3	4	47	1	0	0	0	0	1	0	0	0	10343	884	31	1	179	1	NEDD8	14	24687414	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6437	24687414	82662126	1503	5900										
GZMB	3002	broad.mit.edu	37	chr14	25101153	25101153	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagtcagattcgcactttcGatcttcctgcactgtcatct	6	12	4	1	rs199605460		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:25101153G>A	ENST00000216341.4	-	4	617	c.511C>T	c.(511-513)Cga>Tga	p.R171*	GZMB_ENST00000382540.1_Nonsense_Mutation_p.R126*|GZMB_ENST00000382542.1_Nonsense_Mutation_p.R205*|GZMB_ENST00000526004.1_3'UTR|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000415355.3_Nonsense_Mutation_p.R159*|RP11-104E19.1_ENST00000555300.1_RNA			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	171	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R205*(1)|p.R171*(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		TCGCACTTTCGATCTTCCTGC	0.517																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											161	151	154					14																	25101153		2203	4300	6503	24170993	SO:0001587	stop_gained	3002			BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"fragmentin 2", "cytotoxic serine protease B", "cathepsin G-like 1", "T-cell serine protease 1-3E"	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.511C>T	14.37:g.25101153G>A	ENSP00000216341:p.Arg171*		24170993	Q8N1D2|Q9UCC1	Nonsense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	.	.	.	.	.	.	.	.	.	.	g	12.41	1.928929	0.34002	.	.	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000382539	.	.	.	5.3	-5.55	0.02536	.	1.857220	0.03740	N	0.254823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	1.315	0.02105	0.2399:0.3664:0.1846:0.209	.	.	.	.	X	159;171;205;126;76	.	ENSP00000216341:R171X	R	-	1	2	GZMB	24170993	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.161000	0.01278	-1.007000	0.03408	-0.868000	0.02995	CGA		0.517	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131		A	25101153	G	A	25101153	4	1	47	1	0	0	0	0	0	1	0	0	6937	1066	37	1	240	1	GZMB	14	25101153	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	413739	25101153	82248387	1504	5901										
HECTD1	25831	broad.mit.edu	37	chr14	31572157	31572157	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccagcttaggttcagtgtaAttgataatatcctctgctgc	8	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:31572157A>C	ENST00000399332.1	-	41	8003	c.7515T>G	c.(7513-7515)aaT>aaG	p.N2505K	HECTD1_ENST00000553700.1_Missense_Mutation_p.N2505K	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2505	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.N2505K(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		GTTCAGTGTAATTGATAATAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	14											151	145	147					14																	31572157		1898	4117	6015	30641908	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.7515T>G	14.37:g.31572157A>C	ENSP00000382269:p.Asn2505Lys		30641908	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.19|17.19	3.325232|3.325232	0.60743|0.60743	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332;ENST00000399323	.|T;T	.|0.39229	.|1.09;1.09	5.94|5.94	4.81|4.81	0.61882|0.61882	.|HECT (4);	.|0.062767	.|0.64402	.|U	.|0.000010	T|T	0.28896|0.28896	0.0717|0.0717	N|N	0.25825|0.25825	0.765|0.765	0.58432|0.58432	D|D	0.999999|0.999999	.|P	.|0.38711	.|0.643	.|B	.|0.34652	.|0.187	T|T	0.12837|0.12837	-1.0532|-1.0532	5|10	.|0.52906	.|T	.|0.07	-19.0465|-19.0465	11.4838|11.4838	0.50342|0.50342	0.9306:0.0:0.0694:0.0|0.9306:0.0:0.0694:0.0	.|.	.|2505	.|Q9ULT8	.|HECD1_HUMAN	S|K	871|2505;2507;2505;66	.|ENSP00000450697:N2505K;ENSP00000382269:N2505K	.|ENSP00000261312:N2507K	I|N	-|-	2|3	0|2	HECTD1|HECTD1	30641908|30641908	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.391000|4.391000	0.59652|0.59652	2.275000|2.275000	0.75901|0.75901	0.528000|0.528000	0.53228|0.53228	ATT|AAT		0.368	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31572157	A	C	31572157	3	2	47	1	0	0	0	0	1	0	0	0	7060	98	4	4	329	4	HECTD1	14	31572157	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6471004	31572157	75777383	1505	5902										
ARHGAP5	394	broad.mit.edu	37	chr14	32563226	32563226	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcccagatgatagtcaaaaTcgtattaaaattcgaaactc	6	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:32563226T>G	ENST00000345122.3	+	2	3666	c.3351T>G	c.(3349-3351)aaT>aaG	p.N1117K	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.N1117K|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.N1117K|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.N1117K|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	1117					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.N1117K(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		ATAGTCAAAATCGTATTAAAA	0.368																																					NSCLC(9;77 350 3443 29227 41353)											1	Substitution - Missense(1)	large_intestine(1)	14											52	55	54					14																	32563226		2203	4299	6502	31632977	SO:0001583	missense	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.3351T>G	14.37:g.32563226T>G	ENSP00000371897:p.Asn1117Lys		31632977	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	T	8.546	0.874366	0.17395	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.08546	3.08;3.08;3.08;3.08	5.27	5.27	0.74061	.	0.082034	0.85682	D	0.000000	T	0.08133	0.0203	L	0.36672	1.1	0.43896	D	0.996526	B;B	0.31705	0.336;0.227	B;B	0.35550	0.205;0.101	T	0.36286	-0.9754	10	0.24483	T	0.36	.	9.9324	0.41530	0.0:0.0765:0.0:0.9235	.	1117;1117	Q13017-2;Q13017	.;RHG05_HUMAN	K	1117	ENSP00000452222:N1117K;ENSP00000441692:N1117K;ENSP00000371897:N1117K;ENSP00000393307:N1117K	ENSP00000371897:N1117K	N	+	3	2	ARHGAP5	31632977	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.806000	0.38892	2.123000	0.65237	0.383000	0.25322	AAT		0.368	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		G	32563226	T	G	32563226	3	3	47	1	0	0	0	0	1	0	0	0	886	1432	50	4	3353	4	ARHGAP5	14	32563226	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	991069	32563226	74786314	1506	5903										
SRP54	6729	broad.mit.edu	37	chr14	35468785	35468785	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattgaatgctatgctaaaaGaagtctgtaccgctttgttg	9	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:35468785G>T	ENST00000556994.1	+	4	497	c.100G>T	c.(100-102)Gaa>Taa	p.E34*	SRP54_ENST00000555535.1_3'UTR|SRP54_ENST00000555557.1_Intron|SRP54_ENST00000546080.1_Intron|SRP54_ENST00000216774.6_Nonsense_Mutation_p.E34*			P61011	SRP54_HUMAN	signal recognition particle 54kDa	34	G-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)	p.E34*(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		TATGCTAAAAGAAGTCTGTAC	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											95	99	98					14																	35468785		2203	4300	6503	34538536	SO:0001587	stop_gained	6729			X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.100G>T	14.37:g.35468785G>T	ENSP00000451818:p.Glu34*		34538536	B2R759|B4DUW6|P13624	Nonsense_Mutation	SNP	ENST00000556994.1	37	CCDS9652.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765514	0.90020	.	.	ENSG00000100883	ENST00000556994;ENST00000554803;ENST00000555746;ENST00000216774	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.0883	19.7069	0.96076	0.0:0.0:1.0:0.0	.	.	.	.	X	34	.	ENSP00000216774:E34X	E	+	1	0	SRP54	34538536	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.649000	0.98487	2.654000	0.90174	0.563000	0.77884	GAA		0.299	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		T	35468785	G	T	35468785	4	4	47	1	0	0	0	0	0	1	0	0	15194	943	33	2	106	2	SRP54	14	35468785	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2905559	35468785	71880755	1507	5904										
LRFN5	145581	broad.mit.edu	37	chr14	42356576	42356576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgcaattgtgaattgttgTggttgaggcgtctgtccaga	13	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:42356576T>C	ENST00000298119.4	+	3	1937	c.748T>C	c.(748-750)Tgg>Cgg	p.W250R	LRFN5_ENST00000554171.1_Missense_Mutation_p.W250R|LRFN5_ENST00000554120.1_Missense_Mutation_p.W250R	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	250	LRRCT.					integral component of membrane (GO:0016021)		p.W250R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGAATTGTTGTGGTTGAGGCG	0.443										HNSCC(30;0.082)																																						1	Substitution - Missense(1)	large_intestine(1)	14											162	162	162					14																	42356576		2203	4300	6503	41426326	SO:0001583	missense	145581			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.748T>C	14.37:g.42356576T>C	ENSP00000298119:p.Trp250Arg		41426326	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.098854	0.56183	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.54071	0.59;0.59;0.59	5.69	5.69	0.88448	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.53938	D	0.000058	T	0.78515	0.4295	M	0.92367	3.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.83925	0.0303	10	0.87932	D	0	.	13.9063	0.63839	0.0:0.0:0.0:1.0	.	250;250	G3V364;Q96NI6	.;LRFN5_HUMAN	R	250	ENSP00000298119:W250R;ENSP00000451897:W250R;ENSP00000451067:W250R	ENSP00000298119:W250R	W	+	1	0	LRFN5	41426326	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.161000	0.67846	0.455000	0.32223	TGG		0.443	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		C	42356576	T	C	42356576	3	2	47	1	0	0	0	0	1	0	0	0	8970	1696	59	4	750	4	LRFN5	14	42356576	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	6887791	42356576	64992964	1508	5905										
FAM179B	23116	broad.mit.edu	37	chr14	45481249	45481249	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctgcaaagaaaaaaatttCtcatattgctgaacaaagcc	5	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:45481249C>A	ENST00000361577.3	+	7	3423	c.3209C>A	c.(3208-3210)tCt>tAt	p.S1070Y	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.S1070Y|FAM179B_ENST00000382233.2_Missense_Mutation_p.F992L	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1070	Ser-rich.							p.S1070Y(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						AAAAAAATTTCTCATATTGCT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	14											52	55	54					14																	45481249		2201	4299	6500	44550999	SO:0001583	missense	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3209C>A	14.37:g.45481249C>A	ENSP00000355045:p.Ser1070Tyr		44550999	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.858|4.858	0.159429|0.159429	0.09236|0.09236	.|.	.|.	ENSG00000198718|ENSG00000198718	ENST00000382233|ENST00000429476;ENST00000361577;ENST00000361462	T|T;T	0.28666|0.04406	1.6|3.63;3.63	5.92|5.92	4.1|4.1	0.47936|0.47936	.|Armadillo-type fold (1);	.|0.446471	.|0.24465	.|N	.|0.038299	T|T	0.05364|0.05364	0.0142|0.0142	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|P;P	.|0.40875	.|0.731;0.731	.|B;B	.|0.44224	.|0.444;0.444	T|T	0.27739|0.27739	-1.0065|-1.0065	7|10	0.87932|0.59425	D|D	0|0.04	-3.3036|-3.3036	10.1989|10.1989	0.43071|0.43071	0.0:0.8465:0.0:0.1535|0.0:0.8465:0.0:0.1535	.|.	.|1070;1070	.|G3XAE9;Q9Y4F4	.|.;F179B_HUMAN	L|Y	992|1070	ENSP00000371668:F992L|ENSP00000355045:S1070Y;ENSP00000354917:S1070Y	ENSP00000371668:F992L|ENSP00000354917:S1070Y	F|S	+|+	3|2	2|0	FAM179B|FAM179B	44550999|44550999	0.159000|0.159000	0.22864|0.22864	0.011000|0.011000	0.14972|0.14972	0.008000|0.008000	0.06430|0.06430	2.144000|2.144000	0.42197|0.42197	1.500000|1.500000	0.48636|0.48636	0.650000|0.650000	0.86243|0.86243	TTC|TCT		0.294	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		A	45481249	C	A	45481249	3	1	47	1	0	0	0	0	1	0	0	0	5522	913	32	2	3235	2	FAM179B	14	45481249	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3124673	45481249	61868291	1509	5906										
FANCM	57697	broad.mit.edu	37	chr14	45618082	45618082	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctgctaattgggcagataGagcttcgttctgaagattct	10	8	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:45618082G>T	ENST00000267430.5	+	4	887	c.802G>T	c.(802-804)Gag>Tag	p.E268*	FANCM_ENST00000542564.2_Nonsense_Mutation_p.E242*|FANCM_ENST00000556036.1_Nonsense_Mutation_p.E268*	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	268					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.E268*(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TGGGCAGATAGAGCTTCGTTC	0.328								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Nonsense(1)	large_intestine(1)	14											71	71	71					14																	45618082		2203	4300	6503	44687832	SO:0001587	stop_gained	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.802G>T	14.37:g.45618082G>T	ENSP00000267430:p.Glu268*		44687832	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Nonsense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	37	6.218771	0.97385	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	.	.	.	5.75	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	12.8754	0.57988	0.079:0.0:0.921:0.0	.	.	.	.	X	268;268;242	.	ENSP00000267430:E268X	E	+	1	0	FANCM	44687832	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.702000	0.84576	1.567000	0.49668	0.650000	0.86243	GAG		0.328	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45618082	G	T	45618082	4	4	47	1	0	0	0	0	0	1	0	0	5690	943	33	2	816	2	FANCM	14	45618082	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	136833	45618082	61731458	1510	5907										
FANCM	57697	broad.mit.edu	37	chr14	45644338	45644338	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaagatgttacctcaacatTtattgctcccaggaatgaat	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:45644338T>G	ENST00000267430.5	+	14	2466	c.2381T>G	c.(2380-2382)tTt>tGt	p.F794C	FANCM_ENST00000542564.2_Missense_Mutation_p.F768C	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	794					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.F794C(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ACCTCAACATTTATTGCTCCC	0.333								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	14											85	85	85					14																	45644338		2203	4299	6502	44714088	SO:0001583	missense	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2381T>G	14.37:g.45644338T>G	ENSP00000267430:p.Phe794Cys		44714088	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	T	9.976	1.226886	0.22542	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18502	2.79;2.8;2.21	5.09	-2.67	0.06059	.	1.069690	0.07075	N	0.836004	T	0.12817	0.0311	L	0.44542	1.39	0.09310	N	1	P;P	0.51653	0.947;0.947	B;B	0.43103	0.408;0.408	T	0.21930	-1.0231	10	0.39692	T	0.17	.	2.4942	0.04617	0.1692:0.4597:0.1597:0.2114	.	768;794	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	C	794;768;310	ENSP00000267430:F794C;ENSP00000442493:F768C;ENSP00000452033:F310C	ENSP00000267430:F794C	F	+	2	0	FANCM	44714088	0.000000	0.05858	0.002000	0.10522	0.451000	0.32288	-0.554000	0.06006	-0.268000	0.09312	0.482000	0.46254	TTT		0.333	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45644338	T	G	45644338	3	3	47	1	0	0	0	0	1	0	0	0	5690	1841	64	4	2435	4	FANCM	14	45644338	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	26256	45644338	61705202	1511	5908										
MDGA2	161357	broad.mit.edu	37	chr14	47324284	47324284	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattccatctttgtcctttAttcccacttgaagaccacag	4	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:47324284A>G	ENST00000399232.2	-	15	2983	c.2619T>C	c.(2617-2619)aaT>aaC	p.N873N	MDGA2_ENST00000357362.3_Silent_p.N644N|MDGA2_ENST00000399222.3_Silent_p.N75N|MDGA2_ENST00000439988.3_Silent_p.N942N|MDGA2_ENST00000426342.1_Silent_p.N644N	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	873	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.N644N(2)|p.N942N(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						TTTGTCCTTTATTCCCACTTG	0.313																																																3	Substitution - coding silent(3)	large_intestine(3)	14											137	128	131					14																	47324284		1826	4076	5902	46394034	SO:0001819	synonymous_variant	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.2619T>C	14.37:g.47324284A>G			46394034	F6W3S7|J3KPX6	Silent	SNP	ENST00000399232.2	37																																																																																					0.313	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		G	47324284	A	G	47324284	2	3	47	1	0	0	0	0	0	0	0	1	9437	446	16	4		4	MDGA2	14	47324284	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1679946	47324284	60025256	1512	5909										
KLHDC2	23588	broad.mit.edu	37	chr14	50244957	50244957	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagtattgggaacttttgaaTtcgatgaaacatctttttgg	9	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:50244957T>G	ENST00000298307.5	+	5	1390	c.529T>G	c.(529-531)Ttc>Gtc	p.F177V	KLHDC2_ENST00000554589.1_Missense_Mutation_p.F177V|KLHDC2_ENST00000553538.1_3'UTR|KLHDC2_ENST00000557247.1_Missense_Mutation_p.F177V	NM_014315.2	NP_055130.1	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	177						nucleus (GO:0005634)		p.F177V(1)		endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	all_epithelial(31;0.000959)|Breast(41;0.0117)					AACTTTTGAATTCGATGAAAC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	14											139	139	139					14																	50244957		2203	4300	6503	49314707	SO:0001583	missense	23588			AK001771	CCDS9693.1	14q21.3	2003-01-15			ENSG00000165516	ENSG00000165516			20231	protein-coding gene	gene with protein product		611280				11384994	Standard	NM_014315		Approved	HCLP-1, LCP	uc001wwx.3	Q9Y2U9	OTTHUMG00000140288	ENST00000298307.5:c.529T>G	14.37:g.50244957T>G	ENSP00000298307:p.Phe177Val		49314707	B3KPF9|Q6IAF0|Q86TY9	Missense_Mutation	SNP	ENST00000298307.5	37	CCDS9693.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.276434	0.23307	.	.	ENSG00000165516	ENST00000298307;ENST00000554589;ENST00000557247	T;T;T	0.05382	3.8;3.5;3.45	5.62	5.62	0.85841	Kelch-type beta propeller (1);	0.051372	0.85682	D	0.000000	T	0.06234	0.0161	N	0.12831	0.26	0.58432	D	0.999999	B;P;P	0.46784	0.011;0.884;0.816	B;P;B	0.47864	0.018;0.559;0.357	T	0.53739	-0.8396	10	0.11182	T	0.66	-18.5346	15.8267	0.78711	0.0:0.0:0.0:1.0	.	177;177;177	G3V2H2;G3V3U8;Q9Y2U9	.;.;KLDC2_HUMAN	V	177	ENSP00000298307:F177V;ENSP00000451439:F177V;ENSP00000450658:F177V	ENSP00000298307:F177V	F	+	1	0	KLHDC2	49314707	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.525000	0.60559	2.141000	0.66446	0.528000	0.53228	TTC		0.299	KLHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276869.1			G	50244957	T	G	50244957	3	3	47	1	0	0	0	0	1	0	0	0	8377	1493	52	4	547	4	KLHDC2	14	50244957	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2920673	50244957	57104583	1513	5910										
SDCCAG1	9147	broad.mit.edu	37	chr14	50292653	50292653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaatgtttgctttgttttCttttctgctgacttgaatgc	7	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:50292653C>A	ENST00000298310.5	-	16	1958	c.1509G>T	c.(1507-1509)aaG>aaT	p.K503N	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000545773.1_Missense_Mutation_p.K461N|AL627171.2_ENST00000595378.1_3'UTR|NEMF_ENST00000546046.1_Missense_Mutation_p.K503N			O60524	NEMF_HUMAN	nuclear export mediator factor	503					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.K503N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						GCTTTGTTTTCTTTTCTGCTG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	14											119	113	115					14																	50292653		2201	4297	6498	49362403	SO:0001583	missense	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1509G>T	14.37:g.50292653C>A	ENSP00000298310:p.Lys503Asn		49362403	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.348767	0.61183	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.34	4.45	0.53987	Fibronectin-binding A, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68824	0.3043	M	0.87827	2.91	0.80722	D	1	P;P;P;P;D	0.71674	0.86;0.746;0.86;0.86;0.998	P;P;P;P;D	0.70487	0.561;0.661;0.661;0.661;0.969	T	0.71751	-0.4498	10	0.46703	T	0.11	-14.2237	10.4157	0.44320	0.0:0.8506:0.0:0.1494	.	503;274;478;461;503	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	N	503;461;503;274;461	ENSP00000298310:K503N;ENSP00000438309:K461N;ENSP00000441016:K503N;ENSP00000452540:K461N	ENSP00000298310:K503N	K	-	3	2	NEMF	49362403	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.788000	0.38714	1.407000	0.46875	0.644000	0.83932	AAG		0.279	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		A	50292653	C	A	50292653	3	1	47	1	0	0	0	0	1	0	0	0	13994	912	32	2	1793	2	SDCCAG1	14	50292653	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	47696	50292653	57056887	1514	5911										
SDCCAG1	9147	broad.mit.edu	37	chr14	50295907	50295907	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctggttagctaaagcacttCgaactacctgaatggctctg	9	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:50295907C>T	ENST00000298310.5	-	13	1546	c.1097G>A	c.(1096-1098)cGa>cAa	p.R366Q	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000545773.1_Missense_Mutation_p.R324Q|NEMF_ENST00000546046.1_Missense_Mutation_p.R366Q			O60524	NEMF_HUMAN	nuclear export mediator factor	366					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.R366Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TAAAGCACTTCGAACTACCTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	14											161	153	156					14																	50295907		2203	4300	6503	49365657	SO:0001583	missense	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1097G>A	14.37:g.50295907C>T	ENSP00000298310:p.Arg366Gln		49365657	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.639853	0.47153	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.34	5.34	0.76211	Fibronectin-binding A, N-terminal (1);	0.059837	0.64402	D	0.000002	T	0.48040	0.1478	L	0.51853	1.615	0.80722	D	1	D;P;D;P;P	0.55800	0.973;0.884;0.966;0.925;0.891	P;P;P;P;P	0.51487	0.606;0.485;0.638;0.542;0.671	T	0.30937	-0.9961	10	0.10902	T	0.67	-8.7258	19.0363	0.92980	0.0:1.0:0.0:0.0	.	366;137;341;324;366	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	Q	366;324;366;137;324	ENSP00000298310:R366Q;ENSP00000438309:R324Q;ENSP00000441016:R366Q;ENSP00000452540:R324Q	ENSP00000298310:R366Q	R	-	2	0	NEMF	49365657	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.507000	0.66999	2.496000	0.84212	0.591000	0.81541	CGA		0.388	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		T	50295907	C	T	50295907	3	4	47	1	0	0	0	0	1	0	0	0	13994	884	31	1	2217	1	SDCCAG1	14	50295907	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3254	50295907	57053633	1515	5912										
FBXO34	55030	broad.mit.edu	37	chr14	55818442	55818442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttgtgtcccttactagccGaaatcctgatcaaagaaaag	8	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:55818442G>A	ENST00000313833.4	+	2	1579	c.1334G>A	c.(1333-1335)cGa>cAa	p.R445Q	FBXO34_ENST00000440021.1_Missense_Mutation_p.R445Q	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	445								p.R445Q(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CTTACTAGCCGAAATCCTGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											132	124	127					14																	55818442		2203	4300	6503	54888195	SO:0001583	missense	55030			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1334G>A	14.37:g.55818442G>A	ENSP00000313159:p.Arg445Gln		54888195	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.780903	0.00079	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.16457	2.34;2.34	5.48	3.12	0.35913	.	0.869248	0.09825	N	0.750989	T	0.05181	0.0138	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43669	-0.9377	10	0.13470	T	0.59	-16.8777	1.8293	0.03127	0.5806:0.1391:0.1468:0.1335	.	445	Q9NWN3	FBX34_HUMAN	Q	445	ENSP00000313159:R445Q;ENSP00000394117:R445Q	ENSP00000313159:R445Q	R	+	2	0	FBXO34	54888195	0.000000	0.05858	0.013000	0.15412	0.002000	0.02628	0.404000	0.20999	0.162000	0.19483	-1.189000	0.01698	CGA		0.433	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			A	55818442	G	A	55818442	3	1	47	1	0	0	0	0	1	0	0	0	5763	1058	37	1	1336	1	FBXO34	14	55818442	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5522535	55818442	51531098	1516	5913										
C14orf101	54916	broad.mit.edu	37	chr14	57092245	57092245	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattttcttgaagtaaataAacagtaagcattctttttat	4	5	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:57092245A>C	ENST00000261556.6	+	12	1666	c.1544A>C	c.(1543-1545)aAa>aCa	p.K515T	TMEM260_ENST00000538838.1_3'UTR|TMEM260_ENST00000536419.1_Missense_Mutation_p.K49T	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	515						integral component of membrane (GO:0016021)		p.K515T(1)									GAAGTAAATAAACAGTAAGCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	14											68	70	70					14																	57092245		2203	4300	6503	56161998	SO:0001583	missense	54916			AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.1544A>C	14.37:g.57092245A>C	ENSP00000261556:p.Lys515Thr		56161998	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	37	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	A	15.11	2.734865	0.48939	.	.	ENSG00000070269	ENST00000261556;ENST00000536419	T;T	0.45276	1.49;0.9	5.94	5.94	0.96194	.	0.149996	0.64402	D	0.000012	T	0.30324	0.0761	N	0.22421	0.69	0.35802	D	0.823224	B	0.27229	0.172	B	0.16289	0.015	T	0.28808	-1.0032	10	0.28530	T	0.3	-14.0776	16.4445	0.83913	1.0:0.0:0.0:0.0	.	515	Q9NX78	CN101_HUMAN	T	515;49	ENSP00000261556:K515T;ENSP00000438742:K49T	ENSP00000261556:K515T	K	+	2	0	C14orf101	56161998	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.604000	0.61112	2.284000	0.76573	0.529000	0.55759	AAA		0.333	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		C	57092245	A	C	57092245	3	2	47	1	0	0	0	0	1	0	0	0	1738	14	1	4	1590	4	C14orf101	14	57092245	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1273803	57092245	50257295	1517	5914										
OTX2	5015	broad.mit.edu	37	chr14	57269058	57269058	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggcggcacttagctcttcGattcttaaaccataccttgg	8	11	2	0	rs104894464		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:57269058G>A	ENST00000555006.1	-	4	673	c.265C>T	c.(265-267)Cga>Tga	p.R89*	OTX2_ENST00000554788.1_3'UTR|OTX2_ENST00000408990.3_Nonsense_Mutation_p.R89*|OTX2_ENST00000554559.1_3'UTR|OTX2_ENST00000339475.5_Nonsense_Mutation_p.R97*|RP11-1085N6.6_ENST00000602485.1_lincRNA			P32243	OTX2_HUMAN	orthodenticle homeobox 2	89			R -> G (in MCOPS5). {ECO:0000269|PubMed:15846561}.		axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R97*(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					TTAGCTCTTCGATTCTTAAAC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	14	GRCh37	CM051593	OTX2	M	rs104894464						105	113	110					14																	57269058		2203	4300	6503	56338811	SO:0001587	stop_gained	5015			AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.265C>T	14.37:g.57269058G>A	ENSP00000452336:p.Arg89*		56338811	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Nonsense_Mutation	SNP	ENST00000555006.1	37	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868417	0.91587	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006;ENST00000554845;ENST00000555804	.	.	.	5.78	5.78	0.91487	.	0.000000	0.36628	N	0.002496	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.9921	0.92796	0.0:0.0:1.0:0.0	.	.	.	.	X	97;89;89;97;89	.	ENSP00000343819:R97X	R	-	1	2	OTX2	56338811	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.716000	0.61916	2.722000	0.93159	0.557000	0.71058	CGA		0.423	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		A	57269058	G	A	57269058	4	1	47	1	0	0	0	0	0	1	0	0	11352	1066	37	1	608	1	OTX2	14	57269058	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	176813	57269058	50080482	1518	5915										
SLC35F4	341880	broad.mit.edu	37	chr14	58056127	58056127	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tactgacaagatgatcaagaGtccccagatgcccttcagaa	8	11	2	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:58056127G>T	ENST00000339762.6	-	3	501	c.502C>A	c.(502-504)Ctc>Atc	p.L168I	SLC35F4_ENST00000554729.1_Missense_Mutation_p.L9I|SLC35F4_ENST00000556826.1_Missense_Mutation_p.L132I			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	168					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.L168I(2)		breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATGATCAAGAGTCCCCAGATG	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	14											77	79	79					14																	58056127		2004	4191	6195	57125880	SO:0001583	missense	341880					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"Solute carriers"	19845	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 36"	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.502C>A	14.37:g.58056127G>T	ENSP00000342518:p.Leu168Ile		57125880	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		.	.	.	.	.	.	.	.	.	.	G	14.14	2.446001	0.43429	.	.	ENSG00000151812	ENST00000556826;ENST00000339762;ENST00000554729	T;T;T	0.47869	0.88;0.83;0.95	6.06	5.07	0.68467	.	0.108953	0.64402	D	0.000003	T	0.30386	0.0763	L	0.39898	1.24	0.45541	D	0.998498	B	0.27117	0.168	B	0.17722	0.019	T	0.18053	-1.0349	10	0.18276	T	0.48	-19.0956	4.0572	0.09823	0.3058:0.0:0.6942:0.0	.	168	A4IF30	S35F4_HUMAN	I	132;168;9	ENSP00000452086:L132I;ENSP00000342518:L168I;ENSP00000451990:L9I	ENSP00000342518:L168I	L	-	1	0	SLC35F4	57125880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.473000	0.53122	2.882000	0.98803	0.655000	0.94253	CTC		0.438	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260		T	58056127	G	T	58056127	3	4	47	1	0	0	0	0	1	0	0	0	14628	1029	36	2	1087	2	SLC35F4	14	58056127	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	787069	58056127	49293413	1519	5916										
C14orf37	145407	broad.mit.edu	37	chr14	58598392	58598392	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtgtcactggagatcccaGaactggtgtgaactcctcat	11	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:58598392G>T	ENST00000267485.7	-	4	1863	c.1669C>A	c.(1669-1671)Ctg>Atg	p.L557M	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	557						integral component of membrane (GO:0016021)		p.L557M(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GGAGATCCCAGAACTGGTGTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14											120	121	120					14																	58598392		2203	4300	6503	57668145	SO:0001583	missense	145407				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1669C>A	14.37:g.58598392G>T	ENSP00000267485:p.Leu557Met		57668145	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.138004	0.56936	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.27402	1.67	5.78	-4.23	0.03789	.	1.558920	0.03496	N	0.217296	T	0.21631	0.0521	L	0.56769	1.78	0.09310	N	1	B;P;B;B	0.39022	0.4;0.655;0.4;0.4	B;B;B;B	0.31191	0.075;0.125;0.075;0.075	T	0.15321	-1.0441	10	0.36615	T	0.2	3.301	1.6506	0.02771	0.3086:0.3262:0.2448:0.1204	.	595;557;557;557	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	M	557;595	ENSP00000267485:L557M	ENSP00000267485:L557M	L	-	1	2	C14orf37	57668145	0.000000	0.05858	0.000000	0.03702	0.923000	0.55619	-0.494000	0.06451	-1.090000	0.03069	0.650000	0.86243	CTG		0.488	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		T	58598392	G	T	58598392	3	4	47	1	0	0	0	0	1	0	0	0	1775	933	33	2	675	2	C14orf37	14	58598392	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	542265	58598392	48751148	1520	5917										
ARID4A	5926	broad.mit.edu	37	chr14	58838613	58838613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgattccacagtgtctcatgCgggagcctccatgtcatctg	10	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:58838613C>T	ENST00000355431.3	+	24	4053	c.3680C>T	c.(3679-3681)gCg>gTg	p.A1227V	RP11-517O13.3_ENST00000556390.1_RNA|ARID4A_ENST00000431317.2_Missense_Mutation_p.A1158V|ARID4A_ENST00000348476.3_Missense_Mutation_p.A1158V|ARID4A_ENST00000395168.3_Missense_Mutation_p.A1173V	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1227					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1227V(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GTGTCTCATGCGGGAGCCTCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											108	87	94					14																	58838613		2203	4300	6503	57908366	SO:0001583	missense	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.3680C>T	14.37:g.58838613C>T	ENSP00000347602:p.Ala1227Val		57908366	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.941429	0.34283	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317	T;T;T;T	0.15834	2.39;2.47;2.47;2.47	5.18	4.29	0.51040	.	0.554031	0.18275	N	0.146194	T	0.16128	0.0388	L	0.36672	1.1	0.20307	N	0.999914	B;B;B	0.15719	0.014;0.004;0.014	B;B;B	0.11329	0.006;0.002;0.006	T	0.17440	-1.0369	10	0.87932	D	0	-11.7968	13.6291	0.62186	0.0:0.9257:0.0:0.0743	.	1158;1227;1173	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	V	1227;1158;1173;1158	ENSP00000347602:A1227V;ENSP00000344556:A1158V;ENSP00000378597:A1173V;ENSP00000397368:A1158V	ENSP00000344556:A1158V	A	+	2	0	ARID4A	57908366	1.000000	0.71417	0.921000	0.36526	0.975000	0.68041	5.125000	0.64715	1.414000	0.47017	0.563000	0.77884	GCG		0.393	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		T	58838613	C	T	58838613	3	4	47	1	0	0	0	0	1	0	0	0	919	768	27	1	3770	1	ARID4A	14	58838613	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	240221	58838613	48510927	1521	5918										
DAAM1	23002	broad.mit.edu	37	chr14	59826117	59826117	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcccttcttcaattgtagaaAcattacccttttgcactatc	3	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:59826117A>G	ENST00000395125.1	+	21	2581	c.2558A>G	c.(2557-2559)aAc>aGc	p.N853S	DAAM1_ENST00000553966.1_3'UTR|DAAM1_ENST00000351081.1_Missense_Mutation_p.N853S|DAAM1_ENST00000360909.3_Missense_Mutation_p.N843S	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	853	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)	p.N853S(1)		breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AATTGTAGAAACATTACCCTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	14											82	77	79					14																	59826117		2202	4300	6502	58895870	SO:0001583	missense	23002			AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2558A>G	14.37:g.59826117A>G	ENSP00000378557:p.Asn853Ser		58895870	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	37	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.690872	0.68271	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	T;T;T	0.16324	2.35;2.35;2.35	5.69	5.69	0.88448	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.26593	0.0650	L	0.41906	1.305	0.80722	D	1	B;P	0.42123	0.142;0.771	B;P	0.51355	0.098;0.667	T	0.00681	-1.1612	10	0.34782	T	0.22	.	16.2484	0.82467	1.0:0.0:0.0:0.0	.	843;853	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	S	843;853;822;853	ENSP00000354162:N843S;ENSP00000247170:N853S;ENSP00000378557:N853S	ENSP00000247170:N853S	N	+	2	0	DAAM1	58895870	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.245000	0.95431	2.291000	0.77112	0.533000	0.62120	AAC		0.299	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		G	59826117	A	G	59826117	3	3	47	1	0	0	0	0	1	0	0	0	4221	43	2	4	2640	4	DAAM1	14	59826117	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	987504	59826117	47523423	1522	5919										
JKAMP	51528	broad.mit.edu	37	chr14	59954530	59954530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attggttcttcattgaatggTactcggggaaaaagaggtta	12	4	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:59954530T>C	ENST00000261247.9	+	3	382	c.235T>C	c.(235-237)Tac>Cac	p.Y79H	JKAMP_ENST00000556985.1_Missense_Mutation_p.Y79H|JKAMP_ENST00000554271.1_Missense_Mutation_p.Y93H|JKAMP_ENST00000557560.1_3'UTR|JKAMP_ENST00000356057.5_Missense_Mutation_p.Y87H|JKAMP_ENST00000425728.2_Missense_Mutation_p.Y73H|RP11-701B16.2_ENST00000554253.1_RNA	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	94					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)	p.Y87H(1)		breast(1)|endometrium(1)|kidney(1)|lung(3)	6						CATTGAATGGTACTCGGGGAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	14											288	263	271					14																	59954530		1853	4104	5957	59024283	SO:0001583	missense	51528			AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.235T>C	14.37:g.59954530T>C	ENSP00000261247:p.Tyr79His		59024283	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Missense_Mutation	SNP	ENST00000261247.9	37	CCDS45116.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.347138	0.61183	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000556985;ENST00000554271;ENST00000554795;ENST00000356057	.	.	.	5.6	4.46	0.54185	.	0.053226	0.85682	N	0.000000	T	0.54663	0.1872	L	0.54323	1.7	0.80722	D	1	P;P;P;P;P	0.44309	0.832;0.799;0.799;0.799;0.799	P;B;B;B;B	0.45998	0.5;0.366;0.295;0.366;0.366	T	0.48433	-0.9036	9	0.15952	T	0.53	-46.2585	11.2195	0.48846	0.0:0.0713:0.0:0.9286	.	94;93;73;87;79	Q9P055;G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	JKAMP_HUMAN;.;.;.;.	H	79;73;79;93;87;87	.	ENSP00000261247:Y79H	Y	+	1	0	JKAMP	59024283	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.126000	0.71635	0.966000	0.38159	0.533000	0.62120	TAC		0.373	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		C	59954530	T	C	59954530	3	2	47	1	0	0	0	0	1	0	0	0	7970	1638	57	4	245	4	JKAMP	14	59954530	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	128413	59954530	47395010	1523	5920										
JKAMP	729665	broad.mit.edu	37	chr14	59970584	59970584	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatatagaactgctatgatCttctggtcagaaagaaaaga	8	5	3	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:59970584C>A	ENST00000537690.2	-	0	2616				JKAMP_ENST00000261247.9_Missense_Mutation_p.L244I|JKAMP_ENST00000554271.1_Missense_Mutation_p.L258I|JKAMP_ENST00000356057.5_Missense_Mutation_p.L252I|JKAMP_ENST00000425728.2_Missense_Mutation_p.L238I|RP11-701B16.2_ENST00000554253.1_RNA	NM_001164399.1	NP_001157871.1	P0C221	CC175_HUMAN	coiled-coil domain containing 175									p.L252I(1)									CTGCTATGATCTTCTGGTCAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											96	91	92					14																	59970584		1806	4076	5882	59040337	SO:0001628	intergenic_variant	51528				CCDS53898.1	14q23.1	2012-09-24	2012-09-24	2012-09-24	ENSG00000151838	ENSG00000151838			19847	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 38"	C14orf38			Standard	NM_001164399		Approved		uc021rtw.1	P0C221			14.37:g.59970584C>A			59040337	G3V5J7	Missense_Mutation	SNP	ENST00000537690.2	37	CCDS53898.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403907	0.62288	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000554271;ENST00000356057	.	.	.	5.62	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	M	0.64404	1.975	0.54753	D	0.999982	P;P;P;P;P	0.47484	0.896;0.873;0.703;0.873;0.873	P;B;B;B;B	0.44394	0.448;0.319;0.319;0.319;0.319	T	0.64626	-0.6363	9	0.59425	D	0.04	-7.2	14.5802	0.68282	0.0:0.93:0.0:0.07	.	259;258;238;252;244	Q9P055;G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	JKAMP_HUMAN;.;.;.;.	I	244;238;258;252	.	ENSP00000261247:L244I	L	+	1	0	JKAMP	59040337	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.373000	0.59537	1.384000	0.46424	0.655000	0.94253	CTT		0.323	CCDC175-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471273.1	NM_001164399		A	59970584	C	A	59970584	1	1	47	0	1	0	0	0	0	0	0	0	7970	913	32	2		2	JKAMP	14	59970584	IGR	SNP	C	TCGA-AG-3892-01A-01W-1073-09	16054	59970584	47378956	1524	5921										
SYT16	83851	broad.mit.edu	37	chr14	62463169	62463169	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttctattgcggaggaagaGcatcaccttgaaaagcaaag	10	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:62463169G>T	ENST00000430451.2	+	1	629	c.432G>T	c.(430-432)gaG>gaT	p.E144D	SYT16_ENST00000446982.2_Missense_Mutation_p.E144D	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	144					exocytosis (GO:0006887)			p.E144D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CGGAGGAAGAGCATCACCTTG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	118	120					14																	62463169		1896	4131	6027	61532922	SO:0001583	missense	83851			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.432G>T	14.37:g.62463169G>T	ENSP00000394700:p.Glu144Asp		61532922	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350858	0.24512	.	.	ENSG00000139973	ENST00000446982;ENST00000430451	T;T	0.33216	1.42;3.75	5.55	-11.1	0.00147	.	0.268594	0.26560	N	0.023684	T	0.13157	0.0319	L	0.41236	1.265	0.09310	N	0.999999	B;B	0.21309	0.054;0.003	B;B	0.19666	0.026;0.004	T	0.03784	-1.1004	10	0.39692	T	0.17	-12.6637	1.8919	0.03249	0.4644:0.1399:0.1731:0.2226	.	144;144	B4DZH2;Q17RD7	.;SYT16_HUMAN	D	144	ENSP00000388023:E144D;ENSP00000394700:E144D	ENSP00000394700:E144D	E	+	3	2	SYT16	61532922	0.000000	0.05858	0.020000	0.16555	0.992000	0.81027	-1.730000	0.01855	-2.099000	0.00849	0.655000	0.94253	GAG		0.463	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62463169	G	T	62463169	3	4	47	1	0	0	0	0	1	0	0	0	15511	962	34	2	434	2	SYT16	14	62463169	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2492585	62463169	44886371	1525	5922										
KCNH5	27133	broad.mit.edu	37	chr14	63175164	63175164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcacatcactgatcttacGaaagatgatctgtggaacgg	9	9	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:63175164G>A	ENST00000322893.7	-	11	2297	c.2029C>T	c.(2029-2031)Cgt>Tgt	p.R677C	KCNH5_ENST00000420622.2_Missense_Mutation_p.S611L	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	677					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.R677C(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CTGATCTTACGAAAGATGATC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	14											50	54	53					14																	63175164		2202	4300	6502	62244917	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2029C>T	14.37:g.63175164G>A	ENSP00000321427:p.Arg677Cys		62244917	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.62|13.62	2.291028|2.291028	0.40494|0.40494	.|.	.|.	ENSG00000140015|ENSG00000140015	ENST00000322893|ENST00000420622	T|D	0.18502|0.98531	2.21|-4.98	5.72|5.72	3.85|3.85	0.44370|0.44370	.|.	0.123346|.	0.51477|.	D|.	0.000082|.	D|D	0.96191|0.96191	0.8758|0.8758	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|B	0.89917|0.20052	1.0|0.041	D|B	0.81914|0.12156	0.995|0.007	D|D	0.93426|0.93426	0.6781|0.6781	9|8	0.87932|0.87932	D|D	0|0	.|.	11.31|11.31	0.49358|0.49358	0.0:0.1165:0.6166:0.267|0.0:0.1165:0.6166:0.267	.|.	677|611	Q8NCM2|Q8NCM2-2	KCNH5_HUMAN|.	C|L	677|611	ENSP00000321427:R677C|ENSP00000395439:S611L	ENSP00000321427:R677C|ENSP00000395439:S611L	R|S	-|-	1|2	0|0	KCNH5|KCNH5	62244917|62244917	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.608000|0.608000	0.37181|0.37181	2.738000|2.738000	0.47401|0.47401	0.741000|0.741000	0.32674|0.32674	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.458	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63175164	G	A	63175164	3	1	47	1	0	0	0	0	1	0	0	0	8056	1059	37	1	941	1	KCNH5	14	63175164	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	711995	63175164	44174376	1526	5923										
KCNH5	27133	broad.mit.edu	37	chr14	63468133	63468133	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagaccaccttttcatgttCatttcttattggtgcaattt	5	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:63468133C>A	ENST00000322893.7	-	4	617	c.349G>T	c.(349-351)Gaa>Taa	p.E117*	KCNH5_ENST00000394968.1_Nonsense_Mutation_p.E59*|KCNH5_ENST00000394964.2_Nonsense_Mutation_p.E59*|KCNH5_ENST00000420622.2_Nonsense_Mutation_p.E117*	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	117	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.E117*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TTTTCATGTTCATTTCTTATT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											107	95	99					14																	63468133		2203	4300	6503	62537886	SO:0001587	stop_gained	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.349G>T	14.37:g.63468133C>A	ENSP00000321427:p.Glu117*		62537886	C9JP98	Nonsense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	38	7.180420	0.98118	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.706	0.96072	0.0:1.0:0.0:0.0	.	.	.	.	X	117;117;59;59	.	ENSP00000321427:E117X	E	-	1	0	KCNH5	62537886	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.673000	0.90976	0.591000	0.81541	GAA		0.388	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63468133	C	A	63468133	4	1	47	1	0	0	0	0	0	1	0	0	8056	835	29	2	2683	2	KCNH5	14	63468133	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	292969	63468133	43881407	1527	5924										
SYNE2	23224	broad.mit.edu	37	chr14	64447390	64447390	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaatttattgaagaaaaaGaattcctagctcgacttgat	7	5	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:64447390G>T	ENST00000344113.4	+	15	1800	c.1588G>T	c.(1588-1590)Gaa>Taa	p.E530*	SYNE2_ENST00000554584.1_Nonsense_Mutation_p.E530*|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.E530*	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	530					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.E530*(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGAAGAAAAAGAATTCCTAGC	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											35	33	34					14																	64447390		1786	4051	5837	63517143	SO:0001587	stop_gained	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.1588G>T	14.37:g.64447390G>T	ENSP00000341781:p.Glu530*		63517143	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178096	0.78564	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.93	3.11	0.35812	.	0.862899	0.10116	N	0.714099	.	.	.	.	.	.	0.29596	N	0.848083	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	6.1883	0.20510	0.2216:0.1363:0.6421:0.0	.	.	.	.	X	530	.	ENSP00000261678:E530X	E	+	1	0	SYNE2	63517143	0.870000	0.30015	0.691000	0.30163	0.009000	0.06853	0.795000	0.26972	0.402000	0.25451	0.591000	0.81541	GAA		0.313	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64447390	G	T	64447390	4	4	47	1	0	0	0	0	0	1	0	0	15485	943	33	2	1642	2	SYNE2	14	64447390	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	979257	64447390	42902150	1528	5925										
SYNE2	23224	broad.mit.edu	37	chr14	64519713	64519713	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacccaagtatttgaaaaaGaaaaggaacttgaagaaaaa	7	4	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:64519713G>T	ENST00000344113.4	+	48	9294	c.9082G>T	c.(9082-9084)Gaa>Taa	p.E3028*	SYNE2_ENST00000554584.1_Nonsense_Mutation_p.E3061*|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.E3028*	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3028					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.E3028*(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATTTGAAAAAGAAAAGGAACT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											50	50	50					14																	64519713		1793	4062	5855	63589466	SO:0001587	stop_gained	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9082G>T	14.37:g.64519713G>T	ENSP00000341781:p.Glu3028*		63589466	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	49	15.466095	0.99834	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.69	2.35	0.29111	.	0.350626	0.24012	N	0.042375	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	5.0173	0.14343	0.2608:0.1944:0.5448:0.0	.	.	.	.	X	3028;3028;3061;3061	.	ENSP00000261678:E3061X	E	+	1	0	SYNE2	63589466	1.000000	0.71417	0.613000	0.29037	0.461000	0.32589	1.228000	0.32588	0.721000	0.32231	0.462000	0.41574	GAA		0.313	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64519713	G	T	64519713	4	4	47	1	0	0	0	0	0	1	0	0	15485	943	33	2	9268	2	SYNE2	14	64519713	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	72323	64519713	42829827	1529	5926										
SYNE2	23224	broad.mit.edu	37	chr14	64519940	64519940	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatgtgatgagataataaaGaaattaaatgaaaataagac	7	1	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:64519940G>T	ENST00000344113.4	+	48	9521	c.9309G>T	c.(9307-9309)aaG>aaT	p.K3103N	SYNE2_ENST00000554584.1_Missense_Mutation_p.K3136N|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Missense_Mutation_p.K3103N	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3103					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.K3103N(2)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGATAATAAAGAAATTAAATG	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	14											31	31	31					14																	64519940		1807	4064	5871	63589693	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9309G>T	14.37:g.64519940G>T	ENSP00000341781:p.Lys3103Asn		63589693	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	6.485	0.457708	0.12342	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57107	0.78;0.78;0.42	5.33	2.21	0.28008	.	0.734274	0.12466	N	0.466428	T	0.31918	0.0812	N	0.17082	0.46	0.09310	N	0.999997	B;B	0.16396	0.01;0.017	B;B	0.12156	0.003;0.007	T	0.20974	-1.0259	10	0.56958	D	0.05	.	3.687	0.08332	0.2942:0.0:0.4478:0.2579	.	3103;3103	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	N	3103;3103;3136;3136	ENSP00000350719:K3103N;ENSP00000341781:K3103N;ENSP00000452570:K3136N	ENSP00000261678:K3136N	K	+	3	2	SYNE2	63589693	0.997000	0.39634	0.378000	0.26068	0.293000	0.27360	1.303000	0.33470	0.636000	0.30508	0.462000	0.41574	AAG		0.333	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64519940	G	T	64519940	3	4	47	1	0	0	0	0	1	0	0	0	15485	933	33	2	9495	2	SYNE2	14	64519940	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	227	64519940	42829600	1530	5927										
FUT8	2530	broad.mit.edu	37	chr14	66188690	66188690	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacagccttggctagaaaaaGaaatagaagaagccaccaag	9	9	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:66188690G>T	ENST00000360689.5	+	8	2760	c.1033G>T	c.(1033-1035)Gaa>Taa	p.E345*	FUT8_ENST00000358307.2_Nonsense_Mutation_p.E216*|FUT8_ENST00000417683.1_Intron|FUT8_ENST00000557164.1_Nonsense_Mutation_p.E182*|FUT8_ENST00000394586.2_Nonsense_Mutation_p.E345*|FUT8_ENST00000394585.1_Nonsense_Mutation_p.E345*	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	345	GT23. {ECO:0000255|PROSITE- ProRule:PRU00992}.				cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)	p.E345*(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GCTAGAAAAAGAAATAGAAGA	0.448																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											84	83	83					14																	66188690		2203	4300	6503	65258443	SO:0001587	stop_gained	2530			AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"Fucosyltransferases"	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.1033G>T	14.37:g.66188690G>T	ENSP00000353910:p.Glu345*		65258443	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Nonsense_Mutation	SNP	ENST00000360689.5	37	CCDS9775.1	.	.	.	.	.	.	.	.	.	.	G	43	10.069586	0.99330	.	.	ENSG00000033170	ENST00000360689;ENST00000394586;ENST00000557164;ENST00000394585;ENST00000358307	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-19.5966	17.2877	0.87146	0.0:0.0:1.0:0.0	.	.	.	.	X	345;345;182;345;216	.	ENSP00000351057:E216X	E	+	1	0	FUT8	65258443	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.869000	0.99810	2.668000	0.90789	0.563000	0.77884	GAA		0.448	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480		T	66188690	G	T	66188690	4	4	47	1	0	0	0	0	0	1	0	0	6129	943	33	2	1154	2	FUT8	14	66188690	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1668750	66188690	41160850	1531	5928										
SMOC1	64093	broad.mit.edu	37	chr14	70490005	70490005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggacagcaatagcagcaacGacattaacaagcgggagatg	12	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:70490005G>A	ENST00000381280.4	+	11	1385	c.1132G>A	c.(1132-1134)Gac>Aac	p.D378N	SMOC1_ENST00000361956.3_Missense_Mutation_p.D378N	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	378	EF-hand 1.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)	p.D378N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		TAGCAGCAACGACATTAACAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	14											117	106	110					14																	70490005		2203	4300	6503	69559758	SO:0001583	missense	64093			AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.1132G>A	14.37:g.70490005G>A	ENSP00000370680:p.Asp378Asn		69559758	A8K1S3|B2R7P5|Q96F78	Missense_Mutation	SNP	ENST00000381280.4	37	CCDS9798.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350351	0.82132	.	.	ENSG00000198732	ENST00000361956;ENST00000381280	T;T	0.56941	0.43;0.43	5.34	5.34	0.76211	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.67040	0.2851	L	0.44542	1.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.968	T	0.64024	-0.6504	10	0.39692	T	0.17	-24.6884	19.3898	0.94576	0.0:0.0:1.0:0.0	.	378;378	Q9H4F8-2;Q9H4F8	.;SMOC1_HUMAN	N	378	ENSP00000355110:D378N;ENSP00000370680:D378N	ENSP00000355110:D378N	D	+	1	0	SMOC1	69559758	1.000000	0.71417	0.957000	0.39632	0.360000	0.29518	7.743000	0.85020	2.640000	0.89533	0.655000	0.94253	GAC		0.552	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1			A	70490005	G	A	70490005	3	1	47	1	0	0	0	0	1	0	0	0	14838	1058	37	1	1174	1	SMOC1	14	70490005	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4301315	70490005	36859535	1532	5929										
ADAM21	8747	broad.mit.edu	37	chr14	70924700	70924700	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacacctggtttataagataAacagtaatgagacacaattc	6	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:70924700A>C	ENST00000603540.1	+	2	742	c.484A>C	c.(484-486)Aac>Cac	p.N162H	ADAM21_ENST00000267499.3_Missense_Mutation_p.N162H|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	162					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N162H(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TTATAAGATAAACAGTAATGA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	14											39	49	45					14																	70924700		2183	4298	6481	69994453	SO:0001583	missense	8747			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"ADAM metallopeptidase domain containing"	200	protein-coding gene	gene with protein product		603713	"a disintegrin and metalloproteinase domain 21"			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.484A>C	14.37:g.70924700A>C	ENSP00000474385:p.Asn162His		69994453	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	A	9.086	1.000507	0.19121	.	.	ENSG00000139985	ENST00000267499	T	0.01139	5.28	3.76	-1.69	0.08186	.	0.197979	0.24803	U	0.035465	T	0.01156	0.0038	L	0.51422	1.61	0.09310	N	1	B	0.17852	0.024	B	0.13407	0.009	T	0.43845	-0.9366	10	0.49607	T	0.09	.	4.5533	0.12124	0.2799:0.0:0.5246:0.1955	.	162	Q9UKJ8	ADA21_HUMAN	H	162	ENSP00000267499:N162H	ENSP00000267499:N162H	N	+	1	0	ADAM21	69994453	0.003000	0.15002	0.054000	0.19295	0.421000	0.31385	-0.032000	0.12266	-0.160000	0.11002	-0.379000	0.06801	AAC		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			C	70924700	A	C	70924700	3	2	47	1	0	0	0	0	1	0	0	0	243	14	1	4	486	4	ADAM21	14	70924700	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	434695	70924700	36424840	1533	5930										
HEATR4	399671	broad.mit.edu	37	chr14	73965778	73965778	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactacttctataatacctcGaatggcaaaggccttgattt	6	10	1	1	rs114232158	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:73965778G>A	ENST00000553558.1	-	13	2674	c.2353C>T	c.(2353-2355)Cga>Tga	p.R785*	HEATR4_ENST00000334988.2_Nonsense_Mutation_p.R785*|HEATR4_ENST00000560393.1_Nonsense_Mutation_p.R738*	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	785								p.R738*(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		ATAATACCTCGAATGGCAAAG	0.463													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		20745	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	14						G	stop/ARG,stop/ARG	140,4266	98.9+/-137.6	2,136,2065	227	222	223		2353,2353	4.1	1	14	dbSNP_132	223	0,8600		0,0,4300	yes	stop-gained,stop-gained	HEATR4	NM_001220484.1,NM_203309.2	,	2,136,6365	AA,AG,GG		0.0,3.1775,1.0764	,	785/1027,785/1027	73965778	140,12866	2203	4300	6503	73035531	SO:0001587	stop_gained	399671			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2353C>T	14.37:g.73965778G>A	ENSP00000450444:p.Arg785*		73035531	B7Z7V9|E9KL41	Nonsense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	42	9.368849	0.99150	0.031775	0.0	ENSG00000187105	ENST00000553558;ENST00000334988	.	.	.	5.02	4.06	0.47325	.	0.492618	0.15429	N	0.262809	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	10.3605	0.43991	0.0:0.0:0.6653:0.3347	.	.	.	.	X	785;738	.	ENSP00000335447:R738X	R	-	1	2	HEATR4	73035531	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.720000	0.54933	2.618000	0.88619	0.655000	0.94253	CGA		0.463	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		A	73965778	G	A	73965778	4	1	47	1	0	0	0	0	0	1	0	0	7051	1066	37	1	751	1	HEATR4	14	73965778	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3041078	73965778	33383762	1534	5931										
YLPM1	56252	broad.mit.edu	37	chr14	75282966	75282966	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacatgttgcaaaacttattCgagtgagtatggggaagctg	12	6	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:75282966C>T	ENST00000552421.1	+	11	3569	c.3445C>T	c.(3445-3447)Cga>Tga	p.R1149*	YLPM1_ENST00000325680.7_Nonsense_Mutation_p.R1855*|YLPM1_ENST00000238571.3_Nonsense_Mutation_p.R1660*			P49750	YLPM1_HUMAN	YLP motif containing 1	1660	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R1855*(1)|p.R1660*(1)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		AAAACTTATTCGAGTGAGTAT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											110	105	106					14																	75282966		1885	4118	6003	74352719	SO:0001587	stop_gained	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.3445C>T	14.37:g.75282966C>T	ENSP00000447921:p.Arg1149*		74352719	P49752|Q96I64|Q9P1V7	Nonsense_Mutation	SNP	ENST00000552421.1	37		.	.	.	.	.	.	.	.	.	.	C	43	10.146070	0.99346	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680;ENST00000547879	.	.	.	5.61	5.61	0.85477	.	0.000000	0.51477	D	0.000082	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.1213	12.6949	0.56997	0.2753:0.7247:0.0:0.0	.	.	.	.	X	1149;1855;1660;1568;264	.	ENSP00000238571:R1660X	R	+	1	2	YLPM1	74352719	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.961000	0.49168	2.634000	0.89283	0.563000	0.77884	CGA		0.363	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		T	75282966	C	T	75282966	4	4	47	1	0	0	0	0	0	1	0	0	17526	876	31	1	5609	1	YLPM1	14	75282966	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1317188	75282966	32066574	1535	5932										
MLH3	27030	broad.mit.edu	37	chr14	75514603	75514603	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttccacaattgctagattCtttttttttctctttctctg	3	10	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:75514603C>A	ENST00000556740.1	-	1	1791	c.1756G>T	c.(1756-1758)Gaa>Taa	p.E586*	MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Nonsense_Mutation_p.E586*|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000238662.7_Nonsense_Mutation_p.E586*|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Nonsense_Mutation_p.E586*			Q9UHC1	MLH3_HUMAN	mutL homolog 3	586					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.A577_S588delAQTEKEKKKESS(2)|p.E586*(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TTGCTAGATTCTTTTTTTTTC	0.358								Mismatch excision repair (MMR)																																								3	Deletion - In frame(2)|Substitution - Nonsense(1)	breast(2)|large_intestine(1)	14											116	117	117					14																	75514603		2203	4300	6503	74584356	SO:0001587	stop_gained	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1756G>T	14.37:g.75514603C>A	ENSP00000452316:p.Glu586*		74584356	P49751|Q56DK9|Q9P292|Q9UHC0	Nonsense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454529	0.84209	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	.	.	.	5.81	4.0	0.46444	.	0.607834	0.17195	N	0.183351	.	.	.	.	.	.	0.26897	N	0.967209	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-9.0144	10.117	0.42596	0.0:0.7832:0.1445:0.0724	.	.	.	.	X	586	.	ENSP00000238662:E586X	E	-	1	0	MLH3	74584356	0.006000	0.16342	0.087000	0.20705	0.197000	0.23852	0.915000	0.28638	0.805000	0.34159	0.591000	0.81541	GAA		0.358	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75514603	C	A	75514603	4	1	47	1	0	0	0	0	0	1	0	0	9648	922	32	2	2653	2	MLH3	14	75514603	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	231637	75514603	31834937	1536	5933										
ACYP1	97	broad.mit.edu	37	chr14	75530218	75530218	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgcaccttcccaaaaatTtcataatccactgatatcag	3	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:75530218T>G	ENST00000238618.3	-	2	142	c.39A>C	c.(37-39)gaA>gaC	p.E13D	ACYP1_ENST00000555694.1_Missense_Mutation_p.E13D|ACYP1_ENST00000553302.1_Missense_Mutation_p.E13D|ACYP1_ENST00000555135.1_Missense_Mutation_p.E13D|ACYP1_ENST00000555463.1_Missense_Mutation_p.E43D|ACYP1_ENST00000357971.3_Missense_Mutation_p.E13D	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type	13	Acylphosphatase-like. {ECO:0000255|PROSITE-ProRule:PRU00520}.				phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)	p.E13D(1)		large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		TCCCAAAAATTTCATAATCCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	14											146	130	135					14																	75530218		2203	4300	6503	74599971	SO:0001583	missense	97			X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.39A>C	14.37:g.75530218T>G	ENSP00000238618:p.Glu13Asp		74599971	A6NDV8|B2R590	Missense_Mutation	SNP	ENST00000238618.3	37	CCDS9838.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999716	0.74818	.	.	ENSG00000119640	ENST00000238618;ENST00000555463;ENST00000357971;ENST00000555694;ENST00000555135;ENST00000553302	.	.	.	5.64	-0.765	0.11023	Acylphosphatase-like (3);	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	.	.	.	0.42825	D	0.994004	D;P	0.89917	1.0;0.543	D;B	0.79108	0.992;0.287	T	0.67035	-0.5772	8	0.72032	D	0.01	-21.3872	7.0376	0.25002	0.0:0.3414:0.1179:0.5407	.	13;13	P07311;A6NDV8	ACYP1_HUMAN;.	D	13;43;13;13;13;13	.	ENSP00000238618:E13D	E	-	3	2	ACYP1	74599971	0.951000	0.32395	0.275000	0.24674	0.874000	0.50279	0.825000	0.27393	-0.255000	0.09486	-0.256000	0.11100	GAA		0.483	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1			G	75530218	T	G	75530218	3	3	47	1	0	0	0	0	1	0	0	0	228	1838	64	4	351	4	ACYP1	14	75530218	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	15615	75530218	31819322	1537	5934										
FLVCR2	55640	broad.mit.edu	37	chr14	76101259	76101259	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatggtttccccagggggaaGaagtgaatgctggaagaatt	14	5	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:76101259G>T	ENST00000238667.4	+	5	1383	c.1027G>T	c.(1027-1029)Gaa>Taa	p.E343*	FLVCR2_ENST00000556241.1_3'UTR|FLVCR2_ENST00000556856.1_Intron|FLVCR2_ENST00000553587.1_Nonsense_Mutation_p.E91*|FLVCR2_ENST00000555027.1_Nonsense_Mutation_p.E58*|FLVCR2_ENST00000539311.1_Nonsense_Mutation_p.E138*	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	343					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)	p.E343*(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CCAGGGGGAAGAAGTGAATGC	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											110	92	98					14																	76101259		2203	4300	6503	75171012	SO:0001587	stop_gained	55640			AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"Solute carriers"	20105	protein-coding gene	gene with protein product		610865	"chromosome 14 open reading frame 58", "feline leukemia virus subgroup C cellular receptor 2"	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.1027G>T	14.37:g.76101259G>T	ENSP00000238667:p.Glu343*		75171012	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Nonsense_Mutation	SNP	ENST00000238667.4	37	CCDS9844.1	.	.	.	.	.	.	.	.	.	.	G	38	6.689813	0.97764	.	.	ENSG00000119686	ENST00000238667;ENST00000539311;ENST00000553341;ENST00000553587;ENST00000554580;ENST00000555027	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-12.664	18.3372	0.90293	0.0:0.0:1.0:0.0	.	.	.	.	X	343;138;44;91;43;58	.	ENSP00000238667:E343X	E	+	1	0	AC007182.1	75171012	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.153000	0.94687	2.630000	0.89119	0.591000	0.81541	GAA		0.522	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791		T	76101259	G	T	76101259	4	4	47	1	0	0	0	0	0	1	0	0	5965	943	33	2	1045	2	FLVCR2	14	76101259	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	571041	76101259	31248281	1538	5935										
ADCK1	57143	broad.mit.edu	37	chr14	78392125	78392125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agatgctcacggaagaattcCgcctgaattactgccacctc	8	13	1	3	rs372281167		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:78392125C>T	ENST00000238561.5	+	9	1126	c.1027C>T	c.(1027-1029)Cgc>Tgc	p.R343C	ADCK1_ENST00000341211.5_Missense_Mutation_p.R275C|ADCK1_ENST00000556560.1_3'UTR	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	350	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R343C(1)|p.R275C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		GGAAGAATTCCGCCTGAATTA	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	14											66	69	68					14																	78392125		2203	4300	6503	77461878	SO:0001583	missense	57143			AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.1027C>T	14.37:g.78392125C>T	ENSP00000238561:p.Arg343Cys		77461878	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	37	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.438637	0.62955	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	T;T	0.32753	1.44;1.44	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	H	0.96080	3.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.995;0.995	T	0.81120	-0.1077	10	0.87932	D	0	-33.0312	18.8748	0.92331	0.0:1.0:0.0:0.0	.	350;275;343	Q86TW2;Q9UIE6;Q86TW2-2	ADCK1_HUMAN;.;.	C	343;275	ENSP00000238561:R343C;ENSP00000339663:R275C	ENSP00000238561:R343C	R	+	1	0	ADCK1	77461878	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	3.020000	0.49643	2.461000	0.83175	0.643000	0.83706	CGC		0.587	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		T	78392125	C	T	78392125	3	4	47	1	0	0	0	0	1	0	0	0	288	652	23	1	1057	1	ADCK1	14	78392125	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2290866	78392125	28957415	1539	5936										
DIO2	1734	broad.mit.edu	37	chr14	80669239	80669239	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccacaactcggcactggggCggcaaggagaaacgctccag	14	13	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:80669239C>T	ENST00000557010.1	-	4	1000	c.615G>A	c.(613-615)ccG>ccA	p.P205P	DIO2_ENST00000438257.4_Silent_p.P205P|DIO2_ENST00000422005.3_3'UTR|DIO2_ENST00000557125.1_3'UTR|DIO2_ENST00000555750.1_Silent_p.P241P	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	205					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)	p.P205P(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		GGCACTGGGGCGGCAAGGAGA	0.537											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	14											73	76	75					14																	80669239		2048	4194	6242	79738992	SO:0001819	synonymous_variant	1734			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"thyroxine deiodinase, type II", "deiodonase-2", "deiodinase-2"	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.615G>A	14.37:g.80669239C>T		1200	79738992	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Silent	SNP	ENST00000557010.1	37	CCDS45146.1																																																																																				0.537	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			T	80669239	C	T	80669239	2	4	47	1	0	0	0	0	0	0	0	1	4536	755	27	1		1	DIO2	14	80669239	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2277114	80669239	26680301	1540	5937										
FLRT2	23768	broad.mit.edu	37	chr14	86088030	86088030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcgaagcttgacctcagtgCctcttgggatcccggagggc	14	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:86088030C>T	ENST00000330753.4	+	2	939	c.172C>T	c.(172-174)Cct>Tct	p.P58S	FLRT2_ENST00000554746.1_Missense_Mutation_p.P58S	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	58	LRRNT.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.P58S(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GACCTCAGTGCCTCTTGGGAT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	14											139	127	131					14																	86088030		2203	4300	6503	85157783	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.172C>T	14.37:g.86088030C>T	ENSP00000332879:p.Pro58Ser		85157783	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	34	5.363094	0.95877	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	D;D	0.99857	-7.22;-7.22	5.73	5.73	0.89815	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.99902	0.9953	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96563	0.9417	10	0.87932	D	0	-11.1612	19.9036	0.96999	0.0:1.0:0.0:0.0	.	58	O43155	FLRT2_HUMAN	S	58	ENSP00000332879:P58S;ENSP00000451050:P58S	ENSP00000332879:P58S	P	+	1	0	FLRT2	85157783	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.817000	0.86213	2.706000	0.92434	0.655000	0.94253	CCT		0.522	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			T	86088030	C	T	86088030	3	4	47	1	0	0	0	0	1	0	0	0	5958	739	26	3	174	3	FLRT2	14	86088030	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5418791	86088030	21261510	1541	5938										
PTPN21	11099	broad.mit.edu	37	chr14	88967680	88967680	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctctctacctcctgcatgTacagcatttcagcatcagga	6	13	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:88967680T>G	ENST00000556564.1	-	7	904	c.620A>C	c.(619-621)tAc>tCc	p.Y207S	RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000328736.3_Missense_Mutation_p.Y207S|PTPN21_ENST00000554628.1_5'UTR	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	207	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.Y207S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTCCTGCATGTACAGCATTTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											163	163	163					14																	88967680		2203	4300	6503	88037433	SO:0001583	missense	11099			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.620A>C	14.37:g.88967680T>G	ENSP00000452414:p.Tyr207Ser		88037433		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187762	0.78789	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	D;D	0.85171	-1.95;-1.95	5.34	4.16	0.48862	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.077869	0.53938	D	0.000051	D	0.93789	0.8014	H	0.94306	3.52	0.42271	D	0.992055	D	0.89917	1.0	D	0.91635	0.999	D	0.94112	0.7372	10	0.87932	D	0	.	11.2034	0.48754	0.1377:0.0:0.0:0.8623	.	207	Q16825	PTN21_HUMAN	S	207	ENSP00000330276:Y207S;ENSP00000452414:Y207S	ENSP00000330276:Y207S	Y	-	2	0	PTPN21	88037433	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.704000	0.68347	0.827000	0.34685	0.533000	0.62120	TAC		0.448	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			G	88967680	T	G	88967680	3	3	47	1	0	0	0	0	1	0	0	0	12823	1638	57	4	2956	4	PTPN21	14	88967680	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2879650	88967680	18381860	1542	5939										
C14orf102	55051	broad.mit.edu	37	chr14	90769221	90769221	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaaataaaaggtatttctgCcaaagggctgtattattggg	10	5	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:90769221C>T	ENST00000354366.3	-	6	1486	c.1254G>A	c.(1252-1254)tgG>tgA	p.W418*	NRDE2_ENST00000357904.3_Nonsense_Mutation_p.W187*	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	418								p.W418*(1)									GGTATTTCTGCCAAAGGGCTG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											69	74	72					14																	90769221		2203	4299	6502	89838974	SO:0001587	stop_gained	55051			AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1254G>A	14.37:g.90769221C>T	ENSP00000346335:p.Trp418*		89838974	B4DH71|Q4G0A7|Q9NWH6	Nonsense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	C	41	8.802573	0.98960	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9142	19.4407	0.94820	0.0:1.0:0.0:0.0	.	.	.	.	X	418;187	.	ENSP00000346335:W418X	W	-	3	0	C14orf102	89838974	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	7.731000	0.84895	2.586000	0.87340	0.650000	0.86243	TGG		0.423	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		T	90769221	C	T	90769221	4	4	47	1	0	0	0	0	0	1	0	0	1739	740	26	3	2276	3	C14orf102	14	90769221	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1801541	90769221	16580319	1543	5940										
C14orf102	55051	broad.mit.edu	37	chr14	90784373	90784373	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcagcggtaacccttcagaaAcatgggctggagctgcttca	11	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:90784373A>G	ENST00000354366.3	-	2	381	c.149T>C	c.(148-150)gTt>gCt	p.V50A	NRDE2_ENST00000357904.3_Intron|NRDE2_ENST00000557106.1_5'UTR	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	50								p.V50A(1)									CCCTTCAGAAACATGGGCTGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											147	135	139					14																	90784373		2203	4300	6503	89854126	SO:0001583	missense	55051			AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.149T>C	14.37:g.90784373A>G	ENSP00000346335:p.Val50Ala		89854126	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	A	3.476	-0.106856	0.06924	.	.	ENSG00000119720	ENST00000354366	T	0.20738	2.05	5.14	-0.309	0.12769	.	0.663610	0.13371	N	0.392888	T	0.08670	0.0215	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40079	-0.9582	10	0.08599	T	0.76	-7.437	5.4423	0.16515	0.4091:0.0:0.444:0.1468	.	50	Q9H7Z3	CN102_HUMAN	A	50	ENSP00000346335:V50A	ENSP00000346335:V50A	V	-	2	0	C14orf102	89854126	0.000000	0.05858	0.006000	0.13384	0.362000	0.29581	-0.106000	0.10890	0.028000	0.15324	0.455000	0.32223	GTT		0.448	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		G	90784373	A	G	90784373	3	3	47	1	0	0	0	0	1	0	0	0	1739	43	2	4	3397	4	C14orf102	14	90784373	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	15152	90784373	16565167	1544	5941										
TTC7B	145567	broad.mit.edu	37	chr14	91196424	91196424	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgaagatggcttacccattTttgaaatagaggacatgggc	11	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:91196424T>C	ENST00000328459.6	-	5	814	c.693A>G	c.(691-693)aaA>aaG	p.K231K	TTC7B_ENST00000357056.2_Silent_p.K231K	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	231								p.K231K(1)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				CTTACCCATTTTTGAAATAGA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	14											88	100	96					14																	91196424		2203	4300	6503	90266177	SO:0001819	synonymous_variant	145567			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.693A>G	14.37:g.91196424T>C			90266177	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1																																																																																				0.393	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			C	91196424	T	C	91196424	2	2	47	1	0	0	0	0	0	0	0	1	16753	1838	64	4		4	TTC7B	14	91196424	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	412051	91196424	16153116	1545	5942										
TRIP11	9321	broad.mit.edu	37	chr14	92465697	92465697	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagcttcacgggtataagaAtcttctgattctaaaagatg	8	6	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:92465697A>C	ENST00000267622.4	-	13	5152	c.4779T>G	c.(4777-4779)gaT>gaG	p.D1593E		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1593					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.D1593E(1)		breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GGGTATAAGAATCTTCTGATT	0.378			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	1	Substitution - Missense(1)	large_intestine(1)	14											108	98	102					14																	92465697		2203	4300	6503	91535450	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4779T>G	14.37:g.92465697A>C	ENSP00000267622:p.Asp1593Glu		91535450	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.72|15.72	2.917156|2.917156	0.52546|0.52546	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.03663|.	3.85|.	5.27|5.27	2.97|2.97	0.34412|0.34412	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.42517|0.42517	0.1206|0.1206	L|L	0.35288|0.35288	1.05|1.05	0.39897|0.39897	D|D	0.973845|0.973845	D;D|.	0.89917|.	1.0;0.982|.	D;D|.	0.91635|.	0.999;0.914|.	T|T	0.24476|0.24476	-1.0159|-1.0159	10|5	0.25106|.	T|.	0.35|.	.|.	5.257|5.257	0.15552|0.15552	0.562:0.0:0.438:0.0|0.562:0.0:0.438:0.0	.|.	1329;1593|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	E|V	1593;1329|1309	ENSP00000267622:D1593E|.	ENSP00000267622:D1593E|.	D|F	-|-	3|1	2|0	TRIP11|TRIP11	91535450|91535450	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	1.021000|1.021000	0.30040|0.30040	0.867000|0.867000	0.35654|0.35654	0.533000|0.533000	0.62120|0.62120	GAT|TTC		0.378	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92465697	A	C	92465697	3	2	47	1	0	0	0	0	1	0	0	0	16595	98	4	4	1196	4	TRIP11	14	92465697	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1269273	92465697	14883843	1546	5943										
ASB2	51676	broad.mit.edu	37	chr14	94417349	94417349	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acccttagccactcaccgtaCttggctaagaacctcaaggc	7	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:94417349C>T	ENST00000315988.4	-	4	1220	c.732G>A	c.(730-732)aaG>aaA	p.K244K	ASB2_ENST00000556337.1_Intron|MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000555019.1_Silent_p.K292K	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	244					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)	p.K244K(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		ACTCACCGTACTTGGCTAAGA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	14											217	211	213					14																	94417349		2203	4300	6503	93487102	SO:0001819	synonymous_variant	51676			AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"Ankyrin repeat domain containing"	16012	protein-coding gene	gene with protein product		605759	"ankyrin repeat and SOCS box-containing 2"				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.732G>A	14.37:g.94417349C>T			93487102	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																				0.587	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			T	94417349	C	T	94417349	2	4	47	1	0	0	0	0	0	0	0	1	1024	564	20	3		3	ASB2	14	94417349	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1951652	94417349	12932191	1547	5944										
SERPINA6	866	broad.mit.edu	37	chr14	94780644	94780644	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgtctgactttgcaaagagTtggtgcaggtgctggaaacc	14	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:94780644T>G	ENST00000341584.3	-	2	488	c.342A>C	c.(340-342)caA>caC	p.Q114H		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	114					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)	p.Q114H(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TTGCAAAGAGTTGGTGCAGGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	14											69	67	67					14																	94780644		2203	4300	6503	93850397	SO:0001583	missense	866			J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"Serine (or cysteine) peptidase inhibitors"	1540	protein-coding gene	gene with protein product	"corticosteroid binding globulin", "transcortin"	122500	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.342A>C	14.37:g.94780644T>G	ENSP00000342850:p.Gln114His		93850397	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	.	.	.	.	.	.	.	.	.	.	T	0.242	-1.012895	0.02095	.	.	ENSG00000170099	ENST00000341584;ENST00000557225	D;D	0.84370	-1.84;-1.84	5.07	-2.0	0.07433	Serpin domain (3);	0.520428	0.18065	N	0.152801	T	0.51568	0.1682	N	0.01015	-1.05	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51865	-0.8651	10	0.15952	T	0.53	.	2.8923	0.05680	0.2439:0.2874:0.3663:0.1024	.	114	P08185	CBG_HUMAN	H	114	ENSP00000342850:Q114H;ENSP00000452018:Q114H	ENSP00000342850:Q114H	Q	-	3	2	SERPINA6	93850397	0.001000	0.12720	0.001000	0.08648	0.334000	0.28698	-0.193000	0.09573	-0.212000	0.10109	-0.445000	0.05633	CAA		0.542	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756		G	94780644	T	G	94780644	3	3	47	1	0	0	0	0	1	0	0	0	14130	1722	60	4	891	4	SERPINA6	14	94780644	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	363295	94780644	12568896	1548	5945										
SERPINA1	5265	broad.mit.edu	37	chr14	94849350	94849350	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgatgctcactggggagaaGaagatattggtgctgttgga	16	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:94849350G>T	ENST00000448921.1	-	4	797	c.225C>A	c.(223-225)ttC>ttA	p.F75L	SERPINA1_ENST00000437397.1_Missense_Mutation_p.F75L|SERPINA1_ENST00000404814.4_Missense_Mutation_p.F75L|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000402629.1_Missense_Mutation_p.F75L|SERPINA1_ENST00000393087.4_Missense_Mutation_p.F75L|SERPINA1_ENST00000449399.3_Missense_Mutation_p.F75L|SERPINA1_ENST00000393088.4_Missense_Mutation_p.F75L|SERPINA1_ENST00000440909.1_Missense_Mutation_p.F75L|SERPINA1_ENST00000355814.4_Missense_Mutation_p.F75L	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	75			Missing (in M-Malton, M-Nichinan and M- Palermo; associated with very low serum levels of AAT; homozygosity for allele M- Malton may be associated with a risk for chronic emphysema or infantile liver cirrhosis). {ECO:0000269|PubMed:2309708, ECO:0000269|PubMed:2606478, ECO:0000269|PubMed:2786335}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F75L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CTGGGGAGAAGAAGATATTGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	14											164	137	146					14																	94849350		2203	4300	6503	93919103	SO:0001583	missense	5265			X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.225C>A	14.37:g.94849350G>T	ENSP00000416066:p.Phe75Leu		93919103	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242430	0.58995	.	.	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000556091;ENST00000557492;ENST00000556955;ENST00000553327	D;D;D;D;D;D;D;D;D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9	5.94	2.95	0.34219	Serpin domain (3);	0.074506	0.56097	N	0.000026	T	0.81781	0.4895	M	0.67517	2.055	0.42689	D	0.993577	B;B	0.32543	0.215;0.375	B;B	0.39465	0.114;0.3	T	0.77236	-0.2662	10	0.48119	T	0.1	.	2.4301	0.04470	0.2048:0.1328:0.5252:0.1373	.	75;75	P01009-2;P01009	.;A1AT_HUMAN	L	75	ENSP00000390299:F75L;ENSP00000416066:F75L;ENSP00000408474:F75L;ENSP00000348068:F75L;ENSP00000376802:F75L;ENSP00000376803:F75L;ENSP00000385960:F75L;ENSP00000416354:F75L;ENSP00000386094:F75L;ENSP00000452169:F75L;ENSP00000452452:F75L;ENSP00000451098:F75L;ENSP00000452480:F75L	ENSP00000348068:F75L	F	-	3	2	SERPINA1	93919103	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	2.167000	0.42415	0.835000	0.34877	0.561000	0.74099	TTC		0.542	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		T	94849350	G	T	94849350	3	4	47	1	0	0	0	0	1	0	0	0	14123	933	33	2	1047	2	SERPINA1	14	94849350	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	68706	94849350	12500190	1549	5946										
SERPINA4	5267	broad.mit.edu	37	chr14	95033573	95033573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaggtggaacaacttgttgCggaagaggtaatcagtgtgc	15	5	1	2	rs143608450	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:95033573C>T	ENST00000557004.1	+	3	1337	c.916C>T	c.(916-918)Cgg>Tgg	p.R306W	SERPINA4_ENST00000555095.1_Missense_Mutation_p.R306W|SERPINA4_ENST00000298841.5_Missense_Mutation_p.R306W|SERPINA5_ENST00000553780.1_Intron			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	306					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R306W(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		CAACTTGTTGCGGAAGAGGTA	0.433													C|||	2	0.000399361	0	0	5008	,	,		21498	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14						C	TRP/ARG	0,4406		0,0,2203	80	81	81		916	-0.1	0	14	dbSNP_134	81	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SERPINA4	NM_006215.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	306/428	95033573	2,13004	2203	4300	6503	94103326	SO:0001583	missense	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.916C>T	14.37:g.95033573C>T	ENSP00000450838:p.Arg306Trp		94103326	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	37	CCDS9927.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	15.69	2.907164	0.52333	0.0	2.33E-4	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.84944	-1.92;-1.92;-1.92	4.56	-0.0731	0.13736	Serpin domain (3);	2.512550	0.01659	N	0.025009	D	0.90048	0.6892	L	0.58669	1.825	0.09310	N	1	D;D	0.89917	0.999;1.0	P;D	0.66351	0.892;0.943	T	0.74216	-0.3737	10	0.72032	D	0.01	.	8.1407	0.31082	0.454:0.3986:0.1474:0.0	.	306;306	B2R815;P29622	.;KAIN_HUMAN	W	306	ENSP00000450838:R306W;ENSP00000451172:R306W;ENSP00000298841:R306W	ENSP00000298841:R306W	R	+	1	2	SERPINA4	94103326	0.000000	0.05858	0.000000	0.03702	0.231000	0.25187	-1.854000	0.01664	0.062000	0.16340	0.561000	0.74099	CGG		0.433	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		T	95033573	C	T	95033573	3	4	47	1	0	0	0	0	1	0	0	0	14128	759	27	1	922	1	SERPINA4	14	95033573	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	184223	95033573	12315967	1550	5947										
SERPINA5	5104	broad.mit.edu	37	chr14	95053811	95053811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgaggacctccatgtaggtGccacggtggcccccagcagc	13	15	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:95053811G>A	ENST00000554866.1	+	2	226	c.112G>A	c.(112-114)Gcc>Acc	p.A38T	SERPINA5_ENST00000554276.1_Missense_Mutation_p.A38T|SERPINA5_ENST00000553780.1_Missense_Mutation_p.A38T|SERPINA5_ENST00000329597.7_Missense_Mutation_p.A38T			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	38					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A38T(1)		endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCATGTAGGTGCCACGGTGGC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	56	56					14																	95053811		2203	4300	6503	94123564	SO:0001583	missense	5104			M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"Serine (or cysteine) peptidase inhibitors"	8723	protein-coding gene	gene with protein product		601841	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.112G>A	14.37:g.95053811G>A	ENSP00000451126:p.Ala38Thr		94123564	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	.	.	.	.	.	.	.	.	.	.	G	9.095	1.002632	0.19121	.	.	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554633;ENST00000555681;ENST00000438291;ENST00000554276;ENST00000557598	D;D;D;D;D;T;T;T;T;D;T	0.87809	-1.6;-1.6;-2.3;-1.6;-1.6;-0.83;-0.83;-0.83;-0.83;-1.6;-0.83	4.2	-1.68	0.08212	Serpin domain (1);	2.252930	0.01645	N	0.024261	T	0.73171	0.3553	N	0.08118	0	0.09310	N	1	B;B	0.20459	0.005;0.045	B;B	0.18263	0.005;0.021	T	0.61486	-0.7053	10	0.22109	T	0.4	.	6.1286	0.20194	0.144:0.1205:0.7355:0.0	.	38;38	G3V5Q9;P05154	.;IPSP_HUMAN	T	38	ENSP00000450484:A38T;ENSP00000450837:A38T;ENSP00000452469:A38T;ENSP00000451126:A38T;ENSP00000333203:A38T;ENSP00000450745:A38T;ENSP00000451215:A38T;ENSP00000451697:A38T;ENSP00000451650:A38T;ENSP00000451610:A38T;ENSP00000450485:A38T	ENSP00000333203:A38T	A	+	1	0	SERPINA5	94123564	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.688000	0.05150	-0.442000	0.07190	-0.305000	0.09177	GCC		0.627	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624		A	95053811	G	A	95053811	3	1	47	1	0	0	0	0	1	0	0	0	14129	1319	46	3	114	3	SERPINA5	14	95053811	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	20238	95053811	12295729	1551	5948										
CLMN	79789	broad.mit.edu	37	chr14	95669990	95669990	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctattaggtcgctgttaaAttttgaggcttttaatggga	10	4	1	1	rs201614969		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:95669990A>C	ENST00000298912.4	-	9	1809	c.1696T>G	c.(1696-1698)Ttt>Gtt	p.F566V		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	566					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.F566V(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TCGCTGTTAAATTTTGAGGCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											80	81	80					14																	95669990		2203	4300	6503	94739743	SO:0001583	missense	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1696T>G	14.37:g.95669990A>C	ENSP00000298912:p.Phe566Val		94739743	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	A	8.854	0.945284	0.18356	.	.	ENSG00000165959	ENST00000298912	D	0.92595	-3.07	5.76	1.6	0.23607	.	0.000000	0.42172	D	0.000745	D	0.86830	0.6027	M	0.64997	1.995	0.09310	N	1	B	0.22276	0.067	B	0.15052	0.012	T	0.76255	-0.3026	10	0.42905	T	0.14	.	3.539	0.07804	0.5696:0.1955:0.2349:0.0	.	566	Q96JQ2	CLMN_HUMAN	V	566	ENSP00000298912:F566V	ENSP00000298912:F566V	F	-	1	0	CLMN	94739743	0.055000	0.20627	0.098000	0.21074	0.046000	0.14306	0.969000	0.29370	1.001000	0.39076	0.533000	0.62120	TTT		0.433	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			C	95669990	A	C	95669990	3	2	47	1	0	0	0	0	1	0	0	0	3548	101	4	4	1332	4	CLMN	14	95669990	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	616179	95669990	11679550	1552	5949										
C14orf49	161176	broad.mit.edu	37	chr14	95922049	95922049	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcctcgcccctgggaaaatCtttggcaatgtcctgaagag	10	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:95922049C>A	ENST00000334258.5	-	5	816	c.802G>T	c.(802-804)Gat>Tat	p.D268Y	SYNE3_ENST00000554873.1_Missense_Mutation_p.D25Y|SYNE3_ENST00000557275.1_Missense_Mutation_p.D268Y|SYNE3_ENST00000553340.1_Missense_Mutation_p.D268Y	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	268					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.D268Y(1)		breast(1)|endometrium(2)|lung(25)	28						CTGGGAAAATCTTTGGCAATG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											51	56	54					14																	95922049		2203	4300	6503	94991802	SO:0001583	missense	161176			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.802G>T	14.37:g.95922049C>A	ENSP00000334308:p.Asp268Tyr		94991802	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.477691	0.26511	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.17213	3.46;2.29;3.45;2.89	4.99	4.09	0.47781	.	0.173062	0.27388	N	0.019599	T	0.36110	0.0955	M	0.72118	2.19	0.09310	N	0.999999	D;D;D	0.76494	0.999;0.996;0.999	D;D;P	0.65684	0.937;0.922;0.907	T	0.11743	-1.0575	10	0.62326	D	0.03	-4.6247	9.8866	0.41266	0.0:0.7796:0.1418:0.0785	.	268;268;268	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	Y	268;25;268;268	ENSP00000334308:D268Y;ENSP00000452154:D25Y;ENSP00000450562:D268Y;ENSP00000450774:D268Y	ENSP00000334308:D268Y	D	-	1	0	C14orf49	94991802	0.063000	0.20901	0.009000	0.14445	0.166000	0.22503	1.923000	0.40055	1.081000	0.41110	0.455000	0.32223	GAT		0.547	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95922049	C	A	95922049	3	1	47	1	0	0	0	0	1	0	0	0	1780	913	32	2	2177	2	C14orf49	14	95922049	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	252059	95922049	11427491	1553	5950										
SETD3	84193	broad.mit.edu	37	chr14	99879329	99879329	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catatcccataaaggaatcaGagccagggtcacgcgggaac	11	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:99879329G>T	ENST00000331768.5	-	8	967	c.808C>A	c.(808-810)Ctg>Atg	p.L270M	SETD3_ENST00000436070.2_Missense_Mutation_p.L270M|SETD3_ENST00000329331.3_Missense_Mutation_p.L270M	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	270	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)	p.L270M(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				AAAGGAATCAGAGCCAGGGTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	14											154	143	147					14																	99879329		2203	4300	6503	98949082	SO:0001583	missense	84193			AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.808C>A	14.37:g.99879329G>T	ENSP00000327436:p.Leu270Met		98949082	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Missense_Mutation	SNP	ENST00000331768.5	37	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944548	0.73672	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	T;T;T	0.29917	1.55;1.55;1.55	4.97	4.07	0.47477	SET domain (1);	0.000000	0.64402	D	0.000003	T	0.47911	0.1471	M	0.62209	1.925	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.988;0.999;0.997	T	0.41305	-0.9516	10	0.51188	T	0.08	-3.0096	8.6952	0.34291	0.1685:0.0:0.8315:0.0	.	270;270;270	Q6NXR6;A0PJU3;Q86TU7	.;.;SETD3_HUMAN	M	270	ENSP00000327436:L270M;ENSP00000327910:L270M;ENSP00000408602:L270M	ENSP00000327910:L270M	L	-	1	2	SETD3	98949082	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	3.823000	0.55715	2.454000	0.82982	0.650000	0.86243	CTG		0.483	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		T	99879329	G	T	99879329	3	4	47	1	0	0	0	0	1	0	0	0	14169	933	33	2	1046	2	SETD3	14	99879329	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3957280	99879329	7470211	1554	5951										
WDR25	79446	broad.mit.edu	37	chr14	100847303	100847303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaatggcttcattggtagcGtatgatgattcggactcgga	12	6	1	2	rs368854339		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:100847303G>A	ENST00000335290.6	+	2	268	c.42G>A	c.(40-42)gcG>gcA	p.A14A	WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000554175.1_Silent_p.A14A|WDR25_ENST00000402312.3_Silent_p.A14A|WDR25_ENST00000554998.1_Silent_p.A14A	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	14								p.A14A(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CATTGGTAGCGTATGATGATT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	14						G	,	0,4406		0,0,2203	109	94	99		42,42	-5.8	0.4	14		99	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	WDR25	NM_001161476.1,NM_024515.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	14/545,14/545	100847303	1,13005	2203	4300	6503	99917056	SO:0001819	synonymous_variant	79446			BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"WD repeat domain containing"	21064	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 67"	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.42G>A	14.37:g.100847303G>A			99917056	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																				0.483	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		A	100847303	G	A	100847303	2	1	47	1	0	0	0	0	0	0	0	1	17322	1132	40	1		1	WDR25	14	100847303	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	967974	100847303	6502237	1555	5952										
TRAF3	7187	broad.mit.edu	37	chr14	103341988	103341988	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggataattgctgcaagagaGaaattctggctcttcagatc	10	7	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:103341988G>T	ENST00000560371.1	+	4	542	c.325G>T	c.(325-327)Gaa>Taa	p.E109*	TRAF3_ENST00000351691.5_Nonsense_Mutation_p.E109*|TRAF3_ENST00000347662.4_Nonsense_Mutation_p.E109*|TRAF3_ENST00000539721.1_Nonsense_Mutation_p.E109*|TRAF3_ENST00000392745.2_Nonsense_Mutation_p.E109*	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	109					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E109*(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CTGCAAGAGAGAAATTCTGGC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											131	129	129					14																	103341988		2203	4300	6503	102411741	SO:0001587	stop_gained	7187			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.325G>T	14.37:g.103341988G>T	ENSP00000454207:p.Glu109*		102411741	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Nonsense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	G	40	8.447058	0.98815	.	.	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-51.4831	19.5463	0.95299	0.0:0.0:1.0:0.0	.	.	.	.	X	109	.	ENSP00000328003:E109X	E	+	1	0	TRAF3	102411741	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.570000	0.90748	2.679000	0.91253	0.655000	0.94253	GAA		0.413	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725		T	103341988	G	T	103341988	4	4	47	1	0	0	0	0	0	1	0	0	16479	943	33	2	335	2	TRAF3	14	103341988	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2494685	103341988	4007552	1556	5953										
MARK3	4140	broad.mit.edu	37	chr14	103918266	103918266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcccgcagtgaagttattcGaagtcattgaaactgaaaaa	8	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:103918266G>A	ENST00000429436.2	+	5	868	c.358G>A	c.(358-360)Gaa>Aaa	p.E120K	MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000553942.1_Missense_Mutation_p.E120K|MARK3_ENST00000440884.3_Missense_Mutation_p.E120K|MARK3_ENST00000335102.5_Missense_Mutation_p.E120K|MARK3_ENST00000416682.2_Missense_Mutation_p.E120K|MARK3_ENST00000216288.7_Missense_Mutation_p.E120K|MARK3_ENST00000303622.9_Missense_Mutation_p.E120K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E120K(4)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			GAAGTTATTCGAAGTCATTGA	0.353																																																4	Substitution - Missense(4)	prostate(2)|ovary(1)|large_intestine(1)	14											171	168	169					14																	103918266		1851	4107	5958	102988019	SO:0001583	missense	4140			M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.358G>A	14.37:g.103918266G>A	ENSP00000411397:p.Glu120Lys		102988019	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086533	0.76642	.	.	ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	T;T;T;T;T;T;T	0.26223	1.75;3.07;1.75;1.75;1.75;1.75;1.75	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.70108	2.13	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.87578	0.903;0.997;0.998;0.998;0.993;0.996	T	0.51957	-0.8639	10	0.72032	D	0.01	.	19.0276	0.92939	0.0:0.0:1.0:0.0	.	120;120;120;120;120;120	P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;MARK3_HUMAN;.;.;.	K	120	ENSP00000335347:E120K;ENSP00000402104:E120K;ENSP00000408092:E120K;ENSP00000411397:E120K;ENSP00000303698:E120K;ENSP00000216288:E120K;ENSP00000450772:E120K	ENSP00000216288:E120K	E	+	1	0	MARK3	102988019	1.000000	0.71417	0.999000	0.59377	0.020000	0.10135	8.655000	0.91098	2.797000	0.96272	0.563000	0.77884	GAA		0.353	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		A	103918266	G	A	103918266	3	1	47	1	0	0	0	0	1	0	0	0	9344	1059	37	1	376	1	MARK3	14	103918266	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	576278	103918266	3431274	1557	5954										
BAG5	9529	broad.mit.edu	37	chr14	104026187	104026187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccattcatcagatttcaggtCgagatagctgagaatattct	8	8	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:104026187C>T	ENST00000445922.2	-	2	1561	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	BAG5_ENST00000299204.4_Missense_Mutation_p.D439N|BAG5_ENST00000337322.4_Missense_Mutation_p.D480N|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	439	BAG 5. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.D439N(2)		endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GATTTCAGGTCGAGATAGCTG	0.453																																					NSCLC(171;1832 2055 18950 31566 41632)											2	Substitution - Missense(2)	large_intestine(2)	14											125	122	123					14																	104026187		2203	4300	6503	103095940	SO:0001583	missense	9529			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.1315G>A	14.37:g.104026187C>T	ENSP00000391713:p.Asp439Asn		103095940	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	37	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	C	34	5.314606	0.95655	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.96104	-3.91;-3.91;-3.91	5.87	5.87	0.94306	BAG domain (3);	0.000000	0.85682	D	0.000000	D	0.97629	0.9223	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97641	1.0148	10	0.87932	D	0	-44.4964	20.5827	0.99408	0.0:1.0:0.0:0.0	.	439;480	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	N	439;439;480	ENSP00000299204:D439N;ENSP00000391713:D439N;ENSP00000338814:D480N	ENSP00000299204:D439N	D	-	1	0	BAG5	103095940	1.000000	0.71417	0.949000	0.38748	0.992000	0.81027	7.195000	0.77798	2.941000	0.99782	0.655000	0.94253	GAC		0.453	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			T	104026187	C	T	104026187	3	4	47	1	0	0	0	0	1	0	0	0	1291	884	31	1	32	1	BAG5	14	104026187	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	107921	104026187	3323353	1558	5955										
BAG5	9529	broad.mit.edu	37	chr14	104026640	104026640	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaagttcattttttatttCtctcattctcttgaggacct	6	8	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr14:104026640C>A	ENST00000445922.2	-	2	1108	c.862G>T	c.(862-864)Gaa>Taa	p.E288*	RP11-73M18.2_ENST00000472726.2_5'Flank|BAG5_ENST00000299204.4_Nonsense_Mutation_p.E288*|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000556253.2_5'Flank|BAG5_ENST00000337322.4_Nonsense_Mutation_p.E329*|APOPT1_ENST00000409074.2_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	288	BAG 4. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.E288*(1)		endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			TTTTTTATTTCTCTCATTCTC	0.373																																					NSCLC(171;1832 2055 18950 31566 41632)											1	Substitution - Nonsense(1)	large_intestine(1)	14											94	101	99					14																	104026640		2203	4300	6503	103096393	SO:0001587	stop_gained	9529			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.862G>T	14.37:g.104026640C>A	ENSP00000391713:p.Glu288*		103096393	O94950|Q86W59	Nonsense_Mutation	SNP	ENST00000445922.2	37	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	C	37	5.992948	0.97179	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	.	.	.	5.65	4.77	0.60923	.	0.647217	0.15797	N	0.244149	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-32.3866	10.5004	0.44802	0.0:0.8534:0.0:0.1466	.	.	.	.	X	288;288;329	.	ENSP00000299204:E288X	E	-	1	0	BAG5	103096393	0.996000	0.38824	0.998000	0.56505	0.994000	0.84299	2.747000	0.47475	1.398000	0.46701	0.655000	0.94253	GAA		0.373	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			A	104026640	C	A	104026640	4	1	47	1	0	0	0	0	0	1	0	0	1291	922	32	2	485	2	BAG5	14	104026640	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	453	104026640	3322900	1559	5956										
OR4M2	390538	broad.mit.edu	37	chr15	22368853	22368853	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtggagaggaagataatttCttttgatggatgcattgcac	12	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:22368853C>A	ENST00000332663.2	+	1	376	c.278C>A	c.(277-279)tCt>tAt	p.S93Y	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S93Y(1)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		AAGATAATTTCTTTTGATGGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											327	278	295					15																	22368853		2203	4300	6503	19870217	SO:0001583	missense	390538			AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.278C>A	15.37:g.22368853C>A	ENSP00000329467:p.Ser93Tyr		19870217	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	13.25	2.182527	0.38511	.	.	ENSG00000182974	ENST00000332663	T	0.00745	5.75	2.5	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000272	T	0.05181	0.0138	H	0.94345	3.525	0.09310	N	1	D	0.89917	1.0	D	0.76071	0.987	T	0.08764	-1.0706	10	0.87932	D	0	-16.9563	7.0514	0.25075	0.0:0.8505:0.0:0.1495	.	93	Q8NGB6	OR4M2_HUMAN	Y	93	ENSP00000329467:S93Y	ENSP00000329467:S93Y	S	+	2	0	OR4M2	19870217	0.000000	0.05858	0.872000	0.34217	0.873000	0.50193	0.912000	0.28597	0.390000	0.25115	0.448000	0.29417	TCT		0.438	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			A	22368853	C	A	22368853	3	1	47	1	0	0	0	0	1	0	0	0	11107	913	32	2	280	2	OR4M2	15	22368853	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09		22368853	80162539	1560	5957										
OR4N4	283694	broad.mit.edu	37	chr15	22382489	22382489	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaaatgaagatagcaaacaAcacagtagtgacagaattta	8	5	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:22382489A>C	ENST00000328795.4	+	1	108	c.17A>C	c.(16-18)aAc>aCc	p.N6T	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N6T(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		ATAGCAAACAACACAGTAGTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											171	159	163					15																	22382489		2190	4263	6453	19883853	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.17A>C	15.37:g.22382489A>C	ENSP00000332500:p.Asn6Thr		19883853	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.369045	0.00209	.	.	ENSG00000183706	ENST00000328795	T	0.00514	6.88	3.34	-0.161	0.13371	.	0.504643	0.18478	N	0.140019	T	0.00271	0.0008	N	0.20304	0.555	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.40384	-0.9566	10	0.15066	T	0.55	-1.0899	2.4776	0.04580	0.4292:0.0:0.3507:0.2202	.	6	Q8N0Y3	OR4N4_HUMAN	T	6	ENSP00000332500:N6T	ENSP00000332500:N6T	N	+	2	0	OR4N4	19883853	0.000000	0.05858	0.821000	0.32701	0.029000	0.11900	-2.044000	0.01411	0.097000	0.17492	0.324000	0.21423	AAC		0.348	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382489	A	C	22382489	3	2	47	1	0	0	0	0	1	0	0	0	11109	43	2	4	19	4	OR4N4	15	22382489	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	13636	22382489	80148903	1561	5958										
GABRB3	2562	broad.mit.edu	37	chr15	26793032	26793032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgtctatggcattcacatCggttagatcaggtattttaa	8	7	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:26793032C>T	ENST00000311550.5	-	9	1441	c.1330G>A	c.(1330-1332)Gat>Aat	p.D444N	GABRB3_ENST00000299267.4_Missense_Mutation_p.D444N|GABRB3_ENST00000541819.2_Missense_Mutation_p.D500N|GABRB3_ENST00000545868.1_Missense_Mutation_p.D359N|GABRB3_ENST00000400188.3_Missense_Mutation_p.D373N	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	444					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.D444N(4)|p.D500N(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCATTCACATCGGTTAGATCA	0.458																																																5	Substitution - Missense(5)	cervix(3)|large_intestine(2)	15											121	100	107					15																	26793032		2203	4300	6503	24344125	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1330G>A	15.37:g.26793032C>T	ENSP00000308725:p.Asp444Asn		24344125	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997911	0.54147	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03	6.03	6.03	0.97812	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.84723	0.5535	L	0.48260	1.515	0.80722	D	1	P;P;P	0.50443	0.893;0.92;0.935	B;B;P	0.46362	0.296;0.267;0.514	T	0.82329	-0.0511	10	0.30078	T	0.28	.	19.545	0.95291	0.0:1.0:0.0:0.0	.	500;444;444	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	N	444;500;444;373;359	ENSP00000308725:D444N;ENSP00000442408:D500N;ENSP00000299267:D444N;ENSP00000383049:D373N;ENSP00000439169:D359N	ENSP00000299267:D444N	D	-	1	0	GABRB3	24344125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.984000	0.70548	2.861000	0.98227	0.655000	0.94253	GAT		0.458	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			T	26793032	C	T	26793032	3	4	47	1	0	0	0	0	1	0	0	0	6187	884	31	1	95	1	GABRB3	15	26793032	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4410543	26793032	75738360	1562	5959										
HERC2	8924	broad.mit.edu	37	chr15	28514407	28514407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactcaccagcgtgtcactaTtataggcctgtgtgtacacg	9	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:28514407T>G	ENST00000261609.7	-	11	1541	c.1433A>C	c.(1432-1434)aAt>aCt	p.N478T		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.N478T(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CGTGTCACTATTATAGGCCTG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	15											71	56	61					15																	28514407		2203	4300	6503	26188002	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.1433A>C	15.37:g.28514407T>G	ENSP00000261609:p.Asn478Thr		26188002		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	2.386	-0.340991	0.05243	.	.	ENSG00000128731	ENST00000261609	T	0.79141	-1.24	5.78	3.49	0.39957	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.096395	0.64402	D	0.000001	T	0.69860	0.3158	M	0.65677	2.01	0.39946	D	0.974478	B	0.22800	0.075	B	0.19946	0.027	T	0.59402	-0.7461	10	0.07030	T	0.85	.	9.8485	0.41041	0.0:0.1378:0.0:0.8622	.	478	O95714	HERC2_HUMAN	T	478	ENSP00000261609:N478T	ENSP00000261609:N478T	N	-	2	0	HERC2	26188002	1.000000	0.71417	0.964000	0.40570	0.103000	0.19146	4.335000	0.59298	0.468000	0.27243	0.533000	0.62120	AAT		0.552	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28514407	T	G	28514407	3	3	47	1	0	0	0	0	1	0	0	0	7079	1493	52	4	13403	4	HERC2	15	28514407	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1721375	28514407	74016985	1563	5960										
TJP1	7082	broad.mit.edu	37	chr15	30011134	30011134	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacgatgttcatagtttcgaGaaaactggtccgtatagctt	10	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:30011134G>A	ENST00000346128.6	-	21	3686	c.3212C>T	c.(3211-3213)tCt>tTt	p.S1071F	TJP1_ENST00000545208.2_Missense_Mutation_p.S991F|TJP1_ENST00000356107.6_Missense_Mutation_p.S1071F|TJP1_ENST00000400011.2_Missense_Mutation_p.S995F	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1071					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.S1071F(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		ATAGTTTCGAGAAAACTGGTC	0.488																																					Melanoma(77;681 1843 6309 6570)											1	Substitution - Missense(1)	large_intestine(1)	15											296	289	292					15																	30011134		2059	4206	6265	27798426	SO:0001583	missense	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.3212C>T	15.37:g.30011134G>A	ENSP00000281537:p.Ser1071Phe		27798426	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608421	0.66558	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.07444	3.19;3.25	5.93	5.93	0.95920	.	0.337013	0.37393	N	0.002105	T	0.14960	0.0361	L	0.50333	1.59	0.80722	D	1	P;P;P;P	0.44090	0.608;0.826;0.608;0.731	B;B;B;B	0.44224	0.235;0.299;0.235;0.444	T	0.00162	-1.1971	10	0.52906	T	0.07	.	20.3437	0.98782	0.0:0.0:1.0:0.0	.	1064;991;1071;995	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	F	1071;995;1071;991;991	ENSP00000281537:S1071F;ENSP00000382890:S995F	ENSP00000281537:S1071F	S	-	2	0	TJP1	27798426	1.000000	0.71417	0.934000	0.37439	0.972000	0.66771	9.221000	0.95188	2.802000	0.96397	0.563000	0.77884	TCT		0.488	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30011134	G	A	30011134	3	1	47	1	0	0	0	0	1	0	0	0	15968	942	33	3	2066	3	TJP1	15	30011134	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1496727	30011134	72520258	1564	5961										
MTMR10	54893	broad.mit.edu	37	chr15	31269123	31269123	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgtctgttgcaatgcattTtctcacaaaattgacttcat	6	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:31269123T>G	ENST00000435680.1	-	3	254	c.157A>C	c.(157-159)Aaa>Caa	p.K53Q	MTMR10_ENST00000563714.1_5'UTR|MTMR10_ENST00000314404.8_5'Flank|MTMR10_ENST00000425768.1_Missense_Mutation_p.K53Q	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	53							phosphatase activity (GO:0016791)	p.K53Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		GCAATGCATTTTCTCACAAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	15											116	113	114					15																	31269123		1853	4080	5933	29056415	SO:0001583	missense	54893			AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.157A>C	15.37:g.31269123T>G	ENSP00000402537:p.Lys53Gln		29056415	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651481	0.88056	.	.	ENSG00000166912	ENST00000435680;ENST00000425768	D;D	0.82711	-1.64;-1.64	5.47	5.47	0.80525	.	.	.	.	.	D	0.90219	0.6942	M	0.71206	2.165	0.53688	D	0.999979	D	0.76494	0.999	D	0.80764	0.994	D	0.91168	0.4966	9	0.66056	D	0.02	.	15.559	0.76223	0.0:0.0:0.0:1.0	.	53	Q9NXD2	MTMRA_HUMAN	Q	53	ENSP00000402537:K53Q;ENSP00000412314:K53Q	ENSP00000412314:K53Q	K	-	1	0	MTMR10	29056415	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.621000	0.83083	2.080000	0.62538	0.533000	0.62120	AAA		0.353	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		G	31269123	T	G	31269123	3	3	47	1	0	0	0	0	1	0	0	0	9969	1850	64	4	2232	4	MTMR10	15	31269123	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1257989	31269123	71262269	1565	5962										
ARHGAP11A	9824	broad.mit.edu	37	chr15	32926204	32926204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaggttcgaagatctctgCgtttgaaattcaatctaggg	10	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:32926204C>T	ENST00000361627.3	+	10	2028	c.1306C>T	c.(1306-1308)Cgt>Tgt	p.R436C	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.R247C|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.R436C|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.R247C|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.R408C	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	436					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R436C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AAGATCTCTGCGTTTGAAATT	0.333																																					Colon(45;757 1134 30003 36652)											1	Substitution - Missense(1)	large_intestine(1)	15											38	37	37					15																	32926204		2201	4300	6501	30713496	SO:0001583	missense	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1306C>T	15.37:g.32926204C>T	ENSP00000355090:p.Arg436Cys		30713496	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	29.5	5.009399	0.93346	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	D;D	0.92495	-3.05;-3.05	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000009	D	0.96228	0.8770	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96254	0.9185	10	0.87932	D	0	.	19.7815	0.96417	0.0:1.0:0.0:0.0	.	436;247	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	C	436;247	ENSP00000355090:R436C;ENSP00000440073:R247C	ENSP00000355090:R436C	R	+	1	0	ARHGAP11A	30713496	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.387000	0.79785	2.746000	0.94184	0.655000	0.94253	CGT		0.333	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32926204	C	T	32926204	3	4	47	1	0	0	0	0	1	0	0	0	863	768	27	1	1344	1	ARHGAP11A	15	32926204	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1657081	32926204	69605188	1566	5963										
FMN1	342184	broad.mit.edu	37	chr15	33091014	33091014	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaaccttacctttctttaGatatgtttttactctcccgt	4	10	2	2	rs368124119		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:33091014G>T	ENST00000559047.1	-	16	4120	c.4121C>A	c.(4120-4122)tCt>tAt	p.S1374Y	FMN1_ENST00000334528.9_Missense_Mutation_p.S1151Y|FMN1_ENST00000561249.1_Missense_Mutation_p.S1276Y			Q68DA7	FMN1_HUMAN	formin 1	1374	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S1151Y(1)|p.S1374Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		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)		CCTTTCTTTAGATATGTTTTT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	15											122	109	113					15																	33091014		1831	4087	5918	30878306	SO:0001583	missense	342184			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4121C>A	15.37:g.33091014G>T	ENSP00000454047:p.Ser1374Tyr		30878306	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.187871	0.78789	.	.	ENSG00000248905	ENST00000334528	T	0.63580	-0.05	6.08	6.08	0.98989	.	0.051251	0.85682	D	0.000000	T	0.77458	0.4133	L	0.55481	1.735	.	.	.	D	0.76494	0.999	D	0.76575	0.988	T	0.75243	-0.3386	9	0.52906	T	0.07	.	20.6647	0.99678	0.0:0.0:1.0:0.0	.	1151	Q68DA7-5	.	Y	1151	ENSP00000333950:S1151Y	ENSP00000333950:S1151Y	S	-	2	0	FMN1	30878306	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.396000	0.97270	2.890000	0.99128	0.655000	0.94253	TCT		0.403	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		T	33091014	G	T	33091014	3	4	47	1	0	0	0	0	1	0	0	0	5968	942	33	2	150	2	FMN1	15	33091014	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	164810	33091014	69440378	1567	5964										
RYR3	6263	broad.mit.edu	37	chr15	33955111	33955111	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggaggctcctgtcaaaggcTtgttgcagactcgattaccc	11	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:33955111T>G	ENST00000389232.4	+	35	5450	c.5380T>G	c.(5380-5382)Ttg>Gtg	p.L1794V	RYR3_ENST00000415757.3_Missense_Mutation_p.L1794V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1794	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.L1794V(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTCAAAGGCTTGTTGCAGAC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	15											179	188	185					15																	33955111		2035	4199	6234	31742403	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5380T>G	15.37:g.33955111T>G	ENSP00000373884:p.Leu1794Val		31742403	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.377956	0.61735	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.74106	-0.59;-0.81	4.98	1.28	0.21552	.	0.000000	0.64402	D	0.000012	D	0.83422	0.5251	M	0.79614	2.46	0.45930	D	0.998765	D;D	0.76494	0.994;0.999	D;D	0.85130	0.954;0.997	T	0.82196	-0.0577	10	0.87932	D	0	.	9.756	0.40504	0.0:0.1652:0.0:0.8348	.	1794;1794	Q15413-2;Q15413	.;RYR3_HUMAN	V	1794	ENSP00000373884:L1794V;ENSP00000399610:L1794V	ENSP00000354735:L1794V	L	+	1	2	RYR3	31742403	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	2.989000	0.49393	0.113000	0.18004	0.460000	0.39030	TTG		0.537	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	33955111	T	G	33955111	3	3	47	1	0	0	0	0	1	0	0	0	13807	1606	56	4	5518	4	RYR3	15	33955111	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	864097	33955111	68576281	1568	5965										
RYR3	6263	broad.mit.edu	37	chr15	34047332	34047332	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgcctataagttcttgaaGaagatcctgaaatacgttga	8	6	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:34047332G>A	ENST00000389232.4	+	58	8536	c.8466G>A	c.(8464-8466)aaG>aaA	p.K2822K	RYR3_ENST00000415757.3_Silent_p.K2822K	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2822					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.K2822K(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGTTCTTGAAGAAGATCCTGA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	15											92	93	93					15																	34047332		1890	4115	6005	31834624	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.8466G>A	15.37:g.34047332G>A			31834624	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.398	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34047332	G	A	34047332	2	1	47	1	0	0	0	0	0	0	0	1	13807	933	33	3		3	RYR3	15	34047332	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	92221	34047332	68484060	1569	5966										
RYR3	6263	broad.mit.edu	37	chr15	34072478	34072478	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataccagtggcattcctggaGcccacccttaatcgctacaa	7	14	0	0	rs199647896		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:34072478G>A	ENST00000389232.4	+	65	9274	c.9204G>A	c.(9202-9204)gaG>gaA	p.E3068E	RYR3_ENST00000415757.3_Silent_p.E3068E	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3068					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.E3068E(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CATTCCTGGAGCCCACCCTTA	0.537													G|||	1	0.000199681	0	0	5008	,	,		19882	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											68	67	67					15																	34072478		1936	4150	6086	31859770	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.9204G>A	15.37:g.34072478G>A			31859770	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.537	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34072478	G	A	34072478	2	1	47	1	0	0	0	0	0	0	0	1	13807	962	34	3		3	RYR3	15	34072478	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	25146	34072478	68458914	1570	5967										
CHRM5	1133	broad.mit.edu	37	chr15	34355302	34355302	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggtgatcagttttgaccgTtacttttccatcacaagacc	7	11	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:34355302T>C	ENST00000383263.5	+	3	1054	c.384T>C	c.(382-384)cgT>cgC	p.R128R	CHRM5_ENST00000557872.1_Silent_p.R128R	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	128					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.R128R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GTTTTGACCGTTACTTTTCCA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	15											107	97	100					15																	34355302		2201	4298	6499	32142594	SO:0001819	synonymous_variant	1133				CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.384T>C	15.37:g.34355302T>C			32142594	Q96RG7	Silent	SNP	ENST00000383263.5	37	CCDS10031.1																																																																																				0.532	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			C	34355302	T	C	34355302	2	2	47	1	0	0	0	0	0	0	0	1	3386	1712	60	4		4	CHRM5	15	34355302	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	282824	34355302	68176090	1571	5968										
SLC12A6	9990	broad.mit.edu	37	chr15	34547474	34547474	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attacttaccagaaagatttCaatggcaccaaggatgtaca	7	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:34547474C>A	ENST00000354181.3	-	8	1357	c.865G>T	c.(865-867)Gaa>Taa	p.E289*	SLC12A6_ENST00000458406.2_Nonsense_Mutation_p.E230*|SLC12A6_ENST00000397707.2_Nonsense_Mutation_p.E274*|SLC12A6_ENST00000560611.1_Nonsense_Mutation_p.E289*|SLC12A6_ENST00000558589.1_Nonsense_Mutation_p.E280*|SLC12A6_ENST00000397702.2_Nonsense_Mutation_p.E230*|SLC12A6_ENST00000558667.1_Nonsense_Mutation_p.E289*|SLC12A6_ENST00000451844.2_Nonsense_Mutation_p.E101*|SLC12A6_ENST00000560164.1_Nonsense_Mutation_p.E101*|SLC12A6_ENST00000290209.5_Nonsense_Mutation_p.E238*|RP11-1084A12.2_ENST00000559867.1_RNA			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	289					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)	p.E238*(1)		central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	AGAAAGATTTCAATGGCACCA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											120	129	126					15																	34547474		2201	4298	6499	32334766	SO:0001587	stop_gained	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.865G>T	15.37:g.34547474C>A	ENSP00000346112:p.Glu289*		32334766	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Nonsense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	40	8.206929	0.98706	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.7742	0.88502	0.0:1.0:0.0:0.0	.	.	.	.	X	238;274;280;230;230;101	.	ENSP00000290209:E238X	E	-	1	0	SLC12A6	32334766	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.651000	0.83577	2.724000	0.93272	0.655000	0.94253	GAA		0.423	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		A	34547474	C	A	34547474	4	1	47	1	0	0	0	0	0	1	0	0	14424	835	29	2	2663	2	SLC12A6	15	34547474	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	192172	34547474	67983918	1572	5969										
ZNF770	54989	broad.mit.edu	37	chr15	35274903	35274903	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctttaataaaagagcccGaaaagccttattcctagtat	5	9	1	1	rs35764015		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:35274903G>A	ENST00000356321.4	-	3	1077	c.733C>T	c.(733-735)Cgg>Tgg	p.R245W		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	245					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R245W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		AAAAGAGCCCGAAAAGCCTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											42	44	43					15																	35274903		2201	4297	6498	33062195	SO:0001583	missense	54989			BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"Zinc fingers, C2H2-type"	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.733C>T	15.37:g.35274903G>A	ENSP00000348673:p.Arg245Trp		33062195	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	G	7.312	0.615163	0.14129	.	.	ENSG00000198146	ENST00000356321	T	0.10099	2.91	4.84	4.84	0.62591	.	0.701798	0.12987	N	0.422767	T	0.06554	0.0168	N	0.08118	0	0.23704	N	0.997067	P	0.51653	0.947	B	0.40534	0.332	T	0.23226	-1.0194	10	0.87932	D	0	-0.0257	11.2661	0.49112	0.1312:0.0:0.8688:0.0	.	245	Q6IQ21	ZN770_HUMAN	W	245	ENSP00000348673:R245W	ENSP00000348673:R245W	R	-	1	2	ZNF770	33062195	1.000000	0.71417	1.000000	0.80357	0.148000	0.21650	2.094000	0.41719	2.501000	0.84356	0.555000	0.69702	CGG		0.363	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		A	35274903	G	A	35274903	3	1	47	1	0	0	0	0	1	0	0	0	18182	1057	37	1	1346	1	ZNF770	15	35274903	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	727429	35274903	67256489	1573	5970										
ZNF770	54989	broad.mit.edu	37	chr15	35275374	35275374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcagatttttaaagtgacGctgacaaatactacatttaa	5	7	1	3	rs144467698		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:35275374G>A	ENST00000356321.4	-	3	606	c.262C>T	c.(262-264)Cgt>Tgt	p.R88C		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	88					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R88C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		TTAAAGTGACGCTGACAAATA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	CYS/ARG	0,4402		0,0,2201	84	86	85		262	4.9	1	15	dbSNP_134	85	2,8594	2.2+/-6.3	0,2,4296	no	missense	ZNF770	NM_014106.3	180	0,2,6497	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	88/692	35275374	2,12996	2201	4298	6499	33062666	SO:0001583	missense	54989			BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"Zinc fingers, C2H2-type"	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.262C>T	15.37:g.35275374G>A	ENSP00000348673:p.Arg88Cys		33062666	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204647	0.38905	0.0	2.33E-4	ENSG00000198146	ENST00000356321	T	0.16324	2.35	4.86	4.86	0.63082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.184142	0.36519	N	0.002549	T	0.34716	0.0907	L	0.55743	1.74	0.39240	D	0.963832	D	0.89917	1.0	D	0.68192	0.956	T	0.10706	-1.0618	10	0.87932	D	0	-3.1095	12.7821	0.57483	0.0:0.0:0.8252:0.1748	.	88	Q6IQ21	ZN770_HUMAN	C	88	ENSP00000348673:R88C	ENSP00000348673:R88C	R	-	1	0	ZNF770	33062666	0.987000	0.35691	1.000000	0.80357	0.976000	0.68499	3.100000	0.50275	2.515000	0.84797	0.655000	0.94253	CGT		0.363	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		A	35275374	G	A	35275374	3	1	47	1	0	0	0	0	1	0	0	0	18182	1087	38	1	1817	1	ZNF770	15	35275374	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	471	35275374	67256018	1574	5971										
C15orf41	84529	broad.mit.edu	37	chr15	36950045	36950045	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttataaaggtggactatgcGccctcattaatggctcggct	10	9	1	0	rs372337437		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:36950045G>A	ENST00000566621.1	+	5	535	c.285G>A	c.(283-285)gcG>gcA	p.A95A	C15orf41_ENST00000437989.2_Silent_p.A95A|C15orf41_ENST00000569302.1_Silent_p.A95A|C15orf41_ENST00000338183.4_5'UTR|C15orf41_ENST00000567389.1_5'UTR|C15orf41_ENST00000562877.1_5'UTR|RP11-16L14.2_ENST00000565366.1_RNA	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	95								p.A95A(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TGGACTATGCGCCCTCATTAA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	15						G	,	0,3678		0,0,1839	67	63	64		285,	1.8	1	15		64	1,8159		0,1,4079	no	coding-synonymous,utr-5	C15orf41	NM_001130010.1,NM_032499.4	,	0,1,5918	AA,AG,GG		0.0123,0.0,0.0084	,	95/282,	36950045	1,11837	1839	4080	5919	34737337	SO:0001819	synonymous_variant	84529			BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.285G>A	15.37:g.36950045G>A			34737337	B2RD87	Silent	SNP	ENST00000566621.1	37	CCDS45215.1																																																																																				0.403	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		A	36950045	G	A	36950045	2	1	47	1	0	0	0	0	0	0	0	1	1799	1074	38	1		1	C15orf41	15	36950045	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1674671	36950045	65581347	1575	5972										
MEIS2	4212	broad.mit.edu	37	chr15	37188835	37188835	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacttggaacttgcctgctcGatttgactggtcaatcatgg	10	9	2	1	rs367563077		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:37188835G>A	ENST00000561208.1	-	10	1448	c.1030C>T	c.(1030-1032)Cga>Tga	p.R344*	MEIS2_ENST00000340545.5_Nonsense_Mutation_p.R331*|MEIS2_ENST00000397624.3_Nonsense_Mutation_p.R256*|MEIS2_ENST00000338564.5_Nonsense_Mutation_p.R344*|MEIS2_ENST00000424352.2_Nonsense_Mutation_p.R344*|MEIS2_ENST00000444725.1_Nonsense_Mutation_p.R344*|MEIS2_ENST00000559561.1_Nonsense_Mutation_p.R344*|MEIS2_ENST00000559408.1_5'UTR|MEIS2_ENST00000219869.9_Nonsense_Mutation_p.R198*|MEIS2_ENST00000557796.2_Nonsense_Mutation_p.R331*|MEIS2_ENST00000559085.1_Nonsense_Mutation_p.R331*|MEIS2_ENST00000397620.2_Nonsense_Mutation_p.R256*|MEIS2_ENST00000382766.2_Nonsense_Mutation_p.R344*			O14770	MEIS2_HUMAN	Meis homeobox 2	344	Transcriptional activation domain.				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R344*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TTGCCTGCTCGATTTGACTGG	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	15											179	154	163					15																	37188835		2201	4297	6498	34976127	SO:0001587	stop_gained	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.1030C>T	15.37:g.37188835G>A	ENSP00000453793:p.Arg344*		34976127	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Nonsense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	G	40	8.199426	0.98701	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.3478	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	X	344;344;344;344;344;331;331;256;198	.	ENSP00000219869:R198X	R	-	1	2	MEIS2	34976127	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.807000	0.99171	2.937000	0.99478	0.650000	0.86243	CGA		0.398	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		A	37188835	G	A	37188835	4	1	47	1	0	0	0	0	0	1	0	0	9498	1066	37	1	478	1	MEIS2	15	37188835	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	238790	37188835	65342557	1576	5973										
FAM98B	283742	broad.mit.edu	37	chr15	38765780	38765780	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaatggatttaaattcagaAcaggcggtaaatcccccttt	7	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:38765780A>G	ENST00000491535.1	+	5	614	c.606A>G	c.(604-606)gaA>gaG	p.E202E	FAM98B_ENST00000397609.2_Silent_p.E202E	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	202						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)	p.E202E(2)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		TAAATTCAGAACAGGCGGTAA	0.289																																																2	Substitution - coding silent(2)	large_intestine(2)	15											39	40	40					15																	38765780		2200	4289	6489	36553072	SO:0001819	synonymous_variant	283742				CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.606A>G	15.37:g.38765780A>G			36553072	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	37	CCDS42015.1																																																																																				0.289	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		G	38765780	A	G	38765780	2	3	47	1	0	0	0	0	0	0	0	1	5676	40	2	4		4	FAM98B	15	38765780	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1576945	38765780	63765612	1577	5974										
FSIP1	161835	broad.mit.edu	37	chr15	39910011	39910011	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctcacactgataccatacaGtggatcatctaagaaggagg	10	9	3	2	rs545023586		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:39910011G>C	ENST00000350221.3	-	11	1833	c.1624C>G	c.(1624-1626)Ctg>Gtg	p.L542V		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	542								p.L542V(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ATACCATACAGTGGATCATCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											105	99	101					15																	39910011		2200	4297	6497	37697303	SO:0001583	missense	161835			BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1624C>G	15.37:g.39910011G>C	ENSP00000280236:p.Leu542Val		37697303	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	G	8.853	0.945061	0.18356	.	.	ENSG00000150667	ENST00000350221	T	0.27557	1.66	4.84	0.832	0.18867	.	0.111141	0.33610	N	0.004722	T	0.17408	0.0418	L	0.32530	0.975	0.26343	N	0.97734	P	0.36144	0.539	B	0.36134	0.218	T	0.08126	-1.0737	9	.	.	.	-4.5846	3.4231	0.07401	0.3901:0.1988:0.4111:0.0	.	542	Q8NA03	FSIP1_HUMAN	V	542	ENSP00000280236:L542V	.	L	-	1	2	FSIP1	37697303	0.995000	0.38212	0.934000	0.37439	0.081000	0.17604	1.512000	0.35812	0.334000	0.23590	0.591000	0.81541	CTG		0.413	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		C	39910011	G	C	39910011	3	2	47	1	0	0	0	0	1	0	0	0	6093	1020	36	5	129	5	FSIP1	15	39910011	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1144231	39910011	62621381	1578	5975										
BUB1B	701	broad.mit.edu	37	chr15	40488874	40488874	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaggagaagaaagagaagaTgatgtattgtaaggagaaga	15	0	0	8			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:40488874T>G	ENST00000287598.6	+	9	1382	c.1187T>G	c.(1186-1188)aTg>aGg	p.M396R	BUB1B_ENST00000412359.3_Missense_Mutation_p.M410R	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	396					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.M396R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		AAAGAGAAGATGATGTATTGT	0.433			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																													yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	1	Substitution - Missense(1)	large_intestine(1)	15											107	107	107					15																	40488874		2203	4300	6503	38276166	SO:0001583	missense	701	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"budding uninhibited by benzimidazoles 1 (yeast homolog), beta", "budding uninhibited by benzimidazoles 1 homolog beta (yeast)"			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.1187T>G	15.37:g.40488874T>G	ENSP00000287598:p.Met396Arg		38276166	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.688756	0.48097	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.14391	2.51;2.51	5.58	5.58	0.84498	.	0.283163	0.35378	N	0.003243	T	0.13114	0.0318	L	0.54323	1.7	0.30894	N	0.729994	B;P	0.34412	0.446;0.453	B;B	0.33750	0.169;0.081	T	0.08186	-1.0734	10	0.12430	T	0.62	-3.4531	10.88	0.46933	0.0:0.0733:0.0:0.9267	.	410;396	O60566-3;O60566	.;BUB1B_HUMAN	R	396;410;342	ENSP00000287598:M396R;ENSP00000398470:M410R	ENSP00000287598:M396R	M	+	2	0	BUB1B	38276166	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.095000	0.41729	2.123000	0.65237	0.459000	0.35465	ATG		0.433	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			G	40488874	T	G	40488874	3	3	47	1	0	0	0	0	1	0	0	0	1574	1464	51	4	1221	4	BUB1B	15	40488874	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	578863	40488874	62042518	1579	5976										
DISP2	85455	broad.mit.edu	37	chr15	40662302	40662302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggcagccagtccttgagcGaggccagctcaatgggaagc	15	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:40662302G>A	ENST00000267889.3	+	8	4076	c.3989G>A	c.(3988-3990)cGa>cAa	p.R1330Q	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	1330					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.R1330Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GTCCTTGAGCGAGGCCAGCTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	15											85	87	87					15																	40662302		2203	4300	6503	38449594	SO:0001583	missense	85455			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.3989G>A	15.37:g.40662302G>A	ENSP00000267889:p.Arg1330Gln		38449594	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663553	0.88251	.	.	ENSG00000140323	ENST00000267889	T	0.13657	2.57	5.2	5.2	0.72013	.	0.057426	0.64402	D	0.000002	T	0.26484	0.0647	L	0.29908	0.895	0.36384	D	0.862117	D	0.89917	1.0	D	0.65233	0.933	T	0.06917	-1.0800	10	0.56958	D	0.05	-34.4487	18.9211	0.92525	0.0:0.0:1.0:0.0	.	1330	A7MBM2	DISP2_HUMAN	Q	1330	ENSP00000267889:R1330Q	ENSP00000267889:R1330Q	R	+	2	0	DISP2	38449594	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.178000	0.50879	2.706000	0.92434	0.561000	0.74099	CGA		0.612	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		A	40662302	G	A	40662302	3	1	47	1	0	0	0	0	1	0	0	0	4551	1058	37	1	4019	1	DISP2	15	40662302	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	173428	40662302	61869090	1580	5977										
C15orf23	90417	broad.mit.edu	37	chr15	40685748	40685748	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttatgtaacaatcaagtaAatgatttaacaacagccctt	4	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:40685748A>C	ENST00000249776.8	+	9	1016	c.901A>C	c.(901-903)Aat>Cat	p.N301H	KNSTRN_ENST00000448395.2_3'UTR|KNSTRN_ENST00000416151.2_3'UTR|KNSTRN_ENST00000608100.1_Missense_Mutation_p.N223H	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein									p.N301H(1)									CAATCAAGTAAATGATTTAAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											125	113	117					15																	40685748		1888	4105	5993	38473040	SO:0001583	missense	90417			AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.901A>C	15.37:g.40685748A>C	ENSP00000249776:p.Asn301His		38473040		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.002088	0.35320	.	.	ENSG00000128944	ENST00000249776	T	0.26067	1.76	5.02	2.72	0.32119	.	0.758999	0.12750	N	0.442280	T	0.15522	0.0374	N	0.24115	0.695	0.24200	N	0.995513	B	0.14012	0.009	B	0.14023	0.01	T	0.17379	-1.0371	10	0.52906	T	0.07	-4.3806	4.7744	0.13171	0.7111:0.193:0.0959:0.0	.	301	Q9Y448	T4AF1_HUMAN	H	301	ENSP00000249776:N301H	ENSP00000249776:N301H	N	+	1	0	C15orf23	38473040	0.996000	0.38824	0.552000	0.28243	0.245000	0.25701	1.857000	0.39399	1.023000	0.39654	0.529000	0.55759	AAT		0.413	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		C	40685748	A	C	40685748	3	2	47	1	0	0	0	0	1	0	0	0	1789	14	1	4	978	4	C15orf23	15	40685748	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	23446	40685748	61845644	1581	5978										
C15orf57	90416	broad.mit.edu	37	chr15	40849512	40849512	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggcttgggccagagttcGaagcatgtccttggaagtca	13	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:40849512G>A	ENST00000358005.3	-	3	577	c.304C>T	c.(304-306)Cga>Tga	p.R102*	RP11-111A22.1_ENST00000561460.1_RNA|C15orf57_ENST00000559911.1_Nonsense_Mutation_p.R102*|C15orf57_ENST00000558871.1_Nonsense_Mutation_p.R102*|C15orf57_ENST00000560305.1_Nonsense_Mutation_p.R102*|C15orf57_ENST00000561011.1_Nonsense_Mutation_p.R102*|C15orf57_ENST00000558750.1_Nonsense_Mutation_p.R111*|C15orf57_ENST00000558113.1_Nonsense_Mutation_p.R102*|C15orf57_ENST00000416810.2_Nonsense_Mutation_p.R102*	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	102								p.R102*(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						GCCAGAGTTCGAAGCATGTCC	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											159	140	146					15																	40849512		2203	4300	6503	38636804	SO:0001587	stop_gained	90416			BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"coiled-coil domain containing 32"	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.304C>T	15.37:g.40849512G>A	ENSP00000350695:p.Arg102*		38636804	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Nonsense_Mutation	SNP	ENST00000358005.3	37	CCDS10060.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856286	0.91355	.	.	ENSG00000128891	ENST00000358005;ENST00000416810	.	.	.	5.7	5.7	0.88788	.	0.132361	0.51477	D	0.000084	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2111	19.8354	0.96655	0.0:0.0:1.0:0.0	.	.	.	.	X	102;111	.	ENSP00000350695:R102X	R	-	1	2	C15orf57	38636804	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.952000	0.75989	2.686000	0.91538	0.555000	0.69702	CGA		0.438	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849		A	40849512	G	A	40849512	4	1	47	1	0	0	0	0	0	1	0	0	1809	1066	37	1	261	1	C15orf57	15	40849512	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	163764	40849512	61681880	1582	5979										
CASC5	57082	broad.mit.edu	37	chr15	40914005	40914005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagcagctgcaccaacacccGaaaaagaaatgatgctccaa	7	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:40914005G>A	ENST00000346991.5	+	11	2011	c.1621G>A	c.(1621-1623)Gaa>Aaa	p.E541K	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Missense_Mutation_p.E515K			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	541	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.E541K(2)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ACCAACACCCGAAAAAGAAAT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	15											63	60	61					15																	40914005		1886	4115	6001	38701297	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1621G>A	15.37:g.40914005G>A	ENSP00000335463:p.Glu541Lys		38701297	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.203917	0.38905	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.15139	2.45;2.45	5.21	3.34	0.38264	.	0.361802	0.23795	N	0.044482	T	0.16471	0.0396	M	0.73962	2.25	0.26653	N	0.972067	P;P;P	0.46578	0.88;0.74;0.868	B;B;B	0.34180	0.177;0.127;0.127	T	0.16247	-1.0409	10	0.38643	T	0.18	.	9.3359	0.38049	0.1733:0.0:0.8267:0.0	.	515;541;515	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	K	541;515;515	ENSP00000335463:E541K;ENSP00000382576:E515K	ENSP00000260369:E515K	E	+	1	0	CASC5	38701297	.	.	0.998000	0.56505	0.355000	0.29361	.	.	0.772000	0.33382	0.557000	0.71058	GAA		0.348	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		A	40914005	G	A	40914005	3	1	47	1	0	0	0	0	1	0	0	0	2669	1059	37	1	1659	1	CASC5	15	40914005	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	64493	40914005	61617387	1583	5980										
SPTBN5	51332	broad.mit.edu	37	chr15	42147124	42147124	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggcatacaccttggcctgGcccaggctctgcacttcctt	10	15	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:42147124G>T	ENST00000320955.6	-	56	9701	c.9474C>A	c.(9472-9474)ggC>ggA	p.G3158G	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3158					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.G3158G(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCTTGGCCTGGCCCAGGCTCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	15											60	62	62					15																	42147124		1939	4136	6075	39934416	SO:0001819	synonymous_variant	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9474C>A	15.37:g.42147124G>T			39934416		Silent	SNP	ENST00000320955.6	37																																																																																					0.582	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		T	42147124	G	T	42147124	2	4	47	1	0	0	0	0	0	0	0	1	15161	1190	42	2		2	SPTBN5	15	42147124	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1233119	42147124	60384268	1584	5981										
VPS39	23339	broad.mit.edu	37	chr15	42479509	42479509	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttgaaacccacacagataGaattttcacaccacgccatg	5	13	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:42479509G>T	ENST00000348544.4	-	8	526	c.527C>A	c.(526-528)tCt>tAt	p.S176Y	VPS39_ENST00000318006.5_Missense_Mutation_p.S165Y			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	176	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)	p.S165Y(1)		breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CACACAGATAGAATTTTCACA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	15											83	81	82					15																	42479509		2203	4299	6502	40266801	SO:0001583	missense	23339			AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.527C>A	15.37:g.42479509G>T	ENSP00000335193:p.Ser176Tyr		40266801	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	ENST00000348544.4	37	CCDS10083.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293281	0.80914	.	.	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.14640	2.49;2.49	5.95	5.95	0.96441	Citron-like (2);	0.000000	0.85682	D	0.000000	T	0.15825	0.0381	L	0.49640	1.575	0.80722	D	1	P;B	0.37423	0.594;0.287	B;B	0.38921	0.285;0.188	T	0.02766	-1.1113	10	0.02654	T	1	-9.4469	20.3931	0.98965	0.0:0.0:1.0:0.0	.	176;165	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	Y	165;176	ENSP00000326534:S165Y;ENSP00000335193:S176Y	ENSP00000326534:S165Y	S	-	2	0	VPS39	40266801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	2.824000	0.97209	0.655000	0.94253	TCT		0.353	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		T	42479509	G	T	42479509	3	4	47	1	0	0	0	0	1	0	0	0	17249	942	33	2	2209	2	VPS39	15	42479509	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	332385	42479509	60051883	1585	5982										
CDAN1	146059	broad.mit.edu	37	chr15	43021279	43021279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacgaactctacggtccggcGcaaggagggcggctggttgt	16	11	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:43021279G>A	ENST00000356231.3	-	19	2610	c.2587C>T	c.(2587-2589)Cgc>Tgc	p.R863C		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	863					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R863C(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		ACGGTCCGGCGCAAGGAGGGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	90	90					15																	43021279		2203	4299	6502	40808571	SO:0001583	missense	146059			AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2587C>T	15.37:g.43021279G>A	ENSP00000348564:p.Arg863Cys		40808571	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475578	0.84640	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.84660	-1.88	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.92825	0.7718	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.978	D	0.93715	0.7027	10	0.87932	D	0	-13.6731	18.6595	0.91468	0.0:0.0:1.0:0.0	.	863;861	Q8IWY9;C9K0H8	CDAN1_HUMAN;.	C	863;861	ENSP00000348564:R863C	ENSP00000267892:R861C	R	-	1	0	CDAN1	40808571	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.254000	0.78329	2.404000	0.81709	0.462000	0.41574	CGC		0.582	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		A	43021279	G	A	43021279	3	1	47	1	0	0	0	0	1	0	0	0	3060	1087	38	1	1136	1	CDAN1	15	43021279	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	541770	43021279	59510113	1586	5983										
TMEM62	80021	broad.mit.edu	37	chr15	43426537	43426537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgttctgaaactattgacaTcattcaaccagctctcgtcc	5	13	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:43426537T>A	ENST00000260403.2	+	2	542	c.263T>A	c.(262-264)aTc>aAc	p.I88N		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	88						integral component of membrane (GO:0016021)		p.I88N(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		ACTATTGACATCATTCAACCA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											108	91	97					15																	43426537		2203	4299	6502	41213829	SO:0001583	missense	80021			BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.263T>A	15.37:g.43426537T>A	ENSP00000260403:p.Ile88Asn		41213829	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	37	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145049	0.77888	.	.	ENSG00000137842	ENST00000260403	T	0.53423	0.62	4.97	3.85	0.44370	.	0.251403	0.41194	D	0.000935	T	0.56426	0.1984	L	0.59436	1.845	0.39965	D	0.974713	D	0.67145	0.996	P	0.61201	0.885	T	0.54774	-0.8243	10	0.30854	T	0.27	-3.0947	9.067	0.36469	0.0:0.0843:0.0:0.9157	.	88	Q0P6H9	TMM62_HUMAN	N	88	ENSP00000260403:I88N	ENSP00000260403:I88N	I	+	2	0	TMEM62	41213829	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.372000	0.52387	0.915000	0.36847	-0.256000	0.11100	ATC		0.512	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		A	43426537	T	A	43426537	3	1	47	1	0	0	0	0	1	0	0	0	16228	1435	50	5	269	5	TMEM62	15	43426537	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	405258	43426537	59104855	1587	5984										
TGM5	9333	broad.mit.edu	37	chr15	43544999	43544999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacccagcattgcccgtagcGcacgggctggcagcctgtgg	15	14	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:43544999G>A	ENST00000220420.5	-	6	827	c.820C>T	c.(820-822)Cgc>Tgc	p.R274C	TGM5_ENST00000349114.4_Missense_Mutation_p.R192C	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	274					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R274C(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	TGCCCGTAGCGCACGGGCTGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	73	74					15																	43544999		2202	4299	6501	41332291	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.820C>T	15.37:g.43544999G>A	ENSP00000220420:p.Arg274Cys		41332291	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334291	0.41297	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.57595	0.39;0.39	4.88	1.2	0.21068	Transglutaminase-like (2);	0.146541	0.40064	N	0.001190	T	0.58538	0.2129	L	0.53729	1.69	0.40067	D	0.975968	D;D	0.89917	1.0;0.997	D;P	0.64042	0.921;0.873	T	0.58901	-0.7554	10	0.87932	D	0	-8.2033	5.8747	0.18822	0.098:0.0:0.4086:0.4934	.	192;274	O43548-2;O43548	.;TGM5_HUMAN	C	274;192;273	ENSP00000220420:R274C;ENSP00000220419:R192C	ENSP00000220420:R274C	R	-	1	0	TGM5	41332291	0.043000	0.20138	0.927000	0.36925	0.057000	0.15508	1.149000	0.31626	0.525000	0.28522	0.655000	0.94253	CGC		0.582	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		A	43544999	G	A	43544999	3	1	47	1	0	0	0	0	1	0	0	0	15872	1087	38	1	1374	1	TGM5	15	43544999	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	118462	43544999	58986393	1588	5985										
TP53BP1	7158	broad.mit.edu	37	chr15	43739654	43739654	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtgggatgatatcaccttCtttaggcaaagtgaaatgaa	11	5	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:43739654C>A	ENST00000263801.3	-	13	2983	c.2731G>T	c.(2731-2733)Gaa>Taa	p.E911*	TP53BP1_ENST00000450115.2_Nonsense_Mutation_p.E916*|TP53BP1_ENST00000382044.4_Nonsense_Mutation_p.E916*|TP53BP1_ENST00000382039.3_Nonsense_Mutation_p.E916*|TP53BP1_ENST00000605155.1_5'UTR	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	911					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.E911*(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		ATATCACCTTCTTTAGGCAAA	0.338								Other conserved DNA damage response genes																																								1	Substitution - Nonsense(1)	large_intestine(1)	15											90	87	88					15																	43739654		2201	4298	6499	41526946	SO:0001587	stop_gained	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2731G>T	15.37:g.43739654C>A	ENSP00000263801:p.Glu911*		41526946	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Nonsense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	41	9.099759	0.99066	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000414758	.	.	.	5.67	5.67	0.87782	.	0.059803	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-9.7871	19.1149	0.93334	0.0:1.0:0.0:0.0	.	.	.	.	X	911;916;916;916;55	.	ENSP00000263801:E911X	E	-	1	0	TP53BP1	41526946	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.377000	0.59562	2.834000	0.97654	0.650000	0.86243	GAA		0.338	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43739654	C	A	43739654	4	1	47	1	0	0	0	0	0	1	0	0	16423	922	32	2	3251	2	TP53BP1	15	43739654	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	194655	43739654	58791738	1589	5986										
TP53BP1	7158	broad.mit.edu	37	chr15	43769884	43769884	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtccactttccataagttCttgtgcagacaactgttctt	6	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:43769884C>A	ENST00000263801.3	-	8	1099	c.847G>T	c.(847-849)Gaa>Taa	p.E283*	TP53BP1_ENST00000450115.2_Nonsense_Mutation_p.E288*|TP53BP1_ENST00000382044.4_Nonsense_Mutation_p.E288*|TP53BP1_ENST00000382039.3_Nonsense_Mutation_p.E288*	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	283					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.E283*(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		TCCATAAGTTCTTGTGCAGAC	0.438								Other conserved DNA damage response genes																																								1	Substitution - Nonsense(1)	large_intestine(1)	15											136	131	133					15																	43769884		2201	4298	6499	41557176	SO:0001587	stop_gained	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.847G>T	15.37:g.43769884C>A	ENSP00000263801:p.Glu283*		41557176	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Nonsense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018456	0.54576	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	.	.	.	5.52	5.52	0.82312	.	0.332110	0.29133	N	0.013046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-7.1274	14.9409	0.70992	0.0:1.0:0.0:0.0	.	.	.	.	X	283;288;288;288;288	.	ENSP00000263801:E283X	E	-	1	0	TP53BP1	41557176	0.056000	0.20664	0.162000	0.22713	0.027000	0.11550	1.875000	0.39578	2.588000	0.87417	0.555000	0.69702	GAA		0.438	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43769884	C	A	43769884	4	1	47	1	0	0	0	0	0	1	0	0	16423	922	32	2	5155	2	TP53BP1	15	43769884	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	30230	43769884	58761508	1590	5987										
ELL3	80237	broad.mit.edu	37	chr15	44066403	44066403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtattctggagttcctcgccGaactcttttaatctctgctc	7	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:44066403G>A	ENST00000319359.3	-	9	1656	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	SERF2_ENST00000381359.1_5'Flank|ELL3_ENST00000497465.1_5'UTR|RP11-296A16.1_ENST00000417761.2_3'UTR	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	339					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)	p.R339W(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		GTTCCTCGCCGAACTCTTTTA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	15											92	88	89					15																	44066403		2198	4298	6496	41853695	SO:0001583	missense	80237			AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.1015C>T	15.37:g.44066403G>A	ENSP00000320346:p.Arg339Trp		41853695	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Missense_Mutation	SNP	ENST00000319359.3	37	CCDS10102.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099927	0.56183	.	.	ENSG00000128886	ENST00000319359	T	0.23552	1.9	5.92	5.92	0.95590	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.104977	0.42821	D	0.000652	T	0.19446	0.0467	L	0.32530	0.975	0.31231	N	0.696298	P;P;P	0.37781	0.608;0.608;0.608	B;B;B	0.21917	0.037;0.037;0.037	T	0.16188	-1.0411	10	0.62326	D	0.03	-19.7297	17.8105	0.88614	0.0:0.0:1.0:0.0	.	339;339;293	B3KX08;Q9HB65;B3KQ66	.;ELL3_HUMAN;.	W	339	ENSP00000320346:R339W	ENSP00000320346:R339W	R	-	1	2	ELL3	41853695	0.039000	0.19947	1.000000	0.80357	0.509000	0.34042	1.206000	0.32321	2.809000	0.96659	0.557000	0.71058	CGG		0.507	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165		A	44066403	G	A	44066403	3	1	47	1	0	0	0	0	1	0	0	0	5077	1057	37	1	190	1	ELL3	15	44066403	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	296519	44066403	58464989	1591	5988										
EIF3J	8669	broad.mit.edu	37	chr15	44843634	44843634	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttttttacttttagaggtaAaaatttcagaaaagaaaaaa	5	2	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:44843634A>C	ENST00000535391.1	+	4	220	c.208A>C	c.(208-210)Aaa>Caa	p.K70Q	EIF3J_ENST00000261868.5_Missense_Mutation_p.K70Q|EIF3J_ENST00000424492.3_Intron					eukaryotic translation initiation factor 3, subunit J									p.K70Q(1)		endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		TTTAGAGGTAAAAATTTCaga	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	15											20	23	22					15																	44843634		2172	4258	6430	42630926	SO:0001583	missense	8669			U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000535391.1:c.208A>C	15.37:g.44843634A>C	ENSP00000440221:p.Lys70Gln		42630926		Missense_Mutation	SNP	ENST00000535391.1	37		.	.	.	.	.	.	.	.	.	.	A	13.49	2.252453	0.39797	.	.	ENSG00000104131	ENST00000261868;ENST00000535391	T;T	0.49432	0.78;0.78	5.24	5.24	0.73138	.	0.044146	0.85682	D	0.000000	T	0.58250	0.2109	L	0.50993	1.605	0.35264	D	0.779887	D;D	0.62365	0.991;0.991	D;D	0.76071	0.987;0.987	T	0.61700	-0.7009	10	0.17369	T	0.5	.	11.4555	0.50179	1.0:0.0:0.0:0.0	.	70;70	B4DUI3;O75822	.;EIF3J_HUMAN	Q	70	ENSP00000261868:K70Q;ENSP00000440221:K70Q	ENSP00000261868:K70Q	K	+	1	0	EIF3J	42630926	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.007000	0.57093	2.192000	0.70111	0.533000	0.62120	AAA		0.284	EIF3J-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396804.1	NM_003758		C	44843634	A	C	44843634	3	2	47	1	0	0	0	0	1	0	0	0	5033	15	1	4	222	4	EIF3J	15	44843634	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	777231	44843634	57687758	1592	5989										
SPG11	80208	broad.mit.edu	37	chr15	44890503	44890503	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgctgttccatgtaccttCttctaagagaacaagcaatt	6	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:44890503C>A	ENST00000261866.7	-	23	3977	c.3961G>T	c.(3961-3963)Gaa>Taa	p.E1321*	SPG11_ENST00000427534.2_Nonsense_Mutation_p.E1321*|SPG11_ENST00000535302.2_Nonsense_Mutation_p.E1321*|SPG11_ENST00000558319.1_Nonsense_Mutation_p.E1321*	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1321					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.E1321*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		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)		CATGTACCTTCTTCTAAGAGA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											143	125	131					15																	44890503		2198	4298	6496	42677795	SO:0001587	stop_gained	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3961G>T	15.37:g.44890503C>A	ENSP00000261866:p.Glu1321*		42677795	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Nonsense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	C	42	9.261395	0.99117	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	.	.	.	5.77	5.77	0.91146	.	0.059293	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	17.1387	0.86747	0.0:1.0:0.0:0.0	.	.	.	.	X	1321	.	ENSP00000261866:E1321X	E	-	1	0	SPG11	42677795	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	5.034000	0.64152	2.728000	0.93425	0.655000	0.94253	GAA		0.378	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			A	44890503	C	A	44890503	4	1	47	1	0	0	0	0	0	1	0	0	15080	922	32	2	3442	2	SPG11	15	44890503	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	46869	44890503	57640889	1593	5990										
SPG11	80208	broad.mit.edu	37	chr15	44925797	44925797	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttccttgctcttcaaaaaGaaatttactgtgtccagctg	6	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:44925797G>T	ENST00000261866.7	-	8	1657	c.1641C>A	c.(1639-1641)ttC>ttA	p.F547L	SPG11_ENST00000427534.2_Missense_Mutation_p.F547L|SPG11_ENST00000535302.2_Missense_Mutation_p.F547L|SPG11_ENST00000558319.1_Missense_Mutation_p.F547L|SPG11_ENST00000559193.1_Missense_Mutation_p.F547L	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	547					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.F547L(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		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)		TCTTCAAAAAGAAATTTACTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	15											56	59	58					15																	44925797		2198	4298	6496	42713089	SO:0001583	missense	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1641C>A	15.37:g.44925797G>T	ENSP00000261866:p.Phe547Leu		42713089	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821504	0.50633	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.79554	-1.28;-1.04;-1.02	5.28	4.36	0.52297	.	0.063403	0.64402	D	0.000005	T	0.72479	0.3465	L	0.52126	1.63	0.40127	D	0.976679	B;P;B;B	0.45474	0.414;0.859;0.347;0.244	B;B;B;B	0.43728	0.188;0.429;0.111;0.141	T	0.67937	-0.5541	10	0.12103	T	0.63	.	7.5687	0.27894	0.0859:0.0:0.7483:0.1658	.	547;547;547;547	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	L	547	ENSP00000261866:F547L;ENSP00000445278:F547L;ENSP00000396110:F547L	ENSP00000261866:F547L	F	-	3	2	SPG11	42713089	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.740000	0.38228	2.479000	0.83701	0.655000	0.94253	TTC		0.313	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			T	44925797	G	T	44925797	3	4	47	1	0	0	0	0	1	0	0	0	15080	933	33	2	5822	2	SPG11	15	44925797	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	35294	44925797	57605595	1594	5991										
B2M	567	broad.mit.edu	37	chr15	45007641	45007641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtactccaaagattcaggttTactcacgtcatccagcagag	8	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:45007641T>C	ENST00000558401.1	+	2	158	c.88T>C	c.(88-90)Tac>Cac	p.Y30H	B2M_ENST00000559916.1_Missense_Mutation_p.Y30H|B2M_ENST00000544417.1_Missense_Mutation_p.Y30H|B2M_ENST00000559220.1_Intron	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	30	Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.Y30H(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GATTCAGGTTTACTCACGTCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											157	157	157					15																	45007641		2198	4298	6496	42794933	SO:0001583	missense	567			AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.88T>C	15.37:g.45007641T>C	ENSP00000452780:p.Tyr30His		42794933	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.198181	0.58126	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.08896	3.04	5.82	5.82	0.92795	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.37348	0.1000	M	0.92970	3.365	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.45396	-0.9264	10	0.87932	D	0	.	12.5757	0.56362	0.0:0.0:0.0:1.0	.	30;30;30	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	H	30	ENSP00000437604:Y30H	ENSP00000340858:Y30H	Y	+	1	0	B2M	42794933	1.000000	0.71417	0.316000	0.25252	0.096000	0.18686	5.777000	0.68931	2.222000	0.72286	0.533000	0.62120	TAC		0.418	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		C	45007641	T	C	45007641	3	2	47	1	0	0	0	0	1	0	0	0	1245	1754	61	4	94	4	B2M	15	45007641	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	81844	45007641	57523751	1595	5992										
TRIM69	140691	broad.mit.edu	37	chr15	45059656	45059656	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacagttggagttgtcagaGaatccatcattcggaagggc	14	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:45059656G>T	ENST00000559390.1	+	8	2117	c.1189G>T	c.(1189-1191)Gaa>Taa	p.E397*	TRIM69_ENST00000338264.4_Nonsense_Mutation_p.E238*|TRIM69_ENST00000561043.1_Nonsense_Mutation_p.E160*|TRIM69_ENST00000560442.1_Nonsense_Mutation_p.E193*|TRIM69_ENST00000558173.1_Nonsense_Mutation_p.E193*|TRIM69_ENST00000558329.1_Nonsense_Mutation_p.E176*|TRIM69_ENST00000329464.4_Nonsense_Mutation_p.E397*			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	397	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E397*(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		AGTTGTCAGAGAATCCATCAT	0.468																																					Pancreas(84;519 1450 1802 20427 34706)											1	Substitution - Nonsense(1)	large_intestine(1)	15											99	100	100					15																	45059656		2198	4298	6496	42846948	SO:0001587	stop_gained	140691			AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.1189G>T	15.37:g.45059656G>T	ENSP00000453177:p.Glu397*		42846948	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Nonsense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	37	6.538627	0.97646	.	.	ENSG00000185880	ENST00000329464;ENST00000338264	.	.	.	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.615	0.84904	0.0:0.0:1.0:0.0	.	.	.	.	X	397;238	.	ENSP00000332284:E397X	E	+	1	0	TRIM69	42846948	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.760000	0.85248	2.593000	0.87608	0.655000	0.94253	GAA		0.468	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1			T	45059656	G	T	45059656	4	4	47	1	0	0	0	0	0	1	0	0	16582	943	33	2	1215	2	TRIM69	15	45059656	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	52015	45059656	57471736	1596	5993										
SORD	6652	broad.mit.edu	37	chr15	45365692	45365692	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagggattggggttgaaaatCatgctcaagtgtgaccccag	13	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:45365692C>A	ENST00000267814.9	+	9	1218	c.1038C>A	c.(1036-1038)atC>atA	p.I346I	SORD_ENST00000558580.1_Silent_p.I325I|SORD_ENST00000559562.1_3'UTR|RP11-109D20.2_ENST00000560967.1_RNA	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	346					fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)	p.I346I(1)		endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		GGTTGAAAATCATGCTCAAGT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	15											34	43	40					15																	45365692		2111	4293	6404	43152984	SO:0001819	synonymous_variant	6652				CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.1038C>A	15.37:g.45365692C>A			43152984	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Silent	SNP	ENST00000267814.9	37	CCDS10116.1																																																																																				0.498	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3			A	45365692	C	A	45365692	2	1	47	1	0	0	0	0	0	0	0	1	14970	816	29	2		2	SORD	15	45365692	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	306036	45365692	57165700	1597	5994										
DUOX2	50506	broad.mit.edu	37	chr15	45396172	45396172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccataccgcatcatggtgaaGaattcgtccttggagaggaa	11	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:45396172G>T	ENST00000603300.1	-	20	2842	c.2640C>A	c.(2638-2640)ttC>ttA	p.F880L	DUOX2_ENST00000389039.6_Missense_Mutation_p.F880L	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	880	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)	p.F880L(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		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)		TCATGGTGAAGAATTCGTCCT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	15											149	129	135					15																	45396172		2198	4298	6496	43183464	SO:0001583	missense	50506			AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.2640C>A	15.37:g.45396172G>T	ENSP00000475084:p.Phe880Leu		43183464	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.343544	0.61073	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.23	4.31	0.51392	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46328	0.1387	N	0.16016	0.355	0.53688	D	0.999978	P;P	0.50710	0.84;0.938	P;P	0.60415	0.823;0.874	T	0.32402	-0.9908	9	0.13470	T	0.59	-22.8733	9.0256	0.36227	0.2327:0.0:0.7673:0.0	.	880;442	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	L	880	.	ENSP00000373691:F880L	F	-	3	2	DUOX2	43183464	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.491000	0.35583	1.318000	0.45170	0.563000	0.77884	TTC		0.488	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45396172	G	T	45396172	3	4	47	1	0	0	0	0	1	0	0	0	4812	933	33	2	2066	2	DUOX2	15	45396172	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	30480	45396172	57135220	1598	5995										
FBN1	2200	broad.mit.edu	37	chr15	48888524	48888524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atccgtaagtgcatgcacatCgatttggggccacacacctt	9	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:48888524C>T	ENST00000316623.5	-	6	949	c.494G>A	c.(493-495)cGa>cAa	p.R165Q		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	165	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R165Q(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GCATGCACATCGATTTGGGGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											131	117	122					15																	48888524		2197	4296	6493	46675816	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.494G>A	15.37:g.48888524C>T	ENSP00000325527:p.Arg165Gln		46675816	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.879179	0.91740	.	.	ENSG00000166147	ENST00000316623;ENST00000544030;ENST00000537463	D;T	0.91631	-2.88;0.14	5.87	5.87	0.94306	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.93930	0.8057	L	0.35487	1.065	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.93644	0.6967	10	0.51188	T	0.08	.	20.2182	0.98305	0.0:1.0:0.0:0.0	.	165	P35555	FBN1_HUMAN	Q	165	ENSP00000325527:R165Q;ENSP00000440294:R165Q	ENSP00000325527:R165Q	R	-	2	0	FBN1	46675816	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	7.246000	0.78247	2.785000	0.95823	0.655000	0.94253	CGA		0.418	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48888524	C	T	48888524	3	4	47	1	0	0	0	0	1	0	0	0	5721	884	31	1	8365	1	FBN1	15	48888524	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3492352	48888524	53642868	1599	5996										
CEP152	22995	broad.mit.edu	37	chr15	49048558	49048558	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggatttcttcttgcttttCtttgttccattcactccgag	7	10	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:49048558C>A	ENST00000380950.2	-	20	3074	c.2887G>T	c.(2887-2889)Gaa>Taa	p.E963*	CEP152_ENST00000325747.5_Nonsense_Mutation_p.E870*|CEP152_ENST00000399334.3_Nonsense_Mutation_p.E963*	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	963					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E963*(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TCTTGCTTTTCTTTGTTCCAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											169	156	160					15																	49048558		1839	4093	5932	46835850	SO:0001587	stop_gained	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2887G>T	15.37:g.49048558C>A	ENSP00000370337:p.Glu963*		46835850	E7ER66|Q17RV1|Q6NTA0	Nonsense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	C	42	9.468260	0.99180	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	.	.	.	5.54	4.63	0.57726	.	0.106857	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-22.4214	14.5485	0.68050	0.0:0.9293:0.0:0.0707	.	.	.	.	X	963;870;963	.	ENSP00000321000:E870X	E	-	1	0	CEP152	46835850	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.028000	0.57246	1.463000	0.47967	0.591000	0.81541	GAA		0.408	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49048558	C	A	49048558	4	1	47	1	0	0	0	0	0	1	0	0	3254	922	32	2	2105	2	CEP152	15	49048558	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	160034	49048558	53482834	1600	5997										
CEP152	22995	broad.mit.edu	37	chr15	49088311	49088311	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcagaagactgataaggtTtatatgtcactttattatac	9	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:49088311T>G	ENST00000380950.2	-	6	774	c.587A>C	c.(586-588)aAa>aCa	p.K196T	CEP152_ENST00000325747.5_Missense_Mutation_p.K103T|CEP152_ENST00000399334.3_Missense_Mutation_p.K196T	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	196					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.K196T(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CTGATAAGGTTTATATGTCAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	15											144	138	140					15																	49088311		1856	4088	5944	46875603	SO:0001583	missense	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.587A>C	15.37:g.49088311T>G	ENSP00000370337:p.Lys196Thr		46875603	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.642379	0.67244	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334;ENST00000541880	D;D;D	0.82081	-1.57;-1.57;-1.57	5.79	4.67	0.58626	.	0.099543	0.64402	D	0.000001	D	0.88973	0.6583	M	0.72118	2.19	0.35011	D	0.756864	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.993;0.999	D	0.92051	0.5648	10	0.66056	D	0.02	-29.7978	9.934	0.41539	0.0:0.0763:0.0:0.9237	.	103;196;196	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	T	196;103;196;196	ENSP00000370337:K196T;ENSP00000321000:K103T;ENSP00000382271:K196T	ENSP00000321000:K103T	K	-	2	0	CEP152	46875603	1.000000	0.71417	0.998000	0.56505	0.710000	0.40934	2.488000	0.45276	2.210000	0.71456	0.477000	0.44152	AAA		0.393	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		G	49088311	T	G	49088311	3	3	47	1	0	0	0	0	1	0	0	0	3254	1841	64	4	4461	4	CEP152	15	49088311	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	39753	49088311	53443081	1601	5998										
CEP152	22995	broad.mit.edu	37	chr15	49097786	49097786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctctttcatagtcctcttCgtcatactcttcatcttcat	2	14	8	0	rs187563127	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:49097786C>T	ENST00000380950.2	-	2	248	c.61G>A	c.(61-63)Gaa>Aaa	p.E21K	CEP152_ENST00000325747.5_Missense_Mutation_p.E21K|CEP152_ENST00000399334.3_Missense_Mutation_p.E21K	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	21					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E21K(2)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TAGTCCTCTTCGTCATACTCT	0.363													T|||	5	0.000998403	0.003	0.0014	5008	,	,		15074	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	15						T	LYS/GLU,LYS/GLU	18,3654		2,14,1820	174	149	157		61,61	1.3	1	15		157	0,8172		0,0,4086	yes	missense,missense	CEP152	NM_001194998.1,NM_014985.3	56,56	2,14,5906	TT,TC,CC		0.0,0.4902,0.152	benign,benign	21/1711,21/1655	49097786	18,11826	1836	4086	5922	46885078	SO:0001583	missense	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.61G>A	15.37:g.49097786C>T	ENSP00000370337:p.Glu21Lys		46885078	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	0.957	-0.704547	0.03255	0.004902	0.0	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334;ENST00000541880	T;T;T	0.47528	2.07;0.84;2.07	5.03	1.32	0.21799	.	0.294591	0.37857	N	0.001920	T	0.07007	0.0178	N	0.00246	-1.78	0.21325	N	0.999726	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.04013	0.001;0.0;0.001	T	0.38351	-0.9665	10	0.02654	T	1	-2.7725	6.9884	0.24741	0.0:0.1583:0.3308:0.5109	.	21;21;21	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	K	21	ENSP00000370337:E21K;ENSP00000321000:E21K;ENSP00000382271:E21K	ENSP00000321000:E21K	E	-	1	0	CEP152	46885078	1.000000	0.71417	0.999000	0.59377	0.449000	0.32228	1.177000	0.31969	0.078000	0.16900	-1.301000	0.01330	GAA		0.363	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49097786	C	T	49097786	3	4	47	1	0	0	0	0	1	0	0	0	3254	893	31	1	5003	1	CEP152	15	49097786	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	9475	49097786	53433606	1602	5999										
C15orf33	196951	broad.mit.edu	37	chr15	49882072	49882072	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgattccatgatcaaaagtgCttcaaatattcgaggaacat	7	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:49882072C>T	ENST00000299338.6	-	4	541	c.238G>A	c.(238-240)Gca>Aca	p.A80T	FAM227B_ENST00000558862.1_5'UTR|FAM227B_ENST00000560246.1_Missense_Mutation_p.A80T|FAM227B_ENST00000561064.1_Missense_Mutation_p.A80T|FAM227B_ENST00000558594.1_Missense_Mutation_p.A80T	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	80								p.A80T(1)									ATCAAAAGTGCTTCAAATATT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	15											62	68	66					15																	49882072		2195	4293	6488	47669364	SO:0001583	missense	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.238G>A	15.37:g.49882072C>T	ENSP00000299338:p.Ala80Thr		47669364	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	37	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.458979	0.26248	.	.	ENSG00000166262	ENST00000299338;ENST00000354658	.	.	.	4.62	-0.801	0.10893	.	0.683914	0.13316	N	0.397096	T	0.23094	0.0558	L	0.43152	1.355	0.09310	N	1	B;B	0.19331	0.035;0.035	B;B	0.16289	0.015;0.015	T	0.25293	-1.0136	9	0.07990	T	0.79	-6.5147	0.9331	0.01339	0.162:0.3988:0.158:0.2811	.	80;80	Q96M60-2;Q96M60	.;CO033_HUMAN	T	80	.	ENSP00000299338:A80T	A	-	1	0	C15orf33	47669364	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.542000	0.06091	-0.220000	0.09988	0.591000	0.81541	GCA		0.303	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		T	49882072	C	T	49882072	3	4	47	1	0	0	0	0	1	0	0	0	1795	797	28	3	1340	3	C15orf33	15	49882072	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	784286	49882072	52649320	1603	6000										
C15orf33	196951	broad.mit.edu	37	chr15	49903446	49903446	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaagaattcttcaatgctcTttggaggttcttgcattttc	7	7	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:49903446T>G	ENST00000299338.6	-	3	374	c.71A>C	c.(70-72)aAg>aCg	p.K24T	FAM227B_ENST00000558862.1_5'UTR|FAM227B_ENST00000560246.1_Missense_Mutation_p.K24T|FAM227B_ENST00000561064.1_Missense_Mutation_p.K24T|FAM227B_ENST00000558594.1_Missense_Mutation_p.K24T	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	24								p.K24T(1)									TTCAATGCTCTTTGGAGGTTC	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	15											58	59	59					15																	49903446		2194	4284	6478	47690738	SO:0001583	missense	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.71A>C	15.37:g.49903446T>G	ENSP00000299338:p.Lys24Thr		47690738	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	37	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	T	4.796	0.147996	0.09134	.	.	ENSG00000166262	ENST00000299338;ENST00000354658	.	.	.	4.75	-3.97	0.04094	.	0.627260	0.14785	N	0.298569	T	0.34077	0.0885	L	0.59436	1.845	0.09310	N	1	P;P	0.36535	0.557;0.557	B;B	0.41860	0.368;0.368	T	0.27262	-1.0079	9	0.41790	T	0.15	1.2609	3.7681	0.08630	0.2889:0.3536:0.0:0.3575	.	24;24	Q96M60-2;Q96M60	.;CO033_HUMAN	T	24	.	ENSP00000299338:K24T	K	-	2	0	C15orf33	47690738	0.002000	0.14202	0.003000	0.11579	0.002000	0.02628	-0.634000	0.05477	-0.465000	0.06953	-0.256000	0.11100	AAG		0.264	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		G	49903446	T	G	49903446	3	3	47	1	0	0	0	0	1	0	0	0	1795	1609	56	4	1511	4	C15orf33	15	49903446	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	21374	49903446	52627946	1604	6001										
SLC27A2	11001	broad.mit.edu	37	chr15	50519340	50519340	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggttgaccatgaaaatttCatctatttccacgacagagt	7	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:50519340C>A	ENST00000267842.5	+	7	1654	c.1422C>A	c.(1420-1422)ttC>ttA	p.F474L	SLC27A2_ENST00000380902.4_Missense_Mutation_p.F421L|SLC27A2_ENST00000544960.1_Missense_Mutation_p.F239L	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	474					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.F474L(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		ATGAAAATTTCATCTATTTCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											109	110	110					15																	50519340		2196	4295	6491	48306632	SO:0001583	missense	11001			D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"Acyl-CoA synthetase family", "Solute carriers"	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.1422C>A	15.37:g.50519340C>A	ENSP00000267842:p.Phe474Leu		48306632	A8K2J7|Q53FY6|Q6PF09	Missense_Mutation	SNP	ENST00000267842.5	37	CCDS10133.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.009326	0.75046	.	.	ENSG00000140284	ENST00000380902;ENST00000267842;ENST00000544960	T;T;T	0.49139	0.79;1.04;1.04	5.78	3.89	0.44902	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.59335	0.2186	M	0.64676	1.99	0.54753	D	0.999986	D;D	0.63880	0.97;0.993	P;D	0.67382	0.838;0.951	T	0.57458	-0.7808	10	0.49607	T	0.09	.	7.128	0.25484	0.0:0.7213:0.0:0.2787	.	421;474	Q6PF09;O14975	.;S27A2_HUMAN	L	421;474;239	ENSP00000370289:F421L;ENSP00000267842:F474L;ENSP00000444549:F239L	ENSP00000267842:F474L	F	+	3	2	SLC27A2	48306632	0.035000	0.19736	0.999000	0.59377	0.996000	0.88848	0.356000	0.20181	0.762000	0.33152	0.655000	0.94253	TTC		0.398	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645		A	50519340	C	A	50519340	3	1	47	1	0	0	0	0	1	0	0	0	14563	825	29	2	1448	2	SLC27A2	15	50519340	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	615894	50519340	52012052	1605	6002										
HDC	3067	broad.mit.edu	37	chr15	50534577	50534577	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggcacttttcttcagcatCatcatgtcttctggaaacct	6	11	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:50534577C>A	ENST00000267845.3	-	12	2271	c.1869G>T	c.(1867-1869)atG>atT	p.M623I	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.M590I	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.M623I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TCTTCAGCATCATCATGTCTT	0.512																																					GBM(95;1627 1936 6910 9570)											1	Substitution - Missense(1)	large_intestine(1)	15											97	107	103					15																	50534577		2196	4295	6491	48321869	SO:0001583	missense	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1869G>T	15.37:g.50534577C>A	ENSP00000267845:p.Met623Ile		48321869		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.551968	0.45487	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.09538	3.13;2.97	5.48	4.5	0.54988	.	0.397571	0.24422	N	0.038665	T	0.09468	0.0233	N	0.24115	0.695	0.37716	D	0.924721	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.002	T	0.13282	-1.0515	10	0.72032	D	0.01	-20.366	15.727	0.77770	0.0:0.8632:0.1367:0.0	.	590;623	B7ZM01;P19113	.;DCHS_HUMAN	I	623;590	ENSP00000267845:M623I;ENSP00000440252:M590I	ENSP00000267845:M623I	M	-	3	0	HDC	48321869	0.987000	0.35691	0.980000	0.43619	0.979000	0.70002	2.494000	0.45329	2.570000	0.86706	0.563000	0.77884	ATG		0.512	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50534577	C	A	50534577	3	1	47	1	0	0	0	0	1	0	0	0	7036	826	29	2	123	2	HDC	15	50534577	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15237	50534577	51996815	1606	6003										
HDC	3067	broad.mit.edu	37	chr15	50534738	50534738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcacagacaagtaactgaAcaggaaggaggacagcttgt	12	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:50534738A>G	ENST00000267845.3	-	12	2110	c.1708T>C	c.(1708-1710)Ttc>Ctc	p.F570L	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.F537L	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.F570L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AAGTAACTGAACAGGAAGGAG	0.542																																					GBM(95;1627 1936 6910 9570)											1	Substitution - Missense(1)	large_intestine(1)	15											133	137	135					15																	50534738		2196	4295	6491	48322030	SO:0001583	missense	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1708T>C	15.37:g.50534738A>G	ENSP00000267845:p.Phe570Leu		48322030		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.893144	0.52121	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.13307	2.88;2.6	5.68	4.53	0.55603	.	0.791241	0.11475	N	0.560304	T	0.13157	0.0319	L	0.34521	1.04	0.31962	N	0.608231	B;B	0.13145	0.007;0.007	B;B	0.15870	0.01;0.014	T	0.06481	-1.0824	10	0.87932	D	0	-23.6748	11.3795	0.49748	0.8643:0.0:0.0:0.1357	.	537;570	B7ZM01;P19113	.;DCHS_HUMAN	L	570;537	ENSP00000267845:F570L;ENSP00000440252:F537L	ENSP00000267845:F570L	F	-	1	0	HDC	48322030	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.741000	0.55090	0.948000	0.37687	0.460000	0.39030	TTC		0.542	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			G	50534738	A	G	50534738	3	3	47	1	0	0	0	0	1	0	0	0	7036	43	2	4	284	4	HDC	15	50534738	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	161	50534738	51996654	1607	6004										
TRPM7	54822	broad.mit.edu	37	chr15	50891328	50891328	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaattcttaccatcaatttCgtatgcataaacttcaccaa	2	11	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:50891328C>A	ENST00000313478.7	-	22	3435	c.3154G>T	c.(3154-3156)Gaa>Taa	p.E1052*	TRPM7_ENST00000560955.1_Nonsense_Mutation_p.E1052*	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1052					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.E1052*(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		CCATCAATTTCGTATGCATAA	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											92	91	91					15																	50891328		1803	4063	5866	48678620	SO:0001587	stop_gained	54822			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.3154G>T	15.37:g.50891328C>A	ENSP00000320239:p.Glu1052*		48678620	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Nonsense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	44	11.104457	0.99516	.	.	ENSG00000092439	ENST00000313478	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-23.4378	19.2198	0.93791	0.0:1.0:0.0:0.0	.	.	.	.	X	1052	.	ENSP00000320239:E1052X	E	-	1	0	TRPM7	48678620	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.815000	0.55651	2.629000	0.89072	0.650000	0.86243	GAA		0.289	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50891328	C	A	50891328	4	1	47	1	0	0	0	0	0	1	0	0	16631	893	31	2	2515	2	TRPM7	15	50891328	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	356590	50891328	51640064	1608	6005										
GLDN	342035	broad.mit.edu	37	chr15	51692409	51692409	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgagacttgtgccataccaAatgatgataccttggttgga	11	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:51692409A>C	ENST00000335449.6	+	7	894	c.838A>C	c.(838-840)Aat>Cat	p.N280H	GLDN_ENST00000396399.2_Missense_Mutation_p.N156H	NM_181789.2	NP_861454.2	Q6ZMI3	GLDN_HUMAN	gliomedin	280					clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|microvillus organization (GO:0032528)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N280H(1)		central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		TGCCATACCAAATGATGATAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											106	101	102					15																	51692409		2196	4293	6489	49479701	SO:0001583	missense	342035			AY358144	CCDS10140.2	15q15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000186417	ENSG00000186417			29514	protein-coding gene	gene with protein product		608603	"collomin"	COLM		16039564, 12642876	Standard	XM_005254338		Approved	CRG-L2, CLOM, colmedin, UNC-112	uc002aba.3	Q6ZMI3	OTTHUMG00000131746	ENST00000335449.6:c.838A>C	15.37:g.51692409A>C	ENSP00000335196:p.Asn280His		49479701	Q6UXZ7|Q7Z359	Missense_Mutation	SNP	ENST00000335449.6	37	CCDS10140.2	.	.	.	.	.	.	.	.	.	.	A	27.4	4.826879	0.90955	.	.	ENSG00000186417	ENST00000335449;ENST00000396399;ENST00000537339	D;D	0.92048	-2.96;-2.75	5.79	5.79	0.91817	.	0.000000	0.46442	D	0.000295	D	0.95430	0.8516	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.95836	0.8862	10	0.87932	D	0	.	16.1415	0.81528	1.0:0.0:0.0:0.0	.	280	Q6ZMI3	GLDN_HUMAN	H	280;156;156	ENSP00000335196:N280H;ENSP00000379681:N156H	ENSP00000335196:N280H	N	+	1	0	GLDN	49479701	1.000000	0.71417	0.607000	0.28956	0.992000	0.81027	8.182000	0.89698	2.198000	0.70561	0.533000	0.62120	AAT		0.428	GLDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254667.2	NM_181789		C	51692409	A	C	51692409	3	2	47	1	0	0	0	0	1	0	0	0	6454	14	1	4	864	4	GLDN	15	51692409	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	801081	51692409	50838983	1609	6006										
LEO1	123169	broad.mit.edu	37	chr15	52239507	52239507	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctcatcactggtaagtttCtttgctttgagtaatctttg	7	8	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:52239507C>A	ENST00000299601.5	-	11	1938	c.1878G>T	c.(1876-1878)aaG>aaT	p.K626N	LEO1_ENST00000315141.5_Missense_Mutation_p.K566N	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	626					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)		p.K626N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		TGGTAAGTTTCTTTGCTTTGA	0.398																																					Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)											1	Substitution - Missense(1)	large_intestine(1)	15											249	220	230					15																	52239507		2195	4293	6488	50026799	SO:0001583	missense	123169			AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1878G>T	15.37:g.52239507C>A	ENSP00000299601:p.Lys626Asn		50026799	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	37	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	.	19.50	3.838766	0.71373	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.49	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.71239	0.3316	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.973;0.998	T	0.72364	-0.4316	9	0.72032	D	0.01	.	11.8881	0.52615	0.0:0.8569:0.0:0.1431	.	566;626	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	N	626;604;566	.	ENSP00000299601:K626N	K	-	3	2	LEO1	50026799	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.576000	0.46033	0.711000	0.32018	0.561000	0.74099	AAG		0.398	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		A	52239507	C	A	52239507	3	1	47	1	0	0	0	0	1	0	0	0	8748	912	32	2	130	2	LEO1	15	52239507	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	547098	52239507	50291885	1610	6007										
MYO5C	55930	broad.mit.edu	37	chr15	52537644	52537644	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaatgccgtagcgactgtaGaactcgatgtatgtccacct	10	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:52537644G>T	ENST00000261839.7	-	18	2246	c.2085C>A	c.(2083-2085)ttC>ttA	p.F695L	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	695	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.F695L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		AGCGACTGTAGAACTCGATGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	15											154	153	153					15																	52537644		2033	4199	6232	50324936	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2085C>A	15.37:g.52537644G>T	ENSP00000261839:p.Phe695Leu		50324936	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.063643	0.55432	.	.	ENSG00000128833	ENST00000261839	D	0.89343	-2.5	4.79	3.79	0.43588	Myosin head, motor domain (2);	0.104894	0.64402	D	0.000003	D	0.92980	0.7766	M	0.87097	2.86	0.80722	D	1	D	0.64830	0.994	P	0.61940	0.896	D	0.92663	0.6143	10	0.72032	D	0.01	.	7.0915	0.25287	0.1877:0.0:0.8123:0.0	.	695	Q9NQX4	MYO5C_HUMAN	L	695	ENSP00000261839:F695L	ENSP00000261839:F695L	F	-	3	2	MYO5C	50324936	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.075000	0.41538	2.479000	0.83701	0.555000	0.69702	TTC		0.498	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		T	52537644	G	T	52537644	3	4	47	1	0	0	0	0	1	0	0	0	10110	933	33	2	3239	2	MYO5C	15	52537644	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	298137	52537644	49993748	1611	6008										
UNC13C	440279	broad.mit.edu	37	chr15	54799385	54799385	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagttcacattgtgataaggAaaatgtggtaagtaaaaaat	9	3	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:54799385A>G	ENST00000260323.11	+	22	5372	c.5372A>G	c.(5371-5373)gAa>gGa	p.E1791G	UNC13C_ENST00000537900.1_Missense_Mutation_p.E1789G|UNC13C_ENST00000545554.1_Missense_Mutation_p.E1791G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1791					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.E1791G(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TGTGATAAGGAAAATGTGGTA	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	15											86	80	82					15																	54799385		1831	4087	5918	52586677	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5372A>G	15.37:g.54799385A>G	ENSP00000260323:p.Glu1791Gly		52586677	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.713837	0.89112	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.15139	2.45;2.45;2.45	5.74	5.74	0.90152	.	0.106321	0.64402	D	0.000005	T	0.50939	0.1645	M	0.91663	3.23	0.53005	D	0.999967	D	0.76494	0.999	D	0.80764	0.994	T	0.61739	-0.7001	10	0.66056	D	0.02	.	15.2628	0.73637	1.0:0.0:0.0:0.0	.	1791	Q8NB66	UN13C_HUMAN	G	1791;1791;1789	ENSP00000260323:E1791G;ENSP00000438156:E1791G;ENSP00000442569:E1789G	ENSP00000260323:E1791G	E	+	2	0	UNC13C	52586677	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.108000	0.94275	2.206000	0.71126	0.456000	0.33151	GAA		0.328	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54799385	A	G	54799385	3	3	47	1	0	0	0	0	1	0	0	0	17026	246	9	4	5454	4	UNC13C	15	54799385	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2261741	54799385	47732007	1612	6009										
PRTG	283659	broad.mit.edu	37	chr15	55976069	55976069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgaaatcttgcatgcaaatCgagcaactccaccttcgtgg	8	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:55976069C>T	ENST00000389286.4	-	3	505	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin									p.R153Q(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GCATGCAAATCGAGCAACTCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											90	90	90					15																	55976069		1879	4112	5991	53763361	SO:0001583	missense	283659			AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.458G>A	15.37:g.55976069C>T	ENSP00000373937:p.Arg153Gln		53763361		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	C	34	5.344911	0.95807	.	.	ENSG00000166450	ENST00000389286	T	0.67865	-0.29	5.52	5.52	0.82312	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.000000	0.85682	U	0.000000	T	0.79981	0.4540	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.77576	-0.2536	10	0.32370	T	0.25	-16.9588	16.599	0.84804	0.0:1.0:0.0:0.0	.	153	Q2VWP7	PRTG_HUMAN	Q	153	ENSP00000373937:R153Q	ENSP00000373937:R153Q	R	-	2	0	PRTG	53763361	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.484000	0.81180	2.580000	0.87095	0.455000	0.32223	CGA		0.413	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		T	55976069	C	T	55976069	3	4	47	1	0	0	0	0	1	0	0	0	12672	884	31	1	3066	1	PRTG	15	55976069	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1176684	55976069	46555323	1613	6010										
RNF111	54778	broad.mit.edu	37	chr15	59348038	59348038	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtggaccttaccgttgatGaagatggtaaattgaagtag	12	4	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:59348038G>T	ENST00000557998.1	+	4	1452	c.1165G>T	c.(1165-1167)Gaa>Taa	p.E389*	RNF111_ENST00000561186.1_Nonsense_Mutation_p.E389*|RNF111_ENST00000559209.1_Nonsense_Mutation_p.E389*|RNF111_ENST00000348370.4_Nonsense_Mutation_p.E389*|RNF111_ENST00000434298.1_Nonsense_Mutation_p.E389*	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	389	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E389*(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		TACCGTTGATGAAGATGGTAA	0.418																																					NSCLC(72;983 1365 10746 34387 47081)											1	Substitution - Nonsense(1)	large_intestine(1)	15											58	52	54					15																	59348038		2192	4291	6483	57135330	SO:0001587	stop_gained	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1165G>T	15.37:g.59348038G>T	ENSP00000452732:p.Glu389*		57135330	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Nonsense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	42	9.253824	0.99115	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.4435	19.7762	0.96393	0.0:0.0:1.0:0.0	.	.	.	.	X	389	.	ENSP00000288199:E389X	E	+	1	0	RNF111	57135330	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.793000	0.91862	2.678000	0.91216	0.591000	0.81541	GAA		0.418	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		T	59348038	G	T	59348038	4	4	47	1	0	0	0	0	0	1	0	0	13462	1291	45	2	1175	2	RNF111	15	59348038	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3371969	59348038	43183354	1614	6011										
RNF111	54778	broad.mit.edu	37	chr15	59359277	59359277	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttctggtaccagctatcatGaacaggtatgtggaatttga	11	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:59359277G>T	ENST00000557998.1	+	6	1968	c.1681G>T	c.(1681-1683)Gaa>Taa	p.E561*	RNF111_ENST00000561186.1_Nonsense_Mutation_p.E561*|RNF111_ENST00000559209.1_Nonsense_Mutation_p.E561*|RNF111_ENST00000348370.4_Nonsense_Mutation_p.E561*|RNF111_ENST00000434298.1_Nonsense_Mutation_p.E561*	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	561					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E561*(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CAGCTATCATGAACAGGTATG	0.463																																					NSCLC(72;983 1365 10746 34387 47081)											1	Substitution - Nonsense(1)	large_intestine(1)	15											100	91	94					15																	59359277		2192	4291	6483	57146569	SO:0001587	stop_gained	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1681G>T	15.37:g.59359277G>T	ENSP00000452732:p.Glu561*		57146569	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Nonsense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	43	9.832844	0.99275	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	.	.	.	5.7	5.7	0.88788	.	0.045758	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-5.8722	18.8254	0.92115	0.0:0.0:1.0:0.0	.	.	.	.	X	561	.	ENSP00000288199:E561X	E	+	1	0	RNF111	57146569	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.279000	0.89901	2.695000	0.91970	0.462000	0.41574	GAA		0.463	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		T	59359277	G	T	59359277	4	4	47	1	0	0	0	0	0	1	0	0	13462	1291	45	2	1699	2	RNF111	15	59359277	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	11239	59359277	43172115	1615	6012										
VPS13C	54832	broad.mit.edu	37	chr15	62256067	62256067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcggcgatattgttcttttCgttgcaaacaatgacacaga	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:62256067C>T	ENST00000261517.5	-	32	3371	c.3298G>A	c.(3298-3300)Gaa>Aaa	p.E1100K	VPS13C_ENST00000395898.3_Missense_Mutation_p.E1057K|VPS13C_ENST00000249837.3_Missense_Mutation_p.E1057K|VPS13C_ENST00000395896.4_Missense_Mutation_p.E1100K	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.E1100K(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTGTTCTTTTCGTTGCAAACA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											114	104	107					15																	62256067		2203	4300	6503	60043359	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3298G>A	15.37:g.62256067C>T	ENSP00000261517:p.Glu1100Lys		60043359		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867379	0.72065	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.38401	1.14;1.14;1.14	5.66	5.66	0.87406	.	0.060437	0.64402	D	0.000004	T	0.32466	0.0830	N	0.11560	0.145	0.58432	D	0.999997	D;D;D;D	0.63880	0.991;0.98;0.993;0.976	P;P;P;B	0.52066	0.477;0.559;0.689;0.427	T	0.08534	-1.0717	10	0.17369	T	0.5	.	19.7559	0.96291	0.0:1.0:0.0:0.0	.	1057;1100;1057;1100	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	K	1057;1100;1100;1100	ENSP00000249837:E1057K;ENSP00000261517:E1100K;ENSP00000379233:E1100K	ENSP00000249837:E1057K	E	-	1	0	VPS13C	60043359	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.129000	0.57957	2.656000	0.90262	0.655000	0.94253	GAA		0.348	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62256067	C	T	62256067	3	4	47	1	0	0	0	0	1	0	0	0	17231	893	31	1	8207	1	VPS13C	15	62256067	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2896790	62256067	40275325	1616	6013										
VPS13C	54832	broad.mit.edu	37	chr15	62305311	62305311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcgctaagactatcaagtCgtataagctataagagaaaa	9	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:62305311C>T	ENST00000261517.5	-	11	825	c.752G>A	c.(751-753)cGa>cAa	p.R251Q	VPS13C_ENST00000395898.3_Missense_Mutation_p.R208Q|VPS13C_ENST00000249837.3_Missense_Mutation_p.R208Q|VPS13C_ENST00000395896.4_Missense_Mutation_p.R251Q	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.R251Q(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACTATCAAGTCGTATAAGCTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	15											70	66	68					15																	62305311		2202	4300	6502	60092603	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.752G>A	15.37:g.62305311C>T	ENSP00000261517:p.Arg251Gln		60092603		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111477	0.37242	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.43294	0.96;0.95;1.13	5.83	2.29	0.28610	.	0.467855	0.21430	N	0.074676	T	0.37919	0.1021	L	0.60455	1.87	0.09310	N	1	B;B;B;B	0.29212	0.056;0.237;0.132;0.081	B;B;B;B	0.28991	0.04;0.097;0.027;0.018	T	0.25047	-1.0143	10	0.49607	T	0.09	.	10.3797	0.44104	0.0:0.7738:0.0:0.2262	.	208;251;208;251	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	Q	208;251;251;251	ENSP00000249837:R208Q;ENSP00000261517:R251Q;ENSP00000379233:R251Q	ENSP00000249837:R208Q	R	-	2	0	VPS13C	60092603	0.447000	0.25673	0.039000	0.18376	0.565000	0.35776	2.236000	0.43052	0.145000	0.18977	-0.157000	0.13467	CGA		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62305311	C	T	62305311	3	4	47	1	0	0	0	0	1	0	0	0	17231	884	31	1	10837	1	VPS13C	15	62305311	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	49244	62305311	40226081	1617	6014										
LACTB	114294	broad.mit.edu	37	chr15	63433864	63433864	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctgctggtccttcctgaaGaactggatacagagactata	9	10	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:63433864G>T	ENST00000261893.4	+	6	1576	c.1504G>T	c.(1504-1506)Gaa>Taa	p.E502*	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	502						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.E502*(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CCTTCCTGAAGAACTGGATAC	0.448																																					Melanoma(85;443 1381 6215 27308 35583)											1	Substitution - Nonsense(1)	large_intestine(1)	15											60	55	57					15																	63433864		2203	4300	6503	61220917	SO:0001587	stop_gained	114294			AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1504G>T	15.37:g.63433864G>T	ENSP00000261893:p.Glu502*		61220917	P83096	Nonsense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	G	36	5.640540	0.96693	.	.	ENSG00000103642	ENST00000261893	.	.	.	5.64	5.64	0.86602	.	0.047948	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-26.7563	19.0467	0.93022	0.0:0.0:1.0:0.0	.	.	.	.	X	502	.	ENSP00000261893:E502X	E	+	1	0	LACTB	61220917	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	6.789000	0.75110	2.817000	0.96982	0.563000	0.77884	GAA		0.448	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		T	63433864	G	T	63433864	4	4	47	1	0	0	0	0	0	1	0	0	8619	943	33	2	1530	2	LACTB	15	63433864	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1128553	63433864	39097528	1618	6015										
HERC1	8925	broad.mit.edu	37	chr15	63928190	63928190	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttctccttgtaaggcctcGatctgcctgggccgccgctg	11	15	3	0	rs2228509		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:63928190G>A	ENST00000443617.2	-	65	12471	c.12384C>T	c.(12382-12384)atC>atT	p.I4128I		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4128					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I4128I(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GTAAGGCCTCGATCTGCCTGG	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	15											225	231	229					15																	63928190		2030	4185	6215	61715243	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12384C>T	15.37:g.63928190G>A			61715243	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.478	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63928190	G	A	63928190	2	1	47	1	0	0	0	0	0	0	0	1	7078	1048	37	1		1	HERC1	15	63928190	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	494326	63928190	38603202	1619	6016										
DENND4A	10260	broad.mit.edu	37	chr15	65982886	65982886	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtagtgtatctaagttaaatGaaggtgatgagtgggttaat	13	1	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:65982886G>T	ENST00000431932.2	-	22	4122	c.3914C>A	c.(3913-3915)tCa>tAa	p.S1305*	DENND4A_ENST00000567323.1_5'Flank|DENND4A_ENST00000443035.3_Nonsense_Mutation_p.S1348*	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1305					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.S1307*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TAAGTTAAATGAAGGTGATGA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											115	111	112					15																	65982886		1895	4114	6009	63769940	SO:0001587	stop_gained	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3914C>A	15.37:g.65982886G>T	ENSP00000396830:p.Ser1305*		63769940	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Nonsense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	45	11.991853	0.99625	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	.	.	.	5.46	5.46	0.80206	.	0.307999	0.31884	N	0.006905	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3125	0.94195	0.0:0.0:1.0:0.0	.	.	.	.	X	1348;1305	.	ENSP00000396830:S1305X	S	-	2	0	DENND4A	63769940	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.086000	0.94088	2.576000	0.86940	0.650000	0.86243	TCA		0.408	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65982886	G	T	65982886	4	4	47	1	0	0	0	0	0	1	0	0	4444	1294	45	2	1721	2	DENND4A	15	65982886	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2054696	65982886	36548506	1620	6017										
TIPIN	54962	broad.mit.edu	37	chr15	66641448	66641448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagggagatcaagtcgaattCgttttaaacaggtctgaaaa	10	5	2	2	rs76072153		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:66641448C>T	ENST00000261881.4	-	6	510	c.425G>A	c.(424-426)cGa>cAa	p.R142Q	Y_RNA_ENST00000411339.1_RNA|SCARNA14_ENST00000516903.1_RNA|TIPIN_ENST00000367709.4_Missense_Mutation_p.R41Q	NM_017858.2	NP_060328	Q9BVW5	TIPIN_HUMAN	TIMELESS interacting protein	142	Interaction with TIMELESS.				cell cycle phase transition (GO:0044770)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|regulation of nuclear cell cycle DNA replication (GO:0033262)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)		p.R142Q(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	7						AAGTCGAATTCGTTTTAAACA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	15											60	63	62					15																	66641448		2200	4299	6499	64428502	SO:0001583	missense	54962			BK001386	CCDS10215.1	15q22.31	2012-03-02	2006-08-08		ENSG00000075131	ENSG00000075131			30750	protein-coding gene	gene with protein product	"CSM3 homolog (S. cerevisiae)"	610716				12875843, 17102137	Standard	NM_017858		Approved	FLJ20516	uc002apr.2	Q9BVW5	OTTHUMG00000133188	ENST00000261881.4:c.425G>A	15.37:g.66641448C>T	ENSP00000261881:p.Arg142Gln		64428502	B2CW64|Q9NWZ6	Missense_Mutation	SNP	ENST00000261881.4	37	CCDS10215.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	16.45	3.127047	0.56721	.	.	ENSG00000075131	ENST00000367709;ENST00000261881	T;T	0.44083	0.93;0.93	5.11	4.2	0.49525	Replication fork protection component Swi3 (2);	0.129811	0.50627	N	0.000120	T	0.31389	0.0795	L	0.42245	1.32	0.46167	D	0.998906	P	0.51653	0.947	B	0.38842	0.283	T	0.11767	-1.0574	10	0.54805	T	0.06	-9.7736	9.1058	0.36696	0.0:0.8307:0.0:0.1693	.	142	Q9BVW5	TIPIN_HUMAN	Q	41;142	ENSP00000356682:R41Q;ENSP00000261881:R142Q	ENSP00000261881:R142Q	R	-	2	0	TIPIN	64428502	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.232000	0.51302	1.285000	0.44548	0.555000	0.69702	CGA		0.299	TIPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256897.2	NM_017858		T	66641448	C	T	66641448	3	4	47	1	0	0	0	0	1	0	0	0	15964	884	31	1	492	1	TIPIN	15	66641448	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	658562	66641448	35889944	1621	6018										
IQCH	64799	broad.mit.edu	37	chr15	67664696	67664696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttccagagtttgagctgaCgaataaacttaccagatatg	8	9	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:67664696C>T	ENST00000335894.4	+	9	1067	c.1001C>T	c.(1000-1002)aCg>aTg	p.T334M	IQCH_ENST00000360277.4_Missense_Mutation_p.T86M|IQCH_ENST00000546225.1_Missense_Mutation_p.T82M|IQCH_ENST00000358767.3_Missense_Mutation_p.T161M	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	334								p.T334M(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		TTTGAGCTGACGAATAAACTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											110	118	116					15																	67664696		2201	4299	6500	65451750	SO:0001583	missense	64799			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1001C>T	15.37:g.67664696C>T	ENSP00000336861:p.Thr334Met		65451750	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	.	.	.	.	.	.	.	.	.	.	C	4.045	0.005894	0.07866	.	.	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.44482	0.92;0.93;0.93;0.92	5.53	1.88	0.25563	.	0.578681	0.20079	N	0.099691	T	0.22399	0.0540	N	0.08118	0	0.09310	N	0.999999	P;P;P;P;P	0.49961	0.61;0.61;0.61;0.614;0.93	B;B;B;B;P	0.44477	0.169;0.169;0.169;0.282;0.451	T	0.08700	-1.0709	10	0.51188	T	0.08	0.0259	5.8061	0.18440	0.5928:0.2711:0.1361:0.0	.	161;82;86;334;161	F8WAL8;Q86VS3-2;Q86VS3-4;Q86VS3;Q86VS3-3	.;.;.;IQCH_HUMAN;.	M	161;82;334;86	ENSP00000351617:T161M;ENSP00000444118:T82M;ENSP00000336861:T334M;ENSP00000353419:T86M	ENSP00000336861:T334M	T	+	2	0	IQCH	65451750	0.992000	0.36948	0.287000	0.24848	0.728000	0.41692	3.120000	0.50430	0.117000	0.18138	-1.181000	0.01715	ACG		0.438	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		T	67664696	C	T	67664696	3	4	47	1	0	0	0	0	1	0	0	0	7832	536	19	1	1163	1	IQCH	15	67664696	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1023248	67664696	34866696	1622	6019										
LBXCOR1	390598	broad.mit.edu	37	chr15	68124644	68124644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactgctcctggaacaaatgGagctccgcaagaagctggaa	11	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:68124644G>A	ENST00000380035.2	+	6	2678	c.2620G>A	c.(2620-2622)Gag>Aag	p.E874K	RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000341418.5_Missense_Mutation_p.E777K|SKOR1_ENST00000389002.1_Missense_Mutation_p.E830K|SKOR1_ENST00000554240.1_Missense_Mutation_p.E835K|RP11-34F13.2_ENST00000502156.1_lincRNA|SKOR1_ENST00000554054.1_Missense_Mutation_p.E846K			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	874					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)	p.E830K(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GGAACAAATGGAGCTCCGCAA	0.532											OREG0023215	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											135	137	136					15																	68124644		2200	4298	6498	65911698	SO:0001583	missense	390598				CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"SKI transcriptional corepressors"	21326	protein-coding gene	gene with protein product	"transcriptional corepressor CORL1", "functional smad suppressing element 15", "corepressor for LBX1"	611273	"Lbxcor1 homolog (mouse)"	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2620G>A	15.37:g.68124644G>A	ENSP00000369374:p.Glu874Lys	1104	65911698	A6NIP4|A6NJY0|Q2VWA5	Missense_Mutation	SNP	ENST00000380035.2	37		.	.	.	.	.	.	.	.	.	.	G	34	5.406837	0.96051	.	.	ENSG00000188779	ENST00000341418;ENST00000554240;ENST00000554054;ENST00000380035;ENST00000389002	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	5.33	5.33	0.75918	.	0.059324	0.64402	D	0.000003	T	0.53690	0.1812	N	0.08118	0	0.52501	D	0.99995	P	0.51147	0.942	D	0.65684	0.937	T	0.62900	-0.6756	10	0.56958	D	0.05	-20.6609	16.7928	0.85593	0.0:0.0:1.0:0.0	.	830	P84550-3	.	K	777;835;846;874;830	ENSP00000343200:E777K;ENSP00000451193:E835K;ENSP00000452361:E846K;ENSP00000369374:E874K;ENSP00000373654:E830K	ENSP00000343200:E777K	E	+	1	0	SKOR1	65911698	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.923000	0.92808	2.492000	0.84095	0.561000	0.74099	GAG		0.532	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807		A	68124644	G	A	68124644	3	1	47	1	0	0	0	0	1	0	0	0	8677	1175	41	3	2514	3	LBXCOR1	15	68124644	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	459948	68124644	34406748	1623	6020										
PIAS1	8554	broad.mit.edu	37	chr15	68468982	68468982	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatctcccacatcaccactaAataataaagggtaagtgctg	6	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:68468982A>C	ENST00000249636.6	+	11	1619	c.1471A>C	c.(1471-1473)Aat>Cat	p.N491H	PIAS1_ENST00000545237.1_Missense_Mutation_p.N493H|PIAS1_ENST00000567417.1_3'UTR	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	491					androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.N491H(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						ATCACCACTAAATAATAAAGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	72	73					15																	68468982		1865	4091	5956	66256036	SO:0001583	missense	8554			AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"Zinc fingers, MIZ-type"	2752	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 3"	603566	"DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.1471A>C	15.37:g.68468982A>C	ENSP00000249636:p.Asn491His		66256036	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	A	10.45	1.354758	0.24512	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.30182	1.54;1.54	5.93	5.93	0.95920	.	0.441280	0.29830	N	0.011091	T	0.14874	0.0359	N	0.02539	-0.55	0.19575	N	0.999965	B	0.34147	0.438	B	0.35859	0.212	T	0.19712	-1.0297	10	0.13108	T	0.6	-9.0755	16.3871	0.83514	1.0:0.0:0.0:0.0	.	491	O75925	PIAS1_HUMAN	H	491;493	ENSP00000249636:N491H;ENSP00000438574:N493H	ENSP00000249636:N491H	N	+	1	0	PIAS1	66256036	0.929000	0.31497	0.689000	0.30133	0.994000	0.84299	3.379000	0.52440	2.265000	0.75225	0.533000	0.62120	AAT		0.368	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			C	68468982	A	C	68468982	3	2	47	1	0	0	0	0	1	0	0	0	11906	14	1	4	1513	4	PIAS1	15	68468982	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	344338	68468982	34062410	1624	6021										
ITGA11	22801	broad.mit.edu	37	chr15	68653956	68653956	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggggccacggtcttggaGaacctgaagttggagttgac	16	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:68653956G>T	ENST00000315757.7	-	5	530	c.444C>A	c.(442-444)ttC>ttA	p.F148L	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Missense_Mutation_p.F148L	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	148					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)	p.F148L(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CGGTCTTGGAGAACCTGAAGT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	76	76					15																	68653956		1978	4151	6129	66441010	SO:0001583	missense	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.444C>A	15.37:g.68653956G>T	ENSP00000327290:p.Phe148Leu		66441010	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	G	8.269	0.812932	0.16537	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.57107	0.42;0.44	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.35189	0.0923	N	0.15975	0.35	0.45415	D	0.998396	B;B	0.24317	0.022;0.101	B;B	0.27262	0.024;0.078	T	0.17258	-1.0375	10	0.07325	T	0.83	.	16.915	0.86149	0.0:0.0:1.0:0.0	.	148;148	A8K8T0;Q9UKX5	.;ITA11_HUMAN	L	148	ENSP00000327290:F148L;ENSP00000403392:F148L	ENSP00000327290:F148L	F	-	3	2	ITGA11	66441010	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.654000	0.46699	2.282000	0.76494	0.555000	0.69702	TTC		0.562	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68653956	G	T	68653956	3	4	47	1	0	0	0	0	1	0	0	0	7895	933	33	2	3226	2	ITGA11	15	68653956	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	184974	68653956	33877436	1625	6022										
CORO2B	10391	broad.mit.edu	37	chr15	69011767	69011767	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttagatcccgtgctgatgtCtttgaaagaaggctataaga	10	6	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:69011767C>A	ENST00000566799.1	+	11	1216	c.1187C>A	c.(1186-1188)tCt>tAt	p.S396Y	CORO2B_ENST00000540068.1_Missense_Mutation_p.S391Y|CORO2B_ENST00000543950.1_Missense_Mutation_p.S391Y|CORO2B_ENST00000261861.5_Missense_Mutation_p.S391Y			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	396					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)	p.S396Y(1)		kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						GTGCTGATGTCTTTGAAAGAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15											155	146	149					15																	69011767		2200	4298	6498	66798821	SO:0001583	missense	10391			AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"Coronins", "WD repeat domain containing"	2256	protein-coding gene	gene with protein product	"clipin C", "coronin, actin-binding, 2B"	605002	"coronin, actin-binding protein, 2B"			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.1187C>A	15.37:g.69011767C>A	ENSP00000454783:p.Ser396Tyr		66798821	A8K0W3|O94767|Q8TAN1	Missense_Mutation	SNP	ENST00000566799.1	37	CCDS10229.2	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969903	0.74246	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.38077	1.16;1.16	5.49	5.49	0.81192	Domain of unknown function DUF1900 (1);	.	.	.	.	T	0.62792	0.2457	M	0.82823	2.61	0.58432	D	0.999996	D	0.89917	1.0	D	0.83275	0.996	T	0.67565	-0.5638	9	0.87932	D	0	-7.7866	13.6458	0.62281	0.0:0.8447:0.1553:0.0	.	396	Q9UQ03	COR2B_HUMAN	Y	396;391;391	ENSP00000446250:S391Y;ENSP00000443819:S391Y	ENSP00000261861:S396Y	S	+	2	0	CORO2B	66798821	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.580000	0.67464	2.582000	0.87167	0.462000	0.41574	TCT		0.448	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091		A	69011767	C	A	69011767	3	1	47	1	0	0	0	0	1	0	0	0	3763	913	32	2	1229	2	CORO2B	15	69011767	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	357811	69011767	33519625	1626	6023										
CLK3	1198	broad.mit.edu	37	chr15	74918291	74918291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccggcacatggcctaccagCtctgccacgcccttagatgt	9	16	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:74918291C>A	ENST00000395066.3	+	7	1704	c.1243C>A	c.(1243-1245)Ctc>Atc	p.L415I	CLK3_ENST00000348245.3_3'UTR|CLK3_ENST00000345005.4_Missense_Mutation_p.L267I|CLK3_ENST00000352989.5_Missense_Mutation_p.L244I	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3	415	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.L267I(1)|p.L415I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						GGCCTACCAGCTCTGCCACGC	0.527																																					Ovarian(133;694 1754 28950 29027 31859)											2	Substitution - Missense(2)	large_intestine(2)	15											129	104	113					15																	74918291		2197	4296	6493	72705344	SO:0001583	missense	1198			L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.1243C>A	15.37:g.74918291C>A	ENSP00000378505:p.Leu415Ile		72705344	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Missense_Mutation	SNP	ENST00000395066.3	37	CCDS45304.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.733370	0.48939	.	.	ENSG00000179335	ENST00000345005;ENST00000395066;ENST00000454830;ENST00000352989	T;T	0.19250	2.16;2.16	5.57	4.66	0.58398	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000013	T	0.23133	0.0559	L	0.33624	1.015	0.80722	D	1	B;B;B;B	0.31680	0.024;0.328;0.335;0.012	B;P;B;B	0.45167	0.415;0.472;0.394;0.339	T	0.08848	-1.0702	10	0.21014	T	0.42	.	10.6454	0.45617	0.0:0.8541:0.0:0.1459	.	415;120;194;244	P49761;B3KVF3;B3KUU7;G5E959	CLK3_HUMAN;.;.;.	I	267;267;415;244	ENSP00000344112:L267I;ENSP00000323106:L244I	ENSP00000344112:L267I	L	+	1	0	CLK3	72705344	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.276000	0.33156	1.359000	0.45940	0.655000	0.94253	CTC		0.527	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3			A	74918291	C	A	74918291	3	1	47	1	0	0	0	0	1	0	0	0	3544	797	28	2	1269	2	CLK3	15	74918291	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5906524	74918291	27613101	1627	6024										
CYP1A2	1544	broad.mit.edu	37	chr15	75042427	75042427	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacctctacacctccaccctCatcactgatggccagagctt	6	17	3	2	rs71541923		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:75042427C>T	ENST00000343932.4	+	2	411	c.348C>T	c.(346-348)ctC>ctT	p.L116L		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	116					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.L116L(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"	CCTCCACCCTCATCACTGATG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	15											69	64	65					15																	75042427		2197	4295	6492	72829480	SO:0001819	synonymous_variant	1544			AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"Cytochrome P450s"	2596	protein-coding gene	gene with protein product		124060	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.348C>T	15.37:g.75042427C>T			72829480	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	37	CCDS32293.1																																																																																				0.667	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		T	75042427	C	T	75042427	2	4	47	1	0	0	0	0	0	0	0	1	4156	813	29	3		3	CYP1A2	15	75042427	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	124136	75042427	27488965	1628	6025										
C15orf27	123591	broad.mit.edu	37	chr15	76430069	76430069	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgccatagaaggaggaatTtctgaagttgagatcatctc	10	8	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:76430069T>G	ENST00000388942.3	+	3	336	c.60T>G	c.(58-60)atT>atG	p.I20M		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	20					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)	p.I20M(1)		endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						AAGGAGGAATTTCTGAAGTTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											135	140	139					15																	76430069		1930	4135	6065	74217124	SO:0001583	missense	123591			AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.60T>G	15.37:g.76430069T>G	ENSP00000373594:p.Ile20Met		74217124	Q8N993|Q96LL5	De_novo_Start_OutOfFrame	SNP	ENST00000388942.3	37	CCDS10289.2	.	.	.	.	.	.	.	.	.	.	T	10.73	1.431994	0.25813	.	.	ENSG00000169758	ENST00000388942	T	0.35048	1.33	4.96	3.84	0.44239	.	0.551776	0.16121	N	0.228670	T	0.32704	0.0838	L	0.44542	1.39	0.25753	N	0.985038	B	0.32526	0.374	B	0.36666	0.23	T	0.27606	-1.0069	10	0.72032	D	0.01	-1.0124	8.6202	0.33855	0.0:0.0877:0.0:0.9123	.	20	Q2M3C6	CO027_HUMAN	M	20	ENSP00000373594:I20M	ENSP00000373594:I20M	I	+	3	3	C15orf27	74217124	0.981000	0.34729	0.248000	0.24265	0.048000	0.14542	0.462000	0.21956	0.844000	0.35094	0.533000	0.62120	ATT		0.488	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335		G	76430069	T	G	76430069	3	3	47	1	0	0	0	0	1	0	0	0	1792	1829	64	4	66	4	C15orf27	15	76430069	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1387642	76430069	26101323	1629	6026										
SGK269	79834	broad.mit.edu	37	chr15	77407318	77407318	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggccagagagtctcgcacaAaatcagccacagtaagacat	10	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:77407318A>C	ENST00000560626.2	-	7	4896	c.4421T>G	c.(4420-4422)tTt>tGt	p.F1474C	PEAK1_ENST00000312493.4_Missense_Mutation_p.F1474C			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1474	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.F1474C(2)									GTCTCGCACAAAATCAGCCAC	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	15											113	111	111					15																	77407318		2119	4226	6345	75194373	SO:0001583	missense	79834				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4421T>G	15.37:g.77407318A>C	ENSP00000452796:p.Phe1474Cys		75194373	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.905612	0.72868	.	.	ENSG00000173517	ENST00000312493	T	0.75367	-0.93	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000001	D	0.85978	0.5823	M	0.77486	2.375	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	D	0.88022	0.2769	10	0.87932	D	0	-9.3498	14.9542	0.71098	1.0:0.0:0.0:0.0	.	1474	Q9H792	PEAK1_HUMAN	C	1474	ENSP00000309230:F1474C	ENSP00000309230:F1474C	F	-	2	0	AC087465.1	75194373	1.000000	0.71417	0.986000	0.45419	0.920000	0.55202	9.108000	0.94275	1.957000	0.56846	0.459000	0.35465	TTT		0.522	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			C	77407318	A	C	77407318	3	2	47	1	0	0	0	0	1	0	0	0	14248	14	1	4	823	4	SGK269	15	77407318	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	977249	77407318	25124074	1630	6027										
RASGRF1	5923	broad.mit.edu	37	chr15	79277358	79277358	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgcccgcacctgcttagaGactttgagccacgtcttttt	8	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:79277358G>T	ENST00000419573.3	-	24	3727	c.3453C>A	c.(3451-3453)gtC>gtA	p.V1151V	RASGRF1_ENST00000394745.3_Silent_p.V367V|RP11-16K12.1_ENST00000316148.4_RNA|RASGRF1_ENST00000558480.2_Silent_p.V1135V|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1151	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1151V(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CCTGCTTAGAGACTTTGAGCC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	15											86	67	73					15																	79277358		2196	4293	6489	77064413	SO:0001819	synonymous_variant	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3453C>A	15.37:g.79277358G>T			77064413	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																				0.597	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79277358	G	T	79277358	2	4	47	1	0	0	0	0	0	0	0	1	13109	929	33	2		2	RASGRF1	15	79277358	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1870040	79277358	23254034	1631	6028										
RASGRF1	5923	broad.mit.edu	37	chr15	79339123	79339123	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctgacgtcgtcgtgtgtGatgggaggcttcttggagct	16	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:79339123G>A	ENST00000419573.3	-	5	1117	c.843C>T	c.(841-843)atC>atT	p.I281I	RASGRF1_ENST00000558480.2_Silent_p.I281I|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	281	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I281I(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGTCGTGTGTGATGGGAGGCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	15											186	148	161					15																	79339123		2196	4293	6489	77126178	SO:0001819	synonymous_variant	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.843C>T	15.37:g.79339123G>A			77126178	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																				0.587	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79339123	G	A	79339123	2	1	47	1	0	0	0	0	0	0	0	1	13109	1280	45	3		3	RASGRF1	15	79339123	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	61765	79339123	23192269	1632	6029										
BCL2A1	597	broad.mit.edu	37	chr15	80263050	80263050	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcacacatacccagcctcCgttttgccttatccattctc	3	17	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:80263050C>A	ENST00000267953.3	-	1	738	c.412G>T	c.(412-414)Gga>Tga	p.G138*	BCL2A1_ENST00000335661.6_Nonsense_Mutation_p.G138*	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	138					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G138*(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						ACCCAGCCTCCGTTTTGCCTT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											109	115	113					15																	80263050		2203	4300	6503	78050105	SO:0001587	stop_gained	597				CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.412G>T	15.37:g.80263050C>A	ENSP00000267953:p.Gly138*		78050105	Q6FGZ4|Q6FH19|Q86W13|Q99524	Nonsense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	.	.	.	.	.	.	.	.	.	.	C	39	7.368792	0.98241	.	.	ENSG00000140379	ENST00000267953;ENST00000335661	.	.	.	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-19.9447	17.5676	0.87924	0.0:1.0:0.0:0.0	.	.	.	.	X	138	.	ENSP00000267953:G138X	G	-	1	0	BCL2A1	78050105	0.982000	0.34865	0.959000	0.39883	0.533000	0.34776	2.652000	0.46682	2.572000	0.86782	0.655000	0.94253	GGA		0.368	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		A	80263050	C	A	80263050	4	1	47	1	0	0	0	0	0	1	0	0	1367	661	23	2	183	2	BCL2A1	15	80263050	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	923927	80263050	22268342	1633	6030										
BCL2A1	597	broad.mit.edu	37	chr15	80263115	80263115	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caacaaaatatgaaatctccTtataggtatccacatccggg	6	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:80263115T>G	ENST00000267953.3	-	1	673	c.347A>C	c.(346-348)aAg>aCg	p.K116T	BCL2A1_ENST00000335661.6_Missense_Mutation_p.K116T	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	116					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.K116T(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						TGAAATCTCCTTATAGGTATC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											118	125	123					15																	80263115		2203	4300	6503	78050170	SO:0001583	missense	597				CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.347A>C	15.37:g.80263115T>G	ENSP00000267953:p.Lys116Thr		78050170	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.007207	0.54361	.	.	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.12147	2.71;2.71	5.39	5.39	0.77823	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.373188	0.25487	N	0.030325	T	0.30727	0.0774	M	0.69823	2.125	0.09310	N	0.999999	P;P	0.50443	0.935;0.793	P;P	0.55713	0.782;0.638	T	0.11179	-1.0598	10	0.56958	D	0.05	-14.0008	14.0059	0.64463	0.0:0.0:0.0:1.0	.	116;116	Q86W13;Q16548	.;B2LA1_HUMAN	T	116	ENSP00000267953:K116T;ENSP00000335250:K116T	ENSP00000267953:K116T	K	-	2	0	BCL2A1	78050170	0.156000	0.22821	0.007000	0.13788	0.012000	0.07955	1.925000	0.40074	2.043000	0.60533	0.482000	0.46254	AAG		0.378	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		G	80263115	T	G	80263115	3	3	47	1	0	0	0	0	1	0	0	0	1367	1609	56	4	248	4	BCL2A1	15	80263115	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	65	80263115	22268277	1634	6031										
TMC3	342125	broad.mit.edu	37	chr15	81654629	81654629	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttacaggcgagacgagcaAatttccgccagagctagaca	11	10	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:81654629A>C	ENST00000359440.5	-	4	461	c.326T>G	c.(325-327)tTt>tGt	p.F109C	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.F109C|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3									p.F109C(1)		autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						GAGACGAGCAAATTTCCGCCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											68	65	66					15																	81654629		2006	4177	6183	79441684	SO:0001583	missense	342125			AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.326T>G	15.37:g.81654629A>C	ENSP00000352413:p.Phe109Cys		79441684		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.647341	0.47258	.	.	ENSG00000188869	ENST00000359440	T	0.70399	-0.48	5.02	3.87	0.44632	.	0.272597	0.30185	N	0.010213	T	0.69744	0.3145	M	0.75447	2.3	0.42241	D	0.991933	B;B	0.14805	0.002;0.011	B;B	0.16722	0.009;0.016	T	0.67452	-0.5667	10	0.62326	D	0.03	-6.708	11.7689	0.51947	0.8524:0.1476:0.0:0.0	.	109;109	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	C	109	ENSP00000352413:F109C	ENSP00000352413:F109C	F	-	2	0	TMC3	79441684	1.000000	0.71417	0.927000	0.36925	0.992000	0.81027	6.194000	0.72082	0.730000	0.32425	0.455000	0.32223	TTT		0.473	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		C	81654629	A	C	81654629	3	2	47	1	0	0	0	0	1	0	0	0	16025	14	1	4	3052	4	TMC3	15	81654629	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1391514	81654629	20876763	1635	6032										
FAM154B	283726	broad.mit.edu	37	chr15	82575068	82575068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaaagcatcatgaaagaaGattttccagcatgggaaagt	10	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:82575068G>T	ENST00000339465.5	+	3	931	c.862G>T	c.(862-864)Gat>Tat	p.D288Y	FAM154B_ENST00000427381.2_Missense_Mutation_p.D273Y|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	288								p.D288Y(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						CATGAAAGAAGATTTTCCAGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											65	66	65					15																	82575068		2203	4300	6503	80362123	SO:0001583	missense	283726			AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.862G>T	15.37:g.82575068G>T	ENSP00000340445:p.Asp288Tyr		80362123	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107816	0.56291	.	.	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.38560	1.13;1.13	4.46	3.49	0.39957	.	0.072169	0.52532	D	0.000079	T	0.67608	0.2911	M	0.87682	2.9	0.47698	D	0.999494	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73049	-0.4105	10	0.52906	T	0.07	-21.6491	14.2307	0.65890	0.0:0.1509:0.8491:0.0	.	273;288	B4E2M2;Q658L1	.;F154B_HUMAN	Y	288;273	ENSP00000340445:D288Y;ENSP00000403743:D273Y	ENSP00000340445:D288Y	D	+	1	0	FAM154B	80362123	1.000000	0.71417	0.994000	0.49952	0.631000	0.37964	6.186000	0.72026	0.917000	0.36895	0.404000	0.27445	GAT		0.403	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		T	82575068	G	T	82575068	3	4	47	1	0	0	0	0	1	0	0	0	5480	942	33	2	872	2	FAM154B	15	82575068	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	920439	82575068	19956324	1636	6033										
ADAMTSL3	57188	broad.mit.edu	37	chr15	84639305	84639305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaggctggcagccaaaggtCggcgcatccccctcagtgag	13	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:84639305C>T	ENST00000286744.5	+	20	2784	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	ADAMTSL3_ENST00000567716.1_3'UTR|ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R854W	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	854	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R854W(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGCCAAAGGTCGGCGCATCCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	15											180	160	167					15																	84639305		2203	4300	6503	82430309	SO:0001583	missense	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2560C>T	15.37:g.84639305C>T	ENSP00000286744:p.Arg854Trp		82430309	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442158	0.63067	.	.	ENSG00000156218	ENST00000286744	T	0.53857	0.6	4.39	4.39	0.52855	.	0.414870	0.17881	N	0.158864	T	0.67970	0.2950	M	0.73372	2.23	0.43462	D	0.995666	D;D	0.71674	0.994;0.998	P;P	0.57846	0.711;0.828	T	0.72830	-0.4174	10	0.66056	D	0.02	.	16.75	0.85483	0.0:1.0:0.0:0.0	.	854;854	P82987-2;P82987	.;ATL3_HUMAN	W	854	ENSP00000286744:R854W	ENSP00000286744:R854W	R	+	1	2	ADAMTSL3	82430309	1.000000	0.71417	0.995000	0.50966	0.558000	0.35554	3.356000	0.52269	2.256000	0.74724	0.650000	0.86243	CGG		0.507	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84639305	C	T	84639305	3	4	47	1	0	0	0	0	1	0	0	0	276	875	31	1	2634	1	ADAMTSL3	15	84639305	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2064237	84639305	17892087	1637	6034										
ADAMTSL3	57188	broad.mit.edu	37	chr15	84694131	84694131	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgcccctaaagaccggccTctgggaagaaaaccatgttt	10	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:84694131T>C	ENST00000286744.5	+	27	4823	c.4599T>C	c.(4597-4599)ccT>ccC	p.P1533P	ADAMTSL3_ENST00000567476.1_Silent_p.P1533P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1533	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P1533P(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAGACCGGCCTCTGGGAAGAA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15											114	103	107					15																	84694131		2203	4299	6502	82485135	SO:0001819	synonymous_variant	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4599T>C	15.37:g.84694131T>C			82485135	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																				0.517	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		C	84694131	T	C	84694131	2	2	47	1	0	0	0	0	0	0	0	1	276	1538	54	4		4	ADAMTSL3	15	84694131	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	54826	84694131	17837261	1638	6035										
ZSCAN2	54993	broad.mit.edu	37	chr15	85164941	85164941	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagaaaccctacaaatgcagCgagtgtgggaaatgcttcag	12	8	1	1	rs141281638		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:85164941C>T	ENST00000448803.2	+	3	1807	c.1515C>T	c.(1513-1515)agC>agT	p.S505S	ZSCAN2_ENST00000327179.6_Silent_p.S504S|ZSCAN2_ENST00000546148.1_Silent_p.S505S|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000358472.3_Silent_p.S355S|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000541040.1_Intron	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	505					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S505S(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		ACAAATGCAGCGAGTGTGGGA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C		1,4405	2.1+/-5.4	0,1,2202	97	94	95		1515	-5.1	0	15	dbSNP_134	95	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZSCAN2	NM_181877.3		0,2,6500	TT,TC,CC		0.0116,0.0227,0.0154		505/615	85164941	2,13002	2203	4299	6502	82965945	SO:0001819	synonymous_variant	54993			BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"-", "Zinc fingers, C2H2-type"	20994	protein-coding gene	gene with protein product			"zinc finger protein 29"	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1515C>T	15.37:g.85164941C>T			82965945	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Silent	SNP	ENST00000448803.2	37	CCDS10329.2																																																																																				0.587	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		T	85164941	C	T	85164941	2	4	47	1	0	0	0	0	0	0	0	1	18270	767	27	1		1	ZSCAN2	15	85164941	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	470810	85164941	17366451	1639	6036										
PLIN1	5346	broad.mit.edu	37	chr15	90220717	90220717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgaggcctttgttgactgCcatcctcgctcctcaagctg	11	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:90220717C>T	ENST00000300055.5	-	2	169	c.4G>A	c.(4-6)Gca>Aca	p.A2T	PEX11A_ENST00000557982.1_5'Flank|PLIN1_ENST00000430628.2_Missense_Mutation_p.A2T	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	2					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)	p.A2T(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						TTGTTGACTGCCATCCTCGCT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	15											253	226	235					15																	90220717		2200	4299	6499	88021721	SO:0001583	missense	5346			AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.4G>A	15.37:g.90220717C>T	ENSP00000300055:p.Ala2Thr		88021721	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	37	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872047	0.33069	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.17528	2.27;2.27	5.78	3.86	0.44501	.	0.708385	0.12605	N	0.454349	T	0.06872	0.0175	N	0.08118	0	0.23082	N	0.998323	B	0.29766	0.256	B	0.25614	0.062	T	0.38178	-0.9673	10	0.12766	T	0.61	-5.8261	4.7609	0.13108	0.1806:0.6373:0.0:0.1821	.	2	O60240	PLIN1_HUMAN	T	2	ENSP00000300055:A2T;ENSP00000402167:A2T	ENSP00000300055:A2T	A	-	1	0	PLIN1	88021721	1.000000	0.71417	0.964000	0.40570	0.534000	0.34807	1.535000	0.36061	0.762000	0.33152	0.650000	0.86243	GCA		0.562	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		T	90220717	C	T	90220717	3	4	47	1	0	0	0	0	1	0	0	0	12120	739	26	3	1596	3	PLIN1	15	90220717	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5055776	90220717	12310675	1640	6037										
ANPEP	290	broad.mit.edu	37	chr15	90348345	90348345	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctgcttctccacgtagtcGaactcactgacaatgaaggc	9	13	2	2	rs141615930	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:90348345G>A	ENST00000300060.6	-	4	1174	c.861C>T	c.(859-861)ttC>ttT	p.F287F	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	287	Interaction with HCoV-229E.|Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.F287F(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CCACGTAGTCGAACTCACTGA	0.577													G|||	3	0.000599042	0.0023	0	5008	,	,		20148	0		0	False		,,,				2504	0				NSCLC(30;827 977 2459 19669 26125)											1	Substitution - coding silent(1)	large_intestine(1)	15						G		20,4380	27.2+/-55.0	0,20,2180	276	229	244		861	-0.3	0.2	15	dbSNP_134	244	0,8598		0,0,4299	no	coding-synonymous	ANPEP	NM_001150.2		0,20,6479	AA,AG,GG		0.0,0.4545,0.1539		287/968	90348345	20,12978	2200	4299	6499	88149349	SO:0001819	synonymous_variant	290			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.861C>T	15.37:g.90348345G>A			88149349	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																				0.577	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			A	90348345	G	A	90348345	2	1	47	1	0	0	0	0	0	0	0	1	710	1049	37	1		1	ANPEP	15	90348345	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	127628	90348345	12183047	1641	6038										
TTLL13	440307	broad.mit.edu	37	chr15	90796557	90796557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actctgtactggacagactgCgctgtctcactggaacgagt	11	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:90796557C>T	ENST00000561573.1	+	4	639	c.375C>T	c.(373-375)tgC>tgT	p.C125C	TTLL13_ENST00000438251.1_Silent_p.C125C|TTLL13_ENST00000339615.5_Silent_p.C125C														p.C125C(1)									GGACAGACTGCGCTGTCTCAC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	15											151	98	116					15																	90796557		2199	4298	6497	88597561	SO:0001819	synonymous_variant	440307																														ENST00000561573.1:c.375C>T	15.37:g.90796557C>T			88597561		Silent	SNP	ENST00000561573.1	37																																																																																					0.572	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1			T	90796557	C	T	90796557	2	4	47	1	0	0	0	0	0	0	0	1	16766	776	27	1		1	TTLL13	15	90796557	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	448212	90796557	11734835	1642	6039										
BLM	641	broad.mit.edu	37	chr15	91341469	91341469	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtgaaaagtattgtaagatTtgttcaagaacatagttcat	8	3	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:91341469T>G	ENST00000355112.3	+	17	3378	c.3260T>G	c.(3259-3261)tTt>tGt	p.F1087C	BLM_ENST00000560509.1_Missense_Mutation_p.F1087C|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1087					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)	p.F1087C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			ATTGTAAGATTTGTTCAAGAA	0.318			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																													yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	15											113	113	113					15																	91341469		2198	4297	6495	89142473	SO:0001583	missense	641	Familial Cancer Database		U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3260T>G	15.37:g.91341469T>G	ENSP00000347232:p.Phe1087Cys		89142473	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.178454	0.57692	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.40476	1.03	5.66	5.66	0.87406	RQC domain (2);	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	L	0.58302	1.8	0.80722	D	1	B;B	0.22003	0.063;0.063	B;B	0.27380	0.079;0.079	T	0.23691	-1.0181	10	0.21540	T	0.41	-21.0432	13.8415	0.63441	0.0:0.0:0.0:1.0	.	1087;1087	B2RAN0;P54132	.;BLM_HUMAN	C	1087;717;274	ENSP00000347232:F1087C	ENSP00000347232:F1087C	F	+	2	0	BLM	89142473	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	7.845000	0.86875	2.161000	0.67846	0.477000	0.44152	TTT		0.318	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			G	91341469	T	G	91341469	3	3	47	1	0	0	0	0	1	0	0	0	1446	1841	64	4	3322	4	BLM	15	91341469	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	544912	91341469	11189923	1643	6040										
UNC45A	55898	broad.mit.edu	37	chr15	91482979	91482979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtgcgatacatgtcctcgAcggatgccaaagtggaacag	13	9	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:91482979A>G	ENST00000418476.2	+	5	485	c.445A>G	c.(445-447)Acg>Gcg	p.T149A	UNC45A_ENST00000553671.2_3'UTR|UNC45A_ENST00000394275.2_Missense_Mutation_p.T134A	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	149					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.T149A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CATGTCCTCGACGGATGCCAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											143	123	130					15																	91482979		2198	4298	6496	89283983	SO:0001583	missense	55898				CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.445A>G	15.37:g.91482979A>G	ENSP00000407487:p.Thr149Ala		89283983	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.911568	0.92178	.	.	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.05996	3.36;3.37	5.98	5.98	0.97165	Armadillo-like helical (1);Armadillo-type fold (1);	0.324438	0.32503	N	0.006014	T	0.24851	0.0603	M	0.73962	2.25	0.58432	D	0.999999	D;D;D;D	0.76494	0.997;0.999;0.997;0.997	D;D;D;D	0.79784	0.985;0.993;0.985;0.985	T	0.00448	-1.1733	10	0.37606	T	0.19	-22.171	15.5109	0.75782	1.0:0.0:0.0:0.0	.	149;141;149;134	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	A	134;149	ENSP00000377816:T134A;ENSP00000407487:T149A	ENSP00000377816:T134A	T	+	1	0	UNC45A	89283983	1.000000	0.71417	0.612000	0.29024	0.992000	0.81027	7.745000	0.85046	2.307000	0.77673	0.529000	0.55759	ACG		0.488	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		G	91482979	A	G	91482979	3	3	47	1	0	0	0	0	1	0	0	0	17028	275	10	4	463	4	UNC45A	15	91482979	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	141510	91482979	11048413	1644	6041										
CHD2	1106	broad.mit.edu	37	chr15	93545498	93545498	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaaatgagttctaggaaagAcaaagaaggggacaaggaaa	12	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:93545498A>C	ENST00000394196.4	+	33	5297	c.4229A>C	c.(4228-4230)gAc>gCc	p.D1410A	CHD2_ENST00000557381.1_Missense_Mutation_p.D1410A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1410					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.D1410A(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			tctaggaaagacaaagaaggg	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											121	121	121					15																	93545498		2197	4298	6495	91346502	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4229A>C	15.37:g.93545498A>C	ENSP00000377747:p.Asp1410Ala		91346502	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	10.13	1.266446	0.23136	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;T	0.02197	4.4;4.4	4.89	4.89	0.63831	.	0.231001	0.21408	U	0.075040	T	0.02455	0.0075	L	0.36672	1.1	0.80722	D	1	B;B	0.18741	0.005;0.03	B;B	0.20767	0.014;0.031	T	0.53322	-0.8455	10	0.17369	T	0.5	-21.5003	11.1847	0.48648	1.0:0.0:0.0:0.0	.	1410;1410	O14647;O14647-2	CHD2_HUMAN;.	A	1410	ENSP00000377747:D1410A;ENSP00000451366:D1410A	ENSP00000377747:D1410A	D	+	2	0	CHD2	91346502	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.132000	0.64758	1.954000	0.56735	0.533000	0.62120	GAC		0.388	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93545498	A	C	93545498	3	2	47	1	0	0	0	0	1	0	0	0	3331	275	10	4	4359	4	CHD2	15	93545498	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2062519	93545498	8985894	1645	6042										
LASS3	204219	broad.mit.edu	37	chr15	101016297	101016297	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataagacacttacctttctCttgacatcaaagccaagtct	4	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:101016297C>A	ENST00000394113.1	-	10	1293	c.603G>T	c.(601-603)aaG>aaT	p.K201N	CERS3_ENST00000284382.4_Missense_Mutation_p.K201N|CERS3_ENST00000560944.1_Intron|CERS3_ENST00000538112.2_Missense_Mutation_p.K201N			Q8IU89	CERS3_HUMAN	ceramide synthase 3	201	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.K201N(1)									TTACCTTTCTCTTGACATCAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											64	71	69					15																	101016297		2203	4297	6500	98833820	SO:0001583	missense	204219				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.603G>T	15.37:g.101016297C>A	ENSP00000377672:p.Lys201Asn		98833820	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.150098	0.57151	.	.	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	D;D	0.85955	-2.05;-2.05	5.36	3.48	0.39840	TRAM/LAG1/CLN8 homology domain (3);	0.046039	0.85682	D	0.000000	D	0.92388	0.7584	M	0.91561	3.22	0.53688	D	0.999975	D	0.76494	0.999	D	0.72982	0.979	D	0.92342	0.5882	10	0.87932	D	0	-23.105	8.5461	0.33421	0.0:0.7613:0.0:0.2387	.	201	Q8IU89	CERS3_HUMAN	N	201;212;201	ENSP00000284382:K201N;ENSP00000437640:K201N	ENSP00000284382:K201N	K	-	3	2	CERS3	98833820	1.000000	0.71417	0.999000	0.59377	0.676000	0.39594	0.614000	0.24314	1.269000	0.44280	-0.216000	0.12614	AAG		0.358	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		A	101016297	C	A	101016297	3	1	47	1	0	0	0	0	1	0	0	0	8662	912	32	2	568	2	LASS3	15	101016297	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7470799	101016297	1515095	1646	6043										
LASS3	204219	broad.mit.edu	37	chr15	101031058	101031058	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggaatgtttgaaaaaattCtctaagacagtatttggtgt	10	3	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:101031058C>A	ENST00000394113.1	-	6	942	c.252G>T	c.(250-252)gaG>gaT	p.E84D	CERS3_ENST00000284382.4_Missense_Mutation_p.E84D|CERS3_ENST00000560944.1_Intron|CERS3_ENST00000538112.2_Missense_Mutation_p.E84D			Q8IU89	CERS3_HUMAN	ceramide synthase 3	84					ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.E84D(2)									TGAAAAAATTCTCTAAGACAG	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	15											111	110	110					15																	101031058		2203	4299	6502	98848581	SO:0001583	missense	204219				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.252G>T	15.37:g.101031058C>A	ENSP00000377672:p.Glu84Asp		98848581	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620296	0.87460	.	.	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	D;D	0.97791	-4.54;-4.54	5.53	5.53	0.82687	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98874	0.9619	M	0.89658	3.05	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.99425	1.0934	10	0.87932	D	0	-22.871	15.3311	0.74212	0.0:1.0:0.0:0.0	.	84	Q8IU89	CERS3_HUMAN	D	84;95;84	ENSP00000284382:E84D;ENSP00000437640:E84D	ENSP00000284382:E84D	E	-	3	2	CERS3	98848581	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.111000	0.50360	2.763000	0.94921	0.563000	0.77884	GAG		0.303	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		A	101031058	C	A	101031058	3	1	47	1	0	0	0	0	1	0	0	0	8662	912	32	2	935	2	LASS3	15	101031058	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	14761	101031058	1500334	1647	6044										
ASB7	140460	broad.mit.edu	37	chr15	101188654	101188654	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agactacttaaaacacaaatTtgatgatatctgatatgcca	5	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:101188654T>G	ENST00000332783.7	+	6	1729	c.944T>G	c.(943-945)tTt>tGt	p.F315C	ASB7_ENST00000558747.1_Missense_Mutation_p.F113C	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	315	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.F315C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	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)			AAACACAAATTTGATGATATC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	82	84					15																	101188654		2203	4300	6503	99006177	SO:0001583	missense	140460				CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"Ankyrin repeat domain containing"	17182	protein-coding gene	gene with protein product		615052	"ankyrin repeat and SOCS box-containing 7"				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.944T>G	15.37:g.101188654T>G	ENSP00000328327:p.Phe315Cys		99006177	A8K1E5|Q6GSJ6|Q7Z4S3	Missense_Mutation	SNP	ENST00000332783.7	37	CCDS10387.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.092697	0.76756	.	.	ENSG00000183475	ENST00000332783	T	0.44083	0.93	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	L	0.48642	1.525	0.80722	D	1	D	0.63046	0.992	P	0.60117	0.869	T	0.56902	-0.7902	10	0.62326	D	0.03	-12.2009	15.657	0.77144	0.0:0.0:0.0:1.0	.	315	Q9H672	ASB7_HUMAN	C	315	ENSP00000328327:F315C	ENSP00000328327:F315C	F	+	2	0	ASB7	99006177	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.509000	0.81698	2.097000	0.63578	0.533000	0.62120	TTT		0.348	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708		G	101188654	T	G	101188654	3	3	47	1	0	0	0	0	1	0	0	0	1029	1841	64	4	962	4	ASB7	15	101188654	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	157596	101188654	1342738	1648	6045										
PCSK6	5046	broad.mit.edu	37	chr15	101971646	101971646	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattcatttccgaccggcagCgactgttcttgtcgccacaa	8	14	2	0	rs370069260		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:101971646C>T	ENST00000348070.1	-	5	532	c.533G>A	c.(532-534)cGc>cAc	p.R178H	PCSK6_ENST00000398181.2_Missense_Mutation_p.R178H|PCSK6_ENST00000344273.2_Missense_Mutation_p.R178H|PCSK6_ENST00000358417.3_Missense_Mutation_p.R178H|PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000331826.7_Missense_Mutation_p.R13H	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	179					determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)	p.R178H(3)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGACCGGCAGCGACTGTTCTT	0.527																																																3	Substitution - Missense(3)	large_intestine(3)	15						T	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4168		0,0,2084	63	64	64		534,534,534,534,534,534,534,534	4.8	1	15		64	1,8433		0,1,4216	no	missense,missense,missense,missense,missense,missense,missense,missense	PCSK6	NM_002570.3,NM_138319.2,NM_138320.1,NM_138321.1,NM_138322.2,NM_138323.1,NM_138324.1,NM_138325.2	29,29,29,29,29,29,29,29	0,1,6300	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	179/970,179/957,179/976,179/963,179/488,179/624,179/653,179/665	101971646	1,12601	2084	4217	6301	99789169	SO:0001583	missense	5046				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"subtilisin-like protease", "subtilisin-like proprotein convertase 4", "subtilisin/kexin-like protease PACE4"	167405	"paired basic amino acid cleaving system 4"	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.533G>A	15.37:g.101971646C>T	ENSP00000305056:p.Arg178His		99789169	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Missense_Mutation	SNP	ENST00000348070.1	37		.	.	.	.	.	.	.	.	.	.	c	14.75	2.629658	0.46944	0.0	1.19E-4	ENSG00000140479	ENST00000348070;ENST00000358417;ENST00000398185;ENST00000344273;ENST00000398181;ENST00000331826	T;T;T;T;T;T	0.70749	0.92;0.92;-0.26;0.92;0.92;-0.51	5.67	4.76	0.60689	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.053107	0.85682	N	0.000000	T	0.68238	0.2979	N	0.10707	0.03	0.36438	D	0.865298	D;D;B;B;B;B;D;P;B	0.89917	1.0;0.998;0.038;0.211;0.134;0.134;1.0;0.5;0.119	D;P;B;B;B;B;D;B;B	0.78314	0.991;0.862;0.01;0.052;0.023;0.023;0.964;0.106;0.072	T	0.73442	-0.3981	10	0.29301	T	0.29	-42.069	13.9808	0.64304	0.0:0.9276:0.0:0.0724	.	179;84;178;179;178;178;179;179;178	P29122;Q59H04;E7EUC8;P29122-4;E7EWH5;E7EQ62;P29122-8;P29122-7;E7EM82	PCSK6_HUMAN;.;.;.;.;.;.;.;.	H	178;178;83;178;178;13	ENSP00000305056:R178H;ENSP00000351193:R178H;ENSP00000381246:R83H;ENSP00000344410:R178H;ENSP00000381243:R178H;ENSP00000332052:R13H	ENSP00000332052:R13H	R	-	2	0	PCSK6	99789169	1.000000	0.71417	0.994000	0.49952	0.912000	0.54170	1.692000	0.37731	1.431000	0.47355	-0.119000	0.15052	CGC		0.527	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570		T	101971646	C	T	101971646	3	4	47	1	0	0	0	0	1	0	0	0	11635	768	27	1	2928	1	PCSK6	15	101971646	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	782992	101971646	559746	1649	6046										
OR4F15	390649	broad.mit.edu	37	chr15	102358805	102358805	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgaccatcatgagcccaaGaatgtgtctatactttttag	7	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr15:102358805G>T	ENST00000332238.4	+	1	440	c.416G>T	c.(415-417)aGa>aTa	p.R139I		NM_001001674.1	NP_001001674.1	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F, member 15	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R139I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(10)	19	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			ATGAGCCCAAGAATGTGTCTA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	15											229	212	218					15																	102358805		2203	4300	6503	100176328	SO:0001583	missense	390649			BK004405	CCDS32342.1	15q26.3	2012-08-09				ENSG00000182854		"GPCR / Class A : Olfactory receptors"	15078	protein-coding gene	gene with protein product							Standard	NM_001001674		Approved		uc010uts.2	Q8NGB8		ENST00000332238.4:c.416G>T	15.37:g.102358805G>T	ENSP00000333184:p.Arg139Ile		100176328	B2RNQ5|Q6IF57|Q96R70	Missense_Mutation	SNP	ENST00000332238.4	37	CCDS32342.1	.	.	.	.	.	.	.	.	.	.	.	12.40	1.928104	0.34002	.	.	ENSG00000182854	ENST00000332238	T	0.43294	0.95	5.57	0.346	0.16017	GPCR, rhodopsin-like superfamily (1);	0.424311	0.21782	N	0.069193	T	0.57975	0.2090	M	0.88570	2.965	0.09310	N	1	P	0.42078	0.77	P	0.52710	0.707	T	0.53351	-0.8451	9	.	.	.	.	8.5575	0.33489	0.559:0.0:0.441:0.0	.	139	Q8NGB8	O4F15_HUMAN	I	139	ENSP00000333184:R139I	.	R	+	2	0	OR4F15	100176328	0.000000	0.05858	0.000000	0.03702	0.276000	0.26787	-0.510000	0.06328	-0.078000	0.12730	0.650000	0.86243	AGA		0.443	OR4F15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417594.1	NM_001001674		T	102358805	G	T	102358805	3	4	47	1	0	0	0	0	1	0	0	0	11092	942	33	2	418	2	OR4F15	15	102358805	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	387159	102358805	172587	1650	6047										
ZNF200	7752	broad.mit.edu	37	chr16	3274570	3274570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatcttcattttctacaggTtccctctcaggatcttcacc	4	13	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:3274570T>A	ENST00000431561.3	-	5	1122	c.510A>T	c.(508-510)gaA>gaT	p.E170D	AJ003147.9_ENST00000576468.1_RNA|ZNF200_ENST00000414144.2_Missense_Mutation_p.E170D|ZNF200_ENST00000396868.3_Missense_Mutation_p.E169D|ZNF200_ENST00000575948.1_Missense_Mutation_p.E169D|ZNF200_ENST00000396871.4_Missense_Mutation_p.E169D|ZNF200_ENST00000396870.4_Missense_Mutation_p.E169D	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.E170D(1)		breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						TTTCTACAGGTTCCCTCTCAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	16											80	80	80					16																	3274570		2197	4300	6497	3214571	SO:0001583	missense	7752			AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.510A>T	16.37:g.3274570T>A	ENSP00000395723:p.Glu170Asp		3214571	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	37	CCDS10497.1	.	.	.	.	.	.	.	.	.	.	T	9.877	1.200474	0.22121	.	.	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T	0.07114	3.22;3.25;3.31	5.0	3.89	0.44902	.	0.175046	0.27535	N	0.018934	T	0.09512	0.0234	L	0.54323	1.7	0.09310	N	1	B;B;B	0.14805	0.006;0.006;0.011	B;B;B	0.18263	0.009;0.009;0.021	T	0.20605	-1.0270	10	0.62326	D	0.03	-5.0367	7.9476	0.29995	0.1821:0.0:0.0:0.8179	.	169;170;169	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	D	170;169;169;169;170	ENSP00000380077:E169D;ENSP00000380080:E169D;ENSP00000395723:E170D	ENSP00000380077:E169D	E	-	3	2	ZNF200	3214571	0.173000	0.23056	0.303000	0.25071	0.009000	0.06853	0.688000	0.25422	0.889000	0.36185	0.374000	0.22700	GAA		0.418	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			A	3274570	T	A	3274570	3	1	47	1	0	0	0	0	1	0	0	0	17801	1722	60	5	681	5	ZNF200	16	3274570	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09		3274570	87080183	1651	6048										
UBN1	29855	broad.mit.edu	37	chr16	4910871	4910871	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaccccttgctctcactctTtggctctacttctgacaacg	6	15	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:4910871T>G	ENST00000396658.4	+	6	1581	c.878T>G	c.(877-879)tTt>tGt	p.F293C	UBN1_ENST00000585857.1_3'UTR|UBN1_ENST00000590769.1_Missense_Mutation_p.F293C|UBN1_ENST00000545171.1_Missense_Mutation_p.F293C|UBN1_ENST00000262376.6_Missense_Mutation_p.F293C	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	293					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F293C(1)		NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						CTCTCACTCTTTGGCTCTACT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											158	127	137					16																	4910871		2197	4300	6497	4850872	SO:0001583	missense	29855			AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.878T>G	16.37:g.4910871T>G	ENSP00000379894:p.Phe293Cys		4850872	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	37	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.196696	0.58126	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.51325	1.3;0.71;1.3	5.77	5.77	0.91146	.	0.162599	0.56097	D	0.000036	T	0.62877	0.2464	L	0.59436	1.845	0.39588	D	0.969542	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.949	T	0.66689	-0.5860	10	0.62326	D	0.03	-17.2381	11.4648	0.50232	0.1342:0.0:0.0:0.8658	.	293;293	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	C	293	ENSP00000262376:F293C;ENSP00000442379:F293C;ENSP00000379894:F293C	ENSP00000262376:F293C	F	+	2	0	UBN1	4850872	1.000000	0.71417	0.995000	0.50966	0.605000	0.37080	4.451000	0.60047	2.326000	0.78906	0.533000	0.62120	TTT		0.572	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		G	4910871	T	G	4910871	3	3	47	1	0	0	0	0	1	0	0	0	16932	1841	64	4	900	4	UBN1	16	4910871	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1636301	4910871	85443882	1652	6049										
GRIN2A	2903	broad.mit.edu	37	chr16	9857657	9857657	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaagcatctggtcttcatcGatgtcatagaggttccccat	9	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:9857657G>A	ENST00000396573.2	-	14	4053	c.3744C>T	c.(3742-3744)atC>atT	p.I1248I	GRIN2A_ENST00000404927.2_Silent_p.I1248I|GRIN2A_ENST00000562109.1_Silent_p.I1248I|GRIN2A_ENST00000396575.2_Silent_p.I1248I|GRIN2A_ENST00000330684.3_Silent_p.I1248I|GRIN2A_ENST00000535259.1_Silent_p.I1091I	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1248					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.I1248I(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GGTCTTCATCGATGTCATAGA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	16											121	113	116					16																	9857657		2197	4300	6497	9765158	SO:0001819	synonymous_variant	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3744C>T	16.37:g.9857657G>A			9765158	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.547	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9857657	G	A	9857657	2	1	47	1	0	0	0	0	0	0	0	1	6800	1048	37	1		1	GRIN2A	16	9857657	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4946786	9857657	80497096	1653	6050										
CLEC16A	23274	broad.mit.edu	37	chr16	11071092	11071092	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcctggcaggcatcggaatCggggtaaactgagtgatctg	14	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:11071092C>T	ENST00000409790.1	+	8	969	c.739C>T	c.(739-741)Cgg>Tgg	p.R247W	CLEC16A_ENST00000409552.3_Missense_Mutation_p.R245W	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.R247W(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCATCGGAATCGGGGTAAACT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	16											131	130	130					16																	11071092		2040	4191	6231	10978593	SO:0001583	missense	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.739C>T	16.37:g.11071092C>T	ENSP00000387122:p.Arg247Trp		10978593		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047592	0.75846	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.48522	0.81	5.81	4.81	0.61882	.	0.045054	0.85682	D	0.000000	T	0.62539	0.2436	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.95	T	0.63642	-0.6591	10	0.72032	D	0.01	-22.7045	11.1775	0.48607	0.3505:0.6495:0.0:0.0	.	247;245	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	W	247;247;245	ENSP00000387122:R247W	ENSP00000386495:R245W	R	+	1	2	CLEC16A	10978593	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.561000	0.53770	2.746000	0.94184	0.655000	0.94253	CGG		0.517	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11071092	C	T	11071092	3	4	47	1	0	0	0	0	1	0	0	0	3506	875	31	1	765	1	CLEC16A	16	11071092	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1213435	11071092	79283661	1654	6051										
PRM1	5619	broad.mit.edu	37	chr16	11375010	11375010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctcctccgtgtctggcagCtccgcctccttcgtctgcga	9	18	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:11375010C>T	ENST00000312511.3	-	1	197	c.86G>A	c.(85-87)aGc>aAc	p.S29N	RMI2_ENST00000572173.1_Intron	NM_002761.2	NP_002752.1	P04553	HSP1_HUMAN	protamine 1	29					cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)	DNA binding (GO:0003677)	p.0?(1)|p.S29N(1)		large_intestine(2)|skin(2)	4						TGTCTGGCAGCTCCGCCTCCT	0.627																																																2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											117	107	110					16																	11375010		2197	4300	6497	11282511	SO:0001583	missense	5619				CCDS10547.1	16p13.2	2009-08-06			ENSG00000175646	ENSG00000175646			9447	protein-coding gene	gene with protein product	"cancer/testis antigen family 94, member 1"	182880					Standard	NM_002761		Approved	CT94.1	uc002dav.3	P04553	OTTHUMG00000090521	ENST00000312511.3:c.86G>A	16.37:g.11375010C>T	ENSP00000310515:p.Ser29Asn		11282511		Missense_Mutation	SNP	ENST00000312511.3	37	CCDS10547.1	.	.	.	.	.	.	.	.	.	.	C	8.476	0.858743	0.17178	.	.	ENSG00000175646	ENST00000312511	.	.	.	4.49	1.23	0.21249	.	1.115980	0.06875	N	0.801427	T	0.33059	0.0850	.	.	.	0.09310	N	1	B	0.30211	0.273	B	0.34093	0.175	T	0.41466	-0.9507	8	0.87932	D	0	-2.9089	3.1596	0.06516	0.1787:0.5477:0.1736:0.1	.	29	P04553	HSP1_HUMAN	N	29	.	ENSP00000310515:S29N	S	-	2	0	PRM1	11282511	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.538000	0.23160	0.482000	0.27582	0.484000	0.47621	AGC		0.627	PRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207010.1			T	11375010	C	T	11375010	3	4	47	1	0	0	0	0	1	0	0	0	12566	797	28	3	77	3	PRM1	16	11375010	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	303918	11375010	78979743	1655	6052										
RSL1D1	26156	broad.mit.edu	37	chr16	11941570	11941570	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtttaaaagctttctataAaactgttctgtcttttcagg	6	6	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:11941570A>C	ENST00000571133.1	-	3	411	c.339T>G	c.(337-339)ttT>ttG	p.F113L	RSL1D1_ENST00000542106.1_5'UTR	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	113					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.F113L(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						GCTTTCTATAAAACTGTTCTG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	16											97	92	93					16																	11941570		2197	4300	6497	11849071	SO:0001583	missense	26156			AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.339T>G	16.37:g.11941570A>C	ENSP00000460871:p.Phe113Leu		11849071	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.092185	0.36952	.	.	ENSG00000171490	ENST00000355674;ENST00000396503	T	0.38560	1.13	5.0	2.73	0.32206	Ribosomal protein L1, superfamily (1);	0.343779	0.34291	N	0.004083	T	0.32255	0.0823	L	0.41573	1.285	0.80722	D	1	P;P	0.42337	0.776;0.47	P;B	0.44811	0.461;0.178	T	0.06445	-1.0826	10	0.14656	T	0.56	-10.7138	6.3555	0.21398	0.3746:0.0:0.6254:0.0	.	113;113	Q32Q62;O76021	.;RL1D1_HUMAN	L	113	ENSP00000347897:F113L	ENSP00000347897:F113L	F	-	3	2	RSL1D1	11849071	1.000000	0.71417	0.928000	0.36995	0.453000	0.32348	0.653000	0.24902	0.462000	0.27095	-0.624000	0.04008	TTT		0.343	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		C	11941570	A	C	11941570	3	2	47	1	0	0	0	0	1	0	0	0	13737	11	1	4	1161	4	RSL1D1	16	11941570	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	566560	11941570	78413183	1656	6053										
MYH11	4629	broad.mit.edu	37	chr16	15851731	15851731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtaggtccagcccaaagtCgatgaagttccactcgatgc	10	12	0	1	rs112553563	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:15851731C>T	ENST00000300036.5	-	13	1637	c.1528G>A	c.(1528-1530)Gac>Aac	p.D510N	MYH11_ENST00000576790.2_Missense_Mutation_p.D510N|MYH11_ENST00000396324.3_Missense_Mutation_p.D517N|MYH11_ENST00000452625.2_Missense_Mutation_p.D517N	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	510	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.D510N(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						AGCCCAAAGTCGATGAAGTTC	0.602			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - Missense(1)	large_intestine(1)	16											166	130	142					16																	15851731		2197	4300	6497	15759232	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1528G>A	16.37:g.15851731C>T	ENSP00000300036:p.Asp510Asn		15759232	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	35	5.514322	0.96402	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	4.91	4.91	0.64330	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.84727	0.5536	M	0.82323	2.585	0.80722	D	1	P;D;D;D;D;D	0.53462	0.884;0.96;0.96;0.96;0.96;0.96	D;P;P;D;P;P	0.66196	0.942;0.89;0.89;0.917;0.89;0.89	D	0.87449	0.2400	10	0.87932	D	0	.	17.1125	0.86679	0.0:1.0:0.0:0.0	.	517;510;510;517;510;517	B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;.;MYH11_HUMAN;.;.;.	N	510;510;517;517;517	ENSP00000300036:D510N;ENSP00000345136:D510N;ENSP00000379616:D517N;ENSP00000407821:D517N	ENSP00000300036:D510N	D	-	1	0	MYH11	15759232	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.747000	0.85070	2.265000	0.75225	0.462000	0.41574	GAC		0.602	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15851731	C	T	15851731	3	4	47	1	0	0	0	0	1	0	0	0	10061	884	31	1	4541	1	MYH11	16	15851731	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3910161	15851731	74503022	1657	6054										
TMC5	79838	broad.mit.edu	37	chr16	19451918	19451918	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaccatccaggatccagaaaGaatctggaacatacaagttt	7	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:19451918G>T	ENST00000396229.2	+	3	1307	c.558G>T	c.(556-558)aaG>aaT	p.K186N	TMC5_ENST00000381414.4_Missense_Mutation_p.K186N|TMC5_ENST00000541464.1_Missense_Mutation_p.K186N|TMC5_ENST00000542583.2_Missense_Mutation_p.K186N	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	186					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K186N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						GATCCAGAAAGAATCTGGAAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	16											101	98	99					16																	19451918		1924	4158	6082	19359419	SO:0001583	missense	79838			AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.558G>T	16.37:g.19451918G>T	ENSP00000379531:p.Lys186Asn		19359419	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	3.495	-0.103121	0.06967	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583	T;T;T;T	0.70164	-0.38;-0.25;-0.46;-0.46	5.04	-2.18	0.07037	.	5.593870	0.00166	N	0.000000	T	0.35480	0.0933	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.15178	-1.0446	10	0.24483	T	0.36	-9.137	0.9522	0.01378	0.3751:0.1535:0.3146:0.1568	.	186;186;186	F5GYU8;Q6UXY8;Q6UXY8-2	.;TMC5_HUMAN;.	N	186	ENSP00000441227:K186N;ENSP00000370822:K186N;ENSP00000379531:K186N;ENSP00000446274:K186N	ENSP00000370822:K186N	K	+	3	2	TMC5	19359419	0.048000	0.20356	0.066000	0.19879	0.247000	0.25773	-0.169000	0.09911	-0.116000	0.11893	0.591000	0.81541	AAG		0.468	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		T	19451918	G	T	19451918	3	4	47	1	0	0	0	0	1	0	0	0	16027	933	33	2	560	2	TMC5	16	19451918	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3600187	19451918	70902835	1658	6055										
GDE1	51573	broad.mit.edu	37	chr16	19522173	19522173	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactgtaccttgtgtgcatgGcctttgacatcaaagaagat	9	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:19522173G>A	ENST00000353258.3	-	3	711	c.531C>T	c.(529-531)ggC>ggT	p.G177G		NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	177	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)	p.G177G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						TGTGTGCATGGCCTTTGACAT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	16											177	167	170					16																	19522173		2197	4300	6497	19429674	SO:0001819	synonymous_variant	51573				CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"membrane interacting protein of RGS16"	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.531C>T	16.37:g.19522173G>A			19429674	O43334|Q6PKF7|Q7KYR4	Silent	SNP	ENST00000353258.3	37	CCDS10578.1																																																																																				0.373	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641		A	19522173	G	A	19522173	2	1	47	1	0	0	0	0	0	0	0	1	6330	1190	42	3		3	GDE1	16	19522173	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	70255	19522173	70832580	1659	6056										
PDILT	204474	broad.mit.edu	37	chr16	20373756	20373756	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgctggggaacagcctgaaGaatgggtaccggtccaggta	15	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:20373756G>T	ENST00000302451.4	-	10	1634	c.1386C>A	c.(1384-1386)ttC>ttA	p.F462L		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	462					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.F462L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						ACAGCCTGAAGAATGGGTACC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	16											170	135	147					16																	20373756		2203	4300	6503	20281257	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1386C>A	16.37:g.20373756G>T	ENSP00000305465:p.Phe462Leu		20281257	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921363	0.52653	.	.	ENSG00000169340	ENST00000302451	T	0.03152	4.03	5.0	4.05	0.47172	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.163737	0.56097	D	0.000030	T	0.05686	0.0149	N	0.11427	0.14	0.32319	N	0.562667	D	0.63046	0.992	D	0.65773	0.938	T	0.19353	-1.0308	10	0.72032	D	0.01	.	7.643	0.28305	0.1865:0.0:0.8135:0.0	.	462	Q8N807	PDILT_HUMAN	L	462	ENSP00000305465:F462L	ENSP00000305465:F462L	F	-	3	2	PDILT	20281257	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	2.647000	0.46639	1.336000	0.45506	0.563000	0.77884	TTC		0.463	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20373756	G	T	20373756	3	4	47	1	0	0	0	0	1	0	0	0	11705	933	33	2	380	2	PDILT	16	20373756	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	851583	20373756	69980997	1660	6057										
ERN2	10595	broad.mit.edu	37	chr16	23722319	23722319	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtggacaccagcaggaggttCtctggcctgagagtatgaac	14	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:23722319C>A	ENST00000457008.2	-	2	152	c.114G>T	c.(112-114)gaG>gaT	p.E38D	CTD-2385L22.1_ENST00000563611.1_RNA|ERN2_ENST00000256797.4_Missense_Mutation_p.E86D					endoplasmic reticulum to nucleus signaling 2									p.E86D(1)		large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		GCAGGAGGTTCTCTGGCCTGA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	98	101					16																	23722319		2197	4300	6497	23629820	SO:0001583	missense	10595			AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.114G>T	16.37:g.23722319C>A	ENSP00000413812:p.Glu38Asp		23629820		Missense_Mutation	SNP	ENST00000457008.2	37		.	.	.	.	.	.	.	.	.	.	C	12.60	1.986300	0.35036	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.55588	0.51;0.51	5.61	-0.587	0.11690	.	0.100033	0.64402	N	0.000003	T	0.43233	0.1238	M	0.64404	1.975	0.40887	D	0.984043	B;B	0.16603	0.018;0.001	B;B	0.19666	0.026;0.002	T	0.21348	-1.0248	10	0.36615	T	0.2	.	6.9666	0.24627	0.0:0.5286:0.2376:0.2338	.	38;38	E7ETG2;A5YM65	.;.	D	86;38	ENSP00000256797:E86D;ENSP00000413812:E38D	ENSP00000256797:E86D	E	-	3	2	ERN2	23629820	0.975000	0.34042	0.943000	0.38184	0.977000	0.68977	0.189000	0.17037	0.039000	0.15632	0.563000	0.77884	GAG		0.582	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			A	23722319	C	A	23722319	3	1	47	1	0	0	0	0	1	0	0	0	5251	912	32	2	2750	2	ERN2	16	23722319	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3348563	23722319	66632434	1661	6058										
CACNG3	10368	broad.mit.edu	37	chr16	24372804	24372804	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttctctttcatcatcgcaGaaattgtaggagtggttgcc	9	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:24372804G>T	ENST00000005284.3	+	4	1770	c.568G>T	c.(568-570)Gaa>Taa	p.E190*		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	190					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.E190*(1)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CATCATCGCAGAAATTGTAGG	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											126	127	127					16																	24372804		2197	4300	6497	24280305	SO:0001587	stop_gained	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.568G>T	16.37:g.24372804G>T	ENSP00000005284:p.Glu190*		24280305		Nonsense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	g	46	12.905747	0.99705	.	.	ENSG00000006116	ENST00000005284	.	.	.	4.96	4.01	0.46588	.	0.049960	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-11.2351	15.153	0.72717	0.0:0.1421:0.8579:0.0	.	.	.	.	X	190	.	ENSP00000005284:E190X	E	+	1	0	CACNG3	24280305	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	7.662000	0.83803	1.081000	0.41110	-0.121000	0.15023	GAA		0.468	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24372804	G	T	24372804	4	4	47	1	0	0	0	0	0	1	0	0	2564	943	33	2	582	2	CACNG3	16	24372804	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	650485	24372804	65981949	1662	6059										
RBBP6	5930	broad.mit.edu	37	chr16	24581622	24581622	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacaaaatttctttaagtgCgccagccaaaaaaatcaaac	6	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:24581622C>T	ENST00000319715.4	+	17	4043	c.3611C>T	c.(3610-3612)gCg>gTg	p.A1204V	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Missense_Mutation_p.A1170V	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1204					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A1204V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TCTTTAAGTGCGCCAGCCAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	16											42	47	45					16																	24581622		2197	4298	6495	24489123	SO:0001583	missense	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3611C>T	16.37:g.24581622C>T	ENSP00000317872:p.Ala1204Val		24489123	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	c	9.642	1.139303	0.21205	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.17213	2.29;2.29	5.59	4.65	0.58169	.	0.314743	0.27227	N	0.020321	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.06405	0.002;0.001	T	0.19679	-1.0298	10	0.41790	T	0.15	-2.5212	6.7918	0.23703	0.1431:0.7081:0.0:0.1488	.	1170;1204	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	V	1204;1170	ENSP00000317872:A1204V;ENSP00000316291:A1170V	ENSP00000317872:A1204V	A	+	2	0	RBBP6	24489123	0.998000	0.40836	0.735000	0.30896	0.050000	0.14768	2.636000	0.46545	1.368000	0.46115	-0.119000	0.15052	GCG		0.368	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24581622	C	T	24581622	3	4	47	1	0	0	0	0	1	0	0	0	13140	768	27	1	3731	1	RBBP6	16	24581622	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	208818	24581622	65773131	1663	6060										
ZKSCAN2	342357	broad.mit.edu	37	chr16	25258337	25258337	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagacttttgaacttggttcGacactgttctggggttctaa	11	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:25258337G>A	ENST00000328086.7	-	5	1983	c.1180C>T	c.(1180-1182)Cga>Tga	p.R394*		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	394					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R394*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		AACTTGGTTCGACACTGTTCT	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											139	129	132					16																	25258337		2197	4300	6497	25165838	SO:0001587	stop_gained	342357			AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1180C>T	16.37:g.25258337G>A	ENSP00000331626:p.Arg394*		25165838	A1L3B4|Q6ZN77	Nonsense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	G	44	11.192526	0.99528	.	.	ENSG00000155592	ENST00000328086;ENST00000536768	.	.	.	5.76	3.65	0.41850	.	0.000000	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.0843	11.7888	0.52057	0.0:0.0:0.6854:0.3146	.	.	.	.	X	394	.	ENSP00000331626:R394X	R	-	1	2	ZKSCAN2	25165838	0.997000	0.39634	0.997000	0.53966	0.994000	0.84299	1.924000	0.40065	1.531000	0.49152	0.655000	0.94253	CGA		0.473	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		A	25258337	G	A	25258337	4	1	47	1	0	0	0	0	0	1	0	0	17726	1066	37	1	1735	1	ZKSCAN2	16	25258337	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	676715	25258337	65096416	1664	6061										
HS3ST4	9951	broad.mit.edu	37	chr16	26147061	26147061	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaactgattgtggtggtgaGaaaccccgtgaccagggcca	13	10	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:26147061G>T	ENST00000331351.5	+	2	1255	c.863G>T	c.(862-864)aGa>aTa	p.R288I	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	288					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.R288I(1)		breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GTGGTGGTGAGAAACCCCGTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	16											143	131	135					16																	26147061		1568	3582	5150	26054562	SO:0001583	missense	9951			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.863G>T	16.37:g.26147061G>T	ENSP00000330606:p.Arg288Ile		26054562	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.236830	0.79800	.	.	ENSG00000182601	ENST00000331351	D	0.84370	-1.84	5.35	5.35	0.76521	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000007	D	0.92414	0.7592	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91291	0.5059	10	0.33940	T	0.23	.	18.0433	0.89325	0.0:0.0:1.0:0.0	.	288	Q9Y661	HS3S4_HUMAN	I	288	ENSP00000330606:R288I	ENSP00000330606:R288I	R	+	2	0	HS3ST4	26054562	1.000000	0.71417	0.815000	0.32552	0.985000	0.73830	9.787000	0.99055	2.491000	0.84063	0.655000	0.94253	AGA		0.512	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		T	26147061	G	T	26147061	3	4	47	1	0	0	0	0	1	0	0	0	7388	942	33	2	869	2	HS3ST4	16	26147061	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	888724	26147061	64207692	1665	6062										
SEZ6L2	26470	broad.mit.edu	37	chr16	29907158	29907158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccacatacccttcgccctCggagatgttgttattacaca	6	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:29907158C>T	ENST00000308713.5	-	4	1062	c.535G>A	c.(535-537)Gag>Aag	p.E179K	SEZ6L2_ENST00000350527.3_Missense_Mutation_p.E109K|SEZ6L2_ENST00000346932.5_Intron|SEZ6L2_ENST00000562159.1_Intron|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.E135K	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	179	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.E179K(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTTCGCCCTCGGAGATGTTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	16											77	77	77					16																	29907158		2197	4300	6497	29814659	SO:0001583	missense	26470			AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.535G>A	16.37:g.29907158C>T	ENSP00000312550:p.Glu179Lys		29814659	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629999	0.87660	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000537485	T;T;T	0.18338	2.22;2.22;2.22	5.69	5.69	0.88448	CUB (5);	0.231262	0.29940	N	0.010806	T	0.23846	0.0577	L	0.46157	1.445	0.42555	D	0.993122	P;D;P;P;P	0.53745	0.89;0.962;0.893;0.912;0.953	P;P;B;B;B	0.48334	0.483;0.574;0.251;0.367;0.438	T	0.01010	-1.1482	10	0.21540	T	0.41	.	18.5897	0.91206	0.0:1.0:0.0:0.0	.	135;179;109;179;109	F5H293;B7Z5L4;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;SE6L2_HUMAN;.	K	109;179;135	ENSP00000310206:E109K;ENSP00000312550:E179K;ENSP00000439412:E135K	ENSP00000312550:E179K	E	-	1	0	SEZ6L2	29814659	0.962000	0.33011	0.995000	0.50966	0.995000	0.86356	6.753000	0.74904	2.700000	0.92200	0.561000	0.74099	GAG		0.557	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		T	29907158	C	T	29907158	3	4	47	1	0	0	0	0	1	0	0	0	14181	893	31	1	2296	1	SEZ6L2	16	29907158	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3760097	29907158	60447595	1666	6063										
ABCC11	85320	broad.mit.edu	37	chr16	48244912	48244912	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggcccaggctgttcccttCttcctctggcccgagggcat	12	15	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:48244912C>A	ENST00000394747.1	-	10	1904	c.1555G>T	c.(1555-1557)Gaa>Taa	p.E519*	ABCC11_ENST00000394748.1_Nonsense_Mutation_p.E519*|ABCC11_ENST00000353782.5_Nonsense_Mutation_p.E519*|ABCC11_ENST00000356608.2_Nonsense_Mutation_p.E519*|ABCC11_ENST00000537808.1_Nonsense_Mutation_p.E519*	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	519	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)	p.E519*(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CTGTTCCCTTCTTCCTCTGGC	0.622																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											102	85	91					16																	48244912		2201	4300	6501	46802413	SO:0001587	stop_gained	85320			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1555G>T	16.37:g.48244912C>A	ENSP00000378230:p.Glu519*		46802413	Q8TDJ0|Q96JA6|Q9BX80	Nonsense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929042	0.92389	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	.	.	.	4.64	0.708	0.18144	.	0.889352	0.09855	N	0.747087	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-1.9391	5.4001	0.16291	0.0:0.0981:0.3734:0.5286	.	.	.	.	X	519	.	ENSP00000311326:E519X	E	-	1	0	ABCC11	46802413	0.000000	0.05858	0.051000	0.19133	0.116000	0.19942	-0.103000	0.10940	-0.134000	0.11516	-0.300000	0.09419	GAA		0.622	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48244912	C	A	48244912	4	1	47	1	0	0	0	0	0	1	0	0	51	922	32	2	2673	2	ABCC11	16	48244912	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	18337754	48244912	42109841	1667	6064										
LONP2	83752	broad.mit.edu	37	chr16	48385596	48385596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgagggaatcccaggcaaCgtacgacaggatttaagttt	11	8	0	1	rs150743514		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:48385596C>T	ENST00000285737.4	+	15	2535	c.2442C>T	c.(2440-2442)aaC>aaT	p.N814N	LONP2_ENST00000535754.1_Silent_p.N770N|LONP2_ENST00000564259.1_3'UTR	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal									p.N814N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCCAGGCAACGTACGACAGG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	16						C		0,4400		0,0,2200	91	88	89		2442	-12.1	0	16	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LONP2	NM_031490.2		0,1,6499	TT,TC,CC		0.0116,0.0,0.0077		814/853	48385596	1,12999	2200	4300	6500	46943097	SO:0001819	synonymous_variant	83752			AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.2442C>T	16.37:g.48385596C>T			46943097		Silent	SNP	ENST00000285737.4	37	CCDS10734.1																																																																																				0.473	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		T	48385596	C	T	48385596	2	4	47	1	0	0	0	0	0	0	0	1	8922	535	19	1		1	LONP2	16	48385596	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	140684	48385596	41969157	1668	6065										
N4BP1	9683	broad.mit.edu	37	chr16	48595229	48595229	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttgaatggtaactgagaaAatttttctaccatattttgc	6	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:48595229A>C	ENST00000262384.3	-	2	1561	c.1325T>G	c.(1324-1326)tTt>tGt	p.F442C	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	442					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)		p.F442C(1)		breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				TAACTGAGAAAATTTTTCTAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	16											104	97	99					16																	48595229		1857	4100	5957	47152730	SO:0001583	missense	9683			AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.1325T>G	16.37:g.48595229A>C	ENSP00000262384:p.Phe442Cys		47152730	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	37	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	A	9.122	1.009348	0.19277	.	.	ENSG00000102921	ENST00000262384	T	0.44482	0.92	5.38	1.46	0.22682	.	1.017860	0.07817	N	0.959136	T	0.28067	0.0692	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24012	-1.0172	10	0.39692	T	0.17	-3.8546	6.7142	0.23294	0.6535:0.1262:0.2203:0.0	.	442	O75113	N4BP1_HUMAN	C	442	ENSP00000262384:F442C	ENSP00000262384:F442C	F	-	2	0	N4BP1	47152730	0.000000	0.05858	0.017000	0.16124	0.827000	0.46813	0.418000	0.21230	0.431000	0.26258	0.383000	0.25322	TTT		0.358	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		C	48595229	A	C	48595229	3	2	47	1	0	0	0	0	1	0	0	0	10139	14	1	4	1389	4	N4BP1	16	48595229	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	209633	48595229	41759524	1669	6066										
N4BP1	9683	broad.mit.edu	37	chr16	48595972	48595972	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcctgtttcaaagagattCtcctcaccttgtgtgagtgt	8	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:48595972C>T	ENST00000262384.3	-	2	818	c.582G>A	c.(580-582)gaG>gaA	p.E194E	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	194					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)		p.E194E(1)		breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CAAAGAGATTCTCCTCACCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	16											102	90	93					16																	48595972		1855	4094	5949	47153473	SO:0001819	synonymous_variant	9683			AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.582G>A	16.37:g.48595972C>T			47153473	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	37	CCDS45479.1																																																																																				0.383	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		T	48595972	C	T	48595972	2	4	47	1	0	0	0	0	0	0	0	1	10139	912	32	3		3	N4BP1	16	48595972	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	743	48595972	41758781	1670	6067										
NOD2	64127	broad.mit.edu	37	chr16	50744798	50744798	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcaagacttccaggaatttCtctttgtcttcccattcagc	7	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:50744798C>A	ENST00000300589.2	+	4	1081	c.976C>A	c.(976-978)Ctc>Atc	p.L326I	NOD2_ENST00000526417.2_3'UTR|RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	326	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.L326I(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CCAGGAATTTCTCTTTGTCTT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											45	42	43					16																	50744798		2198	4300	6498	49302299	SO:0001583	missense	64127			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.976C>A	16.37:g.50744798C>A	ENSP00000300589:p.Leu326Ile		49302299	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	C	7.424	0.637229	0.14386	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.79352	-1.26	5.62	2.63	0.31362	NACHT nucleoside triphosphatase (1);	0.000000	0.56097	D	0.000027	T	0.82263	0.4999	M	0.72894	2.215	0.24537	N	0.994084	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.87578	0.998;0.948;0.998	T	0.69624	-0.5095	10	0.18710	T	0.47	.	5.0975	0.14740	0.2893:0.5555:0.0:0.1552	.	110;299;326	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	I	299;326	ENSP00000300589:L326I	ENSP00000300589:L326I	L	+	1	0	NOD2	49302299	0.151000	0.22747	0.323000	0.25347	0.082000	0.17680	0.503000	0.22610	0.328000	0.23435	-0.463000	0.05309	CTC		0.592	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50744798	C	A	50744798	3	1	47	1	0	0	0	0	1	0	0	0	10548	913	32	2	990	2	NOD2	16	50744798	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2148826	50744798	39609955	1671	6068										
CHD9	80205	broad.mit.edu	37	chr16	53326847	53326847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ataccagcgtactaataaaaAcagacaaattcagcagatac	5	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:53326847A>G	ENST00000398510.3	+	28	5480	c.5393A>G	c.(5392-5394)aAc>aGc	p.N1798S	CHD9_ENST00000564845.1_Missense_Mutation_p.N1798S|CHD9_ENST00000447540.1_Missense_Mutation_p.N1798S|CHD9_ENST00000566029.1_Missense_Mutation_p.N1798S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1798					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.N1798S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ACTAATAAAAACAGACAAATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	16											114	107	109					16																	53326847		1902	4128	6030	51884348	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.5393A>G	16.37:g.53326847A>G	ENSP00000381522:p.Asn1798Ser		51884348	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	A	13.53	2.264997	0.40095	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	T;T	0.78816	-1.21;-1.21	5.35	4.21	0.49690	.	0.000000	0.64402	D	0.000009	T	0.56572	0.1994	N	0.08118	0	0.28447	N	0.916534	B;B;B;B	0.14438	0.001;0.01;0.002;0.003	B;B;B;B	0.17433	0.002;0.018;0.002;0.004	T	0.52328	-0.8590	10	0.56958	D	0.05	-13.7578	7.106	0.25364	0.777:0.1485:0.0745:0.0	.	166;1798;1798;1798	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	S	1798;1798;166	ENSP00000396345:N1798S;ENSP00000381522:N1798S	ENSP00000381522:N1798S	N	+	2	0	CHD9	51884348	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.534000	0.53568	2.023000	0.59567	0.482000	0.46254	AAC		0.438	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53326847	A	G	53326847	3	3	47	1	0	0	0	0	1	0	0	0	3338	43	2	4	5503	4	CHD9	16	53326847	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2582049	53326847	37027906	1672	6069										
NLRC5	84166	broad.mit.edu	37	chr16	57115519	57115519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggtctagcatccaagtcaTccggtaacagaggcctgcag	13	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:57115519T>C	ENST00000262510.6	+	48	5711	c.5486T>C	c.(5485-5487)aTc>aCc	p.I1829T	NLRC5_ENST00000436936.1_3'UTR|NLRC5_ENST00000539144.1_Missense_Mutation_p.I1800T|NLRC5_ENST00000308149.7_Missense_Mutation_p.I1800T	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1829					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.I1829T(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				ATCCAAGTCATCCGGTAACAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	16											88	92	91					16																	57115519		2198	4300	6498	55673020	SO:0001583	missense	84166			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.5486T>C	16.37:g.57115519T>C	ENSP00000262510:p.Ile1829Thr		55673020	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	17.54	3.416129	0.62511	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000539144	T;T;T	0.56941	0.43;0.43;0.43	4.45	4.45	0.53987	.	.	.	.	.	T	0.67515	0.2901	M	0.76170	2.325	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.71331	-0.4625	9	0.72032	D	0.01	.	10.3736	0.44068	0.0:0.0:0.0:1.0	.	1829	Q86WI3	NLRC5_HUMAN	T	1829;1800;1800	ENSP00000262510:I1829T;ENSP00000308886:I1800T;ENSP00000441727:I1800T	ENSP00000262510:I1829T	I	+	2	0	NLRC5	55673020	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	3.490000	0.53245	1.762000	0.52044	0.459000	0.35465	ATC		0.622	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57115519	T	C	57115519	3	2	47	1	0	0	0	0	1	0	0	0	10501	1435	50	4	5668	4	NLRC5	16	57115519	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3788672	57115519	33239234	1673	6070										
RSPRY1	89970	broad.mit.edu	37	chr16	57246917	57246917	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattgactgaaattctcaatTtaaatggagaagtagcttgc	8	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:57246917T>G	ENST00000537866.1	+	5	1423	c.550T>G	c.(550-552)Tta>Gta	p.L184V	RSPRY1_ENST00000394420.4_Missense_Mutation_p.L184V			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	184						extracellular region (GO:0005576)	zinc ion binding (GO:0008270)	p.L184V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						AATTCTCAATTTAAATGGAGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	112	110					16																	57246917		2198	4300	6498	55804418	SO:0001583	missense	89970			AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.550T>G	16.37:g.57246917T>G	ENSP00000443176:p.Leu184Val		55804418	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	37	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.868577	0.51588	.	.	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.64085	-0.08;-0.08	5.37	4.28	0.50868	.	0.238371	0.36409	N	0.002609	T	0.52075	0.1712	L	0.53249	1.67	0.58432	D	0.999999	P	0.35411	0.5	B	0.25614	0.062	T	0.52079	-0.8623	10	0.49607	T	0.09	.	11.1537	0.48476	0.0:0.0722:0.0:0.9278	.	184	Q96DX4	RSPRY_HUMAN	V	184	ENSP00000377942:L184V;ENSP00000443176:L184V	ENSP00000377942:L184V	L	+	1	2	RSPRY1	55804418	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.698000	0.54771	0.887000	0.36136	0.529000	0.55759	TTA		0.433	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		G	57246917	T	G	57246917	3	3	47	1	0	0	0	0	1	0	0	0	13750	1838	64	4	564	4	RSPRY1	16	57246917	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	131398	57246917	33107836	1674	6071										
TSNAXIP1	55815	broad.mit.edu	37	chr16	67858496	67858496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctgcttagcccaccaaagGgagaagattcgggctctgga	12	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:67858496G>T	ENST00000388833.3	+	6	707	c.330G>T	c.(328-330)agG>agT	p.R110S	TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.R95S|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.R164S|TSNAXIP1_ENST00000562321.1_Intron	NM_018430.2	NP_060900.2			translin-associated factor X interacting protein 1									p.R110S(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|soft_tissue(1)|urinary_tract(1)	22		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)		CCCACCAAAGGGAGAAGATTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											53	53	53					16																	67858496		1910	4138	6048	66415997	SO:0001583	missense	55815			AF132730	CCDS10846.2, CCDS73903.1, CCDS73904.1	16q22.2	2008-02-05			ENSG00000102904	ENSG00000102904			18586	protein-coding gene	gene with protein product		607720				12036294	Standard	XM_005256051		Approved	TXI1	uc002euj.3	Q2TAA8	OTTHUMG00000137545	ENST00000388833.3:c.330G>T	16.37:g.67858496G>T	ENSP00000373485:p.Arg110Ser		66415997		Missense_Mutation	SNP	ENST00000388833.3	37	CCDS10846.2	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357853	0.61403	.	.	ENSG00000102904	ENST00000415766;ENST00000388833	T;T	0.00995	5.46;5.46	6.17	4.19	0.49359	.	0.146689	0.43416	D	0.000574	T	0.01835	0.0058	M	0.66939	2.045	0.38429	D	0.946384	P;P;P	0.46142	0.873;0.873;0.763	B;B;B	0.42282	0.382;0.382;0.242	T	0.59118	-0.7514	10	0.72032	D	0.01	-29.0475	11.8927	0.52638	0.1397:0.0:0.8603:0.0	.	95;164;110	E7ENJ7;B4DXD0;Q2TAA8	.;.;TXIP1_HUMAN	S	95;110	ENSP00000411472:R95S;ENSP00000373485:R110S	ENSP00000373485:R110S	R	+	3	2	TSNAXIP1	66415997	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.332000	0.33805	1.599000	0.50093	0.655000	0.94253	AGG		0.542	TSNAXIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268876.2	NM_018430		T	67858496	G	T	67858496	3	4	47	1	0	0	0	0	1	0	0	0	16672	1223	43	2	344	2	TSNAXIP1	16	67858496	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	10611579	67858496	22496257	1675	6072										
CDH1	999	broad.mit.edu	37	chr16	68857307	68857307	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattgctttctccagcccaaGaatctatcattttgaagcca	5	11	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:68857307G>T	ENST00000261769.5	+	13	2133	c.1942G>T	c.(1942-1944)Gaa>Taa	p.E648*	CDH1_ENST00000422392.2_Nonsense_Mutation_p.E587*|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	648	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.E648*(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TCCAGCCCAAGAATCTATCAT	0.398			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	1	Substitution - Nonsense(1)	large_intestine(1)	16											63	65	64					16																	68857307		2198	4300	6498	67414808	SO:0001587	stop_gained	999	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1942G>T	16.37:g.68857307G>T	ENSP00000261769:p.Glu648*		67414808	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Nonsense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	35	5.472817	0.96274	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	.	.	.	6.04	5.09	0.68999	.	0.120446	0.36932	N	0.002339	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	13.0494	0.58946	0.0744:0.0:0.9256:0.0	.	.	.	.	X	648;666;587	.	ENSP00000261769:E648X	E	+	1	0	CDH1	67414808	0.998000	0.40836	0.021000	0.16686	0.013000	0.08279	3.321000	0.51999	1.561000	0.49584	0.563000	0.77884	GAA		0.398	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68857307	G	T	68857307	4	4	47	1	0	0	0	0	0	1	0	0	3101	943	33	2	1992	2	CDH1	16	68857307	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	998811	68857307	21497446	1676	6073										
COG4	25839	broad.mit.edu	37	chr16	70551549	70551549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggccaggtcaagctgacGaactttgctggacacattct	10	11	2	1	rs149620212	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:70551549G>A	ENST00000323786.5	-	3	370	c.349C>T	c.(349-351)Cgt>Tgt	p.R117C	COG4_ENST00000564653.1_Missense_Mutation_p.R117C|COG4_ENST00000393612.4_Missense_Mutation_p.R113C	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	113	Interacts with STX5.				Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.R117C(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				TCAAGCTGACGAACTTTGCTG	0.458													g|||	2	0.000399361	0	0.0014	5008	,	,		15606	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16							CYS/ARG,CYS/ARG	0,4396		0,0,2198	137	121	126		349,349	5.3	1	16	dbSNP_134	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	COG4	NM_001195139.1,NM_015386.2	180,180	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	117/769,117/790	70551549	1,12995	2198	4300	6498	69109050	SO:0001583	missense	25839			AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.349C>T	16.37:g.70551549G>A	ENSP00000315775:p.Arg117Cys		69109050	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	37	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	g	20.6	4.015934	0.75161	0.0	1.16E-4	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.47869	0.83;0.83;0.83	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.72953	0.3525	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	T	0.77365	-0.2615	10	0.87932	D	0	-5.2429	19.0495	0.93038	0.0:0.0:1.0:0.0	.	112;113	Q6PIW8;Q9H9E3	.;COG4_HUMAN	C	117;113;113;40	ENSP00000315775:R117C;ENSP00000377236:R113C;ENSP00000461912:R40C	ENSP00000315775:R117C	R	-	1	0	COG4	69109050	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.144000	0.58057	2.496000	0.84212	0.450000	0.29827	CGT		0.458	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			A	70551549	G	A	70551549	3	1	47	1	0	0	0	0	1	0	0	0	3666	1058	37	1	2088	1	COG4	16	70551549	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1694242	70551549	19803204	1677	6074										
SF3B3	23450	broad.mit.edu	37	chr16	70582330	70582330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaacgctgtctggacagtgCgtcgacacattgaaggtaag	12	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:70582330C>T	ENST00000302516.5	+	11	1598	c.1387C>T	c.(1387-1389)Cgt>Tgt	p.R463C		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	463					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.R463C(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CTGGACAGTGCGTCGACACAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											159	135	143					16																	70582330		2198	4300	6498	69139831	SO:0001583	missense	23450			AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.1387C>T	16.37:g.70582330C>T	ENSP00000305790:p.Arg463Cys		69139831	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.327134	0.41197	.	.	ENSG00000189091	ENST00000302516	T	0.47177	0.85	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.47857	0.1468	L	0.57536	1.79	0.80722	D	1	P	0.34662	0.462	B	0.37239	0.244	T	0.51100	-0.8748	10	0.72032	D	0.01	.	13.0613	0.59008	0.2657:0.7343:0.0:0.0	.	463	Q15393	SF3B3_HUMAN	C	463	ENSP00000305790:R463C	ENSP00000305790:R463C	R	+	1	0	SF3B3	69139831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.991000	0.56973	2.752000	0.94435	0.655000	0.94253	CGT		0.478	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70582330	C	T	70582330	3	4	47	1	0	0	0	0	1	0	0	0	14189	768	27	1	1425	1	SF3B3	16	70582330	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	30781	70582330	19772423	1678	6075										
HYDIN	54768	broad.mit.edu	37	chr16	71218803	71218803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcccccatatctaagagttCgatgatctgtggtcggcaca	9	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:71218803C>T	ENST00000393567.2	-	3	376	c.226G>A	c.(226-228)Gaa>Aaa	p.E76K	HYDIN_ENST00000448089.2_Missense_Mutation_p.E76K|HYDIN_ENST00000321489.5_Missense_Mutation_p.E76K|HYDIN_ENST00000448691.1_Missense_Mutation_p.E76K|HYDIN_ENST00000538248.1_Missense_Mutation_p.E103K|HYDIN_ENST00000393550.2_Missense_Mutation_p.E76K|HYDIN_ENST00000541601.1_Missense_Mutation_p.E93K|HYDIN_ENST00000288168.10_Missense_Mutation_p.E93K	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	76					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.E76K(4)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCTAAGAGTTCGATGATCTGT	0.468																																																4	Substitution - Missense(4)	large_intestine(4)	16											169	151	157					16																	71218803		2198	4299	6497	69776304	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.226G>A	16.37:g.71218803C>T	ENSP00000377197:p.Glu76Lys		69776304	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927616	0.73327	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550	T;T;T;T;T;T;T;T	0.17370	5.38;3.54;3.52;3.52;3.53;3.54;3.16;2.28	5.86	3.91	0.45181	.	0.667620	0.11055	U	0.604588	T	0.36608	0.0973	M	0.73217	2.22	0.31277	N	0.691014	D;D;P;D;P	0.67145	0.996;0.996;0.948;0.996;0.77	P;D;P;D;B	0.63793	0.867;0.918;0.577;0.918;0.138	T	0.23440	-1.0188	10	0.30078	T	0.28	.	10.4921	0.44756	0.0:0.5218:0.4039:0.0743	.	103;93;93;76;76	B4DRN4;F5H6V3;F8WD03;Q4G0P3-5;F8WD23	.;.;.;.;.	K	76;76;76;76;76;103;93;93;76	ENSP00000377197:E76K;ENSP00000398544:E76K;ENSP00000394826:E76K;ENSP00000314736:E76K;ENSP00000444970:E103K;ENSP00000437341:E93K;ENSP00000288168:E93K;ENSP00000377181:E76K	ENSP00000288168:E93K	E	-	1	0	HYDIN	69776304	0.399000	0.25287	0.832000	0.32986	0.924000	0.55760	0.817000	0.27281	0.821000	0.34540	-0.136000	0.14681	GAA		0.468	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	71218803	C	T	71218803	3	4	47	1	0	0	0	0	1	0	0	0	7488	893	31	1	15484	1	HYDIN	16	71218803	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	636473	71218803	19135950	1679	6076										
ZNF23	7571	broad.mit.edu	37	chr16	71482693	71482693	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctcgcctgtgtgaattCtctggtgttggattaacttc	10	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:71482693C>A	ENST00000393539.2	-	6	2048	c.1235G>T	c.(1234-1236)aGa>aTa	p.R412I	ZNF23_ENST00000358700.2_3'UTR|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000357254.4_Missense_Mutation_p.R412I|ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000417828.1_Missense_Mutation_p.R412I|ZNF23_ENST00000564528.1_Missense_Mutation_p.R354I|ZNF23_ENST00000428724.2_Missense_Mutation_p.R354I|ZNF23_ENST00000539742.1_5'UTR	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R412I(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TGTGTGAATTCTCTGGTGTTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	16											59	53	55					16																	71482693		2198	4300	6498	70040194	SO:0001583	missense	7571			X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.1235G>T	16.37:g.71482693C>A	ENSP00000377171:p.Arg412Ile		70040194	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.197587	0.58126	.	.	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.14	4.14	0.48551	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000188	T	0.48660	0.1512	M	0.65975	2.015	0.49582	D	0.999802	D;D	0.89917	0.994;1.0	P;D	0.91635	0.863;0.999	T	0.51204	-0.8735	10	0.87932	D	0	-30.0404	14.7277	0.69357	0.0:1.0:0.0:0.0	.	412;412	B3KR55;P17027	.;ZNF23_HUMAN	I	412;412;412;354;354	ENSP00000377171:R412I;ENSP00000349796:R412I;ENSP00000395712:R412I;ENSP00000387673:R354I	ENSP00000349796:R412I	R	-	2	0	ZNF23	70040194	0.001000	0.12720	1.000000	0.80357	0.986000	0.74619	1.010000	0.29898	2.595000	0.87683	0.555000	0.69702	AGA		0.458	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		A	71482693	C	A	71482693	3	1	47	1	0	0	0	0	1	0	0	0	17822	913	32	2	700	2	ZNF23	16	71482693	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	263890	71482693	18872060	1680	6077										
ADAMTS18	170692	broad.mit.edu	37	chr16	77353835	77353835	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtattcaaacgtggtcccagCgaaggggaactccccaggcc	12	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:77353835C>T	ENST00000282849.5	-	16	2861	c.2443G>A	c.(2443-2445)Gct>Act	p.A815T		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	815	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A815T(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GTGGTCCCAGCGAAGGGGAAC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	16											60	58	59					16																	77353835		2198	4300	6498	75911336	SO:0001583	missense	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2443G>A	16.37:g.77353835C>T	ENSP00000282849:p.Ala815Thr		75911336	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036634	0.93630	.	.	ENSG00000140873	ENST00000282849	T	0.54071	0.59	5.54	4.58	0.56647	ADAM-TS Spacer 1 (1);	0.121893	0.53938	D	0.000049	T	0.78355	0.4270	M	0.93375	3.41	0.58432	D	0.999997	D;D	0.76494	0.999;0.99	D;P	0.68353	0.957;0.869	D	0.84635	0.0692	10	0.72032	D	0.01	.	14.8208	0.70070	0.145:0.855:0.0:0.0	.	815;815	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	T	815	ENSP00000282849:A815T	ENSP00000282849:A815T	A	-	1	0	ADAMTS18	75911336	1.000000	0.71417	0.048000	0.18961	0.966000	0.64601	5.698000	0.68302	1.319000	0.45190	0.563000	0.77884	GCT		0.577	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77353835	C	T	77353835	3	4	47	1	0	0	0	0	1	0	0	0	263	768	27	1	1254	1	ADAMTS18	16	77353835	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5871142	77353835	13000918	1681	6078										
ADAMTS18	170692	broad.mit.edu	37	chr16	77387721	77387721	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatctgtcctggtagtttgTccggatatttatactgtcct	8	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:77387721T>G	ENST00000282849.5	-	10	1941	c.1523A>C	c.(1522-1524)gAc>gCc	p.D508A		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	508	Disintegrin.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D508A(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TGGTAGTTTGTCCGGATATTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											350	315	327					16																	77387721		2198	4300	6498	75945222	SO:0001583	missense	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.1523A>C	16.37:g.77387721T>G	ENSP00000282849:p.Asp508Ala		75945222	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.531481	0.45073	.	.	ENSG00000140873	ENST00000282849	T	0.03272	3.99	5.22	5.22	0.72569	Metallopeptidase, catalytic domain (1);	0.169099	0.50627	D	0.000105	T	0.03434	0.0099	N	0.25647	0.755	0.50632	D	0.999886	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.48080	-0.9066	10	0.11794	T	0.64	.	14.4909	0.67649	0.0:0.0:0.0:1.0	.	508;508	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	A	508	ENSP00000282849:D508A	ENSP00000282849:D508A	D	-	2	0	ADAMTS18	75945222	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.436000	0.80404	2.200000	0.70718	0.524000	0.50904	GAC		0.428	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			G	77387721	T	G	77387721	3	3	47	1	0	0	0	0	1	0	0	0	263	1667	58	4	2198	4	ADAMTS18	16	77387721	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	33886	77387721	12967032	1682	6079										
CDH13	1012	broad.mit.edu	37	chr16	83520245	83520245	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcactgttgtgtcacctgcGctgctggaccgagaggtgag	15	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:83520245G>A	ENST00000566620.1	+	7	1235	c.945G>A	c.(943-945)gcG>gcA	p.A315A	CDH13_ENST00000569454.1_3'UTR|CDH13_ENST00000268613.10_Silent_p.A362A|CDH13_ENST00000428848.3_Silent_p.A276A	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	315	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)	p.A315A(2)		large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TGTCACCTGCGCTGCTGGACC	0.488																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	16											84	81	82					16																	83520245		2034	4207	6241	82077746	SO:0001819	synonymous_variant	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.945G>A	16.37:g.83520245G>A			82077746	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																				0.488	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		A	83520245	G	A	83520245	2	1	47	1	0	0	0	0	0	0	0	1	3105	1074	38	1		1	CDH13	16	83520245	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6132524	83520245	6834508	1683	6080										
ATP2C2	9914	broad.mit.edu	37	chr16	84456274	84456274	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggaaagctctcagttcggaGaagtgtttaagatgatgcag	14	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:84456274G>T	ENST00000262429.4	+	9	903	c.814G>T	c.(814-816)Gaa>Taa	p.E272*	ATP2C2_ENST00000416219.2_Nonsense_Mutation_p.E272*|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	272					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.E272*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCAGTTCGGAGAAGTGTTTAA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											193	194	194					16																	84456274		1885	4112	5997	83013775	SO:0001587	stop_gained	9914			AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.814G>T	16.37:g.84456274G>T	ENSP00000262429:p.Glu272*		83013775	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Nonsense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	G	38	7.265832	0.98175	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	.	.	.	5.16	5.16	0.70880	.	0.080192	0.51477	D	0.000100	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	17.1945	0.86888	0.0:0.0:1.0:0.0	.	.	.	.	X	272;272;121	.	ENSP00000262429:E272X	E	+	1	0	ATP2C2	83013775	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	9.201000	0.95017	2.381000	0.81170	0.650000	0.86243	GAA		0.498	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		T	84456274	G	T	84456274	4	4	47	1	0	0	0	0	0	1	0	0	1145	943	33	2	848	2	ATP2C2	16	84456274	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	936029	84456274	5898479	1684	6081										
FAM92B	339145	broad.mit.edu	37	chr16	85135925	85135925	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaatagttacaaagtcacaAaaaaatttctgtggggagag	9	5	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:85135925A>C	ENST00000539556.1	-	7	701	c.546T>G	c.(544-546)ttT>ttG	p.F182L		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	182								p.F182L(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						CAAAGTCACAAAAAAATTTCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											56	56	56					16																	85135925		2198	4300	6498	83693426	SO:0001583	missense	339145				CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.546T>G	16.37:g.85135925A>C	ENSP00000443411:p.Phe182Leu		83693426		Missense_Mutation	SNP	ENST00000539556.1	37	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.478898	0.26511	.	.	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.56275	0.47	5.78	-4.24	0.03777	.	0.074089	0.56097	N	0.000032	T	0.35998	0.0951	L	0.37697	1.125	0.09310	N	1	B	0.27316	0.175	B	0.33339	0.162	T	0.39742	-0.9599	10	0.11182	T	0.66	-10.908	12.0023	0.53237	0.2021:0.1065:0.6913:0.0	.	182	Q6ZTR7	FA92B_HUMAN	L	182	ENSP00000443411:F182L	ENSP00000376937:F182L	F	-	3	2	FAM92B	83693426	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	-0.139000	0.10358	-0.792000	0.04480	-0.451000	0.05528	TTT		0.507	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491		C	85135925	A	C	85135925	3	2	47	1	0	0	0	0	1	0	0	0	5672	11	1	4	380	4	FAM92B	16	85135925	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	679651	85135925	5218828	1685	6082										
CDH15	1013	broad.mit.edu	37	chr16	89245927	89245928	+	Frame_Shift_Ins	INS	-	-	C													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgcggagggcctgggtcatINSccccccgatcagcgtatccg							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:89245927_89245928insC	ENST00000289746.2	+	2	211_212	c.146_147insC	c.(145-150)atccccfs	p.IP49fs	CDH15_ENST00000521087.1_3'UTR	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	49					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I52fs*38(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		GCCTGGGTCATCCCCCCGATCA	0.683																																																1	Insertion - Frameshift(1)	large_intestine(1)	16																																								87773429	SO:0001589	frameshift_variant	1013			D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.152dupC	16.37:g.89245933_89245933dupC	ENSP00000289746:p.Ile49fs		87773428		Frame_Shift_Ins	INS	ENST00000289746.2	37	CCDS10976.1																																																																																				0.683	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		C	89245928	-	C	89245927	7	5	47	1	0	1	1	0	0	0	0	0	3106	1435	50	0	152	0	CDH15	16	89245927	Frame_Shift_Ins	INS	-	TCGA-AG-3892-01A-01W-1073-09	4110002	89245927	1108826	1686	6083										
ANKRD11	29123	broad.mit.edu	37	chr16	89349029	89349029	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctgccctcggtccgtgaaGctgtcagaggagacctcgct	12	14	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:89349029G>A	ENST00000301030.4	-	9	4381	c.3921C>T	c.(3919-3921)agC>agT	p.S1307S	ANKRD11_ENST00000378330.2_Silent_p.S1307S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1307	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S1307S(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GGTCCGTGAAGCTGTCAGAGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	16											44	44	44					16																	89349029		2198	4300	6498	87876530	SO:0001819	synonymous_variant	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3921C>T	16.37:g.89349029G>A			87876530	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																				0.582	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89349029	G	A	89349029	2	1	47	1	0	0	0	0	0	0	0	1	639	962	34	3		3	ANKRD11	16	89349029	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	103102	89349029	1005724	1687	6084										
PRDM7	11105	broad.mit.edu	37	chr16	90126843	90126843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taccagaccagcagttcacaGcctggcctaatgactcggca	9	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr16:90126843G>A	ENST00000449207.2	-	9	1158	c.1139C>T	c.(1138-1140)gCt>gTt	p.A380V	PRDM7_ENST00000407825.1_Intron|PRDM7_ENST00000325921.6_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	380					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)	p.A380V(1)		lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GCAGTTCACAGCCTGGCCTAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16											98	99	99					16																	90126843		1932	4137	6069	88654344	SO:0001583	missense	11105			AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1139C>T	16.37:g.90126843G>A	ENSP00000396732:p.Ala380Val		88654344	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	.	.	.	.	.	.	.	.	.	.	.	8.846	0.943443	0.18281	.	.	ENSG00000126856	ENST00000449207	T	0.11495	2.77	2.07	0.823	0.18812	.	.	.	.	.	T	0.06096	0.0158	N	0.08118	0	0.80722	D	1	D	0.61080	0.989	P	0.48488	0.579	T	0.47873	-0.9083	8	.	.	.	-5.6063	5.6999	0.17877	0.0:0.3462:0.6538:0.0	.	380	Q9NQW5	PRDM7_HUMAN	V	380	ENSP00000396732:A380V	.	A	-	2	0	PRDM7	88654344	0.024000	0.19004	0.980000	0.43619	0.845000	0.48019	0.641000	0.24720	1.151000	0.42436	0.398000	0.26397	GCT		0.552	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			A	90126843	G	A	90126843	3	1	47	1	0	0	0	0	1	0	0	0	12495	971	34	3	347	3	PRDM7	16	90126843	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	777814	90126843	227910	1688	6085										
SRR	63826	broad.mit.edu	37	chr17	2224606	2224606	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatgtactttcagtccagaGaaaatgttgcaaaaagagtt	8	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:2224606G>T	ENST00000344595.5	+	5	724	c.406G>T	c.(406-408)Gaa>Taa	p.E136*	SRR_ENST00000576848.1_Intron	NM_021947.1	NP_068766.1	Q9GZT4	SRR_HUMAN	serine racemase	136					aging (GO:0007568)|brain development (GO:0007420)|D-serine biosynthetic process (GO:0070179)|D-serine metabolic process (GO:0070178)|L-serine metabolic process (GO:0006563)|protein homotetramerization (GO:0051289)|pyruvate biosynthetic process (GO:0042866)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|serine family amino acid metabolic process (GO:0009069)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|D-serine ammonia-lyase activity (GO:0008721)|glycine binding (GO:0016594)|L-serine ammonia-lyase activity (GO:0003941)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|serine racemase activity (GO:0030378)|threonine racemase activity (GO:0018114)	p.E136*(1)		NS(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)	TCAGTCCAGAGAAAATGTTGC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											91	101	98					17																	2224606		2203	4300	6503	2171356	SO:0001587	stop_gained	63826			AF169974	CCDS11017.1	17p13	2007-01-18			ENSG00000167720	ENSG00000167720			14398	protein-coding gene	gene with protein product		606477				17067558, 15953485, 15193426	Standard	NM_021947		Approved	ILV1, ISO1	uc002fue.1	Q9GZT4	OTTHUMG00000090583	ENST00000344595.5:c.406G>T	17.37:g.2224606G>T	ENSP00000339435:p.Glu136*		2171356	D3DTI5|Q6IA55	Nonsense_Mutation	SNP	ENST00000344595.5	37	CCDS11017.1	.	.	.	.	.	.	.	.	.	.	G	37	6.226365	0.97394	.	.	ENSG00000167720	ENST00000344595	.	.	.	5.86	4.82	0.62117	.	0.353536	0.32819	N	0.005615	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-2.7794	8.6011	0.33745	0.1909:0.0:0.8091:0.0	.	.	.	.	X	136	.	ENSP00000339435:E136X	E	+	1	0	SRR	2171356	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	2.205000	0.42770	2.771000	0.95319	0.563000	0.77884	GAA		0.393	SRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207129.2	NM_021947		T	2224606	G	T	2224606	4	4	47	1	0	0	0	0	0	1	0	0	15205	943	33	2	420	2	SRR	17	2224606	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09		2224606	78970604	1689	6086										
TSR1	55720	broad.mit.edu	37	chr17	2237999	2237999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atgggcaaataggtaggcccGccgatctcgaaaagcaagat	12	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:2237999G>A	ENST00000301364.5	-	5	1827	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	SGSM2_ENST00000574563.1_5'Flank|TSR1_ENST00000576112.2_Missense_Mutation_p.R234W|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000268989.3_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	250					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.R250W(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						AGGTAGGCCCGCCGATCTCGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											91	90	90					17																	2237999		2203	4300	6503	2184749	SO:0001583	missense	55720			AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.748C>T	17.37:g.2237999G>A	ENSP00000301364:p.Arg250Trp		2184749	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879816	0.72294	.	.	ENSG00000167721	ENST00000301364	T	0.58506	0.33	5.4	4.42	0.53409	AARP2CN (2);	0.000000	0.85682	D	0.000000	T	0.82019	0.4946	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87242	0.2267	10	0.87932	D	0	-5.8917	14.5363	0.67963	0.0:0.0:0.8523:0.1477	.	250	Q2NL82	TSR1_HUMAN	W	250	ENSP00000301364:R250W	ENSP00000301364:R250W	R	-	1	2	TSR1	2184749	1.000000	0.71417	0.993000	0.49108	0.624000	0.37722	6.189000	0.72051	1.257000	0.44085	-0.181000	0.13052	CGG		0.483	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		A	2237999	G	A	2237999	3	1	47	1	0	0	0	0	1	0	0	0	16704	1086	38	1	1710	1	TSR1	17	2237999	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	13393	2237999	78957211	1690	6087										
METT10D	79066	broad.mit.edu	37	chr17	2344815	2344815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagctcctccttcagaggcGccaggctgcatttctttccc	9	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:2344815G>A	ENST00000263092.6	-	7	894	c.767C>T	c.(766-768)gCg>gTg	p.A256V	METTL16_ENST00000538844.1_Missense_Mutation_p.A38V|METTL16_ENST00000571669.2_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	256							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.A256V(2)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						CTTCAGAGGCGCCAGGCTGCA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	17											74	74	74					17																	2344815		1864	4098	5962	2291565	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.767C>T	17.37:g.2344815G>A	ENSP00000263092:p.Ala256Val		2291565	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.118941	0.77323	.	.	ENSG00000127804	ENST00000263092;ENST00000538844	T;T	0.48522	0.87;0.81	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.32285	0.0824	N	0.14661	0.345	0.80722	D	1	P	0.42584	0.784	B	0.38458	0.274	T	0.12630	-1.0540	10	0.37606	T	0.19	-8.8415	15.433	0.75116	0.0:0.0:1.0:0.0	.	256	Q86W50	MET16_HUMAN	V	256;38	ENSP00000263092:A256V;ENSP00000443633:A38V	ENSP00000263092:A256V	A	-	2	0	METTL16	2291565	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.246000	0.89828	2.714000	0.92807	0.650000	0.86243	GCG		0.418	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		A	2344815	G	A	2344815	3	1	47	1	0	0	0	0	1	0	0	0	9520	1087	38	1	937	1	METT10D	17	2344815	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	106816	2344815	78850395	1691	6088										
TRPV3	162514	broad.mit.edu	37	chr17	3427599	3427599	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacgaggcaggcgaggtactCtttgtaggcaaacaagtaca	12	9	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:3427599C>A	ENST00000576742.1	-	13	1957	c.1636G>T	c.(1636-1638)Gag>Tag	p.E546*	TRPV3_ENST00000572519.1_Nonsense_Mutation_p.E546*|TRPV3_ENST00000301365.4_Nonsense_Mutation_p.E546*	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	546					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)	p.E546K(1)|p.E546*(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GCGAGGTACTCTTTGTAGGCA	0.522																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|skin(1)	17											118	107	110					17																	3427599		2203	4300	6503	3374349	SO:0001587	stop_gained	162514			AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.1636G>T	17.37:g.3427599C>A	ENSP00000461518:p.Glu546*		3374349	Q8NDW7|Q8NET9|Q8NFH2	Nonsense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	c	16.22	3.062595	0.55432	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	.	.	.	5.16	5.16	0.70880	.	0.225469	0.33253	N	0.005101	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-15.5807	13.0489	0.58944	0.1607:0.8393:0.0:0.0	.	.	.	.	X	546;546;530	.	ENSP00000301365:E546X	E	-	1	0	TRPV3	3374349	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.935000	0.48963	2.593000	0.87608	0.563000	0.77884	GAG		0.522	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		A	3427599	C	A	3427599	4	1	47	1	0	0	0	0	0	1	0	0	16637	922	32	2	760	2	TRPV3	17	3427599	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1082784	3427599	77767611	1692	6089										
ZZEF1	23140	broad.mit.edu	37	chr17	3962535	3962535	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagttgatagtaagtgtctcGaatttctttgtgtagatcag	10	4	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:3962535G>A	ENST00000381638.2	-	31	5057	c.4933C>T	c.(4933-4935)Cga>Tga	p.R1645*	RNA5SP434_ENST00000516647.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1645							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R1645*(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						TAAGTGTCTCGAATTTCTTTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											93	89	90					17																	3962535		2203	4300	6503	3909284	SO:0001587	stop_gained	23140			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.4933C>T	17.37:g.3962535G>A	ENSP00000371051:p.Arg1645*		3909284	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Nonsense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.623732	0.66901	.	.	ENSG00000074755	ENST00000381638	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8145	13.7494	0.62897	0.0:0.0:0.8462:0.1538	.	.	.	.	X	1645	.	ENSP00000371051:R1645X	R	-	1	2	ZZEF1	3909284	1.000000	0.71417	1.000000	0.80357	0.542000	0.35054	2.543000	0.45752	2.447000	0.82792	0.555000	0.69702	CGA		0.363	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		A	3962535	G	A	3962535	4	1	47	1	0	0	0	0	0	1	0	0	18294	1066	37	1	4052	1	ZZEF1	17	3962535	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	534936	3962535	77232675	1693	6090										
ZFP3	124961	broad.mit.edu	37	chr17	4995549	4995549	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagagaatccatactggagaGaaaccatatgaatgtaatga	9	6	0	4	rs369205257		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:4995549G>T	ENST00000318833.3	+	2	1086	c.750G>T	c.(748-750)gaG>gaT	p.E250D		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E250D(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						ATACTGGAGAGAAACCATATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	64	65	65		750	2	1	17		65	0,8600		0,0,4300	no	missense	ZFP3	NM_153018.2	45	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging	250/503	4995549	1,13005	2203	4300	6503	4936273	SO:0001583	missense	124961			BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"Zinc fingers, C2H2-type"	12861	protein-coding gene	gene with protein product		194480	"zinc finger protein homologous to Zfp-3 in mouse", "zinc finger protein 3 homolog (mouse)"				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.750G>T	17.37:g.4995549G>T	ENSP00000320347:p.Glu250Asp		4936273	A5PLL4	Missense_Mutation	SNP	ENST00000318833.3	37	CCDS11067.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162951	0.57476	2.27E-4	0.0	ENSG00000180787	ENST00000318833	T	0.26810	1.71	3.93	1.96	0.26148	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36972	N	0.002308	T	0.37544	0.1007	M	0.67397	2.05	0.35045	D	0.760062	P	0.45672	0.864	P	0.54346	0.749	T	0.50955	-0.8766	10	0.72032	D	0.01	-14.2886	8.2559	0.31756	0.2006:0.0:0.7994:0.0	.	250	Q96NJ6	ZFP3_HUMAN	D	250	ENSP00000320347:E250D	ENSP00000320347:E250D	E	+	3	2	ZFP3	4936273	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.208000	0.42797	0.640000	0.30582	-0.253000	0.11424	GAG		0.383	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018		T	4995549	G	T	4995549	3	4	47	1	0	0	0	0	1	0	0	0	17682	933	33	2	752	2	ZFP3	17	4995549	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1033014	4995549	76199661	1694	6091										
USP6	9098	broad.mit.edu	37	chr17	5051946	5051946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccccaatggaatgccaaacActgttgtgccatgtggaact	9	11	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:5051946A>G	ENST00000574788.1	+	30	4757	c.2527A>G	c.(2527-2529)Act>Gct	p.T843A	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000250066.6_Missense_Mutation_p.T843A|USP6_ENST00000304328.5_Missense_Mutation_p.T526A			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	843	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.T843A(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AATGCCAAACACTGTTGTGCC	0.438			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	1	Substitution - Missense(1)	large_intestine(1)	17											150	127	135					17																	5051946		2203	4300	6503	4992670	SO:0001583	missense	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.2527A>G	17.37:g.5051946A>G	ENSP00000460380:p.Thr843Ala		4992670	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	A	10.11	1.260811	0.23051	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.14144	2.95;2.53	2.79	2.79	0.32731	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.23014	0.0556	L	0.40543	1.245	0.44852	D	0.997863	D;B	0.67145	0.996;0.327	D;B	0.76071	0.987;0.299	T	0.01249	-1.1406	10	0.32370	T	0.25	.	9.0444	0.36338	1.0:0.0:0.0:0.0	.	526;843	P35125-2;P35125	.;UBP6_HUMAN	A	843;526	ENSP00000250066:T843A;ENSP00000305473:T526A	ENSP00000250066:T843A	T	+	1	0	USP6	4992670	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	8.323000	0.90002	1.281000	0.44480	0.163000	0.16589	ACT		0.438	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		G	5051946	A	G	5051946	3	3	47	1	0	0	0	0	1	0	0	0	17126	159	6	4	2609	4	USP6	17	5051946	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	56397	5051946	76143264	1695	6092										
NUP88	4927	broad.mit.edu	37	chr17	5308516	5308516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaccatagttatcttcagccGcaggatgcatgggcaatgga	11	9	2	0	rs370008628		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:5308516G>A	ENST00000573584.1	-	6	1414	c.905C>T	c.(904-906)gCg>gTg	p.A302V		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	302					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.A302V(2)		endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						ATCTTCAGCCGCAGGATGCAT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	17						G	VAL/ALA	0,4406		0,0,2203	171	133	146		905	4.8	1	17		146	1,8599	1.2+/-3.3	0,1,4299	no	missense	NUP88	NM_002532.4	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	302/742	5308516	1,13005	2203	4300	6503	5249240	SO:0001583	missense	4927			Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.905C>T	17.37:g.5308516G>A	ENSP00000458954:p.Ala302Val		5249240	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	G	32	5.145788	0.94603	0.0	1.16E-4	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.77837	0.4190	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;P;D	0.91635	0.936;0.874;0.999	T	0.75912	-0.3150	9	0.35671	T	0.21	-13.1062	17.4474	0.87581	0.0:0.0:1.0:0.0	.	302;171;302	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	V	302;171	.	ENSP00000225696:A302V	A	-	2	0	NUP88	5249240	1.000000	0.71417	0.968000	0.41197	0.952000	0.60782	9.497000	0.97970	2.677000	0.91161	0.655000	0.94253	GCG		0.438	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		A	5308516	G	A	5308516	3	1	47	1	0	0	0	0	1	0	0	0	10802	1087	38	1	1368	1	NUP88	17	5308516	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	256570	5308516	75886694	1696	6093										
NLRP1	22861	broad.mit.edu	37	chr17	5461802	5461802	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacacatgcccatttcttcGaaatgggccatcacttgtgt	7	12	2	0	rs199601083		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:5461802G>A	ENST00000572272.1	-	4	2213	c.2214C>T	c.(2212-2214)ttC>ttT	p.F738F	NLRP1_ENST00000354411.3_Silent_p.F738F|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000269280.4_Silent_p.F738F|NLRP1_ENST00000345221.3_Silent_p.F738F|NLRP1_ENST00000262467.5_Silent_p.F738F|NLRP1_ENST00000577119.1_Silent_p.F738F			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	738					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.F738F(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CCATTTCTTCGAAATGGGCCA	0.512													G|||	1	0.000199681	0	0	5008	,	,		21748	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											83	84	84					17																	5461802		2203	4300	6503	5402526	SO:0001819	synonymous_variant	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2214C>T	17.37:g.5461802G>A			5402526	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	37	CCDS42246.1																																																																																				0.512	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		A	5461802	G	A	5461802	2	1	47	1	0	0	0	0	0	0	0	1	10502	1049	37	1		1	NLRP1	17	5461802	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	153286	5461802	75733408	1697	6094										
NLRP1	22861	broad.mit.edu	37	chr17	5462129	5462129	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acataggacattgctgcaaaGaactcttggaaacagaggtg	11	7	1	2	rs149035689	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:5462129G>T	ENST00000572272.1	-	4	1886	c.1887C>A	c.(1885-1887)ttC>ttA	p.F629L	NLRP1_ENST00000354411.3_Missense_Mutation_p.F629L|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000269280.4_Missense_Mutation_p.F629L|NLRP1_ENST00000345221.3_Missense_Mutation_p.F629L|NLRP1_ENST00000262467.5_Missense_Mutation_p.F629L|NLRP1_ENST00000577119.1_Missense_Mutation_p.F629L			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	629	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.F629L(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTGCTGCAAAGAACTCTTGGA	0.443													G|||	22	0.00439297	0	0	5008	,	,		23678	0		0	False		,,,				2504	0.0225															1	Substitution - Missense(1)	large_intestine(1)	17						G	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	0,4406		0,0,2203	70	67	68		1887,1887,1887,1887,1887	3.3	1	17	dbSNP_134	68	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	22,22,22,22,22	0,4,6499	TT,TG,GG		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	629/1376,629/1430,629/1474,629/1444,629/1400	5462129	4,13002	2203	4300	6503	5402853	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1887C>A	17.37:g.5462129G>T	ENSP00000460475:p.Phe629Leu		5402853	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092846	0.76756	0.0	4.65E-4	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	D;D;D;D;D	0.87256	-2.23;-2.23;-2.11;-2.08;-2.11	4.31	3.34	0.38264	NACHT nucleoside triphosphatase (1);	0.000000	0.40728	N	0.001038	D	0.92303	0.7558	M	0.85099	2.735	0.31181	N	0.702059	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.999;0.997	D	0.89301	0.3626	10	0.66056	D	0.02	.	7.4972	0.27496	0.1147:0.0:0.8853:0.0	.	629;629;629;629;629	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	L	629	ENSP00000442029:F629L;ENSP00000262467:F629L;ENSP00000269280:F629L;ENSP00000346390:F629L;ENSP00000324366:F629L	ENSP00000262467:F629L	F	-	3	2	NLRP1	5402853	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.667000	0.25112	2.438000	0.82558	0.650000	0.86243	TTC		0.443	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5462129	G	T	5462129	3	4	47	1	0	0	0	0	1	0	0	0	10502	933	33	2	2665	2	NLRP1	17	5462129	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	327	5462129	75733081	1698	6095										
KIAA0753	9851	broad.mit.edu	37	chr17	6526372	6526372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacaaacatctgtaaggcccGaatggctcctcgatgggcag	12	11	1	0	rs199499810		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:6526372G>A	ENST00000361413.3	-	6	1292	c.934C>T	c.(934-936)Cgg>Tgg	p.R312W	KIAA0753_ENST00000542606.1_Missense_Mutation_p.R13W|KIAA0753_ENST00000589033.1_5'Flank|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R13W	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	312						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R312W(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TGTAAGGCCCGAATGGCTCCT	0.488													G|||	0	0	0	0	5008	,	,		17516	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											39	39	39					17																	6526372		1910	4109	6019	6467096	SO:0001583	missense	9851				CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.934C>T	17.37:g.6526372G>A	ENSP00000355250:p.Arg312Trp		6467096	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	26.4	4.734461	0.89482	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.11169	2.8;2.8	5.7	5.7	0.88788	.	0.179664	0.47852	D	0.000209	T	0.28167	0.0695	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.01386	-1.1368	10	0.87932	D	0	-7.4425	17.7581	0.88456	0.0:0.0:1.0:0.0	.	312	Q2KHM9	K0753_HUMAN	W	312;13	ENSP00000355250:R312W;ENSP00000444634:R13W	ENSP00000355250:R312W	R	-	1	2	KIAA0753	6467096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.796000	0.55507	2.878000	0.98634	0.650000	0.86243	CGG		0.488	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		A	6526372	G	A	6526372	3	1	47	1	0	0	0	0	1	0	0	0	8212	1057	37	1	2025	1	KIAA0753	17	6526372	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1064243	6526372	74668838	1699	6096										
TEKT1	83659	broad.mit.edu	37	chr17	6704232	6704232	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttcaagagctgtaatatTtttctcctgggaagcaatct	7	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:6704232T>G	ENST00000338694.2	-	7	1012	c.883A>C	c.(883-885)Aat>Cat	p.N295H	TEKT1_ENST00000535086.1_Missense_Mutation_p.N149H	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	295						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.N295H(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				GCTGTAATATTTTTCTCCTGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	17											118	121	120					17																	6704232		2203	4300	6503	6644956	SO:0001583	missense	83659				CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.883A>C	17.37:g.6704232T>G	ENSP00000341346:p.Asn295His		6644956	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.428077	0.83667	.	.	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.02787	4.16;4.16	5.85	5.85	0.93711	.	0.091207	0.64402	D	0.000001	T	0.10551	0.0258	M	0.73319	2.225	0.53688	D	0.999978	P	0.47677	0.899	P	0.54431	0.752	T	0.01114	-1.1447	10	0.42905	T	0.14	.	14.4944	0.67674	0.0:0.0:0.0:1.0	.	295	Q969V4	TEKT1_HUMAN	H	295;149	ENSP00000341346:N295H;ENSP00000444142:N149H	ENSP00000341346:N295H	N	-	1	0	TEKT1	6644956	1.000000	0.71417	0.967000	0.41034	0.935000	0.57460	5.675000	0.68123	2.371000	0.80710	0.533000	0.62120	AAT		0.512	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		G	6704232	T	G	6704232	3	3	47	1	0	0	0	0	1	0	0	0	15791	1841	64	4	381	4	TEKT1	17	6704232	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	177860	6704232	74490978	1700	6097										
GPS2	2874	broad.mit.edu	37	chr17	7217623	7217623	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcccacctctgttcctttcGcctccgtttttcttcctcat	3	17	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:7217623G>A	ENST00000380728.2	-	4	604	c.304C>T	c.(304-306)Cga>Tga	p.R102*	NEURL4_ENST00000574120.1_5'Flank|GPS2_ENST00000389167.5_Nonsense_Mutation_p.R102*|GPS2_ENST00000391950.3_Nonsense_Mutation_p.R102*|RP11-542C16.2_ENST00000575474.1_3'UTR			Q13227	GPS2_HUMAN	G protein pathway suppressor 2	102					cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)	p.R102*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				TGTTCCTTTCGCCTCCGTTTT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											157	152	154					17																	7217623		2203	4300	6503	7158347	SO:0001587	stop_gained	2874			U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.304C>T	17.37:g.7217623G>A	ENSP00000370104:p.Arg102*		7158347	B4DXA1|Q6FHM8	Nonsense_Mutation	SNP	ENST00000380728.2	37	CCDS11100.1	.	.	.	.	.	.	.	.	.	.	G	37	6.142223	0.97320	.	.	ENSG00000132522	ENST00000391950;ENST00000380728;ENST00000389167;ENST00000315601	.	.	.	4.69	3.7	0.42460	.	0.000000	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4307	0.50038	0.0:0.0:0.8189:0.1811	.	.	.	.	X	102	.	ENSP00000319371:R102X	R	-	1	2	GPS2	7158347	1.000000	0.71417	0.999000	0.59377	0.864000	0.49448	4.711000	0.61881	1.185000	0.42971	-0.282000	0.10007	CGA		0.453	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489		A	7217623	G	A	7217623	4	1	47	1	0	0	0	0	0	1	0	0	6754	1095	38	1	711	1	GPS2	17	7217623	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	513391	7217623	73977587	1701	6098										
FXR2	9513	broad.mit.edu	37	chr17	7496783	7496783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catagctgcccccataggttCgagtcgcatggagggaggag	15	10	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:7496783C>T	ENST00000250113.7	-	12	1602	c.1268G>A	c.(1267-1269)cGa>cAa	p.R423Q	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	423						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R423Q(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		CCCATAGGTTCGAGTCGCATG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											21	24	23					17																	7496783		2087	4197	6284	7437508	SO:0001583	missense	9513			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1268G>A	17.37:g.7496783C>T	ENSP00000250113:p.Arg423Gln		7437508	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	C	36	5.794949	0.96952	.	.	ENSG00000129245	ENST00000250113	T	0.56275	0.47	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.67627	0.2913	M	0.62723	1.935	0.58432	D	0.999999	D	0.69078	0.997	D	0.70227	0.968	T	0.62020	-0.6942	10	0.23891	T	0.37	-2.7089	16.162	0.81727	0.0:1.0:0.0:0.0	.	423	P51116	FXR2_HUMAN	Q	423	ENSP00000250113:R423Q	ENSP00000250113:R423Q	R	-	2	0	FXR2	7437508	0.994000	0.37717	0.979000	0.43373	0.974000	0.67602	5.559000	0.67326	2.683000	0.91414	0.313000	0.20887	CGA		0.647	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			T	7496783	C	T	7496783	3	4	47	1	0	0	0	0	1	0	0	0	6135	884	31	1	677	1	FXR2	17	7496783	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	279160	7496783	73698427	1702	6099										
SHBG	6462	broad.mit.edu	37	chr17	7535297	7535297	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgctcttgggacaccagaGaacccatcttggctcagtct	9	13	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:7535297G>T	ENST00000380450.4	+	6	847	c.816G>T	c.(814-816)gaG>gaT	p.E272D	SHBG_ENST00000570547.1_Intron|SHBG_ENST00000575314.1_Missense_Mutation_p.E214D|SHBG_ENST00000575903.1_Missense_Mutation_p.E254D|SHBG_ENST00000416273.3_Missense_Mutation_p.E272D|SHBG_ENST00000572262.1_Missense_Mutation_p.E160D|SHBG_ENST00000576728.1_Missense_Mutation_p.E160D|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000441599.2_Intron|SHBG_ENST00000574539.1_Missense_Mutation_p.E214D|SHBG_ENST00000340624.5_Missense_Mutation_p.E214D	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	272	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.0?(1)|p.?(1)|p.E272D(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	GGACACCAGAGAACCCATCTT	0.582																																																3	Substitution - Missense(1)|Unknown(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)	17											132	137	135					17																	7535297		2203	4300	6503	7476022	SO:0001583	missense	6462				CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.816G>T	17.37:g.7535297G>T	ENSP00000369816:p.Glu272Asp		7476022	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	G	8.809	0.934832	0.18206	.	.	ENSG00000129214	ENST00000340624;ENST00000416273;ENST00000441313;ENST00000380450	D;D;T	0.87966	-2.32;-2.1;-1.11	4.62	-0.463	0.12164	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.556821	0.17944	N	0.156745	T	0.78666	0.4319	M	0.65975	2.015	0.09310	N	1	P;P;P;P;P;P	0.45827	0.867;0.729;0.665;0.61;0.791;0.61	B;B;B;B;B;B	0.38264	0.21;0.269;0.119;0.104;0.212;0.073	T	0.67772	-0.5584	10	0.15952	T	0.53	-7.1549	4.0269	0.09692	0.3301:0.4235:0.2464:0.0	.	272;267;218;191;272;214	F5H5Z8;P04278-2;E9PH59;B0FWH5;P04278;B4DYU0	.;.;.;.;SHBG_HUMAN;.	D	214;272;218;272	ENSP00000345675:E214D;ENSP00000388867:E272D;ENSP00000369816:E272D	ENSP00000345675:E214D	E	+	3	2	SHBG	7476022	0.000000	0.05858	0.037000	0.18230	0.334000	0.28698	-0.120000	0.10660	0.069000	0.16605	0.563000	0.77884	GAG		0.582	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		T	7535297	G	T	7535297	3	4	47	1	0	0	0	0	1	0	0	0	14306	933	33	2	838	2	SHBG	17	7535297	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	38514	7535297	73659913	1703	6100										
KRBA2	124751	broad.mit.edu	37	chr17	8274700	8274700	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttgagagccttctaaataAttccaatctttggtcatatt	5	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:8274700A>C	ENST00000331336.2	-	1	158	c.153T>G	c.(151-153)aaT>aaG	p.N51K	RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.5_ENST00000583963.1_RNA|RP11-849F2.7_ENST00000582471.1_3'UTR|KRBA2_ENST00000396267.1_Intron	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	51	KRAB.				DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.N51K(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						CTTCTAAATAATTCCAATCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	128	127					17																	8274700		2203	4300	6503	8215425	SO:0001583	missense	124751			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"-"	26989	protein-coding gene	gene with protein product			"KRAB A domain containing 2"			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.153T>G	17.37:g.8274700A>C	ENSP00000328017:p.Asn51Lys		8215425	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	A	0.120	-1.126787	0.01770	.	.	ENSG00000184619	ENST00000331336	T	0.01516	4.81	2.26	-2.85	0.05734	Krueppel-associated box (3);	.	.	.	.	T	0.00524	0.0017	N	0.00465	-1.465	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45366	-0.9266	9	0.30854	T	0.27	.	0.9757	0.01425	0.4088:0.2672:0.1824:0.1417	.	51	Q6ZNG9	KRBA2_HUMAN	K	51	ENSP00000328017:N51K	ENSP00000328017:N51K	N	-	3	2	KRBA2	8215425	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-2.504000	0.00964	-0.684000	0.05183	-0.396000	0.06452	AAT		0.443	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		C	8274700	A	C	8274700	3	2	47	1	0	0	0	0	1	0	0	0	8461	98	4	4	1333	4	KRBA2	17	8274700	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	739403	8274700	72920510	1704	6101										
NDEL1	81565	broad.mit.edu	37	chr17	8366645	8366645	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcttttattaggcaagaaAaagtcatatttcccacgttg	6	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:8366645A>C	ENST00000334527.7	+	8	1141				NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Intron|NDEL1_ENST00000402554.3_Missense_Mutation_p.K318Q|NDEL1_ENST00000299734.7_Intron	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1						activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)	p.K318Q(1)		large_intestine(6)|lung(4)|skin(3)	13						TAGGCAAGAAAAAGTCATATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	17											288	264	272					17																	8366645		2202	4298	6500	8307370	SO:0001627	intron_variant	81565			AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.944+3167A>C	17.37:g.8366645A>C			8307370	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	37	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168693	0.57584	.	.	ENSG00000166579	ENST00000380025	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	T	0.52041	0.1710	L	0.36672	1.1	0.80722	D	1	P	0.42078	0.77	B	0.42995	0.404	T	0.55736	-0.8094	8	0.51188	T	0.08	.	14.3373	0.66600	1.0:0.0:0.0:0.0	.	318	A6NIZ0	.	Q	318	.	ENSP00000369364:K318Q	K	+	1	0	NDEL1	8307370	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.294000	0.72738	2.167000	0.68274	0.482000	0.46254	AAA		0.378	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		C	8366645	A	C	8366645	1	2	47	0	1	0	0	0	0	0	0	0	10275	15	1	4		4	NDEL1	17	8366645	Intron	SNP	A	TCGA-AG-3892-01A-01W-1073-09	91945	8366645	72828565	1705	6102										
STX8	9482	broad.mit.edu	37	chr17	9471774	9471774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcaatttgacaagtagaatCgtatgtggagaacctgcacc	11	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:9471774C>T	ENST00000306357.4	-	2	458	c.31G>A	c.(31-33)Gat>Aat	p.D11N	STX8_ENST00000573373.1_5'UTR|STX8_ENST00000574431.1_Intron	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	11					endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.D11N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						CAAGTAGAATCGTATGTGGAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	101	109					17																	9471774		2203	4300	6503	9412499	SO:0001583	missense	9482			AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310			11443	protein-coding gene	gene with protein product		604203				9852078, 10198254	Standard	NM_004853		Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.31G>A	17.37:g.9471774C>T	ENSP00000305255:p.Asp11Asn		9412499	O60712|Q53XT8	Missense_Mutation	SNP	ENST00000306357.4	37	CCDS32565.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831684	0.91036	.	.	ENSG00000170310	ENST00000306357	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.73560	0.3602	M	0.71581	2.175	0.52099	D	0.999948	D	0.69078	0.997	P	0.56088	0.791	T	0.73094	-0.4091	9	0.40728	T	0.16	0.7227	16.6943	0.85330	0.0:1.0:0.0:0.0	.	11	Q9UNK0	STX8_HUMAN	N	11	.	ENSP00000305255:D11N	D	-	1	0	STX8	9412499	0.995000	0.38212	0.965000	0.40720	0.975000	0.68041	4.039000	0.57325	2.680000	0.91292	0.655000	0.94253	GAT		0.403	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439206.3	NM_004853		T	9471774	C	T	9471774	3	4	47	1	0	0	0	0	1	0	0	0	15390	884	31	1	707	1	STX8	17	9471774	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1105129	9471774	71723436	1706	6103										
MYH13	8735	broad.mit.edu	37	chr17	10227345	10227345	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgggtttgctcaccttgttCtctgtggcatgcttctcctt	9	11	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:10227345C>A	ENST00000418404.3	-	22	3091	c.2928G>T	c.(2926-2928)gaG>gaT	p.E976D	MYH13_ENST00000252172.4_Missense_Mutation_p.E976D|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	976					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E976D(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						TCACCTTGTTCTCTGTGGCAT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	17											93	88	90					17																	10227345		2197	4299	6496	10168070	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2928G>T	17.37:g.10227345C>A	ENSP00000404570:p.Glu976Asp		10168070	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.488425	0.64074	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	D	0.85861	-2.04	4.37	3.4	0.38934	.	.	.	.	.	T	0.79873	0.4521	L	0.48935	1.535	0.31492	N	0.665896	B;B	0.28512	0.182;0.214	B;B	0.32289	0.076;0.143	T	0.75102	-0.3436	9	0.23891	T	0.37	.	9.884	0.41251	0.0:0.8342:0.0:0.1658	.	602;976	B4DFX9;Q9UKX3	.;MYH13_HUMAN	D	976;602	ENSP00000252172:E976D	ENSP00000252172:E976D	E	-	3	2	MYH13	10168070	0.026000	0.19158	1.000000	0.80357	0.981000	0.71138	-0.686000	0.05161	1.174000	0.42811	0.655000	0.94253	GAG		0.483	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		A	10227345	C	A	10227345	3	1	47	1	0	0	0	0	1	0	0	0	10062	912	32	2	2964	2	MYH13	17	10227345	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	755571	10227345	70967865	1707	6104										
MYH2	4620	broad.mit.edu	37	chr17	10443995	10443995	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgggtaatcatatgggttCgtggtaatcagaagcatttc	11	5	2	1	rs374415748		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:10443995C>A	ENST00000245503.5	-	11	1308	c.924G>T	c.(922-924)acG>acT	p.T308T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Silent_p.T308T|MYH2_ENST00000397183.2_Silent_p.T308T	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	308	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T308T(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CATATGGGTTCGTGGTAATCA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	17											97	89	92					17																	10443995		2203	4300	6503	10384720	SO:0001819	synonymous_variant	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.924G>T	17.37:g.10443995C>A			10384720	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																				0.388	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10443995	C	A	10443995	2	1	47	1	0	0	0	0	0	0	0	1	10065	871	31	2		2	MYH2	17	10443995	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	216650	10443995	70751215	1708	6105										
DNAH9	1770	broad.mit.edu	37	chr17	11556132	11556132	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tattcatgatcttgaacaaaGaattcagaaaactaaagaca	5	6	3	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:11556132G>T	ENST00000262442.4	+	14	2476	c.2408G>T	c.(2407-2409)aGa>aTa	p.R803I	DNAH9_ENST00000454412.2_Missense_Mutation_p.R803I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	803	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R803I(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		CTTGAACAAAGAATTCAGAAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	17											110	108	108					17																	11556132		2203	4300	6503	11496857	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.2408G>T	17.37:g.11556132G>T	ENSP00000262442:p.Arg803Ile		11496857	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872174	0.91587	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25912	1.81;1.77	5.38	5.38	0.77491	.	0.132404	0.50627	D	0.000104	T	0.56046	0.1959	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.54609	-0.8268	10	0.31617	T	0.26	.	19.4938	0.95064	0.0:0.0:1.0:0.0	.	803	Q9NYC9	DYH9_HUMAN	I	803	ENSP00000262442:R803I;ENSP00000414874:R803I	ENSP00000262442:R803I	R	+	2	0	DNAH9	11496857	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.860000	0.92272	2.691000	0.91804	0.650000	0.86243	AGA		0.358	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11556132	G	T	11556132	3	4	47	1	0	0	0	0	1	0	0	0	4619	942	33	2	2462	2	DNAH9	17	11556132	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1112137	11556132	69639078	1709	6106										
ZNF624	57547	broad.mit.edu	37	chr17	16527011	16527011	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagttttgatttatcactaaAagctttcccgcattcactac	4	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:16527011A>C	ENST00000311331.7	-	6	1280	c.1189T>G	c.(1189-1191)Ttt>Gtt	p.F397V		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	397					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F397V(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTATCACTAAAAGCTTTCCCG	0.403																																					NSCLC(186;1023 2134 13330 38202 39800)											1	Substitution - Missense(1)	large_intestine(1)	17											97	97	97					17																	16527011		2203	4300	6503	16467736	SO:0001583	missense	57547			AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"Zinc fingers, C2H2-type", "-"	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.1189T>G	17.37:g.16527011A>C	ENSP00000310472:p.Phe397Val		16467736	Q3SY62|Q3SY63|Q6ZN27	Missense_Mutation	SNP	ENST00000311331.7	37	CCDS11180.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.976164	0.53720	.	.	ENSG00000197566	ENST00000311331	T	0.46063	0.88	2.78	2.78	0.32641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.70281	0.3206	H	0.95645	3.7	0.37254	D	0.906693	D	0.76494	0.999	D	0.74348	0.983	T	0.79152	-0.1921	9	0.87932	D	0	.	9.3624	0.38203	1.0:0.0:0.0:0.0	.	397	Q9P2J8	ZN624_HUMAN	V	397	ENSP00000310472:F397V	ENSP00000310472:F397V	F	-	1	0	ZNF624	16467736	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	8.390000	0.90175	1.528000	0.49103	0.455000	0.32223	TTT		0.403	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617		C	16527011	A	C	16527011	3	2	47	1	0	0	0	0	1	0	0	0	18087	14	1	4	1412	4	ZNF624	17	16527011	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4970879	16527011	64668199	1710	6107										
KCNJ12	3768	broad.mit.edu	37	chr17	21319683	21319683	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagtacaagattgactactcGcacttccacaagacctatga	6	12	0	4	rs111482429	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:21319683G>A	ENST00000583088.1	+	3	1924	c.1029G>A	c.(1027-1029)tcG>tcA	p.S343S	KCNJ12_ENST00000331718.5_Silent_p.S343S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	343				S -> L (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.S343S(2)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TTGACTACTCGCACTTCCACA	0.582										Prostate(3;0.18)																																						2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	17						G		1,4405	2.1+/-5.4	0,1,2202	154	153	153		1029	-5.5	1	17	dbSNP_132	153	0,8600		0,0,4300	no	coding-synonymous	KCNJ12	NM_021012.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		343/434	21319683	1,13005	2203	4300	6503	21260276	SO:0001819	synonymous_variant	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1029G>A	17.37:g.21319683G>A			21260276	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				0.582	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319683	G	A	21319683	2	1	47	1	0	0	0	0	0	0	0	1	8067	1074	38	1		1	KCNJ12	17	21319683	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4792672	21319683	59875527	1711	6108										
EFCAB5	374786	broad.mit.edu	37	chr17	28296034	28296034	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataatagataaggaaaatcTgaagaaggaactagaaaaaa	8	2	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:28296034T>G	ENST00000394835.3	+	4	608	c.416T>G	c.(415-417)cTg>cGg	p.L139R	EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000378738.3_Missense_Mutation_p.L139R|EFCAB5_ENST00000394832.2_Missense_Mutation_p.L139R|EFCAB5_ENST00000320856.5_Missense_Mutation_p.L139R|EFCAB5_ENST00000536908.2_Missense_Mutation_p.L83R	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	139							calcium ion binding (GO:0005509)	p.L139R(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						AAGGAAAATCTGAAGAAGGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	17											37	34	35					17																	28296034		1816	4069	5885	25320160	SO:0001583	missense	374786			AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.416T>G	17.37:g.28296034T>G	ENSP00000378312:p.Leu139Arg		25320160	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	T	7.818	0.717225	0.15372	.	.	ENSG00000176927	ENST00000448319;ENST00000536908;ENST00000421238;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598	T;T;T;T;T	0.26660	1.73;2.76;2.76;2.06;1.72	5.48	4.39	0.52855	.	.	.	.	.	T	0.34337	0.0894	L	0.43152	1.355	0.21256	N	0.999747	P;P;P;P	0.50369	0.934;0.934;0.585;0.836	P;P;P;P	0.58077	0.832;0.784;0.577;0.577	T	0.13308	-1.0514	9	0.59425	D	0.04	0.572	6.0214	0.19630	0.1476:0.0834:0.0:0.769	.	83;139;139;139	F5GYL2;B5MEA3;E7EVS9;A4FU69	.;.;.;EFCB5_HUMAN	R	83;83;83;139;139;139;139;83	ENSP00000440619:L83R;ENSP00000378312:L139R;ENSP00000322003:L139R;ENSP00000378309:L139R;ENSP00000368012:L139R	ENSP00000322003:L139R	L	+	2	0	EFCAB5	25320160	0.009000	0.17119	0.823000	0.32752	0.121000	0.20230	0.229000	0.17833	0.991000	0.38814	0.482000	0.46254	CTG		0.378	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		G	28296034	T	G	28296034	3	3	47	1	0	0	0	0	1	0	0	0	4949	1580	55	4	430	4	EFCAB5	17	28296034	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	6976351	28296034	52899176	1712	6109										
CPD	1362	broad.mit.edu	37	chr17	28789449	28789449	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttgacacagataaccggaTatttggtttgccaagggagc	11	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:28789449T>G	ENST00000225719.4	+	20	3954	c.3878T>G	c.(3877-3879)aTa>aGa	p.I1293R	CPD_ENST00000543464.2_Missense_Mutation_p.I1046R	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	1293	Carboxypeptidase-like 3.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)	p.I1293R(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						GATAACCGGATATTTGGTTTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	17											188	170	176					17																	28789449		2203	4300	6503	25813575	SO:0001583	missense	1362			U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.3878T>G	17.37:g.28789449T>G	ENSP00000225719:p.Ile1293Arg		25813575	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Missense_Mutation	SNP	ENST00000225719.4	37	CCDS11257.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594303	0.86953	.	.	ENSG00000108582	ENST00000225719;ENST00000543464	T;T	0.13196	2.61;2.61	5.39	5.39	0.77823	Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.051948	0.64402	D	0.000001	T	0.22166	0.0534	N	0.19112	0.55	0.80722	D	1	D;D	0.76494	0.989;0.999	P;D	0.66196	0.77;0.942	T	0.03354	-1.1045	10	0.62326	D	0.03	-5.3444	14.5957	0.68403	0.0:0.0:0.0:1.0	.	1046;1293	F5GZH6;O75976	.;CBPD_HUMAN	R	1293;1046	ENSP00000225719:I1293R;ENSP00000444443:I1046R	ENSP00000225719:I1293R	I	+	2	0	CPD	25813575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.499000	0.81566	2.028000	0.59812	0.528000	0.53228	ATA		0.358	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		G	28789449	T	G	28789449	3	3	47	1	0	0	0	0	1	0	0	0	3804	1406	49	4	3956	4	CPD	17	28789449	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	493415	28789449	52405761	1713	6110										
ATAD5	79915	broad.mit.edu	37	chr17	29161838	29161838	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaatactacaagccatgcaAactctagagataacgtaact	6	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:29161838A>C	ENST00000321990.4	+	2	1117	c.739A>C	c.(739-741)Aac>Cac	p.N247H	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	247					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.N247H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGCCATGCAAACTCTAGAGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											80	84	83					17																	29161838		2202	4300	6502	26185964	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.739A>C	17.37:g.29161838A>C	ENSP00000313171:p.Asn247His		26185964	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	0.920	-0.716215	0.03206	.	.	ENSG00000176208	ENST00000321990	T	0.17854	2.25	5.22	-3.02	0.05446	.	1.430800	0.04024	N	0.300303	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.06405	0.002;0.001	T	0.36744	-0.9735	10	0.51188	T	0.08	.	7.4208	0.27071	0.4801:0.1193:0.4006:0.0	.	247;247	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	H	247	ENSP00000313171:N247H	ENSP00000313171:N247H	N	+	1	0	ATAD5	26185964	0.011000	0.17503	0.000000	0.03702	0.259000	0.26198	1.249000	0.32839	-0.759000	0.04684	0.524000	0.50904	AAC		0.338	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		C	29161838	A	C	29161838	3	2	47	1	0	0	0	0	1	0	0	0	1077	14	1	4	745	4	ATAD5	17	29161838	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	372389	29161838	52033372	1714	6111										
C17orf42	79736	broad.mit.edu	37	chr17	29226442	29226442	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccccactgcatttcgattCatgctcagcacctgatgctg	7	14	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:29226442C>A	ENST00000581216.1	-	4	1449	c.828G>T	c.(826-828)atG>atT	p.M276I	TEFM_ENST00000579183.1_5'Flank|TEFM_ENST00000580840.1_3'UTR	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	276					DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)	p.M276I(1)									CATTTCGATTCATGCTCAGCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											126	120	122					17																	29226442		1914	4134	6048	26250568	SO:0001583	missense	79736				CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 42"	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.828G>T	17.37:g.29226442C>A	ENSP00000462963:p.Met276Ile		26250568	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Missense_Mutation	SNP	ENST00000581216.1	37	CCDS42291.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240548	0.39598	.	.	ENSG00000172171	ENST00000306049	.	.	.	6.06	1.85	0.25348	Ribonuclease H-like (1);	0.146425	0.85682	N	0.000000	T	0.44052	0.1275	L	0.42245	1.32	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20174	-1.0283	9	0.39692	T	0.17	-0.5288	6.9729	0.24658	0.1241:0.6825:0.0:0.1934	.	276	Q96QE5	TEFM_HUMAN	I	276	.	ENSP00000306574:M276I	M	-	3	0	C17orf42	26250568	1.000000	0.71417	0.417000	0.26559	0.978000	0.69477	3.253000	0.51469	0.137000	0.18759	-0.127000	0.14921	ATG		0.418	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683		A	29226442	C	A	29226442	3	1	47	1	0	0	0	0	1	0	0	0	1861	826	29	2	258	2	C17orf42	17	29226442	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	64604	29226442	51968768	1715	6112										
NF1	4763	broad.mit.edu	37	chr17	29556891	29556891	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatactcaatttgtagaacaAaccatagctataatgaagaa	5	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:29556891A>C	ENST00000358273.4	+	22	3272	c.2889A>C	c.(2887-2889)caA>caC	p.Q963H	NF1_ENST00000356175.3_Missense_Mutation_p.Q963H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	963					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.Q963H(2)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTGTAGAACAAACCATAGCTA	0.363			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	14	Whole gene deletion(8)|Unknown(4)|Substitution - Missense(2)	soft_tissue(7)|large_intestine(2)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17											92	93	93					17																	29556891		2203	4299	6502	26581017	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2889A>C	17.37:g.29556891A>C	ENSP00000351015:p.Gln963His		26581017	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	.	14.92	2.680169	0.47886	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.65178	-0.14;2.69;2.37	5.66	4.55	0.56014	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62962	0.2471	L	0.28400	0.85	0.80722	D	1	B;D;B	0.60575	0.005;0.988;0.028	B;D;B	0.74674	0.003;0.984;0.062	T	0.58584	-0.7611	10	0.22109	T	0.4	.	7.7302	0.28783	0.8155:0.0:0.1845:0.0	.	963;963;963	E1P657;P21359-2;P21359	.;.;NF1_HUMAN	H	963;963;629	ENSP00000351015:Q963H;ENSP00000348498:Q963H;ENSP00000389907:Q629H	ENSP00000348498:Q963H	Q	+	3	2	NF1	26581017	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	3.643000	0.54374	2.145000	0.66743	0.374000	0.22700	CAA		0.363	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29556891	A	C	29556891	3	2	47	1	0	0	0	0	1	0	0	0	10387	11	1	4	3036	4	NF1	17	29556891	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	330449	29556891	51638319	1716	6113										
EVI2B	2124	broad.mit.edu	37	chr17	29631380	29631380	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cactggatctcaaggttggaAtcttcttggtttttcataaa	8	7	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:29631380A>C	ENST00000330927.4	-	2	1402	c.1248T>G	c.(1246-1248)gaT>gaG	p.D416E	EVI2B_ENST00000577894.1_Missense_Mutation_p.D416E|EVI2B_ENST00000544462.1_Missense_Mutation_p.D431E|NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	416						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)|p.D416E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		CAAGGTTGGAATCTTCTTGGT	0.418																																																12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|large_intestine(1)|central_nervous_system(1)	17											117	108	111					17																	29631380		2203	4300	6503	26655506	SO:0001583	missense	2124				CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"CD molecules"	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.1248T>G	17.37:g.29631380A>C	ENSP00000333779:p.Asp416Glu		26655506	B7Z4A7	Missense_Mutation	SNP	ENST00000330927.4	37	CCDS11266.1	.	.	.	.	.	.	.	.	.	.	A	8.431	0.848544	0.17034	.	.	ENSG00000185862	ENST00000330927;ENST00000544462	T;T	0.40476	1.04;1.03	4.98	-0.546	0.11840	.	0.815812	0.10505	N	0.666826	T	0.24084	0.0583	L	0.27053	0.805	0.19775	N	0.999952	B;B	0.15930	0.015;0.015	B;B	0.16722	0.016;0.016	T	0.28138	-1.0053	10	0.56958	D	0.05	-0.1565	0.8717	0.01215	0.3464:0.1581:0.1028:0.3927	.	431;416	B7Z4A7;P34910	.;EVI2B_HUMAN	E	416;431	ENSP00000333779:D416E;ENSP00000439738:D431E	ENSP00000333779:D416E	D	-	3	2	EVI2B	26655506	0.000000	0.05858	0.009000	0.14445	0.314000	0.28054	-0.389000	0.07342	0.201000	0.20466	-0.438000	0.05819	GAT		0.418	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495		C	29631380	A	C	29631380	3	2	47	1	0	0	0	0	1	0	0	0	5301	98	4	4	102	4	EVI2B	17	29631380	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	74489	29631380	51563830	1717	6114										
EVI2B	2124	broad.mit.edu	37	chr17	29632028	29632028	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtatggcagctattgaattAtaattgtttttttgtggggt	11	2	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:29632028A>C	ENST00000330927.4	-	2	754	c.600T>G	c.(598-600)taT>taG	p.Y200*	EVI2B_ENST00000577894.1_Nonsense_Mutation_p.Y200*|EVI2B_ENST00000544462.1_Nonsense_Mutation_p.Y215*|NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	200						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)|p.Y200*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		CTATTGAATTATAATTGTTTT	0.343																																																12	Whole gene deletion(8)|Unknown(3)|Substitution - Nonsense(1)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|large_intestine(1)|central_nervous_system(1)	17											165	169	168					17																	29632028		2203	4300	6503	26656154	SO:0001587	stop_gained	2124				CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"CD molecules"	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.600T>G	17.37:g.29632028A>C	ENSP00000333779:p.Tyr200*		26656154	B7Z4A7	Nonsense_Mutation	SNP	ENST00000330927.4	37	CCDS11266.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.614437	0.28712	.	.	ENSG00000185862	ENST00000330927;ENST00000544462	.	.	.	5.46	-1.29	0.09288	.	0.896613	0.09320	N	0.818396	.	.	.	.	.	.	0.22066	N	0.99938	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6017	1.5382	0.02550	0.2741:0.1733:0.384:0.1686	.	.	.	.	X	200;215	.	ENSP00000333779:Y200X	Y	-	3	2	EVI2B	26656154	0.000000	0.05858	0.085000	0.20634	0.255000	0.26057	-0.477000	0.06583	0.054000	0.16065	0.402000	0.26972	TAT		0.343	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495		C	29632028	A	C	29632028	4	2	47	1	0	0	0	0	0	1	0	0	5301	456	16	4	750	4	EVI2B	17	29632028	Nonsense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	648	29632028	51563182	1718	6115										
SUZ12	23512	broad.mit.edu	37	chr17	30310020	30310020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgtgtttgtctaacaggcGcttacagcttttagatgggg	12	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:30310020G>A	ENST00000322652.5	+	9	1149	c.920G>A	c.(919-921)cGc>cAc	p.R307H	SUZ12_ENST00000580398.1_Missense_Mutation_p.R284H	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	307					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)	p.R307H(1)	SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				TCTAACAGGCGCTTACAGCTT	0.333			T	JAZF1	endometrial stromal tumours																																		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	1	Substitution - Missense(1)	large_intestine(1)	17											55	58	57					17																	30310020		2202	4280	6482	27334133	SO:0001583	missense	23512			D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.920G>A	17.37:g.30310020G>A	ENSP00000316578:p.Arg307His		27334133	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	37	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318426	0.40996	.	.	ENSG00000178691	ENST00000322652	T	0.52526	0.66	4.59	3.61	0.41365	.	0.050738	0.85682	N	0.000000	T	0.57740	0.2074	L	0.55834	1.745	0.58432	D	0.999998	P;D	0.76494	0.926;0.999	B;P	0.59703	0.158;0.862	T	0.58707	-0.7589	10	0.51188	T	0.08	-1.5675	12.7291	0.57187	0.0808:0.0:0.9192:0.0	.	307;307	A8K1U9;Q15022	.;SUZ12_HUMAN	H	307	ENSP00000316578:R307H	ENSP00000316578:R307H	R	+	2	0	SUZ12	27334133	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.865000	0.99609	0.925000	0.37094	0.597000	0.82753	CGC		0.333	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355		A	30310020	G	A	30310020	3	1	47	1	0	0	0	0	1	0	0	0	15455	1087	38	1	954	1	SUZ12	17	30310020	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	677992	30310020	50885190	1719	6116										
C17orf75	64149	broad.mit.edu	37	chr17	30658941	30658941	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taacatttaaacaaagcataAtgattcatttctgcctgtcg	5	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:30658941A>C	ENST00000577809.1	-	10	1081	c.1032T>G	c.(1030-1032)caT>caG	p.H344Q	RP11-227G15.3_ENST00000581915.1_RNA|RP11-227G15.2_ENST00000580360.1_lincRNA|C17orf75_ENST00000225805.4_Missense_Mutation_p.H344Q	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	344								p.H344Q(1)		ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ACAAAGCATAATGATTCATTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	17											121	116	118					17																	30658941		1814	4080	5894	27683054	SO:0001583	missense	64149			AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.1032T>G	17.37:g.30658941A>C	ENSP00000464275:p.His344Gln		27683054	Q7Z2H4	Missense_Mutation	SNP	ENST00000577809.1	37	CCDS58537.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.786158	0.31593	.	.	ENSG00000108666	ENST00000225805	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.71039	0.3293	M	0.63843	1.955	0.48040	D	0.999571	D	0.89917	1.0	D	0.83275	0.996	T	0.74044	-0.3791	9	0.87932	D	0	-17.1406	9.5439	0.39268	0.9156:0.0:0.0844:0.0	.	344	Q9HAS0	NJMU_HUMAN	Q	344	.	ENSP00000225805:H344Q	H	-	3	2	C17orf75	27683054	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.495000	0.45337	2.254000	0.74563	0.459000	0.35465	CAT		0.328	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344		C	30658941	A	C	30658941	3	2	47	1	0	0	0	0	1	0	0	0	1885	98	4	4	162	4	C17orf75	17	30658941	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	348921	30658941	50536269	1720	6117										
MYO1D	4642	broad.mit.edu	37	chr17	31094749	31094749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcagcaacaactctgaattCggcagcatcattgatagaag	8	9	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:31094749C>T	ENST00000318217.5	-	7	1040	c.736G>A	c.(736-738)Gaa>Aaa	p.E246K	MYO1D_ENST00000583621.1_Missense_Mutation_p.E246K|MYO1D_ENST00000394649.4_Missense_Mutation_p.E158K|MYO1D_ENST00000579584.1_Missense_Mutation_p.E246K	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	246	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E246K(2)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ACTCTGAATTCGGCAGCATCA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	17											88	77	81					17																	31094749		2203	4300	6503	28118862	SO:0001583	missense	4642			AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.736G>A	17.37:g.31094749C>T	ENSP00000324527:p.Glu246Lys		28118862	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571597	0.65765	.	.	ENSG00000176658	ENST00000318217	T	0.72835	-0.69	6.0	5.01	0.66863	Myosin head, motor domain (2);	0.187967	0.25099	U	0.033151	T	0.70064	0.3181	M	0.62723	1.935	0.50467	D	0.999873	B;B	0.22080	0.064;0.064	B;B	0.26202	0.067;0.067	T	0.68534	-0.5383	10	0.56958	D	0.05	.	14.8407	0.70220	0.0:0.8553:0.1447:0.0	.	157;246	Q7Z3N6;O94832	.;MYO1D_HUMAN	K	246	ENSP00000324527:E246K	ENSP00000324527:E246K	E	-	1	0	MYO1D	28118862	1.000000	0.71417	0.942000	0.38095	0.967000	0.64934	7.487000	0.81328	1.505000	0.48720	0.655000	0.94253	GAA		0.363	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			T	31094749	C	T	31094749	3	4	47	1	0	0	0	0	1	0	0	0	10101	893	31	1	2348	1	MYO1D	17	31094749	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	435808	31094749	50100461	1721	6118										
CCT6B	10693	broad.mit.edu	37	chr17	33269504	33269504	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctaaactttctttctcaccTtttgattaatgacgacaaat	3	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:33269504T>G	ENST00000314144.5	-	7	999	c.884A>C	c.(883-885)aAg>aCg	p.K295T	CCT6B_ENST00000421975.3_Splice_Site_p.K258T|CCT6B_ENST00000436961.3_Splice_Site_p.K250T	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	295					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)	p.K295T(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				CTTTCTCACCTTTTGATTAAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	17											61	58	59					17																	33269504		2203	4296	6499	30293617	SO:0001630	splice_region_variant	10693			D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.885+1A>C	17.37:g.33269504T>G			30293617	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.247073	0.59103	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	D;D;D	0.82526	-1.62;-1.62;-1.62	3.74	3.74	0.42951	.	0.000000	0.85682	D	0.000000	D	0.94545	0.8243	H	0.99565	4.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.997;0.995;0.986	D	0.95174	0.8293	10	0.87932	D	0	-10.1058	10.7098	0.45977	0.0:0.0:0.0:1.0	.	250;258;295	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	T	258;295;250	ENSP00000398044:K258T;ENSP00000327191:K295T;ENSP00000400917:K250T	ENSP00000327191:K295T	K	-	2	0	CCT6B	30293617	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.230000	0.78097	1.676000	0.50930	0.383000	0.25322	AAG		0.328	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	Missense_Mutation	G	33269504	T	G	33269504	5	3	47	1	0	0	0	0	0	0	1	0	2964	1623	56	4	740	4	CCT6B	17	33269504	Splice_Site	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2174755	33269504	47925706	1722	6119										
SLFN5	162394	broad.mit.edu	37	chr17	33591298	33591298	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttaataaatacagaaatgcGccctttctctcaaggaatat	5	9	2	1	rs568188480		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:33591298G>A	ENST00000299977.4	+	4	1383	c.1235G>A	c.(1234-1236)cGc>cAc	p.R412H	SLFN5_ENST00000542451.1_Intron	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	412					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.R412H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		ACAGAAATGCGCCCTTTCTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	17											85	84	84					17																	33591298		2203	4300	6503	30615411	SO:0001583	missense	162394			BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.1235G>A	17.37:g.33591298G>A	ENSP00000299977:p.Arg412His		30615411	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622580	0.46840	.	.	ENSG00000166750	ENST00000299977	T	0.01963	4.53	3.5	2.52	0.30459	.	0.194705	0.25570	N	0.029777	T	0.03390	0.0098	L	0.46614	1.455	0.09310	N	0.999997	D	0.69078	0.997	P	0.50082	0.63	T	0.44907	-0.9297	10	0.23891	T	0.37	.	6.6918	0.23177	0.134:0.0:0.866:0.0	.	412	Q08AF3	SLFN5_HUMAN	H	412	ENSP00000299977:R412H	ENSP00000299977:R412H	R	+	2	0	SLFN5	30615411	0.000000	0.05858	0.017000	0.16124	0.779000	0.44077	-1.723000	0.01866	0.810000	0.34279	0.563000	0.77884	CGC		0.403	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		A	33591298	G	A	33591298	3	1	47	1	0	0	0	0	1	0	0	0	14774	1087	38	1	1245	1	SLFN5	17	33591298	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	321794	33591298	47603912	1723	6120										
SLFN13	146857	broad.mit.edu	37	chr17	33767977	33767977	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaaagtttttaataatcttTgtgttgcctggaacacctgg	9	6	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:33767977T>G	ENST00000285013.6	-	6	2606	c.2331A>C	c.(2329-2331)acA>acC	p.T777T	SLFN13_ENST00000360502.2_Silent_p.T459T|SLFN13_ENST00000526861.1_Silent_p.T777T|SLFN13_ENST00000534689.1_Silent_p.T459T|SLFN13_ENST00000533791.1_Silent_p.T777T|SLFN13_ENST00000542635.1_Silent_p.T777T	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	777						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.T777T(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TAATAATCTTTGTGTTGCCTG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	17											82	83	82					17																	33767977		2203	4300	6503	30792090	SO:0001819	synonymous_variant	146857			AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.2331A>C	17.37:g.33767977T>G			30792090	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																				0.408	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		G	33767977	T	G	33767977	2	3	47	1	0	0	0	0	0	0	0	1	14773	1799	63	4		4	SLFN13	17	33767977	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	176679	33767977	47427233	1724	6121										
GAS2L2	246176	broad.mit.edu	37	chr17	34073222	34073222	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtggggtggggttcccggCgtcggttccccagctgtctg	17	11	1	0	rs139833672	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:34073222C>T	ENST00000254466.6	-	6	1321	c.1294G>A	c.(1294-1296)Gcc>Acc	p.A432T	GAS2L2_ENST00000587565.1_Missense_Mutation_p.A416T	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	432					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)	p.A432T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGGTTCCCGGCGTCGGTTCCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	123	135	131		1294	-3.3	0	17	dbSNP_134	131	0,8600		0,0,4300	no	missense	GAS2L2	NM_139285.3	58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	432/881	34073222	3,13003	2203	4300	6503	31097335	SO:0001583	missense	246176			AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1294G>A	17.37:g.34073222C>T	ENSP00000254466:p.Ala432Thr		31097335	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	4.071	0.011006	0.07912	6.81E-4	0.0	ENSG00000132139	ENST00000254466	T	0.19105	2.17	5.3	-3.26	0.05064	.	1.554330	0.03483	N	0.215314	T	0.09202	0.0227	N	0.14661	0.345	0.09310	N	1	B	0.21688	0.059	B	0.10450	0.005	T	0.16394	-1.0404	10	0.11182	T	0.66	-0.1705	1.8325	0.03133	0.1273:0.3663:0.1243:0.3821	.	432	Q8NHY3	GA2L2_HUMAN	T	432	ENSP00000254466:A432T	ENSP00000254466:A432T	A	-	1	0	GAS2L2	31097335	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.557000	0.02166	-0.740000	0.04803	0.655000	0.94253	GCC		0.587	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34073222	C	T	34073222	3	4	47	1	0	0	0	0	1	0	0	0	6267	768	27	1	1352	1	GAS2L2	17	34073222	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	305245	34073222	47121988	1725	6122										
GPR179	440435	broad.mit.edu	37	chr17	36485803	36485803	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgccacccgacaggggtttCttttgattgcttgatgtttt	10	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:36485803C>A	ENST00000342292.4	-	11	3669	c.3649G>T	c.(3649-3651)Gaa>Taa	p.E1217*	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1217					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E1217*(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				ACAGGGGTTTCTTTTGATTGC	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											129	134	132					17																	36485803		1921	4125	6046	33739329	SO:0001587	stop_gained	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3649G>T	17.37:g.36485803C>A	ENSP00000345060:p.Glu1217*		33739329		Nonsense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	36	5.929904	0.97116	.	.	ENSG00000188888	ENST00000342292	.	.	.	5.32	4.29	0.51040	.	0.497197	0.18488	N	0.139732	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-3.7248	5.3536	0.16050	0.2032:0.694:0.0:0.1028	.	.	.	.	X	1217	.	ENSP00000345060:E1217X	E	-	1	0	GPR179	33739329	0.001000	0.12720	0.057000	0.19452	0.002000	0.02628	1.105000	0.31086	2.770000	0.95276	0.407000	0.27541	GAA		0.577	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36485803	C	A	36485803	4	1	47	1	0	0	0	0	0	1	0	0	6694	922	32	2	3458	2	GPR179	17	36485803	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2412581	36485803	44709407	1726	6123										
FBXO47	494188	broad.mit.edu	37	chr17	37119113	37119113	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcacctgacaaatattttaAaattatctggaatatttcca	3	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:37119113A>C	ENST00000378079.2	-	2	365	c.166T>G	c.(166-168)Tta>Gta	p.L56V		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	56	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.							p.L56V(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						AAATATTTTAAAATTATCTGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											34	37	36					17																	37119113		2202	4296	6498	34372639	SO:0001583	missense	494188				CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.166T>G	17.37:g.37119113A>C	ENSP00000367319:p.Leu56Val		34372639	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	37	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.817403	0.50633	.	.	ENSG00000204952	ENST00000378079	T	0.66638	-0.22	5.14	1.72	0.24424	F-box domain, cyclin-like (2);	0.000000	0.64402	D	0.000002	T	0.67915	0.2944	L	0.29908	0.895	0.34007	D	0.65097	D	0.76494	0.999	D	0.87578	0.998	T	0.72127	-0.4384	10	0.66056	D	0.02	-10.1803	7.4931	0.27473	0.7459:0.0:0.2541:0.0	.	56	Q5MNV8	FBX47_HUMAN	V	56	ENSP00000367319:L56V	ENSP00000367319:L56V	L	-	1	2	FBXO47	34372639	0.946000	0.32159	0.833000	0.33012	0.919000	0.55068	1.311000	0.33562	0.010000	0.14839	-0.543000	0.04237	TTA		0.363	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		C	37119113	A	C	37119113	3	2	47	1	0	0	0	0	1	0	0	0	5775	11	1	4	1232	4	FBXO47	17	37119113	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	633310	37119113	44076097	1727	6124										
PLXDC1	57125	broad.mit.edu	37	chr17	37235397	37235397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccatccactcctggcgatagCggtcaaagccactggagcat	10	14	1	0	rs143709538		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:37235397C>T	ENST00000315392.4	-	10	1221	c.1010G>A	c.(1009-1011)cGc>cAc	p.R337H	PLXDC1_ENST00000539608.1_3'UTR|CTD-2206N4.4_ENST00000583447.1_RNA|PLXDC1_ENST00000444911.2_Missense_Mutation_p.R297H|PLXDC1_ENST00000493200.1_5'UTR|AC091178.1_ENST00000410562.1_RNA	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	337					angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)	p.R337H(1)		kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTGGCGATAGCGGTCAAAGCC	0.532													C|||	1	0.000199681	0	0.0014	5008	,	,		23654	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17						C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	105	95	98		1010	5.4	1	17	dbSNP_134	98	0,8600		0,0,4300	yes	missense	PLXDC1	NM_020405.4	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging	337/501	37235397	2,13004	2203	4300	6503	34488923	SO:0001583	missense	57125			AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"tumor endothelial marker 7 precursor"	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.1010G>A	17.37:g.37235397C>T	ENSP00000323927:p.Arg337His		34488923	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Missense_Mutation	SNP	ENST00000315392.4	37	CCDS11333.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.30	2.495114	0.44352	4.54E-4	0.0	ENSG00000161381	ENST00000315392;ENST00000444911	T;T	0.17054	2.3;2.3	5.41	5.41	0.78517	.	0.059890	0.64402	D	0.000003	T	0.37999	0.1024	M	0.82132	2.575	0.80722	D	1	D;P	0.56521	0.976;0.858	P;B	0.55455	0.776;0.303	T	0.19063	-1.0317	10	0.87932	D	0	-36.7282	14.5769	0.68255	0.0:1.0:0.0:0.0	.	297;337	B4E173;Q8IUK5	.;PXDC1_HUMAN	H	337;297	ENSP00000323927:R337H;ENSP00000409687:R297H	ENSP00000323927:R337H	R	-	2	0	PLXDC1	34488923	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.447000	0.66606	2.826000	0.97356	0.561000	0.74099	CGC		0.532	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405		T	37235397	C	T	37235397	3	4	47	1	0	0	0	0	1	0	0	0	12148	768	27	1	512	1	PLXDC1	17	37235397	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	116284	37235397	43959813	1728	6125										
CDK12	51755	broad.mit.edu	37	chr17	37665962	37665962	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttttttgttttacagtgggCaaatcaaactagcagatttt	8	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:37665962C>T	ENST00000447079.4	+	7	2647	c.2614C>T	c.(2614-2616)Caa>Taa	p.Q872*	CDK12_ENST00000430627.2_Nonsense_Mutation_p.Q872*	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	872	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.Q872*(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						TTACAGTGGGCAAATCAAACT	0.368			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	1	Substitution - Nonsense(1)	large_intestine(1)	17											126	125	125					17																	37665962		2203	4300	6503	34919488	SO:0001587	stop_gained	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2614C>T	17.37:g.37665962C>T	ENSP00000398880:p.Gln872*		34919488	A7E2B2|B4DYX4|B9EIQ6|O94978	Nonsense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	39	7.859526	0.98528	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	.	.	.	5.11	5.11	0.69529	.	0.000000	0.43747	D	0.000539	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-9.923	18.92	0.92521	0.0:1.0:0.0:0.0	.	.	.	.	X	872	.	ENSP00000407720:Q872X	Q	+	1	0	CDK12	34919488	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.776000	0.85560	2.551000	0.86045	0.650000	0.86243	CAA		0.368	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37665962	C	T	37665962	4	4	47	1	0	0	0	0	0	1	0	0	3134	711	25	3	2640	3	CDK12	17	37665962	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	430565	37665962	43529248	1729	6126										
IKZF3	22806	broad.mit.edu	37	chr17	37948975	37948975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acattgaagctgatgcaggaTaatccacacacatcgcagtt	8	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:37948975T>C	ENST00000346872.3	-	4	436	c.375A>G	c.(373-375)ttA>ttG	p.L125L	IKZF3_ENST00000377958.2_Intron|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000377945.3_Silent_p.L125L|IKZF3_ENST00000467757.1_Silent_p.L125L|IKZF3_ENST00000439167.2_Silent_p.L91L|IKZF3_ENST00000535189.1_Silent_p.L91L|IKZF3_ENST00000346243.3_Silent_p.L125L|IKZF3_ENST00000377944.3_Intron|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000351680.3_Silent_p.L125L|IKZF3_ENST00000439016.2_Silent_p.L125L|IKZF3_ENST00000350532.3_Silent_p.L125L	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	125					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L125L(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGATGCAGGATAATCCACACA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	17											170	149	156					17																	37948975		2203	4300	6503	35202501	SO:0001819	synonymous_variant	22806			AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.375A>G	17.37:g.37948975T>C			35202501	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Silent	SNP	ENST00000346872.3	37	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	T	9.351	1.065453	0.20067	.	.	ENSG00000161405	ENST00000439167;ENST00000439016	.	.	.	5.96	-0.123	0.13527	.	.	.	.	.	T	0.53546	0.1803	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41270	-0.9518	4	.	.	.	-6.4298	7.3906	0.26907	0.0:0.3893:0.1227:0.488	.	.	.	.	C	79	.	.	Y	-	2	0	IKZF3	35202501	0.992000	0.36948	0.988000	0.46212	0.998000	0.95712	0.247000	0.18179	-0.321000	0.08627	0.533000	0.62120	TAT		0.388	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		C	37948975	T	C	37948975	2	2	47	1	0	0	0	0	0	0	0	1	7637	1403	49	4		4	IKZF3	17	37948975	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	283013	37948975	43246235	1730	6127										
TOP2A	7153	broad.mit.edu	37	chr17	38556814	38556814	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgacgggaagctctgagatTtcaatggttgtagaattaag	12	5	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:38556814T>G	ENST00000423485.1	-	22	2924	c.2766A>C	c.(2764-2766)gaA>gaC	p.E922D		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	922					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)	p.E922D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GCTCTGAGATTTCAATGGTTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	17											90	76	81					17																	38556814		1821	4083	5904	35810340	SO:0001583	missense	7153				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.2766A>C	17.37:g.38556814T>G	ENSP00000411532:p.Glu922Asp		35810340	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652757	0.47362	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.27256	1.68	5.31	1.81	0.25067	DNA topoisomerase, type IIA, subunit A/C-terminal (2);Arginine repressor, C-terminal (1);DNA topoisomerase, type IIA, central (1);	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	M	0.80982	2.52	0.58432	D	0.999999	D	0.62365	0.991	D	0.67103	0.949	T	0.41734	-0.9492	10	0.52906	T	0.07	.	9.657	0.39932	0.0:0.2765:0.0:0.7235	.	922	P11388	TOP2A_HUMAN	D	922;1002;945;958	ENSP00000411532:E922D	ENSP00000269577:E1002D	E	-	3	2	TOP2A	35810340	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.631000	0.37092	0.393000	0.25203	0.533000	0.62120	GAA		0.348	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			G	38556814	T	G	38556814	3	3	47	1	0	0	0	0	1	0	0	0	16405	1838	64	4	1885	4	TOP2A	17	38556814	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	607839	38556814	42638396	1731	6128										
CCR7	1236	broad.mit.edu	37	chr17	38711971	38711971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaccaggctttaaagttccGcacgtccttcttggagcaca	9	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:38711971G>A	ENST00000246657.2	-	3	222	c.160C>T	c.(160-162)Cgg>Tgg	p.R54W	CCR7_ENST00000579344.1_Missense_Mutation_p.R48W	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	54					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)	p.R54W(1)		breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				TTAAAGTTCCGCACGTCCTTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											113	98	103					17																	38711971		2203	4300	6503	35965497	SO:0001583	missense	1236				CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.160C>T	17.37:g.38711971G>A	ENSP00000246657:p.Arg54Trp		35965497		Missense_Mutation	SNP	ENST00000246657.2	37	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597060	0.66332	.	.	ENSG00000126353	ENST00000246657	T	0.37915	1.17	4.74	3.75	0.43078	.	0.076485	0.56097	D	0.000034	T	0.58680	0.2139	M	0.87547	2.89	0.54753	D	0.999989	D	0.62365	0.991	P	0.56474	0.799	T	0.69764	-0.5057	10	0.87932	D	0	.	14.5151	0.67814	0.0:0.0:0.8522:0.1478	.	54	P32248	CCR7_HUMAN	W	54	ENSP00000246657:R54W	ENSP00000246657:R54W	R	-	1	2	CCR7	35965497	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.460000	0.53028	1.309000	0.44985	0.561000	0.74099	CGG		0.483	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			A	38711971	G	A	38711971	3	1	47	1	0	0	0	0	1	0	0	0	2952	1086	38	1	980	1	CCR7	17	38711971	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	155157	38711971	42483239	1732	6129										
KRT37	8688	broad.mit.edu	37	chr17	39580489	39580489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccattcagggtgtttttgCcgtaggccccacagattccg	12	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:39580489C>T	ENST00000225550.3	-	1	286	c.287G>A	c.(286-288)gGc>gAc	p.G96D	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	96	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.G96D(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GGTGTTTTTGCCGTAGGCCCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17											89	74	79					17																	39580489		2203	4300	6503	36834015	SO:0001583	missense	8688			Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.287G>A	17.37:g.39580489C>T	ENSP00000225550:p.Gly96Asp		36834015		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	5.376	0.254543	0.10185	.	.	ENSG00000108417	ENST00000225550	D	0.82433	-1.61	4.69	4.69	0.59074	.	0.260506	0.27181	N	0.020552	T	0.77519	0.4142	L	0.49778	1.585	0.09310	N	1	B	0.15473	0.013	B	0.14023	0.01	T	0.62821	-0.6773	10	0.23302	T	0.38	.	13.103	0.59231	0.0:1.0:0.0:0.0	.	96	O76014	KRT37_HUMAN	D	96	ENSP00000225550:G96D	ENSP00000225550:G96D	G	-	2	0	KRT37	36834015	0.001000	0.12720	0.003000	0.11579	0.089000	0.18198	1.043000	0.30316	2.169000	0.68431	0.655000	0.94253	GGC		0.592	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39580489	C	T	39580489	3	4	47	1	0	0	0	0	1	0	0	0	8495	739	26	3	1090	3	KRT37	17	39580489	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	868518	39580489	41614721	1733	6130										
KRT9	3857	broad.mit.edu	37	chr17	39724630	39724630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttccaagctcttctccagaGctgctttctaagggttagga	9	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:39724630G>A	ENST00000246662.4	-	6	1243	c.1178C>T	c.(1177-1179)gCt>gTt	p.A393V	KRT9_ENST00000588431.1_Missense_Mutation_p.A160V	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	393	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.A393V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				CTTCTCCAGAGCTGCTTTCTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											112	113	113					17																	39724630		2203	4300	6503	36978156	SO:0001583	missense	3857				CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1178C>T	17.37:g.39724630G>A	ENSP00000246662:p.Ala393Val		36978156	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.683158	0.68157	.	.	ENSG00000171403	ENST00000246662	D	0.90261	-2.64	5.03	4.05	0.47172	Filament (1);	0.000000	0.32314	N	0.006268	D	0.94735	0.8301	M	0.82517	2.595	0.28936	N	0.891297	D	0.76494	0.999	D	0.69824	0.966	D	0.90662	0.4591	10	0.72032	D	0.01	.	11.817	0.52216	0.0:0.1327:0.7294:0.1378	.	393	P35527	K1C9_HUMAN	V	393	ENSP00000246662:A393V	ENSP00000246662:A393V	A	-	2	0	KRT9	36978156	0.025000	0.19082	0.948000	0.38648	0.598000	0.36846	2.016000	0.40971	1.083000	0.41159	0.471000	0.43371	GCT		0.522	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39724630	G	A	39724630	3	1	47	1	0	0	0	0	1	0	0	0	8522	971	34	3	701	3	KRT9	17	39724630	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	144141	39724630	41470580	1734	6131										
TTC25	83538	broad.mit.edu	37	chr17	40094922	40094922	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcagcagaagccgatctaCgccagggagcgggaccggaa	16	11	1	1	rs549565054		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:40094922C>T	ENST00000591658.1	+	0	806							Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm (GO:0005737)		p.Y246Y(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				AGCCGATCTACGCCAGGGAGC	0.587													C|||	1	0.000199681	0	0	5008	,	,		20129	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	17											127	134	132					17																	40094922		2059	4192	6251	37348448			83538			AK055498	CCDS74063.1	17q21.2	2014-08-12			ENSG00000204815	ENSG00000204815		"Tetratricopeptide (TTC) repeat domain containing"	25280	protein-coding gene	gene with protein product							Standard	XM_006722129		Approved	DKFZP434H0115	uc002hyj.4	Q96NG3	OTTHUMG00000175837		17.37:g.40094922C>T			37348448	Q6NX40|Q6PJ04|Q9H0K5	Silent	SNP	ENST00000591658.1	37																																																																																					0.587	TTC25-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000449237.1	NM_031421		T	40094922	C	T	40094922	1	4	47	0	1	0	0	0	0	0	0	0	16733	547	19	1		1	TTC25	17	40094922	RNA	SNP	C	TCGA-AG-3892-01A-01W-1073-09	370292	40094922	41100288	1735	6132										
DHX58	79132	broad.mit.edu	37	chr17	40257053	40257053	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacctggaccatggagatttCattggtcaagagcccataac	9	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:40257053C>A	ENST00000251642.3	-	10	1606	c.1384G>T	c.(1384-1386)Gaa>Taa	p.E462*		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	462	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.E462*(1)		breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ATGGAGATTTCATTGGTCAAG	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											96	97	97					17																	40257053		2203	4300	6503	37510579	SO:0001587	stop_gained	79132			BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1384G>T	17.37:g.40257053C>A	ENSP00000251642:p.Glu462*		37510579	Q9HAM6	Nonsense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	C	39	7.856709	0.98528	.	.	ENSG00000108771	ENST00000251642;ENST00000423748	.	.	.	4.77	4.77	0.60923	.	0.108403	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-12.3231	16.5266	0.84332	0.0:1.0:0.0:0.0	.	.	.	.	X	462;425	.	ENSP00000251642:E462X	E	-	1	0	DHX58	37510579	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.620000	0.83070	2.491000	0.84063	0.462000	0.41574	GAA		0.577	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		A	40257053	C	A	40257053	4	1	47	1	0	0	0	0	0	1	0	0	4525	835	29	2	672	2	DHX58	17	40257053	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	162131	40257053	40938157	1736	6133										
RND2	8153	broad.mit.edu	37	chr17	41180148	41180148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggctgtaaactggacatgcGgactgacctggccacactga	12	11	0	2	rs369361646		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:41180148G>A	ENST00000587250.2	+	4	478	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	RND2_ENST00000544533.1_Missense_Mutation_p.R124Q|CTD-3199J23.4_ENST00000225973.5_lincRNA			P52198	RND2_HUMAN	Rho family GTPase 2	124					GTP catabolic process (GO:0006184)|positive regulation of collateral sprouting (GO:0048672)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R124Q(1)		large_intestine(1)|skin(1)	2		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CTGGACATGCGGACTGACCTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	GLN/ARG	0,4406		0,0,2203	145	103	118		371	5.3	1	17		118	1,8599	1.2+/-3.3	0,1,4299	no	missense	RND2	NM_005440.4	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	124/228	41180148	1,13005	2203	4300	6503	38433674	SO:0001583	missense	8153			X95456	CCDS11452.1	17q21.31	2012-10-02	2005-01-24	2005-01-24	ENSG00000108830	ENSG00000108830			18315	protein-coding gene	gene with protein product		601555	"ras homolog gene family, member N"	ARHN			Standard	XM_005257706		Approved	Rho7, RhoN	uc002icn.3	P52198	OTTHUMG00000180817	ENST00000587250.2:c.371G>A	17.37:g.41180148G>A	ENSP00000466680:p.Arg124Gln		38433674	A8K2D4|O00690|O00734|Q5U0P6|Q99535	Missense_Mutation	SNP	ENST00000587250.2	37	CCDS11452.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411799	0.83340	0.0	1.16E-4	ENSG00000108830	ENST00000544533;ENST00000225973	T	0.77229	-1.08	5.29	5.29	0.74685	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90614	0.7057	M	0.90650	3.135	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.92015	0.5621	10	0.87932	D	0	.	19.1238	0.93374	0.0:0.0:1.0:0.0	.	124	P52198	RND2_HUMAN	Q	124	ENSP00000439328:R124Q	ENSP00000225973:R124Q	R	+	2	0	RND2	38433674	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	9.623000	0.98386	2.765000	0.95021	0.591000	0.81541	CGG		0.532	RND2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453111.2	NM_005440		A	41180148	G	A	41180148	3	1	47	1	0	0	0	0	1	0	0	0	13457	1116	39	1	385	1	RND2	17	41180148	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	923095	41180148	40015062	1737	6134										
NAGS	162417	broad.mit.edu	37	chr17	42085916	42085916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctatgagttggtcaaccacGccaagggactgccagactcc	10	14	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:42085916G>A	ENST00000293404.3	+	7	1670	c.1552G>A	c.(1552-1554)Gcc>Acc	p.A518T		NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	518	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.		A -> T (in NAGSD; markedly decreases activity). {ECO:0000269|PubMed:15878741}.		arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)	p.A518T(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GGTCAACCACGCCAAGGGACT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17	GRCh37	CM052024	NAGS	M							171	162	165					17																	42085916		2203	4300	6503	39441442	SO:0001583	missense	162417			AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1552G>A	17.37:g.42085916G>A	ENSP00000293404:p.Ala518Thr		39441442	B2RAZ9|Q8IWR4	Missense_Mutation	SNP	ENST00000293404.3	37	CCDS11473.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956848	0.92726	.	.	ENSG00000161653	ENST00000541745;ENST00000293404	D	0.94138	-3.36	5.33	5.33	0.75918	GCN5-related N-acetyltransferase (GNAT) domain (1);Domain of unknown function DUF619 (1);	0.000000	0.85682	D	0.000000	D	0.95636	0.8581	M	0.63843	1.955	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93987	0.7263	10	0.23302	T	0.38	-28.0339	16.505	0.84270	0.0:0.0:1.0:0.0	.	352;518	Q2NKP2;Q8N159	.;NAGS_HUMAN	T	352;518	ENSP00000293404:A518T	ENSP00000293404:A518T	A	+	1	0	NAGS	39441442	1.000000	0.71417	0.998000	0.56505	0.858000	0.48976	8.210000	0.89753	2.479000	0.83701	0.462000	0.41574	GCC		0.552	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		A	42085916	G	A	42085916	3	1	47	1	0	0	0	0	1	0	0	0	10175	1087	38	1	1578	1	NAGS	17	42085916	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	905768	42085916	39109294	1738	6135										
MAP3K14	9020	broad.mit.edu	37	chr17	43366611	43366611	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccctgcttacctgtactgtTtggacccagcgatgaaaatg	9	12	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:43366611T>G	ENST00000344686.2	-	0	425							Q99558	M3K14_HUMAN	mitogen-activated protein kinase kinase kinase 14						cellular response to mechanical stimulus (GO:0071260)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|T cell costimulation (GO:0031295)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|NF-kappaB-inducing kinase activity (GO:0004704)|protein kinase activity (GO:0004672)	p.K106T(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCTGTACTGTTTGGACCCAGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											92	89	90					17																	43366611		1965	4166	6131	40722394			9020			Y10256	CCDS74079.1	17q21.31	2014-06-16			ENSG00000006062	ENSG00000006062	2.7.11.25	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6853	protein-coding gene	gene with protein product	"serine/threonine protein-kinase"	604655				9020361	Standard	NM_003954		Approved	NIK, HSNIK, FTDCR1B, HS	uc002iiw.1	Q99558	OTTHUMG00000180364		17.37:g.43366611T>G			40722394	A8K2D8|D3DX67|Q8IYN1	Missense_Mutation	SNP	ENST00000344686.2	37		.	.	.	.	.	.	.	.	.	.	T	20.5	3.996725	0.74818	.	.	ENSG00000006062	ENST00000344686	.	.	.	5.3	5.3	0.74995	.	0.077061	0.53938	D	0.000057	T	0.56202	0.1969	.	.	.	0.34876	D	0.744093	P	0.52577	0.954	P	0.47981	0.563	T	0.71659	-0.4526	7	0.87932	D	0	.	12.9883	0.58604	0.0:0.0:0.0:1.0	.	106	Q99558	M3K14_HUMAN	T	106	.	ENSP00000342059:K106T	K	-	2	0	MAP3K14	40722394	1.000000	0.71417	0.897000	0.35233	0.844000	0.47949	4.805000	0.62561	2.009000	0.58944	0.379000	0.24179	AAA		0.552	MAP3K14-201	KNOWN	basic	processed_transcript	processed_transcript		NM_003954		G	43366611	T	G	43366611	1	3	47	0	1	0	0	0	0	0	0	0	9278	1841	64	4		4	MAP3K14	17	43366611	RNA	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1280695	43366611	37828599	1739	6136										
MAPT	4137	broad.mit.edu	37	chr17	44039727	44039727	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgagccccgccaggagttCgaagtgatggaagatcacgc	14	11	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:44039727C>T	ENST00000571987.1	+	1	24	c.24C>T	c.(22-24)ttC>ttT	p.F8F	MAPT_ENST00000347967.5_5'UTR|MAPT_ENST00000574436.1_Silent_p.F8F|MAPT_ENST00000344290.5_Silent_p.F8F|MAPT_ENST00000420682.2_Silent_p.F8F|MAPT_ENST00000535772.1_Silent_p.F8F|MAPT_ENST00000262410.5_Silent_p.F8F|MAPT_ENST00000340799.5_Silent_p.F8F|MAPT_ENST00000415613.2_Silent_p.F8F|MAPT_ENST00000351559.5_Silent_p.F8F|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000431008.3_Silent_p.F8F|MAPT_ENST00000446361.3_Silent_p.F8F|MAPT_ENST00000334239.8_Silent_p.F8F			P10636	TAU_HUMAN	microtubule-associated protein tau	8					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.F8F(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCCAGGAGTTCGAAGTGATGG	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	17											45	40	42					17																	44039727		2203	4300	6503	41395563	SO:0001819	synonymous_variant	4137			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.24C>T	17.37:g.44039727C>T			41395563	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																				0.582	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		T	44039727	C	T	44039727	2	4	47	1	0	0	0	0	0	0	0	1	9327	883	31	1		1	MAPT	17	44039727	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	673116	44039727	37155483	1740	6137										
CDC27	996	broad.mit.edu	37	chr17	45216112	45216112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttggttaacatacctctggcGaatttttatccatgtctgtt	7	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:45216112G>A	ENST00000066544.3	-	13	1790	c.1697C>T	c.(1696-1698)tCg>tTg	p.S566L	CDC27_ENST00000531206.1_Missense_Mutation_p.S572L|CDC27_ENST00000446365.2_Missense_Mutation_p.S505L|CDC27_ENST00000527547.1_Missense_Mutation_p.S565L	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	566					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.S572L(1)|p.S566L(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TACCTCTGGCGAATTTTTATC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	17											50	55	53					17																	45216112		2202	4299	6501	42571111	SO:0001583	missense	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1697C>T	17.37:g.45216112G>A	ENSP00000066544:p.Ser566Leu		42571111	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682257	0.88542	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.058252	0.64402	D	0.000001	T	0.67382	0.2887	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.76494	0.998;0.997;0.999;0.996	P;P;P;P	0.61940	0.896;0.814;0.876;0.685	T	0.76055	-0.3099	10	0.87932	D	0	-9.281	17.1488	0.86773	0.0:0.0:1.0:0.0	.	505;565;572;566	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	L	566;572;505;565	ENSP00000066544:S566L;ENSP00000434614:S572L;ENSP00000392802:S505L;ENSP00000437339:S565L	ENSP00000066544:S566L	S	-	2	0	CDC27	42571111	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.133000	0.77259	2.650000	0.89964	0.650000	0.86243	TCG		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			A	45216112	G	A	45216112	3	1	47	1	0	0	0	0	1	0	0	0	3072	1059	37	1	805	1	CDC27	17	45216112	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1176385	45216112	35979098	1741	6138										
ITGB3	3690	broad.mit.edu	37	chr17	45361953	45361953	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagctggccacccagatgcGaaagctcaccagtaacctgc	9	15	1	1	rs5917	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:45361953G>A	ENST00000559488.1	+	4	522	c.506G>A	c.(505-507)cGa>cAa	p.R169Q	ITGB3_ENST00000435993.2_Missense_Mutation_p.R122Q|ITGB3_ENST00000560629.1_Silent_p.A157A|ITGB3_ENST00000571680.1_Missense_Mutation_p.R169Q	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	169	VWFA.		R -> Q (in alloantigen HPA-4B; dbSNP:rs5917). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:1430225}.		activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R169Q(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	ACCCAGATGCGAAAGCTCACC	0.532													G|||	13	0.00259585	0	0.0115	5008	,	,		17059	0.004		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	17						G	GLN/ARG	0,4406		0,0,2203	124	121	122	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	506	4.9	1	17	dbSNP_52	122	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ITGB3	NM_000212.2	43	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	169/789	45361953	2,13004	2203	4300	6503	42716952	SO:0001583	missense	3690				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.506G>A	17.37:g.45361953G>A	ENSP00000452786:p.Arg169Gln		42716952	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	8	0.003663003663003663	0	0.0	6	0.016574585635359115	2	0.0034965034965034965	0	0.0	G	13.41	2.228941	0.39399	0.0	2.33E-4	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.92348	-3.02	5.86	4.89	0.63831	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.286751	0.44483	D	0.000455	T	0.77191	0.4094	N	0.17901	0.54	0.37985	D	0.933725	P;P	0.49358	0.923;0.551	B;B	0.42188	0.379;0.08	D	0.83827	0.0250	10	0.42905	T	0.14	.	12.9189	0.58220	0.0787:0.0:0.9213:0.0	rs5917;rs52822157;rs61156821;rs5917	169;169	P05106;Q2YFE1	ITB3_HUMAN;.	Q	169;122	ENSP00000407801:R122Q	ENSP00000262017:R169Q	R	+	2	0	C17orf57	42716952	0.998000	0.40836	0.991000	0.47740	0.150000	0.21749	2.422000	0.44696	1.482000	0.48325	0.655000	0.94253	CGA		0.532	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		A	45361953	G	A	45361953	3	1	47	1	0	0	0	0	1	0	0	0	7916	1058	37	1	520	1	ITGB3	17	45361953	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	145841	45361953	35833257	1742	6139										
C17orf57	124989	broad.mit.edu	37	chr17	45438851	45438851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatccctataaaccgtgaaAttttagaagaagtgacaaaa	7	6	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:45438851A>G	ENST00000331493.2	+	10	1180	c.769A>G	c.(769-771)Att>Gtt	p.I257V	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	257						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.I257V(1)									AAACCGTGAAATTTTAGAAGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	17											161	159	160					17																	45438851		2203	4300	6503	42793850	SO:0001583	missense	124989			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.769A>G	17.37:g.45438851A>G	ENSP00000332111:p.Ile257Val		42793850	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	A	3.849	-0.032291	0.07543	.	.	ENSG00000178852	ENST00000331493;ENST00000344176	T	0.40756	1.02	3.78	3.78	0.43462	EF-hand-like domain (1);	0.795723	0.10704	N	0.643726	T	0.34135	0.0887	L	0.36672	1.1	0.26277	N	0.978333	B;B	0.15473	0.013;0.013	B;B	0.11329	0.006;0.006	T	0.24799	-1.0150	10	0.72032	D	0.01	-11.5194	9.0868	0.36586	1.0:0.0:0.0:0.0	.	209;257	Q8N7U2;Q8IY85	.;CQ057_HUMAN	V	257;209	ENSP00000332111:I257V	ENSP00000332111:I257V	I	+	1	0	C17orf57	42793850	0.031000	0.19500	0.009000	0.14445	0.027000	0.11550	1.991000	0.40727	1.696000	0.51158	0.482000	0.46254	ATT		0.333	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45438851	A	G	45438851	3	3	47	1	0	0	0	0	1	0	0	0	1870	101	4	4	795	4	C17orf57	17	45438851	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	76898	45438851	35756359	1743	6140										
MYST2	11143	broad.mit.edu	37	chr17	47875855	47875855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctctcatcgccccaagcGccgtcgcttccatgaaagct	7	17	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:47875855G>A	ENST00000259021.4	+	4	795	c.515G>A	c.(514-516)cGc>cAc	p.R172H	KAT7_ENST00000435742.2_Missense_Mutation_p.R16H|KAT7_ENST00000424009.2_Missense_Mutation_p.R172H|KAT7_ENST00000454930.2_Intron|KAT7_ENST00000509773.1_Intron|KAT7_ENST00000503935.2_Missense_Mutation_p.R16H|KAT7_ENST00000510819.1_Intron	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	172					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R172H(1)									CGCCCCAAGCGCCGTCGCTTC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											120	104	109					17																	47875855		2203	4300	6503	45230854	SO:0001583	missense	11143			AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.515G>A	17.37:g.47875855G>A	ENSP00000259021:p.Arg172His		45230854	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665634	0.88251	.	.	ENSG00000136504	ENST00000259021;ENST00000424009;ENST00000506533;ENST00000503935;ENST00000435742	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.76779	0.4035	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69824	0.925;0.925;0.966	T	0.74586	-0.3616	9	0.51188	T	0.08	-14.468	20.2388	0.98366	0.0:0.0:1.0:0.0	.	165;172;172	B4DGY4;O95251;G5E9K7	.;KAT7_HUMAN;.	H	172;172;16;16;16	.	ENSP00000259021:R172H	R	+	2	0	KAT7	45230854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.841000	0.99482	2.890000	0.99128	0.650000	0.86243	CGC		0.502	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		A	47875855	G	A	47875855	3	1	47	1	0	0	0	0	1	0	0	0	10133	1087	38	1	529	1	MYST2	17	47875855	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2437004	47875855	33319355	1744	6141										
TOB1	10140	broad.mit.edu	37	chr17	48940590	48940590	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaggagaaagagcagaggtTttctgctgttgttgctgctg	14	5	1	3	rs575736346		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:48940590T>G	ENST00000268957.3	-	3	1217	c.789A>C	c.(787-789)aaA>aaC	p.K263N	TOB1_ENST00000499247.2_Missense_Mutation_p.K263N|TOB1_ENST00000509385.1_5'Flank	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	263					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)	p.K263N(1)		breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GAGCAGAGGTTTTctgctgtt	0.537																																					NSCLC(144;643 1919 24513 29423 40686)											1	Substitution - Missense(1)	large_intestine(1)	17											49	47	48					17																	48940590		2203	4300	6503	46295589	SO:0001583	missense	10140			D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.789A>C	17.37:g.48940590T>G	ENSP00000268957:p.Lys263Asn		46295589	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	T	10.67	1.414415	0.25465	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.46063	0.88;0.88	6.06	4.96	0.65561	.	0.442853	0.18251	N	0.146950	T	0.31979	0.0814	L	0.51422	1.61	0.58432	D	0.999993	B	0.17852	0.024	B	0.10450	0.005	T	0.15867	-1.0422	10	0.18710	T	0.47	.	5.609	0.17394	0.0:0.2278:0.0:0.7722	.	263	P50616	TOB1_HUMAN	N	263	ENSP00000427695:K263N;ENSP00000268957:K263N	ENSP00000268957:K263N	K	-	3	2	TOB1	46295589	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.460000	0.45031	2.323000	0.78572	0.528000	0.53228	AAA		0.537	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			G	48940590	T	G	48940590	3	3	47	1	0	0	0	0	1	0	0	0	16386	1838	64	4	252	4	TOB1	17	48940590	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1064735	48940590	32254620	1745	6142										
SPAG9	9043	broad.mit.edu	37	chr17	49071214	49071214	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacagcatcaataataagaActtttgtagccgaatgagtg	9	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:49071214A>C	ENST00000262013.7	-	19	2517	c.2309T>G	c.(2308-2310)gTt>gGt	p.V770G	SPAG9_ENST00000505279.1_Missense_Mutation_p.V760G|SPAG9_ENST00000510283.1_Missense_Mutation_p.V613G|SPAG9_ENST00000357122.4_Missense_Mutation_p.V756G	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	770					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.V756G(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			AATAATAAGAACTTTTGTAGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											113	98	103					17																	49071214		2203	4300	6503	46426213	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2309T>G	17.37:g.49071214A>C	ENSP00000262013:p.Val770Gly		46426213	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.2|23.2	4.382207|4.382207	0.82792|0.82792	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000513906|ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.|T;T;T;T	.|0.47528	.|0.84;0.84;0.84;0.85	5.93|5.93	5.93|5.93	0.95920|0.95920	.|WD40 repeat-like-containing domain (1);	.|0.115737	.|0.64402	.|D	.|0.000017	T|T	0.71710|0.71710	0.3372|0.3372	M|M	0.84948|0.84948	2.725|2.725	0.80722|0.80722	D|D	1|1	.|P;D;D;D;D;D	.|0.67145	.|0.906;0.979;0.979;0.963;0.989;0.996	.|P;P;D;P;P;D	.|0.66847	.|0.713;0.897;0.947;0.852;0.869;0.929	T|T	0.76948|0.76948	-0.2770|-0.2770	5|10	.|0.87932	.|D	.|0	-17.3557|-17.3557	16.3766|16.3766	0.83401|0.83401	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|756;770;760;770;756;613	.|O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.|.;.;.;JIP4_HUMAN;.;.	V|G	29|770;527;517;307;613;760;756;368	.|ENSP00000262013:V770G;ENSP00000423165:V613G;ENSP00000426900:V760G;ENSP00000349636:V756G	.|ENSP00000262013:V770G	F|V	-|-	1|2	0|0	SPAG9|SPAG9	46426213|46426213	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	4.346000|4.346000	0.59367|0.59367	2.263000|2.263000	0.75096|0.75096	0.533000|0.533000	0.62120|0.62120	TTC|GTT		0.418	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		C	49071214	A	C	49071214	3	2	47	1	0	0	0	0	1	0	0	0	15024	43	2	4	1704	4	SPAG9	17	49071214	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	130624	49071214	32123996	1746	6143										
KIF2B	84643	broad.mit.edu	37	chr17	51901813	51901813	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaggggcagagattaacaaGagtcttctagccctcaaaga	11	8	3	3	rs139282377		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:51901813G>T	ENST00000268919.4	+	1	1575	c.1419G>T	c.(1417-1419)aaG>aaT	p.K473N		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	473	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K473N(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AGATTAACAAGAGTCTTCTAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											48	44	45					17																	51901813		2203	4300	6503	49256812	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1419G>T	17.37:g.51901813G>T	ENSP00000268919:p.Lys473Asn		49256812	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.961346	0.53400	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.77620	-1.11	5.73	-0.141	0.13452	Kinesin, motor domain (4);	0.000000	0.46758	D	0.000269	D	0.85600	0.5734	M	0.86651	2.83	0.39734	D	0.971651	D	0.56287	0.975	P	0.61275	0.886	D	0.85703	0.1314	10	0.66056	D	0.02	.	10.3473	0.43913	0.5117:0.0:0.4883:0.0	.	473	Q8N4N8	KIF2B_HUMAN	N	473;361	ENSP00000268919:K473N	ENSP00000268919:K473N	K	+	3	2	KIF2B	49256812	0.998000	0.40836	0.997000	0.53966	0.941000	0.58515	0.352000	0.20113	0.058000	0.16222	-0.345000	0.07892	AAG		0.507	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901813	G	T	51901813	3	4	47	1	0	0	0	0	1	0	0	0	8319	933	33	2	1421	2	KIF2B	17	51901813	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2830599	51901813	29293397	1747	6144										
STXBP4	252983	broad.mit.edu	37	chr17	53124456	53124456	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttttaaatataggaaaaaTtattggaatcagataagcaa	7	2	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:53124456T>G	ENST00000376352.2	+	12	1159	c.952T>G	c.(952-954)Tta>Gta	p.L318V	STXBP4_ENST00000434978.2_Intron	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	318					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L318V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						ATAGGAAAAATTATTGGAATC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	17											71	80	77					17																	53124456		2203	4300	6503	50479455	SO:0001583	missense	252983			BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.952T>G	17.37:g.53124456T>G	ENSP00000365530:p.Leu318Val		50479455	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	37	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	T	15.84	2.950935	0.53186	.	.	ENSG00000166263	ENST00000376352	T	0.60920	0.15	4.8	-0.669	0.11388	.	0.000000	0.64402	D	0.000001	T	0.70701	0.3254	M	0.81239	2.535	0.33062	D	0.534177	D	0.89917	1.0	D	0.91635	0.999	T	0.74044	-0.3791	10	0.87932	D	0	-9.5534	7.6642	0.28421	0.0:0.4938:0.0:0.5061	.	318	Q6ZWJ1	STXB4_HUMAN	V	318	ENSP00000365530:L318V	ENSP00000365530:L318V	L	+	1	2	STXBP4	50479455	0.092000	0.21681	0.474000	0.27266	0.879000	0.50718	-0.087000	0.11215	-0.015000	0.14150	0.477000	0.44152	TTA		0.323	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		G	53124456	T	G	53124456	3	3	47	1	0	0	0	0	1	0	0	0	15394	1490	52	4	990	4	STXBP4	17	53124456	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1222643	53124456	28070754	1748	6145										
MPO	4353	broad.mit.edu	37	chr17	56353037	56353037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtgtgcatggaggtgagctCgggcatctcactggaacggg	18	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:56353037C>T	ENST00000225275.3	-	8	1407	c.1231G>A	c.(1231-1233)Gag>Aag	p.E411K	MPO_ENST00000340482.3_Missense_Mutation_p.E443K|MPO_ENST00000578493.1_5'UTR	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	411					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.E411K(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	GAGGTGAGCTCGGGCATCTCA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											99	77	84					17																	56353037		2203	4300	6503	53708036	SO:0001583	missense	4353				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1231G>A	17.37:g.56353037C>T	ENSP00000225275:p.Glu411Lys		53708036	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434659	0.25813	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.68331	-0.32;-0.32	4.5	4.5	0.54988	.	0.052888	0.64402	D	0.000001	T	0.54095	0.1837	L	0.28504	0.86	0.42072	D	0.991216	P	0.47677	0.899	B	0.43478	0.421	T	0.54662	-0.8260	10	0.06625	T	0.88	-16.8629	16.5452	0.84443	0.0:1.0:0.0:0.0	.	411	P05164	PERM_HUMAN	K	443;411	ENSP00000344419:E443K;ENSP00000225275:E411K	ENSP00000225275:E411K	E	-	1	0	MPO	53708036	0.999000	0.42202	0.957000	0.39632	0.900000	0.52787	7.749000	0.85096	2.217000	0.71921	0.462000	0.41574	GAG		0.577	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56353037	C	T	56353037	3	4	47	1	0	0	0	0	1	0	0	0	9762	893	31	1	1026	1	MPO	17	56353037	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3228581	56353037	24842173	1749	6146										
PPM1E	22843	broad.mit.edu	37	chr17	57050201	57050201	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgctgtttaggatgaaaaGcagagaattgaggcccttgg	13	5	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:57050201G>T	ENST00000308249.2	+	6	1254	c.1125G>T	c.(1123-1125)aaG>aaT	p.K375N		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	98					protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)	p.K375N(1)		biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			AGGATGAAAAGCAGAGAATTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											202	191	195					17																	57050201		2203	4300	6503	54404983	SO:0001583	missense	22843			AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.1125G>T	17.37:g.57050201G>T	ENSP00000312411:p.Lys375Asn		54404983	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389730	0.82902	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.19394	2.15	5.58	4.62	0.57501	.	0.089858	0.85682	D	0.000000	T	0.47581	0.1453	M	0.78637	2.42	0.54753	D	0.999989	D;D	0.76494	0.997;0.999	D;D	0.75484	0.963;0.986	T	0.53387	-0.8446	10	0.87932	D	0	-14.5582	14.4122	0.67121	0.071:0.0:0.929:0.0	.	384;375	Q8WY54-3;Q8WY54-2	.;.	N	375;226	ENSP00000312411:K375N	ENSP00000312411:K375N	K	+	3	2	PPM1E	54404983	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.752000	0.68728	1.353000	0.45828	0.563000	0.77884	AAG		0.388	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		T	57050201	G	T	57050201	3	4	47	1	0	0	0	0	1	0	0	0	12372	962	34	2	1147	2	PPM1E	17	57050201	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	697164	57050201	24145009	1750	6147										
PPM1E	4591	broad.mit.edu	37	chr17	57057918	57057918	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttggtcctggtgcaccaaaGaaagcaaatcttattaatga	8	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:57057918G>T	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Missense_Mutation_p.K598N	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K598N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GTGCACCAAAGAAAGCAAATC	0.423									Mulibrey Nanism																																							1	Substitution - Missense(1)	large_intestine(1)	17											89	87	88					17																	57057918		2203	4300	6503	54412700	SO:0001628	intergenic_variant	22843	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			17.37:g.57057918G>T			54412700	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000393066.3	37	CCDS45746.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.387043	0.61956	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.24538	1.85	5.58	5.58	0.84498	.	0.496191	0.23768	N	0.044747	T	0.37679	0.1012	L	0.27053	0.805	0.45852	D	0.998717	D;D	0.63046	0.99;0.992	P;P	0.59357	0.814;0.856	T	0.17992	-1.0351	10	0.87932	D	0	-13.8069	19.5533	0.95330	0.0:0.0:1.0:0.0	.	607;598	Q8WY54-3;Q8WY54-2	.;.	N	598;449	ENSP00000312411:K598N	ENSP00000312411:K598N	K	+	3	2	PPM1E	54412700	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.778000	0.75043	2.639000	0.89480	0.491000	0.48974	AAG		0.423	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294		T	57057918	G	T	57057918	1	4	47	0	1	0	0	0	0	0	0	0	12372	933	33	2		2	PPM1E	17	57057918	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7717	57057918	24137292	1751	6148										
C17orf71	55181	broad.mit.edu	37	chr17	57288143	57288143	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgccgctccttaaaacagCcattaaggattgtccagttg	8	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:57288143C>G	ENST00000543872.2	+	2	995	c.731C>G	c.(730-732)gCc>gGc	p.A244G	CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000580498.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.A244G|SMG8_ENST00000578922.1_Missense_Mutation_p.A244G			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	244					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.A244G(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CTTAAAACAGCCATTAAGGAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											69	77	74					17																	57288143		2203	4300	6503	54642925	SO:0001583	missense	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.731C>G	17.37:g.57288143C>G	ENSP00000438748:p.Ala244Gly		54642925	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.804006	0.50315	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.46063	0.88;0.88	5.99	5.99	0.97316	.	0.092240	0.85682	D	0.000000	T	0.40932	0.1137	L	0.44542	1.39	0.50171	D	0.99985	P	0.47253	0.892	B	0.43018	0.405	T	0.33343	-0.9872	10	0.72032	D	0.01	-11.7805	15.0003	0.71466	0.0:0.8583:0.1417:0.0	.	244	Q8ND04	SMG8_HUMAN	G	244	ENSP00000300917:A244G;ENSP00000438748:A244G	ENSP00000300917:A244G	A	+	2	0	SMG8	54642925	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.696000	0.68287	2.840000	0.97914	0.655000	0.94253	GCC		0.488	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		G	57288143	C	G	57288143	3	3	47	1	0	0	0	0	1	0	0	0	1883	739	26	5	733	5	C17orf71	17	57288143	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	230225	57288143	23907067	1752	6149										
C17orf71	55181	broad.mit.edu	37	chr17	57288341	57288341	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctggaggaccagatctataGaatcttccggaagagtcgtg	12	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:57288341G>T	ENST00000543872.2	+	2	1193	c.929G>T	c.(928-930)aGa>aTa	p.R310I	CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000580498.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.R310I|SMG8_ENST00000578922.1_Missense_Mutation_p.R310I			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	310					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.R310I(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CAGATCTATAGAATCTTCCGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	17											66	65	65					17																	57288341		2203	4300	6503	54643123	SO:0001583	missense	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.929G>T	17.37:g.57288341G>T	ENSP00000438748:p.Arg310Ile		54643123	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.490954	0.64074	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.45276	0.9;0.9	5.88	5.88	0.94601	.	0.133149	0.64402	D	0.000003	T	0.58581	0.2132	L	0.50333	1.59	0.80722	D	1	D	0.65815	0.995	P	0.61658	0.892	T	0.56171	-0.8023	10	0.56958	D	0.05	-19.5567	19.2147	0.93772	0.0:0.0:1.0:0.0	.	310	Q8ND04	SMG8_HUMAN	I	310	ENSP00000300917:R310I;ENSP00000438748:R310I	ENSP00000300917:R310I	R	+	2	0	SMG8	54643123	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.592000	0.82676	2.769000	0.95229	0.655000	0.94253	AGA		0.512	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		T	57288341	G	T	57288341	3	4	47	1	0	0	0	0	1	0	0	0	1883	942	33	2	931	2	C17orf71	17	57288341	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	198	57288341	23906869	1753	6150										
USP32	84669	broad.mit.edu	37	chr17	58260756	58260756	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcccgaggaaatttgacaAttttctgtgattttatccac	6	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:58260756A>C	ENST00000300896.4	-	31	4087	c.3893T>G	c.(3892-3894)aTt>aGt	p.I1298S	USP32_ENST00000592339.1_Missense_Mutation_p.I968S	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1298	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.I1298S(1)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AAATTTGACAATTTTCTGTGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											67	72	70					17																	58260756		2203	4300	6503	55615538	SO:0001583	missense	84669			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.3893T>G	17.37:g.58260756A>C	ENSP00000300896:p.Ile1298Ser		55615538	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.601683	0.87055	.	.	ENSG00000170832	ENST00000300896	T	0.27890	1.64	5.78	5.78	0.91487	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.40171	0.1106	L	0.43152	1.355	0.80722	D	1	D	0.57257	0.979	P	0.52343	0.696	T	0.15838	-1.0423	10	0.52906	T	0.07	.	16.1069	0.81230	1.0:0.0:0.0:0.0	.	1298	Q8NFA0	UBP32_HUMAN	S	1298	ENSP00000300896:I1298S	ENSP00000300896:I1298S	I	-	2	0	USP32	55615538	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.803000	0.91915	2.198000	0.70561	0.528000	0.53228	ATT		0.418	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		C	58260756	A	C	58260756	3	2	47	1	0	0	0	0	1	0	0	0	17103	101	4	4	937	4	USP32	17	58260756	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	972415	58260756	22934454	1754	6151										
DCAF7	10238	broad.mit.edu	37	chr17	61655832	61655832	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caactttggtatgttacaggTtcagcttgttggtttagatg	11	5	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:61655832T>C	ENST00000310827.4	+	2	357	c.140T>C	c.(139-141)gTt>gCt	p.V47A	DCAF7_ENST00000415273.2_Intron|DCAF7_ENST00000577702.1_3'UTR|DCAF7_ENST00000431926.1_Splice_Site_p.V47A	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	47					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.V47A(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						ATGTTACAGGTTCAGCTTGTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											148	146	147					17																	61655832		1942	4155	6097	59009564	SO:0001630	splice_region_variant	10238			U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30915	protein-coding gene	gene with protein product	"seven-WD-repeat protein of the AN11 family-1", "human anthocyanin"	605973	"WD repeat domain 68"	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.139-1T>C	17.37:g.61655832T>C			59009564	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	37		.	.	.	.	.	.	.	.	.	.	T	26.4	4.732582	0.89482	.	.	ENSG00000136485	ENST00000310827;ENST00000431926	T;T	0.70045	-0.45;-0.45	5.6	5.6	0.85130	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83184	0.5199	M	0.92367	3.3	0.80722	D	1	D	0.53885	0.963	P	0.56127	0.792	D	0.87677	0.2545	10	0.87932	D	0	-16.2529	15.8433	0.78868	0.0:0.0:0.0:1.0	.	47	P61962	DCAF7_HUMAN	A	47	ENSP00000308344:V47A;ENSP00000402312:V47A	ENSP00000308344:V47A	V	+	2	0	DCAF7	59009564	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	8.040000	0.89188	2.154000	0.67381	0.524000	0.50904	GTT		0.418	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	Missense_Mutation	C	61655832	T	C	61655832	5	2	47	1	0	0	0	0	0	0	1	0	4281	1739	60	4	146	4	DCAF7	17	61655832	Splice_Site	SNP	T	TCGA-AG-3892-01A-01W-1073-09	3395076	61655832	19539378	1755	6152										
DDX42	11325	broad.mit.edu	37	chr17	61886998	61886998	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtgtttgatgaagcagatCgaatgtttgacatgggattt	12	3	0	4	rs200692919		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:61886998C>T	ENST00000578681.1	+	12	1832	c.1231C>T	c.(1231-1233)Cga>Tga	p.R411*	DDX42_ENST00000389924.2_Nonsense_Mutation_p.R411*|DDX42_ENST00000457800.2_Nonsense_Mutation_p.R411*|DDX42_ENST00000359353.5_Nonsense_Mutation_p.R292*|DDX42_ENST00000583590.1_Nonsense_Mutation_p.R411*	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	411	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.R411*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						TGAAGCAGATCGAATGTTTGA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											236	208	217					17																	61886998		2203	4300	6503	59240730	SO:0001587	stop_gained	11325			BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1231C>T	17.37:g.61886998C>T	ENSP00000464050:p.Arg411*		59240730	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Nonsense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	38	7.195534	0.98129	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	.	.	.	5.65	3.53	0.40419	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7788	13.7118	0.62672	0.3953:0.6047:0.0:0.0	.	.	.	.	X	411;411;147	.	ENSP00000352308:R147X	R	+	1	2	DDX42	59240730	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.353000	0.52247	1.339000	0.45563	0.563000	0.77884	CGA		0.368	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		T	61886998	C	T	61886998	4	4	47	1	0	0	0	0	0	1	0	0	4368	876	31	1	1269	1	DDX42	17	61886998	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	231166	61886998	19308212	1756	6153										
FTSJ3	5705	broad.mit.edu	37	chr17	61902489	61902489	+	5'Flank	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggcaaatttggggtcaaaGaatttactgtcaaccttgtc	9	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:61902489G>T	ENST00000310144.6	+	0	0				FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000375812.4_5'Flank|PSMC5_ENST00000580864.1_5'Flank|PSMC5_ENST00000581882.1_5'Flank|FTSJ3_ENST00000427159.2_Missense_Mutation_p.F210L	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.F210L(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGGGGTCAAAGAATTTACTGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											79	83	82					17																	61902489		2203	4300	6503	59256221	SO:0001631	upstream_gene_variant	117246			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61902489G>T	Exception_encountered		59256221	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419466	0.25552	.	.	ENSG00000108592	ENST00000427159	T	0.39592	1.07	5.04	2.02	0.26589	.	0.000000	0.85682	D	0.000000	T	0.25901	0.0631	N	0.17901	0.54	0.41463	D	0.988053	B	0.29432	0.244	B	0.37198	0.243	T	0.04065	-1.0980	10	0.08837	T	0.75	-13.7967	8.4788	0.33030	0.2544:0.0:0.7456:0.0	.	210	Q8IY81	RRMJ3_HUMAN	L	210	ENSP00000396673:F210L	ENSP00000396673:F210L	F	-	3	2	FTSJ3	59256221	1.000000	0.71417	1.000000	0.80357	0.505000	0.33919	0.614000	0.24314	0.322000	0.23283	-0.219000	0.12488	TTC		0.428	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61902489	G	T	61902489	1	4	47	0	1	0	0	0	0	0	0	0	6108	933	33	2		2	FTSJ3	17	61902489	5'Flank	SNP	G	TCGA-AG-3892-01A-01W-1073-09	15491	61902489	19292721	1757	6154										
GH1	2688	broad.mit.edu	37	chr17	61995750	61995750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagctggtgcagacgatgggCgcggagcatagcgttgtcaa	16	9	1	1	rs140787052		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:61995750C>T	ENST00000323322.5	-	2	169	c.127G>A	c.(127-129)Gcc>Acc	p.A43T	GH1_ENST00000458650.2_Missense_Mutation_p.A43T|GH1_ENST00000342364.4_Missense_Mutation_p.A43T|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Missense_Mutation_p.A43T	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	43					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)	p.A43T(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						AGACGATGGGCGCGGAGCATA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,	0,4406		0,0,2203	163	170	168		127,127,127,127,	2.9	1	17	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,intron	GH1	NM_000515.3,NM_022559.2,NM_022560.2,NM_022561.2,NM_022562.2	58,58,58,58,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,	43/218,43/203,43/178,43/123,	61995750	1,13005	2203	4300	6503	59349482	SO:0001583	missense	2688			M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"Endogenous ligands"	4261	protein-coding gene	gene with protein product	"pituitary growth hormone", "somatotropin"	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.127G>A	17.37:g.61995750C>T	ENSP00000312673:p.Ala43Thr		59349482	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Missense_Mutation	SNP	ENST00000323322.5	37	CCDS11653.1	.	.	.	.	.	.	.	.	.	.	c	16.76	3.211959	0.58452	0.0	1.16E-4	ENSG00000204414	ENST00000323322;ENST00000458650;ENST00000351388;ENST00000342364	D;D;D;D	0.93307	-3.2;-2.84;-3.2;-3.2	2.86	2.86	0.33363	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.118143	0.64402	D	0.000020	D	0.96907	0.8990	M	0.93939	3.475	0.25871	N	0.983703	D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.972;0.995;1.0;1.0	D	0.90653	0.4584	10	0.87932	D	0	.	9.3531	0.38151	0.0:1.0:0.0:0.0	.	43;43;43;43;43	C9JYZ1;B1A4G9;A6NEF6;P01241;B1A4G7	.;.;.;SOMA_HUMAN;.	T	43	ENSP00000312673:A43T;ENSP00000408486:A43T;ENSP00000343791:A43T;ENSP00000339278:A43T	ENSP00000312673:A43T	A	-	1	0	GH1	59349482	0.985000	0.35326	0.999000	0.59377	0.598000	0.36846	2.748000	0.47483	1.594000	0.50039	0.298000	0.19748	GCC		0.587	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		T	61995750	C	T	61995750	3	4	47	1	0	0	0	0	1	0	0	0	6387	768	27	1	542	1	GH1	17	61995750	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	93261	61995750	19199460	1758	6155										
SCN4A	6329	broad.mit.edu	37	chr17	62022957	62022957	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcagacaagcagcacattCatgatggaggggatggcgcc	15	9	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:62022957C>A	ENST00000435607.1	-	19	3559	c.3483G>T	c.(3481-3483)atG>atT	p.M1161I	SCN4A_ENST00000578147.1_Missense_Mutation_p.M1161I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1161					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.M1161I(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCAGCACATTCATGATGGAGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											173	174	174					17																	62022957		2202	4300	6502	59376689	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3483G>T	17.37:g.62022957C>A	ENSP00000396320:p.Met1161Ile		59376689	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	c	17.47	3.398430	0.62177	.	.	ENSG00000007314	ENST00000435607	D	0.98313	-4.86	3.9	3.9	0.45041	Ion transport (1);	0.087528	0.85682	D	0.000000	D	0.96642	0.8904	L	0.55103	1.725	0.31123	N	0.708629	B	0.22003	0.063	B	0.22152	0.038	D	0.96766	0.9565	10	0.72032	D	0.01	.	15.4374	0.75157	0.0:1.0:0.0:0.0	.	1161	P35499	SCN4A_HUMAN	I	1161	ENSP00000396320:M1161I	ENSP00000396320:M1161I	M	-	3	0	SCN4A	59376689	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.682000	0.54656	2.193000	0.70182	0.556000	0.70494	ATG		0.582	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62022957	C	A	62022957	3	1	47	1	0	0	0	0	1	0	0	0	13957	826	29	2	2051	2	SCN4A	17	62022957	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	27207	62022957	19172253	1759	6156										
CCDC45	90799	broad.mit.edu	37	chr17	62528035	62528035	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatacagaggagaagctgttCgtaaaggaactccagaatgt	11	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:62528035C>T	ENST00000556440.2	+	14	2077	c.1567C>T	c.(1567-1569)Cgt>Tgt	p.R523C	CEP95_ENST00000577476.1_3'UTR|AC009994.2_ENST00000579926.1_RNA|CEP95_ENST00000553412.1_Missense_Mutation_p.R359C	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	523						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)		p.R523C(2)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						AGAAGCTGTTCGTAAAGGAAC	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	17											49	45	46					17																	62528035		1813	4080	5893	59958497	SO:0001583	missense	90799			AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.1567C>T	17.37:g.62528035C>T	ENSP00000450461:p.Arg523Cys		59958497	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	c	4.165	0.029042	0.08054	.	.	ENSG00000258890	ENST00000556440;ENST00000553412	T;T	0.30448	1.54;1.53	5.87	0.414	0.16406	.	0.820841	0.11437	N	0.564153	T	0.10423	0.0255	N	0.03608	-0.345	0.09310	N	1	P	0.45078	0.85	B	0.36885	0.235	T	0.12553	-1.0543	10	0.38643	T	0.18	0.0101	4.3562	0.11179	0.0:0.3761:0.3064:0.3176	.	523	Q96GE4	CEP95_HUMAN	C	523;359	ENSP00000450461:R523C;ENSP00000450906:R359C	ENSP00000440121:R359C	R	+	1	0	CEP95	59958497	1.000000	0.71417	0.024000	0.17045	0.002000	0.02628	1.725000	0.38074	0.102000	0.17638	-0.808000	0.03180	CGT		0.363	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		T	62528035	C	T	62528035	3	4	47	1	0	0	0	0	1	0	0	0	2822	884	31	1	1621	1	CCDC45	17	62528035	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	505078	62528035	18667175	1760	6157										
RGS9	8787	broad.mit.edu	37	chr17	63204065	63204065	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttatgctcgctatttaaaatCtccgatctataaggacatgc	6	9	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:63204065C>A	ENST00000262406.9	+	16	1296	c.1229C>A	c.(1228-1230)tCt>tAt	p.S410Y	RGS9_ENST00000443584.3_Missense_Mutation_p.S407Y|RGS9_ENST00000449996.3_Missense_Mutation_p.S407Y	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	410	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.S410Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						TATTTAAAATCTCCGATCTAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	17											111	95	100					17																	63204065		1834	4084	5918	60634527	SO:0001583	missense	8787			AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"Regulators of G-protein signaling"	10004	protein-coding gene	gene with protein product	"regulator of G protein signalling 9", "regulator of G protein signalling 9L", "regulator of G-protein signaling 9L"	604067	"regulator of G-protein signalling 9"			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1229C>A	17.37:g.63204065C>A	ENSP00000262406:p.Ser410Tyr		60634527	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694561	0.48202	.	.	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.53423	0.62;0.62	5.34	5.34	0.76211	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	H	0.96662	3.86	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87105	0.2181	10	0.87932	D	0	.	19.412	0.94677	0.0:1.0:0.0:0.0	.	410;410;407	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	Y	410;407	ENSP00000262406:S410Y;ENSP00000396329:S407Y	ENSP00000262406:S410Y	S	+	2	0	RGS9	60634527	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	7.618000	0.83043	2.646000	0.89796	0.655000	0.94253	TCT		0.398	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835		A	63204065	C	A	63204065	3	1	47	1	0	0	0	0	1	0	0	0	13350	913	32	2	1291	2	RGS9	17	63204065	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	676030	63204065	17991145	1761	6158										
NOL11	25926	broad.mit.edu	37	chr17	65733770	65733770	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattttatccccggaactgTctgatgcagcttatccaaac	6	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:65733770T>G	ENST00000253247.4	+	12	1480	c.1365T>G	c.(1363-1365)tgT>tgG	p.C455W	NOL11_ENST00000535137.1_Missense_Mutation_p.C273W	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	455					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)	p.C455W(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			CCCGGAACTGTCTGATGCAGC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											144	129	134					17																	65733770		2203	4300	6503	63164232	SO:0001583	missense	25926			AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1365T>G	17.37:g.65733770T>G	ENSP00000253247:p.Cys455Trp		63164232	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	37	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	T	4.299	0.054754	0.08291	.	.	ENSG00000130935	ENST00000253247;ENST00000535137	T	0.44083	0.93	4.87	4.87	0.63330	.	1.047520	0.07348	N	0.881885	T	0.35682	0.0940	L	0.44542	1.39	0.48830	D	0.99971	P	0.52463	0.953	B	0.40101	0.319	T	0.32981	-0.9886	10	0.62326	D	0.03	-1.9099	6.4717	0.22011	0.0:0.1796:0.0:0.8204	.	455	Q9H8H0	NOL11_HUMAN	W	455;273	ENSP00000253247:C455W	ENSP00000253247:C455W	C	+	3	2	NOL11	63164232	0.033000	0.19621	0.996000	0.52242	0.188000	0.23474	0.157000	0.16402	1.930000	0.55929	0.533000	0.62120	TGT		0.428	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		G	65733770	T	G	65733770	3	3	47	1	0	0	0	0	1	0	0	0	10552	1673	58	4	1411	4	NOL11	17	65733770	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2529705	65733770	15461440	1762	6159										
ABCA8	10351	broad.mit.edu	37	chr17	66880487	66880487	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttacaattaggaataccagAaatggctgtacatccattcg	7	9	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:66880487A>G	ENST00000269080.2	-	26	3617	c.3480T>C	c.(3478-3480)ttT>ttC	p.F1160F	ABCA8_ENST00000586539.1_Silent_p.F1200F|ABCA8_ENST00000430352.2_Silent_p.F1200F	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1160					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.F1160F(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GGAATACCAGAAATGGCTGTA	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	17											51	58	56					17																	66880487		2200	4298	6498	64392082	SO:0001819	synonymous_variant	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3480T>C	17.37:g.66880487A>G			64392082	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																				0.308	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		G	66880487	A	G	66880487	2	3	47	1	0	0	0	0	0	0	0	1	38	243	9	4		4	ABCA8	17	66880487	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1146717	66880487	14314723	1763	6160										
ABCA9	10350	broad.mit.edu	37	chr17	66987015	66987015	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagccatagcattcactgttCtcattctttccatctggata	5	12	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:66987015C>T	ENST00000340001.4	-	29	4011	c.3800G>A	c.(3799-3801)aGa>aAa	p.R1267K	ABCA9_ENST00000453985.2_Missense_Mutation_p.R1229K|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000370732.2_Missense_Mutation_p.R1267K	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1267					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1267K(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					ATTCACTGTTCTCATTCTTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											204	172	183					17																	66987015		2203	4300	6503	64498610	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.3800G>A	17.37:g.66987015C>T	ENSP00000342216:p.Arg1267Lys		64498610	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.363188	0.24684	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732	D;D	0.88896	-2.28;-2.44	5.4	4.43	0.53597	.	0.128183	0.34750	N	0.003707	D	0.85712	0.5760	L	0.53780	1.695	0.27761	N	0.943823	B;B	0.27286	0.174;0.025	B;B	0.33254	0.16;0.053	T	0.76438	-0.2959	10	0.30854	T	0.27	.	9.3295	0.38012	0.0:0.7734:0.146:0.0806	.	1267;1267	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	K	1267;1212;1267	ENSP00000342216:R1267K;ENSP00000359767:R1267K	ENSP00000342216:R1267K	R	-	2	0	ABCA9	64498610	0.947000	0.32204	0.835000	0.33067	0.178000	0.23041	0.250000	0.18235	1.291000	0.44653	0.655000	0.94253	AGA		0.388	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	66987015	C	T	66987015	3	4	47	1	0	0	0	0	1	0	0	0	39	913	32	3	1118	3	ABCA9	17	66987015	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	106528	66987015	14208195	1764	6161										
ABCA10	10349	broad.mit.edu	37	chr17	67183946	67183946	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttcaggaagagaacaaaGaacctgttccatttcagact	8	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:67183946G>T	ENST00000269081.4	-	20	3115	c.2206C>A	c.(2206-2208)Ctt>Att	p.L736I	ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	736					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L736I(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					AGAGAACAAAGAACCTGTTCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											173	162	166					17																	67183946		2203	4300	6503	64695541	SO:0001583	missense	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.2206C>A	17.37:g.67183946G>T	ENSP00000269081:p.Leu736Ile		64695541	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104852	0.37145	.	.	ENSG00000154263	ENST00000269081	T	0.78595	-1.19	2.76	-1.03	0.10102	.	.	.	.	.	T	0.70343	0.3213	M	0.83603	2.65	0.09310	N	1	B;P	0.39022	0.439;0.655	B;B	0.35859	0.097;0.212	T	0.58847	-0.7564	9	0.32370	T	0.25	.	0.5859	0.00720	0.2199:0.1523:0.3196:0.3083	.	736;736	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	I	736	ENSP00000269081:L736I	ENSP00000269081:L736I	L	-	1	0	ABCA10	64695541	0.000000	0.05858	0.000000	0.03702	0.560000	0.35617	-1.186000	0.03070	-0.484000	0.06763	0.411000	0.27672	CTT		0.383	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67183946	G	T	67183946	3	4	47	1	0	0	0	0	1	0	0	0	29	942	33	2	2509	2	ABCA10	17	67183946	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	196931	67183946	14011264	1765	6162										
ST6GALNAC2	10610	broad.mit.edu	37	chr17	74574851	74574851	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actctacctttcctgtccaaGaattcgatgccttggattga	7	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:74574851G>A	ENST00000225276.5	-	2	492	c.173C>T	c.(172-174)tCt>tTt	p.S58F	ST6GALNAC2_ENST00000586520.1_5'UTR	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	58					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)	p.S58F(2)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						TCCTGTCCAAGAATTCGATGC	0.493																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	17											165	139	148					17																	74574851		2203	4300	6503	72086446	SO:0001583	missense	10610			U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"Sialyltransferases"	10867	protein-coding gene	gene with protein product		610137	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)", "sialyltransferase-like 1"	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.173C>T	17.37:g.74574851G>A	ENSP00000225276:p.Ser58Phe		72086446	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	G	9.131	1.011432	0.19277	.	.	ENSG00000070731	ENST00000225276	T	0.33216	1.42	4.31	2.23	0.28157	.	0.762517	0.11741	N	0.534072	T	0.25382	0.0617	L	0.48642	1.525	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24119	-1.0169	10	0.54805	T	0.06	-0.9307	6.1582	0.20350	0.2579:0.0:0.7421:0.0	.	58	Q9UJ37	SIA7B_HUMAN	F	58	ENSP00000225276:S58F	ENSP00000225276:S58F	S	-	2	0	ST6GALNAC2	72086446	0.001000	0.12720	0.000000	0.03702	0.136000	0.21042	0.744000	0.26245	0.348000	0.23949	0.561000	0.74099	TCT		0.493	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		A	74574851	G	A	74574851	3	1	47	1	0	0	0	0	1	0	0	0	15263	942	33	3	983	3	ST6GALNAC2	17	74574851	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	7390905	74574851	6620359	1766	6163										
TNRC6C	57690	broad.mit.edu	37	chr17	76089174	76089174	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaatctgacagtgataaaatCtcaaatggctctagcatcaa	6	8	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:76089174C>A	ENST00000588061.1	+	17	4858	c.4131C>A	c.(4129-4131)atC>atA	p.I1377I	TNRC6C_ENST00000541771.1_Silent_p.I1377I|TNRC6C_ENST00000335749.4_Silent_p.I1374I|TNRC6C_ENST00000544502.1_Silent_p.I1374I|TNRC6C_ENST00000301624.4_Silent_p.I1377I|TNRC6C_ENST00000588847.1_Silent_p.I1374I			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1377	Required for interaction with PABPC1.|Silencing domain; interaction with CNOT1 and PAN3.|Sufficient for translational repression when tethered to a target mRNA.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.I1377I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GTGATAAAATCTCAAATGGCT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	17											63	60	61					17																	76089174		2004	4188	6192	73600769	SO:0001819	synonymous_variant	57690			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4131C>A	17.37:g.76089174C>A			73600769	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																				0.512	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76089174	C	A	76089174	2	1	47	1	0	0	0	0	0	0	0	1	16381	903	32	2		2	TNRC6C	17	76089174	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1514323	76089174	5106036	1767	6164										
RPTOR	57521	broad.mit.edu	37	chr17	78704377	78704377	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagaactacacgcagtacatCcctctgtccatatatgacct	5	13	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr17:78704377C>T	ENST00000306801.3	+	5	887	c.525C>T	c.(523-525)atC>atT	p.I175I	RPTOR_ENST00000544334.2_Silent_p.I175I|RPTOR_ENST00000570891.1_Silent_p.I175I|RPTOR_ENST00000537330.1_5'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	175					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.I175I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CGCAGTACATCCCTCTGTCCA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	17											161	110	127					17																	78704377		2203	4300	6503	76318972	SO:0001819	synonymous_variant	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.525C>T	17.37:g.78704377C>T			76318972	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																				0.512	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78704377	C	T	78704377	2	4	47	1	0	0	0	0	0	0	0	1	13702	845	30	3		3	RPTOR	17	78704377	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2615203	78704377	2490833	1768	6165										
LAMA1	284217	broad.mit.edu	37	chr18	6959369	6959369	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaccaaggagatggaatgCgcttgtccatcactgcaggt	12	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:6959369C>T	ENST00000389658.3	-	54	7842	c.7749G>A	c.(7747-7749)gcG>gcA	p.A2583A	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2583	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A2583A(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGATGGAATGCGCTTGTCCAT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	18											161	132	142					18																	6959369		2203	4300	6503	6949369	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7749G>A	18.37:g.6959369C>T			6949369		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.562	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6959369	C	T	6959369	2	4	47	1	0	0	0	0	0	0	0	1	8627	755	27	1		1	LAMA1	18	6959369	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09		6959369	71117879	1769	6166										
LRRC30	339291	broad.mit.edu	37	chr18	7231358	7231358	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggggcttgtccgaggtccaGaaactcaatctgtctcacaa	10	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:7231358G>T	ENST00000383467.2	+	1	236	c.222G>T	c.(220-222)caG>caT	p.Q74H		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	74								p.Q74H(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CCGAGGTCCAGAAACTCAATC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	18											56	60	59					18																	7231358		1955	4158	6113	7221358	SO:0001583	missense	339291				CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422			30219	protein-coding gene	gene with protein product							Standard	NM_001105581		Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.222G>T	18.37:g.7231358G>T	ENSP00000372959:p.Gln74His		7221358		Missense_Mutation	SNP	ENST00000383467.2	37	CCDS42409.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432974	0.62844	.	.	ENSG00000206422	ENST00000383467	T	0.11930	2.73	5.65	4.78	0.61160	.	0.217497	0.48767	D	0.000171	T	0.28928	0.0718	L	0.53249	1.67	0.36428	D	0.864721	D	0.89917	1.0	D	0.72982	0.979	T	0.19516	-1.0303	10	0.33940	T	0.23	.	11.004	0.47622	0.1423:0.0:0.8577:0.0	.	74	A6NM36	LRC30_HUMAN	H	74	ENSP00000372959:Q74H	ENSP00000372959:Q74H	Q	+	3	2	LRRC30	7221358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.115000	0.31209	1.534000	0.49203	0.650000	0.86243	CAG		0.597	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442140.1	XM_292678		T	7231358	G	T	7231358	3	4	47	1	0	0	0	0	1	0	0	0	9014	933	33	2	224	2	LRRC30	18	7231358	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	271989	7231358	70845890	1770	6167										
PTPRM	5797	broad.mit.edu	37	chr18	7888350	7888350	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagggcagaactggccattaGtactttctggcctaactttt	9	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:7888350G>T	ENST00000332175.8	+	3	1480	c.443G>T	c.(442-444)aGt>aTt	p.S148I	PTPRM_ENST00000400060.4_Missense_Mutation_p.S148I|PTPRM_ENST00000580170.1_Missense_Mutation_p.S148I|PTPRM_ENST00000400053.4_Missense_Mutation_p.S86I	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	148	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S148I(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CTGGCCATTAGTACTTTCTGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	18											73	76	75					18																	7888350		2203	4300	6503	7878350	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.443G>T	18.37:g.7888350G>T	ENSP00000331418:p.Ser148Ile		7878350	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694050	0.88735	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.02446	4.29;4.29;4.29	6.07	6.07	0.98685	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.083104	0.85682	D	0.000000	T	0.21468	0.0517	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00120	-1.2030	10	0.87932	D	0	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	148;148	A7MBN1;P28827	.;PTPRM_HUMAN	I	148;148;86	ENSP00000331418:S148I;ENSP00000382933:S148I;ENSP00000382927:S86I	ENSP00000331418:S148I	S	+	2	0	PTPRM	7878350	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	5.636000	0.67848	2.885000	0.99019	0.655000	0.94253	AGT		0.363	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7888350	G	T	7888350	3	4	47	1	0	0	0	0	1	0	0	0	12843	1029	36	2	453	2	PTPRM	18	7888350	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	656992	7888350	70188898	1771	6168										
ANKRD12	23253	broad.mit.edu	37	chr18	9255359	9255359	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatagagaattttggaaagaGaatttttttaaaagtgatga	10	0	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:9255359G>T	ENST00000262126.4	+	9	2334	c.2094G>T	c.(2092-2094)gaG>gaT	p.E698D	ANKRD12_ENST00000400020.3_Missense_Mutation_p.E675D|ANKRD12_ENST00000383440.2_Missense_Mutation_p.E675D	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	698						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E698D(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						tttggaaagagaattttttta	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	18											41	45	44					18																	9255359		2125	4177	6302	9245359	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2094G>T	18.37:g.9255359G>T	ENSP00000262126:p.Glu698Asp		9245359	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369121	0.42003	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000359158	D;D	0.91843	-2.92;-2.92	5.06	2.22	0.28083	.	0.000000	0.85682	D	0.000000	D	0.93956	0.8065	M	0.67953	2.075	0.50632	D	0.999881	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.77557	0.99;0.99;0.918	D	0.92349	0.5888	10	0.66056	D	0.02	-22.5349	7.6147	0.28150	0.4325:0.0:0.5675:0.0	.	325;675;698	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	D	675;698;405	ENSP00000372932:E675D;ENSP00000262126:E698D	ENSP00000262126:E698D	E	+	3	2	ANKRD12	9245359	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.797000	0.26999	0.624000	0.30286	0.460000	0.39030	GAG		0.274	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9255359	G	T	9255359	3	4	47	1	0	0	0	0	1	0	0	0	640	933	33	2	2124	2	ANKRD12	18	9255359	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1367009	9255359	68821889	1772	6169										
ANKRD12	23253	broad.mit.edu	37	chr18	9275530	9275530	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttattcaactaggaaaaactCattgtatccaacgaacaaga	5	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:9275530C>A	ENST00000262126.4	+	11	6012	c.5772C>A	c.(5770-5772)ctC>ctA	p.L1924L	ANKRD12_ENST00000400020.3_Silent_p.L1901L|snoU13_ENST00000459594.1_RNA|ANKRD12_ENST00000383440.2_Silent_p.L1901L	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1924						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L1924L(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AGGAAAAACTCATTGTATCCA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	18											113	108	110					18																	9275530		2203	4300	6503	9265530	SO:0001819	synonymous_variant	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5772C>A	18.37:g.9275530C>A			9265530	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	37	CCDS11843.1																																																																																				0.358	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9275530	C	A	9275530	2	1	47	1	0	0	0	0	0	0	0	1	640	813	29	2		2	ANKRD12	18	9275530	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	20171	9275530	68801718	1773	6170										
SEH1L	81929	broad.mit.edu	37	chr18	12984076	12984076	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaagtgtactggtattttGaaaggtaatgggagcccagt	14	4	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:12984076G>T	ENST00000262124.11	+	8	1084	c.957G>T	c.(955-957)ttG>ttT	p.L319F	SEH1L_ENST00000399892.2_Missense_Mutation_p.L319F|RP11-773H22.4_ENST00000588211.1_RNA|SEH1L_ENST00000592582.1_3'UTR	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	319					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.L319F(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CTGGTATTTTGAAAGGTAATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	18											99	103	102					18																	12984076		2203	4300	6503	12974076	SO:0001583	missense	81929			BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"WD repeat domain containing"	30379	protein-coding gene	gene with protein product	"sec13 like protein", "nucleoporin Seh1"	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.957G>T	18.37:g.12984076G>T	ENSP00000262124:p.Leu319Phe		12974076	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Missense_Mutation	SNP	ENST00000262124.11	37	CCDS45832.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.527835	0.64860	.	.	ENSG00000085415	ENST00000399892;ENST00000262124	T;T	0.68025	-0.3;-0.3	6.04	4.27	0.50696	WD40/YVTN repeat-like-containing domain (1);	0.063541	0.64402	D	0.000005	T	0.66127	0.2758	M	0.71581	2.175	0.52099	D	0.999943	B;B	0.33826	0.012;0.427	B;B	0.36808	0.03;0.233	T	0.66512	-0.5905	10	0.62326	D	0.03	-7.3081	10.7195	0.46032	0.0648:0.2468:0.6884:0.0	.	319;319	Q96EE3;Q96EE3-1	SEH1_HUMAN;.	F	319	ENSP00000382779:L319F;ENSP00000262124:L319F	ENSP00000262124:L319F	L	+	3	2	SEH1L	12974076	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.505000	0.60421	0.895000	0.36342	-0.222000	0.12452	TTG		0.373	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216		T	12984076	G	T	12984076	3	4	47	1	0	0	0	0	1	0	0	0	14046	1281	45	2	987	2	SEH1L	18	12984076	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3708546	12984076	65093172	1774	6171										
RNMT	8731	broad.mit.edu	37	chr18	13731605	13731605	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttctgaaacagagtcttcatTcaatattaatgaaaacacaa	4	7	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:13731605T>G	ENST00000383314.2	+	3	329	c.89T>G	c.(88-90)tTc>tGc	p.F30C	RNMT_ENST00000592764.1_Missense_Mutation_p.F30C|RNMT_ENST00000543302.2_Missense_Mutation_p.F30C|RNMT_ENST00000535051.1_Intron|RNMT_ENST00000589866.1_Missense_Mutation_p.F30C|RNMT_ENST00000262173.3_Missense_Mutation_p.F30C			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	30					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)	p.F30C(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						GAGTCTTCATTCAATATTAAT	0.363																																					GBM(29;474 594 19092 36647 41529)											1	Substitution - Missense(1)	large_intestine(1)	18											107	120	116					18																	13731605		2203	4300	6503	13721605	SO:0001583	missense	8731			AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.89T>G	18.37:g.13731605T>G	ENSP00000372804:p.Phe30Cys		13721605	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Missense_Mutation	SNP	ENST00000383314.2	37	CCDS11867.1	.	.	.	.	.	.	.	.	.	.	T	5.727	0.318584	0.10845	.	.	ENSG00000101654	ENST00000383314;ENST00000543302;ENST00000262173	.	.	.	5.23	-0.545	0.11843	.	1.206160	0.05829	N	0.617194	T	0.17066	0.0410	N	0.14661	0.345	0.09310	N	1	P;P	0.51351	0.944;0.681	B;B	0.44163	0.443;0.174	T	0.08764	-1.0706	9	0.38643	T	0.18	1.3669	1.0373	0.01551	0.3195:0.0941:0.1649:0.4215	.	30;30	O43148-2;O43148	.;MCES_HUMAN	C	30	.	ENSP00000262173:F30C	F	+	2	0	RNMT	13721605	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	0.055000	0.14229	0.047000	0.15862	0.533000	0.62120	TTC		0.363	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		G	13731605	T	G	13731605	3	3	47	1	0	0	0	0	1	0	0	0	13543	1783	62	4	91	4	RNMT	18	13731605	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	747529	13731605	64345643	1775	6172										
MC5R	4161	broad.mit.edu	37	chr18	13825953	13825953	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcataggggccatagtgaaGaacaaaaacctgcactcccc	9	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:13825953G>T	ENST00000324750.3	+	1	411	c.189G>T	c.(187-189)aaG>aaT	p.K63N	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	63					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)	p.K63N(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						CCATAGTGAAGAACAAAAACC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	18											122	116	118					18																	13825953		2203	4300	6503	13815953	SO:0001583	missense	4161			AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"GPCR / Class A : Melanocortin receptors"	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.189G>T	18.37:g.13825953G>T	ENSP00000318077:p.Lys63Asn		13815953	B0YJ34|Q502V1	Missense_Mutation	SNP	ENST00000324750.3	37	CCDS11868.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781587	0.49891	.	.	ENSG00000176136	ENST00000324750	T	0.00567	6.54	5.01	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.046425	0.85682	D	0.000000	T	0.02888	0.0086	H	0.94808	3.585	0.58432	D	0.999997	D	0.67145	0.996	D	0.65773	0.938	T	0.11227	-1.0596	10	0.87932	D	0	.	11.0517	0.47894	0.1575:0.0:0.8425:0.0	.	63	P33032	MC5R_HUMAN	N	63	ENSP00000318077:K63N	ENSP00000318077:K63N	K	+	3	2	MC5R	13815953	1.000000	0.71417	0.995000	0.50966	0.494000	0.33585	2.010000	0.40913	1.065000	0.40693	0.455000	0.32223	AAG		0.532	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913		T	13825953	G	T	13825953	3	4	47	1	0	0	0	0	1	0	0	0	9397	933	33	2	191	2	MC5R	18	13825953	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	94348	13825953	64251295	1776	6173										
ROCK1	6093	broad.mit.edu	37	chr18	18690795	18690795	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcaccagcaaacaatccgaaTtcacttccgatttgggatcc	6	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:18690795T>G	ENST00000399799.2	-	1	1017	c.77A>C	c.(76-78)aAt>aCt	p.N26T		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	26					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N26T(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					ACAATCCGAATTCACTTCCGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	18											227	201	210					18																	18690795		2203	4300	6503	16944793	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.77A>C	18.37:g.18690795T>G	ENSP00000382697:p.Asn26Thr		16944793	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	23.3	4.404809	0.83230	.	.	ENSG00000067900	ENST00000399799	T	0.65549	-0.16	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.78233	0.4251	M	0.83603	2.65	0.54753	D	0.999984	D	0.76494	0.999	P	0.61800	0.894	T	0.82084	-0.0632	10	0.87932	D	0	.	13.9814	0.64306	0.0:0.0:0.0:1.0	.	26	Q13464	ROCK1_HUMAN	T	26	ENSP00000382697:N26T	ENSP00000382697:N26T	N	-	2	0	ROCK1	16944793	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.802000	0.69122	2.127000	0.65507	0.533000	0.62120	AAT		0.478	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		G	18690795	T	G	18690795	3	3	47	1	0	0	0	0	1	0	0	0	13554	1493	52	4	4119	4	ROCK1	18	18690795	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	4864842	18690795	59386453	1777	6174										
ESCO1	114799	broad.mit.edu	37	chr18	19153782	19153782	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttcaacactggtctcttcCaattttatttctgtgggctt	6	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:19153782C>A	ENST00000269214.5	-	4	1960	c.1023G>T	c.(1021-1023)ttG>ttT	p.L341F		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	341					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)	p.L341F(1)		breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TGGTCTCTTCCAATTTTATTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											122	123	123					18																	19153782		2203	4300	6503	17407780	SO:0001583	missense	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.1023G>T	18.37:g.19153782C>A	ENSP00000269214:p.Leu341Phe		17407780	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.163317	0.38217	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.65364	-0.15;1.35	5.74	2.98	0.34508	.	0.000000	0.47852	D	0.000217	T	0.63379	0.2506	M	0.64997	1.995	0.28976	N	0.888967	D	0.56746	0.977	P	0.52267	0.694	T	0.59768	-0.7392	10	0.51188	T	0.08	-0.5787	6.0635	0.19850	0.1358:0.6559:0.0:0.2083	.	341	Q5FWF5	ESCO1_HUMAN	F	341	ENSP00000269214:L341F;ENSP00000372763:L341F	ENSP00000269214:L341F	L	-	3	2	ESCO1	17407780	0.200000	0.23398	0.999000	0.59377	0.768000	0.43524	-0.023000	0.12456	0.772000	0.33382	0.655000	0.94253	TTG		0.348	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		A	19153782	C	A	19153782	3	1	47	1	0	0	0	0	1	0	0	0	5261	593	21	2	1535	2	ESCO1	18	19153782	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	462987	19153782	58923466	1778	6175										
ZNF521	25925	broad.mit.edu	37	chr18	22804543	22804543	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcccaagcctggtctattCgtgccgggagggacgttaat	14	10	1	0	rs149562357		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:22804543C>A	ENST00000361524.3	-	4	3487	c.3339G>T	c.(3337-3339)acG>acT	p.T1113T	ZNF521_ENST00000584787.1_Silent_p.T893T|ZNF521_ENST00000538137.2_Silent_p.T1113T	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1113					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.T1113T(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CTGGTCTATTCGTGCCGGGAG	0.547			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - coding silent(1)	large_intestine(1)	18											106	95	99					18																	22804543		2203	4300	6503	21058541	SO:0001819	synonymous_variant	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3339G>T	18.37:g.22804543C>A			21058541	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																				0.547	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22804543	C	A	22804543	2	1	47	1	0	0	0	0	0	0	0	1	18004	871	31	2		2	ZNF521	18	22804543	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3650761	22804543	55272705	1779	6176										
CHST9	83539	broad.mit.edu	37	chr18	24497266	24497266	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctcagaattgagtagaaGattttcctttttttctcgta	6	7	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:24497266G>T	ENST00000284224.8	-	6	566	c.289C>A	c.(289-291)Ctt>Att	p.L97I	CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000579964.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.L97I	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	97					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.L97I(1)|p.L12I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					TTGAGTAGAAGATTTTCCTTT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	18											206	186	192					18																	24497266		1852	4087	5939	22751264	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.289C>A	18.37:g.24497266G>T	ENSP00000284224:p.Leu97Ile		22751264	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400452	0.25291	.	.	ENSG00000154080	ENST00000284224	T	0.65549	-0.16	5.36	-0.153	0.13403	.	2.395520	0.01510	N	0.017876	T	0.41003	0.1140	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09952	-1.0651	10	0.22706	T	0.39	-0.0457	0.1921	0.00135	0.2522:0.1837:0.2095:0.3546	.	97	Q7L1S5	CHST9_HUMAN	I	97	ENSP00000284224:L97I	ENSP00000284224:L97I	L	-	1	0	CHST9	22751264	0.004000	0.15560	0.002000	0.10522	0.210000	0.24377	0.434000	0.21494	0.057000	0.16193	-0.181000	0.13052	CTT		0.413	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		T	24497266	G	T	24497266	3	4	47	1	0	0	0	0	1	0	0	0	3417	942	33	2	1046	2	CHST9	18	24497266	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1692723	24497266	53579982	1780	6177										
DSC1	1823	broad.mit.edu	37	chr18	28714673	28714673	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attctgacaaatggtcacttCtttgtcaatttgaggtgcgt	9	7	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:28714673C>A	ENST00000257198.5	-	12	1999	c.1738G>T	c.(1738-1740)Gaa>Taa	p.E580*	RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_Nonsense_Mutation_p.E580*|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	580	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E580*(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			ATGGTCACTTCTTTGTCAATT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											81	72	75					18																	28714673		2203	4300	6503	26968671	SO:0001587	stop_gained	1823			AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"Cadherins / Major cadherins"	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1738G>T	18.37:g.28714673C>A	ENSP00000257198:p.Glu580*		26968671	Q9HB01	Nonsense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	C	37	6.453685	0.97581	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	.	.	.	5.57	2.76	0.32466	.	0.789852	0.11299	N	0.578457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	5.8527	0.18701	0.0:0.6268:0.1516:0.2215	.	.	.	.	X	580	.	ENSP00000257197:E580X	E	-	1	0	DSC1	26968671	0.016000	0.18221	0.011000	0.14972	0.570000	0.35934	0.149000	0.16243	0.814000	0.34374	0.591000	0.81541	GAA		0.363	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		A	28714673	C	A	28714673	4	1	47	1	0	0	0	0	0	1	0	0	4776	922	32	2	1006	2	DSC1	18	28714673	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4217407	28714673	49362575	1781	6178										
DSG4	147409	broad.mit.edu	37	chr18	28972226	28972226	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggttggctcaatatttaattCtctctggaaatgatgggaat	10	5	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:28972226C>A	ENST00000308128.4	+	8	1063	c.928C>A	c.(928-930)Ctc>Atc	p.L310I	RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.L310I|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	310	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L310I(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ATATTTAATTCTCTCTGGAAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	18											105	104	105					18																	28972226		2203	4300	6503	27226224	SO:0001583	missense	147409			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.928C>A	18.37:g.28972226C>A	ENSP00000311859:p.Leu310Ile		27226224	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.395536	0.25205	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.56611	0.45;0.45	5.44	4.51	0.55191	Cadherin (4);Cadherin-like (1);	0.000000	0.29814	N	0.011140	T	0.19167	0.0460	N	0.00729	-1.24	0.32892	D	0.511996	B;B	0.20261	0.043;0.007	B;B	0.27380	0.079;0.028	T	0.30357	-0.9981	10	0.13853	T	0.58	.	7.9024	0.29742	0.1965:0.5155:0.288:0.0	.	310;310	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	I	310	ENSP00000311859:L310I;ENSP00000352785:L310I	ENSP00000311859:L310I	L	+	1	0	DSG4	27226224	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.082000	0.30803	2.716000	0.92895	0.650000	0.86243	CTC		0.358	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		A	28972226	C	A	28972226	3	1	47	1	0	0	0	0	1	0	0	0	4790	913	32	2	958	2	DSG4	18	28972226	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	257553	28972226	49105022	1782	6179										
FAM59A	64762	broad.mit.edu	37	chr18	29867438	29867438	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggtgagctcatcgcgggcGtagctgagcgaattgggcac	17	9	1	2	rs138770869	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:29867438G>A	ENST00000269209.6	-	4	1125	c.1122C>T	c.(1120-1122)taC>taT	p.Y374Y	GAREM_ENST00000399218.4_Silent_p.Y374Y|RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000578619.1_5'Flank			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	374					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.Y374Y(1)									CATCGCGGGCGTAGCTGAGCG	0.567													G|||	6	0.00119808	0.0045	0	5008	,	,		19394	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	18						G	,	2,4404	4.2+/-10.8	0,2,2201	100	98	98		1122,1122	-8.8	0.4	18	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	374/877,374/876	29867438	2,13004	2203	4300	6503	28121436	SO:0001819	synonymous_variant	64762			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1122C>T	18.37:g.29867438G>A			28121436	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																				0.567	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29867438	G	A	29867438	2	1	47	1	0	0	0	0	0	0	0	1	5611	1140	40	1		1	FAM59A	18	29867438	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	895212	29867438	48209810	1783	6180										
ASXL3	80816	broad.mit.edu	37	chr18	31324231	31324231	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgatcaattccgtgtaaagtCatcgttgaccacagcaccac	7	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:31324231C>A	ENST00000269197.5	+	12	4419	c.4419C>A	c.(4417-4419)gtC>gtA	p.V1473V		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V1473V(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CGTGTAAAGTCATCGTTGACC	0.532											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	18											72	78	76					18																	31324231		2203	4299	6502	29578229	SO:0001819	synonymous_variant	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.4419C>A	18.37:g.31324231C>A		823	29578229	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	37	CCDS45847.1																																																																																				0.532	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31324231	C	A	31324231	2	1	47	1	0	0	0	0	0	0	0	1	1069	813	29	2		2	ASXL3	18	31324231	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1456793	31324231	46753017	1784	6181										
ZNF397OS	100101467	broad.mit.edu	37	chr18	32833937	32833937	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctctctccagtatgaattCtctgatgtctaatcagcttt	6	10	5	2	rs200243252	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:32833937C>A	ENST00000420878.3	-	5	1417	c.962G>T	c.(961-963)aGa>aTa	p.R321I	ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000355632.4_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.R321I|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000261333.6_Intron	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	321					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R321I(1)		large_intestine(5)|lung(3)|urinary_tract(1)	9						AGTATGAATTCTCTGATGTCT	0.428													C|||	2	0.000399361	0	0	5008	,	,		22239	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											99	90	93					18																	32833937		1568	3582	5150	31087935	SO:0001583	missense	100101467			AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"-", "Zinc fingers, C2H2-type"	33517	protein-coding gene	gene with protein product			"zinc finger protein 397 opposite strand", "ZNF397 opposite strand"	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.962G>T	18.37:g.32833937C>A	ENSP00000392371:p.Arg321Ile		31087935	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	18.84	3.709069	0.68615	.	.	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.24908	1.83;1.83	4.5	4.5	0.54988	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38959	N	0.001502	T	0.34019	0.0883	M	0.68952	2.095	0.80722	D	1	D	0.59357	0.985	P	0.49361	0.608	T	0.09185	-1.0686	10	0.54805	T	0.06	.	10.1691	0.42900	0.1989:0.8011:0.0:0.0	.	321	Q86W11	ZSC30_HUMAN	I	321;321;256	ENSP00000392371:R321I;ENSP00000329738:R321I	ENSP00000329738:R321I	R	-	2	0	ZSCAN30	31087935	0.051000	0.20477	1.000000	0.80357	0.995000	0.86356	1.849000	0.39318	2.480000	0.83734	0.643000	0.83706	AGA		0.428	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		A	32833937	C	A	32833937	3	1	47	1	0	0	0	0	1	0	0	0	17923	913	32	2	526	2	ZNF397OS	18	32833937	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1509706	32833937	45243311	1785	6182										
MOCOS	55034	broad.mit.edu	37	chr18	33793366	33793366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctttacaacatccacctgcGaactggctgcttctgtaaca	6	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:33793366G>A	ENST00000261326.5	+	7	1277	c.1256G>A	c.(1255-1257)cGa>cAa	p.R419Q		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase									p.R419Q(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						ATCCACCTGCGAACTGGCTGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	18											70	62	65					18																	33793366		2203	4300	6503	32047364	SO:0001583	missense	55034			AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1256G>A	18.37:g.33793366G>A	ENSP00000261326:p.Arg419Gln		32047364		Missense_Mutation	SNP	ENST00000261326.5	37	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.657160	0.88154	.	.	ENSG00000075643	ENST00000261326	D	0.88896	-2.44	5.56	5.56	0.83823	Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.96256	0.8779	H	0.96365	3.81	0.51767	D	0.999939	D	0.89917	1.0	D	0.85130	0.997	D	0.97216	0.9874	10	0.87932	D	0	-14.882	15.0208	0.71630	0.0:0.0:1.0:0.0	.	419	Q96EN8	MOCOS_HUMAN	Q	419	ENSP00000261326:R419Q	ENSP00000261326:R419Q	R	+	2	0	MOCOS	32047364	1.000000	0.71417	0.987000	0.45799	0.464000	0.32679	9.452000	0.97615	2.619000	0.88677	0.555000	0.69702	CGA		0.498	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			A	33793366	G	A	33793366	3	1	47	1	0	0	0	0	1	0	0	0	9719	1058	37	1	1282	1	MOCOS	18	33793366	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	959429	33793366	44283882	1786	6183										
SETBP1	26040	broad.mit.edu	37	chr18	42531727	42531727	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttgaaaactatgccaaatCtccagcccatcagtgctctt	6	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:42531727C>A	ENST00000282030.5	+	4	2718	c.2422C>A	c.(2422-2424)Ctc>Atc	p.L808I		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	808						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L754I(1)|p.L808I(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TATGCCAAATCTCCAGCCCAT	0.498									Schinzel-Giedion syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	18											65	65	65					18																	42531727		2203	4300	6503	40785725	SO:0001583	missense	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.2422C>A	18.37:g.42531727C>A	ENSP00000282030:p.Leu808Ile		40785725	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	C	16.71	3.197710	0.58126	.	.	ENSG00000152217	ENST00000282030	D	0.90620	-2.7	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.92260	0.7545	N	0.19112	0.55	0.37400	D	0.912795	D	0.76494	0.999	D	0.73380	0.98	D	0.93675	0.6993	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	808	Q9Y6X0	SETBP_HUMAN	I	808	ENSP00000282030:L808I	ENSP00000282030:L808I	L	+	1	0	SETBP1	40785725	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.986000	0.70563	2.941000	0.99782	0.655000	0.94253	CTC		0.498	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42531727	C	A	42531727	3	1	47	1	0	0	0	0	1	0	0	0	14166	913	32	2	2625	2	SETBP1	18	42531727	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	8738361	42531727	35545521	1787	6184										
KIAA1632	57724	broad.mit.edu	37	chr18	43459165	43459165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaaagtctgaaagccactgTatagtctccattacctggaa	7	9	2	1	rs372631564		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:43459165T>C	ENST00000282041.5	-	33	5716	c.5682A>G	c.(5680-5682)atA>atG	p.I1894M	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1894					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.I1894M(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AAAGCCACTGTATAGTCTCCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	18						T	MET/ILE	0,3604		0,0,1802	57	55	56		5682	-1.2	1	18		56	1,8137		0,1,4068	no	missense	EPG5	NM_020964.2	10	0,1,5870	CC,CT,TT		0.0123,0.0,0.0085	possibly-damaging	1894/2580	43459165	1,11741	1802	4069	5871	41713163	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5682A>G	18.37:g.43459165T>C	ENSP00000282041:p.Ile1894Met		41713163	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	15.38	2.817440	0.50633	0.0	1.23E-4	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.11277	2.79	4.67	-1.25	0.09405	.	.	.	.	.	T	0.13756	0.0333	L	0.46157	1.445	0.39665	D	0.970663	P	0.46512	0.879	P	0.51385	0.668	T	0.19257	-1.0311	9	0.56958	D	0.05	-9.0854	6.3982	0.21624	0.4548:0.0:0.2352:0.31	.	1894	Q9HCE0	EPG5_HUMAN	M	1894;769	ENSP00000282041:I1894M	ENSP00000282041:I1894M	I	-	3	3	EPG5	41713163	0.262000	0.24073	0.981000	0.43875	0.900000	0.52787	-0.723000	0.04952	-0.049000	0.13379	-0.433000	0.05886	ATA		0.343	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43459165	T	C	43459165	3	2	47	1	0	0	0	0	1	0	0	0	8270	1628	57	4	2105	4	KIAA1632	18	43459165	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	927438	43459165	34618083	1788	6185										
TCEB3B	51224	broad.mit.edu	37	chr18	44560390	44560390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcacgagtgcccttggattCgtttgctttcctttgtttat	8	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:44560390C>T	ENST00000332567.4	-	1	1598	c.1246G>A	c.(1246-1248)Gaa>Aaa	p.E416K	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	416					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E416K(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CCCTTGGATTCGTTTGCTTTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	18											113	99	104					18																	44560390		2203	4300	6503	42814388	SO:0001583	missense	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1246G>A	18.37:g.44560390C>T	ENSP00000331302:p.Glu416Lys		42814388	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	C	7.702	0.693246	0.15039	.	.	ENSG00000206181	ENST00000332567	T	0.06608	3.28	2.19	-1.07	0.09968	.	4.080680	0.02912	U	0.136767	T	0.03011	0.0089	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.35525	-0.9785	10	0.05833	T	0.94	.	5.2426	0.15479	0.2203:0.3461:0.4336:0.0	.	416	Q8IYF1	ELOA2_HUMAN	K	416	ENSP00000331302:E416K	ENSP00000331302:E416K	E	-	1	0	TCEB3B	42814388	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.385000	0.07379	-0.285000	0.09089	-0.257000	0.10917	GAA		0.507	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44560390	C	T	44560390	3	4	47	1	0	0	0	0	1	0	0	0	15721	893	31	1	1019	1	TCEB3B	18	44560390	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1101225	44560390	33516858	1789	6186										
KATNAL2	83473	broad.mit.edu	37	chr18	44584718	44584718	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgctcaataaggagcatcctAatcaggtcaggatggcttgg	12	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:44584718A>C	ENST00000245121.5	+	4	423	c.229A>C	c.(229-231)Aat>Cat	p.N77H	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Missense_Mutation_p.N149H	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2									p.N77H(1)		central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GGAGCATCCTAATCAGGTCAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	18											84	82	83					18																	44584718		2203	4300	6503	42838716	SO:0001583	missense	83473			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.229A>C	18.37:g.44584718A>C	ENSP00000245121:p.Asn77His		42838716		Missense_Mutation	SNP	ENST00000245121.5	37	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	A	8.736	0.917844	0.17982	.	.	ENSG00000167216	ENST00000356157;ENST00000245121	D;D	0.93547	-3.24;-3.24	5.35	2.98	0.34508	.	0.573895	0.19374	N	0.115838	D	0.83321	0.5229	N	0.08118	0	0.20074	N	0.999939	B	0.12013	0.005	B	0.08055	0.003	T	0.72404	-0.4304	10	0.44086	T	0.13	-1.7133	7.6972	0.28602	0.83:0.0:0.17:0.0	.	149	Q8IYT4	KATL2_HUMAN	H	149;77	ENSP00000348478:N149H;ENSP00000245121:N77H	ENSP00000245121:N77H	N	+	1	0	KATNAL2	42838716	0.993000	0.37304	0.328000	0.25416	0.864000	0.49448	3.466000	0.53071	0.363000	0.24346	0.459000	0.35465	AAT		0.458	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		C	44584718	A	C	44584718	3	2	47	1	0	0	0	0	1	0	0	0	8007	362	13	4	239	4	KATNAL2	18	44584718	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	24328	44584718	33492530	1790	6187										
MBD2	8932	broad.mit.edu	37	chr18	51731393	51731393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgattgagaggatcgtttCgcagtctctgtttgttcttc	10	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:51731393C>T	ENST00000256429.3	-	2	905	c.677G>A	c.(676-678)cGa>cAa	p.R226Q	MBD2_ENST00000398398.2_Missense_Mutation_p.R226Q|MBD2_ENST00000583046.1_Missense_Mutation_p.R226Q	NM_003927.4	NP_003918.1	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2	226					ATP-dependent chromatin remodeling (GO:0043044)|cellular protein complex assembly (GO:0043623)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|protein domain specific binding (GO:0019904)|satellite DNA binding (GO:0003696)|siRNA binding (GO:0035197)	p.R226Q(1)		breast(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)		AGGATCGTTTCGCAGTCTCTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	18											292	273	280					18																	51731393		2203	4300	6503	49985391	SO:0001583	missense	8932			AF072242	CCDS11953.1, CCDS45871.1	18q21	2008-08-01			ENSG00000134046	ENSG00000134046			6917	protein-coding gene	gene with protein product		603547				9774669, 10441743	Standard	NM_003927		Approved		uc002lfg.2	Q9UBB5	OTTHUMG00000132705	ENST00000256429.3:c.677G>A	18.37:g.51731393C>T	ENSP00000256429:p.Arg226Gln		49985391	O95242|Q9UIS8	Missense_Mutation	SNP	ENST00000256429.3	37	CCDS11953.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550478	0.65311	.	.	ENSG00000134046	ENST00000256429;ENST00000398398	D;D	0.96619	-4.07;-4.07	5.78	5.78	0.91487	Methyl-CpG DNA binding (1);DNA-binding, integrase-type (1);	0.000000	0.64402	D	0.000003	D	0.97059	0.9039	L	0.43923	1.385	0.49299	D	0.999773	D;P	0.89917	1.0;0.899	D;B	0.85130	0.997;0.372	D	0.95840	0.8865	10	0.27785	T	0.31	-17.5094	18.7852	0.91952	0.0:1.0:0.0:0.0	.	226;226	Q9UBB5-3;Q9UBB5	.;MBD2_HUMAN	Q	226	ENSP00000256429:R226Q;ENSP00000381435:R226Q	ENSP00000256429:R226Q	R	-	2	0	MBD2	49985391	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.622000	0.83099	2.739000	0.93911	0.643000	0.83706	CGA		0.363	MBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256003.2	NM_003927		T	51731393	C	T	51731393	3	4	47	1	0	0	0	0	1	0	0	0	9373	884	31	1	789	1	MBD2	18	51731393	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7146675	51731393	26345855	1791	6188										
C18orf54	162681	broad.mit.edu	37	chr18	51900601	51900601	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taggtttcagaagatgatttCtctaaattacagttgaagga	9	4	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:51900601C>A	ENST00000300091.5	+	7	1325	c.993C>A	c.(991-993)ttC>ttA	p.F331L	C18orf54_ENST00000382911.4_Missense_Mutation_p.F492L|C18orf54_ENST00000582188.1_3'UTR|C18orf54_ENST00000578138.1_Missense_Mutation_p.F110L	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	331						extracellular region (GO:0005576)		p.F331L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		AAGATGATTTCTCTAAATTAC	0.249																																																1	Substitution - Missense(1)	large_intestine(1)	18											33	37	36					18																	51900601		2185	4255	6440	50154599	SO:0001583	missense	162681			AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"lung adenoma susceptibility protein 2"	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.993C>A	18.37:g.51900601C>A	ENSP00000300091:p.Phe331Leu		50154599	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	37	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504523	0.26949	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	T;T	0.14391	2.51;2.51	5.2	0.31	0.15825	.	1.170710	0.05950	N	0.638513	T	0.06781	0.0173	N	0.12471	0.22	0.09310	N	0.999993	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.41197	-0.9522	10	0.11794	T	0.64	.	4.8849	0.13697	0.0:0.2272:0.1772:0.5956	.	492;331	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	L	331;492	ENSP00000300091:F331L;ENSP00000372368:F492L	ENSP00000300091:F331L	F	+	3	2	C18orf54	50154599	0.802000	0.28943	0.950000	0.38849	0.952000	0.60782	-0.348000	0.07740	-0.024000	0.13941	0.585000	0.79938	TTC		0.249	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529		A	51900601	C	A	51900601	3	1	47	1	0	0	0	0	1	0	0	0	1910	912	32	2	1015	2	C18orf54	18	51900601	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	169208	51900601	26176647	1792	6189										
CCDC68	80323	broad.mit.edu	37	chr18	52575087	52575087	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctacctgggtttttagttCtttattctaaaattgaaaaa	6	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:52575087C>A	ENST00000591504.1	-	11	1154	c.880G>T	c.(880-882)Gaa>Taa	p.E294*	CCDC68_ENST00000432185.1_Nonsense_Mutation_p.E294*|CCDC68_ENST00000337363.4_Nonsense_Mutation_p.E294*	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	294								p.E294*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		GTTTTTAGTTCTTTATTCTAA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											126	123	124					18																	52575087		2203	4300	6503	50726085	SO:0001587	stop_gained	80323				CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma associated antigen"					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.880G>T	18.37:g.52575087C>A	ENSP00000466690:p.Glu294*		50726085	B2R9I3	Nonsense_Mutation	SNP	ENST00000591504.1	37	CCDS11959.1	.	.	.	.	.	.	.	.	.	.	C	37	6.499095	0.97616	.	.	ENSG00000166510	ENST00000337363;ENST00000432185	.	.	.	5.51	5.51	0.81932	.	0.105580	0.42548	D	0.000682	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-23.51	15.2741	0.73728	0.0:1.0:0.0:0.0	.	.	.	.	X	294	.	ENSP00000337209:E294X	E	-	1	0	CCDC68	50726085	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.381000	0.52455	2.738000	0.93877	0.655000	0.94253	GAA		0.408	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214		A	52575087	C	A	52575087	4	1	47	1	0	0	0	0	0	1	0	0	2846	922	32	2	135	2	CCDC68	18	52575087	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	674486	52575087	25502161	1793	6190										
TCF4	6925	broad.mit.edu	37	chr18	52937154	52937154	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaaagtggacatcggaggaAgactggaattgatgtctgct	15	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:52937154A>C	ENST00000356073.4	-	11	1441	c.830T>G	c.(829-831)cTt>cGt	p.L277R	TCF4_ENST00000457482.3_Missense_Mutation_p.L117R|TCF4_ENST00000566279.1_Missense_Mutation_p.L217R|TCF4_ENST00000561831.3_Missense_Mutation_p.L117R|TCF4_ENST00000564228.1_Missense_Mutation_p.L206R|TCF4_ENST00000537578.1_Missense_Mutation_p.L253R|TCF4_ENST00000567880.1_Missense_Mutation_p.L217R|TCF4_ENST00000398339.1_Missense_Mutation_p.L379R|TCF4_ENST00000543082.1_Missense_Mutation_p.L235R|TCF4_ENST00000544241.2_Missense_Mutation_p.L206R|TCF4_ENST00000354452.3_Missense_Mutation_p.L277R|TCF4_ENST00000565018.2_Missense_Mutation_p.L277R|TCF4_ENST00000561992.1_Missense_Mutation_p.L147R|TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000568673.1_Missense_Mutation_p.L253R|TCF4_ENST00000564999.1_Missense_Mutation_p.L277R|TCF4_ENST00000564403.2_Missense_Mutation_p.L283R|TCF4_ENST00000570177.2_Missense_Mutation_p.L147R|TCF4_ENST00000566286.1_Missense_Mutation_p.L275R|TCF4_ENST00000540999.1_Missense_Mutation_p.L253R|TCF4_ENST00000537856.3_Missense_Mutation_p.L147R|TCF4_ENST00000570287.2_Missense_Mutation_p.L117R|TCF4_ENST00000568740.1_Missense_Mutation_p.L252R	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	277					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)	p.L277R(1)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		CATCGGAGGAAGACTGGAATT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	18											180	153	162					18																	52937154		2203	4300	6503	51088152	SO:0001583	missense	6925			M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.830T>G	18.37:g.52937154A>C	ENSP00000348374:p.Leu277Arg		51088152	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	37	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.960975	0.92791	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.78039	0.4221	M	0.83223	2.63	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.997;1.0;0.999;0.998;0.999;1.0;1.0;0.991;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.85130	0.973;0.997;0.985;0.978;0.979;0.972;0.987;0.944;0.975;0.984	T	0.81577	-0.0869	10	0.87932	D	0	-6.4758	15.1189	0.72426	1.0:0.0:0.0:0.0	.	253;277;253;117;379;277;235;206;117;275	B7Z5M6;G0LNT9;B7Z6Y1;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;.;ITF2_HUMAN;.;.;.;.	R	277;117;277;235;253;253;206;147;379	ENSP00000346440:L277R;ENSP00000409447:L117R;ENSP00000348374:L277R;ENSP00000439656:L235R;ENSP00000445202:L253R;ENSP00000440731:L253R;ENSP00000441562:L206R;ENSP00000439827:L147R;ENSP00000381382:L379R	ENSP00000346440:L277R	L	-	2	0	TCF4	51088152	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.514000	0.90545	2.207000	0.71202	0.377000	0.23210	CTT		0.443	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		C	52937154	A	C	52937154	3	2	47	1	0	0	0	0	1	0	0	0	15734	72	3	4	1221	4	TCF4	18	52937154	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	362067	52937154	25140094	1794	6191										
NARS	4677	broad.mit.edu	37	chr18	55273959	55273959	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgtcaaaagtcaggaaaggAcactcagcttccacgtgagt	10	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:55273959A>G	ENST00000256854.5	-	10	1481	c.1026T>C	c.(1024-1026)tgT>tgC	p.C342C	NARS_ENST00000423481.2_Silent_p.C93C	NM_004539.3	NP_004530.1	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase	342					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.C342C(1)		breast(1)|endometrium(5)|large_intestine(5)|lung(8)|skin(1)	20		Colorectal(73;0.227)			L-Asparagine(DB00174)	TCAGGAAAGGACACTCAGCTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	18											183	151	162					18																	55273959		2203	4300	6503	53424957	SO:0001819	synonymous_variant	4677			D84273	CCDS32837.1	18q21.31	2014-05-06			ENSG00000134440	ENSG00000134440	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	7643	protein-coding gene	gene with protein product	"asparagine tRNA ligase 1, cytoplasmic"	108410				6836455, 9421509	Standard	NM_004539		Approved	NARS1	uc002lgs.2	O43776	OTTHUMG00000180125	ENST00000256854.5:c.1026T>C	18.37:g.55273959A>G			53424957	B4DG16|Q53GU6	Silent	SNP	ENST00000256854.5	37	CCDS32837.1																																																																																				0.473	NARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449872.2	NM_004539		G	55273959	A	G	55273959	2	3	47	1	0	0	0	0	0	0	0	1	10200	273	10	4		4	NARS	18	55273959	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2336805	55273959	22803289	1795	6192										
ATP8B1	5205	broad.mit.edu	37	chr18	55319293	55319293	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaaatgcagatggaaagaGaacatgtattccagcactat	9	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:55319293G>T	ENST00000283684.4	-	25	3372	c.3373C>A	c.(3373-3375)Ctc>Atc	p.L1125I	RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.L1125I|RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	1125					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.L1125I(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				GATGGAAAGAGAACATGTATT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	18											82	78	79					18																	55319293		2203	4300	6503	53470291	SO:0001583	missense	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.3373C>A	18.37:g.55319293G>T	ENSP00000283684:p.Leu1125Ile		53470291	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	G	5.975	0.363907	0.11296	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	D;D	0.89050	-2.46;-2.46	5.7	4.8	0.61643	.	0.199921	0.45126	N	0.000385	T	0.79787	0.4506	N	0.21194	0.64	0.47374	D	0.999406	B	0.10296	0.003	B	0.09377	0.004	T	0.72587	-0.4248	10	0.02654	T	1	.	15.6861	0.77411	0.0:0.0:0.8532:0.1468	.	1125	O43520	AT8B1_HUMAN	I	1125	ENSP00000283684:L1125I;ENSP00000445359:L1125I	ENSP00000283684:L1125I	L	-	1	0	ATP8B1	53470291	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	2.917000	0.48821	1.319000	0.45190	0.655000	0.94253	CTC		0.308	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		T	55319293	G	T	55319293	3	4	47	1	0	0	0	0	1	0	0	0	1195	942	33	2	394	2	ATP8B1	18	55319293	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	45334	55319293	22757955	1796	6193										
MC4R	4160	broad.mit.edu	37	chr18	58039221	58039221	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccgagtcaatgacattatcaAtattcactgtgaaactctgt	6	9	4	2	rs13447330		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:58039221A>C	ENST00000299766.3	-	1	780	c.362T>G	c.(361-363)aTt>aGt	p.I121S		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	121					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)	p.I121S(1)		endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				GACATTATCAATATTCACTGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18	GRCh37	CM032286	MC4R	M	rs13447330						101	90	94					18																	58039221		2203	4300	6503	56190201	SO:0001583	missense	4160			AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"GPCR / Class A : Melanocortin receptors"	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.362T>G	18.37:g.58039221A>C	ENSP00000299766:p.Ile121Ser		56190201	B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	37	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.961619	0.74016	.	.	ENSG00000166603	ENST00000299766	T	0.36878	1.23	5.71	5.71	0.89125	GPCR, rhodopsin-like superfamily (1);	0.091092	0.85682	D	0.000000	T	0.54078	0.1836	M	0.80847	2.515	0.58432	D	0.99999	P	0.45212	0.853	P	0.51297	0.665	T	0.60429	-0.7265	10	0.87932	D	0	.	13.9343	0.64015	1.0:0.0:0.0:0.0	.	121	P32245	MC4R_HUMAN	S	121	ENSP00000299766:I121S	ENSP00000299766:I121S	I	-	2	0	MC4R	56190201	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	9.339000	0.96797	2.186000	0.69663	0.533000	0.62120	ATT		0.423	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		C	58039221	A	C	58039221	3	2	47	1	0	0	0	0	1	0	0	0	9396	101	4	4	640	4	MC4R	18	58039221	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2719928	58039221	20038027	1797	6194										
CDH20	28316	broad.mit.edu	37	chr18	59203827	59203827	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctagaccgggaagaattttCttggcataatatcactgtcc	8	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:59203827C>A	ENST00000262717.4	+	8	1771	c.1373C>A	c.(1372-1374)tCt>tAt	p.S458Y	CDH20_ENST00000536675.2_Missense_Mutation_p.S458Y|CDH20_ENST00000538374.1_Missense_Mutation_p.S458Y			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	458	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S458Y(1)		breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GAAGAATTTTCTTGGCATAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	18											120	120	120					18																	59203827		2203	4300	6503	57354807	SO:0001583	missense	28316			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1373C>A	18.37:g.59203827C>A	ENSP00000262717:p.Ser458Tyr		57354807	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.038185	0.54896	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.62639	0.01;0.01;0.01	5.22	5.22	0.72569	Cadherin (4);Cadherin-like (1);	0.236222	0.44688	D	0.000425	T	0.75273	0.3827	M	0.85197	2.74	0.47183	D	0.99934	B	0.27013	0.166	B	0.40101	0.319	T	0.76484	-0.2942	10	0.62326	D	0.03	.	19.1249	0.93378	0.0:1.0:0.0:0.0	.	458	Q9HBT6	CAD20_HUMAN	Y	458	ENSP00000444767:S458Y;ENSP00000442226:S458Y;ENSP00000262717:S458Y	ENSP00000262717:S458Y	S	+	2	0	CDH20	57354807	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.733000	0.62036	2.599000	0.87857	0.542000	0.68232	TCT		0.408	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		A	59203827	C	A	59203827	3	1	47	1	0	0	0	0	1	0	0	0	3112	913	32	2	1399	2	CDH20	18	59203827	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1164606	59203827	18873421	1798	6195										
TNFRSF11A	8792	broad.mit.edu	37	chr18	60015457	60015457	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagcattatgagcatctgggAcggtgctgtaacaaatgtga	12	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:60015457A>G	ENST00000586569.1	+	2	170	c.132A>G	c.(130-132)ggA>ggG	p.G44G	TNFRSF11A_ENST00000269485.7_Silent_p.G44G	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	44					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)	p.G44G(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				AGCATCTGGGACGGTGCTGTA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	18											146	120	129					18																	60015457		2203	4300	6503	58166437	SO:0001819	synonymous_variant	8792			AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"Tumor necrosis factor receptor superfamily", "CD molecules"	11908	protein-coding gene	gene with protein product		603499	"tumor necrosis factor receptor superfamily, member 11a, activator of NFKB", "Paget disease of bone 2", "loss of heterozygosity, 18, chromosomal region 1"	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.132A>G	18.37:g.60015457A>G			58166437	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	37	CCDS11980.1																																																																																				0.493	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			G	60015457	A	G	60015457	2	3	47	1	0	0	0	0	0	0	0	1	16323	262	10	4		4	TNFRSF11A	18	60015457	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	811630	60015457	18061791	1799	6196										
SERPINB12	89777	broad.mit.edu	37	chr18	61232724	61232724	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacgcaaaaaggcctctacaGaattggcttcatagaggagg	12	8	2	2	rs34833530		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:61232724G>T	ENST00000269491.1	+	6	692	c.692G>T	c.(691-693)aGa>aTa	p.R231I	SERPINB12_ENST00000382768.1_Missense_Mutation_p.R251I	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	231					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R231I(1)		kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						GGCCTCTACAGAATTGGCTTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											150	134	139					18																	61232724		2203	4300	6503	59383704	SO:0001583	missense	89777			AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"Serine (or cysteine) peptidase inhibitors"	14220	protein-coding gene	gene with protein product		615662	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.692G>T	18.37:g.61232724G>T	ENSP00000269491:p.Arg231Ile		59383704	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	37	CCDS11984.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.707356	0.30322	.	.	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.84730	-1.89;-1.89	5.35	0.483	0.16820	Serpin domain (3);	0.508110	0.21035	N	0.081277	D	0.90349	0.6980	M	0.82716	2.605	0.21020	N	0.99981	D;D	0.60160	0.987;0.966	P;P	0.62885	0.908;0.837	D	0.83571	0.0112	10	0.59425	D	0.04	.	11.0541	0.47907	0.5384:0.0:0.4616:0.0	.	251;231	Q3SYB4;Q96P63	.;SPB12_HUMAN	I	231;251	ENSP00000269491:R231I;ENSP00000372218:R251I	ENSP00000269491:R231I	R	+	2	0	SERPINB12	59383704	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.135000	0.15952	-0.122000	0.11766	-0.145000	0.13849	AGA		0.473	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		T	61232724	G	T	61232724	3	4	47	1	0	0	0	0	1	0	0	0	14136	942	33	2	714	2	SERPINB12	18	61232724	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1217267	61232724	16844524	1800	6197										
SERPINB13	5275	broad.mit.edu	37	chr18	61261696	61261696	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggacagggagtttaagaaaGaaaatactaaggaagagaaa	13	2	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:61261696G>T	ENST00000344731.5	+	6	682	c.580G>T	c.(580-582)Gaa>Taa	p.E194*	SERPINB13_ENST00000269489.5_Nonsense_Mutation_p.E194*	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	194					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E194*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						GTTTAAGAAAGAAAATACTAA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											92	90	91					18																	61261696		2203	4300	6503	59412676	SO:0001587	stop_gained	5275			AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.580G>T	18.37:g.61261696G>T	ENSP00000341584:p.Glu194*		59412676	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Nonsense_Mutation	SNP	ENST00000344731.5	37	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	G	37	6.154267	0.97329	.	.	ENSG00000197641	ENST00000269489;ENST00000539341;ENST00000344731	.	.	.	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	19.2577	0.93952	0.0:0.0:1.0:0.0	.	.	.	.	X	194;112;194	.	ENSP00000269489:E194X	E	+	1	0	SERPINB13	59412676	0.008000	0.16893	1.000000	0.80357	0.996000	0.88848	1.474000	0.35398	2.854000	0.98071	0.655000	0.94253	GAA		0.393	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		T	61261696	G	T	61261696	4	4	47	1	0	0	0	0	0	1	0	0	14137	943	33	2	598	2	SERPINB13	18	61261696	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	28972	61261696	16815552	1801	6198										
RTTN	25914	broad.mit.edu	37	chr18	67817852	67817852	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaatgtcatacctcactttCgggctcttgaatgccaaata	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:67817852C>T	ENST00000255674.6	-	15	2333	c.2047G>A	c.(2047-2049)Gaa>Aaa	p.E683K	RTTN_ENST00000454359.1_Missense_Mutation_p.E683K|RTTN_ENST00000437017.1_Missense_Mutation_p.E683K	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	683					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.E683K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				ACCTCACTTTCGGGCTCTTGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											102	101	101					18																	67817852		1817	4079	5896	65968832	SO:0001583	missense	25914			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.2047G>A	18.37:g.67817852C>T	ENSP00000255674:p.Glu683Lys		65968832	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	T	2.189	-0.385805	0.04966	.	.	ENSG00000176225	ENST00000255674;ENST00000454359;ENST00000437017	T;T;T	0.64618	3.53;-0.11;-0.11	5.55	2.93	0.34026	Armadillo-type fold (1);	0.195181	0.48286	N	0.000191	T	0.17789	0.0427	N	0.00170	-1.935	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39941	-0.9589	10	0.02654	T	1	.	8.1482	0.31124	0.0:0.071:0.3675:0.5615	.	683	Q86VV8	RTTN_HUMAN	K	683	ENSP00000255674:E683K;ENSP00000402352:E683K;ENSP00000399520:E683K	ENSP00000255674:E683K	E	-	1	0	RTTN	65968832	0.052000	0.20516	0.893000	0.35052	0.685000	0.39939	-0.061000	0.11693	0.364000	0.24374	-0.360000	0.07572	GAA		0.338	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		T	67817852	C	T	67817852	3	4	47	1	0	0	0	0	1	0	0	0	13774	893	31	1	4773	1	RTTN	18	67817852	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	6556156	67817852	10259396	1802	6199										
ZNF407	55628	broad.mit.edu	37	chr18	72343698	72343698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacaagcacatgggccacaGaaggtcttttcctgtgatct	9	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:72343698G>T	ENST00000299687.5	+	1	723	c.723G>T	c.(721-723)caG>caT	p.Q241H	ZNF407_ENST00000582337.1_Missense_Mutation_p.Q241H|ZNF407_ENST00000577538.1_Missense_Mutation_p.Q241H|ZNF407_ENST00000309902.6_Missense_Mutation_p.Q241H	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Q241H(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		ATGGGCCACAGAAGGTCTTTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	18											137	140	139					18																	72343698		2056	4214	6270	70472686	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.723G>T	18.37:g.72343698G>T	ENSP00000299687:p.Gln241His		70472686	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	9.173	1.021582	0.19433	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.15372	2.43;2.43	5.3	1.29	0.21616	Zinc finger, U1-type (1);	1.276180	0.06487	U	0.733928	T	0.16938	0.0407	L	0.47016	1.485	0.09310	N	1	B;B;B	0.14438	0.004;0.01;0.006	B;B;B	0.16289	0.01;0.015;0.005	T	0.33675	-0.9859	10	0.59425	D	0.04	.	7.2177	0.25969	0.0726:0.4969:0.3137:0.1168	.	241;241;241	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	H	241	ENSP00000299687:Q241H;ENSP00000310359:Q241H	ENSP00000299687:Q241H	Q	+	3	2	ZNF407	70472686	0.000000	0.05858	0.000000	0.03702	0.262000	0.26303	0.017000	0.13399	0.408000	0.25621	0.533000	0.62120	CAG		0.448	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72343698	G	T	72343698	3	4	47	1	0	0	0	0	1	0	0	0	17926	933	33	2	725	2	ZNF407	18	72343698	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4525846	72343698	5733550	1803	6200										
ZNF407	55628	broad.mit.edu	37	chr18	72344389	72344389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacacagatgaaaacacacGatgcagaatcagtgctgaaa	9	8	1	4	rs199633454	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:72344389G>A	ENST00000299687.5	+	1	1414	c.1414G>A	c.(1414-1416)Gat>Aat	p.D472N	ZNF407_ENST00000582337.1_Missense_Mutation_p.D472N|ZNF407_ENST00000577538.1_Missense_Mutation_p.D472N|ZNF407_ENST00000309902.6_Missense_Mutation_p.D472N	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D472N(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAAAACACACGATGCAGAATC	0.463													G|||	4	0.000798722	0.003	0	5008	,	,		21783	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18						G	ASN/ASP,ASN/ASP,ASN/ASP	11,4131		0,11,2060	48	52	50		1414,1414,1414	5.8	0	18		50	0,8410		0,0,4205	yes	missense,missense,missense	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	23,23,23	0,11,6265	AA,AG,GG		0.0,0.2656,0.0876	possibly-damaging,possibly-damaging,possibly-damaging	472/1816,472/1661,472/2249	72344389	11,12541	2071	4205	6276	70473377	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1414G>A	18.37:g.72344389G>A	ENSP00000299687:p.Asp472Asn		70473377	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591501	0.46214	0.002656	0.0	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.10860	2.83;3.31	5.83	5.83	0.93111	.	7.056580	0.02175	U	0.060001	T	0.28863	0.0716	L	0.43152	1.355	0.20307	N	0.999919	D;B;D	0.67145	0.996;0.333;0.993	P;B;P	0.57009	0.811;0.061;0.652	T	0.55309	-0.8161	10	0.27082	T	0.32	.	18.3161	0.90221	0.0:0.0:1.0:0.0	.	472;472;472	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	N	472	ENSP00000299687:D472N;ENSP00000310359:D472N	ENSP00000299687:D472N	D	+	1	0	ZNF407	70473377	0.808000	0.29022	0.018000	0.16275	0.013000	0.08279	2.748000	0.47483	0.774000	0.33427	0.528000	0.53228	GAT		0.463	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72344389	G	A	72344389	3	1	47	1	0	0	0	0	1	0	0	0	17926	1058	37	1	1416	1	ZNF407	18	72344389	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	691	72344389	5732859	1804	6201										
ZNF407	55628	broad.mit.edu	37	chr18	72344916	72344916	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattcattggttcaaccaaaGactttgcaatcatctaacag	5	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:72344916G>T	ENST00000299687.5	+	1	1941	c.1941G>T	c.(1939-1941)aaG>aaT	p.K647N	ZNF407_ENST00000582337.1_Missense_Mutation_p.K647N|ZNF407_ENST00000577538.1_Missense_Mutation_p.K647N|ZNF407_ENST00000309902.6_Missense_Mutation_p.K647N	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	647					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K647N(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TTCAACCAAAGACTTTGCAAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	18											74	74	74					18																	72344916		1849	4085	5934	70473904	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1941G>T	18.37:g.72344916G>T	ENSP00000299687:p.Lys647Asn		70473904	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067877	0.36470	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.10860	2.83;3.27	5.76	1.76	0.24704	.	0.419632	0.14960	U	0.288439	T	0.18882	0.0453	M	0.61703	1.905	0.09310	N	1	D;D;P	0.71674	0.986;0.998;0.868	P;P;B	0.59889	0.663;0.865;0.383	T	0.14504	-1.0470	10	0.25106	T	0.35	.	4.4974	0.11844	0.2456:0.0:0.5289:0.2256	.	647;647;647	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	N	647	ENSP00000299687:K647N;ENSP00000310359:K647N	ENSP00000299687:K647N	K	+	3	2	ZNF407	70473904	0.087000	0.21565	0.003000	0.11579	0.877000	0.50540	1.921000	0.40035	-0.115000	0.11915	0.377000	0.23210	AAG		0.358	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72344916	G	T	72344916	3	4	47	1	0	0	0	0	1	0	0	0	17926	933	33	2	1943	2	ZNF407	18	72344916	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	527	72344916	5732332	1805	6202										
ZNF407	55628	broad.mit.edu	37	chr18	72775641	72775641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccccccgaggcatcctcagcCctggatgcattgctctgtgc	10	17	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:72775641C>T	ENST00000299687.5	+	8	5964	c.5964C>T	c.(5962-5964)gcC>gcT	p.A1988A		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1988					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A1988A(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CATCCTCAGCCCTGGATGCAT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	18											15	19	18					18																	72775641		2086	4208	6294	70904629	SO:0001819	synonymous_variant	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.5964C>T	18.37:g.72775641C>T			70904629	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.617	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72775641	C	T	72775641	2	4	47	1	0	0	0	0	0	0	0	1	17926	610	22	3		3	ZNF407	18	72775641	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	430725	72775641	5301607	1806	6203										
ADNP2	22850	broad.mit.edu	37	chr18	77894049	77894049	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataagcttagatctgtgatTtcagaacatattaagaggac	8	5	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr18:77894049T>G	ENST00000262198.4	+	4	1208	c.753T>G	c.(751-753)atT>atG	p.I251M		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	251					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I251M(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GATCTGTGATTTCAGAACATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	18											73	74	74					18																	77894049		2203	4300	6503	75995040	SO:0001583	missense	22850			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.753T>G	18.37:g.77894049T>G	ENSP00000262198:p.Ile251Met		75995040	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	37	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755595	0.69648	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.41	-6.42	0.01932	.	0.000000	0.64402	D	0.000004	T	0.41558	0.1164	L	0.32530	0.975	0.29063	N	0.883761	D	0.89917	1.0	D	0.91635	0.999	T	0.45948	-0.9226	8	.	.	.	-27.2991	8.9059	0.35523	0.1076:0.494:0.0:0.3985	.	251	Q6IQ32	ADNP2_HUMAN	M	251	.	.	I	+	3	3	ADNP2	75995040	0.994000	0.37717	0.720000	0.30636	0.999000	0.98932	0.035000	0.13797	-1.500000	0.01819	0.533000	0.62120	ATT		0.448	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		G	77894049	T	G	77894049	3	3	47	1	0	0	0	0	1	0	0	0	324	1829	64	4	763	4	ADNP2	18	77894049	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	5118408	77894049	183199	1807	6204										
RPS15	6209	broad.mit.edu	37	chr19	1440147	1440147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgccgcccatggagaagccGgaagtggtgaagacgcacct	15	12	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:1440147G>A	ENST00000586686.2	+	3	258	c.219G>A	c.(217-219)ccG>ccA	p.P73P	RPS15_ENST00000586096.2_Silent_p.P73P|RPS15_ENST00000585665.1_Silent_p.P40P|AC027307.3_ENST00000594262.1_5'Flank|RPS15_ENST00000593052.1_Silent_p.P80P|RPS15_ENST00000589656.2_Silent_p.P73P|RPS15_ENST00000233609.4_Silent_p.P46P|RPS15_ENST00000591032.1_Silent_p.P40P|RPS15_ENST00000591804.2_Silent_p.P40P			P62841	RS15_HUMAN	ribosomal protein S15	73					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|osteoblast differentiation (GO:0001649)|ribosomal small subunit biogenesis (GO:0042274)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.P73P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGAGAAGCCGGAAGTGGTGA	0.657																																					Ovarian(170;79 2680 5719 44260)											1	Substitution - coding silent(1)	large_intestine(1)	19											23	28	26					19																	1440147		2203	4299	6502	1391147	SO:0001819	synonymous_variant	6209				CCDS12067.1	19p13.3	2012-12-20			ENSG00000115268	ENSG00000115268		"S ribosomal proteins"	10388	protein-coding gene	gene with protein product	"40S ribosomal protein S15", "homolog of rat insulinoma", "insulinoma protein"	180535				2159154	Standard	NM_001018		Approved	RIG, MGC111130, S15	uc002lsp.1	P62841	OTTHUMG00000140099	ENST00000586686.2:c.219G>A	19.37:g.1440147G>A			1391147	A5D8V9|P11174|Q3KRA1|Q9UDC2	Silent	SNP	ENST00000586686.2	37	CCDS12067.1																																																																																				0.657	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018		A	1440147	G	A	1440147	2	1	47	1	0	0	0	0	0	0	0	1	13662	1103	39	1		1	RPS15	19	1440147	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09		1440147	57688836	1808	6205										
ITGB1BP3	27231	broad.mit.edu	37	chr19	3941108	3941108	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgatccccccggcctcttCgatggccacgtgtggcccat	10	18	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:3941108C>T	ENST00000168977.2	+	7	725	c.435C>T	c.(433-435)ttC>ttT	p.F145F	NMRK2_ENST00000593949.1_Silent_p.F150F|NMRK2_ENST00000599576.1_Intron	NM_170678.2	NP_733778.1	Q9NPI5	NRK2_HUMAN	nicotinamide riboside kinase 2	145					NAD biosynthetic process (GO:0009435)|negative regulation of myoblast differentiation (GO:0045662)	intracellular (GO:0005622)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)	p.F145F(1)									CCGGCCTCTTCGATGGCCACG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	19											140	122	128					19																	3941108		2203	4300	6503	3892108	SO:0001819	synonymous_variant	27231			AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009			17871	protein-coding gene	gene with protein product	"muscle-specific beta 1 integrin binding protein", "nicotinamide riboside kinase 2"	608705	"integrin beta 1 binding protein 3"	ITGB1BP3		10613898, 15137942	Standard	NM_170678		Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.435C>T	19.37:g.3941108C>T			3892108	B7ZKR3|Q52M81|Q9NZK3	Silent	SNP	ENST00000168977.2	37	CCDS12115.1																																																																																				0.582	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1	NM_014446, NM_170678		T	3941108	C	T	3941108	2	4	47	1	0	0	0	0	0	0	0	1	7914	883	31	1		1	ITGB1BP3	19	3941108	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2500961	3941108	55187875	1809	6206										
ANKRD24	170961	broad.mit.edu	37	chr19	4217067	4217067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agagaccacgggagtggaggCcatgggggtggaggccacaa	19	8	0	1	rs537535275		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:4217067C>T	ENST00000600132.1	+	18	2186	c.1910C>T	c.(1909-1911)gCc>gTc	p.A637V	ANKRD24_ENST00000262970.5_Missense_Mutation_p.A727V|ANKRD24_ENST00000318934.4_Missense_Mutation_p.A637V	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	637								p.A727V(1)|p.A503V(1)|p.A637V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GGAGTGGAGGCCATGGGGGTG	0.567													C|||	1	0.000199681	0	0	5008	,	,		19551	0.001		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	19											55	66	62					19																	4217067		2088	4201	6289	4168067	SO:0001583	missense	170961			AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1910C>T	19.37:g.4217067C>T	ENSP00000471252:p.Ala637Val		4168067	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	-	4.327	0.059997	0.08339	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.37411	1.2;1.28	2.81	0.487	0.16842	.	.	.	.	.	T	0.13030	0.0316	N	0.08118	0	0.09310	N	1	P;P	0.38677	0.51;0.642	B;B	0.25405	0.016;0.06	T	0.13980	-1.0489	9	0.27785	T	0.31	.	6.3276	0.21253	0.1815:0.7084:0.0:0.1102	.	637;727	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	V	637;727	ENSP00000321731:A637V;ENSP00000262970:A727V	ENSP00000262970:A727V	A	+	2	0	ANKRD24	4168067	0.030000	0.19436	0.011000	0.14972	0.219000	0.24729	0.196000	0.17176	0.204000	0.20548	0.185000	0.17295	GCC		0.567	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		T	4217067	C	T	4217067	3	4	47	1	0	0	0	0	1	0	0	0	653	739	26	3	1976	3	ANKRD24	19	4217067	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	275959	4217067	54911916	1810	6207										
TMEM146	257062	broad.mit.edu	37	chr19	5745965	5745965	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caccccctcaaccggagtttCgggctgtcttttgactataa	8	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:5745965C>T	ENST00000381624.3	+	9	760	c.699C>T	c.(697-699)ttC>ttT	p.F233F	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	233					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.F233F(3)									ACCGGAGTTTCGGGCTGTCTT	0.532																																																3	Substitution - coding silent(3)	large_intestine(3)	19											167	160	163					19																	5745965		1888	4121	6009	5696965	SO:0001819	synonymous_variant	257062			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.699C>T	19.37:g.5745965C>T			5696965	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																				0.532	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5745965	C	T	5745965	2	4	47	1	0	0	0	0	0	0	0	1	16099	883	31	1		1	TMEM146	19	5745965	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1528898	5745965	53383018	1811	6208										
ACSBG2	81616	broad.mit.edu	37	chr19	6182780	6182780	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggcaccttggtaagtactCtaaaggaggtaaaacctact	10	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:6182780C>A	ENST00000586696.1	+	9	1201	c.925C>A	c.(925-927)Cta>Ata	p.L309I	ACSBG2_ENST00000591403.1_Missense_Mutation_p.L309I|ACSBG2_ENST00000588304.1_Missense_Mutation_p.L259I|ACSBG2_ENST00000252669.5_Missense_Mutation_p.L309I|ACSBG2_ENST00000588485.1_Missense_Mutation_p.L122I|ACSBG2_ENST00000591741.1_3'UTR			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	309					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.L309I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGTAAGTACTCTAAAGGAGGT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	60	63					19																	6182780		2203	4300	6503	6133780	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.925C>A	19.37:g.6182780C>A	ENSP00000465589:p.Leu309Ile		6133780	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.746575	0.49257	.	.	ENSG00000130377	ENST00000252669	T	0.38401	1.14	5.01	-3.16	0.05217	AMP-dependent synthetase/ligase (1);	0.000000	0.34291	N	0.004088	T	0.51736	0.1692	M	0.80332	2.49	0.20975	N	0.999818	D;D	0.64830	0.994;0.993	D;D	0.75484	0.986;0.951	T	0.43877	-0.9364	10	0.87932	D	0	-23.4973	6.7632	0.23552	0.1138:0.5013:0.0:0.3849	.	309;309	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	I	309	ENSP00000252669:L309I	ENSP00000252669:L309I	L	+	1	2	ACSBG2	6133780	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.025000	0.13577	-0.328000	0.08539	0.455000	0.32223	CTA		0.478	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		A	6182780	C	A	6182780	3	1	47	1	0	0	0	0	1	0	0	0	174	912	32	2	955	2	ACSBG2	19	6182780	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	436815	6182780	52946203	1812	6209										
FBN3	84467	broad.mit.edu	37	chr19	8183824	8183824	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcagctcatgcccagggggAcactggcacttgtagctccc	12	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:8183824A>G	ENST00000600128.1	-	26	3708	c.3294T>C	c.(3292-3294)tgT>tgC	p.C1098C	FBN3_ENST00000270509.2_Silent_p.C1098C|FBN3_ENST00000601739.1_Silent_p.C1098C			Q75N90	FBN3_HUMAN	fibrillin 3	1098	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.C1098C(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCCCAGGGGGACACTGGCACT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											160	117	131					19																	8183824		2203	4300	6503	8089824	SO:0001819	synonymous_variant	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3294T>C	19.37:g.8183824A>G			8089824	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																				0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		G	8183824	A	G	8183824	2	3	47	1	0	0	0	0	0	0	0	1	5723	273	10	4		4	FBN3	19	8183824	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2001044	8183824	50945159	1813	6210										
PRAM1	84106	broad.mit.edu	37	chr19	8563890	8563890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaggcctttttgggaaaggCgctggagtcgcgcttcggct	17	9	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:8563890C>T	ENST00000423345.4	-	2	1322	c.802G>A	c.(802-804)Gcc>Acc	p.A268T	PRAM1_ENST00000255612.3_Missense_Mutation_p.A268T			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	316	Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)	p.A268T(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						TTGGGAAAGGCGCTGGAGTCG	0.642																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	19											37	41	40					19																	8563890		2188	4287	6475	8469890	SO:0001583	missense	84106			BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.802G>A	19.37:g.8563890C>T	ENSP00000408342:p.Ala268Thr		8469890	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	C	4.798	0.148302	0.09134	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.16457	2.34;2.34	3.73	-7.45	0.01374	.	1.283650	0.05976	N	0.643324	T	0.04634	0.0126	N	0.01576	-0.805	0.09310	N	1	B;B	0.24963	0.03;0.115	B;B	0.12156	0.005;0.007	T	0.40813	-0.9543	10	0.21014	T	0.42	.	8.0552	0.30602	0.0:0.1214:0.2274:0.6512	.	268;316	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	T	268	ENSP00000255612:A268T;ENSP00000408342:A268T	ENSP00000255612:A268T	A	-	1	0	PRAM1	8469890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.672000	0.05244	-2.019000	0.00942	-0.218000	0.12543	GCC		0.642	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		T	8563890	C	T	8563890	3	4	47	1	0	0	0	0	1	0	0	0	12457	768	27	1	1243	1	PRAM1	19	8563890	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	380066	8563890	50565093	1814	6211										
MUC16	94025	broad.mit.edu	37	chr19	9048443	9048443	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtttctagttcaccaggaGaaagaatcagagttggaata	11	5	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9048443G>T	ENST00000397910.4	-	5	33391	c.33188C>A	c.(33187-33189)tCt>tAt	p.S11063Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11065	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S11063Y(1)|p.S6696Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCACCAGGAGAAAGAATCAG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	19											85	77	80					19																	9048443		1896	4124	6020	8909443	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33188C>A	19.37:g.9048443G>T	ENSP00000381008:p.Ser11063Tyr		8909443	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.351	0.432881	0.12045	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.05	1.98	0.26296	.	.	.	.	.	T	0.04227	0.0117	L	0.55481	1.735	.	.	.	P	0.40332	0.713	B	0.40410	0.328	T	0.14504	-1.0470	8	0.87932	D	0	.	7.6016	0.28079	0.0:0.0:0.7483:0.2517	.	11063	B5ME49	.	Y	11063	ENSP00000381008:S11063Y	ENSP00000381008:S11063Y	S	-	2	0	MUC16	8909443	0.000000	0.05858	0.001000	0.08648	0.158000	0.22134	0.100000	0.15231	0.803000	0.34113	0.431000	0.28591	TCT		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9048443	G	T	9048443	3	4	47	1	0	0	0	0	1	0	0	0	10003	942	33	2	10655	2	MUC16	19	9048443	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	484553	9048443	50080540	1815	6212										
MUC16	94025	broad.mit.edu	37	chr19	9050212	9050212	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcagagctgtggtggtggtCtccattctttttgtccctcc	10	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9050212C>A	ENST00000397910.4	-	5	31622	c.31419G>T	c.(31417-31419)gaG>gaT	p.E10473D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10475	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E6106D(1)|p.E10473D(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGTGGTGGTCTCCATTCTTT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											345	340	342					19																	9050212		2079	4206	6285	8911212	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31419G>T	19.37:g.9050212C>A	ENSP00000381008:p.Glu10473Asp		8911212	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	11.35	1.613375	0.28712	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	4.18	3.13	0.36017	.	.	.	.	.	T	0.04815	0.0130	L	0.40543	1.245	.	.	.	P	0.46142	0.873	P	0.47134	0.539	T	0.22173	-1.0224	8	0.87932	D	0	.	10.3616	0.43998	0.0:0.8025:0.1975:0.0	.	10473	B5ME49	.	D	10473	ENSP00000381008:E10473D	ENSP00000381008:E10473D	E	-	3	2	MUC16	8911212	0.021000	0.18746	0.803000	0.32268	0.035000	0.12851	0.054000	0.14205	1.332000	0.45431	0.580000	0.79431	GAG		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9050212	C	A	9050212	3	1	47	1	0	0	0	0	1	0	0	0	10003	912	32	2	12424	2	MUC16	19	9050212	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1769	9050212	50078771	1816	6213										
MUC16	94025	broad.mit.edu	37	chr19	9065503	9065503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgattctgccaggatgggggAagtagggaacttaatgattt	14	4	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9065503A>G	ENST00000397910.4	-	3	22146	c.21943T>C	c.(21943-21945)Tcc>Ccc	p.S7315P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7317	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S7315P(2)|p.S2948P(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGATGGGGGAAGTAGGGAAC	0.448																																																3	Substitution - Missense(3)	large_intestine(3)	19											138	132	134					19																	9065503		1913	4110	6023	8926503	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21943T>C	19.37:g.9065503A>G	ENSP00000381008:p.Ser7315Pro		8926503	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	N	5.840	0.339144	0.11069	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	2.97	2.97	0.34412	.	.	.	.	.	T	0.07279	0.0184	L	0.32530	0.975	.	.	.	D	0.71674	0.998	D	0.77004	0.989	T	0.16689	-1.0394	8	0.87932	D	0	.	7.7229	0.28742	1.0:0.0:0.0:0.0	.	7315	B5ME49	.	P	7315	ENSP00000381008:S7315P	ENSP00000381008:S7315P	S	-	1	0	MUC16	8926503	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.201000	0.17276	1.598000	0.50083	0.317000	0.21355	TCC		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9065503	A	G	9065503	3	3	47	1	0	0	0	0	1	0	0	0	10003	246	9	4	21908	4	MUC16	19	9065503	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	15291	9065503	50063480	1817	6214										
MUC16	94025	broad.mit.edu	37	chr19	9073357	9073357	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtttccaaggttgatgtgtCtaaggcaagtggaatctttg	13	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9073357C>A	ENST00000397910.4	-	3	14292	c.14089G>T	c.(14089-14091)Gac>Tac	p.D4697Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4699	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.D4697Y(2)|p.D330Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTTGATGTGTCTAAGGCAAGT	0.473																																																3	Substitution - Missense(3)	large_intestine(3)	19											184	172	176					19																	9073357		1945	4149	6094	8934357	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14089G>T	19.37:g.9073357C>A	ENSP00000381008:p.Asp4697Tyr		8934357	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	6.409	0.443599	0.12164	.	.	ENSG00000181143	ENST00000397910	T	0.24350	1.86	1.8	-0.635	0.11512	.	.	.	.	.	T	0.25975	0.0633	L	0.39898	1.24	.	.	.	D	0.62365	0.991	P	0.54238	0.746	T	0.29058	-1.0024	8	0.87932	D	0	.	2.1919	0.03901	0.3045:0.4965:0.0:0.1991	.	4697	B5ME49	.	Y	4697	ENSP00000381008:D4697Y	ENSP00000381008:D4697Y	D	-	1	0	MUC16	8934357	0.000000	0.05858	0.000000	0.03702	0.578000	0.36192	0.167000	0.16602	-0.093000	0.12396	0.313000	0.20887	GAC		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9073357	C	A	9073357	3	1	47	1	0	0	0	0	1	0	0	0	10003	913	32	2	29762	2	MUC16	19	9073357	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7854	9073357	50055626	1818	6215										
ZNF560	147741	broad.mit.edu	37	chr19	9578100	9578100	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttctcaccagtgtgagttCtcaaatgagcaaaaagagat	9	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9578100C>T	ENST00000301480.4	-	10	1736	c.1523G>A	c.(1522-1524)aGa>aAa	p.R508K		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R508K(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						AGTGTGAGTTCTCAAATGAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	117	115					19																	9578100		2203	4300	6503	9439100	SO:0001583	missense	147741			AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1523G>A	19.37:g.9578100C>T	ENSP00000301480:p.Arg508Lys		9439100	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298785	0.40694	.	.	ENSG00000198028	ENST00000301480	T	0.18338	2.22	2.05	2.05	0.26809	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18800	0.0451	L	0.28115	0.83	0.20764	N	0.999853	D	0.58268	0.982	P	0.53518	0.728	T	0.12451	-1.0547	9	0.35671	T	0.21	.	10.1291	0.42667	0.0:1.0:0.0:0.0	.	508	Q96MR9	ZN560_HUMAN	K	508	ENSP00000301480:R508K	ENSP00000301480:R508K	R	-	2	0	ZNF560	9439100	0.000000	0.05858	0.004000	0.12327	0.312000	0.27988	-1.174000	0.03105	1.446000	0.47643	0.491000	0.48974	AGA		0.408	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		T	9578100	C	T	9578100	3	4	47	1	0	0	0	0	1	0	0	0	18030	913	32	3	853	3	ZNF560	19	9578100	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	504743	9578100	49550883	1819	6216										
ZNF121	7675	broad.mit.edu	37	chr19	9677536	9677536	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgtattcaaaggatttgtCtcctatccacgttctctggt	7	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9677536C>T	ENST00000586602.1	-	6	669	c.253G>A	c.(253-255)Gac>Aac	p.D85N	ZNF121_ENST00000320451.6_Missense_Mutation_p.D85N			P58317	ZN121_HUMAN	zinc finger protein 121	85					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D85N(1)		breast(3)|kidney(4)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	24						AAGGATTTGTCTCCTATCCAC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											112	97	102					19																	9677536		2203	4300	6503	9538536	SO:0001583	missense	7675			M99593	CCDS32902.1	19p13.2	2013-01-08	2006-08-22			ENSG00000197961		"Zinc fingers, C2H2-type"	12904	protein-coding gene	gene with protein product		194628	"zinc finger protein 121 (clone ZHC32)"	D19S204		8468057	Standard	NM_001008727		Approved	ZHC32, ZNF20	uc010xkp.1	P58317		ENST00000586602.1:c.253G>A	19.37:g.9677536C>T	ENSP00000468643:p.Asp85Asn		9538536		Missense_Mutation	SNP	ENST00000586602.1	37		.	.	.	.	.	.	.	.	.	.	C	9.828	1.187675	0.21870	.	.	ENSG00000197961	ENST00000538300;ENST00000320451	T	0.15487	2.42	1.29	-1.2	0.09554	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12050	0.0293	L	0.37561	1.115	0.09310	N	1	B	0.21147	0.052	B	0.18871	0.023	T	0.30119	-0.9989	9	0.87932	D	0	.	5.5037	0.16842	0.0:0.6357:0.0:0.3643	.	85	P58317	ZN121_HUMAN	N	85	ENSP00000326967:D85N	ENSP00000326967:D85N	D	-	1	0	ZNF121	9538536	0.037000	0.19845	0.000000	0.03702	0.024000	0.10985	1.512000	0.35812	-0.279000	0.09167	0.484000	0.47621	GAC		0.448	ZNF121-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000449910.1	NM_001008727		T	9677536	C	T	9677536	3	4	47	1	0	0	0	0	1	0	0	0	17758	913	32	3	923	3	ZNF121	19	9677536	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	99436	9677536	49451447	1820	6217										
ZNF846	162993	broad.mit.edu	37	chr19	9868848	9868848	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttctttccactgtggattCttgtatgatcagtaaggtat	9	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:9868848C>A	ENST00000397902.2	-	6	1318	c.905G>T	c.(904-906)aGa>aTa	p.R302I	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Missense_Mutation_p.R173I|ZNF846_ENST00000588267.1_Missense_Mutation_p.R173I	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R302I(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						ACTGTGGATTCTTGTATGATC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	71	70					19																	9868848		2102	4245	6347	9729848	SO:0001583	missense	162993			AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.905G>T	19.37:g.9868848C>A	ENSP00000380999:p.Arg302Ile		9729848	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	20.8	4.042914	0.75732	.	.	ENSG00000196605	ENST00000397902	T	0.24908	1.83	1.91	1.91	0.25777	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33294	0.0858	L	0.53561	1.675	0.33168	D	0.547947	D	0.63046	0.992	P	0.53689	0.732	T	0.47849	-0.9085	8	.	.	.	.	9.9091	0.41394	0.0:1.0:0.0:0.0	.	302	Q147U1	ZN846_HUMAN	I	302	ENSP00000380999:R302I	.	R	-	2	0	ZNF846	9729848	0.000000	0.05858	0.010000	0.14722	0.762000	0.43233	-0.009000	0.12765	1.397000	0.46682	0.456000	0.33151	AGA		0.388	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		A	9868848	C	A	9868848	3	1	47	1	0	0	0	0	1	0	0	0	18231	913	32	2	700	2	ZNF846	19	9868848	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	191312	9868848	49260135	1821	6218										
RGL3	57139	broad.mit.edu	37	chr19	11508132	11508132	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcccctcaccaagatgcttcGatacaggttcccgtggtcat	9	14	2	1	rs201152952		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:11508132G>A	ENST00000380456.3	-	17	1951	c.1888C>T	c.(1888-1890)Cga>Tga	p.R630*	RGL3_ENST00000393423.3_Nonsense_Mutation_p.R636*|RGL3_ENST00000568628.1_5'UTR	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	630	Interaction with HRAS, MRAS and RIT1. {ECO:0000250}.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.R394*(1)|p.R630*(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						AAGATGCTTCGATACAGGTTC	0.677																																					GBM(174;751 2067 17998 27979 33959)											2	Substitution - Nonsense(2)	large_intestine(2)	19						G	stop/ARG,stop/ARG	0,4402		0,0,2201	39	40	40		1888,1906	4.5	1	19		40	2,8594		0,2,4296	yes	stop-gained,stop-gained	RGL3	NM_001035223.2,NM_001161616.1	,	0,2,6497	AA,AG,GG		0.0233,0.0,0.0154	,	630/711,636/717	11508132	2,12996	2201	4298	6499	11369132	SO:0001587	stop_gained	57139			BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.1888C>T	19.37:g.11508132G>A	ENSP00000369823:p.Arg630*		11369132	B5ME84|B7ZL22|Q0P6G0	Nonsense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	G	39	7.673344	0.98425	0.0	2.33E-4	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	.	.	.	4.48	4.48	0.54585	.	0.062472	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	10.1235	0.42634	0.0:0.0:0.8002:0.1998	.	.	.	.	X	427;636;630	.	ENSP00000344665:R427X	R	-	1	2	RGL3	11369132	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.711000	0.68400	2.479000	0.83701	0.555000	0.69702	CGA		0.677	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		A	11508132	G	A	11508132	4	1	47	1	0	0	0	0	0	1	0	0	13315	1066	37	1	256	1	RGL3	19	11508132	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1639284	11508132	47620851	1822	6219										
ZNF491	126069	broad.mit.edu	37	chr19	11917068	11917068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaggcctcacactagagaGaaaccttttgattgtaagga	10	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:11917068G>T	ENST00000323169.5	+	3	631	c.300G>T	c.(298-300)gaG>gaT	p.E100D	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E100D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						ACACTAGAGAGAAACCTTTTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	56	55					19																	11917068		2202	4300	6502	11778068	SO:0001583	missense	126069			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"Zinc fingers, C2H2-type"	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.300G>T	19.37:g.11917068G>T	ENSP00000313443:p.Glu100Asp		11778068	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	.	.	.	.	.	.	.	.	.	.	g	12.68	2.011904	0.35511	.	.	ENSG00000177599	ENST00000323169;ENST00000455048;ENST00000450087	T;T	0.34859	1.34;1.71	0.914	-0.253	0.12996	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40932	0.1137	L	0.47190	1.495	0.27352	N	0.956218	P	0.51057	0.941	P	0.55577	0.779	T	0.30416	-0.9979	9	0.66056	D	0.02	.	6.4321	0.21803	0.193:0.0:0.807:0.0	.	100	Q8N8L2	ZN491_HUMAN	D	100	ENSP00000313443:E100D;ENSP00000392176:E100D	ENSP00000313443:E100D	E	+	3	2	ZNF491	11778068	0.965000	0.33210	0.051000	0.19133	0.018000	0.09664	0.838000	0.27572	-0.045000	0.13468	0.511000	0.50034	GAG		0.383	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		T	11917068	G	T	11917068	3	4	47	1	0	0	0	0	1	0	0	0	17981	933	33	2	302	2	ZNF491	19	11917068	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	408936	11917068	47211915	1823	6220										
ZNF700	90592	broad.mit.edu	37	chr19	12059355	12059355	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcaacaacctaaaaataaGaaagccttcaggtatcgccc	6	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12059355G>T	ENST00000254321.5	+	4	659	c.516G>T	c.(514-516)aaG>aaT	p.K172N	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000590798.1_Intron|ZNF700_ENST00000482090.1_Missense_Mutation_p.K154N|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000591944.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K172N(1)	ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						CTAAAAATAAGAAAGCCTTCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	109	110					19																	12059355		2203	4300	6503	11920355	SO:0001583	missense	90592			AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.516G>T	19.37:g.12059355G>T	ENSP00000254321:p.Lys172Asn		11920355	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	g	10.96	1.498070	0.26861	.	.	ENSG00000196757	ENST00000254321	T	0.07021	3.23	0.596	0.596	0.17496	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09862	0.0242	N	0.08118	0	0.21220	N	0.999751	D	0.71674	0.998	D	0.65987	0.94	T	0.33854	-0.9852	8	0.62326	D	0.03	.	.	.	.	.	172	Q9H0M5	ZN700_HUMAN	N	172	ENSP00000254321:K172N	ENSP00000254321:K172N	K	+	3	2	ZNF700	11920355	0.000000	0.05858	0.121000	0.21740	0.082000	0.17680	-0.501000	0.06398	0.570000	0.29347	0.305000	0.20034	AAG		0.398	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12059355	G	T	12059355	3	4	47	1	0	0	0	0	1	0	0	0	18143	933	33	2	530	2	ZNF700	19	12059355	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	142287	12059355	47069628	1824	6221										
ZNF878	729747	broad.mit.edu	37	chr19	12155891	12155891	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaagacctatgccgatttCtccacacacactgctttcat	5	13	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12155891C>A	ENST00000547628.1	-	4	462	c.325G>T	c.(325-327)Gaa>Taa	p.E109*	ZNF878_ENST00000602107.1_Nonsense_Mutation_p.E156*|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000591838.1_RNA|CTD-2006C1.10_ENST00000547473.1_Intron	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	109					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						ATGCCGATTTCTCCACACACA	0.438																																																0			19											74	72	73					19																	12155891		2055	4224	6279	12016891	SO:0001587	stop_gained	729747				CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"Zinc fingers, C2H2-type", "-"	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.325G>T	19.37:g.12155891C>A	ENSP00000447931:p.Glu109*		12016891		Nonsense_Mutation	SNP	ENST00000547628.1	37	CCDS45984.2	.	.	.	.	.	.	.	.	.	.	C	13.40	2.225337	0.39300	.	.	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	.	.	.	1.3	-2.6	0.06190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.3446	0.04268	0.0:0.2559:0.2951:0.449	.	.	.	.	X	109;156	.	ENSP00000447931:E109X	E	-	1	0	AC022415.4;ZNF878	12016891	0.012000	0.17670	0.006000	0.13384	0.038000	0.13279	0.076000	0.14712	-1.054000	0.03214	0.313000	0.20887	GAA		0.438	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404		A	12155891	C	A	12155891	4	1	47	1	0	0	0	0	0	1	0	0	18235	922	32	2	1274	2	ZNF878	19	12155891	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	96536	12155891	46973092	1825	6222										
ZNF625	90589	broad.mit.edu	37	chr19	12256528	12256528	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgagttctttcatgtattcGaaggctaccagaatgactaa	9	7	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12256528G>A	ENST00000355738.1	-	4	854	c.505C>T	c.(505-507)Cga>Tga	p.R169*	ZNF625-ZNF20_ENST00000430024.1_Intron|ZNF625_ENST00000542938.1_Nonsense_Mutation_p.R169*|ZNF625_ENST00000455799.1_3'UTR|ZNF625_ENST00000439556.2_Nonsense_Mutation_p.R235*|CTC-359D24.3_ENST00000472362.1_RNA			Q96I27	ZN625_HUMAN	zinc finger protein 625	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R169*(1)		breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TCATGTATTCGAAGGCTACCA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											133	121	125					19																	12256528		2203	4300	6503	12117528	SO:0001587	stop_gained	90589			BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"Zinc fingers, C2H2-type", "-"	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.505C>T	19.37:g.12256528G>A	ENSP00000347977:p.Arg169*		12117528	A4FU45|I3L0E9	Nonsense_Mutation	SNP	ENST00000355738.1	37		.	.	.	.	.	.	.	.	.	.	G	37	5.980486	0.97168	.	.	ENSG00000257591	ENST00000542938;ENST00000355738;ENST00000439556	.	.	.	0.856	0.856	0.19019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	4.7449	0.13033	0.0:0.4054:0.5946:0.0	.	.	.	.	X	169;169;235	.	ENSP00000347977:R169X	R	-	1	2	AC022415.5	12117528	0.000000	0.05858	0.016000	0.15963	0.828000	0.46876	-0.321000	0.08018	0.765000	0.33221	0.313000	0.20887	CGA		0.413	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233		A	12256528	G	A	12256528	4	1	47	1	0	0	0	0	0	1	0	0	18088	1066	37	1	419	1	ZNF625	19	12256528	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	100637	12256528	46872455	1826	6223										
ZNF563	147837	broad.mit.edu	37	chr19	12433451	12433451	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcacatatctgtataaattCttctgtgatggacccagcaa	6	9	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12433451C>A	ENST00000293725.5	-	2	283	c.78G>T	c.(76-78)aaG>aaT	p.K26N	ZNF563_ENST00000595977.1_Missense_Mutation_p.K26N	NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K26N(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TGTATAAATTCTTCTGTGATG	0.428																																					GBM(39;623 795 5132 29510 31476)											2	Substitution - Missense(2)	large_intestine(2)	19											135	122	126					19																	12433451		2203	4300	6503	12294451	SO:0001583	missense	147837			BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"Zinc fingers, C2H2-type", "-"	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.78G>T	19.37:g.12433451C>A	ENSP00000293725:p.Lys26Asn		12294451	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972745	0.34848	.	.	ENSG00000188868	ENST00000293725;ENST00000318168	T	0.02944	4.1	1.27	0.0423	0.14217	Krueppel-associated box (4);	.	.	.	.	T	0.16300	0.0392	M	0.92219	3.285	0.22796	N	0.998726	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.03121	-1.1070	9	0.72032	D	0.01	.	6.2568	0.20877	0.2977:0.7023:0.0:0.0	.	26;26	Q8TA94-2;Q8TA94	.;ZN563_HUMAN	N	26	ENSP00000293725:K26N	ENSP00000293725:K26N	K	-	3	2	ZNF563	12294451	0.016000	0.18221	0.665000	0.29768	0.054000	0.15201	-0.040000	0.12104	-0.124000	0.11724	-0.692000	0.03713	AAG		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		A	12433451	C	A	12433451	3	1	47	1	0	0	0	0	1	0	0	0	18033	912	32	2	1364	2	ZNF563	19	12433451	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	176923	12433451	46695532	1827	6224										
MAN2B1	4125	broad.mit.edu	37	chr19	12758323	12758323	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcctacggcaaactggtgCtccaagcgcagcagcaccat	9	15	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12758323C>T	ENST00000456935.2	-	22	2794	c.2754G>A	c.(2752-2754)gaG>gaA	p.E918E	MAN2B1_ENST00000221363.4_Silent_p.E917E|CTD-2192J16.22_ENST00000597692.1_Missense_Mutation_p.A105T	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	918					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.E918E(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CAAACTGGTGCTCCAAGCGCA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	19											85	85	85					19																	12758323		2203	4300	6503	12619323	SO:0001819	synonymous_variant	4125				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2754G>A	19.37:g.12758323C>T			12619323	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	37	CCDS32919.1																																																																																				0.622	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			T	12758323	C	T	12758323	2	4	47	1	0	0	0	0	0	0	0	1	9246	796	28	3		3	MAN2B1	19	12758323	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	324872	12758323	46370660	1828	6225										
PRDX2	7001	broad.mit.edu	37	chr19	12910788	12910788	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgaaggacacccttgccatcGatgataaagaggcccctgaa	10	12	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:12910788G>A	ENST00000301522.2	-	5	524	c.396C>T	c.(394-396)atC>atT	p.I132I	PRDX2_ENST00000334482.5_Intron|CTD-2659N19.10_ENST00000585496.1_RNA	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2	132	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)	p.I132I(1)		endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						CCTTGCCATCGATGATAAAGA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	19											69	62	64					19																	12910788		2203	4300	6503	12771788	SO:0001819	synonymous_variant	7001				CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.396C>T	19.37:g.12910788G>A			12771788	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Silent	SNP	ENST00000301522.2	37	CCDS12281.1																																																																																				0.572	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		A	12910788	G	A	12910788	2	1	47	1	0	0	0	0	0	0	0	1	12499	1048	37	1		1	PRDX2	19	12910788	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	152465	12910788	46218195	1829	6226										
CACNA1A	773	broad.mit.edu	37	chr19	13365981	13365981	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgaaaggcggagacaccacGaactgccacatgcggtactg	12	12	0	1	rs377082780		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:13365981G>A	ENST00000360228.5	-	29	4682	c.4683C>T	c.(4681-4683)ttC>ttT	p.F1561F	CACNA1A_ENST00000573710.2_Silent_p.F1562F|CACNA1A_ENST00000574822.1_5'Flank	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1562					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.F1562F(3)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGACACCACGAACTGCCACA	0.587																																																3	Substitution - coding silent(3)	large_intestine(3)	19						G	,,,,	0,4300		0,0,2150	84	94	91		4695,4686,4683,4686,4695	-0.2	1	19		91	1,8513		0,1,4256	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	0,1,6406	AA,AG,GG		0.0117,0.0,0.0078	,,,,	1565/2267,1562/2262,1561/2507,1562/2264,1565/2513	13365981	1,12813	2150	4257	6407	13226981	SO:0001819	synonymous_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.4683C>T	19.37:g.13365981G>A			13226981	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																				0.587	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13365981	G	A	13365981	2	1	47	1	0	0	0	0	0	0	0	1	2544	1049	37	1		1	CACNA1A	19	13365981	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	455193	13365981	45763002	1830	6227										
PRKACA	5566	broad.mit.edu	37	chr19	14203926	14203926	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggggcacaggcatgcccctAaaactcagaaaactccttgc	10	13	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:14203926A>G	ENST00000308677.4	-	10	1250	c.1054T>C	c.(1054-1056)Tag>Cag	p.*352Q	PRKACA_ENST00000589994.1_Nonstop_Mutation_p.*344Q|SAMD1_ENST00000533683.2_5'Flank|SAMD1_ENST00000541938.1_5'Flank|PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000350356.3_5'UTR	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	0					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)	p.*352Q(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						GCATGCCCCTAAAACTCAGAA	0.493																																																1	Nonstop extension(1)	large_intestine(1)	19											59	47	51					19																	14203926		2203	4300	6503	14064926	SO:0001578	stop_lost	5566				CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.1054T>C	19.37:g.14203926A>G	ENSP00000309591:p.*352Gluext*26		14064926	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Nonstop_Mutation	SNP	ENST00000308677.4	37	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.336448	0.41398	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3773	0.49735	1.0:0.0:0.0:0.0	.	.	.	.	Q	352;344;352	.	.	X	-	1	0	PRKACA	14064926	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	8.892000	0.92491	1.861000	0.53984	0.347000	0.21830	TAG		0.493	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		G	14203926	A	G	14203926	4	3	47	1	0	0	0	0	0	0	0	0	12531	375	13	4	5	4	PRKACA	19	14203926	Nonstop_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	837945	14203926	44925057	1831	6228										
EMR3	84658	broad.mit.edu	37	chr19	14772866	14772866	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgacagtagaaacttccttcGacattgtaacacacagcgtt	7	10	0	2	rs150826128		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:14772866G>A	ENST00000253673.5	-	4	364	c.264C>T	c.(262-264)gtC>gtT	p.V88V	EMR3_ENST00000599900.1_5'UTR|EMR3_ENST00000443157.2_Intron|EMR3_ENST00000344373.4_Intron	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	88	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.V88V(4)		NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						AACTTCCTTCGACATTGTAAC	0.393																																																4	Substitution - coding silent(4)	large_intestine(4)	19						G		1,4405	2.1+/-5.4	0,1,2202	197	165	176		264	-8.2	0	19	dbSNP_134	176	0,8600		0,0,4300	no	coding-synonymous	EMR3	NM_032571.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		88/653	14772866	1,13005	2203	4300	6503	14633866	SO:0001819	synonymous_variant	84658			AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.264C>T	19.37:g.14772866G>A			14633866		Silent	SNP	ENST00000253673.5	37	CCDS12315.1																																																																																				0.393	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		A	14772866	G	A	14772866	2	1	47	1	0	0	0	0	0	0	0	1	5119	1045	37	1		1	EMR3	19	14772866	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	568940	14772866	44356117	1832	6229										
OR7C2	26658	broad.mit.edu	37	chr19	15052891	15052891	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacaccttcatcaataacatCgtgatgtattttgtgaccat	6	9	2	2	rs145894974		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:15052891C>T	ENST00000248072.3	+	1	591	c.591C>T	c.(589-591)atC>atT	p.I197I		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I197I(1)		large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					TCAATAACATCGTGATGTATT	0.433													.|||	1	0.000199681	0	0	5008	,	,		23359	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											212	196	201					19																	15052891		2203	4300	6503	14913891	SO:0001819	synonymous_variant	26658			U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.591C>T	19.37:g.15052891C>T			14913891	O43881|Q6IFP9	Silent	SNP	ENST00000248072.3	37	CCDS12320.1																																																																																				0.433	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			T	15052891	C	T	15052891	2	4	47	1	0	0	0	0	0	0	0	1	11249	874	31	1		1	OR7C2	19	15052891	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	280025	15052891	44076092	1833	6230										
NOTCH3	4854	broad.mit.edu	37	chr19	15276215	15276215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgacatcagcatggctggCgatgagctcttccaccatgc	10	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:15276215C>T	ENST00000263388.2	-	31	5854	c.5779G>A	c.(5779-5781)Gcc>Acc	p.A1927T		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1927					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.A1927T(2)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GCATGGCTGGCGATGAGCTCT	0.577																																																2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	19											91	77	82					19																	15276215		2203	4300	6503	15137215	SO:0001583	missense	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5779G>A	19.37:g.15276215C>T	ENSP00000263388:p.Ala1927Thr		15137215	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.297690	0.40694	.	.	ENSG00000074181	ENST00000263388	T	0.64991	-0.13	5.14	5.14	0.70334	Ankyrin repeat-containing domain (4);	0.000000	0.32190	N	0.006458	T	0.49184	0.1542	L	0.35249	1.045	0.38489	D	0.947938	B	0.32396	0.369	B	0.32805	0.153	T	0.50709	-0.8796	10	0.30854	T	0.27	.	11.0253	0.47741	0.0:0.9143:0.0:0.0857	.	1927	Q9UM47	NOTC3_HUMAN	T	1927	ENSP00000263388:A1927T	ENSP00000263388:A1927T	A	-	1	0	NOTCH3	15137215	0.967000	0.33354	0.989000	0.46669	0.471000	0.32888	2.016000	0.40971	2.676000	0.91093	0.561000	0.74099	GCC		0.577	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15276215	C	T	15276215	3	4	47	1	0	0	0	0	1	0	0	0	10581	768	27	1	1198	1	NOTCH3	19	15276215	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	223324	15276215	43852768	1834	6231										
CYP4F22	126410	broad.mit.edu	37	chr19	15654824	15654824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagacgaggatatccgagccGaagcagacaccttcatgttt	10	11	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:15654824G>A	ENST00000269703.3	+	9	1181	c.982G>A	c.(982-984)Gaa>Aaa	p.E328K	CYP4F22_ENST00000601005.2_Missense_Mutation_p.E328K	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	328						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.E328K(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						TATCCGAGCCGAAGCAGACAC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19											114	83	93					19																	15654824		2203	4300	6503	15515824	SO:0001583	missense	126410				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.982G>A	19.37:g.15654824G>A	ENSP00000269703:p.Glu328Lys		15515824	Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345161	0.82022	.	.	ENSG00000171954	ENST00000269703	T	0.70045	-0.45	5.49	5.49	0.81192	.	0.054221	0.64402	D	0.000001	D	0.88492	0.6451	H	0.97564	4.03	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.92298	0.5847	10	0.87932	D	0	.	16.8674	0.86033	0.0:0.0:1.0:0.0	.	328	Q6NT55	CP4FN_HUMAN	K	328	ENSP00000269703:E328K	ENSP00000269703:E328K	E	+	1	0	CYP4F22	15515824	1.000000	0.71417	0.950000	0.38849	0.335000	0.28730	7.107000	0.77047	2.592000	0.87571	0.655000	0.94253	GAA		0.547	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		A	15654824	G	A	15654824	3	1	47	1	0	0	0	0	1	0	0	0	4195	1059	37	1	1008	1	CYP4F22	19	15654824	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	378609	15654824	43474159	1835	6232										
CYP4F12	66002	broad.mit.edu	37	chr19	15794313	15794313	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctctgcaggaggcccagtGaatatattgccaccatcttg	10	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:15794313G>T	ENST00000550308.1	+	7	1038	c.658G>T	c.(658-660)Gaa>Taa	p.E220*	CYP4F12_ENST00000324632.10_Nonsense_Mutation_p.E220*	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	220					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)	p.E220*(1)		NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GAGGCCCAGTGAATATATTGC	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											69	68	68					19																	15794313		2201	4299	6500	15655313	SO:0001587	stop_gained	66002			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"Cytochrome P450s"	18857	protein-coding gene	gene with protein product		611485	"cytochrome P450, subfamily IVF, polypeptide 12"			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.658G>T	19.37:g.15794313G>T	ENSP00000448998:p.Glu220*		15655313	E7ET51|O60389|Q5JPJ7|Q9HCS1	Nonsense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	.	.	.	.	.	.	.	.	.	.	.	39	7.308537	0.98203	.	.	ENSG00000186204	ENST00000550308;ENST00000324632	.	.	.	2.46	1.37	0.22104	.	0.652316	0.12737	U	0.443324	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	9.0899	0.36603	0.0:0.2282:0.7717:0.0	.	.	.	.	X	220	.	ENSP00000321821:E220X	E	+	1	0	CYP4F12	15655313	0.943000	0.32029	0.925000	0.36789	0.342000	0.28953	0.548000	0.23314	0.570000	0.29347	0.484000	0.47621	GAA		0.532	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15794313	G	T	15794313	4	4	47	1	0	0	0	0	0	1	0	0	4193	1291	45	2	680	2	CYP4F12	19	15794313	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	139489	15794313	43334670	1836	6233										
CALR3	125972	broad.mit.edu	37	chr19	16601326	16601326	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttttccctttattgctgaaCggtttgaagcgtgcagagat	11	7	0	3	rs570064234		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:16601326C>T	ENST00000269881.3	-	3	311	c.249G>A	c.(247-249)ccG>ccA	p.P83P	CTD-3222D19.2_ENST00000409035.1_Intron	NM_145046.4	NP_659483.2	Q96L12	CALR3_HUMAN	calreticulin 3	83	N-domain.				cell differentiation (GO:0030154)|protein folding (GO:0006457)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.P83P(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|prostate(1)|skin(1)	15						TATTGCTGAACGGTTTGAAGC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	19											169	160	163					19																	16601326		2203	4300	6503	16462326	SO:0001819	synonymous_variant	125972			AK058084	CCDS12344.1	19p13.11	2014-09-17				ENSG00000269058			20407	protein-coding gene	gene with protein product	"cancer/testis antigen 93", "calsperin"	611414				12384296	Standard	NM_145046		Approved	CRT2, FLJ25355, MGC26577, CT93	uc002ned.3	Q96L12		ENST00000269881.3:c.249G>A	19.37:g.16601326C>T			16462326	D9N574|Q96LN3	Silent	SNP	ENST00000269881.3	37	CCDS12344.1																																																																																				0.453	CALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461089.1	NM_145046		T	16601326	C	T	16601326	2	4	47	1	0	0	0	0	0	0	0	1	2599	523	19	1		1	CALR3	19	16601326	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	807013	16601326	42527657	1837	6234										
TMEM38A	79041	broad.mit.edu	37	chr19	16791313	16791313	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggtggtgcgagtccgcaaGatcgcggtgggcatccatca	16	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:16791313G>T	ENST00000187762.2	+	3	478	c.387G>T	c.(385-387)aaG>aaT	p.K129N		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	129						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)	p.K129K(1)|p.K129N(1)		central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						GAGTCCGCAAGATCGCGGTGG	0.532																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|central_nervous_system(1)	19											175	161	166					19																	16791313		2203	4300	6503	16652313	SO:0001583	missense	79041			AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.387G>T	19.37:g.16791313G>T	ENSP00000187762:p.Lys129Asn		16652313	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	37	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	19.61	3.859670	0.71834	.	.	ENSG00000072954	ENST00000187762	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.78020	0.4218	M	0.84219	2.685	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.79818	-0.1643	9	0.59425	D	0.04	-23.8134	9.5009	0.39017	0.1631:0.0:0.8369:0.0	.	129	Q9H6F2	TM38A_HUMAN	N	129	.	ENSP00000187762:K129N	K	+	3	2	TMEM38A	16652313	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.432000	0.52824	2.459000	0.83118	0.561000	0.74099	AAG		0.532	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074		T	16791313	G	T	16791313	3	4	47	1	0	0	0	0	1	0	0	0	16198	933	33	2	397	2	TMEM38A	19	16791313	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	189987	16791313	42337670	1838	6235										
FAM129C	199786	broad.mit.edu	37	chr19	17664141	17664141	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctccaaatcttaacttggtGtcaagtttcctggctgggag	11	9	2	0	rs575613569		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:17664141G>A	ENST00000335393.4	+	16	2001	c.1863G>A	c.(1861-1863)gtG>gtA	p.V621V	FAM129C_ENST00000601861.1_Silent_p.V590V|COLGALT1_ENST00000252599.4_5'Flank|FAM129C_ENST00000449408.2_Silent_p.V347V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	621								p.V621V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						TTAACTTGGTGTCAAGTTTCC	0.453													g|||	1	0.000199681	0	0	5008	,	,		17138	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											129	139	136					19																	17664141		2203	4300	6503	17525141	SO:0001819	synonymous_variant	199786			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1863G>A	19.37:g.17664141G>A			17525141	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																				0.453	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		A	17664141	G	A	17664141	2	1	47	1	0	0	0	0	0	0	0	1	5454	1364	48	3		3	FAM129C	19	17664141	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	872828	17664141	41464842	1839	6236										
UNC13A	23025	broad.mit.edu	37	chr19	17756824	17756824	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggttgaggttcccatagatgGtttttgtccgtttcttggtc	12	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:17756824G>T	ENST00000519716.2	-	18	2140	c.2141C>A	c.(2140-2142)aCc>aAc	p.T714N	UNC13A_ENST00000550896.1_Missense_Mutation_p.T712N|UNC13A_ENST00000551649.1_Missense_Mutation_p.T714N|UNC13A_ENST00000552293.1_Missense_Mutation_p.T714N|UNC13A_ENST00000428389.2_Missense_Mutation_p.T802N|UNC13A_ENST00000252773.7_Missense_Mutation_p.T714N	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	714	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.T802N(1)|p.T714N(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CCCATAGATGGTTTTTGTCCG	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	19											83	79	80					19																	17756824		1959	4172	6131	17617824	SO:0001583	missense	23025			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2141C>A	19.37:g.17756824G>T	ENSP00000429562:p.Thr714Asn		17617824	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.093769	0.76870	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57;-0.57	3.85	3.85	0.44370	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.86301	0.5900	M	0.91406	3.205	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	D	0.89555	0.3802	10	0.87932	D	0	-27.8132	13.6311	0.62196	0.0:0.0:1.0:0.0	.	714	Q9UPW8	UN13A_HUMAN	N	714;802;714;714;714;712	ENSP00000429562:T714N;ENSP00000400409:T802N;ENSP00000252773:T714N;ENSP00000447236:T714N;ENSP00000447572:T714N;ENSP00000446831:T712N	ENSP00000252773:T714N	T	-	2	0	UNC13A	17617824	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	9.620000	0.98373	1.874000	0.54306	0.313000	0.20887	ACC		0.592	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17756824	G	T	17756824	3	4	47	1	0	0	0	0	1	0	0	0	17024	1261	44	2	3074	2	UNC13A	19	17756824	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	92683	17756824	41372159	1840	6237										
LOC729991-MEF2B	100271849	broad.mit.edu	37	chr19	19257365	19257366	+	Splice_Site	INS	-	-	G													0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaggttaggggatgtacctINSggggggcctccggggaggaa							TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:19257365_19257366insG	ENST00000602424.2	-	9	1493_1494	c.767_768insC	c.(766-768)cca>ccCa	p.P256fs	MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000410050.1_Splice_Site_p.P256fs|MEF2B_ENST00000162023.5_Splice_Site_p.P256fs|MEF2B_ENST00000409447.2_Splice_Site_p.S212fs|MEF2BNB-MEF2B_ENST00000514819.3_Splice_Site_p.P273fs|MEF2BNB-MEF2B_ENST00000444486.3_Splice_Site_p.P256fs|MEF2B_ENST00000424583.2_Splice_Site_p.P256fs|MEF2B_ENST00000409224.1_Splice_Site_p.P259fs	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	256					muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E257fs*28(1)|p.V257fs*76(1)		breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			GGGATGTACCTGGGGGGCCTCC	0.653																																																2	Insertion - Frameshift(2)	large_intestine(2)	19																																								19118366	SO:0001630	splice_region_variant	4207			X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"Myocyte enhancer factors"	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.769+1->C	19.37:g.19257371_19257371dupG			19118365	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Frame_Shift_Ins	INS	ENST00000602424.2	37	CCDS12394.1																																																																																				0.653	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919	Frame_Shift_Ins	G	19257366	-	G	19257365	8	5	47	1	0	1	1	0	0	0	1	0	8918	1594	55	0	337	0	LOC729991-MEF2B	19	19257365	Splice_Site	INS	-	TCGA-AG-3892-01A-01W-1073-09	1500541	19257365	39871618	1841	6238										
ZNF506	440515	broad.mit.edu	37	chr19	19905706	19905706	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagtatgaattctcttatgTttagtaaggtttgaggaacg	10	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:19905706T>C	ENST00000540806.2	-	4	1078	c.990A>G	c.(988-990)aaA>aaG	p.K330K	ZNF506_ENST00000443905.2_Silent_p.K330K|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000450683.2_Silent_p.K298K|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K330K(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						TTCTCTTATGTTTAGTAAGGT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	19											64	69	67					19																	19905706		2194	4289	6483	19766706	SO:0001819	synonymous_variant	440515			AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.990A>G	19.37:g.19905706T>C			19766706	B3KTH6	Silent	SNP	ENST00000540806.2	37	CCDS42531.1																																																																																				0.393	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		C	19905706	T	C	19905706	2	2	47	1	0	0	0	0	0	0	0	1	17991	1722	60	4		4	ZNF506	19	19905706	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	648341	19905706	39223277	1842	6239										
ZNF506	440515	broad.mit.edu	37	chr19	19906181	19906181	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catattctatacatttaaaaGatttttttccagtatctctt	2	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:19906181G>T	ENST00000540806.2	-	4	603	c.515C>A	c.(514-516)tCt>tAt	p.S172Y	ZNF506_ENST00000443905.2_Missense_Mutation_p.S172Y|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000450683.2_Missense_Mutation_p.S140Y|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S172Y(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						ACATTTAAAAGATTTTTTTCC	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	39	40					19																	19906181		1876	4126	6002	19767181	SO:0001583	missense	440515			AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.515C>A	19.37:g.19906181G>T	ENSP00000440625:p.Ser172Tyr		19767181	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	.	.	.	.	.	.	.	.	.	.	g	3.450	-0.112302	0.06881	.	.	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.15372	2.43;2.43;2.43	1.16	-2.32	0.06745	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13927	0.0337	M	0.79343	2.45	0.09310	N	1	B;P	0.36599	0.084;0.56	B;B	0.23574	0.025;0.047	T	0.15321	-1.0441	9	0.52906	T	0.07	.	2.9574	0.05881	0.2131:0.0:0.525:0.2619	.	172;140	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	Y	172;172;140	ENSP00000393835:S172Y;ENSP00000440625:S172Y;ENSP00000408892:S140Y	ENSP00000393835:S172Y	S	-	2	0	ZNF506	19767181	0.042000	0.20092	0.000000	0.03702	0.001000	0.01503	1.717000	0.37991	-0.375000	0.07955	-0.751000	0.03497	TCT		0.284	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		T	19906181	G	T	19906181	3	4	47	1	0	0	0	0	1	0	0	0	17991	942	33	2	823	2	ZNF506	19	19906181	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	475	19906181	39222802	1843	6240										
ZNF626	199777	broad.mit.edu	37	chr19	20807937	20807937	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctctccagtatgatttCtcttatgtgtagtaagagtg	9	6	2	2	rs533816037	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:20807937C>A	ENST00000601440.1	-	4	892	c.746G>T	c.(745-747)aGa>aTa	p.R249I	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R249I(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						AGTATGATTTCTCTTATGTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	58	57					19																	20807937		2195	4295	6490	20599777	SO:0001583	missense	199777			BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.746G>T	19.37:g.20807937C>A	ENSP00000469958:p.Arg249Ile		20599777	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	0.390	-0.924191	0.02377	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	0.798	0.798	0.18660	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38214	0.1032	M	0.64567	1.98	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.30822	-0.9965	8	0.27082	T	0.32	.	3.2332	0.06756	0.0:0.6487:0.0:0.3513	.	249	Q68DY1	ZN626_HUMAN	I	249;173;249	.	ENSP00000445201:R249I	R	-	2	0	ZNF626	20599777	0.000000	0.05858	0.508000	0.27688	0.506000	0.33950	-1.548000	0.02184	0.162000	0.19483	0.165000	0.16767	AGA		0.378	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		A	20807937	C	A	20807937	3	1	47	1	0	0	0	0	1	0	0	0	18089	913	32	2	844	2	ZNF626	19	20807937	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	901756	20807937	38321046	1844	6241										
ZNF714	148206	broad.mit.edu	37	chr19	21300554	21300554	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttactacacataagatgattCatactggagagaaaccctac	6	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:21300554C>A	ENST00000596143.1	+	5	1409	c.1084C>A	c.(1084-1086)Cat>Aat	p.H362N	ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H362N(1)		endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TAAGATGATTCATACTGGAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	44	43					19																	21300554		2169	4283	6452	21092394	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1084C>A	19.37:g.21300554C>A	ENSP00000472368:p.His362Asn		21092394	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	11.21	1.572974	0.28092	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75162	0.3812	M	0.92649	3.33	0.29451	N	0.85844	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.998;0.998	T	0.67914	-0.5547	8	0.87932	D	0	.	8.8708	0.35314	0.0:1.0:0.0:0.0	.	363;362;363	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	N	362	.	ENSP00000291770:H362N	H	+	1	0	ZNF714	21092394	0.999000	0.42202	0.441000	0.26858	0.428000	0.31595	5.289000	0.65656	0.446000	0.26666	0.449000	0.29647	CAT		0.358	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21300554	C	A	21300554	3	1	47	1	0	0	0	0	1	0	0	0	18157	826	29	2	1094	2	ZNF714	19	21300554	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	492617	21300554	37828429	1845	6242										
ZNF493	284443	broad.mit.edu	37	chr19	21607170	21607170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagagaattcatactggacAcaaaccctacaaatgtaaag	6	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:21607170A>G	ENST00000355504.4	+	2	1591	c.1325A>G	c.(1324-1326)cAc>cGc	p.H442R	ZNF493_ENST00000392288.2_Missense_Mutation_p.H570R|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H442R(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CATACTGGACACAAACCCTAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	40	41					19																	21607170		2202	4298	6500	21399010	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1325A>G	19.37:g.21607170A>G	ENSP00000347691:p.His442Arg		21399010	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	9.798	1.179688	0.21787	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.17691	2.26;2.26	0.741	0.741	0.18336	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05502	0.0145	N	0.01417	-0.88	0.80722	D	1	B;B	0.22480	0.004;0.07	B;B	0.21151	0.003;0.033	T	0.21484	-1.0244	9	0.87932	D	0	.	7.0351	0.24989	1.0:0.0:0.0:0.0	.	442;570	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	R	570;442	ENSP00000376110:H570R;ENSP00000347691:H442R	ENSP00000347691:H442R	H	+	2	0	ZNF493	21399010	0.154000	0.22792	0.002000	0.10522	0.006000	0.05464	2.694000	0.47035	0.561000	0.29186	0.383000	0.25322	CAC		0.358	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21607170	A	G	21607170	3	3	47	1	0	0	0	0	1	0	0	0	17983	159	6	4	1786	4	ZNF493	19	21607170	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	306616	21607170	37521813	1846	6243										
ZNF429	353088	broad.mit.edu	37	chr19	21712526	21712526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtggcagtgcctggacacaGcacaacagaacttatataga	10	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:21712526G>A	ENST00000358491.4	+	2	278	c.70G>A	c.(70-72)Gca>Aca	p.A24T	ZNF429_ENST00000594022.1_3'UTR|ZNF429_ENST00000597078.1_Missense_Mutation_p.A24T	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A24T(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						CCTGGACACAGCACAACAGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											106	118	114					19																	21712526		2203	4300	6503	21504366	SO:0001583	missense	353088			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.70G>A	19.37:g.21712526G>A	ENSP00000351280:p.Ala24Thr		21504366	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	37	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	8.310	0.821990	0.16678	.	.	ENSG00000197013	ENST00000358491	T	0.02236	4.38	0.926	-1.35	0.09114	Krueppel-associated box (4);	.	.	.	.	T	0.03263	0.0095	M	0.64630	1.985	0.09310	N	1	P	0.36974	0.576	B	0.38921	0.285	T	0.38607	-0.9653	9	0.48119	T	0.1	.	6.7281	0.23369	0.0:0.0:0.727:0.273	.	24	Q86V71	ZN429_HUMAN	T	24	ENSP00000351280:A24T	ENSP00000351280:A24T	A	+	1	0	ZNF429	21504366	0.000000	0.05858	0.098000	0.21074	0.100000	0.18952	0.082000	0.14847	0.308000	0.22923	0.313000	0.20887	GCA		0.418	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		A	21712526	G	A	21712526	3	1	47	1	0	0	0	0	1	0	0	0	17941	971	34	3	76	3	ZNF429	19	21712526	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	105356	21712526	37416457	1847	6244										
ZNF429	353088	broad.mit.edu	37	chr19	21719517	21719517	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcccttactaaccataagaGaatttatgttggtgagaaac	8	7	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:21719517G>T	ENST00000358491.4	+	4	870	c.662G>T	c.(661-663)aGa>aTa	p.R221I	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R221I(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						AACCATAAGAGAATTTATGTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											56	61	59					19																	21719517		2161	4270	6431	21511357	SO:0001583	missense	353088			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.662G>T	19.37:g.21719517G>T	ENSP00000351280:p.Arg221Ile		21511357	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	37	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	7.183	0.589908	0.13812	.	.	ENSG00000197013	ENST00000358491	T	0.02446	4.29	0.81	-0.534	0.11883	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	L	0.27053	0.805	0.32895	D	0.512448	B	0.19073	0.033	B	0.06405	0.002	T	0.26643	-1.0097	9	0.44086	T	0.13	.	6.0723	0.19895	0.2437:0.0:0.7563:0.0	.	221	Q86V71	ZN429_HUMAN	I	221	ENSP00000351280:R221I	ENSP00000351280:R221I	R	+	2	0	ZNF429	21511357	0.000000	0.05858	0.158000	0.22627	0.157000	0.22087	0.205000	0.17356	0.181000	0.19994	0.184000	0.17185	AGA		0.358	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		T	21719517	G	T	21719517	3	4	47	1	0	0	0	0	1	0	0	0	17941	942	33	2	676	2	ZNF429	19	21719517	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	6991	21719517	37409466	1848	6245										
ZNF100	163227	broad.mit.edu	37	chr19	21910188	21910188	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttcactccagtatgaattCttttatgtgtagtaaggtgt	9	5	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:21910188C>A	ENST00000358296.6	-	5	1124	c.926G>T	c.(925-927)aGa>aTa	p.R309I	ZNF100_ENST00000305570.6_Missense_Mutation_p.R245I	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R309I(1)|p.R309T(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						AGTATGAATTCTTTTATGTGT	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											46	49	48					19																	21910188		2192	4296	6488	21702028	SO:0001583	missense	163227			BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"Zinc fingers, C2H2-type", "-"	12880	protein-coding gene	gene with protein product		603982	"zinc finger protein 100 (Y1)"			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.926G>T	19.37:g.21910188C>A	ENSP00000351042:p.Arg309Ile		21702028	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	37	CCDS42538.1	.	.	.	.	.	.	.	.	.	.	.	0.398	-0.919898	0.02396	.	.	ENSG00000197020	ENST00000358296	T	0.02446	4.29	0.907	-1.81	0.07882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03053	0.0090	M	0.69185	2.1	0.39550	D	0.968959	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.42103	-0.9471	9	0.23302	T	0.38	.	2.6738	0.05075	0.2733:0.5235:0.0:0.2032	.	309;363	Q8IYN0;Q4G131	ZN100_HUMAN;.	I	309	ENSP00000351042:R309I	ENSP00000351042:R309I	R	-	2	0	ZNF100	21702028	0.000000	0.05858	0.045000	0.18777	0.045000	0.14185	0.024000	0.13555	-0.888000	0.03956	-0.898000	0.02899	AGA		0.388	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		A	21910188	C	A	21910188	3	1	47	1	0	0	0	0	1	0	0	0	17752	913	32	2	706	2	ZNF100	19	21910188	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	190671	21910188	37218795	1849	6246										
ZNF208	7757	broad.mit.edu	37	chr19	22155133	22155133	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatgtttagtaaggatggaGaacatactaaaacctttgcc	8	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22155133G>T	ENST00000397126.4	-	4	2851	c.2703C>A	c.(2701-2703)ttC>ttA	p.F901L	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	901					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.F801L(2)|p.F901L(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TAAGGATGGAGAACATACTAA	0.383																																																3	Substitution - Missense(3)	large_intestine(3)	19											51	55	54					19																	22155133		2102	4230	6332	21946973	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2703C>A	19.37:g.22155133G>T	ENSP00000380315:p.Phe901Leu		21946973		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	0.250	-1.007447	0.02112	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.13901	2.55	2.9	-5.81	0.02340	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05868	0.0153	.	.	.	0.09310	N	1	P	0.42248	0.774	B	0.43331	0.416	T	0.14980	-1.0453	8	0.09590	T	0.72	.	1.3826	0.02233	0.3123:0.148:0.391:0.1486	.	801	O43345	ZN208_HUMAN	L	901;801	ENSP00000380315:F901L	ENSP00000380315:F901L	F	-	3	2	ZNF208	21946973	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.183000	0.03079	-1.808000	0.01234	0.289000	0.19496	TTC		0.383	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155133	G	T	22155133	3	4	47	1	0	0	0	0	1	0	0	0	17805	933	33	2	1143	2	ZNF208	19	22155133	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	244945	22155133	36973850	1850	6247										
ZNF208	7757	broad.mit.edu	37	chr19	22157350	22157350	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagtatgccttatcttatgTctgtttgaatttgaacattt	6	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22157350T>C	ENST00000397126.4	-	4	634	c.486A>G	c.(484-486)agA>agG	p.R162R	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R162R(3)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTATCTTATGTCTGTTTGAAT	0.308																																																3	Substitution - coding silent(3)	large_intestine(3)	19											116	112	114					19																	22157350		2031	4227	6258	21949190	SO:0001819	synonymous_variant	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.486A>G	19.37:g.22157350T>C			21949190		Silent	SNP	ENST00000397126.4	37	CCDS54240.1																																																																																				0.308	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22157350	T	C	22157350	2	2	47	1	0	0	0	0	0	0	0	1	17805	1664	58	4		4	ZNF208	19	22157350	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2217	22157350	36971633	1851	6248										
ZNF98	148198	broad.mit.edu	37	chr19	22574592	22574592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttctctccagtatgaattAccttatgtttagaaagagtt	7	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22574592A>G	ENST00000357774.5	-	4	1566	c.1445T>C	c.(1444-1446)gTa>gCa	p.V482A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	482					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V482A(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AGTATGAATTACCTTATGTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	19											56	50	52					19																	22574592		2107	4182	6289	22366432	SO:0001583	missense	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1445T>C	19.37:g.22574592A>G	ENSP00000350418:p.Val482Ala		22366432		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	3.630	-0.075815	0.07184	.	.	ENSG00000197360	ENST00000357774	T	0.16196	2.36	1.26	-2.53	0.06326	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09069	0.0224	N	0.17312	0.475	0.09310	N	1	B	0.15473	0.013	B	0.22152	0.038	T	0.32929	-0.9888	9	0.34782	T	0.22	.	5.767	0.18231	0.2557:0.5668:0.1775:0.0	.	482	A6NK75	ZNF98_HUMAN	A	482	ENSP00000350418:V482A	ENSP00000350418:V482A	V	-	2	0	ZNF98	22366432	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.690000	0.05138	-1.449000	0.01938	-0.805000	0.03199	GTA		0.378	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		G	22574592	A	G	22574592	3	3	47	1	0	0	0	0	1	0	0	0	18242	391	14	4	277	4	ZNF98	19	22574592	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	417242	22574592	36554391	1852	6249										
ZNF99	7652	broad.mit.edu	37	chr19	22940528	22940528	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atttgtagggtttctctccaGtatgaattatctcatgtttt	7	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22940528G>T	ENST00000596209.1	-	4	2273	c.2183C>A	c.(2182-2184)aCt>aAt	p.T728N	ZNF99_ENST00000397104.3_Missense_Mutation_p.T637N|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	728					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T637N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTCTCTCCAGTATGAATTAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											32	34	33					19																	22940528		2023	4180	6203	22732368	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2183C>A	19.37:g.22940528G>T	ENSP00000472969:p.Thr728Asn		22732368	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	g	11.46	1.644673	0.29246	.	.	ENSG00000213973	ENST00000397104	T	0.26067	1.76	0.726	0.726	0.18248	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28566	0.0707	L	0.52759	1.655	0.28780	N	0.899902	P	0.37061	0.58	B	0.43867	0.434	T	0.28964	-1.0027	9	0.66056	D	0.02	.	8.9692	0.35897	0.0:0.0:1.0:0.0	.	637	A8MXY4	ZNF99_HUMAN	N	637	ENSP00000380293:T637N	ENSP00000380293:T637N	T	-	2	0	ZNF99	22732368	0.753000	0.28349	0.018000	0.16275	0.041000	0.13682	0.935000	0.28924	0.680000	0.31366	0.400000	0.26472	ACT		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22940528	G	T	22940528	3	4	47	1	0	0	0	0	1	0	0	0	18243	1029	36	2	1214	2	ZNF99	19	22940528	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	365936	22940528	36188455	1853	6250										
ZNF99	7652	broad.mit.edu	37	chr19	22940986	22940986	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctagtaagatgtgaagattgCttaaaagctttgccacattc	8	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22940986C>A	ENST00000596209.1	-	4	1815	c.1725G>T	c.(1723-1725)aaG>aaT	p.K575N	ZNF99_ENST00000397104.3_Missense_Mutation_p.K484N	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	575					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K484N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GTGAAGATTGCTTAAAAGCTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											50	54	53					19																	22940986		2099	4234	6333	22732826	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1725G>T	19.37:g.22940986C>A	ENSP00000472969:p.Lys575Asn		22732826	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.001	-3.401707	0.00014	.	.	ENSG00000213973	ENST00000397104	T	0.08102	3.13	1.44	-2.88	0.05682	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03178	0.0093	N	0.16037	0.36	0.09310	N	1	B	0.12630	0.006	B	0.17722	0.019	T	0.46005	-0.9222	9	0.11485	T	0.65	.	0.4596	0.00514	0.2006:0.161:0.202:0.4364	.	484	A8MXY4	ZNF99_HUMAN	N	484	ENSP00000380293:K484N	ENSP00000380293:K484N	K	-	3	2	ZNF99	22732826	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-7.797000	0.00029	-1.053000	0.03218	0.194000	0.17425	AAG		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22940986	C	A	22940986	3	1	47	1	0	0	0	0	1	0	0	0	18243	796	28	2	1672	2	ZNF99	19	22940986	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	458	22940986	36187997	1854	6251										
ZNF99	7652	broad.mit.edu	37	chr19	22941342	22941342	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctaaaagctttgctgcattCttcacatttgtagggttgct	9	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:22941342C>A	ENST00000596209.1	-	4	1459	c.1369G>T	c.(1369-1371)Gaa>Taa	p.E457*	ZNF99_ENST00000397104.3_Nonsense_Mutation_p.E366*	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E366*(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTGCTGCATTCTTCACATTTG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											71	74	73					19																	22941342		2041	4221	6262	22733182	SO:0001587	stop_gained	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1369G>T	19.37:g.22941342C>A	ENSP00000472969:p.Glu457*		22733182	M0R335	Nonsense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	13.41	2.227511	0.39399	.	.	ENSG00000213973	ENST00000397104	.	.	.	1.28	-2.28	0.06826	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	5.0864	0.14684	0.0:0.618:0.2123:0.1697	.	.	.	.	X	366	.	ENSP00000380293:E366X	E	-	1	0	ZNF99	22733182	0.000000	0.05858	0.003000	0.11579	0.059000	0.15707	-0.889000	0.04144	-0.130000	0.11599	0.395000	0.25975	GAA		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22941342	C	A	22941342	4	1	47	1	0	0	0	0	0	1	0	0	18243	922	32	2	2028	2	ZNF99	19	22941342	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	356	22941342	36187641	1855	6252										
ZNF675	171392	broad.mit.edu	37	chr19	23836153	23836153	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttctctccagtatgaattaTcttatgttcagtaagttttg	6	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:23836153T>G	ENST00000359788.4	-	4	1750	c.1582A>C	c.(1582-1584)Ata>Cta	p.I528L	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	528					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I528L(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GTATGAATTATCTTATGTTCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19											65	67	66					19																	23836153		2202	4299	6501	23627993	SO:0001583	missense	171392				CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.1582A>C	19.37:g.23836153T>G	ENSP00000352836:p.Ile528Leu		23627993	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	1.771	-0.484398	0.04383	.	.	ENSG00000197372	ENST00000359788	T	0.18016	2.24	0.886	0.886	0.19194	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05777	0.0151	N	0.01228	-0.945	0.23624	N	0.997263	B	0.18741	0.03	B	0.18561	0.022	T	0.34875	-0.9811	9	0.59425	D	0.04	.	6.7351	0.23405	0.0:0.0:0.0:1.0	.	528	Q8TD23	ZN675_HUMAN	L	528	ENSP00000352836:I528L	ENSP00000352836:I528L	I	-	1	0	ZNF675	23627993	0.000000	0.05858	0.874000	0.34290	0.873000	0.50193	-1.723000	0.01866	0.257000	0.21650	0.254000	0.18369	ATA		0.348	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		G	23836153	T	G	23836153	3	3	47	1	0	0	0	0	1	0	0	0	18121	1435	50	4	128	4	ZNF675	19	23836153	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	894811	23836153	35292830	1856	6253										
ZNF681	148213	broad.mit.edu	37	chr19	23928124	23928124	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgggcaaaatgagaacaaatAactgaaagaaataaaaataa	7	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:23928124A>C	ENST00000402377.3	-	4	369	c.228T>G	c.(226-228)gtT>gtG	p.V76V	ZNF681_ENST00000395385.3_Splice_Site_p.V7V	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V7V(1)|p.V76V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GAGAACAAATAACTGAAAGAA	0.299																																																2	Substitution - coding silent(2)	large_intestine(2)	19											16	16	16					19																	23928124		2185	4272	6457	23719964	SO:0001630	splice_region_variant	148213			AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.227-1T>G	19.37:g.23928124A>C			23719964	B3KVF7	Silent	SNP	ENST00000402377.3	37	CCDS12414.2																																																																																				0.299	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	Silent	C	23928124	A	C	23928124	5	2	47	1	0	0	0	0	0	0	1	0	18127	376	13	4	1713	4	ZNF681	19	23928124	Splice_Site	SNP	A	TCGA-AG-3892-01A-01W-1073-09	91971	23928124	35200859	1857	6254										
C19orf2	8725	broad.mit.edu	37	chr19	30477222	30477222	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttttgccttcatgccaggaAaacttgtccatactaatgaa	6	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:30477222A>C	ENST00000542441.2	+	4	562	c.265A>C	c.(265-267)Aaa>Caa	p.K89Q	URI1_ENST00000312051.6_Missense_Mutation_p.K49Q|URI1_ENST00000360605.4_Missense_Mutation_p.K71Q|URI1_ENST00000392271.1_Missense_Mutation_p.K13Q			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	89					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.K89Q(1)									CATGCCAGGAAAACTTGTCCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											147	140	142					19																	30477222		2203	4300	6503	35169062	SO:0001583	missense	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.265A>C	19.37:g.30477222A>C	ENSP00000442436:p.Lys89Gln		35169062	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970016	0.53614	.	.	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T;T;T	0.43688	0.94;0.94;0.94	5.25	4.18	0.49190	Prefoldin (1);Prefoldin subunit (1);	0.144833	0.64402	D	0.000007	T	0.35770	0.0943	L	0.31371	0.925	0.47949	D	0.999559	P;P;P	0.39576	0.514;0.489;0.679	B;B;B	0.43052	0.187;0.328;0.406	T	0.17349	-1.0372	10	0.41790	T	0.15	-25.6984	12.7194	0.57134	0.8636:0.1364:0.0:0.0	.	49;89;87	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	Q	87;13;89;49	ENSP00000376097:K13Q;ENSP00000442436:K89Q;ENSP00000312530:K49Q	ENSP00000312530:K49Q	K	+	1	0	C19orf2	35169062	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.750000	0.68712	2.121000	0.65114	0.460000	0.39030	AAA		0.373	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		C	30477222	A	C	30477222	3	2	47	1	0	0	0	0	1	0	0	0	1917	15	1	4	279	4	C19orf2	19	30477222	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6549098	30477222	28651761	1858	6255										
GPATCH1	55094	broad.mit.edu	37	chr19	33600679	33600679	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagacaaagagagaatcaaaGaaatgaagcaggcaactgac	10	6	1	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:33600679G>T	ENST00000170564.2	+	11	1656	c.1342G>T	c.(1342-1344)Gaa>Taa	p.E448*		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	448					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)	p.E448*(1)		breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					GAGAATCAAAGAAATGAAGCA	0.473																																					Pancreas(67;88 1713 4567 18227)											1	Substitution - Nonsense(1)	large_intestine(1)	19											41	45	43					19																	33600679		2203	4300	6503	38292519	SO:0001587	stop_gained	55094			AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.1342G>T	19.37:g.33600679G>T	ENSP00000170564:p.Glu448*		38292519	Q8IZV6|Q8N3B7|Q9NW94	Nonsense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	G	41	8.848263	0.98976	.	.	ENSG00000076650	ENST00000170564	.	.	.	5.74	5.74	0.90152	.	0.260679	0.46442	D	0.000294	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-37.4643	18.9258	0.92544	0.0:0.0:1.0:0.0	.	.	.	.	X	448	.	ENSP00000170564:E448X	E	+	1	0	GPATCH1	38292519	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.221000	0.58574	2.719000	0.93026	0.655000	0.94253	GAA		0.473	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		T	33600679	G	T	33600679	4	4	47	1	0	0	0	0	0	1	0	0	6610	943	33	2	1384	2	GPATCH1	19	33600679	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3123457	33600679	25528304	1859	6256										
LSM14A	26065	broad.mit.edu	37	chr19	34699900	34699900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taccttaccccaaagtagtgCggttggttctgcctttacac	8	12	1	0	rs572136254		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:34699900C>T	ENST00000433627.5	+	4	557	c.482C>T	c.(481-483)gCg>gTg	p.A161V	LSM14A_ENST00000540746.2_Intron|LSM14A_ENST00000544216.3_Missense_Mutation_p.A161V	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	161					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.A161V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CAAAGTAGTGCGGTTGGTTCT	0.343													C|||	1	0.000199681	8e-04	0	5008	,	,		17464	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											75	69	71					19																	34699900		2202	4300	6502	39391740	SO:0001583	missense	26065			AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.482C>T	19.37:g.34699900C>T	ENSP00000413964:p.Ala161Val		39391740	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983721	0.53827	.	.	ENSG00000257103	ENST00000544216;ENST00000433627	T;T	0.33654	1.41;1.4	5.3	4.24	0.50183	.	0.561534	0.19616	N	0.110002	T	0.26268	0.0641	L	0.33485	1.01	0.39388	D	0.966372	B;B	0.31837	0.342;0.007	B;B	0.20577	0.03;0.002	T	0.05852	-1.0860	10	0.19590	T	0.45	-4.4257	16.1108	0.81261	0.0:0.8659:0.1341:0.0	.	161;161	Q8ND56;Q8ND56-2	LS14A_HUMAN;.	V	161	ENSP00000446271:A161V;ENSP00000413964:A161V	ENSP00000314768:A161V	A	+	2	0	LSM14A	39391740	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	5.652000	0.67959	1.316000	0.45131	0.557000	0.71058	GCG		0.343	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		T	34699900	C	T	34699900	3	4	47	1	0	0	0	0	1	0	0	0	9083	768	27	1	496	1	LSM14A	19	34699900	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1099221	34699900	24429083	1860	6257										
ZNF181	339318	broad.mit.edu	37	chr19	35232812	35232812	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaccttaccgtacatcagaGaattcacactggagaaaagc	7	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:35232812G>T	ENST00000492450.1	+	4	1615	c.1526G>T	c.(1525-1527)aGa>aTa	p.R509I	ZNF181_ENST00000459757.2_Missense_Mutation_p.R508I|ZNF181_ENST00000392232.3_Missense_Mutation_p.R553I			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R445I(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GTACATCAGAGAATTCACACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	61	59					19																	35232812		2203	4300	6503	39924652	SO:0001583	missense	339318			BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"Zinc fingers, C2H2-type", "-"	12971	protein-coding gene	gene with protein product		606741	"zinc finger protein 181 (HHZ181)"				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1526G>T	19.37:g.35232812G>T	ENSP00000420727:p.Arg509Ile		39924652	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715158	0.48622	.	.	ENSG00000197841	ENST00000392232;ENST00000492450;ENST00000459757	T;T;T	0.24908	1.83;1.83;1.83	2.72	2.72	0.32119	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39937	0.1097	M	0.79011	2.435	0.39036	D	0.960039	D;D	0.62365	0.991;0.991	P;P	0.57468	0.821;0.821	T	0.39121	-0.9629	9	0.51188	T	0.08	.	5.6258	0.17482	0.1499:0.0:0.8501:0.0	.	508;509	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	I	553;509;508	ENSP00000376065:R553I;ENSP00000420727:R509I;ENSP00000419435:R508I	ENSP00000376065:R553I	R	+	2	0	ZNF181	39924652	0.112000	0.22096	1.000000	0.80357	0.998000	0.95712	2.678000	0.46900	1.839000	0.53478	0.655000	0.94253	AGA		0.388	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		T	35232812	G	T	35232812	3	4	47	1	0	0	0	0	1	0	0	0	17788	942	33	2	1540	2	ZNF181	19	35232812	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	532912	35232812	23896171	1861	6258										
ZNF599	148103	broad.mit.edu	37	chr19	35250402	35250402	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatgttgaattaaggaagagCtgtcacaaaaggccttccca	9	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:35250402C>T	ENST00000329285.8	-	4	1677	c.1304G>A	c.(1303-1305)aGc>aAc	p.S435N		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	435					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S435N(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TAAGGAAGAGCTGTCACAAAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											61	59	60					19																	35250402		2203	4300	6503	39942242	SO:0001583	missense	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1304G>A	19.37:g.35250402C>T	ENSP00000333802:p.Ser435Asn		39942242	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	3.999	-0.002907	0.07773	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.36157	1.27	2.53	1.4	0.22301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24236	0.0587	L	0.37800	1.135	0.09310	N	0.999999	B	0.14012	0.009	B	0.11329	0.006	T	0.23726	-1.0180	9	0.21014	T	0.42	.	6.2269	0.20714	0.2978:0.7022:0.0:0.0	.	435	Q96NL3	ZN599_HUMAN	N	434;435;209	ENSP00000333802:S435N	ENSP00000333802:S435N	S	-	2	0	ZNF599	39942242	0.000000	0.05858	0.292000	0.24919	0.996000	0.88848	-1.306000	0.02735	0.564000	0.29238	0.491000	0.48974	AGC		0.448	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		T	35250402	C	T	35250402	3	4	47	1	0	0	0	0	1	0	0	0	18068	797	28	3	466	3	ZNF599	19	35250402	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	17590	35250402	23878581	1862	6259										
ZNF599	148103	broad.mit.edu	37	chr19	35251262	35251262	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatgtttataactcaacttCtcagggcatatctctttgtg	6	9	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:35251262C>A	ENST00000329285.8	-	4	817	c.444G>T	c.(442-444)gaG>gaT	p.E148D		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E148D(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AACTCAACTTCTCAGGGCATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											135	141	139					19																	35251262		2203	4300	6503	39943102	SO:0001583	missense	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.444G>T	19.37:g.35251262C>A	ENSP00000333802:p.Glu148Asp		39943102	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	5.159	0.214996	0.09810	.	.	ENSG00000153896	ENST00000392231;ENST00000329285	T	0.25749	1.78	2.57	1.49	0.22878	.	.	.	.	.	T	0.12050	0.0293	N	0.14661	0.345	0.23156	N	0.998202	B	0.19583	0.037	B	0.18263	0.021	T	0.32640	-0.9899	9	0.21014	T	0.42	.	4.0339	0.09721	0.0:0.5035:0.0:0.4965	.	148	Q96NL3	ZN599_HUMAN	D	147;148	ENSP00000333802:E148D	ENSP00000333802:E148D	E	-	3	2	ZNF599	39943102	0.000000	0.05858	0.015000	0.15790	0.171000	0.22731	0.064000	0.14437	0.514000	0.28300	0.491000	0.48974	GAG		0.448	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35251262	C	A	35251262	3	1	47	1	0	0	0	0	1	0	0	0	18068	912	32	2	1326	2	ZNF599	19	35251262	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	860	35251262	23877721	1863	6260										
NPHS1	4868	broad.mit.edu	37	chr19	36339600	36339600	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagccaccatcgtagcagaAcccgcgggcgactggacttg	12	15	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:36339600A>G	ENST00000378910.5	-	9	1108	c.1109T>C	c.(1108-1110)gTt>gCt	p.V370A	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Missense_Mutation_p.V370A	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	370	Ig-like C2-type 4.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.V370A(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TCGTAGCAGAACCCGCGGGCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	51	52					19																	36339600		2203	4300	6503	41031440	SO:0001583	missense	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.1109T>C	19.37:g.36339600A>G	ENSP00000368190:p.Val370Ala		41031440	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	A	13.15	2.151548	0.38021	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.74526	-0.85;-0.85	5.43	4.41	0.53225	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	N	0.12502	0.225	0.47183	D	0.999345	D	0.58970	0.984	P	0.56563	0.801	T	0.59579	-0.7428	10	0.09084	T	0.74	-30.7701	8.8504	0.35196	0.9119:0.0:0.0881:0.0	.	370	O60500	NPHN_HUMAN	A	370	ENSP00000368190:V370A;ENSP00000343634:V370A	ENSP00000343634:V370A	V	-	2	0	NPHS1	41031440	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	3.675000	0.54605	2.081000	0.62600	0.378000	0.23410	GTT		0.602	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			G	36339600	A	G	36339600	3	3	47	1	0	0	0	0	1	0	0	0	10613	43	2	4	2700	4	NPHS1	19	36339600	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1088338	36339600	22789383	1864	6261										
ZFP14	57677	broad.mit.edu	37	chr19	36832236	36832236	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttttctccattatgaacGatctgatactcagtaagaaa	5	9	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:36832236G>A	ENST00000270001.7	-	5	607	c.492C>T	c.(490-492)atC>atT	p.I164I		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I164I(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					CATTATGAACGATCTGATACT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	19											164	158	160					19																	36832236		2203	4300	6503	41524076	SO:0001819	synonymous_variant	57677			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.492C>T	19.37:g.36832236G>A			41524076	A7MD23	Silent	SNP	ENST00000270001.7	37	CCDS33002.1																																																																																				0.388	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		A	36832236	G	A	36832236	2	1	47	1	0	0	0	0	0	0	0	1	17678	1048	37	1		1	ZFP14	19	36832236	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	492636	36832236	22296747	1865	6262										
ZNF382	84911	broad.mit.edu	37	chr19	37118264	37118264	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcacagaatacatacaggaGaaaaatccaatgggtgtcct	8	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37118264G>T	ENST00000292928.2	+	5	1578	c.1465G>T	c.(1465-1467)Gaa>Taa	p.E489*	ZNF382_ENST00000423582.1_Nonsense_Mutation_p.E440*|CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000435416.1_Nonsense_Mutation_p.E488*|ZNF382_ENST00000439428.1_Nonsense_Mutation_p.E488*	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	489	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E489*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACATACAGGAGAAAAATCCAA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											59	62	61					19																	37118264		2203	4300	6503	41810104	SO:0001587	stop_gained	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1465G>T	19.37:g.37118264G>T	ENSP00000292928:p.Glu489*		41810104	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Nonsense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	G	49	15.278673	0.99828	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	.	.	.	4.27	4.27	0.50696	.	0.000000	0.43919	D	0.000511	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.5487	0.68050	0.0:0.0:1.0:0.0	.	.	.	.	X	440;489;488;488	.	ENSP00000292928:E489X	E	+	1	0	ZNF382	41810104	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	5.280000	0.65603	2.375000	0.81037	0.591000	0.81541	GAA		0.443	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		T	37118264	G	T	37118264	4	4	47	1	0	0	0	0	0	1	0	0	17912	943	33	2	1475	2	ZNF382	19	37118264	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	286028	37118264	22010719	1866	6263										
ZNF790	388536	broad.mit.edu	37	chr19	37309484	37309484	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagtctgtccattcacagaGatttgcactattatgaattt	6	7	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37309484G>T	ENST00000356725.4	-	5	1882	c.1762C>A	c.(1762-1764)Ctc>Atc	p.L588I	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	588					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L588I(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CATTCACAGAGATTTGCACTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	107	106					19																	37309484		2203	4300	6503	42001324	SO:0001583	missense	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1762C>A	19.37:g.37309484G>T	ENSP00000349161:p.Leu588Ile		42001324		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649820	0.29336	.	.	ENSG00000197863	ENST00000356725	T	0.15603	2.41	2.75	1.65	0.23941	.	.	.	.	.	T	0.14141	0.0342	L	0.37850	1.14	0.09310	N	1	B	0.24186	0.099	B	0.16722	0.016	T	0.21827	-1.0234	9	0.72032	D	0.01	.	10.3963	0.44203	0.0:0.2024:0.7976:0.0	.	588	Q6PG37	ZN790_HUMAN	I	588	ENSP00000349161:L588I	ENSP00000349161:L588I	L	-	1	0	ZNF790	42001324	0.061000	0.20836	0.233000	0.24025	0.659000	0.38960	2.219000	0.42899	0.459000	0.27016	-0.282000	0.10007	CTC		0.333	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		T	37309484	G	T	37309484	3	4	47	1	0	0	0	0	1	0	0	0	18201	942	33	2	152	2	ZNF790	19	37309484	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	191220	37309484	21819499	1867	6264										
ZNF568	374900	broad.mit.edu	37	chr19	37427732	37427732	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctcaaagaaacttgtatCgagatgtgatgctggagaac	11	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37427732C>T	ENST00000333987.7	+	5	726	c.220C>T	c.(220-222)Cga>Tga	p.R74*	ZNF568_ENST00000455427.2_Nonsense_Mutation_p.R10*|ZNF568_ENST00000415168.1_Nonsense_Mutation_p.R10*|ZNF568_ENST00000427117.1_Nonsense_Mutation_p.R74*	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R10*(1)|p.R74*(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAACTTGTATCGAGATGTGAT	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											109	109	109					19																	37427732		2203	4300	6503	42119572	SO:0001587	stop_gained	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.220C>T	19.37:g.37427732C>T	ENSP00000334685:p.Arg74*		42119572	B4DS92|E7ER33|Q6N060|Q8NA64	Nonsense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	C	38	6.962021	0.97967	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000415168;ENST00000444991;ENST00000455427	.	.	.	4.69	2.4	0.29515	.	0.000000	0.32081	N	0.006601	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.8634	0.41129	0.3679:0.6321:0.0:0.0	.	.	.	.	X	74;74;10;74;10	.	ENSP00000334685:R74X	R	+	1	2	ZNF568	42119572	0.463000	0.25799	0.992000	0.48379	0.967000	0.64934	-0.049000	0.11924	1.154000	0.42482	0.655000	0.94253	CGA		0.423	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37427732	C	T	37427732	4	4	47	1	0	0	0	0	0	1	0	0	18038	876	31	1	230	1	ZNF568	19	37427732	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	118248	37427732	21701251	1868	6265										
ZNF585A	199704	broad.mit.edu	37	chr19	37642672	37642672	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttctctccagtgtgaattCgctgatgcacttggagctgt	11	10	1	2	rs144602706		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37642672C>T	ENST00000356958.4	-	5	2387	c.2129G>A	c.(2128-2130)cGa>cAa	p.R710Q	ZNF585A_ENST00000355533.2_Missense_Mutation_p.R347Q|ZNF585A_ENST00000292841.5_Missense_Mutation_p.R655Q|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.R655Q			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	710					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R655Q(1)		breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTGTGAATTCGCTGATGCAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	86	73	78		1964,1964	3.2	0.8	19	dbSNP_134	78	0,8594		0,0,4297	no	missense,missense	ZNF585A	NM_152655.2,NM_199126.1	43,43	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	655/715,655/715	37642672	1,12999	2203	4297	6500	42334512	SO:0001583	missense	199704			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.2129G>A	19.37:g.37642672C>T	ENSP00000349440:p.Arg710Gln		42334512	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	37		.	.	.	.	.	.	.	.	.	.	C	20.5	3.997914	0.74818	2.27E-4	0.0	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	3.16	3.16	0.36331	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.30510	N	0.009464	T	0.44414	0.1292	.	.	.	0.26273	N	0.978392	D	0.89917	1.0	D	0.80764	0.994	T	0.14008	-1.0488	9	0.72032	D	0.01	.	9.1822	0.37149	0.2177:0.7823:0.0:0.0	.	710	Q6P3V2	Z585A_HUMAN	Q	710;655;655;347	ENSP00000349440:R710Q;ENSP00000292841:R655Q;ENSP00000375998:R655Q;ENSP00000347724:R347Q	ENSP00000292841:R655Q	R	-	2	0	ZNF585A	42334512	0.000000	0.05858	0.753000	0.31225	0.983000	0.72400	1.273000	0.33121	1.753000	0.51906	0.655000	0.94253	CGA		0.438	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		T	37642672	C	T	37642672	3	4	47	1	0	0	0	0	1	0	0	0	18056	884	31	1	184	1	ZNF585A	19	37642672	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	214940	37642672	21486311	1869	6266										
ZNF585A	199704	broad.mit.edu	37	chr19	37643409	37643409	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catttattgcacatatagggCttttctcctgtgtgaattcg	8	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37643409C>A	ENST00000356958.4	-	5	1650	c.1392G>T	c.(1390-1392)aaG>aaT	p.K464N	ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000292841.5_Missense_Mutation_p.K409N|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.K409N			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K409N(1)		breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACATATAGGGCTTTTCTCCTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											125	121	122					19																	37643409		2203	4300	6503	42335249	SO:0001583	missense	199704			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1392G>T	19.37:g.37643409C>A	ENSP00000349440:p.Lys464Asn		42335249	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	37		.	.	.	.	.	.	.	.	.	.	C	12.53	1.965659	0.34659	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157	T;T;T	0.26067	1.76;1.76;1.76	2.63	0.363	0.16118	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.195067	0.25189	N	0.032462	T	0.22627	0.0546	.	.	.	0.80722	D	1	P	0.45531	0.86	B	0.42959	0.403	T	0.02654	-1.1128	9	0.87932	D	0	.	6.0242	0.19646	0.0:0.2595:0.0:0.7405	.	464	Q6P3V2	Z585A_HUMAN	N	464;409;409	ENSP00000349440:K464N;ENSP00000292841:K409N;ENSP00000375998:K409N	ENSP00000292841:K409N	K	-	3	2	ZNF585A	42335249	0.000000	0.05858	0.923000	0.36655	0.719000	0.41307	-1.378000	0.02556	-0.129000	0.11620	-1.817000	0.00601	AAG		0.393	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		A	37643409	C	A	37643409	3	1	47	1	0	0	0	0	1	0	0	0	18056	796	28	2	921	2	ZNF585A	19	37643409	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	737	37643409	21485574	1870	6267										
ZNF569	148266	broad.mit.edu	37	chr19	37903537	37903537	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctggtgtctaacaaggtgcgActtttggctgaaagccttgc	12	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37903537A>G	ENST00000316950.6	-	6	2580	c.2023T>C	c.(2023-2025)Tcg>Ccg	p.S675P	ZNF569_ENST00000392149.2_Missense_Mutation_p.S675P|ZNF569_ENST00000392150.2_Missense_Mutation_p.S516P	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	675					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S675P(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACAAGGTGCGACTTTTGGCTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											116	118	117					19																	37903537		2203	4300	6503	42595377	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.2023T>C	19.37:g.37903537A>G	ENSP00000325018:p.Ser675Pro		42595377	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.307277	0.40795	.	.	ENSG00000196437	ENST00000316950;ENST00000392149;ENST00000392150	T;T	0.32988	1.43;2.2	3.93	2.81	0.32909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.28376	N	0.015564	T	0.51295	0.1666	M	0.79805	2.47	0.09310	N	1	B;D	0.54601	0.115;0.967	B;D	0.65874	0.052;0.939	T	0.33445	-0.9868	10	0.72032	D	0.01	.	9.1541	0.36983	0.7077:0.2923:0.0:0.0	.	516;675	Q17RR6;Q5MCW4	.;ZN569_HUMAN	P	675;331;516	ENSP00000325018:S675P;ENSP00000375993:S516P	ENSP00000325018:S675P	S	-	1	0	ZNF569	42595377	0.000000	0.05858	1.000000	0.80357	0.972000	0.66771	0.054000	0.14205	1.770000	0.52166	0.460000	0.39030	TCG		0.413	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		G	37903537	A	G	37903537	3	3	47	1	0	0	0	0	1	0	0	0	18039	275	10	4	41	4	ZNF569	19	37903537	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	260128	37903537	21225446	1871	6268										
ZNF569	148266	broad.mit.edu	37	chr19	37904585	37904585	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccacattcattacatgcataAggtttctccccagtatgaac	5	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:37904585A>C	ENST00000316950.6	-	6	1532	c.975T>G	c.(973-975)ccT>ccG	p.P325P	ZNF569_ENST00000392149.2_Silent_p.P325P|ZNF569_ENST00000392150.2_Silent_p.P166P	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P325P(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TACATGCATAAGGTTTCTCCC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	19											138	136	137					19																	37904585		2203	4300	6503	42596425	SO:0001819	synonymous_variant	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.975T>G	19.37:g.37904585A>C			42596425	A8K1S2|Q15925|Q17RR6|Q96MQ2	Silent	SNP	ENST00000316950.6	37	CCDS12503.1																																																																																				0.388	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		C	37904585	A	C	37904585	2	2	47	1	0	0	0	0	0	0	0	1	18039	59	3	4		4	ZNF569	19	37904585	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1048	37904585	21224398	1872	6269										
ZNF793	390927	broad.mit.edu	37	chr19	38023267	38023267	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtttcaacagatacctgtgTcattcaaagatgtggttgtg	10	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38023267T>C	ENST00000587143.1	+	4	260	c.25T>C	c.(25-27)Tca>Cca	p.S9P	ZNF793_ENST00000587986.1_Missense_Mutation_p.S9P|ZNF793_ENST00000589319.1_Missense_Mutation_p.S9P|ZNF793_ENST00000542455.1_Missense_Mutation_p.S9P|ZNF793_ENST00000445217.1_Missense_Mutation_p.S9P|ZNF793_ENST00000588578.1_Missense_Mutation_p.S9P			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	9	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S9P(1)		kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GATACCTGTGTCATTCAAAGA	0.493																																					Melanoma(44;400 1431 1499 19093)											1	Substitution - Missense(1)	large_intestine(1)	19											53	55	54					19																	38023267		2161	4289	6450	42715107	SO:0001583	missense	390927			AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.25T>C	19.37:g.38023267T>C	ENSP00000468605:p.Ser9Pro		42715107	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	37	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663075	0.47572	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.01981	4.52;4.52	3.53	2.39	0.29439	Krueppel-associated box (4);	.	.	.	.	T	0.06690	0.0171	M	0.93720	3.45	0.23043	N	0.99838	P;P	0.48503	0.911;0.801	B;B	0.42163	0.378;0.378	T	0.26052	-1.0114	9	0.87932	D	0	.	5.787	0.18338	0.3658:0.0:0.0:0.6342	.	9;9	Q6ZN11;E9PGN4	ZN793_HUMAN;.	P	9;9;9;8	ENSP00000444355:S9P;ENSP00000396402:S9P	ENSP00000318811:S8P	S	+	1	0	ZNF793	42715107	0.998000	0.40836	1.000000	0.80357	0.518000	0.34316	1.072000	0.30678	1.590000	0.49995	0.460000	0.39030	TCA		0.493	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		C	38023267	T	C	38023267	3	2	47	1	0	0	0	0	1	0	0	0	18204	1667	58	4	31	4	ZNF793	19	38023267	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	118682	38023267	21105716	1873	6270										
ZNF571	51276	broad.mit.edu	37	chr19	38056518	38056518	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttttcaccactatgaattCtctgatgaagagtatattgt	7	6	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38056518C>A	ENST00000328550.2	-	4	911	c.812G>T	c.(811-813)aGa>aTa	p.R271I	ZNF571_ENST00000451802.2_Missense_Mutation_p.R271I|ZNF571_ENST00000358744.3_Missense_Mutation_p.R271I|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.R271I|ZNF571-AS1_ENST00000589750.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000589802.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R271I(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACTATGAATTCTCTGATGAAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	42	42					19																	38056518		2203	4298	6501	42748358	SO:0001583	missense	51276			AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"Zinc fingers, C2H2-type", "-"	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.812G>T	19.37:g.38056518C>A	ENSP00000333660:p.Arg271Ile		42748358	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.205309	0.39003	.	.	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.24908	1.83;1.83;1.83	3.7	2.66	0.31614	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35770	0.0943	M	0.64170	1.965	0.42382	D	0.992492	P	0.43431	0.807	P	0.51135	0.66	T	0.10800	-1.0614	9	0.49607	T	0.09	.	10.1108	0.42561	0.0:0.8958:0.0:0.1042	.	271	Q7Z3V5	ZN571_HUMAN	I	271	ENSP00000333660:R271I;ENSP00000392638:R271I;ENSP00000351594:R271I	ENSP00000333660:R271I	R	-	2	0	ZNF571	42748358	0.000000	0.05858	0.993000	0.49108	0.324000	0.28378	-0.903000	0.04084	0.747000	0.32809	0.313000	0.20887	AGA		0.373	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536		A	38056518	C	A	38056518	3	1	47	1	0	0	0	0	1	0	0	0	18042	913	32	2	1021	2	ZNF571	19	38056518	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	33251	38056518	21072465	1874	6271										
ZNF540	163255	broad.mit.edu	37	chr19	38102515	38102515	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagaaaaaagtaaaactcttCgtctgaaaggatccattttt	6	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38102515C>T	ENST00000592533.1	+	5	666	c.334C>T	c.(334-336)Cgt>Tgt	p.R112C	ZNF540_ENST00000589117.1_Missense_Mutation_p.R80C|ZNF540_ENST00000316433.4_Missense_Mutation_p.R112C|ZNF540_ENST00000586792.1_3'UTR|ZNF540_ENST00000343599.5_Missense_Mutation_p.R112C	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	112					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.R112C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAAAACTCTTCGTCTGAAAGG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	121	116					19																	38102515		2203	4300	6503	42794355	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.334C>T	19.37:g.38102515C>T	ENSP00000466274:p.Arg112Cys		42794355	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	C	8.700	0.909450	0.17833	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.09163	3.01	2.04	-1.6	0.08426	.	.	.	.	.	T	0.04003	0.0112	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38628	-0.9652	9	0.56958	D	0.05	.	3.7901	0.08716	0.0:0.4232:0.3393:0.2375	.	80;112	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	C	112;80	ENSP00000324598:R112C	ENSP00000324598:R112C	R	+	1	0	ZNF540	42794355	0.155000	0.22806	0.000000	0.03702	0.164000	0.22412	-0.129000	0.10515	-0.255000	0.09486	0.313000	0.20887	CGT		0.333	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		T	38102515	C	T	38102515	3	4	47	1	0	0	0	0	1	0	0	0	18014	884	31	1	348	1	ZNF540	19	38102515	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	45997	38102515	21026468	1875	6272										
ZNF540	163255	broad.mit.edu	37	chr19	38103730	38103730	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttactgaacaccagagaattCacactggtgaaaagccctat	7	10	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38103730C>A	ENST00000592533.1	+	5	1881	c.1549C>A	c.(1549-1551)Cac>Aac	p.H517N	ZNF540_ENST00000589117.1_Missense_Mutation_p.H485N|ZNF540_ENST00000316433.4_Missense_Mutation_p.H517N|ZNF540_ENST00000343599.5_Missense_Mutation_p.H517N	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	517					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.H517N(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGAGAATTCACACTGGTGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	78	76					19																	38103730		2203	4300	6503	42795570	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.1549C>A	19.37:g.38103730C>A	ENSP00000466274:p.His517Asn		42795570	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982560	0.93044	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T;T	0.67345	-0.26;1.34	2.39	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85075	0.5614	H	0.94183	3.505	0.30648	N	0.755686	D;D	0.76494	0.999;0.999	D;D	0.79108	0.986;0.992	T	0.83131	-0.0113	9	0.87932	D	0	.	11.8424	0.52361	0.0:1.0:0.0:0.0	.	485;517	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	N	517;485	ENSP00000324598:H517N;ENSP00000343768:H485N	ENSP00000324598:H517N	H	+	1	0	ZNF540	42795570	0.991000	0.36638	0.115000	0.21578	0.985000	0.73830	3.854000	0.55949	1.313000	0.45069	0.305000	0.20034	CAC		0.363	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		A	38103730	C	A	38103730	3	1	47	1	0	0	0	0	1	0	0	0	18014	826	29	2	1563	2	ZNF540	19	38103730	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1215	38103730	21025253	1876	6273										
ZNF781	163115	broad.mit.edu	37	chr19	38160221	38160221	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttctcaccagtgtgaattCtctggtgttgaataagagct	9	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38160221C>A	ENST00000590008.1	-	5	1681	c.829G>T	c.(829-831)Gaa>Taa	p.E277*	ZNF781_ENST00000358582.4_Nonsense_Mutation_p.E277*|ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000593040.1_5'Flank			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	277					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E277*(1)		NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						AGTGTGAATTCTCTGGTGTTG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											87	90	89					19																	38160221		2203	4300	6503	42852061	SO:0001587	stop_gained	163115			AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.829G>T	19.37:g.38160221C>A	ENSP00000466370:p.Glu277*		42852061	Q2VPJ8	Nonsense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	C	38	7.054786	0.98032	.	.	ENSG00000196381	ENST00000358582;ENST00000545586	.	.	.	2.47	-0.0973	0.13633	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999987	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-6.1485	5.7755	0.18277	0.0:0.5062:0.3728:0.121	.	.	.	.	X	277	.	ENSP00000351391:E277X	E	-	1	0	ZNF781	42852061	0.000000	0.05858	0.031000	0.17742	0.010000	0.07245	-0.012000	0.12699	-0.062000	0.13088	-0.385000	0.06624	GAA		0.368	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		A	38160221	C	A	38160221	4	1	47	1	0	0	0	0	0	1	0	0	18193	922	32	2	158	2	ZNF781	19	38160221	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	56491	38160221	20968762	1877	6274										
ZNF573	126231	broad.mit.edu	37	chr19	38230678	38230678	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcttcccaccagtgtgaattCtctcatgttgaacaatgtgt	8	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:38230678C>A	ENST00000590414.2	-	4	734	c.713G>T	c.(712-714)aGa>aTa	p.R238I	ZNF573_ENST00000357309.3_Missense_Mutation_p.R150I|ZNF573_ENST00000536220.1_Missense_Mutation_p.R150I|ZNF573_ENST00000339503.4_Missense_Mutation_p.R180I|ZNF573_ENST00000392138.1_Missense_Mutation_p.R151I			Q86YE8	ZN573_HUMAN	zinc finger protein 573	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R180I(1)		NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			AGTGTGAATTCTCTCATGTTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											116	108	111					19																	38230678		2203	4300	6503	42922518	SO:0001583	missense	126231			AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.713G>T	19.37:g.38230678C>A	ENSP00000465020:p.Arg238Ile		42922518	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	ENST00000590414.2	37	CCDS59381.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212986	0.58452	.	.	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	2.64	1.59	0.23543	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33177	0.0854	L	0.39467	1.215	0.35935	D	0.832796	D;D;D;D	0.76494	0.996;0.996;0.999;0.998	P;P;P;P	0.61800	0.887;0.829;0.894;0.829	T	0.32824	-0.9892	9	0.52906	T	0.07	.	8.1637	0.31213	0.0:0.8701:0.0:0.1299	.	151;180;218;150	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	I	151;150;150;180;150	ENSP00000375983:R151I;ENSP00000440464:R150I;ENSP00000349861:R150I;ENSP00000340171:R180I	ENSP00000340171:R180I	R	-	2	0	ZNF573	42922518	0.000000	0.05858	0.870000	0.34147	0.986000	0.74619	-1.676000	0.01946	0.315000	0.23110	0.650000	0.86243	AGA		0.448	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		A	38230678	C	A	38230678	3	1	47	1	0	0	0	0	1	0	0	0	18044	913	32	2	1288	2	ZNF573	19	38230678	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	70457	38230678	20898305	1878	6275										
RYR1	6261	broad.mit.edu	37	chr19	39005728	39005728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctactccctgggaaccaccAagaacacttatgtggaaaag	8	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:39005728A>G	ENST00000359596.3	+	64	9535	c.9535A>G	c.(9535-9537)Aag>Gag	p.K3179E	RYR1_ENST00000355481.4_Missense_Mutation_p.K3179E|RYR1_ENST00000360985.3_Missense_Mutation_p.K3179E			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3179					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.K3179E(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGAACCACCAAGAACACTTA	0.607											OREG0025449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	19											62	55	57					19																	39005728		2203	4300	6503	43697568	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9535A>G	19.37:g.39005728A>G	ENSP00000352608:p.Lys3179Glu	882	43697568	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417389	0.62622	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	T;T;T	0.64991	-0.13;-0.13;-0.13	4.67	4.67	0.58626	.	0.069980	0.53938	U	0.000053	T	0.66187	0.2764	M	0.80982	2.52	0.31753	N	0.634284	B;B;B	0.33694	0.421;0.167;0.104	B;B;B	0.37601	0.254;0.169;0.081	T	0.73062	-0.4101	10	0.36615	T	0.2	.	13.9206	0.63928	1.0:0.0:0.0:0.0	.	3179;3179;3179	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	E	3179;3179;3179;99	ENSP00000352608:K3179E;ENSP00000347667:K3179E;ENSP00000354254:K3179E	ENSP00000347667:K3179E	K	+	1	0	RYR1	43697568	1.000000	0.71417	0.949000	0.38748	0.839000	0.47603	7.245000	0.78237	1.944000	0.56390	0.533000	0.62120	AAG		0.607	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	39005728	A	G	39005728	3	3	47	1	0	0	0	0	1	0	0	0	13805	131	5	4	9789	4	RYR1	19	39005728	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	775050	39005728	20123255	1879	6276										
DLL3	10683	broad.mit.edu	37	chr19	39991276	39991276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaccttctctttcatcatcGaaacctggagagaggagtta	9	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:39991276G>A	ENST00000205143.4	+	3	380	c.373G>A	c.(373-375)Gaa>Aaa	p.E125K	DLL3_ENST00000356433.5_Missense_Mutation_p.E125K	NM_016941.3	NP_058637.1	Q9NYJ7	DLL3_HUMAN	delta-like 3 (Drosophila)	125					compartment pattern specification (GO:0007386)|negative regulation of neurogenesis (GO:0050768)|Notch signaling pathway (GO:0007219)|paraxial mesoderm development (GO:0048339)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)	integral component of membrane (GO:0016021)	Notch binding (GO:0005112)	p.E125K(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)	19	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TTTCATCATCGAAACCTGGAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											146	141	143					19																	39991276		2203	4300	6503	44683116	SO:0001583	missense	10683			AF241373	CCDS12537.1, CCDS12538.1	19q13.2	2008-05-14	2001-12-03			ENSG00000090932			2909	protein-coding gene	gene with protein product		602768	"delta (Drosophila)-like 3"			10364530, 10742114	Standard	NM_203486		Approved	SCDO1	uc002olx.2	Q9NYJ7		ENST00000205143.4:c.373G>A	19.37:g.39991276G>A	ENSP00000205143:p.Glu125Lys		44683116	E9PFG2|Q8NBS4	Missense_Mutation	SNP	ENST00000205143.4	37	CCDS12538.1	.	.	.	.	.	.	.	.	.	.	G	32	5.144960	0.94603	.	.	ENSG00000090932	ENST00000356433;ENST00000205143	D;D	0.92805	-3.04;-3.11	4.45	4.45	0.53987	.	0.339252	0.21369	N	0.075669	D	0.96062	0.8717	M	0.84846	2.72	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.991;0.991	D	0.96052	0.9032	9	.	.	.	.	14.8434	0.70243	0.0:0.0:1.0:0.0	.	125;125;125	Q8NBS4;Q9NYJ7;E9PFG2	.;DLL3_HUMAN;.	K	125	ENSP00000348810:E125K;ENSP00000205143:E125K	.	E	+	1	0	DLL3	44683116	1.000000	0.71417	0.951000	0.38953	0.969000	0.65631	7.364000	0.79526	2.426000	0.82243	0.561000	0.74099	GAA		0.537	DLL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464958.1			A	39991276	G	A	39991276	3	1	47	1	0	0	0	0	1	0	0	0	4578	1059	37	1	383	1	DLL3	19	39991276	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	985548	39991276	19137707	1880	6277										
LGALS14	56891	broad.mit.edu	37	chr19	40197310	40197310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggacaccgatcctcacttTtgtgtgagtactccatggtc	10	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:40197310T>G	ENST00000392052.3	+	2	312	c.89T>G	c.(88-90)tTt>tGt	p.F30C	LGALS14_ENST00000360675.3_Missense_Mutation_p.F59C	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	30	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)	p.F59C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			ATCCTCACTTTTGTGTGAGTA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	19											222	178	193					19																	40197310		2203	4300	6503	44889150	SO:0001583	missense	56891			AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"Lectins, galactoside-binding"	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.89T>G	19.37:g.40197310T>G	ENSP00000375905:p.Phe30Cys		44889150	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	.	.	.	.	.	.	.	.	.	.	.	8.368	0.834598	0.16820	.	.	ENSG00000006659	ENST00000392052;ENST00000360675	T;T	0.18016	2.24;2.24	0.906	-0.182	0.13287	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.22399	0.0540	M	0.64080	1.96	0.46260	D	0.998954	P;P	0.45594	0.806;0.862	P;P	0.51999	0.687;0.614	T	0.09422	-1.0675	9	0.49607	T	0.09	.	3.0038	0.06021	0.0:0.3013:0.0:0.6987	.	30;59	Q8TCE9;A8MPV8	PPL13_HUMAN;.	C	30;59	ENSP00000375905:F30C;ENSP00000353893:F59C	ENSP00000353893:F59C	F	+	2	0	LGALS14	44889150	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.160000	0.16462	-0.146000	0.11274	-0.815000	0.03128	TTT		0.488	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129		G	40197310	T	G	40197310	3	3	47	1	0	0	0	0	1	0	0	0	8763	1841	64	4	201	4	LGALS14	19	40197310	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	206034	40197310	18931673	1881	6278										
LYPD4	147719	broad.mit.edu	37	chr19	42342062	42342062	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tagaagcagccaaggggcaaGaattagtggtgacaaaattt	12	5	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:42342062G>T	ENST00000330743.3	-	4	1696	c.485C>A	c.(484-486)tCt>tAt	p.S162Y	LYPD4_ENST00000343055.4_Missense_Mutation_p.S127Y|LYPD4_ENST00000601246.1_Missense_Mutation_p.S127Y|AC020956.3_ENST00000593354.1_lincRNA	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	162	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.S162Y(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						CAAGGGGCAAGAATTAGTGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											76	73	74					19																	42342062		2203	4300	6503	47033902	SO:0001583	missense	147719			AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.485C>A	19.37:g.42342062G>T	ENSP00000328737:p.Ser162Tyr		47033902	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	g	10.11	1.260194	0.23051	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.70749	-0.51;-0.51	4.13	-0.535	0.11879	CD59 antigen (1);	0.798013	0.10997	N	0.610978	T	0.60779	0.2295	L	0.51422	1.61	0.09310	N	1	P;P	0.36392	0.495;0.551	B;B	0.38562	0.181;0.276	T	0.54616	-0.8267	10	0.62326	D	0.03	-0.0648	3.7443	0.08542	0.268:0.0:0.5476:0.1844	.	127;162	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	Y	162;127	ENSP00000328737:S162Y;ENSP00000339568:S127Y	ENSP00000328737:S162Y	S	-	2	0	LYPD4	47033902	0.136000	0.22515	0.066000	0.19879	0.045000	0.14185	0.279000	0.18771	0.016000	0.14998	0.457000	0.33378	TCT		0.493	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506		T	42342062	G	T	42342062	3	4	47	1	0	0	0	0	1	0	0	0	9142	942	33	2	263	2	LYPD4	19	42342062	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2144752	42342062	16786921	1882	6279										
ATP1A3	478	broad.mit.edu	37	chr19	42482426	42482426	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagttcacgtcatcacagtcGaaggcaaagcccttggggaa	11	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:42482426G>A	ENST00000302102.5	-	13	1833	c.1683C>T	c.(1681-1683)ttC>ttT	p.F561F	ATP1A3_ENST00000545399.1_Silent_p.F574F|ATP1A3_ENST00000602133.1_Silent_p.F531F|ATP1A3_ENST00000543770.1_Silent_p.F572F	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	561					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.F561F(2)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						CATCACAGTCGAAGGCAAAGC	0.607																																																2	Substitution - coding silent(2)	large_intestine(2)	19											75	72	73					19																	42482426		2203	4300	6503	47174266	SO:0001819	synonymous_variant	478				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1683C>T	19.37:g.42482426G>A			47174266	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Silent	SNP	ENST00000302102.5	37	CCDS12594.1																																																																																				0.607	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42482426	G	A	42482426	2	1	47	1	0	0	0	0	0	0	0	1	1131	1049	37	1		1	ATP1A3	19	42482426	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	140364	42482426	16646557	1883	6280										
POU2F2	5452	broad.mit.edu	37	chr19	42626525	42626525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgtctggtccatttctttCggtgtctgcaaagagaggga	13	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:42626525C>T	ENST00000526816.2	-	3	115	c.100G>A	c.(100-102)Gaa>Aaa	p.E34K	POU2F2_ENST00000342301.4_Missense_Mutation_p.E34K|POU2F2_ENST00000524801.2_5'UTR|POU2F2_ENST00000389341.5_Missense_Mutation_p.E34K|POU2F2_ENST00000533720.1_Missense_Mutation_p.E34K|POU2F2_ENST00000560398.1_Missense_Mutation_p.E34K|POU2F2_ENST00000529952.1_Missense_Mutation_p.E34K|POU2F2_ENST00000560558.1_Missense_Mutation_p.E34K|POU2F2_ENST00000529067.1_Missense_Mutation_p.E34K			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	34					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E34K(1)		kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	CCATTTCTTTCGGTGTCTGCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											137	125	129					19																	42626525		2203	4300	6503	47318365	SO:0001583	missense	5452				CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.100G>A	19.37:g.42626525C>T	ENSP00000431603:p.Glu34Lys		47318365	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.582937	0.65992	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952;ENST00000531773	D;D;D;D;D	0.85088	-1.87;-1.94;-1.94;-1.68;-1.86	3.56	3.56	0.40772	.	2.677360	0.01454	N	0.015615	T	0.78272	0.4257	L	0.29908	0.895	0.38021	D	0.934831	B;P;B	0.47253	0.196;0.892;0.196	B;B;B	0.32677	0.011;0.15;0.011	T	0.72554	-0.4258	10	0.59425	D	0.04	.	12.5321	0.56122	0.0:1.0:0.0:0.0	.	34;34;34	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	K	34;34;34;34;33;34;34;22	ENSP00000373992:E34K;ENSP00000339369:E34K;ENSP00000437221:E34K;ENSP00000437224:E34K;ENSP00000436988:E34K	ENSP00000292077:E34K	E	-	1	0	POU2F2	47318365	0.994000	0.37717	0.976000	0.42696	0.989000	0.77384	3.421000	0.52742	2.005000	0.58758	0.478000	0.44815	GAA		0.582	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			T	42626525	C	T	42626525	3	4	47	1	0	0	0	0	1	0	0	0	12303	893	31	1	1339	1	POU2F2	19	42626525	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	144099	42626525	16502458	1884	6281										
CEACAM8	1088	broad.mit.edu	37	chr19	43093759	43093759	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcctgggactgaccgggaGactctgaccatttacccacc	10	15	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:43093759G>T	ENST00000244336.5	-	3	654	c.553C>A	c.(553-555)Ctc>Atc	p.L185I	CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	185	Ig-like C2-type 1.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.L185I(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				CTGACCGGGAGACTCTGACCA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											239	210	220					19																	43093759		2203	4300	6503	47785599	SO:0001583	missense	1088			D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.553C>A	19.37:g.43093759G>T	ENSP00000244336:p.Leu185Ile		47785599	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	g	13.39	2.221609	0.39300	.	.	ENSG00000124469	ENST00000244336	T	0.49139	0.79	2.46	1.23	0.21249	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61198	0.2328	M	0.73753	2.245	0.09310	N	1	D	0.54601	0.967	D	0.63488	0.915	T	0.46317	-0.9200	9	0.87932	D	0	.	6.3657	0.21453	0.0:0.3131:0.6869:0.0	.	185	P31997	CEAM8_HUMAN	I	185	ENSP00000244336:L185I	ENSP00000244336:L185I	L	-	1	0	CEACAM8	47785599	0.001000	0.12720	0.011000	0.14972	0.077000	0.17291	0.101000	0.15251	1.387000	0.46486	0.313000	0.20887	CTC		0.527	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			T	43093759	G	T	43093759	3	4	47	1	0	0	0	0	1	0	0	0	3204	942	33	2	508	2	CEACAM8	19	43093759	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	467234	43093759	16035224	1885	6282										
PSG11	5680	broad.mit.edu	37	chr19	43529161	43529161	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgggtggctgggcttcaaTcatgacttgggcagtggtag	16	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:43529161T>G	ENST00000401740.1	-	2	215	c.112A>C	c.(112-114)Att>Ctt	p.I38L	PSG11_ENST00000306322.7_Intron|PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.I38L			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	38	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.I38L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				TGGGCTTCAATCATGACTTGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	19											199	202	201					19																	43529161		2201	4295	6496	48221001	SO:0001583	missense	5675			U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.112A>C	19.37:g.43529161T>G	ENSP00000384995:p.Ile38Leu		48221001	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	t	12.05	1.821771	0.32237	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.01725	4.67;4.67	0.929	-0.193	0.13244	Immunoglobulin-like fold (1);	.	.	.	.	T	0.07818	0.0196	M	0.83852	2.665	0.09310	N	1	D	0.61697	0.99	D	0.87578	0.998	T	0.21999	-1.0229	9	0.87932	D	0	.	2.7795	0.05357	0.0:0.3533:0.0:0.6467	.	38	Q9UQ72	PSG11_HUMAN	L	38	ENSP00000319140:I38L;ENSP00000384995:I38L	ENSP00000319140:I38L	I	-	1	0	PSG11	48221001	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-0.460000	0.06720	-0.109000	0.12044	0.155000	0.16302	ATT		0.468	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		G	43529161	T	G	43529161	3	3	47	1	0	0	0	0	1	0	0	0	12688	1435	50	4	911	4	PSG11	19	43529161	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	435402	43529161	15599822	1886	6283										
PSG4	5672	broad.mit.edu	37	chr19	43699230	43699230	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gataaggtcctgtttcatttCtcgtgacattgggtagaatg	11	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:43699230C>T	ENST00000405312.3	-	4	1142	c.905G>A	c.(904-906)aGa>aAa	p.R302K	PSG4_ENST00000244295.9_Intron|PSG4_ENST00000433626.2_Missense_Mutation_p.R209K	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	302	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.R302K(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				TGTTTCATTTCTCGTGACATT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											223	204	210					19																	43699230		2202	4295	6497	48391070	SO:0001583	missense	5672				CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9521	protein-coding gene	gene with protein product	"pregnancy-specific beta-1-glycoprotein 4"	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.905G>A	19.37:g.43699230C>T	ENSP00000384770:p.Arg302Lys		48391070	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	c	3.363	-0.130030	0.06753	.	.	ENSG00000243137	ENST00000405312;ENST00000433626	T;T	0.12039	2.72;2.72	1.45	1.45	0.22620	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.17874	0.0429	M	0.74258	2.255	0.09310	N	1	B;B	0.22604	0.072;0.041	B;B	0.39339	0.297;0.097	T	0.48906	-0.8993	9	0.05436	T	0.98	.	6.2719	0.20959	0.0:1.0:0.0:0.0	.	209;302	E7EX79;Q00888	.;PSG4_HUMAN	K	302;209	ENSP00000384770:R302K;ENSP00000387864:R209K	ENSP00000384770:R302K	R	-	2	0	PSG4	48391070	0.001000	0.12720	0.067000	0.19924	0.007000	0.05969	0.713000	0.25794	0.774000	0.33427	0.391000	0.25812	AGA		0.478	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		T	43699230	C	T	43699230	3	4	47	1	0	0	0	0	1	0	0	0	12691	913	32	3	366	3	PSG4	19	43699230	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	170069	43699230	15429753	1887	6284										
ZNF404	342908	broad.mit.edu	37	chr19	44378171	44378171	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctcctgatggtacgcattTacttcataatttcttttttc	5	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:44378171T>C	ENST00000587539.1	-	3	194	c.195A>G	c.(193-195)gtA>gtG	p.V65V	ZNF404_ENST00000324394.6_Silent_p.V63V	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	65	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V63V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				GGTACGCATTTACTTCATAAT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	19											41	42	42					19																	44378171		1810	4059	5869	49070011	SO:0001819	synonymous_variant	342908			XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.195A>G	19.37:g.44378171T>C			49070011	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																				0.318	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		C	44378171	T	C	44378171	2	2	47	1	0	0	0	0	0	0	0	1	17925	1741	61	4		4	ZNF404	19	44378171	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	678941	44378171	14750812	1888	6285										
ZNF224	7767	broad.mit.edu	37	chr19	44611396	44611396	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaggcgagatctttatacGcatcatatggtccacacggg	11	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:44611396G>A	ENST00000336976.6	+	6	1337	c.1083G>A	c.(1081-1083)acG>acA	p.T361T	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	361					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T361T(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				ATCTTTATACGCATCATATGG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	19											106	102	103					19																	44611396		2203	4300	6503	49303236	SO:0001819	synonymous_variant	7767			AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1083G>A	19.37:g.44611396G>A			49303236	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																				0.438	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		A	44611396	G	A	44611396	2	1	47	1	0	0	0	0	0	0	0	1	17817	1074	38	1		1	ZNF224	19	44611396	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	233225	44611396	14517587	1889	6286										
ZNF235	9310	broad.mit.edu	37	chr19	44793149	44793149	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacagaagcttgaatagattCtcctgctcccacttgacagg	8	12	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:44793149C>A	ENST00000291182.4	-	5	541	c.439G>T	c.(439-441)Gaa>Taa	p.E147*	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	147					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E147*(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TGAATAGATTCTCCTGCTCCC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											89	91	90					19																	44793149		2203	4300	6503	49484989	SO:0001587	stop_gained	9310			X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"Zinc fingers, C2H2-type", "-"	12866	protein-coding gene	gene with protein product		604749	"zinc finger protein homologous to Zfp93 in mouse"	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.439G>T	19.37:g.44793149C>A	ENSP00000291182:p.Glu147*		49484989	B4DTQ7|O14898|O14899|Q17RR8	Nonsense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067505	0.93898	.	.	ENSG00000159917	ENST00000433015;ENST00000391957;ENST00000291182;ENST00000359844	.	.	.	3.92	0.384	0.16244	.	0.778461	0.10471	N	0.670758	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	4.4299	0.11522	0.0:0.5144:0.1749:0.3107	.	.	.	.	X	143;147;147;69	.	ENSP00000291182:E147X	E	-	1	0	ZNF235	49484989	0.014000	0.17966	0.047000	0.18901	0.858000	0.48976	0.588000	0.23924	0.339000	0.23719	0.462000	0.41574	GAA		0.428	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			A	44793149	C	A	44793149	4	1	47	1	0	0	0	0	0	1	0	0	17827	922	32	2	1781	2	ZNF235	19	44793149	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	181753	44793149	14335834	1890	6287										
ZNF229	7772	broad.mit.edu	37	chr19	44934151	44934151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgaagccatttctgtattCgttacttttcaagccattct	5	11	3	1	rs553024331		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:44934151C>T	ENST00000588931.1	-	6	1238	c.805G>A	c.(805-807)Gaa>Aaa	p.E269K	ZNF229_ENST00000291187.4_Missense_Mutation_p.E263K|ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E269K(1)		breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				TTTCTGTATTCGTTACTTTTC	0.423													C|||	1	0.000199681	8e-04	0	5008	,	,		19489	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											88	82	84					19																	44934151		1920	4120	6040	49625991	SO:0001583	missense	7772			AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.805G>A	19.37:g.44934151C>T	ENSP00000466519:p.Glu269Lys		49625991	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980874	0.53827	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.92	0.298	0.15766	.	.	.	.	.	T	0.23133	0.0559	N	0.14661	0.345	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.21177	-1.0253	8	0.54805	T	0.06	.	5.8196	0.18520	0.0:0.6443:0.1609:0.1948	.	269	Q9UJW7	ZN229_HUMAN	K	269	.	ENSP00000291187:E269K	E	-	1	0	ZNF229	49625991	0.000000	0.05858	0.008000	0.14137	0.048000	0.14542	0.282000	0.18829	0.629000	0.30376	-0.192000	0.12808	GAA		0.423	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		T	44934151	C	T	44934151	3	4	47	1	0	0	0	0	1	0	0	0	17821	893	31	1	1676	1	ZNF229	19	44934151	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	141002	44934151	14194832	1891	6288										
ZNF180	7733	broad.mit.edu	37	chr19	44981076	44981076	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctctccagtgtgagttCtttgatgtgcaacaagctga	10	8	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:44981076C>A	ENST00000221327.4	-	5	1903	c.1622G>T	c.(1621-1623)aGa>aTa	p.R541I	ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000592529.1_Missense_Mutation_p.R514I|ZNF180_ENST00000391956.4_Missense_Mutation_p.R516I|AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	541					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R541I(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AGTGTGAGTTCTTTGATGTGC	0.428																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - Missense(1)	large_intestine(1)	19											77	77	77					19																	44981076		2203	4300	6503	49672916	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1622G>T	19.37:g.44981076C>A	ENSP00000221327:p.Arg541Ile		49672916	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.332220	0.60853	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.02446	4.29;4.29	5.23	4.15	0.48705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45126	D	0.000394	T	0.05044	0.0135	M	0.61703	1.905	0.80722	D	1	P;P;P	0.39717	0.633;0.684;0.684	B;B;B	0.36959	0.152;0.237;0.237	T	0.26258	-1.0108	10	0.87932	D	0	-27.6018	14.0615	0.64802	0.1515:0.8485:0.0:0.0	.	516;540;541	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	I	541;516	ENSP00000221327:R541I;ENSP00000375818:R516I	ENSP00000221327:R541I	R	-	2	0	ZNF180	49672916	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	0.299000	0.19138	2.437000	0.82529	0.467000	0.42956	AGA		0.428	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44981076	C	A	44981076	3	1	47	1	0	0	0	0	1	0	0	0	17787	913	32	2	460	2	ZNF180	19	44981076	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	46925	44981076	14147907	1892	6289										
PNMAL1	55228	broad.mit.edu	37	chr19	46973998	46973998	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcggcatcctgggtagggtCtctacagaccactctccaga	10	14	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:46973998C>A	ENST00000313683.10	-	2	600	c.295G>T	c.(295-297)Gac>Tac	p.D99Y	PNMAL1_ENST00000438932.2_Missense_Mutation_p.D99Y|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	99								p.D99Y(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		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)		tgggtagggtctctacagacc	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											48	45	46					19																	46973998		2203	4300	6503	51665838	SO:0001583	missense	55228			BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"Paraneoplastic Ma antigens"	25578	protein-coding gene	gene with protein product			"PNMA-like 1"			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.295G>T	19.37:g.46973998C>A	ENSP00000318131:p.Asp99Tyr		51665838	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Missense_Mutation	SNP	ENST00000313683.10	37	CCDS33059.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.316886	0.60524	.	.	ENSG00000182013	ENST00000438932;ENST00000313683;ENST00000417103	T;T	0.12039	2.72;2.72	3.36	2.32	0.28847	.	0.197542	0.25127	N	0.032933	T	0.28234	0.0697	M	0.67953	2.075	0.34277	D	0.681746	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.964	T	0.35101	-0.9802	10	0.59425	D	0.04	-15.5645	6.6377	0.22891	0.0:0.8695:0.0:0.1305	.	99;99	Q86V59-2;Q86V59	.;PNML1_HUMAN	Y	99	ENSP00000410273:D99Y;ENSP00000318131:D99Y	ENSP00000318131:D99Y	D	-	1	0	PNMAL1	51665838	0.899000	0.30636	0.997000	0.53966	0.995000	0.86356	1.165000	0.31822	0.992000	0.38840	0.655000	0.94253	GAC		0.542	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		A	46973998	C	A	46973998	3	1	47	1	0	0	0	0	1	0	0	0	12188	913	32	2	1054	2	PNMAL1	19	46973998	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1992922	46973998	12154985	1893	6290										
ZC3H4	23211	broad.mit.edu	37	chr19	47597336	47597336	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcgctagaagaagcatggCgctgtaatgacaggggaagg	15	7	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:47597336C>T	ENST00000253048.5	-	4	420	c.383G>A	c.(382-384)cGc>cAc	p.R128H	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	128							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R128H(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		AGAAGCATGGCGCTGTAATGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											59	61	61					19																	47597336		2047	4193	6240	52289176	SO:0001630	splice_region_variant	23211			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.382-1G>A	19.37:g.47597336C>T			52289176	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014052	0.75161	.	.	ENSG00000130749	ENST00000253048	T	0.17054	2.3	5.9	5.9	0.94986	.	0.373373	0.27109	N	0.020899	T	0.25158	0.0611	N	0.13140	0.3	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.08027	-1.0742	10	0.10902	T	0.67	.	19.0504	0.93041	0.0:1.0:0.0:0.0	.	128	Q9UPT8	ZC3H4_HUMAN	H	128	ENSP00000253048:R128H	ENSP00000253048:R128H	R	-	2	0	ZC3H4	52289176	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.214000	0.77958	2.788000	0.95919	0.650000	0.86243	CGC		0.567	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		Missense_Mutation	T	47597336	C	T	47597336	5	4	47	1	0	0	0	0	0	0	1	0	17609	782	27	1	3576	1	ZC3H4	19	47597336	Splice_Site	SNP	C	TCGA-AG-3892-01A-01W-1073-09	623338	47597336	11531647	1894	6291										
NAPA	8775	broad.mit.edu	37	chr19	48006731	48006731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgctgctctggcgtagatttCgcatgcttcctctattttgg	10	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:48006731C>T	ENST00000263354.3	-	2	426	c.127G>A	c.(127-129)Gaa>Aaa	p.E43K	NAPA-AS1_ENST00000594367.1_RNA|NAPA_ENST00000595227.1_Missense_Mutation_p.E43K|NAPA_ENST00000593785.1_5'UTR	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	43					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)		p.E43K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		GCGTAGATTTCGCATGCTTCC	0.478																																					Ovarian(185;1135 2042 27703 31345 42493)											1	Substitution - Missense(1)	large_intestine(1)	19											192	168	176					19																	48006731		2203	4300	6503	52698543	SO:0001583	missense	8775			U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.127G>A	19.37:g.48006731C>T	ENSP00000263354:p.Glu43Lys		52698543	A8K879|Q96IK3|Q9BVJ3	Missense_Mutation	SNP	ENST00000263354.3	37	CCDS12702.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791893	0.90453	.	.	ENSG00000105402	ENST00000263354	T	0.37584	1.19	5.27	5.27	0.74061	Tetratricopeptide-like helical (1);	0.100973	0.64402	D	0.000003	T	0.52661	0.1748	M	0.91038	3.17	0.80722	D	1	P	0.37636	0.603	B	0.38106	0.265	T	0.64647	-0.6358	10	0.72032	D	0.01	-4.4277	17.8382	0.88707	0.0:1.0:0.0:0.0	.	43	P54920	SNAA_HUMAN	K	43	ENSP00000263354:E43K	ENSP00000263354:E43K	E	-	1	0	NAPA	52698543	1.000000	0.71417	0.964000	0.40570	0.990000	0.78478	7.321000	0.79088	2.735000	0.93741	0.655000	0.94253	GAA		0.478	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		T	48006731	C	T	48006731	3	4	47	1	0	0	0	0	1	0	0	0	10191	893	31	1	800	1	NAPA	19	48006731	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	409395	48006731	11122252	1895	6292										
PLA2G4C	8605	broad.mit.edu	37	chr19	48565266	48565266	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcgattacctcgaaaggatCtccggcactgaagtcgaagg	11	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:48565266C>T	ENST00000599921.1	-	14	1603	c.1246G>A	c.(1246-1248)Gat>Aat	p.D416N	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.D416N|CTD-2265M8.2_ENST00000596552.1_RNA|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.D426N|CTD-2265M8.2_ENST00000601950.1_RNA|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.D416N|CTD-2265M8.2_ENST00000601548.1_RNA			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	416	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)	p.D416N(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		TCGAAAGGATCTCCGGCACTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	88	89					19																	48565266		2203	4300	6503	53257078	SO:0001583	missense	8605			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1246G>A	19.37:g.48565266C>T	ENSP00000469473:p.Asp416Asn		53257078	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.777654	0.49786	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.11063	2.81;2.81	2.79	2.79	0.32731	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.174869	0.36482	U	0.002575	T	0.09730	0.0239	L	0.47716	1.5	0.26216	N	0.979236	B;B	0.31227	0.212;0.314	B;B	0.31869	0.137;0.073	T	0.20240	-1.0281	10	0.25106	T	0.35	-5.1386	9.3872	0.38349	0.0:1.0:0.0:0.0	.	426;416	B4DI40;Q9UP65	.;PA24C_HUMAN	N	416	ENSP00000346228:D416N;ENSP00000400036:D416N	ENSP00000346228:D416N	D	-	1	0	PLA2G4C	53257078	0.984000	0.35163	0.395000	0.26283	0.569000	0.35902	3.267000	0.51577	1.270000	0.44297	0.405000	0.27470	GAT		0.627	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			T	48565266	C	T	48565266	3	4	47	1	0	0	0	0	1	0	0	0	12034	913	32	3	399	3	PLA2G4C	19	48565266	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	558535	48565266	10563717	1896	6293										
CCDC114	93233	broad.mit.edu	37	chr19	48801292	48801292	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaagtggggccatcttcttCggaaggtcctccaggctctg	13	11	3	1	rs201076998		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:48801292C>T	ENST00000315396.7	-	12	2038	c.1356G>A	c.(1354-1356)ccG>ccA	p.P452P		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	452					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)		p.P245P(1)|p.P452P(1)		cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CCATCTTCTTCGGAAGGTCCT	0.672																																																2	Substitution - coding silent(2)	large_intestine(2)	19											44	44	44					19																	48801292		2203	4300	6503	53493104	SO:0001819	synonymous_variant	93233			BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1356G>A	19.37:g.48801292C>T			53493104	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																				0.672	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		T	48801292	C	T	48801292	2	4	47	1	0	0	0	0	0	0	0	1	2757	871	31	1		1	CCDC114	19	48801292	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	236026	48801292	10327691	1897	6294										
LMTK3	114783	broad.mit.edu	37	chr19	49004638	49004638	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgcagtgggatccacaggcgCtctggggtcaggtagtagtc	16	10	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:49004638C>A	ENST00000600059.1	-	9	1130	c.903G>T	c.(901-903)gaG>gaT	p.E301D	LMTK3_ENST00000270238.3_Missense_Mutation_p.E330D			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	301	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E330D(1)|p.E316D(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		TCCACAGGCGCTCTGGGGTCA	0.677																																																2	Substitution - Missense(2)	large_intestine(2)	19											44	53	50					19																	49004638		1973	4141	6114	53696450	SO:0001583	missense	114783			AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.903G>T	19.37:g.49004638C>A	ENSP00000472020:p.Glu301Asp		53696450	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	37		.	.	.	.	.	.	.	.	.	.	C	6.028	0.373450	0.11409	.	.	ENSG00000142235	ENST00000270238	D	0.83163	-1.69	4.13	1.87	0.25490	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.075250	0.50627	D	0.000120	T	0.53045	0.1772	N	0.02854	-0.475	0.27757	N	0.943972	B	0.19331	0.035	B	0.21917	0.037	T	0.50233	-0.8852	10	0.02654	T	1	.	4.5995	0.12347	0.1764:0.6162:0.0:0.2074	.	301	Q96Q04	LMTK3_HUMAN	D	330	ENSP00000270238:E330D	ENSP00000270238:E330D	E	-	3	2	LMTK3	53696450	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.969000	0.29370	0.866000	0.35629	0.449000	0.29647	GAG		0.677	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		A	49004638	C	A	49004638	3	1	47	1	0	0	0	0	1	0	0	0	8884	796	28	2	3507	2	LMTK3	19	49004638	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	203346	49004638	10124345	1898	6295										
KLK12	43849	broad.mit.edu	37	chr19	51532592	51532592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgatcatccggatccagtccAcatacttgcaaatataggtg	8	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:51532592A>G	ENST00000525263.1	-	5	832	c.713T>C	c.(712-714)gTg>gCg	p.V238A	CTC-518B2.9_ENST00000594910.1_RNA|KLK11_ENST00000319720.7_5'Flank|KLK11_ENST00000600362.1_5'Flank|KLK11_ENST00000453757.3_5'Flank|KLK12_ENST00000250351.4_Intron|KLK12_ENST00000250352.11_Intron|KLK11_ENST00000594458.1_5'Flank|KLK11_ENST00000594768.1_5'Flank|KLK12_ENST00000319590.4_Missense_Mutation_p.V238A|KLK12_ENST00000529888.1_3'UTR|KLK11_ENST00000391804.3_5'Flank			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12	238	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.?(1)		endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		GATCCAGTCCACATACTTGCA	0.562																																																1	Unknown(1)	large_intestine(1)	19											143	137	139					19																	51532592		2203	4300	6503	56224404	SO:0001583	missense	43849				CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"Kallikreins"	6360	protein-coding gene	gene with protein product		605539	"kallikrein 12"			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.713T>C	19.37:g.51532592A>G	ENSP00000436458:p.Val238Ala		56224404	Q9UKR1|Q9UKR2	Missense_Mutation	SNP	ENST00000525263.1	37	CCDS12821.1	.	.	.	.	.	.	.	.	.	.	a	6.271	0.418151	0.11870	.	.	ENSG00000186474	ENST00000525263;ENST00000319590	D;D	0.93133	-3.17;-3.17	4.33	-0.4	0.12411	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.88526	0.6460	L	0.36672	1.1	0.09310	N	1	B;B	0.34200	0.441;0.161	B;B	0.40256	0.324;0.091	T	0.79720	-0.1685	9	0.52906	T	0.07	.	3.7101	0.08416	0.5457:0.0:0.2953:0.159	.	128;238	B9EGA9;Q9UKR0	.;KLK12_HUMAN	A	238	ENSP00000436458:V238A;ENSP00000324181:V238A	ENSP00000324181:V238A	V	-	2	0	KLK12	56224404	0.000000	0.05858	0.650000	0.29550	0.090000	0.18270	0.116000	0.15561	-0.243000	0.09653	-0.463000	0.05309	GTG		0.562	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598		G	51532592	A	G	51532592	3	3	47	1	0	0	0	0	1	0	0	0	8421	159	6	4	99	4	KLK12	19	51532592	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2527954	51532592	7596391	1899	6296										
CD33	945	broad.mit.edu	37	chr19	51728611	51728611	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaactccccagttcatggtTactggttccgggaaggagcc	12	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:51728611T>G	ENST00000262262.4	+	2	196	c.175T>G	c.(175-177)Tac>Gac	p.Y59D	CD33_ENST00000421133.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.Y59D|CD33_ENST00000436584.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	59	Ig-like V-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.Y59D(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AGTTCATGGTTACTGGTTCCG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											89	87	88					19																	51728611		2203	4300	6503	56420423	SO:0001583	missense	945			M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1659	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 3"	159590	"CD33 antigen (gp67)"			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.175T>G	19.37:g.51728611T>G	ENSP00000262262:p.Tyr59Asp		56420423	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	.	.	.	.	.	.	.	.	.	.	.	15.43	2.832303	0.50845	.	.	ENSG00000105383	ENST00000262262;ENST00000391796	T;T	0.68181	-0.31;-0.31	3.49	3.49	0.39957	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.29178	U	0.012901	T	0.82079	0.4959	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.989;0.995	D	0.83903	0.0291	10	0.87932	D	0	.	8.5496	0.33444	0.0:0.0:0.0:1.0	.	59;59	F8WAL2;P20138	.;CD33_HUMAN	D	59	ENSP00000262262:Y59D;ENSP00000375673:Y59D	ENSP00000262262:Y59D	Y	+	1	0	CD33	56420423	0.313000	0.24554	0.814000	0.32528	0.595000	0.36748	1.407000	0.34657	1.593000	0.50029	0.533000	0.62120	TAC		0.537	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		G	51728611	T	G	51728611	3	3	47	1	0	0	0	0	1	0	0	0	3011	1754	61	4	181	4	CD33	19	51728611	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	196019	51728611	7400372	1900	6297										
SIGLEC12	89858	broad.mit.edu	37	chr19	52000625	52000625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacgaagatgatgcagaagtAcaggaagaccagggctgtgg	15	6	0	4	rs567922711		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52000625A>G	ENST00000291707.3	-	6	1535	c.1480T>C	c.(1480-1482)Tac>Cac	p.Y494H	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.Y376H	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	494			Y -> S (in dbSNP:rs3752135).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.Y494H(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		ATGCAGAAGTACAGGAAGACC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											164	144	151					19																	52000625		2203	4300	6503	56692437	SO:0001583	missense	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1480T>C	19.37:g.52000625A>G	ENSP00000291707:p.Tyr494His		56692437	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	0.711	-0.787231	0.02907	.	.	ENSG00000254521	ENST00000291707	T	0.37584	1.19	1.5	0.367	0.16140	.	1.213390	0.06410	U	0.720387	T	0.15609	0.0376	N	0.08118	0	0.09310	N	1	B;B	0.27068	0.104;0.167	B;B	0.18263	0.008;0.021	T	0.22382	-1.0218	10	0.15952	T	0.53	.	4.3007	0.10923	0.6402:0.3598:0.0:0.0	.	494;376	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	H	494	ENSP00000291707:Y494H	ENSP00000291707:Y494H	Y	-	1	0	SIGLEC12	56692437	0.000000	0.05858	0.002000	0.10522	0.232000	0.25224	0.062000	0.14389	0.054000	0.16065	0.325000	0.21440	TAC		0.557	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		G	52000625	A	G	52000625	3	3	47	1	0	0	0	0	1	0	0	0	14345	391	14	4	319	4	SIGLEC12	19	52000625	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	272014	52000625	7128358	1901	6298										
SIGLEC12	89858	broad.mit.edu	37	chr19	52003562	52003562	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtcctgggacgctgtggaGaaacgagggtcagcccagcc	16	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52003562G>T	ENST00000291707.3	-	2	483				SIGLEC12_ENST00000598614.1_Missense_Mutation_p.F22L	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.?(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		ACGCTGTGGAGAAACGAGGGT	0.607																																																1	Unknown(1)	large_intestine(1)	19											57	51	53					19																	52003562		2203	4300	6503	56695374	SO:0001627	intron_variant	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.428-8C>A	19.37:g.52003562G>T			56695374	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1																																																																																				0.607	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		T	52003562	G	T	52003562	1	4	47	0	1	0	0	0	0	0	0	0	14345	933	33	2		2	SIGLEC12	19	52003562	Intron	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2937	52003562	7125421	1902	6299										
ZNF613	79898	broad.mit.edu	37	chr19	52447560	52447560	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tactgaaatcaaatttaagtTtagtcaaccagaacaaaagg	6	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52447560T>G	ENST00000293471.6	+	6	1103	c.424T>G	c.(424-426)Tta>Gta	p.L142V	ZNF613_ENST00000391794.4_Missense_Mutation_p.L106V	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	142					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L142V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		AAATTTAAGTTTAGTCAACCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	71	71					19																	52447560		2203	4300	6503	57139372	SO:0001583	missense	79898			AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.424T>G	19.37:g.52447560T>G	ENSP00000293471:p.Leu142Val		57139372	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	37	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	T	1.355	-0.590255	0.03799	.	.	ENSG00000176024	ENST00000293471;ENST00000391794	T;T	0.07216	3.35;3.21	3.14	-0.425	0.12317	.	0.326503	0.17289	N	0.179731	T	0.05227	0.0139	L	0.41236	1.265	0.09310	N	1	B	0.25850	0.136	B	0.18871	0.023	T	0.35051	-0.9804	10	0.62326	D	0.03	.	0.3871	0.00404	0.2242:0.1373:0.2305:0.4081	.	142	Q6PF04	ZN613_HUMAN	V	142;106	ENSP00000293471:L142V;ENSP00000375671:L106V	ENSP00000293471:L142V	L	+	1	2	ZNF613	57139372	0.067000	0.21026	0.021000	0.16686	0.012000	0.07955	0.779000	0.26746	-0.025000	0.13918	0.528000	0.53228	TTA		0.333	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		G	52447560	T	G	52447560	3	3	47	1	0	0	0	0	1	0	0	0	18077	1838	64	4	438	4	ZNF613	19	52447560	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	443998	52447560	6681423	1903	6300										
ZNF614	80110	broad.mit.edu	37	chr19	52519387	52519387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtgtgaataggattttccGcactcggtacatacaaaggg	11	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52519387G>A	ENST00000270649.6	-	5	2008	c.1464C>T	c.(1462-1464)tgC>tgT	p.C488C	ZNF614_ENST00000356322.6_Intron	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	488					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C488C(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		AGGATTTTCCGCACTCGGTAC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	19											171	158	163					19																	52519387		2203	4300	6503	57211199	SO:0001819	synonymous_variant	80110			BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"Zinc fingers, C2H2-type", "-"	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.1464C>T	19.37:g.52519387G>A			57211199	Q494T8|Q8TCF4|Q9BSN8	Silent	SNP	ENST00000270649.6	37	CCDS12847.1																																																																																				0.413	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040		A	52519387	G	A	52519387	2	1	47	1	0	0	0	0	0	0	0	1	18078	1079	38	1		1	ZNF614	19	52519387	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	71827	52519387	6609596	1904	6301										
ZNF836	162962	broad.mit.edu	37	chr19	52658321	52658321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgaggcaagaaaaccgcCcaaaggccttgccacattca	9	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52658321C>T	ENST00000322146.8	-	5	3136	c.2615G>A	c.(2614-2616)gGg>gAg	p.G872E	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.G872E	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	872					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G872E(1)		endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						AGAAAACCGCCCAAAGGCCTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											101	110	107					19																	52658321		2193	4296	6489	57350133	SO:0001583	missense	162962			BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2615G>A	19.37:g.52658321C>T	ENSP00000325038:p.Gly872Glu		57350133		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.291553	0.40494	.	.	ENSG00000196267	ENST00000322146	T	0.17528	2.27	2.15	-2.01	0.07410	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18882	0.0453	N	0.11789	0.175	0.09310	N	1	D	0.76494	0.999	D	0.70487	0.969	T	0.33394	-0.9870	9	0.18276	T	0.48	.	12.9141	0.58197	0.0:0.2662:0.7338:0.0	.	872	Q6ZNA1	ZN836_HUMAN	E	872	ENSP00000325038:G872E	ENSP00000325038:G872E	G	-	2	0	ZNF836	57350133	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	-3.429000	0.00474	-0.252000	0.09528	0.484000	0.47621	GGG		0.403	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		T	52658321	C	T	52658321	3	4	47	1	0	0	0	0	1	0	0	0	18226	623	22	3	197	3	ZNF836	19	52658321	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	138934	52658321	6470662	1905	6302										
ZNF836	162962	broad.mit.edu	37	chr19	52659104	52659104	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccttgccacacacattacatTtgtaaggtttctgcccagta	6	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52659104T>G	ENST00000322146.8	-	5	2353	c.1832A>C	c.(1831-1833)aAa>aCa	p.K611T	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.K611T	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	611					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K611T(1)		endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CACATTACATTTGTAAGGTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											127	138	134					19																	52659104		2150	4277	6427	57350916	SO:0001583	missense	162962			BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.1832A>C	19.37:g.52659104T>G	ENSP00000325038:p.Lys611Thr		57350916		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.660339	0.29515	.	.	ENSG00000196267	ENST00000322146	T	0.18810	2.19	2.09	1.02	0.19986	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31734	0.0806	L	0.48218	1.51	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12528	-1.0544	9	0.33940	T	0.23	.	4.8695	0.13625	0.0:0.3097:0.0:0.6903	.	611	Q6ZNA1	ZN836_HUMAN	T	611	ENSP00000325038:K611T	ENSP00000325038:K611T	K	-	2	0	ZNF836	57350916	0.000000	0.05858	0.400000	0.26346	0.786000	0.44442	-0.027000	0.12371	0.087000	0.17167	0.397000	0.26171	AAA		0.418	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		G	52659104	T	G	52659104	3	3	47	1	0	0	0	0	1	0	0	0	18226	1841	64	4	980	4	ZNF836	19	52659104	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	783	52659104	6469879	1906	6303										
ZNF610	162963	broad.mit.edu	37	chr19	52869103	52869103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaaaagtttacaaaccatCgttcctcagtttcaccactt	4	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:52869103C>T	ENST00000403906.3	+	6	928	c.472C>T	c.(472-474)Cgt>Tgt	p.R158C	ZNF610_ENST00000601151.1_Missense_Mutation_p.R115C|ZNF610_ENST00000321287.8_Missense_Mutation_p.R158C|ZNF610_ENST00000327920.8_Missense_Mutation_p.R158C	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R158C(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		TACAAACCATCGTTCCTCAGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	92	89					19																	52869103		2203	4300	6503	57560915	SO:0001583	missense	162963			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"Zinc fingers, C2H2-type", "-"	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.472C>T	19.37:g.52869103C>T	ENSP00000383922:p.Arg158Cys		57560915	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	CCDS12851.1	.	.	.	.	.	.	.	.	.	.	C	9.779	1.174739	0.21704	.	.	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.05649	3.41;3.41	1.11	-2.21	0.06973	.	.	.	.	.	T	0.03136	0.0092	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42344	-0.9457	9	0.45353	T	0.12	.	2.0091	0.03484	0.4052:0.3103:0.0:0.2845	.	115;158	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	C	158;115;158	ENSP00000383922:R158C;ENSP00000327597:R158C	ENSP00000324441:R115C	R	+	1	0	ZNF610	57560915	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.603000	0.02077	-0.778000	0.04566	-0.823000	0.03104	CGT		0.343	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		T	52869103	C	T	52869103	3	4	47	1	0	0	0	0	1	0	0	0	18075	884	31	1	486	1	ZNF610	19	52869103	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	209999	52869103	6259880	1907	6304										
ZNF578	147660	broad.mit.edu	37	chr19	53015178	53015178	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaccttacaagtgtaatgAatgtgggaagacttttaatg	10	4	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53015178A>C	ENST00000421239.2	+	6	1788	c.1544A>C	c.(1543-1545)gAa>gCa	p.E515A	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E515A(1)							GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		AAGTGTAATGAATGTGGGAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	89	88					19																	53015178		2203	4300	6503	57706990	SO:0001583	missense	147660			AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1544A>C	19.37:g.53015178A>C	ENSP00000459216:p.Glu515Ala		57706990	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	12.82	2.052265	0.36181	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	0.247	0.15521	.	.	.	.	.	T	0.27594	0.0678	L	0.39326	1.205	0.09310	N	1	B	0.27765	0.188	B	0.21360	0.034	T	0.16808	-1.0390	7	.	.	.	.	5.4535	0.16578	0.7501:0.0:0.0:0.2498	.	515	G3V4F6	.	A	515	.	.	E	+	2	0	ZNF578	57706990	0.001000	0.12720	0.001000	0.08648	0.219000	0.24729	1.049000	0.30392	-0.138000	0.11434	0.246000	0.17985	GAA		0.408	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		C	53015178	A	C	53015178	3	2	47	1	0	0	0	0	1	0	0	0	18049	246	9	4	1554	4	ZNF578	19	53015178	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	146075	53015178	6113805	1908	6305										
ZNF808	388558	broad.mit.edu	37	chr19	53058676	53058676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaacaatcacacctttcacGtcatcatagaattcatactg	4	11	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53058676G>A	ENST00000359798.4	+	5	2687	c.2507G>A	c.(2506-2508)cGt>cAt	p.R836H		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	836					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		CACCTTTCACGTCATCATAGA	0.353																																																0			19											103	107	106					19																	53058676		2203	4300	6503	57750488	SO:0001583	missense	388558			CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.2507G>A	19.37:g.53058676G>A	ENSP00000352846:p.Arg836His		57750488	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	6.370	0.436408	0.12104	.	.	ENSG00000198482	ENST00000359798	T	0.26810	1.71	1.51	0.377	0.16198	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33381	0.0861	M	0.64997	1.995	0.09310	N	1	D	0.59357	0.985	P	0.54706	0.759	T	0.13845	-1.0494	9	0.42905	T	0.14	.	4.8058	0.13319	0.3625:0.0:0.6375:0.0	.	836	Q8N4W9	ZN808_HUMAN	H	836	ENSP00000352846:R836H	ENSP00000352846:R836H	R	+	2	0	ZNF808	57750488	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	-5.262000	0.00136	-0.021000	0.14009	0.205000	0.17691	CGT		0.353	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		A	53058676	G	A	53058676	3	1	47	1	0	0	0	0	1	0	0	0	18212	1145	40	1	2517	1	ZNF808	19	53058676	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	43498	53058676	6070307	1909	6306										
ZNF611	81856	broad.mit.edu	37	chr19	53209724	53209724	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttggggcctacaggaaattCtttggaatgttgaaactgag	12	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53209724C>A	ENST00000319783.1	-	7	900	c.584G>T	c.(583-585)aGa>aTa	p.R195I	ZNF611_ENST00000602162.1_Missense_Mutation_p.R126I|ZNF611_ENST00000453741.2_Missense_Mutation_p.R126I|ZNF611_ENST00000540744.1_Missense_Mutation_p.R195I|ZNF611_ENST00000595798.1_Missense_Mutation_p.R126I|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000543227.1_Missense_Mutation_p.R195I	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R195I(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		ACAGGAAATTCTTTGGAATGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											122	127	125					19																	53209724		2203	4300	6503	57901536	SO:0001583	missense	81856			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.584G>T	19.37:g.53209724C>A	ENSP00000322427:p.Arg195Ile		57901536	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	6.008	0.369794	0.11352	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.10763	2.99;2.99;2.84;2.99	1.97	0.841	0.18918	.	.	.	.	.	T	0.12561	0.0305	M	0.71871	2.18	0.09310	N	1	B	0.15141	0.012	B	0.13407	0.009	T	0.25117	-1.0141	9	0.54805	T	0.06	.	5.6776	0.17757	0.3195:0.6805:0.0:0.0	.	195	Q8N823	ZN611_HUMAN	I	195;195;126;195	ENSP00000437616:R195I;ENSP00000439211:R195I;ENSP00000443505:R126I;ENSP00000322427:R195I	ENSP00000322427:R195I	R	-	2	0	ZNF611	57901536	0.000000	0.05858	0.006000	0.13384	0.007000	0.05969	-0.299000	0.08254	0.147000	0.19030	-0.864000	0.03007	AGA		0.388	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		A	53209724	C	A	53209724	3	1	47	1	0	0	0	0	1	0	0	0	18076	913	32	2	1537	2	ZNF611	19	53209724	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	151048	53209724	5919259	1910	6307										
ZNF28	7576	broad.mit.edu	37	chr19	53303034	53303034	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcattacacttgtaaggtttCtctccagtatgaactctctg	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53303034C>A	ENST00000457749.2	-	4	2183	c.2064G>T	c.(2062-2064)gaG>gaT	p.E688D	ZNF28_ENST00000414252.2_Missense_Mutation_p.E635D|ZNF28_ENST00000438150.2_Missense_Mutation_p.E635D|ZNF28_ENST00000360272.4_Missense_Mutation_p.E635D	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E635D(2)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TGTAAGGTTTCTCTCCAGTAT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	19											145	140	142					19																	53303034		2203	4300	6503	57994846	SO:0001583	missense	7576			X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.2064G>T	19.37:g.53303034C>A	ENSP00000397693:p.Glu688Asp		57994846	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	13.37	2.215968	0.39201	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	1.94	0.852	0.18995	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20495	0.0493	L	0.41632	1.29	0.22389	N	0.99914	B	0.29481	0.245	B	0.33568	0.166	T	0.29488	-1.0010	9	0.59425	D	0.04	.	5.0498	0.14503	0.0:0.673:0.0:0.327	.	688	P17035	ZNF28_HUMAN	D	635;688;635;635	ENSP00000412143:E635D;ENSP00000397693:E688D;ENSP00000353410:E635D;ENSP00000444965:E635D	ENSP00000353410:E635D	E	-	3	2	ZNF28	57994846	0.000000	0.05858	0.041000	0.18516	0.042000	0.13812	-0.578000	0.05841	0.150000	0.19136	0.454000	0.30748	GAG		0.408	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		A	53303034	C	A	53303034	3	1	47	1	0	0	0	0	1	0	0	0	17852	912	32	2	96	2	ZNF28	19	53303034	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	93310	53303034	5825949	1911	6308										
ZNF816A	125893	broad.mit.edu	37	chr19	53454606	53454606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcatgcctgtgatcacttCggtctgtactaccagtcaac	8	13	3	1	rs544136644		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53454606C>T	ENST00000357666.4	-	5	722	c.422G>A	c.(421-423)cGa>cAa	p.R141Q	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.R141Q|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000391786.2_3'UTR	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R141Q(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						GTGATCACTTCGGTCTGTACT	0.408													c|||	1	0.000199681	0	0	5008	,	,		19126	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											178	182	181					19																	53454606		2203	4300	6503	58146418	SO:0001583	missense	125893			BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.422G>A	19.37:g.53454606C>T	ENSP00000350295:p.Arg141Gln		58146418	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	37	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	0.019	-1.452459	0.01080	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.04970	3.52;3.52	1.46	0.389	0.16269	.	.	.	.	.	T	0.02267	0.0070	N	0.10618	0.005	0.20196	N	0.999925	B	0.09022	0.002	B	0.06405	0.002	T	0.46261	-0.9204	9	0.02654	T	1	.	3.1278	0.06413	0.0:0.2739:0.0:0.7261	.	141	Q0VGE8	ZN816_HUMAN	Q	141	ENSP00000350295:R141Q;ENSP00000403266:R141Q	ENSP00000350295:R141Q	R	-	2	0	ZNF816	58146418	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.049000	0.03514	0.060000	0.16281	0.205000	0.17691	CGA		0.408	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		T	53454606	C	T	53454606	3	4	47	1	0	0	0	0	1	0	0	0	18216	884	31	1	1537	1	ZNF816A	19	53454606	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	151572	53454606	5674377	1912	6309										
ZNF677	342926	broad.mit.edu	37	chr19	53741152	53741152	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctgatgattagtgaggttCgaacttttgctaaaagcctt	9	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:53741152C>T	ENST00000598513.1	-	5	978	c.828G>A	c.(826-828)tcG>tcA	p.S276S	ZNF677_ENST00000333952.4_Silent_p.S276S|CTD-2245F17.6_ENST00000596041.1_RNA	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S276S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TAGTGAGGTTCGAACTTTTGC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	19											84	77	79					19																	53741152		2203	4300	6503	58432964	SO:0001819	synonymous_variant	342926			BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.828G>A	19.37:g.53741152C>T			58432964		Silent	SNP	ENST00000598513.1	37	CCDS12861.1																																																																																				0.388	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		T	53741152	C	T	53741152	2	4	47	1	0	0	0	0	0	0	0	1	18123	871	31	1		1	ZNF677	19	53741152	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	286546	53741152	5387831	1913	6310										
NLRP12	91662	broad.mit.edu	37	chr19	54314024	54314024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaagaaggcttgagctcatCgaagccgtcgatgatgaaaa	12	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:54314024C>T	ENST00000324134.6	-	3	1057	c.889G>A	c.(889-891)Gat>Aat	p.D297N	NLRP12_ENST00000391772.1_Missense_Mutation_p.D297N|NLRP12_ENST00000354278.3_Missense_Mutation_p.D297N|NLRP12_ENST00000391773.1_Missense_Mutation_p.D297N|NLRP12_ENST00000391775.3_Missense_Mutation_p.D297N|NLRP12_ENST00000535162.1_Missense_Mutation_p.D297N|NLRP12_ENST00000345770.5_Missense_Mutation_p.D297N|NLRP12_ENST00000351894.4_Missense_Mutation_p.D297N	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	297	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.D297N(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TTGAGCTCATCGAAGCCGTCG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											46	48	47					19																	54314024		2203	4300	6503	59005836	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.889G>A	19.37:g.54314024C>T	ENSP00000319377:p.Asp297Asn		59005836	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735969	0.69189	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	4.47	0.849	0.18972	NACHT nucleoside triphosphatase (1);	0.520533	0.15742	N	0.246874	D	0.90304	0.6967	H	0.95294	3.65	0.80722	D	1	P;B;P;B	0.40731	0.536;0.159;0.728;0.3	B;B;B;B	0.30495	0.116;0.027;0.116;0.104	D	0.89831	0.3996	10	0.87932	D	0	.	13.8241	0.63340	0.0:0.5602:0.4398:0.0	.	297;297;297;297	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	N	297	ENSP00000319377:D297N;ENSP00000438030:D297N;ENSP00000340473:D297N;ENSP00000346231:D297N;ENSP00000375655:D297N;ENSP00000375653:D297N;ENSP00000375652:D297N	ENSP00000319377:D297N	D	-	1	0	NLRP12	59005836	0.976000	0.34144	0.006000	0.13384	0.922000	0.55478	2.588000	0.46137	0.068000	0.16574	0.306000	0.20318	GAT		0.582	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54314024	C	T	54314024	3	4	47	1	0	0	0	0	1	0	0	0	10505	884	31	1	2424	1	NLRP12	19	54314024	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	572872	54314024	4814959	1914	6311										
LILRA4	23547	broad.mit.edu	37	chr19	54845008	54845008	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacccatgcggatgagattCtccactgtgtaatcctggag	10	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:54845008C>A	ENST00000291759.4	-	8	1391	c.1335G>T	c.(1333-1335)gaG>gaT	p.E445D	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	445					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.E445D(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		GGATGAGATTCTCCACTGTGT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											106	95	99					19																	54845008		2203	4300	6503	59536820	SO:0001583	missense	23547			AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.1335G>T	19.37:g.54845008C>A	ENSP00000291759:p.Glu445Asp		59536820	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	12.64	1.999098	0.35226	.	.	ENSG00000239961	ENST00000291759	T	0.00514	6.88	3.08	2.04	0.26737	.	7.488640	0.00397	N	0.000043	T	0.00845	0.0028	M	0.71581	2.175	0.09310	N	1	P	0.47302	0.893	B	0.43680	0.427	T	0.49925	-0.8887	10	0.72032	D	0.01	.	6.1842	0.20488	0.0:0.8582:0.0:0.1418	.	445	P59901	LIRA4_HUMAN	D	445	ENSP00000291759:E445D	ENSP00000291759:E445D	E	-	3	2	LILRA4	59536820	0.822000	0.29219	0.055000	0.19348	0.148000	0.21650	1.472000	0.35376	0.870000	0.35726	0.563000	0.77884	GAG		0.562	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54845008	C	A	54845008	3	1	47	1	0	0	0	0	1	0	0	0	8810	912	32	2	168	2	LILRA4	19	54845008	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	530984	54845008	4283975	1915	6312										
NLRP7	199713	broad.mit.edu	37	chr19	55452922	55452922	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaccagaatttctgccagtTtcttgccatcagcctcttcc	6	14	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:55452922T>G	ENST00000590030.1	-	1	198	c.158A>C	c.(157-159)aAa>aCa	p.K53T	NLRP7_ENST00000588756.1_Missense_Mutation_p.K53T|NLRP7_ENST00000592784.1_Missense_Mutation_p.K53T|NLRP7_ENST00000446217.1_Missense_Mutation_p.K81T|NLRP7_ENST00000328092.5_Missense_Mutation_p.K53T|NLRP7_ENST00000340844.2_Missense_Mutation_p.K53T|NLRP7_ENST00000448121.2_Missense_Mutation_p.K53T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	53	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)	p.K53T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTCTGCCAGTTTCTTGCCATC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											115	109	111					19																	55452922		2203	4300	6503	60144734	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.158A>C	19.37:g.55452922T>G	ENSP00000465520:p.Lys53Thr		60144734	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	T	9.279	1.047587	0.19827	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	1.53	-1.25	0.09405	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.38558	0.1045	L	0.50333	1.59	0.09310	N	1	P;P;P;P	0.44877	0.845;0.845;0.845;0.814	P;P;P;B	0.44394	0.448;0.448;0.448;0.32	T	0.24584	-1.0156	9	0.46703	T	0.11	.	2.3556	0.04294	0.2562:0.0:0.3132:0.4307	.	81;53;53;53	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	T	53;53;53;81;53	ENSP00000329568:K53T;ENSP00000409137:K53T;ENSP00000339491:K53T;ENSP00000414273:K81T	ENSP00000329568:K53T	K	-	2	0	NLRP7	60144734	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.433000	0.21477	-0.411000	0.07530	0.260000	0.18958	AAA		0.443	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		G	55452922	T	G	55452922	3	3	47	1	0	0	0	0	1	0	0	0	10513	1841	64	4	2995	4	NLRP7	19	55452922	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	607914	55452922	3676061	1916	6313										
NLRP9	338321	broad.mit.edu	37	chr19	56241243	56241243	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgagccagcgctttgcaaaGaatcgccagggagggatcat	13	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56241243G>T	ENST00000332836.2	-	3	1975	c.1948C>A	c.(1948-1950)Ctt>Att	p.L650I		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	650						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.L650I(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		GCTTTGCAAAGAATCGCCAGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	89	89					19																	56241243		2203	4300	6503	60933055	SO:0001583	missense	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1948C>A	19.37:g.56241243G>T	ENSP00000331857:p.Leu650Ile		60933055	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	g	10.20	1.284803	0.23392	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.63744	-0.06	3.4	3.4	0.38934	.	.	.	.	.	T	0.70193	0.3196	M	0.82323	2.585	0.09310	N	1	P	0.44816	0.844	P	0.47705	0.555	T	0.63620	-0.6596	9	0.59425	D	0.04	.	10.6498	0.45642	0.0:0.0:1.0:0.0	.	650	Q7RTR0	NALP9_HUMAN	I	650	ENSP00000331857:L650I	ENSP00000331857:L650I	L	-	1	0	NLRP9	60933055	0.030000	0.19436	0.027000	0.17364	0.009000	0.06853	0.927000	0.28818	2.234000	0.73211	0.632000	0.83419	CTT		0.438	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56241243	G	T	56241243	3	4	47	1	0	0	0	0	1	0	0	0	10515	942	33	2	1055	2	NLRP9	19	56241243	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	788321	56241243	2887740	1917	6314										
NLRP11	204801	broad.mit.edu	37	chr19	56297079	56297079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatgtaatccaaattagaaTtaggtattattgaacctggc	7	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56297079T>G	ENST00000589093.1	-	10	3107	c.3014A>C	c.(3013-3015)aAt>aCt	p.N1005T	NLRP11_ENST00000589824.2_Missense_Mutation_p.N951T|NLRP11_ENST00000360133.3_Missense_Mutation_p.N951T|NLRP11_ENST00000443188.1_Missense_Mutation_p.N1005T|NLRP11_ENST00000592953.1_Missense_Mutation_p.N906T			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	1005							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.N1005T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		CAAATTAGAATTAGGTATTAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	93	93					19																	56297079		2203	4300	6503	60988891	SO:0001583	missense	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.3014A>C	19.37:g.56297079T>G	ENSP00000466285:p.Asn1005Thr		60988891	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	T	4.906	0.168408	0.09339	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.74526	-0.85;-0.8	1.4	0.344	0.16006	.	.	.	.	.	T	0.49762	0.1576	N	0.08118	0	0.09310	N	1	D;D	0.58620	0.971;0.983	B;B	0.42386	0.215;0.386	T	0.46693	-0.9173	9	0.59425	D	0.04	.	3.2203	0.06713	0.0:0.2494:0.0:0.7506	.	1005;951	P59045;P59045-2	NAL11_HUMAN;.	T	1005;951	ENSP00000409898:N1005T;ENSP00000353251:N951T	ENSP00000353251:N951T	N	-	2	0	NLRP11	60988891	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.282000	0.18829	0.050000	0.15949	0.533000	0.62120	AAT		0.398	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		G	56297079	T	G	56297079	3	3	47	1	0	0	0	0	1	0	0	0	10504	1493	52	4	91	4	NLRP11	19	56297079	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	55836	56297079	2831904	1918	6315										
NLRP4	147945	broad.mit.edu	37	chr19	56370482	56370482	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcagtgaacctcctccaaGaagctaactttcatattatt	6	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56370482G>T	ENST00000301295.6	+	3	2145	c.1723G>T	c.(1723-1725)Gaa>Taa	p.E575*	NLRP4_ENST00000587891.1_Nonsense_Mutation_p.E500*|NLRP4_ENST00000346986.5_Nonsense_Mutation_p.E575*	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	575					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.E575*(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CCTCCTCCAAGAAGCTAACTT	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											79	74	76					19																	56370482		2203	4300	6503	61062294	SO:0001587	stop_gained	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1723G>T	19.37:g.56370482G>T	ENSP00000301295:p.Glu575*		61062294	Q86W87|Q96AY6	Nonsense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	38	7.237921	0.98157	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	.	.	.	4.0	0.498	0.16908	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	6.2033	0.20587	0.2021:0.1617:0.6362:0.0	.	.	.	.	X	575	.	ENSP00000301295:E575X	E	+	1	0	NLRP4	61062294	0.004000	0.15560	0.000000	0.03702	0.027000	0.11550	1.137000	0.31479	-0.123000	0.11745	-1.094000	0.02160	GAA		0.443	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56370482	G	T	56370482	4	4	47	1	0	0	0	0	0	1	0	0	10510	943	33	2	1729	2	NLRP4	19	56370482	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	73403	56370482	2758501	1919	6316										
NLRP13	126204	broad.mit.edu	37	chr19	56422033	56422033	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggtctagctcatgcagattCtcatttgtgaccaacgtaga	9	9	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56422033C>A	ENST00000342929.3	-	6	2177	c.2178G>T	c.(2176-2178)gaG>gaT	p.E726D	NLRP13_ENST00000588751.1_Missense_Mutation_p.E726D	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	726							ATP binding (GO:0005524)	p.E726D(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CATGCAGATTCTCATTTGTGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											198	171	180					19																	56422033		2203	4300	6503	61113845	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2178G>T	19.37:g.56422033C>A	ENSP00000343891:p.Glu726Asp		61113845	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	C	7.348	0.622330	0.14193	.	.	ENSG00000173572	ENST00000342929	T	0.42131	0.98	2.8	-3.06	0.05379	.	.	.	.	.	T	0.21881	0.0527	L	0.33339	1.005	0.09310	N	1	B	0.25441	0.126	B	0.18263	0.021	T	0.26292	-1.0107	9	0.12766	T	0.61	.	3.459	0.07526	0.0:0.3862:0.2032:0.4106	.	726	Q86W25	NAL13_HUMAN	D	726	ENSP00000343891:E726D	ENSP00000343891:E726D	E	-	3	2	NLRP13	61113845	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.105000	0.03323	-0.657000	0.05373	-0.300000	0.09419	GAG		0.458	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		A	56422033	C	A	56422033	3	1	47	1	0	0	0	0	1	0	0	0	10506	912	32	2	975	2	NLRP13	19	56422033	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	51551	56422033	2706950	1920	6317										
ZNF583	147949	broad.mit.edu	37	chr19	56935168	56935168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atactggagagagaccctacGaatgtaaggaatgtaggaaa	12	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56935168G>A	ENST00000333201.9	+	5	1351	c.1141G>A	c.(1141-1143)Gaa>Aaa	p.E381K	ZNF583_ENST00000291598.7_Missense_Mutation_p.E381K|ZNF583_ENST00000585612.1_3'UTR	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	381					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E381K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		GAGACCCTACGAATGTAAGGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	88	88					19																	56935168		2203	4300	6503	61626980	SO:0001583	missense	147949			AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1141G>A	19.37:g.56935168G>A	ENSP00000388502:p.Glu381Lys		61626980	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.147337	0.37923	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.06608	3.28;3.28	4.33	-0.45	0.12223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.157085	0.29995	N	0.010670	T	0.03220	0.0094	N	0.03967	-0.31	0.09310	N	1	P	0.47191	0.891	P	0.49332	0.607	T	0.43114	-0.9411	9	.	.	.	.	4.2789	0.10822	0.3527:0.3129:0.3344:0.0	.	381	Q96ND8	ZN583_HUMAN	K	381	ENSP00000291598:E381K;ENSP00000388502:E381K	.	E	+	1	0	ZNF583	61626980	0.000000	0.05858	0.544000	0.28141	0.975000	0.68041	-1.296000	0.02762	0.172000	0.19760	0.462000	0.41574	GAA		0.413	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		A	56935168	G	A	56935168	3	1	47	1	0	0	0	0	1	0	0	0	18054	1059	37	1	1155	1	ZNF583	19	56935168	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	513135	56935168	2193815	1921	6318										
ZNF583	147949	broad.mit.edu	37	chr19	56935646	56935646	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acatcttgctcatcatgagaGaattcatactatggagtcat	7	8	5	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:56935646G>T	ENST00000333201.9	+	5	1829	c.1619G>T	c.(1618-1620)aGa>aTa	p.R540I	ZNF583_ENST00000291598.7_Missense_Mutation_p.R540I|ZNF583_ENST00000585612.1_Intron	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	540					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R540I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		CATCATGAGAGAATTCATact	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	90	92					19																	56935646		2203	4300	6503	61627458	SO:0001583	missense	147949			AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1619G>T	19.37:g.56935646G>T	ENSP00000388502:p.Arg540Ile		61627458	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811212	0.32053	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.10005	2.92;2.92	4.44	-1.09	0.09904	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.282809	0.25666	N	0.029106	T	0.03959	0.0111	N	0.08118	0	0.22034	N	0.999401	P	0.34892	0.474	B	0.35655	0.207	T	0.40289	-0.9571	9	.	.	.	.	4.1695	0.10322	0.4213:0.0:0.4253:0.1534	.	540	Q96ND8	ZN583_HUMAN	I	540	ENSP00000291598:R540I;ENSP00000388502:R540I	.	R	+	2	0	ZNF583	61627458	0.000000	0.05858	0.014000	0.15608	0.992000	0.81027	-0.980000	0.03770	-0.161000	0.10983	0.650000	0.86243	AGA		0.418	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		T	56935646	G	T	56935646	3	4	47	1	0	0	0	0	1	0	0	0	18054	942	33	2	1633	2	ZNF583	19	56935646	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	478	56935646	2193337	1922	6319										
ZNF471	57573	broad.mit.edu	37	chr19	57036620	57036620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggacttattctgcataggaGaattcatacaggagagaaac	10	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57036620G>T	ENST00000308031.5	+	5	1317	c.1184G>T	c.(1183-1185)aGa>aTa	p.R395I	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R395I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CTGCATAGGAGAATTCATACA	0.423																																					Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)											1	Substitution - Missense(1)	large_intestine(1)	19											83	86	85					19																	57036620		2203	4300	6503	61728432	SO:0001583	missense	57573			AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1184G>T	19.37:g.57036620G>T	ENSP00000309161:p.Arg395Ile		61728432	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.797872	0.50208	.	.	ENSG00000196263	ENST00000308031	T	0.24908	1.83	2.94	2.94	0.34122	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45418	0.1341	L	0.61218	1.895	0.80722	D	1	D	0.63880	0.993	D	0.72075	0.976	T	0.45848	-0.9233	9	0.56958	D	0.05	.	12.7014	0.57035	0.0:0.0:1.0:0.0	.	395	Q9BX82	ZN471_HUMAN	I	395	ENSP00000309161:R395I	ENSP00000309161:R395I	R	+	2	0	ZNF471	61728432	.	.	1.000000	0.80357	0.737000	0.42083	.	.	1.485000	0.48380	0.462000	0.41574	AGA		0.423	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		T	57036620	G	T	57036620	3	4	47	1	0	0	0	0	1	0	0	0	17969	942	33	2	1198	2	ZNF471	19	57036620	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	100974	57036620	2092363	1923	6320										
ZNF471	57573	broad.mit.edu	37	chr19	57036956	57036956	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acagctggctactcatcagaGaattcatactggagagaagc	10	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57036956G>T	ENST00000308031.5	+	5	1653	c.1520G>T	c.(1519-1521)aGa>aTa	p.R507I	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	507					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R507I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		ACTCATCAGAGAATTCATACT	0.378																																					Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)											1	Substitution - Missense(1)	large_intestine(1)	19											62	66	65					19																	57036956		2203	4300	6503	61728768	SO:0001583	missense	57573			AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1520G>T	19.37:g.57036956G>T	ENSP00000309161:p.Arg507Ile		61728768	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702367	0.48307	.	.	ENSG00000196263	ENST00000308031	T	0.24908	1.83	3.31	3.31	0.37934	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28896	0.0717	L	0.28608	0.87	0.80722	D	1	D	0.67145	0.996	P	0.58873	0.847	T	0.04294	-1.0962	9	0.66056	D	0.02	.	6.299	0.21101	0.1375:0.0:0.8625:0.0	.	507	Q9BX82	ZN471_HUMAN	I	507	ENSP00000309161:R507I	ENSP00000309161:R507I	R	+	2	0	ZNF471	61728768	0.000000	0.05858	1.000000	0.80357	0.986000	0.74619	0.674000	0.25218	1.690000	0.51089	0.462000	0.41574	AGA		0.378	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		T	57036956	G	T	57036956	3	4	47	1	0	0	0	0	1	0	0	0	17969	942	33	2	1534	2	ZNF471	19	57036956	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	336	57036956	2092027	1924	6321										
ZNF470	388566	broad.mit.edu	37	chr19	57089047	57089047	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggacttattcagcataagaGaactcatactggagagagac	10	7	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57089047G>T	ENST00000330619.8	+	6	1936	c.1250G>T	c.(1249-1251)aGa>aTa	p.R417I	ZNF470_ENST00000391709.3_Missense_Mutation_p.R417I|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	417					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R417I(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CAGCATAAGAGAACTCATACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	84	83					19																	57089047		2203	4300	6503	61780859	SO:0001583	missense	388566			AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1250G>T	19.37:g.57089047G>T	ENSP00000333223:p.Arg417Ile		61780859	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.011176	0.35511	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.02446	4.29;4.29	4.26	3.18	0.36537	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	L	0.60012	1.86	0.36453	D	0.866185	P	0.39717	0.684	B	0.35510	0.204	T	0.45891	-0.9230	9	0.54805	T	0.06	.	6.2006	0.20573	0.0973:0.0:0.7151:0.1876	.	417	Q6ECI4	ZN470_HUMAN	I	417	ENSP00000375590:R417I;ENSP00000333223:R417I	ENSP00000333223:R417I	R	+	2	0	ZNF470	61780859	0.612000	0.27000	0.991000	0.47740	0.222000	0.24845	3.579000	0.53900	0.965000	0.38133	0.650000	0.86243	AGA		0.418	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		T	57089047	G	T	57089047	3	4	47	1	0	0	0	0	1	0	0	0	17968	942	33	2	1264	2	ZNF470	19	57089047	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	52091	57089047	2039936	1925	6322										
ZNF470	388566	broad.mit.edu	37	chr19	57089719	57089719	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcccttactctgcatcagaGaattcatacaggagagaaac	7	10	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57089719G>T	ENST00000330619.8	+	6	2608	c.1922G>T	c.(1921-1923)aGa>aTa	p.R641I	ZNF470_ENST00000391709.3_Missense_Mutation_p.R641I|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	641					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R641I(2)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTGCATCAGAGAATTCATACA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	19											79	76	77					19																	57089719		2203	4300	6503	61781531	SO:0001583	missense	388566			AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1922G>T	19.37:g.57089719G>T	ENSP00000333223:p.Arg641Ile		61781531	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.850213	0.51270	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.24908	1.83;1.83	4.24	1.97	0.26223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27765	0.0683	M	0.81112	2.525	0.35346	D	0.786935	P	0.45672	0.864	B	0.42995	0.404	T	0.43798	-0.9369	9	0.62326	D	0.03	.	1.6506	0.02771	0.1823:0.1701:0.4729:0.1748	.	641	Q6ECI4	ZN470_HUMAN	I	641	ENSP00000375590:R641I;ENSP00000333223:R641I	ENSP00000333223:R641I	R	+	2	0	ZNF470	61781531	0.000000	0.05858	1.000000	0.80357	0.961000	0.63080	0.046000	0.14035	0.974000	0.38366	0.561000	0.74099	AGA		0.398	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		T	57089719	G	T	57089719	3	4	47	1	0	0	0	0	1	0	0	0	17968	942	33	2	1936	2	ZNF470	19	57089719	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	672	57089719	2039264	1926	6323										
PEG3	5178	broad.mit.edu	37	chr19	57327215	57327215	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgcttatcattaaggtctgaGatataaatggaggattctcc	9	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57327215G>T	ENST00000326441.9	-	10	2958	c.2595C>A	c.(2593-2595)atC>atA	p.I865I	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Silent_p.I865I|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000593695.1_Silent_p.I739I|PEG3_ENST00000598410.1_Silent_p.I741I	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	865					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.I865I(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TAAGGTCTGAGATATAAATGG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	19											103	98	100					19																	57327215		2203	4300	6503	62019027	SO:0001819	synonymous_variant	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2595C>A	19.37:g.57327215G>T			62019027	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																				0.433	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57327215	G	T	57327215	2	4	47	1	0	0	0	0	0	0	0	1	11751	932	33	2		2	PEG3	19	57327215	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	237496	57327215	1801768	1927	6324										
USP29	57663	broad.mit.edu	37	chr19	57641759	57641759	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcaggagatgatttctgaGatcaacagcccattgacacc	8	11	3	4	rs527678550	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57641759G>T	ENST00000254181.4	+	4	2170	c.1716G>T	c.(1714-1716)gaG>gaT	p.E572D	USP29_ENST00000598197.1_Missense_Mutation_p.E572D	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	572	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.E572D(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGATTTCTGAGATCAACAGCC	0.468													G|||	2	0.000399361	0	0	5008	,	,		19848	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	19											89	92	91					19																	57641759		2203	4300	6503	62333571	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1716G>T	19.37:g.57641759G>T	ENSP00000254181:p.Glu572Asp		62333571		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239571	0.22711	.	.	ENSG00000131864	ENST00000254181	T	0.50813	0.73	2.52	1.48	0.22813	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.141710	0.06980	U	0.819757	T	0.57446	0.2054	L	0.54323	1.7	0.09310	N	1	D	0.64830	0.994	D	0.64506	0.926	T	0.40869	-0.9540	10	0.36615	T	0.2	-1.8874	5.068	0.14592	0.1703:0.0:0.8297:0.0	.	572	Q9HBJ7	UBP29_HUMAN	D	572	ENSP00000254181:E572D	ENSP00000254181:E572D	E	+	3	2	USP29	62333571	0.001000	0.12720	0.012000	0.15200	0.014000	0.08584	0.234000	0.17930	0.590000	0.29694	0.467000	0.42956	GAG		0.468	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			T	57641759	G	T	57641759	3	4	47	1	0	0	0	0	1	0	0	0	17099	933	33	2	1718	2	USP29	19	57641759	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	314544	57641759	1487224	1928	6325										
USP29	57663	broad.mit.edu	37	chr19	57642793	57642793	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggggaatacgaaggtgactCtttgtacagacctgcttgac	13	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57642793C>A	ENST00000254181.4	+	4	3204	c.2750C>A	c.(2749-2751)tCt>tAt	p.S917Y	U3_ENST00000516874.1_RNA|USP29_ENST00000598197.1_Missense_Mutation_p.S917Y	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	917					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.S917Y(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GAAGGTGACTCTTTGTACAGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	80	77					19																	57642793		2200	4300	6500	62334605	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.2750C>A	19.37:g.57642793C>A	ENSP00000254181:p.Ser917Tyr		62334605		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	C	1.629	-0.519391	0.04171	.	.	ENSG00000131864	ENST00000254181	T	0.51574	0.7	1.73	-1.76	0.08006	.	.	.	.	.	T	0.23014	0.0556	N	0.08118	0	0.09310	N	1	P	0.40638	0.725	B	0.37833	0.259	T	0.14392	-1.0474	9	0.87932	D	0	.	5.0034	0.14275	0.0:0.4381:0.0:0.5619	.	917	Q9HBJ7	UBP29_HUMAN	Y	917	ENSP00000254181:S917Y	ENSP00000254181:S917Y	S	+	2	0	USP29	62334605	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.798000	0.04565	-0.472000	0.06881	-0.469000	0.05056	TCT		0.483	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			A	57642793	C	A	57642793	3	1	47	1	0	0	0	0	1	0	0	0	17099	913	32	2	2752	2	USP29	19	57642793	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1034	57642793	1486190	1929	6326										
ZIM3	114026	broad.mit.edu	37	chr19	57647398	57647398	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttattgattgatgggacttCtcttgcgagactctctttca	8	9	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57647398C>A	ENST00000269834.1	-	5	692	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E103*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GATGGGACTTCTCTTGCGAGA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											180	176	177					19																	57647398		2203	4300	6503	62339210	SO:0001587	stop_gained	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.307G>T	19.37:g.57647398C>A	ENSP00000269834:p.Glu103*		62339210	Q14CA6	Nonsense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822222	0.90873	.	.	ENSG00000141946	ENST00000269834	.	.	.	2.18	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	8.8171	0.35002	0.0:0.7652:0.2348:0.0	.	.	.	.	X	103	.	ENSP00000269834:E103X	E	-	1	0	ZIM3	62339210	0.001000	0.12720	0.002000	0.10522	0.116000	0.19942	0.725000	0.25970	0.479000	0.27511	-0.676000	0.03789	GAA		0.398	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			A	57647398	C	A	57647398	4	1	47	1	0	0	0	0	0	1	0	0	17724	922	32	2	1115	2	ZIM3	19	57647398	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4605	57647398	1481585	1930	6327										
ZNF547	284306	broad.mit.edu	37	chr19	57883210	57883210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggaggagtgggggcatctcGatgaggctcagagattgctg	18	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57883210G>A	ENST00000282282.3	+	3	235	c.85G>A	c.(85-87)Gat>Aat	p.D29N	AC003002.4_ENST00000597658.1_Missense_Mutation_p.D29N	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	29	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D29N(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GGGGCATCTCGATGAGGCTCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	19											369	337	348					19																	57883210		2203	4300	6503	62575022	SO:0001583	missense	284306			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.85G>A	19.37:g.57883210G>A	ENSP00000282282:p.Asp29Asn		62575022	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726801	0.48833	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.02525	4.26	2.01	0.958	0.19619	Krueppel-associated box (4);	.	.	.	.	T	0.03348	0.0097	M	0.75615	2.305	0.09310	N	1	P;B	0.50710	0.938;0.011	B;B	0.34873	0.191;0.006	T	0.42292	-0.9460	9	0.49607	T	0.09	.	4.2858	0.10855	0.2049:0.0:0.7951:0.0	.	29;29	Q8IVP9-2;Q8IVP9	.;ZN547_HUMAN	N	29	ENSP00000282282:D29N	ENSP00000282282:D29N	D	+	1	0	ZNF547	62575022	0.648000	0.27313	0.055000	0.19348	0.967000	0.64934	1.692000	0.37731	0.407000	0.25591	0.561000	0.74099	GAT		0.498	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		A	57883210	G	A	57883210	3	1	47	1	0	0	0	0	1	0	0	0	18018	1058	37	1	91	1	ZNF547	19	57883210	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	235812	57883210	1245773	1931	6328										
ZNF749	388567	broad.mit.edu	37	chr19	57956327	57956327	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caaacttgttattcatcagaGaattcacactggagaaaagc	7	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:57956327G>T	ENST00000334181.4	+	3	2061	c.1811G>T	c.(1810-1812)aGa>aTa	p.R604I	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R517I(1)		breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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)		ATTCATCAGAGAATTCACACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	69	68					19																	57956327		2203	4300	6503	62648139	SO:0001583	missense	388567			AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1811G>T	19.37:g.57956327G>T	ENSP00000333980:p.Arg604Ile		62648139		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347979	0.61183	.	.	ENSG00000186230	ENST00000334181	T	0.24908	1.83	2.36	-1.68	0.08212	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28067	0.0692	L	0.61387	1.9	0.09310	N	1	D	0.56521	0.976	P	0.49528	0.614	T	0.15292	-1.0442	9	0.59425	D	0.04	.	3.6848	0.08324	0.3492:0.0:0.4811:0.1697	.	604	O43361	ZN749_HUMAN	I	604	ENSP00000333980:R604I	ENSP00000333980:R604I	R	+	2	0	ZNF749	62648139	0.000000	0.05858	0.000000	0.03702	0.783000	0.44284	-0.730000	0.04915	-0.443000	0.07180	0.313000	0.20887	AGA		0.393	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		T	57956327	G	T	57956327	3	4	47	1	0	0	0	0	1	0	0	0	18170	942	33	2	1821	2	ZNF749	19	57956327	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	73117	57956327	1172656	1932	6329										
ZIK1	284307	broad.mit.edu	37	chr19	58102275	58102275	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctttagtcaaagtgccattCttaatcaacaccgaagaatt	5	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58102275C>A	ENST00000597850.1	+	4	1311	c.1096C>A	c.(1096-1098)Ctt>Att	p.L366I	ZIK1_ENST00000536878.2_Missense_Mutation_p.L353I|ZIK1_ENST00000599456.1_Missense_Mutation_p.L311I|ZIK1_ENST00000307468.4_3'UTR	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L366I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAGTGCCATTCTTAATCAACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	72	72					19																	58102275		2203	4300	6503	62794087	SO:0001583	missense	284307			AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.1096C>A	19.37:g.58102275C>A	ENSP00000472867:p.Leu366Ile		62794087	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	37	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932450	0.52866	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.53857	0.6	3.37	3.37	0.38596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.74520	0.3727	M	0.90019	3.08	0.19575	N	0.999961	D;D	0.76494	0.999;0.999	D;D	0.91635	0.992;0.999	T	0.62728	-0.6793	9	0.87932	D	0	.	8.7183	0.34425	0.0:0.884:0.0:0.116	.	353;366	F5H435;Q3SY52	.;ZIK1_HUMAN	I	353;319;366	ENSP00000438487:L353I	ENSP00000303820:L366I	L	+	1	0	ZIK1	62794087	0.007000	0.16637	0.014000	0.15608	0.968000	0.65278	0.121000	0.15667	1.881000	0.54492	0.655000	0.94253	CTT		0.428	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		A	58102275	C	A	58102275	3	1	47	1	0	0	0	0	1	0	0	0	17722	913	32	2	1110	2	ZIK1	19	58102275	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	145948	58102275	1026708	1933	6330										
ZNF530	348327	broad.mit.edu	37	chr19	58117315	58117315	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccagctccagaagcttgataAtggagagaagctctttaaag	10	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58117315A>G	ENST00000332854.6	+	3	642	c.422A>G	c.(421-423)aAt>aGt	p.N141S	ZNF530_ENST00000597864.1_Intron	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N141S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAGCTTGATAATGGAGAGAAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	55	54					19																	58117315		2203	4300	6503	62809127	SO:0001583	missense	348327			AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"Zinc fingers, C2H2-type", "-"	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.422A>G	19.37:g.58117315A>G	ENSP00000332861:p.Asn141Ser		62809127	O43340|Q9P220	Missense_Mutation	SNP	ENST00000332854.6	37	CCDS12955.1	.	.	.	.	.	.	.	.	.	.	A	1.285	-0.609231	0.03690	.	.	ENSG00000183647	ENST00000332854	T	0.04654	3.58	2.01	-3.07	0.05363	.	.	.	.	.	T	0.01661	0.0053	N	0.02802	-0.49	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.47636	-0.9102	9	0.19590	T	0.45	.	3.3452	0.07132	0.3095:0.3062:0.3843:0.0	.	141	Q6P9A1	ZN530_HUMAN	S	141	ENSP00000332861:N141S	ENSP00000332861:N141S	N	+	2	0	ZNF530	62809127	0.000000	0.05858	0.003000	0.11579	0.030000	0.12068	-0.777000	0.04669	-0.493000	0.06678	-0.467000	0.05162	AAT		0.488	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880		G	58117315	A	G	58117315	3	3	47	1	0	0	0	0	1	0	0	0	18010	101	4	4	432	4	ZNF530	19	58117315	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	15040	58117315	1011668	1934	6331										
ZNF154	7710	broad.mit.edu	37	chr19	58213365	58213365	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgtgaaccctatggtgttCaatgaggctagagttttggc	13	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58213365C>A	ENST00000512439.2	-	3	1148	c.952G>T	c.(952-954)Gaa>Taa	p.E318*	ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|ZNF154_ENST00000426889.1_Nonsense_Mutation_p.E318*|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E318*(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		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;0.0257)		CTATGGTGTTCAATGAGGCTA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											94	94	94					19																	58213365		2201	4299	6500	62905177	SO:0001587	stop_gained	7710			U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"Zinc fingers, C2H2-type", "-"	12939	protein-coding gene	gene with protein product		604085	"zinc finger protein 154 (pHZ-92)"			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.952G>T	19.37:g.58213365C>A	ENSP00000421258:p.Glu318*		62905177	A7MCY3|Q8IVG7|Q8NAR0	Nonsense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831401	0.91036	.	.	ENSG00000179909	ENST00000512439;ENST00000426889;ENST00000396157	.	.	.	2.86	-5.71	0.02413	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	15.4957	0.75646	0.0:0.1411:0.7694:0.0895	.	.	.	.	X	318;318;133	.	ENSP00000440907:E133X	E	-	1	0	ZNF154	62905177	0.000000	0.05858	0.000000	0.03702	0.949000	0.60115	-10.123000	0.00007	-2.122000	0.00824	0.462000	0.41574	GAA		0.463	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			A	58213365	C	A	58213365	4	1	47	1	0	0	0	0	0	1	0	0	17774	835	29	2	365	2	ZNF154	19	58213365	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	96050	58213365	915618	1935	6332										
ZNF671	79891	broad.mit.edu	37	chr19	58231911	58231911	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtctgtttccggatgaattCtctcccgcactcactacaca	6	14	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58231911C>A	ENST00000317398.6	-	4	1638	c.1543G>T	c.(1543-1545)Gaa>Taa	p.E515*	ZNF671_ENST00000335820.3_Nonsense_Mutation_p.E417*|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF671_ENST00000594803.1_5'Flank	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E515*(1)		kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CGGATGAATTCTCTCCCGCAC	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											210	208	209					19																	58231911		2203	4300	6503	62923723	SO:0001587	stop_gained	79891				CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"Zinc fingers, C2H2-type", "-"	26279	protein-coding gene	gene with protein product	"hypothetical protein FLJ23506"					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.1543G>T	19.37:g.58231911C>A	ENSP00000321848:p.Glu515*		62923723	A6NF07|Q9H5E9	Nonsense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	.	.	.	.	.	.	.	.	.	.	C	34	5.376440	0.95945	.	.	ENSG00000083814	ENST00000317398;ENST00000335820	.	.	.	1.88	-3.76	0.04359	.	.	.	.	.	.	.	.	.	.	.	0.37728	D	0.925184	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	7.4745	0.27368	0.5273:0.4727:0.0:0.0	.	.	.	.	X	515;417	.	ENSP00000321848:E515X	E	-	1	0	ZNF671	62923723	0.000000	0.05858	0.001000	0.08648	0.689000	0.40095	-2.320000	0.01119	-0.780000	0.04553	0.467000	0.42956	GAA		0.502	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833		A	58231911	C	A	58231911	4	1	47	1	0	0	0	0	0	1	0	0	18117	922	32	2	65	2	ZNF671	19	58231911	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	18546	58231911	897072	1936	6333										
ZNF544	27300	broad.mit.edu	37	chr19	58772549	58772549	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcccaactcacaagttaaaGagttgaaacaaaattcagct	6	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58772549G>T	ENST00000596652.1	+	6	811	c.577G>T	c.(577-579)Gag>Tag	p.E193*	ZNF544_ENST00000269829.4_Nonsense_Mutation_p.E193*|ZNF544_ENST00000415203.2_Nonsense_Mutation_p.E165*|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000600220.1_Nonsense_Mutation_p.E165*|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000600044.1_Nonsense_Mutation_p.E165*|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596929.1_Intron|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000599953.1_Nonsense_Mutation_p.E51*			Q6NX49	ZN544_HUMAN	zinc finger protein 544	193					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E193*(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		ACAAGTTAAAGAGTTGAAACA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											62	58	60					19																	58772549		2203	4299	6502	63464361	SO:0001587	stop_gained	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.577G>T	19.37:g.58772549G>T	ENSP00000469635:p.Glu193*		63464361	A8K6J1|Q9UEX4	Nonsense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	32	5.116090	0.94339	.	.	ENSG00000198131	ENST00000269829;ENST00000415203	.	.	.	3.27	-3.12	0.05282	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	5.4275	0.16433	0.3165:0.1829:0.5006:0.0	.	.	.	.	X	193;165	.	ENSP00000269829:E193X	E	+	1	0	ZNF544	63464361	0.083000	0.21467	0.000000	0.03702	0.002000	0.02628	0.269000	0.18589	-0.628000	0.05582	-0.819000	0.03115	GAG		0.403	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		T	58772549	G	T	58772549	4	4	47	1	0	0	0	0	0	1	0	0	18016	943	33	2	591	2	ZNF544	19	58772549	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	540638	58772549	356434	1937	6334										
ZNF584	201514	broad.mit.edu	37	chr19	58928205	58928205	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgtagagtggaggatgagaGagcccatcctgagcatctaa	14	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:58928205G>A	ENST00000306910.4	+	4	843	c.320G>A	c.(319-321)aGa>aAa	p.R107K	ZNF584_ENST00000322834.7_Missense_Mutation_p.E140K|ZNF584_ENST00000593920.1_Missense_Mutation_p.R62K|ZNF584_ENST00000599238.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000596921.1_3'UTR	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	107					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R107K(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|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;0.0271)		GAGGATGAGAGAGCCCATCCT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											67	57	60					19																	58928205		2203	4300	6503	63620017	SO:0001583	missense	201514			AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"Zinc fingers, C2H2-type", "-"	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.320G>A	19.37:g.58928205G>A	ENSP00000306756:p.Arg107Lys		63620017	A8K203	Missense_Mutation	SNP	ENST00000306910.4	37	CCDS12979.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.25|11.25	1.582513|1.582513	0.28180|0.28180	.|.	.|.	ENSG00000171574|ENSG00000171574	ENST00000322834|ENST00000306910	T|T	0.01369|0.05580	4.97|3.42	2.75|2.75	0.543|0.543	0.17179|0.17179	.|.	.|.	.|.	.|.	.|.	T|T	0.03011|0.03011	0.0089|0.0089	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.10296|0.02656	0.003|0.0	B|B	0.06405|0.01281	0.002|0.0	T|T	0.44205|0.44205	-0.9343|-0.9343	8|9	.|0.37606	.|T	.|0.19	.|.	4.3915|4.3915	0.11343|0.11343	0.6026:0.0:0.3974:0.0|0.6026:0.0:0.3974:0.0	.|.	140|107	F6W0P0|Q8IVC4	.|ZN584_HUMAN	K|K	140|107	ENSP00000320731:E140K|ENSP00000306756:R107K	.|ENSP00000306756:R107K	E|R	+|+	1|2	0|0	ZNF584|ZNF584	63620017|63620017	0.367000|0.367000	0.25023|0.25023	0.005000|0.005000	0.12908|0.12908	0.016000|0.016000	0.09150|0.09150	0.427000|0.427000	0.21379|0.21379	0.068000|0.068000	0.16574|0.16574	-0.471000|-0.471000	0.05019|0.05019	GAG|AGA		0.483	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548		A	58928205	G	A	58928205	3	1	47	1	0	0	0	0	1	0	0	0	18055	942	33	3	334	3	ZNF584	19	58928205	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	155656	58928205	200778	1938	6335										
MZF1	7593	broad.mit.edu	37	chr19	59080942	59080942	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggtggcagctagaggcccagActccaggaaatctagagagg	15	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr19:59080942A>C	ENST00000215057.2	-	4	1152	c.592T>G	c.(592-594)Tct>Gct	p.S198A	MZF1_ENST00000599369.1_Missense_Mutation_p.S198A|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594108.1_Missense_Mutation_p.S198A|MZF1_ENST00000594234.1_Missense_Mutation_p.S198A|AC016629.8_ENST00000600726.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	198					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S198A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		AGAGGCCCAGACTCCAGGAAA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											46	46	46					19																	59080942		2203	4300	6503	63772754	SO:0001583	missense	7593			M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.592T>G	19.37:g.59080942A>C	ENSP00000215057:p.Ser198Ala		63772754	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	7.492	0.650821	0.14516	.	.	ENSG00000099326	ENST00000215057	T	0.06371	3.31	4.11	0.786	0.18590	.	0.386006	0.19212	N	0.119907	T	0.02193	0.0068	N	0.08118	0	0.09310	N	1	B;B	0.32918	0.39;0.075	B;B	0.21917	0.037;0.027	T	0.45877	-0.9231	9	.	.	.	-8.1177	3.778	0.08668	0.6486:0.0:0.1904:0.161	.	198;198	Q7Z729;P28698	.;MZF1_HUMAN	A	198	ENSP00000215057:S198A	.	S	-	1	0	MZF1	63772754	0.089000	0.21612	0.002000	0.10522	0.210000	0.24377	0.199000	0.17237	0.046000	0.15833	0.375000	0.23000	TCT		0.582	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		C	59080942	A	C	59080942	3	2	47	1	0	0	0	0	1	0	0	0	10138	275	10	4	1624	4	MZF1	19	59080942	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	152737	59080942	48041	1939	6336										
CPXM1	56265	broad.mit.edu	37	chr20	2779472	2779472	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcgagttagagttagcttCttccgcttcttcataatgac	10	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:2779472C>A	ENST00000380605.2	-	2	304	c.240G>T	c.(238-240)aaG>aaT	p.K80N		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	80					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.K80N(1)		endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GAGTTAGCTTCTTCCGCTTCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											144	143	143					20																	2779472		2203	4300	6503	2727472	SO:0001583	missense	56265			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.240G>T	20.37:g.2779472C>A	ENSP00000369979:p.Lys80Asn		2727472	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996111	0.74703	.	.	ENSG00000088882	ENST00000380605	D	0.95949	-3.86	4.75	4.75	0.60458	.	0.135079	0.29225	N	0.012764	D	0.91653	0.7362	L	0.27053	0.805	0.37516	D	0.917343	B;B	0.29301	0.241;0.241	B;B	0.33454	0.164;0.164	D	0.91763	0.5421	10	0.54805	T	0.06	-31.5535	13.1188	0.59314	0.0:1.0:0.0:0.0	.	80;80	Q8N2E1;Q96SM3	.;CPXM1_HUMAN	N	80	ENSP00000369979:K80N	ENSP00000369979:K80N	K	-	3	2	CPXM1	2727472	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	1.425000	0.34859	2.479000	0.83701	0.563000	0.77884	AAG		0.567	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2779472	C	A	2779472	3	1	47	1	0	0	0	0	1	0	0	0	3843	912	32	2	2016	2	CPXM1	20	2779472	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09		2779472	60246048	1940	6337										
PCNA	5111	broad.mit.edu	37	chr20	5099467	5099467	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgttatcttcggcccttagTgtaatgatatcttcattgcc	8	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:5099467T>G	ENST00000379160.3	-	3	509	c.267A>C	c.(265-267)acA>acC	p.T89T	SNORA26_ENST00000391215.1_RNA|PCNA_ENST00000379143.5_Silent_p.T89T	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	89	Interaction with NUDT15.				base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)	p.T89T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CGGCCCTTAGTGTAATGATAT	0.433								DNA polymerases (catalytic subunits)																																								1	Substitution - coding silent(1)	large_intestine(1)	20											231	223	226					20																	5099467		2203	4300	6503	5047467	SO:0001819	synonymous_variant	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.267A>C	20.37:g.5099467T>G			5047467	B2R897|D3DW02	Silent	SNP	ENST00000379160.3	37	CCDS13087.1																																																																																				0.433	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			G	5099467	T	G	5099467	2	3	47	1	0	0	0	0	0	0	0	1	11619	1683	59	4		4	PCNA	20	5099467	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2319995	5099467	57926053	1941	6338										
CHGB	1114	broad.mit.edu	37	chr20	5903440	5903440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaggagttagtggccagatCggaaacacatgctgccgggc	15	9	0	2	rs560272361		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:5903440C>T	ENST00000378961.4	+	4	854	c.650C>T	c.(649-651)tCg>tTg	p.S217L		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	217						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.S217L(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GTGGCCAGATCGGAAACACAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	20											55	61	59					20																	5903440		2203	4300	6503	5851440	SO:0001583	missense	1114				CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.650C>T	20.37:g.5903440C>T	ENSP00000368244:p.Ser217Leu		5851440	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	C	7.416	0.635663	0.14322	.	.	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.04970	3.52;4.9	5.57	-0.924	0.10462	.	1.420380	0.04885	N	0.448430	T	0.03783	0.0107	N	0.22421	0.69	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.44159	-0.9346	10	0.19590	T	0.45	-0.2802	0.2008	0.00145	0.3654:0.209:0.1978:0.2279	.	217	P05060	SCG1_HUMAN	L	217;197	ENSP00000368244:S217L;ENSP00000416643:S197L	ENSP00000368244:S217L	S	+	2	0	CHGB	5851440	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.629000	0.24538	-0.086000	0.12550	0.563000	0.77884	TCG		0.498	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		T	5903440	C	T	5903440	3	4	47	1	0	0	0	0	1	0	0	0	3345	893	31	1	664	1	CHGB	20	5903440	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	803973	5903440	57122080	1942	6339										
TASP1	55617	broad.mit.edu	37	chr20	13539737	13539737	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctctagtttcctcttgtttCttttaaatgcagctaaactg	6	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:13539737C>A	ENST00000337743.4	-	8	713	c.593G>T	c.(592-594)aGa>aTa	p.R198I	TASP1_ENST00000539805.1_Intron|TASP1_ENST00000480436.1_5'UTR	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	198					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)	p.R198I(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CCTCTTGTTTCTTTTAAATGC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	20											131	128	129					20																	13539737		2203	4300	6503	13487737	SO:0001583	missense	55617			AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.593G>T	20.37:g.13539737C>A	ENSP00000338624:p.Arg198Ile		13487737	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	37	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.461781	0.84425	.	.	ENSG00000089123	ENST00000378157;ENST00000337743;ENST00000455532	D;D	0.87571	-2.27;-2.27	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.93979	0.8072	M	0.91249	3.19	0.80722	D	1	P;D	0.58620	0.838;0.983	P;P	0.58331	0.51;0.837	D	0.94816	0.7983	10	0.66056	D	0.02	-17.3473	17.1826	0.86858	0.0:1.0:0.0:0.0	.	198;175	Q9H6P5;Q5JWM4	TASP1_HUMAN;.	I	175;198;175	ENSP00000338624:R198I;ENSP00000400580:R175I	ENSP00000338624:R198I	R	-	2	0	TASP1	13487737	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.410000	0.73294	2.652000	0.90054	0.591000	0.81541	AGA		0.313	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		A	13539737	C	A	13539737	3	1	47	1	0	0	0	0	1	0	0	0	15628	913	32	2	697	2	TASP1	20	13539737	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	7636297	13539737	49485783	1943	6340										
TASP1	55617	broad.mit.edu	37	chr20	13604143	13604143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtcagttgcaagagcaccggCctgcagcttttcaattgcct	10	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:13604143C>T	ENST00000337743.4	-	4	352	c.232G>A	c.(232-234)Gcc>Acc	p.A78T	TASP1_ENST00000544472.1_Missense_Mutation_p.A78T|TASP1_ENST00000539805.1_Missense_Mutation_p.A78T|TASP1_ENST00000480436.1_5'UTR	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	78					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)	p.A78T(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						AGAGCACCGGCCTGCAGCTTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	20											13	16	15					20																	13604143		2178	4267	6445	13552143	SO:0001583	missense	55617			AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.232G>A	20.37:g.13604143C>T	ENSP00000338624:p.Ala78Thr		13552143	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	37	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.444940	0.83993	.	.	ENSG00000089123	ENST00000539805;ENST00000337743;ENST00000544472	D	0.88586	-2.4	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.87474	0.6186	L	0.58354	1.805	0.80722	D	1	P;B	0.35745	0.518;0.071	B;B	0.36418	0.224;0.033	D	0.84535	0.0635	10	0.15952	T	0.53	-11.6658	19.7441	0.96245	0.0:1.0:0.0:0.0	.	78;78	B7Z963;Q9H6P5	.;TASP1_HUMAN	T	78	ENSP00000338624:A78T	ENSP00000338624:A78T	A	-	1	0	TASP1	13552143	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.473000	0.45145	2.669000	0.90835	0.585000	0.79938	GCC		0.383	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		T	13604143	C	T	13604143	3	4	47	1	0	0	0	0	1	0	0	0	15628	739	26	3	1074	3	TASP1	20	13604143	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	64406	13604143	49421377	1944	6341										
ESF1	51575	broad.mit.edu	37	chr20	13714414	13714414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctctttcttcttctctaaaAattgttcccaaggggtcagt	6	10	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:13714414A>G	ENST00000202816.1	-	10	2011	c.1904T>C	c.(1903-1905)tTt>tCt	p.F635S		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	635	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.F635S(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CTTCTCTAAAAATTGTTCCCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	20											139	145	143					20																	13714414		2203	4299	6502	13662414	SO:0001583	missense	51575				CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.1904T>C	20.37:g.13714414A>G	ENSP00000202816:p.Phe635Ser		13662414	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.565312	0.65651	.	.	ENSG00000089048	ENST00000202816	T	0.75938	-0.98	5.5	5.5	0.81552	.	0.189583	0.46758	D	0.000272	D	0.83362	0.5238	M	0.70595	2.14	0.40972	D	0.984703	D	0.71674	0.998	D	0.75484	0.986	D	0.84642	0.0696	10	0.52906	T	0.07	.	9.9201	0.41459	0.8479:0.0:0.0:0.1521	.	635	Q9H501	ESF1_HUMAN	S	635	ENSP00000202816:F635S	ENSP00000202816:F635S	F	-	2	0	ESF1	13662414	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.421000	0.44688	2.084000	0.62774	0.528000	0.53228	TTT		0.328	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		G	13714414	A	G	13714414	3	3	47	1	0	0	0	0	1	0	0	0	5264	14	1	4	671	4	ESF1	20	13714414	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	110271	13714414	49311106	1945	6342										
ESF1	51575	broad.mit.edu	37	chr20	13763225	13763225	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcagaggtgcctgagtctaAtgtcctttgtttttcttcga	9	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:13763225A>C	ENST00000202816.1	-	2	669	c.562T>G	c.(562-564)Tta>Gta	p.L188V	NDUFAF5_ENST00000463598.1_5'Flank|NDUFAF5_ENST00000378106.5_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L188V(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CCTGAGTCTAATGTCCTTTGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	20											63	63	63					20																	13763225		2203	4300	6503	13711225	SO:0001583	missense	51575				CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.562T>G	20.37:g.13763225A>C	ENSP00000202816:p.Leu188Val		13711225	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	.	.	.	.	.	.	.	.	.	.	A	2.009	-0.427505	0.04701	.	.	ENSG00000089048	ENST00000202816	T	0.21361	2.01	4.99	-4.3	0.03710	.	1.844080	0.02894	N	0.134487	T	0.08670	0.0215	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26815	-1.0092	10	0.29301	T	0.29	.	4.6031	0.12363	0.4417:0.1978:0.0:0.3606	.	188	Q9H501	ESF1_HUMAN	V	188	ENSP00000202816:L188V	ENSP00000202816:L188V	L	-	1	2	ESF1	13711225	0.000000	0.05858	0.000000	0.03702	0.189000	0.23516	0.006000	0.13152	-0.174000	0.10743	-0.565000	0.04167	TTA		0.343	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		C	13763225	A	C	13763225	3	2	47	1	0	0	0	0	1	0	0	0	5264	98	4	4	2045	4	ESF1	20	13763225	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	48811	13763225	49262295	1946	6343										
SEL1L2	80343	broad.mit.edu	37	chr20	13847414	13847414	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacatcttggccagataataAatggcaaggggctgcccact	10	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:13847414A>C	ENST00000284951.5	-	15	1412	c.1338T>G	c.(1336-1338)atT>atG	p.I446M	SEL1L2_ENST00000378072.5_Missense_Mutation_p.I446M|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	446						integral component of membrane (GO:0016021)		p.I446M(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CCAGATAATAAATGGCAAGGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	20											108	104	105					20																	13847414		1856	4096	5952	13795414	SO:0001583	missense	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1338T>G	20.37:g.13847414A>C	ENSP00000284951:p.Ile446Met		13795414	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	A	11.86	1.764571	0.31228	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.50813	0.73;0.73	6.03	3.81	0.43845	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000004	T	0.55529	0.1926	L	0.47716	1.5	0.37085	D	0.899154	P;D	0.76494	0.636;0.999	P;D	0.73708	0.451;0.981	T	0.56715	-0.7933	10	0.34782	T	0.22	-13.098	7.4379	0.27166	0.7623:0.0:0.2377:0.0	.	446;446	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	M	446	ENSP00000367312:I446M;ENSP00000284951:I446M	ENSP00000284951:I446M	I	-	3	3	SEL1L2	13795414	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.620000	0.46410	0.536000	0.28733	-0.379000	0.06801	ATT		0.393	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		C	13847414	A	C	13847414	3	2	47	1	0	0	0	0	1	0	0	0	14048	10	1	4	752	4	SEL1L2	20	13847414	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	84189	13847414	49178106	1947	6344										
KIF16B	55614	broad.mit.edu	37	chr20	16360507	16360507	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttctcgttgttgttgagttCtttgagtcgttggagttctt	11	6	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:16360507C>A	ENST00000354981.2	-	19	2297	c.2140G>T	c.(2140-2142)Gaa>Taa	p.E714*	KIF16B_ENST00000408042.1_Nonsense_Mutation_p.E714*|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Nonsense_Mutation_p.E714*	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	714	Glu-rich.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.E714*(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TTGTTGAGTTCTTTGAGTCGT	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											155	142	147					20																	16360507		2203	4300	6503	16308507	SO:0001587	stop_gained	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2140G>T	20.37:g.16360507C>A	ENSP00000347076:p.Glu714*		16308507	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Nonsense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.4|27.4	4.830927|4.830927	0.91036|0.91036	.|.	.|.	ENSG00000089177|ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000408042|ENST00000450176	.|T	.|0.17854	.|2.25	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.057994|.	0.64402|.	D|.	0.000003|.	.|T	.|0.39733	.|0.1089	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.11275	.|-1.0594	.|6	0.07813|0.54805	T|T	0.8|0.06	.|.	18.7471|18.7471	0.91797|0.91797	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	714|148	.|ENSP00000396264:K148N	ENSP00000347076:E714X|ENSP00000396264:K148N	E|K	-|-	1|3	0|2	KIF16B|KIF16B	16308507|16308507	1.000000|1.000000	0.71417|0.71417	0.174000|0.174000	0.22961|0.22961	0.012000|0.012000	0.07955|0.07955	6.670000|6.670000	0.74467|0.74467	2.531000|2.531000	0.85337|0.85337	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.458	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16360507	C	A	16360507	4	1	47	1	0	0	0	0	0	1	0	0	8299	922	32	2	1845	2	KIF16B	20	16360507	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2513093	16360507	46665013	1948	6345										
SEC23B	10483	broad.mit.edu	37	chr20	18496339	18496339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaggtgaatcaacctgccGaattgatgccccagttttct	9	11	2	3	rs121918221		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:18496339G>A	ENST00000336714.3	+	4	757	c.325G>A	c.(325-327)Gaa>Aaa	p.E109K	SEC23B_ENST00000262544.2_Missense_Mutation_p.E109K|SEC23B_ENST00000377475.3_Missense_Mutation_p.E109K|SEC23B_ENST00000377465.1_Missense_Mutation_p.E109K|SEC23B_ENST00000494645.1_3'UTR	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	109			E -> K (in CDAN2; the mutant protein is unstable with less than 5% of protein detectable compared to wild-type). {ECO:0000269|PubMed:19561605, ECO:0000269|PubMed:19621418}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)	p.E109K(2)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						TCAACCTGCCGAATTGATGCC	0.353													G|||	1	0.000199681	8e-04	0	5008	,	,		22584	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	20						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	174	127	143	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	325,325,325,325,325	5	1	20	dbSNP_133	143	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	56,56,56,56,56	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	109/768,109/750,109/768,109/768,109/768	18496339	3,13003	2203	4300	6503	18444339	SO:0001583	missense	10483			X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.325G>A	20.37:g.18496339G>A	ENSP00000338844:p.Glu109Lys		18444339	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	36	5.675861	0.96764	2.27E-4	2.33E-4	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46	5.04	5.04	0.67666	Zinc finger, Sec23/Sec24-type (1);	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	H	0.96208	3.785	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	D	0.97400	0.9995	9	0.87932	D	0	-23.8649	17.9094	0.88929	0.0:0.0:1.0:0.0	.	109;109	B4DJW8;Q15437	.;SC23B_HUMAN	K	109	ENSP00000403971:E109K;ENSP00000338844:E109K;ENSP00000262544:E109K;ENSP00000366695:E109K;ENSP00000366685:E109K	ENSP00000262544:E109K	E	+	1	0	SEC23B	18444339	1.000000	0.71417	0.986000	0.45419	0.939000	0.58152	9.433000	0.97501	2.776000	0.95493	0.650000	0.86243	GAA		0.353	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			A	18496339	G	A	18496339	3	1	47	1	0	0	0	0	1	0	0	0	14029	1059	37	1	335	1	SEC23B	20	18496339	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2135832	18496339	44529181	1949	6346										
CRNKL1	51340	broad.mit.edu	37	chr20	20018119	20018119	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccttttcttcacagtttcGcatggttttgttagcttctt	6	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:20018119G>A	ENST00000377340.2	-	14	2258	c.2227C>T	c.(2227-2229)Cga>Tga	p.R743*	CRNKL1_ENST00000377327.4_Nonsense_Mutation_p.R731*|CRNKL1_ENST00000521379.1_5'UTR|CRNKL1_ENST00000536226.1_Nonsense_Mutation_p.R582*	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	743					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R743*(1)		breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TCACAGTTTCGCATGGTTTTG	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											187	183	185					20																	20018119		2203	4300	6503	19966119	SO:0001587	stop_gained	51340			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.2227C>T	20.37:g.20018119G>A	ENSP00000366557:p.Arg743*		19966119	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Nonsense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	G	37	6.429326	0.97559	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	.	.	.	5.02	-1.55	0.08558	.	0.051632	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-10.4844	16.7856	0.85573	0.0:0.0:0.308:0.692	.	.	.	.	X	731;743;582	.	ENSP00000366544:R731X	R	-	1	2	CRNKL1	19966119	1.000000	0.71417	0.993000	0.49108	0.872000	0.50106	1.273000	0.33121	-0.041000	0.13558	-0.516000	0.04426	CGA		0.383	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			A	20018119	G	A	20018119	4	1	47	1	0	0	0	0	0	1	0	0	3897	1095	38	1	327	1	CRNKL1	20	20018119	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1521780	20018119	43007401	1950	6347										
C20orf26	26074	broad.mit.edu	37	chr20	20278850	20278850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaactagtaaccggcagtgCgaaaaatgggacttacttcc	10	9	0	1	rs189288996	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:20278850C>T	ENST00000245957.5	+	25	3318	c.3242C>T	c.(3241-3243)gCg>gTg	p.A1081V	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1081								p.A1081V(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		ACCGGCAGTGCGAAAAATGGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	20											75	75	75					20																	20278850		2203	4300	6503	20226850	SO:0001583	missense	26074																														ENST00000245957.5:c.3242C>T	20.37:g.20278850C>T	ENSP00000245957:p.Ala1081Val		20226850	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675759	0.29783	.	.	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.46063	0.88	5.27	-0.251	0.13003	.	0.338388	0.30193	N	0.010197	T	0.32496	0.0831	L	0.54323	1.7	0.40981	D	0.984779	B	0.21821	0.061	B	0.17098	0.017	T	0.10660	-1.0620	10	0.25106	T	0.35	.	9.5984	0.39589	0.0:0.635:0.0:0.365	.	1081	Q8NHU2	CT026_HUMAN	V	1021;1047;1081	ENSP00000245957:A1081V	ENSP00000245957:A1081V	A	+	2	0	C20orf26	20226850	0.061000	0.20836	0.000000	0.03702	0.017000	0.09413	0.574000	0.23714	-0.189000	0.10482	-0.136000	0.14681	GCG		0.423	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20278850	C	T	20278850	3	4	47	1	0	0	0	0	1	0	0	0	2112	768	27	1	3368	1	C20orf26	20	20278850	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	260731	20278850	42746670	1951	6348										
PLK1S1	100873719	broad.mit.edu	37	chr20	21117112	21117112	+	RNA	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggctcatactcgaaaccaAgaatatttaaagcgatttga	7	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:21117112A>C	ENST00000362639.1	-	0	119									RNA, 5S ribosomal pseudogene 477																		CTCGAAACCAAGAATATTTAA	0.338																																																0			20											76	69	71					20																	21117112		1833	4088	5921	21065112			55857					20p11.23	2012-08-07	2012-08-09	2012-08-09	ENSG00000199509	ENSG00000199509			43377	pseudogene	RNA, pseudogene			"RNA, 5S ribosomal 477"	RN5S477			Standard	NG_033710		Approved						20.37:g.21117112A>C			21065112		Missense_Mutation	SNP	ENST00000362639.1	37																																																																																					0.338	RNA5SP477-201	KNOWN	basic	rRNA	rRNA				C	21117112	A	C	21117112	1	2	47	0	1	0	0	0	0	0	0	0	12126	69	3	4		4	PLK1S1	20	21117112	RNA	SNP	A	TCGA-AG-3892-01A-01W-1073-09	838262	21117112	41908408	1952	6349										
KIF3B	9371	broad.mit.edu	37	chr20	30898370	30898370	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacaaggggagagattaaaaGaagctaccaagatcaacctc	9	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:30898370G>T	ENST00000375712.3	+	2	957	c.790G>T	c.(790-792)Gaa>Taa	p.E264*	KIF3B_ENST00000418717.2_5'UTR	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	264	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)	p.E264*(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GAGATTAAAAGAAGCTACCAA	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											89	85	86					20																	30898370		2203	4300	6503	30362031	SO:0001587	stop_gained	9371			AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"Kinesins"	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.790G>T	20.37:g.30898370G>T	ENSP00000364864:p.Glu264*		30362031	B2RMP4|B4DSR5|E1P5M5	Nonsense_Mutation	SNP	ENST00000375712.3	37	CCDS13200.1	.	.	.	.	.	.	.	.	.	.	G	38	6.919954	0.97936	.	.	ENSG00000101350	ENST00000375712	.	.	.	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.4488	0.87586	0.0:0.0:1.0:0.0	.	.	.	.	X	264	.	ENSP00000364864:E264X	E	+	1	0	KIF3B	30362031	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.657000	0.98554	2.336000	0.79503	0.462000	0.41574	GAA		0.493	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798		T	30898370	G	T	30898370	4	4	47	1	0	0	0	0	0	1	0	0	8322	943	33	2	792	2	KIF3B	20	30898370	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	9781258	30898370	32127150	1953	6350										
ASXL1	171023	broad.mit.edu	37	chr20	31020765	31020765	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacaatggaaagaaaagttCtttgaagactactatggaca	9	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:31020765C>A	ENST00000375687.4	+	11	1486	c.1062C>A	c.(1060-1062)ttC>ttA	p.F354L	ASXL1_ENST00000306058.5_Missense_Mutation_p.F349L	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	354	Interaction with KDM1A. {ECO:0000250}.|Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.F354L(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						AAGAAAAGTTCTTTGAAGACT	0.418			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	1	Substitution - Missense(1)	large_intestine(1)	20											96	93	94					20																	31020765		2203	4300	6503	30484426	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1062C>A	20.37:g.31020765C>A	ENSP00000364839:p.Phe354Leu		30484426	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429351	0.62844	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058;ENST00000553345	T;T	0.33216	1.44;1.42	4.6	2.67	0.31697	.	0.000000	0.85682	D	0.000000	T	0.47985	0.1475	L	0.59436	1.845	0.58432	D	0.99999	D;D	0.76494	0.999;0.999	D;D	0.91635	0.996;0.999	T	0.41592	-0.9500	10	0.62326	D	0.03	-7.7604	10.4924	0.44758	0.0:0.842:0.0:0.158	.	349;354	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	L	354;354;354;293;349;126	ENSP00000364839:F354L;ENSP00000305119:F349L	ENSP00000305119:F349L	F	+	3	2	ASXL1	30484426	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.363000	0.44178	0.563000	0.29222	0.561000	0.74099	TTC		0.418	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31020765	C	A	31020765	3	1	47	1	0	0	0	0	1	0	0	0	1067	912	32	2	1110	2	ASXL1	20	31020765	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	122395	31020765	32004755	1954	6351										
ASXL1	171023	broad.mit.edu	37	chr20	31023615	31023615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcggtggacaaggatgagAaacccaattggaaccaatct	10	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:31023615A>G	ENST00000375687.4	+	13	3524	c.3100A>G	c.(3100-3102)Aaa>Gaa	p.K1034E	ASXL1_ENST00000306058.5_Missense_Mutation_p.K1029E	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1034					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.K1034E(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CAAGGATGAGAAACCCAATTG	0.527			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	1	Substitution - Missense(1)	large_intestine(1)	20											219	183	195					20																	31023615		2203	4300	6503	30487276	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3100A>G	20.37:g.31023615A>G	ENSP00000364839:p.Lys1034Glu		30487276	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	A	8.723	0.914830	0.17907	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.25085	1.82;1.82	4.32	4.32	0.51571	.	0.468058	0.24162	N	0.040969	T	0.15089	0.0364	L	0.34521	1.04	0.09310	N	1	B;B	0.24721	0.11;0.11	B;B	0.20577	0.03;0.03	T	0.18777	-1.0326	10	0.13108	T	0.6	-2.6869	6.0685	0.19875	0.7466:0.1657:0.0876:0.0	.	1029;1034	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	E	1034;1034;1034;955;1029	ENSP00000364839:K1034E;ENSP00000305119:K1029E	ENSP00000305119:K1029E	K	+	1	0	ASXL1	30487276	0.078000	0.21339	0.090000	0.20809	0.094000	0.18550	2.874000	0.48483	2.174000	0.68829	0.459000	0.35465	AAA		0.527	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31023615	A	G	31023615	3	3	47	1	0	0	0	0	1	0	0	0	1067	247	9	4	3156	4	ASXL1	20	31023615	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2850	31023615	32001905	1955	6352										
DNMT3B	1789	broad.mit.edu	37	chr20	31383464	31383464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttctcaatagaacaaatgGcttcagatgttgccaacaac	6	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:31383464G>A	ENST00000328111.2	+	12	1582	c.1261G>A	c.(1261-1263)Gct>Act	p.A421T	DNMT3B_ENST00000344505.4_Missense_Mutation_p.A401T|DNMT3B_ENST00000456297.2_Missense_Mutation_p.A325T|DNMT3B_ENST00000201963.3_Missense_Mutation_p.A413T|DNMT3B_ENST00000348286.2_Missense_Mutation_p.A401T|DNMT3B_ENST00000353855.2_Missense_Mutation_p.A401T|DNMT3B_ENST00000375623.4_Nonsense_Mutation_p.W310*|DNMT3B_ENST00000443239.3_Missense_Mutation_p.A359T	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	421					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.A413T(1)|p.A421T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGAACAAATGGCTTCAGATGT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	20											119	102	108					20																	31383464		2203	4300	6503	30847125	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1261G>A	20.37:g.31383464G>A	ENSP00000328547:p.Ala421Thr		30847125	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.87|19.87	3.906854|3.906854	0.72868|0.72868	.|.	.|.	ENSG00000088305|ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963|ENST00000375623	D;D;D;D;D;D;D|.	0.96802|.	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13|.	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	0.241171|.	0.41605|.	D|.	0.000844|.	T|.	0.63721|.	0.2535|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	A|A	1|1	P;P;B;B;P;B;B|.	0.37985|.	0.478;0.478;0.243;0.356;0.613;0.356;0.349|.	B;B;B;B;B;B;B|.	0.41271|.	0.191;0.191;0.09;0.185;0.352;0.185;0.108|.	T|.	0.70842|.	-0.4762|.	9|.	0.59425|0.66056	D|D	0.04|0.02	-6.9251|-6.9251	16.2076|16.2076	0.82138|0.82138	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	325;359;120;413;401;401;421|.	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3|.	.;.;.;.;.;.;DNM3B_HUMAN|.	T|X	421;487;401;401;359;325;401;413|310	ENSP00000328547:A421T;ENSP00000313397:A401T;ENSP00000337764:A401T;ENSP00000403169:A359T;ENSP00000412305:A325T;ENSP00000345105:A401T;ENSP00000201963:A413T|.	ENSP00000201963:A413T|ENSP00000364774:W310X	A|W	+|+	1|3	0|0	DNMT3B|DNMT3B	30847125|30847125	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.242000|0.242000	0.25591|0.25591	5.388000|5.388000	0.66249|0.66249	2.687000|2.687000	0.91594|0.91594	0.563000|0.563000	0.77884|0.77884	GCT|TGG		0.532	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31383464	G	A	31383464	3	1	47	1	0	0	0	0	1	0	0	0	4688	1203	42	3	1343	3	DNMT3B	20	31383464	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	359849	31383464	31642056	1956	6353										
TGM2	7052	broad.mit.edu	37	chr20	36759606	36759606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acacctcagccaccagcttgCgtttctgcttgggctcccca	8	17	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:36759606C>T	ENST00000361475.2	-	12	1975	c.1802G>A	c.(1801-1803)cGc>cAc	p.R601H	TGM2_ENST00000536724.1_Missense_Mutation_p.R541H|TGM2_ENST00000536701.1_Missense_Mutation_p.R520H	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	601					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R601H(1)		endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	CACCAGCTTGCGTTTCTGCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	20											89	81	84					20																	36759606		2203	4300	6503	36193020	SO:0001583	missense	7052			M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"Transglutaminases"	11778	protein-coding gene	gene with protein product	"C polypeptide, protein-glutamine-gamma-glutamyltransferase"	190196	"transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1802G>A	20.37:g.36759606C>T	ENSP00000355330:p.Arg601His		36193020	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Missense_Mutation	SNP	ENST00000361475.2	37	CCDS13302.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.761313	0.89932	.	.	ENSG00000198959	ENST00000361475;ENST00000536701;ENST00000536724	T;T;T	0.69040	-0.37;-0.37;-0.37	5.06	4.11	0.48088	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.175763	0.49916	D	0.000125	T	0.81678	0.4873	M	0.85630	2.765	0.54753	D	0.999984	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.78314	0.976;0.987;0.986;0.989;0.991	D	0.84290	0.0499	10	0.72032	D	0.01	-42.8195	11.9835	0.53133	0.0:0.9167:0.0:0.0833	.	541;520;541;601;7	F5H6P0;B4DIT7;B4DTN7;P21980;Q6DKH2	.;.;.;TGM2_HUMAN;.	H	601;520;541	ENSP00000355330:R601H;ENSP00000444701:R520H;ENSP00000437479:R541H	ENSP00000355330:R601H	R	-	2	0	TGM2	36193020	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	4.608000	0.61141	2.337000	0.79520	0.561000	0.74099	CGC		0.622	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951		T	36759606	C	T	36759606	3	4	47	1	0	0	0	0	1	0	0	0	15869	768	27	1	269	1	TGM2	20	36759606	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5376142	36759606	26265914	1957	6354										
TOP1	7150	broad.mit.edu	37	chr20	39744918	39744918	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgctttgtctcctccagActggtattctgaataagcat	8	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:39744918A>C	ENST00000361337.2	+	17	1958	c.1708A>C	c.(1708-1710)Act>Cct	p.T570P	RP1-1J6.2_ENST00000454626.1_RNA	NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	570					chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)	p.T570P(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	TCTCCTCCAGACTGGTATTCT	0.463			T	NUP98	AML*																																		Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	1	Substitution - Missense(1)	large_intestine(1)	20											87	76	79					20																	39744918		2203	4300	6503	39178332	SO:0001630	splice_region_variant	7150				CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.1708-1A>C	20.37:g.39744918A>C			39178332	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Missense_Mutation	SNP	ENST00000361337.2	37	CCDS13312.1	.	.	.	.	.	.	.	.	.	.	A	32	5.119079	0.94385	.	.	ENSG00000198900	ENST00000361337	T	0.44083	0.93	5.87	5.87	0.94306	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (1);	0.000000	0.85682	D	0.000000	T	0.64649	0.2617	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64588	-0.6372	9	.	.	.	-13.6266	16.5764	0.84681	1.0:0.0:0.0:0.0	.	570	P11387	TOP1_HUMAN	P	570	ENSP00000354522:T570P	.	T	+	1	0	TOP1	39178332	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	ACT		0.463	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2		Missense_Mutation	C	39744918	A	C	39744918	5	2	47	1	0	0	0	0	0	0	1	0	16403	289	10	4	1774	4	TOP1	20	39744918	Splice_Site	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2985312	39744918	23280602	1958	6355										
PTPRT	11122	broad.mit.edu	37	chr20	41100972	41100972	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcggggttagacagcaagaGtcgcagccggatggtcatga	15	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:41100972G>T	ENST00000373187.1	-	8	1383	c.1384C>A	c.(1384-1386)Ctc>Atc	p.L462I	PTPRT_ENST00000356100.2_Missense_Mutation_p.L462I|PTPRT_ENST00000373190.1_Missense_Mutation_p.L462I|PTPRT_ENST00000373198.4_Missense_Mutation_p.L462I|PTPRT_ENST00000373201.1_Missense_Mutation_p.L462I|PTPRT_ENST00000373193.3_Missense_Mutation_p.L462I|PTPRT_ENST00000373184.1_Missense_Mutation_p.L462I			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	462	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.L462I(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GACAGCAAGAGTCGCAGCCGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	20											56	61	60					20																	41100972		2137	4245	6382	40534386	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1384C>A	20.37:g.41100972G>T	ENSP00000362283:p.Leu462Ile		40534386	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.936013	0.52972	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.28	4.27	0.50696	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.069253	0.64402	D	0.000013	T	0.60431	0.2268	M	0.75615	2.305	0.49130	D	0.999751	P;P	0.42649	0.786;0.68	P;P	0.57679	0.825;0.672	T	0.59915	-0.7364	10	0.42905	T	0.14	.	7.8276	0.29324	0.1239:0.0:0.7297:0.1464	.	462;462	O14522-1;O14522	.;PTPRT_HUMAN	I	462	ENSP00000362286:L462I;ENSP00000362283:L462I;ENSP00000362289:L462I;ENSP00000348408:L462I;ENSP00000362294:L462I;ENSP00000362280:L462I;ENSP00000362297:L462I	ENSP00000348408:L462I	L	-	1	0	PTPRT	40534386	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	3.263000	0.51546	2.480000	0.83734	0.455000	0.32223	CTC		0.612	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	41100972	G	T	41100972	3	4	47	1	0	0	0	0	1	0	0	0	12849	1029	36	2	3098	2	PTPRT	20	41100972	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1356054	41100972	21924548	1959	6356										
RIMS4	140730	broad.mit.edu	37	chr20	43386386	43386386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacctccaactgaccgttccGctcctgcagaccgatctcca	6	19	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:43386386G>A	ENST00000372851.3	-	4	442	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	RIMS4_ENST00000541604.2_Missense_Mutation_p.R127W	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	126	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)		p.R126W(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				TGACCGTTCCGCTCCTGCAGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											118	94	102					20																	43386386		2203	4300	6503	42819800	SO:0001583	missense	140730				CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546	ENST00000372851.3:c.376C>T	20.37:g.43386386G>A	ENSP00000361942:p.Arg126Trp		42819800	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688146	0.68271	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	T;T	0.79141	-1.24;-1.24	5.91	4.89	0.63831	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.88058	0.6335	M	0.84433	2.695	0.58432	D	0.999998	D;D	0.76494	0.998;0.999	P;D	0.63793	0.772;0.918	D	0.89645	0.3865	10	0.87932	D	0	.	15.8828	0.79216	0.0:0.0:0.7778:0.2222	.	127;126	E1P613;Q9H426	.;RIMS4_HUMAN	W	126;127	ENSP00000361942:R126W;ENSP00000439287:R127W	ENSP00000361942:R126W	R	-	1	2	RIMS4	42819800	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	4.181000	0.58303	2.802000	0.96397	0.655000	0.94253	CGG		0.567	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		A	43386386	G	A	43386386	3	1	47	1	0	0	0	0	1	0	0	0	13407	1086	38	1	445	1	RIMS4	20	43386386	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2285414	43386386	19639134	1960	6357										
SEMG2	6407	broad.mit.edu	37	chr20	43851053	43851053	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttactacccaagatgagctCctagtatataacaagaatca	5	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:43851053C>T	ENST00000372769.3	+	2	870	c.780C>T	c.(778-780)ctC>ctT	p.L260L		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	260	Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.L260L(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				AAGATGAGCTCCTAGTATATA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	20											105	105	105					20																	43851053		2203	4300	6503	43284467	SO:0001819	synonymous_variant	6407				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.780C>T	20.37:g.43851053C>T			43284467	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	37	CCDS13346.1																																																																																				0.413	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		T	43851053	C	T	43851053	2	4	47	1	0	0	0	0	0	0	0	1	14082	842	30	3		3	SEMG2	20	43851053	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	464667	43851053	19174467	1961	6358										
ZNF334	55713	broad.mit.edu	37	chr20	45132940	45132940	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacatctggtttgctaacatGataccctgttaatgggaaat	8	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:45132940G>T	ENST00000347606.4	-	4	336	c.154C>A	c.(154-156)Cat>Aat	p.H52N	ZNF334_ENST00000457685.2_Missense_Mutation_p.H14N|ZNF334_ENST00000593880.1_Missense_Mutation_p.H75N	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	52	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H52N(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TTGCTAACATGATACCCTGTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	20											92	77	82					20																	45132940		2203	4300	6503	44566347	SO:0001583	missense	55713			AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.154C>A	20.37:g.45132940G>T	ENSP00000255129:p.His52Asn		44566347	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	37	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	G	2.105	-0.405247	0.04832	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.40476	5.69;1.03	3.0	0.892	0.19230	Krueppel-associated box (3);	.	.	.	.	T	0.26882	0.0658	L	0.35542	1.07	0.09310	N	1	B;B;B	0.20261	0.024;0.024;0.043	B;B;B	0.21151	0.023;0.023;0.033	T	0.26430	-1.0103	9	0.18276	T	0.48	.	5.8506	0.18691	0.1201:0.1967:0.6832:0.0	.	14;52;75	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	N	14;52	ENSP00000402582:H14N;ENSP00000255129:H52N	ENSP00000255129:H52N	H	-	1	0	ZNF334	44566347	0.000000	0.05858	0.001000	0.08648	0.884000	0.51177	-0.613000	0.05610	0.113000	0.18004	0.591000	0.81541	CAT		0.398	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			T	45132940	G	T	45132940	3	4	47	1	0	0	0	0	1	0	0	0	17890	1290	45	2	1896	2	ZNF334	20	45132940	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1281887	45132940	17892580	1962	6359										
SLC9A8	23315	broad.mit.edu	37	chr20	48456127	48456127	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagagtttaaaaaactggcGaattggaaggtaggtttgcc	12	4	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:48456127G>A	ENST00000361573.2	+	4	381	c.339G>A	c.(337-339)gcG>gcA	p.A113A	SLC9A8_ENST00000417961.1_Silent_p.A113A|SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000539601.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	113					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)	p.A113A(2)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			AAAAACTGGCGAATTGGAAGG	0.299																																																2	Substitution - coding silent(2)	large_intestine(2)	20											76	83	80					20																	48456127		2203	4300	6503	47889534	SO:0001819	synonymous_variant	23315			AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.339G>A	20.37:g.48456127G>A			47889534	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																				0.299	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		A	48456127	G	A	48456127	2	1	47	1	0	0	0	0	0	0	0	1	14757	1045	37	1		1	SLC9A8	20	48456127	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3323187	48456127	14569393	1963	6360										
SLC9A8	23315	broad.mit.edu	37	chr20	48472087	48472087	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtctttggagaaagtattCtcaacgatgcagtctccatt	9	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:48472087C>A	ENST00000361573.2	+	8	724	c.682C>A	c.(682-684)Ctc>Atc	p.L228I	SLC9A8_ENST00000417961.1_Missense_Mutation_p.L244I|SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000539601.1_Missense_Mutation_p.L9I			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	228					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)	p.L228I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			AGAAAGTATTCTCAACGATGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	20											131	112	118					20																	48472087		2203	4300	6503	47905494	SO:0001583	missense	23315			AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.682C>A	20.37:g.48472087C>A	ENSP00000354966:p.Leu228Ile		47905494	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Missense_Mutation	SNP	ENST00000361573.2	37	CCDS13421.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089107	0.94100	.	.	ENSG00000197818	ENST00000417961;ENST00000361573;ENST00000539601	T;T;T	0.17528	2.27;2.27;2.27	5.24	5.24	0.73138	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.53642	0.1809	M	0.92122	3.275	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.65919	-0.6051	10	0.87932	D	0	.	19.2019	0.93714	0.0:1.0:0.0:0.0	.	228	Q9Y2E8	SL9A8_HUMAN	I	244;228;9	ENSP00000416418:L244I;ENSP00000354966:L228I;ENSP00000441716:L9I	ENSP00000354966:L228I	L	+	1	0	SLC9A8	47905494	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	5.947000	0.70242	2.598000	0.87819	0.650000	0.86243	CTC		0.463	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		A	48472087	C	A	48472087	3	1	47	1	0	0	0	0	1	0	0	0	14757	913	32	2	712	2	SLC9A8	20	48472087	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	15960	48472087	14553433	1964	6361										
C20orf43	51507	broad.mit.edu	37	chr20	55049745	55049745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctattgcagactttataacaAagatgccgtcattgaatttc	6	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:55049745A>G	ENST00000023939.4	+	3	283	c.176A>G	c.(175-177)aAa>aGa	p.K59R	snoU13_ENST00000459416.1_RNA|RTFDC1_ENST00000357348.5_Missense_Mutation_p.K89R|RTFDC1_ENST00000395881.3_Missense_Mutation_p.K59R	NM_001283035.1|NM_001283036.1|NM_016407.3	NP_001269964.1|NP_001269965.1|NP_057491.2	Q9BY42	RTF2_HUMAN	replication termination factor 2 domain containing 1	59								p.K59R(1)									CTTTATAACAAAGATGCCGTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	20											120	126	124					20																	55049745		2203	4300	6503	54483152	SO:0001583	missense	51507			AF161513	CCDS13453.1, CCDS63316.1, CCDS63317.1	20q13	2012-10-29	2012-10-29	2012-10-29	ENSG00000022277	ENSG00000022277			15890	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 43"	C20orf43			Standard	NM_001283035		Approved	HSPC164, CDAO5	uc002xxt.2	Q9BY42	OTTHUMG00000032801	ENST00000023939.4:c.176A>G	20.37:g.55049745A>G	ENSP00000023939:p.Lys59Arg		54483152	E1P5Z9|Q9BYL7|Q9HCV9|Q9NX29|Q9NZZ8|Q9P002|Q9UHW3	Missense_Mutation	SNP	ENST00000023939.4	37	CCDS13453.1	.	.	.	.	.	.	.	.	.	.	A	32	5.165389	0.94768	.	.	ENSG00000022277	ENST00000023939;ENST00000395881;ENST00000357348;ENST00000449062	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.87097	2.86	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.985;1.0	D;D;D;D	0.97110	1.0;0.999;0.963;1.0	T	0.74743	-0.3562	10	0.59425	D	0.04	-28.7749	16.3141	0.82909	1.0:0.0:0.0:0.0	.	89;59;59;59	A8MSH5;A2A2L6;B2RB99;Q9BY42	.;.;.;CT043_HUMAN	R	59;59;89;89	ENSP00000023939:K59R;ENSP00000379220:K59R;ENSP00000349906:K89R;ENSP00000400322:K89R	ENSP00000023939:K59R	K	+	2	0	C20orf43	54483152	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.285000	0.89914	2.326000	0.78906	0.533000	0.62120	AAA		0.358	RTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079817.2	NM_016407		G	55049745	A	G	55049745	3	3	47	1	0	0	0	0	1	0	0	0	2118	14	1	4	186	4	C20orf43	20	55049745	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	6577658	55049745	7975775	1965	6362										
CTCFL	140690	broad.mit.edu	37	chr20	56090847	56090847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actggcaacactgaaaggggCgctccccagtgtgggatcgg	15	11	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:56090847C>T	ENST00000608263.1	-	5	1764	c.1103G>A	c.(1102-1104)cGc>cAc	p.R368H	CTCFL_ENST00000433949.3_Missense_Mutation_p.R163H|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000539382.1_Missense_Mutation_p.R163H|CTCFL_ENST00000608903.1_Missense_Mutation_p.R106H|CTCFL_ENST00000608440.1_Missense_Mutation_p.R368H|CTCFL_ENST00000371196.2_Missense_Mutation_p.R368H|CTCFL_ENST00000609232.1_Missense_Mutation_p.R368H|CTCFL_ENST00000608425.1_Missense_Mutation_p.R368H|CTCFL_ENST00000422869.2_Missense_Mutation_p.R368H|CTCFL_ENST00000429804.3_Missense_Mutation_p.R368H|CTCFL_ENST00000423479.3_Missense_Mutation_p.R368H|CTCFL_ENST00000243914.3_Missense_Mutation_p.R368H|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000502686.2_Missense_Mutation_p.R106H	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	368					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)	p.R368H(1)		NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	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)			CTGAAAGGGGCGCTCCCCAGT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	20											168	160	162					20																	56090847		2203	4300	6503	55524253	SO:0001583	missense	140690				CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1103G>A	20.37:g.56090847C>T	ENSP00000476783:p.Arg368His		55524253	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	34	5.309861	0.95629	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08	5.24	5.24	0.73138	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000406	T	0.46073	0.1374	M	0.64260	1.97	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	T	0.39418	-0.9615	10	0.72032	D	0.01	-44.5807	17.9608	0.89084	0.0:1.0:0.0:0.0	.	368;368;368;368;368	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	H	368;368;368;368;368;106;368;368;163;368	ENSP00000415579:R368H;ENSP00000243914:R368H;ENSP00000360239:R368H;ENSP00000415329:R368H;ENSP00000392034:R368H;ENSP00000437999:R106H;ENSP00000413713:R368H;ENSP00000403369:R368H;ENSP00000439998:R163H;ENSP00000399061:R368H	ENSP00000243914:R368H	R	-	2	0	CTCFL	55524253	1.000000	0.71417	0.949000	0.38748	0.796000	0.44982	7.493000	0.81493	2.608000	0.88229	0.650000	0.86243	CGC		0.478	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		T	56090847	C	T	56090847	3	4	47	1	0	0	0	0	1	0	0	0	4007	768	27	1	912	1	CTCFL	20	56090847	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1041102	56090847	6934673	1966	6363										
PCK1	5105	broad.mit.edu	37	chr20	56139236	56139236	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actctccaggtcatttaaggGccatcaacccagaaaatggc	8	12	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:56139236G>A	ENST00000319441.4	+	7	1137	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	PCK1_ENST00000543666.1_Missense_Mutation_p.A8T|PCK1_ENST00000535860.1_Missense_Mutation_p.A193T	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	325					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)	p.A325T(1)		endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCATTTAAGGGCCATCAACCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	20											59	58	58					20																	56139236		2203	4300	6503	55572642	SO:0001583	missense	5105				CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.973G>A	20.37:g.56139236G>A	ENSP00000319814:p.Ala325Thr		55572642	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.404074	0.83230	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.21191	2.02;2.02;2.02	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	H	0.98559	4.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80719	-0.1257	10	0.87932	D	0	-21.2458	19.6793	0.95956	0.0:0.0:1.0:0.0	.	8;325	B4DT64;P35558	.;PCKGC_HUMAN	T	7;325;8;193	ENSP00000319814:A325T;ENSP00000445767:A8T;ENSP00000444342:A193T	ENSP00000319814:A325T	A	+	1	0	PCK1	55572642	1.000000	0.71417	0.998000	0.56505	0.326000	0.28443	9.282000	0.95840	2.713000	0.92767	0.655000	0.94253	GCC		0.448	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56139236	G	A	56139236	3	1	47	1	0	0	0	0	1	0	0	0	11612	1203	42	3	995	3	PCK1	20	56139236	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	48389	56139236	6886284	1967	6364										
ZBP1	81030	broad.mit.edu	37	chr20	56185363	56185363	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cggcttccccctcagggtgaGttcctggactgggaattctt	12	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:56185363G>T	ENST00000371173.3	-	7	1112	c.935C>A	c.(934-936)aCt>aAt	p.T312N	ZBP1_ENST00000343535.4_Missense_Mutation_p.T312N|ZBP1_ENST00000340462.4_Missense_Mutation_p.T289N|ZBP1_ENST00000395822.3_Missense_Mutation_p.T237N	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	312					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)	p.T312N(1)		large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CTCAGGGTGAGTTCCTGGACT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20											174	190	184					20																	56185363		2203	4300	6503	55618769	SO:0001583	missense	81030			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.935C>A	20.37:g.56185363G>T	ENSP00000360215:p.Thr312Asn		55618769	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.529522	0.27387	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535	T;T;T;T	0.12569	3.04;2.67;3.04;3.0	4.03	1.84	0.25277	.	0.783334	0.10889	N	0.622963	T	0.08935	0.0221	L	0.36672	1.1	0.09310	N	1	B;B;P	0.34977	0.312;0.005;0.478	B;B;B	0.25987	0.036;0.005;0.065	T	0.26883	-1.0090	10	0.56958	D	0.05	-3.0645	4.7394	0.13005	0.1235:0.225:0.6515:0.0	.	312;237;312	A2RRL9;A2A2F7;Q9H171	.;.;ZBP1_HUMAN	N	312;237;289;312;312	ENSP00000360215:T312N;ENSP00000379167:T237N;ENSP00000344954:T289N;ENSP00000340584:T312N	ENSP00000344954:T289N	T	-	2	0	ZBP1	55618769	0.007000	0.16637	0.001000	0.08648	0.004000	0.04260	1.644000	0.37228	0.994000	0.38892	0.491000	0.48974	ACT		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		T	56185363	G	T	56185363	3	4	47	1	0	0	0	0	1	0	0	0	17560	1029	36	2	362	2	ZBP1	20	56185363	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	46127	56185363	6840157	1968	6365										
ZNF831	128611	broad.mit.edu	37	chr20	57768921	57768921	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaggttacctcaggcagaGacccccttaccactgcccat	7	17	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:57768921G>T	ENST00000371030.2	+	1	2847	c.2847G>T	c.(2845-2847)gaG>gaT	p.E949D		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	949							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.E949D(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CTCAGGCAGAGACCCCCTTAC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	20											87	88	88					20																	57768921		2008	4171	6179	57202316	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2847G>T	20.37:g.57768921G>T	ENSP00000360069:p.Glu949Asp		57202316	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	6.729	0.503225	0.12822	.	.	ENSG00000124203	ENST00000371030	T	0.05447	3.44	5.05	0.658	0.17855	.	0.373374	0.23266	N	0.050066	T	0.05090	0.0136	L	0.40543	1.245	0.09310	N	1	B	0.25521	0.128	B	0.23275	0.045	T	0.34354	-0.9832	10	0.39692	T	0.17	-13.948	6.368	0.21465	0.1576:0.2823:0.56:0.0	.	949	Q5JPB2	ZN831_HUMAN	D	949	ENSP00000360069:E949D	ENSP00000360069:E949D	E	+	3	2	ZNF831	57202316	.	.	0.041000	0.18516	0.485000	0.33311	.	.	-0.026000	0.13895	0.655000	0.94253	GAG		0.602	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57768921	G	T	57768921	3	4	47	1	0	0	0	0	1	0	0	0	18224	933	33	2	2849	2	ZNF831	20	57768921	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1583558	57768921	5256599	1969	6366										
C20orf177	63939	broad.mit.edu	37	chr20	58519083	58519083	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtaaatcccaagtaccccacGcttcttcccagccgagaagc	7	16	1	1	rs200508394		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:58519083G>A	ENST00000358293.3	+	5	500	c.85G>A	c.(85-87)Gct>Act	p.A29T	FAM217B_ENST00000360816.3_Missense_Mutation_p.A29T|FAM217B_ENST00000469084.1_Intron	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	29								p.A29T(1)									AGTACCCCACGCTTCTTCCCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	20											49	50	49					20																	58519083		2203	4300	6503	57952478	SO:0001583	missense	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.85G>A	20.37:g.58519083G>A	ENSP00000351040:p.Ala29Thr		57952478	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.497217	0.26861	.	.	ENSG00000196227	ENST00000358293;ENST00000360816;ENST00000421092	T;T	0.30714	1.52;1.52	5.46	-6.8	0.01709	.	1.144810	0.06668	N	0.765698	T	0.09818	0.0241	N	0.08118	0	0.09310	N	1	P	0.35612	0.512	B	0.22386	0.039	T	0.23762	-1.0179	10	0.59425	D	0.04	-0.0836	3.1458	0.06471	0.522:0.2218:0.1444:0.1119	.	29	Q9NTX9	CT177_HUMAN	T	29	ENSP00000351040:A29T;ENSP00000354056:A29T	ENSP00000351040:A29T	A	+	1	0	C20orf177	57952478	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.036000	0.13819	-0.836000	0.04229	-0.136000	0.14681	GCT		0.453	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		A	58519083	G	A	58519083	3	1	47	1	0	0	0	0	1	0	0	0	2102	1087	38	1	87	1	C20orf177	20	58519083	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	750162	58519083	4506437	1970	6367										
TAF4	6874	broad.mit.edu	37	chr20	60584202	60584202	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaacgtagataggaaatttTtacatttcttcacgttttcc	5	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:60584202T>G	ENST00000252996.4	-	5	1789	c.1790A>C	c.(1789-1791)aAa>aCa	p.K597T	TAF4_ENST00000609045.1_5'Flank	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	597	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.K597T(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			TAGGAAATTTTTACATTTCTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	20											78	79	79					20																	60584202		2203	4300	6503	60017597	SO:0001583	missense	6874			Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1790A>C	20.37:g.60584202T>G	ENSP00000252996:p.Lys597Thr		60017597	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	.	.	.	.	.	.	.	.	.	.	T	19.15	3.771128	0.69992	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.52754	0.65;0.65	5.15	5.15	0.70609	TAFH/NHR1 (3);	0.109901	0.64402	D	0.000016	T	0.60483	0.2272	M	0.85710	2.77	0.53688	D	0.999972	P	0.46987	0.888	P	0.48627	0.584	T	0.63849	-0.6544	10	0.30078	T	0.28	-15.5144	14.9411	0.70994	0.0:0.0:0.0:1.0	.	597	O00268	TAF4_HUMAN	T	597;461	ENSP00000252996:K597T;ENSP00000399091:K461T	ENSP00000252996:K597T	K	-	2	0	TAF4	60017597	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.040000	0.49799	1.930000	0.55929	0.459000	0.35465	AAA		0.353	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		G	60584202	T	G	60584202	3	3	47	1	0	0	0	0	1	0	0	0	15565	1841	64	4	1511	4	TAF4	20	60584202	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2065119	60584202	2441318	1971	6368										
PRPF6	57473	broad.mit.edu	37	chr20	62614401	62614401	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcttgggggtctcctgcagcGccactggcttcaccacgcgg	13	15	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:62614401G>A	ENST00000450537.1	-	2	56				PRPF6_ENST00000535781.1_Splice_Site_p.A25T|ZNF512B_ENST00000217130.3_Intron			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A25T(1)		NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTCCTGCAGCGCCACTGGCTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	20											37	34	35					20																	62614401		2203	4300	6503	62084845	SO:0001627	intron_variant	24148			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-15093C>T	20.37:g.62614401G>A			62084845	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.065722	0.76187	.	.	ENSG00000101161	ENST00000266079;ENST00000535781	D;D	0.88124	-2.29;-2.34	4.78	4.78	0.61160	PRP1 splicing factor, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95787	0.8629	H	0.95884	3.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97443	1.0023	10	0.87932	D	0	-14.1554	17.8432	0.88721	0.0:0.0:1.0:0.0	.	25;25	O94906-2;O94906	.;PRP6_HUMAN	T	25	ENSP00000266079:A25T;ENSP00000446216:A25T	ENSP00000266079:A25T	A	+	1	0	PRPF6	62084845	1.000000	0.71417	0.945000	0.38365	0.100000	0.18952	9.608000	0.98331	2.219000	0.72066	0.585000	0.79938	GCC		0.557	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		A	62614401	G	A	62614401	1	1	47	0	1	0	0	0	0	0	0	0	12608	1101	38	1		1	PRPF6	20	62614401	Intron	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2030199	62614401	411119	1972	6369										
MYT1	4661	broad.mit.edu	37	chr20	62839225	62839225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggatgccgaggaggtcgtcGaagtcaccaccgagcgctcc	14	13	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr20:62839225G>A	ENST00000328439.1	+	7	1040	c.676G>A	c.(676-678)Gaa>Aaa	p.E226K	MYT1_ENST00000536311.1_Missense_Mutation_p.E226K|MYT1_ENST00000360149.4_Intron	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E226K(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GGAGGTCGTCGAAGTCACCAC	0.612																																					GBM(59;481 1041 20555 21139 33705)											2	Substitution - Missense(2)	large_intestine(2)	20											37	39	38					20																	62839225		2203	4300	6503	62309669	SO:0001583	missense	4661			M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.676G>A	20.37:g.62839225G>A	ENSP00000327465:p.Glu226Lys		62309669	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	g	7.369	0.626445	0.14257	.	.	ENSG00000196132	ENST00000328439;ENST00000536311	T;T	0.28895	2.52;1.59	4.46	4.46	0.54185	.	0.118515	0.53938	D	0.000048	T	0.24392	0.0591	L	0.53249	1.67	0.80722	D	1	P	0.39404	0.672	B	0.25884	0.064	T	0.10543	-1.0625	10	0.46703	T	0.11	-11.0582	12.6632	0.56826	0.0833:0.0:0.9166:0.0	.	226	Q01538	MYT1_HUMAN	K	226	ENSP00000327465:E226K;ENSP00000442412:E226K	ENSP00000327465:E226K	E	+	1	0	MYT1	62309669	1.000000	0.71417	0.020000	0.16555	0.114000	0.19823	6.319000	0.72871	2.051000	0.60960	0.552000	0.68991	GAA		0.612	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62839225	G	A	62839225	3	1	47	1	0	0	0	0	1	0	0	0	10136	1059	37	1	694	1	MYT1	20	62839225	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	224824	62839225	186295	1973	6370										
POTED	317754	broad.mit.edu	37	chr21	14983023	14983023	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtccccagaaaggatctcatCgtcatgctcagggacactga	10	12	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:14983023C>T	ENST00000299443.5	+	1	526	c.474C>T	c.(472-474)atC>atT	p.I158I		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	158						plasma membrane (GO:0005886)		p.I158I(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						AGGATCTCATCGTCATGCTCA	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	21											8	13	12					21																	14983023		644	2835	3479	13904894	SO:0001819	synonymous_variant	317754			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	23822	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 1"	607549	"ankyrin repeat domain 21", "ANKRD26-like family B, member 3"	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.474C>T	21.37:g.14983023C>T			13904894	C9JCF7	Silent	SNP	ENST00000299443.5	37	CCDS13562.1																																																																																				0.567	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981		T	14983023	C	T	14983023	2	4	47	1	0	0	0	0	0	0	0	1	12294	874	31	1		1	POTED	21	14983023	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09		14983023	33146872	1974	6371										
LIPI	149998	broad.mit.edu	37	chr21	15558316	15558316	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttgaccatgaaatatcttTccaacaaatccactgatatg	5	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:15558316T>G	ENST00000536861.1	-	3	506	c.507A>C	c.(505-507)ggA>ggC	p.G169G	LIPI_ENST00000344577.2_Silent_p.G190G			Q6XZB0	LIPI_HUMAN	lipase, member I	169					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.G190G(1)		endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GAAATATCTTTCCAACAAATC	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	21											102	101	101					21																	15558316		2203	4300	6503	14480187	SO:0001819	synonymous_variant	149998			BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.507A>C	21.37:g.15558316T>G			14480187	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	37		.	.	.	.	.	.	.	.	.	.	T	9.493	1.101071	0.20552	.	.	ENSG00000188992	ENST00000400211	.	.	.	5.12	3.94	0.45596	.	.	.	.	.	T	0.55545	0.1927	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50775	-0.8788	4	.	.	.	.	6.6752	0.23090	0.0:0.0786:0.1555:0.7658	.	.	.	.	Q	49	.	.	K	-	1	0	LIPI	14480187	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.031000	0.30165	0.869000	0.35703	0.528000	0.53228	AAA		0.313	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		G	15558316	T	G	15558316	2	3	47	1	0	0	0	0	0	0	0	1	8849	1770	62	4		4	LIPI	21	15558316	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	575293	15558316	32571579	1975	6372										
SAMSN1	64092	broad.mit.edu	37	chr21	15882734	15882734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggggccatcgtcatccagtCgaaagctgtcccggttactt	11	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:15882734C>T	ENST00000400566.1	-	5	539	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	SAMSN1_ENST00000285670.2_Missense_Mutation_p.R221Q|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	153					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)	p.R153Q(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GTCATCCAGTCGAAAGCTGTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	21											117	113	115					21																	15882734		2123	4253	6376	14804605	SO:0001583	missense	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.458G>A	21.37:g.15882734C>T	ENSP00000383411:p.Arg153Gln		14804605	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656334	0.88056	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.53423	0.62;0.62	5.78	5.78	0.91487	.	0.065563	0.64402	D	0.000018	T	0.72145	0.3424	M	0.83483	2.645	0.52099	D	0.999947	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.68236	-0.5462	10	0.27082	T	0.32	-9.5361	20.012	0.97458	0.0:1.0:0.0:0.0	.	221;153	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	Q	221;153	ENSP00000285670:R221Q;ENSP00000383411:R153Q	ENSP00000285670:R221Q	R	-	2	0	SAMSN1	14804605	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.451000	0.60047	2.731000	0.93534	0.655000	0.94253	CGA		0.478	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			T	15882734	C	T	15882734	3	4	47	1	0	0	0	0	1	0	0	0	13867	884	31	1	679	1	SAMSN1	21	15882734	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	324418	15882734	32247161	1976	6373										
CXADR	1525	broad.mit.edu	37	chr21	18924180	18924180	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgcatcaataaatgtaacGaatttacaactgtcagatat	6	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:18924180G>A	ENST00000284878.7	+	3	1072	c.324G>A	c.(322-324)acG>acA	p.T108T	CXADR_ENST00000306618.10_Silent_p.T108T|CXADR_ENST00000356275.6_Intron|CXADR_ENST00000400166.1_Silent_p.T108T|CXADR_ENST00000400165.1_Silent_p.T108T|CXADR_ENST00000400169.1_Silent_p.T108T	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	108	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)	p.T108T(2)		endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		TAAATGTAACGAATTTACAAC	0.358																																																2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	21											80	81	80					21																	18924180		2203	4300	6503	17846051	SO:0001819	synonymous_variant	1525			Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.324G>A	21.37:g.18924180G>A			17846051	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Silent	SNP	ENST00000284878.7	37	CCDS33519.1																																																																																				0.358	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			A	18924180	G	A	18924180	2	1	47	1	0	0	0	0	0	0	0	1	4082	1045	37	1		1	CXADR	21	18924180	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3041446	18924180	29205715	1977	6374										
TMPRSS15	5651	broad.mit.edu	37	chr21	19666595	19666595	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcacactcacccatacacGcagtgtgcggcggacaccag	9	16	2	0	rs370908748		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:19666595G>A	ENST00000284885.3	-	21	2511	c.2478C>T	c.(2476-2478)tgC>tgT	p.C826C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	826	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.C826C(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						ACCCATACACGCAGTGTGCGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	21						G		1,4405	2.1+/-5.4	0,1,2202	56	56	56		2478	-9.1	0.4	21		56	0,8600		0,0,4300	no	coding-synonymous	TMPRSS15	NM_002772.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		826/1020	19666595	1,13005	2203	4300	6503	18588466	SO:0001819	synonymous_variant	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2478C>T	21.37:g.19666595G>A			18588466	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																				0.582	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19666595	G	A	19666595	2	1	47	1	0	0	0	0	0	0	0	1	16285	1079	38	1		1	TMPRSS15	21	19666595	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	742415	19666595	28463300	1978	6375										
NCAM2	4685	broad.mit.edu	37	chr21	22707852	22707852	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagctcattgaagaaaatgaGaagtacatattgaaagggag	11	3	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:22707852G>T	ENST00000400546.1	+	7	1014	c.765G>T	c.(763-765)gaG>gaT	p.E255D	NCAM2_ENST00000535285.1_Missense_Mutation_p.E280D|NCAM2_ENST00000284894.7_Missense_Mutation_p.E113D	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	255	Ig-like C2-type 3.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E255D(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AAGAAAATGAGAAGTACATAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	21											78	72	74					21																	22707852		1861	4102	5963	21629723	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.765G>T	21.37:g.22707852G>T	ENSP00000383392:p.Glu255Asp		21629723	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	9.515	1.106700	0.20714	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.34859	1.34;1.34;1.34	5.32	2.92	0.33932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.047118	0.85682	D	0.000000	T	0.22044	0.0531	N	0.21373	0.66	0.58432	D	0.999996	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.14578	0.011;0.006;0.004	T	0.05099	-1.0906	10	0.25106	T	0.35	-27.8052	8.8264	0.35059	0.7728:0.0:0.2272:0.0	.	280;113;255	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	D	255;113;280	ENSP00000383392:E255D;ENSP00000284894:E113D;ENSP00000441887:E280D	ENSP00000284894:E113D	E	+	3	2	NCAM2	21629723	0.957000	0.32711	0.995000	0.50966	0.339000	0.28857	0.069000	0.14552	0.349000	0.23975	-0.550000	0.04213	GAG		0.368	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22707852	G	T	22707852	3	4	47	1	0	0	0	0	1	0	0	0	10234	933	33	2	791	2	NCAM2	21	22707852	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3041257	22707852	25422043	1979	6376										
ADAMTS5	11096	broad.mit.edu	37	chr21	28307000	28307000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttgcactgctgggtggcatCgtaggtctgtcctgggagtt	16	8	1	0	rs546124249	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:28307000C>T	ENST00000284987.5	-	4	1595	c.1474G>A	c.(1474-1476)Gat>Aat	p.D492N	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	492	Disintegrin.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D492N(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TGGGTGGCATCGTAGGTCTGT	0.572													C|||	2	0.000399361	0	0	5008	,	,		17153	0		0	False		,,,				2504	0.002				Esophageal Squamous(53;683 1080 10100 14424 45938)											1	Substitution - Missense(1)	large_intestine(1)	21											105	85	92					21																	28307000		2203	4300	6503	27228871	SO:0001583	missense	11096			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1474G>A	21.37:g.28307000C>T	ENSP00000284987:p.Asp492Asn		27228871	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.962868	0.92791	.	.	ENSG00000154736	ENST00000284987	T	0.08896	3.04	5.0	5.0	0.66597	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.46947	1.48	0.58432	D	0.999999	D	0.76494	0.999	P	0.54856	0.762	T	0.00394	-1.1767	10	0.40728	T	0.16	.	18.5013	0.90882	0.0:1.0:0.0:0.0	.	492	Q9UNA0	ATS5_HUMAN	N	492	ENSP00000284987:D492N	ENSP00000284987:D492N	D	-	1	0	ADAMTS5	27228871	1.000000	0.71417	0.827000	0.32855	0.863000	0.49368	5.553000	0.67287	2.624000	0.88883	0.557000	0.71058	GAT		0.572	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28307000	C	T	28307000	3	4	47	1	0	0	0	0	1	0	0	0	269	884	31	1	1338	1	ADAMTS5	21	28307000	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	5599148	28307000	19822895	1980	6377										
RWDD2B	10069	broad.mit.edu	37	chr21	30378937	30378937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaggaatgtcttctcgatggCgaattaaaattctcttccag	8	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:30378937C>T	ENST00000493196.1	-	5	861	c.761G>A	c.(760-762)cGc>cAc	p.R254H	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	254								p.R254H(2)		endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						TTCTCGATGGCGAATTAAAAT	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	21											65	60	62					21																	30378937		2203	4300	6503	29300808	SO:0001583	missense	10069			AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.761G>A	21.37:g.30378937C>T	ENSP00000418693:p.Arg254His		29300808		Missense_Mutation	SNP	ENST00000493196.1	37	CCDS13582.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.823178	0.71143	.	.	ENSG00000156253	ENST00000493196	.	.	.	5.45	3.61	0.41365	Domain of unknown function DUF1115 (1);	0.162838	0.56097	D	0.000026	T	0.80082	0.4558	M	0.89840	3.065	0.45194	D	0.998203	D;B	0.89917	1.0;0.445	D;B	0.81914	0.995;0.077	T	0.80079	-0.1532	9	0.40728	T	0.16	-15.0736	10.6268	0.45512	0.1323:0.7992:0.0:0.0685	.	254;254	Q53FD2;P57060	.;RWD2B_HUMAN	H	254	.	ENSP00000418693:R254H	R	-	2	0	RWDD2B	29300808	1.000000	0.71417	0.904000	0.35570	0.567000	0.35839	7.264000	0.78432	0.825000	0.34637	0.650000	0.86243	CGC		0.308	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			T	30378937	C	T	30378937	3	4	47	1	0	0	0	0	1	0	0	0	13793	768	27	1	202	1	RWDD2B	21	30378937	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2071937	30378937	17750958	1981	6378										
RWDD2B	10069	broad.mit.edu	37	chr21	30380791	30380791	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatcgcccctccattgtcttCttttcaatacaatctttcag	4	13	5	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:30380791C>A	ENST00000493196.1	-	2	319	c.219G>T	c.(217-219)aaG>aaT	p.K73N	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	73	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.							p.K73N(1)		endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						CCATTGTCTTCTTTTCAATAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	21											103	97	99					21																	30380791		2203	4300	6503	29302662	SO:0001583	missense	10069			AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.219G>T	21.37:g.30380791C>A	ENSP00000418693:p.Lys73Asn		29302662		Missense_Mutation	SNP	ENST00000493196.1	37	CCDS13582.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.170880	0.38315	.	.	ENSG00000156253	ENST00000493196	T	0.28895	1.59	5.65	5.65	0.86999	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.272209	0.44097	D	0.000482	T	0.26774	0.0655	L	0.38838	1.175	0.40436	D	0.979993	P	0.36110	0.537	B	0.42282	0.382	T	0.03524	-1.1028	10	0.20519	T	0.43	-30.0093	9.036	0.36289	0.1577:0.7676:0.0:0.0747	.	73	P57060	RWD2B_HUMAN	N	73	ENSP00000418693:K73N	ENSP00000418693:K73N	K	-	3	2	RWDD2B	29302662	0.602000	0.26916	1.000000	0.80357	0.991000	0.79684	0.635000	0.24629	2.941000	0.99782	0.655000	0.94253	AAG		0.408	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			A	30380791	C	A	30380791	3	1	47	1	0	0	0	0	1	0	0	0	13793	912	32	2	756	2	RWDD2B	21	30380791	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1854	30380791	17749104	1982	6379										
CLDN8	9073	broad.mit.edu	37	chr21	31587958	31587958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgccaaggatggccatcaTgaaagccaagaaggacatca	10	10	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:31587958T>C	ENST00000399899.1	-	1	433	c.286A>G	c.(286-288)Atg>Gtg	p.M96V	CLDN8_ENST00000286809.1_Missense_Mutation_p.M96V	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	96					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.M96V(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						ATGGCCATCATGAAAGCCAAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	21											115	93	100					21																	31587958		2203	4300	6503	30509829	SO:0001583	missense	9073			AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"Claudins"	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.286A>G	21.37:g.31587958T>C	ENSP00000382783:p.Met96Val		30509829	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	.	.	.	.	.	.	.	.	.	.	T	9.690	1.151545	0.21371	.	.	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.87491	-2.26;-2.26	4.84	2.4	0.29515	.	0.145348	0.64402	D	0.000011	T	0.75398	0.3844	L	0.28776	0.89	0.30607	N	0.75985	B	0.02656	0.0	B	0.12156	0.007	T	0.62905	-0.6755	10	0.22706	T	0.39	.	5.4049	0.16316	0.0:0.1539:0.2796:0.5665	.	96	P56748	CLD8_HUMAN	V	96	ENSP00000382783:M96V;ENSP00000286809:M96V	ENSP00000286809:M96V	M	-	1	0	CLDN8	30509829	0.006000	0.16342	1.000000	0.80357	0.964000	0.63967	-0.225000	0.09151	0.410000	0.25675	0.528000	0.53228	ATG		0.522	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328		C	31587958	T	C	31587958	3	2	47	1	0	0	0	0	1	0	0	0	3497	1464	51	4	395	4	CLDN8	21	31587958	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1207167	31587958	16541937	1983	6380										
CLDN8	9073	broad.mit.edu	37	chr21	31588225	31588225	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagaaacagcccagcgatttCtaaggcatgggttgccatta	10	9	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:31588225C>A	ENST00000399899.1	-	1	166	c.19G>T	c.(19-21)Gaa>Taa	p.E7*	CLDN8_ENST00000286809.1_Nonsense_Mutation_p.E7*	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	7					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.E7*(1)|p.E7Q(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						CCAGCGATTTCTAAGGCATGG	0.512																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	21											69	62	64					21																	31588225		2203	4300	6503	30510096	SO:0001587	stop_gained	9073			AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"Claudins"	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.19G>T	21.37:g.31588225C>A	ENSP00000382783:p.Glu7*		30510096	D3DSE3|Q53EX7	Nonsense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.296636	0.60086	.	.	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	.	.	.	5.17	4.28	0.50868	.	0.118364	0.56097	D	0.000022	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.91	0.79467	0.0:0.1377:0.8623:0.0	.	.	.	.	X	7	.	ENSP00000286809:E7X	E	-	1	0	CLDN8	30510096	1.000000	0.71417	0.519000	0.27824	0.050000	0.14768	1.440000	0.35024	1.548000	0.49413	-0.153000	0.13522	GAA		0.512	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328		A	31588225	C	A	31588225	4	1	47	1	0	0	0	0	0	1	0	0	3497	922	32	2	662	2	CLDN8	21	31588225	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	267	31588225	16541670	1984	6381										
KRTAP24-1	643803	broad.mit.edu	37	chr21	31655189	31655189	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgggatataacagtgagttCtgtatgatgtggtactgcag	13	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:31655189C>A	ENST00000340345.4	-	1	87	c.62G>T	c.(61-63)aGa>aTa	p.R21I		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	21						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R21I(1)		breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						ACAGTGAGTTCTGTATGATGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	21											54	55	54					21																	31655189		1989	4186	6175	30577060	SO:0001583	missense	643803			AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"Keratin associated proteins"	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.62G>T	21.37:g.31655189C>A	ENSP00000339238:p.Arg21Ile		30577060	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	37	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.718876	0.30503	.	.	ENSG00000188694	ENST00000340345	T	0.06687	3.27	5.06	3.22	0.36961	.	0.467297	0.19537	N	0.111895	T	0.24160	0.0585	M	0.75777	2.31	0.09310	N	0.999993	D	0.69078	0.997	D	0.70487	0.969	T	0.02837	-1.1104	10	0.72032	D	0.01	-7.3789	8.2231	0.31554	0.0:0.8087:0.0:0.1913	.	21	Q3LI83	KR241_HUMAN	I	21	ENSP00000339238:R21I	ENSP00000339238:R21I	R	-	2	0	KRTAP24-1	30577060	0.012000	0.17670	0.005000	0.12908	0.080000	0.17528	0.658000	0.24979	0.772000	0.33382	0.591000	0.81541	AGA		0.493	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455		A	31655189	C	A	31655189	3	1	47	1	0	0	0	0	1	0	0	0	8564	913	32	2	706	2	KRTAP24-1	21	31655189	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	66964	31655189	16474706	1985	6382										
KRTAP13-3	337960	broad.mit.edu	37	chr21	31798108	31798108	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agctggcaggtgctgggagaGcagaggtcagtgctgtagac	18	7	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:31798108G>T	ENST00000390690.2	-	1	178	c.123C>A	c.(121-123)tgC>tgA	p.C41*		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	41						intermediate filament (GO:0005882)		p.C41*(1)		endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						TGCTGGGAGAGCAGAGGTCAG	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											66	73	71					21																	31798108		2203	4300	6503	30719979	SO:0001587	stop_gained	337960			AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"Keratin associated proteins"	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.123C>A	21.37:g.31798108G>T	ENSP00000375109:p.Cys41*		30719979	Q3LI78	Nonsense_Mutation	SNP	ENST00000390690.2	37	CCDS13591.1	.	.	.	.	.	.	.	.	.	.	-	12.64	1.997274	0.35226	.	.	ENSG00000240432	ENST00000390690;ENST00000448917	.	.	.	4.12	1.22	0.21188	.	0.000000	0.45606	U	0.000359	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.7465	6.3725	0.21489	0.1894:0.1532:0.6574:0.0	.	.	.	.	X	41	.	ENSP00000375109:C41X	C	-	3	2	KRTAP13-3	30719979	0.693000	0.27728	0.798000	0.32154	0.111000	0.19643	0.131000	0.15870	0.022000	0.15160	-0.813000	0.03139	TGC		0.592	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			T	31798108	G	T	31798108	4	4	47	1	0	0	0	0	0	1	0	0	8545	963	34	2	399	2	KRTAP13-3	21	31798108	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	142919	31798108	16331787	1986	6383										
SFRS15	57466	broad.mit.edu	37	chr21	33065732	33065732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctatccctggaccgagatCgagaacgtcgatgccgagac	12	12	1	3	rs139069393	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:33065732C>T	ENST00000286835.7	-	12	1770	c.1388G>A	c.(1387-1389)cGa>cAa	p.R463Q	SCAF4_ENST00000434667.3_Missense_Mutation_p.R448Q|SCAF4_ENST00000399804.1_Missense_Mutation_p.R463Q	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	463						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R463Q(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GGACCGAGATCGAGAACGTCG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	21						C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	109	88	95		1343,1388,1388	5.2	1	21	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SCAF4	NM_001145444.1,NM_001145445.1,NM_020706.2	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	448/1133,463/1126,463/1148	33065732	1,13005	2203	4300	6503	31987603	SO:0001583	missense	57466			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.1388G>A	21.37:g.33065732C>T	ENSP00000286835:p.Arg463Gln		31987603	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045109	0.93685	0.0	1.16E-4	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.41758	0.99;0.99;0.99	5.2	5.2	0.72013	.	0.162764	0.42294	D	0.000738	T	0.68348	0.2991	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.992;0.988;0.996;0.992	T	0.73129	-0.4080	10	0.72032	D	0.01	-13.2899	18.7325	0.91741	0.0:1.0:0.0:0.0	.	448;463;463;463	C9JLZ0;C9J1W7;O95104-2;O95104	.;.;.;SFR15_HUMAN	Q	448;463;463	ENSP00000402377:R448Q;ENSP00000286835:R463Q;ENSP00000382703:R463Q	ENSP00000286835:R463Q	R	-	2	0	SCAF4	31987603	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.555000	0.82223	2.413000	0.81919	0.557000	0.71058	CGA		0.493	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		T	33065732	C	T	33065732	3	4	47	1	0	0	0	0	1	0	0	0	14208	884	31	1	2091	1	SFRS15	21	33065732	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1267624	33065732	15064163	1987	6384										
SYNJ1	8867	broad.mit.edu	37	chr21	34029021	34029021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taagtataacttcaccaaaaCttgcaaactgctgcagaagc	6	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:34029021C>A	ENST00000322229.7	-	20	2770	c.2771G>T	c.(2770-2772)aGt>aTt	p.S924I	SYNJ1_ENST00000382499.2_Missense_Mutation_p.S963I|SYNJ1_ENST00000464778.1_5'UTR|SYNJ1_ENST00000382491.3_Missense_Mutation_p.S919I|SYNJ1_ENST00000357345.3_Missense_Mutation_p.S924I|SYNJ1_ENST00000433931.2_Missense_Mutation_p.S963I			O43426	SYNJ1_HUMAN	synaptojanin 1	924	Pro-rich.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.S924I(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TTCACCAAAACTTGCAAACTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	21											34	35	34					21																	34029021		2202	4300	6502	32950892	SO:0001583	missense	8867			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.2771G>T	21.37:g.34029021C>A	ENSP00000322234:p.Ser924Ile		32950892	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.772113	0.31320	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.93712	-2.43;-3.27;-3.27;-2.43;-2.43	5.35	2.96	0.34315	Domain of unknown function DUF1866 (1);Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.569294	0.20445	N	0.092204	D	0.84606	0.5509	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.27013	0.051;0.166;0.135;0.052;0.145	B;B;B;B;B	0.28784	0.049;0.094;0.043;0.094;0.029	T	0.75199	-0.3402	10	0.54805	T	0.06	.	5.2177	0.15352	0.0:0.2277:0.2512:0.5211	.	919;963;924;924;924	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	I	919;924;963;963;924	ENSP00000371931:S919I;ENSP00000349903:S924I;ENSP00000371939:S963I;ENSP00000409667:S963I;ENSP00000322234:S924I	ENSP00000322234:S924I	S	-	2	0	SYNJ1	32950892	0.977000	0.34250	0.997000	0.53966	0.981000	0.71138	0.828000	0.27435	0.340000	0.23745	-0.339000	0.08088	AGT		0.328	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34029021	C	A	34029021	3	1	47	1	0	0	0	0	1	0	0	0	15491	565	20	2	2023	2	SYNJ1	21	34029021	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	963289	34029021	14100874	1988	6385										
GCFC1	94104	broad.mit.edu	37	chr21	34107355	34107355	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcgaacacttgcaaggagtTttactatctgttttatgttt	7	7	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:34107355T>G	ENST00000331923.4	-	18	2849	c.2660A>C	c.(2659-2661)aAa>aCa	p.K887T	PAXBP1-AS1_ENST00000458479.1_RNA|PAXBP1-AS1_ENST00000440052.1_RNA|PAXBP1-AS1_ENST00000455170.1_RNA	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	887					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K887T(1)									TGCAAGGAGTTTTACTATCTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	21											68	62	64					21																	34107355		2201	4299	6500	33029226	SO:0001583	missense	94104			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.2660A>C	21.37:g.34107355T>G	ENSP00000328992:p.Lys887Thr		33029226	D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.973932	0.53720	.	.	ENSG00000159086	ENST00000331923	T	0.26223	1.75	4.98	4.98	0.66077	.	0.153604	0.56097	D	0.000026	T	0.38719	0.1051	L	0.47716	1.5	0.80722	D	1	D;D	0.64830	0.991;0.994	P;P	0.58013	0.831;0.725	T	0.08472	-1.0720	10	0.42905	T	0.14	-14.1959	15.0402	0.71785	0.0:0.0:0.0:1.0	.	887;396	Q9Y5B6;B3KSC0	GCFC1_HUMAN;.	T	887	ENSP00000328992:K887T	ENSP00000328992:K887T	K	-	2	0	GCFC1	33029226	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.343000	0.59348	2.178000	0.69098	0.460000	0.39030	AAA		0.318	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		G	34107355	T	G	34107355	3	3	47	1	0	0	0	0	1	0	0	0	6309	1841	64	4	97	4	GCFC1	21	34107355	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	78334	34107355	14022540	1989	6386										
DNAJC28	54943	broad.mit.edu	37	chr21	34861073	34861073	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctccttttgccatggattCttgaatgaggtcctccacta	8	11	2	2	rs138072076	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:34861073C>A	ENST00000314399.3	-	2	1066	c.628G>T	c.(628-630)Gaa>Taa	p.E210*	DNAJC28_ENST00000381947.3_Nonsense_Mutation_p.E210*|DNAJC28_ENST00000402202.1_Nonsense_Mutation_p.E210*	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	210								p.E210*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GCCATGGATTCTTGAATGAGG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	21						C	stop/GLU,stop/GLU	0,4406		0,0,2203	176	170	172		628,628	5.4	1	21	dbSNP_134	172	4,8596	3.7+/-12.6	0,4,4296	no	stop-gained,stop-gained	DNAJC28	NM_001040192.1,NM_017833.3	,	0,4,6499	AA,AC,CC		0.0465,0.0,0.0308	,	210/389,210/389	34861073	4,13002	2203	4300	6503	33782943	SO:0001587	stop_gained	54943			AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.628G>T	21.37:g.34861073C>A	ENSP00000320303:p.Glu210*		33782943	D3DSF2	Nonsense_Mutation	SNP	ENST00000314399.3	37	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	C	39	7.632363	0.98399	0.0	4.65E-4	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-25.8209	17.9044	0.88914	0.0:1.0:0.0:0.0	.	.	.	.	X	210	.	ENSP00000320303:E210X	E	-	1	0	DNAJC28	33782943	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.257000	0.78362	2.530000	0.85305	0.655000	0.94253	GAA		0.378	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34861073	C	A	34861073	4	1	47	1	0	0	0	0	0	1	0	0	4657	922	32	2	542	2	DNAJC28	21	34861073	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	753718	34861073	13268822	1990	6387										
TTC3	7267	broad.mit.edu	37	chr21	38460148	38460148	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttagggtgtgcaatataaaGattatatccaaagtgagagg	11	3	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:38460148G>T	ENST00000399017.2	+	3	2907	c.160G>T	c.(160-162)Gat>Tat	p.D54Y	TTC3_ENST00000540756.1_Intron|TTC3_ENST00000354749.2_Missense_Mutation_p.D54Y|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000399010.1_Missense_Mutation_p.D54Y|TTC3_ENST00000355666.1_Missense_Mutation_p.D54Y	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	54					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D54Y(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCAATATAAAGATTATATCCA	0.313																																					Ovarian(38;194 1649 35661)											1	Substitution - Missense(1)	large_intestine(1)	21											71	73	72					21																	38460148		2203	4299	6502	37382018	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.160G>T	21.37:g.38460148G>T	ENSP00000381981:p.Asp54Tyr		37382018	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819241	0.50633	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000399010;ENST00000399017;ENST00000354749	T;T;T;T;T;T	0.50813	2.55;0.73;2.55;2.88;2.88;2.88	3.99	3.1	0.35709	.	0.653275	0.13886	N	0.355963	T	0.58264	0.2110	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58983	-0.7539	10	0.72032	D	0.01	-16.8034	6.848	0.23998	0.1243:0.0:0.8757:0.0	.	54	P53804	TTC3_HUMAN	Y	54	ENSP00000403943:D54Y;ENSP00000408456:D54Y;ENSP00000391891:D54Y;ENSP00000347889:D54Y;ENSP00000381981:D54Y;ENSP00000346791:D54Y	ENSP00000346791:D54Y	D	+	1	0	TTC3	37382018	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	1.805000	0.38883	2.198000	0.70561	0.655000	0.94253	GAT		0.313	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38460148	G	T	38460148	3	4	47	1	0	0	0	0	1	0	0	0	16737	942	33	2	166	2	TTC3	21	38460148	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3599075	38460148	9669747	1991	6388										
TTC3	7267	broad.mit.edu	37	chr21	38523141	38523141	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgaacacaaggtcataaaaGaaaaggttcctccaagacct	7	9	1	3	rs546272125		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:38523141G>T	ENST00000399017.2	+	25	4980	c.2233G>T	c.(2233-2235)Gaa>Taa	p.E745*	TTC3_ENST00000540756.1_Nonsense_Mutation_p.E435*|TTC3_ENST00000354749.2_Nonsense_Mutation_p.E745*|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Nonsense_Mutation_p.E745*	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	745					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E745*(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GGTCATAAAAGAAAAGGTTCC	0.303																																					Ovarian(38;194 1649 35661)											1	Substitution - Nonsense(1)	large_intestine(1)	21											59	63	62					21																	38523141		2202	4297	6499	37445011	SO:0001587	stop_gained	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2233G>T	21.37:g.38523141G>T	ENSP00000381981:p.Glu745*		37445011	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Nonsense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.265286|7.265286	0.98175|0.98175	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749|ENST00000414818	.|T	.|0.60920	.|0.15	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	0.347184|.	0.24896|.	N|.	0.034736|.	.|T	.|0.61837	.|0.2379	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72969	.|-0.4130	.|5	0.25106|0.66056	T|D	0.35|0.02	-27.9912|-27.9912	7.8839|7.8839	0.29637|0.29637	0.0862:0.1637:0.7501:0.0|0.0862:0.1637:0.7501:0.0	.|.	.|.	.|.	.|.	X|N	745;745;727;745;435;745;745|108	.|ENSP00000414658:K108N	ENSP00000346791:E745X|ENSP00000414658:K108N	E|K	+|+	1|3	0|2	TTC3|TTC3	37445011|37445011	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.477000|1.477000	0.35431|0.35431	2.610000|2.610000	0.88304|0.88304	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.303	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38523141	G	T	38523141	4	4	47	1	0	0	0	0	0	1	0	0	16737	943	33	2	2327	2	TTC3	21	38523141	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	62993	38523141	9606754	1992	6389										
TTC3	7267	broad.mit.edu	37	chr21	38564433	38564433	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctcagtttgaagaacaaatTaaggcaattaaaaatggttc	7	5	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:38564433T>G	ENST00000399017.2	+	41	7883	c.5136T>G	c.(5134-5136)atT>atG	p.I1712M	TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000354749.2_Missense_Mutation_p.I1712M|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.I1712M	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1712					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I1712M(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAGAACAAATTAAGGCAATTA	0.353																																					Ovarian(38;194 1649 35661)											1	Substitution - Missense(1)	large_intestine(1)	21											60	59	60					21																	38564433		2202	4300	6502	37486303	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5136T>G	21.37:g.38564433T>G	ENSP00000381981:p.Ile1712Met		37486303	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.589308	0.28357	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.16196	2.36;2.36;2.36	5.09	-0.234	0.13074	.	0.095787	0.45606	D	0.000360	T	0.12817	0.0311	L	0.58810	1.83	0.43569	D	0.995893	B	0.09022	0.002	B	0.09377	0.004	T	0.16364	-1.0405	10	0.87932	D	0	-14.423	0.8314	0.01131	0.1598:0.1817:0.1661:0.4923	.	1712	P53804	TTC3_HUMAN	M	1712	ENSP00000347889:I1712M;ENSP00000381981:I1712M;ENSP00000346791:I1712M	ENSP00000346791:I1712M	I	+	3	3	TTC3	37486303	0.437000	0.25593	0.057000	0.19452	0.978000	0.69477	0.451000	0.21779	-0.202000	0.10268	-0.481000	0.04817	ATT		0.353	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38564433	T	G	38564433	3	3	47	1	0	0	0	0	1	0	0	0	16737	1742	61	4	5294	4	TTC3	21	38564433	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	41292	38564433	9565462	1993	6390										
BRWD1	54014	broad.mit.edu	37	chr21	40578199	40578199	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atctcaaggtcatactataaAtctgcaaggatataaaaaca	5	7	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:40578199A>C	ENST00000333229.2	-	37	4526	c.4199T>G	c.(4198-4200)aTt>aGt	p.I1400S	BRWD1_ENST00000380800.3_Splice_Site_p.I1400S|BRWD1_ENST00000342449.3_Splice_Site_p.I1400S	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1400	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.I1400S(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CATACTATAAATCTGCAAGGA	0.264																																					Melanoma(170;988 1986 4794 16843 39731)											2	Substitution - Missense(2)	large_intestine(2)	21											24	26	25					21																	40578199		2198	4293	6491	39500069	SO:0001630	splice_region_variant	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.4198-1T>G	21.37:g.40578199A>C			39500069	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.83|18.83	3.708152|3.708152	0.68615|0.68615	.|.	.|.	ENSG00000185658|ENSG00000185658	ENST00000424441|ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783	.|T;T;T	.|0.22743	.|1.94;1.94;1.94	4.87|4.87	4.87|4.87	0.63330|0.63330	.|Bromodomain (6);	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.58878|0.58878	0.2153|0.2153	H|H	0.95114|0.95114	3.625|3.625	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.992;0.996;1.0	T|T	0.73062|0.73062	-0.4101|-0.4101	5|10	.|0.87932	.|D	.|0	-8.1425|-8.1425	14.4775|14.4775	0.67557|0.67557	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1400;1400;1400	.|Q9NSI6-3;Q9NSI6-2;Q9NSI6	.|.;.;BRWD1_HUMAN	E|S	337|1400;1400;1400;356	.|ENSP00000330753:I1400S;ENSP00000344333:I1400S;ENSP00000370178:I1400S	.|ENSP00000330753:I1400S	D|I	-|-	3|2	2|0	BRWD1|BRWD1	39500069|39500069	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.815000|0.815000	0.46073|0.46073	8.392000|8.392000	0.90180|0.90180	1.831000|1.831000	0.53308|0.53308	0.459000|0.459000	0.35465|0.35465	GAT|ATT		0.264	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	Missense_Mutation	C	40578199	A	C	40578199	5	2	47	1	0	0	0	0	0	0	1	0	1528	115	4	4	3026	4	BRWD1	21	40578199	Splice_Site	SNP	A	TCGA-AG-3892-01A-01W-1073-09	2013766	40578199	7551696	1994	6391										
TMPRSS2	7113	broad.mit.edu	37	chr21	42870052	42870052	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aattaaccacttactgagttCaaagccatcttgctgttatc	5	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:42870052C>A	ENST00000332149.5	-	2	143	c.9G>T	c.(7-9)ttG>ttT	p.L3F	TMPRSS2_ENST00000497881.1_5'UTR|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.L3F|TMPRSS2_ENST00000398585.3_Missense_Mutation_p.L40F	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	3					positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.L3F(2)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				TTACTGAGTTCAAAGCCATCT	0.393			T	"ERG, ETV1, ETV4, ETV5"	prostate																																		Dom	yes		21	21q22.3	7113	"transmembrane protease, serine 2"		E	2	Substitution - Missense(2)	large_intestine(2)	21											130	110	117					21																	42870052		2203	4300	6503	41791922	SO:0001583	missense	7113			U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"Serine peptidases / Transmembrane"	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.9G>T	21.37:g.42870052C>A	ENSP00000330330:p.Leu3Phe		41791922	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744818	0.30865	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093;ENST00000455813	D;D;D;D;T	0.90004	-2.5;-2.6;-2.5;-2.51;-0.44	4.65	-0.526	0.11913	.	0.626656	0.12995	N	0.422136	D	0.89223	0.6654	L	0.59436	1.845	0.32745	N	0.507216	D;D	0.56746	0.977;0.961	P;P	0.56648	0.803;0.64	D	0.85969	0.1475	10	0.39692	T	0.17	.	7.6167	0.28163	0.0:0.3781:0.0:0.6219	.	40;3	F8WES1;O15393	.;TMPS2_HUMAN	F	3;40;3;3;3;3	ENSP00000330330:L3F;ENSP00000381588:L40F;ENSP00000391216:L3F;ENSP00000389006:L3F;ENSP00000397846:L3F	ENSP00000330330:L3F	L	-	3	2	TMPRSS2	41791922	0.961000	0.32948	0.797000	0.32132	0.953000	0.61014	-0.177000	0.09796	-0.276000	0.09206	-0.768000	0.03414	TTG		0.393	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1			A	42870052	C	A	42870052	3	1	47	1	0	0	0	0	1	0	0	0	16286	825	29	2	1521	2	TMPRSS2	21	42870052	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2291853	42870052	5259843	1995	6392										
UMODL1	89766	broad.mit.edu	37	chr21	43536048	43536048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actcagaatcctttcgcaacGcaagcagccaggagtatcga	9	12	1	1	rs371088374		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:43536048G>A	ENST00000408910.2	+	14	2428	c.2428G>A	c.(2428-2430)Gca>Aca	p.A810T	UMODL1_ENST00000400427.1_Missense_Mutation_p.A866T|UMODL1_ENST00000408989.2_Missense_Mutation_p.A938T|UMODL1_ENST00000400424.2_Missense_Mutation_p.A738T	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	810	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)	p.A738T(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CTTTCGCAACGCAAGCAGCCA	0.468																																					Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)											1	Substitution - Missense(1)	large_intestine(1)	21						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1,3875		0,1,1937	94	96	96		2428,2596,2212,2812	-8.5	0	21		96	0,8284		0,0,4142	no	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	58,58,58,58	0,1,6079	AA,AG,GG		0.0,0.0258,0.0082	benign,benign,benign,benign	810/1319,866/1375,738/1247,938/1447	43536048	1,12159	1938	4142	6080	42409117	SO:0001583	missense	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.2428G>A	21.37:g.43536048G>A	ENSP00000386147:p.Ala810Thr		42409117	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	8.281	0.815527	0.16607	2.58E-4	0.0	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	4.39	-8.46	0.00942	SEA (1);	1.311000	0.05592	N	0.574917	T	0.13157	0.0319	N	0.14661	0.345	0.09310	N	1	B;P	0.43431	0.078;0.807	B;B	0.31495	0.016;0.131	T	0.25012	-1.0144	9	.	.	.	-0.7016	6.3136	0.21178	0.5089:0.0:0.2453:0.2458	.	938;810	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	866;738;938;810	ENSP00000383279:A866T;ENSP00000383276:A738T;ENSP00000386126:A938T;ENSP00000386147:A810T	.	A	+	1	0	UMODL1	42409117	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.784000	0.04633	-1.673000	0.01462	-0.367000	0.07326	GCA		0.468	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43536048	G	A	43536048	3	1	47	1	0	0	0	0	1	0	0	0	17020	1087	38	1	2862	1	UMODL1	21	43536048	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	665996	43536048	4593847	1996	6393										
UBASH3A	53347	broad.mit.edu	37	chr21	43838606	43838606	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggaccccacgcagcaggacGaagccagcgagggctgggtg	17	12	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr21:43838606G>A	ENST00000319294.6	+	7	965	c.934G>A	c.(934-936)Gaa>Aaa	p.E312K	UBASH3A_ENST00000291535.6_Missense_Mutation_p.E274K|UBASH3A_ENST00000398367.1_Missense_Mutation_p.E274K|RNU6-1149P_ENST00000516810.1_RNA	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	312	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.E312K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						GCAGCAGGACGAAGCCAGCGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	21											75	75	75					21																	43838606		2203	4300	6503	42711675	SO:0001583	missense	53347			AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.934G>A	21.37:g.43838606G>A	ENSP00000317327:p.Glu312Lys		42711675	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Missense_Mutation	SNP	ENST00000319294.6	37	CCDS13687.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112384	0.77210	.	.	ENSG00000160185	ENST00000291535;ENST00000319294;ENST00000398367	T;T;T	0.28069	1.63;1.63;1.63	5.13	5.13	0.70059	Src homology-3 domain (4);	0.000000	0.64402	D	0.000006	T	0.51193	0.1660	M	0.83012	2.62	0.20563	N	0.999881	D;D;D	0.76494	0.999;0.996;0.997	P;P;P	0.61328	0.853;0.806;0.887	T	0.50250	-0.8850	10	0.40728	T	0.16	-22.353	9.4398	0.38661	0.1624:0.0:0.8376:0.0	.	274;274;312	G5E9E4;P57075-2;P57075	.;.;UBS3A_HUMAN	K	274;312;274	ENSP00000291535:E274K;ENSP00000317327:E312K;ENSP00000381408:E274K	ENSP00000291535:E274K	E	+	1	0	UBASH3A	42711675	0.926000	0.31397	1.000000	0.80357	0.988000	0.76386	3.282000	0.51693	2.389000	0.81357	0.591000	0.81541	GAA		0.592	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895		A	43838606	G	A	43838606	3	1	47	1	0	0	0	0	1	0	0	0	16879	1059	37	1	960	1	UBASH3A	21	43838606	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	302558	43838606	4291289	1997	6394										
CECR2	27443	broad.mit.edu	37	chr22	17978513	17978513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggcactatattggtatttCtatggaacacgaatgtacaa	10	6	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:17978513C>A	ENST00000400573.5	+	4	418	c.411C>A	c.(409-411)ttC>ttA	p.F137L	CECR2_ENST00000400585.2_5'UTR|CECR2_ENST00000262608.8_Missense_Mutation_p.F118L|CECR2_ENST00000342247.5_Missense_Mutation_p.F117L			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	159					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.F137L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		ATTGGTATTTCTATGGAACAC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	22											84	80	82					22																	17978513		1861	4102	5963	16358513	SO:0001583	missense	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400573.5:c.411C>A	22.37:g.17978513C>A	ENSP00000383417:p.Phe137Leu		16358513	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400573.5	37		.	.	.	.	.	.	.	.	.	.	C	23.8	4.462504	0.84425	.	.	ENSG00000099954	ENST00000342247;ENST00000400573;ENST00000262608	T;T;T	0.40756	1.02;1.02;1.02	6.01	1.57	0.23409	.	0.000000	0.37809	U	0.001922	T	0.59636	0.2208	M	0.76574	2.34	0.39456	D	0.967484	D	0.69078	0.997	D	0.75020	0.985	T	0.61734	-0.7002	10	0.87932	D	0	-11.3464	10.3322	0.43829	0.0:0.6819:0.0:0.3181	.	159	Q9BXF3	CECR2_HUMAN	L	117;137;118	ENSP00000341219:F117L;ENSP00000383417:F137L;ENSP00000262608:F118L	ENSP00000262608:F118L	F	+	3	2	CECR2	16358513	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.773000	0.26661	0.134000	0.18681	0.655000	0.94253	TTC		0.483	CECR2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316104.5	NM_031413		A	17978513	C	A	17978513	3	1	47	1	0	0	0	0	1	0	0	0	3212	912	32	2	363	2	CECR2	22	17978513	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09		17978513	33326053	1998	6395										
CECR2	27443	broad.mit.edu	37	chr22	18022359	18022359	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcagggtacatgcgaccgCcctgcaagtctgccggacat	11	15	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:18022359C>T	ENST00000400585.2	+	16	2476	c.2038C>T	c.(2038-2040)Ccc>Tcc	p.P680S	CECR2_ENST00000262608.8_Missense_Mutation_p.P822S|CECR2_ENST00000400573.5_Missense_Mutation_p.P821S			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	863					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.P821S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		CATGCGACCGCCCTGCAAGTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	22											64	68	67					22																	18022359		2075	4211	6286	16402359	SO:0001583	missense	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.2038C>T	22.37:g.18022359C>T	ENSP00000383428:p.Pro680Ser		16402359	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	C	13.92	2.380996	0.42207	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.36340	1.34;1.34;1.26	5.29	4.27	0.50696	.	0.118599	0.38164	N	0.001783	T	0.38719	0.1051	M	0.67953	2.075	0.40583	D	0.981418	P;P;P	0.39060	0.518;0.657;0.657	B;B;B	0.37650	0.115;0.255;0.255	T	0.41431	-0.9509	10	0.45353	T	0.12	-4.8339	14.5598	0.68128	0.0:0.8545:0.1455:0.0	.	863;680;821	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	S	680;821;822	ENSP00000383428:P680S;ENSP00000383417:P821S;ENSP00000262608:P822S	ENSP00000262608:P822S	P	+	1	0	CECR2	16402359	0.990000	0.36364	0.862000	0.33874	0.587000	0.36485	3.047000	0.49854	1.460000	0.47911	0.561000	0.74099	CCC		0.602	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		T	18022359	C	T	18022359	3	4	47	1	0	0	0	0	1	0	0	0	3212	739	26	3	2521	3	CECR2	22	18022359	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	43846	18022359	33282207	1999	6396										
IGLL1	3543	broad.mit.edu	37	chr22	23915765	23915765	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtgaccgagggggtggccttGggctgacctgtgtggacaga	19	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:23915765G>T	ENST00000330377.2	-	3	447	c.330C>A	c.(328-330)ccC>ccA	p.P110P	AP000345.2_ENST00000458318.1_RNA|AP000345.2_ENST00000454863.1_RNA|IGLL1_ENST00000249053.3_Missense_Mutation_p.Q72K	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	110	C region (By similarity to lambda light- chain).				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.P110P(1)		kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						GGGTGGCCTTGGGCTGACCTG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	22											45	43	44					22																	23915765		2203	4300	6503	22245765	SO:0001819	synonymous_variant	3543			X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.330C>A	22.37:g.23915765G>T			22245765	Q0P681	Missense_Mutation	SNP	ENST00000330377.2	37	CCDS13809.1	.	.	.	.	.	.	.	.	.	.	-	0.268	-0.994883	0.02145	.	.	ENSG00000128322	ENST00000249053	.	.	.	2.45	1.29	0.21616	.	.	.	.	.	T	0.28863	0.0716	.	.	.	0.35274	D	0.780761	P	0.39424	0.673	B	0.26614	0.071	T	0.33979	-0.9847	7	0.87932	D	0	.	4.9963	0.14242	0.0:0.2351:0.5257:0.2392	.	72	Q0P681	.	K	72	.	ENSP00000249053:Q72K	Q	-	1	0	IGLL1	22245765	0.886000	0.30341	0.520000	0.27837	0.027000	0.11550	0.765000	0.26546	0.291000	0.22468	0.165000	0.16767	CAA		0.577	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070		T	23915765	G	T	23915765	2	4	47	1	0	0	0	0	0	0	0	1	7614	1357	47	2		2	IGLL1	22	23915765	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5893406	23915765	27388801	2000	6397										
ZNF70	7621	broad.mit.edu	37	chr22	24086597	24086597	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtctctctcctgtatgaattCtctcgtgttttctgaggctg	9	10	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:24086597C>A	ENST00000341976.3	-	2	1191	c.731G>T	c.(730-732)aGa>aTa	p.R244I		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R244I(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TGTATGAATTCTCTCGTGTTT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	22											66	64	64					22																	24086597		2203	4300	6503	22416597	SO:0001583	missense	7621			X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"Zinc fingers, C2H2-type"	13140	protein-coding gene	gene with protein product		194544	"zinc finger protein 70 (Cos17)"			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.731G>T	22.37:g.24086597C>A	ENSP00000339314:p.Arg244Ile		22416597		Missense_Mutation	SNP	ENST00000341976.3	37	CCDS13812.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815916	0.50527	.	.	ENSG00000187792	ENST00000341976	T	0.24908	1.83	3.34	3.34	0.38264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40719	0.1128	M	0.69463	2.115	0.32029	N	0.599817	D	0.76494	0.999	P	0.61397	0.888	T	0.48948	-0.8989	9	0.59425	D	0.04	-17.2837	6.7019	0.23230	0.0:0.8724:0.0:0.1276	.	244	Q9UC06	ZNF70_HUMAN	I	244	ENSP00000339314:R244I	ENSP00000339314:R244I	R	-	2	0	ZNF70	22416597	0.000000	0.05858	0.050000	0.19076	0.859000	0.49053	0.957000	0.29215	2.175000	0.68902	0.456000	0.33151	AGA		0.517	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916		A	24086597	C	A	24086597	3	1	47	1	0	0	0	0	1	0	0	0	18142	913	32	2	613	2	ZNF70	22	24086597	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	170832	24086597	27217969	2001	6398										
PIWIL3	440822	broad.mit.edu	37	chr22	25124201	25124201	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caattcatctgctgggcaatCttggtgacgatggtccttgc	11	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:25124201C>A	ENST00000332271.5	-	15	2291	c.1875G>T	c.(1873-1875)aaG>aaT	p.K625N	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Missense_Mutation_p.K507N|PIWIL3_ENST00000527701.1_Missense_Mutation_p.K507N	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	625	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.K625N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GCTGGGCAATCTTGGTGACGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	22											246	221	230					22																	25124201		2203	4300	6503	23454201	SO:0001583	missense	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1875G>T	22.37:g.25124201C>A	ENSP00000330031:p.Lys625Asn		23454201		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.569694	0.28003	.	.	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.19105	2.17;2.17;2.17	2.54	1.49	0.22878	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	U	0.000000	T	0.29158	0.0725	L	0.46670	1.46	0.48696	D	0.99969	D;P;D	0.89917	1.0;0.754;1.0	D;P;D	0.97110	1.0;0.804;0.998	T	0.16012	-1.0417	10	0.20046	T	0.44	.	4.7608	0.13108	0.0:0.686:0.0:0.314	.	507;616;625	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	N	625;507;507	ENSP00000330031:K625N;ENSP00000431843:K507N;ENSP00000435718:K507N	ENSP00000330031:K625N	K	-	3	2	PIWIL3	23454201	0.996000	0.38824	0.625000	0.29200	0.023000	0.10783	0.249000	0.18216	0.418000	0.25898	0.491000	0.48974	AAG		0.433	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25124201	C	A	25124201	3	1	47	1	0	0	0	0	1	0	0	0	11990	912	32	2	801	2	PIWIL3	22	25124201	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1037604	25124201	26180365	2002	6399										
ADRBK2	157	broad.mit.edu	37	chr22	26059644	26059644	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtacaaagtcatttatccaaGaaacaagtgacatcaactct	5	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:26059644G>T	ENST00000324198.6	+	5	606	c.414G>T	c.(412-414)aaG>aaT	p.K138N		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	138	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)	p.K138N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	ATTTATCCAAGAAACAAGTGA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	22											51	55	54					22																	26059644		2203	4297	6500	24389644	SO:0001583	missense	157			X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.414G>T	22.37:g.26059644G>T	ENSP00000317578:p.Lys138Asn		24389644	Q9UGW9	Missense_Mutation	SNP	ENST00000324198.6	37	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830657	0.50845	.	.	ENSG00000100077	ENST00000324198;ENST00000545323	T	0.01998	4.51	5.64	4.63	0.57726	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.052145	0.85682	D	0.000000	T	0.05868	0.0153	M	0.70595	2.14	0.80722	D	1	B;B	0.32051	0.354;0.046	B;B	0.41088	0.347;0.126	T	0.08764	-1.0706	10	0.66056	D	0.02	-21.7042	10.3914	0.44171	0.0898:0.0:0.9102:0.0	.	138;138	A8K869;P35626	.;ARBK2_HUMAN	N	138	ENSP00000317578:K138N	ENSP00000317578:K138N	K	+	3	2	ADRBK2	24389644	1.000000	0.71417	0.977000	0.42913	0.924000	0.55760	3.884000	0.56175	1.392000	0.46585	0.563000	0.77884	AAG		0.289	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		T	26059644	G	T	26059644	3	4	47	1	0	0	0	0	1	0	0	0	344	933	33	2	432	2	ADRBK2	22	26059644	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	935443	26059644	25244922	2003	6400										
MTMR3	8897	broad.mit.edu	37	chr22	30421762	30421762	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcattgaccttgaactggAtaagcccattgctgccactt	8	12	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:30421762A>G	ENST00000401950.2	+	20	3911	c.3569A>G	c.(3568-3570)gAt>gGt	p.D1190G	CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000323630.5_Missense_Mutation_p.D1054G|MTMR3_ENST00000333027.3_Missense_Mutation_p.D1162G|MTMR3_ENST00000351488.3_Missense_Mutation_p.D1153G|MTMR3_ENST00000406629.1_Missense_Mutation_p.D1162G|CTA-85E5.10_ENST00000429350.1_RNA	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	1190					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)	p.D1190G(1)		breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CTTGAACTGGATAAGCCCATT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	22											98	86	90					22																	30421762		2203	4300	6503	28751762	SO:0001583	missense	8897			U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.3569A>G	22.37:g.30421762A>G	ENSP00000384651:p.Asp1190Gly		28751762	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306864	0.81247	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	4.93	4.93	0.64822	Zinc finger, FYVE/PHD-type (1);	0.242332	0.39687	N	0.001300	T	0.48642	0.1511	L	0.44542	1.39	0.80722	D	1	D;P;P	0.56287	0.975;0.915;0.949	P;B;P	0.53861	0.736;0.366;0.57	T	0.50717	-0.8795	10	0.62326	D	0.03	.	13.9295	0.63986	1.0:0.0:0.0:0.0	.	1153;1190;1162	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	G	1190;1162;1054;1153;1162	ENSP00000384651:D1190G;ENSP00000331649:D1162G;ENSP00000318070:D1054G;ENSP00000307271:D1153G;ENSP00000384077:D1162G	ENSP00000318070:D1054G	D	+	2	0	MTMR3	28751762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.695000	0.91298	2.092000	0.63282	0.533000	0.62120	GAT		0.552	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		G	30421762	A	G	30421762	3	3	47	1	0	0	0	0	1	0	0	0	9975	333	12	4	3670	4	MTMR3	22	30421762	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	4362118	30421762	20882804	2004	6401										
MORC2	22880	broad.mit.edu	37	chr22	31328993	31328993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaccactccctgttcacaCgcacctccacgtgcagccct	6	19	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:31328993C>T	ENST00000397641.3	-	22	2813	c.2405G>A	c.(2404-2406)cGt>cAt	p.R802H	MORC2_ENST00000215862.4_Missense_Mutation_p.R740H|MORC2-AS1_ENST00000441558.1_RNA			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	802						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R740H(2)		breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCTGTTCACACGCACCTCCAC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	22											248	222	231					22																	31328993		2203	4300	6503	29658993	SO:0001583	missense	22880			AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.2405G>A	22.37:g.31328993C>T	ENSP00000380763:p.Arg802His		29658993	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.079949	0.76528	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.14516	2.51;2.5	5.94	5.94	0.96194	.	0.050797	0.85682	D	0.000000	T	0.37598	0.1009	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.01363	-1.1374	10	0.62326	D	0.03	.	20.3658	0.98878	0.0:1.0:0.0:0.0	.	802	Q9Y6X9	MORC2_HUMAN	H	802;740	ENSP00000380763:R802H;ENSP00000215862:R740H	ENSP00000215862:R740H	R	-	2	0	MORC2	29658993	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.988000	0.56951	2.820000	0.97059	0.650000	0.86243	CGT		0.572	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		T	31328993	C	T	31328993	3	4	47	1	0	0	0	0	1	0	0	0	9732	536	19	1	713	1	MORC2	22	31328993	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	907231	31328993	19975573	2005	6402										
SFI1	9814	broad.mit.edu	37	chr22	31927078	31927078	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttcttatatttatggattCgaatgacttttggaagagta	9	3	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:31927078C>T	ENST00000400288.2	+	4	406	c.301C>T	c.(301-303)Cga>Tga	p.R101*	SFI1_ENST00000414585.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000540643.1_Intron|SFI1_ENST00000432498.1_Nonsense_Mutation_p.R101*	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	101					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.R101*(2)		NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						TTTATGGATTCGAATGACTTT	0.323																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											120	112	115					22																	31927078		1830	4079	5909	30257078	SO:0001587	stop_gained	9814			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.301C>T	22.37:g.31927078C>T	ENSP00000383145:p.Arg101*		30257078	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Nonsense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.976926	0.53720	.	.	ENSG00000198089	ENST00000432498;ENST00000400288;ENST00000450787	.	.	.	4.26	3.15	0.36227	.	0.274240	0.27151	N	0.020686	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.831	0.35085	0.2239:0.7761:0.0:0.0	.	.	.	.	X	101;101;52	.	ENSP00000383145:R101X	R	+	1	2	SFI1	30257078	0.920000	0.31207	1.000000	0.80357	0.976000	0.68499	1.841000	0.39240	2.377000	0.81083	0.442000	0.29010	CGA		0.323	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		T	31927078	C	T	31927078	4	4	47	1	0	0	0	0	0	1	0	0	14193	876	31	1	311	1	SFI1	22	31927078	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	598085	31927078	19377488	2006	6403										
DEPDC5	9681	broad.mit.edu	37	chr22	32302008	32302008	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaatattctgcctctgcttTtaacttccctgctgagaaca	5	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:32302008T>G	ENST00000382112.3	+	41	4518	c.4448T>G	c.(4447-4449)tTt>tGt	p.F1483C	DEPDC5_ENST00000539165.1_Missense_Mutation_p.F309C|DEPDC5_ENST00000382111.2_Missense_Mutation_p.L1472V|DEPDC5_ENST00000400246.1_Missense_Mutation_p.L1472V|DEPDC5_ENST00000535622.1_Missense_Mutation_p.F1392C|DEPDC5_ENST00000382105.2_3'UTR|DEPDC5_ENST00000400248.2_Missense_Mutation_p.F1461C|DEPDC5_ENST00000400249.2_Missense_Mutation_p.F1461C|DEPDC5_ENST00000266091.3_Missense_Mutation_p.F1470C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1492					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.F1461C(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCCTCTGCTTTTAACTTCCCT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	22											88	84	86					22																	32302008		1947	4136	6083	30632008	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.4448T>G	22.37:g.32302008T>G	ENSP00000371546:p.Phe1483Cys		30632008	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	20.3|20.3|20.3	3.974186|3.974186|3.974186	0.74246|0.74246|0.74246	.|.|.	.|.|.	ENSG00000100150|ENSG00000100150|ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000382112;ENST00000400248;ENST00000539165|ENST00000433147|ENST00000400246;ENST00000382111	T;T;T;T;T|.|T;T	0.36157|.|0.22945	1.27;1.69;1.7;1.69;1.7|.|1.93;1.93	5.12|5.12|5.12	5.12|5.12|5.12	0.69794|0.69794|0.69794	.|.|.	0.000000|0.000000|.	0.64402|0.64402|.	D|D|.	0.000001|0.000001|.	T|T|T	0.33089|0.33089|0.33089	0.0851|0.0851|0.0851	L|L|L	0.43152|0.43152|0.43152	1.355|1.355|1.355	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D;D;D;D;D|.|.	0.89917|.|.	0.999;0.999;1.0;0.999;0.999;0.999|.|.	D;D;D;D;D;D|.|.	0.85130|.|.	0.993;0.987;0.997;0.995;0.993;0.99|.|.	T|T|T	0.02736|0.02736|0.02736	-1.1117|-1.1117|-1.1117	10|6|7	0.54805|.|0.30078	T|.|T	0.06|.|0.28	.|.|.	14.412|14.412|14.412	0.67119|0.67119|0.67119	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	1492;1392;878;1470;1483;1461|.|.	B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140|.|.	.;.;.;.;.;DEPD5_HUMAN|.|.	C|L|V	1392;1470;1461;1392;1483;1461;309|867|1472	ENSP00000440210:F1392C;ENSP00000266091:F1470C;ENSP00000383108:F1461C;ENSP00000371546:F1483C;ENSP00000383107:F1461C|.|ENSP00000383105:L1472V;ENSP00000371545:L1472V	ENSP00000266091:F1470C|.|ENSP00000371545:L1472V	F|F|L	+|+|+	2|3|1	0|2|2	DEPDC5|DEPDC5|DEPDC5	30632008|30632008|30632008	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.992000|0.992000|0.992000	0.81027|0.81027|0.81027	7.259000|7.259000|7.259000	0.78381|0.78381|0.78381	2.077000|2.077000|2.077000	0.62373|0.62373|0.62373	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	TTT|TTT|TTA		0.498	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32302008	T	G	32302008	3	3	47	1	0	0	0	0	1	0	0	0	4453	1841	64	4	4628	4	DEPDC5	22	32302008	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	374930	32302008	19002558	2007	6404										
YWHAH	7533	broad.mit.edu	37	chr22	32352269	32352269	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atggctgatggaaacgaaaaGaaattggagaaagttaaagc	12	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:32352269G>T	ENST00000248975.5	+	2	504	c.231G>T	c.(229-231)aaG>aaT	p.K77N	snoU13_ENST00000459049.1_RNA|YWHAH_ENST00000471374.1_3'UTR|YWHAH_ENST00000397492.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	77					apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)	p.K77N(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						GAAACGAAAAGAAATTGGAGA	0.468																																					Ovarian(98;460 2060 9263 44007)											1	Substitution - Missense(1)	large_intestine(1)	22											81	74	77					22																	32352269		2203	4300	6503	30682269	SO:0001583	missense	7533			X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.231G>T	22.37:g.32352269G>T	ENSP00000248975:p.Lys77Asn		30682269		Missense_Mutation	SNP	ENST00000248975.5	37	CCDS13901.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973667	0.53720	.	.	ENSG00000128245	ENST00000248975;ENST00000420430	T;T	0.39997	1.05;1.05	5.95	4.93	0.64822	14-3-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.56031	0.1958	L	0.42632	1.34	0.80722	D	1	B;D	0.89917	0.114;1.0	B;D	0.91635	0.136;0.999	T	0.53287	-0.8460	10	0.51188	T	0.08	-6.9559	14.6808	0.69015	0.0704:0.0:0.9296:0.0	.	77;77	B2R6N6;Q04917	.;1433F_HUMAN	N	77;64	ENSP00000248975:K77N;ENSP00000406747:K64N	ENSP00000248975:K77N	K	+	3	2	YWHAH	30682269	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.018000	0.57174	2.824000	0.97209	0.655000	0.94253	AAG		0.468	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		T	32352269	G	T	32352269	3	4	47	1	0	0	0	0	1	0	0	0	17544	933	33	2	237	2	YWHAH	22	32352269	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	50261	32352269	18952297	2008	6405										
LARGE	9215	broad.mit.edu	37	chr22	34157362	34157362	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggcttccattcttaccttcGaagctcccagaaaacaggta	7	12	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:34157362G>A	ENST00000354992.2	-	3	673	c.102C>T	c.(100-102)ttC>ttT	p.F34F	LARGE_ENST00000397394.2_Silent_p.F34F|LARGE_ENST00000402320.1_Silent_p.F34F|LARGE_ENST00000437602.2_Silent_p.F34F|LARGE_ENST00000337431.2_Silent_p.F34F	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	34					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.F34F(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TCTTACCTTCGAAGCTCCCAG	0.483																																					Colon(70;397 1175 4573 19089 45288)											1	Substitution - coding silent(1)	large_intestine(1)	22											139	138	138					22																	34157362		2203	4300	6503	32487362	SO:0001819	synonymous_variant	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.102C>T	22.37:g.34157362G>A			32487362	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																				0.483	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	34157362	G	A	34157362	2	1	47	1	0	0	0	0	0	0	0	1	8649	1049	37	1		1	LARGE	22	34157362	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1805093	34157362	17147204	2009	6406										
LARGE	9215	broad.mit.edu	37	chr22	34157441	34157441	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcagccaagaatttccgtCtccccctgcagattcccagc	8	16	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:34157441C>T	ENST00000354992.2	-	3	594	c.23G>A	c.(22-24)aGa>aAa	p.R8K	LARGE_ENST00000397394.2_Missense_Mutation_p.R8K|LARGE_ENST00000402320.1_Missense_Mutation_p.R8K|LARGE_ENST00000437602.2_Missense_Mutation_p.R8K|LARGE_ENST00000337431.2_Missense_Mutation_p.R8K	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	8					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.R8K(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				GAATTTCCGTCTCCCCCTGCA	0.527																																					Colon(70;397 1175 4573 19089 45288)											1	Substitution - Missense(1)	large_intestine(1)	22											126	116	119					22																	34157441		2203	4300	6503	32487441	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.23G>A	22.37:g.34157441C>T	ENSP00000347088:p.Arg8Lys		32487441	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	37	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.080163	0.36662	.	.	ENSG00000133424	ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000437602;ENST00000430220;ENST00000413114;ENST00000434071;ENST00000432776;ENST00000423375	T;T;T;T;T;T;T;T	0.52526	1.16;1.13;1.16;1.13;0.66;1.39;1.37;1.35	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.20042	-1.0287	10	0.07990	T	0.79	.	19.1142	0.93331	0.0:1.0:0.0:0.0	.	8;8;8	B7Z2I9;O95461-2;O95461	.;.;LARGE_HUMAN	K	8	ENSP00000347088:R8K;ENSP00000336636:R8K;ENSP00000380549:R8K;ENSP00000385223:R8K;ENSP00000388544:R8K;ENSP00000396277:R8K;ENSP00000415546:R8K;ENSP00000389605:R8K	ENSP00000336636:R8K	R	-	2	0	LARGE	32487441	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.819000	0.75262	2.749000	0.94314	0.655000	0.94253	AGA		0.527	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		T	34157441	C	T	34157441	3	4	47	1	0	0	0	0	1	0	0	0	8649	913	32	3	2303	3	LARGE	22	34157441	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	79	34157441	17147125	2010	6407										
MYH9	4627	broad.mit.edu	37	chr22	36690158	36690158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcagcttggtgaccttgtCggccagctctgtgcgcacgc	13	14	1	1	rs147031322		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:36690158C>T	ENST00000216181.5	-	28	4047	c.3817G>A	c.(3817-3819)Gac>Aac	p.D1273N		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1273					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.D1273N(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GTGACCTTGTCGGCCAGCTCT	0.657			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																														Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	22						C	ASN/ASP	0,4406		0,0,2203	68	65	66		3817	5	1	22	dbSNP_134	66	2,8598	2.2+/-6.3	0,2,4298	no	missense	MYH9	NM_002473.4	23	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1273/1961	36690158	2,13004	2203	4300	6503	35020104	SO:0001583	missense	4627	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.3817G>A	22.37:g.36690158C>T	ENSP00000216181:p.Asp1273Asn		35020104	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.608292	0.87258	0.0	2.33E-4	ENSG00000100345	ENST00000216181	D	0.82893	-1.66	4.98	4.98	0.66077	Myosin tail (1);	0.107359	0.64402	D	0.000006	T	0.77096	0.4080	N	0.20986	0.625	0.80722	D	1	B	0.28178	0.202	B	0.35353	0.201	T	0.72497	-0.4275	10	0.25751	T	0.34	.	18.6261	0.91340	0.0:1.0:0.0:0.0	.	1273	P35579	MYH9_HUMAN	N	1273	ENSP00000216181:D1273N	ENSP00000216181:D1273N	D	-	1	0	MYH9	35020104	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.954000	0.70298	2.454000	0.82982	0.561000	0.74099	GAC		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36690158	C	T	36690158	3	4	47	1	0	0	0	0	1	0	0	0	10072	884	31	1	2121	1	MYH9	22	36690158	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2532717	36690158	14614408	2011	6408										
NCF4	4689	broad.mit.edu	37	chr22	37273855	37273855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caactacagggtctacaacaCgatgccatgagctgacggtg	11	11	1	2	rs147550660		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:37273855C>T	ENST00000248899.6	+	10	1194	c.1010C>T	c.(1009-1011)aCg>aTg	p.T337M	NCF4_ENST00000397147.4_3'UTR	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	337					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)	p.T337M(1)		cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	GTCTACAACACGATGCCATGA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	22						C	MET/THR,	1,4405	2.1+/-5.4	0,1,2202	40	34	36		1010,	5.3	0.9	22	dbSNP_134	36	0,8600		0,0,4300	no	missense,utr-3	NCF4	NM_000631.4,NM_013416.3	81,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,	337/340,	37273855	1,13005	2203	4300	6503	35603801	SO:0001583	missense	4689			X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.1010C>T	22.37:g.37273855C>T	ENSP00000248899:p.Thr337Met		35603801	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Missense_Mutation	SNP	ENST00000248899.6	37	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.139361	0.56936	2.27E-4	0.0	ENSG00000100365	ENST00000248899	T	0.48201	0.82	5.31	5.31	0.75309	.	.	.	.	.	T	0.65471	0.2694	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.68569	-0.5374	9	0.87932	D	0	.	11.6037	0.51020	0.0:0.9182:0.0:0.0818	.	337	Q15080	NCF4_HUMAN	M	337	ENSP00000248899:T337M	ENSP00000248899:T337M	T	+	2	0	NCF4	35603801	0.991000	0.36638	0.946000	0.38457	0.478000	0.33099	3.005000	0.49521	2.487000	0.83934	0.557000	0.71058	ACG		0.597	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		T	37273855	C	T	37273855	3	4	47	1	0	0	0	0	1	0	0	0	10249	536	19	1	1289	1	NCF4	22	37273855	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	583697	37273855	14030711	2012	6409										
DMC1	11144	broad.mit.edu	37	chr22	38935386	38935386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcatggtctacattaaagcGatcagcaatgtccctaaggc	8	10	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:38935386G>A	ENST00000216024.2	-	9	802	c.526C>T	c.(526-528)Cgc>Tgc	p.R176C	DMC1_ENST00000428462.2_Intron	NM_007068.2	NP_008999.2	Q14565	DMC1_HUMAN	DNA meiotic recombinase 1	176					female gamete generation (GO:0007292)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	chromosome (GO:0005694)|chromosome, telomeric region (GO:0000781)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.R176C(1)		large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11	Melanoma(58;0.0286)					ACATTAAAGCGATCAGCAATG	0.423								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	22											173	144	154					22																	38935386		2203	4300	6503	37265332	SO:0001583	missense	11144			D63882	CCDS13973.1, CCDS63477.1	22q13.1	2013-05-02	2013-05-02		ENSG00000100206	ENSG00000100206			2927	protein-coding gene	gene with protein product		602721	"DMC1 (dosage suppressor of mck1, yeast homolog) meiosis-specific homologous recombination", "DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast)"			8602360, 8590282, 17541404	Standard	NM_007068		Approved	LIM15	uc003avz.2	Q14565	OTTHUMG00000151088	ENST00000216024.2:c.526C>T	22.37:g.38935386G>A	ENSP00000216024:p.Arg176Cys		37265332	A8K9A2|B4DMW6|Q08AI1|Q99498|Q9UH11	Missense_Mutation	SNP	ENST00000216024.2	37	CCDS13973.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184189	0.78677	.	.	ENSG00000100206	ENST00000216024	T	0.52983	0.64	5.51	5.51	0.81932	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.111469	0.56097	D	0.000035	T	0.78742	0.4331	M	0.94142	3.5	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.84770	0.0767	10	0.87932	D	0	-4.2799	19.4131	0.94683	0.0:0.0:1.0:0.0	.	176	Q14565	DMC1_HUMAN	C	176	ENSP00000216024:R176C	ENSP00000216024:R176C	R	-	1	0	DMC1	37265332	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.541000	0.60670	2.588000	0.87417	0.591000	0.81541	CGC		0.423	DMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321246.2	NM_007068		A	38935386	G	A	38935386	3	1	47	1	0	0	0	0	1	0	0	0	4590	1058	37	1	520	1	DMC1	22	38935386	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1661531	38935386	12369180	2013	6410										
PPPDE2	27351	broad.mit.edu	37	chr22	42000089	42000089	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaggagaggtactccagaaaGatttcttctgtgacttctgt	11	7	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:42000089G>T	ENST00000263256.6	-	4	505	c.249C>A	c.(247-249)atC>atA	p.I83I	DESI1_ENST00000463886.1_5'UTR	NM_015704.2	NP_056519.1	Q6ICB0	DESI1_HUMAN	desumoylating isopeptidase 1	83	PPPDE peptidase.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)	p.I83I(1)									ACTCCAGAAAGATTTCTTCTG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	22											99	100	99					22																	42000089		2203	4300	6503	40330035	SO:0001819	synonymous_variant	27351			AF038183	CCDS33652.1	22q13.2	2012-05-16	2012-05-16	2012-05-16	ENSG00000100418	ENSG00000100418			24577	protein-coding gene	gene with protein product		614637	"family with sequence similarity 152, member B", "PPPDE peptidase domain containing 2"	FAM152B, PPPDE2		8619474, 9110174, 22370726	Standard	NM_015704		Approved	D15Wsu75e	uc003bam.2	Q6ICB0	OTTHUMG00000044632	ENST00000263256.6:c.249C>A	22.37:g.42000089G>T			40330035		Silent	SNP	ENST00000263256.6	37	CCDS33652.1																																																																																				0.522	DESI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000104124.3	NM_015704		T	42000089	G	T	42000089	2	4	47	1	0	0	0	0	0	0	0	1	12443	932	33	2		2	PPPDE2	22	42000089	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3064703	42000089	9304477	2014	6411										
SEPT3	55964	broad.mit.edu	37	chr22	42390746	42390746	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggacacagaggaaagccacGacagtaacccatgacgacca	10	12	0	2	rs200288550	byFrequency	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:42390746G>A	ENST00000396426.3	+	10	1266				SEPT3_ENST00000396425.3_Missense_Mutation_p.D347N|SEPT3_ENST00000291236.11_Missense_Mutation_p.D283N|SEPT3_ENST00000406029.1_Intron|SEPT3_ENST00000328414.8_Intron	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3						cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)	p.D347N(1)		breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						GGAAAGCCACGACAGTAACCC	0.522													G|||	2	0.000399361	0	0	5008	,	,		18952	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											162	120	134					22																	42390746		2203	4300	6503	40720692	SO:0001627	intron_variant	55964			AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"Septins"	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.1011+28G>A	22.37:g.42390746G>A			40720692	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Missense_Mutation	SNP	ENST00000396426.3	37	CCDS14026.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.92	1.782923	0.31502	.	.	ENSG00000100167	ENST00000396425;ENST00000291236	T;T	0.53857	0.6;0.61	5.1	0.894	0.19242	.	.	.	.	.	T	0.31358	0.0794	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05903	-1.0857	8	.	.	.	.	7.9037	0.29750	0.1713:0.1239:0.7048:0.0	.	283;347	B7Z686;Q9UH03-2	.;.	N	347;283	ENSP00000379703:D347N;ENSP00000291236:D283N	.	D	+	1	0	SEPT3	40720692	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.594000	0.54008	0.163000	0.19507	-0.404000	0.06349	GAC		0.522	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734		A	42390746	G	A	42390746	1	1	47	0	1	0	0	0	0	0	0	0	14102	1058	37	1		1	SEPT3	22	42390746	Intron	SNP	G	TCGA-AG-3892-01A-01W-1073-09	390657	42390746	8913820	2015	6412										
TCF20	6942	broad.mit.edu	37	chr22	42610400	42610400	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgttgggtcccttgtggaatCtttgcctgttcaaaattctt	9	8	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:42610400C>A	ENST00000359486.3	-	1	1048	c.912G>T	c.(910-912)aaG>aaT	p.K304N	TCF20_ENST00000335626.4_Missense_Mutation_p.K304N	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.K304N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CTTGTGGAATCTTTGCCTGTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	22											113	105	107					22																	42610400		2203	4300	6503	40940344	SO:0001583	missense	6942			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.912G>T	22.37:g.42610400C>A	ENSP00000352463:p.Lys304Asn		40940344	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	37	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.185685	0.57909	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.38401	1.14;1.14	5.33	4.32	0.51571	.	0.000000	0.64402	D	0.000001	T	0.43366	0.1244	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.40365	-0.9567	10	0.59425	D	0.04	-24.9728	10.4996	0.44798	0.0:0.8524:0.0:0.1476	.	304;304	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	N	304	ENSP00000352463:K304N;ENSP00000335561:K304N	ENSP00000335561:K304N	K	-	3	2	TCF20	40940344	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.800000	0.38833	1.484000	0.48361	-0.137000	0.14449	AAG		0.473	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		A	42610400	C	A	42610400	3	1	47	1	0	0	0	0	1	0	0	0	15729	912	32	2	5008	2	TCF20	22	42610400	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	219654	42610400	8694166	2016	6413										
POLDIP3	84271	broad.mit.edu	37	chr22	42998970	42998970	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgcactttccctttgattcGaaatcgggcatctttctgca	7	12	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:42998970G>A	ENST00000252115.5	-	2	360	c.256C>T	c.(256-258)Cga>Tga	p.R86*	POLDIP3_ENST00000339677.6_Nonsense_Mutation_p.R86*|POLDIP3_ENST00000348657.2_Nonsense_Mutation_p.R86*|POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000451060.2_5'UTR	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	86					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R86*(2)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CCTTTGATTCGAAATCGGGCA	0.567																																					Ovarian(52;967 1128 5875 19997 42537)											2	Substitution - Nonsense(2)	large_intestine(2)	22											101	99	100					22																	42998970		2203	4300	6503	41328914	SO:0001587	stop_gained	84271				CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.256C>T	22.37:g.42998970G>A	ENSP00000252115:p.Arg86*		41328914	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Nonsense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	G	32	5.175667	0.94807	.	.	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	6.08	5.01	0.66863	.	0.107634	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5184	14.6756	0.68978	0.0:0.0:0.7885:0.2115	.	.	.	.	X	86	.	ENSP00000252115:R86X	R	-	1	2	POLDIP3	41328914	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	2.679000	0.46909	2.894000	0.99253	0.591000	0.81541	CGA		0.567	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		A	42998970	G	A	42998970	4	1	47	1	0	0	0	0	0	1	0	0	12226	1066	37	1	1041	1	POLDIP3	22	42998970	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	388570	42998970	8305596	2017	6414										
TTLL1	25809	broad.mit.edu	37	chr22	43442535	43442535	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcaggttgtacttgaggatTcggtcattggcagtgctgga	14	6	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:43442535T>G	ENST00000266254.7	-	10	1263	c.1023A>C	c.(1021-1023)cgA>cgC	p.R341R	AL022476.2_ENST00000443063.1_RNA|TTLL1_ENST00000331018.7_Silent_p.R312R	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	341	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)	p.R341R(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		ACTTGAGGATTCGGTCATTGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	22											348	300	316					22																	43442535		2203	4300	6503	41772479	SO:0001819	synonymous_variant	25809			AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"Tubulin tyrosine ligase-like family"	1312	protein-coding gene	gene with protein product		608955	"tubulin tyrosine ligase-like 1"	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.1023A>C	22.37:g.43442535T>G			41772479	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	T	6.170	0.399507	0.11696	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.55	-10.9	0.00192	.	.	.	.	.	T	0.47764	0.1463	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60860	-0.7179	4	.	.	.	.	10.5642	0.45163	0.072:0.1905:0.6194:0.1181	.	.	.	.	A	267	.	.	E	-	2	0	TTLL1	41772479	0.001000	0.12720	0.016000	0.15963	0.439000	0.31926	-2.100000	0.01345	-2.092000	0.00857	-0.455000	0.05494	GAA		0.507	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		G	43442535	T	G	43442535	2	3	47	1	0	0	0	0	0	0	0	1	16762	1770	62	4		4	TTLL1	22	43442535	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	443565	43442535	7862031	2018	6415										
TTLL1	25809	broad.mit.edu	37	chr22	43471560	43471560	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgatcagcactgacttctcGatatcagtgacccattttac	6	11	3	3	rs148475049		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:43471560G>A	ENST00000266254.7	-	3	273	c.33C>T	c.(31-33)atC>atT	p.I11I	TTLL1_ENST00000445824.1_Silent_p.I11I|TTLL1_ENST00000331018.7_Silent_p.I11I	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	11	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)	p.I11I(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		CTGACTTCTCGATATCAGTGA	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		18476	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	22						G		11,4393	17.9+/-39.9	0,11,2191	201	188	192		33	-0.2	1	22	dbSNP_134	192	0,8600		0,0,4300	no	coding-synonymous	TTLL1	NM_012263.4		0,11,6491	AA,AG,GG		0.0,0.2498,0.0846		11/424	43471560	11,12993	2202	4300	6502	41801504	SO:0001819	synonymous_variant	25809			AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"Tubulin tyrosine ligase-like family"	1312	protein-coding gene	gene with protein product		608955	"tubulin tyrosine ligase-like 1"	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.33C>T	22.37:g.43471560G>A			41801504	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1																																																																																				0.413	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		A	43471560	G	A	43471560	2	1	47	1	0	0	0	0	0	0	0	1	16762	1048	37	1		1	TTLL1	22	43471560	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	29025	43471560	7833006	2019	6416										
SMC1B	27127	broad.mit.edu	37	chr22	45795093	45795093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgtctccagggcttttataTcatcttcctgtttagaacat	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:45795093T>C	ENST00000357450.4	-	6	994	c.995A>G	c.(994-996)gAt>gGt	p.D332G	SMC1B_ENST00000404354.3_Missense_Mutation_p.D332G	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	332					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.D332G(2)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GGCTTTTATATCATCTTCCTG	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	22											201	179	186					22																	45795093		1839	4094	5933	44173757	SO:0001583	missense	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.995A>G	22.37:g.45795093T>C	ENSP00000350036:p.Asp332Gly		44173757	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.005549	0.54254	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.79845	-1.31;-1.16	5.7	4.67	0.58626	RecF/RecN/SMC (1);	0.278906	0.30809	N	0.008840	T	0.73063	0.3539	L	0.40543	1.245	0.46981	D	0.999279	B;B;B	0.18013	0.008;0.007;0.025	B;B;B	0.26416	0.033;0.019;0.069	T	0.65957	-0.6042	10	0.32370	T	0.25	.	10.83	0.46654	0.0:0.0748:0.0:0.9252	.	332;332;332	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	G	332	ENSP00000350036:D332G;ENSP00000385902:D332G	ENSP00000350036:D332G	D	-	2	0	SMC1B	44173757	1.000000	0.71417	0.907000	0.35723	0.991000	0.79684	4.556000	0.60775	1.006000	0.39211	0.533000	0.62120	GAT		0.358	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		C	45795093	T	C	45795093	3	2	47	1	0	0	0	0	1	0	0	0	14819	1435	50	4	2792	4	SMC1B	22	45795093	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2323533	45795093	5509473	2020	6417										
TBC1D22A	25771	broad.mit.edu	37	chr22	47287218	47287218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actctccagagaaaacaaaaAgaatattttgcatttattga	5	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:47287218A>C	ENST00000337137.4	+	6	931	c.765A>C	c.(763-765)aaA>aaC	p.K255N	TBC1D22A_ENST00000355704.3_Missense_Mutation_p.K177N|TBC1D22A_ENST00000407381.3_Missense_Mutation_p.K196N|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.K208N|TBC1D22A_ENST00000406733.1_Missense_Mutation_p.K208N	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	255	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)	p.K255N(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		GAAAACAAAAAGAATATTTTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	22											87	90	89					22																	47287218		2203	4300	6503	45665882	SO:0001583	missense	25771			AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.765A>C	22.37:g.47287218A>C	ENSP00000336724:p.Lys255Asn		45665882	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	37	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.305525	0.40795	.	.	ENSG00000054611	ENST00000337137;ENST00000380995;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73	4.68	-1.96	0.07525	Rab-GAP/TBC domain (4);	0.167671	0.52532	D	0.000068	T	0.07638	0.0192	N	0.20685	0.6	0.44098	D	0.996868	B;B;B;B	0.21225	0.052;0.042;0.053;0.052	B;B;B;B	0.18871	0.022;0.023;0.022;0.022	T	0.23726	-1.0180	10	0.38643	T	0.18	.	10.3282	0.43807	0.4788:0.0:0.5212:0.0	.	255;177;196;255	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	N	255;208;196;177;208	ENSP00000336724:K255N;ENSP00000370383:K208N;ENSP00000384036:K196N;ENSP00000347932:K177N;ENSP00000385634:K208N	ENSP00000336724:K255N	K	+	3	2	TBC1D22A	45665882	0.980000	0.34600	0.496000	0.27539	0.987000	0.75469	0.208000	0.17415	-0.680000	0.05211	0.455000	0.32223	AAA		0.398	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		C	47287218	A	C	47287218	3	2	47	1	0	0	0	0	1	0	0	0	15650	69	3	4	787	4	TBC1D22A	22	47287218	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1492125	47287218	4017348	2021	6418										
BRD1	23774	broad.mit.edu	37	chr22	50217866	50217866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taccatcctttgagcttgagCgtaggtcagcgtttctcgcg	11	11	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:50217866C>T	ENST00000216267.8	-	1	586	c.100G>A	c.(100-102)Gct>Act	p.A34T	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Missense_Mutation_p.A34T|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Missense_Mutation_p.A34T|BRD1_ENST00000457780.2_Missense_Mutation_p.A34T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	34					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.A34T(1)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		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)		TGAGCTTGAGCGTAGGTCAGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	22											140	130	134					22																	50217866		2203	4300	6503	48603870	SO:0001583	missense	23774			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"BR140-like"	604589	"bromodomain-containing 1"			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.100G>A	22.37:g.50217866C>T	ENSP00000216267:p.Ala34Thr		48603870	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035101	0.75617	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780	T;T;T;T	0.23147	2.22;2.22;2.19;1.92	5.12	5.12	0.69794	.	0.105878	0.64402	D	0.000004	T	0.56366	0.1980	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.60890	-0.7173	9	.	.	.	.	18.5465	0.91048	0.0:1.0:0.0:0.0	.	34;34;34	Q86X06;O95696;O95696-2	.;BRD1_HUMAN;.	T	34	ENSP00000216267:A34T;ENSP00000384076:A34T;ENSP00000385858:A34T;ENSP00000410042:A34T	.	A	-	1	0	BRD1	48603870	1.000000	0.71417	0.974000	0.42286	0.421000	0.31385	7.322000	0.79097	2.385000	0.81259	0.448000	0.29417	GCT		0.498	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		T	50217866	C	T	50217866	3	4	47	1	0	0	0	0	1	0	0	0	1504	768	27	1	3124	1	BRD1	22	50217866	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2930648	50217866	1086700	2022	6419										
MOV10L1	54456	broad.mit.edu	37	chr22	50552974	50552974	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atcagatgaaaatattaattCattaaatagccacacaaaaa	3	6	2	2	rs78907950		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:50552974C>T	ENST00000262794.5	+	7	1132	c.1049C>T	c.(1048-1050)tCa>tTa	p.S350L	MOV10L1_ENST00000545383.1_Missense_Mutation_p.S350L|MOV10L1_ENST00000540615.1_Missense_Mutation_p.S330L|MOV10L1_ENST00000395858.3_Missense_Mutation_p.S350L|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	350					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.S350L(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		AATATTAATTCATTAAATAGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	22											53	57	56					22																	50552974		2203	4300	6503	48895101	SO:0001583	missense	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1049C>T	22.37:g.50552974C>T	ENSP00000262794:p.Ser350Leu		48895101	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	C	6.783	0.513491	0.12944	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.87029	-2.01;-2.01;-1.6;-2.2	5.76	-0.82	0.10826	.	0.946920	0.08921	N	0.874448	D	0.84061	0.5389	M	0.73598	2.24	0.19775	N	0.999957	B;B;B;B	0.21753	0.06;0.002;0.0;0.0	B;B;B;B	0.20577	0.03;0.006;0.003;0.003	T	0.72239	-0.4351	10	0.62326	D	0.03	-4.0133	4.8339	0.13454	0.1813:0.5322:0.0:0.2865	.	111;330;350;350	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	L	350;350;350;330	ENSP00000438978:S350L;ENSP00000262794:S350L;ENSP00000379199:S350L;ENSP00000438542:S330L	ENSP00000262794:S350L	S	+	2	0	MOV10L1	48895101	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.127000	0.10547	-0.273000	0.09246	-0.222000	0.12452	TCA		0.413	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50552974	C	T	50552974	3	4	47	1	0	0	0	0	1	0	0	0	9749	838	29	3	1116	3	MOV10L1	22	50552974	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	335108	50552974	751592	2023	6420										
MOV10L1	54456	broad.mit.edu	37	chr22	50563961	50563961	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatctgctggttctggaggtCccagggttggccgaagggag	18	8	2	0	rs140640371		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:50563961C>T	ENST00000262794.5	+	11	1793	c.1710C>T	c.(1708-1710)gtC>gtT	p.V570V	MOV10L1_ENST00000545383.1_Silent_p.V570V|MOV10L1_ENST00000540615.1_Silent_p.V550V|MOV10L1_ENST00000395858.3_Silent_p.V570V|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	570					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.V570V(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TTCTGGAGGTCCCAGGGTTGG	0.488													C|||	1	0.000199681	0	0	5008	,	,		16988	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	22											132	132	132					22																	50563961		2203	4300	6503	48906088	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1710C>T	22.37:g.50563961C>T			48906088	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.488	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50563961	C	T	50563961	2	4	47	1	0	0	0	0	0	0	0	1	9749	842	30	3		3	MOV10L1	22	50563961	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	10987	50563961	740605	2024	6421										
MOV10L1	54456	broad.mit.edu	37	chr22	50572973	50572973	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taaaagtgttgtttccagaaGaaattattttacagtctcca	6	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:50572973G>T	ENST00000262794.5	+	15	2067	c.1984G>T	c.(1984-1986)Gaa>Taa	p.E662*	MOV10L1_ENST00000545383.1_Nonsense_Mutation_p.E662*|MOV10L1_ENST00000540615.1_Nonsense_Mutation_p.E642*|MOV10L1_ENST00000395858.3_Nonsense_Mutation_p.E662*|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	662					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E662*(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GTTTCCAGAAGAAATTATTTT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											128	127	127					22																	50572973		2203	4300	6503	48915100	SO:0001587	stop_gained	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1984G>T	22.37:g.50572973G>T	ENSP00000262794:p.Glu662*		48915100	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Nonsense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	39	7.889989	0.98545	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	.	.	.	5.78	2.27	0.28462	.	0.583581	0.20472	N	0.091680	.	.	.	.	.	.	0.39714	D	0.971378	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-25.12	2.1238	0.03732	0.3689:0.0:0.393:0.2381	.	.	.	.	X	662;662;662;642	.	ENSP00000262794:E662X	E	+	1	0	MOV10L1	48915100	1.000000	0.71417	0.934000	0.37439	0.872000	0.50106	4.462000	0.60121	0.777000	0.33496	0.655000	0.94253	GAA		0.373	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50572973	G	T	50572973	4	4	47	1	0	0	0	0	0	1	0	0	9749	943	33	2	2083	2	MOV10L1	22	50572973	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	9012	50572973	731593	2025	6422										
ACR	49	broad.mit.edu	37	chr22	51182536	51182536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcacgtgtggatctcatcGacctggacttgtgtaactcg	12	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chr22:51182536G>A	ENST00000216139.5	+	4	653	c.613G>A	c.(613-615)Gac>Aac	p.D205N	AC002056.5_ENST00000532913.1_RNA	NM_001097.2	NP_001088.2	P10323	ACRO_HUMAN	acrosin	205	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acrosome matrix dispersal (GO:0002077)|acrosome reaction (GO:0007340)|activation of adenylate cyclase activity (GO:0007190)|binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|response to steroid hormone (GO:0048545)|single fertilization (GO:0007338)	acrosomal matrix (GO:0043159)|extracellular region (GO:0005576)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|protein complex (GO:0043234)	amidase activity (GO:0004040)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|drug binding (GO:0008144)|fucose binding (GO:0042806)|mannose binding (GO:0005537)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.D205N(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	7		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		GGATCTCATCGACCTGGACTT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	22											171	152	159					22																	51182536		2203	4300	6503	49529402	SO:0001583	missense	49			CR456366	CCDS14101.1	22q13.33	2012-10-23	2012-10-23		ENSG00000100312	ENSG00000100312	3.4.21.10		126	protein-coding gene	gene with protein product	"preproacrosin", "acrosin light and heavy chain prepropeptide"	102480				2298447, 12398221	Standard	NM_001097		Approved		uc003bnh.4	P10323	OTTHUMG00000150155	ENST00000216139.5:c.613G>A	22.37:g.51182536G>A	ENSP00000216139:p.Asp205Asn		49529402	Q6ICK2	Missense_Mutation	SNP	ENST00000216139.5	37	CCDS14101.1	.	.	.	.	.	.	.	.	.	.	N	13.19	2.162115	0.38217	.	.	ENSG00000100312	ENST00000216139	T	0.60299	0.2	4.48	1.03	0.20045	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.460605	0.18488	N	0.139729	T	0.33059	0.0850	N	0.14661	0.345	0.24069	N	0.995982	B	0.28760	0.221	B	0.24701	0.055	T	0.13548	-1.0505	10	0.32370	T	0.25	-21.0446	6.549	0.22423	0.4528:0.0:0.5472:0.0	.	205	P10323	ACRO_HUMAN	N	205	ENSP00000216139:D205N	ENSP00000216139:D205N	D	+	1	0	ACR	49529402	0.004000	0.15560	0.953000	0.39169	0.968000	0.65278	0.632000	0.24583	0.458000	0.26988	0.450000	0.29827	GAC		0.562	ACR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000316605.2	NM_001097		A	51182536	G	A	51182536	3	1	47	1	0	0	0	0	1	0	0	0	169	1058	37	1	627	1	ACR	22	51182536	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	609563	51182536	122030	2026	6423										
CSF2RA	1438	broad.mit.edu	37	chrX	1428404	1428404	+	3'UTR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtaggaatggcatggacatCtccgcctccgcgacacgggg	14	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:1428404C>A	ENST00000381524.3	+	0	1421				CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000501036.2_3'UTR|CSF2RA_ENST00000498153.1_3'UTR|CSF2RA_ENST00000355432.3_Silent_p.I352I|CSF2RA_ENST00000432318.2_3'UTR|CSF2RA_ENST00000361536.3_3'UTR|CSF2RA_ENST00000381500.1_3'UTR|CSF2RA_ENST00000417535.2_3'UTR|CSF2RA_ENST00000355805.2_3'UTR|CSF2RA_ENST00000381529.3_3'UTR			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)						response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.I352I(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	GCATGGACATCTCCGCCTCCG	0.478																																					Esophageal Squamous(131;723 1707 25334 40494 41806)											1	Substitution - coding silent(1)	large_intestine(1)	X											261	243	249					X																	1428404		2203	4296	6499	1388404	SO:0001624	3_prime_UTR_variant	1438			M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.*32C>A	X.37:g.1428404C>A			1388404	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	37	CCDS35191.1																																																																																				0.478	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			A	1428404	C	A	1428404	1	1	47	0	1	0	0	0	0	0	0	0	3940	903	32	2		2	CSF2RA	23	1428404	3'UTR	SNP	C	TCGA-AG-3892-01A-01W-1073-09		1428404	153842156	2027	6424										
MXRA5	25878	broad.mit.edu	37	chrX	3240135	3240135	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctgtaggaaccagagaactCtccacttgacttgaaatctt	8	10	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:3240135C>T	ENST00000217939.6	-	5	3745	c.3591G>A	c.(3589-3591)gaG>gaA	p.E1197E		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1197						extracellular vesicular exosome (GO:0070062)		p.E1197E(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CCAGAGAACTCTCCACTTGAC	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	X											117	112	114					X																	3240135		2203	4300	6503	3250135	SO:0001819	synonymous_variant	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3591G>A	X.37:g.3240135C>T			3250135	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.468	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3240135	C	T	3240135	2	4	47	1	0	0	0	0	0	0	0	1	10033	912	32	3		3	MXRA5	23	3240135	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1811731	3240135	152030425	2028	6425										
NLGN4X	57502	broad.mit.edu	37	chrX	5811344	5811344	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttgtgtcctcaggccctgtTttgtgagggtccttagagtg	14	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:5811344T>C	ENST00000381095.3	-	6	2592	c.1965A>G	c.(1963-1965)aaA>aaG	p.K655K	NLGN4X_ENST00000381093.2_Silent_p.K675K|NLGN4X_ENST00000381092.1_Silent_p.K655K|NLGN4X_ENST00000275857.6_Silent_p.K655K|NLGN4X_ENST00000538097.1_Silent_p.K655K	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	655					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.K655K(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						CAGGCCCTGTTTTGTGAGGGT	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	X											232	210	218					X																	5811344		2203	4300	6503	5821344	SO:0001819	synonymous_variant	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1965A>G	X.37:g.5811344T>C			5821344	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.537	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		C	5811344	T	C	5811344	2	2	47	1	0	0	0	0	0	0	0	1	10495	1838	64	4		4	NLGN4X	23	5811344	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2571209	5811344	149459216	2029	6426										
FAM9B	171483	broad.mit.edu	37	chrX	8997410	8997410	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgctcgtctgtgatgtattCttcaaggacatttagcaact	8	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:8997410C>A	ENST00000327220.5	-	6	695	c.331G>T	c.(331-333)Gaa>Taa	p.E111*	FAM9B_ENST00000362066.3_Nonsense_Mutation_p.E151*|FAM9B_ENST00000428477.1_Nonsense_Mutation_p.E111*			Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B	111						nucleus (GO:0005634)		p.E111*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11		Hepatocellular(5;0.219)				GTGATGTATTCTTCAAGGACA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											206	154	172					X																	8997410		2203	4300	6503	8957410	SO:0001587	stop_gained	171483				CCDS14132.1	Xp22.31	2014-02-17			ENSG00000177138	ENSG00000177138			18404	protein-coding gene	gene with protein product	"testis expressed 39B"	300478				12213195, 21085121, 21998597, 22936694	Standard	XM_005274456		Approved	TEX39B	uc011mhu.2	Q8IZU0	OTTHUMG00000021114	ENST00000327220.5:c.331G>T	X.37:g.8997410C>A	ENSP00000318716:p.Glu111*		8957410	Q0IJ68|Q8N7Z8	Nonsense_Mutation	SNP	ENST00000327220.5	37	CCDS14132.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.279860	0.40294	.	.	ENSG00000177138	ENST00000362066;ENST00000327220;ENST00000428477	.	.	.	0.43	0.43	0.16515	.	.	.	.	.	.	.	.	.	.	.	0.58432	A	0.999993	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	.	.	.	.	.	.	.	X	151;111;111	.	ENSP00000318716:E111X	E	-	1	0	FAM9B	8957410	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.342000	0.02645	0.434000	0.26340	0.436000	0.28706	GAA		0.363	FAM9B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055702.2	NM_205849		A	8997410	C	A	8997410	4	1	47	1	0	0	0	0	0	1	0	0	5679	922	32	2	241	2	FAM9B	23	8997410	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3186066	8997410	146273150	2030	6427										
GPR143	4935	broad.mit.edu	37	chrX	9711655	9711655	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatcggatcttgatcacggcTcccatcctcctctcgttctc	6	16	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:9711655T>C	ENST00000467482.1	-	6	863	c.717A>G	c.(715-717)ggA>ggG	p.G239G	GPR143_ENST00000380929.2_Silent_p.G259G			P51810	GP143_HUMAN	G protein-coupled receptor 143	239					calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)	p.G259G(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				TGATCACGGCTCCCATCCTCC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	X											168	144	152					X																	9711655		2203	4300	6503	9671655	SO:0001819	synonymous_variant	4935			Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"GPCR / Unclassified : 7TM orphan receptors"	20145	protein-coding gene	gene with protein product	"ocular albinism 1"	300808	"ocular albinism 1 (Nettleship-Falls)"	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.717A>G	X.37:g.9711655T>C			9671655	Q6NTI7	Silent	SNP	ENST00000467482.1	37	CCDS14134.2	.	.	.	.	.	.	.	.	.	.	T	6.497	0.459810	0.12342	.	.	ENSG00000101850	ENST00000447366	.	.	.	5.15	0.153	0.14897	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.54753	D	0.99998	.	.	.	.	.	.	T	0.31336	-0.9947	4	.	.	.	-12.6199	4.8248	0.13410	0.0:0.3415:0.3151:0.3434	.	.	.	.	G	175	.	.	S	-	1	0	GPR143	9671655	0.446000	0.25665	0.449000	0.26957	0.680000	0.39746	-0.702000	0.05069	-0.363000	0.08101	0.417000	0.27973	AGC		0.388	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273		C	9711655	T	C	9711655	2	2	47	1	0	0	0	0	0	0	0	1	6671	1538	54	4		4	GPR143	23	9711655	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	714245	9711655	145558905	2031	6428										
WWC3	55841	broad.mit.edu	37	chrX	10085339	10085339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagccagcttctacgcttcGacctcattcccttcgactct	6	17	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:10085339G>A	ENST00000380861.4	+	11	1631	c.1240G>A	c.(1240-1242)Gac>Aac	p.D414N	WWC3_ENST00000454666.1_Missense_Mutation_p.D414N	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	414	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.D414N(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TCTACGCTTCGACCTCATTCC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	X											75	72	73					X																	10085339		2203	4300	6503	10045339	SO:0001583	missense	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1240G>A	X.37:g.10085339G>A	ENSP00000370242:p.Asp414Asn		10045339	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	7.621	0.676917	0.14841	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.05139	3.49;3.49	5.43	4.53	0.55603	.	0.281377	0.39475	N	0.001357	T	0.19805	0.0476	M	0.75264	2.295	0.31783	N	0.630623	D	0.69078	0.997	P	0.59012	0.85	T	0.15407	-1.0438	10	0.26408	T	0.33	-7.3742	15.2219	0.73316	0.0:0.1378:0.8622:0.0	.	414	Q9ULE0	WWC3_HUMAN	N	414;414;78;414	ENSP00000370242:D414N;ENSP00000399584:D414N	ENSP00000370242:D414N	D	+	1	0	WWC3	10045339	1.000000	0.71417	0.401000	0.26359	0.287000	0.27160	5.148000	0.64857	1.045000	0.40225	0.464000	0.42555	GAC		0.657	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10085339	G	A	10085339	3	1	47	1	0	0	0	0	1	0	0	0	17453	1058	37	1	1278	1	WWC3	23	10085339	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	373684	10085339	145185221	2032	6429										
ARHGAP6	395	broad.mit.edu	37	chrX	11160378	11160378	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attcctgggtctttggatccGctttttaatgttgaatgcca	9	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:11160378G>A	ENST00000337414.4	-	12	3104	c.2232C>T	c.(2230-2232)agC>agT	p.S744S	ARHGAP6_ENST00000303025.6_Silent_p.S541S|ARHGAP6_ENST00000534860.1_Silent_p.S569S|ARHGAP6_ENST00000380736.1_Silent_p.S541S	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	744					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)	p.S744S(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CTTTGGATCCGCTTTTTAATG	0.303													G|||	1	0.000264901	0	0	3775	,	,		12406	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X											104	102	103					X																	11160378		2203	4300	6503	11070299	SO:0001819	synonymous_variant	395			AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"Rho GTPase activating proteins"	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.2232C>T	X.37:g.11160378G>A			11070299	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Silent	SNP	ENST00000337414.4	37	CCDS14140.1																																																																																				0.303	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		A	11160378	G	A	11160378	2	1	47	1	0	0	0	0	0	0	0	1	887	1078	38	1		1	ARHGAP6	23	11160378	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1075039	11160378	144110182	2033	6430										
ARHGAP6	395	broad.mit.edu	37	chrX	11162360	11162360	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaacttccgactgcagcatgTcagggcttctggcacaatga	10	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:11162360T>G	ENST00000337414.4	-	11	2788	c.1916A>C	c.(1915-1917)gAc>gCc	p.D639A	ARHGAP6_ENST00000303025.6_Missense_Mutation_p.D436A|ARHGAP6_ENST00000413512.3_3'UTR|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.D639A|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.D464A|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.D436A	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	639					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)	p.D639A(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CTGCAGCATGTCAGGGCTTCT	0.468											OREG0019666	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	X											63	66	65					X																	11162360		2203	4295	6498	11072281	SO:0001583	missense	395			AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"Rho GTPase activating proteins"	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.1916A>C	X.37:g.11162360T>G	ENSP00000338967:p.Asp639Ala	670	11072281	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	T	14.74	2.625341	0.46840	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414;ENST00000380717;ENST00000380718	T;T;T;T;T;T	0.23147	1.94;1.98;1.98;1.98;1.92;1.94	5.51	5.51	0.81932	.	0.487586	0.18460	N	0.140558	T	0.25306	0.0615	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.19935	0.002;0.008;0.022;0.04	B;B;B;B	0.12837	0.001;0.004;0.008;0.008	T	0.06215	-1.0839	10	0.12766	T	0.61	.	14.7411	0.69455	0.0:0.0:0.0:1.0	.	436;639;639;639	O43182-5;O43182-2;O43182;A8KAL3	.;.;RHG06_HUMAN;.	A	464;436;436;639;475;639	ENSP00000438135:D464A;ENSP00000370112:D436A;ENSP00000302312:D436A;ENSP00000338967:D639A;ENSP00000370093:D475A;ENSP00000370094:D639A	ENSP00000302312:D436A	D	-	2	0	ARHGAP6	11072281	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.209000	0.58493	1.863000	0.54032	0.412000	0.27726	GAC		0.468	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		G	11162360	T	G	11162360	3	3	47	1	0	0	0	0	1	0	0	0	887	1667	58	4	1142	4	ARHGAP6	23	11162360	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1982	11162360	144108200	2034	6431										
FRMPD4	9758	broad.mit.edu	37	chrX	12720127	12720127	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaaatctccctcaaatacatCgagtaagtgttgactctcag	6	10	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:12720127C>T	ENST00000380682.1	+	10	1574	c.1068C>T	c.(1066-1068)atC>atT	p.I356I		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	356	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I346I(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TCAAATACATCGAGTAAGTGT	0.468											OREG0019670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	X											124	103	110					X																	12720127		2203	4300	6503	12630048	SO:0001819	synonymous_variant	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1068C>T	X.37:g.12720127C>T		682	12630048	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																				0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12720127	C	T	12720127	2	4	47	1	0	0	0	0	0	0	0	1	6078	874	31	1		1	FRMPD4	23	12720127	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1557767	12720127	142550433	2035	6432										
TLR7	51284	broad.mit.edu	37	chrX	12904321	12904321	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctactttaacagaactatatCtctacaacaacatgattgca	3	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:12904321C>A	ENST00000380659.3	+	3	833	c.694C>A	c.(694-696)Ctc>Atc	p.L232I		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	232					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.L232I(1)		NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	AGAACTATATCTCTACAACAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	X											65	60	62					X																	12904321		2203	4300	6503	12814242	SO:0001583	missense	51284			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.694C>A	X.37:g.12904321C>A	ENSP00000370034:p.Leu232Ile		12814242	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.137093	0.37728	.	.	ENSG00000196664	ENST00000380659	T	0.06933	3.24	5.41	5.41	0.78517	.	0.080132	0.51477	D	0.000098	T	0.13841	0.0335	L	0.46567	1.45	0.46725	D	0.999177	P	0.50710	0.938	P	0.48770	0.589	T	0.00664	-1.1620	10	0.52906	T	0.07	.	13.944	0.64073	0.1616:0.8384:0.0:0.0	.	232	Q9NYK1	TLR7_HUMAN	I	232	ENSP00000370034:L232I	ENSP00000370034:L232I	L	+	1	0	TLR7	12814242	1.000000	0.71417	0.932000	0.37286	0.201000	0.24016	5.001000	0.63946	2.242000	0.73789	0.589000	0.80489	CTC		0.358	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12904321	C	A	12904321	3	1	47	1	0	0	0	0	1	0	0	0	15995	913	32	2	700	2	TLR7	23	12904321	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	184194	12904321	142366239	2036	6433										
OFD1	8481	broad.mit.edu	37	chrX	13764500	13764500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accctcagcgtatcaagttcGaatctttagaaataaagcta	6	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:13764500G>A	ENST00000340096.6	+	7	907	c.580G>A	c.(580-582)Gaa>Aaa	p.E194K	OFD1_ENST00000380550.3_Missense_Mutation_p.E194K|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000398395.3_Missense_Mutation_p.E194K|OFD1_ENST00000380567.1_Missense_Mutation_p.E54K	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	194					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)	p.E194K(2)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TATCAAGTTCGAATCTTTAGA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	X											71	64	67					X																	13764500		2203	4300	6503	13674421	SO:0001583	missense	8481			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.580G>A	X.37:g.13764500G>A	ENSP00000344314:p.Glu194Lys		13674421	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.151123	0.38021	.	.	ENSG00000046651	ENST00000380550;ENST00000398395;ENST00000340096;ENST00000380567;ENST00000543598	D;D;D;D	0.95756	-3.72;-3.49;-3.8;-1.72	5.65	4.77	0.60923	.	0.240997	0.44688	D	0.000438	D	0.96806	0.8957	M	0.74881	2.28	0.31448	N	0.671105	D;D;D;D	0.76494	0.998;0.993;0.999;0.997	P;P;P;P	0.62298	0.9;0.709;0.887;0.775	D	0.95598	0.8660	10	0.22109	T	0.4	-13.6563	15.7197	0.77697	0.0:0.1334:0.8666:0.0	.	194;194;54;194	A8K2T9;O75665-3;A6NF31;O75665	.;.;.;OFD1_HUMAN	K	194;194;194;54;57	ENSP00000369923:E194K;ENSP00000381432:E194K;ENSP00000344314:E194K;ENSP00000369941:E54K	ENSP00000344314:E194K	E	+	1	0	OFD1	13674421	1.000000	0.71417	0.197000	0.23402	0.030000	0.12068	6.343000	0.72986	1.133000	0.42147	-0.218000	0.12543	GAA		0.343	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		A	13764500	G	A	13764500	3	1	47	1	0	0	0	0	1	0	0	0	10869	1059	37	1	606	1	OFD1	23	13764500	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	860179	13764500	141506060	2037	6434										
OFD1	8481	broad.mit.edu	37	chrX	13764901	13764901	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttgtgatcaatttgcagttGaagttttttaaagataccga	8	4	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:13764901G>T	ENST00000340096.6	+	8	984	c.657G>T	c.(655-657)ttG>ttT	p.L219F	OFD1_ENST00000380550.3_Missense_Mutation_p.L219F|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000398395.3_Missense_Mutation_p.L219F|OFD1_ENST00000380567.1_Missense_Mutation_p.L79F	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	219					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)	p.L219F(2)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						ATTTGCAGTTGAAGTTTTTTA	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	X											27	27	27					X																	13764901		2196	4291	6487	13674822	SO:0001583	missense	8481			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.657G>T	X.37:g.13764901G>T	ENSP00000344314:p.Leu219Phe		13674822	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.355822	0.41700	.	.	ENSG00000046651	ENST00000380550;ENST00000398395;ENST00000340096;ENST00000380567;ENST00000543598	D;D;D;D	0.97066	-4.23;-3.87;-4.22;-2.26	5.61	1.81	0.25067	.	0.143865	0.44902	D	0.000418	D	0.97346	0.9132	M	0.74258	2.255	0.31794	N	0.629272	D;D;D;D;D	0.76494	0.983;0.999;0.999;0.997;0.999	P;D;D;D;D	0.72625	0.822;0.978;0.976;0.964;0.978	D	0.94832	0.7997	10	0.66056	D	0.02	-1.1838	4.4496	0.11614	0.4665:0.0:0.3816:0.1519	.	82;219;219;79;219	F5H2Z4;A8K2T9;O75665-3;A6NF31;O75665	.;.;.;.;OFD1_HUMAN	F	219;219;219;79;82	ENSP00000369923:L219F;ENSP00000381432:L219F;ENSP00000344314:L219F;ENSP00000369941:L79F	ENSP00000344314:L219F	L	+	3	2	OFD1	13674822	0.887000	0.30362	0.060000	0.19600	0.724000	0.41520	0.867000	0.27968	-0.065000	0.13021	0.544000	0.68410	TTG		0.279	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		T	13764901	G	T	13764901	3	4	47	1	0	0	0	0	1	0	0	0	10869	1281	45	2	687	2	OFD1	23	13764901	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	401	13764901	141505659	2038	6435										
MOSPD2	158747	broad.mit.edu	37	chrX	14915235	14915235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggtgaagtatcatgtaaaaGaccagaaaaccatattggac	10	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:14915235G>T	ENST00000380492.3	+	5	440	c.352G>T	c.(352-354)Gac>Tac	p.D118Y	MOSPD2_ENST00000482354.1_Missense_Mutation_p.D118Y|MOSPD2_ENST00000495110.1_3'UTR	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	118	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)	p.D118Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					TCATGTAAAAGACCAGAAAAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											112	105	108					X																	14915235		2203	4300	6503	14825156	SO:0001583	missense	158747			AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.352G>T	X.37:g.14915235G>T	ENSP00000369860:p.Asp118Tyr		14825156	Q8N3H2|Q8NA83	Missense_Mutation	SNP	ENST00000380492.3	37	CCDS14162.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316863	0.81469	.	.	ENSG00000130150	ENST00000380492	T	0.75821	-0.97	5.23	5.23	0.72850	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.85906	0.5806	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87261	0.2279	10	0.66056	D	0.02	.	18.2	0.89834	0.0:0.0:1.0:0.0	.	118	Q8NHP6	MSPD2_HUMAN	Y	118	ENSP00000369860:D118Y	ENSP00000369860:D118Y	D	+	1	0	MOSPD2	14825156	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.470000	0.80973	2.322000	0.78497	0.529000	0.55759	GAC		0.338	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581		T	14915235	G	T	14915235	3	4	47	1	0	0	0	0	1	0	0	0	9746	942	33	2	370	2	MOSPD2	23	14915235	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1150334	14915235	140355325	2039	6436										
PIGA	5277	broad.mit.edu	37	chrX	15339715	15339715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcaccccgtggcccagtggcAtctattgcaacatcaatgat	9	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:15339715A>G	ENST00000333590.4	-	6	1452	c.1368T>C	c.(1366-1368)gaT>gaC	p.D456D	PIGA_ENST00000482148.1_5'UTR|PIGA_ENST00000428964.1_Silent_p.D141D|PIGA_ENST00000542278.1_Silent_p.D222D	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	456					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194)	p.D456D(1)		endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Hepatocellular(33;0.183)					GCCCAGTGGCATCTATTGCAA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	X											120	116	117					X																	15339715		2203	4300	6503	15249636	SO:0001819	synonymous_variant	5277			BC038236	CCDS14165.1, CCDS48086.1, CCDS48086.2	Xp22.1	2014-09-17	2008-07-31		ENSG00000165195	ENSG00000165195	2.4.1.198	"Glycosyltransferase group 1 domain containing", "Phosphatidylinositol glycan anchor biosynthesis"	8957	protein-coding gene	gene with protein product	"paroxysmal nocturnal hemoglobinuria", "phosphatidylinositol N-acetylglucosaminyltransferase"	311770	"phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)"			8500164	Standard	NM_002641		Approved	GPI3	uc004cwr.3	P37287	OTTHUMG00000021174	ENST00000333590.4:c.1368T>C	X.37:g.15339715A>G			15249636	B4E0V2|Q16025|Q16250	Silent	SNP	ENST00000333590.4	37	CCDS14165.1																																																																																				0.428	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055854.1	NM_002641		G	15339715	A	G	15339715	2	3	47	1	0	0	0	0	0	0	0	1	11915	214	8	4		4	PIGA	23	15339715	Silent	SNP	A	TCGA-AG-3892-01A-01W-1073-09	424480	15339715	139930845	2040	6437										
FIGF	2277	broad.mit.edu	37	chrX	15376294	15376294	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctctagggctgcactgagttCtttgccattcttcatctata	7	11	5	1	rs78901600		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:15376294C>A	ENST00000297904.3	-	3	752	c.323G>T	c.(322-324)aGa>aTa	p.R108I		NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	108					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)	p.R108I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					GCACTGAGTTCTTTGCCATTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	X											188	158	168					X																	15376294		2203	4300	6503	15286215	SO:0001583	missense	2277			AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.323G>T	X.37:g.15376294C>A	ENSP00000297904:p.Arg108Ile		15286215	B2R7Z3	Missense_Mutation	SNP	ENST00000297904.3	37	CCDS14166.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678385	0.68042	.	.	ENSG00000165197	ENST00000297904	.	.	.	5.11	4.24	0.50183	Platelet-derived growth factor (PDGF) (1);	0.121948	0.64402	D	0.000012	T	0.50667	0.1629	L	0.54323	1.7	0.49299	D	0.999774	D	0.59357	0.985	P	0.48089	0.566	T	0.53486	-0.8432	9	0.87932	D	0	-15.9467	6.5385	0.22367	0.0:0.6947:0.0:0.3053	.	108	O43915	VEGFD_HUMAN	I	108	.	ENSP00000297904:R108I	R	-	2	0	FIGF	15286215	0.956000	0.32656	0.675000	0.29917	0.986000	0.74619	1.799000	0.38824	1.054000	0.40438	0.529000	0.55759	AGA		0.522	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469		A	15376294	C	A	15376294	3	1	47	1	0	0	0	0	1	0	0	0	5908	913	32	2	761	2	FIGF	23	15376294	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36579	15376294	139894266	2041	6438										
MAP7D2	256714	broad.mit.edu	37	chrX	20028972	20028972	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ccaggactgttaaatccttcGataaggtttttgttacagtc	8	8	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:20028972G>A	ENST00000379651.3	-	15	2166	c.2148C>T	c.(2146-2148)atC>atT	p.I716I	MAP7D2_ENST00000379643.5_Silent_p.I757I|MAP7D2_ENST00000443379.3_Silent_p.I671I|MAP7D2_ENST00000543767.1_Silent_p.I601I|MAP7D2_ENST00000452324.3_Silent_p.I664I	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	716					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)		p.I716I(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						TAAATCCTTCGATAAGGTTTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	X											119	114	116					X																	20028972		2203	4300	6503	19938893	SO:0001819	synonymous_variant	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.2148C>T	X.37:g.20028972G>A			19938893	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Silent	SNP	ENST00000379651.3	37	CCDS14195.1																																																																																				0.423	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		A	20028972	G	A	20028972	2	1	47	1	0	0	0	0	0	0	0	1	9298	1048	37	1		1	MAP7D2	23	20028972	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	4652678	20028972	135241588	2042	6439										
RPS6KA3	6197	broad.mit.edu	37	chrX	20222187	20222187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcatggcataaagctgcctaGcatcagagcctgagattttt	9	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:20222187G>T	ENST00000379565.3	-	4	485	c.278C>A	c.(277-279)gCt>gAt	p.A93D	RPS6KA3_ENST00000379548.4_Missense_Mutation_p.A64D|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.A65D|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.A65D	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	93	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A93D(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	AAGCTGCCTAGCATCAGAGCC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	X											128	117	121					X																	20222187		2203	4300	6503	20132108	SO:0001583	missense	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.278C>A	X.37:g.20222187G>T	ENSP00000368884:p.Ala93Asp		20132108	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323858	0.60634	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145;ENST00000438357	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;3.3	5.42	5.42	0.78866	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.185721	0.46758	D	0.000270	T	0.22044	0.0531	N	0.04994	-0.135	0.80722	D	1	B;B;D;B	0.56968	0.096;0.191;0.978;0.344	B;B;P;B	0.55112	0.055;0.022;0.769;0.055	T	0.25363	-1.0134	10	0.49607	T	0.09	.	18.2983	0.90154	0.0:0.0:1.0:0.0	.	65;64;65;93	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	D	93;65;64;65;64;65	ENSP00000368884:A93D;ENSP00000440220:A65D;ENSP00000368865:A64D;ENSP00000444837:A65D;ENSP00000407655:A64D;ENSP00000388512:A65D	ENSP00000368865:A64D	A	-	2	0	RPS6KA3	20132108	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.035000	0.70940	2.260000	0.74910	0.600000	0.82982	GCT		0.323	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		T	20222187	G	T	20222187	3	4	47	1	0	0	0	0	1	0	0	0	13689	971	34	2	2020	2	RPS6KA3	23	20222187	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	193215	20222187	135048373	2043	6440										
ACOT9	23597	broad.mit.edu	37	chrX	23751331	23751331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctatctcccgcaacttatctCgaactgaaacaaaaataaag	4	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:23751331C>T	ENST00000336430.7	-	3	253	c.122G>A	c.(121-123)cGa>cAa	p.R41Q	ACOT9_ENST00000379303.5_Missense_Mutation_p.R50Q|ACOT9_ENST00000379295.1_5'UTR|ACOT9_ENST00000492081.1_5'UTR	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	41					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)	p.R41Q(2)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						CAACTTATCTCGAACTGAAAC	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	X											118	99	105					X																	23751331		2203	4300	6503	23661252	SO:0001583	missense	23597			AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.122G>A	X.37:g.23751331C>T	ENSP00000336580:p.Arg41Gln		23661252	B3KNC9|B7ZM94	Missense_Mutation	SNP	ENST00000336430.7	37	CCDS35216.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364865	0.82463	.	.	ENSG00000123130	ENST00000379303;ENST00000336430	T;T	0.35048	1.34;1.33	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	M	0.83118	2.625	0.80722	D	1	B;P	0.40398	0.345;0.716	B;B	0.35770	0.041;0.21	T	0.52298	-0.8594	10	0.41790	T	0.15	-6.5708	18.2181	0.89893	0.0:1.0:0.0:0.0	.	41;50	Q9Y305;Q9Y305-4	ACOT9_HUMAN;.	Q	50;41	ENSP00000368605:R50Q;ENSP00000336580:R41Q	ENSP00000336580:R41Q	R	-	2	0	ACOT9	23661252	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.108000	0.77055	2.239000	0.73571	0.600000	0.82982	CGA		0.368	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		T	23751331	C	T	23751331	3	4	47	1	0	0	0	0	1	0	0	0	157	884	31	1	1249	1	ACOT9	23	23751331	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3529144	23751331	131519229	2044	6441										
CXorf58	254158	broad.mit.edu	37	chrX	23956728	23956728	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcaaaatcaagttaaatttCtgggtcgtcgatccaagcaa	8	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:23956728C>A	ENST00000379211.3	+	8	1399	c.850C>A	c.(850-852)Ctg>Atg	p.L284M		NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	284								p.L284M(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						AGTTAAATTTCTGGGTCGTCG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											86	85	86					X																	23956728		2202	4300	6502	23866649	SO:0001583	missense	254158			AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.850C>A	X.37:g.23956728C>A	ENSP00000368511:p.Leu284Met		23866649		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311527	0.23821	.	.	ENSG00000165182	ENST00000379211	T	0.29917	1.55	4.76	-0.504	0.11997	.	0.563117	0.14962	N	0.288285	T	0.24736	0.0600	L	0.57536	1.79	0.09310	N	1	P;P	0.41102	0.6;0.738	B;B	0.40009	0.316;0.276	T	0.10894	-1.0610	10	0.34782	T	0.22	-0.0379	4.571	0.12210	0.4284:0.3919:0.0:0.1797	.	284;284	B7ZLS7;Q96LI9	.;CX058_HUMAN	M	284	ENSP00000368511:L284M	ENSP00000368511:L284M	L	+	1	2	CXorf58	23866649	0.020000	0.18652	0.000000	0.03702	0.049000	0.14656	0.506000	0.22658	-0.106000	0.12110	0.523000	0.50628	CTG		0.338	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761		A	23956728	C	A	23956728	3	1	47	1	0	0	0	0	1	0	0	0	4120	912	32	2	876	2	CXorf58	23	23956728	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	205397	23956728	131313832	2045	6442										
POLA1	5422	broad.mit.edu	37	chrX	24751927	24751927	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctttcaaagaagtcattgaGaaaaaggtaaagtgctcatt	9	5	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:24751927G>T	ENST00000379059.3	+	17	1824	c.1809G>T	c.(1807-1809)gaG>gaT	p.E603D	POLA1_ENST00000493342.1_3'UTR|POLA1_ENST00000379068.3_Missense_Mutation_p.E609D	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	603					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.E603D(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	AAGTCATTGAGAAAAAGGTAA	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	X											46	45	45					X																	24751927		2201	4295	6496	24661848	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1809G>T	X.37:g.24751927G>T	ENSP00000368349:p.Glu603Asp		24661848	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	G	6.693	0.496510	0.12762	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.40756	1.02;1.02	4.81	-1.07	0.09968	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.497273	0.24054	N	0.041974	T	0.18173	0.0436	N	0.10809	0.05	0.09310	N	1	B	0.16396	0.017	B	0.20577	0.03	T	0.08994	-1.0695	10	0.38643	T	0.18	0.0	4.0849	0.09943	0.312:0.0:0.2758:0.4122	.	603	P09884	DPOLA_HUMAN	D	609;603	ENSP00000368358:E609D;ENSP00000368349:E603D	ENSP00000368349:E603D	E	+	3	2	POLA1	24661848	0.995000	0.38212	0.000000	0.03702	0.215000	0.24574	0.777000	0.26718	-0.154000	0.11118	0.422000	0.28245	GAG		0.338	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24751927	G	T	24751927	3	4	47	1	0	0	0	0	1	0	0	0	12218	933	33	2	1875	2	POLA1	23	24751927	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	795199	24751927	130518633	2046	6443										
IL1RAPL1	11141	broad.mit.edu	37	chrX	29301120	29301120	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttggtgggagagcctgttCgaatcaaatgtgcactcttt	11	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:29301120C>T	ENST00000378993.1	+	3	821	c.148C>T	c.(148-150)Cga>Tga	p.R50*	IL1RAPL1_ENST00000302196.4_Nonsense_Mutation_p.R50*	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	50	Ig-like C2-type 1.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.R50*(2)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						AGAGCCTGTTCGAATCAAATG	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											143	126	132					X																	29301120		2202	4300	6502	29211041	SO:0001587	stop_gained	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.148C>T	X.37:g.29301120C>T	ENSP00000368278:p.Arg50*		29211041	A0AVG4|Q9UJ53	Nonsense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	C	43	9.909426	0.99293	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	.	.	.	5.51	4.62	0.57501	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	13.7032	0.62622	0.1586:0.8414:0.0:0.0	.	.	.	.	X	50	.	ENSP00000305200:R50X	R	+	1	2	IL1RAPL1	29211041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.745000	0.38278	1.161000	0.42604	0.600000	0.82982	CGA		0.413	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29301120	C	T	29301120	4	4	47	1	0	0	0	0	0	1	0	0	7682	876	31	1	154	1	IL1RAPL1	23	29301120	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	4549193	29301120	125969440	2047	6444										
IL1RAPL1	11141	broad.mit.edu	37	chrX	29414495	29414495	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacttagcaaaagcaaggaAatttcatgccgtgacataga	9	7	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:29414495A>C	ENST00000378993.1	+	4	1156	c.483A>C	c.(481-483)gaA>gaC	p.E161D	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.E161D	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	161	Ig-like C2-type 2.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.E161D(2)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						AAAGCAAGGAAATTTCATGCC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	X											113	107	109					X																	29414495		2202	4300	6502	29324416	SO:0001583	missense	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.483A>C	X.37:g.29414495A>C	ENSP00000368278:p.Glu161Asp		29324416	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419734	0.25552	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.77620	-1.11;-1.11	5.26	1.48	0.22813	Immunoglobulin subtype (1);	0.116150	0.56097	D	0.000021	T	0.64405	0.2595	L	0.39397	1.21	0.27308	N	0.957389	B	0.11235	0.004	B	0.16289	0.015	T	0.49908	-0.8889	9	.	.	.	.	8.0377	0.30502	0.752:0.0:0.248:0.0	.	161	Q9NZN1	IRPL1_HUMAN	D	161	ENSP00000368278:E161D;ENSP00000305200:E161D	.	E	+	3	2	IL1RAPL1	29324416	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.090000	0.30902	0.228000	0.21019	0.417000	0.27973	GAA		0.403	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		C	29414495	A	C	29414495	3	2	47	1	0	0	0	0	1	0	0	0	7682	11	1	4	493	4	IL1RAPL1	23	29414495	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	113375	29414495	125856065	2048	6445										
TAB3	257397	broad.mit.edu	37	chrX	30864739	30864739	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagttgtctgttcatgcttCtcaatcttgtcatttcctca	7	10	6	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:30864739C>A	ENST00000378933.1	-	5	1910	c.1733G>T	c.(1732-1734)aGa>aTa	p.R578I	TAB3_ENST00000288422.2_Missense_Mutation_p.R578I|TAB3_ENST00000378930.3_Missense_Mutation_p.R578I|TAB3_ENST00000378932.2_Missense_Mutation_p.R578I|TAB3_ENST00000378928.1_Missense_Mutation_p.R29I	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	578					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.R578I(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						GTTCATGCTTCTCAATCTTGT	0.373																																					Pancreas(164;1598 1985 29022 43301 49529)											1	Substitution - Missense(1)	large_intestine(1)	X											192	160	171					X																	30864739		2202	4300	6502	30774660	SO:0001583	missense	257397			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.1733G>T	X.37:g.30864739C>A	ENSP00000368215:p.Arg578Ile		30774660	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970344	0.92919	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932;ENST00000378928	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.97110	1.0;0.991	D	0.91249	0.5028	10	0.87932	D	0	-4.4184	18.0063	0.89210	0.0:1.0:0.0:0.0	.	578;578	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	I	578;578;578;578;29	ENSP00000368215:R578I;ENSP00000368212:R578I;ENSP00000288422:R578I;ENSP00000368214:R578I	ENSP00000288422:R578I	R	-	2	0	TAB3	30774660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.648000	0.67930	2.186000	0.69663	0.538000	0.68166	AGA		0.373	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		A	30864739	C	A	30864739	3	1	47	1	0	0	0	0	1	0	0	0	15536	913	32	2	421	2	TAB3	23	30864739	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1450244	30864739	124405821	2049	6446										
DMD	1756	broad.mit.edu	37	chrX	32361363	32361363	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtactgataccactgatgaGaaatttctagagcctttttt	7	7	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:32361363G>T	ENST00000357033.4	-	40	5833	c.5627C>A	c.(5626-5628)tCt>tAt	p.S1876Y	DMD_ENST00000378677.2_Missense_Mutation_p.S1872Y	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1876	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.S1871Y(1)|p.S1872Y(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CCACTGATGAGAAATTTCTAG	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	X											108	98	101					X																	32361363		2202	4300	6502	32271284	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5627C>A	X.37:g.32361363G>T	ENSP00000354923:p.Ser1876Tyr		32271284	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.504634	0.64410	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000493412	T;T;T	0.59083	0.29;0.29;0.29	5.92	5.92	0.95590	.	0.000000	0.37095	U	0.002258	T	0.58864	0.2152	N	0.08118	0	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.998;0.995;0.995	D;D;D;P;P	0.68943	0.961;0.915;0.915;0.88;0.88	T	0.62798	-0.6778	10	0.31617	T	0.26	.	19.2285	0.93827	0.0:0.0:1.0:0.0	.	1868;1876;1872;535;532	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	Y	1868;535;532;1872;1876;1876;1753;95	ENSP00000367948:S1872Y;ENSP00000354923:S1876Y;ENSP00000417725:S95Y	ENSP00000354923:S1876Y	S	-	2	0	DMD	32271284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.537000	0.90631	2.493000	0.84123	0.594000	0.82650	TCT		0.388	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32361363	G	T	32361363	3	4	47	1	0	0	0	0	1	0	0	0	4591	942	33	2	5738	2	DMD	23	32361363	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1496624	32361363	122909197	2050	6447										
DMD	1756	broad.mit.edu	37	chrX	32662382	32662382	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagcttacttcccaattgtaGaatattaccaacccggccct	5	14	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:32662382G>T	ENST00000357033.4	-	11	1404	c.1198C>A	c.(1198-1200)Cta>Ata	p.L400I	DMD_ENST00000288447.4_Missense_Mutation_p.L392I|DMD_ENST00000378677.2_Missense_Mutation_p.L396I|MIR548F5_ENST00000408421.1_RNA	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	400					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L396I(1)|p.L395I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CCCAATTGTAGAATATTACCA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	X											131	112	118					X																	32662382		2202	4300	6502	32572303	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.1198C>A	X.37:g.32662382G>T	ENSP00000354923:p.Leu400Ile		32572303	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990965	0.54041	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	T;T;T	0.51574	0.7;0.7;0.7	5.73	4.86	0.63082	.	0.000000	0.28036	U	0.016850	T	0.67088	0.2856	M	0.86740	2.835	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.984;0.999	D;D;D;D	0.87578	0.998;0.996;0.986;0.998	T	0.70773	-0.4781	10	0.59425	D	0.04	.	4.862	0.13588	0.3178:0.0:0.6821:0.0	.	392;392;400;396	Q4G0X0;P11532-4;P11532;E9PDN5	.;.;DMD_HUMAN;.	I	392;396;400;400;277;392	ENSP00000367948:L396I;ENSP00000354923:L400I;ENSP00000288447:L392I	ENSP00000288447:L392I	L	-	1	2	DMD	32572303	1.000000	0.71417	0.892000	0.35008	0.178000	0.23041	6.121000	0.71602	2.435000	0.82474	0.591000	0.81541	CTA		0.393	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32662382	G	T	32662382	3	4	47	1	0	0	0	0	1	0	0	0	4591	933	33	2	10378	2	DMD	23	32662382	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	301019	32662382	122608178	2051	6448										
FAM47A	158724	broad.mit.edu	37	chrX	34150200	34150200	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcgacaaacgagagtatcttCgggagacggacagccgtagc	14	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:34150200C>T	ENST00000346193.3	-	1	247	c.196G>A	c.(196-198)Gaa>Aaa	p.E66K		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	66								p.E66K(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						AGAGTATCTTCGGGAGACGGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	X											82	79	80					X																	34150200		2202	4300	6502	34060121	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.196G>A	X.37:g.34150200C>T	ENSP00000345029:p.Glu66Lys		34060121	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257576	0.39896	.	.	ENSG00000185448	ENST00000346193	T	0.19806	2.12	1.17	1.17	0.20885	.	.	.	.	.	T	0.14570	0.0352	L	0.46741	1.465	0.09310	N	1	P	0.41159	0.74	B	0.35240	0.198	T	0.14839	-1.0458	9	0.33940	T	0.23	.	5.3637	0.16101	0.0:1.0:0.0:0.0	.	66	Q5JRC9	FA47A_HUMAN	K	66	ENSP00000345029:E66K	ENSP00000345029:E66K	E	-	1	0	FAM47A	34060121	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.167000	0.16602	0.880000	0.35969	0.544000	0.68410	GAA		0.552	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34150200	C	T	34150200	3	4	47	1	0	0	0	0	1	0	0	0	5588	893	31	1	2183	1	FAM47A	23	34150200	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1487818	34150200	121120360	2052	6449										
CXorf22	170063	broad.mit.edu	37	chrX	35993965	35993965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taatcgtcagaattgttgtgCtcagtttcaatggcaacccg	9	9	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:35993965C>T	ENST00000297866.5	+	15	2714	c.2648C>T	c.(2647-2649)gCt>gTt	p.A883V		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	883								p.A883V(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AATTGTTGTGCTCAGTTTCAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											168	151	157					X																	35993965		2202	4300	6502	35903886	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2648C>T	X.37:g.35993965C>T	ENSP00000297866:p.Ala883Val		35903886	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463312	0.26248	.	.	ENSG00000165164	ENST00000297866	T	0.20738	2.05	5.31	4.43	0.53597	.	0.053920	0.64402	N	0.000001	T	0.19327	0.0464	L	0.52905	1.665	0.09310	N	0.999993	P	0.50710	0.938	P	0.45377	0.478	T	0.09400	-1.0676	10	0.02654	T	1	-7.2283	9.8937	0.41304	0.0:0.8943:0.0:0.1057	.	883	Q6ZTR5	CX022_HUMAN	V	883	ENSP00000297866:A883V	ENSP00000297866:A883V	A	+	2	0	CXorf22	35903886	0.417000	0.25432	0.018000	0.16275	0.008000	0.06430	1.143000	0.31553	0.967000	0.38186	0.600000	0.82982	GCT		0.378	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		T	35993965	C	T	35993965	3	4	47	1	0	0	0	0	1	0	0	0	4108	797	28	3	2706	3	CXorf22	23	35993965	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1843765	35993965	119276595	2053	6450										
XK	7504	broad.mit.edu	37	chrX	37587406	37587406	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcttttcaagactgacatCtatatgtatgtgtgcgcacc	7	9	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:37587406C>A	ENST00000378616.3	+	3	1229	c.1026C>A	c.(1024-1026)atC>atA	p.I342I	TM4SF2_ENST00000465127.1_Intron	NM_021083.2	NP_066569.1	P51811	XK_HUMAN	X-linked Kx blood group	342					amino acid transport (GO:0006865)|transport (GO:0006810)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.I342I(1)		breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		all_lung(315;0.175)				AGACTGACATCTATATGTATG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	X											156	139	144					X																	37587406		2202	4300	6502	37472345	SO:0001819	synonymous_variant	7504			Z32684	CCDS14241.1	Xp21.1	2014-07-19	2014-06-18		ENSG00000047597	ENSG00000047597		"Blood group antigens"	12811	protein-coding gene	gene with protein product	"Kx antigen", "McLeod syndrome"	314850	"Kell blood group precursor (McLeod phenotype)", "XK, Kell blood group complex subunit (McLeod syndrome)", "neuroacanthocytosis", "neurocanthocytosis"	NA, NAC		8004674, 11761473	Standard	NM_021083		Approved	XKR1, Kx, X1k	uc004ddq.3	P51811	OTTHUMG00000033171	ENST00000378616.3:c.1026C>A	X.37:g.37587406C>A			37472345	Q4TTN6|Q8IUK6|Q9UC77	Silent	SNP	ENST00000378616.3	37	CCDS14241.1																																																																																				0.453	XK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080875.1	NM_021083		A	37587406	C	A	37587406	2	1	47	1	0	0	0	0	0	0	0	1	17471	903	32	2		2	XK	23	37587406	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1593441	37587406	117683154	2054	6451										
CYBB	1536	broad.mit.edu	37	chrX	37651246	37651246	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtgctgctcaacaagagttCgaagacaactggacaggaat	11	8	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:37651246C>T	ENST00000378588.4	+	4	338	c.271C>T	c.(271-273)Cga>Tga	p.R91*	CYBB_ENST00000536160.1_5'UTR|CYBB_ENST00000545017.1_Nonsense_Mutation_p.R59*|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	91	Ferric oxidoreductase.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)	p.R91*(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AACAAGAGTTCGAAGACAACT	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	X	GRCh37	CM960436	CYBB	M							119	104	109					X																	37651246		2202	4300	6502	37536186	SO:0001587	stop_gained	1536			X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"Cytochrome b genes"	2578	protein-coding gene	gene with protein product		300481	"chronic granulomatous disease"	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.271C>T	X.37:g.37651246C>T	ENSP00000367851:p.Arg91*		37536186	A8K138|Q2PP16	Nonsense_Mutation	SNP	ENST00000378588.4	37	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	C	37	6.114353	0.97296	.	.	ENSG00000165168	ENST00000378588;ENST00000545017	.	.	.	5.87	3.96	0.45880	.	0.137493	0.46442	D	0.000295	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.9743	0.53083	0.5639:0.4361:0.0:0.0	.	.	.	.	X	91;59	.	ENSP00000367851:R91X	R	+	1	2	CYBB	37536186	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	2.097000	0.41748	1.193000	0.43086	0.594000	0.82650	CGA		0.383	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			T	37651246	C	T	37651246	4	4	47	1	0	0	0	0	0	1	0	0	4139	876	31	1	285	1	CYBB	23	37651246	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	63840	37651246	117619314	2055	6452										
RPGR	6103	broad.mit.edu	37	chrX	38158349	38158349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatttcttttgccacaccacGatgaggagcagcaaaaacta	7	10	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:38158349G>A	ENST00000339363.3	-	10	1272	c.1105C>T	c.(1105-1107)Cgt>Tgt	p.R369C	RPGR_ENST00000338898.3_Missense_Mutation_p.R369C|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.R369C|RPGR_ENST00000342811.3_Missense_Mutation_p.R369C|RPGR_ENST00000318842.7_Missense_Mutation_p.R369C|RPGR_ENST00000309513.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	369					cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)	p.R369C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						GCCACACCACGATGAGGAGCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											97	71	80					X																	38158349		2202	4300	6502	38043293	SO:0001583	missense	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1105C>T	X.37:g.38158349G>A	ENSP00000343671:p.Arg369Cys		38043293	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	G	15.39	2.820378	0.50633	.	.	ENSG00000156313	ENST00000339363;ENST00000338898;ENST00000318842;ENST00000342811;ENST00000378505	T;T;T;T;T	0.51325	1.3;0.71;2.13;1.31;1.31	5.14	-0.189	0.13260	.	1.778700	0.03233	N	0.179277	T	0.43433	0.1247	N	0.08118	0	0.09310	N	1	D;D	0.63880	0.993;0.992	P;P	0.59703	0.835;0.862	T	0.35992	-0.9766	10	0.56958	D	0.05	.	6.0155	0.19601	0.0729:0.365:0.4345:0.1276	.	369;369	E9PE28;Q92834-2	.;.	C	369	ENSP00000343671:R369C;ENSP00000340208:R369C;ENSP00000322219:R369C;ENSP00000339531:R369C;ENSP00000367766:R369C	ENSP00000322219:R369C	R	-	1	0	RPGR	38043293	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.562000	0.23531	-0.216000	0.10048	-0.235000	0.12190	CGT		0.403	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		A	38158349	G	A	38158349	3	1	47	1	0	0	0	0	1	0	0	0	13585	1058	37	1	2936	1	RPGR	23	38158349	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	507103	38158349	117112211	2056	6453										
MID1IP1	58526	broad.mit.edu	37	chrX	38664317	38664317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtgcccagcttgctgcgcGacgtgcccctggctgacccc	13	17	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:38664317G>A	ENST00000336949.6	+	2	1063	c.118G>A	c.(118-120)Gac>Aac	p.D40N	MID1IP1_ENST00000378474.3_Missense_Mutation_p.D40N|MID1IP1-AS1_ENST00000436893.1_RNA|MID1IP1_ENST00000457894.1_Missense_Mutation_p.D40N	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN	MID1 interacting protein 1	40					lipid metabolic process (GO:0006629)|negative regulation of microtubule depolymerization (GO:0007026)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of ligase activity (GO:0051351)|protein polymerization (GO:0051258)|regulation of lipid biosynthetic process (GO:0046890)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.D40N(1)		kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						CTTGCTGCGCGACGTGCCCCT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	X											81	55	64					X																	38664317		2202	4300	6502	38549261	SO:0001583	missense	58526				CCDS14249.1	Xp11.4	2012-02-23	2012-02-23		ENSG00000165175	ENSG00000165175			20715	protein-coding gene	gene with protein product	"gastrulation specific G12 homolog (zebrafish)"		"MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish))"				Standard	NM_001098790		Approved	STRAIT11499, FLJ10386, MIG12, THRSPL, G12-like	uc010ngz.3	Q9NPA3	OTTHUMG00000024092	ENST00000336949.6:c.118G>A	X.37:g.38664317G>A	ENSP00000338706:p.Asp40Asn		38549261	D3DWB2	Missense_Mutation	SNP	ENST00000336949.6	37	CCDS14249.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529746	0.85706	.	.	ENSG00000165175	ENST00000457894;ENST00000378474;ENST00000336949	.	.	.	4.84	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.79644	0.4481	M	0.85373	2.75	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.82149	-0.0600	9	0.87932	D	0	-11.9323	11.9075	0.52721	0.0875:0.0:0.9125:0.0	.	40	Q9NPA3	M1IP1_HUMAN	N	40	.	ENSP00000338706:D40N	D	+	1	0	MID1IP1	38549261	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.054000	0.93866	1.035000	0.39972	0.529000	0.55759	GAC		0.632	MID1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060655.1			A	38664317	G	A	38664317	3	1	47	1	0	0	0	0	1	0	0	0	9607	1058	37	1	120	1	MID1IP1	23	38664317	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	505968	38664317	116606243	2057	6454										
BCOR	54880	broad.mit.edu	37	chrX	39914628	39914628	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aactttgtcatacctgttaaGaacttttccataagttcact	4	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:39914628G>T	ENST00000378444.4	-	12	4962	c.4734C>A	c.(4732-4734)ttC>ttA	p.F1578L	BCOR_ENST00000342274.4_Missense_Mutation_p.F1544L|BCOR_ENST00000378463.1_Missense_Mutation_p.F421L|BCOR_ENST00000397354.3_Missense_Mutation_p.F1544L|BCOR_ENST00000378455.4_Missense_Mutation_p.F1526L	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1578					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.F1544L(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TACCTGTTAAGAACTTTTCCA	0.378			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		1	Substitution - Missense(1)	large_intestine(1)	X											96	85	89					X																	39914628		2202	4300	6502	39799572	SO:0001583	missense	54880			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4734C>A	X.37:g.39914628G>T	ENSP00000367705:p.Phe1578Leu		39799572	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.99|16.99	3.274207|3.274207	0.59649|0.59649	.|.	.|.	ENSG00000183337|ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018|ENST00000427012	T;T;T;T;T;T;T|.	0.69685|.	-0.42;0.97;1.06;1.04;1.02;1.04;-0.37|.	5.53|5.53	-0.751|-0.751	0.11076|0.11076	Ankyrin repeat-containing domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.68265|0.68265	0.2982|0.2982	M|M	0.72118|0.72118	2.19|2.19	0.51482|0.51482	D|D	0.999926|0.999926	D;D;D|.	0.76494|.	0.999;0.994;0.999|.	D;D;D|.	0.85130|.	0.997;0.977;0.997|.	T|T	0.66101|0.66101	-0.6007|-0.6007	9|5	0.36615|.	T|.	0.2|.	-15.5601|-15.5601	12.2164|12.2164	0.54408|0.54408	0.383:0.0:0.617:0.0|0.383:0.0:0.617:0.0	.|.	1526;1578;1544|.	Q6W2J9-4;Q6W2J9;Q6W2J9-2|.	.;BCOR_HUMAN;.|.	L|Y	448;421;1526;1544;1578;1544;251|273	ENSP00000408006:F448L;ENSP00000367724:F421L;ENSP00000367716:F1526L;ENSP00000380512:F1544L;ENSP00000367705:F1578L;ENSP00000345923:F1544L;ENSP00000387552:F251L|.	ENSP00000345923:F1544L|.	F|S	-|-	3|2	2|0	BCOR|BCOR	39799572|39799572	1.000000|1.000000	0.71417|0.71417	0.203000|0.203000	0.23512|0.23512	0.822000|0.822000	0.46500|0.46500	1.024000|1.024000	0.30077|0.30077	-0.273000|-0.273000	0.09246|0.09246	-0.340000|-0.340000	0.08031|0.08031	TTC|TCT		0.378	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39914628	G	T	39914628	3	4	47	1	0	0	0	0	1	0	0	0	1387	933	33	2	549	2	BCOR	23	39914628	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1250311	39914628	115355932	2058	6455										
USP9X	8239	broad.mit.edu	37	chrX	40996156	40996156	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacttcttgccatggccttaAatcctcattgcaaattccat	4	12	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:40996156A>C	ENST00000324545.8	+	6	1168	c.535A>C	c.(535-537)Aat>Cat	p.N179H	USP9X_ENST00000378308.2_Missense_Mutation_p.N179H	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	179					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.N172H(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CATGGCCTTAAATCCTCATTG	0.428																																					Ovarian(172;1807 2695 35459 49286)											1	Substitution - Missense(1)	large_intestine(1)	X											160	138	145					X																	40996156		2203	4300	6503	40881100	SO:0001583	missense	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.535A>C	X.37:g.40996156A>C	ENSP00000316357:p.Asn179His		40881100	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394391	0.83011	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.04194	3.68;3.68	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.987	T	0.00425	-1.1747	10	0.87932	D	0	.	14.2447	0.65981	1.0:0.0:0.0:0.0	.	179;179	Q93008-1;Q93008	.;USP9X_HUMAN	H	179	ENSP00000367558:N179H;ENSP00000316357:N179H	ENSP00000316357:N179H	N	+	1	0	USP9X	40881100	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	1.743000	0.51761	0.437000	0.28790	AAT		0.428	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		C	40996156	A	C	40996156	3	2	47	1	0	0	0	0	1	0	0	0	17130	14	1	4	553	4	USP9X	23	40996156	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1081528	40996156	114274404	2059	6456										
EFHC2	80258	broad.mit.edu	37	chrX	44094668	44094668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gactagttttgcaaaaaaacGgagtatattgcttttggagc	10	5	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:44094668G>A	ENST00000420999.1	-	9	1389	c.1306C>T	c.(1306-1308)Cgt>Tgt	p.R436C		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	436	DM10 3. {ECO:0000255|PROSITE- ProRule:PRU00665}.						calcium ion binding (GO:0005509)	p.R436C(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						GCAAAAAAACGGAGTATATTG	0.348													G|||	1	0.000264901	0	0.0014	3775	,	,		13254	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											57	51	53					X																	44094668		1838	4080	5918	43979612	SO:0001583	missense	80258			AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1306C>T	X.37:g.44094668G>A	ENSP00000404232:p.Arg436Cys		43979612	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	14.42|14.42|14.42	2.528607|2.528607|2.528607	0.44969|0.44969|0.44969	.|.|.	.|.|.	ENSG00000183690|ENSG00000183690|ENSG00000183690	ENST00000378056|ENST00000441230|ENST00000333807;ENST00000420999	.|.|T;T	.|.|0.75938	.|.|-0.96;-0.98	5.61|5.61|5.61	5.61|5.61|5.61	0.85477|0.85477|0.85477	.|.|Uncharacterised domain DM10 (2);	.|.|0.139782	.|.|0.46145	.|.|D	.|.|0.000307	.|D|D	.|0.87245|0.87245	.|0.6129|0.6129	M|M|M	0.84156|0.84156|0.84156	2.68|2.68|2.68	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D	.|.|0.89917	.|.|1.0	.|.|D	.|.|0.81914	.|.|0.995	.|D|D	.|0.88926|0.88926	.|0.3369|0.3369	.|5|10	.|.|0.72032	.|.|D	.|.|0.01	.|-10.7512|-10.7512	16.8203|16.8203|16.8203	0.85744|0.85744|0.85744	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|436	.|.|Q5JST6	.|.|EFHC2_HUMAN	.|L|C	-1|416|436;464	.|.|ENSP00000333823:R436C;ENSP00000404232:R464C	.|.|ENSP00000333823:R436C	.|P|R	-|-|-	.|2|1	.|0|0	EFHC2|EFHC2|EFHC2	43979612|43979612|43979612	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.453000|0.453000|0.453000	0.27007|0.27007|0.27007	0.097000|0.097000|0.097000	0.18754|0.18754|0.18754	6.066000|6.066000|6.066000	0.71185|0.71185|0.71185	2.348000|2.348000|2.348000	0.79779|0.79779|0.79779	0.597000|0.597000|0.597000	0.82753|0.82753|0.82753	.|CCG|CGT		0.348	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		A	44094668	G	A	44094668	3	1	47	1	0	0	0	0	1	0	0	0	4958	1116	39	1	971	1	EFHC2	23	44094668	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3098512	44094668	111175892	2060	6457										
ZNF673	55634	broad.mit.edu	37	chrX	46332295	46332295	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaaggatgaaagcggtcaaGaatccagaacatgtagaaaa	11	5	1	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:46332295G>A	ENST00000344302.4	+	6	995	c.364G>A	c.(364-366)Gaa>Aaa	p.E122K	KRBOX4_ENST00000298190.6_Missense_Mutation_p.E117K|KRBOX4_ENST00000487081.1_3'UTR|KRBOX4_ENST00000360017.5_3'UTR|KRBOX4_ENST00000478600.1_Intron	NM_001129898.1|NM_017776.2	NP_001123370.1|NP_060246.2	Q5JUW0	KRBX4_HUMAN	KRAB box domain containing 4	122					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.E117K(1)									AAGCGGTCAAGAATCCAGAAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	91	96					X																	46332295		2203	4300	6503	46217239	SO:0001583	missense	55634				CCDS14267.1, CCDS48097.1, CCDS48098.1	Xp11.3	2013-01-08	2013-01-08	2013-01-08	ENSG00000147121	ENSG00000147121		"-"	26007	protein-coding gene	gene with protein product	"hypothetical protein FLJ20344"	300585	"zinc finger protein 673", "zinc finger family member 673"	ZNF673		11944989	Standard	NM_001129898		Approved	FLJ20344	uc004dgn.4	Q5JUW0	OTTHUMG00000021421	ENST00000344302.4:c.364G>A	X.37:g.46332295G>A	ENSP00000345797:p.Glu122Lys		46217239	A8K0Y8|B3KU22|Q96EA3|Q9NXB1	Missense_Mutation	SNP	ENST00000344302.4	37	CCDS48097.1	.	.	.	.	.	.	.	.	.	.	G	9.075	0.997944	0.19043	.	.	ENSG00000147121	ENST00000344302;ENST00000298190;ENST00000397212	T;T	0.00808	5.67;5.85	2.68	2.68	0.31781	.	.	.	.	.	T	0.00998	0.0033	N	0.17474	0.49	0.80722	D	1	P;P	0.41947	0.655;0.766	B;P	0.45971	0.303;0.499	T	0.79669	-0.1707	9	0.19590	T	0.45	.	10.4216	0.44354	0.0:0.0:1.0:0.0	.	122;117	Q5JUW0;Q5JUW0-2	ZN673_HUMAN;.	K	122;117;122	ENSP00000345797:E122K;ENSP00000298190:E117K	ENSP00000298190:E117K	E	+	1	0	ZNF673	46217239	0.002000	0.14202	0.438000	0.26821	0.455000	0.32408	0.426000	0.21363	1.338000	0.45544	0.422000	0.28245	GAA		0.398	KRBOX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056359.2	NM_017776		A	46332295	G	A	46332295	3	1	47	1	0	0	0	0	1	0	0	0	18119	943	33	3	426	3	ZNF673	23	46332295	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2237627	46332295	108938265	2061	6458										
ZNF674	641339	broad.mit.edu	37	chrX	46359514	46359514	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgacttcctactgaaggcttTtttacagtcagtgcattcat	7	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:46359514T>G	ENST00000523374.1	-	6	1720	c.1510A>C	c.(1510-1512)Aaa>Caa	p.K504Q	ZNF674_ENST00000518795.1_5'Flank|ZNF674_ENST00000414387.2_Missense_Mutation_p.K498Q	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	504					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						CTGAAGGCTTTTTTACAGTCA	0.403																																																0			X											75	68	70					X																	46359514		2166	4278	6444	46244458	SO:0001583	missense	641339			AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"Zinc fingers, C2H2-type", "-"	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.1510A>C	X.37:g.46359514T>G	ENSP00000429148:p.Lys504Gln		46244458	B4DHE2|E9PHQ4	Missense_Mutation	SNP	ENST00000523374.1	37	CCDS48099.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.776932	0.31411	.	.	ENSG00000251192	ENST00000523374;ENST00000414387	T;T	0.27256	1.68;1.68	2.33	2.33	0.28932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48696	0.1514	M	0.81497	2.545	0.24490	N	0.994305	D;D	0.76494	0.999;0.973	D;P	0.79784	0.993;0.685	T	0.21245	-1.0251	9	0.87932	D	0	.	7.894	0.29695	0.0:0.0:0.0:1.0	.	498;504	E9PHQ4;Q2M3X9	.;ZN674_HUMAN	Q	504;498	ENSP00000429148:K504Q;ENSP00000428248:K498Q	ENSP00000428248:K498Q	K	-	1	0	ZNF674	46244458	0.999000	0.42202	0.022000	0.16811	0.071000	0.16799	3.175000	0.50855	1.193000	0.43086	0.430000	0.28490	AAA		0.403	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056357.2	NM_001039891		G	46359514	T	G	46359514	3	3	47	1	0	0	0	0	1	0	0	0	18120	1850	64	4	239	4	ZNF674	23	46359514	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	27219	46359514	108911046	2062	6459										
PHF16	9767	broad.mit.edu	37	chrX	46917620	46917620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	actgttttacccaccaccaaGaattaccttgaagttaaaaa	4	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:46917620G>T	ENST00000218343.4	+	11	1911	c.1613G>T	c.(1612-1614)aGa>aTa	p.R538I	PHF16_ENST00000397189.1_Missense_Mutation_p.R538I	NM_014735.3	NP_055550.1												p.R538I(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CCACCACCAAGAATTACCTTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											85	81	82					X																	46917620		2203	4300	6503	46802564	SO:0001583	missense	9767																														ENST00000218343.4:c.1613G>T	X.37:g.46917620G>T	ENSP00000218343:p.Arg538Ile		46802564		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.780948	0.70222	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.56776	0.44;0.44	5.88	5.02	0.67125	.	0.082552	0.85682	D	0.000000	T	0.67702	0.2921	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	D	0.67103	0.949	T	0.68262	-0.5455	10	0.46703	T	0.11	.	14.034	0.64634	0.074:0.0:0.926:0.0	.	538	Q92613	JADE3_HUMAN	I	538	ENSP00000380373:R538I;ENSP00000218343:R538I	ENSP00000218343:R538I	R	+	2	0	PHF16	46802564	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.545000	0.82128	1.230000	0.43646	0.600000	0.82982	AGA		0.423	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			T	46917620	G	T	46917620	3	4	47	1	0	0	0	0	1	0	0	0	11858	942	33	2	1651	2	PHF16	23	46917620	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	558106	46917620	108352940	2063	6460										
CDK16	5127	broad.mit.edu	37	chrX	47083885	47083885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctccagtgagagtgcgtatgCgcaaccatcccccacgcaag	10	15	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:47083885C>T	ENST00000357227.4	+	3	728	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	CDK16_ENST00000518022.1_Missense_Mutation_p.R102C|CDK16_ENST00000457458.2_Missense_Mutation_p.R108C|CDK16_ENST00000276052.6_Missense_Mutation_p.R176C	NM_006201.4	NP_006192.1	Q00536	CDK16_HUMAN	cyclin-dependent kinase 16	102					exocytosis (GO:0006887)|growth hormone secretion (GO:0030252)|neuron projection development (GO:0031175)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|spermatogenesis (GO:0007283)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein serine/threonine kinase activity (GO:0004674)	p.R102C(2)		breast(1)|endometrium(3)|large_intestine(4)|lung(3)	11						AGTGCGTATGCGCAACCATCC	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	X											106	67	80					X																	47083885		2203	4300	6503	46968829	SO:0001583	missense	5127				CCDS14276.1, CCDS48101.1, CCDS55408.1	Xp11	2011-11-08	2009-12-16	2009-12-16	ENSG00000102225	ENSG00000102225		"Cyclin-dependent kinases"	8749	protein-coding gene	gene with protein product	"serine/threonine-protein kinase"	311550	"PCTAIRE protein kinase 1"	PCTK1		1437147, 19884882	Standard	NM_033018		Approved	PCTAIRE, PCTAIRE1, PCTGAIRE, FLJ16665	uc011mll.2	Q00536	OTTHUMG00000021438	ENST00000357227.4:c.304C>T	X.37:g.47083885C>T	ENSP00000349762:p.Arg102Cys		46968829	A8K280|B7Z7C8|J3KN74|J3KQP7	Missense_Mutation	SNP	ENST00000357227.4	37	CCDS14276.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911228	0.72983	.	.	ENSG00000102225	ENST00000457458;ENST00000357227;ENST00000519758;ENST00000520893;ENST00000540877;ENST00000540311;ENST00000517426;ENST00000518391;ENST00000518022;ENST00000276052	T;T;T;T;T;T	0.74526	-0.66;-0.65;-0.85;0.43;-0.65;-0.7	5.96	4.17	0.49024	.	0.055231	0.64402	D	0.000002	T	0.81721	0.4882	M	0.71036	2.16	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.998;0.998	P;P;P;P	0.61275	0.886;0.836;0.799;0.841	T	0.81376	-0.0961	10	0.87932	D	0	-8.4029	9.416	0.38521	0.1435:0.7792:0.0:0.0774	.	176;102;200;102	B7Z7C8;B7Z461;B7Z8T0;Q00536	.;.;.;CDK16_HUMAN	C	108;102;102;102;200;54;102;102;102;176	ENSP00000405798:R108C;ENSP00000349762:R102C;ENSP00000429985:R102C;ENSP00000429044:R102C;ENSP00000429751:R102C;ENSP00000276052:R176C	ENSP00000276052:R176C	R	+	1	0	CDK16	46968829	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.006000	0.29847	0.611000	0.30052	0.600000	0.82982	CGC		0.587	CDK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056406.2	NM_006201		T	47083885	C	T	47083885	3	4	47	1	0	0	0	0	1	0	0	0	3138	768	27	1	552	1	CDK16	23	47083885	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	166265	47083885	108186675	2064	6461										
ARAF	369	broad.mit.edu	37	chrX	47424488	47424488	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tacaagttccaccagcattgTtcctccaaggtccccacagt	6	15	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:47424488T>C	ENST00000377045.4	+	5	602	c.408T>C	c.(406-408)tgT>tgC	p.C136C	ARAF_ENST00000290277.6_Silent_p.C136C|ARAF_ENST00000377039.2_Silent_p.C136C	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	136					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.C136C(1)		biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	ACCAGCATTGTTCCTCCAAGG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	X											115	85	95					X																	47424488		2203	4300	6503	47309432	SO:0001819	synonymous_variant	369			X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.408T>C	X.37:g.47424488T>C			47309432	P07557|Q5H9B2|Q5H9B3	Silent	SNP	ENST00000377045.4	37	CCDS35232.1																																																																																				0.572	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			C	47424488	T	C	47424488	2	2	47	1	0	0	0	0	0	0	0	1	837	1731	60	4		4	ARAF	23	47424488	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	340603	47424488	107846072	2065	6462										
ZNF81	347344	broad.mit.edu	37	chrX	47775514	47775514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaactccagatgcataagaGaattcatacaggagagaaac	8	8	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:47775514G>T	ENST00000376954.1	+	6	1837	c.1469G>T	c.(1468-1470)aGa>aTa	p.R490I	ZNF81_ENST00000338637.7_Missense_Mutation_p.R490I			P51508	ZNF81_HUMAN	zinc finger protein 81	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R490I(1)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				ATGCATAAGAGAATTCATACA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											43	43	43					X																	47775514		2201	4296	6497	47660458	SO:0001583	missense	347344			AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"Zinc fingers, C2H2-type", "-"	13156	protein-coding gene	gene with protein product		314998	"zinc finger protein 81 (HFZ20)", "mental retardation, X-linked 45"	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.1469G>T	X.37:g.47775514G>T	ENSP00000366153:p.Arg490Ile		47660458	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.227190	0.58668	.	.	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.24908	1.83;1.83	3.96	3.96	0.45880	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34133	N	0.004234	T	0.42223	0.1193	L	0.61218	1.895	0.40405	D	0.979681	D	0.89917	1.0	D	0.79784	0.993	T	0.36016	-0.9765	10	0.62326	D	0.03	.	6.6912	0.23171	0.1278:0.0:0.8722:0.0	.	490	P51508	ZNF81_HUMAN	I	490	ENSP00000366153:R490I;ENSP00000341151:R490I	ENSP00000341151:R490I	R	+	2	0	ZNF81	47660458	0.213000	0.23551	1.000000	0.80357	0.979000	0.70002	2.941000	0.49011	2.237000	0.73441	0.544000	0.68410	AGA		0.408	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137		T	47775514	G	T	47775514	3	4	47	1	0	0	0	0	1	0	0	0	18213	942	33	2	1483	2	ZNF81	23	47775514	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	351026	47775514	107495046	2066	6463										
ZNF182	7569	broad.mit.edu	37	chrX	47836137	47836137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtttctctcctgaatgagttCtctgatgtacaccaaggttt	8	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:47836137C>A	ENST00000396965.1	-	7	1699	c.1349G>T	c.(1348-1350)aGa>aTa	p.R450I	ZNF182_ENST00000305127.6_Missense_Mutation_p.R450I|ZNF182_ENST00000376943.3_Missense_Mutation_p.R431I	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	450					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R450I(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						TGAATGAGTTCTCTGATGTAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											63	56	58					X																	47836137		2203	4300	6503	47721081	SO:0001583	missense	7569			AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"Zinc fingers, C2H2-type", "-"	13001	protein-coding gene	gene with protein product		314993	"zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)"	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.1349G>T	X.37:g.47836137C>A	ENSP00000380165:p.Arg450Ile		47721081	A2IDD7|Q3KP67|Q96QH7	Missense_Mutation	SNP	ENST00000396965.1	37	CCDS35236.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815093	0.50527	.	.	ENSG00000147118	ENST00000376943;ENST00000396965;ENST00000305127	T;T;T	0.02446	4.29;4.29;4.29	4.47	4.47	0.54385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10121	0.0248	L	0.58354	1.805	0.47737	D	0.999507	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.998	T	0.00589	-1.1656	9	0.87932	D	0	.	7.5705	0.27904	0.0:0.8823:0.0:0.1177	.	430;431;450	B4DRM0;Q96QH7;P17025	.;.;ZN182_HUMAN	I	431;450;450	ENSP00000366142:R431I;ENSP00000380165:R450I;ENSP00000306351:R450I	ENSP00000306351:R450I	R	-	2	0	ZNF182	47721081	0.005000	0.15991	0.999000	0.59377	0.977000	0.68977	1.826000	0.39092	2.208000	0.71279	0.544000	0.68410	AGA		0.428	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962		A	47836137	C	A	47836137	3	1	47	1	0	0	0	0	1	0	0	0	17789	913	32	2	574	2	ZNF182	23	47836137	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	60623	47836137	107434423	2067	6464										
WDR13	64743	broad.mit.edu	37	chrX	48460469	48460469	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcagggaagctgaccaaagcCaagcgtttggtggtgcatga	15	8	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:48460469C>A	ENST00000218056.5	+	7	1534	c.1029C>A	c.(1027-1029)gcC>gcA	p.A343A	WDR13_ENST00000376729.5_Silent_p.A343A	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	343						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A343A(2)		endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TGACCAAAGCCAAGCGTTTGG	0.647																																																2	Substitution - coding silent(2)	large_intestine(2)	X											70	53	59					X																	48460469		2203	4300	6503	48345413	SO:0001819	synonymous_variant	64743			AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.1029C>A	X.37:g.48460469C>A			48345413	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Silent	SNP	ENST00000218056.5	37	CCDS14302.1																																																																																				0.647	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			A	48460469	C	A	48460469	2	1	47	1	0	0	0	0	0	0	0	1	17315	581	21	2		2	WDR13	23	48460469	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	624332	48460469	106810091	2068	6465										
GRIPAP1	56850	broad.mit.edu	37	chrX	48847485	48847485	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggccctcactgacagctgaGaacttcccggcttctttccc	8	16	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:48847485G>T	ENST00000376441.1	-	7	529	c.495C>A	c.(493-495)ttC>ttA	p.F165L	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.F165L|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.F120L|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.F112L	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	165						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.F165L(1)|p.F112L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TGACAGCTGAGAACTTCCCGG	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	X											31	28	29					X																	48847485		2203	4297	6500	48732429	SO:0001583	missense	56850			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.495C>A	X.37:g.48847485G>T	ENSP00000365624:p.Phe165Leu		48732429	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	G	2.828	-0.243320	0.05906	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	4.6	-0.616	0.11583	.	1.418770	0.04137	N	0.318921	T	0.09992	0.0245	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.09377	0.003;0.004;0.003	T	0.25813	-1.0121	10	0.25751	T	0.34	7.0375	3.6516	0.08205	0.223:0.0:0.3963:0.3807	.	112;55;165	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	L	165;120;165;165;112	ENSP00000365608:F165L;ENSP00000365627:F120L;ENSP00000365624:F165L;ENSP00000365606:F112L	ENSP00000365606:F112L	F	-	3	2	GRIPAP1	48732429	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.173000	0.16724	-0.116000	0.11893	-0.255000	0.11280	TTC		0.612	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		T	48847485	G	T	48847485	3	4	47	1	0	0	0	0	1	0	0	0	6810	933	33	2	2164	2	GRIPAP1	23	48847485	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	387016	48847485	106423075	2069	6466										
CLCN5	1184	broad.mit.edu	37	chrX	49851224	49851224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gcctggtgtcggaagcgaaaGaccacccagttgggcaagta	14	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:49851224G>T	ENST00000307367.2	+	8	1335	c.1044G>T	c.(1042-1044)aaG>aaT	p.K348N	CLCN5_ENST00000376091.3_Missense_Mutation_p.K418N|CLCN5_ENST00000376108.3_Missense_Mutation_p.K348N|CLCN5_ENST00000376088.3_Missense_Mutation_p.K418N			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	348					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.K348N(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					GGAAGCGAAAGACCACCCAGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	X											110	87	95					X																	49851224		2203	4300	6503	49737964	SO:0001583	missense	1184			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1044G>T	X.37:g.49851224G>T	ENSP00000304257:p.Lys348Asn		49737964	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Missense_Mutation	SNP	ENST00000307367.2	37	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.913937	0.52439	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46	5.7	3.91	0.45181	Chloride channel, core (2);	0.044743	0.85682	D	0.000000	D	0.94666	0.8280	M	0.73372	2.23	0.58432	D	0.999999	B;P	0.51351	0.148;0.944	B;P	0.52957	0.232;0.714	D	0.92749	0.6214	10	0.56958	D	0.05	0.1161	7.8198	0.29282	0.2691:0.0:0.7309:0.0	.	348;418	P51795;P51795-2	CLCN5_HUMAN;.	N	418;250;418;348;348	ENSP00000365256:K418N;ENSP00000365259:K418N;ENSP00000365276:K348N;ENSP00000304257:K348N	ENSP00000304257:K348N	K	+	3	2	CLCN5	49737964	1.000000	0.71417	0.984000	0.44739	0.791000	0.44710	4.145000	0.58065	0.561000	0.29186	0.436000	0.28706	AAG		0.507	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			T	49851224	G	T	49851224	3	4	47	1	0	0	0	0	1	0	0	0	3472	933	33	2	1288	2	CLCN5	23	49851224	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1003739	49851224	105419336	2070	6467										
AKAP4	8852	broad.mit.edu	37	chrX	49961560	49961560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	accttagactggtctttcttCtcagtgtccttgatcacgat	7	11	4	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:49961560C>A	ENST00000376056.2	-	4	381	c.231G>T	c.(229-231)gaG>gaT	p.E77D	AKAP4_ENST00000376064.3_Missense_Mutation_p.E77D|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.E77D|AKAP4_ENST00000358526.2_Missense_Mutation_p.E86D					A kinase (PRKA) anchor protein 4									p.E86D(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					GGTCTTTCTTCTCAGTGTCCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											248	194	213					X																	49961560		2203	4300	6503	49848300	SO:0001583	missense	8852			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.231G>T	X.37:g.49961560C>A	ENSP00000365224:p.Glu77Asp		49848300		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669276	0.29604	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064;ENST00000448865;ENST00000437370	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	4.57	-0.672	0.11377	.	0.000000	0.40222	N	0.001155	T	0.26666	0.0652	M	0.68317	2.08	0.20196	N	0.999925	B;B	0.32467	0.048;0.372	B;B	0.26969	0.015;0.075	T	0.12091	-1.0561	9	.	.	.	-6.9981	4.4576	0.11650	0.0:0.4341:0.1601:0.4059	.	86;77	Q5JQC9;A6ND82	AKAP4_HUMAN;.	D	77;77;86;77;77;77	ENSP00000365224:E77D;ENSP00000365226:E77D;ENSP00000351327:E86D;ENSP00000365232:E77D;ENSP00000402403:E77D;ENSP00000412279:E77D	.	E	-	3	2	AKAP4	49848300	0.998000	0.40836	0.904000	0.35570	0.635000	0.38103	0.160000	0.16462	-0.587000	0.05890	0.513000	0.50165	GAG		0.438	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		A	49961560	C	A	49961560	3	1	47	1	0	0	0	0	1	0	0	0	453	912	32	2	2318	2	AKAP4	23	49961560	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	110336	49961560	105309000	2071	6468										
CCNB3	85417	broad.mit.edu	37	chrX	50053969	50053969	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgaagatatgatagctctgAatgagaaacccaccactggg	10	9	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:50053969A>C	ENST00000376042.1	+	6	3098	c.2800A>C	c.(2800-2802)Aat>Cat	p.N934H	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.N934H			Q8WWL7	CCNB3_HUMAN	cyclin B3	934					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)		p.N934H(2)		breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					GATAGCTCTGAATGAGAAACC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	X											85	79	81					X																	50053969		2203	4300	6503	50070709	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2800A>C	X.37:g.50053969A>C	ENSP00000365210:p.Asn934His		50070709	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	A	7.073	0.568681	0.13560	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.17854	2.25;2.25	3.34	-6.67	0.01783	.	37.836400	0.00166	N	0.000000	T	0.17323	0.0416	L	0.38175	1.15	0.09310	N	1	D	0.61080	0.989	P	0.47673	0.554	T	0.40156	-0.9578	9	.	.	.	.	9.5556	0.39337	0.1643:0.6368:0.1989:0.0	.	934	Q8WWL7	CCNB3_HUMAN	H	934	ENSP00000365210:N934H;ENSP00000276014:N934H	.	N	+	1	0	CCNB3	50070709	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-4.549000	0.00217	-2.529000	0.00492	-0.496000	0.04628	AAT		0.453	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			C	50053969	A	C	50053969	3	2	47	1	0	0	0	0	1	0	0	0	2920	246	9	4	2814	4	CCNB3	23	50053969	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	92409	50053969	105216591	2072	6469										
NUDT11	55190	broad.mit.edu	37	chrX	51239150	51239150	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcctcgggctccatgcccccGcccggcacgatccagcggtc	11	20	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:51239150G>A	ENST00000375992.3	-	1	298	c.147C>T	c.(145-147)ggC>ggT	p.G49G		NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 11	49	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)	p.G49G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9	Ovarian(276;0.236)					CCATGCCCCCGCCCGGCACGA	0.687										HNSCC(48;0.14)																											GBM(38;198 791 1498 11752 13599)											1	Substitution - coding silent(1)	large_intestine(1)	X											15	19	18					X																	51239150		2178	4263	6441	51255890	SO:0001819	synonymous_variant	55190			AK001490	CCDS43952.1	Xp11.22-p11.1	2014-05-20			ENSG00000196368	ENSG00000196368		"Nudix motif containing"	18011	protein-coding gene	gene with protein product						12105228	Standard	NM_018159		Approved	DIPP3b, FLJ10628, hDIPP3beta	uc010njt.3	Q96G61	OTTHUMG00000021531	ENST00000375992.3:c.147C>T	X.37:g.51239150G>A			51255890	Q9NVN0	Silent	SNP	ENST00000375992.3	37	CCDS43952.1																																																																																				0.687	NUDT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056579.1			A	51239150	G	A	51239150	2	1	47	1	0	0	0	0	0	0	0	1	10758	1074	38	1		1	NUDT11	23	51239150	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1185181	51239150	104031410	2073	6470										
PHF8	23133	broad.mit.edu	37	chrX	54040961	54040961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttcgacccatgacagctttCgaacaatcttcggtgtctcc	7	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54040961C>T	ENST00000357988.5	-	7	1098	c.740G>A	c.(739-741)cGa>cAa	p.R247Q	PHF8_ENST00000338946.6_Missense_Mutation_p.R211Q|PHF8_ENST00000338154.6_Missense_Mutation_p.R211Q|PHF8_ENST00000322659.8_Missense_Mutation_p.R211Q	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	247	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.R211Q(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						TGACAGCTTTCGAACAATCTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	X											111	74	86					X																	54040961		2203	4300	6503	54057686	SO:0001583	missense	23133			AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.740G>A	X.37:g.54040961C>T	ENSP00000350676:p.Arg247Gln		54057686	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Missense_Mutation	SNP	ENST00000357988.5	37	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.9|22.9	4.353794|4.353794	0.82243|0.82243	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000396282|ENST00000357988;ENST00000338154;ENST00000338946;ENST00000396277;ENST00000322659	.|T;T;T;T	.|0.70749	.|-0.51;-0.51;-0.51;-0.51	5.35|5.35	5.35|5.35	0.76521|0.76521	.|Transcription factor jumonji/aspartyl beta-hydroxylase (2);	.|0.056066	.|0.64402	.|D	.|0.000001	T|T	0.67258|0.67258	0.2874|0.2874	L|L	0.46947|0.46947	1.48|1.48	0.58432|0.58432	D|D	0.999999|0.999999	.|P;P;D	.|0.62365	.|0.862;0.915;0.991	.|B;B;B	.|0.43331	.|0.059;0.125;0.416	T|T	0.70335|0.70335	-0.4900|-0.4900	5|10	.|0.45353	.|T	.|0.12	-10.2179|-10.2179	16.8548|16.8548	0.86003|0.86003	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|211;247;247	.|B7Z911;Q9UPP1-3;Q9UPP1	.|.;.;PHF8_HUMAN	K|Q	115|247;211;211;241;211	.|ENSP00000350676:R247Q;ENSP00000338868:R211Q;ENSP00000340051:R211Q;ENSP00000319473:R211Q	.|ENSP00000319473:R211Q	E|R	-|-	1|2	0|0	PHF8|PHF8	54057686|54057686	0.975000|0.975000	0.34042|0.34042	0.999000|0.999000	0.59377|0.59377	0.967000|0.967000	0.64934|0.64934	2.725000|2.725000	0.47294|0.47294	2.241000|2.241000	0.73720|0.73720	0.494000|0.494000	0.49563|0.49563	GAA|CGA		0.463	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		T	54040961	C	T	54040961	3	4	47	1	0	0	0	0	1	0	0	0	11871	884	31	1	2676	1	PHF8	23	54040961	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2801811	54040961	101229599	2074	6471										
WNK3	65267	broad.mit.edu	37	chrX	54337635	54337635	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	atagattcccaggaatcataAaatcgaactatattggggtg	9	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54337635A>C	ENST00000375159.2	-	2	626	c.627T>G	c.(625-627)ttT>ttG	p.F209L	WNK3_ENST00000375169.3_Missense_Mutation_p.F209L|WNK3_ENST00000354646.2_Missense_Mutation_p.F209L			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F209L(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AGGAATCATAAAATCGAACTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											103	91	95					X																	54337635		2203	4300	6503	54354360	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.627T>G	X.37:g.54337635A>C	ENSP00000364301:p.Phe209Leu		54354360	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	19.76	3.887238	0.72410	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.17054	2.3;2.3;2.3	5.18	1.41	0.22369	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000014	T	0.20618	0.0496	N	0.17594	0.5	0.34655	D	0.722098	D;D	0.58620	0.983;0.969	D;D	0.68192	0.925;0.956	T	0.20338	-1.0278	10	0.59425	D	0.04	-14.78	8.67	0.34145	0.7446:0.0:0.2554:0.0	.	209;209	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	L	209	ENSP00000364312:F209L;ENSP00000346667:F209L;ENSP00000364301:F209L	ENSP00000346667:F209L	F	-	3	2	WNK3	54354360	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.856000	0.39389	0.233000	0.21120	0.486000	0.48141	TTT		0.388	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		C	54337635	A	C	54337635	3	2	47	1	0	0	0	0	1	0	0	0	17419	11	1	4	4863	4	WNK3	23	54337635	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	296674	54337635	100932925	2075	6472										
FGD1	2245	broad.mit.edu	37	chrX	54495270	54495270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggccttctcagtttgcaggaGctcattggcaatgtgaaaca	11	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54495270G>A	ENST00000375135.3	-	5	1874	c.1141C>T	c.(1141-1143)Ctc>Ttc	p.L381F		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	381	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.L381F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTTTGCAGGAGCTCATTGGCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	75	87					X																	54495270		2203	4300	6503	54511995	SO:0001583	missense	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.1141C>T	X.37:g.54495270G>A	ENSP00000364277:p.Leu381Phe		54511995	Q5H999|Q8N4D9	Missense_Mutation	SNP	ENST00000375135.3	37	CCDS14359.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482897	0.84747	.	.	ENSG00000102302	ENST00000375135	T	0.78246	-1.16	5.33	5.33	0.75918	Dbl homology (DH) domain (5);	0.000000	0.46145	D	0.000310	D	0.90556	0.7040	M	0.91038	3.17	0.52099	D	0.999949	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.92741	0.6208	10	0.87932	D	0	-19.468	16.8196	0.85742	0.0:0.0:1.0:0.0	.	139;381	B4DS99;P98174	.;FGD1_HUMAN	F	381	ENSP00000364277:L381F	ENSP00000364277:L381F	L	-	1	0	FGD1	54511995	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.696000	0.84270	2.232000	0.73038	0.422000	0.28245	CTC		0.542	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		A	54495270	G	A	54495270	3	1	47	1	0	0	0	0	1	0	0	0	5851	971	34	3	1800	3	FGD1	23	54495270	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	157635	54495270	100775290	2076	6473										
MAGED2	10916	broad.mit.edu	37	chrX	54841721	54841721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaatgggcagctcagtaccGagaggcgatggaagcggatt	17	7	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54841721G>A	ENST00000375068.1	+	12	1660	c.1427G>A	c.(1426-1428)cGa>cAa	p.R476Q	MAGED2_ENST00000218439.4_Missense_Mutation_p.R476Q|MAGED2_ENST00000375060.1_Missense_Mutation_p.R391Q|MAGED2_ENST00000396224.1_Missense_Mutation_p.R476Q|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375058.1_Missense_Mutation_p.R476Q|MAGED2_ENST00000375062.4_Missense_Mutation_p.R391Q|MAGED2_ENST00000347546.4_Missense_Mutation_p.R458Q|MAGED2_ENST00000375053.2_Missense_Mutation_p.R476Q			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	476	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					membrane (GO:0016020)		p.R476Q(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						GCTCAGTACCGAGAGGCGATG	0.507													G|||	1	0.000264901	8e-04	0	3775	,	,		14098	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											41	41	41					X																	54841721		2202	4298	6500	54858446	SO:0001583	missense	10916			AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated protein", "breast cancer associated gene 1", "melanoma-associated antigen D2", "hepatocellular carcinoma-associated protein HCA10"	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1427G>A	X.37:g.54841721G>A	ENSP00000364209:p.Arg476Gln		54858446	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030460	0.35797	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.44482	4.06;4.06;4.15;4.06;0.92;4.06;4.06;0.92;4.06	4.73	3.84	0.44239	.	0.000000	0.37012	N	0.002288	T	0.21881	0.0527	N	0.14661	0.345	0.33789	D	0.625204	B;B	0.33494	0.274;0.414	B;B	0.31101	0.087;0.124	T	0.27226	-1.0080	10	0.34782	T	0.22	.	7.1708	0.25717	0.2031:0.0:0.7969:0.0	.	391;476	Q5H907;Q9UNF1	.;MAGD2_HUMAN	Q	476;476;420;458;391;476;476;391;476	ENSP00000364209:R476Q;ENSP00000364193:R476Q;ENSP00000336962:R420Q;ENSP00000340290:R458Q;ENSP00000364202:R391Q;ENSP00000218439:R476Q;ENSP00000364198:R476Q;ENSP00000364200:R391Q;ENSP00000379526:R476Q	ENSP00000218439:R476Q	R	+	2	0	MAGED2	54858446	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.314000	0.33597	2.098000	0.63641	0.513000	0.50165	CGA		0.507	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		A	54841721	G	A	54841721	3	1	47	1	0	0	0	0	1	0	0	0	9214	1058	37	1	1469	1	MAGED2	23	54841721	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	346451	54841721	100428839	2077	6474										
TRO	7216	broad.mit.edu	37	chrX	54956783	54956783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gttaagcaccaatgctggatTtggtggtggactgaacacca	12	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54956783T>C	ENST00000173898.7	+	12	3738	c.3626T>C	c.(3625-3627)tTt>tCt	p.F1209S	TRO_ENST00000399736.1_Intron|TRO_ENST00000319167.8_Intron|TRO_ENST00000375022.4_Intron|TRO_ENST00000375041.2_Missense_Mutation_p.F812S|TRO_ENST00000420798.2_Missense_Mutation_p.F740S|SNORA11_ENST00000408823.1_RNA	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	1209	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.F1209S(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						AATGCTGGATTTGGTGGTGGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											58	57	57					X																	54956783		2061	4183	6244	54973508	SO:0001583	missense	7216			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.3626T>C	X.37:g.54956783T>C	ENSP00000173898:p.Phe1209Ser		54973508	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.883577	0.33255	.	.	ENSG00000067445	ENST00000173898;ENST00000420798;ENST00000375041	T;T;T	0.09445	2.98;2.98;2.98	2.62	1.44	0.22558	.	.	.	.	.	T	0.20129	0.0484	L	0.50333	1.59	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.66979	0.925;0.948	T	0.10245	-1.0638	9	0.87932	D	0	.	3.8587	0.08986	0.0:0.1871:0.0:0.8129	.	812;1209	B1AKE9;Q12816	.;TROP_HUMAN	S	1209;740;812	ENSP00000173898:F1209S;ENSP00000405126:F740S;ENSP00000364181:F812S	ENSP00000173898:F1209S	F	+	2	0	TRO	54973508	0.000000	0.05858	0.012000	0.15200	0.011000	0.07611	-0.188000	0.09642	0.307000	0.22880	0.376000	0.23039	TTT		0.542	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		C	54956783	T	C	54956783	3	2	47	1	0	0	0	0	1	0	0	0	16614	1841	64	4	3668	4	TRO	23	54956783	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	115062	54956783	100313777	2078	6475										
PFKFB1	5207	broad.mit.edu	37	chrX	54982637	54982637	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgacctcatagcactcaattCtctttagaaagtcttccaga	5	11	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:54982637C>A	ENST00000375006.3	-	7	657	c.587G>T	c.(586-588)aGa>aTa	p.R196I	PFKFB1_ENST00000374992.2_Intron|PFKFB1_ENST00000545676.1_Missense_Mutation_p.R131I	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	196	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)	p.R196I(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						GCACTCAATTCTCTTTAGAAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	X											112	94	100					X																	54982637		2203	4300	6503	54999362	SO:0001583	missense	5207				CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.587G>T	X.37:g.54982637C>A	ENSP00000364145:p.Arg196Ile		54999362	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	37	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.419189	0.83559	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	.	.	.	4.65	3.78	0.43462	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	D	0.88407	0.6428	H	0.98980	4.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91743	0.5406	9	0.87932	D	0	-12.7489	12.8287	0.57735	0.1655:0.8345:0.0:0.0	.	131;196	B4DUN5;P16118	.;F261_HUMAN	I	196;131	.	ENSP00000364145:R196I	R	-	2	0	PFKFB1	54999362	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.585000	0.82584	1.037000	0.40024	0.600000	0.82982	AGA		0.473	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			A	54982637	C	A	54982637	3	1	47	1	0	0	0	0	1	0	0	0	11791	913	32	2	860	2	PFKFB1	23	54982637	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	25854	54982637	100287923	2079	6476										
FAM123B	139285	broad.mit.edu	37	chrX	63411546	63411546	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggacaaaaagggctcaaagtTtaagaaggggtcaaacatct	11	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:63411546T>G	ENST00000330258.3	-	2	1893	c.1621A>C	c.(1621-1623)Aac>Cac	p.N541H	AMER1_ENST00000403336.1_Missense_Mutation_p.N541H|AMER1_ENST00000374869.3_Missense_Mutation_p.N541H	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	541					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.N541H(2)									GGCTCAAAGTTTAAGAAGGGG	0.507																																																69	Whole gene deletion(67)|Substitution - Missense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											51	50	50					X																	63411546		2203	4300	6503	63328271	SO:0001583	missense	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1621A>C	X.37:g.63411546T>G	ENSP00000329117:p.Asn541His		63328271	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	10.67	1.414861	0.25465	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.50813	0.74;0.73;0.74	4.97	2.49	0.30216	.	0.538293	0.18503	N	0.139295	T	0.36276	0.0961	L	0.51422	1.61	0.29095	N	0.881838	P	0.47350	0.894	B	0.41723	0.365	T	0.43540	-0.9385	10	0.72032	D	0.01	-6.73	2.2698	0.04087	0.2311:0.3455:0.0:0.4234	.	541	Q5JTC6	F123B_HUMAN	H	541	ENSP00000364003:N541H;ENSP00000329117:N541H;ENSP00000384722:N541H	ENSP00000329117:N541H	N	-	1	0	FAM123B	63328271	1.000000	0.71417	0.998000	0.56505	0.299000	0.27559	1.363000	0.34159	0.851000	0.35264	0.486000	0.48141	AAC		0.507	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63411546	T	G	63411546	3	3	47	1	0	0	0	0	1	0	0	0	5439	1841	64	4	1790	4	FAM123B	23	63411546	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	8428909	63411546	91859014	2080	6477										
FAM123B	139285	broad.mit.edu	37	chrX	63412118	63412118	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggtcccatctcggtttgctCtctggcccccagaggccatg	11	15	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:63412118C>T	ENST00000330258.3	-	2	1321	c.1049G>A	c.(1048-1050)aGa>aAa	p.R350K	AMER1_ENST00000403336.1_Missense_Mutation_p.R350K|AMER1_ENST00000374869.3_Missense_Mutation_p.R350K	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	350					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R350K(2)									TCGGTTTGCTCTCTGGCCCCC	0.522																																																69	Whole gene deletion(67)|Substitution - Missense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											160	141	148					X																	63412118		2203	4300	6503	63328843	SO:0001583	missense	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1049G>A	X.37:g.63412118C>T	ENSP00000329117:p.Arg350Lys		63328843	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	16.86	3.238688	0.58995	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.16457	2.34;2.34;2.34	5.18	5.18	0.71444	.	0.089481	0.49916	D	0.000132	T	0.21347	0.0514	N	0.20685	0.6	0.38599	D	0.950611	D	0.55385	0.971	P	0.62435	0.902	T	0.05852	-1.0860	10	0.14656	T	0.56	-17.0043	12.991	0.58618	0.0:1.0:0.0:0.0	.	350	Q5JTC6	F123B_HUMAN	K	350	ENSP00000364003:R350K;ENSP00000329117:R350K;ENSP00000384722:R350K	ENSP00000329117:R350K	R	-	2	0	FAM123B	63328843	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.979000	0.40608	2.566000	0.86566	0.529000	0.55759	AGA		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		T	63412118	C	T	63412118	3	4	47	1	0	0	0	0	1	0	0	0	5439	913	32	3	2362	3	FAM123B	23	63412118	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	572	63412118	91858442	2081	6478										
ZC3H12B	340554	broad.mit.edu	37	chrX	64719098	64719098	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagcggttgctgatgtattCttttgtgaatgacaagtgcg	14	5	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:64719098C>A	ENST00000338957.4	+	3	1035	c.968C>A	c.(967-969)tCt>tAt	p.S323Y	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.S312Y	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	323							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.S173Y(1)|p.S259Y(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTGATGTATTCTTTTGTGAAT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	X											44	40	41					X																	64719098		1859	4099	5958	64635823	SO:0001583	missense	340554			BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.968C>A	X.37:g.64719098C>A	ENSP00000340839:p.Ser323Tyr		64635823	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	37	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	C	18.45	3.626721	0.66901	.	.	ENSG00000102053	ENST00000338957;ENST00000423889;ENST00000218172	T;T	0.47528	0.84;0.84	5.19	5.19	0.71726	Ribonuclease Zc3h12a-like (1);	0.118510	0.64402	D	0.000015	T	0.76176	0.3951	M	0.92833	3.35	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.83129	-0.0114	10	0.87932	D	0	-17.2949	16.3038	0.82841	0.0:1.0:0.0:0.0	.	312	Q5HYM0	ZC12B_HUMAN	Y	323;312;259	ENSP00000340839:S323Y;ENSP00000408077:S312Y	ENSP00000218172:S259Y	S	+	2	0	ZC3H12B	64635823	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.828000	0.69307	2.159000	0.67721	0.513000	0.50165	TCT		0.363	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		A	64719098	C	A	64719098	3	1	47	1	0	0	0	0	1	0	0	0	17601	913	32	2	978	2	ZC3H12B	23	64719098	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1306980	64719098	90551462	2082	6479										
MSN	4478	broad.mit.edu	37	chrX	64951737	64951737	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatatctgaagattgctcaaGatctggagatgtatggtgtg	12	4	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:64951737G>T	ENST00000360270.5	+	6	761	c.589G>T	c.(589-591)Gat>Tat	p.D197Y		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	197	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.D197Y(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						GATTGCTCAAGATCTGGAGAT	0.493			T	ALK	ALCL																																		Dom	yes		X	Xq11.2-q12	4478	moesin		L	1	Substitution - Missense(1)	large_intestine(1)	X											149	128	135					X																	64951737		2203	4300	6503	64868462	SO:0001583	missense	4478			M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.589G>T	X.37:g.64951737G>T	ENSP00000353408:p.Asp197Tyr		64868462		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.865441	0.91511	.	.	ENSG00000147065	ENST00000360270	D	0.83335	-1.71	5.92	5.92	0.95590	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94275	0.8161	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95765	0.8804	10	0.87932	D	0	.	17.6359	0.88122	0.0:0.0:1.0:0.0	.	197	P26038	MOES_HUMAN	Y	197	ENSP00000353408:D197Y	ENSP00000353408:D197Y	D	+	1	0	MSN	64868462	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	9.760000	0.98935	2.492000	0.84095	0.600000	0.82982	GAT		0.493	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		T	64951737	G	T	64951737	3	4	47	1	0	0	0	0	1	0	0	0	9915	942	33	2	611	2	MSN	23	64951737	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	232639	64951737	90318823	2083	6480										
HEPH	9843	broad.mit.edu	37	chrX	65480093	65480093	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggagaccctcttcactgtttTttctcgaacaggtaagtcct	8	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:65480093T>G	ENST00000343002.2	+	18	3852	c.3188T>G	c.(3187-3189)tTt>tGt	p.F1063C	HEPH_ENST00000519389.1_Missense_Mutation_p.F1117C|HEPH_ENST00000419594.1_Missense_Mutation_p.F874C|HEPH_ENST00000374727.3_Missense_Mutation_p.F1066C|HEPH_ENST00000441993.2_Missense_Mutation_p.F1066C|HEPH_ENST00000336279.5_Missense_Mutation_p.F796C			Q9BQS7	HEPH_HUMAN	hephaestin	1063	Plastocyanin-like 6.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)	p.F1063C(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						TTCACTGTTTTTTCTCGAACA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	X											94	76	82					X																	65480093		2203	4300	6503	65396818	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.3188T>G	X.37:g.65480093T>G	ENSP00000343939:p.Phe1063Cys		65396818	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	T	21.1	4.100731	0.76983	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002	D;D;D;D;D;D	0.99706	-6.47;-6.47;-6.47;-6.47;-6.47;-6.47	4.81	4.81	0.61882	Cupredoxin (2);	0.891873	0.09660	N	0.772529	D	0.99127	0.9699	N	0.14661	0.345	0.46981	D	0.999271	P;D;P	0.57257	0.711;0.979;0.88	P;D;P	0.67231	0.704;0.95;0.838	D	0.96502	0.9372	10	0.62326	D	0.03	.	10.7601	0.46259	0.0:0.0:0.0:1.0	.	1117;874;1063	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	C	1117;1066;796;1066;874;1063	ENSP00000430620:F1117C;ENSP00000363859:F1066C;ENSP00000337418:F796C;ENSP00000411687:F1066C;ENSP00000413211:F874C;ENSP00000343939:F1063C	ENSP00000337418:F796C	F	+	2	0	HEPH	65396818	0.453000	0.25721	0.055000	0.19348	0.444000	0.32077	5.349000	0.66010	1.770000	0.52166	0.486000	0.48141	TTT		0.473	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		G	65480093	T	G	65480093	3	3	47	1	0	0	0	0	1	0	0	0	7075	1841	64	4	3424	4	HEPH	23	65480093	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	528356	65480093	89790467	2084	6481										
OPHN1	4983	broad.mit.edu	37	chrX	67421471	67421471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacagcttacctttcattagTttctatgtcaaaacagaacc	4	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:67421471T>C	ENST00000355520.5	-	11	1656	c.1015A>G	c.(1015-1017)Act>Gct	p.T339A	OPHN1_ENST00000540071.1_Missense_Mutation_p.T339A	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	339	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.T339A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						CTTTCATTAGTTTCTATGTCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X											184	139	154					X																	67421471		2203	4300	6503	67338196	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.1015A>G	X.37:g.67421471T>C	ENSP00000347710:p.Thr339Ala		67338196	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	T	3.464	-0.109274	0.06924	.	.	ENSG00000079482	ENST00000355520;ENST00000540071	T;T	0.48201	0.82;0.82	4.82	3.6	0.41247	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.050839	0.85682	N	0.000000	T	0.22627	0.0546	N	0.12637	0.245	0.50467	D	0.999873	B;B	0.10296	0.001;0.003	B;B	0.08055	0.002;0.003	T	0.13282	-1.0515	10	0.02654	T	1	.	8.161	0.31198	0.0:0.0988:0.0:0.9012	.	339;339	F5H2E3;O60890	.;OPHN1_HUMAN	A	339	ENSP00000347710:T339A;ENSP00000438617:T339A	ENSP00000347710:T339A	T	-	1	0	OPHN1	67338196	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.512000	0.53407	0.731000	0.32448	0.486000	0.48141	ACT		0.458	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		C	67421471	T	C	67421471	3	2	47	1	0	0	0	0	1	0	0	0	10906	1725	60	4	1449	4	OPHN1	23	67421471	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	1941378	67421471	87849089	2085	6482										
OPHN1	4983	broad.mit.edu	37	chrX	67652711	67652711	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgaagccttgcacttacttCtcatagcgctgataagcgcg	9	12	1	1	rs374573197		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:67652711C>A	ENST00000355520.5	-	2	793	c.152G>T	c.(151-153)aGa>aTa	p.R51I	OPHN1_ENST00000540071.1_Missense_Mutation_p.R51I	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	51					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.R51I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						GCACTTACTTCTCATAGCGCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	X											167	129	142					X																	67652711		2203	4300	6503	67569436	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.152G>T	X.37:g.67652711C>A	ENSP00000347710:p.Arg51Ile		67569436	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.989052	0.35131	.	.	ENSG00000079482	ENST00000355520;ENST00000540071	T;T	0.31510	1.49;1.49	4.59	3.73	0.42828	IRSp53/MIM homology domain (IMD) (1);	0.323521	0.32719	N	0.005727	T	0.27559	0.0677	M	0.64404	1.975	0.58432	D	0.999999	P;B;B	0.44195	0.828;0.38;0.396	B;B;B	0.38842	0.282;0.283;0.133	T	0.08066	-1.0740	10	0.87932	D	0	.	6.4549	0.21924	0.0:0.7767:0.0:0.2233	.	51;51;51	F5H2E3;Q6PCC1;O60890	.;.;OPHN1_HUMAN	I	51	ENSP00000347710:R51I;ENSP00000438617:R51I	ENSP00000347710:R51I	R	-	2	0	OPHN1	67569436	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	1.664000	0.37439	1.066000	0.40716	-0.322000	0.08575	AGA		0.507	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		A	67652711	C	A	67652711	3	1	47	1	0	0	0	0	1	0	0	0	10906	913	32	2	2348	2	OPHN1	23	67652711	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	231240	67652711	87617849	2086	6483										
IGBP1	3476	broad.mit.edu	37	chrX	69366635	69366635	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agaagagattgagagcattgAccaggaaataaagatcctga	11	5	0	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:69366635A>G	ENST00000342206.6	+	3	1134	c.635A>G	c.(634-636)gAc>gGc	p.D212G	IGBP1-AS2_ENST00000403371.2_RNA|IGBP1_ENST00000356413.4_Missense_Mutation_p.D212G			P78318	IGBP1_HUMAN	immunoglobulin (CD79A) binding protein 1	212					B cell activation (GO:0042113)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dephosphorylation (GO:0035306)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microtubule-based movement (GO:0060632)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	protein phosphatase type 2A regulator activity (GO:0008601)	p.D212G(1)		kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(2)	11						GAGAGCATTGACCAGGAAATA	0.423																																					NSCLC(167;1189 1558 6576 8216 30387 37980 41450)											1	Substitution - Missense(1)	large_intestine(1)	X											62	52	55					X																	69366635		2203	4300	6503	69283360	SO:0001583	missense	3476			Y08915	CCDS14396.1	Xq13.1-q13.3	2008-02-05			ENSG00000089289	ENSG00000089289			5461	protein-coding gene	gene with protein product	"alpha 4"	300139		IBP1		9441740	Standard	NM_001551		Approved		uc004dxw.3	P78318	OTTHUMG00000021767	ENST00000342206.6:c.635A>G	X.37:g.69366635A>G	ENSP00000363661:p.Asp212Gly		69283360	Q8TAB2	Missense_Mutation	SNP	ENST00000342206.6	37	CCDS14396.1	.	.	.	.	.	.	.	.	.	.	.	18.10	3.548764	0.65311	.	.	ENSG00000089289	ENST00000342206;ENST00000356413	T;T	0.42900	0.96;0.96	5.14	5.14	0.70334	.	0.133510	0.64402	D	0.000002	T	0.56834	0.2012	L	0.58969	1.84	0.50313	D	0.999864	D	0.69078	0.997	D	0.63957	0.92	T	0.60591	-0.7233	10	0.87932	D	0	.	11.9037	0.52699	1.0:0.0:0.0:0.0	.	212	P78318	IGBP1_HUMAN	G	212	ENSP00000363661:D212G;ENSP00000348784:D212G	ENSP00000363661:D212G	D	+	2	0	IGBP1	69283360	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.194000	0.72082	2.014000	0.59158	0.481000	0.45027	GAC		0.423	IGBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057052.1			G	69366635	A	G	69366635	3	3	47	1	0	0	0	0	1	0	0	0	7588	275	10	4	645	4	IGBP1	23	69366635	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	1713924	69366635	85903925	2087	6484										
RAB41	407	broad.mit.edu	37	chrX	69502681	69502681	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggaattgacttcttgtctaaGaccatgtacttggaggacca	10	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:69502681G>T	ENST00000307959.8	+	0	1292				RAB41_ENST00000374473.2_Missense_Mutation_p.K71N|RAB41_ENST00000276066.4_Missense_Mutation_p.K70N	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)						endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)		p.K71N(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						TCTTGTCTAAGACCATGTACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	X											205	166	179					X																	69502681		2203	4300	6503	69419406	SO:0001628	intergenic_variant	347517				CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768		X.37:g.69502681G>T			69419406	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Missense_Mutation	SNP	ENST00000307959.8	37	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.782134	0.49891	.	.	ENSG00000147127	ENST00000509895;ENST00000374473;ENST00000276066	T;T;T	0.81415	-1.49;-1.23;-1.23	4.22	1.35	0.21983	Small GTP-binding protein domain (1);	0.000000	0.64402	U	0.000010	D	0.88851	0.6549	M	0.91717	3.235	0.32811	D	0.501445	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	D	0.86784	0.1981	10	0.87932	D	0	.	4.711	0.12872	0.3098:0.1604:0.5298:0.0	.	70;71	Q5JT25-2;Q5JT25	.;RAB41_HUMAN	N	20;71;70	ENSP00000421643:K20N;ENSP00000363597:K71N;ENSP00000276066:K70N	ENSP00000276066:K70N	K	+	3	2	RAB41	69419406	1.000000	0.71417	0.005000	0.12908	0.842000	0.47809	0.948000	0.29096	0.047000	0.15862	0.513000	0.50165	AAG		0.433	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		T	69502681	G	T	69502681	1	4	47	0	1	0	0	0	0	0	0	0	12980	933	33	2		2	RAB41	23	69502681	IGR	SNP	G	TCGA-AG-3892-01A-01W-1073-09	136046	69502681	85767879	2088	6485										
KIF4A	24137	broad.mit.edu	37	chrX	69518977	69518977	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tatcagatttacaatgaagaAattttggatcttctatgccc	6	7	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:69518977A>C	ENST00000374403.3	+	5	523	c.441A>C	c.(439-441)gaA>gaC	p.E147D	KIF4A_ENST00000374388.3_Missense_Mutation_p.E147D	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	147	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E147D(1)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						ACAATGAAGAAATTTTGGATC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											69	60	63					X																	69518977		2203	4298	6501	69435702	SO:0001583	missense	24137			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.441A>C	X.37:g.69518977A>C	ENSP00000363524:p.Glu147Asp		69435702	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.776401	0.31411	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.76060	-0.99;-0.99	4.59	3.46	0.39613	Kinesin, motor domain (4);	0.466172	0.17947	N	0.156657	T	0.58652	0.2137	L	0.37850	1.14	0.29910	N	0.823641	B;B	0.17465	0.022;0.016	B;B	0.24974	0.057;0.026	T	0.53592	-0.8417	10	0.44086	T	0.13	.	0.1735	0.00116	0.3639:0.2348:0.1681:0.2332	.	147;147	O95239;O95239-2	KIF4A_HUMAN;.	D	147	ENSP00000363509:E147D;ENSP00000363524:E147D	ENSP00000363509:E147D	E	+	3	2	KIF4A	69435702	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.506000	0.22658	1.533000	0.49186	0.435000	0.28638	GAA		0.338	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		C	69518977	A	C	69518977	3	2	47	1	0	0	0	0	1	0	0	0	8324	11	1	4	455	4	KIF4A	23	69518977	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	16296	69518977	85751583	2089	6486										
GDPD2	54857	broad.mit.edu	37	chrX	69644908	69644908	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtatagctgccactggaggaAatgccccagagagaggatgc	14	9	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:69644908A>C	ENST00000374382.3	+	2	325	c.74A>C	c.(73-75)aAa>aCa	p.K25T	GDPD2_ENST00000453994.2_Missense_Mutation_p.K25T|GDPD2_ENST00000536730.1_Intron|GDPD2_ENST00000538649.1_Intron	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	25					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)	p.K25T(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					CACTGGAGGAAATGCCCCAGA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	X											24	17	20					X																	69644908		2202	4298	6500	69561633	SO:0001583	missense	54857			AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"osteoblast differentiation promoting factor"					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.74A>C	X.37:g.69644908A>C	ENSP00000363503:p.Lys25Thr		69561633	B4DRH4|B4DVC9|Q9NXJ6	Missense_Mutation	SNP	ENST00000374382.3	37	CCDS14402.1	.	.	.	.	.	.	.	.	.	.	A	12.63	1.995231	0.35226	.	.	ENSG00000130055	ENST00000453994;ENST00000374382	T;T	0.29917	1.55;1.55	5.25	2.71	0.32032	.	0.709430	0.14152	N	0.337970	T	0.17408	0.0418	N	0.22421	0.69	0.09310	N	1	B;B	0.15141	0.012;0.004	B;B	0.11329	0.006;0.004	T	0.28299	-1.0048	9	.	.	.	-2.2303	5.235	0.15441	0.5623:0.3437:0.094:0.0	.	25;25	B4DVC9;Q9HCC8	.;GDPD2_HUMAN	T	25	ENSP00000414019:K25T;ENSP00000363503:K25T	.	K	+	2	0	GDPD2	69561633	0.845000	0.29573	0.162000	0.22713	0.964000	0.63967	1.426000	0.34870	0.244000	0.21351	0.486000	0.48141	AAA		0.637	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711		C	69644908	A	C	69644908	3	2	47	1	0	0	0	0	1	0	0	0	6344	14	1	4	76	4	GDPD2	23	69644908	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	125931	69644908	85625652	2090	6487										
TEX11	56159	broad.mit.edu	37	chrX	69830386	69830386	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agtcaaaagtcgatccatttCtttcttcctaaaaataaaga	4	8	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:69830386C>A	ENST00000395889.2	-	22	1959	c.1804G>T	c.(1804-1806)Gaa>Taa	p.E602*	TEX11_ENST00000374333.2_Nonsense_Mutation_p.E587*|TEX11_ENST00000374320.2_Nonsense_Mutation_p.E277*|TEX11_ENST00000344304.3_Nonsense_Mutation_p.E602*	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	602					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.E587*(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					CGATCCATTTCTTTCTTCCTA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											130	129	130					X																	69830386		2203	4300	6503	69747111	SO:0001587	stop_gained	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1804G>T	X.37:g.69830386C>A	ENSP00000379226:p.Glu602*		69747111	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Nonsense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	C	32	5.184468	0.94885	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	.	.	.	4.08	2.27	0.28462	.	0.842741	0.10529	N	0.664031	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.2546	4.9891	0.14205	0.0:0.6664:0.2111:0.1225	.	.	.	.	X	587;602;277;602	.	.	E	-	1	0	TEX11	69747111	1.000000	0.71417	0.751000	0.31187	0.517000	0.34286	1.161000	0.31773	0.324000	0.23333	0.600000	0.82982	GAA		0.338	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			A	69830386	C	A	69830386	4	1	47	1	0	0	0	0	0	1	0	0	15813	922	32	2	1058	2	TEX11	23	69830386	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	185478	69830386	85440174	2091	6488										
MED12	9968	broad.mit.edu	37	chrX	70360705	70360705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcagcagcagcagatcctgCgggtaaggcactgggatttc	14	10	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:70360705C>T	ENST00000374080.3	+	42	6297	c.6265C>T	c.(6265-6267)Cgg>Tgg	p.R2089W	MED12_ENST00000374102.1_Missense_Mutation_p.R2088W|MED12_ENST00000333646.6_Missense_Mutation_p.R2092W|AL590764.1_ENST00000579622.1_RNA			Q93074	MED12_HUMAN	mediator complex subunit 12	2089	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R2089W(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					gcagATCCTGCGGGTAAGGCA	0.572			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																																Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	2	Substitution - Missense(2)	large_intestine(2)	X											23	25	24					X																	70360705		2168	4209	6377	70277430	SO:0001583	missense	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6265C>T	X.37:g.70360705C>T	ENSP00000363193:p.Arg2089Trp		70277430	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477279	0.44044	.	.	ENSG00000184634	ENST00000333646;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03	4.48	1.29	0.21616	.	2.487750	0.01159	N	0.006612	T	0.14614	0.0353	N	0.08118	0	0.28039	N	0.933811	P;D;P	0.53885	0.938;0.963;0.938	B;P;B	0.44561	0.265;0.453;0.265	T	0.17471	-1.0368	10	0.62326	D	0.03	0.0216	6.6946	0.23191	0.5019:0.3485:0.1496:0.0	.	1939;2088;2089	Q7Z3Z5;Q93074-3;Q93074	.;.;MED12_HUMAN	W	2092;2088;2089;2039;837	ENSP00000333125:R2092W;ENSP00000363215:R2088W;ENSP00000363193:R2089W;ENSP00000414203:R2039W;ENSP00000408388:R837W	ENSP00000333125:R2092W	R	+	1	2	MED12	70277430	0.438000	0.25602	0.923000	0.36655	0.977000	0.68977	-0.038000	0.12144	0.327000	0.23409	0.422000	0.28245	CGG		0.572	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		T	70360705	C	T	70360705	3	4	47	1	0	0	0	0	1	0	0	0	9458	759	27	1	6431	1	MED12	23	70360705	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	530319	70360705	84909855	2092	6489										
NLGN3	54413	broad.mit.edu	37	chrX	70384117	70384117	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacccccgccggatcactgtCtttggctcgggcattggtgc	13	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:70384117C>A	ENST00000358741.3	+	6	1155	c.852C>A	c.(850-852)gtC>gtA	p.V284V	NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000536169.1_Silent_p.V244V|NLGN3_ENST00000374051.3_Silent_p.V264V	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	284					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.V264V(1)		biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					GGATCACTGTCTTTGGCTCGG	0.582																																					Esophageal Squamous(103;760 1488 16849 22250 40351)											1	Substitution - coding silent(1)	large_intestine(1)	X											79	70	73					X																	70384117		2203	4300	6503	70300842	SO:0001819	synonymous_variant	54413			AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.852C>A	X.37:g.70384117C>A			70300842	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Silent	SNP	ENST00000358741.3	37	CCDS55441.1																																																																																				0.582	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		A	70384117	C	A	70384117	2	1	47	1	0	0	0	0	0	0	0	1	10494	900	32	2		2	NLGN3	23	70384117	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	23412	70384117	84886443	2093	6490										
TAF1	6872	broad.mit.edu	37	chrX	70617214	70617214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caagatttatcgcacgtttcGagatgaagaggggaaagagt	13	5	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:70617214G>A	ENST00000373790.4	+	23	3566	c.3515G>A	c.(3514-3516)cGa>cAa	p.R1172Q	TAF1_ENST00000423759.1_Missense_Mutation_p.R1193Q|TAF1_ENST00000276072.3_Missense_Mutation_p.R1193Q|TAF1_ENST00000449580.1_Missense_Mutation_p.R1172Q	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1172					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R1172Q(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CGCACGTTTCGAGATGAAGAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											181	126	145					X																	70617214		2203	4300	6503	70533939	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3515G>A	X.37:g.70617214G>A	ENSP00000362895:p.Arg1172Gln		70533939	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	17.14|17.14	3.312520|3.312520	0.60414|0.60414	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000483985|ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	.|T;T;T;T	.|0.17213	.|2.29;2.29;2.29;2.29	4.91|4.91	4.05|4.05	0.47172|0.47172	.|.	.|0.199527	.|0.46758	.|D	.|0.000269	T|T	0.16085|0.16085	0.0387|0.0387	L|L	0.41124|0.41124	1.26|1.26	0.45284|0.45284	D|D	0.998284|0.998284	.|B;B;B	.|0.30851	.|0.297;0.098;0.256	.|B;B;B	.|0.32533	.|0.147;0.015;0.08	T|T	0.03739|0.03739	-1.1008|-1.1008	5|10	.|0.42905	.|T	.|0.14	.|.	12.6353|12.6353	0.56679|0.56679	0.0819:0.0:0.9181:0.0|0.0819:0.0:0.9181:0.0	.|.	.|1172;1172;1193	.|P21675-4;P21675;P21675-2	.|.;TAF1_HUMAN;.	K|Q	83|1172;1172;1193;1193	.|ENSP00000362895:R1172Q;ENSP00000389000:R1172Q;ENSP00000406549:R1193Q;ENSP00000276072:R1193Q	.|ENSP00000276072:R1193Q	E|R	+|+	1|2	0|0	TAF1|TAF1	70533939|70533939	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.119000|5.119000	0.64679|0.64679	1.105000|1.105000	0.41606|0.41606	0.449000|0.449000	0.29647|0.29647	GAG|CGA		0.478	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70617214	G	A	70617214	3	1	47	1	0	0	0	0	1	0	0	0	15552	1058	37	1	3668	1	TAF1	23	70617214	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	233097	70617214	84653346	2094	6491										
OGT	8473	broad.mit.edu	37	chrX	70782802	70782802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgctgagcagtattccgagAaattggcttatatgccccac	9	10	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:70782802A>G	ENST00000373719.3	+	16	2300	c.2083A>G	c.(2083-2085)Aaa>Gaa	p.K695E	OGT_ENST00000373701.3_Missense_Mutation_p.K685E	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	695					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)	p.K685E(1)|p.K695E(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					GTATTCCGAGAAATTGGCTTA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	X											129	117	121					X																	70782802		2203	4300	6503	70699527	SO:0001583	missense	8473			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2083A>G	X.37:g.70782802A>G	ENSP00000362824:p.Lys695Glu		70699527	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	37	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377747	0.61735	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.17528	2.27;2.27	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	M	0.75777	2.31	0.80722	D	1	B;B;P	0.39071	0.447;0.394;0.658	B;B;P	0.46685	0.202;0.116;0.524	T	0.03025	-1.1081	10	0.36615	T	0.2	.	14.3726	0.66852	1.0:0.0:0.0:0.0	.	569;685;695	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	E	695;685	ENSP00000362824:K695E;ENSP00000362805:K685E	ENSP00000362805:K685E	K	+	1	0	OGT	70699527	1.000000	0.71417	0.999000	0.59377	0.906000	0.53458	9.108000	0.94275	1.970000	0.57323	0.481000	0.45027	AAA		0.438	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		G	70782802	A	G	70782802	3	3	47	1	0	0	0	0	1	0	0	0	10878	247	9	4	2145	4	OGT	23	70782802	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	165588	70782802	84487758	2095	6492										
ERCC6L	54821	broad.mit.edu	37	chrX	71427103	71427103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagtaactgtcccatcgattCgcaatgtcttaaagtgccta	8	10	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:71427103C>T	ENST00000334463.3	-	2	1649	c.1514G>A	c.(1513-1515)cGa>cAa	p.R505Q	ERCC6L_ENST00000373657.1_Missense_Mutation_p.R382Q|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	505	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R505Q(2)		breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					CCCATCGATTCGCAATGTCTT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	X											107	99	102					X																	71427103		2203	4300	6503	71343828	SO:0001583	missense	54821			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.1514G>A	X.37:g.71427103C>T	ENSP00000334675:p.Arg505Gln		71343828	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.690921	0.48097	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	T;T	0.75704	-0.96;-0.96	5.72	4.86	0.63082	Helicase, C-terminal (3);	.	.	.	.	D	0.86772	0.6013	M	0.86573	2.825	0.43777	D	0.996303	D	0.89917	1.0	D	0.97110	1.0	D	0.88077	0.2804	9	0.87932	D	0	-9.5779	11.3697	0.49692	0.0:0.9106:0.0:0.0894	.	505	Q2NKX8	ERC6L_HUMAN	Q	382;505	ENSP00000362761:R382Q;ENSP00000334675:R505Q	ENSP00000334675:R505Q	R	-	2	0	ERCC6L	71343828	1.000000	0.71417	0.077000	0.20336	0.607000	0.37147	5.816000	0.69222	1.181000	0.42912	0.600000	0.82982	CGA		0.373	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71427103	C	T	71427103	3	4	47	1	0	0	0	0	1	0	0	0	5231	884	31	1	2242	1	ERCC6L	23	71427103	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	644301	71427103	83843457	2096	6493										
PHKA1	5255	broad.mit.edu	37	chrX	71802367	71802367	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gacaaggatggcttcaaccaGcagctgacggtactctggct	12	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:71802367G>T	ENST00000373542.4	-	31	3538	c.3379C>A	c.(3379-3381)Ctg>Atg	p.L1127M	PHKA1_ENST00000373545.3_Missense_Mutation_p.L1085M|PHKA1_ENST00000339490.3_Missense_Mutation_p.L1114M|PHKA1_ENST00000373539.3_Missense_Mutation_p.L1144M|PHKA1_ENST00000541944.1_Missense_Mutation_p.L1055M	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1127					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.L1127M(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GCTTCAACCAGCAGCTGACGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											104	80	88					X																	71802367		2203	4300	6503	71719092	SO:0001583	missense	5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3379C>A	X.37:g.71802367G>T	ENSP00000362643:p.Leu1127Met		71719092	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.364702	0.41902	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91464	-2.85;-2.84;-2.83;-2.81;-2.83	5.12	4.25	0.50352	.	0.000000	0.64402	D	0.000001	D	0.93145	0.7817	L	0.49256	1.55	0.49130	D	0.999759	D;D;P;D	0.89917	0.999;0.964;0.934;1.0	D;P;P;D	0.87578	0.998;0.757;0.661;0.996	D	0.91088	0.4904	10	0.39692	T	0.17	-5.7589	13.7127	0.62678	0.0872:0.0:0.9128:0.0	.	1055;1085;1114;1127	B7ZL07;A6NIT2;P46020-2;P46020	.;.;.;KPB1_HUMAN	M	1085;1127;1055;1114;1144	ENSP00000362646:L1085M;ENSP00000362643:L1127M;ENSP00000441251:L1055M;ENSP00000342469:L1114M;ENSP00000362640:L1144M	ENSP00000342469:L1114M	L	-	1	2	PHKA1	71719092	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.877000	0.63086	0.409000	0.25649	-0.923000	0.02734	CTG		0.438	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71802367	G	T	71802367	3	4	47	1	0	0	0	0	1	0	0	0	11874	962	34	2	300	2	PHKA1	23	71802367	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	375264	71802367	83468193	2097	6494										
ABCB7	22	broad.mit.edu	37	chrX	74288917	74288917	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttgaccagcaagataaatGctacccttttgaggctcata	7	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:74288917G>A	ENST00000373394.3	-	12	1591	c.1584C>T	c.(1582-1584)agC>agT	p.S528S	ABCB7_ENST00000339447.4_Silent_p.S488S|ABCB7_ENST00000253577.3_Silent_p.S529S|ABCB7_ENST00000534570.1_5'UTR			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	528	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)	p.S529S(1)		breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						CAAGATAAATGCTACCCTTTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	X											128	113	118					X																	74288917		2203	4300	6503	74205642	SO:0001819	synonymous_variant	22			AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1584C>T	X.37:g.74288917G>A			74205642	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Silent	SNP	ENST00000373394.3	37																																																																																					0.383	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		A	74288917	G	A	74288917	2	1	47	1	0	0	0	0	0	0	0	1	46	1310	46	3		3	ABCB7	23	74288917	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2486550	74288917	80981643	2098	6495										
BRWD3	254065	broad.mit.edu	37	chrX	79948460	79948460	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacactgtaacactggaaaGaactatcaggatactctggt	9	8	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:79948460G>T	ENST00000373275.4	-	28	3458	c.3242C>A	c.(3241-3243)tCt>tAt	p.S1081Y	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1081					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.S1081Y(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						ACACTGGAAAGAACTATCAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											161	143	149					X																	79948460		2203	4300	6503	79835116	SO:0001583	missense	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.3242C>A	X.37:g.79948460G>T	ENSP00000362372:p.Ser1081Tyr		79835116	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	5.177	0.218150	0.09810	.	.	ENSG00000165288	ENST00000373275	T	0.43688	0.94	4.97	4.97	0.65823	.	0.078002	0.56097	D	0.000029	T	0.25195	0.0612	N	0.14661	0.345	0.40929	D	0.984372	P	0.39831	0.69	B	0.38106	0.265	T	0.07443	-1.0772	9	.	.	.	-13.8132	10.9953	0.47571	0.0873:0.0:0.9127:0.0	.	1081	Q6RI45	BRWD3_HUMAN	Y	1081	ENSP00000362372:S1081Y	.	S	-	2	0	BRWD3	79835116	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.891000	0.75639	2.292000	0.77174	0.600000	0.82982	TCT		0.393	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		T	79948460	G	T	79948460	3	4	47	1	0	0	0	0	1	0	0	0	1529	942	33	2	2222	2	BRWD3	23	79948460	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5659543	79948460	75322100	2099	6496										
BRWD3	254065	broad.mit.edu	37	chrX	79984252	79984252	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctaaaaataaaatacttacaGataatgtatgaagaagctgt	6	4	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:79984252G>T	ENST00000373275.4	-	14	1601	c.1385C>A	c.(1384-1386)tCt>tAt	p.S462Y		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	462					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.S462Y(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AATACTTACAGATAATGTATG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	X											36	31	33					X																	79984252		2201	4296	6497	79870908	SO:0001630	splice_region_variant	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1386+1C>A	X.37:g.79984252G>T			79870908	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.491057	0.44249	.	.	ENSG00000165288	ENST00000373275	T	0.60040	0.22	4.86	3.96	0.45880	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);WD40-repeat-containing domain (1);	0.060048	0.64402	D	0.000002	T	0.50752	0.1634	L	0.43701	1.375	0.44373	D	0.997272	B	0.18741	0.03	B	0.29440	0.102	T	0.45934	-0.9227	9	.	.	.	-1.5467	14.4085	0.67099	0.0:0.1436:0.8564:0.0	.	462	Q6RI45	BRWD3_HUMAN	Y	462	ENSP00000362372:S462Y	.	S	-	2	0	BRWD3	79870908	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.142000	0.64820	2.247000	0.74100	0.544000	0.68410	TCT		0.323	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	Missense_Mutation	T	79984252	G	T	79984252	5	4	47	1	0	0	0	0	0	0	1	0	1529	956	33	2	4135	2	BRWD3	23	79984252	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	35792	79984252	75286308	2100	6497										
BRWD3	254065	broad.mit.edu	37	chrX	80001174	80001174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggtaagcagatgaagggAaaatatgaccaaagcgacta	12	6	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:80001174A>G	ENST00000373275.4	-	7	701	c.485T>C	c.(484-486)tTc>tCc	p.F162S		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	162					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.F162S(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AGATGAAGGGAAAATATGACC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											46	41	43					X																	80001174		2203	4299	6502	79887830	SO:0001583	missense	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.485T>C	X.37:g.80001174A>G	ENSP00000362372:p.Phe162Ser		79887830	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859232	0.71834	.	.	ENSG00000165288	ENST00000373275	T	0.23348	1.91	4.96	4.96	0.65561	.	0.069527	0.64402	D	0.000013	T	0.26846	0.0657	M	0.61703	1.905	0.40996	D	0.984893	B	0.29862	0.259	B	0.26770	0.073	T	0.06215	-1.0839	9	.	.	.	-7.8262	13.8084	0.63248	1.0:0.0:0.0:0.0	.	162	Q6RI45	BRWD3_HUMAN	S	162	ENSP00000362372:F162S	.	F	-	2	0	BRWD3	79887830	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.038000	0.93771	1.835000	0.53391	0.441000	0.28932	TTC		0.393	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		G	80001174	A	G	80001174	3	3	47	1	0	0	0	0	1	0	0	0	1529	246	9	4	5063	4	BRWD3	23	80001174	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	16922	80001174	75269386	2101	6498										
POU3F4	5456	broad.mit.edu	37	chrX	82763852	82763852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gagagcccccggatcacggcGaactgggctcgcaccattgc	13	15	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:82763852G>A	ENST00000373200.2	+	1	584	c.520G>A	c.(520-522)Gaa>Aaa	p.E174K	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	174					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E174K(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						GGATCACGGCGAACTGGGCTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	X											22	22	22					X																	82763852		2203	4299	6502	82650508	SO:0001583	missense	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.520G>A	X.37:g.82763852G>A	ENSP00000362296:p.Glu174Lys		82650508	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	37	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	G	0.380	-0.929159	0.02359	.	.	ENSG00000196767	ENST00000373200	D	0.84730	-1.89	5.31	5.31	0.75309	.	0.265992	0.36167	N	0.002752	T	0.74928	0.3781	L	0.29908	0.895	0.33195	D	0.551385	B	0.21309	0.054	B	0.17433	0.018	T	0.69971	-0.5000	10	0.06625	T	0.88	.	14.2825	0.66221	0.0:0.1458:0.8542:0.0	.	174	P49335	PO3F4_HUMAN	K	174	ENSP00000362296:E174K	ENSP00000362296:E174K	E	+	1	0	POU3F4	82650508	0.999000	0.42202	0.051000	0.19133	0.028000	0.11728	4.870000	0.63035	2.357000	0.79964	0.525000	0.51046	GAA		0.602	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		A	82763852	G	A	82763852	3	1	47	1	0	0	0	0	1	0	0	0	12308	1059	37	1	522	1	POU3F4	23	82763852	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2762678	82763852	72506708	2102	6499										
CYLC1	1538	broad.mit.edu	37	chrX	83128166	83128166	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tccaagcaaatagtagaagaGaaaactaaaagacaaaatga	7	5	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:83128166G>T	ENST00000329312.4	+	4	487	c.450G>T	c.(448-450)gaG>gaT	p.E150D		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	150					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E149D(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TAGTAGAAGAGAAAACTAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	X											22	20	20					X																	83128166		2194	4270	6464	83014822	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.450G>T	X.37:g.83128166G>T	ENSP00000331556:p.Glu150Asp		83014822	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	6.005	0.369311	0.11352	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.47528	0.84	4.54	-2.85	0.05734	.	.	.	.	.	T	0.30823	0.0777	L	0.42245	1.32	0.09310	N	1	B;B	0.17667	0.023;0.023	B;B	0.14023	0.01;0.01	T	0.23762	-1.0179	9	0.21014	T	0.42	-1.294	3.6433	0.08176	0.4895:0.0:0.2057:0.3049	.	150;150	P35663;F5H4V5	CYLC1_HUMAN;.	D	150	ENSP00000331556:E150D	ENSP00000331556:E150D	E	+	3	2	CYLC1	83014822	0.000000	0.05858	0.005000	0.12908	0.043000	0.13939	-1.079000	0.03410	-0.630000	0.05567	0.513000	0.50165	GAG		0.343	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83128166	G	T	83128166	3	4	47	1	0	0	0	0	1	0	0	0	4147	933	33	2	464	2	CYLC1	23	83128166	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	364314	83128166	72142394	2103	6500										
CYLC1	1538	broad.mit.edu	37	chrX	83129044	83129044	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgtcaagaatgatgaagagtCtactgatgctgactctgaac	10	7	3	7			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:83129044C>A	ENST00000329312.4	+	4	1365	c.1328C>A	c.(1327-1329)tCt>tAt	p.S443Y		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	443					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.S442Y(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						GATGAAGAGTCTACTGATGCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											24	21	22					X																	83129044		2198	4296	6494	83015700	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1328C>A	X.37:g.83129044C>A	ENSP00000331556:p.Ser443Tyr		83015700	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	c	8.869	0.948823	0.18356	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.27104	1.69	4.08	4.08	0.47627	.	.	.	.	.	T	0.49643	0.1569	M	0.77313	2.365	0.33674	D	0.611266	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63994	-0.6511	9	0.87932	D	0	-9.3653	10.6449	0.45615	0.0:1.0:0.0:0.0	.	443;443	P35663;F5H4V5	CYLC1_HUMAN;.	Y	443	ENSP00000331556:S443Y	ENSP00000331556:S443Y	S	+	2	0	CYLC1	83015700	0.188000	0.23250	0.965000	0.40720	0.009000	0.06853	1.156000	0.31712	2.274000	0.75844	0.600000	0.82982	TCT		0.348	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		A	83129044	C	A	83129044	3	1	47	1	0	0	0	0	1	0	0	0	4147	913	32	2	1342	2	CYLC1	23	83129044	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	878	83129044	72141516	2104	6501										
RPS6KA6	27330	broad.mit.edu	37	chrX	83361979	83361979	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttttatattcttctgcaataGaagttgcaacaaagctgaat	6	6	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:83361979G>A	ENST00000262752.2	-	14	1188	c.1181C>T	c.(1180-1182)tCt>tTt	p.S394F	RPS6KA6_ENST00000495332.1_5'Flank|RPS6KA6_ENST00000543399.1_Missense_Mutation_p.S394F	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	394	AGC-kinase C-terminal.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S394F(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TTCTGCAATAGAAGTTGCAAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											76	71	73					X																	83361979		2203	4300	6503	83248635	SO:0001583	missense	27330			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1181C>T	X.37:g.83361979G>A	ENSP00000262752:p.Ser394Phe		83248635	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	37	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642429	0.67244	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.71341	-0.56;-0.56	4.93	4.93	0.64822	AGC-kinase, C-terminal (1);	0.294799	0.37577	N	0.002038	D	0.82857	0.5128	M	0.84433	2.695	0.38100	D	0.937235	B;P	0.41498	0.152;0.752	B;P	0.52267	0.232;0.694	D	0.87454	0.2403	10	0.72032	D	0.01	.	17.563	0.87912	0.0:0.0:1.0:0.0	.	394;394	B7ZL90;Q9UK32	.;KS6A6_HUMAN	F	394	ENSP00000262752:S394F;ENSP00000440830:S394F	ENSP00000262752:S394F	S	-	2	0	RPS6KA6	83248635	0.942000	0.31987	0.958000	0.39756	0.989000	0.77384	4.236000	0.58675	2.162000	0.67917	0.600000	0.82982	TCT		0.338	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		A	83361979	G	A	83361979	3	1	47	1	0	0	0	0	1	0	0	0	13692	942	33	3	1092	3	RPS6KA6	23	83361979	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	232935	83361979	71908581	2105	6502										
HDX	139324	broad.mit.edu	37	chrX	83723904	83723904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gggcatttcctcccagaattCtctgggggtaatcgctaact	10	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:83723904C>A	ENST00000297977.5	-	3	938	c.827G>T	c.(826-828)aGa>aTa	p.R276I	HDX_ENST00000506585.2_Missense_Mutation_p.R218I|HDX_ENST00000373177.2_Missense_Mutation_p.R276I	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	276						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R276I(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TCCCAGAATTCTCTGGGGGTA	0.448																																					Pancreas(53;231 1169 36156 43751 51139)											1	Substitution - Missense(1)	large_intestine(1)	X											94	89	91					X																	83723904		2203	4300	6503	83610560	SO:0001583	missense	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.827G>T	X.37:g.83723904C>A	ENSP00000297977:p.Arg276Ile		83610560	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.605246	0.46423	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.49139	0.87;0.79;0.87	5.45	2.69	0.31865	.	0.161807	0.52532	D	0.000063	T	0.45994	0.1370	L	0.61218	1.895	0.54753	D	0.99998	P	0.42123	0.771	B	0.41088	0.347	T	0.49643	-0.8918	10	0.87932	D	0	-32.91	11.2073	0.48778	0.0:0.7917:0.0:0.2083	.	276	Q7Z353	HDX_HUMAN	I	276;218;276	ENSP00000297977:R276I;ENSP00000362272:R218I;ENSP00000423670:R276I	ENSP00000297977:R276I	R	-	2	0	HDX	83610560	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.187000	0.42602	0.590000	0.29694	0.513000	0.50165	AGA		0.448	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83723904	C	A	83723904	3	1	47	1	0	0	0	0	1	0	0	0	7047	913	32	2	1277	2	HDX	23	83723904	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	361925	83723904	71546656	2106	6503										
DACH2	117154	broad.mit.edu	37	chrX	86069731	86069731	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagaaggagaaaaaaaccaaGagaaaattgcaggaagcctt	10	5	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:86069731G>A	ENST00000373125.4	+	10	1578	c.1578G>A	c.(1576-1578)aaG>aaA	p.K526K	DACH2_ENST00000508860.1_Silent_p.K359K|DACH2_ENST00000373131.1_Silent_p.K513K|DACH2_ENST00000510272.1_Silent_p.K307K	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	526	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K513K(1)|p.K526K(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AAAAAACCAAGAGAAAATTGC	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	X											61	57	58					X																	86069731		2203	4300	6503	85956387	SO:0001819	synonymous_variant	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1578G>A	X.37:g.86069731G>A			85956387	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Silent	SNP	ENST00000373125.4	37	CCDS14455.1																																																																																				0.448	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		A	86069731	G	A	86069731	2	1	47	1	0	0	0	0	0	0	0	1	4227	933	33	3		3	DACH2	23	86069731	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2345827	86069731	69200829	2107	6504										
KLHL4	56062	broad.mit.edu	37	chrX	86773235	86773235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctaaatcagttccagagaaGaatttattcaaagaagcttg	7	7	2	3	rs186431341		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:86773235G>T	ENST00000373119.4	+	1	484	c.339G>T	c.(337-339)aaG>aaT	p.K113N	KLHL4_ENST00000373114.4_Missense_Mutation_p.K113N	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	113						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.K113N(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						TTCCAGAGAAGAATTTATTCA	0.408													G|||	1	0.000264901	0	0	3775	,	,		14280	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											60	60	60					X																	86773235		2203	4300	6503	86659891	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.339G>T	X.37:g.86773235G>T	ENSP00000362211:p.Lys113Asn		86659891	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.011	-1.726874	0.00694	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.74209	-0.82;-0.78	5.05	2.22	0.28083	.	2.867830	0.00961	N	0.003113	T	0.56790	0.2009	N	0.08118	0	0.09310	N	1	B;B	0.19200	0.006;0.034	B;B	0.28011	0.017;0.085	T	0.48581	-0.9023	10	0.12103	T	0.63	.	6.082	0.19946	0.2507:0.1347:0.6146:0.0	.	113;113	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	N	113	ENSP00000362211:K113N;ENSP00000362206:K113N	ENSP00000362206:K113N	K	+	3	2	KLHL4	86659891	0.939000	0.31865	0.004000	0.12327	0.078000	0.17371	-0.078000	0.11375	0.131000	0.18576	0.513000	0.50165	AAG		0.408	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			T	86773235	G	T	86773235	3	4	47	1	0	0	0	0	1	0	0	0	8412	933	33	2	341	2	KLHL4	23	86773235	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	703504	86773235	68497325	2108	6505										
CPXCR1	53336	broad.mit.edu	37	chrX	88009305	88009305	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attaagacaacattcatgcaGctcttctgggaattaaatta	6	7	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:88009305G>T	ENST00000276127.4	+	3	1149	c.890G>T	c.(889-891)aGc>aTc	p.S297I	CPXCR1_ENST00000373111.1_Missense_Mutation_p.S297I	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	297							metal ion binding (GO:0046872)	p.S297I(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						CATTCATGCAGCTCTTCTGGG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	X											35	36	35					X																	88009305		2193	4289	6482	87895961	SO:0001583	missense	53336			AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.890G>T	X.37:g.88009305G>T	ENSP00000276127:p.Ser297Ile		87895961	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	G	6.472	0.455236	0.12283	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.29917	1.55;1.55	3.57	-1.73	0.08081	Zinc finger, C2H2 (1);	0.734274	0.12186	N	0.491677	T	0.22044	0.0531	N	0.19112	0.55	0.09310	N	1	P	0.45176	0.852	P	0.47705	0.555	T	0.21552	-1.0242	9	.	.	.	0.1075	8.0203	0.30406	0.6336:0.0:0.3664:0.0	.	297	Q8N123	CPXCR_HUMAN	I	297	ENSP00000276127:S297I;ENSP00000362203:S297I	.	S	+	2	0	CPXCR1	87895961	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.551000	0.06027	-0.604000	0.05760	-1.350000	0.01237	AGC		0.294	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		T	88009305	G	T	88009305	3	4	47	1	0	0	0	0	1	0	0	0	3842	971	34	2	892	2	CPXCR1	23	88009305	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1236070	88009305	67261255	2109	6506										
PCDH11X	27328	broad.mit.edu	37	chrX	91132097	91132097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaatgccaagatccacttCtctttcagcaatctagtctc	5	12	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:91132097C>A	ENST00000373094.1	+	2	1703	c.858C>A	c.(856-858)ttC>ttA	p.F286L	PCDH11X_ENST00000395337.2_Missense_Mutation_p.F286L|PCDH11X_ENST00000406881.1_Missense_Mutation_p.F286L|PCDH11X_ENST00000298274.8_Missense_Mutation_p.F286L|PCDH11X_ENST00000373088.1_Missense_Mutation_p.F286L|PCDH11X_ENST00000361655.2_Missense_Mutation_p.F286L|PCDH11X_ENST00000373097.1_Missense_Mutation_p.F286L|PCDH11X_ENST00000504220.2_Missense_Mutation_p.F286L|PCDH11X_ENST00000361724.1_Missense_Mutation_p.F286L	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	286	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F286L(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						AGATCCACTTCTCTTTCAGCA	0.438																																					NSCLC(38;925 1092 2571 38200 45895)											2	Substitution - Missense(2)	large_intestine(2)	X											15	14	14					X																	91132097		2167	4238	6405	91018753	SO:0001583	missense	27328			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.858C>A	X.37:g.91132097C>A	ENSP00000362186:p.Phe286Leu		91018753	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.263940	0.39995	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	4.63	3.75	0.43078	Cadherin (4);Cadherin-like (1);	0.052199	0.85682	D	0.000000	T	0.57695	0.2071	M	0.65320	2	0.39067	D	0.96063	P;D;D;D;D;D;P;P	0.55172	0.928;0.968;0.963;0.963;0.963;0.97;0.928;0.928	P;P;P;P;P;P;P;P	0.60068	0.591;0.729;0.792;0.792;0.792;0.868;0.591;0.591	T	0.60657	-0.7220	10	0.87932	D	0	.	7.3335	0.26596	0.0:0.7918:0.0:0.2082	.	286;286;286;286;286;286;286;286	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	L	286	ENSP00000378746:F286L;ENSP00000362186:F286L;ENSP00000362189:F286L;ENSP00000355040:F286L;ENSP00000362180:F286L;ENSP00000423762:F286L;ENSP00000355105:F286L;ENSP00000384758:F286L;ENSP00000298274:F286L	ENSP00000298274:F286L	F	+	3	2	PCDH11X	91018753	1.000000	0.71417	0.972000	0.41901	0.216000	0.24613	0.704000	0.25661	0.723000	0.32274	0.544000	0.68410	TTC		0.438	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91132097	C	A	91132097	3	1	47	1	0	0	0	0	1	0	0	0	11539	912	32	2	864	2	PCDH11X	23	91132097	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3122792	91132097	64138463	2110	6507										
NAP1L3	4675	broad.mit.edu	37	chrX	92927556	92927556	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggggacttctttaggatcttCttttacttcaggggttgcct	11	8	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:92927556C>A	ENST00000373079.3	-	1	1011	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000322139.4_5'Flank|NAP1L3_ENST00000475430.2_Nonsense_Mutation_p.E243*|FAM133A_ENST00000355813.5_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	250	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.E250*(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TTAGGATCTTCTTTTACTTCA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											144	137	140					X																	92927556		2203	4300	6503	92814212	SO:0001587	stop_gained	4675				CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.748G>T	X.37:g.92927556C>A	ENSP00000362171:p.Glu250*		92814212	B2RCM0|O60788	Nonsense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508891	0.85282	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	.	.	.	3.18	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	11.548	0.50704	0.0:1.0:0.0:0.0	.	.	.	.	X	250;243	.	ENSP00000362171:E250X	E	-	1	0	NAP1L3	92814212	0.948000	0.32251	0.988000	0.46212	0.513000	0.34164	1.617000	0.36943	1.858000	0.53909	0.529000	0.55759	GAA		0.423	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92927556	C	A	92927556	4	1	47	1	0	0	0	0	0	1	0	0	10188	922	32	2	776	2	NAP1L3	23	92927556	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1795459	92927556	62343004	2111	6508										
FAM133A	286499	broad.mit.edu	37	chrX	92965096	92965096	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaaaaagtaaagaagaagaaGaagaaacagcacaagaaaca	9	4	0	6			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:92965096G>A	ENST00000355813.5	+	4	1204	c.678G>A	c.(676-678)aaG>aaA	p.K226K	FAM133A_ENST00000538690.1_Silent_p.K226K|FAM133A_ENST00000332647.4_Silent_p.K226K|FAM133A_ENST00000322139.4_Silent_p.K226K	NM_001171109.1|NM_173698.2	NP_001164580.1|NP_775969.1	Q8N9E0	F133A_HUMAN	family with sequence similarity 133, member A	226	Lys-rich.							p.K226K(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(7)|upper_aerodigestive_tract(1)	20						agaagaagaagaagaaacagc	0.368													g|||	1	0.000264901	0	0	3775	,	,		14404	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X											23	22	22					X																	92965096		2194	4290	6484	92851752	SO:0001819	synonymous_variant	286499			AK094978	CCDS14466.1	Xq21.32	2010-05-04			ENSG00000179083	ENSG00000179083			26748	protein-coding gene	gene with protein product	"cancer/testis antigen 115"						Standard	NM_173698		Approved	RP1-32F7.2, FLJ37659, CT115	uc022bzv.1	Q8N9E0	OTTHUMG00000021975	ENST00000355813.5:c.678G>A	X.37:g.92965096G>A			92851752		Silent	SNP	ENST00000355813.5	37	CCDS14466.1																																																																																				0.368	FAM133A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057452.1	NM_173698		A	92965096	G	A	92965096	2	1	47	1	0	0	0	0	0	0	0	1	5459	933	33	3		3	FAM133A	23	92965096	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	37540	92965096	62305464	2112	6509										
DIAPH2	1730	broad.mit.edu	37	chrX	96213131	96213131	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acctgaagtgtccatgaagaGaatcaattggtcaaaggtaa	10	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:96213131G>T	ENST00000324765.8	+	16	2266	c.1919G>T	c.(1918-1920)aGa>aTa	p.R640I	DIAPH2_ENST00000373061.3_Missense_Mutation_p.R640I|DIAPH2_ENST00000373054.4_Missense_Mutation_p.R636I|DIAPH2_ENST00000355827.4_Missense_Mutation_p.R640I|DIAPH2_ENST00000373049.4_Missense_Mutation_p.R640I			O60879	DIAP2_HUMAN	diaphanous-related formin 2	640	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)	p.R640I(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TCCATGAAGAGAATCAATTGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	X											42	46	44					X																	96213131		2202	4300	6502	96099787	SO:0001583	missense	1730			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.1919G>T	X.37:g.96213131G>T	ENSP00000321348:p.Arg640Ile		96099787	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	37	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963712	0.53507	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2	5.23	4.37	0.52481	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.50854	0.1640	M	0.90369	3.11	0.80722	D	1	D;D	0.69078	0.997;0.997	D;P	0.65874	0.939;0.899	T	0.60667	-0.7218	10	0.87932	D	0	.	12.7484	0.57293	0.0828:0.0:0.9172:0.0	.	640;640	O60879;O60879-2	DIAP2_HUMAN;.	I	640;636;640;640;640;647	ENSP00000362152:R640I;ENSP00000362145:R636I;ENSP00000348082:R640I;ENSP00000362140:R640I;ENSP00000321348:R640I	ENSP00000321348:R640I	R	+	2	0	DIAPH2	96099787	1.000000	0.71417	0.953000	0.39169	0.229000	0.25112	9.233000	0.95337	0.979000	0.38497	0.594000	0.82650	AGA		0.363	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		T	96213131	G	T	96213131	3	4	47	1	0	0	0	0	1	0	0	0	4530	942	33	2	1981	2	DIAPH2	23	96213131	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	3248035	96213131	59057429	2113	6510										
PCDH19	57526	broad.mit.edu	37	chrX	99663286	99663286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattgagctggacatgacctCgagcgagatgatgcacttgg	13	9	0	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:99663286C>T	ENST00000373034.4	-	1	1985	c.310G>A	c.(310-312)Gag>Aag	p.E104K	PCDH19_ENST00000255531.7_Missense_Mutation_p.E104K|PCDH19_ENST00000420881.2_Missense_Mutation_p.E104K	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E104K(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GACATGACCTCGAGCGAGATG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	X											110	104	106					X																	99663286		2145	4240	6385	99549942	SO:0001583	missense	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.310G>A	X.37:g.99663286C>T	ENSP00000362125:p.Glu104Lys		99549942	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487049	0.84854	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.30448	1.53;1.53;1.53	5.7	5.7	0.88788	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53578	0.1805	L	0.56124	1.755	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.999;0.999	T	0.54616	-0.8267	10	0.87932	D	0	.	18.367	0.90394	0.0:1.0:0.0:0.0	.	104;104;104	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	K	104	ENSP00000400327:E104K;ENSP00000362125:E104K;ENSP00000255531:E104K	ENSP00000255531:E104K	E	-	1	0	PCDH19	99549942	1.000000	0.71417	0.938000	0.37757	0.978000	0.69477	7.770000	0.85390	2.385000	0.81259	0.544000	0.68410	GAG		0.557	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		T	99663286	C	T	99663286	3	4	47	1	0	0	0	0	1	0	0	0	11545	893	31	1	3160	1	PCDH19	23	99663286	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3450155	99663286	55607274	2114	6511										
XKRX	402415	broad.mit.edu	37	chrX	100169474	100169474	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatggatgcaagtactggaaGaaaaggagcatgaagccaat	12	5	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:100169474G>T	ENST00000372956.2	-	3	1807	c.1203C>A	c.(1201-1203)ttC>ttA	p.F401L	XKRX_ENST00000468904.1_3'UTR|XKRX_ENST00000328526.5_Missense_Mutation_p.F414L			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	401						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F414L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						AGTACTGGAAGAAAAGGAGCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											181	149	160					X																	100169474		2203	4300	6503	100056130	SO:0001583	missense	402415			AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"X Kell blood group precursor-related, X-linked"				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.1203C>A	X.37:g.100169474G>T	ENSP00000362047:p.Phe401Leu		100056130	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	37	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614201	0.66672	.	.	ENSG00000182489	ENST00000328526;ENST00000372956	T;T	0.68025	-0.3;-0.3	5.74	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.79118	0.4392	M	0.74647	2.275	0.53005	D	0.99996	D	0.76494	0.999	D	0.83275	0.996	T	0.78617	-0.2134	10	0.87932	D	0	-20.0011	9.5211	0.39135	0.2239:0.0:0.7761:0.0	.	401	Q6PP77	XKR2_HUMAN	L	414;401	ENSP00000327570:F414L;ENSP00000362047:F401L	ENSP00000327570:F414L	F	-	3	2	XKRX	100056130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.197000	0.32211	0.561000	0.29186	0.538000	0.68166	TTC		0.448	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559		T	100169474	G	T	100169474	3	4	47	1	0	0	0	0	1	0	0	0	17479	933	33	2	150	2	XKRX	23	100169474	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	506188	100169474	55101086	2115	6512										
DRP2	1821	broad.mit.edu	37	chrX	100497323	100497323	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tggttctccagctgttcaaaGaagaattctcccccatgaaa	7	11	3	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:100497323G>T	ENST00000395209.3	+	8	1365	c.838G>T	c.(838-840)Gaa>Taa	p.E280*	DRP2_ENST00000402866.1_Nonsense_Mutation_p.E280*|DRP2_ENST00000541709.1_Nonsense_Mutation_p.E202*|DRP2_ENST00000538510.1_Nonsense_Mutation_p.E280*	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	280					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.E277*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GCTGTTCAAAGAAGAATTCTC	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											200	196	197					X																	100497323		2203	4300	6503	100383979	SO:0001587	stop_gained	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.838G>T	X.37:g.100497323G>T	ENSP00000378635:p.Glu280*		100383979	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Nonsense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	G	38	7.236830	0.98154	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-10.591	18.3989	0.90509	0.0:0.0:1.0:0.0	.	.	.	.	X	280;280;202;280	.	ENSP00000362007:E280X	E	+	1	0	DRP2	100383979	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.476000	0.97823	2.285000	0.76669	0.594000	0.82650	GAA		0.478	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100497323	G	T	100497323	4	4	47	1	0	0	0	0	0	1	0	0	4775	943	33	2	860	2	DRP2	23	100497323	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	327849	100497323	54773237	2116	6513										
TAF7L	54457	broad.mit.edu	37	chrX	100534008	100534008	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagctgcttttttccatttCtttgacatcagggacctatg	7	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:100534008C>A	ENST00000372907.3	-	7	747	c.736G>T	c.(736-738)Gaa>Taa	p.E246*	TAF7L_ENST00000324762.6_Nonsense_Mutation_p.E160*|TAF7L_ENST00000372905.2_Nonsense_Mutation_p.E160*|TAF7L_ENST00000356784.1_Nonsense_Mutation_p.E160*	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	246					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)		p.E246*(1)		NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TTTTCCATTTCTTTGACATCA	0.284																																					Ovarian(104;431 1530 3210 15406 18594)											1	Substitution - Nonsense(1)	large_intestine(1)	X											107	108	107					X																	100534008		2202	4296	6498	100420664	SO:0001587	stop_gained	54457			AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"cancer/testis antigen 40"	300314	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.736G>T	X.37:g.100534008C>A	ENSP00000361998:p.Glu246*		100420664	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Nonsense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793485	0.70452	.	.	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	.	.	.	3.99	-3.03	0.05429	.	1.795170	0.03127	N	0.164591	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-0.0667	6.719	0.23321	0.0976:0.6135:0.1728:0.1161	.	.	.	.	X	246;160;160;160	.	ENSP00000320283:E160X	E	-	1	0	TAF7L	100420664	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.302000	0.08221	-0.910000	0.03847	-1.342000	0.01247	GAA		0.284	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			A	100534008	C	A	100534008	4	1	47	1	0	0	0	0	0	1	0	0	15572	922	32	2	680	2	TAF7L	23	100534008	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	36685	100534008	54736552	2117	6514										
GPRASP1	9737	broad.mit.edu	37	chrX	101912765	101912765	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatttgtctgaaaatcttttCatgacaaaagaactactcag	5	7	4	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:101912765C>A	ENST00000361600.5	+	5	4725	c.3924C>A	c.(3922-3924)ttC>ttA	p.F1308L	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000444152.1_Missense_Mutation_p.F1308L|GPRASP1_ENST00000537097.1_Missense_Mutation_p.F1308L|GPRASP1_ENST00000415986.1_Missense_Mutation_p.F1308L	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1308	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)		p.F1308L(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AAAATCTTTTCATGACAAAAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											61	59	60					X																	101912765		2203	4300	6503	101799421	SO:0001583	missense	9737			AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3924C>A	X.37:g.101912765C>A	ENSP00000355146:p.Phe1308Leu		101799421	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	37	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.376478	0.01214	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	2.9	-0.0792	0.13711	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.12902	0.0313	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.33369	-0.9871	9	0.19590	T	0.45	-0.5056	5.3102	0.15825	0.3081:0.5716:0.0:0.1203	.	1308	Q5JY77	GASP1_HUMAN	L	1308	ENSP00000393691:F1308L;ENSP00000409420:F1308L;ENSP00000355146:F1308L;ENSP00000445683:F1308L	ENSP00000355146:F1308L	F	+	3	2	GPRASP1	101799421	0.001000	0.12720	0.040000	0.18447	0.315000	0.28087	-0.812000	0.04496	-0.468000	0.06922	-2.259000	0.00280	TTC		0.348	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		A	101912765	C	A	101912765	3	1	47	1	0	0	0	0	1	0	0	0	6743	825	29	2	3926	2	GPRASP1	23	101912765	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1378757	101912765	53357795	2118	6515										
GLRA4	203562	broad.mit.edu	37	chrX	102968540	102968540	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcatactccagcaaggcagCgaacacaaagagcagacaca	9	12	0	2	rs199835307		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:102968540C>T	ENST00000319560.6	+	3	312	c.121C>T	c.(121-123)Cga>Tga	p.R41*	GLRA4_ENST00000372617.4_Missense_Mutation_p.A331T	NM_182541.2	NP_872347.2	Q5JXX7	TMM31_HUMAN	transmembrane protein 31	41						integral component of membrane (GO:0016021)		p.R41*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						AGCAAGGCAGCGAACACAAAG	0.483													C|||	1	0.000264901	0	0	3775	,	,		14622	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	X											152	117	128					X																	102968540		2203	4300	6503	102855196	SO:0001587	stop_gained	203562			BC029575	CCDS35359.1	Xq22.2	2008-02-05			ENSG00000179363	ENSG00000179363			28601	protein-coding gene	gene with protein product						12477932	Standard	NM_182541		Approved	MGC39655	uc004elh.3	Q5JXX7	OTTHUMG00000022109	ENST00000319560.6:c.121C>T	X.37:g.102968540C>T	ENSP00000316940:p.Arg41*		102855196	Q8NHR4	Nonsense_Mutation	SNP	ENST00000319560.6	37	CCDS35359.1	1|1	6.027727546714888E-4|6.027727546714888E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	37|37	6.076671|6.076671	0.97262|0.97262	.|.	.|.	ENSG00000188828|ENSG00000179363	ENST00000372617|ENST00000319560	D|.	0.84660|.	-1.88|.	5.5|5.5	3.71|3.71	0.42584|0.42584	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.052982|.	0.85682|.	D|.	0.000000|.	T|.	0.29321|.	0.0730|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.34977|.	0.478|.	B|.	0.38106|.	0.265|.	T|.	0.12941|.	-1.0528|.	9|.	0.44086|0.02654	T|T	0.13|1	0.0062|0.0062	7.9431|7.9431	0.29969|0.29969	0.3242:0.5217:0.1541:0.0|0.3242:0.5217:0.1541:0.0	.|.	331|.	Q5JXX5|.	GLRA4_HUMAN|.	T|X	331|41	ENSP00000361700:A331T|.	ENSP00000361700:A331T|ENSP00000316940:R41X	A|R	-|+	1|1	0|2	GLRA4|TMEM31	102855196|102855196	0.994000|0.994000	0.37717|0.37717	0.497000|0.497000	0.27552|0.27552	0.939000|0.939000	0.58152|0.58152	3.137000|3.137000	0.50562|0.50562	0.493000|0.493000	0.27837|0.27837	0.523000|0.523000	0.50628|0.50628	GCT|CGA		0.483	TMEM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057741.1	NM_182541		T	102968540	C	T	102968540	4	4	47	1	0	0	0	0	0	1	0	0	6477	769	27	1	269	1	GLRA4	23	102968540	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1055775	102968540	52302020	2119	6516										
PLP1	5354	broad.mit.edu	37	chrX	103040659	103040659	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aagctaattgagacctatttCtccaaaaactaccaagacta	4	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:103040659C>A	ENST00000303958.2	+	2	299	c.153C>A	c.(151-153)ttC>ttA	p.F51L	PLP1_ENST00000361621.2_Missense_Mutation_p.F51L|PLP1_ENST00000418604.1_Missense_Mutation_p.F51L	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	51			F -> S (in HLD1). {ECO:0000269|PubMed:11093273}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)	p.F51L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						AGACCTATTTCTCCAAAAACT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											190	170	177					X																	103040659		2203	4300	6503	102927315	SO:0001583	missense	5354			M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.153C>A	X.37:g.103040659C>A	ENSP00000305152:p.Phe51Leu		102927315	P04400|P06905|Q502Y1|Q6FHZ6	Missense_Mutation	SNP	ENST00000303958.2	37	CCDS14513.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857759	0.71834	.	.	ENSG00000123560	ENST00000434483;ENST00000429977;ENST00000455268;ENST00000422393;ENST00000433491;ENST00000418604;ENST00000443502;ENST00000303958;ENST00000361621;ENST00000428755	D;D;D;D;D;D;D;D;D	0.99515	-6.06;-6.06;-6.06;-6.06;-6.06;-6.06;-6.06;-6.06;-6.06	5.58	4.53	0.55603	.	0.000000	0.85682	D	0.000000	D	0.99287	0.9751	M	0.78049	2.395	0.49687	D	0.999817	D;D;P	0.63046	0.979;0.992;0.927	D;D;P	0.76071	0.973;0.987;0.801	D	0.98931	1.0787	10	0.59425	D	0.04	-5.5143	7.5371	0.27717	0.0:0.7924:0.0:0.2076	.	51;51;51	B1B1G6;P60201;P60201-2	.;MYPR_HUMAN;.	L	51	ENSP00000403335:F51L;ENSP00000399913:F51L;ENSP00000409802:F51L;ENSP00000413931:F51L;ENSP00000393391:F51L;ENSP00000405750:F51L;ENSP00000391853:F51L;ENSP00000305152:F51L;ENSP00000354860:F51L	ENSP00000305152:F51L	F	+	3	2	PLP1	102927315	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.493000	0.45320	2.337000	0.79520	0.600000	0.82982	TTC		0.478	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			A	103040659	C	A	103040659	3	1	47	1	0	0	0	0	1	0	0	0	12135	912	32	2	159	2	PLP1	23	103040659	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	72119	103040659	52229901	2120	6517										
ESX1	80712	broad.mit.edu	37	chrX	103498876	103498876	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagattcatcgaaaaagttCtctagctcctgcagctgaaa	8	9	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:103498876C>A	ENST00000372588.4	-	2	548	c.465G>T	c.(463-465)gaG>gaT	p.E155D		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	155					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)	p.E155D(1)		endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CGAAAAAGTTCTCTAGCTCCT	0.622																																					Pancreas(200;1705 2227 25194 28471 45274)											1	Substitution - Missense(1)	large_intestine(1)	X											51	51	51					X																	103498876		2203	4298	6501	103385532	SO:0001583	missense	80712			AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"Homeoboxes / PRD class"	14865	protein-coding gene	gene with protein product		300154	"extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.465G>T	X.37:g.103498876C>A	ENSP00000361669:p.Glu155Asp		103385532	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	20.9	4.072116	0.76415	.	.	ENSG00000123576	ENST00000372588	D	0.97791	-4.54	4.48	1.77	0.24775	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);	.	.	.	.	D	0.98570	0.9522	M	0.90870	3.155	0.09310	N	0.999999	D	0.76494	0.999	D	0.91635	0.999	D	0.93791	0.7092	9	0.62326	D	0.03	-26.7401	5.8601	0.18743	0.0:0.6563:0.0:0.3437	.	155	Q8N693	ESX1_HUMAN	D	155	ENSP00000361669:E155D	ENSP00000361669:E155D	E	-	3	2	ESX1	103385532	0.174000	0.23070	0.039000	0.18376	0.451000	0.32288	0.285000	0.18883	0.250000	0.21479	0.534000	0.68092	GAG		0.622	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		A	103498876	C	A	103498876	3	1	47	1	0	0	0	0	1	0	0	0	5276	912	32	2	767	2	ESX1	23	103498876	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	458217	103498876	51771684	2121	6518										
NRK	203447	broad.mit.edu	37	chrX	105167182	105167182	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acgaatgggtaggctataatGcactctctgaaatcttccgg	10	9	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:105167182G>A	ENST00000243300.9	+	18	2986	c.2683G>A	c.(2683-2685)Gca>Aca	p.A895T	NRK_ENST00000428173.2_Missense_Mutation_p.A896T	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	895					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.A896T(1)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						AGGCTATAATGCACTCTCTGA	0.433										HNSCC(51;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	X											113	104	107					X																	105167182		1932	4121	6053	105053838	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2683G>A	X.37:g.105167182G>A	ENSP00000434830:p.Ala895Thr		105053838	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	G	14.42	2.531436	0.45073	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.78707	-1.19;-1.2	3.58	1.71	0.24356	.	0.432093	0.17111	N	0.186605	T	0.62024	0.2394	N	0.24115	0.695	0.80722	D	1	P;B	0.40180	0.705;0.437	B;B	0.40864	0.342;0.098	T	0.53613	-0.8414	10	0.39692	T	0.17	.	5.5303	0.16980	0.0:0.2174:0.5549:0.2278	.	563;895	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	T	895;896	ENSP00000434830:A895T;ENSP00000438378:A896T	ENSP00000434830:A895T	A	+	1	0	NRK	105053838	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.449000	0.35123	0.311000	0.23014	0.597000	0.82753	GCA		0.433	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105167182	G	A	105167182	3	1	47	1	0	0	0	0	1	0	0	0	10686	1319	46	3	2753	3	NRK	23	105167182	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1668306	105167182	50103378	2122	6519										
NRK	203447	broad.mit.edu	37	chrX	105190453	105190453	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tctgatgtgaccctgccaaaGaatgtaagataacaccttca	7	10	2	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:105190453G>T	ENST00000243300.9	+	26	4653	c.4350G>T	c.(4348-4350)aaG>aaT	p.K1450N	NRK_ENST00000540278.1_5'Flank|NRK_ENST00000428173.2_Missense_Mutation_p.K1451N	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1450	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.K1450N(1)|p.K1451N(1)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						CCCTGCCAAAGAATGTAAGAT	0.353										HNSCC(51;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	X											110	98	102					X																	105190453		1861	4083	5944	105077109	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.4350G>T	X.37:g.105190453G>T	ENSP00000434830:p.Lys1450Asn		105077109	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	G	0.079	-1.187229	0.01620	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.04502	3.61;3.61	5.98	3.62	0.41486	Citron-like (2);	0.645901	0.14530	N	0.313937	T	0.01835	0.0058	N	0.05230	-0.09	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35674	-0.9779	10	0.06625	T	0.88	.	1.4948	0.02464	0.2842:0.0854:0.1434:0.4871	.	1450	Q7Z2Y5	NRK_HUMAN	N	1450;1451	ENSP00000434830:K1450N;ENSP00000438378:K1451N	ENSP00000434830:K1450N	K	+	3	2	NRK	105077109	1.000000	0.71417	0.993000	0.49108	0.754000	0.42855	1.316000	0.33620	0.852000	0.35287	-0.327000	0.08410	AAG		0.353	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105190453	G	T	105190453	3	4	47	1	0	0	0	0	1	0	0	0	10686	933	33	2	4452	2	NRK	23	105190453	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	23271	105190453	50080107	2123	6520										
SERPINA7	6906	broad.mit.edu	37	chrX	105280447	105280447	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctttaaagtgaatatagttCactaagaccatgatggtgtt	8	6	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:105280447C>A	ENST00000327674.4	-	1	938	c.603G>T	c.(601-603)gtG>gtT	p.V201V	SERPINA7_ENST00000372563.1_Silent_p.V201V|SERPINA7_ENST00000487487.1_5'Flank			P05543	THBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	201					aging (GO:0007568)|negative regulation of endopeptidase activity (GO:0010951)|post-embryonic development (GO:0009791)|regulation of proteolysis (GO:0030162)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to peptide hormone (GO:0043434)|response to prostaglandin E (GO:0034695)|response to vitamin A (GO:0033189)|thyroid hormone transport (GO:0070327)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone binding (GO:0042562)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.V201V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|skin(3)	24					Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GAATATAGTTCACTAAGACCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	X											132	120	124					X																	105280447		2203	4300	6503	105167103	SO:0001819	synonymous_variant	6906			M14091	CCDS14518.1	Xq21-q22	2014-02-18	2005-08-18		ENSG00000123561	ENSG00000123561		"Serine (or cysteine) peptidase inhibitors"	11583	protein-coding gene	gene with protein product	"thyroxin-binding globulin", "thyroxine-binding globulin", "alpha-1 antiproteinase, antitrypsin"	314200	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	TBG		24172014	Standard	NM_000354		Approved		uc004eme.2	P05543	OTTHUMG00000022144	ENST00000327674.4:c.603G>T	X.37:g.105280447C>A			105167103	D3DUX1	Silent	SNP	ENST00000327674.4	37	CCDS14518.1																																																																																				0.433	SERPINA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057790.1	NM_000354		A	105280447	C	A	105280447	2	1	47	1	0	0	0	0	0	0	0	1	14131	813	29	2		2	SERPINA7	23	105280447	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	89994	105280447	49990113	2124	6521										
CLDN2	9075	broad.mit.edu	37	chrX	106171673	106171673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catctatagcacccttctggGcctgcccgctgacatccagg	9	16	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:106171673G>A	ENST00000541806.1	+	2	734	c.215G>A	c.(214-216)gGc>gAc	p.G72D	CLDN2_ENST00000336803.1_Missense_Mutation_p.G72D|CLDN2_ENST00000540876.1_Missense_Mutation_p.G72D	NM_001171092.1	NP_001164563.1	P57739	CLD2_HUMAN	claudin 2	72					calcium-independent cell-cell adhesion (GO:0016338)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.G72D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						ACCCTTCTGGGCCTGCCCGCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	X											111	91	98					X																	106171673		2203	4300	6503	106058329	SO:0001583	missense	9075			AK075405	CCDS14524.1	Xq22.3-q23	2008-05-14			ENSG00000165376	ENSG00000165376		"Claudins"	2041	protein-coding gene	gene with protein product		300520				9892664	Standard	NM_020384		Approved		uc022ccc.1	P57739	OTTHUMG00000022154	ENST00000541806.1:c.215G>A	X.37:g.106171673G>A	ENSP00000441283:p.Gly72Asp		106058329	B2R6B9	Missense_Mutation	SNP	ENST00000541806.1	37	CCDS14524.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.774710	0.70107	.	.	ENSG00000165376	ENST00000541806;ENST00000540876;ENST00000336803	D;D;D	0.88201	-2.35;-2.35;-2.35	5.46	5.46	0.80206	.	0.152598	0.56097	D	0.000028	D	0.90683	0.7077	L	0.41710	1.295	0.52501	D	0.999958	D	0.63046	0.992	P	0.60117	0.869	D	0.91099	0.4913	10	0.52906	T	0.07	.	15.6452	0.77042	0.0:0.0:1.0:0.0	.	72	P57739	CLD2_HUMAN	D	72	ENSP00000441283:G72D;ENSP00000443230:G72D;ENSP00000336571:G72D	ENSP00000336571:G72D	G	+	2	0	CLDN2	106058329	1.000000	0.71417	0.935000	0.37517	0.977000	0.68977	2.774000	0.47694	2.291000	0.77112	0.523000	0.50628	GGC		0.567	CLDN2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057815.1			A	106171673	G	A	106171673	3	1	47	1	0	0	0	0	1	0	0	0	3487	1203	42	3	217	3	CLDN2	23	106171673	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	891226	106171673	49098887	2125	6522										
GUCY2F	2986	broad.mit.edu	37	chrX	108673541	108673541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaagatttctcataccatttCgaacacatcacttgctcttg	5	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:108673541C>T	ENST00000218006.2	-	8	2077	c.1786G>A	c.(1786-1788)Gaa>Aaa	p.E596K		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	596	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.E596K(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						CATACCATTTCGAACACATCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											193	193	193					X																	108673541		2203	4300	6503	108560197	SO:0001583	missense	2986			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1786G>A	X.37:g.108673541C>T	ENSP00000218006:p.Glu596Lys		108560197	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	C	6.611	0.481156	0.12581	.	.	ENSG00000101890	ENST00000218006	D	0.81996	-1.56	4.43	3.56	0.40772	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.167790	0.50627	N	0.000114	T	0.59689	0.2212	N	0.05619	-0.005	0.50632	D	0.999882	B	0.06786	0.001	B	0.04013	0.001	T	0.53330	-0.8454	10	0.02654	T	1	.	7.7475	0.28877	0.0:0.8762:0.0:0.1238	.	596	P51841	GUC2F_HUMAN	K	596	ENSP00000218006:E596K	ENSP00000218006:E596K	E	-	1	0	GUCY2F	108560197	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.545000	0.36169	0.951000	0.37770	0.600000	0.82982	GAA		0.383	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108673541	C	T	108673541	3	4	47	1	0	0	0	0	1	0	0	0	6919	893	31	1	1588	1	GUCY2F	23	108673541	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2501868	108673541	46597019	2126	6523										
CHRDL1	91851	broad.mit.edu	37	chrX	109924837	109924837	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcatcgtttcttccccgcaGaagtagcctttattgtcaaa	8	11	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:109924837G>T	ENST00000372045.1	-	10	1136	c.1005C>A	c.(1003-1005)ttC>ttA	p.F335L	CHRDL1_ENST00000482160.1_Missense_Mutation_p.F263L|CHRDL1_ENST00000218054.4_Missense_Mutation_p.F341L|CHRDL1_ENST00000444321.2_Missense_Mutation_p.F342L|CHRDL1_ENST00000394797.4_Missense_Mutation_p.F341L|CHRDL1_ENST00000372042.1_Missense_Mutation_p.F343L|CHRDL1_ENST00000434224.1_Missense_Mutation_p.F262L			Q9BU40	CRDL1_HUMAN	chordin-like 1	335					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.F341L(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						CTTCCCCGCAGAAGTAGCCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											153	125	135					X																	109924837		2203	4300	6503	109811493	SO:0001583	missense	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.1005C>A	X.37:g.109924837G>T	ENSP00000361115:p.Phe335Leu		109811493	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Missense_Mutation	SNP	ENST00000372045.1	37		.	.	.	.	.	.	.	.	.	.	G	2.049	-0.418160	0.04766	.	.	ENSG00000101938	ENST00000372045;ENST00000434224;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000482160;ENST00000444321	T;T;T;T;T;T;T	0.28666	2.34;1.6;2.34;2.34;2.65;1.62;2.39	4.97	1.44	0.22558	.	0.343854	0.34777	N	0.003698	T	0.12817	0.0311	N	0.14661	0.345	0.35351	D	0.787354	P;B;B;B;B;B	0.41080	0.737;0.0;0.001;0.001;0.0;0.001	B;B;B;B;B;B	0.36922	0.236;0.001;0.001;0.001;0.001;0.001	T	0.20273	-1.0280	9	.	.	.	-15.406	3.773	0.08649	0.3192:0.0:0.4688:0.212	.	263;342;322;335;343;262	B4DMP3;E9PGS5;Q59FB2;Q9BU40;D3DUY6;D3YTA8	.;.;.;CRDL1_HUMAN;.;.	L	335;262;341;341;343;263;342	ENSP00000361115:F335L;ENSP00000389627:F262L;ENSP00000218054:F341L;ENSP00000378276:F341L;ENSP00000361112:F343L;ENSP00000418443:F263L;ENSP00000399739:F342L	.	F	-	3	2	CHRDL1	109811493	0.990000	0.36364	1.000000	0.80357	0.863000	0.49368	0.105000	0.15333	0.303000	0.22785	-0.512000	0.04463	TTC		0.443	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		T	109924837	G	T	109924837	3	4	47	1	0	0	0	0	1	0	0	0	3379	933	33	2	359	2	CHRDL1	23	109924837	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1251296	109924837	45345723	2127	6524										
CHRDL1	91851	broad.mit.edu	37	chrX	110002960	110002960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaacatttggacatctgactCggctgcaaagcacattccca	8	12	1	1	rs149609884		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:110002960C>T	ENST00000372045.1	-	4	343	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	CHRDL1_ENST00000482160.1_Missense_Mutation_p.R77Q|CHRDL1_ENST00000218054.4_Missense_Mutation_p.R77Q|CHRDL1_ENST00000444321.2_Missense_Mutation_p.R77Q|CHRDL1_ENST00000394797.4_Missense_Mutation_p.R77Q|CHRDL1_ENST00000372042.1_Missense_Mutation_p.R77Q|CHRDL1_ENST00000434224.1_Missense_Mutation_p.R77Q			Q9BU40	CRDL1_HUMAN	chordin-like 1	71	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.R77Q(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						ACATCTGACTCGGCTGCAAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,3835		0,0,1632,571	160	138	145		230,230,230,230	5.4	1	X	dbSNP_134	145	1,6727		0,1,2427,1872	no	missense,missense,missense,missense	CHRDL1	NM_001143981.1,NM_001143982.1,NM_001143983.2,NM_145234.3	43,43,43,43	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging	77/459,77/458,77/379,77/457	110002960	1,10562	2203	4300	6503	109889616	SO:0001583	missense	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.212G>A	X.37:g.110002960C>T	ENSP00000361115:p.Arg71Gln		109889616	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Missense_Mutation	SNP	ENST00000372045.1	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.633960	0.87660	0.0	1.49E-4	ENSG00000101938	ENST00000372045;ENST00000434224;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000482160;ENST00000444321	T;T;T;T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61;-0.61;-0.61;-0.61	5.45	5.45	0.79879	von Willebrand factor, type C (4);	0.059052	0.64402	D	0.000003	T	0.81158	0.4764	L	0.56199	1.76	0.46954	D	0.999262	B;D;D;D;D;D;P	0.76494	0.415;0.999;0.999;0.998;0.999;0.999;0.879	B;D;D;D;D;D;P	0.80764	0.024;0.994;0.99;0.992;0.994;0.994;0.613	T	0.79564	-0.1751	9	.	.	.	-10.5114	17.5649	0.87917	0.0:1.0:0.0:0.0	.	77;77;71;56;71;77;77	B4DMP3;E9PGS5;Q9BU40-2;Q59FB2;Q9BU40;D3DUY6;D3YTA8	.;.;.;.;CRDL1_HUMAN;.;.	Q	71;77;77;77;77;77;77	ENSP00000361115:R71Q;ENSP00000389627:R77Q;ENSP00000218054:R77Q;ENSP00000378276:R77Q;ENSP00000361112:R77Q;ENSP00000418443:R77Q;ENSP00000399739:R77Q	.	R	-	2	0	CHRDL1	109889616	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.084000	0.64462	2.618000	0.88619	0.600000	0.82982	CGA		0.443	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		T	110002960	C	T	110002960	3	4	47	1	0	0	0	0	1	0	0	0	3379	884	31	1	1182	1	CHRDL1	23	110002960	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	78123	110002960	45267600	2128	6525										
AGTR2	186	broad.mit.edu	37	chrX	115303997	115303997	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccctttctgtctcaaagaaGaaatccctggcaagcatctt	6	13	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:115303997G>T	ENST00000371906.4	+	3	654	c.464G>T	c.(463-465)aGa>aTa	p.R155I		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	155					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)	p.R155I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TCTCAAAGAAGAAATCCCTGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											187	174	178					X																	115303997		2203	4300	6503	115218025	SO:0001583	missense	186			AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.464G>T	X.37:g.115303997G>T	ENSP00000360973:p.Arg155Ile		115218025	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702805	0.68501	.	.	ENSG00000180772	ENST00000371906	T	0.38722	1.12	4.69	4.69	0.59074	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71367	0.3331	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79274	-0.1871	10	0.72032	D	0.01	-7.0867	13.9669	0.64213	0.0:0.0:1.0:0.0	.	155	P50052	AGTR2_HUMAN	I	155	ENSP00000360973:R155I	ENSP00000360973:R155I	R	+	2	0	AGTR2	115218025	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.908000	0.92640	2.163000	0.67991	0.506000	0.49869	AGA		0.398	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		T	115303997	G	T	115303997	3	4	47	1	0	0	0	0	1	0	0	0	402	942	33	2	466	2	AGTR2	23	115303997	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	5301037	115303997	39966563	2129	6526										
SLC6A14	11254	broad.mit.edu	37	chrX	115585563	115585563	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agggttcccataactttgggCtgctgcttggttttgtttct	11	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:115585563C>T	ENST00000371900.4	+	10	1447	c.1359C>T	c.(1357-1359)ggC>ggT	p.G453G		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	453					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)	p.G453G(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TAACTTTGGGCTGCTGCTTGG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	X											210	153	172					X																	115585563		2203	4300	6503	115499591	SO:0001819	synonymous_variant	11254			AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.1359C>T	X.37:g.115585563C>T			115499591	Q5H942	Silent	SNP	ENST00000371900.4	37	CCDS14570.1																																																																																				0.368	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			T	115585563	C	T	115585563	2	4	47	1	0	0	0	0	0	0	0	1	14714	784	28	3		3	SLC6A14	23	115585563	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	281566	115585563	39684997	2130	6527										
KLHL13	90293	broad.mit.edu	37	chrX	117043380	117043380	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttgcatccatttattgtatCgaggatcaaatctgaagact	7	8	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:117043380C>T	ENST00000262820.3	-	5	2159	c.1250G>A	c.(1249-1251)cGa>cAa	p.R417Q	KLHL13_ENST00000540167.1_Missense_Mutation_p.R401Q|KLHL13_ENST00000539496.1_Missense_Mutation_p.R420Q|KLHL13_ENST00000371882.1_Missense_Mutation_p.R366Q|KLHL13_ENST00000541812.1_Missense_Mutation_p.R401Q|KLHL13_ENST00000371876.1_Missense_Mutation_p.R366Q|KLHL13_ENST00000545703.1_Missense_Mutation_p.R375Q|KLHL13_ENST00000371878.1_Missense_Mutation_p.R366Q|KLHL13_ENST00000469946.1_Missense_Mutation_p.R366Q	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	417					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)		p.R417Q(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TTTATTGTATCGAGGATCAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											87	72	77					X																	117043380		2203	4300	6503	116927408	SO:0001583	missense	90293			AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.1250G>A	X.37:g.117043380C>T	ENSP00000262820:p.Arg417Gln		116927408	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	37	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590136	0.86851	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946	T;T;T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.02	5.02	0.67125	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.83658	0.5302	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.89917	0.994;1.0;0.987;0.991	P;D;P;P	0.97110	0.742;1.0;0.782;0.845	T	0.79072	-0.1953	10	0.12103	T	0.63	.	17.4247	0.87524	0.0:1.0:0.0:0.0	.	401;420;411;417	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	Q	366;366;366;366;401;401;420;417;375;366	ENSP00000360949:R366Q;ENSP00000360943:R366Q;ENSP00000360945:R366Q;ENSP00000412640:R366Q;ENSP00000444450:R401Q;ENSP00000441029:R401Q;ENSP00000443191:R420Q;ENSP00000262820:R417Q;ENSP00000440707:R375Q;ENSP00000419803:R366Q	ENSP00000262820:R417Q	R	-	2	0	KLHL13	116927408	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.297000	0.77311	0.594000	0.82650	CGA		0.408	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		T	117043380	C	T	117043380	3	4	47	1	0	0	0	0	1	0	0	0	8390	884	31	1	729	1	KLHL13	23	117043380	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1457817	117043380	38227180	2131	6528										
DOCK11	139818	broad.mit.edu	37	chrX	117777428	117777428	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aatgttttatagacccaactTttaaataatgatggccataa	5	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:117777428T>G	ENST00000276202.7	+	40	4332	c.4269T>G	c.(4267-4269)ctT>ctG	p.L1423L	DOCK11_ENST00000276204.6_Silent_p.L1423L	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1423					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1423L(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AGACCCAACTTTTAAATAATG	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	X											123	131	129					X																	117777428		2203	4300	6503	117661456	SO:0001819	synonymous_variant	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.4269T>G	X.37:g.117777428T>G			117661456	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																				0.323	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117777428	T	G	117777428	2	3	47	1	0	0	0	0	0	0	0	1	4697	1828	64	4		4	DOCK11	23	117777428	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	734048	117777428	37493132	2132	6529										
KIAA1210	57481	broad.mit.edu	37	chrX	118238991	118238991	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcttatgtggtaaagccttCttttgtggattcttaggtga	10	6	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:118238991C>A	ENST00000402510.2	-	7	1031	c.1032G>T	c.(1030-1032)aaG>aaT	p.K344N		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	344								p.K344N(1)|p.K204N(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						GTAAAGCCTTCTTTTGTGGAT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	X											158	151	153					X																	118238991		1905	4123	6028	118123019	SO:0001583	missense	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.1032G>T	X.37:g.118238991C>A	ENSP00000384670:p.Lys344Asn		118123019	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627984	0.28978	.	.	ENSG00000250423;ENSG00000241087	ENST00000402510;ENST00000420240	T	0.10960	2.82	4.55	1.74	0.24563	.	.	.	.	.	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	P	0.35844	0.524	B	0.35353	0.201	T	0.39210	-0.9625	9	0.31617	T	0.26	.	4.523	0.11968	0.0:0.5991:0.1814:0.2195	.	344	Q9ULL0	K1210_HUMAN	N	344;180	ENSP00000384670:K344N	ENSP00000396164:K180N	K	-	3	2	RP13-347D8.5;RP13-347D8.6	118123019	0.001000	0.12720	0.002000	0.10522	0.105000	0.19272	0.182000	0.16900	0.096000	0.17463	-0.315000	0.08773	AAG		0.428	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		A	118238991	C	A	118238991	3	1	47	1	0	0	0	0	1	0	0	0	8235	912	32	2	4129	2	KIAA1210	23	118238991	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	461563	118238991	37031569	2133	6530										
KIAA1210	57481	broad.mit.edu	37	chrX	118284421	118284421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgcaacagccttgggaatacGctcgacttccaatcctggcc	9	14	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:118284421G>A	ENST00000402510.2	-	1	121	c.122C>T	c.(121-123)gCg>gTg	p.A41V		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	41								p.A41V(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TTGGGAATACGCTCGACTTCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	X											45	49	48					X																	118284421		1989	4143	6132	118168449	SO:0001583	missense	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.122C>T	X.37:g.118284421G>A	ENSP00000384670:p.Ala41Val		118168449	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.570444	0.28003	.	.	ENSG00000250423	ENST00000402510	T	0.12672	2.66	3.43	-4.03	0.04021	.	.	.	.	.	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	B	0.22480	0.07	B	0.11329	0.006	T	0.34775	-0.9815	9	0.87932	D	0	.	0.3813	0.00395	0.2209:0.2843:0.1925:0.3023	.	41	Q9ULL0	K1210_HUMAN	V	41	ENSP00000384670:A41V	ENSP00000384670:A41V	A	-	2	0	RP13-347D8.6	118168449	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.517000	0.02248	-1.234000	0.02548	0.600000	0.82982	GCG		0.602	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		A	118284421	G	A	118284421	3	1	47	1	0	0	0	0	1	0	0	0	8235	1087	38	1	5063	1	KIAA1210	23	118284421	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	45430	118284421	36986139	2134	6531										
UPF3B	65109	broad.mit.edu	37	chrX	118971941	118971941	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttcagcctctctctttctcGaagtatgcgctcctgatctc	6	15	5	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:118971941G>A	ENST00000276201.2	-	10	1150	c.1081C>T	c.(1081-1083)Cga>Tga	p.R361*	UPF3B_ENST00000345865.2_Nonsense_Mutation_p.R348*|UPF3B_ENST00000478840.1_5'Flank	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	361	Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R361*(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						TCTCTTTCTCGAAGTATGCGC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											156	134	142					X																	118971941		2203	4300	6503	118855969	SO:0001587	stop_gained	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.1081C>T	X.37:g.118971941G>A	ENSP00000276201:p.Arg361*		118855969	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Nonsense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	G	33	5.221315	0.95139	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	.	.	.	5.83	4.01	0.46588	.	0.266734	0.40728	N	0.001037	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.0023	0.24817	0.0813:0.0:0.4406:0.4781	.	.	.	.	X	361;348	.	ENSP00000276201:R361X	R	-	1	2	UPF3B	118855969	0.825000	0.29262	0.071000	0.20095	0.982000	0.71751	1.125000	0.31332	0.572000	0.29383	0.526000	0.51066	CGA		0.463	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			A	118971941	G	A	118971941	4	1	47	1	0	0	0	0	0	1	0	0	17046	1066	37	1	378	1	UPF3B	23	118971941	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	687520	118971941	36298619	2135	6532										
UPF3B	65109	broad.mit.edu	37	chrX	118972442	118972442	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gtccaatttcttggctttttCtcttttgtccaattcttttt	4	9	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:118972442C>A	ENST00000276201.2	-	9	964	c.895G>T	c.(895-897)Gaa>Taa	p.E299*	UPF3B_ENST00000345865.2_Nonsense_Mutation_p.E286*|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	299	Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E299*(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						TTGGCTTTTTCTCTTTTGTCC	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											196	171	179					X																	118972442		2203	4300	6503	118856470	SO:0001587	stop_gained	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.895G>T	X.37:g.118972442C>A	ENSP00000276201:p.Glu299*		118856470	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Nonsense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	31	5.094927	0.94197	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	.	.	.	5.43	5.43	0.79202	.	0.435785	0.27906	N	0.017367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	11.9636	0.53021	0.1732:0.8268:0.0:0.0	.	.	.	.	X	299;286	.	ENSP00000276201:E299X	E	-	1	0	UPF3B	118856470	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	3.280000	0.51677	2.275000	0.75901	0.526000	0.51066	GAA		0.368	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			A	118972442	C	A	118972442	4	1	47	1	0	0	0	0	0	1	0	0	17046	922	32	2	568	2	UPF3B	23	118972442	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	501	118972442	36298118	2136	6533										
FAM70A	55026	broad.mit.edu	37	chrX	119394745	119394745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttagggactgtaaggtggtgGcttttcaaaaggtggatagt	15	3	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:119394745G>A	ENST00000309720.5	-	10	1153	c.1030C>T	c.(1030-1032)Cca>Tca	p.P344S	TMEM255A_ENST00000371352.1_Missense_Mutation_p.P180S|TMEM255A_ENST00000371369.4_Missense_Mutation_p.P320S|TMEM255A_ENST00000440464.1_Missense_Mutation_p.P236S	NM_017938.3	NP_060408.3	Q5JRV8	T255A_HUMAN	transmembrane protein 255A	344	Pro-rich.					integral component of membrane (GO:0016021)		p.P344S(1)									TAAGGTGGTGGCTTTTCAAAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											131	108	115					X																	119394745		2203	4300	6503	119278773	SO:0001583	missense	55026			BC047054	CCDS14597.1, CCDS43986.1, CCDS48157.1	Xq24	2012-11-30	2012-11-30	2012-11-30	ENSG00000125355	ENSG00000125355			26086	protein-coding gene	gene with protein product			"family with sequence similarity 70, member A"	FAM70A		12477932	Standard	NM_017938		Approved	FLJ20716	uc004eso.4	Q5JRV8	OTTHUMG00000022298	ENST00000309720.5:c.1030C>T	X.37:g.119394745G>A	ENSP00000310110:p.Pro344Ser		119278773	A8K0W9|B1APR4|B3KPI6|E9PAR3|Q86Y72|Q9NWN8	Missense_Mutation	SNP	ENST00000309720.5	37	CCDS14597.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889785	0.72524	.	.	ENSG00000125355	ENST00000309720;ENST00000371369;ENST00000371352;ENST00000440464	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.77558	0.4148	M	0.77313	2.365	0.41821	D	0.990029	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	T	0.80652	-0.1287	10	0.87932	D	0	-6.6072	17.6499	0.88161	0.0:0.0:1.0:0.0	.	236;320;344	E9PAR3;B1APR4;Q5JRV8	.;.;FA70A_HUMAN	S	344;320;180;236	ENSP00000310110:P344S;ENSP00000360420:P320S;ENSP00000360403:P180S;ENSP00000405781:P236S	ENSP00000310110:P344S	P	-	1	0	FAM70A	119278773	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.370000	0.90120	2.471000	0.83476	0.600000	0.82982	CCA		0.488	TMEM255A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058091.1	NM_017938		A	119394745	G	A	119394745	3	1	47	1	0	0	0	0	1	0	0	0	5624	1203	42	3	23	3	FAM70A	23	119394745	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	422303	119394745	35875815	2137	6534										
FAM70A	55026	broad.mit.edu	37	chrX	119438238	119438238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aataacctcctacagtcacaTtctgggtcctggtggttgca	9	11	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:119438238T>A	ENST00000309720.5	-	2	290	c.167A>T	c.(166-168)aAt>aTt	p.N56I	TMEM255A_ENST00000371369.4_Missense_Mutation_p.N56I|TMEM255A_ENST00000440464.1_Missense_Mutation_p.N56I	NM_017938.3	NP_060408.3	Q5JRV8	T255A_HUMAN	transmembrane protein 255A	56						integral component of membrane (GO:0016021)		p.N56I(2)									TACAGTCACATTCTGGGTCCT	0.478																																																2	Substitution - Missense(2)	large_intestine(1)|NS(1)	X											173	150	158					X																	119438238		2203	4300	6503	119322266	SO:0001583	missense	55026			BC047054	CCDS14597.1, CCDS43986.1, CCDS48157.1	Xq24	2012-11-30	2012-11-30	2012-11-30	ENSG00000125355	ENSG00000125355			26086	protein-coding gene	gene with protein product			"family with sequence similarity 70, member A"	FAM70A		12477932	Standard	NM_017938		Approved	FLJ20716	uc004eso.4	Q5JRV8	OTTHUMG00000022298	ENST00000309720.5:c.167A>T	X.37:g.119438238T>A	ENSP00000310110:p.Asn56Ile		119322266	A8K0W9|B1APR4|B3KPI6|E9PAR3|Q86Y72|Q9NWN8	Missense_Mutation	SNP	ENST00000309720.5	37	CCDS14597.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.262665	0.80358	.	.	ENSG00000125355	ENST00000309720;ENST00000371369;ENST00000440464;ENST00000519908	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.73110	0.3545	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.996;0.996;0.999	T	0.77509	-0.2561	10	0.87932	D	0	-11.1777	13.4024	0.60891	0.0:0.0:0.0:1.0	.	56;56;56	E9PAR3;B1APR4;Q5JRV8	.;.;FA70A_HUMAN	I	56	ENSP00000310110:N56I;ENSP00000360420:N56I;ENSP00000405781:N56I;ENSP00000428013:N56I	ENSP00000310110:N56I	N	-	2	0	FAM70A	119322266	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.763000	0.68818	1.758000	0.51981	0.486000	0.48141	AAT		0.478	TMEM255A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058091.1	NM_017938		A	119438238	T	A	119438238	3	1	47	1	0	0	0	0	1	0	0	0	5624	1493	52	5	918	5	FAM70A	23	119438238	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	43493	119438238	35832322	2138	6535										
LAMP2	3920	broad.mit.edu	37	chrX	119581785	119581785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgaataggttccagcttctgGtttttcctttggagtaggtg	12	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:119581785G>T	ENST00000200639.4	-	5	788	c.652C>A	c.(652-654)Cca>Aca	p.P218T	LAMP2_ENST00000538785.1_Missense_Mutation_p.P107T|LAMP2_ENST00000540603.1_Missense_Mutation_p.P171T|LAMP2_ENST00000434600.2_Missense_Mutation_p.P218T|LAMP2_ENST00000371335.4_Missense_Mutation_p.P218T			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	218	Hinge.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)	p.P218T(2)		endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						CCAGCTTCTGGTTTTTCCTTT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	X											264	226	239					X																	119581785		2203	4300	6503	119465813	SO:0001583	missense	3920			X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"CD molecules"	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.652C>A	X.37:g.119581785G>T	ENSP00000200639:p.Pro218Thr		119465813	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Missense_Mutation	SNP	ENST00000200639.4	37	CCDS14599.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789453	0.49997	.	.	ENSG00000005893	ENST00000434600;ENST00000538785;ENST00000200639;ENST00000371335;ENST00000540603	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.73458	0.3589	M	0.91090	3.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.79359	-0.1836	10	0.87932	D	0	-15.2412	18.3507	0.90337	0.0:0.0:1.0:0.0	.	171;107;218;218;218	B4E2S7;B7Z2R9;P13473-2;P13473;Q6Q3G8	.;.;.;LAMP2_HUMAN;.	T	218;107;218;218;171	ENSP00000408411:P218T;ENSP00000440506:P107T;ENSP00000200639:P218T;ENSP00000360386:P218T;ENSP00000440479:P171T	ENSP00000200639:P218T	P	-	1	0	LAMP2	119465813	1.000000	0.71417	0.103000	0.21229	0.037000	0.13140	5.783000	0.68982	2.559000	0.86315	0.597000	0.82753	CCA		0.448	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1			T	119581785	G	T	119581785	3	4	47	1	0	0	0	0	1	0	0	0	8640	1261	44	2	891	2	LAMP2	23	119581785	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	143547	119581785	35688775	2139	6536										
STAG2	10735	broad.mit.edu	37	chrX	123164930	123164930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	caacagaatggagtggaaaaCatgatgttgtttgaagttgt	12	3	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:123164930C>T	ENST00000371160.1	+	5	533	c.243C>T	c.(241-243)aaC>aaT	p.N81N	STAG2_ENST00000218089.9_Silent_p.N81N|STAG2_ENST00000371157.3_Silent_p.N81N|STAG2_ENST00000371144.3_Silent_p.N81N|STAG2_ENST00000371145.3_Silent_p.N81N|STAG2_ENST00000354548.5_Silent_p.N12N|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	81					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.N81N(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GAGTGGAAAACATGATGTTGT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	X											255	206	222					X																	123164930		2203	4300	6503	122992611	SO:0001819	synonymous_variant	10735			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.243C>T	X.37:g.123164930C>T			122992611	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	37	CCDS14607.1																																																																																				0.408	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123164930	C	T	123164930	2	4	47	1	0	0	0	0	0	0	0	1	15282	477	17	3		3	STAG2	23	123164930	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3583145	123164930	32105630	2140	6537										
DCAF12L2	340578	broad.mit.edu	37	chrX	125298618	125298618	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtagcagtgggtgtagagCgcattggggaactctcccat	14	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:125298618C>T	ENST00000360028.2	-	1	1316	c.1290G>A	c.(1288-1290)gcG>gcA	p.A430A	DCAF12L2_ENST00000538699.1_Silent_p.A430A			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	430								p.A430A(3)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GGGTGTAGAGCGCATTGGGGA	0.597																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	X											117	118	118					X																	125298618		2203	4300	6503	125126299	SO:0001819	synonymous_variant	340578			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.1290G>A	X.37:g.125298618C>T			125126299	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																				0.597	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		T	125298618	C	T	125298618	2	4	47	1	0	0	0	0	0	0	0	1	4271	755	27	1		1	DCAF12L2	23	125298618	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2133688	125298618	29971942	2141	6538										
SMARCA1	6594	broad.mit.edu	37	chrX	128649957	128649957	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catcttcttcttgctctgtgCgcctatggcggtagctgaaa	10	11	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:128649957C>T	ENST00000371122.4	-	4	572	c.443G>A	c.(442-444)cGc>cAc	p.R148H	SMARCA1_ENST00000371123.1_Missense_Mutation_p.R148H|SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371121.3_Missense_Mutation_p.R148H	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	148					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R148H(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TTGCTCTGTGCGCCTATGGCG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	X											156	125	136					X																	128649957		2203	4300	6503	128477638	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.443G>A	X.37:g.128649957C>T	ENSP00000360163:p.Arg148His		128477638	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	31	5.101303	0.94245	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000003	D	0.95335	0.8486	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.61080	0.982;0.982;0.989;0.982	P;P;P;P	0.59288	0.635;0.72;0.855;0.72	D	0.95948	0.8952	10	0.87932	D	0	-4.2057	17.7766	0.88510	0.0:1.0:0.0:0.0	.	127;148;148;148	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	H	148;148;148;127	ENSP00000360162:R148H;ENSP00000360164:R148H;ENSP00000360163:R148H;ENSP00000404275:R127H	ENSP00000360162:R148H	R	-	2	0	SMARCA1	128477638	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.047000	0.71038	2.129000	0.65627	0.544000	0.68410	CGC		0.368	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		T	128649957	C	T	128649957	3	4	47	1	0	0	0	0	1	0	0	0	14805	768	27	1	2805	1	SMARCA1	23	128649957	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3351339	128649957	26620603	2142	6539										
OCRL	4952	broad.mit.edu	37	chrX	128709967	128709967	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctgccatttttctttcatcCctaaacttaatgacagccag	4	13	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:128709967C>T	ENST00000371113.4	+	17	1972	c.1807C>T	c.(1807-1809)Cct>Tct	p.P603S	OCRL_ENST00000357121.5_Missense_Mutation_p.P603S	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	603	ASH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.P603S(2)		breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						TTCTTTCATCCCTAAACTTAA	0.453																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	X											140	136	137					X																	128709967		2203	4300	6503	128537648	SO:0001583	missense	4952			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.1807C>T	X.37:g.128709967C>T	ENSP00000360154:p.Pro603Ser		128537648	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.832250	0.50845	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94497	-3.44;-3.43	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	L	0.33668	1.02	0.80722	D	1	B;B	0.27853	0.191;0.005	B;B	0.17098	0.017;0.003	D	0.87332	0.2325	10	0.16896	T	0.51	.	17.6594	0.88188	0.0:1.0:0.0:0.0	.	603;603	Q01968-2;Q01968	.;OCRL_HUMAN	S	603	ENSP00000360154:P603S;ENSP00000349635:P603S	ENSP00000349635:P603S	P	+	1	0	OCRL	128537648	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.759000	0.68785	2.388000	0.81334	0.600000	0.82982	CCT		0.453	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		T	128709967	C	T	128709967	3	4	47	1	0	0	0	0	1	0	0	0	10854	623	22	3	1873	3	OCRL	23	128709967	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	60010	128709967	26560593	2143	6540										
XPNPEP2	7512	broad.mit.edu	37	chrX	128886229	128886229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tcgaggattacagccaagttCgtgacagcatccaggcctac	10	12	0	1	rs151254296		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:128886229C>T	ENST00000371106.3	+	10	1117	c.925C>T	c.(925-927)Cgt>Tgt	p.R309C		NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	309						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.R309C(1)		endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						CAGCCAAGTTCGTGACAGCAT	0.483													C|||	1	0.000264901	0	0.0014	3775	,	,		16086	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X						C	CYS/ARG	0,3835		0,0,0,1632,571	157	124	135		925	5	0.6	X	dbSNP_134	135	2,6725		0,1,1,2427,1870	yes	missense	XPNPEP2	NM_003399.5	180	0,1,1,4059,2441	TT,TC,T,CC,C		0.0297,0.0,0.0189	probably-damaging	309/675	128886229	2,10560	2203	4299	6502	128713910	SO:0001583	missense	7512			U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.925C>T	X.37:g.128886229C>T	ENSP00000360147:p.Arg309Cys		128713910	A0AV16|O75994	Missense_Mutation	SNP	ENST00000371106.3	37	CCDS14613.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.122117	0.56613	0.0	2.97E-4	ENSG00000122121	ENST00000371106	T	0.74106	-0.81	5.89	5.03	0.67393	.	0.215747	0.49305	D	0.000146	T	0.75889	0.3911	L	0.56769	1.78	0.31008	N	0.719574	D	0.76494	0.999	P	0.53360	0.724	T	0.76200	-0.3046	10	0.38643	T	0.18	-17.2641	8.6409	0.33976	0.1511:0.7677:0.0:0.0812	.	309	O43895	XPP2_HUMAN	C	309	ENSP00000360147:R309C	ENSP00000360147:R309C	R	+	1	0	XPNPEP2	128713910	0.025000	0.19082	0.617000	0.29091	0.966000	0.64601	0.306000	0.19279	1.257000	0.44085	0.529000	0.55759	CGT		0.483	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399		T	128886229	C	T	128886229	3	4	47	1	0	0	0	0	1	0	0	0	17483	884	31	1	963	1	XPNPEP2	23	128886229	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	176262	128886229	26384331	2144	6541										
ELF4	2000	broad.mit.edu	37	chrX	129200947	129200947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acccctggaaaccacctgggTtggaagtggctgaagatgag	14	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129200947T>C	ENST00000308167.5	-	9	2120	c.1741A>G	c.(1741-1743)Acc>Gcc	p.T581A	ELF4_ENST00000335997.7_Missense_Mutation_p.T581A	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)									p.T581A(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						ACCACCTGGGTTGGAAGTGGC	0.617			T	ERG	AML																																		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	1	Substitution - Missense(1)	large_intestine(1)	X											91	95	94					X																	129200947		2203	4300	6503	129028628	SO:0001583	missense	2000			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1741A>G	X.37:g.129200947T>C	ENSP00000311280:p.Thr581Ala		129028628		Missense_Mutation	SNP	ENST00000308167.5	37	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	t	10.78	1.445863	0.25987	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	T;T	0.19938	2.11;2.11	4.52	2.11	0.27256	.	0.804528	0.10676	N	0.646944	T	0.11067	0.0270	N	0.19112	0.55	0.21256	N	0.999747	B	0.02656	0.0	B	0.01281	0.0	T	0.38045	-0.9679	10	0.16896	T	0.51	.	4.4948	0.11831	0.0:0.2963:0.0:0.7037	.	581	Q99607	ELF4_HUMAN	A	581	ENSP00000338608:T581A;ENSP00000311280:T581A	ENSP00000311280:T581A	T	-	1	0	ELF4	129028628	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	0.703000	0.25646	0.596000	0.29794	0.414000	0.27820	ACC		0.617	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		C	129200947	T	C	129200947	3	2	47	1	0	0	0	0	1	0	0	0	5069	1725	60	4	254	4	ELF4	23	129200947	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	314718	129200947	26069613	2145	6542										
AIFM1	9131	broad.mit.edu	37	chrX	129273794	129273794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctgaaaagcgttgttctactCttcacctctgctccagccct	6	15	4	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129273794C>A	ENST00000287295.3	-	8	1064	c.834G>T	c.(832-834)aaG>aaT	p.K278N	AIFM1_ENST00000319908.3_Missense_Mutation_p.K274N|AIFM1_ENST00000535724.1_Missense_Mutation_p.K191N|AIFM1_ENST00000460436.2_5'Flank|AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000440263.1_5'Flank	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	278	FAD-dependent oxidoreductase. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.K274N(1)|p.K278N(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	TTGTTCTACTCTTCACCTCTG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	X											183	156	165					X																	129273794		2203	4300	6503	129101475	SO:0001583	missense	9131			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.834G>T	X.37:g.129273794C>A	ENSP00000287295:p.Lys278Asn		129101475	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	37	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307269	0.40795	.	.	ENSG00000156709	ENST00000319908;ENST00000535724;ENST00000287295	D;D;T	0.84146	-1.81;-1.79;-0.81	4.66	4.66	0.58398	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.263259	0.42821	D	0.000652	T	0.78123	0.4234	L	0.52364	1.645	0.50813	D	0.999892	P;B;B	0.37594	0.601;0.127;0.151	B;B;B	0.30251	0.113;0.069;0.072	T	0.77811	-0.2449	10	0.35671	T	0.21	-7.6674	11.8682	0.52505	0.1744:0.8255:0.0:0.0	.	278;274;278	Q1L6K6;O95831-3;O95831	.;.;AIFM1_HUMAN	N	274;191;278	ENSP00000315122:K274N;ENSP00000446113:K191N;ENSP00000287295:K278N	ENSP00000287295:K278N	K	-	3	2	AIFM1	129101475	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.067000	0.30616	2.303000	0.77524	0.600000	0.82982	AAG		0.448	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			A	129273794	C	A	129273794	3	1	47	1	0	0	0	0	1	0	0	0	426	912	32	2	1055	2	AIFM1	23	129273794	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	72847	129273794	25996766	2146	6543										
ZNF280C	55609	broad.mit.edu	37	chrX	129339306	129339306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cttggcaagtatgagttttaCgttgacttaagtgtttagcc	10	6	0	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129339306C>T	ENST00000370978.4	-	17	2279	c.2126G>A	c.(2125-2127)cGt>cAt	p.R709H		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	709					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R709H(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						ATGAGTTTTACGTTGACTTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											104	91	95					X																	129339306		2203	4300	6503	129166987	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.2126G>A	X.37:g.129339306C>T	ENSP00000360017:p.Arg709His		129166987	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	C	9.782	1.175634	0.21704	.	.	ENSG00000056277	ENST00000370978	T	0.02579	4.24	3.66	3.66	0.41972	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.03178	0.0093	L	0.38531	1.155	0.29887	N	0.825515	B	0.21821	0.061	B	0.17979	0.02	T	0.18272	-1.0342	9	0.22706	T	0.39	.	12.1794	0.54204	0.0:1.0:0.0:0.0	.	709	Q8ND82	Z280C_HUMAN	H	709	ENSP00000360017:R709H	ENSP00000360017:R709H	R	-	2	0	ZNF280C	129166987	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.803000	0.38863	1.805000	0.52779	0.292000	0.19580	CGT		0.338	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129339306	C	T	129339306	3	4	47	1	0	0	0	0	1	0	0	0	17855	536	19	1	99	1	ZNF280C	23	129339306	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	65512	129339306	25931254	2147	6544										
ZNF280C	55609	broad.mit.edu	37	chrX	129361684	129361684	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catatggcatttcaccaggtTtatgggtgtccttcatatgt	9	8	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129361684T>G	ENST00000370978.4	-	11	1373	c.1220A>C	c.(1219-1221)aAa>aCa	p.K407T		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K407T(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TTCACCAGGTTTATGGGTGTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	X											156	139	144					X																	129361684		2203	4298	6501	129189365	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1220A>C	X.37:g.129361684T>G	ENSP00000360017:p.Lys407Thr		129189365	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	t	21.0	4.077416	0.76528	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.27720	1.65;3.17	4.39	4.39	0.52855	.	.	.	.	.	T	0.33089	0.0851	N	0.05574	-0.02	0.40453	D	0.980169	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	T	0.39035	-0.9633	9	0.72032	D	0.01	.	10.7332	0.46109	0.0:0.0:0.0:1.0	.	407;407	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	T	407	ENSP00000360017:K407T;ENSP00000408521:K407T	ENSP00000066465:K407T	K	-	2	0	ZNF280C	129189365	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.822000	0.86651	1.732000	0.51606	0.427000	0.28365	AAA		0.318	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		G	129361684	T	G	129361684	3	3	47	1	0	0	0	0	1	0	0	0	17855	1841	64	4	1029	4	ZNF280C	23	129361684	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	22378	129361684	25908876	2148	6545										
ZNF280C	55609	broad.mit.edu	37	chrX	129380861	129380861	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gctggttttgaacttgatatCtctccaacaaagatcagttc	7	9	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129380861C>T	ENST00000370978.4	-	3	303	c.150G>A	c.(148-150)gaG>gaA	p.E50E		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E50E(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						AACTTGATATCTCTCCAACAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	X											252	206	222					X																	129380861		2203	4300	6503	129208542	SO:0001819	synonymous_variant	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.150G>A	X.37:g.129380861C>T			129208542	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																				0.358	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129380861	C	T	129380861	2	4	47	1	0	0	0	0	0	0	0	1	17855	912	32	3		3	ZNF280C	23	129380861	Silent	SNP	C	TCGA-AG-3892-01A-01W-1073-09	19177	129380861	25889699	2149	6546										
ENOX2	10495	broad.mit.edu	37	chrX	129771326	129771326	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acttcattccggtaggcatcGagctgccaacggaggctgtc	12	12	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:129771326G>A	ENST00000370927.1	-	9	1296	c.1275C>T	c.(1273-1275)ctC>ctT	p.L425L	ENOX2_ENST00000394363.1_Silent_p.L396L|ENOX2_ENST00000338144.3_Silent_p.L425L|ENOX2_ENST00000370935.1_Silent_p.L396L			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	425					cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)	p.L425L(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						GGTAGGCATCGAGCTGCCAAC	0.433													G|||	5	0.0013245	0	0	3775	,	,		14142	0		0	False		,,,				2504	0.0051				Ovarian(101;828 1506 2951 9500 35258)											1	Substitution - coding silent(1)	large_intestine(1)	X											244	191	209					X																	129771326		2203	4300	6503	129599007	SO:0001819	synonymous_variant	10495			AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"RNA binding motif (RRM) containing"	2259	protein-coding gene	gene with protein product		300282	"cytosolic ovarian carcinoma antigen 1"	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.1275C>T	X.37:g.129771326G>A			129599007	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Silent	SNP	ENST00000370927.1	37	CCDS14626.1																																																																																				0.433	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314		A	129771326	G	A	129771326	2	1	47	1	0	0	0	0	0	0	0	1	5140	1045	37	1		1	ENOX2	23	129771326	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	390465	129771326	25499234	2150	6547										
ARHGAP36	158763	broad.mit.edu	37	chrX	130218328	130218328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gatgagtctcaatccgattgCgaaacaaatcccccaggttg	9	11	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:130218328C>T	ENST00000276211.5	+	5	1040	c.695C>T	c.(694-696)gCg>gTg	p.A232V	ARHGAP36_ENST00000370922.1_Missense_Mutation_p.A220V|ARHGAP36_ENST00000370921.1_Missense_Mutation_p.A96V	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	232	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.A232V(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						AATCCGATTGCGAAACAAATC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	X											47	45	45					X																	130218328		2203	4300	6503	130046009	SO:0001583	missense	158763				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.695C>T	X.37:g.130218328C>T	ENSP00000276211:p.Ala232Val		130046009	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	C	8.845	0.943270	0.18281	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432;ENST00000370921	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	4.99	3.18	0.36537	Rho GTPase-activating protein domain (1);Rho GTPase activation protein (1);	0.130363	0.35349	N	0.003270	T	0.25568	0.0622	L	0.27053	0.805	0.28130	N	0.930236	P;P;P	0.48911	0.814;0.917;0.866	B;B;B	0.42245	0.272;0.381;0.14	T	0.07233	-1.0783	10	0.29301	T	0.29	.	5.2243	0.15385	0.0:0.6804:0.2075:0.1121	.	201;220;232	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	V	232;220;184;201;96	ENSP00000276211:A232V;ENSP00000359960:A220V;ENSP00000409218:A184V;ENSP00000408515:A201V;ENSP00000359959:A96V	ENSP00000276211:A232V	A	+	2	0	ARHGAP36	130046009	0.937000	0.31787	0.518000	0.27811	0.083000	0.17756	1.553000	0.36255	1.192000	0.43071	0.529000	0.55759	GCG		0.468	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130218328	C	T	130218328	3	4	47	1	0	0	0	0	1	0	0	0	883	768	27	1	709	1	ARHGAP36	23	130218328	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	447002	130218328	25052232	2151	6548										
FRMD7	90167	broad.mit.edu	37	chrX	131212720	131212720	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtttggaaggagcttagaGaactcctctctgaaaaaatg	10	6	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:131212720G>T	ENST00000298542.4	-	12	1500	c.1325C>A	c.(1324-1326)tCt>tAt	p.S442Y	FRMD7_ENST00000370879.1_Missense_Mutation_p.S322Y|FRMD7_ENST00000464296.1_Missense_Mutation_p.S427Y	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	442					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.S442Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GGAGCTTAGAGAACTCCTCTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											166	164	164					X																	131212720		2203	4300	6503	131040401	SO:0001583	missense	90167			AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1325C>A	X.37:g.131212720G>T	ENSP00000298542:p.Ser442Tyr		131040401	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527182	0.44969	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.86562	-2.14;-1.8;-1.91	5.76	5.76	0.90799	.	0.267689	0.32852	N	0.005563	T	0.77611	0.4156	N	0.08118	0	0.24087	N	0.995921	P;P	0.41131	0.739;0.49	B;B	0.39152	0.292;0.153	T	0.74858	-0.3521	10	0.72032	D	0.01	.	16.6966	0.85337	0.0:0.0:1.0:0.0	.	427;442	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	Y	322;442;427	ENSP00000359916:S322Y;ENSP00000298542:S442Y;ENSP00000417996:S427Y	ENSP00000298542:S442Y	S	-	2	0	FRMD7	131040401	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	4.937000	0.63513	2.418000	0.82041	0.600000	0.82982	TCT		0.428	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		T	131212720	G	T	131212720	3	4	47	1	0	0	0	0	1	0	0	0	6074	942	33	2	823	2	FRMD7	23	131212720	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	994392	131212720	24057840	2152	6549										
MBNL3	55796	broad.mit.edu	37	chrX	131525102	131525102	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	acaatttccacgctgaaattCtcggcaaaccttagaacaca	5	12	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:131525102C>A	ENST00000370853.3	-	4	622	c.544G>T	c.(544-546)Gaa>Taa	p.E182*	MBNL3_ENST00000394311.2_Nonsense_Mutation_p.E86*|MBNL3_ENST00000473364.1_5'UTR|MBNL3_ENST00000538204.1_Nonsense_Mutation_p.E132*|MBNL3_ENST00000370839.3_Nonsense_Mutation_p.E182*|MBNL3_ENST00000370844.1_Nonsense_Mutation_p.E86*|RAP2C-AS1_ENST00000421483.2_RNA|MBNL3_ENST00000370857.3_Nonsense_Mutation_p.E182*|RAP2C-AS1_ENST00000441399.2_RNA|MBNL3_ENST00000370849.3_Nonsense_Mutation_p.E132*	NM_018388.3	NP_060858.2	Q9NUK0	MBNL3_HUMAN	muscleblind-like splicing regulator 3	182					mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|negative regulation of myoblast differentiation (GO:0045662)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.E182*(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)	16	Acute lymphoblastic leukemia(192;0.000127)					CGCTGAAATTCTCGGCAAACC	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											90	78	82					X																	131525102		2203	4300	6503	131352783	SO:0001587	stop_gained	55796			AF491305	CCDS14633.1, CCDS14634.1, CCDS55492.1, CCDS55493.1, CCDS55494.1	Xq26.2	2013-01-18	2012-02-23		ENSG00000076770	ENSG00000076770		"Zinc fingers, CCCH-type domain containing"	20564	protein-coding gene	gene with protein product		300413	"muscleblind-like 3 (Drosophila)"			12297108, 10970838	Standard	NM_018388		Approved	CHCR, FLJ11316, MBLX39, MBXL	uc004ewv.4	Q9NUK0	OTTHUMG00000022426	ENST00000370853.3:c.544G>T	X.37:g.131525102C>A	ENSP00000359890:p.Glu182*		131352783	Q5JXN8|Q5JXN9|Q5JXP4|Q6UDQ1|Q8IUR4|Q8TAD9|Q8TAF4|Q9H0Z7|Q9UF37	Nonsense_Mutation	SNP	ENST00000370853.3	37	CCDS14633.1	.	.	.	.	.	.	.	.	.	.	C	38	6.651068	0.97734	.	.	ENSG00000076770	ENST00000394311;ENST00000538204;ENST00000370857;ENST00000370853;ENST00000370849;ENST00000370839;ENST00000370844;ENST00000436215;ENST00000421707	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.8846	19.0362	0.92980	0.0:1.0:0.0:0.0	.	.	.	.	X	86;132;182;182;132;182;86;86;86	.	ENSP00000359876:E182X	E	-	1	0	MBNL3	131352783	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.776000	0.85560	2.445000	0.82738	0.513000	0.50165	GAA		0.433	MBNL3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058319.1	NM_018388		A	131525102	C	A	131525102	4	1	47	1	0	0	0	0	0	1	0	0	9385	922	32	2	601	2	MBNL3	23	131525102	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	312382	131525102	23745458	2153	6550										
USP26	83844	broad.mit.edu	37	chrX	132159678	132159678	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctaacacccgcatatcatcGtaagtgaaccagatctgttt	6	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:132159678G>A	ENST00000511190.1	-	6	3040	c.2571C>T	c.(2569-2571)taC>taT	p.Y857Y	USP26_ENST00000406273.1_Silent_p.Y857Y|USP26_ENST00000370832.1_Silent_p.Y857Y	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	857	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.Y857Y(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GCATATCATCGTAAGTGAACC	0.453																																					NSCLC(104;342 1621 36940 47097 52632)											1	Substitution - coding silent(1)	large_intestine(1)	X											145	122	130					X																	132159678		2203	4300	6503	131987344	SO:0001819	synonymous_variant	83844			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2571C>T	X.37:g.132159678G>A			131987344	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	37	CCDS14635.1																																																																																				0.453	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132159678	G	A	132159678	2	1	47	1	0	0	0	0	0	0	0	1	17097	1140	40	1		1	USP26	23	132159678	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	634576	132159678	23110882	2154	6551										
USP26	83844	broad.mit.edu	37	chrX	132160488	132160488	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gattcctttgttgcaggccaTgatacactgatgtttccaga	9	9	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:132160488T>G	ENST00000511190.1	-	6	2230	c.1761A>C	c.(1759-1761)tcA>tcC	p.S587S	USP26_ENST00000406273.1_Silent_p.S587S|USP26_ENST00000370832.1_Silent_p.S587S	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	587	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.S587S(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					TTGCAGGCCATGATACACTGA	0.413																																					NSCLC(104;342 1621 36940 47097 52632)											1	Substitution - coding silent(1)	large_intestine(1)	X											82	74	77					X																	132160488		2203	4299	6502	131988154	SO:0001819	synonymous_variant	83844			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1761A>C	X.37:g.132160488T>G			131988154	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	37	CCDS14635.1																																																																																				0.413	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		G	132160488	T	G	132160488	2	3	47	1	0	0	0	0	0	0	0	1	17097	1451	51	4		4	USP26	23	132160488	Silent	SNP	T	TCGA-AG-3892-01A-01W-1073-09	810	132160488	23110072	2155	6552										
USP26	83844	broad.mit.edu	37	chrX	132161838	132161838	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aaagatttgctacttgatttCtcatcaactttgtggaatga	7	6	2	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:132161838C>A	ENST00000511190.1	-	6	880	c.411G>T	c.(409-411)gaG>gaT	p.E137D	USP26_ENST00000406273.1_Missense_Mutation_p.E137D|USP26_ENST00000370832.1_Missense_Mutation_p.E137D	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	137					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.E137D(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					TACTTGATTTCTCATCAACTT	0.433																																					NSCLC(104;342 1621 36940 47097 52632)											1	Substitution - Missense(1)	large_intestine(1)	X											76	55	62					X																	132161838		2203	4299	6502	131989504	SO:0001583	missense	83844			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.411G>T	X.37:g.132161838C>A	ENSP00000423390:p.Glu137Asp		131989504	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	C	3.454	-0.111488	0.06881	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.54866	0.55;0.55;0.55	3.79	-2.85	0.05734	.	2.177290	0.02597	N	0.100626	T	0.30386	0.0763	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.04078	-1.0979	10	0.14656	T	0.56	3.4871	0.9248	0.01322	0.4361:0.2233:0.1417:0.1989	.	137	Q9BXU7	UBP26_HUMAN	D	137	ENSP00000359869:E137D;ENSP00000423390:E137D;ENSP00000384360:E137D	ENSP00000359869:E137D	E	-	3	2	USP26	131989504	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.352000	0.07701	-0.921000	0.03794	-0.360000	0.07572	GAG		0.433	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132161838	C	A	132161838	3	1	47	1	0	0	0	0	1	0	0	0	17097	912	32	2	2333	2	USP26	23	132161838	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1350	132161838	23108722	2156	6553										
GPC3	2719	broad.mit.edu	37	chrX	132730611	132730611	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gaactctacctttgggcataGacatggttctcaggagctga	11	9	2	2	rs139301532		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:132730611G>T	ENST00000370818.3	-	7	1875	c.1430C>A	c.(1429-1431)tCt>tAt	p.S477Y	GPC3_ENST00000394299.2_Missense_Mutation_p.S500Y|GPC3_ENST00000543339.1_Missense_Mutation_p.S423Y	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	477					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)	p.S477F(1)|p.S477Y(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					TTTGGGCATAGACATGGTTCT	0.453			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome																													yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	X											178	154	162					X																	132730611		2203	4300	6503	132558277	SO:0001583	missense	2719	Familial Cancer Database	SGBS	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"Proteoglycans / Cell Surface : Glypicans"	4451	protein-coding gene	gene with protein product	"glypican proteoglycan 3"	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1430C>A	X.37:g.132730611G>T	ENSP00000359854:p.Ser477Tyr		132558277	C9JLE3|G3V1R0|Q2L880|Q2L882	Missense_Mutation	SNP	ENST00000370818.3	37	CCDS14638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.66|19.66	3.868533|3.868533	0.72065|0.72065	.|.	.|.	ENSG00000147257|ENSG00000147257	ENST00000406757|ENST00000370818;ENST00000394299;ENST00000543339	.|T;T;T	.|0.57752	.|0.43;0.38;0.44	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	.|1.378240	.|0.04343	.|N	.|0.354369	T|T	0.69351|0.69351	0.3101|0.3101	L|L	0.43923|0.43923	1.385|1.385	0.38526|0.38526	D|D	0.94884|0.94884	.|D;D;D;D	.|0.65815	.|0.993;0.995;0.995;0.984	.|D;P;D;D	.|0.68943	.|0.914;0.861;0.961;0.914	T|T	0.55379|0.55379	-0.8150|-0.8150	5|10	.|0.87932	.|D	.|0	.|.	14.2975|14.2975	0.66325|0.66325	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|461;423;500;477	.|B4DTD8;G3V1R0;C9JLE3;P51654	.|.;.;.;GPC3_HUMAN	I|Y	207|477;500;423	.|ENSP00000359854:S477Y;ENSP00000377836:S500Y;ENSP00000444222:S423Y	.|ENSP00000359854:S477Y	L|S	-|-	1|2	2|0	GPC3|GPC3	132558277|132558277	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.671000|5.671000	0.68095|0.68095	2.093000|2.093000	0.63338|0.63338	0.468000|0.468000	0.43344|0.43344	CTA|TCT		0.453	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		T	132730611	G	T	132730611	3	4	47	1	0	0	0	0	1	0	0	0	6619	942	33	2	320	2	GPC3	23	132730611	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	568773	132730611	22539949	2157	6554										
CCDC160	347475	broad.mit.edu	37	chrX	133379807	133379807	+	Nonstop_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctttactggggattttttttAaaacttaaaaaaatccttcc	4	7	0	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:133379807A>T	ENST00000517294.1	+	3	1360	c.977A>T	c.(976-978)tAa>tTa	p.*326L	CCDC160_ENST00000370809.4_Nonstop_Mutation_p.*326L			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	0								p.*326L(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GATTTTTTTTAAAACTTAAAA	0.318																																																1	Nonstop extension(1)	large_intestine(1)	X											12	11	11					X																	133379807		1732	3939	5671	133207473	SO:0001578	stop_lost	347475			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.977A>T	X.37:g.133379807A>T	ENSP00000427951:p.*326Leuext*8		133207473		Nonstop_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.730866	0.30684	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	.	.	.	5.25	-0.308	0.12773	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.8751	0.01222	0.4976:0.161:0.1831:0.1583	.	.	.	.	L	326	.	.	X	+	2	2	CCDC160	133207473	0.996000	0.38824	0.007000	0.13788	0.059000	0.15707	1.238000	0.32707	-0.335000	0.08451	-1.400000	0.01143	TAA		0.318	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		T	133379807	A	T	133379807	4	4	47	1	0	0	0	0	0	0	0	0	2798	377	13	5	979	5	CCDC160	23	133379807	Nonstop_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	649196	133379807	21890753	2158	6555										
PLAC1	10761	broad.mit.edu	37	chrX	133700589	133700589	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cacatcgttgtttagcatgaAggggtgcactgtgaccatga	12	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:133700589A>C	ENST00000359237.4	-	3	409	c.124T>G	c.(124-126)Ttc>Gtc	p.F42V	PLAC1_ENST00000476971.1_5'UTR	NM_021796.3	NP_068568.1			placenta-specific 1									p.F42V(1)		large_intestine(4)|lung(1)|pancreas(1)	6	Acute lymphoblastic leukemia(192;0.000127)					TTTAGCATGAAGGGGTGCACT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	X											227	199	209					X																	133700589		2203	4300	6503	133528255	SO:0001583	missense	10761			AF234654	CCDS14642.1	Xq26.3	2013-10-14			ENSG00000170965	ENSG00000170965			9044	protein-coding gene	gene with protein product	"cancer/testis antigen 92"	300296				10995572	Standard	NM_021796		Approved	CT92, OOSP2L	uc004exo.1	Q9HBJ0	OTTHUMG00000022457	ENST00000359237.4:c.124T>G	X.37:g.133700589A>C	ENSP00000352173:p.Phe42Val		133528255		Missense_Mutation	SNP	ENST00000359237.4	37	CCDS14642.1	.	.	.	.	.	.	.	.	.	.	A	9.797	1.179487	0.21787	.	.	ENSG00000170965	ENST00000359237	D	0.81908	-1.55	4.35	1.93	0.25924	.	0.899500	0.09330	N	0.817068	T	0.79435	0.4445	M	0.72479	2.2	0.09310	N	1	P	0.36909	0.573	B	0.36666	0.23	T	0.64769	-0.6329	10	0.33940	T	0.23	-13.1094	5.2739	0.15639	0.7625:0.0:0.2375:0.0	.	42	Q9HBJ0	PLAC1_HUMAN	V	42	ENSP00000352173:F42V	ENSP00000352173:F42V	F	-	1	0	PLAC1	133528255	0.831000	0.29352	0.007000	0.13788	0.132000	0.20833	2.177000	0.42509	0.290000	0.22444	-0.360000	0.07572	TTC		0.512	PLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058375.1	NM_021796		C	133700589	A	C	133700589	3	2	47	1	0	0	0	0	1	0	0	0	12043	72	3	4	518	4	PLAC1	23	133700589	Missense_Mutation	SNP	A	TCGA-AG-3892-01A-01W-1073-09	320782	133700589	21569971	2159	6556										
FAM122B	159090	broad.mit.edu	37	chrX	133923269	133923269	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	taacctttcatgtgcagtttCtctgttcaccatatccaggc	6	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:133923269C>A	ENST00000370790.1	-	3	1133	c.205G>T	c.(205-207)Gaa>Taa	p.E69*	FAM122B_ENST00000493333.1_5'UTR|FAM122B_ENST00000486347.1_Nonsense_Mutation_p.E69*|FAM122B_ENST00000298090.6_Nonsense_Mutation_p.E88*|FAM122B_ENST00000343004.5_Nonsense_Mutation_p.E88*	NM_001166599.2|NM_145284.5	NP_001160071.1|NP_660327.2	Q7Z309	F122B_HUMAN	family with sequence similarity 122B	69								p.E69*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|skin(1)	6	Acute lymphoblastic leukemia(192;0.000127)					TGTGCAGTTTCTCTGTTCACC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											156	130	139					X																	133923269		2203	4300	6503	133750935	SO:0001587	stop_gained	159090			BX538218	CCDS14643.1, CCDS55497.1, CCDS55498.1	Xq26.3	2008-02-05			ENSG00000156504	ENSG00000156504			30490	protein-coding gene	gene with protein product						12477932	Standard	NM_145284		Approved	DKFZp686L20116, RP11-308B5.5	uc004exq.3	Q7Z309	OTTHUMG00000022461	ENST00000370790.1:c.205G>T	X.37:g.133923269C>A	ENSP00000359826:p.Glu69*		133750935	A8K902|Q6PIM2|Q6ZU47|Q6ZV64|Q6ZVE4|Q8TB75	Nonsense_Mutation	SNP	ENST00000370790.1	37	CCDS55497.1	.	.	.	.	.	.	.	.	.	.	C	37	6.352118	0.97498	.	.	ENSG00000156504	ENST00000370790;ENST00000298090;ENST00000343004;ENST00000394270;ENST00000486347	.	.	.	5.86	5.0	0.66597	.	0.076841	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.9168	0.58211	0.0:0.9207:0.0:0.0793	.	.	.	.	X	69;88;88;88;69	.	ENSP00000298090:E88X	E	-	1	0	FAM122B	133750935	1.000000	0.71417	0.777000	0.31699	0.662000	0.39071	5.779000	0.68948	1.215000	0.43411	0.594000	0.82650	GAA		0.413	FAM122B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058382.1	NM_145284		A	133923269	C	A	133923269	4	1	47	1	0	0	0	0	0	1	0	0	5436	922	32	2	643	2	FAM122B	23	133923269	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	222680	133923269	21347291	2160	6557										
ZNF449	203523	broad.mit.edu	37	chrX	134481164	134481164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcagttccagtacagagaaGcagctgggcctcatgaagca	13	10	1	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:134481164G>A	ENST00000339249.4	+	2	261	c.121G>A	c.(121-123)Gca>Aca	p.A41T	ZNF449_ENST00000370761.3_Missense_Mutation_p.A41T|ZNF449_ENST00000370760.3_Missense_Mutation_p.A41T	NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	41	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A41T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GTACAGAGAAGCAGCTGGGCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	X											96	90	92					X																	134481164		2203	4300	6503	134308830	SO:0001583	missense	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.121G>A	X.37:g.134481164G>A	ENSP00000339585:p.Ala41Thr		134308830	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	37	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	G	9.199	1.028066	0.19512	.	.	ENSG00000173275	ENST00000370761;ENST00000339249;ENST00000370760	T;T;T	0.04502	3.61;3.61;3.61	4.6	3.74	0.42951	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.43110	D	0.000606	T	0.06005	0.0156	N	0.22421	0.69	0.09310	N	1	P;D;P	0.67145	0.856;0.996;0.733	P;P;P	0.60541	0.723;0.876;0.55	T	0.12319	-1.0552	10	0.02654	T	1	.	7.4423	0.27190	0.117:0.0:0.883:0.0	.	41;41;41	Q6P9G9;Q6P9G9-2;Q6P9G9-3	ZN449_HUMAN;.;.	T	41	ENSP00000359797:A41T;ENSP00000339585:A41T;ENSP00000359796:A41T	ENSP00000339585:A41T	A	+	1	0	ZNF449	134308830	1.000000	0.71417	0.051000	0.19133	0.965000	0.64279	3.488000	0.53229	1.282000	0.44496	0.594000	0.82650	GCA		0.473	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		A	134481164	G	A	134481164	3	1	47	1	0	0	0	0	1	0	0	0	17959	971	34	3	123	3	ZNF449	23	134481164	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	557895	134481164	20789396	2161	6558										
SAGE1	55511	broad.mit.edu	37	chrX	134993887	134993887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cattggattctttctctcacGacttcacaagtctcagcaaa	5	12	5	0	rs146408420		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:134993887G>A	ENST00000370709.3	+	17	2296	c.2296G>A	c.(2296-2298)Gac>Aac	p.D766N	SAGE1_ENST00000537770.1_Missense_Mutation_p.D390N|SAGE1_ENST00000535938.1_Missense_Mutation_p.D766N|SAGE1_ENST00000324447.3_Missense_Mutation_p.D766N			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	766						nucleus (GO:0005634)		p.D766N(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					TTTCTCTCACGACTTCACAAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	ASN/ASP	1,3834		0,1,1631,571	167	158	161		2296	1.8	0	X	dbSNP_134	161	0,6728		0,0,2428,1872	no	missense	SAGE1	NM_018666.2	23	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	probably-damaging	766/905	134993887	1,10562	2203	4300	6503	134821553	SO:0001583	missense	55511			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2296G>A	X.37:g.134993887G>A	ENSP00000359743:p.Asp766Asn		134821553	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.673551	0.29693	2.61E-4	0.0	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.39229	1.09;1.09;1.13;1.09	2.67	1.75	0.24633	.	0.896444	0.09542	N	0.788152	T	0.25901	0.0631	N	0.25890	0.77	0.09310	N	1	P;B	0.34662	0.462;0.102	B;B	0.20184	0.028;0.014	T	0.06770	-1.0808	10	0.33940	T	0.23	.	10.043	0.42169	0.0:0.2036:0.7964:0.0	.	390;766	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	N	766;766;390;766	ENSP00000323191:D766N;ENSP00000445959:D766N;ENSP00000438276:D390N;ENSP00000359743:D766N	ENSP00000323191:D766N	D	+	1	0	SAGE1	134821553	0.001000	0.12720	0.001000	0.08648	0.162000	0.22319	0.285000	0.18883	0.111000	0.17947	0.179000	0.17066	GAC		0.448	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		A	134993887	G	A	134993887	3	1	47	1	0	0	0	0	1	0	0	0	13846	1058	37	1	2362	1	SAGE1	23	134993887	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	512723	134993887	20276673	2162	6559										
MAP7D3	79649	broad.mit.edu	37	chrX	135308162	135308162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctcttgagcttttattttgGcgtcccctttctaggaaatt	7	10	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:135308162G>A	ENST00000316077.9	-	13	2265	c.2045C>T	c.(2044-2046)gCc>gTc	p.A682V	MAP7D3_ENST00000495432.1_5'UTR|MAP7D3_ENST00000370661.1_Missense_Mutation_p.A647V|MAP7D3_ENST00000370663.5_Missense_Mutation_p.A664V	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	682					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.A979V(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TTTTATTTTGGCGTCCCCTTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											175	144	154					X																	135308162		1817	4072	5889	135135828	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.2045C>T	X.37:g.135308162G>A	ENSP00000318086:p.Ala682Val		135135828	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	G	8.228	0.804058	0.16467	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	4.48	1.67	0.24075	.	.	.	.	.	T	0.41604	0.1166	M	0.84948	2.725	0.09310	N	1	P;P;P;P	0.49559	0.925;0.908;0.925;0.908	P;B;P;B	0.48270	0.572;0.436;0.572;0.436	T	0.34354	-0.9832	9	0.87932	D	0	-0.8427	5.2049	0.15285	0.1955:0.0:0.64:0.1644	.	664;641;682;647	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	V	647;682;664;641	ENSP00000359695:A647V;ENSP00000318086:A682V;ENSP00000359697:A664V;ENSP00000359694:A641V	ENSP00000318086:A682V	A	-	2	0	MAP7D3	135135828	0.799000	0.28903	0.008000	0.14137	0.015000	0.08874	1.234000	0.32660	0.082000	0.17018	-0.245000	0.11935	GCC		0.338	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			A	135308162	G	A	135308162	3	1	47	1	0	0	0	0	1	0	0	0	9299	1203	42	3	609	3	MAP7D3	23	135308162	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	314275	135308162	19962398	2163	6560										
GPR112	139378	broad.mit.edu	37	chrX	135428507	135428507	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agcacaaagggtgacagcttCtgtcactgtttcctcttttc	8	11	3	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:135428507C>A	ENST00000394143.1	+	6	2933	c.2642C>A	c.(2641-2643)tCt>tAt	p.S881Y	GPR112_ENST00000287534.4_Missense_Mutation_p.S818Y|GPR112_ENST00000412101.1_Missense_Mutation_p.S676Y|GPR112_ENST00000394141.1_Missense_Mutation_p.S676Y|GPR112_ENST00000370652.1_Missense_Mutation_p.S881Y	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	881					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S881Y(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GTGACAGCTTCTGTCACTGTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											127	120	122					X																	135428507		2203	4300	6503	135256173	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.2642C>A	X.37:g.135428507C>A	ENSP00000377699:p.Ser881Tyr		135256173	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	C	6.965	0.548081	0.13312	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.41065	1.05;1.05;1.01;1.12;1.01	2.75	0.761	0.18448	.	.	.	.	.	T	0.42832	0.1220	L	0.29908	0.895	0.09310	N	1	D;P;P	0.58268	0.982;0.82;0.886	P;B;B	0.62184	0.899;0.445;0.259	T	0.24368	-1.0162	9	0.87932	D	0	.	4.0218	0.09668	0.0:0.5937:0.2435:0.1629	.	818;676;881	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	Y	881;881;676;818;676	ENSP00000377699:S881Y;ENSP00000359686:S881Y;ENSP00000416526:S676Y;ENSP00000287534:S818Y;ENSP00000377697:S676Y	ENSP00000287534:S818Y	S	+	2	0	GPR112	135256173	0.002000	0.14202	0.005000	0.12908	0.206000	0.24218	-0.332000	0.07904	-0.044000	0.13491	0.284000	0.19432	TCT		0.398	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			A	135428507	C	A	135428507	3	1	47	1	0	0	0	0	1	0	0	0	6649	913	32	2	2652	2	GPR112	23	135428507	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	120345	135428507	19842053	2164	6561										
GPR112	139378	broad.mit.edu	37	chrX	135429806	135429806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttccagtcaccaaacacattCgccttcagagattccacttg	5	14	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:135429806C>T	ENST00000394143.1	+	6	4232	c.3941C>T	c.(3940-3942)tCg>tTg	p.S1314L	GPR112_ENST00000287534.4_Missense_Mutation_p.S1251L|GPR112_ENST00000412101.1_Missense_Mutation_p.S1109L|GPR112_ENST00000394141.1_Missense_Mutation_p.S1109L|GPR112_ENST00000370652.1_Missense_Mutation_p.S1314L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1314					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S1314L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAAACACATTCGCCTTCAGAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	X											81	70	74					X																	135429806		2203	4300	6503	135257472	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3941C>T	X.37:g.135429806C>T	ENSP00000377699:p.Ser1314Leu		135257472	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	0.014	-1.605054	0.00842	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.28666	1.63;1.63;1.6;1.74;1.6	2.92	-2.66	0.06077	.	.	.	.	.	T	0.13586	0.0329	N	0.08118	0	0.09310	N	1	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.0	T	0.23404	-1.0189	9	0.35671	T	0.21	.	7.724	0.28748	0.0:0.4304:0.0:0.5696	.	1251;1109;1314	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	L	1314;1314;1109;1251;1109	ENSP00000377699:S1314L;ENSP00000359686:S1314L;ENSP00000416526:S1109L;ENSP00000287534:S1251L;ENSP00000377697:S1109L	ENSP00000287534:S1251L	S	+	2	0	GPR112	135257472	0.623000	0.27094	0.148000	0.22405	0.086000	0.17979	0.029000	0.13666	-0.757000	0.04697	-1.221000	0.01599	TCG		0.433	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135429806	C	T	135429806	3	4	47	1	0	0	0	0	1	0	0	0	6649	893	31	1	3951	1	GPR112	23	135429806	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1299	135429806	19840754	2165	6562										
HTATSF1	27336	broad.mit.edu	37	chrX	135584989	135584989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggatgaagatgaaattagagGctacaaattacatgttgagg	12	3	0	5			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:135584989G>A	ENST00000218364.4	+	5	797	c.623G>A	c.(622-624)gGc>gAc	p.G208D	HTATSF1_ENST00000535601.1_Missense_Mutation_p.G208D	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	208	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G208D(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					GAAATTAGAGGCTACAAATTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	X											87	88	87					X																	135584989		2203	4298	6501	135412655	SO:0001583	missense	27336			U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.623G>A	X.37:g.135584989G>A	ENSP00000218364:p.Gly208Asp		135412655	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	37	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.360520	0.82353	.	.	ENSG00000102241	ENST00000535601;ENST00000448450;ENST00000425695;ENST00000218364;ENST00000415377	T;T;T;T	0.53206	2.71;0.63;0.63;2.71	5.4	5.4	0.78164	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.70745	0.3259	M	0.81942	2.565	0.80722	D	1	D	0.60575	0.988	D	0.68192	0.956	T	0.73874	-0.3845	10	0.52906	T	0.07	-7.5642	18.3147	0.90215	0.0:0.0:1.0:0.0	.	208	O43719	HTSF1_HUMAN	D	208	ENSP00000442699:G208D;ENSP00000411381:G208D;ENSP00000412420:G208D;ENSP00000218364:G208D	ENSP00000218364:G208D	G	+	2	0	HTATSF1	135412655	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.294000	0.96088	2.264000	0.75181	0.468000	0.43344	GGC		0.328	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		A	135584989	G	A	135584989	3	1	47	1	0	0	0	0	1	0	0	0	7454	1203	42	3	641	3	HTATSF1	23	135584989	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	155183	135584989	19685571	2166	6563										
GPR101	83550	broad.mit.edu	37	chrX	136113725	136113725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ggcgaggaagataaccagcaCggttgagcggatgatgccgt	16	8	0	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:136113725C>T	ENST00000298110.1	-	1	108	c.109G>A	c.(109-111)Gtg>Atg	p.V37M		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.V37M(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					ATAACCAGCACGGTTGAGCGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	X											95	72	80					X																	136113725		2203	4300	6503	135941391	SO:0001583	missense	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.109G>A	X.37:g.136113725C>T	ENSP00000298110:p.Val37Met		135941391	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703343	0.30232	.	.	ENSG00000165370	ENST00000298110	T	0.41758	0.99	5.09	3.06	0.35304	.	.	.	.	.	T	0.45577	0.1349	L	0.27053	0.805	0.31296	N	0.688839	D	0.76494	0.999	D	0.64042	0.921	T	0.48007	-0.9072	9	0.87932	D	0	-14.7588	8.7317	0.34503	0.1639:0.6785:0.1575:0.0	.	37	Q96P66	GP101_HUMAN	M	37	ENSP00000298110:V37M	ENSP00000298110:V37M	V	-	1	0	GPR101	135941391	0.537000	0.26386	0.878000	0.34440	0.353000	0.29299	1.011000	0.29911	2.100000	0.63781	0.544000	0.68410	GTG		0.597	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136113725	C	T	136113725	3	4	47	1	0	0	0	0	1	0	0	0	6642	536	19	1	1420	1	GPR101	23	136113725	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	528736	136113725	19156835	2167	6564										
MCF2	4168	broad.mit.edu	37	chrX	138678795	138678795	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgcaaaaaacaatggctttTtcatacaagaaaaggtgtcg	8	6	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:138678795T>G	ENST00000370576.4	-	19	2399	c.2190A>C	c.(2188-2190)gaA>gaC	p.E730D	MCF2_ENST00000370573.4_Missense_Mutation_p.E730D|MCF2_ENST00000414978.1_Missense_Mutation_p.E790D|MCF2_ENST00000338585.6_Missense_Mutation_p.E746D|MCF2_ENST00000519895.1_Missense_Mutation_p.E806D|MCF2_ENST00000520602.1_Missense_Mutation_p.E790D|MCF2_ENST00000536274.1_Missense_Mutation_p.E691D|MCF2_ENST00000370578.4_Missense_Mutation_p.E875D|AL033403.1_ENST00000401295.2_RNA	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	730	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E806D(1)|p.E730D(1)		NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					CAATGGCTTTTTCATACAAGA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	X											122	102	109					X																	138678795		2203	4300	6503	138506461	SO:0001583	missense	4168				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.2190A>C	X.37:g.138678795T>G	ENSP00000359608:p.Glu730Asp		138506461	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.24|15.24	2.775332|2.775332	0.49786|0.49786	.|.	.|.	ENSG00000101977|ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000446225;ENST00000519895;ENST00000370573;ENST00000338585|ENST00000437564	T;T;T;T;T;T;T;T;T|.	0.14766|.	2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48|.	5.88|5.88	-2.21|-2.21	0.06973|0.06973	Pleckstrin homology-type (1);Pleckstrin homology domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61578|0.61578	0.2358|0.2358	M|M	0.78049|0.78049	2.395|2.395	0.31063|0.31063	N|N	0.713893|0.713893	B;B;B;B;B;B;P;B|.	0.34757|.	0.252;0.337;0.119;0.252;0.119;0.252;0.467;0.252|.	B;B;B;B;B;B;B;B|.	0.41236|.	0.076;0.191;0.113;0.076;0.159;0.076;0.351;0.076|.	T|T	0.66360|0.66360	-0.5943|-0.5943	10|5	0.52906|.	T|.	0.07|.	.|.	12.8873|12.8873	0.58051|0.58051	0.0:0.5183:0.0:0.4817|0.0:0.5183:0.0:0.4817	.|.	806;875;691;730;730;875;746;730|.	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911|.	.;.;.;.;.;.;.;MCF2_HUMAN|.	D|Q	790;730;691;875;790;333;806;730;746|234	ENSP00000427745:E790D;ENSP00000359608:E730D;ENSP00000438155:E691D;ENSP00000359610:E875D;ENSP00000397055:E790D;ENSP00000405848:E333D;ENSP00000430276:E806D;ENSP00000359605:E730D;ENSP00000342204:E746D|.	ENSP00000342204:E746D|.	E|K	-|-	3|1	2|0	MCF2|MCF2	138506461|138506461	0.972000|0.972000	0.33761|0.33761	0.988000|0.988000	0.46212|0.46212	0.924000|0.924000	0.55760|0.55760	0.149000|0.149000	0.16243|0.16243	-0.480000|-0.480000	0.06803|0.06803	-0.314000|-0.314000	0.08810|0.08810	GAA|AAA		0.403	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		G	138678795	T	G	138678795	3	3	47	1	0	0	0	0	1	0	0	0	9408	1838	64	4	643	4	MCF2	23	138678795	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	2565070	138678795	16591765	2168	6565										
ATP11C	286410	broad.mit.edu	37	chrX	138884448	138884448	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	attgctgctcggagggtatcGatggattctgctgtacacag	13	8	1	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:138884448G>T	ENST00000327569.3	-	7	713	c.615C>A	c.(613-615)atC>atA	p.I205I	ATP11C_ENST00000359686.2_Silent_p.I205I|ATP11C_ENST00000370543.1_Silent_p.I205I|ATP11C_ENST00000370557.1_Silent_p.I202I|ATP11C_ENST00000361648.2_Silent_p.I205I	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	205					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.I205I(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					GGAGGGTATCGATGGATTCTG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	X											274	221	239					X																	138884448		2203	4300	6503	138712114	SO:0001819	synonymous_variant	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.615C>A	X.37:g.138884448G>T			138712114	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Silent	SNP	ENST00000327569.3	37	CCDS14668.1																																																																																				0.398	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		T	138884448	G	T	138884448	2	4	47	1	0	0	0	0	0	0	0	1	1122	1048	37	2		2	ATP11C	23	138884448	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	205653	138884448	16386112	2169	6566										
MAGEC3	139081	broad.mit.edu	37	chrX	140969505	140969505	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccagaaccgcctcctgattCttattctgagtgtgatcttc	7	13	3	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:140969505C>A	ENST00000298296.1	+	4	832	c.832C>A	c.(832-834)Ctt>Att	p.L278I	MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000448920.1_Intron	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	278	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.L278I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCCTGATTCTTATTCTGAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	X											134	128	130					X																	140969505		2202	4300	6502	140797171	SO:0001583	missense	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.832C>A	X.37:g.140969505C>A	ENSP00000298296:p.Leu278Ile		140797171	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	C	4.095	0.015647	0.07959	.	.	ENSG00000165509	ENST00000298296	T	0.05081	3.5	2.26	-4.53	0.03462	.	.	.	.	.	T	0.02193	0.0068	N	0.13272	0.32	0.09310	N	1	B	0.20780	0.048	B	0.14023	0.01	T	0.44513	-0.9323	9	0.02654	T	1	.	1.3204	0.02115	0.2003:0.3623:0.2812:0.1562	.	278	Q8TD91	MAGC3_HUMAN	I	278	ENSP00000298296:L278I	ENSP00000298296:L278I	L	+	1	0	MAGEC3	140797171	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.582000	0.05814	-1.942000	0.01040	-1.459000	0.01027	CTT		0.502	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		A	140969505	C	A	140969505	3	1	47	1	0	0	0	0	1	0	0	0	9212	913	32	2	846	2	MAGEC3	23	140969505	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2085057	140969505	14301055	2170	6567										
MAGEC1	9947	broad.mit.edu	37	chrX	140993373	140993373	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cagagtcgttctgagggggaGgactcctcggatcctctcca	13	12	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:140993373G>T	ENST00000285879.4	+	4	469	c.183G>T	c.(181-183)gaG>gaT	p.E61D	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	61								p.E61D(1)|p.E61E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTGAGGGGGAGGACTCCTCGG	0.602										HNSCC(15;0.026)																																						2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	X											79	80	80					X																	140993373		2203	4300	6503	140821039	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.183G>T	X.37:g.140993373G>T	ENSP00000285879:p.Glu61Asp		140821039	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	g	4.405	0.074873	0.08485	.	.	ENSG00000155495	ENST00000285879	T	0.02812	4.15	0.149	0.149	0.14863	.	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	0.58432	D	0.999993	P	0.42584	0.784	B	0.33690	0.168	T	0.64101	-0.6486	9	0.87932	D	0	.	5.9897	0.19454	6.0E-4:0.0:0.9994:0.0	.	61	O60732	MAGC1_HUMAN	D	61	ENSP00000285879:E61D	ENSP00000285879:E61D	E	+	3	2	MAGEC1	140821039	0.003000	0.15002	0.019000	0.16419	0.019000	0.09904	0.213000	0.17521	0.177000	0.19895	0.179000	0.17066	GAG		0.602	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140993373	G	T	140993373	3	4	47	1	0	0	0	0	1	0	0	0	9210	991	35	2	189	2	MAGEC1	23	140993373	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	23868	140993373	14277187	2171	6568										
MAGEC1	9947	broad.mit.edu	37	chrX	140993858	140993858	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcccctgagagaactcagaGtacttttgagggttttgccc	10	10	1	4			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:140993858G>T	ENST00000285879.4	+	4	954	c.668G>T	c.(667-669)aGt>aTt	p.S223I	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	223				TQSTF -> SQRTS (in Ref. 1 and 2). {ECO:0000305}.				p.S223I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					AGAACTCAGAGTACTTTTGAG	0.493										HNSCC(15;0.026)																																						1	Substitution - Missense(1)	large_intestine(1)	X											112	116	115					X																	140993858		2202	4290	6492	140821524	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.668G>T	X.37:g.140993858G>T	ENSP00000285879:p.Ser223Ile		140821524	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	-	0.537	-0.855117	0.02630	.	.	ENSG00000155495	ENST00000285879	T	0.02552	4.25	.	.	.	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	B	0.26876	0.162	B	0.24394	0.053	T	0.49370	-0.8947	8	0.27785	T	0.31	.	5.8503	0.18689	9.0E-4:0.0:0.9991:0.0	.	223	O60732	MAGC1_HUMAN	I	223	ENSP00000285879:S223I	ENSP00000285879:S223I	S	+	2	0	MAGEC1	140821524	0.004000	0.15560	0.019000	0.16419	0.019000	0.09904	-0.191000	0.09601	0.054000	0.16065	0.054000	0.15206	AGT		0.493	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140993858	G	T	140993858	3	4	47	1	0	0	0	0	1	0	0	0	9210	1029	36	2	674	2	MAGEC1	23	140993858	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	485	140993858	14276702	2172	6569										
MAGEC1	9947	broad.mit.edu	37	chrX	140996068	140996068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cccgtgagttcatagagataCtttttggcatttccctgaga	9	9	1	3			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:140996068C>T	ENST00000285879.4	+	4	3164	c.2878C>T	c.(2878-2880)Ctt>Ttt	p.L960F	MAGEC1_ENST00000406005.2_Missense_Mutation_p.L27F	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	960	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.L960F(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CATAGAGATACTTTTTGGCAT	0.488										HNSCC(15;0.026)																																						1	Substitution - Missense(1)	large_intestine(1)	X											144	137	140					X																	140996068		2203	4300	6503	140823734	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2878C>T	X.37:g.140996068C>T	ENSP00000285879:p.Leu960Phe		140823734	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	7.720	0.697013	0.15106	.	.	ENSG00000155495	ENST00000285879;ENST00000406005	T;T	0.04917	3.53;3.53	0.837	-1.67	0.08238	.	.	.	.	.	T	0.09992	0.0245	L	0.48986	1.54	0.09310	N	1	P	0.52061	0.95	P	0.53224	0.721	T	0.14755	-1.0461	8	0.87932	D	0	.	.	.	.	.	960	O60732	MAGC1_HUMAN	F	960;27	ENSP00000285879:L960F;ENSP00000385500:L27F	ENSP00000285879:L960F	L	+	1	0	MAGEC1	140823734	0.012000	0.17670	0.007000	0.13788	0.189000	0.23516	0.010000	0.13242	-0.887000	0.03961	0.279000	0.19357	CTT		0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140996068	C	T	140996068	3	4	47	1	0	0	0	0	1	0	0	0	9210	565	20	3	2884	3	MAGEC1	23	140996068	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	2210	140996068	14274492	2173	6570										
SLITRK4	139065	broad.mit.edu	37	chrX	142717256	142717256	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aggcgtctcacatttcagttCtttcacaacaatcccgtcgc	6	14	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:142717256C>A	ENST00000381779.4	-	2	1894	c.1669G>T	c.(1669-1671)Gaa>Taa	p.E557*	SLITRK4_ENST00000356928.1_Nonsense_Mutation_p.E557*|SLITRK4_ENST00000338017.4_Nonsense_Mutation_p.E557*	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	557	LRRCT 2.					integral component of membrane (GO:0016021)		p.E557*(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CATTTCAGTTCTTTCACAACA	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											135	131	133					X																	142717256		2203	4300	6503	142544922	SO:0001587	stop_gained	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1669G>T	X.37:g.142717256C>A	ENSP00000371198:p.Glu557*		142544922	Q5JXG3|Q8TCM8|Q96DL3	Nonsense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	C	38	7.048728	0.98029	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	.	.	.	5.41	5.41	0.78517	.	0.057097	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-10.1026	16.9315	0.86191	0.0:1.0:0.0:0.0	.	.	.	.	X	557	.	ENSP00000336627:E557X	E	-	1	0	SLITRK4	142544922	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.776000	0.85560	2.404000	0.81709	0.600000	0.82982	GAA		0.448	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142717256	C	A	142717256	4	1	47	1	0	0	0	0	0	1	0	0	14782	922	32	2	848	2	SLITRK4	23	142717256	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1721188	142717256	12553304	2174	6571										
SLITRK2	84631	broad.mit.edu	37	chrX	144906092	144906092	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cctattaccgaaacctgcaaGagttcagctatagcaacctg	7	12	1	1	rs147521566		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:144906092G>T	ENST00000370490.1	+	1	6404	c.2149G>T	c.(2149-2151)Gag>Tag	p.E717*	SLITRK2_ENST00000428560.2_Nonsense_Mutation_p.E717*|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000434188.2_Nonsense_Mutation_p.E717*|SLITRK2_ENST00000413937.2_Nonsense_Mutation_p.E717*|SLITRK2_ENST00000447897.2_Nonsense_Mutation_p.E717*			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	717					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.E717*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					AAACCTGCAAGAGTTCAGCTA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											83	86	85					X																	144906092		2203	4300	6503	144713784	SO:0001587	stop_gained	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2149G>T	X.37:g.144906092G>T	ENSP00000359521:p.Glu717*		144713784	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Nonsense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	59	36.074161	0.99983	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	.	.	.	5.34	5.34	0.76211	.	0.054551	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-4.1666	15.3882	0.74718	0.0:0.0:1.0:0.0	.	.	.	.	X	717	.	ENSP00000334374:E717X	E	+	1	0	SLITRK2	144713784	1.000000	0.71417	0.988000	0.46212	0.896000	0.52359	7.569000	0.82380	2.224000	0.72417	0.513000	0.50165	GAG		0.498	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144906092	G	T	144906092	4	4	47	1	0	0	0	0	0	1	0	0	14780	943	33	2	2151	2	SLITRK2	23	144906092	Nonsense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2188836	144906092	10364468	2175	6572										
AFF2	2334	broad.mit.edu	37	chrX	148038084	148038084	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agactgccacaaaacccaagCgtcagacagctgtcacagct	8	14	2	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:148038084C>T	ENST00000370460.2	+	11	2988	c.2509C>T	c.(2509-2511)Cgt>Tgt	p.R837C	AFF2_ENST00000342251.3_Missense_Mutation_p.R804C|AFF2_ENST00000286437.5_Missense_Mutation_p.R478C|AFF2_ENST00000370457.5_Missense_Mutation_p.R804C	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	837					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.R837C(1)|p.R478C(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AAAACCCAAGCGTCAGACAGC	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	X											71	71	71					X																	148038084		2203	4300	6503	147845784	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2509C>T	X.37:g.148038084C>T	ENSP00000359489:p.Arg837Cys		147845784	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737810	0.69304	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.87	5.87	0.94306	.	1.118720	0.06880	N	0.802281	D	0.83922	0.5359	M	0.72894	2.215	0.53005	D	0.99996	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.71414	0.973;0.953;0.953;0.953;0.953;0.973	T	0.75850	-0.3172	10	0.59425	D	0.04	.	19.1236	0.93374	0.0:1.0:0.0:0.0	.	478;802;804;798;827;837	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	C	837;804;804;478	ENSP00000359489:R837C;ENSP00000359486:R804C;ENSP00000345459:R804C;ENSP00000286437:R478C	ENSP00000286437:R478C	R	+	1	0	AFF2	147845784	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	2.776000	0.47709	2.467000	0.83353	0.600000	0.82982	CGT		0.532	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	148038084	C	T	148038084	3	4	47	1	0	0	0	0	1	0	0	0	357	768	27	1	2606	1	AFF2	23	148038084	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	3131992	148038084	7232476	2176	6573										
TMEM185A	84548	broad.mit.edu	37	chrX	148690511	148690511	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tttaaactccacacacgtttCtccttctgctctaaaaaagg	4	12	3	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:148690511C>A	ENST00000316916.8	-	3	530	c.226G>T	c.(226-228)Gaa>Taa	p.E76*	TMEM185A_ENST00000536359.1_Nonsense_Mutation_p.E17*|TMEM185A_ENST00000507237.1_Nonsense_Mutation_p.E76*	NM_032508.2	NP_115897.1	Q8NFB2	T185A_HUMAN	transmembrane protein 185A	76						dendrite (GO:0030425)|integral component of membrane (GO:0016021)		p.E76*(1)		kidney(1)|large_intestine(3)|lung(10)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACACACGTTTCTCCTTCTGCT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											107	91	96					X																	148690511		2202	4299	6501	148498307	SO:0001587	stop_gained	84548			AF353675	CCDS14689.1, CCDS55523.1, CCDS76041.1	Xq28	2014-01-28	2007-02-05	2007-02-05	ENSG00000155984	ENSG00000269556			17125	protein-coding gene	gene with protein product		300031	"chromosome X open reading frame 13", "family with sequence similarity 11, member A"	CXorf13, FAM11A		12404111	Standard	NM_032508		Approved		uc022cgl.1	Q8NFB2	OTTHUMG00000022625	ENST00000316916.8:c.226G>T	X.37:g.148690511C>A	ENSP00000359449:p.Glu76*		148498307	B3KTZ3|Q3SYH1|Q96CW3|Q96KE8	Nonsense_Mutation	SNP	ENST00000316916.8	37	CCDS14689.1	.	.	.	.	.	.	.	.	.	.	C	37	6.294642	0.97449	.	.	ENSG00000155984	ENST00000316916;ENST00000536359;ENST00000507237;ENST00000511776	.	.	.	5.46	5.46	0.80206	.	0.047505	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-11.9027	17.2137	0.86937	0.0:1.0:0.0:0.0	.	.	.	.	X	76;17;76;17	.	ENSP00000359449:E76X	E	-	1	0	TMEM185A	148498307	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.438000	0.80431	2.275000	0.75901	0.513000	0.50165	GAA		0.418	TMEM185A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058710.4	NM_032508		A	148690511	C	A	148690511	4	1	47	1	0	0	0	0	0	1	0	0	16146	922	32	2	846	2	TMEM185A	23	148690511	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	652427	148690511	6580049	2177	6574										
TMEM185A	84548	broad.mit.edu	37	chrX	148692971	148692971	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttgtataaagcagtattaccGatattgaggatttcgtgccc	9	7	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:148692971G>A	ENST00000316916.8	-	2	518	c.214C>T	c.(214-216)Cga>Tga	p.R72*	TMEM185A_ENST00000536359.1_Intron|TMEM185A_ENST00000507237.1_Splice_Site_p.R72*	NM_032508.2	NP_115897.1	Q8NFB2	T185A_HUMAN	transmembrane protein 185A	72						dendrite (GO:0030425)|integral component of membrane (GO:0016021)		p.R72*(1)		kidney(1)|large_intestine(3)|lung(10)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					CAGTATTACCGATATTGAGGA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											236	232	233					X																	148692971		2203	4299	6502	148500772	SO:0001630	splice_region_variant	84548			AF353675	CCDS14689.1, CCDS55523.1, CCDS76041.1	Xq28	2014-01-28	2007-02-05	2007-02-05	ENSG00000155984	ENSG00000269556			17125	protein-coding gene	gene with protein product		300031	"chromosome X open reading frame 13", "family with sequence similarity 11, member A"	CXorf13, FAM11A		12404111	Standard	NM_032508		Approved		uc022cgl.1	Q8NFB2	OTTHUMG00000022625	ENST00000316916.8:c.215+1C>T	X.37:g.148692971G>A			148500772	B3KTZ3|Q3SYH1|Q96CW3|Q96KE8	Nonsense_Mutation	SNP	ENST00000316916.8	37	CCDS14689.1	.	.	.	.	.	.	.	.	.	.	G	40	8.290624	0.98745	.	.	ENSG00000155984	ENST00000316916;ENST00000507237	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5255	0.50578	0.0:0.0:0.8213:0.1787	.	.	.	.	X	72	.	ENSP00000359449:R72X	R	-	1	2	TMEM185A	148500772	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.579000	0.74036	2.040000	0.60383	0.594000	0.82650	CGA		0.423	TMEM185A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058710.4	NM_032508	Nonsense_Mutation	A	148692971	G	A	148692971	5	1	47	1	0	0	0	0	0	0	1	0	16146	1072	37	1	862	1	TMEM185A	23	148692971	Splice_Site	SNP	G	TCGA-AG-3892-01A-01W-1073-09	2460	148692971	6577589	2178	6575										
MTMR1	8776	broad.mit.edu	37	chrX	149919217	149919217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttaagtttccttcagcattcGagtttaatgagctattcttg	7	7	2	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:149919217G>A	ENST00000370390.3	+	13	1715	c.1558G>A	c.(1558-1560)Gag>Aag	p.E520K	MTMR1_ENST00000445323.2_Missense_Mutation_p.E528K|MTMR1_ENST00000451863.2_Missense_Mutation_p.E520K|MTMR1_ENST00000541925.1_Missense_Mutation_p.E426K|MTMR1_ENST00000538506.1_Missense_Mutation_p.E345K|MTMR1_ENST00000544228.1_Missense_Mutation_p.E520K	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	520	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)	p.E520K(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					TTCAGCATTCGAGTTTAATGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	X											193	162	172					X																	149919217		2203	4299	6502	149669875	SO:0001583	missense	8776			U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1558G>A	X.37:g.149919217G>A	ENSP00000359417:p.Glu520Lys		149669875	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349269	0.95830	.	.	ENSG00000063601	ENST00000541925;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96;-3.96;-3.96	6.14	6.14	0.99180	Myotubularin phosphatase domain (1);	0.212522	0.48767	D	0.000180	D	0.98988	0.9655	H	0.99130	4.44	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.60117	0.869;0.843	D	0.99038	1.0823	10	0.87932	D	0	.	19.7229	0.96150	0.0:0.0:1.0:0.0	.	520;528	Q13613;F8WA39	MTMR1_HUMAN;.	K	426;520;528;520;520;345	ENSP00000441879:E426K;ENSP00000359417:E520K;ENSP00000414178:E528K;ENSP00000440534:E520K;ENSP00000387446:E520K;ENSP00000443444:E345K	ENSP00000359417:E520K	E	+	1	0	MTMR1	149669875	1.000000	0.71417	0.979000	0.43373	0.971000	0.66376	9.476000	0.97823	2.615000	0.88500	0.596000	0.82720	GAG		0.328	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		A	149919217	G	A	149919217	3	1	47	1	0	0	0	0	1	0	0	0	9968	1059	37	1	1608	1	MTMR1	23	149919217	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1226246	149919217	5351343	2179	6576										
CNGA2	1260	broad.mit.edu	37	chrX	150911720	150911720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	gccctgaggtgcgcttcaacCgcctgctgcactttgcccgc	11	17	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:150911720C>T	ENST00000329903.4	+	6	778	c.745C>T	c.(745-747)Cgc>Tgc	p.R249C		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	249					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.R249C(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					GCGCTTCAACCGCCTGCTGCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	X											170	128	142					X																	150911720		2203	4300	6503	150662376	SO:0001583	missense	1260			S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.745C>T	X.37:g.150911720C>T	ENSP00000328478:p.Arg249Cys		150662376	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008471	0.75046	.	.	ENSG00000183862	ENST00000329903	D	0.99369	-5.78	5.49	5.49	0.81192	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99667	0.9876	H	0.97874	4.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97404	0.9998	10	0.87932	D	0	.	15.6554	0.77129	0.0:1.0:0.0:0.0	.	249	Q16280	CNGA2_HUMAN	C	249	ENSP00000328478:R249C	ENSP00000328478:R249C	R	+	1	0	CNGA2	150662376	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	3.572000	0.53849	2.293000	0.77203	0.600000	0.82982	CGC		0.532	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		T	150911720	C	T	150911720	3	4	47	1	0	0	0	0	1	0	0	0	3603	652	23	1	767	1	CNGA2	23	150911720	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	992503	150911720	4358840	2180	6577										
MAGEA3	4102	broad.mit.edu	37	chrX	151935533	151935533	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ctcaggggcacagtcgccctCtcttgcgattatggccagga	12	13	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:151935533C>A	ENST00000393902.3	-	3	1201	c.634G>T	c.(634-636)Gag>Tag	p.E212*	MAGEA3_ENST00000370278.3_Nonsense_Mutation_p.E212*			P43357	MAGA3_HUMAN	melanoma antigen family A, 3	212	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.E212*(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CAGTCGCCCTCTCTTGCGATT	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											148	146	146					X																	151935533		2202	4292	6494	151686189	SO:0001587	stop_gained	4102				CCDS76045.1	Xq28	2009-03-13			ENSG00000221867	ENSG00000221867			6801	protein-coding gene	gene with protein product	"melanoma-associated antigen 3", "antigen MZ2-D", "MAGE-3 antigen", "cancer/testis antigen family 1, member 3"	300174		MAGE3		1840703, 8575766	Standard	NM_005362		Approved	HYPD, HIP8, MGC14613, CT1.3	uc004fgp.3	P43357	OTTHUMG00000022640	ENST00000393902.3:c.634G>T	X.37:g.151935533C>A	ENSP00000377480:p.Glu212*		151686189	Q6FHI6	Nonsense_Mutation	SNP	ENST00000393902.3	37	CCDS14715.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.549159	0.86127	.	.	ENSG00000221867	ENST00000370278;ENST00000393902	.	.	.	1.42	-1.11	0.09840	.	0.574103	0.19007	N	0.125183	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	2.4772	0.04579	0.0:0.4344:0.3185:0.2471	.	.	.	.	X	212	.	ENSP00000359301:E212X	E	-	1	0	MAGEA3	151686189	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.163000	0.03138	-0.392000	0.07751	0.358000	0.22013	GAG		0.567	MAGEA3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058744.1	NM_005362		A	151935533	C	A	151935533	4	1	47	1	0	0	0	0	0	1	0	0	9197	922	32	2	314	2	MAGEA3	23	151935533	Nonsense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	1023813	151935533	3335027	2181	6578										
L1CAM	3897	broad.mit.edu	37	chrX	153130322	153130322	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	cgtacgatggcttcaccaggGccctctttggtggtggcctg	14	12	2	0	rs149420127		TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:153130322G>A	ENST00000370060.1	-	23	3189	c.3000C>T	c.(2998-3000)ggC>ggT	p.G1000G	L1CAM_ENST00000370055.1_Silent_p.G995G|L1CAM_ENST00000361981.3_Silent_p.G995G|L1CAM_ENST00000361699.4_Silent_p.G1000G|L1CAM_ENST00000538883.1_Silent_p.G1002G|L1CAM_ENST00000543994.1_Silent_p.G1002G|L1CAM_ENST00000370057.3_Silent_p.G1000G	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1000	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.G1000G(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTCACCAGGGCCCTCTTTGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	X						G	,,	0,3835		0,0,1632,571	121	113	115		3000,2985,3000	-1.8	0.5	X	dbSNP_134	115	1,6727		0,1,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	L1CAM	NM_000425.3,NM_001143963.1,NM_024003.2	,,	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	,,	1000/1258,995/1249,1000/1254	153130322	1,10562	2203	4300	6503	152783516	SO:0001819	synonymous_variant	3897			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3000C>T	X.37:g.153130322G>A			152783516	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Silent	SNP	ENST00000370060.1	37	CCDS14733.1																																																																																				0.632	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153130322	G	A	153130322	2	1	47	1	0	0	0	0	0	0	0	1	8610	1190	42	3		3	L1CAM	23	153130322	Silent	SNP	G	TCGA-AG-3892-01A-01W-1073-09	1194789	153130322	2140238	2182	6579										
TKTL1	8277	broad.mit.edu	37	chrX	153549234	153549234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	tgagagcaacatcaacattaTtggttcccactgtggggtat	10	8	1	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:153549234T>C	ENST00000369915.3	+	8	1349	c.1160T>C	c.(1159-1161)aTt>aCt	p.I387T	TKTL1_ENST00000217905.7_Missense_Mutation_p.I127T|TKTL1_ENST00000369912.2_Missense_Mutation_p.I331T	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	387					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.I387T(1)		NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATCAACATTATTGGTTCCCAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	X											236	187	203					X																	153549234		2203	4300	6503	153202428	SO:0001583	missense	8277			X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.1160T>C	X.37:g.153549234T>C	ENSP00000358931:p.Ile387Thr		153202428	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Missense_Mutation	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	T	7.478	0.648136	0.14516	.	.	ENSG00000007350	ENST00000369915;ENST00000441970;ENST00000217905;ENST00000369912	D;D;D	0.92299	-3.01;-3.01;-3.01	4.82	1.99	0.26369	Transketolase-like, pyrimidine-binding domain (2);	0.669311	0.14857	N	0.294328	D	0.92378	0.7581	M	0.86805	2.84	0.30684	N	0.752026	B;B;B	0.32467	0.202;0.372;0.372	B;B;B	0.39771	0.145;0.309;0.309	D	0.90017	0.4125	10	0.72032	D	0.01	-4.4662	5.3193	0.15872	0.0:0.1224:0.3517:0.5259	.	127;381;387	B7Z7M4;B7Z7I0;P51854	.;.;TKTL1_HUMAN	T	387;331;127;331	ENSP00000358931:I387T;ENSP00000217905:I127T;ENSP00000358928:I331T	ENSP00000217905:I127T	I	+	2	0	TKTL1	153202428	0.004000	0.15560	0.136000	0.22124	0.158000	0.22134	1.025000	0.30090	0.523000	0.28482	0.356000	0.21956	ATT		0.468	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		C	153549234	T	C	153549234	3	2	47	1	0	0	0	0	1	0	0	0	15974	1493	52	4	1190	4	TKTL1	23	153549234	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	418912	153549234	1721326	2183	6580										
DKC1	1736	broad.mit.edu	37	chrX	154003541	154003541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	agttgccgaagcagcaaaaaCtgcgaaggtgagtggcatgc	14	8	0	1			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:154003541C>T	ENST00000369550.5	+	13	1541	c.1331C>T	c.(1330-1332)aCt>aTt	p.T444I	SNORA56_ENST00000383966.1_RNA|DKC1_ENST00000475966.1_3'UTR	NM_001142463.1|NM_001363.3	NP_001135935.1|NP_001354.1	O60832	DKC1_HUMAN	dyskeratosis congenita 1, dyskerin	444					cell proliferation (GO:0008283)|pseudouridine synthesis (GO:0001522)|RNA processing (GO:0006396)|rRNA processing (GO:0006364)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)|telomerase activity (GO:0003720)	p.T444I(1)		breast(2)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)	15	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCAGCAAAAACTGCGAAGGTG	0.478									Congenital Dyskeratosis																																							1	Substitution - Missense(1)	large_intestine(1)	X											112	91	98					X																	154003541		2203	4300	6503	153656735	SO:0001583	missense	1736	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AJ224481	CCDS14761.1, CCDS76062.1	Xq28	2014-09-17			ENSG00000130826	ENSG00000130826			2890	protein-coding gene	gene with protein product		300126		DKC		9590285, 9888995	Standard	NM_001142463		Approved	XAP101, dyskerin, NAP57, NOLA4	uc004fmm.3	O60832	OTTHUMG00000024242	ENST00000369550.5:c.1331C>T	X.37:g.154003541C>T	ENSP00000358563:p.Thr444Ile		153656735	F5BSB3|O43845|Q96G67|Q9Y505	Missense_Mutation	SNP	ENST00000369550.5	37	CCDS14761.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.242568	0.22796	.	.	ENSG00000130826	ENST00000369550	D	0.97303	-4.33	5.49	-0.764	0.11027	.	2.732900	0.00926	N	0.002658	D	0.93093	0.7801	N	0.25647	0.755	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	D	0.84535	0.0635	10	0.38643	T	0.18	2.2064	5.3391	0.15974	0.0:0.4356:0.1382:0.4262	.	444;444	A8MUT5;O60832	.;DKC1_HUMAN	I	444	ENSP00000358563:T444I	ENSP00000358563:T444I	T	+	2	0	DKC1	153656735	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.176000	0.16782	-0.373000	0.07979	0.600000	0.82982	ACT		0.478	DKC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061180.5	NM_001363		T	154003541	C	T	154003541	3	4	47	1	0	0	0	0	1	0	0	0	4553	565	20	3	1381	3	DKC1	23	154003541	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	454307	154003541	1267019	2184	6581										
F8	2157	broad.mit.edu	37	chrX	154158356	154158356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	catgaaattcttagtgccagTcactgtatgtatctgaggca	9	8	3	2			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:154158356T>C	ENST00000360256.4	-	14	3909	c.3709A>G	c.(3709-3711)Act>Gct	p.T1237A		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1237	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.T1237A(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTAGTGCCAGTCACTGTATGT	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	X											57	47	50					X																	154158356		2202	4299	6501	153811550	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3709A>G	X.37:g.154158356T>C	ENSP00000353393:p.Thr1237Ala		153811550	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	t	6.503	0.460959	0.12342	.	.	ENSG00000185010	ENST00000360256	D	0.99129	-5.46	5.87	0.283	0.15696	.	0.669254	0.15409	N	0.263901	D	0.96386	0.8821	L	0.55481	1.735	0.09310	N	1	B	0.22346	0.068	B	0.13407	0.009	D	0.91929	0.5553	10	0.39692	T	0.17	-0.5718	2.8663	0.05602	0.3201:0.1833:0.0:0.4966	.	1237	P00451	FA8_HUMAN	A	1237	ENSP00000353393:T1237A	ENSP00000353393:T1237A	T	-	1	0	F8	153811550	0.000000	0.05858	0.000000	0.03702	0.835000	0.47333	0.141000	0.16076	0.293000	0.22520	0.483000	0.47432	ACT		0.343	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			C	154158356	T	C	154158356	3	2	47	1	0	0	0	0	1	0	0	0	5363	1667	58	4	3426	4	F8	23	154158356	Missense_Mutation	SNP	T	TCGA-AG-3892-01A-01W-1073-09	154815	154158356	1112204	2185	6582										
RAB39B	116442	broad.mit.edu	37	chrX	154490417	154490417	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	aacgtgtactttggtctcttCtaaccactcatggacattct	6	11	4	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:154490417C>G	ENST00000369454.3	-	2	613	c.313G>C	c.(313-315)Gaa>Caa	p.E105Q		NM_171998.2	NP_741995.1	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	105					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|synapse organization (GO:0050808)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)	p.E105Q(1)		breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12)	19	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TTGGTCTCTTCTAACCACTCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											195	183	187					X																	154490417		2203	4300	6503	154143611	SO:0001583	missense	116442			AY052478	CCDS14766.1	Xq28	2014-01-31			ENSG00000155961	ENSG00000155961		"RAB, member RAS oncogene"	16499	protein-coding gene	gene with protein product		300774	"mental retardation, X-linked 72"	MRX72		12438742, 20159109	Standard	NM_171998		Approved		uc004fne.3	Q96DA2	OTTHUMG00000022659	ENST00000369454.3:c.313G>C	X.37:g.154490417C>G	ENSP00000358466:p.Glu105Gln		154143611	Q5JT79|Q8NEX3	Missense_Mutation	SNP	ENST00000369454.3	37	CCDS14766.1	.	.	.	.	.	.	.	.	.	.	c	18.43	3.622281	0.66787	.	.	ENSG00000155961	ENST00000369454	T	0.77358	-1.09	4.6	3.74	0.42951	Small GTP-binding protein domain (1);	0.056069	0.64402	D	0.000001	T	0.72700	0.3493	N	0.14661	0.345	0.51767	D	0.999932	D	0.59767	0.986	P	0.56398	0.797	T	0.75036	-0.3459	10	0.56958	D	0.05	.	11.5198	0.50545	0.1813:0.8187:0.0:0.0	.	105	Q96DA2	RB39B_HUMAN	Q	105	ENSP00000358466:E105Q	ENSP00000358466:E105Q	E	-	1	0	RAB39B	154143611	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.005000	0.70716	1.020000	0.39573	-0.274000	0.10170	GAA		0.488	RAB39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058792.1	NM_171998		G	154490417	C	G	154490417	3	3	47	1	0	0	0	0	1	0	0	0	12967	922	32	5	332	5	RAB39B	23	154490417	Missense_Mutation	SNP	C	TCGA-AG-3892-01A-01W-1073-09	332061	154490417	780143	2186	6583										
SPRY3	10251	broad.mit.edu	37	chrX	155003874	155003874	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333790580704161	73	1	0.457490445778188	2.14331140350877	0.447573851909185	1.10909463699096e-19	6.76547728564486e-18	0	ttcaggccaatccatcatccGaacccaacctggagcagggg	10	14	2	0			TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-3892-01A-01W-1073-09	TCGA-AG-3892-10A-01W-1073-09	g.chrX:155003874G>A	ENST00000302805.2	+	2	772	c.341G>A	c.(340-342)cGa>cAa	p.R114Q		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	114					multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R114Q(1)|p.R114L(1)				all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TCCATCATCCGAACCCAACCT	0.547																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	X						G	GLN/ARG	1,4405		0,1,2202	110	105	107		341	3.1	1	X	dbSNP_134	107	0,8592		0,0,4296	no	missense	SPRY3	NM_005840.1	43	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	114/289	155003874	1,12997	2203	4296	6499	154657068	SO:0001583	missense	10251			AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.341G>A	X.37:g.155003874G>A	ENSP00000302978:p.Arg114Gln		154657068	A8K0H8	Missense_Mutation	SNP	ENST00000302805.2	37	CCDS14769.4	.	.	.	.	.	.	.	.	.	.	G	13.12	2.141827	0.37825	2.27E-4	0.0	ENSG00000168939	ENST00000302805	T	0.57595	0.39	3.14	3.14	0.36123	.	0.168000	0.39020	N	0.001489	T	0.47135	0.1429	.	.	.	0.09310	N	1	D	0.59357	0.985	P	0.44673	0.457	T	0.46484	-0.9188	9	0.62326	D	0.03	-0.4995	11.3539	0.49605	0.0:0.0:1.0:0.0	.	114	O43610	SPY3_HUMAN	Q	114	ENSP00000302978:R114Q	ENSP00000302978:R114Q	R	+	2	0	SPRY3	154657068	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	4.847000	0.62867	1.593000	0.50029	0.279000	0.19357	CGA		0.547	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		A	155003874	G	A	155003874	3	1	47	1	0	0	0	0	1	0	0	0	15146	1058	37	1	343	1	SPRY3	23	155003874	Missense_Mutation	SNP	G	TCGA-AG-3892-01A-01W-1073-09	513457	155003874	266686	2187	6584										
PTCH2	8643	broad.mit.edu	37	chr1	45295378	45295378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgatagtcaccccggaaatGctcgtacagctggcggggac	13	12	1	1	rs200534670		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr1:45295378G>A	ENST00000372192.3	-	8	1121	c.991C>T	c.(991-993)Cat>Tat	p.H331Y	PTCH2_ENST00000447098.2_Missense_Mutation_p.H331Y	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	331					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)	p.H331Y(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					CCCCGGAAATGCTCGTACAGC	0.607									Basal Cell Nevus syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	1											67	67	67					1																	45295378		2203	4300	6503	45067965	SO:0001583	missense	8643	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.991C>T	1.37:g.45295378G>A	ENSP00000361266:p.His331Tyr		45067965	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.445478	0.43429	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.92495	-3.04;-3.05	4.63	4.63	0.57726	.	0.000000	0.56097	D	0.000027	D	0.93112	0.7807	L	0.38649	1.16	0.49915	D	0.999838	B;D	0.76494	0.007;0.999	B;D	0.87578	0.032;0.998	D	0.90250	0.4293	10	0.14656	T	0.56	-12.767	17.2969	0.87172	0.0:0.0:1.0:0.0	.	331;331	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	Y	331	ENSP00000389703:H331Y;ENSP00000361266:H331Y	ENSP00000361266:H331Y	H	-	1	0	PTCH2	45067965	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	9.173000	0.94815	2.415000	0.81967	0.561000	0.74099	CAT		0.607	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		A	45295378	G	A	45295378	3	1	48	1	0	0	0	0	1	0	0	0	12765	1319	46	3	2700	3	PTCH2	1	45295378	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		45295378	203955243	1	6585										
CACHD1	57685	broad.mit.edu	37	chr1	65130314	65130314	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	caatggcgtcctcagaatttAtcctggttccctcatggaca	8	12	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr1:65130314A>G	ENST00000371073.2	+	15	2228	c.2228A>G	c.(2227-2229)tAt>tGt	p.Y743C	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.Y692C			Q5VU97	CAHD1_HUMAN	cache domain containing 1	743					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.Y692C(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CTCAGAATTTATCCTGGTTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											178	158	165					1																	65130314		2203	4300	6503	64902902	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2228A>G	1.37:g.65130314A>G	ENSP00000360113:p.Tyr743Cys		64902902	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	A	23.1	4.378173	0.82682	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.30448	1.53;1.54	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	M	0.78285	2.405	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.56378	-0.7989	10	0.72032	D	0.01	-23.9082	16.5655	0.84588	1.0:0.0:0.0:0.0	.	743	Q5VU97	CAHD1_HUMAN	C	743;692	ENSP00000360113:Y743C;ENSP00000290039:Y692C	ENSP00000290039:Y692C	Y	+	2	0	CACHD1	64902902	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.027000	0.76463	2.302000	0.77476	0.533000	0.62120	TAT		0.468	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		G	65130314	A	G	65130314	3	3	48	1	0	0	0	0	1	0	0	0	2543	449	16	4	2133	4	CACHD1	1	65130314	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	19834936	65130314	184120307	2	6586										
OTUD7B	56957	broad.mit.edu	37	chr1	149936185	149936185	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgctgccacctccagcgccTtttcaacgcttccttctcaa	5	18	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr1:149936185T>C	ENST00000369135.4	-	6	988	c.694A>G	c.(694-696)Agg>Ggg	p.R232G	OTUD7B_ENST00000479905.1_5'UTR	NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	232	Catalytic.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R232G(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CTCCAGCGCCTTTTCAACGCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											109	120	117					1																	149936185		2115	4244	6359	148202809	SO:0001583	missense	56957			AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.694A>G	1.37:g.149936185T>C	ENSP00000358131:p.Arg232Gly		148202809	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.653667	0.67472	.	.	ENSG00000163113	ENST00000369135;ENST00000543330;ENST00000417191	T;T	0.36520	1.25;1.32	4.87	2.83	0.33086	Ovarian tumour, otubain (2);	0.000000	0.85682	D	0.000000	T	0.46600	0.1401	M	0.74389	2.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.48681	-0.9014	9	.	.	.	-33.3308	12.242	0.54549	0.0:0.0:0.5726:0.4274	.	232;232	B7Z643;Q6GQQ9	.;OTU7B_HUMAN	G	232	ENSP00000358131:R232G;ENSP00000408231:R232G	.	R	-	1	2	OTUD7B	148202809	0.895000	0.30542	0.928000	0.36995	0.859000	0.49053	0.241000	0.18065	0.615000	0.30124	-0.264000	0.10439	AGG		0.522	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		C	149936185	T	C	149936185	3	2	48	1	0	0	0	0	1	0	0	0	11350	1608	56	4	1865	4	OTUD7B	1	149936185	Missense_Mutation	SNP	T	TCGA-AG-3893-01A-01W-1073-09	84805871	149936185	99314436	3	6587										
HRNR	388697	broad.mit.edu	37	chr1	152192976	152192976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgccctgacgtagatccatGttgtccctggctagaggagt	12	11	0	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr1:152192976G>A	ENST00000368801.2	-	3	1204	c.1129C>T	c.(1129-1131)Cat>Tat	p.H377Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	377					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.H377Y(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGATCCATGTTGTCCCTGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											177	156	163					1																	152192976		2203	4300	6503	150459600	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1129C>T	1.37:g.152192976G>A	ENSP00000357791:p.His377Tyr		150459600	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	7.086	0.571232	0.13623	.	.	ENSG00000197915	ENST00000368801	T	0.05139	3.49	4.53	3.61	0.41365	.	.	.	.	.	T	0.01320	0.0043	N	0.14661	0.345	0.09310	N	1	D	0.56968	0.978	P	0.49140	0.601	T	0.16041	-1.0416	9	0.02654	T	1	.	6.3961	0.21613	0.0987:0.1866:0.7147:0.0	.	377	Q86YZ3	HORN_HUMAN	Y	377	ENSP00000357791:H377Y	ENSP00000357791:H377Y	H	-	1	0	HRNR	150459600	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.341000	0.19909	1.096000	0.41439	0.644000	0.83932	CAT		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152192976	G	A	152192976	3	1	48	1	0	0	0	0	1	0	0	0	7380	1377	48	3	7427	3	HRNR	1	152192976	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	2256791	152192976	97057645	4	6588										
KIDINS220	57498	broad.mit.edu	37	chr2	8871762	8871762	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggatccaggggggaagcatcGttggtggaaacccctgatga	16	8	0	2	rs77234849		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:8871762G>A	ENST00000256707.3	-	30	4585	c.4404C>T	c.(4402-4404)aaC>aaT	p.N1468N	KIDINS220_ENST00000418530.1_Silent_p.N1369N|KIDINS220_ENST00000473731.1_Silent_p.N1449N|KIDINS220_ENST00000427284.1_Silent_p.N1449N	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1468					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.N1468N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGGAAGCATCGTTGGTGGAAA	0.473													G|||	1	0.000199681	0	0	5008	,	,		19530	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											94	90	92					2																	8871762		1889	4101	5990	8789213	SO:0001819	synonymous_variant	57498			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4404C>T	2.37:g.8871762G>A			8789213	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Silent	SNP	ENST00000256707.3	37	CCDS42650.1																																																																																				0.473	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		A	8871762	G	A	8871762	2	1	48	1	0	0	0	0	0	0	0	1	8292	1136	40	1		1	KIDINS220	2	8871762	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09		8871762	234327611	5	6589										
LRPPRC	10128	broad.mit.edu	37	chr2	44132856	44132856	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aaataatcccgcctaacttgCgttatgatgaggcggctgtt	10	9	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:44132856C>T	ENST00000260665.7	-	31	3396	c.3339G>A	c.(3337-3339)acG>acA	p.T1113T		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1113					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.T1113T(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCCTAACTTGCGTTATGATGA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											146	125	133					2																	44132856		2203	4300	6503	43986360	SO:0001819	synonymous_variant	10128			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.3339G>A	2.37:g.44132856C>T			43986360	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																				0.443	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		T	44132856	C	T	44132856	2	4	48	1	0	0	0	0	0	0	0	1	8994	755	27	1		1	LRPPRC	2	44132856	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	35261094	44132856	199066517	6	6590										
TET3	200424	broad.mit.edu	37	chr2	74274629	74274629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agaaggcccagaccgccctgCagcagcacctccaccacaag	9	18	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:74274629C>A	ENST00000409262.3	+	1	1180	c.1180C>A	c.(1180-1182)Cag>Aag	p.Q394K		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	394					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.Q394K(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GACCGCCCTGCAGCAGCACCT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	71	65					2																	74274629		2157	4260	6417	74128137	SO:0001583	missense	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1180C>A	2.37:g.74274629C>A	ENSP00000386869:p.Gln394Lys		74128137	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281694	0.80692	.	.	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.39229	1.09;2.16	5.29	5.29	0.74685	.	.	.	.	.	T	0.50599	0.1625	N	0.19112	0.55	0.53005	D	0.999965	D	0.69078	0.997	D	0.73380	0.98	T	0.51576	-0.8688	9	0.45353	T	0.12	.	18.0716	0.89408	0.0:1.0:0.0:0.0	.	394	O43151	TET3_HUMAN	K	436;394;394	ENSP00000307803:Q436K;ENSP00000386869:Q394K	ENSP00000233310:Q394K	Q	+	1	0	TET3	74128137	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.217000	0.77982	2.635000	0.89317	0.561000	0.74099	CAG		0.672	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			A	74274629	C	A	74274629	3	1	48	1	0	0	0	0	1	0	0	0	15810	711	25	2	1182	2	TET3	2	74274629	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	30141773	74274629	168924744	7	6591										
GLI2	2736	broad.mit.edu	37	chr2	121747300	121747300	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aaccagttcccccaatcctgCagcaacatgccagccaagcc	6	18	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:121747300C>A	ENST00000452319.1	+	14	3870	c.3810C>A	c.(3808-3810)tgC>tgA	p.C1270*	GLI2_ENST00000361492.4_Nonsense_Mutation_p.C1270*|GLI2_ENST00000314490.11_Intron					GLI family zinc finger 2									p.C1270*(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCCAATCCTGCAGCAACATGC	0.627																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											31	32	32					2																	121747300		2200	4299	6499	121463770	SO:0001587	stop_gained	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3810C>A	2.37:g.121747300C>A	ENSP00000390436:p.Cys1270*		121463770		Nonsense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	37	6.233104	0.97399	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	.	.	.	4.72	0.619	0.17630	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5772	0.22573	0.0:0.4079:0.0:0.5921	.	.	.	.	X	1270	.	.	C	+	3	2	GLI2	121463770	0.992000	0.36948	0.986000	0.45419	0.347000	0.29111	0.149000	0.16243	0.226000	0.20979	0.455000	0.32223	TGC		0.627	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121747300	C	A	121747300	4	1	48	1	0	0	0	0	0	1	0	0	6458	718	25	2	3860	2	GLI2	2	121747300	Nonsense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	47472671	121747300	121452073	8	6592										
ANKAR	150709	broad.mit.edu	37	chr2	190592782	190592782	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctcttatacagaaagcatttCtggaaaaatcgttaactaaa	5	7	2	1	rs540415324		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:190592782C>T	ENST00000520309.1	+	13	2924	c.2836C>T	c.(2836-2838)Ctg>Ttg	p.L946L	ANKAR_ENST00000438402.2_Silent_p.L946L|ANKAR_ENST00000313581.4_Silent_p.L946L|ANKAR_ENST00000281412.6_Silent_p.L721L|ANKAR_ENST00000431575.2_Silent_p.L875L	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	946						integral component of membrane (GO:0016021)		p.L875L(1)		breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GAAAGCATTTCTGGAAAAATC	0.333													C|||	1	0.000199681	8e-04	0	5008	,	,		15960	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											52	57	55					2																	190592782		2203	4300	6503	190301027	SO:0001819	synonymous_variant	150709			AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2836C>T	2.37:g.190592782C>T			190301027	Q3ZCS6|Q4G0M2|Q6ZU02	Silent	SNP	ENST00000520309.1	37	CCDS33351.2																																																																																				0.333	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		T	190592782	C	T	190592782	2	4	48	1	0	0	0	0	0	0	0	1	623	912	32	3		3	ANKAR	2	190592782	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	68845482	190592782	52606591	9	6593										
UGT1A4	54657	broad.mit.edu	37	chr2	234627798	234627798	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acatcttctgaagagatattCtagaagtatggcaattatga	8	5	3	4			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:234627798C>A	ENST00000373409.3	+	1	375	c.332C>A	c.(331-333)tCt>tAt	p.S111Y	UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	111					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S111Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	AAGAGATATTCTAGAAGTATG	0.448																																					Melanoma(99;1011 1962 13201 26492)											1	Substitution - Missense(1)	large_intestine(1)	2											164	163	163					2																	234627798		2203	4300	6503	234292537	SO:0001583	missense	54657			M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"UDP glucuronosyltransferases"	12536	other	complex locus constituent		606429	"UDP glycosyltransferase 1 family, polypeptide A4"			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.332C>A	2.37:g.234627798C>A	ENSP00000362508:p.Ser111Tyr		234292537	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	37	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	C	0.403	-0.917516	0.02396	.	.	ENSG00000244474	ENST00000373409	T	0.60171	0.21	4.16	0.319	0.15873	.	.	.	.	.	T	0.43433	0.1247	L	0.49350	1.555	0.09310	N	1	B;B	0.29136	0.234;0.01	B;B	0.34536	0.185;0.063	T	0.38222	-0.9671	9	0.02654	T	1	.	4.9994	0.14257	0.0:0.3631:0.1623:0.4747	.	111;111	B8K288;P22310	.;UD14_HUMAN	Y	111	ENSP00000362508:S111Y	ENSP00000362508:S111Y	S	+	2	0	UGT1A4	234292537	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.386000	0.07370	-0.226000	0.09899	-0.339000	0.08088	TCT		0.448	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1	NM_007120		A	234627798	C	A	234627798	3	1	48	1	0	0	0	0	1	0	0	0	16987	913	32	2	334	2	UGT1A4	2	234627798	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	44035016	234627798	8571575	10	6594										
CXCR7	57007	broad.mit.edu	37	chr2	237489126	237489126	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acgatggatctgcatctcttCgactactcagagccagggaa	10	11	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:237489126C>T	ENST00000272928.3	+	2	328	c.18C>T	c.(16-18)ttC>ttT	p.F6F		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	6					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.F6F(1)									TGCATCTCTTCGACTACTCAG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	2											116	91	99					2																	237489126		2203	4300	6503	237153865	SO:0001819	synonymous_variant	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.18C>T	2.37:g.237489126C>T			237153865	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	37	CCDS2516.1																																																																																				0.493	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489126	C	T	237489126	2	4	48	1	0	0	0	0	0	0	0	1	4102	883	31	1		1	CXCR7	2	237489126	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	2861328	237489126	5710247	11	6595										
OR6B2	389090	broad.mit.edu	37	chr2	240969461	240969461	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	caaggacgtggtagcgcagcGggtggcagatggccacgtag	18	9	0	1	rs376640191	byFrequency	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr2:240969461G>A	ENST00000402971.2	-	1	445	c.386C>T	c.(385-387)cCg>cTg	p.P129L		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P129L(1)		endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		GTAGCGCAGCGGGTGGCAGAT	0.602													G|||	14	0.00279553	0.0106	0	5008	,	,		21571	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	LEU/PRO	24,3528		0,24,1752	7	7	7		386	4.3	0.9	2		7	0,7966		0,0,3983	no	missense	OR6B2	NM_001005853.1	98	0,24,5735	AA,AG,GG		0.0,0.6757,0.2084	probably-damaging	129/313	240969461	24,11494	1776	3983	5759	240618134	SO:0001583	missense	389090				CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.386C>T	2.37:g.240969461G>A	ENSP00000384563:p.Pro129Leu		240618134	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	37	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	g	15.82	2.945740	0.53079	0.006757	0.0	ENSG00000182083	ENST00000402971	T	0.01902	4.57	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000292	T	0.13372	0.0324	H	0.94582	3.555	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.03514	-1.1029	10	0.87932	D	0	.	14.62	0.68576	0.0:0.0:1.0:0.0	.	129	Q6IFH4	OR6B2_HUMAN	L	129	ENSP00000384563:P129L	ENSP00000384563:P129L	P	-	2	0	OR6B2	240618134	1.000000	0.71417	0.928000	0.36995	0.010000	0.07245	8.835000	0.92100	2.357000	0.79964	0.591000	0.81541	CCG		0.602	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		A	240969461	G	A	240969461	3	1	48	1	0	0	0	0	1	0	0	0	11219	1116	39	1	554	1	OR6B2	2	240969461	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	3480335	240969461	2229912	12	6596										
SETD5	55209	broad.mit.edu	37	chr3	9516836	9516836	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagcccttccagatacagctAccaggtgagatgagaaattg	10	10	0	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr3:9516836A>G	ENST00000406341.1	+	21	3906	c.3716A>G	c.(3715-3717)tAc>tGc	p.Y1239C	SETD5_ENST00000302463.6_Missense_Mutation_p.Y1141C|SETD5_ENST00000402198.1_Missense_Mutation_p.Y1239C|SETD5_ENST00000402466.1_Missense_Mutation_p.Y1141C|SETD5_ENST00000407969.1_Missense_Mutation_p.Y1258C			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1239	Ser-rich.							p.Y1239C(1)|p.Y1141C(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		AGATACAGCTACCAGGTGAGA	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	3											49	46	47					3																	9516836		1941	4148	6089	9491836	SO:0001583	missense	55209			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.3716A>G	3.37:g.9516836A>G	ENSP00000383939:p.Tyr1239Cys		9491836	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238400	0.79800	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.92805	-2.78;-3.11;-2.78;-2.76;-3.11	5.76	5.76	0.90799	.	0.155285	0.46145	D	0.000305	D	0.93148	0.7818	L	0.27053	0.805	0.40588	D	0.981466	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.994	D	0.94086	0.7348	10	0.52906	T	0.07	-9.6189	16.0843	0.81031	1.0:0.0:0.0:0.0	.	908;1141;1239	B3KXG4;Q9C0A6-3;Q9C0A6	.;.;SETD5_HUMAN	C	1239;1141;1239;1258;1141	ENSP00000385852:Y1239C;ENSP00000384429:Y1141C;ENSP00000383939:Y1239C;ENSP00000384114:Y1258C;ENSP00000302028:Y1141C	ENSP00000302028:Y1141C	Y	+	2	0	SETD5	9491836	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.668000	0.74457	2.191000	0.70037	0.533000	0.62120	TAC		0.478	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9516836	A	G	9516836	3	3	48	1	0	0	0	0	1	0	0	0	14171	391	14	4	3794	4	SETD5	3	9516836	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09		9516836	188505594	13	6597										
SCN10A	6336	broad.mit.edu	37	chr3	38740002	38740002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggcggatgactctgaagagcGttggggagaagtaactttga	16	5	1	5			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr3:38740002G>A	ENST00000449082.2	-	27	4708	c.4709C>T	c.(4708-4710)aCg>aTg	p.T1570M		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1570					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.T1570M(3)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TCTGAAGAGCGTTGGGGAGAA	0.483																																																3	Substitution - Missense(3)	large_intestine(2)|central_nervous_system(1)	3											67	68	68					3																	38740002		2203	4300	6503	38715006	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4709C>T	3.37:g.38740002G>A	ENSP00000390600:p.Thr1570Met		38715006	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924514	0.52653	.	.	ENSG00000185313	ENST00000449082	D	0.97575	-4.44	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99108	0.9693	H	0.97291	3.975	0.58432	D	0.999998	D	0.89917	1.0	D	0.77557	0.99	D	0.99091	1.0840	10	0.87932	D	0	.	18.9486	0.92632	0.0:0.0:1.0:0.0	.	1570	Q9Y5Y9	SCNAA_HUMAN	M	1570	ENSP00000390600:T1570M	ENSP00000390600:T1570M	T	-	2	0	SCN10A	38715006	1.000000	0.71417	0.102000	0.21198	0.303000	0.27691	7.716000	0.84723	2.713000	0.92767	0.655000	0.94253	ACG		0.483	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38740002	G	A	38740002	3	1	48	1	0	0	0	0	1	0	0	0	13949	1145	40	1	1165	1	SCN10A	3	38740002	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	29223166	38740002	159282428	14	6598										
CADPS	8618	broad.mit.edu	37	chr3	62423781	62423781	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gagaaggcatttacttacatCaaataacctttctatgtaca	5	8	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr3:62423781C>A	ENST00000383710.4	-	28	4124	c.3775G>T	c.(3775-3777)Gat>Tat	p.D1259Y	CADPS_ENST00000283269.9_Missense_Mutation_p.D1220Y|CADPS_ENST00000357948.3_Missense_Mutation_p.D1180Y	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1259	Mediates targeting and association with DCVs. {ECO:0000250}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.D1220Y(1)|p.D1259Y(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTACTTACATCAAATAACCTT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	3											80	75	77					3																	62423781		2203	4300	6503	62398821	SO:0001583	missense	8618			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3775G>T	3.37:g.62423781C>A	ENSP00000373215:p.Asp1259Tyr		62398821	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	37	CCDS46858.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	20.1|20.1|20.1	3.932276|3.932276|3.932276	0.73442|0.73442|0.73442	.|.|.	.|.|.	ENSG00000163618|ENSG00000163618|ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269|ENST00000473635|ENST00000466621	T;T;T|.|.	0.32023|.|.	1.47;1.47;1.47|.|.	5.65|5.65|5.65	5.65|5.65|5.65	0.86999|0.86999|0.86999	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|.	0.76688|0.76688|.	0.4022|0.4022|.	M|M|M	0.72118|0.72118|0.72118	2.19|2.19|2.19	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D;D;D|.|.	0.89917|.|.	0.999;1.0;0.976;0.996|.|.	D;D;P;D|.|.	0.85130|.|.	0.967;0.997;0.726;0.959|.|.	T|T|.	0.74748|0.74748|.	-0.3560|-0.3560|.	10|5|.	0.87932|.|.	D|.|.	0|.|.	.|.|.	19.7806|19.7806|19.7806	0.96414|0.96414|0.96414	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	1180;1220;1259;1264|.|.	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4|.|.	.;.;CAPS1_HUMAN;.|.|.	Y|F|L	1265;1259;1180;1220|250|159	ENSP00000373215:D1259Y;ENSP00000350632:D1180Y;ENSP00000283269:D1220Y|.|.	ENSP00000283269:D1220Y|.|.	D|L|X	-|-|-	1|3|2	0|2|2	CADPS|CADPS|CADPS	62398821|62398821|62398821	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.770000|7.770000|7.770000	0.85390|0.85390|0.85390	2.668000|2.668000|2.668000	0.90789|0.90789|0.90789	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	GAT|TTG|TGA		0.453	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62423781	C	A	62423781	3	1	48	1	0	0	0	0	1	0	0	0	2576	826	29	2	298	2	CADPS	3	62423781	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	23683779	62423781	135598649	15	6599										
CCRL1	51554	broad.mit.edu	37	chr3	132319843	132319843	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	atcaatgaaagcattgattcAaatgctagagatctgcattg	8	6	3	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr3:132319843A>T	ENST00000249887.2	+	2	698	c.602A>T	c.(601-603)cAa>cTa	p.Q201L	ACAD11_ENST00000355458.3_Intron|ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000545291.1_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	201					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.Q201L(1)									GCATTGATTCAAATGCTAGAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											20	20	20					3																	132319843		2200	4294	6494	133802533	SO:0001583	missense	51554			AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"GPCR / Class A : Chemokine receptors : Atypical"	1611	protein-coding gene	gene with protein product		606065	"chemokine (C-C motif) receptor-like 1"	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.602A>T	3.37:g.132319843A>T	ENSP00000249887:p.Gln201Leu		133802533	B2R9U7	Missense_Mutation	SNP	ENST00000249887.2	37	CCDS3075.1	.	.	.	.	.	.	.	.	.	.	A	0.906	-0.720526	0.03182	.	.	ENSG00000129048	ENST00000249887;ENST00000424114	T	0.34859	1.34	5.66	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.227351	0.45867	D	0.000332	T	0.25005	0.0607	N	0.26042	0.785	0.44719	D	0.997715	P	0.49253	0.921	B	0.39935	0.314	T	0.02042	-1.1224	10	0.42905	T	0.14	.	11.4514	0.50156	0.9294:0.0:0.0706:0.0	.	201	Q9NPB9	CCRL1_HUMAN	L	201	ENSP00000249887:Q201L	ENSP00000249887:Q201L	Q	+	2	0	CCRL1	133802533	1.000000	0.71417	0.847000	0.33407	0.275000	0.26752	3.391000	0.52530	0.977000	0.38444	0.533000	0.62120	CAA		0.408	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557		T	132319843	A	T	132319843	3	4	48	1	0	0	0	0	1	0	0	0	2955	130	5	5	604	5	CCRL1	3	132319843	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	69896062	132319843	65702587	16	6600										
IQCG	84223	broad.mit.edu	37	chr3	197670674	197670674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agatgctctgtctcccttcgTactgaacgggcatgatgtag	11	10	2	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr3:197670674T>C	ENST00000265239.6	-	4	681	c.257A>G	c.(256-258)tAc>tGc	p.Y86C	IQCG_ENST00000455191.1_Missense_Mutation_p.Y86C|IQCG_ENST00000480302.1_5'UTR|IQCG_ENST00000453254.1_Missense_Mutation_p.Y86C	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	86						extracellular vesicular exosome (GO:0070062)		p.Y86C(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		TCTCCCTTCGTACTGAACGGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											140	138	138					3																	197670674		2203	4300	6503	199155071	SO:0001583	missense	84223			AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 9"	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.257A>G	3.37:g.197670674T>C	ENSP00000265239:p.Tyr86Cys		199155071	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.906336	0.52333	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.57595	0.39;0.39;0.93;0.93	5.4	-0.499	0.12015	.	0.249234	0.29616	N	0.011656	T	0.65123	0.2661	M	0.76002	2.32	0.09310	N	1	D;D	0.76494	0.999;0.998	D;P	0.65443	0.935;0.847	T	0.58702	-0.7590	10	0.48119	T	0.1	-1.0614	10.8036	0.46504	0.5025:0.0:0.0:0.4975	.	86;86	C9JKX8;Q9H095	.;IQCG_HUMAN	C	86;86;86;67	ENSP00000265239:Y86C;ENSP00000407736:Y86C;ENSP00000389897:Y86C;ENSP00000406411:Y67C	ENSP00000265239:Y86C	Y	-	2	0	IQCG	199155071	0.034000	0.19679	0.040000	0.18447	0.003000	0.03518	0.632000	0.24583	0.004000	0.14682	-0.516000	0.04426	TAC		0.458	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		C	197670674	T	C	197670674	3	2	48	1	0	0	0	0	1	0	0	0	7831	1638	57	4	1110	4	IQCG	3	197670674	Missense_Mutation	SNP	T	TCGA-AG-3893-01A-01W-1073-09	65350831	197670674	351756	17	6601										
SMR3A	26952	broad.mit.edu	37	chr4	71232569	71232569	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tccaccctatggtccagggaGaattcaatcacactctcttc	6	14	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:71232569G>T	ENST00000226460.4	+	3	359	c.263G>T	c.(262-264)aGa>aTa	p.R88I		NM_012390.3	NP_036522.3	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3A	88	Pro-rich.					extracellular region (GO:0005576)		p.R88I(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)	15		all_hematologic(202;0.196)				GGTCCAGGGAGAATTCAATCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	4											177	158	164					4																	71232569		2203	4300	6503	71267158	SO:0001583	missense	26952			D89501	CCDS34000.1	4q13.3	2009-04-17	2008-02-27	2005-02-07	ENSG00000109208	ENSG00000109208			19216	protein-coding gene	gene with protein product			"proline rich 5 (salivary)", "submaxillary gland androgen regulated protein 3 homolog A (mouse)"	PROL5		9354371, 17512016	Standard	NM_012390		Approved	PBI, PRL5	uc003hfg.1	Q99954	OTTHUMG00000160839	ENST00000226460.4:c.263G>T	4.37:g.71232569G>T	ENSP00000226460:p.Arg88Ile		71267158		Missense_Mutation	SNP	ENST00000226460.4	37	CCDS34000.1	.	.	.	.	.	.	.	.	.	.	G	5.099	0.203993	0.09704	.	.	ENSG00000109208	ENST00000226460	T	0.27890	1.64	3.25	0.151	0.14888	.	.	.	.	.	T	0.15782	0.0380	N	0.14661	0.345	0.09310	N	1	B	0.27229	0.172	B	0.25140	0.058	T	0.30621	-0.9972	9	0.20046	T	0.44	.	8.9647	0.35869	0.0:0.0:0.3668:0.6332	.	88	Q99954	SMR3A_HUMAN	I	88	ENSP00000226460:R88I	ENSP00000226460:R88I	R	+	2	0	SMR3A	71267158	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.136000	0.10405	-0.006000	0.14370	-0.397000	0.06425	AGA		0.552	SMR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362574.1	NM_012390		T	71232569	G	T	71232569	3	4	48	1	0	0	0	0	1	0	0	0	14848	942	33	2	269	2	SMR3A	4	71232569	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		71232569	119921707	18	6602										
AMBN	258	broad.mit.edu	37	chr4	71472251	71472251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagcgtcaccccagcagctgCtgacccactgatgacccctg	9	18	1	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:71472251C>T	ENST00000322937.6	+	13	1251	c.1148C>T	c.(1147-1149)gCt>gTt	p.A383V	AMBN_ENST00000449493.2_Missense_Mutation_p.A368V	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	383				A -> V (in Ref. 3; AAG35772). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)	p.A383V(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			CCAGCAGCTGCTGACCCACTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	66	66					4																	71472251		2203	4300	6503	71506840	SO:0001583	missense	258			AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"ameloblastin, enamel matrix protein"			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.1148C>T	4.37:g.71472251C>T	ENSP00000313809:p.Ala383Val		71506840	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	37	CCDS3543.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.006410	0.54361	.	.	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.42131	0.98;0.98	5.79	5.79	0.91817	.	0.162219	0.41396	D	0.000898	T	0.55465	0.1922	M	0.76574	2.34	0.40409	D	0.979739	P	0.42908	0.793	P	0.48815	0.591	T	0.59215	-0.7496	10	0.59425	D	0.04	-0.7487	15.5384	0.76021	0.0:1.0:0.0:0.0	.	383	Q9NP70	AMBN_HUMAN	V	383;382;368	ENSP00000313809:A383V;ENSP00000391234:A368V	ENSP00000313809:A383V	A	+	2	0	AMBN	71506840	0.516000	0.26218	0.739000	0.30968	0.102000	0.19082	3.995000	0.57001	2.747000	0.94245	0.655000	0.94253	GCT		0.557	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519		T	71472251	C	T	71472251	3	4	48	1	0	0	0	0	1	0	0	0	563	797	28	3	1198	3	AMBN	4	71472251	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	239682	71472251	119682025	19	6603										
SMARCAD1	56916	broad.mit.edu	37	chr4	95206150	95206150	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctaataagccaagggacgatTgaagaatccatgctaaaaat	8	7	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:95206150T>A	ENST00000354268.4	+	23	3022	c.2949T>A	c.(2947-2949)atT>atA	p.I983I	SMARCAD1_ENST00000457823.2_Silent_p.I985I|SMARCAD1_ENST00000509418.1_Silent_p.I553I			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	983	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.I983I(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AAGGGACGATTGAAGAATCCA	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	4											101	108	106					4																	95206150		2203	4299	6502	95425173	SO:0001819	synonymous_variant	56916			AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2949T>A	4.37:g.95206150T>A			95425173	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Silent	SNP	ENST00000354268.4	37	CCDS3639.1																																																																																				0.289	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		A	95206150	T	A	95206150	2	1	48	1	0	0	0	0	0	0	0	1	14809	1800	63	5		5	SMARCAD1	4	95206150	Silent	SNP	T	TCGA-AG-3893-01A-01W-1073-09	23733899	95206150	95948126	20	6604										
C4orf17	84103	broad.mit.edu	37	chr4	100443847	100443847	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gccccaaacggtgccaaagtGcctccacggcctcattctgg	10	16	2	0	rs376797865		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:100443847G>A	ENST00000326581.4	+	3	680	c.318G>A	c.(316-318)gtG>gtA	p.V106V	C4orf17_ENST00000503257.1_3'UTR|C4orf17_ENST00000514652.1_Silent_p.V106V	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	106								p.V106V(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTGCCAAAGTGCCTCCACGGC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G		0,4406		0,0,2203	60	59	59		318	3.5	0	4		59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C4orf17	NM_032149.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		106/360	100443847	1,13005	2203	4300	6503	100662870	SO:0001819	synonymous_variant	84103			AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.318G>A	4.37:g.100443847G>A			100662870	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Silent	SNP	ENST00000326581.4	37	CCDS3649.1																																																																																				0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149		A	100443847	G	A	100443847	2	1	48	1	0	0	0	0	0	0	0	1	2258	1306	46	3		3	C4orf17	4	100443847	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	5237697	100443847	90710429	21	6605										
FAT4	79633	broad.mit.edu	37	chr4	126412296	126412296	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gggagtcgcctaaagcagccGattgggcagattccactgga	14	10	0	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:126412296G>T	ENST00000394329.3	+	17	14332	c.14319G>T	c.(14317-14319)ccG>ccT	p.P4773P	FAT4_ENST00000335110.5_Silent_p.P3014P	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4773	Necessary and sufficient for interaction with MPDZ. {ECO:0000250}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P4716P(1)|p.P4773P(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TAAAGCAGCCGATTGGGCAGA	0.517																																																2	Substitution - coding silent(2)	large_intestine(2)	4											47	49	48					4																	126412296		2203	4300	6503	126631746	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.14319G>T	4.37:g.126412296G>T			126631746	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.517	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126412296	G	T	126412296	2	4	48	1	0	0	0	0	0	0	0	1	5711	1045	37	2		2	FAT4	4	126412296	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	25968449	126412296	64741980	22	6606										
PCDH10	57575	broad.mit.edu	37	chr4	134072612	134072612	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gtagtggctcgggaccggggCgagcctgcgctctccaccag	16	14	1	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:134072612C>T	ENST00000264360.5	+	1	2143	c.1317C>T	c.(1315-1317)ggC>ggT	p.G439G	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G439G(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		GGGACCGGGGCGAGCCTGCGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	4											91	103	99					4																	134072612		2203	4300	6503	134292062	SO:0001819	synonymous_variant	57575			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1317C>T	4.37:g.134072612C>T			134292062	Q4W5F6|Q96SF0	Silent	SNP	ENST00000264360.5	37	CCDS34063.1																																																																																				0.587	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		T	134072612	C	T	134072612	2	4	48	1	0	0	0	0	0	0	0	1	11538	755	27	1		1	PCDH10	4	134072612	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	7660316	134072612	57081664	23	6607										
TLL1	7092	broad.mit.edu	37	chr4	166915629	166915629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagagccgctacatcaagaaCggaaagaatatggcctggag	12	9	1	3	rs115824698	byFrequency	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:166915629C>T	ENST00000061240.2	+	4	1105	c.458C>T	c.(457-459)aCg>aTg	p.T153M	TLL1_ENST00000513213.1_Missense_Mutation_p.T153M|TLL1_ENST00000507499.1_Missense_Mutation_p.T153M	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	153	Metalloprotease. {ECO:0000250}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T153M(2)|p.T153K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		ACATCAAGAACGGAAAGAATA	0.413													C|||	4	0.000798722	0	0	5008	,	,		16422	0.004		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(2)|kidney(1)	4						C	MET/THR,MET/THR	0,4406		0,0,2203	72	71	71		458,458	5.5	1	4	dbSNP_132	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TLL1	NM_001204760.1,NM_012464.4	81,81	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	153/393,153/1014	166915629	2,13004	2203	4300	6503	167135079	SO:0001583	missense	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.458C>T	4.37:g.166915629C>T	ENSP00000061240:p.Thr153Met		167135079	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	37	CCDS3811.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	C	16.45	3.125917	0.56721	0.0	2.33E-4	ENSG00000038295	ENST00000061240;ENST00000507499;ENST00000513213;ENST00000506144	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.51	5.51	0.81932	Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.063495	0.64402	U	0.000005	T	0.51873	0.1700	N	0.19112	0.55	0.54753	D	0.999987	D;D	0.76494	0.998;0.999	P;P	0.51016	0.585;0.656	T	0.61322	-0.7086	10	0.51188	T	0.08	.	19.4226	0.94727	0.0:1.0:0.0:0.0	.	153;153	E9PD25;O43897	.;TLL1_HUMAN	M	153;153;153;53	ENSP00000061240:T153M;ENSP00000426082:T153M;ENSP00000422937:T153M;ENSP00000423748:T53M	ENSP00000061240:T153M	T	+	2	0	TLL1	167135079	1.000000	0.71417	0.961000	0.40146	0.002000	0.02628	6.005000	0.70716	2.593000	0.87608	0.655000	0.94253	ACG		0.413	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	166915629	C	T	166915629	3	4	48	1	0	0	0	0	1	0	0	0	15984	536	19	1	472	1	TLL1	4	166915629	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	32843017	166915629	24238647	24	6608										
NEK1	4750	broad.mit.edu	37	chr4	170428889	170428889	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagtgattcgatttttttgcGcctcatgtcagcctcttcac	7	12	4	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr4:170428889G>T	ENST00000439128.2	-	20	2444	c.1804C>A	c.(1804-1806)Cgc>Agc	p.R602S	NEK1_ENST00000512193.1_Missense_Mutation_p.R533S|NEK1_ENST00000511633.1_Missense_Mutation_p.R586S|NEK1_ENST00000510533.1_Missense_Mutation_p.R558S|NEK1_ENST00000507142.1_Missense_Mutation_p.R630S	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	602				R -> RK (in Ref. 2; CAI45943). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R630S(2)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		ATTTTTTTGCGCCTCATGTCA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	4											128	117	121					4																	170428889		1839	4092	5931	170665464	SO:0001583	missense	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.1804C>A	4.37:g.170428889G>T	ENSP00000408020:p.Arg602Ser		170665464	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.551721	0.45487	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.74421	-0.84;-0.83;-0.66;-0.81;-0.62	5.53	3.81	0.43845	.	0.194647	0.36854	N	0.002370	T	0.80433	0.4622	M	0.64997	1.995	0.31051	N	0.715259	D;D;D;D;D	0.71674	0.998;0.997;0.998;0.997;0.997	D;D;D;D;P	0.68353	0.957;0.933;0.957;0.933;0.907	T	0.78303	-0.2256	10	0.56958	D	0.05	.	6.4185	0.21730	0.1509:0.0:0.7025:0.1466	.	533;586;630;558;602	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	S	602;586;558;630;533	ENSP00000408020:R602S;ENSP00000423332:R586S;ENSP00000427653:R558S;ENSP00000424757:R630S;ENSP00000424938:R533S	ENSP00000408020:R602S	R	-	1	0	NEK1	170665464	1.000000	0.71417	0.672000	0.29872	0.219000	0.24729	1.900000	0.39828	0.806000	0.34183	0.655000	0.94253	CGC		0.343	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			T	170428889	G	T	170428889	3	4	48	1	0	0	0	0	1	0	0	0	10352	1087	38	2	2032	2	NEK1	4	170428889	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	3513260	170428889	20725387	25	6609										
LIFR	3977	broad.mit.edu	37	chr5	38493781	38493781	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aggcatggttccgaccgagaCgagttacaccacttaatgac	10	11	0	2	rs142392717		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr5:38493781C>T	ENST00000263409.4	-	14	2154	c.1992G>A	c.(1990-1992)tcG>tcA	p.S664S	LIFR_ENST00000453190.2_Silent_p.S664S|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	664	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> L (in dbSNP:rs3729744).		cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.S664S(3)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					CCGACCGAGACGAGTTACACC	0.438			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	3	Substitution - coding silent(3)	large_intestine(2)|breast(1)	5						C	,	1,4405	2.1+/-5.4	0,1,2202	179	159	165		1992,1992	-8.2	0	5	dbSNP_134	165	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	664/1098,664/1098	38493781	2,13004	2203	4300	6503	38529538	SO:0001819	synonymous_variant	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1992G>A	5.37:g.38493781C>T			38529538	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																				0.438	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38493781	C	T	38493781	2	4	48	1	0	0	0	0	0	0	0	1	8803	523	19	1		1	LIFR	5	38493781	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09		38493781	142421479	26	6610										
APC	324	broad.mit.edu	37	chr5	112175358	112175358	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	caaagctgttgaattttcttCaggagcgaaatctccctcca	7	11	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr5:112175358C>G	ENST00000457016.1	+	16	4447	c.4067C>G	c.(4066-4068)tCa>tGa	p.S1356*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1356*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1356*			P25054	APC_HUMAN	adenomatous polyposis coli	1356	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1356*(11)|p.G1357fs*13(2)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATTTTCTTCAGGAGCGAAA	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(11)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5											62	64	63					5																	112175358		2202	4300	6502	112203257	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4067C>G	5.37:g.112175358C>G	ENSP00000413133:p.Ser1356*		112203257	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	9.058983	0.99051	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.141330	0.49916	D	0.000133	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.6466	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1356	.	.	S	+	2	0	APC	112203257	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCA		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175358	C	G	112175358	4	3	48	1	0	0	0	0	0	1	0	0	763	838	29	5	4125	5	APC	5	112175358	Nonsense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	73681577	112175358	68739902	27	6611										
H2AFY	9555	broad.mit.edu	37	chr5	134670687	134670687	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tagttggcgtccagcttggcCatttcctgcacatagatgcc	10	12	0	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr5:134670687C>G	ENST00000511689.1	-	9	1691	c.1098G>C	c.(1096-1098)atG>atC	p.M366I	CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000512507.1_5'UTR|H2AFY_ENST00000304332.4_Missense_Mutation_p.M365I|H2AFY_ENST00000312469.4_Missense_Mutation_p.M363I|H2AFY_ENST00000423969.2_Missense_Mutation_p.M194I|H2AFY_ENST00000510038.1_Missense_Mutation_p.M366I	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	366	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)	p.M366I(1)|p.M363I(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAGCTTGGCCATTTCCTGCA	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	5											139	126	131					5																	134670687		2203	4300	6503	134698586	SO:0001583	missense	9555			AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1098G>C	5.37:g.134670687C>G	ENSP00000423563:p.Met366Ile		134698586	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Missense_Mutation	SNP	ENST00000511689.1	37	CCDS4185.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.714237	0.68730	.	.	ENSG00000113648	ENST00000511689;ENST00000304332;ENST00000312469;ENST00000423969;ENST00000510038	T;T;T;T	0.24151	1.91;1.87;1.9;1.91	5.17	5.17	0.71159	Appr-1-p processing (1);	0.000000	0.85682	D	0.000000	T	0.48572	0.1507	M	0.66939	2.045	0.80722	D	1	P;B;P;B	0.49635	0.899;0.244;0.926;0.158	P;B;P;B	0.59825	0.462;0.231;0.864;0.116	T	0.47886	-0.9082	10	0.87932	D	0	.	18.8759	0.92334	0.0:1.0:0.0:0.0	.	194;365;363;366	B4DJC3;O75367-3;O75367-2;O75367	.;.;.;H2AY_HUMAN	I	366;365;363;194;366	ENSP00000423563:M366I;ENSP00000302572:M365I;ENSP00000310169:M363I;ENSP00000424971:M366I	ENSP00000302572:M365I	M	-	3	0	H2AFY	134698586	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.683000	0.91414	0.655000	0.94253	ATG		0.463	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		G	134670687	C	G	134670687	3	3	48	1	0	0	0	0	1	0	0	0	6950	594	21	5	24	5	H2AFY	5	134670687	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	22495329	134670687	46244573	28	6612										
PCDHA13	56136	broad.mit.edu	37	chr5	140263105	140263105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gcgccctggaccgcgagagcGtatcagcctatgaactggtg	14	12	1	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr5:140263105G>A	ENST00000289272.2	+	1	1252	c.1252G>A	c.(1252-1254)Gta>Ata	p.V418I	PCDHA13_ENST00000409494.1_Missense_Mutation_p.V418I|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	418	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V418I(2)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCGAGAGCGTATCAGCCTA	0.637																																					Melanoma(147;1739 1852 5500 27947 37288)											2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	5											129	129	129					5																	140263105		2203	4300	6503	140243289	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1252G>A	5.37:g.140263105G>A	ENSP00000289272:p.Val418Ile		140243289	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	1.597	-0.527658	0.04141	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.49139	0.79;0.79	5.19	0.3	0.15776	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.36138	0.0956	L	0.33792	1.035	0.09310	N	1	B;B;B	0.27416	0.178;0.085;0.148	B;B;B	0.29716	0.106;0.068;0.041	T	0.26258	-1.0108	9	0.41790	T	0.15	.	10.2037	0.43101	0.433:0.0:0.567:0.0	.	418;418;418	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	I	418	ENSP00000386821:V418I;ENSP00000289272:V418I	ENSP00000289272:V418I	V	+	1	0	PCDHA13	140243289	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-0.312000	0.08113	-0.177000	0.10690	-0.459000	0.05422	GTA		0.637	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263105	G	A	140263105	3	1	48	1	0	0	0	0	1	0	0	0	11554	1145	40	1	1254	1	PCDHA13	5	140263105	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	5592418	140263105	40652155	29	6613										
PCDHB2	56133	broad.mit.edu	37	chr5	140475487	140475487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	accctcattgctgtattcagCgtttcagatcctgactccgg	8	13	3	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr5:140475487C>T	ENST00000194155.4	+	1	1261	c.1113C>T	c.(1111-1113)agC>agT	p.S371S		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	371	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S371S(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTATTCAGCGTTTCAGATC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	5											66	61	63					5																	140475487		2203	4300	6503	140455671	SO:0001819	synonymous_variant	56133			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1113C>T	5.37:g.140475487C>T			140455671	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																				0.433	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		T	140475487	C	T	140475487	2	4	48	1	0	0	0	0	0	0	0	1	11573	767	27	1		1	PCDHB2	5	140475487	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	212382	140475487	40439773	30	6614										
FAM65B	9750	broad.mit.edu	37	chr6	24865566	24865566	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agctccgattgatctctgtcAgactctcccgggcagctttg	10	13	3	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:24865566A>C	ENST00000259698.4	-	7	702	c.527T>G	c.(526-528)cTg>cGg	p.L176R	FAM65B_ENST00000538035.1_Missense_Mutation_p.L205R|FAM65B_ENST00000540914.1_Missense_Mutation_p.L176R|FAM65B_ENST00000510784.2_Missense_Mutation_p.L210R|FAM65B_ENST00000378023.4_Missense_Mutation_p.L176R	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	176					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)		p.L176R(2)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GATCTCTGTCAGACTCTCCCG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	6											89	88	88					6																	24865566		1922	4134	6056	24973545	SO:0001583	missense	9750			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.527T>G	6.37:g.24865566A>C	ENSP00000259698:p.Leu176Arg		24973545	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	A	18.37	3.609165	0.66558	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.02323	4.34;4.34;4.34;4.34;4.34	5.59	5.59	0.84812	.	0.068970	0.64402	D	0.000015	T	0.09818	0.0241	M	0.74467	2.265	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.989;1.0;0.989;1.0	T	0.00961	-1.1499	10	0.87932	D	0	-13.4911	15.7744	0.78198	1.0:0.0:0.0:0.0	.	210;205;176;176	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	R	176;205;176;176;210	ENSP00000259698:L176R;ENSP00000441138:L205R;ENSP00000367262:L176R;ENSP00000438425:L176R;ENSP00000441305:L210R	ENSP00000259698:L176R	L	-	2	0	FAM65B	24973545	1.000000	0.71417	0.112000	0.21494	0.504000	0.33889	8.740000	0.91579	2.120000	0.65058	0.459000	0.35465	CTG		0.507	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			C	24865566	A	C	24865566	3	2	48	1	0	0	0	0	1	0	0	0	5619	188	7	4	2757	4	FAM65B	6	24865566	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09		24865566	146249501	31	6615										
LRRC16A	55604	broad.mit.edu	37	chr6	25488808	25488808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acgtccttcgtggagatgacCtctcagtaagttttcttttc	8	10	2	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:25488808C>T	ENST00000329474.6	+	13	1428	c.1060C>T	c.(1060-1062)Ctc>Ttc	p.L354F		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	354					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.L354F(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TGGAGATGACCTCTCAGTAAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											162	156	158					6																	25488808		1917	4128	6045	25596787	SO:0001583	missense	55604			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.1060C>T	6.37:g.25488808C>T	ENSP00000331983:p.Leu354Phe		25596787	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911097	0.33721	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.55930	0.49	4.99	4.11	0.48088	.	0.199515	0.44285	D	0.000465	T	0.20047	0.0482	N	0.11845	0.185	0.80722	D	1	B;B;B	0.21821	0.043;0.036;0.061	B;B;B	0.21151	0.03;0.022;0.033	T	0.05818	-1.0862	10	0.36615	T	0.2	.	13.1093	0.59265	0.0:0.922:0.0:0.0779	.	354;354;354	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	F	354	ENSP00000331983:L354F	ENSP00000331983:L354F	L	+	1	0	LRRC16A	25596787	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.326000	0.52037	2.465000	0.83290	0.655000	0.94253	CTC		0.453	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		T	25488808	C	T	25488808	3	4	48	1	0	0	0	0	1	0	0	0	9000	681	24	3	1110	3	LRRC16A	6	25488808	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	623242	25488808	145626259	32	6616										
LSM2	57819	broad.mit.edu	37	chr6	31773919	31773919	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cttgaaaaaagaatagaagaGctattgggagagagggggaa	15	2	0	5			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:31773919G>C	ENST00000375661.5	-	2	230	c.4C>G	c.(4-6)Ctc>Gtc	p.L2V	LSM2_ENST00000491421.1_5'UTR	NM_021177.4	NP_067000.1	Q9Y333	LSM2_HUMAN	LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)	2					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|U6 snRNA binding (GO:0017070)	p.L2V(1)		large_intestine(1)|lung(1)	2						GAATAGAAGAGCTATTGGGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											61	54	56					6																	31773919		1510	2709	4219	31881898	SO:0001630	splice_region_variant	57819			AF182288	CCDS4722.1	6p21.3	2010-02-17	2003-02-17	2003-02-21	ENSG00000204392	ENSG00000204392			13940	protein-coding gene	gene with protein product		607282	"chromosome 6 open reading frame 28"	C6orf28		10523320, 8428774	Standard	NM_021177		Approved	G7b, YBL026W	uc003nxg.3	Q9Y333	OTTHUMG00000031121	ENST00000375661.5:c.4-1C>G	6.37:g.31773919G>C			31881898	Q6FGG1	Missense_Mutation	SNP	ENST00000375661.5	37	CCDS4722.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875656	0.91664	.	.	ENSG00000204392	ENST00000375661	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68888	0.3050	.	.	.	0.80722	D	1	D	0.60160	0.987	P	0.54856	0.762	T	0.70970	-0.4727	8	0.62326	D	0.03	-12.6367	17.8572	0.88769	0.0:0.0:1.0:0.0	.	2	Q9Y333	LSM2_HUMAN	V	2	.	ENSP00000364813:L2V	L	-	1	0	LSM2	31881898	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.362000	0.66098	2.890000	0.99128	0.655000	0.94253	CTC		0.473	LSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076205.2	NM_021177	Missense_Mutation	C	31773919	G	C	31773919	5	2	48	1	0	0	0	0	0	0	1	0	9085	985	34	5	299	5	LSM2	6	31773919	Splice_Site	SNP	G	TCGA-AG-3893-01A-01W-1073-09	6285111	31773919	139341148	33	6617										
PKHD1	5314	broad.mit.edu	37	chr6	51524264	51524264	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggaaacacctgagcgtatttCaatgggctcctctccttgta	9	11	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:51524264C>G	ENST00000371117.3	-	61	10935	c.10660G>C	c.(10660-10662)Gaa>Caa	p.E3554Q		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3554					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E3554Q(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAGCGTATTTCAATGGGCTCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	70	70					6																	51524264		2203	4300	6503	51632223	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10660G>C	6.37:g.51524264C>G	ENSP00000360158:p.Glu3554Gln		51632223	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324171	0.81580	.	.	ENSG00000170927	ENST00000371117	D	0.89343	-2.5	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.90277	0.6959	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.66716	0.946	D	0.90859	0.4737	10	0.66056	D	0.02	.	19.3249	0.94258	0.0:1.0:0.0:0.0	.	3554	P08F94	PKHD1_HUMAN	Q	3554	ENSP00000360158:E3554Q	ENSP00000360158:E3554Q	E	-	1	0	PKHD1	51632223	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.143000	0.64826	2.805000	0.96524	0.655000	0.94253	GAA		0.408	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51524264	C	G	51524264	3	3	48	1	0	0	0	0	1	0	0	0	12002	835	29	5	1592	5	PKHD1	6	51524264	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	19750345	51524264	119590803	34	6618										
WASF1	8936	broad.mit.edu	37	chr6	110429848	110429848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggtcttgaattgtagaacttCggaaagctttcctcattgtt	9	7	2	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:110429848C>T	ENST00000392589.1	-	6	1141	c.305G>A	c.(304-306)cGa>cAa	p.R102Q	WASF1_ENST00000392588.1_Missense_Mutation_p.R102Q|WASF1_ENST00000392586.1_Missense_Mutation_p.R102Q|WASF1_ENST00000392587.2_Missense_Mutation_p.R102Q|WASF1_ENST00000359451.2_Missense_Mutation_p.R102Q	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	102					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)	p.R102Q(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		TGTAGAACTTCGGAAAGCTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											82	76	78					6																	110429848		2203	4300	6503	110536541	SO:0001583	missense	8936			D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.305G>A	6.37:g.110429848C>T	ENSP00000376368:p.Arg102Gln		110536541	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656883	0.88154	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451;ENST00000444391;ENST00000265601;ENST00000368938	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	6.06	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.16981	0.0408	L	0.49126	1.545	0.52099	D	0.999946	P	0.39847	0.691	B	0.18871	0.023	T	0.04281	-1.0963	10	0.22706	T	0.39	.	15.5809	0.76439	0.0:0.934:0.0:0.066	.	102	Q92558	WASF1_HUMAN	Q	102	ENSP00000376365:R102Q;ENSP00000376366:R102Q;ENSP00000376368:R102Q;ENSP00000376367:R102Q;ENSP00000352425:R102Q;ENSP00000407041:R102Q;ENSP00000265601:R102Q;ENSP00000357934:R102Q	ENSP00000265601:R102Q	R	-	2	0	WASF1	110536541	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.777000	0.55364	1.574000	0.49760	0.650000	0.86243	CGA		0.353	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		T	110429848	C	T	110429848	3	4	48	1	0	0	0	0	1	0	0	0	17292	884	31	1	1398	1	WASF1	6	110429848	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	58905584	110429848	60685219	35	6619										
TXLNB	167838	broad.mit.edu	37	chr6	139564112	139564112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctctggctccttgagagcggCgtcagcactctcctgagaac	11	14	3	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr6:139564112C>T	ENST00000358430.3	-	10	1838	c.1606G>A	c.(1606-1608)Gcc>Acc	p.A536T	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	536						cytoplasm (GO:0005737)		p.A536T(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TTGAGAGCGGCGTCAGCACTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											77	84	81					6																	139564112		2203	4300	6503	139605805	SO:0001583	missense	167838				CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1606G>A	6.37:g.139564112C>T	ENSP00000351206:p.Ala536Thr		139605805	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	37	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	C	5.295	0.239808	0.10023	.	.	ENSG00000164440	ENST00000358430	T	0.14391	2.51	3.95	-7.9	0.01169	.	2.538650	0.01279	N	0.009686	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32613	-0.9900	9	.	.	.	5.6381	1.2535	0.01987	0.365:0.2665:0.0915:0.277	.	536	Q8N3L3	TXLNB_HUMAN	T	536	ENSP00000351206:A536T	.	A	-	1	0	TXLNB	139605805	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.799000	0.00762	-3.131000	0.00236	-1.340000	0.01251	GCC		0.567	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		T	139564112	C	T	139564112	3	4	48	1	0	0	0	0	1	0	0	0	16828	768	27	1	452	1	TXLNB	6	139564112	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	29134264	139564112	31550955	36	6620										
PMS2	5395	broad.mit.edu	37	chr7	6022481	6022481	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agcctctgcccctggagcacGgtgtgctgctgcagcatctc	12	15	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:6022481G>A	ENST00000265849.7	-	12	2253	c.2148C>T	c.(2146-2148)acC>acT	p.T716T	PMS2_ENST00000469652.1_5'Flank|PMS2_ENST00000441476.2_Silent_p.T610T|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000382321.4_Silent_p.T315T	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	716					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.T716T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		CCTGGAGCACGGTGTGCTGCT	0.488			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	1	Substitution - coding silent(1)	large_intestine(1)	7											20	20	20					7																	6022481		2199	4277	6476	5989007	SO:0001819	synonymous_variant	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2148C>T	7.37:g.6022481G>A			5989007	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.488	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		A	6022481	G	A	6022481	2	1	48	1	0	0	0	0	0	0	0	1	12174	1103	39	1		1	PMS2	7	6022481	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09		6022481	153116182	37	6621										
THSD7A	221981	broad.mit.edu	37	chr7	11632996	11632996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gatggttcgtgtccttacacGagtgcctgcaggggacacca	13	11	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:11632996G>A	ENST00000423059.4	-	3	1407	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	386	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R386C(1)		NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTCCTTACACGAGTGCCTGCA	0.507										HNSCC(18;0.044)																																						1	Substitution - Missense(1)	large_intestine(1)	7											99	96	97					7																	11632996		1937	4131	6068	11599521	SO:0001583	missense	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1156C>T	7.37:g.11632996G>A	ENSP00000406482:p.Arg386Cys		11599521		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107037	0.56291	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.58210	0.35	5.26	5.26	0.73747	.	0.099634	0.64402	D	0.000001	T	0.82125	0.4969	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87696	0.2557	10	0.62326	D	0.03	.	18.8505	0.92227	0.0:0.0:1.0:0.0	.	386	Q9UPZ6	THS7A_HUMAN	C	386	ENSP00000406482:R386C	ENSP00000262042:R386C	R	-	1	0	THSD7A	11599521	1.000000	0.71417	0.028000	0.17463	0.011000	0.07611	6.453000	0.73488	2.460000	0.83146	0.561000	0.74099	CGT		0.507	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11632996	G	A	11632996	3	1	48	1	0	0	0	0	1	0	0	0	15918	1058	37	1	3917	1	THSD7A	7	11632996	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	5610515	11632996	147505667	38	6622										
HDAC9	9734	broad.mit.edu	37	chr7	18767335	18767335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cccctgctgcctctgttttaCctcacccagcaatggaccgc	7	18	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:18767335C>T	ENST00000432645.2	+	12	1855	c.1855C>T	c.(1855-1857)Cct>Tct	p.P619S	HDAC9_ENST00000441542.2_Missense_Mutation_p.P622S|HDAC9_ENST00000401921.1_Missense_Mutation_p.P578S|HDAC9_ENST00000406451.4_Missense_Mutation_p.P619S	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	619					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.P622S(2)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CTCTGTTTTACCTCACCCAGC	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	7											49	54	53					7																	18767335		2004	4155	6159	18733860	SO:0001583	missense	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1855C>T	7.37:g.18767335C>T	ENSP00000410337:p.Pro619Ser		18733860	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797854	0.70567	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.59083	0.31;0.29;0.3;0.3	5.64	5.64	0.86602	.	0.113597	0.39759	N	0.001265	T	0.76695	0.4023	M	0.69823	2.125	0.80722	D	1	B;D;D;D;D;D;D	0.89917	0.192;1.0;1.0;1.0;1.0;1.0;1.0	B;D;D;D;D;D;D	0.87578	0.392;0.998;0.996;0.996;0.992;0.996;0.992	T	0.75013	-0.3467	10	0.46703	T	0.11	-35.6953	20.0585	0.97663	0.0:1.0:0.0:0.0	.	619;531;578;622;619;619;597	Q9UKV0-4;Q9UKV0-2;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q8N879	.;.;.;.;HDAC9_HUMAN;.;.	S	619;578;619;622;531	ENSP00000384657:P619S;ENSP00000383912:P578S;ENSP00000410337:P619S;ENSP00000408617:P622S	ENSP00000339165:P531S	P	+	1	0	HDAC9	18733860	1.000000	0.71417	0.961000	0.40146	0.975000	0.68041	3.964000	0.56780	2.812000	0.96745	0.557000	0.71058	CCT		0.562	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18767335	C	T	18767335	3	4	48	1	0	0	0	0	1	0	0	0	7035	507	18	3	1961	3	HDAC9	7	18767335	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	7134339	18767335	140371328	39	6623										
CACNA2D1	781	broad.mit.edu	37	chr7	81596502	81596502	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tacgtcactgtttcttttgcAgtcacaaactggaccagcac	7	12	3	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:81596502A>C	ENST00000356253.5	-	31	2776	c.2521T>G	c.(2521-2523)Tgc>Ggc	p.C841G	CACNA2D1_ENST00000535308.1_Missense_Mutation_p.C41G|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.C829G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	841					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.C829G(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTTCTTTTGCAGTCACAAACT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	7											77	74	75					7																	81596502		2202	4296	6498	81434438	SO:0001583	missense	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2521T>G	7.37:g.81596502A>C	ENSP00000348589:p.Cys841Gly		81434438	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	A	19.46	3.832608	0.71258	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.79940	-1.32;-1.32;-1.32	5.31	5.31	0.75309	.	0.223505	0.48767	D	0.000162	D	0.88577	0.6474	M	0.73962	2.25	0.44807	D	0.99781	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.984	D	0.87908	0.2695	10	0.36615	T	0.2	-13.0731	14.4354	0.67277	1.0:0.0:0.0:0.0	.	41;829	B7Z658;P54289-2	.;.	G	829;848;841;41	ENSP00000349320:C829G;ENSP00000348589:C841G;ENSP00000443124:C41G	ENSP00000284088:C848G	C	-	1	0	CACNA2D1	81434438	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.669000	0.61575	2.005000	0.58758	0.482000	0.46254	TGC		0.294	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81596502	A	C	81596502	3	2	48	1	0	0	0	0	1	0	0	0	2554	188	7	4	826	4	CACNA2D1	7	81596502	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	62829167	81596502	77542161	40	6624										
FBXO24	26261	broad.mit.edu	37	chr7	100192116	100192116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cccactacctgcctcacctgCgcgtggcctgcatgacttcc	8	19	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:100192116C>T	ENST00000241071.6	+	6	1226	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	FBXO24_ENST00000465843.1_Missense_Mutation_p.R288C|FBXO24_ENST00000360609.2_Missense_Mutation_p.R288C|PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000468962.1_Missense_Mutation_p.R290C|FBXO24_ENST00000427939.2_Missense_Mutation_p.R340C	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	302			R -> H (in dbSNP:rs7801492).		protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.R302C(1)		NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GCCTCACCTGCGCGTGGCCTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	7											100	74	83					7																	100192116		2203	4300	6503	100030052	SO:0001583	missense	26261			AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.904C>T	7.37:g.100192116C>T	ENSP00000241071:p.Arg302Cys		100030052	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523346	0.64747	.	.	ENSG00000106336	ENST00000241071;ENST00000360609;ENST00000465843;ENST00000468962;ENST00000427939	T;T;T;T;T	0.81330	-1.48;0.77;0.77;-1.48;-1.48	5.03	4.15	0.48705	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.206931	0.34223	N	0.004150	T	0.71779	0.3380	N	0.08118	0	0.44587	D	0.997559	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	P;P;P;P	0.56700	0.676;0.676;0.676;0.804	T	0.73603	-0.3930	10	0.54805	T	0.06	-3.1175	7.2647	0.26224	0.0:0.7404:0.1692:0.0903	.	290;340;302;288	B4DY42;B4DX91;O75426;O75426-2	.;.;FBX24_HUMAN;.	C	302;288;288;290;340	ENSP00000241071:R302C;ENSP00000353821:R288C;ENSP00000419602:R288C;ENSP00000420239:R290C;ENSP00000416558:R340C	ENSP00000241071:R302C	R	+	1	0	FBXO24	100030052	0.972000	0.33761	1.000000	0.80357	0.842000	0.47809	1.026000	0.30103	1.377000	0.46286	0.478000	0.44815	CGC		0.597	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			T	100192116	C	T	100192116	3	4	48	1	0	0	0	0	1	0	0	0	5754	768	27	1	1083	1	FBXO24	7	100192116	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	18595614	100192116	58946547	41	6625										
SLC12A9	56996	broad.mit.edu	37	chr7	100459163	100459163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gctcaccgcgcgaggaggccCcagtagctggggctatgtca	15	13	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:100459163C>T	ENST00000354161.3	+	11	1618	c.1493C>T	c.(1492-1494)cCc>cTc	p.P498L	SLC12A9_ENST00000540482.1_Missense_Mutation_p.P498L|SLC12A9_ENST00000275729.3_Missense_Mutation_p.P409L|SLC12A9_ENST00000415287.1_Missense_Mutation_p.P409L|SLC12A9_ENST00000428758.1_Missense_Mutation_p.P498L	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	498					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)	p.P498L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CGAGGAGGCCCCAGTAGCTGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	7											45	47	46					7																	100459163		2203	4300	6503	100297099	SO:0001583	missense	56996			AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.1493C>T	7.37:g.100459163C>T	ENSP00000275730:p.Pro498Leu		100297099	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.860205	0.51482	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000539308	D;D;D;D;D	0.98968	-5.28;-5.28;-5.28;-5.28;-5.28	5.51	5.51	0.81932	Amino acid permease domain (1);	0.154474	0.56097	D	0.000035	D	0.97247	0.9100	L	0.51422	1.61	0.58432	D	0.999998	B;B	0.34214	0.442;0.168	B;B	0.36186	0.219;0.166	D	0.97115	0.9807	10	0.59425	D	0.04	.	14.8945	0.70633	0.0:1.0:0.0:0.0	.	409;498	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	L	498;498;409;409;498;124	ENSP00000443702:P498L;ENSP00000408301:P498L;ENSP00000275729:P409L;ENSP00000413796:P409L;ENSP00000275730:P498L	ENSP00000275729:P409L	P	+	2	0	SLC12A9	100297099	1.000000	0.71417	1.000000	0.80357	0.259000	0.26198	2.290000	0.43531	2.590000	0.87494	0.491000	0.48974	CCC		0.642	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		T	100459163	C	T	100459163	3	4	48	1	0	0	0	0	1	0	0	0	14427	623	22	3	1531	3	SLC12A9	7	100459163	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	267047	100459163	58679500	42	6626										
SPAM1	6677	broad.mit.edu	37	chr7	123594019	123594019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	caaagctaagaaagacattaCattttatatgccagtagaca	6	7	0	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:123594019C>A	ENST00000439500.1	+	4	1008	c.395C>A	c.(394-396)aCa>aAa	p.T132K	SPAM1_ENST00000460182.1_Missense_Mutation_p.T132K|SPAM1_ENST00000340011.5_Missense_Mutation_p.T132K|SPAM1_ENST00000223028.7_Missense_Mutation_p.T132K|SPAM1_ENST00000402183.2_Missense_Mutation_p.T132K	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	132					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)	p.T132K(2)		breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AAAGACATTACATTTTATATG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	7											88	90	89					7																	123594019		2203	4300	6503	123381255	SO:0001583	missense	6677			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.395C>A	7.37:g.123594019C>A	ENSP00000402123:p.Thr132Lys		123381255	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	C	5.381	0.255573	0.10185	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	6.03	-9.7	0.00521	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	4.007680	0.00166	N	0.000002	T	0.07279	0.0184	N	0.02802	-0.49	0.09310	N	1	B;B	0.12013	0.002;0.005	B;B	0.24701	0.034;0.055	T	0.22695	-1.0209	9	.	.	.	11.6006	6.4722	0.22015	0.3396:0.3097:0.0:0.3507	.	132;132	Q8TC30;P38567	.;HYALP_HUMAN	K	132	ENSP00000386028:T132K;ENSP00000417934:T132K;ENSP00000345849:T132K;ENSP00000402123:T132K;ENSP00000223028:T132K	.	T	+	2	0	SPAM1	123381255	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.739000	0.04866	-1.284000	0.02390	-1.053000	0.02334	ACA		0.398	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			A	123594019	C	A	123594019	3	1	48	1	0	0	0	0	1	0	0	0	15025	478	17	2	397	2	SPAM1	7	123594019	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	23134856	123594019	35544644	43	6627										
PAX4	5078	broad.mit.edu	37	chr7	127253858	127253858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggagaagatagtccgattccGgtggccggtccctgggtggg	18	9	0	2	rs121917718		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:127253858G>A	ENST00000341640.2	-	4	695	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	PAX4_ENST00000338516.3_Missense_Mutation_p.R172W|PAX4_ENST00000463946.1_Missense_Mutation_p.R162W|PAX4_ENST00000378740.2_Missense_Mutation_p.R164W	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	172					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.R164W(1)		cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GTCCGATTCCGGTGGCCGGTC	0.582																																					Ovarian(113;737 1605 7858 27720 34092)											1	Substitution - Missense(1)	large_intestine(1)	7	GRCh37	CM073257	PAX4	M	rs121917718						80	78	79					7																	127253858		2203	4300	6503	127041094	SO:0001583	missense	5078				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.490C>T	7.37:g.127253858G>A	ENSP00000339906:p.Arg164Trp		127041094	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907612	0.72868	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740;ENST00000463946	D;D;D	0.96940	-4.18;-4.18;-4.18	5.18	1.8	0.24995	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.071031	0.52532	D	0.000074	D	0.98298	0.9436	M	0.93638	3.44	0.49389	A	0.999782	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	D	0.99927	1.1290	9	0.87932	D	0	.	12.3749	0.55275	0.0:0.0:0.477:0.523	.	164;162;172;162	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	W	164;172;172;162	ENSP00000339906:R164W;ENSP00000344297:R172W;ENSP00000451923:R162W	ENSP00000344297:R172W	R	-	1	2	PAX4	127041094	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.090000	0.30902	0.501000	0.28013	-0.175000	0.13238	CGG		0.582	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			A	127253858	G	A	127253858	3	1	48	1	0	0	0	0	1	0	0	0	11512	1115	39	1	565	1	PAX4	7	127253858	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	3659839	127253858	31884805	44	6628										
LRGUK	136332	broad.mit.edu	37	chr7	133884080	133884080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggagaaaaggattattcagtCgtgcagaaattgaatttgct	11	4	1	3	rs150378173		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr7:133884080C>T	ENST00000285928.2	+	14	1723	c.1654C>T	c.(1654-1656)Cgt>Tgt	p.R552C		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	552	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)	p.R552C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ATTATTCAGTCGTGCAGAAAT	0.363													C|||	1	0.000199681	0	0.0014	5008	,	,		15031	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						C	CYS/ARG	0,4406		0,0,2203	109	120	117		1654	6.2	1	7	dbSNP_134	117	3,8597	3.0+/-9.4	0,3,4297	yes	missense	LRGUK	NM_144648.1	180	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	552/826	133884080	3,13003	2203	4300	6503	133534620	SO:0001583	missense	136332			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1654C>T	7.37:g.133884080C>T	ENSP00000285928:p.Arg552Cys		133534620	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	20.2	3.949185	0.73787	0.0	3.49E-4	ENSG00000155530	ENST00000285928	T	0.43688	0.94	6.17	6.17	0.99709	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.204143	0.42682	D	0.000679	T	0.59838	0.2223	L	0.54323	1.7	0.43467	D	0.995676	D	0.89917	1.0	D	0.76071	0.987	T	0.59423	-0.7457	10	0.87932	D	0	-19.6321	14.2257	0.65858	0.246:0.754:0.0:0.0	.	552	Q96M69	LRGUK_HUMAN	C	552	ENSP00000285928:R552C	ENSP00000285928:R552C	R	+	1	0	LRGUK	133534620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.289000	0.43523	2.941000	0.99782	0.655000	0.94253	CGT		0.363	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		T	133884080	C	T	133884080	3	4	48	1	0	0	0	0	1	0	0	0	8972	884	31	1	1708	1	LRGUK	7	133884080	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	6630222	133884080	25254583	45	6629										
LOXL2	4017	broad.mit.edu	37	chr8	23217682	23217682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acaccacaccgacatcctccGtgtgcttgcagtcagtgacg	9	15	1	1	rs186026557		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr8:23217682G>A	ENST00000389131.3	-	3	821	c.452C>T	c.(451-453)aCg>aTg	p.T151M	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	151	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)	p.T151M(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		GACATCCTCCGTGTGCTTGCA	0.527													G|||	1	0.000199681	0	0	5008	,	,		20224	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						G	MET/THR	0,4406		0,0,2203	105	87	93		452	5.6	1	8		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOXL2	NM_002318.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	151/775	23217682	1,13005	2203	4300	6503	23273627	SO:0001583	missense	4017			U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.452C>T	8.37:g.23217682G>A	ENSP00000373783:p.Thr151Met		23273627	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	37	CCDS34864.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.75	3.885817	0.72410	0.0	1.16E-4	ENSG00000134013	ENST00000389131;ENST00000524144;ENST00000520871;ENST00000518083	T;T;T;T	0.47528	0.84;0.84;0.84;4.09	5.62	5.62	0.85841	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.202118	0.51477	D	0.000093	T	0.52964	0.1767	L	0.43646	1.37	0.32528	N	0.535298	D	0.53462	0.96	P	0.53062	0.717	T	0.63875	-0.6538	10	0.66056	D	0.02	.	14.2324	0.65903	0.0:0.1493:0.8507:0.0	.	151	Q9Y4K0	LOXL2_HUMAN	M	151;232;192;151	ENSP00000373783:T151M;ENSP00000427883:T232M;ENSP00000429778:T192M;ENSP00000430519:T151M	ENSP00000373783:T151M	T	-	2	0	LOXL2	23273627	0.999000	0.42202	0.983000	0.44433	0.915000	0.54546	2.951000	0.49089	2.804000	0.96469	0.655000	0.94253	ACG		0.527	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			A	23217682	G	A	23217682	3	1	48	1	0	0	0	0	1	0	0	0	8929	1145	40	1	1920	1	LOXL2	8	23217682	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		23217682	123146340	46	6630										
EFCAB1	79645	broad.mit.edu	37	chr8	49641699	49641699	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agacagcttcccatcatggtCatgatcctaggggaatgaga	11	9	2	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr8:49641699C>A	ENST00000262103.3	-	5	558	c.478G>T	c.(478-480)Gac>Tac	p.D160Y	EFCAB1_ENST00000433756.1_Missense_Mutation_p.D108Y|EFCAB1_ENST00000521002.1_Intron|EFCAB1_ENST00000523092.1_Missense_Mutation_p.D108Y	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	160	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.D160Y(1)		endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				CCATCATGGTCATGATCCTAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											110	93	99					8																	49641699		2203	4300	6503	49804252	SO:0001583	missense	79645				CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.478G>T	8.37:g.49641699C>A	ENSP00000262103:p.Asp160Tyr		49804252	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	37	CCDS6145.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.239734|4.239734	0.79800|0.79800	.|.	.|.	ENSG00000034239|ENSG00000034239	ENST00000433756;ENST00000262103;ENST00000450553;ENST00000523092|ENST00000523008;ENST00000522254	T;T;T|.	0.76060|.	-0.99;-0.99;-0.99|.	5.09|5.09	5.09|5.09	0.68999|0.68999	EF-hand-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.91503|.	0.7317|.	H|H	0.99619|0.99619	4.66|4.66	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	D|.	0.94961|.	0.8108|.	9|.	.|.	.|.	.|.	.|.	16.0365|16.0365	0.80635|0.80635	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	108;160|.	Q9HAE3-2;Q9HAE3|.	.;EFCB1_HUMAN|.	Y|L	108;160;160;108|26;77	ENSP00000400873:D108Y;ENSP00000262103:D160Y;ENSP00000430765:D108Y|.	.|.	D|X	-|-	1|2	0|2	EFCAB1|EFCAB1	49804252|49804252	1.000000|1.000000	0.71417|0.71417	0.958000|0.958000	0.39756|0.39756	0.876000|0.876000	0.50452|0.50452	7.352000|7.352000	0.79404|0.79404	2.641000|2.641000	0.89580|0.89580	0.455000|0.455000	0.32223|0.32223	GAC|TGA		0.413	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		A	49641699	C	A	49641699	3	1	48	1	0	0	0	0	1	0	0	0	4944	826	29	2	165	2	EFCAB1	8	49641699	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	26424017	49641699	96722323	47	6631										
RP1	6101	broad.mit.edu	37	chr8	55539894	55539894	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cttctgtcaagttgatgctcAcaaggctaccaacaaatctt	6	11	4	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr8:55539894A>T	ENST00000220676.1	+	4	3600	c.3452A>T	c.(3451-3453)cAc>cTc	p.H1151L		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1151					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.H1151L(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			GTTGATGCTCACAAGGCTACC	0.413																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											95	90	92					8																	55539894		2203	4300	6503	55702447	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3452A>T	8.37:g.55539894A>T	ENSP00000220676:p.His1151Leu		55702447		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.894966	0.00522	.	.	ENSG00000104237	ENST00000220676	T	0.19938	2.11	5.7	-2.17	0.07059	.	1.314670	0.05011	N	0.470926	T	0.10294	0.0252	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24870	-1.0148	10	0.02654	T	1	1.2284	2.7699	0.05330	0.5068:0.158:0.068:0.2671	.	1151	P56715	RP1_HUMAN	L	1151	ENSP00000220676:H1151L	ENSP00000220676:H1151L	H	+	2	0	RP1	55702447	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	0.552000	0.23376	-0.171000	0.10797	0.460000	0.39030	CAC		0.413	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55539894	A	T	55539894	3	4	48	1	0	0	0	0	1	0	0	0	13569	159	6	5	3462	5	RP1	8	55539894	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	5898195	55539894	90824128	48	6632										
CLVS1	157807	broad.mit.edu	37	chr8	62370877	62370877	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tctttacagattttcctgcaTggaaacaatttaaacagcct	5	9	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr8:62370877T>C	ENST00000519846.1	+	6	1225	c.753T>C	c.(751-753)caT>caC	p.H251H	CLVS1_ENST00000518592.1_5'UTR|CLVS1_ENST00000325897.4_Silent_p.H251H			Q8IUQ0	CLVS1_HUMAN	clavesin 1	251	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)	p.H251H(1)		endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						TTTTCCTGCATGGAAACAATT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	8											115	110	112					8																	62370877		2203	4300	6503	62533431	SO:0001819	synonymous_variant	157807			AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"retinaldehyde binding protein 1-like 1"	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.753T>C	8.37:g.62370877T>C			62533431	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																				0.368	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519		C	62370877	T	C	62370877	2	2	48	1	0	0	0	0	0	0	0	1	3577	1461	51	4		4	CLVS1	8	62370877	Silent	SNP	T	TCGA-AG-3893-01A-01W-1073-09	6830983	62370877	83993145	49	6633										
ZFPM2	23414	broad.mit.edu	37	chr8	106814517	106814517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gcagagaaccatgcgcacacGcaagcgcagaaagatgtatg	12	10	0	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr8:106814517G>A	ENST00000407775.2	+	8	2457	c.2207G>A	c.(2206-2208)cGc>cAc	p.R736H	ZFPM2_ENST00000517361.1_Missense_Mutation_p.R604H|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000378472.4_Missense_Mutation_p.R467H|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.R604H|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520433.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	736					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R736H(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATGCGCACACGCAAGCGCAGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8											48	47	48					8																	106814517		2086	4219	6305	106883693	SO:0001583	missense	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2207G>A	8.37:g.106814517G>A	ENSP00000384179:p.Arg736His		106883693	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674769	0.88445	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.54675	0.56;1.13;1.13;2.36	5.72	5.72	0.89469	.	0.044995	0.85682	D	0.000000	T	0.73418	0.3584	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72268	-0.4343	10	0.48119	T	0.1	.	19.88	0.96892	0.0:0.0:1.0:0.0	.	736	Q8WW38	FOG2_HUMAN	H	736;604;604;467	ENSP00000384179:R736H;ENSP00000430757:R604H;ENSP00000428720:R604H;ENSP00000367733:R467H	ENSP00000367733:R467H	R	+	2	0	ZFPM2	106883693	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	9.869000	0.99810	2.708000	0.92522	0.561000	0.74099	CGC		0.507	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106814517	G	A	106814517	3	1	48	1	0	0	0	0	1	0	0	0	17697	1087	38	1	2237	1	ZFPM2	8	106814517	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	44443640	106814517	39549505	50	6634										
DOCK8	81704	broad.mit.edu	37	chr9	441900	441900	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	taagagaatgtttggaacctActtccgagttggtttctttg	10	6	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:441900A>T	ENST00000453981.1	+	42	5493	c.5381A>T	c.(5380-5382)tAc>tTc	p.Y1794F	DOCK8_ENST00000382329.1_Missense_Mutation_p.Y1261F|DOCK8_ENST00000432829.2_Missense_Mutation_p.Y1726F|DOCK8_ENST00000469391.1_Missense_Mutation_p.Y1694F			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1794	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Y1794F(1)|p.Y1726F(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TTTGGAACCTACTTCCGAGTT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	9											106	103	104					9																	441900		2203	4300	6503	431900	SO:0001583	missense	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5381A>T	9.37:g.441900A>T	ENSP00000408464:p.Tyr1794Phe		431900	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	A	28.6	4.934990	0.92458	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.47869	1.06;1.07;1.07;0.83	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.65322	0.2680	M	0.66506	2.035	0.80722	D	1	D;D;D	0.61080	0.989;0.989;0.989	D;P;D	0.64410	0.925;0.88;0.925	T	0.64744	-0.6335	10	0.42905	T	0.14	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	1694;1261;1794	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	F	1794;1762;1726;1694;1261	ENSP00000408464:Y1794F;ENSP00000394888:Y1726F;ENSP00000419438:Y1694F;ENSP00000371766:Y1261F	ENSP00000287364:Y1762F	Y	+	2	0	DOCK8	431900	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.033000	0.93741	2.371000	0.80710	0.533000	0.62120	TAC		0.428	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	441900	A	T	441900	3	4	48	1	0	0	0	0	1	0	0	0	4704	391	14	5	5547	5	DOCK8	9	441900	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09		441900	140771531	51	6635										
MPDZ	8777	broad.mit.edu	37	chr9	13224414	13224414	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgatcaaattcatcacaagCaggtttcccattaatgtgtg	7	9	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:13224414C>A	ENST00000319217.7	-	4	599	c.352G>T	c.(352-354)Gct>Tct	p.A118S	MPDZ_ENST00000536827.1_Missense_Mutation_p.A118S|MPDZ_ENST00000546205.1_Missense_Mutation_p.A118S|MPDZ_ENST00000381022.2_Missense_Mutation_p.A118S|MPDZ_ENST00000447879.1_Missense_Mutation_p.A118S|MPDZ_ENST00000541718.1_Missense_Mutation_p.A118S|MPDZ_ENST00000381015.4_Missense_Mutation_p.A118S	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	118					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.A118S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TCATCACAAGCAGGTTTCCCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											132	126	128					9																	13224414		1843	4089	5932	13214414	SO:0001583	missense	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.352G>T	9.37:g.13224414C>A	ENSP00000320006:p.Ala118Ser		13214414	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	3.285	-0.146096	0.06627	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.09538	3.02;2.97;2.97;2.97;3.02;3.02;3.02	5.72	1.36	0.22044	.	0.877885	0.09597	N	0.780779	T	0.04588	0.0125	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.42582	-0.9443	10	0.33940	T	0.23	.	6.0574	0.19819	0.1613:0.5302:0.0:0.3085	.	118;118;118	B7ZMI4;O75970-3;O75970-2	.;.;.	S	118	ENSP00000320006:A118S;ENSP00000439807:A118S;ENSP00000370410:A118S;ENSP00000444151:A118S;ENSP00000415208:A118S;ENSP00000370403:A118S;ENSP00000446358:A118S	ENSP00000320006:A118S	A	-	1	0	MPDZ	13214414	0.000000	0.05858	0.521000	0.27850	0.992000	0.81027	0.011000	0.13264	0.331000	0.23511	0.655000	0.94253	GCT		0.358	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13224414	C	A	13224414	3	1	48	1	0	0	0	0	1	0	0	0	9752	710	25	2	5945	2	MPDZ	9	13224414	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	12782514	13224414	127989017	52	6636										
ZDHHC21	340481	broad.mit.edu	37	chr9	14674311	14674311	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gcagcaccaaccatgtgggtCaacaacaaagtgaatccgga	10	11	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:14674311C>A	ENST00000380916.4	-	4	494	c.28G>T	c.(28-30)Gac>Tac	p.D10Y		NM_178566.4	NP_848661.1	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21	10					hair follicle development (GO:0001942)|nitric oxide metabolic process (GO:0046209)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)|regulation of nitric-oxide synthase activity (GO:0050999)|sebaceous gland development (GO:0048733)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.D10Y(1)		endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9				GBM - Glioblastoma multiforme(50;4.31e-06)		CCATGTGGGTCAACAACAAAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	107	105					9																	14674311		2203	4300	6503	14664311	SO:0001583	missense	340481			AF161360	CCDS6475.1	9p22.3	2010-02-09			ENSG00000175893	ENSG00000175893		"Zinc fingers, DHHC-type"	20750	protein-coding gene	gene with protein product		614605				19956733	Standard	NM_178566		Approved	HSPC097, DNZ1	uc003zlg.2	Q8IVQ6	OTTHUMG00000019573	ENST00000380916.4:c.28G>T	9.37:g.14674311C>A	ENSP00000370303:p.Asp10Tyr		14664311	A8KA95|D3DRI7|Q5VWG1	Missense_Mutation	SNP	ENST00000380916.4	37	CCDS6475.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449468	0.84101	.	.	ENSG00000175893	ENST00000380916	T	0.52526	0.66	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.59932	0.2230	L	0.27053	0.805	0.58432	D	0.999999	D	0.76494	0.999	D	0.77557	0.99	T	0.62148	-0.6915	10	0.87932	D	0	-17.0095	20.2956	0.98549	0.0:1.0:0.0:0.0	.	10	Q8IVQ6	ZDH21_HUMAN	Y	10	ENSP00000370303:D10Y	ENSP00000370303:D10Y	D	-	1	0	ZDHHC21	14664311	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.628000	0.74262	2.805000	0.96524	0.460000	0.39030	GAC		0.388	ZDHHC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051748.2	NM_178566		A	14674311	C	A	14674311	3	1	48	1	0	0	0	0	1	0	0	0	17651	825	29	2	789	2	ZDHHC21	9	14674311	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	1449897	14674311	126539120	53	6637										
AKNA	80709	broad.mit.edu	37	chr9	117139205	117139205	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tttgtctgcttccagatgtgTtccttgggctgagggcagaa	13	8	1	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:117139205T>C	ENST00000307564.4	-	3	1043	c.882A>G	c.(880-882)gaA>gaG	p.E294E	AKNA_ENST00000374075.5_Silent_p.E213E|AKNA_ENST00000374088.3_Silent_p.E294E|AKNA_ENST00000223791.3_5'UTR|AKNA_ENST00000312033.3_Silent_p.E294E	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	294					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E294E(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TCCAGATGTGTTCCTTGGGCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9											125	110	115					9																	117139205		2203	4300	6503	116179026	SO:0001819	synonymous_variant	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.882A>G	9.37:g.117139205T>C			116179026	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1																																																																																				0.582	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117139205	T	C	117139205	2	2	48	1	0	0	0	0	0	0	0	1	463	1722	60	4		4	AKNA	9	117139205	Silent	SNP	T	TCGA-AG-3893-01A-01W-1073-09	102464894	117139205	24074226	54	6638										
GLE1	2733	broad.mit.edu	37	chr9	131271183	131271183	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agaagaatgtatgtctcttcCcaagctatcttcttattctg	6	9	4	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:131271183C>G	ENST00000309971.4	+	2	234	c.128C>G	c.(127-129)cCc>cGc	p.P43R	GLE1_ENST00000539582.1_5'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.P43R	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	43					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.P43R(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						ATGTCTCTTCCCAAGCTATCT	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	9											145	137	140					9																	131271183		2203	4300	6503	130311004	SO:0001583	missense	2733			AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.128C>G	9.37:g.131271183C>G	ENSP00000308622:p.Pro43Arg		130311004	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	37	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289853	0.40494	.	.	ENSG00000119392	ENST00000309971;ENST00000372770	T;T	0.66815	-0.23;0.18	5.47	5.47	0.80525	.	0.301441	0.37761	N	0.001954	T	0.62295	0.2416	M	0.63843	1.955	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.003;0.006	T	0.59815	-0.7383	10	0.44086	T	0.13	-17.5558	10.4085	0.44278	0.0:0.9111:0.0:0.0889	.	43;43	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	R	43	ENSP00000308622:P43R;ENSP00000361856:P43R	ENSP00000308622:P43R	P	+	2	0	GLE1	130311004	0.823000	0.29233	1.000000	0.80357	0.960000	0.62799	2.668000	0.46816	2.582000	0.87167	0.455000	0.32223	CCC		0.443	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722		G	131271183	C	G	131271183	3	3	48	1	0	0	0	0	1	0	0	0	6455	623	22	5	134	5	GLE1	9	131271183	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	14131978	131271183	9942248	55	6639										
LAMC3	10319	broad.mit.edu	37	chr9	133917079	133917079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cctgtgacccccgcagtgggCgctgcccctgcaaagagaat	12	15	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr9:133917079C>T	ENST00000361069.4	+	7	1472	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	447	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.R447C(2)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCGCAGTGGGCGCTGCCCCTG	0.547																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	9											51	46	48					9																	133917079		2203	4300	6503	132906900	SO:0001583	missense	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1339C>T	9.37:g.133917079C>T	ENSP00000354360:p.Arg447Cys		132906900	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692866	0.68271	.	.	ENSG00000050555	ENST00000361069;ENST00000355048;ENST00000320021	T	0.62364	0.03	4.97	3.01	0.34805	EGF-like, laminin (3);	0.558844	0.19673	N	0.108699	T	0.79370	0.4434	M	0.89095	3.005	0.09310	N	0.999995	D	0.76494	0.999	D	0.64877	0.93	T	0.71590	-0.4547	10	0.54805	T	0.06	.	12.3069	0.54908	0.3029:0.6971:0.0:0.0	.	447	Q9Y6N6	LAMC3_HUMAN	C	447	ENSP00000354360:R447C	ENSP00000325873:R447C	R	+	1	0	LAMC3	132906900	0.008000	0.16893	0.529000	0.27951	0.961000	0.63080	1.954000	0.40362	0.430000	0.26230	0.462000	0.41574	CGC		0.547	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		T	133917079	C	T	133917079	3	4	48	1	0	0	0	0	1	0	0	0	8638	768	27	1	1365	1	LAMC3	9	133917079	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	2645896	133917079	7296352	56	6640										
ARHGAP21	57584	broad.mit.edu	37	chr10	24909176	24909176	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggaacctcgaaaagatttatGaatttcttgctgcctaggtc	9	8	1	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr10:24909176G>C	ENST00000396432.2	-	9	2134	c.1648C>G	c.(1648-1650)Cat>Gat	p.H550D	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.H337D	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	549					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.H549D(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						AAAGATTTATGAATTTCTTGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											82	84	83					10																	24909176		2203	4300	6503	24949182	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.1648C>G	10.37:g.24909176G>C	ENSP00000379709:p.His550Asp		24949182	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	16.02	3.003465	0.54254	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.50277	2.72;2.83;0.75;0.77	5.5	5.5	0.81552	.	0.336409	0.35466	N	0.003189	T	0.64505	0.2604	M	0.68317	2.08	0.37622	D	0.921358	D;B	0.59357	0.985;0.226	P;B	0.56916	0.809;0.064	T	0.68773	-0.5320	10	0.56958	D	0.05	.	19.7622	0.96325	0.0:0.0:1.0:0.0	.	540;549	F8W9U9;Q5T5U3	.;RHG21_HUMAN	D	550;539;337;540;550;385	ENSP00000379709:H550D;ENSP00000365604:H337D;ENSP00000365592:H540D;ENSP00000405018:H550D	ENSP00000365604:H337D	H	-	1	0	ARHGAP21	24949182	1.000000	0.71417	0.201000	0.23476	0.966000	0.64601	5.313000	0.65798	2.732000	0.93576	0.650000	0.86243	CAT		0.418	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24909176	G	C	24909176	3	2	48	1	0	0	0	0	1	0	0	0	871	1290	45	5	4300	5	ARHGAP21	10	24909176	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		24909176	110625571	57	6641										
GPR158	57512	broad.mit.edu	37	chr10	25887089	25887090	+	Missense_Mutation	DNP	AA	AA	TT													0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ccaagaggaggagacaacagAaaattccacactggaatccc							TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr10:25887089_25887090AA>TT	ENST00000376351.3	+	11	2893_2894	c.2534_2535AA>TT	c.(2533-2535)gAA>gTT	p.E845V	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	845					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E845>?(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GAGACAACAGAAAATTCCACAC	0.485																																																1	Complex(1)	large_intestine(1)	10																																								25927096	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	Exception_encountered	10.37:g.25887089_25887090delinsTT	ENSP00000365529:p.Glu845Val		25927095	Q6QR81|Q9ULT3	Missense_Mutation	DNP	ENST00000376351.3	37	CCDS31166.1																																																																																				0.485	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		TT	25887090	AA	TT	25887089	3	4	48	1	0	0	0	0	1	0	0	0	6683	246	9	5	2576	5	GPR158	10	25887089	Missense_Mutation	DNP	AA	TCGA-AG-3893-01A-01W-1073-09	977913	25887089	109647658	58	6642										
PTCHD3	374308	broad.mit.edu	37	chr10	27702772	27702772	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agcaggaagatccaggggtgCgcgcccacctgccaccccag	13	16	0	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr10:27702772C>T	ENST00000438700.3	-	1	525	c.408G>A	c.(406-408)gcG>gcA	p.A136A		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	136					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)	p.A136A(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TCCAGGGGTGCGCGCCCACCT	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	10											28	33	31					10																	27702772		2203	4299	6502	27742778	SO:0001819	synonymous_variant	374308			AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.408G>A	10.37:g.27702772C>T			27742778	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																				0.667	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		T	27702772	C	T	27702772	2	4	48	1	0	0	0	0	0	0	0	1	12768	755	27	1		1	PTCHD3	10	27702772	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	1815683	27702772	107831975	59	6643										
KIAA0913	23053	broad.mit.edu	37	chr10	75548921	75548921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gggatcagctcttccgcatgCgggctgtgaaggacccattg	14	11	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr10:75548921C>T	ENST00000605216.1	+	3	647	c.430C>T	c.(430-432)Cgg>Tgg	p.R144W	ZSWIM8_ENST00000603114.1_Missense_Mutation_p.R144W|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.R144W|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.R144W|ZSWIM8_ENST00000604524.1_Missense_Mutation_p.R144W	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	144							zinc ion binding (GO:0008270)	p.R144W(4)									CTTCCGCATGCGGGCTGTGAA	0.572																																																4	Substitution - Missense(4)	urinary_tract(2)|large_intestine(2)	10											97	102	100					10																	75548921		2104	4225	6329	75218927	SO:0001583	missense	23053			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.430C>T	10.37:g.75548921C>T	ENSP00000474748:p.Arg144Trp		75218927	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	37		.	.	.	.	.	.	.	.	.	.	C	18.15	3.560024	0.65538	.	.	ENSG00000214655	ENST00000398706	T	0.42513	0.97	5.61	1.98	0.26296	.	.	.	.	.	T	0.56702	0.2003	M	0.65498	2.005	0.51012	D	0.999909	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.965;0.977;0.965	T	0.55159	-0.8184	9	0.72032	D	0.01	.	8.091	0.30801	0.6771:0.2563:0.0666:0.0	.	144;144;144	A7E2V4;A7E2V4-5;A7E2V4-4	K0913_HUMAN;.;.	W	144	ENSP00000381693:R144W	ENSP00000381693:R144W	R	+	1	2	KIAA0913	75218927	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.696000	0.25541	0.385000	0.24970	-0.264000	0.10439	CGG		0.572	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		T	75548921	C	T	75548921	3	4	48	1	0	0	0	0	1	0	0	0	8221	759	27	1	440	1	KIAA0913	10	75548921	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	47846149	75548921	59985826	60	6644										
MPEG1	219972	broad.mit.edu	37	chr11	58980158	58980158	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gtaagtcaattccataactcGtcccatgtccacattccgca	5	14	1	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:58980158G>A	ENST00000361050.3	-	1	266	c.181C>T	c.(181-183)Cga>Tga	p.R61*	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	61	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)		p.R61*(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TCCATAACTCGTCCCATGTCC	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											170	169	169					11																	58980158		2017	4174	6191	58736734	SO:0001587	stop_gained	219972			AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.181C>T	11.37:g.58980158G>A	ENSP00000354335:p.Arg61*		58736734	Q2M1T6|Q8TEF8	Nonsense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994369	0.93167	.	.	ENSG00000197629	ENST00000361050;ENST00000545098	.	.	.	5.41	3.33	0.38152	.	0.064428	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1937	10.4012	0.44231	0.0:0.0:0.5005:0.4995	.	.	.	.	X	61	.	ENSP00000354335:R61X	R	-	1	2	MPEG1	58736734	0.994000	0.37717	1.000000	0.80357	0.940000	0.58332	2.854000	0.48325	1.262000	0.44165	0.644000	0.83932	CGA		0.478	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58980158	G	A	58980158	4	1	48	1	0	0	0	0	0	1	0	0	9753	1153	40	1	1973	1	MPEG1	11	58980158	Nonsense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		58980158	76026358	61	6645										
FERMT3	83706	broad.mit.edu	37	chr11	63988498	63988498	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggtcccgcagctcaccccacGgatcctggaagcccaccaga	10	18	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:63988498G>A	ENST00000279227.5	+	13	1663	c.1568G>A	c.(1567-1569)cGg>cAg	p.R523Q	FERMT3_ENST00000345728.5_Missense_Mutation_p.R519Q	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	523	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)	p.R523Q(1)|p.R519Q(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CTCACCCCACGGATCCTGGAA	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	11											97	83	88					11																	63988498		2201	4297	6498	63745074	SO:0001583	missense	83706			L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"Fermitins", "Pleckstrin homology (PH) domain containing"	23151	protein-coding gene	gene with protein product	"kindlin-3"	607901	"fermitin family homolog 3 (Drosophila)"				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1568G>A	11.37:g.63988498G>A	ENSP00000279227:p.Arg523Gln		63745074	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909337	0.92107	.	.	ENSG00000149781	ENST00000345728;ENST00000279227	T;T	0.80653	-1.4;-1.4	4.29	4.29	0.51040	Band 4.1 domain (1);FERM central domain (2);	0.000000	0.85682	D	0.000000	D	0.86134	0.5860	L	0.46947	1.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.985	D	0.87494	0.2429	10	0.66056	D	0.02	-41.2461	16.0438	0.80704	0.0:0.0:1.0:0.0	.	519;523	Q86UX7-2;Q86UX7	.;URP2_HUMAN	Q	519;523	ENSP00000339950:R519Q;ENSP00000279227:R523Q	ENSP00000279227:R523Q	R	+	2	0	FERMT3	63745074	1.000000	0.71417	0.947000	0.38551	0.593000	0.36681	7.368000	0.79567	2.386000	0.81285	0.462000	0.41574	CGG		0.652	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		A	63988498	G	A	63988498	3	1	48	1	0	0	0	0	1	0	0	0	5838	1116	39	1	1614	1	FERMT3	11	63988498	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	5008340	63988498	71018018	62	6646										
DLG2	1740	broad.mit.edu	37	chr11	84245744	84245744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tcgaggtaaggaatgatcatGtggagcgtcctcatcttgat	12	7	3	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:84245744G>A	ENST00000532653.1	-	2	375	c.73C>T	c.(73-75)Cat>Tat	p.H25Y	DLG2_ENST00000524982.1_Missense_Mutation_p.H25Y|DLG2_ENST00000376104.2_Missense_Mutation_p.H130Y|DLG2_ENST00000543673.1_Missense_Mutation_p.H130Y|DLG2_ENST00000398309.2_Missense_Mutation_p.H25Y			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.H25Y(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GAATGATCATGTGGAGCGTCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											185	172	176					11																	84245744		1879	4114	5993	83923392	SO:0001583	missense	1740			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.73C>T	11.37:g.84245744G>A	ENSP00000435849:p.His25Tyr		83923392	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	G	27.6	4.848669	0.91277	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000543673;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000527088	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.88	5.88	0.94601	Membrane-associated guanylate kinase (MAGUK), PEST domain, N-terminal (1);	0.090245	0.45126	D	0.000396	T	0.33760	0.0874	N	0.19112	0.55	0.80722	D	1	B;P;P;P	0.42296	0.432;0.773;0.775;0.647	B;B;B;B	0.40602	0.227;0.334;0.201;0.334	T	0.03608	-1.1020	9	.	.	.	.	20.2279	0.98344	0.0:0.0:1.0:0.0	.	25;25;130;25	B7Z2T4;E9PN83;Q15700-2;Q15700	.;.;.;DLG2_HUMAN	Y	25;130;130;25;25;130;46	ENSP00000381355:H25Y;ENSP00000365272:H130Y;ENSP00000441994:H130Y;ENSP00000432894:H25Y;ENSP00000435849:H25Y;ENSP00000435809:H46Y	.	H	-	1	0	DLG2	83923392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.270000	0.95690	2.778000	0.95560	0.655000	0.94253	CAT		0.388	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		A	84245744	G	A	84245744	3	1	48	1	0	0	0	0	1	0	0	0	4566	1377	48	3	2786	3	DLG2	11	84245744	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	20257246	84245744	50760772	63	6647										
FAT3	120114	broad.mit.edu	37	chr11	92533683	92533683	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ccttttcacaaagcacatacGtagctgaggtgagagagaac	10	9	1	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:92533683G>A	ENST00000298047.6	+	9	7521	c.7504G>A	c.(7504-7506)Gta>Ata	p.V2502I	FAT3_ENST00000409404.2_Missense_Mutation_p.V2502I|FAT3_ENST00000525166.1_Missense_Mutation_p.V2352I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2502	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2502I(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAGCACATACGTAGCTGAGGT	0.498										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											84	81	82					11																	92533683		2056	4199	6255	92173331	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7504G>A	11.37:g.92533683G>A	ENSP00000298047:p.Val2502Ile		92173331	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	15.96	2.986499	0.53934	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.53423	0.62;0.62;0.62	5.95	5.95	0.96441	.	.	.	.	.	T	0.38108	0.1028	N	0.25789	0.76	0.80722	D	1	P	0.49961	0.93	B	0.38225	0.268	T	0.22417	-1.0217	9	0.42905	T	0.14	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	2502	Q8TDW7-3	.	I	2502;2502;2352	ENSP00000298047:V2502I;ENSP00000387040:V2502I;ENSP00000432586:V2352I	ENSP00000298047:V2502I	V	+	1	0	FAT3	92173331	1.000000	0.71417	0.948000	0.38648	0.891000	0.51852	6.668000	0.74457	2.824000	0.97209	0.655000	0.94253	GTA		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92533683	G	A	92533683	3	1	48	1	0	0	0	0	1	0	0	0	5710	1145	40	1	7538	1	FAT3	11	92533683	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	8287939	92533683	42472833	64	6648										
HTR3A	3359	broad.mit.edu	37	chr11	113857531	113857531	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tgcatgtgtctcttgcctctGccctgggctgcacaggtgtc	12	13	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:113857531G>T	ENST00000504030.2	+	8	1361				HTR3A_ENST00000506841.2_Missense_Mutation_p.A333S|HTR3A_ENST00000299961.5_Intron|HTR3A_ENST00000535865.1_Intron|HTR3A_ENST00000375498.2_Intron|HTR3A_ENST00000355556.2_Missense_Mutation_p.A339S			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)	p.A333S(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	TCTTGCCTCTGCCCTGGGCTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	11											117	102	107					11																	113857531		2201	4296	6497	113362741	SO:0001627	intron_variant	3359			D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.917-16G>T	11.37:g.113857531G>T			113362741	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	G	2.902	-0.227281	0.06022	.	.	ENSG00000166736	ENST00000355556;ENST00000506841	D;D	0.87650	-2.28;-2.28	2.81	-5.63	0.02474	.	0.915429	0.08980	N	0.865952	T	0.65831	0.2729	N	0.08118	0	0.09310	N	1	B	0.22683	0.073	B	0.19391	0.025	T	0.55192	-0.8179	9	.	.	.	-0.6469	3.3351	0.07098	0.2651:0.4612:0.1571:0.1166	.	339	G5E986	.	S	339;333	ENSP00000347754:A339S;ENSP00000424776:A333S	.	A	+	1	0	HTR3A	113362741	.	.	0.000000	0.03702	0.159000	0.22180	.	.	-1.366000	0.02155	-0.258000	0.10820	GCC		0.582	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		T	113857531	G	T	113857531	1	4	48	0	1	0	0	0	0	0	0	0	7465	1319	46	2		2	HTR3A	11	113857531	Intron	SNP	G	TCGA-AG-3893-01A-01W-1073-09	21323848	113857531	21148985	65	6649										
TECTA	7007	broad.mit.edu	37	chr11	120989269	120989269	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gctcctgtgcctacttgctgGcccgacagtgtttgcagact	11	13	0	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr11:120989269G>T	ENST00000392793.1	+	7	1316	c.1045G>T	c.(1045-1047)Gcc>Tcc	p.A349S	TECTA_ENST00000264037.2_Missense_Mutation_p.A349S			O75443	TECTA_HUMAN	tectorin alpha	349	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.A349S(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CTACTTGCTGGCCCGACAGTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11											139	123	128					11																	120989269		2203	4299	6502	120494479	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1045G>T	11.37:g.120989269G>T	ENSP00000376543:p.Ala349Ser		120494479		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081468	0.76528	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.62498	0.02;0.02	5.72	5.72	0.89469	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.69214	0.3086	N	0.21142	0.635	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.65594	-0.6130	10	0.27785	T	0.31	.	19.8885	0.96919	0.0:0.0:1.0:0.0	.	349	O75443	TECTA_HUMAN	S	349	ENSP00000376543:A349S;ENSP00000264037:A349S	ENSP00000264037:A349S	A	+	1	0	TECTA	120494479	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.742000	0.74843	2.700000	0.92200	0.563000	0.77884	GCC		0.572	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	120989269	G	T	120989269	3	4	48	1	0	0	0	0	1	0	0	0	15786	1203	42	2	1067	2	TECTA	11	120989269	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	7131738	120989269	14017247	66	6650										
KCNA1	3736	broad.mit.edu	37	chr12	5021087	5021087	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	atggtcatcctcatctccatCgtcatcttttgcctggagac	7	13	5	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr12:5021087C>T	ENST00000382545.3	+	2	1650	c.543C>T	c.(541-543)atC>atT	p.I181I	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	181					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)	p.I181I(1)		NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	TCATCTCCATCGTCATCTTTT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	12											89	85	86					12																	5021087		2203	4300	6503	4891348	SO:0001819	synonymous_variant	3736			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.543C>T	12.37:g.5021087C>T			4891348	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																				0.597	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		T	5021087	C	T	5021087	2	4	48	1	0	0	0	0	0	0	0	1	8022	874	31	1		1	KCNA1	12	5021087	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09		5021087	128830808	67	6651										
LAG3	3902	broad.mit.edu	37	chr12	6884504	6884504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ccagggtggggctgccctgcCgcctgcctgctggtgtgggg	19	13	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr12:6884504C>T	ENST00000203629.2	+	5	1180	c.847C>T	c.(847-849)Cgc>Tgc	p.R283C	LAG3_ENST00000441671.2_Missense_Mutation_p.R283C	NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	283	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)	p.R283C(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GCTGCCCTGCCGCCTGCCTGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	84	82					12																	6884504		2203	4300	6503	6754765	SO:0001583	missense	3902				CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.847C>T	12.37:g.6884504C>T	ENSP00000203629:p.Arg283Cys		6754765	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826486	0.71143	.	.	ENSG00000089692	ENST00000441671;ENST00000203629	T;T	0.13196	2.61;2.61	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.692253	0.14181	N	0.336059	T	0.30479	0.0766	L	0.54323	1.7	0.38867	D	0.956607	D;D	0.76494	0.997;0.999	P;P	0.60609	0.828;0.877	T	0.00795	-1.1563	10	0.46703	T	0.11	-7.5573	15.0046	0.71501	0.0:1.0:0.0:0.0	.	283;283	P18627;Q7Z643	LAG3_HUMAN;.	C	283	ENSP00000413825:R283C;ENSP00000203629:R283C	ENSP00000203629:R283C	R	+	1	0	LAG3	6754765	0.108000	0.22018	0.968000	0.41197	0.638000	0.38207	0.361000	0.20267	2.623000	0.88846	0.462000	0.41574	CGC		0.607	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			T	6884504	C	T	6884504	3	4	48	1	0	0	0	0	1	0	0	0	8622	652	23	1	865	1	LAG3	12	6884504	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	1863417	6884504	126967391	68	6652										
CALCOCO1	57658	broad.mit.edu	37	chr12	54110049	54110049	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aggggcctcactcaccacccGctgctgggcctggcctaggg	14	16	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr12:54110049G>A	ENST00000550804.1	-	8	1060	c.1000C>T	c.(1000-1002)Cgg>Tgg	p.R334W	CALCOCO1_ENST00000548263.1_Missense_Mutation_p.R334W|CALCOCO1_ENST00000262059.4_Missense_Mutation_p.R334W|CALCOCO1_ENST00000430117.2_Intron			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	334					intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.R334W(1)		NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						CTCACCACCCGCTGCTGGGCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											83	75	78					12																	54110049		2203	4300	6503	52396316	SO:0001583	missense	57658			AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.1000C>T	12.37:g.54110049G>A	ENSP00000449960:p.Arg334Trp		52396316	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Missense_Mutation	SNP	ENST00000550804.1	37	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.121726	0.56613	.	.	ENSG00000012822	ENST00000342760;ENST00000262059;ENST00000413257;ENST00000548263;ENST00000550804;ENST00000549935;ENST00000454332	T;T;T	0.10668	2.85;2.85;2.85	4.78	3.79	0.43588	.	0.415778	0.18263	N	0.146576	T	0.07818	0.0196	N	0.08118	0	0.28894	N	0.893688	D;P;P;P	0.56035	0.974;0.894;0.894;0.913	B;B;B;P	0.47206	0.438;0.406;0.406;0.541	T	0.07481	-1.0770	10	0.72032	D	0.01	-12.1252	9.7553	0.40500	0.0:0.0:0.7144:0.2856	.	327;334;334;334	B4DG60;Q9P1Z2-3;Q9P1Z2-2;Q9P1Z2	.;.;.;CACO1_HUMAN	W	11;334;272;334;334;327;211	ENSP00000262059:R334W;ENSP00000447647:R334W;ENSP00000449960:R334W	ENSP00000262059:R334W	R	-	1	2	CALCOCO1	52396316	0.995000	0.38212	0.998000	0.56505	0.953000	0.61014	1.430000	0.34914	1.161000	0.42604	0.655000	0.94253	CGG		0.577	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54110049	G	A	54110049	3	1	48	1	0	0	0	0	1	0	0	0	2583	1086	38	1	1107	1	CALCOCO1	12	54110049	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	47225545	54110049	79741846	69	6653										
MBD6	114785	broad.mit.edu	37	chr12	57921641	57921642	+	Frame_Shift_Del	DEL	TT	TT	-													0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ttctcaacaggtgacctgtcTtcactgaccagcagccctgg							TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	TT	TT	TT	-	TT	TT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr12:57921641_57921642delTT	ENST00000355673.3	+	9	2603_2604	c.2247_2248delTT	c.(2245-2250)tcttcafs	p.SS749fs	MBD6_ENST00000431731.2_Frame_Shift_Del_p.SS749fs	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	749	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S750fs*42(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						GTGACCTGTCTTCACTGACCAG	0.579																																																1	Deletion - Frameshift(1)	large_intestine(1)	12																																								56207909	SO:0001589	frameshift_variant	114785			AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.2247_2248delTT	12.37:g.57921641_57921642delTT	ENSP00000347896:p.Ser749fs		56207908	Q8N3M0|Q8NA81|Q96Q00	Frame_Shift_Del	DEL	ENST00000355673.3	37	CCDS8944.1																																																																																				0.579	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			-	57921642	TT	-	57921641	7	5	48	1	0	1	0	1	0	0	0	0	9378	1596	56	0	2273	0	MBD6	12	57921641	Frame_Shift_Del	DEL	TT	TCGA-AG-3893-01A-01W-1073-09	3811592	57921641	75930254	70	6654										
TBX5	6910	broad.mit.edu	37	chr12	114804048	114804048	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gggtggaggcaggaggtcctGggaggggccggaaacaccat	20	8	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr12:114804048G>T	ENST00000310346.4	-	8	1570	c.904C>A	c.(904-906)Cag>Aag	p.Q302K	TBX5_ENST00000526441.1_Missense_Mutation_p.Q302K|TBX5_ENST00000349716.5_Missense_Mutation_p.Q252K|TBX5_ENST00000405440.2_Missense_Mutation_p.Q302K	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	302					apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Q302K(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		AGGAGGTCCTGGGAGGGGCCG	0.557																																					NSCLC(152;1358 1980 4050 23898 40356)											1	Substitution - Missense(1)	large_intestine(1)	12											116	102	107					12																	114804048		2203	4300	6503	113288431	SO:0001583	missense	6910			U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.904C>A	12.37:g.114804048G>T	ENSP00000309913:p.Gln302Lys		113288431	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.256528	0.80246	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440;ENST00000526441	T;T;T;D	0.87179	0.98;0.98;0.98;-2.22	5.62	4.72	0.59763	.	0.113864	0.64402	D	0.000008	D	0.91546	0.7330	M	0.80746	2.51	0.58432	D	0.999996	P;P	0.50528	0.936;0.817	P;B	0.56127	0.792;0.169	D	0.90187	0.4247	10	0.24483	T	0.36	.	16.0386	0.80648	0.0:0.0:0.865:0.135	.	302;302	Q99593-2;Q99593	.;TBX5_HUMAN	K	252;302;199;302;302	ENSP00000337723:Q252K;ENSP00000309913:Q302K;ENSP00000384152:Q302K;ENSP00000433292:Q302K	ENSP00000309913:Q302K	Q	-	1	0	TBX5	113288431	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.609000	0.82925	1.357000	0.45904	0.655000	0.94253	CAG		0.557	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		T	114804048	G	T	114804048	3	4	48	1	0	0	0	0	1	0	0	0	15700	1357	47	2	727	2	TBX5	12	114804048	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	56882407	114804048	19047847	71	6655										
TPTE2	93492	broad.mit.edu	37	chr13	20039679	20039679	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tcttatcagaataataagtcGtagaagtcgaactaaatgtg	8	5	2	2	rs202071055		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr13:20039679G>A	ENST00000400230.2	-	8	582	c.538C>T	c.(538-540)Cga>Tga	p.R180*	TPTE2_ENST00000382975.4_Nonsense_Mutation_p.R140*|TPTE2_ENST00000382977.4_Nonsense_Mutation_p.R180*|TPTE2_ENST00000255310.6_Nonsense_Mutation_p.R103*|TPTE2_ENST00000457266.2_Nonsense_Mutation_p.R69*|TPTE2_ENST00000382978.1_Nonsense_Mutation_p.R140*|TPTE2_ENST00000390680.2_Nonsense_Mutation_p.R103*|TPTE2_ENST00000400103.2_Nonsense_Mutation_p.R69*			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	180					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R103*(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ATAATAAGTCGTAGAAGTCGA	0.318													g|||	1	0.000199681	8e-04	0	5008	,	,		18760	0		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	13						G	stop/ARG,stop/ARG,stop/ARG	0,4400		0,0,2200	38	37	37		205,307,538	1.9	0	13		37	1,8597		0,1,4298	yes	stop-gained,stop-gained,stop-gained	TPTE2	NM_001141968.1,NM_130785.3,NM_199254.2	,,	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	,,	69/412,103/446,180/523	20039679	1,12997	2200	4299	6499	18937679	SO:0001587	stop_gained	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.538C>T	13.37:g.20039679G>A	ENSP00000383089:p.Arg180*		18937679	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Nonsense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	g	19.37	3.815305	0.70912	0.0	1.16E-4	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	.	.	.	2.79	1.9	0.25705	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.2096	6.8484	0.24000	0.0:0.0:0.7234:0.2766	.	.	.	.	X	140;69;180;103;103;180;140;69;180;49	.	.	R	-	1	2	TPTE2	18937679	1.000000	0.71417	0.002000	0.10522	0.004000	0.04260	1.957000	0.40392	0.688000	0.31529	0.467000	0.42956	CGA		0.318	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		A	20039679	G	A	20039679	4	1	48	1	0	0	0	0	0	1	0	0	16471	1153	40	1	1082	1	TPTE2	13	20039679	Nonsense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		20039679	95130199	72	6656										
SACS	26278	broad.mit.edu	37	chr13	23904434	23904434	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aaactgtctacaccataagcTtccaatgtgtgaacatcatt	5	10	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr13:23904434T>G	ENST00000382292.3	-	9	13854	c.13581A>C	c.(13579-13581)gaA>gaC	p.E4527D	SACS_ENST00000382298.3_Missense_Mutation_p.E4527D|SACS_ENST00000402364.1_Missense_Mutation_p.E3777D			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4527	HEPN. {ECO:0000255|PROSITE- ProRule:PRU00105}.				cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.E4380D(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CACCATAAGCTTCCAATGTGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											187	165	173					13																	23904434		2203	4300	6503	22802434	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.13581A>C	13.37:g.23904434T>G	ENSP00000371729:p.Glu4527Asp		22802434	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	16.13	3.035718	0.54896	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.85773	-2.03;-2.03;-2.03	5.85	-3.7	0.04437	HEPN (3);	0.000000	0.85682	D	0.000000	D	0.84547	0.5496	L	0.34521	1.04	0.43385	D	0.995496	D	0.57257	0.979	D	0.66196	0.942	T	0.80705	-0.1263	10	0.27082	T	0.32	.	15.4777	0.75497	0.0:0.5578:0.0:0.4421	.	4527	Q9NZJ4	SACS_HUMAN	D	4527;3777;4527	ENSP00000371729:E4527D;ENSP00000385844:E3777D;ENSP00000371735:E4527D	ENSP00000371729:E4527D	E	-	3	2	SACS	22802434	0.899000	0.30636	0.909000	0.35828	0.333000	0.28666	-0.003000	0.12901	-0.647000	0.05444	0.460000	0.39030	GAA		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23904434	T	G	23904434	3	3	48	1	0	0	0	0	1	0	0	0	13841	1606	56	4	162	4	SACS	13	23904434	Missense_Mutation	SNP	T	TCGA-AG-3893-01A-01W-1073-09	3864755	23904434	91265444	73	6657										
F7	2155	broad.mit.edu	37	chr13	113771901	113771901	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	agaactggaggaacctgatcGcggtgctgggtgggtaccac	16	9	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr13:113771901G>A	ENST00000375581.3	+	8	831	c.796G>A	c.(796-798)Gcg>Acg	p.A266T	F7_ENST00000541084.1_Missense_Mutation_p.A197T|F7_ENST00000346342.3_Missense_Mutation_p.A244T	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	266	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> T (in FA7D). {ECO:0000269|PubMed:10862079, ECO:0000269|PubMed:18976247}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A266T(1)		large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	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)	GAACCTGATCGCGGTGCTGGG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	13	GRCh37	CM001149	F7	M							149	141	144					13																	113771901		2203	4300	6503	112819902	SO:0001583	missense	2155				CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"eptacog alfa", "FVII coagulation protein", "factor VII"	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.796G>A	13.37:g.113771901G>A	ENSP00000364731:p.Ala266Thr		112819902	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Missense_Mutation	SNP	ENST00000375581.3	37	CCDS9528.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.170365	0.38315	.	.	ENSG00000057593	ENST00000346342;ENST00000541084;ENST00000375581	D;D;D	0.82081	-1.57;-1.57;-1.57	4.32	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.430428	0.22519	N	0.058994	T	0.74928	0.3781	L	0.48174	1.505	0.09310	N	1	P;P;P	0.48834	0.854;0.897;0.916	B;B;B	0.40038	0.317;0.185;0.282	T	0.67304	-0.5704	10	0.72032	D	0.01	.	8.5566	0.33485	0.2725:0.0:0.7275:0.0	.	197;244;266	F5H8B0;P08709-2;P08709	.;.;FA7_HUMAN	T	244;197;266	ENSP00000329546:A244T;ENSP00000442051:A197T;ENSP00000364731:A266T	ENSP00000329546:A244T	A	+	1	0	F7	112819902	0.448000	0.25681	0.011000	0.14972	0.004000	0.04260	2.582000	0.46085	0.471000	0.27319	-0.269000	0.10298	GCG		0.632	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131		A	113771901	G	A	113771901	3	1	48	1	0	0	0	0	1	0	0	0	5362	1087	38	1	826	1	F7	13	113771901	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	89867467	113771901	1397977	74	6658										
CPNE6	9362	broad.mit.edu	37	chr14	24546153	24546153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tccagctctacggccccaccAatgtggcccccatcatcaac	6	19	3	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr14:24546153A>G	ENST00000397016.2	+	15	1542	c.1231A>G	c.(1231-1233)Aat>Gat	p.N411D	CPNE6_ENST00000537691.1_Missense_Mutation_p.N466D|CPNE6_ENST00000216775.2_Missense_Mutation_p.N411D	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	411	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.N411D(1)		endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		CGGCCCCACCAATGTGGCCCC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	52	53					14																	24546153		2203	4300	6503	23615993	SO:0001583	missense	9362			AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.1231A>G	14.37:g.24546153A>G	ENSP00000380211:p.Asn411Asp		23615993	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	37	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	A	33	5.249172	0.95305	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.24723	1.84;1.84;1.84	5.08	5.08	0.68730	von Willebrand factor, type A (2);Copine (1);	0.000000	0.64402	D	0.000010	T	0.51363	0.1670	M	0.78049	2.395	0.46499	D	0.999077	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;1.0;0.999	T	0.56715	-0.7933	10	0.87932	D	0	-14.5398	12.8026	0.57594	1.0:0.0:0.0:0.0	.	466;236;411	F5GXN1;B3KWK1;O95741	.;.;CPNE6_HUMAN	D	466;411;411	ENSP00000440077:N466D;ENSP00000380211:N411D;ENSP00000216775:N411D	ENSP00000216775:N411D	N	+	1	0	CPNE6	23615993	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	9.339000	0.96797	1.907000	0.55213	0.460000	0.39030	AAT		0.612	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			G	24546153	A	G	24546153	3	3	48	1	0	0	0	0	1	0	0	0	3822	130	5	4	1281	4	CPNE6	14	24546153	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09		24546153	82803387	75	6659										
NYNRIN	57523	broad.mit.edu	37	chr14	24886265	24886265	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ggtgagtcaaggctcacggaGcccctgtggtgggagatgag	18	8	2	3	rs534007372		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr14:24886265G>A	ENST00000382554.3	+	9	5628	c.5310G>A	c.(5308-5310)gaG>gaA	p.E1770E		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1770	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.				DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.E1770E(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GGCTCACGGAGCCCCTGTGGT	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	14											42	46	45					14																	24886265		2054	4192	6246	23956105	SO:0001819	synonymous_variant	57523			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.5310G>A	14.37:g.24886265G>A			23956105	Q6P153|Q86TR3|Q9HAC4	Silent	SNP	ENST00000382554.3	37	CCDS45090.1																																																																																				0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			A	24886265	G	A	24886265	2	1	48	1	0	0	0	0	0	0	0	1	10827	962	34	3		3	NYNRIN	14	24886265	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	340112	24886265	82463275	76	6660										
AHNAK2	113146	broad.mit.edu	37	chr14	105416366	105416366	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cttgtcggccagggacaggtCaccctccagccgcacactgt	11	16	1	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr14:105416366C>A	ENST00000333244.5	-	7	5541	c.5422G>T	c.(5422-5424)Gac>Tac	p.D1808Y	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1808						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.D1808Y(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			AGGGACAGGTCACCCTCCAGC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	14											137	167	157					14																	105416366		2001	4143	6144	104487411	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.5422G>T	14.37:g.105416366C>A	ENSP00000353114:p.Asp1808Tyr		104487411	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	17.43	3.387988	0.61956	.	.	ENSG00000185567	ENST00000333244	T	0.01313	5.02	4.52	3.62	0.41486	.	.	.	.	.	T	0.08044	0.0201	M	0.90082	3.085	0.24518	N	0.99418	D	0.71674	0.998	D	0.63877	0.919	T	0.11397	-1.0589	9	0.66056	D	0.02	.	6.2627	0.20910	0.185:0.7171:0.0:0.0979	.	1808	Q8IVF2	AHNK2_HUMAN	Y	1808	ENSP00000353114:D1808Y	ENSP00000353114:D1808Y	D	-	1	0	AHNAK2	104487411	.	.	0.206000	0.23566	0.101000	0.19017	.	.	2.087000	0.62958	0.456000	0.33151	GAC		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105416366	C	A	105416366	3	1	48	1	0	0	0	0	1	0	0	0	415	826	29	2	11969	2	AHNAK2	14	105416366	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	80530101	105416366	1933174	77	6661										
SPINT1	6692	broad.mit.edu	37	chr15	41137042	41137042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgctgcaccacccagaactGcaacttggcgctagtggagc	11	14	0	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr15:41137042G>T	ENST00000344051.4	+	2	524	c.290G>T	c.(289-291)tGc>tTc	p.C97F	RP11-532F12.5_ENST00000565315.1_RNA|RP11-532F12.5_ENST00000568525.1_RNA|RP11-532F12.5_ENST00000564302.1_RNA|SPINT1_ENST00000431806.1_Missense_Mutation_p.C97F|SPINT1_ENST00000562057.1_Missense_Mutation_p.C97F|RP11-532F12.5_ENST00000568419.1_RNA			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	97	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.C97F(1)		central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		ACCCAGAACTGCAACTTGGCG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	15											32	31	31					15																	41137042		2203	4299	6502	38924334	SO:0001583	missense	6692				CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.290G>T	15.37:g.41137042G>T	ENSP00000342098:p.Cys97Phe		38924334	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	37	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671079	0.88348	.	.	ENSG00000166145	ENST00000344051;ENST00000536281;ENST00000431806	T;T	0.56444	0.46;0.46	4.98	4.98	0.66077	Seven cysteines (1);Seven cysteines, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.76630	0.4014	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.81174	-0.1053	10	0.87932	D	0	-28.9488	18.6124	0.91290	0.0:0.0:1.0:0.0	.	97;97;97	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	F	97;64;97	ENSP00000342098:C97F;ENSP00000409935:C97F	ENSP00000342098:C97F	C	+	2	0	SPINT1	38924334	1.000000	0.71417	0.996000	0.52242	0.850000	0.48378	9.721000	0.98766	2.471000	0.83476	0.563000	0.77884	TGC		0.662	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		T	41137042	G	T	41137042	3	4	48	1	0	0	0	0	1	0	0	0	15107	1319	46	2	292	2	SPINT1	15	41137042	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		41137042	61394350	78	6662										
UNC13C	440279	broad.mit.edu	37	chr15	54590085	54590085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gagataaaaggagaagagaaGgttgctccatatcatattca	10	5	2	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr15:54590085G>A	ENST00000260323.11	+	11	4065	c.4065G>A	c.(4063-4065)aaG>aaA	p.K1355K	UNC13C_ENST00000537900.1_Silent_p.K1353K|UNC13C_ENST00000545554.1_Silent_p.K1355K	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1355					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.K1355K(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GAGAAGAGAAGGTTGCTCCAT	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	15											74	71	72					15																	54590085		1840	4082	5922	52377377	SO:0001819	synonymous_variant	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4065G>A	15.37:g.54590085G>A			52377377	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																				0.313	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54590085	G	A	54590085	2	1	48	1	0	0	0	0	0	0	0	1	17026	991	35	3		3	UNC13C	15	54590085	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	13453043	54590085	47941307	79	6663										
AQP9	366	broad.mit.edu	37	chr15	58467220	58467220	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ccgtatctatctctggcgaaCgcatttgcagatcaagtaag	9	10	3	1	rs562183896		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr15:58467220C>T	ENST00000219919.4	+	4	850	c.480C>T	c.(478-480)aaC>aaT	p.N160N	ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000558772.1_Silent_p.N95N|AQP9_ENST00000536493.1_Silent_p.N160N	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	160					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)	p.N160N(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		CTCTGGCGAACGCATTTGCAG	0.418													c|||	1	0.000199681	0	0.0014	5008	,	,		22102	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											144	130	135					15																	58467220		2192	4292	6484	56254512	SO:0001819	synonymous_variant	366			AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"Ion channels / Aquaporins"	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.480C>T	15.37:g.58467220C>T			56254512	Q9NP32	Silent	SNP	ENST00000219919.4	37	CCDS10165.1																																																																																				0.418	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980		T	58467220	C	T	58467220	2	4	48	1	0	0	0	0	0	0	0	1	833	535	19	1		1	AQP9	15	58467220	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	3877135	58467220	44064172	80	6664										
ITGAM	3684	broad.mit.edu	37	chr16	31283239	31283239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gagttccagaacaaccctaaCccaagatcactggtgaagcc	8	13	1	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr16:31283239C>A	ENST00000287497.8	+	7	705	c.630C>A	c.(628-630)aaC>aaA	p.N210K	ITGAM_ENST00000544665.3_Missense_Mutation_p.N210K			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	210	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.N210K(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						ACAACCCTAACCCAAGATCAC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	79	80					16																	31283239		1927	4154	6081	31190740	SO:0001583	missense	3684			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.630C>A	16.37:g.31283239C>A	ENSP00000287497:p.Asn210Lys		31190740	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	C	8.996	0.978966	0.18812	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	D;D	0.82344	-1.6;-1.6	5.5	1.29	0.21616	von Willebrand factor, type A (3);	.	.	.	.	T	0.69628	0.3132	N	0.21508	0.67	0.09310	N	1	B;B	0.15930	0.015;0.015	B;B	0.17433	0.018;0.018	T	0.58814	-0.7570	9	0.52906	T	0.07	.	5.6306	0.17508	0.0:0.4974:0.29:0.2125	.	210;210	Q4VAK1;P11215	.;ITAM_HUMAN	K	210	ENSP00000441691:N210K;ENSP00000287497:N210K	ENSP00000287497:N210K	N	+	3	2	ITGAM	31190740	0.001000	0.12720	0.016000	0.15963	0.007000	0.05969	0.233000	0.17911	0.384000	0.24942	-0.218000	0.12543	AAC		0.527	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31283239	C	A	31283239	3	1	48	1	0	0	0	0	1	0	0	0	7908	506	18	2	656	2	ITGAM	16	31283239	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09		31283239	59071514	81	6665										
ESRP2	80004	broad.mit.edu	37	chr16	68266361	68266361	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acaaagcggatgagggcctcGccatttctgcggccctgggc	14	13	1	1	rs570243647		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr16:68266361G>C	ENST00000565858.1	-	8	983	c.897C>G	c.(895-897)ggC>ggG	p.G299G	ESRP2_ENST00000473183.2_Silent_p.G289G	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	299	RRM 1.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G289G(2)		NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						TGAGGGCCTCGCCATTTCTGC	0.627																																																2	Substitution - coding silent(2)	large_intestine(2)	16											56	55	56					16																	68266361		2198	4300	6498	66823862	SO:0001819	synonymous_variant	80004			AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.897C>G	16.37:g.68266361G>C			66823862	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	37																																																																																					0.627	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		C	68266361	G	C	68266361	2	2	48	1	0	0	0	0	0	0	0	1	5272	1074	38	5		5	ESRP2	16	68266361	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	36983122	68266361	22088392	82	6666										
TP53	7157	broad.mit.edu	37	chr17	7578517	7578517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gctgcacagggcaggtcttgGccagttggcaaaacatcttg	13	10	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:7578517G>A	ENST00000269305.4	-	5	602	c.413C>T	c.(412-414)gCc>gTc	p.A138V	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.A138V|TP53_ENST00000455263.2_Missense_Mutation_p.A138V|TP53_ENST00000359597.4_Missense_Mutation_p.A138V|TP53_ENST00000413465.2_Missense_Mutation_p.A138V|TP53_ENST00000445888.2_Missense_Mutation_p.A138V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	138	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934875).|A -> S (in LFS; germline mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A138V(20)|p.0?(8)|p.A138_P142delAKTCP(4)|p.C135fs*9(3)|p.N131fs*27(2)|p.A138fs*31(1)|p.L137_W146del10(1)|p.K139fs*4(1)|p.F134_T140>S(1)|p.A45_P49delAKTCP(1)|p.V73fs*9(1)|p.K132_A138delKMFCQLA(1)|p.A138_V143delAKTCPV(1)|p.A6_P10delAKTCP(1)|p.C3fs*9(1)|p.A138del(1)|p.C42fs*9(1)|p.A6V(1)|p.C135_A138delCQLA(1)|p.Q136_K139delQLAK(1)|p.C135_T140delCQLAKT(1)|p.A45V(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGTCTTGGCCAGTTGGCA	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	54	Substitution - Missense(22)|Deletion - In frame(13)|Deletion - Frameshift(10)|Whole gene deletion(8)|Complex - deletion inframe(1)	large_intestine(9)|ovary(7)|haematopoietic_and_lymphoid_tissue(6)|urinary_tract(6)|breast(6)|stomach(4)|lung(4)|bone(4)|central_nervous_system(3)|soft_tissue(1)|endometrium(1)|skin(1)|oesophagus(1)|liver(1)	17											54	54	54					17																	7578517		2203	4300	6503	7519242	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.413C>T	17.37:g.7578517G>A	ENSP00000269305:p.Ala138Val		7519242	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.067507	0.76301	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99859	-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23	5.48	5.48	0.80851	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99819	0.9920	M	0.70595	2.14	0.58432	D	0.999998	P;P;D;P;D;D;D	0.89917	0.821;0.952;0.981;0.886;0.984;0.98;1.0	P;P;P;B;P;P;D	0.91635	0.528;0.716;0.646;0.328;0.813;0.771;0.999	D	0.96765	0.9564	10	0.87932	D	0	-15.6629	17.2272	0.86973	0.0:0.0:1.0:0.0	.	99;138;138;45;138;138;138	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	138;138;138;138;138;138;127;45;6;45;6;138	ENSP00000410739:A138V;ENSP00000352610:A138V;ENSP00000269305:A138V;ENSP00000398846:A138V;ENSP00000391127:A138V;ENSP00000391478:A138V;ENSP00000425104:A6V;ENSP00000423862:A45V;ENSP00000424104:A138V	ENSP00000269305:A138V	A	-	2	0	TP53	7519242	1.000000	0.71417	0.989000	0.46669	0.377000	0.30045	5.601000	0.67606	2.733000	0.93635	0.655000	0.94253	GCC		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578517	G	A	7578517	3	1	48	1	0	0	0	0	1	0	0	0	16421	1203	42	3	885	3	TP53	17	7578517	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		7578517	73616693	83	6667										
GAS7	8522	broad.mit.edu	37	chr17	9828912	9828912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gccgctctgtgagggctttcCgggcctggggtccaaggaca	16	12	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:9828912C>T	ENST00000432992.2	-	11	1179	c.1019G>A	c.(1018-1020)cGg>cAg	p.R340Q	GAS7_ENST00000542249.1_Missense_Mutation_p.R276Q|GAS7_ENST00000437099.2_Missense_Mutation_p.R276Q|GAS7_ENST00000579158.1_Missense_Mutation_p.R276Q|GAS7_ENST00000323816.4_Missense_Mutation_p.R280Q|GAS7_ENST00000585266.1_Missense_Mutation_p.R280Q|GAS7_ENST00000580865.1_Missense_Mutation_p.R200Q|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000583882.1_Intron	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	340					actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R340Q(2)|p.R200Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						GAGGGCTTTCCGGGCCTGGGG	0.617			T	MLL	AML*																																		Dom	yes		17	17p	8522	growth arrest-specific 7		L	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	17											107	88	95					17																	9828912		2203	4300	6503	9769637	SO:0001583	missense	8522			AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.1019G>A	17.37:g.9828912C>T	ENSP00000407552:p.Arg340Gln		9769637	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Missense_Mutation	SNP	ENST00000432992.2	37	CCDS11152.1	.	.	.	.	.	.	.	.	.	.	C	34	5.389495	0.95988	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	T	0.45276	0.9	4.73	4.73	0.59995	.	0.143577	0.47455	D	0.000226	T	0.43389	0.1245	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.76494	0.999;0.992;0.96;0.992	P;P;B;P	0.56751	0.805;0.46;0.44;0.543	T	0.26189	-1.0110	9	.	.	.	-4.3585	16.6524	0.85220	0.0:1.0:0.0:0.0	.	292;280;200;340	B7Z2L1;A8KAC2;O60861-2;O60861	.;.;.;GAS7_HUMAN	Q	340;280;279;200;280;154	ENSP00000379421:R280Q	.	R	-	2	0	GAS7	9769637	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.549000	0.82163	2.458000	0.83093	0.655000	0.94253	CGG		0.617	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433		T	9828912	C	T	9828912	3	4	48	1	0	0	0	0	1	0	0	0	6270	652	23	1	427	1	GAS7	17	9828912	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	2250395	9828912	71366298	84	6668										
DNAH9	1770	broad.mit.edu	37	chr17	11648155	11648155	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cgggccatcaagtccgtgctGgtggtggcaggatccctgaa	15	11	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:11648155G>C	ENST00000262442.4	+	31	6221	c.6153G>C	c.(6151-6153)ctG>ctC	p.L2051L	DNAH9_ENST00000454412.2_Silent_p.L2051L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2051	AAA 1. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.L2051L(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		AGTCCGTGCTGGTGGTGGCAG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	17											65	58	61					17																	11648155		2203	4300	6503	11588880	SO:0001819	synonymous_variant	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6153G>C	17.37:g.11648155G>C			11588880	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.572	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11648155	G	C	11648155	2	2	48	1	0	0	0	0	0	0	0	1	4619	1335	47	5		5	DNAH9	17	11648155	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	1819243	11648155	69547055	85	6669										
GGNBP2	79893	broad.mit.edu	37	chr17	34942326	34942326	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	attcatctagcatggaagggAgtgaaacaggttctcgggag	14	6	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:34942326A>C	ENST00000304718.4	+	11	1739	c.1423A>C	c.(1423-1425)Agt>Cgt	p.S475R		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	475					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.S475R(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CATGGAAGGGAGTGAAACAGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	17											159	159	159					17																	34942326		2203	4300	6503	32016439	SO:0001583	missense	79893			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1423A>C	17.37:g.34942326A>C	ENSP00000307617:p.Ser475Arg		32016439	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	37	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.807042	0.90623	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.67683	0.2919	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.994;0.996	T	0.70945	-0.4734	9	0.72032	D	0.01	-16.6878	15.9962	0.80250	1.0:0.0:0.0:0.0	.	475;475	A8K3S2;Q9H3C7	.;GGNB2_HUMAN	R	475	.	ENSP00000307617:S475R	S	+	1	0	GGNBP2	32016439	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.605000	0.90883	2.180000	0.69256	0.459000	0.35465	AGT		0.413	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		C	34942326	A	C	34942326	3	2	48	1	0	0	0	0	1	0	0	0	6379	304	11	4	1461	4	GGNBP2	17	34942326	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	23294171	34942326	46252884	86	6670										
ACACA	31	broad.mit.edu	37	chr17	35536342	35536342	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	atagactcccagagtttgatCagggactagtggagaaaaga	12	6	1	5			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:35536342C>T	ENST00000394406.2	-	41	5017	c.4827G>A	c.(4825-4827)ctG>ctA	p.L1609L	ACACA_ENST00000353139.5_Silent_p.L1646L|ACACA_ENST00000335166.5_Silent_p.L1531L|ACACA_ENST00000360679.3_Silent_p.L1551L	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1609					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.L1551L(1)|p.L1646L(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGAGTTTGATCAGGGACTAGT	0.388																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											2	Substitution - coding silent(2)	large_intestine(2)	17											102	97	99					17																	35536342		2203	4300	6503	32610455	SO:0001819	synonymous_variant	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.4827G>A	17.37:g.35536342C>T			32610455	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.388	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35536342	C	T	35536342	2	4	48	1	0	0	0	0	0	0	0	1	106	813	29	3		3	ACACA	17	35536342	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	594016	35536342	45658868	87	6671										
PLCD3	113026	broad.mit.edu	37	chr17	43195807	43195807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tccaaggcagccccctccggCgacaacaggtacatcatgaa	9	15	1	1	rs563660926	byFrequency	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:43195807C>T	ENST00000322765.5	-	6	1079	c.966G>A	c.(964-966)tcG>tcA	p.S322S	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	322					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.S322S(2)		breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						CCCCCTCCGGCGACAACAGGT	0.577													c|||	4	0.000798722	0	0	5008	,	,		18637	0.004		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	17											115	127	123					17																	43195807		2119	4228	6347	40551333	SO:0001819	synonymous_variant	113026			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.966G>A	17.37:g.43195807C>T			40551333	Q8TEC1|Q8TF37|Q96FL6	Silent	SNP	ENST00000322765.5	37																																																																																					0.577	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_133373		T	43195807	C	T	43195807	2	4	48	1	0	0	0	0	0	0	0	1	12063	755	27	1		1	PLCD3	17	43195807	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	7659465	43195807	37999403	88	6672										
HELZ	9931	broad.mit.edu	37	chr17	65174933	65174933	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctgataagaaggctcttctcCaaatcagtagtttcattagg	8	8	4	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:65174933C>T	ENST00000358691.5	-	13	1438	c.1272G>A	c.(1270-1272)ttG>ttA	p.L424L	HELZ_ENST00000580168.1_Silent_p.L424L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	424						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.L424L(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GGCTCTTCTCCAAATCAGTAG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	17											145	140	142					17																	65174933		1834	4095	5929	62605395	SO:0001819	synonymous_variant	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1272G>A	17.37:g.65174933C>T			62605395	I6L9H4	Silent	SNP	ENST00000358691.5	37	CCDS42374.1																																																																																				0.398	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65174933	C	T	65174933	2	4	48	1	0	0	0	0	0	0	0	1	7070	593	21	3		3	HELZ	17	65174933	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	21979126	65174933	16020277	89	6673										
ABCA8	10351	broad.mit.edu	37	chr17	66871834	66871834	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gtagtgggtggttaggagggCacccctttccgtgtttctaa	14	8	1	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:66871834C>A	ENST00000269080.2	-	34	4428	c.4291G>T	c.(4291-4293)Gcc>Tcc	p.A1431S	ABCA8_ENST00000586539.1_Missense_Mutation_p.A1471S|ABCA8_ENST00000430352.2_Missense_Mutation_p.A1471S	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1431	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A1431S(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GTTAGGAGGGCACCCCTTTCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											87	67	74					17																	66871834		2203	4300	6503	64383429	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.4291G>T	17.37:g.66871834C>A	ENSP00000269080:p.Ala1431Ser		64383429	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719216	0.89205	.	.	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.95412	-3.7;-3.7	4.36	4.36	0.52297	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.248824	0.28047	N	0.016813	D	0.96175	0.8753	L	0.40543	1.245	0.51233	D	0.999916	D;D;D	0.76494	0.994;0.998;0.999	P;D;D	0.71414	0.902;0.973;0.94	D	0.96722	0.9533	10	0.72032	D	0.01	.	16.4175	0.83746	0.0:1.0:0.0:0.0	.	1471;1471;1431	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	S	1431;1471	ENSP00000269080:A1431S;ENSP00000402814:A1471S	ENSP00000269080:A1431S	A	-	1	0	ABCA8	64383429	1.000000	0.71417	0.986000	0.45419	0.872000	0.50106	5.577000	0.67444	2.441000	0.82636	0.650000	0.86243	GCC		0.507	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66871834	C	A	66871834	3	1	48	1	0	0	0	0	1	0	0	0	38	710	25	2	474	2	ABCA8	17	66871834	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	1696901	66871834	14323376	90	6674										
RNF213	57674	broad.mit.edu	37	chr17	78354648	78354648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagagacaaggcagacagaaCgcagaccggccacgtgctgg	14	12	0	4			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr17:78354648C>T	ENST00000582970.1	+	56	13801	c.13658C>T	c.(13657-13659)aCg>aTg	p.T4553M	CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.T4602M|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.T2626M	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4553					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T4602M(1)|p.T2626M(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCAGACAGAACGCAGACCGGC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	17											125	126	125					17																	78354648		2203	4300	6503	75969243	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13658C>T	17.37:g.78354648C>T	ENSP00000464087:p.Thr4553Met		75969243	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.231563	0.58777	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.27557	1.91;1.66	5.26	5.26	0.73747	.	0.060324	0.64402	D	0.000004	T	0.59473	0.2196	M	0.81497	2.545	0.39606	D	0.969809	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.65298	-0.6202	10	0.87932	D	0	.	17.2359	0.86998	0.0:1.0:0.0:0.0	.	4602;2626	C9JCP4;Q63HN8	.;RN213_HUMAN	M	4553;4602;2626	ENSP00000425956:T4553M;ENSP00000338218:T2626M	ENSP00000338218:T2626M	T	+	2	0	RNF213	75969243	1.000000	0.71417	0.938000	0.37757	0.005000	0.04900	6.106000	0.71511	2.728000	0.93425	0.655000	0.94253	ACG		0.602	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78354648	C	T	78354648	3	4	48	1	0	0	0	0	1	0	0	0	13514	536	19	1	14195	1	RNF213	17	78354648	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	11482814	78354648	2840562	91	6675										
PTPRM	5797	broad.mit.edu	37	chr18	7926618	7926618	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gtggaagttaatgctggccaGtttgctaccttccagtgcag	12	9	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr18:7926618G>C	ENST00000332175.8	+	5	1637	c.600G>C	c.(598-600)caG>caC	p.Q200H	PTPRM_ENST00000580170.1_Missense_Mutation_p.Q200H|PTPRM_ENST00000400053.4_Missense_Mutation_p.Q138H|PTPRM_ENST00000400060.4_Missense_Mutation_p.Q200H	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	200	Ig-like C2-type.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.Q200H(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ATGCTGGCCAGTTTGCTACCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	18											100	92	95					18																	7926618		2203	4300	6503	7916618	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.600G>C	18.37:g.7926618G>C	ENSP00000331418:p.Gln200His		7916618	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.036170	0.35893	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.23754	1.89;1.89;1.89	5.72	4.84	0.62591	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49881	0.1583	M	0.68317	2.08	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.74348	0.983;0.983	T	0.51260	-0.8728	10	0.72032	D	0.01	.	15.6781	0.77344	0.1273:0.0:0.8727:0.0	.	200;200	A7MBN1;P28827	.;PTPRM_HUMAN	H	200;200;138	ENSP00000331418:Q200H;ENSP00000382933:Q200H;ENSP00000382927:Q138H	ENSP00000331418:Q200H	Q	+	3	2	PTPRM	7916618	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	3.104000	0.50306	0.785000	0.33685	-1.119000	0.02030	CAG		0.453	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			C	7926618	G	C	7926618	3	2	48	1	0	0	0	0	1	0	0	0	12843	1020	36	5	618	5	PTPRM	18	7926618	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		7926618	70150630	92	6676										
PHLPP1	23239	broad.mit.edu	37	chr18	60646088	60646088	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cccatctgtctgtccaactcCttccagcgccagctatccag	6	18	2	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr18:60646088C>G	ENST00000262719.5	+	17	4812	c.4578C>G	c.(4576-4578)tcC>tcG	p.S1526S	PHLPP1_ENST00000400316.4_Silent_p.S1014S			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1526					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.S1013S(1)		endometrium(2)|kidney(2)|lung(13)	17						TGTCCAACTCCTTCCAGCGCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	18											44	47	46					18																	60646088		2118	4242	6360	58797068	SO:0001819	synonymous_variant	23239			AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.4578C>G	18.37:g.60646088C>G			58797068	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Silent	SNP	ENST00000262719.5	37	CCDS45881.2																																																																																				0.637	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		G	60646088	C	G	60646088	2	3	48	1	0	0	0	0	0	0	0	1	11885	668	24	5		5	PHLPP1	18	60646088	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	52719470	60646088	17431160	93	6677										
ZNF407	55628	broad.mit.edu	37	chr18	72347113	72347113	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	accagtctgaagagggcttgAtagcaacgggagtgagaatt	14	6	1	4			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr18:72347113A>T	ENST00000299687.5	+	1	4138	c.4138A>T	c.(4138-4140)Ata>Tta	p.I1380L	ZNF407_ENST00000582337.1_Missense_Mutation_p.I1380L|ZNF407_ENST00000577538.1_Missense_Mutation_p.I1380L|ZNF407_ENST00000309902.6_Missense_Mutation_p.I1380L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1380					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.I1380L(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		AGAGGGCTTGATAGCAACGGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	18											124	125	125					18																	72347113		1909	4127	6036	70476101	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4138A>T	18.37:g.72347113A>T	ENSP00000299687:p.Ile1380Leu		70476101	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.851266	0.32699	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.08896	3.04;3.49	5.84	-11.7	0.00046	.	1.168720	0.05876	N	0.625545	T	0.02727	0.0082	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.55166	-0.8183	10	0.10111	T	0.7	.	4.7926	0.13256	0.2292:0.1638:0.4465:0.1605	.	1380;1380;1380	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	L	1380	ENSP00000299687:I1380L;ENSP00000310359:I1380L	ENSP00000299687:I1380L	I	+	1	0	ZNF407	70476101	0.000000	0.05858	0.001000	0.08648	0.956000	0.61745	-1.103000	0.03329	0.984000	0.38629	0.533000	0.62120	ATA		0.458	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72347113	A	T	72347113	3	4	48	1	0	0	0	0	1	0	0	0	17926	333	12	5	4140	5	ZNF407	18	72347113	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	11701025	72347113	5730135	94	6678										
PARD6G	84552	broad.mit.edu	37	chr18	77960793	77960793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gcttatgacggtccagagagAaccttcggaattccgcccca	10	13	0	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr18:77960793A>G	ENST00000353265.3	-	2	292	c.95T>C	c.(94-96)tTc>tCc	p.F32S	AC139100.3_ENST00000588950.1_RNA|PARD6G_ENST00000470488.2_Missense_Mutation_p.F32S	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	32	OPR.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.F32S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		GTCCAGAGAGAACCTTCGGAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	18											64	61	62					18																	77960793		2203	4300	6503	76061784	SO:0001583	missense	84552				CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"par-6 (partitioning defective 6, C.elegans) homolog gamma", "par-6 partitioning defective 6 homolog gamma (C. elegans)"			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.95T>C	18.37:g.77960793A>G	ENSP00000343144:p.Phe32Ser		76061784	A8QM57	Missense_Mutation	SNP	ENST00000353265.3	37	CCDS12022.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.598339	0.87055	.	.	ENSG00000178184	ENST00000353265	T	0.30182	1.54	5.43	5.43	0.79202	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.939;0.998	T	0.63274	-0.6674	9	.	.	.	-36.6998	14.5927	0.68378	1.0:0.0:0.0:0.0	.	32;32	A8QM57;Q9BYG4	.;PAR6G_HUMAN	S	32	ENSP00000343144:F32S	.	F	-	2	0	PARD6G	76061784	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.931000	0.87625	2.282000	0.76494	0.533000	0.62120	TTC		0.463	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510		G	77960793	A	G	77960793	3	3	48	1	0	0	0	0	1	0	0	0	11478	246	9	4	1043	4	PARD6G	18	77960793	Missense_Mutation	SNP	A	TCGA-AG-3893-01A-01W-1073-09	5613680	77960793	116455	95	6679										
ZNF99	7652	broad.mit.edu	37	chr19	22941524	22941524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cacattcttcacatttgtagGgtttctgtccagtatgaatt	7	8	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:22941524G>A	ENST00000596209.1	-	4	1277	c.1187C>T	c.(1186-1188)cCc>cTc	p.P396L	ZNF99_ENST00000397104.3_Missense_Mutation_p.P305L	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P305L(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ACATTTGTAGGGTTTCTGTCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											65	70	69					19																	22941524		2029	4219	6248	22733364	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1187C>T	19.37:g.22941524G>A	ENSP00000472969:p.Pro396Leu		22733364	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	14.94	2.686765	0.48097	.	.	ENSG00000213973	ENST00000397104	T	0.27557	1.66	1.28	1.28	0.21552	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50000	0.1590	M	0.80616	2.505	0.51482	D	0.999924	D	0.71674	0.998	D	0.64144	0.922	T	0.52442	-0.8575	9	0.54805	T	0.06	.	9.4929	0.38971	0.0:0.0:1.0:0.0	.	305	A8MXY4	ZNF99_HUMAN	L	305	ENSP00000380293:P305L	ENSP00000380293:P305L	P	-	2	0	ZNF99	22733364	0.941000	0.31946	0.012000	0.15200	0.259000	0.26198	1.462000	0.35266	0.675000	0.31264	0.395000	0.25975	CCC		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22941524	G	A	22941524	3	1	48	1	0	0	0	0	1	0	0	0	18243	1232	43	3	2210	3	ZNF99	19	22941524	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		22941524	36187459	96	6680										
RYR1	6261	broad.mit.edu	37	chr19	39062846	39062846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctacatggaacccgccctgcGgtgtctgagcctcctgcata	10	15	1	1	rs193922860		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:39062846G>A	ENST00000359596.3	+	95	13934	c.13934G>A	c.(13933-13935)cGg>cAg	p.R4645Q	RYR1_ENST00000355481.4_Missense_Mutation_p.R4640Q|RYR1_ENST00000360985.3_Missense_Mutation_p.R4640Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4645					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R4645Q(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCCGCCCTGCGGTGTCTGAGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19	GRCh37	CM064219	RYR1	M							129	111	117					19																	39062846		2203	4300	6503	43754686	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.13934G>A	19.37:g.39062846G>A	ENSP00000352608:p.Arg4645Gln		43754686	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.214457	0.39102	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.94232	-3.38;-3.38;-3.38	5.11	5.11	0.69529	Ryanodine Receptor TM 4-6 (1);	0.598876	0.15295	U	0.269946	D	0.92176	0.7519	M	0.80183	2.485	0.23653	N	0.997197	B;B	0.21309	0.043;0.054	B;B	0.12837	0.005;0.008	D	0.84620	0.0683	10	0.46703	T	0.11	.	9.0998	0.36662	0.162:0.0:0.838:0.0	.	4640;4645	P21817-2;P21817	.;RYR1_HUMAN	Q	4645;4640;4640	ENSP00000352608:R4645Q;ENSP00000347667:R4640Q;ENSP00000354254:R4640Q	ENSP00000347667:R4640Q	R	+	2	0	RYR1	43754686	0.711000	0.27906	0.989000	0.46669	0.843000	0.47879	2.546000	0.45778	2.659000	0.90383	0.561000	0.74099	CGG		0.577	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39062846	G	A	39062846	3	1	48	1	0	0	0	0	1	0	0	0	13805	1116	39	1	14312	1	RYR1	19	39062846	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	16121322	39062846	20066137	97	6681										
HNRNPL	3191	broad.mit.edu	37	chr19	39330793	39330793	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	actcggtcacagttcatcttAgattgatccaagccatagac	7	11	3	3			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:39330793A>C	ENST00000221419.5	-	8	1542	c.1176T>G	c.(1174-1176)tcT>tcG	p.S392S	HNRNPL_ENST00000600873.1_Silent_p.S259S|AC104534.3_ENST00000594769.1_Missense_Mutation_p.L9R	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	392	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)	p.S259S(1)|p.S392S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			AGTTCATCTTAGATTGATCCA	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	19											41	45	43					19																	39330793		2159	4231	6390	44022633	SO:0001819	synonymous_variant	3191			X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1176T>G	19.37:g.39330793A>C			44022633	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																				0.602	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			C	39330793	A	C	39330793	2	2	48	1	0	0	0	0	0	0	0	1	7291	407	15	4		4	HNRNPL	19	39330793	Silent	SNP	A	TCGA-AG-3893-01A-01W-1073-09	267947	39330793	19798190	98	6682										
RELB	5971	broad.mit.edu	37	chr19	45537542	45537542	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aagcggaaacgggggatgccCgacgtccttggggagctgaa	17	9	0	1	rs368632431		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:45537542C>T	ENST00000221452.8	+	10	1398	c.1248C>T	c.(1246-1248)ccC>ccT	p.P416P	RELB_ENST00000540120.1_Silent_p.P416P|RELB_ENST00000505236.1_Silent_p.P413P	NM_006509.3	NP_006500.2	Q01201	RELB_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog B	416	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				antigen processing and presentation (GO:0019882)|circadian regulation of gene expression (GO:0032922)|myeloid dendritic cell differentiation (GO:0043011)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of gene expression (GO:0010628)|T-helper 1 cell differentiation (GO:0045063)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P416P(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(3)|skin(1)	12		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)		GGGGGATGCCCGACGTCCTTG	0.552													C|||	1	0.000199681	8e-04	0	5008	,	,		15107	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		2,3916		0,2,1957	53	57	56		1248	-9.6	0.1	19		56	0,8290		0,0,4145	no	coding-synonymous	RELB	NM_006509.3		0,2,6102	TT,TC,CC		0.0,0.051,0.0164		416/580	45537542	2,12206	1959	4145	6104	50229382	SO:0001819	synonymous_variant	5971			M83221	CCDS46110.1	19q13.32	2013-07-09	2013-07-09		ENSG00000104856	ENSG00000104856			9956	protein-coding gene	gene with protein product		604758	"v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of kappa light polypeptide gene enhancer in B-cells 3)"			1531086	Standard	NM_006509		Approved	REL-B	uc021uvp.1	Q01201	OTTHUMG00000162116	ENST00000221452.8:c.1248C>T	19.37:g.45537542C>T			50229382	Q6GTX7|Q9UEI7	Silent	SNP	ENST00000221452.8	37	CCDS46110.1																																																																																				0.552	RELB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000367361.2			T	45537542	C	T	45537542	2	4	48	1	0	0	0	0	0	0	0	1	13254	639	23	1		1	RELB	19	45537542	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	6206749	45537542	13591441	99	6683										
FPR2	2358	broad.mit.edu	37	chr19	52272425	52272425	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctacagtaactattccaaatGgggacacatactgtactttc	6	10	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:52272425G>T	ENST00000598776.1	+	2	1286	c.514G>T	c.(514-516)Ggg>Tgg	p.G172W	FPR2_ENST00000340023.6_Missense_Mutation_p.G172W|FPR2_ENST00000598953.1_Missense_Mutation_p.G172W	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	172					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)	p.G172W(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						TATTCCAAATGGGGACACATA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	19											129	122	125					19																	52272425		2203	4300	6503	56964237	SO:0001583	missense	2358			M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"GPCR / Class A : Formyl peptide receptors", "GPCR / Class A : Leukotriene receptors"	3827	protein-coding gene	gene with protein product		136538	"formyl peptide receptor-like 1"	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.514G>T	19.37:g.52272425G>T	ENSP00000468897:p.Gly172Trp		56964237	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	37	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.230912	0.39399	.	.	ENSG00000171049	ENST00000340023	T	0.38240	1.15	3.09	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.169329	0.41294	U	0.000903	T	0.65207	0.2669	H	0.96111	3.77	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.56208	-0.8017	10	0.87932	D	0	.	5.1974	0.15245	0.2704:0.0:0.7296:0.0	.	172	P25090	FPR2_HUMAN	W	172	ENSP00000340191:G172W	ENSP00000340191:G172W	G	+	1	0	FPR2	56964237	0.107000	0.21998	0.005000	0.12908	0.006000	0.05464	1.050000	0.30404	0.870000	0.35726	-0.339000	0.08088	GGG		0.498	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738		T	52272425	G	T	52272425	3	4	48	1	0	0	0	0	1	0	0	0	6058	1348	47	2	516	2	FPR2	19	52272425	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	6734883	52272425	6856558	100	6684										
ZNF610	162963	broad.mit.edu	37	chr19	52869685	52869685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	aatgtaatgaatgtggcaagGtctttagtctgctttcatac	9	6	3	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:52869685G>A	ENST00000403906.3	+	6	1510	c.1054G>A	c.(1054-1056)Gtc>Atc	p.V352I	ZNF610_ENST00000601151.1_Missense_Mutation_p.V309I|ZNF610_ENST00000327920.8_Missense_Mutation_p.V352I|ZNF610_ENST00000321287.8_Missense_Mutation_p.V352I	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	352					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V352I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		ATGTGGCAAGGTCTTTAGTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											89	90	90					19																	52869685		2203	4300	6503	57561497	SO:0001583	missense	162963			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"Zinc fingers, C2H2-type", "-"	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.1054G>A	19.37:g.52869685G>A	ENSP00000383922:p.Val352Ile		57561497	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	CCDS12851.1	.	.	.	.	.	.	.	.	.	.	G	5.854	0.341687	0.11069	.	.	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.19105	2.17;2.17	1.58	0.138	0.14793	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16428	0.0395	L	0.37507	1.11	0.09310	N	1	P;P	0.36048	0.478;0.534	B;B	0.38562	0.181;0.276	T	0.25433	-1.0132	9	0.66056	D	0.02	.	5.7688	0.18241	0.0:0.0:0.399:0.601	.	309;352	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	I	352;309;352	ENSP00000383922:V352I;ENSP00000327597:V352I	ENSP00000324441:V309I	V	+	1	0	ZNF610	57561497	0.000000	0.05858	0.539000	0.28077	0.288000	0.27193	-0.635000	0.05471	0.835000	0.34877	0.313000	0.20887	GTC		0.408	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		A	52869685	G	A	52869685	3	1	48	1	0	0	0	0	1	0	0	0	18075	1261	44	3	1068	3	ZNF610	19	52869685	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	597260	52869685	6259298	101	6685										
LILRB5	10990	broad.mit.edu	37	chr19	54754670	54754670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctagtggatggccaggggggCgtagatgctgggttcagctg	19	7	1	1	rs201610708		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:54754670C>A	ENST00000316219.5	-	13	1860	c.1753G>T	c.(1753-1755)Gcc>Tcc	p.A585S	LILRB5_ENST00000449561.2_Missense_Mutation_p.A586S|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_3'UTR|LILRB5_ENST00000345866.6_Missense_Mutation_p.A486S	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	585					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.A585S(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCCAGGGGGGCGTAGATGCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											67	68	67					19																	54754670		2203	4300	6503	59446482	SO:0001583	missense	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1753G>T	19.37:g.54754670C>A	ENSP00000320390:p.Ala585Ser		59446482	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	9.630	1.136148	0.21123	.	.	ENSG00000105609	ENST00000316219;ENST00000449561;ENST00000345866	T;T;T	0.00545	6.67;6.67;6.7	2.75	0.562	0.17290	.	.	.	.	.	T	0.00724	0.0024	M	0.67397	2.05	0.09310	N	1	B;B;P	0.47484	0.214;0.388;0.896	B;B;P	0.44647	0.118;0.106;0.456	T	0.50083	-0.8869	9	0.59425	D	0.04	.	4.4004	0.11383	0.0:0.6624:0.0:0.3376	.	486;586;585	O75023-2;O75023-3;O75023	.;.;LIRB5_HUMAN	S	585;586;486	ENSP00000320390:A585S;ENSP00000406478:A586S;ENSP00000263430:A486S	ENSP00000320390:A585S	A	-	1	0	LILRB5	59446482	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.070000	0.11523	0.504000	0.28082	-0.237000	0.12165	GCC		0.607	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			A	54754670	C	A	54754670	3	1	48	1	0	0	0	0	1	0	0	0	8817	768	27	2	23	2	LILRB5	19	54754670	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	1884985	54754670	4374313	102	6686										
NLRP7	199713	broad.mit.edu	37	chr19	55450708	55450708	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	acgtccccgatgtcccaggcGtggccgtccctgtcctcccc	10	20	0	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:55450708G>A	ENST00000590030.1	-	3	1519	c.1479C>T	c.(1477-1479)caC>caT	p.H493H	NLRP7_ENST00000340844.2_Silent_p.H493H|NLRP7_ENST00000446217.1_Silent_p.H521H|NLRP7_ENST00000592784.1_Silent_p.H493H|NLRP7_ENST00000588756.1_Silent_p.H493H|NLRP7_ENST00000448121.2_Silent_p.H493H|NLRP7_ENST00000328092.5_Silent_p.H493H			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	493							ATP binding (GO:0005524)	p.H493H(4)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TGTCCCAGGCGTGGCCGTCCC	0.567																																																4	Substitution - coding silent(4)	large_intestine(2)|kidney(2)	19											65	63	64					19																	55450708		2203	4300	6503	60142520	SO:0001819	synonymous_variant	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1479C>T	19.37:g.55450708G>A			60142520	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																				0.567	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55450708	G	A	55450708	2	1	48	1	0	0	0	0	0	0	0	1	10513	1136	40	1		1	NLRP7	19	55450708	Silent	SNP	G	TCGA-AG-3893-01A-01W-1073-09	696038	55450708	3678275	103	6687										
ZIM3	114026	broad.mit.edu	37	chr19	57646558	57646558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cttttccccagtatggatttTtttatgttgaatgaggtttt	8	5	0	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr19:57646558T>G	ENST00000269834.1	-	5	1532	c.1147A>C	c.(1147-1149)Aaa>Caa	p.K383Q	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	383					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K383Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTATGGATTTTTTTATGTTGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	116	115					19																	57646558		2203	4300	6503	62338370	SO:0001583	missense	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1147A>C	19.37:g.57646558T>G	ENSP00000269834:p.Lys383Gln		62338370	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.327466	0.41197	.	.	ENSG00000141946	ENST00000269834	T	0.23950	1.88	2.71	2.71	0.32032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30103	0.0754	N	0.16602	0.42	0.25556	N	0.987037	D	0.55800	0.973	D	0.64506	0.926	T	0.08249	-1.0731	9	0.72032	D	0.01	.	8.871	0.35316	0.0:0.0:0.0:1.0	.	383	Q96PE6	ZIM3_HUMAN	Q	383	ENSP00000269834:K383Q	ENSP00000269834:K383Q	K	-	1	0	ZIM3	62338370	0.000000	0.05858	0.454000	0.27019	0.248000	0.25809	-0.114000	0.10757	1.237000	0.43756	0.260000	0.18958	AAA		0.383	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			G	57646558	T	G	57646558	3	3	48	1	0	0	0	0	1	0	0	0	17724	1850	64	4	275	4	ZIM3	19	57646558	Missense_Mutation	SNP	T	TCGA-AG-3893-01A-01W-1073-09	2195850	57646558	1482425	104	6688										
C20orf103	24141	broad.mit.edu	37	chr20	9510366	9510366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tggggctcatcttgggcctcGtcatcatggtaacactcgcg	12	12	4	0			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr20:9510366G>A	ENST00000246070.2	+	6	1234	c.742G>A	c.(742-744)Gtc>Atc	p.V248I	LAMP5_ENST00000427562.2_Missense_Mutation_p.V204I	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	248						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)		p.V248I(1)									CTTGGGCCTCGTCATCATGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	20											129	103	112					20																	9510366		2203	4300	6503	9458366	SO:0001583	missense	24141			AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.742G>A	20.37:g.9510366G>A	ENSP00000246070:p.Val248Ile		9458366	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	G	6.483	0.457336	0.12342	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.34072	1.38;1.38	6.16	4.24	0.50183	.	0.174292	0.51477	N	0.000094	T	0.13798	0.0334	N	0.02539	-0.55	0.36554	D	0.872034	B;B	0.15473	0.013;0.001	B;B	0.12156	0.007;0.002	T	0.12578	-1.0542	9	.	.	.	-15.3548	8.8869	0.35409	0.1241:0.0:0.7538:0.1221	.	204;248	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	I	248;204	ENSP00000246070:V248I;ENSP00000406360:V204I	.	V	+	1	0	C20orf103	9458366	0.980000	0.34600	0.928000	0.36995	0.459000	0.32528	1.879000	0.39618	0.948000	0.37687	-0.806000	0.03193	GTC		0.517	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		A	9510366	G	A	9510366	3	1	48	1	0	0	0	0	1	0	0	0	2081	1145	40	1	764	1	C20orf103	20	9510366	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		9510366	53515154	105	6689										
BPIL3	128859	broad.mit.edu	37	chr20	31625416	31625416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ccatcaagcttgctgatgccGgggaggccctcacgttccct	11	15	2	1	rs202105575		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr20:31625416G>A	ENST00000349552.1	+	8	718	c.718G>A	c.(718-720)Ggg>Agg	p.G240R		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	240						extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.G240R(1)									TGCTGATGCCGGGGAGGCCCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	20											102	87	92					20																	31625416		2203	4300	6503	31089077	SO:0001583	missense	128859			AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"BPI fold containing"	16504	protein-coding gene	gene with protein product		614110	"bactericidal/permeability-increasing protein-like 3"	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.718G>A	20.37:g.31625416G>A	ENSP00000344929:p.Gly240Arg		31089077		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.239474	0.01493	.	.	ENSG00000167104	ENST00000349552	T	0.06687	3.27	4.15	0.761	0.18448	.	1.335750	0.05192	N	0.503217	T	0.06325	0.0163	N	0.25031	0.7	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.43507	-0.9387	10	0.23891	T	0.37	.	6.4558	0.21928	0.3564:0.0:0.6436:0.0	.	240	Q8NFQ5	BPIB6_HUMAN	R	240	ENSP00000344929:G240R	ENSP00000344929:G240R	G	+	1	0	BPIFB6	31089077	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.234000	0.17930	0.009000	0.14813	-0.254000	0.11334	GGG		0.607	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		A	31625416	G	A	31625416	3	1	48	1	0	0	0	0	1	0	0	0	1496	1116	39	1	748	1	BPIL3	20	31625416	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	22115050	31625416	31400104	106	6690										
NCOA6	23054	broad.mit.edu	37	chr20	33329481	33329481	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tgtgggaatgacagatgcttTtttgaggtcctccccagaaa	11	8	0	4			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr20:33329481T>C	ENST00000374796.2	-	12	7149	c.4579A>G	c.(4579-4581)Aaa>Gaa	p.K1527E	NCOA6_ENST00000359003.2_Missense_Mutation_p.K1527E			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1527					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.K1527E(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						ACAGATGCTTTTTTGAGGTCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	20											107	108	108					20																	33329481		2203	4300	6503	32793142	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4579A>G	20.37:g.33329481T>C	ENSP00000363929:p.Lys1527Glu		32793142	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.568499	0.65651	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.27256	1.68;1.68	5.55	5.55	0.83447	.	0.097805	0.53938	D	0.000050	T	0.36552	0.0971	N	0.24115	0.695	0.53005	D	0.999969	D	0.69078	0.997	D	0.75020	0.985	T	0.09378	-1.0677	10	0.35671	T	0.21	-8.9733	15.8689	0.79091	0.0:0.0:0.0:1.0	.	1527	Q14686	NCOA6_HUMAN	E	1527	ENSP00000363929:K1527E;ENSP00000351894:K1527E	ENSP00000351894:K1527E	K	-	1	0	NCOA6	32793142	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.173000	0.58249	2.333000	0.79357	0.482000	0.46254	AAA		0.448	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33329481	T	C	33329481	3	2	48	1	0	0	0	0	1	0	0	0	10264	1850	64	4	1632	4	NCOA6	20	33329481	Missense_Mutation	SNP	T	TCGA-AG-3893-01A-01W-1073-09	1704065	33329481	29696039	107	6691										
CEP250	11190	broad.mit.edu	37	chr20	34099299	34099299	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gcaggcctgcaccacagcctCtcacactcacttcttgccgt	7	18	3	0	rs549300192		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr20:34099299C>T	ENST00000397527.1	+	35	7893	c.7173C>T	c.(7171-7173)ctC>ctT	p.L2391L	CEP250_ENST00000342580.4_Silent_p.L2335L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2391					centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.L2391L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			ACCACAGCCTCTCACACTCAC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	20											62	58	59					20																	34099299		2203	4300	6503	33562713	SO:0001819	synonymous_variant	11190			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.7173C>T	20.37:g.34099299C>T			33562713	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																				0.612	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34099299	C	T	34099299	2	4	48	1	0	0	0	0	0	0	0	1	3258	900	32	3		3	CEP250	20	34099299	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09	769818	34099299	28926221	108	6692										
LSS	4047	broad.mit.edu	37	chr21	47626630	47626630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gctccagcaagtgccccccaCgcttggtctcataggtggcg	12	15	1	0	rs199896537		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr21:47626630C>T	ENST00000397728.3	-	16	1598	c.1520G>A	c.(1519-1521)cGt>cAt	p.R507H	LSS_ENST00000356396.4_Missense_Mutation_p.R507H|LSS_ENST00000522411.1_Missense_Mutation_p.R496H|LSS_ENST00000457828.2_Missense_Mutation_p.R427H	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	507					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)	p.R507H(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GTGCCCCCCACGCTTGGTCTC	0.607																																					Pancreas(114;955 2313 34923 50507)											1	Substitution - Missense(1)	large_intestine(1)	21						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	80	72	75		1520,1487,1280,1520	5.4	1	21		75	0,8600		0,0,4300	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	507/733,496/722,427/653,507/733	47626630	1,13005	2203	4300	6503	46451058	SO:0001583	missense	4047			U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1520G>A	21.37:g.47626630C>T	ENSP00000380837:p.Arg507His		46451058	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	C	36	5.674156	0.96764	2.27E-4	0.0	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.44	5.44	0.79542	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.094753	0.64402	D	0.000001	T	0.65984	0.2744	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70716	0.97;0.934	T	0.77574	-0.2537	10	0.87932	D	0	.	19.2365	0.93862	0.0:1.0:0.0:0.0	.	496;507	E9PEI9;P48449	.;ERG7_HUMAN	H	507;427;507;496	ENSP00000348762:R507H;ENSP00000409191:R427H;ENSP00000380837:R507H;ENSP00000429133:R496H	ENSP00000348762:R507H	R	-	2	0	LSS	46451058	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.538000	0.82048	2.732000	0.93576	0.655000	0.94253	CGT		0.607	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			T	47626630	C	T	47626630	3	4	48	1	0	0	0	0	1	0	0	0	9094	536	19	1	706	1	LSS	21	47626630	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09		47626630	503265	109	6693										
FBXO7	25793	broad.mit.edu	37	chr22	32875253	32875253	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cagtctggtgtttggaatgaCgacagtatggtgggtattaa	14	4	1	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chr22:32875253C>T	ENST00000266087.7	+	2	735	c.408C>T	c.(406-408)gaC>gaT	p.D136D	FBXO7_ENST00000397426.1_Silent_p.D22D|FBXO7_ENST00000382058.3_Silent_p.D57D	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	136	Important for interaction with CDK6.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.D136D(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TTTGGAATGACGACAGTATGG	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	22											55	54	54					22																	32875253		2203	4300	6503	31205253	SO:0001819	synonymous_variant	25793			AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.408C>T	22.37:g.32875253C>T			31205253	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	37	CCDS13907.1																																																																																				0.428	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			T	32875253	C	T	32875253	2	4	48	1	0	0	0	0	0	0	0	1	5779	535	19	1		1	FBXO7	22	32875253	Silent	SNP	C	TCGA-AG-3893-01A-01W-1073-09		32875253	18429313	110	6694										
VCX3B	425054	broad.mit.edu	37	chrX	8434341	8434341	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	cactgagtcaggagagccagGtggaggaaccactgagtcag	15	9	2	3	rs200360954		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chrX:8434341G>A	ENST00000381032.1	+	3	965	c.658G>A	c.(658-660)Gtg>Atg	p.V220M	VCX3B_ENST00000440654.2_Missense_Mutation_p.V170M|VCX3B_ENST00000444481.1_Missense_Mutation_p.V190M|VCX3B_ENST00000381029.4_Missense_Mutation_p.V188M|VCX3B_ENST00000453306.1_Intron	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	220	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)		p.V190M(1)		NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						GGAGAGCCAGGTGGAGGAACC	0.567													-|||	8	0.00211921	0	0.0029	3775	,	,		7799	0		0.003	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	X						G	MET/VAL	0,3809		0,0,0,1626,557	87	167	140		658		0	X		140	14,6655		1,7,5,2416,1816	no	missense	VCX3B	NM_001001888.3	21	1,7,5,4042,2373	AA,AG,A,GG,G		0.2099,0.0,0.1336		220/247	8434341	14,10464	2183	4245	6428	8394341	SO:0001583	missense	425054				CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.658G>A	X.37:g.8434341G>A	ENSP00000370420:p.Val220Met		8394341	C9JS46|Q4KN12	Missense_Mutation	SNP	ENST00000381032.1	37	CCDS48077.2	.	.	.	.	.	.	.	.	.	.	N	2.887	-0.230465	0.05983	0.0	0.002099	ENSG00000205642	ENST00000381032;ENST00000444481;ENST00000440654;ENST00000381029	T;T;T;T	0.22539	2.09;2.09;1.95;2.09	.	.	.	.	.	.	.	.	T	0.10508	0.0257	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.31586	-0.9938	5	0.44086	T	0.13	.	.	.	.	.	190;170	Q9H321;E7ERZ8	VCX3B_HUMAN;.	M	220;190;170;188	ENSP00000370420:V220M;ENSP00000414780:V190M;ENSP00000410372:V170M;ENSP00000370417:V188M	ENSP00000370417:V188M	V	+	1	0	VCX3B	8394341	0.009000	0.17119	0.001000	0.08648	0.001000	0.01503	-1.939000	0.01545	0.328000	0.23435	0.330000	0.21533	GTG		0.567	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1			A	8434341	G	A	8434341	3	1	48	1	0	0	0	0	1	0	0	0	17185	1261	44	3	578	3	VCX3B	23	8434341	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09		8434341	146836219	111	6695										
PHEX	5251	broad.mit.edu	37	chrX	22065266	22065266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	taagcaataatccaattcccGaagatatgccaagctatggg	8	9	0	1	rs149168023		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chrX:22065266G>A	ENST00000379374.4	+	3	851	c.286G>A	c.(286-288)Gaa>Aaa	p.E96K	PHEX_ENST00000537599.1_Missense_Mutation_p.E96K|PHEX_ENST00000535894.1_5'UTR	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	96					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E96K(1)		breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						TCCAATTCCCGAAGATATGCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	LYS/GLU	0,3835		0,0,1632,571	183	151	162		286	5.6	1	X	dbSNP_134	162	2,6726		0,2,2426,1872	no	missense	PHEX	NM_000444.4	56	0,2,4058,2443	AA,AG,GG,G		0.0297,0.0,0.0189	probably-damaging	96/750	22065266	2,10561	2203	4300	6503	21975187	SO:0001583	missense	5251			U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.286G>A	X.37:g.22065266G>A	ENSP00000368682:p.Glu96Lys		21975187	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	37	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617147	0.87359	0.0	2.97E-4	ENSG00000102174	ENST00000379374;ENST00000537599	T;T	0.74526	-0.85;-0.85	5.6	5.6	0.85130	Peptidase M13 (1);	0.045657	0.85682	D	0.000000	T	0.66829	0.2829	L	0.33137	0.985	0.80722	D	1	P;P	0.44776	0.812;0.843	B;B	0.38616	0.182;0.277	T	0.70594	-0.4829	10	0.51188	T	0.08	.	18.6748	0.91525	0.0:0.0:1.0:0.0	.	96;96	F5GXU4;P78562	.;PHEX_HUMAN	K	96	ENSP00000368682:E96K;ENSP00000440362:E96K	ENSP00000368682:E96K	E	+	1	0	PHEX	21975187	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.771000	0.91751	2.355000	0.79922	0.594000	0.82650	GAA		0.418	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		A	22065266	G	A	22065266	3	1	48	1	0	0	0	0	1	0	0	0	11850	1059	37	1	296	1	PHEX	23	22065266	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	13630925	22065266	133205294	112	6696										
GAGE10	643832	broad.mit.edu	37	chrX	49161343	49161343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	gttttcagtgtgaaatatgaGttggcgaggaagatcgacct	13	5	1	3	rs202043957		TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chrX:49161343G>A	ENST00000407599.3	+	2	98	c.5G>A	c.(4-6)aGt>aAt	p.S2N		NM_001098413.2	NP_001091883.2	A6NGK3	GAG10_HUMAN	G antigen 10	2								p.S2N(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	Ovarian(276;0.236)					TGAAATATGAGTTGGCGAGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	ASN/SER	0,3835		0,0,0,1632,571	197	198	198		5	0.3	0	X		198	1,6727		0,0,1,2428,1871	no	missense	GAGE10	NM_001098413.2	46	0,0,1,4060,2442	AA,AG,A,GG,G		0.0149,0.0,0.0095	benign	2/117	49161343	1,10562	2203	4300	6503	49048287	SO:0001583	missense	643832					Xp11.23	2010-06-03			ENSG00000215274	ENSG00000215274			30968	protein-coding gene	gene with protein product							Standard	XM_006710256		Approved	OTTHUMG00000024136	uc010nir.1	A6NGK3	OTTHUMG00000024136	ENST00000407599.3:c.5G>A	X.37:g.49161343G>A	ENSP00000385415:p.Ser2Asn		49048287		Missense_Mutation	SNP	ENST00000407599.3	37	CCDS43938.1	.	.	.	.	.	.	.	.	.	.	G	3.691	-0.063503	0.07273	0.0	1.49E-4	ENSG00000215274	ENST00000407599	T	0.12039	2.72	1.2	0.288	0.15719	.	.	.	.	.	T	0.12347	0.0300	M	0.61703	1.905	0.09310	N	1	B	0.11235	0.004	B	0.18263	0.021	T	0.36383	-0.9750	9	0.26408	T	0.33	.	3.4447	0.07477	0.2917:0.0:0.7083:0.0	.	2	A6NGK3	GAG10_HUMAN	N	2	ENSP00000385415:S2N	ENSP00000385415:S2N	S	+	2	0	GAGE10	49048287	0.712000	0.27916	0.010000	0.14722	0.028000	0.11728	0.679000	0.25291	0.029000	0.15352	0.292000	0.19580	AGT		0.458	GAGE10-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060816.1	NM_001098413		A	49161343	G	A	49161343	3	1	48	1	0	0	0	0	1	0	0	0	6206	1029	36	3	7	3	GAGE10	23	49161343	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	27096077	49161343	106109217	113	6697										
ZCCHC16	340595	broad.mit.edu	37	chrX	111698287	111698287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	ctcagcagttagaaagttgtGggatcatatctgggcctgac	12	8	3	2			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chrX:111698287G>A	ENST00000340433.2	+	1	561	c.331G>A	c.(331-333)Ggg>Agg	p.G111R		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	111							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.G111R(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGAAAGTTGTGGGATCATATC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	90	93					X																	111698287		2203	4300	6503	111584943	SO:0001583	missense	340595			AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"Zinc fingers, CCHC domain containing"	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.331G>A	X.37:g.111698287G>A	ENSP00000340590:p.Gly111Arg		111584943	B2RPG1	Missense_Mutation	SNP	ENST00000340433.2	37	CCDS35369.1	.	.	.	.	.	.	.	.	.	.	G	4.933	0.173268	0.09391	.	.	ENSG00000187823	ENST00000340433	T	0.42513	0.97	3.9	-0.543	0.11851	.	0.843995	0.09756	N	0.759928	T	0.25382	0.0617	L	0.32530	0.975	0.09310	N	1	B	0.15930	0.015	B	0.17433	0.018	T	0.28364	-1.0046	10	0.16420	T	0.52	0.175	3.635	0.08146	0.3953:0.1906:0.4141:0.0	.	111	Q6ZR62	ZCH16_HUMAN	R	111	ENSP00000340590:G111R	ENSP00000340590:G111R	G	+	1	0	ZCCHC16	111584943	0.071000	0.21146	0.000000	0.03702	0.009000	0.06853	0.177000	0.16801	-0.235000	0.09767	0.523000	0.50628	GGG		0.403	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308		A	111698287	G	A	111698287	3	1	48	1	0	0	0	0	1	0	0	0	17623	1348	47	3	333	3	ZCCHC16	23	111698287	Missense_Mutation	SNP	G	TCGA-AG-3893-01A-01W-1073-09	62536944	111698287	43572273	114	6698										
ATP11C	286410	broad.mit.edu	37	chrX	138871554	138871554	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0521739130434783	6	1	0.607784431137725	2.18802395209581	0.352907089047711	1	1	0	tccatcaacctcttgagttaCacctttatatttgtggccat	5	11	2	1			TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3893-01A-01W-1073-09	TCGA-AG-3893-10A-01W-1073-09	g.chrX:138871554C>A	ENST00000327569.3	-	13	1407	c.1309G>T	c.(1309-1311)Gta>Tta	p.V437L	ATP11C_ENST00000370557.1_Missense_Mutation_p.V434L|ATP11C_ENST00000361648.2_Missense_Mutation_p.V437L|ATP11C_ENST00000370543.1_Missense_Mutation_p.V437L|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000359686.2_Missense_Mutation_p.V437L	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	437					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V437L(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TCTTGAGTTACACCTTTATAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	X											191	150	163					X																	138871554		2202	4299	6501	138699220	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1309G>T	X.37:g.138871554C>A	ENSP00000332756:p.Val437Leu		138699220	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	C	7.147	0.582952	0.13749	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2	5.84	4.05	0.47172	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	1.156480	0.06444	N	0.726459	T	0.42291	0.1196	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.36138	-0.9760	10	0.13853	T	0.58	.	0.9798	0.01433	0.1668:0.4179:0.1579:0.2575	.	437;437	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	L	434;437;437;437;437	ENSP00000359588:V434L;ENSP00000355165:V437L;ENSP00000332756:V437L;ENSP00000359574:V437L;ENSP00000352715:V437L	ENSP00000332756:V437L	V	-	1	0	ATP11C	138699220	0.000000	0.05858	0.335000	0.25508	0.933000	0.57130	0.643000	0.24750	1.213000	0.43380	0.529000	0.55759	GTA		0.328	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		A	138871554	C	A	138871554	3	1	48	1	0	0	0	0	1	0	0	0	1122	478	17	2	2224	2	ATP11C	23	138871554	Missense_Mutation	SNP	C	TCGA-AG-3893-01A-01W-1073-09	27173267	138871554	16399006	115	6699										
C1orf38	9473	broad.mit.edu	37	chr1	28208860	28208860	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgacctcctaggtgctttccAgccaggccggccactccggg	12	16	0	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:28208860A>C	ENST00000373921.3	+	4	1029	c.1025A>C	c.(1024-1026)cAg>cCg	p.Q342P	THEMIS2_ENST00000328928.7_Intron|THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	342	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.Q342P(1)									GGTGCTTTCCAGCCAGGCCGG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	1											21	26	24					1																	28208860		1964	4157	6121	28081447	SO:0001583	missense	9473			AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"induced by contact to basement membrane 1"		"chromosome 1 open reading frame 38"	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1025A>C	1.37:g.28208860A>C	ENSP00000363031:p.Gln342Pro		28081447	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.756904	0.49362	.	.	ENSG00000130775	ENST00000442118;ENST00000373921	T;T	0.14391	2.51;2.51	5.32	1.66	0.24008	.	0.785740	0.12579	N	0.456566	T	0.21387	0.0515	M	0.70595	2.14	0.38288	D	0.942639	P	0.49696	0.927	P	0.52109	0.69	T	0.19386	-1.0307	10	0.38643	T	0.18	-24.9168	4.1701	0.10326	0.6061:0.0:0.152:0.2419	.	342	Q5TEJ8	THMS2_HUMAN	P	205;342	ENSP00000413725:Q205P;ENSP00000363031:Q342P	ENSP00000363031:Q342P	Q	+	2	0	C1orf38	28081447	0.000000	0.05858	1.000000	0.80357	0.939000	0.58152	-0.247000	0.08866	0.975000	0.38392	0.454000	0.30748	CAG		0.662	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848		C	28208860	A	C	28208860	3	2	49	1	0	0	0	0	1	0	0	0	2045	188	7	4	1039	4	C1orf38	1	28208860	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09		28208860	221041761	1	6700										
GJB3	2707	broad.mit.edu	37	chr1	35251004	35251005	+	Missense_Mutation	DNP	TC	TC	AA													0	0	1	0	0	0	1	1	0	ctacctcatctgccacagggTcctgcgaggcctgcacaagg							TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	TC	TC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:35251004_35251005TC>AA	ENST00000373366.2	+	2	1256_1257	c.641_642TC>AA	c.(640-642)gTC>gAA	p.V214E	RP1-34M23.5_ENST00000542839.1_RNA|GJB3_ENST00000373362.3_Missense_Mutation_p.V214E	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	214					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)	p.V214>?(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGCCACAGGGTCCTGCGAGGCC	0.624																																																1	Complex(1)	large_intestine(1)	1																																								35023592	SO:0001583	missense	2707			BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"Ion channels / Gap junction proteins (connexins)"	4285	protein-coding gene	gene with protein product	"connexin 31"	603324	"gap junction protein, beta 3, 31kD (connexin 31)", "gap junction protein, beta 3, 31kDa (connexin 31)", "erythrokeratodermia variabilis"	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	Exception_encountered	1.37:g.35251004_35251005delinsAA	ENSP00000362464:p.Val214Glu		35023591	B2R790|Q2TAZ8	Missense_Mutation	DNP	ENST00000373366.2	37	CCDS384.1																																																																																				0.624	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009		AA	35251005	TC	AA	35251004	3	1	49	1	0	0	0	0	1	0	0	0	6429	1667	58	5	643	5	GJB3	1	35251004	Missense_Mutation	DNP	TC	TCGA-AG-3894-01A-01W-1073-09	7042144	35251004	213999617	2	6701										
STXBP3	6814	broad.mit.edu	37	chr1	109299379	109299379	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gctctttatttcatcactccGacatcaaaggtgagtatttt	6	9	4	1	rs572320628		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:109299379G>A	ENST00000370008.3	+	4	299	c.249G>A	c.(247-249)ccG>ccA	p.P83P		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	83	Mediates interaction with DOC2B. {ECO:0000250}.				blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)	p.P83P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TCATCACTCCGACATCAAAGG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	1											40	41	40					1																	109299379		2202	4292	6494	109100902	SO:0001819	synonymous_variant	6814			D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.249G>A	1.37:g.109299379G>A			109100902	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	37	CCDS790.1																																																																																				0.308	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		A	109299379	G	A	109299379	2	1	49	1	0	0	0	0	0	0	0	1	15393	1045	37	1		1	STXBP3	1	109299379	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	74048375	109299379	139951242	3	6702										
TRIM33	51592	broad.mit.edu	37	chr1	114976275	114976277	+	In_Frame_Del	DEL	TTC	TTC	-													0	0	1	0	0	0	1	1	0	tagctgcaaaatgaacataaTtcttcttctcaagaagtttc							TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	TTC	TTC	TTC	-	TTC	TTC	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:114976275_114976277delTTC	ENST00000358465.2	-	5	1085_1087	c.1002_1004delGAA	c.(1000-1005)aagaat>aat	p.K334del	TRIM33_ENST00000369543.2_In_Frame_Del_p.K334del|TRIM33_ENST00000450349.2_5'UTR	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	334	Necessary for oligomerization.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K334delK(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		ATGAACATAATTCTTCTTCTCAA	0.335			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	1	Deletion - In frame(1)	large_intestine(1)	1																																								114777800	SO:0001651	inframe_deletion	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.1002_1004delGAA	1.37:g.114976281_114976283delTTC	ENSP00000351250:p.Lys334del		114777798	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	In_Frame_Del	DEL	ENST00000358465.2	37	CCDS872.1																																																																																				0.335	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		-	114976277	TTC	-	114976275	7	5	49	1	0	1	0	1	0	0	0	0	16547	1493	52	0	2443	0	TRIM33	1	114976275	In_Frame_Del	DEL	TTC	TCGA-AG-3894-01A-01W-1073-09	5676896	114976275	134274346	4	6703										
NRAS	4893	broad.mit.edu	37	chr1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catggcactgtactcttcttGtccagctgtatccagtatgt	8	11	2	0	rs121913254		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:115256530G>T	ENST00000369535.4	-	3	434	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61K(595)|p.Q61E(9)|p.Q61L(3)|p.Q61R(2)|p.G60>?(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		TACTCTTCTTGTCCAGCTGTA	0.458	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	610	Substitution - Missense(609)|Complex(1)	skin(372)|haematopoietic_and_lymphoid_tissue(73)|thyroid(55)|NS(29)|large_intestine(28)|soft_tissue(16)|lung(12)|autonomic_ganglia(6)|liver(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|cervix(2)|endometrium(2)|pancreas(2)|meninges(1)|kidney(1)|biliary_tract(1)|stomach(1)|ovary(1)|bone(1)	1											180	156	164					1																	115256530		2203	4300	6503	115058053	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.181C>A	1.37:g.115256530G>T	ENSP00000358548:p.Gln61Lys		115058053	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	33	5.255564	0.95336	.	.	ENSG00000213281	ENST00000369535	D	0.83506	-1.73	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.91845	0.7419	H	0.95850	3.73	0.80722	D	1	P	0.51791	0.948	P	0.54759	0.76	D	0.93711	0.7024	10	0.62326	D	0.03	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	61	P01111	RASN_HUMAN	K	61	ENSP00000358548:Q61K	ENSP00000358548:Q61K	Q	-	1	0	NRAS	115058053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.520000	0.98027	2.624000	0.88883	0.655000	0.94253	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115256530	G	T	115256530	3	4	49	1	0	0	0	0	1	0	0	0	10671	1386	48	2	400	2	NRAS	1	115256530	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	280255	115256530	133994091	5	6704										
SYCP1	6847	broad.mit.edu	37	chr1	115489889	115489889	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gattgaactatccaatctcaAagctgaacttttgtctgtta	6	8	2	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:115489889A>T	ENST00000369522.3	+	27	2510	c.2270A>T	c.(2269-2271)aAa>aTa	p.K757I	SYCP1_ENST00000369518.1_Missense_Mutation_p.K757I	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	757					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.K757I(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		TCCAATCTCAAAGCTGAACTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	65	64					1																	115489889		2203	4294	6497	115291412	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2270A>T	1.37:g.115489889A>T	ENSP00000358535:p.Lys757Ile		115291412	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.857935	0.32791	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.52526	0.66;0.66;0.66	5.12	1.55	0.23275	.	0.165879	0.52532	D	0.000075	T	0.37019	0.0988	L	0.55481	1.735	0.29877	N	0.826383	P	0.41131	0.739	P	0.52881	0.712	T	0.29305	-1.0016	10	0.66056	D	0.02	-8.1621	8.254	0.31743	0.7549:0.0:0.2451:0.0	.	757	Q15431	SYCP1_HUMAN	I	757	ENSP00000358535:K757I;ENSP00000410011:K757I;ENSP00000358531:K757I	ENSP00000358531:K757I	K	+	2	0	SYCP1	115291412	0.930000	0.31532	0.649000	0.29536	0.028000	0.11728	1.825000	0.39081	0.071000	0.16664	-0.280000	0.10049	AAA		0.328	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115489889	A	T	115489889	3	4	49	1	0	0	0	0	1	0	0	0	15470	14	1	5	2372	5	SYCP1	1	115489889	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	233359	115489889	133760732	6	6705										
MRPS21	54460	broad.mit.edu	37	chr1	150280640	150280640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttgatgcgaaagaatcgggCagatccgtggcagggctgct	15	9	0	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:150280640C>T	ENST00000369084.5	+	2	689	c.242C>T	c.(241-243)gCa>gTa	p.A81V	MRPS21_ENST00000309092.7_Missense_Mutation_p.A81V	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	81					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A81V(1)		kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AAGAATCGGGCAGATCCGTGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											50	46	47					1																	150280640		2203	4300	6503	148547264	SO:0001583	missense	54460			AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"Mitochondrial ribosomal proteins / small subunits"	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.242C>T	1.37:g.150280640C>T	ENSP00000358080:p.Ala81Val		148547264	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.239273	0.22711	.	.	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.30448	1.53;1.53	4.94	2.93	0.34026	.	.	.	.	.	T	0.04952	0.0133	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40001	-0.9586	8	0.14656	T	0.56	.	5.626	0.17482	0.3342:0.5477:0.0:0.1181	.	81	P82921	RT21_HUMAN	V	81	ENSP00000312395:A81V;ENSP00000358080:A81V	ENSP00000312395:A81V	A	+	2	0	MRPS21	148547264	0.014000	0.17966	0.952000	0.39060	0.958000	0.62258	1.886000	0.39688	1.323000	0.45263	-0.127000	0.14921	GCA		0.537	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997		T	150280640	C	T	150280640	3	4	49	1	0	0	0	0	1	0	0	0	9862	710	25	3	248	3	MRPS21	1	150280640	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	34790751	150280640	98969981	7	6706										
C1orf226	400793	broad.mit.edu	37	chr1	162351811	162351811	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggctctggtgagcctgggggGccaggactctgggtgggcag	21	9	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:162351811G>T	ENST00000458626.2	+	1	292	c.120G>T	c.(118-120)ggG>ggT	p.G40G	C1orf226_ENST00000426197.2_Silent_p.G83G|RP11-565P22.6_ENST00000431696.1_Silent_p.G149G	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	40								p.G83G(2)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						AGCCTGGGGGGCCAGGACTCT	0.662																																																2	Substitution - coding silent(2)	large_intestine(2)	1											10	13	12					1																	162351811		1842	4059	5901	160618435	SO:0001819	synonymous_variant	400793			AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.120G>T	1.37:g.162351811G>T			160618435	B4DF31	Silent	SNP	ENST00000458626.2	37	CCDS53422.1																																																																																				0.662	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		T	162351811	G	T	162351811	2	4	49	1	0	0	0	0	0	0	0	1	2038	1190	42	2		2	C1orf226	1	162351811	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	12071171	162351811	86898810	8	6707										
CTSE	1510	broad.mit.edu	37	chr1	206320205	206320205	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgcacttctttccagagacGcacagcaggttccagccttc	9	14	1	1	rs149390455		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:206320205G>T	ENST00000358184.2	+	4	466	c.348G>T	c.(346-348)acG>acT	p.T116T	CTSE_ENST00000468617.1_3'UTR|CTSE_ENST00000432969.2_Silent_p.T41T|CTSE_ENST00000361052.3_Silent_p.T116T|CTSE_ENST00000360218.2_Silent_p.T116T	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	116					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)	p.T116T(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			TTCCAGAGACGCACAGCAGGT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,	0,4406		0,0,2203	116	103	108		348,348	-9.2	0	1	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CTSE	NM_001910.3,NM_148964.2	,	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	,	116/397,116/364	206320205	1,13005	2203	4300	6503	204486828	SO:0001819	synonymous_variant	1510			BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"Cathepsins"	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.348G>T	1.37:g.206320205G>T			204486828	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	37	CCDS1462.1																																																																																				0.577	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910		T	206320205	G	T	206320205	2	4	49	1	0	0	0	0	0	0	0	1	4039	1074	38	2		2	CTSE	1	206320205	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	43968394	206320205	42930416	9	6708										
OR11L1	391189	broad.mit.edu	37	chr1	248004661	248004661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ctgcatgagtggcgggaggtCgcagaagaaatggttaatct	15	6	1	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr1:248004661C>T	ENST00000355784.2	-	1	593	c.538G>A	c.(538-540)Gac>Aac	p.D180N		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	180						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D180N(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGCGGGAGGTCGCAGAAGAAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	83	82					1																	248004661		2203	4300	6503	246071284	SO:0001583	missense	391189			AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"GPCR / Class A : Olfactory receptors"	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.538G>A	1.37:g.248004661C>T	ENSP00000348033:p.Asp180Asn		246071284		Missense_Mutation	SNP	ENST00000355784.2	37	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.798668	0.70567	.	.	ENSG00000197591	ENST00000355784	T	0.00188	8.59	4.27	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38548	U	0.001657	T	0.00524	0.0017	M	0.75264	2.295	0.34296	D	0.683767	D	0.89917	1.0	D	0.85130	0.997	T	0.66701	-0.5857	10	0.72032	D	0.01	.	14.1813	0.65577	0.0:0.8489:0.151:0.0	.	180	Q8NGX0	O11L1_HUMAN	N	180	ENSP00000348033:D180N	ENSP00000348033:D180N	D	-	1	0	OR11L1	246071284	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	3.847000	0.55895	1.125000	0.41998	0.543000	0.68304	GAC		0.507	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959		T	248004661	C	T	248004661	3	4	49	1	0	0	0	0	1	0	0	0	10961	884	31	1	434	1	OR11L1	1	248004661	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	41684456	248004661	1245960	10	6709										
PNPT1	87178	broad.mit.edu	37	chr2	55894202	55894202	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctcacaacttacattcctaAgtgaagtcaaatcccgacca	4	14	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:55894202A>T	ENST00000447944.2	-	13	1186	c.1100T>A	c.(1099-1101)cTt>cAt	p.L367H		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	367					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)	p.L367H(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TACATTCCTAAGTGAAGTCAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	95	97					2																	55894202		2203	4300	6503	55747706	SO:0001583	missense	87178			BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1100T>A	2.37:g.55894202A>T	ENSP00000400646:p.Leu367His		55747706	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680995	0.88542	.	.	ENSG00000138035	ENST00000447944	T	0.69040	-0.37	5.65	5.65	0.86999	Polynucleotide phosphorylase, phosphorolytic RNA-binding, bacterial/organelle-type (1);Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.070917	0.56097	D	0.000026	T	0.82130	0.4970	M	0.78285	2.405	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.84540	0.0638	10	0.87932	D	0	-9.4002	16.2323	0.82352	1.0:0.0:0.0:0.0	.	367	Q8TCS8	PNPT1_HUMAN	H	367	ENSP00000400646:L367H	ENSP00000386075:L367H	L	-	2	0	PNPT1	55747706	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.017000	0.93651	2.288000	0.76882	0.529000	0.55759	CTT		0.348	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		T	55894202	A	T	55894202	3	4	49	1	0	0	0	0	1	0	0	0	12204	72	3	5	1315	5	PNPT1	2	55894202	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09		55894202	187305171	11	6710										
PCBP1	5093	broad.mit.edu	37	chr2	70315180	70315180	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcccccggtcaccctgaggcTggtggtgccggccacccagt	14	17	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:70315180T>A	ENST00000303577.5	+	1	596	c.305T>A	c.(304-306)cTg>cAg	p.L102Q	PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	102	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L102Q(2)|p.L102P(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						ACCCTGAGGCTGGTGGTGCCG	0.612																																					Colon(85;1146 1307 3484 18706 25380)											3	Substitution - Missense(3)	large_intestine(3)	2											57	70	66					2																	70315180		2200	4299	6499	70168684	SO:0001583	missense	5093				CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.305T>A	2.37:g.70315180T>A	ENSP00000305556:p.Leu102Gln		70168684	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	37	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469571	0.63625	.	.	ENSG00000169564	ENST00000303577	T	0.34859	1.34	4.16	4.16	0.48862	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.082382	0.49916	U	0.000122	T	0.72070	0.3415	H	0.97783	4.075	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.81777	-0.0777	10	0.87932	D	0	.	11.8577	0.52449	0.0:0.0:0.0:1.0	.	102	Q15365	PCBP1_HUMAN	Q	102	ENSP00000305556:L102Q	ENSP00000305556:L102Q	L	+	2	0	PCBP1	70168684	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	4.781000	0.62389	2.120000	0.65058	0.477000	0.44152	CTG		0.612	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70315180	T	A	70315180	3	1	49	1	0	0	0	0	1	0	0	0	11531	1580	55	5	307	5	PCBP1	2	70315180	Missense_Mutation	SNP	T	TCGA-AG-3894-01A-01W-1073-09	14420978	70315180	172884193	12	6711										
FMNL2	114793	broad.mit.edu	37	chr2	153473648	153473648	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agagaatgaagccatgtccaAgattgtggaactggaaaagc	12	6	0	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:153473648A>C	ENST00000288670.9	+	13	1623	c.1256A>C	c.(1255-1257)aAg>aCg	p.K419T	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	419	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.K419T(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						GCCATGTCCAAGATTGTGGAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	129	132					2																	153473648		1928	4143	6071	153181894	SO:0001583	missense	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1256A>C	2.37:g.153473648A>C	ENSP00000288670:p.Lys419Thr		153181894	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.554891	0.86231	.	.	ENSG00000157827	ENST00000288670	T	0.50277	0.75	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.69895	0.3162	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69154	-0.5220	10	0.30854	T	0.27	.	16.2167	0.82231	1.0:0.0:0.0:0.0	.	419	Q96PY5-3	.	T	419	ENSP00000288670:K419T	ENSP00000288670:K419T	K	+	2	0	FMNL2	153181894	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.231000	0.72958	0.533000	0.62120	AAG		0.443	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		C	153473648	A	C	153473648	3	2	49	1	0	0	0	0	1	0	0	0	5971	72	3	4	1306	4	FMNL2	2	153473648	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	83158468	153473648	89725725	13	6712										
TTN	7273	broad.mit.edu	37	chr2	179435825	179435825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gacaatgattgcctctggccGtcctggtggatcacatgggt	13	10	2	1	rs368914555	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:179435825G>A	ENST00000591111.1	-	276	70335	c.70111C>T	c.(70111-70113)Cgg>Tgg	p.R23371W	TTN_ENST00000359218.5_Missense_Mutation_p.R16072W|TTN_ENST00000460472.2_Missense_Mutation_p.R15947W|TTN_ENST00000342992.6_Missense_Mutation_p.R22444W|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16139W|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R25012W|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23371	Fibronectin type-III 70. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R16139W(1)|p.R16072W(1)|p.R22442W(1)|p.R15947W(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCTCTGGCCGTCCTGGTGGA	0.458													G|||	10	0.00199681	0	0	5008	,	,		21269	0		0	False		,,,				2504	0.0102															4	Substitution - Missense(4)	large_intestine(4)	2						G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,3974		0,0,1987	121	126	124		47839,67330,48214,48415	3.5	0.4	2		124	1,8311		0,1,4155	no	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	101,101,101,101	0,1,6142	AA,AG,GG		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging	15947/26927,22444/33424,16072/27052,16139/27119	179435825	1,12285	1987	4156	6143	179144071	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.70111C>T	2.37:g.179435825G>A	ENSP00000465570:p.Arg23371Trp		179144071	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	10.13	1.264803	0.23136	0.0	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.28	3.45	0.39498	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71467	0.3343	M	0.80616	2.505	0.37131	D	0.901288	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.65987	0.94;0.94;0.94;0.914	T	0.79699	-0.1694	9	0.87932	D	0	.	14.5479	0.68044	0.0:0.0:0.7219:0.278	.	15947;16072;16139;23371	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	W	22444;15947;16139;16072;15945	ENSP00000343764:R22444W;ENSP00000434586:R15947W;ENSP00000340554:R16139W;ENSP00000352154:R16072W	ENSP00000340554:R16139W	R	-	1	2	TTN	179144071	1.000000	0.71417	0.428000	0.26697	0.936000	0.57629	3.558000	0.53749	0.696000	0.31696	-0.158000	0.13435	CGG		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179435825	G	A	179435825	3	1	49	1	0	0	0	0	1	0	0	0	16775	1144	40	1	33093	1	TTN	2	179435825	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	25962177	179435825	63763548	14	6713										
PTPRN	5798	broad.mit.edu	37	chr2	220161201	220161201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tatgggacagcgggccctgcGtggctatgtaggctggcatc	16	10	0	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:220161201G>A	ENST00000295718.2	-	17	2588	c.2348C>T	c.(2347-2349)aCg>aTg	p.T783M	PTPRN_ENST00000409251.3_Missense_Mutation_p.T754M|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.T693M|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000497977.1_5'UTR	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	783	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T783M(1)		breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGGGCCCTGCGTGGCTATGTA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	74	76					2																	220161201		2203	4300	6503	219869445	SO:0001583	missense	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2348C>T	2.37:g.220161201G>A	ENSP00000295718:p.Thr783Met		219869445	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615140	0.66672	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	D;D;D	0.88046	-2.33;-2.33;-2.33	4.56	4.56	0.56223	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	D	0.95862	0.8653	H	0.96720	3.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97614	1.0131	10	0.87932	D	0	.	17.3328	0.87271	0.0:0.0:1.0:0.0	.	754;783	Q6NSL1;Q16849	.;PTPRN_HUMAN	M	754;783;754;693	ENSP00000386638:T754M;ENSP00000295718:T783M;ENSP00000444244:T693M	ENSP00000295718:T783M	T	-	2	0	PTPRN	219869445	1.000000	0.71417	0.944000	0.38274	0.526000	0.34562	9.734000	0.98822	2.245000	0.73994	0.655000	0.94253	ACG		0.607	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220161201	G	A	220161201	3	1	49	1	0	0	0	0	1	0	0	0	12844	1145	40	1	619	1	PTPRN	2	220161201	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	40725376	220161201	23038172	15	6714										
KIAA1486	57624	broad.mit.edu	37	chr2	226447508	226447508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaggcctcccccttacgacGctgtgcattcgggcagcctc	10	16	0	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:226447508G>A	ENST00000272907.6	+	4	1788	c.1375G>A	c.(1375-1377)Gct>Act	p.A459T	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	459	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.A459T(2)									CCCTTACGACGCTGTGCATTC	0.627																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											45	50	48					2																	226447508		2039	4199	6238	226155752	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1375G>A	2.37:g.226447508G>A	ENSP00000272907:p.Ala459Thr		226155752	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145976	0.37923	.	.	ENSG00000144460	ENST00000272907	T	0.30714	1.52	5.19	4.22	0.49857	.	0.247464	0.41823	D	0.000812	T	0.15522	0.0374	N	0.14661	0.345	0.80722	D	1	P	0.49961	0.93	B	0.38194	0.267	T	0.02533	-1.1145	10	0.28530	T	0.3	-13.4619	10.5722	0.45206	0.0:0.0:0.5605:0.4395	.	459	Q9P242	K1486_HUMAN	T	459	ENSP00000272907:A459T	ENSP00000272907:A459T	A	+	1	0	KIAA1486	226155752	0.998000	0.40836	0.977000	0.42913	0.941000	0.58515	3.662000	0.54510	2.415000	0.81967	0.563000	0.77884	GCT		0.627	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		A	226447508	G	A	226447508	3	1	49	1	0	0	0	0	1	0	0	0	8258	1087	38	1	1385	1	KIAA1486	2	226447508	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	6286307	226447508	16751865	16	6715										
DNER	92737	broad.mit.edu	37	chr2	230456484	230456484	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagactgggaagtgcctgttCacagttgggaccttcatagc	13	9	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr2:230456484C>A	ENST00000341772.4	-	2	531	c.397G>T	c.(397-399)Gaa>Taa	p.E133*		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	133	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Interaction with NOTCH1. {ECO:0000250}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.E133*(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		AGTGCCTGTTCACAGTTGGGA	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											78	62	67					2																	230456484		2203	4300	6503	230164728	SO:0001587	stop_gained	92737			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.397G>T	2.37:g.230456484C>A	ENSP00000345229:p.Glu133*		230164728	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Nonsense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	C	37	6.271630	0.97431	.	.	ENSG00000187957	ENST00000341772	.	.	.	5.69	5.69	0.88448	.	0.210162	0.49305	D	0.000141	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.7953	0.96478	0.0:1.0:0.0:0.0	.	.	.	.	X	133	.	ENSP00000345229:E133X	E	-	1	0	DNER	230164728	1.000000	0.71417	0.953000	0.39169	0.506000	0.33950	6.734000	0.74801	2.673000	0.90976	0.655000	0.94253	GAA		0.567	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		A	230456484	C	A	230456484	4	1	49	1	0	0	0	0	0	1	0	0	4678	835	29	2	1864	2	DNER	2	230456484	Nonsense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	4008976	230456484	12742889	17	6716										
C3orf20	84077	broad.mit.edu	37	chr3	14799047	14799047	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggagcgcttcctgttggcgCcccgagaccccagccaagtg	13	15	0	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr3:14799047C>G	ENST00000253697.3	+	13	2562	c.2110C>G	c.(2110-2112)Ccc>Gcc	p.P704A	C3orf20_ENST00000412910.1_Missense_Mutation_p.P582A|C3orf20_ENST00000435614.1_Missense_Mutation_p.P582A	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	704						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.P704A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCTGTTGGCGCCCCGAGACCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	3											51	50	50					3																	14799047		2203	4300	6503	14774051	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.2110C>G	3.37:g.14799047C>G	ENSP00000253697:p.Pro704Ala		14774051	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270909	0.40194	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08634	3.36;3.07;3.07	4.95	4.95	0.65309	.	0.000000	0.49916	D	0.000126	T	0.27349	0.0671	M	0.72479	2.2	0.38726	D	0.953558	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.02625	-1.1132	10	0.56958	D	0.05	-27.3471	13.7034	0.62622	0.0:1.0:0.0:0.0	.	582;704	Q8ND61-2;Q8ND61	.;CC020_HUMAN	A	704;582;582	ENSP00000253697:P704A;ENSP00000402933:P582A;ENSP00000396081:P582A	ENSP00000253697:P704A	P	+	1	0	C3orf20	14774051	0.972000	0.33761	0.886000	0.34754	0.006000	0.05464	2.415000	0.44635	2.299000	0.77371	0.297000	0.19635	CCC		0.607	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		G	14799047	C	G	14799047	3	3	49	1	0	0	0	0	1	0	0	0	2219	739	26	5	2152	5	C3orf20	3	14799047	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		14799047	183223383	18	6717										
CACNA2D2	9254	broad.mit.edu	37	chr3	50417407	50417407	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ctgctcactcacacatccacGatgatgaccatgtctttggg	8	13	3	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr3:50417407G>A	ENST00000479441.1	-	9	884	c.885C>T	c.(883-885)atC>atT	p.I295I	CACNA2D2_ENST00000435965.1_Silent_p.I295I|CACNA2D2_ENST00000360963.3_Silent_p.I226I|CACNA2D2_ENST00000429770.1_Silent_p.I295I|CACNA2D2_ENST00000423994.2_Silent_p.I295I|CACNA2D2_ENST00000424201.2_Silent_p.I295I|CACNA2D2_ENST00000395083.1_Silent_p.I295I|CACNA2D2_ENST00000266039.3_Silent_p.I295I			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	295	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.I295I(1)		breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	ACACATCCACGATGATGACCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											146	125	132					3																	50417407		2203	4300	6503	50392411	SO:0001819	synonymous_variant	9254			AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.885C>T	3.37:g.50417407G>A			50392411	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Silent	SNP	ENST00000479441.1	37	CCDS54588.1																																																																																				0.602	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		A	50417407	G	A	50417407	2	1	49	1	0	0	0	0	0	0	0	1	2555	1048	37	1		1	CACNA2D2	3	50417407	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	35618360	50417407	147605023	19	6718										
PLS1	5357	broad.mit.edu	37	chr3	142402999	142402999	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctttttgctgatattgagaTttccaggaatgaaggtaaga	10	5	0	4			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr3:142402999T>A	ENST00000337777.3	+	7	944	c.731T>A	c.(730-732)aTt>aAt	p.I244N	PLS1_ENST00000457734.2_Missense_Mutation_p.I244N|PLS1_ENST00000497002.1_Missense_Mutation_p.I244N	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	244	Actin-binding 1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.I244N(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						GATATTGAGATTTCCAGGAAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											160	155	157					3																	142402999		2203	4300	6503	143885689	SO:0001583	missense	5357			L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.731T>A	3.37:g.142402999T>A	ENSP00000336831:p.Ile244Asn		143885689	A8K2Q1|D3DNG3|Q8NEG6	Missense_Mutation	SNP	ENST00000337777.3	37	CCDS3125.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446004	0.63178	.	.	ENSG00000120756	ENST00000457734;ENST00000476044;ENST00000337777;ENST00000497002	D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78	4.89	4.89	0.63831	Calponin homology domain (2);	0.243774	0.46442	D	0.000298	D	0.94676	0.8283	M	0.74467	2.265	0.58432	D	0.999997	P	0.36789	0.57	B	0.36885	0.235	D	0.95251	0.8360	10	0.87932	D	0	-12.4595	14.9516	0.71080	0.0:0.0:0.0:1.0	.	244	Q14651	PLSI_HUMAN	N	244;165;244;244	ENSP00000387890:I244N;ENSP00000417481:I165N;ENSP00000336831:I244N;ENSP00000418700:I244N	ENSP00000336831:I244N	I	+	2	0	PLS1	143885689	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.409000	0.80053	2.169000	0.68431	0.477000	0.44152	ATT		0.403	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		A	142402999	T	A	142402999	3	1	49	1	0	0	0	0	1	0	0	0	12138	1493	52	5	753	5	PLS1	3	142402999	Missense_Mutation	SNP	T	TCGA-AG-3894-01A-01W-1073-09	91985592	142402999	55619431	20	6719										
SMC4	10051	broad.mit.edu	37	chr3	160138629	160138629	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctattgatatagcccaagaAtgtgtaaacttccttaaaag	6	7	1	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr3:160138629A>T	ENST00000357388.3	+	13	2410	c.1959A>T	c.(1957-1959)gaA>gaT	p.E653D	SMC4_ENST00000360111.2_Missense_Mutation_p.E653D|SMC4_ENST00000469762.1_Missense_Mutation_p.E628D|SMC4_ENST00000344722.5_Missense_Mutation_p.E653D|SMC4_ENST00000462787.1_Missense_Mutation_p.E653D|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	653	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.E653D(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TAGCCCAAGAATGTGTAAACT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	109	112					3																	160138629		2203	4300	6503	161621323	SO:0001583	missense	10051			AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1959A>T	3.37:g.160138629A>T	ENSP00000349961:p.Glu653Asp		161621323	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.795166	0.31777	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05	5.43	1.22	0.21188	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.281414	0.40385	N	0.001101	T	0.73233	0.3561	L	0.33093	0.98	0.37653	D	0.922487	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.001	T	0.61850	-0.6978	10	0.13853	T	0.58	-13.3025	9.9803	0.41809	0.584:0.3181:0.0:0.098	.	653;628;628;653	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	D	653;653;628;653;653;247	ENSP00000349961:E653D;ENSP00000353225:E653D;ENSP00000417964:E628D;ENSP00000420734:E653D;ENSP00000341382:E653D	ENSP00000341382:E653D	E	+	3	2	SMC4	161621323	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.088000	0.41663	0.317000	0.23160	0.445000	0.29226	GAA		0.353	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			T	160138629	A	T	160138629	3	4	49	1	0	0	0	0	1	0	0	0	14822	98	4	5	2005	5	SMC4	3	160138629	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	17735630	160138629	37883801	21	6720										
HTR3D	200909	broad.mit.edu	37	chr3	183756569	183756569	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtatcagcagggcagatgCcaggccctggggaggcagag	18	9	1	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr3:183756569C>G	ENST00000382489.3	+	8	1171	c.1171C>G	c.(1171-1173)Cca>Gca	p.P391A	HTR3D_ENST00000453435.1_Missense_Mutation_p.P170A|HTR3D_ENST00000334128.2_Missense_Mutation_p.P216A|HTR3D_ENST00000428798.2_Missense_Mutation_p.P341A	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	391					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.P216A(1)|p.P391A(1)		large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	AGGGCAGATGCCAGGCCCTGG	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	3											48	48	48					3																	183756569		2203	4300	6503	185239263	SO:0001583	missense	200909			AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24004	protein-coding gene	gene with protein product		610122	"5-hydroxytryptamine (serotonin) receptor 3 family member D"			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1171C>G	3.37:g.183756569C>G	ENSP00000371929:p.Pro391Ala		185239263	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	.	.	.	.	.	.	.	.	.	.	C	9.884	1.202333	0.22121	.	.	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59	3.77	1.37	0.22104	Neurotransmitter-gated ion-channel transmembrane domain (1);	1.058060	0.07471	N	0.902282	T	0.82029	0.4948	M	0.86028	2.79	0.09310	N	1	B;B;B;B	0.29162	0.118;0.235;0.036;0.12	B;B;B;B	0.29440	0.07;0.102;0.023;0.09	T	0.63107	-0.6711	10	0.20046	T	0.44	-4.579	5.8752	0.18824	0.0:0.6833:0.0:0.3167	.	391;216;170;216	Q70Z44;Q70Z44-2;Q70Z44-3;F6WC43	5HT3D_HUMAN;.;.;.	A	216;341;391;170	ENSP00000334315:P216A;ENSP00000405409:P341A;ENSP00000371929:P391A;ENSP00000389268:P170A	ENSP00000334315:P216A	P	+	1	0	HTR3D	185239263	0.000000	0.05858	0.004000	0.12327	0.037000	0.13140	-0.424000	0.07025	0.154000	0.19237	0.558000	0.71614	CCA		0.617	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537		G	183756569	C	G	183756569	3	3	49	1	0	0	0	0	1	0	0	0	7468	739	26	5	1371	5	HTR3D	3	183756569	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	23617940	183756569	14265861	22	6721										
KIAA1109	84162	broad.mit.edu	37	chr4	123120528	123120528	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tattaggttacactcctgctAttaagggacaactcttacat	6	9	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr4:123120528A>C	ENST00000264501.4	+	14	1676	c.1303A>C	c.(1303-1305)Att>Ctt	p.I435L	KIAA1109_ENST00000455637.1_Missense_Mutation_p.I435L|KIAA1109_ENST00000388738.3_Missense_Mutation_p.I435L|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	435					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.I435L(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CACTCCTGCTATTAAGGGACA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											189	159	169					4																	123120528		1844	4088	5932	123339978	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1303A>C	4.37:g.123120528A>C	ENSP00000264501:p.Ile435Leu		123339978	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.87|17.87	3.495920|3.495920	0.64186|0.64186	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	D;D;D|.	0.94138|.	-3.36;-3.36;-3.36|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.528136|.	0.17756|.	N|.	0.163068|.	T|T	0.52484|0.52484	0.1737|0.1737	N|N	0.21194|0.21194	0.64|0.64	0.46458|0.46458	D|D	0.999054|0.999054	B|.	0.25312|.	0.123|.	B|.	0.21917|.	0.037|.	T|T	0.49523|0.49523	-0.8931|-0.8931	10|5	0.17832|.	T|.	0.49|.	.|.	15.671|15.671	0.77274|0.77274	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	435|.	Q2LD37|.	K1109_HUMAN|.	L|S	435|267	ENSP00000264501:I435L;ENSP00000373390:I435L;ENSP00000389925:I435L|.	ENSP00000264501:I435L|.	I|Y	+|+	1|2	0|0	KIAA1109|KIAA1109	123339978|123339978	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	7.038000|7.038000	0.76537|0.76537	2.119000|2.119000	0.64992|0.64992	0.482000|0.482000	0.46254|0.46254	ATT|TAT		0.373	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123120528	A	C	123120528	3	2	49	1	0	0	0	0	1	0	0	0	8229	449	16	4	1349	4	KIAA1109	4	123120528	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09		123120528	68033748	23	6722										
FAT4	79633	broad.mit.edu	37	chr4	126336582	126336582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgataacaaccccatctttgCacaagctttgtataaagtgg	7	9	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr4:126336582C>T	ENST00000394329.3	+	5	6477	c.6464C>T	c.(6463-6465)gCa>gTa	p.A2155V	FAT4_ENST00000335110.5_Missense_Mutation_p.A453V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2155	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A2155V(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCATCTTTGCACAAGCTTTG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											94	88	90					4																	126336582		2203	4300	6503	126556032	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6464C>T	4.37:g.126336582C>T	ENSP00000377862:p.Ala2155Val		126556032	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705768	0.48412	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01804	4.63;4.63	5.42	4.55	0.56014	Cadherin (2);Cadherin-like (1);	0.552403	0.12951	U	0.425838	T	0.02610	0.0079	L	0.43923	1.385	0.42608	D	0.9933	B;B	0.18968	0.01;0.032	B;B	0.19946	0.025;0.027	T	0.51919	-0.8644	10	0.26408	T	0.33	.	13.3256	0.60457	0.0:0.9209:0.0:0.0791	.	453;2155	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	2155;453	ENSP00000377862:A2155V;ENSP00000335169:A453V	ENSP00000335169:A453V	A	+	2	0	FAT4	126556032	1.000000	0.71417	0.025000	0.17156	0.827000	0.46813	5.946000	0.70234	1.219000	0.43474	0.557000	0.71058	GCA		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126336582	C	T	126336582	3	4	49	1	0	0	0	0	1	0	0	0	5711	710	25	3	6482	3	FAT4	4	126336582	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	3216054	126336582	64817694	24	6723										
STOX2	56977	broad.mit.edu	37	chr4	184938359	184938359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gccttcaacttccgagcgagCgcggagcccccgacaaatga	11	15	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr4:184938359C>T	ENST00000308497.4	+	4	4138	c.2703C>T	c.(2701-2703)agC>agT	p.S901S		NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	901					embryo development (GO:0009790)|maternal placenta development (GO:0001893)			p.S901S(1)		breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		TCCGAGCGAGCGCGGAGCCCC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	4											58	61	60					4																	184938359		1893	4115	6008	185175353	SO:0001819	synonymous_variant	56977			AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.2703C>T	4.37:g.184938359C>T			185175353	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																				0.532	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		T	184938359	C	T	184938359	2	4	49	1	0	0	0	0	0	0	0	1	15359	767	27	1		1	STOX2	4	184938359	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	58601777	184938359	6215917	25	6724										
CDH12	1010	broad.mit.edu	37	chr5	22078605	22078606	+	Frame_Shift_Ins	INS	-	-	G													0	0	1	0	0	0	1	1	0	tattcttccagcacaaaaaaINSttgattccatacccagccac					rs142320441	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:22078605_22078606insG	ENST00000382254.1	-	5	1266_1267	c.180_181insC	c.(178-183)caatttfs	p.F61fs	CDH12_ENST00000504376.2_Frame_Shift_Ins_p.F61fs|CDH12_ENST00000522262.1_Frame_Shift_Ins_p.F61fs	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F61fs*45(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						AGCACAAAAAATTGATTCCATA	0.465										HNSCC(59;0.17)																																						1	Insertion - Frameshift(1)	large_intestine(1)	5																																								22114363	SO:0001589	frameshift_variant	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.180_181insC	5.37:g.22078605_22078606insG	ENSP00000371689:p.Phe61fs		22114362	B2RBT1|B7Z2U6|Q86UD2	Frame_Shift_Ins	INS	ENST00000382254.1	37	CCDS3890.1																																																																																				0.465	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		G	22078606	-	G	22078605	7	5	49	1	0	1	1	0	0	0	0	0	3104	101	4	0	2247	0	CDH12	5	22078605	Frame_Shift_Ins	INS	-	TCGA-AG-3894-01A-01W-1073-09		22078605	158836655	26	6725										
GZMK	3003	broad.mit.edu	37	chr5	54320566	54320566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ggcctccatccagtatggcgGacatcacgtttgtggaggtg	14	10	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:54320566G>A	ENST00000231009.2	+	2	213	c.143G>A	c.(142-144)gGa>gAa	p.G48E	CTD-2313F11.1_ENST00000596137.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000608929.1_RNA|ESM1_ENST00000598310.1_5'Flank|CTD-2313F11.1_ENST00000608466.1_RNA|CTD-2313F11.1_ENST00000607910.1_RNA|CTD-2313F11.1_ENST00000371487.3_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000596909.2_RNA	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	48	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G48E(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CAGTATGGCGGACATCACGTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	58	57					5																	54320566		2203	4300	6503	54356323	SO:0001583	missense	3003			BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"granzyme K (serine protease, granzyme 3; tryptase II)"			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.143G>A	5.37:g.54320566G>A	ENSP00000231009:p.Gly48Glu		54356323	B2R563	Missense_Mutation	SNP	ENST00000231009.2	37	CCDS3964.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.264835	0.40095	.	.	ENSG00000113088	ENST00000231009	D	0.88586	-2.4	5.11	4.23	0.50019	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.458056	0.20870	N	0.084197	D	0.90868	0.7131	L	0.58669	1.825	0.09310	N	1	P	0.43314	0.803	P	0.51615	0.675	D	0.85007	0.0903	10	0.54805	T	0.06	.	14.9433	0.71012	0.0:0.1442:0.8558:0.0	.	48	P49863	GRAK_HUMAN	E	48	ENSP00000231009:G48E	ENSP00000231009:G48E	G	+	2	0	GZMK	54356323	0.003000	0.15002	0.007000	0.13788	0.405000	0.30901	1.364000	0.34171	1.507000	0.48752	0.591000	0.81541	GGA		0.473	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104		A	54320566	G	A	54320566	3	1	49	1	0	0	0	0	1	0	0	0	6939	1174	41	3	149	3	GZMK	5	54320566	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	32241961	54320566	126594694	27	6726										
APC	324	broad.mit.edu	37	chr5	112128143	112128143	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtttcttgttttattttagCgaagaatagccagaattcag	9	5	2	2	rs62619935		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:112128143C>T	ENST00000457016.1	+	7	1026	c.646C>T	c.(646-648)Cga>Tga	p.R216*	APC_ENST00000508376.2_Splice_Site_p.R216*|APC_ENST00000257430.4_Splice_Site_p.R216*			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R216*(12)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATTTTAGCGAAGAATAGC	0.323		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	12	Substitution - Nonsense(12)	large_intestine(12)	5	GRCh37	CM992133	APC	M	rs62619935						52	51	51					5																	112128143		2202	4300	6502	112156042	SO:0001630	splice_region_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.646-1C>T	5.37:g.112128143C>T			112156042	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.466758	0.98302	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	2.99	0.34606	.	0.630262	0.16042	N	0.232387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2274	1.7088	0.02888	0.2899:0.3634:0.2259:0.1208	rs62619935	.	.	.	X	216	.	.	R	+	1	2	APC	112156042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.662000	0.25038	1.304000	0.44892	-0.158000	0.13435	CGA		0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation	T	112128143	C	T	112128143	5	4	49	1	0	0	0	0	0	0	1	0	763	782	27	1	668	1	APC	5	112128143	Splice_Site	SNP	C	TCGA-AG-3894-01A-01W-1073-09	57807577	112128143	68787117	28	6727										
PCDHB16	57717	broad.mit.edu	37	chr5	140564100	140564100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcctccgcgctcggccaccGccacgctgcacgtgctcctg	11	20	0	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:140564100G>A	ENST00000361016.2	+	1	3121	c.1966G>A	c.(1966-1968)Gcc>Acc	p.A656T		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	656	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A656T(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCGGCCACCGCCACGCTGCA	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	5											21	25	23					5																	140564100		2165	4244	6409	140544284	SO:0001583	missense	57717			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1966G>A	5.37:g.140564100G>A	ENSP00000354293:p.Ala656Thr		140544284	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	13.48	2.251085	0.39797	.	.	ENSG00000196963	ENST00000361016	T	0.50548	0.74	3.75	3.75	0.43078	Cadherin (4);Cadherin-like (1);	0.573872	0.13146	N	0.410254	T	0.43831	0.1265	L	0.43554	1.36	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.43988	-0.9357	10	0.62326	D	0.03	.	15.2277	0.73364	0.0:0.0:1.0:0.0	.	656	Q9NRJ7	PCDBG_HUMAN	T	656	ENSP00000354293:A656T	ENSP00000354293:A656T	A	+	1	0	PCDHB16	140544284	0.001000	0.12720	1.000000	0.80357	0.782000	0.44232	0.923000	0.28757	1.638000	0.50547	0.298000	0.19748	GCC		0.706	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140564100	G	A	140564100	3	1	49	1	0	0	0	0	1	0	0	0	11572	1087	38	1	1968	1	PCDHB16	5	140564100	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	28435957	140564100	40351160	29	6728										
PCDHB13	56123	broad.mit.edu	37	chr5	140595300	140595300	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttccgcgtgggcgcttcagaCcacggctccccggcgctgag	14	16	1	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:140595300C>G	ENST00000341948.4	+	1	1792	c.1605C>G	c.(1603-1605)gaC>gaG	p.D535E		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	535	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D535E(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGCTTCAGACCACGGCTCCC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	5											52	59	57					5																	140595300		2203	4300	6503	140575484	SO:0001583	missense	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1605C>G	5.37:g.140595300C>G	ENSP00000345491:p.Asp535Glu		140575484	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	N	15.74	2.923741	0.52653	.	.	ENSG00000187372	ENST00000341948;ENST00000430318	T	0.80304	-1.36	3.42	2.17	0.27698	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.89466	0.6723	M	0.91196	3.185	0.23704	N	0.997062	D	0.89917	1.0	D	0.81914	0.995	T	0.77270	-0.2650	9	0.87932	D	0	.	5.478	0.16706	0.0:0.6053:0.0:0.3947	.	535	Q9Y5F0	PCDBD_HUMAN	E	535	ENSP00000345491:D535E	ENSP00000345491:D535E	D	+	3	2	PCDHB13	140575484	0.010000	0.17322	0.037000	0.18230	0.002000	0.02628	0.230000	0.17852	1.644000	0.50603	0.449000	0.29647	GAC		0.677	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		G	140595300	C	G	140595300	3	3	49	1	0	0	0	0	1	0	0	0	11569	506	18	5	1607	5	PCDHB13	5	140595300	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	31200	140595300	40319960	30	6729										
PCDHGB7	56099	broad.mit.edu	37	chr5	140798415	140798415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccgaggatctctctcaacacGgtgtaaagtaattgtagaag	10	8	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:140798415G>A	ENST00000398594.2	+	1	989	c.989G>A	c.(988-990)cGg>cAg	p.R330Q	PCDHGA7_ENST00000518325.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	330	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R330Q(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTCAACACGGTGTAAAGTA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											75	71	72					5																	140798415		1880	4105	5985	140778599	SO:0001583	missense	56099			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.989G>A	5.37:g.140798415G>A	ENSP00000381594:p.Arg330Gln		140778599	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	6.226	0.409788	0.11812	.	.	ENSG00000254122	ENST00000398594	T	0.52295	0.67	5.7	2.07	0.26955	Cadherin (4);Cadherin-like (1);	0.957125	0.08379	N	0.954798	T	0.20536	0.0494	N	0.01668	-0.77	0.20563	N	0.999884	B;B	0.11235	0.004;0.002	B;B	0.08055	0.003;0.002	T	0.24548	-1.0157	10	0.20046	T	0.44	.	8.9543	0.35807	0.7812:0.0:0.2188:0.0	.	330;330	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	Q	330	ENSP00000381594:R330Q	ENSP00000381594:R330Q	R	+	2	0	PCDHGB7	140778599	0.001000	0.12720	0.993000	0.49108	0.387000	0.30353	1.094000	0.30951	0.125000	0.18397	-0.367000	0.07326	CGG		0.403	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		A	140798415	G	A	140798415	3	1	49	1	0	0	0	0	1	0	0	0	11599	1116	39	1	991	1	PCDHGB7	5	140798415	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	203115	140798415	40116845	31	6730										
ITK	3702	broad.mit.edu	37	chr5	156649874	156649874	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgttgtctctcttccccagcGaccactttgggaacctgaag	9	13	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:156649874G>A	ENST00000422843.3	+	6	649	c.497G>A	c.(496-498)cGa>cAa	p.R166Q	CTB-4E7.1_ENST00000519375.1_RNA	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	166					activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R166Q(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	CTTCCCCAGCGACCACTTTGG	0.493			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	1	Substitution - Missense(1)	large_intestine(1)	5											83	80	81					5																	156649874		2203	4300	6503	156582452	SO:0001630	splice_region_variant	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.496-1G>A	5.37:g.156649874G>A			156582452	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.503528	0.26949	.	.	ENSG00000113263	ENST00000521769;ENST00000422843	D;T	0.89617	-2.54;-0.9	5.81	4.03	0.46877	.	0.434100	0.23014	N	0.052940	D	0.82838	0.5124	L	0.52573	1.65	0.35863	D	0.827628	B	0.21905	0.062	B	0.12156	0.007	T	0.79364	-0.1834	10	0.25751	T	0.34	.	7.2212	0.25988	0.243:0.0:0.757:0.0	.	166	Q08881	ITK_HUMAN	Q	41;166	ENSP00000430327:R41Q;ENSP00000398655:R166Q	ENSP00000398655:R166Q	R	+	2	0	ITK	156582452	0.166000	0.22962	0.952000	0.39060	0.120000	0.20174	0.904000	0.28491	1.463000	0.47967	0.591000	0.81541	CGA		0.493	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2		Missense_Mutation	A	156649874	G	A	156649874	5	1	49	1	0	0	0	0	0	0	1	0	7930	1072	37	1	519	1	ITK	5	156649874	Splice_Site	SNP	G	TCGA-AG-3894-01A-01W-1073-09	15851459	156649874	24265386	32	6731										
FGF18	8817	broad.mit.edu	37	chr5	170863255	170863255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggccgcaggatcagtgcccgCggcgaggatggggacaagta	18	10	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr5:170863255C>T	ENST00000274625.5	+	3	772	c.228C>T	c.(226-228)cgC>cgT	p.R76R		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	76					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)	p.R76R(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCAGTGCCCGCGGCGAGGATG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5											76	70	72					5																	170863255		2202	4300	6502	170795860	SO:0001819	synonymous_variant	8817			AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.228C>T	5.37:g.170863255C>T			170795860	D3DQL7|Q6UWF1	Silent	SNP	ENST00000274625.5	37	CCDS4378.1																																																																																				0.592	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252857.2	NM_033649, NM_003862		T	170863255	C	T	170863255	2	4	49	1	0	0	0	0	0	0	0	1	5865	755	27	1		1	FGF18	5	170863255	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	14213381	170863255	10052005	33	6732										
UHRF1BP1	54887	broad.mit.edu	37	chr6	34824039	34824039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atagctgcaaacattgggtaCgccactgtgaggccatggag	13	9	0	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr6:34824039C>T	ENST00000192788.5	+	10	1315	c.1144C>T	c.(1144-1146)Cgc>Tgc	p.R382C	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.R382C	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	382							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.R382C(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						ACATTGGGTACGCCACTGTGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											129	136	134					6																	34824039		2050	4199	6249	34932017	SO:0001583	missense	54887			AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1144C>T	6.37:g.34824039C>T	ENSP00000192788:p.Arg382Cys		34932017	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901144	0.52227	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.09630	2.96;2.96	5.67	2.65	0.31530	.	0.127712	0.50627	D	0.000112	T	0.14830	0.0358	L	0.42245	1.32	0.58432	D	0.999998	D	0.89917	1.0	D	0.80764	0.994	T	0.01608	-1.1313	10	0.59425	D	0.04	-11.9209	14.4575	0.67425	0.4605:0.5395:0.0:0.0	.	382	Q6BDS2	URFB1_HUMAN	C	382	ENSP00000192788:R382C;ENSP00000400628:R382C	ENSP00000192788:R382C	R	+	1	0	UHRF1BP1	34932017	0.972000	0.33761	0.334000	0.25495	0.970000	0.65996	2.162000	0.42367	0.797000	0.33971	0.655000	0.94253	CGC		0.473	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		T	34824039	C	T	34824039	3	4	49	1	0	0	0	0	1	0	0	0	17008	536	19	1	1182	1	UHRF1BP1	6	34824039	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		34824039	136291028	34	6733										
COL12A1	1303	broad.mit.edu	37	chr6	75887464	75887464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gatacttcatatttcgtgtcTggaatcaagttctccagtgt	8	8	4	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr6:75887464T>C	ENST00000322507.8	-	12	2661	c.2352A>G	c.(2350-2352)ccA>ccG	p.P784P	COL12A1_ENST00000416123.2_Silent_p.P784P|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Silent_p.P784P	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	784	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.P784P(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATTTCGTGTCTGGAATCAAGT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6											288	281	283					6																	75887464		1874	4100	5974	75944184	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2352A>G	6.37:g.75887464T>C			75944184	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.423	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75887464	T	C	75887464	2	2	49	1	0	0	0	0	0	0	0	1	3675	1567	55	4		4	COL12A1	6	75887464	Silent	SNP	T	TCGA-AG-3894-01A-01W-1073-09	41063425	75887464	95227603	35	6734										
C6orf204	387119	broad.mit.edu	37	chr6	118803034	118803034	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgctttttgatctcttcaagTtttttttctgtatctatcaa	4	7	5	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr6:118803034T>A	ENST00000368491.3	-	8	2274	c.1653A>T	c.(1651-1653)aaA>aaT	p.K551N	CEP85L_ENST00000368488.5_Missense_Mutation_p.K554N	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	551						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.K551N(1)									TCTCTTCAAGTTTTTTTTCTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	72	76					6																	118803034		1792	4058	5850	118909727	SO:0001583	missense	387119			AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1653A>T	6.37:g.118803034T>A	ENSP00000357477:p.Lys551Asn		118909727	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	.	.	.	.	.	.	.	.	.	.	T	4.466	0.086359	0.08583	.	.	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604	T;T;T	0.11821	2.74;2.74;2.74	5.24	-1.29	0.09288	.	0.434840	0.26013	N	0.026874	T	0.02571	0.0078	L	0.50333	1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.42899	-0.9424	10	0.23302	T	0.38	-1.323	1.6485	0.02766	0.1692:0.4201:0.2061:0.2046	.	554;551	F8W6J2;Q5SZL2	.;CF204_HUMAN	N	551;554;554	ENSP00000357477:K551N;ENSP00000357474:K554N;ENSP00000392131:K554N	ENSP00000357474:K554N	K	-	3	2	C6orf204	118909727	0.030000	0.19436	0.676000	0.29932	0.507000	0.33981	-1.040000	0.03546	-0.225000	0.09913	-0.366000	0.07423	AAA		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		A	118803034	T	A	118803034	3	1	49	1	0	0	0	0	1	0	0	0	2359	1722	60	5	788	5	C6orf204	6	118803034	Missense_Mutation	SNP	T	TCGA-AG-3894-01A-01W-1073-09	42915570	118803034	52312033	36	6735										
VNN1	8876	broad.mit.edu	37	chr6	133014198	133014198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggggtaatgtatgttggatGcaaggaaattgaccctcatg	13	5	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr6:133014198G>T	ENST00000367928.4	-	4	804	c.791C>A	c.(790-792)gCa>gAa	p.A264E		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	264	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)	p.A264E(1)		NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TATGTTGGATGCAAGGAAATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	104	109					6																	133014198		2203	4300	6503	133055891	SO:0001583	missense	8876			AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.791C>A	6.37:g.133014198G>T	ENSP00000356905:p.Ala264Glu		133055891	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846418	0.71603	.	.	ENSG00000112299	ENST00000367928	D	0.87571	-2.27	6.07	5.03	0.67393	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.068718	0.64402	D	0.000012	D	0.94178	0.8132	H	0.95043	3.615	0.45979	D	0.998796	D	0.64830	0.994	P	0.59288	0.855	D	0.95115	0.8241	10	0.87932	D	0	-13.3355	16.2658	0.82579	0.073:0.0:0.927:0.0	.	264	O95497	VNN1_HUMAN	E	264	ENSP00000356905:A264E	ENSP00000356905:A264E	A	-	2	0	VNN1	133055891	0.560000	0.26570	0.981000	0.43875	0.801000	0.45260	4.153000	0.58118	2.884000	0.98904	0.655000	0.94253	GCA		0.388	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			T	133014198	G	T	133014198	3	4	49	1	0	0	0	0	1	0	0	0	17222	1319	46	2	766	2	VNN1	6	133014198	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	14211164	133014198	38100869	37	6736										
SYNE1	23345	broad.mit.edu	37	chr6	152523014	152523014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ggtgatccgggagagactgcGaaagcttctttttgaaagtt	13	6	1	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr6:152523014G>A	ENST00000367255.5	-	127	23691	c.23090C>T	c.(23089-23091)tCg>tTg	p.S7697L	SYNE1_ENST00000356820.4_Missense_Mutation_p.S2221L|SYNE1_ENST00000341594.5_Missense_Mutation_p.S7309L|SYNE1_ENST00000265368.4_Missense_Mutation_p.S7697L|SYNE1_ENST00000448038.1_Missense_Mutation_p.S7626L|SYNE1_ENST00000423061.1_Missense_Mutation_p.S7626L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7697					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S7697L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGAGACTGCGAAAGCTTCTT	0.428										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											102	108	106					6																	152523014		2203	4300	6503	152564707	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23090C>T	6.37:g.152523014G>A	ENSP00000356224:p.Ser7697Leu		152564707	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167508	0.78339	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29	6.08	6.08	0.98989	.	0.206543	0.34507	N	0.003905	T	0.55130	0.1901	M	0.78223	2.4	0.58432	D	0.999999	D;D;D;D	0.71674	0.994;0.994;0.998;0.997	P;P;P;P	0.60012	0.74;0.74;0.867;0.74	T	0.57452	-0.7809	10	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	7697;7697;7626;7626	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	L	7697;343;7626;7697;7626;7309;2221;619	ENSP00000356224:S7697L;ENSP00000356226:S343L;ENSP00000396024:S7626L;ENSP00000265368:S7697L;ENSP00000390975:S7626L;ENSP00000341887:S7309L;ENSP00000349276:S2221L;ENSP00000356220:S619L	ENSP00000265368:S7697L	S	-	2	0	SYNE1	152564707	1.000000	0.71417	0.909000	0.35828	0.423000	0.31445	6.753000	0.74904	2.894000	0.99253	0.591000	0.81541	TCG		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152523014	G	A	152523014	3	1	49	1	0	0	0	0	1	0	0	0	15484	1059	37	1	3456	1	SYNE1	6	152523014	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	19508816	152523014	18592053	38	6737										
NEUROD6	63974	broad.mit.edu	37	chr7	31377932	31377932	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gattggctgcgcagatgtaaGtcgtaagggaagtggctgtc	16	6	0	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:31377932G>C	ENST00000297142.3	-	2	1273	c.951C>G	c.(949-951)gaC>gaG	p.D317E		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	317					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.D317E(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GCAGATGTAAGTCGTAAGGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											82	80	81					7																	31377932		2203	4300	6503	31344457	SO:0001583	missense	63974			AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.951C>G	7.37:g.31377932G>C	ENSP00000297142:p.Asp317Glu		31344457	Q548T9|Q9H3H6	Missense_Mutation	SNP	ENST00000297142.3	37	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461642	0.43736	.	.	ENSG00000164600	ENST00000297142	D	0.96774	-4.12	5.13	4.23	0.50019	.	0.000000	0.85682	D	0.000000	D	0.93141	0.7816	L	0.46157	1.445	0.53688	D	0.999974	B	0.11235	0.004	B	0.10450	0.005	D	0.89208	0.3562	10	0.36615	T	0.2	-15.0027	9.9129	0.41417	0.0757:0.1407:0.7836:0.0	.	317	Q96NK8	NDF6_HUMAN	E	317	ENSP00000297142:D317E	ENSP00000297142:D317E	D	-	3	2	NEUROD6	31344457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.836000	0.55813	1.117000	0.41842	0.650000	0.86243	GAC		0.463	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		C	31377932	G	C	31377932	3	2	49	1	0	0	0	0	1	0	0	0	10382	1020	36	5	66	5	NEUROD6	7	31377932	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09		31377932	127760731	39	6738										
WBSCR17	64409	broad.mit.edu	37	chr7	70800614	70800614	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tccggctactctttccccggCtgaagaagaaaaggctaagg	11	11	1	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:70800614C>G	ENST00000333538.5	+	2	951	c.317C>G	c.(316-318)gCt>gGt	p.A106G	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	106					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A106G(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CTTTCCCCGGCTGAAGAAGAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											45	49	48					7																	70800614		2203	4300	6503	70438550	SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.317C>G	7.37:g.70800614C>G	ENSP00000329654:p.Ala106Gly		70438550	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	6.920	0.539400	0.13250	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.55413	0.52;1.88	4.89	3.03	0.35002	.	0.357352	0.14576	U	0.311156	T	0.33381	0.0861	N	0.17872	0.535	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17137	-1.0379	10	0.33940	T	0.23	.	6.2244	0.20700	0.4635:0.4469:0.0:0.0896	.	106	Q6IS24	GLTL3_HUMAN	G	106;84	ENSP00000329654:A106G;ENSP00000392019:A84G	ENSP00000329654:A106G	A	+	2	0	WBSCR17	70438550	0.067000	0.21026	0.022000	0.16811	0.381000	0.30169	0.638000	0.24674	0.606000	0.29965	0.491000	0.48974	GCT		0.483	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		G	70800614	C	G	70800614	3	3	49	1	0	0	0	0	1	0	0	0	17304	797	28	5	323	5	WBSCR17	7	70800614	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	39422682	70800614	88338049	40	6739										
PEX1	5189	broad.mit.edu	37	chr7	92147524	92147524	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ggcttttggaaaaactattcGaatttgatctagaagatgtt	9	4	1	3	rs201415996		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:92147524G>A	ENST00000248633.4	-	4	498	c.403C>T	c.(403-405)Cga>Tga	p.R135*	PEX1_ENST00000541751.1_5'Flank|PEX1_ENST00000428214.1_Nonsense_Mutation_p.R135*|PEX1_ENST00000438045.1_Intron	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	135					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R135*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	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)			AAAACTATTCGAATTTGATCT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											100	98	99					7																	92147524		2203	4300	6503	91985460	SO:0001587	stop_gained	5189			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.403C>T	7.37:g.92147524G>A	ENSP00000248633:p.Arg135*		91985460	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Nonsense_Mutation	SNP	ENST00000248633.4	37	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	G	37	6.325113	0.97476	.	.	ENSG00000127980	ENST00000248633;ENST00000428214;ENST00000545192	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3009	20.3397	0.98756	0.0:0.0:1.0:0.0	.	.	.	.	X	135	.	ENSP00000248633:R135X	R	-	1	2	PEX1	91985460	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.725000	0.54970	2.803000	0.96430	0.585000	0.79938	CGA		0.353	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		A	92147524	G	A	92147524	4	1	49	1	0	0	0	0	0	1	0	0	11766	1066	37	1	3532	1	PEX1	7	92147524	Nonsense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	21346910	92147524	66991139	41	6740										
SAMD9L	219285	broad.mit.edu	37	chr7	92761965	92761965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgctttcattttggcctgaCgtgcccagtccagagctgtg	12	11	1	2	rs369116471		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:92761965C>T	ENST00000318238.4	-	5	4536	c.3320G>A	c.(3319-3321)cGt>cAt	p.R1107H	SAMD9L_ENST00000437805.1_Missense_Mutation_p.R1107H|SAMD9L_ENST00000411955.1_Missense_Mutation_p.R1107H	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1107					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.R1107H(2)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTGGCCTGACGTGCCCAGTC	0.393																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	119	120	120		3320	1.2	0	7		120	0,8598		0,0,4299	no	missense	SAMD9L	NM_152703.2	29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	1107/1585	92761965	1,13003	2203	4299	6502	92599901	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.3320G>A	7.37:g.92761965C>T	ENSP00000326247:p.Arg1107His		92599901	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	C	4.282	0.051557	0.08291	2.27E-4	0.0	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.22539	1.95;1.95;1.95	5.02	1.16	0.20824	.	1.398570	0.04865	N	0.444851	T	0.10423	0.0255	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.29427	-1.0012	10	0.44086	T	0.13	-0.9941	1.8039	0.03076	0.1346:0.1566:0.1398:0.569	.	1107	Q8IVG5	SAM9L_HUMAN	H	1107	ENSP00000326247:R1107H;ENSP00000405760:R1107H;ENSP00000408796:R1107H	ENSP00000326247:R1107H	R	-	2	0	SAMD9L	92599901	0.000000	0.05858	0.005000	0.12908	0.118000	0.20060	0.265000	0.18515	0.037000	0.15575	-0.373000	0.07131	CGT		0.393	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		T	92761965	C	T	92761965	3	4	49	1	0	0	0	0	1	0	0	0	13864	536	19	1	1438	1	SAMD9L	7	92761965	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	614441	92761965	66376698	42	6741										
ZNF3	7551	broad.mit.edu	37	chr7	99673177	99673177	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagctcacctgggacttggcCtttaggagcgcagccgccaa	12	14	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:99673177C>G	ENST00000424697.1	-	4	438	c.132G>C	c.(130-132)aaG>aaC	p.K44N	ZNF3_ENST00000413658.2_Missense_Mutation_p.K44N|ZNF3_ENST00000303915.6_Missense_Mutation_p.K44N|ZNF3_ENST00000299667.4_Missense_Mutation_p.K44N	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	44					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.K44N(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			GGGACTTGGCCTTTAGGAGCG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											73	80	77					7																	99673177		2040	4195	6235	99511113	SO:0001583	missense	7551			AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.132G>C	7.37:g.99673177C>G	ENSP00000415358:p.Lys44Asn		99511113	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	37	CCDS43619.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.218940	0.58560	.	.	ENSG00000166526	ENST00000413658;ENST00000424697;ENST00000303915;ENST00000299667;ENST00000412947;ENST00000449785;ENST00000428683;ENST00000441298;ENST00000415068;ENST00000292393	T;T;T;T;T;T;T;T;T	0.06449	4.75;3.3;3.3;3.3;5.17;5.31;5.31;5.05;5.0	4.63	1.6	0.23607	Krueppel-associated box (1);	0.000000	0.42294	D	0.000740	T	0.13157	0.0319	L	0.43152	1.355	0.25354	N	0.988848	D;P	0.71674	0.998;0.939	D;P	0.76071	0.987;0.514	T	0.02925	-1.1093	10	0.87932	D	0	-17.7308	5.6783	0.17761	0.0:0.6469:0.0:0.3531	.	44;44	P17036;P17036-2	ZNF3_HUMAN;.	N	44;44;44;44;8;44;44;8;44;8	ENSP00000399951:K44N;ENSP00000415358:K44N;ENSP00000306372:K44N;ENSP00000299667:K44N;ENSP00000416088:K8N;ENSP00000405970:K44N;ENSP00000388042:K44N;ENSP00000394113:K8N;ENSP00000416686:K44N	ENSP00000292393:K8N	K	-	3	2	ZNF3	99511113	0.718000	0.27976	1.000000	0.80357	0.998000	0.95712	0.178000	0.16820	0.586000	0.29626	0.650000	0.86243	AAG		0.507	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		G	99673177	C	G	99673177	3	3	49	1	0	0	0	0	1	0	0	0	17868	680	24	5	1349	5	ZNF3	7	99673177	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	6911212	99673177	59465486	43	6742										
LRCH4	4034	broad.mit.edu	37	chr7	100176019	100176020	+	Intron	INS	-	-	A													0	0	1	0	0	0	1	1	0	ttcctccccacctaggacttINSaccagggactgaaactcggg							TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:100176019_100176020insA	ENST00000310300.6	-	6	901				LRCH4_ENST00000497245.1_Intron	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4						nervous system development (GO:0007399)	PML body (GO:0016605)		p.?(1)		NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACCTAGGACTTACCAGGGACTG	0.634																																																1	Unknown(1)	large_intestine(1)	7																																								100013956	SO:0001627	intron_variant	4034			AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.848+1->T	7.37:g.100176020_100176020dupA			100013955	A4D2D5|Q8WV85|Q96ID0	Splice_Site	INS	ENST00000310300.6	37	CCDS34706.1																																																																																				0.634	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319		A	100176020	-	A	100176019	6	5	49	0	1	1	1	0	0	0	0	0	8964	1769	61	0		0	LRCH4	7	100176019	Intron	INS	-	TCGA-AG-3894-01A-01W-1073-09	502842	100176019	58962644	44	6743										
MUC17	140453	broad.mit.edu	37	chr7	100677009	100677009	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tagcaccctttcaacaactcCtcttgacacaagcacacata	3	15	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:100677009C>G	ENST00000306151.4	+	3	2376	c.2312C>G	c.(2311-2313)cCt>cGt	p.P771R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	771	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.P771R(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAACAACTCCTCTTGACACA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											282	285	284					7																	100677009		2203	4300	6503	100463729	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2312C>G	7.37:g.100677009C>G	ENSP00000302716:p.Pro771Arg		100463729	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	1.547	-0.540294	0.04053	.	.	ENSG00000169876	ENST00000306151	T	0.03272	3.99	0.932	-0.342	0.12635	.	.	.	.	.	T	0.01835	0.0058	N	0.24115	0.695	0.09310	N	1	P	0.42993	0.797	B	0.31191	0.125	T	0.48927	-0.8991	9	0.17369	T	0.5	.	5.5733	0.17208	0.3215:0.6785:0.0:0.0	.	771	Q685J3	MUC17_HUMAN	R	771	ENSP00000302716:P771R	ENSP00000302716:P771R	P	+	2	0	MUC17	100463729	0.001000	0.12720	0.000000	0.03702	0.024000	0.10985	1.023000	0.30065	-0.073000	0.12842	0.134000	0.15878	CCT		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100677009	C	G	100677009	3	3	49	1	0	0	0	0	1	0	0	0	10004	681	24	5	2322	5	MUC17	7	100677009	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	500990	100677009	58461654	45	6744										
DUS4L	11062	broad.mit.edu	37	chr7	107215731	107215731	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	aaatcaagtggaaacccctgGattttcagtttctattaaaa	6	7	3	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:107215731G>C	ENST00000265720.3	+	6	817	c.455G>C	c.(454-456)gGa>gCa	p.G152A	DUS4L_ENST00000402620.1_Missense_Mutation_p.G31A	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	152							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)	p.G152A(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						GAAACCCCTGGATTTTCAGTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											76	85	82					7																	107215731		2202	4300	6502	107002967	SO:0001583	missense	11062			U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.455G>C	7.37:g.107215731G>C	ENSP00000265720:p.Gly152Ala		107002967	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	37	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	G	1.893	-0.454953	0.04540	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.32023	1.5;1.47	5.63	3.7	0.42460	Aldolase-type TIM barrel (1);	0.469692	0.26677	N	0.023067	T	0.21801	0.0525	L	0.51914	1.62	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.19946	0.027;0.027	T	0.20840	-1.0263	10	0.10111	T	0.7	.	5.6645	0.17687	0.1177:0.1252:0.6284:0.1287	.	152;152	A4D0R5;O95620	.;DUS4L_HUMAN	A	152;31	ENSP00000265720:G152A;ENSP00000385274:G31A	ENSP00000265720:G152A	G	+	2	0	DUS4L	107002967	0.990000	0.36364	0.993000	0.49108	0.344000	0.29017	2.135000	0.42112	2.805000	0.96524	0.655000	0.94253	GGA		0.353	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		C	107215731	G	C	107215731	3	2	49	1	0	0	0	0	1	0	0	0	4819	1174	41	5	469	5	DUS4L	7	107215731	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	6538722	107215731	51922932	46	6745										
SLC26A4	5172	broad.mit.edu	37	chr7	107314664	107314664	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttgttctgagcatggccccCgacgaacactttctcgtatc	9	13	2	1	rs557892300		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:107314664C>T	ENST00000265715.3	+	5	695	c.471C>T	c.(469-471)ccC>ccT	p.P157P		NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	157					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.P157P(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GCATGGCCCCCGACGAACACT	0.423									Pendred syndrome				C|||	1	0.000199681	0	0	5008	,	,		14887	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	7											154	145	148					7																	107314664		2203	4300	6503	107101900	SO:0001819	synonymous_variant	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.471C>T	7.37:g.107314664C>T			107101900	B7Z266|O43170	Silent	SNP	ENST00000265715.3	37	CCDS5746.1																																																																																				0.423	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		T	107314664	C	T	107314664	2	4	49	1	0	0	0	0	0	0	0	1	14556	639	23	1		1	SLC26A4	7	107314664	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	98933	107314664	51823999	47	6746										
GPR37	2861	broad.mit.edu	37	chr7	124404372	124404372	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cacccaaggatccattctggGccagcgcccggcccgggagt	13	16	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:124404372G>C	ENST00000303921.2	-	1	1309	c.659C>G	c.(658-660)gCc>gGc	p.A220G		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	220					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)	p.A220G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TCCATTCTGGGCCAGCGCCCG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	7											36	40	39					7																	124404372		2203	4300	6503	124191608	SO:0001583	missense	2861				CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.659C>G	7.37:g.124404372G>C	ENSP00000306449:p.Ala220Gly		124191608	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	37	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.238792	0.39598	.	.	ENSG00000170775	ENST00000303921	T	0.72051	-0.62	5.49	5.49	0.81192	.	0.117763	0.56097	D	0.000022	T	0.55768	0.1941	N	0.22421	0.69	0.25417	N	0.988303	B	0.06786	0.001	B	0.06405	0.002	T	0.30060	-0.9991	10	0.16420	T	0.52	-14.4855	14.8127	0.70008	0.0:0.0:1.0:0.0	.	220	O15354	GPR37_HUMAN	G	220	ENSP00000306449:A220G	ENSP00000306449:A220G	A	-	2	0	GPR37	124191608	0.798000	0.28890	1.000000	0.80357	0.904000	0.53231	1.606000	0.36826	2.872000	0.98467	0.638000	0.83543	GCC		0.642	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		C	124404372	G	C	124404372	3	2	49	1	0	0	0	0	1	0	0	0	6711	1203	42	5	1190	5	GPR37	7	124404372	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	17089708	124404372	34734291	48	6747										
PLXNA4	91584	broad.mit.edu	37	chr7	131853173	131853173	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tccagcttgctctgcagcacGgtcatgatgagtgaggccac	12	12	2	3	rs369419660		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:131853173G>A	ENST00000359827.3	-	22	5138	c.4176C>T	c.(4174-4176)acC>acT	p.T1392T	PLXNA4_ENST00000321063.4_Silent_p.T1392T			Q9HCM2	PLXA4_HUMAN	plexin A4	1392					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.T1392T(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TCTGCAGCACGGTCATGATGA	0.572																																																2	Substitution - coding silent(2)	large_intestine(2)	7						G		5,4401	9.9+/-24.2	0,5,2198	91	90	90		4176	-11	0.4	7		90	0,8600		0,0,4300	no	coding-synonymous	PLXNA4	NM_020911.1		0,5,6498	AA,AG,GG		0.0,0.1135,0.0384		1392/1895	131853173	5,13001	2203	4300	6503	131503713	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4176C>T	7.37:g.131853173G>A			131503713	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.572	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131853173	G	A	131853173	2	1	49	1	0	0	0	0	0	0	0	1	12153	1103	39	1		1	PLXNA4	7	131853173	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	7448801	131853173	27285490	49	6748										
TAS2R3	50831	broad.mit.edu	37	chr7	141464109	141464109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgacttcatcatcaccaccCtggcactcttgaggatcatt	6	14	5	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:141464109C>T	ENST00000247879.2	+	1	213	c.151C>T	c.(151-153)Ctg>Ttg	p.L51L	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	51					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.L51L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					CATCACCACCCTGGCACTCTT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	7											252	243	246					7																	141464109		2203	4300	6503	141110578	SO:0001819	synonymous_variant	50831			AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.151C>T	7.37:g.141464109C>T			141110578	A4D1U2|Q645W2|Q75MV6	Silent	SNP	ENST00000247879.2	37	CCDS5867.1																																																																																				0.398	TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1			T	141464109	C	T	141464109	2	4	49	1	0	0	0	0	0	0	0	1	15611	680	24	3		3	TAS2R3	7	141464109	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	9610936	141464109	17674554	50	6749										
ABCF2	10061	broad.mit.edu	37	chr7	150921944	150921944	+	Frame_Shift_Del	DEL	A	A	-													0	0	1	0	0	0	1	1	0	ctgagcagctcttgaccatgAaaggtaagtgagaggttgat							TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr7:150921944delA	ENST00000287844.2	-	3	394	c.285delT	c.(283-285)tttfs	p.F95fs	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Frame_Shift_Del_p.F95fs	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	95	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)	p.H96fs*13(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTTGACCATGAAAGGTAAGTG	0.493																																																1	Deletion - Frameshift(1)	large_intestine(1)	7											122	108	113					7																	150921944		2203	4300	6503	150552877	SO:0001589	frameshift_variant	10061			AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.285delT	7.37:g.150921944delA	ENSP00000287844:p.Phe95fs		150552877	O60864|Q75MJ0|Q75MJ1|Q96TE8	Frame_Shift_Del	DEL	ENST00000287844.2	37	CCDS5923.1																																																																																				0.493	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		-	150921944	A	-	150921944	7	5	49	1	0	1	0	1	0	0	0	0	66	243	9	0	1679	0	ABCF2	7	150921944	Frame_Shift_Del	DEL	A	TCGA-AG-3894-01A-01W-1073-09	9457835	150921944	8216719	51	6750										
LOXL2	4017	broad.mit.edu	37	chr8	23179790	23179790	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tcgttgaggtggatgggtccGatccctgcaaggggagaata	16	7	0	2	rs199848147		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr8:23179790G>A	ENST00000389131.3	-	7	1524	c.1155C>T	c.(1153-1155)atC>atT	p.I385I		NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	385	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)	p.I385I(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		GGATGGGTCCGATCCCTGCAA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	8											111	84	93					8																	23179790		2203	4300	6503	23235735	SO:0001819	synonymous_variant	4017			U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.1155C>T	8.37:g.23179790G>A			23235735	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	G	1.534	-0.543577	0.04053	.	.	ENSG00000134013	ENST00000520349	.	.	.	5.49	-11.0	0.00169	.	.	.	.	.	T	0.33789	0.0875	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42189	-0.9466	4	.	.	.	.	3.3297	0.07080	0.2404:0.372:0.2775:0.1102	.	.	.	.	L	102	.	.	S	-	2	0	LOXL2	23235735	0.863000	0.29885	0.384000	0.26145	0.223000	0.24884	0.005000	0.13129	-2.503000	0.00509	-3.090000	0.00065	TCG		0.502	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			A	23179790	G	A	23179790	2	1	49	1	0	0	0	0	0	0	0	1	8929	1048	37	1		1	LOXL2	8	23179790	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09		23179790	123184232	52	6751										
HOOK3	84376	broad.mit.edu	37	chr8	42761359	42761359	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accatgccagaccgtggaagAtttaacgaatggggttgtga	13	7	0	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr8:42761359A>C	ENST00000307602.4	+	2	301	c.101A>C	c.(100-102)gAt>gCt	p.D34A		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	34	Sufficient for interaction with microtubules.				cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.D34A(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			ACCGTGGAAGATTTAACGAAT	0.408			T	RET	papillary thyroid																																		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - Missense(1)	large_intestine(1)	8											132	134	133					8																	42761359		2203	4300	6503	42880516	SO:0001583	missense	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.101A>C	8.37:g.42761359A>C	ENSP00000305699:p.Asp34Ala		42880516	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	37	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485590	0.84854	.	.	ENSG00000168172	ENST00000307602	T	0.52526	0.66	5.44	5.44	0.79542	.	0.207230	0.49305	D	0.000147	T	0.66046	0.2750	M	0.70595	2.14	0.50813	D	0.999895	D;D	0.67145	0.996;0.986	D;D	0.74023	0.982;0.914	T	0.67381	-0.5685	10	0.48119	T	0.1	-20.2464	13.2929	0.60280	1.0:0.0:0.0:0.0	.	34;34	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	A	34	ENSP00000305699:D34A	ENSP00000305699:D34A	D	+	2	0	HOOK3	42880516	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.388000	0.79795	2.178000	0.69098	0.528000	0.53228	GAT		0.408	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		C	42761359	A	C	42761359	3	2	49	1	0	0	0	0	1	0	0	0	7305	333	12	4	107	4	HOOK3	8	42761359	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	19581569	42761359	103602663	53	6752										
ZFHX4	79776	broad.mit.edu	37	chr8	77764140	77764140	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttagcagctgtaaacagcaaAgatacccatttagatgccaa	7	9	0	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr8:77764140A>C	ENST00000521891.2	+	10	5431	c.4983A>C	c.(4981-4983)aaA>aaC	p.K1661N	ZFHX4_ENST00000518282.1_Missense_Mutation_p.K1635N|ZFHX4_ENST00000050961.6_Missense_Mutation_p.K1616N|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K1616N	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1616	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.K1661N(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TAAACAGCAAAGATACCCATT	0.458										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											87	85	86					8																	77764140		1930	4133	6063	77926695	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4983A>C	8.37:g.77764140A>C	ENSP00000430497:p.Lys1661Asn		77926695	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542992	0.27563	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51574	0.7;0.75;0.72;0.71	4.41	1.98	0.26296	.	0.000000	0.47455	U	0.000237	T	0.47507	0.1449	L	0.38531	1.155	0.58432	D	0.999997	D;D;D	0.58268	0.97;0.982;0.982	P;P;P	0.60345	0.683;0.832;0.873	T	0.27365	-1.0076	10	0.21540	T	0.41	.	8.1875	0.31348	0.7605:0.0:0.2395:0.0	.	1616;1616;1661	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	N	1661;1661;1616;1616;1635	ENSP00000430497:K1661N;ENSP00000399605:K1616N;ENSP00000050961:K1616N;ENSP00000430848:K1635N	ENSP00000050961:K1616N	K	+	3	2	ZFHX4	77926695	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.053000	0.57427	0.320000	0.23234	0.443000	0.29094	AAA		0.458	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77764140	A	C	77764140	3	2	49	1	0	0	0	0	1	0	0	0	17674	69	3	4	5017	4	ZFHX4	8	77764140	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	35002781	77764140	68599882	54	6753										
TSPYL5	85453	broad.mit.edu	37	chr8	98289688	98289688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcatttttcggccttcccaCggttcccgctgttcccacga	9	16	0	0	rs115912728	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr8:98289688C>T	ENST00000322128.3	-	1	488	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	129					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)		p.V129M(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					GGCCTTCCCACGGTTCCCGCT	0.711													C|||	3	0.000599042	0.0023	0	5008	,	,		12869	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	MET/VAL	2,4376		0,2,2187	15	18	17		385	0.8	0	8	dbSNP_132	17	0,8540		0,0,4270	no	missense	TSPYL5	NM_033512.2	21	0,2,6457	TT,TC,CC		0.0,0.0457,0.0155	possibly-damaging	129/418	98289688	2,12916	2189	4270	6459	98358864	SO:0001583	missense	85453			AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.385G>A	8.37:g.98289688C>T	ENSP00000322802:p.Val129Met		98358864	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	11.62	1.691822	0.30052	4.57E-4	0.0	ENSG00000180543	ENST00000322128	T	0.16073	2.37	3.73	0.748	0.18376	.	0.657622	0.11658	N	0.542173	T	0.05090	0.0136	N	0.22421	0.69	0.09310	N	1	P	0.35242	0.492	B	0.20384	0.029	T	0.27773	-1.0064	10	0.46703	T	0.11	-7.327	2.2944	0.04146	0.2041:0.5024:0.1825:0.1109	.	129	Q86VY4	TSYL5_HUMAN	M	129	ENSP00000322802:V129M	ENSP00000322802:V129M	V	-	1	0	TSPYL5	98358864	0.000000	0.05858	0.048000	0.18961	0.929000	0.56500	0.207000	0.17395	0.138000	0.18790	0.650000	0.86243	GTG		0.711	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		T	98289688	C	T	98289688	3	4	49	1	0	0	0	0	1	0	0	0	16702	536	19	1	872	1	TSPYL5	8	98289688	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	20525548	98289688	48074334	55	6754										
FAM49B	51571	broad.mit.edu	37	chr8	130883640	130883640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctctcgtatttcgtggccaGctcctctgtatgactgcaag	9	13	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr8:130883640G>T	ENST00000519824.2	-	4	449	c.176C>A	c.(175-177)gCt>gAt	p.A59D	SNORA25_ENST00000363205.1_RNA|FAM49B_ENST00000517654.1_Missense_Mutation_p.A59D|FAM49B_ENST00000523509.1_Missense_Mutation_p.A59D|FAM49B_ENST00000519540.1_Missense_Mutation_p.A59D|FAM49B_ENST00000519110.1_Missense_Mutation_p.A59D|FAM49B_ENST00000401979.2_Missense_Mutation_p.A59D|FAM49B_ENST00000522250.1_De_novo_Start_OutOfFrame|FAM49B_ENST00000518879.1_Intron|FAM49B_ENST00000522941.1_De_novo_Start_OutOfFrame|FAM49B_ENST00000522746.1_Missense_Mutation_p.A59D	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	59						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)		p.A59D(1)		kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TTCGTGGCCAGCTCCTCTGTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	110	111					8																	130883640		2203	4300	6503	130952822	SO:0001583	missense	51571			AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.176C>A	8.37:g.130883640G>T	ENSP00000429150:p.Ala59Asp		130952822	Q96AZ5|Q9NW21|Q9NZE7	De_novo_Start_OutOfFrame	SNP	ENST00000519824.2	37	CCDS6361.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.5|29.5	5.008367|5.008367	0.93346|0.93346	.|.	.|.	ENSG00000153310|ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142;ENST00000520204;ENST00000518283;ENST00000523993;ENST00000520254;ENST00000519020;ENST00000518167;ENST00000517672|ENST00000311292	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.55760|.	0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84620|0.84620	0.5512|0.5512	M|M	0.88377|0.88377	2.95|2.95	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.85938|0.85938	0.1456|0.1456	10|6	0.72032|0.54805	D|T	0.01|0.06	-9.5159|-9.5159	19.0946|19.0946	0.93244|0.93244	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	59|.	Q9NUQ9|.	FA49B_HUMAN|.	D|M	59|15	ENSP00000428117:A59D;ENSP00000429802:A59D;ENSP00000384880:A59D;ENSP00000429078:A59D;ENSP00000429150:A59D;ENSP00000430674:A59D;ENSP00000429499:A59D;ENSP00000430806:A59D;ENSP00000429051:A59D;ENSP00000430694:A59D;ENSP00000429074:A59D;ENSP00000430127:A59D;ENSP00000429659:A59D;ENSP00000427994:A59D;ENSP00000430434:A59D|.	ENSP00000384880:A59D|ENSP00000311651:L15M	A|L	-|-	2|1	0|2	FAM49B|FAM49B	130952822|130952822	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.476000|9.476000	0.97823|0.97823	2.745000|2.745000	0.94114|0.94114	0.650000|0.650000	0.86243|0.86243	GCT|CTG		0.408	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623		T	130883640	G	T	130883640	3	4	49	1	0	0	0	0	1	0	0	0	5595	971	34	2	834	2	FAM49B	8	130883640	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	32593952	130883640	15480382	56	6755										
CREB3	7094	broad.mit.edu	37	chr9	35732997	35732997	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttggaaccctgcgcaggtacCgagcgactgggaagtagatg	15	9	0	1	rs376045014		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr9:35732997C>G	ENST00000314888.9	-	0	0				TLN1_ENST00000540444.1_5'Flank|CREB3_ENST00000353704.2_Missense_Mutation_p.P45R|CREB3_ENST00000486056.1_3'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.P45R(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCGCAGGTACCGAGCGACTGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											160	167	165					9																	35732997		2203	4300	6503	35722997	SO:0001631	upstream_gene_variant	10488			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874		9.37:g.35732997C>G	Exception_encountered		35722997	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.838655	0.51057	.	.	ENSG00000107175	ENST00000353704	T	0.63580	-0.05	5.03	2.47	0.30058	.	0.538653	0.18456	N	0.140665	T	0.40670	0.1126	N	0.22421	0.69	0.28951	N	0.890412	P	0.37176	0.586	B	0.40134	0.32	T	0.34976	-0.9807	10	0.07175	T	0.84	-8.4347	4.4241	0.11495	0.1652:0.1105:0.0:0.7243	.	45	O43889-2	.	R	45	ENSP00000342136:P45R	ENSP00000342136:P45R	P	+	2	0	CREB3	35722997	0.918000	0.31147	0.367000	0.25926	0.401000	0.30781	1.313000	0.33585	0.280000	0.22209	0.585000	0.79938	CCG		0.557	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		G	35732997	C	G	35732997	1	3	49	0	1	0	0	0	0	0	0	0	3861	652	23	5		5	CREB3	9	35732997	5'Flank	SNP	C	TCGA-AG-3894-01A-01W-1073-09		35732997	105480434	57	6756										
DBH	1621	broad.mit.edu	37	chr9	136508566	136508566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgtcaccaagggcaatgaggCccttgtccaccacatggaag	11	13	1	1	rs201600007	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr9:136508566C>A	ENST00000393056.2	+	4	788	c.776C>A	c.(775-777)gCc>gAc	p.A259D		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	259					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)	p.A259D(1)		central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GGCAATGAGGCCCTTGTCCAC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	9											74	72	73					9																	136508566		2203	4300	6503	135498387	SO:0001583	missense	1621			X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.776C>A	9.37:g.136508566C>A	ENSP00000376776:p.Ala259Asp		135498387	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	.	.	.	.	.	.	.	.	.	.	C	12.83	2.055530	0.36277	.	.	ENSG00000123454	ENST00000393056;ENST00000371880;ENST00000263611	T;T	0.33438	1.41;1.41	5.04	4.13	0.48395	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	T	0.36166	0.0957	L	0.49699	1.58	0.58432	D	0.999996	B	0.33528	0.416	B	0.41666	0.363	T	0.18272	-1.0342	10	0.48119	T	0.1	-7.9464	14.6342	0.68678	0.0:0.8534:0.1466:0.0	.	259	P09172	DOPO_HUMAN	D	259;196;196	ENSP00000376776:A259D;ENSP00000263611:A196D	ENSP00000263611:A196D	A	+	2	0	DBH	135498387	0.998000	0.40836	0.997000	0.53966	0.018000	0.09664	3.583000	0.53928	1.099000	0.41499	-0.156000	0.13503	GCC		0.672	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787		A	136508566	C	A	136508566	3	1	49	1	0	0	0	0	1	0	0	0	4256	739	26	2	790	2	DBH	9	136508566	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	100775569	136508566	4704865	58	6757										
TUBB8	347688	broad.mit.edu	37	chr10	93397	93397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccctgaaaatggcagccgccGttaggtagcggccgtgacgg	15	12	0	2	rs559882106		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr10:93397G>A	ENST00000309812.4	-	4	997	c.935C>T	c.(934-936)aCg>aTg	p.T312M	TUBB8_ENST00000413237.3_5'Flank|TUBB8_ENST00000447903.2_Missense_Mutation_p.T240M	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	312					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.T312M(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GGCAGCCGCCGTTAGGTAGCG	0.537													g|||	1	0.000199681	0	0	5008	,	,		19635	0		0	False		,,,				2504	0.001				Pancreas(192;2041 3010 9013 18103)											1	Substitution - Missense(1)	large_intestine(1)	10											56	71	66					10																	93397		1843	3629	5472	83397	SO:0001583	missense	347688			AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"Tubulins"	20773	protein-coding gene	gene with protein product	"class VIII beta-tubulin"						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.935C>T	10.37:g.93397G>A	ENSP00000311042:p.Thr312Met		83397	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	G	9.714	1.157837	0.21454	.	.	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	D	0.85171	-1.95	.	.	.	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.180284	0.33327	U	0.005023	D	0.91546	0.7330	H	0.97659	4.05	0.36099	D	0.843982	B;D	0.76494	0.3;0.999	B;P	0.54372	0.018;0.75	D	0.90420	0.4416	9	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	275;312	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	M	240;278;275;312	ENSP00000403895:T240M	ENSP00000272035:T278M	T	-	2	0	RP11-631M21.2	83397	1.000000	0.71417	0.016000	0.15963	0.016000	0.09150	6.635000	0.74295	0.119000	0.18210	0.121000	0.15741	ACG		0.537	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		A	93397	G	A	93397	3	1	49	1	0	0	0	0	1	0	0	0	16801	1145	40	1	403	1	TUBB8	10	93397	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09		93397	135441350	59	6758										
ATRNL1	26033	broad.mit.edu	37	chr10	117226742	117226742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caactttaatctcaacattaCgtggtctgtcggttcaacag	7	10	3	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr10:117226742C>T	ENST00000355044.3	+	23	3602	c.3476C>T	c.(3475-3477)aCg>aTg	p.T1159M	ATRNL1_ENST00000423111.2_Missense_Mutation_p.T210M|ATRNL1_ENST00000303745.7_Intron	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1159					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.T1159K(1)|p.T1159M(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTCAACATTACGTGGTCTGTC	0.299																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	10											131	126	128					10																	117226742		2202	4296	6498	117216732	SO:0001583	missense	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3476C>T	10.37:g.117226742C>T	ENSP00000347152:p.Thr1159Met		117216732	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439717	0.83885	.	.	ENSG00000107518	ENST00000355044;ENST00000423111	T;T	0.52526	0.66;0.66	4.69	4.69	0.59074	.	0.096790	0.64402	D	0.000001	T	0.66761	0.2822	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	P;P	0.60609	0.877;0.877	T	0.72782	-0.4189	10	0.87932	D	0	-9.0931	17.9819	0.89144	0.0:1.0:0.0:0.0	.	210;1159	B4DH41;Q5VV63	.;ATRN1_HUMAN	M	1159;210	ENSP00000347152:T1159M;ENSP00000409624:T210M	ENSP00000347152:T1159M	T	+	2	0	ATRNL1	117216732	1.000000	0.71417	0.918000	0.36340	0.882000	0.50991	7.580000	0.82523	2.311000	0.77944	0.655000	0.94253	ACG		0.299	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117226742	C	T	117226742	3	4	49	1	0	0	0	0	1	0	0	0	1208	536	19	1	3566	1	ATRNL1	10	117226742	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	117133345	117226742	18308005	60	6759										
OR51B4	79339	broad.mit.edu	37	chr11	5322906	5322906	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtgaaacaggcagcatgggCaatctccctctggtctagca	12	11	3	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:5322906C>A	ENST00000380224.1	-	1	320	c.271G>T	c.(271-273)Gcc>Tcc	p.A91S	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	91					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A91S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCAGCATGGGCAATCTCCCTC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											146	131	136					11																	5322906		2201	4297	6498	5279482	SO:0001583	missense	79339			BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.271G>T	11.37:g.5322906C>A	ENSP00000369573:p.Ala91Ser		5279482	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.266480	0.00259	.	.	ENSG00000183251	ENST00000380224	T	0.30448	1.53	4.39	-3.48	0.04739	GPCR, rhodopsin-like superfamily (1);	1.364310	0.04873	N	0.446276	T	0.04815	0.0130	N	0.00217	-1.83	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31613	-0.9937	10	0.02654	T	1	.	0.7886	0.01053	0.3726:0.2692:0.114:0.2442	.	91	Q9Y5P0	O51B4_HUMAN	S	91	ENSP00000369573:A91S	ENSP00000369573:A91S	A	-	1	0	OR51B4	5279482	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.643000	0.00058	-0.487000	0.06735	-0.345000	0.07892	GCC		0.502	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		A	5322906	C	A	5322906	3	1	49	1	0	0	0	0	1	0	0	0	11121	710	25	2	664	2	OR51B4	11	5322906	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		5322906	129683610	61	6760										
SPON1	10418	broad.mit.edu	37	chr11	14284473	14284473	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagggaggcccgagagagcCggcggagtgagcagctgaag	21	8	0	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:14284473C>T	ENST00000534587.1	-	0	158				SPON1_ENST00000310358.7_RNA														p.R737W(1)									CCGAGAGAGCCGGCGGAGTGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											38	40	39					11																	14284473		1919	4114	6033	14241049			10418																															11.37:g.14284473C>T			14241049		Missense_Mutation	SNP	ENST00000534587.1	37		.	.	.	.	.	.	.	.	.	.	C	19.68	3.872510	0.72180	.	.	ENSG00000152268	ENST00000310358	.	.	.	6.04	1.34	0.21922	.	0.045895	0.85682	D	0.000000	T	0.77068	0.4076	.	.	.	0.53005	D	0.999969	D	0.89917	1.0	D	0.72075	0.976	D	0.83492	0.0070	7	0.66056	D	0.02	.	14.4744	0.67537	0.5911:0.4089:0.0:0.0	.	738	Q9HCB6	SPON1_HUMAN	W	737	.	ENSP00000309297:R737W	R	+	1	2	SPON1	14241049	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.383000	0.34385	0.361000	0.24292	0.561000	0.74099	CGG		0.587	RP11-21L19.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000386031.1			T	14284473	C	T	14284473	1	4	49	0	1	0	0	0	0	0	0	0	15121	643	23	1		1	SPON1	11	14284473	RNA	SNP	C	TCGA-AG-3894-01A-01W-1073-09	8961567	14284473	120722043	62	6761										
SAAL1	113174	broad.mit.edu	37	chr11	18105187	18105187	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcagtccttttagtttcctcTgtgttagactctgccgagtt	8	10	3	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:18105187T>C	ENST00000524803.1	-	10	1183	c.1134A>G	c.(1132-1134)acA>acG	p.T378T	SAAL1_ENST00000300013.4_Silent_p.T377T|SAAL1_ENST00000529318.1_Silent_p.T380T			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	378								p.T378T(1)		breast(2)|large_intestine(5)|lung(8)	15						TAGTTTCCTCTGTGTTAGACT	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	11											138	135	136					11																	18105187		2200	4293	6493	18061763	SO:0001819	synonymous_variant	113174			AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.1134A>G	11.37:g.18105187T>C			18061763	A6NH05	Silent	SNP	ENST00000524803.1	37	CCDS31439.1																																																																																				0.338	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		C	18105187	T	C	18105187	2	2	49	1	0	0	0	0	0	0	0	1	13838	1567	55	4		4	SAAL1	11	18105187	Silent	SNP	T	TCGA-AG-3894-01A-01W-1073-09	3820714	18105187	116901329	63	6762										
OR5D18	219438	broad.mit.edu	37	chr11	55587894	55587894	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcttcctttactgtgtgccCaactccaaaaactccaggca	5	15	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:55587894C>G	ENST00000333976.4	+	1	809	c.789C>G	c.(787-789)ccC>ccG	p.P263P		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P263P(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				ACTGTGTGCCCAACTCCAAAA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	11											93	87	89					11																	55587894		2200	4296	6496	55344470	SO:0001819	synonymous_variant	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.789C>G	11.37:g.55587894C>G			55344470	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	37	CCDS31510.1																																																																																				0.522	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		G	55587894	C	G	55587894	2	3	49	1	0	0	0	0	0	0	0	1	11188	581	21	5		5	OR5D18	11	55587894	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	37482707	55587894	79418622	64	6763										
SAPS3	55291	broad.mit.edu	37	chr11	68377454	68377454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agactgcagaggcgaagtgcGcggcgcccaggcctcccagc	15	15	0	2	rs199837553		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:68377454G>A	ENST00000393800.2	+	23	2787	c.2533G>A	c.(2533-2535)Gcg>Acg	p.A845T	PPP6R3_ENST00000393801.3_Missense_Mutation_p.A851T|PPP6R3_ENST00000529710.1_Missense_Mutation_p.A765T|PPP6R3_ENST00000527403.2_Missense_Mutation_p.A810T|PPP6R3_ENST00000265637.4_Missense_Mutation_p.A799T|PPP6R3_ENST00000524904.1_Missense_Mutation_p.A839T|PPP6R3_ENST00000393799.2_Missense_Mutation_p.A851T|PPP6R3_ENST00000524845.1_Missense_Mutation_p.A816T|PPP6R3_ENST00000534534.1_Missense_Mutation_p.A613T|PPP6R3_ENST00000265636.5_Missense_Mutation_p.A765T	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	845					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.A765T(1)|p.A851T(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGCGAAGTGCGCGGCGCCCAG	0.607													g|||	1	0.000199681	8e-04	0	5008	,	,		18275	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	11						A	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4400		0,0,2200	76	70	72		2551,2533,2515,2446,2293,2293	-3.4	0	11		72	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense,missense,missense,missense,missense	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	58,58,58,58,58,58	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	851/880,845/874,839/868,816/845,765/792,765/794	68377454	1,12987	2200	4294	6494	68134030	SO:0001583	missense	55291			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2533G>A	11.37:g.68377454G>A	ENSP00000377389:p.Ala845Thr		68134030	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	7.497	0.651791	0.14516	0.0	1.16E-4	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84	5.2	-3.41	0.04839	.	1.693780	0.03025	N	0.151328	T	0.18383	0.0441	N	0.02011	-0.69	0.09310	N	1	B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.001;0.0	B;B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0;0.001;0.001	T	0.08411	-1.0723	10	0.16420	T	0.52	.	4.1507	0.10237	0.5346:0.0971:0.2609:0.1075	.	528;613;765;816;839;845;851;765	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	T	851;845;613;816;799;839;851;765;765;810;552	ENSP00000377388:A851T;ENSP00000377389:A845T;ENSP00000434429:A613T;ENSP00000431415:A816T;ENSP00000265637:A799T;ENSP00000433058:A839T;ENSP00000377390:A851T;ENSP00000265636:A765T;ENSP00000437329:A765T;ENSP00000433565:A810T;ENSP00000436209:A552T	ENSP00000265636:A765T	A	+	1	0	PPP6R3	68134030	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.044000	0.12023	-1.159000	0.02807	-0.993000	0.02533	GCG		0.607	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68377454	G	A	68377454	3	1	49	1	0	0	0	0	1	0	0	0	13875	1087	38	1	2637	1	SAPS3	11	68377454	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	12789560	68377454	66629062	65	6764										
BTG4	54766	broad.mit.edu	37	chr11	111365923	111365923	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atagcaggcctgtaacacttAggatgcttctgcgagccatg	11	10	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr11:111365923A>T	ENST00000356018.2	-	5	826	c.627T>A	c.(625-627)ccT>ccA	p.P209P		NM_017589.3	NP_060059.1	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4	209					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|neuron differentiation (GO:0030182)			p.P209P(1)		large_intestine(2)|upper_aerodigestive_tract(1)	3		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		TGTAACACTTAGGATGCTTCT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	11											109	86	94					11																	111365923		2201	4297	6498	110871133	SO:0001819	synonymous_variant	54766			AJ271351	CCDS8346.1	11q23	2008-05-27				ENSG00000137707			13862	protein-coding gene	gene with protein product		605673				10995567	Standard	NM_017589		Approved	PC3B	uc001plj.3	Q9NY30		ENST00000356018.2:c.627T>A	11.37:g.111365923A>T			110871133	Q8NEH7	Silent	SNP	ENST00000356018.2	37	CCDS8346.1																																																																																				0.562	BTG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391177.1			T	111365923	A	T	111365923	2	4	49	1	0	0	0	0	0	0	0	1	1559	407	15	5		5	BTG4	11	111365923	Silent	SNP	A	TCGA-AG-3894-01A-01W-1073-09	42988469	111365923	23640593	66	6765										
KLRB1	3820	broad.mit.edu	37	chr12	9750672	9750672	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttaaaaaagagccgtttatcCacttccagttcttttctgat	5	9	2	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:9750672C>T	ENST00000229402.3	-	5	546	c.500G>A	c.(499-501)tGg>tAg	p.W167*		NM_002258.2	NP_002249.1	Q12918	KLRB1_HUMAN	killer cell lectin-like receptor subfamily B, member 1	167	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.W167*(1)		endometrium(2)|large_intestine(6)|lung(4)	12						GCCGTTTATCCACTTCCAGTT	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											48	46	47					12																	9750672		2202	4292	6494	9641939	SO:0001587	stop_gained	3820			U11276	CCDS8601.1	12p13	2014-05-22			ENSG00000111796	ENSG00000111796		"Killer cell lectin-like receptors", "CD molecules", "C-type lectin domain containing"	6373	protein-coding gene	gene with protein product		602890		NKR		8077657	Standard	NM_002258		Approved	CD161, NKR-P1, NKR-P1A, hNKR-P1A, CLEC5B	uc010sgt.2	Q12918	OTTHUMG00000168581	ENST00000229402.3:c.500G>A	12.37:g.9750672C>T	ENSP00000229402:p.Trp167*		9641939	Q24K24	Nonsense_Mutation	SNP	ENST00000229402.3	37	CCDS8601.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.093799	0.56075	.	.	ENSG00000111796	ENST00000229402	.	.	.	3.06	3.06	0.35304	.	0.000000	0.40222	N	0.001142	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.6897	9.8491	0.41046	0.0:1.0:0.0:0.0	.	.	.	.	X	167	.	ENSP00000229402:W167X	W	-	2	0	KLRB1	9641939	1.000000	0.71417	1.000000	0.80357	0.607000	0.37147	2.227000	0.42972	2.022000	0.59522	0.655000	0.94253	TGG		0.318	KLRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400280.1	NM_002258		T	9750672	C	T	9750672	4	4	49	1	0	0	0	0	0	1	0	0	8435	595	21	3	184	3	KLRB1	12	9750672	Nonsense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		9750672	124101223	67	6766										
OVCH1	341350	broad.mit.edu	37	chr12	29624865	29624865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaggcttcttcccctcctgCgattcttctggaaagccact	8	15	3	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:29624865C>T	ENST00000318184.5	-	16	1725	c.1726G>A	c.(1726-1728)Gca>Aca	p.A576T	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	576	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.A576T(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TCCCCTCCTGCGATTCTTCTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	12											53	54	54					12																	29624865		1937	4131	6068	29516132	SO:0001583	missense	341350			BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1726G>A	12.37:g.29624865C>T	ENSP00000326708:p.Ala576Thr		29516132		Missense_Mutation	SNP	ENST00000318184.5	37		.	.	.	.	.	.	.	.	.	.	C	11.84	1.758403	0.31137	.	.	ENSG00000187950	ENST00000318184	D	0.88354	-2.37	2.31	1.42	0.22433	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.71879	0.3392	N	0.08118	0	0.09310	N	1	P	0.48230	0.907	B	0.36845	0.234	T	0.66184	-0.5987	9	0.59425	D	0.04	.	4.3494	0.11148	0.0:0.5551:0.0:0.4449	.	576	Q7RTY7	OVCH1_HUMAN	T	576	ENSP00000326708:A576T	ENSP00000326708:A576T	A	-	1	0	OVCH1	29516132	0.001000	0.12720	0.047000	0.18901	0.979000	0.70002	0.101000	0.15251	0.549000	0.28973	0.655000	0.94253	GCA		0.507	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		T	29624865	C	T	29624865	3	4	49	1	0	0	0	0	1	0	0	0	11354	768	27	1	1730	1	OVCH1	12	29624865	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	19874193	29624865	104227030	68	6767										
PRICKLE1	144165	broad.mit.edu	37	chr12	42858385	42858385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcctgggtggctgccataaGcagaatcgcccagtccatct	12	13	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:42858385G>A	ENST00000455697.1	-	7	1736	c.1451C>T	c.(1450-1452)gCt>gTt	p.A484V	PRICKLE1_ENST00000552240.1_Missense_Mutation_p.A484V|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.A484V|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.A484V|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.A484V|RP11-328C8.4_ENST00000547824.1_RNA	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	484					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.A484V(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GCTGCCATAAGCAGAATCGCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											61	58	59					12																	42858385		2203	4300	6503	41144652	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1451C>T	12.37:g.42858385G>A	ENSP00000401060:p.Ala484Val		41144652	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	35	5.434968	0.96150	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.64103	0.2568	N	0.14661	0.345	0.80722	D	1	D	0.57899	0.981	P	0.57911	0.829	T	0.67956	-0.5536	10	0.59425	D	0.04	-6.3067	20.3277	0.98707	0.0:0.0:1.0:0.0	.	484	Q96MT3	PRIC1_HUMAN	V	484	ENSP00000401060:A484V;ENSP00000398947:A484V;ENSP00000448359:A484V;ENSP00000345064:A484V;ENSP00000449819:A484V	ENSP00000345064:A484V	A	-	2	0	PRICKLE1	41144652	1.000000	0.71417	0.959000	0.39883	0.995000	0.86356	9.420000	0.97426	2.879000	0.98667	0.650000	0.86243	GCT		0.468	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42858385	G	A	42858385	3	1	49	1	0	0	0	0	1	0	0	0	12520	971	34	3	1052	3	PRICKLE1	12	42858385	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	13233520	42858385	90993510	69	6768										
GPR84	53831	broad.mit.edu	37	chr12	54757284	54757284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgggcaatgaggaggtagcGtcccagtgcgatgaggcaga	18	7	0	3	rs145386200	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:54757284G>A	ENST00000551809.1	-	1	987	c.352C>T	c.(352-354)Cgc>Tgc	p.R118C	GPR84_ENST00000267015.3_Missense_Mutation_p.R118C|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.R118C(1)		NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						AGGAGGTAGCGTCCCAGTGCG	0.587													G|||	3	0.000599042	8e-04	0	5008	,	,		21756	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	90	79	83		352	4.3	1	12	dbSNP_134	83	0,8600		0,0,4300	no	missense	GPR84	NM_020370.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	118/397	54757284	1,13005	2203	4300	6503	53043551	SO:0001583	missense	53831			AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.352C>T	12.37:g.54757284G>A	ENSP00000450310:p.Arg118Cys		53043551	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	37	CCDS8878.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.03	3.747977	0.69533	2.27E-4	0.0	ENSG00000139572	ENST00000267015;ENST00000551809	D;D	0.97186	-4.28;-4.28	5.21	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000009	D	0.98526	0.9508	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.98776	1.0730	10	0.87932	D	0	-19.9123	13.6225	0.62144	0.0:0.0:0.845:0.155	.	118	Q9NQS5	GPR84_HUMAN	C	118	ENSP00000267015:R118C;ENSP00000450310:R118C	ENSP00000267015:R118C	R	-	1	0	GPR84	53043551	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	2.733000	0.47360	2.602000	0.87976	0.555000	0.69702	CGC		0.587	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			A	54757284	G	A	54757284	3	1	49	1	0	0	0	0	1	0	0	0	6734	1145	40	1	842	1	GPR84	12	54757284	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	11898899	54757284	79094611	70	6769										
PLEKHG7	440107	broad.mit.edu	37	chr12	93150130	93150130	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacatcttgtcaccaaccagCagacaccttctctatgaagg	6	13	3	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:93150130C>T	ENST00000344636.3	+	8	847	c.663C>T	c.(661-663)agC>agT	p.S221S		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	221							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S221S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						CACCAACCAGCAGACACCTTC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	12											90	90	90					12																	93150130		2203	4300	6503	91674261	SO:0001819	synonymous_variant	440107			AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.663C>T	12.37:g.93150130C>T			91674261	B2RNR7	Silent	SNP	ENST00000344636.3	37	CCDS31873.1																																																																																				0.368	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330		T	93150130	C	T	93150130	2	4	49	1	0	0	0	0	0	0	0	1	12106	709	25	3		3	PLEKHG7	12	93150130	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	38392846	93150130	40701765	71	6770										
GNPTAB	79158	broad.mit.edu	37	chr12	102183810	102183810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attcacccaggtgtaaacaaCgtcaatcggcatgggcagac	10	11	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr12:102183810C>T	ENST00000299314.7	-	3	491	c.229G>A	c.(229-231)Gtt>Att	p.V77I	snoU13_ENST00000459085.1_RNA|GNPTAB_ENST00000549940.1_Missense_Mutation_p.V77I	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	77					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)	p.V77I(2)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						GTGTAAACAACGTCAATCGGC	0.428																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											207	184	192					12																	102183810		2203	4300	6503	100707941	SO:0001583	missense	79158			AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.229G>A	12.37:g.102183810C>T	ENSP00000299314:p.Val77Ile		100707941	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	37	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289333	0.59976	.	.	ENSG00000111670	ENST00000299314;ENST00000549940	D;D	0.97480	-4.07;-4.4	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.97387	0.9145	L	0.45137	1.4	0.80722	D	1	P;D	0.89917	0.897;1.0	B;D	0.64237	0.127;0.923	D	0.96193	0.9139	10	0.28530	T	0.3	-19.639	20.2182	0.98305	0.0:1.0:0.0:0.0	.	77;77	Q3T906-2;Q3T906	.;GNPTA_HUMAN	I	77	ENSP00000299314:V77I;ENSP00000449150:V77I	ENSP00000299314:V77I	V	-	1	0	GNPTAB	100707941	1.000000	0.71417	0.987000	0.45799	0.793000	0.44817	7.412000	0.80091	2.785000	0.95823	0.655000	0.94253	GTT		0.428	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			T	102183810	C	T	102183810	3	4	49	1	0	0	0	0	1	0	0	0	6565	536	19	1	3617	1	GNPTAB	12	102183810	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	9033680	102183810	31668085	72	6771										
ATP12A	479	broad.mit.edu	37	chr13	25281181	25281181	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gatgctgttgttgctgtgacCggggatggagttaatgactc	15	6	0	2	rs2289908	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:25281181C>T	ENST00000381946.3	+	16	2357	c.2190C>T	c.(2188-2190)acC>acT	p.T730T	ATP12A_ENST00000218548.6_Silent_p.T736T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	730					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.T730T(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTGCTGTGACCGGGGATGGAG	0.562													c|||	3	0.000599042	0	0	5008	,	,		17883	0.003		0	False		,,,				2504	0				Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - coding silent(1)	large_intestine(1)	13											73	64	67					13																	25281181		2203	4300	6503	24179181	SO:0001819	synonymous_variant	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2190C>T	13.37:g.25281181C>T			24179181	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																				0.562	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25281181	C	T	25281181	2	4	49	1	0	0	0	0	0	0	0	1	1123	639	23	1		1	ATP12A	13	25281181	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09		25281181	89888697	73	6772										
FAM123A	219287	broad.mit.edu	37	chr13	25745584	25745584	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttattaatcttccccgacggCggctcggcggccggcgtttc	12	14	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:25745584C>T	ENST00000515384.1	-	1	841	c.174G>A	c.(172-174)ccG>ccA	p.P58P	AMER2_ENST00000381853.3_Silent_p.P58P|AMER2_ENST00000357816.2_Silent_p.P58P|AMER2-AS1_ENST00000413501.1_lincRNA			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	58	Gly-rich.				ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P58P(2)									TCCCCGACGGCGGCTCGGCGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	13											26	32	30					13																	25745584		2176	4271	6447	24643584	SO:0001819	synonymous_variant	219287			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.174G>A	13.37:g.25745584C>T			24643584	Q5RL80|Q5VX56|Q8N593|Q96NN5	Silent	SNP	ENST00000515384.1	37	CCDS53859.1																																																																																				0.597	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25745584	C	T	25745584	2	4	49	1	0	0	0	0	0	0	0	1	5438	755	27	1		1	FAM123A	13	25745584	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	464403	25745584	89424294	74	6773										
SHISA2	387914	broad.mit.edu	37	chr13	26620912	26620912	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgttgttcatggtcccttcCggcaagcaacagttggtctg	11	11	2	0	rs138455555	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:26620912C>T	ENST00000319420.3	-	2	682	c.627G>A	c.(625-627)ccG>ccA	p.P209P		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	209					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.P209P(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						TGGTCCCTTCCGGCAAGCAAC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	13						C		0,4406		0,0,2203	147	136	140		627	-8.4	0.9	13	dbSNP_134	140	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	SHISA2	NM_001007538.1		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		209/296	26620912	7,12999	2203	4300	6503	25518912	SO:0001819	synonymous_variant	387914				CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.627G>A	13.37:g.26620912C>T			25518912	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																				0.587	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		T	26620912	C	T	26620912	2	4	49	1	0	0	0	0	0	0	0	1	14317	639	23	1		1	SHISA2	13	26620912	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	875328	26620912	88548966	75	6774										
PCDH9	5101	broad.mit.edu	37	chr13	67205527	67205527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agccatcagggagatgaaacGtaacacggcgctgcgactac	12	11	1	2	rs150709677		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:67205527G>A	ENST00000377865.2	-	3	3289	c.3155C>T	c.(3154-3156)aCg>aTg	p.T1052M	PCDH9_ENST00000456367.1_Missense_Mutation_p.T1018M|RNU7-87P_ENST00000459343.1_RNA|PCDH9_ENST00000328454.5_Missense_Mutation_p.T1018M|PCDH9_ENST00000544246.1_Missense_Mutation_p.T1052M			Q9HC56	PCDH9_HUMAN	protocadherin 9	1052					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T1052M(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GAGATGAAACGTAACACGGCG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	81	71	75		3053,3155	5.6	1	13	dbSNP_134	75	0,8600		0,0,4300	no	missense,missense	PCDH9	NM_020403.4,NM_203487.2	81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1018/1204,1052/1238	67205527	1,13005	2203	4300	6503	66103528	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3155C>T	13.37:g.67205527G>A	ENSP00000367096:p.Thr1052Met		66103528	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541342	0.85917	2.27E-4	0.0	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.68479	-0.33;-0.33;0.13;0.13	5.63	5.63	0.86233	.	0.000000	0.45867	D	0.000336	T	0.77082	0.4078	L	0.61036	1.89	0.44956	D	0.997973	B;D	0.63880	0.33;0.993	B;P	0.55303	0.079;0.773	T	0.79125	-0.1932	10	0.87932	D	0	.	19.6801	0.95958	0.0:0.0:1.0:0.0	.	1018;1052	Q9HC56-2;Q9HC56	.;PCDH9_HUMAN	M	1052;1052;1018;1018	ENSP00000442186:T1052M;ENSP00000367096:T1052M;ENSP00000401699:T1018M;ENSP00000332060:T1018M	ENSP00000332060:T1018M	T	-	2	0	PCDH9	66103528	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	9.476000	0.97823	2.652000	0.90054	0.655000	0.94253	ACG		0.498	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67205527	G	A	67205527	3	1	49	1	0	0	0	0	1	0	0	0	11549	1145	40	1	566	1	PCDH9	13	67205527	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	40584615	67205527	47964351	76	6775										
EDNRB	1910	broad.mit.edu	37	chr13	78474707	78474707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gattataaagagtgagcttcAgaatcctgctgaggtgaagg	13	5	1	5			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:78474707A>G	ENST00000334286.5	-	5	1270	c.1034T>C	c.(1033-1035)cTg>cCg	p.L345P	EDNRB_ENST00000446573.1_Missense_Mutation_p.L345P|EDNRB_ENST00000377211.4_Missense_Mutation_p.L435P	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	345					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.L345P(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AGTGAGCTTCAGAATCCTGCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	13											84	88	87					13																	78474707		2203	4300	6503	77372708	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1034T>C	13.37:g.78474707A>G	ENSP00000335311:p.Leu345Pro		77372708	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.548178	0.86022	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.44482	0.92;0.92;0.92	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.75243	0.3823	H	0.95745	3.715	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.99;0.999	D	0.83475	0.0061	10	0.87932	D	0	-14.6951	16.1323	0.81449	1.0:0.0:0.0:0.0	.	345;435;345	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	P	435;345;345	ENSP00000366416:L435P;ENSP00000403401:L345P;ENSP00000335311:L345P	ENSP00000335311:L345P	L	-	2	0	EDNRB	77372708	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.910000	0.92685	2.277000	0.76020	0.528000	0.53228	CTG		0.423	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			G	78474707	A	G	78474707	3	3	49	1	0	0	0	0	1	0	0	0	4931	188	7	4	427	4	EDNRB	13	78474707	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09	11269180	78474707	36695171	77	6776										
HS6ST3	266722	broad.mit.edu	37	chr13	97484897	97484897	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgcctacctgctaccctggGgatgactggtctggggtcag	14	12	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:97484897G>T	ENST00000376705.2	+	2	885	c.861G>T	c.(859-861)ggG>ggT	p.G287G		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	287					heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)	p.G287G(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					GCTACCCTGGGGATGACTGGT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	13											63	57	59					13																	97484897		2203	4300	6503	96282898	SO:0001819	synonymous_variant	266722			AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.861G>T	13.37:g.97484897G>T			96282898	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	37	CCDS9481.1																																																																																				0.562	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		T	97484897	G	T	97484897	2	4	49	1	0	0	0	0	0	0	0	1	7393	1219	43	2		2	HS6ST3	13	97484897	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	19010190	97484897	17684981	78	6777										
PCCA	5095	broad.mit.edu	37	chr13	100807321	100807321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catggatgccatcatggaagCcattaagaaaaccagggccc	10	11	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr13:100807321C>T	ENST00000376285.1	+	5	427	c.389C>T	c.(388-390)gCc>gTc	p.A130V	PCCA_ENST00000485946.1_3'UTR|PCCA_ENST00000376279.3_Missense_Mutation_p.A130V|PCCA_ENST00000376286.4_Missense_Mutation_p.A104V	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	130	Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.A130V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	ATCATGGAAGCCATTAAGAAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	13											108	106	107					13																	100807321		2203	4300	6503	99605322	SO:0001583	missense	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.389C>T	13.37:g.100807321C>T	ENSP00000365462:p.Ala130Val		99605322	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419210	0.62622	.	.	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285	D;D;D	0.97303	-4.33;-4.33;-4.33	5.69	5.69	0.88448	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.062827	0.64402	D	0.000006	D	0.95809	0.8636	L	0.50333	1.59	0.80722	D	1	B;P;P	0.39326	0.412;0.668;0.486	B;B;B	0.43916	0.436;0.197;0.298	D	0.94588	0.7785	10	0.36615	T	0.2	.	13.4914	0.61397	0.0:0.9194:0.0:0.0806	.	130;104;130	C9JPQ8;P05165-2;P05165	.;.;PCCA_HUMAN	V	104;130;130	ENSP00000365463:A104V;ENSP00000365456:A130V;ENSP00000365462:A130V	ENSP00000365456:A130V	A	+	2	0	PCCA	99605322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.772000	0.68889	2.685000	0.91497	0.655000	0.94253	GCC		0.448	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			T	100807321	C	T	100807321	3	4	49	1	0	0	0	0	1	0	0	0	11535	739	26	3	407	3	PCCA	13	100807321	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	3322424	100807321	14362557	79	6778										
TOX4	9878	broad.mit.edu	37	chr14	21960730	21960730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaactccttctccacctcctAtggctactgttgacccagca	5	16	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr14:21960730A>G	ENST00000405508.1	+	8	1231	c.955A>G	c.(955-957)Atg>Gtg	p.M319V	TOX4_ENST00000262709.3_Missense_Mutation_p.M319V|TOX4_ENST00000448790.2_Missense_Mutation_p.M296V			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	319						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)	p.M319V(1)		large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		TCCACCTCCTATGGCTACTGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	118	121					14																	21960730		2203	4300	6503	21030570	SO:0001583	missense	9878			AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"chromosome 14 open reading frame 92", "KIAA0737"	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.955A>G	14.37:g.21960730A>G	ENSP00000385102:p.Met319Val		21030570	B4DPY8|B4DSM0|E7EV69	Missense_Mutation	SNP	ENST00000405508.1	37	CCDS32043.1	.	.	.	.	.	.	.	.	.	.	A	0.294	-0.978107	0.02197	.	.	ENSG00000092203	ENST00000405508;ENST00000262709;ENST00000448790;ENST00000545559	T;T;T	0.10382	2.88;2.88;2.88	4.8	-3.78	0.04333	.	0.972226	0.08534	N	0.931560	T	0.04363	0.0120	N	0.08118	0	0.22639	N	0.998902	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47471	-0.9115	10	0.13108	T	0.6	.	8.1372	0.31061	0.4001:0.1054:0.4945:0.0	.	296;319	B4DPY8;O94842	.;TOX4_HUMAN	V	319;319;296;247	ENSP00000385102:M319V;ENSP00000262709:M319V;ENSP00000393080:M296V	ENSP00000262709:M319V	M	+	1	0	TOX4	21030570	0.479000	0.25925	0.980000	0.43619	0.974000	0.67602	0.143000	0.16115	-0.711000	0.04995	0.397000	0.26171	ATG		0.473	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828		G	21960730	A	G	21960730	3	3	49	1	0	0	0	0	1	0	0	0	16420	449	16	4	981	4	TOX4	14	21960730	Missense_Mutation	SNP	A	TCGA-AG-3894-01A-01W-1073-09		21960730	85388810	80	6779										
NARG2	79664	broad.mit.edu	37	chr15	60734742	60734742	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtagtacataaactggaaaTtgctgcaatgcaaaattata	8	5	0	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr15:60734742T>C	ENST00000261520.4	-	12	2532	c.2298A>G	c.(2296-2298)caA>caG	p.Q766Q	NARG2_ENST00000439632.1_Silent_p.Q629Q	NM_024611.4	NP_078887.2												p.Q766Q(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						AAACTGGAAATTGCTGCAATG	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	15											77	71	73					15																	60734742		2203	4299	6502	58522034	SO:0001819	synonymous_variant	79664																														ENST00000261520.4:c.2298A>G	15.37:g.60734742T>C			58522034		Missense_Mutation	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																				0.323	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			C	60734742	T	C	60734742	2	2	49	1	0	0	0	0	0	0	0	1	10199	1490	52	4		4	NARG2	15	60734742	Silent	SNP	T	TCGA-AG-3894-01A-01W-1073-09		60734742	41796650	81	6780										
TIGD7	91151	broad.mit.edu	37	chr16	3350349	3350349	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caccggctgagcgtttctgtTggtaccacatgtagaccgca	11	12	1	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr16:3350349T>G	ENST00000396862.1	-	2	2094	c.266A>C	c.(265-267)cAa>cCa	p.Q89P	TIGD7_ENST00000268674.2_Missense_Mutation_p.Q89P|TIGD7_ENST00000574598.1_5'Flank	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	89	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Q89P(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						GCGTTTCTGTTGGTACCACAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	16											142	137	139					16																	3350349		2197	4300	6497	3290350	SO:0001583	missense	91151			AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.266A>C	16.37:g.3350349T>G	ENSP00000380071:p.Gln89Pro		3290350	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	37	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058381	0.36277	.	.	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.32515	1.45;1.45	4.38	4.38	0.52667	Homeodomain-related (1);Pogo transposase / Cenp-B / PDC2, DNA-binding HTH domain (3);Homeodomain-like (1);	0.000000	0.34555	U	0.003875	T	0.46718	0.1407	L	0.58810	1.83	0.29759	N	0.835736	D	0.71674	0.998	D	0.76575	0.988	T	0.39583	-0.9607	10	0.31617	T	0.26	.	9.9239	0.41481	0.0:0.0:0.0:1.0	.	89	Q6NT04	TIGD7_HUMAN	P	89	ENSP00000380071:Q89P;ENSP00000268674:Q89P	ENSP00000268674:Q89P	Q	-	2	0	TIGD7	3290350	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.039000	0.41193	1.852000	0.53769	0.533000	0.62120	CAA		0.512	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208		G	3350349	T	G	3350349	3	3	49	1	0	0	0	0	1	0	0	0	15940	1812	63	4	1387	4	TIGD7	16	3350349	Missense_Mutation	SNP	T	TCGA-AG-3894-01A-01W-1073-09		3350349	87004404	82	6781										
SCNN1G	6340	broad.mit.edu	37	chr16	23226531	23226531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttctctatcattgcccgccGccagtggcagaaagccaagg	10	14	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr16:23226531G>A	ENST00000300061.2	+	13	1834	c.1691G>A	c.(1690-1692)cGc>cAc	p.R564H	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	564					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)	p.R564H(1)		NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	ATTGCCCGCCGCCAGTGGCAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	16											92	87	89					16																	23226531		2197	4300	6497	23134032	SO:0001583	missense	6340			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1691G>A	16.37:g.23226531G>A	ENSP00000300061:p.Arg564His		23134032	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	37	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	G	5.103	0.204701	0.09704	.	.	ENSG00000166828	ENST00000300061	T	0.73575	-0.76	5.22	-0.291	0.12843	.	0.550372	0.18016	N	0.154418	T	0.48892	0.1525	N	0.08118	0	0.18873	N	0.999981	B	0.11235	0.004	B	0.06405	0.002	T	0.28235	-1.0050	10	0.15499	T	0.54	-39.1964	10.5884	0.45296	0.4739:0.0:0.5261:0.0	.	564	P51170	SCNNG_HUMAN	H	564	ENSP00000300061:R564H	ENSP00000300061:R564H	R	+	2	0	SCNN1G	23134032	0.000000	0.05858	0.161000	0.22692	0.615000	0.37417	-0.164000	0.09983	-0.292000	0.08999	-0.258000	0.10820	CGC		0.587	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23226531	G	A	23226531	3	1	49	1	0	0	0	0	1	0	0	0	13967	1087	38	1	1737	1	SCNN1G	16	23226531	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	19876182	23226531	67128222	83	6782										
CACNG3	10368	broad.mit.edu	37	chr16	24366271	24366271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acacaacgtcattctcagcgCgggcatcttttttgtctctg	8	12	4	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr16:24366271C>T	ENST00000005284.3	+	3	1615	c.413C>T	c.(412-414)gCg>gTg	p.A138V		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	138					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.A138V(2)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		ATTCTCAGCGCGGGCATCTTT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	16											58	53	55					16																	24366271		2197	4300	6497	24273772	SO:0001583	missense	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.413C>T	16.37:g.24366271C>T	ENSP00000005284:p.Ala138Val		24273772		Missense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	C	33	5.213030	0.95069	.	.	ENSG00000006116	ENST00000005284	D	0.91068	-2.78	5.41	4.45	0.53987	.	0.112679	0.64402	D	0.000015	D	0.93314	0.7869	M	0.88031	2.925	0.80722	D	1	P	0.51653	0.947	P	0.47827	0.558	D	0.94124	0.7382	10	0.59425	D	0.04	-12.7101	15.2787	0.73764	0.1414:0.8586:0.0:0.0	.	138	O60359	CCG3_HUMAN	V	138	ENSP00000005284:A138V	ENSP00000005284:A138V	A	+	2	0	CACNG3	24273772	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	7.089000	0.76909	1.487000	0.48415	0.561000	0.74099	GCG		0.567	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24366271	C	T	24366271	3	4	49	1	0	0	0	0	1	0	0	0	2564	768	27	1	423	1	CACNG3	16	24366271	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	1139740	24366271	65988482	84	6783										
SALL1	6299	broad.mit.edu	37	chr16	51175491	51175491	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ccagaggccccgccgcacctCgcttcctgggagaactgggc	13	17	0	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr16:51175491C>T	ENST00000251020.4	-	2	675	c.642G>A	c.(640-642)gcG>gcA	p.A214A	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.A117A|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	214					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A214A(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			CGCCGCACCTCGCTTCCTGGG	0.602																																					GBM(103;1352 1446 1855 4775 8890)											1	Substitution - coding silent(1)	large_intestine(1)	16											73	78	76					16																	51175491		2198	4300	6498	49732992	SO:0001819	synonymous_variant	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.642G>A	16.37:g.51175491C>T			49732992	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																				0.602	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51175491	C	T	51175491	2	4	49	1	0	0	0	0	0	0	0	1	13847	871	31	1		1	SALL1	16	51175491	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	26809220	51175491	39179262	85	6784										
CHD9	80205	broad.mit.edu	37	chr16	53358218	53358218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	taccggccttccttctggagGagaagctaaaaacatggctg	11	10	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr16:53358218G>A	ENST00000398510.3	+	38	8192	c.8105G>A	c.(8104-8106)gGa>gAa	p.G2702E	CHD9_ENST00000564845.1_Missense_Mutation_p.G2686E|CHD9_ENST00000566029.1_Missense_Mutation_p.G2686E|CHD9_ENST00000447540.1_Missense_Mutation_p.G2687E			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2702					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.G2703E(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CCTTCTGGAGGAGAAGCTAAA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											60	59	60					16																	53358218		1897	4124	6021	51915719	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8105G>A	16.37:g.53358218G>A	ENSP00000381522:p.Gly2702Glu		51915719	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	G	8.015	0.758311	0.15846	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.85484	-1.99	5.47	4.5	0.54988	.	0.113275	0.39274	N	0.001411	T	0.71837	0.3387	N	0.12182	0.205	0.41841	D	0.990127	B;B;P;B	0.39480	0.261;0.004;0.675;0.42	B;B;B;B	0.35353	0.028;0.011;0.201;0.198	T	0.74237	-0.3730	10	0.33940	T	0.23	-19.5627	15.1708	0.72872	0.0713:0.0:0.9287:0.0	.	768;2687;2702;2686	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	E	2687;2686;768	ENSP00000396345:G2687E	ENSP00000381522:G2686E	G	+	2	0	CHD9	51915719	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.911000	0.63328	2.729000	0.93468	0.655000	0.94253	GGA		0.498	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53358218	G	A	53358218	3	1	49	1	0	0	0	0	1	0	0	0	3338	1174	41	3	8207	3	CHD9	16	53358218	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	2182727	53358218	36996535	86	6785										
CYB5D1	124637	broad.mit.edu	37	chr17	7762101	7762101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgccaagacccggagcatcCgcatcattaacacgctcacg	8	16	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr17:7762101C>T	ENST00000332439.4	+	3	567	c.415C>T	c.(415-417)Cgc>Tgc	p.R139C	LSMD1_ENST00000333775.5_5'Flank|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000575771.1_5'Flank|CYB5D1_ENST00000570446.1_Intron|LSMD1_ENST00000575071.1_5'Flank|LSMD1_ENST00000575208.1_5'Flank|LSMD1_ENST00000335155.5_5'Flank|LSMD1_ENST00000570555.1_5'UTR|CYB5D1_ENST00000571846.1_Missense_Mutation_p.R139C	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	139							heme binding (GO:0020037)|metal ion binding (GO:0046872)	p.R139C(1)		breast(1)|endometrium(1)|large_intestine(2)|skin(2)	6		all_cancers(10;0.11)|Prostate(122;0.219)				CCGGAGCATCCGCATCATTAA	0.577											OREG0024147	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	17											44	41	42					17																	7762101		2203	4300	6503	7702826	SO:0001583	missense	124637			AK057061	CCDS11123.1	17p13.1	2006-01-12	2006-01-12						26516	protein-coding gene	gene with protein product						12477932	Standard	NM_144607		Approved	FLJ32499	uc002gjb.4	Q6P9G0		ENST00000332439.4:c.415C>T	17.37:g.7762101C>T	ENSP00000331479:p.Arg139Cys	644	7702826	D3DTQ8|Q96DM7	Missense_Mutation	SNP	ENST00000332439.4	37	CCDS11123.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068770	0.76301	.	.	ENSG00000182224	ENST00000332439;ENST00000541486	T	0.55234	0.53	5.33	3.36	0.38483	Cytochrome b5 (1);	0.061993	0.64402	N	0.000003	T	0.51193	0.1660	M	0.77406	2.37	0.80722	D	1	P;P	0.45768	0.866;0.572	B;B	0.38616	0.277;0.104	T	0.57112	-0.7867	10	0.87932	D	0	-4.1499	10.6921	0.45877	0.0:0.8421:0.0:0.1579	.	139;139	Q6P9G0-2;Q6P9G0	.;CB5D1_HUMAN	C	139	ENSP00000331479:R139C	ENSP00000331479:R139C	R	+	1	0	CYB5D1	7702826	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	5.443000	0.66581	0.640000	0.30582	0.462000	0.41574	CGC		0.577	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607		T	7762101	C	T	7762101	3	4	49	1	0	0	0	0	1	0	0	0	4130	652	23	1	425	1	CYB5D1	17	7762101	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		7762101	73433109	87	6786										
KRT26	353288	broad.mit.edu	37	chr17	38926622	38926622	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgcgaagaccactggtgtcGgcctcaacactgtggtgcag	13	12	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr17:38926622G>A	ENST00000335552.4	-	3	612	c.564C>T	c.(562-564)gcC>gcT	p.A188A		NM_181539.4	NP_853517.2			keratin 26									p.A188A(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				CACTGGTGTCGGCCTCAACAC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	17											132	125	127					17																	38926622		2203	4300	6503	36180148	SO:0001819	synonymous_variant	353288			AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.564C>T	17.37:g.38926622G>A			36180148		Silent	SNP	ENST00000335552.4	37	CCDS11374.1																																																																																				0.493	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		A	38926622	G	A	38926622	2	1	49	1	0	0	0	0	0	0	0	1	8484	1103	39	1		1	KRT26	17	38926622	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	31164521	38926622	42268588	88	6787										
ACLY	47	broad.mit.edu	37	chr17	40063716	40063716	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tctggatatgcctcccgcccGaaggggggagggaactcgat	15	11	1	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr17:40063716G>A	ENST00000352035.2	-	7	856	c.726C>T	c.(724-726)ttC>ttT	p.F242F	ACLY_ENST00000353196.1_Silent_p.F242F|ACLY_ENST00000590151.1_Silent_p.F242F|ACLY_ENST00000393896.2_Silent_p.F242F|ACLY_ENST00000537919.1_Intron	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	242	ATP-grasp.				ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)	p.F242F(1)	NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CCTCCCGCCCGAAGGGGGGAG	0.582																																					Colon(64;807 1396 15971 30971)											1	Substitution - coding silent(1)	large_intestine(1)	17											74	74	74					17																	40063716		2203	4300	6503	37317242	SO:0001819	synonymous_variant	47			X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.726C>T	17.37:g.40063716G>A			37317242	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	37	CCDS11412.1																																																																																				0.582	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40063716	G	A	40063716	2	1	49	1	0	0	0	0	0	0	0	1	143	1049	37	1		1	ACLY	17	40063716	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	1137094	40063716	41131494	89	6788										
PTPRM	5797	broad.mit.edu	37	chr18	8069983	8069983	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagaactcatagtgcagacaGatgaagaccgtgagtacctt	10	8	1	6			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr18:8069983G>T	ENST00000332175.8	+	8	2469	c.1432G>T	c.(1432-1434)Gat>Tat	p.D478Y	PTPRM_ENST00000580170.1_Missense_Mutation_p.D478Y|PTPRM_ENST00000578571.1_3'UTR|PTPRM_ENST00000400053.4_Missense_Mutation_p.D416Y|PTPRM_ENST00000444013.1_Missense_Mutation_p.D265Y|PTPRM_ENST00000400060.4_Missense_Mutation_p.D478Y	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	478	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D478Y(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AGTGCAGACAGATGAAGACCG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											83	67	72					18																	8069983		2203	4300	6503	8059983	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1432G>T	18.37:g.8069983G>T	ENSP00000331418:p.Asp478Tyr		8059983	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876511	0.91664	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.52	5.52	0.82312	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72779	0.3503	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.979;0.997;0.997	T	0.74562	-0.3624	10	0.72032	D	0.01	.	19.4558	0.94889	0.0:0.0:1.0:0.0	.	265;478;478	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	Y	478;478;416;265	ENSP00000331418:D478Y;ENSP00000382933:D478Y;ENSP00000382927:D416Y;ENSP00000387608:D265Y	ENSP00000331418:D478Y	D	+	1	0	PTPRM	8059983	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.380000	0.97202	2.611000	0.88343	0.655000	0.94253	GAT		0.418	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8069983	G	T	8069983	3	4	49	1	0	0	0	0	1	0	0	0	12843	942	33	2	1462	2	PTPRM	18	8069983	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09		8069983	70007265	90	6789										
TCEB3B	51224	broad.mit.edu	37	chr18	44561432	44561432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcttccaccgggccgctaaGtctctggcaaagtcgcccac	9	16	2	0	rs576550803	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr18:44561432G>A	ENST00000332567.4	-	1	556	c.204C>T	c.(202-204)gaC>gaT	p.D68D	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	68	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D68D(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGGCCGCTAAGTCTCTGGCAA	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	18											18	19	19					18																	44561432		2200	4294	6494	42815430	SO:0001819	synonymous_variant	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.204C>T	18.37:g.44561432G>A			42815430	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																				0.652	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		A	44561432	G	A	44561432	2	1	49	1	0	0	0	0	0	0	0	1	15721	1020	36	3		3	TCEB3B	18	44561432	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09	36491449	44561432	33515816	91	6790										
ST8SIA3	51046	broad.mit.edu	37	chr18	55027257	55027257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acaaacatttgtcacctaaaCggctgagcacaggtattctt	7	10	2	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr18:55027257C>T	ENST00000324000.3	+	4	2926	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	298					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.R298W(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GTCACCTAAACGGCTGAGCAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											101	95	97					18																	55027257		2203	4300	6503	53178255	SO:0001583	missense	51046			AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.892C>T	18.37:g.55027257C>T	ENSP00000320431:p.Arg298Trp		53178255	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.021529	0.93462	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.35236	1.32	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65479	-0.6158	10	0.87932	D	0	-7.2102	20.3293	0.98710	0.0:1.0:0.0:0.0	.	298	O43173	SIA8C_HUMAN	W	405;298	ENSP00000320431:R298W	ENSP00000320431:R298W	R	+	1	2	ST8SIA3	53178255	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.576000	0.60915	2.906000	0.99361	0.655000	0.94253	CGG		0.418	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		T	55027257	C	T	55027257	3	4	49	1	0	0	0	0	1	0	0	0	15272	527	19	1	906	1	ST8SIA3	18	55027257	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	10465825	55027257	23049991	92	6791										
FBXO15	201456	broad.mit.edu	37	chr18	71740898	71740898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caggcgatctcaggcacaccGgggaactgaaacaccaaaag	11	12	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr18:71740898G>A	ENST00000419743.2	-	10	1410	c.1331C>T	c.(1330-1332)cCg>cTg	p.P444L	FBXO15_ENST00000580806.1_5'UTR|FBXO15_ENST00000269500.5_Missense_Mutation_p.P368L	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	444						SCF ubiquitin ligase complex (GO:0019005)		p.P368L(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		CAGGCACACCGGGGAACTGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	18											183	172	175					18																	71740898		2203	4300	6503	69891878	SO:0001583	missense	201456			AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1331C>T	18.37:g.71740898G>A	ENSP00000393154:p.Pro444Leu		69891878	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	g	24.2	4.509540	0.85282	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.42131	0.98;0.98	5.9	5.9	0.94986	.	0.049509	0.85682	D	0.000000	T	0.64338	0.2589	M	0.77103	2.36	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.58172	0.834;0.834	T	0.66909	-0.5804	10	0.87932	D	0	-11.1147	20.2814	0.98513	0.0:0.0:1.0:0.0	.	444;368	B3KST3;Q8NCQ5	.;FBX15_HUMAN	L	368;444	ENSP00000269500:P368L;ENSP00000393154:P444L	ENSP00000269500:P368L	P	-	2	0	FBXO15	69891878	1.000000	0.71417	0.958000	0.39756	0.650000	0.38633	7.058000	0.76676	2.809000	0.96659	0.651000	0.88453	CCG		0.478	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		A	71740898	G	A	71740898	3	1	49	1	0	0	0	0	1	0	0	0	5747	1116	39	1	205	1	FBXO15	18	71740898	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	16713641	71740898	6336350	93	6792										
MUC16	94025	broad.mit.edu	37	chr19	9049723	9049723	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttgttggaatggctgagctGacgtctgccccatgactggt	13	9	1	3			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr19:9049723G>T	ENST00000397910.4	-	5	32111	c.31908C>A	c.(31906-31908)gtC>gtA	p.V10636V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10638	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V6269V(1)|p.V10636V(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGCTGAGCTGACGTCTGCCC	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	19											120	110	113					19																	9049723		2003	4175	6178	8910723	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31908C>A	19.37:g.9049723G>T			8910723	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9049723	G	T	9049723	2	4	49	1	0	0	0	0	0	0	0	1	10003	1277	45	2		2	MUC16	19	9049723	Silent	SNP	G	TCGA-AG-3894-01A-01W-1073-09		9049723	50079260	94	6793										
CYP4F11	57834	broad.mit.edu	37	chr19	16038110	16038110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcgtcaacatccgacggtggCggctccacttgtcaccacca	10	16	2	0			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr19:16038110C>T	ENST00000402119.4	-	4	863	c.437G>A	c.(436-438)cGc>cAc	p.R146H	CYP4F11_ENST00000326742.8_Missense_Mutation_p.R146H|CYP4F11_ENST00000591841.1_5'UTR|CYP4F11_ENST00000248041.8_Missense_Mutation_p.R146H	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11									p.R146H(1)		NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						CCGACGGTGGCGGCTCCACTT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	86	87					19																	16038110		2203	4300	6503	15899110	SO:0001583	missense	57834			AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"Cytochrome P450s"	13265	protein-coding gene	gene with protein product		611517	"cytochrome P450, subfamily IVF, polypeptide 11"			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.437G>A	19.37:g.16038110C>T	ENSP00000384588:p.Arg146His		15899110		Missense_Mutation	SNP	ENST00000402119.4	37	CCDS12337.1	.	.	.	.	.	.	.	.	.	.	c	7.904	0.734949	0.15574	.	.	ENSG00000171903	ENST00000402119;ENST00000248041;ENST00000326742	T;T;T	0.69306	-0.39;-0.39;-0.39	2.57	0.0749	0.14397	.	0.084182	0.49305	U	0.000143	T	0.53384	0.1793	L	0.55103	1.725	0.47862	D	0.999532	P;B	0.34757	0.467;0.075	B;B	0.33846	0.171;0.104	T	0.39354	-0.9618	10	0.44086	T	0.13	.	5.2688	0.15613	0.0:0.5083:0.0:0.4917	.	146;146	F8W978;Q9HBI6	.;CP4FB_HUMAN	H	146	ENSP00000384588:R146H;ENSP00000248041:R146H;ENSP00000319859:R146H	ENSP00000248041:R146H	R	-	2	0	CYP4F11	15899110	0.426000	0.25506	0.991000	0.47740	0.429000	0.31625	-0.189000	0.09629	-0.020000	0.14032	0.298000	0.19748	CGC		0.527	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187		T	16038110	C	T	16038110	3	4	49	1	0	0	0	0	1	0	0	0	4192	768	27	1	1173	1	CYP4F11	19	16038110	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	6988387	16038110	43090873	95	6794										
ZNF43	7594	broad.mit.edu	37	chr19	21990430	21990430	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tattttatgtttgaaaaagtTtgaggtgttgtcaaaatcac	8	3	2	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr19:21990430T>G	ENST00000354959.4	-	4	2578	c.2409A>C	c.(2407-2409)caA>caC	p.Q803H	ZNF43_ENST00000595461.1_Missense_Mutation_p.Q797H|ZNF43_ENST00000598381.1_Missense_Mutation_p.Q797H|ZNF43_ENST00000594012.1_Missense_Mutation_p.Q797H	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	803					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q803H(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TTGAAAAAGTTTGAGGTGTTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	19											37	39	38					19																	21990430		2202	4296	6498	21782270	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.2409A>C	19.37:g.21990430T>G	ENSP00000347045:p.Gln803His		21782270	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	T	2.727	-0.265316	0.05754	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.05081	3.5	1.76	-1.36	0.09085	.	.	.	.	.	T	0.03959	0.0111	N	0.25245	0.725	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41752	-0.9491	9	0.62326	D	0.03	.	3.2116	0.06685	0.2288:0.0:0.4586:0.3126	.	803	P17038	ZNF43_HUMAN	H	802;803	ENSP00000347045:Q803H	ENSP00000347045:Q803H	Q	-	3	2	ZNF43	21782270	0.000000	0.05858	0.001000	0.08648	0.116000	0.19942	-4.105000	0.00294	-0.057000	0.13199	0.254000	0.18369	CAA		0.313	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		G	21990430	T	G	21990430	3	3	49	1	0	0	0	0	1	0	0	0	17942	1838	64	4	24	4	ZNF43	19	21990430	Missense_Mutation	SNP	T	TCGA-AG-3894-01A-01W-1073-09	5952320	21990430	37138553	96	6795										
SLC7A9	11136	broad.mit.edu	37	chr19	33355008	33355008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctcaggtactcacagatggCggcggcggccaggcatttca	14	12	3	1	rs140134166	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr19:33355008C>T	ENST00000023064.4	-	4	663	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Missense_Mutation_p.A158T|SLC7A9_ENST00000590341.1_Missense_Mutation_p.A158T	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	158			A -> AA (in CSNU). {ECO:0000269|PubMed:11157794}.		amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)	p.A158T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	TCACAGATGGCGGCGGCGGCC	0.607													C|||	3	0.000599042	0.0023	0	5008	,	,		19212	0		0	False		,,,				2504	0				GBM(181;1335 2108 9644 44178 46689)											1	Substitution - Missense(1)	large_intestine(1)	19						C	THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	49	45	47		472,472	3.9	0.9	19	dbSNP_134	47	0,8600		0,0,4300	no	missense,missense	SLC7A9	NM_001126335.1,NM_014270.4	58,58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign	158/488,158/488	33355008	3,13003	2203	4300	6503	38046848	SO:0001583	missense	11136			AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.472G>A	19.37:g.33355008C>T	ENSP00000023064:p.Ala158Thr		38046848	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331194	0.41297	6.81E-4	0.0	ENSG00000021488	ENST00000023064	D	0.90133	-2.62	4.97	3.92	0.45320	Amino acid permease domain (1);	0.323891	0.37012	N	0.002300	D	0.87637	0.6227	L	0.43598	1.365	0.41734	D	0.989572	B	0.30526	0.283	B	0.32624	0.149	D	0.86194	0.1614	10	0.51188	T	0.08	.	15.5266	0.75915	0.0:0.861:0.139:0.0	.	158	P82251	BAT1_HUMAN	T	158	ENSP00000023064:A158T	ENSP00000023064:A158T	A	-	1	0	SLC7A9	38046848	0.707000	0.27866	0.931000	0.37212	0.059000	0.15707	1.374000	0.34283	1.200000	0.43188	-0.479000	0.04858	GCC		0.607	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			T	33355008	C	T	33355008	3	4	49	1	0	0	0	0	1	0	0	0	14742	768	27	1	1031	1	SLC7A9	19	33355008	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	11364578	33355008	25773975	97	6796										
TULP2	7288	broad.mit.edu	37	chr19	49387079	49387079	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gagaatcacagtcattttccGaggccccaggtatcctaaga	9	11	2	2			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr19:49387079G>A	ENST00000221399.3	-	11	1351	c.1207C>T	c.(1207-1209)Cgg>Tgg	p.R403W		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	403					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.R403W(1)		NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GTCATTTTCCGAGGCCCCAGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	106	107					19																	49387079		2203	4300	6503	54078891	SO:0001583	missense	7288			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1207C>T	19.37:g.49387079G>A	ENSP00000221399:p.Arg403Trp		54078891	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640180	0.47153	.	.	ENSG00000104804	ENST00000221399	D	0.98313	-4.86	4.91	3.85	0.44370	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99171	0.9713	H	0.95574	3.69	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	D	0.99139	1.0855	10	0.87932	D	0	-31.5079	12.4909	0.55899	0.0:0.0:0.8316:0.1684	.	403	O00295	TULP2_HUMAN	W	403	ENSP00000221399:R403W	ENSP00000221399:R403W	R	-	1	2	TULP2	54078891	1.000000	0.71417	0.993000	0.49108	0.034000	0.12701	4.922000	0.63404	1.403000	0.46800	0.650000	0.86243	CGG		0.517	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		A	49387079	G	A	49387079	3	1	49	1	0	0	0	0	1	0	0	0	16814	1057	37	1	367	1	TULP2	19	49387079	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	16032071	49387079	9741904	98	6797										
DEFB119	245932	broad.mit.edu	37	chr20	29976953	29976953	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgactaggaacacagcaccGtttacgatttcggcagcgta	10	11	0	0	rs150443667	byFrequency	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr20:29976953G>A	ENST00000376321.3	-	1	181				DEFB119_ENST00000339144.3_Intron|DEFB119_ENST00000376315.2_Missense_Mutation_p.R48W|DEFB119_ENST00000492344.1_Intron	NM_153289.3	NP_695021.2	Q8N690	DB119_HUMAN	defensin, beta 119						defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.R48W(2)|p.R48R(1)		large_intestine(2)|lung(1)|prostate(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			ACACAGCACCGTTTACGATTT	0.458													G|||	3	0.000599042	0.0023	0	5008	,	,		20150	0		0	False		,,,				2504	0															3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(1)|breast(1)|endometrium(1)	20						G	,TRP/ARG,	2,4404	4.2+/-10.8	0,2,2201	205	176	186		,142,	2.5	0.4	20	dbSNP_134	186	0,8600		0,0,4300	no	intron,missense,intron	DEFB119	NM_153289.2,NM_153323.3,NM_173460.1	,101,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,,	,48/89,	29976953	2,13004	2203	4300	6503	29440614	SO:0001627	intron_variant	245932			AA939044	CCDS13178.1, CCDS33455.1	20q11.21	2007-02-19	2003-10-06		ENSG00000180483	ENSG00000180483		"Defensins, beta"	18099	protein-coding gene	gene with protein product			"defensin, beta 120"	DEFB120		11854508	Standard	NM_153289		Approved	DEFB-19, DEFB-20	uc002wvu.2	Q8N690	OTTHUMG00000032172	ENST00000376321.3:c.61+1272C>T	20.37:g.29976953G>A			29440614	Q5GRG1|Q5JWP1|Q5TH42|Q8N689	Missense_Mutation	SNP	ENST00000376321.3	37	CCDS13178.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	26.1	4.700900	0.88924	4.54E-4	0.0	ENSG00000180483	ENST00000376315	T	0.11821	2.74	3.49	2.54	0.30619	.	1.825100	0.03092	N	0.159957	T	0.10981	0.0268	.	.	.	0.09310	N	0.999994	B	0.33549	0.417	B	0.23018	0.043	T	0.26744	-1.0094	9	0.87932	D	0	-4.3313	7.0046	0.24830	0.1256:0.0:0.8744:0.0	.	48	Q8N690-2	.	W	48	ENSP00000365492:R48W	ENSP00000365492:R48W	R	-	1	2	DEFB119	29440614	0.628000	0.27138	0.391000	0.26233	0.980000	0.70556	0.817000	0.27281	1.053000	0.40415	0.563000	0.77884	CGG		0.458	DEFB119-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078514.1	NM_153289		A	29976953	G	A	29976953	1	1	49	0	1	0	0	0	0	0	0	0	4417	1144	40	1		1	DEFB119	20	29976953	Intron	SNP	G	TCGA-AG-3894-01A-01W-1073-09		29976953	33048567	99	6798										
SLC17A9	63910	broad.mit.edu	37	chr20	61597051	61597051	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtggtctttgcatcagcctcCatcggcctccagaccttcaa	8	15	3	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr20:61597051C>T	ENST00000370351.4	+	10	1166	c.1035C>T	c.(1033-1035)tcC>tcT	p.S345S	SLC17A9_ENST00000370349.3_Silent_p.S339S|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	345					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S345S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CATCAGCCTCCATCGGCCTCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	20											106	115	112					20																	61597051		2088	4215	6303	61067496	SO:0001819	synonymous_variant	63910			AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.1035C>T	20.37:g.61597051C>T			61067496	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Silent	SNP	ENST00000370351.4	37	CCDS42901.1																																																																																				0.637	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		T	61597051	C	T	61597051	2	4	49	1	0	0	0	0	0	0	0	1	14461	581	21	3		3	SLC17A9	20	61597051	Silent	SNP	C	TCGA-AG-3894-01A-01W-1073-09	31620098	61597051	1428469	100	6799										
USP18	11274	broad.mit.edu	37	chr22	18640570	18640570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcccagagagcgtcccagggCctgggactaccctcatggtc	13	15	1	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr22:18640570C>T	ENST00000215794.7	+	2	570	c.140C>T	c.(139-141)gCc>gTc	p.A47V		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	47					cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.A47V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						CGTCCCAGGGCCTGGGACTAC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	22											101	99	100					22																	18640570		2203	4300	6503	17020570	SO:0001583	missense	11274			AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"Ubiquitin-specific peptidases"	12616	protein-coding gene	gene with protein product		607057	"ubiquitin specific protease 18"			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.140C>T	22.37:g.18640570C>T	ENSP00000215794:p.Ala47Val		17020570	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	.	.	.	.	.	.	.	.	.	.	.	17.88	3.497655	0.64186	.	.	ENSG00000184979	ENST00000215794	T	0.06933	3.24	4.76	4.76	0.60689	.	0.764858	0.11957	N	0.513084	T	0.07143	0.0181	L	0.27053	0.805	0.26190	N	0.979593	P	0.35077	0.483	B	0.30943	0.122	T	0.25082	-1.0142	10	0.34782	T	0.22	.	13.4545	0.61191	0.0:1.0:0.0:0.0	.	47	Q9UMW8	UBP18_HUMAN	V	47	ENSP00000215794:A47V	ENSP00000215794:A47V	A	+	2	0	USP18	17020570	0.805000	0.28982	0.957000	0.39632	0.365000	0.29674	1.746000	0.38288	2.626000	0.88956	0.591000	0.81541	GCC		0.557	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1			T	18640570	C	T	18640570	3	4	49	1	0	0	0	0	1	0	0	0	17089	739	26	3	142	3	USP18	22	18640570	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		18640570	32663996	101	6800										
BPIL2	254240	broad.mit.edu	37	chr22	32829708	32829708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaaccctgagcacttacccGggagagcacgttgccaaggc	11	14	0	2	rs371535232		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chr22:32829708G>A	ENST00000397452.1	-	10	1086	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W	BPIFC_ENST00000534972.1_Missense_Mutation_p.R50W|BPIFC_ENST00000432451.2_Missense_Mutation_p.R140W|BPIFC_ENST00000300399.3_Missense_Mutation_p.R326W			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	326						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)	p.R326W(1)									GCACTTACCCGGGAGAGCACG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	22						G	TRP/ARG	0,4406		0,0,2203	99	93	95		976	1.2	0.9	22		95	1,8599	1.2+/-3.3	0,1,4299	no	missense	BPIFC	NM_174932.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	326/508	32829708	1,13005	2203	4300	6503	31159708	SO:0001583	missense	254240			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.976C>T	22.37:g.32829708G>A	ENSP00000380594:p.Arg326Trp		31159708	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511912	0.44660	0.0	1.16E-4	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	5.75	1.23	0.21249	.	0.510840	0.21369	N	0.075663	T	0.06781	0.0173	L	0.44542	1.39	0.27177	N	0.960751	B;B	0.20780	0.048;0.038	B;B	0.15052	0.012;0.008	T	0.25012	-1.0144	10	0.62326	D	0.03	-0.2263	4.6379	0.12534	0.1646:0.0:0.5195:0.3159	.	140;326	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	W	326;326;50;140	ENSP00000380594:R326W;ENSP00000300399:R326W;ENSP00000439123:R50W;ENSP00000408920:R140W	ENSP00000300399:R326W	R	-	1	2	BPIFC	31159708	1.000000	0.71417	0.854000	0.33618	0.912000	0.54170	0.880000	0.28159	0.057000	0.16193	0.655000	0.94253	CGG		0.418	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32829708	G	A	32829708	3	1	49	1	0	0	0	0	1	0	0	0	1495	1115	39	1	575	1	BPIL2	22	32829708	Missense_Mutation	SNP	G	TCGA-AG-3894-01A-01W-1073-09	14189138	32829708	18474858	102	6801										
IL1RAPL2	26280	broad.mit.edu	37	chrX	104984642	104984642	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atacctgccatgttgaaaacCgaaatggacggaaacatgcc	9	10	0	1			TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chrX:104984642C>T	ENST00000372582.1	+	8	1762	c.1006C>T	c.(1006-1008)Cga>Tga	p.R336*	IL1RAPL2_ENST00000344799.4_Nonsense_Mutation_p.R336*|IL1RAPL2_ENST00000485671.1_3'UTR	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	336	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R336*(2)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGTTGAAAACCGAAATGGACG	0.378																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											76	67	70					X																	104984642		2203	4300	6503	104871298	SO:0001587	stop_gained	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1006C>T	X.37:g.104984642C>T	ENSP00000361663:p.Arg336*		104871298	Q2M3U3|Q9NZN0	Nonsense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	39	7.831195	0.98513	.	.	ENSG00000189108	ENST00000372582;ENST00000344799	.	.	.	5.61	3.59	0.41128	.	0.000000	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	14.7819	0.69774	0.3377:0.6623:0.0:0.0	.	.	.	.	X	336	.	ENSP00000344976:R336X	R	+	1	2	IL1RAPL2	104871298	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.084000	0.30828	1.077000	0.40990	0.600000	0.82982	CGA		0.378	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	104984642	C	T	104984642	4	4	49	1	0	0	0	0	0	1	0	0	7683	644	23	1	1032	1	IL1RAPL2	23	104984642	Nonsense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09		104984642	50285918	103	6802										
CNGA2	1260	broad.mit.edu	37	chrX	150908119	150908119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcctgactcattcctcgagCgttttcgtgggcctgaactc	11	13	1	2	rs141559818		TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3894-01A-01W-1073-09	TCGA-AG-3894-10A-01W-1073-09	g.chrX:150908119C>T	ENST00000329903.4	+	3	322	c.289C>T	c.(289-291)Cgt>Tgt	p.R97C		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	97			R -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.R97C(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					ATTCCTCGAGCGTTTTCGTGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	CYS/ARG	1,3834		0,1,0,1631,571	123	92	103		289	4.6	1	X	dbSNP_134	103	1,6727		0,0,1,2428,1871	no	missense	CNGA2	NM_005140.1	180	0,1,1,4059,2442	TT,TC,T,CC,C		0.0149,0.0261,0.0189	possibly-damaging	97/665	150908119	2,10561	2203	4300	6503	150658775	SO:0001583	missense	1260			S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.289C>T	X.37:g.150908119C>T	ENSP00000328478:p.Arg97Cys		150658775	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.111017	0.77210	2.61E-4	1.49E-4	ENSG00000183862	ENST00000329903	T	0.61627	0.09	5.58	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.73814	0.3635	M	0.81802	2.56	0.50813	D	0.999892	D	0.89917	1.0	D	0.83275	0.996	T	0.76033	-0.3107	10	0.59425	D	0.04	.	9.2713	0.37673	0.3734:0.6265:0.0:0.0	.	97	Q16280	CNGA2_HUMAN	C	97	ENSP00000328478:R97C	ENSP00000328478:R97C	R	+	1	0	CNGA2	150658775	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	2.903000	0.48711	2.338000	0.79540	0.529000	0.55759	CGT		0.547	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		T	150908119	C	T	150908119	3	4	49	1	0	0	0	0	1	0	0	0	3603	768	27	1	299	1	CNGA2	23	150908119	Missense_Mutation	SNP	C	TCGA-AG-3894-01A-01W-1073-09	45923477	150908119	4362441	104	6803										
NPPB	4879	broad.mit.edu	37	chr1	11918387	11918387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gggtgtagaggaccattttgCggtgcccacggatgccctcg	15	11	0	1	rs143526178	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:11918387C>T	ENST00000376468.3	-	2	369	c.272G>A	c.(271-273)cGc>cAc	p.R91H		NM_002521.2	NP_002512.1	P16860	ANFB_HUMAN	natriuretic peptide B	91					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|protein complex (GO:0043234)	diuretic hormone activity (GO:0008613)|hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.R91H(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Carvedilol(DB01136)	GACCATTTTGCGGTGCCCACG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	1						T	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	49	46	47		272	-7.9	0	1	dbSNP_134	47	0,8600		0,0,4300	yes	missense	NPPB	NM_002521.2	29	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	91/135	11918387	3,13003	2203	4300	6503	11840974	SO:0001583	missense	4879			BC025785	CCDS140.1	1p36.2	2014-01-30	2010-11-09		ENSG00000120937	ENSG00000120937		"Endogenous ligands"	7940	protein-coding gene	gene with protein product		600295	"natriuretic peptide precursor B"			2597152	Standard	NM_002521		Approved		uc001atj.3	P16860	OTTHUMG00000002389	ENST00000376468.3:c.272G>A	1.37:g.11918387C>T	ENSP00000365651:p.Arg91His		11840974	B0ZBE9|Q6FGY0|Q9P2Q7	Missense_Mutation	SNP	ENST00000376468.3	37	CCDS140.1	.	.	.	.	.	.	.	.	.	.	c	11.17	1.559003	0.27827	6.81E-4	0.0	ENSG00000120937	ENST00000376468	T	0.25414	1.8	3.96	-7.91	0.01165	.	.	.	.	.	T	0.13841	0.0335	N	0.25647	0.755	0.09310	N	1	B	0.22414	0.069	B	0.15052	0.012	T	0.18085	-1.0348	9	0.24483	T	0.36	.	10.6283	0.45521	0.107:0.1661:0.0:0.727	.	91	P16860	ANFB_HUMAN	H	91	ENSP00000365651:R91H	ENSP00000365651:R91H	R	-	2	0	NPPB	11840974	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.301000	0.00133	-3.508000	0.00150	-1.979000	0.00458	CGC		0.642	NPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006854.1	NM_002521		T	11918387	C	T	11918387	3	4	50	1	0	0	0	0	1	0	0	0	10623	768	27	1	140	1	NPPB	1	11918387	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09		11918387	237332234	1	6804										
ARHGEF10L	55160	broad.mit.edu	37	chr1	17953898	17953898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggccctcacagagctggagaCgctggctgagaagctgaacg	15	11	1	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:17953898C>T	ENST00000361221.3	+	15	1643	c.1484C>T	c.(1483-1485)aCg>aTg	p.T495M	ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.T456M|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.T495M|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.T456M|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.T273M|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.T203M|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375420.3_Missense_Mutation_p.T253M	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	495	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T495M(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GAGCTGGAGACGCTGGCTGAG	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	1											43	46	45					1																	17953898		2203	4300	6503	17826485	SO:0001583	missense	55160			AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.1484C>T	1.37:g.17953898C>T	ENSP00000355060:p.Thr495Met		17826485	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719917	0.68844	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375420;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09;1.52	4.94	4.94	0.65067	Dbl homology (DH) domain (5);	0.107908	0.64402	D	0.000007	T	0.76357	0.3976	M	0.77486	2.375	0.40610	D	0.981666	D;P;D;D;D;D;D;P	0.63046	0.979;0.882;0.992;0.969;0.979;0.987;0.969;0.956	P;B;P;P;P;P;P;P	0.58660	0.663;0.393;0.843;0.625;0.611;0.782;0.625;0.742	T	0.79460	-0.1794	10	0.52906	T	0.07	-24.3543	16.8823	0.86066	0.0:1.0:0.0:0.0	.	273;253;495;203;261;456;456;495	Q5VXI4;B4DTE2;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;.;ARGAL_HUMAN	M	495;456;495;456;253;273;273;203	ENSP00000355060:T495M;ENSP00000399401:T456M;ENSP00000394621:T495M;ENSP00000364564:T456M;ENSP00000364569:T253M;ENSP00000364557:T273M;ENSP00000167825:T203M	ENSP00000167825:T203M	T	+	2	0	ARHGEF10L	17826485	0.990000	0.36364	1.000000	0.80357	0.940000	0.58332	2.890000	0.48609	2.568000	0.86640	0.462000	0.41574	ACG		0.622	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		T	17953898	C	T	17953898	3	4	50	1	0	0	0	0	1	0	0	0	895	536	19	1	1538	1	ARHGEF10L	1	17953898	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	6035511	17953898	231296723	2	6805										
HMGCL	3155	broad.mit.edu	37	chr1	24147022	24147022	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tttcattttgtagtccatctCggggaccaacttccacaatt	6	11	2	0	rs121964997		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:24147022C>T	ENST00000374490.3	-	2	165	c.122G>A	c.(121-123)cGa>cAa	p.R41Q	HMGCL_ENST00000374483.4_Missense_Mutation_p.R16Q|HMGCL_ENST00000509389.1_5'UTR|HMGCL_ENST00000436439.2_Missense_Mutation_p.R41Q	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	41			R -> Q (in HMGCLD; loss of activity and of proton exchange). {ECO:0000269|PubMed:17173698, ECO:0000269|PubMed:9463337}.		acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R41Q(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		TAGTCCATCTCGGGGACCAAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM980987	HMGCL	M	rs121964997						161	142	148					1																	24147022		2203	4300	6503	24019609	SO:0001583	missense	3155			BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.122G>A	1.37:g.24147022C>T	ENSP00000363614:p.Arg41Gln		24019609	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Missense_Mutation	SNP	ENST00000374490.3	37	CCDS243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.275565|5.275565	0.95459|0.95459	.|.	.|.	ENSG00000117305|ENSG00000117305	ENST00000235958|ENST00000374490;ENST00000436439;ENST00000374483;ENST00000543166	.|D;D;D	.|0.99860	.|-7.25;-7.19;-7.25	5.27|5.27	4.36|4.36	0.52297|0.52297	.|Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	.|0.158981	.|0.53938	.|D	.|0.000045	D|D	0.99919|0.99919	0.9962|0.9962	H|H	0.99391|0.99391	4.545|4.545	0.58432|0.58432	A|A	0.999998|0.999998	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.79108	.|0.99;0.992;0.986;0.992	D|D	0.96097|0.96097	0.9066|0.9066	4|9	.|0.87932	.|D	.|0	-24.786|-24.786	13.0874|13.0874	0.59149|0.59149	0.0:0.9216:0.0:0.0784|0.0:0.9216:0.0:0.0784	.|.	.|41;41;16;41	.|B4DUP4;Q6IBC0;B1AK13;P35914	.|.;.;.;HMGCL_HUMAN	K|Q	37|41;41;16;16	.|ENSP00000363614:R41Q;ENSP00000389281:R41Q;ENSP00000363607:R16Q	.|ENSP00000363607:R16Q	E|R	-|-	1|2	0|0	HMGCL|HMGCL	24019609|24019609	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.070000|7.070000	0.76763|0.76763	1.474000|1.474000	0.48178|0.48178	0.558000|0.558000	0.71614|0.71614	GAG|CGA		0.403	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		T	24147022	C	T	24147022	3	4	50	1	0	0	0	0	1	0	0	0	7250	884	31	1	887	1	HMGCL	1	24147022	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	6193124	24147022	225103599	3	6806										
GMEB1	10691	broad.mit.edu	37	chr1	29040687	29040687	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gatgcctgtgagcactcctaAgcctccaaaaaggccccggc	10	15	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:29040687A>T	ENST00000294409.2	+	10	1214	c.1124A>T	c.(1123-1125)aAg>aTg	p.K375M	GMEB1_ENST00000373816.1_Missense_Mutation_p.K365M|GMEB1_ENST00000480454.1_3'UTR|GMEB1_ENST00000361872.4_Missense_Mutation_p.K365M	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	375					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.K365M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		AGCACTCCTAAGCCTCCAAAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	84	83					1																	29040687		2203	4300	6503	28913274	SO:0001583	missense	10691			AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.1124A>T	1.37:g.29040687A>T	ENSP00000294409:p.Lys375Met		28913274	B1AT48|Q9NWH1|Q9UKD0	Missense_Mutation	SNP	ENST00000294409.2	37	CCDS327.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912999	0.72983	.	.	ENSG00000162419	ENST00000373816;ENST00000456852;ENST00000361872;ENST00000294409	T;T;T	0.57752	0.39;0.39;0.38	5.86	5.86	0.93980	.	0.051827	0.64402	D	0.000001	T	0.66674	0.2813	L	0.47716	1.5	0.34213	D	0.67454	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.99	T	0.76435	-0.2960	10	0.66056	D	0.02	1.1832	15.2494	0.73532	1.0:0.0:0.0:0.0	.	375;365	Q9Y692;B1AT47	GMEB1_HUMAN;.	M	365;341;365;375	ENSP00000362922:K365M;ENSP00000355186:K365M;ENSP00000294409:K375M	ENSP00000294409:K375M	K	+	2	0	GMEB1	28913274	1.000000	0.71417	0.998000	0.56505	0.918000	0.54935	7.514000	0.81750	2.240000	0.73641	0.533000	0.62120	AAG		0.557	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582		T	29040687	A	T	29040687	3	4	50	1	0	0	0	0	1	0	0	0	6507	72	3	5	1158	5	GMEB1	1	29040687	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	4893665	29040687	220209934	4	6807										
POGZ	23126	broad.mit.edu	37	chr1	151384851	151384851	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gtggctcactttcaaacgccCattcacagatcttgcacttg	7	13	4	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:151384851C>T	ENST00000271715.2	-	11	2014	c.1700G>A	c.(1699-1701)tGg>tAg	p.W567*	POGZ_ENST00000531094.1_Nonsense_Mutation_p.W505*|POGZ_ENST00000392723.1_Nonsense_Mutation_p.W514*|POGZ_ENST00000368863.2_Nonsense_Mutation_p.W472*|POGZ_ENST00000409503.1_Nonsense_Mutation_p.W558*|POGZ_ENST00000361398.3_Nonsense_Mutation_p.W514*|POGZ_ENST00000491586.1_Nonsense_Mutation_p.W514*|POGZ_ENST00000540984.1_5'UTR	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	567					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W567*(1)|p.W514*(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTCAAACGCCCATTCACAGAT	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											92	85	87					1																	151384851		2203	4300	6503	149651475	SO:0001587	stop_gained	23126			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.1700G>A	1.37:g.151384851C>T	ENSP00000271715:p.Trp567*		149651475	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Nonsense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	C	37	6.034781	0.97221	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000529669	.	.	.	4.95	4.02	0.46733	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-8.1352	13.3574	0.60635	0.1589:0.8411:0.0:0.0	.	.	.	.	X	514;567;514;472;558;505;514;16	.	ENSP00000271715:W567X	W	-	2	0	POGZ	149651475	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.579000	0.53900	1.274000	0.44362	0.557000	0.71058	TGG		0.398	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		T	151384851	C	T	151384851	4	4	50	1	0	0	0	0	0	1	0	0	12217	595	21	3	2568	3	POGZ	1	151384851	Nonsense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	122344164	151384851	97865770	5	6808										
FLG	2312	broad.mit.edu	37	chr1	152279751	152279751	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gagctgtcggcccgagaggaAgcttcatggtgacgcgaccc	15	12	1	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:152279751A>T	ENST00000368799.1	-	3	7646	c.7611T>A	c.(7609-7611)gcT>gcA	p.A2537A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2537	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.A2537A(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCGAGAGGAAGCTTCATGGT	0.587									Ichthyosis																																							1	Substitution - coding silent(1)	large_intestine(1)	1											239	259	252					1																	152279751		2203	4299	6502	150546375	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7611T>A	1.37:g.152279751A>T			150546375	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152279751	A	T	152279751	2	4	50	1	0	0	0	0	0	0	0	1	5941	59	3	5		5	FLG	1	152279751	Silent	SNP	A	TCGA-AG-3896-01A-01W-1073-09	894900	152279751	96970870	6	6809										
CACNA1S	779	broad.mit.edu	37	chr1	201029943	201029943	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gggcatactgtacacattggCgctgtgacacatacaacagg	11	10	0	1	rs1800559		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:201029943C>T	ENST00000362061.3	-	26	3483	c.3257G>A	c.(3256-3258)cGc>cAc	p.R1086H	CACNA1S_ENST00000367338.3_Splice_Site_p.R1086H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1086			R -> H (in MHS5; dbSNP:rs1800559). {ECO:0000269|PubMed:9199552}.		axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R1086H(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TACACATTGGCGCTGTGACAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM970210	CACNA1S	M	rs1800559						211	204	206					1																	201029943		2203	4300	6503	199296566	SO:0001630	splice_region_variant	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.3256-1G>A	1.37:g.201029943C>T			199296566	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044776	0.55110	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96885	-4.16;-4.08	5.17	4.26	0.50523	.	0.152379	0.64402	D	0.000015	D	0.98460	0.9487	M	0.93638	3.44	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.99342	1.0912	10	0.87932	D	0	.	13.6178	0.62120	0.0:0.9234:0.0:0.0766	rs1800559;rs28931587	1086	Q13698	CAC1S_HUMAN	H	1086	ENSP00000355192:R1086H;ENSP00000356307:R1086H	ENSP00000355192:R1086H	R	-	2	0	CACNA1S	199296566	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	7.774000	0.85478	1.297000	0.44761	-0.136000	0.14681	CGC		0.562	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	Missense_Mutation	T	201029943	C	T	201029943	5	4	50	1	0	0	0	0	0	0	1	0	2553	782	27	1	2440	1	CACNA1S	1	201029943	Splice_Site	SNP	C	TCGA-AG-3896-01A-01W-1073-09	48750192	201029943	48220678	7	6810										
SLC30A1	7779	broad.mit.edu	37	chr1	211749320	211749320	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tggatctaaatatagcacccAgcaaggaccagcctcataaa	7	11	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:211749320A>T	ENST00000367001.4	-	2	1063	c.934T>A	c.(934-936)Tgg>Agg	p.W312R		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	312					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.W312R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TATAGCACCCAGCAAGGACCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											139	149	145					1																	211749320		2203	4300	6503	209815943	SO:0001583	missense	7779			AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.934T>A	1.37:g.211749320A>T	ENSP00000355968:p.Trp312Arg		209815943	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	37	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650585	0.67472	.	.	ENSG00000170385	ENST00000367001	T	0.74002	-0.8	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.89529	0.6741	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91989	0.5601	10	0.62326	D	0.03	-7.5743	15.4963	0.75653	1.0:0.0:0.0:0.0	.	312	Q9Y6M5	ZNT1_HUMAN	R	312	ENSP00000355968:W312R	ENSP00000355968:W312R	W	-	1	0	SLC30A1	209815943	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.994000	0.93529	2.061000	0.61500	0.460000	0.39030	TGG		0.373	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			T	211749320	A	T	211749320	3	4	50	1	0	0	0	0	1	0	0	0	14590	188	7	5	593	5	SLC30A1	1	211749320	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	10719377	211749320	37501301	8	6811										
USH2A	7399	broad.mit.edu	37	chr1	216062088	216062088	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aatcacagatgttggagtatCagagaacagctctggacttg	11	7	3	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:216062088C>T	ENST00000307340.3	-	41	8289	c.7903G>A	c.(7903-7905)Gat>Aat	p.D2635N	USH2A_ENST00000366943.2_Missense_Mutation_p.D2635N|RP5-1111A8.3_ENST00000414995.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2635	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.D2635N(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTTGGAGTATCAGAGAACAGC	0.498										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											84	89	88					1																	216062088		2203	4300	6503	214128711	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7903G>A	1.37:g.216062088C>T	ENSP00000305941:p.Asp2635Asn		214128711	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665357	0.88251	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.56776	0.44;0.44	5.3	4.36	0.52297	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.159730	0.28706	N	0.014401	T	0.63721	0.2535	L	0.56769	1.78	0.41257	D	0.986755	D	0.76494	0.999	D	0.65323	0.934	T	0.60525	-0.7246	10	0.12103	T	0.63	.	14.8673	0.70427	0.1489:0.8511:0.0:0.0	.	2635	O75445	USH2A_HUMAN	N	2635	ENSP00000305941:D2635N;ENSP00000355910:D2635N	ENSP00000305941:D2635N	D	-	1	0	USH2A	214128711	1.000000	0.71417	0.986000	0.45419	0.964000	0.63967	4.378000	0.59568	1.165000	0.42670	0.655000	0.94253	GAT		0.498	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216062088	C	T	216062088	3	4	50	1	0	0	0	0	1	0	0	0	17076	826	29	3	7833	3	USH2A	1	216062088	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	4312768	216062088	33188533	9	6812										
RYR2	6262	broad.mit.edu	37	chr1	237947690	237947690	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gaaagcgagaaggagaggccGgaagagcaggggccgaggat	20	6	0	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr1:237947690G>A	ENST00000366574.2	+	90	12995	c.12678G>A	c.(12676-12678)ccG>ccA	p.P4226P	RYR2_ENST00000542537.1_Silent_p.P4210P|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.P4232P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4226					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.P4224P(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGAGAGGCCGGAAGAGCAGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	1											59	66	64					1																	237947690		1978	4163	6141	236014313	SO:0001819	synonymous_variant	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12678G>A	1.37:g.237947690G>A			236014313	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.547	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237947690	G	A	237947690	2	1	50	1	0	0	0	0	0	0	0	1	13806	1103	39	1		1	RYR2	1	237947690	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	21885602	237947690	11302931	10	6813										
TMEM214	54867	broad.mit.edu	37	chr2	27259422	27259422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	caccatcatgtgggccctggGtcaagcaggttttgccaacc	11	13	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:27259422G>A	ENST00000238788.9	+	6	850	c.788G>A	c.(787-789)gGt>gAt	p.G263D	TMEM214_ENST00000404032.3_Missense_Mutation_p.G218D	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	263					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.G263D(1)		kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TGGGCCCTGGGTCAAGCAGGT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	109	109					2																	27259422		1934	4142	6076	27112926	SO:0001583	missense	54867				CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.788G>A	2.37:g.27259422G>A	ENSP00000238788:p.Gly263Asp		27112926	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.188699|5.188699	0.94923|0.94923	.|.	.|.	ENSG00000119777|ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397|ENST00000425720	T;T|.	0.69561|.	-0.41;-0.41|.	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77096|0.77096	0.4080|0.4080	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.996;0.999|.	T|T	0.76041|0.76041	-0.3104|-0.3104	10|5	0.48119|.	T|.	0.1|.	-11.1876|-11.1876	19.0913|19.0913	0.93228|0.93228	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	218;263|.	Q6NUQ4-2;Q6NUQ4|.	.;TM214_HUMAN|.	D|I	263;218;5|22	ENSP00000238788:G263D;ENSP00000384417:G218D|.	ENSP00000238788:G263D|.	G|V	+|+	2|1	0|0	TMEM214|TMEM214	27112926|27112926	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.976000|0.976000	0.68499|0.68499	9.234000|9.234000	0.95347|0.95347	2.634000|2.634000	0.89283|0.89283	0.561000|0.561000	0.74099|0.74099	GGT|GTC		0.557	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		A	27259422	G	A	27259422	3	1	50	1	0	0	0	0	1	0	0	0	16176	1261	44	3	810	3	TMEM214	2	27259422	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		27259422	215939951	11	6814										
RASGRP3	25780	broad.mit.edu	37	chr2	33783344	33783344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggcctgcaggagatttgcccGggcgccctccttgagcagtg	15	13	0	2	rs375130686		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:33783344G>A	ENST00000403687.3	+	16	2386	c.1646G>A	c.(1645-1647)cGg>cAg	p.R549Q	RASGRP3_ENST00000402538.3_Missense_Mutation_p.R549Q|AC020594.5_ENST00000437680.1_RNA|RASGRP3_ENST00000407811.1_Missense_Mutation_p.R548Q	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	549					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.R549Q(2)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					AGATTTGCCCGGGCGCCCTCC	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	2						G	GLN/ARG,GLN/ARG,GLN/ARG	0,3830		0,0,1915	52	54	53		1646,1643,1646	5.1	1	2		53	2,8212		0,2,4105	no	missense,missense,missense	RASGRP3	NM_001139488.1,NM_015376.2,NM_170672.2	43,43,43	0,2,6020	AA,AG,GG		0.0243,0.0,0.0166	possibly-damaging,possibly-damaging,possibly-damaging	549/691,548/690,549/691	33783344	2,12042	1915	4107	6022	33636848	SO:0001583	missense	25780			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1646G>A	2.37:g.33783344G>A	ENSP00000384192:p.Arg549Gln		33636848	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.584040	0.28268	0.0	2.43E-4	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.77358	-1.08;-1.08;-1.09	5.14	5.14	0.70334	.	0.625289	0.15897	N	0.239273	T	0.68348	0.2991	L	0.28608	0.87	0.35828	D	0.825086	B;B	0.21821	0.061;0.061	B;B	0.17722	0.019;0.019	T	0.65944	-0.6045	10	0.11794	T	0.64	-15.3144	18.9666	0.92698	0.0:0.0:1.0:0.0	.	548;549	D6W583;Q8IV61	.;GRP3_HUMAN	Q	549;549;548	ENSP00000385886:R549Q;ENSP00000384192:R549Q;ENSP00000383917:R548Q	ENSP00000385886:R549Q	R	+	2	0	RASGRP3	33636848	1.000000	0.71417	0.996000	0.52242	0.697000	0.40408	3.043000	0.49823	2.537000	0.85549	0.650000	0.86243	CGG		0.552	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		A	33783344	G	A	33783344	3	1	50	1	0	0	0	0	1	0	0	0	13113	1116	39	1	1700	1	RASGRP3	2	33783344	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	6523922	33783344	209416029	12	6815										
VRK2	7444	broad.mit.edu	37	chr2	58386817	58386817	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgttagtatttcttgctttaTtttttctctgaagatgatac	6	5	2	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:58386817T>G	ENST00000435505.2	+	16	2261	c.1516T>G	c.(1516-1518)Ttt>Gtt	p.F506V	VRK2_ENST00000412104.2_3'UTR|VRK2_ENST00000340157.4_Missense_Mutation_p.F506V|FANCL_ENST00000403295.3_3'UTR|FANCL_ENST00000233741.4_3'UTR|VRK2_ENST00000440705.2_Missense_Mutation_p.F483V|FANCL_ENST00000402135.3_3'UTR|VRK2_ENST00000417641.2_3'UTR			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	506	Interaction with MAP3K7.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F506V(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TCTTGCTTTATTTTTTCTCTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											141	143	142					2																	58386817		2203	4300	6503	58240321	SO:0001583	missense	7444			AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.1516T>G	2.37:g.58386817T>G	ENSP00000408002:p.Phe506Val		58240321	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.902599	0.52227	.	.	ENSG00000028116	ENST00000435505;ENST00000340157;ENST00000440705	T;T;T	0.04917	3.53;3.53;3.53	6.16	4.95	0.65309	.	0.681687	0.14169	N	0.336844	T	0.04497	0.0123	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42172	-0.9467	10	0.87932	D	0	-2.9189	12.1733	0.54172	0.128:0.0:0.0:0.872	.	506	Q86Y07	VRK2_HUMAN	V	506;506;483	ENSP00000408002:F506V;ENSP00000342381:F506V;ENSP00000398323:F483V	ENSP00000342381:F506V	F	+	1	0	VRK2	58240321	0.983000	0.35010	0.980000	0.43619	0.739000	0.42172	3.491000	0.53252	2.367000	0.80283	0.528000	0.53228	TTT		0.318	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		G	58386817	T	G	58386817	3	3	50	1	0	0	0	0	1	0	0	0	17260	1493	52	4	1575	4	VRK2	2	58386817	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09	24603473	58386817	184812556	13	6816										
MOGS	7841	broad.mit.edu	37	chr2	74688817	74688817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atgaggtggggtccagcagtCgcagcagcaagggaaaaaga	16	7	0	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:74688817C>T	ENST00000233616.4	-	4	2261	c.2099G>A	c.(2098-2100)cGa>cAa	p.R700Q	MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000452063.2_Missense_Mutation_p.R594Q	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	700					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)	p.R700Q(1)		cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						GTCCAGCAGTCGCAGCAGCAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											65	77	73					2																	74688817		2026	4181	6207	74542325	SO:0001583	missense	7841			X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"glucosidase I", "processing A-glucosidase I"	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.2099G>A	2.37:g.74688817C>T	ENSP00000233616:p.Arg700Gln		74542325	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	C	0.085	-1.177173	0.01633	.	.	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.41758	0.99;0.99	5.01	3.2	0.36748	Six-hairpin glycosidase-like (1);	0.250170	0.40222	N	0.001153	T	0.15609	0.0376	N	0.03967	-0.31	0.29795	N	0.83294	B	0.16396	0.017	B	0.12837	0.008	T	0.22836	-1.0205	10	0.08837	T	0.75	-10.4167	6.558	0.22471	0.0:0.7041:0.0:0.2959	.	700	Q13724	MOGS_HUMAN	Q	700;594	ENSP00000233616:R700Q;ENSP00000388201:R594Q	ENSP00000233616:R700Q	R	-	2	0	MOGS	74542325	1.000000	0.71417	0.492000	0.27490	0.829000	0.46940	3.367000	0.52350	0.696000	0.31696	-0.448000	0.05591	CGA		0.617	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		T	74688817	C	T	74688817	3	4	50	1	0	0	0	0	1	0	0	0	9727	884	31	1	418	1	MOGS	2	74688817	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	16302000	74688817	168510556	14	6817										
TSGA10	80705	broad.mit.edu	37	chr2	99636911	99636911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tctgactcctcaggagttcaAtttcagaatgagcagaatct	8	9	5	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:99636911A>G	ENST00000393483.3	-	18	2493	c.1649T>C	c.(1648-1650)aTt>aCt	p.I550T	TSGA10_ENST00000410001.1_Missense_Mutation_p.I550T|TSGA10_ENST00000355053.4_Missense_Mutation_p.I550T|TSGA10_ENST00000539964.1_Missense_Mutation_p.I550T	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	550					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.I550T(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CAGGAGTTCAATTTCAGAATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											52	51	51					2																	99636911		2203	4300	6503	99003343	SO:0001583	missense	80705			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.1649T>C	2.37:g.99636911A>G	ENSP00000377123:p.Ile550Thr		99003343	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.029073	0.54790	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	T;T;T;T;T;T	0.77877	2.56;2.56;2.56;2.56;-1.13;2.56	5.49	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.74215	0.3687	L	0.43152	1.355	0.39652	D	0.970478	P	0.51351	0.944	P	0.49999	0.628	T	0.71337	-0.4623	10	0.27082	T	0.32	-19.6474	9.5464	0.39284	0.8538:0.0:0.1462:0.0	.	550	Q9BZW7	TSG10_HUMAN	T	550;550;550;550;480;550	ENSP00000377123:I550T;ENSP00000386956:I550T;ENSP00000347161:I550T;ENSP00000444419:I550T;ENSP00000386508:I480T;ENSP00000377122:I550T	ENSP00000347161:I550T	I	-	2	0	TSGA10	99003343	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.892000	0.48625	1.089000	0.41292	0.528000	0.53228	ATT		0.373	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		G	99636911	A	G	99636911	3	3	50	1	0	0	0	0	1	0	0	0	16657	101	4	4	463	4	TSGA10	2	99636911	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	24948094	99636911	143562462	15	6818										
RAPGEF4	11069	broad.mit.edu	37	chr2	173882219	173882219	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cagaagcgccagcctatccgCggctctgatgaaggtgagaa	13	11	1	4	rs34965602	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:173882219C>T	ENST00000397081.3	+	21	2138	c.1995C>T	c.(1993-1995)cgC>cgT	p.R665R	RAPGEF4_ENST00000535187.1_Silent_p.R445R|RAPGEF4_ENST00000409036.1_Silent_p.R665R|RAPGEF4_ENST00000538974.1_Silent_p.R494R|RAPGEF4_ENST00000540783.1_Silent_p.R512R|RAPGEF4_ENST00000397087.3_Silent_p.R521R|RAPGEF4_ENST00000264111.6_Silent_p.R664R|RAPGEF4_ENST00000539331.1_Silent_p.R512R	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	665					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.R665R(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			AGCCTATCCGCGGCTCTGATG	0.473													C|||	4	0.000798722	0	0.0014	5008	,	,		19508	0		0	False		,,,				2504	0.0031															1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	1,3809		0,1,1904	56	58	57		1563,1995	-9.7	0.3	2	dbSNP_126	57	7,8261		0,7,4127	no	coding-synonymous,coding-synonymous	RAPGEF4	NM_001100397.1,NM_007023.3	,	0,8,6031	TT,TC,CC		0.0847,0.0262,0.0662	,	521/868,665/1012	173882219	8,12070	1905	4134	6039	173590465	SO:0001819	synonymous_variant	11069			U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1995C>T	2.37:g.173882219C>T			173590465	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Silent	SNP	ENST00000397081.3	37	CCDS42775.1																																																																																				0.473	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		T	173882219	C	T	173882219	2	4	50	1	0	0	0	0	0	0	0	1	13083	755	27	1		1	RAPGEF4	2	173882219	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	74245308	173882219	69317154	16	6819										
GIGYF2	26058	broad.mit.edu	37	chr2	233681635	233681635	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	caaaacgggaagaggaagagCgaaagaggcaggaagaactc	15	6	0	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr2:233681635C>T	ENST00000409547.1	+	22	2574	c.2263C>T	c.(2263-2265)Cga>Tga	p.R755*	GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.R755*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.R749*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.R776*|GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.R777*|GIGYF2_ENST00000452341.2_Nonsense_Mutation_p.R586*|GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.R777*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	755	Gln-rich.|Glu-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.R755*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGAGGAAGAGCGAAAGAGGCA	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											155	140	145					2																	233681635		2203	4300	6503	233389879	SO:0001587	stop_gained	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2263C>T	2.37:g.233681635C>T	ENSP00000386537:p.Arg755*		233389879	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945982	0.73672	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	.	.	.	3.89	1.91	0.25777	.	0.060381	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7047	8.2865	0.31932	0.2045:0.7033:0.0:0.0922	.	.	.	.	X	777;698;755;777;755;755;698;749;776;749;586	.	ENSP00000362664:R755X	R	+	1	2	GIGYF2	233389879	1.000000	0.71417	0.992000	0.48379	0.112000	0.19704	2.279000	0.43435	0.986000	0.38683	-0.258000	0.10820	CGA		0.478	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233681635	C	T	233681635	4	4	50	1	0	0	0	0	0	1	0	0	6398	760	27	1	2403	1	GIGYF2	2	233681635	Nonsense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	59799416	233681635	9517738	17	6820										
DCLK3	85443	broad.mit.edu	37	chr3	36779763	36779763	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aatttcacccgaggtcttttCaatctccaccccaagatgct	5	14	4	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr3:36779763C>A	ENST00000416516.2	-	2	878	c.388G>T	c.(388-390)Gaa>Taa	p.E130*		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	130						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E130*(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						GAGGTCTTTTCAATCTCCACC	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											145	146	146					3																	36779763		1890	4115	6005	36754767	SO:0001587	stop_gained	85443			AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"doublecortin and CaM kinase-like 3"	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.388G>T	3.37:g.36779763C>A	ENSP00000394484:p.Glu130*		36754767		Nonsense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	C	39	7.776827	0.98483	.	.	ENSG00000163673	ENST00000416516	.	.	.	4.7	2.83	0.33086	.	0.254751	0.20568	N	0.089791	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.1919	0.20528	0.0:0.6776:0.1591:0.1633	.	.	.	.	X	130	.	ENSP00000394484:E130X	E	-	1	0	DCLK3	36754767	0.802000	0.28943	0.705000	0.30386	0.885000	0.51271	2.105000	0.41825	1.078000	0.41014	0.655000	0.94253	GAA		0.572	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		A	36779763	C	A	36779763	4	1	50	1	0	0	0	0	0	1	0	0	4299	835	29	2	1574	2	DCLK3	3	36779763	Nonsense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09		36779763	161242667	18	6821										
SCN5A	6331	broad.mit.edu	37	chr3	38597231	38597231	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ttcttctgctcctctgtcatGaagatgtcctggccccctaa	7	14	4	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr3:38597231G>A	ENST00000333535.4	-	26	4607	c.4458C>T	c.(4456-4458)ttC>ttT	p.F1486F	SCN5A_ENST00000414099.2_Silent_p.F1468F|SCN5A_ENST00000449557.2_Silent_p.F1432F|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000413689.1_Silent_p.F1486F|SCN5A_ENST00000451551.2_Silent_p.F1432F|SCN5A_ENST00000423572.2_Silent_p.F1485F|SCN5A_ENST00000455624.2_Silent_p.F1485F|SCN5A_ENST00000443581.1_Silent_p.F1485F|SCN5A_ENST00000425664.1_Silent_p.F1468F|SCN5A_ENST00000450102.2_Silent_p.F1432F			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1486			F -> L (in LQT3).		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.F1486F(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CCTCTGTCATGAAGATGTCCT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	3											99	106	104					3																	38597231		2203	4300	6503	38572235	SO:0001819	synonymous_variant	6331			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.4458C>T	3.37:g.38597231G>A			38572235	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																				0.572	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38597231	G	A	38597231	2	1	50	1	0	0	0	0	0	0	0	1	13959	1281	45	3		3	SCN5A	3	38597231	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	1817468	38597231	159425199	19	6822										
MITF	4286	broad.mit.edu	37	chr3	69988260	69988260	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tttttgcagggattttataaGtttgaagagcaaaacagggc	11	4	0	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr3:69988260G>C	ENST00000448226.2	+	4	721	c.594G>C	c.(592-594)aaG>aaC	p.K198N	MITF_ENST00000394351.3_Missense_Mutation_p.K91N|MITF_ENST00000328528.6_Missense_Mutation_p.K197N|MITF_ENST00000314557.6_Missense_Mutation_p.K91N|MITF_ENST00000472437.1_Missense_Mutation_p.K146N|MITF_ENST00000394355.2_Missense_Mutation_p.K173N|MITF_ENST00000314589.5_Missense_Mutation_p.K182N|MITF_ENST00000531774.1_Missense_Mutation_p.K35N|MITF_ENST00000352241.4_Missense_Mutation_p.K198N			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	198					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.K91N(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GATTTTATAAGTTTGAAGAGC	0.438			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	1	Substitution - Missense(1)	large_intestine(1)	3											96	93	94					3																	69988260		2203	4300	6503	70070950	SO:0001583	missense	4286				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.594G>C	3.37:g.69988260G>C	ENSP00000391803:p.Lys198Asn		70070950	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	G	12.23	1.874745	0.33069	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000433517;ENST00000472437;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	T;T;T;T;T;T;T;T;T;T	0.24538	2.67;2.19;2.45;2.67;1.85;2.66;2.67;2.44;1.86;2.42	5.99	0.153	0.14897	.	0.187157	0.36932	N	0.002336	T	0.16214	0.0390	N	0.08118	0	0.36938	D	0.892242	P;P;P;P;D;P;P	0.56035	0.808;0.589;0.589;0.936;0.974;0.936;0.893	B;B;B;P;P;P;B	0.50659	0.225;0.211;0.288;0.634;0.647;0.634;0.394	T	0.11690	-1.0577	9	.	.	.	.	10.2273	0.43233	0.5817:0.0:0.4183:0.0	.	146;91;91;173;182;197;198	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	N	198;198;90;146;197;182;182;173;91;91;35	ENSP00000295600:K198N;ENSP00000391803:K198N;ENSP00000418845:K146N;ENSP00000327867:K197N;ENSP00000398639:K182N;ENSP00000324443:K182N;ENSP00000377884:K173N;ENSP00000324246:K91N;ENSP00000377880:K91N;ENSP00000435909:K35N	.	K	+	3	2	MITF	70070950	0.997000	0.39634	0.988000	0.46212	0.990000	0.78478	0.253000	0.18296	-0.265000	0.09352	-0.140000	0.14226	AAG		0.438	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		C	69988260	G	C	69988260	3	2	50	1	0	0	0	0	1	0	0	0	9626	1020	36	5	829	5	MITF	3	69988260	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	31391029	69988260	128034170	20	6823										
WDR49	151790	broad.mit.edu	37	chr3	167293922	167293922	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atggacagctggtgttgaatAtcccagagtctcaaaacctg	10	9	1	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr3:167293922A>G	ENST00000308378.3	-	4	575	c.270T>C	c.(268-270)gaT>gaC	p.D90D	WDR49_ENST00000453925.2_Silent_p.D143D|WDR49_ENST00000479765.1_Silent_p.D431D|WDR49_ENST00000476376.1_5'Flank	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	90								p.D90D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						GGTGTTGAATATCCCAGAGTC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3											67	64	65					3																	167293922		2203	4300	6503	168776616	SO:0001819	synonymous_variant	151790			AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.270T>C	3.37:g.167293922A>G			168776616	Q8N297	Silent	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	A	7.148	0.583281	0.13749	.	.	ENSG00000174776	ENST00000472600	.	.	.	5.76	3.09	0.35607	.	.	.	.	.	T	0.55049	0.1896	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49925	-0.8887	4	.	.	.	.	6.2961	0.21087	0.7212:0.0:0.2788:0.0	.	.	.	.	T	155	.	.	I	-	2	0	WDR49	168776616	1.000000	0.71417	0.999000	0.59377	0.845000	0.48019	0.900000	0.28431	1.041000	0.40125	0.529000	0.55759	ATA		0.388	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		G	167293922	A	G	167293922	2	3	50	1	0	0	0	0	0	0	0	1	17342	446	16	4		4	WDR49	3	167293922	Silent	SNP	A	TCGA-AG-3896-01A-01W-1073-09	97305662	167293922	30728508	21	6824										
CORIN	10699	broad.mit.edu	37	chr4	47597796	47597796	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	taatccattcgacgaaatatGacacattactataaacgcca	4	10	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr4:47597796G>A	ENST00000273857.4	-	22	3070	c.3071C>T	c.(3070-3072)tCa>tTa	p.S1024L	CORIN_ENST00000502252.1_Missense_Mutation_p.S957L|CORIN_ENST00000505909.1_Missense_Mutation_p.S987L|CORIN_ENST00000508498.1_Missense_Mutation_p.S885L	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	1024	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.S1024L(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						GACGAAATATGACACATTACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											80	84	83					4																	47597796		2203	4300	6503	47292553	SO:0001583	missense	10699			AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.3071C>T	4.37:g.47597796G>A	ENSP00000273857:p.Ser1024Leu		47292553	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	37	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	G	10.97	1.502076	0.26949	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.46	5.46	0.80206	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.161023	0.42682	D	0.000661	D	0.88254	0.6387	L	0.41415	1.275	0.80722	D	1	P;P	0.36909	0.573;0.488	B;B	0.44315	0.345;0.446	D	0.87089	0.2171	10	0.39692	T	0.17	.	17.4819	0.87674	0.0:0.0:1.0:0.0	.	957;1024	B4E1Y7;Q9Y5Q5	.;CORIN_HUMAN	L	1024;885;957;987	ENSP00000273857:S1024L;ENSP00000425597:S885L;ENSP00000424212:S957L;ENSP00000425401:S987L	ENSP00000273857:S1024L	S	-	2	0	CORIN	47292553	1.000000	0.71417	0.953000	0.39169	0.011000	0.07611	9.727000	0.98787	2.574000	0.86865	0.462000	0.41574	TCA		0.418	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			A	47597796	G	A	47597796	3	1	50	1	0	0	0	0	1	0	0	0	3758	1294	45	3	61	3	CORIN	4	47597796	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		47597796	143556480	22	6825										
SGCB	6443	broad.mit.edu	37	chr4	52899746	52899746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	actgttgtgctctttattgaCactccttctctcaacagcct	5	13	3	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr4:52899746C>T	ENST00000381431.5	-	2	316	c.94G>A	c.(94-96)Gtc>Atc	p.V32I	SGCB_ENST00000535450.1_Intron	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	32					cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.V32I(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TCTTTATTGACACTCCTTCTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											226	197	207					4																	52899746		2203	4300	6503	52594503	SO:0001583	missense	6443			U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.94G>A	4.37:g.52899746C>T	ENSP00000370839:p.Val32Ile		52594503	B7Z635|O00661	Missense_Mutation	SNP	ENST00000381431.5	37	CCDS3488.1	.	.	.	.	.	.	.	.	.	.	C	8.513	0.866886	0.17250	.	.	ENSG00000163069	ENST00000381431	D	0.88818	-2.43	5.29	5.29	0.74685	.	0.174926	0.51477	D	0.000090	T	0.76456	0.3990	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.71017	-0.4714	10	0.23302	T	0.38	-5.7478	11.4019	0.49875	0.0:0.9176:0.0:0.0824	.	32	Q16585	SGCB_HUMAN	I	32	ENSP00000370839:V32I	ENSP00000370839:V32I	V	-	1	0	SGCB	52594503	0.132000	0.22450	0.401000	0.26359	0.020000	0.10135	0.684000	0.25364	2.476000	0.83614	0.650000	0.86243	GTC		0.408	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			T	52899746	C	T	52899746	3	4	50	1	0	0	0	0	1	0	0	0	14237	478	17	3	882	3	SGCB	4	52899746	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	5301950	52899746	138254530	23	6826										
FAT4	79633	broad.mit.edu	37	chr4	126372252	126372252	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agatttatgtttctggaattCttgatcgagaaaaagaagaa	9	3	2	5	rs61163957		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr4:126372252C>G	ENST00000394329.3	+	9	10094	c.10081C>G	c.(10081-10083)Ctt>Gtt	p.L3361V	FAT4_ENST00000335110.5_Missense_Mutation_p.L1659V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3361	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L3361V(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTCTGGAATTCTTGATCGAGA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											117	120	119					4																	126372252		2203	4300	6503	126591702	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10081C>G	4.37:g.126372252C>G	ENSP00000377862:p.Leu3361Val		126591702	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852109	0.32699	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.73152	-0.72;-0.72	5.27	5.27	0.74061	Cadherin (4);Cadherin-like (1);	0.000000	0.31450	U	0.007623	D	0.83995	0.5375	M	0.71871	2.18	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.91635	0.996;0.999;0.994	D	0.85076	0.0943	10	0.59425	D	0.04	.	18.9292	0.92558	0.0:1.0:0.0:0.0	.	1659;3361;3361	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	3361;1659	ENSP00000377862:L3361V;ENSP00000335169:L1659V	ENSP00000335169:L1659V	L	+	1	0	FAT4	126591702	1.000000	0.71417	0.993000	0.49108	0.052000	0.14988	5.919000	0.70005	2.461000	0.83175	0.655000	0.94253	CTT		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126372252	C	G	126372252	3	3	50	1	0	0	0	0	1	0	0	0	5711	913	32	5	10115	5	FAT4	4	126372252	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	73472506	126372252	64782024	24	6827										
RGS7BP	401190	broad.mit.edu	37	chr5	63871616	63871616	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgcagcccggaagatggtgaGatccatccagaaatctgtcg	12	10	1	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:63871616G>T	ENST00000334025.2	+	3	674	c.348G>T	c.(346-348)gaG>gaT	p.E116D	RNU6-294P_ENST00000364999.1_RNA|RGS7BP_ENST00000508162.1_3'UTR	NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	116					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E116D(1)		breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		AAGATGGTGAGATCCATCCAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											90	87	88					5																	63871616		2203	4300	6503	63907372	SO:0001583	missense	401190			BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"regulator of G-protein signalling 7 binding protein"			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.348G>T	5.37:g.63871616G>T	ENSP00000334851:p.Glu116Asp		63907372	B7Z3X1	Missense_Mutation	SNP	ENST00000334025.2	37	CCDS34170.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996745	0.74818	.	.	ENSG00000186479	ENST00000334025	T	0.36878	1.23	5.91	3.18	0.36537	.	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	L	0.34521	1.04	0.47949	D	0.999551	D	0.61697	0.99	D	0.73380	0.98	T	0.19160	-1.0314	10	0.39692	T	0.17	-2.286	9.6994	0.40178	0.3234:0.0:0.6766:0.0	.	116	Q6MZT1	R7BP_HUMAN	D	116	ENSP00000334851:E116D	ENSP00000334851:E116D	E	+	3	2	RGS7BP	63907372	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.398000	0.34554	0.842000	0.35045	0.655000	0.94253	GAG		0.448	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875		T	63871616	G	T	63871616	3	4	50	1	0	0	0	0	1	0	0	0	13348	933	33	2	358	2	RGS7BP	5	63871616	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		63871616	117043644	25	6828										
RAD17	5884	broad.mit.edu	37	chr5	68680652	68680652	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ttccatatgtttccctatcaGtctcagatagcagttttcaa	5	10	3	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:68680652G>T	ENST00000509734.1	+	7	1248	c.570G>T	c.(568-570)caG>caT	p.Q190H	RAD17_ENST00000380774.3_Missense_Mutation_p.Q190H|RAD17_ENST00000354868.5_Missense_Mutation_p.Q179H|RAD17_ENST00000354312.3_Missense_Mutation_p.Q179H|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000282891.6_Missense_Mutation_p.Q93H|RAD17_ENST00000361732.2_Missense_Mutation_p.Q179H|RAD17_ENST00000358030.2_Missense_Mutation_p.Q14H|RAD17_ENST00000305138.4_Missense_Mutation_p.Q179H|RAD17_ENST00000345306.6_Missense_Mutation_p.Q179H|RAD17_ENST00000521422.1_Missense_Mutation_p.Q14H			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	190					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.Q179H(1)					Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		TTCCCTATCAGTCTCAGATAG	0.313								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	5											75	75	75					5																	68680652		2203	4300	6503	68716408	SO:0001583	missense	5884			AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"RAD1 (S. pombe) homolog"			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.570G>T	5.37:g.68680652G>T	ENSP00000426191:p.Gln190His		68716408	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506714	0.64410	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000512785;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.05	-1.09	0.09904	ATPase, AAA+ type, core (1);	0.178511	0.51477	D	0.000083	T	0.40619	0.1124	M	0.78637	2.42	0.34823	D	0.738928	P;D;P	0.54397	0.536;0.966;0.941	B;P;P	0.58970	0.396;0.849;0.849	T	0.51560	-0.8690	10	0.42905	T	0.14	-6.611	9.8064	0.40795	0.4258:0.0:0.5742:0.0	.	190;93;179	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	H	179;190;179;14;179;179;14;179;93;14;190	ENSP00000355226:Q179H;ENSP00000426191:Q190H;ENSP00000346938:Q179H;ENSP00000427743:Q14H;ENSP00000346271:Q179H;ENSP00000311227:Q179H;ENSP00000427673:Q14H;ENSP00000303134:Q179H;ENSP00000282891:Q93H;ENSP00000350725:Q14H;ENSP00000370151:Q190H	ENSP00000282891:Q93H	Q	+	3	2	RAD17	68716408	1.000000	0.71417	0.985000	0.45067	0.970000	0.65996	1.034000	0.30204	-0.186000	0.10533	0.305000	0.20034	CAG		0.313	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344		T	68680652	G	T	68680652	3	4	50	1	0	0	0	0	1	0	0	0	13016	1020	36	2	601	2	RAD17	5	68680652	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	4809036	68680652	112234608	26	6829										
APC	324	broad.mit.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	50	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	43493265	112173917	68741343	27	6830										
PCDHA1	56147	broad.mit.edu	37	chr5	140167397	140167397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agcgcgcgctgtcgaactacGtgtcagtgcacgcggagagc	15	12	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:140167397G>A	ENST00000504120.2	+	1	1522	c.1522G>A	c.(1522-1524)Gtg>Atg	p.V508M	PCDHA1_ENST00000394633.3_Missense_Mutation_p.V508M|PCDHA1_ENST00000378133.3_Missense_Mutation_p.V508M	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	508	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V508M(2)		breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCGAACTACGTGTCAGTGCA	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	5											66	67	67					5																	140167397		2203	4300	6503	140147581	SO:0001583	missense	56147			AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1522G>A	5.37:g.140167397G>A	ENSP00000420840:p.Val508Met		140147581	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	g	15.95	2.983011	0.53827	.	.	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.61392	0.11;0.11;0.11	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	0.000000	0.37304	U	0.002143	T	0.72187	0.3429	M	0.79926	2.475	0.23886	N	0.99657	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.72338	0.977;0.889;0.964	T	0.62464	-0.6849	10	0.87932	D	0	.	7.469	0.27338	0.1995:0.0:0.8005:0.0	.	508;508;508	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	M	508	ENSP00000420840:V508M;ENSP00000378129:V508M;ENSP00000367373:V508M	ENSP00000367373:V508M	V	+	1	0	PCDHA1	140147581	1.000000	0.71417	0.999000	0.59377	0.711000	0.40976	1.173000	0.31920	1.768000	0.52137	0.549000	0.68633	GTG		0.687	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		A	140167397	G	A	140167397	3	1	50	1	0	0	0	0	1	0	0	0	11550	1145	40	1	1524	1	PCDHA1	5	140167397	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	27993480	140167397	40747863	28	6831										
PCDH12	51294	broad.mit.edu	37	chr5	141325081	141325081	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctgagggtcctcccgcagacCgagagccgccgcagcgcctc	13	18	0	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:141325081C>T	ENST00000231484.3	-	4	4630	c.3420G>A	c.(3418-3420)tcG>tcA	p.S1140S		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1140					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S1140S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCCGCAGACCGAGAGCCGCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	5											21	21	21					5																	141325081		2203	4300	6503	141305265	SO:0001819	synonymous_variant	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3420G>A	5.37:g.141325081C>T			141305265	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																				0.637	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141325081	C	T	141325081	2	4	50	1	0	0	0	0	0	0	0	1	11541	639	23	1		1	PCDH12	5	141325081	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	1157684	141325081	39590179	29	6832										
POU4F3	5459	broad.mit.edu	37	chr5	145719863	145719863	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gagaagcgttcactcgaggcCtatttcgctatccagccacg	10	13	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr5:145719863C>G	ENST00000230732.4	+	2	962	c.873C>G	c.(871-873)gcC>gcG	p.A291A	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	291					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A291A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACTCGAGGCCTATTTCGCTA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	5											51	50	50					5																	145719863		2203	4300	6503	145700056	SO:0001819	synonymous_variant	5459			U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.873C>G	5.37:g.145719863C>G			145700056	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																				0.562	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		G	145719863	C	G	145719863	2	3	50	1	0	0	0	0	0	0	0	1	12311	668	24	5		5	POU4F3	5	145719863	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	4394782	145719863	35195397	30	6833										
HIST1H1B	3009	broad.mit.edu	37	chr6	27835017	27835017	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gcaccagtgcccttggtctgCaccagggtgcccttgctcac	11	16	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:27835017C>T	ENST00000331442.3	-	1	342	c.291G>A	c.(289-291)gtG>gtA	p.V97V		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	97	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)	p.V97V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCTTGGTCTGCACCAGGGTGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	6											126	137	133					6																	27835017		2203	4300	6503	27942996	SO:0001819	synonymous_variant	3009			AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"Histones / Replication-dependent"	4719	protein-coding gene	gene with protein product		142711	"H1 histone family, member 5", "histone 1, H1b"	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.291G>A	6.37:g.27835017C>T			27942996	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																				0.587	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		T	27835017	C	T	27835017	2	4	50	1	0	0	0	0	0	0	0	1	7144	697	25	3		3	HIST1H1B	6	27835017	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09		27835017	143280050	31	6834										
NOTCH4	4855	broad.mit.edu	37	chr6	32187428	32187428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gacaggtgcttcctgggtggCagggctgggagaggcactca	18	9	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:32187428C>T	ENST00000375023.3	-	8	1589	c.1451G>A	c.(1450-1452)tGc>tAc	p.C484Y		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	484	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.C484Y(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCCTGGGTGGCAGGGCTGGGA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											93	65	75					6																	32187428		1510	2709	4219	32295406	SO:0001583	missense	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1451G>A	6.37:g.32187428C>T	ENSP00000364163:p.Cys484Tyr		32295406	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602829	0.66445	.	.	ENSG00000204301	ENST00000375023	D	0.94828	-3.53	4.0	4.0	0.46444	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.45606	D	0.000356	D	0.98535	0.9511	H	0.99740	4.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98824	1.0748	10	0.87932	D	0	.	13.6604	0.62363	0.0:1.0:0.0:0.0	.	484;484	Q6P3V5;Q99466	.;NOTC4_HUMAN	Y	484	ENSP00000364163:C484Y	ENSP00000364163:C484Y	C	-	2	0	NOTCH4	32295406	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	7.140000	0.77322	2.069000	0.61940	0.455000	0.32223	TGC		0.607	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32187428	C	T	32187428	3	4	50	1	0	0	0	0	1	0	0	0	10582	710	25	3	4652	3	NOTCH4	6	32187428	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	4352411	32187428	138927639	32	6835										
NFYA	4800	broad.mit.edu	37	chr6	41059354	41059354	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aacaggagccaataccaacaCaaccagcagtgggcaaggga	11	11	0	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:41059354C>G	ENST00000341376.6	+	7	836	c.635C>G	c.(634-636)aCa>aGa	p.T212R	NFYA_ENST00000353205.5_Missense_Mutation_p.T183R|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	212					cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T212R(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					AATACCAACACAACCAGCAGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											213	177	189					6																	41059354		2203	4300	6503	41167332	SO:0001583	missense	4800				CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.635C>G	6.37:g.41059354C>G	ENSP00000345702:p.Thr212Arg		41167332	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	37	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901261	0.92035	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	L	0.51422	1.61	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.78314	0.991;0.979	T	0.67067	-0.5764	9	0.41790	T	0.15	-15.4413	19.1684	0.93567	0.0:1.0:0.0:0.0	.	183;212	P23511-2;P23511	.;NFYA_HUMAN	R	212;183	.	ENSP00000345702:T212R	T	+	2	0	NFYA	41167332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.734000	0.84928	2.777000	0.95525	0.655000	0.94253	ACA		0.468	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			G	41059354	C	G	41059354	3	3	50	1	0	0	0	0	1	0	0	0	10420	478	17	5	657	5	NFYA	6	41059354	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	8871926	41059354	130055713	33	6836										
TCTE1	202500	broad.mit.edu	37	chr6	44250254	44250254	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aaggcttcgaattatgatgcGtgccttgtcatcatccacct	8	11	2	1	rs112092930		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:44250254G>A	ENST00000371505.4	-	4	1011	c.889C>T	c.(889-891)Cgc>Tgc	p.R297C	TCTE1_ENST00000371504.1_Intron|TCTE1_ENST00000371503.3_Intron|TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	297								p.R297C(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ATTATGATGCGTGCCTTGTCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6											113	100	105					6																	44250254		2203	4300	6503	44358232	SO:0001583	missense	202500			BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.889C>T	6.37:g.44250254G>A	ENSP00000360560:p.Arg297Cys		44358232	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	G	8.982	0.975525	0.18736	.	.	ENSG00000146221	ENST00000371505	T	0.53857	0.6	5.37	5.37	0.77165	.	0.169046	0.51477	D	0.000093	T	0.29684	0.0741	L	0.58354	1.805	0.80722	D	1	P	0.35107	0.484	B	0.25291	0.059	T	0.34825	-0.9813	10	0.49607	T	0.09	-53.6838	8.815	0.34989	0.0774:0.0:0.7625:0.1601	.	297	Q5JU00	TCTE1_HUMAN	C	297	ENSP00000360560:R297C	ENSP00000360560:R297C	R	-	1	0	TCTE1	44358232	1.000000	0.71417	0.989000	0.46669	0.108000	0.19459	4.388000	0.59633	2.695000	0.91970	0.455000	0.32223	CGC		0.562	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		A	44250254	G	A	44250254	3	1	50	1	0	0	0	0	1	0	0	0	15756	1145	40	1	624	1	TCTE1	6	44250254	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	3190900	44250254	126864813	34	6837										
BAI3	577	broad.mit.edu	37	chr6	70071001	70071001	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agaaaatagtgaattgcggaGaactgtgtacttatgtacgg	12	4	0	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:70071001G>T	ENST00000370598.1	+	29	4657	c.3836G>T	c.(3835-3837)aGa>aTa	p.R1279I	BAI3_ENST00000546190.1_Missense_Mutation_p.R243I|BAI3_ENST00000238918.8_Missense_Mutation_p.R485I	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1279					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1279I(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GAATTGCGGAGAACTGTGTAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	85	86					6																	70071001		2203	4298	6501	70127722	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3836G>T	6.37:g.70071001G>T	ENSP00000359630:p.Arg1279Ile		70127722	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184372	0.78677	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.10763	2.84;2.84;2.84	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	L	0.47716	1.5	0.80722	D	1	D;D	0.65815	0.995;0.972	D;P	0.75484	0.986;0.549	T	0.00724	-1.1593	10	0.66056	D	0.02	.	19.3944	0.94601	0.0:0.0:1.0:0.0	.	485;1279	B7Z356;O60242	.;BAI3_HUMAN	I	1279;485;243	ENSP00000359630:R1279I;ENSP00000238918:R485I;ENSP00000441821:R243I	ENSP00000238918:R485I	R	+	2	0	BAI3	70127722	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	9.174000	0.94824	2.665000	0.90641	0.591000	0.81541	AGA		0.413	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	70071001	G	T	70071001	3	4	50	1	0	0	0	0	1	0	0	0	1301	942	33	2	3942	2	BAI3	6	70071001	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	25820747	70071001	101044066	35	6838										
FILIP1	27145	broad.mit.edu	37	chr6	76023352	76023352	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tcttctttgttcattaattcGtgaatcttctctttaagagc	5	8	5	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:76023352G>A	ENST00000237172.7	-	5	2526	c.2196C>T	c.(2194-2196)caC>caT	p.H732H	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Silent_p.H633H|FILIP1_ENST00000393004.2_Silent_p.H732H	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	732								p.H732H(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TCATTAATTCGTGAATCTTCT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	6											112	118	116					6																	76023352		2203	4300	6503	76080072	SO:0001819	synonymous_variant	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2196C>T	6.37:g.76023352G>A			76080072	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	37	CCDS4984.1																																																																																				0.373	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023352	G	A	76023352	2	1	50	1	0	0	0	0	0	0	0	1	5913	1136	40	1		1	FILIP1	6	76023352	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	5952351	76023352	95091715	36	6839										
GPR126	57211	broad.mit.edu	37	chr6	142688889	142688889	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agaagctcccaattgcatttAtgactcattatcccttgata	5	10	1	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:142688889A>C	ENST00000230173.6	+	3	763	c.287A>C	c.(286-288)tAt>tCt	p.Y96S	GPR126_ENST00000367609.3_Missense_Mutation_p.Y96S|GPR126_ENST00000545477.1_3'UTR|GPR126_ENST00000367608.2_Missense_Mutation_p.Y96S|GPR126_ENST00000296932.8_Missense_Mutation_p.Y96S	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	96	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Y95S(1)|p.Y96S(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		AATTGCATTTATGACTCATTA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	6											79	79	79					6																	142688889		1862	4103	5965	142730582	SO:0001583	missense	57211			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.287A>C	6.37:g.142688889A>C	ENSP00000230173:p.Tyr96Ser		142730582	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.743865	0.89663	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609;ENST00000541199;ENST00000435011	T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1	6.06	6.06	0.98353	CUB (5);	0.000000	0.64402	D	0.000011	T	0.37183	0.0994	M	0.64630	1.985	0.54753	D	0.999985	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999	T	0.18650	-1.0330	10	0.87932	D	0	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	96;96;96;96;95	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4;F5H2L1	.;.;.;GP126_HUMAN;.	S	96;96;96;96;95;96	ENSP00000230173:Y96S;ENSP00000356580:Y96S;ENSP00000296932:Y96S;ENSP00000356581:Y96S;ENSP00000446287:Y95S;ENSP00000438366:Y96S	ENSP00000230173:Y96S	Y	+	2	0	GPR126	142730582	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.323000	0.78572	0.528000	0.53228	TAT		0.438	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			C	142688889	A	C	142688889	3	2	50	1	0	0	0	0	1	0	0	0	6660	449	16	4	297	4	GPR126	6	142688889	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	66665537	142688889	28426178	37	6840										
TAGAP	117289	broad.mit.edu	37	chr6	159456927	159456927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cggctggctacatcgtcgcaCgagacagtcccgcttattcc	10	15	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:159456927C>T	ENST00000367066.3	-	10	2459	c.2128G>A	c.(2128-2130)Gtg>Atg	p.V710M	RP1-111C20.4_ENST00000606470.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.V532M|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	710					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.V710M(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CATCGTCGCACGAGACAGTCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	64	66					6																	159456927		2203	4300	6503	159376915	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.2128G>A	6.37:g.159456927C>T	ENSP00000356033:p.Val710Met		159376915	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	C	9.424	1.083896	0.20309	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	T;T	0.17370	2.28;2.54	5.82	-7.41	0.01392	.	1.853500	0.02343	N	0.075080	T	0.04137	0.0115	L	0.44542	1.39	0.09310	N	1	B	0.30851	0.297	B	0.14023	0.01	T	0.07328	-1.0778	10	0.46703	T	0.11	-0.4464	10.7124	0.45990	0.0:0.5576:0.2347:0.2077	.	710	Q8N103	TAGAP_HUMAN	M	710;532	ENSP00000356033:V710M;ENSP00000322650:V532M	ENSP00000322650:V532M	V	-	1	0	TAGAP	159376915	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.278000	0.08490	-1.905000	0.01090	-2.611000	0.00159	GTG		0.577	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159456927	C	T	159456927	3	4	50	1	0	0	0	0	1	0	0	0	15576	536	19	1	71	1	TAGAP	6	159456927	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	16768038	159456927	11658140	38	6841										
PDE10A	10846	broad.mit.edu	37	chr6	165848819	165848819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgggcccagcagggatgaggCggggttttccttcctttatc	14	10	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr6:165848819C>T	ENST00000366882.1	-	7	567	c.413G>A	c.(412-414)cGc>cAc	p.R138H	PDE10A_ENST00000354448.4_Missense_Mutation_p.R138H|PDE10A_ENST00000539869.2_Missense_Mutation_p.R148H			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	138	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.R138H(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AGGGATGAGGCGGGGTTTTCC	0.488																																					Esophageal Squamous(22;308 615 5753 12038 40624)											1	Substitution - Missense(1)	large_intestine(1)	6											146	125	132					6																	165848819		2203	4300	6503	165768809	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.413G>A	6.37:g.165848819C>T	ENSP00000355847:p.Arg138His		165768809	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	C	16.42	3.118205	0.56505	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69306	-0.39;-0.39	5.32	2.57	0.30868	GAF (1);	0.473990	0.25535	N	0.030018	T	0.36441	0.0967	L	0.38175	1.15	0.21527	N	0.999651	P;P	0.52842	0.66;0.956	B;P	0.47102	0.149;0.537	T	0.28713	-1.0035	10	0.45353	T	0.12	.	2.4185	0.04442	0.1336:0.5251:0.1293:0.212	.	148;138	Q9ULW9;Q9Y233	.;PDE10_HUMAN	H	138;166;148;138;137	ENSP00000355847:R138H;ENSP00000346435:R138H	ENSP00000341187:R148H	R	-	2	0	PDE10A	165768809	0.001000	0.12720	0.070000	0.20053	0.702000	0.40608	0.827000	0.27421	0.321000	0.23259	0.460000	0.39030	CGC		0.488	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165848819	C	T	165848819	3	4	50	1	0	0	0	0	1	0	0	0	11661	768	27	1	1994	1	PDE10A	6	165848819	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	6391892	165848819	5266248	39	6842										
MACC1	346389	broad.mit.edu	37	chr7	20198970	20198970	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tacattacctgactcaagtcGattagcttgacttggatggt	9	8	1	2	rs535443647		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:20198970G>A	ENST00000400331.5	-	5	1322	c.1014C>T	c.(1012-1014)atC>atT	p.I338I	MACC1_ENST00000332878.4_Silent_p.I338I|MACC1_ENST00000589011.1_Silent_p.I338I	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	338					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.I338I(1)		endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						GACTCAAGTCGATTAGCTTGA	0.418													G|||	1	0.000199681	0	0	5008	,	,		20577	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	7											62	58	60					7																	20198970		2203	4300	6503	20165495	SO:0001819	synonymous_variant	346389				CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.1014C>T	7.37:g.20198970G>A			20165495	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Silent	SNP	ENST00000400331.5	37	CCDS5369.1																																																																																				0.418	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20198970	G	A	20198970	2	1	50	1	0	0	0	0	0	0	0	1	9173	1048	37	1		1	MACC1	7	20198970	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09		20198970	138939693	40	6843										
ZNF117	51351	broad.mit.edu	37	chr7	64438652	64438652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atgaattctcttatgtccaaTaagggttgaagatcggttaa	9	5	1	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:64438652T>C	ENST00000282869.6	-	4	2581	c.1297A>G	c.(1297-1299)Att>Gtt	p.I433V		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	433					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.I433V(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TTATGTCCAATAAGGGTTGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											65	68	67					7																	64438652		2102	4254	6356	64076087	SO:0001583	missense	51351			M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"Zinc fingers, C2H2-type"	12897	protein-coding gene	gene with protein product		194624	"zinc finger protein 117 (HPF9)"			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.1297A>G	7.37:g.64438652T>C	ENSP00000282869:p.Ile433Val		64076087	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	.	.	.	.	.	.	.	.	.	.	.	4.859	0.159682	0.09287	.	.	ENSG00000152926	ENST00000282869	T	0.07216	3.21	1.1	1.1	0.20463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03783	0.0107	N	0.04655	-0.195	0.09310	N	1	B	0.14012	0.009	B	0.21151	0.033	T	0.40627	-0.9553	9	0.56958	D	0.05	.	4.2658	0.10763	0.0:0.0:0.0:1.0	.	433	Q03924	ZN117_HUMAN	V	433	ENSP00000282869:I433V	ENSP00000282869:I433V	I	-	1	0	ZNF117	64076087	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.053000	0.11846	0.432000	0.26286	0.255000	0.18592	ATT		0.353	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498		C	64438652	T	C	64438652	3	2	50	1	0	0	0	0	1	0	0	0	17756	1406	49	4	158	4	ZNF117	7	64438652	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09	44239682	64438652	94700011	41	6844										
ZNF804B	219578	broad.mit.edu	37	chr7	88964664	88964664	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggaactgcaaattgtgggaaTcatttaaaaatgaaaaatac	8	4	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:88964664T>A	ENST00000333190.4	+	4	2977	c.2368T>A	c.(2368-2370)Tca>Aca	p.S790T		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	790							metal ion binding (GO:0046872)	p.S790T(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATTGTGGGAATCATTTAAAAA	0.358										HNSCC(36;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	7											44	42	43					7																	88964664		2203	4300	6503	88802600	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2368T>A	7.37:g.88964664T>A	ENSP00000329638:p.Ser790Thr		88802600	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	T	8.991	0.977646	0.18812	.	.	ENSG00000182348	ENST00000333190	T	0.05258	3.47	5.4	4.24	0.50183	.	0.365590	0.23420	N	0.048362	T	0.03871	0.0109	N	0.20986	0.625	0.09310	N	1	B	0.31077	0.307	B	0.25759	0.063	T	0.36625	-0.9740	10	0.36615	T	0.2	-7.7891	5.3711	0.16140	0.2103:0.0:0.1577:0.632	.	790	A4D1E1	Z804B_HUMAN	T	790	ENSP00000329638:S790T	ENSP00000329638:S790T	S	+	1	0	ZNF804B	88802600	0.458000	0.25760	0.067000	0.19924	0.844000	0.47949	2.404000	0.44539	2.274000	0.75844	0.533000	0.62120	TCA		0.358	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88964664	T	A	88964664	3	1	50	1	0	0	0	0	1	0	0	0	18210	1435	50	5	2382	5	ZNF804B	7	88964664	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09	24526012	88964664	70173999	42	6845										
PUS7	54517	broad.mit.edu	37	chr7	105135670	105135670	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cgaagtggcagtaacttcccCtagattttggccaagaatgt	10	9	0	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:105135670C>T	ENST00000356362.2	-	6	975	c.761G>A	c.(760-762)aGg>aAg	p.R254K	PUS7_ENST00000469408.1_Missense_Mutation_p.R254K	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	254					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)	p.R254K(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						GTAACTTCCCCTAGATTTTGG	0.328																																					Colon(138;2387 3051 17860)											1	Substitution - Missense(1)	large_intestine(1)	7											201	204	203					7																	105135670		2203	4300	6503	104922906	SO:0001583	missense	54517			AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.761G>A	7.37:g.105135670C>T	ENSP00000348722:p.Arg254Lys		104922906	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	37	CCDS34725.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.018237	0.93404	.	.	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.41065	1.01;1.01	5.35	5.35	0.76521	Pseudouridine synthase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	L	0.43701	1.375	0.58432	D	0.999999	D;P	0.58970	0.984;0.843	P;B	0.49561	0.615;0.336	T	0.21552	-1.0242	10	0.06494	T	0.89	-11.54	18.0541	0.89358	0.0:1.0:0.0:0.0	.	254;254	B3KY42;Q96PZ0	.;PUS7_HUMAN	K	254	ENSP00000348722:R254K;ENSP00000417402:R254K	ENSP00000348722:R254K	R	-	2	0	PUS7	104922906	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.280000	0.78610	2.505000	0.84491	0.650000	0.86243	AGG		0.328	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		T	105135670	C	T	105135670	3	4	50	1	0	0	0	0	1	0	0	0	12870	681	24	3	1268	3	PUS7	7	105135670	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	16171006	105135670	54002993	43	6846										
PTPRZ1	5803	broad.mit.edu	37	chr7	121651200	121651200	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tctgcaggcccagtgatgtcAcagggtccctcagttacaga	11	12	3	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:121651200A>C	ENST00000393386.2	+	12	2511	c.2100A>C	c.(2098-2100)tcA>tcC	p.S700S	PTPRZ1_ENST00000449182.1_Silent_p.S700S	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	700					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S700S(2)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CAGTGATGTCACAGGGTCCCT	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	7											111	94	100					7																	121651200		2203	4300	6503	121438436	SO:0001819	synonymous_variant	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2100A>C	7.37:g.121651200A>C			121438436	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																				0.468	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121651200	A	C	121651200	2	2	50	1	0	0	0	0	0	0	0	1	12851	146	6	4		4	PTPRZ1	7	121651200	Silent	SNP	A	TCGA-AG-3896-01A-01W-1073-09	16515530	121651200	37487463	44	6847										
RNF148	378925	broad.mit.edu	37	chr7	122342770	122342770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aaagtccagatgaaacagaaCtatgcgtcgaaggggtaatt	11	6	0	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:122342770C>T	ENST00000434824.1	-	1	251	c.35G>A	c.(34-36)aGt>aAt	p.S12N	RNF148_ENST00000447240.1_Missense_Mutation_p.S12N|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	12						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.S12N(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						TGAAACAGAACTATGCGTCGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											36	31	33					7																	122342770		1863	4094	5957	122130006	SO:0001583	missense	378925			BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.35G>A	7.37:g.122342770C>T	ENSP00000388207:p.Ser12Asn		122130006	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	37	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	C	0.432	-0.902940	0.02453	.	.	ENSG00000235631	ENST00000434824;ENST00000447240	T	0.04360	3.64	5.4	1.18	0.20946	.	.	.	.	.	T	0.03011	0.0089	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.48948	-0.8989	9	0.12766	T	0.61	.	4.1241	0.10119	0.3168:0.4975:0.0:0.1857	.	12;12	C9JVJ0;Q8N7C7	.;RN148_HUMAN	N	12	ENSP00000388207:S12N	ENSP00000388207:S12N	S	-	2	0	RNF148	122130006	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-0.083000	0.11286	0.216000	0.20781	0.555000	0.69702	AGT		0.383	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		T	122342770	C	T	122342770	3	4	50	1	0	0	0	0	1	0	0	0	13486	565	20	3	886	3	RNF148	7	122342770	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	691570	122342770	36795893	45	6848										
LUC7L2	100996928	broad.mit.edu	37	chr7	139102364	139102364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gagaactcgatccaaatctcGggagaaacgccatcgccaca	9	13	1	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr7:139102364G>A	ENST00000354926.4	+	9	1244	c.890G>A	c.(889-891)cGg>cAg	p.R297Q	C7orf55-LUC7L2_ENST00000482860.1_3'UTR|LUC7L2_ENST00000541515.3_Missense_Mutation_p.R363Q|C7orf55-LUC7L2_ENST00000263545.6_Missense_Mutation_p.R296Q|C7orf55-LUC7L2_ENST00000541170.3_Missense_Mutation_p.R294Q	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough									p.R297Q(1)									TCCAAATCTCGGGAGAAACGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											71	81	78					7																	139102364		2128	4235	6363	138752904	SO:0001583	missense	51631				CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.890G>A	7.37:g.139102364G>A	ENSP00000347005:p.Arg297Gln		138752904		Missense_Mutation	SNP	ENST00000354926.4	37	CCDS43656.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.704223	0.68615	.	.	ENSG00000146963	ENST00000541170;ENST00000541515;ENST00000545899;ENST00000354926;ENST00000263545	T;T;T;T	0.28895	3.36;1.59;3.36;3.36	5.69	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	L	0.48642	1.525	0.51012	D	0.999907	P;P;P;P	0.43352	0.553;0.804;0.681;0.553	B;B;B;B	0.31337	0.06;0.06;0.128;0.06	T	0.47071	-0.9145	9	0.54805	T	0.06	-1.6322	15.0572	0.71925	0.0692:0.0:0.9308:0.0	.	363;294;296;297	B7Z4Q3;B7Z500;Q9Y383-2;Q9Y383	.;.;.;LC7L2_HUMAN	Q	294;363;297;297;296	ENSP00000441604:R294Q;ENSP00000440222:R363Q;ENSP00000347005:R297Q;ENSP00000263545:R296Q	ENSP00000263545:R296Q	R	+	2	0	LUC7L2	138752904	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.902000	0.69869	2.698000	0.92095	0.563000	0.77884	CGG		0.552	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			A	139102364	G	A	139102364	3	1	50	1	0	0	0	0	1	0	0	0	9112	1116	39	1	924	1	LUC7L2	7	139102364	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	16759594	139102364	20036299	46	6849										
PNMA2	10687	broad.mit.edu	37	chr8	26365513	26365513	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tcctgataggtcttcagataCctcacctgggctgtcctgcg	10	13	3	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:26365513C>T	ENST00000522362.2	-	3	1653	c.759G>A	c.(757-759)agG>agA	p.R253R	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	253					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)		p.R253R(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		tcttcagatacctcacctggg	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	8											62	61	61					8																	26365513		2203	4300	6503	26421430	SO:0001819	synonymous_variant	10687				CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"Paraneoplastic Ma antigens"	9159	protein-coding gene	gene with protein product		603970	"paraneoplastic antigen MA2"			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.759G>A	8.37:g.26365513C>T			26421430	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Silent	SNP	ENST00000522362.2	37	CCDS34868.1																																																																																				0.552	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375709.2	NM_007257		T	26365513	C	T	26365513	2	4	50	1	0	0	0	0	0	0	0	1	12185	506	18	3		3	PNMA2	8	26365513	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09		26365513	119998509	47	6850										
ST18	9705	broad.mit.edu	37	chr8	53071513	53071513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgtctgtggcttccctgcagCgggtggaaaggttcaggatg	16	8	2	0	rs200417136	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:53071513C>T	ENST00000276480.7	-	15	2434	c.1751G>A	c.(1750-1752)cGc>cAc	p.R584H		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	584					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R584H(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTCCCTGCAGCGGGTGGAAAG	0.592													C|||	2	0.000399361	0	0	5008	,	,		14818	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											107	113	111					8																	53071513		2203	4300	6503	53234066	SO:0001583	missense	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1751G>A	8.37:g.53071513C>T	ENSP00000276480:p.Arg584His		53234066	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	19.46	3.831179	0.71258	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.60920	0.15;0.15	6.08	6.08	0.98989	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.61986	0.2391	M	0.83223	2.63	0.80722	D	1	P;P	0.38767	0.641;0.646	B;B	0.36244	0.165;0.22	T	0.67925	-0.5544	10	0.66056	D	0.02	-20.4449	14.7703	0.69671	0.0:0.9316:0.0:0.0684	.	584;584	E5RHS3;O60284	.;ST18_HUMAN	H	584	ENSP00000276480:R584H;ENSP00000428521:R584H	ENSP00000276480:R584H	R	-	2	0	ST18	53234066	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.774000	0.68906	2.894000	0.99253	0.655000	0.94253	CGC		0.592	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53071513	C	T	53071513	3	4	50	1	0	0	0	0	1	0	0	0	15251	768	27	1	1440	1	ST18	8	53071513	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	26706000	53071513	93292509	48	6851										
NSMAF	8439	broad.mit.edu	37	chr8	59518550	59518550	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggttcatagaactttaggtaGatgtcggaacacagatcatc	10	7	2	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:59518550G>T	ENST00000038176.3	-	12	1016	c.804C>A	c.(802-804)atC>atA	p.I268I	NSMAF_ENST00000427130.2_Silent_p.I299I|NSMAF_ENST00000519858.1_5'UTR	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	268					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.I268I(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				ACTTTAGGTAGATGTCGGAAC	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	8											89	83	85					8																	59518550		2203	4300	6503	59681104	SO:0001819	synonymous_variant	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.804C>A	8.37:g.59518550G>T			59681104	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																				0.333	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		T	59518550	G	T	59518550	2	4	50	1	0	0	0	0	0	0	0	1	10705	932	33	2		2	NSMAF	8	59518550	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	6447037	59518550	86845472	49	6852										
ZFHX4	79776	broad.mit.edu	37	chr8	77765849	77765849	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cagtaaaaggtcttctagaaCgagatttactgactaccagc	8	9	2	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:77765849C>T	ENST00000521891.2	+	10	7140	c.6692C>T	c.(6691-6693)aCg>aTg	p.T2231M	ZFHX4_ENST00000518282.1_Missense_Mutation_p.T2205M|ZFHX4_ENST00000455469.2_Missense_Mutation_p.T2186M|ZFHX4_ENST00000050961.6_Missense_Mutation_p.T2186M	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.T2215M(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TCTTCTAGAACGAGATTTACT	0.383										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											71	68	69					8																	77765849		1891	4097	5988	77928404	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6692C>T	8.37:g.77765849C>T	ENSP00000430497:p.Thr2231Met		77928404	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735213	0.48939	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.97352	-4.35;-4.35;-4.35;-4.35	4.05	4.05	0.47172	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.45867	U	0.000338	D	0.98576	0.9524	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.99655	1.0992	10	0.87932	D	0	.	16.7528	0.85490	0.0:1.0:0.0:0.0	.	2186;2186;2231	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	M	2231;2215;2186;2186;2205	ENSP00000430497:T2231M;ENSP00000399605:T2186M;ENSP00000050961:T2186M;ENSP00000430848:T2205M	ENSP00000050961:T2186M	T	+	2	0	ZFHX4	77928404	1.000000	0.71417	0.047000	0.18901	0.893000	0.52053	7.548000	0.82154	2.270000	0.75569	0.555000	0.69702	ACG		0.383	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77765849	C	T	77765849	3	4	50	1	0	0	0	0	1	0	0	0	17674	536	19	1	6726	1	ZFHX4	8	77765849	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	18247299	77765849	68598173	50	6853										
KCNS2	3788	broad.mit.edu	37	chr8	99441154	99441154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	caggcactccactggcctccGctccctgggggccactttga	11	17	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:99441154G>A	ENST00000287042.4	+	2	1297	c.947G>A	c.(946-948)cGc>cAc	p.R316H	KCNS2_ENST00000521839.1_Missense_Mutation_p.R316H	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	316					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R316H(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			ACTGGCCTCCGCTCCCTGGGG	0.577																																					Pancreas(138;844 2489 9202 24627)											1	Substitution - Missense(1)	large_intestine(1)	8											83	75	78					8																	99441154		2203	4300	6503	99510330	SO:0001583	missense	3788			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.947G>A	8.37:g.99441154G>A	ENSP00000287042:p.Arg316His		99510330	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358219	0.82243	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	D;D	0.97959	-4.63;-4.63	5.83	5.83	0.93111	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98979	0.9652	M	0.89478	3.035	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.99544	1.0964	10	0.87932	D	0	.	20.1184	0.97949	0.0:0.0:1.0:0.0	.	316	Q9ULS6	KCNS2_HUMAN	H	316	ENSP00000287042:R316H;ENSP00000430712:R316H	ENSP00000287042:R316H	R	+	2	0	KCNS2	99510330	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	2.769000	0.95229	0.655000	0.94253	CGC		0.577	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		A	99441154	G	A	99441154	3	1	50	1	0	0	0	0	1	0	0	0	8110	1087	38	1	949	1	KCNS2	8	99441154	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	21675305	99441154	46922868	51	6854										
RSPO2	340419	broad.mit.edu	37	chr8	108970375	108970375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atggttggacacagtattgtGtctttcactggctttttaac	9	7	2	0	rs151165897	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:108970375G>T	ENST00000276659.5	-	5	1169	c.549C>A	c.(547-549)gaC>gaA	p.D183E	RSPO2_ENST00000378439.2_Missense_Mutation_p.D119E|RSPO2_ENST00000517781.1_Missense_Mutation_p.D119E|RSPO2_ENST00000517939.1_Missense_Mutation_p.D116E	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	183	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.D183E(1)	EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			ACAGTATTGTGTCTTTCACTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											321	277	292					8																	108970375		2203	4300	6503	109039551	SO:0001583	missense	340419			AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.549C>A	8.37:g.108970375G>T	ENSP00000276659:p.Asp183Glu		109039551	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451651	0.84209	.	.	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.9	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.71813	0.3384	N	0.16066	0.365	0.51012	D	0.999905	D;B	0.61697	0.99;0.22	D;B	0.75484	0.986;0.101	T	0.65545	-0.6142	10	0.12430	T	0.62	-7.7256	12.515	0.56028	0.1347:0.0:0.8653:0.0	.	183;119	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	E	116;119;119;183;116	ENSP00000428940:D116E;ENSP00000427937:D119E;ENSP00000367698:D119E;ENSP00000276659:D183E;ENSP00000428614:D116E	ENSP00000276659:D183E	D	-	3	2	RSPO2	109039551	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	1.794000	0.38774	0.829000	0.34733	0.563000	0.77884	GAC		0.443	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		T	108970375	G	T	108970375	3	4	50	1	0	0	0	0	1	0	0	0	13747	1368	48	2	190	2	RSPO2	8	108970375	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	9529221	108970375	37393647	52	6855										
CSMD3	114788	broad.mit.edu	37	chr8	113569062	113569062	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cacttgagaaggctacttccGtggagagtgtagcctggatt	13	8	0	2	rs140111920		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:113569062G>A	ENST00000297405.5	-	25	4408	c.4164C>T	c.(4162-4164)caC>caT	p.H1388H	CSMD3_ENST00000352409.3_Silent_p.H1388H|CSMD3_ENST00000343508.3_Silent_p.H1348H|CSMD3_ENST00000455883.2_Silent_p.H1284H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1388	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.H1388H(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGCTACTTCCGTGGAGAGTGT	0.463										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8						G	,,	0,4406		0,0,2203	110	97	101		3852,4164,4044	1.3	1	8	dbSNP_134	101	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,	1284/3539,1388/3708,1348/3668	113569062	1,13003	2203	4299	6502	113638238	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4164C>T	8.37:g.113569062G>A			113638238	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.463	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113569062	G	A	113569062	2	1	50	1	0	0	0	0	0	0	0	1	3952	1136	40	1		1	CSMD3	8	113569062	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	4598687	113569062	32794960	53	6856										
RAD21	5885	broad.mit.edu	37	chr8	117864329	117864329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggcttggctcttcaataatgGgctcatctgcaattggtcat	10	9	5	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:117864329G>A	ENST00000297338.2	-	11	1615	c.1328C>T	c.(1327-1329)cCc>cTc	p.P443L	RAD21_ENST00000518055.1_5'UTR|RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000523986.1_5'UTR	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	443					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.P443L(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TTCAATAATGGGCTCATCTGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	8											58	53	55					8																	117864329		2203	4300	6503	117933510	SO:0001583	missense	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1328C>T	8.37:g.117864329G>A	ENSP00000297338:p.Pro443Leu		117933510	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457875	0.63401	.	.	ENSG00000164754	ENST00000297338	T	0.51071	0.72	5.71	5.71	0.89125	.	0.046947	0.85682	D	0.000000	T	0.42337	0.1198	L	0.38531	1.155	0.80722	D	1	B	0.23377	0.084	B	0.20767	0.031	T	0.15093	-1.0449	10	0.28530	T	0.3	-21.5991	19.8625	0.96789	0.0:0.0:1.0:0.0	.	443	O60216	RAD21_HUMAN	L	443	ENSP00000297338:P443L	ENSP00000297338:P443L	P	-	2	0	RAD21	117933510	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.611000	0.82962	2.689000	0.91719	0.655000	0.94253	CCC		0.418	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117864329	G	A	117864329	3	1	50	1	0	0	0	0	1	0	0	0	13018	1232	43	3	583	3	RAD21	8	117864329	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	4295267	117864329	28499693	54	6857										
PTP4A3	11156	broad.mit.edu	37	chr8	142432393	142432393	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggtgagctacaaacacatgcGcttcctcatcacccacaacc	6	16	2	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:142432393G>T	ENST00000521578.1	+	2	998	c.53G>T	c.(52-54)cGc>cTc	p.R18L	PTP4A3_ENST00000520105.1_Missense_Mutation_p.R18L|PTP4A3_ENST00000329397.1_Missense_Mutation_p.R18L|PTP4A3_ENST00000349124.1_Missense_Mutation_p.R18L|PTP4A3_ENST00000524028.1_Missense_Mutation_p.R18L			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	18					peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)	p.R18L(1)		endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			AAACACATGCGCTTCCTCATC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	8											125	115	118					8																	142432393		2203	4300	6503	142501575	SO:0001583	missense	11156			AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.53G>T	8.37:g.142432393G>T	ENSP00000428976:p.Arg18Leu		142501575	Q8IVN5|Q99849|Q9BTW5	Missense_Mutation	SNP	ENST00000521578.1	37	CCDS6383.1	.	.	.	.	.	.	.	.	.	.	G	33	5.287413	0.95517	.	.	ENSG00000184489	ENST00000521578;ENST00000520105;ENST00000523147;ENST00000329397;ENST00000349124;ENST00000524028	D;T;D;T	0.95949	-3.86;0.7;-3.86;0.7	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.97864	0.9298	M	0.87456	2.885	0.80722	D	1	D;B	0.71674	0.998;0.294	D;B	0.80764	0.994;0.29	D	0.98715	1.0706	10	0.66056	D	0.02	-14.7022	16.6165	0.84917	0.0:0.0:1.0:0.0	.	18;18	O75365-2;O75365	.;TP4A3_HUMAN	L	18	ENSP00000428976:R18L;ENSP00000428758:R18L;ENSP00000332274:R18L;ENSP00000331730:R18L	ENSP00000332274:R18L	R	+	2	0	PTP4A3	142501575	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.644000	0.98468	2.268000	0.75426	0.491000	0.48974	CGC		0.657	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611		T	142432393	G	T	142432393	3	4	50	1	0	0	0	0	1	0	0	0	12807	1087	38	2	55	2	PTP4A3	8	142432393	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	24568064	142432393	3931629	55	6858										
CYP11B1	1584	broad.mit.edu	37	chr8	143960554	143960554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cacctgttgcagcttctccaCgtcctccggcagcatcacac	7	18	2	0	rs200867786		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr8:143960554C>T	ENST00000292427.4	-	2	321	c.289G>A	c.(289-291)Gtg>Atg	p.V97M	CYP11B1_ENST00000517471.1_Missense_Mutation_p.V97M|CYP11B1_ENST00000377675.3_Missense_Mutation_p.V142M	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	97					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.V97L(1)|p.V97M(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	AGCTTCTCCACGTCCTCCGGC	0.622									Familial Hyperaldosteronism type I																																							2	Substitution - Missense(2)	large_intestine(1)|lung(1)	8											205	150	169					8																	143960554		2203	4300	6503	143957556	SO:0001583	missense	1584	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.289G>A	8.37:g.143960554C>T	ENSP00000292427:p.Val97Met		143957556	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900515	0.33535	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.76968	-0.62;-0.62;-1.06	3.55	3.55	0.40652	.	0.766622	0.10813	N	0.631407	T	0.75384	0.3842	L	0.54323	1.7	0.19575	N	0.999968	P;P;P	0.46578	0.841;0.8;0.88	B;B;B	0.43386	0.241;0.418;0.329	T	0.66551	-0.5895	10	0.66056	D	0.02	.	10.9711	0.47441	0.0:1.0:0.0:0.0	.	142;97;97	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	M	97;97;142	ENSP00000292427:V97M;ENSP00000428043:V97M;ENSP00000366903:V142M	ENSP00000292427:V97M	V	-	1	0	CYP11B1	143957556	0.024000	0.19004	0.033000	0.17914	0.457000	0.32468	2.857000	0.48349	1.677000	0.50941	0.484000	0.47621	GTG		0.622	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143960554	C	T	143960554	3	4	50	1	0	0	0	0	1	0	0	0	4151	536	19	1	1254	1	CYP11B1	8	143960554	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	1528161	143960554	2403468	56	6859										
RFX3	5991	broad.mit.edu	37	chr9	3228886	3228886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agacacggcatttaaatcacCaaactgcaaaacaatagtca	5	10	2	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr9:3228886C>T	ENST00000382004.3	-	17	2283	c.1972G>A	c.(1972-1974)Ggt>Agt	p.G658S		NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	658					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G658S(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TTTAAATCACCAAACTGCAAA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	9											52	52	52					9																	3228886		2202	4291	6493	3218886	SO:0001583	missense	5991			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1972G>A	9.37:g.3228886C>T	ENSP00000371434:p.Gly658Ser		3218886	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981858	0.53827	.	.	ENSG00000080298	ENST00000382004	T	0.40476	1.03	5.77	5.77	0.91146	.	0.402843	0.30383	N	0.009747	T	0.30823	0.0777	N	0.16790	0.44	0.80722	D	1	B	0.11235	0.004	B	0.16722	0.016	T	0.10941	-1.0608	10	0.14252	T	0.57	-12.1489	19.9928	0.97374	0.0:1.0:0.0:0.0	.	658	P48380	RFX3_HUMAN	S	658	ENSP00000371434:G658S	ENSP00000371434:G658S	G	-	1	0	RFX3	3218886	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.480000	0.73604	2.745000	0.94114	0.650000	0.86243	GGT		0.294	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		T	3228886	C	T	3228886	3	4	50	1	0	0	0	0	1	0	0	0	13301	594	21	3	285	3	RFX3	9	3228886	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09		3228886	137984545	57	6860										
BNC2	54796	broad.mit.edu	37	chr9	16419344	16419344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atcccctcatcgctgcctgcGtcggattctctggaggaatg	11	13	2	0	rs374901966		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr9:16419344G>A	ENST00000380672.4	-	7	3000	c.2943C>T	c.(2941-2943)gaC>gaT	p.D981D	BNC2_ENST00000380667.2_Silent_p.D914D|BNC2_ENST00000545497.1_Silent_p.D886D	NM_017637.5	NP_060107.3			basonuclin 2									p.D981D(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CGCTGCCTGCGTCGGATTCTC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	9						G		0,4406		0,0,2203	91	87	88		2943	-0.1	1	9		88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BNC2	NM_017637.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		981/1100	16419344	1,13005	2203	4300	6503	16409344	SO:0001819	synonymous_variant	54796			AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2943C>T	9.37:g.16419344G>A			16409344		Silent	SNP	ENST00000380672.4	37	CCDS6482.2																																																																																				0.612	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16419344	G	A	16419344	2	1	50	1	0	0	0	0	0	0	0	1	1476	1136	40	1		1	BNC2	9	16419344	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	13190458	16419344	124794087	58	6861										
SMC5	23137	broad.mit.edu	37	chr9	72967217	72967217	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aaggctttccaaaggcggcgGcgccgtattacattcactca	10	12	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr9:72967217G>A	ENST00000361138.5	+	25	3334	c.3276G>A	c.(3274-3276)cgG>cgA	p.R1092R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	1092					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.R1092R(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						AAAGGCGGCGGCGCCGTATTA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	89	87					9																	72967217		2203	4300	6503	72157037	SO:0001819	synonymous_variant	23137			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.3276G>A	9.37:g.72967217G>A			72157037	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	37	CCDS6632.1																																																																																				0.368	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		A	72967217	G	A	72967217	2	1	50	1	0	0	0	0	0	0	0	1	14823	1190	42	3		3	SMC5	9	72967217	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	56547873	72967217	68246214	59	6862										
KIAA1958	158405	broad.mit.edu	37	chr9	115422112	115422112	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctcctctacaagtacatgtaCatccaccggccgcccaccca	5	19	1	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr9:115422112C>T	ENST00000337530.6	+	4	2210	c.1914C>T	c.(1912-1914)taC>taT	p.Y638Y	KIAA1958_ENST00000536272.1_Silent_p.Y666Y	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	638								p.Y638Y(1)		endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						AGTACATGTACATCCACCGGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	9											56	49	51					9																	115422112		2203	4300	6503	114461933	SO:0001819	synonymous_variant	158405			AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1914C>T	9.37:g.115422112C>T			114461933	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	37	CCDS35108.1																																																																																				0.587	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		T	115422112	C	T	115422112	2	4	50	1	0	0	0	0	0	0	0	1	8285	489	17	3		3	KIAA1958	9	115422112	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	42454895	115422112	25791319	60	6863										
PITRM1	10531	broad.mit.edu	37	chr10	3207621	3207621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ataccagaaatccagctcgcGtaaacatgggaaaaaggtgg	11	8	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr10:3207621G>A	ENST00000224949.4	-	5	551	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	PITRM1_ENST00000451104.2_Missense_Mutation_p.R141C|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.R173C|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	173					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R173C(1)		breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TCCAGCTCGCGTAAACATGGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											93	94	94					10																	3207621		1880	4120	6000	3197621	SO:0001583	missense	10531			AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.517C>T	10.37:g.3207621G>A	ENSP00000224949:p.Arg173Cys		3197621	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.158781	0.57368	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.30448	1.53;1.53;1.53	5.37	3.23	0.37069	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.59662	0.2210	M	0.86573	2.825	0.58432	D	0.999997	D;D;D;D;D;D	0.76494	0.998;0.998;0.999;0.999;0.999;0.999	P;D;D;D;D;D	0.72338	0.772;0.953;0.921;0.969;0.969;0.977	T	0.70605	-0.4826	10	0.87932	D	0	.	15.2762	0.73742	0.0:0.0:0.654:0.346	.	166;141;173;173;173;166	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	C	173;166;173;141	ENSP00000224949:R173C;ENSP00000370377:R173C;ENSP00000401201:R141C	ENSP00000224949:R173C	R	-	1	0	PITRM1	3197621	1.000000	0.71417	0.989000	0.46669	0.773000	0.43773	3.316000	0.51960	1.200000	0.43188	0.586000	0.80456	CGC		0.393	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			A	3207621	G	A	3207621	3	1	50	1	0	0	0	0	1	0	0	0	11984	1145	40	1	2688	1	PITRM1	10	3207621	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		3207621	132327126	61	6864										
ZNF518A	9849	broad.mit.edu	37	chr10	97919838	97919838	+	RNA	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agaaaaaagacttccaaaaaAattttttcaaaaacaaaaac	2	6	1	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr10:97919838A>C	ENST00000534948.1	+	0	4616							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K1253N(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		CTTCCAAAAAAATTTTTTCAA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	10											28	30	29					10																	97919838		1782	4039	5821	97909828			9849			AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"Zinc fingers, C2H2-type"	29009	protein-coding gene	gene with protein product			"zinc finger protein 518"	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97919838A>C			97909828	A0PJI5|O15044|Q32MP4	Missense_Mutation	SNP	ENST00000534948.1	37																																																																																					0.333	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		C	97919838	A	C	97919838	1	2	50	0	1	0	0	0	0	0	0	0	18001	11	1	4		4	ZNF518A	10	97919838	RNA	SNP	A	TCGA-AG-3896-01A-01W-1073-09	94712217	97919838	37614909	62	6865										
PPRC1	23082	broad.mit.edu	37	chr10	103899635	103899635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	accaggttcccagagagctcGaaagggcaggaagaagaaga	14	8	0	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr10:103899635G>A	ENST00000278070.2	+	5	1409	c.1370G>A	c.(1369-1371)cGa>cAa	p.R457Q	PPRC1_ENST00000413464.2_Missense_Mutation_p.R457Q|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	457	Necessary for interaction with CREB1 and NRF1 and for transcriptional coactivation.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R457Q(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CAGAGAGCTCGAAAGGGCAGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	10											55	52	53					10																	103899635		2203	4300	6503	103889625	SO:0001583	missense	23082			AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.1370G>A	10.37:g.103899635G>A	ENSP00000278070:p.Arg457Gln		103889625	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304770	0.60305	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.38722	1.12;1.12	6.03	2.73	0.32206	.	0.550027	0.17427	N	0.174619	T	0.25827	0.0629	L	0.32530	0.975	0.26452	N	0.975583	B;B;B	0.31817	0.231;0.341;0.231	B;B;B	0.21151	0.022;0.033;0.022	T	0.09997	-1.0649	10	0.33940	T	0.23	.	7.4616	0.27298	0.1636:0.0:0.6964:0.14	.	457;337;457	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	Q	457	ENSP00000278070:R457Q;ENSP00000399743:R457Q	ENSP00000278070:R457Q	R	+	2	0	PPRC1	103889625	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.584000	0.36589	0.862000	0.35528	0.555000	0.69702	CGA		0.597	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103899635	G	A	103899635	3	1	50	1	0	0	0	0	1	0	0	0	12444	1058	37	1	1388	1	PPRC1	10	103899635	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	5979797	103899635	31635112	63	6866										
PDCD11	22984	broad.mit.edu	37	chr10	105181166	105181166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgttgagggccagacagtagCggcaaaggtgaccaatgtgg	16	7	0	3	rs145404572	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr10:105181166C>T	ENST00000369797.3	+	17	2433	c.2339C>T	c.(2338-2340)gCg>gTg	p.A780V		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	780	S1 motif 8. {ECO:0000255|PROSITE- ProRule:PRU00180}.		A -> S (in dbSNP:rs11591914).		mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.A780V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CAGACAGTAGCGGCAAAGGTG	0.537													C|||	2	0.000399361	8e-04	0	5008	,	,		16448	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											67	57	60					10																	105181166		2203	4300	6503	105171156	SO:0001583	missense	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.2339C>T	10.37:g.105181166C>T	ENSP00000358812:p.Ala780Val		105171156	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	0.013	-1.639427	0.00799	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.42900	0.96	5.74	2.05	0.26809	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.496053	0.24443	N	0.038497	T	0.11623	0.0283	N	0.00303	-1.675	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29366	-1.0014	10	0.16420	T	0.52	-11.4892	12.0084	0.53272	0.0:0.1304:0.0:0.8696	.	780	Q14690	RRP5_HUMAN	V	780	ENSP00000358812:A780V	ENSP00000358812:A780V	A	+	2	0	PDCD11	105171156	1.000000	0.71417	0.040000	0.18447	0.041000	0.13682	3.097000	0.50251	0.521000	0.28445	-1.421000	0.01109	GCG		0.537	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105181166	C	T	105181166	3	4	50	1	0	0	0	0	1	0	0	0	11648	768	27	1	2401	1	PDCD11	10	105181166	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	1281531	105181166	30353581	64	6867										
SLC43A3	29015	broad.mit.edu	37	chr11	57185285	57185285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gggcatcaggaggaaagtgcGtgctacatgccaggtactgc	15	9	1	0	rs201915801		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr11:57185285G>A	ENST00000395123.2	-	8	911	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	SLC43A3_ENST00000395124.1_Missense_Mutation_p.R203C|SLC43A3_ENST00000533524.1_Missense_Mutation_p.R216C|SLC43A3_ENST00000352187.1_Missense_Mutation_p.R203C|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000529554.1_Missense_Mutation_p.R203C	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	203					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.R203C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						AGGAAAGTGCGTGCTACATGC	0.537													G|||	1	0.000199681	8e-04	0	5008	,	,		19315	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											109	97	101					11																	57185285		2201	4296	6497	56941861	SO:0001583	missense	5553			AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.607C>T	11.37:g.57185285G>A	ENSP00000378555:p.Arg203Cys		56941861	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	19.34	3.809051	0.70797	.	.	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005	T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;0.35	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90116	0.6912	M	0.83483	2.645	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;0.998;0.996	D	0.89383	0.3683	10	0.38643	T	0.18	-17.5211	17.1335	0.86733	0.0:0.0:1.0:0.0	.	203;216;203;203	B4DV87;E7EQD2;Q8NBI5;A8K2X6	.;.;S43A3_HUMAN;.	C	203;203;203;203;216;203	ENSP00000378555:R203C;ENSP00000378556:R203C;ENSP00000337561:R203C;ENSP00000436254:R203C;ENSP00000434515:R216C;ENSP00000435893:R203C	ENSP00000337561:R203C	R	-	1	0	SLC43A3	56941861	1.000000	0.71417	0.118000	0.21660	0.644000	0.38419	4.872000	0.63050	2.586000	0.87340	0.462000	0.41574	CGC		0.537	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		A	57185285	G	A	57185285	3	1	50	1	0	0	0	0	1	0	0	0	14671	1145	40	1	896	1	SLC43A3	11	57185285	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		57185285	77821231	65	6868										
SORL1	6653	broad.mit.edu	37	chr11	121360759	121360759	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cttgtctttgcagctgtggaAgtcagatgactttggccaga	12	8	2	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr11:121360759A>T	ENST00000260197.7	+	5	827	c.698A>T	c.(697-699)aAg>aTg	p.K233M	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	233					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.K233M(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CAGCTGTGGAAGTCAGATGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											208	166	180					11																	121360759		2203	4299	6502	120865969	SO:0001583	missense	6653			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.698A>T	11.37:g.121360759A>T	ENSP00000260197:p.Lys233Met		120865969	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	a	18.66	3.671055	0.67814	.	.	ENSG00000137642	ENST00000260197	T	0.23552	1.9	5.68	4.43	0.53597	VPS10 (1);	0.050237	0.85682	D	0.000000	T	0.30479	0.0766	L	0.33485	1.01	0.80722	D	1	D	0.67145	0.996	P	0.55871	0.786	T	0.01600	-1.1315	10	0.30854	T	0.27	.	11.5368	0.50641	0.9247:0.0:0.0753:0.0	.	233	Q92673	SORL_HUMAN	M	233	ENSP00000260197:K233M	ENSP00000260197:K233M	K	+	2	0	SORL1	120865969	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	4.876000	0.63079	0.963000	0.38082	0.529000	0.55759	AAG		0.428	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		T	121360759	A	T	121360759	3	4	50	1	0	0	0	0	1	0	0	0	14971	72	3	5	716	5	SORL1	11	121360759	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	64175474	121360759	13645757	66	6869										
KCNJ1	3758	broad.mit.edu	37	chr11	128709642	128709642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tggtcttggcacgttttttgGgcctggagatcttggctaag	14	7	2	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr11:128709642G>A	ENST00000392664.2	-	2	670	c.554C>T	c.(553-555)cCc>cTc	p.P185L	KCNJ1_ENST00000392665.2_Missense_Mutation_p.P166L|KCNJ1_ENST00000392666.1_Missense_Mutation_p.P166L|KCNJ1_ENST00000440599.2_Missense_Mutation_p.P166L|KCNJ1_ENST00000324036.3_Missense_Mutation_p.P166L	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	185					cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P185L(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	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)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	ACGTTTTTTGGGCCTGGAGAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											79	75	76					11																	128709642		2201	4296	6497	128214852	SO:0001583	missense	3758			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.554C>T	11.37:g.128709642G>A	ENSP00000376432:p.Pro185Leu		128214852	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824768	0.90955	.	.	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664	D;D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63;-3.63	5.98	5.98	0.97165	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.202538	0.53938	D	0.000058	D	0.98036	0.9353	M	0.92122	3.275	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	D	0.98287	1.0511	10	0.87932	D	0	.	20.4464	0.99123	0.0:0.0:1.0:0.0	.	185	P48048	IRK1_HUMAN	L	166;166;166;166;185	ENSP00000376433:P166L;ENSP00000376434:P166L;ENSP00000406320:P166L;ENSP00000316233:P166L;ENSP00000376432:P185L	ENSP00000316233:P166L	P	-	2	0	KCNJ1	128214852	1.000000	0.71417	0.970000	0.41538	0.988000	0.76386	9.852000	0.99516	2.838000	0.97847	0.514000	0.50259	CCC		0.468	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		A	128709642	G	A	128709642	3	1	50	1	0	0	0	0	1	0	0	0	8064	1232	43	3	625	3	KCNJ1	11	128709642	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	7348883	128709642	6296874	67	6870										
FGF6	2251	broad.mit.edu	37	chr12	4554551	4554551	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atctctccagctagcccggcGcgagacctggacagcagggt	13	14	1	1	rs202212518		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:4554551G>A	ENST00000228837.2	-	1	229	c.186C>T	c.(184-186)cgC>cgT	p.R62R		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	62					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.R62R(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			CTAGCCCGGCGCGAGACCTGG	0.652													G|||	1	0.000199681	0	0	5008	,	,		17362	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											86	81	83					12																	4554551		2203	4300	6503	4424812	SO:0001819	synonymous_variant	2251			X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"Endogenous ligands"	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.186C>T	12.37:g.4554551G>A			4424812	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																				0.652	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		A	4554551	G	A	4554551	2	1	50	1	0	0	0	0	0	0	0	1	5875	1074	38	1		1	FGF6	12	4554551	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09		4554551	129297344	68	6871										
KRAS	3845	broad.mit.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000311936.3_Missense_Mutation_p.G12C|KRAS_ENST00000557334.1_Missense_Mutation_p.G12C|KRAS_ENST00000556131.1_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	12.37:g.25398285C>A	ENSP00000256078:p.Gly12Cys		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398285	C	A	25398285	3	1	50	1	0	0	0	0	1	0	0	0	8459	594	21	2	672	2	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	20843734	25398285	108453610	69	6872										
KRT6A	3853	broad.mit.edu	37	chr12	52886927	52886927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgagttggcactgaaaccccGgcggctgctgctgtggctcc	14	13	0	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:52886927G>A	ENST00000330722.6	-	1	114	c.46C>T	c.(46-48)Cgg>Tgg	p.R16W		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	16	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.R16W(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGAAACCCCGGCGGCTGCTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											18	24	22					12																	52886927		2159	4229	6388	51173194	SO:0001583	missense	3853			BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.46C>T	12.37:g.52886927G>A	ENSP00000369317:p.Arg16Trp		51173194	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	37	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.319937	0.23994	.	.	ENSG00000205420	ENST00000330722	T	0.76316	-1.01	5.05	-0.648	0.11464	.	0.102760	0.40908	D	0.000991	T	0.75295	0.3830	M	0.89601	3.045	0.09310	N	0.999998	P	0.50617	0.937	B	0.40565	0.333	T	0.69778	-0.5053	10	0.66056	D	0.02	.	5.1459	0.14985	0.0662:0.1712:0.4034:0.3593	.	16	P02538	K2C6A_HUMAN	W	16	ENSP00000369317:R16W	ENSP00000369317:R16W	R	-	1	2	KRT6A	51173194	0.000000	0.05858	0.010000	0.14722	0.559000	0.35586	0.300000	0.19156	-0.019000	0.14055	-0.264000	0.10439	CGG		0.652	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		A	52886927	G	A	52886927	3	1	50	1	0	0	0	0	1	0	0	0	8501	1115	39	1	1684	1	KRT6A	12	52886927	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	27488642	52886927	80964968	70	6873										
PPFIA2	8499	broad.mit.edu	37	chr12	81734925	81734926	+	In_Frame_Ins	INS	-	-	GGG													0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gggctctaggggtaggaggaINSggagaagtttcacatttaat							TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	-	-	-	GGG	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:81734925_81734926insGGG	ENST00000549396.1	-	20	2484_2485	c.2324_2325insCCC	c.(2323-2325)cct>ccCCCt	p.775_775P>PP	PPFIA2_ENST00000333447.7_In_Frame_Ins_p.757_757P>PP|PPFIA2_ENST00000552948.1_In_Frame_Ins_p.775_775P>PP|PPFIA2_ENST00000541017.1_5'UTR|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000443686.3_In_Frame_Ins_p.676_676P>PP|PPFIA2_ENST00000550359.2_In_Frame_Ins_p.622_622P>PP|PPFIA2_ENST00000550584.2_In_Frame_Ins_p.775_775P>PP|PPFIA2_ENST00000407050.4_In_Frame_Ins_p.701_701P>PP|PPFIA2_ENST00000548586.1_In_Frame_Ins_p.775_775P>PP|PPFIA2_ENST00000549325.1_In_Frame_Ins_p.757_757P>PP|PPFIA2_ENST00000541570.2_In_Frame_Ins_p.342_342P>PP	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	775					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.P777_T778insP(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						GGGTAGGAGGAGGAGAAGTTTC	0.436																																																1	Insertion - In frame(1)	large_intestine(1)	12																																								80259057	SO:0001652	inframe_insertion	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2324_2325insCCC	12.37:g.81734925_81734926insGGG	ENSP00000450337:p.Pro777dup		80259056	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	In_Frame_Ins	INS	ENST00000549396.1	37	CCDS55857.1																																																																																				0.436	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			GGG	81734926	-	GGG	81734925	7	5	50	1	0	1	1	0	0	0	0	0	12341	291	11	0	1500	0	PPFIA2	12	81734925	In_Frame_Ins	INS	-	TCGA-AG-3896-01A-01W-1073-09	28847998	81734925	52116970	71	6874										
RASSF9	9182	broad.mit.edu	37	chr12	86198974	86198974	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tattcggtaatatttcagtcGttcttccagctgttcaattc	6	9	3	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:86198974G>A	ENST00000361228.3	-	2	1182	c.814C>T	c.(814-816)Cga>Tga	p.R272*		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	272					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.R272*(2)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TATTTCAGTCGTTCTTCCAGC	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											113	108	110					12																	86198974		1886	4108	5994	84723105	SO:0001587	stop_gained	9182				CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.814C>T	12.37:g.86198974G>A	ENSP00000354884:p.Arg272*		84723105	B3KMQ4|Q8N5U8	Nonsense_Mutation	SNP	ENST00000361228.3	37	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.685307	0.68157	.	.	ENSG00000198774	ENST00000361228	.	.	.	4.9	1.88	0.25563	.	0.581472	0.16373	U	0.217227	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-15.3805	10.6117	0.45425	0.0:0.1108:0.2861:0.6031	.	.	.	.	X	272	.	ENSP00000354884:R272X	R	-	1	2	RASSF9	84723105	0.009000	0.17119	0.003000	0.11579	0.198000	0.23893	0.492000	0.22435	0.148000	0.19059	-0.188000	0.12872	CGA		0.398	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			A	86198974	G	A	86198974	4	1	50	1	0	0	0	0	0	1	0	0	13130	1153	40	1	497	1	RASSF9	12	86198974	Nonsense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	4464049	86198974	47652921	72	6875										
NAA25	80018	broad.mit.edu	37	chr12	112485550	112485550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atggaatgtcatcttcttctGgcctaaggttcattgacttt	8	8	5	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:112485550G>A	ENST00000261745.4	-	17	2173	c.1925C>T	c.(1924-1926)cCa>cTa	p.P642L		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	642						cytoplasm (GO:0005737)		p.P642L(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						ATCTTCTTCTGGCCTAAGGTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											236	248	244					12																	112485550		2203	4300	6503	110969933	SO:0001583	missense	80018			AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.1925C>T	12.37:g.112485550G>A	ENSP00000261745:p.Pro642Leu		110969933	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990319	0.93106	.	.	ENSG00000111300	ENST00000261745	T	0.43688	0.94	5.71	5.71	0.89125	.	0.056738	0.64402	D	0.000001	T	0.63663	0.2530	M	0.83223	2.63	0.80722	D	1	D;D	0.58268	0.982;0.982	P;P	0.55055	0.767;0.767	T	0.65010	-0.6272	10	0.44086	T	0.13	-9.3324	19.8505	0.96738	0.0:0.0:1.0:0.0	.	642;642	A8K8X0;Q14CX7	.;NAA25_HUMAN	L	642	ENSP00000261745:P642L	ENSP00000261745:P642L	P	-	2	0	NAA25	110969933	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	9.476000	0.97823	2.688000	0.91661	0.655000	0.94253	CCA		0.348	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		A	112485550	G	A	112485550	3	1	50	1	0	0	0	0	1	0	0	0	10151	1348	47	3	1025	3	NAA25	12	112485550	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	26286576	112485550	21366345	73	6876										
ATP6V0A2	23545	broad.mit.edu	37	chr12	124239011	124239011	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	acccaagtaatccattccatCgagtactgtctgggatgcat	8	11	1	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr12:124239011C>T	ENST00000330342.3	+	18	2468	c.2220C>T	c.(2218-2220)atC>atT	p.I740I	ATP6V0A2_ENST00000544833.1_Silent_p.I22I	NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	740					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)	p.I740I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TCCATTCCATCGAGTACTGTC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	12											119	106	111					12																	124239011		2203	4300	6503	122804964	SO:0001819	synonymous_variant	23545			AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"ATPases / V-type"	18481	protein-coding gene	gene with protein product	"infantile malignant osteopetrosis"	611716	"infantile malignant osteopetrosis", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 2", "ATPase, H+ transporting, lysosomal V0 subunit A2"			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.2220C>T	12.37:g.124239011C>T			122804964	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																				0.453	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463		T	124239011	C	T	124239011	2	4	50	1	0	0	0	0	0	0	0	1	1170	874	31	1		1	ATP6V0A2	12	124239011	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	11753461	124239011	9612884	74	6877										
C14orf43	91748	broad.mit.edu	37	chr14	74196574	74196574	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggtgatgttggagtagacggGaggggcgatgaaagtgcccg	20	5	0	3			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr14:74196574G>C	ENST00000286523.5	-	4	2646	c.1864C>G	c.(1864-1866)Ccc>Gcc	p.P622A	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.P622A	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	622					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.P622A(1)									GAGTAGACGGGAGGGGCGATG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	56	56					14																	74196574		2203	4300	6503	73266327	SO:0001583	missense	91748			BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1864C>G	14.37:g.74196574G>C	ENSP00000286523:p.Pro622Ala		73266327	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.901546	0.52227	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.14144	2.53;2.53;2.53;2.53	5.4	5.4	0.78164	.	0.195138	0.36591	N	0.002518	T	0.17323	0.0416	N	0.19112	0.55	0.50039	D	0.999848	B;D	0.62365	0.089;0.991	B;P	0.60541	0.037;0.876	T	0.05354	-1.0890	10	0.08381	T	0.77	-11.8994	14.7518	0.69530	0.0:0.1443:0.8557:0.0	.	622;622	A0PJD3;Q6PJG2	.;CN043_HUMAN	A	622	ENSP00000377634:P622A;ENSP00000286523:P622A;ENSP00000407767:P622A;ENSP00000402380:P622A	ENSP00000286523:P622A	P	-	1	0	C14orf43	73266327	0.999000	0.42202	0.989000	0.46669	0.808000	0.45660	2.677000	0.46892	2.511000	0.84671	0.579000	0.79373	CCC		0.637	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		C	74196574	G	C	74196574	3	2	50	1	0	0	0	0	1	0	0	0	1778	1174	41	5	1309	5	C14orf43	14	74196574	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		74196574	33152966	75	6878										
DUOX1	53905	broad.mit.edu	37	chr15	45454506	45454506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggagggggcattggggtcacCccttttgcctccatcctcaa	12	13	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr15:45454506C>T	ENST00000321429.4	+	32	4586	c.4179C>T	c.(4177-4179)acC>acT	p.T1393T	DUOX1_ENST00000389037.3_Silent_p.T1393T|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Silent_p.T1039T	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1393					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.T1393T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		TTGGGGTCACCCCTTTTGCCT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	15											150	130	137					15																	45454506		2198	4298	6496	43241798	SO:0001819	synonymous_variant	53905			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.4179C>T	15.37:g.45454506C>T			43241798	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																				0.547	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45454506	C	T	45454506	2	4	50	1	0	0	0	0	0	0	0	1	4811	610	22	3		3	DUOX1	15	45454506	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09		45454506	57076886	76	6879										
UNC13C	440279	broad.mit.edu	37	chr15	54305554	54305554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cacacacaatgccagttagaCgcaacagaaagagttcaagc	8	11	1	3	rs536918048		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr15:54305554C>T	ENST00000260323.11	+	1	454	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	UNC13C_ENST00000545554.1_Missense_Mutation_p.R152C|UNC13C_ENST00000537900.1_Missense_Mutation_p.R152C	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	152					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.R152C(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GCCAGTTAGACGCAACAGAAA	0.468													C|||	1	0.000199681	0	0	5008	,	,		20857	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	15											87	87	87					15																	54305554		2020	4188	6208	52092846	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.454C>T	15.37:g.54305554C>T	ENSP00000260323:p.Arg152Cys		52092846	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864614	0.51482	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.83673	-1.75;-1.75;-1.75	5.16	5.16	0.70880	.	.	.	.	.	D	0.86957	0.6058	L	0.32530	0.975	0.58432	D	0.999999	D	0.89917	1.0	D	0.73708	0.981	D	0.88664	0.3191	9	0.87932	D	0	.	17.6434	0.88143	0.0:1.0:0.0:0.0	.	152	Q8NB66	UN13C_HUMAN	C	152	ENSP00000260323:R152C;ENSP00000438156:R152C;ENSP00000442569:R152C	ENSP00000260323:R152C	R	+	1	0	UNC13C	52092846	1.000000	0.71417	0.522000	0.27862	0.365000	0.29674	4.576000	0.60915	2.394000	0.81467	0.655000	0.94253	CGC		0.468	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54305554	C	T	54305554	3	4	50	1	0	0	0	0	1	0	0	0	17026	536	19	1	456	1	UNC13C	15	54305554	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	8851048	54305554	48225838	77	6880										
SMAD3	4088	broad.mit.edu	37	chr15	67473630	67473630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cttctggtgctccatctcctActacgagctgaaccagcgcg	9	15	2	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr15:67473630A>G	ENST00000327367.4	+	6	1020	c.710A>G	c.(709-711)tAc>tGc	p.Y237C	SMAD3_ENST00000439724.3_Missense_Mutation_p.Y193C|SMAD3_ENST00000537194.2_Missense_Mutation_p.Y42C|SMAD3_ENST00000540846.2_Missense_Mutation_p.Y132C	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	237	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y237C(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		TCCATCTCCTACTACGAGCTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	15											80	61	68					15																	67473630		2201	4299	6500	65260684	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.710A>G	15.37:g.67473630A>G	ENSP00000332973:p.Tyr237Cys		65260684	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.576616	0.86645	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.99706	-6.47;-6.47;-6.47;-6.47	5.1	5.1	0.69264	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99832	0.9924	H	0.97516	4.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96608	0.9450	10	0.87932	D	0	.	15.1773	0.72924	1.0:0.0:0.0:0.0	.	193;237	B7Z4Z5;P84022	.;SMAD3_HUMAN	C	237;237;132;193;42	ENSP00000332973:Y237C;ENSP00000437757:Y132C;ENSP00000401133:Y193C;ENSP00000445348:Y42C	ENSP00000332973:Y237C	Y	+	2	0	SMAD3	65260684	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.164000	0.94755	2.035000	0.60131	0.454000	0.30748	TAC		0.612	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		G	67473630	A	G	67473630	3	3	50	1	0	0	0	0	1	0	0	0	14796	391	14	4	810	4	SMAD3	15	67473630	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	13168076	67473630	35057762	78	6881										
TMC3	342125	broad.mit.edu	37	chr15	81625262	81625262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gctgtggggagggaggctggCgggggacccgggatgcatat	22	7	0	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr15:81625262C>T	ENST00000359440.5	-	22	2936	c.2801G>A	c.(2800-2802)cGc>cAc	p.R934H	RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.R935H|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3									p.R938H(1)		autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						GGGAGGCTGGCGGGGGACCCG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	15											35	38	37					15																	81625262		1942	4106	6048	79412317	SO:0001583	missense	342125			AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2801G>A	15.37:g.81625262C>T	ENSP00000352413:p.Arg934His		79412317		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	C	6.093	0.385429	0.11524	.	.	ENSG00000188869	ENST00000359440	T	0.61158	0.13	4.94	-9.89	0.00464	.	1.218680	0.06653	N	0.763174	T	0.24005	0.0581	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08027	-1.0742	10	0.13470	T	0.59	0.504	3.5438	0.07820	0.1756:0.433:0.2085:0.1828	.	934	Q7Z5M5	TMC3_HUMAN	H	934	ENSP00000352413:R934H	ENSP00000352413:R934H	R	-	2	0	TMC3	79412317	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.397000	0.07269	-3.958000	0.00087	-0.165000	0.13383	CGC		0.552	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		T	81625262	C	T	81625262	3	4	50	1	0	0	0	0	1	0	0	0	16025	768	27	1	505	1	TMC3	15	81625262	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	14151632	81625262	20906130	79	6882										
MYLK3	91807	broad.mit.edu	37	chr16	46771731	46771731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tcagcctcgtgccttcctctAagggctcagggtcaggcctg	12	14	4	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr16:46771731A>G	ENST00000394809.4	-	3	1008	c.893T>C	c.(892-894)tTa>tCa	p.L298S	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	298					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.L349S(1)|p.L298S(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GCCTTCCTCTAAGGGCTCAGG	0.667																																																2	Substitution - Missense(2)	large_intestine(2)	16											70	69	70					16																	46771731		2203	4300	6503	45329232	SO:0001583	missense	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.893T>C	16.37:g.46771731A>G	ENSP00000378288:p.Leu298Ser		45329232	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.439046	0.01098	.	.	ENSG00000140795	ENST00000394809	T	0.65916	-0.18	4.75	0.458	0.16670	.	1.527450	0.04890	N	0.449400	T	0.29716	0.0742	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27365	-1.0076	10	0.06236	T	0.91	.	3.456	0.07515	0.2975:0.0:0.5258:0.1766	.	298	Q32MK0	MYLK3_HUMAN	S	298	ENSP00000378288:L298S	ENSP00000378288:L298S	L	-	2	0	MYLK3	45329232	0.342000	0.24809	0.000000	0.03702	0.005000	0.04900	0.752000	0.26362	0.025000	0.15241	-0.912000	0.02778	TTA		0.667	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		G	46771731	A	G	46771731	3	3	50	1	0	0	0	0	1	0	0	0	10088	372	13	4	1610	4	MYLK3	16	46771731	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09		46771731	43583022	80	6883										
HYDIN	54768	broad.mit.edu	37	chr16	70871736	70871736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgtgtttcctggctttaccaCatcaacacgggagttcacct	8	12	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr16:70871736C>T	ENST00000393567.2	-	77	13249	c.13099G>A	c.(13099-13101)Gtg>Atg	p.V4367M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4367					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.V4366M(1)|p.V4318M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGCTTTACCACATCAACACGG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	16											86	80	82					16																	70871736		1876	4114	5990	69429237	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13099G>A	16.37:g.70871736C>T	ENSP00000377197:p.Val4367Met		69429237	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.557734	0.45590	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.47869	0.83	5.04	4.01	0.46588	.	0.333086	0.16838	U	0.197453	T	0.59756	0.2217	M	0.65975	2.015	0.80722	D	1	P	0.49961	0.93	P	0.61533	0.89	T	0.53294	-0.8459	10	0.28530	T	0.3	.	9.7648	0.40554	0.0:0.7758:0.1439:0.0802	.	4366	F8WD23	.	M	4367;4366	ENSP00000377197:V4367M	ENSP00000313052:V4366M	V	-	1	0	HYDIN	69429237	0.472000	0.25870	0.886000	0.34754	0.328000	0.28507	1.060000	0.30530	2.506000	0.84524	0.511000	0.50034	GTG		0.433	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70871736	C	T	70871736	3	4	50	1	0	0	0	0	1	0	0	0	7488	478	17	3	2306	3	HYDIN	16	70871736	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	24100005	70871736	19483017	81	6884										
TP53	7157	broad.mit.edu	37	chr17	7578454	7578454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	actgcttgtagatggccatgGcgcggacgcgggtgccgggc	18	11	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr17:7578454G>A	ENST00000269305.4	-	5	665	c.476C>T	c.(475-477)gCc>gTc	p.A159V	TP53_ENST00000413465.2_Missense_Mutation_p.A159V|TP53_ENST00000359597.4_Missense_Mutation_p.A159V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.A159V|TP53_ENST00000455263.2_Missense_Mutation_p.A159V|TP53_ENST00000445888.2_Missense_Mutation_p.A159V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	159	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A159V(33)|p.0?(8)|p.A159D(7)|p.R158fs(6)|p.R65fs(2)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.R26fs(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.R158fs*11(1)|p.A66V(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.A27V(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.A159_Q167delAMAIYKQSQ(1)|p.V157fs*21(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGCCATGGCGCGGACGCG	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	81	Substitution - Missense(42)|Deletion - In frame(12)|Complex(10)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - frameshift(2)	central_nervous_system(15)|large_intestine(13)|lung(13)|stomach(6)|breast(6)|ovary(6)|oesophagus(4)|bone(4)|liver(4)|haematopoietic_and_lymphoid_tissue(3)|pancreas(2)|upper_aerodigestive_tract(1)|endometrium(1)|urinary_tract(1)|skin(1)|prostate(1)	17											50	51	51					17																	7578454		2203	4300	6503	7519179	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.476C>T	17.37:g.7578454G>A	ENSP00000269305:p.Ala159Val		7519179	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211949	0.58452	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99859	-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23	5.59	2.42	0.29668	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.053992	0.64402	D	0.000001	D	0.99594	0.9853	L	0.49513	1.565	0.50171	D	0.999855	D;P;B;D;P;P;D	0.67145	0.984;0.881;0.358;0.989;0.832;0.769;0.996	P;P;B;P;P;P;P	0.59703	0.774;0.616;0.255;0.741;0.814;0.632;0.862	D	0.98152	1.0442	10	0.87932	D	0	-9.0177	10.7596	0.46258	0.0:0.2672:0.5942:0.1386	.	120;159;159;66;159;159;159	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	159;159;159;159;159;159;148;66;27;66;27;159	ENSP00000410739:A159V;ENSP00000352610:A159V;ENSP00000269305:A159V;ENSP00000398846:A159V;ENSP00000391127:A159V;ENSP00000391478:A159V;ENSP00000425104:A27V;ENSP00000423862:A66V;ENSP00000424104:A159V	ENSP00000269305:A159V	A	-	2	0	TP53	7519179	1.000000	0.71417	0.377000	0.26055	0.171000	0.22731	7.969000	0.87988	0.364000	0.24374	-0.176000	0.13171	GCC		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578454	G	A	7578454	3	1	50	1	0	0	0	0	1	0	0	0	16421	1203	42	3	822	3	TP53	17	7578454	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		7578454	73616756	82	6885										
TTYH2	94015	broad.mit.edu	37	chr17	72249925	72249925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgctctttggtaggaacccaCgctacgagaacgtgccacta	10	12	1	1	rs114644256	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr17:72249925C>T	ENST00000269346.4	+	13	1551	c.1477C>T	c.(1477-1479)Cgc>Tgc	p.R493C	TTYH2_ENST00000529107.1_Missense_Mutation_p.R472C|TTYH2_ENST00000441391.2_Missense_Mutation_p.R172C	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	493						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.R493C(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						TAGGAACCCACGCTACGAGAA	0.557													C|||	57	0.0113818	0.0401	0.0058	5008	,	,		18357	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17						C	CYS/ARG,CYS/ARG	135,4271	97.1+/-135.8	2,131,2070	168	135	146		1477,514	4.8	1	17	dbSNP_132	146	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	TTYH2	NM_032646.5,NM_052869.1	180,180	2,135,6366	TT,TC,CC		0.0465,3.064,1.0687	probably-damaging,probably-damaging	493/535,172/214	72249925	139,12867	2203	4300	6503	69761520	SO:0001583	missense	94015				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1477C>T	17.37:g.72249925C>T	ENSP00000269346:p.Arg493Cys		69761520	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	C	22.8	4.333797	0.81801	0.03064	4.65E-4	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.49139	0.79;0.79;0.79	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.45756	0.1358	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69479	0.95;0.964	T	0.67233	-0.5722	10	0.87932	D	0	-28.8769	16.5959	0.84796	0.0:1.0:0.0:0.0	.	472;493	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	C	493;472;172	ENSP00000269346:R493C;ENSP00000433089:R472C;ENSP00000394576:R172C	ENSP00000269346:R493C	R	+	1	0	TTYH2	69761520	1.000000	0.71417	0.982000	0.44146	0.891000	0.51852	4.897000	0.63231	2.205000	0.71048	0.563000	0.77884	CGC		0.557	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			T	72249925	C	T	72249925	3	4	50	1	0	0	0	0	1	0	0	0	16780	536	19	1	1527	1	TTYH2	17	72249925	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	64671471	72249925	8945285	83	6886										
C19orf21	126353	broad.mit.edu	37	chr19	759987	759987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctcaaacgtggcgtggacagTggaagatccagtggacagtg	15	8	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:759987T>C	ENST00000215582.6	+	3	1962	c.1859T>C	c.(1858-1860)gTg>gCg	p.V620A		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	620					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V620A(1)									GCGTGGACAGTGGAAGATCCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											121	103	109					19																	759987		2203	4300	6503	710987	SO:0001583	missense	126353			BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1859T>C	19.37:g.759987T>C	ENSP00000215582:p.Val620Ala		710987		Missense_Mutation	SNP	ENST00000215582.6	37	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	T	7.183	0.590068	0.13812	.	.	ENSG00000099812	ENST00000215582	T	0.31769	1.48	4.81	-4.96	0.03038	.	1.047520	0.07567	N	0.917928	T	0.13072	0.0317	N	0.25144	0.715	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38001	-0.9681	10	0.02654	T	1	-14.6643	5.0585	0.14546	0.1592:0.2221:0.0:0.6187	.	620	Q8IVT2	CS021_HUMAN	A	620	ENSP00000215582:V620A	ENSP00000215582:V620A	V	+	2	0	C19orf21	710987	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.932000	0.03963	-0.435000	0.07264	-1.405000	0.01134	GTG		0.597	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		C	759987	T	C	759987	3	2	50	1	0	0	0	0	1	0	0	0	1919	1696	59	4	1865	4	C19orf21	19	759987	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09		759987	58368996	84	6887										
PLIN4	729359	broad.mit.edu	37	chr19	4513405	4513405	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gtcttggtggtgtccacaccGgcctgtacggtccctttggc	13	13	1	0	rs142527003	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:4513405G>A	ENST00000301286.3	-	3	524	c.525C>T	c.(523-525)gcC>gcT	p.A175A		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	175	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.A103A(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGTCCACACCGGCCTGTACGG	0.617													G|||	3	0.000599042	0	0	5008	,	,		20440	0		0.003	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4122		0,0,2061	82	89	87		525	-10.9	0	19	dbSNP_134	87	2,8380		0,2,4189	no	coding-synonymous	PLIN4	NM_001080400.1		0,2,6250	AA,AG,GG		0.0239,0.0,0.016		175/1358	4513405	2,12502	2061	4191	6252	4464405	SO:0001819	synonymous_variant	729359			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.525C>T	19.37:g.4513405G>A			4464405	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																				0.617	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4513405	G	A	4513405	2	1	50	1	0	0	0	0	0	0	0	1	12123	1103	39	1		1	PLIN4	19	4513405	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	3753418	4513405	54615578	85	6888										
ACTL9	284382	broad.mit.edu	37	chr19	8808159	8808159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gggggttgaacagcagctccGgacactggaacagctccttg	14	11	0	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:8808159G>A	ENST00000324436.3	-	1	1013	c.893C>T	c.(892-894)cCg>cTg	p.P298L		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	298						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.P298L(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						CAGCAGCTCCGGACACTGGAA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											37	40	39					19																	8808159		2203	4298	6501	8669159	SO:0001583	missense	284382				CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.893C>T	19.37:g.8808159G>A	ENSP00000316674:p.Pro298Leu		8669159	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	g	26.1	4.706836	0.89018	.	.	ENSG00000181786	ENST00000324436	D	0.95588	-3.75	4.63	4.63	0.57726	.	0.148034	0.31102	N	0.008244	D	0.98267	0.9426	M	0.93898	3.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99222	1.0879	10	0.87932	D	0	.	16.5967	0.84798	0.0:0.0:1.0:0.0	.	298	Q8TC94	ACTL9_HUMAN	L	298	ENSP00000316674:P298L	ENSP00000316674:P298L	P	-	2	0	ACTL9	8669159	1.000000	0.71417	0.969000	0.41365	0.929000	0.56500	8.950000	0.93019	2.581000	0.87130	0.306000	0.20318	CCG		0.652	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525		A	8808159	G	A	8808159	3	1	50	1	0	0	0	0	1	0	0	0	203	1116	39	1	361	1	ACTL9	19	8808159	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	4294754	8808159	50320824	86	6889										
MUC16	94025	broad.mit.edu	37	chr19	9019615	9019615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctcactgctgctggtgggcaCagaggtccgatgggtgaaac	15	10	1	2	rs375258130		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:9019615C>T	ENST00000397910.4	-	22	37734	c.37531G>A	c.(37531-37533)Gtg>Atg	p.V12511M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12513					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V12511M(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGGTGGGCACAGAGGTCCGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19						T	MET/VAL	0,3922		0,0,1961	152	133	139		37531	-2.9	0	19		139	1,8297		0,1,4148	no	missense	MUC16	NM_024690.2	21	0,1,6109	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging	12511/14508	9019615	1,12219	1961	4149	6110	8880615	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37531G>A	19.37:g.9019615C>T	ENSP00000381008:p.Val12511Met		8880615	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	1.154	-0.645881	0.03531	0.0	1.21E-4	ENSG00000181143	ENST00000397910	T	0.30448	1.53	1.43	-2.86	0.05717	.	.	.	.	.	T	0.13670	0.0331	N	0.20610	0.595	.	.	.	D	0.53462	0.96	B	0.38156	0.266	T	0.13845	-1.0494	8	0.87932	D	0	.	2.7421	0.05256	0.0:0.3733:0.2524:0.3742	.	12511	B5ME49	.	M	12511	ENSP00000381008:V12511M	ENSP00000381008:V12511M	V	-	1	0	MUC16	8880615	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.550000	0.06034	-0.749000	0.04747	-1.691000	0.00728	GTG		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9019615	C	T	9019615	3	4	50	1	0	0	0	0	1	0	0	0	10003	478	17	3	6244	3	MUC16	19	9019615	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	211456	9019615	50109368	87	6890										
MAN2B1	4125	broad.mit.edu	37	chr19	12759995	12759995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	aggctgctgcccccctgggaGcggtcagtcagcacagtcag	14	14	3	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:12759995G>A	ENST00000456935.2	-	20	2431	c.2391C>T	c.(2389-2391)cgC>cgT	p.R797R	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Silent_p.R796R	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	797					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.R797R(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CCCCCTGGGAGCGGTCAGTCA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19											58	50	53					19																	12759995		2203	4300	6503	12620995	SO:0001819	synonymous_variant	4125				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2391C>T	19.37:g.12759995G>A			12620995	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	37	CCDS32919.1																																																																																				0.617	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			A	12759995	G	A	12759995	2	1	50	1	0	0	0	0	0	0	0	1	9246	958	34	3		3	MAN2B1	19	12759995	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	3740380	12759995	46368988	88	6891										
OR10H2	26538	broad.mit.edu	37	chr19	15839268	15839268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	acaacgtgctcatgagcccaCggggctgcgcctgcctggtg	14	14	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:15839268C>T	ENST00000305899.3	+	1	435	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R139W(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					CATGAGCCCACGGGGCTGCGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	73	79					19																	15839268		2203	4300	6503	15700268	SO:0001583	missense	26538			AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.415C>T	19.37:g.15839268C>T	ENSP00000306095:p.Arg139Trp		15700268	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	37	CCDS12333.1	.	.	.	.	.	.	.	.	.	.	.	13.86	2.363639	0.41902	.	.	ENSG00000171942	ENST00000305899	T	0.42900	0.96	3.4	1.15	0.20763	GPCR, rhodopsin-like superfamily (1);	0.152141	0.30969	N	0.008513	T	0.43389	0.1245	L	0.54908	1.71	0.09310	N	1	D	0.63046	0.992	P	0.56088	0.791	T	0.32851	-0.9891	10	0.59425	D	0.04	.	2.1438	0.03782	0.1997:0.487:0.195:0.1183	.	139	O60403	O10H2_HUMAN	W	139	ENSP00000306095:R139W	ENSP00000306095:R139W	R	+	1	2	OR10H2	15700268	0.000000	0.05858	0.010000	0.14722	0.691000	0.40173	-0.896000	0.04114	0.009000	0.14813	-0.336000	0.08194	CGG		0.637	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			T	15839268	C	T	15839268	3	4	50	1	0	0	0	0	1	0	0	0	10937	527	19	1	417	1	OR10H2	19	15839268	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	3079273	15839268	43289715	89	6892										
ZNF230	7773	broad.mit.edu	37	chr19	44514982	44514982	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tgggagggccttcattcacgAtttccagcttcagaaacatc	9	11	3	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:44514982A>G	ENST00000429154.2	+	5	1019	c.791A>G	c.(790-792)gAt>gGt	p.D264G		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	264					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D264G(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				TTCATTCACGATTTCCAGCTT	0.408																																					GBM(175;914 2069 22996 47111 52600)											1	Substitution - Missense(1)	large_intestine(1)	19											116	121	119					19																	44514982		2203	4300	6503	49206822	SO:0001583	missense	7773			U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"Zinc fingers, C2H2-type", "-"	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.791A>G	19.37:g.44514982A>G	ENSP00000409318:p.Asp264Gly		49206822	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	.	.	.	.	.	.	.	.	.	.	A	4.357	0.065705	0.08388	.	.	ENSG00000159882	ENST00000429154	T	0.07567	3.18	2.33	-2.31	0.06765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02688	0.0081	N	0.03238	-0.38	0.09310	N	1	P	0.37548	0.599	B	0.32677	0.15	T	0.44483	-0.9325	9	0.30078	T	0.28	.	5.7688	0.18241	0.316:0.3818:0.3022:0.0	.	264	Q9UIE0	ZN230_HUMAN	G	264	ENSP00000409318:D264G	ENSP00000409318:D264G	D	+	2	0	ZNF230	49206822	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-4.045000	0.00306	-0.113000	0.11958	0.172000	0.16884	GAT		0.408	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			G	44514982	A	G	44514982	3	3	50	1	0	0	0	0	1	0	0	0	17823	333	12	4	805	4	ZNF230	19	44514982	Missense_Mutation	SNP	A	TCGA-AG-3896-01A-01W-1073-09	28675714	44514982	14614001	90	6893										
TRPM4	54795	broad.mit.edu	37	chr19	49684698	49684698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ttgcccagagtgaactctttCggggggacatccaatggcgg	14	10	1	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:49684698C>T	ENST00000252826.5	+	10	1369	c.1243C>T	c.(1243-1245)Cgg>Tgg	p.R415W	TRPM4_ENST00000427978.2_Missense_Mutation_p.R415W|TRPM4_ENST00000601347.1_Intron|TRPM4_ENST00000355712.5_Intron	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	415					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)	p.R415W(1)		breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		TGAACTCTTTCGGGGGGACAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											59	56	57					19																	49684698		2203	4300	6503	54376510	SO:0001583	missense	54795			AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.1243C>T	19.37:g.49684698C>T	ENSP00000252826:p.Arg415Trp		54376510	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Missense_Mutation	SNP	ENST00000252826.5	37	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.849165	0.71603	.	.	ENSG00000130529	ENST00000252826;ENST00000427978	D;D	0.83163	-1.69;-1.69	3.92	3.92	0.45320	.	0.139448	0.48286	D	0.000199	D	0.89543	0.6745	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72625	0.958;0.978;0.937	D	0.90113	0.4193	10	0.49607	T	0.09	-17.107	15.0744	0.72066	0.0:1.0:0.0:0.0	.	241;415;415	Q8TD43-2;Q8TD43-3;Q8TD43	.;.;TRPM4_HUMAN	W	415	ENSP00000252826:R415W;ENSP00000407492:R415W	ENSP00000252826:R415W	R	+	1	2	TRPM4	54376510	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.514000	0.45503	1.899000	0.54978	0.455000	0.32223	CGG		0.587	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49684698	C	T	49684698	3	4	50	1	0	0	0	0	1	0	0	0	16628	875	31	1	1281	1	TRPM4	19	49684698	Missense_Mutation	SNP	C	TCGA-AG-3896-01A-01W-1073-09	5169716	49684698	9444285	91	6894										
KLK10	5655	broad.mit.edu	37	chr19	51519274	51519274	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	agcttcagcaacatgagatcGtgctcatccgttcgccttgg	10	12	2	1	rs139432866		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:51519274G>A	ENST00000309958.3	-	4	626	c.408C>T	c.(406-408)caC>caT	p.H136H	KLK10_ENST00000358789.3_Silent_p.H136H|KLK10_ENST00000391805.1_Silent_p.H136H|CTC-518B2.12_ENST00000596286.1_RNA	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	136	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.H136H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		ACATGAGATCGTGCTCATCCG	0.657													G|||	1	0.000199681	8e-04	0	5008	,	,		15885	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G	,,	2,4384		0,2,2191	39	35	36		408,408,408	-5.7	0.8	19	dbSNP_134	36	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	KLK10	NM_001077500.1,NM_002776.4,NM_145888.2	,,	0,2,6484	AA,AG,GG		0.0,0.0456,0.0154	,,	136/277,136/277,136/277	51519274	2,12970	2193	4293	6486	56211086	SO:0001819	synonymous_variant	5655			AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.408C>T	19.37:g.51519274G>A			56211086	A6NC12|Q53YL3|Q99920|Q9GZW9	Silent	SNP	ENST00000309958.3	37	CCDS12817.1																																																																																				0.657	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		A	51519274	G	A	51519274	2	1	50	1	0	0	0	0	0	0	0	1	8419	1136	40	1		1	KLK10	19	51519274	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	1834576	51519274	7609709	92	6895										
C19orf75	284369	broad.mit.edu	37	chr19	51770648	51770648	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gtgaaacatatcagaaagaaGcaggcgaagaaagctgcagc	12	7	1	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr19:51770648G>T	ENST00000316401.7	+	5	813	c.432G>T	c.(430-432)aaG>aaT	p.K144N	CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Missense_Mutation_p.K50N	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	508	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.K144N(1)									TCAGAAAGAAGCAGGCGAAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											123	125	124					19																	51770648		2203	4300	6503	56462460	SO:0001583	missense	284369			AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.432G>T	19.37:g.51770648G>T	ENSP00000321249:p.Lys144Asn		56462460	Q8IYH7	Missense_Mutation	SNP	ENST00000316401.7	37	CCDS12827.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.667600	0.47677	.	.	ENSG00000179213	ENST00000316401	T	0.39056	1.1	3.7	-0.037	0.13886	.	1.565550	0.04098	N	0.312430	T	0.45657	0.1353	M	0.75615	2.305	0.09310	N	1	P;P	0.45126	0.851;0.462	B;B	0.44224	0.444;0.175	T	0.36163	-0.9759	10	0.59425	D	0.04	.	3.292	0.06952	0.1449:0.0:0.4084:0.4467	.	50;144	B7ZLS6;Q8N7X8	.;CS075_HUMAN	N	144	ENSP00000321249:K144N	ENSP00000321249:K144N	K	+	3	2	C19orf75	56462460	0.036000	0.19791	0.001000	0.08648	0.899000	0.52679	0.587000	0.23909	0.064000	0.16427	0.650000	0.86243	AAG		0.458	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		T	51770648	G	T	51770648	3	4	50	1	0	0	0	0	1	0	0	0	1955	962	34	2	446	2	C19orf75	19	51770648	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	251374	51770648	7358335	93	6896										
RBCK1	10616	broad.mit.edu	37	chr20	390535	390535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	tggctttcagcagaggaaatGgccctgagcctcacccgagc	12	13	2	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr20:390535G>A	ENST00000356286.5	+	2	738	c.33G>A	c.(31-33)atG>atA	p.M11I	RBCK1_ENST00000353660.3_Intron|RBCK1_ENST00000400245.3_3'UTR|RBCK1_ENST00000382181.2_Intron|RBCK1_ENST00000475269.1_Missense_Mutation_p.M11I|RBCK1_ENST00000400247.3_Intron	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	11	Interaction with IRF3.|Interaction with TAB2.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M11I(1)		kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				CAGAGGAAATGGCCCTGAGCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	20											116	126	122					20																	390535		2203	4300	6503	338535	SO:0001583	missense	10616			U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"RING-type (C3HC4) zinc fingers", "Zinc fingers, RAN-binding domain containing"	15864	protein-coding gene	gene with protein product	"heme-oxidized IRP2 ubiquitin ligase 1"	610924	"chromosome 20 open reading frame 18"	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.33G>A	20.37:g.390535G>A	ENSP00000348632:p.Met11Ile		338535	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	37	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.30|15.30	2.792379|2.792379	0.50102|0.50102	.|.	.|.	ENSG00000125826|ENSG00000125826	ENST00000411647;ENST00000356286;ENST00000475269;ENST00000441733;ENST00000400244;ENST00000400243|ENST00000414880	T;T;T|.	0.40225|.	1.05;2.39;1.04|.	4.68|4.68	4.68|4.68	0.58851|0.58851	.|.	0.360076|.	0.28889|.	N|.	0.013811|.	T|.	0.53932|.	0.1827|.	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	B;P|.	0.35383|.	0.0;0.498|.	B;B|.	0.26770|.	0.001;0.073|.	T|.	0.49725|.	-0.8909|.	10|.	0.25751|.	T|.	0.34|.	-8.7986|-8.7986	8.6702|8.6702	0.34145|0.34145	0.1013:0.0:0.8987:0.0|0.1013:0.0:0.8987:0.0	.|.	1;11|.	B4E0F5;Q9BYM8|.	.;HOIL1_HUMAN|.	I|X	11;11;11;10;11;11|3	ENSP00000415080:M11I;ENSP00000348632:M11I;ENSP00000387799:M10I|.	ENSP00000348632:M11I|.	M|W	+|+	3|2	0|0	RBCK1|RBCK1	338535|338535	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.757000|0.757000	0.42996|0.42996	6.944000|6.944000	0.75940|0.75940	2.397000|2.397000	0.81536|0.81536	0.563000|0.563000	0.77884|0.77884	ATG|TGG		0.572	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229		A	390535	G	A	390535	3	1	50	1	0	0	0	0	1	0	0	0	13144	1348	47	3	58	3	RBCK1	20	390535	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		390535	62634985	94	6897										
TSHZ2	128553	broad.mit.edu	37	chr20	51871431	51871431	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	accagcaaggatgagaaagtCgtgaaaagcgaggactatga	13	6	0	3	rs183008464		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr20:51871431C>T	ENST00000371497.5	+	2	2321	c.1434C>T	c.(1432-1434)gtC>gtT	p.V478V	TSHZ2_ENST00000603338.2_Silent_p.V475V|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Silent_p.V475V	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	478					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V478V(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			ATGAGAAAGTCGTGAAAAGCG	0.413													C|||	1	0.000199681	8e-04	0	5008	,	,		20958	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	20											92	98	96					20																	51871431		2203	4300	6503	51304838	SO:0001819	synonymous_variant	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1434C>T	20.37:g.51871431C>T			51304838	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Silent	SNP	ENST00000371497.5	37	CCDS33490.1																																																																																				0.413	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		T	51871431	C	T	51871431	2	4	50	1	0	0	0	0	0	0	0	1	16664	871	31	1		1	TSHZ2	20	51871431	Silent	SNP	C	TCGA-AG-3896-01A-01W-1073-09	51480896	51871431	11154089	95	6898										
KCNQ2	3785	broad.mit.edu	37	chr20	62070997	62070997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cgatgagggtgaaggttgccGcaaggagcctgccgttccag	16	10	0	2	rs118192211		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr20:62070997G>A	ENST00000359125.2	-	6	1055	c.881C>T	c.(880-882)gCg>gTg	p.A294V	KCNQ2_ENST00000344425.5_Missense_Mutation_p.A294V|KCNQ2_ENST00000370224.1_Missense_Mutation_p.A294V|KCNQ2_ENST00000357249.2_Missense_Mutation_p.A294V|KCNQ2_ENST00000360480.3_Missense_Mutation_p.A294V|KCNQ2_ENST00000354587.3_Missense_Mutation_p.A294V|KCNQ2_ENST00000359689.1_Missense_Mutation_p.A294V|KCNQ2_ENST00000344462.4_Missense_Mutation_p.A294V	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	294					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.A294V(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GAAGGTTGCCGCAAGGAGCCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	20	GRCh37	CM073161	KCNQ2	M	rs118192211						216	159	178					20																	62070997		2203	4300	6503	61541441	SO:0001583	missense	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.881C>T	20.37:g.62070997G>A	ENSP00000352035:p.Ala294Val		61541441	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.248795	0.59103	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222;ENST00000370221;ENST00000344425	D;D;D;D;D;D;D;D;D;D;D;D	0.98474	-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95	4.01	4.01	0.46588	Ion transport (1);	0.142257	0.46145	D	0.000306	D	0.98532	0.9510	M	0.64630	1.985	0.58432	D	0.999998	D;P;D;D;D;D	0.76494	0.999;0.782;0.995;0.991;0.991;0.993	D;B;P;P;P;P	0.72338	0.977;0.426;0.726;0.726;0.726;0.821	D	0.99852	1.1073	10	0.87932	D	0	-13.0776	16.4798	0.84155	0.0:0.0:1.0:0.0	.	294;294;294;294;294;294	B4DEP4;Q53Y30;O43526-3;O43526-2;O43526-4;O43526	.;.;.;.;.;KCNQ2_HUMAN	V	294	ENSP00000349789:A294V;ENSP00000352035:A294V;ENSP00000359246:A294V;ENSP00000346601:A294V;ENSP00000352718:A294V;ENSP00000399612:A294V;ENSP00000353668:A294V;ENSP00000339611:A294V;ENSP00000359244:A294V;ENSP00000359242:A294V;ENSP00000359241:A294V;ENSP00000345523:A294V	ENSP00000345523:A294V	A	-	2	0	KCNQ2	61541441	1.000000	0.71417	0.569000	0.28460	0.117000	0.20001	5.273000	0.65564	1.908000	0.55244	0.561000	0.74099	GCG		0.627	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62070997	G	A	62070997	3	1	50	1	0	0	0	0	1	0	0	0	8104	1087	38	1	1849	1	KCNQ2	20	62070997	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	10199566	62070997	954523	96	6899										
GMEB2	26205	broad.mit.edu	37	chr20	62229213	62229213	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gctgattacatgctcgtcgtActgtgggggacacagtcatg	13	9	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr20:62229213A>T	ENST00000266068.1	-	4	836	c.358T>A	c.(358-360)Tac>Aac	p.Y120N	GMEB2_ENST00000370069.1_Splice_Site_p.Y69N|GMEB2_ENST00000370077.1_Splice_Site_p.Y120N			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	120	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.Y120N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			TGCTCGTCGTACTGTGGGGGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											107	81	90					20																	62229213		2203	4300	6503	61699657	SO:0001630	splice_region_variant	26205			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.358-1T>A	20.37:g.62229213A>T			61699657	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Missense_Mutation	SNP	ENST00000266068.1	37	CCDS13528.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.723358	0.48728	.	.	ENSG00000101216	ENST00000370069;ENST00000370077;ENST00000266068	T;T;T	0.71698	-0.59;-0.59;-0.59	5.02	5.02	0.67125	SAND domain-like (2);SAND domain (3);	0.188387	0.47093	D	0.000244	T	0.75170	0.3813	L	0.36672	1.1	0.54753	D	0.999982	D	0.60160	0.987	P	0.62649	0.905	T	0.74853	-0.3523	10	0.38643	T	0.18	0.1356	14.7287	0.69365	1.0:0.0:0.0:0.0	.	120	Q9UKD1	GMEB2_HUMAN	N	69;120;120	ENSP00000359086:Y69N;ENSP00000359094:Y120N;ENSP00000266068:Y120N	ENSP00000266068:Y120N	Y	-	1	0	GMEB2	61699657	1.000000	0.71417	0.991000	0.47740	0.163000	0.22366	6.911000	0.75746	1.894000	0.54839	0.459000	0.35465	TAC		0.587	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	Missense_Mutation	T	62229213	A	T	62229213	5	4	50	1	0	0	0	0	0	0	1	0	6508	405	14	5	1258	5	GMEB2	20	62229213	Splice_Site	SNP	A	TCGA-AG-3896-01A-01W-1073-09	158216	62229213	796307	97	6900										
KRTAP10-9	386676	broad.mit.edu	37	chr21	46047906	46047906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctgtgtgtcccttctctgccGccctgtgtgctcccgcccgg	11	18	1	0	rs587668632		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr21:46047906G>A	ENST00000397911.3	+	1	867	c.818G>A	c.(817-819)cGc>cAc	p.R273H	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	273						keratin filament (GO:0045095)		p.R273H(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CTTCTCTGCCGCCCTGTGTGC	0.706													G|||	1	0.000199681	0	0	5008	,	,		18503	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	21											64	79	74					21																	46047906		2196	4293	6489	44872334	SO:0001583	missense	386676			AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"Keratin associated proteins"	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.818G>A	21.37:g.46047906G>A	ENSP00000381009:p.Arg273His		44872334	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	.	.	.	.	.	.	.	.	.	.	g	4.155	0.027215	0.08054	.	.	ENSG00000221837	ENST00000397911	T	0.01015	5.44	3.5	0.186	0.15105	.	.	.	.	.	T	0.01254	0.0041	M	0.84326	2.69	0.09310	N	1	P	0.39250	0.665	B	0.29862	0.108	T	0.43245	-0.9403	8	.	.	.	.	1.4446	0.02361	0.2259:0.162:0.4478:0.1643	.	273	P60411	KR109_HUMAN	H	273	ENSP00000381009:R273H	.	R	+	2	0	KRTAP10-9	44872334	0.000000	0.05858	0.034000	0.17996	0.002000	0.02628	-0.499000	0.06413	0.127000	0.18452	-0.251000	0.11542	CGC		0.706	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1			A	46047906	G	A	46047906	3	1	50	1	0	0	0	0	1	0	0	0	8537	1087	38	1	820	1	KRTAP10-9	21	46047906	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		46047906	2081989	98	6901										
PI4KA	5297	broad.mit.edu	37	chr22	21157556	21157556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ccaggaagtctcgcaaggacGgtgtcacagagtgcaccacc	12	13	2	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr22:21157556G>A	ENST00000572273.1	-	13	1570	c.1340C>T	c.(1339-1341)cCg>cTg	p.P447L	PI4KA_ENST00000255882.6_Missense_Mutation_p.P505L			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	447					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.P447L(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			TCGCAAGGACGGTGTCACAGA	0.557																																					GBM(136;1332 1831 3115 23601 50806)											2	Substitution - Missense(2)	large_intestine(2)	22											179	129	146					22																	21157556		2203	4300	6503	19487556	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1340C>T	22.37:g.21157556G>A	ENSP00000458238:p.Pro447Leu		19487556	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	G	10.97	1.500200	0.26861	.	.	ENSG00000241973	ENST00000255882	.	.	.	4.89	4.89	0.63831	.	0.205291	0.45867	D	0.000323	T	0.25269	0.0614	N	0.01352	-0.895	0.80722	D	1	B;B	0.12013	0.005;0.002	B;B	0.06405	0.002;0.001	T	0.19257	-1.0311	9	0.11182	T	0.66	-26.4369	18.2178	0.89892	0.0:0.0:1.0:0.0	.	505;447	D3DX33;P42356	.;PI4KA_HUMAN	L	447	.	ENSP00000255882:P447L	P	-	2	0	PI4KA	19487556	0.999000	0.42202	0.788000	0.31933	0.974000	0.67602	4.457000	0.60088	2.533000	0.85409	0.491000	0.48974	CCG		0.557	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21157556	G	A	21157556	3	1	50	1	0	0	0	0	1	0	0	0	11904	1116	39	1	4966	1	PI4KA	22	21157556	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09		21157556	30147010	99	6902										
MGAT3	4248	broad.mit.edu	37	chr22	39883628	39883628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cccagcaaggcggccgaggaGctccaccgggtggacttggt	16	13	0	0	rs527409773		TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chr22:39883628G>A	ENST00000341184.6	+	2	491	c.276G>A	c.(274-276)gaG>gaA	p.E92E		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	92					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)	p.E92E(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					CGGCCGAGGAGCTCCACCGGG	0.692																																																1	Substitution - coding silent(1)	large_intestine(1)	22											19	23	22					22																	39883628		2196	4280	6476	38213574	SO:0001819	synonymous_variant	4248			D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.276G>A	22.37:g.39883628G>A			38213574	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Silent	SNP	ENST00000341184.6	37	CCDS13994.2																																																																																				0.692	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		A	39883628	G	A	39883628	2	1	50	1	0	0	0	0	0	0	0	1	9574	962	34	3		3	MGAT3	22	39883628	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	18726072	39883628	11420938	100	6903										
FAM47A	158724	broad.mit.edu	37	chrX	34149087	34149087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	atcccatacgtccttcagcgTcctcccagaatccagcactt	5	17	1	1			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:34149087T>C	ENST00000346193.3	-	1	1360	c.1309A>G	c.(1309-1311)Acg>Gcg	p.T437A		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	437								p.T437A(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TCCTTCAGCGTCCTCCCAGAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	X											44	45	44					X																	34149087		2117	4243	6360	34059008	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1309A>G	X.37:g.34149087T>C	ENSP00000345029:p.Thr437Ala		34059008	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	t	3.300	-0.143110	0.06669	.	.	ENSG00000185448	ENST00000346193	T	0.13307	2.6	0.866	-1.73	0.08081	.	.	.	.	.	T	0.06005	0.0156	N	0.22421	0.69	0.09310	N	1	P	0.40834	0.73	B	0.37387	0.248	T	0.29397	-1.0013	8	0.10111	T	0.7	.	.	.	.	.	437	Q5JRC9	FA47A_HUMAN	A	437	ENSP00000345029:T437A	ENSP00000345029:T437A	T	-	1	0	FAM47A	34059008	0.072000	0.21174	0.010000	0.14722	0.151000	0.21798	-0.314000	0.08092	-1.023000	0.03342	0.237000	0.17872	ACG		0.552	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		C	34149087	T	C	34149087	3	2	50	1	0	0	0	0	1	0	0	0	5588	1667	58	4	1070	4	FAM47A	23	34149087	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09		34149087	121121473	101	6904										
ITIH5L	347365	broad.mit.edu	37	chrX	54785075	54785075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	gccacccaggtagttcagacGcacatctgccagcagaggca	11	14	2	2			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:54785075G>A	ENST00000218436.6	-	8	1461	c.1432C>T	c.(1432-1434)Cgt>Tgt	p.R478C		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	478					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R478C(1)									TAGTTCAGACGCACATCTGCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	X											45	40	42					X																	54785075		2203	4300	6503	54801800	SO:0001583	missense	347365			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1432C>T	X.37:g.54785075G>A	ENSP00000218436:p.Arg478Cys		54801800	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	6.725	0.502448	0.12822	.	.	ENSG00000102313	ENST00000218436	T	0.11821	2.74	3.66	0.383	0.16239	.	0.849036	0.10374	N	0.682431	T	0.08582	0.0213	N	0.24115	0.695	0.24611	N	0.993722	B	0.06786	0.001	B	0.01281	0.0	T	0.32693	-0.9897	10	0.66056	D	0.02	.	4.9584	0.14054	0.2486:0.3734:0.378:0.0	.	478	Q6UXX5	ITH5L_HUMAN	C	478	ENSP00000218436:R478C	ENSP00000218436:R478C	R	-	1	0	ITIH5L	54801800	0.001000	0.12720	0.489000	0.27452	0.417000	0.31264	0.222000	0.17699	0.386000	0.24997	-0.196000	0.12772	CGT		0.597	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54785075	G	A	54785075	3	1	50	1	0	0	0	0	1	0	0	0	7929	1087	38	1	2533	1	ITIH5L	23	54785075	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	20635988	54785075	100485485	102	6905										
FAM123B	139285	broad.mit.edu	37	chrX	63411291	63411291	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ctctcgggcctgggcttctcGggttctggcctccctgccat	12	16	3	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:63411291G>A	ENST00000330258.3	-	2	2148	c.1876C>T	c.(1876-1878)Cga>Tga	p.R626*	AMER1_ENST00000374869.3_Nonsense_Mutation_p.R626*|AMER1_ENST00000403336.1_Nonsense_Mutation_p.R626*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	626					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R626*(2)									TGGGCTTCTCGGGTTCTGGCC	0.617																																																69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											27	23	24					X																	63411291		2203	4300	6503	63328016	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1876C>T	X.37:g.63411291G>A	ENSP00000329117:p.Arg626*		63328016	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	27.0	4.788975	0.90367	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	4.24	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.8451	4.4728	0.11720	0.1079:0.0:0.4881:0.404	.	.	.	.	X	626	.	ENSP00000329117:R626X	R	-	1	2	FAM123B	63328016	0.002000	0.14202	0.008000	0.14137	0.053000	0.15095	0.259000	0.18405	1.098000	0.41479	0.600000	0.82982	CGA		0.617	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411291	G	A	63411291	4	1	50	1	0	0	0	0	0	1	0	0	5439	1124	39	1	1535	1	FAM123B	23	63411291	Nonsense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	8626216	63411291	91859269	103	6906										
AR	367	broad.mit.edu	37	chrX	66942701	66942701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ggctgaaaaatcaaaaattcTttgatgaacttcgaatgaac	7	6	2	4			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:66942701T>C	ENST00000374690.3	+	7	3006	c.2482T>C	c.(2482-2484)Ttt>Ctt	p.F828L	AR_ENST00000396043.2_Missense_Mutation_p.F296L|AR_ENST00000396044.3_Intron	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	827	Interaction with KAT7.|Interaction with LPXN.|Ligand-binding.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.F646L(1)|p.F828L(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	TCAAAAATTCTTTGATGAACT	0.448									Androgen Insensitivity Syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	X	GRCh37	CM014507	AR	M							75	65	68					X																	66942701		2203	4300	6503	66859426	SO:0001583	missense	367	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.2482T>C	X.37:g.66942701T>C	ENSP00000363822:p.Phe828Leu		66859426	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	-	18.85	3.711175	0.68730	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000396043	D;D	0.96200	-3.94;-3.94	5.19	5.19	0.71726	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97377	0.9142	M	0.80982	2.52	0.80722	D	1	P;D	0.89917	0.65;1.0	B;D	0.83275	0.398;0.996	D	0.97868	1.0284	10	0.87932	D	0	.	11.864	0.52482	0.0:0.0:0.0:1.0	.	296;827	F1D8N5;P10275	.;ANDR_HUMAN	L	646;828;296	ENSP00000363822:F828L;ENSP00000379358:F296L	ENSP00000363822:F828L	F	+	1	0	AR	66859426	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.862000	0.87013	1.930000	0.55929	0.478000	0.44815	TTT		0.448	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66942701	T	C	66942701	3	2	50	1	0	0	0	0	1	0	0	0	836	1609	56	4	2532	4	AR	23	66942701	Missense_Mutation	SNP	T	TCGA-AG-3896-01A-01W-1073-09	3531410	66942701	88327859	104	6907										
PCDH11X	27328	broad.mit.edu	37	chrX	91873897	91873897	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	ccacgccaacaggccagaccGtccagaggtgattcccccat	9	17	0	3	rs80336085	byFrequency	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:91873897G>A	ENST00000373094.1	+	7	4847	c.4002G>A	c.(4000-4002)ccG>ccA	p.P1334P	PCDH11X_ENST00000373097.1_Silent_p.P1324P|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000361655.2_Silent_p.P1316P|PCDH11X_ENST00000298274.8_Silent_p.P1297P|PCDH11X_ENST00000373088.1_Silent_p.P1297P|PCDH11X_ENST00000406881.1_Silent_p.P1326P	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1334					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1334P(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						AGGCCAGACCGTCCAGAGGTG	0.378													G|||	7	0.0018543	0.0053	0	3775	,	,		15380	0		0	False		,,,				2504	0				NSCLC(38;925 1092 2571 38200 45895)											1	Substitution - coding silent(1)	large_intestine(1)	X						A	,,,,,	42,3793		0,33,9,1599,562	116	112	113		3978,,3891,3948,4002,3972	-1.1	0	X	dbSNP_131	113	0,6728		0,0,0,2428,1872	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH11X	NM_001168360.1,NM_001168361.1,NM_001168362.1,NM_001168363.1,NM_032968.3,NM_032969.3	,,,,,	0,33,9,4027,2434	AA,AG,A,GG,G		0.0,1.0952,0.3976	,,,,,	1326/1340,,1297/1311,1316/1330,1334/1348,1324/1338	91873897	42,10521	2203	4300	6503	91760553	SO:0001819	synonymous_variant	27328			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.4002G>A	X.37:g.91873897G>A			91760553	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	37	CCDS14461.1																																																																																				0.378	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91873897	G	A	91873897	2	1	50	1	0	0	0	0	0	0	0	1	11539	1132	40	1		1	PCDH11X	23	91873897	Silent	SNP	G	TCGA-AG-3896-01A-01W-1073-09	24931196	91873897	63396663	105	6908										
COL4A5	1287	broad.mit.edu	37	chrX	107936015	107936015	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	4	1	0.383603367316722	1.23072747014115	0.312015414965362	0.569230769230769	1	0	cttcgtcgctttagtaccatGcctttcatgttctgcaacat	6	12	2	0			TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3896-01A-01W-1073-09	TCGA-AG-3896-10A-01W-1073-09	g.chrX:107936015G>C	ENST00000361603.2	+	48	4792	c.4548G>C	c.(4546-4548)atG>atC	p.M1516I	COL4A5_ENST00000328300.6_Missense_Mutation_p.M1522I	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1516	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.M1516I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						TTAGTACCATGCCTTTCATGT	0.438									Alport syndrome with Diffuse Leiomyomatosis																																							1	Substitution - Missense(1)	large_intestine(1)	X											129	99	109					X																	107936015		2203	4300	6503	107822671	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4548G>C	X.37:g.107936015G>C	ENSP00000354505:p.Met1516Ile		107822671	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992232	0.93167	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.94330	-3.4;-3.4	5.82	5.82	0.92795	C-type lectin fold (1);	0.000000	0.85682	D	0.000000	D	0.97009	0.9023	M	0.84219	2.685	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	D	0.97086	0.9787	10	0.59425	D	0.04	.	19.0941	0.93242	0.0:0.0:1.0:0.0	.	1519;1516	E7EVY4;P29400	.;CO4A5_HUMAN	I	1522;1516;1522	ENSP00000331902:M1522I;ENSP00000354505:M1516I	ENSP00000331902:M1522I	M	+	3	0	COL4A5	107822671	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.459000	0.83118	0.594000	0.82650	ATG		0.438	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			C	107936015	G	C	107936015	3	2	50	1	0	0	0	0	1	0	0	0	3700	1319	46	5	4749	5	COL4A5	23	107936015	Missense_Mutation	SNP	G	TCGA-AG-3896-01A-01W-1073-09	16062118	107936015	47334545	106	6909										
PUM1	9698	broad.mit.edu	37	chr1	31441267	31441267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cactgctgcagctgccacaaGgggatccgtttgctgtccct	11	14	0	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:31441267G>A	ENST00000257075.5	-	11	1672	c.1579C>T	c.(1579-1581)Ctt>Ttt	p.L527F	PUM1_ENST00000423018.2_Missense_Mutation_p.L431F|PUM1_ENST00000373742.2_Missense_Mutation_p.L468F|PUM1_ENST00000426105.2_Missense_Mutation_p.L527F|PUM1_ENST00000373741.4_Missense_Mutation_p.L563F|PUM1_ENST00000424085.2_Missense_Mutation_p.L285F|PUM1_ENST00000440538.2_Missense_Mutation_p.L528F|PUM1_ENST00000490546.1_5'UTR|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000373747.3_Missense_Mutation_p.L528F	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	527	Ala-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)	p.L527F(1)		breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		GCTGCCACAAGGGGATCCGTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	87	90					1																	31441267		2203	4300	6503	31213854	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1579C>T	1.37:g.31441267G>A	ENSP00000257075:p.Leu527Phe		31213854	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.0|25.0	4.587431|4.587431	0.86851|0.86851	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742|ENST00000525843;ENST00000498419;ENST00000532678	T;T;T;T;T;T;T;T|T;T;T	0.21031|0.44881	2.1;2.03;2.27;2.28;2.19;2.27;2.25;2.03|2.23;2.48;0.91	5.77|5.77	4.86|4.86	0.63082|0.63082	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.51500|0.51500	0.1678|0.1678	M|M	0.63843|0.63843	1.955|1.955	0.58432|0.58432	D|D	0.999996|0.999996	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.995;1.0;0.997;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.85130|.	0.997;0.979;0.997;0.991;0.997;0.997;0.997;0.997|.	T|T	0.48536|0.48536	-0.9027|-0.9027	10|7	0.30078|0.34782	T|T	0.28|0.22	-6.1257|-6.1257	12.2468|12.2468	0.54574|0.54574	0.1371:0.0:0.8629:0.0|0.1371:0.0:0.8629:0.0	.|.	468;431;563;528;527;527;528;527|.	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5|.	.;.;.;.;PUM1_HUMAN;.;.;.|.	F|L	285;527;528;265;527;528;563;431;468|544;238;214	ENSP00000400141:L285F;ENSP00000257075:L527F;ENSP00000362852:L528F;ENSP00000391723:L527F;ENSP00000401777:L528F;ENSP00000362846:L563F;ENSP00000399440:L431F;ENSP00000362847:L468F|ENSP00000435825:P544L;ENSP00000433850:P238L;ENSP00000435589:P214L	ENSP00000257075:L527F|ENSP00000433850:P238L	L|P	-|-	1|2	0|0	PUM1|PUM1	31213854|31213854	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.993000|0.993000	0.82548|0.82548	5.233000|5.233000	0.65337|0.65337	1.576000|1.576000	0.49790|0.49790	0.655000|0.655000	0.94253|0.94253	CTT|CCT		0.532	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			A	31441267	G	A	31441267	3	1	51	1	0	0	0	0	1	0	0	0	12862	1000	35	3	2035	3	PUM1	1	31441267	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		31441267	217809354	1	6910										
RNF19B	127544	broad.mit.edu	37	chr1	33413875	33413875	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	acaaagccaacagaattcacAgccacacactgcacaggtca	6	14	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:33413875A>T	ENST00000373456.7	-	3	933	c.934T>A	c.(934-936)Tgt>Agt	p.C312S	RNF19B_ENST00000235150.4_Missense_Mutation_p.C311S|RNF19B_ENST00000356990.5_Missense_Mutation_p.C311S	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	312					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.C311S(1)|p.C121S(1)		endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CAGAATTCACAGCCACACACT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	1											205	159	175					1																	33413875		2203	4300	6503	33186462	SO:0001583	missense	127544			AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"RING-type (C3HC4) zinc fingers"	26886	protein-coding gene	gene with protein product		610872	"IBR domain containing 3"	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.934T>A	1.37:g.33413875A>T	ENSP00000362555:p.Cys312Ser		33186462	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Missense_Mutation	SNP	ENST00000373456.7	37	CCDS372.2	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399648	0.62177	.	.	ENSG00000116514	ENST00000373456;ENST00000356990;ENST00000235150;ENST00000405457	T;T;T	0.80033	-1.33;-1.33;-1.33	5.71	5.71	0.89125	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.83972	0.5370	L	0.31664	0.95	0.80722	D	1	B;D;P	0.89917	0.376;1.0;0.785	B;D;P	0.87578	0.198;0.998;0.674	T	0.82930	-0.0213	10	0.33141	T	0.24	.	16.2911	0.82752	1.0:0.0:0.0:0.0	.	311;312;311	G3XA82;Q6ZMZ0;E9PAW6	.;RN19B_HUMAN;.	S	312;311;311;210	ENSP00000362555:C312S;ENSP00000349482:C311S;ENSP00000235150:C311S	ENSP00000235150:C311S	C	-	1	0	RNF19B	33186462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.334000	0.96470	2.302000	0.77476	0.533000	0.62120	TGT		0.428	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341		T	33413875	A	T	33413875	3	4	51	1	0	0	0	0	1	0	0	0	13508	188	7	5	1318	5	RNF19B	1	33413875	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	1972608	33413875	215836746	2	6911										
ABCA4	24	broad.mit.edu	37	chr1	94474421	94474421	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	atgggctccttagtgggctcGgcaatcctagatgaagaaaa	12	8	0	3	rs368502305		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:94474421G>A	ENST00000370225.3	-	41	5807	c.5721C>T	c.(5719-5721)gcC>gcT	p.A1907A	ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000535881.1_Silent_p.A26A|ABCA4_ENST00000536513.1_Silent_p.A177A	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1907					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.A1907A(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TAGTGGGCTCGGCAATCCTAG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	1						A		0,4406		0,0,2203	108	102	104		5721	-11.3	0	1		104	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	ABCA4	NM_000350.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1907/2274	94474421	1,13005	2203	4300	6503	94247009	SO:0001819	synonymous_variant	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5721C>T	1.37:g.94474421G>A			94247009	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.463	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94474421	G	A	94474421	2	1	51	1	0	0	0	0	0	0	0	1	34	1103	39	1		1	ABCA4	1	94474421	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	61060546	94474421	154776200	3	6912										
HSPA6	3310	broad.mit.edu	37	chr1	161496144	161496144	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gccttagggacaagattcccGaagaggacaggcgcaaaatg	13	9	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:161496144G>A	ENST00000309758.4	+	1	2109	c.1696G>A	c.(1696-1698)Gaa>Aaa	p.E566K	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	566					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)	p.E566K(1)		endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CAAGATTCCCGAAGAGGACAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											28	27	27					1																	161496144		2203	4300	6503	159762768	SO:0001583	missense	3310				CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"Heat shock proteins / HSP70"	5239	protein-coding gene	gene with protein product		140555	"heat shock 70kD protein 6 (HSP70B')"			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1696G>A	1.37:g.161496144G>A	ENSP00000310219:p.Glu566Lys		159762768	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	12.77	2.036081	0.35893	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.16457	2.34	3.39	0.403	0.16350	.	0.000000	0.32736	U	0.005707	T	0.06462	0.0166	L	0.55017	1.72	0.26207	N	0.979351	P	0.47545	0.897	B	0.43658	0.426	T	0.18304	-1.0341	10	0.87932	D	0	.	4.1865	0.10400	0.2155:0.0:0.6025:0.182	.	566	P17066	HSP76_HUMAN	K	566;542	ENSP00000310219:E566K	ENSP00000310219:E566K	E	+	1	0	HSPA6	159762768	0.986000	0.35501	0.253000	0.24343	0.534000	0.34807	2.368000	0.44222	-0.122000	0.11766	-0.216000	0.12614	GAA		0.542	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		A	161496144	G	A	161496144	3	1	51	1	0	0	0	0	1	0	0	0	7436	1059	37	1	1698	1	HSPA6	1	161496144	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	67021723	161496144	87754477	4	6913										
CFHR5	81494	broad.mit.edu	37	chr1	196953228	196953228	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agaaaaacatttcgtgtgtaGaacggggctggtccactcct	11	9	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:196953228G>T	ENST00000256785.4	+	3	500	c.391G>T	c.(391-393)Gaa>Taa	p.E131*	CFHR5_ENST00000367414.5_Nonsense_Mutation_p.E155*			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	131	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)		p.E131*(1)		NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						TTCGTGTGTAGAACGGGGCTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											90	81	84					1																	196953228		2203	4300	6503	195219851	SO:0001587	stop_gained	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.391G>T	1.37:g.196953228G>T	ENSP00000256785:p.Glu131*		195219851	Q2NKK2	Nonsense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.569552	0.45798	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	.	.	.	3.66	2.39	0.29439	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	4.4322	0.11533	0.2438:0.0:0.7562:0.0	.	.	.	.	X	155;131	.	ENSP00000256785:E131X	E	+	1	0	CFHR5	195219851	0.053000	0.20554	0.010000	0.14722	0.004000	0.04260	0.869000	0.27996	1.769000	0.52152	0.467000	0.42956	GAA		0.363	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		T	196953228	G	T	196953228	4	4	51	1	0	0	0	0	0	1	0	0	3294	943	33	2	401	2	CFHR5	1	196953228	Nonsense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	35457084	196953228	52297393	5	6914										
KIAA1804	84451	broad.mit.edu	37	chr1	233482308	233482308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gagcacagcaggcacctatgCctggatggcccccgaagtga	13	13	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:233482308C>T	ENST00000366624.3	+	2	1187	c.926C>T	c.(925-927)gCc>gTc	p.A309V	MLK4_ENST00000366623.3_Missense_Mutation_p.A309V	NM_032435.2	NP_115811.2												p.A309V(1)									GGCACCTATGCCTGGATGGCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											95	90	92					1																	233482308		2203	4300	6503	231548931	SO:0001583	missense	84451																														ENST00000366624.3:c.926C>T	1.37:g.233482308C>T	ENSP00000355583:p.Ala309Val		231548931		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	32	5.185378	0.94885	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.82984	-1.67;-1.67	4.49	4.49	0.54785	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.074602	0.56097	D	0.000031	D	0.86389	0.5921	L	0.31752	0.955	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.984	D	0.88581	0.3136	10	0.87932	D	0	.	17.3739	0.87386	0.0:1.0:0.0:0.0	.	309;309	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	V	309	ENSP00000355582:A309V;ENSP00000355583:A309V	ENSP00000355582:A309V	A	+	2	0	RP5-862P8.2	231548931	1.000000	0.71417	0.977000	0.42913	0.969000	0.65631	7.645000	0.83430	2.319000	0.78375	0.563000	0.77884	GCC		0.478	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233482308	C	T	233482308	3	4	51	1	0	0	0	0	1	0	0	0	8280	739	26	3	932	3	KIAA1804	1	233482308	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	36529080	233482308	15768313	6	6915										
CEP170	9859	broad.mit.edu	37	chr1	243329021	243329021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctttgttcttgttgttgaagTtttgctaatgtttgctttac	8	5	1	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:243329021T>A	ENST00000366542.1	-	13	2292	c.2241A>T	c.(2239-2241)aaA>aaT	p.K747N	RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Missense_Mutation_p.K649N|CEP170_ENST00000366543.1_Missense_Mutation_p.K649N|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	747						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.K747N(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTTGTTGAAGTTTTGCTAATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											240	231	234					1																	243329021		1866	4100	5966	241395644	SO:0001583	missense	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2241A>T	1.37:g.243329021T>A	ENSP00000355500:p.Lys747Asn		241395644	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.16|13.16	2.153847|2.153847	0.38021|0.38021	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543|ENST00000336415	T;T;T|.	0.51817|.	0.8;0.7;0.69|.	5.25|5.25	4.13|4.13	0.48395|0.48395	.|.	0.087564|.	0.49305|.	D|.	0.000157|.	T|T	0.40040|0.40040	0.1101|0.1101	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	P;P;P;B|.	0.46142|.	0.604;0.873;0.763;0.381|.	B;P;P;B|.	0.44897|.	0.433;0.447;0.463;0.115|.	T|T	0.17715|0.17715	-1.0360|-1.0360	10|5	0.22706|.	T|.	0.39|.	-8.9138|-8.9138	8.3988|8.3988	0.32572|0.32572	0.0:0.0884:0.0:0.9116|0.0:0.0884:0.0:0.9116	.|.	710;649;649;747|.	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;.;CE170_HUMAN|.	N|I	747;649;649|711	ENSP00000355500:K747N;ENSP00000355502:K649N;ENSP00000355501:K649N|.	ENSP00000355500:K747N|.	K|N	-|-	3|2	2|0	CEP170|CEP170	241395644|241395644	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.896000|0.896000	0.52359|0.52359	2.904000|2.904000	0.48719|0.48719	1.980000|1.980000	0.57719|0.57719	0.397000|0.397000	0.26171|0.26171	AAA|AAC		0.388	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243329021	T	A	243329021	3	1	51	1	0	0	0	0	1	0	0	0	3256	1722	60	5	2575	5	CEP170	1	243329021	Missense_Mutation	SNP	T	TCGA-AG-3898-01A-01W-1073-09	9846713	243329021	5921600	7	6916										
OR1C1	26188	broad.mit.edu	37	chr1	247920899	247920899	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	atgatggttgacagagtgtcGctctcaggcatatgggggga	16	6	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:247920899G>A	ENST00000408896.2	-	1	1083	c.810C>T	c.(808-810)agC>agT	p.S270S		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S270S(2)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	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)			ACAGAGTGTCGCTCTCAGGCA	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	1											91	87	88					1																	247920899		2014	4202	6216	245987522	SO:0001819	synonymous_variant	26188			X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"GPCR / Class A : Olfactory receptors"	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.810C>T	1.37:g.247920899G>A			245987522	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Silent	SNP	ENST00000408896.2	37	CCDS41481.1																																																																																				0.502	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1			A	247920899	G	A	247920899	2	1	51	1	0	0	0	0	0	0	0	1	10983	1078	38	1		1	OR1C1	1	247920899	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	4591878	247920899	1329722	8	6917										
OR1C1	26188	broad.mit.edu	37	chr1	247921116	247921116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gacctcctactgcaaaaatgAtcattacattgaaggagacg	8	9	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr1:247921116A>G	ENST00000408896.2	-	1	866	c.593T>C	c.(592-594)aTc>aCc	p.I198T		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	198					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I198T(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	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)			TGCAAAAATGATCATTACATT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	57	58					1																	247921116		2063	4214	6277	245987739	SO:0001583	missense	26188			X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"GPCR / Class A : Olfactory receptors"	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.593T>C	1.37:g.247921116A>G	ENSP00000386138:p.Ile198Thr		245987739	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Missense_Mutation	SNP	ENST00000408896.2	37	CCDS41481.1	.	.	.	.	.	.	.	.	.	.	A	4.737	0.137050	0.09032	.	.	ENSG00000221888	ENST00000408896	T	0.38077	1.16	3.22	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.21227	0.0511	N	0.05510	-0.035	0.09310	N	1	P	0.38729	0.644	B	0.43082	0.407	T	0.12502	-1.0545	9	0.72032	D	0.01	.	4.2077	0.10497	0.614:0.177:0.209:0.0	.	198	Q15619	OR1C1_HUMAN	T	198	ENSP00000386138:I198T	ENSP00000386138:I198T	I	-	2	0	OR1C1	245987739	0.002000	0.14202	0.013000	0.15412	0.017000	0.09413	1.617000	0.36943	0.423000	0.26033	0.482000	0.46254	ATC		0.453	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1			G	247921116	A	G	247921116	3	3	51	1	0	0	0	0	1	0	0	0	10983	333	12	4	353	4	OR1C1	1	247921116	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	217	247921116	1329505	9	6918										
PXDN	7837	broad.mit.edu	37	chr2	1652579	1652579	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	atgcggttgtgctcgcggaaCcacagcgtgtgcatgctggt	15	10	0	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:1652579C>A	ENST00000252804.4	-	17	3023	c.2973G>T	c.(2971-2973)tgG>tgT	p.W991C		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	991					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.W991C(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GCTCGCGGAACCACAGCGTGT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											27	28	28					2																	1652579		2168	4263	6431	1631586	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2973G>T	2.37:g.1652579C>A	ENSP00000252804:p.Trp991Cys		1631586	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068284	0.76301	.	.	ENSG00000130508	ENST00000252804	T	0.71934	-0.61	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.89846	0.6833	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92722	0.6192	10	0.87932	D	0	-31.1989	19.4416	0.94823	0.0:1.0:0.0:0.0	.	991	Q92626	PXDN_HUMAN	C	991	ENSP00000252804:W991C	ENSP00000252804:W991C	W	-	3	0	PXDN	1631586	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	6.015000	0.70791	2.596000	0.87737	0.558000	0.71614	TGG		0.647	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1652579	C	A	1652579	3	1	51	1	0	0	0	0	1	0	0	0	12884	508	18	2	1494	2	PXDN	2	1652579	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		1652579	241546794	10	6919										
ATAD2B	54454	broad.mit.edu	37	chr2	23977531	23977531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gcttaccttcaatctctcacGatcaactataagaggaggca	7	11	4	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:23977531G>A	ENST00000238789.5	-	26	4535	c.4192C>T	c.(4192-4194)Cgt>Tgt	p.R1398C	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1398						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.R1398C(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATCTCTCACGATCAACTATA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	90	89					2																	23977531		1858	4089	5947	23831035	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.4192C>T	2.37:g.23977531G>A	ENSP00000238789:p.Arg1398Cys		23831035	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641578	0.67244	.	.	ENSG00000119778	ENST00000238789;ENST00000546030	D	0.91686	-2.89	5.39	5.39	0.77823	.	0.279593	0.29438	N	0.012153	D	0.82412	0.5031	N	0.08118	0	0.37928	D	0.931901	P;D	0.54772	0.83;0.968	B;B	0.36719	0.116;0.231	D	0.87211	0.2247	10	0.54805	T	0.06	.	16.6994	0.85344	0.0:0.0:1.0:0.0	.	1398;1393	Q9ULI0;Q9ULI0-2	ATD2B_HUMAN;.	C	1398;566	ENSP00000238789:R1398C	ENSP00000238789:R1398C	R	-	1	0	ATAD2B	23831035	1.000000	0.71417	0.967000	0.41034	0.991000	0.79684	6.011000	0.70760	2.712000	0.92718	0.650000	0.86243	CGT		0.398	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	23977531	G	A	23977531	3	1	51	1	0	0	0	0	1	0	0	0	1073	1058	37	1	196	1	ATAD2B	2	23977531	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	22324952	23977531	219221842	11	6920										
TP53I3	9540	broad.mit.edu	37	chr2	24305898	24305898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggcccccaccggggagcagaGccatggctgtgtccccgatc	14	16	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:24305898G>A	ENST00000238721.4	-	2	1117	c.263C>T	c.(262-264)gCt>gTt	p.A88V	TP53I3_ENST00000417886.1_5'UTR|TP53I3_ENST00000407482.1_Missense_Mutation_p.A88V|TP53I3_ENST00000313482.4_Missense_Mutation_p.A88V|TP53I3_ENST00000335934.4_Missense_Mutation_p.A88V|FAM228B_ENST00000461972.1_Intron	NM_004881.4	NP_004872.2	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	88					NADP metabolic process (GO:0006739)	extracellular vesicular exosome (GO:0070062)	NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)	p.A88V(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(3)|urinary_tract(2)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGAGCAGAGCCATGGCTGT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	64	64					2																	24305898		2203	4300	6503	24159402	SO:0001583	missense	9540			AF010309	CCDS1708.1, CCDS56112.1	2p23.3	2009-06-12			ENSG00000115129	ENSG00000115129			19373	protein-coding gene	gene with protein product		605171				11919562, 10840161, 19349281	Standard	NM_004881		Approved	PIG3	uc002rez.2	Q53FA7	OTTHUMG00000090817	ENST00000238721.4:c.263C>T	2.37:g.24305898G>A	ENSP00000238721:p.Ala88Val		24159402	D6W533|O14679|O14685|Q38G78|Q6JLE7|Q9BWB8	Missense_Mutation	SNP	ENST00000238721.4	37	CCDS1708.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.272406	0.80580	.	.	ENSG00000115129	ENST00000335934;ENST00000238721;ENST00000313482;ENST00000407482;ENST00000413037	T;T;T;T;T	0.16743	3.78;3.78;2.32;2.32;2.37	4.98	3.06	0.35304	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.114905	0.64402	N	0.000018	T	0.17238	0.0414	L	0.48986	1.54	0.42869	D	0.99413	B;P	0.39551	0.318;0.678	B;B	0.39027	0.134;0.288	T	0.02132	-1.1208	10	0.62326	D	0.03	-0.9857	10.4747	0.44657	0.1343:0.0:0.8657:0.0	.	88;88	Q53FA7;Q53FA7-2	QORX_HUMAN;.	V	88;88;88;88;83	ENSP00000337834:A88V;ENSP00000238721:A88V;ENSP00000322298:A88V;ENSP00000384414:A88V;ENSP00000389620:A83V	ENSP00000238721:A88V	A	-	2	0	TP53I3	24159402	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.412000	0.52679	0.524000	0.28502	0.655000	0.94253	GCT		0.632	TP53I3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207618.2	NM_004881		A	24305898	G	A	24305898	3	1	51	1	0	0	0	0	1	0	0	0	16427	971	34	3	751	3	TP53I3	2	24305898	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	328367	24305898	218893475	12	6921										
PPM1B	5495	broad.mit.edu	37	chr2	44428909	44428909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gaggcagcgtgatgatacaaCgtgttaatggttcattagca	12	6	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:44428909C>T	ENST00000282412.4	+	2	983	c.571C>T	c.(571-573)Cgt>Tgt	p.R191C	PPM1B_ENST00000409432.3_Missense_Mutation_p.R191C|PPM1B_ENST00000378551.2_Missense_Mutation_p.R191C|PPM1B_ENST00000409895.4_Missense_Mutation_p.R191C|PPM1B_ENST00000345249.4_Intron|PPM1B_ENST00000378540.4_3'UTR	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	191					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.R191S(3)|p.R191C(1)		kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GATGATACAACGTGTTAATGG	0.468																																																4	Substitution - Missense(4)	kidney(3)|large_intestine(1)	2											182	169	173					2																	44428909		2203	4300	6503	44282413	SO:0001583	missense	5495			AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.571C>T	2.37:g.44428909C>T	ENSP00000282412:p.Arg191Cys		44282413	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Missense_Mutation	SNP	ENST00000282412.4	37	CCDS1817.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611873	0.66558	.	.	ENSG00000138032	ENST00000419807;ENST00000409895;ENST00000409432;ENST00000282412;ENST00000378551;ENST00000409473	T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38	5.68	5.68	0.88126	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.79811	0.4510	H	0.99746	4.745	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.89014	0.3430	10	0.87932	D	0	-14.9137	19.8002	0.96504	0.0:1.0:0.0:0.0	.	191;191;191;191;191	Q4J6C0;O75688-2;Q4J6C1;O75688;Q4J6C2	.;.;.;PPM1B_HUMAN;.	C	191	ENSP00000390087:R191C;ENSP00000387341:R191C;ENSP00000387287:R191C;ENSP00000282412:R191C;ENSP00000367813:R191C;ENSP00000386982:R191C	ENSP00000282412:R191C	R	+	1	0	PPM1B	44282413	1.000000	0.71417	0.948000	0.38648	0.900000	0.52787	3.804000	0.55568	2.674000	0.91012	0.655000	0.94253	CGT		0.468	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		T	44428909	C	T	44428909	3	4	51	1	0	0	0	0	1	0	0	0	12370	536	19	1	573	1	PPM1B	2	44428909	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	20123011	44428909	198770464	13	6922										
USP39	10713	broad.mit.edu	37	chr2	85872186	85872186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agccctccgagggctcctacCggatccacgtgcttcatcat	9	16	2	0	rs143344250		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:85872186C>T	ENST00000323701.6	+	11	1553	c.1543C>T	c.(1543-1545)Cgg>Tgg	p.R515W	USP39_ENST00000409025.1_Missense_Mutation_p.R515W|USP39_ENST00000409766.3_Intron|USP39_ENST00000450066.2_Missense_Mutation_p.R412W|USP39_ENST00000409470.1_Missense_Mutation_p.R515W|USP39_ENST00000459775.1_3'UTR	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	515	USP.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)	p.R515W(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						GGGCTCCTACCGGATCCACGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	99	86	90		1543	5.2	1	2	dbSNP_134	90	0,8600		0,0,4300	no	missense	USP39	NM_006590.2	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	515/566	85872186	1,13005	2203	4300	6503	85725697	SO:0001583	missense	10713			AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"Ubiquitin-specific peptidases"	20071	protein-coding gene	gene with protein product	"snRNP assembly defective 1 homolog (S.cerevisiae)", "small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"	611594	"ubiquitin specific protease 39"			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.1543C>T	2.37:g.85872186C>T	ENSP00000312981:p.Arg515Trp		85725697	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Missense_Mutation	SNP	ENST00000323701.6	37	CCDS33234.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114049	0.77210	2.27E-4	0.0	ENSG00000168883	ENST00000450066;ENST00000409268;ENST00000409025;ENST00000409470;ENST00000323701	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	6.13	5.24	0.73138	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.84082	2.675	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.991;0.997;0.997	T	0.65586	-0.6132	10	0.72032	D	0.01	-24.9534	14.3044	0.66375	0.1543:0.8457:0.0:0.0	.	412;437;515;515	B4DHT4;B7Z7L9;B9A018;Q53GS9	.;.;.;SNUT2_HUMAN	W	412;452;515;515;515	ENSP00000396133:R412W;ENSP00000386572:R515W;ENSP00000386864:R515W;ENSP00000312981:R515W	ENSP00000312981:R515W	R	+	1	2	USP39	85725697	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.220000	0.32491	1.560000	0.49568	0.650000	0.86243	CGG		0.517	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590		T	85872186	C	T	85872186	3	4	51	1	0	0	0	0	1	0	0	0	17110	643	23	1	1585	1	USP39	2	85872186	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	41443277	85872186	157327187	14	6923										
FAHD2B	151313	broad.mit.edu	37	chr2	97749739	97749739	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	acacctgggggggtcccagtTaggatgacatcccctgggta	14	11	0	1	rs374707075		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:97749739T>C	ENST00000414820.1	-	8	1098	c.828A>G	c.(826-828)ctA>ctG	p.L276L	FAHD2B_ENST00000468548.1_5'Flank|FAHD2B_ENST00000272610.3_Silent_p.L276L|FAHD2B_ENST00000440566.2_Silent_p.L276L			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	276							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.L276L(2)		kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						GGGTCCCAGTTAGGATGACAT	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	2											34	34	34					2																	97749739		2203	4299	6502	97113466	SO:0001819	synonymous_variant	151313				CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.828A>G	2.37:g.97749739T>C			97113466	D3DXH7|Q8NDK1	Silent	SNP	ENST00000414820.1	37	CCDS2030.1																																																																																				0.557	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336		C	97749739	T	C	97749739	2	2	51	1	0	0	0	0	0	0	0	1	5390	1741	61	4		4	FAHD2B	2	97749739	Silent	SNP	T	TCGA-AG-3898-01A-01W-1073-09	11877553	97749739	145449634	15	6924										
TUBA4A	7277	broad.mit.edu	37	chr2	220115325	220115325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctgcaccttggccaggtcacCcccaggcaccacagtgggag	12	16	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:220115325C>T	ENST00000248437.4	-	4	1269	c.1096G>A	c.(1096-1098)Ggt>Agt	p.G366S	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000392088.2_Missense_Mutation_p.G351S|TUBA4A_ENST00000498660.1_5'Flank	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	366					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.G351S(1)|p.G366S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	GCCAGGTCACCCCCAGGCACC	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	2											62	51	54					2																	220115325		2203	4300	6503	219823569	SO:0001583	missense	7277			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.1096G>A	2.37:g.220115325C>T	ENSP00000248437:p.Gly366Ser		219823569	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.033360	0.54896	.	.	ENSG00000127824	ENST00000248437;ENST00000392088	T;T	0.79454	-1.27;-1.27	5.11	5.11	0.69529	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81823	0.4904	L	0.43554	1.36	0.80722	D	1	P	0.34757	0.467	P	0.48677	0.586	T	0.82829	-0.0264	10	0.87932	D	0	.	18.7287	0.91726	0.0:1.0:0.0:0.0	.	366	P68366	TBA4A_HUMAN	S	366;351	ENSP00000248437:G366S;ENSP00000375938:G351S	ENSP00000248437:G366S	G	-	1	0	TUBA4A	219823569	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.622000	0.83099	2.644000	0.89710	0.650000	0.86243	GGT		0.617	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		T	220115325	C	T	220115325	3	4	51	1	0	0	0	0	1	0	0	0	16789	623	22	3	254	3	TUBA4A	2	220115325	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	122365586	220115325	23084048	16	6925										
WDR69	164781	broad.mit.edu	37	chr2	228758615	228758615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gaatgtggtttatgccatagCattcaacaatccttacgggt	9	8	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:228758615C>A	ENST00000309931.2	+	5	505	c.422C>A	c.(421-423)gCa>gAa	p.A141E	DAW1_ENST00000472604.1_3'UTR|DAW1_ENST00000545118.1_Missense_Mutation_p.A126E|DAW1_ENST00000373666.2_Missense_Mutation_p.A141E	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	141						cilium (GO:0005929)		p.A141E(1)									TATGCCATAGCATTCAACAAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	95	98					2																	228758615		2203	4300	6503	228466859	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.422C>A	2.37:g.228758615C>A	ENSP00000311899:p.Ala141Glu		228466859	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761661	0.69763	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000545118	T;T;T	0.63913	-0.07;-0.07;-0.07	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.113903	0.64402	D	0.000016	T	0.69033	0.3066	L	0.41710	1.295	0.48511	D	0.999667	D	0.58970	0.984	P	0.61275	0.886	T	0.71119	-0.4685	10	0.87932	D	0	.	13.4576	0.61208	0.1566:0.8433:0.0:0.0	.	141	Q8N136	WDR69_HUMAN	E	141;141;126	ENSP00000362770:A141E;ENSP00000311899:A141E;ENSP00000437887:A126E	ENSP00000311899:A141E	A	+	2	0	WDR69	228466859	1.000000	0.71417	0.970000	0.41538	0.618000	0.37518	5.033000	0.64146	2.692000	0.91855	0.650000	0.86243	GCA		0.468	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		A	228758615	C	A	228758615	3	1	51	1	0	0	0	0	1	0	0	0	17359	710	25	2	440	2	WDR69	2	228758615	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	8643290	228758615	14440758	17	6926										
NDUFA10	4705	broad.mit.edu	37	chr2	240960762	240960762	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttgccattatagtcggtggcGaggggcttcccatctcctgt	12	11	1	0	rs145407882		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr2:240960762G>A	ENST00000252711.2	-	3	412	c.312C>T	c.(310-312)ctC>ctT	p.L104L	NDUFA10_ENST00000307300.4_Silent_p.L104L|NDUFA10_ENST00000407129.3_Silent_p.L104L|NDUFA10_ENST00000404554.1_Silent_p.L104L	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	104					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206)	p.L104L(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)	16		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)		AGTCGGTGGCGAGGGGCTTCC	0.488											OREG0015348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	8e-04	0	5008	,	,		20148	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G		1,4405	2.1+/-5.4	0,1,2202	89	89	89		312	-3.2	0	2	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NDUFA10	NM_004544.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		104/356	240960762	2,13004	2203	4300	6503	240609435	SO:0001819	synonymous_variant	4705			AF087661	CCDS2531.1	2q37.3	2011-07-04	2002-08-29		ENSG00000130414	ENSG00000130414		"Mitochondrial respiratory chain complex / Complex I"	7684	protein-coding gene	gene with protein product	"complex I 42kDa subunit"	603835	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)"			9878551	Standard	NM_004544		Approved	CI-42k	uc002vyn.3	O95299	OTTHUMG00000133350	ENST00000252711.2:c.312C>T	2.37:g.240960762G>A		2423	240609435	Q8WXC9	Silent	SNP	ENST00000252711.2	37	CCDS2531.1																																																																																				0.488	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544		A	240960762	G	A	240960762	2	1	51	1	0	0	0	0	0	0	0	1	10291	1045	37	1		1	NDUFA10	2	240960762	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	12202147	240960762	2238611	18	6927										
TATDN2	9797	broad.mit.edu	37	chr3	10302277	10302277	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gtgaggagccccttggggacCgaaggactgtcattgacaaa	14	9	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr3:10302277C>T	ENST00000287652.4	+	3	1922	c.871C>T	c.(871-873)Cga>Tga	p.R291*	TATDN2_ENST00000448281.2_Nonsense_Mutation_p.R291*|RP11-438J1.1_ENST00000450534.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	291					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.R291*(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CCTTGGGGACCGAAGGACTGT	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											84	87	86					3																	10302277		2203	4300	6503	10277277	SO:0001587	stop_gained	9797			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.871C>T	3.37:g.10302277C>T	ENSP00000287652:p.Arg291*		10277277	Q3MIL9|Q5BKU0	Nonsense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	C	35	5.462442	0.96240	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	.	.	.	5.15	3.34	0.38264	.	0.359136	0.16607	N	0.207078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.9973	6.5947	0.22666	0.1773:0.7322:0.0:0.0905	.	.	.	.	X	291	.	ENSP00000287652:R291X	R	+	1	2	TATDN2	10277277	0.017000	0.18338	0.448000	0.26945	0.964000	0.63967	0.332000	0.19751	0.852000	0.35287	0.655000	0.94253	CGA		0.488	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10302277	C	T	10302277	4	4	51	1	0	0	0	0	0	1	0	0	15631	644	23	1	877	1	TATDN2	3	10302277	Nonsense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		10302277	187720153	19	6928										
IL17RD	54756	broad.mit.edu	37	chr3	57136546	57136546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	catcacagtgaagagcgtcgCgaatgccgatatgactacca	10	11	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr3:57136546C>T	ENST00000296318.7	-	10	1028	c.940G>A	c.(940-942)Gcg>Acg	p.A314T	IL17RD_ENST00000320057.5_Missense_Mutation_p.A170T|IL17RD_ENST00000463523.1_Missense_Mutation_p.A170T|IL17RD_ENST00000427856.2_Missense_Mutation_p.A290T	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	314					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A170T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		AAGAGCGTCGCGAATGCCGAT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											70	69	69					3																	57136546		2203	4300	6503	57111586	SO:0001583	missense	54756			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.940G>A	3.37:g.57136546C>T	ENSP00000296318:p.Ala314Thr		57111586	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629876	0.87660	.	.	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.13778	2.56;2.58;2.57;2.58	5.48	5.48	0.80851	.	0.052258	0.85682	D	0.000000	T	0.17365	0.0417	L	0.29908	0.895	0.80722	D	1	D;D;D	0.62365	0.976;0.991;0.974	B;P;P	0.47251	0.432;0.532;0.542	T	0.00426	-1.1746	10	0.66056	D	0.02	-14.5417	19.5489	0.95310	0.0:1.0:0.0:0.0	.	170;314;290	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	T	314;170;290;170	ENSP00000296318:A314T;ENSP00000322250:A170T;ENSP00000399209:A290T;ENSP00000417516:A170T	ENSP00000296318:A314T	A	-	1	0	IL17RD	57111586	1.000000	0.71417	0.853000	0.33588	0.420000	0.31355	7.273000	0.78527	2.850000	0.98022	0.655000	0.94253	GCG		0.557	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		T	57136546	C	T	57136546	3	4	51	1	0	0	0	0	1	0	0	0	7663	768	27	1	1295	1	IL17RD	3	57136546	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	46834269	57136546	140885884	20	6929										
WDR52	55779	broad.mit.edu	37	chr3	113138965	113138965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gttcccagctatgtatatggCgatactgtcgtccagaagtt	10	9	0	1	rs370318076		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr3:113138965C>T	ENST00000295868.2	-	5	631	c.469G>A	c.(469-471)Gcc>Acc	p.A157T	WDR52_ENST00000393845.2_Missense_Mutation_p.A157T|WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA	NM_018338.3	NP_060808.2												p.A157T(2)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						ATGTATATGGCGATACTGTCG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	3						C	THR/ALA,THR/ALA	0,4406		0,0,2203	133	122	126		469,469	-8	0	3		126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	WDR52	NM_001164496.1,NM_018338.3	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	157/1855,157/983	113138965	1,13005	2203	4300	6503	114621655	SO:0001583	missense	55779																														ENST00000295868.2:c.469G>A	3.37:g.113138965C>T	ENSP00000295868:p.Ala157Thr		114621655		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314456	0.23908	0.0	1.16E-4	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.42513	5.04;0.97	5.44	-8.02	0.01118	.	.	.	.	.	T	0.15955	0.0384	L	0.29908	0.895	0.09310	N	1	P	0.36768	0.569	B	0.19148	0.024	T	0.16247	-1.0409	9	0.41790	T	0.15	.	0.1572	0.00099	0.2433:0.241:0.2158:0.2999	.	157	Q96MT7	WDR52_HUMAN	T	157	ENSP00000377428:A157T;ENSP00000295868:A157T	ENSP00000295868:A157T	A	-	1	0	WDR52	114621655	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.367000	0.02583	-0.990000	0.03481	-0.140000	0.14226	GCC		0.428	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			T	113138965	C	T	113138965	3	4	51	1	0	0	0	0	1	0	0	0	17344	768	27	1	5234	1	WDR52	3	113138965	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	56002419	113138965	84883465	21	6930										
ACAD9	28976	broad.mit.edu	37	chr3	128627864	128627864	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gtcatggataccgttggccgGaggcttcgggactccctggg	16	11	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr3:128627864G>A	ENST00000308982.7	+	14	1488	c.1407G>A	c.(1405-1407)cgG>cgA	p.R469R	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	469						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.R469R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						CCGTTGGCCGGAGGCTTCGGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	3											66	62	64					3																	128627864		2203	4300	6503	130110554	SO:0001819	synonymous_variant	28976			AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.1407G>A	3.37:g.128627864G>A			130110554	D3DNB8|Q8WXX3	Silent	SNP	ENST00000308982.7	37	CCDS3053.1																																																																																				0.597	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		A	128627864	G	A	128627864	2	1	51	1	0	0	0	0	0	0	0	1	111	1161	41	3		3	ACAD9	3	128627864	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	15488899	128627864	69394566	22	6931										
IGSF10	285313	broad.mit.edu	37	chr3	151156169	151156169	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	actggggagccggaagctttGcaatctacttggaaatcttt	11	8	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr3:151156169G>A	ENST00000282466.3	-	6	6179	c.6180C>T	c.(6178-6180)tgC>tgT	p.C2060C	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2060	Ig-like C2-type 7.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.C2060C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CGGAAGCTTTGCAATCTACTT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											126	121	123					3																	151156169		2203	4300	6503	152638859	SO:0001819	synonymous_variant	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6180C>T	3.37:g.151156169G>A			152638859	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																				0.458	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151156169	G	A	151156169	2	1	51	1	0	0	0	0	0	0	0	1	7618	1311	46	3		3	IGSF10	3	151156169	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	22528305	151156169	46866261	23	6932										
LPHN3	23284	broad.mit.edu	37	chr4	62910254	62910254	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggagacataaacagttcagcGtcactcaacagaggtaatta	9	8	3	2	rs182596389	byFrequency	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:62910254G>A	ENST00000514591.1	+	24	3926	c.3597G>A	c.(3595-3597)gcG>gcA	p.A1199A	LPHN3_ENST00000508693.1_Silent_p.A1267A|LPHN3_ENST00000506700.1_Silent_p.A1190A|LPHN3_ENST00000508946.1_Silent_p.A1199A|LPHN3_ENST00000504896.1_Silent_p.A1199A|LPHN3_ENST00000507625.1_Silent_p.A1258A|LPHN3_ENST00000512091.2_Silent_p.A1199A|LPHN3_ENST00000514996.1_Silent_p.A1190A|LPHN3_ENST00000514157.1_Silent_p.A1190A|LPHN3_ENST00000545650.1_Silent_p.A1199A|LPHN3_ENST00000509896.1_Silent_p.A1267A|LPHN3_ENST00000506720.1_Silent_p.A1267A|LPHN3_ENST00000506746.1_Silent_p.A1258A|LPHN3_ENST00000511324.1_Silent_p.A1258A|LPHN3_ENST00000507164.1_Silent_p.A1258A			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1177					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.A1199A(5)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						ACAGTTCAGCGTCACTCAACA	0.368													G|||	6	0.00119808	0.0045	0	5008	,	,		16079	0		0	False		,,,				2504	0															5	Substitution - coding silent(5)	large_intestine(5)	4						G		16,3770		0,16,1877	45	42	43		3597	-5.4	0.9	4		43	1,8249		0,1,4124	no	coding-synonymous	LPHN3	NM_015236.4		0,17,6001	AA,AG,GG		0.0121,0.4226,0.1412		1199/1470	62910254	17,12019	1893	4125	6018	62592849	SO:0001819	synonymous_variant	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3597G>A	4.37:g.62910254G>A			62592849	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.943	0.743102	0.15642	0.004226	1.21E-4	ENSG00000150471	ENST00000502815	.	.	.	5.95	-5.37	0.02681	.	.	.	.	.	T	0.46852	0.1414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46162	-0.9211	4	.	.	.	.	5.8064	0.18442	0.6148:0.0803:0.1569:0.148	.	.	.	.	I	648	.	.	V	+	1	0	LPHN3	62592849	0.001000	0.12720	0.919000	0.36401	0.993000	0.82548	-1.345000	0.02637	-0.951000	0.03654	-0.244000	0.11960	GTC		0.368	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62910254	G	A	62910254	2	1	51	1	0	0	0	0	0	0	0	1	8946	1132	40	1		1	LPHN3	4	62910254	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09		62910254	128244022	24	6933										
C4orf37	285555	broad.mit.edu	37	chr4	98893481	98893481	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agcttctttctgaaccgagaAgaaagtccgaggaacagaag	11	8	2	4			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:98893481A>C	ENST00000295268.3	-	7	972	c.883T>G	c.(883-885)Ttc>Gtc	p.F295V		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	295								p.F295V(1)									TGAACCGAGAAGAAAGTCCGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	83	83					4																	98893481		2203	4300	6503	99112504	SO:0001583	missense	285555			BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.883T>G	4.37:g.98893481A>C	ENSP00000295268:p.Phe295Val		99112504		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	1.538	-0.542494	0.04053	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.43688	0.94;2.71	5.45	0.206	0.15208	.	0.585021	0.17397	N	0.175693	T	0.22437	0.0541	L	0.34521	1.04	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.11743	-1.0575	10	0.15952	T	0.53	-8.6868	1.8653	0.03197	0.5767:0.1472:0.1333:0.1428	.	295	Q8N412	CD037_HUMAN	V	9;295	ENSP00000428346:F9V;ENSP00000295268:F295V	ENSP00000295268:F295V	F	-	1	0	C4orf37	99112504	0.000000	0.05858	0.003000	0.11579	0.450000	0.32258	-0.256000	0.08757	0.314000	0.23086	0.455000	0.32223	TTC		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98893481	A	C	98893481	3	2	51	1	0	0	0	0	1	0	0	0	2273	72	3	4	516	4	C4orf37	4	98893481	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	35983227	98893481	92260795	25	6934										
ADH7	131	broad.mit.edu	37	chr4	100349246	100349246	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaaatgactgaaacctactcGctcctaatgcaaaggttgcc	7	11	0	2	rs141541308	byFrequency	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:100349246G>A	ENST00000209665.4	-	4	621	c.381C>T	c.(379-381)agC>agT	p.S127S	ADH7_ENST00000476959.1_Silent_p.S135S|ADH7_ENST00000482593.1_Silent_p.S58S|ADH7_ENST00000437033.2_Silent_p.S115S	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	127					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)	p.S127S(1)		breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		AAACCTACTCGCTCCTAATGC	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	4											141	140	140					4																	100349246		2203	4300	6503	100568269	SO:0001819	synonymous_variant	131			X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"Alcohol dehydrogenases"	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.381C>T	4.37:g.100349246G>A			100568269	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Silent	SNP	ENST00000209665.4	37	CCDS34034.1																																																																																				0.343	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673		A	100349246	G	A	100349246	2	1	51	1	0	0	0	0	0	0	0	1	313	1078	38	1		1	ADH7	4	100349246	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	1455765	100349246	90805030	26	6935										
TRPC3	7222	broad.mit.edu	37	chr4	122828635	122828635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	catttgcagggaggatgtacGcaatccgagagaagctgagc	14	8	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:122828635G>A	ENST00000379645.3	-	7	1953	c.1880C>T	c.(1879-1881)gCg>gTg	p.A627V	TRPC3_ENST00000513531.1_Missense_Mutation_p.A499V|TRPC3_ENST00000264811.5_Missense_Mutation_p.A554V	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	542					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.A554V(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GAGGATGTACGCAATCCGAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											110	108	109					4																	122828635		2203	4299	6502	123048085	SO:0001583	missense	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1880C>T	4.37:g.122828635G>A	ENSP00000368966:p.Ala627Val		123048085	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596481	0.86953	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.98329	-4.87;-4.87;-4.87	5.5	5.5	0.81552	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97870	0.9300	L	0.39467	1.215	0.80722	D	1	P;P;D	0.89917	0.801;0.796;1.0	P;P;D	0.81914	0.59;0.49;0.995	D	0.95404	0.8492	10	0.02654	T	1	-40.157	19.4029	0.94637	0.0:0.0:1.0:0.0	.	542;499;627	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	V	554;627;499	ENSP00000264811:A554V;ENSP00000368966:A627V;ENSP00000426899:A499V	ENSP00000264811:A554V	A	-	2	0	TRPC3	123048085	1.000000	0.71417	0.930000	0.37139	0.929000	0.56500	9.753000	0.98904	2.571000	0.86741	0.655000	0.94253	GCG		0.453	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		A	122828635	G	A	122828635	3	1	51	1	0	0	0	0	1	0	0	0	16619	1087	38	1	909	1	TRPC3	4	122828635	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	22479389	122828635	68325641	27	6936										
LRBA	987	broad.mit.edu	37	chr4	151356760	151356760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ccttaatatcagaggtatcaCgctgactgtttcgccaagct	8	11	2	2	rs371873204		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:151356760C>T	ENST00000357115.3	-	47	7298	c.7055G>A	c.(7054-7056)cGt>cAt	p.R2352H	LRBA_ENST00000510413.1_Missense_Mutation_p.R2341H|LRBA_ENST00000507224.1_Missense_Mutation_p.R2341H|LRBA_ENST00000535741.1_Missense_Mutation_p.R2341H|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2352	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R2352H(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AGAGGTATCACGCTGACTGTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	95	103	100		7055,7055	5.2	1	4		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LRBA	NM_001199282.2,NM_006726.4	29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	2352/2864,2352/2864	151356760	2,13004	2203	4300	6503	151576210	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.7055G>A	4.37:g.151356760C>T	ENSP00000349629:p.Arg2352His		151576210	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.159784|5.159784	0.94727|0.94727	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000198589|ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224|ENST00000509835	T;T;T;T|.	0.80393|.	-1.37;-1.37;-1.37;-1.37|.	5.2|5.2	5.2|5.2	0.72013|0.72013	BEACH domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74772|0.74772	0.3760|0.3760	M|M	0.66560|0.66560	2.04|2.04	0.80722|0.80722	D|D	1|1	D;P;D|.	0.89917|.	1.0;0.688;0.999|.	D;B;D|.	0.78314|.	0.991;0.258;0.953|.	T|T	0.73235|0.73235	-0.4047|-0.4047	10|5	0.44086|.	T|.	0.13|.	.|.	19.0835|19.0835	0.93192|0.93192	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2352;2341;242|.	P50851;P50851-2;Q68D03|.	LRBA_HUMAN;.;.|.	H|M	2341;2341;2352;2341|994	ENSP00000446299:R2341H;ENSP00000421552:R2341H;ENSP00000349629:R2352H;ENSP00000422180:R2341H|.	ENSP00000349629:R2352H|.	R|V	-|-	2|1	0|0	LRBA|LRBA	151576210|151576210	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.701000|7.701000	0.84566|0.84566	2.574000|2.574000	0.86865|0.86865	0.591000|0.591000	0.81541|0.81541	CGT|GTG		0.358	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151356760	C	T	151356760	3	4	51	1	0	0	0	0	1	0	0	0	8960	536	19	1	1584	1	LRBA	4	151356760	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	28528125	151356760	39797516	28	6937										
FBXW7	55294	broad.mit.edu	37	chr4	153249385	153249385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttcatgaagatgcatacaacGcacagtggaagtatgcccat	9	9	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr4:153249385G>A	ENST00000281708.4	-	9	2622	c.1393C>T	c.(1393-1395)Cgt>Tgt	p.R465C	FBXW7_ENST00000263981.5_Missense_Mutation_p.R385C|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465C|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289C|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347C|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465C	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465C(71)|p.R226C(11)|p.R385C(11)|p.R347C(3)|p.R465Y(2)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGCATACAACGCACAGTGGAA	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	99	Substitution - Missense(98)|Unknown(1)	haematopoietic_and_lymphoid_tissue(41)|large_intestine(27)|endometrium(20)|stomach(6)|biliary_tract(4)|pancreas(1)	4											260	223	235					4																	153249385		2203	4300	6503	153468835	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1393C>T	4.37:g.153249385G>A	ENSP00000281708:p.Arg465Cys		153468835	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909959	0.92107	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67287	0.2877	M	0.71206	2.165	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67130	-0.5748	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:0.0:1.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	C	465;347;385;289	ENSP00000281708:R465C;ENSP00000296555:R347C;ENSP00000263981:R385C;ENSP00000377528:R289C	ENSP00000263981:R385C	R	-	1	0	FBXW7	153468835	1.000000	0.71417	0.959000	0.39883	0.996000	0.88848	9.869000	0.99810	2.878000	0.98634	0.650000	0.86243	CGT		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249385	G	A	153249385	3	1	51	1	0	0	0	0	1	0	0	0	5788	1087	38	1	746	1	FBXW7	4	153249385	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	1892625	153249385	37904891	29	6938										
CDH12	1010	broad.mit.edu	37	chr5	21751945	21751945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gtcagatagtcatagtcctgGtcggcttctgtggtgagaga	14	7	3	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:21751945G>T	ENST00000382254.1	-	15	3372	c.2286C>A	c.(2284-2286)gaC>gaA	p.D762E	CDH12_ENST00000522262.1_Missense_Mutation_p.D722E|CDH12_ENST00000521384.1_5'UTR|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000504376.2_Missense_Mutation_p.D762E	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	762					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D762E(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						CATAGTCCTGGTCGGCTTCTG	0.512										HNSCC(59;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	5											124	116	119					5																	21751945		2203	4300	6503	21787702	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2286C>A	5.37:g.21751945G>T	ENSP00000371689:p.Asp762Glu		21787702	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	G	9.230	1.035613	0.19590	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.75704	-0.96;-0.96;-0.96	5.18	4.3	0.51218	Cadherin, cytoplasmic domain (1);	0.102346	0.64402	D	0.000002	T	0.59101	0.2169	L	0.31578	0.945	0.36707	D	0.880413	B;B	0.17038	0.02;0.002	B;B	0.25405	0.06;0.001	T	0.55211	-0.8176	10	0.20046	T	0.44	.	6.7287	0.23371	0.1518:0.0:0.7056:0.1425	.	722;762	B7Z2U6;P55289	.;CAD12_HUMAN	E	762;762;722	ENSP00000423577:D762E;ENSP00000371689:D762E;ENSP00000428786:D722E	ENSP00000371689:D762E	D	-	3	2	CDH12	21787702	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	1.672000	0.37523	1.179000	0.42884	0.467000	0.42956	GAC		0.512	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		T	21751945	G	T	21751945	3	4	51	1	0	0	0	0	1	0	0	0	3104	1252	44	2	102	2	CDH12	5	21751945	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		21751945	159163315	30	6939										
CDH9	1007	broad.mit.edu	37	chr5	26881462	26881462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cgtcgttttcttttaatcttCgatggataaaatcttgtaca	6	7	3	0	rs535692550		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:26881462C>T	ENST00000231021.4	-	12	2325	c.2153G>A	c.(2152-2154)cGa>cAa	p.R718Q		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	718					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R718Q(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TTTTAATCTTCGATGGATAAA	0.418													C|||	1	0.000199681	0	0	5008	,	,		18360	0		0	False		,,,				2504	0.001				Melanoma(8;187 585 15745 40864 52829)											1	Substitution - Missense(1)	large_intestine(1)	5											151	144	146					5																	26881462		2203	4300	6503	26917219	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2153G>A	5.37:g.26881462C>T	ENSP00000231021:p.Arg718Gln		26917219	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	6.509	0.462107	0.12342	.	.	ENSG00000113100	ENST00000231021	T	0.75938	-0.98	5.06	4.19	0.49359	Cadherin, cytoplasmic domain (1);	0.430312	0.25581	N	0.029685	T	0.40040	0.1101	N	0.00750	-1.22	0.32895	D	0.512351	B;B	0.13594	0.008;0.0	B;B	0.14023	0.01;0.001	T	0.44236	-0.9341	9	.	.	.	.	8.8413	0.35144	0.0:0.8274:0.0:0.1726	.	311;718	B4DFP0;Q9ULB4	.;CADH9_HUMAN	Q	718	ENSP00000231021:R718Q	.	R	-	2	0	CDH9	26917219	0.781000	0.28676	0.955000	0.39395	0.957000	0.61999	1.501000	0.35693	1.260000	0.44134	0.557000	0.71058	CGA		0.418	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26881462	C	T	26881462	3	4	51	1	0	0	0	0	1	0	0	0	3123	884	31	1	220	1	CDH9	5	26881462	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	5129517	26881462	154033798	31	6940										
BHMT2	23743	broad.mit.edu	37	chr5	78376648	78376648	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctagaattaaaaaactttttCgacaacagctagaagttttt	5	6	0	2	rs374028274		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:78376648C>T	ENST00000255192.3	+	4	463	c.397C>T	c.(397-399)Cga>Tga	p.R133*	DMGDH_ENST00000520388.1_Intron|BHMT2_ENST00000521567.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	133	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.R133*(2)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		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)	AAAACTTTTTCGACAACAGCT	0.418																																																2	Substitution - Nonsense(2)	large_intestine(1)|skin(1)	5						C	,stop/ARG	0,4406		0,0,2203	86	88	88		,397	4.4	0	5		88	1,8599	1.2+/-3.3	0,1,4299	no	intron,stop-gained	BHMT2	NM_001178005.1,NM_017614.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,133/364	78376648	1,13005	2203	4300	6503	78412404	SO:0001587	stop_gained	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.397C>T	5.37:g.78376648C>T	ENSP00000255192:p.Arg133*		78412404	B7Z516|Q9NXX7	Nonsense_Mutation	SNP	ENST00000255192.3	37	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.322087	0.41096	0.0	1.16E-4	ENSG00000132840	ENST00000255192	.	.	.	6.16	4.41	0.53225	.	0.304797	0.34802	N	0.003679	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4616	7.8641	0.29526	0.1311:0.7366:0.0:0.1323	.	.	.	.	X	133	.	ENSP00000255192:R133X	R	+	1	2	BHMT2	78412404	0.998000	0.40836	0.022000	0.16811	0.248000	0.25809	4.618000	0.61211	0.948000	0.37687	0.650000	0.86243	CGA		0.418	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		T	78376648	C	T	78376648	4	4	51	1	0	0	0	0	0	1	0	0	1427	876	31	1	411	1	BHMT2	5	78376648	Nonsense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	51495186	78376648	102538612	32	6941										
ERAP2	64167	broad.mit.edu	37	chr5	96253166	96253166	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttttcttcaatattttacagGtgaaactattttttgaatct	4	5	3	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:96253166G>A	ENST00000437043.3	+	19	3451	c.2740G>A	c.(2740-2742)Gtg>Atg	p.V914M	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000379904.4_Splice_Site_p.V869M	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	914					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V914M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TATTTTACAGGTGAAACTATT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											60	65	63					5																	96253166		2203	4300	6503	96278922	SO:0001630	splice_region_variant	64167			AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.2740-1G>A	5.37:g.96253166G>A			96278922	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286184	0.80803	.	.	ENSG00000164308	ENST00000437043;ENST00000379904	T;T	0.08282	3.11;3.11	4.6	4.6	0.57074	.	0.000000	0.64402	D	0.000004	T	0.22126	0.0533	L	0.53729	1.69	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.72338	0.977;0.968	T	0.00333	-1.1810	9	.	.	.	.	13.269	0.60150	0.0:0.0:1.0:0.0	.	869;914	Q6P179-3;Q6P179	.;ERAP2_HUMAN	M	914;869	ENSP00000400376:V914M;ENSP00000369235:V869M	.	V	+	1	0	ERAP2	96278922	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.575000	0.60908	2.280000	0.76307	0.557000	0.71058	GTG		0.398	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	Missense_Mutation	A	96253166	G	A	96253166	5	1	51	1	0	0	0	0	0	0	1	0	5217	1275	44	3	2810	3	ERAP2	5	96253166	Splice_Site	SNP	G	TCGA-AG-3898-01A-01W-1073-09	17876518	96253166	84662094	33	6942										
APC	324	broad.mit.edu	37	chr5	112173704	112173704	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	attatgtttttgacaccaatCgacatgatgataataggtca	7	6	1	3	rs587779783		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:112173704C>T	ENST00000457016.1	+	16	2793	c.2413C>T	c.(2413-2415)Cga>Tga	p.R805*	APC_ENST00000257430.4_Nonsense_Mutation_p.R805*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R805*			P25054	APC_HUMAN	adenomatous polyposis coli	805	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R805*(10)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGACACCAATCGACATGATGA	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	11	Substitution - Nonsense(10)|Unknown(1)	large_intestine(10)|skin(1)	5	GRCh37	CM960067	APC	M							77	78	78					5																	112173704		2202	4300	6502	112201603	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2413C>T	5.37:g.112173704C>T	ENSP00000413133:p.Arg805*		112201603	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.853935	0.97030	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.16	4.36	0.52297	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-10.8016	14.7295	0.69372	0.4961:0.5038:0.0:0.0	.	.	.	.	X	805;787;805;805;805	.	ENSP00000257430:R805X	R	+	1	2	APC	112201603	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.615000	0.36922	0.896000	0.36366	-0.188000	0.12872	CGA		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173704	C	T	112173704	4	4	51	1	0	0	0	0	0	1	0	0	763	876	31	1	2471	1	APC	5	112173704	Nonsense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	15920538	112173704	68741556	34	6943										
APC	324	broad.mit.edu	37	chr5	112174412	112174412	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agcagttgaactctggaaggCaaagtccttcacagaatgaa	10	8	2	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:112174412C>G	ENST00000457016.1	+	16	3501	c.3121C>G	c.(3121-3123)Caa>Gaa	p.Q1041E	APC_ENST00000257430.4_Missense_Mutation_p.Q1041E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.Q1041E			P25054	APC_HUMAN	adenomatous polyposis coli	1041	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1041E(1)|p.Q1041*(1)|p.?(1)|p.S1042fs*6(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCTGGAAGGCAAAGTCCTTC	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Substitution - Nonsense(1)|Unknown(1)|Insertion - Frameshift(1)|Substitution - Missense(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CM920045	APC	M							65	66	66					5																	112174412		2202	4300	6502	112202311	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3121C>G	5.37:g.112174412C>G	ENSP00000413133:p.Gln1041Glu		112202311	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.077596	0.55753	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94576	-2.71;-3.46;-2.71;-2.71;-2.89	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.94291	0.8166	L	0.27053	0.805	0.51482	D	0.999923	D;D	0.54964	0.969;0.969	D;D	0.64877	0.93;0.93	D	0.92953	0.6382	10	0.30854	T	0.27	-12.6463	15.141	0.72609	0.0:0.9305:0.0:0.0695	.	1043;1041	Q4LE70;P25054	.;APC_HUMAN	E	1041;1023;1041;1041;1041	ENSP00000413133:Q1041E;ENSP00000423224:Q1023E;ENSP00000257430:Q1041E;ENSP00000427089:Q1041E;ENSP00000423828:Q1041E	ENSP00000257430:Q1041E	Q	+	1	0	APC	112202311	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.294000	0.78760	2.726000	0.93360	0.655000	0.94253	CAA		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174412	C	G	112174412	3	3	51	1	0	0	0	0	1	0	0	0	763	711	25	5	3179	5	APC	5	112174412	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	708	112174412	68740848	35	6944										
FEM1C	56929	broad.mit.edu	37	chr5	114860764	114860764	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaattgctctgctgcatatcCaaagcatacttccataggtt	6	10	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:114860764C>T	ENST00000274457.3	-	3	1656	c.1095G>A	c.(1093-1095)ttG>ttA	p.L365L		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	365					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.L365L(1)		breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		GCTGCATATCCAAAGCATACT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	5											95	92	93					5																	114860764		2202	4300	6502	114888663	SO:0001819	synonymous_variant	56929				CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1095G>A	5.37:g.114860764C>T			114888663	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	ENST00000274457.3	37	CCDS4118.1																																																																																				0.413	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		T	114860764	C	T	114860764	2	4	51	1	0	0	0	0	0	0	0	1	5830	593	21	3		3	FEM1C	5	114860764	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	2686352	114860764	66054496	36	6945										
FTMT	94033	broad.mit.edu	37	chr5	121188027	121188027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	caccagtcccgggaggagacCgagcacgcggagaagctgat	15	12	0	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:121188027C>T	ENST00000321339.1	+	1	378	c.369C>T	c.(367-369)acC>acT	p.T123T		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	123	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)	p.T123T(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GGGAGGAGACCGAGCACGCGG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5											59	58	58					5																	121188027		2203	4300	6503	121215926	SO:0001819	synonymous_variant	94033			BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.369C>T	5.37:g.121188027C>T			121215926		Silent	SNP	ENST00000321339.1	37	CCDS4128.1																																																																																				0.592	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		T	121188027	C	T	121188027	2	4	51	1	0	0	0	0	0	0	0	1	6104	639	23	1		1	FTMT	5	121188027	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	6327263	121188027	59727233	37	6946										
TRPC7	57113	broad.mit.edu	37	chr5	135692763	135692763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cagcagcgcgtcccccacccGtgccaggttctccttcttca	8	19	3	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:135692763G>A	ENST00000513104.1	-	2	595	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	TRPC7_ENST00000355180.3_Missense_Mutation_p.R105W|TRPC7_ENST00000426057.2_Missense_Mutation_p.R105W	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	105					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R105W(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCCCCCACCCGTGCCAGGTTC	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	5											56	65	62					5																	135692763		2203	4300	6503	135720662	SO:0001583	missense	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.313C>T	5.37:g.135692763G>A	ENSP00000426070:p.Arg105Trp		135720662	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	37	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.06|18.06	3.540262|3.540262	0.65085|0.65085	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193|ENST00000352189;ENST00000378459;ENST00000502753	T;T;T|.	0.71103|.	-0.54;-0.54;-0.54|.	5.0|5.0	4.06|4.06	0.47325|0.47325	Ankyrin repeat-containing domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71854|0.71854	0.3389|0.3389	M|M	0.78637|0.78637	2.42|2.42	0.33398|0.33398	D|D	0.576973|0.576973	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.993;0.982;0.999;0.998|.	T|T	0.79364|0.79364	-0.1834|-0.1834	10|5	0.87932|.	D|.	0|.	-15.3684|-15.3684	16.0147|16.0147	0.80427|0.80427	0.0:0.0:0.8568:0.1432|0.0:0.0:0.8568:0.1432	.|.	105;105;105;105|.	Q8IWP7;F5H5U9;Q70T25;Q9HCX4|.	.;.;.;TRPC7_HUMAN|.	W|M	105|104	ENSP00000347312:R105W;ENSP00000441628:R105W;ENSP00000426070:R105W|.	ENSP00000265193:R105W|.	R|T	-|-	1|2	2|0	TRPC7|TRPC7	135720662|135720662	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.980000|0.980000	0.70556|0.70556	3.406000|3.406000	0.52637|0.52637	2.608000|2.608000	0.88229|0.88229	0.561000|0.561000	0.74099|0.74099	CGG|ACG		0.652	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692763	G	A	135692763	3	1	51	1	0	0	0	0	1	0	0	0	16624	1144	40	1	2319	1	TRPC7	5	135692763	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	14504736	135692763	45222497	38	6947										
PCDHB3	56132	broad.mit.edu	37	chr5	140481822	140481822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cctgcaggcgttcgagttccGcgtgggcgccacagaccgtg	15	14	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:140481822G>A	ENST00000231130.2	+	1	1589	c.1589G>A	c.(1588-1590)cGc>cAc	p.R530H	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	530	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R530H(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCGAGTTCCGCGTGGGCGCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	5											59	63	62					5																	140481822		2203	4300	6503	140462006	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1589G>A	5.37:g.140481822G>A	ENSP00000231130:p.Arg530His		140462006	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	0.185	-1.058176	0.01950	.	.	ENSG00000113205	ENST00000231130	T	0.01767	4.65	4.14	1.03	0.20045	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01092	0.0036	N	0.11064	0.09	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.48854	-0.8998	9	0.15499	T	0.54	.	6.6896	0.23163	0.1992:0.224:0.5769:0.0	.	530	Q9Y5E6	PCDB3_HUMAN	H	530	ENSP00000231130:R530H	ENSP00000231130:R530H	R	+	2	0	PCDHB3	140462006	0.000000	0.05858	0.989000	0.46669	0.065000	0.16274	-0.362000	0.07602	0.834000	0.34852	0.650000	0.86243	CGC		0.667	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		A	140481822	G	A	140481822	3	1	51	1	0	0	0	0	1	0	0	0	11574	1087	38	1	1591	1	PCDHB3	5	140481822	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	4789059	140481822	40433438	39	6948										
GPX3	10318	broad.mit.edu	37	chr5	150407549	150407549	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	catgaaggttcacgacatccGctggaactttgagaagttcc	10	10	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:150407549G>A	ENST00000389378.2	-	0	3268				GPX3_ENST00000388825.4_Missense_Mutation_p.R180H|GPX3_ENST00000517973.1_3'UTR	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1						defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)	p.R180H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACGACATCCGCTGGAACTTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	5											53	56	55					5																	150407549		2034	4218	6252	150387742	SO:0001628	intergenic_variant	2878			AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025			5.37:g.150407549G>A			150387742	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.710208	0.89018	.	.	ENSG00000211445	ENST00000388825	T	0.04194	3.68	5.33	3.51	0.40186	Thioredoxin-like fold (2);	0.124148	0.50627	D	0.000119	T	0.12561	0.0305	M	0.89534	3.04	0.80722	D	1	D	0.58620	0.983	P	0.48425	0.577	T	0.00939	-1.1507	10	0.72032	D	0.01	.	4.0691	0.09874	0.2916:0.1795:0.529:0.0	.	180	P22352	GPX3_HUMAN	H	180	ENSP00000373477:R180H	ENSP00000373477:R180H	R	+	2	0	GPX3	150387742	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.555000	0.60767	0.587000	0.29643	0.655000	0.94253	CGC		0.572	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		A	150407549	G	A	150407549	1	1	51	0	1	0	0	0	0	0	0	0	6762	1087	38	1		1	GPX3	5	150407549	IGR	SNP	G	TCGA-AG-3898-01A-01W-1073-09	9925727	150407549	30507711	40	6949										
CDHR2	54825	broad.mit.edu	37	chr5	176011567	176011567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gggctacctccggctgccccCggacgtgagcctggattacg	14	15	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:176011567C>T	ENST00000510636.1	+	19	2559	c.2285C>T	c.(2284-2286)cCg>cTg	p.P762L	CDHR2_ENST00000506348.1_Missense_Mutation_p.P762L|CDHR2_ENST00000261944.5_Missense_Mutation_p.P762L	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	762	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P762L(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CGGCTGCCCCCGGACGTGAGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	5											67	70	69					5																	176011567		2203	4300	6503	175944173	SO:0001583	missense	54825			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2285C>T	5.37:g.176011567C>T	ENSP00000424565:p.Pro762Leu		175944173	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	C	7.204	0.593983	0.13875	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.44881	0.91;0.91;0.91	5.12	2.12	0.27331	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.33089	0.0851	L	0.41415	1.275	0.23325	N	0.997907	B	0.23316	0.083	B	0.21546	0.035	T	0.22243	-1.0222	9	0.44086	T	0.13	-0.3685	9.0917	0.36614	0.0:0.7348:0.0:0.2652	.	762	Q9BYE9	CDHR2_HUMAN	L	762	ENSP00000424565:P762L;ENSP00000261944:P762L;ENSP00000421078:P762L	ENSP00000261944:P762L	P	+	2	0	CDHR2	175944173	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.819000	0.27308	0.175000	0.19841	0.549000	0.68633	CCG		0.622	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	176011567	C	T	176011567	3	4	51	1	0	0	0	0	1	0	0	0	3125	652	23	1	2355	1	CDHR2	5	176011567	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	25604018	176011567	4903693	41	6950										
RNF130	55819	broad.mit.edu	37	chr5	179405271	179405271	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cagactgcacaatgatcaaaGtctgggtcagtttcctaaaa	8	9	3	2	rs145652271		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr5:179405271G>A	ENST00000261947.4	-	5	1178	c.780C>T	c.(778-780)gaC>gaT	p.D260D	RNF130_ENST00000521389.1_Silent_p.D260D|RNF130_ENST00000522208.2_Silent_p.D260D	NM_001280801.1	NP_001267730.1			ring finger protein 130									p.D260D(1)		breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AATGATCAAAGTCTGGGTCAG	0.393																																					GBM(24;432 554 38471 39699 51728)											1	Substitution - coding silent(1)	large_intestine(1)	5						G		0,4406		0,0,2203	115	104	108		780	1.9	1	5	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RNF130	NM_018434.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		260/420	179405271	1,13005	2203	4300	6503	179337877	SO:0001819	synonymous_variant	55819			AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"RING-type (C3HC4) zinc fingers"	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.780C>T	5.37:g.179405271G>A			179337877		Silent	SNP	ENST00000261947.4	37																																																																																					0.393	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434		A	179405271	G	A	179405271	2	1	51	1	0	0	0	0	0	0	0	1	13475	1020	36	3		3	RNF130	5	179405271	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	3393704	179405271	1509989	42	6951										
HSP90AB1	3326	broad.mit.edu	37	chr6	44219536	44219536	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gagctgctgcgctatcatacCtcccagtctggagatgagat	11	11	2	2	rs190938365	byFrequency	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr6:44219536C>A	ENST00000371554.1	+	9	1591	c.1377C>A	c.(1375-1377)acC>acA	p.T459T	HSP90AB1_ENST00000353801.3_Silent_p.T459T|HSP90AB1_ENST00000371646.5_Silent_p.T459T|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000495706.1_5'Flank			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	459					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.T459T(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCTATCATACCTCCCAGTCTG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	6											109	108	108					6																	44219536		2203	4300	6503	44327514	SO:0001819	synonymous_variant	3326			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.1377C>A	6.37:g.44219536C>A			44327514	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Silent	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	C	9.431	1.085532	0.20390	.	.	ENSG00000096384	ENST00000435812;ENST00000415133;ENST00000428822	.	.	.	4.77	-5.18	0.02840	.	.	.	.	.	T	0.19248	0.0462	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40720	-0.9548	4	.	.	.	-14.7785	1.4246	0.02320	0.1776:0.1976:0.1829:0.4419	.	.	.	.	H	85	.	.	P	+	2	0	HSP90AB1	44327514	0.000000	0.05858	0.952000	0.39060	0.950000	0.60333	-2.277000	0.01160	-0.773000	0.04596	-0.230000	0.12252	CCT		0.498	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		A	44219536	C	A	44219536	2	1	51	1	0	0	0	0	0	0	0	1	7423	668	24	2		2	HSP90AB1	6	44219536	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09		44219536	126895531	43	6952										
GPR110	266977	broad.mit.edu	37	chr6	46996732	46996732	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	acatagcaccaactcaccccCaggaagccaccgtggccgtc	8	18	1	0	rs149265399		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr6:46996732C>T	ENST00000371253.2	-	2	281	c.66G>A	c.(64-66)ctG>ctA	p.L22L	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000371243.2_Silent_p.L22L	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	22					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L22L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AACTCACCCCCAGGAAGCCAC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	2,4404	4.2+/-10.8	0,2,2201	133	106	115		66,66	-2.4	0	6	dbSNP_134	115	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPR110	NM_025048.2,NM_153840.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	22/219,22/911	46996732	2,13004	2203	4300	6503	47104691	SO:0001819	synonymous_variant	266977			AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.66G>A	6.37:g.46996732C>T			47104691	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																				0.517	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		T	46996732	C	T	46996732	2	4	51	1	0	0	0	0	0	0	0	1	6647	581	21	3		3	GPR110	6	46996732	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	2777196	46996732	124118335	44	6953										
IRAK1BP1	134728	broad.mit.edu	37	chr6	79595106	79595106	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctgtttcaggcagaaaatatAactgtgacaaaggattttag	9	5	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr6:79595106A>T	ENST00000369940.2	+	2	432	c.327A>T	c.(325-327)atA>atT	p.I109I	IRAK1BP1_ENST00000607739.1_Silent_p.I22I	NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	109					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.I109I(1)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		CAGAAAATATAACTGTGACAA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	6											97	106	103					6																	79595106		2203	4299	6502	79651825	SO:0001819	synonymous_variant	134728			AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243			17368	protein-coding gene	gene with protein product		615375				11096118	Standard	XM_005248654		Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.327A>T	6.37:g.79595106A>T			79651825		Silent	SNP	ENST00000369940.2	37	CCDS34488.1																																																																																				0.313	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729		T	79595106	A	T	79595106	2	4	51	1	0	0	0	0	0	0	0	1	7843	352	13	5		5	IRAK1BP1	6	79595106	Silent	SNP	A	TCGA-AG-3898-01A-01W-1073-09	32598374	79595106	91519961	45	6954										
FAM184A	79632	broad.mit.edu	37	chr6	119337950	119337950	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	atccctaattgcattactgtGgacagcttcaattgccatat	6	10	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr6:119337950G>A	ENST00000338891.7	-	5	1935	c.1492C>T	c.(1492-1494)Cac>Tac	p.H498Y	FAM184A_ENST00000368475.4_Missense_Mutation_p.H378Y|FAM184A_ENST00000352896.5_Missense_Mutation_p.H378Y|FAM184A_ENST00000521531.1_Missense_Mutation_p.H498Y|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000522284.1_Missense_Mutation_p.H378Y	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	498						extracellular space (GO:0005615)		p.H498Y(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GCATTACTGTGGACAGCTTCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											130	120	123					6																	119337950		1825	4098	5923	119379649	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1492C>T	6.37:g.119337950G>A	ENSP00000342604:p.His498Tyr		119379649	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026595	0.75390	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.00342	8.03;8.03;8.03;8.03;8.03	5.18	5.18	0.71444	.	0.125961	0.56097	D	0.000023	T	0.00300	0.0009	L	0.56769	1.78	0.41786	D	0.989847	P;P;D	0.53745	0.952;0.952;0.962	P;P;P	0.53490	0.636;0.536;0.727	D	0.87998	0.2754	10	0.59425	D	0.04	-12.1478	18.6868	0.91567	0.0:0.0:1.0:0.0	.	498;378;498	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	Y	498;378;378;498;378	ENSP00000342604:H498Y;ENSP00000326608:H378Y;ENSP00000357460:H378Y;ENSP00000430442:H498Y;ENSP00000429826:H378Y	ENSP00000342604:H498Y	H	-	1	0	FAM184A	119379649	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.200000	0.77838	2.433000	0.82419	0.491000	0.48974	CAC		0.358	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119337950	G	A	119337950	3	1	51	1	0	0	0	0	1	0	0	0	5527	1348	47	3	1986	3	FAM184A	6	119337950	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	39742844	119337950	51777117	46	6955										
SYTL3	94120	broad.mit.edu	37	chr6	159178252	159178252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgcctctgcagtatcaggtgGcccctgcccagctggtgacc	12	15	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr6:159178252G>A	ENST00000297239.9	+	13	1341	c.1147G>A	c.(1147-1149)Gcc>Acc	p.A383T	SYTL3_ENST00000360448.3_Missense_Mutation_p.A315T|SYTL3_ENST00000367081.3_Missense_Mutation_p.A109T			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	383	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)	p.A315T(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		GTATCAGGTGGCCCCTGCCCA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											28	27	28					6																	159178252		2203	4299	6502	159098240	SO:0001583	missense	94120			AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.1147G>A	6.37:g.159178252G>A	ENSP00000297239:p.Ala383Thr		159098240	Q496J4|Q496J6|Q5U3B9	Missense_Mutation	SNP	ENST00000297239.9	37	CCDS56458.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.695276	0.48202	.	.	ENSG00000164674	ENST00000360448;ENST00000543689;ENST00000297239;ENST00000367081	T;T;T	0.07444	3.19;3.19;3.19	5.07	5.07	0.68467	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.719506	0.13853	N	0.358226	T	0.02119	0.0066	N	0.05467	-0.045	0.37242	D	0.906182	B;B;B	0.15719	0.011;0.014;0.008	B;B;B	0.21151	0.02;0.033;0.012	T	0.46076	-0.9217	10	0.12430	T	0.62	.	18.4301	0.90622	0.0:0.0:1.0:0.0	.	109;383;315	F8W7H4;Q4VX76;Q4VX76-2	.;SYTL3_HUMAN;.	T	315;383;383;109	ENSP00000353631:A315T;ENSP00000297239:A383T;ENSP00000356048:A109T	ENSP00000297239:A383T	A	+	1	0	SYTL3	159098240	1.000000	0.71417	0.802000	0.32245	0.244000	0.25665	5.672000	0.68102	2.356000	0.79943	0.491000	0.48974	GCC		0.647	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1			A	159178252	G	A	159178252	3	1	51	1	0	0	0	0	1	0	0	0	15523	1203	42	3	977	3	SYTL3	6	159178252	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	39840302	159178252	11936815	47	6956										
FTSJ2	29960	broad.mit.edu	37	chr7	2279173	2279173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cctctcgttcacctccaggaGcttgaaggcgcttcgacacc	9	16	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr7:2279173G>A	ENST00000242257.8	-	2	206	c.178C>T	c.(178-180)Ctc>Ttc	p.L60F	FTSJ2_ENST00000407040.1_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|NUDT1_ENST00000356714.1_5'Flank|FTSJ2_ENST00000440306.2_Missense_Mutation_p.L60F|NUDT1_ENST00000397048.1_5'Flank|NUDT1_ENST00000397046.1_5'Flank|NUDT1_ENST00000397049.1_5'Flank	NM_013393.1	NP_037525.1			FtsJ RNA methyltransferase homolog 2 (E. coli)									p.L60F(1)		endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.7e-14)		ACCTCCAGGAGCTTGAAGGCG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	7											69	65	67					7																	2279173		2203	4300	6503	2245699	SO:0001583	missense	29960			AF093415	CCDS5328.1	7p22	2012-06-12	2012-06-12		ENSG00000122687	ENSG00000122687			16352	protein-coding gene	gene with protein product	"rRNA (uridine-2'-O-)-methyltransferase", "MRM2 RNA methyltransferase homolog (S. cerevisiae)"	606906				11827451	Standard	NM_013393		Approved	FJH1, MRM2	uc003slm.3	Q9UI43	OTTHUMG00000023866	ENST00000242257.8:c.178C>T	7.37:g.2279173G>A	ENSP00000242257:p.Leu60Phe		2245699		Missense_Mutation	SNP	ENST00000242257.8	37	CCDS5328.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.581482	0.86748	.	.	ENSG00000122687	ENST00000242257;ENST00000440306	T;T	0.64803	-0.12;-0.12	5.96	5.96	0.96718	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.000000	0.64402	D	0.000001	D	0.85234	0.5650	H	0.95884	3.735	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88912	0.3360	10	0.87932	D	0	-0.3659	14.0108	0.64495	0.0772:0.0:0.9228:0.0	.	60	Q9UI43	RRMJ2_HUMAN	F	60	ENSP00000242257:L60F;ENSP00000392343:L60F	ENSP00000242257:L60F	L	-	1	0	FTSJ2	2245699	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	5.201000	0.65163	2.832000	0.97577	0.655000	0.94253	CTC		0.627	FTSJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060187.1	NM_013393		A	2279173	G	A	2279173	3	1	51	1	0	0	0	0	1	0	0	0	6107	971	34	3	570	3	FTSJ2	7	2279173	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		2279173	156859490	48	6957										
RNF133	168433	broad.mit.edu	37	chr7	122338728	122338728	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgggattacatgcattttggAtttttccctctggtggcact	10	8	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr7:122338728A>T	ENST00000340112.2	-	1	482	c.245T>A	c.(244-246)aTc>aAc	p.I82N	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000412584.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	82	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.I82N(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						TGCATTTTGGATTTTTCCCTC	0.458																																					Colon(198;1778 2057 7449 19869 45985)											1	Substitution - Missense(1)	large_intestine(1)	7											125	133	130					7																	122338728		2203	4299	6502	122125964	SO:0001583	missense	168433			AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"RING-type (C3HC4) zinc fingers"	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.245T>A	7.37:g.122338728A>T	ENSP00000344489:p.Ile82Asn		122125964	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	A	2.356	-0.347693	0.05208	.	.	ENSG00000188050	ENST00000340112	T	0.13089	2.62	6.06	-8.6	0.00889	.	1.896570	0.03151	N	0.167944	T	0.03915	0.0110	N	0.01493	-0.835	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37454	-0.9705	10	0.39692	T	0.17	.	4.5968	0.12334	0.594:0.1548:0.1252:0.126	.	82	Q8WVZ7	RN133_HUMAN	N	82	ENSP00000344489:I82N	ENSP00000344489:I82N	I	-	2	0	RNF133	122125964	0.000000	0.05858	0.000000	0.03702	0.361000	0.29550	-0.994000	0.03716	-1.415000	0.02022	-1.815000	0.00603	ATC		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		T	122338728	A	T	122338728	3	4	51	1	0	0	0	0	1	0	0	0	13476	333	12	5	889	5	RNF133	7	122338728	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	120059555	122338728	36799935	49	6958										
ZC3HAV1	56829	broad.mit.edu	37	chr7	138774426	138774426	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cactgctaattcctctttgtTcagtccagagagttcgtgat	8	10	2	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr7:138774426T>G	ENST00000242351.5	-	2	704	c.388A>C	c.(388-390)Aac>Cac	p.N130H	ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.N130H|ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.N130H	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	130	N-terminal domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.N130H(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TCCTCTTTGTTCAGTCCAGAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											121	109	113					7																	138774426		2203	4300	6503	138424966	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.388A>C	7.37:g.138774426T>G	ENSP00000242351:p.Asn130His		138424966	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.741287	0.49151	.	.	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652	T;T;T	0.45668	0.89;0.89;0.89	4.21	2.96	0.34315	.	0.292580	0.24886	N	0.034816	T	0.53850	0.1822	L	0.60455	1.87	0.21445	N	0.99969	D;D	0.89917	0.999;1.0	D;D	0.76071	0.987;0.97	T	0.33624	-0.9861	10	0.72032	D	0.01	.	6.4587	0.21944	0.2167:0.0:0.0:0.7833	.	130;130	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	H	130	ENSP00000242351:N130H;ENSP00000418385:N130H;ENSP00000419855:N130H	ENSP00000242351:N130H	N	-	1	0	ZC3HAV1	138424966	0.850000	0.29656	0.900000	0.35374	0.703000	0.40648	2.673000	0.46858	1.895000	0.54865	0.528000	0.53228	AAC		0.408	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		G	138774426	T	G	138774426	3	3	51	1	0	0	0	0	1	0	0	0	17614	1783	62	4	2372	4	ZC3HAV1	7	138774426	Missense_Mutation	SNP	T	TCGA-AG-3898-01A-01W-1073-09	16435698	138774426	20364237	50	6959										
FAM115C	285966	broad.mit.edu	37	chr7	143417092	143417092	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	taaaagatctgtgtcctctcCtatcggagcatggcctgcaa	9	11	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr7:143417092C>G	ENST00000441159.2	+	3	1006	c.940C>G	c.(940-942)Cta>Gta	p.L314V	FAM115C_ENST00000411497.2_Missense_Mutation_p.L33V|FAM115C_ENST00000409703.3_Missense_Mutation_p.L150V|FAM115C_ENST00000444908.2_Missense_Mutation_p.L314V|FAM115C_ENST00000411935.1_Missense_Mutation_p.L150V|FAM115C_ENST00000357344.4_Missense_Mutation_p.L314V|FAM115C_ENST00000425618.2_Missense_Mutation_p.L33V			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	314					hematopoietic progenitor cell differentiation (GO:0002244)			p.L314V(1)		endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						GTGTCCTCTCCTATCGGAGCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	7											4	4	4					7																	143417092		1106	2465	3571	143048025	SO:0001583	missense	285966			AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"family with sequence similarity 139, member A"	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.940C>G	7.37:g.143417092C>G	ENSP00000404265:p.Leu314Val		143048025	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Missense_Mutation	SNP	ENST00000441159.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	5.437|5.437	0.265728|0.265728	0.10294|0.10294	.|.	.|.	ENSG00000170379|ENSG00000170379	ENST00000444908;ENST00000411497;ENST00000357344;ENST00000441159;ENST00000411935;ENST00000409703;ENST00000425618|ENST00000518791	T;T;T;T;T|.	0.21734|.	1.99;1.99;1.99;1.99;1.99|.	3.58|3.58	1.69|1.69	0.24217|0.24217	.|.	0.067496|.	0.64402|.	D|.	0.000011|.	T|T	0.48642|0.48642	0.1511|0.1511	M|M	0.77103|0.77103	2.36|2.36	0.09310|0.09310	N|N	1|1	D;D;D;D|.	0.58268|.	0.982;0.969;0.969;0.982|.	P;P;P;P|.	0.55055|.	0.713;0.45;0.52;0.767|.	T|T	0.40664|0.40664	-0.9551|-0.9551	10|5	0.42905|.	T|.	0.14|.	-23.1762|-23.1762	5.8374|5.8374	0.18615|0.18615	0.0:0.6143:0.0:0.3857|0.0:0.6143:0.0:0.3857	.|.	150;314;33;314|.	A6NFQ2-3;A6NFQ2;Q8N1I1;A6NFQ2-2|.	.;F115C_HUMAN;.;.|.	V|R	314;33;314;314;150;150;33|128	ENSP00000412724:L314V;ENSP00000349902:L314V;ENSP00000404265:L314V;ENSP00000389100:L150V;ENSP00000386405:L150V|.	ENSP00000349902:L314V|.	L|P	+|+	1|2	2|0	FAM115C|FAM115C	143048025|143048025	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.126000|0.126000	0.20510|0.20510	-0.169000|-0.169000	0.09911|0.09911	0.259000|0.259000	0.21709|0.21709	0.411000|0.411000	0.27672|0.27672	CTA|CCT		0.557	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330287.1	NM_173678		G	143417092	C	G	143417092	3	3	51	1	0	0	0	0	1	0	0	0	5422	680	24	5	1081	5	FAM115C	7	143417092	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	4642666	143417092	15721571	51	6960										
WDR60	55112	broad.mit.edu	37	chr7	158672383	158672383	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cgtgttttacagctgcagtaCggagacagcaaggacaaccc	11	11	0	1	rs368847195		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr7:158672383C>T	ENST00000407559.3	+	5	740	c.582C>T	c.(580-582)taC>taT	p.Y194Y		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	194					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.Y194Y(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	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)		AGCTGCAGTACGGAGACAGCA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	7								1,3947		0,1,1973	48	50	50		582	-2.3	0.3	7		50	0,8340		0,0,4170	no	coding-synonymous	WDR60	NM_018051.4		0,1,6143	TT,TC,CC		0.0,0.0253,0.0081		194/1067	158672383	1,12287	1974	4170	6144	158365144	SO:0001819	synonymous_variant	55112				CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.582C>T	7.37:g.158672383C>T			158365144	Q9NW58	Silent	SNP	ENST00000407559.3	37	CCDS47757.1																																																																																				0.522	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		T	158672383	C	T	158672383	2	4	51	1	0	0	0	0	0	0	0	1	17351	547	19	1		1	WDR60	7	158672383	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	15255291	158672383	466280	52	6961										
FAM167A	83648	broad.mit.edu	37	chr8	11281913	11281913	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agaacctccgagagttgatgTtcatcttggtcacgccaata	9	10	3	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:11281913T>A	ENST00000528897.1	-	3	1233	c.614A>T	c.(613-615)aAc>aTc	p.N205I	C8orf12_ENST00000529305.1_Intron|C8orf12_ENST00000284481.3_Intron|FAM167A_ENST00000284486.4_Missense_Mutation_p.N205I|FAM167A_ENST00000531564.1_5'UTR|FAM167A_ENST00000534308.1_Missense_Mutation_p.N205I			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	205								p.N205I(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						AGAGTTGATGTTCATCTTGGT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	8											129	109	116					8																	11281913		2203	4300	6503	11319323	SO:0001583	missense	83648				CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"chromosome 8 open reading frame 13"	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.614A>T	8.37:g.11281913T>A	ENSP00000436655:p.Asn205Ile		11319323	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548913	0.86127	.	.	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897	T;T;T	0.51325	0.71;0.71;0.71	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.65186	0.2667	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69003	-0.5260	10	0.87932	D	0	-0.8951	13.6866	0.62520	0.0:0.0:0.0:1.0	.	205	Q96KS9	F167A_HUMAN	I	205	ENSP00000284486:N205I;ENSP00000432232:N205I;ENSP00000436655:N205I	ENSP00000284486:N205I	N	-	2	0	FAM167A	11319323	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.368000	0.79567	2.008000	0.58898	0.529000	0.55759	AAC		0.607	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1			A	11281913	T	A	11281913	3	1	51	1	0	0	0	0	1	0	0	0	5499	1725	60	5	34	5	FAM167A	8	11281913	Missense_Mutation	SNP	T	TCGA-AG-3898-01A-01W-1073-09		11281913	135082109	53	6962										
MTUS1	57509	broad.mit.edu	37	chr8	17573410	17573410	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgatgacagcggcattaccaGctgtaataaaacagaaaagt	9	7	0	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:17573410G>T	ENST00000262102.6	-	5	2674	c.2450C>A	c.(2449-2451)tCt>tAt	p.S817Y	MTUS1_ENST00000544260.1_De_novo_Start_OutOfFrame|MTUS1_ENST00000381861.3_Splice_Site_p.T64N|MTUS1_ENST00000519263.1_Splice_Site_p.A763D|MTUS1_ENST00000381869.3_Splice_Site_p.A763D	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	817					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T64N(1)|p.S817Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		GGCATTACCAGCTGTAATAAA	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	8											98	96	97					8																	17573410		1847	4090	5937	17617690	SO:0001630	splice_region_variant	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2450-1C>A	8.37:g.17573410G>T			17617690	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	11.11|11.11|11.11	1.543252|1.543252|1.543252	0.27563|0.27563|0.27563	.|.|.	.|.|.	ENSG00000129422|ENSG00000129422|ENSG00000129422	ENST00000381869;ENST00000519263|ENST00000262102|ENST00000381861	T;T|T|T	0.07800|0.37915|0.14766	3.16;3.16|1.17|2.48	4.85|4.85|4.85	3.95|3.95|3.95	0.45737|0.45737|0.45737	.|.|.	.|0.604741|.	.|0.16174|.	.|N|.	.|0.226180|.	T|T|T	0.17023|0.17023|0.17023	0.0409|0.0409|0.0409	L|L|L	0.51422|0.51422|0.51422	1.61|1.61|1.61	0.80722|0.80722|0.80722	D|D|D	1|1|1	B|P|B	0.20988|0.36315|0.33612	0.05|0.547|0.419	B|B|B	0.26202|0.40228|0.37239	0.067|0.323|0.244	T|T|T	0.03673|0.03673|0.03673	-1.1014|-1.1014|-1.1014	9|10|9	0.52906|0.72032|0.66056	T|D|D	0.07|0.01|0.02	.|.|.	13.8518|13.8518|13.8518	0.63501|0.63501|0.63501	0.0:0.1594:0.8406:0.0|0.0:0.1594:0.8406:0.0|0.0:0.1594:0.8406:0.0	.|.|.	763|817|64	Q9ULD2-2|Q9ULD2|Q9ULD2-6	.|MTUS1_HUMAN|.	D|Y|N	763|817|64	ENSP00000371293:A763D;ENSP00000430167:A763D|ENSP00000262102:S817Y|ENSP00000371285:T64N	ENSP00000371293:A763D|ENSP00000262102:S817Y|ENSP00000371285:T64N	A|S|T	-|-|-	2|2|2	0|0|0	MTUS1|MTUS1|MTUS1	17617690|17617690|17617690	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.914000|0.914000|0.914000	0.36105|0.36105|0.36105	0.203000|0.203000|0.203000	0.24098|0.24098|0.24098	2.996000|2.996000|2.996000	0.49449|0.49449|0.49449	1.314000|1.314000|1.314000	0.45095|0.45095|0.45095	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GCT|TCT|ACT		0.373	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	Missense_Mutation	T	17573410	G	T	17573410	5	4	51	1	0	0	0	0	0	0	1	0	9995	985	34	2	1531	2	MTUS1	8	17573410	Splice_Site	SNP	G	TCGA-AG-3898-01A-01W-1073-09	6291497	17573410	128790612	54	6963										
ZFHX4	79776	broad.mit.edu	37	chr8	77768157	77768157	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cctttcatgatcaatcaaggCggaacggaaggcaccaaacc	9	12	3	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:77768157C>T	ENST00000521891.2	+	10	9448	c.9000C>T	c.(8998-9000)ggC>ggT	p.G3000G	ZFHX4_ENST00000518282.1_Silent_p.G2974G|ZFHX4_ENST00000050961.6_Silent_p.G2955G|ZFHX4_ENST00000455469.2_Silent_p.G2955G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2955					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.G2984G(3)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TCAATCAAGGCGGAACGGAAG	0.468										HNSCC(33;0.089)																																						3	Substitution - coding silent(3)	ovary(1)|large_intestine(1)|endometrium(1)	8											45	44	44					8																	77768157		1913	4126	6039	77930712	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9000C>T	8.37:g.77768157C>T			77930712	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.468	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77768157	C	T	77768157	2	4	51	1	0	0	0	0	0	0	0	1	17674	755	27	1		1	ZFHX4	8	77768157	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	60194747	77768157	68595865	55	6964										
CSMD3	114788	broad.mit.edu	37	chr8	113323315	113323315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcctcgatcacaggcccaacGgaccacactgttaagctgcc	8	16	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:113323315G>T	ENST00000297405.5	-	50	8021	c.7777C>A	c.(7777-7779)Cgt>Agt	p.R2593S	CSMD3_ENST00000343508.3_Missense_Mutation_p.R2553S|CSMD3_ENST00000352409.3_Missense_Mutation_p.R2523S|CSMD3_ENST00000455883.2_Missense_Mutation_p.R2489S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2593	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2593S(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAGGCCCAACGGACCACACTG	0.468										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											153	125	135					8																	113323315		2203	4300	6503	113392491	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7777C>A	8.37:g.113323315G>T	ENSP00000297405:p.Arg2593Ser		113392491	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323657	0.95708	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.62	5.62	0.85841	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.70771	0.3262	L	0.38175	1.15	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.987	D;D;P	0.91635	0.998;0.999;0.875	T	0.62666	-0.6806	10	0.12430	T	0.62	.	19.6449	0.95773	0.0:0.0:1.0:0.0	.	2489;2593;2553	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	2553;2593;1863;2489;2523	ENSP00000345799:R2553S;ENSP00000297405:R2593S;ENSP00000341558:R1863S;ENSP00000412263:R2489S;ENSP00000343124:R2523S	ENSP00000297405:R2593S	R	-	1	0	CSMD3	113392491	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.750000	0.74888	2.628000	0.89032	0.655000	0.94253	CGT		0.468	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113323315	G	T	113323315	3	4	51	1	0	0	0	0	1	0	0	0	3952	1116	39	2	3434	2	CSMD3	8	113323315	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	35555158	113323315	33040707	56	6965										
CSMD3	114788	broad.mit.edu	37	chr8	113564872	113564872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	catccacatgcaacgcaggtTattgtcatatggaaaaggat	9	8	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:113564872T>C	ENST00000297405.5	-	26	4556	c.4312A>G	c.(4312-4314)Aac>Gac	p.N1438D	CSMD3_ENST00000343508.3_Missense_Mutation_p.N1398D|CSMD3_ENST00000352409.3_Missense_Mutation_p.N1438D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1334D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1438	CUB 8. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N1438D(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAACGCAGGTTATTGTCATAT	0.358										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											84	79	81					8																	113564872		2203	4300	6503	113634048	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4312A>G	8.37:g.113564872T>C	ENSP00000297405:p.Asn1438Asp		113634048	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.453465	0.84209	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	4.74	4.74	0.60224	CUB (5);	0.000000	0.85682	D	0.000000	T	0.77184	0.4093	M	0.69823	2.125	0.38549	D	0.949405	D;D;D	0.76494	0.999;0.999;0.986	D;D;P	0.76071	0.978;0.987;0.814	T	0.80957	-0.1150	10	0.54805	T	0.06	.	14.7021	0.69162	0.0:0.0:0.0:1.0	.	1334;1438;1398	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1398;1438;778;1334;1438	ENSP00000345799:N1398D;ENSP00000297405:N1438D;ENSP00000341558:N778D;ENSP00000412263:N1334D;ENSP00000343124:N1438D	ENSP00000297405:N1438D	N	-	1	0	CSMD3	113634048	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	7.825000	0.86693	2.115000	0.64714	0.533000	0.62120	AAC		0.358	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113564872	T	C	113564872	3	2	51	1	0	0	0	0	1	0	0	0	3952	1754	61	4	6995	4	CSMD3	8	113564872	Missense_Mutation	SNP	T	TCGA-AG-3898-01A-01W-1073-09	241557	113564872	32799150	57	6966										
KIAA0196	9897	broad.mit.edu	37	chr8	126088592	126088592	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaaattagcaatacttgcccAattatctggaaagtatttat	5	6	1	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr8:126088592A>C	ENST00000318410.7	-	7	1211	c.862T>G	c.(862-864)Tgg>Ggg	p.W288G	KIAA0196_ENST00000517845.1_Missense_Mutation_p.W140G	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	288					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)		p.W288G(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ATACTTGCCCAATTATCTGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	8											126	123	124					8																	126088592		2203	4300	6503	126157774	SO:0001583	missense	9897				CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.862T>G	8.37:g.126088592A>C	ENSP00000318016:p.Trp288Gly		126157774	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.278409	0.80692	.	.	ENSG00000164961	ENST00000318410;ENST00000517845;ENST00000523297	D;D;D	0.96073	-3.9;-3.9;-3.9	5.84	5.84	0.93424	.	0.054045	0.85682	D	0.000000	D	0.96383	0.8820	M	0.88105	2.93	0.80722	D	1	B	0.29481	0.245	B	0.35182	0.197	D	0.95749	0.8790	10	0.87932	D	0	-7.683	16.215	0.82206	1.0:0.0:0.0:0.0	.	288	Q12768	STRUM_HUMAN	G	288;140;140	ENSP00000318016:W288G;ENSP00000429676:W140G;ENSP00000427946:W140G	ENSP00000318016:W288G	W	-	1	0	KIAA0196	126157774	1.000000	0.71417	0.969000	0.41365	0.981000	0.71138	9.228000	0.95250	2.239000	0.73571	0.533000	0.62120	TGG		0.378	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		C	126088592	A	C	126088592	3	2	51	1	0	0	0	0	1	0	0	0	8182	130	5	4	2709	4	KIAA0196	8	126088592	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	12523720	126088592	20275430	58	6967										
NTNG2	84628	broad.mit.edu	37	chr9	135073918	135073918	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	catgcggctgctgcgcccggCgctgggcggcacctatgtgc	16	15	0	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr9:135073918C>T	ENST00000393229.3	+	3	1555	c.779C>T	c.(778-780)gCg>gTg	p.A260V	NTNG2_ENST00000393228.4_Missense_Mutation_p.A260V|NTNG2_ENST00000372179.3_Missense_Mutation_p.A260V|NTNG2_ENST00000360670.3_Missense_Mutation_p.A260V	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	260	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)		p.A260V(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		CTGCGCCCGGCGCTGGGCGGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											37	43	41					9																	135073918		2202	4296	6498	134063739	SO:0001583	missense	84628			AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"Netrins"	14288	protein-coding gene	gene with protein product	"Netrin-G2"		"netrin G1"	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.779C>T	9.37:g.135073918C>T	ENSP00000376921:p.Ala260Val		134063739	Q5JUJ2|Q6UXY0|Q96JH0	Missense_Mutation	SNP	ENST00000393229.3	37	CCDS6946.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236627	0.95240	.	.	ENSG00000196358	ENST00000393229;ENST00000393228;ENST00000360670;ENST00000372179	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.34	5.34	0.76211	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.84624	0.5513	M	0.65975	2.015	0.58432	D	0.999999	D	0.89917	1.0	D	0.71414	0.973	D	0.83855	0.0265	10	0.40728	T	0.16	.	18.0304	0.89282	0.0:1.0:0.0:0.0	.	260	Q96CW9	NTNG2_HUMAN	V	260	ENSP00000376921:A260V;ENSP00000376920:A260V;ENSP00000353888:A260V;ENSP00000361252:A260V	ENSP00000353888:A260V	A	+	2	0	NTNG2	134063739	1.000000	0.71417	0.991000	0.47740	0.882000	0.50991	6.084000	0.71335	2.485000	0.83878	0.491000	0.48974	GCG		0.637	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536		T	135073918	C	T	135073918	3	4	51	1	0	0	0	0	1	0	0	0	10736	768	27	1	785	1	NTNG2	9	135073918	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		135073918	6139513	59	6968										
CUBN	8029	broad.mit.edu	37	chr10	16916455	16916455	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gtagtctgcgtatgaataggCaggacttgtgatgattccag	13	6	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:16916455C>A	ENST00000377833.4	-	58	9219	c.9154G>T	c.(9154-9156)Gcc>Tcc	p.A3052S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3052	CUB 23. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.A3052S(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TATGAATAGGCAGGACTTGTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											185	148	161					10																	16916455		2203	4300	6503	16956461	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9154G>T	10.37:g.16916455C>A	ENSP00000367064:p.Ala3052Ser		16956461	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	3.514	-0.099089	0.07010	.	.	ENSG00000107611	ENST00000377833	T	0.26957	1.7	5.44	-0.323	0.12709	CUB (5);	1.471140	0.04665	N	0.409585	T	0.10165	0.0249	N	0.02412	-0.56	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.31194	-0.9952	10	0.07175	T	0.84	.	9.2745	0.37692	0.606:0.2775:0.0:0.1166	.	3052	O60494	CUBN_HUMAN	S	3052	ENSP00000367064:A3052S	ENSP00000367064:A3052S	A	-	1	0	CUBN	16956461	0.036000	0.19791	0.001000	0.08648	0.007000	0.05969	0.005000	0.13129	-0.587000	0.05890	-0.808000	0.03180	GCC		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16916455	C	A	16916455	3	1	51	1	0	0	0	0	1	0	0	0	4057	710	25	2	1757	2	CUBN	10	16916455	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		16916455	118618292	60	6969										
TLL2	7093	broad.mit.edu	37	chr10	98156950	98156950	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	acctcgcacaaaccttcgtaCgctgcaaagaagcccttgcc	7	16	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:98156950C>T	ENST00000357947.3	-	11	1602	c.1377G>A	c.(1375-1377)gcG>gcA	p.A459A	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	459	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A459A(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AACCTTCGTACGCTGCAAAGA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	10											75	62	66					10																	98156950		2203	4300	6503	98146940	SO:0001819	synonymous_variant	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1377G>A	10.37:g.98156950C>T			98146940	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Silent	SNP	ENST00000357947.3	37	CCDS7449.1																																																																																				0.622	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			T	98156950	C	T	98156950	2	4	51	1	0	0	0	0	0	0	0	1	15985	523	19	1		1	TLL2	10	98156950	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	81240495	98156950	37377797	61	6970										
GOLGA7B	401647	broad.mit.edu	37	chr10	99623944	99623944	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggttctcaagaagatttcccGctacatccaggagcagaatg	10	10	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:99623944G>A	ENST00000370602.1	+	4	376	c.311G>A	c.(310-312)cGc>cAc	p.R104H		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	104						Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.R104H(1)		endometrium(1)|large_intestine(3)|prostate(1)	5						AAGATTTCCCGCTACATCCAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	10											81	74	76					10																	99623944		2203	4300	6503	99613934	SO:0001583	missense	401647			BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.311G>A	10.37:g.99623944G>A	ENSP00000359634:p.Arg104His		99613934	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	37	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.875259	0.33162	.	.	ENSG00000155265	ENST00000370602	.	.	.	5.31	3.48	0.39840	Golgin subfamily A member 7/ERF4 (1);	0.114380	0.56097	D	0.000036	T	0.36054	0.0953	L	0.59436	1.845	0.24039	N	0.996086	D	0.60575	0.988	P	0.46389	0.515	T	0.29518	-1.0009	9	0.72032	D	0.01	-45.8472	6.7581	0.23526	0.3365:0.0:0.6635:0.0	.	104	Q2TAP0	GOG7B_HUMAN	H	104	.	ENSP00000359634:R104H	R	+	2	0	GOLGA7B	99613934	0.986000	0.35501	0.985000	0.45067	0.034000	0.12701	2.375000	0.44283	0.841000	0.35020	-0.136000	0.14681	CGC		0.562	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917		A	99623944	G	A	99623944	3	1	51	1	0	0	0	0	1	0	0	0	6582	1087	38	1	325	1	GOLGA7B	10	99623944	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	1466994	99623944	35910803	62	6971										
TCF7L2	6934	broad.mit.edu	37	chr10	114901075	114901075	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ccgacgtagaccccaaaacaGgtaggctgtgggctacggag	14	11	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:114901075G>A	ENST00000355995.4	+	6	1192	c.685G>A	c.(685-687)Gga>Aga	p.G229R	TCF7L2_ENST00000534894.1_Splice_Site_p.G229R|TCF7L2_ENST00000536810.1_Splice_Site_p.G229R|TCF7L2_ENST00000545257.1_Splice_Site_p.G229R|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000355717.4_Splice_Site_p.G253R|TCF7L2_ENST00000369397.4_Splice_Site_p.G206R|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000352065.5_Splice_Site_p.G206R|TCF7L2_ENST00000543371.1_Splice_Site_p.G229R|TCF7L2_ENST00000349937.2_Splice_Site_p.G229R|TCF7L2_ENST00000369395.1_Splice_Site_p.G254R|TCF7L2_ENST00000538897.1_Splice_Site_p.G229R			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	229	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G206R(1)|p.G229R(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCCCAAAACAGGTAGGCTGTG	0.602			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	2	Substitution - Missense(2)	large_intestine(2)	10											103	89	93					10																	114901075		2203	4300	6503	114891065	SO:0001630	splice_region_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.685+1G>A	10.37:g.114901075G>A			114891065	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	g	36	5.664229	0.96745	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000349937;ENST00000352065;ENST00000369395	D;D;D;D;D;D;D;D;D	0.99769	-6.14;-6.17;-6.25;-6.25;-6.52;-6.7;-6.57;-6.17;-6.56	5.45	5.45	0.79879	CTNNB1 binding, N-teminal (1);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	M	0.83384	2.64	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.998;0.999;1.0;1.0;1.0;1.0;0.999;1.0;0.999;0.999;0.999;0.999;1.0;1.0;0.999;0.999;0.999;1.0	D	0.97374	0.9978	10	0.87932	D	0	-6.0561	19.2979	0.94131	0.0:0.0:1.0:0.0	.	86;46;123;229;100;148;206;206;206;172;229;206;206;206;253;206;229;206;206	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	R	229;229;229;229;253;229;229;206;229;206;254	ENSP00000348274:G229R;ENSP00000440547:G229R;ENSP00000444972:G229R;ENSP00000446238:G229R;ENSP00000347949:G253R;ENSP00000446172:G229R;ENSP00000443626:G229R;ENSP00000358404:G206R;ENSP00000344823:G206R	ENSP00000298692:G229R	G	+	1	0	TCF7L2	114891065	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.864000	0.99589	2.559000	0.86315	0.650000	0.86243	GGA		0.602	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	Missense_Mutation	A	114901075	G	A	114901075	5	1	51	1	0	0	0	0	0	0	1	0	15737	1014	35	3	852	3	TCF7L2	10	114901075	Splice_Site	SNP	G	TCGA-AG-3898-01A-01W-1073-09	15277131	114901075	20633672	63	6972										
PNLIPRP3	119548	broad.mit.edu	37	chr10	118220738	118220738	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tacccaaatggagggaagcaCatgccaggatgtgaagactt	12	8	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:118220738C>T	ENST00000369230.3	+	7	890	c.744C>T	c.(742-744)caC>caT	p.H248H		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	248					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.H248H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GAGGGAAGCACATGCCAGGAT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	10											159	152	154					10																	118220738		2203	4300	6503	118210728	SO:0001819	synonymous_variant	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.744C>T	10.37:g.118220738C>T			118210728		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.353	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		T	118220738	C	T	118220738	2	4	51	1	0	0	0	0	0	0	0	1	12183	477	17	3		3	PNLIPRP3	10	118220738	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	3319663	118220738	17314009	64	6973										
LHPP	64077	broad.mit.edu	37	chr10	126176996	126176996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tctctctctttccaggagtcCgctcagaatttgatcagatc	7	12	4	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr10:126176996C>T	ENST00000368842.5	+	3	347	c.319C>T	c.(319-321)Cgc>Tgc	p.R107C	LHPP_ENST00000392757.4_Missense_Mutation_p.R107C|LHPP_ENST00000368839.1_Missense_Mutation_p.R107C	NM_022126.3	NP_071409.3	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	107					phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|phosphohistidine phosphatase activity (GO:0008969)|protein homodimerization activity (GO:0042803)	p.R107C(1)		large_intestine(2)|lung(2)	4		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		TCCAGGAGTCCGCTCAGAATT	0.507																																					GBM(165;1980 2715 15999 18454)											1	Substitution - Missense(1)	large_intestine(1)	10											85	85	85					10																	126176996		2203	4300	6503	126166986	SO:0001583	missense	64077			AB049629	CCDS7640.1, CCDS53587.1	10q26.2	2010-02-17			ENSG00000107902	ENSG00000107902	3.6.1.1		30042	protein-coding gene	gene with protein product						12801912, 16430861	Standard	NM_022126		Approved	HDHD2B	uc001lhs.2	Q9H008	OTTHUMG00000019214	ENST00000368842.5:c.319C>T	10.37:g.126176996C>T	ENSP00000357835:p.Arg107Cys		126166986	B3KP20|Q2TBE9|Q5VUV9|Q5VUW0	Missense_Mutation	SNP	ENST00000368842.5	37	CCDS7640.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490540	0.64074	.	.	ENSG00000107902	ENST00000392757;ENST00000368842;ENST00000368839	T;T;T	0.23754	1.89;1.89;1.89	5.04	5.04	0.67666	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Nitrophenylphosphatase-like  domain (1);	0.244845	0.35151	N	0.003411	T	0.44519	0.1297	M	0.66506	2.035	0.51482	D	0.999928	D;D;P	0.76494	0.999;0.998;0.945	P;P;P	0.59357	0.856;0.695;0.762	T	0.23547	-1.0185	10	0.37606	T	0.19	-18.4755	15.4244	0.75041	0.0:0.8511:0.1488:0.0	.	107;107;107	Q5T1Z0;Q9H008-2;Q9H008	.;.;LHPP_HUMAN	C	107	ENSP00000376512:R107C;ENSP00000357835:R107C;ENSP00000357832:R107C	ENSP00000357832:R107C	R	+	1	0	LHPP	126166986	1.000000	0.71417	0.998000	0.56505	0.840000	0.47671	2.296000	0.43584	2.512000	0.84698	0.655000	0.94253	CGC		0.507	LHPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050870.1	NM_022126		T	126176996	C	T	126176996	3	4	51	1	0	0	0	0	1	0	0	0	8792	652	23	1	329	1	LHPP	10	126176996	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	7956258	126176996	9357751	65	6974										
OR2AG2	338755	broad.mit.edu	37	chr11	6789509	6789509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcccctcatttgatggcataCgaagcacagtgaataggact	9	10	1	2	rs569276635		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr11:6789509C>T	ENST00000338569.2	-	1	777	c.680G>A	c.(679-681)cGt>cAt	p.R227H		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R227H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGATGGCATACGAAGCACAGT	0.483													C|||	1	0.000199681	0	0	5008	,	,		19355	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											98	85	89					11																	6789509		2201	4296	6497	6746085	SO:0001583	missense	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"GPCR / Class A : Olfactory receptors"	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.680G>A	11.37:g.6789509C>T	ENSP00000342697:p.Arg227His		6746085		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.702188	0.00719	.	.	ENSG00000188124	ENST00000338569	T	0.00262	8.4	4.47	-3.56	0.04626	GPCR, rhodopsin-like superfamily (1);	0.499410	0.18634	N	0.135502	T	0.00109	0.0003	L	0.35854	1.095	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28996	-1.0026	10	0.13853	T	0.58	.	6.003	0.19531	0.1199:0.3487:0.0:0.5314	.	227	A6NM03	O2AG2_HUMAN	H	227	ENSP00000342697:R227H	ENSP00000342697:R227H	R	-	2	0	OR2AG2	6746085	0.000000	0.05858	0.103000	0.21229	0.008000	0.06430	-2.009000	0.01455	-0.688000	0.05155	-2.240000	0.00288	CGT		0.483	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		T	6789509	C	T	6789509	3	4	51	1	0	0	0	0	1	0	0	0	11016	536	19	1	274	1	OR2AG2	11	6789509	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		6789509	128217007	66	6975										
TNKS1BP1	85456	broad.mit.edu	37	chr11	57076324	57076324	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gcccctggggccatgtttctCagcccaaggtcaggtgtcca	12	14	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr11:57076324C>T	ENST00000532437.1	-	5	4172	c.3861G>A	c.(3859-3861)ctG>ctA	p.L1287L	TNKS1BP1_ENST00000358252.3_Silent_p.L1287L|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1287	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)	p.L1287L(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CCATGTTTCTCAGCCCAAGGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	11											109	110	110					11																	57076324		2201	4296	6497	56832900	SO:0001819	synonymous_variant	85456			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3861G>A	11.37:g.57076324C>T			56832900	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																				0.597	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57076324	C	T	57076324	2	4	51	1	0	0	0	0	0	0	0	1	16359	813	29	3		3	TNKS1BP1	11	57076324	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	50286815	57076324	77930192	67	6976										
FADS2	9415	broad.mit.edu	37	chr11	61607828	61607828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaagatcactgaggacttccGggccctgaggaagacggctg	14	10	1	4			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr11:61607828G>A	ENST00000278840.4	+	3	971	c.341G>A	c.(340-342)cGg>cAg	p.R114Q	FADS2_ENST00000257261.6_Missense_Mutation_p.R92Q|FADS2_ENST00000521849.1_Missense_Mutation_p.R114Q|FADS2_ENST00000522056.1_Missense_Mutation_p.R83Q	NM_004265.2	NP_004256.1	O95864	FADS2_HUMAN	fatty acid desaturase 2	114					alpha-linolenic acid metabolic process (GO:0036109)|linoleic acid metabolic process (GO:0043651)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.R114Q(1)		breast(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20					Alpha-Linolenic Acid(DB00132)	GAGGACTTCCGGGCCCTGAGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	11											108	101	104					11																	61607828		2202	4299	6501	61364404	SO:0001583	missense	9415			AF084559	CCDS8012.1, CCDS60807.1, CCDS60808.1	11q12.2	2013-01-25			ENSG00000134824	ENSG00000134824	1.14.19.3	"Fatty acid desaturases"	3575	protein-coding gene	gene with protein product	"delta-6-desaturase"	606149		LLCDL2			Standard	NM_004265		Approved	FADSD6, D6D, TU13, DES6, SLL0262	uc001nsl.1	O95864	OTTHUMG00000163794	ENST00000278840.4:c.341G>A	11.37:g.61607828G>A	ENSP00000278840:p.Arg114Gln		61364404	A8K2M6|B7Z634|Q6MZQ7|Q96H07|Q96SV8|Q9H3G3|Q9Y3X4	Missense_Mutation	SNP	ENST00000278840.4	37	CCDS8012.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.866504	0.32977	.	.	ENSG00000134824	ENST00000257261;ENST00000522056;ENST00000278840;ENST00000521849	T;T;T;T	0.27104	1.69;1.69;1.74;1.69	4.65	2.79	0.32731	.	0.125201	0.34435	N	0.003963	T	0.21841	0.0526	L	0.55990	1.75	0.43777	D	0.996309	B;B;B;B	0.31859	0.343;0.136;0.053;0.322	B;B;B;B	0.24848	0.042;0.024;0.036;0.056	T	0.03717	-1.1010	10	0.42905	T	0.14	-5.6524	10.4506	0.44520	0.1609:0.0:0.8391:0.0	.	83;114;114;92	B7Z634;O95864;O95864-3;O95864-2	.;FADS2_HUMAN;.;.	Q	92;83;114;114	ENSP00000257261:R92Q;ENSP00000429500:R83Q;ENSP00000278840:R114Q;ENSP00000431091:R114Q	ENSP00000257261:R92Q	R	+	2	0	FADS2	61364404	1.000000	0.71417	0.992000	0.48379	0.512000	0.34134	4.497000	0.60367	0.592000	0.29728	0.436000	0.28706	CGG		0.552	FADS2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375586.2	NM_004265		A	61607828	G	A	61607828	3	1	51	1	0	0	0	0	1	0	0	0	5382	1116	39	1	351	1	FADS2	11	61607828	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	4531504	61607828	73398688	68	6977										
GRIA4	2893	broad.mit.edu	37	chr11	105774640	105774640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctcaaggagaggaaatgctgGggattgtctggcaaatcctg	14	7	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr11:105774640G>A	ENST00000530497.1	+	7	986	c.986G>A	c.(985-987)gGg>gAg	p.G329E	GRIA4_ENST00000282499.5_Missense_Mutation_p.G329E|GRIA4_ENST00000393125.2_Missense_Mutation_p.G329E|GRIA4_ENST00000525187.1_Missense_Mutation_p.G329E|GRIA4_ENST00000393127.2_Missense_Mutation_p.G329E|GRIA4_ENST00000428631.2_Missense_Mutation_p.G329E			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	329					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.G329E(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GGAAATGCTGGGGATTGTCTG	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	11											110	112	111					11																	105774640		2202	4299	6501	105279850	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.986G>A	11.37:g.105774640G>A	ENSP00000435775:p.Gly329Glu		105279850	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	34	5.344065	0.95807	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	T;T;T;T;T;T	0.19105	2.17;2.71;2.55;2.17;2.71;2.55	5.63	5.63	0.86233	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	T	0.49490	0.1560	M	0.71581	2.175	0.80722	D	1	P;D;D	0.89917	0.956;1.0;1.0	P;D;D	0.97110	0.67;1.0;0.992	T	0.45352	-0.9267	10	0.72032	D	0.01	.	20.0499	0.97621	0.0:0.0:1.0:0.0	.	329;329;329	P48058;G3V164;Q86XE8	GRIA4_HUMAN;.;.	E	329	ENSP00000376833:G329E;ENSP00000282499:G329E;ENSP00000376835:G329E;ENSP00000415551:G329E;ENSP00000435775:G329E;ENSP00000432180:G329E	ENSP00000282499:G329E	G	+	2	0	GRIA4	105279850	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	9.420000	0.97426	2.798000	0.96311	0.655000	0.94253	GGG		0.438	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105774640	G	A	105774640	3	1	51	1	0	0	0	0	1	0	0	0	6791	1232	43	3	1012	3	GRIA4	11	105774640	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	44166812	105774640	29231876	69	6978										
KCNA6	3742	broad.mit.edu	37	chr12	4919894	4919894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gaggaagaggaggatgaagaCgattcctacacatttcatca	11	7	2	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr12:4919894C>T	ENST00000280684.3	+	1	1553	c.687C>T	c.(685-687)gaC>gaT	p.D229D	KCNA6_ENST00000433855.1_Silent_p.D229D|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	229					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.D229D(1)		NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	AGGATGAAGACGATTCCTACA	0.557										HNSCC(72;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											91	91	91					12																	4919894		2203	4300	6503	4790155	SO:0001819	synonymous_variant	3742			X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.687C>T	12.37:g.4919894C>T			4790155		Silent	SNP	ENST00000280684.3	37	CCDS8534.1																																																																																				0.557	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		T	4919894	C	T	4919894	2	4	51	1	0	0	0	0	0	0	0	1	8028	535	19	1		1	KCNA6	12	4919894	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09		4919894	128932001	70	6979										
SLC38A1	81539	broad.mit.edu	37	chr12	46601356	46601356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctccaaagattacgaacttcCctgtggtgccaaagacttgt	8	11	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr12:46601356C>T	ENST00000398637.5	-	7	1131	c.437G>A	c.(436-438)gGg>gAg	p.G146E	SLC38A1_ENST00000439706.1_Missense_Mutation_p.G146E|SLC38A1_ENST00000549049.1_Missense_Mutation_p.G146E|SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000552197.1_Missense_Mutation_p.G146E|SLC38A1_ENST00000546893.1_Missense_Mutation_p.G146E	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	146					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.G146E(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	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)			TACGAACTTCCCTGTGGTGCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											125	123	124					12																	46601356		1843	4089	5932	44887623	SO:0001583	missense	81539			AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.437G>A	12.37:g.46601356C>T	ENSP00000381634:p.Gly146Glu		44887623	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.042850	0.93685	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197	T;T;T;T;T	0.02631	4.22;4.22;4.22;4.22;4.22	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000001	T	0.20740	0.0499	M	0.87900	2.915	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.994;0.986	T	0.00525	-1.1689	10	0.87932	D	0	-10.9887	19.6512	0.95812	0.0:1.0:0.0:0.0	.	146;146;146	B5MEC5;F8VX04;Q9H2H9	.;.;S38A1_HUMAN	E	146	ENSP00000449607:G146E;ENSP00000398142:G146E;ENSP00000381634:G146E;ENSP00000447853:G146E;ENSP00000449756:G146E	ENSP00000381634:G146E	G	-	2	0	SLC38A1	44887623	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.435000	0.80391	2.646000	0.89796	0.563000	0.77884	GGG		0.403	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			T	46601356	C	T	46601356	3	4	51	1	0	0	0	0	1	0	0	0	14638	623	22	3	1070	3	SLC38A1	12	46601356	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	41681462	46601356	87250539	71	6980										
CEP290	80184	broad.mit.edu	37	chr12	88524943	88524943	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aactactaaaattttttaccTctcttcttaatttgctgttt	2	8	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr12:88524943T>A	ENST00000552810.1	-	7	837	c.494A>T	c.(493-495)gAg>gTg	p.E165V	CEP290_ENST00000397838.3_5'Flank|CEP290_ENST00000309041.7_Splice_Site_p.E165V	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	165					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.E165V(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATTTTTTACCTCTCTTCTTAA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	12											93	88	90					12																	88524943		1768	4039	5807	87049074	SO:0001630	splice_region_variant	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.495+1A>T	12.37:g.88524943T>A			87049074	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949217	0.92660	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.70282	-0.47;-0.47	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.74245	0.3691	L	0.27053	0.805	0.80722	D	1	D	0.67145	0.996	D	0.64410	0.925	T	0.76088	-0.3087	10	0.48119	T	0.1	.	15.555	0.76187	0.0:0.0:0.0:1.0	.	165	O15078	CE290_HUMAN	V	165;165;165;67	ENSP00000448012:E165V;ENSP00000308021:E165V	ENSP00000308021:E165V	E	-	2	0	CEP290	87049074	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.293000	0.72731	2.081000	0.62600	0.460000	0.39030	GAG		0.279	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	Missense_Mutation	A	88524943	T	A	88524943	5	1	51	1	0	0	0	0	0	0	1	0	3259	1565	54	5	7137	5	CEP290	12	88524943	Splice_Site	SNP	T	TCGA-AG-3898-01A-01W-1073-09	41923587	88524943	45326952	72	6981										
TMPO	7112	broad.mit.edu	37	chr12	98927741	98927741	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcagcagttggacttagcacTctgtagagcatatgaagctg	11	8	2	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr12:98927741T>G	ENST00000556029.1	+	3	921				TMPO_ENST00000266732.4_Missense_Mutation_p.L569R|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000261210.5_Intron|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)	p.L569R(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GACTTAGCACTCTGTAGAGCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											75	66	69					12																	98927741		2203	4300	6503	97451872	SO:0001627	intron_variant	7112				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.565+2125T>G	12.37:g.98927741T>G			97451872	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.119622	0.56613	.	.	ENSG00000120802	ENST00000266732	T	0.64618	-0.11	5.96	5.96	0.96718	.	0.388184	0.28279	N	0.015929	T	0.66665	0.2812	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.70208	-0.4935	10	0.66056	D	0.02	-2.9727	12.8402	0.57797	0.0:0.0:0.0:1.0	.	569	P42166	LAP2A_HUMAN	R	569	ENSP00000266732:L569R	ENSP00000266732:L569R	L	+	2	0	TMPO	97451872	0.994000	0.37717	0.465000	0.27155	0.932000	0.56968	3.640000	0.54350	2.285000	0.76669	0.533000	0.62120	CTC		0.468	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		G	98927741	T	G	98927741	1	3	51	0	1	0	0	0	0	0	0	0	16276	1551	54	4		4	TMPO	12	98927741	Intron	SNP	T	TCGA-AG-3898-01A-01W-1073-09	10402798	98927741	34924154	73	6982										
FAM109A	144717	broad.mit.edu	37	chr12	111801236	111801236	+	5'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gctcgttcagcttcatggtgGcaatcgcggggcctggaggg	17	10	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr12:111801236G>A	ENST00000547838.2	-	0	93				FAM109A_ENST00000361483.3_Missense_Mutation_p.A12V|FAM109A_ENST00000392658.5_5'UTR|FAM109A_ENST00000548163.1_5'UTR|FAM109A_ENST00000450786.2_5'UTR			Q8N4B1	SESQ1_HUMAN	family with sequence similarity 109, member A						endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)	p.A12V(1)		breast(1)|endometrium(1)|lung(1)|ovary(1)	4						CTTCATGGTGGCAATCGCGGG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											13	16	15					12																	111801236		2192	4274	6466	110285619	SO:0001623	5_prime_UTR_variant	144717			BC034809	CCDS9152.1, CCDS53833.1	12q24.12	2013-01-10			ENSG00000198324	ENSG00000198324		"Pleckstrin homology (PH) domain containing"	26509	protein-coding gene	gene with protein product		614239				12477932	Standard	NM_144671		Approved	FLJ32356	uc009zvu.3	Q8N4B1	OTTHUMG00000169547	ENST00000547838.2:c.-5C>T	12.37:g.111801236G>A			110285619	J3KP50|Q6PJL9|Q96MH8	Missense_Mutation	SNP	ENST00000547838.2	37	CCDS9152.1	.	.	.	.	.	.	.	.	.	.	G	8.996	0.978988	0.18812	.	.	ENSG00000198324	ENST00000361483	T	0.30714	1.52	4.2	-0.249	0.13011	.	.	.	.	.	T	0.24774	0.0601	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26643	-1.0097	6	0.38643	T	0.18	.	6.2364	0.20766	0.2024:0.5076:0.29:0.0	.	.	.	.	V	12	ENSP00000354461:A12V	ENSP00000354461:A12V	A	-	2	0	FAM109A	110285619	0.001000	0.12720	0.000000	0.03702	0.032000	0.12392	0.708000	0.25719	-0.448000	0.07128	-0.304000	0.09214	GCC		0.652	FAM109A-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404768.2	NM_144671		A	111801236	G	A	111801236	1	1	51	0	1	0	0	0	0	0	0	0	5410	1203	42	3		3	FAM109A	12	111801236	5'UTR	SNP	G	TCGA-AG-3898-01A-01W-1073-09	12873495	111801236	22050659	74	6983										
LRCH1	23143	broad.mit.edu	37	chr13	47260087	47260087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttgacttttcctgcaacaaaGtgctcgtgattccaatttgt	7	9	0	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr13:47260087G>A	ENST00000389798.3	+	5	930	c.733G>A	c.(733-735)Gtg>Atg	p.V245M	LRCH1_ENST00000389797.3_Missense_Mutation_p.V245M|LRCH1_ENST00000311191.6_Missense_Mutation_p.V245M	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	245								p.V245M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CTGCAACAAAGTGCTCGTGAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	13											62	58	59					13																	47260087		2203	4300	6503	46158088	SO:0001583	missense	23143			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.733G>A	13.37:g.47260087G>A	ENSP00000374448:p.Val245Met		46158088	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419222	0.83559	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.18960	2.18;2.18;2.18	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.48370	0.1496	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.994	D;D;D;D	0.97110	0.999;1.0;0.999;0.972	T	0.38520	-0.9657	10	0.87932	D	0	-20.2544	19.3421	0.94347	0.0:0.0:1.0:0.0	.	245;245;245;245	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	M	245	ENSP00000308493:V245M;ENSP00000374448:V245M;ENSP00000374447:V245M	ENSP00000308493:V245M	V	+	1	0	LRCH1	46158088	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.192000	0.72069	2.826000	0.97356	0.655000	0.94253	GTG		0.363	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		A	47260087	G	A	47260087	3	1	51	1	0	0	0	0	1	0	0	0	8961	1029	36	3	751	3	LRCH1	13	47260087	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		47260087	67909791	75	6984										
PCDH17	27253	broad.mit.edu	37	chr13	58208285	58208285	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	cccacgaacggggccatctaCgccctgcgctcctttaactt	8	17	1	0	rs143619660		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr13:58208285C>T	ENST00000377918.3	+	1	1631	c.1605C>T	c.(1603-1605)taC>taT	p.Y535Y		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	535	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y535Y(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GGGCCATCTACGCCCTGCGCT	0.587																																					Melanoma(72;952 1291 1619 12849 33676)											1	Substitution - coding silent(1)	large_intestine(1)	13						C		0,4406		0,0,2203	52	51	51		1605	-0.6	1	13	dbSNP_134	51	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PCDH17	NM_001040429.2		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		535/1160	58208285	3,13003	2203	4300	6503	57106286	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1605C>T	13.37:g.58208285C>T			57106286	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.587	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58208285	C	T	58208285	2	4	51	1	0	0	0	0	0	0	0	1	11543	547	19	1		1	PCDH17	13	58208285	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	10948198	58208285	56961593	76	6985										
ARHGEF7	8874	broad.mit.edu	37	chr13	111926252	111926252	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgagcaaacccttcatgcgcCtggataaataccctacgctg	8	13	1	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr13:111926252C>T	ENST00000375741.2	+	11	1478	c.1228C>T	c.(1228-1230)Ctg>Ttg	p.L410L	ARHGEF7_ENST00000317133.5_Silent_p.L389L|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000375723.1_Silent_p.L232L|ARHGEF7_ENST00000375736.4_Silent_p.L232L|ARHGEF7_ENST00000375737.5_Silent_p.L307L|ARHGEF7_ENST00000370623.3_Silent_p.L317L|ARHGEF7_ENST00000218789.5_Silent_p.L232L|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000375739.2_Silent_p.L360L|ARHGEF7_ENST00000426073.2_Silent_p.L232L|ARHGEF7_ENST00000478679.1_Silent_p.L154L	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	410	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L232L(1)|p.L389L(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	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)			CTTCATGCGCCTGGATAAATA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	13											87	78	81					13																	111926252		2203	4300	6503	110724253	SO:0001819	synonymous_variant	8874			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1228C>T	13.37:g.111926252C>T			110724253	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																				0.552	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		T	111926252	C	T	111926252	2	4	51	1	0	0	0	0	0	0	0	1	911	680	24	3		3	ARHGEF7	13	111926252	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	53717967	111926252	3243626	77	6986										
MKRN3	7681	broad.mit.edu	37	chr15	23811699	23811699	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	agtttgctttcgtggggagaGctgtatgtacctccatggag	14	7	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr15:23811699G>T	ENST00000314520.3	+	1	1246	c.770G>T	c.(769-771)aGc>aTc	p.S257I	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568945.1_3'UTR|MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	257					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.S257I(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		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)		CGTGGGGAGAGCTGTATGTAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											106	110	109					15																	23811699		2203	4300	6503	21362792	SO:0001583	missense	7681			U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.770G>T	15.37:g.23811699G>T	ENSP00000313881:p.Ser257Ile		21362792		Missense_Mutation	SNP	ENST00000314520.3	37	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.703121	0.30232	.	.	ENSG00000179455	ENST00000314520	T	0.48522	0.81	4.07	1.09	0.20402	Zinc finger, CCCH-type (2);	0.198500	0.52532	D	0.000066	T	0.43055	0.1230	M	0.73217	2.22	0.26912	N	0.966869	P	0.44578	0.838	B	0.41691	0.364	T	0.37174	-0.9717	10	0.51188	T	0.08	.	6.805	0.23772	0.3743:0.0:0.6257:0.0	.	257	Q13064	MKRN3_HUMAN	I	257	ENSP00000313881:S257I	ENSP00000313881:S257I	S	+	2	0	MKRN3	21362792	1.000000	0.71417	0.429000	0.26710	0.075000	0.17131	2.761000	0.47589	0.258000	0.21686	0.655000	0.94253	AGC		0.542	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		T	23811699	G	T	23811699	3	4	51	1	0	0	0	0	1	0	0	0	9638	971	34	2	772	2	MKRN3	15	23811699	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		23811699	78719693	78	6987										
ATP10A	57194	broad.mit.edu	37	chr15	25947069	25947069	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgaaacccacctacctgggaGgtggcattcagggtgatgac	13	10	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr15:25947069G>T	ENST00000356865.6	-	13	2865	c.2754C>A	c.(2752-2754)acC>acA	p.T918T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	918					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.T918T(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTACCTGGGAGGTGGCATTCA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	15											151	130	137					15																	25947069		2203	4300	6503	23498162	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2754C>A	15.37:g.25947069G>T			23498162	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.552	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25947069	G	T	25947069	2	4	51	1	0	0	0	0	0	0	0	1	1117	987	35	2		2	ATP10A	15	25947069	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	2135370	25947069	76584323	79	6988										
SEMA6D	80031	broad.mit.edu	37	chr15	48063804	48063804	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggtggactatattcagggaaCaccagtgagtgttcatctgc	12	8	3	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr15:48063804C>A	ENST00000316364.5	+	19	3483	c.3044C>A	c.(3043-3045)aCa>aAa	p.T1015K	SEMA6D_ENST00000389433.2_Missense_Mutation_p.T996K|SEMA6D_ENST00000537942.1_Missense_Mutation_p.T953K|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389428.3_Missense_Mutation_p.T940K|SEMA6D_ENST00000354744.4_Missense_Mutation_p.T959K|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Missense_Mutation_p.T953K|SEMA6D_ENST00000389432.2_Missense_Mutation_p.T972K|SEMA6D_ENST00000536845.2_Missense_Mutation_p.T1015K|SEMA6D_ENST00000558014.1_Missense_Mutation_p.T953K	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	1015					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.T1015K(1)		biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ATTCAGGGAACACCAGTGAGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											125	118	121					15																	48063804		2198	4297	6495	45851096	SO:0001583	missense	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.3044C>A	15.37:g.48063804C>A	ENSP00000324857:p.Thr1015Lys		45851096	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.228819	0.39399	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.17854	2.26;2.29;2.29;2.28;2.25;2.25;2.26;2.26	5.8	5.8	0.92144	.	0.282280	0.39615	N	0.001320	T	0.14960	0.0361	L	0.29908	0.895	0.80722	D	1	B;B;B;P	0.35684	0.056;0.099;0.381;0.515	B;B;B;B	0.29267	0.033;0.075;0.046;0.1	T	0.02526	-1.1146	10	0.42905	T	0.14	.	20.0693	0.97712	0.0:1.0:0.0:0.0	.	940;959;1015;953	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	K	953;1015;1015;996;972;959;953;940	ENSP00000442040:T953K;ENSP00000446152:T1015K;ENSP00000324857:T1015K;ENSP00000374084:T996K;ENSP00000374083:T972K;ENSP00000346786:T959K;ENSP00000350770:T953K;ENSP00000374079:T940K	ENSP00000324857:T1015K	T	+	2	0	SEMA6D	45851096	1.000000	0.71417	0.996000	0.52242	0.865000	0.49528	3.520000	0.53465	2.758000	0.94735	0.563000	0.77884	ACA		0.517	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48063804	C	A	48063804	3	1	51	1	0	0	0	0	1	0	0	0	14079	478	17	2	3157	2	SEMA6D	15	48063804	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	22116735	48063804	54467588	80	6989										
RNPS1	10921	broad.mit.edu	37	chr16	2312776	2312776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggtgagtctcccaatgtgcaCtttggtgggcttaggagatg	15	7	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr16:2312776C>T	ENST00000565678.1	-	5	1032	c.487G>A	c.(487-489)Gtg>Atg	p.V163M	RNPS1_ENST00000566458.1_Missense_Mutation_p.V140M|RNPS1_ENST00000568631.1_Missense_Mutation_p.V163M|RNPS1_ENST00000566397.1_De_novo_Start_InFrame|RNPS1_ENST00000397086.2_Missense_Mutation_p.V163M|RNPS1_ENST00000301730.8_Missense_Mutation_p.V163M|RNPS1_ENST00000320225.5_Missense_Mutation_p.V163M|RNPS1_ENST00000561718.1_De_novo_Start_InFrame|RNPS1_ENST00000569598.2_Missense_Mutation_p.V69M|RNPS1_ENST00000567147.1_Missense_Mutation_p.V140M			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	163	Interaction with SAP18 and ACIN1.|Necessary for interaction with PNN and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.V163M(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						CCAATGTGCACTTTGGTGGGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											137	114	122					16																	2312776		2198	4300	6498	2252777	SO:0001583	missense	10921			AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"RNA binding motif (RRM) containing"	10080	protein-coding gene	gene with protein product		606447	"RNA-binding protein S1, serine-rich domain"			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.487G>A	16.37:g.2312776C>T	ENSP00000457723:p.Val163Met		2252777	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Missense_Mutation	SNP	ENST00000565678.1	37	CCDS10465.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.460290	0.63401	.	.	ENSG00000205937	ENST00000320225;ENST00000397086;ENST00000301730	T;T;T	0.54279	0.58;0.58;0.58	5.95	5.95	0.96441	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.437565	0.24303	N	0.039710	T	0.72104	0.3419	M	0.66560	2.04	0.50039	D	0.999841	D;D	0.71674	0.997;0.998	D;D	0.75484	0.984;0.986	T	0.72646	-0.4230	10	0.72032	D	0.01	-10.323	17.8666	0.88796	0.0:1.0:0.0:0.0	.	140;163	Q15287-2;Q15287	.;RNPS1_HUMAN	M	163	ENSP00000315859:V163M;ENSP00000380275:V163M;ENSP00000301730:V163M	ENSP00000301730:V163M	V	-	1	0	RNPS1	2252777	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	4.387000	0.59626	2.826000	0.97356	0.579000	0.79373	GTG		0.498	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594		T	2312776	C	T	2312776	3	4	51	1	0	0	0	0	1	0	0	0	13548	565	20	3	446	3	RNPS1	16	2312776	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09		2312776	88041977	81	6990										
POLR3E	55718	broad.mit.edu	37	chr16	22326413	22326413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tccccttcccaccgcaggtgCggttctcccggccggagtca	11	18	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr16:22326413C>T	ENST00000299853.5	+	9	693	c.526C>T	c.(526-528)Cgg>Tgg	p.R176W	POLR3E_ENST00000564209.1_Missense_Mutation_p.R176W|POLR3E_ENST00000418581.2_Missense_Mutation_p.R140W|POLR3E_ENST00000359210.4_Missense_Mutation_p.R176W	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	176					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)	p.R176W(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		ACCGCAGGTGCGGTTCTCCCG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	16											44	40	41					16																	22326413		2197	4300	6497	22233914	SO:0001583	missense	55718			AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.526C>T	16.37:g.22326413C>T	ENSP00000299853:p.Arg176Trp		22233914	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	37	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333288	0.81801	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	T;T;T	0.52057	0.68;0.68;0.68	5.47	5.47	0.80525	.	0.052732	0.85682	D	0.000000	T	0.67011	0.2848	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.997;0.994;0.998;0.995;0.997;0.997	T	0.69669	-0.5083	10	0.87932	D	0	-25.3685	14.9971	0.71439	0.143:0.857:0.0:0.0	.	120;140;176;176;176;176	B4DDR0;B4DL24;B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;.;.;RPC5_HUMAN;.	W	176;176;140	ENSP00000299853:R176W;ENSP00000352140:R176W;ENSP00000399254:R140W	ENSP00000299853:R176W	R	+	1	2	POLR3E	22233914	0.999000	0.42202	0.998000	0.56505	0.879000	0.50718	3.020000	0.49643	2.553000	0.86117	0.655000	0.94253	CGG		0.637	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		T	22326413	C	T	22326413	3	4	51	1	0	0	0	0	1	0	0	0	12263	759	27	1	556	1	POLR3E	16	22326413	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	20013637	22326413	68028340	82	6991										
USP10	9100	broad.mit.edu	37	chr16	84806210	84806210	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcctcgtgctgcacctgaaaCgattcgtttatgagaagact	9	10	0	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr16:84806210C>T	ENST00000219473.7	+	12	2175	c.2062C>T	c.(2062-2064)Cga>Tga	p.R688*	USP10_ENST00000570191.1_Nonsense_Mutation_p.R692*	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	688	USP.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R688*(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GCACCTGAAACGATTCGTTTA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											176	171	173					16																	84806210		1952	4155	6107	83363711	SO:0001587	stop_gained	9100			D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"Ubiquitin-specific peptidases"	12608	protein-coding gene	gene with protein product		609818	"ubiquitin specific protease 10"			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.2062C>T	16.37:g.84806210C>T	ENSP00000219473:p.Arg688*		83363711	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Nonsense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656867	0.47467	.	.	ENSG00000103194	ENST00000219473	.	.	.	4.38	4.38	0.52667	.	0.133168	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.3595	13.0564	0.58982	0.161:0.839:0.0:0.0	.	.	.	.	X	688	.	ENSP00000219473:R688X	R	+	1	2	USP10	83363711	0.983000	0.35010	0.829000	0.32907	0.204000	0.24138	2.270000	0.43355	2.157000	0.67596	0.563000	0.77884	CGA		0.443	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			T	84806210	C	T	84806210	4	4	51	1	0	0	0	0	0	1	0	0	17081	528	19	1	2108	1	USP10	16	84806210	Nonsense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	62479797	84806210	5548543	83	6992										
TP53	7157	broad.mit.edu	37	chr17	7576891	7576892	+	Frame_Shift_Ins	INS	-	-	TGGC													0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ccatccagtggtttcttcttINStggctggggagaggagctgg							TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:7576891_7576892insTGGC	ENST00000269305.4	-	9	1143_1144	c.954_955insGCCA	c.(952-957)ccaaagfs	p.PK318fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.PK318fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Frame_Shift_Ins_p.PK318fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.PK318fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.PK318fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	318	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		P -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.K319*(8)|p.P318fs*15(2)|p.K319fs*19(2)|p.K319E(2)|p.P318fs*21(1)|p.S315fs*22(1)|p.?(1)|p.S314fs*25(1)|p.L308fs*15(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGTTTCTTCTTTGGCTGGGGAG	0.47		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	27	Substitution - Nonsense(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Insertion - Frameshift(2)|Substitution - Missense(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(6)|bone(4)|upper_aerodigestive_tract(3)|breast(3)|large_intestine(2)|stomach(2)|central_nervous_system(2)|urinary_tract(1)|lung(1)|skin(1)|ovary(1)|liver(1)	17																																								7517617	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.951_954dupGCCA	17.37:g.7576892_7576895dupTGGC	ENSP00000269305:p.Pro318fs		7517616	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.47	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		TGGC	7576892	-	TGGC	7576891	7	5	51	1	0	1	1	0	0	0	0	0	16421	1850	64	0	327	0	TP53	17	7576891	Frame_Shift_Ins	INS	-	TCGA-AG-3898-01A-01W-1073-09		7576891	73618319	84	6993										
NEK8	284086	broad.mit.edu	37	chr17	27064382	27064382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ctttgcacctatctctgaccGgtacagccctgagcttcgcc	8	16	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:27064382G>A	ENST00000268766.6	+	5	711	c.677G>A	c.(676-678)cGg>cAg	p.R226Q	AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R226Q(1)|p.R226L(1)		breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					ATCTCTGACCGGTACAGCCCT	0.587																																					NSCLC(6;19 293 14866 25253 49845)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	17											55	47	50					17																	27064382		2203	4300	6503	24088509	SO:0001583	missense	284086			AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.677G>A	17.37:g.27064382G>A	ENSP00000268766:p.Arg226Gln		24088509	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	37	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	g	18.26	3.585426	0.66105	.	.	ENSG00000160602	ENST00000543014;ENST00000268766	T;T	0.63913	-0.07;-0.07	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47619	0.1455	N	0.16656	0.425	0.80722	D	1	B	0.25486	0.127	B	0.21546	0.035	T	0.39643	-0.9604	10	0.15066	T	0.55	.	19.2155	0.93776	0.0:0.0:1.0:0.0	.	226	Q86SG6	NEK8_HUMAN	Q	226	ENSP00000465859:R226Q;ENSP00000268766:R226Q	ENSP00000268766:R226Q	R	+	2	0	NEK8	24088509	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	7.787000	0.85759	2.779000	0.95612	0.651000	0.88453	CGG		0.587	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			A	27064382	G	A	27064382	3	1	51	1	0	0	0	0	1	0	0	0	10361	1116	39	1	695	1	NEK8	17	27064382	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	19487491	27064382	54130828	85	6994										
LASP1	3927	broad.mit.edu	37	chr17	37074956	37074956	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aacgtgcagcagatcgacgaCggctggatgtacgggacggt	16	9	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:37074956C>T	ENST00000318008.6	+	7	1042	c.711C>T	c.(709-711)gaC>gaT	p.D237D	LASP1_ENST00000435347.3_Silent_p.D237D|LASP1_ENST00000433206.2_Silent_p.D181D|RP1-56K13.3_ENST00000580121.1_RNA	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	237	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)	p.D237D(1)		breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						AGATCGACGACGGCTGGATGT	0.657			T	MLL	AML																																		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	1	Substitution - coding silent(1)	large_intestine(1)	17											114	99	104					17																	37074956		2203	4300	6503	34328482	SO:0001819	synonymous_variant	3927				CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.711C>T	17.37:g.37074956C>T			34328482	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	37	CCDS11331.1																																																																																				0.657	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148		T	37074956	C	T	37074956	2	4	51	1	0	0	0	0	0	0	0	1	8659	535	19	1		1	LASP1	17	37074956	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	10010574	37074956	44120254	86	6995										
ERBB2	2064	broad.mit.edu	37	chr17	37881332	37881332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	acctggaggatgtgcggctcGtacacagggacttggccgct	15	11	0	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:37881332G>A	ENST00000269571.5	+	21	2683	c.2524G>A	c.(2524-2526)Gta>Ata	p.V842I	ERBB2_ENST00000584601.1_Missense_Mutation_p.V812I|ERBB2_ENST00000540147.1_Missense_Mutation_p.V812I|ERBB2_ENST00000445658.2_Missense_Mutation_p.V566I|ERBB2_ENST00000541774.1_Missense_Mutation_p.V827I|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000406381.2_Missense_Mutation_p.V812I|ERBB2_ENST00000584450.1_Missense_Mutation_p.V842I			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	842	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.V842I(6)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGTGCGGCTCGTACACAGGGA	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	6	Substitution - Missense(6)	large_intestine(5)|stomach(1)	17											70	61	64					17																	37881332		2203	4300	6503	35134858	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2524G>A	17.37:g.37881332G>A	ENSP00000269571:p.Val842Ile		35134858	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.241303	0.58995	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	5.09	5.09	0.68999	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.85106	0.5621	N	0.21142	0.635	0.80722	D	1	D;D;D	0.76494	0.997;0.979;0.999	D;P;D	0.64506	0.92;0.559;0.926	D	0.87344	0.2333	9	0.87932	D	0	.	18.2846	0.90110	0.0:0.0:1.0:0.0	.	566;827;842	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	I	812;827;566;842;812	ENSP00000385185:V812I;ENSP00000446466:V827I;ENSP00000404047:V566I;ENSP00000269571:V842I;ENSP00000443562:V812I	ENSP00000269571:V842I	V	+	1	0	ERBB2	35134858	1.000000	0.71417	0.919000	0.36401	0.900000	0.52787	9.657000	0.98554	2.651000	0.90000	0.563000	0.77884	GTA		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37881332	G	A	37881332	3	1	51	1	0	0	0	0	1	0	0	0	5219	1145	40	1	2606	1	ERBB2	17	37881332	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	806376	37881332	43313878	87	6996										
KRT38	8687	broad.mit.edu	37	chr17	39593678	39593678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aggaattcagaatcggcttcCggtggtgctggctccacagg	14	10	1	1	rs148086126	byFrequency	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:39593678C>T	ENST00000246646.3	-	7	1356	c.1357G>A	c.(1357-1359)Gga>Aga	p.G453R		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	453	Tail.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.G453R(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				AATCGGCTTCCGGTGGTGCTG	0.592													C|||	9	0.00179712	0	0	5008	,	,		17678	0		0.007	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	17						C	ARG/GLY	0,4406		0,0,2203	20	20	20		1357	1.2	0	17	dbSNP_134	20	3,8595		0,3,4296	yes	missense	KRT38	NM_006771.3	125	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	453/457	39593678	3,13001	2203	4299	6502	36847204	SO:0001583	missense	8687			Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.1357G>A	17.37:g.39593678C>T	ENSP00000246646:p.Gly453Arg		36847204	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	.	10.38	1.333283	0.24167	0.0	3.49E-4	ENSG00000171360	ENST00000246646	D	0.81659	-1.52	2.25	1.25	0.21368	.	0.722437	0.11102	N	0.599518	T	0.61949	0.2388	N	0.08118	0	0.09310	N	1	D	0.57899	0.981	P	0.53146	0.719	T	0.56932	-0.7897	10	0.54805	T	0.06	.	4.8148	0.13362	0.0:0.8159:0.0:0.1841	.	453	O76015	KRT38_HUMAN	R	453	ENSP00000246646:G453R	ENSP00000246646:G453R	G	-	1	0	KRT38	36847204	0.000000	0.05858	0.008000	0.14137	0.072000	0.16883	0.008000	0.13197	0.521000	0.28445	0.555000	0.69702	GGA		0.592	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		T	39593678	C	T	39593678	3	4	51	1	0	0	0	0	1	0	0	0	8496	661	23	1	17	1	KRT38	17	39593678	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	1712346	39593678	41601532	88	6997										
TNRC6C	57690	broad.mit.edu	37	chr17	76046266	76046266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcaccagccagaaccctaccGtacagcctggtggtgaacac	9	15	1	2	rs202206566		TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr17:76046266G>A	ENST00000588061.1	+	5	1850	c.1123G>A	c.(1123-1125)Gta>Ata	p.V375I	TNRC6C_ENST00000335749.4_Missense_Mutation_p.V375I|TNRC6C_ENST00000544502.1_Missense_Mutation_p.V375I|TNRC6C_ENST00000588847.1_Missense_Mutation_p.V375I|TNRC6C_ENST00000301624.4_Missense_Mutation_p.V375I|TNRC6C_ENST00000541771.1_Missense_Mutation_p.V375I			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	375	Gly-rich.|Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.V375I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GAACCCTACCGTACAGCCTGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											59	59	59					17																	76046266		1988	4154	6142	73557861	SO:0001583	missense	57690			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.1123G>A	17.37:g.76046266G>A	ENSP00000468647:p.Val375Ile		73557861	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	37	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	9.211	1.030999	0.19590	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	5.12	-9.34	0.00636	.	1.100860	0.07055	N	0.832741	T	0.05227	0.0139	N	0.14661	0.345	0.19300	N	0.999977	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.0	T	0.35525	-0.9785	10	0.21014	T	0.42	1.9699	4.9047	0.13793	0.5787:0.2184:0.0926:0.1103	.	375;375;375	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	I	375	ENSP00000336783:V375I;ENSP00000301624:V375I;ENSP00000440310:V375I;ENSP00000442421:V375I	ENSP00000301624:V375I	V	+	1	0	TNRC6C	73557861	0.376000	0.25098	0.244000	0.24202	0.880000	0.50808	-0.586000	0.05787	-1.757000	0.01316	0.655000	0.94253	GTA		0.522	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76046266	G	A	76046266	3	1	51	1	0	0	0	0	1	0	0	0	16381	1145	40	1	1125	1	TNRC6C	17	76046266	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	36452588	76046266	5148944	89	6998										
MUC16	94025	broad.mit.edu	37	chr19	9075143	9075143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ggtgcacttagtgatgtagcGccaggtggacttgtttgcat	14	7	0	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr19:9075143G>A	ENST00000397910.4	-	3	12506	c.12303C>T	c.(12301-12303)ggC>ggT	p.G4101G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4103	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.G4101G(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGATGTAGCGCCAGGTGGAC	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	19											123	119	120					19																	9075143		2102	4229	6331	8936143	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12303C>T	19.37:g.9075143G>A			8936143	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9075143	G	A	9075143	2	1	51	1	0	0	0	0	0	0	0	1	10003	1074	38	1		1	MUC16	19	9075143	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09		9075143	50053840	90	6999										
HKR1	284459	broad.mit.edu	37	chr19	37854172	37854172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	caaacaccagaggtcacacaCgggggagaagccatttgtat	11	10	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr19:37854172C>T	ENST00000324411.4	+	6	1744	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	HKR1_ENST00000591471.1_Missense_Mutation_p.T219M|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000392153.3_Missense_Mutation_p.T473M|HKR1_ENST00000544914.1_Missense_Mutation_p.T219M|HKR1_ENST00000541583.2_Missense_Mutation_p.T431M|HKR1_ENST00000589392.1_Missense_Mutation_p.T474M	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	492					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T492M(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGGTCACACACGGGGGAGAAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	80	81					19																	37854172		2203	4300	6503	42546012	SO:0001583	missense	284459			M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"Zinc fingers, C2H2-type", "-"	4928	protein-coding gene	gene with protein product	"oncogene HKR1"	165250	"GLI-Kruppel family member HKR1"			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.1475C>T	19.37:g.37854172C>T	ENSP00000315505:p.Thr492Met		42546012	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926900	0.34002	.	.	ENSG00000181666	ENST00000544914;ENST00000414402;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	3.04	0.571	0.17352	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50820	0.1638	M	0.89601	3.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.991	D;D;D;P	0.81914	0.995;0.988;0.958;0.638	T	0.53648	-0.8409	9	0.87932	D	0	.	6.5745	0.22557	0.1766:0.7113:0.0:0.1121	.	431;473;492;474	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	M	219;271;473;528;492;431	ENSP00000437774:T219M;ENSP00000375994:T473M;ENSP00000315505:T492M;ENSP00000438261:T431M	ENSP00000315505:T492M	T	+	2	0	HKR1	42546012	0.002000	0.14202	0.460000	0.27093	0.360000	0.29518	0.173000	0.16724	0.604000	0.29930	-0.145000	0.13849	ACG		0.537	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37854172	C	T	37854172	3	4	51	1	0	0	0	0	1	0	0	0	7215	536	19	1	1489	1	HKR1	19	37854172	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	28779029	37854172	21274811	91	7000										
SIGLEC11	114132	broad.mit.edu	37	chr19	50453238	50453239	+	Missense_Mutation	DNP	CC	CC	AA													0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gagacctcttcactttggaaCcatccctgacatctccctct							TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr19:50453238_50453239CC>AA	ENST00000447370.2	-	11	2175_2176	c.2085_2086GG>TT	c.(2083-2088)atGGtt>atTTtt	p.695_696MV>IF	CTC-326K19.6_ENST00000451973.1_Intron|U3_ENST00000408198.1_RNA|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.599_600MV>IF	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	695					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.M683>?(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		CACTTTGGAACCATCCCTGACA	0.579																																																1	Complex(1)	large_intestine(1)	19																																								55145051	SO:0001583	missense	114132			AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.2085_2086delinsAA	19.37:g.50453238_50453239delinsAA	ENSP00000412361:p.M695_V696delinsIF		55145050		Missense_Mutation	DNP	ENST00000447370.2	37	CCDS12790.2																																																																																				0.579	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		AA	50453239	CC	AA	50453238	3	1	51	1	0	0	0	0	1	0	0	0	14344	507	18	2	14	2	SIGLEC11	19	50453238	Missense_Mutation	DNP	CC	TCGA-AG-3898-01A-01W-1073-09	12599066	50453238	8675745	92	7001										
ZNF578	147660	broad.mit.edu	37	chr19	53014180	53014180	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	attgctaatcaagtggagaaGtctgtcaacgatgcttcctc	9	9	3	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr19:53014180G>A	ENST00000421239.2	+	6	790	c.546G>A	c.(544-546)aaG>aaA	p.K182K	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	182					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K182K(1)							GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		AAGTGGAGAAGTCTGTCAACG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	19											89	93	92					19																	53014180		2202	4300	6502	57705992	SO:0001819	synonymous_variant	147660			AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.546G>A	19.37:g.53014180G>A			57705992	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	37	CCDS54310.1																																																																																				0.368	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		A	53014180	G	A	53014180	2	1	51	1	0	0	0	0	0	0	0	1	18049	1020	36	3		3	ZNF578	19	53014180	Silent	SNP	G	TCGA-AG-3898-01A-01W-1073-09	2560942	53014180	6114803	93	7002										
ZNF415	55786	broad.mit.edu	37	chr19	53612947	53612947	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tggtctctcctacaagtaagAttttcttttggggccgtagt	10	8	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr19:53612947A>T	ENST00000500065.4	-	4	684	c.351T>A	c.(349-351)aaT>aaA	p.N117K	ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000601215.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.N117K|ZNF415_ENST00000455735.2_Missense_Mutation_p.N165K|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.N165K|ZNF415_ENST00000421033.1_Missense_Mutation_p.N129K|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000440291.1_Missense_Mutation_p.N104K	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N117K(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TACAAGTAAGATTTTCTTTTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											120	109	113					19																	53612947		2203	4300	6503	58304759	SO:0001583	missense	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.351T>A	19.37:g.53612947A>T	ENSP00000439435:p.Asn117Lys		58304759	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	A	3.918	-0.018721	0.07681	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11;3.11	2.74	-2.82	0.05787	.	.	.	.	.	T	0.04861	0.0131	N	0.12182	0.205	0.09310	N	1	B;D;B;B;B;B	0.60575	0.078;0.988;0.148;0.078;0.078;0.231	B;P;B;B;B;B	0.52343	0.06;0.696;0.027;0.06;0.06;0.06	T	0.07177	-1.0786	9	0.02654	T	1	.	4.1075	0.10043	0.3812:0.2073:0.4115:0.0	.	117;165;165;117;104;129	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	K	117;117;165;129;165;104	ENSP00000243643:N117K;ENSP00000439435:N117K;ENSP00000396492:N165K;ENSP00000395055:N129K;ENSP00000388787:N165K;ENSP00000414601:N104K	ENSP00000243643:N117K	N	-	3	2	ZNF415	58304759	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	0.088000	0.14979	-0.963000	0.03600	0.260000	0.18958	AAT		0.398	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		T	53612947	A	T	53612947	3	4	51	1	0	0	0	0	1	0	0	0	17931	330	12	5	1320	5	ZNF415	19	53612947	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	598767	53612947	5516036	94	7003										
TASP1	55617	broad.mit.edu	37	chr20	13463941	13463941	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcagcttgtaaagcatgtgaAcattctctagccagtatggt	9	8	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:13463941A>G	ENST00000337743.4	-	11	1038	c.918T>C	c.(916-918)tgT>tgC	p.C306C	TASP1_ENST00000480436.1_5'UTR|TASP1_ENST00000539805.1_Missense_Mutation_p.V109A	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	306					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)	p.C306C(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						AAGCATGTGAACATTCTCTAG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	20											166	154	158					20																	13463941		2203	4300	6503	13411941	SO:0001819	synonymous_variant	55617			AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.918T>C	20.37:g.13463941A>G			13411941	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Silent	SNP	ENST00000337743.4	37	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.742900	0.30865	.	.	ENSG00000089123	ENST00000539805	.	.	.	5.72	3.47	0.39725	.	.	.	.	.	T	0.30854	0.0778	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11842	-1.0571	5	0.02654	T	1	-0.6388	9.9838	0.41830	0.8612:0.0:0.1388:0.0	.	.	.	.	A	109	.	ENSP00000444062:V109A	V	-	2	0	TASP1	13411941	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.501000	0.60393	0.520000	0.28426	-0.263000	0.10527	GTT		0.418	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		G	13463941	A	G	13463941	2	3	51	1	0	0	0	0	0	0	0	1	15628	41	2	4		4	TASP1	20	13463941	Silent	SNP	A	TCGA-AG-3898-01A-01W-1073-09		13463941	49561579	95	7004										
FLRT3	23767	broad.mit.edu	37	chr20	14307773	14307773	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gtaattcttccagatagggaAtttttgaaagtgaatcataa	8	4	2	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:14307773A>T	ENST00000378053.3	-	2	636	c.380T>A	c.(379-381)aTt>aAt	p.I127N	MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron|FLRT3_ENST00000341420.4_Missense_Mutation_p.I127N|FLRT3_ENST00000462077.1_5'Flank	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	127					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.I127N(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		CAGATAGGGAATTTTTGAAAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	20											129	135	133					20																	14307773		2203	4300	6503	14255773	SO:0001583	missense	23767			AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"Fibronectin type III domain containing"	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.380T>A	20.37:g.14307773A>T	ENSP00000367292:p.Ile127Asn		14255773	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	37	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.896384	0.91962	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.57107	0.42;0.42	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.55909	0.1950	N	0.19112	0.55	0.80722	D	1	D	0.54397	0.966	P	0.58620	0.842	T	0.59841	-0.7378	10	0.56958	D	0.05	-14.7729	16.6093	0.84858	1.0:0.0:0.0:0.0	.	127	Q9NZU0	FLRT3_HUMAN	N	127	ENSP00000367292:I127N;ENSP00000339912:I127N	ENSP00000339912:I127N	I	-	2	0	FLRT3	14255773	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.324000	0.78689	0.533000	0.62120	ATT		0.368	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281		T	14307773	A	T	14307773	3	4	51	1	0	0	0	0	1	0	0	0	5959	101	4	5	1573	5	FLRT3	20	14307773	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	843832	14307773	48717747	96	7005										
CSRP2BP	57325	broad.mit.edu	37	chr20	18163911	18163911	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ccaaatcacatcccaacgatCaactccatgtgtcaggagtt	6	13	3	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:18163911C>G	ENST00000435364.3	+	8	2294	c.1953C>G	c.(1951-1953)atC>atG	p.I651M	CSRP2BP_ENST00000489634.2_Missense_Mutation_p.I523M|CSRP2BP_ENST00000377681.3_Missense_Mutation_p.I650M	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	651	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)	p.I651M(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						TCCCAACGATCAACTCCATGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	20											137	129	132					20																	18163911		2203	4300	6503	18111911	SO:0001583	missense	57325			AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1953C>G	20.37:g.18163911C>G	ENSP00000392318:p.Ile651Met		18111911	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903271	0.72754	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	6.04	3.91	0.45181	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.048340	0.85682	D	0.000000	T	0.58906	0.2155	M	0.71581	2.175	0.49051	D	0.999749	D;P	0.55800	0.973;0.954	P;P	0.59889	0.865;0.736	T	0.59337	-0.7473	10	0.87932	D	0	-18.4013	6.2852	0.21029	0.3816:0.417:0.0:0.2014	.	523;651	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	M	651;650;651;523	ENSP00000278816:I651M;ENSP00000366909:I650M;ENSP00000392318:I651M;ENSP00000425909:I523M	ENSP00000278816:I651M	I	+	3	3	CSRP2BP	18111911	0.993000	0.37304	0.998000	0.56505	0.989000	0.77384	0.466000	0.22019	0.683000	0.31428	0.563000	0.77884	ATC		0.498	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		G	18163911	C	G	18163911	3	3	51	1	0	0	0	0	1	0	0	0	3974	816	29	5	1983	5	CSRP2BP	20	18163911	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	3856138	18163911	44861609	97	7006										
CSRP2BP	57325	broad.mit.edu	37	chr20	18165310	18165310	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gttgttctttataaaaaagtCatcattgcctttggcttcat	6	7	4	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:18165310C>T	ENST00000435364.3	+	9	2390	c.2049C>T	c.(2047-2049)gtC>gtT	p.V683V	CSRP2BP_ENST00000489634.2_Silent_p.V555V|CSRP2BP_ENST00000377681.3_Silent_p.V682V	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	683	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)	p.V683V(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						ATAAAAAAGTCATCATTGCCT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	20											221	191	201					20																	18165310		2203	4300	6503	18113310	SO:0001819	synonymous_variant	57325			AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.2049C>T	20.37:g.18165310C>T			18113310	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Silent	SNP	ENST00000435364.3	37	CCDS13133.1																																																																																				0.413	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		T	18165310	C	T	18165310	2	4	51	1	0	0	0	0	0	0	0	1	3974	813	29	3		3	CSRP2BP	20	18165310	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	1399	18165310	44860210	98	7007										
CHMP4B	128866	broad.mit.edu	37	chr20	32439957	32439957	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttgctggaaatcagtggaccCgaaacagtccctctaccaaa	8	12	2	0	rs79766928	byFrequency	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:32439957C>T	ENST00000217402.2	+	4	723	c.558C>T	c.(556-558)ccC>ccT	p.P186P		NM_176812.4	NP_789782.1	Q9H444	CHM4B_HUMAN	charged multivesicular body protein 4B	186					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|positive regulation of viral release from host cell (GO:1902188)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.P186P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13						TCAGTGGACCCGAAACAGTCC	0.478													C|||	46	0.0091853	0.0303	0.0072	5008	,	,		19331	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	20						C		86,4320	73.1+/-111.1	4,78,2121	154	143	147		558	-7	1	20	dbSNP_131	147	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CHMP4B	NM_176812.4		4,81,6418	TT,TC,CC		0.0349,1.9519,0.6843		186/225	32439957	89,12917	2203	4300	6503	31903618	SO:0001819	synonymous_variant	128866			AL050349	CCDS13228.1	20q11.22	2011-09-21	2011-09-21	2005-04-04	ENSG00000101421	ENSG00000101421		"Charged multivesicular body proteins"	16171	protein-coding gene	gene with protein product		610897	"chromosome 20 open reading frame 178", "chromatin modifying protein 4B"	C20orf178		14678797	Standard	NM_176812		Approved	dJ553F4.4, Shax1, SNF7-2, VPS32B	uc002xaa.3	Q9H444	OTTHUMG00000032272	ENST00000217402.2:c.558C>T	20.37:g.32439957C>T			31903618	E1P5N4|Q53ZD6	Silent	SNP	ENST00000217402.2	37	CCDS13228.1																																																																																				0.478	CHMP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078738.2			T	32439957	C	T	32439957	2	4	51	1	0	0	0	0	0	0	0	1	3363	639	23	1		1	CHMP4B	20	32439957	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09	14274647	32439957	30585563	99	7008										
YTHDF1	54915	broad.mit.edu	37	chr20	61835065	61835065	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tcggagggtcccctgcagtaGaccacggagcctcattgagg	14	12	1	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr20:61835065G>T	ENST00000370339.3	-	4	568	c.227C>A	c.(226-228)tCt>tAt	p.S76Y	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.S26Y	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	76							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)	p.S76Y(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						CCCTGCAGTAGACCACGGAGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	20											98	104	102					20																	61835065		2203	4300	6503	61305510	SO:0001583	missense	54915			AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.227C>A	20.37:g.61835065G>T	ENSP00000359364:p.Ser76Tyr		61305510	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	37	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469416	0.63625	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.54279	0.58;0.58	5.24	5.24	0.73138	.	0.049239	0.85682	D	0.000000	T	0.74412	0.3713	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76575	-0.2909	10	0.54805	T	0.06	-18.0279	18.8357	0.92162	0.0:0.0:1.0:0.0	.	76	Q9BYJ9	YTHD1_HUMAN	Y	76;26	ENSP00000359364:S76Y;ENSP00000359358:S26Y	ENSP00000359358:S26Y	S	-	2	0	YTHDF1	61305510	1.000000	0.71417	0.942000	0.38095	0.403000	0.30841	9.725000	0.98778	2.448000	0.82819	0.561000	0.74099	TCT		0.537	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		T	61835065	G	T	61835065	3	4	51	1	0	0	0	0	1	0	0	0	17538	942	33	2	1460	2	YTHDF1	20	61835065	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	29395108	61835065	1190455	100	7009										
HSF2BP	11077	broad.mit.edu	37	chr21	44949838	44949838	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tgaaggcacacctctgcatcTggatctagggaaaagaggta	12	8	3	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr21:44949838T>C	ENST00000291560.2	-	9	1132	c.801A>G	c.(799-801)ccA>ccG	p.P267P	HSF2BP_ENST00000542962.1_Silent_p.P192P	NM_007031.1	NP_008962.1	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding protein	267					spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)		p.P267P(1)		kidney(2)|large_intestine(3)|prostate(1)|skin(1)	7				STAD - Stomach adenocarcinoma(101;0.18)		CCTCTGCATCTGGATCTAGGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	21											44	45	45					21																	44949838		2203	4300	6503	43774266	SO:0001819	synonymous_variant	11077			AB007131	CCDS13697.1	21q22.3	2008-07-31			ENSG00000160207	ENSG00000160207			5226	protein-coding gene	gene with protein product	"heat shock factor 2 binding protein"	604554				9651507	Standard	XM_005261090		Approved		uc002zdi.3	O75031	OTTHUMG00000086863	ENST00000291560.2:c.801A>G	21.37:g.44949838T>C			43774266	B4DX36	Silent	SNP	ENST00000291560.2	37	CCDS13697.1																																																																																				0.458	HSF2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195620.1	NM_007031		C	44949838	T	C	44949838	2	2	51	1	0	0	0	0	0	0	0	1	7418	1567	55	4		4	HSF2BP	21	44949838	Silent	SNP	T	TCGA-AG-3898-01A-01W-1073-09		44949838	3180057	101	7010										
CECR5	27440	broad.mit.edu	37	chr22	17624004	17624004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	ttaccttcaatgcgggggaaGtcattcctcgggaggggctg	15	9	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chr22:17624004G>C	ENST00000336737.4	-	5	580	c.555C>G	c.(553-555)gaC>gaG	p.D185E	CECR5_ENST00000155674.5_Missense_Mutation_p.D155E|CECR5_ENST00000399852.3_Missense_Mutation_p.D48E	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	185						mitochondrion (GO:0005739)		p.D185E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				TGCGGGGGAAGTCATTCCTCG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											93	81	85					22																	17624004		2203	4300	6503	16004004	SO:0001583	missense	27440			AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.555C>G	22.37:g.17624004G>C	ENSP00000337358:p.Asp185Glu		16004004	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931654	0.52866	.	.	ENSG00000069998	ENST00000155674;ENST00000336737;ENST00000399852	T;T;T	0.22539	2.0;2.0;1.95	5.62	4.6	0.57074	HAD-like domain (1);	0.289501	0.38111	N	0.001806	T	0.27205	0.0667	L	0.52266	1.64	0.27895	N	0.9392	B;P;B	0.48089	0.004;0.905;0.017	B;P;B	0.50860	0.008;0.652;0.009	T	0.07597	-1.0764	10	0.17369	T	0.5	-20.3512	12.5239	0.56075	0.078:0.0:0.922:0.0	.	155;48;185	Q9BXW7-2;A8MYZ9;Q9BXW7	.;.;CECR5_HUMAN	E	155;185;48	ENSP00000155674:D155E;ENSP00000337358:D185E;ENSP00000382745:D48E	ENSP00000155674:D155E	D	-	3	2	CECR5	16004004	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	3.046000	0.49846	1.389000	0.46526	0.561000	0.74099	GAC		0.567	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829		C	17624004	G	C	17624004	3	2	51	1	0	0	0	0	1	0	0	0	3213	1020	36	5	732	5	CECR5	22	17624004	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09		17624004	33680562	102	7011										
SHROOM2	357	broad.mit.edu	37	chrX	9862668	9862668	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aacatcctctacactgtgggCctctgggaggctcccaggca	11	14	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:9862668C>A	ENST00000380913.3	+	4	810	c.720C>A	c.(718-720)ggC>ggA	p.G240G		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	240					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)	p.G240G(1)		breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				ACACTGTGGGCCTCTGGGAGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	X											42	34	36					X																	9862668		2202	4300	6502	9822668	SO:0001819	synonymous_variant	357			X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.720C>A	X.37:g.9862668C>A			9822668	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																				0.662	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		A	9862668	C	A	9862668	2	1	51	1	0	0	0	0	0	0	0	1	14331	726	26	2		2	SHROOM2	23	9862668	Silent	SNP	C	TCGA-AG-3898-01A-01W-1073-09		9862668	145407892	103	7012										
CNKSR2	22866	broad.mit.edu	37	chrX	21488902	21488902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aggattgtactgtatatgaaAcagagaataaaattcttcac	7	5	2	2			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:21488902A>G	ENST00000379510.3	+	5	574	c.538A>G	c.(538-540)Aca>Gca	p.T180A	CNKSR2_ENST00000279451.4_Missense_Mutation_p.T180A|CNKSR2_ENST00000543067.1_Missense_Mutation_p.T180A|CNKSR2_ENST00000425654.2_Missense_Mutation_p.T180A	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	180					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.T180A(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						TGTATATGAAACAGAGAATAA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	X											48	55	53					X																	21488902		2187	4270	6457	21398823	SO:0001583	missense	22866			AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.538A>G	X.37:g.21488902A>G	ENSP00000368824:p.Thr180Ala		21398823	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	37	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533958	0.45073	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.19105	2.45;2.22;2.17;2.44	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	N	0.22421	0.69	0.53005	D	0.999961	D;P;B	0.89917	1.0;0.573;0.222	D;B;B	0.83275	0.996;0.119;0.085	T	0.05582	-1.0876	10	0.36615	T	0.2	0.0583	12.4401	0.55619	1.0:0.0:0.0:0.0	.	180;180;180	B7ZLJ1;B4DGR4;Q8WXI2	.;.;CNKR2_HUMAN	A	180	ENSP00000397906:T180A;ENSP00000444633:T180A;ENSP00000279451:T180A;ENSP00000368824:T180A	ENSP00000279451:T180A	T	+	1	0	CNKSR2	21398823	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.315000	0.72853	1.844000	0.53588	0.441000	0.28932	ACA		0.254	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		G	21488902	A	G	21488902	3	3	51	1	0	0	0	0	1	0	0	0	3613	43	2	4	556	4	CNKSR2	23	21488902	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	11626234	21488902	133781658	104	7013										
POLA1	5422	broad.mit.edu	37	chrX	24830827	24830827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gcttgaaatagacattgatgGggttttcaagtctctgctac	10	7	2	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:24830827G>A	ENST00000379059.3	+	29	3140	c.3125G>A	c.(3124-3126)gGg>gAg	p.G1042E	POLA1_ENST00000379068.3_Missense_Mutation_p.G1048E	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1042					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.G1042E(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GACATTGATGGGGTTTTCAAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											88	86	87					X																	24830827		2203	4300	6503	24740748	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3125G>A	X.37:g.24830827G>A	ENSP00000368349:p.Gly1042Glu		24740748	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.768651	0.69878	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.16897	2.31;2.31	4.81	3.94	0.45596	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.051519	0.85682	D	0.000000	T	0.45196	0.1330	M	0.84585	2.705	0.80722	D	1	D	0.69078	0.997	D	0.70487	0.969	T	0.54016	-0.8356	10	0.72032	D	0.01	-8.8542	14.5572	0.68109	0.0:0.1427:0.8573:0.0	.	1042	P09884	DPOLA_HUMAN	E	1048;1042	ENSP00000368358:G1048E;ENSP00000368349:G1042E	ENSP00000368349:G1042E	G	+	2	0	POLA1	24740748	1.000000	0.71417	0.849000	0.33467	0.906000	0.53458	7.432000	0.80349	1.011000	0.39340	0.513000	0.50165	GGG		0.373	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24830827	G	A	24830827	3	1	51	1	0	0	0	0	1	0	0	0	12218	1232	43	3	3239	3	POLA1	23	24830827	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	3341925	24830827	130439733	105	7014										
ZNF630	57232	broad.mit.edu	37	chrX	47918364	47918364	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaggattttccacattcagtAcacatataaggtttctctcc	5	10	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:47918364A>G	ENST00000409324.3	-	5	1693	c.1467T>C	c.(1465-1467)tgT>tgC	p.C489C	ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000276054.4_Silent_p.C365C|ZNF630_ENST00000442455.3_Silent_p.C475C	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	489					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C489C(1)		endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						CACATTCAGTACACATATAAG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	X											72	69	70					X																	47918364		2195	4289	6484	47803308	SO:0001819	synonymous_variant	57232			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1467T>C	X.37:g.47918364A>G			47803308	F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																				0.418	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		G	47918364	A	G	47918364	2	3	51	1	0	0	0	0	0	0	0	1	18093	389	14	4		4	ZNF630	23	47918364	Silent	SNP	A	TCGA-AG-3898-01A-01W-1073-09	23087537	47918364	107352196	106	7015										
AR	367	broad.mit.edu	37	chrX	66905930	66905930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gaaaaattgtccatcttgtcGtcttcggaaatgttatgaag	9	6	2	1			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:66905930G>A	ENST00000374690.3	+	3	2371	c.1847G>A	c.(1846-1848)cGt>cAt	p.R616H	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.R616H|AR_ENST00000396043.2_Missense_Mutation_p.R84H|AR_ENST00000396044.3_Missense_Mutation_p.R616H	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	615	Interaction with HIPK3. {ECO:0000250}.|Interaction with LPXN.		L -> P (in AIS). {ECO:0000269|PubMed:8647313}.|L -> R (in PAIS). {ECO:0000269|PubMed:8126121}.		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R616H(1)|p.R426H(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CCATCTTGTCGTCTTCGGAAA	0.438									Androgen Insensitivity Syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	X	GRCh37	CD942043|CM910043|CM930035	AR	D|M							129	108	115					X																	66905930		2203	4300	6503	66822655	SO:0001583	missense	367	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1847G>A	X.37:g.66905930G>A	ENSP00000363822:p.Arg616His		66822655	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	G	30	5.055738	0.93793	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000396043	D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01	5.42	5.42	0.78866	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.99378	0.9781	H	0.98111	4.15	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	D	0.98457	1.0594	10	0.87932	D	0	.	15.3078	0.74008	0.0:0.0:1.0:0.0	.	616;616;84;615	E7EVX6;D3YPQ2;F1D8N5;P10275	.;.;.;ANDR_HUMAN	H	426;616;616;616;84	ENSP00000363822:R616H;ENSP00000421155:R616H;ENSP00000379359:R616H;ENSP00000379358:R84H	ENSP00000363822:R616H	R	+	2	0	AR	66822655	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.054000	0.93866	2.499000	0.84300	0.594000	0.82650	CGT		0.438	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66905930	G	A	66905930	3	1	51	1	0	0	0	0	1	0	0	0	836	1145	40	1	1881	1	AR	23	66905930	Missense_Mutation	SNP	G	TCGA-AG-3898-01A-01W-1073-09	18987566	66905930	88364630	107	7016										
ZCCHC5	203430	broad.mit.edu	37	chrX	77913213	77913213	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	aaagtgtattgcagggggaaAtctgtagcctctaacccaat	10	8	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:77913213A>C	ENST00000321110.1	-	2	1000	c.705T>G	c.(703-705)gaT>gaG	p.D235E		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	235							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.D235E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						GCAGGGGGAAATCTGTAGCCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	X											27	26	27					X																	77913213		2203	4300	6503	77799869	SO:0001583	missense	203430			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"Zinc fingers, CCHC domain containing"	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.705T>G	X.37:g.77913213A>C	ENSP00000316794:p.Asp235Glu		77799869	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.945262	0.00052	.	.	ENSG00000179300	ENST00000321110	T	0.16073	2.37	3.29	3.29	0.37713	.	.	.	.	.	T	0.06371	0.0164	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41142	-0.9525	9	0.02654	T	1	.	5.1713	0.15112	0.7365:0.0:0.0:0.2634	.	235	Q8N8U3	ZCHC5_HUMAN	E	235	ENSP00000316794:D235E	ENSP00000316794:D235E	D	-	3	2	ZCCHC5	77799869	0.031000	0.19500	0.014000	0.15608	0.008000	0.06430	1.797000	0.38804	1.525000	0.49052	0.417000	0.27973	GAT		0.502	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		C	77913213	A	C	77913213	3	2	51	1	0	0	0	0	1	0	0	0	17630	98	4	4	726	4	ZCCHC5	23	77913213	Missense_Mutation	SNP	A	TCGA-AG-3898-01A-01W-1073-09	11007283	77913213	77357347	108	7017										
PCDH19	57526	broad.mit.edu	37	chrX	99551715	99551715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	gccgcagtcgtcataagcctCgacatcagcagcagtagctt	10	13	2	0			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:99551715C>T	ENST00000373034.4	-	6	4682	c.3007G>A	c.(3007-3009)Gag>Aag	p.E1003K	PCDH19_ENST00000255531.7_Missense_Mutation_p.E956K|PCDH19_ENST00000464981.1_5'Flank|PCDH19_ENST00000420881.2_Missense_Mutation_p.E955K	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1003					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E456K(1)|p.E1003K(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TCATAAGCCTCGACATCAGCA	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	X											81	80	80					X																	99551715		2107	4218	6325	99438371	SO:0001583	missense	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3007G>A	X.37:g.99551715C>T	ENSP00000362125:p.Glu1003Lys		99438371	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985339	0.74474	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.56776	0.44;0.5;0.44	5.84	5.84	0.93424	.	0.122561	0.56097	D	0.000026	T	0.65228	0.2671	L	0.59436	1.845	0.53688	D	0.999978	P;D;D	0.69078	0.902;0.997;0.994	B;P;P	0.55871	0.207;0.786;0.616	T	0.62779	-0.6782	10	0.38643	T	0.18	.	19.1326	0.93413	0.0:1.0:0.0:0.0	.	1003;956;955	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	K	955;1003;956	ENSP00000400327:E955K;ENSP00000362125:E1003K;ENSP00000255531:E956K	ENSP00000255531:E956K	E	-	1	0	PCDH19	99438371	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.347000	0.65998	2.469000	0.83416	0.600000	0.82982	GAG		0.577	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		T	99551715	C	T	99551715	3	4	51	1	0	0	0	0	1	0	0	0	11545	893	31	1	443	1	PCDH19	23	99551715	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	21638502	99551715	55718845	109	7018										
ARHGAP36	158763	broad.mit.edu	37	chrX	130217770	130217770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0272727272727273	3	1	0.304604810996564	1.90378006872852	0.21451043027927	1	1	0	tggtgaacgagtttacccgcCgcaagcatcttgaactgaca	10	11	1	3			TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3898-01A-01W-1073-09	TCGA-AG-3898-10A-01W-1073-09	g.chrX:130217770C>T	ENST00000276211.5	+	4	727	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	ARHGAP36_ENST00000370921.1_5'UTR|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.R116C	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	128					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R128C(2)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GTTTACCCGCCGCAAGCATCT	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	X											134	132	133					X																	130217770		2203	4300	6503	130045451	SO:0001583	missense	158763				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.382C>T	X.37:g.130217770C>T	ENSP00000276211:p.Arg128Cys		130045451	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535966	0.27475	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432	T;T;T	0.13307	2.6;2.6;2.63	4.3	3.43	0.39272	.	0.137816	0.34156	N	0.004215	T	0.09992	0.0245	N	0.24115	0.695	0.80722	D	1	D;D;D	0.58620	0.957;0.983;0.971	B;B;B	0.43950	0.437;0.437;0.253	T	0.09530	-1.0670	10	0.51188	T	0.08	.	8.4459	0.32841	0.2315:0.7685:0.0:0.0	.	97;116;128	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	C	128;116;80;97	ENSP00000276211:R128C;ENSP00000359960:R116C;ENSP00000408515:R97C	ENSP00000276211:R128C	R	+	1	0	ARHGAP36	130045451	0.999000	0.42202	0.996000	0.52242	0.044000	0.14063	1.640000	0.37186	1.134000	0.42165	0.600000	0.82982	CGC		0.562	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130217770	C	T	130217770	3	4	51	1	0	0	0	0	1	0	0	0	883	652	23	1	392	1	ARHGAP36	23	130217770	Missense_Mutation	SNP	C	TCGA-AG-3898-01A-01W-1073-09	30666055	130217770	25052790	110	7019										
DLGAP3	58512	broad.mit.edu	37	chr1	35370070	35370070	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cagcggccttccgacccgccCgagcgccccttgaagctcaa	10	19	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:35370070C>T	ENST00000373347.1	-	3	1183	c.915G>A	c.(913-915)tcG>tcA	p.S305S	DLGAP3_ENST00000235180.4_Silent_p.S305S|DLGAP3_ENST00000495979.1_5'Flank			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	305					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)	p.S305S(2)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CCGACCCGCCCGAGCGCCCCT	0.657																																																2	Substitution - coding silent(2)	urinary_tract(1)|large_intestine(1)	1											44	47	46					1																	35370070		2203	4300	6503	35142657	SO:0001819	synonymous_variant	58512			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.915G>A	1.37:g.35370070C>T			35142657	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	37	CCDS30670.1																																																																																				0.657	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35370070	C	T	35370070	2	4	52	1	0	0	0	0	0	0	0	1	4572	639	23	1		1	DLGAP3	1	35370070	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09		35370070	213880551	1	7020										
FOXJ3	22887	broad.mit.edu	37	chr1	42657097	42657097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ctgggggtgaggggactggaGctggctgtgttgctgtgggt	22	5	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:42657097G>A	ENST00000372572.1	-	11	1539	c.1228C>T	c.(1228-1230)Ctc>Ttc	p.L410F	FOXJ3_ENST00000372571.1_5'Flank|FOXJ3_ENST00000361776.1_Missense_Mutation_p.L376F|FOXJ3_ENST00000545068.1_Missense_Mutation_p.L410F|FOXJ3_ENST00000372573.1_Missense_Mutation_p.L410F|FOXJ3_ENST00000361346.1_Missense_Mutation_p.L410F	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	410					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L410F(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGACTGGAGCTGGCTGTGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											311	234	260					1																	42657097		2203	4300	6503	42429684	SO:0001583	missense	22887			AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"Forkhead boxes"	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.1228C>T	1.37:g.42657097G>A	ENSP00000361653:p.Leu410Phe		42429684	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	37	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.960604	0.34565	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	5.31	5.31	0.75309	.	0.913255	0.08856	U	0.883748	T	0.31857	0.0810	N	0.08118	0	0.45567	D	0.998517	P;P	0.47677	0.899;0.838	B;B	0.41813	0.367;0.202	T	0.17715	-1.0360	10	0.10111	T	0.7	.	16.8252	0.85929	0.0:0.0:1.0:0.0	.	376;410	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	F	410;410;410;376;410;376	ENSP00000361654:L410F;ENSP00000361653:L410F;ENSP00000354620:L410F;ENSP00000354449:L376F;ENSP00000439044:L410F;ENSP00000393408:L376F	ENSP00000354620:L410F	L	-	1	0	FOXJ3	42429684	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.983000	0.88140	2.646000	0.89796	0.555000	0.69702	CTC		0.602	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		A	42657097	G	A	42657097	3	1	52	1	0	0	0	0	1	0	0	0	6032	971	34	3	660	3	FOXJ3	1	42657097	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	7287027	42657097	206593524	2	7021										
PAPPA2	60676	broad.mit.edu	37	chr1	176525833	176525833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aggggtgcagttgaagagccGgctgccccatgggtagggga	19	8	0	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:176525833G>A	ENST00000367662.3	+	2	1539	c.375G>A	c.(373-375)ccG>ccA	p.P125P	PAPPA2_ENST00000367661.3_Silent_p.P125P	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	125					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P125P(2)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TTGAAGAGCCGGCTGCCCCAT	0.542																																																2	Substitution - coding silent(2)	large_intestine(2)	1											114	115	114					1																	176525833		2052	4198	6250	174792456	SO:0001819	synonymous_variant	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.375G>A	1.37:g.176525833G>A			174792456	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																				0.542	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176525833	G	A	176525833	2	1	52	1	0	0	0	0	0	0	0	1	11464	1103	39	1		1	PAPPA2	1	176525833	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	133868736	176525833	72724788	3	7022										
KCNT2	343450	broad.mit.edu	37	chr1	196227479	196227479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ggccttttctgctcagtcttCgggcccactgcatgcttttt	9	13	3	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:196227479C>T	ENST00000294725.9	-	26	3971	c.3056G>A	c.(3055-3057)cGa>cAa	p.R1019Q	KCNT2_ENST00000367433.5_Missense_Mutation_p.R995Q|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.R952Q|KCNT2_ENST00000367431.4_Missense_Mutation_p.R953Q			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1019					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.R1019Q(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GCTCAGTCTTCGGGCCCACTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	127	134					1																	196227479		2203	4300	6503	194494102	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.3056G>A	1.37:g.196227479C>T	ENSP00000294725:p.Arg1019Gln		194494102	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.444207	0.83993	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.23950	1.88;1.93;2.23	5.74	4.83	0.62350	.	0.000000	0.49305	D	0.000152	T	0.49847	0.1581	M	0.78916	2.43	0.80722	D	1	D;D;D;D	0.76494	0.999;0.99;0.967;0.983	D;P;P;P	0.65443	0.935;0.674;0.556;0.474	T	0.51803	-0.8659	10	0.41790	T	0.15	-7.0387	14.7148	0.69259	0.0:0.9307:0.0:0.0693	.	984;995;952;1019	Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	Q	995;953;1019	ENSP00000356403:R995Q;ENSP00000356401:R953Q;ENSP00000294725:R1019Q	ENSP00000294725:R1019Q	R	-	2	0	KCNT2	194494102	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	7.487000	0.81328	1.437000	0.47472	-0.148000	0.13756	CGA		0.512	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196227479	C	T	196227479	3	4	52	1	0	0	0	0	1	0	0	0	8113	884	31	1	363	1	KCNT2	1	196227479	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	19701646	196227479	53023142	4	7023										
CRB1	23418	broad.mit.edu	37	chr1	197396689	197396689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cctctccatgtttgtccgaaCgcttcaaccatcaggcttac	6	15	3	0	rs28939720		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:197396689C>T	ENST00000367400.3	+	7	2369	c.2234C>T	c.(2233-2235)aCg>aTg	p.T745M	CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367399.2_Missense_Mutation_p.T633M|CRB1_ENST00000544212.1_Missense_Mutation_p.T226M|CRB1_ENST00000367397.1_Missense_Mutation_p.T126M|CRB1_ENST00000535699.1_Missense_Mutation_p.T676M|CRB1_ENST00000543483.1_3'UTR	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	745	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> M (in RP12 and LCA8; dbSNP:rs28939720). {ECO:0000269|PubMed:10508521, ECO:0000269|PubMed:15024725, ECO:0000269|PubMed:15459956, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17724218, ECO:0000269|PubMed:20591486, ECO:0000269|PubMed:20956273, ECO:0000269|PubMed:22334370}.		cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T745M(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TTTGTCCGAACGCTTCAACCA	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	1	GRCh37	CM992150	CRB1	M	rs28939720	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	84	75	78	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1898,2234	4.8	0.2	1	dbSNP_125	78	0,8600		0,0,4300	no	missense,missense	CRB1	NM_001193640.1,NM_201253.2	81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	633/1295,745/1407	197396689	1,13005	2203	4300	6503	195663312	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2234C>T	1.37:g.197396689C>T	ENSP00000356370:p.Thr745Met		195663312	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723780	0.48728	2.27E-4	0.0	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55;-2.55	5.75	4.85	0.62838	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.95004	0.8383	M	0.88906	2.99	0.80722	A	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.986;0.999	D	0.95323	0.8422	8	0.54805	T	0.06	.	14.531	0.67926	0.0:0.9302:0.0:0.0698	rs28939720	676;633;394;745	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	M	676;745;633;226;126;394	ENSP00000438786:T676M;ENSP00000356370:T745M;ENSP00000356369:T633M;ENSP00000444556:T226M;ENSP00000356367:T126M	ENSP00000356367:T126M	T	+	2	0	CRB1	195663312	1.000000	0.71417	0.222000	0.23844	0.022000	0.10575	5.591000	0.67536	1.425000	0.47237	0.650000	0.86243	ACG		0.483	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197396689	C	T	197396689	3	4	52	1	0	0	0	0	1	0	0	0	3854	536	19	1	2260	1	CRB1	1	197396689	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	1169210	197396689	51853932	5	7024										
PIGR	5284	broad.mit.edu	37	chr1	207110869	207110869	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gagcctgagttggttgatgaCaacgctgaacagtaactggc	13	8	0	4			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:207110869C>T	ENST00000356495.4	-	4	799	c.616G>A	c.(616-618)Gtc>Atc	p.V206I		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	206	Ig-like V-type 2.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.V206I(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TGGTTGATGACAACGCTGAAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	73	75					1																	207110869		2203	4300	6503	205177492	SO:0001583	missense	5284				CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.616G>A	1.37:g.207110869C>T	ENSP00000348888:p.Val206Ile		205177492	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	9.198	1.027709	0.19512	.	.	ENSG00000162896	ENST00000356495	T	0.64991	-0.13	6.08	-5.18	0.02840	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	1.516540	0.03262	N	0.183419	T	0.46795	0.1411	L	0.38175	1.15	0.09310	N	1	B	0.22080	0.064	B	0.16289	0.015	T	0.23940	-1.0174	10	0.35671	T	0.21	-24.8877	5.4409	0.16509	0.2062:0.272:0.0:0.5218	.	206	P01833	PIGR_HUMAN	I	206	ENSP00000348888:V206I	ENSP00000348888:V206I	V	-	1	0	PIGR	205177492	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.708000	0.01891	-0.833000	0.04245	-0.302000	0.09304	GTC		0.478	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		T	207110869	C	T	207110869	3	4	52	1	0	0	0	0	1	0	0	0	11928	478	17	3	1710	3	PIGR	1	207110869	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	9714180	207110869	42139752	6	7025										
NLRP3	114548	broad.mit.edu	37	chr1	247593021	247593021	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gatgagagtgttgtgtgaaaCgctccagcatcctggctgta	13	8	0	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr1:247593021C>T	ENST00000336119.3	+	4	3037	c.2291C>T	c.(2290-2292)aCg>aTg	p.T764M	NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000366496.2_Missense_Mutation_p.T764M|NLRP3_ENST00000391828.3_Missense_Mutation_p.T764M|NLRP3_ENST00000366497.2_Missense_Mutation_p.T764M|NLRP3_ENST00000391827.2_Intron	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	764					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.T764M(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TTGTGTGAAACGCTCCAGCAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	91	93					1																	247593021		2203	4300	6503	245659644	SO:0001583	missense	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2291C>T	1.37:g.247593021C>T	ENSP00000337383:p.Thr764Met		245659644	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	3.108	-0.183351	0.06340	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000366496	D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35	4.21	0.862	0.19056	.	0.886354	0.09463	N	0.798745	T	0.79845	0.4516	L	0.31926	0.97	0.09310	N	1	B;B;B	0.30542	0.092;0.069;0.284	B;B;B	0.26310	0.012;0.027;0.068	T	0.68176	-0.5478	10	0.49607	T	0.09	.	3.5037	0.07683	0.0:0.5216:0.211:0.2674	.	764;764;764	B7ZKS9;Q96P20-5;Q96P20	.;.;NALP3_HUMAN	M	764	ENSP00000375704:T764M;ENSP00000355453:T764M;ENSP00000337383:T764M;ENSP00000355452:T764M	ENSP00000337383:T764M	T	+	2	0	NLRP3	245659644	0.004000	0.15560	0.001000	0.08648	0.075000	0.17131	0.690000	0.25451	0.393000	0.25203	0.536000	0.68110	ACG		0.512	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247593021	C	T	247593021	3	4	52	1	0	0	0	0	1	0	0	0	10509	536	19	1	2305	1	NLRP3	1	247593021	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	40482152	247593021	1657600	7	7026										
SCN1A	6323	broad.mit.edu	37	chr2	166868748	166868748	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ttgtcagcatattccaacatCgtcttaatcgtctttcgctg	6	11	3	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr2:166868748C>T	ENST00000303395.4	-	19	3749	c.3750G>A	c.(3748-3750)acG>acA	p.T1250T	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Silent_p.T1222T|SCN1A_ENST00000375405.3_Silent_p.T1239T|SCN1A_ENST00000423058.2_Silent_p.T1250T|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1250					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.T1239T(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATTCCAACATCGTCTTAATCG	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	2											80	75	77					2																	166868748		2202	4299	6501	166576994	SO:0001819	synonymous_variant	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3750G>A	2.37:g.166868748C>T			166576994	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																				0.318	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166868748	C	T	166868748	2	4	52	1	0	0	0	0	0	0	0	1	13951	871	31	1		1	SCN1A	2	166868748	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09		166868748	76330625	8	7027										
RBM45	129831	broad.mit.edu	37	chr2	178990777	178990777	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gtggggtatgccaagtatgcCgatagaataagtgctaatga	13	5	0	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr2:178990777C>T	ENST00000286070.5	+	9	1391	c.1299C>T	c.(1297-1299)gcC>gcT	p.A433A		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	435	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A433A(2)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			CCAAGTATGCCGATAGAATAA	0.388																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	2											159	144	149					2																	178990777		2203	4300	6503	178699023	SO:0001819	synonymous_variant	129831			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"RNA binding motif (RRM) containing"	24468	protein-coding gene	gene with protein product	"developmentally regulated RNA binding protein 1"	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.1299C>T	2.37:g.178990777C>T			178699023	Q6NYL0|Q8NFC9	Silent	SNP	ENST00000286070.5	37	CCDS33335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.565|9.565	1.119453|1.119453	0.20877|0.20877	.|.	.|.	ENSG00000155636|ENSG00000155636	ENST00000455903|ENST00000424099	.|.	.|.	.|.	5.74|5.74	-2.19|-2.19	0.07015|0.07015	.|.	.|.	.|.	.|.	.|.	T|.	0.41026|.	0.1141|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.27400|.	-1.0075|.	4|.	.|.	.|.	.|.	-18.3773|-18.3773	2.3916|2.3916	0.04379|0.04379	0.2966:0.2297:0.0646:0.4091|0.2966:0.2297:0.0646:0.4091	.|.	.|.	.|.	.|.	L|X	94|32	.|.	.|.	P|R	+|+	2|1	0|2	RBM45|RBM45	178699023|178699023	0.990000|0.990000	0.36364|0.36364	0.986000|0.986000	0.45419|0.45419	0.947000|0.947000	0.59692|0.59692	0.419000|0.419000	0.21247|0.21247	-0.648000|-0.648000	0.05437|0.05437	-1.072000|-1.072000	0.02254|0.02254	CCG|CGA		0.388	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		T	178990777	C	T	178990777	2	4	52	1	0	0	0	0	0	0	0	1	13176	639	23	1		1	RBM45	2	178990777	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09	12122029	178990777	64208596	9	7028										
TTN	7273	broad.mit.edu	37	chr2	179452756	179452756	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gtaacagtgaattccttgcgTacaagctgtgctgcagcatt	10	9	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr2:179452756T>A	ENST00000591111.1	-	255	58679	c.58455A>T	c.(58453-58455)gtA>gtT	p.V19485V	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Silent_p.V12186V|TTN_ENST00000460472.2_Silent_p.V12061V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.V12253V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Silent_p.V18558V|TTN_ENST00000589042.1_Silent_p.V21126V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19485	Fibronectin type-III 41. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V12253V(1)|p.V12186V(1)|p.V18556V(1)|p.V12061V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTCCTTGCGTACAAGCTGTG	0.478																																																4	Substitution - coding silent(4)	large_intestine(4)	2											92	87	89					2																	179452756		1961	4158	6119	179161002	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58455A>T	2.37:g.179452756T>A			179161002	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179452756	T	A	179452756	2	1	52	1	0	0	0	0	0	0	0	1	16775	1625	57	5		5	TTN	2	179452756	Silent	SNP	T	TCGA-AG-3901-01A-01W-1073-09	461979	179452756	63746617	10	7029										
DIRC1	116093	broad.mit.edu	37	chr2	189599428	189599428	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ttcagacctagaagaaagttGatcctttgttattggtttat	8	5	1	4			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr2:189599428G>C	ENST00000308100.4	-	2	490	c.220C>G	c.(220-222)Caa>Gaa	p.Q74E	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	74								p.Q74E(1)		large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			GAAGAAAGTTGATCCTTTGTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											155	154	155					2																	189599428		2203	4300	6503	189307673	SO:0001583	missense	116093			AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.220C>G	2.37:g.189599428G>C	ENSP00000307860:p.Gln74Glu		189307673	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	.	.	.	.	.	.	.	.	.	.	G	2.034	-0.421666	0.04734	.	.	ENSG00000174325	ENST00000308100	T	0.32023	1.47	2.27	-2.2	0.06994	.	.	.	.	.	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	P	0.35481	0.504	B	0.29598	0.104	T	0.14924	-1.0455	9	0.87932	D	0	.	6.7864	0.23675	0.4825:0.0:0.5175:0.0	.	74	Q969H9	DIRC1_HUMAN	E	74	ENSP00000307860:Q74E	ENSP00000307860:Q74E	Q	-	1	0	DIRC1	189307673	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.353000	0.07691	-0.665000	0.05317	0.655000	0.94253	CAA		0.378	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952		C	189599428	G	C	189599428	3	2	52	1	0	0	0	0	1	0	0	0	4544	1299	45	5	98	5	DIRC1	2	189599428	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	10146672	189599428	53599945	11	7030										
PSMD1	5707	broad.mit.edu	37	chr2	231943382	231943382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgttgttgcaggatgcagtaCggaattctgtatgtcatact	11	6	2	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr2:231943382C>T	ENST00000308696.6	+	10	1243	c.1081C>T	c.(1081-1083)Cgg>Tgg	p.R361W	PSMD1_ENST00000373635.4_Missense_Mutation_p.R361W|PSMD1_ENST00000409643.1_Missense_Mutation_p.R361W	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	361					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.R361W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GGATGCAGTACGGAATTCTGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											121	113	116					2																	231943382		2203	4300	6503	231651626	SO:0001583	missense	5707			D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.1081C>T	2.37:g.231943382C>T	ENSP00000309474:p.Arg361Trp		231651626	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	37	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812542	0.70912	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643	.	.	.	5.68	4.79	0.61399	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85089	0.5617	M	0.92691	3.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.984	D	0.88549	0.3115	9	0.87932	D	0	-11.8035	13.7724	0.63034	0.4187:0.5813:0.0:0.0	.	361;361	Q99460;Q99460-2	PSMD1_HUMAN;.	W	361	.	ENSP00000309474:R361W	R	+	1	2	PSMD1	231651626	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.985000	0.40668	1.362000	0.46000	0.585000	0.79938	CGG		0.398	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231943382	C	T	231943382	3	4	52	1	0	0	0	0	1	0	0	0	12726	527	19	1	1119	1	PSMD1	2	231943382	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	42343954	231943382	11255991	12	7031										
PIK3CA	5290	broad.mit.edu	37	chr3	178921549	178921549	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aattctttgtgcaacctacgTgaatgtaaatattcgagaca	7	7	1	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr3:178921549T>G	ENST00000263967.3	+	5	1188	c.1031T>G	c.(1030-1032)gTg>gGg	p.V344G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	344	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.V344G(8)|p.V344A(5)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GCAACCTACGTGAATGTAAAT	0.303		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	13	Substitution - Missense(13)	endometrium(6)|large_intestine(4)|cervix(2)|central_nervous_system(1)	3											68	67	67					3																	178921549		1808	4073	5881	180404243	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1031T>G	3.37:g.178921549T>G	ENSP00000263967:p.Val344Gly		180404243	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391827	0.83011	.	.	ENSG00000121879	ENST00000263967	T	0.71103	-0.54	5.41	5.41	0.78517	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	D	0.83367	0.5239	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	D	0.84581	0.0661	10	0.49607	T	0.09	-22.945	15.721	0.77710	0.0:0.0:0.0:1.0	.	344	P42336	PK3CA_HUMAN	G	344	ENSP00000263967:V344G	ENSP00000263967:V344G	V	+	2	0	PIK3CA	180404243	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.606000	0.82863	2.166000	0.68216	0.402000	0.26972	GTG		0.303	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178921549	T	G	178921549	3	3	52	1	0	0	0	0	1	0	0	0	11944	1696	59	4	1045	4	PIK3CA	3	178921549	Missense_Mutation	SNP	T	TCGA-AG-3901-01A-01W-1073-09		178921549	19100881	13	7032										
KCNMB3	27094	broad.mit.edu	37	chr3	178968641	178968641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cggtcctctccagcactggaTggcagcctcttgtgcacatc	10	15	2	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr3:178968641T>C	ENST00000314235.5	-	2	661	c.150A>G	c.(148-150)ccA>ccG	p.P50P	KCNMB3_ENST00000485523.1_Silent_p.P28P|KCNMB3_ENST00000497599.1_Silent_p.P48P|KCNMB3_ENST00000392685.2_Silent_p.P46P|KCNMB3_ENST00000349697.2_Silent_p.P48P	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	50					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)	p.P50P(1)		NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	CAGCACTGGATGGCAGCCTCT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											107	99	102					3																	178968641		2203	4300	6503	180451335	SO:0001819	synonymous_variant	27094			AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"Potassium channels"	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.150A>G	3.37:g.178968641T>C			180451335	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000314235.5	37	CCDS3226.1																																																																																				0.527	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1			C	178968641	T	C	178968641	2	2	52	1	0	0	0	0	0	0	0	1	8097	1451	51	4		4	KCNMB3	3	178968641	Silent	SNP	T	TCGA-AG-3901-01A-01W-1073-09	47092	178968641	19053789	14	7033										
DGKG	1608	broad.mit.edu	37	chr3	185986590	185986590	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cgccctgggcgccaacccacCgtcatccggcaccacacgca	9	21	1	0	rs533768857		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr3:185986590C>T	ENST00000265022.3	-	12	1655	c.1116G>A	c.(1114-1116)acG>acA	p.T372T	DGKG_ENST00000544847.1_Intron|DGKG_ENST00000344484.4_Splice_Site_p.T372T|DGKG_ENST00000382164.4_Intron	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	372					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.T372T(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	GCCAACCCACCGTCATCCGGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	3											58	50	53					3																	185986590		2203	4300	6503	187469284	SO:0001630	splice_region_variant	1608			AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1116+1G>A	3.37:g.185986590C>T			187469284	B2RAH4|Q2M1H4|Q5FWG1	Silent	SNP	ENST00000265022.3	37	CCDS3274.1																																																																																				0.597	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		Silent	T	185986590	C	T	185986590	5	4	52	1	0	0	0	0	0	0	1	0	4480	666	23	1	1315	1	DGKG	3	185986590	Splice_Site	SNP	C	TCGA-AG-3901-01A-01W-1073-09	7017949	185986590	12035840	15	7034										
TNIP2	79155	broad.mit.edu	37	chr4	2749534	2749534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gcggcacaggacgtcactggCggcccgggcgcgctcccctt	15	17	1	0	rs545493843		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr4:2749534C>T	ENST00000315423.7	-	2	501	c.415G>A	c.(415-417)Gcc>Acc	p.A139T	TNIP2_ENST00000503235.1_Missense_Mutation_p.A139T|TNIP2_ENST00000505186.1_5'Flank|TNIP2_ENST00000510267.1_Missense_Mutation_p.A32T	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2									p.A139T(2)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACGTCACTGGCGGCCCGGGCG	0.657													c|||	1	0.000199681	0	0	5008	,	,		15662	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	4											96	94	95					4																	2749534		2203	4300	6503	2719332	SO:0001583	missense	79155			BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.415G>A	4.37:g.2749534C>T	ENSP00000321203:p.Ala139Thr		2719332		Missense_Mutation	SNP	ENST00000315423.7	37	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	c	6.971	0.549043	0.13312	.	.	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	T;T;T	0.28454	1.61;1.71;1.75	3.81	2.43	0.29744	.	0.196706	0.42548	D	0.000683	T	0.11239	0.0274	N	0.17345	0.48	0.30654	N	0.755072	P;B	0.36354	0.549;0.2	B;B	0.29176	0.099;0.019	T	0.13388	-1.0511	10	0.07990	T	0.79	-10.2482	4.1522	0.10244	0.0:0.5588:0.0:0.4412	.	139;139	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	T	32;139;139	ENSP00000427613:A32T;ENSP00000321203:A139T;ENSP00000426314:A139T	ENSP00000321203:A139T	A	-	1	0	TNIP2	2719332	1.000000	0.71417	0.143000	0.22291	0.719000	0.41307	2.535000	0.45685	0.962000	0.38057	0.550000	0.68814	GCC		0.657	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		T	2749534	C	T	2749534	3	4	52	1	0	0	0	0	1	0	0	0	16354	768	27	1	894	1	TNIP2	4	2749534	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		2749534	188404742	16	7035										
AFAP1	60312	broad.mit.edu	37	chr4	7770717	7770717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gggcgagttttccagggtccGgtgccggaacactggagact	16	10	0	1	rs149064401		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr4:7770717G>A	ENST00000360265.4	-	15	2254	c.2020C>T	c.(2020-2022)Cgg>Tgg	p.R674W	AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000420658.1_Missense_Mutation_p.R758W|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000382543.3_Missense_Mutation_p.R758W|AFAP1_ENST00000358461.2_Missense_Mutation_p.R674W			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	674						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)		p.R674W(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TCCAGGGTCCGGTGCCGGAAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	80	95	90		2272,2020	3.6	1	4	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AFAP1	NM_001134647.1,NM_198595.2	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	758/815,674/731	7770717	1,13005	2203	4300	6503	7821617	SO:0001583	missense	60312			AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.2020C>T	4.37:g.7770717G>A	ENSP00000353402:p.Arg674Trp		7821617	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176272	0.78564	0.0	1.16E-4	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.15834	2.41;2.39;2.41;2.39	4.48	3.59	0.41128	.	0.074746	0.56097	D	0.000035	T	0.28499	0.0705	L	0.60455	1.87	0.58432	D	0.999993	D;D	0.76494	0.999;0.998	P;P	0.53185	0.72;0.634	T	0.09596	-1.0667	10	0.87932	D	0	-37.4538	13.6873	0.62524	0.0:0.0:0.845:0.155	.	758;674	E9PDT7;Q8N556	.;AFAP1_HUMAN	W	674;758;674;758	ENSP00000353402:R674W;ENSP00000410689:R758W;ENSP00000351245:R674W;ENSP00000371983:R758W	ENSP00000351245:R674W	R	-	1	2	AFAP1	7821617	1.000000	0.71417	0.989000	0.46669	0.770000	0.43624	3.888000	0.56204	2.030000	0.59900	0.561000	0.74099	CGG		0.572	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		A	7770717	G	A	7770717	3	1	52	1	0	0	0	0	1	0	0	0	353	1115	39	1	180	1	AFAP1	4	7770717	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	5021183	7770717	183383559	17	7036										
CLNK	116449	broad.mit.edu	37	chr4	10560059	10560059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ttttggcttctgacgtccttGgaaatgggtttgtccacctg	11	9	1	1	rs371671172		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr4:10560059G>A	ENST00000226951.6	-	8	656	c.417C>T	c.(415-417)tcC>tcT	p.S139S	CLNK_ENST00000442825.2_Silent_p.S97S|CLNK_ENST00000507719.1_Silent_p.S97S	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	139					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)	p.S139S(2)		NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TGACGTCCTTGGAAATGGGTT	0.383													g|||	1	0.000199681	0	0	5008	,	,		22046	0		0.001	False		,,,				2504	0				GBM(87;402 1286 6949 13902 35851)											2	Substitution - coding silent(2)	large_intestine(2)	4						A		0,3838		0,0,1919	215	201	205		417	0.5	0.3	4		205	1,8271		0,1,4135	no	coding-synonymous	CLNK	NM_052964.2		0,1,6054	AA,AG,GG		0.0121,0.0,0.0083		139/429	10560059	1,12109	1919	4136	6055	10169157	SO:0001819	synonymous_variant	116449			AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.417C>T	4.37:g.10560059G>A			10169157	Q05C27|Q9P2U9	Silent	SNP	ENST00000226951.6	37	CCDS47024.1																																																																																				0.383	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		A	10560059	G	A	10560059	2	1	52	1	0	0	0	0	0	0	0	1	3553	1335	47	3		3	CLNK	4	10560059	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	2789342	10560059	180594217	18	7037										
CHRNA9	55584	broad.mit.edu	37	chr4	40356303	40356303	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	atgaacaaacgcttaaagaaCgacctgggctgccagggtaa	11	9	0	2	rs144758556	byFrequency	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr4:40356303C>T	ENST00000310169.2	+	5	1345	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	402					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)	p.N402N(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	GCTTAAAGAACGACCTGGGCT	0.483																																					Esophageal Squamous(115;1297 1602 22235 25158 43327)											1	Substitution - coding silent(1)	large_intestine(1)	4						C		2,4404	4.2+/-10.8	0,2,2201	84	74	78		1206	-3	1	4	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	CHRNA9	NM_017581.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		402/480	40356303	2,13004	2203	4300	6503	40051060	SO:0001819	synonymous_variant	55584			AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	14079	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 9 (neuronal)"	605116	"cholinergic receptor, nicotinic, alpha polypeptide 9"				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.1206C>T	4.37:g.40356303C>T			40051060	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																				0.483	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			T	40356303	C	T	40356303	2	4	52	1	0	0	0	0	0	0	0	1	3395	535	19	1		1	CHRNA9	4	40356303	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09	29796244	40356303	150797973	19	7038										
NIPBL	25836	broad.mit.edu	37	chr5	37044545	37044545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gtgaaacttttcttgccactAttgaggaagatctaatgaag	9	6	2	4			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr5:37044545A>G	ENST00000282516.8	+	35	6704	c.6205A>G	c.(6205-6207)Att>Gtt	p.I2069V	NIPBL_ENST00000448238.2_Missense_Mutation_p.I2069V	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2069					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.I2069V(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			TCTTGCCACTATTGAGGAAGA	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	5											90	88	89					5																	37044545		2203	4300	6503	37080302	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.6205A>G	5.37:g.37044545A>G	ENSP00000282516:p.Ile2069Val		37080302	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103020	0.56183	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	T;T	0.66815	-0.23;-0.23	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51109	0.1655	N	0.14661	0.345	0.54753	D	0.999984	B;B	0.17852	0.014;0.024	B;B	0.20384	0.013;0.029	T	0.45614	-0.9249	10	0.28530	T	0.3	-12.0682	15.4716	0.75443	1.0:0.0:0.0:0.0	.	2069;2069	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	V	2069	ENSP00000282516:I2069V;ENSP00000406266:I2069V	ENSP00000282516:I2069V	I	+	1	0	NIPBL	37080302	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.958000	0.93099	2.124000	0.65301	0.477000	0.44152	ATT		0.348	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37044545	A	G	37044545	3	3	52	1	0	0	0	0	1	0	0	0	10459	449	16	4	6339	4	NIPBL	5	37044545	Missense_Mutation	SNP	A	TCGA-AG-3901-01A-01W-1073-09		37044545	143870715	20	7039										
ATXN1	6310	broad.mit.edu	37	chr6	16327144	16327144	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gtgattgcttgctgctggccGctcaggtagccgatgacagg	15	10	1	2	rs144916658		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr6:16327144G>A	ENST00000244769.4	-	8	2334	c.1398C>T	c.(1396-1398)agC>agT	p.S466S	ATXN1_ENST00000436367.1_Silent_p.S466S	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	466					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.S466S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GCTGCTGGCCGCTCAGGTAGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	1,4405	2.1+/-5.4	0,1,2202	70	79	76		1398,1398	2.1	1	6	dbSNP_134	76	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ATXN1	NM_000332.3,NM_001128164.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	466/816,466/816	16327144	1,13005	2203	4300	6503	16435123	SO:0001819	synonymous_variant	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1398C>T	6.37:g.16327144G>A			16435123	Q17S02|Q9UJG2|Q9Y4J1	Silent	SNP	ENST00000244769.4	37	CCDS34342.1																																																																																				0.647	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327144	G	A	16327144	2	1	52	1	0	0	0	0	0	0	0	1	1210	1078	38	1		1	ATXN1	6	16327144	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09		16327144	154787923	21	7040										
TDRD6	221400	broad.mit.edu	37	chr6	46657943	46657943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgtttcaaaccactttactaCggagagtaacaaaatacctt	5	9	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr6:46657943C>T	ENST00000316081.6	+	1	2078	c.2078C>T	c.(2077-2079)aCg>aTg	p.T693M	RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.T693M|RP11-446F17.3_ENST00000434329.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	693					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)		p.T693R(1)|p.T693M(1)		NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			CACTTTACTACGGAGAGTAAC	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	6											49	50	50					6																	46657943		2203	4300	6503	46765902	SO:0001583	missense	221400			AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2078C>T	6.37:g.46657943C>T	ENSP00000346065:p.Thr693Met		46765902	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	C	9.935	1.215963	0.22373	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.15139	2.45;2.46	5.85	1.13	0.20643	.	1.246180	0.05029	N	0.474317	T	0.03871	0.0109	N	0.22421	0.69	0.09310	N	1	P;P	0.39181	0.663;0.592	B;B	0.32289	0.143;0.092	T	0.41324	-0.9515	10	0.48119	T	0.1	-1.759	9.7906	0.40704	0.0:0.6787:0.0:0.3213	.	693;693	F5H5M3;O60522	.;TDRD6_HUMAN	M	693	ENSP00000443299:T693M;ENSP00000346065:T693M	ENSP00000346065:T693M	T	+	2	0	TDRD6	46765902	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.055000	0.03493	-0.077000	0.12752	-0.782000	0.03352	ACG		0.418	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		T	46657943	C	T	46657943	3	4	52	1	0	0	0	0	1	0	0	0	15773	536	19	1	2080	1	TDRD6	6	46657943	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	30330799	46657943	124457124	22	7041										
OPRM1	4988	broad.mit.edu	37	chr6	154412611	154412611	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	atagaactaatcatcaggtaCgcagtctctagaattaggta	8	7	3	2	rs79668187		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr6:154412611C>T	ENST00000330432.7	+	3	1401				OPRM1_ENST00000522236.1_Intron|OPRM1_ENST00000428397.2_Missense_Mutation_p.R390C|OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000360422.4_Intron|OPRM1_ENST00000414028.2_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000229768.5_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000419506.2_Intron|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000524163.1_Intron	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)	p.?(3)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	TCATCAGGTACGCAGTCTCTA	0.408													C|||	1	0.000199681	0	0	5008	,	,		18905	0.001		0	False		,,,				2504	0															3	Unknown(3)	large_intestine(3)	6						C	,,CYS/ARG,,,,,,,,,,	0,3560		0,0,1780	32	32	32		,,1168,,,,,,,,,,	-9.9	0	6	dbSNP_131	32	5,7725		0,5,3860	yes	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron	OPRM1	NM_000914.3,NM_001008503.1,NM_001008504.2,NM_001008505.1,NM_001145279.2,NM_001145280.2,NM_001145281.1,NM_001145282.1,NM_001145283.1,NM_001145284.2,NM_001145285.1,NM_001145286.1,NM_001145287.1	,,180,,,,,,,,,,	0,5,5640	TT,TC,CC		0.0647,0.0,0.0443	,,,,,,,,,,,,	,,390/393,,,,,,,,,,	154412611	5,11285	1780	3865	5645	154454304	SO:0001627	intron_variant	4988			L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1164+4C>T	6.37:g.154412611C>T			154454304	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	7.121	0.577903	0.13686	0.0	6.47E-4	ENSG00000112038	ENST00000428397	T	0.70986	-0.53	6.16	-9.95	0.00446	.	.	.	.	.	T	0.21590	0.0520	.	.	.	0.80722	D	1	B;B	0.23490	0.0;0.086	B;B	0.12156	0.0;0.007	T	0.04165	-1.0972	7	.	.	.	.	3.887	0.09102	0.0799:0.2197:0.164:0.5365	.	290;390	Q6UPP1;P35372-2	.;.	C	390	ENSP00000411903:R390C	.	R	+	1	0	OPRM1	154454304	.	.	0.003000	0.11579	0.052000	0.14988	.	.	-2.203000	0.00744	-1.128000	0.01989	CGC		0.408	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		T	154412611	C	T	154412611	1	4	52	0	1	0	0	0	0	0	0	0	10918	536	19	1		1	OPRM1	6	154412611	Intron	SNP	C	TCGA-AG-3901-01A-01W-1073-09	107754668	154412611	16702456	23	7042										
HOXA5	3202	broad.mit.edu	37	chr7	27181483	27181483	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gaaggcccctcctgccgcggCcatgctcatgcttttcagct	10	16	2	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr7:27181483C>A	ENST00000222726.3	-	2	844	c.784G>T	c.(784-786)Gcc>Tcc	p.A262S	HOXA-AS3_ENST00000518848.1_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA5_ENST00000520854.1_5'UTR|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5	262					anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A262S(1)		central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						CCTGCCGCGGCCATGCTCATG	0.473											OREG0017911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(119;75 2200 7557 42868)											1	Substitution - Missense(1)	large_intestine(1)	7											112	110	111					7																	27181483		2203	4300	6503	27148008	SO:0001583	missense	3202				CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"Homeoboxes / ANTP class : HOXL subclass"	5106	protein-coding gene	gene with protein product		142952	"homeo box A5"	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214	ENST00000222726.3:c.784G>T	7.37:g.27181483C>A	ENSP00000222726:p.Ala262Ser	792	27148008	A4D179|O43367|Q96CY6	Missense_Mutation	SNP	ENST00000222726.3	37	CCDS5406.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.916948	0.52546	.	.	ENSG00000106004	ENST00000222726	D	0.91843	-2.92	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.83036	0.5167	N	0.04203	-0.255	0.80722	D	1	P	0.39809	0.689	B	0.36378	0.223	D	0.84597	0.0670	10	0.37606	T	0.19	.	18.9046	0.92455	0.0:1.0:0.0:0.0	.	262	P20719	HXA5_HUMAN	S	262	ENSP00000222726:A262S	ENSP00000222726:A262S	A	-	1	0	HOXA5	27148008	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.424000	0.80242	2.548000	0.85928	0.543000	0.68304	GCC		0.473	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1			A	27181483	C	A	27181483	3	1	52	1	0	0	0	0	1	0	0	0	7316	739	26	2	32	2	HOXA5	7	27181483	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		27181483	131957180	24	7043										
GRM3	2913	broad.mit.edu	37	chr7	86468760	86468760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	caccagtcatctgtgcattgCgccgactcgggctggggagt	14	12	2	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr7:86468760C>T	ENST00000361669.2	+	4	3029	c.1930C>T	c.(1930-1932)Cgc>Tgc	p.R644C	GRM3_ENST00000439827.1_Intron|GRM3_ENST00000536043.1_Missense_Mutation_p.R516C|GRM3_ENST00000546348.1_Missense_Mutation_p.R236C|GRM3_ENST00000394720.2_Intron	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	644					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.R644C(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CTGTGCATTGCGCCGACTCGG	0.532																																					GBM(52;969 1098 3139 52280)											1	Substitution - Missense(1)	large_intestine(1)	7											217	182	194					7																	86468760		2203	4300	6503	86306696	SO:0001583	missense	2913				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.1930C>T	7.37:g.86468760C>T	ENSP00000355316:p.Arg644Cys		86306696	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269599	0.80469	.	.	ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043	D;D;D	0.90788	-2.73;-2.73;-2.73	5.95	5.95	0.96441	GPCR, family 3, C-terminal (2);	0.050608	0.85682	D	0.000000	D	0.96125	0.8737	M	0.87038	2.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.978;0.99;0.994	D	0.96138	0.9098	10	0.87932	D	0	.	19.3629	0.94448	0.0:1.0:0.0:0.0	.	236;516;644	B7Z204;F5GYZ2;Q14832	.;.;GRM3_HUMAN	C	644;236;516	ENSP00000355316:R644C;ENSP00000444064:R236C;ENSP00000441407:R516C	ENSP00000355316:R644C	R	+	1	0	GRM3	86306696	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	7.818000	0.86416	2.817000	0.96982	0.563000	0.77884	CGC		0.532	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			T	86468760	C	T	86468760	3	4	52	1	0	0	0	0	1	0	0	0	6819	768	27	1	1940	1	GRM3	7	86468760	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	59287277	86468760	72669903	25	7044										
CASD1	64921	broad.mit.edu	37	chr7	94167097	94167097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	atatttctatatgtgtgaccGtgcaaatctgttcatgaagg	9	6	3	2	rs371554475		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr7:94167097G>A	ENST00000297273.4	+	9	1444	c.1157G>A	c.(1156-1158)cGt>cAt	p.R386H		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	386			R -> S (in dbSNP:rs17855797). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.R386H(1)		NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	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)			ATGTGTGACCGTGCAAATCTG	0.289													G|||	1	0.000199681	8e-04	0	5008	,	,		18079	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						G	HIS/ARG	0,4404		0,0,2202	97	108	104		1157	4.6	1	7		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	CASD1	NM_022900.4	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	386/798	94167097	1,13003	2202	4300	6502	94005033	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1157G>A	7.37:g.94167097G>A	ENSP00000297273:p.Arg386His		94005033	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586622	0.86851	0.0	1.16E-4	ENSG00000127995	ENST00000297273	T	0.64438	-0.1	5.51	4.63	0.57726	.	0.049300	0.85682	N	0.000000	T	0.65933	0.2739	M	0.79693	2.465	0.58432	D	0.999998	B;B	0.17038	0.02;0.02	B;B	0.19946	0.027;0.027	T	0.67577	-0.5635	10	0.87932	D	0	.	14.4995	0.67711	0.0709:0.0:0.9291:0.0	.	386;386	Q8WZ77;Q96PB1	.;CASD1_HUMAN	H	386	ENSP00000297273:R386H	ENSP00000297273:R386H	R	+	2	0	CASD1	94005033	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.606000	0.98325	1.475000	0.48197	0.585000	0.79938	CGT		0.289	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		A	94167097	G	A	94167097	3	1	52	1	0	0	0	0	1	0	0	0	2670	1145	40	1	1191	1	CASD1	7	94167097	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	7698337	94167097	64971566	26	7045										
IMPDH1	3614	broad.mit.edu	37	chr7	128033072	128033072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ccgctgtcctcagtacagccGcttttcgtaactgtggggac	11	13	1	0	rs530357590		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr7:128033072G>A	ENST00000480861.1	-	14	1596	c.1519C>T	c.(1519-1521)Cgg>Tgg	p.R507W	IMPDH1_ENST00000338791.6_Missense_Mutation_p.R597W|IMPDH1_ENST00000496200.1_Missense_Mutation_p.R487W|IMPDH1_ENST00000470772.1_Missense_Mutation_p.R511W|IMPDH1_ENST00000343214.4_Missense_Mutation_p.R487W|IMPDH1_ENST00000354269.5_Missense_Mutation_p.R587W|IMPDH1_ENST00000419067.2_Missense_Mutation_p.R564W|IMPDH1_ENST00000378717.4_Missense_Mutation_p.R528W|IMPDH1_ENST00000348127.6_Missense_Mutation_p.R561W	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1									p.R597W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						CAGTACAGCCGCTTTTCGTAA	0.602													G|||	1	0.000199681	0	0.0014	5008	,	,		19139	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7											103	79	88					7																	128033072		2203	4300	6503	127820308	SO:0001583	missense	3614				CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"retinitis pigmentosa 10 (autosomal dominant)", "IMP (inosine monophosphate) dehydrogenase 1"	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1519C>T	7.37:g.128033072G>A	ENSP00000420185:p.Arg507Trp		127820308		Missense_Mutation	SNP	ENST00000480861.1	37	CCDS55161.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.985951	0.53934	.	.	ENSG00000106348	ENST00000419067;ENST00000338791;ENST00000496200;ENST00000354269;ENST00000378717;ENST00000348127;ENST00000343214;ENST00000470772;ENST00000480861	T;T;T;T;T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23	5.16	5.16	0.70880	Aldolase-type TIM barrel (1);	0.131624	0.37178	U	0.002215	T	0.78786	0.4338	M	0.87097	2.86	0.58432	D	0.999996	B;B;B;B;B;B;B	0.31655	0.017;0.024;0.024;0.012;0.207;0.334;0.041	B;B;B;B;B;B;B	0.17433	0.002;0.0;0.0;0.005;0.018;0.008;0.007	T	0.81378	-0.0960	10	0.87932	D	0	-18.527	14.1242	0.65210	0.0:0.0:1.0:0.0	.	564;507;512;528;561;597;487	C9JV30;B4DE09;P20839;E7EQS0;P20839-3;A4D0Z6;P20839-2	.;.;IMDH1_HUMAN;.;.;.;.	W	564;597;487;587;528;561;487;511;507	ENSP00000399400:R564W;ENSP00000345096:R597W;ENSP00000420803:R487W;ENSP00000346219:R587W;ENSP00000367989:R528W;ENSP00000265385:R561W;ENSP00000342438:R487W;ENSP00000417296:R511W;ENSP00000420185:R507W	ENSP00000345096:R597W	R	-	1	2	IMPDH1	127820308	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.200000	0.65158	2.389000	0.81357	0.297000	0.19635	CGG		0.602	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883		A	128033072	G	A	128033072	3	1	52	1	0	0	0	0	1	0	0	0	7747	1086	38	1	14	1	IMPDH1	7	128033072	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	33865975	128033072	31105591	27	7046										
ZNF425	155054	broad.mit.edu	37	chr7	148815402	148815402	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aggatctcccactcttgttcCgaaaaatataaggccacatc	6	12	2	0	rs560790723		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr7:148815402C>T	ENST00000378061.2	-	2	189	c.57G>A	c.(55-57)tcG>tcA	p.S19S		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	19	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S19S(1)		breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ACTCTTGTTCCGAAAAATATA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	7											216	200	205					7																	148815402		2203	4300	6503	148446335	SO:0001819	synonymous_variant	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.57G>A	7.37:g.148815402C>T			148446335	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																				0.393	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148815402	C	T	148815402	2	4	52	1	0	0	0	0	0	0	0	1	17938	639	23	1		1	ZNF425	7	148815402	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09	20782330	148815402	10323261	28	7047										
SLC24A2	25769	broad.mit.edu	37	chr9	19619585	19619585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	caaagcttgatgtttaccttCggcgagtgggtcaagggtgt	14	7	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr9:19619585C>T	ENST00000341998.2	-	3	1136	c.1075G>A	c.(1075-1077)Gaa>Aaa	p.E359K	SLC24A2_ENST00000286344.3_Missense_Mutation_p.E359K	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	359					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)	p.E359K(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		TGTTTACCTTCGGCGAGTGGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											204	188	193					9																	19619585		2203	4300	6503	19609585	SO:0001583	missense	25769			AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1075G>A	9.37:g.19619585C>T	ENSP00000344801:p.Glu359Lys		19609585	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	37	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.257455	0.80246	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.77098	-1.07;-1.0	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.85164	0.5634	M	0.80183	2.485	0.80722	D	1	D;D	0.57571	0.976;0.98	P;P	0.51324	0.457;0.666	D	0.85408	0.1135	9	.	.	.	.	19.6614	0.95875	0.0:1.0:0.0:0.0	.	359;359	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	K	359	ENSP00000344801:E359K;ENSP00000286344:E359K	.	E	-	1	0	SLC24A2	19609585	1.000000	0.71417	0.997000	0.53966	0.407000	0.30961	5.834000	0.69361	2.740000	0.93945	0.650000	0.86243	GAA		0.517	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		T	19619585	C	T	19619585	3	4	52	1	0	0	0	0	1	0	0	0	14503	893	31	1	942	1	SLC24A2	9	19619585	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		19619585	121593846	29	7048										
CBWD3	445571	broad.mit.edu	37	chr9	70871837	70871837	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgaatattatatattttcacGtgcagtggcttctatgtttt	7	5	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr9:70871837G>A	ENST00000360171.6	+	5	982	c.431G>A	c.(430-432)gGt>gAt	p.G144D	CBWD3_ENST00000377342.5_Intron	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3	144							ATP binding (GO:0005524)	p.G144D(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		ATATTTTCACGTGCAGTGGCT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	9											25	31	29					9																	70871837		2190	4253	6443	70061657	SO:0001630	splice_region_variant	445571			BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.431-1G>A	9.37:g.70871837G>A			70061657	B4DNG9|Q6VB91	Missense_Mutation	SNP	ENST00000360171.6	37	CCDS35038.1	.	.	.	.	.	.	.	.	.	.	.	17.89	3.499164	0.64298	.	.	ENSG00000196873	ENST00000360171;ENST00000447896;ENST00000455061;ENST00000455820;ENST00000377344	T	0.43294	0.95	3.38	3.38	0.38709	Cobalamin (vitamin B12) biosynthesis CobW-like (1);	0.000000	0.85682	D	0.000000	T	0.63271	0.2497	M	0.88979	2.995	0.80722	D	1	D	0.57899	0.981	P	0.56823	0.807	T	0.72669	-0.4223	9	.	.	.	.	13.8697	0.63610	0.0:0.0:1.0:0.0	.	144	Q5JTY5	CBWD3_HUMAN	D	144;144;144;144;108	ENSP00000353295:G144D	.	G	+	2	0	CBWD3	70061657	1.000000	0.71417	0.991000	0.47740	0.822000	0.46500	8.848000	0.92172	1.602000	0.50124	0.305000	0.20034	GGT		0.284	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453	Missense_Mutation	A	70871837	G	A	70871837	5	1	52	1	0	0	0	0	0	0	1	0	2720	1159	40	1	1697	1	CBWD3	9	70871837	Splice_Site	SNP	G	TCGA-AG-3901-01A-01W-1073-09	51252252	70871837	70341594	30	7049										
SHC3	53358	broad.mit.edu	37	chr9	91667023	91667023	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cggagctcaaaggcttgtccGatggagccgatgacatcctg	13	11	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr9:91667023G>A	ENST00000375835.4	-	7	1197	c.891C>T	c.(889-891)atC>atT	p.I297I	SHC3_ENST00000375830.1_5'UTR	NM_016848.5	NP_058544.3	Q92529	SHC3_HUMAN	SHC (Src homology 2 domain containing) transforming protein 3	297	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|insulin receptor signaling pathway (GO:0008286)|learning or memory (GO:0007611)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	signal transducer activity (GO:0004871)	p.I297I(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|skin(3)	28						AGGCTTGTCCGATGGAGCCGA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	9											91	85	87					9																	91667023		2203	4300	6503	90856843	SO:0001819	synonymous_variant	53358			D84361	CCDS6681.1	9q22.1	2013-02-14	2005-05-24		ENSG00000148082	ENSG00000148082		"SH2 domain containing"	18181	protein-coding gene	gene with protein product		605263	"src homology 2 domain containing transforming protein C3"			8808684	Standard	NM_016848		Approved	N-Shc, NSHC, SHCC	uc004aqf.2	Q92529	OTTHUMG00000020179	ENST00000375835.4:c.891C>T	9.37:g.91667023G>A			90856843	Q5T7I7|Q8TAP2|Q9UCX5	Silent	SNP	ENST00000375835.4	37	CCDS6681.1																																																																																				0.498	SHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052986.1	NM_016848		A	91667023	G	A	91667023	2	1	52	1	0	0	0	0	0	0	0	1	14309	1048	37	1		1	SHC3	9	91667023	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	20795186	91667023	49546408	31	7050										
SLC35D2	11046	broad.mit.edu	37	chr9	99084293	99084293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cactcaccaaatatttaaccCtacaaagtttaacaaagaga	3	10	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr9:99084293C>T	ENST00000253270.7	-	11	963	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	SLC35D2_ENST00000375259.4_Missense_Mutation_p.G213R	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	301					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)	p.G301R(1)		endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				ATATTTAACCCTACAAAGTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											73	79	77					9																	99084293		2203	4300	6503	98124114	SO:0001583	missense	11046			AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.901G>A	9.37:g.99084293C>T	ENSP00000253270:p.Gly301Arg		98124114	O95454|Q498C1|Q75W21|Q7Z5X5	Missense_Mutation	SNP	ENST00000253270.7	37	CCDS6717.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185579	0.78677	.	.	ENSG00000130958	ENST00000253270;ENST00000375259	T;T	0.80123	-1.34;-1.34	4.84	4.84	0.62591	Domain of unknown function DUF250 (1);	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	M	0.90019	3.08	0.33749	D	0.620376	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94993	0.8136	10	0.87932	D	0	.	15.4797	0.75514	0.0:1.0:0.0:0.0	.	213;301	Q76EJ3-2;Q76EJ3	.;S35D2_HUMAN	R	301;213	ENSP00000253270:G301R;ENSP00000364408:G213R	ENSP00000253270:G301R	G	-	1	0	SLC35D2	98124114	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	5.904000	0.69886	2.522000	0.85027	0.563000	0.77884	GGG		0.363	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			T	99084293	C	T	99084293	3	4	52	1	0	0	0	0	1	0	0	0	14619	681	24	3	120	3	SLC35D2	9	99084293	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	7417270	99084293	42129138	32	7051										
NCBP1	4686	broad.mit.edu	37	chr9	100407910	100407910	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	taggtgcgacgagattggtaTgtgtatgcatttctgtcatc	12	6	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr9:100407910T>C	ENST00000375147.3	+	6	763	c.507T>C	c.(505-507)taT>taC	p.Y169Y		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	169	MIF4G.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)	p.Y169Y(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				GAGATTGGTATGTGTATGCAT	0.338																																					Ovarian(36;879 898 2893 44212 50307)											1	Substitution - coding silent(1)	large_intestine(1)	9											131	118	122					9																	100407910		2203	4300	6503	99447731	SO:0001819	synonymous_variant	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.507T>C	9.37:g.100407910T>C			99447731	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	37	CCDS6728.1																																																																																				0.338	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		C	100407910	T	C	100407910	2	2	52	1	0	0	0	0	0	0	0	1	10242	1471	51	4		4	NCBP1	9	100407910	Silent	SNP	T	TCGA-AG-3901-01A-01W-1073-09	1323617	100407910	40805521	33	7052										
MCM10	55388	broad.mit.edu	37	chr10	13234299	13234299	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gctctgaggagttcaaggaaCtgatggacctgccgacgtgt	14	9	2	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr10:13234299C>A	ENST00000484800.2	+	12	1667	c.1564C>A	c.(1564-1566)Ctg>Atg	p.L522M	MCM10_ENST00000378714.3_Missense_Mutation_p.L521M|MCM10_ENST00000378694.1_Missense_Mutation_p.L521M			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	522					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.L522M(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						GTTCAAGGAACTGATGGACCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											116	98	104					10																	13234299		2203	4300	6503	13274305	SO:0001583	missense	55388			AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1564C>A	10.37:g.13234299C>A	ENSP00000418268:p.Leu522Met		13274305	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710072	0.68730	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.28454	1.65;1.65;1.61	5.52	-8.72	0.00845	.	0.000000	0.85682	D	0.000000	T	0.35480	0.0933	L	0.32530	0.975	0.45216	D	0.99822	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.987	T	0.62784	-0.6781	10	0.36615	T	0.2	-10.436	16.184	0.81934	0.0:0.4046:0.0:0.5954	.	521;521;522	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	M	521;522;522;521	ENSP00000367986:L521M;ENSP00000418268:L522M;ENSP00000367966:L521M	ENSP00000354945:L522M	L	+	1	2	MCM10	13274305	0.620000	0.27068	0.163000	0.22734	0.992000	0.81027	0.014000	0.13333	-1.981000	0.00989	-0.152000	0.13540	CTG		0.507	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		A	13234299	C	A	13234299	3	1	52	1	0	0	0	0	1	0	0	0	9415	564	20	2	1606	2	MCM10	10	13234299	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		13234299	122300448	34	7053										
PTEN	5728	broad.mit.edu	37	chr10	89685307	89685307	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	ataaaaaccattacaagataTacaatctgtaagtatgtttt	4	5	1	1	rs398123317		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr10:89685307T>A	ENST00000371953.3	+	3	1559	c.202T>A	c.(202-204)Tac>Aac	p.Y68N		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	68	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> H (in CWS1 and BRRS; loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3; retains the ability to bind phospholipid membranes). {ECO:0000269|PubMed:10400993, ECO:0000269|PubMed:11494117, ECO:0000269|PubMed:9600246}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.Y68H(8)|p.?(6)|p.R55fs*1(5)|p.Y68N(2)|p.Y68fs*5(2)|p.Y27fs*1(2)|p.I67_Y68insY(1)|p.V54fs*29(1)|p.R55_L70>S(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTACAAGATATACAATCTGTA	0.274		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	66	Whole gene deletion(37)|Deletion - Frameshift(11)|Substitution - Missense(10)|Unknown(6)|Insertion - In frame(1)|Complex - deletion inframe(1)	prostate(16)|central_nervous_system(15)|skin(7)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|lung(5)|ovary(4)|urinary_tract(2)|breast(2)|large_intestine(1)|soft_tissue(1)|kidney(1)|pancreas(1)	10	GRCh37	CM061927|CM981667	PTEN	M							41	42	42					10																	89685307		2186	4275	6461	89675287	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.202T>A	10.37:g.89685307T>A	ENSP00000361021:p.Tyr68Asn		89675287	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.443705	0.83993	.	.	ENSG00000171862	ENST00000371953	D	0.98666	-5.06	5.46	5.46	0.80206	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99211	0.9726	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99331	1.0909	9	.	.	.	-6.2149	15.5246	0.75894	0.0:0.0:0.0:1.0	.	68	P60484	PTEN_HUMAN	N	68	ENSP00000361021:Y68N	.	Y	+	1	0	PTEN	89675287	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.448000	0.80631	2.072000	0.62099	0.533000	0.62120	TAC		0.274	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89685307	T	A	89685307	3	1	52	1	0	0	0	0	1	0	0	0	12772	1406	49	5	212	5	PTEN	10	89685307	Missense_Mutation	SNP	T	TCGA-AG-3901-01A-01W-1073-09	76451008	89685307	45849440	35	7054										
TCTN3	26123	broad.mit.edu	37	chr10	97423975	97423975	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tccagtccattttgggttggCcccttggaggctgtggcttc	13	11	0	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr10:97423975C>G	ENST00000371217.5	-	14	1696	c.1673G>C	c.(1672-1674)gGc>gCc	p.G558A	TCTN3_ENST00000430368.2_Missense_Mutation_p.G410A|TCTN3_ENST00000265993.9_Missense_Mutation_p.G576A			Q6NUS6	TECT3_HUMAN	tectonic family member 3	558					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.G380A(1)|p.G558A(1)		breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		TTTGGGTTGGCCCCTTGGAGG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	10											263	263	263					10																	97423975		2203	4300	6503	97413965	SO:0001583	missense	26123			AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.1673G>C	10.37:g.97423975C>G	ENSP00000360261:p.Gly558Ala		97413965	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Missense_Mutation	SNP	ENST00000371217.5	37	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018249	0.54576	.	.	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000343162	T	0.80994	-1.44	6.04	4.17	0.49024	.	0.150322	0.43919	D	0.000504	T	0.75975	0.3923	L	0.33485	1.01	0.26455	N	0.975532	D;P;P	0.63880	0.993;0.78;0.956	P;B;P	0.58331	0.837;0.265;0.78	T	0.65907	-0.6054	10	0.02654	T	1	-25.9825	8.8988	0.35481	0.0:0.8234:0.0:0.1766	.	410;558;380	B4DR81;Q6NUS6;Q6NUS6-3	.;TECT3_HUMAN;.	A	558;410;576;380	ENSP00000265993:G558A	ENSP00000265993:G558A	G	-	2	0	TCTN3	97413965	0.994000	0.37717	1.000000	0.80357	0.987000	0.75469	1.195000	0.32186	1.539000	0.49286	0.563000	0.77884	GGC		0.458	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631		G	97423975	C	G	97423975	3	3	52	1	0	0	0	0	1	0	0	0	15763	739	26	5	154	5	TCTN3	10	97423975	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	7738668	97423975	38110772	36	7055										
GFRA1	2674	broad.mit.edu	37	chr10	117884958	117884958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gttgcagacatcgttggacaCgctggtggtgcacggggtga	17	8	0	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr10:117884958C>T	ENST00000355422.6	-	6	1094	c.544G>A	c.(544-546)Gtg>Atg	p.V182M	GFRA1_ENST00000439649.3_Missense_Mutation_p.V177M|GFRA1_ENST00000544592.1_Missense_Mutation_p.V61M|GFRA1_ENST00000369236.1_Missense_Mutation_p.V177M	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	182					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.V177M(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		TCGTTGGACACGCTGGTGGTG	0.587																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - Missense(1)	large_intestine(1)	10											79	65	70					10																	117884958		2203	4300	6503	117874948	SO:0001583	missense	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.544G>A	10.37:g.117884958C>T	ENSP00000347591:p.Val182Met		117874948	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	C	5.955	0.360260	0.11296	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.63255	-0.03;-0.03	5.74	3.29	0.37713	GDNF/GAS1 (2);	0.304234	0.40908	N	0.000986	T	0.44664	0.1304	L	0.28740	0.885	0.29512	N	0.854152	B;B	0.24533	0.105;0.068	B;B	0.21151	0.033;0.014	T	0.35425	-0.9789	10	0.30854	T	0.27	-17.6791	7.414	0.27034	0.0:0.147:0.1323:0.7207	.	182;177	P56159;P56159-2	GFRA1_HUMAN;.	M	182;177;177;61;177	ENSP00000358239:V177M;ENSP00000442179:V61M	ENSP00000347591:V177M	V	-	1	0	GFRA1	117874948	1.000000	0.71417	1.000000	0.80357	0.222000	0.24845	1.370000	0.34238	1.020000	0.39573	-0.367000	0.07326	GTG		0.587	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		T	117884958	C	T	117884958	3	4	52	1	0	0	0	0	1	0	0	0	6367	536	19	1	877	1	GFRA1	10	117884958	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	20460983	117884958	17649789	37	7056										
KAT5	10524	broad.mit.edu	37	chr11	65482088	65482088	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	attgagtgcattgagctgggCcggcaccgcctcaagccgtg	14	12	1	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr11:65482088C>T	ENST00000377046.3	+	8	986	c.714C>T	c.(712-714)ggC>ggT	p.G238G	KAT5_ENST00000530446.1_Silent_p.G219G|KAT5_ENST00000352980.4_Silent_p.G186G|KAT5_ENST00000534650.1_Silent_p.G27G|KAT5_ENST00000341318.4_Silent_p.G271G	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	238	MYST-type HAT.				androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)	p.G271G(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						TTGAGCTGGGCCGGCACCGCC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											154	126	136					11																	65482088		2201	4297	6498	65238664	SO:0001819	synonymous_variant	10524			U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.714C>T	11.37:g.65482088C>T			65238664	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Silent	SNP	ENST00000377046.3	37	CCDS31610.1																																																																																				0.582	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		T	65482088	C	T	65482088	2	4	52	1	0	0	0	0	0	0	0	1	8004	726	26	3		3	KAT5	11	65482088	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09		65482088	69524428	38	7057										
TYR	7299	broad.mit.edu	37	chr11	88911235	88911235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gagaaggaatgctgtccaccGtggagcggggacaggagtcc	17	9	0	1	rs1939261	byFrequency	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr11:88911235G>A	ENST00000263321.5	+	1	616	c.114G>A	c.(112-114)ccG>ccA	p.P38P	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	38					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.P38P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GCTGTCCACCGTGGAGCGGGG	0.542													G|||	64	0.0127796	0.0484	0	5008	,	,		19065	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						G		222,4180	132.9+/-169.3	8,206,1987	67	63	65		114	-12.1	0	11	dbSNP_92	65	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	TYR	NM_000372.4		8,208,6284	AA,AG,GG		0.0233,5.0432,1.7231		38/530	88911235	224,12776	2201	4299	6500	88550883	SO:0001819	synonymous_variant	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.114G>A	11.37:g.88911235G>A			88550883	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Silent	SNP	ENST00000263321.5	37	CCDS8284.1																																																																																				0.542	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		A	88911235	G	A	88911235	2	1	52	1	0	0	0	0	0	0	0	1	16853	1132	40	1		1	TYR	11	88911235	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	23429147	88911235	46095281	39	7058										
DYNC2H1	79659	broad.mit.edu	37	chr11	103157020	103157020	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tttatcagaccctctgctttGaagatgcagctctgtggcgt	10	10	3	3			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr11:103157020G>T	ENST00000375735.2	+	74	11071	c.10927G>T	c.(10927-10929)Gaa>Taa	p.E3643*	DYNC2H1_ENST00000398093.3_Nonsense_Mutation_p.E3650*|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3643					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E1083*(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCTCTGCTTTGAAGATGCAGC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											188	192	191					11																	103157020		1894	4142	6036	102662230	SO:0001587	stop_gained	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10927G>T	11.37:g.103157020G>T	ENSP00000364887:p.Glu3643*		102662230	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Nonsense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	52	19.475371	0.99920	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	.	.	.	5.41	5.41	0.78517	.	0.328595	0.36066	N	0.002815	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	15.2116	0.73227	0.0:0.1412:0.8588:0.0	.	.	.	.	X	3643;3650	.	ENSP00000364887:E3643X	E	+	1	0	DYNC2H1	102662230	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.185000	0.58330	2.530000	0.85305	0.655000	0.94253	GAA		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103157020	G	T	103157020	4	4	52	1	0	0	0	0	0	1	0	0	4857	1291	45	2	11246	2	DYNC2H1	11	103157020	Nonsense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	14245785	103157020	31849496	40	7059										
KRAS	3845	broad.mit.edu	37	chr12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	acttacctgtcttgtctttgCtgatgtttcaataaaaggaa	7	7	3	1	rs121913527		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	12											207	188	195					12																	25378562		2203	4300	6503	25269829	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr		25269829	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA		0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25378562	C	T	25378562	3	4	52	1	0	0	0	0	1	0	0	0	8459	797	28	3	262	3	KRAS	12	25378562	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		25378562	108473333	41	7060										
UGGT2	55757	broad.mit.edu	37	chr13	96684169	96684169	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gcttataaattgctaattctTgcacagtttccaaaaactgc	5	9	1	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr13:96684169T>C	ENST00000376747.3	-	2	285	c.215A>G	c.(214-216)cAa>cGa	p.Q72R	UGGT2_ENST00000397618.3_Missense_Mutation_p.Q72R|UGGT2_ENST00000376714.3_Missense_Mutation_p.Q72R|UGGT2_ENST00000376712.4_Missense_Mutation_p.Q72R	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	72					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.Q72R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TGCTAATTCTTGCACAGTTTC	0.249																																																1	Substitution - Missense(1)	large_intestine(1)	13											60	63	62					13																	96684169		2198	4280	6478	95482170	SO:0001583	missense	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.215A>G	13.37:g.96684169T>C	ENSP00000365938:p.Gln72Arg		95482170	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.481689	0.26598	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.30448	3.13;1.53	5.93	-2.12	0.07165	.	0.722577	0.14026	N	0.346490	T	0.14743	0.0356	N	0.20685	0.6	0.20489	N	0.999897	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.16041	-1.0416	10	0.87932	D	0	-9.0E-4	2.748	0.05273	0.1157:0.3733:0.1173:0.3937	.	72;72;72	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	R	72	ENSP00000365938:Q72R;ENSP00000380743:Q72R	ENSP00000365902:Q72R	Q	-	2	0	UGGT2	95482170	0.070000	0.21116	0.215000	0.23724	0.991000	0.79684	0.235000	0.17948	-0.241000	0.09681	0.533000	0.62120	CAA		0.249	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		C	96684169	T	C	96684169	3	2	52	1	0	0	0	0	1	0	0	0	16982	1812	63	4	4487	4	UGGT2	13	96684169	Missense_Mutation	SNP	T	TCGA-AG-3901-01A-01W-1073-09		96684169	18485709	42	7061										
DOCK9	23348	broad.mit.edu	37	chr13	99479090	99479090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gaataattccttacctttccGtgtgagatattctgccacta	6	10	1	1	rs371892069		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr13:99479090G>A	ENST00000376460.1	-	44	5028	c.4948C>T	c.(4948-4950)Cgg>Tgg	p.R1650W	DOCK9_ENST00000448493.2_3'UTR|DOCK9_ENST00000339416.2_Missense_Mutation_p.R1651W	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1651	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1651W(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TTACCTTTCCGTGTGAGATAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	TRP/ARG,TRP/ARG	1,3823		0,1,1911	104	93	97		4948,4951	4.1	1	13		97	0,8268		0,0,4134	no	missense,missense	DOCK9	NM_001130048.1,NM_015296.2	101,101	0,1,6045	AA,AG,GG		0.0,0.0262,0.0083	probably-damaging,probably-damaging	1650/2069,1651/2070	99479090	1,12091	1912	4134	6046	98277091	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.4948C>T	13.37:g.99479090G>A	ENSP00000365643:p.Arg1650Trp		98277091	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.96|17.96	3.516310|3.516310	0.64634|0.64634	2.62E-4|2.62E-4	0.0|0.0	ENSG00000088387|ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453;ENST00000451563;ENST00000340449|ENST00000400228	T;T;T;T|T	0.46819|0.23552	2.33;2.41;0.97;0.86|1.9	5.1|5.1	4.12|4.12	0.48240|0.48240	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.49474|0.49474	0.1559|0.1559	M|M	0.83852|0.83852	2.665|2.665	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0;1.0;0.999;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.85130|.	0.997;0.991;0.991;0.994;0.967;0.937;0.986;0.996|.	T|T	0.52931|0.52931	-0.8509|-0.8509	10|7	0.66056|0.46703	D|T	0.02|0.11	.|.	14.9842|14.9842	0.71332|0.71332	0.0:0.0:0.8138:0.1862|0.0:0.0:0.8138:0.1862	.|.	1651;370;294;1650;294;1651;343;293|.	A8MWZ5;B7Z6H5;B7Z2J2;Q9BZ29-5;Q5JUD8;Q9BZ29;B7Z6G9;F5H1Q4|.	.;.;.;.;.;DOCK9_HUMAN;.;.|.	W|M	1650;1651;1643;1651;1650;581;1651;293;38;294|237	ENSP00000365643:R1650W;ENSP00000341086:R1651W;ENSP00000407610:R38W;ENSP00000344702:R294W|ENSP00000383087:T237M	ENSP00000341086:R1651W|ENSP00000383087:T237M	R|T	-|-	1|2	2|0	DOCK9|DOCK9	98277091|98277091	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.676000|0.676000	0.39594|0.39594	2.040000|2.040000	0.41203|0.41203	2.512000|2.512000	0.84698|0.84698	0.460000|0.460000	0.39030|0.39030	CGG|ACG		0.403	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		A	99479090	G	A	99479090	3	1	52	1	0	0	0	0	1	0	0	0	4705	1144	40	1	1306	1	DOCK9	13	99479090	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	2794921	99479090	15690788	43	7062										
PML	5371	broad.mit.edu	37	chr15	74326969	74326969	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gactctcagacttgccttgcGcctggggaattttccagtga	11	11	1	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr15:74326969G>A	ENST00000268058.3	+	7	1806				PML_ENST00000569477.1_Intron|PML_ENST00000435786.2_Missense_Mutation_p.R603H|PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000354026.6_Intron|PML_ENST00000268059.6_Intron|PML_ENST00000563500.1_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000565898.1_Intron|PML_ENST00000436891.3_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R603H(1)|p.R603L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CTTGCCTTGCGCCTGGGGAAT	0.602			T	"RARA, PAX5"	"APL, ALL"																																		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	15											53	51	52					15																	74326969		1322	2306	3628	72114022	SO:0001627	intron_variant	5371			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+98G>A	15.37:g.74326969G>A			72114022	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	.	.	.	.	.	.	.	.	.	.	G	3.157	-0.172854	0.06421	.	.	ENSG00000140464	ENST00000435786	.	.	.	3.18	-6.35	0.01975	.	.	.	.	.	T	0.29126	0.0724	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22765	-1.0207	6	.	.	.	.	13.3877	0.60805	0.6699:0.0:0.3301:0.0	.	603	P29590-2	.	H	603	.	.	R	+	2	0	PML	72114022	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.955000	0.01523	-2.553000	0.00478	-2.069000	0.00389	CGC		0.602	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74326969	G	A	74326969	1	1	52	0	1	0	0	0	0	0	0	0	12166	1087	38	1		1	PML	15	74326969	Intron	SNP	G	TCGA-AG-3901-01A-01W-1073-09		74326969	28204423	44	7063										
CPPED1	55313	broad.mit.edu	37	chr16	12798724	12798724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gttgaggaccaggaacaggaCgcccccgacccagaagctga	13	13	0	3	rs145004672	byFrequency	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr16:12798724C>T	ENST00000381774.4	-	3	712	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	CPPED1_ENST00000433677.2_Intron|CPPED1_ENST00000261660.4_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	158	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.V158I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						AGGAACAGGACGCCCCCGACC	0.612													C|||	42	0.00838658	0.0272	0.0029	5008	,	,		17716	0.003		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16						C	,ILE/VAL	69,3929		1,67,1931	57	62	60		,472	4.4	0.8	16	dbSNP_134	60	1,8319		0,1,4159	yes	intron,missense	CPPED1	NM_001099455.1,NM_018340.2	,29	1,68,6090	TT,TC,CC		0.012,1.7259,0.5683	,possibly-damaging	,158/315	12798724	70,12248	1999	4160	6159	12706225	SO:0001583	missense	55313			AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"complete S transactivated protein 1"	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.472G>A	16.37:g.12798724C>T	ENSP00000371193:p.Val158Ile		12706225	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	27	0.012362637362637362	23	0.046747967479674794	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	C	16.61	3.171078	0.57584	0.017259	1.2E-4	ENSG00000103381	ENST00000381774	T	0.72505	-0.66	5.32	4.37	0.52481	Metallophosphoesterase domain (1);	0.053983	0.64402	D	0.000001	T	0.29882	0.0747	M	0.67397	2.05	0.80722	D	1	P	0.47191	0.891	B	0.43194	0.411	T	0.56165	-0.8024	10	0.46703	T	0.11	-31.751	12.0777	0.53653	0.0:0.9163:0.0:0.0837	.	158	Q9BRF8	CPPED_HUMAN	I	158	ENSP00000371193:V158I	ENSP00000371193:V158I	V	-	1	0	CPPED1	12706225	0.998000	0.40836	0.840000	0.33206	0.315000	0.28087	3.848000	0.55903	1.256000	0.44068	-0.128000	0.14901	GTC		0.612	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340		T	12798724	C	T	12798724	3	4	52	1	0	0	0	0	1	0	0	0	3828	536	19	1	480	1	CPPED1	16	12798724	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		12798724	77556029	45	7064										
LCMT1	51451	broad.mit.edu	37	chr16	25180479	25180479	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gatcatgattgaaaacctgcGgagacgccagtgtgacctgg	13	9	1	4	rs35016949	byFrequency	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr16:25180479G>T	ENST00000399069.3	+	8	892	c.737G>T	c.(736-738)cGg>cTg	p.R246L	LCMT1_ENST00000572869.1_3'UTR|LCMT1_ENST00000380966.4_Missense_Mutation_p.R191L	NM_016309.2	NP_057393.2	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1	246					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|negative regulation of protein complex assembly (GO:0031333)|protein methylation (GO:0006479)|regulation of apoptotic process (GO:0042981)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	cytosol (GO:0005829)	protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.R246L(1)							GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	GAAAACCTGCGGAGACGCCAG	0.488																																					Colon(200;565 2072 24396 47922 50898)											1	Substitution - Missense(1)	large_intestine(1)	16											118	119	118					16																	25180479		1925	4132	6057	25087980	SO:0001583	missense	51451			AF037601	CCDS45445.1, CCDS45446.1	16p12.1	2014-08-01			ENSG00000205629	ENSG00000205629			17557	protein-coding gene	gene with protein product	"protein phosphatase methyltransferase 1"	610286				10810093	Standard	XM_005255354		Approved	CGI-68, PPMT1	uc002dnx.1	Q9UIC8	OTTHUMG00000177182	ENST00000399069.3:c.737G>T	16.37:g.25180479G>T	ENSP00000382021:p.Arg246Leu		25087980	A6NL89|A8K770|Q53FC5|Q96CI5|Q9H6I9|Q9NTG4|Q9Y378	Missense_Mutation	SNP	ENST00000399069.3	37	CCDS45445.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.428959	0.62844	.	.	ENSG00000205629	ENST00000399069;ENST00000380966;ENST00000380962	T;T	0.25912	1.77;1.77	5.97	5.97	0.96955	.	0.195654	0.46145	D	0.000301	T	0.27349	0.0671	L	0.55990	1.75	0.39913	D	0.97405	B;B	0.15141	0.012;0.005	B;B	0.24394	0.053;0.006	T	0.05937	-1.0855	10	0.59425	D	0.04	-17.0698	11.2276	0.48892	0.0823:0.0:0.9177:0.0	.	191;246	Q9UIC8-3;Q9UIC8	.;LCMT1_HUMAN	L	246;191;263	ENSP00000382021:R246L;ENSP00000370353:R191L	ENSP00000370349:R263L	R	+	2	0	LCMT1	25087980	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.622000	0.61240	2.836000	0.97738	0.655000	0.94253	CGG		0.488	LCMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435747.4	NM_016309		T	25180479	G	T	25180479	3	4	52	1	0	0	0	0	1	0	0	0	8700	1116	39	2	767	2	LCMT1	16	25180479	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	12381755	25180479	65174274	46	7065										
GSG1L	146395	broad.mit.edu	37	chr16	27840214	27840214	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cggaactcaatgaccgtcttGgtgtaggagttgagcgtggt	15	7	2	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr16:27840214G>T	ENST00000447459.2	-	5	810	c.726C>A	c.(724-726)acC>acA	p.T242T	GSG1L_ENST00000395724.3_Silent_p.T191T|GSG1L_ENST00000380897.3_Silent_p.T87T|GSG1L_ENST00000569166.1_Silent_p.T87T|GSG1L_ENST00000380898.2_Silent_p.T87T	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	242					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T87T(1)|p.T242T(1)		endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						TGACCGTCTTGGTGTAGGAGT	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	16											88	65	73					16																	27840214		2197	4300	6497	27747715	SO:0001819	synonymous_variant	146395			AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.726C>A	16.37:g.27840214G>T			27747715	Q7Z6F8|Q8TB81	Silent	SNP	ENST00000447459.2	37	CCDS45450.1																																																																																				0.587	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		T	27840214	G	T	27840214	2	4	52	1	0	0	0	0	0	0	0	1	6842	1335	47	2		2	GSG1L	16	27840214	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	2659735	27840214	62514539	47	7066										
PKD1L2	114780	broad.mit.edu	37	chr16	81253925	81253925	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tcctctggcttaacagtggtGgccctaagcctcagagcaag	11	12	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr16:81253925G>T	ENST00000525539.1	-	0	50				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.A17A(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TAACAGTGGTGGCCCTAAGCC	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	16											66	66	66					16																	81253925		2035	4194	6229	79811426			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253925G>T			79811426	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																					0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81253925	G	T	81253925	1	4	52	0	1	0	0	0	0	0	0	0	11996	1335	47	2		2	PKD1L2	16	81253925	RNA	SNP	G	TCGA-AG-3901-01A-01W-1073-09	53413711	81253925	9100828	48	7067										
SLC5A10	125206	broad.mit.edu	37	chr17	18872425	18872425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgggctggaacttctacctcTccaccatcctcacgctcggc	8	17	3	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr17:18872425T>C	ENST00000395645.3	+	6	532	c.514T>C	c.(514-516)Tcc>Ccc	p.S172P	SLC5A10_ENST00000417251.2_Missense_Mutation_p.S172P|SLC5A10_ENST00000395643.2_Missense_Mutation_p.S172P|SLC5A10_ENST00000395642.1_Missense_Mutation_p.S116P|SLC5A10_ENST00000317977.6_Missense_Mutation_p.S116P|FAM83G_ENST00000388995.6_3'UTR|SLC5A10_ENST00000395647.2_Missense_Mutation_p.S172P	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	172					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.S172P(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						CTTCTACCTCTCCACCATCCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											156	117	130					17																	18872425		2203	4300	6503	18813150	SO:0001583	missense	125206				CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.514T>C	17.37:g.18872425T>C	ENSP00000379007:p.Ser172Pro		18813150	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	37	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.828449	0.90955	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.91521	-2.86;-2.52;-2.86;-2.52;-2.52;-2.39	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.95162	0.8432	M	0.93854	3.465	0.80722	D	1	P;P;P;P;P	0.41848	0.584;0.72;0.763;0.72;0.694	P;P;P;P;P	0.51016	0.539;0.525;0.656;0.525;0.557	D	0.96145	0.9103	10	0.72032	D	0.01	.	14.3297	0.66548	0.0:0.0:0.0:1.0	.	172;172;172;172;116	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	P	116;172;116;172;172;172	ENSP00000324346:S116P;ENSP00000379008:S172P;ENSP00000379004:S116P;ENSP00000401875:S172P;ENSP00000379007:S172P;ENSP00000379005:S172P	ENSP00000324346:S116P	S	+	1	0	SLC5A10	18813150	1.000000	0.71417	0.976000	0.42696	0.983000	0.72400	4.801000	0.62532	1.943000	0.56356	0.379000	0.24179	TCC		0.602	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		C	18872425	T	C	18872425	3	2	52	1	0	0	0	0	1	0	0	0	14699	1551	54	4	536	4	SLC5A10	17	18872425	Missense_Mutation	SNP	T	TCGA-AG-3901-01A-01W-1073-09		18872425	62322785	49	7068										
KCNH4	23415	broad.mit.edu	37	chr17	40328102	40328102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gagcatttccacggcgatgtCgctgacaagggtgtgtcgcg	15	10	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr17:40328102C>T	ENST00000264661.3	-	5	1131	c.799G>A	c.(799-801)Gac>Aac	p.D267N	KCNH4_ENST00000607371.1_Missense_Mutation_p.D267N	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	267					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.D267N(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ACGGCGATGTCGCTGACAAGG	0.597																																					NSCLC(117;707 1703 2300 21308 31858)											1	Substitution - Missense(1)	large_intestine(1)	17											137	122	127					17																	40328102		2203	4300	6503	37581628	SO:0001583	missense	23415			AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.799G>A	17.37:g.40328102C>T	ENSP00000264661:p.Asp267Asn		37581628		Missense_Mutation	SNP	ENST00000264661.3	37	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	36	5.968645	0.97156	.	.	ENSG00000089558	ENST00000264661	D	0.97752	-4.52	5.53	5.53	0.82687	Ion transport (1);	0.000000	0.43260	D	0.000600	D	0.98723	0.9571	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.99548	1.0965	10	0.87932	D	0	.	19.6556	0.95837	0.0:1.0:0.0:0.0	.	267	Q9UQ05	KCNH4_HUMAN	N	267	ENSP00000264661:D267N	ENSP00000264661:D267N	D	-	1	0	KCNH4	37581628	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	7.617000	0.83032	2.882000	0.98803	0.655000	0.94253	GAC		0.597	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		T	40328102	C	T	40328102	3	4	52	1	0	0	0	0	1	0	0	0	8055	884	31	1	2302	1	KCNH4	17	40328102	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	21455677	40328102	40867108	50	7069										
ABCA8	10351	broad.mit.edu	37	chr17	66873754	66873754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgtcaggttgggccacagcgCgttctcctgagggcagtacc	14	12	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr17:66873754C>T	ENST00000269080.2	-	31	4122	c.3985G>A	c.(3985-3987)Gcg>Acg	p.A1329T	ABCA8_ENST00000586539.1_Missense_Mutation_p.A1369T|ABCA8_ENST00000430352.2_Missense_Mutation_p.A1369T	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1329	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A1329T(2)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GGCCACAGCGCGTTCTCCTGA	0.597																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	17											138	118	125					17																	66873754		2203	4300	6503	64385349	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3985G>A	17.37:g.66873754C>T	ENSP00000269080:p.Ala1329Thr		64385349	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867711	0.32977	.	.	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.93426	-3.22;-3.22	4.34	2.17	0.27698	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.455820	0.18056	N	0.153094	D	0.85673	0.5751	L	0.28192	0.835	0.26055	N	0.981424	B;B;B	0.18166	0.026;0.024;0.026	B;B;B	0.21917	0.037;0.024;0.025	T	0.76780	-0.2833	10	0.66056	D	0.02	.	3.1347	0.06435	0.1493:0.4633:0.2869:0.1006	.	1369;1369;1329	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	T	1329;1369	ENSP00000269080:A1329T;ENSP00000402814:A1369T	ENSP00000269080:A1329T	A	-	1	0	ABCA8	64385349	0.052000	0.20516	0.012000	0.15200	0.600000	0.36913	0.695000	0.25527	1.192000	0.43071	0.637000	0.83480	GCG		0.597	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66873754	C	T	66873754	3	4	52	1	0	0	0	0	1	0	0	0	38	768	27	1	792	1	ABCA8	17	66873754	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	26545652	66873754	14321456	51	7070										
SDK2	54549	broad.mit.edu	37	chr17	71389755	71389755	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tggggctgccgtccccgatgCgtgtgaaggccagcacctgg	16	13	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr17:71389755C>T	ENST00000392650.3	-	27	3842	c.3842G>A	c.(3841-3843)cGc>cAc	p.R1281H	SDK2_ENST00000388726.3_Missense_Mutation_p.R1281H	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1281	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.R1281H(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GTCCCCGATGCGTGTGAAGGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											61	55	57					17																	71389755		2203	4300	6503	68901350	SO:0001583	missense	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.3842G>A	17.37:g.71389755C>T	ENSP00000376421:p.Arg1281His		68901350	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	33	5.215483	0.95104	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.57595	0.39;0.39;0.39	5.41	5.41	0.78517	Fibronectin, type III (5);Immunoglobulin-like fold (1);	0.058360	0.64402	D	0.000002	T	0.76856	0.4046	M	0.85099	2.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.994;0.997;0.994	T	0.79364	-0.1834	10	0.54805	T	0.06	.	19.1974	0.93695	0.0:1.0:0.0:0.0	.	1281;1281;1281	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	H	905;1281;1281;457;1281	ENSP00000376421:R1281H;ENSP00000373378:R1281H;ENSP00000407098:R457H	ENSP00000324967:R1281H	R	-	2	0	SDK2	68901350	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	7.324000	0.79115	2.527000	0.85204	0.563000	0.77884	CGC		0.637	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		T	71389755	C	T	71389755	3	4	52	1	0	0	0	0	1	0	0	0	14006	768	27	1	2752	1	SDK2	17	71389755	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	4516001	71389755	9805455	52	7071										
ZNF521	25925	broad.mit.edu	37	chr18	22804983	22804983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	agttaaaagggagggaaaccGctctccgcaaatagggcaca	12	9	1	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr18:22804983G>A	ENST00000361524.3	-	4	3047	c.2899C>T	c.(2899-2901)Cgg>Tgg	p.R967W	ZNF521_ENST00000538137.2_Missense_Mutation_p.R967W|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.R747W	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	967					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.R967W(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GAGGGAAACCGCTCTCCGCAA	0.498			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - Missense(1)	large_intestine(1)	18											89	84	85					18																	22804983		2203	4300	6503	21058981	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2899C>T	18.37:g.22804983G>A	ENSP00000354794:p.Arg967Trp		21058981	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398830	0.25291	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.19938	2.11;2.11	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.44201	0.1282	L	0.60845	1.875	0.41388	D	0.987597	D	0.89917	1.0	D	0.97110	1.0	T	0.17653	-1.0362	10	0.62326	D	0.03	-30.0479	15.968	0.79987	0.0:0.0:0.8646:0.1353	.	967	Q96K83	ZN521_HUMAN	W	967;1001;967	ENSP00000354794:R967W;ENSP00000382352:R967W	ENSP00000354794:R967W	R	-	1	2	ZNF521	21058981	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	3.628000	0.54259	2.828000	0.97474	0.655000	0.94253	CGG		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22804983	G	A	22804983	3	1	52	1	0	0	0	0	1	0	0	0	18004	1086	38	1	1056	1	ZNF521	18	22804983	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09		22804983	55272265	53	7072										
SMAD4	4089	broad.mit.edu	37	chr18	48591904	48591904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tgttgatggatacgtggaccCttctggaggagatcgctttt	13	7	1	2			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr18:48591904C>T	ENST00000342988.3	+	9	1605	c.1067C>T	c.(1066-1068)cCt>cTt	p.P356L	SMAD4_ENST00000398417.2_Missense_Mutation_p.P356L|SMAD4_ENST00000588745.1_Missense_Mutation_p.P260L	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	356	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.P356L(2)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TACGTGGACCCTTCTGGAGGA	0.433																																																40	Whole gene deletion(36)|Substitution - Missense(2)|Unknown(2)	pancreas(26)|large_intestine(5)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											208	173	185					18																	48591904		2203	4300	6503	46845902	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1067C>T	18.37:g.48591904C>T	ENSP00000341551:p.Pro356Leu		46845902	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	34	5.405615	0.96051	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.97114	-4.25;-4.25	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98213	0.9409	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99016	1.0816	10	0.87932	D	0	.	18.9646	0.92691	0.0:1.0:0.0:0.0	.	356	Q13485	SMAD4_HUMAN	L	356	ENSP00000341551:P356L;ENSP00000381452:P356L	ENSP00000341551:P356L	P	+	2	0	SMAD4	46845902	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.672000	0.83956	2.771000	0.95319	0.563000	0.77884	CCT		0.433	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48591904	C	T	48591904	3	4	52	1	0	0	0	0	1	0	0	0	14797	681	24	3	1097	3	SMAD4	18	48591904	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	25786921	48591904	29485344	54	7073										
ZFP82	284406	broad.mit.edu	37	chr19	36884213	36884213	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	cgcactctaaaggccttcccGcattccttacattcataggg	7	14	2	0	rs112210948		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr19:36884213G>A	ENST00000392161.3	-	5	1271	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	ZFP82_ENST00000392171.1_Silent_p.C343C	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C343C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGGCCTTCCCGCATTCCTTAC	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	19											96	97	96					19																	36884213		2203	4300	6503	41576053	SO:0001819	synonymous_variant	284406			AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1029C>T	19.37:g.36884213G>A			41576053	Q8NC63|Q8TF53	Silent	SNP	ENST00000392161.3	37	CCDS12493.1																																																																																				0.428	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		A	36884213	G	A	36884213	2	1	52	1	0	0	0	0	0	0	0	1	17692	1079	38	1		1	ZFP82	19	36884213	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09		36884213	22244770	55	7074										
DDX27	55661	broad.mit.edu	37	chr20	47851609	47851609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gcaacttgtcacagacgcagCggctggaggccctccggtaa	13	13	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr20:47851609C>T	ENST00000371764.4	+	12	1513	c.1504C>T	c.(1504-1506)Cgg>Tgg	p.R502W	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	502	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.R502W(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACAGACGCAGCGGCTGGAGGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	20											54	51	52					20																	47851609		2203	4300	6503	47285016	SO:0001583	missense	55661			AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"DEAD-boxes"	15837	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.1504C>T	20.37:g.47851609C>T	ENSP00000360828:p.Arg502Trp		47285016	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.024379	0.75390	.	.	ENSG00000124228	ENST00000371764	D	0.82893	-1.66	5.18	5.18	0.71444	Helicase, C-terminal (3);	0.049847	0.85682	D	0.000000	D	0.95162	0.8432	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97262	0.9905	10	0.87932	D	0	-10.0097	16.1918	0.81996	0.0:1.0:0.0:0.0	.	502	Q96GQ7	DDX27_HUMAN	W	502	ENSP00000360828:R502W	ENSP00000360828:R502W	R	+	1	2	DDX27	47285016	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.624000	0.61254	2.417000	0.82017	0.655000	0.94253	CGG		0.602	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			T	47851609	C	T	47851609	3	4	52	1	0	0	0	0	1	0	0	0	4360	759	27	1	1550	1	DDX27	20	47851609	Missense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09		47851609	15173911	56	7075										
SERPIND1	3053	broad.mit.edu	37	chr22	21133658	21133658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tcataacatctgcgtggggtGggagcaaaggcccgctggat	15	9	2	0			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr22:21133658G>A	ENST00000215727.5	+	2	341	c.58G>A	c.(58-60)Ggg>Agg	p.G20R	SERPIND1_ENST00000406799.1_Missense_Mutation_p.G20R|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000572273.1_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	20					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G20R(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	TGCGTGGGGTGGGAGCAAAGG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	22											56	58	58					22																	21133658		2203	4300	6503	19463658	SO:0001583	missense	3053			M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"Serine (or cysteine) peptidase inhibitors"	4838	protein-coding gene	gene with protein product	"heparin cofactor II"	142360	"serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.58G>A	22.37:g.21133658G>A	ENSP00000215727:p.Gly20Arg		19463658	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	37	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877228	0.51801	.	.	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.83419	-1.72;-1.72	5.54	1.98	0.26296	.	0.356504	0.35179	N	0.003383	T	0.64929	0.2643	N	0.08118	0	0.09310	N	1	B;B	0.15930	0.015;0.006	B;B	0.14578	0.011;0.011	T	0.61466	-0.7057	10	0.72032	D	0.01	.	9.1906	0.37197	0.1523:0.1258:0.7219:0.0	.	20;20	Q8IVC0;P05546	.;HEP2_HUMAN	R	20	ENSP00000215727:G20R;ENSP00000384050:G20R	ENSP00000215727:G20R	G	+	1	0	SERPIND1	19463658	0.174000	0.23070	0.002000	0.10522	0.002000	0.02628	1.554000	0.36266	1.347000	0.45714	0.655000	0.94253	GGG		0.488	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21133658	G	A	21133658	3	1	52	1	0	0	0	0	1	0	0	0	14147	1348	47	3	60	3	SERPIND1	22	21133658	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09		21133658	30170908	57	7076										
UPB1	51733	broad.mit.edu	37	chr22	24911250	24911250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	tcgcggtgaacatttgctacGggcggcaccaccccctcaac	10	16	1	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr22:24911250G>A	ENST00000326010.5	+	6	1047	c.703G>A	c.(703-705)Ggg>Agg	p.G235R	AP000355.2_ENST00000432032.1_RNA|UPB1_ENST00000413389.2_Missense_Mutation_p.G167R	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	235	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)	p.G235R(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					CATTTGCTACGGGCGGCACCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	22											128	102	111					22																	24911250		2203	4300	6503	23241250	SO:0001583	missense	51733			AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.703G>A	22.37:g.24911250G>A	ENSP00000324343:p.Gly235Arg		23241250	A3KMF8|Q9UIR3	Missense_Mutation	SNP	ENST00000326010.5	37	CCDS13827.1	.	.	.	.	.	.	.	.	.	.	G	34	5.395696	0.96009	.	.	ENSG00000100024	ENST00000413389;ENST00000326010	D;D	0.85556	-2.0;-2.0	5.11	5.11	0.69529	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.094539	0.64402	D	0.000001	D	0.94644	0.8273	H	0.94503	3.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95823	0.8851	10	0.87932	D	0	-7.9849	17.7088	0.88316	0.0:0.0:1.0:0.0	.	235;167	Q9UBR1;E7EUZ5	BUP1_HUMAN;.	R	167;235	ENSP00000406057:G167R;ENSP00000324343:G235R	ENSP00000324343:G235R	G	+	1	0	UPB1	23241250	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.007000	0.93597	2.663000	0.90544	0.650000	0.86243	GGG		0.557	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1			A	24911250	G	A	24911250	3	1	52	1	0	0	0	0	1	0	0	0	17042	1116	39	1	725	1	UPB1	22	24911250	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	3777592	24911250	26393316	58	7077										
C22orf23	84645	broad.mit.edu	37	chr22	38343397	38343397	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	atgggaggcaggtagatgggCgaggctatttgcttggaagg	19	4	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chr22:38343397C>T	ENST00000249079.2	-	4	496	c.240G>A	c.(238-240)tcG>tcA	p.S80S	C22orf23_ENST00000403305.1_Silent_p.S80S|C22orf23_ENST00000403026.1_Silent_p.S80S			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	80								p.S80S(1)		endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					GGTAGATGGGCGAGGCTATTT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	22											146	125	132					22																	38343397		2203	4300	6503	36673343	SO:0001819	synonymous_variant	84645			AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.240G>A	22.37:g.38343397C>T			36673343	Q5JYU9|Q96M68	Silent	SNP	ENST00000249079.2	37	CCDS13962.1																																																																																				0.607	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561		T	38343397	C	T	38343397	2	4	52	1	0	0	0	0	0	0	0	1	2143	755	27	1		1	C22orf23	22	38343397	Silent	SNP	C	TCGA-AG-3901-01A-01W-1073-09	13432147	38343397	12961169	59	7078										
CXorf21	80231	broad.mit.edu	37	chrX	30578217	30578217	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aaacacaggattggggtttgTctgcagcactgtgactctct	11	9	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:30578217T>G	ENST00000378962.3	-	3	578	c.256A>C	c.(256-258)Aca>Cca	p.T86P		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	86								p.T86P(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						TTGGGGTTTGTCTGCAGCACT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											159	156	157					X																	30578217		2202	4300	6502	30488138	SO:0001583	missense	80231			BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.256A>C	X.37:g.30578217T>G	ENSP00000368245:p.Thr86Pro		30488138		Missense_Mutation	SNP	ENST00000378962.3	37	CCDS14224.1	.	.	.	.	.	.	.	.	.	.	T	7.894	0.732966	0.15507	.	.	ENSG00000120280	ENST00000378962	.	.	.	5.11	2.6	0.31112	.	0.763914	0.12002	N	0.508749	T	0.25269	0.0614	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.17684	-1.0361	9	0.31617	T	0.26	-0.112	1.6743	0.02818	0.2329:0.097:0.1325:0.5376	.	86	Q9HAI6	CX021_HUMAN	P	86	.	ENSP00000368245:T86P	T	-	1	0	CXorf21	30488138	0.015000	0.18098	0.924000	0.36721	0.994000	0.84299	0.102000	0.15272	0.790000	0.33803	0.381000	0.24937	ACA		0.453	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159		G	30578217	T	G	30578217	3	3	52	1	0	0	0	0	1	0	0	0	4107	1667	58	4	653	4	CXorf21	23	30578217	Missense_Mutation	SNP	T	TCGA-AG-3901-01A-01W-1073-09		30578217	124692343	60	7079										
FGD1	2245	broad.mit.edu	37	chrX	54496875	54496875	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gggactggtctatccgaggcGacaatcacaggctctctgag	13	11	3	1	rs149366519		TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:54496875G>A	ENST00000375135.3	-	4	1408	c.675C>T	c.(673-675)gtC>gtT	p.V225V		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	225	Pro-rich.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.V225V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TATCCGAGGCGACAATCACAG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	X						G		0,3827		0,0,1628,571	30	36	34		675	-4.8	0.2	X	dbSNP_134	34	1,6711		0,1,2424,1862	no	coding-synonymous	FGD1	NM_004463.2		0,1,4052,2433	AA,AG,GG,G		0.0149,0.0,0.0095		225/962	54496875	1,10538	2199	4287	6486	54513600	SO:0001819	synonymous_variant	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.675C>T	X.37:g.54496875G>A			54513600	Q5H999|Q8N4D9	Silent	SNP	ENST00000375135.3	37	CCDS14359.1																																																																																				0.627	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		A	54496875	G	A	54496875	2	1	52	1	0	0	0	0	0	0	0	1	5851	1045	37	1		1	FGD1	23	54496875	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	23918658	54496875	100773685	61	7080										
BRWD3	254065	broad.mit.edu	37	chrX	79945323	79945323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aattttattataagtatccaGtatatcagtacagctctgat	5	6	2	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:79945323G>C	ENST00000373275.4	-	33	3967	c.3751C>G	c.(3751-3753)Ctg>Gtg	p.L1251V	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1251					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.L1251V(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TAAGTATCCAGTATATCAGTA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	X											99	79	86					X																	79945323		2199	4298	6497	79831979	SO:0001583	missense	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.3751C>G	X.37:g.79945323G>C	ENSP00000362372:p.Leu1251Val		79831979	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382646	0.25031	.	.	ENSG00000165288	ENST00000373275	T	0.55588	0.51	5.27	0.2	0.15181	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.69823	2.125	0.36990	D	0.894758	P	0.37985	0.613	B	0.41466	0.358	T	0.45411	-0.9263	9	.	.	.	-5.6635	6.1556	0.20335	0.5312:0.1326:0.3361:0.0	.	1251	Q6RI45	BRWD3_HUMAN	V	1251	ENSP00000362372:L1251V	.	L	-	1	2	BRWD3	79831979	1.000000	0.71417	0.992000	0.48379	0.996000	0.88848	1.120000	0.31271	-0.111000	0.12001	0.594000	0.82650	CTG		0.279	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		C	79945323	G	C	79945323	3	2	52	1	0	0	0	0	1	0	0	0	1529	1020	36	5	1693	5	BRWD3	23	79945323	Missense_Mutation	SNP	G	TCGA-AG-3901-01A-01W-1073-09	25448448	79945323	75325237	62	7081										
CYLC1	1538	broad.mit.edu	37	chrX	83128791	83128791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	aaaaattaaagaaagatgacAagaaaaaggacacaaagaag	8	3	0	5			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:83128791A>G	ENST00000329312.4	+	4	1112	c.1075A>G	c.(1075-1077)Aag>Gag	p.K359E		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	359					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.K358E(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						gaaagatgacaagaaaaagga	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	X											36	32	33					X																	83128791		2191	4289	6480	83015447	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1075A>G	X.37:g.83128791A>G	ENSP00000331556:p.Lys359Glu		83015447	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	3.960	-0.010548	0.07727	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.28255	1.62	3.08	1.88	0.25563	.	.	.	.	.	T	0.24044	0.0582	L	0.47016	1.485	0.09310	N	1	B;B	0.34181	0.44;0.221	B;B	0.35240	0.198;0.133	T	0.16689	-1.0394	9	0.27082	T	0.32	.	5.6714	0.17725	0.721:0.279:0.0:0.0	.	359;359	P35663;F5H4V5	CYLC1_HUMAN;.	E	359	ENSP00000331556:K359E	ENSP00000331556:K359E	K	+	1	0	CYLC1	83015447	0.019000	0.18553	0.095000	0.20976	0.094000	0.18550	1.019000	0.30014	0.422000	0.26005	0.451000	0.29950	AAG		0.353	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		G	83128791	A	G	83128791	3	3	52	1	0	0	0	0	1	0	0	0	4147	131	5	4	1089	4	CYLC1	23	83128791	Missense_Mutation	SNP	A	TCGA-AG-3901-01A-01W-1073-09	3183468	83128791	72141769	63	7082										
IL1RAPL2	26280	broad.mit.edu	37	chrX	104984642	104984642	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	atacctgccatgttgaaaacCgaaatggacggaaacatgcc	9	10	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:104984642C>T	ENST00000372582.1	+	8	1762	c.1006C>T	c.(1006-1008)Cga>Tga	p.R336*	IL1RAPL2_ENST00000485671.1_3'UTR|IL1RAPL2_ENST00000344799.4_Nonsense_Mutation_p.R336*	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	336	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R336*(2)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGTTGAAAACCGAAATGGACG	0.378																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											76	67	70					X																	104984642		2203	4300	6503	104871298	SO:0001587	stop_gained	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1006C>T	X.37:g.104984642C>T	ENSP00000361663:p.Arg336*		104871298	Q2M3U3|Q9NZN0	Nonsense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	39	7.831195	0.98513	.	.	ENSG00000189108	ENST00000372582;ENST00000344799	.	.	.	5.61	3.59	0.41128	.	0.000000	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	14.7819	0.69774	0.3377:0.6623:0.0:0.0	.	.	.	.	X	336	.	ENSP00000344976:R336X	R	+	1	2	IL1RAPL2	104871298	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.084000	0.30828	1.077000	0.40990	0.600000	0.82982	CGA		0.378	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	104984642	C	T	104984642	4	4	52	1	0	0	0	0	0	1	0	0	7683	644	23	1	1032	1	IL1RAPL2	23	104984642	Nonsense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	21855851	104984642	50285918	64	7083										
DOCK11	139818	broad.mit.edu	37	chrX	117744321	117744321	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	attccccatgtgactattcgGtatgcggagattcccgatga	10	10	0	3			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:117744321G>A	ENST00000276202.7	+	28	3099	c.3036G>A	c.(3034-3036)cgG>cgA	p.R1012R	DOCK11_ENST00000276204.6_Silent_p.R1012R	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1012					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1012R(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGACTATTCGGTATGCGGAGA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	X											135	110	119					X																	117744321		2203	4300	6503	117628349	SO:0001819	synonymous_variant	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3036G>A	X.37:g.117744321G>A			117628349	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																				0.448	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117744321	G	A	117744321	2	1	52	1	0	0	0	0	0	0	0	1	4697	1248	44	3		3	DOCK11	23	117744321	Silent	SNP	G	TCGA-AG-3901-01A-01W-1073-09	12759679	117744321	37526239	65	7084										
BCORL1	63035	broad.mit.edu	37	chrX	129150016	129150016	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0151515151515152	1	1	0.167831325301205	2.79718875502008	0	1	1	0	gggctaaggccgggcaggctCgagtgaaacaggaaagcgta	17	8	0	1			TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3901-01A-01W-1073-09	TCGA-AG-3901-10A-01W-1073-09	g.chrX:129150016C>T	ENST00000218147.7	+	4	3465	c.3268C>T	c.(3268-3270)Cga>Tga	p.R1090*	BCORL1_ENST00000303743.5_Nonsense_Mutation_p.R1090*|BCORL1_ENST00000540052.1_Nonsense_Mutation_p.R1090*|BCORL1_ENST00000359304.2_Nonsense_Mutation_p.R1090*			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1090					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1090*(1)		breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CGGGCAGGCTCGAGTGAAACA	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											75	67	70					X																	129150016		2203	4300	6503	128977697	SO:0001587	stop_gained	63035			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.3268C>T	X.37:g.129150016C>T	ENSP00000218147:p.Arg1090*		128977697	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Nonsense_Mutation	SNP	ENST00000218147.7	37	CCDS14616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.399452|8.399452	0.98794|0.98794	.|.	.|.	ENSG00000085185|ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822|ENST00000441294	.|.	.|.	.|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|.	0.30134|.	N|.	0.010337|.	.|T	.|0.74359	.|0.3706	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73949	.|-0.3821	.|3	0.06365|.	T|.	0.9|.	-2.9752|-2.9752	18.0554|18.0554	0.89363|0.89363	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1090;1090;1090;1090;690|525	.|.	ENSP00000218147:R1090X|.	R|S	+|+	1|2	2|0	BCORL1|BCORL1	128977697|128977697	0.997000|0.997000	0.39634|0.39634	0.973000|0.973000	0.42090|0.42090	0.924000|0.924000	0.55760|0.55760	5.080000|5.080000	0.64437|0.64437	2.200000|2.200000	0.70718|0.70718	0.600000|0.600000	0.82982|0.82982	CGA|TCG		0.572	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		T	129150016	C	T	129150016	4	4	52	1	0	0	0	0	0	1	0	0	1388	876	31	1	3278	1	BCORL1	23	129150016	Nonsense_Mutation	SNP	C	TCGA-AG-3901-01A-01W-1073-09	11405695	129150016	26120544	66	7085										
LZIC	84328	broad.mit.edu	37	chr1	9996591	9996591	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcttacctgcattcctccagAtcttgtaattgttgcatgag	7	10	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:9996591A>T	ENST00000377223.1	-	3	334	c.87T>A	c.(85-87)gaT>gaA	p.D29E	LZIC_ENST00000541052.1_Missense_Mutation_p.D50E|LZIC_ENST00000400903.2_Missense_Mutation_p.D29E|LZIC_ENST00000377213.1_Missense_Mutation_p.D29E	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	29					response to ionizing radiation (GO:0010212)			p.D29E(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		ATTCCTCCAGATCTTGTAATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											251	223	232					1																	9996591		2203	4300	6503	9919178	SO:0001583	missense	84328			AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.87T>A	1.37:g.9996591A>T	ENSP00000366430:p.Asp29Glu		9919178	B2R6F0|B4E2N0|Q96IU1	Missense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.980217	0.74474	.	.	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.67	0.438	0.16560	.	0.000000	0.85682	D	0.000000	T	0.42944	0.1225	M	0.67397	2.05	0.50313	D	0.999865	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.10543	-1.0625	9	.	.	.	-5.9897	9.5843	0.39506	0.637:0.0:0.363:0.0	.	50;29	B4E2N0;Q8WZA0	.;LZIC_HUMAN	E	29;29;50;29	ENSP00000366430:D29E;ENSP00000383695:D29E;ENSP00000437432:D50E;ENSP00000366418:D29E	.	D	-	3	2	LZIC	9919178	0.982000	0.34865	0.996000	0.52242	0.997000	0.91878	0.245000	0.18142	-0.171000	0.10797	0.459000	0.35465	GAT		0.403	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368		T	9996591	A	T	9996591	3	4	53	1	0	0	0	0	1	0	0	0	9165	330	12	5	509	5	LZIC	1	9996591	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09		9996591	239254030	1	7086										
ZSCAN20	7579	broad.mit.edu	37	chr1	33960677	33960677	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgtgccgaatgtgggaaaagCttcagtaagagctccaccct	11	10	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:33960677C>G	ENST00000361328.3	+	8	2886	c.2733C>G	c.(2731-2733)agC>agG	p.S911R		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	911					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S911R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTGGGAAAAGCTTCAGTAAGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	90	87					1																	33960677		2128	4258	6386	33733264	SO:0001583	missense	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.2733C>G	1.37:g.33960677C>G	ENSP00000355053:p.Ser911Arg		33733264	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.928704	0.52759	.	.	ENSG00000121903	ENST00000326544;ENST00000361328;ENST00000401072	.	.	.	5.76	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.153488	0.46758	D	0.000270	T	0.43986	0.1272	N	0.25094	0.71	0.31142	N	0.706457	P;D	0.76494	0.638;0.999	B;D	0.75020	0.218;0.985	T	0.46105	-0.9215	9	0.72032	D	0.01	-8.3849	7.8342	0.29360	0.0:0.6159:0.0:0.3841	.	910;911	P17040-3;P17040	.;ZSC20_HUMAN	R	911;845;845	.	ENSP00000324450:S911R	S	+	3	2	ZSCAN20	33733264	0.851000	0.29673	1.000000	0.80357	0.994000	0.84299	0.863000	0.27913	0.752000	0.32923	0.655000	0.94253	AGC		0.507	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		G	33960677	C	G	33960677	3	3	53	1	0	0	0	0	1	0	0	0	18271	796	28	5	2759	5	ZSCAN20	1	33960677	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	23964086	33960677	215289944	2	7087										
EIF2C4	192670	broad.mit.edu	37	chr1	36316529	36316529	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gcagatgaactccagctactGacttaccagctgtgtcacac	8	13	1	3	rs150907205		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:36316529G>C	ENST00000373210.3	+	17	2597	c.2352G>C	c.(2350-2352)ctG>ctC	p.L784L	AGO4_ENST00000488778.1_3'UTR	NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	784	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)	p.L784L(1)									TCCAGCTACTGACTTACCAGC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											124	108	113					1																	36316529		2203	4300	6503	36089116	SO:0001819	synonymous_variant	192670			AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.2352G>C	1.37:g.36316529G>C			36089116	A7MD27	Silent	SNP	ENST00000373210.3	37	CCDS397.1																																																																																				0.498	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		C	36316529	G	C	36316529	2	2	53	1	0	0	0	0	0	0	0	1	5019	1277	45	5		5	EIF2C4	1	36316529	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	2355852	36316529	212934092	3	7088										
GRIK3	2899	broad.mit.edu	37	chr1	37324825	37324825	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gcacacggacacgatatggaCggcgtcgtacagtaaggctg	14	10	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:37324825C>T	ENST00000373091.3	-	7	1004	c.988G>A	c.(988-990)Gtc>Atc	p.V330I	GRIK3_ENST00000462621.1_5'Flank|GRIK3_ENST00000373093.4_Missense_Mutation_p.V330I	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	330					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.V330I(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				ACGATATGGACGGCGTCGTAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	1											138	118	125					1																	37324825		2203	4300	6503	37097412	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.988G>A	1.37:g.37324825C>T	ENSP00000362183:p.Val330Ile		37097412	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	33	5.211136	0.95069	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	D;D	0.90069	-2.61;-2.61	5.68	5.68	0.88126	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.92251	0.7542	M	0.77103	2.36	0.58432	D	0.999999	B;B	0.32753	0.176;0.383	B;B	0.43301	0.415;0.324	D	0.91112	0.4923	10	0.51188	T	0.08	.	19.7849	0.96432	0.0:1.0:0.0:0.0	.	330;330	A9Z1Z8;Q13003	.;GRIK3_HUMAN	I	330	ENSP00000362183:V330I;ENSP00000362185:V330I	ENSP00000362183:V330I	V	-	1	0	GRIK3	37097412	1.000000	0.71417	0.970000	0.41538	0.683000	0.39861	7.482000	0.81143	2.671000	0.90904	0.650000	0.86243	GTC		0.647	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37324825	C	T	37324825	3	4	53	1	0	0	0	0	1	0	0	0	6796	536	19	1	1811	1	GRIK3	1	37324825	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	1008296	37324825	211925796	4	7089										
NRD1	4898	broad.mit.edu	37	chr1	52275053	52275053	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gaaattactattccacagttCagcccaagagttttcaatat	5	9	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:52275053C>A	ENST00000354831.7	-	19	2317	c.2128G>T	c.(2128-2130)Gaa>Taa	p.E710*	NRD1_ENST00000544028.1_Nonsense_Mutation_p.E510*|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000539524.1_Nonsense_Mutation_p.E578*|NRD1_ENST00000352171.7_Nonsense_Mutation_p.E642*	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	641					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.E710*(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TTCCACAGTTCAGCCCAAGAG	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											151	162	158					1																	52275053		2203	4300	6503	52047641	SO:0001587	stop_gained	4898			X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2128G>T	1.37:g.52275053C>A	ENSP00000346890:p.Glu710*		52047641	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Nonsense_Mutation	SNP	ENST00000354831.7	37	CCDS559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.06|14.06	2.424089|2.424089	0.43020|0.43020	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169;ENST00000544028|ENST00000440943	.|.	.|.	.|.	5.55|5.55	4.64|4.64	0.57946|0.57946	.|.	0.222920|.	0.45867|.	D|.	0.000324|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.27785|.	T|.	0.31|.	-9.2672|-9.2672	14.3582|14.3582	0.66752|0.66752	0.0:0.9288:0.0:0.0712|0.0:0.9288:0.0:0.0712	.|.	.|.	.|.	.|.	X|L	642;710;578;112;642;510|96	.|.	ENSP00000262679:E642X|.	E|X	-|-	1|2	0|2	NRD1|NRD1	52047641|52047641	0.982000|0.982000	0.34865|0.34865	1.000000|1.000000	0.80357|0.80357	0.252000|0.252000	0.25951|0.25951	2.718000|2.718000	0.47236|0.47236	1.353000|1.353000	0.45828|0.45828	-0.136000|-0.136000	0.14681|0.14681	GAA|TGA		0.303	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52275053	C	A	52275053	4	1	53	1	0	0	0	0	0	1	0	0	10676	835	29	2	1591	2	NRD1	1	52275053	Nonsense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	14950228	52275053	196975568	5	7090										
DAB1	1600	broad.mit.edu	37	chr1	57537209	57537209	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gtatacctggtacacagcttGttcacactgcttatcctttt	6	11	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:57537209G>C	ENST00000371231.1	-	5	578	c.544C>G	c.(544-546)Caa>Gaa	p.Q182E	DAB1_ENST00000420954.2_Missense_Mutation_p.Q182E|DAB1_ENST00000371236.2_Missense_Mutation_p.Q182E|DAB1_ENST00000371230.1_Missense_Mutation_p.Q182E|DAB1_ENST00000439789.2_Intron|DAB1_ENST00000414851.2_Missense_Mutation_p.Q182E|DAB1_ENST00000371234.4_Missense_Mutation_p.Q182E|DAB1_ENST00000485760.1_5'UTR			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	182	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.Q182E(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						TACACAGCTTGTTCACACTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											250	218	229					1																	57537209		2203	4300	6503	57309797	SO:0001583	missense	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.544C>G	1.37:g.57537209G>C	ENSP00000360275:p.Gln182Glu		57309797	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	G	17.61	3.432422	0.62844	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000371231;ENST00000332102;ENST00000371230	T;T;T;T;T;T;T	0.64260	0.86;0.86;1.13;1.19;0.84;0.11;-0.09	6.16	6.16	0.99307	.	0.052644	0.85682	D	0.000000	T	0.48314	0.1493	N	0.19112	0.55	0.80722	D	1	P;B;B;B	0.39480	0.675;0.136;0.087;0.087	B;B;B;B	0.39258	0.295;0.037;0.063;0.063	T	0.47315	-0.9127	10	0.02654	T	1	-19.2076	20.8598	0.99761	0.0:0.0:1.0:0.0	.	182;182;182;182	O75553-4;O75553;O75553-6;O75553-5	.;DAB1_HUMAN;.;.	E	182	ENSP00000360280:Q182E;ENSP00000360278:Q182E;ENSP00000395296:Q182E;ENSP00000387581:Q182E;ENSP00000360275:Q182E;ENSP00000329120:Q182E;ENSP00000360274:Q182E	ENSP00000329120:Q182E	Q	-	1	0	DAB1	57309797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	CAA		0.398	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		C	57537209	G	C	57537209	3	2	53	1	0	0	0	0	1	0	0	0	4223	1386	48	5	1159	5	DAB1	1	57537209	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	5262156	57537209	191713412	6	7091										
ROR1	4919	broad.mit.edu	37	chr1	64624706	64624706	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gaataaaatggaaatcctgtAcatactagtgccaagtgtgg	10	6	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:64624706A>G	ENST00000371079.1	+	8	1592	c.1217A>G	c.(1216-1218)tAc>tGc	p.Y406C	ROR1_ENST00000545203.1_5'UTR|RP11-24J23.2_ENST00000424995.1_RNA	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	406					peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.Y406C(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						GAAATCCTGTACATACTAGTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	105	106					1																	64624706		2203	4300	6503	64397294	SO:0001583	missense	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1217A>G	1.37:g.64624706A>G	ENSP00000360120:p.Tyr406Cys		64397294	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.852525	0.71719	.	.	ENSG00000185483	ENST00000371079;ENST00000544776	T	0.76448	-1.02	5.77	5.77	0.91146	Kringle-like fold (1);	0.000000	0.39210	N	0.001430	T	0.74658	0.3745	L	0.32530	0.975	0.80722	D	1	D	0.67145	0.996	P	0.58077	0.832	T	0.79598	-0.1737	10	0.87932	D	0	.	14.9523	0.71083	1.0:0.0:0.0:0.0	.	406	Q01973	ROR1_HUMAN	C	406;409	ENSP00000360120:Y406C	ENSP00000360120:Y406C	Y	+	2	0	ROR1	64397294	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	9.255000	0.95524	2.330000	0.79161	0.528000	0.53228	TAC		0.408	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		G	64624706	A	G	64624706	3	3	53	1	0	0	0	0	1	0	0	0	13563	391	14	4	1255	4	ROR1	1	64624706	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	7087497	64624706	184625915	7	7092										
GBP7	388646	broad.mit.edu	37	chr1	89616102	89616102	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aattttctgattgcatctggAaattactatccagttggtct	7	7	3	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:89616102A>T	ENST00000294671.2	-	6	920	c.782T>A	c.(781-783)tTc>tAc	p.F261Y		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	261	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F261Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTGCATCTGGAAATTACTATC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	121	123					1																	89616102		2203	4300	6503	89388690	SO:0001583	missense	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.782T>A	1.37:g.89616102A>T	ENSP00000294671:p.Phe261Tyr		89388690		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.004258	0.54254	.	.	ENSG00000213512	ENST00000294671	D	0.83837	-1.77	3.4	3.4	0.38934	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88444	0.6438	M	0.84773	2.715	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.89531	0.3785	10	0.87932	D	0	.	9.8308	0.40941	1.0:0.0:0.0:0.0	.	261	Q8N8V2	GBP7_HUMAN	Y	261	ENSP00000294671:F261Y	ENSP00000294671:F261Y	F	-	2	0	GBP7	89388690	0.998000	0.40836	0.011000	0.14972	0.005000	0.04900	5.981000	0.70524	1.424000	0.47217	0.338000	0.21704	TTC		0.398	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		T	89616102	A	T	89616102	3	4	53	1	0	0	0	0	1	0	0	0	6299	246	9	5	1158	5	GBP7	1	89616102	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	24991396	89616102	159634519	8	7093										
LRRC8C	84230	broad.mit.edu	37	chr1	90178694	90178694	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	actcagaagaaaaggacaacAggaagaacaacatgaacagg	10	7	1	4			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:90178694A>C	ENST00000370454.4	+	3	820	c.565A>C	c.(565-567)Agg>Cgg	p.R189R	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	189					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R189R(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		AAAGGACAACAGGAAGAACAA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											63	64	64					1																	90178694		2203	4300	6503	89951282	SO:0001819	synonymous_variant	84230				CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.565A>C	1.37:g.90178694A>C			89951282	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																				0.458	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90178694	A	C	90178694	2	2	53	1	0	0	0	0	0	0	0	1	9052	179	7	4		4	LRRC8C	1	90178694	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	562592	90178694	159071927	9	7094										
WNT2B	7482	broad.mit.edu	37	chr1	113057699	113057699	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ccgggaccacaccgtctttgGccgtgtcatgctcagaagta	11	13	3	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:113057699G>C	ENST00000369684.4	+	2	871	c.386G>C	c.(385-387)gGc>gCc	p.G129A	WNT2B_ENST00000369686.5_Missense_Mutation_p.G110A|WNT2B_ENST00000478360.1_3'UTR|WNT2B_ENST00000256640.5_Missense_Mutation_p.G37A|RP4-671G15.2_ENST00000608357.1_RNA	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	129					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|chondrocyte differentiation (GO:0002062)|cornea development in camera-type eye (GO:0061303)|forebrain regionalization (GO:0021871)|hematopoietic stem cell proliferation (GO:0071425)|iris morphogenesis (GO:0061072)|lens development in camera-type eye (GO:0002088)|lung induction (GO:0060492)|male gonad development (GO:0008584)|mesenchymal-epithelial cell signaling (GO:0060638)|neuron differentiation (GO:0030182)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.G129A(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|stomach(1)	18	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCGTCTTTGGCCGTGTCATG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	50	57					1																	113057699		2203	4300	6503	112859222	SO:0001583	missense	7482			AB045116	CCDS847.1, CCDS846.1	1p13	2008-07-18			ENSG00000134245	ENSG00000134245		"Wingless-type MMTV integration sites"	12781	protein-coding gene	gene with protein product	"XWNT2, Xenopus, homolog of", "wingless-type MMTV integration site family, member 13"	601968		WNT13		8761309, 10944466	Standard	NM_024494		Approved	XWNT2	uc001ecb.3	Q93097	OTTHUMG00000011157	ENST00000369684.4:c.386G>C	1.37:g.113057699G>C	ENSP00000358698:p.Gly129Ala		112859222	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Missense_Mutation	SNP	ENST00000369684.4	37	CCDS847.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.751041	0.89753	.	.	ENSG00000134245	ENST00000256640;ENST00000369686;ENST00000369684	T;T;T	0.75938	-0.98;-0.98;-0.98	4.96	4.96	0.65561	.	0.092424	0.85682	D	0.000000	D	0.85758	0.5771	M	0.83118	2.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.87833	0.2646	10	0.87932	D	0	.	18.238	0.89956	0.0:0.0:1.0:0.0	.	129;110	Q93097;Q93097-2	WNT2B_HUMAN;.	A	37;110;129	ENSP00000256640:G37A;ENSP00000358700:G110A;ENSP00000358698:G129A	ENSP00000256640:G37A	G	+	2	0	WNT2B	112859222	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.469000	0.83416	0.555000	0.69702	GGC		0.597	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030692.1	NM_004185		C	113057699	G	C	113057699	3	2	53	1	0	0	0	0	1	0	0	0	17427	1203	42	5	525	5	WNT2B	1	113057699	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	22879005	113057699	136192922	10	7095										
HAO2	51179	broad.mit.edu	37	chr1	119923775	119923775	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agctgtctaagtcaactcggGattttattgaaggtggagca	12	6	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:119923775G>T	ENST00000325945.3	+	2	140	c.67G>T	c.(67-69)Gat>Tat	p.D23Y	HAO2_ENST00000361035.4_Missense_Mutation_p.D36Y	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	23	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)	p.D23Y(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		GTCAACTCGGGATTTTATTGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											198	187	190					1																	119923775		2203	4300	6503	119725298	SO:0001583	missense	51179			AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"(S)-2-hydroxy-acid oxidase", "glycolate oxidase", "long-chain L-2-hydroxy acid oxidase", "growth-inhibiting protein 16"	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.67G>T	1.37:g.119923775G>T	ENSP00000316339:p.Asp23Tyr		119725298	Q2TU86|Q5QP00|Q9UJS6	Missense_Mutation	SNP	ENST00000325945.3	37	CCDS901.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211186	0.58343	.	.	ENSG00000116882	ENST00000457318;ENST00000361035;ENST00000325945	T;T;T	0.34667	1.35;1.35;1.35	5.4	5.4	0.78164	Aldolase-type TIM barrel (1);FMN-dependent dehydrogenase (1);	0.091701	0.64402	D	0.000001	T	0.59169	0.2174	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61936	-0.6960	9	.	.	.	-25.1974	19.1748	0.93600	0.0:0.0:1.0:0.0	.	23	Q9NYQ3	HAOX2_HUMAN	Y	23;36;23	ENSP00000393955:D23Y;ENSP00000354314:D36Y;ENSP00000316339:D23Y	.	D	+	1	0	HAO2	119725298	1.000000	0.71417	0.996000	0.52242	0.067000	0.16453	9.139000	0.94554	2.542000	0.85734	0.655000	0.94253	GAT		0.458	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783		T	119923775	G	T	119923775	3	4	53	1	0	0	0	0	1	0	0	0	6973	1174	41	2	69	2	HAO2	1	119923775	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	6866076	119923775	129326846	11	7096										
ELF3	1999	broad.mit.edu	37	chr1	201982405	201982405	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aagagtactgggactgtctcGagggcaagaagagcaagcac	14	8	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:201982405G>T	ENST00000359651.3	+	6	3976	c.784G>T	c.(784-786)Gag>Tag	p.E262*	ELF3_ENST00000367283.3_Nonsense_Mutation_p.E262*|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_Nonsense_Mutation_p.E262*|RP11-465N4.4_ENST00000419190.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.E262*(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						GGACTGTCTCGAGGGCAAGAA	0.632																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											71	77	75					1																	201982405		2203	4300	6503	200249028	SO:0001587	stop_gained	1999			AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.784G>T	1.37:g.201982405G>T	ENSP00000352673:p.Glu262*		200249028		Nonsense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	.	.	.	.	.	.	.	.	.	.	G	37	6.256485	0.97417	.	.	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044	.	.	.	5.6	5.6	0.85130	.	1.419500	0.03867	N	0.275079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	17.4077	0.87477	0.0:0.0:1.0:0.0	.	.	.	.	X	262;262;262;239	.	ENSP00000311348:E239X	E	+	1	0	ELF3	200249028	0.468000	0.25839	0.994000	0.49952	0.974000	0.67602	1.618000	0.36954	2.633000	0.89246	0.561000	0.74099	GAG		0.632	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		T	201982405	G	T	201982405	4	4	53	1	0	0	0	0	0	1	0	0	5068	1059	37	2	806	2	ELF3	1	201982405	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	82058630	201982405	47268216	12	7097										
SOX13	9580	broad.mit.edu	37	chr1	204092051	204092051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gcagctgctgcacagccacaGtggggccttggatggctccc	14	14	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:204092051G>A	ENST00000367204.1	+	10	1203	c.1094G>A	c.(1093-1095)aGt>aAt	p.S365N		NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	365					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S365N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CACAGCCACAGTGGGGCCTTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1											27	31	30					1																	204092051		2037	4189	6226	202358674	SO:0001583	missense	9580				CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"SRY (sex determining region Y)-boxes"	11192	protein-coding gene	gene with protein product	"islet cell antibody 12", "SRY-related HMG-box gene 13", "type 1 diabetes autoantigen", "SRY-box 13"	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.1094G>A	1.37:g.204092051G>A	ENSP00000356172:p.Ser365Asn		202358674	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Missense_Mutation	SNP	ENST00000367204.1	37	CCDS44299.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584932	0.46110	.	.	ENSG00000143842	ENST00000367204	D	0.97994	-4.65	5.31	4.38	0.52667	.	0.407005	0.31392	N	0.007738	D	0.94496	0.8228	L	0.43152	1.355	0.25250	N	0.989689	B;B;B	0.24963	0.002;0.115;0.002	B;B;B	0.22880	0.002;0.042;0.004	D	0.86902	0.2055	10	0.26408	T	0.33	.	9.12	0.36782	0.0777:0.1486:0.7737:0.0	.	232;232;365	B4DX26;B4E3N9;Q9UN79	.;.;SOX13_HUMAN	N	365	ENSP00000356172:S365N	ENSP00000356172:S365N	S	+	2	0	SOX13	202358674	0.999000	0.42202	0.525000	0.27900	0.976000	0.68499	4.303000	0.59098	1.195000	0.43115	0.655000	0.94253	AGT		0.617	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686		A	204092051	G	A	204092051	3	1	53	1	0	0	0	0	1	0	0	0	14981	1029	36	3	1128	3	SOX13	1	204092051	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	2109646	204092051	45158570	13	7098										
CENPF	1063	broad.mit.edu	37	chr1	214818039	214818039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	caatctagacattgagaaaaTaactgagactggtgcagtga	10	6	1	4			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:214818039T>C	ENST00000366955.3	+	13	5294	c.5126T>C	c.(5125-5127)aTa>aCa	p.I1709T		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1805					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.I1709T(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		ATTGAGAAAATAACTGAGACT	0.448																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											65	64	64					1																	214818039		2203	4300	6503	212884662	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.5126T>C	1.37:g.214818039T>C	ENSP00000355922:p.Ile1709Thr		212884662	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	3.675	-0.066641	0.07273	.	.	ENSG00000117724	ENST00000366955	T	0.03242	4.0	5.04	1.48	0.22813	.	0.759033	0.10916	N	0.620050	T	0.03095	0.0091	L	0.51422	1.61	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.50092	-0.8868	10	0.10636	T	0.68	.	0.4042	0.00430	0.209:0.2497:0.156:0.3853	.	1805	P49454	CENPF_HUMAN	T	1709	ENSP00000355922:I1709T	ENSP00000355922:I1709T	I	+	2	0	CENPF	212884662	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.045000	0.12003	0.083000	0.17047	0.496000	0.49642	ATA		0.448	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214818039	T	C	214818039	3	2	53	1	0	0	0	0	1	0	0	0	3237	1406	49	4	5172	4	CENPF	1	214818039	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	10725988	214818039	34432582	14	7099										
ACTN2	88	broad.mit.edu	37	chr1	236923041	236923041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cagaggaagaatggcctgatGgatcatgaggatttcagagc	14	6	2	5			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:236923041G>A	ENST00000366578.4	+	19	2485	c.2319G>A	c.(2317-2319)atG>atA	p.M773I	ACTN2_ENST00000542672.1_Missense_Mutation_p.M773I|ACTN2_ENST00000546208.1_Missense_Mutation_p.M267I	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	773	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)	p.M773I(1)		endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	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)			ATGGCCTGATGGATCATGAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											149	133	139					1																	236923041		2203	4300	6503	234989664	SO:0001583	missense	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2319G>A	1.37:g.236923041G>A	ENSP00000355537:p.Met773Ile		234989664	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.842906	0.71488	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000546208;ENST00000545611	T;T;T	0.63096	-0.02;-0.02;-0.02	5.41	5.41	0.78517	EF-hand-like domain (1);	0.036669	0.85682	D	0.000000	T	0.43344	0.1243	N	0.01817	-0.705	0.80722	D	1	B;B;B;B	0.19073	0.033;0.002;0.015;0.007	B;B;B;B	0.28784	0.094;0.025;0.094;0.013	T	0.48468	-0.9033	10	0.87932	D	0	.	19.1936	0.93677	0.0:0.0:1.0:0.0	.	558;773;543;773	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	I	773;773;267;542	ENSP00000443495:M773I;ENSP00000355537:M773I;ENSP00000438384:M267I	ENSP00000355537:M773I	M	+	3	0	ACTN2	234989664	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.427000	0.97472	2.540000	0.85666	0.655000	0.94253	ATG		0.418	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236923041	G	A	236923041	3	1	53	1	0	0	0	0	1	0	0	0	205	1348	47	3	2393	3	ACTN2	1	236923041	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	22105002	236923041	12327580	15	7100										
AHCTF1	25909	broad.mit.edu	37	chr1	247067334	247067334	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	caaactcaaaacatccccttCactgaaacagaaattaacga	3	12	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr1:247067334C>T	ENST00000391829.2	-	7	1006	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	AHCTF1_ENST00000326225.3_Splice_Site_p.E304K|AHCTF1_ENST00000366508.1_Splice_Site_p.E330K			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	295	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E295K(1)		NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	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)			ACATCCCCTTCACTGAAACAG	0.373																																					Colon(145;197 1800 4745 15099 26333)											1	Substitution - Missense(1)	large_intestine(1)	1											70	67	68					1																	247067334		2203	4300	6503	245133957	SO:0001630	splice_region_variant	25909				CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.882-1G>A	1.37:g.247067334C>T			245133957	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	C	30	5.052023	0.93793	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.21191	2.02;2.02;2.02	5.37	5.37	0.77165	.	0.051464	0.85682	D	0.000000	T	0.36608	0.0973	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68765	0.96;0.936	T	0.03630	-1.1018	10	0.40728	T	0.16	-24.8108	19.1058	0.93294	0.0:1.0:0.0:0.0	.	330;295	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	K	330;304;295	ENSP00000355464:E330K;ENSP00000355465:E304K;ENSP00000375705:E295K	ENSP00000355465:E304K	E	-	1	0	AHCTF1	245133957	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.298000	0.78815	2.506000	0.84524	0.557000	0.71058	GAA		0.373	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	Missense_Mutation	T	247067334	C	T	247067334	5	4	53	1	0	0	0	0	0	0	1	0	408	840	29	3	6037	3	AHCTF1	1	247067334	Splice_Site	SNP	C	TCGA-AG-3902-01A-01W-1073-09	10144293	247067334	2183287	16	7101										
KCNS3	3790	broad.mit.edu	37	chr2	18112879	18112879	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgctggcctccatcgtggccAtgtgcgttcacagcatgtcg	12	13	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:18112879A>T	ENST00000403915.1	+	3	1055	c.604A>T	c.(604-606)Atg>Ttg	p.M202L	KCNS3_ENST00000304101.4_Missense_Mutation_p.M202L|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	202					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)	p.M202L(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CATCGTGGCCATGTGCGTTCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	63	63					2																	18112879		2203	4300	6503	17976360	SO:0001583	missense	3790			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.604A>T	2.37:g.18112879A>T	ENSP00000385968:p.Met202Leu		17976360	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295917	0.60086	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.97041	-4.22;-4.22	6.07	6.07	0.98685	.	0.035762	0.85682	D	0.000000	D	0.93654	0.7973	L	0.36672	1.1	0.58432	D	0.999997	B	0.19706	0.038	B	0.21546	0.035	D	0.89850	0.4009	10	0.02654	T	1	.	16.6288	0.85011	1.0:0.0:0.0:0.0	.	202	Q9BQ31	KCNS3_HUMAN	L	202	ENSP00000385968:M202L;ENSP00000305824:M202L	ENSP00000305824:M202L	M	+	1	0	KCNS3	17976360	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	ATG		0.542	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		T	18112879	A	T	18112879	3	4	53	1	0	0	0	0	1	0	0	0	8111	217	8	5	606	5	KCNS3	2	18112879	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09		18112879	225086494	17	7102										
GCC2	9648	broad.mit.edu	37	chr2	109087283	109087283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aactgggggaatctgctggaAaaataagtcaagagttcgaa	12	5	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:109087283A>G	ENST00000309863.6	+	6	2212	c.1498A>G	c.(1498-1500)Aaa>Gaa	p.K500E		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	500					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)	p.K500E(1)		breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ATCTGCTGGAAAAATAAGTCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											60	62	61					2																	109087283		2202	4297	6499	108453715	SO:0001583	missense	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.1498A>G	2.37:g.109087283A>G	ENSP00000307939:p.Lys500Glu		108453715	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.307123	0.60305	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	T	0.36699	1.24	5.4	4.24	0.50183	.	0.179384	0.49305	D	0.000153	T	0.34571	0.0902	M	0.69823	2.125	0.38980	D	0.958924	B	0.21606	0.058	B	0.20184	0.028	T	0.17745	-1.0359	10	0.12103	T	0.63	.	11.2765	0.49170	0.9281:0.0:0.0719:0.0	.	500	Q8IWJ2	GCC2_HUMAN	E	500;463;245	ENSP00000307939:K500E	ENSP00000307939:K500E	K	+	1	0	GCC2	108453715	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.624000	0.67764	0.990000	0.38787	0.528000	0.53228	AAA		0.373	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		G	109087283	A	G	109087283	3	3	53	1	0	0	0	0	1	0	0	0	6306	15	1	4	1520	4	GCC2	2	109087283	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	90974404	109087283	134112090	18	7103										
THSD7B	80731	broad.mit.edu	37	chr2	137814212	137814212	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgtgcttgttccttacgctcGcggtgaagtcaagcctcgga	12	11	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:137814212G>A	ENST00000409968.1	+	3	540	c.362G>A	c.(361-363)cGc>cAc	p.R121H	THSD7B_ENST00000413152.2_Missense_Mutation_p.R90H|THSD7B_ENST00000272643.3_Missense_Mutation_p.R121H|THSD7B_ENST00000543459.1_5'Flank			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	121	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.R121H(2)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CCTTACGCTCGCGGTGAAGTC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	2											75	82	79					2																	137814212		2061	4206	6267	137530682	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.362G>A	2.37:g.137814212G>A	ENSP00000387145:p.Arg121His		137530682		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	g	5.876	0.345696	0.11126	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.23754	2.43;2.29;1.89	6.07	1.07	0.20283	.	0.972227	0.08512	N	0.934707	T	0.07818	0.0196	N	0.01705	-0.755	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.36286	-0.9754	9	.	.	.	.	1.4505	0.02374	0.5177:0.1143:0.2233:0.1447	.	90	C9JKN6	.	H	121;121;90	ENSP00000387145:R121H;ENSP00000272643:R121H;ENSP00000413841:R90H	.	R	+	2	0	THSD7B	137530682	0.000000	0.05858	0.002000	0.10522	0.135000	0.20990	0.037000	0.13840	-0.046000	0.13446	-0.385000	0.06624	CGC		0.542	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		A	137814212	G	A	137814212	3	1	53	1	0	0	0	0	1	0	0	0	15919	1087	38	1	275	1	THSD7B	2	137814212	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	28726929	137814212	105385161	19	7104										
OSBPL6	114880	broad.mit.edu	37	chr2	179259117	179259117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	actccagagatctcggagacGatatatggaagaaaacaatc	9	8	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:179259117G>T	ENST00000190611.4	+	24	3027	c.2651G>T	c.(2650-2652)cGa>cTa	p.R884L	OSBPL6_ENST00000409045.3_Missense_Mutation_p.R853L|OSBPL6_ENST00000409631.1_Missense_Mutation_p.R848L|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R909L|OSBPL6_ENST00000359685.3_Missense_Mutation_p.R848L|OSBPL6_ENST00000315022.2_Missense_Mutation_p.R888L	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	884					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R884L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCTCGGAGACGATATATGGAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	119	115					2																	179259117		2203	4300	6503	178967363	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.2651G>T	2.37:g.179259117G>T	ENSP00000190611:p.Arg884Leu		178967363	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585811	0.86748	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35	6.07	6.07	0.98685	.	0.128204	0.56097	D	0.000027	T	0.67126	0.2860	M	0.92169	3.28	0.58432	D	0.999998	P;P;D;D;D	0.71674	0.758;0.875;0.998;0.98;0.965	P;P;D;P;P	0.68039	0.628;0.774;0.955;0.774;0.83	T	0.74210	-0.3739	10	0.87932	D	0	-9.5297	13.7999	0.63192	0.0696:0.0:0.9304:0.0	.	853;888;848;909;884	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3	.;.;.;.;OSBL6_HUMAN	L	909;848;853;884;848;888	ENSP00000376293:R909L;ENSP00000352713:R848L;ENSP00000387248:R853L;ENSP00000190611:R884L;ENSP00000386885:R848L;ENSP00000318723:R888L	ENSP00000190611:R884L	R	+	2	0	OSBPL6	178967363	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.145000	0.58065	2.890000	0.99128	0.585000	0.79938	CGA		0.373	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		T	179259117	G	T	179259117	3	4	53	1	0	0	0	0	1	0	0	0	11312	1058	37	2	2859	2	OSBPL6	2	179259117	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	41444905	179259117	63940256	20	7105										
COL5A2	1290	broad.mit.edu	37	chr2	189910538	189910538	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctccttaccggatctcctctTtgtcctgcatctcctggagc	7	16	3	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:189910538T>G	ENST00000374866.3	-	46	3571	c.3297A>C	c.(3295-3297)caA>caC	p.Q1099H		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1099					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.Q1099H(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GATCTCCTCTTTGTCCTGCAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											88	82	84					2																	189910538		2203	4300	6503	189618783	SO:0001583	missense	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3297A>C	2.37:g.189910538T>G	ENSP00000364000:p.Gln1099His		189618783	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.051939	0.55218	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.93189	-3.18	5.21	-1.54	0.08584	.	0.138683	0.32703	N	0.005742	D	0.85336	0.5673	L	0.41079	1.255	0.36453	D	0.866232	B;P	0.38677	0.187;0.642	B;B	0.34452	0.037;0.183	T	0.78871	-0.2033	10	0.13470	T	0.59	.	9.9567	0.41671	0.0:0.3939:0.0:0.6061	.	739;1099	Q5PR22;P05997	.;CO5A2_HUMAN	H	1099;739	ENSP00000364000:Q1099H	ENSP00000364000:Q1099H	Q	-	3	2	COL5A2	189618783	0.999000	0.42202	0.989000	0.46669	0.996000	0.88848	0.635000	0.24629	-0.405000	0.07599	0.528000	0.53228	CAA		0.537	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		G	189910538	T	G	189910538	3	3	53	1	0	0	0	0	1	0	0	0	3703	1838	64	4	1238	4	COL5A2	2	189910538	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	10651421	189910538	53288835	21	7106										
ALS2CR12	130540	broad.mit.edu	37	chr2	202163982	202163982	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tctttggtttttctcagctcTtctaattgcaaggtgtcact	7	9	5	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:202163982T>A	ENST00000286190.5	-	11	967	c.921A>T	c.(919-921)gaA>gaT	p.E307D	ALS2CR12_ENST00000392257.3_Missense_Mutation_p.E307D|ALS2CR12_ENST00000439709.1_Missense_Mutation_p.E307D|ALS2CR12_ENST00000405148.2_Missense_Mutation_p.E307D			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	307					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)		p.E307D(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						TTCTCAGCTCTTCTAATTGCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											214	209	211					2																	202163982		2203	4300	6503	201872227	SO:0001583	missense	130540			AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.921A>T	2.37:g.202163982T>A	ENSP00000286190:p.Glu307Asp		201872227	G5E9S3|Q53TT6|Q8N1B6	Missense_Mutation	SNP	ENST00000286190.5	37	CCDS2346.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.35|12.35	1.910910|1.910910	0.33721|0.33721	.|.	.|.	ENSG00000155749|ENSG00000155749	ENST00000286190;ENST00000405148;ENST00000392257;ENST00000439709|ENST00000415745	T;T;T;T|.	0.43688|.	0.94;0.94;0.94;0.94|.	4.52|4.52	-0.9|-0.9	0.10544|0.10544	.|.	0.262894|.	0.26891|.	N|.	0.021979|.	T|T	0.30166|0.30166	0.0756|0.0756	L|L	0.29908|0.29908	0.895|0.895	0.21822|0.21822	N|N	0.999521|0.999521	P;P|.	0.50156|.	0.932;0.827|.	P;B|.	0.46543|.	0.52;0.442|.	T|T	0.31696|0.31696	-0.9934|-0.9934	10|5	0.29301|.	T|.	0.29|.	-6.2128|-6.2128	7.7233|7.7233	0.28744|0.28744	0.0:0.3791:0.0:0.6209|0.0:0.3791:0.0:0.6209	.|.	307;307|.	Q96Q35;G5E9S3|.	AL2SB_HUMAN;.|.	D|M	307|82	ENSP00000286190:E307D;ENSP00000385098:E307D;ENSP00000376086:E307D;ENSP00000412073:E307D|.	ENSP00000286190:E307D|.	E|K	-|-	3|2	2|0	ALS2CR12|ALS2CR12	201872227|201872227	0.951000|0.951000	0.32395|0.32395	0.988000|0.988000	0.46212|0.46212	0.512000|0.512000	0.34134|0.34134	0.131000|0.131000	0.15870|0.15870	-0.069000|-0.069000	0.12931|0.12931	-0.468000|-0.468000	0.05107|0.05107	GAA|AAG		0.368	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163		A	202163982	T	A	202163982	3	1	53	1	0	0	0	0	1	0	0	0	553	1606	56	5	432	5	ALS2CR12	2	202163982	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	12253444	202163982	41035391	22	7107										
NCL	4691	broad.mit.edu	37	chr2	232326411	232326411	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcctcatcctcctcactgtcAtcatcctcctcttcatcact	1	19	7	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr2:232326411A>G	ENST00000322723.4	-	3	693	c.453T>C	c.(451-453)gaT>gaC	p.D151D	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	151	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.D151D(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		cctcactgtcatcatcctcct	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	2											474	283	348					2																	232326411		2203	4300	6503	232034655	SO:0001819	synonymous_variant	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.453T>C	2.37:g.232326411A>G			232034655	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																				0.532	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		G	232326411	A	G	232326411	2	3	53	1	0	0	0	0	0	0	0	1	10257	214	8	4		4	NCL	2	232326411	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	30162429	232326411	10872962	23	7108										
ATP2B2	491	broad.mit.edu	37	chr3	10442664	10442664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cagcatggggtccttgtccaCggacttgcgcacctggtcag	13	13	1	0	rs375973812		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr3:10442664C>T	ENST00000352432.4	-	4	823	c.754G>A	c.(754-756)Gtg>Atg	p.V252M	ATP2B2_ENST00000383800.4_Missense_Mutation_p.V252M|ATP2B2_ENST00000397077.1_Missense_Mutation_p.V252M|ATP2B2_ENST00000360273.2_Missense_Mutation_p.V252M|ATP2B2_ENST00000343816.4_Missense_Mutation_p.V252M			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	252					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.V252M(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TCCTTGTCCACGGACTTGCGC	0.587																																					Ovarian(125;1619 1709 15675 19819 38835)											1	Substitution - Missense(1)	large_intestine(1)	3						C	MET/VAL,MET/VAL	0,4406		0,0,2203	146	117	127		754,754	5.6	1	3		127	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ATP2B2	NM_001001331.2,NM_001683.3	21,21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	252/1244,252/1199	10442664	1,13005	2203	4300	6503	10417664	SO:0001583	missense	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.754G>A	3.37:g.10442664C>T	ENSP00000324172:p.Val252Met		10417664	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.729415	0.89390	0.0	1.16E-4	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69;-2.69	5.61	5.61	0.85477	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.122884	0.53938	D	0.000046	D	0.92315	0.7562	M	0.75615	2.305	0.48185	D	0.999609	P;P;P	0.48230	0.906;0.907;0.616	P;P;B	0.46339	0.511;0.513;0.19	D	0.92413	0.5939	10	0.51188	T	0.08	-25.5035	19.6383	0.95746	0.0:1.0:0.0:0.0	.	252;264;252	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	M	252;252;252;252;252;218;139;252	ENSP00000324172:V252M;ENSP00000373311:V252M;ENSP00000380267:V252M;ENSP00000353414:V252M;ENSP00000344677:V252M;ENSP00000414854:V139M	ENSP00000342954:V252M	V	-	1	0	ATP2B2	10417664	0.789000	0.28775	0.996000	0.52242	0.999000	0.98932	1.646000	0.37249	2.631000	0.89168	0.655000	0.94253	GTG		0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		T	10442664	C	T	10442664	3	4	53	1	0	0	0	0	1	0	0	0	1141	536	19	1	3053	1	ATP2B2	3	10442664	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09		10442664	187579766	24	7109										
ROBO1	6091	broad.mit.edu	37	chr3	78666887	78666887	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	atcagtgaaaaaggagccgtCcgaagaactaacactggagc	11	9	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr3:78666887C>G	ENST00000464233.1	-	27	4293	c.4180G>C	c.(4180-4182)Gac>Cac	p.D1394H	ROBO1_ENST00000467549.1_Missense_Mutation_p.D1294H|ROBO1_ENST00000495273.1_Missense_Mutation_p.D1349H|ROBO1_ENST00000436010.2_Missense_Mutation_p.D1355H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1394					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.D1394H(1)|p.D1349H(1)|p.D1371H(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AAGGAGCCGTCCGAAGAACTA	0.577																																																3	Substitution - Missense(3)	large_intestine(3)	3											56	61	59					3																	78666887		1971	4137	6108	78749577	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4180G>C	3.37:g.78666887C>G	ENSP00000420321:p.Asp1394His		78749577	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.126909	0.56721	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.79653	-1.24;-1.29;-1.12;-1.23	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.86377	0.5918	L	0.39245	1.2	0.80722	D	1	D;D;D;D;B	0.89917	1.0;0.981;1.0;0.982;0.052	D;P;D;P;B	0.87578	0.998;0.662;0.956;0.856;0.014	D	0.83779	0.0224	9	.	.	.	.	20.1554	0.98111	0.0:1.0:0.0:0.0	.	1358;1394;1349;1294;1355	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	H	1355;1349;1394;1349;1294;1398	ENSP00000406043:D1355H;ENSP00000420321:D1394H;ENSP00000420637:D1349H;ENSP00000417992:D1294H	.	D	-	1	0	ROBO1	78749577	1.000000	0.71417	0.123000	0.21794	0.048000	0.14542	7.445000	0.80570	2.838000	0.97847	0.591000	0.81541	GAC		0.577	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		G	78666887	C	G	78666887	3	3	53	1	0	0	0	0	1	0	0	0	13550	855	30	5	795	5	ROBO1	3	78666887	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	68224223	78666887	119355543	25	7110										
CLSTN2	64084	broad.mit.edu	37	chr3	140285015	140285015	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aagaggaggaggaggaggaaGggatgggcagaggcagacat	21	3	0	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr3:140285015G>C	ENST00000458420.3	+	17	2978	c.2788G>C	c.(2788-2790)Ggg>Cgg	p.G930R		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	930					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.G930R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GGAGGAGGAAGGGATGGGCAG	0.602										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)	large_intestine(1)	3											97	87	91					3																	140285015		2203	4300	6503	141767705	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2788G>C	3.37:g.140285015G>C	ENSP00000402460:p.Gly930Arg		141767705	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	7.575	0.667574	0.14710	.	.	ENSG00000158258	ENST00000458420	T	0.39229	1.09	5.59	3.76	0.43208	.	0.796683	0.10880	N	0.623905	T	0.29524	0.0736	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24048	-1.0171	9	.	.	.	-17.509	7.8831	0.29633	0.0834:0.3095:0.6071:0.0	.	930	Q9H4D0	CSTN2_HUMAN	R	930	ENSP00000402460:G930R	.	G	+	1	0	CLSTN2	141767705	0.999000	0.42202	0.006000	0.13384	0.439000	0.31926	3.492000	0.53259	0.681000	0.31386	0.655000	0.94253	GGG		0.602	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		C	140285015	G	C	140285015	3	2	53	1	0	0	0	0	1	0	0	0	3568	1000	35	5	2854	5	CLSTN2	3	140285015	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	61618128	140285015	57737415	26	7111										
SLITRK3	22865	broad.mit.edu	37	chr3	164905727	164905727	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tccaggacttcgaggtaatcCggcttggtttgaagtttggc	13	8	0	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr3:164905727C>T	ENST00000475390.1	-	2	3335	c.2892G>A	c.(2890-2892)ccG>ccA	p.P964P	SLITRK3_ENST00000241274.3_Silent_p.P964P			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	964					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.P964P(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						CGAGGTAATCCGGCTTGGTTT	0.393										HNSCC(40;0.11)																																						2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	3											150	148	149					3																	164905727		2203	4300	6503	166388421	SO:0001819	synonymous_variant	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.2892G>A	3.37:g.164905727C>T			166388421	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																				0.393	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164905727	C	T	164905727	2	4	53	1	0	0	0	0	0	0	0	1	14781	639	23	1		1	SLITRK3	3	164905727	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	24620712	164905727	33116703	27	7112										
GNB4	59345	broad.mit.edu	37	chr3	179134313	179134313	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	atagctatcccaaataattaAttttccatcttgagaagcac	4	9	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr3:179134313A>G	ENST00000232564.3	-	5	521	c.235T>C	c.(235-237)Tta>Cta	p.L79L	GNB4_ENST00000468623.1_Silent_p.L79L|GNB4_ENST00000465153.1_5'Flank	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	79					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)	p.L79L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			CAAATAATTAATTTTCCATCT	0.308																																					Melanoma(105;1405 1491 7265 20440 33721)											1	Substitution - coding silent(1)	large_intestine(1)	3											47	51	50					3																	179134313		2202	4282	6484	180617007	SO:0001819	synonymous_variant	59345			AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"WD repeat domain containing"	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.235T>C	3.37:g.179134313A>G			180617007	B3KMH5|D3DNR8	Silent	SNP	ENST00000232564.3	37	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.285442	0.23478	.	.	ENSG00000114450	ENST00000466899	.	.	.	5.45	4.32	0.51571	.	.	.	.	.	T	0.60418	0.2267	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58713	-0.7588	4	.	.	.	-45.0162	9.9401	0.41576	0.8895:0.0:0.1105:0.0	.	.	.	.	T	1	.	.	I	-	2	0	GNB4	180617007	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.215000	0.32431	2.061000	0.61500	0.533000	0.62120	ATT		0.308	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629		G	179134313	A	G	179134313	2	3	53	1	0	0	0	0	0	0	0	1	6540	98	4	4		4	GNB4	3	179134313	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	14228586	179134313	18888117	28	7113										
AASDH	132949	broad.mit.edu	37	chr4	57244559	57244559	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tttttccagtgaagtctgaaGagcactaggtcattatgttc	9	7	2	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr4:57244559G>A	ENST00000205214.6	-	4	603	c.423C>T	c.(421-423)ctC>ctT	p.L141L	AASDH_ENST00000434343.2_Intron|AASDH_ENST00000513376.1_Silent_p.L41L|AASDH_ENST00000602986.1_5'UTR|AASDH_ENST00000451613.1_Silent_p.L141L|AASDH_ENST00000502617.1_Silent_p.L141L|AASDH_ENST00000510762.1_5'UTR	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	141					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.L141L(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GAAGTCTGAAGAGCACTAGGT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											80	79	79					4																	57244559		2203	4299	6502	56939316	SO:0001819	synonymous_variant	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.423C>T	4.37:g.57244559G>A			56939316	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																				0.318	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		A	57244559	G	A	57244559	2	1	53	1	0	0	0	0	0	0	0	1	22	929	33	3		3	AASDH	4	57244559	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09		57244559	133909717	29	7114										
UGT2B4	7363	broad.mit.edu	37	chr4	70361243	70361243	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aaatgtccacatgatttcttGtacttgtgaaaaatatgacc	6	7	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr4:70361243G>A	ENST00000305107.6	-	1	383	c.337C>T	c.(337-339)Caa>Taa	p.Q113*	UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000512583.1_Nonsense_Mutation_p.Q113*|UGT2B4_ENST00000381096.3_Intron	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	113					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.Q113*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ATGATTTCTTGTACTTGTGAA	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											48	44	45					4																	70361243		1964	4209	6173	70395832	SO:0001587	stop_gained	7363			BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.337C>T	4.37:g.70361243G>A	ENSP00000305221:p.Gln113*		70395832	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Nonsense_Mutation	SNP	ENST00000305107.6	37	CCDS43234.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.491596	0.26774	.	.	ENSG00000156096	ENST00000512583;ENST00000305107	.	.	.	2.41	-3.99	0.04069	.	0.285346	0.26428	U	0.024426	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	5.5245	0.16951	0.0:0.312:0.2196:0.4684	.	.	.	.	X	113	.	ENSP00000305221:Q113X	Q	-	1	0	UGT2B4	70395832	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.415000	0.02469	-0.580000	0.05944	0.306000	0.20318	CAA		0.318	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		A	70361243	G	A	70361243	4	1	53	1	0	0	0	0	0	1	0	0	17001	1386	48	3	1273	3	UGT2B4	4	70361243	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	13116684	70361243	120793033	30	7115										
SLC25A31	83447	broad.mit.edu	37	chr4	128651781	128651781	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gggaaggaccttctggccggCggagtcgcggcagctgtgtc	18	11	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr4:128651781C>T	ENST00000281154.4	+	1	249	c.81C>T	c.(79-81)ggC>ggT	p.G27G		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	27					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.G27G(1)		NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						TTCTGGCCGGCGGAGTCGCGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	4											53	50	51					4																	128651781		2203	4300	6503	128871231	SO:0001819	synonymous_variant	83447			AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.81C>T	4.37:g.128651781C>T			128871231		Silent	SNP	ENST00000281154.4	37	CCDS3733.1																																																																																				0.597	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		T	128651781	C	T	128651781	2	4	53	1	0	0	0	0	0	0	0	1	14532	755	27	1		1	SLC25A31	4	128651781	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	58290538	128651781	62502495	31	7116										
TTC29	83894	broad.mit.edu	37	chr4	147724726	147724726	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgtaagcatcatctgatgagCttttgctattccatagtgaa	8	7	2	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr4:147724726C>G	ENST00000325106.4	-	11	1439	c.1213G>C	c.(1213-1215)Gct>Cct	p.A405P	TTC29_ENST00000398886.4_Missense_Mutation_p.A431P|TTC29_ENST00000513335.1_Missense_Mutation_p.A431P|TTC29_ENST00000506019.1_5'UTR	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	405								p.A405P(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					ATCTGATGAGCTTTTGCTATT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	97	97					4																	147724726		1920	4148	6068	147944176	SO:0001583	missense	83894			AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.1213G>C	4.37:g.147724726C>G	ENSP00000316740:p.Ala405Pro		147944176	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.602002	0.87055	.	.	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000504425	T;T;T;T	0.30448	1.53;1.53;1.56;1.55	5.84	5.84	0.93424	.	0.118165	0.56097	D	0.000031	T	0.56455	0.1986	M	0.65498	2.005	0.47778	D	0.999512	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.69142	0.924;0.962;0.924	T	0.55792	-0.8085	10	0.72032	D	0.01	-5.9448	20.1551	0.98106	0.0:1.0:0.0:0.0	.	405;431;405	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	P	431;431;405;405	ENSP00000423505:A431P;ENSP00000381861:A431P;ENSP00000316740:A405P;ENSP00000425778:A405P	ENSP00000316740:A405P	A	-	1	0	TTC29	147944176	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	3.070000	0.50033	2.760000	0.94817	0.655000	0.94253	GCT		0.428	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		G	147724726	C	G	147724726	3	3	53	1	0	0	0	0	1	0	0	0	16736	797	28	5	226	5	TTC29	4	147724726	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	19072945	147724726	43429550	32	7117										
ODZ3	55714	broad.mit.edu	37	chr4	183713656	183713656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agctttcttgggtacaagtcGgagggtcttattcaaataca	10	7	3	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr4:183713656G>A	ENST00000511685.1	+	26	5954	c.5831G>A	c.(5830-5832)cGg>cAg	p.R1944Q	TENM3_ENST00000406950.2_Missense_Mutation_p.R1944Q			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1944					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R1944Q(1)									GGTACAAGTCGGAGGGTCTTA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	60	60					4																	183713656		1882	4101	5983	183950650	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5831G>A	4.37:g.183713656G>A	ENSP00000424226:p.Arg1944Gln		183950650	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358002	0.82243	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.87179	-2.22;-2.22	4.74	4.74	0.60224	.	.	.	.	.	D	0.91405	0.7288	L	0.58428	1.81	0.80722	D	1	D	0.69078	0.997	D	0.67725	0.953	D	0.89411	0.3703	9	0.29301	T	0.29	.	18.268	0.90057	0.0:0.0:1.0:0.0	.	1944	Q9P273	TEN3_HUMAN	Q	1944	ENSP00000424226:R1944Q;ENSP00000385276:R1944Q	ENSP00000385276:R1944Q	R	+	2	0	ODZ3	183950650	1.000000	0.71417	0.992000	0.48379	0.917000	0.54804	9.321000	0.96353	2.608000	0.88229	0.591000	0.81541	CGG		0.453	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183713656	G	A	183713656	3	1	53	1	0	0	0	0	1	0	0	0	10867	1116	39	1	5929	1	ODZ3	4	183713656	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	35988930	183713656	7440620	33	7118										
PRLR	5618	broad.mit.edu	37	chr5	35068332	35068332	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	acttacctccaacagatgagCatcaaatccttttatttttg	4	10	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:35068332C>G	ENST00000382002.5	-	9	1267	c.841G>C	c.(841-843)Gct>Cct	p.A281P	PRLR_ENST00000348262.3_Intron|PRLR_ENST00000511486.1_Missense_Mutation_p.A180P|PRLR_ENST00000310101.5_Missense_Mutation_p.A281P|PRLR_ENST00000397391.3_Intron|PRLR_ENST00000542609.1_Missense_Mutation_p.A281P|PRLR_ENST00000509934.1_5'UTR|PRLR_ENST00000513753.1_Missense_Mutation_p.A281P|PRLR_ENST00000342362.5_Missense_Mutation_p.A180P|PRLR_ENST00000231423.3_Missense_Mutation_p.A281P	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	281					activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)	p.A281P(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	AACAGATGAGCATCAAATCCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											173	156	161					5																	35068332		2203	4300	6503	35104089	SO:0001583	missense	5618				CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.841G>C	5.37:g.35068332C>G	ENSP00000371432:p.Ala281Pro		35104089	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.764450	0.49574	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101	T;T;T;D;T;D;T	0.86497	-0.85;-0.83;-0.83;-2.13;-1.22;-2.13;-0.82	5.54	1.77	0.24775	.	0.416111	0.29908	N	0.010900	T	0.64983	0.2648	N	0.01631	-0.79	0.21802	N	0.999533	P;P;P;P	0.43885	0.725;0.82;0.731;0.731	B;B;B;B	0.42692	0.177;0.331;0.306;0.395	T	0.62310	-0.6881	10	0.24483	T	0.36	-3.4131	4.9522	0.14021	0.1256:0.2144:0.0:0.6599	.	281;180;281;281	P16471;P16471-2;P16471-6;P16471-4	PRLR_HUMAN;.;.;.	P	281;281;281;180;281;180;281	ENSP00000231423:A281P;ENSP00000424841:A281P;ENSP00000441813:A281P;ENSP00000339213:A180P;ENSP00000371432:A281P;ENSP00000422556:A180P;ENSP00000309008:A281P	ENSP00000231423:A281P	A	-	1	0	PRLR	35104089	0.995000	0.38212	0.999000	0.59377	0.922000	0.55478	0.310000	0.19356	0.120000	0.18254	-0.302000	0.09304	GCT		0.418	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2			G	35068332	C	G	35068332	3	3	53	1	0	0	0	0	1	0	0	0	12565	710	25	5	1035	5	PRLR	5	35068332	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09		35068332	145846928	34	7119										
RGNEF	64283	broad.mit.edu	37	chr5	73166009	73166009	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aataggcaggagaaggatgtCatcaaaagacaggatgtcat	12	5	3	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:73166009C>T	ENST00000426542.2	+	20	2561	c.2541C>T	c.(2539-2541)gtC>gtT	p.V847V	ARHGEF28_ENST00000437974.1_Silent_p.V847V|ARHGEF28_ENST00000296794.6_Silent_p.V847V|ARHGEF28_ENST00000545377.1_Silent_p.V847V|ARHGEF28_ENST00000513042.2_Silent_p.V847V|ARHGEF28_ENST00000296799.4_Silent_p.V534V|ARHGEF28_ENST00000287898.5_Silent_p.V847V			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	847					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)	p.V847V(2)									AGAAGGATGTCATCAAAAGAC	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	5											129	119	122					5																	73166009		1899	4126	6025	73201765	SO:0001819	synonymous_variant	64283				CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2541C>T	5.37:g.73166009C>T			73201765	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																				0.448	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73166009	C	T	73166009	2	4	53	1	0	0	0	0	0	0	0	1	13320	813	29	3		3	RGNEF	5	73166009	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	38097677	73166009	107749251	35	7120										
POU5F2	134187	broad.mit.edu	37	chr5	93076993	93076993	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggcgccttcggaggggcgtcGcaaccagtcccctgcctcac	13	17	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:93076993G>A	ENST00000510627.4	-	1	350	c.277C>T	c.(277-279)Cga>Tga	p.R93*	POU5F2_ENST00000606183.1_5'Flank|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000395965.3_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	93					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-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;0.0415)|all cancers(79;2.03e-19)		GAGGGGCGTCGCAACCAGTCC	0.652																																																0			5											22	24	24					5																	93076993		1882	4108	5990	93102749	SO:0001587	stop_gained	134187				CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.277C>T	5.37:g.93076993G>A	ENSP00000464890:p.Arg93*		93102749	Q15169|Q6MZL7|Q8N748	Nonsense_Mutation	SNP	ENST00000510627.4	37	CCDS59489.1																																																																																				0.652	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		A	93076993	G	A	93076993	4	1	53	1	0	0	0	0	0	1	0	0	12314	1095	38	1	713	1	POU5F2	5	93076993	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	19910984	93076993	87838267	36	7121										
APC	324	broad.mit.edu	37	chr5	112175153	112175153	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	catcagctgaagatgaaataGgatgtaatcagacgacacag	10	7	2	4			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:112175153G>T	ENST00000457016.1	+	16	4242	c.3862G>T	c.(3862-3864)Gga>Tga	p.G1288*	APC_ENST00000508376.2_Nonsense_Mutation_p.G1288*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.G1288*			P25054	APC_HUMAN	adenomatous polyposis coli	1288	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.G1288*(2)|p.K1192fs*3(1)|p.?(1)|p.I1287fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGATGAAATAGGATGTAATCA	0.358		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Substitution - Nonsense(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5											56	58	57					5																	112175153		2202	4300	6502	112203052	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3862G>T	5.37:g.112175153G>T	ENSP00000413133:p.Gly1288*		112203052	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	39	7.661470	0.98419	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	5.73	0.89815	.	0.058979	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-20.3238	19.8705	0.96849	0.0:0.0:1.0:0.0	.	.	.	.	X	1288	.	.	G	+	1	0	APC	112203052	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	5.057000	0.64294	2.861000	0.98227	0.655000	0.94253	GGA		0.358	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175153	G	T	112175153	4	4	53	1	0	0	0	0	0	1	0	0	763	1001	35	2	3920	2	APC	5	112175153	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	19098160	112175153	68740107	37	7122										
SLC27A6	28965	broad.mit.edu	37	chr5	128302276	128302276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctccctcctgaattgcatccGcgcctgtgggcccagagccc	10	18	0	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:128302276G>A	ENST00000262462.4	+	1	1456	c.446G>A	c.(445-447)cGc>cAc	p.R149H	SLC27A6_ENST00000395266.1_Missense_Mutation_p.R149H|SLC27A6_ENST00000506176.1_Missense_Mutation_p.R149H			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	149					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.R149H(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		AATTGCATCCGCGCCTGTGGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	30	34					5																	128302276		2203	4300	6503	128330175	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.446G>A	5.37:g.128302276G>A	ENSP00000262462:p.Arg149His		128330175	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	7.373	0.627191	0.14257	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.42900	0.96;0.96;0.96	4.18	-0.984	0.10259	AMP-dependent synthetase/ligase (1);	0.969547	0.08601	N	0.921544	T	0.28400	0.0702	L	0.42245	1.32	0.09310	N	1	B	0.16396	0.017	B	0.18561	0.022	T	0.29882	-0.9997	10	0.34782	T	0.22	-4.4793	0.9223	0.01318	0.3473:0.1122:0.3121:0.2284	.	149	Q9Y2P4	S27A6_HUMAN	H	149	ENSP00000262462:R149H;ENSP00000378684:R149H;ENSP00000421024:R149H	ENSP00000262462:R149H	R	+	2	0	SLC27A6	128330175	0.000000	0.05858	0.477000	0.27303	0.557000	0.35523	0.285000	0.18883	-0.202000	0.10268	0.561000	0.74099	CGC		0.582	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		A	128302276	G	A	128302276	3	1	53	1	0	0	0	0	1	0	0	0	14567	1087	38	1	448	1	SLC27A6	5	128302276	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	16127123	128302276	52612984	38	7123										
RAPGEF6	51735	broad.mit.edu	37	chr5	130928157	130928157	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aacatctggcaatcgtttctGaactgtttaaataaataagt	6	6	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:130928157G>C	ENST00000509018.1	-	4	405	c.200C>G	c.(199-201)tCa>tGa	p.S67*	RAPGEF6_ENST00000503398.2_5'Flank|RAPGEF6_ENST00000307984.5_Nonsense_Mutation_p.S67*|RAPGEF6_ENST00000308008.6_Nonsense_Mutation_p.S67*|CTC-432M15.3_ENST00000514667.1_Nonsense_Mutation_p.S117*|RAPGEF6_ENST00000296859.6_Nonsense_Mutation_p.S67*|RAPGEF6_ENST00000510071.1_Nonsense_Mutation_p.S67*|RAPGEF6_ENST00000507093.1_Nonsense_Mutation_p.S67*	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	67					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.S67*(2)|p.S117*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AATCGTTTCTGAACTGTTTAA	0.323																																					Melanoma(168;435 1955 13113 13877 23213)											3	Substitution - Nonsense(3)	large_intestine(3)	5											67	56	60					5																	130928157		2203	4300	6503	130956056	SO:0001587	stop_gained	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.200C>G	5.37:g.130928157G>C	ENSP00000421684:p.Ser67*		130956056	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Nonsense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	38	7.052717	0.98029	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000308008;ENST00000510071;ENST00000514667	.	.	.	4.73	4.73	0.59995	.	0.232089	0.28671	N	0.014523	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	16.8241	0.85926	0.0:0.0:1.0:0.0	.	.	.	.	X	67;67;67;67;67;67;67;117	.	ENSP00000426948:S117X	S	-	2	0	RAPGEF6;FNIP1	130956056	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.920000	0.70017	2.317000	0.78254	0.563000	0.77884	TCA		0.323	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130928157	G	C	130928157	4	2	53	1	0	0	0	0	0	1	0	0	13085	1294	45	5	5191	5	RAPGEF6	5	130928157	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	2625881	130928157	49987103	39	7124										
C5orf15	56951	broad.mit.edu	37	chr5	133292560	133292560	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcacagtgctttaaaaaataTaatcattggtaatcttcaaa	4	6	4	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:133292560T>A	ENST00000231512.3	-	3	990	c.788A>T	c.(787-789)tAt>tTt	p.Y263F	C5orf15_ENST00000507191.1_5'Flank	NM_020199.2	NP_064584.1	Q8NC54	KCT2_HUMAN	chromosome 5 open reading frame 15	263						integral component of membrane (GO:0016021)		p.Y263F(1)		endometrium(2)|large_intestine(1)|lung(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)			TTAAAAAATATAATCATTGGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											67	66	66					5																	133292560		2203	4300	6503	133320459	SO:0001583	missense	56951			AF226055	CCDS4167.1	5q31.1	2012-02-22			ENSG00000113583	ENSG00000113583			20656	protein-coding gene	gene with protein product	"keratinocytes associated transmembrane protein 2"						Standard	NM_020199		Approved	KCT2, HTGN29	uc003kyo.3	Q8NC54	OTTHUMG00000129125	ENST00000231512.3:c.788A>T	5.37:g.133292560T>A	ENSP00000231512:p.Tyr263Phe		133320459	B2RD10|D3DQ92|Q9NRG2	Missense_Mutation	SNP	ENST00000231512.3	37	CCDS4167.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.474523	0.84640	.	.	ENSG00000113583	ENST00000231512;ENST00000451255	.	.	.	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000010	T	0.77725	0.4173	M	0.66939	2.045	0.53688	D	0.999971	D	0.89917	1.0	D	0.85130	0.997	T	0.79869	-0.1621	9	0.72032	D	0.01	-17.0445	15.327	0.74172	0.0:0.0:0.0:1.0	.	263	Q8NC54	KCT2_HUMAN	F	263;163	.	ENSP00000231512:Y263F	Y	-	2	0	C5orf15	133320459	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.476000	0.81055	2.221000	0.72209	0.528000	0.53228	TAT		0.338	C5orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251175.1	NM_020199		A	133292560	T	A	133292560	3	1	53	1	0	0	0	0	1	0	0	0	2289	1406	49	5	13	5	C5orf15	5	133292560	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	2364403	133292560	47622700	40	7125										
PCDHA9	9752	broad.mit.edu	37	chr5	140228226	140228226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	caccttcgtgggccgcatcgCgcaggacctggggctggagc	16	14	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:140228226C>T	ENST00000532602.1	+	1	1179	c.146C>T	c.(145-147)gCg>gTg	p.A49V	PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.A49V|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	49	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A49V(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCGCATCGCGCAGGACCTG	0.652																																					Melanoma(55;1800 1972 14909)											2	Substitution - Missense(2)	large_intestine(2)	5											51	57	55					5																	140228226		2196	4266	6462	140208410	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.146C>T	5.37:g.140228226C>T	ENSP00000436042:p.Ala49Val		140208410	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.744705	0.89663	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53423	0.62;0.62	3.69	3.69	0.42338	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.72455	0.3462	M	0.86805	2.84	0.34935	D	0.749779	D;D	0.89917	1.0;1.0	D;D	0.87578	0.932;0.998	D	0.84215	0.0458	9	0.87932	D	0	.	16.0581	0.80820	0.0:1.0:0.0:0.0	.	49;49	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	V	49	ENSP00000436042:A49V;ENSP00000367362:A49V	ENSP00000367362:A49V	A	+	2	0	PCDHA9	140208410	0.711000	0.27906	1.000000	0.80357	0.918000	0.54935	1.450000	0.35134	2.047000	0.60756	0.586000	0.80456	GCG		0.652	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140228226	C	T	140228226	3	4	53	1	0	0	0	0	1	0	0	0	11562	768	27	1	148	1	PCDHA9	5	140228226	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	6935666	140228226	40687034	41	7126										
PCDHA13	56136	broad.mit.edu	37	chr5	140263460	140263460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gctgttgcagttccaggtgaGcgcgcgcgactctggcgtgc	16	12	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:140263460G>A	ENST00000289272.2	+	1	1607	c.1607G>A	c.(1606-1608)aGc>aAc	p.S536N	PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.S536N|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S536N(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGGTGAGCGCGCGCGAC	0.682																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											73	79	77					5																	140263460		2203	4299	6502	140243644	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1607G>A	5.37:g.140263460G>A	ENSP00000289272:p.Ser536Asn		140243644	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466932	0.26335	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.61510	0.1;0.1	4.54	1.58	0.23477	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.36166	0.0957	N	0.11756	0.17	0.19775	N	0.999956	B;B;B	0.20261	0.013;0.03;0.043	B;B;B	0.24848	0.033;0.044;0.056	T	0.27434	-1.0074	9	0.49607	T	0.09	.	5.3606	0.16085	0.1989:0.3303:0.4708:0.0	.	536;536;536	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	N	536	ENSP00000386821:S536N;ENSP00000289272:S536N	ENSP00000289272:S536N	S	+	2	0	PCDHA13	140243644	0.000000	0.05858	1.000000	0.80357	0.912000	0.54170	-1.319000	0.02702	1.079000	0.41038	0.561000	0.74099	AGC		0.682	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263460	G	A	140263460	3	1	53	1	0	0	0	0	1	0	0	0	11554	971	34	3	1609	3	PCDHA13	5	140263460	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	35234	140263460	40651800	42	7127										
PCDHB15	56121	broad.mit.edu	37	chr5	140626409	140626409	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gccgagtacaacatcaccatCaccatcacagacttggggac	8	14	3	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:140626409C>A	ENST00000231173.3	+	1	1263	c.1263C>A	c.(1261-1263)atC>atA	p.I421I		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	421	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.I421I(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATCACCATCACCATCACAG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	5											103	95	98					5																	140626409		2203	4300	6503	140606593	SO:0001819	synonymous_variant	56121			AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1263C>A	5.37:g.140626409C>A			140606593	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																				0.517	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		A	140626409	C	A	140626409	2	1	53	1	0	0	0	0	0	0	0	1	11571	816	29	2		2	PCDHB15	5	140626409	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	362949	140626409	40288851	43	7128										
GABRB2	2561	broad.mit.edu	37	chr5	160757952	160757952	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agccttctcagctgctttctTttggcgttggggccccctcc	10	15	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr5:160757952T>A	ENST00000393959.1	-	8	1014	c.1015A>T	c.(1015-1017)Aag>Tag	p.K339*	GABRB2_ENST00000274547.2_Nonsense_Mutation_p.K339*|GABRB2_ENST00000517547.1_Nonsense_Mutation_p.K179*|GABRB2_ENST00000517901.1_Nonsense_Mutation_p.K276*|GABRB2_ENST00000353437.6_Nonsense_Mutation_p.K339*|GABRB2_ENST00000520240.1_Nonsense_Mutation_p.K339*			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	339					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.K339*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	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)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCTGCTTTCTTTTGGCGTTGG	0.498																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											97	101	100					5																	160757952		2203	4300	6503	160690530	SO:0001587	stop_gained	2561				CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1015A>T	5.37:g.160757952T>A	ENSP00000377531:p.Lys339*		160690530	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Nonsense_Mutation	SNP	ENST00000393959.1	37	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	T	39	7.872728	0.98537	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	.	.	.	5.26	5.26	0.73747	.	0.556823	0.19671	N	0.108749	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1774	0.72924	0.0:0.0:0.0:1.0	.	.	.	.	X	339;339;339;339;276;179	.	ENSP00000274547:K339X	K	-	1	0	GABRB2	160690530	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.946000	0.87746	1.984000	0.57885	0.460000	0.39030	AAG		0.498	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			A	160757952	T	A	160757952	4	1	53	1	0	0	0	0	0	1	0	0	6186	1850	64	5	535	5	GABRB2	5	160757952	Nonsense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	20131543	160757952	20157308	44	7129										
HIVEP1	3096	broad.mit.edu	37	chr6	12089420	12089420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttctctgtttttcttagacaAaattgaagaagcacaaaaag	6	6	2	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:12089420A>G	ENST00000379388.2	+	3	376	c.44A>G	c.(43-45)aAa>aGa	p.K15R		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	15					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K15R(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTCTTAGACAAAATTGAAGAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	6											46	42	43					6																	12089420		1780	4037	5817	12197406	SO:0001583	missense	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.44A>G	6.37:g.12089420A>G	ENSP00000368698:p.Lys15Arg		12197406	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.984154	0.53827	.	.	ENSG00000095951	ENST00000491710;ENST00000487103;ENST00000379388;ENST00000442081;ENST00000478545	T	0.16073	2.37	5.95	5.95	0.96441	.	0.000000	0.34268	U	0.004105	T	0.25005	0.0607	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.01863	-1.1258	10	0.87932	D	0	-21.038	12.8206	0.57690	1.0:0.0:0.0:0.0	.	15	P15822	ZEP1_HUMAN	R	15;15;15;24;15	ENSP00000368698:K15R	ENSP00000368698:K15R	K	+	2	0	HIVEP1	12197406	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.836000	0.62789	2.282000	0.76494	0.533000	0.62120	AAA		0.274	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		G	12089420	A	G	12089420	3	3	53	1	0	0	0	0	1	0	0	0	7207	14	1	4	50	4	HIVEP1	6	12089420	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09		12089420	159025647	45	7130										
RANBP9	10048	broad.mit.edu	37	chr6	13697041	13697041	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctcttcccttactgacaattTttacttcaaaataataaatc	1	10	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:13697041T>G	ENST00000011619.3	-	2	717	c.659A>C	c.(658-660)aAa>aCa	p.K220T		NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	220	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)	p.K220T(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			ACTGACAATTTTTACTTCAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											91	96	94					6																	13697041		2203	4300	6503	13805020	SO:0001583	missense	10048			AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.659A>C	6.37:g.13697041T>G	ENSP00000011619:p.Lys220Thr		13805020	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	37	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358840	0.41801	.	.	ENSG00000010017	ENST00000011619;ENST00000283152	T	0.70749	-0.51	5.64	5.64	0.86602	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.61261	0.2333	N	0.11364	0.135	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66019	-0.6027	10	0.25106	T	0.35	-23.7751	15.5275	0.75923	0.0:0.0:0.0:1.0	.	220	Q96S59	RANB9_HUMAN	T	220	ENSP00000011619:K220T	ENSP00000011619:K220T	K	-	2	0	RANBP9	13805020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.677000	0.84024	2.142000	0.66516	0.528000	0.53228	AAA		0.378	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			G	13697041	T	G	13697041	3	3	53	1	0	0	0	0	1	0	0	0	13069	1841	64	4	1582	4	RANBP9	6	13697041	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	1607621	13697041	157418026	46	7131										
PRL	5617	broad.mit.edu	37	chr6	22290562	22290562	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gatcgcaatatgctgactatCaggctcagaaagtctttttg	9	8	3	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:22290562C>G	ENST00000306482.1	-	4	851	c.333G>C	c.(331-333)ctG>ctC	p.L111L	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	111				SL -> VS (in Ref. 7; AA sequence). {ECO:0000305}.	cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)	p.L111L(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					TGCTGACTATCAGGCTCAGAA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	6											107	101	103					6																	22290562		2203	4300	6503	22398541	SO:0001819	synonymous_variant	5617			D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.333G>C	6.37:g.22290562C>G			22398541	Q15199|Q92996	Silent	SNP	ENST00000306482.1	37	CCDS4548.1																																																																																				0.418	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948		G	22290562	C	G	22290562	2	3	53	1	0	0	0	0	0	0	0	1	12562	813	29	5		5	PRL	6	22290562	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	8593521	22290562	148824505	47	7132										
FTSJD2	23070	broad.mit.edu	37	chr6	37421042	37421042	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aatgaagatggctaacatggAttttgtatttgatcgcatgt	10	4	0	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:37421042A>G	ENST00000373451.4	+	8	895	c.731A>G	c.(730-732)gAt>gGt	p.D244G		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	244	RrmJ-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00945}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.D244G(1)									GCTAACATGGATTTTGTATTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											204	186	192					6																	37421042		2203	4300	6503	37529020	SO:0001583	missense	23070			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.731A>G	6.37:g.37421042A>G	ENSP00000362550:p.Asp244Gly		37529020	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	37	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505672	0.85282	.	.	ENSG00000137200	ENST00000373451	T	0.36157	1.27	5.92	5.92	0.95590	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.000000	0.85682	D	0.000000	T	0.65739	0.2720	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76675	-0.2872	10	0.72032	D	0.01	-20.7239	15.5593	0.76229	1.0:0.0:0.0:0.0	.	244	Q8N1G2	MTR1_HUMAN	G	244	ENSP00000362550:D244G	ENSP00000362550:D244G	D	+	2	0	FTSJD2	37529020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.277000	0.76020	0.528000	0.53228	GAT		0.433	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		G	37421042	A	G	37421042	3	3	53	1	0	0	0	0	1	0	0	0	6110	333	12	4	757	4	FTSJD2	6	37421042	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	15130480	37421042	133694025	48	7133										
DNAH8	1769	broad.mit.edu	37	chr6	38939412	38939412	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aaggacaagaagtacatgctCgaaagctgattcagatgtca	10	7	2	3	rs150428096		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:38939412C>T	ENST00000359357.3	+	81	12099	c.11845C>T	c.(11845-11847)Cga>Tga	p.R3949*	DNAH8_ENST00000441566.1_Nonsense_Mutation_p.R3913*|DNAH8_ENST00000449981.2_Nonsense_Mutation_p.R4166*			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3949	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R3949*(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGTACATGCTCGAAAGCTGAT	0.418													C|||	1	0.000199681	8e-04	0	5008	,	,		20158	0		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(2)	6						C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	160	131	141		12496	3.2	1	6	dbSNP_134	141	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained	DNAH8	NM_001206927.1		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		4166/4708	38939412	3,13003	2203	4300	6503	39047390	SO:0001587	stop_gained	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11845C>T	6.37:g.38939412C>T	ENSP00000352312:p.Arg3949*		39047390	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Nonsense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	C	53	21.383550	0.99940	2.27E-4	2.33E-4	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	5.04	3.19	0.36642	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7075	0.62648	0.2814:0.7186:0.0:0.0	.	.	.	.	X	4154;4154;3949;3913	.	ENSP00000333363:R4154X	R	+	1	2	DNAH8	39047390	0.833000	0.29383	0.992000	0.48379	0.924000	0.55760	1.464000	0.35288	0.480000	0.27534	-0.324000	0.08512	CGA		0.418	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38939412	C	T	38939412	4	4	53	1	0	0	0	0	0	1	0	0	4618	876	31	1	12159	1	DNAH8	6	38939412	Nonsense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	1518370	38939412	132175655	49	7134										
TREM1	54210	broad.mit.edu	37	chr6	41250471	41250471	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	catacttttcctcagttaatTtagttgcagctcggagttct	7	9	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:41250471T>G	ENST00000244709.4	-	2	131	c.68A>C	c.(67-69)aAa>aCa	p.K23T	TREM1_ENST00000334475.6_Missense_Mutation_p.K23T|TREM1_ENST00000591620.1_Missense_Mutation_p.K23T|TREM1_ENST00000589614.1_Missense_Mutation_p.K23T	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	23					blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.K23T(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CTCAGTTAATTTAGTTGCAGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											93	100	98					6																	41250471		2203	4300	6503	41358449	SO:0001583	missense	54210			AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.68A>C	6.37:g.41250471T>G	ENSP00000244709:p.Lys23Thr		41358449	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	37	CCDS4854.1	.	.	.	.	.	.	.	.	.	.	T	8.281	0.815641	0.16607	.	.	ENSG00000124731	ENST00000244709;ENST00000334475	T;T	0.12255	3.08;2.7	3.65	-3.76	0.04359	.	2.028980	0.02444	N	0.084868	T	0.01976	0.0062	N	0.22421	0.69	0.09310	N	1	B;B	0.15719	0.014;0.008	B;B	0.25140	0.035;0.058	T	0.39623	-0.9605	10	0.20519	T	0.43	1.8266	0.0987	0.00046	0.3367:0.21:0.1609:0.2924	.	23;23	Q9NP99-2;Q9NP99	.;TREM1_HUMAN	T	23	ENSP00000244709:K23T;ENSP00000334284:K23T	ENSP00000244709:K23T	K	-	2	0	TREM1	41358449	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.946000	0.01536	-0.703000	0.05049	0.482000	0.46254	AAA		0.468	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643		G	41250471	T	G	41250471	3	3	53	1	0	0	0	0	1	0	0	0	16510	1841	64	4	648	4	TREM1	6	41250471	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	2311059	41250471	129864596	50	7135										
OGFRL1	79627	broad.mit.edu	37	chr6	72011438	72011438	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctatgcacaaaaaagccaagGactccaaaaattcctcctca	4	13	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:72011438G>A	ENST00000370435.4	+	7	1176	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	348						membrane (GO:0016020)	receptor activity (GO:0004872)	p.D348N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						AAAAGCCAAGGACTCCAAAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											43	49	47					6																	72011438		2203	4300	6503	72068159	SO:0001583	missense	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.1042G>A	6.37:g.72011438G>A	ENSP00000359464:p.Asp348Asn		72068159	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.530338	0.64860	.	.	ENSG00000119900	ENST00000370435	T	0.51817	0.69	6.04	6.04	0.98038	.	0.373147	0.28006	N	0.016974	T	0.41627	0.1167	L	0.56769	1.78	0.33385	D	0.575402	P	0.46395	0.877	P	0.45829	0.494	T	0.50866	-0.8777	10	0.62326	D	0.03	-24.4858	16.0072	0.80372	0.0:0.1336:0.8664:0.0	.	348	Q5TC84	OGRL1_HUMAN	N	348	ENSP00000359464:D348N	ENSP00000359464:D348N	D	+	1	0	OGFRL1	72068159	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	5.393000	0.66279	2.873000	0.98535	0.563000	0.77884	GAC		0.463	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		A	72011438	G	A	72011438	3	1	53	1	0	0	0	0	1	0	0	0	10875	1174	41	3	1068	3	OGFRL1	6	72011438	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	30760967	72011438	99103629	51	7136										
NMBR	4829	broad.mit.edu	37	chr6	142396914	142396914	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agtaggtagctggttcctctCtcttgataggacttcctccc	9	12	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:142396914C>T	ENST00000258042.1	-	3	1184	c.1044G>A	c.(1042-1044)gaG>gaA	p.E348E	NMBR_ENST00000480652.1_5'UTR	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	348					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)	p.E348E(1)		breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		TGGTTCCTCTCTCTTGATAGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	6											126	117	120					6																	142396914		2203	4300	6503	142438607	SO:0001819	synonymous_variant	4829				CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.1044G>A	6.37:g.142396914C>T			142438607	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																				0.458	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			T	142396914	C	T	142396914	2	4	53	1	0	0	0	0	0	0	0	1	10518	912	32	3		3	NMBR	6	142396914	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	70385476	142396914	28718153	52	7137										
MAP3K4	4216	broad.mit.edu	37	chr6	161470018	161470018	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttgctaaagcttacctcagtCtcaaagaaaaaagacaggga	8	8	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr6:161470018C>G	ENST00000392142.4	+	3	862	c.714C>G	c.(712-714)gtC>gtG	p.V238V	MAP3K4_ENST00000348824.7_Silent_p.V238V|MAP3K4_ENST00000366919.2_Silent_p.V238V|MAP3K4_ENST00000366920.2_Silent_p.V238V	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	238					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.V238V(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TTACCTCAGTCTCAAAGAAAA	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	6											41	41	41					6																	161470018		2203	4300	6503	161390008	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.714C>G	6.37:g.161470018C>G			161390008	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.438	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			G	161470018	C	G	161470018	2	3	53	1	0	0	0	0	0	0	0	1	9282	900	32	5		5	MAP3K4	6	161470018	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	19073104	161470018	9645049	53	7138										
PHF14	9678	broad.mit.edu	37	chr7	11022332	11022332	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gaatgtggctgcttctgctgCtgccaccacaccagccacaa	9	15	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:11022332C>G	ENST00000403050.3	+	3	898	c.446C>G	c.(445-447)gCt>gGt	p.A149G	PHF14_ENST00000445996.2_Intron	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	149					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.A149G(1)		NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		GCTTCTGCTGCTGCCACCACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7											27	34	31					7																	11022332		1999	4169	6168	10988857	SO:0001583	missense	9678			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.446C>G	7.37:g.11022332C>G	ENSP00000385795:p.Ala149Gly		10988857	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	C	9.274	1.046527	0.19748	.	.	ENSG00000106443	ENST00000403050	T	0.63744	-0.06	4.25	2.45	0.29901	.	.	.	.	.	T	0.35856	0.0946	N	0.08118	0	0.80722	D	1	B;B	0.27498	0.18;0.079	B;B	0.23018	0.043;0.043	T	0.09662	-1.0664	9	0.33940	T	0.23	.	6.752	0.23491	0.0:0.7887:0.0:0.2113	.	149;149	A8MSQ1;O94880	.;PHF14_HUMAN	G	149	ENSP00000385795:A149G	ENSP00000385795:A149G	A	+	2	0	PHF14	10988857	0.002000	0.14202	0.962000	0.40283	0.794000	0.44872	1.506000	0.35747	0.739000	0.32628	0.585000	0.79938	GCT		0.458	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		G	11022332	C	G	11022332	3	3	53	1	0	0	0	0	1	0	0	0	11856	797	28	5	456	5	PHF14	7	11022332	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09		11022332	148116331	54	7139										
ANKMY2	57037	broad.mit.edu	37	chr7	16666720	16666720	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgttcatgctgatgacaattTacatcggctccatgtcgcag	9	10	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:16666720T>G	ENST00000306999.2	-	3	459	c.216A>C	c.(214-216)gtA>gtC	p.V72V	ANKMY2_ENST00000421746.1_5'UTR	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	72						cilium (GO:0005929)	metal ion binding (GO:0046872)	p.V72V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GATGACAATTTACATCGGCTC	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	7											96	83	87					7																	16666720		2203	4300	6503	16633245	SO:0001819	synonymous_variant	57037			AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.216A>C	7.37:g.16666720T>G			16633245	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																				0.363	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		G	16666720	T	G	16666720	2	3	53	1	0	0	0	0	0	0	0	1	635	1741	61	4		4	ANKMY2	7	16666720	Silent	SNP	T	TCGA-AG-3902-01A-01W-1073-09	5644388	16666720	142471943	55	7140										
HDAC9	9734	broad.mit.edu	37	chr7	18687500	18687500	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cagtatggaggcagcatcccGgcatcttccagccaccctca	9	16	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:18687500G>A	ENST00000432645.2	+	9	1119	c.1119G>A	c.(1117-1119)ccG>ccA	p.P373P	HDAC9_ENST00000406072.1_Silent_p.P360P|HDAC9_ENST00000428307.2_Silent_p.P329P|HDAC9_ENST00000417496.2_Silent_p.P371P|HDAC9_ENST00000405010.3_Silent_p.P373P|HDAC9_ENST00000441542.2_Silent_p.P376P|HDAC9_ENST00000524023.1_Silent_p.P296P|HDAC9_ENST00000456174.2_Silent_p.P345P|HDAC9_ENST00000401921.1_Silent_p.P332P|HDAC9_ENST00000406451.4_Silent_p.P373P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	373					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.P376P(2)|p.P373P(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GCAGCATCCCGGCATCTTCCA	0.512																																																3	Substitution - coding silent(3)	large_intestine(3)	7											38	41	40					7																	18687500		2071	4220	6291	18654025	SO:0001819	synonymous_variant	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1119G>A	7.37:g.18687500G>A			18654025	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																				0.512	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18687500	G	A	18687500	2	1	53	1	0	0	0	0	0	0	0	1	7035	1103	39	1		1	HDAC9	7	18687500	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	2020780	18687500	140451163	56	7141										
LANCL2	55915	broad.mit.edu	37	chr7	55493099	55493099	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	taccgtctcacgcaggataaGaagtacctctaccgagcttg	9	12	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:55493099G>T	ENST00000254770.2	+	7	1739	c.1161G>T	c.(1159-1161)aaG>aaT	p.K387N		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	387					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.K387N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			CGCAGGATAAGAAGTACCTCT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	7											161	143	149					7																	55493099		2203	4300	6503	55460593	SO:0001583	missense	55915			AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"testis-specific adriamycin sensitivity protein", "G protein-coupled receptor 69B"	612919	"LanC (bacterial lantibiotic synthetase component C)-like 2"	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.1161G>T	7.37:g.55493099G>T	ENSP00000254770:p.Lys387Asn		55460593	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Missense_Mutation	SNP	ENST00000254770.2	37	CCDS5517.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.394290	0.42410	.	.	ENSG00000132434	ENST00000254770	T	0.42513	0.97	5.27	-7.42	0.01388	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.131990	0.64402	D	0.000002	T	0.41213	0.1149	M	0.80746	2.51	0.27131	N	0.961893	P	0.38335	0.627	B	0.41412	0.356	T	0.45877	-0.9231	10	0.17832	T	0.49	.	15.7739	0.78193	0.7442:0.0:0.2558:0.0	.	387	Q9NS86	LANC2_HUMAN	N	387	ENSP00000254770:K387N	ENSP00000254770:K387N	K	+	3	2	LANCL2	55460593	0.005000	0.15991	0.013000	0.15412	0.976000	0.68499	-0.187000	0.09656	-1.513000	0.01789	0.557000	0.71058	AAG		0.542	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697		T	55493099	G	T	55493099	3	4	53	1	0	0	0	0	1	0	0	0	8643	933	33	2	1187	2	LANCL2	7	55493099	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	36805599	55493099	103645564	57	7142										
ASNS	440	broad.mit.edu	37	chr7	97482429	97482429	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gaattcttaactgaagttatTccatcactgaaggcttcttt	6	8	3	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:97482429T>C	ENST00000394309.3	-	12	1890	c.1419A>G	c.(1417-1419)ggA>ggG	p.G473G	ASNS_ENST00000437628.1_Silent_p.G390G|ASNS_ENST00000175506.4_Silent_p.G473G|ASNS_ENST00000455086.1_Silent_p.G390G|ASNS_ENST00000444334.1_Silent_p.G452G|ASNS_ENST00000422745.1_Silent_p.G452G|ASNS_ENST00000394308.3_Silent_p.G473G	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	473	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)	p.G473G(1)		ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	CTGAAGTTATTCCATCACTGA	0.368																																					Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)											1	Substitution - coding silent(1)	large_intestine(1)	7											43	41	42					7																	97482429		2203	4300	6503	97320365	SO:0001819	synonymous_variant	440			M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1419A>G	7.37:g.97482429T>C			97320365	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Silent	SNP	ENST00000394309.3	37	CCDS5652.1																																																																																				0.368	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		C	97482429	T	C	97482429	2	2	53	1	0	0	0	0	0	0	0	1	1049	1770	62	4		4	ASNS	7	97482429	Silent	SNP	T	TCGA-AG-3902-01A-01W-1073-09	41989330	97482429	61656234	58	7143										
TAF6	6878	broad.mit.edu	37	chr7	99706133	99706133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctgattgtcaggcggtgggcGcagctttgccagaacaggag	16	9	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:99706133G>A	ENST00000344095.4	-	13	1840	c.1315C>T	c.(1315-1317)Cgc>Tgc	p.R439C	TAF6_ENST00000418432.2_Missense_Mutation_p.R363C|TAF6_ENST00000452041.1_Missense_Mutation_p.R439C|TAF6_ENST00000437822.2_Missense_Mutation_p.R476C|TAF6_ENST00000453269.2_Missense_Mutation_p.R439C|TAF6_ENST00000472509.1_Missense_Mutation_p.R496C|AP4M1_ENST00000421755.1_Intron	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	439					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R439C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGCGGTGGGCGCAGCTTTGCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	7											60	67	65					7																	99706133		2203	4300	6503	99544069	SO:0001583	missense	6878				CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1315C>T	7.37:g.99706133G>A	ENSP00000344537:p.Arg439Cys		99544069	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	37	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382507	0.82792	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T	0.60797	0.23;0.16;0.23;0.23;0.17	5.69	3.77	0.43336	.	0.000000	0.85682	D	0.000000	T	0.71525	0.3350	M	0.74647	2.275	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.983;0.993;0.983;0.983;0.983	T	0.73439	-0.3982	10	0.87932	D	0	-11.6419	8.261	0.31786	0.0867:0.0:0.7611:0.1522	.	476;439;429;439;363	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	C	439;496;439;439;363;476	ENSP00000389575:R439C;ENSP00000419760:R496C;ENSP00000416396:R439C;ENSP00000344537:R439C;ENSP00000399982:R476C	ENSP00000344537:R439C	R	-	1	0	TAF6	99544069	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	5.509000	0.67012	1.344000	0.45657	0.491000	0.48974	CGC		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		A	99706133	G	A	99706133	3	1	53	1	0	0	0	0	1	0	0	0	15569	1087	38	1	730	1	TAF6	7	99706133	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	2223704	99706133	59432530	59	7144										
ZAN	7455	broad.mit.edu	37	chr7	100334192	100334192	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cagacgatgaagactgggttCgagccagtgggccctctccc	13	13	1	3	rs200760090		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:100334192C>T	ENST00000348028.3	+	0	358				ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000542585.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R65*(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AGACTGGGTTCGAGCCAGTGG	0.622																																																1	Substitution - Nonsense(1)	large_intestine(1)	7						C	stop/ARG,stop/ARG	0,3648		0,0,1824	82	80	80		193,193	4.7	0.5	7		80	2,7762		0,2,3880	yes	stop-gained,stop-gained	ZAN	NM_003386.1,NM_173059.1	,	0,2,5704	TT,TC,CC		0.0258,0.0,0.0175	,	65/2813,65/2722	100334192	2,11410	1824	3882	5706	100172128			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100334192C>T			100172128	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Nonsense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	C	27.9	4.869836	0.91587	0.0	2.58E-4	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	.	.	.	4.7	4.7	0.59300	.	0.000000	0.29009	N	0.013438	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8686	0.63603	0.0:1.0:0.0:0.0	.	.	.	.	X	65	.	ENSP00000423579:R65X	R	+	1	2	ZAN	100172128	0.062000	0.20869	0.490000	0.27465	0.318000	0.28184	2.025000	0.41059	2.551000	0.86045	0.561000	0.74099	CGA		0.622	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100334192	C	T	100334192	1	4	53	0	1	0	0	0	0	0	0	0	17553	876	31	1		1	ZAN	7	100334192	RNA	SNP	C	TCGA-AG-3902-01A-01W-1073-09	628059	100334192	58804471	60	7145										
MUC17	140453	broad.mit.edu	37	chr7	100682302	100682303	+	Missense_Mutation	DNP	TT	TT	AC													0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agtcctgaggctagcaccctTtcaacaactcctgttgactc							TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	TT	TT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr7:100682302_100682303TT>AC	ENST00000306151.4	+	3	7669_7670	c.7605_7606TT>AC	c.(7603-7608)ctTTca>ctACca	p.S2536P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2536	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.L2535>?(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTAGCACCCTTTCAACAACTCC	0.48																																																1	Complex(1)	large_intestine(1)	7																																								100469023	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	Exception_encountered	7.37:g.100682302_100682303delinsAC	ENSP00000302716:p.Ser2536Pro		100469022	O14761|Q685J2|Q8TDH7	Missense_Mutation	DNP	ENST00000306151.4	37	CCDS34711.1																																																																																				0.48	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		AC	100682303	TT	AC	100682302	3	1	53	1	0	0	0	0	1	0	0	0	10004	1828	64	5	7615	5	MUC17	7	100682302	Missense_Mutation	DNP	TT	TCGA-AG-3902-01A-01W-1073-09	348110	100682302	58456361	61	7146										
MCPH1	79648	broad.mit.edu	37	chr8	6302622	6302622	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aagcatatttgaaatgtctgAtttttcctgcgttggcaaaa	8	6	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:6302622A>T	ENST00000344683.5	+	8	1455	c.1379A>T	c.(1378-1380)gAt>gTt	p.D460V	MCPH1_ENST00000522905.1_Missense_Mutation_p.D412V|MCPH1_ENST00000519480.1_Missense_Mutation_p.D460V	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	460					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)	p.D460V(1)	AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GAAATGTCTGATTTTTCCTGC	0.438																																					Colon(95;1448 1467 8277 34473 35819)											1	Substitution - Missense(1)	large_intestine(1)	8											85	84	84					8																	6302622		1865	4114	5979	6290030	SO:0001583	missense	79648			AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1379A>T	8.37:g.6302622A>T	ENSP00000342924:p.Asp460Val		6290030	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.096918	0.76870	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.26373	1.74;1.74;1.74	5.76	4.57	0.56435	.	0.592362	0.17984	N	0.155449	T	0.49626	0.1568	M	0.77486	2.375	0.22342	N	0.999186	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.42155	-0.9468	10	0.87932	D	0	-23.2935	9.2142	0.37337	0.8386:0.0:0.0:0.1614	.	412;460;460	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	V	460;460;412	ENSP00000342924:D460V;ENSP00000430962:D460V;ENSP00000430768:D412V	ENSP00000342924:D460V	D	+	2	0	MCPH1	6290030	0.011000	0.17503	0.014000	0.15608	0.707000	0.40811	2.001000	0.40825	1.076000	0.40961	0.533000	0.62120	GAT		0.438	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		T	6302622	A	T	6302622	3	4	53	1	0	0	0	0	1	0	0	0	9428	333	12	5	1409	5	MCPH1	8	6302622	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09		6302622	140061400	62	7147										
DUSP26	78986	broad.mit.edu	37	chr8	33451178	33451178	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cccagcccctcataggcctcGggcgtgcctcgccaccggct	11	20	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:33451178G>A	ENST00000256261.4	-	3	826	c.309C>T	c.(307-309)ccC>ccT	p.P103P	DUSP26_ENST00000523956.1_Silent_p.P103P	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	103	Tyrosine-protein phosphatase.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)	p.P103P(1)		NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		CATAGGCCTCGGGCGTGCCTC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	8											54	47	49					8																	33451178		2203	4300	6503	33570720	SO:0001819	synonymous_variant	78986			AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.309C>T	8.37:g.33451178G>A			33570720	D3DSV8|Q9BTW0	Silent	SNP	ENST00000256261.4	37	CCDS6092.1																																																																																				0.637	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025		A	33451178	G	A	33451178	2	1	53	1	0	0	0	0	0	0	0	1	4834	1103	39	1		1	DUSP26	8	33451178	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	27148556	33451178	112912844	63	7148										
RB1CC1	9821	broad.mit.edu	37	chr8	53569095	53569095	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctaatttctgttctcaaattTtctgtctcttgttcaagaag	5	8	5	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:53569095T>C	ENST00000025008.5	-	15	3817	c.3294A>G	c.(3292-3294)gaA>gaG	p.E1098E	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Silent_p.E1098E|RB1CC1_ENST00000539297.1_Silent_p.E1098E	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1098					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.E1098E(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTCTCAAATTTTCTGTCTCTT	0.358																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - coding silent(1)	large_intestine(1)	8											58	60	59					8																	53569095		2202	4298	6500	53731648	SO:0001819	synonymous_variant	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3294A>G	8.37:g.53569095T>C			53731648	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																				0.358	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		C	53569095	T	C	53569095	2	2	53	1	0	0	0	0	0	0	0	1	13136	1838	64	4		4	RB1CC1	8	53569095	Silent	SNP	T	TCGA-AG-3902-01A-01W-1073-09	20117917	53569095	92794927	64	7149										
SGK3	23678	broad.mit.edu	37	chr8	67771662	67771662	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttaggctggaccagatgataTcagaaactttgacacagcat	9	8	1	4	rs150440508		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:67771662T>C	ENST00000396596.1	+	17	1551	c.1337T>C	c.(1336-1338)aTc>aCc	p.I446T	C8orf44-SGK3_ENST00000519289.1_Missense_Mutation_p.I446T|SGK3_ENST00000345714.4_Missense_Mutation_p.I446T|SGK3_ENST00000521198.2_Missense_Mutation_p.I446T|SGK3_ENST00000520976.1_Missense_Mutation_p.I414T|SGK3_ENST00000522398.1_Missense_Mutation_p.I446T	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	446	AGC-kinase C-terminal.				ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.I379T(1)|p.I446T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CCAGATGATATCAGAAACTTT	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	8											179	157	164					8																	67771662		2203	4300	6503	67934216	SO:0001583	missense	23678				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"serum/glucocorticoid regulated kinase-like"	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.1337T>C	8.37:g.67771662T>C	ENSP00000379842:p.Ile446Thr		67934216	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Missense_Mutation	SNP	ENST00000396596.1	37	CCDS6195.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643713	0.67244	.	.	ENSG00000104205	ENST00000519289;ENST00000521198;ENST00000262211;ENST00000522398;ENST00000520976;ENST00000396596;ENST00000345714	T;T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15;1.15	5.51	5.51	0.81932	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.24547	0.0595	N	0.12887	0.27	0.45205	D	0.998213	B;B	0.25719	0.109;0.132	B;B	0.29353	0.061;0.101	T	0.27536	-1.0071	9	0.26408	T	0.33	.	15.6124	0.76737	0.0:0.0:0.0:1.0	.	414;446	Q96BR1-2;Q96BR1	.;SGK3_HUMAN	T	446;446;446;446;414;446;446	ENSP00000429022:I446T;ENSP00000430463:I446T;ENSP00000430256:I446T;ENSP00000430691:I414T;ENSP00000379842:I446T;ENSP00000331816:I446T	ENSP00000262211:I446T	I	+	2	0	SGK3	67934216	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.690000	0.84178	2.096000	0.63516	0.528000	0.53228	ATC		0.328	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3			C	67771662	T	C	67771662	3	2	53	1	0	0	0	0	1	0	0	0	14249	1435	50	4	1399	4	SGK3	8	67771662	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	14202567	67771662	78592360	65	7150										
COPS5	10987	broad.mit.edu	37	chr8	67958095	67958095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cttctgattttcggtcatgcGtttctaaacccaacatgaaa	6	10	3	2	rs143525514		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:67958095G>A	ENST00000357849.4	-	7	1192	c.872C>T	c.(871-873)aCg>aTg	p.T291M	COPS5_ENST00000517736.1_3'UTR|PPP1R42_ENST00000517834.1_Intron	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	291					cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)	p.T291M(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			TCGGTCATGCGTTTCTAAACC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	163	155	158		872	5.7	1	8	dbSNP_134	158	1,8599	1.2+/-3.3	0,1,4299	no	missense	COPS5	NM_006837.2	81	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	291/335	67958095	2,13004	2203	4300	6503	68120649	SO:0001583	missense	10987			U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5", "COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.872C>T	8.37:g.67958095G>A	ENSP00000350512:p.Thr291Met		68120649	O15386|Q6AW95|Q86WQ4|Q9BQ17	Missense_Mutation	SNP	ENST00000357849.4	37	CCDS6198.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978093	0.53720	2.27E-4	1.16E-4	ENSG00000121022	ENST00000357849	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.53367	0.1792	L	0.46157	1.445	0.80722	D	1	P	0.36110	0.537	B	0.32677	0.15	T	0.54892	-0.8225	9	0.48119	T	0.1	-2.3839	19.4585	0.94906	0.0:0.0:1.0:0.0	.	291	Q92905	CSN5_HUMAN	M	291	.	ENSP00000350512:T291M	T	-	2	0	COPS5	68120649	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.856000	0.86956	2.705000	0.92388	0.650000	0.86243	ACG		0.418	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			A	67958095	G	A	67958095	3	1	53	1	0	0	0	0	1	0	0	0	3742	1145	40	1	140	1	COPS5	8	67958095	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	186433	67958095	78405927	66	7151										
PREX2	80243	broad.mit.edu	37	chr8	68939513	68939513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gttcccttggaaggatatttAgtaacaccaatacaaagaat	7	7	0	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:68939513A>T	ENST00000288368.4	+	5	775	c.498A>T	c.(496-498)ttA>ttT	p.L166F	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	166	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.L166F(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAGGATATTTAGTAACACCAA	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	8											140	132	135					8																	68939513		2203	4300	6503	69102067	SO:0001583	missense	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.498A>T	8.37:g.68939513A>T	ENSP00000288368:p.Leu166Phe		69102067	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.965443	0.74131	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	D	0.83914	-1.78	5.66	-2.1	0.07210	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000003	D	0.90310	0.6969	M	0.92077	3.27	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87509	0.2438	10	0.87932	D	0	.	7.2562	0.26177	0.5405:0.0:0.3566:0.103	.	166;166;166	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	F	166	ENSP00000288368:L166F	ENSP00000288368:L166F	L	+	3	2	PREX2	69102067	1.000000	0.71417	0.984000	0.44739	0.989000	0.77384	1.112000	0.31172	-0.279000	0.09167	-0.290000	0.09829	TTA		0.348	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68939513	A	T	68939513	3	4	53	1	0	0	0	0	1	0	0	0	12511	417	15	5	516	5	PREX2	8	68939513	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	981418	68939513	77424509	67	7152										
FZD6	8323	broad.mit.edu	37	chr8	104337008	104337008	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tacttttttaattgatgttaGaagattcagatacccagaga	7	5	1	5			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:104337008G>A	ENST00000358755.4	+	4	991	c.674G>A	c.(673-675)aGa>aAa	p.R225K	FZD6_ENST00000522566.1_Missense_Mutation_p.R225K|FZD6_ENST00000523739.1_Missense_Mutation_p.R193K|FZD6_ENST00000540287.1_Intron	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	225					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R225K(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			ATTGATGTTAGAAGATTCAGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	8											50	51	50					8																	104337008		2203	4300	6503	104406184	SO:0001583	missense	8323			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.674G>A	8.37:g.104337008G>A	ENSP00000351605:p.Arg225Lys		104406184	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	G	2.158	-0.392939	0.04899	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000539487	T;T;T	0.81163	-1.46;-1.46;-1.46	5.6	-0.0437	0.13858	GPCR, family 2-like (1);	0.246549	0.46758	N	0.000263	T	0.54175	0.1842	N	0.11154	0.105	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.19549	-1.0302	10	0.11485	T	0.65	.	4.9812	0.14166	0.5649:0.146:0.2891:0.0	.	170;225;225	B4E236;B2R9H9;O60353	.;.;FZD6_HUMAN	K	225;225;193;170	ENSP00000429055:R225K;ENSP00000351605:R225K;ENSP00000429528:R193K	ENSP00000351605:R225K	R	+	2	0	FZD6	104406184	1.000000	0.71417	0.862000	0.33874	0.980000	0.70556	2.628000	0.46477	-0.162000	0.10964	-0.658000	0.03865	AGA		0.333	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		A	104337008	G	A	104337008	3	1	53	1	0	0	0	0	1	0	0	0	6153	942	33	3	684	3	FZD6	8	104337008	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	35397495	104337008	42027014	68	7153										
ZFPM2	23414	broad.mit.edu	37	chr8	106815014	106815014	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttccgaatccagaaagcgaaCgaaacagccctgatgtcagc	9	12	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:106815014C>T	ENST00000407775.2	+	8	2954	c.2704C>T	c.(2704-2706)Cga>Tga	p.R902*	ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000517361.1_Nonsense_Mutation_p.R770*|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000520492.1_Nonsense_Mutation_p.R770*|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000378472.4_Nonsense_Mutation_p.R633*	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	902					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R902*(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AGAAAGCGAACGAAACAGCCC	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											46	45	45					8																	106815014		1930	4141	6071	106884190	SO:0001587	stop_gained	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2704C>T	8.37:g.106815014C>T	ENSP00000384179:p.Arg902*		106884190	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Nonsense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	37	5.984063	0.97173	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	.	.	.	5.57	3.73	0.42828	.	0.176149	0.51477	D	0.000099	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	14.4956	0.67685	0.5405:0.4595:0.0:0.0	.	.	.	.	X	902;770;770;633	.	ENSP00000367733:R633X	R	+	1	2	ZFPM2	106884190	1.000000	0.71417	0.973000	0.42090	0.869000	0.49853	1.600000	0.36762	0.663000	0.31027	-0.284000	0.09977	CGA		0.458	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			T	106815014	C	T	106815014	4	4	53	1	0	0	0	0	0	1	0	0	17697	528	19	1	2734	1	ZFPM2	8	106815014	Nonsense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	2478006	106815014	39549008	69	7154										
PKHD1L1	93035	broad.mit.edu	37	chr8	110504156	110504156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agggaatttgattgcactttCggtttggccaggaacctatc	11	8	0	1	rs541350761	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:110504156C>T	ENST00000378402.5	+	62	10273	c.10169C>T	c.(10168-10170)tCg>tTg	p.S3390L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3390					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.S3392L(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATTGCACTTTCGGTTTGGCCA	0.353										HNSCC(38;0.096)			C|||	2	0.000399361	0.0015	0	5008	,	,		14555	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											42	44	43					8																	110504156		1817	4075	5892	110573332	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10169C>T	8.37:g.110504156C>T	ENSP00000367655:p.Ser3390Leu		110573332	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.764903	0.69878	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85773	-2.03;-1.84	5.61	5.61	0.85477	Pectin lyase fold/virulence factor (1);	0.262894	0.32175	N	0.006466	T	0.79930	0.4531	L	0.34521	1.04	0.30014	N	0.814901	B	0.30021	0.265	B	0.29267	0.1	T	0.77191	-0.2678	10	0.45353	T	0.12	.	17.1443	0.86762	0.0:1.0:0.0:0.0	.	3390	Q86WI1	PKHL1_HUMAN	L	3390;318	ENSP00000367655:S3390L;ENSP00000437376:S318L	ENSP00000367655:S3390L	S	+	2	0	PKHD1L1	110573332	1.000000	0.71417	0.976000	0.42696	0.955000	0.61496	6.015000	0.70791	2.635000	0.89317	0.563000	0.77884	TCG		0.353	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110504156	C	T	110504156	3	4	53	1	0	0	0	0	1	0	0	0	12003	893	31	1	10415	1	PKHD1L1	8	110504156	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	3689142	110504156	35859866	70	7155										
KIAA0196	9897	broad.mit.edu	37	chr8	126049483	126049483	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	taaatgttatacgtacccagAtttttgttgtattgaagttt	7	4	0	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:126049483A>G	ENST00000318410.7	-	26	3526	c.3177T>C	c.(3175-3177)aaT>aaC	p.N1059N	KIAA0196_ENST00000517845.1_Silent_p.N911N	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	1059					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)		p.N1059N(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ACGTACCCAGATTTTTGTTGT	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	8											110	113	112					8																	126049483		2203	4300	6503	126118665	SO:0001819	synonymous_variant	9897				CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.3177T>C	8.37:g.126049483A>G			126118665	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	A	8.292	0.817861	0.16607	.	.	ENSG00000164961	ENST00000523273	.	.	.	6.04	3.07	0.35406	.	.	.	.	.	T	0.57858	0.2082	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50242	-0.8851	4	.	.	.	-29.3312	8.5922	0.33695	0.373:0.0:0.627:0.0	.	.	.	.	T	676	.	.	I	-	2	0	KIAA0196	126118665	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	2.472000	0.45136	0.335000	0.23614	0.459000	0.35465	ATC		0.308	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		G	126049483	A	G	126049483	2	3	53	1	0	0	0	0	0	0	0	1	8182	330	12	4		4	KIAA0196	8	126049483	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	15545327	126049483	20314539	71	7156										
TG	7038	broad.mit.edu	37	chr8	133899528	133899528	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgcttttccggagagtgctgGtgtgtgaattcctggggcaa	15	7	0	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr8:133899528G>A	ENST00000220616.4	+	9	1951	c.1911G>A	c.(1909-1911)tgG>tgA	p.W637*	TG_ENST00000377869.1_Nonsense_Mutation_p.W637*	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	637	Thyroglobulin type-1 5. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.W637*(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		GAGAGTGCTGGTGTGTGAATT	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											119	98	105					8																	133899528		2203	4300	6503	133968710	SO:0001587	stop_gained	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1911G>A	8.37:g.133899528G>A	ENSP00000220616:p.Trp637*		133968710	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Nonsense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	39	7.358002	0.98235	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	.	.	.	5.03	5.03	0.67393	.	0.000000	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.5379	0.87839	0.0:0.0:1.0:0.0	.	.	.	.	X	637	.	ENSP00000220616:W637X	W	+	3	0	TG	133968710	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	8.793000	0.91862	2.613000	0.88420	0.655000	0.94253	TGG		0.532	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133899528	G	A	133899528	4	1	53	1	0	0	0	0	0	1	0	0	15852	1270	44	3	1945	3	TG	8	133899528	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	7850045	133899528	12464494	72	7157										
ELAVL2	1993	broad.mit.edu	37	chr9	23701471	23701471	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggcctgattggttttttggcTtgggttattagcaaacttta	11	5	0	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:23701471T>G	ENST00000397312.2	-	5	893	c.619A>C	c.(619-621)Agc>Cgc	p.S207R	ELAVL2_ENST00000544538.1_Missense_Mutation_p.S207R|ELAVL2_ENST00000223951.6_Missense_Mutation_p.S207R|ELAVL2_ENST00000380110.4_Missense_Mutation_p.S236R|ELAVL2_ENST00000380117.1_Missense_Mutation_p.S207R	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	207					regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S207R(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		GTTTTTTGGCTTGGGTTATTA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											303	304	303					9																	23701471		2203	4300	6503	23691471	SO:0001583	missense	1993			BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"RNA binding motif (RRM) containing"	3313	protein-coding gene	gene with protein product	"Hu antigen B"	601673	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.619A>C	9.37:g.23701471T>G	ENSP00000380479:p.Ser207Arg		23691471	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	37	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.736129	0.69189	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000423281	T;T;T;T;T	0.35605	1.3;3.39;3.39;3.39;1.3	5.92	5.92	0.95590	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.42223	0.1193	M	0.72353	2.195	0.80722	D	1	B;P	0.34412	0.248;0.453	B;B	0.33620	0.015;0.167	T	0.42068	-0.9473	10	0.66056	D	0.02	.	16.3663	0.83325	0.0:0.0:0.0:1.0	.	207;207	Q12926;Q12926-2	ELAV2_HUMAN;.	R	207;207;207;207;207;235;72	ENSP00000223951:S207R;ENSP00000380479:S207R;ENSP00000440998:S207R;ENSP00000369460:S207R;ENSP00000391757:S72R	ENSP00000223951:S207R	S	-	1	0	ELAVL2	23691471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.678000	0.84035	2.269000	0.75478	0.460000	0.39030	AGC		0.493	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		G	23701471	T	G	23701471	3	3	53	1	0	0	0	0	1	0	0	0	5063	1609	56	4	472	4	ELAVL2	9	23701471	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09		23701471	117511960	73	7158										
DAPK1	1612	broad.mit.edu	37	chr9	90262278	90262278	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ccacgtcgataccttgaaatTtctcagtgagaacaaatgcc	7	11	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:90262278T>A	ENST00000408954.3	+	14	1624	c.1289T>A	c.(1288-1290)tTt>tAt	p.F430Y	DAPK1_ENST00000472284.1_Missense_Mutation_p.F430Y|DAPK1_ENST00000469640.2_Missense_Mutation_p.F430Y|DAPK1_ENST00000358077.5_Missense_Mutation_p.F430Y|DAPK1_ENST00000491893.1_Missense_Mutation_p.F430Y	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	430					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F430Y(2)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						ACCTTGAAATTTCTCAGTGAG	0.502									Chronic Lymphocytic Leukemia, Familial Clustering of																																							2	Substitution - Missense(2)	large_intestine(2)	9											114	118	117					9																	90262278		2025	4179	6204	89452098	SO:0001583	missense	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.1289T>A	9.37:g.90262278T>A	ENSP00000386135:p.Phe430Tyr		89452098	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.522040	0.44866	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.64260	-0.02;-0.02;-0.09;-0.02;-0.09	4.74	4.74	0.60224	Ankyrin repeat-containing domain (4);	0.000000	0.52532	D	0.000069	T	0.75199	0.3817	M	0.74881	2.28	0.80722	D	1	B;D;D	0.62365	0.059;0.991;0.981	B;D;D	0.74023	0.043;0.982;0.931	T	0.72286	-0.4338	10	0.11485	T	0.65	.	14.6995	0.69147	0.0:0.0:0.0:1.0	.	430;430;430	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	Y	430	ENSP00000350785:F430Y;ENSP00000417076:F430Y;ENSP00000418885:F430Y;ENSP00000386135:F430Y;ENSP00000419026:F430Y	ENSP00000350785:F430Y	F	+	2	0	DAPK1	89452098	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.885000	0.69736	2.125000	0.65367	0.533000	0.62120	TTT		0.502	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		A	90262278	T	A	90262278	3	1	53	1	0	0	0	0	1	0	0	0	4241	1841	64	5	1339	5	DAPK1	9	90262278	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	66560807	90262278	50951153	74	7159										
C9orf79	286234	broad.mit.edu	37	chr9	90501795	90501795	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggccaaatgtgctgttcccaAgtctgacacccacaggaaac	9	13	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:90501795A>G	ENST00000325643.5	+	4	2459	c.2393A>G	c.(2392-2394)aAg>aGg	p.K798R		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	798					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.K798R(1)									GCTGTTCCCAAGTCTGACACC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	85	83					9																	90501795		2203	4300	6503	89691615	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2393A>G	9.37:g.90501795A>G	ENSP00000322640:p.Lys798Arg		89691615	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	a	8.515	0.867384	0.17250	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.03982	3.74	2.43	0.031	0.14169	.	2.533380	0.01756	N	0.030228	T	0.06280	0.0162	L	0.34521	1.04	0.09310	N	1	P;P	0.49185	0.92;0.666	P;B	0.48030	0.564;0.362	T	0.31806	-0.9930	10	0.19590	T	0.45	.	4.3425	0.11117	0.6557:0.0:0.3443:0.0	.	798;450	Q6ZUB1;Q8NA33	CI079_HUMAN;.	R	798;450	ENSP00000322640:K798R	ENSP00000322640:K798R	K	+	2	0	C9orf79	89691615	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.033000	0.13754	-0.003000	0.14444	0.455000	0.32223	AAG		0.592	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		G	90501795	A	G	90501795	3	3	53	1	0	0	0	0	1	0	0	0	2503	72	3	4	2407	4	C9orf79	9	90501795	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	239517	90501795	50711636	75	7160										
C5	727	broad.mit.edu	37	chr9	123751902	123751902	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttaatgggtcagaatgaaaaAtgttccaatgatttcctgtt	8	5	1	3	rs41311881	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:123751902A>T	ENST00000223642.1	-	24	3127	c.3098T>A	c.(3097-3099)aTt>aAt	p.I1033N		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1033			I -> T (in dbSNP:rs41311881). {ECO:0000269|Ref.2}.		activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.I1033N(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	AGAATGAAAAATGTTCCAATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											52	54	53					9																	123751902		2203	4300	6503	122791723	SO:0001583	missense	727			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.3098T>A	9.37:g.123751902A>T	ENSP00000223642:p.Ile1033Asn		122791723	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.45|16.45	3.126388|3.126388	0.56721|0.56721	.|.	.|.	ENSG00000106804|ENSG00000106804	ENST00000430906|ENST00000223642	.|T	.|0.38722	.|1.12	5.73|5.73	4.6|4.6	0.57074|0.57074	.|Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	.|0.331184	.|0.33650	.|N	.|0.004689	T|T	0.59266|0.59266	0.2181|0.2181	M|M	0.74881|0.74881	2.28|2.28	0.42608|0.42608	D|D	0.993304|0.993304	.|D	.|0.71674	.|0.998	.|D	.|0.65573	.|0.936	T|T	0.60840|0.60840	-0.7183|-0.7183	6|10	0.33940|0.52906	T|T	0.23|0.07	.|.	9.127|9.127	0.36821|0.36821	0.917:0.0:0.0829:0.0|0.917:0.0:0.0829:0.0	.|.	.|1033	.|P01031	.|CO5_HUMAN	Q|N	1102|1033	.|ENSP00000223642:I1033N	ENSP00000394199:H1102Q|ENSP00000223642:I1033N	H|I	-|-	3|2	2|0	C5|C5	122791723|122791723	0.532000|0.532000	0.26346|0.26346	0.967000|0.967000	0.41034|0.41034	0.615000|0.615000	0.37417|0.37417	2.188000|2.188000	0.42612|0.42612	1.013000|1.013000	0.39391|0.39391	0.460000|0.460000	0.39030|0.39030	CAT|ATT		0.363	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123751902	A	T	123751902	3	4	53	1	0	0	0	0	1	0	0	0	2286	101	4	5	2004	5	C5	9	123751902	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	33250107	123751902	17461529	76	7161										
PTGS1	5742	broad.mit.edu	37	chr9	125154645	125154645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agggaatcccatctgttctcCggagtactggaagccgagca	12	11	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:125154645C>T	ENST00000362012.2	+	11	1627	c.1622C>T	c.(1621-1623)cCg>cTg	p.P541L	PTGS1_ENST00000373698.5_Missense_Mutation_p.P432L|PTGS1_ENST00000223423.4_Missense_Mutation_p.P504L|PTGS1_ENST00000540753.1_Missense_Mutation_p.P479L	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	541					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.P541L(1)		large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	ATCTGTTCTCCGGAGTACTGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											108	110	110					9																	125154645		2203	4300	6503	124194466	SO:0001583	missense	5742			M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.1622C>T	9.37:g.125154645C>T	ENSP00000354612:p.Pro541Leu		124194466	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	C	34	5.303898	0.95601	.	.	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000373698	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.44074	0.1276	M	0.92026	3.265	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.55055	-0.8200	10	0.87932	D	0	-10.2139	18.2032	0.89846	0.0:1.0:0.0:0.0	.	479;541;504	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	L	479;541;504;432	ENSP00000437709:P479L;ENSP00000354612:P541L;ENSP00000223423:P504L;ENSP00000362802:P432L	ENSP00000223423:P504L	P	+	2	0	PTGS1	124194466	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	7.814000	0.86154	2.539000	0.85634	0.655000	0.94253	CCG		0.517	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1			T	125154645	C	T	125154645	3	4	53	1	0	0	0	0	1	0	0	0	12790	652	23	1	1664	1	PTGS1	9	125154645	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	1402743	125154645	16058786	77	7162										
RABGAP1	23637	broad.mit.edu	37	chr9	125751741	125751741	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cacgtcttccggtgtgaaatAcaagaagctgtaagtcctca	9	10	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:125751741A>T	ENST00000373647.4	+	5	890	c.756A>T	c.(754-756)atA>atT	p.I252I		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	252	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)	p.I252I(1)|p.I180I(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						GGTGTGAAATACAAGAAGCTG	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	9											62	60	60					9																	125751741		2203	4300	6503	124791562	SO:0001819	synonymous_variant	23637			AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.756A>T	9.37:g.125751741A>T			124791562	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																				0.408	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		T	125751741	A	T	125751741	2	4	53	1	0	0	0	0	0	0	0	1	13001	381	14	5		5	RABGAP1	9	125751741	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	597096	125751741	15461690	78	7163										
DENND1A	57706	broad.mit.edu	37	chr9	126202686	126202686	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ccggtcttctcggagcttggGgtccttggcctccaccagtg	13	14	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:126202686G>A	ENST00000373624.2	-	19	1642	c.1441C>T	c.(1441-1443)Ccc>Tcc	p.P481S	DENND1A_ENST00000394215.2_Missense_Mutation_p.P451S|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000373618.1_Missense_Mutation_p.P449S|DENND1A_ENST00000542603.1_Missense_Mutation_p.P223S|DENND1A_ENST00000373620.3_Missense_Mutation_p.P481S|DENND1A_ENST00000394219.3_Missense_Mutation_p.P449S	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	481					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.P481S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						CGGAGCTTGGGGTCCTTGGCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	9											59	51	54					9																	126202686		2203	4300	6503	125242507	SO:0001583	missense	57706			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1441C>T	9.37:g.126202686G>A	ENSP00000362727:p.Pro481Ser		125242507	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.494914	0.26774	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T;T	0.20332	3.51;2.08;3.41;3.53;3.39;3.37	5.31	3.04	0.35103	.	0.763124	0.12802	N	0.437906	T	0.08846	0.0219	N	0.10837	0.055	0.30122	N	0.805566	B;B;B;B;B;B;B	0.21071	0.008;0.008;0.0;0.006;0.001;0.001;0.051	B;B;B;B;B;B;B	0.16722	0.006;0.006;0.002;0.007;0.003;0.002;0.016	T	0.32161	-0.9917	10	0.07030	T	0.85	-14.0218	6.4754	0.22033	0.082:0.1303:0.6542:0.1334	.	449;439;449;451;481;481;301	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4	.;.;.;.;.;DEN1A_HUMAN;.	S	481;223;449;481;451;449	ENSP00000362727:P481S;ENSP00000437457:P223S;ENSP00000377766:P449S;ENSP00000362722:P481S;ENSP00000377763:P451S;ENSP00000362720:P449S	ENSP00000362720:P449S	P	-	1	0	DENND1A	125242507	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.710000	0.37920	1.189000	0.43028	0.655000	0.94253	CCC		0.552	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126202686	G	A	126202686	3	1	53	1	0	0	0	0	1	0	0	0	4437	1232	43	3	1711	3	DENND1A	9	126202686	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	450945	126202686	15010745	79	7164										
SETX	23064	broad.mit.edu	37	chr9	135202893	135202893	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gtactttcacaatcagaaagTcttcgtctatttttttgtga	6	7	4	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr9:135202893T>G	ENST00000224140.5	-	10	4274	c.4092A>C	c.(4090-4092)agA>agC	p.R1364S	SETX_ENST00000393220.1_Missense_Mutation_p.R1364S|SETX_ENST00000372169.2_Missense_Mutation_p.R1364S	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1364					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.R1364S(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AATCAGAAAGTCTTCGTCTAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	102	102					9																	135202893		2203	4300	6503	134192714	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.4092A>C	9.37:g.135202893T>G	ENSP00000224140:p.Arg1364Ser		134192714	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	4.249	0.045246	0.08196	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86956	-2.09;-2.19;-1.81	5.63	-1.41	0.08941	.	2.192920	0.01617	N	0.022834	T	0.80949	0.4722	L	0.36672	1.1	0.09310	N	1	B;B;B	0.20368	0.034;0.044;0.034	B;B;B	0.24394	0.053;0.024;0.053	T	0.62358	-0.6871	10	0.15066	T	0.55	.	8.1432	0.31095	0.0:0.5044:0.1355:0.3602	.	1364;1364;1364	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	S	1364	ENSP00000224140:R1364S;ENSP00000361242:R1364S;ENSP00000376913:R1364S	ENSP00000224140:R1364S	R	-	3	2	SETX	134192714	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.045000	0.14013	-0.508000	0.06540	-0.417000	0.06048	AGA		0.363	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135202893	T	G	135202893	3	3	53	1	0	0	0	0	1	0	0	0	14178	1664	58	4	4009	4	SETX	9	135202893	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	9000207	135202893	6010538	80	7165										
SEPHS1	22929	broad.mit.edu	37	chr10	13386833	13386833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctgtaaagattccagcaattTttgcaggacatcttggggca	10	8	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:13386833T>C	ENST00000327347.5	-	2	493	c.118A>G	c.(118-120)Aaa>Gaa	p.K40E	SEPHS1_ENST00000378614.4_Missense_Mutation_p.K40E|SEPHS1_ENST00000494329.1_5'UTR|SEPHS1_ENST00000545675.1_Missense_Mutation_p.K40E|SEPHS1_ENST00000537130.1_Intron	NM_001195602.1|NM_012247.4	NP_001182531.1|NP_036379.2	P49903	SPS1_HUMAN	selenophosphate synthetase 1	40					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|selenide, water dikinase activity (GO:0004756)	p.K40E(2)		cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|stomach(1)	16						TCCAGCAATTTTTGCAGGACA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	10											120	124	123					10																	13386833		2203	4300	6503	13426839	SO:0001583	missense	22929			BC000941	CCDS7098.1, CCDS55702.1, CCDS55703.1	10p14	2006-10-06			ENSG00000086475	ENSG00000086475			19685	protein-coding gene	gene with protein product		600902				7665581	Standard	NM_012247		Approved	SPS, SPS1	uc001imk.3	P49903	OTTHUMG00000017696	ENST00000327347.5:c.118A>G	10.37:g.13386833T>C	ENSP00000367893:p.Lys40Glu		13426839	B4DWK0|D3DRS9|D6PSQ9|Q5T5U8|Q5T5U9|Q9BVT4	Missense_Mutation	SNP	ENST00000327347.5	37	CCDS7098.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208576	0.58343	.	.	ENSG00000086475	ENST00000327347;ENST00000319684;ENST00000378614;ENST00000545675;ENST00000413411	T;T;T	0.44482	0.92;0.93;0.94	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	L	0.50333	1.59	0.80722	D	1	B;B;B;B	0.14012	0.003;0.009;0.009;0.009	B;B;B;B	0.17098	0.002;0.017;0.009;0.017	T	0.15838	-1.0423	10	0.23891	T	0.37	-5.4924	13.53	0.61617	0.0:0.0:0.0:1.0	.	40;40;40;40	Q5T5U9;P49903;D6PSQ9;D3DRS9	.;SPS1_HUMAN;.;.	E	40	ENSP00000367893:K40E;ENSP00000367877:K40E;ENSP00000441119:K40E	ENSP00000367887:K40E	K	-	1	0	SEPHS1	13426839	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	7.985000	0.88162	1.783000	0.52377	0.260000	0.18958	AAA		0.468	SEPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046856.1	NM_012247		C	13386833	T	C	13386833	3	2	53	1	0	0	0	0	1	0	0	0	14091	1850	64	4	1092	4	SEPHS1	10	13386833	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09		13386833	122147914	81	7166										
ENKUR	219670	broad.mit.edu	37	chr10	25273712	25273712	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttttcaattatgccaatgtcGtgttctagttgtttcatttc	6	7	3	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:25273712G>A	ENST00000331161.4	-	5	936	c.717C>T	c.(715-717)caC>caT	p.H239H	ENKUR_ENST00000376363.1_Silent_p.H239H	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	239	Enkurin. {ECO:0000255|PROSITE- ProRule:PRU01000}.					motile cilium (GO:0031514)		p.H239H(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						TGCCAATGTCGTGTTCTAGTT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	10											128	120	123					10																	25273712		2203	4300	6503	25313718	SO:0001819	synonymous_variant	219670			AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"chromosome 10 open reading frame 63"	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.717C>T	10.37:g.25273712G>A			25313718	A8K8Y0|D3DRV2	Silent	SNP	ENST00000331161.4	37	CCDS7146.1																																																																																				0.348	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010		A	25273712	G	A	25273712	2	1	53	1	0	0	0	0	0	0	0	1	5133	1136	40	1		1	ENKUR	10	25273712	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	11886879	25273712	110261035	82	7167										
ANKRD30A	91074	broad.mit.edu	37	chr10	37508552	37508552	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gctgaacacatgtatcaaaaCgaacaagataatgtgaacaa	7	7	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:37508552C>T	ENST00000602533.1	+	34	3843	c.3744C>T	c.(3742-3744)aaC>aaT	p.N1248N	ANKRD30A_ENST00000374660.1_Silent_p.N1367N|ANKRD30A_ENST00000361713.1_Silent_p.N1248N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1304					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N1248N(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TGTATCAAAACGAACAAGATA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	10											77	65	69					10																	37508552		1915	4122	6037	37548558	SO:0001819	synonymous_variant	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3744C>T	10.37:g.37508552C>T			37548558	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																					0.368	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37508552	C	T	37508552	2	4	53	1	0	0	0	0	0	0	0	1	658	535	19	1		1	ANKRD30A	10	37508552	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	12234840	37508552	98026195	83	7168										
PCDH15	65217	broad.mit.edu	37	chr10	55582288	55582288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgtttggtggatgggcaaaaTtttcaaaaatatttctttcg	9	4	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:55582288T>C	ENST00000320301.6	-	33	5592	c.5198A>G	c.(5197-5199)aAt>aGt	p.N1733S	PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.N1735S|PCDH15_ENST00000395430.1_Missense_Mutation_p.N1730S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.N1710S|PCDH15_ENST00000395432.2_Missense_Mutation_p.N1693S|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.N1664S|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000373957.3_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1733					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.N1733S(1)|p.N1740S(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGGGCAAAATTTTCAAAAAT	0.453										HNSCC(58;0.16)																																						2	Substitution - Missense(2)	large_intestine(2)	10											37	39	38					10																	55582288		2203	4299	6502	55252294	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.5198A>G	10.37:g.55582288T>C	ENSP00000322604:p.Asn1733Ser		55252294	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	0.060	-1.226185	0.01518	.	.	ENSG00000150275	ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T	0.56275	0.5;0.47;0.51;0.48;0.48;0.49	5.0	2.52	0.30459	.	.	.	.	.	T	0.29556	0.0737	N	0.19112	0.55	0.22112	N	0.999355	B;B;B;B;B;B;B;B	0.13145	0.007;0.007;0.007;0.007;0.004;0.007;0.007;0.007	B;B;B;B;B;B;B;B	0.12156	0.007;0.004;0.004;0.004;0.006;0.004;0.007;0.004	T	0.27157	-1.0082	9	0.07644	T	0.81	.	4.6763	0.12713	0.3082:0.0808:0.0:0.611	.	1710;1733;1735;1740;1664;1693;1730;1733	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;Q96QU1	.;.;.;.;.;.;.;PCD15_HUMAN	S	1693;1735;1710;1733;1730;1740;1664	ENSP00000378820:N1693S;ENSP00000354950:N1735S;ENSP00000378821:N1710S;ENSP00000322604:N1733S;ENSP00000378818:N1730S;ENSP00000412628:N1664S	ENSP00000322604:N1733S	N	-	2	0	PCDH15	55252294	0.063000	0.20901	0.518000	0.27811	0.261000	0.26267	0.031000	0.13710	0.201000	0.20466	0.533000	0.62120	AAT		0.453	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55582288	T	C	55582288	3	2	53	1	0	0	0	0	1	0	0	0	11542	1493	52	4	2279	4	PCDH15	10	55582288	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	18073736	55582288	79952459	84	7169										
TLL2	7093	broad.mit.edu	37	chr10	98133419	98133419	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cgaataaaacctgagaaacaTactgctgccggaagccaccg	9	12	0	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:98133419T>A	ENST00000357947.3	-	19	2821	c.2596A>T	c.(2596-2598)Atg>Ttg	p.M866L		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	866	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.M866L(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		CTGAGAAACATACTGCTGCCG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											72	73	73					10																	98133419		2203	4300	6503	98123409	SO:0001583	missense	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2596A>T	10.37:g.98133419T>A	ENSP00000350630:p.Met866Leu		98123409	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	T	9.642	1.139131	0.21205	.	.	ENSG00000095587	ENST00000357947	T	0.15834	2.39	4.85	0.568	0.17333	CUB (5);	0.344834	0.19558	N	0.111394	T	0.07234	0.0183	N	0.16833	0.445	0.41503	D	0.988291	B	0.02656	0.0	B	0.01281	0.0	T	0.29640	-1.0005	10	0.09338	T	0.73	.	5.0535	0.14520	0.1715:0.0:0.3841:0.4444	.	866	Q9Y6L7	TLL2_HUMAN	L	866	ENSP00000350630:M866L	ENSP00000350630:M866L	M	-	1	0	TLL2	98123409	1.000000	0.71417	0.999000	0.59377	0.875000	0.50365	1.674000	0.37544	0.334000	0.23590	-0.302000	0.09304	ATG		0.592	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98133419	T	A	98133419	3	1	53	1	0	0	0	0	1	0	0	0	15985	1406	49	5	463	5	TLL2	10	98133419	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	42551131	98133419	37401328	85	7170										
PAX2	5076	broad.mit.edu	37	chr10	102510632	102510632	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	acaatgacacagtgcccagcGtctcttccatcaacaggtga	8	13	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:102510632G>A	ENST00000428433.1	+	3	944	c.394G>A	c.(394-396)Gtc>Atc	p.V132I	PAX2_ENST00000355243.3_Missense_Mutation_p.V132I|PAX2_ENST00000370296.2_Missense_Mutation_p.V132I|PAX2_ENST00000556085.1_Missense_Mutation_p.V131I|PAX2_ENST00000553492.1_Intron|PAX2_ENST00000361791.3_Missense_Mutation_p.V132I	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	132	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)	p.V132I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		AGTGCCCAGCGTCTCTTCCAT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	10											55	59	58					10																	102510632		2203	4299	6502	102500622	SO:0001583	missense	5076				CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"Paired boxes", "Homeoboxes / PRD class"	8616	protein-coding gene	gene with protein product		167409	"paired box gene 2"			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.394G>A	10.37:g.102510632G>A	ENSP00000396259:p.Val132Ile		102500622	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Missense_Mutation	SNP	ENST00000428433.1	37	CCDS53569.1	.	.	.	.	.	.	.	.	.	.	G	32	5.187093	0.94923	.	.	ENSG00000075891	ENST00000370294;ENST00000370296;ENST00000428433;ENST00000361791;ENST00000355243;ENST00000556085;ENST00000427256;ENST00000554172	D;D;D;D;D;D;D	0.99494	-6.01;-6.01;-6.01;-6.01;-6.01;-6.01;-6.01	5.93	5.93	0.95920	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.055638	0.64402	D	0.000001	D	0.99396	0.9787	M	0.80332	2.49	0.80722	D	1	P;D;B;P;P;P;P	0.59767	0.736;0.986;0.406;0.948;0.867;0.736;0.935	P;P;B;P;P;P;P	0.55749	0.489;0.783;0.191;0.727;0.623;0.489;0.489	D	0.99517	1.0957	10	0.87932	D	0	.	20.3437	0.98782	0.0:0.0:1.0:0.0	.	131;132;132;136;132;132;136	G3V5U4;Q02962-2;Q02962-3;Q6YFJ8;Q02962;Q02962-4;G3V5S4	.;.;.;.;PAX2_HUMAN;.;.	I	24;132;132;132;132;131;132;136	ENSP00000359319:V132I;ENSP00000396259:V132I;ENSP00000355069:V132I;ENSP00000347385:V132I;ENSP00000452527:V131I;ENSP00000398652:V132I;ENSP00000452489:V136I	ENSP00000347385:V132I	V	+	1	0	PAX2	102500622	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.815000	0.96918	0.561000	0.74099	GTC		0.597	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding				A	102510632	G	A	102510632	3	1	53	1	0	0	0	0	1	0	0	0	11510	1145	40	1	404	1	PAX2	10	102510632	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	4377213	102510632	33024115	86	7171										
KNDC1	85442	broad.mit.edu	37	chr10	135013012	135013012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cctttgccactttctgtggcGccatttccgagaagttctgt	9	12	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr10:135013012G>A	ENST00000304613.3	+	15	2830	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	KNDC1_ENST00000368572.2_Missense_Mutation_p.A939T|KNDC1_ENST00000368571.2_Missense_Mutation_p.A872T			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	937					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.A937T(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTTCTGTGGCGCCATTTCCGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											177	150	159					10																	135013012		2203	4300	6503	134863002	SO:0001583	missense	85442			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2809G>A	10.37:g.135013012G>A	ENSP00000304437:p.Ala937Thr		134863002	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244556	0.59103	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.12984	2.63;2.63;2.63	3.99	3.99	0.46301	.	0.479232	0.18727	N	0.132851	T	0.34571	0.0902	M	0.66939	2.045	0.41003	D	0.984944	D;D;D	0.89917	0.993;1.0;0.997	D;D;P	0.72338	0.919;0.977;0.74	T	0.18116	-1.0347	10	0.72032	D	0.01	-25.397	13.9012	0.63804	0.0:0.0:1.0:0.0	.	937;872;937	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	T	937;939;872	ENSP00000304437:A937T;ENSP00000357561:A939T;ENSP00000357560:A872T	ENSP00000304437:A937T	A	+	1	0	KNDC1	134863002	0.937000	0.31787	0.821000	0.32701	0.124000	0.20399	2.706000	0.47135	1.957000	0.56846	0.313000	0.20887	GCC		0.532	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135013012	G	A	135013012	3	1	53	1	0	0	0	0	1	0	0	0	8447	1087	38	1	2867	1	KNDC1	10	135013012	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	32502380	135013012	521735	87	7172										
OR51A7	119687	broad.mit.edu	37	chr11	4929276	4929276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gatcttgaagactatactcaGcattgcatctttggcagaga	9	8	3	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:4929276G>A	ENST00000359350.4	+	1	677	c.677G>A	c.(676-678)aGc>aAc	p.S226N	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S226N(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACTATACTCAGCATTGCATCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											237	197	211					11																	4929276		2201	4298	6499	4885852	SO:0001583	missense	119687			AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.677G>A	11.37:g.4929276G>A	ENSP00000352305:p.Ser226Asn		4885852	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	37	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	G	7.246	0.602247	0.13939	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.37752	1.18	5.02	3.16	0.36331	GPCR, rhodopsin-like superfamily (1);	0.380742	0.23093	N	0.052002	T	0.25082	0.0609	N	0.25789	0.76	0.09310	N	1	B	0.12013	0.005	B	0.21151	0.033	T	0.17561	-1.0365	10	0.40728	T	0.16	.	9.8726	0.41185	0.1656:0.0:0.8344:0.0	.	226	Q8NH64	O51A7_HUMAN	N	226;226;215	ENSP00000352305:S226N	ENSP00000352305:S226N	S	+	2	0	OR51A7	4885852	0.000000	0.05858	0.954000	0.39281	0.232000	0.25224	-0.421000	0.07053	0.709000	0.31976	0.655000	0.94253	AGC		0.468	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		A	4929276	G	A	4929276	3	1	53	1	0	0	0	0	1	0	0	0	11119	971	34	3	679	3	OR51A7	11	4929276	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09		4929276	130077240	88	7173										
OR51B2	79345	broad.mit.edu	37	chr11	5345396	5345396	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tggtcatgcttgatgaggtaGaggagcatgccattgcccag	14	8	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:5345396G>C	ENST00000328813.2	-	1	186	c.132C>G	c.(130-132)ctC>ctG	p.L44L	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L44L(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGATGAGGTAGAGGAGCATGC	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	11											136	114	121					11																	5345396		2201	4297	6498	5301972	SO:0001819	synonymous_variant	79345			AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"GPCR / Class A : Olfactory receptors"	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.132C>G	11.37:g.5345396G>C			5301972	Q96RD4	Silent	SNP	ENST00000328813.2	37	CCDS31377.1																																																																																				0.527	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180		C	5345396	G	C	5345396	2	2	53	1	0	0	0	0	0	0	0	1	11120	929	33	5		5	OR51B2	11	5345396	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	416120	5345396	129661120	89	7174										
OR5T1	390155	broad.mit.edu	37	chr11	56043937	56043937	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcttcatgtatgtgagaccaAgttccagctacacttcggac	8	11	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:56043937A>C	ENST00000313033.2	+	1	909	c.823A>C	c.(823-825)Agt>Cgt	p.S275R		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S275R(2)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					TGTGAGACCAAGTTCCAGCTA	0.423																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	11											226	194	205					11																	56043937		2201	4296	6497	55800513	SO:0001583	missense	390155			AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"GPCR / Class A : Olfactory receptors"	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.823A>C	11.37:g.56043937A>C	ENSP00000323612:p.Ser275Arg		55800513	B2RNM9	Missense_Mutation	SNP	ENST00000313033.2	37	CCDS31525.1	.	.	.	.	.	.	.	.	.	.	A	11.58	1.681141	0.29872	.	.	ENSG00000181698	ENST00000313033	T	0.00137	8.68	3.48	0.87	0.19102	GPCR, rhodopsin-like superfamily (1);	0.112616	0.39274	N	0.001405	T	0.00178	0.0005	M	0.61703	1.905	0.09310	N	1	B	0.24132	0.098	B	0.37387	0.248	T	0.36841	-0.9731	10	0.72032	D	0.01	.	4.2507	0.10693	0.6692:0.1991:0.1316:0.0	.	275	Q8NG75	OR5T1_HUMAN	R	275	ENSP00000323612:S275R	ENSP00000323612:S275R	S	+	1	0	OR5T1	55800513	0.000000	0.05858	0.275000	0.24674	0.923000	0.55619	0.261000	0.18442	0.052000	0.16007	0.381000	0.24937	AGT		0.423	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745		C	56043937	A	C	56043937	3	2	53	1	0	0	0	0	1	0	0	0	11212	72	3	4	825	4	OR5T1	11	56043937	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	50698541	56043937	78962579	90	7175										
DPF2	5977	broad.mit.edu	37	chr11	65113720	65113720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcacttcccccactacagggCatccatcttgcctccaattt	4	17	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:65113720C>T	ENST00000528416.1	+	9	1040	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	DPF2_ENST00000252268.4_Missense_Mutation_p.H317Y|DPF2_ENST00000415073.2_Intron	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	303					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)	p.H303Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						CACTACAGGGCATCCATCTTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											140	105	117					11																	65113720		2201	4297	6498	64870296	SO:0001583	missense	5977			U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.907C>T	11.37:g.65113720C>T	ENSP00000436901:p.His303Tyr		64870296	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	37	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.020289	0.75275	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.94046	-3.2;-3.34	5.62	5.62	0.85841	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38778	N	0.001576	D	0.97870	0.9300	H	0.96142	3.775	0.80722	D	1	D	0.60160	0.987	D	0.79784	0.993	D	0.98886	1.0771	10	0.87932	D	0	-23.2646	17.1512	0.86778	0.0:1.0:0.0:0.0	.	303	Q92785	REQU_HUMAN	Y	303;317	ENSP00000436901:H303Y;ENSP00000252268:H317Y	ENSP00000252268:H317Y	H	+	1	0	DPF2	64870296	1.000000	0.71417	1.000000	0.80357	0.284000	0.27059	7.701000	0.84566	2.667000	0.90743	0.561000	0.74099	CAT		0.547	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		T	65113720	C	T	65113720	3	4	53	1	0	0	0	0	1	0	0	0	4728	710	25	3	941	3	DPF2	11	65113720	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	9069783	65113720	69892796	91	7176										
RELA	5970	broad.mit.edu	37	chr11	65425864	65425864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gcctgcaggctggggtctgcGtagggaggggtccggaacac	19	10	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:65425864G>A	ENST00000406246.3	-	8	1032	c.771C>T	c.(769-771)taC>taT	p.Y257Y	RELA_ENST00000308639.9_Silent_p.Y254Y|RELA_ENST00000525693.1_Silent_p.Y257Y	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	257	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.Y257Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						TGGGGTCTGCGTAGGGAGGGG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	11											82	75	77					11																	65425864		2201	4297	6498	65182440	SO:0001819	synonymous_variant	5970			Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.771C>T	11.37:g.65425864G>A			65182440	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1																																																																																				0.627	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		A	65425864	G	A	65425864	2	1	53	1	0	0	0	0	0	0	0	1	13253	1140	40	1		1	RELA	11	65425864	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	312144	65425864	69580652	92	7177										
RBM14	10432	broad.mit.edu	37	chr11	66392424	66392424	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gcctcttcctatggggttcgTgcagctgcttcttcctacaa	9	13	2	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:66392424T>G	ENST00000310137.4	+	2	1216	c.1077T>G	c.(1075-1077)cgT>cgG	p.R359R	RBM14-RBM4_ENST00000511114.1_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	359	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)	p.R359R(1)	RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						ATGGGGTTCGTGCAGCTGCTT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	11											72	80	77					11																	66392424		2200	4295	6495	66149000	SO:0001819	synonymous_variant	10432			AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1077T>G	11.37:g.66392424T>G			66149000	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	37	CCDS8147.1																																																																																				0.612	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		G	66392424	T	G	66392424	2	3	53	1	0	0	0	0	0	0	0	1	13152	1683	59	4		4	RBM14	11	66392424	Silent	SNP	T	TCGA-AG-3902-01A-01W-1073-09	966560	66392424	68614092	93	7178										
FAT3	120114	broad.mit.edu	37	chr11	92531511	92531511	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tttctcaatactcaggcagcCtaagtgaggctgccccaatt	8	12	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr11:92531511C>G	ENST00000298047.6	+	9	5349	c.5332C>G	c.(5332-5334)Cta>Gta	p.L1778V	FAT3_ENST00000409404.2_Missense_Mutation_p.L1778V|FAT3_ENST00000525166.1_Missense_Mutation_p.L1628V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1778	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1778V(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CTCAGGCAGCCTAAGTGAGGC	0.453										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											29	29	29					11																	92531511		1884	4117	6001	92171159	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.5332C>G	11.37:g.92531511C>G	ENSP00000298047:p.Leu1778Val		92171159	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	12.43	1.935438	0.34189	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.57752	0.38;0.38;0.38	5.93	5.93	0.95920	.	.	.	.	.	T	0.21881	0.0527	N	0.00670	-1.27	0.80722	D	1	B	0.15930	0.015	B	0.15870	0.014	T	0.29088	-1.0023	9	0.17832	T	0.49	.	13.2493	0.60041	0.261:0.739:0.0:0.0	.	1778	Q8TDW7-3	.	V	1778;1778;1628	ENSP00000298047:L1778V;ENSP00000387040:L1778V;ENSP00000432586:L1628V	ENSP00000298047:L1778V	L	+	1	2	FAT3	92171159	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.690000	0.61731	2.818000	0.97014	0.591000	0.81541	CTA		0.453	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92531511	C	G	92531511	3	3	53	1	0	0	0	0	1	0	0	0	5710	680	24	5	5366	5	FAT3	11	92531511	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	26139087	92531511	42475005	94	7179										
KRAS	3845	broad.mit.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	53	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09		25398281	108453614	95	7180										
IPO8	10526	broad.mit.edu	37	chr12	30818779	30818779	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgccatcatttttggcaacaCctaaagaaacagaagaatcc	6	10	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:30818779C>A	ENST00000256079.4	-	12	1560	c.1222G>T	c.(1222-1224)Gtg>Ttg	p.V408L	IPO8_ENST00000544829.1_Splice_Site_p.V203L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	408					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)	p.V408L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTTGGCAACACCTAAAGAAAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											85	85	85					12																	30818779		2203	4300	6503	30710046	SO:0001630	splice_region_variant	10526			U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1222-1G>T	12.37:g.30818779C>A			30710046	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	37	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055631	0.93793	.	.	ENSG00000133704	ENST00000256079;ENST00000544829	T;T	0.67865	-0.29;-0.29	4.52	4.52	0.55395	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	T	0.76593	0.4009	M	0.74881	2.28	0.80722	D	1	P;D	0.56287	0.877;0.975	P;P	0.55391	0.678;0.775	T	0.74456	-0.3659	10	0.23891	T	0.37	-20.8154	17.7744	0.88503	0.0:1.0:0.0:0.0	.	203;408	B7Z7M3;O15397	.;IPO8_HUMAN	L	408;203	ENSP00000256079:V408L;ENSP00000444520:V203L	ENSP00000256079:V408L	V	-	1	0	IPO8	30710046	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.556000	0.67307	2.497000	0.84241	0.585000	0.79938	GTG		0.358	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390	Missense_Mutation	A	30818779	C	A	30818779	5	1	53	1	0	0	0	0	0	0	1	0	7819	521	18	2	1947	2	IPO8	12	30818779	Splice_Site	SNP	C	TCGA-AG-3902-01A-01W-1073-09	5420498	30818779	103033116	96	7181										
DENND5B	160518	broad.mit.edu	37	chr12	31540608	31540608	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctgaatggtctgcagaattcGgataagggagttgacagtca	13	6	2	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:31540608G>A	ENST00000389082.5	-	21	4018	c.3754C>T	c.(3754-3756)Cga>Tga	p.R1252*	DENND5B_ENST00000536562.1_Nonsense_Mutation_p.R1287*|DENND5B_ENST00000306833.6_Nonsense_Mutation_p.R1287*	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1252	RUN 2. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1252*(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TGCAGAATTCGGATAAGGGAG	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											106	100	102					12																	31540608		1990	4156	6146	31431875	SO:0001587	stop_gained	160518			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.3754C>T	12.37:g.31540608G>A	ENSP00000373734:p.Arg1252*		31431875	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Nonsense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	G	42	9.640961	0.99227	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562	.	.	.	4.98	4.98	0.66077	.	0.157591	0.42821	D	0.000642	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.7112	18.4229	0.90597	0.0:0.0:1.0:0.0	.	.	.	.	X	1252;1287;1287	.	ENSP00000306482:R1287X	R	-	1	2	DENND5B	31431875	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	1.035000	0.30216	2.597000	0.87782	0.591000	0.81541	CGA		0.488	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31540608	G	A	31540608	4	1	53	1	0	0	0	0	0	1	0	0	4448	1124	39	1	74	1	DENND5B	12	31540608	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	721829	31540608	102311287	97	7182										
SOAT2	8435	broad.mit.edu	37	chr12	53509273	53509273	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctgtccaccctgttggcgccGtaccaggccctacggctgtg	12	16	0	0	rs151267658	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:53509273G>A	ENST00000301466.3	+	6	603	c.543G>A	c.(541-543)ccG>ccA	p.P181P		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	181					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)	p.P181P(1)		endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	TGTTGGCGCCGTACCAGGCCC	0.677													G|||	2	0.000399361	0.0015	0	5008	,	,		17361	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						G		3,4403	6.2+/-15.9	0,3,2200	41	41	41		543	2.7	1	12	dbSNP_134	41	0,8600		0,0,4300	no	coding-synonymous	SOAT2	NM_003578.3		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		181/523	53509273	3,13003	2203	4300	6503	51795540	SO:0001819	synonymous_variant	8435			AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.543G>A	12.37:g.53509273G>A			51795540	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Silent	SNP	ENST00000301466.3	37	CCDS8847.1																																																																																				0.677	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1			A	53509273	G	A	53509273	2	1	53	1	0	0	0	0	0	0	0	1	14948	1132	40	1		1	SOAT2	12	53509273	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	21968665	53509273	80342622	98	7183										
CALCOCO1	57658	broad.mit.edu	37	chr12	54117514	54117514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cccacacacctggccctggcGgttcacatatcggaactggt	10	15	1	0	rs377219497		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:54117514G>A	ENST00000550804.1	-	4	373	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	CALCOCO1_ENST00000262059.4_Missense_Mutation_p.R105C|CALCOCO1_ENST00000430117.2_Intron|CALCOCO1_ENST00000548263.1_Missense_Mutation_p.R105C|CALCOCO1_ENST00000547885.1_5'Flank			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	105	N-terminal AD (CTNNB1 binding site). {ECO:0000250}.				intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.R105C(1)		NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						TGGCCCTGGCGGTTCACATAT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	CYS/ARG,	0,4406		0,0,2203	52	55	54		313,	4.8	1	12		54	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	CALCOCO1	NM_020898.2,NM_001143682.1	180,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	105/692,	54117514	1,13005	2203	4300	6503	52403781	SO:0001583	missense	57658			AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.313C>T	12.37:g.54117514G>A	ENSP00000449960:p.Arg105Cys		52403781	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Missense_Mutation	SNP	ENST00000550804.1	37	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552327	0.86127	0.0	1.16E-4	ENSG00000012822	ENST00000262059;ENST00000548263;ENST00000550804;ENST00000549935;ENST00000551900;ENST00000546619;ENST00000547949;ENST00000553154;ENST00000549784;ENST00000549173;ENST00000548177;ENST00000552623	T;T;T;T;T;T;T;T;T	0.11169	2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8	4.79	4.79	0.61399	.	0.000000	0.46442	D	0.000290	T	0.19208	0.0461	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.69078	0.997;0.996;0.996;0.997	P;P;P;P	0.57846	0.828;0.736;0.736;0.828	T	0.00901	-1.1521	10	0.62326	D	0.03	-10.8076	17.4946	0.87714	0.0:0.0:1.0:0.0	.	98;105;105;105	B4DG60;Q9P1Z2-3;Q9P1Z2-2;Q9P1Z2	.;.;.;CACO1_HUMAN	C	105;105;105;98;105;105;105;105;105;125;105;105	ENSP00000262059:R105C;ENSP00000447647:R105C;ENSP00000449960:R105C;ENSP00000450083:R105C;ENSP00000448621:R105C;ENSP00000447117:R105C;ENSP00000449058:R125C;ENSP00000446820:R105C;ENSP00000448026:R105C	ENSP00000262059:R105C	R	-	1	0	CALCOCO1	52403781	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.688000	0.37690	2.586000	0.87340	0.655000	0.94253	CGC		0.592	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54117514	G	A	54117514	3	1	53	1	0	0	0	0	1	0	0	0	2583	1116	39	1	1810	1	CALCOCO1	12	54117514	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	608241	54117514	79734381	99	7184										
HNRNPA1	3178	broad.mit.edu	37	chr12	54675593	54675593	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tctcaggtaatgagagatccAaacaccaagcgctccagggg	11	11	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:54675593A>C	ENST00000340913.6	+	3	200	c.147A>C	c.(145-147)ccA>ccC	p.P49P	CBX5_ENST00000209875.4_5'Flank|RP11-968A15.2_ENST00000547177.1_RNA|HNRNPA1_ENST00000547276.1_Silent_p.P49P|HNRNPA1_ENST00000330752.8_Silent_p.P49P|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000546500.1_Silent_p.P49P	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	49	Globular A domain.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)	p.P49P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						TGAGAGATCCAAACACCAAGC	0.443																																					Colon(83;502 1289 8436 16406 24870)											1	Substitution - coding silent(1)	large_intestine(1)	12											46	46	46					12																	54675593		1976	4197	6173	52961860	SO:0001819	synonymous_variant	3178			BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"RNA binding motif (RRM) containing"	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.147A>C	12.37:g.54675593A>C			52961860	A8K4Z8|Q3MIB7|Q6PJZ7	Silent	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																				0.443	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		C	54675593	A	C	54675593	2	2	53	1	0	0	0	0	0	0	0	1	7278	117	5	4		4	HNRNPA1	12	54675593	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	558079	54675593	79176302	100	7185										
ANKS1B	56899	broad.mit.edu	37	chr12	99192716	99192716	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agtttggcagacttacccgcAtttttgcacaagcatcttgg	9	10	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:99192716A>T	ENST00000547776.2	-	21	3262	c.3263T>A	c.(3262-3264)aTg>aAg	p.M1088K	ANKS1B_ENST00000546568.1_Missense_Mutation_p.M254K|ANKS1B_ENST00000332712.7_Missense_Mutation_p.M278K|ANKS1B_ENST00000550693.2_Missense_Mutation_p.M278K|ANKS1B_ENST00000547446.1_Missense_Mutation_p.M223K|ANKS1B_ENST00000329257.7_Missense_Mutation_p.M1088K|ANKS1B_ENST00000546960.1_Missense_Mutation_p.M314K|ANKS1B_ENST00000333732.7_Missense_Mutation_p.M118K|ANKS1B_ENST00000549025.2_Missense_Mutation_p.M186K|ANKS1B_ENST00000549493.2_Missense_Mutation_p.M338K|ANKS1B_ENST00000549558.2_Missense_Mutation_p.M254K|ANKS1B_ENST00000341752.7_Missense_Mutation_p.M94K|ANKS1B_ENST00000547010.1_Missense_Mutation_p.M604K	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	1088	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.M1088K(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACTTACCCGCATTTTTGCACA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											108	103	105					12																	99192716		1818	4076	5894	97716847	SO:0001583	missense	56899			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3263T>A	12.37:g.99192716A>T	ENSP00000449629:p.Met1088Lys		97716847	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.5|27.5	4.833239|4.833239	0.91036|0.91036	.|.	.|.	ENSG00000185046|ENSG00000185046	ENST00000550778|ENST00000341752;ENST00000549558;ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000333732;ENST00000546568;ENST00000332712;ENST00000407362;ENST00000546960	.|T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.19669	.|2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.93|5.93	5.93|5.93	0.95920|0.95920	.|Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.45337|0.45337	0.1337|0.1337	M|M	0.61703|0.61703	1.905|1.905	0.58432|0.58432	D|D	0.999993|0.999993	.|P;D;D;P;D;D;P;P;D;D;D;D;P	.|0.64830	.|0.952;0.988;0.99;0.76;0.994;0.98;0.76;0.869;0.988;0.964;0.975;0.987;0.928	.|P;P;P;P;P;P;P;P;P;P;P;D;P	.|0.72982	.|0.647;0.717;0.814;0.66;0.896;0.701;0.66;0.563;0.717;0.681;0.883;0.979;0.775	T|T	0.38308|0.38308	-0.9667|-0.9667	5|10	.|0.87932	.|D	.|0	-15.393|-15.393	16.3797|16.3797	0.83452|0.83452	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|223;118;118;314;278;228;302;254;338;186;604;1088;254	.|F8VPM3;F8VR14;B7Z9I9;Q7Z6G8-4;Q7Z6G8-5;B1VKB5;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9;Q7Z6G8-6;Q7Z6G8;Q7Z6G8-7	.|.;.;.;.;.;.;.;.;.;.;.;ANS1B_HUMAN;.	S|K	360|94;254;1088;604;1088;603;278;186;338;223;118;254;278;179;314	.|ENSP00000345510:M94K;ENSP00000448993:M254K;ENSP00000449629:M1088K;ENSP00000448512:M604K;ENSP00000331381:M1088K;ENSP00000447999:M278K;ENSP00000447312:M186K;ENSP00000448203:M338K;ENSP00000450015:M223K;ENSP00000331256:M118K;ENSP00000448205:M254K;ENSP00000332683:M278K;ENSP00000447839:M314K	.|ENSP00000331381:M1088K	C|M	-|-	1|2	0|0	ANKS1B|ANKS1B	97716847|97716847	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	8.562000|8.562000	0.90719|0.90719	2.271000|2.271000	0.75665|0.75665	0.533000|0.533000	0.62120|0.62120	TGC|ATG		0.333	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		T	99192716	A	T	99192716	3	4	53	1	0	0	0	0	1	0	0	0	689	217	8	5	622	5	ANKS1B	12	99192716	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	44517123	99192716	34659179	101	7186										
TMEM132D	121256	broad.mit.edu	37	chr12	129558551	129558551	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gttcctggtggggtactcgtCgtctgaggagacggcggtga	18	8	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:129558551C>T	ENST00000422113.2	-	9	3495	c.3169G>A	c.(3169-3171)Gac>Aac	p.D1057N	TMEM132D_ENST00000389441.4_Missense_Mutation_p.D595N	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	1057					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.D1057N(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		GGGTACTCGTCGTCTGAGGAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	12											153	150	151					12																	129558551		2203	4300	6503	128124504	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.3169G>A	12.37:g.129558551C>T	ENSP00000408581:p.Asp1057Asn		128124504	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513069	0.44660	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.10192	2.9;3.69	4.16	4.16	0.48862	.	0.175073	0.37577	N	0.002040	T	0.11793	0.0287	M	0.65975	2.015	0.24021	N	0.996143	P;B	0.48230	0.907;0.17	B;B	0.31495	0.131;0.016	T	0.28713	-1.0035	9	.	.	.	-15.9856	16.8313	0.85945	0.0:1.0:0.0:0.0	.	1057;595	Q14C87;Q14C87-2	T132D_HUMAN;.	N	595;1057	ENSP00000374092:D595N;ENSP00000408581:D1057N	.	D	-	1	0	TMEM132D	128124504	0.001000	0.12720	0.002000	0.10522	0.008000	0.06430	1.239000	0.32719	2.018000	0.59344	0.563000	0.77884	GAC		0.512	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	129558551	C	T	129558551	3	4	53	1	0	0	0	0	1	0	0	0	16086	884	31	1	134	1	TMEM132D	12	129558551	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	30365835	129558551	4293344	102	7187										
STX2	2054	broad.mit.edu	37	chr12	131297522	131297522	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cctttaacttggctcgaattTtattcgcagttttcttgatt	6	8	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr12:131297522T>G	ENST00000392373.2	-	4	354	c.260A>C	c.(259-261)aAa>aCa	p.K87T	RP11-989F5.1_ENST00000546264.1_lincRNA|RP11-989F5.3_ENST00000542821.1_lincRNA|snoU13_ENST00000459050.1_RNA|STX2_ENST00000261653.6_Missense_Mutation_p.K87T	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	87					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)	p.K87T(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		GGCTCGAATTTTATTCGCAGT	0.259																																																2	Substitution - Missense(2)	large_intestine(2)	12											95	99	98					12																	131297522		2202	4296	6498	129863475	SO:0001583	missense	2054			D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"epimorphin"	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.260A>C	12.37:g.131297522T>G	ENSP00000376178:p.Lys87Thr		129863475	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.911874	0.33721	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.20200	2.09;2.09	4.38	2.04	0.26737	t-SNARE (1);Syntaxin, N-terminal (2);	0.354250	0.32231	N	0.006387	T	0.21347	0.0514	M	0.70903	2.155	0.27454	N	0.953349	B;B;B	0.17268	0.021;0.008;0.015	B;B;B	0.19946	0.011;0.011;0.027	T	0.16660	-1.0395	10	0.32370	T	0.25	-14.6089	7.8165	0.29263	0.0:0.1566:0.0:0.8434	.	87;87;87	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	T	87	ENSP00000261653:K87T;ENSP00000376178:K87T	ENSP00000261653:K87T	K	-	2	0	STX2	129863475	0.936000	0.31750	0.480000	0.27341	0.712000	0.41017	1.439000	0.35013	0.333000	0.23563	0.533000	0.62120	AAA		0.259	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356		G	131297522	T	G	131297522	3	3	53	1	0	0	0	0	1	0	0	0	15384	1841	64	4	716	4	STX2	12	131297522	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09	1738971	131297522	2554373	103	7188										
KIAA0564	23078	broad.mit.edu	37	chr13	42465571	42465571	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cttactcggagaagtttgtcGtaacgctcagcagacatcag	10	10	2	2	rs57255143		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr13:42465571G>T	ENST00000379310.3	-	5	704	c.636C>A	c.(634-636)taC>taA	p.Y212*	VWA8_ENST00000281496.6_Nonsense_Mutation_p.Y212*	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	212						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.Y212*(1)									GAAGTTTGTCGTAACGCTCAG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											158	149	152					13																	42465571		2203	4300	6503	41363571	SO:0001587	stop_gained	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.636C>A	13.37:g.42465571G>T	ENSP00000368612:p.Tyr212*		41363571	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Nonsense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	G	34	5.322326	0.95708	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	.	.	.	5.71	-9.4	0.00616	.	0.153522	0.43747	D	0.000529	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	21.3045	0.99951	0.8612:0.0:0.1388:0.0	.	.	.	.	X	116;212;212;212	.	ENSP00000251030:Y116X	Y	-	3	2	KIAA0564	41363571	0.001000	0.12720	0.058000	0.19502	0.955000	0.61496	-1.350000	0.02624	-2.368000	0.00604	-0.808000	0.03180	TAC		0.438	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42465571	G	T	42465571	4	4	53	1	0	0	0	0	0	1	0	0	8206	1140	40	2	5249	2	KIAA0564	13	42465571	Nonsense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09		42465571	72704307	104	7189										
AKAP11	11215	broad.mit.edu	37	chr13	42875055	42875055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttagtgtctctacggataatAtcaagtatgtgagtgcagaa	10	5	2	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr13:42875055A>G	ENST00000025301.2	+	8	2348	c.2173A>G	c.(2173-2175)Atc>Gtc	p.I725V		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	725					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.I725V(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TACGGATAATATCAAGTATGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											147	137	140					13																	42875055		2203	4300	6503	41773055	SO:0001583	missense	11215			AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2173A>G	13.37:g.42875055A>G	ENSP00000025301:p.Ile725Val		41773055	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.896971	0.00517	.	.	ENSG00000023516	ENST00000025301	T	0.15487	2.42	5.98	-2.45	0.06481	.	0.712950	0.13507	N	0.382818	T	0.05777	0.0151	N	0.04880	-0.145	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.41980	-0.9478	10	0.06365	T	0.9	.	8.9651	0.35872	0.3292:0.2141:0.4567:0.0	.	725	Q9UKA4	AKA11_HUMAN	V	725	ENSP00000025301:I725V	ENSP00000025301:I725V	I	+	1	0	AKAP11	41773055	0.293000	0.24371	0.000000	0.03702	0.013000	0.08279	0.573000	0.23699	-0.630000	0.05567	0.482000	0.46254	ATC		0.408	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42875055	A	G	42875055	3	3	53	1	0	0	0	0	1	0	0	0	447	449	16	4	2195	4	AKAP11	13	42875055	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	409484	42875055	72294823	105	7190										
SERPINE3	647174	broad.mit.edu	37	chr13	51929218	51929218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttcaacttaaaaagcattttAaattcttggggagtcaccga	7	7	3	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr13:51929218A>C	ENST00000521255.1	+	5	999	c.939A>C	c.(937-939)ttA>ttC	p.L313F	SERPINE3_ENST00000524365.1_Missense_Mutation_p.L313F|SERPINE3_ENST00000400389.4_Missense_Mutation_p.L313F	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	313					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L313F(1)		ovary(2)	2						AAAGCATTTTAAATTCTTGGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											58	52	54					13																	51929218		1782	4017	5799	50827219	SO:0001583	missense	647174			AX772926	CCDS53870.1	13q14.3	2014-02-18			ENSG00000253309	ENSG00000253309		"Serine (or cysteine) peptidase inhibitors"	24774	protein-coding gene	gene with protein product						24172014	Standard	NM_001101320		Approved		uc001vfh.2	A8MV23	OTTHUMG00000016943	ENST00000521255.1:c.939A>C	13.37:g.51929218A>C	ENSP00000428316:p.Leu313Phe		50827219	B1V8P3	Missense_Mutation	SNP	ENST00000521255.1	37	CCDS53870.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020547	0.35606	.	.	ENSG00000253309	ENST00000524365;ENST00000521255;ENST00000400389	D;D;D	0.95035	-3.59;-3.59;-3.59	4.69	3.52	0.40303	Serpin domain (3);	0.158172	0.29646	U	0.011569	D	0.95614	0.8574	M	0.80332	2.49	0.54753	D	0.999986	D;P	0.58268	0.982;0.898	P;P	0.58520	0.84;0.567	D	0.94319	0.7552	10	0.87932	D	0	.	5.9336	0.19152	0.7981:0.0:0.2019:0.0	.	313;313	A8MV23-2;A8MV23	.;SERP3_HUMAN	F	313	ENSP00000430755:L313F;ENSP00000428316:L313F;ENSP00000441468:L313F	ENSP00000441468:L313F	L	+	3	2	SERPINE3	50827219	0.671000	0.27521	0.717000	0.30585	0.736000	0.42039	0.770000	0.26618	0.844000	0.35094	0.460000	0.39030	TTA		0.338	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320		C	51929218	A	C	51929218	3	2	53	1	0	0	0	0	1	0	0	0	14150	359	13	4	957	4	SERPINE3	13	51929218	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	9054163	51929218	63240660	106	7191										
HECTD1	25831	broad.mit.edu	37	chr14	31617997	31617997	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cagtccagccagtcacaaatTctgaaccttggggggaaaaa	10	10	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:31617997T>A	ENST00000399332.1	-	15	2914	c.2426A>T	c.(2425-2427)gAa>gTa	p.E809V	HECTD1_ENST00000553700.1_Missense_Mutation_p.E809V	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	809					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.E809V(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		AGTCACAAATTCTGAACCTTG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											81	76	78					14																	31617997		1797	4062	5859	30687748	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2426A>T	14.37:g.31617997T>A	ENSP00000382269:p.Glu809Val		30687748	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826007	0.71143	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	6.1	6.1	0.99115	Armadillo-type fold (1);	0.069128	0.56097	U	0.000035	T	0.33440	0.0863	L	0.54323	1.7	0.80722	D	1	D;P	0.67145	0.996;0.759	P;B	0.56788	0.806;0.245	T	0.02121	-1.1210	10	0.87932	D	0	-15.2432	16.3594	0.83251	0.0:0.0:0.0:1.0	.	809;809	D3DS86;Q9ULT8	.;HECD1_HUMAN	V	809;809;809;283;809	ENSP00000450697:E809V;ENSP00000382269:E809V;ENSP00000451860:E283V;ENSP00000452015:E809V	ENSP00000261312:E809V	E	-	2	0	HECTD1	30687748	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.021000	0.88750	2.340000	0.79590	0.528000	0.53228	GAA		0.323	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31617997	T	A	31617997	3	1	53	1	0	0	0	0	1	0	0	0	7060	1783	62	5	5522	5	HECTD1	14	31617997	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09		31617997	75731543	107	7192										
EXOC5	10640	broad.mit.edu	37	chr14	57676674	57676674	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgaatgattttactcacattAgtatattgaatcaaaacatt	4	5	2	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:57676674A>C	ENST00000413566.2	-	16	2078	c.1719T>G	c.(1717-1719)acT>acG	p.T573T	EXOC5_ENST00000340918.7_Silent_p.T508T	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	573					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.T575T(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						TACTCACATTAGTATATTGAA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	14											59	54	56					14																	57676674		1831	4062	5893	56746427	SO:0001819	synonymous_variant	10640			U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"SEC10 (S. cerevisiae)-like 1", "SEC10-like 1 (S. cerevisiae)"	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1719T>G	14.37:g.57676674A>C			56746427	B2R6C5	Silent	SNP	ENST00000413566.2	37	CCDS45111.1																																																																																				0.284	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		C	57676674	A	C	57676674	2	2	53	1	0	0	0	0	0	0	0	1	5320	407	15	4		4	EXOC5	14	57676674	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	26058677	57676674	49672866	108	7193										
TOMM20L	387990	broad.mit.edu	37	chr14	58874096	58874096	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aatgcccttttagtgtgcgaGcaaccacgggaacttctgaa	10	10	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:58874096G>A	ENST00000360945.2	+	4	357	c.315G>A	c.(313-315)gaG>gaA	p.E105E	TIMM9_ENST00000216463.4_5'Flank|RP11-517O13.1_ENST00000556734.1_RNA	NM_207377.2	NP_997260.1	Q6UXN7	TO20L_HUMAN	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	105					protein targeting (GO:0006605)	integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)		p.E105E(1)		large_intestine(2)|lung(2)	4						TAGTGTGCGAGCAACCACGGG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	14											103	98	99					14																	58874096		2203	4300	6503	57943849	SO:0001819	synonymous_variant	387990				CCDS9734.1	14q23.1	2009-01-14			ENSG00000196860	ENSG00000196860			33752	protein-coding gene	gene with protein product	"translocase of outer mitochondrial membrane 20 homolog type I"					15733919	Standard	NM_207377		Approved	UNQ9438	uc001xdr.1	Q6UXN7	OTTHUMG00000140323	ENST00000360945.2:c.315G>A	14.37:g.58874096G>A			57943849	B2RPR0	Silent	SNP	ENST00000360945.2	37	CCDS9734.1																																																																																				0.428	TOMM20L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276937.1	NM_207377		A	58874096	G	A	58874096	2	1	53	1	0	0	0	0	0	0	0	1	16394	962	34	3		3	TOMM20L	14	58874096	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09	1197422	58874096	48475444	109	7194										
GPHN	10243	broad.mit.edu	37	chr14	67646310	67646310	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgtagttatcatgtgatgtaAaacttgatcctcgtccagaa	8	7	1	3			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:67646310A>C	ENST00000315266.5	+	21	3117	c.1996A>C	c.(1996-1998)Aaa>Caa	p.K666Q	GPHN_ENST00000478722.1_Missense_Mutation_p.K699Q|GPHN_ENST00000305960.9_Missense_Mutation_p.K635Q|GPHN_ENST00000543237.1_Missense_Mutation_p.K712Q|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	666	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)	p.K699Q(1)		large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		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)		ATGTGATGTAAAACTTGATCC	0.388			T	MLL	AL																																		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	1	Substitution - Missense(1)	large_intestine(1)	14											149	118	129					14																	67646310		2203	4300	6503	66716063	SO:0001583	missense	10243			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1996A>C	14.37:g.67646310A>C	ENSP00000312771:p.Lys666Gln		66716063	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.437742	0.62955	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.79	5.79	0.91817	MoeA, C-terminal, domain IV (3);	0.000000	0.85682	D	0.000000	T	0.59155	0.2173	L	0.57536	1.79	0.80722	D	1	B;B;B;B	0.33583	0.161;0.418;0.123;0.077	B;B;B;B	0.28385	0.039;0.089;0.066;0.069	T	0.62845	-0.6768	9	0.66056	D	0.02	-10.2587	16.1342	0.81471	1.0:0.0:0.0:0.0	.	635;712;666;699	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	Q	666;699;712;635	.	ENSP00000303019:K635Q	K	+	1	0	GPHN	66716063	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.237000	0.95368	2.209000	0.71365	0.533000	0.62120	AAA		0.388	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67646310	A	C	67646310	3	2	53	1	0	0	0	0	1	0	0	0	6630	15	1	4	2181	4	GPHN	14	67646310	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	8772214	67646310	39703230	110	7195										
FAM164C	79696	broad.mit.edu	37	chr14	75538609	75538609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	actggaaggggccagcttcaGccaaggtaacaagagcctta	12	10	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:75538609G>A	ENST00000524913.1	+	2	1822	c.1333G>A	c.(1333-1335)Gcc>Acc	p.A445T	ZC2HC1C_ENST00000238686.8_Intron|ACYP1_ENST00000555463.1_5'Flank|ZC2HC1C_ENST00000439583.2_Intron|ZC2HC1C_ENST00000526748.1_Intron	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	445							metal ion binding (GO:0046872)	p.A445T(1)									GCCAGCTTCAGCCAAGGTAAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	14											39	40	40					14																	75538609		1968	4145	6113	74608362	SO:0001583	missense	79696			AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"Zinc fingers, C2HC-type containing"	20354	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 140", "family with sequence similarity 164, member C"	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.1333G>A	14.37:g.75538609G>A	ENSP00000435550:p.Ala445Thr		74608362	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	37	CCDS41972.1	.	.	.	.	.	.	.	.	.	.	G	10.64	1.406127	0.25378	.	.	ENSG00000119703	ENST00000524913	T	0.46451	0.87	5.01	3.19	0.36642	.	1.181490	0.06382	N	0.715439	T	0.25158	0.0611	N	0.19112	0.55	0.09310	N	0.999999	B	0.29716	0.255	B	0.24394	0.053	T	0.23119	-1.0197	9	.	.	.	-1.4665	3.8568	0.08979	0.1536:0.1373:0.5831:0.1261	.	445	E9PJQ0	.	T	445	ENSP00000435550:A445T	.	A	+	1	0	FAM164C	74608362	0.000000	0.05858	0.090000	0.20809	0.983000	0.72400	0.737000	0.26144	0.830000	0.34757	0.655000	0.94253	GCC		0.493	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430		A	75538609	G	A	75538609	3	1	53	1	0	0	0	0	1	0	0	0	5495	971	34	3	1335	3	FAM164C	14	75538609	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	7892299	75538609	31810931	111	7196										
EML1	2009	broad.mit.edu	37	chr14	100361034	100361034	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	acatgcccaaagatcaagtgGattcttacagcttggaagca	9	9	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr14:100361034G>C	ENST00000262233.6	+	6	755	c.616G>C	c.(616-618)Gat>Cat	p.D206H	EML1_ENST00000327921.9_Missense_Mutation_p.D194H|EML1_ENST00000334192.4_Missense_Mutation_p.D225H	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	206	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.D225H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGATCAAGTGGATTCTTACAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	14											124	109	114					14																	100361034		2203	4300	6503	99430787	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.616G>C	14.37:g.100361034G>C	ENSP00000262233:p.Asp206His		99430787	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829029	0.90955	.	.	ENSG00000066629	ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138;ENST00000556714	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.32	5.32	0.75619	HELP (1);	0.190072	0.56097	D	0.000040	T	0.39937	0.1097	L	0.29908	0.895	0.80722	D	1	P;P;B;P;P	0.48162	0.676;0.906;0.011;0.676;0.723	P;P;B;P;P	0.49226	0.603;0.571;0.063;0.603;0.576	T	0.29274	-1.0017	10	0.62326	D	0.03	-15.1866	18.9766	0.92740	0.0:0.0:1.0:0.0	.	194;194;206;225;225	F8W717;B7Z650;O00423;O00423-3;B3KXA3	.;.;EMAL1_HUMAN;.;.	H	193;194;206;225;225;175	ENSP00000451346:D193H;ENSP00000327384:D194H;ENSP00000262233:D206H;ENSP00000334314:D225H;ENSP00000452089:D175H	ENSP00000262233:D206H	D	+	1	0	EML1	99430787	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	9.869000	0.99810	2.471000	0.83476	0.585000	0.79938	GAT		0.383	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		C	100361034	G	C	100361034	3	2	53	1	0	0	0	0	1	0	0	0	5109	1174	41	5	699	5	EML1	14	100361034	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	24822425	100361034	6988506	112	7197										
RYR3	6263	broad.mit.edu	37	chr15	33927942	33927942	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	actggaggagacatgcgagtCggctgggcgaggccaggctg	19	9	0	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr15:33927942C>T	ENST00000389232.4	+	26	3373	c.3303C>T	c.(3301-3303)gtC>gtT	p.V1101V	RYR3_ENST00000415757.3_Silent_p.V1101V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1101	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.V1101V(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACATGCGAGTCGGCTGGGCGA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	15											62	65	64					15																	33927942		2027	4198	6225	31715234	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3303C>T	15.37:g.33927942C>T			31715234	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.502	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33927942	C	T	33927942	2	4	53	1	0	0	0	0	0	0	0	1	13807	871	31	1		1	RYR3	15	33927942	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09		33927942	68603450	113	7198										
LEO1	123169	broad.mit.edu	37	chr15	52258693	52258693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	agaatctgagtcagatccagAatcagaatctatggggtcat	10	7	5	5			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr15:52258693A>T	ENST00000299601.5	-	2	127	c.67T>A	c.(67-69)Tct>Act	p.S23T	LEO1_ENST00000315141.5_Missense_Mutation_p.S23T	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	23	Asp-rich.				endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)		p.S23T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		TCAGATCCAGAATCAGAATCT	0.418																																					Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)											1	Substitution - Missense(1)	large_intestine(1)	15											78	76	77					15																	52258693		2190	4292	6482	50045985	SO:0001583	missense	123169			AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.67T>A	15.37:g.52258693A>T	ENSP00000299601:p.Ser23Thr		50045985	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	37	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.131372	0.77549	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	L	0.34521	1.04	0.80722	D	1	D;D	0.58268	0.974;0.982	D;D	0.70487	0.969;0.952	T	0.65372	-0.6184	9	0.39692	T	0.17	.	15.5373	0.76013	1.0:0.0:0.0:0.0	.	23;23	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	T	23	.	ENSP00000299601:S23T	S	-	1	0	LEO1	50045985	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.153000	0.89640	2.068000	0.61886	0.460000	0.39030	TCT		0.418	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		T	52258693	A	T	52258693	3	4	53	1	0	0	0	0	1	0	0	0	8748	246	9	5	1977	5	LEO1	15	52258693	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09	18330751	52258693	50272699	114	7199										
CCPG1	9236	broad.mit.edu	37	chr15	55664032	55664032	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgctgattgcaatcaccaaaGcaagtataacacacttattg	6	9	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr15:55664032G>T	ENST00000310958.6	-	6	963	c.665C>A	c.(664-666)gCt>gAt	p.A222D	CCPG1_ENST00000569205.1_Missense_Mutation_p.A222D|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Missense_Mutation_p.A222D|MIR628_ENST00000385229.1_RNA|CCPG1_ENST00000425574.3_Missense_Mutation_p.A222D	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	222	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)		p.A222D(1)		autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		AATCACCAAAGCAAGTATAAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	15											120	107	111					15																	55664032		1899	4119	6018	53451324	SO:0001583	missense	9236			AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.665C>A	15.37:g.55664032G>T	ENSP00000311656:p.Ala222Asp		53451324	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394725	0.83011	.	.	ENSG00000256061	ENST00000310958;ENST00000442196;ENST00000425574	T;T;T	0.51817	3.03;3.03;0.69	5.74	4.82	0.62117	.	0.049620	0.85682	D	0.000000	T	0.69566	0.3125	M	0.78916	2.43	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.74765	-0.3554	10	0.87932	D	0	.	15.3284	0.74186	0.0:0.0:0.8594:0.1406	.	222;222;222;78	A8K9T0;Q9ULG6-3;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	D	222	ENSP00000311656:A222D;ENSP00000403400:A222D;ENSP00000415128:A222D	ENSP00000311656:A222D	A	-	2	0	DYX1C1	53451324	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.778000	0.85637	1.416000	0.47057	0.655000	0.94253	GCT		0.393	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748		T	55664032	G	T	55664032	3	4	53	1	0	0	0	0	1	0	0	0	2944	971	34	2	1620	2	CCPG1	15	55664032	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	3405339	55664032	46867360	115	7200										
TLN2	83660	broad.mit.edu	37	chr15	63063276	63063276	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctggaccagaccaagactctCgcagagtctgccttgcagat	10	13	2	4	rs200255870	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr15:63063276C>T	ENST00000561311.1	+	41	5540	c.5310C>T	c.(5308-5310)ctC>ctT	p.L1770L	TLN2_ENST00000472902.1_Silent_p.L163L|TLN2_ENST00000306829.6_Silent_p.L1770L			Q9Y4G6	TLN2_HUMAN	talin 2	1770					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.L1770L(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCAAGACTCTCGCAGAGTCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C		1,4405	2.1+/-5.4	0,1,2202	119	108	112		5310	-10.8	0	15		112	0,8600		0,0,4300	no	coding-synonymous	TLN2	NM_015059.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1770/2543	63063276	1,13005	2203	4300	6503	60850568	SO:0001819	synonymous_variant	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.5310C>T	15.37:g.63063276C>T			60850568	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																				0.517	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63063276	C	T	63063276	2	4	53	1	0	0	0	0	0	0	0	1	15987	871	31	1		1	TLN2	15	63063276	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	7399244	63063276	39468116	116	7201										
ALPK3	57538	broad.mit.edu	37	chr15	85402523	85402523	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gagcagtttcctgatgcctcCggtagcctgaagctgtggtg	14	10	0	2	rs188837127	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr15:85402523C>A	ENST00000258888.5	+	7	4640	c.4473C>A	c.(4471-4473)tcC>tcA	p.S1491S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1491	Ig-like 2.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S1491S(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTGATGCCTCCGGTAGCCTGA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	15											91	77	82					15																	85402523		2203	4299	6502	83203527	SO:0001819	synonymous_variant	57538			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4473C>A	15.37:g.85402523C>A			83203527	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																				0.582	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85402523	C	A	85402523	2	1	53	1	0	0	0	0	0	0	0	1	546	639	23	2		2	ALPK3	15	85402523	Silent	SNP	C	TCGA-AG-3902-01A-01W-1073-09	22339247	85402523	17128869	117	7202										
TP53	7157	broad.mit.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	53	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09		7577120	73618090	118	7203										
CCDC144A	9720	broad.mit.edu	37	chr17	16593740	16593740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctcctggggtggagaaaagcGgggaggggctgaggggtctc	21	7	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr17:16593740G>A	ENST00000360524.8	+	1	102	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	CCDC144A_ENST00000340621.5_Missense_Mutation_p.R9Q|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.R9Q|CCDC144A_ENST00000443444.2_Missense_Mutation_p.R9Q|CCDC144A_ENST00000456009.1_Missense_Mutation_p.R9Q|RNU6-405P_ENST00000516637.1_RNA|CCDC144A_ENST00000436374.1_3'UTR|CCDC144A_ENST00000399273.1_Missense_Mutation_p.R9Q	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	9								p.R9Q(1)									GGAGAAAAGCGGGGAGGGGCT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											13	16	15					17																	16593740		2197	4293	6490	16534465	SO:0001583	missense	9720			BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.26G>A	17.37:g.16593740G>A	ENSP00000353717:p.Arg9Gln		16534465	O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	37	CCDS45621.1	.	.	.	.	.	.	.	.	.	.	.	10.09	1.254907	0.22965	.	.	ENSG00000170160	ENST00000420937;ENST00000340621;ENST00000399273;ENST00000436374;ENST00000399264;ENST00000443444;ENST00000448331;ENST00000360524;ENST00000456009;ENST00000360495	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	0.407	0.407	0.16371	.	.	.	.	.	T	0.14485	0.0350	N	0.22421	0.69	0.09310	N	1	P	0.36065	0.535	B	0.14023	0.01	T	0.12734	-1.0536	8	0.52906	T	0.07	.	.	.	.	.	9	A2RUR9	C144A_HUMAN	Q	9	ENSP00000344740:R9Q;ENSP00000382215:R9Q;ENSP00000439262:R9Q;ENSP00000440655:R9Q;ENSP00000353717:R9Q;ENSP00000394201:R9Q;ENSP00000353685:R9Q	ENSP00000344740:R9Q	R	+	2	0	CCDC144A	16534465	0.323000	0.24643	0.001000	0.08648	0.022000	0.10575	0.199000	0.17237	0.443000	0.26582	0.184000	0.17185	CGG		0.657	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			A	16593740	G	A	16593740	3	1	53	1	0	0	0	0	1	0	0	0	2783	1116	39	1	28	1	CCDC144A	17	16593740	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	9016620	16593740	64601470	119	7204										
ERBB2	2064	broad.mit.edu	37	chr17	37881332	37881332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	acctggaggatgtgcggctcGtacacagggacttggccgct	15	11	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr17:37881332G>A	ENST00000269571.5	+	21	2683	c.2524G>A	c.(2524-2526)Gta>Ata	p.V842I	MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000541774.1_Missense_Mutation_p.V827I|ERBB2_ENST00000445658.2_Missense_Mutation_p.V566I|ERBB2_ENST00000584601.1_Missense_Mutation_p.V812I|ERBB2_ENST00000406381.2_Missense_Mutation_p.V812I|ERBB2_ENST00000540147.1_Missense_Mutation_p.V812I|ERBB2_ENST00000584450.1_Missense_Mutation_p.V842I			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	842	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.V842I(6)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGTGCGGCTCGTACACAGGGA	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	6	Substitution - Missense(6)	large_intestine(5)|stomach(1)	17											70	61	64					17																	37881332		2203	4300	6503	35134858	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2524G>A	17.37:g.37881332G>A	ENSP00000269571:p.Val842Ile		35134858	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.241303	0.58995	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	5.09	5.09	0.68999	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.85106	0.5621	N	0.21142	0.635	0.80722	D	1	D;D;D	0.76494	0.997;0.979;0.999	D;P;D	0.64506	0.92;0.559;0.926	D	0.87344	0.2333	9	0.87932	D	0	.	18.2846	0.90110	0.0:0.0:1.0:0.0	.	566;827;842	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	I	812;827;566;842;812	ENSP00000385185:V812I;ENSP00000446466:V827I;ENSP00000404047:V566I;ENSP00000269571:V842I;ENSP00000443562:V812I	ENSP00000269571:V842I	V	+	1	0	ERBB2	35134858	1.000000	0.71417	0.919000	0.36401	0.900000	0.52787	9.657000	0.98554	2.651000	0.90000	0.563000	0.77884	GTA		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37881332	G	A	37881332	3	1	53	1	0	0	0	0	1	0	0	0	5219	1145	40	1	2606	1	ERBB2	17	37881332	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	21287592	37881332	43313878	120	7205										
NFIC	4782	broad.mit.edu	37	chr19	3434304	3434304	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	tgactggaacaggacccaacTtctccctgggggagctgcag	13	12	1	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr19:3434304T>G	ENST00000443272.2	+	5	790	c.739T>G	c.(739-741)Ttc>Gtc	p.F247V	NFIC_ENST00000586919.1_Missense_Mutation_p.F214V|NFIC_ENST00000589123.1_Missense_Mutation_p.F238V|NFIC_ENST00000346156.5_Missense_Mutation_p.F214V|NFIC_ENST00000590282.1_Missense_Mutation_p.F247V|NFIC_ENST00000341919.3_Missense_Mutation_p.F247V|NFIC_ENST00000395111.3_Missense_Mutation_p.F238V	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	247					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F238V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		AGGACCCAACTTCTCCCTGGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											101	95	97					19																	3434304		2203	4300	6503	3385304	SO:0001583	missense	4782			X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.739T>G	19.37:g.3434304T>G	ENSP00000396843:p.Phe247Val		3385304	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	37	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.672397	0.67928	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.59364	0.27;0.27;0.27	3.48	3.48	0.39840	.	0.142329	0.50627	D	0.000102	T	0.70789	0.3264	M	0.76838	2.35	0.47862	D	0.999537	P;D;P;D;D	0.61697	0.891;0.99;0.867;0.988;0.976	P;P;B;P;P	0.61722	0.596;0.893;0.269;0.829;0.743	T	0.73461	-0.3975	10	0.52906	T	0.07	.	10.9743	0.47456	0.0:0.0:0.0:1.0	.	247;247;238;247;238	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	V	238;238;214;247;247;247	ENSP00000378543:F238V;ENSP00000301935:F214V;ENSP00000342194:F247V	ENSP00000269778:F247V	F	+	1	0	NFIC	3385304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.752000	0.74898	1.459000	0.47892	0.379000	0.24179	TTC		0.612	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		G	3434304	T	G	3434304	3	3	53	1	0	0	0	0	1	0	0	0	10403	1609	56	4	764	4	NFIC	19	3434304	Missense_Mutation	SNP	T	TCGA-AG-3902-01A-01W-1073-09		3434304	55694679	121	7206										
RAB11B	9230	broad.mit.edu	37	chr19	8467073	8467073	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aggagctgcgggaccacgcaGacagcaacatcgtcatcatg	12	12	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr19:8467073G>T	ENST00000328024.6	+	3	558	c.340G>T	c.(340-342)Gac>Tac	p.D114Y	RAB11B_ENST00000601897.1_5'UTR|RAB11B_ENST00000594216.1_Missense_Mutation_p.D114Y	NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	114					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.D114Y(1)		large_intestine(2)|lung(1)|ovary(1)	4						GGACCACGCAGACAGCAACAT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											72	41	52					19																	8467073		2201	4299	6500	8373073	SO:0001583	missense	9230			X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"RAB, member RAS oncogene"	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.340G>T	19.37:g.8467073G>T	ENSP00000333547:p.Asp114Tyr		8373073	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Missense_Mutation	SNP	ENST00000328024.6	37	CCDS12201.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.024112	0.54683	.	.	ENSG00000185236	ENST00000328024	T	0.77750	-1.12	4.65	3.59	0.41128	Small GTP-binding protein domain (1);	0.095427	0.64402	D	0.000001	T	0.81809	0.4901	L	0.40543	1.245	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.68621	0.959;0.955	D	0.83628	0.0143	10	0.87932	D	0	.	13.1333	0.59395	0.0:0.0:0.8384:0.1616	.	114;114	B4DMK0;Q15907	.;RB11B_HUMAN	Y	114	ENSP00000333547:D114Y	ENSP00000333547:D114Y	D	+	1	0	RAB11B	8373073	1.000000	0.71417	0.855000	0.33649	0.252000	0.25951	9.657000	0.98554	1.290000	0.44636	0.561000	0.74099	GAC		0.642	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218		T	8467073	G	T	8467073	3	4	53	1	0	0	0	0	1	0	0	0	12929	942	33	2	350	2	RAB11B	19	8467073	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	5032769	8467073	50661910	122	7207										
PDCD2L	84306	broad.mit.edu	37	chr19	34916980	34916980	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	catcagactcccatggaagaAttttgtattatacaagaaga	7	7	1	4			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr19:34916980A>G	ENST00000246535.3	+	7	1079	c.1032A>G	c.(1030-1032)gaA>gaG	p.E344E	PDCD2L_ENST00000587065.2_Silent_p.E42E|CTD-2588C8.8_ENST00000592220.1_RNA|UBA2_ENST00000439527.2_5'Flank|UBA2_ENST00000246548.4_5'Flank	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	344					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.E344E(1)		breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CCATGGAAGAATTTTGTATTA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	19											70	73	72					19																	34916980		2203	4300	6503	39608820	SO:0001819	synonymous_variant	84306			BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.1032A>G	19.37:g.34916980A>G			39608820		Silent	SNP	ENST00000246535.3	37	CCDS12438.1																																																																																				0.318	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		G	34916980	A	G	34916980	2	3	53	1	0	0	0	0	0	0	0	1	11651	98	4	4		4	PDCD2L	19	34916980	Silent	SNP	A	TCGA-AG-3902-01A-01W-1073-09	26449907	34916980	24212003	123	7208										
CADM4	199731	broad.mit.edu	37	chr19	44131040	44131040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cgccctctaccgcctgctccCggacctccaccacaggattc	7	21	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr19:44131040C>T	ENST00000222374.2	-	4	443	c.395G>A	c.(394-396)cGg>cAg	p.R132Q	CADM4_ENST00000593506.1_5'Flank	NM_145296.1	NP_660339.1	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4	132	Ig-like C2-type 1.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R132Q(1)		endometrium(2)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	12		Prostate(69;0.0199)				CGCCTGCTCCCGGACCTCCAC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	19											28	31	30					19																	44131040		2203	4300	6503	48822880	SO:0001583	missense	199731			AF363368	CCDS12627.1	19q13.32	2013-01-29	2007-02-07	2007-02-07		ENSG00000105767		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30825	protein-coding gene	gene with protein product	"nectin-like 4"	609744	"immunoglobulin superfamily, member 4C"	IGSF4C		11536053	Standard	NM_145296		Approved	TSLL2, Necl-4, SynCAM4	uc002oxc.1	Q8NFZ8		ENST00000222374.2:c.395G>A	19.37:g.44131040C>T	ENSP00000222374:p.Arg132Gln		48822880	B2R7L5|Q9Y4A4	Missense_Mutation	SNP	ENST00000222374.2	37	CCDS12627.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966960	0.53507	.	.	ENSG00000105767	ENST00000222374	T	0.75704	-0.96	5.62	3.52	0.40303	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.209202	0.38548	N	0.001645	T	0.52289	0.1725	N	0.17474	0.49	0.31161	N	0.704355	B	0.16396	0.017	B	0.16722	0.016	T	0.47005	-0.9150	10	0.14252	T	0.57	.	6.7186	0.23318	0.0:0.7344:0.0:0.2656	.	132	Q8NFZ8	CADM4_HUMAN	Q	132	ENSP00000222374:R132Q	ENSP00000222374:R132Q	R	-	2	0	CADM4	48822880	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.973000	0.40550	1.381000	0.46364	0.591000	0.81541	CGG		0.667	CADM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463352.1	NM_145296		T	44131040	C	T	44131040	3	4	53	1	0	0	0	0	1	0	0	0	2575	652	23	1	795	1	CADM4	19	44131040	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	9214060	44131040	14997943	124	7209										
EXOC3L2	90332	broad.mit.edu	37	chr19	45716583	45716583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	cggctgtgttgcgcaggccaCggatgtcgaggagggctgcc	18	11	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr19:45716583C>T	ENST00000252482.3	-	9	1001	c.974G>A	c.(973-975)cGt>cAt	p.R325H	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.R325H|AC006126.3_ENST00000591569.1_Intron			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	325					exocytosis (GO:0006887)	exocyst (GO:0000145)		p.R325H(1)		endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		GCGCAGGCCACGGATGTCGAG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											39	42	41					19																	45716583		2203	4300	6503	50408423	SO:0001583	missense	90332			AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.974G>A	19.37:g.45716583C>T	ENSP00000252482:p.Arg325His		50408423	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064226	0.76187	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.29142	1.58;1.58	4.39	4.39	0.52855	.	0.136296	0.48286	D	0.000196	T	0.54029	0.1833	M	0.75777	2.31	0.37754	D	0.926064	D	0.89917	1.0	D	0.97110	1.0	T	0.63743	-0.6568	10	0.87932	D	0	.	12.4574	0.55712	0.0:1.0:0.0:0.0	.	325	Q2M3D2	EX3L2_HUMAN	H	325	ENSP00000252482:R325H;ENSP00000400713:R325H	ENSP00000252482:R325H	R	-	2	0	EXOC3L2	50408423	0.999000	0.42202	0.842000	0.33263	0.617000	0.37484	5.375000	0.66173	1.983000	0.57843	0.455000	0.32223	CGT		0.672	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		T	45716583	C	T	45716583	3	4	53	1	0	0	0	0	1	0	0	0	5318	536	19	1	259	1	EXOC3L2	19	45716583	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	1585543	45716583	13412400	125	7210										
DEFB126	81623	broad.mit.edu	37	chr20	126092	126092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aaagtgtctaaacgacgttgGaatttgcaagaagaagtgca	11	5	1	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr20:126092G>A	ENST00000382398.3	+	2	355	c.95G>A	c.(94-96)gGa>gAa	p.G32E	DEFB126_ENST00000542572.1_3'UTR	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	32					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)		p.G32E(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AACGACGTTGGAATTTGCAAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	20											140	132	135					20																	126092		2203	4300	6503	74092	SO:0001583	missense	81623				CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"Defensins, beta"	15900	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 8"	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.95G>A	20.37:g.126092G>A	ENSP00000371835:p.Gly32Glu		74092	Q562G3|Q9H1M5	Missense_Mutation	SNP	ENST00000382398.3	37	CCDS12990.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.770367	0.49680	.	.	ENSG00000125788	ENST00000382398	T	0.63417	-0.04	3.74	3.74	0.42951	.	0.000000	0.46145	D	0.000316	T	0.64216	0.2578	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55829	-0.8079	10	0.87932	D	0	-31.0193	11.3542	0.49607	0.0:0.0:1.0:0.0	.	32	Q9BYW3	DB126_HUMAN	E	32	ENSP00000371835:G32E	ENSP00000371835:G32E	G	+	2	0	DEFB126	74092	0.457000	0.25752	0.037000	0.18230	0.005000	0.04900	3.056000	0.49923	2.371000	0.80710	0.561000	0.74099	GGA		0.383	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931		A	126092	G	A	126092	3	1	53	1	0	0	0	0	1	0	0	0	4422	1174	41	3	101	3	DEFB126	20	126092	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09		126092	62899428	126	7211										
CENPB	1059	broad.mit.edu	37	chr20	3765546	3765546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	atcctcctcatcatcatcgtCgtcttcatcttcatcatcct	2	16	8	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr20:3765546C>T	ENST00000379751.4	-	1	1791	c.1585G>A	c.(1585-1587)Gac>Aac	p.D529N	CDC25B_ENST00000344256.6_5'Flank|CDC25B_ENST00000379598.5_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	529	Asp/Glu-rich (acidic).				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)	p.D529N(1)		kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						tcatcatcgtcgtcttcatct	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	20											233	173	193					20																	3765546		2203	4300	6503	3713546	SO:0001583	missense	1059			X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"centromere protein B (80kD)"			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.1585G>A	20.37:g.3765546C>T	ENSP00000369075:p.Asp529Asn		3713546	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	37	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	C	5.735	0.320134	0.10845	.	.	ENSG00000125817	ENST00000379751;ENST00000536335	T	0.26223	1.75	4.32	4.32	0.51571	Centromere protein Cenp-B, dimerisation domain (1);	.	.	.	.	T	0.23611	0.0571	L	0.27053	0.805	0.21325	N	0.999724	D	0.55385	0.971	P	0.48189	0.57	T	0.06338	-1.0832	9	0.26408	T	0.33	.	12.2756	0.54733	0.0:1.0:0.0:0.0	.	529	P07199	CENPB_HUMAN	N	529;68	ENSP00000369075:D529N	ENSP00000369075:D529N	D	-	1	0	CENPB	3713546	0.255000	0.24002	0.133000	0.22050	0.021000	0.10359	3.285000	0.51716	1.952000	0.56665	0.655000	0.94253	GAC		0.537	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3765546	C	T	3765546	3	4	53	1	0	0	0	0	1	0	0	0	3233	884	31	1	218	1	CENPB	20	3765546	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	3639454	3765546	59259974	127	7212										
DSCAM	1826	broad.mit.edu	37	chr21	41450657	41450657	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	aagttggcctgcttctccgcGcagcccgcactgttgcacac	10	16	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr21:41450657G>A	ENST00000400454.1	-	26	5145	c.4668C>T	c.(4666-4668)tgC>tgT	p.C1556C		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1556	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.C1556C(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GCTTCTCCGCGCAGCCCGCAC	0.587																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - coding silent(1)	large_intestine(1)	21											75	79	78					21																	41450657		2190	4290	6480	40372527	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4668C>T	21.37:g.41450657G>A			40372527	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.587	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41450657	G	A	41450657	2	1	53	1	0	0	0	0	0	0	0	1	4779	1079	38	1		1	DSCAM	21	41450657	Silent	SNP	G	TCGA-AG-3902-01A-01W-1073-09		41450657	6679238	128	7213										
ITGB2	3689	broad.mit.edu	37	chr21	46306689	46306689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	gagcttctccttctcaaagcGcctgtactcccggaggtcgc	10	15	2	0	rs568682818	byFrequency	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr21:46306689G>A	ENST00000397850.2	-	16	2661	c.2209C>T	c.(2209-2211)Cgc>Tgc	p.R737C	ITGB2_ENST00000397852.1_Missense_Mutation_p.R737C|ITGB2_ENST00000355153.4_Missense_Mutation_p.R737C|ITGB2_ENST00000397857.1_Missense_Mutation_p.R737C|ITGB2_ENST00000302347.5_Missense_Mutation_p.R737C|ITGB2_ENST00000397854.3_Missense_Mutation_p.R680C			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	737					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.R737C(1)		breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	TTCTCAAAGCGCCTGTACTCC	0.612													G|||	2	0.000399361	0	0	5008	,	,		17604	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	21											100	83	89					21																	46306689		2203	4300	6503	45131117	SO:0001583	missense	3689			AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.2209C>T	21.37:g.46306689G>A	ENSP00000380948:p.Arg737Cys		45131117	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	37	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292327	0.40594	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347	D;D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65;-2.65	4.51	3.55	0.40652	Integrin beta subunit, cytoplasmic (2);	.	.	.	.	D	0.93644	0.7970	M	0.72894	2.215	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.93363	0.6728	9	0.87932	D	0	.	9.0891	0.36598	0.0:0.0:0.6439:0.3561	.	680;737	A8MYE6;P05107	.;ITB2_HUMAN	C	737;737;680;737;737;737	ENSP00000380950:R737C;ENSP00000380955:R737C;ENSP00000380952:R680C;ENSP00000347279:R737C;ENSP00000380948:R737C;ENSP00000303242:R737C	ENSP00000303242:R737C	R	-	1	0	ITGB2	45131117	1.000000	0.71417	0.976000	0.42696	0.091000	0.18340	2.861000	0.48380	2.055000	0.61198	0.655000	0.94253	CGC		0.612	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		A	46306689	G	A	46306689	3	1	53	1	0	0	0	0	1	0	0	0	7915	1087	38	1	108	1	ITGB2	21	46306689	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09	4856032	46306689	1823206	129	7214										
SLC25A18	83733	broad.mit.edu	37	chr22	18070018	18070018	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ttgcctgggagctgctccgcActcagggcctggctgggctc	15	14	1	0	rs201336926		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr22:18070018A>C	ENST00000327451.6	+	8	1064	c.526A>C	c.(526-528)Act>Cct	p.T176P	SLC25A18_ENST00000399813.1_Missense_Mutation_p.T176P|AC004019.13_ENST00000443935.1_RNA	NM_031481.1	NP_113669.1	Q9H1K4	GHC2_HUMAN	solute carrier family 25 (glutamate carrier), member 18	176						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	symporter activity (GO:0015293)	p.T176P(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)	18				Lung(27;0.124)		GCTGCTCCGCACTCAGGGCCT	0.662													A|||	1	0.000199681	0	0	5008	,	,		16786	0		0.001	False		,,,				2504	0				Colon(118;1560 1625 18964 29606 50093)											1	Substitution - Missense(1)	large_intestine(1)	22											72	71	72					22																	18070018		2203	4300	6503	16450018	SO:0001583	missense	83733			AY008285	CCDS13744.1	22q11.2	2013-05-22	2012-03-29		ENSG00000182902	ENSG00000182902		"Solute carriers"	10988	protein-coding gene	gene with protein product		609303	"solute carrier family 25 (mitochondrial carrier), member 18"			11381032, 11897791	Standard	NM_031481		Approved		uc002zmp.1	Q9H1K4	OTTHUMG00000150089	ENST00000327451.6:c.526A>C	22.37:g.18070018A>C	ENSP00000329033:p.Thr176Pro		16450018		Missense_Mutation	SNP	ENST00000327451.6	37	CCDS13744.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	15.67	2.901129	0.52227	.	.	ENSG00000182902	ENST00000327451;ENST00000399813	T;T	0.79454	-1.27;-1.27	4.95	3.9	0.45041	Mitochondrial carrier domain (2);	0.150965	0.64402	D	0.000016	D	0.87916	0.6298	M	0.92507	3.315	0.30223	N	0.796678	P	0.52463	0.953	P	0.59825	0.864	D	0.85943	0.1459	10	0.62326	D	0.03	.	10.3833	0.44125	0.9153:0.0:0.0847:0.0	.	176	Q9H1K4	GHC2_HUMAN	P	176	ENSP00000329033:T176P;ENSP00000382710:T176P	ENSP00000329033:T176P	T	+	1	0	SLC25A18	16450018	0.065000	0.20965	0.173000	0.22940	0.767000	0.43475	2.592000	0.46171	2.002000	0.58637	0.397000	0.26171	ACT		0.662	SLC25A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316214.3	NM_031481		C	18070018	A	C	18070018	3	2	53	1	0	0	0	0	1	0	0	0	14517	159	6	4	548	4	SLC25A18	22	18070018	Missense_Mutation	SNP	A	TCGA-AG-3902-01A-01W-1073-09		18070018	33234548	130	7215										
ZNF74	7625	broad.mit.edu	37	chr22	20761176	20761176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggacgtggatcccatcgacgCgctggatgtggcaaagctct	14	11	1	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr22:20761176C>T	ENST00000400451.2	+	5	2367	c.1853C>T	c.(1852-1854)gCg>gTg	p.A618V	ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000405993.1_Missense_Mutation_p.A586V|ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000356671.5_Missense_Mutation_p.A618V	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	618					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A618V(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	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)			CCCATCGACGCGCTGGATGTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											54	59	58					22																	20761176		2133	4240	6373	19091176	SO:0001583	missense	7625			X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"Zinc fingers, C2H2-type", "-"	13144	protein-coding gene	gene with protein product		194548	"zinc finger protein 74 (Cos52)"			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.1853C>T	22.37:g.20761176C>T	ENSP00000383301:p.Ala618Val		19091176	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	37	CCDS42982.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737747	0.49045	.	.	ENSG00000185252	ENST00000400451;ENST00000356671;ENST00000405993	T;T;T	0.07021	3.33;3.33;3.23	4.04	4.04	0.47022	.	0.457832	0.16223	N	0.223973	T	0.07999	0.0200	L	0.34521	1.04	0.09310	N	1	B	0.30146	0.27	B	0.24394	0.053	T	0.20338	-1.0278	10	0.59425	D	0.04	.	14.5044	0.67743	0.0:1.0:0.0:0.0	.	618	Q16587	ZNF74_HUMAN	V	618;618;586	ENSP00000383301:A618V;ENSP00000349098:A618V;ENSP00000385855:A586V	ENSP00000349098:A618V	A	+	2	0	ZNF74	19091176	0.003000	0.15002	0.014000	0.15608	0.007000	0.05969	1.835000	0.39181	2.535000	0.85469	0.563000	0.77884	GCG		0.572	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426		T	20761176	C	T	20761176	3	4	53	1	0	0	0	0	1	0	0	0	18166	768	27	1	1871	1	ZNF74	22	20761176	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	2691158	20761176	30543390	131	7216										
NPTXR	23467	broad.mit.edu	37	chr22	39222678	39222678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ctcgggcagagccttccgcaCgcgggcgtacatgtagttgt	14	12	0	1	rs368736692		TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chr22:39222678C>T	ENST00000333039.2	-	3	1048	c.925G>A	c.(925-927)Gtg>Atg	p.V309M		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	309	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.V309M(1)		central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					GCCTTCCGCACGCGGGCGTAC	0.622																																					Pancreas(139;2521 3281 36965)											1	Substitution - Missense(1)	large_intestine(1)	22						C	MET/VAL	0,4406		0,0,2203	91	81	84		925	2.2	1	22		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPTXR	NM_014293.3	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	309/501	39222678	1,13005	2203	4300	6503	37552624	SO:0001583	missense	23467			AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.925G>A	22.37:g.39222678C>T	ENSP00000327545:p.Val309Met		37552624		Missense_Mutation	SNP	ENST00000333039.2	37	CCDS33647.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633610	0.67015	0.0	1.16E-4	ENSG00000221890	ENST00000333039	T	0.61980	0.06	4.64	2.24	0.28232	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.270890	0.35903	N	0.002909	T	0.56062	0.1960	L	0.43701	1.375	0.42244	D	0.991943	P	0.50272	0.933	P	0.45946	0.498	T	0.68550	-0.5379	9	0.59425	D	0.04	-47.7375	10.8239	0.46620	0.0:0.7442:0.0:0.2558	.	309	O95502	NPTXR_HUMAN	M	309	ENSP00000327545:V309M	ENSP00000327545:V309M	V	-	1	0	NPTXR	37552624	0.245000	0.23899	1.000000	0.80357	0.930000	0.56654	0.260000	0.18424	0.740000	0.32651	0.655000	0.94253	GTG		0.622	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293		T	39222678	C	T	39222678	3	4	53	1	0	0	0	0	1	0	0	0	10635	536	19	1	589	1	NPTXR	22	39222678	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	18461502	39222678	12081888	132	7217										
CNKSR2	22866	broad.mit.edu	37	chrX	21627703	21627703	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggaggaggaggaggaggaagGggaggcagcaggggaaaaca	23	3	0	0			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chrX:21627703G>T	ENST00000379510.3	+	20	2696	c.2660G>T	c.(2659-2661)gGg>gTg	p.G887V	CNKSR2_ENST00000543067.1_Missense_Mutation_p.G838V|CNKSR2_ENST00000279451.4_Missense_Mutation_p.G887V|CNKSR2_ENST00000425654.2_Missense_Mutation_p.G857V	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	887	Poly-Glu.				regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.G887V(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						gaggaggaaggggaggCAGCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											31	23	26					X																	21627703		2199	4292	6491	21537624	SO:0001583	missense	22866			AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.2660G>T	X.37:g.21627703G>T	ENSP00000368824:p.Gly887Val		21537624	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	37	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	7.202	0.593591	0.13875	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.19938	2.47;2.11;2.14;2.5	5.38	3.56	0.40772	.	0.301293	0.33235	N	0.005127	T	0.12433	0.0302	L	0.29908	0.895	0.39018	D	0.959683	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.12708	-1.0537	10	0.32370	T	0.25	.	3.9224	0.09250	0.2424:0.0:0.4682:0.2894	.	857;838;479;887	B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2	.;.;.;CNKR2_HUMAN	V	857;838;887;887	ENSP00000397906:G857V;ENSP00000444633:G838V;ENSP00000279451:G887V;ENSP00000368824:G887V	ENSP00000279451:G887V	G	+	2	0	CNKSR2	21537624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.862000	0.39448	1.120000	0.41904	0.513000	0.50165	GGG		0.488	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		T	21627703	G	T	21627703	3	4	53	1	0	0	0	0	1	0	0	0	3613	1232	43	2	2738	2	CNKSR2	23	21627703	Missense_Mutation	SNP	G	TCGA-AG-3902-01A-01W-1073-09		21627703	133642857	133	7218										
RBM10	8241	broad.mit.edu	37	chrX	47028790	47028790	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	atggtggggagaaccgcagcCgagaccacgactaccgggac	15	12	0	2			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chrX:47028790C>T	ENST00000377604.3	+	3	836	c.94C>T	c.(94-96)Cga>Tga	p.R32*	RBM10_ENST00000345781.6_Nonsense_Mutation_p.R32*|RBM10_ENST00000329236.7_Nonsense_Mutation_p.R32*	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	32					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.R32*(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						GAACCGCAGCCGAGACCACGA	0.592																																					Melanoma(171;120 2705 19495 39241)											2	Substitution - Nonsense(2)	large_intestine(2)	X											98	67	78					X																	47028790		2203	4300	6503	46913734	SO:0001587	stop_gained	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.94C>T	X.37:g.47028790C>T	ENSP00000366829:p.Arg32*		46913734	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Nonsense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	39	7.573321	0.98368	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	.	.	.	4.62	2.79	0.32731	.	0.000000	0.41938	D	0.000797	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8986	9.4105	0.38489	0.3851:0.6149:0.0:0.0	.	.	.	.	X	32	.	ENSP00000328848:R32X	R	+	1	2	RBM10	46913734	1.000000	0.71417	0.983000	0.44433	0.991000	0.79684	1.426000	0.34870	0.324000	0.23333	0.436000	0.28706	CGA		0.592	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47028790	C	T	47028790	4	4	53	1	0	0	0	0	0	1	0	0	13148	644	23	1	100	1	RBM10	23	47028790	Nonsense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	25401087	47028790	108241770	134	7219										
PABPC5	140886	broad.mit.edu	37	chrX	90690912	90690912	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	10	1	0.917497670887823	2.23257766582704	0.577390775644923	1	1	0	ggaaatatattcatcaaaaaCctggacaaatccatagacaa	5	8	2	1			TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3902-01A-01W-1073-09	TCGA-AG-3902-10A-01W-1073-09	g.chrX:90690912C>A	ENST00000312600.3	+	2	550	c.336C>A	c.(334-336)aaC>aaA	p.N112K	PABPC5-AS1_ENST00000456187.1_RNA|PABPC5_ENST00000373105.1_Intron	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	112	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.N112K(1)		central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						TCATCAAAAACCTGGACAAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											73	68	70					X																	90690912		2203	4300	6503	90577568	SO:0001583	missense	140886			AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.336C>A	X.37:g.90690912C>A	ENSP00000308012:p.Asn112Lys		90577568	A8K240|Q5JQF4|Q6P529|Q9UFE5	Missense_Mutation	SNP	ENST00000312600.3	37	CCDS14460.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052021	0.36181	.	.	ENSG00000174740	ENST00000312600;ENST00000402906	T	0.27720	1.65	4.43	1.74	0.24563	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.043066	0.85682	D	0.000000	T	0.32071	0.0817	M	0.78916	2.43	0.45502	D	0.998463	P	0.35575	0.51	B	0.35353	0.201	T	0.11842	-1.0571	10	0.87932	D	0	.	7.7233	0.28744	0.0:0.702:0.0:0.298	.	112	Q96DU9	PABP5_HUMAN	K	112;80	ENSP00000308012:N112K	ENSP00000308012:N112K	N	+	3	2	PABPC5	90577568	0.965000	0.33210	0.999000	0.59377	0.954000	0.61252	0.169000	0.16641	0.239000	0.21243	-0.208000	0.12717	AAC		0.408	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		A	90690912	C	A	90690912	3	1	53	1	0	0	0	0	1	0	0	0	11398	506	18	2	338	2	PABPC5	23	90690912	Missense_Mutation	SNP	C	TCGA-AG-3902-01A-01W-1073-09	43662122	90690912	64579648	135	7220										
DIO1	1733	broad.mit.edu	37	chr1	54371958	54371958	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ataatccaggagggcaggatCctctacaaggtggtgacctg	13	9	1	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:54371958C>T	ENST00000361921.3	+	3	696	c.672C>T	c.(670-672)atC>atT	p.I224I	DIO1_ENST00000322679.6_Intron|DIO1_ENST00000532493.1_Intron|DIO1_ENST00000525202.1_Silent_p.I160I|DIO1_ENST00000388876.3_Silent_p.I176I|DIO1_ENST00000524406.1_Silent_p.I95I	NM_000792.5|NM_213593.3	NP_000783.2|NP_998758.1	P49895	IOD1_HUMAN	deiodinase, iodothyronine, type I	224					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)	p.I224I(1)|p.I176I(1)		cervix(1)|endometrium(2)|large_intestine(3)|lung(2)|skin(1)	9						AGGGCAGGATCCTCTACAAGG	0.617																																																2	Substitution - coding silent(2)	large_intestine(2)	1											27	26	26					1																	54371958		2203	4300	6503	54144546	SO:0001819	synonymous_variant	1733				CCDS30722.1, CCDS41339.1, CCDS41340.1, CCDS53320.1	1p33-p32	2012-03-01			ENSG00000211452	ENSG00000211452	1.97.1.10		2883	protein-coding gene	gene with protein product		147892		TXDI1		8964838	Standard	NM_000792		Approved		uc001cwb.3	P49895	OTTHUMG00000008435	ENST00000361921.3:c.672C>T	1.37:g.54371958C>T			54144546	Q1RN02|Q3KNP8|Q6Q4C1|Q6Q4C2|Q6Q4C3|Q6Q4C4|Q6Q4C5|Q6Q4C6|Q6Q4C7|Q6Q4C9|Q8WWC6	Silent	SNP	ENST00000361921.3	37	CCDS41339.1																																																																																				0.617	DIO1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000023247.3			T	54371958	C	T	54371958	2	4	54	1	0	0	0	0	0	0	0	1	4535	845	30	3		3	DIO1	1	54371958	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09		54371958	194878663	1	7221										
DPYD	1806	broad.mit.edu	37	chr1	97544581	97544581	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cgcctctctttggttcataaGgtgttgtcctggaaaccatt	9	10	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:97544581G>T	ENST00000370192.3	-	23	3129	c.3029C>A	c.(3028-3030)cCt>cAt	p.P1010H		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	1010					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.P1010H(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TGGTTCATAAGGTGTTGTCCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											245	226	233					1																	97544581		2203	4300	6503	97317169	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.3029C>A	1.37:g.97544581G>T	ENSP00000359211:p.Pro1010His		97317169	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.002107	0.93227	.	.	ENSG00000188641	ENST00000370192	D	0.90620	-2.7	5.46	5.46	0.80206	.	0.057159	0.64402	D	0.000001	D	0.90913	0.7144	M	0.80422	2.495	0.80722	D	1	P	0.44195	0.828	B	0.43082	0.407	D	0.92369	0.5904	10	0.87932	D	0	-10.792	19.6731	0.95918	0.0:0.0:1.0:0.0	.	1010	Q12882	DPYD_HUMAN	H	1010	ENSP00000359211:P1010H	ENSP00000359211:P1010H	P	-	2	0	DPYD	97317169	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.849000	0.86908	2.735000	0.93741	0.561000	0.74099	CCT		0.463	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	97544581	G	T	97544581	3	4	54	1	0	0	0	0	1	0	0	0	4756	1000	35	2	52	2	DPYD	1	97544581	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	43172623	97544581	151706040	2	7222										
CAPZA1	829	broad.mit.edu	37	chr1	113197127	113197127	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tgacctgggtaatagcagatTtttagatccaagaaacaaaa	8	6	0	4			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:113197127T>G	ENST00000263168.3	+	5	932	c.260T>G	c.(259-261)tTt>tGt	p.F87C	CAPZA1_ENST00000476936.1_Intron|snoU13_ENST00000459345.1_RNA	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	87					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)	p.F87C(1)		breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATAGCAGATTTTTAGATCCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	83	80					1																	113197127		2202	4300	6502	112998650	SO:0001583	missense	829			U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.260T>G	1.37:g.113197127T>G	ENSP00000263168:p.Phe87Cys		112998650	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	37	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057762	0.76074	.	.	ENSG00000116489	ENST00000263168	.	.	.	4.69	4.69	0.59074	.	0.057902	0.64402	D	0.000001	T	0.66416	0.2787	M	0.89968	3.075	0.49389	D	0.99978	B	0.18013	0.025	B	0.28991	0.097	T	0.73553	-0.3946	9	0.87932	D	0	-19.5832	14.245	0.65983	0.0:0.0:0.0:1.0	.	87	P52907	CAZA1_HUMAN	C	87	.	ENSP00000263168:F87C	F	+	2	0	CAPZA1	112998650	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.977000	0.70492	2.090000	0.63153	0.477000	0.44152	TTT		0.383	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		G	113197127	T	G	113197127	3	3	54	1	0	0	0	0	1	0	0	0	2646	1841	64	4	278	4	CAPZA1	1	113197127	Missense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09	15652546	113197127	136053494	3	7223										
KISS1	3814	broad.mit.edu	37	chr1	204159823	204159823	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cggggggcggggacagcgagGtcccccgacggctcagcctg	19	14	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:204159823G>T	ENST00000367194.4	-	3	354	c.206C>A	c.(205-207)aCc>aAc	p.T69N		NM_002256.3	NP_002247.3	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor	69					cytoskeleton organization (GO:0007010)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of synaptic transmission (GO:0050806)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.T69N(1)		large_intestine(1)|lung(1)|ovary(1)	3	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		GGACAGCGAGGTCCCCCGACG	0.751																																																1	Substitution - Missense(1)	large_intestine(1)	1											5	7	6					1																	204159823		1432	3382	4814	202426446	SO:0001583	missense	3814			U43527	CCDS41454.1	1q32	2014-01-30			ENSG00000170498	ENSG00000170498		"Endogenous ligands"	6341	protein-coding gene	gene with protein product	"prepro-kisspeptin", "kisspeptin"	603286				9192814, 9806840	Standard	NM_002256		Approved		uc001har.3	Q15726	OTTHUMG00000036060	ENST00000367194.4:c.206C>A	1.37:g.204159823G>T	ENSP00000356162:p.Thr69Asn		202426446	A8K6N0|Q9HBP1	Missense_Mutation	SNP	ENST00000367194.4	37	CCDS41454.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.305143	0.23736	.	.	ENSG00000170498	ENST00000367194	D	0.81659	-1.52	4.83	3.87	0.44632	.	0.290042	0.24343	N	0.039346	T	0.67316	0.2880	N	0.24115	0.695	0.09310	N	1	B	0.21905	0.062	B	0.15052	0.012	T	0.61446	-0.7061	10	0.56958	D	0.05	-1.9756	10.4774	0.44674	0.0:0.0:0.8072:0.1928	.	69	Q15726	KISS1_HUMAN	N	69	ENSP00000356162:T69N	ENSP00000356162:T69N	T	-	2	0	KISS1	202426446	0.060000	0.20803	0.003000	0.11579	0.010000	0.07245	3.103000	0.50298	2.191000	0.70037	0.609000	0.83330	ACC		0.751	KISS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087892.1	NM_002256		T	204159823	G	T	204159823	3	4	54	1	0	0	0	0	1	0	0	0	8348	1261	44	2	214	2	KISS1	1	204159823	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	90962696	204159823	45090798	4	7224										
KCNK1	3775	broad.mit.edu	37	chr1	233802421	233802421	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcattggcattcccttcaccCtcctgttcctgacggctgtg	8	15	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:233802421C>G	ENST00000366621.3	+	2	604	c.436C>G	c.(436-438)Ctc>Gtc	p.L146V	KCNK1_ENST00000366620.1_Missense_Mutation_p.L30V|KCNK1_ENST00000472190.1_3'UTR	NM_002245.3	NP_002236.1	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1	146					potassium ion transport (GO:0006813)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.L146V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	11		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)	TCCCTTCACCCTCCTGTTCCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											209	144	166					1																	233802421		2203	4300	6503	231869044	SO:0001583	missense	3775			U33632	CCDS1599.1	1q42-q43	2012-03-07			ENSG00000135750	ENSG00000135750		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6272	protein-coding gene	gene with protein product		601745				8661042, 16382106	Standard	NM_002245		Approved	K2p1.1, DPK, TWIK-1	uc010pxo.1	O00180	OTTHUMG00000037923	ENST00000366621.3:c.436C>G	1.37:g.233802421C>G	ENSP00000355580:p.Leu146Val		231869044	Q13307|Q5T5E8	Missense_Mutation	SNP	ENST00000366621.3	37	CCDS1599.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763552	0.89932	.	.	ENSG00000135750	ENST00000366621;ENST00000366620;ENST00000446915	T;T;T	0.30981	1.51;1.51;1.51	5.91	5.91	0.95273	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.52354	0.1729	M	0.62209	1.925	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.44034	-0.9354	10	0.44086	T	0.13	.	14.4428	0.67330	0.0:0.9303:0.0:0.0697	.	146	O00180	KCNK1_HUMAN	V	146;30;64	ENSP00000355580:L146V;ENSP00000355579:L30V;ENSP00000409626:L64V	ENSP00000355579:L30V	L	+	1	0	KCNK1	231869044	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.896000	0.69822	2.793000	0.96121	0.655000	0.94253	CTC		0.587	KCNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092565.1	NM_002245		G	233802421	C	G	233802421	3	3	54	1	0	0	0	0	1	0	0	0	8079	681	24	5	442	5	KCNK1	1	233802421	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	29642598	233802421	15448200	5	7225										
HEATR1	55127	broad.mit.edu	37	chr1	236721766	236721766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gattgcttgttcttcttcccCttcctttttcttacgctgca	5	13	3	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:236721766C>T	ENST00000366582.3	-	36	5089	c.4975G>A	c.(4975-4977)Ggg>Agg	p.G1659R	HEATR1_ENST00000366581.2_Missense_Mutation_p.G1578R	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1659					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.G1659R(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCTTCTTCCCCTTCCTTTTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	111	116					1																	236721766		2203	4300	6503	234788389	SO:0001583	missense	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.4975G>A	1.37:g.236721766C>T	ENSP00000355541:p.Gly1659Arg		234788389	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843729	0.32606	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.05855	3.38;3.39	6.03	-2.61	0.06171	Armadillo-like helical (1);Armadillo-type fold (1);	1.238380	0.05810	N	0.613785	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	B;B	0.24823	0.044;0.112	B;B	0.19148	0.017;0.024	T	0.45571	-0.9252	10	0.16896	T	0.51	.	3.5187	0.07734	0.2851:0.4203:0.1767:0.1179	.	1578;1659	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	R	1659;1578	ENSP00000355541:G1659R;ENSP00000355540:G1578R	ENSP00000355540:G1578R	G	-	1	0	HEATR1	234788389	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.521000	0.22893	-0.325000	0.08577	0.655000	0.94253	GGG		0.428	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236721766	C	T	236721766	3	4	54	1	0	0	0	0	1	0	0	0	7048	681	24	3	1499	3	HEATR1	1	236721766	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	2919345	236721766	12528855	6	7226										
RYR2	6262	broad.mit.edu	37	chr1	237777815	237777815	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	caaaaccatacagatgctgaCagaagctgttaaagagggca	10	8	0	4			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:237777815C>A	ENST00000366574.2	+	37	5704	c.5387C>A	c.(5386-5388)aCa>aAa	p.T1796K	RYR2_ENST00000360064.6_Missense_Mutation_p.T1794K|RYR2_ENST00000542537.1_Missense_Mutation_p.T1780K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1796	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.T1794K(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CAGATGCTGACAGAAGCTGTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											159	152	155					1																	237777815		1945	4144	6089	235844438	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5387C>A	1.37:g.237777815C>A	ENSP00000355533:p.Thr1796Lys		235844438	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461575	0.26248	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.74947	-0.89;-0.89;-0.89	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000008	T	0.64843	0.2635	L	0.38838	1.175	0.80722	D	1	B	0.26672	0.156	B	0.24848	0.056	T	0.61787	-0.6991	10	0.06236	T	0.91	.	19.6609	0.95871	0.0:1.0:0.0:0.0	.	1796	Q92736	RYR2_HUMAN	K	1796;1794;1780	ENSP00000355533:T1796K;ENSP00000353174:T1794K;ENSP00000443798:T1780K	ENSP00000353174:T1794K	T	+	2	0	RYR2	235844438	1.000000	0.71417	0.962000	0.40283	0.400000	0.30750	7.776000	0.85560	2.665000	0.90641	0.650000	0.86243	ACA		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237777815	C	A	237777815	3	1	54	1	0	0	0	0	1	0	0	0	13806	478	17	2	5533	2	RYR2	1	237777815	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	1056049	237777815	11472806	7	7227										
OR2T8	343172	broad.mit.edu	37	chr1	248084470	248084470	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ttctcctgattcactgggacCaccggctccacacgcccatg	8	17	2	1	rs140846339|rs547311711	byFrequency	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr1:248084470C>G	ENST00000319968.4	+	1	151	c.151C>G	c.(151-153)Cac>Gac	p.H51D		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCACTGGGACCACCGGCTCCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	60	60					1																	248084470		2201	4297	6498	246151093	SO:0001583	missense	343172				CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"GPCR / Class A : Olfactory receptors"	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.151C>G	1.37:g.248084470C>G	ENSP00000326225:p.His51Asp		246151093		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	c	8.583	0.882849	0.17467	.	.	ENSG00000177462	ENST00000319968	T	0.00428	7.44	3.65	0.32	0.15878	GPCR, rhodopsin-like superfamily (1);	3.036110	0.01499	U	0.017405	T	0.00356	0.0011	L	0.41492	1.28	0.09310	N	1	B	0.09022	0.002	B	0.16289	0.015	T	0.48502	-0.9030	10	0.66056	D	0.02	.	2.7852	0.05372	0.0:0.3992:0.2448:0.3561	.	51	A6NH00	OR2T8_HUMAN	D	51	ENSP00000326225:H51D	ENSP00000326225:H51D	H	+	1	0	OR2T8	246151093	0.118000	0.22208	0.005000	0.12908	0.016000	0.09150	-0.265000	0.08644	0.228000	0.21019	0.603000	0.83216	CAC		0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522		G	248084470	C	G	248084470	3	3	54	1	0	0	0	0	1	0	0	0	11061	594	21	5	153	5	OR2T8	1	248084470	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	10306655	248084470	1166151	8	7228										
NRXN1	9378	broad.mit.edu	37	chr2	50149358	50149358	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acttctgctgagcctggataCggctctctgccgcctgctcg	11	15	2	1	rs151195816		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:50149358C>T	ENST00000406316.2	-	22	5634	c.4158G>A	c.(4156-4158)ccG>ccA	p.P1386P	NRXN1_ENST00000406859.3_Silent_p.P1386P|NRXN1_ENST00000401669.2_Silent_p.P1416P|NRXN1_ENST00000402717.3_Silent_p.P1408P|NRXN1_ENST00000401710.1_Silent_p.P404P|NRXN1_ENST00000342183.5_Silent_p.P351P|NRXN1_ENST00000405472.3_Silent_p.P1408P|NRXN1_ENST00000404971.1_Silent_p.P1456P	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1386					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.P1386P(1)|p.P351P(1)|p.P1457P(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AGCCTGGATACGGCTCTCTGC	0.527													C|||	1	0.000199681	0	0	5008	,	,		16427	0		0	False		,,,				2504	0.001															3	Substitution - coding silent(3)	large_intestine(3)	2						C	,,	0,4406		0,0,2203	48	42	44		4368,4158,1053	-11.9	0	2	dbSNP_134	44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	1456/1548,1386/1478,351/443	50149358	1,13005	2203	4300	6503	50002862	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.4158G>A	2.37:g.50149358C>T			50002862	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.933|0.933	-0.712039|-0.712039	0.03206|0.03206	0.0|0.0	1.16E-4|1.16E-4	ENSG00000179915|ENSG00000179915	ENST00000412315|ENST00000378262	.|.	.|.	.|.	5.95|5.95	-11.9|-11.9	0.00025|0.00025	.|.	.|.	.|.	.|.	.|.	T|T	0.23451|0.23451	0.0567|0.0567	.|.	.|.	.|.	0.27274|0.27274	N|N	0.958287|0.958287	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.32402|0.32402	-0.9908|-0.9908	4|4	.|.	.|.	.|.	.|.	7.8463|7.8463	0.29426|0.29426	0.1256:0.51:0.2001:0.1642|0.1256:0.51:0.2001:0.1642	.|.	.|.	.|.	.|.	H|I	119|53	.|.	.|.	R|V	-|-	2|1	0|0	NRXN1|NRXN1	50002862|50002862	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.787000|0.787000	0.44495|0.44495	-2.706000|-2.706000	0.00821|0.00821	-5.262000|-5.262000	0.00018|0.00018	-0.986000|-0.986000	0.02555|0.02555	CGT|GTA		0.527	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50149358	C	T	50149358	2	4	54	1	0	0	0	0	0	0	0	1	10696	523	19	1		1	NRXN1	2	50149358	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09		50149358	193050015	9	7229										
NRXN1	9378	broad.mit.edu	37	chr2	50847278	50847278	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcatggtataatcttcttgcGtgtagcccgttgtggtaaga	12	7	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:50847278G>A	ENST00000406316.2	-	8	2678	c.1202C>T	c.(1201-1203)aCg>aTg	p.T401M	NRXN1_ENST00000406859.3_Missense_Mutation_p.T401M|NRXN1_ENST00000401669.2_Missense_Mutation_p.T401M|NRXN1_ENST00000402717.3_Missense_Mutation_p.T393M|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Missense_Mutation_p.T393M|NRXN1_ENST00000404971.1_Missense_Mutation_p.T441M	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	401	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.T442M(1)|p.T401M(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATCTTCTTGCGTGTAGCCCGT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	2											64	65	65					2																	50847278		2058	4234	6292	50700782	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1202C>T	2.37:g.50847278G>A	ENSP00000384311:p.Thr401Met		50700782	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.704527	0.68615	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.79749	-1.12;-1.12;-1.3;-1.12;-1.3;-1.12	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.91129	0.7207	M	0.83774	2.66	0.54753	D	0.999982	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	D	0.90074	0.4165	10	0.52906	T	0.07	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	441;401;393	Q9ULB1-3;F8WB18;A7E294	.;.;.	M	441;401;393;401;442;393;401	ENSP00000385142:T441M;ENSP00000384311:T401M;ENSP00000434015:T393M;ENSP00000385017:T401M;ENSP00000385434:T393M;ENSP00000385681:T401M	ENSP00000385017:T401M	T	-	2	0	NRXN1	50700782	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	ACG		0.468	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50847278	G	A	50847278	3	1	54	1	0	0	0	0	1	0	0	0	10696	1145	40	1	3648	1	NRXN1	2	50847278	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	697920	50847278	192352095	10	7230										
SLC4A5	57835	broad.mit.edu	37	chr2	74483058	74483058	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcttcatgaatttgtttttcCgctggacagggaggggaaac	12	7	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:74483058C>T	ENST00000377634.4	-	13	1268	c.869G>A	c.(868-870)cGg>cAg	p.R290Q	SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000346834.4_Splice_Site_p.R290Q|SLC4A5_ENST00000394019.2_Splice_Site_p.R290Q|SLC4A5_ENST00000358683.4_Splice_Site_p.R226Q|SLC4A5_ENST00000359484.4_Splice_Site_p.R226Q|SLC4A5_ENST00000423644.1_Splice_Site_p.R290Q|SLC4A5_ENST00000357822.5_Splice_Site_p.R290Q|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Splice_Site_p.R290Q					solute carrier family 4 (sodium bicarbonate cotransporter), member 5									p.R290Q(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TTTGTTTTTCCGCTGGACAGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											111	82	92					2																	74483058		2203	4300	6503	74336566	SO:0001630	splice_region_variant	57835			AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"Solute carriers"	18168	protein-coding gene	gene with protein product		606757	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.868-1G>A	2.37:g.74483058C>T			74336566		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.639759	0.47153	.	.	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000423644;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634;ENST00000425249	T;T;T;T;T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28	4.92	2.96	0.34315	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.281578	0.34700	N	0.003745	T	0.62097	0.2400	N	0.20483	0.58	0.80722	D	1	P;P;B;P;B	0.50943	0.634;0.94;0.04;0.566;0.019	B;B;B;B;B	0.41332	0.103;0.354;0.011;0.084;0.017	T	0.57991	-0.7715	10	0.28530	T	0.3	.	5.4941	0.16793	0.286:0.6131:0.0:0.1009	.	290;290;226;290;290	Q9BY07-4;E7EQT3;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;.;S4A5_HUMAN;.	Q	290;290;290;226;290;226;290;290;290;290	ENSP00000377587:R290Q;ENSP00000251768:R290Q;ENSP00000352461:R226Q;ENSP00000395804:R290Q;ENSP00000351513:R226Q;ENSP00000350475:R290Q;ENSP00000366859:R290Q;ENSP00000366861:R290Q;ENSP00000405678:R290Q	ENSP00000251768:R290Q	R	-	2	0	SLC4A5	74336566	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.557000	0.60782	1.307000	0.44944	0.655000	0.94253	CGG		0.527	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		Missense_Mutation	T	74483058	C	T	74483058	5	4	54	1	0	0	0	0	0	0	1	0	14694	666	23	1	2620	1	SLC4A5	2	74483058	Splice_Site	SNP	C	TCGA-AG-3909-01A-01W-1073-09	23635780	74483058	168716315	11	7231										
PCDP1	200373	broad.mit.edu	37	chr2	120369269	120369269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tttggatgaggaatttcagcGacttaaaacagaagttagcc	10	6	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:120369269G>A	ENST00000413369.3	+	13	1349	c.1262G>A	c.(1261-1263)cGa>cAa	p.R421Q	PCDP1_ENST00000597189.1_3'UTR|PCDP1_ENST00000602047.1_Missense_Mutation_p.R135Q	NM_001271049.1	NP_001257978												p.R135Q(1)				Colorectal(110;0.196)					GAATTTCAGCGACTTAAAACA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	88	88					2																	120369269		2203	4300	6503	120085739	SO:0001583	missense	200373																														ENST00000413369.3:c.1262G>A	2.37:g.120369269G>A	ENSP00000393222:p.Arg421Gln		120085739		Missense_Mutation	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141068	0.77775	.	.	ENSG00000163075	ENST00000295220;ENST00000413369	T	0.19938	2.11	4.39	4.39	0.52855	.	0.234819	0.28453	N	0.015299	T	0.42086	0.1187	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.33854	-0.9852	10	0.87932	D	0	-13.7282	13.815	0.63285	0.0:0.0:1.0:0.0	.	265;421	Q4G0U5-3;Q4G0U5	.;PCDP1_HUMAN	Q	135;421	ENSP00000393222:R421Q	ENSP00000295220:R135Q	R	+	2	0	AC069154.2	120085739	1.000000	0.71417	0.998000	0.56505	0.787000	0.44495	5.567000	0.67378	2.253000	0.74438	0.650000	0.86243	CGA		0.338	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			A	120369269	G	A	120369269	3	1	54	1	0	0	0	0	1	0	0	0	11603	1058	37	1	422	1	PCDP1	2	120369269	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	45886211	120369269	122830104	12	7232										
LRP1B	53353	broad.mit.edu	37	chr2	141806753	141806753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcctctaacaattcctgggcGtcctttcccataaaagagga	7	12	1	1	rs371410109		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:141806753G>A	ENST00000389484.3	-	11	2562	c.1591C>T	c.(1591-1593)Cgc>Tgc	p.R531C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	531					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.R531C(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ATTCCTGGGCGTCCTTTCCCA	0.398										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2						G	CYS/ARG	0,4406		0,0,2203	107	109	108		1591	4.6	1	2		108	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP1B	NM_018557.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	531/4600	141806753	1,13005	2203	4300	6503	141523223	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1591C>T	2.37:g.141806753G>A	ENSP00000374135:p.Arg531Cys		141523223	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.262951	0.39995	0.0	1.16E-4	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90676	-2.71	5.49	4.61	0.57282	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	U	0.000001	D	0.89626	0.6769	M	0.84082	2.675	0.58432	D	0.999999	B	0.25809	0.135	B	0.17722	0.019	D	0.87612	0.2504	10	0.87932	D	0	.	9.1244	0.36805	0.0739:0.0:0.7802:0.1458	.	531	Q9NZR2	LRP1B_HUMAN	C	531;469	ENSP00000374135:R531C	ENSP00000374135:R531C	R	-	1	0	LRP1B	141523223	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	4.314000	0.59166	1.295000	0.44724	0.563000	0.77884	CGC		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141806753	G	A	141806753	3	1	54	1	0	0	0	0	1	0	0	0	8984	1145	40	1	12532	1	LRP1B	2	141806753	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	21437484	141806753	101392620	13	7233										
COBLL1	22837	broad.mit.edu	37	chr2	165584560	165584560	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gtcaagaggctcctgcgattGataatctttcaacaatagtg	9	8	3	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:165584560G>C	ENST00000392717.2	-	5	698	c.694C>G	c.(694-696)Caa>Gaa	p.Q232E	COBLL1_ENST00000491126.2_Intron|COBLL1_ENST00000194871.6_Missense_Mutation_p.Q247E|COBLL1_ENST00000342193.4_Missense_Mutation_p.Q194E|COBLL1_ENST00000375458.2_Missense_Mutation_p.Q194E|COBLL1_ENST00000409184.3_Missense_Mutation_p.Q232E			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	232						extracellular vesicular exosome (GO:0070062)		p.Q194*(1)|p.Q194E(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						TCCTGCGATTGATAATCTTTC	0.393																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	2											124	121	122					2																	165584560		2203	4300	6503	165292806	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.694C>G	2.37:g.165584560G>C	ENSP00000376478:p.Gln232Glu		165292806	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.29|17.29	3.351725|3.351725	0.61183|0.61183	.|.	.|.	ENSG00000082438|ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871;ENST00000456693|ENST00000452626	D;D;D;D;D;D|.	0.91740|.	-2.9;-2.9;-2.9;-2.9;-2.9;-2.9|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Cordon-bleu domain (1);|.	0.331824|.	0.34906|.	N|.	0.003597|.	T|.	0.76630|.	0.4014|.	M|M	0.67953|0.67953	2.075|2.075	0.50039|0.50039	D|D	0.999843|0.999843	D;D;D|.	0.89917|.	1.0;1.0;0.999|.	D;D;D|.	0.87578|.	0.998;0.998;0.997|.	T|.	0.72050|.	-0.4407|.	10|.	0.35671|.	T|.	0.21|.	-14.2422|-14.2422	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	232;247;232|.	Q53SF7;B7Z2P5;Q53SF7-2|.	COBL1_HUMAN;.;.|.	E|X	194;194;232;232;247;169|196	ENSP00000364607:Q194E;ENSP00000341360:Q194E;ENSP00000387326:Q232E;ENSP00000376478:Q232E;ENSP00000194871:Q247E;ENSP00000397520:Q169E|.	ENSP00000194871:Q247E|.	Q|S	-|-	1|2	0|0	COBLL1|COBLL1	165292806|165292806	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.082000|0.082000	0.17680|0.17680	6.557000|6.557000	0.73937|0.73937	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	CAA|TCA		0.393	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		C	165584560	G	C	165584560	3	2	54	1	0	0	0	0	1	0	0	0	3660	1299	45	5	2964	5	COBLL1	2	165584560	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	23777807	165584560	77614813	14	7234										
CHRNA1	1134	broad.mit.edu	37	chr2	175624081	175624081	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gtttcagacgcacattggttGtcacgatctgatttacttca	8	9	4	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:175624081G>T	ENST00000261007.5	-	3	278	c.212C>A	c.(211-213)aCa>aAa	p.T71K	AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000348749.5_Missense_Mutation_p.T71K|CHRNA1_ENST00000409542.1_Missense_Mutation_p.T71K|CHRNA1_ENST00000409219.1_Missense_Mutation_p.T71K|CHRNA1_ENST00000409323.1_Missense_Mutation_p.T71K	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	71					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)	p.T71K(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	CACATTGGTTGTCACGATCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	102	104					2																	175624081		2203	4300	6503	175332327	SO:0001583	missense	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.212C>A	2.37:g.175624081G>T	ENSP00000261007:p.Thr71Lys		175332327	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.580264	0.86645	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41	5.95	5.95	0.96441	Neurotransmitter-gated ion-channel ligand-binding (3);	0.091297	0.85682	D	0.000000	D	0.88187	0.6369	L	0.61218	1.895	0.58432	D	0.999999	D;D;D	0.60160	0.987;0.96;0.958	P;B;P	0.62560	0.754;0.387;0.904	D	0.87581	0.2484	10	0.59425	D	0.04	.	20.3789	0.98926	0.0:0.0:1.0:0.0	.	71;71;71	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	K	71	ENSP00000261008:T71K;ENSP00000261007:T71K;ENSP00000387026:T71K;ENSP00000386611:T71K;ENSP00000386684:T71K	ENSP00000261007:T71K	T	-	2	0	CHRNA1	175332327	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.498000	0.60373	2.826000	0.97356	0.563000	0.77884	ACA		0.443	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			T	175624081	G	T	175624081	3	4	54	1	0	0	0	0	1	0	0	0	3387	1377	48	2	1268	2	CHRNA1	2	175624081	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	10039521	175624081	67575292	15	7235										
TTN	7273	broad.mit.edu	37	chr2	179440531	179440531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cctttgtgatgtctgtaggcCgcaggttgaggactgggcct	15	9	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:179440531C>T	ENST00000591111.1	-	276	65629	c.65405G>A	c.(65404-65406)cGg>cAg	p.R21802Q	TTN_ENST00000589042.1_Missense_Mutation_p.R23443Q|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R20875Q|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R14378Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R14503Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R14570Q			Q8WZ42	TITIN_HUMAN	titin	21802	Fibronectin type-III 58. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R20873Q(1)|p.R14503Q(1)|p.R14378Q(1)|p.R14570Q(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCTGTAGGCCGCAGGTTGAG	0.502																																																4	Substitution - Missense(4)	large_intestine(4)	2											94	99	97					2																	179440531		2103	4239	6342	179148777	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65405G>A	2.37:g.179440531C>T	ENSP00000465570:p.Arg21802Gln		179148777	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.88	1.770101	0.31320	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.66	3.88	0.44766	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32346	0.0826	N	0.12887	0.27	0.31869	N	0.619964	B;B;B;B	0.30179	0.271;0.271;0.271;0.271	B;B;B;B	0.28139	0.086;0.086;0.086;0.086	T	0.38972	-0.9636	9	0.87932	D	0	.	6.9044	0.24301	0.0:0.6193:0.0:0.3807	.	14378;14503;14570;21802	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	20875;14378;14570;14503;14376	ENSP00000343764:R20875Q;ENSP00000434586:R14378Q;ENSP00000340554:R14570Q;ENSP00000352154:R14503Q	ENSP00000340554:R14570Q	R	-	2	0	TTN	179148777	1.000000	0.71417	0.880000	0.34516	0.782000	0.44232	2.760000	0.47581	0.770000	0.33336	0.650000	0.86243	CGG		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179440531	C	T	179440531	3	4	54	1	0	0	0	0	1	0	0	0	16775	652	23	1	37799	1	TTN	2	179440531	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	3816450	179440531	63758842	16	7236										
TTN	7273	broad.mit.edu	37	chr2	179473120	179473120	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	aacccaaaatggggcttccaTtatcttttggttcattccat	6	10	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:179473120T>C	ENST00000591111.1	-	225	47791	c.47567A>G	c.(47566-47568)aAt>aGt	p.N15856S	TTN_ENST00000589042.1_Missense_Mutation_p.N17497S|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N14929S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N8432S|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N8557S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N8624S			Q8WZ42	TITIN_HUMAN	titin	15856	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.N8432S(1)|p.N8624S(1)|p.N8557S(1)|p.N14929S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGGCTTCCATTATCTTTTGG	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											44	40	41					2																	179473120		1863	4098	5961	179181365	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.47567A>G	2.37:g.179473120T>C	ENSP00000465570:p.Asn15856Ser		179181365	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	11.26	1.586406	0.28268	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.72	4.55	0.56014	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.68742	0.3034	M	0.63208	1.945	0.48341	D	0.999635	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.71115	-0.4686	9	0.87932	D	0	.	13.0115	0.58733	0.0:0.0:0.1348:0.8652	.	8432;8557;8624;15856	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	14929;8432;8624;8557;8432	ENSP00000343764:N14929S;ENSP00000434586:N8432S;ENSP00000340554:N8624S;ENSP00000352154:N8557S	ENSP00000340554:N8624S	N	-	2	0	TTN	179181365	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	6.255000	0.72466	0.974000	0.38366	0.460000	0.39030	AAT		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179473120	T	C	179473120	3	2	54	1	0	0	0	0	1	0	0	0	16775	1493	52	4	55555	4	TTN	2	179473120	Missense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09	32589	179473120	63726253	17	7237										
TTN	7273	broad.mit.edu	37	chr2	179486705	179486705	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gtcatattttttgcccttttTaatttcagcaccatctttaa	3	9	3	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:179486705T>A	ENST00000591111.1	-	194	40245	c.40021A>T	c.(40021-40023)Aaa>Taa	p.K13341*	TTN_ENST00000589042.1_Nonsense_Mutation_p.K14982*|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.K12414*|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.K5917*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.K6042*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.K6109*			Q8WZ42	TITIN_HUMAN	titin	13341	Ig-like 89.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K6042*(1)|p.K6109*(1)|p.K12414*(1)|p.K5917*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGCCCTTTTTAATTTCAGCA	0.343																																																4	Substitution - Nonsense(4)	large_intestine(4)	2											148	128	135					2																	179486705		1872	4100	5972	179194950	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40021A>T	2.37:g.179486705T>A	ENSP00000465570:p.Lys13341*		179194950	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	58	31.686368	0.99979	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.0568	0.58984	0.0:0.0:0.1339:0.8661	.	.	.	.	X	12414;5917;6109;6042;5917	.	ENSP00000340554:K6109X	K	-	1	0	TTN	179194950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.186000	0.72026	2.323000	0.78572	0.528000	0.53228	AAA		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179486705	T	A	179486705	4	1	54	1	0	0	0	0	0	1	0	0	16775	1763	61	5	63225	5	TTN	2	179486705	Nonsense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09	13585	179486705	63712668	18	7238										
ABCA12	26154	broad.mit.edu	37	chr2	215876238	215876238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	agtcaaaaaatccttggtgtGgttgccttttggcctctggg	12	8	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr2:215876238G>T	ENST00000272895.7	-	17	2476	c.2257C>A	c.(2257-2259)Cac>Aac	p.H753N	ABCA12_ENST00000389661.4_Missense_Mutation_p.H435N	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	753					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.H753N(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TCCTTGGTGTGGTTGCCTTTT	0.368																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											101	106	104					2																	215876238		2203	4300	6503	215584483	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2257C>A	2.37:g.215876238G>T	ENSP00000272895:p.His753Asn		215584483	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144862	0.57044	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87571	-2.27;-2.26	5.11	5.11	0.69529	.	0.284014	0.30639	N	0.009188	D	0.87200	0.6118	N	0.22421	0.69	0.80722	D	1	D;P	0.63880	0.993;0.735	D;B	0.70227	0.968;0.319	T	0.82824	-0.0266	10	0.11485	T	0.65	.	15.8141	0.78586	0.0:0.0:1.0:0.0	.	753;435	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	753;435	ENSP00000272895:H753N;ENSP00000374312:H435N	ENSP00000272895:H753N	H	-	1	0	ABCA12	215584483	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.024000	0.41049	2.530000	0.85305	0.655000	0.94253	CAC		0.368	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215876238	G	T	215876238	3	4	54	1	0	0	0	0	1	0	0	0	30	1348	47	2	5678	2	ABCA12	2	215876238	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	36389533	215876238	27323135	19	7239										
CAND2	23066	broad.mit.edu	37	chr3	12858310	12858310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcctgcggaatgagatcaccCggctgcccgccatcaaggcg	13	15	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:12858310C>T	ENST00000456430.2	+	10	1920	c.1879C>T	c.(1879-1881)Cgg>Tgg	p.R627W	CAND2_ENST00000295989.5_Missense_Mutation_p.R534W	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	627					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.R534W(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGAGATCACCCGGCTGCCCGC	0.632																																					GBM(43;676 868 1633 6395 37496)											1	Substitution - Missense(1)	large_intestine(1)	3											67	76	73					3																	12858310		2100	4217	6317	12833310	SO:0001583	missense	23066				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1879C>T	3.37:g.12858310C>T	ENSP00000387641:p.Arg627Trp		12833310	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.386485	0.61956	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.71341	-0.56;-0.56	4.82	4.82	0.62117	Armadillo-like helical (1);Armadillo-type fold (1);	0.068282	0.56097	D	0.000033	D	0.87884	0.6290	M	0.93550	3.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.91089	0.4905	10	0.87932	D	0	-35.2501	15.7833	0.78281	0.0:1.0:0.0:0.0	.	627;534	O75155;O75155-2	CAND2_HUMAN;.	W	534;627	ENSP00000295989:R534W;ENSP00000387641:R627W	ENSP00000295989:R534W	R	+	1	2	CAND2	12833310	0.317000	0.24589	1.000000	0.80357	0.837000	0.47467	0.913000	0.28611	2.395000	0.81488	0.561000	0.74099	CGG		0.632	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		T	12858310	C	T	12858310	3	4	54	1	0	0	0	0	1	0	0	0	2622	643	23	1	1917	1	CAND2	3	12858310	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		12858310	185164120	20	7240										
SGOL1	151648	broad.mit.edu	37	chr3	20212291	20212291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acacaaatctgtaaaagggtCccctcttctcagtttcctgt	6	12	3	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:20212291C>T	ENST00000263753.4	-	8	1628	c.1489G>A	c.(1489-1491)Gac>Aac	p.D497N	SGOL1_ENST00000417364.1_Missense_Mutation_p.D245N|SGOL1_ENST00000460637.1_5'UTR|SGOL1_ENST00000412868.1_Missense_Mutation_p.D497N|SGOL1_ENST00000443724.1_Intron|SGOL1_ENST00000421451.1_Missense_Mutation_p.D497N|SGOL1_ENST00000437051.1_Missense_Mutation_p.D245N|SGOL1_ENST00000306698.2_Missense_Mutation_p.D228N|SGOL1_ENST00000425061.1_Missense_Mutation_p.D245N|SGOL1_ENST00000452020.1_Missense_Mutation_p.D228N|SGOL1_ENST00000412997.1_Missense_Mutation_p.D497N|SGOL1_ENST00000383774.1_Intron|SGOL1_ENST00000419233.2_Missense_Mutation_p.D245N|SGOL1_ENST00000442720.1_Missense_Mutation_p.D228N|SGOL1_ENST00000429446.3_Missense_Mutation_p.D228N	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	497					attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)	p.D497N(1)		kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						GTAAAAGGGTCCCCTCTTCTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	61	61					3																	20212291		2203	4300	6503	20187295	SO:0001583	missense	151648			BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.1489G>A	3.37:g.20212291C>T	ENSP00000263753:p.Asp497Asn		20187295	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Missense_Mutation	SNP	ENST00000263753.4	37	CCDS33716.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532295	0.85812	.	.	ENSG00000129810	ENST00000306698;ENST00000419233;ENST00000263753;ENST00000425061;ENST00000421451;ENST00000452020;ENST00000442720;ENST00000412997;ENST00000437051;ENST00000412868;ENST00000429446;ENST00000417364	T;T;T;T;T;T;T;T	0.73897	-0.79;-0.75;-0.79;-0.75;-0.33;-0.69;-0.33;-0.69	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.82296	0.5006	L	0.41492	1.28	0.29813	N	0.831446	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.99;0.99;0.99;0.999;0.976;0.991	T	0.79624	-0.1726	10	0.87932	D	0	.	18.235	0.89947	0.0:1.0:0.0:0.0	.	497;228;245;245;497;228	B5BUA4;Q5FBB7-5;Q5FBB7-4;Q5FBB7-2;Q5FBB7;Q5FBB7-3	.;.;.;.;SGOL1_HUMAN;.	N	228;245;497;245;497;228;228;497;245;497;228;245	ENSP00000394625:D245N;ENSP00000263753:D497N;ENSP00000414960:D245N;ENSP00000414129:D497N;ENSP00000410458:D497N;ENSP00000389034:D245N;ENSP00000406880:D497N;ENSP00000394613:D245N	ENSP00000263753:D497N	D	-	1	0	SGOL1	20187295	0.999000	0.42202	1.000000	0.80357	0.808000	0.45660	4.798000	0.62510	2.746000	0.94184	0.591000	0.81541	GAC		0.338	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484		T	20212291	C	T	20212291	3	4	54	1	0	0	0	0	1	0	0	0	14253	855	30	3	224	3	SGOL1	3	20212291	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	7353981	20212291	177810139	21	7241										
COL7A1	1294	broad.mit.edu	37	chr3	48621941	48621941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tggtccagggtcccctttccGcccaggaagcccaggtcctt	11	16	0	0	rs147089666	byFrequency	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:48621941G>A	ENST00000328333.8	-	35	4203	c.4096C>T	c.(4096-4098)Cgg>Tgg	p.R1366W	COL7A1_ENST00000454817.1_Missense_Mutation_p.R1366W	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1366	Interrupted collagenous region.|Triple-helical region.		R -> W (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R1366W(2)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCCCCTTTCCGCCCAGGAAGC	0.617																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	3						G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	167	171	170		4096	2.3	0	3	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL7A1	NM_000094.3	101	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	probably-damaging	1366/2945	48621941	4,13002	2203	4300	6503	48596945	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.4096C>T	3.37:g.48621941G>A	ENSP00000332371:p.Arg1366Trp		48596945	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351467	0.24512	6.81E-4	1.16E-4	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.93659	-3.26;-3.26	5.62	2.3	0.28687	.	0.767870	0.11135	N	0.595954	D	0.91348	0.7271	M	0.64404	1.975	0.09310	N	1	D	0.62365	0.991	B	0.40410	0.328	T	0.82649	-0.0353	10	0.66056	D	0.02	.	13.2901	0.60267	0.0:0.0:0.5165:0.4835	.	1366	Q02388	CO7A1_HUMAN	W	1366	ENSP00000332371:R1366W;ENSP00000412569:R1366W	ENSP00000332371:R1366W	R	-	1	2	COL7A1	48596945	0.008000	0.16893	0.005000	0.12908	0.964000	0.63967	1.644000	0.37228	0.637000	0.30526	0.655000	0.94253	CGG		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48621941	G	A	48621941	3	1	54	1	0	0	0	0	1	0	0	0	3710	1086	38	1	5074	1	COL7A1	3	48621941	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	28409650	48621941	149400489	22	7242										
PROS1	5627	broad.mit.edu	37	chr3	93617367	93617367	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	caagtgtaacctccagggtaAttgacacaaagctgagcaca	9	10	0	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:93617367A>G	ENST00000394236.3	-	8	1090	c.774T>C	c.(772-774)aaT>aaC	p.N258N	PROS1_ENST00000407433.1_Silent_p.N127N	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	258	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		N -> S (in THPH5; produces around 30% of PROS1 levels compared to wild-type; has impaired secretion; intracellular degradation of unsecreted material is found). {ECO:0000269|PubMed:11858485, ECO:0000269|PubMed:7545463, ECO:0000269|Ref.14}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)	p.N258N(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CTCCAGGGTAATTGACACAAA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	3											99	91	94					3																	93617367		2203	4300	6503	95100057	SO:0001819	synonymous_variant	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.774T>C	3.37:g.93617367A>G			95100057	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Silent	SNP	ENST00000394236.3	37	CCDS2923.1																																																																																				0.373	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		G	93617367	A	G	93617367	2	3	54	1	0	0	0	0	0	0	0	1	12592	98	4	4		4	PROS1	3	93617367	Silent	SNP	A	TCGA-AG-3909-01A-01W-1073-09	44995426	93617367	104405063	23	7243										
GUCA1C	9626	broad.mit.edu	37	chr3	108672582	108672582	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tgtaggaactgctttctgatCaccagctatagatttgccat	8	9	2	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:108672582C>T	ENST00000261047.3	-	1	160	c.28G>A	c.(28-30)Gat>Aat	p.D10N	GUCA1C_ENST00000393963.3_Missense_Mutation_p.D10N|GUCA1C_ENST00000471108.1_Missense_Mutation_p.D10N	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	10					phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.D10N(1)		endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						GCTTTCTGATCACCAGCTATA	0.418																																					NSCLC(157;1360 1999 30631 40189 44208)											1	Substitution - Missense(1)	large_intestine(1)	3											141	142	141					3																	108672582		2203	4300	6503	110155272	SO:0001583	missense	9626			AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"EF-hand domain containing"	4680	protein-coding gene	gene with protein product	"guanylyl cyclase-activating protein 3"	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.28G>A	3.37:g.108672582C>T	ENSP00000261047:p.Asp10Asn		110155272	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.604986	0.28623	.	.	ENSG00000138472	ENST00000393963;ENST00000261047;ENST00000471108	T;T;T	0.72505	-0.4;-0.66;-0.28	5.6	2.75	0.32379	.	2.645310	0.01387	N	0.013129	T	0.67804	0.2932	L	0.59436	1.845	0.09310	N	1	P;P	0.34462	0.454;0.454	B;B	0.32677	0.15;0.107	T	0.53215	-0.8470	10	0.49607	T	0.09	.	6.1526	0.20320	0.1538:0.6829:0.0:0.1633	.	10;10	C9JNI2;O95843	.;GUC1C_HUMAN	N	10	ENSP00000377535:D10N;ENSP00000261047:D10N;ENSP00000417761:D10N	ENSP00000261047:D10N	D	-	1	0	GUCA1C	110155272	0.003000	0.15002	0.004000	0.12327	0.007000	0.05969	0.633000	0.24598	0.808000	0.34231	0.650000	0.86243	GAT		0.418	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459		T	108672582	C	T	108672582	3	4	54	1	0	0	0	0	1	0	0	0	6911	826	29	3	617	3	GUCA1C	3	108672582	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	15055215	108672582	89349848	24	7244										
FBXO40	51725	broad.mit.edu	37	chr3	121340299	121340299	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggggaaagcccgcagatcccCgccagggcaccacaggcatt	13	15	0	1	rs141957650		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:121340299C>T	ENST00000338040.4	+	3	437	c.23C>T	c.(22-24)cCg>cTg	p.P8L		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	8					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P8L(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CGCAGATCCCCGCCAGGGCAC	0.532													C|||	1	0.000199681	0	0	5008	,	,		16862	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											72	74	73					3																	121340299		2203	4300	6503	122822989	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.23C>T	3.37:g.121340299C>T	ENSP00000337510:p.Pro8Leu		122822989	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.082	-1.181803	0.01633	.	.	ENSG00000163833	ENST00000338040	T	0.40225	1.04	5.73	3.89	0.44902	.	0.609592	0.17228	N	0.182079	T	0.25827	0.0629	N	0.22421	0.69	0.09310	N	0.999999	B	0.15719	0.014	B	0.11329	0.006	T	0.16541	-1.0399	10	0.14656	T	0.56	0.2054	9.1779	0.37123	0.0:0.8191:0.0:0.1809	.	8	Q9UH90	FBX40_HUMAN	L	8	ENSP00000337510:P8L	ENSP00000337510:P8L	P	+	2	0	FBXO40	122822989	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	1.113000	0.31184	1.372000	0.46190	0.655000	0.94253	CCG		0.532	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121340299	C	T	121340299	3	4	54	1	0	0	0	0	1	0	0	0	5768	652	23	1	29	1	FBXO40	3	121340299	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	12667717	121340299	76682131	25	7245										
MCF2L2	23101	broad.mit.edu	37	chr3	183145690	183145690	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	aaaattaaagcttcgtttacCgacatgagtgatcactgtgg	9	7	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:183145690C>T	ENST00000328913.3	-	1	373	c.76G>A	c.(76-78)Gat>Aat	p.D26N	MCF2L2_ENST00000447025.2_Splice_Site_p.D26N|MCF2L2_ENST00000414362.2_Splice_Site_p.D26N|MCF2L2_ENST00000473233.1_Splice_Site_p.D26N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	26	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D26N(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CTTCGTTTACCGACATGAGTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											87	91	90					3																	183145690		2203	4300	6503	184628384	SO:0001630	splice_region_variant	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.76+1G>A	3.37:g.183145690C>T			184628384	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026540	0.93518	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.06933	4.35;4.4;3.54;3.24	5.31	5.31	0.75309	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.64402	U	0.000020	T	0.21550	0.0519	L	0.61387	1.9	0.44890	D	0.997909	D;D	0.76494	0.984;0.999	P;P	0.58970	0.671;0.849	T	0.00180	-1.1948	9	.	.	.	.	14.4771	0.67554	0.0:1.0:0.0:0.0	.	26;26	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	N	26	ENSP00000328118:D26N;ENSP00000420070:D26N;ENSP00000388190:D26N;ENSP00000414131:D26N	.	D	-	1	0	MCF2L2	184628384	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.065000	0.57513	2.474000	0.83562	0.655000	0.94253	GAT		0.522	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	Missense_Mutation	T	183145690	C	T	183145690	5	4	54	1	0	0	0	0	0	0	1	0	9410	666	23	1	3388	1	MCF2L2	3	183145690	Splice_Site	SNP	C	TCGA-AG-3909-01A-01W-1073-09	61805391	183145690	14876740	26	7246										
ABCC5	10057	broad.mit.edu	37	chr3	183670905	183670905	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcttgatccagtaactcaacCaccaggtgctgaaggcggtg	12	11	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr3:183670905C>T	ENST00000334444.6	-	18	2876	c.2636G>A	c.(2635-2637)tGg>tAg	p.W879*	ABCC5_ENST00000265586.6_Nonsense_Mutation_p.W879*	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	879	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.W879*(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GTAACTCAACCACCAGGTGCT	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											104	102	103					3																	183670905		1917	4120	6037	185153599	SO:0001587	stop_gained	10057			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.2636G>A	3.37:g.183670905C>T	ENSP00000333926:p.Trp879*		185153599	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Nonsense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	C	40	8.246463	0.98724	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	.	.	.	5.62	5.62	0.85841	.	0.059276	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7591	19.69	0.95996	0.0:1.0:0.0:0.0	.	.	.	.	X	879	.	ENSP00000265586:W879X	W	-	2	0	ABCC5	185153599	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	7.380000	0.79704	2.648000	0.89879	0.650000	0.86243	TGG		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		T	183670905	C	T	183670905	4	4	54	1	0	0	0	0	0	1	0	0	56	595	21	3	1729	3	ABCC5	3	183670905	Nonsense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	525215	183670905	14351525	27	7247										
BANK1	55024	broad.mit.edu	37	chr4	102946615	102946615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gacctcctctccccccgccgCgacctgtagctaatgccttc	7	20	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr4:102946615C>T	ENST00000322953.4	+	9	1817	c.1543C>T	c.(1543-1545)Cga>Tga	p.R515*	BANK1_ENST00000504592.1_Nonsense_Mutation_p.R500*|BANK1_ENST00000444316.2_Nonsense_Mutation_p.R485*|BANK1_ENST00000428908.1_Nonsense_Mutation_p.R382*|BANK1_ENST00000510950.1_3'UTR|RP11-498M5.2_ENST00000505091.1_RNA|BANK1_ENST00000508653.1_Nonsense_Mutation_p.R382*	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	515					B cell activation (GO:0042113)			p.R515*(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CCCCCCGCCGCGACCTGTAGC	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											57	58	57					4																	102946615		2203	4300	6503	103165638	SO:0001587	stop_gained	55024			AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1543C>T	4.37:g.102946615C>T	ENSP00000320509:p.Arg515*		103165638	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Nonsense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104110	0.94245	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	.	.	.	4.9	3.0	0.34707	.	0.211219	0.31507	N	0.007539	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8154	0.46573	0.3423:0.6577:0.0:0.0	.	.	.	.	X	500;515;382;382;485	.	ENSP00000320509:R515X	R	+	1	2	BANK1	103165638	0.200000	0.23398	0.008000	0.14137	0.018000	0.09664	0.745000	0.26259	1.029000	0.39812	0.591000	0.81541	CGA		0.438	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		T	102946615	C	T	102946615	4	4	54	1	0	0	0	0	0	1	0	0	1310	760	27	1	1577	1	BANK1	4	102946615	Nonsense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		102946615	88207661	28	7248										
TRIML2	205860	broad.mit.edu	37	chr4	189012782	189012782	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cttttcagaggggggaagacCcagagagtccactcggtccc	13	12	1	3			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr4:189012782C>G	ENST00000512729.1	-	7	1283	c.909G>C	c.(907-909)tgG>tgC	p.W303C	TRIML2_ENST00000326754.3_Missense_Mutation_p.W328C	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	303	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.W303C(1)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		GGGGGAAGACCCAGAGAGTCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	4											132	148	143					4																	189012782		2203	4300	6503	189249776	SO:0001583	missense	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.909G>C	4.37:g.189012782C>G	ENSP00000422581:p.Trp303Cys		189249776	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	37	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	C	11.92	1.783874	0.31593	.	.	ENSG00000179046	ENST00000512729;ENST00000326754	T;T	0.61980	0.06;0.06	5.85	4.09	0.47781	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.47455	D	0.000222	T	0.69387	0.3105	L	0.48935	1.535	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	T	0.69978	-0.4998	10	0.54805	T	0.06	.	8.8899	0.35427	0.1517:0.7705:0.0:0.0778	.	328;303	B7ZLC3;Q8N7C3	.;TRIMM_HUMAN	C	303;328	ENSP00000422581:W303C;ENSP00000317498:W328C	ENSP00000317498:W328C	W	-	3	0	TRIML2	189249776	0.042000	0.20092	1.000000	0.80357	0.104000	0.19210	1.557000	0.36299	1.610000	0.50200	0.655000	0.94253	TGG		0.552	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		G	189012782	C	G	189012782	3	3	54	1	0	0	0	0	1	0	0	0	16591	624	22	5	258	5	TRIML2	4	189012782	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	86066167	189012782	2141494	29	7249										
MYO10	4651	broad.mit.edu	37	chr5	16680134	16680134	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acgttttgaatggcactggaCcaccgggtggcctcgttgag	14	10	0	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:16680134C>A	ENST00000513610.1	-	33	4918	c.4464G>T	c.(4462-4464)tgG>tgT	p.W1488C	MYO10_ENST00000274203.9_Missense_Mutation_p.W845C|MYO10_ENST00000505695.1_Missense_Mutation_p.W827C|MYO10_ENST00000515803.1_Missense_Mutation_p.W827C|MYO10_ENST00000427430.2_Missense_Mutation_p.W845C	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1488	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.W1488C(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TGGCACTGGACCACCGGGTGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	88	88					5																	16680134		2038	4189	6227	16733134	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4464G>T	5.37:g.16680134C>A	ENSP00000421280:p.Trp1488Cys		16733134	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794413	0.90453	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.99882	-7.48;-7.48;-7.48;-7.48;-7.48	5.46	5.46	0.80206	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.99910	0.9957	M	0.90977	3.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.96411	0.9304	9	0.87932	D	0	.	19.6953	0.96022	0.0:1.0:0.0:0.0	.	367;1128;1488	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	C	1488;827;845;827;845	ENSP00000421280:W1488C;ENSP00000425051:W827C;ENSP00000274203:W845C;ENSP00000421170:W827C;ENSP00000391106:W845C	ENSP00000274203:W845C	W	-	3	0	MYO10	16733134	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.798000	0.85924	2.741000	0.93983	0.655000	0.94253	TGG		0.582	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16680134	C	A	16680134	3	1	54	1	0	0	0	0	1	0	0	0	10092	508	18	2	1748	2	MYO10	5	16680134	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		16680134	164235126	30	7250										
PAPD4	167153	broad.mit.edu	37	chr5	78938706	78938706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cacggcatatactcaccttaGtccataaacacttctgtact	4	13	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:78938706G>A	ENST00000296783.3	+	8	1023	c.724G>A	c.(724-726)Gtc>Atc	p.V242I	PAPD4_ENST00000504233.1_Missense_Mutation_p.V242I|PAPD4_ENST00000453514.1_Missense_Mutation_p.V242I|PAPD4_ENST00000428308.2_Missense_Mutation_p.V242I|PAPD4_ENST00000423041.2_Missense_Mutation_p.V238I			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	242					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)	p.V242I(1)		biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		ACTCACCTTAGTCCATAAACA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	5											96	85	89					5																	78938706		2203	4300	6503	78974462	SO:0001583	missense	167153			AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.724G>A	5.37:g.78938706G>A	ENSP00000296783:p.Val242Ile		78974462	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	37	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.531509	0.45073	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	5.88	5.0	0.66597	.	0.175573	0.49916	D	0.000131	T	0.32376	0.0827	L	0.35723	1.085	0.40164	D	0.977097	B;B;B	0.30406	0.047;0.078;0.278	B;B;B	0.27887	0.018;0.041;0.084	T	0.09773	-1.0659	10	0.13108	T	0.6	-2.9437	15.6317	0.76917	0.0:0.3855:0.6145:0.0	.	242;238;242	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	I	242;238;242;242;242	ENSP00000397563:V242I;ENSP00000393412:V238I;ENSP00000421966:V242I;ENSP00000396861:V242I;ENSP00000296783:V242I	ENSP00000296783:V242I	V	+	1	0	PAPD4	78974462	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.958000	0.49145	1.468000	0.48064	-0.291000	0.09656	GTC		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		A	78938706	G	A	78938706	3	1	54	1	0	0	0	0	1	0	0	0	11455	1029	36	3	746	3	PAPD4	5	78938706	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	62258572	78938706	101976554	31	7251										
WDR36	134430	broad.mit.edu	37	chr5	110428046	110428046	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cagcgggcgccggaagcggtGttgtgtctgcagctctggca	17	11	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:110428046G>T	ENST00000513710.2	+	1	64	c.60G>T	c.(58-60)gtG>gtT	p.V20V	WDR36_ENST00000506538.2_Silent_p.V20V|CTC-551A13.2_ENST00000507269.3_RNA|WDR36_ENST00000505303.1_5'UTR			Q8NI36	WDR36_HUMAN	WD repeat domain 36	20					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.V20V(1)		cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CGGAAGCGGTGTTGTGTCTGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	5											75	83	80					5																	110428046		2202	4300	6502	110455945	SO:0001819	synonymous_variant	134430			AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.60G>T	5.37:g.110428046G>T			110455945	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																				0.587	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110428046	G	T	110428046	2	4	54	1	0	0	0	0	0	0	0	1	17330	1364	48	2		2	WDR36	5	110428046	Silent	SNP	G	TCGA-AG-3909-01A-01W-1073-09	31489340	110428046	70487214	32	7252										
APC	324	broad.mit.edu	37	chr5	112173780	112173780	+	Frame_Shift_Del	DEL	T	T	-													0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	accatatttgaatactacagTgttacccagctcctcttcat							TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:112173780delT	ENST00000457016.1	+	16	2869	c.2489delT	c.(2488-2490)gtgfs	p.V830fs	APC_ENST00000508376.2_Frame_Shift_Del_p.V830fs|APC_ENST00000257430.4_Frame_Shift_Del_p.V830fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	830	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.V830fs*12(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AATACTACAGTGTTACCCAGC	0.393		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	large_intestine(1)|skin(1)	5											63	64	64					5																	112173780		2202	4300	6502	112201679	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2489delT	5.37:g.112173780delT	ENSP00000413133:p.Val830fs		112201679	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.393	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112173780	T	-	112173780	7	5	54	1	0	1	0	1	0	0	0	0	763	1696	59	0	2547	0	APC	5	112173780	Frame_Shift_Del	DEL	T	TCGA-AG-3909-01A-01W-1073-09	1745734	112173780	68741480	33	7253			1	8		3	3	4804	N	T_G_AC	8.618201e-05
APC	324	broad.mit.edu	37	chr5	112175168	112175169	+	Frame_Shift_Del	DEL	AC	AC	-													0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	aaataggatgtaatcagacgAcacaggaagcagattctgct							TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	AC	AC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:112175168_112175169delAC	ENST00000457016.1	+	16	4257_4258	c.3877_3878delAC	c.(3877-3879)acafs	p.T1293fs	APC_ENST00000508376.2_Frame_Shift_Del_p.T1293fs|APC_ENST00000257430.4_Frame_Shift_Del_p.T1293fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1293	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1294fs*6(2)|p.T1293fs*2(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAATCAGACGACACAGGAAGCA	0.381		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Deletion - Frameshift(4)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5																																								112203068	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3877_3878delAC	5.37:g.112175170_112175171delAC	ENSP00000413133:p.Thr1293fs		112203067	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.381	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175169	AC	-	112175168	7	5	54	1	0	1	0	1	0	0	0	0	763	275	10	0	3935	0	APC	5	112175168	Frame_Shift_Del	DEL	AC	TCGA-AG-3909-01A-01W-1073-09	1388	112175168	68740092	34	7254			1	8		3	3	4804	N	T_G_AC	8.618201e-05
APC	324	broad.mit.edu	37	chr5	112178583	112178583	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	aagtggaagtgaatctgataGatcagaaagacctgtattag	11	4	2	5			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:112178583G>A	ENST00000457016.1	+	16	7672	c.7292G>A	c.(7291-7293)aGa>aAa	p.R2431K	APC_ENST00000508376.2_Missense_Mutation_p.R2431K|APC_ENST00000257430.4_Missense_Mutation_p.R2431K|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	2431	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R2431K(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATCTGATAGATCAGAAAGA	0.363		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											72	73	73					5																	112178583		2202	4300	6502	112206482	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.7292G>A	5.37:g.112178583G>A	ENSP00000413133:p.Arg2431Lys		112206482	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043513	0.36085	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89875	-2.58;-2.58;-2.58	6.06	5.19	0.71726	Adenomatous polyposis coli protein basic domain (1);	0.089706	0.85682	D	0.000000	D	0.86920	0.6049	L	0.51422	1.61	0.43412	D	0.995558	B;B	0.23735	0.09;0.09	B;B	0.31442	0.089;0.13	T	0.82739	-0.0308	9	.	.	.	-16.5528	15.3394	0.74284	0.0665:0.0:0.9335:0.0	.	2433;2431	Q4LE70;P25054	.;APC_HUMAN	K	2431	ENSP00000413133:R2431K;ENSP00000257430:R2431K;ENSP00000427089:R2431K	.	R	+	2	0	APC	112206482	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	7.842000	0.86851	1.585000	0.49928	-0.136000	0.14681	AGA		0.363	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112178583	G	A	112178583	3	1	54	1	0	0	0	0	1	0	0	0	763	942	33	3	7350	3	APC	5	112178583	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	3415	112178583	68736677	35	7255			1	8		3	3	4804	N	T_G_AC	8.618201e-05
TRPC7	57113	broad.mit.edu	37	chr5	135692752	135692752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ctgatggccagcagcagcgcGtcccccacccgtgccaggtt	12	17	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:135692752G>A	ENST00000513104.1	-	2	606	c.324C>T	c.(322-324)gaC>gaT	p.D108D	TRPC7_ENST00000355180.3_Silent_p.D108D|TRPC7_ENST00000426057.2_Silent_p.D108D	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	108					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.D108D(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCAGCAGCGCGTCCCCCACCC	0.667																																																2	Substitution - coding silent(2)	large_intestine(2)	5											56	65	62					5																	135692752		2203	4300	6503	135720651	SO:0001819	synonymous_variant	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.324C>T	5.37:g.135692752G>A			135720651	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	De_novo_Start_OutOfFrame	SNP	ENST00000513104.1	37	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	8.425	0.847192	0.17034	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	5.0	-0.142	0.13448	.	.	.	.	.	T	0.56046	0.1959	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50189	-0.8857	4	.	.	.	-29.7479	9.6183	0.39706	0.5936:0.0:0.4064:0.0	.	.	.	.	C	108	.	.	R	-	1	0	TRPC7	135720651	0.924000	0.31332	0.998000	0.56505	0.988000	0.76386	0.115000	0.15540	0.050000	0.15949	0.561000	0.74099	CGC		0.667	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692752	G	A	135692752	2	1	54	1	0	0	0	0	0	0	0	1	16624	1136	40	1		1	TRPC7	5	135692752	Silent	SNP	G	TCGA-AG-3909-01A-01W-1073-09	23514169	135692752	45222508	36	7256										
PCDHA2	56146	broad.mit.edu	37	chr5	140175915	140175915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acgacaacgcgccggcgttcGcacagcctgagtacacagta	11	14	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:140175915G>A	ENST00000526136.1	+	1	1366	c.1366G>A	c.(1366-1368)Gca>Aca	p.A456T	PCDHA2_ENST00000378132.1_Missense_Mutation_p.A456T|PCDHA2_ENST00000520672.2_Missense_Mutation_p.A456T|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	456	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A456T(2)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCGGCGTTCGCACAGCCTGA	0.657																																																2	Substitution - Missense(2)	large_intestine(2)	5											77	78	77					5																	140175915		2203	4300	6503	140156099	SO:0001583	missense	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1366G>A	5.37:g.140175915G>A	ENSP00000431748:p.Ala456Thr		140156099	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	g	4.798	0.148314	0.09134	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.59906	0.23;0.23;0.23	3.98	3.98	0.46160	Cadherin (3);Cadherin-like (1);	0.409515	0.17250	U	0.181211	T	0.26702	0.0653	N	0.01417	-0.88	0.09310	N	1	P;B;P	0.35656	0.514;0.072;0.514	B;B;B	0.29077	0.098;0.079;0.098	T	0.14980	-1.0453	10	0.44086	T	0.13	.	12.6262	0.56630	0.0:0.3099:0.6901:0.0	.	456;456;456	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	T	456	ENSP00000430584:A456T;ENSP00000367372:A456T;ENSP00000431748:A456T	ENSP00000367372:A456T	A	+	1	0	PCDHA2	140156099	0.000000	0.05858	0.977000	0.42913	0.178000	0.23041	-0.575000	0.05861	1.920000	0.55613	0.650000	0.86243	GCA		0.657	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140175915	G	A	140175915	3	1	54	1	0	0	0	0	1	0	0	0	11555	1087	38	1	1368	1	PCDHA2	5	140175915	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	4483163	140175915	40739345	37	7257										
FAT2	2196	broad.mit.edu	37	chr5	150932903	150932903	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gatccactcaatgtgtagccGgacactggctgagagtggtg	14	9	1	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:150932903G>A	ENST00000261800.5	-	5	4003	c.3991C>T	c.(3991-3993)Cgg>Tgg	p.R1331W		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1331	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1331W(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATGTGTAGCCGGACACTGGCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	5											81	63	69					5																	150932903		2203	4300	6503	150913096	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3991C>T	5.37:g.150932903G>A	ENSP00000261800:p.Arg1331Trp		150913096	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907779	0.72868	.	.	ENSG00000086570	ENST00000261800	T	0.53206	0.63	5.49	4.54	0.55810	Cadherin (4);Cadherin-like (1);	0.000000	0.53938	D	0.000043	T	0.67988	0.2952	M	0.73598	2.24	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.68232	-0.5463	10	0.41790	T	0.15	.	16.3383	0.83074	0.0:0.0:0.816:0.184	.	1331	Q9NYQ8	FAT2_HUMAN	W	1331	ENSP00000261800:R1331W	ENSP00000261800:R1331W	R	-	1	2	FAT2	150913096	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	3.614000	0.54160	2.583000	0.87209	0.561000	0.74099	CGG		0.572	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150932903	G	A	150932903	3	1	54	1	0	0	0	0	1	0	0	0	5709	1115	39	1	9134	1	FAT2	5	150932903	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	10756988	150932903	29982357	38	7258										
FAT2	2196	broad.mit.edu	37	chr5	150946724	150946724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggttctgaagctcatccacaTctatggctgacatagtcatt	8	10	4	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr5:150946724T>C	ENST00000261800.5	-	1	1781	c.1769A>G	c.(1768-1770)gAt>gGt	p.D590G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	590	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D590G(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCATCCACATCTATGGCTGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	98	97					5																	150946724		2203	4300	6503	150926917	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1769A>G	5.37:g.150946724T>C	ENSP00000261800:p.Asp590Gly		150926917	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.751940	0.69533	.	.	ENSG00000086570	ENST00000261800	T	0.61627	0.09	5.75	5.75	0.90469	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000003	D	0.83769	0.5326	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89089	0.3481	10	0.87932	D	0	.	16.0518	0.80769	0.0:0.0:0.0:1.0	.	590	Q9NYQ8	FAT2_HUMAN	G	590	ENSP00000261800:D590G	ENSP00000261800:D590G	D	-	2	0	FAT2	150926917	1.000000	0.71417	0.994000	0.49952	0.896000	0.52359	7.975000	0.88055	2.191000	0.70037	0.533000	0.62120	GAT		0.418	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150946724	T	C	150946724	3	2	54	1	0	0	0	0	1	0	0	0	5709	1435	50	4	11372	4	FAT2	5	150946724	Missense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09	13821	150946724	29968536	39	7259										
SCAND3	114821	broad.mit.edu	37	chr6	28541599	28541599	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	aagtccagtgaagcttgtttCgccatctgaaattaggaata	9	7	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr6:28541599C>T	ENST00000452236.2	-	4	2684	c.2067G>A	c.(2065-2067)gcG>gcA	p.A689A	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1												p.A689A(1)		NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						aagcttgtttcgccatctgaa	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	6											16	16	16					6																	28541599		2095	4173	6268	28649578	SO:0001819	synonymous_variant	114821																														ENST00000452236.2:c.2067G>A	6.37:g.28541599C>T			28649578		Silent	SNP	ENST00000452236.2	37	CCDS34355.1																																																																																				0.299	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			T	28541599	C	T	28541599	2	4	54	1	0	0	0	0	0	0	0	1	13913	871	31	1		1	SCAND3	6	28541599	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09		28541599	142573468	40	7260										
PTCRA	171558	broad.mit.edu	37	chr6	42890846	42890846	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcagcagatggtggtggtctGcctggtccttgatgttgcac	15	9	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr6:42890846G>T	ENST00000304672.1	+	2	221	c.140G>T	c.(139-141)tGc>tTc	p.C47F	PTCRA_ENST00000441198.1_Intron|PTCRA_ENST00000446507.1_Intron	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	47					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)		p.C47F(1)		large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GTGGTGGTCTGCCTGGTCCTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											150	129	136					6																	42890846		2203	4300	6503	42998824	SO:0001583	missense	171558			AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.140G>T	6.37:g.42890846G>T	ENSP00000304447:p.Cys47Phe		42998824	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.0|21.0	4.086356|4.086356	0.76642|0.76642	.|.	.|.	ENSG00000171611|ENSG00000171611	ENST00000418903|ENST00000304672	.|T	.|0.79247	.|-1.25	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Immunoglobulin-like fold (1);	.|0.000000	.|0.51477	.|D	.|0.000086	T|T	0.80292|0.80292	0.4596|0.4596	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.82460|0.82460	-0.0446|-0.0446	6|10	0.87932|0.87932	D|D	0|0	-27.204|-27.204	15.6455|15.6455	0.77046|0.77046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|47	.|Q6ISU1	.|PTCRA_HUMAN	S|F	58|47	.|ENSP00000304447:C47F	ENSP00000407061:A58S|ENSP00000304447:C47F	A|C	+|+	1|2	0|0	PTCRA|PTCRA	42998824|42998824	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	5.199000|5.199000	0.65152|0.65152	2.748000|2.748000	0.94277|0.94277	0.650000|0.650000	0.86243|0.86243	GCC|TGC		0.597	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296		T	42890846	G	T	42890846	3	4	54	1	0	0	0	0	1	0	0	0	12769	1319	46	2	146	2	PTCRA	6	42890846	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	14349247	42890846	128224221	41	7261										
CUL7	9820	broad.mit.edu	37	chr6	43013368	43013368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tctggatgatgggccagaagCgggtcaggttctccaggagg	17	8	3	2	rs201130952		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr6:43013368C>T	ENST00000265348.3	-	14	2904	c.2819G>A	c.(2818-2820)cGc>cAc	p.R940H	CUL7_ENST00000478630.1_5'UTR|CUL7_ENST00000535468.1_Missense_Mutation_p.R1024H			Q14999	CUL7_HUMAN	cullin 7	940	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.R940H(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGGCCAGAAGCGGGTCAGGTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	71	66	68		3071,2819	1.2	0.7	6		68	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	CUL7	NM_001168370.1,NM_014780.4	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	1024/1783,940/1699	43013368	2,13004	2203	4300	6503	43121346	SO:0001583	missense	9820			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.2819G>A	6.37:g.43013368C>T	ENSP00000265348:p.Arg940His		43121346	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.953766	0.53293	0.0	2.33E-4	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.64085	-0.08;-0.08	5.11	1.2	0.21068	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	0.350509	0.32578	N	0.005917	T	0.38427	0.1040	M	0.65975	2.015	0.80722	D	1	B;B;B	0.19445	0.017;0.036;0.02	B;B;B	0.16289	0.011;0.015;0.015	T	0.27839	-1.0062	10	0.49607	T	0.09	-5.2521	7.934	0.29918	0.0:0.6592:0.0:0.3408	.	1024;1024;940	F5H0L1;B4DYZ0;Q14999	.;.;CUL7_HUMAN	H	940;1024	ENSP00000265348:R940H;ENSP00000438788:R1024H	ENSP00000265348:R940H	R	-	2	0	CUL7	43121346	0.992000	0.36948	0.748000	0.31131	0.978000	0.69477	1.174000	0.31932	-0.069000	0.12931	-0.140000	0.14226	CGC		0.622	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		T	43013368	C	T	43013368	3	4	54	1	0	0	0	0	1	0	0	0	4066	768	27	1	2329	1	CUL7	6	43013368	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	122522	43013368	128101699	42	7262										
ADCY1	107	broad.mit.edu	37	chr7	45747980	45747980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	catctcctcccacctgagcaCgctggcggactttgccattg	9	16	1	1	rs368928291		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr7:45747980C>T	ENST00000297323.7	+	18	2871	c.2849C>T	c.(2848-2850)aCg>aTg	p.T950M		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	950					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.T950M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CACCTGAGCACGCTGGCGGAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	MET/THR	0,4406		0,0,2203	204	159	174		2849	4.4	0.1	7		174	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADCY1	NM_021116.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	950/1120	45747980	1,13005	2203	4300	6503	45714505	SO:0001583	missense	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2849C>T	7.37:g.45747980C>T	ENSP00000297323:p.Thr950Met		45714505	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	37	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.535314	0.64972	0.0	1.16E-4	ENSG00000164742	ENST00000297323;ENST00000545300	T	0.30182	1.54	5.34	4.42	0.53409	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.202759	0.52532	D	0.000065	T	0.41949	0.1181	L	0.46157	1.445	0.50467	D	0.999874	D	0.71674	0.998	P	0.61722	0.893	T	0.22452	-1.0216	10	0.48119	T	0.1	.	9.9422	0.41587	0.0:0.8945:0.0:0.1055	.	950	Q08828	ADCY1_HUMAN	M	950	ENSP00000297323:T950M	ENSP00000297323:T950M	T	+	2	0	ADCY1	45714505	1.000000	0.71417	0.095000	0.20976	0.683000	0.39861	5.486000	0.66856	1.389000	0.46526	0.609000	0.83330	ACG		0.517	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45747980	C	T	45747980	3	4	54	1	0	0	0	0	1	0	0	0	292	536	19	1	2919	1	ADCY1	7	45747980	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		45747980	113390683	43	7263										
SEMA3E	9723	broad.mit.edu	37	chr7	83036445	83036445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cccgaccctggtgtaaattgCgtgagcattgttttctgcct	10	11	1	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr7:83036445C>T	ENST00000307792.3	-	7	1248	c.781G>A	c.(781-783)Gca>Aca	p.A261T	SEMA3E_ENST00000427262.1_Missense_Mutation_p.A201T	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	261	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.A261T(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GTGTAAATTGCGTGAGCATTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											114	107	109					7																	83036445		2203	4300	6503	82874381	SO:0001583	missense	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.781G>A	7.37:g.83036445C>T	ENSP00000303212:p.Ala261Thr		82874381	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.419900	0.25552	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.10960	2.82;2.82	5.43	-1.45	0.08828	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.165821	0.52532	N	0.000062	T	0.05410	0.0143	N	0.17838	0.53	0.35394	D	0.790998	B	0.23854	0.092	B	0.20955	0.032	T	0.44065	-0.9352	10	0.10111	T	0.7	.	11.2273	0.48890	0.0:0.6108:0.0:0.3892	.	261	O15041	SEM3E_HUMAN	T	261;201;261	ENSP00000303212:A261T;ENSP00000405052:A201T	ENSP00000303212:A261T	A	-	1	0	SEMA3E	82874381	0.564000	0.26602	0.005000	0.12908	0.746000	0.42486	1.229000	0.32600	-0.187000	0.10516	-0.489000	0.04712	GCA		0.403	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	83036445	C	T	83036445	3	4	54	1	0	0	0	0	1	0	0	0	14065	768	27	1	1590	1	SEMA3E	7	83036445	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	37288465	83036445	76102218	44	7264										
OR2A14	135941	broad.mit.edu	37	chr7	143826871	143826871	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcctacttgcgcatcctggcCgccatcttgaggatccagtc	9	15	1	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr7:143826871C>T	ENST00000408899.2	+	1	721	c.666C>T	c.(664-666)gcC>gcT	p.A222A		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A222A(1)		large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					GCATCCTGGCCGCCATCTTGA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	7											116	120	119					7																	143826871		2057	4206	6263	143457804	SO:0001819	synonymous_variant	135941				CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"GPCR / Class A : Olfactory receptors"	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.666C>T	7.37:g.143826871C>T			143457804	Q6IF41|Q8NGT8	Silent	SNP	ENST00000408899.2	37	CCDS43672.1																																																																																				0.612	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1			T	143826871	C	T	143826871	2	4	54	1	0	0	0	0	0	0	0	1	11007	639	23	1		1	OR2A14	7	143826871	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09	60790426	143826871	15311792	45	7265										
MCM4	4173	broad.mit.edu	37	chr8	48887410	48887410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gctaaagtaagattgtctaaCaaagttgaagccattgatgt	9	5	1	3			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr8:48887410C>T	ENST00000262105.2	+	14	2462	c.2253C>T	c.(2251-2253)aaC>aaT	p.N751N	MCM4_ENST00000523944.1_Silent_p.N751N	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	751					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.N751N(1)		biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GATTGTCTAACAAAGTTGAAG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	8											148	152	151					8																	48887410		2203	4300	6503	49049963	SO:0001819	synonymous_variant	4173				CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.2253C>T	8.37:g.48887410C>T			49049963	Q8NEH1|Q99658	Silent	SNP	ENST00000262105.2	37	CCDS6143.1																																																																																				0.498	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		T	48887410	C	T	48887410	2	4	54	1	0	0	0	0	0	0	0	1	9419	477	17	3		3	MCM4	8	48887410	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09		48887410	97476612	46	7266										
PXDNL	137902	broad.mit.edu	37	chr8	52396242	52396242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gattagaaaagctcccagctGgaattttagataatttgttg	9	5	0	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr8:52396242G>A	ENST00000356297.4	-	6	585	c.485C>T	c.(484-486)cCa>cTa	p.P162L	PXDNL_ENST00000543296.1_Missense_Mutation_p.P162L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	162					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.P162L(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTCCCAGCTGGAATTTTAGA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	8											29	26	27					8																	52396242		1578	3669	5247	52558795	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.485C>T	8.37:g.52396242G>A	ENSP00000348645:p.Pro162Leu		52558795	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	5.578	0.291369	0.10567	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.60672	0.17;0.17	4.6	-0.399	0.12415	.	.	.	.	.	T	0.52597	0.1744	L	0.55213	1.73	0.25823	N	0.98426	P	0.47910	0.902	P	0.46419	0.516	T	0.45131	-0.9282	9	0.29301	T	0.29	.	8.0724	0.30697	0.4475:0.0:0.5525:0.0	.	162	A1KZ92	PXDNL_HUMAN	L	162	ENSP00000348645:P162L;ENSP00000444865:P162L	ENSP00000348645:P162L	P	-	2	0	PXDNL	52558795	0.061000	0.20836	0.007000	0.13788	0.098000	0.18820	0.545000	0.23268	-0.355000	0.08199	-0.742000	0.03525	CCA		0.284	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52396242	G	A	52396242	3	1	54	1	0	0	0	0	1	0	0	0	12885	1348	47	3	3978	3	PXDNL	8	52396242	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	3508832	52396242	93967780	47	7267										
DENND3	22898	broad.mit.edu	37	chr8	142178177	142178177	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ttccgctggagagcaagtgcGtgcaggcataccatgcccac	12	13	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr8:142178177G>A	ENST00000262585.2	+	13	1866	c.1588G>A	c.(1588-1590)Gtg>Atg	p.V530M	DENND3_ENST00000424248.1_Missense_Mutation_p.V478M|DENND3_ENST00000519811.1_Missense_Mutation_p.V610M	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	530					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.V530M(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	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)			GAGCAAGTGCGTGCAGGCATA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	8											132	120	124					8																	142178177		2203	4300	6503	142247359	SO:0001583	missense	22898			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.1588G>A	8.37:g.142178177G>A	ENSP00000262585:p.Val530Met		142247359	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.43|14.43	2.533069|2.533069	0.45073|0.45073	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000262585;ENST00000424248;ENST00000519811	.|T;T;T	.|0.18338	.|2.69;2.22;2.67	5.36|5.36	3.56|3.56	0.40772|0.40772	.|.	.|0.251684	.|0.39909	.|N	.|0.001239	T|T	0.37461|0.37461	0.1004|0.1004	M|M	0.73598|0.73598	2.24|2.24	0.37110|0.37110	D|D	0.900328|0.900328	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|P;D;P	.|0.64042	.|0.835;0.921;0.835	T|T	0.44314|0.44314	-0.9336|-0.9336	5|10	.|0.87932	.|D	.|0	-11.4822|-11.4822	11.457|11.457	0.50187|0.50187	0.1465:0.0:0.8535:0.0|0.1465:0.0:0.8535:0.0	.|.	.|610;478;530	.|E9PF32;A2RUS2-2;A2RUS2	.|.;.;DEND3_HUMAN	H|M	534|530;478;610	.|ENSP00000262585:V530M;ENSP00000410594:V478M;ENSP00000428714:V610M	.|ENSP00000262585:V530M	R|V	+|+	2|1	0|0	DENND3|DENND3	142247359|142247359	1.000000|1.000000	0.71417|0.71417	0.036000|0.036000	0.18154|0.18154	0.003000|0.003000	0.03518|0.03518	4.456000|4.456000	0.60081|0.60081	0.638000|0.638000	0.30545|0.30545	0.462000|0.462000	0.41574|0.41574	CGT|GTG		0.532	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142178177	G	A	142178177	3	1	54	1	0	0	0	0	1	0	0	0	4443	1145	40	1	1634	1	DENND3	8	142178177	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	89781935	142178177	4185845	48	7268										
C9orf79	286234	broad.mit.edu	37	chr9	90503556	90503556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ccctaaagccacccccaaggGccaccactgtcctgtcaaaa	6	18	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr9:90503556G>A	ENST00000325643.5	+	4	4220	c.4154G>A	c.(4153-4155)gGc>gAc	p.G1385D		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1385					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G1385D(1)									ACCCCCAAGGGCCACCACTGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	9											56	52	53					9																	90503556		2203	4300	6503	89693376	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.4154G>A	9.37:g.90503556G>A	ENSP00000322640:p.Gly1385Asp		89693376	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	g	1.547	-0.540248	0.04053	.	.	ENSG00000177992	ENST00000325643	T	0.03553	3.89	2.05	-0.0152	0.13977	.	1.765340	0.03105	N	0.161626	T	0.03136	0.0092	L	0.38175	1.15	0.09310	N	1	P	0.35745	0.518	B	0.32533	0.147	T	0.40496	-0.9560	10	0.15066	T	0.55	.	2.6183	0.04909	0.1759:0.0:0.5439:0.2802	.	1385	Q6ZUB1	CI079_HUMAN	D	1385	ENSP00000322640:G1385D	ENSP00000322640:G1385D	G	+	2	0	C9orf79	89693376	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-0.313000	0.08103	-0.010000	0.14271	-0.291000	0.09656	GGC		0.617	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		A	90503556	G	A	90503556	3	1	54	1	0	0	0	0	1	0	0	0	2503	1203	42	3	4168	3	C9orf79	9	90503556	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09		90503556	50709875	49	7269										
PSMD13	5719	broad.mit.edu	37	chr11	244118	244118	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcactttgaaaatgagtgcaTtgatgctcggcggtgctcaa	11	8	2	3			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr11:244118T>C	ENST00000532097.1	+	4	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.I58T|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.I58T(1)		NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		AATGAGTGCATTGATGCTCGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											59	64	63					11																	244118		2202	4298	6500	234118	SO:0001627	intron_variant	5719			AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.210-43T>C	11.37:g.244118T>C			234118	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531946	0.27387	.	.	ENSG00000185627	ENST00000431206	T	0.20332	2.08	5.94	0.788	0.18601	.	.	.	.	.	T	0.12220	0.0297	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34976	-0.9807	7	.	.	.	.	9.4574	0.38762	0.0:0.3031:0.0:0.6969	.	58	Q9UNM6-2	.	T	58	ENSP00000396937:I58T	.	I	+	2	0	PSMD13	234118	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.178000	0.16820	0.122000	0.18314	0.460000	0.39030	ATT		0.418	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		C	244118	T	C	244118	1	2	54	0	1	0	0	0	0	0	0	0	12730	1493	52	4		4	PSMD13	11	244118	Intron	SNP	T	TCGA-AG-3909-01A-01W-1073-09		244118	134762398	50	7270										
OR5L1	219437	broad.mit.edu	37	chr11	55579241	55579241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cttcctagggtgcatggtgcAattctacttgttttgcactt	9	9	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr11:55579241A>G	ENST00000333973.2	+	1	388	c.299A>G	c.(298-300)cAa>cGa	p.Q100R		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q100R(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TGCATGGTGCAATTCTACTTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											236	211	219					11																	55579241		2200	4296	6496	55335817	SO:0001583	missense	219437			AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.299A>G	11.37:g.55579241A>G	ENSP00000335529:p.Gln100Arg		55335817	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.945117	0.73672	.	.	ENSG00000186117	ENST00000333973	T	0.00466	7.23	4.18	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000190	T	0.03390	0.0098	H	0.99379	4.54	0.42578	D	0.993203	D	0.89917	1.0	D	0.91635	0.999	T	0.00939	-1.1507	10	0.87932	D	0	-19.5197	12.1272	0.53922	1.0:0.0:0.0:0.0	.	100	Q8NGL2	OR5L1_HUMAN	R	100	ENSP00000335529:Q100R	ENSP00000335529:Q100R	Q	+	2	0	OR5L1	55335817	1.000000	0.71417	0.043000	0.18650	0.065000	0.16274	8.795000	0.91872	1.533000	0.49186	0.358000	0.22013	CAA		0.453	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		G	55579241	A	G	55579241	3	3	54	1	0	0	0	0	1	0	0	0	11201	130	5	4	301	4	OR5L1	11	55579241	Missense_Mutation	SNP	A	TCGA-AG-3909-01A-01W-1073-09	55335123	55579241	79427275	51	7271										
MPEG1	219972	broad.mit.edu	37	chr11	58979642	58979642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	agaggcggtcacggcactacGactgctctggctgtcttgga	14	11	3	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr11:58979642G>A	ENST00000361050.3	-	1	782	c.697C>T	c.(697-699)Cgt>Tgt	p.R233C	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	233	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)		p.R233C(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				ACGGCACTACGACTGCTCTGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											50	49	49					11																	58979642		1943	4125	6068	58736218	SO:0001583	missense	219972			AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.697C>T	11.37:g.58979642G>A	ENSP00000354335:p.Arg233Cys		58736218	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	8.861	0.946866	0.18356	.	.	ENSG00000197629	ENST00000361050	D	0.84442	-1.85	4.95	2.99	0.34606	Membrane attack complex component/perforin (MACPF) domain (3);	0.545245	0.20156	N	0.098042	D	0.86736	0.6004	M	0.61703	1.905	0.09310	N	1	D	0.67145	0.996	P	0.54815	0.761	T	0.78252	-0.2276	10	0.72032	D	0.01	0.7655	8.5853	0.33655	0.0:0.3133:0.525:0.1617	.	233	Q2M385	MPEG1_HUMAN	C	233	ENSP00000354335:R233C	ENSP00000354335:R233C	R	-	1	0	MPEG1	58736218	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.994000	0.29693	0.457000	0.26962	0.650000	0.86243	CGT		0.542	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58979642	G	A	58979642	3	1	54	1	0	0	0	0	1	0	0	0	9753	1058	37	1	1457	1	MPEG1	11	58979642	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	3400401	58979642	76026874	52	7272										
GRM5	2915	broad.mit.edu	37	chr11	88330413	88330413	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tgatgatgttgcttttcttgGaccatacttcatcatcatcc	6	10	4	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr11:88330413G>A	ENST00000305447.4	-	5	1651	c.1502C>T	c.(1501-1503)tCc>tTc	p.S501F	GRM5_ENST00000418177.2_Missense_Mutation_p.S501F|GRM5_ENST00000305432.5_Missense_Mutation_p.S501F|GRM5_ENST00000455756.2_Missense_Mutation_p.S501F|GRM5_ENST00000393297.1_Missense_Mutation_p.S501F	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	501					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.S501F(2)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GCTTTTCTTGGACCATACTTC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	11											222	182	195					11																	88330413		2201	4298	6499	87970061	SO:0001583	missense	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1502C>T	11.37:g.88330413G>A	ENSP00000306138:p.Ser501Phe		87970061	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.444305	0.43429	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.88741	-2.38;-2.38;-2.38;-2.38;-2.42	5.56	5.56	0.83823	.	0.393578	0.31821	N	0.007016	D	0.89146	0.6632	L	0.40543	1.245	0.44485	D	0.997429	D;P	0.59767	0.986;0.612	P;B	0.51135	0.66;0.259	D	0.87775	0.2608	9	.	.	.	.	19.5308	0.95228	0.0:0.0:1.0:0.0	.	501;501	P41594-2;P41594	.;GRM5_HUMAN	F	501	ENSP00000402912:S501F;ENSP00000405690:S501F;ENSP00000305905:S501F;ENSP00000306138:S501F;ENSP00000376975:S501F	.	S	-	2	0	GRM5	87970061	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.556000	0.60775	2.621000	0.88768	0.650000	0.86243	TCC		0.338	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88330413	G	A	88330413	3	1	54	1	0	0	0	0	1	0	0	0	6821	1174	41	3	2156	3	GRM5	11	88330413	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	29350771	88330413	46676103	53	7273										
KRAS	3845	broad.mit.edu	37	chr12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acttacctgtcttgtctttgCtgatgtttcaataaaaggaa	7	7	3	1	rs121913527		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|KRAS_ENST00000557334.1_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	12											207	188	195					12																	25378562		2203	4300	6503	25269829	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr		25269829	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA		0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25378562	C	T	25378562	3	4	54	1	0	0	0	0	1	0	0	0	8459	797	28	3	262	3	KRAS	12	25378562	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		25378562	108473333	54	7274										
TIMELESS	8914	broad.mit.edu	37	chr12	56817487	56817487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ccacgttcctctgggccctgCtgccctatagacagagggag	12	14	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr12:56817487C>T	ENST00000553532.1	-	17	2121	c.1971G>A	c.(1969-1971)caG>caA	p.Q657Q	TIMELESS_ENST00000554616.1_Intron|TIMELESS_ENST00000229201.4_Silent_p.Q656Q					timeless circadian clock									p.Q657Q(1)		NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						CTGGGCCCTGCTGCCCTATAG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	12											50	51	51					12																	56817487		2203	4300	6503	55103754	SO:0001819	synonymous_variant	8914			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1971G>A	12.37:g.56817487C>T			55103754		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																				0.522	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56817487	C	T	56817487	2	4	54	1	0	0	0	0	0	0	0	1	15943	796	28	3		3	TIMELESS	12	56817487	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09	31438925	56817487	77034408	55	7275										
DNAH10	196385	broad.mit.edu	37	chr12	124267807	124267807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggcccaactgaagaagacacCtcaggtagtttgtgcagggc	13	10	1	3			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr12:124267807C>T	ENST00000409039.3	+	7	837	c.812C>T	c.(811-813)cCt>cTt	p.P271L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	271	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P271L(1)|p.P89L(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AAGAAGACACCTCAGGTAGTT	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	12											83	79	80					12																	124267807		2203	4300	6503	122833760	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.812C>T	12.37:g.124267807C>T	ENSP00000386770:p.Pro271Leu		122833760	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254858	0.22965	.	.	ENSG00000197653	ENST00000409039	T	0.50548	0.74	6.01	6.01	0.97437	Dynein heavy chain, domain-1 (1);	0.000000	0.64402	D	0.000001	T	0.64227	0.2579	M	0.82630	2.6	0.80722	D	1	D	0.53151	0.958	P	0.51170	0.661	T	0.61603	-0.7029	10	0.27785	T	0.31	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	271	Q8IVF4	DYH10_HUMAN	L	271	ENSP00000386770:P271L	ENSP00000386770:P271L	P	+	2	0	DNAH10	122833760	1.000000	0.71417	0.794000	0.32065	0.064000	0.16182	7.234000	0.78134	2.861000	0.98227	0.650000	0.86243	CCT		0.542	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124267807	C	T	124267807	3	4	54	1	0	0	0	0	1	0	0	0	4609	681	24	3	838	3	DNAH10	12	124267807	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	67450320	124267807	9584088	56	7276										
TMEM132D	121256	broad.mit.edu	37	chr12	129822278	129822278	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ccggggtactcgacctgccaCgtgaccagctgtgtggctgg	15	13	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr12:129822278C>T	ENST00000422113.2	-	4	1526	c.1200G>A	c.(1198-1200)acG>acA	p.T400T		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	400					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.T400T(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		CGACCTGCCACGTGACCAGCT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											155	138	143					12																	129822278		2203	4300	6503	128388231	SO:0001819	synonymous_variant	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1200G>A	12.37:g.129822278C>T			128388231	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.577	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	129822278	C	T	129822278	2	4	54	1	0	0	0	0	0	0	0	1	16086	523	19	1		1	TMEM132D	12	129822278	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09	5554471	129822278	4029617	57	7277										
PCDH9	5101	broad.mit.edu	37	chr13	67801923	67801923	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ctttgattttcatcacatagGtatctttctgttctctatcc	4	10	5	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr13:67801923G>T	ENST00000377865.2	-	1	784	c.650C>A	c.(649-651)aCc>aAc	p.T217N	PCDH9_ENST00000328454.5_Missense_Mutation_p.T217N|PCDH9_ENST00000377861.3_Missense_Mutation_p.T217N|PCDH9_ENST00000456367.1_Missense_Mutation_p.T217N|PCDH9_ENST00000544246.1_Missense_Mutation_p.T217N			Q9HC56	PCDH9_HUMAN	protocadherin 9	217	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T217N(2)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CATCACATAGGTATCTTTCTG	0.453																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	13											145	139	141					13																	67801923		2203	4300	6503	66699924	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.650C>A	13.37:g.67801923G>T	ENSP00000367096:p.Thr217Asn		66699924	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.062885	0.36373	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	6.17	5.32	0.75619	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.59128	0.2171	L	0.31065	0.9	0.58432	D	0.999997	B;D;D;D	0.89917	0.392;1.0;1.0;1.0	B;D;D;D	0.85130	0.374;0.995;0.991;0.997	T	0.63862	-0.6541	10	0.72032	D	0.01	.	16.966	0.86286	0.0:0.0:0.8712:0.1288	.	217;217;217;217	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	N	217	ENSP00000442186:T217N;ENSP00000367096:T217N;ENSP00000401699:T217N;ENSP00000332060:T217N;ENSP00000367092:T217N	ENSP00000332060:T217N	T	-	2	0	PCDH9	66699924	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	8.062000	0.89475	1.607000	0.50170	-0.181000	0.13052	ACC		0.453	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67801923	G	T	67801923	3	4	54	1	0	0	0	0	1	0	0	0	11549	1261	44	2	3079	2	PCDH9	13	67801923	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09		67801923	47367955	58	7278										
DIO2	1734	broad.mit.edu	37	chr14	80669214	80669214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gttggcgttattgtccatgcGgtcagccacaactcggcact	11	12	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr14:80669214G>A	ENST00000557010.1	-	4	1025	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	DIO2_ENST00000555750.1_Missense_Mutation_p.R250C|DIO2_ENST00000438257.4_Missense_Mutation_p.R214C|DIO2_ENST00000422005.3_3'UTR|DIO2_ENST00000557125.1_3'UTR	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	214					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)	p.R214C(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		TTGTCCATGCGGTCAGCCACA	0.542											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	14											83	85	85					14																	80669214		2055	4192	6247	79738967	SO:0001583	missense	1734			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"thyroxine deiodinase, type II", "deiodonase-2", "deiodinase-2"	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.640C>T	14.37:g.80669214G>A	ENSP00000451419:p.Arg214Cys	1200	79738967	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Missense_Mutation	SNP	ENST00000557010.1	37	CCDS45146.1	.	.	.	.	.	.	.	.	.	.	g	11.83	1.756453	0.31137	.	.	ENSG00000211448	ENST00000438257;ENST00000557010;ENST00000555750	T;T;T	0.33438	1.41;1.41;1.41	5.77	2.6	0.31112	.	0.147221	0.45606	D	0.000345	T	0.05181	0.0138	N	0.00128	-2.045	0.80722	D	1	B;B;B	0.17667	0.001;0.001;0.023	B;B;B	0.08055	0.001;0.002;0.003	T	0.11131	-1.0600	10	0.32370	T	0.25	.	2.1007	0.03679	0.3678:0.0:0.3913:0.2409	.	250;214;250	Q92813-2;Q92813;G3V315	.;IOD2_HUMAN;.	C	214;214;250	ENSP00000405854:R214C;ENSP00000451419:R214C;ENSP00000450980:R250C	ENSP00000405854:R214C	R	-	1	0	DIO2	79738967	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.547000	0.45786	0.802000	0.34089	-0.127000	0.14921	CGC		0.542	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			A	80669214	G	A	80669214	3	1	54	1	0	0	0	0	1	0	0	0	4536	1116	39	1	185	1	DIO2	14	80669214	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09		80669214	26680326	59	7279										
AK7	122481	broad.mit.edu	37	chr14	96944928	96944928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ccgggctctgagcaactaccGggacatcaatatcgacgatg	11	12	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr14:96944928G>A	ENST00000267584.4	+	15	1726	c.1682G>A	c.(1681-1683)cGg>cAg	p.R561Q		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	561	Adenylate kinase.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)	p.R561Q(1)		breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		AGCAACTACCGGGACATCAAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											99	87	91					14																	96944928		2203	4300	6503	96014681	SO:0001583	missense	122481			AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1682G>A	14.37:g.96944928G>A	ENSP00000267584:p.Arg561Gln		96014681	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879111	0.91740	.	.	ENSG00000140057	ENST00000267584	D	0.93133	-3.17	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.96408	0.8828	M	0.74647	2.275	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	D	0.96357	0.9263	10	0.51188	T	0.08	-20.27	18.3825	0.90455	0.0:0.0:1.0:0.0	.	561	Q96M32	KAD7_HUMAN	Q	561	ENSP00000267584:R561Q	ENSP00000267584:R561Q	R	+	2	0	AK7	96014681	1.000000	0.71417	0.996000	0.52242	0.745000	0.42441	9.465000	0.97660	2.340000	0.79590	0.491000	0.48974	CGG		0.453	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			A	96944928	G	A	96944928	3	1	54	1	0	0	0	0	1	0	0	0	444	1116	39	1	1740	1	AK7	14	96944928	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	16275714	96944928	10404612	60	7280										
HERC2	8924	broad.mit.edu	37	chr15	28492013	28492013	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggagggctgtgtacttcttcAgcaaggaaccaacacccatt	10	11	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr15:28492013A>T	ENST00000261609.7	-	22	3374	c.3266T>A	c.(3265-3267)cTg>cAg	p.L1089Q		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.L1089Q(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		GTACTTCTTCAGCAAGGAACC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											95	80	85					15																	28492013		2203	4300	6503	26165608	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.3266T>A	15.37:g.28492013A>T	ENSP00000261609:p.Leu1089Gln		26165608		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.036197	0.75617	.	.	ENSG00000128731	ENST00000261609	T	0.64438	-0.1	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000002	T	0.78136	0.4236	M	0.72353	2.195	0.58432	D	0.999999	D	0.65815	0.995	D	0.75484	0.986	T	0.80544	-0.1335	10	0.66056	D	0.02	.	15.4668	0.75406	1.0:0.0:0.0:0.0	.	1089	O95714	HERC2_HUMAN	Q	1089	ENSP00000261609:L1089Q	ENSP00000261609:L1089Q	L	-	2	0	HERC2	26165608	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	9.339000	0.96797	2.059000	0.61396	0.528000	0.53228	CTG		0.473	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28492013	A	T	28492013	3	4	54	1	0	0	0	0	1	0	0	0	7079	188	7	5	11526	5	HERC2	15	28492013	Missense_Mutation	SNP	A	TCGA-AG-3909-01A-01W-1073-09		28492013	74039379	61	7281										
IGDCC3	9543	broad.mit.edu	37	chr15	65621838	65621838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cagctggccccgctgtccccGtctcgccccatttagggcta	10	18	1	0	rs369729407		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr15:65621838G>A	ENST00000327987.4	-	13	2346	c.2095C>T	c.(2095-2097)Cgg>Tgg	p.R699W	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	699					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)		p.R699W(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CGCTGTCCCCGTCTCGCCCCA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	TRP/ARG	0,4384		0,0,2192	37	45	42		2095	4.9	0	15		42	1,8577		0,1,4288	no	missense	IGDCC3	NM_004884.3	101	0,1,6480	AA,AG,GG		0.0117,0.0,0.0077	benign	699/815	65621838	1,12961	2192	4289	6481	63408891	SO:0001583	missense	9543			AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2095C>T	15.37:g.65621838G>A	ENSP00000332773:p.Arg699Trp		63408891	O95215	De_novo_Start_OutOfFrame	SNP	ENST00000327987.4	37	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	G	9.735	1.163384	0.21538	0.0	1.17E-4	ENSG00000174498	ENST00000327987	T	0.68025	-0.3	5.82	4.91	0.64330	.	0.453489	0.20641	N	0.088402	T	0.54515	0.1863	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.50800	-0.8785	10	0.52906	T	0.07	-3.5926	13.4469	0.61146	0.0726:0.0:0.9274:0.0	.	699	Q8IVU1	IGDC3_HUMAN	W	699	ENSP00000332773:R699W	ENSP00000332773:R699W	R	-	1	2	IGDCC3	63408891	0.035000	0.19736	0.002000	0.10522	0.111000	0.19643	2.213000	0.42844	1.473000	0.48159	-0.254000	0.11334	CGG		0.647	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		A	65621838	G	A	65621838	3	1	54	1	0	0	0	0	1	0	0	0	7589	1144	40	1	357	1	IGDCC3	15	65621838	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	37129825	65621838	36909554	62	7282										
SPATA8	145946	broad.mit.edu	37	chr15	97327474	97327474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gaggcctcaagggcccggtgTggcctgcaaaggaaggtaag	17	9	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr15:97327474T>C	ENST00000328504.3	+	2	448	c.181T>C	c.(181-183)Tgg>Cgg	p.W61R	SPATA8-AS1_ENST00000560888.1_RNA|SPATA8-AS1_ENST00000558722.1_RNA|SPATA8_ENST00000558553.1_Missense_Mutation_p.V20A	NM_173499.3	NP_775770.1	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8	61								p.W61R(1)		large_intestine(4)|lung(8)|ovary(1)|skin(3)	16	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			GGGCCCGGTGTGGCCTGCAAA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15											59	54	56					15																	97327474		2197	4298	6495	95128478	SO:0001583	missense	145946			AY489187	CCDS10376.1	15q26	2008-02-05			ENSG00000185594	ENSG00000185594			28676	protein-coding gene	gene with protein product		613948					Standard	NM_173499		Approved	MGC44294	uc002bue.3	Q6RVD6	OTTHUMG00000149847	ENST00000328504.3:c.181T>C	15.37:g.97327474T>C	ENSP00000328149:p.Trp61Arg		95128478	Q2KJ07	Missense_Mutation	SNP	ENST00000328504.3	37	CCDS10376.1	.	.	.	.	.	.	.	.	.	.	T	7.008	0.556172	0.13436	.	.	ENSG00000185594	ENST00000328504	T	0.49432	0.78	3.28	-2.4	0.06583	.	.	.	.	.	T	0.21062	0.0507	N	0.08118	0	0.09310	N	1	B	0.20671	0.047	B	0.14023	0.01	T	0.13415	-1.0510	9	0.87932	D	0	.	1.1833	0.01849	0.1709:0.1186:0.2928:0.4177	.	61	Q6RVD6	SPAT8_HUMAN	R	61	ENSP00000328149:W61R	ENSP00000328149:W61R	W	+	1	0	SPATA8	95128478	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.257000	0.08745	-0.940000	0.03705	-1.139000	0.01908	TGG		0.567	SPATA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313533.1	NM_173499		C	97327474	T	C	97327474	3	2	54	1	0	0	0	0	1	0	0	0	15054	1696	59	4	187	4	SPATA8	15	97327474	Missense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09	31705636	97327474	5203918	63	7283										
LRRK1	79705	broad.mit.edu	37	chr15	101601396	101601396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gaactacacggtggtgaacaCagagaagggcctcatggagg	15	8	1	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr15:101601396C>A	ENST00000388948.3	+	30	5059	c.4700C>A	c.(4699-4701)aCa>aAa	p.T1567K	LRRK1_ENST00000284395.5_Missense_Mutation_p.T1564K|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.T1567K(1)|p.T1579K(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	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)			GTGGTGAACACAGAGAAGGGC	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	15											82	94	90					15																	101601396		2100	4232	6332	99418919	SO:0001583	missense	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4700C>A	15.37:g.101601396C>A	ENSP00000373600:p.Thr1567Lys		99418919		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747708	0.69533	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.73363	-0.73;-0.74	5.46	5.46	0.80206	.	0.376116	0.30383	N	0.009744	T	0.58892	0.2154	N	0.24115	0.695	0.27751	N	0.944159	P	0.38922	0.651	B	0.35240	0.198	T	0.59984	-0.7351	10	0.46703	T	0.11	.	10.8074	0.46527	0.0:0.8533:0.0:0.1467	.	1567	Q38SD2	LRRK1_HUMAN	K	1567;1564;258;121	ENSP00000373600:T1567K;ENSP00000284395:T1564K	ENSP00000284395:T1564K	T	+	2	0	LRRK1	99418919	1.000000	0.71417	0.984000	0.44739	0.953000	0.61014	4.382000	0.59594	2.576000	0.86940	0.555000	0.69702	ACA		0.622	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101601396	C	A	101601396	3	1	54	1	0	0	0	0	1	0	0	0	9061	478	17	2	4814	2	LRRK1	15	101601396	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	4273922	101601396	929996	64	7284										
GRIN2A	2903	broad.mit.edu	37	chr16	9923459	9923459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggagttattgaacaccaggcCccaaagaagccatatagctt	9	10	0	2			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr16:9923459C>T	ENST00000396573.2	-	10	2137	c.1828G>A	c.(1828-1830)Ggc>Agc	p.G610S	GRIN2A_ENST00000535259.1_Missense_Mutation_p.G453S|GRIN2A_ENST00000404927.2_Missense_Mutation_p.G610S|GRIN2A_ENST00000396575.2_Missense_Mutation_p.G610S|GRIN2A_ENST00000330684.3_Missense_Mutation_p.G610S|GRIN2A_ENST00000562109.1_Missense_Mutation_p.G610S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	610					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.G610S(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AACACCAGGCCCCAAAGAAGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	16											74	68	70					16																	9923459		2197	4300	6497	9830960	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1828G>A	16.37:g.9923459C>T	ENSP00000379818:p.Gly610Ser		9830960	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	34	5.329790	0.95733	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	5.27	5.27	0.74061	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.67933	0.2946	L	0.52364	1.645	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.99	D;D;D	0.83275	0.996;0.992;0.95	T	0.65837	-0.6071	9	.	.	.	.	17.9016	0.88906	0.0:1.0:0.0:0.0	.	453;610;610	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	S	610;610;453;610;610	ENSP00000379818:G610S;ENSP00000385872:G610S;ENSP00000441572:G453S;ENSP00000332549:G610S;ENSP00000379820:G610S	.	G	-	1	0	GRIN2A	9830960	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.681000	0.84073	2.465000	0.83290	0.655000	0.94253	GGC		0.463	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9923459	C	T	9923459	3	4	54	1	0	0	0	0	1	0	0	0	6800	623	22	3	2586	3	GRIN2A	16	9923459	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		9923459	80431294	65	7285										
CMTM2	146225	broad.mit.edu	37	chr16	66613533	66613533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggcacctaaggcggcaaaggGggccaagccagagccagcac	15	13	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr16:66613533G>A	ENST00000268595.2	+	1	174	c.23G>A	c.(22-24)gGg>gAg	p.G8E	CMTM2_ENST00000379486.2_Missense_Mutation_p.G8E|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	8					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.G8E(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		GCGGCAAAGGGGGCCAAGCCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											68	67	67					16																	66613533		2201	4300	6501	65171034	SO:0001583	missense	146225			BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"chemokine-like factor super family 2", "chemokine-like factor superfamily 2"	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.23G>A	16.37:g.66613533G>A	ENSP00000268595:p.Gly8Glu		65171034	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	8.908	0.957990	0.18507	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.50001	0.76;1.36	1.79	-1.69	0.08186	.	2.408040	0.01571	N	0.020584	T	0.50582	0.1624	L	0.48642	1.525	0.09310	N	1	D;P	0.55172	0.97;0.724	P;P	0.53912	0.737;0.531	T	0.39941	-0.9589	10	0.87932	D	0	3.5381	2.6208	0.04916	0.3769:0.2651:0.358:0.0	.	8;8	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	E	8	ENSP00000368800:G8E;ENSP00000268595:G8E	ENSP00000268595:G8E	G	+	2	0	CMTM2	65171034	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.249000	0.18216	-0.434000	0.07275	0.313000	0.20887	GGG		0.597	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			A	66613533	G	A	66613533	3	1	54	1	0	0	0	0	1	0	0	0	3589	1232	43	3	25	3	CMTM2	16	66613533	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	56690074	66613533	23741220	66	7286										
ADAMTS18	170692	broad.mit.edu	37	chr16	77326991	77326991	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acctcgctccacgaagaagcGacccactgtagccggctgtt	10	15	0	1	rs187998780		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr16:77326991G>A	ENST00000282849.5	-	20	3589	c.3171C>T	c.(3169-3171)gtC>gtT	p.V1057V	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1057	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V1057V(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ACGAAGAAGCGACCCACTGTA	0.547													G|||	1	0.000199681	0	0.0014	5008	,	,		16785	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											77	71	73					16																	77326991		2198	4300	6498	75884492	SO:0001819	synonymous_variant	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3171C>T	16.37:g.77326991G>A			75884492	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																				0.547	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77326991	G	A	77326991	2	1	54	1	0	0	0	0	0	0	0	1	263	1045	37	1		1	ADAMTS18	16	77326991	Silent	SNP	G	TCGA-AG-3909-01A-01W-1073-09	10713458	77326991	13027762	67	7287										
ATP2C2	9914	broad.mit.edu	37	chr16	84494312	84494312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tcaggcagccaccacggagtGtgcgggacaccatcctcagc	12	15	2	0	rs200530016		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr16:84494312G>A	ENST00000262429.4	+	24	2475	c.2386G>A	c.(2386-2388)Gtg>Atg	p.V796M	ATP2C2_ENST00000420010.2_3'UTR|RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000416219.2_Missense_Mutation_p.V825M	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	796					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.V796M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						ACCACGGAGTGTGCGGGACAC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	16											112	124	120					16																	84494312		2118	4243	6361	83051813	SO:0001583	missense	9914			AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.2386G>A	16.37:g.84494312G>A	ENSP00000262429:p.Val796Met		83051813	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	G	5.594	0.294430	0.10567	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	D;D	0.95788	-3.81;-3.81	5.41	-1.83	0.07833	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.872740	0.10077	N	0.718988	D	0.93220	0.7840	M	0.71296	2.17	0.09310	N	1	B;B;B;B;B	0.24675	0.079;0.029;0.02;0.109;0.011	B;B;B;B;B	0.32762	0.152;0.098;0.087;0.094;0.098	D	0.84215	0.0458	10	0.32370	T	0.25	.	5.922	0.19088	0.3568:0.2242:0.419:0.0	.	825;645;645;813;796	E7ES94;B3KR57;F8WAA5;O75185-2;O75185	.;.;.;.;AT2C2_HUMAN	M	825;796;645	ENSP00000397925:V825M;ENSP00000262429:V796M	ENSP00000262429:V796M	V	+	1	0	ATP2C2	83051813	0.005000	0.15991	0.000000	0.03702	0.016000	0.09150	-0.242000	0.08928	-0.445000	0.07159	0.655000	0.94253	GTG		0.547	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		A	84494312	G	A	84494312	3	1	54	1	0	0	0	0	1	0	0	0	1145	1377	48	3	2480	3	ATP2C2	16	84494312	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	7167321	84494312	5860441	68	7288										
TP53	7157	broad.mit.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	54	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09		7577094	73618116	69	7289										
DNAH2	146754	broad.mit.edu	37	chr17	7690289	7690289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ggatcgagaacatgaactccGtcatggacgataacaaggtg	12	8	1	2	rs147226714		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr17:7690289G>A	ENST00000572933.1	+	42	8001	c.6541G>A	c.(6541-6543)Gtc>Atc	p.V2181I	DNAH2_ENST00000389173.2_Missense_Mutation_p.V2181I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2181	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V2181I(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CATGAACTCCGTCATGGACGA	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		19618	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17						G	ILE/VAL	0,4406		0,0,2203	95	64	74		6541	5.2	1	17	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH2	NM_020877.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	2181/4428	7690289	1,13005	2203	4300	6503	7631014	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.6541G>A	17.37:g.7690289G>A	ENSP00000458355:p.Val2181Ile		7631014	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	35	5.462838	0.96257	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	D	0.94092	-3.35	5.16	5.16	0.70880	ATPase, dynein-related, AAA domain (1);	0.000000	0.64402	D	0.000001	D	0.97614	0.9218	H	0.94734	3.575	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	D	0.98541	1.0632	10	0.87932	D	0	.	17.5818	0.87970	0.0:0.0:1.0:0.0	.	2181	Q9P225	DYH2_HUMAN	I	2181	ENSP00000373825:V2181I	ENSP00000353818:V2181I	V	+	1	0	DNAH2	7631014	1.000000	0.71417	0.959000	0.39883	0.885000	0.51271	9.474000	0.97718	2.672000	0.90937	0.650000	0.86243	GTC		0.582	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7690289	G	A	7690289	3	1	54	1	0	0	0	0	1	0	0	0	4613	1145	40	1	6703	1	DNAH2	17	7690289	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	113195	7690289	73504921	70	7290										
COLEC12	81035	broad.mit.edu	37	chr18	357502	357502	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gttatttttacatttggtacAttgtgttccttcctgaatac	6	7	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr18:357502A>G	ENST00000400256.3	-	3	286	c.79T>C	c.(79-81)Tgt>Cgt	p.C27R		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	27					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)	p.C27R(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CATTTGGTACATTGTGTTCCT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	18											120	117	118					18																	357502		2202	4298	6500	347502	SO:0001583	missense	81035			AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.79T>C	18.37:g.357502A>G	ENSP00000383115:p.Cys27Arg		347502	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.363542	0.61513	.	.	ENSG00000158270	ENST00000400256	D	0.95137	-3.62	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.95497	0.8537	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96302	0.9222	10	0.87932	D	0	-11.8381	16.3127	0.82898	1.0:0.0:0.0:0.0	.	27	Q5KU26	COL12_HUMAN	R	27	ENSP00000383115:C27R	ENSP00000383115:C27R	C	-	1	0	COLEC12	347502	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.904000	0.92590	2.246000	0.74042	0.533000	0.62120	TGT		0.294	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			G	357502	A	G	357502	3	3	54	1	0	0	0	0	1	0	0	0	3718	217	8	4	2181	4	COLEC12	18	357502	Missense_Mutation	SNP	A	TCGA-AG-3909-01A-01W-1073-09		357502	77719746	71	7291										
MC5R	4161	broad.mit.edu	37	chr18	13826480	13826480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	cagcatgcagggcgcggtcaCcgtcaccatgctgctgggcg	15	14	2	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr18:13826480C>T	ENST00000324750.3	+	1	938	c.716C>T	c.(715-717)aCc>aTc	p.T239I	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	239					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)	p.T239I(2)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						GGCGCGGTCACCGTCACCATG	0.617																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	18											216	174	188					18																	13826480		2203	4300	6503	13816480	SO:0001583	missense	4161			AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"GPCR / Class A : Melanocortin receptors"	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.716C>T	18.37:g.13826480C>T	ENSP00000318077:p.Thr239Ile		13816480	B0YJ34|Q502V1	Missense_Mutation	SNP	ENST00000324750.3	37	CCDS11868.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133428	0.37630	.	.	ENSG00000176136	ENST00000324750	T	0.39056	1.1	4.88	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.55194	0.1905	M	0.87456	2.885	0.80722	D	1	P	0.34639	0.461	B	0.38264	0.269	T	0.65207	-0.6224	10	0.87932	D	0	.	17.0064	0.86394	0.0:1.0:0.0:0.0	.	239	P33032	MC5R_HUMAN	I	239	ENSP00000318077:T239I	ENSP00000318077:T239I	T	+	2	0	MC5R	13816480	1.000000	0.71417	0.999000	0.59377	0.068000	0.16541	7.423000	0.80229	2.246000	0.74042	0.305000	0.20034	ACC		0.617	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913		T	13826480	C	T	13826480	3	4	54	1	0	0	0	0	1	0	0	0	9397	507	18	3	718	3	MC5R	18	13826480	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	13468978	13826480	64250768	72	7292										
TICAM1	148022	broad.mit.edu	37	chr19	4816756	4816756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gttcccgcagggctcgggtgTcctgttccttcctccacatg	11	15	0	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr19:4816756T>C	ENST00000248244.5	-	2	1863	c.1634A>G	c.(1633-1635)gAc>gGc	p.D545G		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	545	Sufficient to induce apoptosis.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.D545G(1)		NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGCTCGGGTGTCCTGTTCCTT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	52	59					19																	4816756		2203	4300	6503	4767756	SO:0001583	missense	148022			AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1634A>G	19.37:g.4816756T>C	ENSP00000248244:p.Asp545Gly		4767756	B3Y691|O75532|Q86XP8|Q96GA0	Missense_Mutation	SNP	ENST00000248244.5	37	CCDS12136.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889551	0.52014	.	.	ENSG00000127666	ENST00000248244	T	0.45276	0.9	4.45	3.34	0.38264	.	0.377447	0.19131	N	0.121924	T	0.29389	0.0732	L	0.57536	1.79	0.09310	N	1	P	0.43477	0.808	B	0.30855	0.121	T	0.37337	-0.9710	10	0.52906	T	0.07	-7.4014	5.356	0.16061	0.0:0.0978:0.1783:0.7239	.	545	Q8IUC6	TCAM1_HUMAN	G	545	ENSP00000248244:D545G	ENSP00000248244:D545G	D	-	2	0	TICAM1	4767756	0.753000	0.28349	0.114000	0.21550	0.570000	0.35934	1.325000	0.33724	1.766000	0.52107	0.260000	0.18958	GAC		0.627	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261		C	4816756	T	C	4816756	3	2	54	1	0	0	0	0	1	0	0	0	15931	1667	58	4	508	4	TICAM1	19	4816756	Missense_Mutation	SNP	T	TCGA-AG-3909-01A-01W-1073-09		4816756	54312227	73	7293										
CATSPERG	57828	broad.mit.edu	37	chr19	38851275	38851275	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	accctcttctacgaagacagCaaactgtaccaggtgcccgg	9	14	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr19:38851275C>T	ENST00000409235.3	+	15	1870	c.1755C>T	c.(1753-1755)agC>agT	p.S585S	AC005625.1_ENST00000590304.1_RNA|CATSPERG_ENST00000215069.4_3'UTR|CATSPERG_ENST00000410018.1_Silent_p.S545S	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	585					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.S225S(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						ACGAAGACAGCAAACTGTACC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	19											107	102	104					19																	38851275		2203	4300	6503	43543115	SO:0001819	synonymous_variant	57828			AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.1755C>T	19.37:g.38851275C>T			43543115	A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	37	CCDS12514.2																																																																																				0.602	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		T	38851275	C	T	38851275	2	4	54	1	0	0	0	0	0	0	0	1	2698	709	25	3		3	CATSPERG	19	38851275	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09	34034519	38851275	20277708	74	7294										
CD177	57126	broad.mit.edu	37	chr19	43858092	43858092	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcaatggacccctaagaacaCcagctgcgacagcggcttgg	12	13	0	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr19:43858092C>T	ENST00000607517.1	+	0	196				CD177_ENST00000378009.4_RNA|CD177_ENST00000378012.2_RNA			Q8N6Q3	CD177_HUMAN	CD177 molecule						blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.T47I(2)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5		Prostate(69;0.00682)				CCTAAGAACACCAGCTGCGAC	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	19											57	57	57					19																	43858092		2047	4207	6254	48549932			57126			AF146747	CCDS62700.1	19q13.31	2013-10-02	2006-03-28		ENSG00000204936	ENSG00000204936		"CD molecules"	30072	protein-coding gene	gene with protein product	"polycythemia rubra vera 1"	162860	"CD177 antigen"			10753836, 5552408	Standard	NM_020406		Approved	PRV1, HNA2A, NB1	uc002owi.3	Q8N6Q3	OTTHUMG00000185320		19.37:g.43858092C>T			48549932	Q711Q2|Q8NCV9|Q96QH1|Q9HDA5	Missense_Mutation	SNP	ENST00000607517.1	37		.	.	.	.	.	.	.	.	.	.	c	4.812	0.150966	0.09185	.	.	ENSG00000204936	ENST00000378009;ENST00000378012;ENST00000457794	T;T;T	0.15017	3.07;2.46;2.46	3.75	-7.51	0.01346	.	.	.	.	.	T	0.10337	0.0253	L	0.42245	1.32	0.09310	N	1	P	0.36282	0.546	B	0.25759	0.063	T	0.01675	-1.1298	9	0.33141	T	0.24	.	11.0326	0.47783	0.1386:0.6106:0.0:0.2509	.	47	Q8N6Q3	CD177_HUMAN	I	47	ENSP00000367248:T47I;ENSP00000367251:T47I;ENSP00000388794:T47I	ENSP00000367248:T47I	T	+	2	0	CD177	48549932	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.639000	0.02011	-2.950000	0.00293	-3.016000	0.00074	ACC		0.632	CD177-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000470162.1	NM_020406		T	43858092	C	T	43858092	1	4	54	0	1	0	0	0	0	0	0	0	2977	507	18	3		3	CD177	19	43858092	RNA	SNP	C	TCGA-AG-3909-01A-01W-1073-09	5006817	43858092	15270891	75	7295										
GRIN2D	2906	broad.mit.edu	37	chr19	48945180	48945180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gctcccgctggaagcggcccAtcgacctggcgttgctgcag	14	15	0	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr19:48945180A>G	ENST00000263269.3	+	11	2495	c.2407A>G	c.(2407-2409)Atc>Gtc	p.I803V		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	803					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.I803V(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GAAGCGGCCCATCGACCTGGC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											37	34	35					19																	48945180		2203	4300	6503	53636992	SO:0001583	missense	2906			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2407A>G	19.37:g.48945180A>G	ENSP00000263269:p.Ile803Val		53636992		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.896692	0.52121	.	.	ENSG00000105464	ENST00000263269	T	0.49720	0.77	4.62	4.62	0.57501	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.067872	0.56097	D	0.000038	T	0.36331	0.0963	N	0.17872	0.535	0.38448	D	0.946879	P	0.40250	0.709	B	0.43445	0.42	T	0.21999	-1.0229	10	0.20519	T	0.43	.	13.4795	0.61328	1.0:0.0:0.0:0.0	.	803	O15399	NMDE4_HUMAN	V	803	ENSP00000263269:I803V	ENSP00000263269:I803V	I	+	1	0	GRIN2D	53636992	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.329000	0.52060	2.090000	0.63153	0.374000	0.22700	ATC		0.672	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			G	48945180	A	G	48945180	3	3	54	1	0	0	0	0	1	0	0	0	6803	217	8	4	2445	4	GRIN2D	19	48945180	Missense_Mutation	SNP	A	TCGA-AG-3909-01A-01W-1073-09	5087088	48945180	10183803	76	7296										
ZNF578	147660	broad.mit.edu	37	chr19	53014805	53014805	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	caacccttgtaattcataagGcaattcatactggagagaaa	7	8	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr19:53014805G>T	ENST00000421239.2	+	6	1415	c.1171G>T	c.(1171-1173)Gca>Tca	p.A391S	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A391S(1)							GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		AATTCATAAGGCAATTCATAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	94	92					19																	53014805		2203	4300	6503	57706617	SO:0001583	missense	147660			AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1171G>T	19.37:g.53014805G>T	ENSP00000459216:p.Ala391Ser		57706617	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	3.437	-0.114858	0.06881	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.85	0.05734	.	.	.	.	.	T	0.13500	0.0327	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30327	-0.9982	7	.	.	.	.	6.4906	0.22113	0.5324:0.0:0.4676:0.0	.	391	G3V4F6	.	S	391	.	.	A	+	1	0	ZNF578	57706617	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.181000	0.00568	-0.712000	0.04988	-0.734000	0.03567	GCA		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014805	G	T	53014805	3	4	54	1	0	0	0	0	1	0	0	0	18049	1203	42	2	1181	2	ZNF578	19	53014805	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	4069625	53014805	6114178	77	7297										
MMP9	4318	broad.mit.edu	37	chr20	44641960	44641960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gcagcccacggctcccccgaCggtctgccccaccggacccc	10	23	1	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr20:44641960C>T	ENST00000372330.3	+	9	1416	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	466					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T466M(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	GCTCCCCCGACGGTCTGCCCC	0.682											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	20											44	59	54					20																	44641960		2186	4273	6459	44075367	SO:0001583	missense	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1397C>T	20.37:g.44641960C>T	ENSP00000361405:p.Thr466Met	925	44075367	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938940	0.34189	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.22134	1.97	4.63	3.62	0.41486	.	.	.	.	.	T	0.19604	0.0471	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	P	0.50231	0.635	T	0.11494	-1.0585	9	0.45353	T	0.12	.	13.8455	0.63466	0.1634:0.8366:0.0:0.0	.	466	P14780	MMP9_HUMAN	M	466;111	ENSP00000361405:T466M	ENSP00000361405:T466M	T	+	2	0	MMP9	44075367	0.002000	0.14202	0.027000	0.17364	0.157000	0.22087	0.842000	0.27627	2.376000	0.81061	0.655000	0.94253	ACG		0.682	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			T	44641960	C	T	44641960	3	4	54	1	0	0	0	0	1	0	0	0	9699	536	19	1	1431	1	MMP9	20	44641960	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09		44641960	18383560	78	7298										
ARFRP1	10139	broad.mit.edu	37	chr20	62338073	62338073	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ttcttgttaaatcgggttttCgactgctccaggaaggtctg	11	8	2	0	rs528376535		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr20:62338073C>T	ENST00000359715.5	-	2	677	c.111G>A	c.(109-111)tcG>tcA	p.S37S	ZGPAT_ENST00000369967.3_5'Flank|ZGPAT_ENST00000448100.2_5'Flank|ARFRP1_ENST00000440854.1_Silent_p.S37S|ZGPAT_ENST00000355969.6_5'Flank|ARFRP1_ENST00000609142.1_Silent_p.S37S|RP4-583P15.15_ENST00000490623.2_5'Flank|ZGPAT_ENST00000357119.4_5'Flank|ARFRP1_ENST00000607873.1_5'UTR|ARFRP1_ENST00000324228.2_Silent_p.S37S|ZGPAT_ENST00000328969.5_5'Flank			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	37					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.S37S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			ATCGGGTTTTCGACTGCTCCA	0.478													C|||	1	0.000199681	8e-04	0	5008	,	,		20245	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	20											208	189	196					20																	62338073		2203	4300	6503	61808517	SO:0001819	synonymous_variant	10139			X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"ADP-ribosylation factors"	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.111G>A	20.37:g.62338073C>T			61808517	B7ZKX7|E1P5J9|Q6IBQ0	Silent	SNP	ENST00000359715.5	37	CCDS13533.1																																																																																				0.478	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			T	62338073	C	T	62338073	2	4	54	1	0	0	0	0	0	0	0	1	856	871	31	1		1	ARFRP1	20	62338073	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09	17696113	62338073	687447	79	7299										
TIAM1	7074	broad.mit.edu	37	chr21	32525053	32525053	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	acttgaaactctaccatttcCgttaaatttccaaaaagcac	3	11	1	1	rs143851539		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chr21:32525053C>T	ENST00000286827.3	-	20	3738	c.3267G>A	c.(3265-3267)acG>acA	p.T1089T	TIAM1_ENST00000541036.1_Silent_p.T1029T	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1089	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T1089T(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CTACCATTTCCGTTAAATTTC	0.333																																																2	Substitution - coding silent(2)	large_intestine(2)	21						C		2,4404	4.2+/-10.8	0,2,2201	61	62	62		3267	-11.3	0.1	21	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous	TIAM1	NM_003253.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		1089/1592	32525053	2,13004	2203	4300	6503	31446924	SO:0001819	synonymous_variant	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3267G>A	21.37:g.32525053C>T			31446924	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.333	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32525053	C	T	32525053	2	4	54	1	0	0	0	0	0	0	0	1	15929	639	23	1		1	TIAM1	21	32525053	Silent	SNP	C	TCGA-AG-3909-01A-01W-1073-09		32525053	15604842	80	7300										
HCCS	3052	broad.mit.edu	37	chrX	11139860	11139860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gttcaccatcctggacgtccGtcctgccttagattcacttt	7	14	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chrX:11139860G>A	ENST00000321143.4	+	7	939	c.737G>A	c.(736-738)cGt>cAt	p.R246H	HCCS_ENST00000380762.4_Missense_Mutation_p.R246H|HCCS_ENST00000380763.3_Missense_Mutation_p.R246H|ARHGAP6_ENST00000534860.1_Intron	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	246					organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)	p.R246H(1)		kidney(1)|large_intestine(3)|lung(3)	7						CTGGACGTCCGTCCTGCCTTA	0.443																																					Ovarian(86;1338 1347 1462 10340 37882)											1	Substitution - Missense(1)	large_intestine(1)	X											149	116	127					X																	11139860		2203	4300	6503	11049781	SO:0001583	missense	3052				CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"cytochrome c heme-lyase"	300056	"holocytochrome c synthase (cytochrome c heme-lyase)", "microphthalamia with linear skin defects"	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.737G>A	X.37:g.11139860G>A	ENSP00000326579:p.Arg246His		11049781	B3KUS1|Q502X8	Missense_Mutation	SNP	ENST00000321143.4	37	CCDS14139.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295180	0.81025	.	.	ENSG00000004961	ENST00000321143;ENST00000380763;ENST00000380762	D;D;D	0.92699	-3.09;-3.09;-3.09	5.83	4.07	0.47477	.	0.048205	0.85682	N	0.000000	D	0.97052	0.9037	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96207	0.9150	10	0.87932	D	0	-13.546	9.8221	0.40889	0.1705:0.0:0.8295:0.0	.	246	P53701	CCHL_HUMAN	H	246	ENSP00000326579:R246H;ENSP00000370140:R246H;ENSP00000370139:R246H	ENSP00000326579:R246H	R	+	2	0	HCCS	11049781	1.000000	0.71417	0.046000	0.18839	0.960000	0.62799	9.239000	0.95389	0.613000	0.30089	0.594000	0.82650	CGT		0.443	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			A	11139860	G	A	11139860	3	1	54	1	0	0	0	0	1	0	0	0	7011	1145	40	1	759	1	HCCS	23	11139860	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09		11139860	144130700	81	7301										
DMD	1756	broad.mit.edu	37	chrX	32867868	32867868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	tttttgccctgtcaggccttCgaggaggtctaggaggcgcc	14	11	2	0	rs398123864		TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chrX:32867868C>T	ENST00000357033.4	-	3	369	c.163G>A	c.(163-165)Gaa>Aaa	p.E55K	DMD_ENST00000288447.4_Missense_Mutation_p.E47K|DMD_ENST00000378677.2_Missense_Mutation_p.E51K|snoU13_ENST00000459244.1_RNA	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	55	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.		Missing (in BMD).		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E50K(1)|p.E51K(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				GTCAGGCCTTCGAGGAGGTCT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	X											80	76	77					X																	32867868		2202	4300	6502	32777789	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.163G>A	X.37:g.32867868C>T	ENSP00000354923:p.Glu55Lys		32777789	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	32	5.107550	0.94292	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000288447;ENST00000447523	D;D;D;D	0.97455	-4.39;-4.39;-4.39;-4.39	5.63	5.63	0.86233	Calponin homology domain (5);	0.000000	0.35805	U	0.002969	D	0.98874	0.9619	M	0.93150	3.385	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.986;0.984;0.992	D	0.99737	1.1014	10	0.87932	D	0	.	17.2721	0.87105	0.0:1.0:0.0:0.0	.	47;47;55;51	Q4G0X0;P11532-4;P11532;E9PDN5	.;.;DMD_HUMAN;.	K	47;51;55;55;47;18	ENSP00000367948:E51K;ENSP00000354923:E55K;ENSP00000288447:E47K;ENSP00000395904:E18K	ENSP00000288447:E47K	E	-	1	0	DMD	32777789	1.000000	0.71417	0.942000	0.38095	0.985000	0.73830	6.051000	0.71072	2.346000	0.79739	0.600000	0.82982	GAA		0.378	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32867868	C	T	32867868	3	4	54	1	0	0	0	0	1	0	0	0	4591	893	31	1	11445	1	DMD	23	32867868	Missense_Mutation	SNP	C	TCGA-AG-3909-01A-01W-1073-09	21728008	32867868	122402692	82	7302										
TEX11	56159	broad.mit.edu	37	chrX	69749016	69749016	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	gttactcaatgcttccacaaGctgactatacagcatattca	5	11	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chrX:69749016G>T	ENST00000395889.2	-	31	2907	c.2752C>A	c.(2752-2754)Ctt>Att	p.L918I	TEX11_ENST00000374333.2_Missense_Mutation_p.L903I|TEX11_ENST00000374320.2_Missense_Mutation_p.L593I|TEX11_ENST00000344304.3_Missense_Mutation_p.L918I	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	918					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.L903I(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GCTTCCACAAGCTGACTATAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											119	84	96					X																	69749016		2203	4300	6503	69665741	SO:0001583	missense	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2752C>A	X.37:g.69749016G>T	ENSP00000379226:p.Leu918Ile		69665741	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	G	2.255	-0.370661	0.05069	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.37584	1.75;1.73;1.19;1.73	4.35	-1.42	0.08913	.	0.394763	0.23072	N	0.052246	T	0.22551	0.0544	L	0.32530	0.975	0.09310	N	1	P;P	0.46064	0.872;0.798	P;B	0.45856	0.495;0.3	T	0.10917	-1.0609	9	.	.	.	-0.8473	1.1711	0.01826	0.212:0.3172:0.3076:0.1632	.	903;918	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	I	903;918;593;918	ENSP00000363453:L903I;ENSP00000379226:L918I;ENSP00000363440:L593I;ENSP00000340995:L918I	.	L	-	1	0	TEX11	69665741	0.046000	0.20272	0.000000	0.03702	0.003000	0.03518	0.073000	0.14640	-0.214000	0.10078	0.589000	0.80489	CTT		0.443	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	69749016	G	T	69749016	3	4	54	1	0	0	0	0	1	0	0	0	15813	971	34	2	74	2	TEX11	23	69749016	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	36881148	69749016	85521544	83	7303										
KIAA2022	340533	broad.mit.edu	37	chrX	73960374	73960374	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ctccatgggttcccaaagggGctctatggaggccatcatga	12	11	2	1			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chrX:73960374G>T	ENST00000055682.6	-	3	4629	c.4018C>A	c.(4018-4020)Ccc>Acc	p.P1340T		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1340					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.P1340T(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TCCCAAAGGGGCTCTATGGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	X											75	72	73					X																	73960374		2203	4300	6503	73877099	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4018C>A	X.37:g.73960374G>T	ENSP00000055682:p.Pro1340Thr		73877099	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.424208	0.62733	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.34072	1.38;1.38	5.55	5.55	0.83447	.	0.097492	0.64402	D	0.000001	T	0.52058	0.1711	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55211	-0.8176	10	0.87932	D	0	-9.5638	18.5251	0.90969	0.0:0.0:1.0:0.0	.	1340	Q5QGS0	K2022_HUMAN	T	1340	ENSP00000362567:P1340T;ENSP00000055682:P1340T	ENSP00000055682:P1340T	P	-	1	0	KIAA2022	73877099	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.317000	0.78254	0.544000	0.68410	CCC		0.473	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		T	73960374	G	T	73960374	3	4	54	1	0	0	0	0	1	0	0	0	8290	1203	42	2	540	2	KIAA2022	23	73960374	Missense_Mutation	SNP	G	TCGA-AG-3909-01A-01W-1073-09	4211358	73960374	81310186	84	7304										
DCAF12L2	340578	broad.mit.edu	37	chrX	125299059	125299059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.439899154196487	2.12617924528302	0.314989517819707	1	1	0	ttccacaggtggaagtagccGtccaaggacaccgctcccag	11	14	0	0			TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3909-01A-01W-1073-09	TCGA-AG-3909-10A-01W-1073-09	g.chrX:125299059G>A	ENST00000360028.2	-	1	875	c.849C>T	c.(847-849)gaC>gaT	p.D283D	DCAF12L2_ENST00000538699.1_Silent_p.D283D			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	283								p.D283D(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GGAAGTAGCCGTCCAAGGACA	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	X											66	70	69					X																	125299059		2203	4300	6503	125126740	SO:0001819	synonymous_variant	340578			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.849C>T	X.37:g.125299059G>A			125126740	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																				0.627	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		A	125299059	G	A	125299059	2	1	54	1	0	0	0	0	0	0	0	1	4271	1136	40	1		1	DCAF12L2	23	125299059	Silent	SNP	G	TCGA-AG-3909-01A-01W-1073-09	51338685	125299059	29971501	85	7305										
PTPRU	10076	broad.mit.edu	37	chr1	29649914	29649914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gtactggccagagccaggccGgcagcaatatggcctcatgg	14	12	1	1	rs373365649		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:29649914G>A	ENST00000345512.3	+	28	4019	c.3890G>A	c.(3889-3891)cGg>cAg	p.R1297Q	PTPRU_ENST00000460170.2_Missense_Mutation_p.R1293Q|PTPRU_ENST00000428026.2_Missense_Mutation_p.R1284Q|PTPRU_ENST00000373779.3_Missense_Mutation_p.R1287Q|PTPRU_ENST00000323874.8_Missense_Mutation_p.R1293Q|PTPRU_ENST00000356870.3_Missense_Mutation_p.R1293Q	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1297	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R1297Q(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GAGCCAGGCCGGCAGCAATAT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	40	38	39		3851,3890,3878,3860	3.8	1	1		39	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	PTPRU	NM_001195001.1,NM_005704.4,NM_133177.3,NM_133178.3	43,43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1284/1434,1297/1447,1293/1441,1287/1437	29649914	1,13005	2203	4300	6503	29522501	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3890G>A	1.37:g.29649914G>A	ENSP00000334941:p.Arg1297Gln		29522501	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231179	0.79688	0.0	1.16E-4	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58	3.84	3.84	0.44239	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.091907	0.43579	U	0.000559	T	0.10981	0.0268	N	0.12182	0.205	0.30744	N	0.745873	D;D;D;D;D	0.57899	0.977;0.977;0.977;0.981;0.981	P;P;P;P;P	0.51550	0.543;0.543;0.543;0.673;0.673	T	0.03717	-1.1010	9	.	.	.	.	9.4043	0.38451	0.0:0.0:0.6606:0.3394	.	1284;1293;1287;1293;1297	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	Q	1297;1287;1293;1293;1284;1293	ENSP00000334941:R1297Q;ENSP00000362884:R1287Q;ENSP00000349333:R1293Q;ENSP00000314987:R1293Q;ENSP00000392332:R1284Q;ENSP00000432906:R1293Q	.	R	+	2	0	PTPRU	29522501	0.962000	0.33011	0.998000	0.56505	0.965000	0.64279	5.631000	0.67812	2.135000	0.66039	0.462000	0.41574	CGG		0.612	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29649914	G	A	29649914	3	1	55	1	0	0	0	0	1	0	0	0	12850	1116	39	1	4022	1	PTPRU	1	29649914	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		29649914	219600707	1	7306										
TDRKH	11022	broad.mit.edu	37	chr1	151751698	151751698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agatgccttacagatagaacGaattgtctcgccgcctctcc	8	13	2	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:151751698G>A	ENST00000368822.1	-	5	1075	c.442C>T	c.(442-444)Cgt>Tgt	p.R148C	TDRKH_ENST00000368827.6_Missense_Mutation_p.R148C|TDRKH_ENST00000368825.3_Intron|TDRKH_ENST00000368824.3_Missense_Mutation_p.R148C|TDRKH_ENST00000458431.2_Missense_Mutation_p.R148C|TDRKH_ENST00000484421.1_5'UTR|TDRKH_ENST00000440583.2_5'UTR|TDRKH_ENST00000368823.1_Missense_Mutation_p.R144C			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	148	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)	p.R148C(1)		breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CAGATAGAACGAATTGTCTCG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	101	104					1																	151751698		1859	4094	5953	150018322	SO:0001583	missense	11022			AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"Tudor domain containing"	11713	protein-coding gene	gene with protein product		609501	"tudor and KH domain containing"			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.442C>T	1.37:g.151751698G>A	ENSP00000357812:p.Arg148Cys		150018322	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Missense_Mutation	SNP	ENST00000368822.1	37	CCDS41394.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423789	0.83667	.	.	ENSG00000182134	ENST00000368827;ENST00000368824;ENST00000368823;ENST00000368822;ENST00000458431	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	5.87	5.87	0.94306	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.053244	0.64402	D	0.000001	T	0.67183	0.2866	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.75522	-0.3288	10	0.87932	D	0	-10.3827	18.7883	0.91964	0.0:0.0:1.0:0.0	.	144;148	Q5SZR4;Q9Y2W6	.;TDRKH_HUMAN	C	148;148;144;148;148	ENSP00000357819:R148C;ENSP00000357815:R148C;ENSP00000357813:R144C;ENSP00000357812:R148C;ENSP00000395718:R148C	ENSP00000357812:R148C	R	-	1	0	TDRKH	150018322	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.477000	0.60223	2.770000	0.95276	0.650000	0.86243	CGT		0.398	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862		A	151751698	G	A	151751698	3	1	55	1	0	0	0	0	1	0	0	0	15776	1058	37	1	1279	1	TDRKH	1	151751698	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	122101784	151751698	97498923	2	7307										
CRTC2	200186	broad.mit.edu	37	chr1	153924880	153924880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agggagtacttacttaattcCagggacttcacaggaccgag	11	9	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:153924880C>T	ENST00000368633.1	-	9	872	c.745G>A	c.(745-747)Gga>Aga	p.G249R	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Intron	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	249					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.G249R(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	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)			TACTTAATTCCAGGGACTTCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	81	80					1																	153924880		2203	4300	6503	152191504	SO:0001583	missense	200186			AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.745G>A	1.37:g.153924880C>T	ENSP00000357622:p.Gly249Arg		152191504	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.557980	0.86231	.	.	ENSG00000160741	ENST00000368633	T	0.56941	0.43	4.67	4.67	0.58626	Transducer of regulated CREB activity, middle domain (1);	0.000000	0.85682	D	0.000000	T	0.65595	0.2706	M	0.71036	2.16	0.50813	D	0.999892	D	0.89917	1.0	D	0.87578	0.998	T	0.69624	-0.5095	10	0.72032	D	0.01	-4.4078	15.1154	0.72397	0.0:1.0:0.0:0.0	.	249	Q53ET0	CRTC2_HUMAN	R	249	ENSP00000357622:G249R	ENSP00000357622:G249R	G	-	1	0	CRTC2	152191504	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	6.421000	0.73353	2.430000	0.82344	0.455000	0.32223	GGA		0.532	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		T	153924880	C	T	153924880	3	4	55	1	0	0	0	0	1	0	0	0	3906	603	21	3	1360	3	CRTC2	1	153924880	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	2173182	153924880	95325741	3	7308										
PKLR	5313	broad.mit.edu	37	chr1	155263069	155263069	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gtgggatcacggcttagtggCgctgcccgacgtagctcctc	14	13	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:155263069C>T	ENST00000342741.4	-	9	1373	c.1335G>A	c.(1333-1335)gcG>gcA	p.A445A	PKLR_ENST00000392414.3_Silent_p.A414A	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	445					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.A445A(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	GGCTTAGTGGCGCTGCCCGAC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	1											81	69	73					1																	155263069		2203	4300	6503	153529693	SO:0001819	synonymous_variant	5313			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.1335G>A	1.37:g.155263069C>T			153529693	O75758|P11973	Silent	SNP	ENST00000342741.4	37	CCDS1109.1																																																																																				0.612	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		T	155263069	C	T	155263069	2	4	55	1	0	0	0	0	0	0	0	1	12007	755	27	1		1	PKLR	1	155263069	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	1338189	155263069	93987552	4	7309										
RGS13	6003	broad.mit.edu	37	chr1	192628477	192628477	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tcacttttcagattaacattGacagttcgacaagagagact	7	8	2	4			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:192628477G>A	ENST00000391995.2	+	7	592	c.304G>A	c.(304-306)Gac>Aac	p.D102N	RGS13_ENST00000482095.1_3'UTR|RGS13_ENST00000543215.1_Missense_Mutation_p.D102N	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	102	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.D102N(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						GATTAACATTGACAGTTCGAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	84	92					1																	192628477		2203	4300	6503	190895100	SO:0001583	missense	6003			AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"Regulators of G-protein signaling"	9995	protein-coding gene	gene with protein product		607190	"regulator of G-protein signalling 13"			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.304G>A	1.37:g.192628477G>A	ENSP00000375853:p.Asp102Asn		190895100	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	G	33	5.225310	0.95173	.	.	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.35605	1.3;1.3	5.69	5.69	0.88448	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67636	0.2914	M	0.90759	3.145	0.58432	D	0.999999	P	0.43287	0.802	P	0.62298	0.9	T	0.71823	-0.4476	10	0.66056	D	0.02	.	17.2892	0.87150	0.0:0.0:1.0:0.0	.	102	O14921	RGS13_HUMAN	N	102	ENSP00000375853:D102N;ENSP00000442837:D102N	ENSP00000375853:D102N	D	+	1	0	RGS13	190895100	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.243000	0.78219	2.685000	0.91497	0.591000	0.81541	GAC		0.343	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927		A	192628477	G	A	192628477	3	1	55	1	0	0	0	0	1	0	0	0	13333	1290	45	3	318	3	RGS13	1	192628477	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	37365408	192628477	56622144	5	7310										
ATP6V1G3	127124	broad.mit.edu	37	chr1	198492551	198492551	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gctctgtagttcacatggatTtctggtttcatgtcacagac	9	9	5	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:198492551T>A	ENST00000367382.1	-	3	411	c.327A>T	c.(325-327)gaA>gaT	p.E109D	ATP6V1G3_ENST00000489986.1_Missense_Mutation_p.E115D|ATP6V1G3_ENST00000367381.1_Missense_Mutation_p.E115D|ATP6V1G3_ENST00000309309.7_3'UTR|ATP6V1G3_ENST00000281087.2_Missense_Mutation_p.E109D			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	109					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)	p.E109D(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	7						TCACATGGATTTCTGGTTTCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											173	143	153					1																	198492551		2203	4300	6503	196759174	SO:0001583	missense	127124			AY039760	CCDS1395.1, CCDS1396.1	1q32.2	2010-04-21	2006-01-13		ENSG00000151418	ENSG00000151418		"ATPases / V-type"	18265	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 13kD, V1 subunit G isoform 3", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3"			9442887	Standard	NM_133262		Approved	ATP6G3, Vma10	uc001gup.3	Q96LB4	OTTHUMG00000035661	ENST00000367382.1:c.327A>T	1.37:g.198492551T>A	ENSP00000356352:p.Glu109Asp		196759174	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185713	0.57909	.	.	ENSG00000151418	ENST00000367382;ENST00000367381;ENST00000281087;ENST00000489986	T;T;T;T	0.52295	0.7;0.67;0.7;0.67	4.65	2.32	0.28847	.	0.104672	0.64402	D	0.000004	T	0.62913	0.2467	M	0.88775	2.98	0.45594	D	0.998533	D;P	0.60160	0.987;0.939	P;P	0.55087	0.768;0.511	T	0.65384	-0.6181	10	0.72032	D	0.01	-29.5629	8.3937	0.32544	0.0:0.1607:0.0:0.8393	.	115;109	Q96LB4-4;Q96LB4	.;VATG3_HUMAN	D	109;115;109;115	ENSP00000356352:E109D;ENSP00000356351:E115D;ENSP00000281087:E109D;ENSP00000417171:E115D	ENSP00000281087:E109D	E	-	3	2	ATP6V1G3	196759174	1.000000	0.71417	0.979000	0.43373	0.955000	0.61496	1.598000	0.36740	0.381000	0.24851	0.533000	0.62120	GAA		0.393	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326		A	198492551	T	A	198492551	3	1	55	1	0	0	0	0	1	0	0	0	1189	1838	64	5	33	5	ATP6V1G3	1	198492551	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	5864074	198492551	50758070	6	7311										
PPFIA4	8497	broad.mit.edu	37	chr1	203033031	203033031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gcctggggctcccgcagtacCgcagctacttcatggagtgc	13	14	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:203033031C>T	ENST00000447715.2	+	30	3325	c.2884C>T	c.(2884-2886)Cgc>Tgc	p.R962C	PPFIA4_ENST00000272198.6_Missense_Mutation_p.R478C|PPFIA4_ENST00000414050.2_Missense_Mutation_p.R691C|PPFIA4_ENST00000599966.1_Missense_Mutation_p.R469C|PPFIA4_ENST00000367240.2_Missense_Mutation_p.R963C|PPFIA4_ENST00000295706.4_Missense_Mutation_p.R469C			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	962	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.R1108C(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CCCGCAGTACCGCAGCTACTT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	66	63					1																	203033031		2203	4300	6503	201299654	SO:0001583	missense	8497			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2884C>T	1.37:g.203033031C>T	ENSP00000402576:p.Arg962Cys		201299654	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	C	28.5	4.927031	0.92389	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	5.14	5.14	0.70334	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.174005	0.27754	U	0.017990	T	0.72423	0.3458	M	0.87038	2.855	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.75020	0.961;0.985;0.937;0.957;0.975	T	0.77485	-0.2570	10	0.87932	D	0	-19.2637	15.8944	0.79323	0.0:0.8649:0.1351:0.0	.	691;962;164;469;478	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	C	963;962;469;691;478	ENSP00000356209:R963C;ENSP00000402576:R962C;ENSP00000295706:R469C;ENSP00000400379:R691C;ENSP00000272198:R478C	ENSP00000272198:R478C	R	+	1	0	PPFIA4	201299654	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.668000	0.90789	0.650000	0.86243	CGC		0.592	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		T	203033031	C	T	203033031	3	4	55	1	0	0	0	0	1	0	0	0	12343	652	23	1	1478	1	PPFIA4	1	203033031	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	4540480	203033031	46217590	7	7312										
NFASC	23114	broad.mit.edu	37	chr1	204948576	204948576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ccggcagcgttaactcagccGtcctccggctgtccccgtat	10	17	1	0	rs562163063		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:204948576G>A	ENST00000401399.1	+	18	2264	c.2065G>A	c.(2065-2067)Gtc>Atc	p.V689I	NFASC_ENST00000404076.1_Missense_Mutation_p.V668I|NFASC_ENST00000338515.6_Missense_Mutation_p.V689I|NFASC_ENST00000367171.4_Missense_Mutation_p.V674I|NFASC_ENST00000513543.1_Missense_Mutation_p.V685I|NFASC_ENST00000539706.1_Missense_Mutation_p.V685I|NFASC_ENST00000367170.4_Missense_Mutation_p.V689I|NFASC_ENST00000404907.1_Missense_Mutation_p.V685I|NFASC_ENST00000339876.6_Missense_Mutation_p.V689I|NFASC_ENST00000367169.4_Missense_Mutation_p.V689I|NFASC_ENST00000338586.6_Missense_Mutation_p.V689I|NFASC_ENST00000367172.4_Missense_Mutation_p.V689I|NFASC_ENST00000360049.4_Missense_Mutation_p.V685I			O94856	NFASC_HUMAN	neurofascin	689	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.V685I(2)|p.V689I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TAACTCAGCCGTCCTCCGGCT	0.587													G|||	1	0.000199681	0	0	5008	,	,		18674	0		0.001	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	1											107	104	105					1																	204948576		2203	4300	6503	203215199	SO:0001583	missense	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.2065G>A	1.37:g.204948576G>A	ENSP00000385637:p.Val689Ile		203215199	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	G	0.497	-0.872707	0.02570	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28	5.43	0.154	0.14901	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.452189	0.18437	N	0.141253	T	0.27489	0.0675	N	0.11255	0.115	0.19300	N	0.999973	B;B;B;B;B;B	0.33022	0.127;0.001;0.008;0.099;0.394;0.008	B;B;B;B;B;B	0.23150	0.044;0.002;0.01;0.012;0.012;0.005	T	0.14117	-1.0484	10	0.22706	T	0.39	.	6.4211	0.21744	0.4377:0.1188:0.4434:0.0	.	689;700;685;674;689;685	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3	NFASC_HUMAN;.;.;.;.;.	I	689;674;689;689;689;689;700;685;685;689;668;689;685;685;676	ENSP00000356140:V689I;ENSP00000356139:V674I;ENSP00000356138:V689I;ENSP00000342128:V689I;ENSP00000344786:V689I;ENSP00000343509:V689I;ENSP00000438614:V685I;ENSP00000353154:V685I;ENSP00000356137:V689I;ENSP00000385676:V668I;ENSP00000385637:V689I;ENSP00000384061:V685I;ENSP00000425908:V685I;ENSP00000415031:V676I	ENSP00000295776:V700I	V	+	1	0	NFASC	203215199	0.038000	0.19896	0.100000	0.21137	0.135000	0.20990	0.371000	0.20450	-0.226000	0.09899	-0.136000	0.14681	GTC		0.587	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204948576	G	A	204948576	3	1	55	1	0	0	0	0	1	0	0	0	10390	1145	40	1	2215	1	NFASC	1	204948576	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	1915545	204948576	44302045	8	7313										
HEATR1	55127	broad.mit.edu	37	chr1	236723029	236723029	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cctaccttatctaacaggtcGtaagctttactaaggagcgc	8	11	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr1:236723029G>A	ENST00000366582.3	-	34	4869	c.4755C>T	c.(4753-4755)taC>taT	p.Y1585Y	HEATR1_ENST00000366581.2_Silent_p.Y1504Y	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1585					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.Y1585Y(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CTAACAGGTCGTAAGCTTTAC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	1											121	104	110					1																	236723029		2203	4300	6503	234789652	SO:0001819	synonymous_variant	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.4755C>T	1.37:g.236723029G>A			234789652	Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																				0.398	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		A	236723029	G	A	236723029	2	1	55	1	0	0	0	0	0	0	0	1	7048	1140	40	1		1	HEATR1	1	236723029	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	31774453	236723029	12527592	9	7314										
TP53I3	9540	broad.mit.edu	37	chr2	24303706	24303706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tacctttggtgaatttcagcGttgcttcagagaaatcctct	8	9	3	2	rs148103343	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr2:24303706G>A	ENST00000238721.4	-	3	1456	c.602C>T	c.(601-603)aCg>aTg	p.T201M	TP53I3_ENST00000407482.1_Missense_Mutation_p.T201M|TP53I3_ENST00000417886.1_5'UTR|TP53I3_ENST00000313482.4_Missense_Mutation_p.T201M|FAM228B_ENST00000461972.1_Intron|TP53I3_ENST00000335934.4_Missense_Mutation_p.T201M	NM_004881.4	NP_004872.2	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	201					NADP metabolic process (GO:0006739)	extracellular vesicular exosome (GO:0070062)	NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)	p.T201M(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(3)|urinary_tract(2)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATTTCAGCGTTGCTTCAGA	0.438													G|||	2	0.000399361	8e-04	0	5008	,	,		18159	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	MET/THR,MET/THR,MET/THR	2,4404	4.2+/-10.8	0,2,2201	179	190	186		602,602,602	1.9	0	2	dbSNP_134	186	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	TP53I3	NM_001206802.2,NM_004881.4,NM_147184.3	81,81,81	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	possibly-damaging,possibly-damaging,possibly-damaging	201/249,201/333,201/333	24303706	4,13002	2203	4300	6503	24157210	SO:0001583	missense	9540			AF010309	CCDS1708.1, CCDS56112.1	2p23.3	2009-06-12			ENSG00000115129	ENSG00000115129			19373	protein-coding gene	gene with protein product		605171				11919562, 10840161, 19349281	Standard	NM_004881		Approved	PIG3	uc002rez.2	Q53FA7	OTTHUMG00000090817	ENST00000238721.4:c.602C>T	2.37:g.24303706G>A	ENSP00000238721:p.Thr201Met		24157210	D6W533|O14679|O14685|Q38G78|Q6JLE7|Q9BWB8	Missense_Mutation	SNP	ENST00000238721.4	37	CCDS1708.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	15.19	2.760699	0.49468	4.54E-4	2.33E-4	ENSG00000115129	ENST00000335934;ENST00000238721;ENST00000313482;ENST00000407482;ENST00000413037	T;T;T;T;T	0.04015	3.73;3.73;3.73;3.73;3.73	5.2	1.91	0.25777	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.772058	0.12394	N	0.472795	T	0.05044	0.0135	N	0.12569	0.235	0.09310	N	1	D;D;D	0.76494	0.997;0.986;0.999	P;B;P	0.55345	0.774;0.419;0.749	T	0.38929	-0.9638	10	0.56958	D	0.05	-24.7596	3.3863	0.07273	0.395:0.2007:0.4043:0.0	.	112;201;201	B4DMQ7;Q53FA7;Q53FA7-2	.;QORX_HUMAN;.	M	201;201;201;201;196	ENSP00000337834:T201M;ENSP00000238721:T201M;ENSP00000322298:T201M;ENSP00000384414:T201M;ENSP00000389620:T196M	ENSP00000238721:T201M	T	-	2	0	TP53I3	24157210	0.075000	0.21258	0.029000	0.17559	0.969000	0.65631	1.479000	0.35453	0.702000	0.31825	0.561000	0.74099	ACG		0.438	TP53I3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207618.2	NM_004881		A	24303706	G	A	24303706	3	1	55	1	0	0	0	0	1	0	0	0	16427	1145	40	1	408	1	TP53I3	2	24303706	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		24303706	218895667	10	7315										
PUS10	150962	broad.mit.edu	37	chr2	61192599	61192599	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gtttctgggtgagcaaagacCacactcacttcaaacaagct	8	11	3	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr2:61192599C>T	ENST00000316752.6	-	7	897	c.636G>A	c.(634-636)gtG>gtA	p.V212V	PUS10_ENST00000407787.1_Silent_p.V212V	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	212					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.V212V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			GAGCAAAGACCACACTCACTT	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	2											137	134	135					2																	61192599		2203	4299	6502	61046103	SO:0001819	synonymous_variant	150962			AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.636G>A	2.37:g.61192599C>T			61046103	Q5JPJ5|Q96MI8	Silent	SNP	ENST00000316752.6	37	CCDS1865.1																																																																																				0.328	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		T	61192599	C	T	61192599	2	4	55	1	0	0	0	0	0	0	0	1	12868	581	21	3		3	PUS10	2	61192599	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	36888893	61192599	182006774	11	7316										
TMEM131	23505	broad.mit.edu	37	chr2	98392321	98392321	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cgtacctccttgaggagcggTtctgtgtcagggttggaggt	16	8	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr2:98392321T>G	ENST00000186436.5	-	32	4533	c.4305A>C	c.(4303-4305)gaA>gaC	p.E1435D		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1435	Lys-rich.					integral component of membrane (GO:0016021)		p.E1435D(1)|p.E1322D(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TGAGGAGCGGTTCTGTGTCAG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	2											152	159	157					2																	98392321		2026	4195	6221	97758753	SO:0001583	missense	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.4305A>C	2.37:g.98392321T>G	ENSP00000186436:p.Glu1435Asp		97758753		Missense_Mutation	SNP	ENST00000186436.5	37	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252036	0.59212	.	.	ENSG00000075568	ENST00000186436	T	0.20598	2.06	5.22	-5.06	0.02946	.	0.000000	0.85682	D	0.000000	T	0.18215	0.0437	M	0.63843	1.955	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.01566	-1.1323	10	0.66056	D	0.02	-5.9685	11.1774	0.48607	0.0:0.3265:0.0837:0.5897	.	1435	Q92545	TM131_HUMAN	D	1435	ENSP00000186436:E1435D	ENSP00000186436:E1435D	E	-	3	2	TMEM131	97758753	0.014000	0.17966	0.361000	0.25849	0.869000	0.49853	-1.058000	0.03482	-1.437000	0.01967	-1.139000	0.01908	GAA		0.517	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		G	98392321	T	G	98392321	3	3	55	1	0	0	0	0	1	0	0	0	16083	1722	60	4	1386	4	TMEM131	2	98392321	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	37199722	98392321	144807052	12	7317										
ABCA12	26154	broad.mit.edu	37	chr2	215884152	215884152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tattttccaagtaattcattTgcagtgcctgttctagaaac	6	8	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr2:215884152T>C	ENST00000272895.7	-	13	1784	c.1565A>G	c.(1564-1566)cAa>cGa	p.Q522R	ABCA12_ENST00000389661.4_Missense_Mutation_p.Q204R|AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	522					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.Q522R(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		GTAATTCATTTGCAGTGCCTG	0.363																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											94	92	93					2																	215884152		2202	4300	6502	215592397	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1565A>G	2.37:g.215884152T>C	ENSP00000272895:p.Gln522Arg		215592397	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.191369	0.38707	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.56275	0.47;0.47	5.93	5.93	0.95920	.	0.097486	0.46758	N	0.000277	T	0.38161	0.1030	N	0.24115	0.695	0.80722	D	1	P;B	0.37612	0.602;0.387	B;B	0.30782	0.088;0.12	T	0.40813	-0.9543	10	0.66056	D	0.02	.	14.6064	0.68481	0.0:0.0:0.0:1.0	.	522;204	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	R	522;204	ENSP00000272895:Q522R;ENSP00000374312:Q204R	ENSP00000272895:Q522R	Q	-	2	0	ABCA12	215592397	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	4.860000	0.62961	2.263000	0.75096	0.533000	0.62120	CAA		0.363	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215884152	T	C	215884152	3	2	55	1	0	0	0	0	1	0	0	0	30	1812	63	4	6386	4	ABCA12	2	215884152	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	117491831	215884152	27315221	13	7318										
ZNF142	7701	broad.mit.edu	37	chr2	219515221	219515222	+	Frame_Shift_Ins	INS	-	-	TC													0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tacctgcttcctgtgaaggtINStctctctctcctggaggcag							TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	-	-	-	TC	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr2:219515221_219515222insTC	ENST00000449707.1	-	5	729_730	c.308_309insGA	c.(307-309)gaafs	p.E103fs	ZNF142_ENST00000411696.2_Frame_Shift_Ins_p.E103fs	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P104fs*21(1)		breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCTGTGAAGGTTCTCTCTCTCC	0.465																																					Colon(170;867 1942 8995 15834 18053)											1	Insertion - Frameshift(1)	large_intestine(1)	2																																								219223466	SO:0001589	frameshift_variant	7701			U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.307_308dupGA	2.37:g.219515230_219515231dupTC	ENSP00000408643:p.Glu103fs		219223465	Q92510	Frame_Shift_Ins	INS	ENST00000449707.1	37	CCDS42817.1																																																																																				0.465	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		TC	219515222	-	TC	219515221	7	5	55	1	0	1	1	0	0	0	0	0	17770	1722	60	0	4778	0	ZNF142	2	219515221	Frame_Shift_Ins	INS	-	TCGA-AG-3999-01A-01W-1073-09	3631069	219515221	23684152	14	7319										
C3orf20	84077	broad.mit.edu	37	chr3	14725825	14725825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cacctcaatgccaaggagatGgccttcaactgcctgatcag	9	13	3	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr3:14725825G>A	ENST00000253697.3	+	4	1013	c.561G>A	c.(559-561)atG>atA	p.M187I	C3orf20_ENST00000412910.1_Missense_Mutation_p.M65I|C3orf20_ENST00000435614.1_Missense_Mutation_p.M65I	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	187						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.M187I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCAAGGAGATGGCCTTCAACT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	3											132	114	120					3																	14725825		2203	4300	6503	14700829	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.561G>A	3.37:g.14725825G>A	ENSP00000253697:p.Met187Ile		14700829	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.491410	0.44249	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08370	3.39;3.1;3.1	4.91	4.91	0.64330	.	0.228619	0.30879	N	0.008693	T	0.06462	0.0166	L	0.34521	1.04	0.35116	D	0.766577	P	0.38677	0.642	B	0.24269	0.052	T	0.25641	-1.0126	10	0.72032	D	0.01	-16.1931	13.9423	0.64064	0.0:0.0:1.0:0.0	.	187	Q8ND61	CC020_HUMAN	I	187;65;65	ENSP00000253697:M187I;ENSP00000402933:M65I;ENSP00000396081:M65I	ENSP00000253697:M187I	M	+	3	0	C3orf20	14700829	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	2.822000	0.48073	2.423000	0.82170	0.467000	0.42956	ATG		0.547	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		A	14725825	G	A	14725825	3	1	55	1	0	0	0	0	1	0	0	0	2219	1348	47	3	567	3	C3orf20	3	14725825	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		14725825	183296605	15	7320										
BSN	8927	broad.mit.edu	37	chr3	49690304	49690304	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cccatcgaggatgcctccccGacggaggagctgaggcaggc	15	14	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr3:49690304G>A	ENST00000296452.4	+	5	3429	c.3315G>A	c.(3313-3315)ccG>ccA	p.P1105P		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1105					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.P1105P(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ATGCCTCCCCGACGGAGGAGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	3											67	70	69					3																	49690304		2203	4300	6503	49665308	SO:0001819	synonymous_variant	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3315G>A	3.37:g.49690304G>A			49665308	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																				0.647	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49690304	G	A	49690304	2	1	55	1	0	0	0	0	0	0	0	1	1533	1045	37	1		1	BSN	3	49690304	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	34964479	49690304	148332126	16	7321										
TF	7018	broad.mit.edu	37	chr3	133478031	133478031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tgccataggcccagaagcccCaacagatgaatgcaagcctg	10	13	0	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr3:133478031C>T	ENST00000402696.3	+	9	1546	c.1061C>T	c.(1060-1062)cCa>cTa	p.P354L	TF_ENST00000264998.3_Missense_Mutation_p.P227L	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	354					blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.P354L(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	CCAGAAGCCCCAACAGATGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											150	153	152					3																	133478031		2203	4300	6503	134960721	SO:0001583	missense	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1061C>T	3.37:g.133478031C>T	ENSP00000385834:p.Pro354Leu		134960721	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	.	.	.	.	.	.	.	.	.	.	C	8.168	0.791135	0.16258	.	.	ENSG00000091513	ENST00000402696;ENST00000264998	T;T	0.02280	4.36;4.41	4.15	1.34	0.21922	.	3.741260	0.00397	N	0.000055	T	0.03263	0.0095	L	0.42245	1.32	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48456	-0.9034	10	0.25751	T	0.34	2.34	7.7128	0.28688	0.0:0.7082:0.0:0.2918	.	354	P02787	TRFE_HUMAN	L	354;227	ENSP00000385834:P354L;ENSP00000264998:P227L	ENSP00000264998:P227L	P	+	2	0	TF	134960721	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.228000	0.17814	0.082000	0.17018	-0.671000	0.03813	CCA		0.488	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133478031	C	T	133478031	3	4	55	1	0	0	0	0	1	0	0	0	15824	594	21	3	1095	3	TF	3	133478031	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	83787727	133478031	64544399	17	7322										
JAKMIP1	152789	broad.mit.edu	37	chr4	6107415	6107415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggccctgcgcgcctcctcgcGcgcctcggtcagcagcgccg	14	20	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr4:6107415G>A	ENST00000282924.5	-	3	894	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R137C|JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000409371.3_Intron|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.R137C|JAKMIP1_ENST00000410077.2_Intron	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	137	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)	p.R137C(2)		NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GCCTCCTCGCGCGCCTCGGTC	0.701																																																2	Substitution - Missense(2)	large_intestine(2)	4											15	14	15					4																	6107415		2198	4290	6488	6158316	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.409C>T	4.37:g.6107415G>A	ENSP00000282924:p.Arg137Cys		6158316	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903758	0.72754	.	.	ENSG00000152969	ENST00000409021;ENST00000418227;ENST00000425341;ENST00000282924;ENST00000409831	T;T;T	0.46451	0.87;0.87;0.87	4.6	3.76	0.43208	.	0.084761	0.46145	D	0.000307	T	0.54367	0.1854	M	0.72894	2.215	0.80722	D	1	B;B;D	0.89917	0.098;0.027;1.0	B;B;P	0.61003	0.016;0.005;0.882	T	0.56378	-0.7989	10	0.87932	D	0	.	6.2909	0.21059	0.0936:0.0:0.6176:0.2887	.	137;137;137	F2Z2K5;Q96N16-2;Q96N16	.;.;JKIP1_HUMAN	C	137	ENSP00000386711:R137C;ENSP00000282924:R137C;ENSP00000386925:R137C	ENSP00000282924:R137C	R	-	1	0	JAKMIP1	6158316	0.997000	0.39634	0.986000	0.45419	0.852000	0.48524	3.343000	0.52167	1.051000	0.40369	0.484000	0.47621	CGC		0.701	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		A	6107415	G	A	6107415	3	1	55	1	0	0	0	0	1	0	0	0	7961	1087	38	1	2237	1	JAKMIP1	4	6107415	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		6107415	185046861	18	7323										
CC2D2A	57545	broad.mit.edu	37	chr4	15516423	15516423	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ttgtagcagtcagacctgcaGattatgaaagcatccatgat	9	8	1	4			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr4:15516423G>T	ENST00000503292.1	+	10	991	c.811G>T	c.(811-813)Gat>Tat	p.D271Y	CC2D2A_ENST00000424120.1_Missense_Mutation_p.D271Y|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000389652.5_Missense_Mutation_p.D222Y|CC2D2A_ENST00000413206.1_Missense_Mutation_p.D271Y	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	271					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.D222Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						CAGACCTGCAGATTATGAAAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											153	154	153					4																	15516423		1964	4158	6122	15125521	SO:0001583	missense	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.811G>T	4.37:g.15516423G>T	ENSP00000421809:p.Asp271Tyr		15125521	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	G	10.20	1.283922	0.23392	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000512702;ENST00000503292;ENST00000389652	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.76	4.02	0.46733	.	0.421591	0.24803	N	0.035469	T	0.22437	0.0541	L	0.36672	1.1	0.80722	D	1	B;B	0.11235	0.004;0.004	B;B	0.11329	0.004;0.006	T	0.03060	-1.1077	10	0.87932	D	0	.	12.7526	0.57316	0.0:0.1259:0.7429:0.1312	.	271;222	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	Y	271;271;222;222;271;271;222	ENSP00000403465:D271Y;ENSP00000398391:D271Y;ENSP00000422875:D271Y;ENSP00000421809:D271Y;ENSP00000374303:D222Y	ENSP00000374303:D222Y	D	+	1	0	CC2D2A	15125521	1.000000	0.71417	0.020000	0.16555	0.286000	0.27126	5.755000	0.68750	0.757000	0.33036	-0.165000	0.13383	GAT		0.448	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		T	15516423	G	T	15516423	3	4	55	1	0	0	0	0	1	0	0	0	2734	942	33	2	1044	2	CC2D2A	4	15516423	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	9409008	15516423	175637853	19	7324										
ADAM29	11086	broad.mit.edu	37	chr4	175897509	175897509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gtggaagtcggagaacattaCgccccggatgcaacatgaca	12	10	0	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr4:175897509C>T	ENST00000359240.3	+	5	1503	c.833C>T	c.(832-834)aCg>aTg	p.T278M	ADAM29_ENST00000445694.1_Missense_Mutation_p.T278M|ADAM29_ENST00000514159.1_Missense_Mutation_p.T278M|ADAM29_ENST00000404450.4_Missense_Mutation_p.T278M|RP13-577H12.2_ENST00000507525.1_RNA	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	278	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T278M(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GAGAACATTACGCCCCGGATG	0.428																																					Ovarian(140;1727 1835 21805 25838 41440)											1	Substitution - Missense(1)	large_intestine(1)	4											145	138	140					4																	175897509		2203	4300	6503	176134084	SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.833C>T	4.37:g.175897509C>T	ENSP00000352177:p.Thr278Met		176134084	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.355578	0.24598	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.09630	2.96;2.96;2.96;2.96	4.13	-8.26	0.01021	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	6.208930	0.00695	U	0.000753	T	0.08935	0.0221	N	0.25647	0.755	0.09310	N	1	P	0.50710	0.938	P	0.49192	0.602	T	0.35051	-0.9804	9	.	.	.	.	2.0652	0.03601	0.458:0.2589:0.0881:0.1951	.	278	Q9UKF5	ADA29_HUMAN	M	278	ENSP00000352177:T278M;ENSP00000414544:T278M;ENSP00000384229:T278M;ENSP00000423517:T278M	.	T	+	2	0	ADAM29	176134084	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.223000	0.00023	-3.644000	0.00127	-2.445000	0.00210	ACG		0.428	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				T	175897509	C	T	175897509	3	4	55	1	0	0	0	0	1	0	0	0	247	536	19	1	835	1	ADAM29	4	175897509	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	160381086	175897509	15256767	20	7325										
APC	324	broad.mit.edu	37	chr5	112116523	112116523	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	atatgaccagaaggcaattgGaatatgaagcaaggcaaatc	10	6	0	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr5:112116523G>T	ENST00000457016.1	+	6	948	c.568G>T	c.(568-570)Gaa>Taa	p.E190*	APC_ENST00000508376.2_Nonsense_Mutation_p.E190*|RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000257430.4_Nonsense_Mutation_p.E190*			P25054	APC_HUMAN	adenomatous polyposis coli	190	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E190*(1)|p.Q188fs*2(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGGCAATTGGAATATGAAGC	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Deletion - Frameshift(1)	large_intestine(2)	5	GRCh37	CM990148	APC	M							72	71	71					5																	112116523		2202	4300	6502	112144422	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.568G>T	5.37:g.112116523G>T	ENSP00000413133:p.Glu190*		112144422	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	37	6.315838	0.97467	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.1281	19.2841	0.94063	0.0:0.0:1.0:0.0	.	.	.	.	X	190;200;190;190;190	.	ENSP00000257430:E190X	E	+	1	0	APC	112144422	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.077000	0.94016	2.535000	0.85469	0.655000	0.94253	GAA		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112116523	G	T	112116523	4	4	55	1	0	0	0	0	0	1	0	0	763	1175	41	2	586	2	APC	5	112116523	Nonsense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		112116523	68798737	21	7326										
TRIM41	90933	broad.mit.edu	37	chr5	180651556	180651556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gtgcttcacatgccctcagtGccgaaagagctttcctcggc	10	14	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr5:180651556G>A	ENST00000315073.5	+	1	1267	c.557G>A	c.(556-558)tGc>tAc	p.C186Y	CTC-338M12.7_ENST00000499096.2_RNA|MIR4638_ENST00000581158.1_RNA|TRIM41_ENST00000351937.5_Missense_Mutation_p.C186Y	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	186					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.C186S(2)|p.C186Y(2)		NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCCCTCAGTGCCGAAAGAGC	0.637																																																4	Substitution - Missense(4)	large_intestine(2)|kidney(2)	5											43	46	45					5																	180651556		2203	4300	6503	180584162	SO:0001583	missense	90933			AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.557G>A	5.37:g.180651556G>A	ENSP00000320869:p.Cys186Tyr		180584162	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134868	0.56828	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	T;T	0.34667	1.35;1.35	5.08	5.08	0.68730	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.000000	0.64402	D	0.000019	T	0.71187	0.3310	H	0.95504	3.68	0.49582	D	0.999804	D;D;D	0.89917	1.0;0.997;0.997	D;D;D	0.81914	0.995;0.943;0.982	T	0.81208	-0.1037	10	0.87932	D	0	.	15.9814	0.80114	0.0:0.0:1.0:0.0	.	186;186;186	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	Y	186;186;65	ENSP00000336749:C186Y;ENSP00000320869:C186Y	ENSP00000320869:C186Y	C	+	2	0	TRIM41	180584162	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.632000	0.74281	2.345000	0.79718	0.491000	0.48974	TGC		0.637	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		A	180651556	G	A	180651556	3	1	55	1	0	0	0	0	1	0	0	0	16556	1319	46	3	559	3	TRIM41	5	180651556	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	68535033	180651556	263704	22	7327										
EHMT2	10919	broad.mit.edu	37	chr6	31860203	31860203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ccttgctgtcggagtccacgCgctcatccacagagtaggaa	11	13	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:31860203C>T	ENST00000375537.4	-	7	851	c.845G>A	c.(844-846)cGc>cAc	p.R282H	EHMT2_ENST00000375530.4_Missense_Mutation_p.R282H|EHMT2_ENST00000395728.3_Missense_Mutation_p.R339H|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Missense_Mutation_p.R339H	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	282					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)	p.R282H(1)		central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GGAGTCCACGCGCTCATCCAC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	69	76					6																	31860203		1511	2709	4220	31968182	SO:0001583	missense	10919			AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.845G>A	6.37:g.31860203C>T	ENSP00000364687:p.Arg282His		31968182	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735648	0.49045	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	T;T;T;T	0.73258	-0.46;-0.73;-0.65;-0.45	4.97	4.97	0.65823	.	0.084955	0.46145	D	0.000320	T	0.31606	0.0802	N	0.08118	0	0.43448	D	0.995635	B;B;B;B	0.14438	0.006;0.01;0.006;0.003	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.31475	-0.9942	10	0.42905	T	0.14	.	7.3862	0.26884	0.0:0.8216:0.0:0.1784	.	339;282;282;96	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	H	339;339;282;282;96	ENSP00000379078:R339H;ENSP00000364678:R339H;ENSP00000364680:R282H;ENSP00000364687:R282H	ENSP00000364678:R339H	R	-	2	0	EHMT2	31968182	0.971000	0.33674	1.000000	0.80357	0.996000	0.88848	2.174000	0.42482	2.582000	0.87167	0.491000	0.48974	CGC		0.622	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		T	31860203	C	T	31860203	3	4	55	1	0	0	0	0	1	0	0	0	4995	768	27	1	2875	1	EHMT2	6	31860203	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		31860203	139254864	23	7328										
LEMD2	221496	broad.mit.edu	37	chr6	33740480	33740480	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tcctctcctgcaacgcggtgGgactccgtctggatccggga	13	14	2	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:33740480G>T	ENST00000293760.5	-	9	1456	c.1437C>A	c.(1435-1437)tcC>tcA	p.S479S	LEMD2_ENST00000508327.1_Silent_p.S177S	NM_181336.3	NP_851853.1	Q8NC56	LEMD2_HUMAN	LEM domain containing 2	479					negative regulation of MAPK cascade (GO:0043409)|skeletal muscle cell differentiation (GO:0035914)	integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear membrane (GO:0031965)		p.S479S(1)		central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)|pancreas(1)	9						CAACGCGGTGGGACTCCGTCT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	6											73	57	62					6																	33740480		2203	4300	6503	33848458	SO:0001819	synonymous_variant	221496				CCDS4785.1, CCDS47411.1	6p21.31	2009-11-06			ENSG00000161904	ENSG00000161904			21244	protein-coding gene	gene with protein product						12477932	Standard	NM_001143944		Approved	dJ482C21.1, NET25	uc011drm.2	Q8NC56	OTTHUMG00000014535	ENST00000293760.5:c.1437C>A	6.37:g.33740480G>T			33848458	B4DVH5|E7EVT2|Q5T972|Q5T974	Silent	SNP	ENST00000293760.5	37	CCDS4785.1																																																																																				0.622	LEMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040209.3	XM_166338		T	33740480	G	T	33740480	2	4	55	1	0	0	0	0	0	0	0	1	8742	1219	43	2		2	LEMD2	6	33740480	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	1880277	33740480	137374587	24	7329										
GPR115	221393	broad.mit.edu	37	chr6	47681990	47681991	+	Missense_Mutation	DNP	GA	GA	TC													0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aagaaatcatactcaccttcGaaaagatcaataaaacccgc					rs116696585	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:47681990_47681991GA>TC	ENST00000283303.2	+	6	1267_1268	c.1009_1010GA>TC	c.(1009-1011)GAa>TCa	p.E337S	GPR115_ENST00000327753.3_Missense_Mutation_p.E337S|GPR115_ENST00000371220.1_Missense_Mutation_p.E394S|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	337					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E337>?(1)		NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						ACTCACCTTCGAAAAGATCAAT	0.455																																					GBM(22;431 510 9010 26644 32828)											1	Complex(1)	large_intestine(1)	6																																								47789950	SO:0001583	missense	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	Exception_encountered	6.37:g.47681990_47681991delinsTC	ENSP00000283303:p.Glu337Ser		47789949	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Missense_Mutation	DNP	ENST00000283303.2	37	CCDS4922.2																																																																																				0.455	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		TC	47681991	GA	TC	47681990	3	4	55	1	0	0	0	0	1	0	0	0	6652	1059	37	2	1027	2	GPR115	6	47681990	Missense_Mutation	DNP	GA	TCGA-AG-3999-01A-01W-1073-09	13941510	47681990	123433077	25	7330										
COL12A1	1303	broad.mit.edu	37	chr6	75798886	75798886	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctttcacctttctctcctggCaaacctaaggagggagaaaa	8	11	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:75798886C>A	ENST00000322507.8	-	64	9255	c.8946G>T	c.(8944-8946)ttG>ttT	p.L2982F	COL12A1_ENST00000345356.6_Missense_Mutation_p.L1818F|COL12A1_ENST00000483888.2_Missense_Mutation_p.L2978F|COL12A1_ENST00000416123.2_Missense_Mutation_p.L2906F|COL12A1_ENST00000511023.1_5'UTR	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2982	Collagen-like 4.|Triple-helical region (COL1) with 2 imperfections.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.L2982F(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCTCTCCTGGCAAACCTAAGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											36	38	38					6																	75798886		1810	4068	5878	75855606	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8946G>T	6.37:g.75798886C>A	ENSP00000325146:p.Leu2982Phe		75855606	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658062	0.47467	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	5.82	4.77	0.60923	.	0.375112	0.26293	N	0.025217	D	0.86234	0.5884	L	0.41710	1.295	0.31510	N	0.663711	P;D	0.56287	0.944;0.975	B;P	0.50136	0.413;0.632	T	0.80549	-0.1333	10	0.19147	T	0.46	.	7.5849	0.27987	0.0:0.6723:0.1512:0.1765	.	1818;2982	Q99715-2;Q99715	.;COCA1_HUMAN	F	2982;620;2906;1818;2906;2978	ENSP00000325146:L2982F;ENSP00000399812:L620F;ENSP00000305147:L1818F;ENSP00000412864:L2906F;ENSP00000421216:L2978F	ENSP00000325146:L2982F	L	-	3	2	COL12A1	75855606	0.305000	0.24481	1.000000	0.80357	0.952000	0.60782	-0.175000	0.09825	2.752000	0.94435	0.655000	0.94253	TTG		0.423	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75798886	C	A	75798886	3	1	55	1	0	0	0	0	1	0	0	0	3675	709	25	2	257	2	COL12A1	6	75798886	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	28116896	75798886	95316181	26	7331										
POPDC3	64208	broad.mit.edu	37	chr6	105606355	105606355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gactttgatgtcatttatcaCagtatcgtctggaattctga	8	7	4	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:105606355C>T	ENST00000254765.3	-	4	1144	c.866G>A	c.(865-867)tGt>tAt	p.C289Y	POPDC3_ENST00000474760.1_5'UTR|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000369120.2_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	289					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)		p.C289Y(1)		NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				TCATTTATCACAGTATCGTCT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											72	75	74					6																	105606355		2203	4300	6503	105713048	SO:0001583	missense	64208			BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.866G>A	6.37:g.105606355C>T	ENSP00000254765:p.Cys289Tyr		105713048	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	37	CCDS5052.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.792489	0.31685	.	.	ENSG00000132429	ENST00000254765	T	0.18960	2.18	5.56	2.77	0.32553	.	0.971060	0.08437	N	0.946071	T	0.05364	0.0142	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40021	-0.9585	10	0.87932	D	0	-3.5707	5.2812	0.15676	0.1633:0.6662:0.0:0.1705	.	289	Q9HBV1	POPD3_HUMAN	Y	289	ENSP00000254765:C289Y	ENSP00000254765:C289Y	C	-	2	0	POPDC3	105713048	0.913000	0.31002	0.744000	0.31058	0.204000	0.24138	1.570000	0.36439	0.899000	0.36444	-0.169000	0.13324	TGT		0.353	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361		T	105606355	C	T	105606355	3	4	55	1	0	0	0	0	1	0	0	0	12287	478	17	3	13	3	POPDC3	6	105606355	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	29807469	105606355	65508712	27	7332										
OPRM1	4988	broad.mit.edu	37	chr6	154412222	154412222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctatggactgatgatcttgcGcctcaagagtgtccgcatgc	11	11	2	3	rs1799974	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr6:154412222G>A	ENST00000330432.7	+	3	1016	c.779G>A	c.(778-780)cGc>cAc	p.R260H	OPRM1_ENST00000524163.1_Missense_Mutation_p.R260H|OPRM1_ENST00000522555.1_Missense_Mutation_p.R160H|OPRM1_ENST00000414028.2_Missense_Mutation_p.R260H|OPRM1_ENST00000434900.2_Missense_Mutation_p.R353H|OPRM1_ENST00000435918.2_Missense_Mutation_p.R260H|OPRM1_ENST00000520708.1_Missense_Mutation_p.R160H|OPRM1_ENST00000428397.2_Missense_Mutation_p.R260H|OPRM1_ENST00000337049.4_Missense_Mutation_p.R260H|OPRM1_ENST00000522236.1_Missense_Mutation_p.R160H|OPRM1_ENST00000229768.5_Missense_Mutation_p.R260H|OPRM1_ENST00000360422.4_Missense_Mutation_p.R260H|OPRM1_ENST00000518759.1_Missense_Mutation_p.R179H|OPRM1_ENST00000452687.2_Missense_Mutation_p.R260H|OPRM1_ENST00000419506.2_Missense_Mutation_p.R260H	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	260			R -> H (rare polymorphism; dbSNP:rs1799974). {ECO:0000269|PubMed:9689128}.		adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)	p.R260H(4)|p.R353H(2)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	ATGATCTTGCGCCTCAAGAGT	0.502													G|||	3	0.000599042	0	0.0014	5008	,	,		20227	0		0	False		,,,				2504	0.002															6	Substitution - Missense(6)	large_intestine(6)	6	GRCh37	CM016140	OPRM1	M	rs1799974	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	5,4359		0,5,2177	172	173	173		779,779,779,779,1058,479,536,779,779,779,779,779,479	6	1	6	dbSNP_89	173	7,8569		0,7,4281	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	OPRM1	NM_000914.3,NM_001008503.1,NM_001008504.2,NM_001008505.1,NM_001145279.2,NM_001145280.2,NM_001145281.1,NM_001145282.1,NM_001145283.1,NM_001145284.2,NM_001145285.1,NM_001145286.1,NM_001145287.1	29,29,29,29,29,29,29,29,29,29,29,29,29	0,12,6458	AA,AG,GG		0.0816,0.1146,0.0927	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	260/401,260/419,260/393,260/447,353/494,160/301,179/320,260/407,260/398,260/404,260/390,260/421,160/301	154412222	12,12928	2182	4288	6470	154453915	SO:0001583	missense	4988			L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.779G>A	6.37:g.154412222G>A	ENSP00000328264:p.Arg260His		154453915	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	G	31	5.084463	0.94100	0.001146	8.16E-4	ENSG00000112038	ENST00000434900;ENST00000520708;ENST00000518759;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049;ENST00000522555;ENST00000522236	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	5.96	5.96	0.96718	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.71871	2.18	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.979;1.0;1.0	T	0.58025	-0.7709	10	0.87932	D	0	.	20.4192	0.99033	0.0:0.0:1.0:0.0	rs1799974	260;260;260;260;353;179;160;260;260;260;260;260	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	H	353;160;179;260;260;260;260;260;260;260;260;260;260;160;160	ENSP00000394624:R353H;ENSP00000430876:R160H;ENSP00000430260:R179H;ENSP00000328264:R260H;ENSP00000353598:R260H;ENSP00000411903:R260H;ENSP00000410497:R260H;ENSP00000229768:R260H;ENSP00000403549:R260H;ENSP00000430097:R260H;ENSP00000399359:R260H;ENSP00000413752:R260H;ENSP00000338381:R260H;ENSP00000429719:R160H;ENSP00000429373:R160H	ENSP00000229768:R260H	R	+	2	0	OPRM1	154453915	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.831000	0.97527	0.650000	0.86243	CGC		0.502	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		A	154412222	G	A	154412222	3	1	55	1	0	0	0	0	1	0	0	0	10918	1087	38	1	1123	1	OPRM1	6	154412222	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	48805867	154412222	16702845	28	7333										
NPC1L1	29881	broad.mit.edu	37	chr7	44578579	44578579	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	attgtccggattgaggggggCgtagcagatgtcctgcaggg	18	7	0	2	rs201421514		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr7:44578579C>T	ENST00000289547.4	-	2	1472	c.1417G>A	c.(1417-1419)Gcc>Acc	p.A473T	NPC1L1_ENST00000381160.3_Missense_Mutation_p.A473T|NPC1L1_ENST00000546276.1_Missense_Mutation_p.A473T|NPC1L1_ENST00000423141.1_Missense_Mutation_p.A473T	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	473					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)	p.A473T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	TTGAGGGGGGCGTAGCAGATG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											124	108	114					7																	44578579		2203	4300	6503	44545104	SO:0001583	missense	29881				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1417G>A	7.37:g.44578579C>T	ENSP00000289547:p.Ala473Thr		44545104	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	37	CCDS5491.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	19.51	3.842100	0.71488	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.94716	0.8295	M	0.88640	2.97	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.999;0.998;0.998	D;P;D;P	0.66084	0.922;0.823;0.941;0.878	D	0.94775	0.7948	10	0.45353	T	0.12	-30.816	15.9151	0.79508	0.0:1.0:0.0:0.0	.	473;473;473;473	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	T	473	ENSP00000289547:A473T;ENSP00000370552:A473T;ENSP00000438033:A473T;ENSP00000404670:A473T	ENSP00000289547:A473T	A	-	1	0	NPC1L1	44545104	1.000000	0.71417	0.487000	0.27428	0.424000	0.31475	7.160000	0.77495	2.353000	0.79882	0.407000	0.27541	GCC		0.592	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		T	44578579	C	T	44578579	3	4	55	1	0	0	0	0	1	0	0	0	10602	768	27	1	2738	1	NPC1L1	7	44578579	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		44578579	114560084	29	7334										
PCLO	27445	broad.mit.edu	37	chr7	82583572	82583572	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	atagtctataatgctgcctgGaaaataagttgatgaagaaa	9	4	1	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr7:82583572G>A	ENST00000333891.9	-	5	7034	c.6697C>T	c.(6697-6699)Cca>Tca	p.P2233S	PCLO_ENST00000423517.2_Missense_Mutation_p.P2233S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.P2233S(2)|p.P2164S(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATGCTGCCTGGAAAATAAGTT	0.378																																																3	Substitution - Missense(3)	large_intestine(3)	7											53	50	51					7																	82583572		1824	4092	5916	82421508	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6697C>T	7.37:g.82583572G>A	ENSP00000334319:p.Pro2233Ser		82421508		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692862	0.30052	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15487	2.42;2.42	5.77	5.77	0.91146	.	.	.	.	.	T	0.30978	0.0782	L	0.44542	1.39	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.54544	0.755;0.755	T	0.00722	-1.1594	9	0.87932	D	0	.	19.9785	0.97317	0.0:0.0:1.0:0.0	.	2233;2233	Q9Y6V0-5;Q9Y6V0-6	.;.	S	2164;2233;2233	ENSP00000334319:P2233S;ENSP00000388393:P2233S	ENSP00000334319:P2233S	P	-	1	0	PCLO	82421508	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.336000	0.65935	2.724000	0.93272	0.650000	0.86243	CCA		0.378	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82583572	G	A	82583572	3	1	55	1	0	0	0	0	1	0	0	0	11614	1174	41	3	8832	3	PCLO	7	82583572	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	38004993	82583572	76555091	30	7335										
PCLO	27445	broad.mit.edu	37	chr7	82583669	82583669	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gttatgctatccagggtagtAatgggtgaagagctatctgt	13	5	1	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr7:82583669A>C	ENST00000333891.9	-	5	6937	c.6600T>G	c.(6598-6600)atT>atG	p.I2200M	PCLO_ENST00000423517.2_Missense_Mutation_p.I2200M	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.I2200M(2)|p.I2131M(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCAGGGTAGTAATGGGTGAAG	0.428																																																3	Substitution - Missense(3)	large_intestine(3)	7											98	93	94					7																	82583669		1946	4156	6102	82421605	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6600T>G	7.37:g.82583669A>C	ENSP00000334319:p.Ile2200Met		82421605		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	3.327	-0.137463	0.06711	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17854	2.25;2.26	5.77	0.232	0.15381	.	.	.	.	.	T	0.12987	0.0315	L	0.44542	1.39	0.53688	D	0.999978	P;P	0.36909	0.573;0.573	B;B	0.37692	0.256;0.256	T	0.11179	-1.0598	9	0.87932	D	0	.	3.6635	0.08247	0.4123:0.0:0.2611:0.3266	.	2200;2200	Q9Y6V0-5;Q9Y6V0-6	.;.	M	2131;2200;2200	ENSP00000334319:I2200M;ENSP00000388393:I2200M	ENSP00000334319:I2200M	I	-	3	3	PCLO	82421605	0.009000	0.17119	0.455000	0.27031	0.710000	0.40934	-0.034000	0.12225	-0.203000	0.10251	0.528000	0.53228	ATT		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82583669	A	C	82583669	3	2	55	1	0	0	0	0	1	0	0	0	11614	358	13	4	8929	4	PCLO	7	82583669	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09	97	82583669	76554994	31	7336										
NUP205	23165	broad.mit.edu	37	chr7	135300734	135300734	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tcaatagagctaagggtaacCtctctgaatcgtcagcggtc	10	10	3	2	rs367706530		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr7:135300734C>T	ENST00000285968.6	+	24	3407	c.3381C>T	c.(3379-3381)acC>acT	p.T1127T		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1127					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.T1127T(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TAAGGGTAACCTCTCTGAATC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	7											140	126	131					7																	135300734		2203	4300	6503	134951274	SO:0001819	synonymous_variant	23165			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.3381C>T	7.37:g.135300734C>T			134951274	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																				0.393	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			T	135300734	C	T	135300734	2	4	55	1	0	0	0	0	0	0	0	1	10790	668	24	3		3	NUP205	7	135300734	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	52717065	135300734	23837929	32	7337										
C8orf80	389643	broad.mit.edu	37	chr8	27898660	27898660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	catgcaggcgaagcactgtgCgatggccttctccagcagct	12	13	1	0	rs199622602		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:27898660C>T	ENST00000413272.2	-	13	1661	c.1519G>A	c.(1519-1521)Gca>Aca	p.A507T	NUGGC_ENST00000341513.6_Missense_Mutation_p.A507T	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	507					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A507T(1)									AAGCACTGTGCGATGGCCTTC	0.542													C|||	1	0.000199681	8e-04	0	5008	,	,		18025	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	THR/ALA	6,4192		0,6,2093	48	50	50		1519	1.9	0	8		50	2,8430		0,2,4214	yes	missense	C8orf80	NM_001010906.1	58	0,8,6307	TT,TC,CC		0.0237,0.1429,0.0633	benign	507/797	27898660	8,12622	2099	4216	6315	27954579	SO:0001583	missense	389643			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1519G>A	8.37:g.27898660C>T	ENSP00000408697:p.Ala507Thr		27954579	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	2.552	-0.303799	0.05495	0.001429	2.37E-4	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.29397	1.57;1.57	5.65	1.92	0.25849	.	0.646882	0.15899	N	0.239164	T	0.13243	0.0321	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.14656	T	0.56	-4.7309	7.8611	0.29509	0.0:0.6702:0.0:0.3298	.	507	Q68CJ6	SLIP_HUMAN	T	507	ENSP00000408697:A507T;ENSP00000345031:A507T	ENSP00000345031:A507T	A	-	1	0	C8orf80	27954579	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.218000	0.17622	0.069000	0.16605	-0.897000	0.02905	GCA		0.542	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		T	27898660	C	T	27898660	3	4	55	1	0	0	0	0	1	0	0	0	2445	768	27	1	899	1	C8orf80	8	27898660	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		27898660	118465362	33	7338										
PLEKHA2	59339	broad.mit.edu	37	chr8	38826183	38826183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ccaggccctcaagtgccaccCcagagtaagtcacttccttt	7	16	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:38826183C>T	ENST00000420274.1	+	11	1145	c.911C>T	c.(910-912)cCc>cTc	p.P304L	PLEKHA2_ENST00000388745.4_3'UTR|CTD-2544N14.3_ENST00000520863.1_RNA|PLEKHA2_ENST00000521746.1_Intron	NM_021623.1	NP_067636.1	Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2	304					positive regulation of cell-matrix adhesion (GO:0001954)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289)	p.P304L(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			AAGTGCCACCCCAGAGTAAGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											93	100	97					8																	38826183		2031	4193	6224	38945340	SO:0001583	missense	59339			AF286164	CCDS75732.1	8p11.21	2013-01-10	2002-01-14			ENSG00000169499		"Pleckstrin homology (PH) domain containing"	14336	protein-coding gene	gene with protein product	"tandem PH Domain containing protein-2"	607773	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"			11001876	Standard	NM_021623		Approved	TAPP2	uc003xmi.4	Q9HB19		ENST00000420274.1:c.911C>T	8.37:g.38826183C>T	ENSP00000393860:p.Pro304Leu		38945340		Missense_Mutation	SNP	ENST00000420274.1	37		.	.	.	.	.	.	.	.	.	.	C	16.26	3.071812	0.55646	.	.	ENSG00000169499	ENST00000420274;ENST00000535929	T	0.05513	3.43	6.16	5.28	0.74379	.	0.228628	0.45606	D	0.000350	T	0.08980	0.0222	M	0.65975	2.015	0.54753	D	0.999988	B;B	0.31383	0.321;0.1	B;B	0.29267	0.1;0.036	T	0.14531	-1.0469	10	0.22706	T	0.39	-11.9401	12.1765	0.54188	0.1353:0.7347:0.13:0.0	.	304;304	Q9HB19;A8K727	PKHA2_HUMAN;.	L	304;254	ENSP00000393860:P304L	ENSP00000393860:P304L	P	+	2	0	PLEKHA2	38945340	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	2.761000	0.47589	1.607000	0.50170	0.650000	0.86243	CCC		0.498	PLEKHA2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021623		T	38826183	C	T	38826183	3	4	55	1	0	0	0	0	1	0	0	0	12087	623	22	3	949	3	PLEKHA2	8	38826183	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	10927523	38826183	107537839	34	7339										
TRPA1	8989	broad.mit.edu	37	chr8	72975174	72975174	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctgtctactgtacccatgctCttcaccttgagaagaaaata	6	11	3	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:72975174C>G	ENST00000262209.4	-	6	874	c.667G>C	c.(667-669)Gag>Cag	p.E223Q		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	223					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.E223Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TACCCATGCTCTTCACCTTGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8											94	88	90					8																	72975174		2203	4300	6503	73137728	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.667G>C	8.37:g.72975174C>G	ENSP00000262209:p.Glu223Gln		73137728	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.719758	0.48728	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.54071	0.59;2.31	5.62	2.71	0.32032	Ankyrin repeat-containing domain (3);	0.281797	0.43747	D	0.000531	T	0.42040	0.1185	L	0.52759	1.655	0.39321	D	0.965244	B	0.24426	0.103	B	0.20184	0.028	T	0.25187	-1.0139	10	0.25751	T	0.34	-9.5954	9.0015	0.36085	0.0:0.7499:0.0:0.2501	.	223	O75762	TRPA1_HUMAN	Q	75;223	ENSP00000428151:E75Q;ENSP00000262209:E223Q	ENSP00000262209:E223Q	E	-	1	0	TRPA1	73137728	0.992000	0.36948	0.048000	0.18961	0.654000	0.38779	0.605000	0.24179	0.640000	0.30582	0.650000	0.86243	GAG		0.328	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		G	72975174	C	G	72975174	3	3	55	1	0	0	0	0	1	0	0	0	16617	922	32	5	2780	5	TRPA1	8	72975174	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	34148991	72975174	73388848	35	7340										
ZFHX4	79776	broad.mit.edu	37	chr8	77618386	77618386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gcctcaccccaggcttgcccGgggtgagagttacacgtgtg	14	13	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:77618386G>A	ENST00000521891.2	+	2	2511	c.2063G>A	c.(2062-2064)cGg>cAg	p.R688Q	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.R688Q|ZFHX4_ENST00000518282.1_Missense_Mutation_p.R688Q|ZFHX4_ENST00000050961.6_Missense_Mutation_p.R688Q	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R688Q(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGGCTTGCCCGGGGTGAGAGT	0.517										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											42	46	45					8																	77618386		2140	4277	6417	77780941	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.2063G>A	8.37:g.77618386G>A	ENSP00000430497:p.Arg688Gln		77780941	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705674	0.48412	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.58060	0.42;0.41;0.38;0.36	4.98	4.98	0.66077	.	0.000000	0.42294	U	0.000731	T	0.72827	0.3509	M	0.70595	2.14	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.988;0.996;0.995;1.0	T	0.75010	-0.3468	10	0.66056	D	0.02	.	18.7896	0.91968	0.0:0.0:1.0:0.0	.	688;688;688;688	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	Q	688	ENSP00000430497:R688Q;ENSP00000399605:R688Q;ENSP00000050961:R688Q;ENSP00000430848:R688Q	ENSP00000050961:R688Q	R	+	2	0	ZFHX4	77780941	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.592000	0.98245	2.737000	0.93849	0.637000	0.83480	CGG		0.517	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77618386	G	A	77618386	3	1	55	1	0	0	0	0	1	0	0	0	17674	1116	39	1	2065	1	ZFHX4	8	77618386	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	4643212	77618386	68745636	36	7341										
C8orf47	203111	broad.mit.edu	37	chr8	99102183	99102183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aagcatggagcatccagcacGaaatgtagaggcaggagcat	13	8	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:99102183G>A	ENST00000318528.3	+	2	1297	c.938G>A	c.(937-939)cGa>cAa	p.R313Q	C8orf47_ENST00000545282.1_Intron	NM_173549.2	NP_775820.2	Q6P6B1	ERIC5_HUMAN		313	Glu-rich.							p.R313Q(2)		kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(2)	13	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			CATCCAGCACGAAATGTAGAG	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	8											117	103	107					8																	99102183		2203	4300	6503	99171359	SO:0001583	missense	203111																														ENST00000318528.3:c.938G>A	8.37:g.99102183G>A	ENSP00000315614:p.Arg313Gln		99171359	G3V1K4|Q8N1L8	Missense_Mutation	SNP	ENST00000318528.3	37	CCDS34929.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.238636	0.22711	.	.	ENSG00000177459	ENST00000318528	T	0.22336	1.96	4.8	1.8	0.24995	.	0.411835	0.20879	N	0.084039	T	0.09642	0.0237	N	0.22421	0.69	0.09310	N	0.999999	B	0.29936	0.262	B	0.22386	0.039	T	0.24764	-1.0151	10	0.18276	T	0.48	-1.6124	4.3678	0.11233	0.1902:0.0:0.6336:0.1762	.	313	Q6P6B1	CH047_HUMAN	Q	313	ENSP00000315614:R313Q	ENSP00000315614:R313Q	R	+	2	0	C8orf47	99171359	0.043000	0.20138	0.021000	0.16686	0.016000	0.09150	0.376000	0.20535	0.730000	0.32425	0.655000	0.94253	CGA		0.438	C8orf47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380465.1			A	99102183	G	A	99102183	3	1	55	1	0	0	0	0	1	0	0	0	2438	1058	37	1	944	1	C8orf47	8	99102183	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	21483797	99102183	47261839	37	7342										
KCNS2	3788	broad.mit.edu	37	chr8	99441321	99441321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggtggtgggctaccgtcagtAtgaccacagtggggtacggg	18	8	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:99441321A>G	ENST00000287042.4	+	2	1464	c.1114A>G	c.(1114-1116)Atg>Gtg	p.M372V	KCNS2_ENST00000521839.1_Missense_Mutation_p.M372V	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	372					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.M372V(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TACCGTCAGTATGACCACAGT	0.617																																					Pancreas(138;844 2489 9202 24627)											1	Substitution - Missense(1)	large_intestine(1)	8											85	80	82					8																	99441321		2203	4300	6503	99510497	SO:0001583	missense	3788			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.1114A>G	8.37:g.99441321A>G	ENSP00000287042:p.Met372Val		99510497	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461620	0.63513	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	D;D	0.98807	-5.15;-5.15	6.07	6.07	0.98685	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98937	0.9639	M	0.71581	2.175	0.58432	D	0.999999	D	0.53885	0.963	D	0.67231	0.95	D	0.99864	1.1087	10	0.87932	D	0	.	16.6288	0.85011	1.0:0.0:0.0:0.0	.	372	Q9ULS6	KCNS2_HUMAN	V	372	ENSP00000287042:M372V;ENSP00000430712:M372V	ENSP00000287042:M372V	M	+	1	0	KCNS2	99510497	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	ATG		0.617	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		G	99441321	A	G	99441321	3	3	55	1	0	0	0	0	1	0	0	0	8110	449	16	4	1116	4	KCNS2	8	99441321	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09	339138	99441321	46922701	38	7343										
UBR5	51366	broad.mit.edu	37	chr8	103299706	103299706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agtgacaacgcttctgcgccCactagcattatcttggttgc	9	12	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr8:103299706C>T	ENST00000520539.1	-	37	5518	c.4912G>A	c.(4912-4914)Ggg>Agg	p.G1638R	UBR5_ENST00000519528.1_5'Flank|UBR5_ENST00000521922.1_Missense_Mutation_p.G1632R|UBR5_ENST00000220959.4_Missense_Mutation_p.G1638R	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1638					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.G1638R(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			CTTCTGCGCCCACTAGCATTA	0.443																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											199	148	165					8																	103299706		2203	4300	6503	103368882	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4912G>A	8.37:g.103299706C>T	ENSP00000429084:p.Gly1638Arg		103368882	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178925	0.94846	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.46819	0.86;0.86;0.86	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.59280	0.2182	N	0.22421	0.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.61783	-0.6992	10	0.72032	D	0.01	.	20.3955	0.98984	0.0:1.0:0.0:0.0	.	1632;1638	E7EMW7;O95071	.;UBR5_HUMAN	R	1638;1638;1632	ENSP00000429084:G1638R;ENSP00000220959:G1638R;ENSP00000427819:G1632R	ENSP00000220959:G1638R	G	-	1	0	UBR5	103368882	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.770000	0.85390	2.830000	0.97506	0.655000	0.94253	GGG		0.443	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103299706	C	T	103299706	3	4	55	1	0	0	0	0	1	0	0	0	16945	594	21	3	3579	3	UBR5	8	103299706	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	3858385	103299706	43064316	39	7344										
WASH1	0	broad.mit.edu	37	chr9	14816	14816	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	catggagccccctacgattcCcagtcgtcctcgtcctcctc	7	19	0	0	rs200377821	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr9:14816C>G								None (None upstream) : MIR1302-2 (12840 downstream)																							CCTACGATTCCCAGTCGTCCT	0.642													.|||	136	0.0271565	0.0023	0.1095	5008	,	,		25373	0		0.0378	False		,,,				2504	0.0194															0			9						C	CYS/TRP	28,2736		1,26,1355	7	10	9		1389	1.2	1	9		9	373,6917		20,333,3292	no	missense	WASH1	NM_182905.4	215	21,359,4647	GG,GC,CC		5.1166,1.013,3.9885	probably-damaging	463/466	14816	401,9653	1382	3645	5027	4816	SO:0001628	intergenic_variant	375690																															9.37:g.14816C>G			4816		Missense_Mutation	SNP		37																																																																																				0	0.642									G	14816	C	G	14816	1	3	55	0	1	0	0	0	0	0	0	0	17295	624	22	5		5	WASH1	9	14816	IGR	SNP	C	TCGA-AG-3999-01A-01W-1073-09		14816	141198615	40	7345										
BAG1	51510	broad.mit.edu	37	chr9	33264430	33264430	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cgggtcaactcctcgctccgGgtcgagcggcgccgggtttt	15	14	1	0	rs140687411	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr9:33264430G>A	ENST00000223500.8	+	0	0				BAG1_ENST00000379704.2_5'UTR|BAG1_ENST00000472232.3_Silent_p.T81T|CHMP5_ENST00000419016.2_5'Flank	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5						endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T81T(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			CCTCGCTCCGGGTCGAGCGGC	0.697																																																1	Substitution - coding silent(1)	large_intestine(1)	9											37	37	37					9																	33264430		2203	4300	6503	33254430	SO:0001631	upstream_gene_variant	573			AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"Charged multivesicular body proteins"	26942	protein-coding gene	gene with protein product		610900	"chromosome 9 open reading frame 83", "chromatin modifying protein 5"	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765		9.37:g.33264430G>A	Exception_encountered		33254430	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Silent	SNP	ENST00000223500.8	37	CCDS6537.1																																																																																				0.697	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410		A	33264430	G	A	33264430	1	1	55	0	1	0	0	0	0	0	0	0	1287	1219	43	3		3	BAG1	9	33264430	5'Flank	SNP	G	TCGA-AG-3999-01A-01W-1073-09	33249614	33264430	107949001	41	7346										
HSD17B3	3293	broad.mit.edu	37	chr9	99015130	99015130	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aagtttttctttaatatgctCgtagatgtcatcttttgtaa	6	5	3	1	rs568096279		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr9:99015130C>T	ENST00000375263.3	-	4	387	c.340G>A	c.(340-342)Gag>Aag	p.E114K	HSD17B3_ENST00000464104.1_5'Flank|RP11-240L7.4_ENST00000448857.1_RNA|HSD17B3_ENST00000375262.2_Missense_Mutation_p.E114K	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	114					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)	p.E114K(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				TTAATATGCTCGTAGATGTCA	0.363													C|||	1	0.000199681	0	0.0014	5008	,	,		17507	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											187	188	187					9																	99015130		2203	4299	6502	98054951	SO:0001583	missense	3293				CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.340G>A	9.37:g.99015130C>T	ENSP00000364412:p.Glu114Lys		98054951	Q5U0Q6	Missense_Mutation	SNP	ENST00000375263.3	37	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	C	7.884	0.730951	0.15507	.	.	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.87571	-2.27;-2.27	4.31	3.41	0.39046	NAD(P)-binding domain (1);	0.505671	0.21335	N	0.076230	T	0.74512	0.3726	N	0.25031	0.7	0.28164	N	0.928844	B;P	0.47409	0.139;0.895	B;B	0.40982	0.072;0.345	T	0.66093	-0.6009	10	0.20519	T	0.43	-35.9645	6.5733	0.22551	0.0:0.7928:0.0:0.2072	.	114;114	Q5U0Q6;P37058	.;DHB3_HUMAN	K	114	ENSP00000364412:E114K;ENSP00000364411:E114K	ENSP00000364411:E114K	E	-	1	0	HSD17B3	98054951	0.994000	0.37717	0.726000	0.30738	0.036000	0.12997	1.301000	0.33447	1.401000	0.46761	0.655000	0.94253	GAG		0.363	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		T	99015130	C	T	99015130	3	4	55	1	0	0	0	0	1	0	0	0	7406	893	31	1	624	1	HSD17B3	9	99015130	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	65750700	99015130	42198301	42	7347										
AKAP2	11217	broad.mit.edu	37	chr9	112899307	112899307	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aacatctggagtcgcacaaaAagtacaaggagcgcaaagag	11	8	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr9:112899307A>C	ENST00000259318.7	+	2	997	c.790A>C	c.(790-792)Aag>Cag	p.K264Q	AKAP2_ENST00000555236.1_Missense_Mutation_p.K495Q|AKAP2_ENST00000374525.1_Missense_Mutation_p.K353Q|AKAP2_ENST00000434623.2_Missense_Mutation_p.K353Q|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.K495Q|AKAP2_ENST00000510514.5_Missense_Mutation_p.K495Q|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.K495Q	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	264								p.K353Q(1)|p.K495Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						GTCGCACAAAAAGTACAAGGA	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	9											32	35	34					9																	112899307		2203	4300	6503	111939128	SO:0001583	missense	445815			AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"A-kinase anchor proteins"	372	protein-coding gene	gene with protein product	"protein kinase A2"	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.790A>C	9.37:g.112899307A>C	ENSP00000259318:p.Lys264Gln		111939128	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	37	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.627178	0.66901	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.72	5.72	0.89469	.	0.047880	0.85682	D	0.000000	T	0.65502	0.2697	M	0.70275	2.135	0.49389	D	0.999783	P;D;P;D;D;P;P;P	0.57257	0.912;0.979;0.883;0.979;0.964;0.934;0.934;0.891	P;P;B;P;P;P;B;B	0.54140	0.535;0.743;0.36;0.743;0.558;0.559;0.44;0.356	T	0.70070	-0.4973	10	0.72032	D	0.01	-30.112	15.2015	0.73142	1.0:0.0:0.0:0.0	.	264;353;347;353;354;495;495;313	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	Q	495;495;495;495;353;353;313;264	ENSP00000363654:K495Q;ENSP00000305861:K495Q;ENSP00000451476:K495Q;ENSP00000421522:K495Q;ENSP00000404782:K353Q;ENSP00000363649:K353Q;ENSP00000419268:K313Q;ENSP00000259318:K264Q	ENSP00000259318:K264Q	K	+	1	0	PALM2-AKAP2;AKAP2	111939128	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	4.721000	0.61951	2.174000	0.68829	0.533000	0.62120	AAG		0.547	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		C	112899307	A	C	112899307	3	2	55	1	0	0	0	0	1	0	0	0	451	15	1	4	1063	4	AKAP2	9	112899307	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09	13884177	112899307	28314124	43	7348										
NTNG2	84628	broad.mit.edu	37	chr9	135073643	135073643	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cagccctaccagttctacgcCgaggactgcatggaggcctt	11	14	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr9:135073643C>T	ENST00000393229.3	+	3	1280	c.504C>T	c.(502-504)gcC>gcT	p.A168A	NTNG2_ENST00000360670.3_Silent_p.A168A|NTNG2_ENST00000372179.3_Silent_p.A168A|NTNG2_ENST00000393228.4_Silent_p.A168A	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	168	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)		p.A168A(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		AGTTCTACGCCGAGGACTGCA	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	9											43	34	37					9																	135073643		2202	4299	6501	134063464	SO:0001819	synonymous_variant	84628			AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"Netrins"	14288	protein-coding gene	gene with protein product	"Netrin-G2"		"netrin G1"	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.504C>T	9.37:g.135073643C>T			134063464	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																				0.667	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536		T	135073643	C	T	135073643	2	4	55	1	0	0	0	0	0	0	0	1	10736	639	23	1		1	NTNG2	9	135073643	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	22174336	135073643	6139788	44	7349										
DDX21	9188	broad.mit.edu	37	chr10	70725230	70725230	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agtggcttgtttttatggtgGaactccctatggaggtcaat	12	6	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr10:70725230G>T	ENST00000354185.4	+	5	982	c.884G>T	c.(883-885)gGa>gTa	p.G295V	RN7SL373P_ENST00000577512.1_RNA	NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	295	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.G295V(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TTTTATGGTGGAACTCCCTAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											90	84	86					10																	70725230		2203	4300	6503	70395236	SO:0001583	missense	9188			U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.884G>T	10.37:g.70725230G>T	ENSP00000346120:p.Gly295Val		70395236	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	37	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.036593	0.93630	.	.	ENSG00000165732	ENST00000354185	T	0.59224	0.28	5.87	5.87	0.94306	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85906	0.5806	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89718	0.3917	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	295	Q9NR30	DDX21_HUMAN	V	295	ENSP00000346120:G295V	ENSP00000346120:G295V	G	+	2	0	DDX21	70395236	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	GGA		0.423	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		T	70725230	G	T	70725230	3	4	55	1	0	0	0	0	1	0	0	0	4355	1174	41	2	902	2	DDX21	10	70725230	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		70725230	64809517	45	7350										
AGAP11	119385	broad.mit.edu	37	chr10	88769651	88769651	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tgcagtacggctgccccgacGagtgcgtgtagtatctgttt	13	10	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr10:88769651G>A	ENST00000444431.1	+	0	4251				RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										CTGCCCCGACGAGTGCGTGTA	0.502																																																0			10											9	10	10					10																	88769651		2180	4252	6432	88759631			119385					10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88769651G>A			88759631	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	37																																																																																					0.502	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		A	88769651	G	A	88769651	1	1	55	0	1	0	0	0	0	0	0	0	367	1059	37	1		1	AGAP11	10	88769651	RNA	SNP	G	TCGA-AG-3999-01A-01W-1073-09	18044421	88769651	46765096	46	7351										
SORCS3	22986	broad.mit.edu	37	chr10	106937890	106937890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tcggttcctctctttgttgaCggggctctggtggaggcagg	16	9	2	1	rs372850065		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr10:106937890C>T	ENST00000369701.3	+	14	2195	c.1968C>T	c.(1966-1968)gaC>gaT	p.D656D	SORCS3_ENST00000369699.4_Intron	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	656					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.D656D(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TCTTTGTTGACGGGGCTCTGG	0.473																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - coding silent(1)	large_intestine(1)	10						C		0,4406		0,0,2203	209	178	189		1968	-7.2	0.1	10		189	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SORCS3	NM_014978.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		656/1223	106937890	1,13005	2203	4300	6503	106927880	SO:0001819	synonymous_variant	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1968C>T	10.37:g.106937890C>T			106927880	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																				0.473	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106937890	C	T	106937890	2	4	55	1	0	0	0	0	0	0	0	1	14969	535	19	1		1	SORCS3	10	106937890	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	18168239	106937890	28596857	47	7352										
PNLIP	5406	broad.mit.edu	37	chr10	118306919	118306919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctccaaaagatgtcaacaccCgcttcctcctatatactaat	3	14	1	1	rs142749694		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr10:118306919C>T	ENST00000369221.2	+	3	188	c.160C>T	c.(160-162)Cgc>Tgc	p.R54C	PNLIP_ENST00000470562.1_3'UTR	NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	54					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)	p.R54C(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	TGTCAACACCCGCTTCCTCCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	77	75	75		160	5.4	1	10	dbSNP_134	75	0,8600		0,0,4300	no	missense	PNLIP	NM_000936.2	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	54/466	118306919	1,13005	2203	4300	6503	118296909	SO:0001583	missense	5406			BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.160C>T	10.37:g.118306919C>T	ENSP00000358223:p.Arg54Cys		118296909	Q5VSQ2	Missense_Mutation	SNP	ENST00000369221.2	37	CCDS7594.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116467	0.77323	2.27E-4	0.0	ENSG00000175535	ENST00000369221	D	0.91945	-2.94	5.36	5.36	0.76844	Lipase, N-terminal (1);	0.079288	0.53938	D	0.000049	D	0.97259	0.9104	H	0.96333	3.805	0.58432	D	0.999994	D	0.89917	1.0	D	0.83275	0.996	D	0.97868	1.0284	10	0.87932	D	0	.	14.225	0.65853	0.0:0.8496:0.1504:0.0	.	54	P16233	LIPP_HUMAN	C	54	ENSP00000358223:R54C	ENSP00000358223:R54C	R	+	1	0	PNLIP	118296909	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.998000	0.49465	2.789000	0.95967	0.591000	0.81541	CGC		0.468	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936		T	118306919	C	T	118306919	3	4	55	1	0	0	0	0	1	0	0	0	12180	652	23	1	166	1	PNLIP	10	118306919	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	11369029	118306919	17227828	48	7353										
MICALCL	84953	broad.mit.edu	37	chr11	12371470	12371470	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aaattaatgcgatatgagtcGgagctcctaatcatgtaagt	9	6	1	1	rs189290736	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr11:12371470G>A	ENST00000256186.2	+	7	2106	c.1815G>A	c.(1813-1815)tcG>tcA	p.S605S		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	605					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.S605S(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		GATATGAGTCGGAGCTCCTAA	0.473													G|||	8	0.00159744	0.0061	0	5008	,	,		19942	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						G		17,3849		0,17,1916	94	89	91		1815	-2.8	1	11		91	0,8254		0,0,4127	no	coding-synonymous	MICALCL	NM_032867.2		0,17,6043	AA,AG,GG		0.0,0.4397,0.1403		605/696	12371470	17,12103	1933	4127	6060	12328046	SO:0001819	synonymous_variant	84953			BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1815G>A	11.37:g.12371470G>A			12328046	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																				0.473	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		A	12371470	G	A	12371470	2	1	55	1	0	0	0	0	0	0	0	1	9602	1103	39	1		1	MICALCL	11	12371470	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09		12371470	122635046	49	7354										
OR5AS1	219447	broad.mit.edu	37	chr11	55798206	55798206	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gcactacaaatgtttttcttCgcttcttttgctgatgctga	7	9	2	2	rs142110904	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr11:55798206C>T	ENST00000313555.1	+	1	312	c.312C>T	c.(310-312)ttC>ttT	p.F104F		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F104F(1)		endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					TGTTTTTCTTCGCTTCTTTTG	0.458													C|||	3	0.000599042	0.0023	0	5008	,	,		19721	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		4,4398	8.1+/-20.4	0,4,2197	102	88	93		312	0.5	1	11	dbSNP_134	93	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous	OR5AS1	NM_001001921.1		0,7,6490	TT,TC,CC		0.0349,0.0909,0.0539		104/325	55798206	7,12987	2201	4296	6497	55554782	SO:0001819	synonymous_variant	219447			AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.312C>T	11.37:g.55798206C>T			55554782	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																				0.458	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		T	55798206	C	T	55798206	2	4	55	1	0	0	0	0	0	0	0	1	11177	883	31	1		1	OR5AS1	11	55798206	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	43426736	55798206	79208310	50	7355										
C2CD3	26005	broad.mit.edu	37	chr11	73820134	73820134	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aagtgaggttggaattccacCagtgctctatcattgggcca	11	9	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr11:73820134C>T	ENST00000334126.7	-	12	2133	c.1907G>A	c.(1906-1908)tGg>tAg	p.W636*	C2CD3_ENST00000313663.7_Nonsense_Mutation_p.W636*			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	636					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.W636*(2)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGAATTCCACCAGTGCTCTAT	0.438																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											123	119	120					11																	73820134		2200	4293	6493	73497782	SO:0001587	stop_gained	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1907G>A	11.37:g.73820134C>T	ENSP00000334379:p.Trp636*		73497782	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Nonsense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	41	8.988336	0.99027	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4669	18.9103	0.92481	0.0:1.0:0.0:0.0	.	.	.	.	X	636	.	ENSP00000323339:W636X	W	-	2	0	C2CD3	73497782	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.479000	0.66813	2.561000	0.86390	0.650000	0.86243	TGG		0.438	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		T	73820134	C	T	73820134	4	4	55	1	0	0	0	0	0	1	0	0	2160	595	21	3	4064	3	C2CD3	11	73820134	Nonsense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	18021928	73820134	61186382	51	7356										
TRPC6	7225	broad.mit.edu	37	chr11	101323775	101323775	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	taggtcttctgtattctgagAtttttcttcaaggagttcat	8	6	6	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr11:101323775A>G	ENST00000344327.3	-	13	3131	c.2707T>C	c.(2707-2709)Tct>Cct	p.S903P	TRPC6_ENST00000532133.1_Missense_Mutation_p.S825P|TRPC6_ENST00000360497.4_Missense_Mutation_p.S848P|TRPC6_ENST00000348423.4_Missense_Mutation_p.S787P	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	903					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.S903P(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		GTATTCTGAGATTTTTCTTCA	0.368																																					Colon(166;1315 1927 11094 12848 34731)											1	Substitution - Missense(1)	large_intestine(1)	11											167	164	165					11																	101323775		2203	4300	6503	100828985	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2707T>C	11.37:g.101323775A>G	ENSP00000340913:p.Ser903Pro		100828985	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.855446	0.51376	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	5.65	3.28	0.37604	.	0.213406	0.49916	D	0.000127	T	0.78349	0.4269	M	0.62723	1.935	0.42471	D	0.992826	P;P	0.45634	0.683;0.863	B;B	0.41374	0.23;0.355	T	0.74973	-0.3481	10	0.56958	D	0.05	-7.3777	6.8796	0.24166	0.6898:0.1175:0.0:0.1927	.	787;903	Q9Y210-2;Q9Y210	.;TRPC6_HUMAN	P	903;825;787;848	ENSP00000340913:S903P;ENSP00000435574:S825P;ENSP00000343672:S787P;ENSP00000353687:S848P	ENSP00000340913:S903P	S	-	1	0	TRPC6	100828985	1.000000	0.71417	0.999000	0.59377	0.851000	0.48451	3.336000	0.52113	0.401000	0.25424	0.529000	0.55759	TCT		0.368	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		G	101323775	A	G	101323775	3	3	55	1	0	0	0	0	1	0	0	0	16623	333	12	4	92	4	TRPC6	11	101323775	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09	27503641	101323775	33682741	52	7357										
BCL9L	283149	broad.mit.edu	37	chr11	118771331	118771331	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctgcgcaattgactcaccctGttccatgttgctcagggtgg	11	12	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr11:118771331G>A	ENST00000334801.3	-	6	4085	c.3121C>T	c.(3121-3123)Cag>Tag	p.Q1041*	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1041	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.Q1041*(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GACTCACCCTGTTCCATGTTG	0.622																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											79	81	80					11																	118771331		2200	4295	6495	118276541	SO:0001587	stop_gained	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.3121C>T	11.37:g.118771331G>A	ENSP00000335320:p.Gln1041*		118276541	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Nonsense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	48	14.592926	0.99802	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	.	.	.	4.96	4.05	0.47172	.	0.000000	0.45361	D	0.000367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	13.0661	0.59034	0.0768:0.0:0.9232:0.0	.	.	.	.	X	1041;1004;334;1041;1041	.	ENSP00000335320:Q1041X	Q	-	1	0	BCL9L	118276541	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	4.890000	0.63178	1.302000	0.44855	0.655000	0.94253	CAG		0.622	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118771331	G	A	118771331	4	1	55	1	0	0	0	0	0	1	0	0	1383	1386	48	3	1390	3	BCL9L	11	118771331	Nonsense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	17447556	118771331	16235185	53	7358										
KRAS	3845	broad.mit.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr12:25398285C>T	ENST00000256078.4	-	2	97	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	KRAS_ENST00000556131.1_Missense_Mutation_p.G12S|KRAS_ENST00000311936.3_Missense_Mutation_p.G12S|KRAS_ENST00000557334.1_Missense_Mutation_p.G12S	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>A	12.37:g.25398285C>T	ENSP00000256078:p.Gly12Ser		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441396	0.96187	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	L	0.28344	0.845	0.80722	D	1	P;P	0.39665	0.557;0.682	P;P	0.50570	0.525;0.644	T	0.80254	-0.1459	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	S	12	ENSP00000308495:G12S;ENSP00000452512:G12S;ENSP00000256078:G12S;ENSP00000451856:G12S	ENSP00000256078:G12S	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398285	C	T	25398285	3	4	55	1	0	0	0	0	1	0	0	0	8459	594	21	3	672	3	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		25398285	108453610	54	7359										
TMTC1	83857	broad.mit.edu	37	chr12	29757205	29757205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gaacaccaggaacaacaagcCgactaaaacctccttgtgct	7	13	0	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr12:29757205C>T	ENST00000539277.1	-	7	1214	c.1156G>A	c.(1156-1158)Ggc>Agc	p.G386S	TMTC1_ENST00000256062.5_Missense_Mutation_p.G278S|TMTC1_ENST00000551659.1_Missense_Mutation_p.G448S|TMTC1_ENST00000552618.1_Missense_Mutation_p.G448S|TMTC1_ENST00000381224.2_Missense_Mutation_p.G340S|TMTC1_ENST00000319685.8_5'UTR	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	386						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.G278S(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AACAACAAGCCGACTAAAACC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											115	104	108					12																	29757205		2203	4300	6503	29648472	SO:0001583	missense	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1156G>A	12.37:g.29757205C>T	ENSP00000442046:p.Gly386Ser		29648472	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120988	0.77436	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	L	0.37697	1.125	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	P;D;D	0.74348	0.882;0.983;0.975	T	0.55679	-0.8103	9	.	.	.	-19.3147	16.74	0.85456	0.0:1.0:0.0:0.0	.	340;386;448	Q8IUR5-3;Q8IUR5;F8VTQ9	.;TMTC1_HUMAN;.	S	149;278;448;448;386;340	ENSP00000256062:G278S;ENSP00000448112:G448S;ENSP00000449043:G448S;ENSP00000442046:G386S;ENSP00000370622:G340S	.	G	-	1	0	TMTC1	29648472	1.000000	0.71417	0.997000	0.53966	0.889000	0.51656	7.185000	0.77714	2.346000	0.79739	0.655000	0.94253	GGC		0.468	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		T	29757205	C	T	29757205	3	4	55	1	0	0	0	0	1	0	0	0	16299	652	23	1	1540	1	TMTC1	12	29757205	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	4358920	29757205	104094690	55	7360										
ASCL4	121549	broad.mit.edu	37	chr12	108169040	108169040	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cggctggccttgccatactcGctgcgcaccgcgcccctggg	13	18	0	0	rs577263861		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr12:108169040G>A	ENST00000342331.4	+	1	879	c.48G>A	c.(46-48)tcG>tcA	p.S16S		NM_203436.2	NP_982260.2	Q6XD76	ASCL4_HUMAN	achaete-scute family bHLH transcription factor 4	15					regulation of transcription from RNA polymerase II promoter (GO:0006357)|skin development (GO:0043588)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S15S(1)		breast(2)|central_nervous_system(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	13						TGCCATACTCGCTGCGCACCG	0.642																																					GBM(170;776 3695 11650)											1	Substitution - coding silent(1)	large_intestine(1)	12											56	63	61					12																	108169040		2203	4299	6502	106693170	SO:0001819	synonymous_variant	121549			AY238895	CCDS31894.2	12q24.11	2013-10-17	2013-10-17		ENSG00000187855	ENSG00000187855		"Basic helix-loop-helix proteins"	24311	protein-coding gene	gene with protein product		609155	"achaete-scute complex-like 4 (Drosophila)", "achaete-scute complex homolog 4 (Drosophila)"				Standard	NM_203436		Approved	HASH4, bHLHa44	uc001tmr.3	Q6XD76	OTTHUMG00000156964	ENST00000342331.4:c.48G>A	12.37:g.108169040G>A			106693170	Q7RTS2	Silent	SNP	ENST00000342331.4	37	CCDS31894.2																																																																																				0.642	ASCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346845.1	NM_203436		A	108169040	G	A	108169040	2	1	55	1	0	0	0	0	0	0	0	1	1037	1074	38	1		1	ASCL4	12	108169040	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	78411835	108169040	25682855	56	7361										
TPCN1	53373	broad.mit.edu	37	chr12	113728005	113728005	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aggaccgtggtggaggaaggCtactattatctcaataattt	11	6	1	0	rs146118100	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr12:113728005C>T	ENST00000335509.6	+	22	2183	c.1869C>T	c.(1867-1869)ggC>ggT	p.G623G	TPCN1_ENST00000541517.1_Silent_p.G695G|TPCN1_ENST00000550785.1_Silent_p.G695G|TPCN1_ENST00000392569.4_Silent_p.G555G	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	623					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)	p.G623G(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TGGAGGAAGGCTACTATTATC	0.557													C|||	7	0.00139776	0	0	5008	,	,		20725	0		0.003	False		,,,				2504	0.0041															1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	4,4402	9.9+/-24.2	0,4,2199	126	95	105		2085,1869	-1.6	0.9	12	dbSNP_134	105	33,8567	21.6+/-65.8	0,33,4267	no	coding-synonymous,coding-synonymous	TPCN1	NM_001143819.1,NM_017901.4	,	0,37,6466	TT,TC,CC		0.3837,0.0908,0.2845	,	695/889,623/817	113728005	37,12969	2203	4300	6503	112212388	SO:0001819	synonymous_variant	53373			AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.1869C>T	12.37:g.113728005C>T			112212388	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																				0.557	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		T	113728005	C	T	113728005	2	4	55	1	0	0	0	0	0	0	0	1	16435	784	28	3		3	TPCN1	12	113728005	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	5558965	113728005	20123890	57	7362										
NPAS3	64067	broad.mit.edu	37	chr14	34269530	34269530	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	actacccgcccaaccgggagAtctccaggaacgagtccccc	9	18	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr14:34269530A>C	ENST00000356141.4	+	12	2017	c.2017A>C	c.(2017-2019)Atc>Ctc	p.I673L	NPAS3_ENST00000551492.1_Missense_Mutation_p.I678L|NPAS3_ENST00000346562.2_Missense_Mutation_p.I641L|NPAS3_ENST00000548645.1_Missense_Mutation_p.I643L|NPAS3_ENST00000357798.5_Missense_Mutation_p.I660L			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	673					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.I660L(1)|p.I641L(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CAACCGGGAGATCTCCAGGAA	0.637																																																2	Substitution - Missense(2)	large_intestine(2)	14											71	74	73					14																	34269530		2203	4300	6503	33339281	SO:0001583	missense	64067			AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2017A>C	14.37:g.34269530A>C	ENSP00000348460:p.Ile673Leu		33339281	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.942620	0.73672	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.70399	-0.48;2.96;2.98;2.97;2.96;2.83	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.56352	0.1979	L	0.27053	0.805	0.80722	D	1	P;B;P;P	0.37101	0.582;0.447;0.582;0.582	B;B;B;B	0.31686	0.134;0.063;0.134;0.134	T	0.58819	-0.7569	10	0.37606	T	0.19	.	15.0046	0.71501	1.0:0.0:0.0:0.0	.	643;673;641;660	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	L	647;678;641;643;673;660	ENSP00000448373:I647L;ENSP00000450392:I678L;ENSP00000319610:I641L;ENSP00000448916:I643L;ENSP00000348460:I673L;ENSP00000350446:I660L	ENSP00000319610:I641L	I	+	1	0	NPAS3	33339281	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.059000	0.76684	1.925000	0.55765	0.454000	0.30748	ATC		0.637	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			C	34269530	A	C	34269530	3	2	55	1	0	0	0	0	1	0	0	0	10595	333	12	4	2118	4	NPAS3	14	34269530	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09		34269530	73080010	58	7363										
RALGAPA1	253959	broad.mit.edu	37	chr14	36197692	36197692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tgcaggttcaagaagaaataTatttgatgagtttataataa	8	2	1	4			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr14:36197692T>C	ENST00000389698.3	-	13	2002	c.1612A>G	c.(1612-1614)Ata>Gta	p.I538V	RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.I538V|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.I538V|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.I538V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	538					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.I538V(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGAAGAAATATATTTGATGAG	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	14											29	31	30					14																	36197692		2196	4271	6467	35267443	SO:0001583	missense	253959			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.1612A>G	14.37:g.36197692T>C	ENSP00000374348:p.Ile538Val		35267443	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	T	6.009	0.370152	0.11352	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.24	5.24	0.73138	.	0.049575	0.85682	D	0.000000	T	0.49270	0.1547	N	0.11364	0.135	0.42075	D	0.991228	B;B;B;B;B	0.14805	0.004;0.002;0.011;0.001;0.002	B;B;B;B;B	0.20184	0.015;0.004;0.028;0.012;0.004	T	0.49495	-0.8934	10	0.02654	T	1	-18.7682	15.4304	0.75092	0.0:0.0:0.0:1.0	.	538;538;538;538;538	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	V	538	ENSP00000374348:I538V;ENSP00000302647:I538V;ENSP00000258840:I538V;ENSP00000371803:I538V;ENSP00000451877:I538V	ENSP00000258840:I538V	I	-	1	0	RALGAPA1	35267443	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.408000	0.59761	2.086000	0.62901	0.460000	0.39030	ATA		0.299	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36197692	T	C	36197692	3	2	55	1	0	0	0	0	1	0	0	0	13050	1406	49	4	4763	4	RALGAPA1	14	36197692	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	1928162	36197692	71151848	59	7364										
SDCCAG1	9147	broad.mit.edu	37	chr14	50280749	50280749	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctagtagctccatgaagatcAgcatgtacataaatgtctcc	7	10	2	2	rs146062067		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr14:50280749A>C	ENST00000298310.5	-	18	2150	c.1701T>G	c.(1699-1701)gcT>gcG	p.A567A	NEMF_ENST00000546046.1_Intron|NEMF_ENST00000545773.1_Silent_p.A525A|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	567					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.A567A(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CATGAAGATCAGCATGTACAT	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	14											63	64	64					14																	50280749		2203	4299	6502	49350499	SO:0001819	synonymous_variant	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1701T>G	14.37:g.50280749A>C			49350499	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	ENST00000298310.5	37	CCDS9694.1																																																																																				0.289	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		C	50280749	A	C	50280749	2	2	55	1	0	0	0	0	0	0	0	1	13994	175	7	4		4	SDCCAG1	14	50280749	Silent	SNP	A	TCGA-AG-3999-01A-01W-1073-09	14083057	50280749	57068791	60	7365										
AHNAK2	113146	broad.mit.edu	37	chr14	105410178	105410178	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggcacgtggccctccaggagTttcatgtccacctggcgagc	13	14	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr14:105410178T>G	ENST00000333244.5	-	7	11729	c.11610A>C	c.(11608-11610)aaA>aaC	p.K3870N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3870						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.K3870N(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CCTCCAGGAGTTTCATGTCCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14											130	138	135					14																	105410178		1965	4151	6116	104481223	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.11610A>C	14.37:g.105410178T>G	ENSP00000353114:p.Lys3870Asn		104481223	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	13.02	2.113670	0.37339	.	.	ENSG00000185567	ENST00000333244	T	0.01599	4.74	3.67	-2.53	0.06326	.	.	.	.	.	T	0.02610	0.0079	M	0.66378	2.025	0.09310	N	1	P	0.47762	0.9	P	0.47645	0.553	T	0.32587	-0.9901	9	0.25106	T	0.35	.	1.0517	0.01581	0.1601:0.227:0.3018:0.3111	.	3870	Q8IVF2	AHNK2_HUMAN	N	3870	ENSP00000353114:K3870N	ENSP00000353114:K3870N	K	-	3	2	AHNAK2	104481223	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.088000	0.00081	-0.467000	0.06932	-0.366000	0.07423	AAA		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105410178	T	G	105410178	3	3	55	1	0	0	0	0	1	0	0	0	415	1722	60	4	5781	4	AHNAK2	14	105410178	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	55129429	105410178	1939362	61	7366										
DISP2	85455	broad.mit.edu	37	chr15	40662376	40662376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tgtatgacccatcattgcccGcttcccatcacagcagcttg	7	15	2	1	rs146679685		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr15:40662376G>A	ENST00000267889.3	+	8	4150	c.4063G>A	c.(4063-4065)Gct>Act	p.A1355T	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	1355					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.A1355T(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		ATCATTGCCCGCTTCCCATCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	85	89	88		4063	-3.4	0.1	15	dbSNP_134	88	0,8600		0,0,4300	no	missense	DISP2	NM_033510.1	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1355/1402	40662376	1,13005	2203	4300	6503	38449668	SO:0001583	missense	85455			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.4063G>A	15.37:g.40662376G>A	ENSP00000267889:p.Ala1355Thr		38449668	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	G	4.202	0.036197	0.08148	2.27E-4	0.0	ENSG00000140323	ENST00000267889	T	0.13196	2.61	5.0	-3.39	0.04868	.	1.044700	0.07477	N	0.903145	T	0.06234	0.0161	N	0.12182	0.205	0.09310	N	1	B	0.16396	0.017	B	0.08055	0.003	T	0.42050	-0.9474	10	0.22706	T	0.39	-0.3538	5.9126	0.19037	0.4994:0.1322:0.3684:0.0	.	1355	A7MBM2	DISP2_HUMAN	T	1355	ENSP00000267889:A1355T	ENSP00000267889:A1355T	A	+	1	0	DISP2	38449668	0.593000	0.26840	0.055000	0.19348	0.551000	0.35334	0.818000	0.27295	-0.872000	0.04037	-1.193000	0.01689	GCT		0.632	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		A	40662376	G	A	40662376	3	1	55	1	0	0	0	0	1	0	0	0	4551	1087	38	1	4093	1	DISP2	15	40662376	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		40662376	61869016	62	7367										
MGA	23269	broad.mit.edu	37	chr15	42052633	42052633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cactgccaatgagcggcggcGgcgtggtgaaatgagggatc	17	9	0	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr15:42052633G>A	ENST00000570161.1	+	19	7304	c.7304G>A	c.(7303-7305)cGg>cAg	p.R2435Q	MGA_ENST00000389936.4_Missense_Mutation_p.R2396Q|MGA_ENST00000545763.1_Missense_Mutation_p.R2226Q|MGA_ENST00000566586.1_Missense_Mutation_p.R2226Q|MGA_ENST00000219905.7_Missense_Mutation_p.R2435Q			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R2484Q(4)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GAGCGGCGGCGGCGTGGTGAA	0.438																																																4	Substitution - Missense(4)	ovary(2)|large_intestine(1)|central_nervous_system(1)	15											109	111	110					15																	42052633		1900	4109	6009	39839925	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7304G>A	15.37:g.42052633G>A	ENSP00000457035:p.Arg2435Gln		39839925	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	34	5.296335	0.95574	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.99722	-6.53;-6.53;-6.53	5.53	5.53	0.82687	.	0.000000	0.49305	D	0.000156	D	0.99711	0.9889	M	0.83223	2.63	0.31601	N	0.652706	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.997;0.978	D	0.97541	1.0086	10	0.87932	D	0	.	19.4485	0.94857	0.0:0.0:1.0:0.0	.	1051;2226;2435	B4DVS1;F5H7K2;E7ENI0	.;.;.	Q	2435;2396;2226	ENSP00000219905:R2435Q;ENSP00000374586:R2396Q;ENSP00000442467:R2226Q	ENSP00000219905:R2435Q	R	+	2	0	MGA	39839925	0.999000	0.42202	0.998000	0.56505	0.992000	0.81027	7.159000	0.77483	2.583000	0.87209	0.655000	0.94253	CGG		0.438	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42052633	G	A	42052633	3	1	55	1	0	0	0	0	1	0	0	0	9570	1116	39	1	7378	1	MGA	15	42052633	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	1390257	42052633	60478759	63	7368										
ISLR	3671	broad.mit.edu	37	chr15	74467645	74467645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ccgcagcctccgtgctctgcGctcgctgcaactcaaccaca	8	19	2	0	rs149796219		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr15:74467645G>A	ENST00000249842.3	+	2	803	c.446G>A	c.(445-447)cGc>cAc	p.R149H	ISLR_ENST00000395118.1_Missense_Mutation_p.R149H|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	149					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)		p.R149H(1)		central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						CGTGCTCTGCGCTCGCTGCAA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	73	72	72		446,446	3.1	0.9	15	dbSNP_134	72	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	ISLR	NM_005545.3,NM_201526.1	29,29	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	149/429,149/429	74467645	1,12989	2198	4297	6495	72254698	SO:0001583	missense	3671			AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.446G>A	15.37:g.74467645G>A	ENSP00000249842:p.Arg149His		72254698		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885881	0.51908	0.0	1.16E-4	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.58506	0.33;0.33	4.05	3.11	0.35812	.	0.125517	0.28431	U	0.015369	T	0.61999	0.2392	L	0.39898	1.24	0.43579	D	0.995915	D	0.89917	1.0	D	0.67231	0.95	T	0.60342	-0.7282	10	0.56958	D	0.05	.	7.4589	0.27283	0.0911:0.1698:0.739:0.0	.	149	O14498	ISLR_HUMAN	H	149	ENSP00000249842:R149H;ENSP00000378550:R149H	ENSP00000249842:R149H	R	+	2	0	ISLR	72254698	1.000000	0.71417	0.880000	0.34516	0.312000	0.27988	4.800000	0.62524	0.672000	0.31204	0.313000	0.20887	CGC		0.622	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		A	74467645	G	A	74467645	3	1	55	1	0	0	0	0	1	0	0	0	7879	1087	38	1	448	1	ISLR	15	74467645	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	32415012	74467645	28063747	64	7369										
MYLK3	91807	broad.mit.edu	37	chr16	46755087	46755087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ttgatgtcctgtctgattgaCgcacaatatgttctccggct	9	10	2	3			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr16:46755087C>T	ENST00000394809.4	-	9	2048	c.1933G>A	c.(1933-1935)Gtc>Atc	p.V645I	MYLK3_ENST00000536476.1_Missense_Mutation_p.V304I	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	645	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.V724I(1)|p.V645I(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GTCTGATTGACGCACAATATG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	16											125	124	125					16																	46755087		2203	4300	6503	45312588	SO:0001583	missense	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1933G>A	16.37:g.46755087C>T	ENSP00000378288:p.Val645Ile		45312588	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699938	0.88924	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.39406	1.08;1.08	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.32518	N	0.005993	T	0.43211	0.1237	L	0.31752	0.955	0.48830	D	0.999719	P	0.39282	0.666	P	0.44623	0.455	T	0.39941	-0.9589	10	0.62326	D	0.03	.	19.4403	0.94817	0.0:1.0:0.0:0.0	.	645	Q32MK0	MYLK3_HUMAN	I	645;304	ENSP00000378288:V645I;ENSP00000439297:V304I	ENSP00000378288:V645I	V	-	1	0	MYLK3	45312588	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.891000	0.56227	2.666000	0.90696	0.557000	0.71058	GTC		0.448	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46755087	C	T	46755087	3	4	55	1	0	0	0	0	1	0	0	0	10088	536	19	1	546	1	MYLK3	16	46755087	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		46755087	43599666	65	7370										
KCNG4	93107	broad.mit.edu	37	chr16	84270675	84270675	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tcctcctggaaggacagcgcGcacatctcctgcagaagcac	10	15	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr16:84270675G>A	ENST00000308251.4	-	2	485	c.417C>T	c.(415-417)tgC>tgT	p.C139C	KCNG4_ENST00000568181.1_Silent_p.C139C	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	139					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.C139C(2)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						AGGACAGCGCGCACATCTCCT	0.652																																																2	Substitution - coding silent(2)	large_intestine(2)	16											47	49	48					16																	84270675		2200	4300	6500	82828176	SO:0001819	synonymous_variant	93107			AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.417C>T	16.37:g.84270675G>A			82828176	Q96H24	Silent	SNP	ENST00000308251.4	37	CCDS10945.1																																																																																				0.652	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347		A	84270675	G	A	84270675	2	1	55	1	0	0	0	0	0	0	0	1	8051	1079	38	1		1	KCNG4	16	84270675	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	37515588	84270675	6084078	66	7371										
SAT2	112483	broad.mit.edu	37	chr17	7529893	7529893	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cctctggttccagtccaggaCggccaggcggaattgggagc	15	12	1	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr17:7529893C>T	ENST00000269298.5	-	6	604	c.385G>A	c.(385-387)Gtc>Atc	p.V129I	SHBG_ENST00000576478.1_Intron|SHBG_ENST00000572262.1_Intron|SAT2_ENST00000573566.1_Missense_Mutation_p.V95I|SAT2_ENST00000380466.2_5'UTR|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000576728.1_Intron	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	129	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.V129I(1)|p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	CAGTCCAGGACGGCCAGGCGG	0.532																																																2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	17											72	71	71					17																	7529893		2203	4300	6503	7470618	SO:0001583	missense	112483			AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"diamine N-acetyltransferase 2"	611463	"spermidine/spermine N1-acetyltransferase 2"			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.385G>A	17.37:g.7529893C>T	ENSP00000269298:p.Val129Ile		7470618		Missense_Mutation	SNP	ENST00000269298.5	37	CCDS11116.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728816	0.89390	.	.	ENSG00000141504	ENST00000380466;ENST00000269298	T	0.31247	1.5	5.1	4.14	0.48551	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	M	0.84433	2.695	0.80722	D	1	D	0.60160	0.987	P	0.50934	0.654	T	0.53683	-0.8404	10	0.87932	D	0	-10.58	9.3141	0.37924	0.0:0.9033:0.0:0.0967	.	129	Q96F10	SAT2_HUMAN	I	208;129	ENSP00000269298:V129I	ENSP00000269298:V129I	V	-	1	0	SAT2	7470618	1.000000	0.71417	0.637000	0.29366	0.888000	0.51559	5.520000	0.67080	1.381000	0.46364	0.655000	0.94253	GTC		0.532	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491		T	7529893	C	T	7529893	3	4	55	1	0	0	0	0	1	0	0	0	13889	536	19	1	131	1	SAT2	17	7529893	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		7529893	73665317	67	7372										
TP53	7157	broad.mit.edu	37	chr17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gggcaccaccacactatgtcGaaaagtgtttctgtcatcca	8	12	2	0	rs397516436		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	large_intestine(89)|breast(45)|lung(37)|upper_aerodigestive_tract(30)|central_nervous_system(18)|skin(16)|oesophagus(15)|stomach(14)|ovary(14)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(9)|biliary_tract(8)|liver(8)|soft_tissue(5)|endometrium(5)|bone(4)|prostate(3)|thyroid(1)|pancreas(1)|autonomic_ganglia(1)	17	GRCh37	CM951226	TP53	M							132	118	123					17																	7578212		2203	4300	6503	7518937	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.637C>T	17.37:g.7578212G>A	ENSP00000269305:p.Arg213*		7518937	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578212	G	A	7578212	4	1	55	1	0	0	0	0	0	1	0	0	16421	1066	37	1	657	1	TP53	17	7578212	Nonsense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	48319	7578212	73616998	68	7373										
KIAA0100	9703	broad.mit.edu	37	chr17	26964917	26964917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	caagtccaccttccacagtaAtgacacagattccccaaatg	5	14	0	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr17:26964917A>T	ENST00000528896.2	-	14	1782	c.1708T>A	c.(1708-1710)Tta>Ata	p.L570I	KIAA0100_ENST00000544884.1_Missense_Mutation_p.L427I|KIAA0100_ENST00000389003.3_Missense_Mutation_p.L427I|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	570						extracellular region (GO:0005576)		p.L570I(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TTCCACAGTAATGACACAGAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											118	101	107					17																	26964917		2203	4300	6503	23989044	SO:0001583	missense	9703			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.1708T>A	17.37:g.26964917A>T	ENSP00000436773:p.Leu570Ile		23989044	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.052192	0.55218	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.25749	1.79;1.78	5.5	3.18	0.36537	FMP27, N-terminal (1);	0.071870	0.64402	D	0.000019	T	0.20047	0.0482	L	0.29908	0.895	0.29186	N	0.876182	D	0.53312	0.959	P	0.50490	0.642	T	0.05517	-1.0880	10	0.18710	T	0.47	.	4.4899	0.11808	0.6588:0.0:0.3412:0.0	.	570	Q14667	K0100_HUMAN	I	570;570;570;427	ENSP00000436773:L570I;ENSP00000446443:L427I	ENSP00000005905:L570I	L	-	1	2	KIAA0100	23989044	0.998000	0.40836	0.927000	0.36925	0.826000	0.46750	3.965000	0.56788	0.917000	0.36895	0.460000	0.39030	TTA		0.473	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		T	26964917	A	T	26964917	3	4	55	1	0	0	0	0	1	0	0	0	8175	98	4	5	5103	5	KIAA0100	17	26964917	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09	19386705	26964917	54230293	69	7374										
FOXK2	3607	broad.mit.edu	37	chr17	80545006	80545006	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gccagccggatcattcagacGgcacagaccaccccggtcca	10	17	2	2	rs148594749	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr17:80545006G>A	ENST00000335255.5	+	8	1818	c.1644G>A	c.(1642-1644)acG>acA	p.T548T	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	548					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T548T(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			TCATTCAGACGGCACAGACCA	0.502													G|||	6	0.00119808	0	0.0014	5008	,	,		17906	0		0.005	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17						G		0,4406		0,0,2203	94	82	86		1644	-3.2	0	17	dbSNP_134	86	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	FOXK2	NM_004514.3		0,15,6488	AA,AG,GG		0.1744,0.0,0.1153		548/661	80545006	15,12991	2203	4300	6503	78138295	SO:0001819	synonymous_variant	3607			U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1644G>A	17.37:g.80545006G>A			78138295	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																				0.502	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		A	80545006	G	A	80545006	2	1	55	1	0	0	0	0	0	0	0	1	6034	1103	39	1		1	FOXK2	17	80545006	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	53580089	80545006	650204	70	7375										
FAM38B	63895	broad.mit.edu	37	chr18	10696470	10696471	+	Missense_Mutation	DNP	CG	CG	AA													0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gagtacatacacgtcagtcaCggcgctatactccgggtgga					rs551918181|rs371890622		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr18:10696470_10696471CG>AA	ENST00000503781.3	-	42	6554_6555	c.6555_6556CG>TT	c.(6553-6558)gcCGtg>gcTTtg	p.V2186L	PIEZO2_ENST00000285141.4_Missense_Mutation_p.V41L|PIEZO2_ENST00000302079.6_Missense_Mutation_p.V2186L|PIEZO2_ENST00000538948.1_Missense_Mutation_p.V143L|PIEZO2_ENST00000580640.1_Missense_Mutation_p.V2211L	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2186					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)	p.A40>?(1)|p.A2185>?(1)									ACGTCAGTCACGGCGCTATACT	0.525																																																2	Complex(2)	large_intestine(2)	18																																								10686471	SO:0001583	missense	63895			AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6555_6556delinsAA	18.37:g.10696470_10696471delinsAA	ENSP00000421377:p.Val2186Leu		10686470	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Missense_Mutation	DNP	ENST00000503781.3	37																																																																																					0.525	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		AA	10696471	CG	AA	10696470	3	1	55	1	0	0	0	0	1	0	0	0	5574	536	19	2	1746	2	FAM38B	18	10696470	Missense_Mutation	DNP	CG	TCGA-AG-3999-01A-01W-1073-09		10696470	67380778	71	7376										
TTR	7276	broad.mit.edu	37	chr18	29178562	29178562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agccaacgactccggcccccGccgctacaccattgccgccc	8	22	0	0	rs148538950		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr18:29178562G>A	ENST00000237014.3	+	4	545	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	123					extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)	p.R123H(1)		cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TCCGGCCCCCGCCGCTACACC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	18						G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	68	62	64		368	6	0.2	18	dbSNP_134	64	0,8600		0,0,4300	no	missense	TTR	NM_000371.3	29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	possibly-damaging	123/148	29178562	3,13003	2203	4300	6503	27432560	SO:0001583	missense	7276			M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"prealbumin, amyloidosis type I", "carpal tunnel syndrome 1"	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.368G>A	18.37:g.29178562G>A	ENSP00000237014:p.Arg123His		27432560	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	37	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732870	0.48939	6.81E-4	0.0	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.96073	-3.9	5.98	5.98	0.97165	Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.000000	0.85682	D	0.000000	D	0.95604	0.8571	M	0.91717	3.235	0.80722	D	1	P	0.49185	0.92	B	0.32533	0.147	D	0.96269	0.9197	10	0.66056	D	0.02	-19.9086	20.0317	0.97542	0.0:0.0:1.0:0.0	.	123	P02766	TTHY_HUMAN	H	123;160;123	ENSP00000237014:R123H	ENSP00000237014:R123H	R	+	2	0	TTR	27432560	1.000000	0.71417	0.242000	0.24170	0.032000	0.12392	7.630000	0.83225	2.837000	0.97791	0.591000	0.81541	CGC		0.562	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371		A	29178562	G	A	29178562	3	1	55	1	0	0	0	0	1	0	0	0	16778	1087	38	1	382	1	TTR	18	29178562	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	18482092	29178562	48898686	72	7377										
NOL4	8715	broad.mit.edu	37	chr18	31709948	31709948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	atcttcaaccacagctacccGtcgtaaagatagcttctcat	5	13	3	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr18:31709948G>A	ENST00000261592.5	-	2	598	c.301C>T	c.(301-303)Cgg>Tgg	p.R101W	NOL4_ENST00000269185.4_De_novo_Start_OutOfFrame|NOL4_ENST00000535475.1_De_novo_Start_InFrame|NOL4_ENST00000589544.1_Missense_Mutation_p.R101W|NOL4_ENST00000538587.1_Missense_Mutation_p.R27W	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	101						nucleolus (GO:0005730)	RNA binding (GO:0003723)	p.R101W(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						ACAGCTACCCGTCGTAAAGAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	18											94	85	88					18																	31709948		2203	4300	6503	29963946	SO:0001583	missense	8715			AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.301C>T	18.37:g.31709948G>A	ENSP00000261592:p.Arg101Trp		29963946	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	37	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820490	0.71028	.	.	ENSG00000101746	ENST00000261592;ENST00000538587	D	0.84223	-1.82	5.61	3.74	0.42951	.	.	.	.	.	D	0.89674	0.6783	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.992;0.988;0.994	D	0.89507	0.3768	9	0.87932	D	0	-5.9031	13.0677	0.59043	0.0:0.0:0.5372:0.4628	.	27;101;101	B4DSQ0;O94818;O94818-2	.;NOL4_HUMAN;.	W	101;27	ENSP00000261592:R101W	ENSP00000261592:R101W	R	-	1	2	NOL4	29963946	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.109000	0.57824	0.626000	0.30322	0.585000	0.79938	CGG		0.388	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		A	31709948	G	A	31709948	3	1	55	1	0	0	0	0	1	0	0	0	10555	1144	40	1	1655	1	NOL4	18	31709948	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	2531386	31709948	46367300	73	7378										
C19orf29	58509	broad.mit.edu	37	chr19	3612375	3612375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ccatgccctccttggcccgcCggaagaagatgtcctcggcg	12	16	0	2	rs371228649		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:3612375C>T	ENST00000429344.2	-	10	1875	c.1823G>A	c.(1822-1824)cGg>cAg	p.R608Q	CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000221899.3_Missense_Mutation_p.R540Q|CACTIN_ENST00000248420.5_Missense_Mutation_p.R608Q	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	608					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R608Q(1)|p.R540Q(1)									CTTGGCCCGCCGGAAGAAGAT	0.711																																																2	Substitution - Missense(2)	large_intestine(2)	19						C	GLN/ARG,GLN/ARG	1,4291		0,1,2145	19	22	21		1823,1823	3.9	1	19		21	0,8496		0,0,4248	no	missense,missense	C19orf29	NM_001080543.1,NM_021231.1	43,43	0,1,6393	TT,TC,CC		0.0,0.0233,0.0078	possibly-damaging,possibly-damaging	608/759,608/759	3612375	1,12787	2146	4248	6394	3563375	SO:0001583	missense	58509			BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.1823G>A	19.37:g.3612375C>T	ENSP00000415078:p.Arg608Gln		3563375	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	37	CCDS45920.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.10|18.10	3.548869|3.548869	0.65311|0.65311	2.33E-4|2.33E-4	0.0|0.0	ENSG00000226800|ENSG00000105298	ENST00000447295|ENST00000429344;ENST00000248420;ENST00000221899	.|.	.|.	.|.	3.88|3.88	3.88|3.88	0.44766|0.44766	.|.	.|0.125578	.|0.56097	.|D	.|0.000039	T|T	0.53562|0.53562	0.1804|0.1804	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|P;P	.|0.50819	.|0.939;0.745	.|B;B	.|0.41440	.|0.357;0.07	T|T	0.59075|0.59075	-0.7522|-0.7522	5|9	.|0.37606	.|T	.|0.19	.|.	14.9374|14.9374	0.70967|0.70967	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|608;608	.|Q8WUQ7-2;Q8WUQ7	.|.;CS029_HUMAN	L|Q	216|608;608;540	.|.	.|ENSP00000221899:R540Q	P|R	+|-	2|2	0|0	C19orf29OS|C19orf29	3563375|3563375	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.543000|0.543000	0.35085|0.35085	7.211000|7.211000	0.77933|0.77933	2.166000|2.166000	0.68216|0.68216	0.549000|0.549000	0.68633|0.68633	CCG|CGG		0.711	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			T	3612375	C	T	3612375	3	4	55	1	0	0	0	0	1	0	0	0	1924	652	23	1	457	1	C19orf29	19	3612375	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		3612375	55516608	74	7379										
OR7G1	125962	broad.mit.edu	37	chr19	9226075	9226075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggtggcaaatggccacatagCggtcgtaggccatgactgca	14	10	0	1	rs140073167	byFrequency	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:9226075C>T	ENST00000541538.1	-	1	364	c.365G>A	c.(364-366)cGc>cAc	p.R122H	OR7G1_ENST00000293614.1_Missense_Mutation_p.R122H	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122H(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						GGCCACATAGCGGTCGTAGGC	0.483													C|||	2	0.000399361	8e-04	0	5008	,	,		19063	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19						C	HIS/ARG	3,4403	8.1+/-20.4	0,3,2200	121	120	120		365	2.7	0.4	19	dbSNP_134	120	0,8600		0,0,4300	yes	missense	OR7G1	NM_001005192.2	29	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	possibly-damaging	122/312	9226075	3,13003	2203	4300	6503	9087075	SO:0001583	missense	125962				CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.365G>A	19.37:g.9226075C>T	ENSP00000444134:p.Arg122His		9087075	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	c	12.65	2.000534	0.35320	6.81E-4	0.0	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.77489	-1.1;-1.1	3.78	2.71	0.32032	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39146	U	0.001442	T	0.81259	0.4785	M	0.93328	3.405	0.27687	N	0.946241	B	0.31256	0.316	B	0.26969	0.075	T	0.77443	-0.2586	10	0.72032	D	0.01	.	12.6859	0.56948	0.0:0.8313:0.1687:0.0	.	122	Q8NGA0	OR7G1_HUMAN	H	122	ENSP00000293614:R122H;ENSP00000444134:R122H	ENSP00000293614:R122H	R	-	2	0	OR7G1	9087075	0.966000	0.33281	0.374000	0.26016	0.265000	0.26407	5.008000	0.63991	0.903000	0.36546	0.501000	0.49751	CGC		0.483	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			T	9226075	C	T	9226075	3	4	55	1	0	0	0	0	1	0	0	0	11253	768	27	1	644	1	OR7G1	19	9226075	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	5613700	9226075	49902908	75	7380										
C19orf66	55337	broad.mit.edu	37	chr19	10202907	10202907	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aagacctggacaacctcatcCtggaggacctgaaggaggag	13	10	1	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:10202907C>T	ENST00000253110.11	+	8	1103	c.805C>T	c.(805-807)Ctg>Ttg	p.L269L	CTD-2240E14.4_ENST00000589622.1_RNA|C19orf66_ENST00000397881.3_Silent_p.L218L|C19orf66_ENST00000591813.1_Silent_p.L233L	NM_018381.2	NP_060851.2	Q9NUL5	CS066_HUMAN	chromosome 19 open reading frame 66	269	Asp/Glu-rich (acidic).							p.L269L(1)		large_intestine(3)|skin(1)	4						CAACCTCATCCTGGAGGACCT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	19											26	31	29					19																	10202907		2031	4185	6216	10063907	SO:0001819	synonymous_variant	55337				CCDS45957.1	19p13.2	2012-10-26			ENSG00000130813	ENSG00000130813			25649	protein-coding gene	gene with protein product						12477932	Standard	NM_018381		Approved	FLJ11286	uc002mmu.4	Q9NUL5		ENST00000253110.11:c.805C>T	19.37:g.10202907C>T			10063907	A8MQT9|Q4G188|Q8IYH6|Q8N8V1	Silent	SNP	ENST00000253110.11	37	CCDS45957.1																																																																																				0.622	C19orf66-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451129.1	NM_018381		T	10202907	C	T	10202907	2	4	55	1	0	0	0	0	0	0	0	1	1952	680	24	3		3	C19orf66	19	10202907	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	976832	10202907	48926076	76	7381										
CYP4F3	4051	broad.mit.edu	37	chr19	15770102	15770102	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctcacgctgctgcgcttccgCgtcctgcctgaccacaccga	9	19	1	1	rs144943990		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:15770102C>T	ENST00000221307.8	+	13	1517	c.1470C>T	c.(1468-1470)cgC>cgT	p.R490R	CYP4F3_ENST00000585846.1_Silent_p.R490R|CYP4F3_ENST00000586182.2_Silent_p.R490R|CYP4F3_ENST00000591058.1_Silent_p.R490R	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	490					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)	p.R490R(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						TGCGCTTCCGCGTCCTGCCTG	0.672													.|||	1	0.000199681	0	0	5008	,	,		15483	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C	,,	0,4404		0,0,2202	26	27	27		1470,1470,1470	-7	0.2	19	dbSNP_134	27	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	CYP4F3	NM_000896.2,NM_001199208.1,NM_001199209.1	,,	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	,,	490/521,490/521,490/521	15770102	2,13002	2202	4300	6502	15631102	SO:0001819	synonymous_variant	4051			AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.1470C>T	19.37:g.15770102C>T			15631102	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																				0.672	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		T	15770102	C	T	15770102	2	4	55	1	0	0	0	0	0	0	0	1	4196	755	27	1		1	CYP4F3	19	15770102	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	5567195	15770102	43358881	77	7382										
ZNF208	7757	broad.mit.edu	37	chr19	22155008	22155008	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	atgcttcacatttgtagaatTtctctccagcatgagttttc	6	9	2	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:22155008T>G	ENST00000397126.4	-	4	2976	c.2828A>C	c.(2827-2829)aAa>aCa	p.K943T	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	943					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K843T(2)|p.K943T(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTTGTAGAATTTCTCTCCAGC	0.363																																																3	Substitution - Missense(3)	large_intestine(3)	19											43	46	45					19																	22155008		2028	4195	6223	21946848	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2828A>C	19.37:g.22155008T>G	ENSP00000380315:p.Lys943Thr		21946848		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.315414	0.40996	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.24908	1.83	2.84	1.78	0.24846	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.44138	0.1279	.	.	.	0.21290	N	0.999739	D	0.57899	0.981	D	0.85130	0.997	T	0.11299	-1.0593	8	0.72032	D	0.01	.	6.3689	0.21471	0.0:0.1359:0.0:0.8641	.	843	O43345	ZN208_HUMAN	T	943;843	ENSP00000380315:K943T	ENSP00000380315:K943T	K	-	2	0	ZNF208	21946848	0.001000	0.12720	0.015000	0.15790	0.256000	0.26092	-0.103000	0.10940	0.970000	0.38263	0.102000	0.15555	AAA		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22155008	T	G	22155008	3	3	55	1	0	0	0	0	1	0	0	0	17805	1841	64	4	1018	4	ZNF208	19	22155008	Missense_Mutation	SNP	T	TCGA-AG-3999-01A-01W-1073-09	6384906	22155008	36973975	78	7383										
PRKD2	25865	broad.mit.edu	37	chr19	47197331	47197331	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cagtgtgggttggtgcccggCggcacaaggctgaagttctg	17	9	1	1	rs61739905		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:47197331C>T	ENST00000291281.4	-	10	1602	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	PRKD2_ENST00000600194.1_Silent_p.P302P|PRKD2_ENST00000433867.1_Silent_p.P459P|PRKD2_ENST00000601806.1_Silent_p.P302P|PRKD2_ENST00000595515.1_Silent_p.P459P			Q9BZL6	KPCD2_HUMAN	protein kinase D2	459	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.P459P(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		TGGTGCCCGGCGGCACAAGGC	0.622													C|||	1	0.000199681	8e-04	0	5008	,	,		17635	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C	,,,	1,4405	2.1+/-5.4	0,1,2202	61	51	54		1377,1377,906,1377	-9.5	0.1	19	dbSNP_129	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKD2	NM_001079880.1,NM_001079881.1,NM_001079882.1,NM_016457.4	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	459/879,459/879,302/722,459/879	47197331	1,13005	2203	4300	6503	51889171	SO:0001819	synonymous_variant	25865			AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.1377G>A	19.37:g.47197331C>T			51889171	Q8TB08|Q9P0T6|Q9Y3X8	Silent	SNP	ENST00000291281.4	37	CCDS12689.1																																																																																				0.622	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		T	47197331	C	T	47197331	2	4	55	1	0	0	0	0	0	0	0	1	12553	755	27	1		1	PRKD2	19	47197331	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	25042323	47197331	11931652	79	7384										
MEIS3	56917	broad.mit.edu	37	chr19	47912429	47912429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agatccccctcttcttgtttCgccgtcgctcctggtccaag	8	16	2	1	rs563242031		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:47912429C>T	ENST00000558555.1	-	8	972	c.785G>A	c.(784-786)cGa>cAa	p.R262Q	MEIS3_ENST00000561096.1_Missense_Mutation_p.R350Q|MEIS3_ENST00000331559.5_Missense_Mutation_p.R245Q|MEIS3_ENST00000561293.1_Missense_Mutation_p.R262Q|MEIS3_ENST00000559524.1_Missense_Mutation_p.R262Q|MEIS3_ENST00000560253.1_5'UTR|MEIS3_ENST00000441740.2_Missense_Mutation_p.R245Q			Q99687	MEIS3_HUMAN	Meis homeobox 3	262					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.R262Q(1)		breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		CTTCTTGTTTCGCCGTCGCTC	0.617													c|||	1	0.000199681	0	0	5008	,	,		18368	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19											96	74	82					19																	47912429		2203	4300	6503	52604241	SO:0001583	missense	56917			BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"Homeoboxes / TALE class"	29537	protein-coding gene	gene with protein product			"Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.785G>A	19.37:g.47912429C>T	ENSP00000454073:p.Arg262Gln		52604241	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	37		.	.	.	.	.	.	.	.	.	.	C	13.40	2.225961	0.39300	.	.	ENSG00000105419	ENST00000331559;ENST00000441740	D	0.83837	-1.77	3.96	2.91	0.33838	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.217385	0.38217	N	0.001778	D	0.85796	0.5780	L	0.44542	1.39	0.40923	D	0.98432	B;B;D;D;B	0.76494	0.041;0.398;0.987;0.999;0.006	B;B;P;D;B	0.77557	0.003;0.042;0.63;0.99;0.002	D	0.86060	0.1531	10	0.62326	D	0.03	-27.5691	10.3134	0.43723	0.0:0.8998:0.0:0.1002	.	154;262;245;262;137	Q8TCW1;Q99687;Q99687-3;Q99687-2;Q59FK5	.;MEIS3_HUMAN;.;.;.	Q	262;245	ENSP00000388667:R245Q	ENSP00000333552:R262Q	R	-	2	0	MEIS3	52604241	0.901000	0.30685	1.000000	0.80357	0.968000	0.65278	2.215000	0.42862	1.227000	0.43598	0.655000	0.94253	CGA		0.617	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929		T	47912429	C	T	47912429	3	4	55	1	0	0	0	0	1	0	0	0	9499	884	31	1	500	1	MEIS3	19	47912429	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	715098	47912429	11216554	80	7385										
GRIN2D	2906	broad.mit.edu	37	chr19	48908432	48908432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gaggcgcccccctgcctgccGggctgtttgcagtgcgctcg	15	16	0	0			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:48908432G>A	ENST00000263269.3	+	3	995	c.907G>A	c.(907-909)Ggg>Agg	p.G303R		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	303					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.G303R(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCTGCCTGCCGGGCTGTTTGC	0.731																																																1	Substitution - Missense(1)	large_intestine(1)	19											8	11	10					19																	48908432		2162	4204	6366	53600244	SO:0001583	missense	2906			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.907G>A	19.37:g.48908432G>A	ENSP00000263269:p.Gly303Arg		53600244		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.710640	0.68730	.	.	ENSG00000105464	ENST00000263269	T	0.08807	3.05	4.45	4.45	0.53987	Extracellular ligand-binding receptor (1);	0.211955	0.37136	N	0.002222	T	0.24122	0.0584	L	0.49126	1.545	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.00989	-1.1489	10	0.72032	D	0.01	.	16.2466	0.82448	0.0:0.0:1.0:0.0	.	303	O15399	NMDE4_HUMAN	R	303	ENSP00000263269:G303R	ENSP00000263269:G303R	G	+	1	0	GRIN2D	53600244	1.000000	0.71417	0.882000	0.34594	0.364000	0.29643	9.117000	0.94347	2.199000	0.70637	0.561000	0.74099	GGG		0.731	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48908432	G	A	48908432	3	1	55	1	0	0	0	0	1	0	0	0	6803	1116	39	1	913	1	GRIN2D	19	48908432	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	996003	48908432	10220551	81	7386										
SIGLEC11	114132	broad.mit.edu	37	chr19	50461734	50461734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gctcctccccaagccaccagCgcagagagggggccgggctg	15	16	0	1	rs200767146		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr19:50461734C>T	ENST00000447370.2	-	8	1547	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H	SIGLEC11_ENST00000426971.2_Intron|CTC-326K19.6_ENST00000451973.1_5'Flank	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	486					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.R474H(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		AAGCCACCAGCGCAGAGAGGG	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	19											11	13	12					19																	50461734		2185	4258	6443	55153546	SO:0001583	missense	114132			AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1457G>A	19.37:g.50461734C>T	ENSP00000412361:p.Arg486His		55153546		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	.	.	.	.	.	.	.	.	.	.	C	9.279	1.047774	0.19827	.	.	ENSG00000161640	ENST00000447370	D	0.86297	-2.1	2.86	1.79	0.24919	.	0.594677	0.16362	N	0.217735	T	0.81370	0.4808	L	0.35723	1.085	0.80722	D	1	D	0.54207	0.965	P	0.47470	0.548	T	0.74931	-0.3496	9	.	.	.	.	6.3602	0.21425	0.0:0.8425:0.0:0.1575	.	486	Q96RL6	SIG11_HUMAN	H	486	ENSP00000412361:R486H	.	R	-	2	0	SIGLEC11	55153546	0.022000	0.18835	0.628000	0.29241	0.012000	0.07955	-0.950000	0.03889	0.486000	0.27676	0.556000	0.70494	CGC		0.706	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		T	50461734	C	T	50461734	3	4	55	1	0	0	0	0	1	0	0	0	14344	768	27	1	655	1	SIGLEC11	19	50461734	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	1553302	50461734	8667249	82	7387										
PCNA	5111	broad.mit.edu	37	chr20	5098192	5098192	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	caagttctccacttgcagaaAatttcactccgtcttttgca	5	12	3	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr20:5098192A>C	ENST00000379160.3	-	5	748	c.506T>G	c.(505-507)tTt>tGt	p.F169C	PCNA_ENST00000379143.5_Missense_Mutation_p.F169C	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	169					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)	p.F169C(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						ACTTGCAGAAAATTTCACTCC	0.378								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	20											89	89	89					20																	5098192		2203	4300	6503	5046192	SO:0001583	missense	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.506T>G	20.37:g.5098192A>C	ENSP00000368458:p.Phe169Cys		5046192	B2R897|D3DW02	Missense_Mutation	SNP	ENST00000379160.3	37	CCDS13087.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.384817	0.82792	.	.	ENSG00000132646	ENST00000379143;ENST00000379160	.	.	.	5.4	5.4	0.78164	Proliferating cell nuclear antigen, PCNA, C-terminal (1);	0.043746	0.85682	D	0.000000	D	0.87947	0.6306	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91968	0.5584	9	0.87932	D	0	-14.8375	14.2529	0.66031	1.0:0.0:0.0:0.0	.	169	P12004	PCNA_HUMAN	C	169	.	ENSP00000368438:F169C	F	-	2	0	PCNA	5046192	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.165000	0.94761	2.055000	0.61198	0.379000	0.24179	TTT		0.378	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			C	5098192	A	C	5098192	3	2	55	1	0	0	0	0	1	0	0	0	11619	14	1	4	291	4	PCNA	20	5098192	Missense_Mutation	SNP	A	TCGA-AG-3999-01A-01W-1073-09		5098192	57927328	83	7388										
C20orf160	140706	broad.mit.edu	37	chr20	30605881	30605881	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cctggcgcgacaatgaagagCtcattctgcgaatccctacg	10	13	2	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr20:30605881C>G	ENST00000300415.8	+	4	395	c.382C>G	c.(382-384)Ctc>Gtc	p.L128V	CCM2L_ENST00000262659.8_Missense_Mutation_p.L128V			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	128								p.L128V(2)									CAATGAAGAGCTCATTCTGCG	0.662																																																2	Substitution - Missense(2)	large_intestine(2)	20											29	27	28					20																	30605881		2203	4300	6503	30069542	SO:0001583	missense	140706			AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 160"	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.382C>G	20.37:g.30605881C>G	ENSP00000300415:p.Leu128Val		30069542	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	37		.	.	.	.	.	.	.	.	.	.	C	14.46	2.541162	0.45280	.	.	ENSG00000101331	ENST00000300415;ENST00000339619;ENST00000262659	T;T	0.37235	1.21;1.21	4.8	4.8	0.61643	.	0.076801	0.56097	D	0.000039	T	0.52403	0.1732	M	0.70275	2.135	0.47476	D	0.99943	D	0.56035	0.974	P	0.53450	0.726	T	0.58634	-0.7602	10	0.66056	D	0.02	-32.5857	16.7764	0.85551	0.0:1.0:0.0:0.0	.	128	Q9NUG4-2	.	V	128	ENSP00000300415:L128V;ENSP00000262659:L128V	ENSP00000262659:L128V	L	+	1	0	C20orf160	30069542	1.000000	0.71417	1.000000	0.80357	0.259000	0.26198	2.390000	0.44416	2.366000	0.80165	0.305000	0.20034	CTC		0.662	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625		G	30605881	C	G	30605881	3	3	55	1	0	0	0	0	1	0	0	0	2099	797	28	5	396	5	C20orf160	20	30605881	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	25507689	30605881	32419639	84	7389										
PTPRT	11122	broad.mit.edu	37	chr20	40714387	40714387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cccgggccatgttacagatgCggaatattctgtggatgatg	13	8	1	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr20:40714387C>T	ENST00000373187.1	-	28	3952	c.3953G>A	c.(3952-3954)cGc>cAc	p.R1318H	PTPRT_ENST00000373198.4_Missense_Mutation_p.R1337H|PTPRT_ENST00000373193.3_Missense_Mutation_p.R1321H|PTPRT_ENST00000373190.1_Missense_Mutation_p.R1317H|PTPRT_ENST00000373201.1_Missense_Mutation_p.R1308H|PTPRT_ENST00000373184.1_Missense_Mutation_p.R1328H|PTPRT_ENST00000356100.2_Missense_Mutation_p.R1327H			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1318	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.R1340H(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GTTACAGATGCGGAATATTCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	20											77	82	80					20																	40714387		1997	4160	6157	40147801	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3953G>A	20.37:g.40714387C>T	ENSP00000362283:p.Arg1318His		40147801	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	35	5.422801	0.96111	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76	5.31	5.31	0.75309	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.057867	0.64402	D	0.000002	D	0.89588	0.6758	L	0.56124	1.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.988;0.993	D	0.90045	0.4145	10	0.87932	D	0	.	19.1694	0.93570	0.0:1.0:0.0:0.0	.	1340;1318	O14522-1;O14522	.;PTPRT_HUMAN	H	1317;1318;1321;1327;1340;1328;1308	ENSP00000362286:R1317H;ENSP00000362283:R1318H;ENSP00000362289:R1321H;ENSP00000348408:R1327H;ENSP00000362294:R1340H;ENSP00000362280:R1328H;ENSP00000362297:R1308H	ENSP00000348408:R1327H	R	-	2	0	PTPRT	40147801	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.570000	0.82390	2.765000	0.95021	0.655000	0.94253	CGC		0.592	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	40714387	C	T	40714387	3	4	55	1	0	0	0	0	1	0	0	0	12849	768	27	1	388	1	PTPRT	20	40714387	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	10108506	40714387	22311133	85	7390										
DIDO1	11083	broad.mit.edu	37	chr20	61511660	61511660	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cgaactggaaaggcgcgccgCctctgcttcccagaaatggg	13	13	1	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr20:61511660C>A	ENST00000266070.4	-	16	5973	c.5648G>T	c.(5647-5649)gGc>gTc	p.G1883V	DIDO1_ENST00000395343.1_Missense_Mutation_p.G1883V	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1883	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G1883V(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					AGGCGCGCCGCCTCTGCTTCC	0.647																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											1	Substitution - Missense(1)	large_intestine(1)	20											34	39	37					20																	61511660		2202	4292	6494	60982105	SO:0001583	missense	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5648G>T	20.37:g.61511660C>A	ENSP00000266070:p.Gly1883Val		60982105	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.906692	0.33628	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.10099	2.91;2.91	4.6	3.64	0.41730	.	0.000000	0.38897	U	0.001539	T	0.29061	0.0722	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.02307	-1.1179	10	0.87932	D	0	-23.8276	13.9595	0.64170	0.0:0.7106:0.2894:0.0	.	1883	Q9BTC0	DIDO1_HUMAN	V	1883	ENSP00000266070:G1883V;ENSP00000378752:G1883V	ENSP00000266070:G1883V	G	-	2	0	DIDO1	60982105	0.697000	0.27767	0.019000	0.16419	0.009000	0.06853	3.158000	0.50723	0.880000	0.35969	0.561000	0.74099	GGC		0.647	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61511660	C	A	61511660	3	1	55	1	0	0	0	0	1	0	0	0	4533	739	26	2	1078	2	DIDO1	20	61511660	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	20797273	61511660	1513860	86	7391										
TRPM2	7226	broad.mit.edu	37	chr21	45811378	45811378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ttgcgcgcccgcggcgccccGcctgcagatgcaccacgtgg	14	18	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr21:45811378G>A	ENST00000397928.1	+	11	2109	c.1664G>A	c.(1663-1665)cGc>cAc	p.R555H	TRPM2_ENST00000397932.2_Missense_Mutation_p.R555H|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300482.5_Missense_Mutation_p.R555H|TRPM2_ENST00000300481.9_Intron	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	555					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.R555L(1)|p.R555H(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						gcggcgccccgccTGCAGATG	0.706																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	21											16	17	17					21																	45811378		2169	4249	6418	44635806	SO:0001583	missense	7226			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1664G>A	21.37:g.45811378G>A	ENSP00000381023:p.Arg555His		44635806	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	7.394	0.631406	0.14322	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000397932	T;T;T	0.63417	-0.04;-0.04;-0.04	4.63	1.2	0.21068	.	1.517800	0.03458	N	0.211825	T	0.62865	0.2463	L	0.60067	1.865	0.80722	D	1	D;D;D	0.60575	0.958;0.98;0.988	B;B;P	0.47981	0.382;0.443;0.563	T	0.58239	-0.7671	10	0.46703	T	0.11	-4.8183	4.3929	0.11350	0.3758:0.1967:0.4274:0.0	.	555;341;555	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	H	555	ENSP00000300482:R555H;ENSP00000381023:R555H;ENSP00000381026:R555H	ENSP00000300482:R555H	R	+	2	0	TRPM2	44635806	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.089000	0.15002	0.376000	0.24707	0.655000	0.94253	CGC		0.706	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45811378	G	A	45811378	3	1	55	1	0	0	0	0	1	0	0	0	16626	1087	38	1	1706	1	TRPM2	21	45811378	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		45811378	2318517	87	7392										
PI4KA	5297	broad.mit.edu	37	chr22	21119206	21119206	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ggaggggggtccagcaggttGatgatagtgctgcggagctc	19	7	0	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr22:21119206G>C	ENST00000572273.1	-	22	2663	c.2433C>G	c.(2431-2433)atC>atG	p.I811M	PI4KA_ENST00000466162.1_5'UTR|PI4KA_ENST00000255882.6_Missense_Mutation_p.I869M			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	811					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.I811M(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CCAGCAGGTTGATGATAGTGC	0.602																																					GBM(136;1332 1831 3115 23601 50806)											2	Substitution - Missense(2)	large_intestine(2)	22											73	65	68					22																	21119206		2203	4300	6503	19449206	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2433C>G	22.37:g.21119206G>C	ENSP00000458238:p.Ile811Met		19449206	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	G	15.04	2.715985	0.48622	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.58	5.58	0.84498	.	0.272982	0.39759	N	0.001264	T	0.57227	0.2039	L	0.40543	1.245	0.80722	D	1	B	0.20550	0.046	B	0.29598	0.104	T	0.54589	-0.8271	9	0.48119	T	0.1	-17.662	15.0461	0.71827	0.0:0.0:0.793:0.207	.	811	P42356	PI4KA_HUMAN	M	811	.	ENSP00000255882:I811M	I	-	3	3	PI4KA	19449206	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.895000	0.48648	2.621000	0.88768	0.650000	0.86243	ATC		0.602	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		C	21119206	G	C	21119206	3	2	55	1	0	0	0	0	1	0	0	0	11904	1280	45	5	3837	5	PI4KA	22	21119206	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09		21119206	30185360	88	7393										
PI4KA	5297	broad.mit.edu	37	chr22	21119493	21119493	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	gacttagtggctatttcacaGaccccctcgtaccattcttc	6	14	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr22:21119493G>A	ENST00000572273.1	-	21	2525	c.2295C>T	c.(2293-2295)gtC>gtT	p.V765V	PI4KA_ENST00000466162.1_5'UTR|PI4KA_ENST00000255882.6_Silent_p.V823V			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	765					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.V765V(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CTATTTCACAGACCCCCTCGT	0.507																																					GBM(136;1332 1831 3115 23601 50806)											2	Substitution - coding silent(2)	large_intestine(2)	22											115	119	117					22																	21119493		2203	4300	6503	19449493	SO:0001819	synonymous_variant	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2295C>T	22.37:g.21119493G>A			19449493	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																					0.507	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21119493	G	A	21119493	2	1	55	1	0	0	0	0	0	0	0	1	11904	929	33	3		3	PI4KA	22	21119493	Silent	SNP	G	TCGA-AG-3999-01A-01W-1073-09	287	21119493	30185073	89	7394										
VPREB3	29802	broad.mit.edu	37	chr22	24095278	24095278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	ctgctggtaccaggacacacCgtagtccctgatggtgacgt	12	12	0	2	rs143409128		TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chr22:24095278C>T	ENST00000248948.3	-	2	261	c.157G>A	c.(157-159)Ggt>Agt	p.G53S	VPREB3_ENST00000398465.3_Missense_Mutation_p.G37S|ZNF70_ENST00000341976.3_5'Flank	NM_013378.2	NP_037510.1	Q9UKI3	VPRE3_HUMAN	pre-B lymphocyte 3	53	Ig-like.					endoplasmic reticulum (GO:0005783)		p.G53S(1)		large_intestine(1)|lung(1)|skin(1)	3		Medulloblastoma(6;7.87e-06)|all_neural(6;0.00334)				CAGGACACACCGTAGTCCCTG	0.637													C|||	1	0.000199681	0	0	5008	,	,		18713	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						C	SER/GLY	2,4404	4.2+/-10.8	0,2,2201	95	71	79		157	-0.4	0	22	dbSNP_134	79	0,8600		0,0,4300	yes	missense	VPREB3	NM_013378.2	56	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	53/124	24095278	2,13004	2203	4300	6503	22425278	SO:0001583	missense	29802				CCDS13813.1	22q11.23	2013-01-11	2008-09-12		ENSG00000128218	ENSG00000128218		"Immunoglobulin superfamily / V-set domain containing"	12710	protein-coding gene	gene with protein product		605017				10702669, 14670953	Standard	NM_013378		Approved	8HS20	uc002zxt.3	Q9UKI3	OTTHUMG00000150738	ENST00000248948.3:c.157G>A	22.37:g.24095278C>T	ENSP00000248948:p.Gly53Ser		22425278	B2R587	Missense_Mutation	SNP	ENST00000248948.3	37	CCDS13813.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.68	2.309109	0.40895	4.54E-4	0.0	ENSG00000128218	ENST00000398465;ENST00000248948	T;T	0.62941	-0.01;-0.01	5.57	-0.428	0.12306	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.488214	0.17443	N	0.174058	T	0.57592	0.2064	N	0.21282	0.65	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50145	-0.8862	10	0.22109	T	0.4	.	5.1186	0.14849	0.2417:0.458:0.234:0.0662	.	53	Q9UKI3	VPRE3_HUMAN	S	37;53	ENSP00000381483:G37S;ENSP00000248948:G53S	ENSP00000248948:G53S	G	-	1	0	VPREB3	22425278	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	1.801000	0.38843	-0.101000	0.12219	-0.187000	0.12897	GGT		0.637	VPREB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319879.2	NM_013378		T	24095278	C	T	24095278	3	4	55	1	0	0	0	0	1	0	0	0	17227	652	23	1	218	1	VPREB3	22	24095278	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	2975785	24095278	27209288	90	7395										
CSF2RA	1438	broad.mit.edu	37	chrX	1407724	1407724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tttaatgaactgtacctgggCgaggggtccgacggcccccc	13	13	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:1407724C>T	ENST00000381524.3	+	6	602	c.416C>T	c.(415-417)gCg>gTg	p.A139V	CSF2RA_ENST00000501036.2_Missense_Mutation_p.A6V|CSF2RA_ENST00000355805.2_Missense_Mutation_p.A139V|BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000355432.3_Missense_Mutation_p.A139V|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000381500.1_Missense_Mutation_p.A139V|CSF2RA_ENST00000432318.2_Missense_Mutation_p.A139V|CSF2RA_ENST00000417535.2_Missense_Mutation_p.A139V|CSF2RA_ENST00000381529.3_Missense_Mutation_p.A139V|CSF2RA_ENST00000361536.3_Missense_Mutation_p.A139V|CSF2RA_ENST00000381509.3_Missense_Mutation_p.A139V			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	139					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.A139V(2)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	TGTACCTGGGCGAGGGGTCCG	0.458																																					Esophageal Squamous(131;723 1707 25334 40494 41806)											2	Substitution - Missense(2)	large_intestine(2)	X											135	145	142					X																	1407724		2203	4296	6499	1367724	SO:0001583	missense	1438			M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.416C>T	X.37:g.1407724C>T	ENSP00000370935:p.Ala139Val		1367724	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	12.62	1.993658	0.35131	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000501036;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;T;D;D;T;T;D;T;T;D;T	0.96073	-3.9;-3.9;0.48;-3.65;-3.9;0.48;0.48;-3.9;0.48;0.48;-3.9;0.48	2.02	1.01	0.19927	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Short hematopoietin receptor, family 2, conserved site (1);Immunoglobulin-like fold (1);	0.749927	0.10657	U	0.649132	D	0.95872	0.8656	.	.	.	0.09310	N	1	D;D;D;D;D;D	0.76494	0.998;0.999;0.996;0.999;0.995;0.998	P;D;P;P;P;P	0.67725	0.862;0.953;0.806;0.895;0.748;0.878	D	0.87842	0.2652	9	0.31617	T	0.26	.	5.887	0.18886	0.0:0.67:0.33:0.0	.	139;139;139;139;139;139	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	V	139;139;139;139;6;139;139;139;139;139;139;139;139	ENSP00000370940:A139V;ENSP00000416437:A139V;ENSP00000354836:A139V;ENSP00000440491:A6V;ENSP00000370935:A139V;ENSP00000410667:A139V;ENSP00000397452:A139V;ENSP00000370920:A139V;ENSP00000348058:A139V;ENSP00000347606:A139V;ENSP00000394227:A139V;ENSP00000370911:A139V	ENSP00000347606:A139V	A	+	2	0	CSF2RA	1367724	0.483000	0.25956	0.002000	0.10522	0.077000	0.17291	0.417000	0.21214	0.104000	0.17725	0.280000	0.19369	GCG		0.458	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			T	1407724	C	T	1407724	3	4	55	1	0	0	0	0	1	0	0	0	3940	768	27	1	430	1	CSF2RA	23	1407724	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09		1407724	153862836	91	7396										
SYTL5	94122	broad.mit.edu	37	chrX	37931343	37931343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	agtggttttttgaagaaaagGcaaaacgtttcaagcaagtc	10	5	1	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:37931343G>A	ENST00000357972.5	+	4	919	c.373G>A	c.(373-375)Gca>Aca	p.A125T	SYTL5_ENST00000297875.2_Missense_Mutation_p.A125T|SYTL5_ENST00000456733.2_Missense_Mutation_p.A125T|TM4SF2_ENST00000465127.1_Intron			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	125					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.A125T(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						TGAAGAAAAGGCAAAACGTTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											184	159	167					X																	37931343		2202	4300	6502	37816287	SO:0001583	missense	94122				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"exophilin 9"						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.373G>A	X.37:g.37931343G>A	ENSP00000350657:p.Ala125Thr		37816287	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	37	CCDS14244.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962655	0.74016	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.76448	-1.02;-1.02;-1.02	5.33	5.33	0.75918	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.115754	0.64402	D	0.000015	T	0.76435	0.3987	M	0.66939	2.045	0.29544	N	0.851873	D;P	0.54397	0.966;0.81	B;B	0.43950	0.437;0.146	T	0.76558	-0.2915	10	0.41790	T	0.15	-22.3867	12.5795	0.56383	0.0:0.0:0.8334:0.1666	.	125;125	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	T	125	ENSP00000297875:A125T;ENSP00000350657:A125T;ENSP00000395220:A125T	ENSP00000297875:A125T	A	+	1	0	SYTL5	37816287	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.321000	0.51999	2.354000	0.79902	0.513000	0.50165	GCA		0.373	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		A	37931343	G	A	37931343	3	1	55	1	0	0	0	0	1	0	0	0	15525	1203	42	3	383	3	SYTL5	23	37931343	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	36523619	37931343	117339217	92	7397										
RBM10	8241	broad.mit.edu	37	chrX	47028790	47028790	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	atggtggggagaaccgcagcCgagaccacgactaccgggac	15	12	0	2			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:47028790C>T	ENST00000377604.3	+	3	836	c.94C>T	c.(94-96)Cga>Tga	p.R32*	RBM10_ENST00000345781.6_Nonsense_Mutation_p.R32*|RBM10_ENST00000329236.7_Nonsense_Mutation_p.R32*	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	32					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.R32*(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						GAACCGCAGCCGAGACCACGA	0.592																																					Melanoma(171;120 2705 19495 39241)											2	Substitution - Nonsense(2)	large_intestine(2)	X											98	67	78					X																	47028790		2203	4300	6503	46913734	SO:0001587	stop_gained	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.94C>T	X.37:g.47028790C>T	ENSP00000366829:p.Arg32*		46913734	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Nonsense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	39	7.573321	0.98368	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	.	.	.	4.62	2.79	0.32731	.	0.000000	0.41938	D	0.000797	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8986	9.4105	0.38489	0.3851:0.6149:0.0:0.0	.	.	.	.	X	32	.	ENSP00000328848:R32X	R	+	1	2	RBM10	46913734	1.000000	0.71417	0.983000	0.44433	0.991000	0.79684	1.426000	0.34870	0.324000	0.23333	0.436000	0.28706	CGA		0.592	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47028790	C	T	47028790	4	4	55	1	0	0	0	0	0	1	0	0	13148	644	23	1	100	1	RBM10	23	47028790	Nonsense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	9097447	47028790	108241770	93	7398										
CACNA1F	778	broad.mit.edu	37	chrX	49086834	49086834	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aattgagcactatgtgcaggCctgcggggagggagggggag	20	6	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:49086834C>A	ENST00000376265.2	-	6	726	c.665G>T	c.(664-666)aGc>aTc	p.S222I	CACNA1F_ENST00000376251.1_Splice_Site_p.S157I|CACNA1F_ENST00000323022.5_Splice_Site_p.S222I	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	222					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S222I(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TATGTGCAGGCCTGCGGGGAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	X											40	34	36					X																	49086834		2203	4300	6503	48973778	SO:0001630	splice_region_variant	778			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.665-1G>T	X.37:g.49086834C>A			48973778	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.428288	0.62844	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98732	-5.1;-5.1;-5.1	4.2	4.2	0.49525	Ion transport (1);	0.041854	0.85682	D	0.000000	D	0.99336	0.9767	H	0.94620	3.56	0.58432	D	0.999991	D;D	0.76494	0.999;0.999	D;D	0.87578	0.996;0.998	D	0.98664	1.0685	10	0.87932	D	0	.	14.9323	0.70926	0.0:1.0:0.0:0.0	.	222;222	F5CIQ9;O60840	.;CAC1F_HUMAN	I	157;222;222	ENSP00000365427:S157I;ENSP00000321618:S222I;ENSP00000365441:S222I	ENSP00000321618:S222I	S	-	2	0	CACNA1F	48973778	1.000000	0.71417	0.997000	0.53966	0.650000	0.38633	5.847000	0.69451	1.843000	0.53566	0.287000	0.19450	AGC		0.607	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	Missense_Mutation	A	49086834	C	A	49086834	5	1	55	1	0	0	0	0	0	0	1	0	2549	753	26	2	5440	2	CACNA1F	23	49086834	Splice_Site	SNP	C	TCGA-AG-3999-01A-01W-1073-09	2058044	49086834	106183726	94	7399										
AKAP4	8852	broad.mit.edu	37	chrX	49958478	49958478	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	tagaaagcttttctggccacCttccctggactcctctccag	7	15	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:49958478C>A	ENST00000376056.2	-	5	1009	c.859G>T	c.(859-861)Ggt>Tgt	p.G287C	AKAP4_ENST00000376064.3_Missense_Mutation_p.G287C|AKAP4_ENST00000376058.2_Intron|AKAP4_ENST00000358526.2_Missense_Mutation_p.G296C|AKAP4_ENST00000481402.1_5'UTR					A kinase (PRKA) anchor protein 4									p.G296C(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TTCTGGCCACCTTCCCTGGAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											52	47	49					X																	49958478		2203	4300	6503	49845218	SO:0001583	missense	8852			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.859G>T	X.37:g.49958478C>A	ENSP00000365224:p.Gly287Cys		49845218		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	5.376	0.254632	0.10185	.	.	ENSG00000147081	ENST00000376056;ENST00000358526;ENST00000376064	T;T;T	0.09163	3.01;3.01;3.01	3.53	2.62	0.31277	A-kinase anchor 110kDa, C-terminal (1);	0.452338	0.16021	U	0.233310	T	0.10937	0.0267	L	0.54323	1.7	0.44807	D	0.997815	B	0.23735	0.09	B	0.26693	0.072	T	0.08066	-1.0740	9	.	.	.	-3.8587	7.7821	0.29070	0.2499:0.7501:0.0:0.0	.	296	Q5JQC9	AKAP4_HUMAN	C	287;296;287	ENSP00000365224:G287C;ENSP00000351327:G296C;ENSP00000365232:G287C	.	G	-	1	0	AKAP4	49845218	0.078000	0.21339	0.420000	0.26596	0.017000	0.09413	0.298000	0.19120	0.567000	0.29293	0.277000	0.19347	GGT		0.478	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		A	49958478	C	A	49958478	3	1	55	1	0	0	0	0	1	0	0	0	453	681	24	2	1686	2	AKAP4	23	49958478	Missense_Mutation	SNP	C	TCGA-AG-3999-01A-01W-1073-09	871644	49958478	105312082	95	7400										
GRIA3	2892	broad.mit.edu	37	chrX	122598806	122598806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	aaacaacagcagacggagtgGcccgagtgcgaaagtccaag	13	10	0	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:122598806G>A	ENST00000371251.1	+	13	2219	c.2167G>A	c.(2167-2169)Gcc>Acc	p.A723T	GRIA3_ENST00000371256.5_Missense_Mutation_p.A723T|AL356213.1_ENST00000577653.1_RNA|GRIA3_ENST00000542149.1_Missense_Mutation_p.A723T|GRIA3_ENST00000264357.5_Missense_Mutation_p.A723T			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	723					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)	p.A723T(2)		breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	AGACGGAGTGGCCCGAGTGCG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	X											95	84	88					X																	122598806		2203	4300	6503	122426487	SO:0001583	missense	2892			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.2167G>A	X.37:g.122598806G>A	ENSP00000360297:p.Ala723Thr		122426487	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	7.734	0.699833	0.15106	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.12	5.12	0.69794	Ionotropic glutamate receptor (2);	0.048712	0.85682	D	0.000000	T	0.37073	0.0990	L	0.39566	1.225	0.80722	D	1	P;P	0.40000	0.698;0.649	B;B	0.38683	0.279;0.183	T	0.13953	-1.0490	10	0.31617	T	0.26	.	16.5308	0.84357	0.0:0.0:1.0:0.0	.	723;723	P42263;P42263-2	GRIA3_HUMAN;.	T	723	ENSP00000264357:A723T;ENSP00000446146:A723T;ENSP00000360302:A723T;ENSP00000360297:A723T	ENSP00000264357:A723T	A	+	1	0	GRIA3	122426487	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.291000	0.65667	2.104000	0.64026	0.415000	0.27848	GCC		0.463	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		A	122598806	G	A	122598806	3	1	55	1	0	0	0	0	1	0	0	0	6790	1203	42	3	2217	3	GRIA3	23	122598806	Missense_Mutation	SNP	G	TCGA-AG-3999-01A-01W-1073-09	72640328	122598806	32671754	96	7401										
SLC25A14	9016	broad.mit.edu	37	chrX	129506897	129506897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.482019363762102	4.33817427385892	0.255186721991701	1	1	0	cctcagttttttattacataCgagcagctaaagaggcttca	7	9	2	1			TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-3999-01A-01W-1073-09	TCGA-AG-3999-10A-01W-1073-09	g.chrX:129506897C>T	ENST00000218197.5	+	10	1178	c.951C>T	c.(949-951)taC>taT	p.Y317Y	SLC25A14_ENST00000361980.5_Silent_p.Y314Y|SLC25A14_ENST00000339231.3_Silent_p.Y345Y	NM_001282195.1|NM_001282196.1|NM_001282198.1	NP_001269124.1|NP_001269125.1|NP_001269127.1	O95258	UCP5_HUMAN	solute carrier family 25 (mitochondrial carrier, brain), member 14	317					aerobic respiration (GO:0009060)|mitochondrial transport (GO:0006839)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.Y317Y(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)	22						TTATTACATACGAGCAGCTAA	0.393																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	X											226	221	222					X																	129506897		2203	4300	6503	129334578	SO:0001819	synonymous_variant	9016			AF078544	CCDS14623.1, CCDS14624.1, CCDS76020.1, CCDS76021.1	Xq24	2013-05-22			ENSG00000102078	ENSG00000102078		"Solute carriers"	10984	protein-coding gene	gene with protein product		300242				9852133	Standard	XM_005262485		Approved	BMCP1, UCP5	uc004evp.1	O95258	OTTHUMG00000022394	ENST00000218197.5:c.951C>T	X.37:g.129506897C>T			129334578	D3DTG2|Q0VDH7|Q9HC60|Q9HC61	Silent	SNP	ENST00000218197.5	37	CCDS14623.1																																																																																				0.393	SLC25A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058253.1	NM_022810, NM_003951		T	129506897	C	T	129506897	2	4	55	1	0	0	0	0	0	0	0	1	14513	547	19	1		1	SLC25A14	23	129506897	Silent	SNP	C	TCGA-AG-3999-01A-01W-1073-09	6908091	129506897	25763663	97	7402										
CLIC4	25932	broad.mit.edu	37	chr1	25167305	25167305	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aactttgatattccaaaagaAatgactggcatctggagata	8	6	1	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:25167305A>G	ENST00000374379.4	+	6	836	c.639A>G	c.(637-639)gaA>gaG	p.E213E		NM_013943.2	NP_039234.1	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	213	GST C-terminal.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|endothelial cell morphogenesis (GO:0001886)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|keratinocyte differentiation (GO:0030216)|multicellular organism growth (GO:0035264)|negative regulation of cell migration (GO:0030336)|regulation of cytoskeleton organization (GO:0051493)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|vacuolar acidification (GO:0007035)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|microvillus (GO:0005902)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.E213E(1)		large_intestine(3)|lung(2)|skin(1)	6		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)		TTCCAAAAGAAATGACTGGCA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	1											122	117	119					1																	25167305		2203	4300	6503	25039892	SO:0001819	synonymous_variant	25932			AF097330	CCDS256.1	1p	2012-09-26			ENSG00000169504	ENSG00000169504		"Ion channels / Chloride channels : Intracellular"	13518	protein-coding gene	gene with protein product		606536				9139710, 10070163	Standard	NM_013943		Approved	DKFZP566G223, CLIC4L, P64H1, H1, huH1, p64H1	uc001bjo.2	Q9Y696	OTTHUMG00000003327	ENST00000374379.4:c.639A>G	1.37:g.25167305A>G			25039892	Q9UFW9|Q9UQJ6	Silent	SNP	ENST00000374379.4	37	CCDS256.1																																																																																				0.383	CLIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009332.1	NM_013943		G	25167305	A	G	25167305	2	3	56	1	0	0	0	0	0	0	0	1	3534	11	1	4		4	CLIC4	1	25167305	Silent	SNP	A	TCGA-AG-4001-01A-02W-1073-09		25167305	224083316	1	7403										
SLC44A5	204962	broad.mit.edu	37	chr1	75708605	75708605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cagtggtcttacagaactgaCggtagtcttcccagtagctt	10	10	2	2	rs373084017		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:75708605C>T	ENST00000370855.5	-	8	550	c.437G>A	c.(436-438)cGt>cAt	p.R146H	SLC44A5_ENST00000370859.3_Missense_Mutation_p.R146H|SLC44A5_ENST00000469525.1_5'UTR|SLC44A5_ENST00000535611.1_Missense_Mutation_p.R16H	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	146					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R146H(2)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						ACAGAACTGACGGTAGTCTTC	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	1						C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	163	166	165		437,437	2.1	0.4	1		165	0,8600		0,0,4300	no	missense,missense	SLC44A5	NM_001130058.1,NM_152697.4	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	146/718,146/720	75708605	1,13005	2203	4300	6503	75481193	SO:0001583	missense	204962			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.437G>A	1.37:g.75708605C>T	ENSP00000359892:p.Arg146His		75481193	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	37	CCDS667.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270806	0.40194	2.27E-4	0.0	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535611;ENST00000535790	T;T;T	0.27104	1.69;1.69;2.36	5.07	2.14	0.27477	.	0.631700	0.16943	N	0.193215	T	0.08626	0.0214	L	0.52573	1.65	0.24652	N	0.993511	B;B;B;P;B	0.36599	0.425;0.425;0.284;0.56;0.427	B;B;B;B;B	0.32090	0.046;0.066;0.046;0.14;0.058	T	0.10753	-1.0616	10	0.44086	T	0.13	0.009	8.7123	0.34391	0.0:0.6837:0.0:0.3163	.	140;185;146;146;185	B7Z5Y4;B7Z470;Q8NCS7;Q8NCS7-2;F5GYS0	.;.;CTL5_HUMAN;.;.	H	146;185;146;16;139	ENSP00000359896:R146H;ENSP00000359892:R146H;ENSP00000443090:R16H	ENSP00000359892:R146H	R	-	2	0	SLC44A5	75481193	0.049000	0.20398	0.442000	0.26870	0.644000	0.38419	0.193000	0.17116	0.649000	0.30751	0.655000	0.94253	CGT		0.378	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		T	75708605	C	T	75708605	3	4	56	1	0	0	0	0	1	0	0	0	14676	536	19	1	1901	1	SLC44A5	1	75708605	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	50541300	75708605	173542016	2	7404										
AMPD2	271	broad.mit.edu	37	chr1	110163651	110163652	+	Missense_Mutation	DNP	CA	CA	TG													0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	acaacatgagaaatcgtggcCagggcctcttccgcctgcgg							TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:110163651_110163652CA>TG	ENST00000256578.3	+	1	376_377	c.16_17CA>TG	c.(16-18)CAg>TGg	p.Q6W	AMPD2_ENST00000342115.4_Intron|AMPD2_ENST00000528667.1_Missense_Mutation_p.Q6W|AMPD2_ENST00000526301.1_Intron|AMPD2_ENST00000528454.1_5'Flank|AMPD2_ENST00000358729.4_5'Flank	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	6					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.Q6>?(1)		breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		AAATCGTGGCCAGGGCCTCTTC	0.663																																																1	Complex(1)	large_intestine(1)	1																																								109965175	SO:0001583	missense	271			S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	Exception_encountered	1.37:g.110163651_110163652delinsTG	ENSP00000256578:p.Gln6Trp		109965174	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	DNP	ENST00000256578.3	37	CCDS805.1																																																																																				0.663	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			TG	110163652	CA	TG	110163651	3	4	56	1	0	0	0	0	1	0	0	0	586	595	21	3	32	3	AMPD2	1	110163651	Missense_Mutation	DNP	CA	TCGA-AG-4001-01A-02W-1073-09	34455046	110163651	139086970	3	7405										
BCL9	607	broad.mit.edu	37	chr1	147091237	147091237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gacctgggccccggacagacGtgggagctccatttggccct	14	14	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:147091237G>A	ENST00000234739.3	+	8	2016	c.1276G>A	c.(1276-1278)Gtg>Atg	p.V426M		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	426	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.V426M(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CCGGACAGACGTGGGAGCTCC	0.532			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	1	Substitution - Missense(1)	large_intestine(1)	1											55	62	60					1																	147091237		2203	4300	6503	145557861	SO:0001583	missense	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1276G>A	1.37:g.147091237G>A	ENSP00000234739:p.Val426Met		145557861	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	G	9.076	0.998055	0.19043	.	.	ENSG00000116128	ENST00000234739	T	0.76316	-1.01	5.61	3.74	0.42951	.	0.308735	0.34460	N	0.003958	T	0.41119	0.1145	N	0.08118	0	0.30715	N	0.748912	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.29640	-1.0005	10	0.49607	T	0.09	-10.853	12.3874	0.55340	0.1354:0.0:0.8646:0.0	.	426;426	Q1JQ81;O00512	.;BCL9_HUMAN	M	426	ENSP00000234739:V426M	ENSP00000234739:V426M	V	+	1	0	BCL9	145557861	1.000000	0.71417	0.988000	0.46212	0.806000	0.45545	3.156000	0.50708	0.937000	0.37394	-0.156000	0.13503	GTG		0.532	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		A	147091237	G	A	147091237	3	1	56	1	0	0	0	0	1	0	0	0	1382	1145	40	1	1294	1	BCL9	1	147091237	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	36927586	147091237	102159384	4	7406										
OR10K2	391107	broad.mit.edu	37	chr1	158390379	158390379	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggatggcacagcccaggaaaGaaatggtcttcttctgggac	13	9	3	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:158390379G>T	ENST00000314902.2	-	1	277	c.278C>A	c.(277-279)tCt>tAt	p.S93Y		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S93Y(1)		NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GCCCAGGAAAGAAATGGTCTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											178	174	175					1																	158390379		2203	4300	6503	156657003	SO:0001583	missense	391107			AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"GPCR / Class A : Olfactory receptors"	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.278C>A	1.37:g.158390379G>T	ENSP00000324251:p.Ser93Tyr		156657003		Missense_Mutation	SNP	ENST00000314902.2	37	CCDS30896.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.117726	0.37339	.	.	ENSG00000180708	ENST00000314902	T	0.00745	5.75	4.1	4.1	0.47936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000280	T	0.04318	0.0119	H	0.96996	3.92	0.35657	D	0.812211	D	0.71674	0.998	P	0.62813	0.907	T	0.02728	-1.1118	10	0.87932	D	0	.	15.5895	0.76517	0.0:0.0:1.0:0.0	.	93	Q6IF99	O10K2_HUMAN	Y	93	ENSP00000324251:S93Y	ENSP00000324251:S93Y	S	-	2	0	OR10K2	156657003	1.000000	0.71417	0.978000	0.43139	0.315000	0.28087	7.168000	0.77570	2.265000	0.75225	0.467000	0.42956	TCT		0.478	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476		T	158390379	G	T	158390379	3	4	56	1	0	0	0	0	1	0	0	0	10945	942	33	2	662	2	OR10K2	1	158390379	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	11299142	158390379	90860242	5	7407										
SPTA1	6708	broad.mit.edu	37	chr1	158626363	158626363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gttagtcttacctggcaggcGtttgcctgattccgcagagc	12	11	1	2	rs371639635	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:158626363G>A	ENST00000368147.4	-	20	3069	c.2889C>T	c.(2887-2889)aaC>aaT	p.N963N		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	963					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.N963N(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTGGCAGGCGTTTGCCTGAT	0.398													G|||	4	0.000798722	0.003	0	5008	,	,		16668	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		2,3722		0,2,1860	168	171	170		2889	-5.2	1	1		170	1,8185		0,1,4092	no	coding-synonymous	SPTA1	NM_003126.2		0,3,5952	AA,AG,GG		0.0122,0.0537,0.0252		963/2420	158626363	3,11907	1862	4093	5955	156892987	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2889C>T	1.37:g.158626363G>A			156892987	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158626363	G	A	158626363	2	1	56	1	0	0	0	0	0	0	0	1	15155	1136	40	1		1	SPTA1	1	158626363	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	235984	158626363	90624258	6	7408										
PIK3C2B	5287	broad.mit.edu	37	chr1	204412619	204412619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	attgacaagccagcactggcGgttaaactcttctctcagcc	8	13	3	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:204412619G>A	ENST00000367187.3	-	20	3530	c.2974C>T	c.(2974-2976)Cgc>Tgc	p.R992C	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R964C	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	992					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R992C(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			CAGCACTGGCGGTTAAACTCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	90	90					1																	204412619		2203	4300	6503	202679242	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2974C>T	1.37:g.204412619G>A	ENSP00000356155:p.Arg992Cys		202679242	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033178	0.75504	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	D;D	0.81579	-1.51;-1.51	5.79	4.8	0.61643	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.87811	0.6271	M	0.74467	2.265	0.44155	D	0.99695	P;D	0.89917	0.753;1.0	P;P	0.62184	0.571;0.899	D	0.88611	0.3156	10	0.62326	D	0.03	.	15.4174	0.74980	0.0:0.0:0.7758:0.2242	.	964;992	F5GWN5;O00750	.;P3C2B_HUMAN	C	992;964	ENSP00000356155:R992C;ENSP00000400561:R964C	ENSP00000356155:R992C	R	-	1	0	PIK3C2B	202679242	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.039000	0.49791	2.742000	0.94016	0.591000	0.81541	CGC		0.607	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		A	204412619	G	A	204412619	3	1	56	1	0	0	0	0	1	0	0	0	11941	1116	39	1	1990	1	PIK3C2B	1	204412619	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	45786256	204412619	44838002	7	7409										
PPP2R5A	5525	broad.mit.edu	37	chr1	212502526	212502526	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttctgtcagaagttgcagcaGtgttgtatactgtttgattt	10	5	2	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:212502526G>A	ENST00000261461.2	+	2	805	c.231G>A	c.(229-231)caG>caA	p.Q77Q	PPP2R5A_ENST00000498129.2_3'UTR|PPP2R5A_ENST00000537030.3_Silent_p.Q20Q|RP11-384C4.7_ENST00000442146.1_RNA	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	77					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)	p.Q77Q(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		AGTTGCAGCAGTGTTGTATAC	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	1											104	102	103					1																	212502526		2203	4300	6503	210569149	SO:0001819	synonymous_variant	5525			BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9309	protein-coding gene	gene with protein product		601643	"protein phosphatase 2, regulatory subunit B (B56), alpha isoform", "protein phosphatase 2, regulatory subunit B', alpha isoform"			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.231G>A	1.37:g.212502526G>A			210569149	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Silent	SNP	ENST00000261461.2	37	CCDS1503.1																																																																																				0.328	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243		A	212502526	G	A	212502526	2	1	56	1	0	0	0	0	0	0	0	1	12426	1020	36	3		3	PPP2R5A	1	212502526	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	8089907	212502526	36748095	8	7410										
OR2G6	391211	broad.mit.edu	37	chr1	248685161	248685161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	acctctcgtgtgtggacatcTgctttaccaccagtgttgcc	9	13	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr1:248685161T>C	ENST00000343414.4	+	1	246	c.214T>C	c.(214-216)Tgc>Cgc	p.C72R		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	72						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C72R(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTGGACATCTGCTTTACCAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											125	108	114					1																	248685161		2203	4300	6503	246751784	SO:0001583	missense	391211				CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.214T>C	1.37:g.248685161T>C	ENSP00000341291:p.Cys72Arg		246751784	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	37	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	-	12.24	1.879932	0.33162	.	.	ENSG00000188558	ENST00000343414	T	0.01106	5.33	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	U	0.000166	T	0.11537	0.0281	H	0.97540	4.025	0.09310	N	0.999997	D	0.89917	1.0	D	0.87578	0.998	T	0.14755	-1.0461	10	0.87932	D	0	.	11.4534	0.50167	0.0:0.0:0.0:1.0	.	72	Q5TZ20	OR2G6_HUMAN	R	72	ENSP00000341291:C72R	ENSP00000341291:C72R	C	+	1	0	OR2G6	246751784	0.000000	0.05858	0.577000	0.28562	0.762000	0.43233	0.192000	0.17096	1.523000	0.49018	0.329000	0.21502	TGC		0.507	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		C	248685161	T	C	248685161	3	2	56	1	0	0	0	0	1	0	0	0	11031	1580	55	4	216	4	OR2G6	1	248685161	Missense_Mutation	SNP	T	TCGA-AG-4001-01A-02W-1073-09	36182635	248685161	565460	9	7411										
TTC15	51112	broad.mit.edu	37	chr2	3405656	3405656	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aatcttttgttggattgaaaCagctaatcgtaagtgacaat	8	5	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:3405656C>T	ENST00000324266.5	+	3	1351	c.1156C>T	c.(1156-1158)Cag>Tag	p.Q386*	TRAPPC12_ENST00000382110.2_Nonsense_Mutation_p.Q386*	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	386					vesicle-mediated transport (GO:0016192)			p.Q386*(1)									TGGATTGAAACAGCTAATCGT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											244	239	240					2																	3405656		2203	4300	6503	3384663	SO:0001587	stop_gained	51112			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1156C>T	2.37:g.3405656C>T	ENSP00000324318:p.Gln386*		3384663	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Nonsense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296062	0.60086	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	.	.	.	5.23	5.23	0.72850	.	0.123739	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	12.7945	0.57553	0.1637:0.8363:0.0:0.0	.	.	.	.	X	386;369;386	.	ENSP00000303612:Q369X	Q	+	1	0	TTC15	3384663	1.000000	0.71417	0.997000	0.53966	0.398000	0.30690	5.039000	0.64185	2.605000	0.88082	0.655000	0.94253	CAG		0.368	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		T	3405656	C	T	3405656	4	4	56	1	0	0	0	0	0	1	0	0	16722	479	17	3	1162	3	TTC15	2	3405656	Nonsense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		3405656	239793717	10	7412										
MEMO1	51072	broad.mit.edu	37	chr2	32093497	32093497	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gccagtttctacactggctcGactgggcataattcaaaaac	8	11	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:32093497G>A	ENST00000295065.5	-	9	1136	c.827C>T	c.(826-828)tCg>tTg	p.S276L	DPY30_ENST00000446765.1_5'UTR|MEMO1_ENST00000426310.2_Missense_Mutation_p.S253L|MEMO1_ENST00000490459.1_5'UTR|MEMO1_ENST00000379383.3_Missense_Mutation_p.S279L|MEMO1_ENST00000404530.1_Missense_Mutation_p.S276L	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	276					regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.S276L(1)		NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					ACACTGGCTCGACTGGGCATA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											20	19	19					2																	32093497		2202	4295	6497	31947001	SO:0001583	missense	51072			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.827C>T	2.37:g.32093497G>A	ENSP00000295065:p.Ser276Leu		31947001	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Missense_Mutation	SNP	ENST00000295065.5	37	CCDS1776.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273718	0.80580	.	.	ENSG00000162959	ENST00000295065;ENST00000379383;ENST00000404530;ENST00000426310	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.86522	0.5953	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.993;1.0	D	0.89610	0.3841	9	0.87932	D	0	0.0	18.7757	0.91911	0.0:0.0:1.0:0.0	.	253;276	Q9Y316-2;Q9Y316	.;MEMO1_HUMAN	L	276;279;276;253	.	ENSP00000295065:S276L	S	-	2	0	MEMO1	31947001	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.560000	0.98139	2.608000	0.88229	0.650000	0.86243	TCG		0.443	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955		A	32093497	G	A	32093497	3	1	56	1	0	0	0	0	1	0	0	0	9501	1059	37	1	70	1	MEMO1	2	32093497	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	28687841	32093497	211105876	11	7413										
MSH6	2956	broad.mit.edu	37	chr2	48028057	48028057	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttggtaggaaccgttaccagCtggaaattcctgagaatttc	10	8	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:48028057C>G	ENST00000234420.5	+	4	3087	c.2935C>G	c.(2935-2937)Ctg>Gtg	p.L979V	MSH6_ENST00000540021.1_Missense_Mutation_p.L849V|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.L677V	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	979					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)|p.L979V(1)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CCGTTACCAGCTGGAAATTCC	0.438			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	3	Whole gene deletion(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	2											51	51	51					2																	48028057		2203	4300	6503	47881561	SO:0001583	missense	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2935C>G	2.37:g.48028057C>G	ENSP00000234420:p.Leu979Val		47881561	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243482	0.39697	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.91577	-2.87;-2.87;-2.87	5.61	-0.99	0.10238	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.101506	0.64402	D	0.000007	D	0.90683	0.7077	M	0.75884	2.315	0.80722	D	1	P;P;P	0.51537	0.946;0.933;0.73	P;P;B	0.53689	0.732;0.718;0.327	D	0.86944	0.2081	10	0.54805	T	0.06	-9.8504	6.5288	0.22316	0.2119:0.4745:0.0:0.3135	.	849;979;979	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	V	979;977;849;677	ENSP00000234420:L979V;ENSP00000446475:L849V;ENSP00000438580:L677V	ENSP00000234420:L979V	L	+	1	2	MSH6	47881561	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	0.902000	0.28459	-0.112000	0.11979	-0.414000	0.06135	CTG		0.438	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48028057	C	G	48028057	3	3	56	1	0	0	0	0	1	0	0	0	9904	796	28	5	2949	5	MSH6	2	48028057	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	15934560	48028057	195171316	12	7414										
CCT4	10575	broad.mit.edu	37	chr2	62099690	62099690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agaaccacgaacaacaattgTaactgtttttccagggctgg	9	9	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:62099690T>C	ENST00000394440.3	-	11	1455	c.1159A>G	c.(1159-1161)Aca>Gca	p.T387A	CCT4_ENST00000461540.2_Intron|CCT4_ENST00000544079.1_Missense_Mutation_p.T357A|CCT4_ENST00000538252.1_Missense_Mutation_p.T331A|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544185.1_Missense_Mutation_p.T237A	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	387					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.T387A(1)		breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	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)			ACAACAATTGTAACTGTTTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											72	68	69					2																	62099690		2203	4300	6503	61953194	SO:0001583	missense	10575				CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.1159A>G	2.37:g.62099690T>C	ENSP00000377958:p.Thr387Ala		61953194	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	37	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818328	0.71028	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000544185;ENST00000538252	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	5.87	5.87	0.94306	.	0.041854	0.85682	D	0.000000	D	0.88680	0.6502	H	0.97291	3.975	0.54753	D	0.999989	B;B	0.18741	0.029;0.03	B;B	0.25759	0.063;0.046	D	0.87864	0.2666	10	0.87932	D	0	-15.0909	16.2496	0.82475	0.0:0.0:0.0:1.0	.	357;387	F5H5W3;P50991	.;TCPD_HUMAN	A	387;357;237;331	ENSP00000377958:T387A;ENSP00000443061:T357A;ENSP00000443451:T237A;ENSP00000442174:T331A	ENSP00000377958:T387A	T	-	1	0	CCT4	61953194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.881000	0.87252	2.371000	0.80710	0.533000	0.62120	ACA		0.428	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62099690	T	C	62099690	3	2	56	1	0	0	0	0	1	0	0	0	2961	1638	57	4	476	4	CCT4	2	62099690	Missense_Mutation	SNP	T	TCGA-AG-4001-01A-02W-1073-09	14071633	62099690	181099683	13	7415										
DYSF	8291	broad.mit.edu	37	chr2	71795413	71795413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agctacccaaggacagcttcCgcccctcggccggctggacc	11	18	0	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:71795413C>T	ENST00000258104.3	+	26	3032	c.2755C>T	c.(2755-2757)Cgc>Tgc	p.R919C	DYSF_ENST00000409651.1_Missense_Mutation_p.R951C|DYSF_ENST00000410041.1_Missense_Mutation_p.R937C|DYSF_ENST00000413539.2_Missense_Mutation_p.R950C|DYSF_ENST00000410020.3_Missense_Mutation_p.R937C|DYSF_ENST00000409366.1_Missense_Mutation_p.R920C|DYSF_ENST00000409582.3_Missense_Mutation_p.R936C|DYSF_ENST00000409744.1_Missense_Mutation_p.R906C|DYSF_ENST00000394120.2_Missense_Mutation_p.R920C|DYSF_ENST00000429174.2_Missense_Mutation_p.R919C|DYSF_ENST00000409762.1_Missense_Mutation_p.R936C	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	919					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R919C(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACAGCTTCCGCCCCTCGGC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											211	222	218					2																	71795413		2203	4300	6503	71648921	SO:0001583	missense	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2755C>T	2.37:g.71795413C>T	ENSP00000258104:p.Arg919Cys		71648921	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.186634	0.57909	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.83419	-1.71;-1.72;-1.72;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.72;-1.72	4.95	4.95	0.65309	Ferlin/Peroxisome membrane (1);	0.059627	0.64402	D	0.000002	D	0.85071	0.5613	L	0.38175	1.15	0.49582	D	0.999803	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.993;0.987;0.993;0.998;1.0;0.998;0.999;1.0;1.0;1.0	D;D;D;D;P;P;P;P;D;P;D;D;D;D	0.68943	0.961;0.961;0.961;0.961;0.827;0.781;0.827;0.827;0.961;0.862;0.921;0.947;0.961;0.915	D	0.85222	0.1027	10	0.52906	T	0.07	-21.8454	10.8993	0.47043	0.1877:0.8123:0.0:0.0	.	951;937;920;906;937;906;936;905;950;936;919;905;920;919	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	C	950;936;936;919;919;951;920;906;920;937;937	ENSP00000407046:R950C;ENSP00000387137:R936C;ENSP00000386547:R936C;ENSP00000398305:R919C;ENSP00000258104:R919C;ENSP00000386683:R951C;ENSP00000377678:R920C;ENSP00000386285:R906C;ENSP00000386512:R920C;ENSP00000386881:R937C;ENSP00000386617:R937C	ENSP00000258104:R919C	R	+	1	0	DYSF	71648921	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	2.998000	0.49465	2.298000	0.77334	0.462000	0.41574	CGC		0.632	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71795413	C	T	71795413	3	4	56	1	0	0	0	0	1	0	0	0	4870	652	23	1	3049	1	DYSF	2	71795413	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	9695723	71795413	171403960	14	7416										
SNRNP200	23020	broad.mit.edu	37	chr2	96944355	96944355	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agaggcgccacgtccatctcGtcctcgatgctgatgcactt	10	14	1	2	rs72937669	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:96944355G>A	ENST00000323853.5	-	38	5495	c.5418C>T	c.(5416-5418)gaC>gaT	p.D1806D	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1806					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.D1806D(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CGTCCATCTCGTCCTCGATGC	0.577													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		21332	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G		44,4362	46.7+/-81.2	0,44,2159	107	97	101		5418	-9.4	0.5	2	dbSNP_130	101	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SNRNP200	NM_014014.4		0,47,6456	AA,AG,GG		0.0349,0.9986,0.3614		1806/2137	96944355	47,12959	2203	4300	6503	96308082	SO:0001819	synonymous_variant	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5418C>T	2.37:g.96944355G>A			96308082	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																				0.577	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		A	96944355	G	A	96944355	2	1	56	1	0	0	0	0	0	0	0	1	14889	1136	40	1		1	SNRNP200	2	96944355	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	25148942	96944355	146255018	15	7417										
AFF3	3899	broad.mit.edu	37	chr2	100210168	100210168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cgatcctgcttagcccccgcGtgcggcgcttctcgcaggtc	12	17	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:100210168G>A	ENST00000409236.2	-	13	2067	c.1955C>T	c.(1954-1956)aCg>aTg	p.T652M	AFF3_ENST00000409579.1_Missense_Mutation_p.T677M|AFF3_ENST00000356421.2_Missense_Mutation_p.T677M|AFF3_ENST00000317233.4_Missense_Mutation_p.T652M			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	652					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.T677M(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TAGCCCCCGCGTGCGGCGCTT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											59	64	63					2																	100210168		2203	4299	6502	99576600	SO:0001583	missense	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1955C>T	2.37:g.100210168G>A	ENSP00000387207:p.Thr652Met		99576600	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113561	0.56398	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.17	4.28	0.50868	.	0.362216	0.26507	N	0.023987	T	0.71986	0.3405	L	0.59436	1.845	0.33979	D	0.647759	D;D;D	0.76494	0.999;0.999;0.988	D;D;P	0.65987	0.94;0.921;0.599	T	0.76987	-0.2755	10	0.33940	T	0.23	.	13.0792	0.59102	0.0775:0.0:0.9225:0.0	.	805;652;677	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	M	652;677;677;652;652;805;677	ENSP00000317421:T652M;ENSP00000348793:T677M;ENSP00000386834:T677M;ENSP00000387207:T652M	ENSP00000317421:T652M	T	-	2	0	AFF3	99576600	0.000000	0.05858	0.947000	0.38551	0.757000	0.42996	0.240000	0.18042	2.426000	0.82243	0.561000	0.74099	ACG		0.632	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		A	100210168	G	A	100210168	3	1	56	1	0	0	0	0	1	0	0	0	358	1145	40	1	1769	1	AFF3	2	100210168	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	3265813	100210168	142989205	16	7418										
PCDP1	200373	broad.mit.edu	37	chr2	120397422	120397422	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gttctctcctccctgccggaCccctccaagatggagaccac	8	18	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:120397422C>T	ENST00000413369.3	+	21	2286	c.2199C>T	c.(2197-2199)gaC>gaT	p.D733D	PCDP1_ENST00000602047.1_Silent_p.D447D	NM_001271049.1	NP_001257978												p.D447D(1)				Colorectal(110;0.196)					CCCTGCCGGACCCCTCCAAGA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	2											93	91	92					2																	120397422		2203	4300	6503	120113892	SO:0001819	synonymous_variant	200373																														ENST00000413369.3:c.2199C>T	2.37:g.120397422C>T			120113892		Silent	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	C	3.201	-0.163689	0.06502	.	.	ENSG00000163075	ENST00000443972;ENST00000434869	.	.	.	5.07	-1.49	0.08718	.	.	.	.	.	T	0.18509	0.0444	.	.	.	0.19945	N	0.999945	.	.	.	.	.	.	T	0.23655	-1.0182	4	.	.	.	-9.8575	0.9151	0.01303	0.2991:0.295:0.2345:0.1714	.	.	.	.	I	292;41	.	.	T	+	2	0	AC069154.2	120113892	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	-0.280000	0.08468	-0.217000	0.10033	0.655000	0.94253	ACC		0.493	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			T	120397422	C	T	120397422	2	4	56	1	0	0	0	0	0	0	0	1	11603	506	18	3		3	PCDP1	2	120397422	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	20187254	120397422	122801951	17	7419										
LRP1B	53353	broad.mit.edu	37	chr2	141812827	141812827	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	acttcacatgcatggcttctGactacaacaaataaaaaaca	4	10	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:141812827G>T	ENST00000389484.3	-	10	2381	c.1410C>A	c.(1408-1410)gtC>gtA	p.V470V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	470					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.V470V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CATGGCTTCTGACTACAACAA	0.403										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - coding silent(1)	large_intestine(1)	2											75	68	71					2																	141812827		2203	4300	6503	141529297	SO:0001630	splice_region_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1409-1C>A	2.37:g.141812827G>T			141529297	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Silent	T	141812827	G	T	141812827	5	4	56	1	0	0	0	0	0	0	1	0	8984	1304	45	2	12717	2	LRP1B	2	141812827	Splice_Site	SNP	G	TCGA-AG-4001-01A-02W-1073-09	21415405	141812827	101386546	18	7420										
XIRP2	129446	broad.mit.edu	37	chr2	168100236	168100236	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tggatgtttgaaacacagccGttggacacaattaacaaaga	9	7	0	2	rs191792139		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:168100236G>A	ENST00000409195.1	+	9	2423	c.2334G>A	c.(2332-2334)ccG>ccA	p.P778P	XIRP2_ENST00000295237.9_Silent_p.P778P|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Silent_p.P556P|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	603					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.P778P(2)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAACACAGCCGTTGGACACAA	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		19011	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	2						G	,,,,	2,3718		0,2,1858	69	65	66		,,1668,,2334	-4.1	0.2	2		66	0,8194		0,0,4097	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	0,2,5955	AA,AG,GG		0.0,0.0538,0.0168	,,,,	,,556/3328,,778/3550	168100236	2,11912	1860	4097	5957	167808482	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2334G>A	2.37:g.168100236G>A			167808482	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																				0.413	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168100236	G	A	168100236	2	1	56	1	0	0	0	0	0	0	0	1	17470	1132	40	1		1	XIRP2	2	168100236	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	26287409	168100236	75099137	19	7421										
ABCB11	8647	broad.mit.edu	37	chr2	169851948	169851948	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ctcctaaagtaaaattttctCattttctgtatctgacgagc	5	9	3	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:169851948C>T	ENST00000263817.6	-	7	646	c.522G>A	c.(520-522)atG>atA	p.M174I		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	174	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.M174I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AAAATTTTCTCATTTTCTGTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	80	82					2																	169851948		1836	4089	5925	169560194	SO:0001583	missense	8647			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.522G>A	2.37:g.169851948C>T	ENSP00000263817:p.Met174Ile		169560194	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	C	2.252	-0.371380	0.05034	.	.	ENSG00000073734	ENST00000263817	D	0.86627	-2.15	4.94	2.85	0.33270	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.089051	0.85682	N	0.000000	T	0.52500	0.1738	N	0.00453	-1.485	0.35297	D	0.782683	B	0.02656	0.0	B	0.04013	0.001	T	0.57934	-0.7725	10	0.02654	T	1	-13.7667	3.825	0.08851	0.0:0.3706:0.2856:0.3437	.	174	O95342	ABCBB_HUMAN	I	174	ENSP00000263817:M174I	ENSP00000263817:M174I	M	-	3	0	ABCB11	169560194	0.876000	0.30132	1.000000	0.80357	0.933000	0.57130	-0.133000	0.10451	1.066000	0.40716	0.655000	0.94253	ATG		0.368	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		T	169851948	C	T	169851948	3	4	56	1	0	0	0	0	1	0	0	0	42	826	29	3	3531	3	ABCB11	2	169851948	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	1751712	169851948	73347425	20	7422										
TTN	7273	broad.mit.edu	37	chr2	179396278	179396278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cgttgcatagtcagaagcttCgcccttgtagttggtgcaca	11	10	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:179396278C>T	ENST00000591111.1	-	308	100365	c.100141G>A	c.(100141-100143)Gaa>Aaa	p.E33381K	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E32454K|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E26082K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E35022K|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E26149K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E25957K|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591867.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33381	Ig-like 146.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E32452K(1)|p.E26082K(1)|p.E25957K(1)|p.E26149K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGAAGCTTCGCCCTTGTAG	0.507																																																4	Substitution - Missense(4)	large_intestine(4)	2											117	117	117					2																	179396278		2017	4188	6205	179104524	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100141G>A	2.37:g.179396278C>T	ENSP00000465570:p.Glu33381Lys		179104524	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	23.5	4.427921	0.83667	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.56	5.56	0.83823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78604	0.4309	M	0.61703	1.905	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.79841	-0.1633	9	0.87932	D	0	.	19.5233	0.95194	0.0:1.0:0.0:0.0	.	25957;26082;26149;33381	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	32454;25957;26149;26082;25954	ENSP00000343764:E32454K;ENSP00000434586:E25957K;ENSP00000340554:E26149K;ENSP00000352154:E26082K	ENSP00000340554:E26149K	E	-	1	0	TTN	179104524	1.000000	0.71417	0.936000	0.37596	0.607000	0.37147	7.810000	0.86072	2.615000	0.88500	0.650000	0.86243	GAA		0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179396278	C	T	179396278	3	4	56	1	0	0	0	0	1	0	0	0	16775	893	31	1	2935	1	TTN	2	179396278	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	9544330	179396278	63803095	21	7423										
ZNF804A	91752	broad.mit.edu	37	chr2	185800807	185800807	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gcgtccgtgaagctagagtcCtcagctgcagccttctctga	11	13	2	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:185800807C>A	ENST00000302277.6	+	4	1278	c.684C>A	c.(682-684)tcC>tcA	p.S228S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	228							metal ion binding (GO:0046872)	p.S228S(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AGCTAGAGTCCTCAGCTGCAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	2											74	73	74					2																	185800807		2203	4299	6502	185509052	SO:0001819	synonymous_variant	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.684C>A	2.37:g.185800807C>A			185509052	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																				0.438	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185800807	C	A	185800807	2	1	56	1	0	0	0	0	0	0	0	1	18209	668	24	2		2	ZNF804A	2	185800807	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	6404529	185800807	57398566	22	7424										
SP110	3431	broad.mit.edu	37	chr2	231050789	231050789	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tctgagttccaggttgagtcGtctttcctttgagtcacctt	9	10	3	3	rs115361843	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr2:231050789G>A	ENST00000358662.4	-	11	1278	c.1200C>T	c.(1198-1200)gaC>gaT	p.D400D	SP110_ENST00000392048.3_Silent_p.D398D|SP110_ENST00000540870.1_Silent_p.D406D|SP110_ENST00000338556.3_Silent_p.D102D|SP110_ENST00000258382.5_Silent_p.D400D|SP110_ENST00000258381.6_Silent_p.D400D	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	400					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.D400D(1)		breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		AGGTTGAGTCGTCTTTCCTTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G	,,,	0,4406		0,0,2203	197	168	178		1218,1200,1200,1200	-5.5	0	2	dbSNP_132	178	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	,,,	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	,,,	406/556,400/690,400/550,400/714	231050789	7,12999	2203	4300	6503	230759033	SO:0001819	synonymous_variant	3431			L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1200C>T	2.37:g.231050789G>A			230759033	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	37	CCDS2474.1																																																																																				0.473	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		A	231050789	G	A	231050789	2	1	56	1	0	0	0	0	0	0	0	1	14998	1136	40	1		1	SP110	2	231050789	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	45249982	231050789	12148584	23	7425										
ZCWPW2	152098	broad.mit.edu	37	chr3	28454693	28454693	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tttgaaatggagattgttatCaagtgaggattcagccaagg	12	4	2	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:28454693C>T	ENST00000383768.2	+	3	322	c.134C>T	c.(133-135)tCa>tTa	p.S45L	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.S45L			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	45							zinc ion binding (GO:0008270)	p.S45L(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AGATTGTTATCAAGTGAGGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	131	133					3																	28454693		2203	4300	6503	28429697	SO:0001583	missense	152098			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.134C>T	3.37:g.28454693C>T	ENSP00000373278:p.Ser45Leu		28429697		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.751436	0.69533	.	.	ENSG00000206559	ENST00000420223;ENST00000383768;ENST00000421010	T;T	0.32023	1.47;1.47	5.46	4.58	0.56647	Zinc finger, CW-type (2);	0.327135	0.22381	N	0.060811	T	0.27313	0.0670	L	0.45285	1.41	0.29178	N	0.876667	B	0.20052	0.041	B	0.23419	0.046	T	0.18871	-1.0323	10	0.52906	T	0.07	-3.1557	10.1793	0.42957	0.0:0.9074:0.0:0.0926	.	45	Q504Y3	ZCPW2_HUMAN	L	45	ENSP00000373278:S45L;ENSP00000412386:S45L	ENSP00000373278:S45L	S	+	2	0	ZCWPW2	28429697	1.000000	0.71417	0.997000	0.53966	0.924000	0.55760	1.931000	0.40134	1.304000	0.44892	0.591000	0.81541	TCA		0.353	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		T	28454693	C	T	28454693	3	4	56	1	0	0	0	0	1	0	0	0	17637	838	29	3	136	3	ZCWPW2	3	28454693	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		28454693	169567737	24	7426										
CLASP2	23122	broad.mit.edu	37	chr3	33725930	33725930	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ataaatctccactatagccaAtattgcagcatctctcacct	3	13	3	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:33725930A>G	ENST00000468888.2	-	6	611	c.565T>C	c.(565-567)Ttg>Ctg	p.L189L	CLASP2_ENST00000399362.4_Silent_p.L189L|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000359576.5_Silent_p.L189L			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1242					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.L189L(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						ACTATAGCCAATATTGCAGCA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	3											136	134	134					3																	33725930		1814	4082	5896	33700934	SO:0001819	synonymous_variant	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.565T>C	3.37:g.33725930A>G			33700934	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																					0.338	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		G	33725930	A	G	33725930	2	3	56	1	0	0	0	0	0	0	0	1	3461	98	4	4		4	CLASP2	3	33725930	Silent	SNP	A	TCGA-AG-4001-01A-02W-1073-09	5271237	33725930	164296500	25	7427										
KIF9	64147	broad.mit.edu	37	chr3	47282501	47282501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tggtttggagggtggggtgtCgggccttgagatgaaaaggt	20	3	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:47282501C>T	ENST00000265529.3	-	18	2394	c.1714G>A	c.(1714-1716)Gac>Aac	p.D572N	KIF9_ENST00000487440.1_5'UTR|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000335044.2_Missense_Mutation_p.D572N|KIF9_ENST00000444589.2_Missense_Mutation_p.D507N|KIF9_ENST00000452770.2_Missense_Mutation_p.D572N|KIF9_ENST00000352910.4_Missense_Mutation_p.D414N			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	572					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)	p.D572N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		GGTGGGGTGTCGGGCCTTGAG	0.478																																					Colon(44;962 1147 15977 24541)											1	Substitution - Missense(1)	large_intestine(1)	3											72	75	74					3																	47282501		2203	4300	6503	47257505	SO:0001583	missense	64147			AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"Kinesins"	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1714G>A	3.37:g.47282501C>T	ENSP00000265529:p.Asp572Asn		47257505	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.806488	0.31961	.	.	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.84	2.15	0.27550	.	0.192471	0.56097	D	0.000033	T	0.22666	0.0547	N	0.14661	0.345	0.29044	N	0.884899	B;B	0.13145	0.001;0.007	B;B	0.04013	0.001;0.001	T	0.12243	-1.0555	10	0.32370	T	0.25	.	8.536	0.33364	0.0:0.2412:0.0:0.7588	.	507;572	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	N	572;572;507;572;414	ENSP00000333942:D572N;ENSP00000265529:D572N;ENSP00000414987:D507N;ENSP00000391100:D572N;ENSP00000292334:D414N	ENSP00000265529:D572N	D	-	1	0	KIF9	47257505	1.000000	0.71417	0.983000	0.44433	0.360000	0.29518	1.348000	0.33987	0.487000	0.27698	-0.302000	0.09304	GAC		0.478	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2			T	47282501	C	T	47282501	3	4	56	1	0	0	0	0	1	0	0	0	8331	884	31	1	678	1	KIF9	3	47282501	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	13556571	47282501	150739929	26	7428										
CNTN3	5067	broad.mit.edu	37	chr3	74474046	74474046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gcacaactccctggccttcaCgcacagacactgtactcctc	6	18	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:74474046C>T	ENST00000263665.6	-	4	431	c.404G>A	c.(403-405)cGt>cAt	p.R135H		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	135	Ig-like C2-type 2.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R135H(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGGCCTTCACGCACAGACAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											85	76	79					3																	74474046		2203	4300	6503	74556736	SO:0001583	missense	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.404G>A	3.37:g.74474046C>T	ENSP00000263665:p.Arg135His		74556736	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.384232	0.82792	.	.	ENSG00000113805	ENST00000263665	T	0.13307	2.6	5.18	5.18	0.71444	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.21387	0.0515	M	0.77103	2.36	0.80722	D	1	P	0.37525	0.598	B	0.36534	0.227	T	0.02214	-1.1194	10	0.39692	T	0.17	.	16.5611	0.84566	0.0:1.0:0.0:0.0	.	135	Q9P232	CNTN3_HUMAN	H	135	ENSP00000263665:R135H	ENSP00000263665:R135H	R	-	2	0	CNTN3	74556736	1.000000	0.71417	0.990000	0.47175	0.959000	0.62525	6.814000	0.75236	2.574000	0.86865	0.549000	0.68633	CGT		0.398	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		T	74474046	C	T	74474046	3	4	56	1	0	0	0	0	1	0	0	0	3648	536	19	1	2758	1	CNTN3	3	74474046	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	27191545	74474046	123548384	27	7429										
MYH15	22989	broad.mit.edu	37	chr3	108248110	108248110	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatgttgggagtccactcacCatgatctttttggtaagatg	10	7	2	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:108248110C>T	ENST00000273353.3	-	1	59	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.M1I(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GTCCACTCACCATGATCTTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	80	81					3																	108248110		1856	4088	5944	109730800	SO:0001630	splice_region_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3+1G>A	3.37:g.108248110C>T			109730800		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416108	0.42918	.	.	ENSG00000144821	ENST00000273353	D	0.84873	-1.91	2.91	-3.98	0.04082	.	.	.	.	.	T	0.67664	0.2917	.	.	.	0.19575	N	0.999966	B	0.02656	0.0	B	0.01281	0.0	T	0.50792	-0.8786	7	.	.	.	.	4.4316	0.11531	0.0:0.4011:0.1876:0.4113	.	1	Q9Y2K3	MYH15_HUMAN	I	1	ENSP00000273353:M1I	.	M	-	3	0	MYH15	109730800	0.000000	0.05858	0.000000	0.03702	0.913000	0.54294	-0.238000	0.08977	-0.715000	0.04968	-0.369000	0.07265	ATG		0.358	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation	T	108248110	C	T	108248110	5	4	56	1	0	0	0	0	0	0	1	0	10064	608	21	3	6005	3	MYH15	3	108248110	Splice_Site	SNP	C	TCGA-AG-4001-01A-02W-1073-09	33774064	108248110	89774320	28	7430										
IQCB1	9657	broad.mit.edu	37	chr3	121489301	121489301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ctccaagcttcttccaccagGgtgcttgtatgtgcttcagg	10	12	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:121489301G>A	ENST00000310864.6	-	15	1902	c.1688C>T	c.(1687-1689)cCc>cTc	p.P563L	IQCB1_ENST00000349820.6_Missense_Mutation_p.P430L	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	563					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)	p.P563L(1)		NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		CTTCCACCAGGGTGCTTGTAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											172	166	168					3																	121489301		2203	4300	6503	122971991	SO:0001583	missense	9657			D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1688C>T	3.37:g.121489301G>A	ENSP00000311505:p.Pro563Leu		122971991	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253250	0.80135	.	.	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.80653	-1.4;-1.4	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.88288	0.6396	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.986	D;P	0.83275	0.996;0.73	D	0.88696	0.3212	10	0.87932	D	0	-8.322	14.7509	0.69525	0.0:0.0:1.0:0.0	.	563;430	Q15051;Q15051-2	IQCB1_HUMAN;.	L	563;430	ENSP00000311505:P563L;ENSP00000323756:P430L	ENSP00000311505:P563L	P	-	2	0	IQCB1	122971991	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.523000	0.60545	2.857000	0.98124	0.650000	0.86243	CCC		0.463	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		A	121489301	G	A	121489301	3	1	56	1	0	0	0	0	1	0	0	0	7824	1232	43	3	112	3	IQCB1	3	121489301	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	13241191	121489301	76533129	29	7431										
ALDH1L1	10840	broad.mit.edu	37	chr3	125872377	125872377	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atgggcaaagcgtctccctcGggcaccaggcctgaagtgtt	13	12	1	1	rs149145858		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:125872377G>A	ENST00000393434.2	-	7	1117	c.768C>T	c.(766-768)ccC>ccT	p.P256P	ALDH1L1_ENST00000472186.1_Silent_p.P256P|ALDH1L1_ENST00000452905.2_Silent_p.P155P|ALDH1L1_ENST00000273450.3_Silent_p.P266P|ALDH1L1_ENST00000413612.1_5'UTR|ALDH1L1_ENST00000455064.2_Silent_p.P81P|ALDH1L1_ENST00000393431.2_Silent_p.P256P	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	256					10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.P256P(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CGTCTCCCTCGGGCACCAGGC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		0,4406		0,0,2203	97	96	97		768	-8.5	0.6	3	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ALDH1L1	NM_012190.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		256/903	125872377	1,13005	2203	4300	6503	127355067	SO:0001819	synonymous_variant	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.768C>T	3.37:g.125872377G>A			127355067	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																				0.537	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		A	125872377	G	A	125872377	2	1	56	1	0	0	0	0	0	0	0	1	494	1103	39	1		1	ALDH1L1	3	125872377	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	4383076	125872377	72150053	30	7432										
MLF1	4291	broad.mit.edu	37	chr3	158317840	158317840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agcaatgagagattctgacaGtggactagaaaaaatggcta	11	5	1	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:158317840G>A	ENST00000355893.5	+	5	584	c.446G>A	c.(445-447)aGt>aAt	p.S149N	MLF1_ENST00000469452.1_Missense_Mutation_p.S81N|MLF1_ENST00000359117.5_Missense_Mutation_p.S124N|MLF1_ENST00000484955.1_Missense_Mutation_p.S124N|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000392822.3_Missense_Mutation_p.S180N|MLF1_ENST00000471745.1_Missense_Mutation_p.S139N|MLF1_ENST00000478894.2_Missense_Mutation_p.S139N|MLF1_ENST00000482628.1_Missense_Mutation_p.S124N	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	149					cell cycle arrest (GO:0007050)|myeloid progenitor cell differentiation (GO:0002318)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)	p.S180N(1)		large_intestine(3)	3		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			GATTCTGACAGTGGACTAGAA	0.338			T	NPM1	AML																																		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	1	Substitution - Missense(1)	large_intestine(1)	3											82	89	87					3																	158317840		2203	4300	6503	159800534	SO:0001583	missense	4291			L49054	CCDS3182.1, CCDS46945.1, CCDS56286.1, CCDS56287.1, CCDS56288.1	3q25	2008-07-18			ENSG00000178053	ENSG00000178053			7125	protein-coding gene	gene with protein product	"myeloid leukemia factor 1 variant 1", "myeloid leukemia factor 1 variant 2", "myeloid leukemia factor 1 variant 3"	601402				8570204	Standard	NM_022443		Approved		uc003fcb.3	P58340	OTTHUMG00000158775	ENST00000355893.5:c.446G>A	3.37:g.158317840G>A	ENSP00000348157:p.Ser149Asn		159800534	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Missense_Mutation	SNP	ENST00000355893.5	37	CCDS3182.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.576760	0.86645	.	.	ENSG00000178053	ENST00000491767;ENST00000355893;ENST00000484955;ENST00000359117;ENST00000498592;ENST00000477042;ENST00000471745;ENST00000469452;ENST00000482628;ENST00000478894;ENST00000392822;ENST00000466246	T;T;T;T;T;T;T;T;T;T	0.52057	0.79;0.68;0.71;0.71;0.75;0.77;0.76;0.71;0.77;0.74	6.06	5.2	0.72013	.	0.126819	0.64402	D	0.000001	T	0.65831	0.2729	L	0.61036	1.89	0.46241	D	0.998948	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.981;0.993;0.99	T	0.67515	-0.5651	10	0.51188	T	0.08	-11.0103	15.3434	0.74314	0.0665:0.0:0.9335:0.0	.	81;180;149	Q2TLE5;Q8N8F8;P58340	.;.;MLF1_HUMAN	N	75;149;124;124;104;139;139;81;124;139;180;164	ENSP00000420410:S75N;ENSP00000348157:S149N;ENSP00000417835:S124N;ENSP00000352025:S124N;ENSP00000419636:S104N;ENSP00000420134:S139N;ENSP00000418595:S81N;ENSP00000417141:S124N;ENSP00000417777:S139N;ENSP00000376568:S180N	ENSP00000348157:S149N	S	+	2	0	MLF1	159800534	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.303000	0.65738	1.582000	0.49881	0.650000	0.86243	AGT		0.338	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443		A	158317840	G	A	158317840	3	1	56	1	0	0	0	0	1	0	0	0	9644	1029	36	3	464	3	MLF1	3	158317840	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	32445463	158317840	39704590	31	7433										
IFT80	57560	broad.mit.edu	37	chr3	159996992	159996992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtaaattaccttaacaaagcGacaaagtctcacagcatctt	5	10	2	0	rs186192085	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr3:159996992G>A	ENST00000326448.7	-	16	2257	c.1825C>T	c.(1825-1827)Cgc>Tgc	p.R609C	IFT80_ENST00000483465.1_Missense_Mutation_p.R472C|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R780C|IFT80_ENST00000496589.1_Missense_Mutation_p.R472C	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	609					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)		p.R609C(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTAACAAAGCGACAAAGTCTC	0.353													G|||	2	0.000399361	0	0.0014	5008	,	,		17885	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											81	78	79					3																	159996992		2203	4300	6503	161479686	SO:0001583	missense	57560			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1825C>T	3.37:g.159996992G>A	ENSP00000312778:p.Arg609Cys		161479686	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	21.5	4.162685	0.78226	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	D;D;D	0.82984	-1.67;-1.67;-1.67	6.16	6.16	0.99307	.	0.000000	0.64402	U	0.000013	D	0.84977	0.5592	M	0.88906	2.99	0.80722	D	1	B	0.29955	0.263	B	0.20767	0.031	D	0.84303	0.0506	10	0.87932	D	0	-14.0768	14.6998	0.69147	0.0:0.0:0.7448:0.2551	.	609	Q9P2H3	IFT80_HUMAN	C	609;472;472	ENSP00000312778:R609C;ENSP00000418196:R472C;ENSP00000420646:R472C	ENSP00000312778:R609C	R	-	1	0	IFT80	161479686	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.225000	0.58600	2.937000	0.99478	0.650000	0.86243	CGC		0.353	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		A	159996992	G	A	159996992	3	1	56	1	0	0	0	0	1	0	0	0	7585	1058	37	1	528	1	IFT80	3	159996992	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	1679152	159996992	38025438	32	7434										
TMPRSS11F	389208	broad.mit.edu	37	chr4	68934470	68934470	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atagctgtttcccttccttgGacaattctttgagtagaaga	8	8	1	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:68934470G>C	ENST00000356291.2	-	7	680	c.621C>G	c.(619-621)gtC>gtG	p.V207V	UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	207	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.V207V(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						CCCTTCCTTGGACAATTCTTT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	4											117	105	109					4																	68934470		2203	4300	6503	68617065	SO:0001819	synonymous_variant	389208			AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.621C>G	4.37:g.68934470G>C			68617065	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																				0.478	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		C	68934470	G	C	68934470	2	2	56	1	0	0	0	0	0	0	0	1	16282	1161	41	5		5	TMPRSS11F	4	68934470	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09		68934470	122219806	33	7435										
AFM	173	broad.mit.edu	37	chr4	74357723	74357723	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gatgatagaccaaaggatttAtctctaagagaaggaaaatt	9	4	1	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:74357723A>C	ENST00000226355.3	+	8	1071	c.978A>C	c.(976-978)ttA>ttC	p.L326F		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	326	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)	p.L326F(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAAAGGATTTATCTCTAAGAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											81	84	83					4																	74357723		2203	4300	6503	74576587	SO:0001583	missense	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.978A>C	4.37:g.74357723A>C	ENSP00000226355:p.Leu326Phe		74576587	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808253	0.50421	.	.	ENSG00000079557	ENST00000226355	T	0.75589	-0.95	4.54	1.94	0.25998	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.333399	0.24456	N	0.038379	D	0.82879	0.5133	M	0.87827	2.91	0.09310	N	1	D	0.69078	0.997	D	0.65874	0.939	T	0.71892	-0.4455	10	0.87932	D	0	.	3.8629	0.09004	0.7108:0.0:0.1047:0.1845	.	326	P43652	AFAM_HUMAN	F	326	ENSP00000226355:L326F	ENSP00000226355:L326F	L	+	3	2	AFM	74576587	0.172000	0.23043	0.205000	0.23548	0.954000	0.61252	0.645000	0.24782	0.626000	0.30322	0.248000	0.18094	TTA		0.373	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			C	74357723	A	C	74357723	3	2	56	1	0	0	0	0	1	0	0	0	361	446	16	4	1008	4	AFM	4	74357723	Missense_Mutation	SNP	A	TCGA-AG-4001-01A-02W-1073-09	5423253	74357723	116796553	34	7436										
FAT4	79633	broad.mit.edu	37	chr4	126373648	126373648	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aagattggctgtgagctccgTattaaaaagccgtgagagtc	12	7	0	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:126373648T>A	ENST00000394329.3	+	9	11490	c.11477T>A	c.(11476-11478)gTa>gAa	p.V3826E	FAT4_ENST00000335110.5_Missense_Mutation_p.V2124E	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3826	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V3826E(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GTGAGCTCCGTATTAAAAAGC	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	4											86	86	86					4																	126373648		2203	4300	6503	126593098	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.11477T>A	4.37:g.126373648T>A	ENSP00000377862:p.Val3826Glu		126593098	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.659225	0.00772	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.74526	-0.71;-0.85	5.47	-10.9	0.00192	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	2.042920	0.04412	N	0.366239	T	0.35740	0.0942	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.29640	-1.0005	10	0.02654	T	1	.	6.558	0.22471	0.164:0.526:0.0772:0.2329	.	2124;3826;3826	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	E	3826;2124	ENSP00000377862:V3826E;ENSP00000335169:V2124E	ENSP00000335169:V2124E	V	+	2	0	FAT4	126593098	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.079000	0.11357	-2.310000	0.00650	-0.379000	0.06801	GTA		0.502	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126373648	T	A	126373648	3	1	56	1	0	0	0	0	1	0	0	0	5711	1638	57	5	11511	5	FAT4	4	126373648	Missense_Mutation	SNP	T	TCGA-AG-4001-01A-02W-1073-09	52015925	126373648	64780628	35	7437										
NR3C2	4306	broad.mit.edu	37	chr4	149357481	149357481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agggcttttaacaacggcgcGcatgacgccaccattcacgg	11	13	1	1	rs375487193		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:149357481G>A	ENST00000358102.3	-	2	894	c.532C>T	c.(532-534)Cgc>Tgc	p.R178C	NR3C2_ENST00000512865.1_Missense_Mutation_p.R178C|NR3C2_ENST00000355292.3_Missense_Mutation_p.R178C|NR3C2_ENST00000344721.4_Missense_Mutation_p.R178C|NR3C2_ENST00000511528.1_Missense_Mutation_p.R178C	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	178	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R178C(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAACGGCGCGCATGACGCCA	0.502																																					Melanoma(27;428 957 40335 51025 51111)											1	Substitution - Missense(1)	large_intestine(1)	4						G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	106	106	106		532,532	4.5	1	4		106	0,8600		0,0,4300	no	missense,missense	NR3C2	NM_000901.4,NM_001166104.1	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	178/985,178/868	149357481	1,13005	2203	4300	6503	149576931	SO:0001583	missense	4306			M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.532C>T	4.37:g.149357481G>A	ENSP00000350815:p.Arg178Cys		149576931	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	9.405	1.078946	0.20227	2.27E-4	0.0	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.2;-2.21;-2.62	5.38	4.54	0.55810	.	0.688531	0.14729	N	0.301876	D	0.85737	0.5766	L	0.36672	1.1	0.42829	D	0.994014	B;D	0.61080	0.003;0.989	B;B	0.44163	0.001;0.443	T	0.82165	-0.0592	9	.	.	.	.	9.1999	0.37251	0.0738:0.0:0.7821:0.1441	.	178;178	B0ZBF5;B0ZBF6	.;.	C	178	ENSP00000341390:R178C;ENSP00000347441:R178C;ENSP00000350815:R178C;ENSP00000423510:R178C;ENSP00000343907:R178C;ENSP00000421481:R178C	.	R	-	1	0	NR3C2	149576931	1.000000	0.71417	0.964000	0.40570	0.154000	0.21943	4.934000	0.63491	1.265000	0.44215	0.467000	0.42956	CGC		0.502	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149357481	G	A	149357481	3	1	56	1	0	0	0	0	1	0	0	0	10662	1087	38	1	2454	1	NR3C2	4	149357481	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	22983833	149357481	41796795	36	7438										
GLRB	2743	broad.mit.edu	37	chr4	158091817	158091817	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aagcgaattgatctttatgcAagagcattgtttcctttctg	8	7	2	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:158091817A>T	ENST00000264428.4	+	10	1701	c.1431A>T	c.(1429-1431)gcA>gcT	p.A477A	GLRB_ENST00000509282.1_Silent_p.A477A|GLRB_ENST00000541722.1_3'UTR|GLRB_ENST00000512619.1_3'UTR	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	477					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)	p.A477A(1)		central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	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)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	ATCTTTATGCAAGAGCATTGT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	4											116	117	117					4																	158091817		2203	4300	6503	158311267	SO:0001819	synonymous_variant	2743			U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.1431A>T	4.37:g.158091817A>T			158311267	A8K3K2|D3DP23|F5GWE1	Silent	SNP	ENST00000264428.4	37	CCDS3796.1																																																																																				0.348	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		T	158091817	A	T	158091817	2	4	56	1	0	0	0	0	0	0	0	1	6478	117	5	5		5	GLRB	4	158091817	Silent	SNP	A	TCGA-AG-4001-01A-02W-1073-09	8734336	158091817	33062459	37	7439										
FSTL5	56884	broad.mit.edu	37	chr4	162376202	162376202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggtgggaatgaaaaaatcatCcactctgtcaaattgctttc	8	8	3	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:162376202C>T	ENST00000306100.5	-	15	2231	c.1795G>A	c.(1795-1797)Gat>Aat	p.D599N	FSTL5_ENST00000379164.4_Missense_Mutation_p.D598N|FSTL5_ENST00000427802.2_Missense_Mutation_p.D589N|FSTL5_ENST00000536695.1_Missense_Mutation_p.D598N	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	599						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D599fs*14(1)|p.D599N(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		AAAAAATCATCCACTCTGTCA	0.413																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4											171	127	142					4																	162376202		2203	4300	6503	162595652	SO:0001583	missense	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1795G>A	4.37:g.162376202C>T	ENSP00000305334:p.Asp599Asn		162595652	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.870929	0.91587	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);	0.094002	0.64402	D	0.000001	T	0.43033	0.1229	M	0.72118	2.19	0.80722	D	1	P;P;P	0.46395	0.877;0.799;0.799	P;B;B	0.45829	0.494;0.275;0.343	T	0.47497	-0.9113	10	0.72032	D	0.01	.	18.1706	0.89744	0.0:1.0:0.0:0.0	.	589;598;599	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	N	599;598;589;598	ENSP00000305334:D599N;ENSP00000368462:D598N;ENSP00000389270:D589N;ENSP00000440409:D598N	ENSP00000305334:D599N	D	-	1	0	FSTL5	162595652	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	7.231000	0.78106	2.606000	0.88127	0.655000	0.94253	GAT		0.413	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162376202	C	T	162376202	3	4	56	1	0	0	0	0	1	0	0	0	6099	855	30	3	756	3	FSTL5	4	162376202	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	4284385	162376202	28778074	38	7440										
SPATA4	132851	broad.mit.edu	37	chr4	177109270	177109270	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agcaaagagttaaaacttacGtaaaacagggacaactcttc	7	8	1	1	rs142260014		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr4:177109270G>A	ENST00000280191.2	-	5	913	c.805C>T	c.(805-807)Cca>Tca	p.P269S	SPATA4_ENST00000515234.1_Splice_Site_p.P96S	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	269						cytoplasm (GO:0005737)		p.P269S(1)		NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TAAAACTTACGTAAAACAGGG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	58	63	61		805	-8.8	0	4	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	SPATA4	NM_144644.2	74	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	269/306	177109270	2,13004	2203	4300	6503	177346264	SO:0001630	splice_region_variant	132851			AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.805+1C>T	4.37:g.177109270G>A			177346264	Q8NCS5|Q8WW15	Missense_Mutation	SNP	ENST00000280191.2	37	CCDS3826.1	.	.	.	.	.	.	.	.	.	.	G	3.674	-0.066955	0.07273	2.27E-4	1.16E-4	ENSG00000150628	ENST00000280191;ENST00000515234	T	0.41400	1.0	4.42	-8.84	0.00803	.	4.529290	0.00597	N	0.000365	T	0.19685	0.0473	N	0.14661	0.345	0.09310	N	0.999997	B	0.10296	0.003	B	0.04013	0.001	T	0.16660	-1.0395	9	.	.	.	.	2.5489	0.04743	0.1083:0.3732:0.1981:0.3204	.	269	Q8NEY3	SPAT4_HUMAN	S	269;96	ENSP00000280191:P269S	.	P	-	1	0	SPATA4	177346264	0.000000	0.05858	0.000000	0.03702	0.186000	0.23388	-4.293000	0.00258	-4.385000	0.00052	-0.479000	0.04858	CCA		0.328	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	Missense_Mutation	A	177109270	G	A	177109270	5	1	56	1	0	0	0	0	0	0	1	0	15049	1159	40	1	120	1	SPATA4	4	177109270	Splice_Site	SNP	G	TCGA-AG-4001-01A-02W-1073-09	14733068	177109270	14045006	39	7441										
SPEF2	79925	broad.mit.edu	37	chr5	35641565	35641565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	caaacttaataatttttctcGcttggagccaacacttaacc	4	11	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr5:35641565G>A	ENST00000356031.3	+	3	348	c.194G>A	c.(193-195)cGc>cAc	p.R65H	SPEF2_ENST00000440995.2_Missense_Mutation_p.R65H|SPEF2_ENST00000509059.1_Missense_Mutation_p.R65H|SPEF2_ENST00000282469.6_Missense_Mutation_p.R65H	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	65	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)		p.R65H(2)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AATTTTTCTCGCTTGGAGCCA	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	5											83	86	85					5																	35641565		2203	4300	6503	35677322	SO:0001583	missense	79925			AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.194G>A	5.37:g.35641565G>A	ENSP00000348314:p.Arg65His		35677322	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761602	0.89932	.	.	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000510777;ENST00000440995	T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88	5.93	5.93	0.95920	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.52789	0.1756	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.987	T	0.50947	-0.8767	10	0.59425	D	0.04	.	16.6094	0.84858	0.0:0.0:0.8694:0.1306	.	65;65;65	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	H	65	ENSP00000282469:R65H;ENSP00000348314:R65H;ENSP00000421593:R65H;ENSP00000426259:R65H;ENSP00000412125:R65H	ENSP00000282469:R65H	R	+	2	0	SPEF2	35677322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.416000	0.66417	2.814000	0.96858	0.655000	0.94253	CGC		0.373	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35641565	G	A	35641565	3	1	56	1	0	0	0	0	1	0	0	0	15074	1087	38	1	204	1	SPEF2	5	35641565	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		35641565	145273695	40	7442										
APC	324	broad.mit.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	56	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	76532352	112173917	68741343	41	7443										
PCDHA13	56136	broad.mit.edu	37	chr5	140264030	140264030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgcgctgcggtgctcggcacCgcccaccgagggcgcgtgcg	17	16	0	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr5:140264030C>T	ENST00000289272.2	+	1	2177	c.2177C>T	c.(2176-2178)cCg>cTg	p.P726L	PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.P726L|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	726					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P726L(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTCGGCACCGCCCACCGAG	0.647																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											55	56	56					5																	140264030		2203	4299	6502	140244214	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2177C>T	5.37:g.140264030C>T	ENSP00000289272:p.Pro726Leu		140244214	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.361579	0.01235	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.11385	2.78;2.78	4.08	2.16	0.27623	.	.	.	.	.	T	0.07908	0.0198	L	0.55990	1.75	0.09310	N	1	B;B;B	0.16802	0.007;0.019;0.012	B;B;B	0.12837	0.001;0.006;0.008	T	0.45011	-0.9290	9	0.09590	T	0.72	.	0.6424	0.00813	0.302:0.3218:0.1831:0.1931	.	726;726;726	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	L	726	ENSP00000386821:P726L;ENSP00000289272:P726L	ENSP00000289272:P726L	P	+	2	0	PCDHA13	140244214	0.000000	0.05858	0.007000	0.13788	0.012000	0.07955	-0.893000	0.04127	0.261000	0.21753	0.655000	0.94253	CCG		0.647	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140264030	C	T	140264030	3	4	56	1	0	0	0	0	1	0	0	0	11554	652	23	1	2179	1	PCDHA13	5	140264030	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	28090113	140264030	40651230	42	7444										
PCDHB6	56130	broad.mit.edu	37	chr5	140531943	140531943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtcgtcgctcttcctcttttCggtgctcctgttcgtggcgg	12	13	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr5:140531943C>T	ENST00000231136.1	+	1	2105	c.2105C>T	c.(2104-2106)tCg>tTg	p.S702L	PCDHB6_ENST00000543635.1_Missense_Mutation_p.S566L	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	702					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S702L(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCCTCTTTTCGGTGCTCCTG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	93	89					5																	140531943		2201	4288	6489	140512127	SO:0001583	missense	56130			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2105C>T	5.37:g.140531943C>T	ENSP00000231136:p.Ser702Leu		140512127	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.320921	0.60634	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.20463	2.07;2.07	4.55	2.65	0.31530	.	.	.	.	.	T	0.55705	0.1937	M	0.92649	3.33	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55573	-0.8120	9	0.87932	D	0	.	14.5088	0.67769	0.0:0.5788:0.4212:0.0	.	702	Q9Y5E3	PCDB6_HUMAN	L	566;702	ENSP00000438466:S566L;ENSP00000231136:S702L	ENSP00000231136:S702L	S	+	2	0	PCDHB6	140512127	0.001000	0.12720	0.003000	0.11579	0.751000	0.42716	0.519000	0.22862	0.410000	0.25675	0.556000	0.70494	TCG		0.687	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140531943	C	T	140531943	3	4	56	1	0	0	0	0	1	0	0	0	11577	893	31	1	2107	1	PCDHB6	5	140531943	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	267913	140531943	40383317	43	7445										
SLC35B3	51000	broad.mit.edu	37	chr6	8430341	8430341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tttcagagttatttttgttgGtttcctggactgttatgttc	9	5	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:8430341G>T	ENST00000379660.4	-	3	502	c.53C>A	c.(52-54)aCc>aAc	p.T18N	SLC35B3_ENST00000426876.1_Missense_Mutation_p.T84N|SLC35B3_ENST00000339306.5_Missense_Mutation_p.T18N	NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	18					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.T18N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					ATTTTTGTTGGTTTCCTGGAC	0.333																																					Melanoma(83;700 1353 9357 11478 30548)											1	Substitution - Missense(1)	large_intestine(1)	6											153	147	149					6																	8430341		2203	4300	6503	8375340	SO:0001583	missense	51000			AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"Solute carriers"	21601	protein-coding gene	gene with protein product	"3' phosphoadenosine 5' phosphosulfate transporter 2"	610845	"chromosome 6 open reading frame 196", "solute carrier family 35, member B3"	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.53C>A	6.37:g.8430341G>T	ENSP00000368981:p.Thr18Asn		8375340	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Missense_Mutation	SNP	ENST00000379660.4	37	CCDS4508.1	.	.	.	.	.	.	.	.	.	.	G	6.659	0.490067	0.12702	.	.	ENSG00000124786	ENST00000379660;ENST00000339306;ENST00000426876	T;T	0.45668	1.5;0.89	5.59	-0.932	0.10435	.	1.160410	0.06280	N	0.697214	T	0.05640	0.0148	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.0	T	0.26883	-1.0090	9	.	.	.	1.4672	1.166	0.01815	0.1661:0.1935:0.2238:0.4166	.	18;18	B4E2F5;Q9H1N7	.;S35B3_HUMAN	N	18;18;84	ENSP00000368981:T18N;ENSP00000345902:T18N	.	T	-	2	0	SLC35B3	8375340	0.891000	0.30450	0.000000	0.03702	0.070000	0.16714	0.574000	0.23714	0.026000	0.15269	-0.296000	0.09543	ACC		0.333	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	NM_015948		T	8430341	G	T	8430341	3	4	56	1	0	0	0	0	1	0	0	0	14614	1261	44	2	1188	2	SLC35B3	6	8430341	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		8430341	162684726	44	7446										
HIST1H2BH	8345	broad.mit.edu	37	chr6	26252218	26252218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tggccaagcacgccgtgtccGagggcactaaggccgtcacc	13	15	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:26252218G>A	ENST00000356350.2	+	1	340	c.340G>A	c.(340-342)Gag>Aag	p.E114K	HIST1H3F_ENST00000446824.2_5'Flank	NM_003524.2	NP_003515.1	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	114					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E114K(2)|p.E114Q(1)		NS(3)|breast(2)|large_intestine(1)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	17						CGCCGTGTCCGAGGGCACTAA	0.537																																																3	Substitution - Missense(3)	large_intestine(1)|NS(1)|lung(1)	6											63	68	66					6																	26252218		2203	4300	6503	26360197	SO:0001583	missense	8345			Z80781	CCDS4601.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000197459	ENSG00000275713		"Histones / Replication-dependent"	4755	protein-coding gene	gene with protein product		602806	"H2B histone family, member J", "histone 1, H2bh"	H2BFJ		9119399, 12408966	Standard	NM_003524		Approved	H2B/j	uc003nhh.3	Q93079	OTTHUMG00000014447	ENST00000356350.2:c.340G>A	6.37:g.26252218G>A	ENSP00000348706:p.Glu114Lys		26360197	B2R541|Q4VB74	Missense_Mutation	SNP	ENST00000356350.2	37	CCDS4601.1	.	.	.	.	.	.	.	.	.	.	.	16.28	3.079141	0.55753	.	.	ENSG00000197459	ENST00000356350	T	0.48201	0.82	4.65	3.78	0.43462	Histone-fold (2);	0.000000	0.40222	U	0.001155	T	0.30696	0.0773	M	0.78801	2.425	0.35286	D	0.781761	B	0.33299	0.407	B	0.23018	0.043	T	0.38908	-0.9639	10	0.52906	T	0.07	.	12.6473	0.56742	0.0824:0.0:0.9176:0.0	.	114	Q93079	H2B1H_HUMAN	K	114	ENSP00000348706:E114K	ENSP00000348706:E114K	E	+	1	0	HIST1H2BH	26360197	1.000000	0.71417	0.962000	0.40283	0.380000	0.30137	7.726000	0.84824	1.271000	0.44313	0.591000	0.81541	GAG		0.537	HIST1H2BH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040110.1	NM_003524		A	26252218	G	A	26252218	3	1	56	1	0	0	0	0	1	0	0	0	7168	1059	37	1	342	1	HIST1H2BH	6	26252218	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	17821877	26252218	144862849	45	7447										
BAT2	7916	broad.mit.edu	37	chr6	31600024	31600024	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggagccctccagccaagtctCtggctcccaagaaacctccc	8	18	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:31600024C>T	ENST00000376033.2	+	16	3808	c.3574C>T	c.(3574-3576)Ctg>Ttg	p.L1192L	PRRC2A_ENST00000376007.4_Silent_p.L1192L	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1192	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L1192L(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						AGCCAAGTCTCTGGCTCCCAA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	6											24	31	28					6																	31600024		1508	2705	4213	31708003	SO:0001819	synonymous_variant	7916			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3574C>T	6.37:g.31600024C>T			31708003	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																				0.642	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31600024	C	T	31600024	2	4	56	1	0	0	0	0	0	0	0	1	1320	912	32	3		3	BAT2	6	31600024	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	5347806	31600024	139515043	46	7448										
DAAM2	23500	broad.mit.edu	37	chr6	39869628	39869628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtgagcggtggcagcggcagCggaaggtcctggctgcaggc	20	10	0	1	rs573237647		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:39869628C>T	ENST00000398904.2	+	25	3204	c.3022C>T	c.(3022-3024)Cgg>Tgg	p.R1008W	DAAM2_ENST00000538976.1_Missense_Mutation_p.R1007W|DAAM2_ENST00000274867.4_Missense_Mutation_p.R1008W|RP11-61I13.3_ENST00000437947.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1008					actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.R1007W(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCAGCGGCAGCGGAAGGTCCT	0.662													C|||	1	0.000199681	8e-04	0	5008	,	,		15990	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											21	29	26					6																	39869628		2092	4211	6303	39977606	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.3022C>T	6.37:g.39869628C>T	ENSP00000381876:p.Arg1008Trp		39977606	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.997134	0.74818	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.80214	-1.34;-1.34;-1.35	5.51	1.33	0.21861	Actin-binding FH2/DRF autoregulatory (1);	0.400623	0.24755	N	0.035864	T	0.79143	0.4396	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.96	T	0.79497	-0.1779	10	0.72032	D	0.01	.	10.5247	0.44941	0.6084:0.2832:0.1083:0.0	.	1007;1008	G5EA45;Q86T65	.;DAAM2_HUMAN	W	1008;1008;1007	ENSP00000274867:R1008W;ENSP00000381876:R1008W;ENSP00000437808:R1007W	ENSP00000274867:R1008W	R	+	1	2	DAAM2	39977606	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.162000	0.31786	0.236000	0.21180	-0.314000	0.08810	CGG		0.662	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39869628	C	T	39869628	3	4	56	1	0	0	0	0	1	0	0	0	4222	759	27	1	3113	1	DAAM2	6	39869628	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	8269604	39869628	131245439	47	7449										
PKHD1	5314	broad.mit.edu	37	chr6	51768525	51768525	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatttccatgtcctgaccagTctaatgtttcaacaaatcca	4	11	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:51768525T>C	ENST00000371117.3	-	43	7141	c.6866A>G	c.(6865-6867)gAc>gGc	p.D2289G	PKHD1_ENST00000340994.4_Splice_Site_p.D2289G	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2289					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.D2289G(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCTGACCAGTCTAATGTTTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											126	119	121					6																	51768525		2203	4300	6503	51876484	SO:0001630	splice_region_variant	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.6866-1A>G	6.37:g.51768525T>C			51876484	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	7.242	0.601388	0.13939	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80566	-1.39;-1.39	5.73	0.704	0.18121	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.296460	0.27060	N	0.021127	T	0.49474	0.1559	L	0.53671	1.685	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.0	B;B;B	0.12156	0.007;0.004;0.001	T	0.41592	-0.9500	10	0.15952	T	0.53	.	5.5774	0.17231	0.0:0.2947:0.1371:0.5682	.	2289;2289;2289	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	G	2289	ENSP00000360158:D2289G;ENSP00000341097:D2289G	ENSP00000341097:D2289G	D	-	2	0	PKHD1	51876484	0.861000	0.29849	0.006000	0.13384	0.421000	0.31385	0.184000	0.16939	-0.102000	0.12197	0.528000	0.53228	GAC		0.403	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	Missense_Mutation	C	51768525	T	C	51768525	5	2	56	1	0	0	0	0	0	0	1	0	12002	1681	58	4	5497	4	PKHD1	6	51768525	Splice_Site	SNP	T	TCGA-AG-4001-01A-02W-1073-09	11898897	51768525	119346542	48	7450										
IBTK	25998	broad.mit.edu	37	chr6	82891706	82891706	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttttcttctagtaagaaatcCcggaatgacttggatgaaac	8	7	2	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:82891706C>T	ENST00000306270.7	-	26	4164	c.3615G>A	c.(3613-3615)cgG>cgA	p.R1205R	IBTK_ENST00000510291.1_Silent_p.R1190R|IBTK_ENST00000503631.1_Silent_p.R1004R	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1205					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.R1205R(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GTAAGAAATCCCGGAATGACT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	6											57	60	59					6																	82891706		2203	4300	6503	82948425	SO:0001819	synonymous_variant	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3615G>A	6.37:g.82891706C>T			82948425	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Silent	SNP	ENST00000306270.7	37	CCDS34490.1																																																																																				0.368	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		T	82891706	C	T	82891706	2	4	56	1	0	0	0	0	0	0	0	1	7497	610	22	3		3	IBTK	6	82891706	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	31123181	82891706	88223361	49	7451										
MAP3K4	4216	broad.mit.edu	37	chr6	161455406	161455406	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cctctccccccagcacacctCgacagatgaaacgcatgtca	6	18	2	2	rs370191115		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr6:161455406C>T	ENST00000392142.4	+	2	416	c.268C>T	c.(268-270)Cga>Tga	p.R90*	MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.R90*|MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.R90*|MAP3K4_ENST00000446500.1_3'UTR|MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.R90*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	90					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.R90*(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CAGCACACCTCGACAGATGAA	0.458																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											84	84	84					6																	161455406		2203	4300	6503	161375396	SO:0001587	stop_gained	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.268C>T	6.37:g.161455406C>T	ENSP00000375986:p.Arg90*		161375396	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	38	6.755629	0.97813	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824;ENST00000544209	.	.	.	5.49	4.61	0.57282	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-21.2332	15.9703	0.80008	0.136:0.864:0.0:0.0	.	.	.	.	X	90;90;90;90;90;69	.	ENSP00000297332:R90X	R	+	1	2	MAP3K4	161375396	1.000000	0.71417	0.867000	0.34043	0.992000	0.81027	5.733000	0.68571	1.440000	0.47531	0.558000	0.71614	CGA		0.458	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161455406	C	T	161455406	4	4	56	1	0	0	0	0	0	1	0	0	9282	876	31	1	274	1	MAP3K4	6	161455406	Nonsense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	78563700	161455406	9659661	50	7452										
FBXL18	80028	broad.mit.edu	37	chr7	5540135	5540135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tcacctgaggtccctcagccGcttgcagtgcttcaacatgt	9	14	3	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr7:5540135G>A	ENST00000382368.3	-	3	1888	c.1765C>T	c.(1765-1767)Cgg>Tgg	p.R589W	FBXL18_ENST00000453700.3_Missense_Mutation_p.R589W	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	589								p.R589W(1)	FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		TCCCTCAGCCGCTTGCAGTGC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	7											39	44	42					7																	5540135		2019	4159	6178	5506661	SO:0001583	missense	80028			AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"F-boxes / Leucine-rich repeats"	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1765C>T	7.37:g.5540135G>A	ENSP00000371805:p.Arg589Trp		5506661	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000382368.3	37	CCDS43546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.59|18.59	3.656834|3.656834	0.67586|0.67586	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000297035|ENST00000382368;ENST00000312577;ENST00000453700	.|T;T	.|0.55234	.|0.53;0.53	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.341140	.|0.33938	.|N	.|0.004410	T|T	0.47002|0.47002	0.1422|0.1422	N|N	0.14661|0.14661	0.345|0.345	0.36710|0.36710	D|D	0.880617|0.880617	.|D;D	.|0.69078	.|0.997;0.987	.|P;P	.|0.53861	.|0.736;0.528	T|T	0.58781|0.58781	-0.7576|-0.7576	6|10	0.87932|0.72032	D|D	0|0.01	.|.	11.4554|11.4554	0.50179|0.50179	0.0919:0.0:0.9081:0.0|0.0919:0.0:0.9081:0.0	.|.	.|589;589	.|F5H4Z4;Q96ME1-4	.|.;.	V|W	148|589	.|ENSP00000371805:R589W;ENSP00000444797:R589W	ENSP00000297035:A148V|ENSP00000311990:R589W	A|R	-|-	2|1	0|2	FBXL18|FBXL18	5506661|5506661	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.467000|4.467000	0.60155|0.60155	2.533000|2.533000	0.85409|0.85409	0.585000|0.585000	0.79938|0.79938	GCG|CGG		0.667	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963		A	5540135	G	A	5540135	3	1	56	1	0	0	0	0	1	0	0	0	5733	1086	38	1	403	1	FBXL18	7	5540135	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		5540135	153598528	51	7453										
ADCY1	107	broad.mit.edu	37	chr7	45753429	45753429	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gatggaaacggctcccaaatCaggtccctgggcttggatcg	13	11	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr7:45753429C>G	ENST00000297323.7	+	20	3217	c.3195C>G	c.(3193-3195)atC>atG	p.I1065M		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	1065					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.I1065M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCTCCCAAATCAGGTCCCTGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	7											117	108	111					7																	45753429		2203	4300	6503	45719954	SO:0001583	missense	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.3195C>G	7.37:g.45753429C>G	ENSP00000297323:p.Ile1065Met		45719954	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	37	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	C	9.244	1.039004	0.19669	.	.	ENSG00000164742	ENST00000297323	T	0.79653	-1.29	5.77	4.89	0.63831	.	0.631499	0.17732	N	0.163866	T	0.64371	0.2592	N	0.08118	0	0.20307	N	0.999915	B	0.09022	0.002	B	0.12156	0.007	T	0.54132	-0.8339	10	0.34782	T	0.22	.	12.6393	0.56700	0.0:0.9199:0.0:0.0801	.	1065	Q08828	ADCY1_HUMAN	M	1065	ENSP00000297323:I1065M	ENSP00000297323:I1065M	I	+	3	3	ADCY1	45719954	0.014000	0.17966	0.035000	0.18076	0.396000	0.30629	0.728000	0.26013	1.447000	0.47661	-0.140000	0.14226	ATC		0.567	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		G	45753429	C	G	45753429	3	3	56	1	0	0	0	0	1	0	0	0	292	816	29	5	3273	5	ADCY1	7	45753429	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	40213294	45753429	113385234	52	7454										
C7orf57	136288	broad.mit.edu	37	chr7	48089541	48089541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	caccccacttggccctaagaAtcctgcaggaagtagactct	8	14	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr7:48089541A>G	ENST00000348904.3	+	6	784	c.572A>G	c.(571-573)aAt>aGt	p.N191S	C7orf57_ENST00000420324.1_Missense_Mutation_p.N236S|C7orf57_ENST00000539619.1_Missense_Mutation_p.N191S|C7orf57_ENST00000430738.1_Missense_Mutation_p.N236S|C7orf57_ENST00000435376.1_Missense_Mutation_p.N69S	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	191								p.N191S(2)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						GGCCCTAAGAATCCTGCAGGA	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	7											61	57	59					7																	48089541		1987	4165	6152	48056066	SO:0001583	missense	136288			BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.572A>G	7.37:g.48089541A>G	ENSP00000335500:p.Asn191Ser		48056066	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	.	.	.	.	.	.	.	.	.	.	A	6.914	0.538213	0.13188	.	.	ENSG00000164746	ENST00000420324;ENST00000435376;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.57	4.41	0.53225	.	0.582317	0.18412	N	0.142022	T	0.29976	0.0750	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.001;0.01	B;B	0.15484	0.004;0.013	T	0.18555	-1.0333	10	0.44086	T	0.13	-10.347	8.3405	0.32241	0.9108:0.0:0.0892:0.0	.	69;191	C9JBJ8;Q8NEG2	.;CG057_HUMAN	S	236;69;236;191;191	ENSP00000394648:N236S;ENSP00000391652:N69S;ENSP00000410944:N236S;ENSP00000335500:N191S;ENSP00000442474:N191S	ENSP00000335500:N191S	N	+	2	0	C7orf57	48056066	0.571000	0.26659	0.008000	0.14137	0.014000	0.08584	2.932000	0.48940	0.954000	0.37851	0.454000	0.30748	AAT		0.537	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159		G	48089541	A	G	48089541	3	3	56	1	0	0	0	0	1	0	0	0	2410	101	4	4	590	4	C7orf57	7	48089541	Missense_Mutation	SNP	A	TCGA-AG-4001-01A-02W-1073-09	2336112	48089541	111049122	53	7455										
KRIT1	889	broad.mit.edu	37	chr7	91851319	91851319	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	attcagcaagtatttctggcCagtcacgaacatgttgcaag	9	9	3	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr7:91851319C>T	ENST00000340022.2	-	14	2478	c.1460G>A	c.(1459-1461)tGg>tAg	p.W487*	KRIT1_ENST00000412043.2_Nonsense_Mutation_p.W487*|KRIT1_ENST00000394503.2_Nonsense_Mutation_p.W439*|KRIT1_ENST00000394507.1_Nonsense_Mutation_p.W487*|KRIT1_ENST00000394505.2_Nonsense_Mutation_p.W487*	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	487	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)	p.W487*(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTTCTGGCCAGTCACGAAC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											110	109	109					7																	91851319		2203	4300	6503	91689255	SO:0001587	stop_gained	889			AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"Ankyrin repeat domain containing"	1573	protein-coding gene	gene with protein product		604214	"cerebral cavernous malformations 1"	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1460G>A	7.37:g.91851319C>T	ENSP00000344668:p.Trp487*		91689255	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Nonsense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	C	41	8.867462	0.98984	.	.	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0998	19.6508	0.95805	0.0:1.0:0.0:0.0	.	.	.	.	X	487;487;487;487;439;487	.	ENSP00000344668:W487X	W	-	2	0	KRIT1	91689255	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.287000	0.78681	2.650000	0.89964	0.471000	0.43371	TGG		0.358	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1			T	91851319	C	T	91851319	4	4	56	1	0	0	0	0	0	1	0	0	8466	595	21	3	774	3	KRIT1	7	91851319	Nonsense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	43761778	91851319	67287344	54	7456										
DGKI	9162	broad.mit.edu	37	chr7	137374734	137374734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccagatgctggaggcctgccCgggagattgctttcctgcag	14	12	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr7:137374734C>T	ENST00000288490.5	-	2	416	c.416G>A	c.(415-417)cGg>cAg	p.R139Q	DGKI_ENST00000446122.1_Missense_Mutation_p.R139Q|DGKI_ENST00000424189.2_Missense_Mutation_p.R139Q|DGKI_ENST00000453654.2_Intron	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	139					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R139Q(1)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GAGGCCTGCCCGGGAGATTGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											59	61	60					7																	137374734		2203	4300	6503	137025274	SO:0001583	missense	9162			AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.416G>A	7.37:g.137374734C>T	ENSP00000288490:p.Arg139Gln		137025274	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	34	5.398092	0.96030	.	.	ENSG00000157680	ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T	0.36878	1.23;1.42	5.83	5.83	0.93111	.	0.175120	0.51477	D	0.000099	T	0.44498	0.1296	L	0.42245	1.32	0.58432	D	0.999999	D	0.61697	0.99	P	0.50270	0.636	T	0.30090	-0.9990	10	0.59425	D	0.04	.	18.9089	0.92474	0.0:1.0:0.0:0.0	.	139	O75912	DGKI_HUMAN	Q	87;139;139;139	ENSP00000288490:R139Q;ENSP00000399131:R139Q	ENSP00000288490:R139Q	R	-	2	0	DGKI	137025274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.377000	0.66184	2.763000	0.94921	0.563000	0.77884	CGG		0.498	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137374734	C	T	137374734	3	4	56	1	0	0	0	0	1	0	0	0	4482	652	23	1	2913	1	DGKI	7	137374734	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	45523415	137374734	21763929	55	7457										
ADAM32	203102	broad.mit.edu	37	chr8	39079179	39079179	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cgaacttgtgtactgaaagaCggagcaaaatgttataaagg	11	5	0	2	rs189440658		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr8:39079179C>T	ENST00000379907.4	+	13	1411	c.1284C>T	c.(1282-1284)gaC>gaT	p.D428D	ADAM32_ENST00000519315.1_Silent_p.D322D|ADAM32_ENST00000437682.2_Silent_p.D329D	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	428	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D427D(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		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)			TACTGAAAGACGGAGCAAAAT	0.338													C|||	1	0.000199681	0	0.0014	5008	,	,		19067	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											132	123	126					8																	39079179		1879	4109	5988	39198336	SO:0001819	synonymous_variant	203102			BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1284C>T	8.37:g.39079179C>T			39198336	Q8TC42	De_novo_Start_InFrame	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																				0.338	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		T	39079179	C	T	39079179	2	4	56	1	0	0	0	0	0	0	0	1	249	535	19	1		1	ADAM32	8	39079179	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09		39079179	107284843	56	7458										
ZFHX4	79776	broad.mit.edu	37	chr8	77620095	77620095	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gcaagactgataaacatatgCagaaatatcaactggtggct	9	7	1	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr8:77620095C>G	ENST00000521891.2	+	3	3353	c.2905C>G	c.(2905-2907)Cag>Gag	p.Q969E	ZFHX4_ENST00000455469.2_Missense_Mutation_p.Q943E|ZFHX4_ENST00000518282.1_Missense_Mutation_p.Q943E|ZFHX4_ENST00000050961.6_Missense_Mutation_p.Q943E|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	943					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.Q969E(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TAAACATATGCAGAAATATCA	0.438										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											99	100	100					8																	77620095		2199	4297	6496	77782650	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.2905C>G	8.37:g.77620095C>G	ENSP00000430497:p.Gln969Glu		77782650	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	9.568	1.120218	0.20877	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.43	5.43	0.79202	Zinc finger, U1-type (1);	0.000000	0.41097	U	0.000946	T	0.76863	0.4047	M	0.87547	2.89	0.80722	D	1	D;D;D;D	0.69078	0.965;0.979;0.979;0.997	P;P;P;D	0.70227	0.542;0.73;0.73;0.968	T	0.78518	-0.2173	10	0.51188	T	0.08	.	19.4288	0.94756	0.0:1.0:0.0:0.0	.	943;943;969;943	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	E	969;969;943;943;943	ENSP00000430497:Q969E;ENSP00000399605:Q943E;ENSP00000050961:Q943E;ENSP00000430848:Q943E	ENSP00000050961:Q943E	Q	+	1	0	ZFHX4	77782650	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.320000	0.79064	2.830000	0.97506	0.585000	0.79938	CAG		0.438	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77620095	C	G	77620095	3	3	56	1	0	0	0	0	1	0	0	0	17674	711	25	5	2911	5	ZFHX4	8	77620095	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	38540916	77620095	68743927	57	7459										
SYBU	55638	broad.mit.edu	37	chr8	110588198	110588198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cctcctcaatccagtcctctCgcatgcgggccagctgggac	10	17	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr8:110588198C>T	ENST00000422135.1	-	8	1444	c.929G>A	c.(928-930)cGa>cAa	p.R310Q	SYBU_ENST00000532779.1_Missense_Mutation_p.R242Q|SYBU_ENST00000446070.2_Missense_Mutation_p.R309Q|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000533895.1_Missense_Mutation_p.R309Q|SYBU_ENST00000533065.1_Missense_Mutation_p.R191Q|SYBU_ENST00000408908.2_Missense_Mutation_p.R310Q|SYBU_ENST00000528647.1_Missense_Mutation_p.R309Q|SYBU_ENST00000419099.1_Missense_Mutation_p.R309Q|SYBU_ENST00000424158.2_Missense_Mutation_p.R315Q|SYBU_ENST00000529690.1_Missense_Mutation_p.R180Q|SYBU_ENST00000533171.1_Missense_Mutation_p.R310Q|SYBU_ENST00000408889.3_Missense_Mutation_p.R191Q|SYBU_ENST00000529175.1_Missense_Mutation_p.R104Q|SYBU_ENST00000528331.1_Missense_Mutation_p.R191Q|SYBU_ENST00000440310.1_Missense_Mutation_p.R310Q|SYBU_ENST00000399066.3_Missense_Mutation_p.R307Q|SYBU_ENST00000433638.1_Missense_Mutation_p.R310Q|SYBU_ENST00000276646.9_Missense_Mutation_p.R310Q	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	310	Sufficient for interaction with KIF5B.|Sufficient for interaction with STX1A.				regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R307Q(1)|p.R307L(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						CCAGTCCTCTCGCATGCGGGC	0.443																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	8											53	54	54					8																	110588198		1988	4214	6202	110657374	SO:0001583	missense	55638			AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"syntaphilin-like"	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.929G>A	8.37:g.110588198C>T	ENSP00000407118:p.Arg310Gln		110657374	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Missense_Mutation	SNP	ENST00000422135.1	37	CCDS47912.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468357	0.63625	.	.	ENSG00000147642	ENST00000533895;ENST00000424158;ENST00000532779;ENST00000399066;ENST00000446070;ENST00000528331;ENST00000529175;ENST00000276646;ENST00000528647;ENST00000422135;ENST00000419099;ENST00000433638;ENST00000408908;ENST00000440310;ENST00000408889;ENST00000533065;ENST00000529690;ENST00000533171	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.72095	0.3418	L	0.44542	1.39	0.54753	D	0.999986	D;D;P;D;D	0.89917	1.0;1.0;0.93;1.0;1.0	D;D;P;D;D	0.85130	0.997;0.996;0.66;0.997;0.997	T	0.63466	-0.6631	9	0.12103	T	0.63	-23.7344	19.0385	0.92989	0.0:1.0:0.0:0.0	.	180;242;309;310;307	B7Z4D2;Q9NX95-2;Q9NX95-3;Q9NX95;Q9NX95-4	.;.;.;SYBU_HUMAN;.	Q	309;315;242;307;309;191;104;310;309;310;309;310;310;310;191;191;180;310	.	ENSP00000276646:R310Q	R	-	2	0	SYBU	110657374	0.997000	0.39634	0.930000	0.37139	0.983000	0.72400	6.019000	0.70818	2.736000	0.93811	0.591000	0.81541	CGA		0.443	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		T	110588198	C	T	110588198	3	4	56	1	0	0	0	0	1	0	0	0	15466	884	31	1	1066	1	SYBU	8	110588198	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	32968103	110588198	35775824	58	7460										
TRPS1	7227	broad.mit.edu	37	chr8	116426341	116426341	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtgaagtcatatttgtccgtGcaaagatgctggcatatgct	11	7	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr8:116426341G>T	ENST00000220888.5	-	6	3915	c.3756C>A	c.(3754-3756)tgC>tgA	p.C1252*	TRPS1_ENST00000520276.1_Nonsense_Mutation_p.C1256*|TRPS1_ENST00000519076.1_Nonsense_Mutation_p.C1006*|TRPS1_ENST00000395715.3_Nonsense_Mutation_p.C1265*			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1252	Transcriptional repressor domain. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.C1252*(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			ATTTGTCCGTGCAAAGATGCT	0.433									Langer-Giedion syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	8											179	168	172					8																	116426341		1967	4155	6122	116495517	SO:0001587	stop_gained	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3756C>A	8.37:g.116426341G>T	ENSP00000220888:p.Cys1252*		116495517	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Nonsense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	G	39	7.584813	0.98374	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2461	0.93902	0.0:0.0:1.0:0.0	.	.	.	.	X	1265;1252;1006;1256	.	ENSP00000220888:C1252X	C	-	3	2	TRPS1	116495517	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.158000	0.58150	2.525000	0.85131	0.655000	0.94253	TGC		0.433	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116426341	G	T	116426341	4	4	56	1	0	0	0	0	0	1	0	0	16633	1311	46	2	93	2	TRPS1	8	116426341	Nonsense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5838143	116426341	29937681	59	7461										
NDUFB9	4715	broad.mit.edu	37	chr8	125562099	125562099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tttgcccccactgtggtggtAtattgtgaccagaccccggg	12	12	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr8:125562099A>G	ENST00000276689.3	+	4	590	c.506A>G	c.(505-507)tAt>tGt	p.Y169C	NDUFB9_ENST00000517367.1_Missense_Mutation_p.Y158C|NDUFB9_ENST00000517830.1_Intron|NDUFB9_ENST00000522532.1_Intron	NM_001278646.1|NM_005005.2	NP_001265575.1|NP_004996.1	Q9Y6M9	NDUB9_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa	169					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.Y169C(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CTGTGGTGGTATATTGTGACC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	8											61	57	58					8																	125562099		2203	4300	6503	125631280	SO:0001583	missense	4715			AF044956	CCDS6352.1	8q24.13	2011-07-04	2002-08-29		ENSG00000147684	ENSG00000147684		"LYR motif containing", "Mitochondrial respiratory chain complex / Complex I"	7704	protein-coding gene	gene with protein product	"complex I B22 subunit"	601445	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9 (22kD, B22)"			8661098	Standard	NM_005005		Approved	B22, UQOR22, LYRM3	uc003yrg.4	Q9Y6M9	OTTHUMG00000165054	ENST00000276689.3:c.506A>G	8.37:g.125562099A>G	ENSP00000276689:p.Tyr169Cys		125631280	B2R8M6|Q9UQE8	Missense_Mutation	SNP	ENST00000276689.3	37	CCDS6352.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066685	0.55539	.	.	ENSG00000147684	ENST00000276689;ENST00000517367	T;T	0.71934	-0.61;-0.61	5.01	5.01	0.66863	.	0.115612	0.64402	D	0.000011	T	0.53286	0.1787	N	0.08118	0	0.32788	N	0.501492	B	0.29805	0.257	B	0.30179	0.112	T	0.66814	-0.5828	10	0.87932	D	0	-13.8005	15.004	0.71498	1.0:0.0:0.0:0.0	.	169	Q9Y6M9	NDUB9_HUMAN	C	169;158	ENSP00000276689:Y169C;ENSP00000430322:Y158C	ENSP00000276689:Y169C	Y	+	2	0	NDUFB9	125631280	1.000000	0.71417	0.998000	0.56505	0.891000	0.51852	6.766000	0.74970	2.018000	0.59344	0.260000	0.18958	TAT		0.512	NDUFB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381606.1	NM_005005		G	125562099	A	G	125562099	3	3	56	1	0	0	0	0	1	0	0	0	10319	449	16	4	520	4	NDUFB9	8	125562099	Missense_Mutation	SNP	A	TCGA-AG-4001-01A-02W-1073-09	9135758	125562099	20801923	60	7462										
NFIB	4781	broad.mit.edu	37	chr9	14120603	14120603	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tggcaacggtgaaggtggagGtggagttcgagttgagatga	19	3	0	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr9:14120603G>C	ENST00000380959.3	-	8	1554	c.1081C>G	c.(1081-1083)Cct>Gct	p.P361A	NFIB_ENST00000397579.2_Missense_Mutation_p.P361A|NFIB_ENST00000380924.1_Missense_Mutation_p.P109A|NFIB_ENST00000380934.4_Missense_Mutation_p.P387A|NFIB_ENST00000380953.1_Missense_Mutation_p.P361A|NFIB_ENST00000397581.2_Missense_Mutation_p.P361A|NFIB_ENST00000397575.3_Missense_Mutation_p.P361A|NFIB_ENST00000543693.1_Missense_Mutation_p.P109A	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	361					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P361A(2)		central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		GAAGGTGGAGGTGGAGTTCGA	0.468			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																Esophageal Squamous(132;921 1730 14828 40753 46471)		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	2	Substitution - Missense(2)	large_intestine(2)	9											159	116	131					9																	14120603		2203	4300	6503	14110603	SO:0001583	missense	4781			U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.1081C>G	9.37:g.14120603G>C	ENSP00000370346:p.Pro361Ala		14110603	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	G	9.591	1.126031	0.20959	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000543693;ENST00000380924	T;T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.40398	0.1115	N	0.05199	-0.095	0.58432	D	0.999998	D;P;D;D	0.69078	0.997;0.942;0.997;0.988	D;P;D;D	0.77004	0.989;0.711;0.989;0.981	T	0.19582	-1.0301	10	0.02654	T	1	.	18.9927	0.92800	0.0:0.0:1.0:0.0	.	361;361;361;109	Q5VW27;Q5VW29;O00712;G3V1P1	.;.;NFIB_HUMAN;.	A	387;361;361;361;361;361;109;109	ENSP00000370321:P387A;ENSP00000370346:P361A;ENSP00000370340:P361A;ENSP00000380705:P361A;ENSP00000380711:P361A;ENSP00000380709:P361A;ENSP00000442888:P109A;ENSP00000370311:P109A	ENSP00000370311:P109A	P	-	1	0	NFIB	14110603	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.011000	0.93618	2.487000	0.83934	0.655000	0.94253	CCT		0.468	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		C	14120603	G	C	14120603	3	2	56	1	0	0	0	0	1	0	0	0	10402	1261	44	5	189	5	NFIB	9	14120603	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		14120603	127092828	61	7463										
TRPM3	80036	broad.mit.edu	37	chr9	73152149	73152149	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtctgacgaggtcctcgagcGgattttgttggactcggccc	14	11	1	1	rs148061413		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr9:73152149G>A	ENST00000377111.2	-	25	4087	c.3844C>T	c.(3844-3846)Cgc>Tgc	p.R1282C	TRPM3_ENST00000396292.4_Missense_Mutation_p.R1154C|TRPM3_ENST00000396280.5_Missense_Mutation_p.R1131C|TRPM3_ENST00000377105.1_Missense_Mutation_p.R1141C|TRPM3_ENST00000408909.2_Missense_Mutation_p.R1141C|TRPM3_ENST00000377110.3_Missense_Mutation_p.R1282C|TRPM3_ENST00000377106.1_Missense_Mutation_p.R1154C|TRPM3_ENST00000357533.2_Missense_Mutation_p.R1286C|TRPM3_ENST00000396285.1_Missense_Mutation_p.R1141C|TRPM3_ENST00000423814.3_Missense_Mutation_p.R1309C|TRPM3_ENST00000360823.2_Missense_Mutation_p.R1144C|TRPM3_ENST00000358082.3_Missense_Mutation_p.R1144C	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1307					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.R1154C(1)|p.R1286C(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GTCCTCGAGCGGATTTTGTTG	0.617													G|||	1	0.000199681	0	0	5008	,	,		16489	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	9						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	86	83	84		3844,3385,3421,3355,3391,3460,3430	6.1	1	9	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	180,180,180,180,180,180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1282/1708,1129/1555,1141/1567,1119/1545,1131/1557,1154/1580,1144/1570	73152149	1,13005	2203	4300	6503	72341969	SO:0001583	missense	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.3844C>T	9.37:g.73152149G>A	ENSP00000366315:p.Arg1282Cys		72341969	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.95|18.95	3.732722|3.732722	0.69189|0.69189	0.0|0.0	1.16E-4|1.16E-4	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T;T	.|0.55413	.|0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.74291|0.74291	0.3697|0.3697	M|M	0.75447|0.75447	2.3|2.3	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D;D;D;D	.|0.89917	.|1.0;0.998;1.0;0.999;0.999;0.999;1.0;0.999	.|D;P;D;P;P;P;D;P	.|0.70487	.|0.954;0.886;0.969;0.899;0.836;0.899;0.962;0.732	T|T	0.73646|0.73646	-0.3917|-0.3917	5|10	.|0.59425	.|D	.|0.04	-14.6718|-14.6718	20.6721|20.6721	0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1282;1282;1272;1286;1144;1141;1254;1141	.|Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|.;.;.;.;.;.;.;.	L|C	1130|1282;1282;1154;1144;1141;1286;1141;1141;1154;1144;1309	.|ENSP00000366315:R1282C;ENSP00000366314:R1282C;ENSP00000366310:R1154C;ENSP00000354066:R1144C;ENSP00000366309:R1141C;ENSP00000350140:R1286C;ENSP00000386127:R1141C;ENSP00000379581:R1141C;ENSP00000379587:R1154C;ENSP00000350791:R1144C;ENSP00000389542:R1309C	.|ENSP00000350140:R1286C	P|R	-|-	2|1	0|0	TRPM3|TRPM3	72341969|72341969	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.185000|6.185000	0.72013|0.72013	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	CCG|CGC		0.617	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73152149	G	A	73152149	3	1	56	1	0	0	0	0	1	0	0	0	16627	1116	39	1	1283	1	TRPM3	9	73152149	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	59031546	73152149	68061282	62	7464										
ANXA1	301	broad.mit.edu	37	chr9	75775279	75775279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atttgatgctgatgaacttcGtgctgccatgaaggtaaatc	10	7	0	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr9:75775279G>A	ENST00000376911.1	+	4	1253	c.371G>A	c.(370-372)cGt>cAt	p.R124H	ANXA1_ENST00000257497.6_Missense_Mutation_p.R124H			P04083	ANXA1_HUMAN	annexin A1	124					alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.R124H(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	GATGAACTTCGTGCTGCCATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	93	94					9																	75775279		2203	4300	6503	74965099	SO:0001583	missense	301			X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"Annexins", "Endogenous ligands"	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.371G>A	9.37:g.75775279G>A	ENSP00000366109:p.Arg124His		74965099		Missense_Mutation	SNP	ENST00000376911.1	37	CCDS6645.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.868205	0.72065	.	.	ENSG00000135046	ENST00000257497;ENST00000456643;ENST00000376911	T;T;T	0.03468	3.92;3.92;3.92	5.92	4.9	0.64082	.	0.139109	0.64402	D	0.000006	T	0.10809	0.0264	L	0.48642	1.525	0.09310	N	0.999995	D	0.89917	1.0	D	0.75484	0.986	T	0.21861	-1.0233	10	0.15499	T	0.54	.	12.4182	0.55506	0.0992:0.0:0.9008:0.0	.	124	P04083	ANXA1_HUMAN	H	124;135;124	ENSP00000257497:R124H;ENSP00000412489:R135H;ENSP00000366109:R124H	ENSP00000257497:R124H	R	+	2	0	ANXA1	74965099	0.969000	0.33509	0.682000	0.30024	0.941000	0.58515	3.640000	0.54350	1.249000	0.43950	0.650000	0.86243	CGT		0.428	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052665.1	NM_000700		A	75775279	G	A	75775279	3	1	56	1	0	0	0	0	1	0	0	0	714	1145	40	1	385	1	ANXA1	9	75775279	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	2623130	75775279	65438152	63	7465										
SETX	23064	broad.mit.edu	37	chr9	135203335	135203335	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aagacttcttttgtgaaaccGtagtggctctctgaatacgt	9	8	2	3	rs140892948		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr9:135203335G>A	ENST00000224140.5	-	10	3832	c.3650C>T	c.(3649-3651)aCg>aTg	p.T1217M	SETX_ENST00000372169.2_Missense_Mutation_p.T1217M|SETX_ENST00000393220.1_Missense_Mutation_p.T1217M	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1217					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.T1217M(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTGTGAAACCGTAGTGGCTCT	0.388													G|||	1	0.000199681	8e-04	0	5008	,	,		19350	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						G	MET/THR	3,4403	6.2+/-15.9	0,3,2200	111	109	109		3650	-2.4	0	9	dbSNP_134	109	0,8600		0,0,4300	yes	missense	SETX	NM_015046.5	81	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	possibly-damaging	1217/2678	135203335	3,13003	2203	4300	6503	134193156	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.3650C>T	9.37:g.135203335G>A	ENSP00000224140:p.Thr1217Met		134193156	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	13.15	2.152651	0.38021	6.81E-4	0.0	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87029	-2.11;-2.2;-1.82	5.69	-2.39	0.06602	.	3.645620	0.00639	N	0.000520	T	0.77644	0.4161	L	0.27053	0.805	0.09310	N	1	D;P;D	0.54397	0.966;0.898;0.966	B;B;B	0.42214	0.38;0.117;0.38	T	0.69595	-0.5103	10	0.48119	T	0.1	.	2.3999	0.04399	0.3201:0.0882:0.3997:0.192	.	1217;1217;1217	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	M	1217	ENSP00000224140:T1217M;ENSP00000361242:T1217M;ENSP00000376913:T1217M	ENSP00000224140:T1217M	T	-	2	0	SETX	134193156	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.578000	0.05841	-0.137000	0.11455	0.650000	0.86243	ACG		0.388	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		A	135203335	G	A	135203335	3	1	56	1	0	0	0	0	1	0	0	0	14178	1145	40	1	4451	1	SETX	9	135203335	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	59428056	135203335	6010096	64	7466										
METTL10	399818	broad.mit.edu	37	chr10	126453968	126453968	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatagtcacttaccttcactGaattcatttagcaactcttc	3	11	4	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr10:126453968G>A	ENST00000368836.2	-	5	645	c.609C>T	c.(607-609)ttC>ttT	p.F203F	Y_RNA_ENST00000362596.1_RNA|RP11-12J10.3_ENST00000494792.1_Missense_Mutation_p.S168L	NM_212554.2	NP_997719.2	Q5JPI9	MET10_HUMAN	methyltransferase like 10	203							methyltransferase activity (GO:0008168)	p.F203F(1)		endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_lung(145;0.0186)|Lung NSC(174;0.0295)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.101)|COAD - Colon adenocarcinoma(40;0.111)		TACCTTCACTGAATTCATTTA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	10											156	151	152					10																	126453968		2203	4300	6503	126443958	SO:0001819	synonymous_variant	399818				CCDS31307.1	10q26.13	2010-01-15			ENSG00000203791	ENSG00000203791			33787	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 138"	C10orf138			Standard	NM_212554		Approved	Em:AC068896.3	uc001lhy.1	Q5JPI9	OTTHUMG00000019217	ENST00000368836.2:c.609C>T	10.37:g.126453968G>A			126443958	A8MPY7	Silent	SNP	ENST00000368836.2	37	CCDS31307.1																																																																																				0.358	METTL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050884.1	NM_212554		A	126453968	G	A	126453968	2	1	56	1	0	0	0	0	0	0	0	1	9524	1281	45	3		3	METTL10	10	126453968	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09		126453968	9080779	65	7467										
ATHL1	80162	broad.mit.edu	37	chr11	294589	294589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ctttccccgctcggctggccGgatacaaatgtcacccccga	9	17	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:294589G>A	ENST00000409548.2	+	14	2169	c.2054G>A	c.(2053-2055)cGg>cAg	p.R685Q	ATHL1_ENST00000409479.1_Missense_Mutation_p.R712Q|ATHL1_ENST00000409655.1_Missense_Mutation_p.R437Q	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	685					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.R508Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		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;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCGGCTGGCCGGATACAAATG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											90	103	99					11																	294589		2203	4300	6503	284589	SO:0001583	missense	80162			AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.2054G>A	11.37:g.294589G>A	ENSP00000387185:p.Arg685Gln		284589	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	37	CCDS31322.2	.	.	.	.	.	.	.	.	.	.	G	3.024	-0.201146	0.06219	.	.	ENSG00000142102	ENST00000409548;ENST00000409655;ENST00000409479	.	.	.	3.54	1.56	0.23342	.	0.636795	0.14851	N	0.294685	T	0.15998	0.0385	N	0.05230	-0.09	0.24200	N	0.995515	B;B	0.18166	0.026;0.004	B;B	0.08055	0.002;0.003	T	0.28364	-1.0046	9	0.14656	T	0.56	.	10.0895	0.42439	0.1957:0.0:0.8043:0.0	.	685;437	Q32M88;B8ZZ60	ATHL1_HUMAN;.	Q	685;437;712	.	ENSP00000387099:R712Q	R	+	2	0	ATHL1	284589	0.970000	0.33590	0.949000	0.38748	0.057000	0.15508	1.866000	0.39489	0.005000	0.14708	-1.598000	0.00824	CGG		0.647	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		A	294589	G	A	294589	3	1	56	1	0	0	0	0	1	0	0	0	1105	1116	39	1	2104	1	ATHL1	11	294589	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		294589	134711927	66	7468										
CREB3L1	90993	broad.mit.edu	37	chr11	46321515	46321515	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gagcacctggaccactttacGgagaacatggaggacttctc	11	11	1	1	rs181804070		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:46321515G>A	ENST00000529193.1	+	2	583	c.132G>A	c.(130-132)acG>acA	p.T44T	CREB3L1_ENST00000288400.3_Silent_p.T44T			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	44	Required for transcriptional activation.				regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.T44T(1)	FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		ACCACTTTACGGAGAACATGG	0.532			T	FUS	myxofibrosarcoma								G|||	1	0.000199681	0	0.0014	5008	,	,		23893	0		0	False		,,,				2504	0				Pancreas(3;159 194 19597 26278 47995)		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	1	Substitution - coding silent(1)	large_intestine(1)	11											107	103	105					11																	46321515		2043	4195	6238	46278091	SO:0001819	synonymous_variant	90993				CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.132G>A	11.37:g.46321515G>A			46278091	Q8N2D5|Q96CP0	Silent	SNP	ENST00000529193.1	37	CCDS53620.1																																																																																				0.532	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854		A	46321515	G	A	46321515	2	1	56	1	0	0	0	0	0	0	0	1	3862	1103	39	1		1	CREB3L1	11	46321515	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	46026926	46321515	88685001	67	7469										
OR5D18	219438	broad.mit.edu	37	chr11	55587548	55587548	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ctgcgtgctgctggttgtggGatcctatgcctggggagtct	16	9	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:55587548G>T	ENST00000333976.4	+	1	463	c.443G>T	c.(442-444)gGa>gTa	p.G148V		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G148V(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				CTGGTTGTGGGATCCTATGCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											194	182	186					11																	55587548		2200	4296	6496	55344124	SO:0001583	missense	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.443G>T	11.37:g.55587548G>T	ENSP00000335025:p.Gly148Val		55344124	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	3.822	-0.037460	0.07497	.	.	ENSG00000186119	ENST00000333976	T	0.36520	1.25	4.66	0.263	0.15602	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38663	N	0.001619	T	0.26702	0.0653	L	0.48174	1.505	0.19945	N	0.999948	B	0.22003	0.063	B	0.30716	0.119	T	0.18241	-1.0343	10	0.40728	T	0.16	-2.2592	3.0288	0.06099	0.1583:0.3757:0.3341:0.1319	.	148	Q8NGL1	OR5DI_HUMAN	V	148	ENSP00000335025:G148V	ENSP00000335025:G148V	G	+	2	0	OR5D18	55344124	0.000000	0.05858	0.001000	0.08648	0.028000	0.11728	0.021000	0.13489	-0.107000	0.12088	0.567000	0.79289	GGA		0.468	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		T	55587548	G	T	55587548	3	4	56	1	0	0	0	0	1	0	0	0	11188	1174	41	2	445	2	OR5D18	11	55587548	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	9266033	55587548	79418968	68	7470										
AMOTL1	154810	broad.mit.edu	37	chr11	94592772	94592772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgtgcgggagaaggaggagcGgatcctggccctggaggccg	20	9	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:94592772G>A	ENST00000433060.2	+	9	2168	c.2027G>A	c.(2026-2028)cGg>cAg	p.R676Q	AMOTL1_ENST00000317829.8_Missense_Mutation_p.R626Q|AMOTL1_ENST00000317837.9_Intron	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	676					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.R677Q(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AAGGAGGAGCGGATCCTGGCC	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	11											45	49	48					11																	94592772		2201	4298	6499	94232420	SO:0001583	missense	154810			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2027G>A	11.37:g.94592772G>A	ENSP00000387739:p.Arg676Gln		94232420	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.326103	0.81580	.	.	ENSG00000166025	ENST00000317829;ENST00000433060	T;T	0.19532	2.15;2.14	6.08	6.08	0.98989	Angiomotin, C-terminal (1);	0.113923	0.42821	D	0.000645	T	0.24392	0.0591	L	0.43152	1.355	0.80722	D	1	P;P	0.44734	0.842;0.659	P;B	0.46049	0.502;0.319	T	0.01033	-1.1474	10	0.15952	T	0.53	-39.5486	16.0688	0.80909	0.0:0.1332:0.8668:0.0	.	626;676	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	Q	626;676	ENSP00000320968:R626Q;ENSP00000387739:R676Q	ENSP00000320968:R626Q	R	+	2	0	AMOTL1	94232420	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.414000	0.73318	2.894000	0.99253	0.655000	0.94253	CGG		0.562	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94592772	G	A	94592772	3	1	56	1	0	0	0	0	1	0	0	0	583	1116	39	1	2061	1	AMOTL1	11	94592772	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	39005224	94592772	40413744	69	7471										
C11orf87	399947	broad.mit.edu	37	chr11	109294680	109294680	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatgagcgggatcactgcagCggcagccgcggtggcggggg	20	10	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:109294680C>T	ENST00000327419.6	+	2	724	c.321C>T	c.(319-321)agC>agT	p.S107S	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	107						integral component of membrane (GO:0016021)		p.S107S(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						ATCACTGCAGCGGCAGCCGCG	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	11											80	83	82					11																	109294680		2201	4298	6499	108799890	SO:0001819	synonymous_variant	399947			AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"neuronal integral membrane protein 1"					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.321C>T	11.37:g.109294680C>T			108799890	B4E169	Silent	SNP	ENST00000327419.6	37	CCDS31672.1																																																																																				0.642	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645		T	109294680	C	T	109294680	2	4	56	1	0	0	0	0	0	0	0	1	1673	767	27	1		1	C11orf87	11	109294680	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	14701908	109294680	25711836	70	7472										
OR10G4	390264	broad.mit.edu	37	chr11	123886963	123886963	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tctgttccatcctgcggatcCgcacctcagatgggaggcgc	12	14	2	1	rs191928020		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr11:123886963C>T	ENST00000320891.4	+	1	682	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R228C(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CCTGCGGATCCGCACCTCAGA	0.527													c|||	1	0.000199681	0	0	5008	,	,		21452	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											186	152	164					11																	123886963		2201	4299	6500	123392173	SO:0001583	missense	390264			AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"GPCR / Class A : Olfactory receptors"	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.682C>T	11.37:g.123886963C>T	ENSP00000325076:p.Arg228Cys		123392173	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	6.344	0.431547	0.12045	.	.	ENSG00000254737	ENST00000320891	T	0.40225	1.04	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.420315	0.20410	N	0.092861	T	0.33731	0.0873	M	0.74546	2.27	0.21553	N	0.999647	B	0.17465	0.022	B	0.21360	0.034	T	0.39292	-0.9621	10	0.62326	D	0.03	.	8.8892	0.35423	0.0:0.8919:0.0:0.1081	.	228	Q8NGN3	O10G4_HUMAN	C	228	ENSP00000325076:R228C	ENSP00000325076:R228C	R	+	1	0	OR10G4	123392173	0.000000	0.05858	0.604000	0.28916	0.295000	0.27426	-0.074000	0.11450	1.878000	0.54408	0.580000	0.79431	CGC		0.527	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		T	123886963	C	T	123886963	3	4	56	1	0	0	0	0	1	0	0	0	10932	652	23	1	684	1	OR10G4	11	123886963	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	14592283	123886963	11119553	71	7473										
CLEC4C	170482	broad.mit.edu	37	chr12	7894041	7894041	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatgtcctttccttccatgaCgcaggtcaggcttggatgat	10	10	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr12:7894041C>T	ENST00000542353.1	-	4	701	c.211G>A	c.(211-213)Gtc>Atc	p.V71I	CLEC4C_ENST00000360345.3_Missense_Mutation_p.V71I|CLEC4C_ENST00000540085.1_Missense_Mutation_p.V40I|CLEC4C_ENST00000354629.5_Missense_Mutation_p.V40I	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	71					innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.V71I(2)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		CCTTCCATGACGCAGGTCAGG	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	12											193	164	174					12																	7894041		2203	4300	6503	7785308	SO:0001583	missense	170482			AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"C-type lectin domain containing", "CD molecules"	13258	protein-coding gene	gene with protein product		606677	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.211G>A	12.37:g.7894041C>T	ENSP00000440428:p.Val71Ile		7785308	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	CCDS8583.1	.	.	.	.	.	.	.	.	.	.	C	2.509	-0.313476	0.05422	.	.	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	1.79	-3.59	0.04583	.	.	.	.	.	T	0.04092	0.0114	N	0.04335	-0.225	0.09310	N	1	P;B	0.45126	0.851;0.342	B;B	0.30179	0.112;0.026	T	0.36696	-0.9737	9	0.22109	T	0.4	.	4.0105	0.09621	0.5588:0.2914:0.0:0.1498	.	40;71	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	I	71;40;40;71	ENSP00000440428:V71I;ENSP00000346648:V40I;ENSP00000445338:V40I;ENSP00000353500:V71I	ENSP00000346648:V40I	V	-	1	0	CLEC4C	7785308	0.000000	0.05858	0.000000	0.03702	0.238000	0.25445	-0.993000	0.03720	-1.359000	0.02174	0.514000	0.50259	GTC		0.418	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503		T	7894041	C	T	7894041	3	4	56	1	0	0	0	0	1	0	0	0	3519	536	19	1	446	1	CLEC4C	12	7894041	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		7894041	125957854	72	7474										
NELL2	4753	broad.mit.edu	37	chr12	45269124	45269124	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tctgtagggaagggtccacaCcaagcccccaaactggtgag	12	12	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr12:45269124C>A	ENST00000429094.2	-	2	572	c.68G>T	c.(67-69)gGt>gTt	p.G23V	NELL2_ENST00000437801.2_Missense_Mutation_p.G73V|NELL2_ENST00000395487.2_Missense_Mutation_p.G22V|NELL2_ENST00000548826.1_Missense_Mutation_p.G23V|NELL2_ENST00000452445.2_Missense_Mutation_p.G23V|NELL2_ENST00000333837.4_Missense_Mutation_p.G46V|NELL2_ENST00000551601.1_Missense_Mutation_p.G22V|NELL2_ENST00000549027.1_Missense_Mutation_p.G22V	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	23						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.G73V(1)|p.G23V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		AGGGTCCACACCAAGCCCCCA	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	12											47	46	46					12																	45269124		2203	4300	6503	43555391	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.68G>T	12.37:g.45269124C>A	ENSP00000390680:p.Gly23Val		43555391	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.381114	0.82792	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684;ENST00000552993;ENST00000553120;ENST00000548826;ENST00000548531	D;D;T;D;D;D;D;T;T;T;T	0.82893	-1.55;-1.55;-1.24;-1.55;-1.55;-1.54;-1.66;2.52;-0.14;0.17;-0.42	4.74	4.74	0.60224	.	0.000000	0.64402	D	0.000001	D	0.90086	0.6903	M	0.67397	2.05	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.994;1.0;1.0;0.994;0.999;1.0	D	0.91329	0.5088	10	0.87932	D	0	-16.0105	16.8676	0.86033	0.0:1.0:0.0:0.0	.	46;73;22;23;23;22	B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2	.;.;.;.;NELL2_HUMAN;.	V	22;23;22;23;22;46;73;22;23;20;23;22	ENSP00000378866:G22V;ENSP00000390680:G23V;ENSP00000449332:G22V;ENSP00000394612:G23V;ENSP00000447927:G22V;ENSP00000327988:G46V;ENSP00000416341:G73V;ENSP00000447085:G23V;ENSP00000447384:G20V;ENSP00000448635:G23V;ENSP00000449068:G22V	ENSP00000327988:G46V	G	-	2	0	NELL2	43555391	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.102000	0.64572	2.337000	0.79520	0.563000	0.77884	GGT		0.537	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		A	45269124	C	A	45269124	3	1	56	1	0	0	0	0	1	0	0	0	10365	507	18	2	2458	2	NELL2	12	45269124	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	37375083	45269124	88582771	73	7475										
ARID2	196528	broad.mit.edu	37	chr12	46233130	46233130	+	Frame_Shift_Del	DEL	T	T	-													0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agacatgttagtgtgtctggTttctatggatattcagatgt							TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr12:46233130delT	ENST00000334344.6	+	11	1521	c.1349delT	c.(1348-1350)gttfs	p.V450fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.V301fs|ARID2_ENST00000444670.1_Intron|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	450					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S451fs*12(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GTGTGTCTGGTTTCTATGGAT	0.348			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Deletion - Frameshift(1)	large_intestine(1)	12											100	94	96					12																	46233130		2203	4300	6503	44519397	SO:0001589	frameshift_variant	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1349delT	12.37:g.46233130delT	ENSP00000335044:p.Val450fs		44519397	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	37	CCDS31783.1																																																																																				0.348	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46233130	T	-	46233130	7	5	56	1	0	1	0	1	0	0	0	0	915	1725	60	0	1391	0	ARID2	12	46233130	Frame_Shift_Del	DEL	T	TCGA-AG-4001-01A-02W-1073-09	964006	46233130	87618765	74	7476										
CACNB3	784	broad.mit.edu	37	chr12	49220218	49220218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgcagctagtagtgttggacGctgacaccatcaaccaccca	9	13	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr12:49220218G>A	ENST00000301050.2	+	10	1010	c.811G>A	c.(811-813)Gct>Act	p.A271T	CACNB3_ENST00000540990.1_Missense_Mutation_p.A258T|CACNB3_ENST00000536187.2_Missense_Mutation_p.A270T|CACNB3_ENST00000547230.1_Missense_Mutation_p.A230T|CACNB3_ENST00000547392.1_Missense_Mutation_p.A244T	NM_000725.3	NP_000716.2	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3 subunit	271					axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.A271T(1)		autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1)	12					Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGTGTTGGACGCTGACACCAT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	82	88					12																	49220218		2203	4300	6503	47506485	SO:0001583	missense	784				CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1	12q13	2008-05-02				ENSG00000167535		"Calcium channel subunits"	1403	protein-coding gene	gene with protein product		601958		CACNLB3		8119293	Standard	NM_000725		Approved		uc010sly.2	P54284		ENST00000301050.2:c.811G>A	12.37:g.49220218G>A	ENSP00000301050:p.Ala271Thr		47506485	A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913	Missense_Mutation	SNP	ENST00000301050.2	37	CCDS8769.1	.	.	.	.	.	.	.	.	.	.	G	36	5.754271	0.96890	.	.	ENSG00000167535	ENST00000540990;ENST00000536187;ENST00000547818;ENST00000547392;ENST00000301050;ENST00000547230	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	5.86	5.86	0.93980	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.000000	0.85682	D	0.000000	T	0.66877	0.2834	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.966;0.952;0.98	T	0.68164	-0.5481	10	0.72032	D	0.01	-11.7483	18.9438	0.92613	0.0:0.0:1.0:0.0	.	270;258;271;258	F5GZW7;F5H2P6;P54284;B7Z973	.;.;CACB3_HUMAN;.	T	258;270;95;244;271;230	ENSP00000445495:A258T;ENSP00000444160:A270T;ENSP00000448137:A95T;ENSP00000446529:A244T;ENSP00000301050:A271T;ENSP00000448304:A230T	ENSP00000301050:A271T	A	+	1	0	CACNB3	47506485	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	9.813000	0.99286	2.768000	0.95171	0.655000	0.94253	GCT		0.567	CACNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408886.1			A	49220218	G	A	49220218	3	1	56	1	0	0	0	0	1	0	0	0	2560	1087	38	1	849	1	CACNB3	12	49220218	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	2987088	49220218	84631677	75	7477										
CRYL1	51084	broad.mit.edu	37	chr13	20978863	20978863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tatgccttcgctgtatctgtCgcagtagcttaacatacctg	8	11	1	0	rs145530540		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr13:20978863C>T	ENST00000298248.7	-	7	819	c.757G>A	c.(757-759)Gac>Aac	p.D253N	CRYL1_ENST00000382812.1_Missense_Mutation_p.D231N	NM_015974.2	NP_057058.2	Q9Y2S2	CRYL1_HUMAN	crystallin, lambda 1	253					fatty acid metabolic process (GO:0006631)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|L-gulonate 3-dehydrogenase activity (GO:0050104)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)	p.D253N(1)		NS(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		CTGTATCTGTCGCAGTAGCTT	0.393													C|||	0	0	0	0	5008	,	,		23800	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13						C	ASN/ASP	7,3725		0,7,1859	165	166	166		757	4.7	1	13	dbSNP_134	166	0,8224		0,0,4112	yes	missense	CRYL1	NM_015974.2	23	0,7,5971	TT,TC,CC		0.0,0.1876,0.0585	benign	253/320	20978863	7,11949	1866	4112	5978	19876863	SO:0001583	missense	51084			AF077049	CCDS41871.1	13q11	2008-07-18			ENSG00000165475	ENSG00000165475			18246	protein-coding gene	gene with protein product	"crystallin, lamda 1", "L-gulonate 3-dehydrogenase", "lambda-crystallin homolog"	609877				12527201	Standard	NM_015974		Approved	GDH, lambda-CRY, MGC149525, MGC149526	uc001une.3	Q9Y2S2	OTTHUMG00000016516	ENST00000298248.7:c.757G>A	13.37:g.20978863C>T	ENSP00000298248:p.Asp253Asn		19876863	A0PJ43|B3KN92|Q0VDI1|Q7Z4Z9|Q9P0G7	Missense_Mutation	SNP	ENST00000298248.7	37	CCDS41871.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	7.146	0.582776	0.13749	0.001876	0.0	ENSG00000165475	ENST00000298248;ENST00000382812	D;D	0.89415	-2.51;-2.51	5.56	4.71	0.59529	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.228632	0.52532	N	0.000074	D	0.84754	0.5542	L	0.46670	1.46	0.36249	D	0.853765	B	0.14438	0.01	B	0.15484	0.013	T	0.82796	-0.0280	10	0.30854	T	0.27	-40.9827	13.0913	0.59167	0.0:0.9216:0.0:0.0784	.	253	Q9Y2S2	CRYL1_HUMAN	N	253;231	ENSP00000298248:D253N;ENSP00000372262:D231N	ENSP00000298248:D253N	D	-	1	0	CRYL1	19876863	1.000000	0.71417	0.999000	0.59377	0.126000	0.20510	2.122000	0.41987	1.346000	0.45694	0.563000	0.77884	GAC		0.393	CRYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044071.1	NM_015974		T	20978863	C	T	20978863	3	4	56	1	0	0	0	0	1	0	0	0	3926	884	31	1	210	1	CRYL1	13	20978863	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		20978863	94191015	76	7478										
SACS	26278	broad.mit.edu	37	chr13	23912013	23912013	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ctgctgaaccaacatctcttCttttaagtatagagtcatct	5	10	4	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr13:23912013C>A	ENST00000382292.3	-	9	6275	c.6002G>T	c.(6001-6003)aGa>aTa	p.R2001I	SACS_ENST00000382298.3_Missense_Mutation_p.R2001I|SACS_ENST00000402364.1_Missense_Mutation_p.R1251I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2001					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.R1854I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AACATCTCTTCTTTTAAGTAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	13											41	42	42					13																	23912013		2202	4298	6500	22810013	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6002G>T	13.37:g.23912013C>A	ENSP00000371729:p.Arg2001Ile		22810013	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344397	0.82022	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87491	-2.12;-2.26;-2.12	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.90417	0.7000	L	0.51422	1.61	0.80722	D	1	D	0.67145	0.996	P	0.56612	0.802	D	0.90018	0.4126	10	0.52906	T	0.07	.	20.0368	0.97565	0.0:1.0:0.0:0.0	.	2001	Q9NZJ4	SACS_HUMAN	I	2001;1251;2001	ENSP00000371729:R2001I;ENSP00000385844:R1251I;ENSP00000371735:R2001I	ENSP00000371729:R2001I	R	-	2	0	SACS	22810013	1.000000	0.71417	0.995000	0.50966	0.955000	0.61496	7.466000	0.80914	2.727000	0.93392	0.591000	0.81541	AGA		0.388	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23912013	C	A	23912013	3	1	56	1	0	0	0	0	1	0	0	0	13841	913	32	2	7741	2	SACS	13	23912013	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	2933150	23912013	91257865	77	7479										
SUCLA2	8803	broad.mit.edu	37	chr13	48523666	48523666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aatttccaagtcttttactgCcatgactataccctgtgcaa	5	11	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr13:48523666C>A	ENST00000378654.3	-	9	1236	c.1180G>T	c.(1180-1182)Gca>Tca	p.A394S	SUCLA2_ENST00000544100.1_Missense_Mutation_p.A260S|SUCLA2_ENST00000534875.1_Missense_Mutation_p.A336S|SUCLA2_ENST00000543413.1_Missense_Mutation_p.A336S	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	394					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)	p.A394S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		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)	TCTTTTACTGCCATGACTATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											103	99	101					13																	48523666		2203	4300	6503	47421667	SO:0001583	missense	8803			AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.1180G>T	13.37:g.48523666C>A	ENSP00000367923:p.Ala394Ser		47421667	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Missense_Mutation	SNP	ENST00000378654.3	37	CCDS9406.1	.	.	.	.	.	.	.	.	.	.	c	18.84	3.709238	0.68615	.	.	ENSG00000136143	ENST00000378654;ENST00000378645;ENST00000544100;ENST00000534875;ENST00000543413;ENST00000541732	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	4.57	4.57	0.56435	Succinyl-CoA synthetase-like (2);ATP-citrate lyase/succinyl-CoA ligase (1);	0.000000	0.85682	D	0.000000	D	0.91492	0.7314	M	0.93678	3.445	0.80722	D	1	P	0.39250	0.665	D	0.65443	0.935	D	0.93048	0.6463	10	0.66056	D	0.02	-15.9032	16.7109	0.85385	0.0:1.0:0.0:0.0	.	394	Q9P2R7	SUCB1_HUMAN	S	394;372;260;336;336;222	ENSP00000367923:A394S;ENSP00000443412:A260S;ENSP00000438182:A336S;ENSP00000441056:A336S	ENSP00000367912:A372S	A	-	1	0	SUCLA2	47421667	1.000000	0.71417	1.000000	0.80357	0.205000	0.24178	7.348000	0.79366	2.228000	0.72767	0.491000	0.48974	GCA		0.358	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1			A	48523666	C	A	48523666	3	1	56	1	0	0	0	0	1	0	0	0	15402	739	26	2	223	2	SUCLA2	13	48523666	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	24611653	48523666	66646212	78	7480										
FOXA1	3169	broad.mit.edu	37	chr14	38061632	38061632	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccattcatggaggccgcctgCtgcgcacccatggcgcccat	11	17	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr14:38061632C>T	ENST00000250448.2	-	2	418	c.357G>A	c.(355-357)caG>caA	p.Q119Q	FOXA1_ENST00000540786.1_Silent_p.Q86Q|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	119					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.Q119Q(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		AGGCCGCCTGCTGCGCACCCA	0.741																																																1	Substitution - coding silent(1)	large_intestine(1)	14											10	11	11					14																	38061632		2094	4130	6224	37131383	SO:0001819	synonymous_variant	3169			U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"Forkhead boxes"	5021	protein-coding gene	gene with protein product		602294	"hepatocyte nuclear factor 3, alpha"	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.357G>A	14.37:g.38061632C>T			37131383	B2R9H6|B7ZAP5|Q9H2A0	Silent	SNP	ENST00000250448.2	37	CCDS9665.1																																																																																				0.741	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1			T	38061632	C	T	38061632	2	4	56	1	0	0	0	0	0	0	0	1	6008	796	28	3		3	FOXA1	14	38061632	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09		38061632	69287908	79	7481										
CLEC14A	161198	broad.mit.edu	37	chr14	38724289	38724289	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggccatgttctctgcggcacGgggctggttgcagtggccgg	18	11	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr14:38724289G>A	ENST00000342213.2	-	1	1285	c.939C>T	c.(937-939)ccC>ccT	p.P313P		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	313						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.P313P(1)		breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	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;0.00439)		TCTGCGGCACGGGGCTGGTTG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	14											64	66	65					14																	38724289		2203	4299	6502	37794040	SO:0001819	synonymous_variant	161198				CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.939C>T	14.37:g.38724289G>A			37794040	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1																																																																																				0.617	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		A	38724289	G	A	38724289	2	1	56	1	0	0	0	0	0	0	0	1	3505	1103	39	1		1	CLEC14A	14	38724289	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	662657	38724289	68625251	80	7482										
PRKCH	5583	broad.mit.edu	37	chr14	61995892	61995892	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atttgcaatggtgtcaccacGgccacattctgtggcacgcc	10	13	2	0	rs113681621	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr14:61995892G>T	ENST00000332981.5	+	11	1918	c.1533G>T	c.(1531-1533)acG>acT	p.T511T	PRKCH_ENST00000555082.1_Silent_p.T350T|RP11-47I22.4_ENST00000556347.1_Missense_Mutation_p.R16L	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	511	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)	p.T511T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		GTGTCACCACGGCCACATTCT	0.517																																					Melanoma(135;863 1779 8064 14443 26348)											1	Substitution - coding silent(1)	large_intestine(1)	14											121	99	106					14																	61995892		2203	4300	6503	61065645	SO:0001819	synonymous_variant	5583			M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1533G>T	14.37:g.61995892G>T			61065645	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	37	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	G	7.233	0.599626	0.13939	.	.	ENSG00000258989	ENST00000556347	.	.	.	5.9	-9.93	0.00452	.	.	.	.	.	T	0.46034	0.1372	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55173	-0.8182	4	.	.	.	.	8.1984	0.31411	0.6366:0.1931:0.0958:0.0745	.	.	.	.	L	16	.	.	R	+	2	0	RP11-47I22.4	61065645	0.000000	0.05858	0.689000	0.30133	0.686000	0.39977	-3.991000	0.00318	-1.562000	0.01682	-0.808000	0.03180	CGG		0.517	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61995892	G	T	61995892	2	4	56	1	0	0	0	0	0	0	0	1	12547	1103	39	2		2	PRKCH	14	61995892	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	23271603	61995892	45353648	81	7483										
ATP10A	57194	broad.mit.edu	37	chr15	26026197	26026197	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	agccgcggaccacctgccgcCgcttcaggttggtctctcca	11	17	2	0	rs539032579		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:26026197C>T	ENST00000356865.6	-	2	734	c.623G>A	c.(622-624)cGg>cAg	p.R208Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	208					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R208Q(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CACCTGCCGCCGCTTCAGGTT	0.602													C|||	1	0.000199681	0	0	5008	,	,		16301	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	15											72	74	74					15																	26026197		2203	4300	6503	23577290	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.623G>A	15.37:g.26026197C>T	ENSP00000349325:p.Arg208Gln		23577290	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	8.388	0.839056	0.16891	.	.	ENSG00000206190	ENST00000356865	D	0.90385	-2.66	4.67	3.67	0.42095	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.121989	0.56097	D	0.000034	T	0.55862	0.1947	N	0.00082	-2.215	0.38704	D	0.953065	B	0.11235	0.004	B	0.09377	0.004	T	0.66803	-0.5831	10	0.02654	T	1	-29.3942	4.2405	0.10645	0.0:0.7173:0.0:0.2827	.	208	O60312	AT10A_HUMAN	Q	208	ENSP00000349325:R208Q	ENSP00000349325:R208Q	R	-	2	0	ATP10A	23577290	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.672000	0.54583	2.428000	0.82296	0.561000	0.74099	CGG		0.602	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	26026197	C	T	26026197	3	4	56	1	0	0	0	0	1	0	0	0	1117	652	23	1	3956	1	ATP10A	15	26026197	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		26026197	76505195	82	7484										
OCA2	4948	broad.mit.edu	37	chr15	28230313	28230313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gatgatcatggcccacacccGtccccgggagagccggtatg	13	14	1	2	rs372899234		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:28230313G>A	ENST00000354638.3	-	13	1416	c.1261C>T	c.(1261-1263)Cgg>Tgg	p.R421W	OCA2_ENST00000382996.2_Missense_Mutation_p.R421W|OCA2_ENST00000353809.5_Missense_Mutation_p.R397W	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	421					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.R421W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GCCCACACCCGTCCCCGGGAG	0.572									Oculocutaneous Albinism				G|||	1	0.000199681	0	0	5008	,	,		19287	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	15						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	107	79	89		1261	0.1	0	15		89	0,8600		0,0,4300	no	missense	OCA2	NM_000275.2	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	421/839	28230313	1,13005	2203	4300	6503	25903908	SO:0001583	missense	4948	Familial Cancer Database			CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1261C>T	15.37:g.28230313G>A	ENSP00000346659:p.Arg421Trp		25903908	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486431	0.63962	2.27E-4	0.0	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.82344	-1.6;-1.6;-1.6	5.35	0.0772	0.14407	Divalent ion symporter (1);	0.140477	0.64402	D	0.000009	D	0.88463	0.6443	M	0.69358	2.11	0.37669	D	0.923076	D;D	0.89917	1.0;1.0	D;D	0.72625	0.971;0.978	D	0.88999	0.3420	10	0.87932	D	0	-4.0634	14.1846	0.65598	0.0:0.0:0.5266:0.4734	.	397;421	Q04671-2;Q04671	.;P_HUMAN	W	421;397;421	ENSP00000346659:R421W;ENSP00000261276:R397W;ENSP00000372457:R421W	ENSP00000261276:R397W	R	-	1	2	OCA2	25903908	0.951000	0.32395	0.017000	0.16124	0.790000	0.44656	3.001000	0.49488	-0.172000	0.10779	-0.262000	0.10625	CGG		0.572	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		A	28230313	G	A	28230313	3	1	56	1	0	0	0	0	1	0	0	0	10846	1144	40	1	1303	1	OCA2	15	28230313	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	2204116	28230313	74301079	83	7485										
CTDSPL2	51496	broad.mit.edu	37	chr15	44811371	44811371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttatttttatgtttaggcacCggcttttccgtgaacattgt	8	7	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:44811371C>T	ENST00000260327.4	+	11	1680	c.1117C>T	c.(1117-1119)Cgg>Tgg	p.R373W	CTD-2329K10.1_ENST00000561324.1_RNA|CTDSPL2_ENST00000558373.1_Missense_Mutation_p.R301W|CTDSPL2_ENST00000558966.1_Missense_Mutation_p.R373W|CTDSPL2_ENST00000396780.1_Missense_Mutation_p.R301W	NM_016396.2	NP_057480.2	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	373	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.						phosphoprotein phosphatase activity (GO:0004721)	p.R373W(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	13		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		GTTTAGGCACCGGCTTTTCCG	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	15											21	22	22					15																	44811371		2179	4288	6467	42598663	SO:0001583	missense	51496			AF161478	CCDS10110.1	15q15.3-q21.1	2010-06-21			ENSG00000137770	ENSG00000137770		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	26936	protein-coding gene	gene with protein product							Standard	NM_016396		Approved	HSPC129, FLJ10523	uc001ztr.3	Q05D32	OTTHUMG00000131159	ENST00000260327.4:c.1117C>T	15.37:g.44811371C>T	ENSP00000260327:p.Arg373Trp		42598663	Q3ZTU1|Q6AI06|Q8IYI9|Q9NVT2|Q9NZX8|Q9P030	Missense_Mutation	SNP	ENST00000260327.4	37	CCDS10110.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333335	0.60853	.	.	ENSG00000137770	ENST00000260327;ENST00000396780	T;T	0.21031	2.03;2.03	5.66	4.74	0.60224	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.61825	0.2378	H	0.98802	4.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73421	-0.3988	10	0.87932	D	0	-4.6394	9.62	0.39716	0.1404:0.7883:0.0:0.0713	.	301;373	Q05D32-2;Q05D32	.;CTSL2_HUMAN	W	373;301	ENSP00000260327:R373W;ENSP00000380000:R301W	ENSP00000260327:R373W	R	+	1	2	CTDSPL2	42598663	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	1.794000	0.38774	1.394000	0.46624	0.557000	0.71058	CGG		0.269	CTDSPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253851.1	NM_016396		T	44811371	C	T	44811371	3	4	56	1	0	0	0	0	1	0	0	0	4012	643	23	1	1155	1	CTDSPL2	15	44811371	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	16581058	44811371	57720021	84	7486										
FBN1	2200	broad.mit.edu	37	chr15	48787710	48787710	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccaaagtactttcagaagaaCattcacaaataaaagagcct	5	9	2	3	rs397515775		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:48787710C>G	ENST00000316623.5	-	21	2950	c.2495G>C	c.(2494-2496)tGt>tCt	p.C832S		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	832	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		C -> Y (in MFS). {ECO:0000269|PubMed:16222657}.		extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.C832S(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTCAGAAGAACATTCACAAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	15	GRCh37	CM972801	FBN1	M							186	199	194					15																	48787710		2197	4296	6493	46575002	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.2495G>C	15.37:g.48787710C>G	ENSP00000325527:p.Cys832Ser		46575002	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.832381	0.91036	.	.	ENSG00000166147	ENST00000316623	D	0.96619	-4.07	5.87	5.87	0.94306	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	H	0.97783	4.075	0.80722	D	1	D	0.55172	0.97	P	0.60886	0.88	D	0.99379	1.0922	10	0.87932	D	0	.	18.7582	0.91839	0.0:1.0:0.0:0.0	.	832	P35555	FBN1_HUMAN	S	832	ENSP00000325527:C832S	ENSP00000325527:C832S	C	-	2	0	FBN1	46575002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.042000	0.70996	2.777000	0.95525	0.555000	0.69702	TGT		0.333	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			G	48787710	C	G	48787710	3	3	56	1	0	0	0	0	1	0	0	0	5721	478	17	5	6304	5	FBN1	15	48787710	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	3976339	48787710	53743682	85	7487										
DENND4A	10260	broad.mit.edu	37	chr15	65964191	65964191	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgaaggaagatgtcacttctGatttcccaggtaaggcaaac	10	8	2	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:65964191G>C	ENST00000431932.2	-	24	4479	c.4271C>G	c.(4270-4272)tCa>tGa	p.S1424*	DENND4A_ENST00000443035.3_Nonsense_Mutation_p.S1467*	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1424					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.S1426*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TGTCACTTCTGATTTCCCAGG	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											142	137	138					15																	65964191		1835	4095	5930	63751245	SO:0001587	stop_gained	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.4271C>G	15.37:g.65964191G>C	ENSP00000396830:p.Ser1424*		63751245	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Nonsense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	44	10.739269	0.99460	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	.	.	.	5.92	5.92	0.95590	.	1.047830	0.07441	N	0.897387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.3151	0.98650	0.0:0.0:1.0:0.0	.	.	.	.	X	1467;1424	.	ENSP00000396830:S1424X	S	-	2	0	DENND4A	63751245	1.000000	0.71417	0.998000	0.56505	0.639000	0.38242	7.832000	0.86757	2.809000	0.96659	0.467000	0.42956	TCA		0.348	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	65964191	G	C	65964191	4	2	56	1	0	0	0	0	0	1	0	0	4444	1294	45	5	1356	5	DENND4A	15	65964191	Nonsense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	17176481	65964191	36567201	86	7488										
SNX33	257364	broad.mit.edu	37	chr15	75949483	75949483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	catgatgcagaactacttgcGccagcagatcctcttctacc	7	14	2	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:75949483G>A	ENST00000308527.5	+	2	2849	c.1652G>A	c.(1651-1653)cGc>cAc	p.R551H		NM_153271.1	NP_695003.1	Q8WV41	SNX33_HUMAN	sorting nexin 33	551	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038)	cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.R551H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	19						AACTACTTGCGCCAGCAGATC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	15											123	109	114					15																	75949483		2197	4294	6491	73736538	SO:0001583	missense	257364			AK091291	CCDS10283.1	15q23	2008-04-18	2008-03-25	2008-03-25	ENSG00000173548	ENSG00000173548			28468	protein-coding gene	gene with protein product			"SH3 and PX domain containing 3"	SH3PX3		16374509, 16782399, 18353773	Standard	NM_153271		Approved	MGC32065, SH3PXD3C, SNX30	uc002bau.3	Q8WV41	OTTHUMG00000142835	ENST00000308527.5:c.1652G>A	15.37:g.75949483G>A	ENSP00000311427:p.Arg551His		73736538	B1NM17	Missense_Mutation	SNP	ENST00000308527.5	37	CCDS10283.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.873255	0.51695	.	.	ENSG00000173548	ENST00000308527	T	0.41065	1.01	5.41	2.48	0.30137	Sorting nexin protein, WASP-binding domain (1);	0.258092	0.37530	N	0.002050	T	0.22936	0.0554	N	0.19112	0.55	0.49582	D	0.999806	B;B	0.28584	0.216;0.216	B;B	0.25987	0.065;0.065	T	0.04495	-1.0947	10	0.37606	T	0.19	-1.6655	5.3192	0.15872	0.2896:0.146:0.5644:0.0	.	551;551	B1NM17;Q8WV41	.;SNX33_HUMAN	H	551	ENSP00000311427:R551H	ENSP00000311427:R551H	R	+	2	0	SNX33	73736538	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.751000	0.38339	0.635000	0.30488	0.591000	0.81541	CGC		0.627	SNX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286471.1	NM_153271		A	75949483	G	A	75949483	3	1	56	1	0	0	0	0	1	0	0	0	14940	1087	38	1	1658	1	SNX33	15	75949483	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	9985292	75949483	26581909	87	7489										
SH3GL3	6457	broad.mit.edu	37	chr15	84237406	84237406	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgaaatacgggaaggagctcGgggaagactccacctttggt	14	8	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:84237406G>T	ENST00000427482.2	+	4	619	c.313G>T	c.(313-315)Ggg>Tgg	p.G105W	SH3GL3_ENST00000434347.1_Missense_Mutation_p.G113W|SH3GL3_ENST00000324537.5_Missense_Mutation_p.G113W|SH3GL3_ENST00000535412.1_Missense_Mutation_p.G105W	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	105	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.G113W(1)		central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						GAAGGAGCTCGGGGAAGACTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											74	78	77					15																	84237406		2203	4300	6503	82028410	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.313G>T	15.37:g.84237406G>T	ENSP00000391372:p.Gly105Trp		82028410	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637043	0.67130	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	4.86	4.86	0.63082	BAR (3);	0.000000	0.85682	D	0.000000	D	0.85177	0.5637	M	0.90483	3.12	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.88637	0.3173	10	0.87932	D	0	-5.9604	17.3782	0.87398	0.0:0.0:1.0:0.0	.	105;105;113	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	W	105;105;113;113	ENSP00000391372:G105W;ENSP00000439239:G105W;ENSP00000320092:G113W;ENSP00000397871:G113W	ENSP00000320092:G113W	G	+	1	0	SH3GL3	82028410	1.000000	0.71417	0.832000	0.32986	0.534000	0.34807	9.384000	0.97219	2.402000	0.81655	0.544000	0.68410	GGG		0.522	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		T	84237406	G	T	84237406	3	4	56	1	0	0	0	0	1	0	0	0	14289	1116	39	2	327	2	SH3GL3	15	84237406	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	8287923	84237406	18293986	88	7490										
SPATA8	145946	broad.mit.edu	37	chr15	97327411	97327411	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cgcgacatttctcagaagccAtgacatgtccctgcggctgg	11	13	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr15:97327411A>T	ENST00000328504.3	+	2	385	c.118A>T	c.(118-120)Atg>Ttg	p.M40L	SPATA8-AS1_ENST00000560888.1_RNA|SPATA8-AS1_ENST00000558722.1_RNA|SPATA8_ENST00000558553.1_De_novo_Start_OutOfFrame	NM_173499.3	NP_775770.1	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8	40								p.M40L(1)		large_intestine(4)|lung(8)|ovary(1)|skin(3)	16	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			CTCAGAAGCCATGACATGTCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	15											79	76	77					15																	97327411		2197	4298	6495	95128415	SO:0001583	missense	145946			AY489187	CCDS10376.1	15q26	2008-02-05			ENSG00000185594	ENSG00000185594			28676	protein-coding gene	gene with protein product		613948					Standard	NM_173499		Approved	MGC44294	uc002bue.3	Q6RVD6	OTTHUMG00000149847	ENST00000328504.3:c.118A>T	15.37:g.97327411A>T	ENSP00000328149:p.Met40Leu		95128415	Q2KJ07	Missense_Mutation	SNP	ENST00000328504.3	37	CCDS10376.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.478010	0.44044	.	.	ENSG00000185594	ENST00000328504	.	.	.	3.84	1.54	0.23209	.	.	.	.	.	T	0.28532	0.0706	N	0.08118	0	0.80722	D	1	P	0.37573	0.6	B	0.42555	0.391	T	0.09100	-1.0690	8	0.87932	D	0	.	5.3629	0.16098	0.7665:0.0:0.2335:0.0	.	40	Q6RVD6	SPAT8_HUMAN	L	40	.	ENSP00000328149:M40L	M	+	1	0	SPATA8	95128415	0.002000	0.14202	0.916000	0.36221	0.834000	0.47266	0.854000	0.27791	0.327000	0.23409	0.533000	0.62120	ATG		0.592	SPATA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313533.1	NM_173499		T	97327411	A	T	97327411	3	4	56	1	0	0	0	0	1	0	0	0	15054	217	8	5	124	5	SPATA8	15	97327411	Missense_Mutation	SNP	A	TCGA-AG-4001-01A-02W-1073-09	13090005	97327411	5203981	89	7491										
SRRM2	23524	broad.mit.edu	37	chr16	2816324	2816324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cagaacgccaccagtaacccGccgtcgttcaaggtctagaa	9	14	2	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:2816324G>A	ENST00000301740.8	+	11	6344	c.5795G>A	c.(5794-5796)cGc>cAc	p.R1932H		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1932	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.R1932H(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CCAGTAACCCGCCGTCGTTCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											76	79	78					16																	2816324		2198	4300	6498	2756325	SO:0001583	missense	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.5795G>A	16.37:g.2816324G>A	ENSP00000301740:p.Arg1932His		2756325	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811263	0.32053	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.31769	1.48	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000008	T	0.33702	0.0872	N	0.08118	0	0.35689	D	0.814703	D	0.76494	0.999	D	0.69654	0.965	T	0.44817	-0.9303	10	0.27082	T	0.32	-8.0496	16.3084	0.82859	0.0:0.0:1.0:0.0	.	1932	Q9UQ35	SRRM2_HUMAN	H	1932;1932;1184	ENSP00000301740:R1932H	ENSP00000301740:R1932H	R	+	2	0	SRRM2	2756325	0.990000	0.36364	1.000000	0.80357	0.985000	0.73830	3.362000	0.52314	2.454000	0.82982	0.650000	0.86243	CGC		0.582	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2816324	G	A	2816324	3	1	56	1	0	0	0	0	1	0	0	0	15208	1087	38	1	5833	1	SRRM2	16	2816324	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		2816324	87538429	90	7492										
GRIN2A	2903	broad.mit.edu	37	chr16	10031860	10031860	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tctggcctctccatctgcccGtagcagctggccttggcctc	10	17	3	0	rs368200727		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:10031860G>A	ENST00000396573.2	-	4	1272	c.963C>T	c.(961-963)taC>taT	p.Y321Y	GRIN2A_ENST00000535259.1_Silent_p.Y164Y|GRIN2A_ENST00000562109.1_Silent_p.Y321Y|GRIN2A_ENST00000404927.2_Silent_p.Y321Y|GRIN2A_ENST00000566670.1_5'Flank|GRIN2A_ENST00000396575.2_Silent_p.Y321Y|GRIN2A_ENST00000330684.3_Silent_p.Y321Y	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	321					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.Y321Y(2)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCATCTGCCCGTAGCAGCTGG	0.562																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	16						G	,,	3,4391	6.2+/-15.9	0,3,2194	67	58	61		963,963,963	-3.6	1	16		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIN2A	NM_000833.3,NM_001134407.1,NM_001134408.1	,,	0,4,6493	AA,AG,GG		0.0116,0.0683,0.0308	,,	321/1465,321/1465,321/1282	10031860	4,12990	2197	4300	6497	9939361	SO:0001819	synonymous_variant	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.963C>T	16.37:g.10031860G>A			9939361	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.562	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	10031860	G	A	10031860	2	1	56	1	0	0	0	0	0	0	0	1	6800	1140	40	1		1	GRIN2A	16	10031860	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	7215536	10031860	80322893	91	7493										
MYH11	4629	broad.mit.edu	37	chr16	15932005	15932005	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttctccgaggggacccagacGagtctcttggcggcccagtc	13	14	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:15932005G>A	ENST00000300036.5	-	2	214	c.105C>T	c.(103-105)ctC>ctT	p.L35L	MYH11_ENST00000452625.2_Silent_p.L35L|MYH11_ENST00000396324.3_Silent_p.L35L|MYH11_ENST00000576790.2_Silent_p.L35L	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	35					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.L35L(2)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GGACCCAGACGAGTCTCTTGG	0.577			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	2	Substitution - coding silent(2)	large_intestine(2)	16											101	103	102					16																	15932005		2197	4300	6497	15839506	SO:0001819	synonymous_variant	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.105C>T	16.37:g.15932005G>A			15839506	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																				0.577	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15932005	G	A	15932005	2	1	56	1	0	0	0	0	0	0	0	1	10061	1045	37	1		1	MYH11	16	15932005	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5900145	15932005	74422748	92	7494										
PRR14	78994	broad.mit.edu	37	chr16	30664362	30664363	+	Frame_Shift_Ins	INS	-	-	C													0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttcacaaaaggtggaccgggINSccccccagcccaccctggtg							TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:30664362_30664363insC	ENST00000542965.2	+	4	898_899	c.442_443insC	c.(442-444)gccfs	p.A148fs	PRR14_ENST00000300835.4_Frame_Shift_Ins_p.A148fs			Q9BWN1	PRR14_HUMAN	proline rich 14	148	Pro-rich.							p.Q150fs*15(1)|p.A148P(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			GGTGGACCGGGCCCCCCAGCCC	0.644																																																2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(1)|endometrium(1)	16																																								30571864	SO:0001589	frameshift_variant	78994			AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.448dupC	16.37:g.30664368_30664368dupC	ENSP00000441641:p.Ala148fs		30571863	Q8WTX2	Frame_Shift_Ins	INS	ENST00000542965.2	37	CCDS10687.1																																																																																				0.644	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		C	30664363	-	C	30664362	7	5	56	1	0	1	1	0	0	0	0	0	12620	1203	42	0	456	0	PRR14	16	30664362	Frame_Shift_Ins	INS	-	TCGA-AG-4001-01A-02W-1073-09	14732357	30664362	59690391	93	7495										
MMP2	4313	broad.mit.edu	37	chr16	55519308	55519308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggagactcccattttgatgaCgatgagctatggaccttggg	13	8	0	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:55519308C>T	ENST00000219070.4	+	4	1136	c.627C>T	c.(625-627)gaC>gaT	p.D209D	MMP2_ENST00000570308.1_Silent_p.D133D|MMP2_ENST00000437642.2_Silent_p.D159D|MMP2_ENST00000543485.1_Silent_p.D133D	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	209	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.D209D(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	ATTTTGATGACGATGAGCTAT	0.577																																																2	Substitution - coding silent(2)	large_intestine(2)	16											111	98	102					16																	55519308		2198	4300	6498	54076809	SO:0001819	synonymous_variant	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.627C>T	16.37:g.55519308C>T			54076809	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																				0.577	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			T	55519308	C	T	55519308	2	4	56	1	0	0	0	0	0	0	0	1	9688	535	19	1		1	MMP2	16	55519308	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	24854946	55519308	34835445	94	7496										
CNGB1	1258	broad.mit.edu	37	chr16	57953079	57953079	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aacttgcagcagagcatgtcGcaatagtgctcctcttccac	8	13	1	1	rs369525244		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr16:57953079G>A	ENST00000251102.8	-	20	1941	c.1881C>T	c.(1879-1881)tgC>tgT	p.C627C	CNGB1_ENST00000564448.1_Silent_p.C621C	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	627					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.C627C(1)		breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AGAGCATGTCGCAATAGTGCT	0.577																																					Colon(156;1293 1853 16336 28962 38659)											1	Substitution - coding silent(1)	large_intestine(1)	16											103	108	107					16																	57953079		2001	4178	6179	56510580	SO:0001819	synonymous_variant	1258			AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.1881C>T	16.37:g.57953079G>A			56510580	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																				0.577	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57953079	G	A	57953079	2	1	56	1	0	0	0	0	0	0	0	1	3606	1079	38	1		1	CNGB1	16	57953079	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	2433771	57953079	32401674	95	7497										
TP53	7157	broad.mit.edu	37	chr17	7579321	7579322	+	Frame_Shift_Del	DEL	CA	CA	-													0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gggcaactgaccgtgcaagtCacagacttggctgtcccaga					rs587780067		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	CA	CA	CA	-	CA	CA	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr17:7579321_7579322delCA	ENST00000269305.4	-	4	554_555	c.365_366delTG	c.(364-366)gtgfs	p.V122fs	TP53_ENST00000359597.4_Frame_Shift_Del_p.V122fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.V122fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.V122fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Frame_Shift_Del_p.V122fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.V122fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	122	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> L (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.V122fs*26(5)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGTGCAAGTCACAGACTTGGC	0.554		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	23	Deletion - Frameshift(13)|Whole gene deletion(8)|Deletion - In frame(2)	upper_aerodigestive_tract(4)|large_intestine(4)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|breast(2)|stomach(1)|liver(1)|ovary(1)	17	GRCh37	CM065494	TP53	M																																				7520047	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.365_366delTG	17.37:g.7579323_7579324delCA	ENSP00000269305:p.Val122fs		7520046	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.554	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579322	CA	-	7579321	7	5	56	1	0	1	0	1	0	0	0	0	16421	813	29	0	936	0	TP53	17	7579321	Frame_Shift_Del	DEL	CA	TCGA-AG-4001-01A-02W-1073-09		7579321	73615889	96	7498										
NCOR1	9611	broad.mit.edu	37	chr17	16004937	16004937	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	actttcatcttcagctggttTtgtacttggaactgctaagg	9	8	3	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr17:16004937T>A	ENST00000268712.3	-	20	2574	c.2317A>T	c.(2317-2319)Aaa>Taa	p.K773*	NCOR1_ENST00000583226.1_5'Flank|NCOR1_ENST00000395848.1_Nonsense_Mutation_p.K680*|NCOR1_ENST00000395851.1_Nonsense_Mutation_p.K789*|RNU6-314P_ENST00000516574.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	773					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.K773*(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TCAGCTGGTTTTGTACTTGGA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											183	165	171					17																	16004937		2203	4300	6503	15945662	SO:0001587	stop_gained	9611			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.2317A>T	17.37:g.16004937T>A	ENSP00000268712:p.Lys773*		15945662	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Nonsense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	33	5.250174	0.95305	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	.	.	.	5.55	3.28	0.37604	.	0.341207	0.33092	N	0.005283	.	.	.	.	.	.	0.21147	N	0.999771	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1724	4.3196	0.11011	0.1226:0.0694:0.1278:0.6802	.	.	.	.	X	773;789;680;680	.	ENSP00000268712:K773X	K	-	1	0	NCOR1	15945662	1.000000	0.71417	0.002000	0.10522	0.937000	0.57800	0.694000	0.25512	0.369000	0.24510	0.533000	0.62120	AAA		0.507	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16004937	T	A	16004937	4	1	56	1	0	0	0	0	0	1	0	0	10266	1850	64	5	5113	5	NCOR1	17	16004937	Nonsense_Mutation	SNP	T	TCGA-AG-4001-01A-02W-1073-09	8425616	16004937	65190273	97	7499										
BCAS3	54828	broad.mit.edu	37	chr17	59024609	59024609	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tagtcacaacagacacccttGgccatgactttcatgtcttc	6	13	3	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr17:59024609G>C	ENST00000390652.5	+	14	1148	c.1117G>C	c.(1117-1119)Ggc>Cgc	p.G373R	BCAS3_ENST00000589222.1_Missense_Mutation_p.G373R|BCAS3_ENST00000585744.1_Missense_Mutation_p.G144R|BCAS3_ENST00000408905.3_Missense_Mutation_p.G373R|BCAS3_ENST00000588874.1_Missense_Mutation_p.G144R|BCAS3_ENST00000407086.3_Missense_Mutation_p.G373R|BCAS3_ENST00000588462.1_Missense_Mutation_p.G373R	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.G373R(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AGACACCCTTGGCCATGACTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											203	186	191					17																	59024609		1903	4133	6036	56379391	SO:0001583	missense	54828			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.1117G>C	17.37:g.59024609G>C	ENSP00000375067:p.Gly373Arg		56379391		Missense_Mutation	SNP	ENST00000390652.5	37	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848929	0.91277	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000405070;ENST00000408905;ENST00000360207;ENST00000405217	T;T;T	0.62498	0.02;0.02;0.02	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81597	0.4856	M	0.80847	2.515	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.985;0.988;0.999;0.997;1.0	T	0.83058	-0.0149	10	0.87932	D	0	.	19.9542	0.97213	0.0:0.0:1.0:0.0	.	164;178;373;373;373	B4E3M9;Q70WD9;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;.;BCAS3_HUMAN;.	R	373;373;373;373;165;178	ENSP00000375067:G373R;ENSP00000385323:G373R;ENSP00000386173:G373R	ENSP00000353336:G165R	G	+	1	0	BCAS3	56379391	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.467000	0.97671	2.788000	0.95919	0.585000	0.79938	GGC		0.388	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		C	59024609	G	C	59024609	3	2	56	1	0	0	0	0	1	0	0	0	1353	1348	47	5	1167	5	BCAS3	17	59024609	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	43019672	59024609	22170601	98	7500										
CACNG5	27091	broad.mit.edu	37	chr17	64880889	64880889	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccacaaccattttggaccccGgaccacccactctacttccc	4	20	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr17:64880889G>A	ENST00000533854.1	+	5	807				CACNG5_ENST00000169565.3_Silent_p.P227P|CACNG5_ENST00000307139.3_Intron			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)	p.P227P(1)		NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			TTTGGACCCCGGACCACCCAC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	17											108	93	98					17																	64880889		2203	4300	6503	62311351	SO:0001627	intron_variant	27091			AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"Calcium channel subunits"	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.570+111G>A	17.37:g.64880889G>A			62311351	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Silent	SNP	ENST00000533854.1	37	CCDS11665.1																																																																																				0.597	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811		A	64880889	G	A	64880889	1	1	56	0	1	0	0	0	0	0	0	0	2566	1103	39	1		1	CACNG5	17	64880889	Intron	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5856280	64880889	16314321	99	7501										
ZNF560	147741	broad.mit.edu	37	chr19	9580372	9580372	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccaagagatcagactgggttTgaagagctggtaacctgtac	12	8	1	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:9580372T>G	ENST00000301480.4	-	8	676	c.463A>C	c.(463-465)Aaa>Caa	p.K155Q		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	155	KRAB 2. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K155Q(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						AGACTGGGTTTGAAGAGCTGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											108	94	99					19																	9580372		2203	4300	6503	9441372	SO:0001583	missense	147741			AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.463A>C	19.37:g.9580372T>G	ENSP00000301480:p.Lys155Gln		9441372	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.288461	0.40494	.	.	ENSG00000198028	ENST00000301480	T	0.00932	5.53	2.43	2.43	0.29744	Krueppel-associated box (3);	.	.	.	.	T	0.02610	0.0079	M	0.73372	2.23	0.21184	N	0.999765	D	0.60160	0.987	P	0.56278	0.795	T	0.45659	-0.9246	9	0.18710	T	0.47	.	8.3437	0.32258	0.0:0.0:0.0:1.0	.	155	Q96MR9	ZN560_HUMAN	Q	155	ENSP00000301480:K155Q	ENSP00000301480:K155Q	K	-	1	0	ZNF560	9441372	0.347000	0.24853	0.053000	0.19242	0.907000	0.53573	1.425000	0.34859	1.098000	0.41479	0.379000	0.24179	AAA		0.463	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		G	9580372	T	G	9580372	3	3	56	1	0	0	0	0	1	0	0	0	18030	1821	63	4	1921	4	ZNF560	19	9580372	Missense_Mutation	SNP	T	TCGA-AG-4001-01A-02W-1073-09		9580372	49548611	100	7502										
SLC1A6	6511	broad.mit.edu	37	chr19	15063790	15063790	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atgtcttccgtgggcaagccGaccgacgtaagcacaatgac	11	12	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:15063790G>A	ENST00000221742.3	-	8	1456	c.1449C>T	c.(1447-1449)gtC>gtT	p.V483V	SLC1A6_ENST00000600144.1_Silent_p.V405V|SLC1A6_ENST00000430939.2_Silent_p.V419V	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	483					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.V483V(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						TGGGCAAGCCGACCGACGTAA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19											189	147	161					19																	15063790		2203	4300	6503	14924790	SO:0001819	synonymous_variant	6511				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1449C>T	19.37:g.15063790G>A			14924790	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1																																																																																				0.617	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		A	15063790	G	A	15063790	2	1	56	1	0	0	0	0	0	0	0	1	14473	1045	37	1		1	SLC1A6	19	15063790	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5483418	15063790	44065193	101	7503										
ZNF507	22847	broad.mit.edu	37	chr19	32851435	32851435	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aagtcttcagtccagaaacaAtatagatgtgatgtgtgtga	10	5	2	4			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:32851435A>G	ENST00000311921.4	+	4	2463	c.2271A>G	c.(2269-2271)caA>caG	p.Q757Q	ZNF507_ENST00000355898.5_Silent_p.Q757Q|ZNF507_ENST00000544431.1_Silent_p.Q757Q	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	757					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q757Q(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					TCCAGAAACAATATAGATGTG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	19											147	140	142					19																	32851435		2203	4300	6503	37543275	SO:0001819	synonymous_variant	22847			AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2271A>G	19.37:g.32851435A>G			37543275	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Silent	SNP	ENST00000311921.4	37	CCDS32985.1																																																																																				0.368	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		G	32851435	A	G	32851435	2	3	56	1	0	0	0	0	0	0	0	1	17992	98	4	4		4	ZNF507	19	32851435	Silent	SNP	A	TCGA-AG-4001-01A-02W-1073-09	17787645	32851435	26277548	102	7504										
ZNF382	84911	broad.mit.edu	37	chr19	37117799	37117799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	atcaatgtggaaaggccttcCgtcagaagacagccctcacc	9	13	3	2	rs374650096		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:37117799C>T	ENST00000292928.2	+	5	1113	c.1000C>T	c.(1000-1002)Cgt>Tgt	p.R334C	ZNF382_ENST00000423582.1_Missense_Mutation_p.R285C|CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000435416.1_Missense_Mutation_p.R333C|ZNF382_ENST00000439428.1_Missense_Mutation_p.R333C	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	334	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R334C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AAAGGCCTTCCGTCAGAAGAC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	CYS/ARG	0,4406		0,0,2203	76	75	75		1000	3.3	1	19		75	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF382	NM_032825.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	334/551	37117799	1,13005	2203	4300	6503	41809639	SO:0001583	missense	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1000C>T	19.37:g.37117799C>T	ENSP00000292928:p.Arg334Cys		41809639	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150089	0.37923	0.0	1.16E-4	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.07444	3.19;3.19;3.19;3.19	4.47	3.34	0.38264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42821	D	0.000651	T	0.16685	0.0401	M	0.64630	1.985	0.41073	D	0.985467	D;D;D	0.76494	0.998;0.998;0.999	P;P;P	0.60886	0.809;0.809;0.88	T	0.00460	-1.1726	10	0.42905	T	0.14	.	5.0872	0.14689	0.2061:0.6881:0.0:0.1058	.	333;333;334	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	C	285;334;333;333	ENSP00000389722:R285C;ENSP00000292928:R334C;ENSP00000407593:R333C;ENSP00000410113:R333C	ENSP00000292928:R334C	R	+	1	0	ZNF382	41809639	0.001000	0.12720	1.000000	0.80357	0.998000	0.95712	0.882000	0.28186	2.481000	0.83766	0.591000	0.81541	CGT		0.448	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		T	37117799	C	T	37117799	3	4	56	1	0	0	0	0	1	0	0	0	17912	652	23	1	1010	1	ZNF382	19	37117799	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	4266364	37117799	22011184	103	7505										
PSG2	5670	broad.mit.edu	37	chr19	43579536	43579536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cagggtgactgggtcactgcGgctggcactccctgagttcc	14	13	1	2	rs529547477		TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:43579536G>A	ENST00000406487.1	-	3	777	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	227	Ig-like C2-type 1.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R227C(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GGGTCACTGCGGCTGGCACTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											221	233	229					19																	43579536		2202	4299	6501	48271376	SO:0001583	missense	5670				CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9519	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta-1-glycoprotein 7", "carcinoembryonic antigen SG8"	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.679C>T	19.37:g.43579536G>A	ENSP00000385706:p.Arg227Cys		48271376	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	.	.	.	.	.	.	.	.	.	.	N	11.11	1.543254	0.27563	.	.	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.12774	2.65	1.33	-0.184	0.13280	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.31544	0.0800	M	0.80616	2.505	0.09310	N	1	P;D	0.89917	0.934;1.0	P;D	0.75484	0.712;0.986	T	0.08973	-1.0696	9	0.87932	D	0	.	3.9393	0.09319	0.0:0.0:0.5847:0.4153	.	227;227	B5MCM8;P11465	.;PSG2_HUMAN	C	227	ENSP00000385706:R227C	ENSP00000332984:R227C	R	-	1	0	PSG2	48271376	0.000000	0.05858	0.007000	0.13788	0.074000	0.17049	-0.263000	0.08670	0.703000	0.31848	0.454000	0.30748	CGC		0.527	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		A	43579536	G	A	43579536	3	1	56	1	0	0	0	0	1	0	0	0	12689	1116	39	1	340	1	PSG2	19	43579536	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	6461737	43579536	15549447	104	7506										
PSG4	5672	broad.mit.edu	37	chr19	43698574	43698574	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	caagcatagagcccactatgCtttgtagttatttgggggat	11	7	0	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:43698574C>T	ENST00000405312.3	-	5	1398	c.1161G>A	c.(1159-1161)aaG>aaA	p.K387K	PSG4_ENST00000433626.2_Silent_p.K294K|PSG4_ENST00000244295.9_Silent_p.K294K	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	387	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.K387K(1)|p.K294K(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				GCCCACTATGCTTTGTAGTTA	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	19											210	210	210					19																	43698574		2202	4295	6497	48390414	SO:0001819	synonymous_variant	5672				CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9521	protein-coding gene	gene with protein product	"pregnancy-specific beta-1-glycoprotein 4"	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.1161G>A	19.37:g.43698574C>T			48390414	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1																																																																																				0.468	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		T	43698574	C	T	43698574	2	4	56	1	0	0	0	0	0	0	0	1	12691	796	28	3		3	PSG4	19	43698574	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	119038	43698574	15430409	105	7507										
NLRP4	147945	broad.mit.edu	37	chr19	56369444	56369444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	aaccggagagactcttgttcGtcatcgacagcttcgaagag	11	10	2	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:56369444G>A	ENST00000301295.6	+	3	1107	c.685G>A	c.(685-687)Gtc>Atc	p.V229I	NLRP4_ENST00000346986.5_Missense_Mutation_p.V229I|NLRP4_ENST00000587891.1_Missense_Mutation_p.V154I	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	229	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.V229I(3)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		ACTCTTGTTCGTCATCGACAG	0.557																																																3	Substitution - Missense(3)	large_intestine(2)|ovary(1)	19											81	80	81					19																	56369444		2203	4300	6503	61061256	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.685G>A	19.37:g.56369444G>A	ENSP00000301295:p.Val229Ile		61061256	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.491014	0.01009	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.83992	-1.79;-1.79	4.1	-2.63	0.06133	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.51568	0.1682	N	0.02854	-0.475	0.23876	N	0.996597	B;B;B	0.27997	0.0;0.0;0.197	B;B;B	0.24006	0.0;0.001;0.05	T	0.50947	-0.8767	9	0.02654	T	1	.	4.8964	0.13753	0.448:0.2809:0.271:0.0	.	229;154;229	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	I	229	ENSP00000301295:V229I;ENSP00000344787:V229I	ENSP00000301295:V229I	V	+	1	0	NLRP4	61061256	0.159000	0.22864	0.009000	0.14445	0.166000	0.22503	-0.124000	0.10595	-0.811000	0.04369	-0.302000	0.09304	GTC		0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		A	56369444	G	A	56369444	3	1	56	1	0	0	0	0	1	0	0	0	10510	1145	40	1	691	1	NLRP4	19	56369444	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	12670870	56369444	2759539	106	7508										
ZNF586	54807	broad.mit.edu	37	chr19	58290302	58290302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tcacaaacacaggaatgttcGcactggagaaaggccttatg	10	9	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr19:58290302G>A	ENST00000396154.2	+	3	520	c.347G>A	c.(346-348)cGc>cAc	p.R116H	ZNF586_ENST00000391702.3_Missense_Mutation_p.R73H|ZNF586_ENST00000598183.1_Intron|ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron|ZNF586_ENST00000396150.4_Missense_Mutation_p.A74T	NM_017652.3	NP_060122.2	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R116H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)	15		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;0.026)		AGGAATGTTCGCACTGGAGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											80	81	81					19																	58290302		2061	4250	6311	62982114	SO:0001583	missense	54807			AK095993	CCDS42640.1, CCDS56107.1, CCDS56108.1	19q13.43	2013-01-08				ENSG00000083828		"Zinc fingers, C2H2-type", "-"	25949	protein-coding gene	gene with protein product						12477932	Standard	NM_017652		Approved	FLJ20070	uc002qqd.3	Q9NXT0		ENST00000396154.2:c.347G>A	19.37:g.58290302G>A	ENSP00000379458:p.Arg116His		62982114	A0JLV8|A8MY63|B3KTS9|E7ERT1|G3XAH3	Missense_Mutation	SNP	ENST00000396154.2	37	CCDS42640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.017|0.017	-1.503189|-1.503189	0.00992|0.00992	.|.	.|.	ENSG00000083828|ENSG00000083828	ENST00000396150|ENST00000449441;ENST00000391702;ENST00000396154	T|T;T	0.06142|0.09911	3.34|2.93;3.08	1.66|1.66	0.513|0.513	0.17000|0.17000	.|Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.01254|0.01254	0.0041|0.0041	N|N	0.00025|0.00025	-2.68|-2.68	0.23126|0.23126	N|N	0.998259|0.998259	B|B	0.22146|0.17465	0.065|0.022	B|B	0.06405|0.08055	0.002|0.003	T|T	0.43310|0.43310	-0.9399|-0.9399	9|9	0.09084|0.02654	T|T	0.74|1	.|.	5.2282|5.2282	0.15406|0.15406	0.8141:0.0:0.1859:0.0|0.8141:0.0:0.1859:0.0	.|.	74|116	A0JLV8|Q9NXT0	.|ZN586_HUMAN	T|H	74|116;73;116	ENSP00000379454:A74T|ENSP00000375583:R73H;ENSP00000379458:R116H	ENSP00000379454:A74T|ENSP00000375583:R73H	A|R	+|+	1|2	0|0	ZNF586|ZNF586	62982114|62982114	0.133000|0.133000	0.22466|0.22466	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	4.205000|4.205000	0.58466|0.58466	-0.081000|-0.081000	0.12662|0.12662	-0.339000|-0.339000	0.08088|0.08088	GCA|CGC		0.418	ZNF586-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466825.2	NM_017652		A	58290302	G	A	58290302	3	1	56	1	0	0	0	0	1	0	0	0	18058	1087	38	1	357	1	ZNF586	19	58290302	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	1920858	58290302	838681	107	7509										
MYL9	10398	broad.mit.edu	37	chr20	35177494	35177494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ccgcaggtttcatccatgagGaccacctccgggagctgctc	11	15	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr20:35177494G>A	ENST00000279022.2	+	4	465	c.361G>A	c.(361-363)Gac>Aac	p.D121N	RP5-977B1.7_ENST00000425233.1_RNA|RP5-977B1.11_ENST00000561134.1_RNA|MYL9_ENST00000346786.2_Missense_Mutation_p.D67N|RP5-977B1.7_ENST00000439595.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	121	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.D121N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				CATCCATGAGGACCACCTCCG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	20											73	66	69					20																	35177494		2203	4300	6503	34610908	SO:0001583	missense	10398			J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"Myosins / Light chain", "EF-hand domain containing"	15754	protein-coding gene	gene with protein product	"myosin regulatory light chain 2, smooth muscle isoform", "myosin regulatory light chain 1"	609905	"myosin, light polypeptide 9, regulatory"			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.361G>A	20.37:g.35177494G>A	ENSP00000279022:p.Asp121Asn		34610908	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Missense_Mutation	SNP	ENST00000279022.2	37	CCDS13276.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028316	0.93518	.	.	ENSG00000101335	ENST00000279022;ENST00000346786	T;T	0.80566	-1.28;-1.39	4.7	4.7	0.59300	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.87533	0.6201	L	0.58510	1.815	0.80722	D	1	D;B	0.69078	0.997;0.173	D;B	0.73380	0.98;0.14	D	0.88741	0.3243	10	0.66056	D	0.02	.	16.5838	0.84722	0.0:0.0:1.0:0.0	.	67;121	Q9BUF9;P24844	.;MYL9_HUMAN	N	121;67	ENSP00000279022:D121N;ENSP00000217313:D67N	ENSP00000279022:D121N	D	+	1	0	MYL9	34610908	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	9.759000	0.98931	2.317000	0.78254	0.655000	0.94253	GAC		0.597	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		A	35177494	G	A	35177494	3	1	56	1	0	0	0	0	1	0	0	0	10084	1174	41	3	371	3	MYL9	20	35177494	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09		35177494	27848026	108	7510										
TSHZ2	128553	broad.mit.edu	37	chr20	51870841	51870841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgaaatgtatgttttgtggcGactcctttgattccctccaa	8	9	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr20:51870841G>A	ENST00000371497.5	+	2	1731	c.844G>A	c.(844-846)Gac>Aac	p.D282N	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.D279N|TSHZ2_ENST00000603338.2_Missense_Mutation_p.D279N	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	282					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D282N(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GTTTTGTGGCGACTCCTTTGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	20											75	60	65					20																	51870841		2203	4300	6503	51304248	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.844G>A	20.37:g.51870841G>A	ENSP00000360552:p.Asp282Asn		51304248	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396175	0.83011	.	.	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.27557	1.66;1.66	5.5	5.5	0.81552	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.047161	0.85682	D	0.000000	T	0.30916	0.0780	N	0.03608	-0.345	0.54753	D	0.999989	D	0.67145	0.996	P	0.58391	0.838	T	0.46952	-0.9154	10	0.52906	T	0.07	-0.7384	19.7465	0.96253	0.0:0.0:1.0:0.0	.	282	Q9NRE2	TSH2_HUMAN	N	282;279	ENSP00000360552:D282N;ENSP00000333114:D279N	ENSP00000333114:D279N	D	+	1	0	TSHZ2	51304248	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	6.934000	0.75880	2.732000	0.93576	0.643000	0.83706	GAC		0.443	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51870841	G	A	51870841	3	1	56	1	0	0	0	0	1	0	0	0	16664	1058	37	1	850	1	TSHZ2	20	51870841	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	16693347	51870841	11154679	109	7511										
CABIN1	23523	broad.mit.edu	37	chr22	24466813	24466813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgttccgatgtggctctgaaCgaggctgtccagcagatggt	14	9	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chr22:24466813C>T	ENST00000398319.2	+	17	2680	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	CABIN1_ENST00000263119.5_Silent_p.N765N|CABIN1_ENST00000405822.2_Silent_p.N715N	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	765					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.N765N(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGGCTCTGAACGAGGCTGTCC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	22											127	116	119					22																	24466813		2203	4300	6503	22796813	SO:0001819	synonymous_variant	23523			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.2295C>T	22.37:g.24466813C>T			22796813	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	37	CCDS13823.1																																																																																				0.587	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24466813	C	T	24466813	2	4	56	1	0	0	0	0	0	0	0	1	2534	535	19	1		1	CABIN1	22	24466813	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09		24466813	26837753	110	7512										
MAOB	4129	broad.mit.edu	37	chrX	43626760	43626760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gtgggccaggaagccaagagCcgttgctgaaaagatggtgg	17	7	0	3			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:43626760C>T	ENST00000378069.4	-	15	1663	c.1516G>A	c.(1516-1518)Gct>Act	p.A506T	MAOB_ENST00000538942.1_3'UTR|MAOB_ENST00000536181.1_Missense_Mutation_p.A490T	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	506					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)	p.A506T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	AAGCCAAGAGCCGTTGCTGAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											84	71	75					X																	43626760		2203	4300	6503	43511704	SO:0001583	missense	4129				CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.1516G>A	X.37:g.43626760C>T	ENSP00000367309:p.Ala506Thr		43511704	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	37	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251481	0.59212	.	.	ENSG00000069535	ENST00000378069;ENST00000536181	T;T	0.18657	2.2;2.23	5.76	5.76	0.90799	.	0.050617	0.85682	D	0.000000	T	0.29524	0.0736	M	0.72479	2.2	0.80722	D	1	B	0.24043	0.096	B	0.23419	0.046	T	0.03863	-1.0997	10	0.54805	T	0.06	-5.748	17.6248	0.88091	0.0:1.0:0.0:0.0	.	506	P27338	AOFB_HUMAN	T	506;490	ENSP00000367309:A506T;ENSP00000441613:A490T	ENSP00000367309:A506T	A	-	1	0	MAOB	43511704	1.000000	0.71417	0.476000	0.27291	0.438000	0.31896	6.803000	0.75180	2.434000	0.82447	0.597000	0.82753	GCT		0.517	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43626760	C	T	43626760	3	4	56	1	0	0	0	0	1	0	0	0	9256	739	26	3	50	3	MAOB	23	43626760	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09		43626760	111643800	111	7513										
SYN1	6853	broad.mit.edu	37	chrX	47436858	47436858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cttgcccatcccagagtgtgCgtgccccatcttcacaacca	7	17	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:47436858C>T	ENST00000295987.7	-	6	941	c.817G>A	c.(817-819)Gca>Aca	p.A273T	SYN1_ENST00000340666.4_Missense_Mutation_p.A273T	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	273	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)	p.A273T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						CCAGAGTGTGCGTGCCCCATC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	X											222	101	142					X																	47436858		2203	4300	6503	47321802	SO:0001583	missense	6853				CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.817G>A	X.37:g.47436858C>T	ENSP00000295987:p.Ala273Thr		47321802	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	37	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	C	19.77	3.888742	0.72524	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.38240	1.63;1.15	4.39	4.39	0.52855	Synapsin, conserved site (1);ATP-grasp fold, subdomain 1 (1);Synapsin, ATP-binding domain (1);	0.000000	0.64402	D	0.000008	T	0.65015	0.2651	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	0.969;1.0	P;D	0.87578	0.64;0.998	T	0.73251	-0.4042	10	0.87932	D	0	-8.2626	13.5758	0.61873	0.0:1.0:0.0:0.0	.	273;273	P17600;P17600-2	SYN1_HUMAN;.	T	273	ENSP00000295987:A273T;ENSP00000343206:A273T	ENSP00000295987:A273T	A	-	1	0	SYN1	47321802	1.000000	0.71417	0.431000	0.26735	0.184000	0.23303	7.094000	0.76944	1.764000	0.52075	0.583000	0.79449	GCA		0.562	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		T	47436858	C	T	47436858	3	4	56	1	0	0	0	0	1	0	0	0	15479	768	27	1	1332	1	SYN1	23	47436858	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	3810098	47436858	107833702	112	7514										
WDR13	64743	broad.mit.edu	37	chrX	48457786	48457786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tgggggcccgtgggcaccgtCgttctgtcagcagaggctcc	16	13	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:48457786C>T	ENST00000218056.5	+	3	833	c.328C>T	c.(328-330)Cgt>Tgt	p.R110C	WDR13_ENST00000376729.5_Missense_Mutation_p.R110C|WDR13_ENST00000492715.1_3'UTR	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	110						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R110C(2)		endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TGGGCACCGTCGTTCTGTCAG	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	X											28	25	26					X																	48457786		2203	4300	6503	48342730	SO:0001583	missense	64743			AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.328C>T	X.37:g.48457786C>T	ENSP00000218056:p.Arg110Cys		48342730	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	37	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447005	0.84101	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.72835	-0.69;-0.69	5.14	5.14	0.70334	.	0.057310	0.64402	D	0.000001	T	0.79287	0.4420	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	P	0.59221	0.854	T	0.80953	-0.1152	10	0.54805	T	0.06	-28.2534	14.9887	0.71368	0.0:1.0:0.0:0.0	.	110	Q9H1Z4	WDR13_HUMAN	C	110	ENSP00000365919:R110C;ENSP00000218056:R110C	ENSP00000218056:R110C	R	+	1	0	WDR13	48342730	1.000000	0.71417	0.990000	0.47175	0.964000	0.63967	3.053000	0.49901	2.124000	0.65301	0.529000	0.55759	CGT		0.617	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			T	48457786	C	T	48457786	3	4	56	1	0	0	0	0	1	0	0	0	17315	884	31	1	338	1	WDR13	23	48457786	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	1020928	48457786	106812774	113	7515										
HSD17B10	3028	broad.mit.edu	37	chrX	53460776	53460776	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggctccctgccccacaagtcGctccgccgtggccaggccca	11	20	0	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:53460776G>A	ENST00000168216.6	-	2	112	c.85C>T	c.(85-87)Cga>Tga	p.R29*	HSD17B10_ENST00000375298.4_Nonsense_Mutation_p.R29*|RP3-339A18.6_ENST00000418049.1_RNA|HSD17B10_ENST00000495986.1_5'UTR|HSD17B10_ENST00000375304.5_Nonsense_Mutation_p.R29*	NM_001037811.2|NM_004493.2	NP_001032900.1|NP_004484.1	Q99714	HCD2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 10	29					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity (GO:0047015)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|cholate 7-alpha-dehydrogenase activity (GO:0008709)|poly(A) RNA binding (GO:0044822)|testosterone dehydrogenase [NAD(P)] activity (GO:0030283)	p.R29*(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	8						CCCACAAGTCGCTCCGCCGTG	0.627																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											33	25	28					X																	53460776		2203	4299	6502	53477501	SO:0001587	stop_gained	3028			U96132	CCDS14354.1, CCDS35300.1	Xp11.2	2014-09-17	2006-11-22	2006-11-22	ENSG00000072506	ENSG00000072506	1.1.1.35	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	4800	protein-coding gene	gene with protein product	"type 10 17b-HSD", "type 10 17beta-hydroxysteroid dehydrogenase", "AB-binding alcohol dehydrogenase", "short chain dehydrogenase/reductase family 5C, member 1", "mitochondrial RNase P subunit 2"	300256	"hydroxyacyl-Coenzyme A dehydrogenase, type II, hydroxyacyl-Coenzyme A dehydrogenase, type II", "mental retardation, X-linked, syndromic 10"	HADH2, MRXS10		9338779, 16899120, 19027726, 18984158, 17236142	Standard	NM_004493		Approved	ERAB, MHBD, 17b-HSD10, ABAD, SDR5C1, MRPP2, CAMR	uc004dsl.1	Q99714	OTTHUMG00000021612	ENST00000168216.6:c.85C>T	X.37:g.53460776G>A	ENSP00000168216:p.Arg29*		53477501	Q5H927|Q6IBS9|Q8TCV9|Q96HD5	Nonsense_Mutation	SNP	ENST00000168216.6	37	CCDS14354.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.703299	0.68501	.	.	ENSG00000072506	ENST00000168216;ENST00000375304;ENST00000375298	.	.	.	5.55	3.53	0.40419	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.17	0.59593	0.0:0.0:0.6684:0.3316	.	.	.	.	X	29	.	ENSP00000168216:R29X	R	-	1	2	HSD17B10	53477501	1.000000	0.71417	0.827000	0.32855	0.140000	0.21249	3.327000	0.52045	1.065000	0.40693	0.513000	0.50165	CGA		0.627	HSD17B10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056750.1	NM_004493		A	53460776	G	A	53460776	4	1	56	1	0	0	0	0	0	1	0	0	7400	1095	38	1	720	1	HSD17B10	23	53460776	Nonsense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5002990	53460776	101809784	114	7516										
ZC4H2	55906	broad.mit.edu	37	chrX	64138962	64138962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gcctgaaggtggccgtctgcCgagtatcctgcttcctagcc	12	14	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:64138962C>T	ENST00000374839.3	-	4	627	c.521G>A	c.(520-522)cGg>cAg	p.R174Q	ZC4H2_ENST00000447788.2_Intron|ZC4H2_ENST00000545618.1_Missense_Mutation_p.R169Q|ZC4H2_ENST00000488608.1_5'UTR|ZC4H2_ENST00000337990.2_Missense_Mutation_p.R151Q	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	174					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)	p.R174Q(1)		endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GGCCGTCTGCCGAGTATCCTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	X											54	50	51					X																	64138962		2203	4300	6503	64055687	SO:0001583	missense	55906			AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"Zinc fingers"	24931	protein-coding gene	gene with protein product		300897	"KIAA1166", "Wieacker-Wolff syndrome"	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.521G>A	X.37:g.64138962C>T	ENSP00000363972:p.Arg174Gln		64055687	B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Missense_Mutation	SNP	ENST00000374839.3	37	CCDS14380.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003970	0.74932	.	.	ENSG00000126970	ENST00000545618;ENST00000374839;ENST00000337990	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.60547	0.2277	L	0.36672	1.1	0.80722	D	1	D	0.65815	0.995	P	0.57283	0.817	T	0.53229	-0.8468	9	0.13853	T	0.58	.	16.0648	0.80863	0.0:1.0:0.0:0.0	.	174	Q9NQZ6	ZC4H2_HUMAN	Q	169;174;151	.	ENSP00000338650:R151Q	R	-	2	0	ZC4H2	64055687	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	7.555000	0.82223	2.482000	0.83794	0.600000	0.82982	CGG		0.612	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684		T	64138962	C	T	64138962	3	4	56	1	0	0	0	0	1	0	0	0	17617	652	23	1	180	1	ZC4H2	23	64138962	Missense_Mutation	SNP	C	TCGA-AG-4001-01A-02W-1073-09	10678186	64138962	91131598	115	7517										
MED12	9968	broad.mit.edu	37	chrX	70342603	70342603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	cttaggcttcaccattggacGggtacttcatactttggaag	10	9	2	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:70342603G>A	ENST00000374080.3	+	10	1396	c.1364G>A	c.(1363-1365)cGg>cAg	p.R455Q	MED12_ENST00000374102.1_Missense_Mutation_p.R455Q|MED12_ENST00000333646.6_Missense_Mutation_p.R455Q			Q93074	MED12_HUMAN	mediator complex subunit 12	455					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R455Q(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					ACCATTGGACGGGTACTTCAT	0.478			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	1	0.000264901	0	0.0014	3775	,	,		13699	0		0	False		,,,				2504	0						Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	2	Substitution - Missense(2)	large_intestine(2)	X											99	85	89					X																	70342603		1931	4133	6064	70259328	SO:0001583	missense	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.1364G>A	X.37:g.70342603G>A	ENSP00000363193:p.Arg455Gln		70259328	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	17.86	3.493322	0.64186	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	4.85	4.85	0.62838	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	M	0.73962	2.25	0.58432	D	0.999999	B;P;B;B	0.48016	0.032;0.904;0.267;0.275	B;P;B;B	0.46479	0.018;0.518;0.083;0.093	T	0.55945	-0.8060	10	0.56958	D	0.05	-22.8441	17.2392	0.87008	0.0:0.0:1.0:0.0	.	455;302;455;455	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	Q	455;455;455;455;423	ENSP00000333125:R455Q;ENSP00000363215:R455Q;ENSP00000363193:R455Q;ENSP00000414203:R423Q	ENSP00000333125:R455Q	R	+	2	0	MED12	70259328	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.152000	0.77419	2.251000	0.74343	0.502000	0.49764	CGG		0.478	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70342603	G	A	70342603	3	1	56	1	0	0	0	0	1	0	0	0	9458	1116	39	1	1402	1	MED12	23	70342603	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	6203641	70342603	84927957	116	7518										
TAF1	6872	broad.mit.edu	37	chrX	70595134	70595134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggaccaggattctattactgGtggtaagtagagattgtcta	12	5	2	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:70595134G>A	ENST00000373790.4	+	4	581	c.530G>A	c.(529-531)gGt>gAt	p.G177D	TAF1_ENST00000423759.1_Missense_Mutation_p.G177D|TAF1_ENST00000276072.3_Missense_Mutation_p.G177D|TAF1_ENST00000449580.1_Missense_Mutation_p.G177D	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	177	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.G177D(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TCTATTACTGGTGGTAAGTAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											96	81	86					X																	70595134		2203	4300	6503	70511859	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.530G>A	X.37:g.70595134G>A	ENSP00000362895:p.Gly177Asp		70511859	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	6.764	0.509787	0.12883	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.09630	2.96;3.02;3.12;3.07	4.83	2.05	0.26809	.	0.970411	0.08475	N	0.940471	T	0.05823	0.0152	N	0.19112	0.55	0.18873	N	0.999983	B;B	0.19200	0.001;0.034	B;B	0.21708	0.002;0.036	T	0.47005	-0.9150	10	0.12103	T	0.63	.	1.4179	0.02306	0.2715:0.3092:0.292:0.1273	.	177;177	P21675;P21675-2	TAF1_HUMAN;.	D	177	ENSP00000362895:G177D;ENSP00000389000:G177D;ENSP00000406549:G177D;ENSP00000276072:G177D	ENSP00000276072:G177D	G	+	2	0	TAF1	70511859	0.629000	0.27146	0.471000	0.27229	0.155000	0.21991	0.587000	0.23909	0.406000	0.25560	0.429000	0.28392	GGT		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70595134	G	A	70595134	3	1	56	1	0	0	0	0	1	0	0	0	15552	1261	44	3	544	3	TAF1	23	70595134	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	252531	70595134	84675426	117	7519										
SLC16A2	6567	broad.mit.edu	37	chrX	73745670	73745670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ggctacctcaggccttgggcGtcttgtgtcaggccacatca	12	13	4	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:73745670G>A	ENST00000587091.1	+	4	1289	c.1112G>A	c.(1111-1113)cGt>cAt	p.R371H	SLC16A2_ENST00000276033.5_Missense_Mutation_p.R445H	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	371					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)	p.R445H(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	GGCCTTGGGCGTCTTGTGTCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											177	150	159					X																	73745670		2203	4300	6503	73662395	SO:0001583	missense	6567				CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"Solute carriers"	10923	protein-coding gene	gene with protein product		300095	"solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)", "Allan-Herndon-Dudley syndrome", "solute carrier family 16 (monocarboxylic acid transporters), member 2", "mental retardation, X-linked 22", "solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.1112G>A	X.37:g.73745670G>A	ENSP00000465734:p.Arg371His		73662395	Q7Z797	Missense_Mutation	SNP	ENST00000587091.1	37	CCDS14426.2	.	.	.	.	.	.	.	.	.	.	G	25.5	4.645668	0.87958	.	.	ENSG00000147100	ENST00000276033	T	0.56941	0.43	4.94	4.94	0.65067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.75265	0.3826	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80493	-0.1358	10	0.87932	D	0	.	17.4803	0.87671	0.0:0.0:1.0:0.0	.	371	P36021	MOT8_HUMAN	H	445	ENSP00000276033:R445H	ENSP00000276033:R445H	R	+	2	0	SLC16A2	73662395	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.472000	0.97709	2.052000	0.61016	0.597000	0.82753	CGT		0.517	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3			A	73745670	G	A	73745670	3	1	56	1	0	0	0	0	1	0	0	0	14445	1145	40	1	1348	1	SLC16A2	23	73745670	Missense_Mutation	SNP	G	TCGA-AG-4001-01A-02W-1073-09	3150536	73745670	81524890	118	7520										
PCDH19	57526	broad.mit.edu	37	chrX	99662660	99662660	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttagcctgcacgtccagttcGtacacgtgcccctcttcgta	8	15	1	0			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:99662660G>A	ENST00000373034.4	-	1	2611	c.936C>T	c.(934-936)taC>taT	p.Y312Y	PCDH19_ENST00000255531.7_Silent_p.Y312Y|PCDH19_ENST00000420881.2_Silent_p.Y312Y	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	312	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y312Y(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CGTCCAGTTCGTACACGTGCC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	X											59	65	63					X																	99662660		2169	4254	6423	99549316	SO:0001819	synonymous_variant	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.936C>T	X.37:g.99662660G>A			99549316	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																				0.602	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99662660	G	A	99662660	2	1	56	1	0	0	0	0	0	0	0	1	11545	1140	40	1		1	PCDH19	23	99662660	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	25916990	99662660	55607900	119	7521										
THOC2	57187	broad.mit.edu	37	chrX	122765683	122765683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	gatgctaaaaacccaccaaaCtgcaccagggtatcatgaca	7	12	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:122765683C>T	ENST00000245838.8	-	22	2368	c.2337G>A	c.(2335-2337)caG>caA	p.Q779Q	THOC2_ENST00000355725.4_Silent_p.Q779Q|THOC2_ENST00000491737.1_Silent_p.Q664Q	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	779					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)	p.Q779Q(1)|p.Q700Q(1)		breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						ACCCACCAAACTGCACCAGGG	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	X											138	129	132					X																	122765683		1829	4082	5911	122593364	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2337G>A	X.37:g.122765683C>T			122593364	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				0.313	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			T	122765683	C	T	122765683	2	4	56	1	0	0	0	0	0	0	0	1	15904	564	20	3		3	THOC2	23	122765683	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	23103023	122765683	32504877	120	7522										
STAG2	10735	broad.mit.edu	37	chrX	123179201	123179201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	acaagtcagagcatttcgacAtacaagcaccctggcaggtc	9	12	1	1			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:123179201A>G	ENST00000371160.1	+	8	940	c.650A>G	c.(649-651)cAt>cGt	p.H217R	STAG2_ENST00000354548.5_Missense_Mutation_p.H148R|STAG2_ENST00000371145.3_Missense_Mutation_p.H217R|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.H217R|STAG2_ENST00000371157.3_Missense_Mutation_p.H217R|STAG2_ENST00000371144.3_Missense_Mutation_p.H217R	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	217					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.H217R(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GCATTTCGACATACAAGCACC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											128	121	123					X																	123179201		2203	4300	6503	123006882	SO:0001583	missense	10735			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.650A>G	X.37:g.123179201A>G	ENSP00000360202:p.His217Arg		123006882	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242660	0.79912	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62;0.62	4.95	4.95	0.65309	STAG (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	H	0.94658	3.565	0.80722	D	1	D;D	0.56035	0.974;0.963	P;P	0.61328	0.887;0.857	T	0.82504	-0.0424	10	0.87932	D	0	-17.2085	13.9391	0.64043	1.0:0.0:0.0:0.0	.	217;217	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	R	217;217;148;217;217;217;217	ENSP00000218089:H217R;ENSP00000397265:H217R;ENSP00000346555:H148R;ENSP00000360202:H217R;ENSP00000360199:H217R;ENSP00000360187:H217R;ENSP00000360186:H217R	ENSP00000218089:H217R	H	+	2	0	STAG2	123006882	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.272000	0.95707	1.736000	0.51660	0.345000	0.21793	CAT		0.348	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123179201	A	G	123179201	3	3	56	1	0	0	0	0	1	0	0	0	15282	217	8	4	672	4	STAG2	23	123179201	Missense_Mutation	SNP	A	TCGA-AG-4001-01A-02W-1073-09	413518	123179201	32091359	121	7523										
ZNF280C	55609	broad.mit.edu	37	chrX	129394415	129394415	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tttggttgaaaaggtttgtcGtcatccatgaagttgcaagg	12	5	1	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:129394415G>A	ENST00000370978.4	-	2	162	c.9C>T	c.(7-9)gaC>gaT	p.D3D		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D3D(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						AAGGTTTGTCGTCATCCATGA	0.348													G|||	1	0.000264901	0	0	3775	,	,		11610	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X											127	106	113					X																	129394415		2203	4300	6503	129222096	SO:0001819	synonymous_variant	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.9C>T	X.37:g.129394415G>A			129222096	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																				0.348	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		A	129394415	G	A	129394415	2	1	56	1	0	0	0	0	0	0	0	1	17855	1136	40	1		1	ZNF280C	23	129394415	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	6215214	129394415	25876145	122	7524										
FHL1	2273	broad.mit.edu	37	chrX	135288597	135288597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	tacaaggtgggcaccatggcGgagaagtttgactgccacta	13	9	0	2			TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:135288597G>A	ENST00000345434.3	+	2	87	c.6G>A	c.(4-6)gcG>gcA	p.A2A	FHL1_ENST00000370690.3_Silent_p.A2A|FHL1_ENST00000370683.1_Silent_p.A18A|FHL1_ENST00000539015.1_Silent_p.A31A|FHL1_ENST00000370676.3_Silent_p.A18A|FHL1_ENST00000477080.1_3'UTR|FHL1_ENST00000394153.2_Silent_p.A2A|FHL1_ENST00000394155.2_Silent_p.A2A|FHL1_ENST00000543669.1_Silent_p.A2A|FHL1_ENST00000535737.1_Silent_p.A2A			Q13642	FHL1_HUMAN	four and a half LIM domains 1	2					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)	p.A2A(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					GCACCATGGCGGAGAAGTTTG	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	X											134	120	125					X																	135288597		2203	4300	6503	135116263	SO:0001819	synonymous_variant	2273			U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"Four-and-a-half LIM domains 1", "LIM protein SLIMMER"	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.6G>A	X.37:g.135288597G>A			135116263	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Silent	SNP	ENST00000345434.3	37	CCDS55507.1																																																																																				0.567	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449		A	135288597	G	A	135288597	2	1	56	1	0	0	0	0	0	0	0	1	5897	1103	39	1		1	FHL1	23	135288597	Silent	SNP	G	TCGA-AG-4001-01A-02W-1073-09	5894182	135288597	19981963	123	7525										
OPN1LW	5956	broad.mit.edu	37	chrX	153420112	153420112	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	6	1	0.490066649577032	1.91942771084337	0.357102829924349	0.619909502262444	1	0	ttcagcggcagctcgtacccCggggtgcagtcttacatgat	12	12	2	1	rs138979991	byFrequency	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4001-01A-02W-1073-09	TCGA-AG-4001-10A-01W-1073-09	g.chrX:153420112C>T	ENST00000369951.4	+	4	702	c.642C>T	c.(640-642)ccC>ccT	p.P214P	OPN1LW_ENST00000463296.1_Intron	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	214					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.P214P(2)		endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTCGTACCCCGGGGTGCAGT	0.607													C|||	2	0.000529801	0.0015	0	3775	,	,		11090	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	X						C		5,3809		1,1,2,1629,550	135	98	111		642	-8.5	0.4	X	dbSNP_134	111	0,6664		0,0,0,2424,1816	no	coding-synonymous	OPN1LW	NM_020061.4		1,1,2,4053,2366	TT,TC,T,CC,C		0.0,0.1311,0.0477		214/365	153420112	5,10473	2183	4240	6423	153073306	SO:0001819	synonymous_variant	5956			Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"GPCR / Class A : Opsin receptors"	9936	protein-coding gene	gene with protein product	"cone dystrophy 5 (X-linked)"	300822	"color blindness, protan", "red cone photoreceptor pigment"	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.642C>T	X.37:g.153420112C>T			153073306		Silent	SNP	ENST00000369951.4	37	CCDS14742.1																																																																																				0.607	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061		T	153420112	C	T	153420112	2	4	56	1	0	0	0	0	0	0	0	1	10908	639	23	1		1	OPN1LW	23	153420112	Silent	SNP	C	TCGA-AG-4001-01A-02W-1073-09	18131515	153420112	1850448	124	7526										
PDPN	10630	broad.mit.edu	37	chr1	13940872	13940872	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcttcattggtgcaatcatcGttgtggttatgcgaaaaatg	11	6	2	0	rs377220172		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:13940872G>A	ENST00000509009.1	+	5	477	c.433G>A	c.(433-435)Gtt>Att	p.V145I	PDPN_ENST00000376061.4_Missense_Mutation_p.V108I|PDPN_ENST00000475043.1_Missense_Mutation_p.V108I|PDPN_ENST00000487038.1_Missense_Mutation_p.V108I|PDPN_ENST00000513143.1_Missense_Mutation_p.V108I|PDPN_ENST00000294489.6_Missense_Mutation_p.V226I|PDPN_ENST00000376057.4_Missense_Mutation_p.V226I					podoplanin									p.V226I(1)		endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-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;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)		TGCAATCATCGTTGTGGTTAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	199	186	191		676,676,322,322	-6.1	0	1		191	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	PDPN	NM_198389.2,NM_006474.4,NM_001006625.1,NM_001006624.1	29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	226/237,226/239,108/119,108/121	13940872	1,13005	2203	4300	6503	13813459	SO:0001583	missense	10630			AB127958, AY194238	CCDS30602.1, CCDS41266.1, CCDS44060.1, CCDS53270.1	1p36.21	2008-02-05			ENSG00000162493	ENSG00000162493			29602	protein-coding gene	gene with protein product	"lung type I cell membrane associated glycoprotein"	608863				10393083, 9651190	Standard	NM_006474		Approved	T1A-2, Gp38, aggrus, GP40, PA2.26	uc001avd.3	Q86YL7	OTTHUMG00000007912	ENST00000509009.1:c.433G>A	1.37:g.13940872G>A	ENSP00000422977:p.Val145Ile		13813459		Missense_Mutation	SNP	ENST00000509009.1	37		.	.	.	.	.	.	.	.	.	.	G	2.798	-0.249812	0.05867	0.0	1.16E-4	ENSG00000162493	ENST00000294489;ENST00000376057;ENST00000510906;ENST00000509009;ENST00000376061;ENST00000513143;ENST00000487038;ENST00000475043	T;T;T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78	5.93	-6.13	0.02118	.	0.570455	0.17214	N	0.182609	T	0.05227	0.0139	N	0.01228	-0.945	0.09310	N	1	B;B;B;B	0.18013	0.003;0.003;0.025;0.025	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.25916	-1.0118	10	0.02654	T	1	-5.211	9.4694	0.38833	0.2042:0.0:0.0712:0.7247	.	150;108;226;226	Q86YL7;E9PB68;Q86YL7-3;Q86YL7-4	PDPN_HUMAN;.;.;.	I	226;226;217;145;108;108;108;108	ENSP00000294489:V226I;ENSP00000365225:V226I;ENSP00000426302:V217I;ENSP00000422977:V145I;ENSP00000365229:V108I;ENSP00000425304:V108I;ENSP00000427537:V108I;ENSP00000426063:V108I	ENSP00000294489:V226I	V	+	1	0	PDPN	13813459	0.002000	0.14202	0.000000	0.03702	0.897000	0.52465	-1.148000	0.03185	-1.453000	0.01928	-0.302000	0.09304	GTT		0.423	PDPN-009	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367736.1	NM_006474		A	13940872	G	A	13940872	3	1	57	1	0	0	0	0	1	0	0	0	11719	1145	40	1	694	1	PDPN	1	13940872	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		13940872	235309749	1	7527										
PADI6	353238	broad.mit.edu	37	chr1	17722085	17722085	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgcctgctataaactgttccGagagaaacagaaggaaggct	11	8	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:17722085G>A	ENST00000434762.2	+	0	1595							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.R514Q(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AAACTGTTCCGAGAGAAACAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											26	28	27					1																	17722085		2020	4223	6243	17594672			353238			AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17722085G>A			17594672	Q330K5|Q70SX3	Missense_Mutation	SNP	ENST00000434762.2	37																																																																																					0.527	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		A	17722085	G	A	17722085	1	1	57	0	1	0	0	0	0	0	0	0	11412	1058	37	1		1	PADI6	1	17722085	RNA	SNP	G	TCGA-AG-4005-01A-01W-1073-09	3781213	17722085	231528536	2	7528										
PTPRU	10076	broad.mit.edu	37	chr1	29587280	29587280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cctgggctgaggtgcacgccGtcagcctgcagacctacaag	13	14	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:29587280G>A	ENST00000345512.3	+	7	1138	c.1009G>A	c.(1009-1011)Gtc>Atc	p.V337I	PTPRU_ENST00000428026.2_Missense_Mutation_p.V337I|PTPRU_ENST00000356870.3_Missense_Mutation_p.V337I|PTPRU_ENST00000460170.2_Missense_Mutation_p.V337I|PTPRU_ENST00000373779.3_Missense_Mutation_p.V337I|PTPRU_ENST00000323874.8_Missense_Mutation_p.V337I	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	337	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V337I(2)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GGTGCACGCCGTCAGCCTGCA	0.657																																																2	Substitution - Missense(2)	large_intestine(2)	1											63	60	61					1																	29587280		2203	4300	6503	29459867	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.1009G>A	1.37:g.29587280G>A	ENSP00000334941:p.Val337Ile		29459867	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.659797	0.67586	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37	5.22	5.22	0.72569	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	T	0.56978	0.2022	M	0.83312	2.635	0.58432	D	0.999998	B;B;B;B;B	0.28552	0.179;0.179;0.179;0.215;0.215	B;B;B;B;B	0.21360	0.02;0.02;0.02;0.034;0.034	T	0.58222	-0.7674	9	.	.	.	.	17.7715	0.88494	0.0:0.0:1.0:0.0	.	337;337;337;337;337	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	I	337	ENSP00000334941:V337I;ENSP00000362884:V337I;ENSP00000349333:V337I;ENSP00000314987:V337I;ENSP00000392332:V337I;ENSP00000432906:V337I	.	V	+	1	0	PTPRU	29459867	1.000000	0.71417	0.998000	0.56505	0.451000	0.32288	9.860000	0.99555	2.418000	0.82041	0.462000	0.41574	GTC		0.657	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29587280	G	A	29587280	3	1	57	1	0	0	0	0	1	0	0	0	12850	1145	40	1	1035	1	PTPRU	1	29587280	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	11865195	29587280	219663341	3	7529										
CSMD2	114784	broad.mit.edu	37	chr1	34164354	34164354	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	agaggaagagccctcctaccGacacaggtgggcagaggccg	15	12	0	3	rs543673574	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:34164354G>A	ENST00000373380.1	-	3	763	c.543C>T	c.(541-543)gtC>gtT	p.V181V	CSMD2_ENST00000373381.4_Splice_Site_p.V1308V|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1268	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V1268V(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCCTCCTACCGACACAGGTGG	0.612													G|||	2	0.000399361	0.0015	0	5008	,	,		18447	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											58	60	59					1																	34164354		2203	4300	6503	33936941	SO:0001630	splice_region_variant	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.544+1C>T	1.37:g.34164354G>A			33936941	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																					0.612	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	Silent	A	34164354	G	A	34164354	5	1	57	1	0	0	0	0	0	0	1	0	3951	1072	37	1	6843	1	CSMD2	1	34164354	Splice_Site	SNP	G	TCGA-AG-4005-01A-01W-1073-09	4577074	34164354	215086267	4	7530										
ZMYM1	79830	broad.mit.edu	37	chr1	35570063	35570063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gtgcagcatgtgccagaagaCtgctattgtaagttccaatt	10	8	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:35570063C>T	ENST00000373330.1	+	6	761	c.587C>T	c.(586-588)aCt>aTt	p.T196I	ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Missense_Mutation_p.T196I			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	196						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.T196I(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGCCAGAAGACTGCTATTGTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	60	62					1																	35570063		1844	4106	5950	35342650	SO:0001583	missense	79830			AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.587C>T	1.37:g.35570063C>T	ENSP00000362427:p.Thr196Ile		35342650	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	37	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622304	0.28889	.	.	ENSG00000197056	ENST00000417119;ENST00000359858;ENST00000373329;ENST00000373330	T;T;T;T	0.18174	2.23;2.5;2.24;2.5	4.86	1.78	0.24846	TRASH (1);	0.387955	0.22770	N	0.055843	T	0.14527	0.0351	L	0.53249	1.67	0.21861	N	0.999503	B;B	0.26195	0.138;0.144	B;B	0.25987	0.065;0.022	T	0.18147	-1.0346	10	0.59425	D	0.04	-6.1195	4.6926	0.12788	0.3189:0.4965:0.0:0.1846	.	196;196	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	I	196;196;121;196	ENSP00000394233:T196I;ENSP00000352920:T196I;ENSP00000362426:T121I;ENSP00000362427:T196I	ENSP00000352920:T196I	T	+	2	0	ZMYM1	35342650	0.998000	0.40836	0.748000	0.31131	0.844000	0.47949	1.582000	0.36568	0.770000	0.33336	-0.150000	0.13652	ACT		0.328	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		T	35570063	C	T	35570063	3	4	57	1	0	0	0	0	1	0	0	0	17738	565	20	3	601	3	ZMYM1	1	35570063	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	1405709	35570063	213680558	5	7531										
DAB1	1600	broad.mit.edu	37	chr1	57602312	57602312	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gaacgagcgccagcaacaacGccctgttgaaaggaagaaca	11	11	0	2	rs143307821		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:57602312G>A	ENST00000371231.1	-	3	244	c.210C>T	c.(208-210)ggC>ggT	p.G70G	DAB1_ENST00000371236.2_Silent_p.G70G|DAB1_ENST00000371234.4_Silent_p.G70G|DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000439789.2_Silent_p.G70G|DAB1_ENST00000420954.2_Silent_p.G70G|DAB1_ENST00000414851.2_Silent_p.G70G|DAB1_ENST00000371230.1_Silent_p.G70G			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	70	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.G70G(2)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						CAGCAACAACGCCCTGTTGAA	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	1						G		0,4406		0,0,2203	61	60	60		210	-2.6	1	1	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DAB1	NM_021080.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		70/556	57602312	1,13005	2203	4300	6503	57374900	SO:0001819	synonymous_variant	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.210C>T	1.37:g.57602312G>A			57374900	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Silent	SNP	ENST00000371231.1	37																																																																																					0.408	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		A	57602312	G	A	57602312	2	1	57	1	0	0	0	0	0	0	0	1	4223	1074	38	1		1	DAB1	1	57602312	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	22032249	57602312	191648309	6	7532										
MYSM1	114803	broad.mit.edu	37	chr1	59156062	59156062	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgatcaagccagactttttcCggttgtgattttttagataa	8	6	1	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:59156062C>T	ENST00000472487.1	-	4	285	c.246G>A	c.(244-246)ccG>ccA	p.P82P	MYSM1_ENST00000493821.1_5'Flank	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	82					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.P82P(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					AGACTTTTTCCGGTTGTGATT	0.249																																																1	Substitution - coding silent(1)	large_intestine(1)	1											70	63	65					1																	59156062		1781	4054	5835	58928650	SO:0001819	synonymous_variant	114803			AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.246G>A	1.37:g.59156062C>T			58928650	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																				0.249	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		T	59156062	C	T	59156062	2	4	57	1	0	0	0	0	0	0	0	1	10131	639	23	1		1	MYSM1	1	59156062	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	1553750	59156062	190094559	7	7533										
C1orf173	127254	broad.mit.edu	37	chr1	75139186	75139186	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ccagttgtcacttacccagcGgggtgagaatggctcatttt	11	10	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:75139186G>A	ENST00000326665.5	-	1	236	c.18C>T	c.(16-18)ccC>ccT	p.P6P		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		6								p.P6P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CTTACCCAGCGGGGTGAGAAT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	1											67	63	65					1																	75139186		2203	4300	6503	74911774	SO:0001819	synonymous_variant	127254																														ENST00000326665.5:c.18C>T	1.37:g.75139186G>A			74911774	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	37	CCDS30755.1																																																																																				0.672	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75139186	G	A	75139186	2	1	57	1	0	0	0	0	0	0	0	1	2020	1103	39	1		1	C1orf173	1	75139186	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	15983124	75139186	174111435	8	7534										
FLG2	388698	broad.mit.edu	37	chr1	152324672	152324672	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggatcctgactgtgtggactGtccatgaccagattgagaat	12	8	0	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:152324672G>T	ENST00000388718.5	-	3	5662	c.5590C>A	c.(5590-5592)Cag>Aag	p.Q1864K	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1864					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.Q1864K(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGTGGACTGTCCATGACCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											331	289	303					1																	152324672		2203	4300	6503	150591296	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5590C>A	1.37:g.152324672G>T	ENSP00000373370:p.Gln1864Lys		150591296	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963415	0.53507	.	.	ENSG00000143520	ENST00000388718	T	0.06768	3.26	4.05	4.05	0.47172	.	.	.	.	.	T	0.05593	0.0147	M	0.70595	2.14	0.09310	N	1	P	0.47034	0.889	B	0.41036	0.346	T	0.19418	-1.0306	9	0.34782	T	0.22	-3.8616	12.0493	0.53498	0.0:0.0:1.0:0.0	.	1864	Q5D862	FILA2_HUMAN	K	1864	ENSP00000373370:Q1864K	ENSP00000373370:Q1864K	Q	-	1	0	FLG2	150591296	0.022000	0.18835	0.013000	0.15412	0.007000	0.05969	0.256000	0.18351	2.292000	0.77174	0.549000	0.68633	CAG		0.488	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152324672	G	T	152324672	3	4	57	1	0	0	0	0	1	0	0	0	5942	1386	48	2	1589	2	FLG2	1	152324672	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	77185486	152324672	96925949	9	7535										
MNDA	4332	broad.mit.edu	37	chr1	158813175	158813175	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcaagaaacaaactgacatcGgaagcaagagggaggattcc	12	8	0	3	rs144118208		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:158813175G>A	ENST00000368141.4	+	3	633	c.372G>A	c.(370-372)tcG>tcA	p.S124S		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	124					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S124S(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AACTGACATCGGAAGCAAGAG	0.463													g|||	1	0.000199681	8e-04	0	5008	,	,		17411	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405		0,1,2202	60	53	56		372	-1.9	0	1	dbSNP_134	56	0,8600		0,0,4300	no	coding-synonymous	MNDA	NM_002432.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		124/408	158813175	1,13005	2203	4300	6503	157079799	SO:0001819	synonymous_variant	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.372G>A	1.37:g.158813175G>A			157079799		Silent	SNP	ENST00000368141.4	37	CCDS1177.1																																																																																				0.463	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		A	158813175	G	A	158813175	2	1	57	1	0	0	0	0	0	0	0	1	9706	1103	39	1		1	MNDA	1	158813175	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	6488503	158813175	90437446	10	7536										
OR10J3	441911	broad.mit.edu	37	chr1	159284400	159284400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gctgccgcctgaagctggagAaaccttcaaagaggaactca	11	11	2	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:159284400A>G	ENST00000332217.5	-	1	49	c.50T>C	c.(49-51)tTc>tCc	p.F17S		NM_001004467.1	NP_001004467.1	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J, member 3	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F17S(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(19)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	47	all_hematologic(112;0.0429)					GAAGCTGGAGAAACCTTCAAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	176	174					1																	159284400		2203	4300	6503	157551024	SO:0001583	missense	441911				CCDS30909.1	1q23.2	2012-08-09		2004-03-10	ENSG00000196266	ENSG00000196266		"GPCR / Class A : Olfactory receptors"	14992	protein-coding gene	gene with protein product				OR10J3P			Standard	NM_001004467		Approved		uc010piu.2	Q5JRS4	OTTHUMG00000037233	ENST00000332217.5:c.50T>C	1.37:g.159284400A>G	ENSP00000331789:p.Phe17Ser		157551024		Missense_Mutation	SNP	ENST00000332217.5	37	CCDS30909.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.146323	0.57044	.	.	ENSG00000196266	ENST00000332217	T	0.00551	6.65	5.13	3.99	0.46301	.	.	.	.	.	T	0.01695	0.0054	H	0.96633	3.855	0.22961	N	0.998502	D	0.89917	1.0	D	0.91635	0.999	T	0.39623	-0.9605	9	0.87932	D	0	.	9.6165	0.39694	0.8437:0.0:0.0:0.1563	.	17	Q5JRS4	O10J3_HUMAN	S	17	ENSP00000331789:F17S	ENSP00000331789:F17S	F	-	2	0	OR10J3	157551024	0.144000	0.22641	0.901000	0.35422	0.875000	0.50365	2.913000	0.48790	0.943000	0.37553	0.459000	0.35465	TTC		0.423	OR10J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090629.1			G	159284400	A	G	159284400	3	3	57	1	0	0	0	0	1	0	0	0	10942	246	9	4	941	4	OR10J3	1	159284400	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	471225	159284400	89966221	11	7537										
TBX19	9095	broad.mit.edu	37	chr1	168260608	168260608	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggggcccactggatgaaagcTcccatctccttcagcaaagt	10	13	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:168260608T>A	ENST00000367821.3	+	2	465	c.414T>A	c.(412-414)gcT>gcA	p.A138A		NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	138					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A138A(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					GGATGAAAGCTCCCATCTCCT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	1											88	98	94					1																	168260608		2203	4300	6503	166527232	SO:0001819	synonymous_variant	9095			AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.414T>A	1.37:g.168260608T>A			166527232	Q52M53	Silent	SNP	ENST00000367821.3	37	CCDS1272.1	.	.	.	.	.	.	.	.	.	.	T	8.633	0.894102	0.17613	.	.	ENSG00000143178	ENST00000431969	.	.	.	5.51	-11.0	0.00169	.	.	.	.	.	T	0.02649	0.0080	.	.	.	.	.	.	.	.	.	.	.	.	T	0.11060	-1.0603	3	.	.	.	.	1.7295	0.02928	0.1888:0.3294:0.2058:0.276	.	.	.	.	T	71	.	.	S	+	1	0	TBX19	166527232	0.000000	0.05858	0.033000	0.17914	0.938000	0.57974	-2.871000	0.00720	-3.546000	0.00143	-1.219000	0.01604	TCC		0.632	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		A	168260608	T	A	168260608	2	1	57	1	0	0	0	0	0	0	0	1	15693	1538	54	5		5	TBX19	1	168260608	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	8976208	168260608	80990013	12	7538										
C1orf125	126859	broad.mit.edu	37	chr1	179364244	179364244	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttatttcagggaactgtgtcTagttcgggcacatgatgtga	12	6	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:179364244T>A	ENST00000367618.3	+	11	1403	c.1016T>A	c.(1015-1017)cTa>cAa	p.L339Q	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.L339Q	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	339								p.L339Q(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						GAACTGTGTCTAGTTCGGGCA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											111	122	118					1																	179364244		2203	4300	6503	177630867	SO:0001583	missense	126859			BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.1016T>A	1.37:g.179364244T>A	ENSP00000356590:p.Leu339Gln		177630867	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.799845	0.31869	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000457238;ENST00000434088	T;T;T	0.41065	2.31;1.01;2.34	5.65	5.65	0.86999	.	0.572784	0.18470	N	0.140258	T	0.48169	0.1485	L	0.35414	1.06	0.24922	N	0.991973	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.999;0.994	T	0.36553	-0.9743	10	0.15499	T	0.54	-19.2927	9.1732	0.37096	0.1622:0.0:0.0:0.8378	.	297;339;339	E9PCJ4;Q5T1B0;F5GWM2	.;AXDN1_HUMAN;.	Q	339;297;339;273	ENSP00000356590:L339Q;ENSP00000416712:L339Q;ENSP00000391716:L273Q	ENSP00000353471:L297Q	L	+	2	0	AXDND1	177630867	0.940000	0.31905	1.000000	0.80357	0.980000	0.70556	2.064000	0.41432	2.142000	0.66516	0.533000	0.62120	CTA		0.338	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		A	179364244	T	A	179364244	3	1	57	1	0	0	0	0	1	0	0	0	1999	1522	53	5	1054	5	C1orf125	1	179364244	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09	11103636	179364244	69886377	13	7539										
NCF2	4688	broad.mit.edu	37	chr1	183529276	183529276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cccttcctgaaactccaggtCctctggttgggtagcctcat	9	14	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:183529276C>T	ENST00000367535.3	-	14	1674	c.1423G>A	c.(1423-1425)Gac>Aac	p.D475N	NCF2_ENST00000413720.1_Missense_Mutation_p.D430N|NCF2_ENST00000418089.1_Missense_Mutation_p.D394N|NCF2_ENST00000367536.1_Missense_Mutation_p.D475N|NCF2_ENST00000469280.1_5'Flank	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	475	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)	p.D475N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	AACTCCAGGTCCTCTGGTTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											198	193	195					1																	183529276		2203	4300	6503	181795899	SO:0001583	missense	4688			BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"Tetratricopeptide (TTC) repeat domain containing"	7661	protein-coding gene	gene with protein product	"NADPH oxidase activator 2", "chronic granulomatous disease, autosomal 2"	608515	"neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.1423G>A	1.37:g.183529276C>T	ENSP00000356505:p.Asp475Asn		181795899	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145310	0.94603	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.45	5.45	0.79879	Src homology-3 domain (5);	0.000000	0.85682	D	0.000000	T	0.81418	0.4818	H	0.94771	3.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.86585	0.1856	10	0.87932	D	0	-2.5811	19.2883	0.94087	0.0:1.0:0.0:0.0	.	394;430;475	E9PHJ2;E9PHX3;P19878	.;.;NCF2_HUMAN	N	475;547;430;394;475	ENSP00000356506:D475N;ENSP00000399294:D430N;ENSP00000407217:D394N;ENSP00000356505:D475N	ENSP00000356505:D475N	D	-	1	0	NCF2	181795899	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.511000	0.73733	2.555000	0.86185	0.655000	0.94253	GAC		0.428	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433		T	183529276	C	T	183529276	3	4	57	1	0	0	0	0	1	0	0	0	10248	855	30	3	165	3	NCF2	1	183529276	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	4165032	183529276	65721345	14	7540										
FAM5C	339479	broad.mit.edu	37	chr1	190067895	190067895	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aaccagctattgaggcgcatGtcattgctgataaaaatggc	10	8	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:190067895G>A	ENST00000367462.3	-	8	1785	c.1554C>T	c.(1552-1554)gaC>gaT	p.D518D	BRINP3_ENST00000534846.1_Silent_p.D416D	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	518					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.D518D(1)									TGAGGCGCATGTCATTGCTGA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											147	140	142					1																	190067895		2203	4300	6503	188334518	SO:0001819	synonymous_variant	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1554C>T	1.37:g.190067895G>A			188334518	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	37	CCDS1373.1																																																																																				0.443	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190067895	G	A	190067895	2	1	57	1	0	0	0	0	0	0	0	1	5613	1368	48	3		3	FAM5C	1	190067895	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	6538619	190067895	59182726	15	7541										
ADORA1	134	broad.mit.edu	37	chr1	203134704	203134704	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aagaaggtgtcggcctcctcCggcgacccgcagaagtacta	12	13	0	2	rs201016113		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:203134704C>T	ENST00000367236.4	+	3	1578	c.657C>T	c.(655-657)tcC>tcT	p.S219S	ADORA1_ENST00000367235.1_3'UTR|ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000337894.4_Silent_p.S219S|ADORA1_ENST00000309502.3_Silent_p.S219S	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	219					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)	p.S219S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	CGGCCTCCTCCGGCGACCCGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											130	118	122					1																	203134704		2203	4300	6503	201401327	SO:0001819	synonymous_variant	134			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.657C>T	1.37:g.203134704C>T			201401327	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1																																																																																				0.582	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		T	203134704	C	T	203134704	2	4	57	1	0	0	0	0	0	0	0	1	326	639	23	1		1	ADORA1	1	203134704	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	13066809	203134704	46115917	16	7542										
TGFB2	7042	broad.mit.edu	37	chr1	218609481	218609481	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cgtgctttggatgcggcctaTtgctttaggtaaaggaaaga	13	6	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:218609481T>C	ENST00000366930.4	+	5	1391	c.924T>C	c.(922-924)taT>taC	p.Y308Y	TGFB2_ENST00000366929.4_Silent_p.Y336Y|TGFB2_ENST00000479322.1_3'UTR	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	308					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.Y308Y(1)|p.Y336Y(1)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		ATGCGGCCTATTGCTTTAGGT	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	1											75	71	73					1																	218609481		2203	4300	6503	216676104	SO:0001819	synonymous_variant	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.924T>C	1.37:g.218609481T>C			216676104	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Silent	SNP	ENST00000366930.4	37	CCDS1521.1																																																																																				0.448	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		C	218609481	T	C	218609481	2	2	57	1	0	0	0	0	0	0	0	1	15857	1500	52	4		4	TGFB2	1	218609481	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	15474777	218609481	30641140	17	7543										
TRIM67	440730	broad.mit.edu	37	chr1	231344894	231344894	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cttcggggtggccagggccaGcgtggtcaaggacatgatgc	17	10	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr1:231344894G>T	ENST00000366653.5	+	8	2021	c.2021G>T	c.(2020-2022)aGc>aTc	p.S674I	TRIM67_ENST00000444294.3_Missense_Mutation_p.S672I|TRIM67_ENST00000366652.2_Missense_Mutation_p.S674I|TRIM67_ENST00000449018.3_Missense_Mutation_p.S612I			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	674	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.S674I(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GCCAGGGCCAGCGTGGTCAAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	94	91					1																	231344894		2195	4298	6493	229411517	SO:0001583	missense	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2021G>T	1.37:g.231344894G>T	ENSP00000355613:p.Ser674Ile		229411517	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.618192	0.66787	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.73	3.7	0.42460	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.135532	0.64402	D	0.000004	T	0.67608	0.2911	L	0.32530	0.975	0.40037	D	0.975607	B	0.30634	0.288	B	0.40038	0.317	T	0.63862	-0.6541	10	0.51188	T	0.08	.	2.2842	0.04122	0.3901:0.2934:0.3166:0.0	.	674	Q6ZTA4	TRI67_HUMAN	I	672;674;612;674	ENSP00000412124:S672I;ENSP00000355612:S674I;ENSP00000400163:S612I;ENSP00000355613:S674I	ENSP00000355612:S674I	S	+	2	0	TRIM67	229411517	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.539000	0.82063	0.754000	0.32968	0.655000	0.94253	AGC		0.622	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231344894	G	T	231344894	3	4	57	1	0	0	0	0	1	0	0	0	16580	971	34	2	2051	2	TRIM67	1	231344894	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	12735413	231344894	17905727	18	7544										
NTSR2	23620	broad.mit.edu	37	chr2	11800224	11800224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gagcctgcgggcatggtacgGcagccagcagatgacataca	14	11	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:11800224G>A	ENST00000306928.5	-	3	968	c.934C>T	c.(934-936)Ccg>Tcg	p.P312S		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	312					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.P312S(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	GCATGGTACGGCAGCCAGCAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	86	90					2																	11800224		2203	4300	6503	11717675	SO:0001583	missense	23620			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.934C>T	2.37:g.11800224G>A	ENSP00000303686:p.Pro312Ser		11717675	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	37	CCDS1681.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908729	0.72868	.	.	ENSG00000169006	ENST00000306928	T	0.80304	-1.36	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.128890	0.34750	N	0.003701	D	0.90923	0.7147	M	0.92555	3.32	0.39942	D	0.974426	D	0.89917	1.0	D	0.77557	0.99	D	0.93217	0.6605	10	0.87932	D	0	-25.8996	12.9419	0.58350	0.0:0.0:1.0:0.0	.	312	O95665	NTR2_HUMAN	S	312	ENSP00000303686:P312S	ENSP00000303686:P312S	P	-	1	0	NTSR2	11717675	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.514000	0.81750	2.149000	0.67028	0.650000	0.86243	CCG		0.562	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			A	11800224	G	A	11800224	3	1	57	1	0	0	0	0	1	0	0	0	10742	1203	42	3	306	3	NTSR2	2	11800224	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		11800224	231399149	19	7545										
APOB	338	broad.mit.edu	37	chr2	21227306	21227306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gggcttttgatattgaggtgCgcttttccttcccattccct	9	11	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:21227306C>T	ENST00000233242.1	-	28	12049	c.11922G>A	c.(11920-11922)gcG>gcA	p.A3974A		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3974					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.A3974A(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATTGAGGTGCGCTTTTCCTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											133	131	132					2																	21227306		2203	4300	6503	21080811	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11922G>A	2.37:g.21227306C>T			21080811	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21227306	C	T	21227306	2	4	57	1	0	0	0	0	0	0	0	1	785	755	27	1		1	APOB	2	21227306	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	9427082	21227306	221972067	20	7546										
APOB	338	broad.mit.edu	37	chr2	21245844	21245844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ccccactcctagcgaagtccGgaatgatgatgcccatattt	8	13	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:21245844G>A	ENST00000233242.1	-	18	2802	c.2675C>T	c.(2674-2676)cCg>cTg	p.P892L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	892					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.P892L(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCGAAGTCCGGAATGATGAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	109	110					2																	21245844		2203	4300	6503	21099349	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2675C>T	2.37:g.21245844G>A	ENSP00000233242:p.Pro892Leu		21099349	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683825	0.88639	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.21031	2.03	5.51	5.51	0.81932	Lipid transport protein, beta-sheet shell (1);Vitellinogen, open beta-sheet (1);Vitellinogen, open beta-sheet, subdomain 2 (1);	0.000000	0.64402	D	0.000009	T	0.53061	0.1773	M	0.82923	2.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55692	-0.8101	10	0.62326	D	0.03	.	19.7977	0.96492	0.0:0.0:1.0:0.0	.	892	P04114	APOB_HUMAN	L	892	ENSP00000233242:P892L	ENSP00000233242:P892L	P	-	2	0	APOB	21099349	1.000000	0.71417	0.902000	0.35471	0.687000	0.40016	9.360000	0.97119	2.765000	0.95021	0.655000	0.94253	CCG		0.483	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21245844	G	A	21245844	3	1	57	1	0	0	0	0	1	0	0	0	785	1116	39	1	11064	1	APOB	2	21245844	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	18538	21245844	221953529	21	7547										
AGBL5	60509	broad.mit.edu	37	chr2	27292470	27292470	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aggttgggccggggctcaccGccgactcgcagagggatgaa	17	11	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:27292470G>A	ENST00000360131.4	+	14	2544	c.2385G>A	c.(2383-2385)ccG>ccA	p.P795P		NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	795					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.P795P(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGCTCACCGCCGACTCGCA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	2											117	132	127					2																	27292470		2203	4300	6503	27145974	SO:0001819	synonymous_variant	60509			BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2385G>A	2.37:g.27292470G>A			27145974	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Silent	SNP	ENST00000360131.4	37	CCDS1732.3																																																																																				0.587	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		A	27292470	G	A	27292470	2	1	57	1	0	0	0	0	0	0	0	1	378	1074	38	1		1	AGBL5	2	27292470	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	6046626	27292470	215906903	22	7548										
CALM2	805	broad.mit.edu	37	chr2	47397889	47397889	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tcacctgcaatctgctcttcAgtcagttggtcagcctacaa	7	13	6	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:47397889A>G	ENST00000272298.7	-	2	175	c.18T>C	c.(16-18)acT>acC	p.T6T	CALM2_ENST00000409563.1_5'UTR|CALM2_ENST00000484408.1_5'UTR|RP11-761B3.1_ENST00000422269.1_Missense_Mutation_p.L29P	NM_001743.4	NP_001734.1	P62158	CALM_HUMAN	calmodulin 2 (phosphorylase kinase, delta)	6					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)	p.0?(2)|p.T6T(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)	5		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	TCTGCTCTTCAGTCAGTTGGT	0.368																																																3	Whole gene deletion(2)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	2											129	130	130					2																	47397889		2203	4300	6503	47251393	SO:0001819	synonymous_variant	805				CCDS1832.1	2p21.3-p21.1	2013-02-25			ENSG00000143933	ENSG00000143933		"EF-hand domain containing", "Endogenous ligands"	1445	protein-coding gene	gene with protein product	"prepro-calmodulin 2"	114182					Standard	NM_001743		Approved	PHKD, CAMII	uc002rvt.2	P62158	OTTHUMG00000128850	ENST00000272298.7:c.18T>C	2.37:g.47397889A>G			47251393	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000272298.7	37	CCDS1832.1																																																																																				0.368	CALM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250789.3	NM_001743		G	47397889	A	G	47397889	2	3	57	1	0	0	0	0	0	0	0	1	2591	175	7	4		4	CALM2	2	47397889	Silent	SNP	A	TCGA-AG-4005-01A-01W-1073-09	20105419	47397889	195801484	23	7549										
CTNNA2	1496	broad.mit.edu	37	chr2	80101313	80101313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	catttctccgccacccagatGtcgccgctacgagagccaac	8	17	1	2	rs559758762		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:80101313G>A	ENST00000402739.4	+	5	702	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	CTNNA2_ENST00000466387.1_Missense_Mutation_p.V233I|CTNNA2_ENST00000541047.1_Missense_Mutation_p.V233I|CTNNA2_ENST00000361291.4_Missense_Mutation_p.V267I|CTNNA2_ENST00000496558.1_Missense_Mutation_p.V233I|CTNNA2_ENST00000540488.1_Missense_Mutation_p.V233I	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	233					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.V233I(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CCACCCAGATGTCGCCGCTAC	0.577													G|||	1	0.000199681	0	0	5008	,	,		16564	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											51	56	54					2																	80101313		2072	4220	6292	79954821	SO:0001583	missense	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.697G>A	2.37:g.80101313G>A	ENSP00000384638:p.Val233Ile		79954821	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	G	18.73	3.687461	0.68157	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	T	0.44138	0.1279	L	0.60845	1.875	0.80722	D	1	B;B;B	0.28400	0.21;0.095;0.095	B;B;B	0.28916	0.089;0.096;0.096	T	0.24835	-1.0149	10	0.24483	T	0.36	.	19.8448	0.96704	0.0:0.0:1.0:0.0	.	233;233;233	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	I	233;233;267;233;233;233	ENSP00000418191:V233I;ENSP00000419295:V233I;ENSP00000355398:V267I;ENSP00000384638:V233I;ENSP00000444675:V233I;ENSP00000441705:V233I	ENSP00000355398:V267I	V	+	1	0	CTNNA2	79954821	1.000000	0.71417	0.979000	0.43373	0.821000	0.46438	9.869000	0.99810	2.686000	0.91538	0.650000	0.86243	GTC		0.577	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80101313	G	A	80101313	3	1	57	1	0	0	0	0	1	0	0	0	4019	1377	48	3	715	3	CTNNA2	2	80101313	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	32703424	80101313	163098060	24	7550										
ANKRD36B	0	broad.mit.edu	37	chr2	98156677	98156677	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	taattaccttcaaggctggtCgtctctgagaagacactgaa	9	9	2	3	rs536823787	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:98156677C>T								AC159540.1 (65628 upstream) : ANKRD36B (7350 downstream)																							CAAGGCTGGTCGTCTCTGAGA	0.313																																																0			2											67	53	58					2																	98156677		1550	2479	4029	97523109	SO:0001628	intergenic_variant	57730																															2.37:g.98156677C>T			97523109		Missense_Mutation	SNP		37																																																																																				0	0.313									T	98156677	C	T	98156677	1	4	57	0	1	0	0	0	0	0	0	0	666	884	31	1		1	ANKRD36B	2	98156677	IGR	SNP	C	TCGA-AG-4005-01A-01W-1073-09	18055364	98156677	145042696	25	7551										
CNTNAP5	129684	broad.mit.edu	37	chr2	125521264	125521264	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgcaggacaaatgatactggCtttctttccttcaaagacca	7	10	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:125521264C>A	ENST00000431078.1	+	15	2611	c.2247C>A	c.(2245-2247)ggC>ggA	p.G749G		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	749	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.G749G(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		ATGATACTGGCTTTCTTTCCT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	2											85	76	78					2																	125521264		1843	4092	5935	125237734	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2247C>A	2.37:g.125521264C>A			125237734	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.408	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125521264	C	A	125521264	2	1	57	1	0	0	0	0	0	0	0	1	3656	784	28	2		2	CNTNAP5	2	125521264	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	27364587	125521264	117678109	26	7552										
MYO7B	4648	broad.mit.edu	37	chr2	128338352	128338352	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gagaacctggacgcctcagaCgtgatggagacgcccgcctt	13	13	1	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:128338352C>T	ENST00000409816.2	+	9	1067	c.1035C>T	c.(1033-1035)gaC>gaT	p.D345D	MYO7B_ENST00000389524.4_Silent_p.D345D|MYO7B_ENST00000428314.1_Silent_p.D345D			Q6PIF6	MYO7B_HUMAN	myosin VIIB	345	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.D345E(2)|p.D345D(2)		breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ACGCCTCAGACGTGATGGAGA	0.602																																																4	Substitution - Missense(2)|Substitution - coding silent(2)	large_intestine(2)|lung(2)	2											55	57	56					2																	128338352		1993	4164	6157	128054822	SO:0001819	synonymous_variant	4648				CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.1035C>T	2.37:g.128338352C>T			128054822	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																				0.602	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128338352	C	T	128338352	2	4	57	1	0	0	0	0	0	0	0	1	10113	535	19	1		1	MYO7B	2	128338352	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	2817088	128338352	114861021	27	7553										
NCKAP5	344148	broad.mit.edu	37	chr2	133539711	133539711	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctgtctcacactgtagttcaGgcttctttttctcttttttt	5	10	4	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:133539711G>C	ENST00000409261.1	-	14	5046	c.4673C>G	c.(4672-4674)cCt>cGt	p.P1558R	NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Missense_Mutation_p.P1558R|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1558								p.P1558R(2)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTGTAGTTCAGGCTTCTTTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											141	130	133					2																	133539711		1849	4096	5945	133256181	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4673C>G	2.37:g.133539711G>C	ENSP00000387128:p.Pro1558Arg		133256181	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908355	0.33721	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.09350	2.99;2.99	5.33	4.43	0.53597	.	0.624337	0.11884	U	0.520243	T	0.08179	0.0204	N	0.19112	0.55	0.22156	N	0.999321	P	0.44380	0.834	B	0.42282	0.382	T	0.19943	-1.0290	10	0.25751	T	0.34	.	9.4479	0.38708	0.0771:0.1426:0.7803:0.0	.	1558	O14513	NCKP5_HUMAN	R	1558	ENSP00000387128:P1558R;ENSP00000380603:P1558R	ENSP00000380603:P1558R	P	-	2	0	NCKAP5	133256181	0.828000	0.29307	0.972000	0.41901	0.941000	0.58515	2.851000	0.48302	2.781000	0.95711	0.591000	0.81541	CCT		0.378	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133539711	G	C	133539711	3	2	57	1	0	0	0	0	1	0	0	0	10254	1000	35	5	1084	5	NCKAP5	2	133539711	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	5201359	133539711	109659662	28	7554										
LRP1B	53353	broad.mit.edu	37	chr2	141643736	141643736	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cagaaagctttccccggtatAttctgtcttctacaacatct	5	12	4	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:141643736A>C	ENST00000389484.3	-	24	4906	c.3935T>G	c.(3934-3936)aTa>aGa	p.I1312R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1312					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.I1312R(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		TCCCCGGTATATTCTGTCTTC	0.303										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											60	61	61					2																	141643736		2202	4299	6501	141360206	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3935T>G	2.37:g.141643736A>C	ENSP00000374135:p.Ile1312Arg		141360206	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.420845	0.83559	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.94138	-3.36;-3.36	5.68	5.68	0.88126	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.97926	0.9318	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.996	D	0.99372	1.0920	10	0.87932	D	0	.	15.9351	0.79698	1.0:0.0:0.0:0.0	.	495;1312	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	R	1312;1250;457	ENSP00000374135:I1312R;ENSP00000413239:I457R	ENSP00000374135:I1312R	I	-	2	0	LRP1B	141360206	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.124000	0.94394	2.159000	0.67721	0.528000	0.53228	ATA		0.303	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141643736	A	C	141643736	3	2	57	1	0	0	0	0	1	0	0	0	8984	449	16	4	10136	4	LRP1B	2	141643736	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	8104025	141643736	101555637	29	7555										
NEB	4703	broad.mit.edu	37	chr2	152500443	152500443	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	acgtcgctgactaaggtctgGcacttcttggccaacaccac	9	14	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:152500443G>A	ENST00000172853.10	-	57	7992	c.7845C>T	c.(7843-7845)tgC>tgT	p.C2615C	NEB_ENST00000409198.1_Silent_p.C2615C|NEB_ENST00000397345.3_Silent_p.C2615C|NEB_ENST00000604864.1_Silent_p.C2615C|NEB_ENST00000427231.2_Silent_p.C2615C|NEB_ENST00000603639.1_Silent_p.C2615C			P20929	NEBU_HUMAN	nebulin	2615					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.C2615C(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTAAGGTCTGGCACTTCTTGG	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	2											347	332	337					2																	152500443		2069	4207	6276	152208689	SO:0001819	synonymous_variant	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7845C>T	2.37:g.152500443G>A			152208689	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.557	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152500443	G	A	152500443	2	1	57	1	0	0	0	0	0	0	0	1	10333	1195	42	3		3	NEB	2	152500443	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	10856707	152500443	90698930	30	7556										
CACNB4	785	broad.mit.edu	37	chr2	152717291	152717291	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gggattatttaggacagaccTcttagcaagagaaatgtcag	11	6	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:152717291T>C	ENST00000539935.1	-	10	869	c.802A>G	c.(802-804)Agg>Ggg	p.R268G	CACNB4_ENST00000201943.5_Missense_Mutation_p.R268G|CACNB4_ENST00000360283.6_Missense_Mutation_p.R235G|CACNB4_ENST00000397327.2_Missense_Mutation_p.R221G|CACNB4_ENST00000427385.1_Missense_Mutation_p.R250G|CACNB4_ENST00000534999.1_Missense_Mutation_p.R234G	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	268					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R268G(2)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGGACAGACCTCTTAGCAAGA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	2											158	150	153					2																	152717291		1880	4112	5992	152425537	SO:0001583	missense	785			AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.802A>G	2.37:g.152717291T>C	ENSP00000438949:p.Arg268Gly		152425537	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.162886	0.78226	.	.	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	D;D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	5.82	4.63	0.57726	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.000000	0.85682	D	0.000000	D	0.95220	0.8450	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.69078	0.994;0.995;0.997;0.994	D;D;D;D	0.83275	0.985;0.989;0.996;0.981	D	0.95401	0.8490	10	0.87932	D	0	-15.9052	12.6562	0.56788	0.0:0.0:0.1382:0.8618	.	268;268;250;234	A7BJ74;O00305;B4DG40;O00305-2	.;CACB4_HUMAN;.;.	G	268;235;225;263;234;221;250;268;269	ENSP00000438949:R268G;ENSP00000353425:R235G;ENSP00000390161:R263G;ENSP00000443893:R234G;ENSP00000380490:R221G;ENSP00000410978:R250G;ENSP00000201943:R268G	ENSP00000201943:R268G	R	-	1	2	CACNB4	152425537	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.359000	0.52292	0.980000	0.38523	0.455000	0.32223	AGG		0.418	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		C	152717291	T	C	152717291	3	2	57	1	0	0	0	0	1	0	0	0	2561	1550	54	4	780	4	CACNB4	2	152717291	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09	216848	152717291	90482082	31	7557										
ITGA4	3676	broad.mit.edu	37	chr2	182388171	182388171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tttttcccattaggaagagaAgcaaataaactgtgaagtca	8	6	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:182388171A>G	ENST00000397033.2	+	19	2511	c.2081A>G	c.(2080-2082)aAg>aGg	p.K694R		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	694					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.K694R(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TAGGAAGAGAAGCAAATAAAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	99	101					2																	182388171		1836	4094	5930	182096416	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2081A>G	2.37:g.182388171A>G	ENSP00000380227:p.Lys694Arg		182096416	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.996769	0.54147	.	.	ENSG00000115232	ENST00000397033	T	0.46063	0.88	4.94	4.94	0.65067	Integrin alpha-2 (1);	0.046879	0.85682	D	0.000000	T	0.54727	0.1876	M	0.61703	1.905	0.44995	D	0.998014	D;D	0.62365	0.991;0.991	D;D	0.64776	0.929;0.929	T	0.51212	-0.8734	10	0.22706	T	0.39	.	10.3183	0.43751	0.8351:0.1649:0.0:0.0	.	516;694	Q59H74;P13612	.;ITA4_HUMAN	R	694	ENSP00000380227:K694R	ENSP00000380227:K694R	K	+	2	0	ITGA4	182096416	1.000000	0.71417	0.995000	0.50966	0.807000	0.45602	3.863000	0.56016	1.975000	0.57531	0.477000	0.44152	AAG		0.343	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			G	182388171	A	G	182388171	3	3	57	1	0	0	0	0	1	0	0	0	7899	72	3	4	2155	4	ITGA4	2	182388171	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	29670880	182388171	60811202	32	7558										
STAT4	6775	broad.mit.edu	37	chr2	191905872	191905872	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tcttcagtcaccatgtgacaGccctaaggaagagagaaata	9	9	3	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:191905872G>T	ENST00000392320.2	-	15	1568	c.1254C>A	c.(1252-1254)ggC>ggA	p.G418G	STAT4_ENST00000470708.1_5'UTR|STAT4_ENST00000358470.4_Silent_p.G418G	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	418					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.G418G(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CCATGTGACAGCCCTAAGGAA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	2											103	97	99					2																	191905872		2203	4300	6503	191614117	SO:0001819	synonymous_variant	6775				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1254C>A	2.37:g.191905872G>T			191614117	Q96NZ6	Silent	SNP	ENST00000392320.2	37	CCDS2310.1																																																																																				0.333	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		T	191905872	G	T	191905872	2	4	57	1	0	0	0	0	0	0	0	1	15306	958	34	2		2	STAT4	2	191905872	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	9517701	191905872	51293501	33	7559										
FN1	2335	broad.mit.edu	37	chr2	216247030	216247030	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctgtgggctgcaagccttcaAtagtcatttctgtttgatct	9	9	4	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:216247030A>G	ENST00000359671.1	-	31	5061	c.4796T>C	c.(4795-4797)aTt>aCt	p.I1599T	FN1_ENST00000443816.1_Missense_Mutation_p.I1599T|FN1_ENST00000432072.2_Missense_Mutation_p.I1690T|FN1_ENST00000421182.1_Missense_Mutation_p.I1599T|FN1_ENST00000345488.5_Missense_Mutation_p.I1599T|FN1_ENST00000357867.4_Missense_Mutation_p.I1599T|FN1_ENST00000446046.1_Missense_Mutation_p.I1599T|FN1_ENST00000356005.4_Missense_Mutation_p.I1599T|FN1_ENST00000354785.4_Missense_Mutation_p.I1690T|FN1_ENST00000490833.1_5'UTR|FN1_ENST00000336916.4_Missense_Mutation_p.I1599T|FN1_ENST00000346544.3_Missense_Mutation_p.I1599T|FN1_ENST00000357009.2_Missense_Mutation_p.I1599T|FN1_ENST00000323926.6_Missense_Mutation_p.I1690T			P02751	FINC_HUMAN	fibronectin 1	1599	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.I1599T(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	CAAGCCTTCAATAGTCATTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	72	75					2																	216247030		2203	4300	6503	215955275	SO:0001583	missense	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4796T>C	2.37:g.216247030A>G	ENSP00000352696:p.Ile1599Thr		215955275	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	A	23.3	4.395075	0.83011	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000002	T	0.79839	0.4515	M	0.86953	2.85	0.80722	D	1	D;D;D;B;P;D;D;P;D;D;D;D	0.71674	0.998;0.981;0.99;0.087;0.733;0.997;0.998;0.938;0.996;0.99;0.99;0.995	D;D;D;B;P;D;D;D;D;D;D;D	0.87578	0.998;0.987;0.987;0.155;0.621;0.996;0.998;0.942;0.998;0.987;0.987;0.993	D	0.83530	0.0090	10	0.87932	D	0	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	1390;1599;1690;1690;1599;1599;1599;1599;1600;1599;1599;1690	Q68CX6;F8W7G7;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.;.	T	1599;1690;1599;1599;1690;1600;1599;1599;1599;1599;1599;1599;1690;1599;406	ENSP00000394423:I1599T;ENSP00000323534:I1690T;ENSP00000338200:I1599T;ENSP00000350534:I1599T;ENSP00000346839:I1690T;ENSP00000352696:I1599T;ENSP00000265312:I1599T;ENSP00000273049:I1599T;ENSP00000349509:I1599T;ENSP00000410422:I1599T;ENSP00000415018:I1599T;ENSP00000399538:I1690T;ENSP00000348285:I1599T;ENSP00000416139:I406T	ENSP00000265313:I1600T	I	-	2	0	FN1	215955275	1.000000	0.71417	0.987000	0.45799	0.973000	0.67179	9.300000	0.96151	2.254000	0.74563	0.533000	0.62120	ATT		0.463	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216247030	A	G	216247030	3	3	57	1	0	0	0	0	1	0	0	0	5981	101	4	4	2424	4	FN1	2	216247030	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	24341158	216247030	26952343	34	7560										
IRS1	3667	broad.mit.edu	37	chr2	227662786	227662786	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	acggcagaacggcccacctcGatgaagaagaagttttccga	11	11	0	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr2:227662786G>A	ENST00000305123.5	-	1	1689	c.669C>T	c.(667-669)atC>atT	p.I223I	RP11-395N3.2_ENST00000607970.1_lincRNA|IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	223	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.I223I(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GGCCCACCTCGATGAAGAAGA	0.607											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - coding silent(2)	large_intestine(2)	2											76	84	82					2																	227662786		2203	4300	6503	227371030	SO:0001819	synonymous_variant	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.669C>T	2.37:g.227662786G>A		2321	227371030		Silent	SNP	ENST00000305123.5	37	CCDS2463.1																																																																																				0.607	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		A	227662786	G	A	227662786	2	1	57	1	0	0	0	0	0	0	0	1	7861	1048	37	1		1	IRS1	2	227662786	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	11415756	227662786	15536587	35	7561										
FBXL2	25827	broad.mit.edu	37	chr3	33420182	33420182	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	catgtttctctccagataacCgacagcacactcatccagct	5	15	2	1	rs377078642		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:33420182C>T	ENST00000484457.1	+	13	991	c.900C>T	c.(898-900)acC>acT	p.T300T	FBXL2_ENST00000507198.1_Silent_p.T232T|FBXL2_ENST00000538892.1_Silent_p.T232T|FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000446237.3_Silent_p.T10T|FBXL2_ENST00000538181.1_Silent_p.T216T|FBXL2_ENST00000542085.1_Silent_p.T10T	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2									p.T300T(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						TCCAGATAACCGACAGCACAC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	3						C	,	1,4405	2.1+/-5.4	0,1,2202	191	163	172		696,900	-2.5	0.9	3		172	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FBXL2	NM_001171713.1,NM_012157.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	232/356,300/424	33420182	1,13005	2203	4300	6503	33395186	SO:0001819	synonymous_variant	25827			AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"F-boxes / Leucine-rich repeats"	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000484457.1:c.900C>T	3.37:g.33420182C>T			33395186		Silent	SNP	ENST00000484457.1	37	CCDS2658.1																																																																																				0.438	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253245.2	NM_012157		T	33420182	C	T	33420182	2	4	57	1	0	0	0	0	0	0	0	1	5735	639	23	1		1	FBXL2	3	33420182	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09		33420182	164602248	36	7562										
ULK4	54986	broad.mit.edu	37	chr3	41757043	41757043	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	acgtccagaaacattagccaAggagttaagaatgtcacctg	9	9	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:41757043A>T	ENST00000301831.4	-	24	2935	c.2473T>A	c.(2473-2475)Ttg>Atg	p.L825M		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	825					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L825M(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ACATTAGCCAAGGAGTTAAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											82	80	81					3																	41757043		1961	4166	6127	41732047	SO:0001583	missense	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2473T>A	3.37:g.41757043A>T	ENSP00000301831:p.Leu825Met		41732047	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	A	17.02	3.281389	0.59758	.	.	ENSG00000168038	ENST00000301831	T	0.70045	-0.45	5.5	0.247	0.15521	Armadillo-type fold (1);	0.000000	0.64402	U	0.000007	T	0.74951	0.3784	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73148	-0.4074	10	0.87932	D	0	.	10.5066	0.44836	0.6696:0.0:0.3304:0.0	.	825	Q96C45	ULK4_HUMAN	M	825	ENSP00000301831:L825M	ENSP00000301831:L825M	L	-	1	2	ULK4	41732047	0.979000	0.34478	0.966000	0.40874	0.723000	0.41478	0.838000	0.27572	-0.174000	0.10743	0.528000	0.53228	TTG		0.458	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		T	41757043	A	T	41757043	3	4	57	1	0	0	0	0	1	0	0	0	17018	69	3	5	1410	5	ULK4	3	41757043	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	8336861	41757043	156265387	37	7563										
DCBLD2	131566	broad.mit.edu	37	chr3	98518393	98518393	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctgtcagtcctggagagaagTgtattgtaagttcccactag	11	8	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:98518393T>A	ENST00000326840.6	-	16	2513	c.2151A>T	c.(2149-2151)acA>acT	p.T717T	DCBLD2_ENST00000326857.9_Silent_p.T731T	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	717					cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.T717T(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						TGGAGAGAAGTGTATTGTAAG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	3											183	184	184					3																	98518393		1966	4162	6128	100001083	SO:0001819	synonymous_variant	131566				CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.2151A>T	3.37:g.98518393T>A			100001083	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																				0.562	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927		A	98518393	T	A	98518393	2	1	57	1	0	0	0	0	0	0	0	1	4287	1683	59	5		5	DCBLD2	3	98518393	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	56761350	98518393	99504037	38	7564										
GAP43	2596	broad.mit.edu	37	chr3	115394917	115394917	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	atggtatcaaaccagaagatAaagctcataaggccgcaacc	8	10	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:115394917A>T	ENST00000305124.6	+	2	454	c.88A>T	c.(88-90)Aaa>Taa	p.K30*	GAP43_ENST00000393780.3_Nonsense_Mutation_p.K66*	NM_002045.3	NP_002036.1	P17677	NEUM_HUMAN	growth associated protein 43	30					axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.K30*(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		ACCAGAAGATAAAGCTCATAA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											90	93	92					3																	115394917		2203	4300	6503	116877607	SO:0001587	stop_gained	2596				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020			4140	protein-coding gene	gene with protein product	"neuron growth-associated protein 43", "neuromodulin", "nerve growth-related peptide GAP43", "axonal membrane protein GAP-43", "protein F1", "calmodulin-binding protein P-57", "neural phosphoprotein B-50"	162060				3272162, 8231732	Standard	NM_002045		Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000305124.6:c.88A>T	3.37:g.115394917A>T	ENSP00000305010:p.Lys30*		116877607	A8K0Y4	Nonsense_Mutation	SNP	ENST00000305124.6	37	CCDS33830.1	.	.	.	.	.	.	.	.	.	.	A	41	8.627007	0.98890	.	.	ENSG00000172020	ENST00000305124;ENST00000393780	.	.	.	4.75	4.75	0.60458	.	0.047299	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6529	14.721	0.69305	1.0:0.0:0.0:0.0	.	.	.	.	X	30;66	.	ENSP00000305010:K30X	K	+	1	0	GAP43	116877607	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.698000	0.91311	2.117000	0.64856	0.460000	0.39030	AAA		0.413	GAP43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258216.2	NM_002045		T	115394917	A	T	115394917	4	4	57	1	0	0	0	0	0	1	0	0	6255	363	13	5	236	5	GAP43	3	115394917	Nonsense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	16876524	115394917	82627513	39	7565										
PAQR9	344838	broad.mit.edu	37	chr3	142681728	142681728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gtccaggtagaagaaggcggCgcgcagacgcagcgacaggc	17	11	0	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:142681728C>T	ENST00000340634.3	-	1	450	c.451G>A	c.(451-453)Gcc>Acc	p.A151T	RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	151						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.A151T(1)		endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						AAGAAGGCGGCGCGCAGACGC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3											42	40	41					3																	142681728		2203	4300	6503	144164418	SO:0001583	missense	344838			AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.451G>A	3.37:g.142681728C>T	ENSP00000341564:p.Ala151Thr		144164418	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608676	0.87258	.	.	ENSG00000188582	ENST00000340634	T	0.30182	1.54	4.8	4.8	0.61643	.	0.257041	0.31784	N	0.007064	T	0.42720	0.1215	L	0.50333	1.59	0.49130	D	0.999753	D	0.63880	0.993	P	0.56127	0.792	T	0.12811	-1.0533	10	0.17369	T	0.5	-24.4567	18.2419	0.89970	0.0:1.0:0.0:0.0	.	151	Q6ZVX9	PAQR9_HUMAN	T	151	ENSP00000341564:A151T	ENSP00000341564:A151T	A	-	1	0	PAQR9	144164418	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.597000	0.61062	2.369000	0.80426	0.462000	0.41574	GCC		0.627	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		T	142681728	C	T	142681728	3	4	57	1	0	0	0	0	1	0	0	0	11473	768	27	1	686	1	PAQR9	3	142681728	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	27286811	142681728	55340702	40	7566										
SGEF	26084	broad.mit.edu	37	chr3	153840411	153840411	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cctgggccccagaaaagttcTtcggaacaaaaactccccct	7	15	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:153840411T>A	ENST00000356448.4	+	2	914	c.630T>A	c.(628-630)tcT>tcA	p.S210S	ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26_ENST00000465093.1_Silent_p.S210S|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26_ENST00000465817.1_Silent_p.S210S	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	210					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S210S(2)		endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						AGAAAAGTTCTTCGGAACAAA	0.597																																					GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)											2	Substitution - coding silent(2)	large_intestine(2)	3											21	23	22					3																	153840411		1818	4075	5893	155323101	SO:0001819	synonymous_variant	26084			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.630T>A	3.37:g.153840411T>A			155323101	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Silent	SNP	ENST00000356448.4	37	CCDS46938.1																																																																																				0.597	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		A	153840411	T	A	153840411	2	1	57	1	0	0	0	0	0	0	0	1	14242	1596	56	5		5	SGEF	3	153840411	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	11158683	153840411	44182019	41	7567										
FNDC3B	64778	broad.mit.edu	37	chr3	172115036	172115036	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gttccgcgtatgtgcgtgtcGtcgctgtttagacacctctc	11	12	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:172115036G>A	ENST00000336824.4	+	26	3485	c.3386G>A	c.(3385-3387)cGt>cAt	p.R1129H	FNDC3B_ENST00000416957.1_Missense_Mutation_p.R1129H|FNDC3B_ENST00000415807.2_Missense_Mutation_p.R1129H	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1129	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.R1129H(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TGTGCGTGTCGTCGCTGTTTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	88	89					3																	172115036		2203	4300	6503	173597730	SO:0001583	missense	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.3386G>A	3.37:g.172115036G>A	ENSP00000338523:p.Arg1129His		173597730	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876106	0.72180	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.53857	0.6;0.6;0.6	6.02	5.14	0.70334	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.76744	0.4030	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81861	-0.0738	10	0.72032	D	0.01	-17.9503	16.5632	0.84572	0.0:0.0:0.8684:0.1316	.	1129	Q53EP0	FND3B_HUMAN	H	1129	ENSP00000411242:R1129H;ENSP00000338523:R1129H;ENSP00000389094:R1129H	ENSP00000338523:R1129H	R	+	2	0	FNDC3B	173597730	1.000000	0.71417	0.675000	0.29917	0.737000	0.42083	9.307000	0.96226	1.525000	0.49052	0.655000	0.94253	CGT		0.522	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	172115036	G	A	172115036	3	1	57	1	0	0	0	0	1	0	0	0	5989	1145	40	1	3484	1	FNDC3B	3	172115036	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	18274625	172115036	25907394	42	7568										
GP5	2814	broad.mit.edu	37	chr3	194118321	194118321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggccccgggtgcgatggaacGgatgtgatttcggtggaact	17	8	0	1	rs369093144		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr3:194118321G>A	ENST00000401815.1	-	1	762	c.691C>T	c.(691-693)Cgt>Tgt	p.R231C	GP5_ENST00000323007.3_Missense_Mutation_p.R231C			P40197	GPV_HUMAN	glycoprotein V (platelet)	231					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R231C(2)|p.R231S(2)		breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		GCGATGGAACGGATGTGATTT	0.582																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	3						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	113	120	118		691	-1.5	0	3		118	0,8600		0,0,4300	no	missense	GP5	NM_004488.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	231/561	194118321	1,13005	2203	4300	6503	195599610	SO:0001583	missense	2814			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"CD molecules"	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.691C>T	3.37:g.194118321G>A	ENSP00000383931:p.Arg231Cys		195599610	D1MER9	Missense_Mutation	SNP	ENST00000401815.1	37	CCDS3307.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.256854	0.22965	2.27E-4	0.0	ENSG00000178732	ENST00000401815;ENST00000323007	T;T	0.58210	0.35;0.35	4.33	-1.47	0.08772	.	0.701509	0.11800	N	0.528186	T	0.53158	0.1779	M	0.70903	2.155	0.09310	N	1	D	0.60575	0.988	P	0.48114	0.567	T	0.50474	-0.8824	10	0.56958	D	0.05	.	8.0813	0.30746	0.0685:0.4933:0.3294:0.1089	.	231	P40197	GPV_HUMAN	C	231	ENSP00000383931:R231C;ENSP00000319286:R231C	ENSP00000319286:R231C	R	-	1	0	GP5	195599610	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	-0.271000	0.08572	-0.186000	0.10533	-0.485000	0.04761	CGT		0.582	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488		A	194118321	G	A	194118321	3	1	57	1	0	0	0	0	1	0	0	0	6603	1116	39	1	995	1	GP5	3	194118321	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	22003285	194118321	3904109	43	7569										
MAPK10	5602	broad.mit.edu	37	chr4	87023093	87023093	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggtgcttaatgccacacaacAtttggtacagcaggtaagac	10	9	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr4:87023093A>G	ENST00000359221.3	-	7	1044	c.518T>C	c.(517-519)aTg>aCg	p.M173T	MAPK10_ENST00000395157.3_Missense_Mutation_p.M28T|MAPK10_ENST00000361569.2_Missense_Mutation_p.M173T|MAPK10_ENST00000395169.3_Missense_Mutation_p.M135T|MAPK10_ENST00000449047.2_Missense_Mutation_p.M28T|MAPK10_ENST00000395166.1_Missense_Mutation_p.M135T|MAPK10_ENST00000395160.3_Missense_Mutation_p.M28T|MAPK10_ENST00000513839.1_5'Flank|MAPK10_ENST00000395161.2_Missense_Mutation_p.M173T			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	173	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)	p.M173T(1)|p.M28T(1)		breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		GCCACACAACATTTGGTACAG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	4											238	223	228					4																	87023093		2203	4300	6503	87242117	SO:0001583	missense	5602			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.518T>C	4.37:g.87023093A>G	ENSP00000352157:p.Met173Thr		87242117	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	37	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208481	0.79240	.	.	ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161	D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87152	0.6106	N	0.17594	0.5	0.80722	D	1	B;B;B;B;B	0.28667	0.013;0.219;0.022;0.146;0.049	P;P;P;P;P	0.60415	0.558;0.874;0.522;0.655;0.687	D	0.87355	0.2340	10	0.72032	D	0.01	-13.8068	16.4127	0.83723	1.0:0.0:0.0:0.0	.	59;28;135;173;173	B7Z1Z1;Q499Y8;P53779-3;P53779-2;P53779	.;.;.;.;MK10_HUMAN	T	135;173;28;173;135;28;28;173	ENSP00000378598:M135T;ENSP00000352157:M173T;ENSP00000378586:M28T;ENSP00000355297:M173T;ENSP00000378595:M135T;ENSP00000378589:M28T;ENSP00000414469:M28T;ENSP00000378590:M173T	ENSP00000352157:M173T	M	-	2	0	MAPK10	87242117	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.231000	0.95317	2.279000	0.76181	0.528000	0.53228	ATG		0.398	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			G	87023093	A	G	87023093	3	3	57	1	0	0	0	0	1	0	0	0	9302	217	8	4	913	4	MAPK10	4	87023093	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09		87023093	104131183	44	7570										
SPOCK3	50859	broad.mit.edu	37	chr4	167675873	167675873	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	caaattggcaagatgctggtAtcgaatcctaaaggcaaaaa	9	7	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr4:167675873A>T	ENST00000357154.3	-	9	863	c.726T>A	c.(724-726)gaT>gaA	p.D242E	SPOCK3_ENST00000512648.1_Missense_Mutation_p.D239E|SPOCK3_ENST00000421836.2_Missense_Mutation_p.D191E|SPOCK3_ENST00000535728.1_Missense_Mutation_p.D110E|SPOCK3_ENST00000534949.1_Missense_Mutation_p.D146E|SPOCK3_ENST00000511531.1_Missense_Mutation_p.D242E|SPOCK3_ENST00000506886.1_Missense_Mutation_p.D242E|SPOCK3_ENST00000512681.1_Missense_Mutation_p.D144E|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000511269.1_Missense_Mutation_p.D239E|SPOCK3_ENST00000504953.1_Missense_Mutation_p.D239E|SPOCK3_ENST00000510741.1_Missense_Mutation_p.D199E|SPOCK3_ENST00000541354.1_Missense_Mutation_p.D122E|SPOCK3_ENST00000541637.1_Missense_Mutation_p.D144E|SPOCK3_ENST00000502330.1_Missense_Mutation_p.D242E|SPOCK3_ENST00000357545.4_Missense_Mutation_p.D239E	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	242					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)	p.D239E(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		AGATGCTGGTATCGAATCCTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	99	102					4																	167675873		2203	4300	6503	167912448	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.726T>A	4.37:g.167675873A>T	ENSP00000349677:p.Asp242Glu		167912448	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.764209	0.49574	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949;ENST00000512648;ENST00000510403	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;D	0.86769	1.5;1.5;1.5;1.5;1.5;1.5;1.52;1.43;0.95;1.5;1.49;1.3;0.95;1.19;2.24;-2.17	5.64	5.64	0.86602	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.107040	0.64402	D	0.000005	D	0.90872	0.7132	L	0.47190	1.495	0.58432	D	0.999992	P;P;D;D;D;P;D;D	0.71674	0.649;0.804;0.963;0.998;0.998;0.804;0.996;0.998	B;P;P;D;D;B;D;D	0.83275	0.402;0.47;0.812;0.996;0.996;0.325;0.99;0.996	D	0.89369	0.3673	10	0.30854	T	0.27	-1.5653	16.1564	0.81670	1.0:0.0:0.0:0.0	.	144;146;191;251;199;242;239;242	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;.;TICN3_HUMAN	E	242;239;239;242;242;242;199;122;144;239;110;191;144;146;239;121	ENSP00000349677:D242E;ENSP00000350153:D239E;ENSP00000425570:D239E;ENSP00000420920:D242E;ENSP00000423421:D242E;ENSP00000423606:D242E;ENSP00000426716:D199E;ENSP00000444789:D122E;ENSP00000426318:D144E;ENSP00000425502:D239E;ENSP00000441396:D110E;ENSP00000411344:D191E;ENSP00000445430:D144E;ENSP00000438142:D146E;ENSP00000426177:D239E;ENSP00000423176:D121E	ENSP00000349677:D242E	D	-	3	2	SPOCK3	167912448	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	3.583000	0.53928	2.274000	0.75844	0.528000	0.53228	GAT		0.388	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			T	167675873	A	T	167675873	3	4	57	1	0	0	0	0	1	0	0	0	15120	446	16	5	600	5	SPOCK3	4	167675873	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	80652780	167675873	23478403	45	7571										
SPOCK3	50859	broad.mit.edu	37	chr4	167921517	167921517	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tacctgtgtgtaagcctccgGtgactaatgcagactgcagt	11	10	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr4:167921517G>T	ENST00000357154.3	-	5	479	c.342C>A	c.(340-342)caC>caA	p.H114Q	SPOCK3_ENST00000512648.1_Missense_Mutation_p.H111Q|SPOCK3_ENST00000421836.2_Missense_Mutation_p.H63Q|SPOCK3_ENST00000535728.1_Missense_Mutation_p.H22Q|SPOCK3_ENST00000534949.1_Intron|SPOCK3_ENST00000511531.1_Missense_Mutation_p.H114Q|SPOCK3_ENST00000506886.1_Missense_Mutation_p.H114Q|SPOCK3_ENST00000512681.1_Intron|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000511269.1_Missense_Mutation_p.H111Q|SPOCK3_ENST00000504953.1_Missense_Mutation_p.H111Q|SPOCK3_ENST00000510741.1_Missense_Mutation_p.H111Q|SPOCK3_ENST00000541354.1_Intron|SPOCK3_ENST00000541637.1_Intron|SPOCK3_ENST00000502330.1_Missense_Mutation_p.H114Q|SPOCK3_ENST00000357545.4_Missense_Mutation_p.H111Q	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	114					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)	p.H111Q(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		TAAGCCTCCGGTGACTAATGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											127	121	123					4																	167921517		2203	4300	6503	168158092	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.342C>A	4.37:g.167921517G>T	ENSP00000349677:p.His114Gln		168158092	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	G	9.675	1.147694	0.21288	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000512648;ENST00000509854;ENST00000506697;ENST00000512042	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.40225	1.62;1.62;1.62;1.62;1.62;1.62;1.63;1.62;1.63;1.42;2.39;1.04;1.04;1.04	5.27	2.6	0.31112	.	0.207410	0.46758	D	0.000276	T	0.21062	0.0507	N	0.20766	0.605	0.80722	D	1	B;B;B;B;B;B	0.20052	0.007;0.031;0.031;0.009;0.041;0.031	B;B;B;B;B;B	0.19391	0.006;0.025;0.025;0.01;0.019;0.025	T	0.10314	-1.0635	10	0.06236	T	0.91	-6.6568	6.9416	0.24496	0.2608:0.1282:0.611:0.0	.	63;123;111;114;111;114	B4DHB4;B4DFW5;E7EP61;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;TICN3_HUMAN	Q	114;111;111;114;114;114;111;111;22;63;111;111;114;114	ENSP00000349677:H114Q;ENSP00000350153:H111Q;ENSP00000425570:H111Q;ENSP00000420920:H114Q;ENSP00000423421:H114Q;ENSP00000423606:H114Q;ENSP00000426716:H111Q;ENSP00000425502:H111Q;ENSP00000441396:H22Q;ENSP00000411344:H63Q;ENSP00000426177:H111Q;ENSP00000423367:H111Q;ENSP00000424168:H114Q;ENSP00000425407:H114Q	ENSP00000349677:H114Q	H	-	3	2	SPOCK3	168158092	0.988000	0.35896	1.000000	0.80357	0.857000	0.48899	0.096000	0.15147	0.308000	0.22923	0.460000	0.39030	CAC		0.408	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			T	167921517	G	T	167921517	3	4	57	1	0	0	0	0	1	0	0	0	15120	1252	44	2	1000	2	SPOCK3	4	167921517	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	245644	167921517	23232759	46	7572										
MAP1B	4131	broad.mit.edu	37	chr5	71490971	71490971	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aagacaagccaataaaaacaGagaccaaaccttcagtgact	6	10	1	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:71490971G>T	ENST00000296755.7	+	5	2087	c.1789G>T	c.(1789-1791)Gag>Tag	p.E597*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	597	Lys-rich (highly basic, contains many KKEE and KKEI/V repeats).				axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E597*(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AATAAAAACAGAGACCAAACC	0.453																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Nonsense(1)	large_intestine(1)	5											63	66	65					5																	71490971		2203	4300	6503	71526727	SO:0001587	stop_gained	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.1789G>T	5.37:g.71490971G>T	ENSP00000296755:p.Glu597*		71526727	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756132	0.89843	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	.	.	.	5.81	5.81	0.92471	.	0.087773	0.48767	D	0.000175	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-13.8229	20.0825	0.97783	0.0:0.0:1.0:0.0	.	.	.	.	X	597;614;471	.	ENSP00000296755:E597X	E	+	1	0	MAP1B	71526727	1.000000	0.71417	0.978000	0.43139	0.977000	0.68977	9.869000	0.99810	2.746000	0.94184	0.655000	0.94253	GAG		0.453	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71490971	G	T	71490971	4	4	57	1	0	0	0	0	0	1	0	0	9258	943	33	2	1807	2	MAP1B	5	71490971	Nonsense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		71490971	109424289	47	7573										
APC	324	broad.mit.edu	37	chr5	112174884	112174884	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gaaacagtcattttcattctCaaagagttcatctggacaaa	6	8	5	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:112174884C>G	ENST00000457016.1	+	16	3973	c.3593C>G	c.(3592-3594)tCa>tGa	p.S1198*	APC_ENST00000257430.4_Nonsense_Mutation_p.S1198*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1198*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1198	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1198*(1)|p.K1192fs*3(1)|p.?(1)|p.S1198fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTTCATTCTCAAAGAGTTCA	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Substitution - Nonsense(1)|Unknown(1)|Complex - frameshift(1)|Deletion - Frameshift(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CM040980|CM990160	APC	M							84	88	87					5																	112174884		2202	4300	6502	112202783	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3593C>G	5.37:g.112174884C>G	ENSP00000413133:p.Ser1198*		112202783	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	7.020417	0.98006	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.91	5.91	0.95273	.	0.413227	0.24818	N	0.035348	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.3231	20.2983	0.98569	0.0:1.0:0.0:0.0	.	.	.	.	X	1198	.	.	S	+	2	0	APC	112202783	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.331000	0.65905	2.802000	0.96397	0.655000	0.94253	TCA		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174884	C	G	112174884	4	3	57	1	0	0	0	0	0	1	0	0	763	838	29	5	3651	5	APC	5	112174884	Nonsense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	40683913	112174884	68740376	48	7574										
APC	324	broad.mit.edu	37	chr5	112175273	112175273	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcgaagttccagcagtgtcaCagcaccctagaaccaaatcc	8	14	1	1	rs398123121		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:112175273C>T	ENST00000457016.1	+	16	4362	c.3982C>T	c.(3982-3984)Cag>Tag	p.Q1328*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1328*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1328*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1328	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			AVSQHPR -> SSVHSTLE (in Ref. 1; AAA60353/ AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1328*(12)|p.Q1328fs*3(2)|p.?(1)|p.?fs(1)|p.K1192fs*3(1)|p.V1326fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGCAGTGTCACAGCACCCTAG	0.448		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	18	Substitution - Nonsense(12)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(15)|soft_tissue(1)|endometrium(1)|skin(1)	5	GRCh37	CM930028	APC	M							61	63	63					5																	112175273		2202	4300	6502	112203172	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3982C>T	5.37:g.112175273C>T	ENSP00000413133:p.Gln1328*		112203172	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.920796	0.97105	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.360425	0.32258	N	0.006349	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.017	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1328	.	.	Q	+	1	0	APC	112203172	1.000000	0.71417	0.958000	0.39756	0.198000	0.23893	4.377000	0.59562	2.861000	0.98227	0.655000	0.94253	CAG		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175273	C	T	112175273	4	4	57	1	0	0	0	0	0	1	0	0	763	479	17	3	4040	3	APC	5	112175273	Nonsense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	389	112175273	68739987	49	7575										
PCDHB16	57717	broad.mit.edu	37	chr5	140563203	140563203	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctgcactcaccagccccatcCcagagaactcgcctgagata	7	17	1	2	rs17857089	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:140563203C>G	ENST00000361016.2	+	1	2224	c.1069C>G	c.(1069-1071)Cca>Gca	p.P357A		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	357	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.			P -> A (in Ref. 7; AAH36062). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P357A(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGCCCCATCCCAGAGAACTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											81	85	84					5																	140563203		2203	4300	6503	140543387	SO:0001583	missense	57717			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1069C>G	5.37:g.140563203C>G	ENSP00000354293:p.Pro357Ala		140543387	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235645	0.39498	.	.	ENSG00000196963	ENST00000361016	T	0.73258	-0.73	4.47	2.6	0.31112	Cadherin (3);Cadherin-like (1);	0.000000	0.34046	N	0.004302	T	0.65037	0.2653	M	0.64676	1.99	0.26717	N	0.970867	B;B	0.16802	0.011;0.019	B;B	0.23150	0.017;0.044	T	0.58741	-0.7583	10	0.44086	T	0.13	.	9.5484	0.39295	0.0:0.7784:0.1415:0.0801	rs17857089;rs17857089	47;357	O15199;Q9NRJ7	.;PCDBG_HUMAN	A	357	ENSP00000354293:P357A	ENSP00000354293:P357A	P	+	1	0	PCDHB16	140543387	0.000000	0.05858	0.693000	0.30195	0.993000	0.82548	0.651000	0.24873	0.823000	0.34589	0.591000	0.81541	CCA		0.532	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		G	140563203	C	G	140563203	3	3	57	1	0	0	0	0	1	0	0	0	11572	623	22	5	1071	5	PCDHB16	5	140563203	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	28387930	140563203	40352057	50	7576										
TCOF1	6949	broad.mit.edu	37	chr5	149776096	149776096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcaggaagggctgggagagcCgcaagcggaagctatcggga	19	8	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:149776096C>T	ENST00000504761.2	+	24	4033	c.4033C>T	c.(4033-4035)Cgc>Tgc	p.R1345C	TCOF1_ENST00000445265.2_Missense_Mutation_p.R1269C|TCOF1_ENST00000439160.2_Missense_Mutation_p.R1308C|TCOF1_ENST00000451292.1_Missense_Mutation_p.R1382C|TCOF1_ENST00000513346.1_Missense_Mutation_p.R1345C|TCOF1_ENST00000377797.3_Missense_Mutation_p.R1346C|TCOF1_ENST00000323668.7_Missense_Mutation_p.R1268C			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1345					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.R1268C(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGGAGAGCCGCAAGCGGAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	5											20	22	21					5																	149776096		2201	4295	6496	149756289	SO:0001583	missense	6949				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.4033C>T	5.37:g.149776096C>T	ENSP00000421655:p.Arg1345Cys		149756289	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.568324	0.45798	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97;-0.97;-0.97;-0.97	4.8	3.01	0.34805	.	.	.	.	.	T	0.70710	0.3255	L	0.27053	0.805	0.09310	N	1	D;D;D;D;D	0.76494	0.996;0.996;0.996;0.999;0.996	P;P;P;P;P	0.56474	0.648;0.648;0.648;0.799;0.648	T	0.59467	-0.7449	9	0.87932	D	0	0.4065	6.311	0.21164	0.1815:0.7229:0.0:0.0956	.	1308;1268;1307;1345;1269	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	C	1382;1346;1269;1268;1308;1307;1345;1345	ENSP00000400939:R1382C;ENSP00000367028:R1346C;ENSP00000409944:R1269C;ENSP00000325223:R1268C;ENSP00000406888:R1308C;ENSP00000390717:R1307C;ENSP00000421655:R1345C;ENSP00000427484:R1345C	ENSP00000325223:R1268C	R	+	1	0	TCOF1	149756289	0.061000	0.20836	0.005000	0.12908	0.818000	0.46254	0.663000	0.25053	0.560000	0.29169	0.561000	0.74099	CGC		0.617	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		T	149776096	C	T	149776096	3	4	57	1	0	0	0	0	1	0	0	0	15747	652	23	1	4152	1	TCOF1	5	149776096	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	9212893	149776096	31139164	51	7577										
CYFIP2	26999	broad.mit.edu	37	chr5	156786108	156786108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgcagactcctgggttatcaGggcatcgctgtggtcatgga	14	9	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr5:156786108G>A	ENST00000442283.2	+	26	2902	c.620G>A	c.(619-621)aGg>aAg	p.R207K	CYFIP2_ENST00000522463.1_Silent_p.Q727Q|CYFIP2_ENST00000521420.1_Silent_p.Q897Q|CYFIP2_ENST00000541131.1_Silent_p.Q848Q|CYFIP2_ENST00000435847.2_Silent_p.Q622Q|CYFIP2_ENST00000347377.6_Silent_p.Q923Q|CYFIP2_ENST00000377576.3_Silent_p.Q923Q|CYFIP2_ENST00000318218.6_Silent_p.Q948Q	NM_001037333.1	NP_001032410.1			cytoplasmic FMR1 interacting protein 2									p.Q948Q(2)		breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGGTTATCAGGGCATCGCTG	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	5											134	134	134					5																	156786108		1994	4178	6172	156718686	SO:0001583	missense	26999			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000442283.2:c.620G>A	5.37:g.156786108G>A	ENSP00000390948:p.Arg207Lys		156718686		Silent	SNP	ENST00000442283.2	37		.	.	.	.	.	.	.	.	.	.	G	20.1	3.940706	0.73557	.	.	ENSG00000055163	ENST00000442283	T	0.33216	1.42	5.28	5.28	0.74379	.	.	.	.	.	T	0.40145	0.1105	.	.	.	0.23628	N	0.997259	.	.	.	.	.	.	T	0.26710	-1.0095	6	0.48119	T	0.1	-27.3022	14.1828	0.65586	0.0736:0.0:0.9264:0.0	.	.	.	.	K	207	ENSP00000390948:R207K	ENSP00000390948:R207K	R	+	2	0	CYFIP2	156718686	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.903000	0.39858	2.455000	0.83008	0.655000	0.94253	AGG		0.498	CYFIP2-205	KNOWN	basic	protein_coding	protein_coding		NM_001037332		A	156786108	G	A	156786108	3	1	57	1	0	0	0	0	1	0	0	0	4144	991	35	3	2859	3	CYFIP2	5	156786108	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	7010012	156786108	24129152	52	7578										
C4A	721	broad.mit.edu	37	chr6	31995115	31995115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gctctgcccggcctgttgccTtctctgtggtgcccacggca	12	16	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr6:31995115T>C	ENST00000435363.2	+	21	2779	c.2695T>C	c.(2695-2697)Ttc>Ctc	p.F899L	C4B_ENST00000425700.2_Missense_Mutation_p.F899L	NM_001002029.3	NP_001002029.3	P0C0L5	CO4B_HUMAN	complement component 4B (Chido blood group)	899					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|detection of molecule of bacterial origin (GO:0032490)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|complement binding (GO:0001848)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	GCCTGTTGCCTTCTCTGTGGT	0.677																																																0			6											5	13	11					6																	31995115		644	1682	2326	32103093	SO:0001583	missense	721			AF019413	CCDS47405.1	6p21.3	2014-09-17	2009-01-06		ENSG00000224389	ENSG00000224389		"Blood group antigens", "Complement system"	1324	protein-coding gene	gene with protein product		120820	"complement component 4B"				Standard	NM_001002029		Approved	CPAMD3, C4F, CO4, C4B1, C4B3, CH	uc011jpm.2	P0C0L5	OTTHUMG00000031187	ENST00000435363.2:c.2695T>C	6.37:g.31995115T>C	ENSP00000415941:p.Phe899Leu		32103093	A2BHY4|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q6U2E9|Q6U2G1|Q6U2I5|Q6U2L1|Q6U2L7|Q6U2L9|Q6U2M5|Q6VCV8|Q96SA7|Q9NPK5|Q9UIP5	Missense_Mutation	SNP	ENST00000435363.2	37	CCDS47405.1	.	.	.	.	.	.	.	.	.	.	t	25.0	4.589608	0.86851	.	.	ENSG00000224389	ENST00000435363;ENST00000425700	T;T	0.46063	0.88;0.88	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.50446	0.1616	M	0.65975	2.015	0.51012	D	0.9999	D;P	0.89917	1.0;0.723	D;P	0.83275	0.996;0.465	T	0.56679	-0.7939	10	0.72032	D	0.01	.	10.1615	0.42855	0.0:0.0:0.0:1.0	.	899;899	F5GXS0;Q6U2E9	.;.	L	899	ENSP00000415941:F899L;ENSP00000391933:F899L	ENSP00000391933:F899L	F	+	1	0	C4B	32103093	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.934000	0.48956	1.638000	0.50547	0.456000	0.33151	TTC		0.677	C4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076368.5	NM_001002029		C	31995115	T	C	31995115	3	2	57	1	0	0	0	0	1	0	0	0	2253	1609	56	4	7839	4	C4A	6	31995115	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09		31995115	139119952	53	7579										
FAM184A	79632	broad.mit.edu	37	chr6	119337983	119337983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgccatatggtgcttccaagCtaattcttccaaagtcttag	7	10	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr6:119337983C>A	ENST00000338891.7	-	5	1902	c.1459G>T	c.(1459-1461)Gct>Tct	p.A487S	FAM184A_ENST00000368475.4_Missense_Mutation_p.A367S|FAM184A_ENST00000522284.1_Missense_Mutation_p.A367S|FAM184A_ENST00000521531.1_Missense_Mutation_p.A487S|FAM184A_ENST00000352896.5_Missense_Mutation_p.A367S|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	487						extracellular space (GO:0005615)		p.A487S(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TGCTTCCAAGCTAATTCTTCC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											137	130	132					6																	119337983		1828	4086	5914	119379682	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1459G>T	6.37:g.119337983C>A	ENSP00000342604:p.Ala487Ser		119379682	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.47|14.47	2.544693|2.544693	0.45280|0.45280	.|.	.|.	ENSG00000111879|ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284|ENST00000448815	T;T;T;T;T|.	0.00333|.	8.07;8.07;8.07;8.07;8.07|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.193514|.	0.44902|.	D|.	0.000405|.	T|.	0.40094|.	0.1103|.	L|L	0.27053|0.27053	0.805|0.805	0.47276|0.47276	D|D	0.999372|0.999372	B;B;B|.	0.32365|.	0.312;0.084;0.367|.	B;B;B|.	0.28232|.	0.064;0.028;0.087|.	T|.	0.30966|.	-0.9960|.	10|.	0.12430|.	T|.	0.62|.	-6.2951|-6.2951	13.6357|13.6357	0.62221|0.62221	0.155:0.845:0.0:0.0|0.155:0.845:0.0:0.0	.|.	487;367;487|.	Q8NB25-2;F8W8D6;Q8NB25|.	.;.;F184A_HUMAN|.	S|Y	487;367;367;487;367|72	ENSP00000342604:A487S;ENSP00000326608:A367S;ENSP00000357460:A367S;ENSP00000430442:A487S;ENSP00000429826:A367S|.	ENSP00000342604:A487S|.	A|X	-|-	1|3	0|2	FAM184A|FAM184A	119379682|119379682	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.227000|3.227000	0.51262|0.51262	2.433000|2.433000	0.82419|0.82419	0.491000|0.491000	0.48974|0.48974	GCT|TAG		0.358	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119337983	C	A	119337983	3	1	57	1	0	0	0	0	1	0	0	0	5527	797	28	2	2019	2	FAM184A	6	119337983	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	87342868	119337983	51777084	54	7580										
PLG	5340	broad.mit.edu	37	chr6	161155034	161155034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttcttgttttcagtactgccGtaaccctgatggtgatgtag	10	8	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr6:161155034G>A	ENST00000308192.9	+	13	1658	c.1595G>A	c.(1594-1596)cGt>cAt	p.R532H		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	532	Kringle 5. {ECO:0000255|PROSITE- ProRule:PRU00121}.		R -> H (in PLGD). {ECO:0000269|PubMed:10233898}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R532H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CAGTACTGCCGTAACCCTGAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	6	GRCh37	CM991052	PLG	M							219	154	176					6																	161155034		2203	4300	6503	161075024	SO:0001583	missense	5340			M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1595G>A	6.37:g.161155034G>A	ENSP00000308938:p.Arg532His		161075024	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	.	17.22	3.332901	0.60853	.	.	ENSG00000122194	ENST00000308192	D	0.93906	-3.31	3.98	3.98	0.46160	Kringle (4);Kringle-like fold (1);Kringle, conserved site (1);	0.000000	0.34110	U	0.004247	D	0.95999	0.8697	H	0.98802	4.335	0.58432	D	0.999998	P	0.43024	0.798	P	0.44990	0.466	D	0.97234	0.9886	10	0.87932	D	0	.	13.0592	0.58997	0.0:0.0:1.0:0.0	.	532	P00747	PLMN_HUMAN	H	532	ENSP00000308938:R532H	ENSP00000308938:R532H	R	+	2	0	PLG	161075024	1.000000	0.71417	0.677000	0.29947	0.220000	0.24768	5.951000	0.70273	2.037000	0.60232	0.462000	0.41574	CGT		0.498	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161155034	G	A	161155034	3	1	57	1	0	0	0	0	1	0	0	0	12117	1145	40	1	1649	1	PLG	6	161155034	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	41817051	161155034	9960033	55	7581										
GET4	51608	broad.mit.edu	37	chr7	931981	931981	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	acgtacacccagaagcacccGtccatcgaggacgggcctcc	10	17	0	1	rs368468235		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr7:931981G>A	ENST00000265857.3	+	6	766	c.672G>A	c.(670-672)ccG>ccA	p.P224P	GET4_ENST00000407192.1_Silent_p.P171P	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	224					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)		p.P224P(1)		breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AGAAGCACCCGTCCATCGAGG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	7						G		1,4405	2.1+/-5.4	0,1,2202	81	87	85		672	-5.6	1	7		85	0,8600		0,0,4300	no	coding-synonymous	GET4	NM_015949.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		224/328	931981	1,13005	2203	4300	6503	898507	SO:0001819	synonymous_variant	51608			AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"CGI-20 protein", "conserved edge protein", "transmembrane domain recognition complex, 35kDa"	612056	"chromosome 7 open reading frame 20"	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.672G>A	7.37:g.931981G>A			898507	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																				0.557	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949		A	931981	G	A	931981	2	1	57	1	0	0	0	0	0	0	0	1	6356	1132	40	1		1	GET4	7	931981	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09		931981	158206682	56	7582										
SDK1	221935	broad.mit.edu	37	chr7	4272918	4272918	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgggacatgtttgtgaaggaCatcccgcggagcgccacatc	13	11	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr7:4272918C>A	ENST00000404826.2	+	41	5998	c.5859C>A	c.(5857-5859)gaC>gaA	p.D1953E	SDK1_ENST00000389531.3_Missense_Mutation_p.D1933E|SDK1_ENST00000466611.1_3'UTR	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1953	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D1953E(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TTGTGAAGGACATCCCGCGGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	81	86					7																	4272918		2203	4300	6503	4239444	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5859C>A	7.37:g.4272918C>A	ENSP00000385899:p.Asp1953Glu		4239444	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270518	0.80469	.	.	ENSG00000146555	ENST00000404826;ENST00000446104;ENST00000389531	T;T	0.56776	0.44;0.44	4.9	4.01	0.46588	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.082111	0.48767	D	0.000171	T	0.55194	0.1905	L	0.35414	1.06	0.31276	N	0.691188	D;D;P;P	0.60160	0.982;0.987;0.932;0.881	P;P;P;B	0.57776	0.769;0.827;0.685;0.42	T	0.60979	-0.7155	10	0.56958	D	0.05	.	12.5734	0.56349	0.0:0.9196:0.0:0.0804	.	1933;13;440;1953	F8W6X9;Q7Z5N4-2;F2Z3E9;Q7Z5N4	.;.;.;SDK1_HUMAN	E	1953;201;1933	ENSP00000385899:D1953E;ENSP00000374182:D1933E	ENSP00000374182:D1933E	D	+	3	2	SDK1	4239444	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.407000	0.34657	2.252000	0.74401	0.655000	0.94253	GAC		0.587	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4272918	C	A	4272918	3	1	57	1	0	0	0	0	1	0	0	0	14005	477	17	2	6021	2	SDK1	7	4272918	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	3340937	4272918	154865745	57	7583										
DNAH11	8701	broad.mit.edu	37	chr7	21727129	21727129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aaatgattcatgatgccatcAgaaacaggaagaagaggtga	11	5	2	6			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr7:21727129A>G	ENST00000409508.3	+	34	5939	c.5908A>G	c.(5908-5910)Aga>Gga	p.R1970G	DNAH11_ENST00000328843.6_Missense_Mutation_p.R1977G	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1977	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1977G(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TGATGCCATCAGAAACAGGAA	0.448									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											54	55	55					7																	21727129		2186	4295	6481	21693654	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5908A>G	7.37:g.21727129A>G	ENSP00000475939:p.Arg1970Gly		21693654	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	A	14.49	2.552316	0.45487	.	.	ENSG00000105877	ENST00000328843	T	0.38887	1.11	5.66	3.26	0.37387	ATPase, AAA+ type, core (1);	0.226531	0.46442	D	0.000298	T	0.58380	0.2118	.	.	.	0.48185	D	0.999607	D	0.76494	0.999	D	0.70487	0.969	T	0.56529	-0.7964	9	0.62326	D	0.03	.	7.1537	0.25624	0.6494:0.279:0.0716:0.0	.	1977	Q96DT5	DYH11_HUMAN	G	1977	ENSP00000330671:R1977G	ENSP00000330671:R1977G	R	+	1	2	DNAH11	21693654	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	2.464000	0.45067	0.419000	0.25927	-0.438000	0.05819	AGA		0.448	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21727129	A	G	21727129	3	3	57	1	0	0	0	0	1	0	0	0	4610	180	7	4	6064	4	DNAH11	7	21727129	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	17454211	21727129	137411534	58	7584										
GNGT1	2792	broad.mit.edu	37	chr7	93540203	93540203	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gacaaaaatcccttcaaggaGctcaaaggaggctgtgtgat	11	8	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr7:93540203G>T	ENST00000248572.5	+	3	346	c.198G>T	c.(196-198)gaG>gaT	p.E66D	GNGT1_ENST00000455502.1_3'UTR|GNGT1_ENST00000429473.1_Missense_Mutation_p.E66D	NM_021955.3	NP_068774.1	P63211	GBG1_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	66					cardiac muscle cell apoptotic process (GO:0010659)|cellular response to hypoxia (GO:0071456)|eye photoreceptor cell development (GO:0042462)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)	p.E66D(1)		endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			CCTTCAAGGAGCTCAAAGGAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7											60	58	58					7																	93540203		2203	4300	6503	93378139	SO:0001583	missense	2792				CCDS5633.1	7q21.3	2008-07-18			ENSG00000127928	ENSG00000127928			4411	protein-coding gene	gene with protein product		189970				8661128	Standard	NM_021955		Approved	GNG1	uc003unc.1	P63211	OTTHUMG00000022908	ENST00000248572.5:c.198G>T	7.37:g.93540203G>T	ENSP00000248572:p.Glu66Asp		93378139	A4D1H2|O43835|Q08447|Q16026|Q6LCP6	Missense_Mutation	SNP	ENST00000248572.5	37	CCDS5633.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116455	0.77323	.	.	ENSG00000127928	ENST00000248572;ENST00000429473	T;T	0.34275	1.37;1.37	5.75	-0.445	0.12242	G-protein gamma domain (5);	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	.	.	.	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	T	0.47674	-0.9099	9	0.33141	T	0.24	-33.4741	11.4219	0.49987	0.3907:0.0:0.6093:0.0	.	66	P63211	GBG1_HUMAN	D	66	ENSP00000248572:E66D;ENSP00000388777:E66D	ENSP00000248572:E66D	E	+	3	2	GNGT1	93378139	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	1.723000	0.38053	-0.048000	0.13401	0.655000	0.94253	GAG		0.343	GNGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254718.2	NM_021955		T	93540203	G	T	93540203	3	4	57	1	0	0	0	0	1	0	0	0	6553	962	34	2	204	2	GNGT1	7	93540203	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	71813074	93540203	65598460	59	7585										
PDIA4	9601	broad.mit.edu	37	chr7	148700977	148700977	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctctgtctccaccctcaaatTtaactgggttctttttgtcc	5	13	4	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr7:148700977T>A	ENST00000286091.4	-	10	2079	c.1847A>T	c.(1846-1848)aAa>aTa	p.K616I		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	616	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)	p.K616I(1)		large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			ACCCTCAAATTTAACTGGGTT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	7											72	72	72					7																	148700977		2203	4300	6503	148331910	SO:0001583	missense	9601			BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1847A>T	7.37:g.148700977T>A	ENSP00000286091:p.Lys616Ile		148331910	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182398	0.78677	.	.	ENSG00000155660	ENST00000286091	T	0.23950	1.88	5.81	3.47	0.39725	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.043280	0.85682	D	0.000000	T	0.48314	0.1493	M	0.70903	2.155	0.80722	D	1	P	0.38535	0.635	P	0.62491	0.903	T	0.34104	-0.9842	10	0.48119	T	0.1	.	11.2458	0.48996	0.0:0.0928:0.0:0.9072	.	616	P13667	PDIA4_HUMAN	I	616	ENSP00000286091:K616I	ENSP00000286091:K616I	K	-	2	0	PDIA4	148331910	1.000000	0.71417	0.220000	0.23810	0.994000	0.84299	4.868000	0.63021	0.482000	0.27582	0.454000	0.30748	AAA		0.522	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		A	148700977	T	A	148700977	3	1	57	1	0	0	0	0	1	0	0	0	11701	1841	64	5	94	5	PDIA4	7	148700977	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09	55160774	148700977	10437686	60	7586										
ANGPT1	284	broad.mit.edu	37	chr8	108264121	108264121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aatcatcatagttgtggaacGtaaggagtaactgggccctt	11	7	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr8:108264121G>A	ENST00000520734.1	-	8	1144	c.859C>T	c.(859-861)Cgt>Tgt	p.R287C	AP000428.1_ENST00000390706.1_RNA|ANGPT1_ENST00000520052.1_Missense_Mutation_p.R286C|ANGPT1_ENST00000518386.1_5'UTR			Q15389	ANGP1_HUMAN	angiopoietin 1	487	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)	p.R487C(1)		NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			GTTGTGGAACGTAAGGAGTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	8											190	175	180					8																	108264121		2203	4300	6503	108333297	SO:0001583	missense	284			D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.859C>T	8.37:g.108264121G>A	ENSP00000430750:p.Arg287Cys		108333297	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	37		.	.	.	.	.	.	.	.	.	.	G	21.2	4.111864	0.77210	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000520734;ENST00000520052	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.9	5.9	0.94986	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.046380	0.85682	D	0.000000	T	0.64080	0.2566	M	0.88512	2.96	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.67725	0.953;0.953	T	0.69316	-0.5177	10	0.87932	D	0	.	20.2768	0.98488	0.0:0.0:1.0:0.0	.	487;487	Q5HYA0;Q15389	.;ANGP1_HUMAN	C	487;486;287;286	ENSP00000428340:R487C;ENSP00000297450:R486C;ENSP00000430750:R287C;ENSP00000429349:R286C	ENSP00000297450:R486C	R	-	1	0	ANGPT1	108333297	1.000000	0.71417	1.000000	0.80357	0.413000	0.31143	9.869000	0.99810	2.808000	0.96608	0.650000	0.86243	CGT		0.433	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		A	108264121	G	A	108264121	3	1	57	1	0	0	0	0	1	0	0	0	610	1145	40	1	41	1	ANGPT1	8	108264121	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		108264121	38099901	61	7587										
NRBP2	340371	broad.mit.edu	37	chr8	144919461	144919461	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gtccagctccatgaaggagaCttccgagtacctggcatgga	12	11	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr8:144919461C>G	ENST00000442628.2	-	13	1226	c.1087G>C	c.(1087-1089)Gtc>Ctc	p.V363L	NRBP2_ENST00000327830.5_Missense_Mutation_p.V120L	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2									p.V369L(1)		central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ATGAAGGAGACTTCCGAGTAC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	8											31	30	30					8																	144919461		2203	4299	6502	144991449	SO:0001583	missense	340371			BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1087G>C	8.37:g.144919461C>G	ENSP00000414055:p.Val363Leu		144991449		Missense_Mutation	SNP	ENST00000442628.2	37	CCDS34959.2	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434912	0.25813	.	.	ENSG00000185189	ENST00000442628;ENST00000327830	T;T	0.20598	2.06;2.06	4.63	2.82	0.32997	.	0.254816	0.31963	U	0.006788	T	0.17831	0.0428	M	0.72118	2.19	0.39649	D	0.970436	B;P;B;B	0.42941	0.058;0.794;0.141;0.005	B;B;B;B	0.36030	0.029;0.216;0.073;0.006	T	0.06197	-1.0840	10	0.32370	T	0.25	-22.9627	4.3967	0.11367	0.177:0.6293:0.0:0.1937	.	363;155;155;120	Q9NSY0;Q9NSY0-4;Q9NSY0-2;D3DWK9	NRBP2_HUMAN;.;.;.	L	363;120	ENSP00000414055:V363L;ENSP00000330271:V120L	ENSP00000330271:V120L	V	-	1	0	NRBP2	144991449	0.952000	0.32445	0.760000	0.31359	0.802000	0.45316	2.560000	0.45896	0.406000	0.25560	0.579000	0.79373	GTC		0.642	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564		G	144919461	C	G	144919461	3	3	57	1	0	0	0	0	1	0	0	0	10674	565	20	5	442	5	NRBP2	8	144919461	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	36655340	144919461	1444561	62	7588										
APBA1	320	broad.mit.edu	37	chr9	72067136	72067136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctccttctggctgagatcttCggggttaatcccattggccc	10	13	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr9:72067136C>T	ENST00000265381.4	-	9	2092	c.1870G>A	c.(1870-1872)Gaa>Aaa	p.E624K		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	624	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.E624K(2)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CTGAGATCTTCGGGGTTAATC	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	9											205	172	183					9																	72067136		2203	4300	6503	71256956	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1870G>A	9.37:g.72067136C>T	ENSP00000265381:p.Glu624Lys		71256956	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.823790	0.90873	.	.	ENSG00000107282	ENST00000265381	T	0.04502	3.61	5.54	5.54	0.83059	Phosphotyrosine interaction domain (1);	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.00098	-1.2070	10	0.45353	T	0.12	-11.9676	19.4843	0.95024	0.0:1.0:0.0:0.0	.	624	Q02410	APBA1_HUMAN	K	624	ENSP00000265381:E624K	ENSP00000265381:E624K	E	-	1	0	APBA1	71256956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.884000	0.63135	2.610000	0.88304	0.655000	0.94253	GAA		0.502	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72067136	C	T	72067136	3	4	57	1	0	0	0	0	1	0	0	0	756	893	31	1	663	1	APBA1	9	72067136	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		72067136	69146295	63	7589										
TSC1	7248	broad.mit.edu	37	chr9	135772645	135772645	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aggccatctttctccaacctGccatataaatctaagatctc	4	13	4	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr9:135772645G>A	ENST00000298552.3	-	22	3122	c.2901C>T	c.(2899-2901)ggC>ggT	p.G967G	TSC1_ENST00000545250.1_Silent_p.G916G|TSC1_ENST00000440111.2_Silent_p.G967G	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	967					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.G967G(1)|p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		TCTCCAACCTGCCATATAAAT	0.443			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																													yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|bone(1)	9											134	140	138					9																	135772645		2203	4300	6503	134762466	SO:0001819	synonymous_variant	7248	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2901C>T	9.37:g.135772645G>A			134762466	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																				0.443	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135772645	G	A	135772645	2	1	57	1	0	0	0	0	0	0	0	1	16645	1306	46	3		3	TSC1	9	135772645	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	63705509	135772645	5440786	64	7590										
SYT15	83849	broad.mit.edu	37	chr10	46968587	46968587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcaaggacactcaccaaggcCgccgctggaggtgtgaggca	15	12	1	1	rs373437721	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr10:46968587C>T	ENST00000374321.4	-	3	415	c.349G>A	c.(349-351)Ggc>Agc	p.G117S	SYT15_ENST00000503753.1_Missense_Mutation_p.G117S|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.G170S|SYT15_ENST00000374325.3_Missense_Mutation_p.G117S	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G117S(2)		cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						TCACCAAGGCCGCCGCTGGAG	0.657													C|||	2	0.000399361	0.0015	0	5008	,	,		33609	0		0	False		,,,				2504	0				Ovarian(57;1152 1428 19651 37745)											2	Substitution - Missense(2)	large_intestine(2)	10																																								46388593	SO:0001583	missense	83849			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.349G>A	10.37:g.46968587C>T	ENSP00000363441:p.Gly117Ser		46388593	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	3.038	-0.198099	0.06219	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374323;ENST00000374321	T;T;T;T	0.12465	2.68;2.68;2.87;2.89	4.37	0.329	0.15924	.	1.202190	0.06237	N	0.689767	T	0.04407	0.0121	N	0.04090	-0.28	0.09310	N	1	B;B	0.17852	0.007;0.024	B;B	0.06405	0.002;0.002	T	0.38520	-0.9657	10	0.06494	T	0.89	.	0.737	0.00967	0.2873:0.1088:0.1665:0.4374	.	117;117	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	S	117;117;117;170;117	ENSP00000363445:G117S;ENSP00000427607:G117S;ENSP00000363443:G170S;ENSP00000363441:G117S	ENSP00000363441:G117S	G	-	1	0	SYT15	46388593	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.273000	0.18662	0.294000	0.22547	-0.391000	0.06502	GGC		0.657	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		T	46968587	C	T	46968587	3	4	57	1	0	0	0	0	1	0	0	0	15510	652	23	1	994	1	SYT15	10	46968587	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		46968587	88566160	65	7591										
TLX1NB	100038246	broad.mit.edu	37	chr10	102849370	102849370	+	Frame_Shift_Del	DEL	T	T	-													0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggattctggatttctccagcTgaggtgacctgggcaccaga					rs200664029	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr10:102849370delT	ENST00000445873.1	-	3	1569	c.293delA	c.(292-294)cagfs	p.Q98fs	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	98																	TTTCTCCAGCTGAGGTGACCT	0.572													T|T|-|deletion	7	0.00139776	8e-04	0.0014	5008	,	,		15955	0		0.005	False		,,,				2504	0															0			10								8,3620		0,8,1806	33	33	33			1.1	0	10		33	75,7807		1,73,3867	no	frameshift	TLX1NB	NM_001085398.1		1,81,5673	A1A1,A1R,RR		0.9515,0.2205,0.7211			102849370	83,11427	1881	4116	5997	102839360	SO:0001589	frameshift_variant	100038246			BC019674	CCDS60615.1	10q24	2014-04-01			ENSG00000236311	ENSG00000236311			37183	protein-coding gene	gene with protein product		612734				17303350	Standard	NM_001085398		Approved	TD1, TDI, APT-B7	uc001ksv.3	P0CAT3	OTTHUMG00000018925	ENST00000445873.1:c.293delA	10.37:g.102849370delT	ENSP00000475001:p.Gln98fs		102839360		Frame_Shift_Del	DEL	ENST00000445873.1	37																																																																																					0.572	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398		-	102849370	T	-	102849370	7	5	57	1	0	1	0	1	0	0	0	0	15999	1580	55	0	79	0	TLX1NB	10	102849370	Frame_Shift_Del	DEL	T	TCGA-AG-4005-01A-01W-1073-09	55880783	102849370	32685377	66	7592										
SH3PXD2A	9644	broad.mit.edu	37	chr10	105526904	105526904	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tccttctggccaccttcaatGggaaacttatccaaaagctg	7	12	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr10:105526904G>A	ENST00000369774.4	-	3	453	c.177C>T	c.(175-177)ccC>ccT	p.P59P	SH3PXD2A_ENST00000355946.2_Silent_p.P59P			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	59	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)	p.P59P(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CACCTTCAATGGGAAACTTAT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	10											95	74	81					10																	105526904		2203	4300	6503	105516894	SO:0001819	synonymous_variant	9644			AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"five SH3 domains"		"SH3 multiple domains 1"	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.177C>T	10.37:g.105526904G>A			105516894	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		.	.	.	.	.	.	.	.	.	.	G	10.10	1.256326	0.22965	.	.	ENSG00000107957	ENST00000420222	.	.	.	5.38	2.5	0.30297	.	.	.	.	.	T	0.57621	0.2066	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49234	-0.8961	4	.	.	.	-21.8477	8.5498	0.33444	0.2532:0.0:0.7468:0.0	.	.	.	.	Y	14	.	.	H	-	1	0	SH3PXD2A	105516894	0.985000	0.35326	0.992000	0.48379	0.998000	0.95712	0.042000	0.13949	0.252000	0.21531	0.561000	0.74099	CAT		0.542	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631		A	105526904	G	A	105526904	2	1	57	1	0	0	0	0	0	0	0	1	14293	1335	47	3		3	SH3PXD2A	10	105526904	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	2677534	105526904	30007843	67	7593										
C10orf46	143384	broad.mit.edu	37	chr10	120514109	120514110	+	Frame_Shift_Ins	INS	-	-	C													0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcgggcaccgccagcagctgINScccccccggaggctctcggg					rs199927390		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr10:120514109_120514110insC	ENST00000369151.3	-	1	648_649	c.165_166insG	c.(163-168)gggcagfs	p.Q56fs	CACUL1_ENST00000340214.4_Frame_Shift_Ins_p.Q56fs	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	56	Pro-rich.				G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)	p.Q56fs*30(1)									GCCAGCAGCTGCCCCCCCGGAG	0.733																																																1	Insertion - Frameshift(1)	large_intestine(1)	10								20,3416		1,18,1699						3.9	1			11	18,7588		0,18,3785	no	frameshift	C10orf46	NM_153810.4		1,36,5484	A1A1,A1R,RR		0.2367,0.5821,0.3441				38,11004				120504100	SO:0001589	frameshift_variant	143384			AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"Cdk-Associated Cullin1"		"chromosome 10 open reading frame 46"	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.166dupG	10.37:g.120514116_120514116dupC	ENSP00000358147:p.Gln56fs		120504099	Q5XPL7|Q8IY11|Q8N7S4	Frame_Shift_Ins	INS	ENST00000369151.3	37	CCDS41570.1																																																																																				0.733	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810		C	120514110	-	C	120514109	7	5	57	1	0	1	1	0	0	0	0	0	1608	1328	46	0	979	0	C10orf46	10	120514109	Frame_Shift_Ins	INS	-	TCGA-AG-4005-01A-01W-1073-09	14987205	120514109	15020638	68	7594										
OR52B4	143496	broad.mit.edu	37	chr11	4388604	4388604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tttctgttttataaacaaaaActgaaccacctgttcctgga	5	9	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:4388604A>C	ENST00000408920.2	-	1	1012	c.922T>G	c.(922-924)Ttt>Gtt	p.F308V		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	308					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F308V(1)		NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATAAACAAAAACTGAACCACC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											45	45	45					11																	4388604		1848	4088	5936	4345180	SO:0001583	missense	143496			AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.922T>G	11.37:g.4388604A>C	ENSP00000386160:p.Phe308Val		4345180	A6NP68|Q6IFK6	Missense_Mutation	SNP	ENST00000408920.2	37	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	A	4.474	0.087778	0.08583	.	.	ENSG00000221996	ENST00000408920	T	0.35421	1.31	5.17	-5.42	0.02640	.	2.593500	0.01875	N	0.037463	T	0.15262	0.0368	N	0.10645	0.015	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14559	-1.0468	10	0.11182	T	0.66	.	4.862	0.13588	0.3075:0.2822:0.0:0.4103	.	308	Q8NGK2	O52B4_HUMAN	V	308	ENSP00000386160:F308V	ENSP00000386160:F308V	F	-	1	0	OR52B4	4345180	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.100000	0.00604	-0.957000	0.03627	-0.418000	0.06021	TTT		0.408	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		C	4388604	A	C	4388604	3	2	57	1	0	0	0	0	1	0	0	0	11143	43	2	4	26	4	OR52B4	11	4388604	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09		4388604	130617912	69	7595										
NAT10	55226	broad.mit.edu	37	chr11	34156800	34156801	+	Missense_Mutation	DNP	CT	CT	TC													0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cttgtctggaggaaaaggtcCttgagacaccacaggaaatt							TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:34156800_34156801CT>TC	ENST00000257829.3	+	19	2196_2197	c.1990_1991CT>TC	c.(1990-1992)CTt>TCt	p.L664S	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.L592S	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	664	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)	p.L664>?(1)		endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				GGAAAAGGTCCTTGAGACACCA	0.51																																																1	Complex(1)	large_intestine(1)	11																																								34113377	SO:0001583	missense	55226			AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	Exception_encountered	11.37:g.34156800_34156801delinsTC	ENSP00000257829:p.Leu664Ser		34113376	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	DNP	ENST00000257829.3	37	CCDS7889.1																																																																																				0.51	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		TC	34156801	CT	TC	34156800	3	4	57	1	0	0	0	0	1	0	0	0	10204	681	24	3	2060	3	NAT10	11	34156800	Missense_Mutation	DNP	CT	TCGA-AG-4005-01A-01W-1073-09	29768196	34156800	100849716	70	7596										
OR5B21	219968	broad.mit.edu	37	chr11	58274728	58274728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tcctaaggctgtatatcaagGgattcagcatgggaatcacc	10	9	3	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:58274728G>A	ENST00000360374.2	-	1	850	c.851C>T	c.(850-852)cCc>cTc	p.P284L		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P284L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GTATATCAAGGGATTCAGCAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											148	145	146					11																	58274728		2201	4295	6496	58031304	SO:0001583	missense	219968				CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.851C>T	11.37:g.58274728G>A	ENSP00000353537:p.Pro284Leu		58031304		Missense_Mutation	SNP	ENST00000360374.2	37	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622855	0.66901	.	.	ENSG00000198283	ENST00000360374	T	0.63417	-0.04	5.11	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	U	0.002444	D	0.83216	0.5206	H	0.94964	3.605	0.51767	D	0.999935	D	0.76494	0.999	D	0.76071	0.987	D	0.87195	0.2237	10	0.87932	D	0	-10.3482	12.1723	0.54165	0.083:0.0:0.9169:0.0	.	284	A6NL26	OR5BL_HUMAN	L	284	ENSP00000353537:P284L	ENSP00000353537:P284L	P	-	2	0	OR5B21	58031304	1.000000	0.71417	0.102000	0.21198	0.979000	0.70002	7.729000	0.84864	1.371000	0.46172	0.655000	0.94253	CCC		0.418	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		A	58274728	G	A	58274728	3	1	57	1	0	0	0	0	1	0	0	0	11182	1232	43	3	80	3	OR5B21	11	58274728	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	24117928	58274728	76731788	71	7597										
OR5A1	219982	broad.mit.edu	37	chr11	59210836	59210836	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cacacacccatgtacttcttCctaagcaacttatctttcat	2	14	3	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:59210836C>T	ENST00000302030.2	+	1	220	c.195C>T	c.(193-195)ttC>ttT	p.F65F		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F65F(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						TGTACTTCTTCCTAAGCAACT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	11											156	151	152					11																	59210836		2201	4295	6496	58967412	SO:0001819	synonymous_variant	219982			AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"GPCR / Class A : Olfactory receptors"	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.195C>T	11.37:g.59210836C>T			58967412	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																				0.483	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728		T	59210836	C	T	59210836	2	4	57	1	0	0	0	0	0	0	0	1	11170	854	30	3		3	OR5A1	11	59210836	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	936108	59210836	75795680	72	7598										
OR5A1	219982	broad.mit.edu	37	chr11	59211280	59211280	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gtcactgtcggaggaacatcGttcctccaactccttatctc	7	14	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:59211280G>A	ENST00000302030.2	+	1	664	c.639G>A	c.(637-639)tcG>tcA	p.S213S		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S213S(2)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						GAGGAACATCGTTCCTCCAAC	0.547																																																2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	11											224	209	214					11																	59211280		2201	4295	6496	58967856	SO:0001819	synonymous_variant	219982			AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"GPCR / Class A : Olfactory receptors"	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.639G>A	11.37:g.59211280G>A			58967856	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																				0.547	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728		A	59211280	G	A	59211280	2	1	57	1	0	0	0	0	0	0	0	1	11170	1132	40	1		1	OR5A1	11	59211280	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	444	59211280	75795236	73	7599										
ESRRA	2101	broad.mit.edu	37	chr11	64083421	64083421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	agctgttcttggagatgctcGaggccatgatggactgaggc	15	8	1	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:64083421G>A	ENST00000405666.1	+	7	1489	c.1255G>A	c.(1255-1257)Gag>Aag	p.E419K	ESRRA_ENST00000406310.1_Missense_Mutation_p.E418K|PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|PRDX5_ENST00000352435.4_5'Flank|ESRRA_ENST00000000442.6_Missense_Mutation_p.E419K	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	419	AF-2 domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E419K(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GGAGATGCTCGAGGCCATGAT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											36	38	38					11																	64083421		2013	4172	6185	63839997	SO:0001583	missense	2101			X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"Nuclear hormone receptors"	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.1255G>A	11.37:g.64083421G>A	ENSP00000384851:p.Glu419Lys		63839997	Q14514	Missense_Mutation	SNP	ENST00000405666.1	37	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611047	0.66558	.	.	ENSG00000173153	ENST00000406310;ENST00000000442;ENST00000405666	T;T;T	0.36520	1.25;1.25;1.25	4.58	4.58	0.56647	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.59932	0.2230	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.78314	0.922;0.991	T	0.64605	-0.6368	10	0.87932	D	0	.	15.2562	0.73588	0.0:0.0:1.0:0.0	.	418;419	P11474-2;P11474	.;ERR1_HUMAN	K	418;419;419	ENSP00000385971:E418K;ENSP00000000442:E419K;ENSP00000384851:E419K	ENSP00000000442:E419K	E	+	1	0	ESRRA	63839997	1.000000	0.71417	0.994000	0.49952	0.914000	0.54420	9.587000	0.98229	2.554000	0.86153	0.561000	0.74099	GAG		0.642	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		A	64083421	G	A	64083421	3	1	57	1	0	0	0	0	1	0	0	0	5273	1059	37	1	1277	1	ESRRA	11	64083421	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	4872141	64083421	70923095	74	7600										
UBASH3B	84959	broad.mit.edu	37	chr11	122672021	122672021	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	agttagctgcagccaacctgAgtgttgatacaacctacagg	10	10	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:122672021A>T	ENST00000284273.5	+	11	1951	c.1576A>T	c.(1576-1578)Agt>Tgt	p.S526C		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	526	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.S526C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		AGCCAACCTGAGTGTTGATAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											152	141	145					11																	122672021		2202	4299	6501	122177231	SO:0001583	missense	84959			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1576A>T	11.37:g.122672021A>T	ENSP00000284273:p.Ser526Cys		122177231	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211427	0.58343	.	.	ENSG00000154127	ENST00000284273	T	0.72615	-0.67	5.47	4.27	0.50696	Histidine phosphatase superfamily, clade-1 (1);	0.038489	0.85682	D	0.000000	T	0.60971	0.2310	L	0.32530	0.975	0.58432	D	0.999997	B	0.26902	0.163	B	0.32211	0.142	T	0.62487	-0.6844	10	0.52906	T	0.07	-3.9306	11.0744	0.48023	0.8612:0.0:0.0:0.1388	.	526	Q8TF42	UBS3B_HUMAN	C	526	ENSP00000284273:S526C	ENSP00000284273:S526C	S	+	1	0	UBASH3B	122177231	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.273000	0.51623	2.058000	0.61347	0.533000	0.62120	AGT		0.517	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		T	122672021	A	T	122672021	3	4	57	1	0	0	0	0	1	0	0	0	16880	304	11	5	1618	5	UBASH3B	11	122672021	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09	58588600	122672021	12334495	75	7601										
OPCML	4978	broad.mit.edu	37	chr11	132290088	132290088	+	Nonstop_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gaggacctaggatttcttatCaaaacttgatgaagaagtgg	11	5	2	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr11:132290088C>G	ENST00000331898.7	-	7	1615	c.1037G>C	c.(1036-1038)tGa>tCa	p.*346S	OPCML_ENST00000524381.1_Nonstop_Mutation_p.*339S|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Nonstop_Mutation_p.*355S|OPCML_ENST00000374778.4_Nonstop_Mutation_p.*305S	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	0					cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.*346S(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GATTTCTTATCAAAACTTGAT	0.488																																																1	Nonstop extension(1)	large_intestine(1)	11											94	87	89					11																	132290088		2201	4297	6498	131795298	SO:0001578	stop_lost	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.1037G>C	11.37:g.132290088C>G			131795298	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Nonstop_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.931083	0.92389	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.999925	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8403	0.85967	0.0:1.0:0.0:0.0	.	.	.	.	S	346;339;305;313;355	.	.	X	-	2	2	OPCML	131795298	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.621000	0.61233	2.504000	0.84457	0.563000	0.77884	TGA		0.488	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		G	132290088	C	G	132290088	4	3	57	1	0	0	0	0	0	0	0	0	10905	837	29	5	4	5	OPCML	11	132290088	Nonstop_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	9618067	132290088	2716428	76	7602										
CLEC1A	51267	broad.mit.edu	37	chr12	10233859	10233859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cagctttgttatacagctcaCgacagagtttttcagccaca	7	11	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr12:10233859C>T	ENST00000315330.4	-	3	430	c.368G>A	c.(367-369)cGt>cAt	p.R123H	CLEC1A_ENST00000457018.2_Missense_Mutation_p.R90H|CLEC1A_ENST00000420265.2_Intron|RN7SKP161_ENST00000411110.1_RNA	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	123					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R123H(2)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						ATACAGCTCACGACAGAGTTT	0.463																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	12											109	112	111					12																	10233859		2203	4300	6503	10125126	SO:0001583	missense	51267			AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.368G>A	12.37:g.10233859C>T	ENSP00000326407:p.Arg123His		10125126	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	37	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946124	0.73672	.	.	ENSG00000150048	ENST00000315330;ENST00000457018	T;T	0.17370	2.28;2.28	5.06	3.2	0.36748	.	0.159238	0.30752	N	0.008952	T	0.33818	0.0876	M	0.69823	2.125	0.53688	D	0.99997	D;D	0.76494	0.999;0.999	P;D	0.72338	0.828;0.977	T	0.02244	-1.1189	10	0.38643	T	0.18	.	7.6201	0.28181	0.0:0.8287:0.0:0.1713	.	90;123	E9PFB4;Q8NC01	.;CLC1A_HUMAN	H	123;90	ENSP00000326407:R123H;ENSP00000415048:R90H	ENSP00000326407:R123H	R	-	2	0	CLEC1A	10125126	0.991000	0.36638	0.786000	0.31890	0.940000	0.58332	1.300000	0.33436	2.330000	0.79161	0.563000	0.77884	CGT		0.463	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		T	10233859	C	T	10233859	3	4	57	1	0	0	0	0	1	0	0	0	3511	536	19	1	490	1	CLEC1A	12	10233859	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		10233859	123618036	77	7603										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	57	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	15164425	25398284	108453611	78	7604										
DIP2B	57609	broad.mit.edu	37	chr12	51127944	51127944	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tcagggcctgatccgactacTgtgtatgtggatctgaaatc	11	9	2	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr12:51127944T>G	ENST00000301180.5	+	33	4042	c.4008T>G	c.(4006-4008)acT>acG	p.T1336T		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1336						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.T1336T(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						ATCCGACTACTGTGTATGTGG	0.363																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	12											245	217	227					12																	51127944		2203	4300	6503	49414211	SO:0001819	synonymous_variant	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.4008T>G	12.37:g.51127944T>G			49414211	Q6B011|Q8N1L5|Q8NB38	Silent	SNP	ENST00000301180.5	37	CCDS31799.1																																																																																				0.363	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		G	51127944	T	G	51127944	2	3	57	1	0	0	0	0	0	0	0	1	4539	1567	55	4		4	DIP2B	12	51127944	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	25729660	51127944	82723951	79	7605										
CCDC62	84660	broad.mit.edu	37	chr12	123281894	123281894	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gatgaattgcttaatattgcGaagtcaaagcaagaacgcac	9	7	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr12:123281894G>A	ENST00000253079.6	+	7	1157	c.813G>A	c.(811-813)gcG>gcA	p.A271A	CCDC62_ENST00000392441.4_Silent_p.A271A|CCDC62_ENST00000392440.2_Silent_p.A32A|CCDC62_ENST00000537566.1_Silent_p.A32A	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	271					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.A271A(1)		breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		TTAATATTGCGAAGTCAAAGC	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	12											123	112	116					12																	123281894		2203	4300	6503	121847847	SO:0001819	synonymous_variant	84660				CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.813G>A	12.37:g.123281894G>A			121847847	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Silent	SNP	ENST00000253079.6	37	CCDS9238.1																																																																																				0.353	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		A	123281894	G	A	123281894	2	1	57	1	0	0	0	0	0	0	0	1	2839	1045	37	1		1	CCDC62	12	123281894	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	72153950	123281894	10570001	80	7606										
TPTE2	93492	broad.mit.edu	37	chr13	20049728	20049728	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	catacccaaatgcaaaggatGatacaattgaatgcacaatt	6	8	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:20049728G>T	ENST00000400230.2	-	5	259	c.215C>A	c.(214-216)tCa>tAa	p.S72*	TPTE2_ENST00000382977.4_Nonsense_Mutation_p.S72*|TPTE2_ENST00000382978.1_Nonsense_Mutation_p.S72*|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382975.4_Nonsense_Mutation_p.S72*|TPTE2_ENST00000390680.2_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	72					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S72*(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TGCAAAGGATGATACAATTGA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											29	30	30					13																	20049728		2201	4294	6495	18947728	SO:0001587	stop_gained	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.215C>A	13.37:g.20049728G>T	ENSP00000383089:p.Ser72*		18947728	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Nonsense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	g	19.90	3.913320	0.72983	.	.	ENSG00000132958	ENST00000382978;ENST00000400230;ENST00000382977;ENST00000382975;ENST00000343548	.	.	.	2.29	2.29	0.28610	.	0.376195	0.24717	U	0.036161	.	.	.	.	.	.	0.21184	N	0.999763	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.2474	8.1387	0.31069	0.0:0.0:1.0:0.0	.	.	.	.	X	72	.	.	S	-	2	0	TPTE2	18947728	0.901000	0.30685	0.054000	0.19295	0.169000	0.22640	1.547000	0.36190	1.590000	0.49995	0.467000	0.42956	TCA		0.338	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		T	20049728	G	T	20049728	4	4	57	1	0	0	0	0	0	1	0	0	16471	1294	45	2	1417	2	TPTE2	13	20049728	Nonsense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		20049728	95120150	81	7607										
SACS	26278	broad.mit.edu	37	chr13	23910682	23910682	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tatcttgccataatttttctCacaaaattcttgtttctttt	2	8	4	0	rs564734108		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:23910682C>A	ENST00000382292.3	-	9	7606	c.7333G>T	c.(7333-7335)Gag>Tag	p.E2445*	SACS_ENST00000382298.3_Nonsense_Mutation_p.E2445*|SACS_ENST00000402364.1_Nonsense_Mutation_p.E1695*			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2445					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.E2298*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TAATTTTTCTCACAAAATTCT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											74	77	76					13																	23910682		2203	4299	6502	22808682	SO:0001587	stop_gained	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7333G>T	13.37:g.23910682C>A	ENSP00000371729:p.Glu2445*		22808682	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Nonsense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	56	26.749135	0.99969	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	.	.	.	5.6	5.6	0.85130	.	0.176257	0.50627	D	0.000118	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.6023	0.95568	0.0:1.0:0.0:0.0	.	.	.	.	X	2445;1695;2445	.	ENSP00000371729:E2445X	E	-	1	0	SACS	22808682	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.115000	0.50391	2.653000	0.90120	0.561000	0.74099	GAG		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23910682	C	A	23910682	4	1	57	1	0	0	0	0	0	1	0	0	13841	835	29	2	6410	2	SACS	13	23910682	Nonsense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	3860954	23910682	91259196	82	7608										
WASF3	10810	broad.mit.edu	37	chr13	27250749	27250749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttagaaaagccagaaacaggCgccaggagtggaatatgatg	13	6	0	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:27250749C>T	ENST00000335327.5	+	7	782	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	WASF3_ENST00000361042.4_Intron|WASF3_ENST00000496788.1_3'UTR	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	202					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)		p.R202C(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CAGAAACAGGCGCCAGGAGTG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	13											132	130	131					13																	27250749		2203	4300	6503	26148749	SO:0001583	missense	10810			AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.604C>T	13.37:g.27250749C>T	ENSP00000335055:p.Arg202Cys		26148749	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.954114	0.92726	.	.	ENSG00000132970	ENST00000335327	T	0.49432	0.78	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.67411	0.2890	M	0.79258	2.445	0.80722	D	1	D	0.76494	0.999	P	0.56865	0.808	T	0.70850	-0.4760	10	0.87932	D	0	-11.6242	19.9634	0.97258	0.0:1.0:0.0:0.0	.	202	Q9UPY6	WASF3_HUMAN	C	202	ENSP00000335055:R202C	ENSP00000335055:R202C	R	+	1	0	WASF3	26148749	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.478000	0.66806	2.726000	0.93360	0.591000	0.81541	CGC		0.502	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			T	27250749	C	T	27250749	3	4	57	1	0	0	0	0	1	0	0	0	17294	768	27	1	622	1	WASF3	13	27250749	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	3340067	27250749	87919129	83	7609										
RBM26	64062	broad.mit.edu	37	chr13	79911344	79911344	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	accaggcacacctcgccctcGccctcgccccctgcctcggc	8	24	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:79911344G>A	ENST00000438737.2	-	19	3066	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	RBM26_ENST00000267229.7_Nonsense_Mutation_p.R849*|RBM26_ENST00000438724.1_Nonsense_Mutation_p.R852*			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	876					mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R849*(1)|p.R876*(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		CCTCGCCCTCGCCCTCGCCCC	0.562																																																2	Substitution - Nonsense(2)	large_intestine(2)	13											108	89	96					13																	79911344		2203	4300	6503	78809345	SO:0001587	stop_gained	64062			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.2626C>T	13.37:g.79911344G>A	ENSP00000387531:p.Arg876*		78809345	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Nonsense_Mutation	SNP	ENST00000438737.2	37		.	.	.	.	.	.	.	.	.	.	G	44	11.121188	0.99518	.	.	ENSG00000139746	ENST00000449987;ENST00000267229;ENST00000438737;ENST00000327303;ENST00000438724	.	.	.	4.89	3.98	0.46160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.4544	12.7836	0.57491	0.0:0.0:0.7152:0.2848	.	.	.	.	X	62;849;877;876;852	.	.	R	-	1	2	RBM26	78809345	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	2.678000	0.46900	2.406000	0.81754	0.650000	0.86243	CGA		0.562	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		A	79911344	G	A	79911344	4	1	57	1	0	0	0	0	0	1	0	0	13163	1095	38	1	413	1	RBM26	13	79911344	Nonsense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	52660595	79911344	35258534	84	7610										
HS6ST3	266722	broad.mit.edu	37	chr13	97485095	97485095	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aacatggccttctttgggctCactgagttccagaggaagac	11	10	2	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:97485095C>T	ENST00000376705.2	+	2	1083	c.1059C>T	c.(1057-1059)ctC>ctT	p.L353L		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	353					heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)	p.L353L(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TCTTTGGGCTCACTGAGTTCC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	13											99	102	101					13																	97485095		2203	4300	6503	96283096	SO:0001819	synonymous_variant	266722			AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.1059C>T	13.37:g.97485095C>T			96283096	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	37	CCDS9481.1																																																																																				0.463	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		T	97485095	C	T	97485095	2	4	57	1	0	0	0	0	0	0	0	1	7393	813	29	3		3	HS6ST3	13	97485095	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	17573751	97485095	17684783	85	7611										
FARP1	10160	broad.mit.edu	37	chr13	99061752	99061752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gaccaggcctgcccccggacGgacgatgaggatgagggccg	17	13	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:99061752G>A	ENST00000319562.6	+	14	1840	c.1575G>A	c.(1573-1575)acG>acA	p.T525T	FARP1_ENST00000595437.1_Silent_p.T525T|FARP1_ENST00000376586.2_Silent_p.T525T	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	525					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T525T(2)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GCCCCCGGACGGACGATGAGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	13											28	21	24					13																	99061752		2203	4300	6503	97859753	SO:0001819	synonymous_variant	10160			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.1575G>A	13.37:g.99061752G>A			97859753	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	G	9.017	0.983827	0.18889	.	.	ENSG00000152767	ENST00000457029	.	.	.	5.57	-11.1	0.00147	.	.	.	.	.	T	0.32645	0.0836	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42749	-0.9433	4	.	.	.	.	2.1902	0.03897	0.2377:0.3487:0.0944:0.3193	.	.	.	.	Q	54	.	.	R	+	2	0	FARP1	97859753	0.000000	0.05858	0.064000	0.19789	0.879000	0.50718	-2.950000	0.00678	-3.054000	0.00259	-0.136000	0.14681	CGG		0.597	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		A	99061752	G	A	99061752	2	1	57	1	0	0	0	0	0	0	0	1	5695	1103	39	1		1	FARP1	13	99061752	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	1576657	99061752	16108126	86	7612										
C13orf39	196541	broad.mit.edu	37	chr13	103346751	103346751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ccccggtgctgtctttctgcGgagcccccttcttctcagcc	9	18	4	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:103346751G>A	ENST00000267273.6	-	1	103	c.98C>T	c.(97-99)cCg>cTg	p.P33L		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	33					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)	p.P33L(1)		breast(1)|large_intestine(3)|lung(2)|skin(1)	7						GTCTTTCTGCGGAGCCCCCTT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	13											54	53	53					13																	103346751		2203	4300	6503	102144752	SO:0001583	missense	196541				CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.98C>T	13.37:g.103346751G>A	ENSP00000267273:p.Pro33Leu		102144752		Missense_Mutation	SNP	ENST00000267273.6	37	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	G	3.352	-0.132307	0.06753	.	.	ENSG00000139780	ENST00000267273	T	0.12569	2.67	4.31	-2.77	0.05877	.	1.401160	0.04609	N	0.399880	T	0.05090	0.0136	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39643	-0.9604	10	0.30078	T	0.28	-6.3194	8.8733	0.35330	0.5016:0.0:0.4984:0.0	.	33	Q5VZV1	MT21C_HUMAN	L	33	ENSP00000267273:P33L	ENSP00000267273:P33L	P	-	2	0	METTL21C	102144752	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.105000	0.15333	-0.382000	0.07870	-1.223000	0.01593	CCG		0.577	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		A	103346751	G	A	103346751	3	1	57	1	0	0	0	0	1	0	0	0	1736	1116	39	1	712	1	C13orf39	13	103346751	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	4284999	103346751	11823127	87	7613										
MCF2L	23263	broad.mit.edu	37	chr13	113739450	113739450	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	agcctggactcctacctgctGaagccagtgcagaggatcac	11	13	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr13:113739450G>T	ENST00000375608.3	+	21	2353	c.2295G>T	c.(2293-2295)ctG>ctT	p.L765L	MCF2L_ENST00000397030.1_Silent_p.L768L|MCF2L_ENST00000442652.2_Silent_p.L765L|MCF2L_ENST00000434480.2_Silent_p.L741L|MCF2L_ENST00000423482.2_Silent_p.L733L|MCF2L_ENST00000375604.2_Silent_p.L792L|MCF2L_ENST00000375601.3_Silent_p.L739L|MCF2L_ENST00000375597.4_Silent_p.L733L|MCF2L_ENST00000421756.1_Silent_p.L739L|MCF2L_ENST00000535094.2_Silent_p.L735L			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	765	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L739L(1)		kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	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;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CCTACCTGCTGAAGCCAGTGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	13											71	63	66					13																	113739450		2203	4300	6503	112787451	SO:0001819	synonymous_variant	23263			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.2295G>T	13.37:g.113739450G>T			112787451	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	G	9.251	1.040818	0.19669	.	.	ENSG00000126217	ENST00000397017	.	.	.	4.83	3.99	0.46301	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6485	0.39883	0.161:0.0:0.839:0.0	.	.	.	.	X	396	.	.	E	+	1	0	MCF2L	112787451	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.397000	0.52572	1.035000	0.39972	0.306000	0.20318	GAA		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			T	113739450	G	T	113739450	2	4	57	1	0	0	0	0	0	0	0	1	9409	1277	45	2		2	MCF2L	13	113739450	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	10392699	113739450	1430428	88	7614										
PRKD1	5587	broad.mit.edu	37	chr14	30068249	30068249	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttgcctgaggaaaaggatcaGctgaggctagcaacacattt	11	8	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr14:30068249G>A	ENST00000331968.5	-	15	2379	c.2150C>T	c.(2149-2151)gCt>gTt	p.A717V	PRKD1_ENST00000415220.2_Missense_Mutation_p.A725V	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	717	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.A717D(2)|p.A717V(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AAAAGGATCAGCTGAGGCTAG	0.428																																																4	Substitution - Missense(4)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)	14											150	149	149					14																	30068249		2203	4300	6503	29138000	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2150C>T	14.37:g.30068249G>A	ENSP00000333568:p.Ala717Val		29138000	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914934	0.72983	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.65549	-0.16;-0.16	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.061537	0.64402	D	0.000008	T	0.58235	0.2108	L	0.38733	1.17	0.80722	D	1	B	0.22746	0.074	B	0.29524	0.103	T	0.49753	-0.8906	10	0.29301	T	0.29	-12.2893	20.3754	0.98918	0.0:0.0:1.0:0.0	.	717	Q15139	KPCD1_HUMAN	V	717;725	ENSP00000333568:A717V;ENSP00000390535:A725V	ENSP00000333568:A717V	A	-	2	0	PRKD1	29138000	1.000000	0.71417	0.971000	0.41717	0.998000	0.95712	7.882000	0.87258	2.894000	0.99253	0.591000	0.81541	GCT		0.428	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30068249	G	A	30068249	3	1	57	1	0	0	0	0	1	0	0	0	12552	971	34	3	604	3	PRKD1	14	30068249	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		30068249	77281291	89	7615										
TDRD9	122402	broad.mit.edu	37	chr14	104508489	104508489	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cttgggccagagagagttgcGcagcttcaagacattgcccg	13	11	1	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr14:104508489G>A	ENST00000409874.4	+	34	3987	c.3939G>A	c.(3937-3939)gcG>gcA	p.A1313A	TDRD9_ENST00000339063.5_Silent_p.A1122A	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	1313					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.A1313A(1)|p.A837A(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				AGAGAGTTGCGCAGCTTCAAG	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	14											125	115	119					14																	104508489		2203	4300	6503	103578242	SO:0001819	synonymous_variant	122402			AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.3939G>A	14.37:g.104508489G>A			103578242	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.319602	0.01320	.	.	ENSG00000156414	ENST00000557332	T	0.07114	3.22	4.5	-8.99	0.00751	.	0.483083	0.16726	U	0.202043	T	0.04407	0.0121	.	.	.	0.36944	D	0.892513	.	.	.	.	.	.	T	0.35525	-0.9785	6	.	.	.	.	0.5805	0.00711	0.3832:0.1232:0.2191:0.2745	.	.	.	.	T	849	ENSP00000451637:A849T	.	A	+	1	0	TDRD9	103578242	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-2.868000	0.00722	-2.066000	0.00886	-1.261000	0.01458	GCA		0.468	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		A	104508489	G	A	104508489	2	1	57	1	0	0	0	0	0	0	0	1	15775	1074	38	1		1	TDRD9	14	104508489	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	74440240	104508489	2841051	90	7616										
NARG2	79664	broad.mit.edu	37	chr15	60758802	60758802	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tgtttttttacctctgtgaaGagacgggcatcatcagaaag	10	7	3	3			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr15:60758802G>C	ENST00000261520.4	-	5	753	c.519C>G	c.(517-519)ctC>ctG	p.L173L	NARG2_ENST00000558654.1_5'Flank|NARG2_ENST00000439632.1_Silent_p.L36L|NARG2_ENST00000561114.1_Silent_p.L173L	NM_024611.4	NP_078887.2												p.L173L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CCTCTGTGAAGAGACGGGCAT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	15											97	94	95					15																	60758802		2203	4300	6503	58546094	SO:0001819	synonymous_variant	79664																														ENST00000261520.4:c.519C>G	15.37:g.60758802G>C			58546094		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																				0.378	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			C	60758802	G	C	60758802	2	2	57	1	0	0	0	0	0	0	0	1	10199	929	33	5		5	NARG2	15	60758802	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09		60758802	41772590	91	7617										
CYP11A1	1583	broad.mit.edu	37	chr15	74637524	74637527	+	Frame_Shift_Del	DEL	CTCT	CTCT	-													0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggcaaaaagttcttggtggcCtctggagccatcacctcctg							TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	CTCT	CTCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr15:74637524_74637527delCTCT	ENST00000268053.6	-	3	637_640	c.483_486delAGAG	c.(481-486)ccagagfs	p.PE161fs	CYP11A1_ENST00000358632.4_Frame_Shift_Del_p.PE3fs|CYP11A1_ENST00000541301.1_Intron|CYP11A1_ENST00000419019.2_Frame_Shift_Del_p.PE3fs	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	161					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.E162fs*63(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	TCTTGGTGGCCTCTGGAGCCATCA	0.588																																					Esophageal Squamous(87;818 1337 4093 9268 37314)											1	Deletion - Frameshift(1)	large_intestine(1)	15																																								72424580	SO:0001589	frameshift_variant	1583			AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.483_486delAGAG	15.37:g.74637524_74637527delCTCT	ENSP00000268053:p.Pro161fs		72424577	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Frame_Shift_Del	DEL	ENST00000268053.6	37	CCDS32291.1																																																																																				0.588	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			-	74637527	CTCT	-	74637524	7	5	57	1	0	1	0	1	0	0	0	0	4150	680	24	0	1107	0	CYP11A1	15	74637524	Frame_Shift_Del	DEL	CTCT	TCGA-AG-4005-01A-01W-1073-09	13878722	74637524	27893868	92	7618										
PTX4	390667	broad.mit.edu	37	chr16	1537807	1537807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctcacccaggccttgagctgCgccagctccccctgcaccga	9	20	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr16:1537807C>T	ENST00000447419.2	-	2	331	c.306G>A	c.(304-306)gcG>gcA	p.A102A	PTX4_ENST00000293922.1_Silent_p.A97A|PTX4_ENST00000440447.2_Silent_p.A102A			Q96A99	PTX4_HUMAN	pentraxin 4, long	102						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.A97A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCTTGAGCTGCGCCAGCTCCC	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	16											53	57	56					16																	1537807		2199	4298	6497	1477808	SO:0001819	synonymous_variant	390667				CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.306G>A	16.37:g.1537807C>T			1477808		Silent	SNP	ENST00000447419.2	37																																																																																					0.682	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		T	1537807	C	T	1537807	2	4	57	1	0	0	0	0	0	0	0	1	12860	755	27	1		1	PTX4	16	1537807	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09		1537807	88816946	93	7619										
ZBTB4	57659	broad.mit.edu	37	chr17	7366544	7366544	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aggggccccggccagcccctGtggggggacccccacctcca	14	19	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:7366544G>C	ENST00000311403.4	-	4	2096	c.1757C>G	c.(1756-1758)aCa>aGa	p.T586R	ZBTB4_ENST00000380599.4_Missense_Mutation_p.T586R	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	586					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)	p.T586R(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GCCAGCCCCTGTGGGGGGACC	0.657																																																2	Substitution - Missense(2)	large_intestine(2)	17											12	14	13					17																	7366544		2202	4295	6497	7307268	SO:0001583	missense	57659			AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1757C>G	17.37:g.7366544G>C	ENSP00000307858:p.Thr586Arg		7307268	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	G	1.127	-0.653614	0.03480	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.03920	3.76;3.76	4.87	1.66	0.24008	.	0.872989	0.09942	N	0.735822	T	0.03348	0.0097	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.43065	-0.9414	10	0.32370	T	0.25	-0.2593	3.6784	0.08301	0.2697:0.1965:0.5337:0.0	.	586	Q9P1Z0	ZBTB4_HUMAN	R	586	ENSP00000307858:T586R;ENSP00000369973:T586R	ENSP00000307858:T586R	T	-	2	0	ZBTB4	7307268	0.000000	0.05858	0.445000	0.26908	0.032000	0.12392	0.636000	0.24644	1.268000	0.44264	0.462000	0.41574	ACA		0.657	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899		C	7366544	G	C	7366544	3	2	57	1	0	0	0	0	1	0	0	0	17580	1377	48	5	1288	5	ZBTB4	17	7366544	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09		7366544	73828666	94	7620										
TP53	7157	broad.mit.edu	37	chr17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttgtcctgcttgcttacctcGcttagtgctccctgggggca	11	13	0	0	rs121913344		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:7577022G>A	ENST00000269305.4	-	8	1105	c.916C>T	c.(916-918)Cga>Tga	p.R306*	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	306	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCTTACCTCGCTTAGTGCTC	0.562	R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	147	Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(39)|breast(21)|upper_aerodigestive_tract(15)|ovary(11)|central_nervous_system(10)|oesophagus(10)|stomach(8)|lung(8)|endometrium(6)|bone(4)|pancreas(3)|haematopoietic_and_lymphoid_tissue(3)|biliary_tract(3)|kidney(2)|NS(2)|urinary_tract(1)|liver(1)	17	GRCh37	CM971506	TP53	M	rs121913344						120	106	110					17																	7577022		2203	4300	6503	7517747	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.916C>T	17.37:g.7577022G>A	ENSP00000269305:p.Arg306*		7517747	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782988	0.90282	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	3.21	0.36854	.	1.348720	0.05032	N	0.474808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4785	0.44678	0.0:0.0:0.6334:0.3666	.	.	.	.	X	306;306;306;306;306;295;174	.	ENSP00000269305:R306X	R	-	1	2	TP53	7517747	1.000000	0.71417	0.970000	0.41538	0.345000	0.29048	2.280000	0.43443	0.735000	0.32537	0.561000	0.74099	CGA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577022	G	A	7577022	4	1	57	1	0	0	0	0	0	1	0	0	16421	1095	38	1	370	1	TP53	17	7577022	Nonsense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	210478	7577022	73618188	95	7621										
MPRIP	23164	broad.mit.edu	37	chr17	17077244	17077244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ccccagggaggagctgcagtCggtgcagcgggaactggagg	19	10	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:17077244C>T	ENST00000341712.4	+	18	2444	c.2444C>T	c.(2443-2445)tCg>tTg	p.S815L	RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000395811.5_Missense_Mutation_p.S815L|MPRIP_ENST00000444976.1_Missense_Mutation_p.S777L|MPRIP_ENST00000395804.3_Missense_Mutation_p.S815L			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	815	Interaction with RHOA.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.S815L(1)		biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GAGCTGCAGTCGGTGCAGCGG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											56	52	53					17																	17077244		2202	4300	6502	17017969	SO:0001583	missense	23164			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.2444C>T	17.37:g.17077244C>T	ENSP00000342379:p.Ser815Leu		17017969	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.143078|5.143078	0.94560|0.94560	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000414263|ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712;ENST00000429184	.|T;T;T;T	.|0.26373	.|1.74;1.74;1.74;1.74	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.208516	.|0.42420	.|D	.|0.000719	T|T	0.50463|0.50463	0.1617|0.1617	M|M	0.66939|0.66939	2.045|2.045	0.58432|0.58432	D|D	0.999994|0.999994	.|D;D;D;D;D	.|0.89917	.|0.999;1.0;1.0;0.996;0.999	.|P;D;D;D;D	.|0.73380	.|0.908;0.98;0.92;0.941;0.954	T|T	0.22347|0.22347	-1.0219|-1.0219	5|10	.|0.25751	.|T	.|0.34	-22.84|-22.84	20.0263|20.0263	0.97523|0.97523	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|814;777;1179;815;815	.|B9EGI2;Q6WCQ1-3;Q9Y6X7;Q6WCQ1-2;Q6WCQ1	.|.;.;.;.;MPRIP_HUMAN	W|L	881|777;815;815;815;11	.|ENSP00000400189:S777L;ENSP00000379156:S815L;ENSP00000379149:S815L;ENSP00000342379:S815L	.|ENSP00000342379:S815L	R|S	+|+	1|2	2|0	MPRIP|MPRIP	17017969|17017969	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.794000|0.794000	0.44872|0.44872	6.044000|6.044000	0.71012|0.71012	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.657	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		T	17077244	C	T	17077244	3	4	57	1	0	0	0	0	1	0	0	0	9773	893	31	1	2514	1	MPRIP	17	17077244	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	9500222	17077244	64117966	96	7622										
C17orf42	79736	broad.mit.edu	37	chr17	29231161	29231161	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cggtgactttcttttttcccGtccagtctttggacaaagta	8	10	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:29231161G>A	ENST00000581216.1	-	2	1039	c.418C>T	c.(418-420)Cgg>Tgg	p.R140W	TEFM_ENST00000580840.1_Missense_Mutation_p.R140W	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	140					DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)	p.R140W(2)									CTTTTTTCCCGTCCAGTCTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	17											68	62	64					17																	29231161		1815	4081	5896	26255287	SO:0001583	missense	79736				CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 42"	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.418C>T	17.37:g.29231161G>A	ENSP00000462963:p.Arg140Trp		26255287	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Missense_Mutation	SNP	ENST00000581216.1	37	CCDS42291.1	.	.	.	.	.	.	.	.	.	.	G	4.013	-0.000170	0.07819	.	.	ENSG00000172171	ENST00000306049;ENST00000541382	.	.	.	5.68	-5.78	0.02362	.	1.107800	0.06616	N	0.756446	T	0.18045	0.0433	L	0.29908	0.895	0.09310	N	1	P;P;P	0.52842	0.926;0.956;0.926	B;B;B	0.39152	0.153;0.292;0.182	T	0.38436	-0.9661	9	0.66056	D	0.02	-9.3796	8.1614	0.31201	0.0:0.237:0.2013:0.5617	.	140;140;140	B4DPU1;Q96QE5-4;Q96QE5	.;.;TEFM_HUMAN	W	140	.	ENSP00000306574:R140W	R	-	1	2	C17orf42	26255287	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.255000	0.18333	-0.748000	0.04753	-1.552000	0.00895	CGG		0.378	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683		A	29231161	G	A	29231161	3	1	57	1	0	0	0	0	1	0	0	0	1861	1144	40	1	676	1	C17orf42	17	29231161	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	12153917	29231161	51964049	97	7623										
AOC3	8639	broad.mit.edu	37	chr17	41004707	41004707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	caccactcagatctctactcGcactactttgggggtcttgc	8	14	3	1	rs115107156	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:41004707G>A	ENST00000308423.2	+	1	1507	c.1347G>A	c.(1345-1347)tcG>tcA	p.S449S	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	449					amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)	p.S449S(2)		breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	ATCTCTACTCGCACTACTTTG	0.542													G|||	4	0.000798722	0.003	0	5008	,	,		19486	0		0	False		,,,				2504	0				NSCLC(3;192 220 10664 11501 16477)											2	Substitution - coding silent(2)	large_intestine(2)	17						G		11,4395	17.9+/-39.9	0,11,2192	124	110	114		1347	-4.8	0	17	dbSNP_132	114	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AOC3	NM_003734.2		0,12,6491	AA,AG,GG		0.0116,0.2497,0.0923		449/764	41004707	12,12994	2203	4300	6503	38258233	SO:0001819	synonymous_variant	8639			AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1347G>A	17.37:g.41004707G>A			38258233	B2RCI5|K7ESB3|L0L8N9|Q45F94	Silent	SNP	ENST00000308423.2	37	CCDS11444.1																																																																																				0.542	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		A	41004707	G	A	41004707	2	1	57	1	0	0	0	0	0	0	0	1	728	1074	38	1		1	AOC3	17	41004707	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	11773546	41004707	40190503	98	7624										
AXIN2	8313	broad.mit.edu	37	chr17	63554543	63554543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	atccggagatgcccgcccctCcggctcccccaacccatctt	7	21	1	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:63554543C>T	ENST00000375702.5	-	1	304	c.196G>A	c.(196-198)Gag>Aag	p.E66K	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Missense_Mutation_p.E66K			Q9Y2T1	AXIN2_HUMAN	axin 2	66					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.E66K(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GCCCGCCCCTCCGGCTCCCCC	0.612									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	17											64	66	65					17																	63554543		2203	4300	6503	60985005	SO:0001583	missense	8313	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.196G>A	17.37:g.63554543C>T	ENSP00000364854:p.Glu66Lys		60985005	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		.	.	.	.	.	.	.	.	.	.	C	12.95	2.090795	0.36855	.	.	ENSG00000168646	ENST00000307078;ENST00000544103;ENST00000375702	T;T;T	0.79247	-0.39;-1.25;-0.39	4.74	3.77	0.43336	.	0.055186	0.64402	D	0.000001	D	0.86994	0.6067	M	0.80616	2.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.87005	0.2119	10	0.52906	T	0.07	-25.8748	11.8019	0.52133	0.0:0.9127:0.0:0.0873	.	66;66;66	B7ZKL5;Q9Y2T1;E7ES00	.;AXIN2_HUMAN;.	K	66	ENSP00000302625:E66K;ENSP00000441151:E66K;ENSP00000364854:E66K	ENSP00000302625:E66K	E	-	1	0	AXIN2	60985005	1.000000	0.71417	0.901000	0.35422	0.831000	0.47069	7.667000	0.83888	0.980000	0.38523	0.561000	0.74099	GAG		0.612	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		T	63554543	C	T	63554543	3	4	57	1	0	0	0	0	1	0	0	0	1238	864	30	3	2375	3	AXIN2	17	63554543	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	22549836	63554543	17640667	99	7625										
CD300C	10871	broad.mit.edu	37	chr17	72539113	72539113	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gagctctgggggctggaggcTgtggtcgtcccggctgtggg	21	9	1	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:72539113T>C	ENST00000330793.1	-	3	774	c.414A>G	c.(412-414)acA>acG	p.T138T		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	138	Pro-rich.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.T138T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						GGCTGGAGGCTGTGGTCGTCC	0.592																																					Esophageal Squamous(66;421 1121 20537 25337 27468)											1	Substitution - coding silent(1)	large_intestine(1)	17											117	101	106					17																	72539113		2203	4300	6503	70050708	SO:0001819	synonymous_variant	10871			BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19320	protein-coding gene	gene with protein product		606786	"CD300c antigen"			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.414A>G	17.37:g.72539113T>C			70050708		Silent	SNP	ENST00000330793.1	37	CCDS11701.1																																																																																				0.592	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678		C	72539113	T	C	72539113	2	2	57	1	0	0	0	0	0	0	0	1	3003	1567	55	4		4	CD300C	17	72539113	Silent	SNP	T	TCGA-AG-4005-01A-01W-1073-09	8984570	72539113	8656097	100	7626										
NUP85	79902	broad.mit.edu	37	chr17	73205962	73205962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gcccctttatctatatcatcCgtaaggatgtagatgtttac	7	9	2	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:73205962C>T	ENST00000245544.4	+	3	243	c.172C>T	c.(172-174)Cgt>Tgt	p.R58C	NUP85_ENST00000579324.1_5'UTR|NUP85_ENST00000447371.2_5'UTR|NUP85_ENST00000541827.1_Missense_Mutation_p.R12C|NUP85_ENST00000579298.1_Missense_Mutation_p.R58C|NUP85_ENST00000449421.2_3'UTR	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	58					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.R58C(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			CTATATCATCCGTAAGGATGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											54	58	57					17																	73205962		2203	4300	6503	70717557	SO:0001583	missense	79902			AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.172C>T	17.37:g.73205962C>T	ENSP00000245544:p.Arg58Cys		70717557	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	37	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939963	0.52972	.	.	ENSG00000125450	ENST00000245544;ENST00000541827;ENST00000449421	.	.	.	5.43	3.4	0.38934	.	0.095884	0.64402	D	0.000001	T	0.74199	0.3685	M	0.74881	2.28	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.59643	0.803;0.861	T	0.77027	-0.2740	9	0.66056	D	0.02	-13.2029	13.3096	0.60371	0.2869:0.7131:0.0:0.0	.	12;58	B4DMQ3;Q9BW27	.;NUP85_HUMAN	C	58;12;12	.	ENSP00000245544:R58C	R	+	1	0	NUP85	70717557	1.000000	0.71417	0.656000	0.29637	0.396000	0.30629	1.207000	0.32333	0.753000	0.32945	0.650000	0.86243	CGT		0.368	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844		T	73205962	C	T	73205962	3	4	57	1	0	0	0	0	1	0	0	0	10801	652	23	1	182	1	NUP85	17	73205962	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	666849	73205962	7989248	101	7627										
SPHK1	8877	broad.mit.edu	37	chr17	74382047	74382048	+	Intron	DEL	TT	TT	-													0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tcggttgcggacgtggcctcTttggttttgttttctcagcg							TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	TT	TT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr17:74382047_74382048delTT	ENST00000545180.1	+	5	819				SPHK1_ENST00000323374.4_Intron|SPHK1_ENST00000392496.3_Intron|SPHK1_ENST00000592299.1_Intron|SPHK1_ENST00000590959.1_Frame_Shift_Del_p.F12fs			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	ACGTGGCCTCTTTGGTTTTGTT	0.673											OREG0024750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(90;966 1307 27369 33775 44498)											0			17							,,,	8,3760		3,2,1879					,,,	-3.7	0			25	20,7872		4,12,3930	no	intron,frameshift,intron,intron	SPHK1	NM_182965.2,NM_021972.3,NM_001142602.1,NM_001142601.1	,,,	7,14,5809	A1A1,A1R,RR		0.2534,0.2123,0.2401	,,,	,,,		28,11632				71893643	SO:0001627	intron_variant	8877			BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.11-18TT>-	17.37:g.74382047_74382048delTT		1152	71893642	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Frame_Shift_Del	DEL	ENST00000545180.1	37	CCDS45785.1																																																																																				0.673	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		-	74382048	TT	-	74382047	6	5	57	0	1	1	0	1	0	0	0	0	15085	1609	56	0		0	SPHK1	17	74382047	Intron	DEL	TT	TCGA-AG-4005-01A-01W-1073-09	1176085	74382047	6813163	102	7628										
CHST9	83539	broad.mit.edu	37	chr18	24496749	24496749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctttggtgtaagtatttaagCgggtatatatcccttttagg	10	5	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr18:24496749C>T	ENST00000284224.8	-	6	1083	c.806G>A	c.(805-807)cGc>cAc	p.R269H	AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000578701.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.R269H|CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000568797.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	269					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.R184H(1)|p.R269H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					AGTATTTAAGCGGGTATATAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	18											141	130	134					18																	24496749		1864	4095	5959	22750747	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.806G>A	18.37:g.24496749C>T	ENSP00000284224:p.Arg269His		22750747	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076065	0.55646	.	.	ENSG00000154080	ENST00000284224	T	0.75260	-0.92	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.89121	0.6625	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89295	0.3622	10	0.87932	D	0	-13.6533	20.8794	0.99867	0.0:1.0:0.0:0.0	.	269	Q7L1S5	CHST9_HUMAN	H	269	ENSP00000284224:R269H	ENSP00000284224:R269H	R	-	2	0	CHST9	22750747	1.000000	0.71417	0.958000	0.39756	0.116000	0.19942	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CGC		0.413	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		T	24496749	C	T	24496749	3	4	57	1	0	0	0	0	1	0	0	0	3417	768	27	1	529	1	CHST9	18	24496749	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		24496749	53580499	103	7629										
ST8SIA5	29906	broad.mit.edu	37	chr18	44260284	44260284	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctgagccagtagcgcgacacGttgaccaggtactgcggatg	14	11	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr18:44260284G>A	ENST00000315087.7	-	7	1512	c.852C>T	c.(850-852)aaC>aaT	p.N284N	ST8SIA5_ENST00000538168.1_Silent_p.N320N|ST8SIA5_ENST00000536490.1_Silent_p.N253N|ST8SIA5_ENST00000590497.1_5'UTR	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	284					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)	p.N284N(1)		kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						AGCGCGACACGTTGACCAGGT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	18											112	81	92					18																	44260284		2203	4300	6503	42514282	SO:0001819	synonymous_variant	29906			U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.852C>T	18.37:g.44260284G>A			42514282	B7Z1K9|Q6IAW7	Silent	SNP	ENST00000315087.7	37	CCDS11930.1																																																																																				0.627	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		A	44260284	G	A	44260284	2	1	57	1	0	0	0	0	0	0	0	1	15274	1136	40	1		1	ST8SIA5	18	44260284	Silent	SNP	G	TCGA-AG-4005-01A-01W-1073-09	19763535	44260284	33816964	104	7630										
SMAD4	4089	broad.mit.edu	37	chr18	48591919	48591919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ggacccttctggaggagatcGcttttgtttgggtcaactct	12	9	3	1	rs377767347		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr18:48591919G>A	ENST00000342988.3	+	9	1620	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	SMAD4_ENST00000398417.2_Missense_Mutation_p.R361H|SMAD4_ENST00000588745.1_Missense_Mutation_p.R265H	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	361	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		R -> C (in JPS; dbSNP:rs80338963). {ECO:0000269|PubMed:9811934}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R361H(12)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGAGATCGCTTTTGTTTG	0.413																																																50	Whole gene deletion(36)|Substitution - Missense(12)|Unknown(2)	pancreas(26)|large_intestine(13)|lung(3)|breast(3)|upper_aerodigestive_tract(2)|stomach(2)|oesophagus(1)	18	GRCh37	CM004254	SMAD4	M							167	138	148					18																	48591919		2203	4300	6503	46845917	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1082G>A	18.37:g.48591919G>A	ENSP00000341551:p.Arg361His		46845917	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477304	0.96291	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98120	-4.73;-4.73	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99741	1.1015	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	361	Q13485	SMAD4_HUMAN	H	361	ENSP00000341551:R361H;ENSP00000381452:R361H	ENSP00000341551:R361H	R	+	2	0	SMAD4	46845917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.828000	0.86729	2.771000	0.95319	0.563000	0.77884	CGC		0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48591919	G	A	48591919	3	1	57	1	0	0	0	0	1	0	0	0	14797	1087	38	1	1112	1	SMAD4	18	48591919	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	4331635	48591919	29485329	105	7631										
SGTA	6449	broad.mit.edu	37	chr19	2767633	2767633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gagtctgagggagcgcaaggTcactgtcttctaccgtcacc	12	12	5	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr19:2767633T>C	ENST00000221566.2	-	3	313	c.152A>G	c.(151-153)gAc>gGc	p.D51G		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	51					viral process (GO:0016032)	cytoplasm (GO:0005737)		p.D51G(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		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)		GAGCGCAAGGTCACTGTCTTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	56	60					19																	2767633		2203	4300	6503	2718633	SO:0001583	missense	6449			AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"Tetratricopeptide (TTC) repeat domain containing"	10819	protein-coding gene	gene with protein product		603419	"small glutamine-rich tetratricopeptide repeat (TPR)-containing"	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.152A>G	19.37:g.2767633T>C	ENSP00000221566:p.Asp51Gly		2718633	D6W610|Q6FIA9|Q9BTZ9	Missense_Mutation	SNP	ENST00000221566.2	37	CCDS12094.1	.	.	.	.	.	.	.	.	.	.	T	1.796	-0.478235	0.04414	.	.	ENSG00000104969	ENST00000221566	T	0.37058	1.22	4.36	2.21	0.28008	.	0.310538	0.35903	N	0.002904	T	0.23133	0.0559	L	0.33485	1.01	0.27324	N	0.95696	B	0.02656	0.0	B	0.01281	0.0	T	0.13980	-1.0489	10	0.27785	T	0.31	-3.422	7.3208	0.26526	0.0:0.1997:0.0:0.8003	.	51	O43765	SGTA_HUMAN	G	51	ENSP00000221566:D51G	ENSP00000221566:D51G	D	-	2	0	SGTA	2718633	0.240000	0.23847	0.045000	0.18777	0.012000	0.07955	0.716000	0.25836	0.547000	0.28938	0.402000	0.26972	GAC		0.602	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021		C	2767633	T	C	2767633	3	2	57	1	0	0	0	0	1	0	0	0	14262	1667	58	4	825	4	SGTA	19	2767633	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09		2767633	56361350	106	7632										
ZNF536	9745	broad.mit.edu	37	chr19	31039805	31039805	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	actctgggagagcagaagagCggtgcatggaccggccacgt	16	10	1	3	rs147863190		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr19:31039805C>T	ENST00000355537.3	+	4	3426	c.3279C>T	c.(3277-3279)agC>agT	p.S1093S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1093					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.S1093S(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					AGCAGAAGAGCGGTGCATGGA	0.537													C|||	1	0.000199681	0	0	5008	,	,		18334	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	75	85	81		3279	-4.1	0	19	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF536	NM_014717.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1093/1301	31039805	1,13005	2203	4300	6503	35731645	SO:0001819	synonymous_variant	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3279C>T	19.37:g.31039805C>T			35731645	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																				0.537	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039805	C	T	31039805	2	4	57	1	0	0	0	0	0	0	0	1	18013	767	27	1		1	ZNF536	19	31039805	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	28272172	31039805	28089178	107	7633										
MEGF8	1954	broad.mit.edu	37	chr19	42880528	42880528	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gaccctactgccccggcctcCgcctggaagccggctgggct	13	18	0	0	rs199681302	byFrequency	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr19:42880528C>T	ENST00000251268.6	+	42	8139	c.8139C>T	c.(8137-8139)tcC>tcT	p.S2713S	MEGF8_ENST00000378073.4_Silent_p.S307S|MEGF8_ENST00000334370.4_Silent_p.S2646S	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2713					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.S2254S(1)|p.S2646S(1)|p.S2713S(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCCCGGCCTCCGCCTGGAAGC	0.711													C|||	15	0.00299521	0	0	5008	,	,		12807	0		0.001	False		,,,				2504	0.0143															3	Substitution - coding silent(3)	large_intestine(3)	19						C		2,4394		0,2,2196	28	28	28		7938	-6.7	0	19		28	1,8587		0,1,4293	no	coding-synonymous	MEGF8	NM_001410.2		0,3,6489	TT,TC,CC		0.0116,0.0455,0.0231		2646/2779	42880528	3,12981	2198	4294	6492	47572368	SO:0001819	synonymous_variant	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.8139C>T	19.37:g.42880528C>T			47572368	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																					0.711	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42880528	C	T	42880528	2	4	57	1	0	0	0	0	0	0	0	1	9493	639	23	1		1	MEGF8	19	42880528	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	11840723	42880528	16248455	108	7634										
TSKS	60385	broad.mit.edu	37	chr19	50248605	50248605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	agccgcagggcttcctgcacCgccccctcctcctgatgcca	9	20	0	1			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr19:50248605C>T	ENST00000246801.3	-	7	1123	c.1041G>A	c.(1039-1041)gcG>gcA	p.A347A	TSKS_ENST00000358830.3_Silent_p.A147A	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	347					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.A347A(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CTTCCTGCACCGCCCCCTCCT	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	19											11	12	12					19																	50248605		2194	4282	6476	54940417	SO:0001819	synonymous_variant	60385			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1041G>A	19.37:g.50248605C>T			54940417	Q8WXJ0	Silent	SNP	ENST00000246801.3	37	CCDS12780.1																																																																																				0.706	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50248605	C	T	50248605	2	4	57	1	0	0	0	0	0	0	0	1	16666	639	23	1		1	TSKS	19	50248605	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09	7368077	50248605	8880378	109	7635										
NLRP5	126206	broad.mit.edu	37	chr19	56538575	56538575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	tccccgttagagagatgcagCggaagaaggagagcagtgtc	15	8	0	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr19:56538575C>T	ENST00000390649.3	+	7	976	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	326	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.R326W(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AGAGATGCAGCGGAAGAAGGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											38	40	39					19																	56538575		2072	4209	6281	61230387	SO:0001583	missense	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.976C>T	19.37:g.56538575C>T	ENSP00000375063:p.Arg326Trp		61230387	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	4.088	0.014253	0.07959	.	.	ENSG00000171487	ENST00000390649	T	0.80653	-1.4	3.35	-6.71	0.01760	NACHT nucleoside triphosphatase (1);	2.741520	0.01259	N	0.009110	T	0.60996	0.2312	N	0.11131	0.1	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.56294	-0.8003	10	0.28530	T	0.3	.	6.5283	0.22312	0.1102:0.6213:0.1113:0.1572	.	326	P59047	NALP5_HUMAN	W	326	ENSP00000375063:R326W	ENSP00000375063:R326W	R	+	1	2	NLRP5	61230387	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.882000	0.04174	-3.381000	0.00175	-0.812000	0.03155	CGG		0.567	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56538575	C	T	56538575	3	4	57	1	0	0	0	0	1	0	0	0	10511	759	27	1	1002	1	NLRP5	19	56538575	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	6289970	56538575	2590408	110	7636										
NINL	22981	broad.mit.edu	37	chr20	25459760	25459760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	cctccagcacgctgacctcgCgcctgcgagcctgctccatg	10	19	0	1	rs370541015		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr20:25459760C>T	ENST00000278886.6	-	16	2073	c.2000G>A	c.(1999-2001)cGc>cAc	p.R667H	NINL_ENST00000422516.1_Missense_Mutation_p.R667H	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	667					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.R667H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GCTGACCTCGCGCCTGCGAGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	HIS/ARG	0,4406		0,0,2203	75	72	73		2000	-6.2	0	20		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	NINL	NM_025176.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	667/1383	25459760	1,13005	2203	4300	6503	25407760	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2000G>A	20.37:g.25459760C>T	ENSP00000278886:p.Arg667His		25407760	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	C	0.891	-0.725448	0.03158	0.0	1.16E-4	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.29917	1.79;1.55	4.91	-6.24	0.02046	.	2.237540	0.01716	N	0.028024	T	0.13157	0.0319	N	0.03608	-0.345	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.001	T	0.19943	-1.0290	10	0.38643	T	0.18	8.0E-4	7.1438	0.25570	0.247:0.2738:0.0:0.4792	.	667;667	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	H	667	ENSP00000278886:R667H;ENSP00000410431:R667H	ENSP00000278886:R667H	R	-	2	0	NINL	25407760	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.341000	0.07811	-1.576000	0.01652	-0.812000	0.03155	CGC		0.552	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25459760	C	T	25459760	3	4	57	1	0	0	0	0	1	0	0	0	10451	768	27	1	2184	1	NINL	20	25459760	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		25459760	37565760	111	7637										
NCAM2	4685	broad.mit.edu	37	chr21	22881329	22881329	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	atgtgtggaaagaaaagtggCtccagtggcaaaagtaaaga	13	4	0	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr21:22881329C>T	ENST00000400546.1	+	16	2484	c.2235C>T	c.(2233-2235)ggC>ggT	p.G745G	NCAM2_ENST00000284894.7_Silent_p.G603G	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	745					axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G745G(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGAAAAGTGGCTCCAGTGGCA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	21											114	109	110					21																	22881329		1952	4169	6121	21803200	SO:0001819	synonymous_variant	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.2235C>T	21.37:g.22881329C>T			21803200	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																				0.443	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22881329	C	T	22881329	2	4	57	1	0	0	0	0	0	0	0	1	10234	784	28	3		3	NCAM2	21	22881329	Silent	SNP	C	TCGA-AG-4005-01A-01W-1073-09		22881329	25248566	112	7638										
ZDHHC8	29801	broad.mit.edu	37	chr22	20128426	20128426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gccaccccggctgccgctcgCggtgagtttgaagccgcctt	13	16	0	2	rs548919026		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr22:20128426C>T	ENST00000334554.7	+	7	926	c.785C>T	c.(784-786)gCg>gTg	p.A262V	ZDHHC8_ENST00000468112.1_3'UTR|ZDHHC8_ENST00000405930.3_Missense_Mutation_p.A262V|ZDHHC8_ENST00000320602.7_Missense_Mutation_p.A170V	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	262					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.A262V(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CTGCCGCTCGCGGTGAGTTTG	0.642													C|||	1	0.000199681	0	0	5008	,	,		15183	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											42	46	45					22																	20128426		2202	4300	6502	18508426	SO:0001583	missense	29801			AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.785C>T	22.37:g.20128426C>T	ENSP00000334490:p.Ala262Val		18508426	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	37	CCDS13776.1	.	.	.	.	.	.	.	.	.	.	C	6.849	0.525939	0.13066	.	.	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.72394	1.34;-0.65;1.33	5.08	4.05	0.47172	.	829.068000	0.00166	N	0.000001	T	0.62865	0.2463	N	0.20685	0.6	0.09310	N	1	P;B;B	0.35774	0.519;0.132;0.005	B;B;B	0.32022	0.139;0.027;0.003	T	0.59511	-0.7441	10	0.51188	T	0.08	.	14.9631	0.71171	0.0:0.8564:0.1436:0.0	.	170;262;262	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	V	262;170;262	ENSP00000334490:A262V;ENSP00000317804:A170V;ENSP00000384716:A262V	ENSP00000317804:A170V	A	+	2	0	ZDHHC8	18508426	0.008000	0.16893	0.002000	0.10522	0.020000	0.10135	1.211000	0.32382	1.253000	0.44018	0.655000	0.94253	GCG		0.642	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20128426	C	T	20128426	3	4	57	1	0	0	0	0	1	0	0	0	17660	768	27	1	811	1	ZDHHC8	22	20128426	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09		20128426	31176140	113	7639										
CABIN1	23523	broad.mit.edu	37	chr22	24494116	24494116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctccgattgaccacgattacGtcaaatgtaaaaaaccccac	5	13	1	1	rs568317451		TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chr22:24494116G>A	ENST00000398319.2	+	26	4463	c.4078G>A	c.(4078-4080)Gtc>Atc	p.V1360I	CABIN1_ENST00000405822.2_Intron|CABIN1_ENST00000263119.5_Missense_Mutation_p.V1360I	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1360					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.V1360I(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CCACGATTACGTCAAATGTAA	0.627													G|||	1	0.000199681	0	0	5008	,	,		8441	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											91	87	88					22																	24494116		2203	4300	6503	22824116	SO:0001583	missense	23523			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.4078G>A	22.37:g.24494116G>A	ENSP00000381364:p.Val1360Ile		22824116	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860141	0.32884	.	.	ENSG00000099991	ENST00000263119;ENST00000398319	T;T	0.61742	0.08;0.08	4.77	2.63	0.31362	.	0.245918	0.41712	N	0.000821	T	0.38931	0.1059	L	0.31294	0.92	0.80722	D	1	B	0.26258	0.145	B	0.14023	0.01	T	0.17137	-1.0379	10	0.25751	T	0.34	.	8.778	0.34774	0.249:0.0:0.751:0.0	.	1360	Q9Y6J0	CABIN_HUMAN	I	1360	ENSP00000263119:V1360I;ENSP00000381364:V1360I	ENSP00000263119:V1360I	V	+	1	0	CABIN1	22824116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.868000	0.63021	1.159000	0.42565	0.650000	0.86243	GTC		0.627	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24494116	G	A	24494116	3	1	57	1	0	0	0	0	1	0	0	0	2534	1145	40	1	4176	1	CABIN1	22	24494116	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	4365690	24494116	26810450	114	7640										
NHS	4810	broad.mit.edu	37	chrX	17743893	17743893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	aagcagcccgagtgcccaggAccaccagcctactttgggcc	11	16	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:17743893A>G	ENST00000380060.3	+	6	1942	c.1604A>G	c.(1603-1605)gAc>gGc	p.D535G	NHS_ENST00000398097.3_Missense_Mutation_p.D379G	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	556					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.D535G(1)|p.D379G(1)		breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					AGTGCCCAGGACCACCAGCCT	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	X											61	54	57					X																	17743893		2203	4300	6503	17653814	SO:0001583	missense	4810				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1604A>G	X.37:g.17743893A>G	ENSP00000369400:p.Asp535Gly		17653814	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.713649	0.30413	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.44083	0.93;0.94	5.86	4.71	0.59529	.	0.206541	0.50627	D	0.000111	T	0.29158	0.0725	N	0.22421	0.69	0.46113	D	0.998878	B;B;B;B	0.25850	0.0;0.0;0.0;0.136	B;B;B;B	0.23419	0.0;0.0;0.0;0.046	T	0.14783	-1.0460	10	0.72032	D	0.01	-4.313	10.4431	0.44477	0.9237:0.0:0.0763:0.0	.	556;377;379;535	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	G	535;379;377	ENSP00000369400:D535G;ENSP00000381170:D379G	ENSP00000369397:D377G	D	+	2	0	NHS	17653814	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	5.025000	0.64097	1.974000	0.57490	0.486000	0.48141	GAC		0.542	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		G	17743893	A	G	17743893	3	3	57	1	0	0	0	0	1	0	0	0	10442	275	10	4	1731	4	NHS	23	17743893	Missense_Mutation	SNP	A	TCGA-AG-4005-01A-01W-1073-09		17743893	137526667	115	7641										
FAM47C	442444	broad.mit.edu	37	chrX	37027597	37027597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ctctccgccagctgcctcccGaggctggagtgtcccatctc	10	18	2	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:37027597G>A	ENST00000358047.3	+	1	1166	c.1114G>A	c.(1114-1116)Gag>Aag	p.E372K		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	372								p.E372K(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GCTGCCTCCCGAGGCTGGAGT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	X											62	62	62					X																	37027597		2202	4299	6501	36937518	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1114G>A	X.37:g.37027597G>A	ENSP00000367913:p.Glu372Lys		36937518	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	g	8.268	0.812734	0.16537	.	.	ENSG00000198173	ENST00000358047	T	0.19806	2.12	0.951	0.951	0.19579	.	.	.	.	.	T	0.14527	0.0351	N	0.12182	0.205	0.23546	N	0.997445	D	0.69078	0.997	P	0.54312	0.748	T	0.06481	-1.0824	9	0.06365	T	0.9	.	7.6353	0.28264	1.0E-4:0.0:0.9999:0.0	.	372	Q5HY64	FA47C_HUMAN	K	372	ENSP00000367913:E372K	ENSP00000367913:E372K	E	+	1	0	FAM47C	36937518	0.341000	0.24801	0.019000	0.16419	0.013000	0.08279	0.467000	0.22035	0.181000	0.19994	0.183000	0.17082	GAG		0.637	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37027597	G	A	37027597	3	1	57	1	0	0	0	0	1	0	0	0	5590	1059	37	1	1116	1	FAM47C	23	37027597	Missense_Mutation	SNP	G	TCGA-AG-4005-01A-01W-1073-09	19283704	37027597	118242963	116	7642										
OTC	5009	broad.mit.edu	37	chrX	38260659	38260659	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gtaccatcctatccagatccTggctgattacctcacgctcc	6	16	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:38260659T>G	ENST00000039007.4	+	5	670	c.518T>G	c.(517-519)cTg>cGg	p.L173R	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	173					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)	p.L173R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	ATCCAGATCCTGGCTGATTAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											134	99	111					X																	38260659		2202	4300	6502	38145603	SO:0001583	missense	5009			K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.518T>G	X.37:g.38260659T>G	ENSP00000039007:p.Leu173Arg		38145603	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.520585	0.85495	.	.	ENSG00000036473	ENST00000039007	D	0.99688	-6.41	5.97	5.97	0.96955	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	H	0.99143	4.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96248	0.9181	10	0.87932	D	0	-10.1205	15.388	0.74718	0.0:0.0:0.0:1.0	.	173	P00480	OTC_HUMAN	R	173	ENSP00000039007:L173R	ENSP00000039007:L173R	L	+	2	0	OTC	38145603	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.651000	0.83577	2.018000	0.59344	0.486000	0.48141	CTG		0.388	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			G	38260659	T	G	38260659	3	3	57	1	0	0	0	0	1	0	0	0	11332	1580	55	4	536	4	OTC	23	38260659	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09	1233062	38260659	117009901	117	7643										
GLUD2	2747	broad.mit.edu	37	chrX	120181654	120181654	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	gggccgcggacagcccgccgCcgcctcgcagccggggctcg	17	19	0	0			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:120181654C>A	ENST00000328078.1	+	1	193	c.116C>A	c.(115-117)gCc>gAc	p.A39D		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	39					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)	p.A39D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CAGCCCGCCGCCGCCTCGCAG	0.761																																																1	Substitution - Missense(1)	large_intestine(1)	X											8	10	9					X																	120181654		2065	4029	6094	120009335	SO:0001583	missense	2747			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.116C>A	X.37:g.120181654C>A	ENSP00000327589:p.Ala39Asp		120009335	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608163	0.46527	.	.	ENSG00000182890	ENST00000328078	D	0.96685	-4.09	0.886	0.886	0.19194	.	0.341384	0.25408	U	0.030882	D	0.87313	0.6146	N	0.08118	0	0.30090	N	0.80838	B	0.02656	0.0	B	0.01281	0.0	T	0.79843	-0.1632	10	0.31617	T	0.26	.	4.8548	0.13554	0.0:1.0:0.0:0.0	.	39	P49448	DHE4_HUMAN	D	39	ENSP00000327589:A39D	ENSP00000327589:A39D	A	+	2	0	GLUD2	120009335	0.992000	0.36948	0.003000	0.11579	0.005000	0.04900	2.224000	0.42945	0.727000	0.32360	0.372000	0.22366	GCC		0.761	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120181654	C	A	120181654	3	1	57	1	0	0	0	0	1	0	0	0	6497	739	26	2	118	2	GLUD2	23	120181654	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	81920995	120181654	35088906	118	7644										
GPC3	2719	broad.mit.edu	37	chrX	132887834	132887834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	ttgtgttgatcacttcaattCcaagattcagagcctgaagg	9	8	3	4			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:132887834C>T	ENST00000370818.3	-	3	1152	c.707G>A	c.(706-708)gGa>gAa	p.G236E	GPC3_ENST00000543339.1_Missense_Mutation_p.G182E|GPC3_ENST00000394299.2_Missense_Mutation_p.G236E	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	236					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)	p.G236E(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					CACTTCAATTCCAAGATTCAG	0.463			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome																													yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	1	Substitution - Missense(1)	large_intestine(1)	X											457	307	358					X																	132887834		2203	4300	6503	132715500	SO:0001583	missense	2719	Familial Cancer Database	SGBS	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"Proteoglycans / Cell Surface : Glypicans"	4451	protein-coding gene	gene with protein product	"glypican proteoglycan 3"	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.707G>A	X.37:g.132887834C>T	ENSP00000359854:p.Gly236Glu		132715500	C9JLE3|G3V1R0|Q2L880|Q2L882	Missense_Mutation	SNP	ENST00000370818.3	37	CCDS14638.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768777	0.69878	.	.	ENSG00000147257	ENST00000370818;ENST00000394299;ENST00000543339	T;T;T	0.56941	0.43;0.43;0.43	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.74596	0.3737	M	0.77616	2.38	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	T	0.77544	-0.2548	10	0.87932	D	0	.	17.9336	0.89006	0.0:1.0:0.0:0.0	.	220;182;236;236	B4DTD8;G3V1R0;C9JLE3;P51654	.;.;.;GPC3_HUMAN	E	236;236;182	ENSP00000359854:G236E;ENSP00000377836:G236E;ENSP00000444222:G182E	ENSP00000359854:G236E	G	-	2	0	GPC3	132715500	1.000000	0.71417	0.911000	0.35937	0.978000	0.69477	7.487000	0.81328	2.455000	0.83008	0.594000	0.82650	GGA		0.463	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		T	132887834	C	T	132887834	3	4	57	1	0	0	0	0	1	0	0	0	6619	855	30	3	1132	3	GPC3	23	132887834	Missense_Mutation	SNP	C	TCGA-AG-4005-01A-01W-1073-09	12706180	132887834	22382726	119	7645										
RPL10	6134	broad.mit.edu	37	chrX	153628261	153628261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	4	1	0.40390243902439	3.24564459930314	0.111370157819225	0.569230769230769	1	0	catccgcatcaacaagatgtTgtcctgtgctggggctgaca	11	11	1	2			TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4005-01A-01W-1073-09	TCGA-AG-4005-10A-01W-1073-09	g.chrX:153628261T>C	ENST00000369817.2	+	6	884	c.308T>C	c.(307-309)tTg>tCg	p.L103S	SNORA70_ENST00000384436.1_RNA|RPL10_ENST00000406022.2_Missense_Mutation_p.L52S|RPL10_ENST00000424325.2_Missense_Mutation_p.L103S			P27635	RL10_HUMAN	ribosomal protein L10	103					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.L103S(1)		large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AACAAGATGTTGTCCTGTGCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											56	50	52					X																	153628261		2203	4300	6503	153281455	SO:0001583	missense	6134			AB007170	CCDS14746.1, CCDS76059.1	Xq28	2011-04-06			ENSG00000147403	ENSG00000147403		"L ribosomal proteins"	10298	protein-coding gene	gene with protein product		312173				9582194	Standard	NM_006013		Approved	NOV, QM, DXS648E, DXS648, FLJ23544, L10	uc004fkm.2	P27635	OTTHUMG00000033189	ENST00000369817.2:c.308T>C	X.37:g.153628261T>C	ENSP00000358832:p.Leu103Ser		153281455	A3KQT0|D3DWW6|Q16470|Q2HXT7|Q53FH7|Q6FGN8|Q8TDA5	Missense_Mutation	SNP	ENST00000369817.2	37	CCDS14746.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.792937	0.90453	.	.	ENSG00000147403	ENST00000369817;ENST00000424325;ENST00000436473;ENST00000344746;ENST00000458500;ENST00000406022;ENST00000451365;ENST00000427682;ENST00000449494;ENST00000428169	T;T;T;T	0.77358	-1.07;-1.07;-1.07;-1.09	4.88	4.88	0.63580	Ribosomal protein L10e/L16 (2);	0.000000	0.56097	U	0.000035	D	0.91761	0.7394	H	0.98466	4.24	0.80722	D	1	P;D;P	0.64830	0.88;0.994;0.948	P;D;P	0.67103	0.828;0.949;0.837	D	0.93763	0.7068	10	0.87932	D	0	-24.1658	11.5135	0.50507	0.0:0.0:0.0:1.0	.	52;103;103	F8W7C6;A6QRI9;P27635	.;.;RL10_HUMAN	S	103;103;103;103;103;52;86;13;13;13	ENSP00000358832:L103S;ENSP00000413436:L103S;ENSP00000341730:L103S;ENSP00000385621:L52S	ENSP00000341730:L103S	L	+	2	0	RPL10	153281455	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.369000	0.79578	1.617000	0.50277	0.417000	0.27973	TTG		0.478	RPL10-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127774.5	NM_006013		C	153628261	T	C	153628261	3	2	57	1	0	0	0	0	1	0	0	0	13591	1821	63	4	322	4	RPL10	23	153628261	Missense_Mutation	SNP	T	TCGA-AG-4005-01A-01W-1073-09	20740427	153628261	1642299	120	7646										
AJAP1	55966	broad.mit.edu	37	chr1	4772582	4772583	+	In_Frame_Ins	INS	-	-	CCA													0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	acggaagacaactgtggccgINSccaccaccaccaccaccacc					rs149907194|rs529940202	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:4772582_4772583insCCA	ENST00000378191.4	+	2	1033_1034	c.652_653insCCA	c.(652-654)gcc>gCCAcc	p.225_226insT	AJAP1_ENST00000378190.3_In_Frame_Ins_p.225_226insT	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	225	Thr-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T225_A226insT(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		AACTGTGGccgccaccaccacc	0.639														10	0.00199681	0.0023	0.0029	5008	,	,		14933	0		0.005	False		,,,				2504	0															1	Insertion - In frame(1)	large_intestine(1)	1																																								4672443	SO:0001652	inframe_insertion	55966			AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.671_673dupCCA	1.37:g.4772589_4772591dupCCA	ENSP00000367433:p.Thr226_Thr227dup		4672442	Q9Y229	In_Frame_Ins	INS	ENST00000378191.4	37	CCDS54.1																																																																																				0.639	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		CCA	4772583	-	CCA	4772582	7	5	58	1	0	1	1	0	0	0	0	0	438	1087	38	0	658	0	AJAP1	1	4772582	In_Frame_Ins	INS	-	TCGA-AG-4007-01A-01W-1073-09		4772582	244478039	1	7647										
RNF207	388591	broad.mit.edu	37	chr1	6278400	6278400	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	agtctacagaacacgcacgaCgacagcaggaacaacgcggc	11	13	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:6278400C>T	ENST00000377939.4	+	17	1831	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	568						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.D568D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		ACACGCACGACGACAGCAGGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											69	81	77					1																	6278400		2141	4253	6394	6200987	SO:0001819	synonymous_variant	388591			AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"RING-type (C3HC4) zinc fingers"	32947	protein-coding gene	gene with protein product	"OTTHUMG00000001089"		"chromosome 1 open reading frame 188"	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1704C>T	1.37:g.6278400C>T			6200987	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																				0.577	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396		T	6278400	C	T	6278400	2	4	58	1	0	0	0	0	0	0	0	1	13511	535	19	1		1	RNF207	1	6278400	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	1505818	6278400	242972221	2	7648										
SLC2A7	155184	broad.mit.edu	37	chr1	9082990	9082990	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgtttacctgccgcagctatCaaccagcaggcccacgagca	9	15	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:9082990C>A	ENST00000400906.1	-	3	297	c.298G>T	c.(298-300)Gat>Tat	p.D100Y		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	100					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.D100Y(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CCGCAGCTATCAACCAGCAGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											138	134	135					1																	9082990		2203	4300	6503	9005577	SO:0001583	missense	155184			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.298G>T	1.37:g.9082990C>A	ENSP00000383698:p.Asp100Tyr		9005577	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	.	.	.	.	.	.	.	.	.	.	C	15.00	2.702906	0.48412	.	.	ENSG00000197241	ENST00000400906	T	0.73789	-0.78	4.86	1.88	0.25563	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.196667	0.41194	D	0.000936	T	0.81550	0.4846	M	0.81942	2.565	0.09310	N	1	P	0.49961	0.93	P	0.59948	0.866	T	0.71130	-0.4682	10	0.72032	D	0.01	.	6.8259	0.23883	0.0:0.5246:0.0:0.4754	.	100	Q6PXP3	GTR7_HUMAN	Y	100	ENSP00000383698:D100Y	ENSP00000383698:D100Y	D	-	1	0	SLC2A7	9005577	0.189000	0.23263	0.005000	0.12908	0.026000	0.11368	1.350000	0.34010	0.624000	0.30286	0.561000	0.74099	GAT		0.547	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		A	9082990	C	A	9082990	3	1	58	1	0	0	0	0	1	0	0	0	14587	826	29	2	1280	2	SLC2A7	1	9082990	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	2804590	9082990	240167631	3	7649										
CSMD2	114784	broad.mit.edu	37	chr1	34037186	34037186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttgccattggcctgacagcGgatgaccctttggccagtat	11	11	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:34037186G>A	ENST00000373381.4	-	51	8079	c.7903C>T	c.(7903-7905)Cgc>Tgc	p.R2635C		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2637	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2637C(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCCTGACAGCGGATGACCCTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	76	80					1																	34037186		2203	4300	6503	33809773	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7903C>T	1.37:g.34037186G>A	ENSP00000362479:p.Arg2635Cys		33809773	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	22.5	4.300383	0.81136	.	.	ENSG00000121904	ENST00000373381	T	0.66099	-0.19	5.32	4.4	0.53042	Complement control module (2);Sushi/SCR/CCP (3);	0.121265	0.53938	D	0.000041	T	0.77765	0.4179	M	0.84683	2.71	0.80722	D	1	D;D	0.89917	0.987;1.0	P;D	0.71414	0.846;0.973	T	0.79045	-0.1964	10	0.59425	D	0.04	.	8.6692	0.34140	0.0815:0.0:0.7583:0.1603	.	2637;2635	Q7Z408;E7EUA6	CSMD2_HUMAN;.	C	2635	ENSP00000362479:R2635C	ENSP00000241312:R2637C	R	-	1	0	CSMD2	33809773	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.617000	0.54181	1.237000	0.43756	0.655000	0.94253	CGC		0.572	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34037186	G	A	34037186	3	1	58	1	0	0	0	0	1	0	0	0	3951	1116	39	1	2626	1	CSMD2	1	34037186	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	24954196	34037186	215213435	4	7650										
INADL	10207	broad.mit.edu	37	chr1	62349972	62349972	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccttcctgttgtggctcaaaGgagggagcaagaagatttgc	13	8	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:62349972G>C	ENST00000371158.2	+	22	3137	c.3023G>C	c.(3022-3024)aGg>aCg	p.R1008T	INADL_ENST00000316485.6_Missense_Mutation_p.R1008T	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1008					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.R1008T(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GTGGCTCAAAGGAGGGAGCAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											213	188	196					1																	62349972		2203	4300	6503	62122560	SO:0001583	missense	10207			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3023G>C	1.37:g.62349972G>C	ENSP00000360200:p.Arg1008Thr		62122560	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	g	3.668	-0.068156	0.07228	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.13657	2.72;2.57	5.13	2.21	0.28008	.	0.614978	0.15878	N	0.240200	T	0.12732	0.0309	M	0.65975	2.015	0.09310	N	1	B;B;B	0.24132	0.098;0.085;0.029	B;B;B	0.27608	0.067;0.026;0.081	T	0.32824	-0.9892	10	0.14252	T	0.57	.	4.2443	0.10663	0.0856:0.1565:0.5956:0.1622	.	1008;1008;1008	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	T	1008	ENSP00000360200:R1008T;ENSP00000326199:R1008T	ENSP00000255202:R1008T	R	+	2	0	INADL	62122560	0.132000	0.22450	0.067000	0.19924	0.001000	0.01503	0.816000	0.27267	0.773000	0.33404	-0.233000	0.12211	AGG		0.463	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62349972	G	C	62349972	3	2	58	1	0	0	0	0	1	0	0	0	7752	1000	35	5	3105	5	INADL	1	62349972	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	28312786	62349972	186900649	5	7651										
EPS8L3	79574	broad.mit.edu	37	chr1	110301241	110301241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcggcctttccatagcaggcCccctccatctgtcctggcct	9	18	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:110301241C>T	ENST00000361965.4	-	7	612	c.506G>A	c.(505-507)gGg>gAg	p.G169E	EPS8L3_ENST00000361852.4_Missense_Mutation_p.G169E|EPS8L3_ENST00000494151.1_5'UTR|EPS8L3_ENST00000369805.3_Missense_Mutation_p.G170E|RP4-735C1.4_ENST00000431955.1_RNA	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	169						cytoplasm (GO:0005737)		p.G170E(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		CATAGCAGGCCCCCTCCATCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	54	55					1																	110301241		2203	4300	6503	110102764	SO:0001583	missense	79574			AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.506G>A	1.37:g.110301241C>T	ENSP00000355255:p.Gly169Glu		110102764	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	37	CCDS814.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062007	0.36373	.	.	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.59638	2.61;0.26;0.25	5.35	3.33	0.38152	.	0.800615	0.11900	N	0.518687	T	0.33381	0.0861	M	0.70595	2.14	0.09310	N	1	B;B;B;B	0.24368	0.013;0.023;0.007;0.102	B;B;B;B	0.25759	0.01;0.016;0.004;0.063	T	0.29027	-1.0025	10	0.15952	T	0.53	-19.5781	9.1532	0.36976	0.1631:0.6786:0.1583:0.0	.	169;169;169;170	A8K2J6;Q8TE67-2;Q8TE67;Q8TE67-3	.;.;ES8L3_HUMAN;.	E	169;170;169	ENSP00000354551:G169E;ENSP00000358820:G170E;ENSP00000355255:G169E	ENSP00000354551:G169E	G	-	2	0	EPS8L3	110102764	0.000000	0.05858	0.045000	0.18777	0.331000	0.28603	-0.059000	0.11731	1.343000	0.45638	0.655000	0.94253	GGG		0.607	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526		T	110301241	C	T	110301241	3	4	58	1	0	0	0	0	1	0	0	0	5210	623	22	3	1327	3	EPS8L3	1	110301241	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	47951269	110301241	138949380	6	7652										
LYSMD1	388695	broad.mit.edu	37	chr1	151137721	151137721	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cccctggcgggggctgtctaGacggggaagccatctcttca	14	13	3	1	rs200029870		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:151137721G>A	ENST00000368908.5	-	1	674	c.14C>T	c.(13-15)tCt>tTt	p.S5F	SCNM1_ENST00000368905.4_5'Flank|LYSMD1_ENST00000440902.2_Intron	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1	5								p.S5F(1)		endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			GGGCTGTCTAGACGGGGAAGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											38	41	40					1																	151137721		2203	4300	6503	149404345	SO:0001583	missense	388695			BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.14C>T	1.37:g.151137721G>A	ENSP00000357904:p.Ser5Phe		149404345	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.508010	0.64410	.	.	ENSG00000163155	ENST00000368908	T	0.34472	1.36	5.04	5.04	0.67666	.	0.349858	0.30989	N	0.008479	T	0.32164	0.0820	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.03863	-1.0997	10	0.12430	T	0.62	.	17.3159	0.87224	0.0:0.0:1.0:0.0	.	5	Q96S90	LYSM1_HUMAN	F	5	ENSP00000357904:S5F	ENSP00000357904:S5F	S	-	2	0	LYSMD1	149404345	1.000000	0.71417	1.000000	0.80357	0.464000	0.32679	4.118000	0.57884	2.607000	0.88179	0.557000	0.71058	TCT		0.592	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551		A	151137721	G	A	151137721	3	1	58	1	0	0	0	0	1	0	0	0	9154	942	33	3	681	3	LYSMD1	1	151137721	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	40836480	151137721	98112900	7	7653										
IL6R	3570	broad.mit.edu	37	chr1	154408532	154408532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttcgtgcccaggaggagttcGggcaaggcgagtggagcgag	19	8	0	0	rs375243100		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:154408532G>A	ENST00000368485.3	+	6	1332	c.895G>A	c.(895-897)Ggg>Agg	p.G299R	IL6R_ENST00000344086.4_Missense_Mutation_p.G299R|IL6R_ENST00000507256.1_Intron	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	299	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)	p.G299R(1)	IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	GGAGGAGTTCGGGCAAGGCGA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	87	74	78		895,895,895	1.9	0.4	1		78	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	IL6R	NM_000565.3,NM_001206866.1,NM_181359.2	125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	299/469,299/353,299/366	154408532	1,13005	2203	4300	6503	152675156	SO:0001583	missense	3570			X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.895G>A	1.37:g.154408532G>A	ENSP00000357470:p.Gly299Arg		152675156	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	37	CCDS1067.1	.	.	.	.	.	.	.	.	.	.	G	8.648	0.897580	0.17686	0.0	1.16E-4	ENSG00000160712	ENST00000368485;ENST00000344086	T;T	0.21361	2.34;2.01	5.29	1.93	0.25924	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.823181	0.11253	N	0.583388	T	0.06508	0.0167	M	0.74647	2.275	0.09310	N	1	P;B	0.46621	0.881;0.421	B;B	0.31016	0.123;0.027	T	0.28267	-1.0049	10	0.41790	T	0.15	-9.0432	3.259	0.06842	0.276:0.2246:0.4994:0.0	.	299;299	P08887-2;P08887	.;IL6RA_HUMAN	R	299	ENSP00000357470:G299R;ENSP00000340589:G299R	ENSP00000340589:G299R	G	+	1	0	IL6R	152675156	0.011000	0.17503	0.433000	0.26760	0.073000	0.16967	1.093000	0.30939	0.574000	0.29417	-0.165000	0.13383	GGG		0.637	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		A	154408532	G	A	154408532	3	1	58	1	0	0	0	0	1	0	0	0	7723	1116	39	1	917	1	IL6R	1	154408532	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	3270811	154408532	94842089	8	7654										
PAPPA2	60676	broad.mit.edu	37	chr1	176769219	176769219	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cattgtgtgcactggccggcGtcaatggcacccagaccccg	12	15	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:176769219G>A	ENST00000367662.3	+	21	6317	c.5153G>A	c.(5152-5154)cGt>cAt	p.R1718H		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1718	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1718H(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						ACTGGCCGGCGTCAATGGCAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											133	129	131					1																	176769219		1935	4140	6075	175035842	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5153G>A	1.37:g.176769219G>A	ENSP00000356634:p.Arg1718His		175035842	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.330450	0.60743	.	.	ENSG00000116183	ENST00000367662	T	0.01705	4.68	6.02	3.07	0.35406	.	0.289113	0.33092	N	0.005285	T	0.04048	0.0113	L	0.51422	1.61	0.09310	N	0.999999	D	0.76494	0.999	P	0.58210	0.835	T	0.36286	-0.9754	10	0.38643	T	0.18	-9.571	5.7732	0.18265	0.1489:0.0:0.6041:0.247	.	1718	Q9BXP8	PAPP2_HUMAN	H	1718	ENSP00000356634:R1718H	ENSP00000356634:R1718H	R	+	2	0	PAPPA2	175035842	0.007000	0.16637	0.443000	0.26883	0.918000	0.54935	1.478000	0.35442	0.897000	0.36392	-0.122000	0.15005	CGT		0.493	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176769219	G	A	176769219	3	1	58	1	0	0	0	0	1	0	0	0	11464	1145	40	1	5284	1	PAPPA2	1	176769219	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	22360687	176769219	72481402	9	7655										
RASAL2	9462	broad.mit.edu	37	chr1	178389684	178389684	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgaaaggctccatcaagagGaccaaaagccagtcaaagct	9	11	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:178389684G>A	ENST00000462775.1	+	3	284	c.159G>A	c.(157-159)agG>agA	p.R53R	RASAL2_ENST00000448150.3_Silent_p.R183R|RASAL2_ENST00000367649.3_Silent_p.R201R	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	53	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)	p.R53S(1)|p.R183S(1)|p.R183R(1)|p.R201R(1)|p.R201S(1)		biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CCATCAAGAGGACCAAAAGCC	0.463																																																5	Substitution - Missense(3)|Substitution - coding silent(2)	lung(3)|large_intestine(2)	1											74	68	70					1																	178389684		2203	4300	6503	176656307	SO:0001819	synonymous_variant	9462			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.159G>A	1.37:g.178389684G>A			176656307	F8W755|O95174|Q2TB22|Q5TFU9	Silent	SNP	ENST00000462775.1	37	CCDS1322.1																																																																																				0.463	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		A	178389684	G	A	178389684	2	1	58	1	0	0	0	0	0	0	0	1	13101	1165	41	3		3	RASAL2	1	178389684	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	1620465	178389684	70860937	10	7656										
KDM5B	10765	broad.mit.edu	37	chr1	202702942	202702942	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttggagaggcgacagcaattTcccttcattggcgagtctga	12	9	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:202702942T>G	ENST00000367265.3	-	23	4660	c.3496A>C	c.(3496-3498)Aaa>Caa	p.K1166Q	KDM5B_ENST00000367264.2_Missense_Mutation_p.K1202Q	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1166					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.K1166Q(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GACAGCAATTTCCCTTCATTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	116	114					1																	202702942		2203	4300	6503	200969565	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3496A>C	1.37:g.202702942T>G	ENSP00000356234:p.Lys1166Gln		200969565	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841515	0.71488	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.85013	-1.93;-1.93;-1.93	5.89	5.89	0.94794	Zinc finger, FYVE/PHD-type (1);	0.041875	0.85682	D	0.000000	D	0.90823	0.7118	M	0.68317	2.08	0.80722	D	1	D;D	0.69078	0.997;0.981	P;D	0.63793	0.904;0.918	D	0.91427	0.5163	10	0.62326	D	0.03	-26.7497	16.3036	0.82836	0.0:0.0:0.0:1.0	.	1202;1166	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	Q	1166;1008;1202;1008	ENSP00000356234:K1166Q;ENSP00000356233:K1202Q;ENSP00000235790:K1008Q	ENSP00000235790:K1008Q	K	-	1	0	KDM5B	200969565	1.000000	0.71417	0.977000	0.42913	0.281000	0.26958	7.695000	0.84257	2.251000	0.74343	0.533000	0.62120	AAA		0.473	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		G	202702942	T	G	202702942	3	3	58	1	0	0	0	0	1	0	0	0	8155	1792	62	4	1158	4	KDM5B	1	202702942	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	24313258	202702942	46547679	11	7657										
NEK2	4751	broad.mit.edu	37	chr1	211842487	211842487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cttctcttgctttgagagctCgctctcgctcctgtaactga	8	13	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:211842487C>T	ENST00000366999.4	-	6	1091	c.953G>A	c.(952-954)cGa>cAa	p.R318Q	NEK2_ENST00000366998.3_Missense_Mutation_p.R318Q|NEK2_ENST00000540251.1_Missense_Mutation_p.R275Q|NEK2_ENST00000462283.1_5'UTR	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	318	Interaction with PCNT.|Leucine-zipper.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)	p.R318Q(1)		breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TTTGAGAGCTCGCTCTCGCTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											209	220	216					1																	211842487		2203	4300	6503	209909110	SO:0001583	missense	4751			U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.953G>A	1.37:g.211842487C>T	ENSP00000355966:p.Arg318Gln		209909110	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.785519	0.31593	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.32023	1.47;1.47;1.47	4.76	-1.44	0.08856	.	0.572625	0.19593	N	0.110575	T	0.07683	0.0193	N	0.02158	-0.66	0.28095	N	0.931653	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.36456	-0.9747	10	0.06625	T	0.88	.	5.4603	0.16614	0.0:0.3886:0.1443:0.4671	.	318;318;318	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	Q	318;275;318	ENSP00000355966:R318Q;ENSP00000440237:R275Q;ENSP00000355965:R318Q	ENSP00000355965:R318Q	R	-	2	0	NEK2	209909110	0.000000	0.05858	0.968000	0.41197	0.926000	0.56050	-0.158000	0.10070	-0.075000	0.12798	-0.237000	0.12165	CGA		0.453	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		T	211842487	C	T	211842487	3	4	58	1	0	0	0	0	1	0	0	0	10355	884	31	1	396	1	NEK2	1	211842487	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9139545	211842487	37408134	12	7658										
DISP1	84976	broad.mit.edu	37	chr1	223177920	223177920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tccattatggggttgcctacCgcttggctccagatcccgac	10	14	0	1	rs371849402		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:223177920C>T	ENST00000284476.6	+	8	3345	c.3181C>T	c.(3181-3183)Cgc>Tgc	p.R1061C		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1061					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.R1061C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GGTTGCCTACCGCTTGGCTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	119	113	115		3181	5	1	1		115	0,8600		0,0,4300	no	missense	DISP1	NM_032890.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1061/1525	223177920	1,13005	2203	4300	6503	221244543	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3181C>T	1.37:g.223177920C>T	ENSP00000284476:p.Arg1061Cys		221244543	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278060	0.59758	2.27E-4	0.0	ENSG00000154309	ENST00000284476	D	0.85339	-1.97	5.95	5.03	0.67393	.	0.091610	0.85682	D	0.000000	D	0.84615	0.5511	M	0.67700	2.07	0.80722	D	1	B	0.26400	0.148	B	0.30179	0.112	T	0.81824	-0.0755	10	0.38643	T	0.18	-32.2348	15.4394	0.75171	0.0:0.9329:0.0:0.0671	.	1061	Q96F81	DISP1_HUMAN	C	1061	ENSP00000284476:R1061C	ENSP00000284476:R1061C	R	+	1	0	DISP1	221244543	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.716000	0.61916	1.503000	0.48686	0.491000	0.48974	CGC		0.582	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		T	223177920	C	T	223177920	3	4	58	1	0	0	0	0	1	0	0	0	4550	652	23	1	3207	1	DISP1	1	223177920	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	11335433	223177920	26072701	13	7659										
RYR2	6262	broad.mit.edu	37	chr1	237954780	237954780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gaatgttagccttatttgtcGcatttgctatcaatttcatc	6	8	2	0	rs397516510		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr1:237954780G>A	ENST00000366574.2	+	93	13845	c.13528G>A	c.(13528-13530)Gca>Aca	p.A4510T	RYR2_ENST00000360064.6_Missense_Mutation_p.A4516T|RYR2_ENST00000542537.1_Missense_Mutation_p.A4494T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4510			A -> T (in CPVT1). {ECO:0000269|PubMed:15466642}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.A4508T(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTTATTTGTCGCATTTGCTAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM043079	RYR2	M							208	181	189					1																	237954780		1844	4089	5933	236021403	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13528G>A	1.37:g.237954780G>A	ENSP00000355533:p.Ala4510Thr		236021403	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.036831	0.93630	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97089	-4.24;-4.24;-4.24	4.66	4.66	0.58398	Ryanodine Receptor TM 4-6 (1);	0.000000	0.56097	U	0.000037	D	0.98163	0.9393	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.99482	1.0948	10	0.87932	D	0	.	17.917	0.88954	0.0:0.0:1.0:0.0	.	4510	Q92736	RYR2_HUMAN	T	4510;4516;4494	ENSP00000355533:A4510T;ENSP00000353174:A4516T;ENSP00000443798:A4494T	ENSP00000353174:A4516T	A	+	1	0	RYR2	236021403	1.000000	0.71417	0.969000	0.41365	0.891000	0.51852	9.813000	0.99286	2.309000	0.77851	0.555000	0.69702	GCA		0.323	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237954780	G	A	237954780	3	1	58	1	0	0	0	0	1	0	0	0	13806	1087	38	1	13898	1	RYR2	1	237954780	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	14776860	237954780	11295841	14	7660										
TRIB2	28951	broad.mit.edu	37	chr2	12863517	12863517	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gtgttctttgagcgaagctaTggggacatgcattccttcgt	12	8	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:12863517T>C	ENST00000405331.3	+	2	472	c.402T>C	c.(400-402)taT>taC	p.Y134Y	TRIB2_ENST00000381465.2_5'UTR|TRIB2_ENST00000155926.4_Silent_p.Y134Y					tribbles pseudokinase 2									p.Y134Y(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AGCGAAGCTATGGGGACATGC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	2											113	96	102					2																	12863517		2203	4300	6503	12780968	SO:0001819	synonymous_variant	28951			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000405331.3:c.402T>C	2.37:g.12863517T>C			12780968		Silent	SNP	ENST00000405331.3	37																																																																																					0.522	TRIB2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000323585.1	NM_021643		C	12863517	T	C	12863517	2	2	58	1	0	0	0	0	0	0	0	1	16523	1471	51	4		4	TRIB2	2	12863517	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09		12863517	230335856	15	7661										
OSR1	130497	broad.mit.edu	37	chr2	19553321	19553321	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aaggcgggcagctggaagcgCgcatccaccaagctggacac	14	13	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:19553321C>T	ENST00000272223.2	-	2	590	c.246G>A	c.(244-246)gcG>gcA	p.A82A	OSR1_ENST00000536433.1_Silent_p.A82A	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	82					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A82A(1)		breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				GCTGGAAGCGCGCATCCACCA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	2											37	39	39					2																	19553321		2203	4300	6503	19416802	SO:0001819	synonymous_variant	130497			BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.246G>A	2.37:g.19553321C>T			19416802	B3KV97|D6W521	Silent	SNP	ENST00000272223.2	37	CCDS1694.1																																																																																				0.632	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		T	19553321	C	T	19553321	2	4	58	1	0	0	0	0	0	0	0	1	11324	755	27	1		1	OSR1	2	19553321	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	6689804	19553321	223646052	16	7662										
TSPYL6	388951	broad.mit.edu	37	chr2	54482114	54482114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctggctcccttaccaggcgaCgtctagctctatgggcgtct	11	14	3	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:54482114C>T	ENST00000317802.7	-	1	1295	c.1175G>A	c.(1174-1176)cGt>cAt	p.R392H	ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000394666.3_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	392					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.R392H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						TACCAGGCGACGTCTAGCTCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											73	80	78					2																	54482114		2146	4284	6430	54335618	SO:0001583	missense	388951			AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.1175G>A	2.37:g.54482114C>T	ENSP00000417919:p.Arg392His		54335618	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121605	0.37436	.	.	ENSG00000178021	ENST00000317802	T	0.24538	1.85	1.83	-3.09	0.05331	.	.	.	.	.	T	0.37433	0.1003	M	0.68317	2.08	0.09310	N	1	D	0.89917	1.0	D	0.65987	0.94	T	0.23190	-1.0195	9	0.62326	D	0.03	.	2.987	0.05971	0.2296:0.3162:0.0:0.4541	.	392	Q8N831	TSYL6_HUMAN	H	392	ENSP00000417919:R392H	ENSP00000417919:R392H	R	-	2	0	TSPYL6	54335618	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.487000	0.06505	-1.009000	0.03400	-0.469000	0.05056	CGT		0.527	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		T	54482114	C	T	54482114	3	4	58	1	0	0	0	0	1	0	0	0	16703	536	19	1	61	1	TSPYL6	2	54482114	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	34928793	54482114	188717259	17	7663										
PLEK	5341	broad.mit.edu	37	chr2	68609685	68609685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tctgtgcagtgccttatattTgtccatgaaagacactgaaa	8	8	1	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:68609685T>C	ENST00000234313.7	+	4	571	c.392T>C	c.(391-393)tTg>tCg	p.L131S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	131					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.L131S(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		GCCTTATATTTGTCCATGAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	93	91					2																	68609685		2203	4300	6503	68463189	SO:0001583	missense	5341			X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.392T>C	2.37:g.68609685T>C	ENSP00000234313:p.Leu131Ser		68463189	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	T	3.237	-0.156247	0.06544	.	.	ENSG00000115956	ENST00000234313	T	0.19250	2.16	5.42	5.42	0.78866	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.577827	0.17755	N	0.163086	T	0.15349	0.0370	L	0.36672	1.1	0.30844	N	0.735329	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.15521	-1.0434	10	0.09084	T	0.74	.	10.9229	0.47176	0.14:0.0:0.0:0.86	.	149;131	Q59GZ2;P08567	.;PLEK_HUMAN	S	131	ENSP00000234313:L131S	ENSP00000234313:L131S	L	+	2	0	PLEK	68463189	0.731000	0.28111	1.000000	0.80357	0.986000	0.74619	2.146000	0.42216	2.181000	0.69327	0.496000	0.49642	TTG		0.363	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		C	68609685	T	C	68609685	3	2	58	1	0	0	0	0	1	0	0	0	12084	1821	63	4	406	4	PLEK	2	68609685	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	14127571	68609685	174589688	18	7664										
SEMA4F	10505	broad.mit.edu	37	chr2	74902749	74902749	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccacagccagttgagaacatGaaattgtaccacgtgagttg	10	9	0	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:74902749G>T	ENST00000357877.2	+	11	1619	c.1470G>T	c.(1468-1470)atG>atT	p.M490I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.M335I|SEMA4F_ENST00000473350.1_3'UTR	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	490	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.M490I(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TTGAGAACATGAAATTGTACC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	91	95					2																	74902749		2203	4300	6503	74756257	SO:0001583	missense	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1470G>T	2.37:g.74902749G>T	ENSP00000350547:p.Met490Ile		74756257	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.758270	0.31137	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.32023	1.47;1.47	4.5	3.58	0.41010	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.129054	0.51477	D	0.000093	T	0.17916	0.0430	N	0.12887	0.27	0.34285	D	0.682588	B;B	0.14012	0.003;0.009	B;B	0.15052	0.007;0.012	T	0.15983	-1.0418	10	0.46703	T	0.11	.	12.2822	0.54771	0.0:0.1859:0.814:0.0	.	335;490	O95754-2;O95754	.;SEM4F_HUMAN	I	490;335	ENSP00000350547:M490I;ENSP00000342675:M335I	ENSP00000342675:M335I	M	+	3	0	SEMA4F	74756257	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.936000	0.40183	2.333000	0.79357	0.467000	0.42956	ATG		0.512	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		T	74902749	G	T	74902749	3	4	58	1	0	0	0	0	1	0	0	0	14072	1290	45	2	1512	2	SEMA4F	2	74902749	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	6293064	74902749	168296624	19	7665										
ZC3H8	84524	broad.mit.edu	37	chr2	112991733	112991733	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcaagaaaatatttacaaatTtgttttcccttgcgttccac	4	9	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:112991733T>C	ENST00000409573.2	-	5	714	c.585A>G	c.(583-585)caA>caG	p.Q195Q	ZC3H8_ENST00000272570.5_Silent_p.Q195Q|ZC3H8_ENST00000476902.1_5'Flank			Q8N5P1	ZC3H8_HUMAN	zinc finger CCCH-type containing 8	195					apoptotic process (GO:0006915)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to antibiotic (GO:0046677)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|T cell homeostasis (GO:0043029)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q195Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	7						ATTTACAAATTTGTTTTCCCT	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	2											80	71	74					2																	112991733		1831	4083	5914	112708204	SO:0001819	synonymous_variant	84524			AF334161	CCDS46392.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000144161	ENSG00000144161		"Zinc fingers, CCCH-type domain containing"	30941	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 8"	ZC3HDC8		12477932	Standard	NM_032494		Approved	Fliz1	uc021vmw.1	Q8N5P1	OTTHUMG00000153270	ENST00000409573.2:c.585A>G	2.37:g.112991733T>C			112708204	Q9BZ75	Silent	SNP	ENST00000409573.2	37	CCDS46392.1																																																																																				0.308	ZC3H8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330521.3	NM_032494		C	112991733	T	C	112991733	2	2	58	1	0	0	0	0	0	0	0	1	17613	1838	64	4		4	ZC3H8	2	112991733	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09	38088984	112991733	130207640	20	7666										
UGGT1	56886	broad.mit.edu	37	chr2	128914868	128914868	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aactttttggattgttggggAttttgatagcccttctggac	11	6	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:128914868A>G	ENST00000259253.6	+	22	2350	c.2303A>G	c.(2302-2304)gAt>gGt	p.D768G	UGGT1_ENST00000375990.3_Missense_Mutation_p.D744G	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	768					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.D768G(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ATTGTTGGGGATTTTGATAGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											154	144	148					2																	128914868		2203	4300	6503	128631338	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.2303A>G	2.37:g.128914868A>G	ENSP00000259253:p.Asp768Gly		128631338	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.853066	0.91355	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.28069	1.63;1.63	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.59985	0.2234	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.63844	-0.6545	9	.	.	.	.	16.2962	0.82776	1.0:0.0:0.0:0.0	.	744;768	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	G	744;768	ENSP00000365158:D744G;ENSP00000259253:D768G	.	D	+	2	0	UGGT1	128631338	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.691000	0.91279	2.304000	0.77564	0.528000	0.53228	GAT		0.373	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		G	128914868	A	G	128914868	3	3	58	1	0	0	0	0	1	0	0	0	16981	333	12	4	2389	4	UGGT1	2	128914868	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	15923135	128914868	114284505	21	7667										
LRP1B	53353	broad.mit.edu	37	chr2	141243076	141243076	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	acagcaagtgcattggggacCgctgtgttatgaactaccta	11	9	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:141243076C>T	ENST00000389484.3	-	59	10232	c.9261G>A	c.(9259-9261)gcG>gcA	p.A3087A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3087					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.A3087A(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CATTGGGGACCGCTGTGTTAT	0.368										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - coding silent(1)	large_intestine(1)	2											105	97	100					2																	141243076		2203	4300	6503	140959546	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.9261G>A	2.37:g.141243076C>T			140959546	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.368	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141243076	C	T	141243076	2	4	58	1	0	0	0	0	0	0	0	1	8984	639	23	1		1	LRP1B	2	141243076	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	12328208	141243076	101956297	22	7668										
SCN7A	6332	broad.mit.edu	37	chr2	167300022	167300022	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	attctacttaccatcctgaaTaatcgaagaagagccattcc	5	11	1	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:167300022T>A	ENST00000409855.1	-	13	1917	c.1791A>T	c.(1789-1791)ttA>ttT	p.L597F		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	597					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.L597F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CCATCCTGAATAATCGAAGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	55	56					2																	167300022		1835	4088	5923	167008268	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1791A>T	2.37:g.167300022T>A	ENSP00000386796:p.Leu597Phe		167008268		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.587440	0.28268	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.98792	-5.14;-5.14	4.87	2.51	0.30379	Ion transport (1);	2.578750	0.01291	N	0.010005	D	0.97445	0.9164	L	0.36672	1.1	0.09310	N	1	P	0.37612	0.602	P	0.45377	0.478	D	0.93604	0.6933	10	0.62326	D	0.03	.	5.1412	0.14959	0.0:0.0936:0.3665:0.5398	.	597	Q01118	SCN7A_HUMAN	F	597	ENSP00000386796:L597F;ENSP00000413699:L597F	ENSP00000259060:L597F	L	-	3	2	SCN7A	167008268	0.000000	0.05858	0.124000	0.21820	0.588000	0.36517	-1.382000	0.02546	0.965000	0.38133	0.482000	0.46254	TTA		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167300022	T	A	167300022	3	1	58	1	0	0	0	0	1	0	0	0	13960	1403	49	5	3309	5	SCN7A	2	167300022	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	26056946	167300022	75899351	23	7669										
C2orf77	129881	broad.mit.edu	37	chr2	170502570	170502570	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttgttgtttccgattcaagTtcaattacctctctggcata	6	9	3	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:170502570T>C	ENST00000447353.1	-	9	1545	c.1440A>G	c.(1438-1440)gaA>gaG	p.E480E		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	480								p.E474E(1)									CCGATTCAAGTTCAATTACCT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	2											208	208	208					2																	170502570		1859	4085	5944	170210816	SO:0001819	synonymous_variant	129881			BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"hypothetical LOC129881"		"chromosome 2 open reading frame 77"	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.1440A>G	2.37:g.170502570T>C			170210816	Q6PJF6	Silent	SNP	ENST00000447353.1	37	CCDS46445.1																																																																																				0.418	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		C	170502570	T	C	170502570	2	2	58	1	0	0	0	0	0	0	0	1	2200	1722	60	4		4	C2orf77	2	170502570	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09	3202548	170502570	72696803	24	7670										
HOXD9	3235	broad.mit.edu	37	chr2	176988158	176988159	+	Frame_Shift_Ins	INS	-	-	G													0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gagaaggcggcagcggcgacINSggggggaaccgggcctgggg					rs535219899		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:176988158_176988159insG	ENST00000249499.6	+	1	1071_1072	c.662_663insG	c.(661-666)acggggfs	p.TG221fs	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	221				AATGGT -> GGDGGN (in Ref. 1; CAA42016). {ECO:0000305}.	adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T214fs*48(1)		endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GCAGCGGCGACGGGGGGAACCG	0.718																																					GBM(47;924 952 7959 9248 12176)											1	Insertion - Frameshift(1)	large_intestine(1)	2																																								176696405	SO:0001589	frameshift_variant	3235				CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"Homeoboxes / ANTP class : HOXL subclass"	5140	protein-coding gene	gene with protein product		142982	"homeo box D9"	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.668dupG	2.37:g.176988164_176988164dupG	ENSP00000249499:p.Thr221fs		176696404	Q86ST1	Frame_Shift_Ins	INS	ENST00000249499.6	37	CCDS2267.2																																																																																				0.718	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			G	176988159	-	G	176988158	7	5	58	1	0	1	1	0	0	0	0	0	7347	536	19	0	664	0	HOXD9	2	176988158	Frame_Shift_Ins	INS	-	TCGA-AG-4007-01A-01W-1073-09	6485588	176988158	66211215	25	7671										
TTN	7273	broad.mit.edu	37	chr2	179586845	179586845	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	acaggcttgatgtcaaagaaGggagatttcttgggttctgg	14	5	3	3	rs373496180		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:179586845G>T	ENST00000591111.1	-	76	21818	c.21594C>A	c.(21592-21594)ccC>ccA	p.P7198P	RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Silent_p.P6271P|TTN_ENST00000589042.1_Silent_p.P7515P|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12766	Ig-like 54.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P6271P(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTCAAAGAAGGGAGATTTCT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											171	162	165					2																	179586845		1909	4118	6027	179295090	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.21594C>A	2.37:g.179586845G>T			179295090	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179586845	G	T	179586845	2	4	58	1	0	0	0	0	0	0	0	1	16775	987	35	2		2	TTN	2	179586845	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	2598687	179586845	63612528	26	7672										
ZC3H15	55854	broad.mit.edu	37	chr2	187373395	187373395	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgttcctgttgatgaaaatCttttcactggagaggatttg	10	6	2	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:187373395C>G	ENST00000337859.6	+	10	1443	c.1216C>G	c.(1216-1218)Ctt>Gtt	p.L406V		NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	406					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.L406V(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TGATGAAAATCTTTTCACTGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	127	127					2																	187373395		1861	4112	5973	187081640	SO:0001583	missense	55854				CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"Zinc fingers, CCCH-type domain containing"	29528	protein-coding gene	gene with protein product	"likely ortholog of mouse immediate early response, erythropoietin 4"					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.1216C>G	2.37:g.187373395C>G	ENSP00000338788:p.Leu406Val		187081640	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	37	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804340	0.90623	.	.	ENSG00000065548	ENST00000337859	T	0.44482	0.92	5.81	5.81	0.92471	.	0.192112	0.44902	N	0.000403	T	0.64649	0.2617	M	0.75777	2.31	0.80722	D	1	D	0.67145	0.996	P	0.60473	0.875	T	0.66897	-0.5807	10	0.87932	D	0	-7.0391	20.066	0.97704	0.0:1.0:0.0:0.0	.	406	Q8WU90	ZC3HF_HUMAN	V	406	ENSP00000338788:L406V	ENSP00000338788:L406V	L	+	1	0	ZC3H15	187081640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.405000	0.80007	2.730000	0.93505	0.650000	0.86243	CTT		0.403	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		G	187373395	C	G	187373395	3	3	58	1	0	0	0	0	1	0	0	0	17606	913	32	5	1254	5	ZC3H15	2	187373395	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	7786550	187373395	55825978	27	7673										
CTLA4	1493	broad.mit.edu	37	chr2	204736159	204736159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	atccttgcagcagttagttcGgggttgtttttttatagctt	10	6	0	0	rs375949600		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:204736159G>A	ENST00000302823.3	+	3	673	c.516G>A	c.(514-516)tcG>tcA	p.S172S	CTLA4_ENST00000472206.1_Intron|CTLA4_ENST00000427473.2_Intron|CTLA4_ENST00000487393.1_Intron|CTLA4_ENST00000295854.6_Intron	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	172					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.S172S(1)		large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	CAGTTAGTTCGGGGTTGTTTT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G	,	2,4404	4.2+/-10.8	0,2,2201	199	188	192		,516	-10.8	0.6	2		192	0,8600		0,0,4300	no	intron,coding-synonymous	CTLA4	NM_001037631.2,NM_005214.4	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	,172/224	204736159	2,13004	2203	4300	6503	204444404	SO:0001819	synonymous_variant	1493				CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.516G>A	2.37:g.204736159G>A			204444404	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Silent	SNP	ENST00000302823.3	37	CCDS2362.1																																																																																				0.468	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		A	204736159	G	A	204736159	2	1	58	1	0	0	0	0	0	0	0	1	4017	1103	39	1		1	CTLA4	2	204736159	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	17362764	204736159	38463214	28	7674										
ZDBF2	57683	broad.mit.edu	37	chr2	207174525	207174525	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gtgtgctccccctcttccatCtgatactgatcagcctcaag	7	15	4	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:207174525C>A	ENST00000374423.3	+	5	5659	c.5273C>A	c.(5272-5274)tCt>tAt	p.S1758Y		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1758							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S1758Y(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CCTCTTCCATCTGATACTGAT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	2											59	58	58					2																	207174525		1865	4096	5961	206882770	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5273C>A	2.37:g.207174525C>A	ENSP00000363545:p.Ser1758Tyr		206882770	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.413534	0.42817	.	.	ENSG00000204186	ENST00000374423	T	0.59364	0.27	4.84	1.5	0.22942	.	.	.	.	.	T	0.49745	0.1575	L	0.53249	1.67	0.09310	N	1	P	0.46512	0.879	B	0.41691	0.364	T	0.41840	-0.9486	9	0.87932	D	0	.	6.3204	0.21215	0.0:0.5041:0.2998:0.1961	.	1758	Q9HCK1	ZDBF2_HUMAN	Y	1758	ENSP00000363545:S1758Y	ENSP00000363545:S1758Y	S	+	2	0	ZDBF2	206882770	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.021000	0.12504	0.090000	0.17273	0.650000	0.86243	TCT		0.398	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207174525	C	A	207174525	3	1	58	1	0	0	0	0	1	0	0	0	17638	913	32	2	5283	2	ZDBF2	2	207174525	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	2438366	207174525	36024848	29	7675										
TMEM169	92691	broad.mit.edu	37	chr2	216964670	216964670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gaacctgcctctggacagccGctacgtcaccttaactggga	10	14	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:216964670G>A	ENST00000295658.4	+	3	506	c.299G>A	c.(298-300)cGc>cAc	p.R100H	TMEM169_ENST00000406027.2_Missense_Mutation_p.R100H|TMEM169_ENST00000454545.1_Missense_Mutation_p.R100H|TMEM169_ENST00000437356.2_Missense_Mutation_p.R100H	NM_001142311.1|NM_001142312.1|NM_138390.3	NP_001135783.1|NP_001135784.1|NP_612399.1	Q96HH4	TM169_HUMAN	transmembrane protein 169	100						integral component of membrane (GO:0016021)		p.R100H(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)	13		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGACAGCCGCTACGTCACC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											170	159	163					2																	216964670		2203	4300	6503	216672915	SO:0001583	missense	92691			AK091582	CCDS2401.1	2q35	2008-02-05			ENSG00000163449	ENSG00000163449			25130	protein-coding gene	gene with protein product						12477932	Standard	NM_001142310		Approved	FLJ34263	uc002vfv.4	Q96HH4	OTTHUMG00000133053	ENST00000295658.4:c.299G>A	2.37:g.216964670G>A	ENSP00000295658:p.Arg100His		216672915	B2R8W6	Missense_Mutation	SNP	ENST00000295658.4	37	CCDS2401.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543629	0.86022	.	.	ENSG00000163449	ENST00000433112;ENST00000454545;ENST00000437356;ENST00000295658;ENST00000455479;ENST00000406027	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.59445	0.2194	M	0.63843	1.955	0.58432	D	0.999997	P	0.49559	0.925	B	0.43052	0.406	T	0.67122	-0.5750	9	0.66056	D	0.02	-8.7	17.308	0.87200	0.0:0.0:1.0:0.0	.	100	Q96HH4	TM169_HUMAN	H	100	.	ENSP00000295658:R100H	R	+	2	0	TMEM169	216672915	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.761000	0.85260	2.550000	0.86006	0.655000	0.94253	CGC		0.522	TMEM169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256666.2	NM_138390		A	216964670	G	A	216964670	3	1	58	1	0	0	0	0	1	0	0	0	16123	1087	38	1	305	1	TMEM169	2	216964670	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	9790145	216964670	26234703	30	7676										
GMPPA	29926	broad.mit.edu	37	chr2	220366585	220366585	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ggggacaggtacctgcaggaAtttgcccccctaggcacagg	14	12	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:220366585A>C	ENST00000358215.3	+	5	624	c.255A>C	c.(253-255)gaA>gaC	p.E85D	AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000341142.3_Missense_Mutation_p.E85D|GMPPA_ENST00000313597.5_Missense_Mutation_p.E85D|GMPPA_ENST00000373908.1_Missense_Mutation_p.E85D|GMPPA_ENST00000373917.3_Missense_Mutation_p.E85D	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	85					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)	p.E85D(1)|p.I17L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		ACCTGCAGGAATTTGCCCCCC	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	2											71	67	68					2																	220366585		2203	4300	6503	220074829	SO:0001583	missense	29926			AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.255A>C	2.37:g.220366585A>C	ENSP00000350949:p.Glu85Asp		220074829	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	37	CCDS2441.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.45|19.45	3.829544|3.829544	0.71258|0.71258	.|.	.|.	ENSG00000144591|ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000455657;ENST00000435316;ENST00000341142|ENST00000373924	T;T;T;T;T;T;T|.	0.77098|.	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07|.	4.68|4.68	0.95|0.95	0.19572|0.19572	Nucleotidyl transferase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75206|0.75206	0.3818|0.3818	M|M	0.89095|0.89095	3.005|3.005	0.58432|0.58432	D|D	0.999992|0.999992	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.997;0.999|.	T|T	0.75199|0.75199	-0.3402|-0.3402	10|6	0.87932|0.87932	D|D	0|0	-35.3195|-35.3195	8.405|8.405	0.32610|0.32610	0.6583:0.0:0.3417:0.0|0.6583:0.0:0.3417:0.0	.|.	85;85|.	Q96IJ6-2;Q96IJ6|.	.;GMPPA_HUMAN|.	D|L	85;85;85;85;85;50;85|17	ENSP00000315925:E85D;ENSP00000363027:E85D;ENSP00000350949:E85D;ENSP00000363016:E85D;ENSP00000392465:E85D;ENSP00000411060:E50D;ENSP00000340760:E85D|.	ENSP00000315925:E85D|ENSP00000363034:I17L	E|I	+|+	3|1	2|0	GMPPA|GMPPA	220074829|220074829	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	1.069000|1.069000	0.30641|0.30641	0.172000|0.172000	0.19760|0.19760	0.459000|0.459000	0.35465|0.35465	GAA|ATT		0.592	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		C	220366585	A	C	220366585	3	2	58	1	0	0	0	0	1	0	0	0	6514	98	4	4	269	4	GMPPA	2	220366585	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	3401915	220366585	22832788	31	7677										
KCNE4	23704	broad.mit.edu	37	chr2	223917943	223917943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gagctccgagtcctcctcccCggacgtgcacctcaccattc	8	19	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:223917943C>T	ENST00000281830.3	+	2	879	c.548C>T	c.(547-549)cCg>cTg	p.P183L	KCNE4_ENST00000488477.2_Intron|KCNE4_ENST00000604125.1_Missense_Mutation_p.P132L			Q8WWG9	KCNE4_HUMAN	potassium voltage-gated channel, Isk-related family, member 4	183						apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	voltage-gated potassium channel activity (GO:0005249)	p.P132L(1)		large_intestine(2)|lung(5)|ovary(2)|skin(1)	10		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCCTCCTCCCCGGACGTGCAC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	2											41	43	42					2																	223917943		2203	4300	6503	223626187	SO:0001583	missense	23704			AY065987	CCDS2456.1, CCDS2456.2	2q36.1	2008-02-05			ENSG00000152049	ENSG00000152049		"Potassium channels"	6244	protein-coding gene	gene with protein product		607775				10219239, 12670483	Standard	NM_080671		Approved	MiRP3	uc002vnl.5	Q8WWG9	OTTHUMG00000133161	ENST00000281830.3:c.548C>T	2.37:g.223917943C>T	ENSP00000281830:p.Pro183Leu		223626187	B7Z275|Q53SM4|Q96CC4	Missense_Mutation	SNP	ENST00000281830.3	37		.	.	.	.	.	.	.	.	.	.	C	27.0	4.794290	0.90453	.	.	ENSG00000152049	ENST00000281830	.	.	.	6.17	6.17	0.99709	.	0.054288	0.85682	D	0.000000	T	0.39655	0.1086	N	0.24115	0.695	0.80722	D	1	P	0.44659	0.84	B	0.31390	0.129	T	0.45818	-0.9235	9	0.72032	D	0.01	-16.3701	20.8794	0.99867	0.0:1.0:0.0:0.0	.	132	Q8WWG9	KCNE4_HUMAN	L	132	.	ENSP00000281830:P132L	P	+	2	0	KCNE4	223626187	1.000000	0.71417	0.845000	0.33349	0.953000	0.61014	7.342000	0.79310	2.941000	0.99782	0.655000	0.94253	CCG		0.652	KCNE4-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000330997.2	NM_080671		T	223917943	C	T	223917943	3	4	58	1	0	0	0	0	1	0	0	0	8046	652	23	1	397	1	KCNE4	2	223917943	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	3551358	223917943	19281430	32	7678										
SP140L	93349	broad.mit.edu	37	chr2	231264877	231264877	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gagtgtgaggtgtgccgggaCggaggggagctgttctgttg	21	5	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr2:231264877C>T	ENST00000415673.2	+	15	1319	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D	SP140L_ENST00000243810.6_Silent_p.D411D|SP140L_ENST00000396563.4_Silent_p.D376D|SP140L_ENST00000444636.1_Silent_p.D411D	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	411						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D411D(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						TGTGCCGGGACGGAGGGGAGC	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	2											188	194	192					2																	231264877		2072	4228	6300	230973121	SO:0001819	synonymous_variant	93349			BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1233C>T	2.37:g.231264877C>T			230973121	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																				0.527	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		T	231264877	C	T	231264877	2	4	58	1	0	0	0	0	0	0	0	1	15000	535	19	1		1	SP140L	2	231264877	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	7346934	231264877	11934496	33	7679										
GRM7	2917	broad.mit.edu	37	chr3	7721970	7721970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	agaccgagctctgtgaaaacGtagacccaaacagtaagtaa	9	9	1	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:7721970G>A	ENST00000357716.4	+	9	2960	c.2686G>A	c.(2686-2688)Gta>Ata	p.V896I	GRM7_ENST00000402647.2_Missense_Mutation_p.V896I|GRM7_ENST00000403881.1_Missense_Mutation_p.V896I|GRM7_ENST00000389336.4_Missense_Mutation_p.V896I|GRM7_ENST00000486284.1_Missense_Mutation_p.V896I	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	896					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.V896I(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CTGTGAAAACGTAGACCCAAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											100	69	79					3																	7721970		2203	4300	6503	7696970	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2686G>A	3.37:g.7721970G>A	ENSP00000350348:p.Val896Ile		7696970	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966329	0.53507	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647	D;D;D;D;D	0.89196	-2.44;-2.48;-2.48;-2.48;-2.48	5.07	5.07	0.68467	.	0.330029	0.32819	N	0.005617	T	0.82111	0.4966	L	0.36672	1.1	0.32604	N	0.525576	B;P;B;P	0.40681	0.44;0.66;0.313;0.727	B;B;B;B	0.32393	0.026;0.055;0.011;0.145	D	0.84142	0.0418	10	0.23891	T	0.37	.	17.3817	0.87406	0.0:0.0:1.0:0.0	.	896;651;896;896	Q14831-5;Q59G95;Q14831;Q14831-2	.;.;GRM7_HUMAN;.	I	896	ENSP00000350348:V896I;ENSP00000417536:V896I;ENSP00000373987:V896I;ENSP00000385664:V896I;ENSP00000384585:V896I	ENSP00000350348:V896I	V	+	1	0	GRM7	7696970	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	3.919000	0.56439	2.509000	0.84616	0.591000	0.81541	GTA		0.512	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		A	7721970	G	A	7721970	3	1	58	1	0	0	0	0	1	0	0	0	6823	1145	40	1	2720	1	GRM7	3	7721970	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		7721970	190300460	34	7680										
UBE2E2	7325	broad.mit.edu	37	chr3	23541106	23541106	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgtcttatttcagtgctggaCccaaaggagacaacatttat	8	8	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:23541106C>A	ENST00000396703.1	+	4	415	c.235C>A	c.(235-237)Ccc>Acc	p.P79T	UBE2E2_ENST00000425792.1_Missense_Mutation_p.P79T	NM_152653.3	NP_689866.1	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2	79					ISG15-protein conjugation (GO:0032020)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)		ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)	p.P79T(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(2)	10						CAGTGCTGGACCCAAAGGAGA	0.373																																					GBM(85;1941 2083 9456)											1	Substitution - Missense(1)	large_intestine(1)	3											100	94	96					3																	23541106		2203	4300	6503	23516110	SO:0001583	missense	7325			AK057886	CCDS2637.1	3p24.2	2011-05-19	2011-05-19		ENSG00000182247	ENSG00000182247		"Ubiquitin-conjugating enzymes E2"	12478	protein-coding gene	gene with protein product		602163	"ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)"			9371400	Standard	NM_152653		Approved	UbcH8, FLJ25157	uc003ccg.2	Q96LR5	OTTHUMG00000130482	ENST00000396703.1:c.235C>A	3.37:g.23541106C>A	ENSP00000379931:p.Pro79Thr		23516110		Missense_Mutation	SNP	ENST00000396703.1	37	CCDS2637.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.795097	0.90453	.	.	ENSG00000182247	ENST00000425792;ENST00000452894;ENST00000396703	T;T;T	0.59638	0.25;0.25;0.25	5.84	5.84	0.93424	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000002	D	0.82728	0.5100	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86096	0.1553	10	0.87932	D	0	.	19.7502	0.96265	0.0:1.0:0.0:0.0	.	79	Q96LR5	UB2E2_HUMAN	T	79;103;79	ENSP00000401053:P79T;ENSP00000392800:P103T;ENSP00000379931:P79T	ENSP00000379931:P79T	P	+	1	0	UBE2E2	23516110	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.783000	0.85696	2.760000	0.94817	0.655000	0.94253	CCC		0.373	UBE2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252881.2	NM_152653		A	23541106	C	A	23541106	3	1	58	1	0	0	0	0	1	0	0	0	16893	507	18	2	245	2	UBE2E2	3	23541106	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	15819136	23541106	174481324	35	7681										
SCN5A	6331	broad.mit.edu	37	chr3	38601826	38601826	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cttccccgcaaagaggttcaCgcccatgatgctgaagatga	10	12	1	5	rs199473233		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:38601826C>T	ENST00000333535.4	-	23	4206	c.4057G>A	c.(4057-4059)Gtg>Atg	p.V1353M	SCN5A_ENST00000449557.2_Missense_Mutation_p.V1299M|SCN5A_ENST00000451551.2_Missense_Mutation_p.V1299M|SCN5A_ENST00000413689.1_Missense_Mutation_p.V1353M|SCN5A_ENST00000423572.2_Missense_Mutation_p.V1352M|SCN5A_ENST00000414099.2_Missense_Mutation_p.V1353M|SCN5A_ENST00000455624.2_Missense_Mutation_p.V1352M|SCN5A_ENST00000443581.1_Missense_Mutation_p.V1352M|SCN5A_ENST00000450102.2_Missense_Mutation_p.V1299M|SCN5A_ENST00000425664.1_Missense_Mutation_p.V1353M			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1353					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.V1353M(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	AAGAGGTTCACGCCCATGATG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	111	112					3																	38601826		2203	4300	6503	38576830	SO:0001583	missense	6331			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.4057G>A	3.37:g.38601826C>T	ENSP00000328968:p.Val1353Met		38576830	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676898	0.88445	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.98493	-4.96;-4.96;-4.96;-4.96;-4.96;-4.96;-4.96;-4.96;-4.96;-4.96	4.25	4.25	0.50352	Ion transport (1);	0.067398	0.64402	D	0.000014	D	0.99089	0.9687	M	0.89785	3.06	0.58432	D	0.999997	D;D;D;D;D;D;D	0.89917	0.998;1.0;0.987;0.989;1.0;0.995;0.987	D;D;P;P;D;D;P	0.91635	0.937;0.999;0.782;0.861;0.984;0.928;0.643	D	0.99338	1.0911	10	0.87932	D	0	.	17.2234	0.86963	0.0:1.0:0.0:0.0	.	1299;1352;1353;1353;1353;1352;1353	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	M	1353;1352;1353;1299;1352;1353;1353;1352;1299;1299	ENSP00000398962:V1353M;ENSP00000398266:V1352M;ENSP00000410257:V1353M;ENSP00000388797:V1299M;ENSP00000397915:V1352M;ENSP00000416634:V1353M;ENSP00000328968:V1353M;ENSP00000399524:V1352M;ENSP00000403355:V1299M;ENSP00000413996:V1299M	ENSP00000328968:V1353M	V	-	1	0	SCN5A	38576830	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.575000	0.82447	2.355000	0.79922	0.655000	0.94253	GTG		0.547	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38601826	C	T	38601826	3	4	58	1	0	0	0	0	1	0	0	0	13959	536	19	1	2017	1	SCN5A	3	38601826	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	15060720	38601826	159420604	36	7682										
GRM2	2912	broad.mit.edu	37	chr3	51750037	51750037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cgctttatgccttcaagactCgcaagtgccccgaaaacttc	7	14	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:51750037C>T	ENST00000395052.3	+	4	2482	c.2248C>T	c.(2248-2250)Cgc>Tgc	p.R750C	GRM2_ENST00000442933.2_Missense_Mutation_p.R472C|GRM2_ENST00000475478.1_3'UTR	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	750					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.R750C(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CTTCAAGACTCGCAAGTGCCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	89	96					3																	51750037		2203	4300	6503	51725077	SO:0001583	missense	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.2248C>T	3.37:g.51750037C>T	ENSP00000378492:p.Arg750Cys		51725077	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512621	0.27123	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.91521	-2.86;-2.86	5.08	4.17	0.49024	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96741	0.8936	H	0.96833	3.89	0.27273	N	0.958325	D	0.89917	1.0	D	0.97110	1.0	D	0.92061	0.5656	10	0.87932	D	0	.	13.1596	0.59537	0.2896:0.7104:0.0:0.0	.	750	Q14416	GRM2_HUMAN	C	750;472	ENSP00000378492:R750C;ENSP00000408906:R472C	ENSP00000378492:R750C	R	+	1	0	GRM2	51725077	0.943000	0.32029	0.955000	0.39395	0.553000	0.35397	1.173000	0.31920	1.213000	0.43380	0.549000	0.68633	CGC		0.547	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51750037	C	T	51750037	3	4	58	1	0	0	0	0	1	0	0	0	6818	884	31	1	2258	1	GRM2	3	51750037	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	13148211	51750037	146272393	37	7683										
RRP9	9136	broad.mit.edu	37	chr3	51972119	51972119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccactggctcaccttgctgaCggagctgctctaggtagagc	12	13	2	2	rs374405922		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:51972119C>T	ENST00000232888.6	-	3	345	c.272G>A	c.(271-273)cGt>cAt	p.R91H		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	91	Glu-rich.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.R91H(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		ACCTTGCTGACGGAGCTGCTC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	HIS/ARG	0,4406		0,0,2203	76	59	65		272	2.6	1	3		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	RRP9	NM_004704.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	91/476	51972119	1,13005	2203	4300	6503	51947159	SO:0001583	missense	9136			AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"WD repeat domain containing"	16829	protein-coding gene	gene with protein product			"RNA, U3 small nucleolar interacting protein 2"	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.272G>A	3.37:g.51972119C>T	ENSP00000232888:p.Arg91His		51947159	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039752	0.55003	0.0	1.16E-4	ENSG00000114767	ENST00000232888	T	0.56275	0.47	5.34	2.6	0.31112	.	0.207680	0.48286	D	0.000195	T	0.46249	0.1383	L	0.45581	1.43	0.32210	N	0.576657	P	0.49696	0.927	P	0.44732	0.459	T	0.57225	-0.7848	10	0.66056	D	0.02	-23.5166	8.6788	0.34196	0.0:0.7114:0.0:0.2885	.	91	O43818	U3IP2_HUMAN	H	91	ENSP00000232888:R91H	ENSP00000232888:R91H	R	-	2	0	RRP9	51947159	0.247000	0.23920	0.952000	0.39060	0.861000	0.49209	1.464000	0.35288	0.259000	0.21709	0.563000	0.77884	CGT		0.627	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704		T	51972119	C	T	51972119	3	4	58	1	0	0	0	0	1	0	0	0	13728	536	19	1	1207	1	RRP9	3	51972119	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	222082	51972119	146050311	38	7684										
ROBO1	6091	broad.mit.edu	37	chr3	78796020	78796020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctactgcaaccatgacatccGaagggttttgtctgaagtca	9	10	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:78796020G>A	ENST00000464233.1	-	5	643	c.530C>T	c.(529-531)tCg>tTg	p.S177L	ROBO1_ENST00000436010.2_Missense_Mutation_p.S138L|ROBO1_ENST00000495273.1_Missense_Mutation_p.S138L|ROBO1_ENST00000467549.1_Missense_Mutation_p.S138L	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	177	Ig-like C2-type 2.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.S177*(2)|p.S177L(1)|p.S138*(1)|p.S154*(1)|p.S154L(1)|p.S138L(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CATGACATCCGAAGGGTTTTG	0.458																																																7	Substitution - Nonsense(4)|Substitution - Missense(3)	lung(4)|large_intestine(3)	3											103	100	101					3																	78796020		1914	4136	6050	78878710	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.530C>T	3.37:g.78796020G>A	ENSP00000420321:p.Ser177Leu		78878710	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440972	0.43326	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.83	5.83	0.93111	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.163360	0.56097	D	0.000030	T	0.57286	0.2043	L	0.28504	0.86	0.50171	D	0.999852	P;B;P;P	0.37276	0.589;0.438;0.589;0.534	B;B;B;B	0.35550	0.205;0.205;0.205;0.13	T	0.53655	-0.8408	9	.	.	.	.	20.1133	0.97917	0.0:0.0:1.0:0.0	.	177;138;138;138	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	L	138;138;177;138;138;177	ENSP00000406043:S138L;ENSP00000420321:S177L;ENSP00000420637:S138L;ENSP00000417992:S138L	.	S	-	2	0	ROBO1	78878710	1.000000	0.71417	0.998000	0.56505	0.179000	0.23085	6.669000	0.74462	2.762000	0.94881	0.591000	0.81541	TCG		0.458	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78796020	G	A	78796020	3	1	58	1	0	0	0	0	1	0	0	0	13550	1059	37	1	4546	1	ROBO1	3	78796020	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	26823901	78796020	119226410	39	7685										
SRPRB	58477	broad.mit.edu	37	chr3	133538462	133538462	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cagttccagcactgcccctgCtcagctggggaagaaaggca	12	13	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:133538462C>A	ENST00000466490.2	+	8	953	c.668C>A	c.(667-669)gCt>gAt	p.A223D		NM_021203.3	NP_067026.3	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, B subunit	223					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|small GTPase mediated signal transduction (GO:0007264)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)	p.A223D(1)		breast(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(2)	12						ACTGCCCCTGCTCAGCTGGGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											64	68	67					3																	133538462		2203	4300	6503	135021152	SO:0001583	missense	58477			AK075531	CCDS3081.1	3q22.1	2004-01-29			ENSG00000144867	ENSG00000144867			24085	protein-coding gene	gene with protein product						7844142, 10859309	Standard	NM_021203		Approved	APMCF1	uc003epx.2	Q9Y5M8	OTTHUMG00000159753	ENST00000466490.2:c.668C>A	3.37:g.133538462C>A	ENSP00000418401:p.Ala223Asp		135021152	Q6P595|Q8N2D8	Missense_Mutation	SNP	ENST00000466490.2	37	CCDS3081.1	.	.	.	.	.	.	.	.	.	.	C	9.402	1.078169	0.20227	.	.	ENSG00000144867	ENST00000466490	T	0.14144	2.53	5.83	2.99	0.34606	.	1.114620	0.06770	N	0.783378	T	0.07593	0.0191	N	0.03253	-0.375	0.21967	N	0.999449	B	0.30937	0.301	B	0.30495	0.116	T	0.44847	-0.9301	10	0.31617	T	0.26	0.7643	10.5691	0.45190	0.0:0.7923:0.0:0.2077	.	223	Q9Y5M8	SRPRB_HUMAN	D	223	ENSP00000418401:A223D	ENSP00000418401:A223D	A	+	2	0	SRPRB	135021152	0.973000	0.33851	0.205000	0.23548	0.783000	0.44284	1.335000	0.33839	0.341000	0.23771	-0.355000	0.07637	GCT		0.557	SRPRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357170.2			A	133538462	C	A	133538462	3	1	58	1	0	0	0	0	1	0	0	0	15202	797	28	2	694	2	SRPRB	3	133538462	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	54742442	133538462	64483968	40	7686										
ESYT3	83850	broad.mit.edu	37	chr3	138193103	138193103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcagtggagctgatccctacGtccgtgtctacttgttgcca	11	12	1	1	rs201464827	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:138193103G>A	ENST00000389567.4	+	20	2563	c.2377G>A	c.(2377-2379)Gtc>Atc	p.V793I	ESYT3_ENST00000460133.1_Intron	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	793	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.V793I(1)		breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						TGATCCCTACGTCCGTGTCTA	0.463													G|||	3	0.000599042	0.0023	0	5008	,	,		18298	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	ILE/VAL	12,3928		0,12,1958	150	155	154		2377	4.8	1	3		154	0,8286		0,0,4143	yes	missense	ESYT3	NM_031913.3	29	0,12,6101	AA,AG,GG		0.0,0.3046,0.0982	benign	793/887	138193103	12,12214	1970	4143	6113	139675793	SO:0001583	missense	83850			AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"Synaptotagmins"	24295	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member C"	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.2377G>A	3.37:g.138193103G>A	ENSP00000374218:p.Val793Ile		139675793	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880401	0.72294	0.003046	0.0	ENSG00000158220	ENST00000389567	T	0.21543	2.0	4.75	4.75	0.60458	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.184731	0.33854	N	0.004497	T	0.34308	0.0893	M	0.69185	2.1	0.80722	D	1	P	0.46142	0.873	P	0.49451	0.611	T	0.10965	-1.0607	10	0.59425	D	0.04	-13.1291	15.2928	0.73879	0.0:0.0:1.0:0.0	.	793	A0FGR9	ESYT3_HUMAN	I	793	ENSP00000374218:V793I	ENSP00000374218:V793I	V	+	1	0	ESYT3	139675793	1.000000	0.71417	0.984000	0.44739	0.989000	0.77384	5.507000	0.66999	2.459000	0.83118	0.655000	0.94253	GTC		0.463	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		A	138193103	G	A	138193103	3	1	58	1	0	0	0	0	1	0	0	0	5279	1145	40	1	2455	1	ESYT3	3	138193103	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	4654641	138193103	59829327	41	7687										
TRPC1	7220	broad.mit.edu	37	chr3	142522954	142522954	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	attgttggtacatacaatgtCgtggttgtgattgtgcttac	11	5	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:142522954C>T	ENST00000476941.1	+	11	2379	c.1893C>T	c.(1891-1893)gtC>gtT	p.V631V	TRPC1_ENST00000273482.6_Silent_p.V597V|RNU7-47P_ENST00000515978.1_RNA	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	631					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.V597V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CATACAATGTCGTGGTTGTGA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	3											186	162	170					3																	142522954		2203	4300	6503	144005644	SO:0001819	synonymous_variant	7220			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1893C>T	3.37:g.142522954C>T			144005644	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																				0.393	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		T	142522954	C	T	142522954	2	4	58	1	0	0	0	0	0	0	0	1	16618	871	31	1		1	TRPC1	3	142522954	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	4329851	142522954	55499476	42	7688										
MED12L	116931	broad.mit.edu	37	chr3	151150580	151150580	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gtgactccgtatgggcatccTtcacacttctgaatctgcaa	8	12	3	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:151150580T>G	ENST00000474524.1	+	43	6464	c.6426T>G	c.(6424-6426)ccT>ccG	p.P2142P	MED12L_ENST00000273432.4_Silent_p.P1806P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2142						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.P2142P(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATGGGCATCCTTCACACTTCT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	3											111	98	103					3																	151150580		2203	4300	6503	152633270	SO:0001819	synonymous_variant	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6426T>G	3.37:g.151150580T>G			152633270	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																				0.378	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151150580	T	G	151150580	2	3	58	1	0	0	0	0	0	0	0	1	9459	1596	56	4		4	MED12L	3	151150580	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09	8627626	151150580	46871850	43	7689										
SUCNR1	56670	broad.mit.edu	37	chr3	151598788	151598788	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttgggttttagtaaccttaGagttactacccatacttccc	6	10	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:151598788G>C	ENST00000362032.5	+	3	562	c.457G>C	c.(457-459)Gag>Cag	p.E153Q	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	153						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E153Q(1)		endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	AGTAACCTTAGAGTTACTACC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											132	133	132					3																	151598788		2203	4300	6503	153081478	SO:0001583	missense	56670			AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.457G>C	3.37:g.151598788G>C	ENSP00000355156:p.Glu153Gln		153081478	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	37	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104244	0.37145	.	.	ENSG00000198829	ENST00000362032	T	0.71579	-0.58	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.062950	0.64402	U	0.000011	T	0.72851	0.3512	L	0.33710	1.025	0.35041	D	0.759752	D	0.57899	0.981	D	0.64042	0.921	T	0.74393	-0.3680	10	0.24483	T	0.36	.	12.6389	0.56698	0.0758:0.0:0.9242:0.0	.	153	Q9BXA5	SUCR1_HUMAN	Q	153	ENSP00000355156:E153Q	ENSP00000355156:E153Q	E	+	1	0	SUCNR1	153081478	1.000000	0.71417	0.353000	0.25747	0.036000	0.12997	3.544000	0.53640	2.646000	0.89796	0.655000	0.94253	GAG		0.383	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		C	151598788	G	C	151598788	3	2	58	1	0	0	0	0	1	0	0	0	15405	943	33	5	463	5	SUCNR1	3	151598788	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	448208	151598788	46423642	44	7690										
MME	4311	broad.mit.edu	37	chr3	154884783	154884783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcggcatggtcataggacacGaaatcacccatggcttcgat	10	11	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:154884783G>A	ENST00000460393.1	+	18	1873	c.1753G>A	c.(1753-1755)Gaa>Aaa	p.E585K	MME-AS1_ENST00000484721.1_RNA|MME_ENST00000360490.2_Missense_Mutation_p.E585K|MME_ENST00000462745.1_Missense_Mutation_p.E585K|MME_ENST00000492661.1_Missense_Mutation_p.E585K|MME_ENST00000493237.1_Missense_Mutation_p.E585K	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	585					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.E585K(2)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CATAGGACACGAAATCACCCA	0.448																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	3											147	134	138					3																	154884783		2203	4300	6503	156367477	SO:0001583	missense	4311				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1753G>A	3.37:g.154884783G>A	ENSP00000418525:p.Glu585Lys		156367477	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	G	36	5.841453	0.97009	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	D;D;D;D;D	0.98835	-5.17;-5.17;-5.17;-5.17;-5.17	5.9	5.9	0.94986	Peptidase M13, neprilysin, C-terminal (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99557	0.9841	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97965	1.0340	10	0.87932	D	0	-31.9984	20.2789	0.98501	0.0:0.0:1.0:0.0	.	585	P08473	NEP_HUMAN	K	585	ENSP00000420389:E585K;ENSP00000418525:E585K;ENSP00000419653:E585K;ENSP00000417079:E585K;ENSP00000353679:E585K	ENSP00000353679:E585K	E	+	1	0	MME	156367477	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	9.731000	0.98807	2.788000	0.95919	0.650000	0.86243	GAA		0.448	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154884783	G	A	154884783	3	1	58	1	0	0	0	0	1	0	0	0	9675	1059	37	1	1819	1	MME	3	154884783	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	3285995	154884783	43137647	45	7691										
BCHE	590	broad.mit.edu	37	chr3	165547452	165547452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctcccatccattctggccacGgaagtttggaggatcggtgt	12	11	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:165547452G>A	ENST00000264381.3	-	2	1536	c.1370C>T	c.(1369-1371)cCg>cTg	p.P457L	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	457					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)	p.P457L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TTCTGGCCACGGAAGTTTGGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	102	101					3																	165547452		2203	4300	6503	167030146	SO:0001583	missense	590			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1370C>T	3.37:g.165547452G>A	ENSP00000264381:p.Pro457Leu		167030146	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.901674	0.33535	.	.	ENSG00000114200	ENST00000264381	T	0.65364	-0.15	5.52	5.52	0.82312	Carboxylesterase, type B (1);	0.170167	0.52532	D	0.000063	T	0.44244	0.1284	N	0.16602	0.42	0.80722	D	1	P	0.41910	0.764	B	0.30029	0.11	T	0.49570	-0.8926	10	0.41790	T	0.15	.	18.4281	0.90615	0.0:0.0:1.0:0.0	.	457	P06276	CHLE_HUMAN	L	457	ENSP00000264381:P457L	ENSP00000264381:P457L	P	-	2	0	BCHE	167030146	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.496000	0.81526	2.605000	0.88082	0.591000	0.81541	CCG		0.398	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			A	165547452	G	A	165547452	3	1	58	1	0	0	0	0	1	0	0	0	1359	1116	39	1	450	1	BCHE	3	165547452	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	10662669	165547452	32474978	46	7692										
MASP1	5648	broad.mit.edu	37	chr3	186954338	186954338	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gaccaggcttggcagggagcGggagggctgaccacactctg	17	11	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr3:186954338G>A	ENST00000337774.5	-	10	1693				MASP1_ENST00000495249.1_Intron|MASP1_ENST00000392472.2_Missense_Mutation_p.R328C|MASP1_ENST00000296280.6_Missense_Mutation_p.R441C	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)						complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.R441C(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GGCAGGGAGCGGGAGGGCTGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	79	78					3																	186954338		2203	4300	6503	188437032	SO:0001627	intron_variant	5648			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1303+4930C>T	3.37:g.186954338G>A			188437032	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	37	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923270	0.92319	.	.	ENSG00000127241	ENST00000296280;ENST00000392472;ENST00000541896	D;D	0.83837	-1.75;-1.77	5.91	5.91	0.95273	.	0.440644	0.28683	N	0.014493	D	0.88526	0.6460	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.997;0.998	P;P	0.58520	0.84;0.84	D	0.86406	0.1745	10	0.36615	T	0.2	.	19.2934	0.94112	0.0:0.0:1.0:0.0	.	328;441	P48740-4;P48740-2	.;.	C	441;328;328	ENSP00000296280:R441C;ENSP00000376264:R328C	ENSP00000296280:R441C	R	-	1	0	MASP1	188437032	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.526000	0.81920	2.808000	0.96608	0.655000	0.94253	CGC		0.572	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		A	186954338	G	A	186954338	1	1	58	0	1	0	0	0	0	0	0	0	9352	1116	39	1		1	MASP1	3	186954338	Intron	SNP	G	TCGA-AG-4007-01A-01W-1073-09	21406886	186954338	11068092	47	7693										
SLC30A9	10463	broad.mit.edu	37	chr4	42025372	42025372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgccagagagaaaaaattgcGtaaggaagcagaaatagaat	11	4	0	4	rs144935504	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:42025372G>A	ENST00000264451.7	+	6	761	c.581G>A	c.(580-582)cGt>cAt	p.R194H		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	194					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R194H(3)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AAAAAATTGCGTAAGGAAGCA	0.343													G|||	2	0.000399361	0	0	5008	,	,		17754	0		0.001	False		,,,				2504	0.001															3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	4						G	HIS/ARG	0,4406		0,0,2203	98	103	101		581	5.5	1	4	dbSNP_134	101	3,8597	3.7+/-12.6	0,3,4297	yes	missense	SLC30A9	NM_006345.3	29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	194/569	42025372	3,13003	2203	4300	6503	41720129	SO:0001583	missense	10463			AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.581G>A	4.37:g.42025372G>A	ENSP00000264451:p.Arg194His		41720129	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	34	5.319460	0.95682	0.0	3.49E-4	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.56444	0.46	5.48	5.48	0.80851	DNA binding domain, putative (1);	0.000000	0.85682	D	0.000000	T	0.74869	0.3773	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.69142	0.962	T	0.78270	-0.2269	10	0.87932	D	0	-11.4523	19.3393	0.94335	0.0:0.0:1.0:0.0	.	194	Q6PML9	ZNT9_HUMAN	H	194;22	ENSP00000264451:R194H	ENSP00000264451:R194H	R	+	2	0	SLC30A9	41720129	1.000000	0.71417	0.987000	0.45799	0.987000	0.75469	9.297000	0.96120	2.556000	0.86216	0.585000	0.79938	CGT		0.343	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			A	42025372	G	A	42025372	3	1	58	1	0	0	0	0	1	0	0	0	14599	1145	40	1	603	1	SLC30A9	4	42025372	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		42025372	149128904	48	7694										
POLR2B	5431	broad.mit.edu	37	chr4	57896476	57896476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aggcatcagatccatatcagGttcatgtttgcaatctttgt	8	8	4	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:57896476G>A	ENST00000381227.1	+	25	3759	c.3346G>A	c.(3346-3348)Gtt>Att	p.V1116I	IGFBP7_ENST00000512512.1_5'Flank|POLR2B_ENST00000431623.2_Missense_Mutation_p.V1041I|POLR2B_ENST00000314595.5_Missense_Mutation_p.V1116I|POLR2B_ENST00000441246.2_Missense_Mutation_p.V1109I			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	1116					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)	p.V1116F(2)|p.V1116I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TCCATATCAGGTTCATGTTTG	0.458																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	4											114	111	112					4																	57896476		2203	4300	6503	57591233	SO:0001583	missense	5431				CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.3346G>A	4.37:g.57896476G>A	ENSP00000370625:p.Val1116Ile		57591233	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.915342	0.52546	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.41	5.41	0.78517	RNA polymerase Rpb2, domain 7 (1);	0.000000	0.85682	D	0.000000	T	0.72317	0.3445	L	0.41124	1.26	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.006	T	0.65660	-0.6114	10	0.29301	T	0.29	.	19.2125	0.93763	0.0:0.0:1.0:0.0	.	1041;1116	C9J4M6;P30876	.;RPB2_HUMAN	I	1116;1041;1109;1116	ENSP00000370625:V1116I;ENSP00000391096:V1041I;ENSP00000391452:V1109I;ENSP00000312735:V1116I	ENSP00000312735:V1116I	V	+	1	0	POLR2B	57591233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.623000	0.98386	2.529000	0.85273	0.585000	0.79938	GTT		0.458	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		A	57896476	G	A	57896476	3	1	58	1	0	0	0	0	1	0	0	0	12246	1261	44	3	3440	3	POLR2B	4	57896476	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	15871104	57896476	133257800	49	7695										
NHEDC1	150159	broad.mit.edu	37	chr4	103867924	103867924	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	atgaatggaacattcctaatCgtaaaaccagccagtaacat	6	9	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:103867924C>T	ENST00000296422.7	-	5	546	c.405G>A	c.(403-405)acG>acA	p.T135T	SLC9B1_ENST00000394789.3_Silent_p.T135T	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	135					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.T135T(1)									CATTCCTAATCGTAAAACCAG	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	4											52	52	52					4																	103867924		2203	4298	6501	104087373	SO:0001819	synonymous_variant	150159			AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.405G>A	4.37:g.103867924C>T			104087373	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Silent	SNP	ENST00000296422.7	37	CCDS34041.1																																																																																				0.328	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		T	103867924	C	T	103867924	2	4	58	1	0	0	0	0	0	0	0	1	10431	871	31	1		1	NHEDC1	4	103867924	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	45971448	103867924	87286352	50	7696										
BBS12	166379	broad.mit.edu	37	chr4	123663513	123663513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aacttgaaacatttagtgtaAgtttgtgtccttttctacag	7	6	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:123663513A>C	ENST00000314218.3	+	2	659	c.466A>C	c.(466-468)Agt>Cgt	p.S156R	BBS12_ENST00000542236.1_Missense_Mutation_p.S156R	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	156					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)	p.S156R(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ATTTAGTGTAAGTTTGTGTCC	0.373									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	4											115	102	106					4																	123663513		2203	4300	6503	123882963	SO:0001583	missense	166379	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.466A>C	4.37:g.123663513A>C	ENSP00000319062:p.Ser156Arg		123882963	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	.	.	.	.	.	.	.	.	.	.	A	5.941	0.357554	0.11239	.	.	ENSG00000181004	ENST00000314218;ENST00000542236;ENST00000433287	T;T;T	0.70631	-0.5;-0.5;0.13	5.2	-1.35	0.09114	.	0.931433	0.09170	N	0.838998	T	0.53433	0.1796	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40757	-0.9546	10	0.45353	T	0.12	-34.7595	5.5141	0.16896	0.4917:0.0:0.3764:0.1319	.	156	Q6ZW61	BBS12_HUMAN	R	156	ENSP00000319062:S156R;ENSP00000438273:S156R;ENSP00000398912:S156R	ENSP00000319062:S156R	S	+	1	0	BBS12	123882963	0.000000	0.05858	0.000000	0.03702	0.319000	0.28217	0.551000	0.23361	-0.137000	0.11455	0.528000	0.53228	AGT		0.373	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		C	123663513	A	C	123663513	3	2	58	1	0	0	0	0	1	0	0	0	1338	72	3	4	468	4	BBS12	4	123663513	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	19795589	123663513	67490763	51	7697										
DCHS2	54798	broad.mit.edu	37	chr4	155157679	155157679	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	taagtaaaaatgtcccttctCatttccagagatgatgttgt	7	7	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:155157679C>G	ENST00000357232.4	-	25	6759	c.6760G>C	c.(6760-6762)Gag>Cag	p.E2254Q		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2254	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E2254Q(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGTCCCTTCTCATTTCCAGAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	102	101					4																	155157679		2203	4300	6503	155377129	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6760G>C	4.37:g.155157679C>G	ENSP00000349768:p.Glu2254Gln		155377129	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908492	0.52333	.	.	ENSG00000197410	ENST00000357232	T	0.54279	0.58	5.64	5.64	0.86602	Cadherin (4);Cadherin-like (1);	0.079447	0.51477	D	0.000083	T	0.68668	0.3026	L	0.50847	1.595	0.80722	D	1	D	0.71674	0.998	D	0.69142	0.962	T	0.68784	-0.5317	10	0.59425	D	0.04	.	19.7012	0.96054	0.0:1.0:0.0:0.0	.	2254	Q6V1P9	PCD23_HUMAN	Q	2254	ENSP00000349768:E2254Q	ENSP00000349768:E2254Q	E	-	1	0	DCHS2	155377129	1.000000	0.71417	0.974000	0.42286	0.717000	0.41224	2.582000	0.46085	2.637000	0.89404	0.563000	0.77884	GAG		0.403	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155157679	C	G	155157679	3	3	58	1	0	0	0	0	1	0	0	0	4294	835	29	5	1994	5	DCHS2	4	155157679	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	31494166	155157679	35996597	52	7698										
WDR17	116966	broad.mit.edu	37	chr4	177100635	177100635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgtgtttttccttgaagacGggaaatctgctatctccttg	9	9	2	2	rs146320284		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:177100635G>A	ENST00000280190.4	+	31	4030	c.3874G>A	c.(3874-3876)Ggg>Agg	p.G1292R	WDR17_ENST00000393643.2_Missense_Mutation_p.G1268R|WDR17_ENST00000508596.1_Missense_Mutation_p.G1253R|WDR17_ENST00000507824.2_Missense_Mutation_p.G1267R			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1292								p.G1292R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CCTTGAAGACGGGAAATCTGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	ARG/GLY,ARG/GLY	0,4406		0,0,2203	144	131	136		3874,3757	4.7	1	4	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1292/1323,1253/1284	177100635	1,13005	2203	4300	6503	177337629	SO:0001583	missense	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3874G>A	4.37:g.177100635G>A	ENSP00000280190:p.Gly1292Arg		177337629	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.9|21.9	4.211820|4.211820	0.79240|0.79240	0.0|0.0	1.16E-4|1.16E-4	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.71579|.	-0.44;-0.51;-0.58|.	5.51|5.51	4.66|4.66	0.58398|0.58398	.|.	0.125096|.	0.53938|.	N|.	0.000059|.	T|T	0.73705|0.73705	0.3621|0.3621	M|M	0.74881|0.74881	2.28|2.28	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D|.	0.76494|.	0.999;0.997;0.997|.	P;P;P|.	0.62298|.	0.9;0.847;0.847|.	T|T	0.74780|0.74780	-0.3549|-0.3549	10|5	0.87932|.	D|.	0|.	-16.1458|-16.1458	14.4989|14.4989	0.67707|0.67707	0.0711:0.0:0.9289:0.0|0.0711:0.0:0.9289:0.0	.|.	1268;1253;1292|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	R|Q	1253;1268;1292;1268|526	ENSP00000422763:G1253R;ENSP00000377258:G1268R;ENSP00000280190:G1292R|.	ENSP00000280190:G1292R|.	G|R	+|+	1|2	0|0	WDR17|WDR17	177337629|177337629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	6.273000|6.273000	0.72581|0.72581	1.451000|1.451000	0.47736|0.47736	0.655000|0.655000	0.94253|0.94253	GGG|CGG		0.393	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177100635	G	A	177100635	3	1	58	1	0	0	0	0	1	0	0	0	17317	1116	39	1	3992	1	WDR17	4	177100635	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	21942956	177100635	14053641	53	7699										
KIAA1430	57587	broad.mit.edu	37	chr4	186112011	186112011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aattctatttggaatggacaCgtgtattttaagtcctgttg	9	5	1	0	rs371391407		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr4:186112011C>T	ENST00000458385.2	-	2	459	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	KIAA1430_ENST00000296775.6_Missense_Mutation_p.V114M|KIAA1430_ENST00000514798.1_Missense_Mutation_p.V114M	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		114								p.V114M(1)		endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		GGAATGGACACGTGTATTTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											91	81	84					4																	186112011		1859	4105	5964	186349005	SO:0001583	missense	57587																														ENST00000458385.2:c.340G>A	4.37:g.186112011C>T	ENSP00000409964:p.Val114Met		186349005	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Missense_Mutation	SNP	ENST00000458385.2	37	CCDS47168.1	.	.	.	.	.	.	.	.	.	.	C	0.735	-0.778583	0.02929	.	.	ENSG00000164323	ENST00000458385;ENST00000514798;ENST00000296775;ENST00000503223	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.21	1.25	0.21368	.	0.525227	0.17162	N	0.184648	T	0.12433	0.0302	N	0.03608	-0.345	0.09310	N	1	P;B	0.40476	0.718;0.002	B;B	0.27380	0.079;0.001	T	0.14309	-1.0477	10	0.42905	T	0.14	0.0991	2.5544	0.04756	0.3949:0.3519:0.1462:0.1071	.	114;114	Q9P2B7-2;Q9P2B7	.;K1430_HUMAN	M	114	ENSP00000409964:V114M;ENSP00000423312:V114M;ENSP00000296775:V114M;ENSP00000420832:V114M	ENSP00000296775:V114M	V	-	1	0	KIAA1430	186349005	0.000000	0.05858	0.026000	0.17262	0.023000	0.10783	0.133000	0.15912	0.052000	0.16007	-0.706000	0.03657	GTG		0.363	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2			T	186112011	C	T	186112011	3	4	58	1	0	0	0	0	1	0	0	0	8253	536	19	1	1274	1	KIAA1430	4	186112011	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9011376	186112011	5042265	54	7700										
ADCY2	108	broad.mit.edu	37	chr5	7802364	7802364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	agtcctatgactgcgtctgcGtcatgtttgcctccattccg	9	13	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:7802364G>A	ENST00000338316.4	+	21	2751	c.2662G>A	c.(2662-2664)Gtc>Atc	p.V888I	ADCY2_ENST00000537121.1_Missense_Mutation_p.V708I	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	888					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.V888I(3)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTGCGTCTGCGTCATGTTTGC	0.488																																																3	Substitution - Missense(3)	ovary(2)|large_intestine(1)	5											82	78	79					5																	7802364		2203	4300	6503	7855364	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2662G>A	5.37:g.7802364G>A	ENSP00000342952:p.Val888Ile		7855364	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	31	5.078655	0.94050	.	.	ENSG00000078295	ENST00000338316;ENST00000382532;ENST00000541993;ENST00000537121	T;T	0.80653	-1.4;-1.4	5.24	5.24	0.73138	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.87613	0.6221	L	0.52126	1.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.87987	0.2747	10	0.56958	D	0.05	.	18.8415	0.92186	0.0:0.0:1.0:0.0	.	708;888	B7Z2C1;Q08462	.;ADCY2_HUMAN	I	888;41;721;708	ENSP00000342952:V888I;ENSP00000444803:V708I	ENSP00000342952:V888I	V	+	1	0	ADCY2	7855364	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.506000	0.97992	2.447000	0.82792	0.591000	0.81541	GTC		0.488	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7802364	G	A	7802364	3	1	58	1	0	0	0	0	1	0	0	0	294	1145	40	1	2744	1	ADCY2	5	7802364	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		7802364	173112896	55	7701										
ST8SIA4	7903	broad.mit.edu	37	chr5	100191810	100191810	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cctttccagtcacttaccctCtgacagcatgaataagtctc	5	14	3	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:100191810C>T	ENST00000231461.5	-	4	1104	c.794G>A	c.(793-795)aGa>aAa	p.R265K		NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	265					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.R265K(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		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)		CACTTACCCTCTGACAGCATG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											101	90	94					5																	100191810		2203	4300	6503	100219709	SO:0001583	missense	7903			L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.794G>A	5.37:g.100191810C>T	ENSP00000231461:p.Arg265Lys		100219709	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	37	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974224	0.74246	.	.	ENSG00000113532	ENST00000231461	T	0.30714	1.52	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.26304	0.0642	L	0.45422	1.42	0.80722	D	1	B	0.23735	0.09	B	0.23852	0.049	T	0.08086	-1.0739	10	0.05620	T	0.96	.	18.1509	0.89674	0.0:1.0:0.0:0.0	.	265	Q92187	SIA8D_HUMAN	K	265	ENSP00000231461:R265K	ENSP00000231461:R265K	R	-	2	0	ST8SIA4	100219709	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.619000	0.83057	2.751000	0.94390	0.591000	0.81541	AGA		0.413	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		T	100191810	C	T	100191810	3	4	58	1	0	0	0	0	1	0	0	0	15273	913	32	3	293	3	ST8SIA4	5	100191810	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	92389446	100191810	80723450	56	7702										
APC	324	broad.mit.edu	37	chr5	112175426	112175426	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cacctgaacactatgttcagGagaccccactcatgtttagc	7	13	2	2	rs121913326		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:112175426G>T	ENST00000457016.1	+	16	4515	c.4135G>T	c.(4135-4137)Gag>Tag	p.E1379*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1379*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1379*			P25054	APC_HUMAN	adenomatous polyposis coli	1379	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1379*(21)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTATGTTCAGGAGACCCCACT	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	26	Substitution - Nonsense(21)|Deletion - Frameshift(4)|Unknown(1)	large_intestine(24)|soft_tissue(1)|skin(1)	5											94	89	91					5																	112175426		2202	4300	6502	112203325	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4135G>T	5.37:g.112175426G>T	ENSP00000413133:p.Glu1379*		112203325	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	41	9.025348	0.99040	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.047393	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.4605	20.4898	0.99202	0.0:0.0:1.0:0.0	.	.	.	.	X	1379	.	.	E	+	1	0	APC	112203325	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GAG		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175426	G	T	112175426	4	4	58	1	0	0	0	0	0	1	0	0	763	1175	41	2	4193	2	APC	5	112175426	Nonsense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	11983616	112175426	68739834	57	7703										
PAIP2	51247	broad.mit.edu	37	chr5	138700309	138700309	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cgctgtttccaagaaatgctGgaagaggaagaagagcatga	13	6	0	5			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:138700309G>A	ENST00000394795.2	+	3	1186	c.195G>A	c.(193-195)ctG>ctA	p.L65L	CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000510080.1_Silent_p.L65L|PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000511381.1_3'UTR|PAIP2_ENST00000265192.4_Silent_p.L65L			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	65	Glu-rich.|PABPC1-interacting motif-1 (PAM1).				memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)	p.L65L(1)		kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAGAAATGCTGGAAGAGGAAG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	5											100	93	95					5																	138700309		2203	4300	6503	138728208	SO:0001819	synonymous_variant	51247			AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.195G>A	5.37:g.138700309G>A			138728208	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Silent	SNP	ENST00000394795.2	37	CCDS4211.1																																																																																				0.368	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480		A	138700309	G	A	138700309	2	1	58	1	0	0	0	0	0	0	0	1	11428	1335	47	3		3	PAIP2	5	138700309	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	26524883	138700309	42214951	58	7704										
PSD2	84249	broad.mit.edu	37	chr5	139219669	139219669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	agctgactgcggagctggccGaacacaggtgtcacccagtc	13	13	1	1	rs549742335		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:139219669G>A	ENST00000274710.3	+	14	2231	c.2026G>A	c.(2026-2028)Gaa>Aaa	p.E676K		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	676					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.E676K(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTGGCCGAACACAGGTG	0.567													G|||	1	0.000199681	0	0	5008	,	,		20605	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											115	104	108					5																	139219669		2203	4300	6503	139199853	SO:0001583	missense	84249			AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.2026G>A	5.37:g.139219669G>A	ENSP00000274710:p.Glu676Lys		139199853	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	37	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411924	0.83340	.	.	ENSG00000146005	ENST00000274710	T	0.14266	2.52	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.25791	0.0628	M	0.84948	2.725	0.80722	D	1	P	0.51653	0.947	B	0.41412	0.356	T	0.37842	-0.9688	10	0.87932	D	0	.	18.5248	0.90968	0.0:0.0:1.0:0.0	.	676	Q9BQI7	PSD2_HUMAN	K	676	ENSP00000274710:E676K	ENSP00000274710:E676K	E	+	1	0	PSD2	139199853	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	7.700000	0.84556	2.455000	0.83008	0.555000	0.69702	GAA		0.567	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139219669	G	A	139219669	3	1	58	1	0	0	0	0	1	0	0	0	12681	1059	37	1	2076	1	PSD2	5	139219669	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	519360	139219669	41695591	59	7705										
PCDHB3	56132	broad.mit.edu	37	chr5	140481975	140481975	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gctggtgccccgggcggctgAgccgggctacctggtgacca	17	14	0	2	rs541148618	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:140481975A>C	ENST00000231130.2	+	1	1742	c.1742A>C	c.(1741-1743)gAg>gCg	p.E581A	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	581	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E581A(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGGCGGCTGAGCCGGGCTAC	0.711																																																1	Substitution - Missense(1)	large_intestine(1)	5											19	24	22					5																	140481975		2175	4212	6387	140462159	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1742A>C	5.37:g.140481975A>C	ENSP00000231130:p.Glu581Ala		140462159	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441848	0.63067	.	.	ENSG00000113205	ENST00000231130	T	0.50813	0.73	4.24	4.24	0.50183	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.56217	0.1970	L	0.48986	1.54	0.20196	N	0.999925	P	0.49559	0.925	P	0.56648	0.803	T	0.47686	-0.9098	9	0.87932	D	0	.	10.4481	0.44505	0.8369:0.1631:0.0:0.0	.	581	Q9Y5E6	PCDB3_HUMAN	A	581	ENSP00000231130:E581A	ENSP00000231130:E581A	E	+	2	0	PCDHB3	140462159	0.005000	0.15991	0.989000	0.46669	0.899000	0.52679	2.119000	0.41958	1.689000	0.51079	0.454000	0.30748	GAG		0.711	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		C	140481975	A	C	140481975	3	2	58	1	0	0	0	0	1	0	0	0	11574	304	11	4	1744	4	PCDHB3	5	140481975	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	1262306	140481975	40433285	60	7706										
PCDHB6	56130	broad.mit.edu	37	chr5	140531988	140531988	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gctgtgcaggaggagcagggCggcctcggtgggtcgctact	19	10	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:140531988C>A	ENST00000231136.1	+	1	2150	c.2150C>A	c.(2149-2151)gCg>gAg	p.A717E	PCDHB6_ENST00000543635.1_Missense_Mutation_p.A581E	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	717					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A717E(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGAGCAGGGCGGCCTCGGTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	5											77	91	86					5																	140531988		2202	4300	6502	140512172	SO:0001583	missense	56130			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2150C>A	5.37:g.140531988C>A	ENSP00000231136:p.Ala717Glu		140512172	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.408269	0.25378	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.17054	2.3;2.3	4.45	0.753	0.18404	.	.	.	.	.	T	0.16938	0.0407	L	0.58302	1.8	0.09310	N	1	B	0.17667	0.023	B	0.18263	0.021	T	0.23440	-1.0188	9	0.49607	T	0.09	.	7.7172	0.28710	0.2384:0.5394:0.2222:0.0	.	717	Q9Y5E3	PCDB6_HUMAN	E	581;717	ENSP00000438466:A581E;ENSP00000231136:A717E	ENSP00000231136:A717E	A	+	2	0	PCDHB6	140512172	0.003000	0.15002	0.001000	0.08648	0.204000	0.24138	0.351000	0.20096	0.382000	0.24878	0.556000	0.70494	GCG		0.652	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		A	140531988	C	A	140531988	3	1	58	1	0	0	0	0	1	0	0	0	11577	768	27	2	2152	2	PCDHB6	5	140531988	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	50013	140531988	40383272	61	7707										
PCDHGA11	56105	broad.mit.edu	37	chr5	140802769	140802769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	agccccctctctcggccaccGtcacgctcaccgtggctgtg	10	19	3	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:140802769G>A	ENST00000398587.2	+	1	2008	c.1975G>A	c.(1975-1977)Gtc>Atc	p.V659I	PCDHGA8_ENST00000398604.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	659	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V659I(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCGGCCACCGTCACGCTCAC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	5											34	42	40					5																	140802769		2202	4297	6499	140782953	SO:0001583	missense	56105			AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1975G>A	5.37:g.140802769G>A	ENSP00000381589:p.Val659Ile		140782953	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	g	15.20	2.763662	0.49574	.	.	ENSG00000253873	ENST00000398587	T	0.52983	0.64	5.33	3.53	0.40419	Cadherin (4);Cadherin-like (1);	0.474182	0.12845	U	0.434472	T	0.53094	0.1775	M	0.69823	2.125	0.80722	D	1	P;P	0.40875	0.731;0.538	P;B	0.45232	0.474;0.12	T	0.54543	-0.8278	10	0.54805	T	0.06	.	10.3526	0.43945	0.2135:0.0:0.7865:0.0	.	659;659	Q9Y5H2;Q9Y5H2-2	PCDGB_HUMAN;.	I	659	ENSP00000381589:V659I	ENSP00000381589:V659I	V	+	1	0	PCDHGA11	140782953	0.483000	0.25956	0.097000	0.21041	0.868000	0.49771	3.305000	0.51873	1.272000	0.44329	0.556000	0.70494	GTC		0.672	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		A	140802769	G	A	140802769	3	1	58	1	0	0	0	0	1	0	0	0	11583	1145	40	1	1977	1	PCDHGA11	5	140802769	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	270781	140802769	40112491	62	7708										
CCNJL	79616	broad.mit.edu	37	chr5	159682576	159682576	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	accagcaggatttcaatacaCgtgctgaggtgctccaggga	12	10	1	1	rs544092120	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:159682576C>T	ENST00000393977.3	-	6	1152	c.867G>A	c.(865-867)acG>acA	p.T289T	CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000541762.1_Silent_p.T240T|CCNJL_ENST00000257536.7_Silent_p.T241T|CCNJL_ENST00000519673.1_Silent_p.T241T	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	289						nucleus (GO:0005634)		p.T289T(3)		endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTCAATACACGTGCTGAGGT	0.552													C|||	2	0.000399361	0.0015	0	5008	,	,		16431	0		0	False		,,,				2504	0															3	Substitution - coding silent(3)	large_intestine(1)|endometrium(1)|kidney(1)	5											179	179	179					5																	159682576		1903	4138	6041	159615154	SO:0001819	synonymous_variant	79616			BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.867G>A	5.37:g.159682576C>T			159615154	Q6ZN43|Q9H7W8	Silent	SNP	ENST00000393977.3	37	CCDS4350.2																																																																																				0.552	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565		T	159682576	C	T	159682576	2	4	58	1	0	0	0	0	0	0	0	1	2935	523	19	1		1	CCNJL	5	159682576	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	18879807	159682576	21232684	63	7709										
ADAMTS2	9509	broad.mit.edu	37	chr5	178585754	178585754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ggaaggcccaaagtcctgccGtgtgaggaagatggcgtgat	16	8	0	3	rs371384169		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr5:178585754G>A	ENST00000251582.7	-	6	1203	c.1102C>T	c.(1102-1104)Cgg>Tgg	p.R368W	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.R368W	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	368	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R368W(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AAGTCCTGCCGTGTGAGGAAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	156	135	142		1102,1102	2.6	0.9	5		142	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	368/1212,368/567	178585754	1,13005	2203	4300	6503	178518360	SO:0001583	missense	9509			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1102C>T	5.37:g.178585754G>A	ENSP00000251582:p.Arg368Trp		178518360		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.590408	0.66219	0.0	1.16E-4	ENSG00000087116	ENST00000251582;ENST00000274609	D;D	0.87491	-2.26;-2.26	5.73	2.61	0.31194	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.51477	D	0.000087	D	0.94653	0.8276	M	0.93854	3.465	0.42100	D	0.991334	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.95601	0.8663	10	0.87932	D	0	.	14.1394	0.65311	0.0:0.0:0.4888:0.5112	.	368;368	O95450-2;O95450	.;ATS2_HUMAN	W	368	ENSP00000251582:R368W;ENSP00000274609:R368W	ENSP00000251582:R368W	R	-	1	2	ADAMTS2	178518360	0.665000	0.27466	0.932000	0.37286	0.991000	0.79684	0.944000	0.29043	0.733000	0.32492	0.650000	0.86243	CGG		0.627	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178585754	G	A	178585754	3	1	58	1	0	0	0	0	1	0	0	0	265	1144	40	1	2676	1	ADAMTS2	5	178585754	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	18903178	178585754	2329506	64	7710										
CYP21A2	1589	broad.mit.edu	37	chr6	32007206	32007206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cctcacctgcagcatcatctGttacctcaccttcggagaca	6	16	4	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:32007206G>A	ENST00000418967.2	+	4	679	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	CYP21A2_ENST00000435122.2_Missense_Mutation_p.C144Y	NM_000500.7	NP_000491.4	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A, polypeptide 2	173					glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 21-monooxygenase activity (GO:0004509)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)	p.C174Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	11					Ketoconazole(DB01026)	AGCATCATCTGTTACCTCACC	0.582																																					Melanoma(174;1669 1998 3915 34700 46447)											1	Substitution - Missense(1)	large_intestine(1)	6											60	52	55					6																	32007206		2203	4299	6502	32115185	SO:0001583	missense	1589			X58906	CCDS4735.1, CCDS47406.1	6p21.3	2014-09-17	2003-01-14		ENSG00000231852	ENSG00000231852	1.14.99.10	"Cytochrome P450s"	2600	protein-coding gene	gene with protein product	"Steroid 21-monooxygenase"	613815	"cytochrome P450, subfamily XXIA (steroid 21-hydroxylase, congenital adrenal hyperplasia), polypeptide 2"	CYP21, CYP21B			Standard	NM_000500		Approved	P450c21B, CA21H, CPS1, CAH1	uc021yvd.1	P08686	OTTHUMG00000031069	ENST00000418967.2:c.521G>A	6.37:g.32007206G>A	ENSP00000408860:p.Cys174Tyr		32115185	A2BHY6|P04033|Q01204|Q08AG8|Q16749|Q16806|Q5ST44|Q96NU8	Missense_Mutation	SNP	ENST00000418967.2	37	CCDS4735.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021652	0.54576	.	.	ENSG00000231852	ENST00000418967;ENST00000478281;ENST00000471671;ENST00000435122	T;T;T;T	0.69806	-0.42;-0.43;-0.42;-0.42	4.69	3.81	0.43845	.	0.474215	0.17898	N	0.158294	T	0.70254	0.3203	M	0.76838	2.35	0.22796	N	0.998726	D;D	0.63880	0.984;0.993	D;D	0.63381	0.914;0.914	T	0.64563	-0.6378	10	0.87932	D	0	.	11.0699	0.47997	0.0:0.1869:0.8131:0.0	.	144;174	Q5ST44;Q16874	.;.	Y	174;185;174;144	ENSP00000408860:C174Y;ENSP00000419572:C185Y;ENSP00000418561:C174Y;ENSP00000415043:C144Y	ENSP00000408860:C174Y	C	+	2	0	CYP21A2	32115185	0.993000	0.37304	0.709000	0.30452	0.969000	0.65631	1.980000	0.40618	0.942000	0.37525	0.655000	0.94253	TGT		0.582	CYP21A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268768.2	NM_000500		A	32007206	G	A	32007206	3	1	58	1	0	0	0	0	1	0	0	0	4159	1377	48	3	2056	3	CYP21A2	6	32007206	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		32007206	139107861	65	7711										
TNXB	7148	broad.mit.edu	37	chr6	32036877	32036877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gctcaggcgctggaggggtcGgggccgtggtctcagtttcc	18	11	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:32036877G>A	ENST00000375244.3	-	16	5825	c.5624C>T	c.(5623-5625)cCg>cTg	p.P1875L	TNXB_ENST00000375247.2_Missense_Mutation_p.P1875L			P22105	TENX_HUMAN	tenascin XB	1957	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.P1962L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGGAGGGGTCGGGGCCGTGGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											33	37	35					6																	32036877		1297	2552	3849	32144855	SO:0001583	missense	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5624C>T	6.37:g.32036877G>A	ENSP00000364393:p.Pro1875Leu		32144855	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	G	11.08	1.533957	0.27387	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.66995	-0.07;-0.24	4.5	1.42	0.22433	.	0.258742	0.27673	N	0.018333	T	0.34774	0.0909	M	0.78049	2.395	0.09310	N	1	B	0.16166	0.016	B	0.15870	0.014	T	0.32798	-0.9893	10	0.09590	T	0.72	.	4.5495	0.12105	0.1114:0.0:0.5063:0.3823	.	1875	P22105-3	.	L	1875	ENSP00000364393:P1875L;ENSP00000364396:P1875L	ENSP00000364393:P1875L	P	-	2	0	TNXB	32144855	0.002000	0.14202	0.004000	0.12327	0.040000	0.13550	0.619000	0.24388	0.164000	0.19529	0.655000	0.94253	CCG		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32036877	G	A	32036877	3	1	58	1	0	0	0	0	1	0	0	0	16385	1116	39	1	9205	1	TNXB	6	32036877	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	29671	32036877	139078190	66	7712										
ZNF318	24149	broad.mit.edu	37	chr6	43322831	43322831	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgtggaagtctaattggggcAgatggggctgatggcaacat	16	5	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:43322831A>T	ENST00000361428.2	-	4	2318	c.2241T>A	c.(2239-2241)tcT>tcA	p.S747S	ZNF318_ENST00000318149.3_Silent_p.S747S	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	747					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S747S(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TAATTGGGGCAGATGGGGCTG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	6											128	122	124					6																	43322831		2203	4300	6503	43430809	SO:0001819	synonymous_variant	24149			AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2241T>A	6.37:g.43322831A>T			43430809	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																				0.522	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		T	43322831	A	T	43322831	2	4	58	1	0	0	0	0	0	0	0	1	17875	175	7	5		5	ZNF318	6	43322831	Silent	SNP	A	TCGA-AG-4007-01A-01W-1073-09	11285954	43322831	127792236	67	7713										
PKHD1	5314	broad.mit.edu	37	chr6	51914991	51914991	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ggagctccgtgccacaccccGccagccaggaggtgacactg	13	16	0	1	rs141622697	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:51914991G>A	ENST00000371117.3	-	22	2518	c.2243C>T	c.(2242-2244)gCg>gTg	p.A748V	PKHD1_ENST00000340994.4_Missense_Mutation_p.A748V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	748					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.A748V(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCCACACCCCGCCAGCCAGGA	0.582											OREG0017493	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0015	0	5008	,	,		18230	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	VAL/ALA,VAL/ALA	8,4398	14.3+/-33.2	0,8,2195	62	58	59		2243,2243	2.9	0	6	dbSNP_134	59	0,8600		0,0,4300	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	64,64	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	benign,benign	748/4075,748/3397	51914991	8,12998	2203	4300	6503	52022950	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2243C>T	6.37:g.51914991G>A	ENSP00000360158:p.Ala748Val	981	52022950	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.277	0.608416	0.14002	0.001816	0.0	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87571	-2.07;-2.27	5.64	2.93	0.34026	.	0.376059	0.24715	N	0.036196	T	0.57548	0.2061	N	0.16656	0.425	0.09310	N	1	B;B	0.24483	0.104;0.036	B;B	0.20384	0.029;0.004	T	0.48103	-0.9064	10	0.22706	T	0.39	.	10.0749	0.42355	0.2157:0.0:0.7843:0.0	.	748;748	P08F94-2;P08F94	.;PKHD1_HUMAN	V	748	ENSP00000360158:A748V;ENSP00000341097:A748V	ENSP00000341097:A748V	A	-	2	0	PKHD1	52022950	0.001000	0.12720	0.022000	0.16811	0.210000	0.24377	0.856000	0.27818	0.342000	0.23796	-0.136000	0.14681	GCG		0.582	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51914991	G	A	51914991	3	1	58	1	0	0	0	0	1	0	0	0	12002	1087	38	1	10204	1	PKHD1	6	51914991	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	8592160	51914991	119200076	68	7714										
PHIP	55023	broad.mit.edu	37	chr6	79675473	79675473	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcatcttttctgtatctccaTtgtcccagcttaaagaaaga	5	10	4	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:79675473T>G	ENST00000275034.4	-	29	3493	c.3326A>C	c.(3325-3327)aAt>aCt	p.N1109T	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1109	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.N1109T(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TGTATCTCCATTGTCCCAGCT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	96	95					6																	79675473		2203	4298	6501	79732192	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3326A>C	6.37:g.79675473T>G	ENSP00000275034:p.Asn1109Thr		79732192	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154589	0.57259	.	.	ENSG00000146247	ENST00000275034	T	0.39787	1.06	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.53530	0.1802	M	0.66506	2.035	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.73380	0.98;0.98	T	0.54351	-0.8307	9	.	.	.	-21.7131	15.1344	0.72552	0.0:0.0:0.0:1.0	.	1109;1109	A7J992;Q8WWQ0	.;PHIP_HUMAN	T	1109	ENSP00000275034:N1109T	.	N	-	2	0	PHIP	79732192	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.608000	0.82898	2.232000	0.73038	0.528000	0.53228	AAT		0.279	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			G	79675473	T	G	79675473	3	3	58	1	0	0	0	0	1	0	0	0	11873	1493	52	4	2187	4	PHIP	6	79675473	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	27760482	79675473	91439594	69	7715										
GJB7	375519	broad.mit.edu	37	chr6	87994312	87994312	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgggctgacatagagtttctTtctgtgccttttctctctac	8	10	4	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:87994312T>C	ENST00000525899.1	-	3	664	c.319A>G	c.(319-321)Aag>Gag	p.K107E	GJB7_ENST00000296882.3_Missense_Mutation_p.K107E	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	107					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.K107E(1)		endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		TAGAGTTTCTTTCTGTGCCTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	97	97					6																	87994312		2203	4300	6503	88051031	SO:0001583	missense	375519			AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"Ion channels / Gap junction proteins (connexins)"	16690	protein-coding gene	gene with protein product	"connexin 25"	611921	"gap junction protein, beta 7"				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.319A>G	6.37:g.87994312T>C	ENSP00000435355:p.Lys107Glu		88051031	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	37	CCDS5008.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.729301	0.00687	.	.	ENSG00000164411	ENST00000525899;ENST00000296882;ENST00000369576	D;D;D	0.99042	-5.36;-5.36;-5.36	4.84	3.59	0.41128	Connexin, N-terminal (1);	0.207536	0.20002	U	0.101315	D	0.90830	0.7120	N	0.20445	0.575	0.23743	N	0.996967	B	0.06786	0.001	B	0.04013	0.001	T	0.82265	-0.0543	10	0.02654	T	1	.	10.0214	0.42046	0.0:0.0:0.2576:0.7424	.	107	Q6PEY0	CXB7_HUMAN	E	107	ENSP00000435355:K107E;ENSP00000296882:K107E;ENSP00000358589:K107E	ENSP00000296882:K107E	K	-	1	0	GJB7	88051031	0.974000	0.33945	0.993000	0.49108	0.195000	0.23768	1.112000	0.31172	1.807000	0.52817	0.459000	0.35465	AAG		0.438	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1			C	87994312	T	C	87994312	3	2	58	1	0	0	0	0	1	0	0	0	6433	1850	64	4	356	4	GJB7	6	87994312	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	8318839	87994312	83120755	70	7716										
NUS1	116150	broad.mit.edu	37	chr6	118014243	118014243	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	attccagattgatggatgaaAttttaaaacaacagcaagaa	7	5	0	4			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:118014243A>G	ENST00000368494.3	+	2	623	c.454A>G	c.(454-456)Att>Gtt	p.I152V		NM_138459.3	NP_612468.1	Q96E22	NGBR_HUMAN	nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae)	152					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|intracellular cholesterol transport (GO:0032367)|protein glycosylation (GO:0006486)|sterol homeostasis (GO:0055092)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)	p.I152V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|prostate(2)	8		all_cancers(87;0.0395)|all_epithelial(87;0.0301)		GBM - Glioblastoma multiforme(226;0.02)|OV - Ovarian serous cystadenocarcinoma(136;0.115)|all cancers(137;0.146)		GATGGATGAAATTTTAAAACA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											29	32	31					6																	118014243		2194	4289	6483	118120936	SO:0001583	missense	116150			BC013026	CCDS5118.1	6q22.1	2012-12-13	2006-11-24	2006-11-24	ENSG00000153989	ENSG00000153989			21042	protein-coding gene	gene with protein product	"Nogo-B receptor", "transport and golgi organization 14 homolog (Drosophila)"	610463	"chromosome 6 open reading frame 68"	C6orf68			Standard	NM_138459		Approved	MGC7199, NgBR, TANGO14	uc003pxw.3	Q96E22	OTTHUMG00000015458	ENST00000368494.3:c.454A>G	6.37:g.118014243A>G	ENSP00000357480:p.Ile152Val		118120936	B2RWQ4|O00251	Missense_Mutation	SNP	ENST00000368494.3	37	CCDS5118.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854612	0.51376	.	.	ENSG00000153989	ENST00000368494	T	0.16897	2.31	5.68	5.68	0.88126	.	0.046662	0.85682	D	0.000000	T	0.08582	0.0213	L	0.33753	1.03	0.49798	D	0.999822	P	0.43431	0.807	P	0.45913	0.497	T	0.20538	-1.0272	10	0.24483	T	0.36	-2.9742	10.5563	0.45118	0.9278:0.0:0.0722:0.0	.	152	Q96E22	NGBR_HUMAN	V	152	ENSP00000357480:I152V	ENSP00000357480:I152V	I	+	1	0	NUS1	118120936	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.997000	0.70646	2.289000	0.77006	0.533000	0.62120	ATT		0.313	NUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041989.1	NM_138459		G	118014243	A	G	118014243	3	3	58	1	0	0	0	0	1	0	0	0	10808	101	4	4	460	4	NUS1	6	118014243	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	30019931	118014243	53100824	71	7717										
C6orf174	387104	broad.mit.edu	37	chr6	127796803	127796803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcgagtgggcgtgaggcagcGgatgttgcgcacctcctccg	17	12	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr6:127796803G>A	ENST00000525778.1	-	6	3113	c.2368C>T	c.(2368-2370)Cgc>Tgc	p.R790C	SOGA3_ENST00000556132.1_Missense_Mutation_p.R790C|SOGA3_ENST00000474293.2_5'UTR|SOGA3_ENST00000368268.2_Missense_Mutation_p.R790C|SOGA3_ENST00000481848.2_Missense_Mutation_p.R790C|SOGA3_ENST00000465909.2_Missense_Mutation_p.R790C			Q5TF21	SOGA3_HUMAN	SOGA family member 3	790					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.R790C(1)									GTGAGGCAGCGGATGTTGCGC	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	6											21	27	25					6																	127796803		2124	4232	6356	127838496	SO:0001583	missense	387104			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2368C>T	6.37:g.127796803G>A	ENSP00000434570:p.Arg790Cys		127838496		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928261	0.92389	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.45637	0.1352	L	0.51422	1.61	0.80722	D	1	D	0.69078	0.997	P	0.60286	0.872	T	0.43114	-0.9411	10	0.72032	D	0.01	-15.0059	19.4355	0.94792	0.0:0.0:1.0:0.0	.	790	Q5TF21	CF174_HUMAN	C	790	ENSP00000451768:R790C;ENSP00000357251:R790C;ENSP00000434570:R790C;ENSP00000435559:R790C	ENSP00000435559:R790C	R	-	1	0	C6orf174	127838496	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.508000	0.73721	2.593000	0.87608	0.462000	0.41574	CGC		0.701	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		A	127796803	G	A	127796803	3	1	58	1	0	0	0	0	1	0	0	0	2351	1116	39	1	483	1	C6orf174	6	127796803	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	9782560	127796803	43318264	72	7718										
IQCE	23288	broad.mit.edu	37	chr7	2632682	2632682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ggtgaagcagctcctgcaggCgaaggccgacctggagaagg	17	10	0	2	rs200474974		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:2632682C>T	ENST00000402050.2	+	15	1455	c.1271C>T	c.(1270-1272)gCg>gTg	p.A424V	IQCE_ENST00000325979.7_Missense_Mutation_p.A359V|IQCE_ENST00000404984.1_Missense_Mutation_p.A373V|IQCE_ENST00000438376.2_Missense_Mutation_p.A408V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	424						mitochondrion (GO:0005739)		p.A424V(2)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		CTCCTGCAGGCGAAGGCCGAC	0.572																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	7						C	VAL/ALA,VAL/ALA	0,4256		0,0,2128	106	130	122		1223,1271	2.2	0	7		122	1,8481		0,1,4240	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	64,64	0,1,6368	TT,TC,CC		0.0118,0.0,0.0079	benign,benign	408/680,424/696	2632682	1,12737	2128	4241	6369	2599208	SO:0001583	missense	23288			AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1271C>T	7.37:g.2632682C>T	ENSP00000385597:p.Ala424Val		2599208	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	C	6.604	0.479857	0.12581	0.0	1.18E-4	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.03	2.22	0.28083	.	0.557965	0.17201	N	0.183130	T	0.27731	0.0682	L	0.38175	1.15	0.09310	N	1	B;B;P;B;B;B	0.41784	0.369;0.369;0.762;0.051;0.369;0.068	B;B;B;B;B;B	0.36845	0.041;0.041;0.234;0.013;0.023;0.021	T	0.07558	-1.0766	10	0.31617	T	0.26	-0.6608	7.6824	0.28522	0.0:0.7274:0.0:0.2726	.	359;408;359;424;424;408	B4DXN1;B4DDX4;Q6IPM2-2;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;.;IQCE_HUMAN;.;.	V	424;373;408;359	ENSP00000385597:A424V;ENSP00000385945:A373V;ENSP00000396178:A408V;ENSP00000313772:A359V	ENSP00000313772:A359V	A	+	2	0	IQCE	2599208	0.010000	0.17322	0.000000	0.03702	0.148000	0.21650	0.259000	0.18405	0.246000	0.21394	-0.258000	0.10820	GCG		0.572	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		T	2632682	C	T	2632682	3	4	58	1	0	0	0	0	1	0	0	0	7827	768	27	1	1329	1	IQCE	7	2632682	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		2632682	156505981	73	7719										
OCM	654231	broad.mit.edu	37	chr7	5922227	5922227	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cggttcatagacaacgaccaGagcgggtacctggatgaaga	13	9	1	4	rs541796052		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:5922227G>A	ENST00000242104.5	+	2	257	c.165G>A	c.(163-165)caG>caA	p.Q55Q	OCM_ENST00000416608.1_Silent_p.Q55Q	NM_001097622.1	NP_001091091.1	P0CE72	ONCO_HUMAN	oncomodulin	55	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.Q55Q(1)		endometrium(1)|large_intestine(3)|lung(2)	6		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)		ACAACGACCAGAGCGGGTACC	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	7											134	114	121					7																	5922227		2203	4300	6503	5888753	SO:0001819	synonymous_variant	654231			BC069468	CCDS43548.1	7p22.1	2013-01-10						"EF-hand domain containing"	8105	protein-coding gene	gene with protein product	"oncomodulin 1"	164795				1559707, 8354278	Standard	NM_001097622		Approved	OCM1	uc003spe.4	P0CE72		ENST00000242104.5:c.165G>A	7.37:g.5922227G>A			5888753	B9EJH7|P32930|Q6ISI5|Q75MW0	Silent	SNP	ENST00000242104.5	37	CCDS43548.1																																																																																				0.527	OCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340372.1	NM_001097622		A	5922227	G	A	5922227	2	1	58	1	0	0	0	0	0	0	0	1	10852	933	33	3		3	OCM	7	5922227	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	3289545	5922227	153216436	74	7720										
IGFBP3	3486	broad.mit.edu	37	chr7	45956888	45956888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	actcgtagtcaactttgtagCgctggctgtctttagcatgc	10	10	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:45956888C>T	ENST00000275521.6	-	2	687	c.554G>A	c.(553-555)cGc>cAc	p.R185H	IGFBP3_ENST00000381086.5_Missense_Mutation_p.R88H|IGFBP3_ENST00000381083.4_Missense_Mutation_p.R191H|IGFBP3_ENST00000465642.1_5'UTR	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	185					apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)	p.R185H(1)		large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	AACTTTGTAGCGCTGGCTGTC	0.502											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	7											170	149	156					7																	45956888		2203	4300	6503	45923413	SO:0001583	missense	3486				CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"growth hormone-dependent binding protein", "acid stable subunit of the 140 K IGF complex", "binding protein 53", "binding protein 29", "IGF-binding protein 3"	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.554G>A	7.37:g.45956888C>T	ENSP00000275521:p.Arg185His	935	45923413	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	37	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.649489|4.649489	0.87958|0.87958	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000428530|ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047;ENST00000448817	.|T;T;T;T	.|0.27890	.|2.34;1.68;2.36;1.64	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Thyroglobulin type-1 (1);	.|2.918300	.|0.00843	.|N	.|0.001760	T|T	0.63988|0.63988	0.2558|0.2558	M|M	0.81239|0.81239	2.535|2.535	0.40816|0.40816	D|D	0.983469|0.983469	.|D;D;D	.|0.71674	.|0.998;0.998;0.998	.|D;D;D	.|0.66351	.|0.943;0.943;0.943	T|T	0.38672|0.38672	-0.9650|-0.9650	5|10	.|0.72032	.|D	.|0.01	-52.4084|-52.4084	15.0203|15.0203	0.71624|0.71624	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|88;185;170	.|B3KWK7;P17936;B4DN53	.|.;IBP3_HUMAN;.	T|H	37|162;185;88;171;83;191;157;75	.|ENSP00000275521:R185H;ENSP00000370476:R88H;ENSP00000370473:R191H;ENSP00000389668:R75H	.|ENSP00000275521:R185H	A|R	-|-	1|2	0|0	IGFBP3|IGFBP3	45923413|45923413	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.750000|4.750000	0.62162|0.62162	2.613000|2.613000	0.88420|0.88420	0.655000|0.655000	0.94253|0.94253	GCT|CGC		0.502	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398		T	45956888	C	T	45956888	3	4	58	1	0	0	0	0	1	0	0	0	7601	768	27	1	333	1	IGFBP3	7	45956888	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	40034661	45956888	113181775	75	7721										
TNS3	64759	broad.mit.edu	37	chr7	47342747	47342748	+	Frame_Shift_Ins	INS	-	-	T													0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcagggtcacaccctggcccINStgcaggcctggactgtggtg							TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:47342747_47342748insT	ENST00000398879.1	-	22	3623_3624	c.3257_3258insA	c.(3256-3258)cagfs	p.Q1086fs	TNS3_ENST00000311160.9_Frame_Shift_Ins_p.Q1086fs|TNS3_ENST00000355730.3_Frame_Shift_Ins_p.Q846fs			Q68CZ2	TENS3_HUMAN	tensin 3	1086					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.Q1088fs*13(1)		NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CACCCTGGCCCTGCAGGCCTGG	0.658																																																1	Insertion - Frameshift(1)	large_intestine(1)	7																																								47309273	SO:0001589	frameshift_variant	64759			AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3258dupA	7.37:g.47342748_47342748dupT	ENSP00000381854:p.Gln1086fs		47309272	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Frame_Shift_Ins	INS	ENST00000398879.1	37	CCDS5506.2																																																																																				0.658	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47342748	-	T	47342747	7	5	58	1	0	1	1	0	0	0	0	0	16383	680	24	0	1119	0	TNS3	7	47342747	Frame_Shift_Ins	INS	-	TCGA-AG-4007-01A-01W-1073-09	1385859	47342747	111795916	76	7722										
DNAJC30	84277	broad.mit.edu	37	chr7	73097234	73097234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccgttcccgctccagttgttCcccgtagtgggcctggtaga	12	14	0	1	rs137909145		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:73097234C>T	ENST00000395176.2	-	1	549	c.520G>A	c.(520-522)Gaa>Aaa	p.E174K	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000265758.2_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	174						mitochondrion (GO:0005739)		p.E174K(1)		kidney(1)|large_intestine(2)|lung(1)	4						TCCAGTTGTTCCCCGTAGTGG	0.682													C|||	1	0.000199681	0	0	5008	,	,		12861	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	7						C	LYS/GLU	1,4405		0,1,2202	33	34	34		520	4.3	0.7	7	dbSNP_134	34	0,8600		0,0,4300	no	missense	DNAJC30	NM_032317.2	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	174/227	73097234	1,13005	2203	4300	6503	72735170	SO:0001583	missense	84277			AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"Heat shock proteins / DNAJ (HSP40)"	16410	protein-coding gene	gene with protein product			"Williams Beuren syndrome chromosome region 18"	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.520G>A	7.37:g.73097234C>T	ENSP00000378605:p.Glu174Lys		72735170	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	37	CCDS5556.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685288	0.88639	2.27E-4	0.0	ENSG00000176410	ENST00000395176	T	0.55234	0.53	5.2	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.68072	0.2961	M	0.81239	2.535	0.41980	D	0.990795	D	0.76494	0.999	P	0.59546	0.859	T	0.72924	-0.4144	10	0.62326	D	0.03	.	11.3409	0.49533	0.0:0.9124:0.0:0.0876	.	174	Q96LL9	DJC30_HUMAN	K	174	ENSP00000378605:E174K	ENSP00000378605:E174K	E	-	1	0	DNAJC30	72735170	0.997000	0.39634	0.702000	0.30337	0.978000	0.69477	3.733000	0.55029	1.431000	0.47355	0.555000	0.69702	GAA		0.682	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2			T	73097234	C	T	73097234	3	4	58	1	0	0	0	0	1	0	0	0	4659	864	30	3	164	3	DNAJC30	7	73097234	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	25754487	73097234	86041429	77	7723										
ZP3	7784	broad.mit.edu	37	chr7	76062286	76062286	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gccatcctgcccacctggttGcccttcaggaccacggtgtt	10	16	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:76062286G>T	ENST00000394857.3	+	3	532	c.474G>T	c.(472-474)ttG>ttT	p.L158F	ZP3_ENST00000416245.1_5'UTR|ZP3_ENST00000336517.4_Missense_Mutation_p.L107F	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	158	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)	p.L107F(1)		endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						CCACCTGGTTGCCCTTCAGGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											96	80	85					7																	76062286		2203	4300	6503	75900222	SO:0001583	missense	7784			M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"Zona pellucida glycoproteins"	13189	protein-coding gene	gene with protein product		182889	"zona pellucida glycoprotein 3A (sperm receptor)"	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.474G>T	7.37:g.76062286G>T	ENSP00000378326:p.Leu158Phe		75900222	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474141	0.63737	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121	D;D	0.82526	-1.62;-1.62	5.4	1.01	0.19927	Zona pellucida sperm-binding protein (3);	0.701438	0.13976	N	0.349833	T	0.74711	0.3752	N	0.24115	0.695	0.80722	D	1	D;B	0.54964	0.969;0.205	P;B	0.51385	0.668;0.215	T	0.71567	-0.4554	10	0.72032	D	0.01	-9.1927	3.2396	0.06776	0.0851:0.2096:0.4368:0.2685	.	107;158	P21754-3;P21754	.;ZP3_HUMAN	F	107;158;158	ENSP00000337310:L107F;ENSP00000378326:L158F	ENSP00000337310:L107F	L	+	3	2	ZP3	75900222	0.969000	0.33509	1.000000	0.80357	0.899000	0.52679	0.017000	0.13399	0.616000	0.30141	-0.221000	0.12465	TTG		0.592	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			T	76062286	G	T	76062286	3	4	58	1	0	0	0	0	1	0	0	0	18256	1310	46	2	484	2	ZP3	7	76062286	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	2965052	76062286	83076377	78	7724										
TSC22D4	81628	broad.mit.edu	37	chr7	100065186	100065186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttctcttaccatggcttgctCgattttgttgtcaatgccaa	7	10	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:100065186C>T	ENST00000300181.2	-	4	1721	c.967G>A	c.(967-969)Gag>Aag	p.E323K	TSC22D4_ENST00000496728.1_5'UTR|TSC22D4_ENST00000393991.1_Missense_Mutation_p.E84K	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	323					negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E323K(1)		breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATGGCTTGCTCGATTTTGTTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	7											145	135	139					7																	100065186		2203	4300	6503	99903122	SO:0001583	missense	81628			BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.967G>A	7.37:g.100065186C>T	ENSP00000300181:p.Glu323Lys		99903122	A4D2C3|A8MWR6|D6W5V9	Missense_Mutation	SNP	ENST00000300181.2	37	CCDS5695.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.786748	0.49997	.	.	ENSG00000166925	ENST00000300181;ENST00000393991	.	.	.	4.51	2.65	0.31530	.	0.450054	0.18859	N	0.129193	T	0.25232	0.0613	N	0.19112	0.55	0.47659	D	0.999489	D	0.52996	0.957	B	0.34301	0.179	T	0.04579	-1.0941	9	0.87932	D	0	-1.9329	7.6241	0.28202	0.0:0.7372:0.1678:0.095	.	323	Q9Y3Q8	T22D4_HUMAN	K	323;84	.	ENSP00000300181:E323K	E	-	1	0	TSC22D4	99903122	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	5.451000	0.66632	0.426000	0.26116	-0.181000	0.13052	GAG		0.577	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1	NM_030935		T	100065186	C	T	100065186	3	4	58	1	0	0	0	0	1	0	0	0	16650	893	31	1	228	1	TSC22D4	7	100065186	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	24002900	100065186	59073477	79	7725										
UBN2	254048	broad.mit.edu	37	chr7	138943309	138943309	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	acactggcactctacagtttCgccaagcttcagatactgaa	7	12	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:138943309C>T	ENST00000473989.3	+	4	739	c.739C>T	c.(739-741)Cgc>Tgc	p.R247C	UBN2_ENST00000288561.8_Missense_Mutation_p.R164C	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	247						extracellular space (GO:0005615)|nucleus (GO:0005634)		p.R164C(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						TCTACAGTTTCGCCAAGCTTC	0.363																																																2	Substitution - Missense(2)	urinary_tract(1)|large_intestine(1)	7											103	93	96					7																	138943309		1852	4090	5942	138593849	SO:0001583	missense	254048			AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.739C>T	7.37:g.138943309C>T	ENSP00000418648:p.Arg247Cys		138593849	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Missense_Mutation	SNP	ENST00000473989.3	37	CCDS43655.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289874	0.80914	.	.	ENSG00000157741	ENST00000486663;ENST00000473989;ENST00000288561	T;T;T	0.28069	1.63;1.63;1.63	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.55561	0.1928	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58651	-0.7599	10	0.87932	D	0	-7.8458	14.138	0.65300	0.1501:0.8499:0.0:0.0	.	247	Q6ZU65	UBN2_HUMAN	C	70;247;164	ENSP00000417849:R70C;ENSP00000418648:R247C;ENSP00000288561:R164C	ENSP00000288561:R164C	R	+	1	0	UBN2	138593849	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.521000	0.53472	2.628000	0.89032	0.460000	0.39030	CGC		0.363	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569		T	138943309	C	T	138943309	3	4	58	1	0	0	0	0	1	0	0	0	16933	884	31	1	753	1	UBN2	7	138943309	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	38878123	138943309	20195354	80	7726										
MGAM	8972	broad.mit.edu	37	chr7	141705401	141705402	+	Frame_Shift_Ins	INS	-	-	A													0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gttcttctgcttgtgttgttINStatcatcagtattgttctaa							TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:141705401_141705402insA	ENST00000549489.2	+	2	166_167	c.71_72insA	c.(70-75)tttatcfs	p.FI24fs	MGAM_ENST00000475668.2_Frame_Shift_Ins_p.FI24fs	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	24					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.F24fs*48(3)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTTGTGTTGTTTATCATCAGTA	0.342																																																3	Insertion - Frameshift(3)	large_intestine(3)	7																																								141351871	SO:0001589	frameshift_variant	8972			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	Exception_encountered	7.37:g.141705401_141705402insA	ENSP00000447378:p.Phe24fs		141351870	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Ins	INS	ENST00000549489.2	37	CCDS47727.1																																																																																				0.342	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141705402	-	A	141705401	7	5	58	1	0	1	1	0	0	0	0	0	9571	1841	64	0	73	0	MGAM	7	141705401	Frame_Shift_Ins	INS	-	TCGA-AG-4007-01A-01W-1073-09	2762092	141705401	17433262	81	7727										
CLCN1	1180	broad.mit.edu	37	chr7	143047530	143047530	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gattcctgctgtattgaccaGtctcccttccagctggtgga	10	12	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr7:143047530G>A	ENST00000343257.2	+	21	2556	c.2469G>A	c.(2467-2469)caG>caA	p.Q823Q		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	823	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.Q823Q(1)		breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					GTATTGACCAGTCTCCCTTCC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	7											124	101	108					7																	143047530		2203	4300	6503	142757652	SO:0001819	synonymous_variant	1180			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2469G>A	7.37:g.143047530G>A			142757652	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																				0.557	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143047530	G	A	143047530	2	1	58	1	0	0	0	0	0	0	0	1	3468	1020	36	3		3	CLCN1	7	143047530	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	1342129	143047530	16091133	82	7728										
CSMD1	64478	broad.mit.edu	37	chr8	4495006	4495006	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccaggtgcagttggcatagtTcggatacccgtgaggaaacc	13	10	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr8:4495006T>A	ENST00000520002.1	-	2	715	c.160A>T	c.(160-162)Aac>Tac	p.N54Y	CSMD1_ENST00000537824.1_Missense_Mutation_p.N54Y|CSMD1_ENST00000539096.1_Missense_Mutation_p.N54Y|CSMD1_ENST00000400186.3_Missense_Mutation_p.N54Y|CSMD1_ENST00000542608.1_Missense_Mutation_p.N54Y|CSMD1_ENST00000602557.1_Missense_Mutation_p.N54Y|CSMD1_ENST00000602723.1_Missense_Mutation_p.N54Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	54	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.N54Y(1)		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)		TTGGCATAGTTCGGATACCCG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											106	107	106					8																	4495006		1937	4153	6090	4482414	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.160A>T	8.37:g.4495006T>A	ENSP00000430733:p.Asn54Tyr		4482414	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	T	16.77	3.216358	0.58452	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	5.32	5.32	0.75619	.	.	.	.	.	T	0.61223	0.2330	M	0.89478	3.035	0.39734	D	0.97164	D	0.89917	1.0	D	0.91635	0.999	T	0.70941	-0.4735	9	0.87932	D	0	.	13.2346	0.59963	0.0:0.0:0.0:1.0	.	54	E5RIG2	.	Y	54	ENSP00000383047:N54Y;ENSP00000430733:N54Y;ENSP00000441462:N54Y;ENSP00000446243:N54Y;ENSP00000441675:N54Y	ENSP00000383047:N54Y	N	-	1	0	CSMD1	4482414	1.000000	0.71417	0.897000	0.35233	0.155000	0.21991	7.975000	0.88055	2.029000	0.59856	0.477000	0.44152	AAC		0.468	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	4495006	T	A	4495006	3	1	58	1	0	0	0	0	1	0	0	0	3950	1783	62	5	10623	5	CSMD1	8	4495006	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09		4495006	141869016	83	7729										
XKR4	114786	broad.mit.edu	37	chr8	56436504	56436504	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aacaaccgcagtgttgtcagCgaccgcgatcagaaattcgc	10	12	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr8:56436504C>T	ENST00000327381.6	+	3	1771	c.1671C>T	c.(1669-1671)agC>agT	p.S557S	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	557						integral component of membrane (GO:0016021)		p.S557S(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GTGTTGTCAGCGACCGCGATC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	8											66	68	68					8																	56436504		2203	4300	6503	56599058	SO:0001819	synonymous_variant	114786			AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1671C>T	8.37:g.56436504C>T			56599058	Q96PZ8	Silent	SNP	ENST00000327381.6	37	CCDS34893.1																																																																																				0.592	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		T	56436504	C	T	56436504	2	4	58	1	0	0	0	0	0	0	0	1	17473	767	27	1		1	XKR4	8	56436504	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	51941498	56436504	89927518	84	7730										
ABRA	137735	broad.mit.edu	37	chr8	107782396	107782396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcttggctgggccctccccgCtttccttttcgcccggagcc	10	18	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr8:107782396C>A	ENST00000311955.3	-	1	77	c.23G>T	c.(22-24)aGc>aTc	p.S8I		NM_139166.4	NP_631905.1			actin-binding Rho activating protein									p.S8I(1)		breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			GCCCTCCCCGCTTTCCTTTTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	8											37	41	40					8																	107782396		2201	4298	6499	107851572	SO:0001583	missense	137735			AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.23G>T	8.37:g.107782396C>A	ENSP00000311436:p.Ser8Ile		107851572		Missense_Mutation	SNP	ENST00000311955.3	37	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	C	5.954	0.360073	0.11296	.	.	ENSG00000174429	ENST00000311955	.	.	.	5.29	4.35	0.52113	.	0.493537	0.25601	N	0.029556	T	0.27933	0.0688	N	0.14661	0.345	0.09310	N	1	B	0.24882	0.113	B	0.18871	0.023	T	0.32455	-0.9906	9	0.72032	D	0.01	.	14.8959	0.70644	0.0:0.6747:0.3253:0.0	.	8	Q8N0Z2	ABRA_HUMAN	I	8	.	ENSP00000311436:S8I	S	-	2	0	ABRA	107851572	0.000000	0.05858	0.332000	0.25469	0.135000	0.20990	0.286000	0.18902	2.613000	0.88420	0.609000	0.83330	AGC		0.602	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		A	107782396	C	A	107782396	3	1	58	1	0	0	0	0	1	0	0	0	100	797	28	2	1130	2	ABRA	8	107782396	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	51345892	107782396	38581626	85	7731										
CSMD3	114788	broad.mit.edu	37	chr8	113267642	113267642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttgggcaggtataccagggtCaccacaaaactttgctggaa	11	9	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr8:113267642C>A	ENST00000297405.5	-	62	10121	c.9877G>T	c.(9877-9879)Gac>Tac	p.D3293Y	CSMD3_ENST00000455883.2_Missense_Mutation_p.D3124Y|CSMD3_ENST00000352409.3_Missense_Mutation_p.D3223Y|CSMD3_ENST00000343508.3_Missense_Mutation_p.D3253Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3293	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D3293Y(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATACCAGGGTCACCACAAAAC	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											88	84	85					8																	113267642		2203	4300	6503	113336818	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9877G>T	8.37:g.113267642C>A	ENSP00000297405:p.Asp3293Tyr		113336818	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204153	0.79127	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	4.99	4.99	0.66335	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.80768	0.4686	M	0.81942	2.565	0.80722	D	1	D;D;P	0.76494	0.999;0.999;0.876	D;D;P	0.81914	0.991;0.995;0.457	D	0.83503	0.0076	10	0.87932	D	0	.	18.485	0.90825	0.0:1.0:0.0:0.0	.	3124;3293;3253	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	3253;3293;2563;3124;3223	ENSP00000345799:D3253Y;ENSP00000297405:D3293Y;ENSP00000341558:D2563Y;ENSP00000412263:D3124Y;ENSP00000343124:D3223Y	ENSP00000297405:D3293Y	D	-	1	0	CSMD3	113336818	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.581000	0.82535	2.601000	0.87937	0.650000	0.86243	GAC		0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113267642	C	A	113267642	3	1	58	1	0	0	0	0	1	0	0	0	3952	826	29	2	1286	2	CSMD3	8	113267642	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	5485246	113267642	33096380	86	7732										
C9orf72	203228	broad.mit.edu	37	chr9	27566891	27566891	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttacatctatagcaccactCtctgcatttcgaaggatttc	5	11	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr9:27566891C>G	ENST00000380003.3	-	2	291	c.228G>C	c.(226-228)gaG>gaC	p.E76D	C9orf72_ENST00000379997.3_Missense_Mutation_p.E76D|C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	76					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)	p.E76D(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		TAGCACCACTCTCTGCATTTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	9											100	96	97					9																	27566891		2203	4300	6503	27556891	SO:0001583	missense	203228			AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.228G>C	9.37:g.27566891C>G	ENSP00000369339:p.Glu76Asp		27556891	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307577	0.60305	.	.	ENSG00000147894	ENST00000380003;ENST00000379997;ENST00000379995	T;T;T	0.45276	0.9;0.9;0.9	5.99	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.45577	0.1349	N	0.24115	0.695	0.58432	D	0.999998	D;P	0.61697	0.99;0.892	D;P	0.70935	0.971;0.641	T	0.37291	-0.9712	9	.	.	.	.	9.1847	0.37163	0.0:0.7736:0.0:0.2264	.	76;76	Q96LT7-2;Q96LT7	.;CI072_HUMAN	D	76	ENSP00000369339:E76D;ENSP00000369333:E76D;ENSP00000369331:E76D	.	E	-	3	2	C9orf72	27556891	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.033000	0.41136	1.540000	0.49301	0.655000	0.94253	GAG		0.393	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		G	27566891	C	G	27566891	3	3	58	1	0	0	0	0	1	0	0	0	2501	912	32	5	1261	5	C9orf72	9	27566891	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		27566891	113646540	87	7733										
APBA1	320	broad.mit.edu	37	chr9	72047482	72047482	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcattggagagaatgtggacGatcttctcgtggggggtggc	18	6	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr9:72047482G>A	ENST00000265381.4	-	12	2634	c.2412C>T	c.(2410-2412)atC>atT	p.I804I		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	804	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I804I(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						GAATGTGGACGATCTTCTCGT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	9											91	72	78					9																	72047482		2203	4300	6503	71237302	SO:0001819	synonymous_variant	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.2412C>T	9.37:g.72047482G>A			71237302	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	37	CCDS6630.1																																																																																				0.622	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72047482	G	A	72047482	2	1	58	1	0	0	0	0	0	0	0	1	756	1048	37	1		1	APBA1	9	72047482	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	44480591	72047482	69165949	88	7734										
VPS13A	23230	broad.mit.edu	37	chr9	79929571	79929571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aagacctcatgtcaagaaagCaactcctcggtatgtattgt	8	9	2	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr9:79929571C>T	ENST00000360280.3	+	37	4663	c.4403C>T	c.(4402-4404)gCa>gTa	p.A1468V	VPS13A_ENST00000376636.3_Missense_Mutation_p.A1429V|VPS13A_ENST00000376634.4_Missense_Mutation_p.A1468V|VPS13A_ENST00000357409.5_Missense_Mutation_p.A1468V|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1468					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.A1468V(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GTCAAGAAAGCAACTCCTCGG	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	9											49	52	51					9																	79929571		2188	4284	6472	79119391	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.4403C>T	9.37:g.79929571C>T	ENSP00000353422:p.Ala1468Val		79119391	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.445501	0.43429	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.49139	0.97;0.79;0.88;0.97	5.35	5.35	0.76521	.	0.171825	0.37906	N	0.001882	T	0.41026	0.1141	L	0.45051	1.395	0.80722	D	1	B;B;B;B	0.29766	0.036;0.163;0.256;0.256	B;B;B;B	0.33295	0.09;0.046;0.161;0.161	T	0.18745	-1.0327	10	0.13470	T	0.59	.	14.6651	0.68901	0.1459:0.8541:0.0:0.0	.	1429;1468;1468;1468	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	V	1468;1429;1468;1468	ENSP00000365821:A1468V;ENSP00000365823:A1429V;ENSP00000353422:A1468V;ENSP00000349985:A1468V	ENSP00000349985:A1468V	A	+	2	0	VPS13A	79119391	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.065000	0.64344	2.510000	0.84645	0.557000	0.71058	GCA		0.299	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79929571	C	T	79929571	3	4	58	1	0	0	0	0	1	0	0	0	17229	710	25	3	4549	3	VPS13A	9	79929571	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	7882089	79929571	61283860	89	7735										
CACNB2	783	broad.mit.edu	37	chr10	18803963	18803963	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aactgcaggcttgttttggcGgtttactgtgagtttttcct	11	7	0	1	rs373932682		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:18803963G>A	ENST00000324631.7	+	7	864				CACNB2_ENST00000396576.2_Intron|CACNB2_ENST00000282343.8_Intron|CACNB2_ENST00000352115.6_Missense_Mutation_p.R242Q|CACNB2_ENST00000377331.2_Missense_Mutation_p.R214Q|CACNB2_ENST00000377319.3_Intron|CACNB2_ENST00000377328.1_Intron|CACNB2_ENST00000377329.4_Intron|CACNB2_ENST00000377315.4_Intron|RP11-499P20.2_ENST00000425669.1_RNA	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)	p.R242Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TTGTTTTGGCGGTTTACTGTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											112	108	109					10																	18803963		2203	4300	6503	18843969	SO:0001627	intron_variant	783			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"Calcium channel subunits"	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.804+665G>A	10.37:g.18803963G>A			18843969	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	37	CCDS7125.1	.	.	.	.	.	.	.	.	.	.	G	10.18	1.280572	0.23392	.	.	ENSG00000165995	ENST00000352115;ENST00000377331	D;D	0.82526	-1.62;-1.62	5.43	4.52	0.55395	.	.	.	.	.	T	0.56963	0.2021	N	0.00841	-1.15	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.55444	-0.8140	9	0.42905	T	0.14	.	9.4879	0.38942	0.1763:0.0:0.8237:0.0	.	188;214;242	Q6TME1;A6PVM7;Q08289-8	.;.;.	Q	242;214	ENSP00000344474:R242Q;ENSP00000366548:R214Q	ENSP00000344474:R242Q	R	+	2	0	CACNB2	18843969	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.666000	0.37460	1.426000	0.47256	0.655000	0.94253	CGG		0.378	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724		A	18803963	G	A	18803963	1	1	58	0	1	0	0	0	0	0	0	0	2559	1116	39	1		1	CACNB2	10	18803963	Intron	SNP	G	TCGA-AG-4007-01A-01W-1073-09		18803963	116730784	90	7736										
NRG3	10718	broad.mit.edu	37	chr10	84745020	84745020	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcccttcagtgggtttagagGaaacctgcctgcaaatgcca	10	11	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:84745020G>T	ENST00000404547.1	+	10	1822	c.1822G>T	c.(1822-1824)Gaa>Taa	p.E608*	NRG3_ENST00000404576.2_Nonsense_Mutation_p.E388*|NRG3_ENST00000537893.1_Nonsense_Mutation_p.E234*|NRG3_ENST00000556918.1_Nonsense_Mutation_p.E414*|NRG3_ENST00000372142.2_Nonsense_Mutation_p.E387*|NRG3_ENST00000372141.2_Nonsense_Mutation_p.E584*|NRG3_ENST00000545131.1_Nonsense_Mutation_p.E234*			P56975	NRG3_HUMAN	neuregulin 3	608					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.E584*(1)|p.E387*(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GGGTTTAGAGGAAACCTGCCT	0.463																																																2	Substitution - Nonsense(2)	large_intestine(2)	10											106	110	109					10																	84745020		2203	4300	6503	84735000	SO:0001587	stop_gained	10718			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1822G>T	10.37:g.84745020G>T	ENSP00000384796:p.Glu608*		84735000	A4D7U1|Q0PEH2|Q5VYH3	Nonsense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049770	0.75846	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	.	.	.	5.95	5.95	0.96441	.	0.135483	0.51477	D	0.000095	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-30.5666	17.8962	0.88888	0.0:0.0:1.0:0.0	.	.	.	.	X	584;608;583;387;388;414;234;234	.	ENSP00000361214:E584X	E	+	1	0	NRG3	84735000	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.668000	0.74457	2.827000	0.97445	0.650000	0.86243	GAA		0.463	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		T	84745020	G	T	84745020	4	4	58	1	0	0	0	0	0	1	0	0	10680	1175	41	2	2028	2	NRG3	10	84745020	Nonsense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	65941057	84745020	50789727	91	7737										
KIF20B	9585	broad.mit.edu	37	chr10	91474900	91474900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tccaaaagagaaagatgctgCgcctttcccaagacgtaaag	9	10	0	3	rs138800578	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:91474900C>T	ENST00000371728.3	+	8	966	c.901C>T	c.(901-903)Cgc>Tgc	p.R301C	KIF20B_ENST00000260753.4_Missense_Mutation_p.R301C|KIF20B_ENST00000394289.2_Missense_Mutation_p.R301C|KIF20B_ENST00000416354.1_Missense_Mutation_p.R301C	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	301	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.R301C(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AAAGATGCTGCGCCTTTCCCA	0.313													C|||	5	0.000998403	0	0	5008	,	,		15681	0.005		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											42	46	45					10																	91474900		2197	4285	6482	91464880	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.901C>T	10.37:g.91474900C>T	ENSP00000360793:p.Arg301Cys		91464880	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	22.4	4.288186	0.80803	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.36	5.36	0.76844	Kinesin, motor domain (4);	0.000000	0.47852	D	0.000208	D	0.84538	0.5494	M	0.81942	2.565	0.80722	D	1	D;P	0.89917	1.0;0.783	D;P	0.91635	0.999;0.661	D	0.87388	0.2361	10	0.87932	D	0	-3.9588	14.3059	0.66384	0.1485:0.8515:0.0:0.0	.	301;301	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	C	301	ENSP00000260753:R301C;ENSP00000411545:R301C;ENSP00000377830:R301C;ENSP00000360793:R301C	ENSP00000260753:R301C	R	+	1	0	KIF20B	91464880	0.999000	0.42202	0.960000	0.40013	0.995000	0.86356	4.304000	0.59104	2.674000	0.91012	0.650000	0.86243	CGC		0.313	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		T	91474900	C	T	91474900	3	4	58	1	0	0	0	0	1	0	0	0	8308	768	27	1	927	1	KIF20B	10	91474900	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	6729880	91474900	44059847	92	7738										
LCOR	84458	broad.mit.edu	37	chr10	98715591	98715591	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gaaaaagatgaaattaatgaGgtcggaggggccagatgttt	14	3	0	4			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:98715591G>T	ENST00000371097.4	+	8	1760	c.1214G>T	c.(1213-1215)aGg>aTg	p.R405M	LCOR_ENST00000540664.1_Splice_Site_p.S405I|LCOR_ENST00000356016.3_Missense_Mutation_p.R405M|LCOR_ENST00000371103.3_Missense_Mutation_p.R405M|LCOR_ENST00000498444.1_Intron			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	405					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R405M(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		AAATTAATGAGGTCGGAGGGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											43	46	45					10																	98715591		2203	4300	6503	98705581	SO:0001583	missense	84458				CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233			29503	protein-coding gene	gene with protein product		607698				12535528, 15193453	Standard	NM_001170765		Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000371097.4:c.1214G>T	10.37:g.98715591G>T	ENSP00000360138:p.Arg405Met		98705581	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	Missense_Mutation	SNP	ENST00000371097.4	37	CCDS7451.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.39|13.39	2.224355|2.224355	0.39300|0.39300	.|.	.|.	ENSG00000196233|ENSG00000196233	ENST00000371103;ENST00000371097;ENST00000356016|ENST00000540664	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Homeodomain-like (1);|.	0.075176|.	0.64402|.	D|.	0.000001|.	T|T	0.29684|0.29684	0.0741|0.0741	N|N	0.14661|0.14661	0.345|0.345	0.27937|0.27937	N|N	0.937664|0.937664	P|B	0.47350|0.20368	0.894|0.044	B|B	0.44044|0.17433	0.439|0.018	T|T	0.19063|0.19063	-1.0317|-1.0317	9|8	0.66056|0.87932	D|D	0.02|0	-0.0971|-0.0971	13.0708|13.0708	0.59059|0.59059	0.0736:0.0:0.9264:0.0|0.0736:0.0:0.9264:0.0	.|.	405|405	Q96JN0|Q96JN0-2	LCOR_HUMAN|.	M|I	405|405	.|.	ENSP00000348298:R405M|ENSP00000443431:S405I	R|S	+|+	2|2	0|0	LCOR|LCOR	98705581|98705581	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.883000|4.883000	0.63128|0.63128	2.759000|2.759000	0.94783|0.94783	0.555000|0.555000	0.69702|0.69702	AGG|AGT		0.423	LCOR-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049628.2			T	98715591	G	T	98715591	3	4	58	1	0	0	0	0	1	0	0	0	8711	1014	35	2	1224	2	LCOR	10	98715591	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	7240691	98715591	36819156	93	7739										
SORCS1	114815	broad.mit.edu	37	chr10	108431124	108431124	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctcccatgatacatgcttccCcctgtaagcagagaaggatc	8	13	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:108431124C>T	ENST00000263054.6	-	16	2067	c.2060G>A	c.(2059-2061)gGg>gAg	p.G687E	SORCS1_ENST00000369698.1_Splice_Site_p.G222E|SORCS1_ENST00000344440.6_Splice_Site_p.G687E	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	687					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.G687E(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ACATGCTTCCCCCTGTAAGCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											186	164	171					10																	108431124		2203	4300	6503	108421114	SO:0001630	splice_region_variant	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2059-1G>A	10.37:g.108431124C>T			108421114	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.406782	0.83230	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.51071	0.72;0.72;0.72	5.87	5.87	0.94306	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.68421	0.2999	M	0.62209	1.925	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.999	T	0.63247	-0.6680	9	.	.	.	-23.8546	20.5827	0.99408	0.0:1.0:0.0:0.0	.	687;687;687;687;687	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	E	222;687;687	ENSP00000358712:G222E;ENSP00000263054:G687E;ENSP00000345964:G687E	.	G	-	2	0	SORCS1	108421114	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	5.717000	0.68446	2.941000	0.99782	0.655000	0.94253	GGG		0.438	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	Missense_Mutation	T	108431124	C	T	108431124	5	4	58	1	0	0	0	0	0	0	1	0	14967	637	22	3	1724	3	SORCS1	10	108431124	Splice_Site	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9715533	108431124	27103623	94	7740										
TCF7L2	6934	broad.mit.edu	37	chr10	114920390	114920390	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gctaacagatgcaaatactcCaaagaagtgtcgggcactgt	10	9	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr10:114920390C>A	ENST00000355995.4	+	14	1949				TCF7L2_ENST00000543371.1_Missense_Mutation_p.P444Q|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000352065.5_Intron|TCF7L2_ENST00000466338.1_Intron|TCF7L2_ENST00000369397.4_Intron|TCF7L2_ENST00000536810.1_Intron|TCF7L2_ENST00000369389.1_Intron|TCF7L2_ENST00000545257.1_Missense_Mutation_p.P461Q|TCF7L2_ENST00000534894.1_Silent_p.S485S|TCF7L2_ENST00000538897.1_Intron|TCF7L2_ENST00000355717.4_Intron|TCF7L2_ENST00000369386.1_Silent_p.S111S			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)						blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P444Q(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GCAAATACTCCAAAGAAGTGT	0.448			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	1	Substitution - Missense(1)	large_intestine(1)	10											85	71	76					10																	114920390		1568	3582	5150	114910380	SO:0001627	intron_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1442+639C>A	10.37:g.114920390C>A			114910380	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	C	18.18	3.566503	0.65651	.	.	ENSG00000148737	ENST00000545257;ENST00000543371	D;D	0.98633	-4.94;-5.04	5.15	5.15	0.70609	.	.	.	.	.	D	0.97692	0.9243	.	.	.	0.80722	D	1	B;P;B;B	0.47841	0.23;0.901;0.23;0.202	B;P;B;B	0.45474	0.138;0.482;0.05;0.153	D	0.97439	1.0020	8	0.30854	T	0.27	.	18.9807	0.92754	0.0:1.0:0.0:0.0	.	461;376;421;444	Q9NQB0;C6ZRJ6;C6ZRJ8;Q9NQB0-7	TF7L2_HUMAN;.;.;.	Q	461;444	ENSP00000440547:P461Q;ENSP00000444972:P444Q	ENSP00000444972:P444Q	P	+	2	0	TCF7L2	114910380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.305000	0.78891	2.549000	0.85964	0.655000	0.94253	CCA		0.448	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114920390	C	A	114920390	1	1	58	0	1	0	0	0	0	0	0	0	15737	594	21	2		2	TCF7L2	10	114920390	Intron	SNP	C	TCGA-AG-4007-01A-01W-1073-09	6489266	114920390	20614357	95	7741										
KCNC1	3746	broad.mit.edu	37	chr11	17793429	17793429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	caccttcgagttcctcatgcGtgtcatcttctgccccaaca	6	16	4	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:17793429G>A	ENST00000379472.3	+	2	818	c.788G>A	c.(787-789)cGt>cAt	p.R263H	KCNC1_ENST00000265969.6_Missense_Mutation_p.R263H	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	263					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.R263H(1)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	TTCCTCATGCGTGTCATCTTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11											305	259	275					11																	17793429		2200	4293	6493	17750005	SO:0001583	missense	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.788G>A	11.37:g.17793429G>A	ENSP00000368785:p.Arg263His		17750005	K4DI87	Missense_Mutation	SNP	ENST00000379472.3	37	CCDS7827.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.772471	0.69992	.	.	ENSG00000129159	ENST00000265969;ENST00000379472	D;D	0.98684	-5.07;-5.07	4.77	4.77	0.60923	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99174	0.9714	M	0.84846	2.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.99501	1.0953	10	0.66056	D	0.02	.	17.808	0.88607	0.0:0.0:1.0:0.0	.	263;263	Q3KNS8;P48547	.;KCNC1_HUMAN	H	263	ENSP00000265969:R263H;ENSP00000368785:R263H	ENSP00000265969:R263H	R	+	2	0	KCNC1	17750005	1.000000	0.71417	0.994000	0.49952	0.883000	0.51084	9.869000	0.99810	2.202000	0.70862	0.555000	0.69702	CGT		0.567	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		A	17793429	G	A	17793429	3	1	58	1	0	0	0	0	1	0	0	0	8035	1145	40	1	794	1	KCNC1	11	17793429	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		17793429	117213087	96	7742										
CAT	847	broad.mit.edu	37	chr11	34478355	34478355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	attgaggccagtcctgacaaAatgcttcaggtgagcctggt	12	9	1	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:34478355A>T	ENST00000241052.4	+	8	1136	c.1047A>T	c.(1045-1047)aaA>aaT	p.K349N		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	349					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.K349N(1)		breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	GTCCTGACAAAATGCTTCAGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											77	61	66					11																	34478355		2202	4298	6500	34434931	SO:0001583	missense	847			AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.1047A>T	11.37:g.34478355A>T	ENSP00000241052:p.Lys349Asn		34434931	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Missense_Mutation	SNP	ENST00000241052.4	37	CCDS7891.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.916169	0.73098	.	.	ENSG00000121691	ENST00000241052	D	0.92446	-3.04	6.04	-3.64	0.04515	Catalase domain (1);Catalase, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96895	0.8986	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95841	0.8866	10	0.87932	D	0	-24.192	14.6482	0.68777	0.5116:0.0:0.4884:0.0	.	349	P04040	CATA_HUMAN	N	349	ENSP00000241052:K349N	ENSP00000241052:K349N	K	+	3	2	CAT	34434931	1.000000	0.71417	0.922000	0.36590	0.736000	0.42039	1.155000	0.31700	-0.978000	0.03533	-0.371000	0.07208	AAA		0.478	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		T	34478355	A	T	34478355	3	4	58	1	0	0	0	0	1	0	0	0	2692	11	1	5	1077	5	CAT	11	34478355	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	16684926	34478355	100528161	97	7743										
LRRC55	219527	broad.mit.edu	37	chr11	56954801	56954801	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	actgaggagagcttcaaggcCtgccacctgaccctgaccct	10	15	1	4			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:56954801C>T	ENST00000497933.1	+	2	1020	c.873C>T	c.(871-873)gcC>gcT	p.A291A		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	261					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A291A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						GCTTCAAGGCCTGCCACCTGA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											158	111	127					11																	56954801		2201	4296	6497	56711377	SO:0001819	synonymous_variant	219527				CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.873C>T	11.37:g.56954801C>T			56711377	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																				0.582	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210		T	56954801	C	T	56954801	2	4	58	1	0	0	0	0	0	0	0	1	9040	668	24	3		3	LRRC55	11	56954801	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	22476446	56954801	78051715	98	7744										
APLNR	187	broad.mit.edu	37	chr11	57004033	57004033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcacccaaagaactgccgtgGccacggccccgctgacccgc	11	19	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:57004033G>A	ENST00000606794.1	-	1	642	c.446C>T	c.(445-447)gCc>gTc	p.A149V		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	149					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.A149V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						AACTGCCGTGGCCACGGCCCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	11											35	32	33					11																	57004033		2200	4294	6494	56760609	SO:0001583	missense	187			U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"APJ (apelin) receptor"	600052	"angiotensin II receptor-like 1"	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.446C>T	11.37:g.57004033G>A	ENSP00000475344:p.Ala149Val		56760609		Missense_Mutation	SNP	ENST00000606794.1	37	CCDS7950.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898755	0.33535	.	.	ENSG00000134817	ENST00000257254	T	0.35421	1.31	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.131941	0.52532	D	0.000075	T	0.21962	0.0529	N	0.25060	0.705	0.42160	D	0.991592	B	0.11235	0.004	B	0.17722	0.019	T	0.06041	-1.0849	10	0.02654	T	1	-22.2821	12.866	0.57939	0.0795:0.0:0.9205:0.0	.	149	P35414	APJ_HUMAN	V	149	ENSP00000257254:A149V	ENSP00000257254:A149V	A	-	2	0	APLNR	56760609	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	3.437000	0.52863	2.448000	0.82819	0.555000	0.69702	GCC		0.652	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161		A	57004033	G	A	57004033	3	1	58	1	0	0	0	0	1	0	0	0	777	1203	42	3	700	3	APLNR	11	57004033	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	49232	57004033	78002483	99	7745										
ARAP1	116985	broad.mit.edu	37	chr11	72423599	72423599	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	acggcccgtgggactcggctCggtgggggctcctcctgccc	16	16	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:72423599C>T	ENST00000393609.3	-	6	964	c.762G>A	c.(760-762)ccG>ccA	p.P254P	ARAP1_ENST00000426523.1_Silent_p.P9P|ARAP1_ENST00000334211.8_Silent_p.P9P|ARAP1_ENST00000393605.3_Silent_p.P14P|ARAP1_ENST00000455638.2_Silent_p.P254P|ARAP1_ENST00000429686.1_Silent_p.P9P|ARAP1_ENST00000359373.5_Silent_p.P254P	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	254					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.P254P(1)|p.P14P(1)		cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GGACTCGGCTCGGTGGGGGCT	0.672																																					Ovarian(102;1198 1520 13195 17913 37529)											2	Substitution - coding silent(2)	large_intestine(2)	11											110	99	103					11																	72423599		2200	4293	6493	72101247	SO:0001819	synonymous_variant	116985			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.762G>A	11.37:g.72423599C>T			72101247	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	37	CCDS41687.1																																																																																				0.672	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		T	72423599	C	T	72423599	2	4	58	1	0	0	0	0	0	0	0	1	838	871	31	1		1	ARAP1	11	72423599	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	15419566	72423599	62582917	100	7746										
ODZ4	26011	broad.mit.edu	37	chr11	78380888	78380888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccccatgttatcatactggaCggtcatccagtacatgagcg	9	12	2	1	rs200474747	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:78380888C>T	ENST00000278550.7	-	32	6964	c.6502G>A	c.(6502-6504)Gtc>Atc	p.V2168I		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2168					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.V2168I(2)									TCATACTGGACGGTCATCCAG	0.507													C|||	3	0.000599042	0	0.0014	5008	,	,		24345	0		0	False		,,,				2504	0.002															2	Substitution - Missense(2)	large_intestine(2)	11						C	ILE/VAL	0,4164		0,0,2082	74	76	75		6502	5.1	1	11		75	1,8443		0,1,4221	no	missense	ODZ4	NM_001098816.2	29	0,1,6303	TT,TC,CC		0.0118,0.0,0.0079	benign	2168/2770	78380888	1,12607	2082	4222	6304	78058536	SO:0001583	missense	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6502G>A	11.37:g.78380888C>T	ENSP00000278550:p.Val2168Ile		78058536	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.909110	0.33721	0.0	1.18E-4	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.89270	-2.49;0.97	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.91730	0.7385	L	0.41356	1.27	0.53688	D	0.999978	D	0.76494	0.999	D	0.71184	0.972	D	0.90428	0.4422	9	.	.	.	.	18.8078	0.92045	0.0:1.0:0.0:0.0	.	2168	Q6N022	TEN4_HUMAN	I	2168;632	ENSP00000278550:V2168I;ENSP00000431711:V632I	.	V	-	1	0	ODZ4	78058536	1.000000	0.71417	0.964000	0.40570	0.961000	0.63080	4.672000	0.61597	2.677000	0.91161	0.655000	0.94253	GTC		0.507	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78380888	C	T	78380888	3	4	58	1	0	0	0	0	1	0	0	0	10868	536	19	1	1819	1	ODZ4	11	78380888	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	5957289	78380888	56625628	101	7747										
PCF11	51585	broad.mit.edu	37	chr11	82879949	82879949	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cccctggtctgaggtttgagGgatctccaggtggtttgaga	15	8	2	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:82879949G>T	ENST00000298281.4	+	8	3024	c.2572G>T	c.(2572-2574)Gga>Tga	p.G858*		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	858	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)		p.G858*(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GAGGTTTGAGGGATCTCCAGG	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											74	75	75					11																	82879949		1928	4135	6063	82557597	SO:0001587	stop_gained	51585			AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2572G>T	11.37:g.82879949G>T	ENSP00000298281:p.Gly858*		82557597	A6H8W7|O43671|Q6P0X8	Nonsense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	G	41	8.623808	0.98890	.	.	ENSG00000165494	ENST00000298281;ENST00000530660	.	.	.	5.65	5.65	0.86999	.	0.000000	0.52532	D	0.000067	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.3635	16.751	0.85485	0.0:0.0:1.0:0.0	.	.	.	.	X	858;989	.	.	G	+	1	0	PCF11	82557597	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.126000	0.77201	2.941000	0.99782	0.655000	0.94253	GGA		0.567	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82879949	G	T	82879949	4	4	58	1	0	0	0	0	0	1	0	0	11604	1233	43	2	2602	2	PCF11	11	82879949	Nonsense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	4499061	82879949	52126567	102	7748										
RAB39	54734	broad.mit.edu	37	chr11	107832799	107832799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aaatgtatgtacagccatttCggattgtatttctgctagtg	9	6	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:107832799C>T	ENST00000320578.2	+	2	421	c.355C>T	c.(355-357)Cgg>Tgg	p.R119W		NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	119					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.R119W(1)									ACAGCCATTTCGGATTGTATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	74	76					11																	107832799		2201	4298	6499	107338009	SO:0001583	missense	54734			X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"RAB, member RAS oncogene"	16521	protein-coding gene	gene with protein product	"rab-related GTP-binding protein"		"RAB39, member RAS oncogene family"	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.355C>T	11.37:g.107832799C>T	ENSP00000322594:p.Arg119Trp		107338009	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	37	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.876868	0.72180	.	.	ENSG00000179331	ENST00000320578	T	0.80033	-1.33	5.21	5.21	0.72293	Small GTP-binding protein domain (1);	0.382752	0.22323	N	0.061577	D	0.83202	0.5203	L	0.34521	1.04	0.34607	D	0.717194	D	0.60160	0.987	P	0.57244	0.816	D	0.87944	0.2719	10	0.87932	D	0	.	18.9407	0.92604	0.0:1.0:0.0:0.0	.	119	Q14964	RB39A_HUMAN	W	119	ENSP00000322594:R119W	ENSP00000322594:R119W	R	+	1	2	RAB39	107338009	1.000000	0.71417	0.999000	0.59377	0.819000	0.46315	2.869000	0.48444	2.693000	0.91896	0.655000	0.94253	CGG		0.378	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516		T	107832799	C	T	107832799	3	4	58	1	0	0	0	0	1	0	0	0	12966	875	31	1	361	1	RAB39	11	107832799	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	24952850	107832799	27173717	103	7749										
DSCAML1	57453	broad.mit.edu	37	chr11	117332214	117332214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gacccgatagcctttgaggaCgccattgagggtgctgcgcg	15	11	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr11:117332214C>T	ENST00000321322.6	-	18	3545	c.3544G>A	c.(3544-3546)Gtc>Atc	p.V1182I	DSCAML1_ENST00000527706.1_Missense_Mutation_p.V912I	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1122	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.V1182I(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	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)		CCTTTGAGGACGCCATTGAGG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											83	82	83					11																	117332214		2201	4296	6497	116837424	SO:0001583	missense	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.3544G>A	11.37:g.117332214C>T	ENSP00000315465:p.Val1182Ile		116837424	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961222	0.53400	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.57436	0.4;0.4	4.9	4.9	0.64082	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.31263	0.0791	N	0.11064	0.09	0.80722	D	1	B	0.33807	0.426	B	0.32211	0.142	T	0.26121	-1.0112	9	0.02654	T	1	.	18.2786	0.90091	0.0:1.0:0.0:0.0	.	1122	Q8TD84	DSCL1_HUMAN	I	912;1182;889	ENSP00000434335:V912I;ENSP00000315465:V1182I	ENSP00000315465:V1182I	V	-	1	0	DSCAML1	116837424	1.000000	0.71417	0.971000	0.41717	0.989000	0.77384	5.841000	0.69409	2.547000	0.85894	0.655000	0.94253	GTC		0.627	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117332214	C	T	117332214	3	4	58	1	0	0	0	0	1	0	0	0	4780	536	19	1	2861	1	DSCAML1	11	117332214	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9499415	117332214	17674302	104	7750										
CHD4	1108	broad.mit.edu	37	chr12	6697108	6697108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gcccaatccggtgagctctgCtaaaggcctggagttgaaca	12	11	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:6697108C>A	ENST00000357008.2	-	24	3636	c.3473G>T	c.(3472-3474)aGc>aTc	p.S1158I	CHD4_ENST00000544040.1_Missense_Mutation_p.S1151I|CHD4_ENST00000544484.1_Missense_Mutation_p.S1155I|CHD4_ENST00000309577.6_Missense_Mutation_p.S1158I|CHD4_ENST00000540960.1_5'Flank	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1158	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.S1158I(2)		central_nervous_system(2)	2						GTGAGCTCTGCTAAAGGCCTG	0.448																																					Colon(32;586 792 4568 16848 45314)											2	Substitution - Missense(2)	large_intestine(2)	12											64	63	64					12																	6697108		2203	4300	6503	6567369	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.3473G>T	12.37:g.6697108C>A	ENSP00000349508:p.Ser1158Ile		6567369	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.979196	0.74360	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.91	5.91	0.95273	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89508	0.6735	M	0.90483	3.12	0.80722	D	1	P;P;D	0.69078	0.776;0.744;0.997	P;P;D	0.80764	0.72;0.832;0.994	D	0.90581	0.4529	10	0.87932	D	0	.	20.2882	0.98536	0.0:1.0:0.0:0.0	.	1158;1158;1151	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	I	1155;1151;1158;1158;1132	ENSP00000440392:S1155I;ENSP00000440542:S1151I;ENSP00000312419:S1158I;ENSP00000349508:S1158I	ENSP00000312419:S1158I	S	-	2	0	CHD4	6567369	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	7.448000	0.80631	2.802000	0.96397	0.543000	0.68304	AGC		0.448	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6697108	C	A	6697108	3	1	58	1	0	0	0	0	1	0	0	0	3333	797	28	2	2333	2	CHD4	12	6697108	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		6697108	127154787	105	7751										
CCNT1	904	broad.mit.edu	37	chr12	49087215	49087215	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttagggaagaggatttagtActcttggcaatcttggctgg	13	5	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:49087215A>G	ENST00000261900.3	-	9	2004	c.1782T>C	c.(1780-1782)agT>agC	p.S594S		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	594	Ser-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)	p.S594S(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AGGATTTAGTACTCTTGGCAA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	12											92	92	92					12																	49087215		2203	4300	6503	47373482	SO:0001819	synonymous_variant	904			AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1782T>C	12.37:g.49087215A>G			47373482	A9XU13|E7EX76|O60581	Silent	SNP	ENST00000261900.3	37	CCDS8766.1																																																																																				0.473	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		G	49087215	A	G	49087215	2	3	58	1	0	0	0	0	0	0	0	1	2940	388	14	4		4	CCNT1	12	49087215	Silent	SNP	A	TCGA-AG-4007-01A-01W-1073-09	42390107	49087215	84764680	106	7752										
SLC4A8	9498	broad.mit.edu	37	chr12	51863567	51863567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttggagaagccactgagggaCgcatagtaaggacttttaac	12	7	0	2	rs374704511		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:51863567C>T	ENST00000453097.2	+	12	1736	c.1519C>T	c.(1519-1521)Cgc>Tgc	p.R507C	SLC4A8_ENST00000535225.2_Missense_Mutation_p.R454C|SLC4A8_ENST00000546663.1_3'UTR|SLC4A8_ENST00000394856.1_Missense_Mutation_p.R454C|SLC4A8_ENST00000514353.3_Missense_Mutation_p.R454C|SLC4A8_ENST00000358657.3_Missense_Mutation_p.R534C	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.R454C(1)|p.R507C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		CACTGAGGGACGCATAGTAAG	0.488													C|||	1	0.000199681	8e-04	0	5008	,	,		22189	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12						C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	165	152	157		1519,1519	5.7	1	12		157	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SLC4A8	NM_001039960.1,NM_004858.2	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	507/1094,507/1045	51863567	1,13005	2203	4300	6503	50149834	SO:0001583	missense	9498			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1519C>T	12.37:g.51863567C>T	ENSP00000405812:p.Arg507Cys		50149834		Missense_Mutation	SNP	ENST00000453097.2	37	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.196508	0.79015	0.0	1.16E-4	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000551071	T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25	5.69	5.69	0.88448	Bicarbonate transporter, C-terminal (1);	0.145309	0.64402	D	0.000004	D	0.89361	0.6693	M	0.86178	2.8	0.58432	D	0.999991	D;D;D;D;D;D	0.89917	0.999;0.998;1.0;0.999;0.995;1.0	D;P;D;D;D;D	0.70487	0.916;0.827;0.961;0.969;0.921;0.961	D	0.89528	0.3783	10	0.56958	D	0.05	.	18.9789	0.92748	0.0:1.0:0.0:0.0	.	454;534;454;507;507;507	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6	.;.;.;S4A8_HUMAN;.;.	C	454;534;507;454;507;454;454	ENSP00000441520:R454C;ENSP00000351483:R534C;ENSP00000405812:R507C;ENSP00000378325:R454C;ENSP00000442561:R454C	ENSP00000315789:R507C	R	+	1	0	SLC4A8	50149834	0.973000	0.33851	1.000000	0.80357	0.995000	0.86356	2.534000	0.45676	2.865000	0.98341	0.655000	0.94253	CGC		0.488	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51863567	C	T	51863567	3	4	58	1	0	0	0	0	1	0	0	0	14696	536	19	1	1565	1	SLC4A8	12	51863567	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	2776352	51863567	81988328	107	7753										
KRT6A	3853	broad.mit.edu	37	chr12	52883814	52883814	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgcttggtgttgcgcaggtcGtccccatgtctgcctgctgt	13	12	1	0	rs372043088		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:52883814G>A	ENST00000330722.6	-	6	1184	c.1116C>T	c.(1114-1116)gaC>gaT	p.D372D		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	372	Coil 2.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.D372D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCGCAGGTCGTCCCCATGTC	0.562													g|||	1	0.000199681	0	0	5008	,	,		23467	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	12						G		0,4404		0,0,2202	100	81	88		1116	-5.6	0.8	12		88	1,8555	1.2+/-3.3	0,1,4277	no	coding-synonymous	KRT6A	NM_005554.3		0,1,6479	AA,AG,GG		0.0117,0.0,0.0077		372/565	52883814	1,12959	2202	4278	6480	51170081	SO:0001819	synonymous_variant	3853			BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.1116C>T	12.37:g.52883814G>A			51170081	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																				0.562	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		A	52883814	G	A	52883814	2	1	58	1	0	0	0	0	0	0	0	1	8501	1136	40	1		1	KRT6A	12	52883814	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	1020247	52883814	80968081	108	7754										
PPP1R12A	4659	broad.mit.edu	37	chr12	80199538	80199538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	actatcctcagcccacaaacGatttgaggtactatagcatc	6	12	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:80199538G>A	ENST00000450142.2	-	14	2100	c.1834C>T	c.(1834-1836)Cgt>Tgt	p.R612C	PPP1R12A_ENST00000437004.2_Missense_Mutation_p.R612C|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.R556C|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.R525C|AC073569.1_ENST00000598624.1_Intron|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.R612C	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	612	Ser/Thr-rich.				centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R612C(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						GCCCACAAACGATTTGAGGTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	90	92					12																	80199538		2002	4164	6166	78723669	SO:0001583	missense	4659			D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.1834C>T	12.37:g.80199538G>A	ENSP00000389168:p.Arg612Cys		78723669	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.782956	0.70222	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107	T;T;T;T;T	0.39997	1.09;1.09;1.12;1.12;1.05	5.54	5.54	0.83059	.	0.046039	0.85682	D	0.000000	T	0.63510	0.2517	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.997	P;D;P	0.76575	0.738;0.988;0.551	T	0.64769	-0.6329	10	0.72032	D	0.01	.	19.4766	0.94991	0.0:0.0:1.0:0.0	.	612;556;612	O14974-2;O14974-3;O14974	.;.;MYPT1_HUMAN	C	612;612;612;556;612;612;525;556	ENSP00000261207:R612C;ENSP00000389168:R612C;ENSP00000416769:R612C;ENSP00000449514:R525C;ENSP00000446855:R556C	ENSP00000261207:R612C	R	-	1	0	PPP1R12A	78723669	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.663000	0.61532	2.585000	0.87301	0.591000	0.81541	CGT		0.413	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		A	80199538	G	A	80199538	3	1	58	1	0	0	0	0	1	0	0	0	12388	1058	37	1	1306	1	PPP1R12A	12	80199538	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	27315724	80199538	53652357	109	7755										
SCYL2	55681	broad.mit.edu	37	chr12	100711606	100711606	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gttaattttcctacaaaaaaTggatttgctactaaccaaaa	4	7	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:100711606T>A	ENST00000360820.2	+	10	1735	c.1298T>A	c.(1297-1299)aTg>aAg	p.M433K		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	433					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)	p.M437K(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						CTACAAAAAATGGATTTGCTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											62	59	60					12																	100711606		2203	4300	6503	99235737	SO:0001583	missense	55681			AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1298T>A	12.37:g.100711606T>A	ENSP00000354061:p.Met433Lys		99235737	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.587249	0.86851	.	.	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.33654	1.4;1.4	5.23	5.23	0.72850	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59702	0.2213	M	0.77313	2.365	0.80722	D	1	D	0.65815	0.995	D	0.64144	0.922	T	0.65664	-0.6113	10	0.87932	D	0	.	15.4116	0.74929	0.0:0.0:0.0:1.0	.	433	Q6P3W7	SCYL2_HUMAN	K	433;260;433	ENSP00000448366:M433K;ENSP00000354061:M433K	ENSP00000258506:M260K	M	+	2	0	SCYL2	99235737	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.013000	0.88655	2.099000	0.63709	0.528000	0.53228	ATG		0.343	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		A	100711606	T	A	100711606	3	1	58	1	0	0	0	0	1	0	0	0	13985	1464	51	5	1332	5	SCYL2	12	100711606	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	20512068	100711606	33140289	110	7756										
SH2B3	10019	broad.mit.edu	37	chr12	111886037	111886037	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gtgaatcgagcccgggactcGgactacgaaatggactcatc	12	11	1	1	rs369151728		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:111886037G>A	ENST00000341259.2	+	8	2016	c.1659G>A	c.(1657-1659)tcG>tcA	p.S553S	SH2B3_ENST00000538307.1_Silent_p.S351S	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	553					blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)	p.S553S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	CCCGGGACTCGGACTACGAAA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	12											86	102	97					12																	111886037		2203	4300	6503	110370420	SO:0001819	synonymous_variant	10019			AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	29605	protein-coding gene	gene with protein product	"lymphocyte adaptor protein"	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1659G>A	12.37:g.111886037G>A			110370420	B9EGG5|O95184	Silent	SNP	ENST00000341259.2	37	CCDS9153.1																																																																																				0.602	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475		A	111886037	G	A	111886037	2	1	58	1	0	0	0	0	0	0	0	1	14266	1103	39	1		1	SH2B3	12	111886037	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	11174431	111886037	21965858	111	7757										
DNAH10	196385	broad.mit.edu	37	chr12	124345570	124345570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttgatttaggcttgggctgaCgacaaagttgtacatcctga	11	7	0	3	rs372604094		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr12:124345570C>T	ENST00000409039.3	+	38	6432	c.6407C>T	c.(6406-6408)aCg>aTg	p.T2136M		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2136	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T728M(1)|p.T2136M(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTTGGGCTGACGACAAAGTTG	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	12						T	MET/THR	0,3788		0,0,1894	76	75	75		6407	2	0.1	12		75	1,8231		0,1,4115	no	missense	DNAH10	NM_207437.3	81	0,1,6009	TT,TC,CC		0.0121,0.0,0.0083	benign	2136/4472	124345570	1,12019	1894	4116	6010	122911523	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6407C>T	12.37:g.124345570C>T	ENSP00000386770:p.Thr2136Met		122911523	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	T	5.742	0.321349	0.10845	0.0	1.21E-4	ENSG00000197653	ENST00000409039	T	0.39592	1.07	5.59	1.99	0.26369	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.569325	0.15863	N	0.240912	T	0.36193	0.0958	L	0.50919	1.6	0.09310	N	1	B	0.19200	0.034	B	0.22880	0.042	T	0.26950	-1.0088	10	0.46703	T	0.11	.	9.3607	0.38195	0.0:0.2687:0.0:0.7313	.	2136	Q8IVF4	DYH10_HUMAN	M	2136	ENSP00000386770:T2136M	ENSP00000386770:T2136M	T	+	2	0	DNAH10	122911523	0.996000	0.38824	0.063000	0.19743	0.382000	0.30200	2.814000	0.48010	-0.113000	0.11958	-1.062000	0.02293	ACG		0.483	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124345570	C	T	124345570	3	4	58	1	0	0	0	0	1	0	0	0	4609	536	19	1	6557	1	DNAH10	12	124345570	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	12459533	124345570	9506325	112	7758										
KIAA0564	23078	broad.mit.edu	37	chr13	42263628	42263628	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcactggaaattttatgaggTatgctgaactctgtttctga	9	6	3	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr13:42263628T>G	ENST00000379310.3	-	34	4061	c.3993A>C	c.(3991-3993)atA>atC	p.I1331I	VWA8_ENST00000478987.1_5'UTR	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1331						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.I1331I(1)									TTTTATGAGGTATGCTGAACT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	13											89	80	83					13																	42263628		1820	4086	5906	41161628	SO:0001819	synonymous_variant	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3993A>C	13.37:g.42263628T>G			41161628	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	37	CCDS41881.1																																																																																				0.358	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42263628	T	G	42263628	2	3	58	1	0	0	0	0	0	0	0	1	8206	1628	57	4		4	KIAA0564	13	42263628	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09		42263628	72906250	113	7759										
PCDH17	27253	broad.mit.edu	37	chr13	58207746	58207746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cgtccatcggtttcgtctccGtgcgccagggggcgctgagc	15	14	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr13:58207746G>A	ENST00000377918.3	+	1	1092	c.1066G>A	c.(1066-1068)Gtg>Atg	p.V356M		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	356	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V356M(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TTTCGTCTCCGTGCGCCAGGG	0.672																																					Melanoma(72;952 1291 1619 12849 33676)											1	Substitution - Missense(1)	large_intestine(1)	13											49	50	50					13																	58207746		2203	4300	6503	57105747	SO:0001583	missense	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1066G>A	13.37:g.58207746G>A	ENSP00000367151:p.Val356Met		57105747	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.888282	0.72524	.	.	ENSG00000118946	ENST00000377918	T	0.21543	2.0	5.67	5.67	0.87782	Cadherin (1);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.38427	0.1040	L	0.35854	1.095	0.58432	D	0.999994	D;D	0.89917	0.981;1.0	P;D	0.72625	0.787;0.978	T	0.01771	-1.1277	9	.	.	.	.	19.7768	0.96398	0.0:0.0:1.0:0.0	.	356;356	O14917-2;O14917	.;PCD17_HUMAN	M	356	ENSP00000367151:V356M	.	V	+	1	0	PCDH17	57105747	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.698000	0.92095	0.650000	0.86243	GTG		0.672	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58207746	G	A	58207746	3	1	58	1	0	0	0	0	1	0	0	0	11543	1145	40	1	1068	1	PCDH17	13	58207746	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	15944118	58207746	56962132	114	7760										
SLITRK6	84189	broad.mit.edu	37	chr13	86369420	86369420	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttttgtaatctcgttaggttCataaacgatccttcttcaag	6	8	4	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr13:86369420C>A	ENST00000400286.2	-	2	1822	c.1224G>T	c.(1222-1224)atG>atT	p.M408I		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	408					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.M408I(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TCGTTAGGTTCATAAACGATC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	13											78	73	74					13																	86369420		1848	4092	5940	85267421	SO:0001583	missense	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.1224G>T	13.37:g.86369420C>A	ENSP00000383143:p.Met408Ile		85267421	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	0.258	-1.001577	0.02128	.	.	ENSG00000184564	ENST00000400286	T	0.57107	0.42	5.61	3.89	0.44902	.	0.158438	0.42682	N	0.000665	T	0.27205	0.0667	N	0.04787	-0.16	0.34758	D	0.732438	B	0.02656	0.0	B	0.04013	0.001	T	0.15350	-1.0440	10	0.34782	T	0.22	-3.2485	6.1342	0.20221	0.1505:0.6926:0.0:0.157	.	408	Q9H5Y7	SLIK6_HUMAN	I	408	ENSP00000383143:M408I	ENSP00000383143:M408I	M	-	3	0	SLITRK6	85267421	0.996000	0.38824	0.998000	0.56505	0.483000	0.33249	0.361000	0.20267	0.733000	0.32492	0.585000	0.79938	ATG		0.343	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		A	86369420	C	A	86369420	3	1	58	1	0	0	0	0	1	0	0	0	14784	826	29	2	1305	2	SLITRK6	13	86369420	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	28161674	86369420	28800458	115	7761										
GPC6	10082	broad.mit.edu	37	chr13	95055269	95055269	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttcaatctttccacactagGtgatgaatccagtggctcag	8	10	3	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr13:95055269G>A	ENST00000377047.4	+	9	2081	c.1466G>A	c.(1465-1467)aGt>aAt	p.S489N		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	489					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.S489N(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TCCACACTAGGTGATGAATCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	13											153	165	161					13																	95055269		2203	4300	6503	93853270	SO:0001630	splice_region_variant	10082			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1466-1G>A	13.37:g.95055269G>A			93853270	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483366	0.63962	.	.	ENSG00000183098	ENST00000377047	T	0.52295	0.67	5.84	5.84	0.93424	.	0.043940	0.85682	D	0.000000	T	0.50871	0.1641	M	0.69248	2.105	0.80722	D	1	B	0.28208	0.203	B	0.28709	0.093	T	0.43065	-0.9414	9	.	.	.	.	20.1432	0.98067	0.0:0.0:1.0:0.0	.	489	Q9Y625	GPC6_HUMAN	N	489	ENSP00000366246:S489N	.	S	+	2	0	GPC6	93853270	1.000000	0.71417	0.934000	0.37439	0.885000	0.51271	7.602000	0.82796	2.769000	0.95229	0.561000	0.74099	AGT		0.502	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	Missense_Mutation	A	95055269	G	A	95055269	5	1	58	1	0	0	0	0	0	0	1	0	6622	1275	44	3	1500	3	GPC6	13	95055269	Splice_Site	SNP	G	TCGA-AG-4007-01A-01W-1073-09	8685849	95055269	20114609	116	7762										
DHRS4L1	728635	broad.mit.edu	37	chr14	24505826	24505826	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aaggtggccctggtaacggcCtccaccgactggtgagtgtt	14	11	0	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr14:24505826C>T	ENST00000558293.1	+	0	165					NR_102693.1																						TGGTAACGGCCTCCACCGACT	0.652																																																0			14											38	45	42					14																	24505826		2191	4293	6484	23575666			728635																															14.37:g.24505826C>T			23575666		Silent	SNP	ENST00000558293.1	37																																																																																					0.652	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			T	24505826	C	T	24505826	1	4	58	0	1	0	0	0	0	0	0	0	4504	668	24	3		3	DHRS4L1	14	24505826	RNA	SNP	C	TCGA-AG-4007-01A-01W-1073-09		24505826	82843714	117	7763										
NFATC4	4776	broad.mit.edu	37	chr14	24844904	24844904	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aggaggaggccacagtgaacCgactgcagagcaacgaggta	15	9	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr14:24844904C>T	ENST00000250373.4	+	7	2053	c.1912C>T	c.(1912-1914)Cga>Tga	p.R638*	NFATC4_ENST00000413692.2_Nonsense_Mutation_p.R701*|NFATC4_ENST00000555590.1_Nonsense_Mutation_p.R651*|NFATC4_ENST00000553879.1_Nonsense_Mutation_p.R568*|NFATC4_ENST00000539237.2_Nonsense_Mutation_p.R670*|NFATC4_ENST00000554050.1_Nonsense_Mutation_p.R638*|NFATC4_ENST00000555167.1_Nonsense_Mutation_p.R173*|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000554473.1_Nonsense_Mutation_p.R173*|NFATC4_ENST00000554344.1_Nonsense_Mutation_p.R568*|NFATC4_ENST00000557451.1_Nonsense_Mutation_p.R568*|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000556279.1_Nonsense_Mutation_p.R670*|NFATC4_ENST00000422617.3_Nonsense_Mutation_p.R626*|NFATC4_ENST00000554966.1_Nonsense_Mutation_p.R651*|NFATC4_ENST00000553708.1_Nonsense_Mutation_p.R638*|NFATC4_ENST00000554591.1_Nonsense_Mutation_p.R701*|NFATC4_ENST00000424781.2_Nonsense_Mutation_p.R651*|NFATC4_ENST00000553469.1_Nonsense_Mutation_p.R670*|NFATC4_ENST00000556759.1_Nonsense_Mutation_p.R173*|NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000556169.1_Nonsense_Mutation_p.R626*|NFATC4_ENST00000555453.1_Nonsense_Mutation_p.R626*|NFATC4_ENST00000554661.1_Nonsense_Mutation_p.R568*	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	638	IPT/TIG.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)	p.R638*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		CACAGTGAACCGACTGCAGAG	0.627																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											56	39	45					14																	24844904		2194	4288	6482	23914744	SO:0001587	stop_gained	4776			BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1912C>T	14.37:g.24844904C>T	ENSP00000250373:p.Arg638*		23914744	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Nonsense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	41	8.934063	0.99008	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167	.	.	.	5.41	4.46	0.54185	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.5001	10.6467	0.45623	0.276:0.724:0.0:0.0	.	.	.	.	X	701;701;651;651;651;670;670;670;638;638;638;568;568;568;626;568;626;626;173;173;173	.	ENSP00000250373:R638X	R	+	1	2	NFATC4	23914744	0.939000	0.31865	1.000000	0.80357	0.988000	0.76386	0.057000	0.14279	2.816000	0.96949	0.563000	0.77884	CGA		0.627	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		T	24844904	C	T	24844904	4	4	58	1	0	0	0	0	0	1	0	0	10396	644	23	1	2131	1	NFATC4	14	24844904	Nonsense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	339078	24844904	82504636	118	7764										
EAPP	55837	broad.mit.edu	37	chr14	34998597	34998597	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	catcaacccaggcctgatctCtgttatctttttcaggatca	6	12	5	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr14:34998597C>T	ENST00000250454.3	-	4	518	c.437G>A	c.(436-438)aGa>aAa	p.R146K		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	146					negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.R146K(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		GGCCTGATCTCTGTTATCTTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	14											163	144	150					14																	34998597		1830	4086	5916	34068348	SO:0001583	missense	55837			AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"chromosome 14 open reading frame 11"	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.437G>A	14.37:g.34998597C>T	ENSP00000250454:p.Arg146Lys		34068348	Q9BVF4|Q9NWV5|Q9NZ86	Missense_Mutation	SNP	ENST00000250454.3	37	CCDS41941.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.682787	0.47991	.	.	ENSG00000129518	ENST00000250454;ENST00000554792	T;T	0.41400	1.0;1.0	5.38	4.48	0.54585	.	0.097290	0.64402	D	0.000001	T	0.33644	0.0870	L	0.37561	1.115	0.58432	D	0.999995	B	0.16603	0.018	B	0.19666	0.026	T	0.07252	-1.0782	10	0.28530	T	0.3	-20.1992	13.8651	0.63583	0.0:0.9261:0.0:0.0739	.	146	Q56P03	EAPP_HUMAN	K	146;125	ENSP00000250454:R146K;ENSP00000450908:R125K	ENSP00000250454:R146K	R	-	2	0	EAPP	34068348	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.304000	0.51866	2.705000	0.92388	0.585000	0.79938	AGA		0.308	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453		T	34998597	C	T	34998597	3	4	58	1	0	0	0	0	1	0	0	0	4888	913	32	3	432	3	EAPP	14	34998597	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	10153693	34998597	72350943	119	7765										
RALGAPA1	253959	broad.mit.edu	37	chr14	36041891	36041891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tctagtatgctctgaccaaaCaatgtgcacttcatcatttc	5	11	4	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr14:36041891C>T	ENST00000389698.3	-	37	6115	c.5725G>A	c.(5725-5727)Gtt>Att	p.V1909I	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.V1956I|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.V1909I|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.V1922I	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1909	Minimal domain that binds to TCF3/E12. {ECO:0000250}.|Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.V1909I(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TCTGACCAAACAATGTGCACT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	14											104	104	104					14																	36041891		2203	4300	6503	35111642	SO:0001583	missense	253959			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.5725G>A	14.37:g.36041891C>T	ENSP00000374348:p.Val1909Ile		35111642	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280601	0.80692	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	5.17	4.28	0.50868	Rap/ran-GAP (2);	0.122801	0.53938	N	0.000045	D	0.93858	0.8035	L	0.31120	0.905	0.53005	D	0.999964	D;D;D;D	0.89917	0.997;1.0;0.96;1.0	D;D;P;D	0.91635	0.991;0.999;0.69;0.999	D	0.93869	0.7160	10	0.54805	T	0.06	-10.7572	13.4351	0.61079	0.0:0.9244:0.0:0.0756	.	1956;1922;1909;1909	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	I	1909;1909;1909;1956;547;1922;1956	ENSP00000374348:V1909I;ENSP00000302647:V1909I;ENSP00000258840:V1956I;ENSP00000451133:V547I;ENSP00000371803:V1922I;ENSP00000451877:V1956I	ENSP00000258840:V1956I	V	-	1	0	RALGAPA1	35111642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.861000	0.56002	1.170000	0.42753	0.585000	0.79938	GTT		0.353	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		T	36041891	C	T	36041891	3	4	58	1	0	0	0	0	1	0	0	0	13050	478	17	3	554	3	RALGAPA1	14	36041891	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	1043294	36041891	71307649	120	7766										
VRK1	7443	broad.mit.edu	37	chr14	97312449	97312449	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aaggaacccagtgacaatggAcctctttttactgaattaaa	7	8	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr14:97312449A>C	ENST00000216639.3	+	4	383	c.234A>C	c.(232-234)ggA>ggC	p.G78G		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	78	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G78G(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		GTGACAATGGACCTCTTTTTA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	14											87	89	88					14																	97312449		2203	4295	6498	96382202	SO:0001819	synonymous_variant	7443			AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.234A>C	14.37:g.97312449A>C			96382202	Q3SYL2	Silent	SNP	ENST00000216639.3	37	CCDS9947.1																																																																																				0.318	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384		C	97312449	A	C	97312449	2	2	58	1	0	0	0	0	0	0	0	1	17259	262	10	4		4	VRK1	14	97312449	Silent	SNP	A	TCGA-AG-4007-01A-01W-1073-09	61270558	97312449	10037091	121	7767										
SNX22	79856	broad.mit.edu	37	chr15	64446589	64446589	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttaattctatcccacagagtCgctgcccaacgtggtggtga	10	11	1	2	rs111942276	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr15:64446589C>T	ENST00000325881.4	+	7	523	c.464C>T	c.(463-465)tCg>tTg	p.S155L	PPIB_ENST00000558492.1_5'Flank	NM_024798.2	NP_079074.2	Q96L94	SNX22_HUMAN	sorting nexin 22	155					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.S155L(1)		large_intestine(3)|lung(1)|urinary_tract(2)	6						CCCACAGAGTCGCTGCCCAAC	0.602											OREG0023180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0	0	5008	,	,		18755	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	15											93	90	91					15																	64446589		2203	4300	6503	62233642	SO:0001583	missense	79856			AK024014	CCDS10190.1	15q22.1	2010-01-15			ENSG00000157734	ENSG00000157734		"Sorting nexins"	16315	protein-coding gene	gene with protein product						12461558, 17400918	Standard	NR_073534		Approved	FLJ13952	uc002anc.1	Q96L94	OTTHUMG00000132965	ENST00000325881.4:c.464C>T	15.37:g.64446589C>T	ENSP00000323435:p.Ser155Leu	1076	62233642	Q8WUS9|Q9H844	Missense_Mutation	SNP	ENST00000325881.4	37	CCDS10190.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	4.014	0.000010	0.07819	.	.	ENSG00000157734	ENST00000325881	T	0.78246	-1.16	5.43	3.55	0.40652	.	0.801287	0.11987	N	0.510246	T	0.64811	0.2632	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47045	-0.9147	10	0.26408	T	0.33	-14.4408	12.8442	0.57821	0.0:0.8739:0.0:0.1261	.	155	Q96L94	SNX22_HUMAN	L	155	ENSP00000323435:S155L	ENSP00000323435:S155L	S	+	2	0	SNX22	62233642	0.000000	0.05858	0.125000	0.21846	0.088000	0.18126	0.144000	0.16135	0.289000	0.22422	-1.564000	0.00881	TCG		0.602	SNX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256524.2	NM_024798		T	64446589	C	T	64446589	3	4	58	1	0	0	0	0	1	0	0	0	14931	893	31	1	490	1	SNX22	15	64446589	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		64446589	38084803	122	7768										
ISLR2	57611	broad.mit.edu	37	chr15	74425863	74425863	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgcgcgcaggactggcgttCgtgttacactgcatcgccga	13	13	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr15:74425863C>T	ENST00000361742.3	+	4	1537	c.768C>T	c.(766-768)ttC>ttT	p.F256F	ISLR2_ENST00000565540.1_Silent_p.F256F|ISLR2_ENST00000435464.1_Silent_p.F256F|ISLR2_ENST00000453268.2_Silent_p.F256F|ISLR2_ENST00000419208.1_Silent_p.F256F|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000445793.1_Silent_p.F256F|ISLR2_ENST00000565159.1_Silent_p.F256F	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	256	Ig-like.				positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F256F(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						GACTGGCGTTCGTGTTACACT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	15											40	38	39					15																	74425863		2197	4296	6493	72212916	SO:0001819	synonymous_variant	57611				CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.768C>T	15.37:g.74425863C>T			72212916	A8K352|Q9P263	Silent	SNP	ENST00000361742.3	37	CCDS10259.1																																																																																				0.672	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		T	74425863	C	T	74425863	2	4	58	1	0	0	0	0	0	0	0	1	7880	883	31	1		1	ISLR2	15	74425863	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9979274	74425863	28105529	123	7769										
MYH11	4629	broad.mit.edu	37	chr16	15844149	15844149	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cgctgggcagcgagctctccGtcatcttggccatctggtcc	12	15	4	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr16:15844149G>A	ENST00000300036.5	-	16	2013	c.1904C>T	c.(1903-1905)aCg>aTg	p.T635M	MYH11_ENST00000452625.2_Missense_Mutation_p.T642M|MYH11_ENST00000396324.3_Missense_Mutation_p.T642M|MYH11_ENST00000576790.2_Missense_Mutation_p.T635M	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	635	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.T635M(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CGAGCTCTCCGTCATCTTGGC	0.627			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - Missense(1)	large_intestine(1)	16											93	69	77					16																	15844149		2197	4300	6497	15751650	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1904C>T	16.37:g.15844149G>A	ENSP00000300036:p.Thr635Met		15751650	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993385	0.74703	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	5.47	5.47	0.80525	Myosin head, motor domain (2);	0.123826	0.53938	D	0.000050	D	0.87313	0.6146	L	0.47190	1.495	0.80722	D	1	D;P;P;P;P;P	0.54397	0.966;0.619;0.619;0.619;0.904;0.619	P;P;P;P;P;P	0.49799	0.622;0.5;0.5;0.5;0.5;0.5	D	0.88077	0.2804	10	0.56958	D	0.05	.	15.4747	0.75468	0.0:0.1387:0.8613:0.0	.	642;635;635;642;635;642	B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;.;MYH11_HUMAN;.;.;.	M	635;635;642;642;642	ENSP00000300036:T635M;ENSP00000345136:T635M;ENSP00000379616:T642M;ENSP00000407821:T642M	ENSP00000300036:T635M	T	-	2	0	MYH11	15751650	1.000000	0.71417	0.993000	0.49108	0.977000	0.68977	6.660000	0.74417	2.571000	0.86741	0.561000	0.74099	ACG		0.627	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15844149	G	A	15844149	3	1	58	1	0	0	0	0	1	0	0	0	10061	1145	40	1	4153	1	MYH11	16	15844149	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		15844149	74510604	124	7770										
POLR3E	55718	broad.mit.edu	37	chr16	22334241	22334241	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgaggtgctctgcaggggcCgagacttcgttgtaagtacc	14	10	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr16:22334241C>T	ENST00000299853.5	+	14	1224	c.1057C>T	c.(1057-1059)Cga>Tga	p.R353*	POLR3E_ENST00000418581.2_Nonsense_Mutation_p.R317*|POLR3E_ENST00000359210.4_Nonsense_Mutation_p.R353*|POLR3E_ENST00000564209.1_Nonsense_Mutation_p.R353*	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	353					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)	p.R353*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		CTGCAGGGGCCGAGACTTCGT	0.642																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											58	47	51					16																	22334241		2197	4300	6497	22241742	SO:0001587	stop_gained	55718			AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.1057C>T	16.37:g.22334241C>T	ENSP00000299853:p.Arg353*		22241742	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Nonsense_Mutation	SNP	ENST00000299853.5	37	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	C	37	6.070576	0.97256	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	.	.	.	5.43	5.43	0.79202	.	0.122739	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6457	12.3828	0.55315	0.284:0.716:0.0:0.0	.	.	.	.	X	353;353;317	.	ENSP00000299853:R353X	R	+	1	2	POLR3E	22241742	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.189000	0.42621	2.550000	0.86006	0.655000	0.94253	CGA		0.642	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		T	22334241	C	T	22334241	4	4	58	1	0	0	0	0	0	1	0	0	12263	644	23	1	1107	1	POLR3E	16	22334241	Nonsense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	6490092	22334241	68020512	125	7771										
HYDIN	54768	broad.mit.edu	37	chr16	70975668	70975668	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gagggcggctgcagcattctGagcaaagagagtgtcgaggc	17	8	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr16:70975668G>A	ENST00000393567.2	-	43	6874	c.6724C>T	c.(6724-6726)Cag>Tag	p.Q2242*		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2242			Q -> R (in dbSNP:rs2258307).		cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.Q2241*(1)|p.Q2193*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCAGCATTCTGAGCAAAGAGA	0.537																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											74	75	75					16																	70975668		1973	4158	6131	69533169	SO:0001587	stop_gained	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6724C>T	16.37:g.70975668G>A	ENSP00000377197:p.Gln2242*		69533169	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Nonsense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	44	11.228427	0.99534	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	.	.	.	5.32	3.2	0.36748	.	0.000000	0.31290	U	0.007911	.	.	.	.	.	.	0.44337	D	0.997229	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	14.4735	0.67531	0.0:0.0:0.7365:0.2635	.	.	.	.	X	2242;2241	.	ENSP00000313052:Q2241X	Q	-	1	0	HYDIN	69533169	0.015000	0.18098	0.189000	0.23252	0.128000	0.20619	1.443000	0.35057	1.350000	0.45770	0.508000	0.49915	CAG		0.537	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70975668	G	A	70975668	4	1	58	1	0	0	0	0	0	1	0	0	7488	1299	45	3	8817	3	HYDIN	16	70975668	Nonsense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	48641427	70975668	19379085	126	7772										
NLRP1	22861	broad.mit.edu	37	chr17	5433948	5433948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cacacagaattcaatctcaaCggtcaccgcttctctcatca	4	15	6	1	rs201871081		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:5433948C>T	ENST00000572272.1	-	12	3372	c.3373G>A	c.(3373-3375)Gtt>Att	p.V1125I	NLRP1_ENST00000577119.1_Missense_Mutation_p.V1095I|NLRP1_ENST00000345221.3_Missense_Mutation_p.V1125I|NLRP1_ENST00000262467.5_Missense_Mutation_p.V1129I|NLRP1_ENST00000269280.4_Missense_Mutation_p.V1125I|NLRP1_ENST00000354411.3_Missense_Mutation_p.V1095I|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1125					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.V1125I(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TCAATCTCAACGGTCACCGCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	17											89	82	85					17																	5433948		2203	4300	6503	5374672	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3373G>A	17.37:g.5433948C>T	ENSP00000460475:p.Val1125Ile		5374672	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	C	1.052	-0.675426	0.03378	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2	5.13	-3.0	0.05480	.	0.422499	0.17492	N	0.172302	T	0.04588	0.0125	N	0.01618	-0.8	0.09310	N	1	B;B;B;B;B;B	0.10296	0.002;0.003;0.003;0.003;0.003;0.001	B;B;B;B;B;B	0.09377	0.004;0.003;0.003;0.004;0.003;0.004	T	0.38757	-0.9646	10	0.02654	T	1	.	7.311	0.26475	0.0:0.4184:0.1253:0.4564	.	391;1095;1095;1125;1125;1129	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	I	1129;1129;1125;1095;1125;391	ENSP00000442029:V1129I;ENSP00000262467:V1129I;ENSP00000269280:V1125I;ENSP00000346390:V1095I;ENSP00000324366:V1125I	ENSP00000262467:V1129I	V	-	1	0	NLRP1	5374672	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.078000	0.03413	-0.465000	0.06953	-0.357000	0.07601	GTT		0.572	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5433948	C	T	5433948	3	4	58	1	0	0	0	0	1	0	0	0	10502	536	19	1	1135	1	NLRP1	17	5433948	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		5433948	75761262	127	7773										
TP53	7157	broad.mit.edu	37	chr17	7578551	7578551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	catcttgttgagggcaggggAgtactgtaggaagaggaagg	18	4	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:7578551A>G	ENST00000269305.4	-	5	568	c.379T>C	c.(379-381)Tcc>Ccc	p.S127P	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.S127P|TP53_ENST00000445888.2_Missense_Mutation_p.S127P|TP53_ENST00000455263.2_Missense_Mutation_p.S127P|TP53_ENST00000359597.4_Missense_Mutation_p.S127P|TP53_ENST00000413465.2_Missense_Mutation_p.S127P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	127	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S127T(6)|p.Y126_K132delYSPALNK(6)|p.S127P(6)|p.A129fs*20(3)|p.Y126_S127insQPHH(3)|p.Y126_N131delYSPALN(3)|p.V73fs*9(1)|p.S127fs*43(1)|p.?(1)|p.A36fs*20(1)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.S34P(1)|p.P13fs*18(1)|p.Y33_S34insQPHH(1)|p.S127fs*42(1)|p.Y126fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGGCAGGGGAGTACTGTAGG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	46	Substitution - Missense(13)|Deletion - In frame(10)|Whole gene deletion(8)|Deletion - Frameshift(6)|Insertion - Frameshift(4)|Insertion - In frame(4)|Unknown(1)	large_intestine(7)|upper_aerodigestive_tract(5)|haematopoietic_and_lymphoid_tissue(5)|breast(5)|central_nervous_system(4)|pancreas(4)|prostate(4)|bone(4)|lung(3)|ovary(2)|stomach(1)|urinary_tract(1)|liver(1)	17											43	44	44					17																	7578551		2203	4300	6503	7519276	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.379T>C	17.37:g.7578551A>G	ENSP00000269305:p.Ser127Pro		7519276	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.741786	0.89573	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D;D	0.99940	-8.39;-8.39;-8.39;-8.39;-8.39;-8.39;-8.39;-8.39;-8.39	5.48	5.48	0.80851	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99937	0.9972	M	0.91038	3.17	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.977;1.0;1.0;1.0	D	0.95533	0.8605	10	0.87932	D	0	-30.2503	13.8301	0.63375	1.0:0.0:0.0:0.0	.	88;127;127;34;127;127;127	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	127;127;127;127;127;127;116;34;34;127;127	ENSP00000410739:S127P;ENSP00000352610:S127P;ENSP00000269305:S127P;ENSP00000398846:S127P;ENSP00000391127:S127P;ENSP00000391478:S127P;ENSP00000423862:S34P;ENSP00000424104:S127P;ENSP00000426252:S127P	ENSP00000269305:S127P	S	-	1	0	TP53	7519276	1.000000	0.71417	0.962000	0.40283	0.934000	0.57294	7.419000	0.80179	2.206000	0.71126	0.533000	0.62120	TCC		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578551	A	G	7578551	3	3	58	1	0	0	0	0	1	0	0	0	16421	304	11	4	919	4	TP53	17	7578551	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	2144603	7578551	73616659	128	7774										
MYH10	4628	broad.mit.edu	37	chr17	8413168	8413168	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ttggtcctcgagaagcagaaTctcctcttccatcttcttga	7	12	4	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:8413168T>A	ENST00000269243.4	-	23	3097	c.2959A>T	c.(2959-2961)Att>Ttt	p.I987F	RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000360416.3_Missense_Mutation_p.I1018F|MYH10_ENST00000396239.1_Missense_Mutation_p.I1008F|MYH10_ENST00000379980.4_Missense_Mutation_p.I1003F	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	987					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.I987F(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						AGAAGCAGAATCTCCTCTTCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											143	138	140					17																	8413168		2203	4300	6503	8353893	SO:0001583	missense	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2959A>T	17.37:g.8413168T>A	ENSP00000269243:p.Ile987Phe		8353893	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226789	0.39399	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.04	3.97	0.46021	.	0.110339	0.64402	D	0.000012	D	0.89378	0.6698	M	0.79693	2.465	0.46678	D	0.999159	B;B;B	0.33212	0.104;0.167;0.402	B;B;B	0.31016	0.058;0.123;0.058	D	0.87838	0.2649	10	0.87932	D	0	.	10.013	0.41997	0.0:0.0804:0.0:0.9196	.	996;1018;987	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	F	987;1018;1008;1003	ENSP00000269243:I987F;ENSP00000353590:I1018F;ENSP00000379539:I1008F;ENSP00000369315:I1003F	ENSP00000269243:I987F	I	-	1	0	MYH10	8353893	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.548000	0.45794	0.951000	0.37770	0.482000	0.46254	ATT		0.428	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			A	8413168	T	A	8413168	3	1	58	1	0	0	0	0	1	0	0	0	10060	1435	50	5	3047	5	MYH10	17	8413168	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	834617	8413168	72782042	129	7775										
ABI3	51225	broad.mit.edu	37	chr17	47293951	47293951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cttcactacccaggcactggCcagcgtggcctaccaggtgg	12	15	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:47293951C>T	ENST00000225941.1	+	2	674	c.176C>T	c.(175-177)gCc>gTc	p.A59V	ABI3_ENST00000419580.2_Missense_Mutation_p.A59V	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	59					cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)		p.A59V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			CAGGCACTGGCCAGCGTGGCC	0.652										HNSCC(55;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	17											31	28	29					17																	47293951		2203	4300	6503	44648950	SO:0001583	missense	51225			AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.176C>T	17.37:g.47293951C>T	ENSP00000225941:p.Ala59Val		44648950	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.748941	0.89753	.	.	ENSG00000108798	ENST00000225941;ENST00000419580	D;D	0.92595	-3.07;-3.07	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000002	D	0.96059	0.8716	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.988	D	0.96509	0.9377	10	0.87932	D	0	-29.607	16.8368	0.85958	0.0:1.0:0.0:0.0	.	59;59	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	V	59	ENSP00000225941:A59V;ENSP00000406651:A59V	ENSP00000225941:A59V	A	+	2	0	ABI3	44648950	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	7.133000	0.77259	2.486000	0.83907	0.563000	0.77884	GCC		0.652	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428		T	47293951	C	T	47293951	3	4	58	1	0	0	0	0	1	0	0	0	90	739	26	3	182	3	ABI3	17	47293951	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	38880783	47293951	33901259	130	7776										
CSH1	1442	broad.mit.edu	37	chr17	61972614	61972614	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aagagaaggagaggccaagcGcttgggcactgttccctccc	13	12	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:61972614G>A	ENST00000316193.8	-	5	598				CSH1_ENST00000329882.8_Silent_p.S225S|CSH1_ENST00000453363.3_Intron	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GAGGCCAAGCGCTTGGGCACT	0.542									Russell-Silver syndrome																																							0			17											68	69	69					17																	61972614		2192	4297	6489	59326346	SO:0001627	intron_variant	1442	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.457-35C>T	17.37:g.61972614G>A			59326346	P01243|Q0VDB1|Q14407	Silent	SNP	ENST00000316193.8	37	CCDS11649.1																																																																																				0.542	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		A	61972614	G	A	61972614	1	1	58	0	1	0	0	0	0	0	0	0	3946	1078	38	1		1	CSH1	17	61972614	Intron	SNP	G	TCGA-AG-4007-01A-01W-1073-09	14678663	61972614	19222596	131	7777										
SCN4A	6329	broad.mit.edu	37	chr17	62034860	62034860	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cagcgttggccacgacttggCcagcttgaagacccgcagct	12	14	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:62034860C>A	ENST00000435607.1	-	13	2114	c.2038G>T	c.(2038-2040)Gcc>Tcc	p.A680S	SCN4A_ENST00000578147.1_Missense_Mutation_p.A680S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	680					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A680S(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CACGACTTGGCCAGCTTGAAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											58	65	63					17																	62034860		2125	4244	6369	59388592	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2038G>T	17.37:g.62034860C>A	ENSP00000396320:p.Ala680Ser		59388592	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.394902	0.83011	.	.	ENSG00000007314	ENST00000435607	D	0.98531	-4.98	3.52	3.52	0.40303	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	M	0.87682	2.9	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	D	0.99308	1.0903	10	0.87932	D	0	.	14.5928	0.68383	0.0:1.0:0.0:0.0	.	680	P35499	SCN4A_HUMAN	S	680	ENSP00000396320:A680S	ENSP00000396320:A680S	A	-	1	0	SCN4A	59388592	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.609000	0.82925	1.979000	0.57680	0.561000	0.74099	GCC		0.582	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62034860	C	A	62034860	3	1	58	1	0	0	0	0	1	0	0	0	13957	739	26	2	3520	2	SCN4A	17	62034860	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	62246	62034860	19160350	132	7778										
SCN4A	6329	broad.mit.edu	37	chr17	62049785	62049785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	caggtagagagcaggtgtggCggagaagcggaagatggcct	19	6	0	3	rs538978403		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr17:62049785C>T	ENST00000435607.1	-	2	395	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	SCN4A_ENST00000578147.1_Missense_Mutation_p.A107T|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	107					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A107T(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCAGGTGTGGCGGAGAAGCGG	0.592													C|||	1	0.000199681	0	0	5008	,	,		20555	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	17											81	88	86					17																	62049785		2172	4276	6448	59403517	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.319G>A	17.37:g.62049785C>T	ENSP00000396320:p.Ala107Thr		59403517	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.251406	0.59212	.	.	ENSG00000007314	ENST00000435607	D	0.96913	-4.17	4.23	4.23	0.50019	.	0.054077	0.64402	D	0.000001	D	0.95931	0.8675	M	0.80847	2.515	0.45307	D	0.998308	D	0.59357	0.985	B	0.43623	0.425	D	0.96374	0.9276	10	0.59425	D	0.04	.	15.7671	0.78135	0.0:1.0:0.0:0.0	.	107	P35499	SCN4A_HUMAN	T	107	ENSP00000396320:A107T	ENSP00000396320:A107T	A	-	1	0	SCN4A	59403517	0.978000	0.34361	0.861000	0.33841	0.834000	0.47266	2.510000	0.45468	2.188000	0.69820	0.313000	0.20887	GCC		0.592	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62049785	C	T	62049785	3	4	58	1	0	0	0	0	1	0	0	0	13957	768	27	1	5283	1	SCN4A	17	62049785	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	14925	62049785	19145425	133	7779										
CD226	10666	broad.mit.edu	37	chr18	67562982	67562982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gaaggtttcgttttctcctgCgctggcctgcaagtagcagc	12	11	1	0	rs146723371	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr18:67562982C>T	ENST00000280200.4	-	4	950	c.682G>A	c.(682-684)Gca>Aca	p.A228T	CD226_ENST00000577287.1_Missense_Mutation_p.A73T|CD226_ENST00000582621.1_Missense_Mutation_p.A228T|CD226_ENST00000581982.1_Missense_Mutation_p.A73T	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	228	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)	p.A228T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				TTTTCTCCTGCGCTGGCCTGC	0.542													C|||	4	0.000798722	0.003	0	5008	,	,		18442	0		0	False		,,,				2504	0				NSCLC(184;838 2130 8673 21498 50749)											1	Substitution - Missense(1)	large_intestine(1)	18						C	THR/ALA	4,4402	8.1+/-20.4	0,4,2199	133	134	134		682	-0.9	0	18	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CD226	NM_006566.2	58	0,5,6498	TT,TC,CC		0.0116,0.0908,0.0384	benign	228/337	67562982	5,13001	2203	4300	6503	65713962	SO:0001583	missense	10666			U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	16961	protein-coding gene	gene with protein product		605397	"CD226 antigen"			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.682G>A	18.37:g.67562982C>T	ENSP00000280200:p.Ala228Thr		65713962	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	C	1.448	-0.565719	0.03910	9.08E-4	1.16E-4	ENSG00000150637	ENST00000280200	T	0.12255	2.7	4.82	-0.932	0.10435	Immunoglobulin V-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.434279	0.24513	N	0.037863	T	0.01489	0.0048	N	0.00092	-2.175	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.40776	-0.9545	10	0.02654	T	1	.	2.8128	0.05446	0.318:0.183:0.0:0.499	.	228	Q15762	CD226_HUMAN	T	228	ENSP00000280200:A228T	ENSP00000280200:A228T	A	-	1	0	CD226	65713962	0.012000	0.17670	0.001000	0.08648	0.004000	0.04260	0.019000	0.13444	-0.166000	0.10890	-0.300000	0.09419	GCA		0.542	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566		T	67562982	C	T	67562982	3	4	58	1	0	0	0	0	1	0	0	0	2992	768	27	1	344	1	CD226	18	67562982	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		67562982	10514266	134	7780										
TMIGD2	126259	broad.mit.edu	37	chr19	4298087	4298087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cgctgtggttgaggctcacaGggtccagctgcagggtgaga	17	9	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:4298087G>A	ENST00000301272.2	-	2	347	c.302C>T	c.(301-303)cCt>cTt	p.P101L	TMIGD2_ENST00000600114.1_Intron|TMIGD2_ENST00000595645.1_Missense_Mutation_p.P101L|TMIGD2_ENST00000600349.1_Intron	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	101	Ig-like.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.P101L(1)|p.P101H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCTCACAGGGTCCAGCTG	0.642																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											65	68	67					19																	4298087		2203	4300	6503	4249087	SO:0001583	missense	126259			BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.302C>T	19.37:g.4298087G>A	ENSP00000301272:p.Pro101Leu		4249087	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	.	.	.	.	.	.	.	.	.	.	G	5.391	0.257422	0.10239	.	.	ENSG00000167664	ENST00000301272	T	0.28069	1.63	4.09	-8.19	0.01049	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13372	0.0324	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.002;0.003	T	0.12116	-1.0560	9	0.27785	T	0.31	.	4.0659	0.09859	0.1911:0.4567:0.2033:0.1489	.	101;101	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	L	101	ENSP00000301272:P101L	ENSP00000301272:P101L	P	-	2	0	TMIGD2	4249087	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-5.654000	0.00107	-3.515000	0.00149	-0.350000	0.07774	CCT		0.642	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615		A	4298087	G	A	4298087	3	1	58	1	0	0	0	0	1	0	0	0	16270	1000	35	3	562	3	TMIGD2	19	4298087	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09		4298087	54830896	135	7781										
MUC16	94025	broad.mit.edu	37	chr19	9067649	9067649	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gattccttttcagaagtggtGgtccccacattggttactgc	10	10	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:9067649G>A	ENST00000397910.4	-	3	20000	c.19797C>T	c.(19795-19797)acC>acT	p.T6599T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6601	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T6599T(2)|p.T2232T(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGAAGTGGTGGTCCCCACAT	0.443																																																3	Substitution - coding silent(3)	large_intestine(3)	19											199	181	187					19																	9067649		1931	4133	6064	8928649	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.19797C>T	19.37:g.9067649G>A			8928649	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9067649	G	A	9067649	2	1	58	1	0	0	0	0	0	0	0	1	10003	1335	47	3		3	MUC16	19	9067649	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	4769562	9067649	50061334	136	7782										
ZNF846	162993	broad.mit.edu	37	chr19	9868340	9868340	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	taaggcttttctcctgtgtgCgttcgcatgtgcatattaag	10	8	1	0	rs377731453		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:9868340C>T	ENST00000397902.2	-	6	1826	c.1413G>A	c.(1411-1413)acG>acA	p.T471T	ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T471T(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						CTCCTGTGTGCGTTCGCATGT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4316		0,0,2158	95	104	101		1413	-4	0	19		101	1,8571		0,1,4285	no	coding-synonymous	ZNF846	NM_001077624.1		0,1,6443	TT,TC,CC		0.0117,0.0,0.0078		471/534	9868340	1,12887	2158	4286	6444	9729340	SO:0001819	synonymous_variant	162993			AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1413G>A	19.37:g.9868340C>T			9729340	A8K0H1|B3KUP1	Silent	SNP	ENST00000397902.2	37	CCDS42496.1																																																																																				0.433	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		T	9868340	C	T	9868340	2	4	58	1	0	0	0	0	0	0	0	1	18231	755	27	1		1	ZNF846	19	9868340	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	800691	9868340	49260643	137	7783										
SMARCA4	6597	broad.mit.edu	37	chr19	11135019	11135019	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ccctgcaggtggagtacgtcAtcaagtgcgacatgtctgcg	13	11	3	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:11135019A>T	ENST00000429416.3	+	22	3267	c.2986A>T	c.(2986-2988)Atc>Ttc	p.I996F	SMARCA4_ENST00000413806.3_Missense_Mutation_p.I996F|SMARCA4_ENST00000444061.3_Missense_Mutation_p.I996F|SMARCA4_ENST00000589677.1_Missense_Mutation_p.I996F|SMARCA4_ENST00000541122.2_Missense_Mutation_p.I996F|SMARCA4_ENST00000590574.1_Missense_Mutation_p.I996F|SMARCA4_ENST00000358026.2_Missense_Mutation_p.I996F|SMARCA4_ENST00000450717.3_Missense_Mutation_p.I996F|SMARCA4_ENST00000344626.4_Missense_Mutation_p.I996F	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	996					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.I996F(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGAGTACGTCATCAAGTGCGA	0.627			"F, N, Mis"		NSCLC																																		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|lung(1)	19											91	63	72					19																	11135019		2203	4300	6503	10996019	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2986A>T	19.37:g.11135019A>T	ENSP00000395654:p.Ile996Phe		10996019	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.832490	0.91036	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	5.23	5.23	0.72850	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.86994	0.6067	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D;D;D;D	0.67145	0.993;0.984;0.993;0.996;0.992;0.986;0.993;0.993	D;D;D;D;P;D;D;D	0.75020	0.962;0.949;0.962;0.985;0.889;0.935;0.962;0.962	D	0.88581	0.3136	10	0.87932	D	0	-36.8253	14.2475	0.65997	1.0:0.0:0.0:0.0	.	996;996;996;996;996;216;996;996	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	F	996;996;1060;996;996;996;996;996	ENSP00000395654:I996F;ENSP00000350720:I996F;ENSP00000343896:I996F;ENSP00000445036:I996F;ENSP00000392837:I996F;ENSP00000397783:I996F;ENSP00000414727:I996F	ENSP00000343896:I996F	I	+	1	0	SMARCA4	10996019	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.127000	0.77210	2.202000	0.70862	0.533000	0.62120	ATC		0.627	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11135019	A	T	11135019	3	4	58	1	0	0	0	0	1	0	0	0	14807	217	8	5	3064	5	SMARCA4	19	11135019	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	1266679	11135019	47993964	138	7784										
EMR2	30817	broad.mit.edu	37	chr19	14884750	14884750	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctgccctcaagcctctgtacCgtcacaagtctccatggggg	10	15	4	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:14884750C>T	ENST00000315576.3	-	4	650	c.199G>A	c.(199-201)Gac>Aac	p.D67N	EMR2_ENST00000599423.1_5'UTR|EMR2_ENST00000392965.3_Splice_Site_p.D67N|EMR2_ENST00000595839.1_Splice_Site_p.D67N|EMR2_ENST00000353005.1_Splice_Site_p.D67N|EMR2_ENST00000596991.2_Splice_Site_p.D67N|EMR2_ENST00000601345.1_Splice_Site_p.D67N|EMR2_ENST00000353876.1_Splice_Site_p.D67N|EMR2_ENST00000594294.1_Splice_Site_p.D67N|EMR2_ENST00000392964.3_5'Flank|EMR2_ENST00000594076.1_Splice_Site_p.D67N|EMR2_ENST00000392967.2_Splice_Site_p.D67N|EMR2_ENST00000346057.1_Splice_Site_p.D67N	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	67	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)	p.D67N(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						GCCTCTGTACCGTCACAAGTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											130	122	125					19																	14884750		2203	4300	6503	14745750	SO:0001630	splice_region_variant	30817			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.199+1G>A	19.37:g.14884750C>T			14745750	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.299094	0.60195	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000360222;ENST00000392965;ENST00000392962	D;D;D;D;D;D;D	0.99051	-5.37;-5.37;-5.37;-5.37;-5.37;-5.37;-5.37	3.87	2.83	0.33086	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.99086	0.9686	M	0.83012	2.62	0.24000	N	0.99621	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.991;1.0;1.0	D;D;P;D;P;D;D	0.91635	0.999;0.982;0.908;0.96;0.633;0.985;0.975	D	0.95651	0.8707	8	.	.	.	.	8.0793	0.30735	0.0:0.8795:0.0:0.1205	.	67;67;67;67;67;67;67	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;.;.;.;EMR2_HUMAN;.	N	67	ENSP00000319883:D67N;ENSP00000376694:D67N;ENSP00000263380:D67N;ENSP00000319454:D67N;ENSP00000319838:D67N;ENSP00000376692:D67N;ENSP00000376689:D67N	.	D	-	1	0	EMR2	14745750	0.524000	0.26282	0.330000	0.25442	0.038000	0.13279	2.233000	0.43027	0.930000	0.37217	-0.507000	0.04495	GAC		0.582	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		Missense_Mutation	T	14884750	C	T	14884750	5	4	58	1	0	0	0	0	0	0	1	0	5118	666	23	1	2344	1	EMR2	19	14884750	Splice_Site	SNP	C	TCGA-AG-4007-01A-01W-1073-09	3749731	14884750	44244233	139	7785										
CASP14	23581	broad.mit.edu	37	chr19	15164318	15164318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	atatgatatgtcaggtgcccGcctggccctaatactgtgtg	11	10	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:15164318G>A	ENST00000427043.3	+	3	361	c.53G>A	c.(52-54)cGc>cAc	p.R18H	CASP14_ENST00000221740.1_Missense_Mutation_p.R18H|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	18					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.R18H(1)|p.R18P(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TCAGGTGCCCGCCTGGCCCTA	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											81	79	80					19																	15164318		2203	4300	6503	15025318	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.53G>A	19.37:g.15164318G>A	ENSP00000393417:p.Arg18His		15025318	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.989537	0.74589	.	.	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.03717	3.83;3.83	4.81	4.81	0.61882	Peptidase C14, caspase precursor p45, core (1);	0.238103	0.21366	N	0.075706	T	0.19127	0.0459	M	0.84683	2.71	0.37202	D	0.904416	D	0.89917	1.0	D	0.70935	0.971	T	0.03863	-1.0997	10	0.49607	T	0.09	.	13.3594	0.60646	0.0:0.0:1.0:0.0	.	18	P31944	CASPE_HUMAN	H	18	ENSP00000393417:R18H;ENSP00000221740:R18H	ENSP00000221740:R18H	R	+	2	0	CASP14	15025318	0.996000	0.38824	0.996000	0.52242	0.820000	0.46376	3.077000	0.50089	2.209000	0.71365	0.306000	0.20318	CGC		0.512	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		A	15164318	G	A	15164318	3	1	58	1	0	0	0	0	1	0	0	0	2676	1087	38	1	59	1	CASP14	19	15164318	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	279568	15164318	43964665	140	7786										
NWD1	284434	broad.mit.edu	37	chr19	16899843	16899843	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aagggaccctcgccaactctGcttcaaaggattacacgctg	9	13	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:16899843G>T	ENST00000552788.1	+	11	2782	c.2782G>T	c.(2782-2784)Gct>Tct	p.A928S	NWD1_ENST00000524140.2_Missense_Mutation_p.A928S|NWD1_ENST00000523826.1_Missense_Mutation_p.A722S|NWD1_ENST00000549814.1_Missense_Mutation_p.A928S|NWD1_ENST00000339803.6_Missense_Mutation_p.A793S|NWD1_ENST00000379808.3_Missense_Mutation_p.A928S			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	928							ATP binding (GO:0005524)	p.A793S(1)|p.A928S(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CGCCAACTCTGCTTCAAAGGA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	19											120	115	117					19																	16899843		2203	4300	6503	16760843	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2782G>T	19.37:g.16899843G>T	ENSP00000447224:p.Ala928Ser		16760843	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	G	11.17	1.560318	0.27827	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04	5.65	2.13	0.27403	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.411559	0.24947	N	0.034331	T	0.63307	0.2500	L	0.42529	1.33	0.26405	N	0.97636	D;D;D	0.69078	0.99;0.997;0.957	P;D;P	0.64042	0.846;0.921;0.67	T	0.51426	-0.8707	10	0.27785	T	0.31	-14.0575	6.1517	0.20316	0.0875:0.0:0.5622:0.3503	.	928;928;793	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	S	793;928;928;928;722;928;793	ENSP00000428579:A928S;ENSP00000447548:A928S;ENSP00000369136:A928S;ENSP00000428955:A722S;ENSP00000447224:A928S;ENSP00000340159:A793S	ENSP00000340159:A793S	A	+	1	0	NWD1	16760843	0.922000	0.31269	0.894000	0.35097	0.046000	0.14306	1.305000	0.33493	0.712000	0.32039	0.591000	0.81541	GCT		0.493	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16899843	G	T	16899843	3	4	58	1	0	0	0	0	1	0	0	0	10812	1319	46	2	2411	2	NWD1	19	16899843	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	1735525	16899843	42229140	141	7787										
WDR88	126248	broad.mit.edu	37	chr19	33639806	33639806	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gagaacatcaccaccgtttcCgtcatcaaaggtgagggtgt	11	10	3	2	rs144975503	byFrequency	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:33639806C>T	ENST00000355868.3	+	5	745	c.669C>T	c.(667-669)tcC>tcT	p.S223S	WDR88_ENST00000361680.2_Silent_p.S223S	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	223								p.S223S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					CCACCGTTTCCGTCATCAAAG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	130	99	109		669	-10.9	0	19	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR88	NM_173479.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		223/473	33639806	1,13005	2203	4300	6503	38331646	SO:0001819	synonymous_variant	126248			BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.669C>T	19.37:g.33639806C>T			38331646	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																				0.493	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		T	33639806	C	T	33639806	2	4	58	1	0	0	0	0	0	0	0	1	17375	639	23	1		1	WDR88	19	33639806	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	16739963	33639806	25489177	142	7788										
ATP4A	495	broad.mit.edu	37	chr19	36051502	36051502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctggaatttgtctccatcgcGgatgacagtggcttgctgcg	13	10	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:36051502G>A	ENST00000262623.3	-	6	578	c.550C>T	c.(550-552)Cgc>Tgc	p.R184C		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	184					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)	p.R184C(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	TCTCCATCGCGGATGACAGTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											35	35	35					19																	36051502		2203	4300	6503	40743342	SO:0001583	missense	495				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.550C>T	19.37:g.36051502G>A	ENSP00000262623:p.Arg184Cys		40743342	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	g	16.79	3.220823	0.58560	.	.	ENSG00000105675	ENST00000262623	D	0.94046	-3.34	3.99	3.99	0.46301	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000015	D	0.98121	0.9380	H	0.99197	4.465	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98776	1.0730	10	0.87932	D	0	.	13.9607	0.64177	0.0:0.0:1.0:0.0	.	184	P20648	ATP4A_HUMAN	C	184	ENSP00000262623:R184C	ENSP00000262623:R184C	R	-	1	0	ATP4A	40743342	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	2.179000	0.42528	2.227000	0.72691	0.306000	0.20318	CGC		0.617	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		A	36051502	G	A	36051502	3	1	58	1	0	0	0	0	1	0	0	0	1146	1116	39	1	2625	1	ATP4A	19	36051502	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	2411696	36051502	23077481	143	7789										
APLP1	333	broad.mit.edu	37	chr19	36361838	36361838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgcacgtgtggagcaggctaCgcaggccatccccatggagc	14	13	0	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:36361838C>T	ENST00000221891.4	+	3	524	c.332C>T	c.(331-333)aCg>aTg	p.T111M	APLP1_ENST00000537454.2_Missense_Mutation_p.T72M|APLP1_ENST00000586861.1_Missense_Mutation_p.T105M|NPHS1_ENST00000591817.1_5'Flank	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	111					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)	p.T111M(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGCAGGCTACGCAGGCCATC	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	19											19	21	20					19																	36361838		2203	4299	6502	41053678	SO:0001583	missense	333			U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.332C>T	19.37:g.36361838C>T	ENSP00000221891:p.Thr111Met		41053678	O00113|Q96A92	Missense_Mutation	SNP	ENST00000221891.4	37	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.365860	0.24684	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	D;D	0.93953	-3.25;-3.32	4.96	2.62	0.31277	Amyloidogenic glycoprotein, extracellular (1);Amyloidogenic glycoprotein, heparin-binding (3);	0.912638	0.09172	N	0.838648	D	0.89114	0.6623	N	0.14661	0.345	0.09310	N	1	D;P;P;P	0.59357	0.985;0.917;0.872;0.895	P;B;B;P	0.48921	0.595;0.429;0.36;0.493	T	0.80888	-0.1181	10	0.87932	D	0	-0.1806	9.4215	0.38555	0.3868:0.6132:0.0:0.0	.	105;72;111;111	B7Z4G8;F5GZ08;P51693-2;P51693	.;.;.;APLP1_HUMAN	M	72;111	ENSP00000441501:T72M;ENSP00000221891:T111M	ENSP00000221891:T111M	T	+	2	0	APLP1	41053678	0.001000	0.12720	0.033000	0.17914	0.256000	0.26092	1.513000	0.35823	1.045000	0.40225	0.484000	0.47621	ACG		0.697	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		T	36361838	C	T	36361838	3	4	58	1	0	0	0	0	1	0	0	0	778	536	19	1	342	1	APLP1	19	36361838	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	310336	36361838	22767145	144	7790										
ZFP112	7771	broad.mit.edu	37	chr19	44832911	44832911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gctgttactacacacatagcGtttatatggttgttccttag	8	8	0	0	rs202199443		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:44832911G>A	ENST00000337401.4	-	5	1505	c.1417C>T	c.(1417-1419)Cgc>Tgc	p.R473C	ZNF112_ENST00000354340.4_Missense_Mutation_p.R467C|ZNF112_ENST00000536500.1_Missense_Mutation_p.R490C	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R473C(1)|p.R467C(1)									CACACATAGCGTTTATATGGT	0.403													G|||	1	0.000199681	8e-04	0	5008	,	,		20002	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	19											118	107	110					19																	44832911		2203	4300	6503	49524751	SO:0001583	missense	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1417C>T	19.37:g.44832911G>A	ENSP00000337081:p.Arg473Cys		49524751	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	0.005	-2.172726	0.00315	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.00575	6.46;6.46;6.46	4.73	0.312	0.15837	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.027060	0.07822	N	0.959946	T	0.00073	0.0002	N	0.00000	-3.935	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.50346	-0.8839	10	0.02654	T	1	-0.4915	6.7395	0.23428	0.5532:0.0:0.4468:0.0	.	472;490;473	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	C	473;473;467;490;472	ENSP00000337081:R473C;ENSP00000346305:R467C;ENSP00000441990:R490C	ENSP00000253426:R472C	R	-	1	0	ZNF285	49524751	0.004000	0.15560	0.001000	0.08648	0.135000	0.20990	1.882000	0.39648	0.316000	0.23135	0.561000	0.74099	CGC		0.403	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		A	44832911	G	A	44832911	3	1	58	1	0	0	0	0	1	0	0	0	17677	1145	40	1	1328	1	ZFP112	19	44832911	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	8471073	44832911	14296072	145	7791										
CKM	1158	broad.mit.edu	37	chr19	45821107	45821107	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aggttttcatggttgaggtcAgtcttgtgcttgtcagtggg	15	5	4	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:45821107A>G	ENST00000221476.3	-	3	498	c.324T>C	c.(322-324)acT>acC	p.T108T		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	108					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.T108T(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	GGTTGAGGTCAGTCTTGTGCT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19											146	116	126					19																	45821107		2203	4300	6503	50512947	SO:0001819	synonymous_variant	1158			M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.324T>C	19.37:g.45821107A>G			50512947	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																				0.562	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			G	45821107	A	G	45821107	2	3	58	1	0	0	0	0	0	0	0	1	3454	175	7	4		4	CKM	19	45821107	Silent	SNP	A	TCGA-AG-4007-01A-01W-1073-09	988196	45821107	13307876	146	7792										
NOVA2	4858	broad.mit.edu	37	chr19	46457181	46457181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ggcctctgccgtgccctgtaCtaggcatacccgctctgtgg	12	15	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:46457181C>T	ENST00000263257.5	-	3	447	c.253G>A	c.(253-255)Gta>Ata	p.V85I		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	85	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.V85I(1)		endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		GTGCCCTGTACTAGGCATACC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	19											199	165	177					19																	46457181		2203	4300	6503	51149021	SO:0001583	missense	4858			U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.253G>A	19.37:g.46457181C>T	ENSP00000263257:p.Val85Ile		51149021	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	37	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	C	5.969	0.362750	0.11296	.	.	ENSG00000104967	ENST00000263257	T	0.18174	2.23	5.17	4.13	0.48395	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.063980	0.64402	D	0.000008	T	0.04861	0.0131	N	0.00966	-1.09	0.42916	D	0.994277	B	0.16603	0.018	B	0.20184	0.028	T	0.28396	-1.0045	10	0.02654	T	1	-11.484	11.6811	0.51458	0.0:0.9144:0.0:0.0856	.	85	Q9UNW9	NOVA2_HUMAN	I	85	ENSP00000263257:V85I	ENSP00000263257:V85I	V	-	1	0	NOVA2	51149021	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.338000	0.52128	1.419000	0.47118	0.591000	0.81541	GTA		0.532	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		T	46457181	C	T	46457181	3	4	58	1	0	0	0	0	1	0	0	0	10586	565	20	3	1233	3	NOVA2	19	46457181	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	636074	46457181	12671802	147	7793										
C19orf75	284369	broad.mit.edu	37	chr19	51769106	51769106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctatgcgggaattgtaattgCgctgctcttcctctgcctcc	9	13	2	0	rs149546733		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:51769106C>T	ENST00000316401.7	+	4	761	c.380C>T	c.(379-381)gCg>gTg	p.A127V	SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Missense_Mutation_p.A33V|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	489	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A127V(1)									ATTGTAATTGCGCTGCTCTTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	VAL/ALA	0,4406		0,0,2203	243	224	230		380	0.9	0	19	dbSNP_134	230	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C19orf75	NM_173635.1	64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	127/198	51769106	2,13004	2203	4300	6503	56460918	SO:0001583	missense	284369			AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.380C>T	19.37:g.51769106C>T	ENSP00000321249:p.Ala127Val		56460918	Q8IYH7	Missense_Mutation	SNP	ENST00000316401.7	37	CCDS12827.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.599762	0.28534	0.0	2.33E-4	ENSG00000179213	ENST00000316401	T	0.38560	1.13	4.38	0.863	0.19062	.	1.625570	0.03695	N	0.247752	T	0.42040	0.1185	L	0.55017	1.72	0.09310	N	1	B;D	0.56287	0.0;0.975	B;P	0.46299	0.001;0.511	T	0.28170	-1.0052	10	0.41790	T	0.15	.	4.069	0.09874	0.0:0.5631:0.2137:0.2231	.	33;127	B7ZLS6;Q8N7X8	.;CS075_HUMAN	V	127	ENSP00000321249:A127V	ENSP00000321249:A127V	A	+	2	0	C19orf75	56460918	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.247000	0.08866	0.507000	0.28148	-0.128000	0.14901	GCG		0.557	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		T	51769106	C	T	51769106	3	4	58	1	0	0	0	0	1	0	0	0	1955	768	27	1	390	1	C19orf75	19	51769106	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	5311925	51769106	7359877	148	7794										
ZSCAN5B	342933	broad.mit.edu	37	chr19	56704070	56704070	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcttctgttatttcgtagcaGgtcctccaggtctttgcagc	9	11	3	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:56704070G>C	ENST00000586855.2	-	2	665	c.352C>G	c.(352-354)Ctg>Gtg	p.L118V	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.L118V			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	118	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.L118V(2)		breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TTTCGTAGCAGGTCCTCCAGG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	19											50	54	53					19																	56704070		2202	4294	6496	61395882	SO:0001583	missense	342933				CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"-", "Zinc fingers, C2H2-type"	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.352C>G	19.37:g.56704070G>C	ENSP00000466072:p.Leu118Val		61395882		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.341251	0.24339	.	.	ENSG00000197213	ENST00000358992	T	0.07688	3.17	2.48	-4.95	0.03048	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.17238	0.0414	M	0.64170	1.965	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.07558	-1.0766	9	0.34782	T	0.22	.	5.6768	0.17753	0.0:0.1783:0.2802:0.5416	.	118	A6NJL1	ZSA5B_HUMAN	V	118	ENSP00000351883:L118V	ENSP00000351883:L118V	L	-	1	2	ZSCAN5B	61395882	0.001000	0.12720	0.050000	0.19076	0.166000	0.22503	-1.910000	0.01584	-0.684000	0.05183	0.313000	0.20887	CTG		0.547	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		C	56704070	G	C	56704070	3	2	58	1	0	0	0	0	1	0	0	0	18278	991	35	5	1151	5	ZSCAN5B	19	56704070	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	4934964	56704070	2424913	149	7795										
ZNF471	57573	broad.mit.edu	37	chr19	57027677	57027677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcaaggatgtggcaatagatTtttcccaggaagaatggcaa	11	6	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr19:57027677T>C	ENST00000308031.5	+	3	200	c.67T>C	c.(67-69)Ttt>Ctt	p.F23L	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Missense_Mutation_p.F23L	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F23L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		GGCAATAGATTTTTCCCAGGA	0.418																																					Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)											1	Substitution - Missense(1)	large_intestine(1)	19											149	135	140					19																	57027677		2203	4300	6503	61719489	SO:0001583	missense	57573			AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.67T>C	19.37:g.57027677T>C	ENSP00000309161:p.Phe23Leu		61719489	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.716358	0.68844	.	.	ENSG00000196263	ENST00000308031	T	0.12879	2.64	3.77	3.77	0.43336	Krueppel-associated box (4);	.	.	.	.	T	0.35068	0.0919	M	0.76574	2.34	0.28823	N	0.897584	D	0.76494	0.999	D	0.79108	0.992	T	0.07947	-1.0746	9	0.52906	T	0.07	.	10.7951	0.46455	0.0:0.0:0.0:1.0	.	23	Q9BX82	ZN471_HUMAN	L	23	ENSP00000309161:F23L	ENSP00000309161:F23L	F	+	1	0	ZNF471	61719489	0.998000	0.40836	0.921000	0.36526	0.976000	0.68499	2.040000	0.41203	1.708000	0.51301	0.528000	0.53228	TTT		0.418	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57027677	T	C	57027677	3	2	58	1	0	0	0	0	1	0	0	0	17969	1841	64	4	73	4	ZNF471	19	57027677	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	323607	57027677	2101306	150	7796										
KIAA0406	9675	broad.mit.edu	37	chr20	36641522	36641522	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aaagatctttagggaagataCgacaatgctgtgaccttgtt	10	6	1	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr20:36641522C>T	ENST00000373448.2	-	3	935	c.697G>A	c.(697-699)Gta>Ata	p.V233I	TTI1_ENST00000449821.1_Missense_Mutation_p.V233I|TTI1_ENST00000373447.3_Missense_Mutation_p.V233I|TTI1_ENST00000487362.1_Intron	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	233					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)		p.V233I(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AGGGAAGATACGACAATGCTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	20											157	154	155					20																	36641522		2203	4300	6503	36074936	SO:0001583	missense	9675			BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.697G>A	20.37:g.36641522C>T	ENSP00000362547:p.Val233Ile		36074936	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	C	0.900	-0.722465	0.03182	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.15139	2.45;2.45;2.45	5.45	3.38	0.38709	Armadillo-like helical (1);Armadillo-type fold (1);	0.302894	0.36409	N	0.002618	T	0.11707	0.0285	L	0.38175	1.15	0.09310	N	1	B	0.19331	0.035	B	0.15052	0.012	T	0.15578	-1.0432	10	0.33141	T	0.24	-27.6647	6.4202	0.21740	0.1648:0.6876:0.0:0.1476	.	233	O43156	TTI1_HUMAN	I	233	ENSP00000362547:V233I;ENSP00000362546:V233I;ENSP00000407270:V233I	ENSP00000362546:V233I	V	-	1	0	TTI1	36074936	0.420000	0.25457	0.013000	0.15412	0.755000	0.42902	1.413000	0.34725	1.517000	0.48917	-0.188000	0.12872	GTA		0.428	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		T	36641522	C	T	36641522	3	4	58	1	0	0	0	0	1	0	0	0	8194	536	19	1	2600	1	KIAA0406	20	36641522	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09		36641522	26383998	151	7797										
ZSWIM3	140831	broad.mit.edu	37	chr20	44506472	44506472	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttgtggattacatagacttCtttaataccaaaggcttgaa	7	6	1	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr20:44506472C>A	ENST00000255152.2	+	2	1484	c.1275C>A	c.(1273-1275)ttC>ttA	p.F425L	ZSWIM3_ENST00000454862.2_Missense_Mutation_p.F419L	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	425							zinc ion binding (GO:0008270)	p.F425F(1)|p.F425L(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				ACATAGACTTCTTTAATACCA	0.498																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	20											62	58	60					20																	44506472		2203	4300	6503	43939879	SO:0001583	missense	140831			AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"Zinc fingers, SWIM-type"	16157	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 174"		"chromosome 20 open reading frame 164"	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1275C>A	20.37:g.44506472C>A	ENSP00000255152:p.Phe425Leu		43939879	Q9BR13	Missense_Mutation	SNP	ENST00000255152.2	37	CCDS13381.1	.	.	.	.	.	.	.	.	.	.	C	7.606	0.673794	0.14841	.	.	ENSG00000132801	ENST00000255152;ENST00000454862	T;T	0.23348	1.95;1.91	5.41	0.275	0.15659	.	0.416464	0.25523	N	0.030098	T	0.11623	0.0283	L	0.29908	0.895	0.31958	N	0.608748	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.19418	-1.0306	10	0.10902	T	0.67	-13.6958	1.5419	0.02557	0.1368:0.3903:0.1486:0.3243	.	419;425	E7ETT6;Q96MP5	.;ZSWM3_HUMAN	L	425;419	ENSP00000255152:F425L;ENSP00000406313:F419L	ENSP00000255152:F425L	F	+	3	2	ZSWIM3	43939879	0.986000	0.35501	0.999000	0.59377	0.997000	0.91878	-0.016000	0.12613	0.125000	0.18397	0.655000	0.94253	TTC		0.498	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752		A	44506472	C	A	44506472	3	1	58	1	0	0	0	0	1	0	0	0	18281	912	32	2	1281	2	ZSWIM3	20	44506472	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	7864950	44506472	18519048	152	7798										
ZSWIM3	140831	broad.mit.edu	37	chr20	44506752	44506752	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	atgagtgggaggtggtacagAactccacccacctggtggac	14	10	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr20:44506752A>T	ENST00000255152.2	+	2	1764	c.1555A>T	c.(1555-1557)Aac>Tac	p.N519Y	ZSWIM3_ENST00000454862.2_Missense_Mutation_p.N513Y	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	519							zinc ion binding (GO:0008270)	p.N519Y(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				GGTGGTACAGAACTCCACCCA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											90	74	79					20																	44506752		2203	4300	6503	43940159	SO:0001583	missense	140831			AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"Zinc fingers, SWIM-type"	16157	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 174"		"chromosome 20 open reading frame 164"	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1555A>T	20.37:g.44506752A>T	ENSP00000255152:p.Asn519Tyr		43940159	Q9BR13	Missense_Mutation	SNP	ENST00000255152.2	37	CCDS13381.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.796332	0.50208	.	.	ENSG00000132801	ENST00000255152;ENST00000454862	T;T	0.26067	1.8;1.76	5.51	5.51	0.81932	.	0.207171	0.43110	D	0.000603	T	0.28797	0.0714	L	0.51422	1.61	0.36899	D	0.890312	D;D	0.61080	0.989;0.976	P;P	0.53450	0.726;0.656	T	0.22173	-1.0224	10	0.02654	T	1	-29.3497	9.8798	0.41227	0.9239:0.0:0.0761:0.0	.	513;519	E7ETT6;Q96MP5	.;ZSWM3_HUMAN	Y	519;513	ENSP00000255152:N519Y;ENSP00000406313:N513Y	ENSP00000255152:N519Y	N	+	1	0	ZSWIM3	43940159	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.158000	0.50723	2.317000	0.78254	0.459000	0.35465	AAC		0.567	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752		T	44506752	A	T	44506752	3	4	58	1	0	0	0	0	1	0	0	0	18281	246	9	5	1561	5	ZSWIM3	20	44506752	Missense_Mutation	SNP	A	TCGA-AG-4007-01A-01W-1073-09	280	44506752	18518768	153	7799										
ZNF70	7621	broad.mit.edu	37	chr22	24086665	24086665	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tccctgcactcgtagggcctCtttccggtgtggatcttttg	11	12	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr22:24086665C>T	ENST00000341976.3	-	2	1123	c.663G>A	c.(661-663)aaG>aaA	p.K221K		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K221K(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						CGTAGGGCCTCTTTCCGGTGT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	22											60	51	54					22																	24086665		2203	4300	6503	22416665	SO:0001819	synonymous_variant	7621			X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"Zinc fingers, C2H2-type"	13140	protein-coding gene	gene with protein product		194544	"zinc finger protein 70 (Cos17)"			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.663G>A	22.37:g.24086665C>T			22416665		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																				0.562	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916		T	24086665	C	T	24086665	2	4	58	1	0	0	0	0	0	0	0	1	18142	912	32	3		3	ZNF70	22	24086665	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09		24086665	27217901	154	7800										
ZC3H7B	23264	broad.mit.edu	37	chr22	41742078	41742078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	accatcaggaggagatcgacGtgtggaccgaggagcggaag	17	8	1	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chr22:41742078G>A	ENST00000352645.4	+	14	1788	c.1531G>A	c.(1531-1533)Gtg>Atg	p.V511M	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.V511M	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	527					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.V511M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GGAGATCGACGTGTGGACCGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	22											203	167	179					22																	41742078		2203	4300	6503	40072024	SO:0001583	missense	23264				CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.1531G>A	22.37:g.41742078G>A	ENSP00000345793:p.Val511Met		40072024	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	37	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	G	33	5.290145	0.95546	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.22336	1.96;1.96	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.50803	0.1637	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54669	-0.8259	10	0.87932	D	0	-28.124	19.0939	0.93242	0.0:0.0:1.0:0.0	.	511	Q9UGR2-2	.	M	511	ENSP00000345793:V511M;ENSP00000263243:V511M	ENSP00000263243:V511M	V	+	1	0	ZC3H7B	40072024	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.807000	0.99171	2.523000	0.85059	0.555000	0.69702	GTG		0.587	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		A	41742078	G	A	41742078	3	1	58	1	0	0	0	0	1	0	0	0	17612	1145	40	1	1581	1	ZC3H7B	22	41742078	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	17655413	41742078	9562488	155	7801										
MXRA5	25878	broad.mit.edu	37	chrX	3238174	3238174	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tggtgaggatttgtggctttTccccaagagaccagaatttg	12	7	0	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:3238174T>C	ENST00000217939.6	-	5	5706	c.5552A>G	c.(5551-5553)gAa>gGa	p.E1851G		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1851						extracellular vesicular exosome (GO:0070062)		p.E1851G(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TTGTGGCTTTTCCCCAAGAGA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	X											96	85	89					X																	3238174		2203	4300	6503	3248174	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5552A>G	X.37:g.3238174T>C	ENSP00000217939:p.Glu1851Gly		3248174	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.369042	0.24771	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.68025	-0.3	3.51	3.51	0.40186	.	0.000000	0.39341	U	0.001398	T	0.47691	0.1459	N	0.08118	0	0.21915	N	0.999477	P	0.52842	0.956	B	0.44224	0.444	T	0.45352	-0.9267	10	0.54805	T	0.06	.	11.8172	0.52218	0.0:0.0:0.0:1.0	.	1851	Q9NR99	MXRA5_HUMAN	G	1851	ENSP00000217939:E1851G	ENSP00000217939:E1851G	E	-	2	0	MXRA5	3248174	0.020000	0.18652	0.257000	0.24404	0.156000	0.22039	1.247000	0.32815	1.133000	0.42147	0.372000	0.22366	GAA		0.507	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3238174	T	C	3238174	3	2	58	1	0	0	0	0	1	0	0	0	10033	1783	62	4	2946	4	MXRA5	23	3238174	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09		3238174	152032386	156	7802										
ZNF674	641339	broad.mit.edu	37	chrX	46359623	46359623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cattcgttgcatttatagggTttctctcctgtatgcattct	7	9	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:46359623T>C	ENST00000523374.1	-	6	1611	c.1401A>G	c.(1399-1401)aaA>aaG	p.K467K	ZNF674_ENST00000414387.2_Silent_p.K461K|ZNF674_ENST00000518795.1_5'Flank	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						ATTTATAGGGTTTCTCTCCTG	0.423																																																0			X											78	78	78					X																	46359623		2195	4293	6488	46244567	SO:0001819	synonymous_variant	641339			AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"Zinc fingers, C2H2-type", "-"	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.1401A>G	X.37:g.46359623T>C			46244567	B4DHE2|E9PHQ4	Silent	SNP	ENST00000523374.1	37	CCDS48099.1																																																																																				0.423	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056357.2	NM_001039891		C	46359623	T	C	46359623	2	2	58	1	0	0	0	0	0	0	0	1	18120	1722	60	4		4	ZNF674	23	46359623	Silent	SNP	T	TCGA-AG-4007-01A-01W-1073-09	43121449	46359623	108910937	157	7803										
TRO	7216	broad.mit.edu	37	chrX	54955781	54955781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	ctttggcagtgcacccacaaCgagcacagtcttcagtagtg	10	12	2	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:54955781C>T	ENST00000173898.7	+	12	2736	c.2624C>T	c.(2623-2625)aCg>aTg	p.T875M	TRO_ENST00000375022.4_Intron|TRO_ENST00000319167.8_Intron|TRO_ENST00000375041.2_Missense_Mutation_p.T478M|TRO_ENST00000399736.1_Intron|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Missense_Mutation_p.T406M	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	875	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T875M(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GCACCCACAACGAGCACAGTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	X											55	50	52					X																	54955781		2128	4221	6349	54972506	SO:0001583	missense	7216			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2624C>T	X.37:g.54955781C>T	ENSP00000173898:p.Thr875Met		54972506	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	C	1.206	-0.631151	0.03584	.	.	ENSG00000067445	ENST00000173898;ENST00000420798;ENST00000375041	T;T;T	0.09630	2.96;2.96;2.96	2.84	0.95	0.19572	.	.	.	.	.	T	0.07458	0.0188	L	0.46157	1.445	0.09310	N	1	P;P	0.41848	0.763;0.763	B;B	0.29440	0.102;0.102	T	0.27640	-1.0068	9	0.87932	D	0	.	5.2366	0.15450	0.0:0.6559:0.2082:0.1359	.	478;875	B1AKE9;Q12816	.;TROP_HUMAN	M	875;406;478	ENSP00000173898:T875M;ENSP00000405126:T406M;ENSP00000364181:T478M	ENSP00000173898:T875M	T	+	2	0	TRO	54972506	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.144000	0.16135	0.122000	0.18314	-0.248000	0.11899	ACG		0.572	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		T	54955781	C	T	54955781	3	4	58	1	0	0	0	0	1	0	0	0	16614	536	19	1	2666	1	TRO	23	54955781	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	8596158	54955781	100314779	158	7804										
TBX22	50945	broad.mit.edu	37	chrX	79277903	79277903	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aagggcggagaggaagaggaGgagagaaggagcagcgctgc	21	5	0	3			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:79277903G>A	ENST00000373294.5	+	1	163	c.135G>A	c.(133-135)gaG>gaA	p.E45E	TBX22_ENST00000476373.1_3'UTR|TBX22_ENST00000373291.1_5'Flank|TBX22_ENST00000373296.3_Silent_p.E45E|TBX22_ENST00000442340.1_5'UTR	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	45					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E45E(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						AGGAAGAGGAGGAGAGAAGGA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	X											65	50	55					X																	79277903		2200	4295	6495	79164559	SO:0001819	synonymous_variant	50945			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.135G>A	X.37:g.79277903G>A			79164559	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	37	CCDS14445.1																																																																																				0.592	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		A	79277903	G	A	79277903	2	1	58	1	0	0	0	0	0	0	0	1	15697	991	35	3		3	TBX22	23	79277903	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	24322122	79277903	75992657	159	7805										
GPRASP1	9737	broad.mit.edu	37	chrX	101912025	101912025	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	gtccatggggtagggtcggcTtcccatctataagccccttt	11	12	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:101912025T>G	ENST00000361600.5	+	5	3985	c.3184T>G	c.(3184-3186)Ttc>Gtc	p.F1062V	GPRASP1_ENST00000415986.1_Missense_Mutation_p.F1062V|GPRASP1_ENST00000537097.1_Missense_Mutation_p.F1062V|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000444152.1_Missense_Mutation_p.F1062V	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1062	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)		p.F1062V(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TAGGGTCGGCTTCCCATCTAT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											122	121	121					X																	101912025		2203	4300	6503	101798681	SO:0001583	missense	9737			AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3184T>G	X.37:g.101912025T>G	ENSP00000355146:p.Phe1062Val		101798681	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	37	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.822931	0.32237	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	2.84	2.84	0.33178	.	.	.	.	.	T	0.25269	0.0614	M	0.61703	1.905	0.27121	N	0.962141	D	0.76494	0.999	D	0.78314	0.991	T	0.03060	-1.1077	9	0.52906	T	0.07	-3.9728	6.6244	0.22820	0.0:0.0:0.0:1.0	.	1062	Q5JY77	GASP1_HUMAN	V	1062	ENSP00000393691:F1062V;ENSP00000409420:F1062V;ENSP00000355146:F1062V;ENSP00000445683:F1062V	ENSP00000355146:F1062V	F	+	1	0	GPRASP1	101798681	1.000000	0.71417	0.931000	0.37212	0.948000	0.59901	2.926000	0.48892	1.365000	0.46057	0.235000	0.17854	TTC		0.517	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		G	101912025	T	G	101912025	3	3	58	1	0	0	0	0	1	0	0	0	6743	1609	56	4	3186	4	GPRASP1	23	101912025	Missense_Mutation	SNP	T	TCGA-AG-4007-01A-01W-1073-09	22634122	101912025	53358535	160	7806										
IRS4	8471	broad.mit.edu	37	chrX	107979463	107979463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	aatgagtgcggtcggggttcCcgaggaaagaagcggggtgg	20	6	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:107979463C>T	ENST00000372129.2	-	1	188	c.112G>A	c.(112-114)Gga>Aga	p.G38R	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	38					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.G38R(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GTCGGGGTTCCCGAGGAAAGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	X											27	29	28					X																	107979463		2203	4297	6500	107866119	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.112G>A	X.37:g.107979463C>T	ENSP00000361202:p.Gly38Arg		107866119		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	c	11.57	1.677313	0.29783	.	.	ENSG00000133124	ENST00000372129	T	0.39229	1.09	3.21	1.37	0.22104	.	0.575630	0.13084	U	0.415070	T	0.21550	0.0519	N	0.08118	0	0.27800	N	0.942521	B	0.15930	0.015	B	0.15484	0.013	T	0.17806	-1.0357	10	0.66056	D	0.02	-0.0909	6.7584	0.23526	0.2:0.6093:0.1906:0.0	.	38	O14654	IRS4_HUMAN	R	38	ENSP00000361202:G38R	ENSP00000361202:G38R	G	-	1	0	IRS4	107866119	0.775000	0.28604	0.007000	0.13788	0.548000	0.35241	3.443000	0.52907	0.246000	0.21394	-1.562000	0.00884	GGA		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107979463	C	T	107979463	3	4	58	1	0	0	0	0	1	0	0	0	7863	632	22	3	3665	3	IRS4	23	107979463	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	6067438	107979463	47291097	161	7807										
PAK3	5063	broad.mit.edu	37	chrX	110463652	110463652	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tgattatcgctgcaaaggaaGcaattaagaacagcagccgc	10	9	0	2			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:110463652G>A	ENST00000372010.1	+	19	2099	c.1657G>A	c.(1657-1659)Gca>Aca	p.A553T	PAK3_ENST00000417227.1_Missense_Mutation_p.A559T|PAK3_ENST00000372007.5_Missense_Mutation_p.A538T|PAK3_ENST00000425146.1_Missense_Mutation_p.A538T|PAK3_ENST00000519681.1_Missense_Mutation_p.A559T|PAK3_ENST00000446737.1_Missense_Mutation_p.A538T|PAK3_ENST00000262836.4_Missense_Mutation_p.A553T|PAK3_ENST00000518291.1_Missense_Mutation_p.A574T|PAK3_ENST00000360648.4_Missense_Mutation_p.A574T			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	553					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A538T(1)		breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						TGCAAAGGAAGCAATTAAGAA	0.433										TSP Lung(19;0.15)																																						1	Substitution - Missense(1)	large_intestine(1)	X											50	42	44					X																	110463652		2203	4300	6503	110350308	SO:0001583	missense	5063			AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1657G>A	X.37:g.110463652G>A	ENSP00000361080:p.Ala553Thr		110350308	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	37	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945037	0.73672	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.72167	-0.61;-0.61;-0.62;-0.63;-0.61;-0.61;-0.61;-0.63;-0.62	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70116	0.3187	L	0.45352	1.415	0.80722	D	1	B;P;P;P	0.39665	0.379;0.549;0.554;0.682	B;B;B;B	0.41412	0.251;0.251;0.232;0.356	T	0.71262	-0.4645	10	0.59425	D	0.04	.	19.7362	0.96205	0.0:0.0:1.0:0.0	.	559;574;553;538	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	T	538;538;553;559;538;574;574;559;553	ENSP00000410853:A538T;ENSP00000401982:A538T;ENSP00000361080:A553T;ENSP00000429113:A559T;ENSP00000361077:A538T;ENSP00000428921:A574T;ENSP00000353864:A574T;ENSP00000389172:A559T;ENSP00000262836:A553T	ENSP00000262836:A553T	A	+	1	0	PAK3	110350308	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	9.390000	0.97246	2.618000	0.88619	0.600000	0.82982	GCA		0.433	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110463652	G	A	110463652	3	1	58	1	0	0	0	0	1	0	0	0	11433	971	34	3	1782	3	PAK3	23	110463652	Missense_Mutation	SNP	G	TCGA-AG-4007-01A-01W-1073-09	2484189	110463652	44806908	162	7808										
SLC6A14	11254	broad.mit.edu	37	chrX	115588822	115588822	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tttcatagacctaattatggCgcaattccataccctgactg	6	11	1	2	rs187409232		TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:115588822C>T	ENST00000371900.4	+	13	1750	c.1662C>T	c.(1660-1662)ggC>ggT	p.G554G	SLC6A14_ENST00000463626.1_Intron	NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	554					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)	p.G554G(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTAATTATGGCGCAATTCCAT	0.353													C|||	3	0.000794702	0	0	3775	,	,		11785	0.003		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											190	167	175					X																	115588822		2203	4300	6503	115502850	SO:0001819	synonymous_variant	11254			AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.1662C>T	X.37:g.115588822C>T			115502850	Q5H942	Silent	SNP	ENST00000371900.4	37	CCDS14570.1																																																																																				0.353	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			T	115588822	C	T	115588822	2	4	58	1	0	0	0	0	0	0	0	1	14714	755	27	1		1	SLC6A14	23	115588822	Silent	SNP	C	TCGA-AG-4007-01A-01W-1073-09	5125170	115588822	39681738	163	7809										
DCAF12L2	340578	broad.mit.edu	37	chrX	125299670	125299670	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	cagctcgggcagcctctggaCggcgtagccccgcagctcgc	14	17	1	0			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:125299670C>T	ENST00000360028.2	-	1	264	c.238G>A	c.(238-240)Gtc>Atc	p.V80I	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.V80I			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	80								p.V80I(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						AGCCTCTGGACGGCGTAGCCC	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	X											25	27	26					X																	125299670		2190	4261	6451	125127351	SO:0001583	missense	340578			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.238G>A	X.37:g.125299670C>T	ENSP00000353128:p.Val80Ile		125127351	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	c	13.93	2.385398	0.42308	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.34859	1.34;1.34	3.28	3.28	0.37604	.	.	.	.	.	T	0.25419	0.0618	L	0.46157	1.445	0.31006	N	0.719822	P	0.49358	0.923	B	0.32022	0.139	T	0.26780	-1.0093	9	0.34782	T	0.22	.	11.6703	0.51396	0.0:1.0:0.0:0.0	.	80	Q5VW00	DC122_HUMAN	I	80	ENSP00000441489:V80I;ENSP00000353128:V80I	ENSP00000353128:V80I	V	-	1	0	DCAF12L2	125127351	1.000000	0.71417	0.024000	0.17045	0.059000	0.15707	5.147000	0.64851	1.891000	0.54761	0.287000	0.19450	GTC		0.701	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		T	125299670	C	T	125299670	3	4	58	1	0	0	0	0	1	0	0	0	4271	536	19	1	1157	1	DCAF12L2	23	125299670	Missense_Mutation	SNP	C	TCGA-AG-4007-01A-01W-1073-09	9710848	125299670	29970890	164	7810										
GPR101	83550	broad.mit.edu	37	chrX	136113120	136113120	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0606060606060606	10	1	0.729815638906548	5.35198135198135	0.463152232383002	0.707985303535915	1	0	tcattctccacacagtccttGactcgcacttccaagctgtg	6	15	2	1			TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4007-01A-01W-1073-09	TCGA-AG-4007-10A-01W-1073-09	g.chrX:136113120G>T	ENST00000298110.1	-	1	713	c.714C>A	c.(712-714)gtC>gtA	p.V238V		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.V238V(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					CACAGTCCTTGACTCGCACTT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	X											128	113	118					X																	136113120		2203	4300	6503	135940786	SO:0001819	synonymous_variant	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.714C>A	X.37:g.136113120G>T			135940786	Q5JSM8|Q8NG93	Silent	SNP	ENST00000298110.1	37	CCDS14662.1																																																																																				0.532	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136113120	G	T	136113120	2	4	58	1	0	0	0	0	0	0	0	1	6642	1277	45	2		2	GPR101	23	136113120	Silent	SNP	G	TCGA-AG-4007-01A-01W-1073-09	10813450	136113120	19157440	165	7811										
DAB1	1600	broad.mit.edu	37	chr1	57476850	57476850	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ttcgcttttgctgggactttCaaagccctcttcaaagatgt	8	10	3	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:57476850C>G	ENST00000371231.1	-	14	1673	c.1639G>C	c.(1639-1641)Gaa>Caa	p.E547Q	DAB1_ENST00000439789.2_Missense_Mutation_p.E428Q|DAB1_ENST00000414851.2_Missense_Mutation_p.E496Q|DAB1_ENST00000420954.2_Missense_Mutation_p.E512Q|DAB1_ENST00000371236.2_Missense_Mutation_p.E514Q|DAB1_ENST00000371234.4_Missense_Mutation_p.E514Q|DAB1_ENST00000485760.1_5'UTR			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	547					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.E514Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						CTGGGACTTTCAAAGCCCTCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											136	137	137					1																	57476850		2203	4300	6503	57249438	SO:0001583	missense	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.1639G>C	1.37:g.57476850C>G	ENSP00000360275:p.Glu547Gln		57249438	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.088248	0.76756	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231	T;T;T;T;T;T	0.46063	0.9;0.9;0.88;0.88;1.89;0.89	4.96	4.96	0.65561	.	0.152990	0.64402	D	0.000015	T	0.51907	0.1702	L	0.36672	1.1	0.50813	D	0.999895	D;D;D;D;D	0.69078	0.994;0.99;0.982;0.978;0.997	P;P;P;P;P	0.62435	0.641;0.801;0.792;0.549;0.902	T	0.35301	-0.9794	10	0.25106	T	0.35	-47.9219	18.7462	0.91794	0.0:1.0:0.0:0.0	.	496;547;514;428;512	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	Q	514;514;514;512;496;428;547	ENSP00000360280:E514Q;ENSP00000360278:E514Q;ENSP00000395296:E512Q;ENSP00000387581:E496Q;ENSP00000409328:E428Q;ENSP00000360275:E547Q	ENSP00000360275:E547Q	E	-	1	0	DAB1	57249438	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	5.475000	0.66787	2.724000	0.93272	0.555000	0.69702	GAA		0.438	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		G	57476850	C	G	57476850	3	3	59	1	0	0	0	0	1	0	0	0	4223	835	29	5	135	5	DAB1	1	57476850	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		57476850	191773771	1	7812										
PRDX6	9588	broad.mit.edu	37	chr1	173454529	173454529	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gcttacaattgtgaagagccCacagaaaagttaccttttcc	7	10	0	3			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:173454529C>T	ENST00000340385.5	+	3	414	c.282C>T	c.(280-282)ccC>ccT	p.P94P	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	94	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)	p.P94P(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						GTGAAGAGCCCACAGAAAAGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											147	138	141					1																	173454529		2203	4300	6503	171721152	SO:0001819	synonymous_variant	9588			D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.282C>T	1.37:g.173454529C>T			171721152	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Silent	SNP	ENST00000340385.5	37	CCDS1307.1																																																																																				0.443	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		T	173454529	C	T	173454529	2	4	59	1	0	0	0	0	0	0	0	1	12503	581	21	3		3	PRDX6	1	173454529	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	115977679	173454529	75796092	2	7813										
SERPINC1	462	broad.mit.edu	37	chr1	173878853	173878853	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgcagcacctctggggtgagTtccttctctaccttggccag	11	13	2	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:173878853T>C	ENST00000367698.3	-	5	1108	c.990A>G	c.(988-990)gaA>gaG	p.E330E	SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	330					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E330E(1)		NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	CTGGGGTGAGTTCCTTCTCTA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											150	145	147					1																	173878853		2203	4300	6503	172145476	SO:0001819	synonymous_variant	462			X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"Serine (or cysteine) peptidase inhibitors"	775	protein-coding gene	gene with protein product	"antithrombin III", "signal peptide antithrombin part 1", "coding sequence signal peptide antithrombin part 1", "antithrombin (aa 375-432)"	107300	"serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.990A>G	1.37:g.173878853T>C			172145476	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Silent	SNP	ENST00000367698.3	37	CCDS1313.1																																																																																				0.552	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488		C	173878853	T	C	173878853	2	2	59	1	0	0	0	0	0	0	0	1	14146	1722	60	4		4	SERPINC1	1	173878853	Silent	SNP	T	TCGA-AG-4008-01A-01W-1073-09	424324	173878853	75371768	3	7814										
CRB1	23418	broad.mit.edu	37	chr1	197390846	197390846	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	atggtgttgctctgcttaacTtctataatatgccatccaca	6	10	2	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:197390846T>G	ENST00000367400.3	+	6	2023	c.1888T>G	c.(1888-1890)Ttc>Gtc	p.F630V	CRB1_ENST00000543483.1_Intron|CRB1_ENST00000538660.1_Missense_Mutation_p.F630V|CRB1_ENST00000367399.2_Missense_Mutation_p.F518V|CRB1_ENST00000535699.1_Missense_Mutation_p.F561V|CRB1_ENST00000367397.1_Missense_Mutation_p.F11V|CRB1_ENST00000544212.1_Missense_Mutation_p.F111V	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	630	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F630V(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TCTGCTTAACTTCTATAATAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											152	139	143					1																	197390846		2203	4300	6503	195657469	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.1888T>G	1.37:g.197390846T>G	ENSP00000356370:p.Phe630Val		195657469	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	T	0.262	-0.999185	0.02128	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T;D	0.85339	-1.15;-1.15;-1.15;-1.15;-1.15;-1.97	5.96	-0.386	0.12466	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.62233	0.2411	N	0.04508	-0.205	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.0;0.003;0.001;0.001	T	0.48305	-0.9047	9	0.10377	T	0.69	.	5.6202	0.17453	0.5244:0.0:0.3491:0.1265	.	630;561;518;279;630	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	V	561;630;630;518;111;11;279	ENSP00000438786:F561V;ENSP00000438091:F630V;ENSP00000356370:F630V;ENSP00000356369:F518V;ENSP00000444556:F111V;ENSP00000356367:F11V	ENSP00000356367:F11V	F	+	1	0	CRB1	195657469	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.071000	0.14594	-0.309000	0.08779	-1.415000	0.01116	TTC		0.418	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		G	197390846	T	G	197390846	3	3	59	1	0	0	0	0	1	0	0	0	3854	1609	56	4	1910	4	CRB1	1	197390846	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	23511993	197390846	51859775	4	7815										
PPP1R12B	4660	broad.mit.edu	37	chr1	202464575	202464575	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgagagttcagagactaccaCaaacactacaactgcaaagg	8	10	1	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:202464575C>A	ENST00000608999.1	+	16	2453	c.2300C>A	c.(2299-2301)aCa>aAa	p.T767K	PPP1R12B_ENST00000391959.3_5'UTR|PPP1R12B_ENST00000367270.4_5'UTR|PPP1R12B_ENST00000290419.5_3'UTR|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.T767K	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	767					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)	p.T767K(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GAGACTACCACAAACACTACA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	77	79					1																	202464575		2203	4300	6503	200731198	SO:0001583	missense	4660			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2300C>A	1.37:g.202464575C>A	ENSP00000476755:p.Thr767Lys		200731198	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	37	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	C	3.294	-0.144316	0.06627	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	T;T	0.02890	4.12;4.12	5.34	1.02	0.19986	.	0.663449	0.14535	N	0.313648	T	0.02727	0.0082	M	0.65975	2.015	0.09310	N	0.999999	B;B	0.26258	0.008;0.145	B;B	0.23852	0.007;0.049	T	0.47018	-0.9149	10	0.06891	T	0.86	.	1.4656	0.02405	0.2895:0.4032:0.1411:0.1662	.	767;767	O60237;F8W8M3	MYPT2_HUMAN;.	K	767	ENSP00000384496:T767K;ENSP00000337897:T767K	ENSP00000337897:T767K	T	+	2	0	PPP1R12B	200731198	0.000000	0.05858	0.000000	0.03702	0.790000	0.44656	-0.122000	0.10627	0.307000	0.22880	0.650000	0.86243	ACA		0.443	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		A	202464575	C	A	202464575	3	1	59	1	0	0	0	0	1	0	0	0	12389	478	17	2	2452	2	PPP1R12B	1	202464575	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	5073729	202464575	46786046	5	7816										
ARID4B	51742	broad.mit.edu	37	chr1	235336038	235336038	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ttcttgaagtttttcttgaaGaattgtgatgcgttcggcac	10	6	2	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr1:235336038G>T	ENST00000264183.3	-	23	4203	c.3706C>A	c.(3706-3708)Ctt>Att	p.L1236I	ARID4B-IT1_ENST00000357671.6_RNA|ARID4B_ENST00000349213.3_Missense_Mutation_p.L1150I|ARID4B_ENST00000366603.2_Missense_Mutation_p.L1236I	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1236					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L1236I(1)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TTTTCTTGAAGAATTGTGATG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	72	73					1																	235336038		2202	4300	6502	233402661	SO:0001583	missense	51742			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"-"	15550	protein-coding gene	gene with protein product		609696	"retinoblastoma binding protein 1-like 1", "AT rich interactive domain 4B (RBP1- like)"	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.3706C>A	1.37:g.235336038G>T	ENSP00000264183:p.Leu1236Ile		233402661	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.715070	0.89112	.	.	ENSG00000054267	ENST00000349213;ENST00000366603;ENST00000264183	T;T;T	0.59083	0.29;0.33;0.33	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.72471	0.3464	L	0.48362	1.52	0.54753	D	0.999988	D;D	0.69078	0.99;0.997	D;D	0.78314	0.979;0.991	T	0.73254	-0.4041	10	0.87932	D	0	-11.4728	20.047	0.97613	0.0:0.0:1.0:0.0	.	1150;1236	Q4LE39-2;Q4LE39	.;ARI4B_HUMAN	I	1150;1236;1236	ENSP00000264184:L1150I;ENSP00000355562:L1236I;ENSP00000264183:L1236I	ENSP00000264183:L1236I	L	-	1	0	ARID4B	233402661	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.265000	0.95647	2.821000	0.97095	0.555000	0.69702	CTT		0.313	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		T	235336038	G	T	235336038	3	4	59	1	0	0	0	0	1	0	0	0	920	942	33	2	240	2	ARID4B	1	235336038	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	32871463	235336038	13914583	6	7817										
PXDN	7837	broad.mit.edu	37	chr2	1652070	1652070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ggatcccgtggtcccggcccCgctggatgttgatggccgcc	15	15	0	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:1652070C>T	ENST00000252804.4	-	17	3532	c.3482G>A	c.(3481-3483)cGg>cAg	p.R1161Q		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1161					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R1161Q(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GTCCCGGCCCCGCTGGATGTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	84	81					2																	1652070		2036	4213	6249	1631077	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3482G>A	2.37:g.1652070C>T	ENSP00000252804:p.Arg1161Gln		1631077	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	33	5.281594	0.95489	.	.	ENSG00000130508	ENST00000252804	D	0.83419	-1.72	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.93609	0.7959	M	0.93062	3.375	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94595	0.7791	10	0.87932	D	0	-37.3055	19.6424	0.95763	0.0:1.0:0.0:0.0	.	1161	Q92626	PXDN_HUMAN	Q	1161	ENSP00000252804:R1161Q	ENSP00000252804:R1161Q	R	-	2	0	PXDN	1631077	1.000000	0.71417	0.955000	0.39395	0.974000	0.67602	7.734000	0.84928	2.645000	0.89757	0.650000	0.86243	CGG		0.597	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1652070	C	T	1652070	3	4	59	1	0	0	0	0	1	0	0	0	12884	652	23	1	985	1	PXDN	2	1652070	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		1652070	241547303	7	7818										
ADCY3	109	broad.mit.edu	37	chr2	25050913	25050913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctgcaccagcatgatggtggCgatgagggacagcacggcca	15	11	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:25050913C>T	ENST00000260600.5	-	13	3141	c.2290G>A	c.(2290-2292)Gcc>Acc	p.A764T	ADCY3_ENST00000450524.1_5'UTR|ADCY3_ENST00000405392.1_Intron|RP11-443B20.1_ENST00000606114.1_RNA	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	764					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.A764T(1)		NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ATGATGGTGGCGATGAGGGAC	0.607											OREG0014498	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											108	83	91					2																	25050913		2203	4300	6503	24904417	SO:0001583	missense	109			AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.2290G>A	2.37:g.25050913C>T	ENSP00000260600:p.Ala764Thr	776	24904417	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.549702	0.86127	.	.	ENSG00000138031	ENST00000260600;ENST00000415879;ENST00000455323;ENST00000450524	T;T;T	0.72942	-0.7;-0.7;-0.7	5.38	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.82006	0.4943	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.74023	0.775;0.982	T	0.81773	-0.0779	10	0.36615	T	0.2	.	15.2141	0.73250	0.1419:0.8581:0.0:0.0	.	764;764	B7ZLX9;O60266	.;ADCY3_HUMAN	T	764;739;103;107	ENSP00000260600:A764T;ENSP00000402008:A103T;ENSP00000410972:A107T	ENSP00000260600:A764T	A	-	1	0	ADCY3	24904417	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.573000	0.82421	1.480000	0.48289	-0.181000	0.13052	GCC		0.607	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			T	25050913	C	T	25050913	3	4	59	1	0	0	0	0	1	0	0	0	295	768	27	1	1180	1	ADCY3	2	25050913	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	23398843	25050913	218148460	8	7819										
SRD5A2	6716	broad.mit.edu	37	chr2	31805728	31805728	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cagaagaggcccagaagtacCgtcccaggtggcccgaagag	14	12	0	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:31805728C>T	ENST00000405650.1	-	0	408							P31213	S5A2_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2)						androgen biosynthetic process (GO:0006702)|androgen metabolic process (GO:0008209)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|male gonad development (GO:0008584)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|sterol 5-alpha reductase activity (GO:0009917)					Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)|Finasteride(DB01216)|Spironolactone(DB00421)	CCAGAAGTACCGTCCCAGGTG	0.687																																																0			2											20	24	23					2																	31805728		1937	4141	6078	31659232			6716			M74047	CCDS74503.1	2p23.1	2013-01-31			ENSG00000049319	ENSG00000277893	1.3.99.5		11285	protein-coding gene	gene with protein product		607306				1522235	Standard	NM_000348		Approved		uc002rnw.1	P31213	OTTHUMG00000152057		2.37:g.31805728C>T			31659232	B2RE87|Q2M1R4|Q9BYE6	Silent	SNP	ENST00000405650.1	37																																																																																					0.687	SRD5A2-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000325124.1	NM_000348		T	31805728	C	T	31805728	1	4	59	0	1	0	0	0	0	0	0	0	15178	652	23	1		1	SRD5A2	2	31805728	RNA	SNP	C	TCGA-AG-4008-01A-01W-1073-09	6754815	31805728	211393645	9	7820										
PNPT1	87178	broad.mit.edu	37	chr2	55883321	55883321	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gtgaaaggaaaatctcggggAataacaggatacaaagcttt	11	5	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:55883321A>C	ENST00000447944.2	-	17	1472	c.1386T>G	c.(1384-1386)atT>atG	p.I462M		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	462					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)	p.I462M(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AATCTCGGGGAATAACAGGAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	85	87					2																	55883321		2203	4297	6500	55736825	SO:0001583	missense	87178			BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1386T>G	2.37:g.55883321A>C	ENSP00000400646:p.Ile462Met		55736825	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	A	8.775	0.926829	0.18056	.	.	ENSG00000138035	ENST00000447944	T	0.67171	-0.25	4.82	3.66	0.41972	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	L	0.49571	1.57	0.44660	D	0.997649	P	0.45827	0.867	P	0.60609	0.877	T	0.65142	-0.6240	10	0.30854	T	0.27	-10.9452	4.5499	0.12107	0.7015:0.0:0.1563:0.1422	.	462	Q8TCS8	PNPT1_HUMAN	M	462	ENSP00000400646:I462M	ENSP00000386075:I462M	I	-	3	3	PNPT1	55736825	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.136000	0.31467	0.802000	0.34089	0.460000	0.39030	ATT		0.323	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		C	55883321	A	C	55883321	3	2	59	1	0	0	0	0	1	0	0	0	12204	242	9	4	1013	4	PNPT1	2	55883321	Missense_Mutation	SNP	A	TCGA-AG-4008-01A-01W-1073-09	24077593	55883321	187316052	10	7821										
EHBP1	23301	broad.mit.edu	37	chr2	63223863	63223863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gcaaattgacacccgtgccgCgctggtggagaagcgccttc	13	13	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:63223863C>T	ENST00000263991.5	+	21	3760	c.3278C>T	c.(3277-3279)gCg>gTg	p.A1093V	EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000354487.3_Missense_Mutation_p.A1058V|EHBP1_ENST00000431489.1_Missense_Mutation_p.A1022V|EHBP1_ENST00000405289.1_Missense_Mutation_p.A1058V|EHBP1_ENST00000405015.3_Missense_Mutation_p.A1022V	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	1093						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.A1093V(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ACCCGTGCCGCGCTGGTGGAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											98	92	94					2																	63223863		2203	4300	6503	63077367	SO:0001583	missense	23301			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.3278C>T	2.37:g.63223863C>T	ENSP00000263991:p.Ala1093Val		63077367	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676569	0.88445	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289;ENST00000545092	T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4	5.41	5.41	0.78517	Domain of unknown function DUF3585 (1);	0.000000	0.85682	D	0.000000	T	0.45657	0.1353	N	0.21373	0.66	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.87578	0.854;0.946;0.998	T	0.19910	-1.0291	10	0.12103	T	0.63	.	19.2084	0.93744	0.0:1.0:0.0:0.0	.	1058;1022;1093	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	V	1022;1022;1093;1058;1058;64	ENSP00000384143:A1022V;ENSP00000403783:A1022V;ENSP00000263991:A1093V;ENSP00000346482:A1058V;ENSP00000385524:A1058V	ENSP00000263991:A1093V	A	+	2	0	EHBP1	63077367	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.556000	0.86216	0.650000	0.86243	GCG		0.458	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		T	63223863	C	T	63223863	3	4	59	1	0	0	0	0	1	0	0	0	4986	768	27	1	3356	1	EHBP1	2	63223863	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	7340542	63223863	179975510	11	7822										
WDR92	116143	broad.mit.edu	37	chr2	68365960	68365960	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	attgtcatagccagcacaaaCaacacgttcttcttgattat	5	10	3	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:68365960C>A	ENST00000295121.6	-	5	663	c.547G>T	c.(547-549)Gtt>Ttt	p.V183F	RP11-474G23.1_ENST00000406334.3_3'UTR|WDR92_ENST00000406245.2_Missense_Mutation_p.V82F|WDR92_ENST00000492039.2_5'UTR|WDR92_ENST00000409164.1_Missense_Mutation_p.V183F	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	183					apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)	p.V183F(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						CCAGCACAAACAACACGTTCT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											238	230	233					2																	68365960		2203	4300	6503	68219464	SO:0001583	missense	116143			AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"WD repeat domain containing"	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.547G>T	2.37:g.68365960C>A	ENSP00000295121:p.Val183Phe		68219464	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	37	CCDS1884.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082073	0.94050	.	.	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	T;T;T	0.65916	1.62;1.62;-0.18	5.82	5.82	0.92795	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.52532	D	0.000074	T	0.81828	0.4905	M	0.85099	2.735	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	D	0.83835	0.0254	10	0.87932	D	0	.	20.0991	0.97865	0.0:1.0:0.0:0.0	.	183	Q96MX6	WDR92_HUMAN	F	183;82;183	ENSP00000295121:V183F;ENSP00000384518:V82F;ENSP00000386746:V183F	ENSP00000295121:V183F	V	-	1	0	WDR92	68219464	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.605000	0.82844	2.752000	0.94435	0.655000	0.94253	GTT		0.353	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458		A	68365960	C	A	68365960	3	1	59	1	0	0	0	0	1	0	0	0	17379	478	17	2	542	2	WDR92	2	68365960	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	5142097	68365960	174833413	12	7823										
BMP10	27302	broad.mit.edu	37	chr2	69093668	69093668	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gaagaggagggggtattttcGgagcccattaaaactgaccg	14	7	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:69093668G>A	ENST00000295379.1	-	2	528	c.370C>T	c.(370-372)Cga>Tga	p.R124*		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	124					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)	p.R124*(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						GGGTATTTTCGGAGCCCATTA	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											34	36	36					2																	69093668		2203	4300	6503	68947172	SO:0001587	stop_gained	27302			AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"Bone morphogenetic proteins", "Endogenous ligands"	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.370C>T	2.37:g.69093668G>A	ENSP00000295379:p.Arg124*		68947172	Q53R17|Q6NTE0	Nonsense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.003712	0.93287	.	.	ENSG00000163217	ENST00000295379	.	.	.	5.94	5.05	0.67936	.	0.050449	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3402	0.60540	0.0:0.0:0.7129:0.2871	.	.	.	.	X	124	.	ENSP00000295379:R124X	R	-	1	2	BMP10	68947172	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	1.579000	0.36536	1.484000	0.48361	0.557000	0.71058	CGA		0.433	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482		A	69093668	G	A	69093668	4	1	59	1	0	0	0	0	0	1	0	0	1458	1124	39	1	908	1	BMP10	2	69093668	Nonsense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	727708	69093668	174105705	13	7824										
GPR45	11250	broad.mit.edu	37	chr2	105858990	105858990	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctcaacacggtccgcaagaaCgccgtgcgcgtgcacaacca	10	16	1	1	rs200019068		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:105858990C>T	ENST00000258456.1	+	1	791	c.675C>T	c.(673-675)aaC>aaT	p.N225N		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N225N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						TCCGCAAGAACGCCGTGCGCG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	2											67	67	67					2																	105858990		2203	4300	6503	105225422	SO:0001819	synonymous_variant	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.675C>T	2.37:g.105858990C>T			105225422	Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	37	CCDS2066.1																																																																																				0.667	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		T	105858990	C	T	105858990	2	4	59	1	0	0	0	0	0	0	0	1	6716	535	19	1		1	GPR45	2	105858990	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	36765322	105858990	137340383	14	7825										
YSK4	80122	broad.mit.edu	37	chr2	135738422	135738422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	catgcgcacaaagtctgctgCattttctgagaagtggtctg	11	9	3	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:135738422C>T	ENST00000375845.3	-	9	3919	c.3889G>A	c.(3889-3891)Gca>Aca	p.A1297T	MAP3K19_ENST00000358371.4_Missense_Mutation_p.A1184T|MAP3K19_ENST00000392918.3_Missense_Mutation_p.A431T|MAP3K19_ENST00000392915.1_3'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.A479T|MAP3K19_ENST00000392917.3_Missense_Mutation_p.A429T|MAP3K19_ENST00000315513.3_Missense_Mutation_p.A158T	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1297	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A1297T(1)|p.A649T(1)									AAGTCTGCTGCATTTTCTGAG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	2											48	42	44					2																	135738422		2203	4300	6503	135454892	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3889G>A	2.37:g.135738422C>T	ENSP00000365005:p.Ala1297Thr		135454892	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	22.9	4.353590	0.82243	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000437365;ENST00000315513	T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.76	5.76	0.90799	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44285	D	0.000465	T	0.75561	0.3866	L	0.45051	1.395	0.51767	D	0.999932	D;D;P;P;D	0.89917	0.997;1.0;0.947;0.947;1.0	P;D;P;P;D	0.87578	0.902;0.994;0.58;0.701;0.998	T	0.75462	-0.3309	10	0.52906	T	0.07	.	13.8592	0.63550	0.1525:0.8475:0.0:0.0	.	429;1184;431;479;1297	B7ZMH9;Q56UN5-3;Q56UN5-4;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	T	1297;1184;479;431;429;687;158	ENSP00000365005:A1297T;ENSP00000351140:A1184T;ENSP00000365004:A479T;ENSP00000376650:A431T;ENSP00000376649:A429T;ENSP00000392827:A687T;ENSP00000321160:A158T	ENSP00000321160:A158T	A	-	1	0	YSK4	135454892	1.000000	0.71417	0.193000	0.23327	0.978000	0.69477	5.739000	0.68622	2.706000	0.92434	0.591000	0.81541	GCA		0.517	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		T	135738422	C	T	135738422	3	4	59	1	0	0	0	0	1	0	0	0	17535	710	25	3	105	3	YSK4	2	135738422	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	29879432	135738422	107460951	15	7826										
TTN	7273	broad.mit.edu	37	chr2	179427593	179427593	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tctgacgttaacaaaagctgTtttggagccactattatttt	7	7	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:179427593T>A	ENST00000591111.1	-	276	78567	c.78343A>T	c.(78343-78345)Aca>Tca	p.T26115S	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T18691S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T18816S|TTN_ENST00000589042.1_Missense_Mutation_p.T27756S|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T18883S|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T25188S|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26115	Ig-like 126.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T18816S(1)|p.T18883S(1)|p.T18691S(1)|p.T25186S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACAAAAGCTGTTTTGGAGCCA	0.413																																																4	Substitution - Missense(4)	large_intestine(4)	2											57	54	55					2																	179427593		1883	4125	6008	179135839	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78343A>T	2.37:g.179427593T>A	ENSP00000465570:p.Thr26115Ser		179135839	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	10.76	1.441954	0.25900	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	6.04	4.86	0.63082	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.40645	0.1125	N	0.02775	-0.495	0.37701	D	0.924222	B;B;B;B	0.17465	0.022;0.022;0.022;0.012	B;B;B;B	0.15052	0.012;0.012;0.012;0.008	T	0.38735	-0.9647	9	0.87932	D	0	.	7.3717	0.26804	0.1559:0.0712:0.0:0.7729	.	18691;18816;18883;26115	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	25188;18691;18883;18816;18689	ENSP00000343764:T25188S;ENSP00000434586:T18691S;ENSP00000340554:T18883S;ENSP00000352154:T18816S	ENSP00000340554:T18883S	T	-	1	0	TTN	179135839	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.520000	0.60524	1.066000	0.40716	0.459000	0.35465	ACA		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179427593	T	A	179427593	3	1	59	1	0	0	0	0	1	0	0	0	16775	1725	60	5	24861	5	TTN	2	179427593	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	43689171	179427593	63771780	16	7827										
TTN	7273	broad.mit.edu	37	chr2	179434963	179434963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctggtactacaaatggattcTtggcaactactggctcagat	9	9	2	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:179434963T>C	ENST00000591111.1	-	276	71197	c.70973A>G	c.(70972-70974)aAg>aGg	p.K23658R	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K16234R|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K16359R|TTN_ENST00000589042.1_Missense_Mutation_p.K25299R|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K16426R|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K22731R|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23658	Fibronectin type-III 71. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K16234R(1)|p.K16359R(1)|p.K22729R(1)|p.K16426R(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAATGGATTCTTGGCAACTAC	0.413																																																4	Substitution - Missense(4)	large_intestine(4)	2											101	94	97					2																	179434963		1941	4138	6079	179143209	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.70973A>G	2.37:g.179434963T>C	ENSP00000465570:p.Lys23658Arg		179143209	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	11.93	1.784611	0.31593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.87	5.87	0.94306	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32645	0.0836	N	0.16478	0.41	0.43953	D	0.996624	B;B;B;B	0.09022	0.002;0.002;0.002;0.002	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.14448	-1.0472	9	0.87932	D	0	.	10.5981	0.45349	0.0:0.0714:0.0:0.9286	.	16234;16359;16426;23658	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	22731;16234;16426;16359;16232	ENSP00000343764:K22731R;ENSP00000434586:K16234R;ENSP00000340554:K16426R;ENSP00000352154:K16359R	ENSP00000340554:K16426R	K	-	2	0	TTN	179143209	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.529000	0.35996	2.236000	0.73375	0.528000	0.53228	AAG		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179434963	T	C	179434963	3	2	59	1	0	0	0	0	1	0	0	0	16775	1609	56	4	32231	4	TTN	2	179434963	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	7370	179434963	63764410	17	7828										
TRAF3IP1	26146	broad.mit.edu	37	chr2	239237875	239237875	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	agagacagggaccgagagcgCgaccgggacaaagggaagga	18	8	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr2:239237875C>T	ENST00000373327.4	+	5	1029	c.807C>T	c.(805-807)cgC>cgT	p.R269R	TRAF3IP1_ENST00000391993.3_Silent_p.R269R|TRAF3IP1_ENST00000391994.2_Silent_p.R269R	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	269	Abolishes microtubules-binding when missing.|Arg-rich.|DISC1-interaction domain.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.R269R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		accgagagcgcgaccgggaca	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2											89	100	96					2																	239237875		2202	4300	6502	238902614	SO:0001819	synonymous_variant	26146			AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"Intraflagellar transport homologs"	17861	protein-coding gene	gene with protein product	"microtubule interacting protein that associates with TRAF3"	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.807C>T	2.37:g.239237875C>T			238902614	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Silent	SNP	ENST00000373327.4	37	CCDS33415.1																																																																																				0.582	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650		T	239237875	C	T	239237875	2	4	59	1	0	0	0	0	0	0	0	1	16480	755	27	1		1	TRAF3IP1	2	239237875	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	59802912	239237875	3961498	18	7829										
SEMA3G	56920	broad.mit.edu	37	chr3	52469644	52469644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tggcctccacctcccggggcGtccgattgtgctcggcatgc	13	16	0	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr3:52469644G>A	ENST00000231721.2	-	16	2323	c.2324C>T	c.(2323-2325)aCg>aTg	p.T775M		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	775					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.T775M(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		CTCCCGGGGCGTCCGATTGTG	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	3											58	66	64					3																	52469644		2201	4299	6500	52444684	SO:0001583	missense	56920				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.2324C>T	3.37:g.52469644G>A	ENSP00000231721:p.Thr775Met		52444684	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.445884	0.43429	.	.	ENSG00000010319	ENST00000231721	T	0.77098	-1.07	4.98	4.04	0.47022	.	0.970881	0.08494	N	0.937494	T	0.78761	0.4334	L	0.56769	1.78	0.25366	N	0.988747	D	0.63880	0.993	P	0.52856	0.711	T	0.66582	-0.5887	10	0.36615	T	0.2	.	4.6992	0.12818	0.1405:0.2227:0.6368:0.0	.	775	Q9NS98	SEM3G_HUMAN	M	775	ENSP00000231721:T775M	ENSP00000231721:T775M	T	-	2	0	SEMA3G	52444684	0.989000	0.36119	0.913000	0.36048	0.341000	0.28922	5.479000	0.66813	2.315000	0.78130	0.650000	0.86243	ACG		0.697	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52469644	G	A	52469644	3	1	59	1	0	0	0	0	1	0	0	0	14067	1145	40	1	28	1	SEMA3G	3	52469644	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09		52469644	145552786	19	7830										
BOC	91653	broad.mit.edu	37	chr3	112993524	112993524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tctactatgtggtgaaacacCgcaaggtatggccctggtgt	12	9	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr3:112993524C>T	ENST00000495514.1	+	9	2241	c.1537C>T	c.(1537-1539)Cgc>Tgc	p.R513C	BOC_ENST00000273395.4_Missense_Mutation_p.R513C|BOC_ENST00000355385.3_Missense_Mutation_p.R513C|BOC_ENST00000497495.1_3'UTR			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	513	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.R513C(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GGTGAAACACCGCAAGGTATG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											37	39	38					3																	112993524		2203	4300	6503	114476214	SO:0001583	missense	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1537C>T	3.37:g.112993524C>T	ENSP00000418663:p.Arg513Cys		114476214	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702645	0.88924	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.59364	0.27;0.27;0.27	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055251	0.64402	D	0.000001	T	0.76506	0.3997	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76992	-0.2753	10	0.72032	D	0.01	.	20.0693	0.97712	0.0:1.0:0.0:0.0	.	513;513	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	C	513	ENSP00000418663:R513C;ENSP00000273395:R513C;ENSP00000347546:R513C	ENSP00000273395:R513C	R	+	1	0	BOC	114476214	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	4.655000	0.61476	2.758000	0.94735	0.563000	0.77884	CGC		0.617	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112993524	C	T	112993524	3	4	59	1	0	0	0	0	1	0	0	0	1482	652	23	1	1563	1	BOC	3	112993524	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	60523880	112993524	85028906	20	7831										
ILDR1	286676	broad.mit.edu	37	chr3	121725902	121725902	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	aagcgccatgtcaccaccacGtcctggagctgggcagaggt	13	13	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr3:121725902G>A	ENST00000344209.5	-	2	291	c.165C>T	c.(163-165)gaC>gaT	p.D55D	ILDR1_ENST00000462014.1_Silent_p.D67D|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Silent_p.D55D|ILDR1_ENST00000273691.3_Silent_p.D55D	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	55	Ig-like V-type.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)	p.D55D(2)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TCACCACCACGTCCTGGAGCT	0.542																																																2	Substitution - coding silent(2)	large_intestine(2)	3											164	126	139					3																	121725902		2203	4300	6503	123208592	SO:0001819	synonymous_variant	286676			BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.165C>T	3.37:g.121725902G>A			123208592	Q6ZP61|Q7Z578	Silent	SNP	ENST00000344209.5	37	CCDS56271.1																																																																																				0.542	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121725902	G	A	121725902	2	1	59	1	0	0	0	0	0	0	0	1	7730	1136	40	1		1	ILDR1	3	121725902	Silent	SNP	G	TCGA-AG-4008-01A-01W-1073-09	8732378	121725902	76296528	21	7832										
MECOM	2122	broad.mit.edu	37	chr3	168808021	168808021	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tctttaaaatgactgccattCattctttcaaaagcattaaa	3	8	4	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr3:168808021C>T	ENST00000464456.1	-	13	3777	c.2577G>A	c.(2575-2577)atG>atA	p.M859I	MECOM_ENST00000264674.3_Missense_Mutation_p.M933I|MECOM_ENST00000472280.1_Missense_Mutation_p.M869I|MECOM_ENST00000433243.2_Missense_Mutation_p.M869I|MECOM_ENST00000468789.1_Missense_Mutation_p.M868I|MECOM_ENST00000460814.1_Missense_Mutation_p.M859I|MECOM_ENST00000392736.3_Missense_Mutation_p.M868I|MECOM_ENST00000494292.1_Missense_Mutation_p.M1047I	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M868I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GACTGCCATTCATTCTTTCAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	69	69					3																	168808021		2203	4299	6502	170290715	SO:0001583	missense	2122			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2577G>A	3.37:g.168808021C>T	ENSP00000419770:p.Met859Ile		170290715	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.269993	0.23221	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.05139	3.54;3.54;3.49;3.64;3.49;3.54;3.49;3.64	5.2	5.2	0.72013	.	0.420710	0.22758	N	0.055985	T	0.06096	0.0158	L	0.36672	1.1	0.41047	D	0.985272	B;B;B;B;B	0.15473	0.013;0.0;0.002;0.0;0.0	B;B;B;B;B	0.08055	0.003;0.001;0.002;0.002;0.0	T	0.36359	-0.9751	10	0.16896	T	0.51	-12.2337	12.4667	0.55762	0.0:0.9229:0.0:0.0771	.	1056;860;1047;933;868	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	I	933;868;859;869;1047;868;859;869	ENSP00000264674:M933I;ENSP00000376493:M868I;ENSP00000419770:M859I;ENSP00000420048:M869I;ENSP00000417899:M1047I;ENSP00000419995:M868I;ENSP00000420466:M859I;ENSP00000394302:M869I	ENSP00000264674:M933I	M	-	3	0	MECOM	170290715	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.716000	0.37981	2.571000	0.86741	0.650000	0.86243	ATG		0.318	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		T	168808021	C	T	168808021	3	4	59	1	0	0	0	0	1	0	0	0	9452	826	29	3	563	3	MECOM	3	168808021	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	47082119	168808021	29214409	22	7833										
JAKMIP1	152789	broad.mit.edu	37	chr4	6083355	6083355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ccatttccacgttttcccgcGtgaggttcttgattttctcc	7	13	2	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr4:6083355G>A	ENST00000282924.5	-	6	1567	c.1082C>T	c.(1081-1083)aCg>aTg	p.T361M	JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.T361M|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.T361M|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.T196M|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.T196M	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	361	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)	p.T361M(2)		NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTTTTCCCGCGTGAGGTTCTT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	4											183	158	166					4																	6083355		2203	4300	6503	6134256	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1082C>T	4.37:g.6083355G>A	ENSP00000282924:p.Thr361Met		6134256	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.161084	0.57368	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.36699	1.67;1.27;1.67;1.67;1.24	4.42	3.58	0.41010	.	0.196104	0.35124	N	0.003440	T	0.39279	0.1072	L	0.49126	1.545	0.30703	N	0.75007	B;D;B;B;D	0.64830	0.029;0.981;0.011;0.011;0.994	B;P;B;B;P	0.48454	0.016;0.578;0.01;0.01;0.578	T	0.49082	-0.8976	10	0.87932	D	0	.	11.8578	0.52449	0.0858:0.0:0.9142:0.0	.	196;361;196;361;361	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	M	361;196;361;361;253;361;361;196	ENSP00000386711:T361M;ENSP00000387042:T196M;ENSP00000282924:T361M;ENSP00000386925:T361M;ENSP00000386745:T196M	ENSP00000282924:T361M	T	-	2	0	JAKMIP1	6134256	0.999000	0.42202	0.845000	0.33349	0.722000	0.41435	4.475000	0.60210	0.995000	0.38917	0.561000	0.74099	ACG		0.532	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		A	6083355	G	A	6083355	3	1	59	1	0	0	0	0	1	0	0	0	7961	1145	40	1	1552	1	JAKMIP1	4	6083355	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09		6083355	185070921	23	7834										
MEPE	56955	broad.mit.edu	37	chr4	88767462	88767462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cagacaaaataattctacacGgaataagggtatgccacaag	8	8	1	1	rs138152179		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr4:88767462G>A	ENST00000424957.3	+	4	1515	c.1442G>A	c.(1441-1443)cGg>cAg	p.R481Q	MEPE_ENST00000497649.2_Missense_Mutation_p.R457Q|MEPE_ENST00000395102.4_Missense_Mutation_p.R512Q|MEPE_ENST00000361056.3_Missense_Mutation_p.R481Q|MEPE_ENST00000540395.1_Missense_Mutation_p.R368Q|MEPE_ENST00000560249.1_Missense_Mutation_p.R368Q|MEPE_ENST00000508016.1_3'UTR	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	481					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.R481Q(1)|p.R481L(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		AATTCTACACGGAATAAGGGT	0.423																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	84	84	84		1442,1103,1103,1103,1442	-0.1	0	4	dbSNP_134	84	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	43,43,43,43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign,benign,benign	481/526,368/413,368/413,368/413,481/526	88767462	2,13004	2203	4300	6503	88986486	SO:0001583	missense	56955			AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.1442G>A	4.37:g.88767462G>A	ENSP00000416984:p.Arg481Gln		88986486	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	G	9.311	1.055691	0.19907	4.54E-4	0.0	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.48522	0.82;0.82;0.81;0.83;0.82	4.68	-0.129	0.13502	.	2.142430	0.02126	N	0.055974	T	0.34164	0.0888	L	0.28400	0.85	0.09310	N	1	B	0.20052	0.041	B	0.13407	0.009	T	0.08722	-1.0708	10	0.25751	T	0.34	5.0519	4.6795	0.12727	0.3356:0.1521:0.5123:0.0	.	481	Q9NQ76	MEPE_HUMAN	Q	481;512;457;368;481	ENSP00000416984:R481Q;ENSP00000378534:R512Q;ENSP00000422747:R457Q;ENSP00000443491:R368Q;ENSP00000354341:R481Q	ENSP00000354341:R481Q	R	+	2	0	MEPE	88986486	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.531000	0.23052	0.021000	0.15133	0.563000	0.77884	CGG		0.423	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			A	88767462	G	A	88767462	3	1	59	1	0	0	0	0	1	0	0	0	9508	1116	39	1	1452	1	MEPE	4	88767462	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	82684107	88767462	102386814	24	7835										
NDST3	9348	broad.mit.edu	37	chr4	119148099	119148099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	taaagaaaaaacttgtgatcGcttaccaaaattcttggtaa	6	6	1	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr4:119148099G>A	ENST00000296499.5	+	8	2184	c.1781G>A	c.(1780-1782)cGc>cAc	p.R594H	NDST3_ENST00000433996.2_Missense_Mutation_p.R513H	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	594	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.R594H(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						ACTTGTGATCGCTTACCAAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											78	84	82					4																	119148099		2203	4300	6503	119367547	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1781G>A	4.37:g.119148099G>A	ENSP00000296499:p.Arg594His		119367547	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220099	0.58560	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.58210	0.35;0.35	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.46308	0.1386	L	0.55743	1.74	0.40713	D	0.982599	P;B	0.37824	0.609;0.001	B;B	0.25506	0.061;0.001	T	0.50750	-0.8791	10	0.35671	T	0.21	.	19.0943	0.93244	0.0:0.0:1.0:0.0	.	513;594	B4DI67;O95803	.;NDST3_HUMAN	H	594;513	ENSP00000296499:R594H;ENSP00000396625:R513H	ENSP00000296499:R594H	R	+	2	0	NDST3	119367547	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.810000	0.86072	2.571000	0.86741	0.491000	0.48974	CGC		0.348	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		A	119148099	G	A	119148099	3	1	59	1	0	0	0	0	1	0	0	0	10288	1087	38	1	1807	1	NDST3	4	119148099	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	30380637	119148099	72006177	25	7836										
RASGRF2	5924	broad.mit.edu	37	chr5	80366384	80366384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	agaagacgaagatccagacaTcaagaagattaaaaaggtag	10	5	1	6			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr5:80366384T>C	ENST00000265080.4	+	4	684	c.617T>C	c.(616-618)aTc>aCc	p.I206T	RASGRF2_ENST00000502677.1_3'UTR	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	206	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I206T(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		GATCCAGACATCAAGAAGATT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											130	133	132					5																	80366384		2203	4300	6503	80402140	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.617T>C	5.37:g.80366384T>C	ENSP00000265080:p.Ile206Thr		80402140	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.612796	0.66672	.	.	ENSG00000113319	ENST00000265080	T	0.76968	-1.06	5.69	5.69	0.88448	.	.	.	.	.	T	0.78362	0.4271	L	0.46157	1.445	0.80722	D	1	P;P	0.48998	0.918;0.722	P;B	0.47827	0.558;0.164	T	0.81217	-0.1033	9	0.87932	D	0	.	16.2484	0.82467	0.0:0.0:0.0:1.0	.	206;206	D6RAS9;O14827	.;RGRF2_HUMAN	T	206	ENSP00000265080:I206T	ENSP00000265080:I206T	I	+	2	0	RASGRF2	80402140	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.291000	0.77112	0.533000	0.62120	ATC		0.448	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		C	80366384	T	C	80366384	3	2	59	1	0	0	0	0	1	0	0	0	13110	1435	50	4	631	4	RASGRF2	5	80366384	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09		80366384	100548876	26	7837										
PAM	5066	broad.mit.edu	37	chr5	102326074	102326074	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctaagaataacctggtgattTtccacagaggtgaccatgtc	9	9	0	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr5:102326074T>A	ENST00000438793.3	+	15	2052	c.1582T>A	c.(1582-1584)Ttc>Atc	p.F528I	PAM_ENST00000274392.9_Missense_Mutation_p.F431I|PAM_ENST00000346918.2_Missense_Mutation_p.F528I|PAM_ENST00000348126.2_Missense_Mutation_p.F421I|PAM_ENST00000304400.7_Missense_Mutation_p.F528I|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000455264.2_Missense_Mutation_p.F528I	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	528	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)	p.F528I(2)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CCTGGTGATTTTCCACAGAGG	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	5											57	56	56					5																	102326074		2203	4300	6503	102353973	SO:0001583	missense	5066			AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.1582T>A	5.37:g.102326074T>A	ENSP00000396493:p.Phe528Ile		102353973	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.155652|5.155652	0.94686|0.94686	.|.	.|.	ENSG00000145730|ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000274392;ENST00000455264|ENST00000379799	D;D;D;D;D;D|.	0.89939|.	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.78735|0.78735	0.4330|0.4330	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	0.999;0.999;0.998;0.996;1.0;0.999;0.995|.	D;D;D;D;D;D;D|.	0.75484|.	0.976;0.984;0.948;0.948;0.986;0.976;0.96|.	T|T	0.81339|0.81339	-0.0977|-0.0977	10|6	0.87932|.	D|.	0|.	-14.5741|-14.5741	15.1757|15.1757	0.72910|0.72910	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	431;101;528;528;528;528;421|.	F8WE90;Q13749;P19021;P19021-4;P19021-3;P19021-5;P19021-2|.	.;.;AMD_HUMAN;.;.;.;.|.	I|Y	528;528;421;528;431;528|300	ENSP00000396493:F528I;ENSP00000282992:F528I;ENSP00000314638:F421I;ENSP00000306100:F528I;ENSP00000274392:F431I;ENSP00000403461:F528I|.	ENSP00000274392:F431I|.	F|F	+|+	1|2	0|0	PAM|PAM	102353973|102353973	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.669000|6.669000	0.74462|0.74462	2.075000|2.075000	0.62263|0.62263	0.454000|0.454000	0.30748|0.30748	TTC|TTT		0.388	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102326074	T	A	102326074	3	1	59	1	0	0	0	0	1	0	0	0	11443	1841	64	5	1640	5	PAM	5	102326074	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	21959690	102326074	78589186	27	7838										
REEP2	51308	broad.mit.edu	37	chr5	137780216	137780216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgcacccaacgctgtccaacAaggagaaggtttgcccccac	9	15	0	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr5:137780216A>G	ENST00000254901.5	+	4	417	c.295A>G	c.(295-297)Aag>Gag	p.K99E	REEP2_ENST00000506158.1_Missense_Mutation_p.K61E|REEP2_ENST00000378339.2_Missense_Mutation_p.K99E	NM_016606.2	NP_057690.2	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	99					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein transport into membrane raft (GO:0032596)|regulation of intracellular transport (GO:0032386)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.K99E(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GCTGTCCAACAAGGAGAAGGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											139	111	120					5																	137780216		2203	4300	6503	137808115	SO:0001583	missense	51308			AK056193	CCDS4205.1, CCDS64259.1	5q31	2014-03-12	2006-02-07	2006-02-07	ENSG00000132563	ENSG00000132563		"Receptor accessory proteins"	17975	protein-coding gene	gene with protein product		609347	"chromosome 5 open reading frame 19"	C5orf19		16271481, 15550249, 24388663	Standard	NM_016606		Approved	SGC32445, SPG72	uc003lda.4	Q9BRK0	OTTHUMG00000129205	ENST00000254901.5:c.295A>G	5.37:g.137780216A>G	ENSP00000254901:p.Lys99Glu		137808115	Q53EM8|Q9NYF2	Missense_Mutation	SNP	ENST00000254901.5	37	CCDS4205.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.988253	0.93106	.	.	ENSG00000132563	ENST00000378339;ENST00000254901;ENST00000506158	D;D;D	0.88124	-2.34;-2.34;-1.52	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.89248	0.6661	M	0.73598	2.24	0.58432	D	0.999999	P;P	0.38420	0.63;0.63	P;P	0.44732	0.459;0.459	D	0.90395	0.4398	10	0.72032	D	0.01	-5.2119	14.0341	0.64634	1.0:0.0:0.0:0.0	.	99;99	A8K3D2;Q9BRK0	.;REEP2_HUMAN	E	99;99;61	ENSP00000367590:K99E;ENSP00000254901:K99E;ENSP00000422530:K61E	ENSP00000254901:K99E	K	+	1	0	REEP2	137808115	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.999000	0.76283	2.159000	0.67721	0.533000	0.62120	AAG		0.602	REEP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251284.1	NM_016606		G	137780216	A	G	137780216	3	3	59	1	0	0	0	0	1	0	0	0	13242	131	5	4	309	4	REEP2	5	137780216	Missense_Mutation	SNP	A	TCGA-AG-4008-01A-01W-1073-09	35454142	137780216	43135044	28	7839										
HSPA9	3313	broad.mit.edu	37	chr5	137906735	137906735	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ttgtttgggttggtgacagcCtgtcgcttggccggcattcc	14	10	0	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr5:137906735C>T	ENST00000297185.3	-	4	449	c.324G>A	c.(322-324)caG>caA	p.Q108Q		NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	108					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.Q108Q(1)		breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGGTGACAGCCTGTCGCTTGG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											109	99	102					5																	137906735		2203	4300	6503	137934634	SO:0001819	synonymous_variant	3313			L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.324G>A	5.37:g.137906735C>T			137934634	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Silent	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	C	8.846	0.943363	0.18281	.	.	ENSG00000113013	ENST00000541333	.	.	.	5.34	2.52	0.30459	.	.	.	.	.	T	0.53690	0.1812	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41431	-0.9509	5	0.22706	T	0.39	-10.1034	10.3089	0.43697	0.0:0.7674:0.0:0.2326	.	.	.	.	K	78	.	ENSP00000438817:R78K	R	-	2	0	HSPA9	137934634	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	0.649000	0.24843	0.726000	0.32339	0.655000	0.94253	AGG		0.498	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		T	137906735	C	T	137906735	2	4	59	1	0	0	0	0	0	0	0	1	7438	680	24	3		3	HSPA9	5	137906735	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	126519	137906735	43008525	29	7840										
SLC4A9	83697	broad.mit.edu	37	chr5	139742515	139742515	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	agcaattccagtggtcagttCgtcgggccagcaaccttcat	10	12	2	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr5:139742515C>A	ENST00000230993.6	+	7	933	c.898C>A	c.(898-900)Cgt>Agt	p.R300S	SLC4A9_ENST00000507527.1_Missense_Mutation_p.R300S|SLC4A9_ENST00000506545.1_Missense_Mutation_p.R276S|SLC4A9_ENST00000432095.2_Missense_Mutation_p.R276S|SLC4A9_ENST00000506757.2_Missense_Mutation_p.R276S	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	300					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.R300C(2)|p.R274C(1)|p.R274S(1)|p.R300S(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGTCAGTTCGTCGGGCCAG	0.542											OREG0016461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				5	Substitution - Missense(5)	lung(3)|large_intestine(2)	5											171	172	171					5																	139742515		2042	4182	6224	139722699	SO:0001583	missense	83697			AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.898C>A	5.37:g.139742515C>A	ENSP00000230993:p.Arg300Ser	1651	139722699	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	37	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728337	0.69074	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	5.13	4.18	0.49190	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.165488	0.43579	D	0.000556	T	0.69851	0.3157	L	0.52364	1.645	0.39306	D	0.964995	D;D;P;P	0.63046	0.992;0.974;0.891;0.891	P;P;P;P	0.60236	0.855;0.871;0.616;0.616	T	0.72915	-0.4147	10	0.87932	D	0	.	6.1893	0.20516	0.1673:0.6794:0.0:0.1533	.	276;300;276;276	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	S	300;276;276;276;300	ENSP00000230993:R300S;ENSP00000424424:R276S;ENSP00000410056:R276S;ENSP00000422855:R276S;ENSP00000427661:R300S	ENSP00000230993:R300S	R	+	1	0	SLC4A9	139722699	0.705000	0.27846	1.000000	0.80357	0.836000	0.47400	1.319000	0.33655	2.667000	0.90743	0.462000	0.41574	CGT		0.542	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		A	139742515	C	A	139742515	3	1	59	1	0	0	0	0	1	0	0	0	14697	884	31	2	852	2	SLC4A9	5	139742515	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	1835780	139742515	41172745	30	7841										
TRIM10	10107	broad.mit.edu	37	chr6	30128219	30128219	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tttcctaccctatagggagcCgctgcatcctccaggaagcg	10	14	0	0	rs373243528		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr6:30128219C>T	ENST00000449742.2	-	1	492	c.417G>A	c.(415-417)gcG>gcA	p.A139A	TRIM15_ENST00000376694.4_5'Flank|TRIM10_ENST00000376704.3_Silent_p.A139A	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	139					erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.A139A(1)		ovary(1)	1						TATAGGGAGCCGCTGCATCCT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	0,4406		0,0,2203	51	46	48		417,417	-10.2	0	6		48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TRIM10	NM_006778.3,NM_052828.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	139/482,139/396	30128219	1,13005	2203	4300	6503	30236198	SO:0001819	synonymous_variant	10107			Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.417G>A	6.37:g.30128219C>T			30236198	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	37	CCDS34375.1																																																																																				0.572	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			T	30128219	C	T	30128219	2	4	59	1	0	0	0	0	0	0	0	1	16526	639	23	1		1	TRIM10	6	30128219	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09		30128219	140986848	31	7842										
RIMS1	22999	broad.mit.edu	37	chr6	72960676	72960676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	agaaaatactagaaccaaaaTggaatcaaacttttgtctat	5	6	2	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr6:72960676T>C	ENST00000521978.1	+	14	2425	c.2425T>C	c.(2425-2427)Tgg>Cgg	p.W809R	RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000517960.1_Missense_Mutation_p.W809R|RIMS1_ENST00000520567.1_Missense_Mutation_p.W809R|RIMS1_ENST00000518273.1_Missense_Mutation_p.W809R|RIMS1_ENST00000491071.2_Missense_Mutation_p.W809R|RIMS1_ENST00000517827.1_Missense_Mutation_p.W268R|RIMS1_ENST00000401910.3_Missense_Mutation_p.W283R|RIMS1_ENST00000522291.1_Missense_Mutation_p.W809R|RIMS1_ENST00000348717.5_Missense_Mutation_p.W809R|RIMS1_ENST00000425662.2_Missense_Mutation_p.W202R|RIMS1_ENST00000264839.7_Missense_Mutation_p.W809R|RIMS1_ENST00000523963.1_Missense_Mutation_p.W283R	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	809	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.W809R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGAACCAAAATGGAATCAAAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	79	81					6																	72960676		1814	4062	5876	73017397	SO:0001583	missense	22999			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2425T>C	6.37:g.72960676T>C	ENSP00000428417:p.Trp809Arg		73017397	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.2|22.2	4.257381|4.257381	0.80246|0.80246	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420	.|D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.84298	.|-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.79|5.79	5.79|5.79	0.91817|0.91817	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.100120	.|0.45867	.|D	.|0.000337	D|D	0.94640|0.94640	0.8272|0.8272	H|H	0.96777|0.96777	3.88|3.88	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D;D;D	.|0.97110	.|1.0;1.0;0.997;1.0;1.0;0.999;1.0;0.999;1.0;0.998;0.997;1.0	D|D	0.96365|0.96365	0.9269|0.9269	5|10	.|0.87932	.|D	.|0	-5.501|-5.501	16.1056|16.1056	0.81220|0.81220	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|268;283;809;268;283;809;62;809;809;62;809;809	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	T|R	382|809;809;809;809;809;809;809;809;809;809;809;809;283;283;202;202;268;34	.|ENSP00000430101:W809R;ENSP00000275037:W809R;ENSP00000264839:W809R;ENSP00000429959:W809R;ENSP00000430408:W809R;ENSP00000430502:W809R;ENSP00000430932:W809R;ENSP00000428417:W809R;ENSP00000385649:W283R;ENSP00000428328:W283R;ENSP00000411235:W202R;ENSP00000389503:W202R;ENSP00000428367:W268R;ENSP00000359448:W34R	.|ENSP00000264839:W809R	M|W	+|+	2|1	0|0	RIMS1|RIMS1	73017397|73017397	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	8.005000|8.005000	0.88553|0.88553	2.207000|2.207000	0.71202|0.71202	0.477000|0.477000	0.44152|0.44152	ATG|TGG		0.333	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72960676	T	C	72960676	3	2	59	1	0	0	0	0	1	0	0	0	13404	1464	51	4	2642	4	RIMS1	6	72960676	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	42832457	72960676	98154391	32	7843										
ASCC3	10973	broad.mit.edu	37	chr6	101312034	101312034	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tcattcaaaaattttattatCttcttccatgtcaggcccaa	3	10	5	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr6:101312034C>A	ENST00000369162.2	-	3	491	c.147G>T	c.(145-147)aaG>aaT	p.K49N	ASCC3_ENST00000369143.2_Missense_Mutation_p.K49N|ASCC3_ENST00000522650.1_Missense_Mutation_p.K49N	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	49					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.K49N(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		ATTTTATTATCTTCTTCCATG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											98	109	105					6																	101312034		2201	4297	6498	101418755	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.147G>T	6.37:g.101312034C>A	ENSP00000358159:p.Lys49Asn		101418755	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.181350	0.38511	.	.	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723;ENST00000369143	T;T;T	0.59224	0.36;0.28;0.66	5.32	0.726	0.18248	.	0.108694	0.64402	N	0.000009	T	0.49745	0.1575	L	0.59436	1.845	0.28193	N	0.927686	D;D;D;P	0.89917	0.961;1.0;0.961;0.454	P;D;P;B	0.83275	0.541;0.996;0.541;0.084	T	0.42189	-0.9466	10	0.66056	D	0.02	.	2.0724	0.03616	0.2963:0.4164:0.1471:0.1402	.	49;49;49;49	Q4G1A0;Q9H5A2;E7EW23;Q8N3C0	.;.;.;HELC1_HUMAN	N	49	ENSP00000358159:K49N;ENSP00000430769:K49N;ENSP00000320777:K49N	ENSP00000320777:K49N	K	-	3	2	ASCC3	101418755	1.000000	0.71417	0.994000	0.49952	0.965000	0.64279	0.544000	0.23253	0.189000	0.20188	0.655000	0.94253	AAG		0.299	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101312034	C	A	101312034	3	1	59	1	0	0	0	0	1	0	0	0	1034	912	32	2	6720	2	ASCC3	6	101312034	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	28351358	101312034	69803033	33	7844										
PMS2	5395	broad.mit.edu	37	chr7	6029489	6029489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ttgttgacatcactatcaaaCattcctatcaaagaggtctt	5	9	4	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr7:6029489C>T	ENST00000265849.7	-	10	1191	c.1086G>A	c.(1084-1086)atG>atA	p.M362I	PMS2_ENST00000441476.2_Missense_Mutation_p.M256I|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.M362I	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	362					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.M362I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		CACTATCAAACATTCCTATCA	0.363			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	1	Substitution - Missense(1)	large_intestine(1)	7											119	114	116					7																	6029489		2203	4300	6503	5996015	SO:0001583	missense	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1086G>A	7.37:g.6029489C>T	ENSP00000265849:p.Met362Ile		5996015	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	23.8	4.456063	0.84209	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;T	0.80393	-1.37;-1.37;-1.37	5.73	5.73	0.89815	Ribosomal protein S5 domain 2-type fold (1);	0.088281	0.85682	D	0.000000	T	0.74906	0.3778	L	0.33189	0.99	0.58432	D	0.999999	B;P;P	0.47191	0.266;0.891;0.865	B;B;B	0.43123	0.096;0.409;0.264	T	0.70978	-0.4725	10	0.15066	T	0.55	-22.4835	19.964	0.97260	0.0:1.0:0.0:0.0	.	362;362;256	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	I	362;315;256;362	ENSP00000265849:M362I;ENSP00000392843:M256I;ENSP00000384308:M362I	ENSP00000265849:M362I	M	-	3	0	PMS2	5996015	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.634000	0.61325	2.719000	0.93026	0.650000	0.86243	ATG		0.363	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		T	6029489	C	T	6029489	3	4	59	1	0	0	0	0	1	0	0	0	12174	478	17	3	1526	3	PMS2	7	6029489	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		6029489	153109174	34	7845										
TNS3	64759	broad.mit.edu	37	chr7	47342865	47342865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ggatgctgggggtcggtgacGctccatgagaattggccagc	17	9	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr7:47342865G>A	ENST00000398879.1	-	22	3506	c.3140C>T	c.(3139-3141)gCg>gTg	p.A1047V	TNS3_ENST00000355730.3_Missense_Mutation_p.A807V|TNS3_ENST00000311160.9_Missense_Mutation_p.A1047V			Q68CZ2	TENS3_HUMAN	tensin 3	1047				A -> T (in Ref. 4; CAH18438). {ECO:0000305}.	cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.A1047V(1)		NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GGTCGGTGACGCTCCATGAGA	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	7											17	21	19					7																	47342865		2024	4163	6187	47309390	SO:0001583	missense	64759			AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3140C>T	7.37:g.47342865G>A	ENSP00000381854:p.Ala1047Val		47309390	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	G	4.881	0.163753	0.09287	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.51	1.64	0.23874	.	1.484980	0.04979	N	0.465343	T	0.32406	0.0828	L	0.32530	0.975	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.24764	-1.0151	10	0.49607	T	0.09	-2.7576	5.1032	0.14770	0.2504:0.1494:0.6002:0.0	.	1047	Q68CZ2	TENS3_HUMAN	V	1047;1157;1047;807;503;1150	ENSP00000312143:A1047V;ENSP00000381854:A1047V;ENSP00000347968:A807V;ENSP00000414358:A1150V	ENSP00000312143:A1047V	A	-	2	0	TNS3	47309390	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.771000	0.26633	0.022000	0.15160	-0.228000	0.12330	GCG		0.672	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47342865	G	A	47342865	3	1	59	1	0	0	0	0	1	0	0	0	16383	1087	38	1	1237	1	TNS3	7	47342865	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	41313376	47342865	111795798	35	7846										
CRISPLD1	83690	broad.mit.edu	37	chr8	75941678	75941678	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gtggttcgaaatcacggtggTtatgttgatgtaatgcctgt	13	5	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr8:75941678T>G	ENST00000262207.4	+	14	1845	c.1377T>G	c.(1375-1377)ggT>ggG	p.G459G	RP11-300E4.2_ENST00000520778.1_RNA|CRISPLD1_ENST00000523524.1_Silent_p.G271G|CRISPLD1_ENST00000517786.1_Silent_p.G273G	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	459	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)		p.G459G(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			ATCACGGTGGTTATGTTGATG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	8											108	98	101					8																	75941678		2203	4300	6503	76104233	SO:0001819	synonymous_variant	83690			AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1377T>G	8.37:g.75941678T>G			76104233	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	37	CCDS6219.1																																																																																				0.393	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		G	75941678	T	G	75941678	2	3	59	1	0	0	0	0	0	0	0	1	3888	1712	60	4		4	CRISPLD1	8	75941678	Silent	SNP	T	TCGA-AG-4008-01A-01W-1073-09		75941678	70422344	36	7847										
JAKMIP3	282973	broad.mit.edu	37	chr10	133950773	133950773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cctagacccttgagaccgccGgctacgtgaagagcgtgtta	12	12	0	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr10:133950773G>A	ENST00000298622.4	+	7	1402	c.1264G>A	c.(1264-1266)Ggc>Agc	p.G422S		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	422						Golgi apparatus (GO:0005794)		p.G422S(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TGAGACCGCCGGCTACGTGAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	10											90	92	91					10																	133950773		2044	4184	6228	133800763	SO:0001583	missense	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1264G>A	10.37:g.133950773G>A	ENSP00000298622:p.Gly422Ser		133800763	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.643920	0.29246	.	.	ENSG00000188385	ENST00000298622	T	0.21734	1.99	5.08	5.08	0.68730	.	0.089418	0.42053	D	0.000770	T	0.24812	0.0602	L	0.44542	1.39	0.58432	D	0.999991	D	0.59767	0.986	P	0.47626	0.552	T	0.01566	-1.1323	10	0.23302	T	0.38	-25.0169	16.6701	0.85263	0.0:0.0:1.0:0.0	.	422	Q5VZ66	JKIP3_HUMAN	S	422	ENSP00000298622:G422S	ENSP00000298622:G422S	G	+	1	0	JAKMIP3	133800763	1.000000	0.71417	0.976000	0.42696	0.042000	0.13812	8.489000	0.90461	2.368000	0.80403	0.651000	0.88453	GGC		0.627	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		A	133950773	G	A	133950773	3	1	59	1	0	0	0	0	1	0	0	0	7963	1116	39	1	1290	1	JAKMIP3	10	133950773	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09		133950773	1583974	37	7848										
MRGPRX1	259249	broad.mit.edu	37	chr11	18956223	18956223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgtcagcccgacaagggaaaCgatgcacgtcagcaccgtga	12	12	2	1	rs367640618		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr11:18956223C>T	ENST00000302797.3	-	1	333	c.109G>A	c.(109-111)Gtt>Att	p.V37I	MRGPRX1_ENST00000526914.1_5'UTR|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	37					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V37I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						ACAAGGGAAACGATGCACGTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	11											206	194	198					11																	18956223		2194	4286	6480	18912799	SO:0001583	missense	259249				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.109G>A	11.37:g.18956223C>T	ENSP00000305766:p.Val37Ile		18912799	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.486962	0.00161	.	.	ENSG00000170255	ENST00000302797	T	0.25250	1.81	2.42	-4.84	0.03151	.	1.176060	0.06178	N	0.678998	T	0.07143	0.0181	N	0.03209	-0.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	10	0.02654	T	1	.	1.1666	0.01817	0.3758:0.3123:0.1284:0.1835	.	37	Q96LB2	MRGX1_HUMAN	I	37	ENSP00000305766:V37I	ENSP00000305766:V37I	V	-	1	0	MRGPRX1	18912799	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.194000	0.09559	-3.660000	0.00125	-1.438000	0.01074	GTT		0.557	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18956223	C	T	18956223	3	4	59	1	0	0	0	0	1	0	0	0	9796	536	19	1	863	1	MRGPRX1	11	18956223	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		18956223	116050293	38	7849										
OR4A5	81318	broad.mit.edu	37	chr11	51412308	51412308	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgtcaccaagtatgtgagtaAaaacatgacaaataatgctt	7	6	1	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr11:51412308A>C	ENST00000319760.6	-	1	140	c.88T>G	c.(88-90)Tta>Gta	p.L30V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L30V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				TATGTGAGTAAAAACATGACA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											52	49	50					11																	51412308		2201	4296	6497	51268884	SO:0001583	missense	81318			AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.88T>G	11.37:g.51412308A>C	ENSP00000367664:p.Leu30Val		51268884	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	8.200	0.797894	0.16327	.	.	ENSG00000221840	ENST00000319760	T	0.01902	4.57	2.01	-0.436	0.12275	.	0.194706	0.25302	N	0.031649	T	0.11367	0.0277	H	0.95780	3.72	0.09310	N	1	D	0.57899	0.981	P	0.58721	0.844	T	0.04153	-1.0973	10	0.66056	D	0.02	.	5.6516	0.17620	0.4833:0.0:0.5167:0.0	.	30	Q8NH83	OR4A5_HUMAN	V	30	ENSP00000367664:L30V	ENSP00000367664:L30V	L	-	1	2	OR4A5	51268884	0.000000	0.05858	0.061000	0.19648	0.033000	0.12548	0.525000	0.22956	-0.114000	0.11936	0.136000	0.15936	TTA		0.418	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		C	51412308	A	C	51412308	3	2	59	1	0	0	0	0	1	0	0	0	11074	11	1	4	863	4	OR4A5	11	51412308	Missense_Mutation	SNP	A	TCGA-AG-4008-01A-01W-1073-09	32456085	51412308	83594208	39	7850										
CDC42BPG	55561	broad.mit.edu	37	chr11	64600210	64600210	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cgccggacacctgagggccgCggcacctggcggaaaggcaa	16	14	0	1	rs150950292	byFrequency	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr11:64600210C>T	ENST00000342711.5	-	26	2870	c.2871G>A	c.(2869-2871)ccG>ccA	p.P957P	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)									p.P957P(1)		central_nervous_system(1)|lung(3)	4						CTGAGGGCCGCGGCACCTGGC	0.697													C|||	2	0.000399361	0.0015	0	5008	,	,		13160	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		3,4377		0,3,2187	19	20	20		2871	-8.9	0	11	dbSNP_134	20	1,8563		0,1,4281	no	coding-synonymous	CDC42BPG	NM_017525.2		0,4,6468	TT,TC,CC		0.0117,0.0685,0.0309		957/1552	64600210	4,12940	2190	4282	6472	64356786	SO:0001819	synonymous_variant	55561			AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.2871G>A	11.37:g.64600210C>T			64356786		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																				0.697	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		T	64600210	C	T	64600210	2	4	59	1	0	0	0	0	0	0	0	1	3080	755	27	1		1	CDC42BPG	11	64600210	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	13187902	64600210	70406306	40	7851										
NPAS4	266743	broad.mit.edu	37	chr11	66192375	66192375	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tggagcccctggactccaacCtgtccctgtcaggggcaggc	13	15	1	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr11:66192375C>A	ENST00000311034.2	+	7	2190	c.2014C>A	c.(2014-2016)Ctg>Atg	p.L672M		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	672					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.L672M(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GGACTCCAACCTGTCCCTGTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	94	92					11																	66192375		2200	4295	6495	65948951	SO:0001583	missense	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.2014C>A	11.37:g.66192375C>A	ENSP00000311196:p.Leu672Met		65948951	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.640323	0.47153	.	.	ENSG00000174576	ENST00000311034	T	0.48201	0.82	4.39	4.39	0.52855	.	0.000000	0.43579	D	0.000549	T	0.44244	0.1284	N	0.14661	0.345	0.41114	D	0.98576	D	0.65815	0.995	P	0.59221	0.854	T	0.41016	-0.9532	10	0.46703	T	0.11	-5.3897	10.6578	0.45686	0.0:0.8055:0.1945:0.0	.	672	Q8IUM7	NPAS4_HUMAN	M	672	ENSP00000311196:L672M	ENSP00000311196:L672M	L	+	1	2	NPAS4	65948951	0.970000	0.33590	1.000000	0.80357	0.997000	0.91878	0.138000	0.16016	2.443000	0.82685	0.655000	0.94253	CTG		0.602	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		A	66192375	C	A	66192375	3	1	59	1	0	0	0	0	1	0	0	0	10596	680	24	2	2040	2	NPAS4	11	66192375	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	1592165	66192375	68814141	41	7852										
CHD4	1108	broad.mit.edu	37	chr12	6692269	6692269	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gactggttgtcggactggtcGtcctgccaatctggagggag	16	9	1	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:6692269G>A	ENST00000357008.2	-	27	4234	c.4071C>T	c.(4069-4071)gaC>gaT	p.D1357D	CHD4_ENST00000544040.1_Silent_p.D1350D|CHD4_ENST00000544484.1_Silent_p.D1382D|SCARNA11_ENST00000516089.1_RNA|CHD4_ENST00000309577.6_Silent_p.D1385D|RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000540960.1_5'UTR	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1357					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.D1385D(1)|p.D1357D(1)		central_nervous_system(2)	2						CGGACTGGTCGTCCTGCCAAT	0.587																																					Colon(32;586 792 4568 16848 45314)											2	Substitution - coding silent(2)	large_intestine(2)	12											85	85	85					12																	6692269		2203	4300	6503	6562530	SO:0001819	synonymous_variant	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.4071C>T	12.37:g.6692269G>A			6562530	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																				0.587	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6692269	G	A	6692269	2	1	59	1	0	0	0	0	0	0	0	1	3333	1136	40	1		1	CHD4	12	6692269	Silent	SNP	G	TCGA-AG-4008-01A-01W-1073-09		6692269	127159626	42	7853										
PZP	5858	broad.mit.edu	37	chr12	9318699	9318699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	caggaaaatagcttcgcaccGtttcagggactggccctgaa	11	11	1	1	rs200058002		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:9318699G>A	ENST00000261336.2	-	18	2235	c.2207C>T	c.(2206-2208)aCg>aTg	p.T736M	PZP_ENST00000381997.2_Missense_Mutation_p.T605M|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	736					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T605M(1)|p.T736M(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GCTTCGCACCGTTTCAGGGAC	0.448																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12						G	MET/THR	0,4406		0,0,2203	143	135	138		2207	1.5	0	12		138	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PZP	NM_002864.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	736/1483	9318699	1,13005	2203	4300	6503	9209966	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2207C>T	12.37:g.9318699G>A	ENSP00000261336:p.Thr736Met		9209966	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.298198	0.40694	0.0	1.16E-4	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.38722	1.4;1.12	3.58	1.47	0.22746	.	0.243635	0.20220	U	0.096705	T	0.43299	0.1241	L	0.29908	0.895	0.21020	N	0.999806	D;D;D	0.76494	0.999;0.986;0.999	P;P;P	0.62885	0.908;0.8;0.908	T	0.20306	-1.0279	10	0.62326	D	0.03	.	6.5659	0.22511	0.2768:0.0:0.7232:0.0	.	736;605;736	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	M	736;605	ENSP00000261336:T736M;ENSP00000371427:T605M	ENSP00000261336:T736M	T	-	2	0	PZP	9209966	0.960000	0.32886	0.002000	0.10522	0.335000	0.28730	2.324000	0.43831	0.192000	0.20272	0.460000	0.39030	ACG		0.448	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9318699	G	A	9318699	3	1	59	1	0	0	0	0	1	0	0	0	12906	1145	40	1	2317	1	PZP	12	9318699	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	2626430	9318699	124533196	43	7854										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398285	+	Missense_Mutation	DNP	CC	CC	AA													0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt					rs121913530|rs121913529		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:25398284_25398285CC>AA	ENST00000256078.4	-	2	97_98	c.34_35GG>TT	c.(34-36)GGt>TTt	p.G12F	KRAS_ENST00000311936.3_Missense_Mutation_p.G12F|KRAS_ENST00000557334.1_Missense_Mutation_p.G12F|KRAS_ENST00000556131.1_Missense_Mutation_p.G12F	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12C(3001)|p.G12A(1407)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12fs*3(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAACT	0.347	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	20892	Substitution - Missense(20889)|Insertion - In frame(2)|Deletion - Frameshift(1)	large_intestine(11786)|pancreas(3650)|lung(3132)|ovary(556)|biliary_tract(494)|endometrium(373)|haematopoietic_and_lymphoid_tissue(212)|stomach(145)|thyroid(97)|prostate(70)|small_intestine(56)|upper_aerodigestive_tract(47)|urinary_tract(47)|soft_tissue(42)|cervix(41)|skin(35)|liver(22)|breast(20)|testis(16)|oesophagus(11)|central_nervous_system(8)|peritoneum(6)|kidney(5)|eye(4)|NS(4)|autonomic_ganglia(3)|gastrointestinal_tract_(site_indeterminate)(3)|thymus(3)|penis(1)|adrenal_gland(1)|salivary_gland(1)|bone(1)	12	GRCh37	CM076251	KRAS	M	rs121913530																																			25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34_35delinsAA	12.37:g.25398284_25398285delinsAA	ENSP00000256078:p.Gly12Phe		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	DNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.347	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		AA	25398285	CC	AA	25398284	3	1	59	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	DNP	CC	TCGA-AG-4008-01A-01W-1073-09	16079585	25398284	108453611	44	7855										
KIAA0748	9840	broad.mit.edu	37	chr12	55356419	55356419	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tccttggctggatgggtttcCgtattggtggctggtagact	15	7	0	1	rs200398984	byFrequency	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:55356419C>T	ENST00000449076.1	-	9	1395	c.1263G>A	c.(1261-1263)acG>acA	p.T421T	TESPA1_ENST00000316577.8_Silent_p.T421T|TESPA1_ENST00000532804.1_Silent_p.T283T|TESPA1_ENST00000531122.1_Silent_p.T283T|TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000524622.1_Silent_p.T283T	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	421					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.T421T(2)|p.T283T(2)									GATGGGTTTCCGTATTGGTGG	0.493																																																4	Substitution - coding silent(4)	large_intestine(2)|endometrium(2)	12						C	,	0,3904		0,0,1952	148	151	150		1263,1263	2.3	0	12		150	11,8261		0,11,4125	no	coding-synonymous,coding-synonymous	KIAA0748	NM_001098815.1,NM_001136030.1	,	0,11,6077	TT,TC,CC		0.133,0.0,0.0903	,	421/522,421/522	55356419	11,12165	1952	4136	6088	53642686	SO:0001819	synonymous_variant	9840			AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.1263G>A	12.37:g.55356419C>T			53642686	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Silent	SNP	ENST00000449076.1	37	CCDS44913.1																																																																																				0.493	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		T	55356419	C	T	55356419	2	4	59	1	0	0	0	0	0	0	0	1	8211	639	23	1		1	KIAA0748	12	55356419	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	29958135	55356419	78495476	45	7856										
WSCD2	9671	broad.mit.edu	37	chr12	108634175	108634175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	acggaccatctgcatcaagaCgcacgaaagcggccagaaag	11	12	2	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:108634175C>T	ENST00000332082.4	+	9	2017	c.1199C>T	c.(1198-1200)aCg>aTg	p.T400M	WSCD2_ENST00000547525.1_Missense_Mutation_p.T400M|WSCD2_ENST00000261400.3_Missense_Mutation_p.T400M|WSCD2_ENST00000549903.1_Missense_Mutation_p.T400M			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	400						integral component of membrane (GO:0016021)		p.T400M(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						TGCATCAAGACGCACGAAAGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											130	140	137					12																	108634175		2060	4210	6270	107158305	SO:0001583	missense	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1199C>T	12.37:g.108634175C>T	ENSP00000331933:p.Thr400Met		107158305	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045715	0.93685	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.38401	1.14;4.25;1.14;4.25	4.9	4.9	0.64082	.	0.097827	0.64402	D	0.000001	T	0.64271	0.2583	M	0.90759	3.145	0.80722	D	1	D;D	0.76494	0.999;0.997	P;P	0.60173	0.87;0.745	T	0.72364	-0.4316	10	0.56958	D	0.05	-17.6089	17.3052	0.87192	0.0:1.0:0.0:0.0	.	400;400	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	M	400	ENSP00000448047:T400M;ENSP00000261400:T400M;ENSP00000331933:T400M;ENSP00000447272:T400M	ENSP00000261400:T400M	T	+	2	0	WSCD2	107158305	1.000000	0.71417	0.961000	0.40146	0.987000	0.75469	7.192000	0.77771	2.551000	0.86045	0.644000	0.83932	ACG		0.602	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108634175	C	T	108634175	3	4	59	1	0	0	0	0	1	0	0	0	17447	536	19	1	1225	1	WSCD2	12	108634175	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	53277756	108634175	25217720	46	7857										
C12orf51	283450	broad.mit.edu	37	chr12	112708081	112708081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	acaggtatctccattaaccaTggccttctccataatgtcac	5	13	3	0	rs552018424		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:112708081T>C	ENST00000430131.2	-	11	1974	c.829A>G	c.(829-831)Atg>Gtg	p.M277V	HECTD4_ENST00000377560.5_Missense_Mutation_p.M527V|RN7SKP71_ENST00000364558.1_RNA|HECTD4_ENST00000550722.1_Missense_Mutation_p.M565V			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	277					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.M277V(1)|p.M527V(1)									CCATTAACCATGGCCTTCTCC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	12											249	223	232					12																	112708081		2203	4300	6503	111192464	SO:0001583	missense	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.829A>G	12.37:g.112708081T>C	ENSP00000404379:p.Met277Val		111192464	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	T	16.47	3.131681	0.56828	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.40756	1.02;1.02;1.03	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.33789	0.0875	N	0.08118	0	0.43885	D	0.996507	B;B;B	0.34399	0.452;0.323;0.452	P;B;P	0.44623	0.455;0.354;0.455	T	0.29731	-1.0002	10	0.27785	T	0.31	.	15.6267	0.76863	0.0:0.0:0.0:1.0	.	277;277;277	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	V	527;277;565	ENSP00000366783:M527V;ENSP00000404379:M277V;ENSP00000449784:M565V	ENSP00000366783:M527V	M	-	1	0	C12orf51	111192464	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.665000	0.83852	2.089000	0.63090	0.379000	0.24179	ATG		0.398	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112708081	T	C	112708081	3	2	59	1	0	0	0	0	1	0	0	0	1700	1464	51	4	11421	4	C12orf51	12	112708081	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09	4073906	112708081	21143814	47	7858										
TPCN1	53373	broad.mit.edu	37	chr12	113731118	113731118	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cggcgatcaaggaccaagagCgacctgagcctgaagatgta	13	10	1	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr12:113731118C>T	ENST00000335509.6	+	27	2612	c.2298C>T	c.(2296-2298)agC>agT	p.S766S	TPCN1_ENST00000541517.1_Silent_p.S838S|TPCN1_ENST00000546787.1_3'UTR|TPCN1_ENST00000550785.1_Silent_p.S838S|TPCN1_ENST00000392569.4_Silent_p.S698S	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	766					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)	p.S766S(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GGACCAAGAGCGACCTGAGCC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	12											215	209	211					12																	113731118		2203	4300	6503	112215501	SO:0001819	synonymous_variant	53373			AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.2298C>T	12.37:g.113731118C>T			112215501	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																				0.602	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		T	113731118	C	T	113731118	2	4	59	1	0	0	0	0	0	0	0	1	16435	767	27	1		1	TPCN1	12	113731118	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	1023037	113731118	20120777	48	7859										
OR11H12	440153	broad.mit.edu	37	chr14	19377838	19377838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	catgttcctgggaaatttctCctttttagagatatggtatg	9	6	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr14:19377838C>T	ENST00000550708.1	+	1	317	c.245C>T	c.(244-246)tCc>tTc	p.S82F		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S82F(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGAAATTTCTCCTTTTTAGAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											41	50	47					14																	19377838		1971	4084	6055	18447838	SO:0001583	missense	440153				CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"GPCR / Class A : Olfactory receptors"	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.245C>T	14.37:g.19377838C>T	ENSP00000449002:p.Ser82Phe		18447838		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	c	10.28	1.305674	0.23736	.	.	ENSG00000257115	ENST00000550708	T	0.12361	2.69	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.171384	0.27447	N	0.019339	T	0.42630	0.1211	H	0.95539	3.685	0.25486	N	0.9877	D	0.89917	1.0	D	0.83275	0.996	T	0.57723	-0.7762	9	0.87932	D	0	.	7.1009	0.25336	0.0:0.9999:0.0:1.0E-4	.	82	B2RN74	O11HC_HUMAN	F	82	ENSP00000449002:S82F	ENSP00000449002:S82F	S	+	2	0	CR383656.1	18447838	0.178000	0.23122	0.997000	0.53966	0.280000	0.26924	1.272000	0.33109	0.619000	0.30197	0.064000	0.15345	TCC		0.423	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354		T	19377838	C	T	19377838	3	4	59	1	0	0	0	0	1	0	0	0	10958	855	30	3	247	3	OR11H12	14	19377838	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		19377838	87971702	49	7860										
OR4N2	390429	broad.mit.edu	37	chr14	20296294	20296294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgtcgcatacgagggtcttcTtctgaggcaaaaaacaaggc	11	9	3	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr14:20296294T>C	ENST00000315947.1	+	1	687	c.687T>C	c.(685-687)tcT>tcC	p.S229S	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S229S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GAGGGTCTTCTTCTGAGGCAA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	14											107	108	108					14																	20296294		2203	4300	6503	19366134	SO:0001819	synonymous_variant	390429				CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.687T>C	14.37:g.20296294T>C			19366134	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																				0.488	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			C	20296294	T	C	20296294	2	2	59	1	0	0	0	0	0	0	0	1	11108	1596	56	4		4	OR4N2	14	20296294	Silent	SNP	T	TCGA-AG-4008-01A-01W-1073-09	918456	20296294	87053246	50	7861										
BMP4	652	broad.mit.edu	37	chr14	54417346	54417346	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cacatcaaaagtttcccaccGtgtcacattgtggtggacca	8	12	2	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr14:54417346G>A	ENST00000245451.4	-	4	1024	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	BMP4_ENST00000417573.1_Missense_Mutation_p.R211W|BMP4_ENST00000558984.1_Missense_Mutation_p.R211W|MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000559087.1_Missense_Mutation_p.R211W	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	211					activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)	p.R211W(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						GTTTCCCACCGTGTCACATTG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	14											110	101	104					14																	54417346		2203	4300	6503	53487096	SO:0001583	missense	652			AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"Bone morphogenetic proteins", "Endogenous ligands"	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.631C>T	14.37:g.54417346G>A	ENSP00000245451:p.Arg211Trp		53487096	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	37	CCDS9715.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.413920	0.62511	.	.	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.65916	-0.18;-0.18	5.09	4.19	0.49359	Transforming growth factor-beta, N-terminal (1);	0.417987	0.27126	N	0.020803	T	0.75722	0.3888	M	0.76727	2.345	0.34982	D	0.754164	D	0.64830	0.994	P	0.61722	0.893	D	0.84829	0.0801	10	0.87932	D	0	.	14.0622	0.64806	0.0:0.0:0.8482:0.1518	.	211	P12644	BMP4_HUMAN	W	211	ENSP00000245451:R211W;ENSP00000394165:R211W	ENSP00000245451:R211W	R	-	1	2	BMP4	53487096	0.970000	0.33590	1.000000	0.80357	0.997000	0.91878	2.864000	0.48404	1.355000	0.45865	0.655000	0.94253	CGG		0.537	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202		A	54417346	G	A	54417346	3	1	59	1	0	0	0	0	1	0	0	0	1463	1144	40	1	599	1	BMP4	14	54417346	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	34121052	54417346	52932194	51	7862										
C14orf68	283600	broad.mit.edu	37	chr14	100793639	100793639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	acatctgccggctccggtacGgcaaccctgacgccaagccc	10	18	1	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr14:100793639G>A	ENST00000361529.3	+	4	337	c.259G>A	c.(259-261)Ggc>Agc	p.G87S	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	87					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.G87S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						GCTCCGGTACGGCAACCCTGA	0.692																																					GBM(11;1289 1351)											1	Substitution - Missense(1)	large_intestine(1)	14											91	88	89					14																	100793639		2203	4300	6503	99863392	SO:0001583	missense	283600				CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"Solute carriers"	20115	protein-coding gene	gene with protein product		609911	"chromosome 14 open reading frame 68"	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.259G>A	14.37:g.100793639G>A	ENSP00000354886:p.Gly87Ser		99863392	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.762369	0.49468	.	.	ENSG00000140107	ENST00000361529	T	0.77489	-1.1	4.95	4.95	0.65309	Mitochondrial carrier domain (2);	0.263229	0.43416	D	0.000576	T	0.62624	0.2443	N	0.12182	0.205	0.80722	D	1	B	0.26876	0.162	B	0.20384	0.029	T	0.61262	-0.7098	10	0.39692	T	0.17	-16.9087	16.5884	0.84745	0.0:0.0:1.0:0.0	.	87	Q6Q0C1	S2547_HUMAN	S	87	ENSP00000354886:G87S	ENSP00000354886:G87S	G	+	1	0	SLC25A47	99863392	0.997000	0.39634	0.900000	0.35374	0.520000	0.34377	2.840000	0.48215	2.599000	0.87857	0.485000	0.47835	GGC		0.692	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1			A	100793639	G	A	100793639	3	1	59	1	0	0	0	0	1	0	0	0	1782	1116	39	1	273	1	C14orf68	14	100793639	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	46376293	100793639	6555901	52	7863										
MAPKBP1	23005	broad.mit.edu	37	chr15	42106934	42106934	+	Frame_Shift_Del	DEL	G	G	-													0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tcttcctgcgtctggagtgtGgaggtatgtgggctggctgg					rs141101616		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr15:42106934delG	ENST00000456763.2	+	11	1381	c.1185delG	c.(1183-1185)gtgfs	p.V395fs	MAPKBP1_ENST00000221214.6_Intron|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.V389fs|MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.V389fs|MAPKBP1_ENST00000260357.7_Frame_Shift_Del_p.V277fs	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	395								p.E390fs*6(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TCTGGAGTGTGGAGGTATGTG	0.498																																																1	Deletion - Frameshift(1)	large_intestine(1)	15											180	167	172					15																	42106934		2203	4300	6503	39894226	SO:0001589	frameshift_variant	23005			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1185delG	15.37:g.42106934delG	ENSP00000393099:p.Val395fs		39894226	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	37	CCDS45239.1																																																																																				0.498	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		-	42106934	G	-	42106934	7	5	59	1	0	1	0	1	0	0	0	0	9322	1335	47	0	1223	0	MAPKBP1	15	42106934	Frame_Shift_Del	DEL	G	TCGA-AG-4008-01A-01W-1073-09		42106934	60424458	53	7864										
DNAH3	55567	broad.mit.edu	37	chr16	21145625	21145625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgagcatcatggggttcaccGtgtgcagatgctcctcgttc	12	11	2	2	rs372982554		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr16:21145625G>A	ENST00000261383.3	-	7	1036	c.1037C>T	c.(1036-1038)aCg>aTg	p.T346M	DNAH3_ENST00000415178.1_Missense_Mutation_p.T346M	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	346	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.T346M(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGGGTTCACCGTGTGCAGATG	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	16						G	MET/THR	0,4402		0,0,2201	112	104	106		1037	2.4	0.4	16		106	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH3	NM_017539.1	81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	346/4117	21145625	1,13001	2201	4300	6501	21053126	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1037C>T	16.37:g.21145625G>A	ENSP00000261383:p.Thr346Met		21053126	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637575	0.29157	0.0	1.16E-4	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.23950	1.88;2.04	5.85	2.43	0.29744	.	0.660669	0.14636	N	0.307503	T	0.40767	0.1130	M	0.64404	1.975	0.22888	N	0.998606	P;D	0.65815	0.848;0.995	B;P	0.57283	0.214;0.817	T	0.18366	-1.0339	10	0.62326	D	0.03	.	11.7556	0.51874	0.2321:0.0:0.7679:0.0	.	346;317	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	M	346;346;317	ENSP00000261383:T346M;ENSP00000394245:T346M	ENSP00000261383:T346M	T	-	2	0	DNAH3	21053126	0.892000	0.30473	0.436000	0.26797	0.730000	0.41778	1.521000	0.35910	0.836000	0.34901	-0.140000	0.14226	ACG		0.527	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21145625	G	A	21145625	3	1	59	1	0	0	0	0	1	0	0	0	4614	1145	40	1	11536	1	DNAH3	16	21145625	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09		21145625	69209128	54	7865										
HSF4	3299	broad.mit.edu	37	chr16	67201665	67201666	+	Frame_Shift_Ins	INS	-	-	G													0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	aagaagagccggccagtccaINSgggggggatggcgaggccgg							TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr16:67201665_67201666insG	ENST00000521374.1	+	9	897_898	c.897_898insG	c.(898-900)gggfs	p.G300fs	NOL3_ENST00000564053.1_5'Flank|HSF4_ENST00000584272.1_Intron|NOL3_ENST00000432069.2_5'Flank|HSF4_ENST00000421453.1_Intron|HSF4_ENST00000264009.8_Frame_Shift_Ins_p.G300fs			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	300	Interactions with DUSP26, MAPK1 and MAPK2.				camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.D302fs*14(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		CGGCCAGTCCAGGGGGGGATGG	0.649																																																1	Insertion - Frameshift(1)	large_intestine(1)	16																																								65759167	SO:0001589	frameshift_variant	3299			D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"cataract, Marner"	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.904dupG	16.37:g.67201672_67201672dupG	ENSP00000430947:p.Gly300fs		65759166	Q99472|Q9ULV6	Frame_Shift_Ins	INS	ENST00000521374.1	37	CCDS42175.1																																																																																				0.649	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538		G	67201666	-	G	67201665	7	5	59	1	0	1	1	0	0	0	0	0	7419	175	7	0	945	0	HSF4	16	67201665	Frame_Shift_Ins	INS	-	TCGA-AG-4008-01A-01W-1073-09	46056040	67201665	23153088	55	7866										
C17orf87	388325	broad.mit.edu	37	chr17	5118255	5118255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	aaggccaattcctcggtggcAgaggcggtaattgaactggc	14	9	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr17:5118255A>G	ENST00000574081.1	-	4	352	c.248T>C	c.(247-249)cTg>cCg	p.L83P	SCIMP_ENST00000399600.4_Missense_Mutation_p.L76P|RP11-333E1.1_ENST00000571689.1_RNA|RP11-333E1.1_ENST00000575601.1_RNA|SCIMP_ENST00000571800.1_Missense_Mutation_p.L76P|SCIMP_ENST00000574297.1_Missense_Mutation_p.L83P	NM_001271842.1|NM_207103.3	NP_001258771.1|NP_996986.1	Q6UWF3	SCIMP_HUMAN	SLP adaptor and CSK interacting membrane protein	83	Pro-rich.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)	immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|tetraspanin-enriched microdomain (GO:0097197)|uropod membrane (GO:0031259)		p.L83P(1)									CCTCGGTGGCAGAGGCGGTAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	17											73	75	74					17																	5118255		1932	4131	6063	5058979	SO:0001583	missense	388325			AY358809	CCDS42242.1, CCDS62044.1	17p13.2	2011-11-24	2011-11-23	2011-11-23	ENSG00000161929	ENSG00000161929			33504	protein-coding gene	gene with protein product	"SLP65/SLP76, Csk-interacting membrane protein"	614406	"chromosome 17 open reading frame 87"	C17orf87		21930792	Standard	NM_207103		Approved	DTFT5783, UNQ5783, FLJ32580, MGC163426, MGC163428	uc002gbh.3	Q6UWF3	OTTHUMG00000132914	ENST00000574081.1:c.248T>C	17.37:g.5118255A>G	ENSP00000461269:p.Leu83Pro		5058979	A6XGL4|B4DLK1|Q96MD0	Missense_Mutation	SNP	ENST00000574081.1	37	CCDS42242.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506538	0.44558	.	.	ENSG00000161929	ENST00000399600	.	.	.	4.89	4.89	0.63831	.	0.000000	0.44097	D	0.000490	T	0.75384	0.3842	M	0.66939	2.045	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.77885	-0.2421	9	0.87932	D	0	-11.2481	11.0857	0.48086	1.0:0.0:0.0:0.0	.	76;76;83	A6XGL4;Q6UWF3-2;Q6UWF3	.;.;CQ087_HUMAN	P	83	.	ENSP00000382509:L83P	L	-	2	0	C17orf87	5058979	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	3.838000	0.55828	2.194000	0.70268	0.459000	0.35465	CTG		0.438	SCIMP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256425.2	NM_207103		G	5118255	A	G	5118255	3	3	59	1	0	0	0	0	1	0	0	0	1894	188	7	4	197	4	C17orf87	17	5118255	Missense_Mutation	SNP	A	TCGA-AG-4008-01A-01W-1073-09		5118255	76076955	56	7867										
TP53	7157	broad.mit.edu	37	chr17	7578478	7578478	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ggacgcgggtgccgggcgggGgtgtggaatcaacccacagc	19	11	1	0	rs137852790|rs137852791		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr17:7578478G>T	ENST00000269305.4	-	5	641	c.452C>A	c.(451-453)cCc>cAc	p.P151H	TP53_ENST00000413465.2_Missense_Mutation_p.P151H|TP53_ENST00000455263.2_Missense_Mutation_p.P151H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P151H|TP53_ENST00000445888.2_Missense_Mutation_p.P151H|TP53_ENST00000420246.2_Missense_Mutation_p.P151H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	151	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934874). {ECO:0000269|PubMed:7682763}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P151H(31)|p.P151R(9)|p.0?(8)|p.P151L(7)|p.T150fs*16(6)|p.?(5)|p.P58H(2)|p.P19H(2)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.P151del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*28(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P58R(1)|p.Q144_G154del11(1)|p.P19R(1)|p.Q144fs*16(1)|p.P152fs*14(1)|p.P151fs*30(1)|p.T18fs*16(1)|p.T150_P151delTP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCGGGCGGGGGTGTGGAATC	0.607		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	90	Substitution - Missense(53)|Deletion - Frameshift(14)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Insertion - Frameshift(2)	lung(17)|large_intestine(13)|ovary(10)|skin(8)|oesophagus(8)|breast(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|central_nervous_system(4)|bone(4)|upper_aerodigestive_tract(3)|soft_tissue(2)|urinary_tract(2)|liver(2)|vulva(1)	17											54	55	55					17																	7578478		2203	4300	6503	7519203	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.452C>A	17.37:g.7578478G>T	ENSP00000269305:p.Pro151His		7519203	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040562	0.55003	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99887	-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110207	0.64402	D	0.000007	D	0.99891	0.9948	M	0.91406	3.205	0.53688	D	0.999972	D;P;D;P;P;P;D	0.89917	0.99;0.807;1.0;0.793;0.948;0.84;1.0	P;P;D;P;P;P;D	0.97110	0.84;0.754;0.995;0.625;0.841;0.868;1.0	D	0.96236	0.9172	10	0.87932	D	0	-14.1156	12.4691	0.55777	0.0812:0.0:0.9188:0.0	.	112;151;151;58;151;151;151	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	151;151;151;151;151;151;140;58;19;58;19;151	ENSP00000410739:P151H;ENSP00000352610:P151H;ENSP00000269305:P151H;ENSP00000398846:P151H;ENSP00000391127:P151H;ENSP00000391478:P151H;ENSP00000425104:P19H;ENSP00000423862:P58H;ENSP00000424104:P151H	ENSP00000269305:P151H	P	-	2	0	TP53	7519203	1.000000	0.71417	0.974000	0.42286	0.058000	0.15608	6.711000	0.74675	1.515000	0.48885	0.655000	0.94253	CCC		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578478	G	T	7578478	3	4	59	1	0	0	0	0	1	0	0	0	16421	1232	43	2	846	2	TP53	17	7578478	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	2460223	7578478	73616732	57	7868										
RAB11FIP4	84440	broad.mit.edu	37	chr17	29848366	29848366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctactcggacctggggtcttCggtgtcttccaggtggcccc	13	14	2	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr17:29848366C>T	ENST00000325874.8	+	5	975	c.746C>T	c.(745-747)tCg>tTg	p.S249L	RAB11FIP4_ENST00000394744.2_Missense_Mutation_p.S147L|RN7SL45P_ENST00000578050.1_RNA	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	249	Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.S249L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				CTGGGGTCTTCGGTGTCTTCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	78	87					17																	29848366		2203	4300	6503	26872486	SO:0001583	missense	84440			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"EF-hand domain containing"	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.746C>T	17.37:g.29848366C>T	ENSP00000312837:p.Ser249Leu		26872486	Q52LI1|Q8N829|Q8NDT7|Q969D8	Missense_Mutation	SNP	ENST00000325874.8	37	CCDS11267.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810051	0.90707	.	.	ENSG00000131242	ENST00000325874;ENST00000394744	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.75664	0.3880	L	0.55103	1.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.976;0.994	T	0.72861	-0.4164	8	.	.	.	-11.9493	17.713	0.88327	0.0:1.0:0.0:0.0	.	147;249	Q86YS3-2;Q86YS3	.;RFIP4_HUMAN	L	249	.	.	S	+	2	0	RAB11FIP4	26872486	1.000000	0.71417	0.691000	0.30163	0.674000	0.39518	7.317000	0.79018	2.780000	0.95670	0.655000	0.94253	TCG		0.577	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932		T	29848366	C	T	29848366	3	4	59	1	0	0	0	0	1	0	0	0	12933	893	31	1	764	1	RAB11FIP4	17	29848366	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	22269888	29848366	51346844	58	7869										
RPL19	6143	broad.mit.edu	37	chr17	37360786	37360786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ttccctgaccagtgaccaggCtgaggcccgcaggtctaaga	12	13	1	4			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr17:37360786C>T	ENST00000225430.4	+	6	538	c.476C>T	c.(475-477)gCt>gTt	p.A159V	RPL19_ENST00000579260.1_Missense_Mutation_p.A157V|RPL19_ENST00000579374.1_Missense_Mutation_p.A156V|RPL19_ENST00000582193.1_Missense_Mutation_p.A157V	NM_000981.3	NP_000972.1	P84098	RL19_HUMAN	ribosomal protein L19	159					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.A159V(1)		kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7						AGTGACCAGGCTGAGGCCCGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											73	79	77					17																	37360786		1913	4135	6048	34614312	SO:0001583	missense	6143				CCDS42312.1	17q12	2012-09-20			ENSG00000108298	ENSG00000108298		"L ribosomal proteins"	10312	protein-coding gene	gene with protein product	"60S ribosomal protein L19", "ribosomal protein L19, cytosolic, N-terminus truncated"	180466				1577483	Standard	XM_005257564		Approved	FLJ27452, MGC71997, DKFZp779D216, L19	uc002hrq.1	P84098	OTTHUMG00000178979	ENST00000225430.4:c.476C>T	17.37:g.37360786C>T	ENSP00000225430:p.Ala159Val		34614312	B2R4K2|P14118|P22908|Q502Y6|Q7Z6E4	Missense_Mutation	SNP	ENST00000225430.4	37	CCDS42312.1	.	.	.	.	.	.	.	.	.	.	c	19.17	3.775191	0.70107	.	.	ENSG00000108298	ENST00000225430	.	.	.	5.22	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.60104	0.2243	M	0.90705	3.14	0.80722	D	1	D	0.57571	0.98	B	0.41412	0.356	T	0.68108	-0.5496	9	0.07482	T	0.82	.	13.4094	0.60933	0.0:0.9242:0.0:0.0758	.	159	P84098	RL19_HUMAN	V	159	.	ENSP00000225430:A159V	A	+	2	0	RPL19	34614312	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.621000	0.83083	1.202000	0.43218	0.563000	0.77884	GCT		0.552	RPL19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444190.1	NM_000981		T	37360786	C	T	37360786	3	4	59	1	0	0	0	0	1	0	0	0	13603	797	28	3	498	3	RPL19	17	37360786	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	7512420	37360786	43834424	59	7870										
KRT37	8688	broad.mit.edu	37	chr17	39577794	39577794	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	catctgggccagctctgtgcCgtagcggtcctccgcttcac	11	16	3	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr17:39577794C>T	ENST00000225550.3	-	6	1065	c.1066G>A	c.(1066-1068)Ggc>Agc	p.G356S	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	356	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.G356S(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				AGCTCTGTGCCGTAGCGGTCC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	17											63	60	61					17																	39577794		2203	4300	6503	36831320	SO:0001583	missense	8688			Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.1066G>A	17.37:g.39577794C>T	ENSP00000225550:p.Gly356Ser		36831320		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.759102	0.00657	.	.	ENSG00000108417	ENST00000225550	D	0.87809	-2.3	4.84	2.58	0.30949	Filament (1);	0.125321	0.35772	N	0.002989	T	0.55737	0.1939	N	0.02158	-0.66	0.20703	N	0.999868	P	0.37441	0.595	B	0.29077	0.098	T	0.62746	-0.6789	10	0.02654	T	1	.	3.7803	0.08677	0.1759:0.4743:0.0:0.3498	.	356	O76014	KRT37_HUMAN	S	356	ENSP00000225550:G356S	ENSP00000225550:G356S	G	-	1	0	KRT37	36831320	0.000000	0.05858	0.101000	0.21167	0.163000	0.22366	-3.095000	0.00607	0.388000	0.25054	0.655000	0.94253	GGC		0.557	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39577794	C	T	39577794	3	4	59	1	0	0	0	0	1	0	0	0	8495	652	23	1	291	1	KRT37	17	39577794	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	2217008	39577794	41617416	60	7871										
GMIP	51291	broad.mit.edu	37	chr19	19745480	19745480	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gccagagagatgaaggcgtcGtagaggtggaaggggatcac	18	6	1	4	rs367883715		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:19745480G>A	ENST00000203556.4	-	18	2057	c.1920C>T	c.(1918-1920)taC>taT	p.Y640Y	GMIP_ENST00000586269.1_Intron|GMIP_ENST00000587238.1_Silent_p.Y614Y|GMIP_ENST00000445806.2_Silent_p.Y611Y	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	640	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)	p.Y640Y(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TGAAGGCGTCGTAGAGGTGGA	0.672													G|||	1	0.000199681	0	0	5008	,	,		18158	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	132	135	134		1920	3.5	1	19		134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GMIP	NM_016573.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		640/971	19745480	1,13005	2203	4300	6503	19606480	SO:0001819	synonymous_variant	51291			AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.1920C>T	19.37:g.19745480G>A			19606480	A0AVN9|B7ZLZ0	Silent	SNP	ENST00000203556.4	37	CCDS12408.1																																																																																				0.672	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		A	19745480	G	A	19745480	2	1	59	1	0	0	0	0	0	0	0	1	6511	1140	40	1		1	GMIP	19	19745480	Silent	SNP	G	TCGA-AG-4008-01A-01W-1073-09		19745480	39383503	61	7872										
ZNF492	57615	broad.mit.edu	37	chr19	22847996	22847996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	agaaactctacaaacctgaaAgttgtaacaatgcttgtgac	7	8	1	3			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:22847996A>G	ENST00000456783.2	+	4	1769	c.1525A>G	c.(1525-1527)Agt>Ggt	p.S509G	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S509G(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				CAAACCTGAAAGTTGTAACAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	19											13	14	14					19																	22847996		1810	4057	5867	22639836	SO:0001583	missense	57615			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1525A>G	19.37:g.22847996A>G	ENSP00000413660:p.Ser509Gly		22639836	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	4.917	0.170329	0.09339	.	.	ENSG00000229676	ENST00000456783	T	0.07800	3.16	1.03	-1.4	0.08968	.	.	.	.	.	T	0.04227	0.0117	N	0.12887	0.27	0.09310	N	1	B	0.22480	0.07	B	0.22753	0.041	T	0.40421	-0.9564	9	0.62326	D	0.03	.	3.7962	0.08740	0.3597:0.0:0.6403:0.0	.	509	Q9P255	ZN492_HUMAN	G	509	ENSP00000413660:S509G	ENSP00000413660:S509G	S	+	1	0	ZNF492	22639836	0.000000	0.05858	0.045000	0.18777	0.406000	0.30931	-1.059000	0.03479	-0.373000	0.07979	0.128000	0.15822	AGT		0.338	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		G	22847996	A	G	22847996	3	3	59	1	0	0	0	0	1	0	0	0	17982	72	3	4	1535	4	ZNF492	19	22847996	Missense_Mutation	SNP	A	TCGA-AG-4008-01A-01W-1073-09	3102516	22847996	36280987	62	7873										
ZNF91	7644	broad.mit.edu	37	chr19	23544847	23544847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tccagtatgaattctcttatGtttagcaagggttgaagaat	9	5	1	3			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:23544847G>A	ENST00000300619.7	-	4	1139	c.934C>T	c.(934-936)Cat>Tat	p.H312Y	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.H280Y	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	312					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.H312Y(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ATTCTCTTATGTTTAGCAAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	75	73					19																	23544847		2157	4284	6441	23336687	SO:0001583	missense	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.934C>T	19.37:g.23544847G>A	ENSP00000300619:p.His312Tyr		23336687	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.628819	0.28978	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	D;D	0.86769	-2.17;-2.17	1.97	1.97	0.26223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93746	0.8001	H	0.97918	4.105	0.18873	N	0.999988	P;D	0.58970	0.71;0.984	B;P	0.52267	0.3;0.694	D	0.86791	0.1985	9	0.87932	D	0	.	10.9757	0.47465	0.0:0.0:1.0:0.0	.	280;312	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	312;280	ENSP00000300619:H312Y;ENSP00000380272:H280Y	ENSP00000300619:H312Y	H	-	1	0	ZNF91	23336687	1.000000	0.71417	0.001000	0.08648	0.005000	0.04900	6.514000	0.73746	1.100000	0.41517	0.162000	0.16502	CAT		0.393	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23544847	G	A	23544847	3	1	59	1	0	0	0	0	1	0	0	0	18239	1377	48	3	2645	3	ZNF91	19	23544847	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	696851	23544847	35584136	63	7874										
ARHGAP33	115703	broad.mit.edu	37	chr19	36275939	36275939	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gctggaggaagcccaggcacGcacccagggccggctgggga	18	13	0	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:36275939G>A	ENST00000007510.4	+	17	1796	c.1652G>A	c.(1651-1653)cGc>cAc	p.R551H	ARHGAP33_ENST00000378944.5_Missense_Mutation_p.R415H|ARHGAP33_ENST00000314737.5_Missense_Mutation_p.R551H			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	551					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)	p.R551H(1)		endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GCCCAGGCACGCACCCAGGGC	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	19											4	6	5					19																	36275939		2071	4083	6154	40967779	SO:0001583	missense	115703			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1652G>A	19.37:g.36275939G>A	ENSP00000007510:p.Arg551His		40967779	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	37		.	.	.	.	.	.	.	.	.	.	G	15.35	2.806571	0.50421	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.13307	2.85;2.6;2.94	4.41	3.34	0.38264	.	0.000000	0.64402	D	0.000003	T	0.30448	0.0765	L	0.54323	1.7	0.30718	N	0.748517	D;D;D	0.89917	1.0;1.0;0.996	D;D;P	0.74348	0.972;0.983;0.73	T	0.16630	-1.0396	10	0.59425	D	0.04	.	13.3979	0.60865	0.0:0.1593:0.8407:0.0	.	551;415;551	O14559;O14559-10;O14559-11	RHG33_HUMAN;.;.	H	551;551;415	ENSP00000007510:R551H;ENSP00000320038:R551H;ENSP00000368227:R415H	ENSP00000007510:R551H	R	+	2	0	ARHGAP33	40967779	0.994000	0.37717	0.676000	0.29932	0.169000	0.22640	7.310000	0.78947	1.059000	0.40554	0.305000	0.20034	CGC		0.721	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		A	36275939	G	A	36275939	3	1	59	1	0	0	0	0	1	0	0	0	882	1087	38	1	1718	1	ARHGAP33	19	36275939	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	12731092	36275939	22853044	64	7875										
RSPH6A	81492	broad.mit.edu	37	chr19	46299141	46299141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgggcctcagtcatctgtctCctcgccctcctcctcctcct	6	20	4	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:46299141C>T	ENST00000221538.3	-	6	2282	c.2140G>A	c.(2140-2142)Gag>Aag	p.E714K	RSPH6A_ENST00000600188.1_Missense_Mutation_p.E450K|RSPH6A_ENST00000597055.1_3'UTR	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	714	Glu-rich.					intracellular (GO:0005622)		p.E714K(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						TCATCTGTctcctcgccctcc	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	74	73					19																	46299141		2202	4300	6502	50990981	SO:0001583	missense	81492			AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.2140G>A	19.37:g.46299141C>T	ENSP00000221538:p.Glu714Lys		50990981	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	c	14.91	2.675247	0.47781	.	.	ENSG00000104941	ENST00000221538	T	0.16897	2.31	4.16	4.16	0.48862	.	0.239640	0.40554	N	0.001077	T	0.15998	0.0385	L	0.43923	1.385	0.35045	D	0.76007	B	0.29432	0.244	B	0.21917	0.037	T	0.22208	-1.0223	10	0.87932	D	0	-13.0601	14.4001	0.67037	0.0:1.0:0.0:0.0	.	714	Q9H0K4	RSH6A_HUMAN	K	714	ENSP00000221538:E714K	ENSP00000221538:E714K	E	-	1	0	RSPH6A	50990981	1.000000	0.71417	0.943000	0.38184	0.052000	0.14988	4.180000	0.58296	2.335000	0.79485	0.551000	0.68910	GAG		0.557	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			T	46299141	C	T	46299141	3	4	59	1	0	0	0	0	1	0	0	0	13744	864	30	3	17	3	RSPH6A	19	46299141	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	10023202	46299141	12829842	65	7876										
CACNG7	59284	broad.mit.edu	37	chr19	54418696	54418696	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ccttcgtcatcagcaacatcGgccacatccgcccgcagagg	9	17	2	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr19:54418696G>T	ENST00000391767.1	+	4	573	c.361G>T	c.(361-363)Ggc>Tgc	p.G121C	CACNG7_ENST00000468076.1_3'UTR|CACNG7_ENST00000222212.2_Missense_Mutation_p.G121C|CACNG7_ENST00000391766.1_Missense_Mutation_p.G121C			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	121					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.G121C(1)		NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		CAGCAACATCGGCCACATCCG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											114	98	104					19																	54418696		2203	4300	6503	59110508	SO:0001583	missense	59284			AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.361G>T	19.37:g.54418696G>T	ENSP00000375647:p.Gly121Cys		59110508	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111576	0.77210	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.91295	-2.82;-2.82;-2.82	3.77	3.77	0.43336	.	0.000000	0.85682	D	0.000000	D	0.94719	0.8296	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.94598	0.7793	10	0.52906	T	0.07	-29.004	13.9093	0.63857	0.0:0.0:1.0:0.0	.	121	P62955	CCG7_HUMAN	C	121	ENSP00000375647:G121C;ENSP00000222212:G121C;ENSP00000375646:G121C	ENSP00000222212:G121C	G	+	1	0	CACNG7	59110508	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.081000	0.94049	2.381000	0.81170	0.563000	0.77884	GGC		0.597	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			T	54418696	G	T	54418696	3	4	59	1	0	0	0	0	1	0	0	0	2568	1116	39	2	371	2	CACNG7	19	54418696	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	8119555	54418696	4710287	66	7877										
PCIF1	63935	broad.mit.edu	37	chr20	44569123	44569123	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ccctccaccagtcggaccctTtggggctgaatgcgacccca	10	17	0	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr20:44569123T>A	ENST00000372409.3	+	5	623	c.259T>A	c.(259-261)Ttg>Atg	p.L87M		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	87					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.L87M(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						GTCGGACCCTTTGGGGCTGAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	20											24	20	21					20																	44569123		2203	4300	6503	44002530	SO:0001583	missense	63935			AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.259T>A	20.37:g.44569123T>A	ENSP00000361486:p.Leu87Met		44002530	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.418012	0.62622	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.02	3.89	0.44902	.	0.000000	0.64402	D	0.000001	T	0.71728	0.3374	M	0.77103	2.36	0.49389	D	0.999786	D	0.89917	1.0	D	0.91635	0.999	T	0.71656	-0.4527	9	0.66056	D	0.02	-13.6608	6.3465	0.21353	0.0:0.2003:0.0:0.7997	.	87	Q9H4Z3	PCIF1_HUMAN	M	87	.	ENSP00000361486:L87M	L	+	1	2	PCIF1	44002530	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.499000	0.35671	0.897000	0.36392	0.482000	0.46254	TTG		0.627	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		A	44569123	T	A	44569123	3	1	59	1	0	0	0	0	1	0	0	0	11611	1838	64	5	269	5	PCIF1	20	44569123	Missense_Mutation	SNP	T	TCGA-AG-4008-01A-01W-1073-09		44569123	18456397	67	7878										
CDH22	64405	broad.mit.edu	37	chr20	44803566	44803566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	cgccgaagtcgtagaggctcCgcagcgccgacatgtcgtag	14	13	0	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr20:44803566C>A	ENST00000372262.3	-	11	2466	c.2066G>T	c.(2065-2067)cGg>cTg	p.R689L	CDH22_ENST00000537909.1_Missense_Mutation_p.R689L	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	689					brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R689L(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				GTAGAGGCTCCGCAGCGCCGA	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	20											19	20	19					20																	44803566		2069	4185	6254	44236973	SO:0001583	missense	64405			AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.2066G>T	20.37:g.44803566C>A	ENSP00000361336:p.Arg689Leu		44236973	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916295	0.92249	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.78924	-1.22;-1.22	3.89	3.89	0.44902	Cadherin, cytoplasmic domain (1);	0.000000	0.64402	D	0.000001	D	0.88529	0.6461	M	0.84433	2.695	0.46774	D	0.999193	D	0.89917	1.0	D	0.91635	0.999	D	0.90591	0.4537	10	0.66056	D	0.02	.	15.0128	0.71562	0.0:1.0:0.0:0.0	.	689	Q9UJ99	CAD22_HUMAN	L	689	ENSP00000361336:R689L;ENSP00000437790:R689L	ENSP00000361336:R689L	R	-	2	0	CDH22	44236973	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	2.965000	0.49200	1.999000	0.58509	0.563000	0.77884	CGG		0.721	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		A	44803566	C	A	44803566	3	1	59	1	0	0	0	0	1	0	0	0	3113	652	23	2	424	2	CDH22	20	44803566	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	234443	44803566	18221954	68	7879										
SLC13A3	64849	broad.mit.edu	37	chr20	45242331	45242331	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctccgtgcaccagtacaccgCcatgagcaggatgacaaaca	9	14	0	2			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr20:45242331C>A	ENST00000279027.4	-	2	163	c.145G>T	c.(145-147)Gcg>Tcg	p.A49S	SLC13A3_ENST00000372121.1_Missense_Mutation_p.A49S|SLC13A3_ENST00000495082.1_Missense_Mutation_p.A2S|SLC13A3_ENST00000290317.5_Missense_Mutation_p.A2S|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000396360.1_Missense_Mutation_p.A2S|SLC13A3_ENST00000413164.2_Missense_Mutation_p.A49S|SLC13A3_ENST00000339636.3_Missense_Mutation_p.A49S|SLC13A3_ENST00000417157.2_Missense_Mutation_p.A2S|SLC13A3_ENST00000472148.1_Missense_Mutation_p.A2S	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	49					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.A49S(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAGTACACCGCCATGAGCAGG	0.642																																																2	Substitution - Missense(2)	large_intestine(2)	20											46	36	39					20																	45242331		2203	4300	6503	44675738	SO:0001583	missense	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.145G>T	20.37:g.45242331C>A	ENSP00000279027:p.Ala49Ser		44675738	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	C	35	5.492854	0.96339	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121;ENST00000417157;ENST00000339636	T;T;T;T;T;T;T;T;T;T;T	0.03242	4.0;4.0;4.0;4.0;4.0;4.0;4.0;4.0;4.0;4.0;4.0	5.67	5.67	0.87782	.	0.103441	0.64402	D	0.000003	T	0.21186	0.0510	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;1.0	T	0.00074	-1.2124	10	0.87932	D	0	-18.8515	19.7691	0.96356	0.0:1.0:0.0:0.0	.	49;2;2;2;49	B4DIR8;Q8WWT9-3;F6WI18;C9J4A3;Q8WWT9	.;.;.;.;S13A3_HUMAN	S	2;2;49;2;49;2;2;12;49;2;49	ENSP00000290317:A2S;ENSP00000379648:A2S;ENSP00000279027:A49S;ENSP00000420177:A2S;ENSP00000415852:A49S;ENSP00000419621:A2S;ENSP00000417784:A2S;ENSP00000395095:A12S;ENSP00000361193:A49S;ENSP00000397955:A2S;ENSP00000344912:A49S	ENSP00000279027:A49S	A	-	1	0	SLC13A3	44675738	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.445000	0.80570	2.689000	0.91719	0.462000	0.41574	GCG		0.642	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45242331	C	A	45242331	3	1	59	1	0	0	0	0	1	0	0	0	14430	739	26	2	1711	2	SLC13A3	20	45242331	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	438765	45242331	17783189	69	7880										
KCNB1	3745	broad.mit.edu	37	chr20	47991335	47991335	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gggcccttgaagaacttccaCttcttgggcgaggagaggaa	14	9	1	3			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr20:47991335C>T	ENST00000371741.4	-	2	928	c.762G>A	c.(760-762)aaG>aaA	p.K254K		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	254					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)	p.K254K(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	AGAACTTCCACTTCTTGGGCG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	20											80	71	74					20																	47991335		2203	4300	6503	47424742	SO:0001819	synonymous_variant	3745			AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.762G>A	20.37:g.47991335C>T			47424742	Q14193	Silent	SNP	ENST00000371741.4	37	CCDS13418.1																																																																																				0.557	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		T	47991335	C	T	47991335	2	4	59	1	0	0	0	0	0	0	0	1	8033	564	20	3		3	KCNB1	20	47991335	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09	2749004	47991335	15034185	70	7881										
ZNF831	128611	broad.mit.edu	37	chr20	57767575	57767575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ccaccgtggaatgtgtccccGtcaccaggagcaactcgctg	11	15	1	0	rs546116387		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr20:57767575G>A	ENST00000371030.2	+	1	1501	c.1501G>A	c.(1501-1503)Gtc>Atc	p.V501I		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	501							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.V501I(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					ATGTGTCCCCGTCACCAGGAG	0.687													.|||	1	0.000199681	8e-04	0	5008	,	,		14593	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											19	23	21					20																	57767575		1969	4128	6097	57200970	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1501G>A	20.37:g.57767575G>A	ENSP00000360069:p.Val501Ile		57200970	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	7.684	0.689654	0.14973	.	.	ENSG00000124203	ENST00000371030	T	0.10960	2.82	5.21	4.26	0.50523	.	.	.	.	.	T	0.06234	0.0161	N	0.05078	-0.115	0.18873	N	0.999986	D	0.56968	0.978	B	0.44085	0.44	T	0.24835	-1.0149	9	0.42905	T	0.14	-16.1228	8.1202	0.30967	0.0801:0.0:0.7642:0.1558	.	501	Q5JPB2	ZN831_HUMAN	I	501	ENSP00000360069:V501I	ENSP00000360069:V501I	V	+	1	0	ZNF831	57200970	0.059000	0.20769	0.823000	0.32752	0.571000	0.35966	0.315000	0.19451	1.186000	0.42985	0.655000	0.94253	GTC		0.687	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767575	G	A	57767575	3	1	59	1	0	0	0	0	1	0	0	0	18224	1145	40	1	1503	1	ZNF831	20	57767575	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	9776240	57767575	5257945	71	7882										
NCAM2	4685	broad.mit.edu	37	chr21	22696712	22696712	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ctctccttcagtgccgccagCaatctcaatgcctcagaaat	6	15	4	1			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr21:22696712C>A	ENST00000400546.1	+	6	878	c.629C>A	c.(628-630)gCa>gAa	p.A210E	NCAM2_ENST00000535285.1_Missense_Mutation_p.A235E|NCAM2_ENST00000284894.7_Missense_Mutation_p.A68E	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	210	Ig-like C2-type 3.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A210E(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GTGCCGCCAGCAATCTCAATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	21											120	118	118					21																	22696712		1943	4132	6075	21618583	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.629C>A	21.37:g.22696712C>A	ENSP00000383392:p.Ala210Glu		21618583	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276875	0.40294	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.34667	1.35;1.35;1.35	5.3	3.5	0.40072	Immunoglobulin-like (1);	0.270198	0.42294	D	0.000731	T	0.13670	0.0331	N	0.02842	-0.48	0.39279	D	0.964523	B;B;B	0.15473	0.002;0.013;0.007	B;B;B	0.08055	0.002;0.003;0.002	T	0.06972	-1.0797	10	0.28530	T	0.3	-8.9064	5.7357	0.18065	0.1554:0.6809:0.0:0.1637	.	235;68;210	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	E	210;68;235	ENSP00000383392:A210E;ENSP00000284894:A68E;ENSP00000441887:A235E	ENSP00000284894:A68E	A	+	2	0	NCAM2	21618583	0.463000	0.25799	0.997000	0.53966	0.990000	0.78478	0.551000	0.23361	0.638000	0.30545	0.591000	0.81541	GCA		0.428	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		A	22696712	C	A	22696712	3	1	59	1	0	0	0	0	1	0	0	0	10234	710	25	2	651	2	NCAM2	21	22696712	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		22696712	25433183	72	7883										
GGTLC2	91227	broad.mit.edu	37	chr22	22989502	22989502	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	acgatcatggtgggccaggaCggccaggtccggatggtggt	18	9	1	0	rs149680064		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr22:22989502C>T	ENST00000480559.1	+	3	354	c.354C>T	c.(352-354)gaC>gaT	p.D118D	GGTLC2_ENST00000448514.1_Silent_p.D118D|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	118					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)	p.D118D(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		TGGGCCAGGACGGCCAGGTCC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	22											55	65	61					22																	22989502		2203	4296	6499	21319502	SO:0001819	synonymous_variant	91227			X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"Gamma-glutamyltransferases"	18596	protein-coding gene	gene with protein product		612339	"gamma-glutamyltransferase-like 4"	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.354C>T	22.37:g.22989502C>T			21319502	A1A516|A2VCM9|Q5NV76|Q6ISH0	Silent	SNP	ENST00000480559.1	37	CCDS13802.2																																																																																				0.647	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127		T	22989502	C	T	22989502	2	4	59	1	0	0	0	0	0	0	0	1	6386	535	19	1		1	GGTLC2	22	22989502	Silent	SNP	C	TCGA-AG-4008-01A-01W-1073-09		22989502	28315064	73	7884										
SEZ6L	23544	broad.mit.edu	37	chr22	26709847	26709847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	ccacgtgggagaagagaaacGgatcttcttagatatccagt	11	8	2	3	rs150114413		TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chr22:26709847G>A	ENST00000248933.6	+	9	2089	c.1994G>A	c.(1993-1995)cGg>cAg	p.R665Q	SEZ6L_ENST00000360929.3_Missense_Mutation_p.R665Q|SEZ6L_ENST00000343706.4_Missense_Mutation_p.R665Q|SEZ6L_ENST00000402979.1_Missense_Mutation_p.R438Q|SEZ6L_ENST00000404234.3_Missense_Mutation_p.R665Q|SEZ6L_ENST00000403121.1_Missense_Mutation_p.R438Q|SEZ6L_ENST00000529632.2_Missense_Mutation_p.R665Q			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	665	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.R665Q(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GAAGAGAAACGGATCTTCTTA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	22						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	140	133	136		1994,1994,1994,1994,1994,1994	4.7	1	22	dbSNP_134	136	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	43,43,43,43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	665/1024,665/1014,665/1012,665/950,665/949,665/1025	26709847	1,13005	2203	4300	6503	25039847	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1994G>A	22.37:g.26709847G>A	ENSP00000248933:p.Arg665Gln		25039847	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	35	5.432254	0.96150	2.27E-4	0.0	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27	4.65	4.65	0.58169	CUB (5);	0.000000	0.51477	D	0.000089	T	0.39911	0.1096	M	0.70595	2.14	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.983;0.999;0.983;1.0;0.999;0.999;0.999	P;D;P;D;D;P;P	0.63597	0.753;0.915;0.77;0.916;0.916;0.886;0.886	T	0.31110	-0.9955	10	0.66056	D	0.02	.	16.7223	0.85413	0.0:0.0:1.0:0.0	.	665;665;438;665;665;665;665	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	Q	665;665;665;665;665;438;438	ENSP00000384772:R665Q;ENSP00000437037:R665Q;ENSP00000354185:R665Q;ENSP00000248933:R665Q;ENSP00000342661:R665Q;ENSP00000384838:R438Q;ENSP00000384733:R438Q	ENSP00000248933:R665Q	R	+	2	0	SEZ6L	25039847	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.085000	0.94083	2.422000	0.82143	0.561000	0.74099	CGG		0.463	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26709847	G	A	26709847	3	1	59	1	0	0	0	0	1	0	0	0	14180	1116	39	1	2028	1	SEZ6L	22	26709847	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	3720345	26709847	24594719	74	7885										
NLGN4X	57502	broad.mit.edu	37	chrX	5821698	5821698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gtcgccgtcgatcaccggccCgaaggctatgtggtaggtgg	16	11	1	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chrX:5821698C>T	ENST00000381095.3	-	5	1648	c.1021G>A	c.(1021-1023)Ggg>Agg	p.G341R	NLGN4X_ENST00000381092.1_Missense_Mutation_p.G341R|NLGN4X_ENST00000381093.2_Missense_Mutation_p.G361R|NLGN4X_ENST00000275857.6_Missense_Mutation_p.G341R|NLGN4X_ENST00000538097.1_Missense_Mutation_p.G341R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	341					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.G341R(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						ATCACCGGCCCGAAGGCTATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	X											183	126	146					X																	5821698		2203	4300	6503	5831698	SO:0001583	missense	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1021G>A	X.37:g.5821698C>T	ENSP00000370485:p.Gly341Arg		5831698	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	37	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603652	0.46423	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	3.93	3.93	0.45458	Carboxylesterase, type B (1);	.	.	.	.	T	0.73497	0.3594	M	0.72576	2.205	0.80722	D	1	D;D;D	0.89917	0.993;1.0;1.0	P;D;D	0.83275	0.657;0.996;0.945	T	0.75563	-0.3274	8	.	.	.	.	14.4946	0.67678	0.0:1.0:0.0:0.0	.	398;341;361	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	R	341;361;341;341;341	ENSP00000370485:G341R;ENSP00000370483:G361R;ENSP00000275857:G341R;ENSP00000370482:G341R;ENSP00000439203:G341R	.	G	-	1	0	NLGN4X	5831698	1.000000	0.71417	0.273000	0.24645	0.054000	0.15201	6.722000	0.74735	1.579000	0.49836	0.600000	0.82982	GGG		0.587	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		T	5821698	C	T	5821698	3	4	59	1	0	0	0	0	1	0	0	0	10495	652	23	1	1437	1	NLGN4X	23	5821698	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09		5821698	149448862	75	7886										
MAGEB6	158809	broad.mit.edu	37	chrX	26212565	26212565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	tgtaaagaagaaggcgtgcaCgttggcgcaattcctgcaga	13	8	0	3			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chrX:26212565C>T	ENST00000379034.1	+	2	751	c.602C>T	c.(601-603)aCg>aTg	p.T201M		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	201	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.T201M(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						AAGGCGTGCACGTTGGCGCAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											83	70	75					X																	26212565		2202	4300	6502	26122486	SO:0001583	missense	158809			AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"cancer/testis antigen family 3, member 4"	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.602C>T	X.37:g.26212565C>T	ENSP00000368320:p.Thr201Met		26122486	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	c	0.001	-4.099939	0.00002	.	.	ENSG00000176746	ENST00000379034	T	0.01804	4.63	2.88	-5.76	0.02376	.	0.624921	0.14149	N	0.338154	T	0.00496	0.0016	N	0.00252	-1.77	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.52034	-0.8629	10	0.38643	T	0.18	.	3.784	0.08692	0.6019:0.174:0.0996:0.1246	.	201	Q8N7X4	MAGB6_HUMAN	M	201	ENSP00000368320:T201M	ENSP00000368320:T201M	T	+	2	0	MAGEB6	26122486	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.470000	0.00065	-5.416000	0.00015	-4.040000	0.00012	ACG		0.483	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523		T	26212565	C	T	26212565	3	4	59	1	0	0	0	0	1	0	0	0	9209	536	19	1	604	1	MAGEB6	23	26212565	Missense_Mutation	SNP	C	TCGA-AG-4008-01A-01W-1073-09	20390867	26212565	129057995	76	7887										
ITIH5L	347365	broad.mit.edu	37	chrX	54777771	54777771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.025974025974026	2	1	0.337910072319463	7.94088669950739	0.172627971728422	1	1	0	gagtctggtccttgtggcccGgccttggtggtgcgccaagc	16	12	1	0			TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4008-01A-01W-1073-09	TCGA-AG-4008-10A-01W-1073-09	g.chrX:54777771G>A	ENST00000218436.6	-	12	3424	c.3395C>T	c.(3394-3396)cCg>cTg	p.P1132L		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1132					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P1132L(1)									CTTGTGGCCCGGCCTTGGTGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	X											59	50	53					X																	54777771		2203	4300	6503	54794496	SO:0001583	missense	347365			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3395C>T	X.37:g.54777771G>A	ENSP00000218436:p.Pro1132Leu		54794496	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663062	0.47572	.	.	ENSG00000102313	ENST00000218436	T	0.11604	2.76	3.58	1.7	0.24286	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	1.594190	0.03907	U	0.281200	T	0.09423	0.0232	L	0.41492	1.28	0.29785	N	0.833698	P	0.49090	0.919	B	0.38296	0.27	T	0.25082	-1.0142	10	0.59425	D	0.04	.	3.4161	0.07376	0.2301:0.0:0.5581:0.2118	.	1132	Q6UXX5	ITH5L_HUMAN	L	1132	ENSP00000218436:P1132L	ENSP00000218436:P1132L	P	-	2	0	ITIH5L	54794496	0.000000	0.05858	0.423000	0.26634	0.810000	0.45777	0.559000	0.23485	0.351000	0.24027	0.287000	0.19450	CCG		0.572	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54777771	G	A	54777771	3	1	59	1	0	0	0	0	1	0	0	0	7929	1116	39	1	554	1	ITIH5L	23	54777771	Missense_Mutation	SNP	G	TCGA-AG-4008-01A-01W-1073-09	28565206	54777771	100492789	77	7888										
NUDC	10726	broad.mit.edu	37	chr1	27272144	27272144	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gtccatggggctgccaacttCagacgaacagaagaaacagg	12	10	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:27272144C>T	ENST00000321265.5	+	8	1034	c.911C>T	c.(910-912)tCa>tTa	p.S304L	NUDC_ENST00000484772.1_3'UTR	NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	304					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)		p.S304L(1)		cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		CTGCCAACTTCAGACGAACAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	97	96					1																	27272144		2203	4300	6503	27144731	SO:0001583	missense	10726				CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"nuclear distribution gene C homolog (A. nidulans)", "nuclear distribution C homolog (A. nidulans)"				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.911C>T	1.37:g.27272144C>T	ENSP00000319664:p.Ser304Leu		27144731	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	37	CCDS292.1	.	.	.	.	.	.	.	.	.	.	C	34	5.343841	0.95807	.	.	ENSG00000090273	ENST00000321265	T	0.72051	-0.62	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.89901	0.6849	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93296	0.6672	10	0.87932	D	0	1.5853	18.8328	0.92148	0.0:1.0:0.0:0.0	.	304	Q9Y266	NUDC_HUMAN	L	304	ENSP00000319664:S304L	ENSP00000319664:S304L	S	+	2	0	NUDC	27144731	1.000000	0.71417	0.955000	0.39395	0.927000	0.56198	7.818000	0.86416	2.447000	0.82792	0.655000	0.94253	TCA		0.552	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			T	27272144	C	T	27272144	3	4	60	1	0	0	0	0	1	0	0	0	10752	838	29	3	941	3	NUDC	1	27272144	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		27272144	221978477	1	7889										
ZC3H12A	80149	broad.mit.edu	37	chr1	37947405	37947405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggaagcgcttcatcgaggagCggctgctcatgtactccttc	12	12	2	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:37947405C>T	ENST00000373087.6	+	4	903	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A									p.R263W(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CATCGAGGAGCGGCTGCTCAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	105	109					1																	37947405		2203	4300	6503	37719992	SO:0001583	missense	80149				CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.787C>T	1.37:g.37947405C>T	ENSP00000362179:p.Arg263Trp		37719992		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247399	0.80024	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.53640	0.61	5.8	2.71	0.32032	Ribonuclease Zc3h12a-like (1);	0.000000	0.85682	D	0.000000	T	0.76793	0.4037	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84614	0.0680	10	0.87932	D	0	-36.0734	15.0422	0.71799	0.369:0.631:0.0:0.0	.	263	Q5D1E8	ZC12A_HUMAN	W	263	ENSP00000362179:R263W	ENSP00000362174:R263W	R	+	1	2	ZC3H12A	37719992	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.709000	0.25734	0.730000	0.32425	0.655000	0.94253	CGG		0.587	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37947405	C	T	37947405	3	4	60	1	0	0	0	0	1	0	0	0	17600	759	27	1	797	1	ZC3H12A	1	37947405	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	10675261	37947405	211303216	2	7890										
LEPR	3953	broad.mit.edu	37	chr1	66058425	66058425	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	attgcagtgttcatgaatgtTgtgaatgtcttgtgcctgtg	12	5	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:66058425T>G	ENST00000349533.6	+	6	765	c.580T>G	c.(580-582)Tgt>Ggt	p.C194G	LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.C194G|LEPR_ENST00000371060.3_Missense_Mutation_p.C194G|LEPR_ENST00000344610.8_Missense_Mutation_p.C194G|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371058.1_Missense_Mutation_p.C194G	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.C194G(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TCATGAATGTTGTGAATGTCT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	1											152	137	142					1																	66058425		2203	4300	6503	65831013	SO:0001583	missense	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.580T>G	1.37:g.66058425T>G	ENSP00000330393:p.Cys194Gly		65831013	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.796356	0.50208	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.60040	0.34;0.22;0.35;0.31;0.34	5.68	5.68	0.88126	.	0.252890	0.48286	D	0.000193	T	0.69223	0.3087	M	0.74258	2.255	0.80722	D	1	D;D;D	0.69078	0.991;0.995;0.997	P;D;D	0.67382	0.894;0.951;0.933	T	0.73736	-0.3889	10	0.62326	D	0.03	-7.4788	15.5869	0.76491	0.0:0.0:0.0:1.0	.	194;194;194	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	G	194	ENSP00000340884:C194G;ENSP00000330393:C194G;ENSP00000360099:C194G;ENSP00000360098:C194G;ENSP00000360097:C194G	ENSP00000340884:C194G	C	+	1	0	LEPR	65831013	0.999000	0.42202	0.926000	0.36857	0.156000	0.22039	3.816000	0.55658	2.166000	0.68216	0.528000	0.53228	TGT		0.408	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		G	66058425	T	G	66058425	3	3	60	1	0	0	0	0	1	0	0	0	8750	1812	63	4	594	4	LEPR	1	66058425	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	28111020	66058425	183192196	3	7891										
HHLA3	11147	broad.mit.edu	37	chr1	70832138	70832138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctgtgataggtcttgtcaacGgaaaggggtccctatccaga	12	9	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:70832138G>A	ENST00000359875.5	+	2	409	c.269G>A	c.(268-270)cGg>cAg	p.R90Q	HHLA3_ENST00000370940.5_Missense_Mutation_p.G58R|HHLA3_ENST00000361764.4_Silent_p.T56T|HHLA3_ENST00000531950.1_Missense_Mutation_p.R90Q|HHLA3_ENST00000432224.1_Missense_Mutation_p.G91R	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	90								p.R90Q(1)		large_intestine(3)|lung(1)	4						TCTtgtcaacggaaaggggtc	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											17	21	20					1																	70832138		2182	4283	6465	70604726	SO:0001583	missense	11147			AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.269G>A	1.37:g.70832138G>A	ENSP00000352938:p.Arg90Gln		70604726	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Missense_Mutation	SNP	ENST00000359875.5	37	CCDS30753.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.029|0.029	-1.350342|-1.350342	0.01256|0.01256	.|.	.|.	ENSG00000197568|ENSG00000197568	ENST00000370940;ENST00000432224|ENST00000359875;ENST00000531950	.|.	.|.	.|.	0.137|0.137	-0.274|-0.274	0.12910|0.12910	.|.	.|.	.|.	.|.	.|.	T|T	0.05090|0.05090	0.0136|0.0136	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B	0.30542|0.12630	0.284|0.006	B|B	0.12156|0.01281	0.007|0.0	T|T	0.41875|0.41875	-0.9484|-0.9484	6|6	0.87932|0.17369	D|T	0|0.5	.|.	.|.	.|.	.|.	.|.	58|90	Q9XRX5-2|Q9XRX5	.|HHLA3_HUMAN	R|Q	58;91|90	.|.	ENSP00000359978:G58R|ENSP00000352938:R90Q	G|R	+|+	1|2	0|0	HHLA3|HHLA3	70604726|70604726	0.001000|0.001000	0.12720|0.12720	0.049000|0.049000	0.19019|0.19019	0.059000|0.059000	0.15707|0.15707	-1.656000|-1.656000	0.01980|0.01980	-0.750000|-0.750000	0.04740|0.04740	-0.734000|-0.734000	0.03567|0.03567	GGA|CGG		0.338	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071		A	70832138	G	A	70832138	3	1	60	1	0	0	0	0	1	0	0	0	7117	1117	39	1	275	1	HHLA3	1	70832138	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	4773713	70832138	178418483	4	7892										
AMY2A	279	broad.mit.edu	37	chr1	104160213	104160213	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agcgatatttagctccgaagGgatttggaggggttcaggtg	16	5	1	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:104160213G>T	ENST00000414303.2	+	1	215	c.151G>T	c.(151-153)Gga>Tga	p.G51*		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	51					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)	p.G51*(1)		endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	AGCTCCGAAGGGATTTGGAGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											297	245	263					1																	104160213		2201	4279	6480	103961736	SO:0001587	stop_gained	279			BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"amylase, alpha 2A; pancreatic"	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.151G>T	1.37:g.104160213G>T	ENSP00000397582:p.Gly51*		103961736	B9EJG1|Q9UBH3	Nonsense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.38|15.38	2.815229|2.815229	0.50527|0.50527	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|.	.|.	.|.	3.22|3.22	3.22|3.22	0.36961|0.36961	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.61664|.	0.2365|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.70146|.	-0.4952|.	4|.	.|0.87932	.|D	.|0	.|.	14.5293|14.5293	0.67912|0.67912	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	49|51	.|.	.|ENSP00000377509:G51X	G|G	+|+	2|1	0|0	AMY2A|AMY2A	103961736|103961736	1.000000|1.000000	0.71417|0.71417	0.579000|0.579000	0.28588|0.28588	0.019000|0.019000	0.09904|0.09904	8.935000|8.935000	0.92923|0.92923	1.784000|1.784000	0.52394|0.52394	0.455000|0.455000	0.32223|0.32223	GGG|GGA		0.423	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699		T	104160213	G	T	104160213	4	4	60	1	0	0	0	0	0	1	0	0	594	1233	43	2	153	2	AMY2A	1	104160213	Nonsense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	33328075	104160213	145090408	5	7893										
TCHH	7062	broad.mit.edu	37	chr1	152081237	152081237	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttgttcctcctccaggaattTtctgtcacgctcttggcggt	9	12	3	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:152081237T>C	ENST00000368804.1	-	2	4455	c.4456A>G	c.(4456-4458)Aaa>Gaa	p.K1486E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1486	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.K1486E(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCAGGAATTTTCTGTCACGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											97	97	97					1																	152081237		1898	4107	6005	150347861	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4456A>G	1.37:g.152081237T>C	ENSP00000357794:p.Lys1486Glu		150347861	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	7.748	0.702679	0.15172	.	.	ENSG00000159450	ENST00000368804	T	0.06849	3.25	3.24	0.307	0.15811	.	.	.	.	.	T	0.01976	0.0062	M	0.68593	2.085	0.09310	N	1	P	0.34724	0.465	B	0.30646	0.118	T	0.46091	-0.9216	9	0.08179	T	0.78	.	5.1129	0.14819	0.1612:0.0:0.4932:0.3457	.	1486	Q07283	TRHY_HUMAN	E	1486	ENSP00000357794:K1486E	ENSP00000357794:K1486E	K	-	1	0	TCHH	150347861	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-2.949000	0.00679	-0.047000	0.13423	0.164000	0.16699	AAA		0.552	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152081237	T	C	152081237	3	2	60	1	0	0	0	0	1	0	0	0	15739	1850	64	4	1379	4	TCHH	1	152081237	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	47921024	152081237	97169384	6	7894										
FCRL5	83416	broad.mit.edu	37	chr1	157514324	157514324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agctggctctcagcactggaCgtgtaaatggctctagagag	13	9	2	1	rs140080936		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:157514324C>T	ENST00000361835.3	-	5	729	c.572G>A	c.(571-573)cGt>cAt	p.R191H	FCRL5_ENST00000368191.3_Missense_Mutation_p.R106H|FCRL5_ENST00000368189.3_Missense_Mutation_p.R191H|FCRL5_ENST00000356953.4_Missense_Mutation_p.R191H|FCRL5_ENST00000368190.3_Missense_Mutation_p.R191H	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	191	Ig-like C2-type 2.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.R191H(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CAGCACTGGACGTGTAAATGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	82	80	81		572,572	-5.3	0	1	dbSNP_134	81	4,8596	4.3+/-15.6	0,4,4296	yes	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	29,29	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	benign,benign	191/999,191/978	157514324	5,13001	2203	4300	6503	155780948	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.572G>A	1.37:g.157514324C>T	ENSP00000354691:p.Arg191His		155780948	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	5.974	0.363603	0.11296	2.27E-4	4.65E-4	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73	4.17	-5.26	0.02772	Immunoglobulin-like (1);	.	.	.	.	T	0.02688	0.0081	L	0.34521	1.04	0.09310	N	1	B;B;P;D;P	0.53619	0.441;0.194;0.709;0.961;0.709	B;B;B;B;B	0.43194	0.038;0.042;0.216;0.411;0.216	T	0.19844	-1.0293	9	0.38643	T	0.18	.	3.4039	0.07333	0.1918:0.1433:0.4962:0.1687	.	106;191;191;191;191	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;FCRL5_HUMAN	H	191;191;191;106;191	ENSP00000354691:R191H;ENSP00000349434:R191H;ENSP00000357173:R191H;ENSP00000357174:R106H;ENSP00000357172:R191H	ENSP00000349434:R191H	R	-	2	0	FCRL5	155780948	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.266000	0.02842	-0.919000	0.03803	0.467000	0.42956	CGT		0.537	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157514324	C	T	157514324	3	4	60	1	0	0	0	0	1	0	0	0	5817	536	19	1	2413	1	FCRL5	1	157514324	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	5433087	157514324	91736297	7	7895										
NAV1	89796	broad.mit.edu	37	chr1	201777611	201777611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tgaggaggaggagccagagaAgaaggaggtatcggagctgc	19	5	0	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr1:201777611A>G	ENST00000367296.4	+	19	4331	c.3911A>G	c.(3910-3912)aAg>aGg	p.K1304R	NAV1_ENST00000367300.3_Missense_Mutation_p.K1244R|MIR1231_ENST00000408101.1_RNA|NAV1_ENST00000367295.1_Missense_Mutation_p.K910R|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367302.1_Missense_Mutation_p.K1257R|NAV1_ENST00000367297.4_Missense_Mutation_p.K1296R|NAV1_ENST00000295624.6_Missense_Mutation_p.K1301R	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1304					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.K1301R(1)		breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						GAGCCAGAGAAGAAGGAGGTA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	60	60					1																	201777611		2203	4300	6503	200044234	SO:0001583	missense	89796			AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3911A>G	1.37:g.201777611A>G	ENSP00000356265:p.Lys1304Arg		200044234	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	a	15.18	2.758055	0.49468	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295	T;T;T;T;T;T	0.07114	3.23;3.22;3.22;3.22;3.23;3.22	5.53	4.4	0.53042	.	0.319150	0.33959	N	0.004388	T	0.06872	0.0175	N	0.22421	0.69	0.37557	D	0.918938	B;B	0.21147	0.019;0.052	B;B	0.18561	0.007;0.022	T	0.18178	-1.0345	10	0.66056	D	0.02	-24.0157	11.1622	0.48522	0.9265:0.0:0.0735:0.0	.	910;1301	Q8NEY1-5;Q8NEY1-3	.;.	R	1257;1304;1301;1296;1244;910	ENSP00000356271:K1257R;ENSP00000356265:K1304R;ENSP00000295624:K1301R;ENSP00000356266:K1296R;ENSP00000356269:K1244R;ENSP00000356264:K910R	ENSP00000295624:K1301R	K	+	2	0	NAV1	200044234	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.999000	0.70665	0.929000	0.37192	0.451000	0.29950	AAG		0.557	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		G	201777611	A	G	201777611	3	3	60	1	0	0	0	0	1	0	0	0	10213	72	3	4	4042	4	NAV1	1	201777611	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	44263287	201777611	47473010	8	7896										
NRXN1	9378	broad.mit.edu	37	chr2	50149357	50149357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cacttctgctgagcctggatAcggctctctgccgcctgctc	10	16	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:50149357A>G	ENST00000406316.2	-	22	5635	c.4159T>C	c.(4159-4161)Tat>Cat	p.Y1387H	NRXN1_ENST00000402717.3_Missense_Mutation_p.Y1409H|NRXN1_ENST00000342183.5_Missense_Mutation_p.Y352H|NRXN1_ENST00000401669.2_Missense_Mutation_p.Y1417H|NRXN1_ENST00000406859.3_Missense_Mutation_p.Y1387H|NRXN1_ENST00000405472.3_Missense_Mutation_p.Y1409H|NRXN1_ENST00000404971.1_Missense_Mutation_p.Y1457H|NRXN1_ENST00000401710.1_Missense_Mutation_p.Y405H	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1387					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.Y1458H(1)|p.Y1387H(1)|p.Y352H(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GAGCCTGGATACGGCTCTCTG	0.527																																																3	Substitution - Missense(3)	large_intestine(3)	2											49	42	45					2																	50149357		2203	4300	6503	50002861	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.4159T>C	2.37:g.50149357A>G	ENSP00000384311:p.Tyr1387His		50002861	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.75|12.75	2.030550|2.030550	0.35797|0.35797	.|.	.|.	ENSG00000179915|ENSG00000179915	ENST00000378262|ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.|T;T;T;T;T;T;T;T	.|0.71698	.|0.92;2.13;0.11;0.1;-0.59;-0.48;-0.18;-0.04	5.95|5.95	4.81|4.81	0.61882|0.61882	.|.	.|0.310755	.|0.20291	.|U	.|0.095252	T|T	0.69468|0.69468	0.3114|0.3114	L|L	0.44542|0.44542	1.39|1.39	0.26483|0.26483	N|N	0.975075|0.975075	.|B;D;P;P;P;P	.|0.54601	.|0.003;0.967;0.944;0.904;0.836;0.589	.|B;P;P;B;B;B	.|0.52066	.|0.003;0.689;0.492;0.243;0.285;0.179	T|T	0.62105|0.62105	-0.6924|-0.6924	5|10	.|0.37606	.|T	.|0.19	.|.	10.1757|10.1757	0.42937|0.42937	0.9255:0.0:0.0745:0.0|0.9255:0.0:0.0745:0.0	.|.	.|52;1457;352;1387;1406;49	.|B4DIT5;Q9ULB1-3;P58400;F8WB18;A7E294;Q5HYI0	.|.;.;NRX1B_HUMAN;.;.;.	A|H	53|352;306;405;1457;1387;1409;1417;1458;1409;1387	.|ENSP00000341184:Y352H;ENSP00000385580:Y405H;ENSP00000385142:Y1457H;ENSP00000384311:Y1387H;ENSP00000434015:Y1409H;ENSP00000385017:Y1417H;ENSP00000385434:Y1409H;ENSP00000385681:Y1387H	.|ENSP00000341184:Y352H	V|Y	-|-	2|1	0|0	NRXN1|NRXN1	50002861|50002861	1.000000|1.000000	0.71417|0.71417	0.918000|0.918000	0.36340|0.36340	0.806000|0.806000	0.45545|0.45545	4.863000|4.863000	0.62983|0.62983	2.272000|2.272000	0.75746|0.75746	0.460000|0.460000	0.39030|0.39030	GTA|TAT		0.527	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			G	50149357	A	G	50149357	3	3	60	1	0	0	0	0	1	0	0	0	10696	391	14	4	278	4	NRXN1	2	50149357	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09		50149357	193050016	9	7897										
SFXN5	94097	broad.mit.edu	37	chr2	73268005	73268005	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gttcattggtgacccccgggCgcagggtcccatgcttatag	13	12	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:73268005C>T	ENST00000272433.2	-	3	357	c.227G>A	c.(226-228)cGc>cAc	p.R76H	SFXN5_ENST00000474528.1_5'UTR|SFXN5_ENST00000410065.1_Missense_Mutation_p.R76H	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	76					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)	p.R76H(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						GACCCCCGGGCGCAGGGTCCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											45	45	45					2																	73268005		2203	4300	6503	73121513	SO:0001583	missense	94097			AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"Sideroflexins"	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.227G>A	2.37:g.73268005C>T	ENSP00000272433:p.Arg76His		73121513	A8K116|Q494Y3|Q53T29	Missense_Mutation	SNP	ENST00000272433.2	37	CCDS1922.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.369455	0.42003	.	.	ENSG00000144040	ENST00000272433;ENST00000410065;ENST00000442582	T;T;T	0.30182	1.54;1.54;1.54	5.36	1.11	0.20524	.	0.152130	0.64402	N	0.000017	T	0.13884	0.0336	N	0.12746	0.255	0.31737	N	0.636299	B;B	0.17667	0.023;0.001	B;B	0.14023	0.01;0.001	T	0.05937	-1.0855	10	0.45353	T	0.12	-0.9481	4.6624	0.12648	0.0:0.5233:0.1985:0.2783	.	76;76	B8ZZJ6;Q8TD22	.;SFXN5_HUMAN	H	76	ENSP00000272433:R76H;ENSP00000387076:R76H;ENSP00000396825:R76H	ENSP00000272433:R76H	R	-	2	0	SFXN5	73121513	0.998000	0.40836	0.950000	0.38849	0.862000	0.49288	1.220000	0.32491	0.360000	0.24265	0.655000	0.94253	CGC		0.562	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579		T	73268005	C	T	73268005	3	4	60	1	0	0	0	0	1	0	0	0	14235	768	27	1	843	1	SFXN5	2	73268005	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	23118648	73268005	169931368	10	7898										
BCL2L11	10018	broad.mit.edu	37	chr2	111881594	111881594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aagatcctccctgctgtctcGatcctccagtgggtatttct	8	13	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:111881594G>A	ENST00000393256.3	+	2	545	c.272G>A	c.(271-273)cGa>cAa	p.R91Q	BCL2L11_ENST00000308659.8_Intron|BCL2L11_ENST00000357757.2_Missense_Mutation_p.R91Q|BCL2L11_ENST00000405953.1_Intron|BCL2L11_ENST00000393253.2_Intron|BCL2L11_ENST00000337565.5_Intron	NM_001204106.1|NM_006538.4|NM_138621.4|NM_138627.3	NP_001191035.1|NP_006529.1|NP_619527.1|NP_619533.1	O43521	B2L11_HUMAN	BCL2-like 11 (apoptosis facilitator)	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|brain development (GO:0007420)|cell-matrix adhesion (GO:0007160)|cellular process regulating host cell cycle in response to virus (GO:0060154)|developmental pigmentation (GO:0048066)|ear development (GO:0043583)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of cell cycle (GO:0045787)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|post-embryonic organ morphogenesis (GO:0048563)|regulation of developmental pigmentation (GO:0048070)|regulation of organ growth (GO:0046620)|response to endoplasmic reticulum stress (GO:0034976)|spermatogenesis (GO:0007283)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|thymocyte apoptotic process (GO:0070242)|thymus development (GO:0048538)|tube formation (GO:0035148)	BIM-BCL-2 complex (GO:0097141)|BIM-BCL-xl complex (GO:0097140)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|mitochondrial outer membrane (GO:0005741)		p.R91Q(2)		endometrium(4)|large_intestine(3)|lung(2)|prostate(2)	11						CTGCTGTCTCGATCCTCCAGT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	2											85	91	89					2																	111881594		2203	4300	6503	111598065	SO:0001583	missense	10018			AF032458	CCDS2089.1, CCDS2092.1, CCDS42731.1, CCDS56131.1, CCDS56132.1, CCDS56133.1, CCDS56134.1, CCDS56135.1, CCDS56136.1, CCDS74560.1, CCDS74561.1, CCDS74559.1	2q13	2014-09-17			ENSG00000153094	ENSG00000153094			994	protein-coding gene	gene with protein product		603827				9731710, 9430630	Standard	NM_006538		Approved	BOD, BimL, BimEL, BimS, BIM	uc002tgv.1	O43521	OTTHUMG00000131256	ENST00000393256.3:c.272G>A	2.37:g.111881594G>A	ENSP00000376943:p.Arg91Gln		111598065	A8K2W2|O43522|Q0MSE7|Q0MSE8|Q0MSE9|Q53R28|Q6JTU6|Q6T851|Q6TE14|Q6TE15|Q6TE16|Q6V402|Q8WYL6|Q8WYL7|Q8WYL8|Q8WYL9|Q8WYM0|Q8WYM1	Missense_Mutation	SNP	ENST00000393256.3	37	CCDS2089.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418394	0.83559	.	.	ENSG00000153094	ENST00000432179;ENST00000357757;ENST00000393256	T;T;T	0.43688	0.94;0.94;0.94	5.5	5.5	0.81552	.	0.000000	0.52532	D	0.000079	T	0.37237	0.0996	N	0.24115	0.695	0.80722	D	1	D;D	0.61697	0.976;0.99	P;P	0.50049	0.592;0.629	T	0.19224	-1.0312	10	0.72032	D	0.01	-9.7219	10.6716	0.45762	0.0873:0.0:0.9127:0.0	.	91;91	O43521-11;O43521	.;B2L11_HUMAN	Q	91	ENSP00000411870:R91Q;ENSP00000350398:R91Q;ENSP00000376943:R91Q	ENSP00000350398:R91Q	R	+	2	0	BCL2L11	111598065	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.250000	0.51445	2.755000	0.94549	0.655000	0.94253	CGA		0.567	BCL2L11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254022.3			A	111881594	G	A	111881594	3	1	60	1	0	0	0	0	1	0	0	0	1370	1058	37	1	274	1	BCL2L11	2	111881594	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	38613589	111881594	131317779	11	7899										
LRP2	4036	broad.mit.edu	37	chr2	170007505	170007505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aagtttagccacctcaatgcGtttattcttgacatctgacc	6	11	3	2	rs570499038		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:170007505G>A	ENST00000263816.3	-	68	12778	c.12493C>T	c.(12493-12495)Cgc>Tgc	p.R4165C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4165					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R4165C(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	ACCTCAATGCGTTTATTCTTG	0.428													G|||	1	0.000199681	8e-04	0	5008	,	,		21127	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											180	159	166					2																	170007505		2203	4300	6503	169715751	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12493C>T	2.37:g.170007505G>A	ENSP00000263816:p.Arg4165Cys		169715751	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369471	0.61624	.	.	ENSG00000081479	ENST00000263816	D	0.84370	-1.84	5.86	4.97	0.65823	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.92270	0.7548	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93204	0.6594	10	0.72032	D	0.01	.	16.4444	0.83913	0.0:0.0:0.8676:0.1324	.	4165	P98164	LRP2_HUMAN	C	4165	ENSP00000263816:R4165C	ENSP00000263816:R4165C	R	-	1	0	LRP2	169715751	1.000000	0.71417	0.788000	0.31933	0.490000	0.33462	1.609000	0.36858	1.468000	0.48064	0.655000	0.94253	CGC		0.428	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170007505	G	A	170007505	3	1	60	1	0	0	0	0	1	0	0	0	8985	1145	40	1	1522	1	LRP2	2	170007505	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	58125911	170007505	73191868	12	7900										
HNRNPA3	220988	broad.mit.edu	37	chr2	178080348	178080348	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aaactacagatgatagtttaCgagaacattttgagaaatgg	9	4	0	4			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:178080348C>T	ENST00000392524.2	+	2	391	c.154C>T	c.(154-156)Cga>Tga	p.R52*	AC079305.8_ENST00000455416.1_RNA|HNRNPA3_ENST00000435711.1_Nonsense_Mutation_p.R52*|HNRNPA3_ENST00000411529.2_Nonsense_Mutation_p.R30*|MIR4444-1_ENST00000581696.1_RNA			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	52	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R52*(3)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						TGATAGTTTACGAGAACATTT	0.428																																																3	Substitution - Nonsense(3)	large_intestine(1)|lung(1)|breast(1)	2											66	66	66					2																	178080348		2203	4295	6498	177788594	SO:0001587	stop_gained	220988			AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"RNA binding motif (RRM) containing"	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.154C>T	2.37:g.178080348C>T	ENSP00000376309:p.Arg52*		177788594	D3DPF4|Q53RW7|Q6URK5	Nonsense_Mutation	SNP	ENST00000392524.2	37	CCDS2273.1	.	.	.	.	.	.	.	.	.	.	A	37	6.504984	0.97620	.	.	ENSG00000170144	ENST00000392524;ENST00000411529;ENST00000416446;ENST00000420139;ENST00000435711	.	.	.	4.22	4.22	0.49857	.	0.000000	0.50627	U	0.000108	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1344	0.48367	0.8447:0.1553:0.0:0.0	.	.	.	.	X	52;30;30;30;52	.	ENSP00000376309:R52X	R	+	1	2	HNRNPA3	177788594	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.529000	0.45632	0.615000	0.30124	-0.824000	0.03097	CGA		0.428	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247		T	178080348	C	T	178080348	4	4	60	1	0	0	0	0	0	1	0	0	7281	528	19	1	160	1	HNRNPA3	2	178080348	Nonsense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	8072843	178080348	65119025	13	7901										
GTF3C3	9330	broad.mit.edu	37	chr2	197645302	197645302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cattaagtggttcaagaatgTtgagatgtacaaggcagacc	11	6	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:197645302T>C	ENST00000263956.3	-	9	1288	c.1199A>G	c.(1198-1200)aAc>aGc	p.N400S	GTF3C3_ENST00000409364.3_Missense_Mutation_p.N400S	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	400					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.N400S(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TTCAAGAATGTTGAGATGTAC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											163	138	146					2																	197645302		2203	4300	6503	197353547	SO:0001583	missense	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1199A>G	2.37:g.197645302T>C	ENSP00000263956:p.Asn400Ser		197353547	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.476106	0.63737	.	.	ENSG00000119041	ENST00000263956;ENST00000448087;ENST00000409364	T;T	0.46451	0.87;0.88	5.41	5.41	0.78517	Tetratricopeptide-like helical (1);	0.053247	0.64402	D	0.000001	T	0.37945	0.1022	L	0.43152	1.355	0.50171	D	0.999856	P;B	0.36465	0.554;0.084	B;B	0.35550	0.205;0.024	T	0.26677	-1.0096	10	0.48119	T	0.1	-22.5105	15.612	0.76733	0.0:0.0:0.0:1.0	.	400;400	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	S	400;85;400	ENSP00000263956:N400S;ENSP00000386465:N400S	ENSP00000263956:N400S	N	-	2	0	GTF3C3	197353547	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.362000	0.52314	2.281000	0.76405	0.533000	0.62120	AAC		0.383	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			C	197645302	T	C	197645302	3	2	60	1	0	0	0	0	1	0	0	0	6895	1725	60	4	1501	4	GTF3C3	2	197645302	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	19564954	197645302	45554071	14	7902										
SP140	11262	broad.mit.edu	37	chr2	231112704	231112704	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggggagaaacagggagaggaGgaaggcaggaacagtcccag	19	6	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr2:231112704G>A	ENST00000392045.3	+	8	930	c.816G>A	c.(814-816)gaG>gaA	p.E272E	SP140_ENST00000486687.2_Intron|SP140_ENST00000343805.6_Silent_p.E246E|SP140_ENST00000350136.5_Intron|SP140_ENST00000420434.3_Silent_p.E272E|SP140_ENST00000417495.3_Intron	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	272					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E272E(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGGGAGAGGAGGAAGGCAGGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	2											148	154	152					2																	231112704		1995	4162	6157	230820948	SO:0001819	synonymous_variant	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.816G>A	2.37:g.231112704G>A			230820948	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	37	CCDS42831.1																																																																																				0.488	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		A	231112704	G	A	231112704	2	1	60	1	0	0	0	0	0	0	0	1	14999	991	35	3		3	SP140	2	231112704	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	33467402	231112704	12086669	15	7903										
CCBP2	1238	broad.mit.edu	37	chr3	42907078	42907078	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cccaagaggaaatgactggcAtgaatgaccttggagagagg	14	7	0	5	rs551444331		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr3:42907078A>G	ENST00000422265.1	+	3	1259	c.1084A>G	c.(1084-1086)Atg>Gtg	p.M362V	CYP8B1_ENST00000437102.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|ACKR2_ENST00000442925.1_Missense_Mutation_p.M362V|KRBOX1_ENST00000426937.1_Intron|ACKR2_ENST00000273145.2_Missense_Mutation_p.M362V	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	362	C-terminal cytoplasmic tail.				chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.M362V(1)									AATGACTGGCATGAATGACCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											88	84	86					3																	42907078		2203	4300	6503	42882082	SO:0001583	missense	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.1084A>G	3.37:g.42907078A>G	ENSP00000416996:p.Met362Val		42882082	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	A	7.347	0.622155	0.14193	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.70986	-0.53;-0.53;-0.53	4.43	1.87	0.25490	.	.	.	.	.	T	0.44477	0.1295	N	0.08118	0	0.25192	N	0.990126	B	0.18461	0.028	B	0.19148	0.024	T	0.25984	-1.0116	8	.	.	.	.	4.7446	0.13031	0.6106:0.1986:0.0:0.1908	.	362	O00590	CCBP2_HUMAN	V	362	ENSP00000396150:M362V;ENSP00000416996:M362V;ENSP00000273145:M362V	.	M	+	1	0	CCBP2	42882082	0.940000	0.31905	0.243000	0.24186	0.382000	0.30200	1.906000	0.39887	0.199000	0.20427	0.533000	0.62120	ATG		0.522	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		G	42907078	A	G	42907078	3	3	60	1	0	0	0	0	1	0	0	0	2740	217	8	4	1086	4	CCBP2	3	42907078	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09		42907078	155115352	16	7904										
ALDH1L1	10840	broad.mit.edu	37	chr3	125824614	125824614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tttgaatcctccgaagggagCggccacgtcggtcttgttgt	13	10	1	1	rs200290145		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr3:125824614C>T	ENST00000393434.2	-	22	2957	c.2608G>A	c.(2608-2610)Gct>Act	p.A870T	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.A870T|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.A769T|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.A880T	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	870	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.A870T(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CCGAAGGGAGCGGCCACGTCG	0.493													C|||	1	0.000199681	0	0	5008	,	,		18443	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	3											193	184	187					3																	125824614		2203	4300	6503	127307304	SO:0001583	missense	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2608G>A	3.37:g.125824614C>T	ENSP00000377083:p.Ala870Thr		127307304	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	19.67	3.871783	0.72180	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	4.53	4.53	0.55603	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.132430	0.49916	D	0.000126	T	0.21022	0.0506	L	0.45051	1.395	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.77004	0.973;0.989;0.905	T	0.00448	-1.1733	10	0.52906	T	0.07	.	14.7775	0.69740	0.0:1.0:0.0:0.0	.	769;405;870	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	T	880;870;769;870	ENSP00000273450:A880T;ENSP00000420293:A870T;ENSP00000395881:A769T;ENSP00000377083:A870T	ENSP00000273450:A880T	A	-	1	0	ALDH1L1	127307304	0.859000	0.29813	0.813000	0.32504	0.875000	0.50365	1.695000	0.37763	2.329000	0.79093	0.591000	0.81541	GCT		0.493	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		T	125824614	C	T	125824614	3	4	60	1	0	0	0	0	1	0	0	0	494	768	27	1	108	1	ALDH1L1	3	125824614	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	82917536	125824614	72197816	17	7905										
TRIM42	287015	broad.mit.edu	37	chr3	140401766	140401766	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tgcctcaaggccttccactcGgatgtggccatgcaagacca	10	14	1	1	rs114287544		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr3:140401766G>A	ENST00000286349.3	+	2	995	c.804G>A	c.(802-804)tcG>tcA	p.S268S		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	268						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.S268S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCTTCCACTCGGATGTGGCCA	0.592													G|||	1	0.000199681	0	0	5008	,	,		20505	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						G		3,4403	6.2+/-15.9	0,3,2200	123	108	113		804	3.6	1	3	dbSNP_132	113	0,8600		0,0,4300	no	coding-synonymous	TRIM42	NM_152616.4		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		268/724	140401766	3,13003	2203	4300	6503	141884456	SO:0001819	synonymous_variant	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.804G>A	3.37:g.140401766G>A			141884456	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																				0.592	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401766	G	A	140401766	2	1	60	1	0	0	0	0	0	0	0	1	16557	1103	39	1		1	TRIM42	3	140401766	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	14577152	140401766	57620664	18	7906										
RASA2	5922	broad.mit.edu	37	chr3	141272740	141272740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcctctcataaatggccaaaGctgtgacccttatgcaacag	8	12	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr3:141272740G>A	ENST00000452898.1	+	6	604	c.569G>A	c.(568-570)aGc>aAc	p.S190N	RASA2_ENST00000286364.3_Missense_Mutation_p.S190N	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	190	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.S190N(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						AATGGCCAAAGCTGTGACCCT	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	3											127	126	126					3																	141272740		2203	4300	6503	142755430	SO:0001583	missense	5922			AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"Pleckstrin homology (PH) domain containing"	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.569G>A	3.37:g.141272740G>A	ENSP00000391677:p.Ser190Asn		142755430	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	G	12.14	1.849247	0.32699	.	.	ENSG00000155903	ENST00000286364;ENST00000452898	T;T	0.70045	-0.45;-0.45	5.54	5.54	0.83059	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.095290	0.64402	D	0.000001	T	0.55609	0.1931	L	0.45352	1.415	0.39107	D	0.96139	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.16289	0.015;0.006;0.01	T	0.52064	-0.8625	10	0.19590	T	0.45	.	10.5818	0.45259	0.1173:0.0:0.8827:0.0	.	190;190;190	A8K7K1;G3V0F9;Q15283	.;.;RASA2_HUMAN	N	190	ENSP00000286364:S190N;ENSP00000391677:S190N	ENSP00000286364:S190N	S	+	2	0	RASA2	142755430	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.473000	0.53122	2.607000	0.88179	0.557000	0.71058	AGC		0.318	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506		A	141272740	G	A	141272740	3	1	60	1	0	0	0	0	1	0	0	0	13098	971	34	3	591	3	RASA2	3	141272740	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	870974	141272740	56749690	19	7907										
PIK3CA	5290	broad.mit.edu	37	chr3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	atcctctctctgaaatcactGagcaggagaaagattttcta	7	9	4	4	rs104886003		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)	3											61	60	60					3																	178936091		1813	4072	5885	180418785	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys		180418785	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936091	G	A	178936091	3	1	60	1	0	0	0	0	1	0	0	0	11944	1291	45	3	1667	3	PIK3CA	3	178936091	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	37663351	178936091	19086339	20	7908										
KDR	3791	broad.mit.edu	37	chr4	55964966	55964966	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tccaagttcgtcttttcctgGgcacctggaaagacacaatt	8	11	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:55964966G>A	ENST00000263923.4	-	16	2566	c.2271C>T	c.(2269-2271)gcC>gcT	p.A757A		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	757					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.A757A(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTTTTCCTGGGCACCTGGAA	0.403			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - coding silent(1)	large_intestine(1)	4											88	87	87					4																	55964966		2203	4300	6503	55659723	SO:0001819	synonymous_variant	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2271C>T	4.37:g.55964966G>A			55659723	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																				0.403	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55964966	G	A	55964966	2	1	60	1	0	0	0	0	0	0	0	1	8160	1219	43	3		3	KDR	4	55964966	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09		55964966	135189310	21	7909										
CCDC158	339965	broad.mit.edu	37	chr4	77244562	77244563	+	Splice_Site	DNP	TC	TC	AG													0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctattggcggagactgtgaaTctattagaaaattgcttaga							TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	TC	TC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:77244562_77244563TC>AG	ENST00000388914.3	-	23	3310	c.3158_3158GA>CT	c.(3157-3159)gGAa>gCTaa	p.G1053A		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1053	Ser-rich.							p.?(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						AGACTGTGAATCTATTAGAAAA	0.327																																																1	Unknown(1)	large_intestine(1)	4																																								77463587	SO:0001630	splice_region_variant	339965			BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.3158_3158delinsAG	4.37:g.77244562_77244563delinsAG			77463586	Q8IYQ1|Q8N7D4|Q8N7E3	Splice_Site	DNP	ENST00000388914.3	37	CCDS43242.1																																																																																				0.327	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	Missense_Mutation	AG	77244563	TC	AG	77244562	5	1	60	1	0	0	0	0	0	0	1	0	2796	1449	50	5	191	5	CCDC158	4	77244562	Splice_Site	DNP	TC	TCGA-AG-4015-01A-01W-1073-09	21279596	77244562	113909714	22	7910										
GRID2	2895	broad.mit.edu	37	chr4	94436464	94436464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcatgaaaggactgaatcctTttgagagggacagcatgtat	12	6	0	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:94436464T>C	ENST00000282020.4	+	13	2353	c.2095T>C	c.(2095-2097)Ttt>Ctt	p.F699L	GRID2_ENST00000510992.1_Missense_Mutation_p.F604L	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	699					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.F699L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		ACTGAATCCTTTTGAGAGGGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											119	105	110					4																	94436464		2203	4300	6503	94655487	SO:0001583	missense	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2095T>C	4.37:g.94436464T>C	ENSP00000282020:p.Phe699Leu		94655487	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	T	9.382	1.073197	0.20147	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.14516	2.52;2.5	5.1	5.1	0.69264	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.05960	0.0155	N	0.02916	-0.46	0.58432	D	0.999997	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.27673	-1.0067	10	0.08381	T	0.77	.	15.1709	0.72872	0.0:0.0:0.0:1.0	.	604;699	E9PH24;O43424	.;GRID2_HUMAN	L	699;604	ENSP00000282020:F699L;ENSP00000421257:F604L	ENSP00000282020:F699L	F	+	1	0	GRID2	94655487	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	3.456000	0.53000	2.045000	0.60652	0.477000	0.44152	TTT		0.483	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			C	94436464	T	C	94436464	3	2	60	1	0	0	0	0	1	0	0	0	6793	1841	64	4	2145	4	GRID2	4	94436464	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	17191902	94436464	96717812	23	7911										
CENPE	1062	broad.mit.edu	37	chr4	104030086	104030086	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cacaggatcttgtaaattccGttccttgcattgagagggtg	11	8	1	1	rs187303852	byFrequency	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:104030086G>A	ENST00000265148.3	-	48	7974	c.7885C>T	c.(7885-7887)Cgg>Tgg	p.R2629W	CENPE_ENST00000380026.3_Missense_Mutation_p.R2508W	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2629	Globular autoinhibitory domain. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.R2592W(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGTAAATTCCGTTCCTTGCAT	0.388													G|||	3	0.000599042	0	0	5008	,	,		17838	0.001		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	4						G	TRP/ARG	0,4406		0,0,2203	190	187	188		7885	0.3	0	4		188	1,8599	1.2+/-3.3	0,1,4299	no	missense	CENPE	NM_001813.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	2629/2702	104030086	1,13005	2203	4300	6503	104249535	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.7885C>T	4.37:g.104030086G>A	ENSP00000265148:p.Arg2629Trp		104249535	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.38	2.218621	0.39201	0.0	1.16E-4	ENSG00000138778	ENST00000265148;ENST00000380026	T;T	0.69561	-0.41;-0.4	5.19	0.266	0.15617	.	.	.	.	.	T	0.51398	0.1672	L	0.44542	1.39	0.09310	N	1	B;B	0.17465	0.022;0.013	B;B	0.12156	0.007;0.003	T	0.46133	-0.9213	9	0.62326	D	0.03	.	1.4703	0.02414	0.1657:0.1422:0.3994:0.2926	.	2508;2629	Q02224-3;Q02224	.;CENPE_HUMAN	W	2629;2508	ENSP00000265148:R2629W;ENSP00000369365:R2508W	ENSP00000265148:R2629W	R	-	1	2	CENPE	104249535	0.000000	0.05858	0.000000	0.03702	0.475000	0.33008	0.277000	0.18734	-0.306000	0.08818	-0.150000	0.13652	CGG		0.388	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104030086	G	A	104030086	3	1	60	1	0	0	0	0	1	0	0	0	3236	1144	40	1	228	1	CENPE	4	104030086	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	9593622	104030086	87124190	24	7912										
TRPC3	7222	broad.mit.edu	37	chr4	122853894	122853894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agcagggcgtcgccaatgcgCgccaggttctccttcttgag	13	13	2	1	rs201407818		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:122853894C>T	ENST00000379645.3	-	2	592	c.519G>A	c.(517-519)gcG>gcA	p.A173A	TRPC3_ENST00000513531.1_Silent_p.A100A|TRPC3_ENST00000264811.5_Silent_p.A100A	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	88					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.A100A(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CGCCAATGCGCGCCAGGTTCT	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	4											63	54	57					4																	122853894		2203	4300	6503	123073344	SO:0001819	synonymous_variant	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.519G>A	4.37:g.122853894C>T			123073344	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																				0.637	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122853894	C	T	122853894	2	4	60	1	0	0	0	0	0	0	0	1	16619	755	27	1		1	TRPC3	4	122853894	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	18823808	122853894	68300382	25	7913										
TKTL2	84076	broad.mit.edu	37	chr4	164394816	164394816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tggccctgatggaatggatcCgcaggcggttggctgtgtcc	16	10	0	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr4:164394816C>T	ENST00000280605.3	-	1	231	c.71G>A	c.(70-72)cGg>cAg	p.R24Q		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	24						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.R24Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGAATGGATCCGCAGGCGGTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	45	48					4																	164394816		2203	4300	6503	164614266	SO:0001583	missense	84076			BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.71G>A	4.37:g.164394816C>T	ENSP00000280605:p.Arg24Gln		164614266	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.697334	0.88830	.	.	ENSG00000151005	ENST00000280605	T	0.56941	0.43	4.22	4.22	0.49857	Transketolase, N-terminal (1);	0.000000	0.64402	U	0.000005	T	0.81484	0.4832	H	0.97659	4.05	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.88018	0.2767	10	0.87932	D	0	-8.4083	14.4807	0.67579	0.0:1.0:0.0:0.0	.	24	Q9H0I9	TKTL2_HUMAN	Q	24	ENSP00000280605:R24Q	ENSP00000280605:R24Q	R	-	2	0	TKTL2	164614266	1.000000	0.71417	0.963000	0.40424	0.758000	0.43043	4.253000	0.58791	2.353000	0.79882	0.491000	0.48974	CGG		0.602	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		T	164394816	C	T	164394816	3	4	60	1	0	0	0	0	1	0	0	0	15975	652	23	1	1813	1	TKTL2	4	164394816	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	41540922	164394816	26759460	26	7914										
CDH12	1010	broad.mit.edu	37	chr5	21802319	21802319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	caggtcttgagcagtgacagCgccaatgatggtccctaccg	12	12	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:21802319C>T	ENST00000382254.1	-	10	2299	c.1213G>A	c.(1213-1215)Gct>Act	p.A405T	CDH12_ENST00000504376.2_Missense_Mutation_p.A405T|CDH12_ENST00000521384.1_5'UTR|CDH12_ENST00000522262.1_Missense_Mutation_p.A365T	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	405	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A405T(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						GCAGTGACAGCGCCAATGATG	0.463										HNSCC(59;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	5											102	77	85					5																	21802319		2203	4300	6503	21838076	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.1213G>A	5.37:g.21802319C>T	ENSP00000371689:p.Ala405Thr		21838076	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	C	9.742	1.165171	0.21538	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.47528	0.84;0.84;0.84	5.84	5.84	0.93424	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.37237	0.0996	N	0.03029	-0.43	0.80722	D	1	B;D	0.69078	0.021;0.997	B;P	0.57057	0.051;0.812	T	0.26326	-1.0106	10	0.02654	T	1	.	20.1346	0.98019	0.0:1.0:0.0:0.0	.	365;405	B7Z2U6;P55289	.;CAD12_HUMAN	T	405;405;365	ENSP00000423577:A405T;ENSP00000371689:A405T;ENSP00000428786:A365T	ENSP00000371689:A405T	A	-	1	0	CDH12	21838076	0.998000	0.40836	0.575000	0.28536	0.688000	0.40055	3.759000	0.55227	2.765000	0.95021	0.655000	0.94253	GCT		0.463	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		T	21802319	C	T	21802319	3	4	60	1	0	0	0	0	1	0	0	0	3104	768	27	1	1195	1	CDH12	5	21802319	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		21802319	159112941	27	7915										
DMGDH	29958	broad.mit.edu	37	chr5	78359590	78359590	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctttccattgtgtttctgcaGataagggtggtttttcctct	9	8	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:78359590G>T	ENST00000255189.3	-	2	150	c.122C>A	c.(121-123)tCt>tAt	p.S41Y	DMGDH_ENST00000540686.1_De_novo_Start_InFrame|DMGDH_ENST00000520388.1_Intron|DMGDH_ENST00000380311.4_De_novo_Start_OutOfFrame	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	41					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)	p.S41Y(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TGTTTCTGCAGATAAGGGTGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											238	201	213					5																	78359590		2203	4300	6503	78395346	SO:0001583	missense	29958			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.122C>A	5.37:g.78359590G>T	ENSP00000255189:p.Ser41Tyr		78395346	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	G	6.097	0.386219	0.11524	.	.	ENSG00000132837	ENST00000255189	T	0.75154	-0.91	5.25	3.35	0.38373	.	1.238380	0.05342	N	0.530281	T	0.53286	0.1787	N	0.08118	0	0.18873	N	0.999981	B	0.09022	0.002	B	0.08055	0.003	T	0.41502	-0.9505	10	0.25751	T	0.34	.	5.0967	0.14737	0.2073:0.0:0.6268:0.1659	.	41	Q9UI17	M2GD_HUMAN	Y	41	ENSP00000255189:S41Y	ENSP00000255189:S41Y	S	-	2	0	DMGDH	78395346	0.001000	0.12720	0.008000	0.14137	0.067000	0.16453	0.667000	0.25112	2.610000	0.88304	0.561000	0.74099	TCT		0.463	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		T	78359590	G	T	78359590	3	4	60	1	0	0	0	0	1	0	0	0	4592	942	33	2	2538	2	DMGDH	5	78359590	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	56557271	78359590	102555670	28	7916										
ZFYVE16	9765	broad.mit.edu	37	chr5	79768737	79768737	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gatgctgaagaaaaaggaaaCaaagggtaggaattttttta	11	2	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:79768737C>G	ENST00000338008.5	+	15	4362	c.4182C>G	c.(4180-4182)aaC>aaG	p.N1394K	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.N1394K|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.N1394K	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1394					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)	p.N1394K(1)		breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		AAAAAGGAAACAAAGGGTAGG	0.299																																					Melanoma(150;1452 1854 16018 17851 37292)											1	Substitution - Missense(1)	large_intestine(1)	5											60	62	61					5																	79768737		2203	4300	6503	79804493	SO:0001583	missense	9765			AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.4182C>G	5.37:g.79768737C>G	ENSP00000337159:p.Asn1394Lys		79804493	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	37	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820813	0.71028	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.50001	0.76;0.76;0.76	5.93	3.93	0.45458	Domain of unknown function DUF3480 (1);	0.000000	0.64402	D	0.000005	T	0.66752	0.2821	M	0.81942	2.565	0.58432	D	0.999994	D;D	0.67145	0.993;0.996	D;D	0.75484	0.955;0.986	T	0.67818	-0.5572	10	0.87932	D	0	-15.2725	9.2882	0.37771	0.0:0.74:0.0:0.26	.	204;1394	B3KXA7;Q7Z3T8	.;ZFY16_HUMAN	K	1394	ENSP00000337159:N1394K;ENSP00000423663:N1394K;ENSP00000426848:N1394K	ENSP00000337159:N1394K	N	+	3	2	ZFYVE16	79804493	0.998000	0.40836	0.992000	0.48379	0.989000	0.77384	1.228000	0.32588	0.651000	0.30788	0.655000	0.94253	AAC		0.299	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		G	79768737	C	G	79768737	3	3	60	1	0	0	0	0	1	0	0	0	17703	477	17	5	4236	5	ZFYVE16	5	79768737	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	1409147	79768737	101146523	29	7917										
VCAN	1462	broad.mit.edu	37	chr5	82834349	82834349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gctctggagaagctgctgccGacccagaaaccaccactgtt	10	14	1	2	rs140580494		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:82834349G>A	ENST00000265077.3	+	8	6092	c.5527G>A	c.(5527-5529)Gac>Aac	p.D1843N	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.D856N|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1843	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.D1843N(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AGCTGCTGCCGACCCAGAAAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	,ASN/ASP,,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	93	104	100		,2566,,5527	2.1	0	5	dbSNP_134	100	1,8597	1.2+/-3.3	0,1,4298	no	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,23,,23	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	,benign,,benign	,856/2410,,1843/3397	82834349	2,13002	2203	4299	6502	82870105	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5527G>A	5.37:g.82834349G>A	ENSP00000265077:p.Asp1843Asn		82870105	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	2.205	-0.382149	0.04966	2.27E-4	1.16E-4	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.85013	-1.91;-1.93;3.2	5.81	2.06	0.26882	.	0.886526	0.09842	N	0.748728	T	0.77903	0.4200	L	0.56769	1.78	0.09310	N	1	B;B	0.28605	0.007;0.217	B;B	0.22152	0.007;0.038	T	0.59397	-0.7462	10	0.15066	T	0.55	.	5.378	0.16176	0.3318:0.1385:0.5297:0.0	.	856;1843	P13611-2;P13611	.;CSPG2_HUMAN	N	1843;856;856	ENSP00000265077:D1843N;ENSP00000340062:D856N;ENSP00000426251:D856N	ENSP00000265077:D1843N	D	+	1	0	VCAN	82870105	0.001000	0.12720	0.000000	0.03702	0.040000	0.13550	0.563000	0.23547	0.389000	0.25086	-0.834000	0.03071	GAC		0.507	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82834349	G	A	82834349	3	1	60	1	0	0	0	0	1	0	0	0	17178	1058	37	1	5553	1	VCAN	5	82834349	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	3065612	82834349	98080911	30	7918										
APC	324	broad.mit.edu	37	chr5	112175419	112175419	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aaaagtccacctgaacactaTgttcaggagaccccactcat	6	13	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:112175419T>A	ENST00000457016.1	+	16	4508	c.4128T>A	c.(4126-4128)taT>taA	p.Y1376*	APC_ENST00000508376.2_Nonsense_Mutation_p.Y1376*|APC_ENST00000257430.4_Nonsense_Mutation_p.Y1376*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1376	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Y1376*(6)|p.Y1376fs*9(2)|p.Y1376fs*1(2)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGAACACTATGTTCAGGAGA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	14	Substitution - Nonsense(6)|Deletion - Frameshift(6)|Unknown(1)|Complex - frameshift(1)	large_intestine(12)|soft_tissue(1)|skin(1)	5											89	85	86					5																	112175419		2202	4300	6502	112203318	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4128T>A	5.37:g.112175419T>A	ENSP00000413133:p.Tyr1376*		112203318	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	38	6.976126	0.97975	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	-7.8	0.01214	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.8733	16.6751	0.85276	0.0:0.555:0.0:0.445	.	.	.	.	X	1376	.	.	Y	+	3	2	APC	112203318	0.969000	0.33509	0.756000	0.31282	0.791000	0.44710	0.067000	0.14510	-1.475000	0.01876	-1.044000	0.02363	TAT		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175419	T	A	112175419	4	1	60	1	0	0	0	0	0	1	0	0	763	1471	51	5	4186	5	APC	5	112175419	Nonsense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	29341070	112175419	68739841	31	7919										
PCDHA12	56137	broad.mit.edu	37	chr5	140256741	140256741	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tgctggacgagaacgacaacGcgccggcactgctggcgact	14	13	0	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:140256741G>A	ENST00000398631.2	+	1	1684	c.1684G>A	c.(1684-1686)Gcg>Acg	p.A562T	PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	562	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A562T(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACGACAACGCGCCGGCACT	0.701																																					Pancreas(113;759 1672 13322 24104 50104)											1	Substitution - Missense(1)	large_intestine(1)	5											147	152	150					5																	140256741		2203	4299	6502	140236925	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1684G>A	5.37:g.140256741G>A	ENSP00000381628:p.Ala562Thr		140236925	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	9.970	1.225084	0.22457	.	.	ENSG00000251664	ENST00000398631	T	0.43294	0.95	4.92	3.02	0.34903	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.51160	0.1658	L	0.50333	1.59	0.25271	N	0.989517	P;P	0.52692	0.955;0.609	P;B	0.53912	0.737;0.135	T	0.45629	-0.9248	9	0.49607	T	0.09	.	14.8554	0.70332	0.0:0.2712:0.7287:0.0	.	562;562	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	562	ENSP00000381628:A562T	ENSP00000381628:A562T	A	+	1	0	PCDHA12	140236925	0.000000	0.05858	0.403000	0.26384	0.008000	0.06430	0.753000	0.26376	1.034000	0.39945	0.561000	0.74099	GCG		0.701	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256741	G	A	140256741	3	1	60	1	0	0	0	0	1	0	0	0	11553	1087	38	1	1686	1	PCDHA12	5	140256741	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	28081322	140256741	40658519	32	7920										
PCDHB12	56124	broad.mit.edu	37	chr5	140590534	140590534	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcccaggcccaggccgactcGctcactgtctacctggtggt	12	16	2	0	rs543195348		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr5:140590534G>T	ENST00000239450.2	+	1	2244	c.2055G>T	c.(2053-2055)tcG>tcT	p.S685S	PCDHB12_ENST00000541609.1_Silent_p.S348S|PCDHB13_ENST00000341948.4_5'Flank	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	685					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S685S(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCCGACTCGCTCACTGTCT	0.701													G|||	1	0.000199681	8e-04	0	5008	,	,		15830	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											70	75	74					5																	140590534		2203	4296	6499	140570718	SO:0001819	synonymous_variant	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2055G>T	5.37:g.140590534G>T			140570718	B4DDU1	Silent	SNP	ENST00000239450.2	37	CCDS4254.1																																																																																				0.701	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		T	140590534	G	T	140590534	2	4	60	1	0	0	0	0	0	0	0	1	11568	1074	38	2		2	PCDHB12	5	140590534	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	333793	140590534	40324726	33	7921										
CRISP2	7180	broad.mit.edu	37	chr6	49663583	49663583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tcacagtcatcagggcaaccGgcacaaggtgttccttgttg	11	11	3	0	rs371237410		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr6:49663583G>A	ENST00000339139.4	-	9	806	c.570C>T	c.(568-570)gcC>gcT	p.A190A		NM_001142407.2|NM_001142408.2|NM_001142417.2|NM_001142435.2|NM_001261822.1|NM_003296.3	NP_001135879.1|NP_001135880.1|NP_001135889.1|NP_001135907.1|NP_001248751.1|NP_003287.1	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2	190					single organismal cell-cell adhesion (GO:0016337)	extracellular space (GO:0005615)		p.A190A(1)		kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CAGGGCAACCGGCACAAGGTG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,,,,	0,4406		0,0,2203	101	96	98		570,570,570,570,570	2.2	1	6		98	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRISP2	NM_001142407.1,NM_001142408.1,NM_001142417.1,NM_001142435.1,NM_003296.2	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	190/244,190/244,190/244,190/244,190/244	49663583	1,13005	2203	4300	6503	49771542	SO:0001819	synonymous_variant	7180			X95239	CCDS4928.1	6p12.3	2009-03-12	2003-09-03	2003-09-05	ENSG00000124490	ENSG00000124490			12024	protein-coding gene	gene with protein product	"cancer/testis antigen 36"	187430	"testis specific protein 1 (probe H4-1 p3-1)"	GAPDL5, TPX1		2613236, 8665901	Standard	NM_003296		Approved	CRISP-2, CT36	uc003ozo.3	P16562	OTTHUMG00000014822	ENST00000339139.4:c.570C>T	6.37:g.49663583G>A			49771542	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Silent	SNP	ENST00000339139.4	37	CCDS4928.1																																																																																				0.308	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296		A	49663583	G	A	49663583	2	1	60	1	0	0	0	0	0	0	0	1	3886	1103	39	1		1	CRISP2	6	49663583	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09		49663583	121451484	34	7922										
TFAP2D	83741	broad.mit.edu	37	chr6	50683008	50683008	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	accccgctccaccaccagtcCttccattacgagtttcagca	5	18	1	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr6:50683008C>G	ENST00000008391.3	+	2	447	c.219C>G	c.(217-219)tcC>tcG	p.S73S		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.S73S(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					ACCACCAGTCCTTCCATTACG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	6											239	194	209					6																	50683008		2203	4300	6503	50790967	SO:0001819	synonymous_variant	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.219C>G	6.37:g.50683008C>G			50790967		Silent	SNP	ENST00000008391.3	37	CCDS4933.1																																																																																				0.577	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		G	50683008	C	G	50683008	2	3	60	1	0	0	0	0	0	0	0	1	15829	668	24	5		5	TFAP2D	6	50683008	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	1019425	50683008	120432059	35	7923										
FAM184A	79632	broad.mit.edu	37	chr6	119296268	119296268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttctttggttagggcacttaTattctcatgaaggtgctgaa	10	6	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr6:119296268T>C	ENST00000338891.7	-	13	3132	c.2689A>G	c.(2689-2691)Ata>Gta	p.I897V	FAM184A_ENST00000368475.4_Missense_Mutation_p.I777V|FAM184A_ENST00000352896.5_Missense_Mutation_p.I777V|FAM184A_ENST00000521531.1_Missense_Mutation_p.I897V|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	897						extracellular space (GO:0005615)		p.I897V(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						AGGGCACTTATATTCTCATGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											144	126	132					6																	119296268		1857	4083	5940	119337967	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2689A>G	6.37:g.119296268T>C	ENSP00000342604:p.Ile897Val		119337967	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	T	14.07	2.424979	0.43020	.	.	ENSG00000111879	ENST00000521043;ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.24151	2.48;2.57;1.88;1.87	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.09949	0.0244	L	0.31664	0.95	0.80722	D	1	P;B;P	0.40000	0.514;0.063;0.698	B;B;B	0.36030	0.151;0.044;0.216	T	0.09185	-1.0686	10	0.24483	T	0.36	-16.95	15.7338	0.77827	0.0:0.0:0.0:1.0	.	897;777;897	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	V	60;897;777;777;897	ENSP00000342604:I897V;ENSP00000326608:I777V;ENSP00000357460:I777V;ENSP00000430442:I897V	ENSP00000342604:I897V	I	-	1	0	FAM184A	119337967	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.655000	0.83696	2.185000	0.69588	0.528000	0.53228	ATA		0.383	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119296268	T	C	119296268	3	2	60	1	0	0	0	0	1	0	0	0	5527	1406	49	4	757	4	FAM184A	6	119296268	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	68613260	119296268	51818799	36	7924										
KBTBD2	25948	broad.mit.edu	37	chr7	32909120	32909120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tccccaagtcccacagtacaCgttcagatatatgctgccgc	7	15	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr7:32909120C>T	ENST00000304056.4	-	4	2408	c.1709G>A	c.(1708-1710)cGt>cAt	p.R570H	AVL9_ENST00000404479.1_Intron|KBTBD2_ENST00000485611.1_5'Flank	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	570								p.R570H(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			CCACAGTACACGTTCAGATAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											142	132	135					7																	32909120		2203	4300	6503	32875645	SO:0001583	missense	25948			AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"BTB/POZ domain containing"	21751	protein-coding gene	gene with protein product			"BTB and kelch domain containing 1"	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.1709G>A	7.37:g.32909120C>T	ENSP00000302586:p.Arg570His		32875645	A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Missense_Mutation	SNP	ENST00000304056.4	37	CCDS34614.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.971935	0.74246	.	.	ENSG00000170852	ENST00000304056	T	0.66815	-0.23	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.75657	0.3879	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.77970	-0.2387	10	0.87932	D	0	.	19.4306	0.94762	0.0:1.0:0.0:0.0	.	570	Q8IY47	KBTB2_HUMAN	H	570	ENSP00000302586:R570H	ENSP00000302586:R570H	R	-	2	0	KBTBD2	32875645	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.610000	0.88304	0.591000	0.81541	CGT		0.463	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224		T	32909120	C	T	32909120	3	4	60	1	0	0	0	0	1	0	0	0	8014	536	19	1	166	1	KBTBD2	7	32909120	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		32909120	126229543	37	7925										
PILRB	29990	broad.mit.edu	37	chr7	99956630	99956630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctgtgtatttctgccgagtcGagctggacacccggagatca	12	11	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr7:99956630G>A	ENST00000452089.1	+	7	1441	c.382G>A	c.(382-384)Gag>Aag	p.E128K	STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA|PILRB_ENST00000444073.1_Missense_Mutation_p.E128K|PILRB_ENST00000448382.1_Missense_Mutation_p.R180Q|PILRB_ENST00000610247.1_Missense_Mutation_p.E128K|PILRB_ENST00000609309.1_Missense_Mutation_p.E128K			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	128	Ig-like V-type.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)		p.E128K(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTGCCGAGTCGAGCTGGACAC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7											85	87	87					7																	99956630		2203	4300	6503	99794566	SO:0001583	missense	29990			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"Immunoglobulin superfamily / V-set domain containing"	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.382G>A	7.37:g.99956630G>A	ENSP00000391748:p.Glu128Lys		99794566	Q69YF9|Q9HBS0	Missense_Mutation	SNP	ENST00000452089.1	37	CCDS43622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.021|2.021	-0.424737|-0.424737	0.04734|0.04734	.|.	.|.	ENSG00000121716|ENSG00000121716	ENST00000310771;ENST00000420688;ENST00000452089;ENST00000444073;ENST00000413850|ENST00000444874;ENST00000448382;ENST00000431140	T;T;T|.	0.64618|.	-0.11;-0.11;-0.11|.	2.76|2.76	-4.32|-4.32	0.03688|0.03688	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	3.377880|.	0.00628|.	N|.	0.000462|.	T|T	0.15305|0.15305	0.0369|0.0369	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	P|B	0.51240|0.24576	0.943|0.106	B|B	0.42422|0.18263	0.387|0.021	T|T	0.22103|0.22103	-1.0226|-1.0226	9|7	.|.	.|.	.|.	.|.	1.1418|1.1418	0.01767|0.01767	0.1573:0.2096:0.3736:0.2596|0.1573:0.2096:0.3736:0.2596	.|.	128|58	Q9UKJ0|Q9UKJ0-2	PILRB_HUMAN|.	K|Q	128;128;128;128;233|58;180;58	ENSP00000311153:E128K;ENSP00000391748:E128K;ENSP00000410764:E128K|.	.|.	E|R	+|+	1|2	0|0	PILRB|PILRB	99794566|99794566	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.535000|-0.535000	0.06142|0.06142	-0.906000|-0.906000	0.03866|0.03866	-1.238000|-1.238000	0.01547|0.01547	GAG|CGA		0.587	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238		A	99956630	G	A	99956630	3	1	60	1	0	0	0	0	1	0	0	0	11957	1059	37	1	388	1	PILRB	7	99956630	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	67047510	99956630	59182033	38	7926										
PARP12	64761	broad.mit.edu	37	chr7	139754515	139754515	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aacagatctgatcaccctccTcctggctaagagtgtttggg	10	11	2	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr7:139754515T>A	ENST00000263549.3	-	4	1682	c.809A>T	c.(808-810)gAg>gTg	p.E270V		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	270						nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.E270V(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					ATCACCCTCCTCCTGGCTAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											148	129	136					7																	139754515		2203	4300	6503	139400984	SO:0001583	missense	64761			AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	21919	protein-coding gene	gene with protein product		612481	"zinc finger CCCH-type domain containing 1"	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.809A>T	7.37:g.139754515T>A	ENSP00000263549:p.Glu270Val		139400984	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.351706	0.61183	.	.	ENSG00000059378	ENST00000263549;ENST00000489809	T;T	0.49432	3.16;0.78	5.65	5.65	0.86999	Zinc finger, CCCH-type (2);	0.402745	0.26704	N	0.022922	T	0.44705	0.1306	M	0.62723	1.935	0.37412	D	0.913265	P	0.38078	0.617	B	0.32533	0.147	T	0.55927	-0.8063	10	0.49607	T	0.09	.	14.1166	0.65159	0.0:0.0:0.0:1.0	.	270	Q9H0J9	PAR12_HUMAN	V	270;62	ENSP00000263549:E270V;ENSP00000417606:E62V	ENSP00000263549:E270V	E	-	2	0	PARP12	139400984	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.674000	0.46867	2.157000	0.67596	0.523000	0.50628	GAG		0.443	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		A	139754515	T	A	139754515	3	1	60	1	0	0	0	0	1	0	0	0	11488	1551	54	5	1332	5	PARP12	7	139754515	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	39797885	139754515	19384148	39	7927										
DLGAP2	9228	broad.mit.edu	37	chr8	1626540	1626540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcacccccacccagtacagcGcggtgagaactgtacggacc	11	16	0	1	rs377276862		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:1626540G>A	ENST00000421627.2	+	9	2343	c.2209G>A	c.(2209-2211)Gcg>Acg	p.A737T	DLGAP2_ENST00000524065.1_3'UTR	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	816					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.A745T(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CCAGTACAGCGCGGTGAGAAC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	THR/ALA	2,4026		0,2,2012	45	53	51		2209	5.3	0.5	8		51	0,8338		0,0,4169	no	missense	DLGAP2	NM_004745.3	58	0,2,6181	AA,AG,GG		0.0,0.0497,0.0162	possibly-damaging	737/976	1626540	2,12364	2014	4169	6183	1613947	SO:0001583	missense	9228			AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.2209G>A	8.37:g.1626540G>A	ENSP00000400258:p.Ala737Thr		1613947	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468291	0.84533	4.97E-4	0.0	ENSG00000198010	ENST00000356067;ENST00000421627	T	0.20069	2.1	5.32	5.32	0.75619	.	0.094982	0.64402	D	0.000001	T	0.45418	0.1341	M	0.74258	2.255	0.52501	D	0.999953	D;D	0.71674	0.997;0.998	P;D	0.63192	0.811;0.912	T	0.25222	-1.0138	10	0.29301	T	0.29	-8.3498	18.9967	0.92817	0.0:0.0:1.0:0.0	.	802;816	Q9P1A6-2;Q9P1A6	.;DLGP2_HUMAN	T	768;737	ENSP00000400258:A737T	ENSP00000348366:A768T	A	+	1	0	DLGAP2	1613947	1.000000	0.71417	0.495000	0.27527	0.512000	0.34134	7.328000	0.79160	2.475000	0.83589	0.650000	0.86243	GCG		0.632	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1626540	G	A	1626540	3	1	60	1	0	0	0	0	1	0	0	0	4571	1087	38	1	2239	1	DLGAP2	8	1626540	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		1626540	144737482	40	7928										
CSMD1	64478	broad.mit.edu	37	chr8	3224669	3224669	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gtatgaggcaacaccgacccGgtgagcctggcaacgggctc	14	13	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:3224669G>A	ENST00000520002.1	-	21	3558	c.3003C>T	c.(3001-3003)acC>acT	p.T1001T	CSMD1_ENST00000542608.1_Silent_p.T1000T|CSMD1_ENST00000539096.1_Silent_p.T1000T|CSMD1_ENST00000602557.1_Silent_p.T1001T|CSMD1_ENST00000537824.1_Silent_p.T1000T|CSMD1_ENST00000602723.1_Silent_p.T1001T|CSMD1_ENST00000400186.3_Silent_p.T1001T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1001	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.T729T(1)|p.T1000T(1)		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)		ACACCGACCCGGTGAGCCTGG	0.483																																																2	Substitution - coding silent(2)	large_intestine(2)	8											63	64	64					8																	3224669		1864	4114	5978	3212076	SO:0001819	synonymous_variant	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3003C>T	8.37:g.3224669G>A			3212076	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	0.025	-1.379442	0.01204	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.22	-10.4	0.00318	.	.	.	.	.	T	0.33177	0.0854	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59573	-0.7429	4	.	.	.	.	1.7777	0.03025	0.1409:0.3559:0.2116:0.2916	.	.	.	.	W	481	.	.	R	-	1	2	CSMD1	3212076	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-5.149000	0.00146	-5.432000	0.00014	-2.253000	0.00282	CGG		0.483	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3224669	G	A	3224669	2	1	60	1	0	0	0	0	0	0	0	1	3950	1103	39	1		1	CSMD1	8	3224669	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	1598129	3224669	143139353	41	7929										
CDH17	1015	broad.mit.edu	37	chr8	95142932	95142932	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agtctggtgacctgctggccGgaaacaacttccttccacac	9	14	1	1	rs199497492		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:95142932G>A	ENST00000027335.3	-	17	2444	c.2320C>T	c.(2320-2322)Cgg>Tgg	p.R774W	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Missense_Mutation_p.R774W	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	774	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.R774W(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CCTGCTGGCCGGAAACAACTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	73	75					8																	95142932		2203	4300	6503	95212108	SO:0001583	missense	1015			X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2320C>T	8.37:g.95142932G>A	ENSP00000027335:p.Arg774Trp		95212108	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	37	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.417426	0.25552	.	.	ENSG00000079112	ENST00000027335;ENST00000450165	T;T	0.58358	0.34;0.34	5.84	2.83	0.33086	Cadherin (1);	0.561125	0.16175	N	0.226091	T	0.46014	0.1371	L	0.56769	1.78	0.27273	N	0.95831	D	0.63046	0.992	B	0.40534	0.332	T	0.37549	-0.9701	10	0.37606	T	0.19	-0.1227	11.2752	0.49163	0.0:0.0:0.5163:0.4836	.	774	Q12864	CAD17_HUMAN	W	774	ENSP00000027335:R774W;ENSP00000401468:R774W	ENSP00000027335:R774W	R	-	1	2	CDH17	95212108	0.965000	0.33210	0.969000	0.41365	0.045000	0.14185	1.376000	0.34306	0.760000	0.33108	-0.282000	0.10007	CGG		0.448	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		A	95142932	G	A	95142932	3	1	60	1	0	0	0	0	1	0	0	0	3108	1115	39	1	186	1	CDH17	8	95142932	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	91918263	95142932	51221090	42	7930										
CSMD3	114788	broad.mit.edu	37	chr8	113649165	113649165	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aggtcagagtgtcaccaatcCcaaagttgaacccgattcga	9	11	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:113649165C>T	ENST00000297405.5	-	22	3840	c.3596G>A	c.(3595-3597)gGg>gAg	p.G1199E	CSMD3_ENST00000455883.2_Missense_Mutation_p.G1095E|CSMD3_ENST00000352409.3_Missense_Mutation_p.G1199E|CSMD3_ENST00000343508.3_Missense_Mutation_p.G1159E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1199	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G1199E(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTCACCAATCCCAAAGTTGAA	0.468										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											218	180	193					8																	113649165		2203	4300	6503	113718341	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3596G>A	8.37:g.113649165C>T	ENSP00000297405:p.Gly1199Glu		113718341	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640091	0.67244	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	5.56	5.56	0.83823	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.64907	0.2641	N	0.13140	0.3	0.40241	D	0.97796	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;1.0;0.984	T	0.60239	-0.7302	10	0.12430	T	0.62	.	19.5386	0.95266	0.0:1.0:0.0:0.0	.	1095;1199;1159	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	1159;1199;539;1095;1199	ENSP00000345799:G1159E;ENSP00000297405:G1199E;ENSP00000341558:G539E;ENSP00000412263:G1095E;ENSP00000343124:G1199E	ENSP00000297405:G1199E	G	-	2	0	CSMD3	113718341	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	4.973000	0.63763	2.610000	0.88304	0.650000	0.86243	GGG		0.468	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113649165	C	T	113649165	3	4	60	1	0	0	0	0	1	0	0	0	3952	623	22	3	7727	3	CSMD3	8	113649165	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	18506233	113649165	32714857	43	7931										
TRPS1	7227	broad.mit.edu	37	chr8	116616108	116616108	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cccatgcctcacctgtagtgTcgggaaatctcttcttccac	7	15	3	0	rs559562389		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:116616108T>G	ENST00000220888.5	-	3	2208	c.2049A>C	c.(2047-2049)cgA>cgC	p.R683R	TRPS1_ENST00000519674.1_Silent_p.R683R|TRPS1_ENST00000520276.1_Silent_p.R687R|TRPS1_ENST00000519076.1_Silent_p.R437R|TRPS1_ENST00000395715.3_Silent_p.R696R			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	683	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R683R(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			ACCTGTAGTGTCGGGAAATCT	0.448									Langer-Giedion syndrome				T|||	1	0.000199681	0	0	5008	,	,		17550	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	8											71	66	68					8																	116616108		1859	4094	5953	116685283	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2049A>C	8.37:g.116616108T>G			116685283	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.448	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116616108	T	G	116616108	2	3	60	1	0	0	0	0	0	0	0	1	16633	1654	58	4		4	TRPS1	8	116616108	Silent	SNP	T	TCGA-AG-4015-01A-01W-1073-09	2966943	116616108	29747914	44	7932										
FAM135B	51059	broad.mit.edu	37	chr8	139153530	139153530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggagtttgttgaggtaatacCggaaccggggccgtgtgagg	18	6	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr8:139153530C>T	ENST00000395297.1	-	17	3871	c.3701G>A	c.(3700-3702)cGg>cAg	p.R1234Q		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1234								p.R1234Q(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GAGGTAATACCGGAACCGGGG	0.527										HNSCC(54;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	8											181	191	188					8																	139153530		2019	4189	6208	139222712	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3701G>A	8.37:g.139153530C>T	ENSP00000378710:p.Arg1234Gln		139222712	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	35	5.463394	0.96257	.	.	ENSG00000147724	ENST00000395297	T	0.49139	0.79	5.83	5.83	0.93111	Domain of unknown function DUF676, lipase-like (1);	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	N	0.19112	0.55	0.50632	D	0.999882	D	0.89917	1.0	D	0.75020	0.985	T	0.53802	-0.8387	10	0.54805	T	0.06	-19.2025	12.4236	0.55534	0.0:0.9238:0.0:0.0762	.	1234	Q49AJ0	F135B_HUMAN	Q	1234	ENSP00000378710:R1234Q	ENSP00000378710:R1234Q	R	-	2	0	FAM135B	139222712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.892000	0.63193	2.750000	0.94351	0.655000	0.94253	CGG		0.527	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139153530	C	T	139153530	3	4	60	1	0	0	0	0	1	0	0	0	5465	652	23	1	535	1	FAM135B	8	139153530	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	22537422	139153530	7210492	45	7933										
TRPM6	140803	broad.mit.edu	37	chr9	77431819	77431819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gatactcacccttcagcaaaGctgttaggattgctaagtcc	8	11	2	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr9:77431819G>A	ENST00000360774.1	-	10	1433	c.1196C>T	c.(1195-1197)gCt>gTt	p.A399V	TRPM6_ENST00000361255.3_Missense_Mutation_p.A394V|TRPM6_ENST00000449912.2_Missense_Mutation_p.A394V|TRPM6_ENST00000451710.3_Missense_Mutation_p.A399V|TRPM6_ENST00000376871.3_Missense_Mutation_p.A399V|TRPM6_ENST00000376864.4_Missense_Mutation_p.A399V|TRPM6_ENST00000376872.3_Missense_Mutation_p.A399V	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	399					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A399V(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CTTCAGCAAAGCTGTTAGGAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											198	181	187					9																	77431819		2203	4300	6503	76621639	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1196C>T	9.37:g.77431819G>A	ENSP00000354006:p.Ala399Val		76621639	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970530	0.92919	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	5.93	5.04	0.67666	.	0.194312	0.56097	D	0.000040	D	0.86389	0.5921	H	0.94306	3.52	0.54753	D	0.999988	B;B;D;D	0.89917	0.082;0.082;0.999;1.0	B;B;D;D	0.76071	0.04;0.058;0.96;0.987	D	0.90330	0.4351	10	0.87932	D	0	.	15.1024	0.72292	0.0676:0.0:0.9324:0.0	.	399;399;399;394	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3	.;.;TRPM6_HUMAN;.	V	399;399;399;399;394;394;399;62;62	ENSP00000354006:A399V;ENSP00000407341:A399V;ENSP00000366068:A399V;ENSP00000366067:A399V;ENSP00000396672:A394V;ENSP00000354962:A394V;ENSP00000366060:A399V	ENSP00000309693:A62V	A	-	2	0	TRPM6	76621639	1.000000	0.71417	0.988000	0.46212	0.938000	0.57974	7.945000	0.87732	1.524000	0.49035	0.561000	0.74099	GCT		0.423	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77431819	G	A	77431819	3	1	60	1	0	0	0	0	1	0	0	0	16630	971	34	3	4992	3	TRPM6	9	77431819	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		77431819	63781612	46	7934										
KIAA0368	23392	broad.mit.edu	37	chr9	114134760	114134760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	taaattacattcttctttttCggatttctcctcatcagcaa	3	10	5	0	rs201047834		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr9:114134760C>T	ENST00000338205.5	-	41	4696	c.4477G>A	c.(4477-4479)Gaa>Aaa	p.E1493K	KIAA0368_ENST00000465499.1_5'Flank|KIAA0368_ENST00000259335.4_Missense_Mutation_p.E1671K|KIAA0368_ENST00000374378.3_5'UTR			Q5VYK3	ECM29_HUMAN	KIAA0368	1499					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.E1671K(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TCTTCTTTTTCGGATTTCTCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											117	110	112					9																	114134760		1865	4098	5963	113174581	SO:0001583	missense	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.4477G>A	9.37:g.114134760C>T	ENSP00000339889:p.Glu1493Lys		113174581	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	C	16.97	3.269823	0.59540	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.48201	0.82	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.43211	0.1237	L	0.42245	1.32	0.80722	D	1	P	0.49090	0.919	B	0.39876	0.312	T	0.21075	-1.0256	10	0.23891	T	0.37	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	968	B3KXF2	.	K	1493;1671;968	ENSP00000259335:E1671K	ENSP00000259335:E1671K	E	-	1	0	KIAA0368	113174581	1.000000	0.71417	0.982000	0.44146	0.584000	0.36387	5.660000	0.68018	2.824000	0.97209	0.655000	0.94253	GAA		0.418	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		T	114134760	C	T	114134760	3	4	60	1	0	0	0	0	1	0	0	0	8192	893	31	1	1078	1	KIAA0368	9	114134760	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	36702941	114134760	27078671	47	7935										
BMS1	9790	broad.mit.edu	37	chr10	43282631	43282631	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tataggtaaaaagcgcagacTcaccattattgaatgtgggt	10	6	1	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr10:43282631T>G	ENST00000374518.5	+	4	446	c.383T>G	c.(382-384)cTc>cGc	p.L128R		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	128	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.L128R(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AAGCGCAGACTCACCATTATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											16	22	20					10																	43282631		1221	2197	3418	42602637	SO:0001583	missense	9790			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.383T>G	10.37:g.43282631T>G	ENSP00000363642:p.Leu128Arg		42602637	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	t	16.24	3.067790	0.55539	.	.	ENSG00000165733	ENST00000374518	T	0.11930	2.73	4.81	4.81	0.61882	.	0.067431	0.64402	D	0.000010	T	0.38585	0.1046	M	0.80616	2.505	0.49213	D	0.999764	D	0.89917	1.0	D	0.81914	0.995	T	0.33007	-0.9885	10	0.72032	D	0.01	.	12.9738	0.58527	0.0:0.0:0.0:1.0	.	128	Q14692	BMS1_HUMAN	R	128	ENSP00000363642:L128R	ENSP00000363642:L128R	L	+	2	0	BMS1	42602637	1.000000	0.71417	0.994000	0.49952	0.416000	0.31233	7.743000	0.85020	1.804000	0.52760	0.163000	0.16589	CTC		0.378	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		G	43282631	T	G	43282631	3	3	60	1	0	0	0	0	1	0	0	0	1473	1551	54	4	393	4	BMS1	10	43282631	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09		43282631	92252116	48	7936										
ZNF488	118738	broad.mit.edu	37	chr10	48370641	48370641	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctgaaaacagatggcgacttAgcgaacctgagctgggccgg	14	10	0	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr10:48370641A>C	ENST00000395702.2	+	2	336	c.109A>C	c.(109-111)Agc>Cgc	p.S37R	ZNF488_ENST00000494156.1_Missense_Mutation_p.S37R|ZNF488_ENST00000586537.1_5'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	37					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S37R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						ATGGCGACTTAGCGAACCTGA	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	10											49	57	54					10																	48370641		2202	4299	6501	47990647	SO:0001583	missense	118738			AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.109A>C	10.37:g.48370641A>C	ENSP00000379054:p.Ser37Arg		47990647	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	37	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.796204	0.31777	.	.	ENSG00000165388	ENST00000395702;ENST00000433077;ENST00000442001;ENST00000436850;ENST00000412534;ENST00000444585;ENST00000425196	T;T;T;T;T;T	0.53423	1.93;0.82;0.69;0.62;1.45;1.45	4.9	2.59	0.31030	.	1.429690	0.04130	U	0.317847	T	0.42743	0.1216	L	0.51422	1.61	0.09310	N	0.999992	B	0.09022	0.002	B	0.06405	0.002	T	0.23084	-1.0198	10	0.38643	T	0.18	.	5.2495	0.15515	0.6905:0.0:0.3095:0.0	.	37	Q96MN9	ZN488_HUMAN	R	37	ENSP00000379054:S37R;ENSP00000401469:S37R;ENSP00000415923:S37R;ENSP00000406508:S37R;ENSP00000410326:S37R;ENSP00000412898:S37R	ENSP00000379054:S37R	S	+	1	0	ZNF488	47990647	0.097000	0.21791	0.001000	0.08648	0.013000	0.08279	0.881000	0.28173	0.719000	0.32188	0.459000	0.35465	AGC		0.667	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		C	48370641	A	C	48370641	3	2	60	1	0	0	0	0	1	0	0	0	17979	420	15	4	111	4	ZNF488	10	48370641	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	5088010	48370641	87164106	49	7937										
COPB1	1315	broad.mit.edu	37	chr11	14490905	14490905	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttgggataatttctcttcttCtagtttagcagataacatgt	7	6	3	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:14490905C>T	ENST00000249923.3	-	15	2242	c.1942G>A	c.(1942-1944)Gaa>Aaa	p.E648K	COPB1_ENST00000439561.2_Missense_Mutation_p.E648K	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	648					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.E648K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						TTCTCTTCTTCTAGTTTAGCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											163	164	164					11																	14490905		2200	4294	6494	14447481	SO:0001583	missense	1315			BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.1942G>A	11.37:g.14490905C>T	ENSP00000249923:p.Glu648Lys		14447481	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313429	0.60414	.	.	ENSG00000129083	ENST00000249923;ENST00000439561	T;T	0.44083	0.93;0.93	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.39572	0.1083	L	0.49640	1.575	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31223	-0.9951	10	0.10902	T	0.67	.	19.8405	0.96681	0.0:1.0:0.0:0.0	.	648	P53618	COPB_HUMAN	K	648	ENSP00000249923:E648K;ENSP00000397873:E648K	ENSP00000249923:E648K	E	-	1	0	COPB1	14447481	1.000000	0.71417	0.977000	0.42913	0.985000	0.73830	7.535000	0.82014	2.692000	0.91855	0.655000	0.94253	GAA		0.408	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		T	14490905	C	T	14490905	3	4	60	1	0	0	0	0	1	0	0	0	3734	922	32	3	951	3	COPB1	11	14490905	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		14490905	120515611	50	7938										
TPH1	7166	broad.mit.edu	37	chr11	18048169	18048169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gacggatggaaaaacctgtaCgctctgcaaagcaaaggaga	12	8	1	1	rs368665249		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:18048169C>T	ENST00000250018.2	-	6	1233	c.671G>A	c.(670-672)cGt>cAt	p.R224H	TPH1_ENST00000341556.2_Missense_Mutation_p.R224H	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	224					aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.R224H(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	AAAACCTGTACGCTCTGCAAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG	1,4399	2.1+/-5.4	0,1,2199	67	67	67		671	5.4	1	11		67	0,8586		0,0,4293	no	missense	TPH1	NM_004179.2	29	0,1,6492	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	224/445	18048169	1,12985	2200	4293	6493	18004745	SO:0001583	missense	7166			X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"tryptophan 5-monooxygenase"	191060	"tryptophan hydroxylase (tryptophan 5-monooxygenase)"	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.671G>A	11.37:g.18048169C>T	ENSP00000250018:p.Arg224His		18004745	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Missense_Mutation	SNP	ENST00000250018.2	37	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.881021	0.91740	2.27E-4	0.0	ENSG00000129167	ENST00000250018;ENST00000341556	D;D	0.99578	-6.21;-6.21	5.4	5.4	0.78164	Aromatic amino acid hydroxylase, C-terminal (3);	0.048980	0.85682	D	0.000000	D	0.99426	0.9797	M	0.77103	2.36	0.80722	D	1	D	0.60160	0.987	P	0.55087	0.768	D	0.99651	1.0991	10	0.37606	T	0.19	-5.0466	19.5398	0.95270	0.0:1.0:0.0:0.0	.	224	P17752	TPH1_HUMAN	H	224	ENSP00000250018:R224H;ENSP00000343550:R224H	ENSP00000250018:R224H	R	-	2	0	TPH1	18004745	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.907000	0.63300	2.694000	0.91930	0.467000	0.42956	CGT		0.418	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179		T	18048169	C	T	18048169	3	4	60	1	0	0	0	0	1	0	0	0	16441	536	19	1	683	1	TPH1	11	18048169	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	3557264	18048169	116958347	51	7939										
CCDC73	493860	broad.mit.edu	37	chr11	32674733	32674733	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tattagcttgaatttgttgcCgaagtaactgctgcatatgt	9	6	0	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:32674733C>T	ENST00000335185.5	-	12	918	c.875G>A	c.(874-876)cGg>cAg	p.R292Q	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	292								p.R292Q(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					AATTTGTTGCCGAAGTAACTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	11											150	139	142					11																	32674733		1860	4097	5957	32631309	SO:0001583	missense	493860			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.875G>A	11.37:g.32674733C>T	ENSP00000335325:p.Arg292Gln		32631309	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	C	5.233	0.228431	0.09916	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.63	4.5	0.54988	.	0.241486	0.35040	N	0.003489	T	0.11665	0.0284	N	0.00210	-1.845	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.30060	-0.9991	9	0.02654	T	1	.	10.1764	0.42941	0.0:0.0757:0.0:0.9243	.	282;292	Q6ZRK6-2;Q6ZRK6	.;CCD73_HUMAN	Q	292	.	ENSP00000335325:R292Q	R	-	2	0	CCDC73	32631309	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.342000	0.43992	0.975000	0.38392	-0.475000	0.04921	CGG		0.318	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		T	32674733	C	T	32674733	3	4	60	1	0	0	0	0	1	0	0	0	2852	652	23	1	2392	1	CCDC73	11	32674733	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	14626564	32674733	102331783	52	7940										
FGF19	9965	broad.mit.edu	37	chr11	69514273	69514273	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	accgggaggcggtgcttctcGgatcggtacacattgtagcc	14	11	1	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:69514273G>A	ENST00000294312.3	-	3	1173	c.408C>T	c.(406-408)tcC>tcT	p.S136S		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	136					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)	p.S136>F(1)|p.S136S(1)		large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			GGTGCTTCTCGGATCGGTACA	0.557																																																2	Substitution - coding silent(1)|Complex - compound substitution(1)	large_intestine(1)|skin(1)	11											76	71	72					11																	69514273		2200	4294	6494	69223454	SO:0001819	synonymous_variant	9965			AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.408C>T	11.37:g.69514273G>A			69223454		Silent	SNP	ENST00000294312.3	37	CCDS8193.1																																																																																				0.557	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117		A	69514273	G	A	69514273	2	1	60	1	0	0	0	0	0	0	0	1	5866	1103	39	1		1	FGF19	11	69514273	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	36839540	69514273	65492243	53	7941										
DYNC2H1	79659	broad.mit.edu	37	chr11	103106440	103106440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aattagctactcttcctaaaAgagctcaacttgctgctgca	6	11	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:103106440A>G	ENST00000375735.2	+	62	9751	c.9607A>G	c.(9607-9609)Aga>Gga	p.R3203G	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R3203G|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3203					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R636G(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TCTTCCTAAAAGAGCTCAACT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	68	69					11																	103106440		1847	4088	5935	102611650	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.9607A>G	11.37:g.103106440A>G	ENSP00000364887:p.Arg3203Gly		102611650	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.409919	0.42715	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.73897	-0.79;-0.79	5.68	4.54	0.55810	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	T	0.78207	0.4247	M	0.64170	1.965	0.54753	D	0.999986	P;B	0.38395	0.629;0.371	P;B	0.47251	0.542;0.217	T	0.78643	-0.2124	10	0.66056	D	0.02	.	13.021	0.58787	0.8653:0.1347:0.0:0.0	.	3203;3203	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	G	3203	ENSP00000364887:R3203G;ENSP00000381167:R3203G	ENSP00000364887:R3203G	R	+	1	2	DYNC2H1	102611650	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	2.937000	0.48979	0.964000	0.38108	0.524000	0.50904	AGA		0.378	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103106440	A	G	103106440	3	3	60	1	0	0	0	0	1	0	0	0	4857	64	3	4	9853	4	DYNC2H1	11	103106440	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	33592167	103106440	31900076	54	7942										
HTR3B	9177	broad.mit.edu	37	chr11	113816850	113816850	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tccctctgggcactgtggggCggcgtgtgaagactgaagtg	17	9	1	3	rs151164355	byFrequency	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:113816850C>T	ENST00000260191.2	+	9	1574	c.1317C>T	c.(1315-1317)ggC>ggT	p.G439G	HTR3B_ENST00000537778.1_Silent_p.G428G	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	439					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)	p.G439G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	CACTGTGGGGCGGCGTGTGAA	0.527													C|||	17	0.00339457	0	0	5008	,	,		15373	0		0	False		,,,				2504	0.0174															1	Substitution - coding silent(1)	large_intestine(1)	11						C		1,4401	2.1+/-5.4	0,1,2200	63	59	60		1317	-4.8	0	11	dbSNP_134	60	0,8592		0,0,4296	no	coding-synonymous	HTR3B	NM_006028.4		0,1,6496	TT,TC,CC		0.0,0.0227,0.0077		439/442	113816850	1,12993	2201	4296	6497	113322060	SO:0001819	synonymous_variant	9177			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.1317C>T	11.37:g.113816850C>T			113322060	B0YJ23|Q0VJC3	Silent	SNP	ENST00000260191.2	37	CCDS8364.1																																																																																				0.527	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		T	113816850	C	T	113816850	2	4	60	1	0	0	0	0	0	0	0	1	7466	755	27	1		1	HTR3B	11	113816850	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	10710410	113816850	21189666	55	7943										
MLL	4297	broad.mit.edu	37	chr11	118343890	118343890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggtttttctgcatctggtacCgctgcttcagcccgattgtt	10	11	3	0	rs368516174		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr11:118343890C>T	ENST00000389506.5	+	3	2016	c.2016C>T	c.(2014-2016)acC>acT	p.T672T	KMT2A_ENST00000534358.1_Silent_p.T672T|KMT2A_ENST00000354520.4_Silent_p.T672T			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	672					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.T672T(1)									CATCTGGTACCGCTGCTTCAG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C	,	1,4399	2.1+/-5.4	0,1,2199	74	76	75		2016,2016	0.4	0.7	11		75	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	MLL	NM_001197104.1,NM_005933.3	,	0,1,6495	TT,TC,CC		0.0,0.0227,0.0077	,	672/3973,672/3970	118343890	1,12991	2200	4296	6496	117849100	SO:0001819	synonymous_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.2016C>T	11.37:g.118343890C>T			117849100	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118343890	C	T	118343890	2	4	60	1	0	0	0	0	0	0	0	1	9650	639	23	1		1	MLL	11	118343890	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	4527040	118343890	16662626	56	7944										
LRP6	4040	broad.mit.edu	37	chr12	12291420	12291420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agttttcaaacacagtaagtCccacaggctgcaagatattg	8	9	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:12291420C>T	ENST00000261349.4	-	16	3522	c.3446G>A	c.(3445-3447)gGa>gAa	p.G1149E	LRP6_ENST00000543091.1_Missense_Mutation_p.G1149E|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1149	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.G1149E(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CACAGTAAGTCCCACAGGCTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											177	165	169					12																	12291420		2203	4300	6503	12182687	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3446G>A	12.37:g.12291420C>T	ENSP00000261349:p.Gly1149Glu		12182687	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883596	0.91740	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.97731	-4.51;-4.51	5.47	5.47	0.80525	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.56097	U	0.000024	D	0.99052	0.9675	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99180	1.0867	10	0.46703	T	0.11	.	19.3326	0.94297	0.0:1.0:0.0:0.0	.	1149;1149	F5H7J9;O75581	.;LRP6_HUMAN	E	1149	ENSP00000261349:G1149E;ENSP00000442472:G1149E	ENSP00000261349:G1149E	G	-	2	0	LRP6	12182687	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	7.487000	0.81328	2.561000	0.86390	0.591000	0.81541	GGA		0.398	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12291420	C	T	12291420	3	4	60	1	0	0	0	0	1	0	0	0	8991	855	30	3	1427	3	LRP6	12	12291420	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		12291420	121560475	57	7945										
FGD4	121512	broad.mit.edu	37	chr12	32793313	32793313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	caaactgacccagtctaagtCcgtgcacagctttgctgcag	9	13	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:32793313C>T	ENST00000427716.2	+	17	2571	c.2147C>T	c.(2146-2148)tCc>tTc	p.S716F	FGD4_ENST00000525053.1_Missense_Mutation_p.S828F|FGD4_ENST00000546442.1_Missense_Mutation_p.S623F|FGD4_ENST00000534526.2_Missense_Mutation_p.S853F|FGD4_ENST00000531134.1_Missense_Mutation_p.S801F	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	716	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.S716F(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CAGTCTAAGTCCGTGCACAGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											134	116	122					12																	32793313		2203	4300	6503	32684580	SO:0001583	missense	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.2147C>T	12.37:g.32793313C>T	ENSP00000394487:p.Ser716Phe		32684580	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.670947	0.47781	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68	5.31	4.41	0.53225	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.51477	D	0.000086	T	0.11281	0.0275	L	0.31294	0.92	0.80722	D	1	B;B;B	0.26195	0.126;0.126;0.144	B;B;B	0.32724	0.151;0.151;0.118	T	0.12066	-1.0562	10	0.11794	T	0.64	-13.1109	13.3561	0.60629	0.0:0.924:0.0:0.076	.	828;801;716	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	F	853;801;716;623;828	ENSP00000449273:S853F;ENSP00000431323:S801F;ENSP00000394487:S716F;ENSP00000446695:S623F;ENSP00000433666:S828F	ENSP00000394487:S716F	S	+	2	0	FGD4	32684580	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.627000	0.54252	2.470000	0.83445	0.563000	0.77884	TCC		0.527	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		T	32793313	C	T	32793313	3	4	60	1	0	0	0	0	1	0	0	0	5854	855	30	3	2205	3	FGD4	12	32793313	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	20501893	32793313	101058582	58	7946										
TUBA1B	10376	broad.mit.edu	37	chr12	49521781	49521781	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cctcaccctctccttcaacaGaatccacaccaacctcctca	1	21	4	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:49521781G>T	ENST00000336023.5	-	4	1410	c.1316C>A	c.(1315-1317)tCt>tAt	p.S439Y	RP11-386G11.10_ENST00000552893.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	439					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.S439Y(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						TCCTTCAACAGAATCCACACC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											137	144	142					12																	49521781		2203	4299	6502	47808048	SO:0001583	missense	10376			AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"Tubulins"	18809	protein-coding gene	gene with protein product	"tubulin, alpha, ubiquitous"	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.1316C>A	12.37:g.49521781G>T	ENSP00000336799:p.Ser439Tyr		47808048	P04687|P05209|Q27I68|Q8WU19	Missense_Mutation	SNP	ENST00000336023.5	37	CCDS31792.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.879250	0.33162	.	.	ENSG00000123416	ENST00000336023;ENST00000429203	T	0.78595	-1.19	5.45	5.45	0.79879	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.46442	U	0.000282	D	0.86422	0.5929	M	0.72353	2.195	0.80722	D	1	P	0.52170	0.951	P	0.60012	0.867	D	0.87668	0.2539	10	0.87932	D	0	.	18.058	0.89368	0.0:0.0:1.0:0.0	.	439	P68363	TBA1B_HUMAN	Y	439;170	ENSP00000336799:S439Y	ENSP00000336799:S439Y	S	-	2	0	TUBA1B	47808048	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.467000	0.60155	2.571000	0.86741	0.650000	0.86243	TCT		0.498	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082		T	49521781	G	T	49521781	3	4	60	1	0	0	0	0	1	0	0	0	16784	942	33	2	43	2	TUBA1B	12	49521781	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	16728468	49521781	84330114	59	7947										
ATF1	466	broad.mit.edu	37	chr12	51174016	51174016	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctcacatttctcatattgctCaacaggtaagggagggactg	10	9	3	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:51174016C>A	ENST00000262053.3	+	2	110	c.88C>A	c.(88-90)Caa>Aaa	p.Q30K	ATF1_ENST00000539132.1_5'UTR	NM_005171.4	NP_005162.1	P18846	ATF1_HUMAN	activating transcription factor 1	30					cellular protein complex assembly (GO:0043623)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to cobalt ion (GO:0032025)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q30K(1)	EWSR1/ATF1(347)|FUS/ATF1(4)	breast(1)|large_intestine(1)|ovary(2)	4					Pseudoephedrine(DB00852)	TCATATTGCTCAACAGGTAAG	0.393			T	"EWSR1, FUS"	"malignant melanoma of soft parts , angiomatoid fibrous histiocytoma "																																		Dom	yes		12	12q13	466	activating transcription factor 1		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	12											112	114	114					12																	51174016		2203	4300	6503	49460283	SO:0001583	missense	466			BC029619	CCDS8803.1	12q13	2014-05-13			ENSG00000123268	ENSG00000123268		"basic leucine zipper proteins"	783	protein-coding gene	gene with protein product		123803				8401579	Standard	NM_005171		Approved	TREB36	uc001rww.4	P18846		ENST00000262053.3:c.88C>A	12.37:g.51174016C>A	ENSP00000262053:p.Gln30Lys		49460283	B4DRF9|P25168|Q9H4A8	Missense_Mutation	SNP	ENST00000262053.3	37	CCDS8803.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.617499	0.28801	.	.	ENSG00000123268	ENST00000552510;ENST00000262053;ENST00000552487	T;T;T	0.78126	-1.15;0.48;0.46	5.47	5.47	0.80525	.	0.450874	0.21198	N	0.078506	T	0.56863	0.2014	N	0.08118	0	0.80722	D	1	B	0.19200	0.034	B	0.14023	0.01	T	0.54990	-0.8210	10	0.05959	T	0.93	-25.1398	15.1991	0.73120	0.0:1.0:0.0:0.0	.	30	P18846	ATF1_HUMAN	K	30	ENSP00000448592:Q30K;ENSP00000262053:Q30K;ENSP00000448921:Q30K	ENSP00000262053:Q30K	Q	+	1	0	ATF1	49460283	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	3.618000	0.54188	2.743000	0.94032	0.591000	0.81541	CAA		0.393	ATF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404285.1	NM_005171		A	51174016	C	A	51174016	3	1	60	1	0	0	0	0	1	0	0	0	1080	827	29	2	90	2	ATF1	12	51174016	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	1652235	51174016	82677879	60	7948										
ATF7	11016	broad.mit.edu	37	chr12	53931208	53931208	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agagaatttaccttctccttCagtggtggggaacagggact	12	8	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:53931208C>T	ENST00000548446.2	-	5	538	c.426G>A	c.(424-426)ctG>ctA	p.L142L	ATF7_ENST00000420353.2_Silent_p.L131L|RP11-793H13.10_ENST00000591834.1_Silent_p.L131L|ATF7_ENST00000415113.1_Intron|ATF7_ENST00000328463.7_Silent_p.L142L|ATF7_ENST00000456903.4_Silent_p.L131L			P17544	ATF7_HUMAN	activating transcription factor 7	142	Transactivation domain.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.L142L(2)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	CCTTCTCCTTCAGTGGTGGGG	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	12											109	111	110					12																	53931208		1861	4108	5969	52217475	SO:0001819	synonymous_variant	11016			X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"basic leucine zipper proteins"	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.426G>A	12.37:g.53931208C>T			52217475	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																					0.413	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		T	53931208	C	T	53931208	2	4	60	1	0	0	0	0	0	0	0	1	1087	813	29	3		3	ATF7	12	53931208	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	2757192	53931208	79920687	61	7949										
SILV	6490	broad.mit.edu	37	chr12	56350928	56350928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tgacatctctgccagtgtggTacccatgacctctgaaactg	9	12	2	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:56350928T>C	ENST00000548747.1	-	6	1821	c.1159A>G	c.(1159-1161)Acc>Gcc	p.T387A	PMEL_ENST00000360714.4_Missense_Mutation_p.T387A|PMEL_ENST00000536427.1_Intron|PMEL_ENST00000449260.2_Missense_Mutation_p.T387A|PMEL_ENST00000550464.1_Missense_Mutation_p.T301A|PMEL_ENST00000550447.1_Intron|PMEL_ENST00000548493.1_Missense_Mutation_p.T387A|PMEL_ENST00000548689.1_5'Flank|PMEL_ENST00000539511.1_Missense_Mutation_p.T301A|PMEL_ENST00000552882.1_Missense_Mutation_p.T387A			P40967	PMEL_HUMAN	premelanosome protein	387	10 X 13 AA approximate tandem repeats, RPT domain.				melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)		p.T387A(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCCAGTGTGGTACCCATGACC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											134	106	116					12																	56350928		2203	4300	6503	54637195	SO:0001583	missense	6490			AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"silver (mouse homolog) like", "silver homolog (mouse)"	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.1159A>G	12.37:g.56350928T>C	ENSP00000448828:p.Thr387Ala		54637195	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Missense_Mutation	SNP	ENST00000548747.1	37	CCDS8897.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518406	0.64634	.	.	ENSG00000185664	ENST00000449260;ENST00000552882;ENST00000550464;ENST00000548747;ENST00000548493;ENST00000360714;ENST00000539511;ENST00000547137	T;T;T;T;T;T;T;T	0.14893	3.0;3.04;3.03;3.04;3.04;3.0;3.03;2.47	5.66	4.52	0.55395	.	0.101050	0.43579	N	0.000555	T	0.31420	0.0796	L	0.52573	1.65	0.58432	D	0.999999	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.81914	0.914;0.995;0.989	T	0.01899	-1.1251	10	0.37606	T	0.19	-10.315	8.8846	0.35396	0.0:0.0845:0.0:0.9155	.	301;387;387	P40967-3;P40967-2;P40967	.;.;PMEL_HUMAN	A	387;387;301;387;387;387;301;333	ENSP00000402758:T387A;ENSP00000449690:T387A;ENSP00000450036:T301A;ENSP00000448828:T387A;ENSP00000447374:T387A;ENSP00000353940:T387A;ENSP00000445005:T301A;ENSP00000448849:T333A	ENSP00000353940:T387A	T	-	1	0	PMEL	54637195	0.792000	0.28813	0.871000	0.34182	0.364000	0.29643	1.021000	0.30040	1.087000	0.41251	-0.264000	0.10439	ACC		0.517	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928		C	56350928	T	C	56350928	3	2	60	1	0	0	0	0	1	0	0	0	14359	1638	57	4	850	4	SILV	12	56350928	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	2419720	56350928	77500967	62	7950										
TCP11L2	255394	broad.mit.edu	37	chr12	106717424	106717424	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aaattttggaagaaactccaAgtgagtataatataatgtgt	8	3	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:106717424A>T	ENST00000299045.3	+	6	946	c.772A>T	c.(772-774)Agt>Tgt	p.S258C	TCP11L2_ENST00000552690.1_3'UTR|TCP11L2_ENST00000546625.1_Missense_Mutation_p.S258C|TCP11L2_ENST00000547153.1_Splice_Site_p.R258*	NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	258								p.S258C(1)		endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						AGAAACTCCAAGTGAGTATAA	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	49	47					12																	106717424		2203	4298	6501	105241554	SO:0001630	splice_region_variant	255394			BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.772+1A>T	12.37:g.106717424A>T			105241554	B2RA65|G3V1Y9	Nonsense_Mutation	SNP	ENST00000299045.3	37	CCDS9104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	36|36	5.968119|5.968119	0.97156|0.97156	.|.	.|.	ENSG00000166046|ENSG00000166046	ENST00000547153|ENST00000299045;ENST00000546625	.|T;T	.|0.12569	.|2.67;2.67	5.76|5.76	3.22|3.22	0.36961|0.36961	.|.	.|0.402536	.|0.33670	.|N	.|0.004667	.|T	.|0.24547	.|0.0595	L|L	0.55990|0.55990	1.75|1.75	0.38068|0.38068	D|D	0.936292|0.936292	.|D;D	.|0.63046	.|0.985;0.992	.|P;P	.|0.61874	.|0.895;0.863	.|T	.|0.02417	.|-1.1162	.|10	0.59425|0.38643	D|T	0.04|0.18	-6.1535|-6.1535	7.795|7.795	0.29141|0.29141	0.7379:0.0:0.2621:0.0|0.7379:0.0:0.2621:0.0	.|.	.|258;258	.|Q8N4U5;G3V1Z2	.|T11L2_HUMAN;.	X|C	258|258	.|ENSP00000299045:S258C;ENSP00000449123:S258C	ENSP00000448952:R258X|ENSP00000299045:S258C	R|S	+|+	1|1	2|0	TCP11L2|TCP11L2	105241554|105241554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.170000|4.170000	0.58229|0.58229	0.361000|0.361000	0.24292|0.24292	0.533000|0.533000	0.62120|0.62120	AGA|AGT		0.269	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772	Missense_Mutation	T	106717424	A	T	106717424	5	4	60	1	0	0	0	0	0	0	1	0	15754	86	3	5	790	5	TCP11L2	12	106717424	Splice_Site	SNP	A	TCGA-AG-4015-01A-01W-1073-09	50366496	106717424	27134471	63	7951										
PTPN11	5781	broad.mit.edu	37	chr12	112891129	112891129	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttctttctgtgcgcactggtGatgacaaaggggagagcaat	13	7	2	3	rs398122858		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr12:112891129G>T	ENST00000351677.2	+	4	661	c.463G>T	c.(463-465)Gat>Tat	p.D155Y	PTPN11_ENST00000392597.1_Missense_Mutation_p.D155Y	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	155	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.D155Y(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GCGCACTGGTGATGACAAAGG	0.433			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	12											131	126	128					12																	112891129		2203	4300	6503	111375512	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.463G>T	12.37:g.112891129G>T	ENSP00000340944:p.Asp155Tyr		111375512	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914121	0.92178	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	T;T	0.78481	-1.18;-1.18	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.90092	0.6905	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.68621	0.959;0.959	D	0.91520	0.5234	10	0.87932	D	0	.	19.5088	0.95132	0.0:0.0:1.0:0.0	.	155;155	Q06124-2;Q06124-3	.;.	Y	155	ENSP00000376376:D155Y;ENSP00000340944:D155Y	ENSP00000340944:D155Y	D	+	1	0	PTPN11	111375512	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.860000	0.99555	2.624000	0.88883	0.555000	0.69702	GAT		0.433	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112891129	G	T	112891129	3	4	60	1	0	0	0	0	1	0	0	0	12815	1290	45	2	477	2	PTPN11	12	112891129	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	6173705	112891129	20960766	64	7952										
SACS	26278	broad.mit.edu	37	chr13	23914699	23914699	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggcttcaattttttttgccaCttgcacaacatccttttctt	4	11	2	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr13:23914699C>A	ENST00000382292.3	-	9	3589	c.3316G>T	c.(3316-3318)Gtg>Ttg	p.V1106L	SACS_ENST00000382298.3_Missense_Mutation_p.V1106L|SACS_ENST00000402364.1_Missense_Mutation_p.V356L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1106					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.V959L(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTTTTGCCACTTGCACAACA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	13											189	199	196					13																	23914699		2203	4300	6503	22812699	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.3316G>T	13.37:g.23914699C>A	ENSP00000371729:p.Val1106Leu		22812699	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336964	0.41398	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87179	-2.09;-2.22;-2.09	6.16	6.16	0.99307	.	0.059735	0.64402	D	0.000003	D	0.85652	0.5746	M	0.62723	1.935	0.45554	D	0.998507	B	0.06786	0.001	B	0.06405	0.002	T	0.79167	-0.1915	10	0.26408	T	0.33	.	17.0356	0.86474	0.0:0.8732:0.1268:0.0	.	1106	Q9NZJ4	SACS_HUMAN	L	1106;356;1106	ENSP00000371729:V1106L;ENSP00000385844:V356L;ENSP00000371735:V1106L	ENSP00000371729:V1106L	V	-	1	0	SACS	22812699	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	5.727000	0.68523	2.937000	0.99478	0.650000	0.86243	GTG		0.388	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23914699	C	A	23914699	3	1	60	1	0	0	0	0	1	0	0	0	13841	565	20	2	10427	2	SACS	13	23914699	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		23914699	91255179	65	7953										
DCLK1	9201	broad.mit.edu	37	chr13	36385094	36385094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agtgatttgctgccatcttgGtgctcatacacctaaaacaa	7	10	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr13:36385094G>T	ENST00000360631.3	-	12	1777	c.1566C>A	c.(1564-1566)caC>caA	p.H522Q	DCLK1_ENST00000379893.1_Missense_Mutation_p.H215Q|DCLK1_ENST00000255448.4_Missense_Mutation_p.H522Q			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	522	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.H522Q(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TGCCATCTTGGTGCTCATACA	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	13											134	123	127					13																	36385094		2203	4300	6503	35283094	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1566C>A	13.37:g.36385094G>T	ENSP00000353846:p.His522Gln		35283094	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	16.37	3.103620	0.56291	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893;ENST00000539451	T;T;T	0.63913	-0.07;-0.07;-0.07	5.28	5.28	0.74379	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	N	0.11845	0.185	0.80722	D	1	P;P;P;P	0.41188	0.647;0.741;0.696;0.647	B;P;B;B	0.45610	0.377;0.487;0.355;0.377	T	0.49113	-0.8973	10	0.28530	T	0.3	.	14.514	0.67807	0.0726:0.0:0.9274:0.0	.	215;522;522;215	O15075-4;O15075;O15075-2;O15075-3	.;DCLK1_HUMAN;.;.	Q	214;522;522;215;504	ENSP00000255448:H522Q;ENSP00000353846:H522Q;ENSP00000369223:H215Q	ENSP00000255448:H522Q	H	-	3	2	DCLK1	35283094	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.589000	0.46145	2.630000	0.89119	0.655000	0.94253	CAC		0.453	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		T	36385094	G	T	36385094	3	4	60	1	0	0	0	0	1	0	0	0	4297	1252	44	2	651	2	DCLK1	13	36385094	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	12470395	36385094	78784784	66	7954										
TRPC4	7223	broad.mit.edu	37	chr13	38248384	38248384	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cctttacaaatgcaacaattTtcaaggagattgttgctaaa	6	7	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr13:38248384T>G	ENST00000379705.3	-	5	2212	c.1355A>C	c.(1354-1356)aAa>aCa	p.K452T	TRPC4_ENST00000379673.2_Missense_Mutation_p.K452T|TRPC4_ENST00000447043.1_Missense_Mutation_p.K452T|TRPC4_ENST00000355779.2_Missense_Mutation_p.K452T|TRPC4_ENST00000494529.1_5'UTR|TRPC4_ENST00000358477.2_Missense_Mutation_p.K452T|TRPC4_ENST00000338947.5_Missense_Mutation_p.K279T|TRPC4_ENST00000426868.2_Missense_Mutation_p.K452T|TRPC4_ENST00000379681.3_Missense_Mutation_p.K452T|TRPC4_ENST00000379679.1_Missense_Mutation_p.K279T			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	452					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.K452T(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TGCAACAATTTTCAAGGAGAT	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	13											53	52	53					13																	38248384		2203	4300	6503	37146384	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1355A>C	13.37:g.38248384T>G	ENSP00000369027:p.Lys452Thr		37146384	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	19.91	3.914611	0.72983	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000426868;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	D;D;D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.31	5.31	0.75309	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98741	0.9577	M	0.73962	2.25	0.58432	D	0.999995	D;D;D;D;P;D	0.76494	0.993;0.996;0.999;0.999;0.941;0.996	D;D;D;D;P;D	0.80764	0.936;0.931;0.994;0.986;0.892;0.978	D	0.99866	1.1090	10	0.87932	D	0	-34.4696	15.5566	0.76200	0.0:0.0:0.0:1.0	.	452;452;452;279;452;452	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	T	452;452;279;279;452;452;452;452;452	ENSP00000369027:K452T;ENSP00000369003:K452T;ENSP00000342580:K279T;ENSP00000369001:K279T;ENSP00000410133:K452T;ENSP00000348025:K452T;ENSP00000351264:K452T;ENSP00000368995:K452T;ENSP00000414316:K452T	ENSP00000342580:K279T	K	-	2	0	TRPC4	37146384	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.997000	0.88414	2.122000	0.65172	0.482000	0.46254	AAA		0.303	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		G	38248384	T	G	38248384	3	3	60	1	0	0	0	0	1	0	0	0	16620	1841	64	4	1621	4	TRPC4	13	38248384	Missense_Mutation	SNP	T	TCGA-AG-4015-01A-01W-1073-09	1863290	38248384	76921494	67	7955										
KLHL1	57626	broad.mit.edu	37	chr13	70535466	70535466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	atgcaaattggacaaggtccCagagagcattggggtctatg	13	7	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr13:70535466C>A	ENST00000377844.4	-	3	1550	c.791G>T	c.(790-792)tGg>tTg	p.W264L	KLHL1_ENST00000545028.1_Missense_Mutation_p.W71L	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	264	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)	p.W264*(1)|p.W264L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		GACAAGGTCCCAGAGAGCATT	0.378																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	13											148	131	137					13																	70535466		2203	4300	6503	69433467	SO:0001583	missense	57626			AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.791G>T	13.37:g.70535466C>A	ENSP00000367075:p.Trp264Leu		69433467	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100044	0.37048	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.66099	-0.19;-0.19	5.08	5.08	0.68730	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.243063	0.32134	N	0.006535	T	0.48003	0.1476	N	0.17278	0.47	0.32778	N	0.502838	P;B	0.38395	0.629;0.322	B;B	0.40009	0.316;0.222	T	0.61973	-0.6952	10	0.45353	T	0.12	.	12.2399	0.54536	0.0:0.9218:0.0:0.0782	.	264;264	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	L	264;71	ENSP00000367075:W264L;ENSP00000439602:W71L	ENSP00000367075:W264L	W	-	2	0	KLHL1	69433467	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.272000	0.51616	2.531000	0.85337	0.563000	0.77884	TGG		0.378	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		A	70535466	C	A	70535466	3	1	60	1	0	0	0	0	1	0	0	0	8386	595	21	2	1491	2	KLHL1	13	70535466	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	32287082	70535466	44634412	68	7956										
NALCN	259232	broad.mit.edu	37	chr13	101936303	101936303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cctggaggcaggctggggcgCgtccctggggcttgttgaca	18	11	0	1	rs75772824		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr13:101936303C>T	ENST00000251127.6	-	10	1196	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Missense_Mutation_p.R372H	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	372					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.R372H(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGCTGGGGCGCGTCCCTGGGG	0.473													C|||	1	0.000199681	0	0	5008	,	,		14627	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13						C	HIS/ARG	0,4406		0,0,2203	41	42	42		1115	5.4	1	13	dbSNP_131	42	12,8588	9.1+/-34.3	0,12,4288	yes	missense	NALCN	NM_052867.2	29	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	benign	372/1739	101936303	12,12994	2203	4300	6503	100734304	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1115G>A	13.37:g.101936303C>T	ENSP00000251127:p.Arg372His		100734304	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.51	2.259409	0.39995	0.0	0.001395	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.98732	-4.68;-5.1	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.96626	0.8899	N	0.08118	0	0.80722	D	1	B;D;B	0.71674	0.198;0.998;0.134	B;P;B	0.53649	0.026;0.731;0.026	D	0.95536	0.8608	10	0.15499	T	0.54	.	19.2799	0.94048	0.0:1.0:0.0:0.0	.	372;372;372	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	H	372	ENSP00000251127:R372H;ENSP00000365367:R372H	ENSP00000251127:R372H	R	-	2	0	NALCN	100734304	1.000000	0.71417	0.979000	0.43373	0.998000	0.95712	7.450000	0.80656	2.568000	0.86640	0.543000	0.68304	CGC		0.473	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101936303	C	T	101936303	3	4	60	1	0	0	0	0	1	0	0	0	10178	768	27	1	4241	1	NALCN	13	101936303	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	31400837	101936303	13233575	69	7957										
AQP9	366	broad.mit.edu	37	chr15	58465336	58465336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gatgaaatggttcaaattgcCattttatgtgggagcccagt	11	6	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr15:58465336C>T	ENST00000219919.4	+	3	678	c.308C>T	c.(307-309)cCa>cTa	p.P103L	AQP9_ENST00000536493.1_Missense_Mutation_p.P103L|ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000558772.1_Missense_Mutation_p.P38L	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	103					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)	p.P103L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		TTCAAATTGCCATTTTATGTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											197	194	195					15																	58465336		2192	4292	6484	56252628	SO:0001583	missense	366			AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"Ion channels / Aquaporins"	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.308C>T	15.37:g.58465336C>T	ENSP00000219919:p.Pro103Leu		56252628	Q9NP32	Missense_Mutation	SNP	ENST00000219919.4	37	CCDS10165.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055814	0.76074	.	.	ENSG00000103569	ENST00000219919;ENST00000536493	D;D	0.84298	-1.83;-1.83	5.46	5.46	0.80206	Aquaporin-like (2);	0.000000	0.85682	D	0.000000	D	0.90235	0.6947	L	0.55990	1.75	0.80722	D	1	D	0.59357	0.985	D	0.63381	0.914	D	0.89555	0.3802	10	0.51188	T	0.08	.	19.5125	0.95148	0.0:1.0:0.0:0.0	.	103	O43315	AQP9_HUMAN	L	103	ENSP00000219919:P103L;ENSP00000441390:P103L	ENSP00000219919:P103L	P	+	2	0	AQP9	56252628	1.000000	0.71417	0.760000	0.31359	0.929000	0.56500	7.410000	0.80065	2.840000	0.97914	0.655000	0.94253	CCA		0.488	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980		T	58465336	C	T	58465336	3	4	60	1	0	0	0	0	1	0	0	0	833	594	21	3	318	3	AQP9	15	58465336	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		58465336	44066056	70	7958										
HMG20A	10363	broad.mit.edu	37	chr15	77771527	77771527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttatctcacttcaggaagtgGagagacacctacagtggaca	10	9	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr15:77771527G>T	ENST00000381714.3	+	10	1342	c.914G>T	c.(913-915)gGa>gTa	p.G305V	HMG20A_ENST00000336216.4_Missense_Mutation_p.G305V	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	305					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G305V(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						TCAGGAAGTGGAGAGACACCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											130	131	131					15																	77771527		2196	4294	6490	75558582	SO:0001583	missense	10363			AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.914G>T	15.37:g.77771527G>T	ENSP00000371133:p.Gly305Val		75558582	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321104	0.81580	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.68765	-0.35;-0.35	6.04	6.04	0.98038	.	0.151278	0.64402	N	0.000011	T	0.76162	0.3949	M	0.69823	2.125	0.80722	D	1	D	0.55172	0.97	P	0.53809	0.735	T	0.77435	-0.2589	10	0.59425	D	0.04	-12.4166	16.0072	0.80372	0.0:0.1336:0.8664:0.0	.	305	Q9NP66	HM20A_HUMAN	V	305	ENSP00000336856:G305V;ENSP00000371133:G305V	ENSP00000336856:G305V	G	+	2	0	HMG20A	75558582	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.513000	0.81739	2.873000	0.98535	0.563000	0.77884	GGA		0.368	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		T	77771527	G	T	77771527	3	4	60	1	0	0	0	0	1	0	0	0	7242	1174	41	2	944	2	HMG20A	15	77771527	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	19306191	77771527	24759865	71	7959										
LRRK1	79705	broad.mit.edu	37	chr15	101605592	101605592	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttagcgggcctcgccgatggGcttgtggctgtgtttcccgt	15	11	0	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr15:101605592G>A	ENST00000388948.3	+	32	5309	c.4950G>A	c.(4948-4950)ggG>ggA	p.G1650G	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000532145.1_3'UTR|LRRK1_ENST00000284395.5_Silent_p.G1647G	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.G1662G(1)|p.G1650G(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	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)			TCGCCGATGGGCTTGTGGCTG	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	15											80	92	88					15																	101605592		2085	4217	6302	99423115	SO:0001819	synonymous_variant	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4950G>A	15.37:g.101605592G>A			99423115		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																				0.562	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101605592	G	A	101605592	2	1	60	1	0	0	0	0	0	0	0	1	9061	1190	42	3		3	LRRK1	15	101605592	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	23834065	101605592	925800	72	7960										
NOMO1	23420	broad.mit.edu	37	chr16	14976468	14976468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cagccgggatgtgtgtaccaCgttcagctcaaggcagaagg	14	10	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr16:14976468C>T	ENST00000287667.7	+	26	3216	c.3045C>T	c.(3043-3045)caC>caT	p.H1015H		NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	1015						integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.H1015H(1)		endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						GTGTGTACCACGTTCAGCTCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	16											74	78	76					16																	14976468		2195	4298	6493	14883969	SO:0001819	synonymous_variant	23420			X57398	CCDS10556.1	16p13.11	2008-02-05			ENSG00000103512	ENSG00000103512			30060	protein-coding gene	gene with protein product		609157				1310294, 15257293	Standard	NM_014287		Approved	PM5	uc002dcv.3	Q15155	OTTHUMG00000090541	ENST00000287667.7:c.3045C>T	16.37:g.14976468C>T			14883969	P78421|Q8IW21|Q96DG0	Silent	SNP	ENST00000287667.7	37	CCDS10556.1																																																																																				0.577	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207065.1			T	14976468	C	T	14976468	2	4	60	1	0	0	0	0	0	0	0	1	10562	535	19	1		1	NOMO1	16	14976468	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09		14976468	75378285	73	7961										
PHKB	5257	broad.mit.edu	37	chr16	47723013	47723013	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcggagacaagccagccttgGacttgtatcagctgtcacct	11	12	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr16:47723013G>T	ENST00000323584.5	+	27	2716	c.2692G>T	c.(2692-2694)Gac>Tac	p.D898Y	PHKB_ENST00000455779.1_Missense_Mutation_p.D891Y|PHKB_ENST00000299167.8_Missense_Mutation_p.D898Y|PHKB_ENST00000566044.1_Missense_Mutation_p.D891Y	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	898					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.D898Y(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GCCAGCCTTGGACTTGTATCA	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	16											113	100	104					16																	47723013		2201	4300	6501	46280514	SO:0001583	missense	5257				CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2692G>T	16.37:g.47723013G>T	ENSP00000313504:p.Asp898Tyr		46280514	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963448	0.74016	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91237	-2.81;-2.81	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.93220	0.7840	L	0.38175	1.15	0.80722	D	1	D;D;D	0.89917	0.998;0.967;1.0	D;P;D	0.78314	0.942;0.851;0.991	D	0.93574	0.6906	10	0.62326	D	0.03	-26.1595	19.5522	0.95324	0.0:0.0:1.0:0.0	.	139;898;891	B3KVX5;Q93100;Q93100-4	.;KPBB_HUMAN;.	Y	891;891;898	ENSP00000414345:D891Y;ENSP00000313504:D898Y	ENSP00000299167:D891Y	D	+	1	0	PHKB	46280514	1.000000	0.71417	0.944000	0.38274	0.419000	0.31324	9.399000	0.97285	2.639000	0.89480	0.650000	0.86243	GAC		0.463	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			T	47723013	G	T	47723013	3	4	60	1	0	0	0	0	1	0	0	0	11876	1174	41	2	2952	2	PHKB	16	47723013	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	32746545	47723013	42631740	74	7962										
C16orf80	29105	broad.mit.edu	37	chr16	58147932	58147932	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tcgagtcacaattccagttaTtgctgaagggaaaaaacaga	9	7	1	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr16:58147932T>C	ENST00000262498.3	-	6	913	c.579A>G	c.(577-579)caA>caG	p.Q193Q	C16orf80_ENST00000562443.1_5'Flank|CTB-134F13.1_ENST00000564672.1_RNA	NM_013242.2	NP_037374.1												p.Q193Q(1)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						ATTCCAGTTATTGCTGAAGGG	0.423																																					Pancreas(103;1212 1612 18629 30162 52390)											1	Substitution - coding silent(1)	large_intestine(1)	16											149	148	148					16																	58147932		2198	4300	6498	56705433	SO:0001819	synonymous_variant	29105																														ENST00000262498.3:c.579A>G	16.37:g.58147932T>C			56705433		Silent	SNP	ENST00000262498.3	37	CCDS10793.1																																																																																				0.423	C16orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257388.2			C	58147932	T	C	58147932	2	2	60	1	0	0	0	0	0	0	0	1	1841	1490	52	4		4	C16orf80	16	58147932	Silent	SNP	T	TCGA-AG-4015-01A-01W-1073-09	10424919	58147932	32206821	75	7963										
TP53	7157	broad.mit.edu	37	chr17	7576855	7576855	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggtcccaagacttagtacctGaagggtgaaatattctccat	9	9	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr17:7576855G>A	ENST00000269305.4	-	9	1180	c.991C>T	c.(991-993)Cag>Tag	p.Q331*	TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q331*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q331*|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q331*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q331*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	331	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		Q -> H (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q331*(23)|p.0?(8)|p.Q331fs*6(2)|p.?(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTTAGTACCTGAAGGGTGAAA	0.448		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	34	Substitution - Nonsense(23)|Whole gene deletion(8)|Insertion - Frameshift(2)|Unknown(1)	lung(6)|large_intestine(4)|urinary_tract(4)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|endometrium(2)|skin(2)|ovary(2)|stomach(1)|breast(1)|oesophagus(1)	17											115	108	110					17																	7576855		2203	4300	6503	7517580	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.991C>T	17.37:g.7576855G>A	ENSP00000269305:p.Gln331*		7517580	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117678	0.77323	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	4.95	2.88	0.33553	.	0.253251	0.40469	N	0.001098	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-17.7352	9.751	0.40475	0.0:0.0:0.4869:0.5131	.	.	.	.	X	331;331;331;331;331;320;199	.	ENSP00000269305:Q331X	Q	-	1	0	TP53	7517580	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	1.858000	0.39408	0.557000	0.29117	-0.314000	0.08810	CAG		0.448	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7576855	G	A	7576855	4	1	60	1	0	0	0	0	0	1	0	0	16421	1299	45	3	291	3	TP53	17	7576855	Nonsense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		7576855	73618355	76	7964										
LGALS9	3965	broad.mit.edu	37	chr17	25967751	25967751	+	Frame_Shift_Del	DEL	G	G	-													0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	acacacatgcctttccagaaGgggatgccctttgacctctg							TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr17:25967751delG	ENST00000395473.2	+	3	1753	c.285delG	c.(283-285)aagfs	p.K95fs	AC015688.3_ENST00000584605.1_3'UTR|LGALS9_ENST00000413914.2_Frame_Shift_Del_p.K38fs|LGALS9_ENST00000310394.5_Frame_Shift_Del_p.K95fs|LGALS9_ENST00000313648.6_Frame_Shift_Del_p.K95fs|LGALS9_ENST00000302228.5_Frame_Shift_Del_p.K95fs|LGALS9_ENST00000448970.2_3'UTR	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	95	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)	p.M97fs*16(1)		endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		CTTTCCAGAAGGGGATGCCCT	0.587																																					Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)											1	Deletion - Frameshift(1)	large_intestine(1)	17											139	132	134					17																	25967751		2203	4300	6503	22991878	SO:0001589	frameshift_variant	3965			AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"Lectins, galactoside-binding"	6570	protein-coding gene	gene with protein product	"galectin 9"	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.285delG	17.37:g.25967751delG	ENSP00000378856:p.Lys95fs		22991878	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Frame_Shift_Del	DEL	ENST00000395473.2	37	CCDS11222.1																																																																																				0.587	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587		-	25967751	G	-	25967751	7	5	60	1	0	1	0	1	0	0	0	0	8771	991	35	0	295	0	LGALS9	17	25967751	Frame_Shift_Del	DEL	G	TCGA-AG-4015-01A-01W-1073-09	18390896	25967751	55227459	77	7965										
HLF	3131	broad.mit.edu	37	chr17	53392723	53392723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ccaggaaatgtttgaccctcGcaaacgcaagttctctgagg	10	11	1	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr17:53392723G>A	ENST00000226067.5	+	3	1060	c.587G>A	c.(586-588)cGc>cAc	p.R196H	HLF_ENST00000430986.2_Missense_Mutation_p.R111H|HLF_ENST00000575345.1_Missense_Mutation_p.R111H|HLF_ENST00000573945.1_Missense_Mutation_p.R111H	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	196	Pro-rich (proline/acidic region (PAR)).				multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R196H(1)		large_intestine(1)|ovary(2)	3						TTTGACCCTCGCAAACGCAAG	0.517			T	TCF3	ALL																																		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	1	Substitution - Missense(1)	large_intestine(1)	17											100	93	95					17																	53392723		2203	4300	6503	50747722	SO:0001583	missense	3131				CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.587G>A	17.37:g.53392723G>A	ENSP00000226067:p.Arg196His		50747722	A8K1X8|Q6FHS9	Missense_Mutation	SNP	ENST00000226067.5	37	CCDS11585.1	.	.	.	.	.	.	.	.	.	.	G	35	5.525197	0.96431	.	.	ENSG00000108924	ENST00000226067;ENST00000430986	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.83885	0.5351	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.962;0.996	D	0.85824	0.1387	9	0.87932	D	0	.	18.6178	0.91310	0.0:0.0:1.0:0.0	.	144;196	B4DIQ5;Q16534	.;HLF_HUMAN	H	196;111	.	ENSP00000226067:R196H	R	+	2	0	HLF	50747722	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.644000	0.89710	0.655000	0.94253	CGC		0.517	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126		A	53392723	G	A	53392723	3	1	60	1	0	0	0	0	1	0	0	0	7235	1087	38	1	597	1	HLF	17	53392723	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	27424972	53392723	27802487	78	7966										
ANKFN1	162282	broad.mit.edu	37	chr17	54431352	54431352	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gatattgccatcatgaccaaCaatgtgcccattgcaaggat	8	10	1	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr17:54431352C>A	ENST00000318698.2	+	5	590	c.555C>A	c.(553-555)aaC>aaA	p.N185K	ANKFN1_ENST00000566473.2_Missense_Mutation_p.N185K	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	185								p.N185K(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TCATGACCAACAATGTGCCCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											159	118	132					17																	54431352		2203	4300	6503	51786351	SO:0001583	missense	162282			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.555C>A	17.37:g.54431352C>A	ENSP00000321627:p.Asn185Lys		51786351		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.194551	0.78902	.	.	ENSG00000153930	ENST00000318698	T	0.63913	-0.07	5.22	5.22	0.72569	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.78323	0.4265	M	0.84326	2.69	0.49582	D	0.999807	D	0.89917	1.0	D	0.87578	0.998	T	0.80876	-0.1186	10	0.87932	D	0	-15.7985	9.4991	0.39006	0.0:0.8436:0.0:0.1564	.	185	Q8N957	ANKF1_HUMAN	K	185	ENSP00000321627:N185K	ENSP00000321627:N185K	N	+	3	2	ANKFN1	51786351	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.750000	0.38329	2.426000	0.82243	0.655000	0.94253	AAC		0.473	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		A	54431352	C	A	54431352	3	1	60	1	0	0	0	0	1	0	0	0	625	477	17	2	573	2	ANKFN1	17	54431352	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	1038629	54431352	26763858	79	7967										
RNF213	57674	broad.mit.edu	37	chr17	78328244	78328244	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tttctgcctttgtacagcctCtttcttgcgggtatccaaga	8	11	3	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr17:78328244C>T	ENST00000582970.1	+	36	10873	c.10730C>T	c.(10729-10731)tCt>tTt	p.S3577F	RNF213_ENST00000336301.6_Missense_Mutation_p.S1650F|RNF213_ENST00000508628.2_Missense_Mutation_p.S3626F|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3577					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S1650F(1)|p.S3626F(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TGTACAGCCTCTTTCTTGCGG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	17											95	89	91					17																	78328244		2203	4300	6503	75942839	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10730C>T	17.37:g.78328244C>T	ENSP00000464087:p.Ser3577Phe		75942839	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	2.145	-0.395896	0.04899	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.24723	1.84;1.85	4.93	3.96	0.45880	.	0.500984	0.22481	N	0.059498	T	0.38348	0.1037	M	0.66939	2.045	0.09310	N	1	P;P	0.46220	0.874;0.49	P;B	0.51355	0.667;0.193	T	0.19484	-1.0304	10	0.66056	D	0.02	.	11.2159	0.48825	0.1437:0.7181:0.1383:0.0	.	3626;1650	C9JCP4;Q63HN8	.;RN213_HUMAN	F	3577;3626;1650	ENSP00000425956:S3577F;ENSP00000338218:S1650F	ENSP00000338218:S1650F	S	+	2	0	RNF213	75942839	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	0.609000	0.24238	1.091000	0.41335	-0.127000	0.14921	TCT		0.547	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78328244	C	T	78328244	3	4	60	1	0	0	0	0	1	0	0	0	13514	913	32	3	11187	3	RNF213	17	78328244	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	23896892	78328244	2866966	80	7968										
LILRB1	10859	broad.mit.edu	37	chr19	55144588	55144588	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	actttccttctgaccaaggaGggggcagctgatgacccatg	12	11	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr19:55144588G>T	ENST00000396331.1	+	8	1437	c.1080G>T	c.(1078-1080)gaG>gaT	p.E360D	LILRB1_ENST00000396332.4_Missense_Mutation_p.E360D|LILRB1_ENST00000396315.1_Missense_Mutation_p.E360D|LILRB1_ENST00000448689.1_Missense_Mutation_p.E360D|LILRB1_ENST00000396317.1_Missense_Mutation_p.E360D|LILRB1_ENST00000396321.2_Missense_Mutation_p.E360D|LILRB1_ENST00000427581.2_Missense_Mutation_p.E396D|LILRB1_ENST00000324602.7_Missense_Mutation_p.E360D|LILRB1_ENST00000418536.2_Missense_Mutation_p.E360D|LILRB1_ENST00000434867.2_Missense_Mutation_p.E360D|LILRB1_ENST00000396327.3_Missense_Mutation_p.E360D	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	360	Ig-like C2-type 4.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.E360D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		TGACCAAGGAGGGGGCAGCTG	0.582										HNSCC(37;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	19											103	112	109					19																	55144588		2203	4300	6503	59836400	SO:0001583	missense	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1080G>T	19.37:g.55144588G>T	ENSP00000379622:p.Glu360Asp		59836400	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	8.251	0.808994	0.16537	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00705	5.81;5.81;5.81;5.81;5.81;5.81;5.81;5.81;5.81;5.81;5.81	2.25	-4.49	0.03504	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.785098	0.11056	N	0.604486	T	0.01421	0.0046	M	0.79343	2.45	0.09310	N	1	B;B;B;B;B	0.30068	0.137;0.008;0.267;0.016;0.004	B;B;B;B;B	0.39771	0.215;0.067;0.309;0.067;0.077	T	0.31586	-0.9938	10	0.62326	D	0.03	.	2.9992	0.06008	0.4252:0.0:0.2561:0.3187	.	360;360;360;360;360	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	D	360;360;360;360;360;360;360;360;396;360;360	ENSP00000379614:E360D;ENSP00000391514:E360D;ENSP00000409968:E360D;ENSP00000379622:E360D;ENSP00000379618:E360D;ENSP00000315997:E360D;ENSP00000405243:E360D;ENSP00000379623:E360D;ENSP00000395004:E396D;ENSP00000379610:E360D;ENSP00000379608:E360D	ENSP00000315997:E360D	E	+	3	2	LILRB1	59836400	0.005000	0.15991	0.005000	0.12908	0.000000	0.00434	-0.561000	0.05957	-1.502000	0.01814	-2.554000	0.00176	GAG		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55144588	G	T	55144588	3	4	60	1	0	0	0	0	1	0	0	0	8813	991	35	2	1102	2	LILRB1	19	55144588	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		55144588	3984395	81	7969										
ZNF544	27300	broad.mit.edu	37	chr19	58772536	58772536	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	acaggtttccctaagcccaaCtcacaagttaaagagttgaa	7	10	1	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr19:58772536C>T	ENST00000596652.1	+	6	798	c.564C>T	c.(562-564)aaC>aaT	p.N188N	ZNF544_ENST00000600220.1_Silent_p.N160N|ZNF544_ENST00000599953.1_Silent_p.N46N|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000269829.4_Silent_p.N188N|ZNF544_ENST00000415203.2_Silent_p.N160N|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000600044.1_Silent_p.N160N|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000595981.1_Intron			Q6NX49	ZN544_HUMAN	zinc finger protein 544	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N188N(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		CTAAGCCCAACTCACAAGTTA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	19											67	62	64					19																	58772536		2203	4300	6503	63464348	SO:0001819	synonymous_variant	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.564C>T	19.37:g.58772536C>T			63464348	A8K6J1|Q9UEX4	Silent	SNP	ENST00000596652.1	37	CCDS12973.1																																																																																				0.403	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		T	58772536	C	T	58772536	2	4	60	1	0	0	0	0	0	0	0	1	18016	564	20	3		3	ZNF544	19	58772536	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	3627948	58772536	356447	82	7970										
TM9SF4	9777	broad.mit.edu	37	chr20	30753230	30753230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ttgttcgcaagatctatgctGctgtgaagatagactgattg	11	6	1	5			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr20:30753230G>A	ENST00000398022.2	+	18	2147	c.1912G>A	c.(1912-1914)Gct>Act	p.A638T	TM9SF4_ENST00000217315.5_Missense_Mutation_p.A621T	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	638						integral component of membrane (GO:0016021)		p.A621T(1)		central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GATCTATGCTGCTGTGAAGAT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	20											164	130	141					20																	30753230		2203	4300	6503	30216891	SO:0001583	missense	9777			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.1912G>A	20.37:g.30753230G>A	ENSP00000381104:p.Ala638Thr		30216891	B0QYT7|Q9NUA3	Missense_Mutation	SNP	ENST00000398022.2	37	CCDS13196.2	.	.	.	.	.	.	.	.	.	.	G	33	5.221940	0.95139	.	.	ENSG00000101337	ENST00000398022;ENST00000217315	T;T	0.44881	1.49;0.91	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.55065	0.1897	L	0.52573	1.65	0.80722	D	1	P;D	0.64830	0.633;0.994	B;P	0.58210	0.15;0.835	T	0.53753	-0.8394	10	0.45353	T	0.12	-9.3997	18.3035	0.90172	0.0:0.0:1.0:0.0	.	545;638	B4DH88;Q92544	.;TM9S4_HUMAN	T	638;621	ENSP00000381104:A638T;ENSP00000217315:A621T	ENSP00000217315:A621T	A	+	1	0	TM9SF4	30216891	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.542000	0.73869	2.556000	0.86216	0.561000	0.74099	GCT		0.542	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		A	30753230	G	A	30753230	3	1	60	1	0	0	0	0	1	0	0	0	16019	1319	46	3	1982	3	TM9SF4	20	30753230	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		30753230	32272290	83	7971										
SGK2	10110	broad.mit.edu	37	chr20	42204996	42204996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	tccacaaggaccagaggcagCggctgggctccaaagcagac	13	13	0	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr20:42204996C>T	ENST00000341458.4	+	10	1225	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	SGK2_ENST00000373100.1_Missense_Mutation_p.R276W|SGK2_ENST00000373077.1_Missense_Mutation_p.R275W|SGK2_ENST00000423407.3_Missense_Mutation_p.R276W|SGK2_ENST00000426287.1_Missense_Mutation_p.R302W|SGK2_ENST00000373092.3_Missense_Mutation_p.R276W	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	336	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.R336W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCAGAGGCAGCGGCTGGGCTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	20											39	41	41					20																	42204996		2203	4300	6503	41638410	SO:0001583	missense	10110			AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.1006C>T	20.37:g.42204996C>T	ENSP00000340608:p.Arg336Trp		41638410	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573509	0.65765	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	4.65	-0.0418	0.13866	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050719	0.85682	N	0.000000	D	0.88276	0.6393	H	0.99169	4.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.86256	0.1652	10	0.87932	D	0	.	7.7095	0.28669	0.4735:0.4443:0.0:0.0822	.	302;336;276	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	W	276;276;275;276;336;302	ENSP00000362192:R276W;ENSP00000362184:R276W;ENSP00000362168:R275W;ENSP00000392795:R276W;ENSP00000340608:R336W;ENSP00000412214:R302W	ENSP00000340608:R336W	R	+	1	2	SGK2	41638410	0.847000	0.29606	1.000000	0.80357	0.725000	0.41563	-0.078000	0.11375	0.214000	0.20742	0.655000	0.94253	CGG		0.602	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			T	42204996	C	T	42204996	3	4	60	1	0	0	0	0	1	0	0	0	14246	759	27	1	1044	1	SGK2	20	42204996	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	11451766	42204996	20820524	84	7972										
PREX1	57580	broad.mit.edu	37	chr20	47267958	47267958	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcggtgaggccgaagcagccGcggggctccacgatcttctc	15	14	2	1	rs143006779	byFrequency	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr20:47267958G>A	ENST00000371941.3	-	22	2653	c.2631C>T	c.(2629-2631)cgC>cgT	p.R877R	PREX1_ENST00000396220.1_Silent_p.R877R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	877					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R877R(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGAAGCAGCCGCGGGGCTCCA	0.602													G|||	2	0.000399361	0.0015	0	5008	,	,		20278	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	20						G		5,4401	9.9+/-24.2	0,5,2198	49	42	44		2631	-9.4	0.6	20	dbSNP_134	44	0,8600		0,0,4300	no	coding-synonymous	PREX1	NM_020820.3		0,5,6498	AA,AG,GG		0.0,0.1135,0.0384		877/1660	47267958	5,13001	2203	4300	6503	46701365	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2631C>T	20.37:g.47267958G>A			46701365	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																				0.602	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47267958	G	A	47267958	2	1	60	1	0	0	0	0	0	0	0	1	12510	1074	38	1		1	PREX1	20	47267958	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	5062962	47267958	15757562	85	7973										
DOK5	55816	broad.mit.edu	37	chr20	53208302	53208302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gccgctaagcgccctgcggcGgtatggacgtgatactacgt	14	12	0	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr20:53208302G>A	ENST00000262593.5	+	5	907	c.557G>A	c.(556-558)cGg>cAg	p.R186Q	DOK5_ENST00000395939.1_Missense_Mutation_p.R78Q	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	186	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)	p.R186Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			GCCCTGCGGCGGTATGGACGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	20											128	115	119					20																	53208302		2203	4300	6503	52641709	SO:0001583	missense	55816			AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"Pleckstrin homology (PH) domain containing"	16173	protein-coding gene	gene with protein product		608334	"chromosome 20 open reading frame 180"	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.557G>A	20.37:g.53208302G>A	ENSP00000262593:p.Arg186Gln		52641709	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Missense_Mutation	SNP	ENST00000262593.5	37	CCDS13446.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650920	0.87958	.	.	ENSG00000101134	ENST00000262593;ENST00000395939	T;T	0.80653	-1.4;-1.4	5.66	5.66	0.87406	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.85682	D	0.000000	D	0.90899	0.7140	M	0.90082	3.085	0.54753	D	0.999987	D;D	0.67145	0.996;0.996	B;P	0.61722	0.428;0.893	D	0.92419	0.5944	10	0.87932	D	0	-8.162	18.3134	0.90208	0.0:0.0:1.0:0.0	.	78;186	Q9P104-2;Q9P104	.;DOK5_HUMAN	Q	186;78	ENSP00000262593:R186Q;ENSP00000379270:R78Q	ENSP00000262593:R186Q	R	+	2	0	DOK5	52641709	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.795000	0.99099	2.668000	0.90789	0.650000	0.86243	CGG		0.453	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079777.2			A	53208302	G	A	53208302	3	1	60	1	0	0	0	0	1	0	0	0	4711	1116	39	1	575	1	DOK5	20	53208302	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09	5940344	53208302	9817218	86	7974										
MYT1	4661	broad.mit.edu	37	chr20	62848458	62848458	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gcagctcgaggtccctccatAtgggagctaccggcccaacg	12	15	0	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr20:62848458A>T	ENST00000328439.1	+	11	2034	c.1670A>T	c.(1669-1671)tAt>tTt	p.Y557F	MYT1_ENST00000536311.1_Missense_Mutation_p.Y557F|MYT1_ENST00000360149.4_Missense_Mutation_p.Y259F	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Y557F(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GTCCCTCCATATGGGAGCTAC	0.617																																					GBM(59;481 1041 20555 21139 33705)											1	Substitution - Missense(1)	large_intestine(1)	20											78	72	74					20																	62848458		2203	4300	6503	62318902	SO:0001583	missense	4661			M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1670A>T	20.37:g.62848458A>T	ENSP00000327465:p.Tyr557Phe		62318902	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.496381	0.44352	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.48836	0.88;0.8;0.8	5.67	4.55	0.56014	.	0.063541	0.64402	N	0.000004	T	0.61148	0.2324	L	0.55481	1.735	0.47245	D	0.999361	D;B;D	0.76494	0.999;0.223;0.997	D;B;D	0.75020	0.958;0.235;0.985	T	0.58978	-0.7540	10	0.41790	T	0.15	-11.1292	11.9489	0.52944	0.8698:0.0:0.0:0.1302	.	557;557;259	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	F	259;557;557	ENSP00000353269:Y259F;ENSP00000327465:Y557F;ENSP00000442412:Y557F	ENSP00000327465:Y557F	Y	+	2	0	MYT1	62318902	1.000000	0.71417	0.778000	0.31720	0.980000	0.70556	6.032000	0.70918	0.945000	0.37605	0.533000	0.62120	TAT		0.617	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62848458	A	T	62848458	3	4	60	1	0	0	0	0	1	0	0	0	10136	449	16	5	1704	5	MYT1	20	62848458	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	9640156	62848458	177062	87	7975										
NCAM2	4685	broad.mit.edu	37	chr21	22746210	22746210	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	acggccgtatcgaagtcaaaGggcagcatggaagctcatca	12	10	3	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr21:22746210G>T	ENST00000400546.1	+	9	1321	c.1072G>T	c.(1072-1074)Ggg>Tgg	p.G358W	NCAM2_ENST00000535285.1_Missense_Mutation_p.G383W|NCAM2_ENST00000284894.7_Missense_Mutation_p.G216W	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	358	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G358W(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		CGAAGTCAAAGGGCAGCATGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	21											145	136	139					21																	22746210		1932	4124	6056	21668081	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1072G>T	21.37:g.22746210G>T	ENSP00000383392:p.Gly358Trp		21668081	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948052	0.92593	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.66815	-0.23;-0.23;-0.23	5.54	5.54	0.83059	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83202	0.5203	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	D	0.85007	0.0903	10	0.72032	D	0.01	-14.2	18.1211	0.89572	0.0:0.0:1.0:0.0	.	383;216;358	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	W	358;216;383	ENSP00000383392:G358W;ENSP00000284894:G216W;ENSP00000441887:G383W	ENSP00000284894:G216W	G	+	1	0	NCAM2	21668081	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.226000	0.95229	2.618000	0.88619	0.644000	0.83932	GGG		0.418	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22746210	G	T	22746210	3	4	60	1	0	0	0	0	1	0	0	0	10234	1000	35	2	1106	2	NCAM2	21	22746210	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		22746210	25383685	88	7976										
MYO18B	84700	broad.mit.edu	37	chr22	26422994	26422994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	aaacccaattcagttcctgcGagtccctcttagaatccaga	6	13	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr22:26422994G>A	ENST00000407587.2	+	43	7226	c.7057G>A	c.(7057-7059)Gag>Aag	p.E2353K	MYO18B_ENST00000536101.1_Missense_Mutation_p.E2352K|MYO18B_ENST00000335473.7_Missense_Mutation_p.E2352K			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2352						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E2353K(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CAGTTCCTGCGAGTCCCTCTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											81	90	87					22																	26422994		1935	4140	6075	24752994	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7057G>A	22.37:g.26422994G>A	ENSP00000386096:p.Glu2353Lys		24752994	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	25.3	4.621415	0.87460	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.89050	-2.44;-2.44;-2.46	4.89	4.89	0.63831	.	0.194001	0.31257	N	0.007962	D	0.92861	0.7729	L	0.60455	1.87	0.35534	D	0.802536	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;1.0	P;D;D;D;D	0.68765	0.9;0.912;0.912;0.96;0.96	D	0.95646	0.8702	10	0.66056	D	0.02	.	16.609	0.84838	0.0:0.0:1.0:0.0	.	1865;2354;2352;2353;2352	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	K	2352;2352;2353	ENSP00000441229:E2352K;ENSP00000334563:E2352K;ENSP00000386096:E2353K	ENSP00000334563:E2352K	E	+	1	0	MYO18B	24752994	1.000000	0.71417	0.985000	0.45067	0.823000	0.46562	4.943000	0.63554	2.246000	0.74042	0.462000	0.41574	GAG		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26422994	G	A	26422994	3	1	60	1	0	0	0	0	1	0	0	0	10096	1059	37	1	7220	1	MYO18B	22	26422994	Missense_Mutation	SNP	G	TCGA-AG-4015-01A-01W-1073-09		26422994	24881572	89	7977										
SEC14L3	266629	broad.mit.edu	37	chr22	30866514	30866514	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ctcggagccagcgtagaaggAaataatcatcagggttgggc	14	8	2	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chr22:30866514A>T	ENST00000215812.4	-	2	200	c.110T>A	c.(109-111)tTc>tAc	p.F37Y	SEC14L3_ENST00000402286.1_5'UTR|SEC14L3_ENST00000415957.2_5'UTR|SEC14L3_ENST00000403066.1_5'UTR|SEC14L3_ENST00000539629.1_5'UTR|SEC14L3_ENST00000401751.1_5'UTR|SEC14L3_ENST00000540910.1_5'UTR	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	37						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.F37Y(1)		NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	GCGTAGAAGGAAATAATCATC	0.562																																					Esophageal Squamous(108;290 1516 3584 23771 37333)											1	Substitution - Missense(1)	large_intestine(1)	22											128	109	115					22																	30866514		2203	4300	6503	29196514	SO:0001583	missense	266629			AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.110T>A	22.37:g.30866514A>T	ENSP00000215812:p.Phe37Tyr		29196514	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.36|12.36	1.913549|1.913549	0.33815|0.33815	.|.	.|.	ENSG00000100012|ENSG00000100012	ENST00000435069|ENST00000215812	.|D	.|0.86562	.|-2.14	5.39|5.39	5.39|5.39	0.77823|0.77823	.|Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.052433|0.052433	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79375|0.79375	0.4435|0.4435	L|L	0.31476|0.31476	0.935|0.935	0.80722|0.80722	D|D	1|1	.|B	.|0.17268	.|0.021	.|B	.|0.28139	.|0.086	T|T	0.71659|0.71659	-0.4526|-0.4526	6|10	.|0.13853	.|T	.|0.58	-20.1348|-20.1348	10.1841|10.1841	0.42986|0.42986	0.8508:0.0:0.0:0.1492|0.8508:0.0:0.0:0.1492	.|.	.|37	.|Q9UDX4	.|S14L3_HUMAN	L|Y	17|37	.|ENSP00000215812:F37Y	.|ENSP00000215812:F37Y	F|F	-|-	3|2	2|0	SEC14L3|SEC14L3	29196514|29196514	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.886000|0.886000	0.51366|0.51366	1.269000|1.269000	0.33074|0.33074	2.027000|2.027000	0.59764|0.59764	0.528000|0.528000	0.53228|0.53228	TTT|TTC		0.562	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		T	30866514	A	T	30866514	3	4	60	1	0	0	0	0	1	0	0	0	14020	246	9	5	1136	5	SEC14L3	22	30866514	Missense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	4443520	30866514	20438052	90	7978										
ATXN3L	92552	broad.mit.edu	37	chrX	13337039	13337039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	cataatttctaaaatggtgtCgacagcggcctgtactgtgc	10	9	1	0			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:13337039C>T	ENST00000380622.2	-	1	1479	c.1015G>A	c.(1015-1017)Gac>Aac	p.D339N	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	339					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)	p.D339N(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						AAAATGGTGTCGACAGCGGCC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											158	138	144					X																	13337039		1568	3582	5150	13246960	SO:0001583	missense	92552				CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.1015G>A	X.37:g.13337039C>T	ENSP00000369996:p.Asp339Asn		13246960	B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.956769	0.00465	.	.	ENSG00000123594	ENST00000380622	T	0.15256	2.44	0.657	-0.517	0.11947	.	0.218405	0.38548	N	0.001643	T	0.04907	0.0132	N	0.04508	-0.205	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.39375	-0.9617	9	0.07175	T	0.84	.	.	.	.	.	339	Q9H3M9	ATX3L_HUMAN	N	339	ENSP00000369996:D339N	ENSP00000369996:D339N	D	-	1	0	ATXN3L	13246960	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.901000	0.04093	-0.292000	0.08999	0.284000	0.19432	GAC		0.378	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		T	13337039	C	T	13337039	3	4	60	1	0	0	0	0	1	0	0	0	1215	884	31	1	56	1	ATXN3L	23	13337039	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09		13337039	141933521	91	7979										
RP2	6102	broad.mit.edu	37	chrX	46713275	46713275	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	atggtactatcctgaattagCtttccagttcaaagatgcag	8	8	1	2	rs35565082		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:46713275C>A	ENST00000218340.3	+	2	628	c.467C>A	c.(466-468)gCt>gAt	p.A156D		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	156	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)	p.A156D(1)		NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						CCTGAATTAGCTTTCCAGTTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											111	100	103					X																	46713275		2203	4300	6503	46598219	SO:0001583	missense	6102			AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.467C>A	X.37:g.46713275C>A	ENSP00000218340:p.Ala156Asp		46598219	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	37	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.037099	0.54896	.	.	ENSG00000102218	ENST00000218340	D	0.86297	-2.1	5.62	5.62	0.85841	Tubulin binding cofactor C (1);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.80491	0.4633	L	0.28504	0.86	0.80722	D	1	B	0.30361	0.277	B	0.20384	0.029	T	0.76879	-0.2796	10	0.25106	T	0.35	-18.004	18.6553	0.91450	0.0:1.0:0.0:0.0	.	156	O75695	XRP2_HUMAN	D	156	ENSP00000218340:A156D	ENSP00000218340:A156D	A	+	2	0	RP2	46598219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.371000	0.79600	2.349000	0.79799	0.513000	0.50165	GCT		0.393	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		A	46713275	C	A	46713275	3	1	60	1	0	0	0	0	1	0	0	0	13571	797	28	2	473	2	RP2	23	46713275	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	33376236	46713275	108557285	92	7980										
WDR13	64743	broad.mit.edu	37	chrX	48460237	48460237	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ggcaagaaagtgaaggggggCtccagcaagctgacaggccg	17	9	0	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:48460237C>T	ENST00000218056.5	+	6	1402	c.897C>T	c.(895-897)ggC>ggT	p.G299G	WDR13_ENST00000376729.5_Silent_p.G299G	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	299						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G299G(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TGAAGGGGGGCTCCAGCAAGC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	X											79	57	65					X																	48460237		2203	4300	6503	48345181	SO:0001819	synonymous_variant	64743			AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.897C>T	X.37:g.48460237C>T			48345181	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Silent	SNP	ENST00000218056.5	37	CCDS14302.1																																																																																				0.577	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			T	48460237	C	T	48460237	2	4	60	1	0	0	0	0	0	0	0	1	17315	784	28	3		3	WDR13	23	48460237	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	1746962	48460237	106810323	93	7981										
RPS6KA6	27330	broad.mit.edu	37	chrX	83389795	83389795	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agaaaatctgcatacctgttAatttgatatgtcctatttca	5	7	2	2			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:83389795A>T	ENST00000262752.2	-	8	648	c.641T>A	c.(640-642)tTa>tAa	p.L214*	RPS6KA6_ENST00000543399.1_Nonsense_Mutation_p.L214*	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	214	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L214*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						CATACCTGTTAATTTGATATG	0.239																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											36	35	36					X																	83389795		2181	4237	6418	83276451	SO:0001587	stop_gained	27330			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.641T>A	X.37:g.83389795A>T	ENSP00000262752:p.Leu214*		83276451	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Nonsense_Mutation	SNP	ENST00000262752.2	37	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	A	34	5.405613	0.96051	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	.	.	.	4.62	3.41	0.39046	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5844	0.45273	0.8401:0.1599:0.0:0.0	.	.	.	.	X	214	.	ENSP00000262752:L214X	L	-	2	0	RPS6KA6	83276451	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.524000	0.90579	0.445000	0.26639	0.425000	0.28330	TTA		0.239	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		T	83389795	A	T	83389795	4	4	60	1	0	0	0	0	0	1	0	0	13692	372	13	5	1656	5	RPS6KA6	23	83389795	Nonsense_Mutation	SNP	A	TCGA-AG-4015-01A-01W-1073-09	34929558	83389795	71880765	94	7982										
RGAG1	57529	broad.mit.edu	37	chrX	109696416	109696416	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	agatccacagcctctggaggGatgtccatgccactgatgag	12	11	1	3			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:109696416G>A	ENST00000465301.2	+	3	2817	c.2571G>A	c.(2569-2571)ggG>ggA	p.G857G	RGAG1_ENST00000540313.1_Silent_p.G857G	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	857								p.G857G(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CCTCTGGAGGGATGTCCATGC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	X											174	161	165					X																	109696416		2203	4300	6503	109583072	SO:0001819	synonymous_variant	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2571G>A	X.37:g.109696416G>A			109583072	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																				0.532	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109696416	G	A	109696416	2	1	60	1	0	0	0	0	0	0	0	1	13311	1161	41	3		3	RGAG1	23	109696416	Silent	SNP	G	TCGA-AG-4015-01A-01W-1073-09	26306621	109696416	45574144	95	7983										
MAGEC3	139081	broad.mit.edu	37	chrX	140983314	140983314	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	gatggccgccgagggctgacCgaggcgtccccacaacagaa	14	14	0	2	rs188167309		TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:140983314C>T	ENST00000298296.1	+	6	1092	c.1092C>T	c.(1090-1092)acC>acT	p.T364T	MAGEC3_ENST00000483584.1_Intron|MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000544766.1_Intron|MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000409007.1_5'Flank|MAGEC3_ENST00000448920.1_3'UTR	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	364	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.			GLTEASPQQKKGG -> SSPLPSTLILGVP (in Ref. 3). {ECO:0000305}.				p.T364T(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GAGGGCTGACCGAGGCGTCCC	0.612													G|||	1	0.000264901	0	0	3775	,	,		7247	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											34	35	35					X																	140983314		2201	4296	6497	140810980	SO:0001819	synonymous_variant	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1092C>T	X.37:g.140983314C>T			140810980	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	37	CCDS14676.1																																																																																				0.612	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140983314	C	T	140983314	2	4	60	1	0	0	0	0	0	0	0	1	9212	639	23	1		1	MAGEC3	23	140983314	Silent	SNP	C	TCGA-AG-4015-01A-01W-1073-09	31286898	140983314	14287246	96	7984										
MAGEC2	51438	broad.mit.edu	37	chrX	141290933	141290933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0618556701030928	6	1	0.745009416195857	0	0.771150097465887	0.0108359133126935	0.101690878780662	0	ccgatactccaggtaatgtcCctgcacccaaactttagtga	7	13	0	1			TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-4015-01A-01W-1073-09	TCGA-AG-4015-10A-01W-1073-09	g.chrX:141290933C>T	ENST00000247452.3	-	3	1188	c.841G>A	c.(841-843)Gga>Aga	p.G281R		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	281	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.G281R(1)		NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AGGTAATGTCCCTGCACCCAA	0.522										HNSCC(46;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	X											91	91	91					X																	141290933		2203	4300	6503	141118599	SO:0001583	missense	51438			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.841G>A	X.37:g.141290933C>T	ENSP00000354660:p.Gly281Arg		141118599	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	37	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	6.733	0.504024	0.12822	.	.	ENSG00000046774	ENST00000247452	T	0.04317	3.65	0.988	-0.145	0.13436	.	0.228439	0.36066	U	0.002814	T	0.01523	0.0049	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.43410	-0.9393	10	0.49607	T	0.09	.	4.4166	0.11459	0.0:0.5759:0.4241:0.0	.	281	Q9UBF1	MAGC2_HUMAN	R	281	ENSP00000354660:G281R	ENSP00000354660:G281R	G	-	1	0	MAGEC2	141118599	0.000000	0.05858	0.002000	0.10522	0.119000	0.20118	-0.794000	0.04584	-0.093000	0.12396	0.284000	0.19432	GGA		0.522	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		T	141290933	C	T	141290933	3	4	60	1	0	0	0	0	1	0	0	0	9211	632	22	3	284	3	MAGEC2	23	141290933	Missense_Mutation	SNP	C	TCGA-AG-4015-01A-01W-1073-09	307619	141290933	13979627	97	7985										
NOC2L	26155	broad.mit.edu	37	chr1	892306	892306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccatctctcaaccatggCgacggtcacaggaacagaat	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:892306C>T	ENST00000327044.6	-	4	503	c.454G>A	c.(454-456)Gcc>Acc	p.A152T	NOC2L_ENST00000487214.1_5'UTR	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	152					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)	p.A152T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		TCAACCATGGCGACGGTCACA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											155	156	156					1																	892306		2203	4300	6503	882169	SO:0001583	missense	26155			AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"novel INHAT repressor", "protein phosphatase 1, regulatory subunit 12"	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.454G>A	1.37:g.892306C>T	ENSP00000317992:p.Ala152Thr		882169	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	.	.	.	.	.	.	.	.	.	.	C	1.891	-0.455352	0.04540	.	.	ENSG00000188976	ENST00000327044	T	0.24723	1.84	4.54	1.56	0.23342	.	0.521758	0.19774	N	0.106370	T	0.17619	0.0423	L	0.46157	1.445	0.18873	N	0.999981	B;B	0.20887	0.049;0.049	B;B	0.15052	0.012;0.012	T	0.26849	-1.0091	10	0.14252	T	0.57	-9.3456	7.1513	0.25612	0.0:0.5402:0.0:0.4598	.	152;152	B3KNC3;Q9Y3T9	.;NOC2L_HUMAN	T	152	ENSP00000317992:A152T	ENSP00000317992:A152T	A	-	1	0	NOC2L	882169	0.006000	0.16342	0.540000	0.28089	0.120000	0.20174	0.367000	0.20382	0.466000	0.27193	-0.142000	0.14014	GCC		0.607	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658		T	892306	C	T	892306	3	4	61	1	0	0	0	0	1	0	0	0	10544	768	27	1	1859	1	NOC2L	1	892306	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		892306	248358315	1	7986										
CDK11A	728642	broad.mit.edu	37	chr1	1636056	1636056	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctccacgtagttcatcacGatgtagatcttgtccatgtt	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:1636056G>A	ENST00000378633.1	-	14	1585	c.1506C>T	c.(1504-1506)atC>atT	p.I502I	CDK11A_ENST00000357760.2_Silent_p.I498I|CDK11A_ENST00000356200.3_Silent_p.I465I|CDK11A_ENST00000404249.3_Silent_p.I499I|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000495016.1_5'Flank|CDK11A_ENST00000358779.5_Silent_p.I489I|CDK11A_ENST00000378638.2_Silent_p.I465I			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	502	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I498I(1)|p.I514I(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						AGTTCATCACGATGTAGATCT	0.632																																					Pancreas(186;965 2119 30274 40311 50569)											2	Substitution - coding silent(2)	large_intestine(2)	1																																								1625916	SO:0001819	synonymous_variant	728642			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"Cyclin-dependent kinases"	1730	protein-coding gene	gene with protein product		116951	"cell division cycle 2-like 2", "cell division cycle 2-like 2 (PITSLRE proteins)"	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1506C>T	1.37:g.1636056G>A			1625916	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Silent	SNP	ENST00000378633.1	37																																																																																					0.632	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		A	1636056	G	A	1636056	2	1	61	1	0	0	0	0	0	0	0	1	3132	1048	37	1		1	CDK11A	1	1636056	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	743750	1636056	247614565	2	7987										
KIAA1751	85452	broad.mit.edu	37	chr1	1920015	1920015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggcgctcaggttctgccGcaggtgaaatgcctgcgttc	14	12	2	1	rs199576325		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:1920015G>A	ENST00000434971.2	-	4	264	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W				Q69YW0	CA222_HUMAN		0								p.R78W(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGGTTCTGCCGCAGGTGAAAT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	117	115					1																	1920015		2052	4193	6245	1909875	SO:0001583	missense	85452																														ENST00000434971.2:c.232C>T	1.37:g.1920015G>A	ENSP00000408078:p.Arg78Trp		1909875		Missense_Mutation	SNP	ENST00000434971.2	37		.	.	.	.	.	.	.	.	.	.	G	13.89	2.373030	0.42105	.	.	ENSG00000142609	ENST00000270720;ENST00000378590;ENST00000434971	T;T	0.65549	-0.16;-0.12	3.89	0.178	0.15058	.	0.222162	0.25529	N	0.030045	T	0.73009	0.3532	M	0.67953	2.075	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.64980	-0.6279	10	0.87932	D	0	-20.8805	10.3702	0.44049	0.0:0.0:0.354:0.646	.	78;78	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	W	78;69;78	ENSP00000367853:R69W;ENSP00000408078:R78W	ENSP00000270720:R78W	R	-	1	2	C1orf222	1909875	0.002000	0.14202	0.014000	0.15608	0.012000	0.07955	-0.007000	0.12810	-0.073000	0.12842	-0.493000	0.04662	CGG		0.502	C1orf222-201	KNOWN	basic	protein_coding	protein_coding				A	1920015	G	A	1920015	3	1	61	1	0	0	0	0	1	0	0	0	8277	1086	38	1	2116	1	KIAA1751	1	1920015	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283959	1920015	247330606	3	7988										
PRDM16	63976	broad.mit.edu	37	chr1	3328498	3328498	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggggcccgaggagaagttCgagagccgcctggaggactc	18	11	0	2	rs35579804	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:3328498C>T	ENST00000270722.5	+	9	1786	c.1737C>T	c.(1735-1737)ttC>ttT	p.F579F	PRDM16_ENST00000378398.3_Silent_p.F580F|PRDM16_ENST00000441472.2_Silent_p.F579F|PRDM16_ENST00000511072.1_Silent_p.F580F|PRDM16_ENST00000378391.2_Silent_p.F579F|PRDM16_ENST00000442529.2_Silent_p.F579F|PRDM16_ENST00000514189.1_Silent_p.F580F|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	579					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.F579F(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AGGAGAAGTTCGAGAGCCGCC	0.662			T	EVI1	"MDS, AML"																																		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	1	Substitution - coding silent(1)	large_intestine(1)	1											34	45	41					1																	3328498		2116	4236	6352	3318358	SO:0001819	synonymous_variant	63976			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1737C>T	1.37:g.3328498C>T			3318358	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																				0.662	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3328498	C	T	3328498	2	4	61	1	0	0	0	0	0	0	0	1	12491	883	31	1		1	PRDM16	1	3328498	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1408483	3328498	245922123	4	7989										
CCDC27	148870	broad.mit.edu	37	chr1	3680321	3680321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaagaaacccagctgcGaaagatcaatacggaaaatg	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:3680321G>A	ENST00000294600.2	+	8	1457	c.1373G>A	c.(1372-1374)cGa>cAa	p.R458Q		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	458								p.R458Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		ACCCAGCTGCGAAAGATCAAT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	104	104					1																	3680321		2203	4300	6503	3670181	SO:0001583	missense	148870				CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1373G>A	1.37:g.3680321G>A	ENSP00000294600:p.Arg458Gln		3670181	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	.	.	.	.	.	.	.	.	.	.	G	3.034	-0.198923	0.06219	.	.	ENSG00000162592	ENST00000294600	T	0.19394	2.15	4.76	-1.24	0.09435	.	0.819777	0.10648	N	0.650228	T	0.07369	0.0186	N	0.08118	0	0.09310	N	1	B	0.28178	0.202	B	0.23852	0.049	T	0.38564	-0.9655	10	0.07175	T	0.84	-8.0746	6.0813	0.19942	0.2101:0.0:0.6175:0.1724	.	458	Q2M243	CCD27_HUMAN	Q	458	ENSP00000294600:R458Q	ENSP00000294600:R458Q	R	+	2	0	CCDC27	3670181	0.010000	0.17322	0.004000	0.12327	0.006000	0.05464	0.079000	0.14782	-0.158000	0.11040	0.462000	0.41574	CGA		0.567	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		A	3680321	G	A	3680321	3	1	61	1	0	0	0	0	1	0	0	0	2807	1058	37	1	1403	1	CCDC27	1	3680321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	351823	3680321	245570300	5	7990										
KIAA0562	9731	broad.mit.edu	37	chr1	3753214	3753214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctccccataatgcttacGaatagctggaagaggccgct	10	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:3753214G>A	ENST00000378230.3	-	10	1486	c.1162C>T	c.(1162-1164)Cgt>Tgt	p.R388C	CEP104_ENST00000460038.1_Intron	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	388						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.R388C(1)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						TAATGCTTACGAATAGCTGGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	73	75					1																	3753214		2203	4300	6503	3743074	SO:0001583	missense	9731			AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1162C>T	1.37:g.3753214G>A	ENSP00000367476:p.Arg388Cys		3743074	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.674236	0.29693	.	.	ENSG00000116198	ENST00000378230;ENST00000443466	T;T	0.48522	1.36;0.81	5.68	4.77	0.60923	.	0.569195	0.17844	N	0.160112	T	0.45875	0.1364	M	0.77820	2.39	0.09310	N	0.999996	B;B	0.26041	0.14;0.055	B;B	0.18871	0.023;0.016	T	0.48603	-0.9021	10	0.54805	T	0.06	.	6.6514	0.22965	0.1515:0.0:0.7034:0.1451	.	388;388	O60308-3;O60308	.;CE104_HUMAN	C	388;82	ENSP00000367476:R388C;ENSP00000411927:R82C	ENSP00000367476:R388C	R	-	1	0	CEP104	3743074	0.019000	0.18553	0.008000	0.14137	0.032000	0.12392	1.970000	0.40520	1.395000	0.46643	0.650000	0.86243	CGT		0.562	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3753214	G	A	3753214	3	1	61	1	0	0	0	0	1	0	0	0	8205	1058	37	1	1667	1	KIAA0562	1	3753214	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72893	3753214	245497407	6	7991										
KIAA0562	9731	broad.mit.edu	37	chr1	3765182	3765182	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattcttacccaagtcttcGaaaccgctctgcttgatagg	7	12	4	1	rs145420390		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:3765182G>A	ENST00000378230.3	-	3	601	c.277C>T	c.(277-279)Cga>Tga	p.R93*	CEP104_ENST00000378223.3_Nonsense_Mutation_p.R93*	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	93						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.R93*(3)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						CCAAGTCTTCGAAACCGCTCT	0.358																																																3	Substitution - Nonsense(3)	large_intestine(2)|skin(1)	1											91	92	92					1																	3765182		2203	4300	6503	3755042	SO:0001587	stop_gained	9731			AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.277C>T	1.37:g.3765182G>A	ENSP00000367476:p.Arg93*		3755042	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Nonsense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	40	8.258558	0.98729	.	.	ENSG00000116198	ENST00000378230;ENST00000378223	.	.	.	5.14	5.14	0.70334	.	0.204058	0.42964	D	0.000640	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6015	0.88026	0.0:0.0:1.0:0.0	.	.	.	.	X	93	.	ENSP00000367468:R93X	R	-	1	2	CEP104	3755042	1.000000	0.71417	0.990000	0.47175	0.971000	0.66376	7.156000	0.77453	2.395000	0.81488	0.591000	0.81541	CGA		0.358	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3765182	G	A	3765182	4	1	61	1	0	0	0	0	0	1	0	0	8205	1066	37	1	2580	1	KIAA0562	1	3765182	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11968	3765182	245485439	7	7992										
AJAP1	55966	broad.mit.edu	37	chr1	4829995	4829995	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacaactcttgtcttaaaAaattggtaaggctccttggg	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:4829995A>C	ENST00000378191.4	+	3	1293	c.912A>C	c.(910-912)aaA>aaC	p.K304N	AJAP1_ENST00000378190.3_Missense_Mutation_p.K304N	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	304	Targeting signals.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K304N(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		TTGTCTTAAAAAATTGGTAAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	151	151					1																	4829995		2203	4300	6503	4729855	SO:0001583	missense	55966			AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.912A>C	1.37:g.4829995A>C	ENSP00000367433:p.Lys304Asn		4729855	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	37	CCDS54.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.622575	0.46840	.	.	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.64991	-0.13;-0.13	5.38	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.66177	0.2763	L	0.27053	0.805	0.51233	D	0.999916	D	0.89917	1.0	D	0.87578	0.998	T	0.67848	-0.5564	10	0.87932	D	0	-13.375	10.0175	0.42022	0.9206:0.0:0.0794:0.0	.	304	Q9UKB5	AJAP1_HUMAN	N	304	ENSP00000367432:K304N;ENSP00000367433:K304N	ENSP00000367432:K304N	K	+	3	2	AJAP1	4729855	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.703000	0.54808	0.888000	0.36160	0.383000	0.25322	AAA		0.517	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		C	4829995	A	C	4829995	3	2	61	1	0	0	0	0	1	0	0	0	438	11	1	4	922	4	AJAP1	1	4829995	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1064813	4829995	244420626	8	7993										
AJAP1	55966	broad.mit.edu	37	chr1	4834526	4834526	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcttattcctgtggccttCgtgtctgagaaatggtttga	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:4834526C>T	ENST00000378191.4	+	5	1584	c.1203C>T	c.(1201-1203)ttC>ttT	p.F401F	AJAP1_ENST00000378190.3_Silent_p.F401F	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	401	Targeting signals.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F401F(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		CTGTGGCCTTCGTGTCTGAGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											209	189	196					1																	4834526		2203	4300	6503	4734386	SO:0001819	synonymous_variant	55966			AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.1203C>T	1.37:g.4834526C>T			4734386	Q9Y229	Silent	SNP	ENST00000378191.4	37	CCDS54.1																																																																																				0.522	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		T	4834526	C	T	4834526	2	4	61	1	0	0	0	0	0	0	0	1	438	883	31	1		1	AJAP1	1	4834526	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4531	4834526	244416095	9	7994										
NPHP4	261734	broad.mit.edu	37	chr1	5935092	5935092	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcgatgctctcggccttCgtgcgttcccggtaggcggc	15	14	1	0	rs368320071		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:5935092C>T	ENST00000378156.4	-	21	3151	c.2886G>A	c.(2884-2886)acG>acA	p.T962T	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	962					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.T962T(1)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TCTCGGCCTTCGTGCGTTCCC	0.642													c|||	1	0.000199681	0	0	5008	,	,		17567	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1								0,4388		0,0,2194	64	79	74		2886	-9.3	0	1		74	2,8562	2.2+/-6.3	0,2,4280	no	coding-synonymous	NPHP4	NM_015102.3		0,2,6474	TT,TC,CC		0.0234,0.0,0.0154		962/1427	5935092	2,12950	2194	4282	6476	5857679	SO:0001819	synonymous_variant	261734			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2886G>A	1.37:g.5935092C>T			5857679	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																				0.642	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			T	5935092	C	T	5935092	2	4	61	1	0	0	0	0	0	0	0	1	10612	871	31	1		1	NPHP4	1	5935092	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1100566	5935092	243315529	10	7995										
NPHP4	261734	broad.mit.edu	37	chr1	5964828	5964828	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaaggtgaaatacacagtCtttggccatgatgttcctcg	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:5964828C>A	ENST00000378156.4	-	16	2257	c.1992G>T	c.(1990-1992)aaG>aaT	p.K664N	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	664					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.K664K(2)|p.K664N(1)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		AATACACAGTCTTTGGCCATG	0.577																																																3	Substitution - coding silent(2)|Substitution - Missense(1)	prostate(2)|large_intestine(1)	1											124	127	126					1																	5964828		2104	4228	6332	5887415	SO:0001583	missense	261734			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1992G>T	1.37:g.5964828C>A	ENSP00000367398:p.Lys664Asn		5887415	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747522	0.30955	.	.	ENSG00000131697	ENST00000378156;ENST00000378160	D	0.87887	-2.31	5.1	2.82	0.32997	.	0.575121	0.15995	N	0.234631	T	0.79604	0.4474	L	0.40543	1.245	0.22017	N	0.999414	B	0.19583	0.037	B	0.19666	0.026	T	0.67142	-0.5745	10	0.37606	T	0.19	.	6.7665	0.23571	0.1558:0.6841:0.0:0.1601	.	664	O75161	NPHP4_HUMAN	N	664;67	ENSP00000367398:K664N	ENSP00000367398:K664N	K	-	3	2	NPHP4	5887415	0.028000	0.19301	0.993000	0.49108	0.989000	0.77384	0.098000	0.15189	1.108000	0.41662	0.655000	0.94253	AAG		0.577	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	5964828	C	A	5964828	3	1	61	1	0	0	0	0	1	0	0	0	10612	912	32	2	2348	2	NPHP4	1	5964828	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29736	5964828	243285793	11	7996										
NPHP4	261734	broad.mit.edu	37	chr1	5965483	5965483	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttattggcatccagaatCtcgggaaagccggaggactg	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:5965483C>A	ENST00000378156.4	-	15	2089	c.1824G>T	c.(1822-1824)gaG>gaT	p.E608D	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	608					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.E608D(1)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CATCCAGAATCTCGGGAAAGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	65	65					1																	5965483		1971	4155	6126	5888070	SO:0001583	missense	261734			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1824G>T	1.37:g.5965483C>A	ENSP00000367398:p.Glu608Asp		5888070	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	C	5.534	0.283405	0.10458	.	.	ENSG00000131697	ENST00000378156;ENST00000378160	D	0.86865	-2.18	5.52	3.42	0.39159	.	0.142736	0.45361	D	0.000363	T	0.73721	0.3623	N	0.16201	0.385	0.29932	N	0.821808	P	0.43352	0.804	P	0.44860	0.462	T	0.67405	-0.5679	10	0.21540	T	0.41	.	2.2267	0.03986	0.1542:0.4903:0.1506:0.2049	.	608	O75161	NPHP4_HUMAN	D	608;11	ENSP00000367398:E608D	ENSP00000367398:E608D	E	-	3	2	NPHP4	5888070	0.864000	0.29904	0.999000	0.59377	0.307000	0.27823	-0.141000	0.10327	1.327000	0.45338	0.561000	0.74099	GAG		0.562	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	5965483	C	A	5965483	3	1	61	1	0	0	0	0	1	0	0	0	10612	912	32	2	2520	2	NPHP4	1	5965483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	655	5965483	243285138	12	7997										
CHD5	26038	broad.mit.edu	37	chr1	6191703	6191703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggtaccattgaatctgtCgattgcctcctgccggaggc	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:6191703C>T	ENST00000262450.3	-	21	3349	c.3250G>A	c.(3250-3252)Gac>Aac	p.D1084N	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.D1084N(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TTGAATCTGTCGATTGCCTCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	76	78					1																	6191703		2203	4300	6503	6114290	SO:0001583	missense	26038			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.3250G>A	1.37:g.6191703C>T	ENSP00000262450:p.Asp1084Asn		6114290	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654638	0.67472	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.91180	-2.8	5.09	4.16	0.48862	Helicase, C-terminal (3);	0.000000	0.64402	D	0.000001	D	0.91915	0.7440	L	0.39397	1.21	0.80722	D	1	D	0.65815	0.995	P	0.60012	0.867	D	0.92808	0.6262	10	0.87932	D	0	-41.5577	15.7116	0.77631	0.0:0.8625:0.1375:0.0	.	1084	Q8TDI0	CHD5_HUMAN	N	1084;600;492;492	ENSP00000262450:D1084N	ENSP00000262450:D1084N	D	-	1	0	CHD5	6114290	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	7.699000	0.84547	1.242000	0.43836	0.561000	0.74099	GAC		0.572	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6191703	C	T	6191703	3	4	61	1	0	0	0	0	1	0	0	0	3334	884	31	1	2698	1	CHD5	1	6191703	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	226220	6191703	243058918	13	7998										
CHD5	26038	broad.mit.edu	37	chr1	6212508	6212508	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgttgctgatccccccGaagcggaacttgagcccggc	11	15	1	2	rs200170499	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:6212508G>A	ENST00000262450.3	-	6	933	c.834C>T	c.(832-834)ttC>ttT	p.F278F	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.F278F(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGATCCCCCCGAAGCGGAACT	0.537													G|||	2	0.000399361	0	0	5008	,	,		17959	0.001		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	147	122	130		834	-8.8	0.7	1		130	0,8600		0,0,4300	no	coding-synonymous	CHD5	NM_015557.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		278/1955	6212508	1,13005	2203	4300	6503	6135095	SO:0001819	synonymous_variant	26038			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.834C>T	1.37:g.6212508G>A			6135095	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																				0.537	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6212508	G	A	6212508	2	1	61	1	0	0	0	0	0	0	0	1	3334	1049	37	1		1	CHD5	1	6212508	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20805	6212508	243038113	14	7999										
RNF207	388591	broad.mit.edu	37	chr1	6270289	6270289	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccccctcccccagccaataCgaagagaaggacaaggcctt	8	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:6270289C>T	ENST00000377939.4	+	9	934	c.807C>T	c.(805-807)taC>taT	p.Y269Y	RNF207_ENST00000377948.2_Silent_p.Y42Y	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	269						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.Y269Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CCAGCCAATACGAAGAGAAGG	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	1											48	50	49					1																	6270289		2203	4300	6503	6192876	SO:0001819	synonymous_variant	388591			AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"RING-type (C3HC4) zinc fingers"	32947	protein-coding gene	gene with protein product	"OTTHUMG00000001089"		"chromosome 1 open reading frame 188"	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.807C>T	1.37:g.6270289C>T			6192876	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																				0.672	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396		T	6270289	C	T	6270289	2	4	61	1	0	0	0	0	0	0	0	1	13511	547	19	1		1	RNF207	1	6270289	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57781	6270289	242980332	15	8000										
TAS1R1	80835	broad.mit.edu	37	chr1	6636659	6636659	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaaacataaatgagaccaAaatccagtggcacggaaagg	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:6636659A>C	ENST00000333172.6	+	4	1638	c.1445A>C	c.(1444-1446)aAa>aCa	p.K482T	TAS1R1_ENST00000328191.4_Intron|TAS1R1_ENST00000351136.3_Missense_Mutation_p.K228T	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	482					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)	p.K482T(1)		NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		AATGAGACCAAAATCCAGTGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	75	77					1																	6636659		2203	4300	6503	6559246	SO:0001583	missense	80835				CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1445A>C	1.37:g.6636659A>C	ENSP00000331867:p.Lys482Thr		6559246	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.92|17.92	3.507061|3.507061	0.64410|0.64410	.|.	.|.	ENSG00000173662|ENSG00000173662	ENST00000415267|ENST00000333172;ENST00000437392;ENST00000351136	T|D;T	0.75050|0.86230	-0.9|-2.09;-0.83	5.05|5.05	3.85|3.85	0.44370|0.44370	.|.	0.718258|0.718258	0.14095|0.14095	N|N	0.341726|0.341726	T|T	0.81019|0.81019	0.4736|0.4736	N|N	0.24115|0.24115	0.695|0.695	0.22127|0.22127	N|N	0.999343|0.999343	.|D;P;P	.|0.53462	.|0.96;0.952;0.704	.|P;P;B	.|0.49085	.|0.59;0.6;0.229	T|T	0.69109|0.69109	-0.5232|-0.5232	8|10	0.32370|0.21540	T|T	0.25|0.41	.|.	8.7915|8.7915	0.34854|0.34854	0.8323:0.0:0.0:0.1677|0.8323:0.0:0.0:0.1677	.|.	.|228;228;482	.|Q7RTX1-4;Q7RTX1-2;Q7RTX1	.|.;.;TS1R1_HUMAN	Q|T	154|482;150;228	ENSP00000408448:K154Q|ENSP00000331867:K482T;ENSP00000312558:K228T	ENSP00000408448:K154Q|ENSP00000331867:K482T	K|K	+|+	1|2	0|0	TAS1R1|TAS1R1	6559246|6559246	0.114000|0.114000	0.22134|0.22134	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	0.337000|0.337000	0.19841|0.19841	1.881000|1.881000	0.54492|0.54492	0.482000|0.482000	0.46254|0.46254	AAA|AAA		0.507	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			C	6636659	A	C	6636659	3	2	61	1	0	0	0	0	1	0	0	0	15601	14	1	4	1459	4	TAS1R1	1	6636659	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	366370	6636659	242613962	16	8001										
DNAJC11	55735	broad.mit.edu	37	chr1	6712908	6712908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctccccatccctttgccGaagttactcgtctgagcgca	7	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:6712908G>A	ENST00000377577.5	-	6	734	c.611C>T	c.(610-612)tCg>tTg	p.S204L	DNAJC11_ENST00000542246.1_Missense_Mutation_p.S166L|DNAJC11_ENST00000294401.7_Missense_Mutation_p.S204L|DNAJC11_ENST00000349363.6_Missense_Mutation_p.S166L|DNAJC11_ENST00000377573.5_Missense_Mutation_p.S114L	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	204						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.S204L(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCTTTGCCGAAGTTACTCG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											143	136	139					1																	6712908		2203	4300	6503	6635495	SO:0001583	missense	55735			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.611C>T	1.37:g.6712908G>A	ENSP00000366800:p.Ser204Leu		6635495	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139664	0.94560	.	.	ENSG00000007923	ENST00000377577;ENST00000451196;ENST00000349363;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T;T;T	0.54479	2.12;1.03;0.57;2.12;1.83;1.43;1.98	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.75258	0.3825	M	0.82056	2.57	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.963;0.976;0.997;0.923	T	0.78383	-0.2225	10	0.87932	D	0	-20.2492	18.4511	0.90704	0.0:0.0:1.0:0.0	.	114;180;204;204	B4DGD5;Q5TH61;Q9NVH1-3;Q9NVH1	.;.;.;DJC11_HUMAN	L	204;180;166;204;166;114;204	ENSP00000366800:S204L;ENSP00000415871:S180L;ENSP00000326304:S166L;ENSP00000294401:S204L;ENSP00000444020:S166L;ENSP00000366796:S114L;ENSP00000410194:S204L	ENSP00000294401:S204L	S	-	2	0	DNAJC11	6635495	1.000000	0.71417	0.760000	0.31359	0.972000	0.66771	9.328000	0.96403	2.666000	0.90696	0.655000	0.94253	TCG		0.483	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		A	6712908	G	A	6712908	3	1	61	1	0	0	0	0	1	0	0	0	4641	1059	37	1	1112	1	DNAJC11	1	6712908	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76249	6712908	242537713	17	8002										
CAMTA1	23261	broad.mit.edu	37	chr1	7805038	7805038	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgagctggctggccagTtatctagcggatgctgactg	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:7805038T>G	ENST00000303635.7	+	17	4533	c.4326T>G	c.(4324-4326)agT>agG	p.S1442R	CAMTA1_ENST00000439411.2_Missense_Mutation_p.S1442R|CAMTA1_ENST00000476864.1_Missense_Mutation_p.S6R	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S1442R(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GGCTGGCCAGTTATCTAGCGG	0.522			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	1	Substitution - Missense(1)	large_intestine(1)	1											109	95	100					1																	7805038		2203	4300	6503	7727625	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.4326T>G	1.37:g.7805038T>G	ENSP00000306522:p.Ser1442Arg		7727625	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.88|19.88	3.908689|3.908689	0.72868|0.72868	.|.	.|.	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646;ENST00000476864|ENST00000495233;ENST00000490905	T;T;T|.	0.56444|.	1.85;1.78;0.46|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.240460|.	0.48767|.	D|.	0.000171|.	T|T	0.72423|0.72423	0.3458|0.3458	M|M	0.68593|0.68593	2.085|2.085	0.48696|0.48696	D|D	0.999699|0.999699	P;P;B;P|.	0.42757|.	0.789;0.624;0.255;0.554|.	B;B;B;B|.	0.38106|.	0.265;0.261;0.141;0.241|.	T|T	0.72523|0.72523	-0.4267|-0.4267	10|5	0.46703|.	T|.	0.11|.	-1.5509|-1.5509	15.2307|15.2307	0.73386|0.73386	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1442;505;398;1442|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	R|G	1442;1442;505;398;6|399;22	ENSP00000306522:S1442R;ENSP00000402561:S1442R;ENSP00000452319:S6R|.	ENSP00000306522:S1442R|.	S|V	+|+	3|2	2|0	CAMTA1|CAMTA1	7727625|7727625	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.795000|0.795000	0.44927|0.44927	3.180000|3.180000	0.50895|0.50895	1.998000|1.998000	0.58463|0.58463	0.533000|0.533000	0.62120|0.62120	AGT|GTT		0.522	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	7805038	T	G	7805038	3	3	61	1	0	0	0	0	1	0	0	0	2619	1722	60	4	4392	4	CAMTA1	1	7805038	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1092130	7805038	241445583	18	8003										
VAMP3	9341	broad.mit.edu	37	chr1	7833537	7833537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgccactggcagtaatcGaagacttcagcagacacaaa	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:7833537G>A	ENST00000054666.6	+	2	153	c.38G>A	c.(37-39)cGa>cAa	p.R13Q	VAMP3_ENST00000470357.1_5'UTR|RP3-467L1.6_ENST00000602406.1_RNA	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN	vesicle-associated membrane protein 3	13					calcium ion-dependent exocytosis (GO:0017156)|exocytosis (GO:0006887)|Golgi to plasma membrane protein transport (GO:0043001)|membrane fusion (GO:0061025)|positive regulation of receptor recycling (GO:0001921)|protein complex assembly (GO:0006461)|retrograde transport, endosome to Golgi (GO:0042147)|SNARE complex assembly (GO:0035493)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synapse (GO:0045202)		p.R13Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		GGCAGTAATCGAAGACTTCAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	80	82					1																	7833537		2203	4300	6503	7756124	SO:0001583	missense	9341			BC003570	CCDS88.1	1p36.23	2013-02-13	2012-10-17		ENSG00000049245	ENSG00000049245		"Vesicle-associated membrane proteins"	12644	protein-coding gene	gene with protein product	"cellubrevin"	603657				9885218	Standard	NM_004781		Approved	CEB	uc001aol.3	Q15836	OTTHUMG00000001225	ENST00000054666.6:c.38G>A	1.37:g.7833537G>A	ENSP00000054666:p.Arg13Gln		7756124	Q9BRV4	Missense_Mutation	SNP	ENST00000054666.6	37	CCDS88.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268654	0.80469	.	.	ENSG00000049245	ENST00000054666	T	0.29397	1.57	5.84	5.84	0.93424	Synaptobrevin (1);	0.126333	0.49916	D	0.000123	T	0.33702	0.0872	L	0.47016	1.485	0.80722	D	1	B	0.33379	0.41	B	0.33392	0.163	T	0.08973	-1.0696	10	0.62326	D	0.03	-11.8316	20.1346	0.98019	0.0:0.0:1.0:0.0	.	13	Q15836	VAMP3_HUMAN	Q	13	ENSP00000054666:R13Q	ENSP00000054666:R13Q	R	+	2	0	VAMP3	7756124	1.000000	0.71417	0.940000	0.37924	0.993000	0.82548	5.299000	0.65716	2.765000	0.95021	0.655000	0.94253	CGA		0.363	VAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003625.1	NM_004781		A	7833537	G	A	7833537	3	1	61	1	0	0	0	0	1	0	0	0	17154	1058	37	1	44	1	VAMP3	1	7833537	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28499	7833537	241417084	19	8004										
TNFRSF9	3604	broad.mit.edu	37	chr1	7993247	7993247	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaatatatacaggagtttCtttctgccccgtttaacaac	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:7993247C>A	ENST00000377507.3	-	7	820	c.654G>T	c.(652-654)aaG>aaT	p.K218N		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	218	Interaction with LRR-1.				apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)	p.K218N(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGGAGTTTCTTTCTGCCCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	59	60					1																	7993247		2203	4300	6503	7915834	SO:0001583	missense	3604			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"Tumor necrosis factor receptor superfamily", "CD molecules"	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.654G>T	1.37:g.7993247C>A	ENSP00000366729:p.Lys218Asn		7915834		Missense_Mutation	SNP	ENST00000377507.3	37	CCDS92.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430303	0.83776	.	.	ENSG00000049249	ENST00000377507	T	0.74002	-0.8	4.38	3.45	0.39498	.	1.460060	0.04179	N	0.326063	D	0.84316	0.5445	M	0.68952	2.095	0.30309	N	0.78866	D	0.76494	0.999	D	0.66084	0.941	T	0.66598	-0.5883	10	0.52906	T	0.07	-16.8454	8.796	0.34878	0.0:0.8939:0.0:0.1061	.	218	Q07011	TNR9_HUMAN	N	218	ENSP00000366729:K218N	ENSP00000366729:K218N	K	-	3	2	TNFRSF9	7915834	0.997000	0.39634	0.445000	0.26908	0.811000	0.45836	1.163000	0.31798	1.175000	0.42826	0.563000	0.77884	AAG		0.403	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1			A	7993247	C	A	7993247	3	1	61	1	0	0	0	0	1	0	0	0	16339	912	32	2	121	2	TNFRSF9	1	7993247	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159710	7993247	241257374	20	8005										
SLC45A1	50651	broad.mit.edu	37	chr1	8390911	8390911	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatcagggattctgaagaGacctcagaccttggccatcc	10	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:8390911G>T	ENST00000471889.1	+	5	1743	c.1358G>T	c.(1357-1359)aGa>aTa	p.R453I	SLC45A1_ENST00000289877.8_Missense_Mutation_p.R453I|SLC45A1_ENST00000377479.2_Missense_Mutation_p.R487I|Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000481265.1_3'UTR			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	453					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.R453I(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		ATTCTGAAGAGACCTCAGACC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	63	60					1																	8390911		2203	4300	6503	8313498	SO:0001583	missense	50651			AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"Solute carriers"	17939	protein-coding gene	gene with protein product	"H+/sugar symporter"	605763	"deleted in neuroblastoma 5"	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.1358G>T	1.37:g.8390911G>T	ENSP00000418096:p.Arg453Ile		8313498	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466106	0.63625	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.24723	1.88;1.84;1.88	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.49983	0.1589	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.51482	-0.8700	10	0.66056	D	0.02	-18.5113	17.4452	0.87577	0.0:0.0:1.0:0.0	.	453	Q9Y2W3	S45A1_HUMAN	I	453;487;453	ENSP00000418096:R453I;ENSP00000366699:R487I;ENSP00000289877:R453I	ENSP00000289877:R453I	R	+	2	0	SLC45A1	8313498	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	9.203000	0.95033	2.348000	0.79779	0.561000	0.74099	AGA		0.602	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			T	8390911	G	T	8390911	3	4	61	1	0	0	0	0	1	0	0	0	14677	942	33	2	1372	2	SLC45A1	1	8390911	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	397664	8390911	240859710	21	8006										
SLC2A7	155184	broad.mit.edu	37	chr1	9083095	9083095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccgtccatgaatgttgCgtgtcgctcaaagtaggttt	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:9083095C>T	ENST00000400906.1	-	3	192	c.193G>A	c.(193-195)Gca>Aca	p.A65T		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	65					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.A65T(2)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		ATGAATGTTGCGTGTCGCTCA	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	1											170	157	161					1																	9083095		2203	4300	6503	9005682	SO:0001583	missense	155184			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.193G>A	1.37:g.9083095C>T	ENSP00000383698:p.Ala65Thr		9005682	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917421	0.52546	.	.	ENSG00000197241	ENST00000400906	T	0.73789	-0.78	4.68	1.51	0.23008	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.305652	0.30210	N	0.010158	T	0.59500	0.2198	L	0.38175	1.15	0.09310	N	1	B	0.32188	0.359	B	0.31495	0.131	T	0.54695	-0.8255	10	0.72032	D	0.01	.	5.9715	0.19355	0.1497:0.6776:0.0:0.1726	.	65	Q6PXP3	GTR7_HUMAN	T	65	ENSP00000383698:A65T	ENSP00000383698:A65T	A	-	1	0	SLC2A7	9005682	0.000000	0.05858	0.002000	0.10522	0.306000	0.27790	0.526000	0.22971	0.537000	0.28751	0.556000	0.70494	GCA		0.498	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		T	9083095	C	T	9083095	3	4	61	1	0	0	0	0	1	0	0	0	14587	768	27	1	1385	1	SLC2A7	1	9083095	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	692184	9083095	240167526	22	8007										
SLC2A5	6518	broad.mit.edu	37	chr1	9097720	9097720	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcagacaccttattcatCttggtgaaaatctggttgat	7	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:9097720C>A	ENST00000377424.4	-	12	1610	c.1431G>T	c.(1429-1431)aaG>aaT	p.K477N	SLC2A5_ENST00000536305.1_Missense_Mutation_p.K418N|SLC2A5_ENST00000535586.1_Missense_Mutation_p.K362N	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	477					carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)	p.K477N(1)		endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CCTTATTCATCTTGGTGAAAA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											144	148	146					1																	9097720		2203	4300	6503	9020307	SO:0001583	missense	6518			BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.1431G>T	1.37:g.9097720C>A	ENSP00000366641:p.Lys477Asn		9020307	Q14770|Q5T977|Q8IVB3	Missense_Mutation	SNP	ENST00000377424.4	37	CCDS99.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276032	0.40294	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	T;T;T	0.81415	-1.23;-1.49;-1.15	5.53	3.65	0.41850	.	0.289177	0.39985	N	0.001215	T	0.70692	0.3253	L	0.31120	0.905	0.40393	D	0.97956	P;P;P	0.41313	0.745;0.745;0.611	B;B;B	0.41988	0.287;0.372;0.287	T	0.70396	-0.4883	10	0.59425	D	0.04	.	8.4239	0.32718	0.1526:0.7683:0.0:0.0791	.	433;418;477	B4DG19;B4DU31;P22732	.;.;GTR5_HUMAN	N	477;460;418;362	ENSP00000366641:K477N;ENSP00000440688:K418N;ENSP00000442744:K362N	ENSP00000366641:K477N	K	-	3	2	SLC2A5	9020307	1.000000	0.71417	0.303000	0.25071	0.530000	0.34684	1.229000	0.32600	0.791000	0.33826	-0.137000	0.14449	AAG		0.498	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		A	9097720	C	A	9097720	3	1	61	1	0	0	0	0	1	0	0	0	14585	912	32	2	78	2	SLC2A5	1	9097720	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14625	9097720	240152901	23	8008										
UBE4B	10277	broad.mit.edu	37	chr1	10161225	10161225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggttgatgaaaatgatcGaagagaaaagcggagcctca	14	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:10161225G>A	ENST00000253251.8	+	4	1246	c.407G>A	c.(406-408)cGa>cAa	p.R136Q	UBE4B_ENST00000377157.3_Missense_Mutation_p.R20Q|UBE4B_ENST00000343090.6_Missense_Mutation_p.R136Q					ubiquitination factor E4B									p.R136Q(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GAAAATGATCGAAGAGAAAAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	145	148					1																	10161225		2203	4300	6503	10083812	SO:0001583	missense	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.407G>A	1.37:g.10161225G>A	ENSP00000253251:p.Arg136Gln		10083812		Missense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	35	5.473916	0.96291	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.52526	0.75;0.8;0.66	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.59155	0.2173	L	0.35854	1.095	0.43263	D	0.995204	D;D	0.69078	0.997;0.997	D;D	0.70227	0.968;0.947	T	0.52041	-0.8628	10	0.24483	T	0.36	-9.0481	19.1353	0.93426	0.0:0.0:1.0:0.0	.	136;136	O95155;O95155-2	UBE4B_HUMAN;.	Q	136;20;136	ENSP00000253251:R136Q;ENSP00000366362:R20Q;ENSP00000343001:R136Q	ENSP00000253251:R136Q	R	+	2	0	UBE4B	10083812	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.507000	0.84556	0.557000	0.71058	CGA		0.388	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		A	10161225	G	A	10161225	3	1	61	1	0	0	0	0	1	0	0	0	16923	1058	37	1	421	1	UBE4B	1	10161225	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1063505	10161225	239089396	24	8009										
UBE4B	10277	broad.mit.edu	37	chr1	10177622	10177622	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactacctcatcgagtgtttCgaccgagttggaatagagga	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:10177622C>T	ENST00000253251.8	+	7	1754	c.915C>T	c.(913-915)ttC>ttT	p.F305F	UBE4B_ENST00000377157.3_Silent_p.F189F|UBE4B_ENST00000343090.6_Silent_p.F434F|UBE4B_ENST00000475795.1_3'UTR					ubiquitination factor E4B									p.F305F(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TCGAGTGTTTCGACCGAGTTG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	1											66	65	65					1																	10177622		2203	4300	6503	10100209	SO:0001819	synonymous_variant	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.915C>T	1.37:g.10177622C>T			10100209		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																				0.393	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		T	10177622	C	T	10177622	2	4	61	1	0	0	0	0	0	0	0	1	16923	883	31	1		1	UBE4B	1	10177622	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16397	10177622	239072999	25	8010										
KIF1B	23095	broad.mit.edu	37	chr1	10318593	10318593	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaaaaccgtgtgtacaatGacattggcaaggaaatgctc	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:10318593G>T	ENST00000377086.1	+	4	428	c.226G>T	c.(226-228)Gac>Tac	p.D76Y	KIF1B_ENST00000377083.1_Missense_Mutation_p.D76Y|KIF1B_ENST00000377093.4_Missense_Mutation_p.D76Y|KIF1B_ENST00000263934.6_Missense_Mutation_p.D76Y|KIF1B_ENST00000377081.1_Missense_Mutation_p.D76Y			O60333	KIF1B_HUMAN	kinesin family member 1B	76	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.D76Y(2)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGTGTACAATGACATTGGCAA	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	1											153	143	147					1																	10318593		2203	4300	6503	10241180	SO:0001583	missense	23095			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.226G>T	1.37:g.10318593G>T	ENSP00000366290:p.Asp76Tyr		10241180	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	G	27.6	4.848000	0.91277	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95	5.5	5.5	0.81552	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.85431	0.5695	M	0.62266	1.93	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.958;1.0	D;D;D;D;D;P;D	0.97110	0.999;1.0;1.0;1.0;0.996;0.737;0.999	D	0.86199	0.1617	10	0.72032	D	0.01	.	19.4076	0.94655	0.0:0.0:1.0:0.0	.	76;76;76;76;76;76;76	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	Y	76	ENSP00000263934:D76Y;ENSP00000366297:D76Y;ENSP00000366290:D76Y;ENSP00000366287:D76Y;ENSP00000366284:D76Y	ENSP00000263934:D76Y	D	+	1	0	KIF1B	10241180	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.776000	0.99001	2.586000	0.87340	0.460000	0.39030	GAC		0.373	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10318593	G	T	10318593	3	4	61	1	0	0	0	0	1	0	0	0	8305	1290	45	2	236	2	KIF1B	1	10318593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140971	10318593	238932028	26	8011										
KIF1B	23095	broad.mit.edu	37	chr1	10364222	10364222	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcttaggattccaaaagaCgatgaagcaaggaaagggaa	13	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:10364222C>T	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377083.1_Silent_p.D993D|KIF1B_ENST00000377093.4_Silent_p.D993D|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377081.1_Intron|RN7SL731P_ENST00000584329.1_RNA			O60333	KIF1B_HUMAN	kinesin family member 1B						anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.D993D(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TTCCAAAAGACGATGAAGCAA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	100	98					1																	10364222		2203	4300	6503	10286809	SO:0001627	intron_variant	23095			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2115+6918C>T	1.37:g.10364222C>T			10286809	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																					0.433	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10364222	C	T	10364222	1	4	61	0	1	0	0	0	0	0	0	0	8305	535	19	1		1	KIF1B	1	10364222	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45629	10364222	238886399	27	8012										
DFFA	1676	broad.mit.edu	37	chr1	10529303	10529303	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtattggaaggtagacacaGaaagtaatcgtcatcatcca	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:10529303G>T	ENST00000377038.3	-	2	296	c.229C>A	c.(229-231)Ctg>Atg	p.L77M	DFFA_ENST00000377036.2_Missense_Mutation_p.L77M	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	77	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.L77M(1)		large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		GGTAGACACAGAAAGTAATCG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											178	156	163					1																	10529303		2203	4300	6503	10451890	SO:0001583	missense	1676			AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"DNA fragmentation factor, 45 kD, alpha subunit"	601882	"DNA fragmentation factor, 45 kD, alpha polypeptide"			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.229C>A	1.37:g.10529303G>T	ENSP00000366237:p.Leu77Met		10451890	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861433	0.51482	.	.	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.4	4.49	0.54785	Caspase-activated nuclease CIDE-N (3);	0.071050	0.64402	D	0.000018	T	0.66297	0.2775	L	0.48362	1.52	0.46981	D	0.999272	P;D	0.76494	0.841;0.999	B;D	0.70227	0.39;0.968	T	0.64927	-0.6292	9	0.41790	T	0.15	-4.8286	10.6511	0.45649	0.2023:0.0:0.7977:0.0	.	77;77	O00273-2;O00273	.;DFFA_HUMAN	M	77	.	ENSP00000366235:L77M	L	-	1	2	DFFA	10451890	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	2.032000	0.41127	1.267000	0.44247	0.655000	0.94253	CTG		0.453	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401		T	10529303	G	T	10529303	3	4	61	1	0	0	0	0	1	0	0	0	4463	933	33	2	810	2	DFFA	1	10529303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165081	10529303	238721318	28	8013										
C1orf127	148345	broad.mit.edu	37	chr1	11008835	11008835	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttgcaccactctggggaGaatggaggcagatgtctggc	15	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11008835G>T	ENST00000377008.4	-	11	1302	c.856C>A	c.(856-858)Ctc>Atc	p.L286I	C1orf127_ENST00000377004.4_Missense_Mutation_p.L453I			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	286	Pro-rich.							p.L286I(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	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)		ACTCTGGGGAGAATGGAGGCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	61	58					1																	11008835		2202	4300	6502	10931422	SO:0001583	missense	148345			AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.856C>A	1.37:g.11008835G>T	ENSP00000366207:p.Leu286Ile		10931422	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.827|9.827	1.187375|1.187375	0.21870|0.21870	.|.	.|.	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.25250	.|1.81;1.81	4.64|4.64	-3.99|-3.99	0.04069|0.04069	.|.	.|1.271750	.|0.05547	.|N	.|0.566773	T|T	0.09862|0.09862	0.0242|0.0242	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.11329	.|0.006;0.006;0.006	T|T	0.24476|0.24476	-1.0159|-1.0159	5|10	.|0.19590	.|T	.|0.45	0.0448|0.0448	1.785|1.785	0.03040|0.03040	0.232:0.2624:0.3586:0.147|0.232:0.2624:0.3586:0.147	.|.	.|304;278;286	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	L|I	287;404|453;286	.|ENSP00000366203:L453I;ENSP00000366207:L286I	.|ENSP00000366203:L453I	F|L	-|-	3|1	2|0	C1orf127|C1orf127	10931422|10931422	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	-0.527000|-0.527000	0.06200|0.06200	-0.695000|-0.695000	0.05105|0.05105	-0.490000|-0.490000	0.04691|0.04691	TTC|CTC		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11008835	G	T	11008835	3	4	61	1	0	0	0	0	1	0	0	0	2000	942	33	2	1118	2	C1orf127	1	11008835	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	479532	11008835	238241786	29	8014										
C1orf127	148345	broad.mit.edu	37	chr1	11017789	11017789	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagccaccagctcccctcGaagggacagcagccatggag	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11017789G>A	ENST00000377008.4	-	7	576	c.130C>T	c.(130-132)Cga>Tga	p.R44*	C1orf127_ENST00000377004.4_Nonsense_Mutation_p.R193*			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	44								p.R44*(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	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)		AGCTCCCCTCGAAGGGACAGC	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											85	82	83					1																	11017789		2203	4300	6503	10940376	SO:0001587	stop_gained	148345			AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.130C>T	1.37:g.11017789G>A	ENSP00000366207:p.Arg44*		10940376	A0AVG8|A6NKM7|Q5VXJ2	Nonsense_Mutation	SNP	ENST00000377008.4	37		.	.	.	.	.	.	.	.	.	.	G	36	5.669604	0.96754	.	.	ENSG00000175262	ENST00000377004;ENST00000377008	.	.	.	5.35	3.45	0.39498	.	0.311945	0.17743	N	0.163493	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2661	6.7824	0.23654	0.0901:0.0:0.7357:0.1741	.	.	.	.	X	193;44	.	ENSP00000366203:R193X	R	-	1	2	C1orf127	10940376	0.005000	0.15991	0.493000	0.27502	0.996000	0.88848	0.269000	0.18589	0.612000	0.30071	0.655000	0.94253	CGA		0.577	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11017789	G	A	11017789	4	1	61	1	0	0	0	0	0	1	0	0	2000	1066	37	1	1918	1	C1orf127	1	11017789	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8954	11017789	238232832	30	8015										
MASP2	10747	broad.mit.edu	37	chr1	11086966	11086966	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcactaattatgttctcGatccagggaatatagttaat	6	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11086966G>A	ENST00000400897.3	-	11	2052	c.2037C>T	c.(2035-2037)atC>atT	p.I679I	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	679	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.I679I(1)		biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-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)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		TTATGTTCTCGATCCAGGGAA	0.438																																					GBM(35;611 746 20780 22741 36496)											1	Substitution - coding silent(1)	large_intestine(1)	1											93	98	97					1																	11086966		2203	4300	6503	11009553	SO:0001819	synonymous_variant	10747			X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"mannan-binding lectin serine protease 2", "mannan-binding lectin serine peptidase 1 pseudogene 1", "mannan-binding lectin serine protease 1 pseudogene 1"	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.2037C>T	1.37:g.11086966G>A			11009553	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Silent	SNP	ENST00000400897.3	37	CCDS123.1																																																																																				0.438	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		A	11086966	G	A	11086966	2	1	61	1	0	0	0	0	0	0	0	1	9353	1048	37	1		1	MASP2	1	11086966	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69177	11086966	238163655	31	8016										
MTOR	2475	broad.mit.edu	37	chr1	11189004	11189004	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatcaaaccataaggtgaGaactctgaaaaagaaatgag	8	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11189004G>A	ENST00000361445.4	-	41	5795	c.5719C>T	c.(5719-5721)Ctc>Ttc	p.L1907F	MTOR_ENST00000376838.1_Missense_Mutation_p.L112F|MTOR_ENST00000495435.1_5'Flank	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1907	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.L1907F(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CATAAGGTGAGAACTCTGAAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	59	60					1																	11189004		2203	4300	6503	11111591	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.5719C>T	1.37:g.11189004G>A	ENSP00000354558:p.Leu1907Phe		11111591	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301439	0.81136	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	D;D	0.82619	-1.63;-1.63	6.06	6.06	0.98353	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.000000	0.85682	D	0.000000	D	0.94443	0.8212	H	0.95780	3.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95030	0.8168	10	0.87932	D	0	-20.7712	20.6208	0.99490	0.0:0.0:1.0:0.0	.	1907	P42345	MTOR_HUMAN	F	1907;112	ENSP00000354558:L1907F;ENSP00000366034:L112F	ENSP00000354558:L1907F	L	-	1	0	MTOR	11111591	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.188000	0.77739	2.882000	0.98803	0.655000	0.94253	CTC		0.453	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		A	11189004	G	A	11189004	3	1	61	1	0	0	0	0	1	0	0	0	9984	942	33	3	2002	3	MTOR	1	11189004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102038	11189004	238061617	32	8017										
PTCHD2	57540	broad.mit.edu	37	chr1	11574496	11574496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtttgactatgaagtgCgcaggacgttcaacaatgac	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11574496C>T	ENST00000294484.6	+	4	1504	c.1366C>T	c.(1366-1368)Cgc>Tgc	p.R456C	PTCHD2_ENST00000389575.3_Missense_Mutation_p.R456C	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	456					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)	p.R673C(1)		NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CTATGAAGTGCGCAGGACGTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	134	135					1																	11574496		2049	4192	6241	11497083	SO:0001583	missense	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1366C>T	1.37:g.11574496C>T	ENSP00000294484:p.Arg456Cys		11497083	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687602	0.68157	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.95690	-3.78;-3.78	5.03	3.03	0.35002	.	0.000000	0.85682	D	0.000000	D	0.95376	0.8499	L	0.43152	1.355	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.93981	0.7258	10	0.59425	D	0.04	-25.1376	6.4875	0.22097	0.3132:0.5951:0.0:0.0917	.	456	Q9P2K9	PTHD2_HUMAN	C	456	ENSP00000294484:R456C;ENSP00000374226:R456C	ENSP00000294484:R456C	R	+	1	0	PTCHD2	11497083	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	2.308000	0.43690	1.254000	0.44035	0.655000	0.94253	CGC		0.532	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11574496	C	T	11574496	3	4	61	1	0	0	0	0	1	0	0	0	12767	768	27	1	1376	1	PTCHD2	1	11574496	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385492	11574496	237676125	33	8018										
MTHFR	4524	broad.mit.edu	37	chr1	11854882	11854882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacgtacatcttcctctcggCgcttggggtgggcgctgaga	15	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11854882C>T	ENST00000376592.1	-	6	1198	c.1070G>A	c.(1069-1071)cGc>cAc	p.R357H	MTHFR_ENST00000376590.3_Missense_Mutation_p.R357H|MTHFR_ENST00000376585.1_Missense_Mutation_p.R398H|MTHFR_ENST00000376583.3_Missense_Mutation_p.R398H			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	357			R -> C (in MTHFRD). {ECO:0000269|PubMed:7726158}.		blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)	p.R357H(1)		NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	TTCCTCTCGGCGCTTGGGGTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	60	60					1																	11854882		2203	4300	6503	11777469	SO:0001583	missense	4524			BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"5,10-methylenetetrahydrofolate reductase (NADPH)"			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1070G>A	1.37:g.11854882C>T	ENSP00000365777:p.Arg357His		11777469	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	34	5.376861	0.95945	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.89382	0.6699	M	0.92555	3.32	0.80722	D	1	D;D	0.89917	0.98;1.0	P;D	0.81914	0.53;0.995	D	0.92092	0.5681	10	0.87932	D	0	.	17.4549	0.87604	0.0:1.0:0.0:0.0	.	357;398	P42898;Q5SNW6	MTHR_HUMAN;.	H	357;398;357;398	ENSP00000365777:R357H;ENSP00000365767:R398H;ENSP00000365775:R357H;ENSP00000365770:R398H	ENSP00000365767:R398H	R	-	2	0	MTHFR	11777469	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.338000	0.79269	2.407000	0.81776	0.462000	0.41574	CGC		0.607	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957		T	11854882	C	T	11854882	3	4	61	1	0	0	0	0	1	0	0	0	9961	768	27	1	924	1	MTHFR	1	11854882	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280386	11854882	237395739	34	8019										
CLCN6	1185	broad.mit.edu	37	chr1	11886267	11886267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcccctatttccgaagcGacaggtatggaaaggttaga	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11886267G>A	ENST00000346436.6	+	9	755	c.703G>A	c.(703-705)Gac>Aac	p.D235N	CLCN6_ENST00000376487.3_Missense_Mutation_p.D213N|CLCN6_ENST00000376496.3_Missense_Mutation_p.D235N|CLCN6_ENST00000312413.6_Missense_Mutation_p.D235N|CLCN6_ENST00000376492.3_3'UTR	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	235					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.D235N(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TTTCCGAAGCGACAGGTATGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											133	130	131					1																	11886267		2203	4300	6503	11808854	SO:0001583	missense	1185			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.703G>A	1.37:g.11886267G>A	ENSP00000234488:p.Asp235Asn		11808854	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	36	5.698168	0.96802	.	.	ENSG00000011021	ENST00000312413;ENST00000346436;ENST00000376487;ENST00000376496;ENST00000376490;ENST00000376491;ENST00000376492	D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5	5.76	5.76	0.90799	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.96950	0.9004	M	0.68593	2.085	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.983;0.996;0.999;0.997	D	0.97192	0.9858	10	0.87932	D	0	-43.5354	18.9641	0.92689	0.0:0.0:1.0:0.0	.	213;235;235;235;235	F8W9R3;P51797-3;P51797-4;P51797-2;P51797	.;.;.;.;CLCN6_HUMAN	N	235;235;213;235;235;235;235	ENSP00000308367:D235N;ENSP00000234488:D235N;ENSP00000365670:D213N;ENSP00000365679:D235N	ENSP00000308367:D235N	D	+	1	0	CLCN6	11808854	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.284000	0.95882	2.713000	0.92767	0.655000	0.94253	GAC		0.448	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11886267	G	A	11886267	3	1	61	1	0	0	0	0	1	0	0	0	3473	1058	37	1	737	1	CLCN6	1	11886267	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31385	11886267	237364354	35	8020										
CLCN6	1185	broad.mit.edu	37	chr1	11889342	11889342	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgccgacagatgtcctCttcgagtcaaatcggtaatg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:11889342C>A	ENST00000346436.6	+	13	1263	c.1211C>A	c.(1210-1212)tCt>tAt	p.S404Y	CLCN6_ENST00000376487.3_Missense_Mutation_p.S382Y|CLCN6_ENST00000376496.3_Missense_Mutation_p.S404Y|CLCN6_ENST00000312413.6_Silent_p.L348L|CLCN6_ENST00000376492.3_3'UTR	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	404					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.S404Y(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CAGATGTCCTCTTCGAGTCAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											234	211	218					1																	11889342		2203	4300	6503	11811929	SO:0001583	missense	1185			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1211C>A	1.37:g.11889342C>A	ENSP00000234488:p.Ser404Tyr		11811929	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	C	9.975	1.226555	0.22542	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.91843	-2.92;-2.91;-2.91	5.83	4.92	0.64577	Chloride channel, core (1);	0.315121	0.39985	N	0.001205	D	0.93690	0.7984	.	.	.	0.80722	D	1	P;P	0.47191	0.867;0.891	P;P	0.52267	0.568;0.694	D	0.93639	0.6963	9	0.54805	T	0.06	-8.6969	14.1851	0.65601	0.0:0.9284:0.0:0.0716	.	382;404	F8W9R3;P51797	.;CLCN6_HUMAN	Y	404;382;404	ENSP00000234488:S404Y;ENSP00000365670:S382Y;ENSP00000365679:S404Y	ENSP00000234488:S404Y	S	+	2	0	CLCN6	11811929	0.997000	0.39634	0.005000	0.12908	0.008000	0.06430	6.717000	0.74707	1.470000	0.48102	-0.150000	0.13652	TCT		0.502	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11889342	C	A	11889342	3	1	61	1	0	0	0	0	1	0	0	0	3473	913	32	2	1271	2	CLCN6	1	11889342	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3075	11889342	237361279	36	8021										
TNFRSF8	943	broad.mit.edu	37	chr1	12183391	12183391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccacccctggggacccagCcggactgcaaccccacccca	9	22	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12183391C>T	ENST00000263932.2	+	9	1219	c.997C>T	c.(997-999)Ccg>Tcg	p.P333S	TNFRSF8_ENST00000417814.2_Missense_Mutation_p.P222S|TNFRSF8_ENST00000413146.2_5'Flank	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	333					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.P333S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GGGGACCCAGCCGGACTGCAA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	1											30	31	30					1																	12183391		2203	4299	6502	12105978	SO:0001583	missense	943			M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.997C>T	1.37:g.12183391C>T	ENSP00000263932:p.Pro333Ser		12105978	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	37	CCDS144.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686094	0.29962	.	.	ENSG00000120949	ENST00000263932;ENST00000417814	T;T	0.38560	1.13;1.13	3.15	2.22	0.28083	.	1009.050000	0.00166	N	0.000000	T	0.49830	0.1580	L	0.41492	1.28	0.09310	N	1	D;P	0.89917	1.0;0.833	D;B	0.71414	0.973;0.376	T	0.53892	-0.8374	10	0.02654	T	1	-3.0E-4	6.6268	0.22835	0.0:0.8662:0.0:0.1338	.	222;333	D3YTD8;P28908	.;TNR8_HUMAN	S	333;222	ENSP00000263932:P333S;ENSP00000390650:P222S	ENSP00000263932:P333S	P	+	1	0	TNFRSF8	12105978	0.000000	0.05858	0.002000	0.10522	0.085000	0.17905	0.050000	0.14120	0.906000	0.36621	0.561000	0.74099	CCG		0.642	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			T	12183391	C	T	12183391	3	4	61	1	0	0	0	0	1	0	0	0	16338	739	26	3	1031	3	TNFRSF8	1	12183391	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294049	12183391	237067230	37	8022										
VPS13D	55187	broad.mit.edu	37	chr1	12343196	12343196	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaggacttattggagaaGaatccagattctaaatataa	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12343196G>T	ENST00000358136.3	+	21	5167	c.5037G>T	c.(5035-5037)aaG>aaT	p.K1679N	VPS13D_ENST00000356315.4_Missense_Mutation_p.K1679N	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.K1679N(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TATTGGAGAAGAATCCAGATT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	120	117					1																	12343196		2203	4300	6503	12265783	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.5037G>T	1.37:g.12343196G>T	ENSP00000350854:p.Lys1679Asn		12265783		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.62|11.62	1.692200|1.692200	0.30052|0.30052	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.54071|.	0.59;0.59|.	5.89|5.89	-4.47|-4.47	0.03525|0.03525	.|.	0.212351|.	0.47852|.	D|.	0.000202|.	T|T	0.58163|0.58163	0.2103|0.2103	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	B;B|.	0.30973|.	0.302;0.201|.	B;B|.	0.29942|.	0.109;0.051|.	T|T	0.56117|0.56117	-0.8032|-0.8032	10|5	0.22706|.	T|.	0.39|.	.|.	17.2985|17.2985	0.87175|0.87175	0.3289:0.0:0.6711:0.0|0.3289:0.0:0.6711:0.0	.|.	1679;1679|.	Q5THJ4-2;Q5THJ4|.	.;VP13D_HUMAN|.	N|I	1679|502	ENSP00000348666:K1679N;ENSP00000350854:K1679N|.	ENSP00000348666:K1679N|.	K|R	+|+	3|2	2|0	VPS13D|VPS13D	12265783|12265783	0.096000|0.096000	0.21769|0.21769	0.967000|0.967000	0.41034|0.41034	0.961000|0.961000	0.63080|0.63080	-0.449000|-0.449000	0.06812|0.06812	-0.687000|-0.687000	0.05162|0.05162	-1.166000|-1.166000	0.01754|0.01754	AAG|AGA		0.433	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12343196	G	T	12343196	3	4	61	1	0	0	0	0	1	0	0	0	17232	933	33	2	5115	2	VPS13D	1	12343196	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159805	12343196	236907425	38	8023										
AADACL3	126767	broad.mit.edu	37	chr1	12779665	12779665	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggcatcgtgtactaccaCggtggcgggggcgtcatggg	17	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12779665C>T	ENST00000359318.5	+	2	391	c.186C>T	c.(184-186)caC>caT	p.H62H	AADACL3_ENST00000332530.3_Intron	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	62							hydrolase activity (GO:0016787)	p.H62H(1)		breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGTACTACCACGGTGGCGGGG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	1											74	77	76					1																	12779665		1942	4145	6087	12702252	SO:0001819	synonymous_variant	126767				CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.186C>T	1.37:g.12779665C>T			12702252	B3KXR9|Q5VUY1	Silent	SNP	ENST00000359318.5	37	CCDS41253.1																																																																																				0.527	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		T	12779665	C	T	12779665	2	4	61	1	0	0	0	0	0	0	0	1	12	535	19	1		1	AADACL3	1	12779665	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	436469	12779665	236470956	39	8024										
AADACL3	126767	broad.mit.edu	37	chr1	12785455	12785455	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttcgtttcaacagaggaAaaacatcccactgctcacct	5	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12785455A>C	ENST00000359318.5	+	4	750	c.545A>C	c.(544-546)aAa>aCa	p.K182T	AADACL3_ENST00000332530.3_Missense_Mutation_p.K112T	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	182							hydrolase activity (GO:0016787)	p.K182T(1)|p.K112T(1)		breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CAACAGAGGAAAAACATCCCA	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	1											184	173	176					1																	12785455		1880	4102	5982	12708042	SO:0001583	missense	126767				CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.545A>C	1.37:g.12785455A>C	ENSP00000352268:p.Lys182Thr		12708042	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	37	CCDS41253.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.437476	0.25900	.	.	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.11495	2.77;2.77	5.35	-5.14	0.02875	Alpha/beta hydrolase fold-3 (1);	1.283390	0.04994	N	0.467920	T	0.09247	0.0228	L	0.39633	1.23	0.09310	N	1	B;B	0.30634	0.154;0.288	B;B	0.36186	0.219;0.091	T	0.35226	-0.9797	10	0.19147	T	0.46	-0.0613	6.1592	0.20354	0.2382:0.1194:0.5259:0.1165	.	182;112	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	T	112;182	ENSP00000333352:K112T;ENSP00000352268:K182T	ENSP00000333352:K112T	K	+	2	0	AADACL3	12708042	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.712000	0.05013	-1.393000	0.02079	-1.922000	0.00515	AAA		0.498	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		C	12785455	A	C	12785455	3	2	61	1	0	0	0	0	1	0	0	0	12	14	1	4	563	4	AADACL3	1	12785455	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5790	12785455	236465166	40	8025										
PRAMEF12	390999	broad.mit.edu	37	chr1	12835860	12835860	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctagacctttgcttcaaGaatgggatgctggatgaatg	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12835860G>T	ENST00000357726.4	+	2	489	c.462G>T	c.(460-462)aaG>aaT	p.K154N		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	154					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.K154N(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTTGCTTCAAGAATGGGATGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	124	122					1																	12835860		2203	4300	6503	12758447	SO:0001583	missense	390999				CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.462G>T	1.37:g.12835860G>T	ENSP00000350358:p.Lys154Asn		12758447		Missense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	12.04	1.818368	0.32145	.	.	ENSG00000116726	ENST00000357726	T	0.00824	5.65	2.8	-2.1	0.07210	.	1.757830	0.02967	N	0.143886	T	0.03305	0.0096	M	0.68952	2.095	0.09310	N	1	D	0.71674	0.998	D	0.68353	0.957	T	0.37572	-0.9700	10	0.35671	T	0.21	.	2.6404	0.04969	0.252:0.0:0.3634:0.3847	.	154	O95522	PRA12_HUMAN	N	154	ENSP00000350358:K154N	ENSP00000350358:K154N	K	+	3	2	PRAMEF12	12758447	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.845000	0.01677	-0.462000	0.06984	0.313000	0.20887	AAG		0.537	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12835860	G	T	12835860	3	4	61	1	0	0	0	0	1	0	0	0	12462	933	33	2	468	2	PRAMEF12	1	12835860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50405	12835860	236414761	41	8026										
PRAMEF1	65121	broad.mit.edu	37	chr1	12854441	12854441	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctggccacgtctgataaGaaagcttcgttgttacctga	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12854441G>T	ENST00000332296.7	+	3	768	c.665G>T	c.(664-666)aGa>aTa	p.R222I	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	222					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.R222I(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCTGATAAGAAAGCTTCGT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	1											256	239	245					1																	12854441		2203	4300	6503	12777028	SO:0001583	missense	65121			AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.665G>T	1.37:g.12854441G>T	ENSP00000332134:p.Arg222Ile		12777028	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	5.967	0.362324	0.11296	.	.	ENSG00000116721	ENST00000332296	T	0.00976	5.48	0.401	0.401	0.16338	.	0.654334	0.13897	N	0.355156	T	0.00666	0.0022	N	0.22421	0.69	0.09310	N	1	P	0.45126	0.851	B	0.33750	0.169	T	0.55328	-0.8158	9	0.51188	T	0.08	.	.	.	.	.	222	O95521	PRAM1_HUMAN	I	222	ENSP00000332134:R222I	ENSP00000332134:R222I	R	+	2	0	PRAMEF1	12777028	0.000000	0.05858	0.005000	0.12908	0.009000	0.06853	-0.096000	0.11059	0.436000	0.26393	0.436000	0.28706	AGA		0.403	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		T	12854441	G	T	12854441	3	4	61	1	0	0	0	0	1	0	0	0	12459	942	33	2	671	2	PRAMEF1	1	12854441	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18581	12854441	236396180	42	8027										
PRAMEF2	65122	broad.mit.edu	37	chr1	12919830	12919830	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctggtcaattatctaacGccaattaaatatctcagaaa	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12919830G>A	ENST00000240189.2	+	3	657	c.570G>A	c.(568-570)acG>acA	p.T190T		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	190					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.T190T(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATTATCTAACGCCAATTAAAT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	1											162	177	172					1																	12919830		2202	4294	6496	12842417	SO:0001819	synonymous_variant	65122				CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.570G>A	1.37:g.12919830G>A			12842417		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																				0.398	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		A	12919830	G	A	12919830	2	1	61	1	0	0	0	0	0	0	0	1	12469	1074	38	1		1	PRAMEF2	1	12919830	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65389	12919830	236330791	43	8028										
PRAMEF4	400735	broad.mit.edu	37	chr1	12941936	12941936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctggatacagtctaggTtcaccattttcaggatgctt	8	11	3	0	rs145441347	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12941936T>C	ENST00000235349.5	-	3	684	c.614A>G	c.(613-615)aAc>aGc	p.N205S		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	205					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.N205S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTCTAGGTTCACCATTTT	0.463													t|||	4	0.000798722	0.003	0	5008	,	,		21308	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	SER/ASN	10,2738		1,8,1365	73	92	85		614	1.5	0	1	dbSNP_134	85	0,4766		0,0,2383	no	missense	PRAMEF4	NM_001009611.2	46	1,8,3748	CC,CT,TT		0.0,0.3639,0.1331	possibly-damaging	205/479	12941936	10,7504	1374	2383	3757	12864523	SO:0001583	missense	400735				CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.614A>G	1.37:g.12941936T>C	ENSP00000235349:p.Asn205Ser		12864523	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	t	5.004	0.186349	0.09495	0.003639	0.0	ENSG00000243073	ENST00000235349	T	0.01051	5.4	1.48	1.48	0.22813	.	1.277390	0.05377	N	0.536443	T	0.01835	0.0058	M	0.61703	1.905	0.09310	N	1	B	0.21821	0.061	B	0.16289	0.015	T	0.46555	-0.9183	10	0.41790	T	0.15	.	5.1316	0.14913	0.0:0.0:0.0:1.0	.	205	O60810	PRAM4_HUMAN	S	205	ENSP00000235349:N205S	ENSP00000235349:N205S	N	-	2	0	PRAMEF4	12864523	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.673000	0.25203	0.939000	0.37446	0.329000	0.21502	AAC		0.463	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		C	12941936	T	C	12941936	3	2	61	1	0	0	0	0	1	0	0	0	12471	1725	60	4	830	4	PRAMEF4	1	12941936	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22106	12941936	236308685	44	8029										
PRAMEF10	343071	broad.mit.edu	37	chr1	12952819	12952819	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaagggacgggaccaaaGaagatcctcttgggctgcct	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12952819G>T	ENST00000235347.4	-	4	1432	c.1353C>A	c.(1351-1353)ttC>ttA	p.F451L		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	451					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.F451L(1)		NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CGGGACCAAAGAAGATCCTCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											44	48	47					1																	12952819		1973	4163	6136	12875406	SO:0001583	missense	343071			AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"-"	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.1353C>A	1.37:g.12952819G>T	ENSP00000235347:p.Phe451Leu		12875406	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	g	0.026	-1.369176	0.01225	.	.	ENSG00000187545	ENST00000235347	T	0.44083	0.93	1.45	-2.9	0.05648	.	1.392000	0.04973	N	0.464164	T	0.26195	0.0639	L	0.35414	1.06	0.09310	N	1	B	0.16802	0.019	B	0.18871	0.023	T	0.08310	-1.0728	10	0.23302	T	0.38	.	0.5638	0.00684	0.2793:0.198:0.3261:0.1966	.	451	O60809	PRA10_HUMAN	L	451	ENSP00000235347:F451L	ENSP00000235347:F451L	F	-	3	2	PRAMEF10	12875406	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-2.161000	0.01278	-2.458000	0.00538	-1.050000	0.02344	TTC		0.537	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342		T	12952819	G	T	12952819	3	4	61	1	0	0	0	0	1	0	0	0	12460	933	33	2	75	2	PRAMEF10	1	12952819	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10883	12952819	236297802	45	8030										
PRAMEF7	441871	broad.mit.edu	37	chr1	12979808	12979808	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtgtcacgctgacccatTtcagccctgagcccctcaca	10	16	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:12979808T>G	ENST00000361079.2	+	4	1083	c.1000T>G	c.(1000-1002)Ttc>Gtc	p.F334V	RNU6-1072P_ENST00000384703.1_RNA			Q5VXH5	PRAM7_HUMAN	PRAME family member 7	334					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.F334V(1)		endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGACCCATTTCAGCCCTGA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	132	137					1																	12979808		2201	4297	6498	12902395	SO:0001583	missense	391002				CCDS30593.1	1p36.21	2013-01-17			ENSG00000204510	ENSG00000204510		"-"	28415	protein-coding gene	gene with protein product							Standard	NM_001012277		Approved			Q5VXH5	OTTHUMG00000001982	ENST00000361079.2:c.1000T>G	1.37:g.12979808T>G	ENSP00000354371:p.Phe334Val		12902395	B9EIP0	Missense_Mutation	SNP	ENST00000361079.2	37	CCDS30593.1	.	.	.	.	.	.	.	.	.	.	.	1.576	-0.532744	0.04112	.	.	ENSG00000204510	ENST00000361079;ENST00000330881	T;T	0.07908	3.15;3.15	1.68	-1.17	0.09648	.	1.397780	0.04529	N	0.385999	T	0.05227	0.0139	N	0.25245	0.725	0.09310	N	1	B	0.25441	0.126	B	0.22386	0.039	T	0.38993	-0.9635	10	0.25751	T	0.34	.	2.1167	0.03715	0.2652:0.3667:0.0:0.3681	.	334	Q5VXH5	PRAM7_HUMAN	V	334	ENSP00000354371:F334V;ENSP00000328915:F334V	ENSP00000328915:F334V	F	+	1	0	PRAMEF7	12902395	0.000000	0.05858	0.000000	0.03702	0.212000	0.24457	-0.157000	0.10085	-0.312000	0.08741	0.254000	0.18369	TTC		0.582	PRAMEF7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012277		G	12979808	T	G	12979808	3	3	61	1	0	0	0	0	1	0	0	0	12473	1841	64	4	1010	4	PRAMEF7	1	12979808	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26989	12979808	236270813	46	8031										
PRAMEF13	400736	broad.mit.edu	37	chr1	13448321	13448321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatagacatacaatttctgCcaaagtagaaggtggtgagc	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:13448321C>T	ENST00000376132.3	-	4	1256	c.1154G>A	c.(1153-1155)gGc>gAc	p.G385D		NM_001024661.1	NP_001019832.1	Q5VWM6	PRA13_HUMAN	PRAME family member 13	385					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.G385D(1)		breast(1)|large_intestine(1)|lung(3)|skin(2)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ACAATTTCTGCCAAAGTAGAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											43	42	42					1																	13448321		2202	4295	6497	13320908	SO:0001583	missense	729528					1p36.21	2013-01-17			ENSG00000204495			"-"	13262	protein-coding gene	gene with protein product							Standard	NG_005159		Approved	OTTHUMG00000008034	uc010obi.1	Q5VWM6	OTTHUMG00000008034	ENST00000376132.3:c.1154G>A	1.37:g.13448321C>T	ENSP00000365302:p.Gly385Asp		13320908		Missense_Mutation	SNP	ENST00000376132.3	37	CCDS41257.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.695447	0.00731	.	.	ENSG00000204495	ENST00000376132	T	0.12774	2.65	1.2	-1.61	0.08399	.	1.398020	0.04253	N	0.338926	T	0.14743	0.0356	N	0.14661	0.345	0.09310	N	1	P;D	0.69078	0.82;0.997	P;P	0.58780	0.527;0.845	T	0.15549	-1.0433	10	0.37606	T	0.19	.	5.0833	0.14668	0.5975:0.4025:0.0:0.0	.	385;385	Q5VWM6;A6NFR9	PRA13_HUMAN;.	D	385	ENSP00000365302:G385D	ENSP00000365302:G385D	G	-	2	0	PRAMEF13	13320908	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.181000	0.09740	-0.507000	0.06549	-0.887000	0.02937	GGC		0.562	PRAMEF13-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022040.1	XM_375688		T	13448321	C	T	13448321	3	4	61	1	0	0	0	0	1	0	0	0	12463	739	26	3	274	3	PRAMEF13	1	13448321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	468513	13448321	235802300	47	8032										
PRDM2	7799	broad.mit.edu	37	chr1	14108128	14108128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaataatggcttctggaAtaaagacaaaagatccagat	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:14108128A>G	ENST00000235372.7	+	8	4694	c.3838A>G	c.(3838-3840)Ata>Gta	p.I1280V	PRDM2_ENST00000413440.1_Missense_Mutation_p.I1079V|PRDM2_ENST00000343137.4_Missense_Mutation_p.I1079V|PRDM2_ENST00000311066.5_Missense_Mutation_p.I1280V|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000376048.5_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.I1280V(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	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)		GGCTTCTGGAATAAAGACAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	96	93					1																	14108128		2203	4300	6503	13980715	SO:0001583	missense	7799			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.3838A>G	1.37:g.14108128A>G	ENSP00000235372:p.Ile1280Val		13980715	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	A	5.157	0.214493	0.09810	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01397	5.07;4.94;4.95;4.95	6.17	3.86	0.44501	.	0.284442	0.38778	N	0.001567	T	0.00695	0.0023	N	0.02539	-0.55	0.29609	N	0.847114	B;B;B	0.16802	0.019;0.001;0.002	B;B;B	0.15052	0.012;0.001;0.002	T	0.39375	-0.9617	10	0.25751	T	0.34	.	4.9635	0.14078	0.6528:0.0:0.3472:0.0	.	1138;1280;1280	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	V	1280;1280;1280;1079;1079	ENSP00000235372:I1280V;ENSP00000312352:I1280V;ENSP00000411103:I1079V;ENSP00000341621:I1079V	ENSP00000235372:I1280V	I	+	1	0	PRDM2	13980715	0.998000	0.40836	1.000000	0.80357	0.884000	0.51177	2.323000	0.43823	1.153000	0.42468	-0.264000	0.10439	ATA		0.408	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		G	14108128	A	G	14108128	3	3	61	1	0	0	0	0	1	0	0	0	12492	101	4	4	3864	4	PRDM2	1	14108128	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	659807	14108128	235142493	48	8033										
KAZ	23254	broad.mit.edu	37	chr1	15392182	15392182	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaagagaagatgggattCggctccatctcccgcgtctt	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:15392182C>T	ENST00000376030.2	+	8	1449	c.1155C>T	c.(1153-1155)ttC>ttT	p.F385F	KAZN_ENST00000422387.2_Silent_p.F385F|KAZN_ENST00000361144.5_Silent_p.F379F|KAZN_ENST00000400797.3_Silent_p.F291F|KAZN_ENST00000503743.1_Silent_p.F385F|KAZN_ENST00000400798.2_Silent_p.F291F	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	385					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.F379F(1)|p.F385F(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						AGATGGGATTCGGCTCCATCT	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	1											78	86	83					1																	15392182		2203	4300	6503	15264769	SO:0001819	synonymous_variant	23254			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1155C>T	1.37:g.15392182C>T			15264769	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	37	CCDS152.2																																																																																				0.547	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15392182	C	T	15392182	2	4	61	1	0	0	0	0	0	0	0	1	8009	883	31	1		1	KAZ	1	15392182	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1284054	15392182	233858439	49	8034										
KAZ	23254	broad.mit.edu	37	chr1	15428237	15428237	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagcatcctgctggggatCgagctgctgtaccaagtgaa	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:15428237C>T	ENST00000376030.2	+	11	2040	c.1746C>T	c.(1744-1746)atC>atT	p.I582I		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	582	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.I582I(1)|p.I29I(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						TGCTGGGGATCGAGCTGCTGT	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	1											73	47	56					1																	15428237		2203	4299	6502	15300824	SO:0001819	synonymous_variant	23254			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1746C>T	1.37:g.15428237C>T			15300824	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	37	CCDS152.2																																																																																				0.587	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15428237	C	T	15428237	2	4	61	1	0	0	0	0	0	0	0	1	8009	874	31	1		1	KAZ	1	15428237	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36055	15428237	233822384	50	8035										
DNAJC16	23341	broad.mit.edu	37	chr1	15855713	15855713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagtcctaggggtcagccGaacagccagtcaggctgata	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:15855713G>A	ENST00000375847.3	+	2	277	c.113G>A	c.(112-114)cGa>cAa	p.R38Q	CASP9_ENST00000469637.1_5'Flank|DNAJC16_ENST00000375849.1_Missense_Mutation_p.R38Q|DNAJC16_ENST00000375838.1_Missense_Mutation_p.R38Q	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	38	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.R38Q(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GGGGTCAGCCGAACAGCCAGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											85	86	86					1																	15855713		2203	4300	6503	15728300	SO:0001583	missense	23341			AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.113G>A	1.37:g.15855713G>A	ENSP00000365007:p.Arg38Gln		15728300	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	37	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804758	0.90623	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.32753	1.44;1.44;1.44	5.65	4.74	0.60224	Heat shock protein DnaJ, N-terminal (5);	0.162637	0.51477	N	0.000088	T	0.32376	0.0827	L	0.41356	1.27	0.24066	N	0.995992	D;D	0.60575	0.958;0.988	P;P	0.50791	0.537;0.65	T	0.16571	-1.0398	10	0.72032	D	0.01	-11.1731	8.4752	0.33009	0.173:0.0:0.827:0.0	.	38;38	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	Q	38	ENSP00000365007:R38Q;ENSP00000364998:R38Q;ENSP00000365009:R38Q	ENSP00000364998:R38Q	R	+	2	0	DNAJC16	15728300	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.389000	0.59639	1.391000	0.46566	0.563000	0.77884	CGA		0.438	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		A	15855713	G	A	15855713	3	1	61	1	0	0	0	0	1	0	0	0	4646	1058	37	1	115	1	DNAJC16	1	15855713	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	427476	15855713	233394908	51	8036										
DNAJC16	23341	broad.mit.edu	37	chr1	15873342	15873342	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccttctgtttgaccaaacGcccattgtgccactgttata	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:15873342G>A	ENST00000375847.3	+	6	1004	c.840G>A	c.(838-840)acG>acA	p.T280T	DNAJC16_ENST00000375849.1_Silent_p.T280T|DNAJC16_ENST00000375838.1_Silent_p.T280T	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	280					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.T280T(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TTGACCAAACGCCCATTGTGC	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	1											103	100	101					1																	15873342		2203	4300	6503	15745929	SO:0001819	synonymous_variant	23341			AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.840G>A	1.37:g.15873342G>A			15745929	Q68D57|Q86X32|Q8N5P4	Silent	SNP	ENST00000375847.3	37	CCDS30606.1																																																																																				0.328	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		A	15873342	G	A	15873342	2	1	61	1	0	0	0	0	0	0	0	1	4646	1074	38	1		1	DNAJC16	1	15873342	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17629	15873342	233377279	52	8037										
AGMAT	79814	broad.mit.edu	37	chr1	15909787	15909787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaagattgacattcacatCgcctaggtctgcaaccatga	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:15909787C>T	ENST00000375826.3	-	2	518	c.376G>A	c.(376-378)Gat>Aat	p.D126N	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	126					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)	p.D126N(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		ACATTCACATCGCCTAGGTCT	0.547																																					NSCLC(126;1678 1780 25805 43508 49531)											1	Substitution - Missense(1)	large_intestine(1)	1											76	71	72					1																	15909787		2203	4300	6503	15782374	SO:0001583	missense	79814			AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.376G>A	1.37:g.15909787C>T	ENSP00000364986:p.Asp126Asn		15782374	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738265	0.89573	.	.	ENSG00000116771	ENST00000375826	T	0.36878	1.23	5.17	4.25	0.50352	Ureohydrolase domain (1);	0.048584	0.85682	N	0.000000	T	0.58495	0.2126	M	0.87456	2.885	0.43724	D	0.996204	D	0.61080	0.989	P	0.59056	0.851	T	0.64605	-0.6368	10	0.56958	D	0.05	-15.0396	11.5463	0.50696	0.0:0.9107:0.0:0.0893	.	126	Q9BSE5	SPEB_HUMAN	N	126	ENSP00000364986:D126N	ENSP00000364986:D126N	D	-	1	0	AGMAT	15782374	0.999000	0.42202	0.671000	0.29857	0.869000	0.49853	4.323000	0.59221	1.152000	0.42452	0.563000	0.77884	GAT		0.547	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		T	15909787	C	T	15909787	3	4	61	1	0	0	0	0	1	0	0	0	385	884	31	1	706	1	AGMAT	1	15909787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36445	15909787	233340834	53	8038										
PLEKHM2	23207	broad.mit.edu	37	chr1	16060342	16060342	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccaacaagaagaaattCgaggatgccttgagcctcat	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16060342C>T	ENST00000375799.3	+	20	3200	c.2973C>T	c.(2971-2973)ttC>ttT	p.F991F	RP11-288I21.1_ENST00000453804.1_RNA|SLC25A34_ENST00000294454.5_5'Flank|PLEKHM2_ENST00000477849.1_3'UTR|PLEKHM2_ENST00000375793.2_Silent_p.F971F	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	991					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)	p.F991F(1)|p.F991L(1)|p.F1094L(1)|p.F1094F(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		AGAAGAAATTCGAGGATGCCT	0.637																																																4	Substitution - Missense(2)|Substitution - coding silent(2)	large_intestine(2)|lung(2)	1											70	80	77					1																	16060342		2069	4205	6274	15932929	SO:0001819	synonymous_variant	23207			AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2973C>T	1.37:g.16060342C>T			15932929	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																				0.637	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		T	16060342	C	T	16060342	2	4	61	1	0	0	0	0	0	0	0	1	12112	883	31	1		1	PLEKHM2	1	16060342	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150555	16060342	233190279	54	8039										
FBLIM1	54751	broad.mit.edu	37	chr1	16103737	16103737	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaagatgccttcaaaatCgaatgcatgggaagaaactt	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16103737C>T	ENST00000375766.3	+	8	1603	c.963C>T	c.(961-963)atC>atT	p.I321I	FBLIM1_ENST00000332305.5_Silent_p.I224I|FBLIM1_ENST00000509138.1_3'UTR|FBLIM1_ENST00000375771.1_Silent_p.I321I|FBLIM1_ENST00000400773.1_Silent_p.I224I	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	321	FERMT2-binding.|LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)	p.I321I(1)		large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|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;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		CCTTCAAAATCGAATGCATGG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											114	113	114					1																	16103737		2203	4300	6503	15976324	SO:0001819	synonymous_variant	54751				CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.963C>T	1.37:g.16103737C>T			15976324	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																				0.488	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215		T	16103737	C	T	16103737	2	4	61	1	0	0	0	0	0	0	0	1	5716	874	31	1		1	FBLIM1	1	16103737	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43395	16103737	233146884	55	8040										
SPEN	23013	broad.mit.edu	37	chr1	16255966	16255966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtatttctgttgggtctggCtcaaggcccagctcagacct	11	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16255966C>T	ENST00000375759.3	+	11	3435	c.3231C>T	c.(3229-3231)ggC>ggT	p.G1077G		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1077					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.G1077G(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		TTGGGTCTGGCTCAAGGCCCA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											44	47	46					1																	16255966		2203	4300	6503	16128553	SO:0001819	synonymous_variant	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3231C>T	1.37:g.16255966C>T			16128553	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																				0.438	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16255966	C	T	16255966	2	4	61	1	0	0	0	0	0	0	0	1	15077	784	28	3		3	SPEN	1	16255966	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152229	16255966	232994655	56	8041										
SPEN	23013	broad.mit.edu	37	chr1	16256061	16256061	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaaaaaagcccattccctCaaaaccacagctcaaacagc	3	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16256061C>A	ENST00000375759.3	+	11	3530	c.3326C>A	c.(3325-3327)tCa>tAa	p.S1109*		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1109					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.S1109*(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		CCCATTCCCTCAAAACCACAG	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											40	42	42					1																	16256061		2203	4300	6503	16128648	SO:0001587	stop_gained	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3326C>A	1.37:g.16256061C>A	ENSP00000364912:p.Ser1109*		16128648	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	38	6.655620	0.97739	.	.	ENSG00000065526	ENST00000375759	.	.	.	5.39	2.33	0.28932	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.6168	3.5535	0.07855	0.0:0.3806:0.1916:0.4278	.	.	.	.	X	1109	.	ENSP00000364912:S1109X	S	+	2	0	SPEN	16128648	0.001000	0.12720	0.277000	0.24703	0.625000	0.37756	0.956000	0.29202	0.849000	0.35215	0.650000	0.86243	TCA		0.453	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16256061	C	A	16256061	4	1	61	1	0	0	0	0	0	1	0	0	15077	838	29	2	3368	2	SPEN	1	16256061	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95	16256061	232994560	57	8042										
SPEN	23013	broad.mit.edu	37	chr1	16256750	16256750	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctgaagatgaactaaatCgttgggactctcagatgaaa	9	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16256750C>A	ENST00000375759.3	+	11	4219	c.4015C>A	c.(4015-4017)Cgt>Agt	p.R1339S		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1339					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.R1339S(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		TGAACTAAATCGTTGGGACTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											44	46	45					1																	16256750		2203	4300	6503	16129337	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4015C>A	1.37:g.16256750C>A	ENSP00000364912:p.Arg1339Ser		16129337	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	4.489	0.090683	0.08632	.	.	ENSG00000065526	ENST00000375759	T	0.09350	2.99	5.02	5.02	0.67125	.	.	.	.	.	T	0.12178	0.0296	L	0.29908	0.895	0.23841	N	0.996694	D	0.54207	0.965	P	0.49853	0.624	T	0.15607	-1.0431	9	0.13470	T	0.59	-7.8283	12.7927	0.57543	0.2634:0.7366:0.0:0.0	.	1339	Q96T58	MINT_HUMAN	S	1339	ENSP00000364912:R1339S	ENSP00000364912:R1339S	R	+	1	0	SPEN	16129337	0.571000	0.26659	0.740000	0.30986	0.740000	0.42216	1.172000	0.31908	2.626000	0.88956	0.557000	0.71058	CGT		0.378	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16256750	C	A	16256750	3	1	61	1	0	0	0	0	1	0	0	0	15077	884	31	2	4057	2	SPEN	1	16256750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	689	16256750	232993871	58	8043										
SPEN	23013	broad.mit.edu	37	chr1	16257924	16257924	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaggtgaccagccgccttAtctggatgccaagcctccaa	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16257924A>C	ENST00000375759.3	+	11	5393	c.5189A>C	c.(5188-5190)tAt>tCt	p.Y1730S		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1730					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.Y1730S(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		CAGCCGCCTTATCTGGATGCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											144	157	153					1																	16257924		2203	4300	6503	16130511	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5189A>C	1.37:g.16257924A>C	ENSP00000364912:p.Tyr1730Ser		16130511	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429675	0.43122	.	.	ENSG00000065526	ENST00000375759	T	0.08193	3.12	5.1	-6.14	0.02111	.	.	.	.	.	T	0.02888	0.0086	L	0.29908	0.895	0.09310	N	1	P	0.35433	0.501	B	0.24541	0.054	T	0.44787	-0.9305	9	0.06365	T	0.9	0.5139	2.1015	0.03681	0.3017:0.3818:0.0924:0.2242	.	1730	Q96T58	MINT_HUMAN	S	1730	ENSP00000364912:Y1730S	ENSP00000364912:Y1730S	Y	+	2	0	SPEN	16130511	0.000000	0.05858	0.000000	0.03702	0.830000	0.47004	-0.263000	0.08670	-1.564000	0.01678	0.383000	0.25322	TAT		0.572	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16257924	A	C	16257924	3	2	61	1	0	0	0	0	1	0	0	0	15077	449	16	4	5231	4	SPEN	1	16257924	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1174	16257924	232992697	59	8044										
SPEN	23013	broad.mit.edu	37	chr1	16258934	16258934	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaagttgtagagaaaaaaCcggcccctgaaaaaaactcc	8	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16258934C>A	ENST00000375759.3	+	11	6403	c.6199C>A	c.(6199-6201)Ccg>Acg	p.P2067T		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2067					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.P2067T(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		AGAGAAAAAACCGGCCCCTGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											51	61	58					1																	16258934		2171	4278	6449	16131521	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6199C>A	1.37:g.16258934C>A	ENSP00000364912:p.Pro2067Thr		16131521	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	0.292	-0.979466	0.02197	.	.	ENSG00000065526	ENST00000375759	T	0.08282	3.11	4.79	-3.53	0.04667	.	.	.	.	.	T	0.06690	0.0171	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36335	-0.9752	9	0.38643	T	0.18	0.2818	9.9417	0.41585	0.3702:0.4519:0.1778:0.0	.	2067	Q96T58	MINT_HUMAN	T	2067	ENSP00000364912:P2067T	ENSP00000364912:P2067T	P	+	1	0	SPEN	16131521	0.000000	0.05858	0.300000	0.25030	0.090000	0.18270	-0.513000	0.06305	-0.590000	0.05866	0.462000	0.41574	CCG		0.473	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16258934	C	A	16258934	3	1	61	1	0	0	0	0	1	0	0	0	15077	507	18	2	6241	2	SPEN	1	16258934	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1010	16258934	232991687	60	8045										
SPEN	23013	broad.mit.edu	37	chr1	16259073	16259073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacaggcaggggagagggAatctggggtggtggcagtct	20	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16259073A>G	ENST00000375759.3	+	11	6542	c.6338A>G	c.(6337-6339)gAa>gGa	p.E2113G		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2113					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.E2113G(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		GGGGAGAGGGAATCTGGGGTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	91	88					1																	16259073		2203	4300	6503	16131660	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6338A>G	1.37:g.16259073A>G	ENSP00000364912:p.Glu2113Gly		16131660	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	3.268	-0.149710	0.06585	.	.	ENSG00000065526	ENST00000375759	T	0.10860	2.83	5.16	4.02	0.46733	.	.	.	.	.	T	0.11836	0.0288	M	0.64997	1.995	0.34127	D	0.66482	P	0.35077	0.483	B	0.24974	0.057	T	0.10917	-1.0609	9	0.45353	T	0.12	-20.1733	12.298	0.54859	0.8585:0.1415:0.0:0.0	.	2113	Q96T58	MINT_HUMAN	G	2113	ENSP00000364912:E2113G	ENSP00000364912:E2113G	E	+	2	0	SPEN	16131660	0.993000	0.37304	0.107000	0.21349	0.153000	0.21895	3.280000	0.51677	0.793000	0.33875	0.379000	0.24179	GAA		0.522	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16259073	A	G	16259073	3	3	61	1	0	0	0	0	1	0	0	0	15077	246	9	4	6380	4	SPEN	1	16259073	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	139	16259073	232991548	61	8046										
SPEN	23013	broad.mit.edu	37	chr1	16265285	16265285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgttgtgagccagaccGagtccctcaaggctgccttc	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16265285G>A	ENST00000375759.3	+	14	10981	c.10777G>A	c.(10777-10779)Gag>Aag	p.E3593K		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3593	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.E3593K(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		GAGCCAGACCGAGTCCCTCAA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											115	87	96					1																	16265285		2203	4300	6503	16137872	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.10777G>A	1.37:g.16265285G>A	ENSP00000364912:p.Glu3593Lys		16137872	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143957	0.57044	.	.	ENSG00000065526	ENST00000375759	T	0.08370	3.1	5.62	4.71	0.59529	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	.	.	.	.	T	0.07052	0.0179	N	0.08118	0	0.51012	D	0.999908	P	0.47841	0.901	P	0.46543	0.52	T	0.47598	-0.9105	9	0.37606	T	0.19	-24.3207	14.5815	0.68295	0.0703:0.0:0.9296:0.0	.	3593	Q96T58	MINT_HUMAN	K	3593	ENSP00000364912:E3593K	ENSP00000364912:E3593K	E	+	1	0	SPEN	16137872	1.000000	0.71417	0.896000	0.35187	0.991000	0.79684	6.887000	0.75616	1.373000	0.46208	0.655000	0.94253	GAG		0.597	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16265285	G	A	16265285	3	1	61	1	0	0	0	0	1	0	0	0	15077	1059	37	1	10831	1	SPEN	1	16265285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6212	16265285	232985336	62	8047										
FBXO42	54455	broad.mit.edu	37	chr1	16577169	16577169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggtttagaacacattatCtctttgctcgtacaaagtac	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16577169C>A	ENST00000375592.3	-	10	2366	c.2150G>T	c.(2149-2151)aGa>aTa	p.R717I		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	717								p.R717I(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		AACACATTATCTCTTTGCTCG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	121	122					1																	16577169		2203	4300	6503	16449756	SO:0001583	missense	54455			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.2150G>T	1.37:g.16577169C>A	ENSP00000364742:p.Arg717Ile		16449756	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244333	0.79912	.	.	ENSG00000037637	ENST00000375592	T	0.10960	2.82	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.17831	0.0428	N	0.08118	0	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.28106	-1.0054	10	0.87932	D	0	.	18.7865	0.91957	0.0:1.0:0.0:0.0	.	717	Q6P3S6	FBX42_HUMAN	I	717	ENSP00000364742:R717I	ENSP00000364742:R717I	R	-	2	0	FBXO42	16449756	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.587000	0.82613	2.767000	0.95098	0.655000	0.94253	AGA		0.388	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			A	16577169	C	A	16577169	3	1	61	1	0	0	0	0	1	0	0	0	5770	913	32	2	7	2	FBXO42	1	16577169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	311884	16577169	232673452	63	8048										
NECAP2	55707	broad.mit.edu	37	chr1	16774457	16774457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacttcgtgatccgcatcGaagatggaaatggtaggcat	13	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16774457G>A	ENST00000337132.5	+	3	376	c.286G>A	c.(286-288)Gaa>Aaa	p.E96K	NECAP2_ENST00000457722.2_Missense_Mutation_p.E70K|NECAP2_ENST00000406746.1_Missense_Mutation_p.E96K|NECAP2_ENST00000443980.2_Missense_Mutation_p.E96K|NECAP2_ENST00000504551.2_Missense_Mutation_p.R62Q	NM_001145278.1|NM_018090.4	NP_001138750.1|NP_060560.1	Q9NVZ3	NECP2_HUMAN	NECAP endocytosis associated 2	96					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.E96K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|Kidney(64;0.000181)|KIRC - Kidney renal clear cell carcinoma(64;0.00268)|STAD - Stomach adenocarcinoma(196;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GATCCGCATCGAAGATGGAAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											219	193	202					1																	16774457		2203	4300	6503	16647044	SO:0001583	missense	55707			AK021938	CCDS173.1, CCDS44066.1, CCDS44067.1	1p36.13	2008-02-05			ENSG00000157191	ENSG00000157191			25528	protein-coding gene	gene with protein product		611624				14555962, 15494011	Standard	NM_001145277		Approved	FLJ10420	uc001ayq.3	Q9NVZ3	OTTHUMG00000002313	ENST00000337132.5:c.286G>A	1.37:g.16774457G>A	ENSP00000338746:p.Glu96Lys		16647044	B4DY19|E9PGQ8|Q5VSU4|Q5VSU5|Q9H7L1|Q9H8L1	Missense_Mutation	SNP	ENST00000337132.5	37	CCDS173.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.384306|4.384306	0.82792|0.82792	.|.	.|.	ENSG00000157191|ENSG00000157191	ENST00000337132;ENST00000457722;ENST00000406746;ENST00000263498;ENST00000443980;ENST00000492095|ENST00000504551	T;T;T;T;T|T	0.41758|0.30182	0.99;0.99;0.99;0.99;0.99|1.54	6.17|6.17	5.24|5.24	0.73138|0.73138	.|.	0.042517|.	0.85682|.	D|.	0.000000|.	T|T	0.42877|0.42877	0.1222|0.1222	L|L	0.46157|0.46157	1.445|1.445	0.58432|0.58432	D|D	0.999999|0.999999	B;B;B|.	0.32829|.	0.334;0.376;0.386|.	B;B;B|.	0.23150|.	0.038;0.041;0.044|.	T|T	0.36553|0.36553	-0.9743|-0.9743	10|7	0.27785|0.87932	T|D	0.31|0	-20.0291|-20.0291	15.2654|15.2654	0.73657|0.73657	0.0:0.1408:0.8592:0.0|0.0:0.1408:0.8592:0.0	.|.	70;96;96|.	Q9NVZ3-4;Q9NVZ3-2;Q9NVZ3|.	.;.;NECP2_HUMAN|.	K|Q	96;70;96;96;96;96|62	ENSP00000338746:E96K;ENSP00000407091:E70K;ENSP00000383925:E96K;ENSP00000391942:E96K;ENSP00000427620:E96K|ENSP00000424509:R62Q	ENSP00000263498:E96K|ENSP00000424509:R62Q	E|R	+|+	1|2	0|0	NECAP2|NECAP2	16647044|16647044	0.997000|0.997000	0.39634|0.39634	0.980000|0.980000	0.43619|0.43619	0.789000|0.789000	0.44602|0.44602	1.835000|1.835000	0.39181|0.39181	1.578000|1.578000	0.49821|0.49821	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.552	NECAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006680.2	NM_018090		A	16774457	G	A	16774457	3	1	61	1	0	0	0	0	1	0	0	0	10339	1059	37	1	296	1	NECAP2	1	16774457	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197288	16774457	232476164	64	8049										
NBPF1	55672	broad.mit.edu	37	chr1	16918427	16918427	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgaactgctgtttgttCtctgccagctgggggcgcaa	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:16918427C>T	ENST00000430580.2	-	7	977	c.90G>A	c.(88-90)gaG>gaA	p.E30E		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	30						cytoplasm (GO:0005737)									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)		GCTGTTTGTTCTCTGCCAGCT	0.483																																																0			1											450	450	450					1																	16918427		2203	4299	6502	16791014	SO:0001819	synonymous_variant	55672			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"neuroblastoma breakpoint family"	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.90G>A	1.37:g.16918427C>T			16791014	Q8N4E8|Q9C0H0	Silent	SNP	ENST00000430580.2	37																																																																																					0.483	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940		T	16918427	C	T	16918427	2	4	61	1	0	0	0	0	0	0	0	1	10222	912	32	3		3	NBPF1	1	16918427	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	143970	16918427	232332194	65	8050										
PADI2	11240	broad.mit.edu	37	chr1	17413184	17413184	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggatatagcgttggccGaagaacgggtctggagggaa	17	5	1	1	rs141669259	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:17413184G>A	ENST00000375486.4	-	7	729	c.666C>T	c.(664-666)ttC>ttT	p.F222F	PADI2_ENST00000444885.2_Missense_Mutation_p.S141L|PADI2_ENST00000375481.1_Silent_p.F222F	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	222					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)	p.F222F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	AGCGTTGGCCGAAGAACGGGT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1						A		1,4405	2.1+/-5.4	0,1,2202	70	75	73		666	-1.9	1	1	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		222/666	17413184	1,13005	2203	4300	6503	17285771	SO:0001819	synonymous_variant	11240			AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"Peptidyl arginine deiminases"	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.666C>T	1.37:g.17413184G>A			17285771	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1	.	.	.	.	.	.	.	.	.	.	g	11.31	1.599793	0.28534	2.27E-4	0.0	ENSG00000117115	ENST00000444885	T	0.04862	3.54	4.84	-1.86	0.07760	.	.	.	.	.	T	0.02688	0.0081	.	.	.	0.22961	N	0.998505	B	0.02656	0.0	B	0.01281	0.0	T	0.48647	-0.9017	8	0.09843	T	0.71	-25.7629	6.2439	0.20805	0.5113:0.0:0.3621:0.1266	.	141	B4DIU3	.	L	141	ENSP00000405894:S141L	ENSP00000405894:S141L	S	-	2	0	PADI2	17285771	0.029000	0.19370	0.991000	0.47740	0.677000	0.39632	-1.113000	0.03296	-0.208000	0.10171	-0.993000	0.02533	TCG		0.592	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			A	17413184	G	A	17413184	2	1	61	1	0	0	0	0	0	0	0	1	11409	1049	37	1		1	PADI2	1	17413184	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	494757	17413184	231837437	66	8051										
RCC2	55920	broad.mit.edu	37	chr1	17755625	17755625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtttaggcacttcttttCgaccaatcaagtcccagttg	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:17755625C>T	ENST00000375436.4	-	3	543	c.356G>A	c.(355-357)cGa>cAa	p.R119Q	RCC2_ENST00000375433.3_Missense_Mutation_p.R119Q	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	119					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)	p.R119Q(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		CACTTCTTTTCGACCAATCAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	122	130					1																	17755625		2203	4300	6503	17628212	SO:0001583	missense	55920				CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.356G>A	1.37:g.17755625C>T	ENSP00000364585:p.Arg119Gln		17628212	Q8IVL9|Q9BSN6|Q9NPV8	Missense_Mutation	SNP	ENST00000375436.4	37	CCDS181.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500738	0.85176	.	.	ENSG00000179051	ENST00000375436;ENST00000375433	T;T	0.80480	-1.38;-1.38	5.72	5.72	0.89469	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.87156	0.6107	L	0.52206	1.635	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.85121	0.0969	10	0.39692	T	0.17	-7.6483	18.8071	0.92041	0.0:1.0:0.0:0.0	.	119	Q9P258	RCC2_HUMAN	Q	119	ENSP00000364585:R119Q;ENSP00000364582:R119Q	ENSP00000364582:R119Q	R	-	2	0	RCC2	17628212	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.596000	0.82721	2.865000	0.98341	0.655000	0.94253	CGA		0.443	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007144.1	NM_018715		T	17755625	C	T	17755625	3	4	61	1	0	0	0	0	1	0	0	0	13211	884	31	1	1256	1	RCC2	1	17755625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	342441	17755625	231494996	67	8052										
ARHGEF10L	55160	broad.mit.edu	37	chr1	17948398	17948398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggctccatcgtgcagagcGaaggcagctacgtggagtct	15	10	1	1	rs371515222		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:17948398G>A	ENST00000361221.3	+	11	1141	c.982G>A	c.(982-984)Gaa>Aaa	p.E328K	ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.E328K|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.E289K|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.E106K|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.E106K|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.E289K|ARHGEF10L_ENST00000375420.3_Missense_Mutation_p.E86K	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	328	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E328K(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CGTGCAGAGCGAAGGCAGCTA	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	1						G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	102	94	97		865,982	5.1	1	1		97	0,8600		0,0,4300	no	missense,missense	ARHGEF10L	NM_001011722.2,NM_018125.3	56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	289/1241,328/1280	17948398	1,13005	2203	4300	6503	17820985	SO:0001583	missense	55160			AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.982G>A	1.37:g.17948398G>A	ENSP00000355060:p.Glu328Lys		17820985	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.975751	0.92982	2.27E-4	0.0	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375420;ENST00000375408;ENST00000457829;ENST00000167825	D;D;D;D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58;-3.58;-3.58;-3.58	5.09	5.09	0.68999	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.98280	0.9430	H	0.96691	3.865	0.58432	D	0.999991	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;1.0;1.0;0.995;0.999	D;D;D;P;D;D;P;D	0.83275	0.986;0.976;0.975;0.759;0.996;0.975;0.886;0.968	D	0.99675	1.0997	10	0.72032	D	0.01	-18.5094	17.0479	0.86509	0.0:0.0:1.0:0.0	.	106;86;328;106;94;289;289;328	Q5VXI4;B4DTE2;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;.;ARGAL_HUMAN	K	328;289;328;289;86;106;106;106	ENSP00000355060:E328K;ENSP00000399401:E289K;ENSP00000394621:E328K;ENSP00000364564:E289K;ENSP00000364569:E86K;ENSP00000364557:E106K;ENSP00000167825:E106K	ENSP00000167825:E106K	E	+	1	0	ARHGEF10L	17820985	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	9.076000	0.94009	2.370000	0.80446	0.561000	0.74099	GAA		0.612	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		A	17948398	G	A	17948398	3	1	61	1	0	0	0	0	1	0	0	0	895	1059	37	1	1020	1	ARHGEF10L	1	17948398	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192773	17948398	231302223	68	8053										
IGSF21	84966	broad.mit.edu	37	chr1	18688676	18688676	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagccgctaccaagcccaGaacttcacgctggtctgcat	8	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:18688676G>A	ENST00000251296.1	+	5	875	c.492G>A	c.(490-492)caG>caA	p.Q164Q		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	164						extracellular region (GO:0005576)		p.Q164Q(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		ACCAAGCCCAGAACTTCACGC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	1											73	65	67					1																	18688676		2203	4300	6503	18561263	SO:0001819	synonymous_variant	84966			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.492G>A	1.37:g.18688676G>A			18561263	Q8NBR8	Silent	SNP	ENST00000251296.1	37	CCDS184.1	.	.	.	.	.	.	.	.	.	.	G	9.124	1.009722	0.19277	.	.	ENSG00000117154	ENST00000412684	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	T	0.71626	0.3362	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71417	-0.4599	4	.	.	.	-9.438	16.2704	0.82616	0.0:0.0:1.0:0.0	.	.	.	.	K	117	.	.	E	+	1	0	IGSF21	18561263	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.129000	0.77225	2.271000	0.75665	0.491000	0.48974	GAA		0.602	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		A	18688676	G	A	18688676	2	1	61	1	0	0	0	0	0	0	0	1	7620	933	33	3		3	IGSF21	1	18688676	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	740278	18688676	230561945	69	8054										
PAX7	5081	broad.mit.edu	37	chr1	19062434	19062434	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcccacccccagggcctcCtgcttgtttatggagagcta	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19062434C>A	ENST00000375375.3	+	8	2062	c.1464C>A	c.(1462-1464)tcC>tcA	p.S488S	PAX7_ENST00000420770.2_Intron|PAX7_ENST00000400661.3_Silent_p.S486S	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	488					anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S488S(1)	PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		CCAGGGCCTCCTGCTTGTTTA	0.577			T	FOXO1A	alveolar rhabdomyosarcoma																																		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	1	Substitution - coding silent(1)	large_intestine(1)	1											35	34	35					1																	19062434		2203	4300	6503	18935021	SO:0001819	synonymous_variant	5081			X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709		"Paired boxes", "Homeoboxes / PRD class"	8621	protein-coding gene	gene with protein product		167410	"paired box gene 7"			7981748, 8431641	Standard	NM_001135254		Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000375375.3:c.1464C>A	1.37:g.19062434C>A			18935021	E9PFV9|Q0VA99|Q2PJS5	Silent	SNP	ENST00000375375.3	37	CCDS186.1																																																																																				0.577	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584		A	19062434	C	A	19062434	2	1	61	1	0	0	0	0	0	0	0	1	11515	668	24	2		2	PAX7	1	19062434	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	373758	19062434	230188187	70	8055										
TAS1R2	80834	broad.mit.edu	37	chr1	19166654	19166654	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaggcgcagacgatctgGaaagaacgcacggcgataca	13	9	1	3	rs201114108		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19166654G>T	ENST00000375371.3	-	6	1980	c.1959C>A	c.(1957-1959)ttC>ttA	p.F653L		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	653					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)	p.F653L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	AGACGATCTGGAAAGAACGCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	126	125					1																	19166654		2203	4300	6503	19039241	SO:0001583	missense	80834				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1959C>A	1.37:g.19166654G>T	ENSP00000364520:p.Phe653Leu		19039241	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.672455	0.29693	.	.	ENSG00000179002	ENST00000375371	D	0.87334	-2.24	5.22	4.31	0.51392	GPCR, family 3, C-terminal (2);	0.000000	0.53938	D	0.000043	D	0.90239	0.6948	M	0.76433	2.335	0.41365	D	0.987455	D	0.65815	0.995	D	0.67382	0.951	D	0.88363	0.2989	10	0.02654	T	1	.	11.8638	0.52482	0.086:0.0:0.914:0.0	.	653	Q8TE23	TS1R2_HUMAN	L	653	ENSP00000364520:F653L	ENSP00000364520:F653L	F	-	3	2	TAS1R2	19039241	0.998000	0.40836	1.000000	0.80357	0.146000	0.21551	1.837000	0.39201	1.212000	0.43366	-0.224000	0.12420	TTC		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19166654	G	T	19166654	3	4	61	1	0	0	0	0	1	0	0	0	15602	1165	41	2	564	2	TAS1R2	1	19166654	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104220	19166654	230083967	71	8056										
ALDH4A1	8659	broad.mit.edu	37	chr1	19202928	19202928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggctgggtgaggagcgtgCgtgctccagccacttcttga	16	10	1	2	rs145334067		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19202928C>T	ENST00000375341.3	-	12	1476	c.1219G>A	c.(1219-1221)Gca>Aca	p.A407T	RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.A347T|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.A407T|ALDH4A1_ENST00000538839.1_Intron	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	407					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)	p.A407T(1)		cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAGCGTGCGTGCTCCAGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											41	28	32					1																	19202928		2202	4300	6502	19075515	SO:0001583	missense	8659			U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"Aldehyde dehydrogenases"	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1219G>A	1.37:g.19202928C>T	ENSP00000364490:p.Ala407Thr		19075515	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.862863	0.91511	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538309	T;T;T	0.80304	-1.36;-1.36;-1.36	4.88	3.75	0.43078	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.219657	0.45867	D	0.000330	D	0.90621	0.7059	M	0.92555	3.32	0.80722	D	1	D	0.76494	0.999	D	0.68039	0.955	D	0.92504	0.6011	10	0.87932	D	0	-31.7548	12.8155	0.57663	0.0:0.903:0.0:0.097	.	407	P30038	AL4A1_HUMAN	T	407;407;347	ENSP00000290597:A407T;ENSP00000364490:A407T;ENSP00000442988:A347T	ENSP00000290597:A407T	A	-	1	0	ALDH4A1	19075515	1.000000	0.71417	0.934000	0.37439	0.900000	0.52787	4.410000	0.59774	2.278000	0.76064	0.561000	0.74099	GCA		0.637	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			T	19202928	C	T	19202928	3	4	61	1	0	0	0	0	1	0	0	0	501	768	27	1	488	1	ALDH4A1	1	19202928	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36274	19202928	230047693	72	8057										
UBR4	23352	broad.mit.edu	37	chr1	19408021	19408021	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacttctccttgggctgttCcagaaagccttggaggttct	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19408021C>T	ENST00000375254.3	-	103	15082	c.15055G>A	c.(15055-15057)Gaa>Aaa	p.E5019K	UBR4_ENST00000375224.1_Missense_Mutation_p.E726K|UBR4_ENST00000375225.3_Missense_Mutation_p.E94K|UBR4_ENST00000375267.2_Missense_Mutation_p.E5019K|UBR4_ENST00000429347.2_Missense_Mutation_p.E542K|UBR4_ENST00000543981.1_Missense_Mutation_p.E683K|UBR4_ENST00000375217.2_Missense_Mutation_p.E5012K|AL137127.1_ENST00000582644.1_RNA|UBR4_ENST00000375226.2_Missense_Mutation_p.E4995K	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5019					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E5019K(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTGGGCTGTTCCAGAAAGCCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											160	165	163					1																	19408021		2203	4300	6503	19280608	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.15055G>A	1.37:g.19408021C>T	ENSP00000364403:p.Glu5019Lys		19280608	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496632	0.64186	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375225;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.42562	0.1208	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.57257	0.979;0.979;0.979;0.974	D;D;D;D	0.71414	0.973;0.973;0.973;0.953	T	0.07501	-1.0769	10	0.23891	T	0.37	.	18.3749	0.90432	0.0:1.0:0.0:0.0	.	683;542;5019;4995	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	K	5019;5019;5012;4995;94;726;542;683	ENSP00000364403:E5019K;ENSP00000364416:E5019K;ENSP00000364365:E5012K;ENSP00000364374:E4995K;ENSP00000364373:E94K;ENSP00000364372:E726K;ENSP00000394173:E542K;ENSP00000444070:E683K	ENSP00000364365:E5012K	E	-	1	0	UBR4	19280608	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	7.399000	0.79935	2.756000	0.94617	0.563000	0.77884	GAA		0.537	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19408021	C	T	19408021	3	4	61	1	0	0	0	0	1	0	0	0	16944	864	30	3	512	3	UBR4	1	19408021	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205093	19408021	229842600	73	8058										
UBR4	23352	broad.mit.edu	37	chr1	19426954	19426954	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatccctcatcagcggcccGatgcctggctcattgctgct	9	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19426954G>A	ENST00000375254.3	-	89	13164	c.13137C>T	c.(13135-13137)atC>atT	p.I4379I	UBR4_ENST00000375224.1_Silent_p.I86I|UBR4_ENST00000375267.2_Silent_p.I4379I|UBR4_ENST00000429347.2_5'Flank|UBR4_ENST00000543981.1_Silent_p.I70I|UBR4_ENST00000375217.2_Silent_p.I4372I|UBR4_ENST00000467272.2_5'Flank|UBR4_ENST00000375226.2_Silent_p.I4355I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4379					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I4379I(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TCAGCGGCCCGATGCCTGGCT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											167	155	159					1																	19426954		2203	4300	6503	19299541	SO:0001819	synonymous_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.13137C>T	1.37:g.19426954G>A			19299541	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.517	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19426954	G	A	19426954	2	1	61	1	0	0	0	0	0	0	0	1	16944	1048	37	1		1	UBR4	1	19426954	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18933	19426954	229823667	74	8059										
UBR4	23352	broad.mit.edu	37	chr1	19468011	19468011	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgtctccaggaccatcGactcagactgcagagagaaa	10	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19468011G>T	ENST00000375254.3	-	57	8345	c.8318C>A	c.(8317-8319)tCg>tAg	p.S2773*	UBR4_ENST00000375267.2_Nonsense_Mutation_p.S2773*|UBR4_ENST00000375217.2_Nonsense_Mutation_p.S2801*|UBR4_ENST00000375226.2_Nonsense_Mutation_p.S2784*	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2773					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S2773*(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAGGACCATCGACTCAGACTG	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											64	67	66					1																	19468011		2203	4300	6503	19340598	SO:0001587	stop_gained	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.8318C>A	1.37:g.19468011G>T	ENSP00000364403:p.Ser2773*		19340598	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Nonsense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	43	9.926792	0.99297	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4714	0.94965	0.0:0.0:1.0:0.0	.	.	.	.	X	2773;2773;2801;2784;416;1494	.	ENSP00000364365:S2801X	S	-	2	0	UBR4	19340598	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.202000	0.95026	2.837000	0.97791	0.591000	0.81541	TCG		0.547	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19468011	G	T	19468011	4	4	61	1	0	0	0	0	0	1	0	0	16944	1059	37	2	7433	2	UBR4	1	19468011	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41057	19468011	229782610	75	8060										
UBR4	23352	broad.mit.edu	37	chr1	19475106	19475106	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttccagggcttctaaaGaactcacaaccagcctgggg	10	12	2	1	rs373018513		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19475106G>T	ENST00000375254.3	-	50	7472	c.7445C>A	c.(7444-7446)tCt>tAt	p.S2482Y	UBR4_ENST00000375267.2_Missense_Mutation_p.S2482Y|UBR4_ENST00000375217.2_Missense_Mutation_p.S2482Y|UBR4_ENST00000375226.2_Missense_Mutation_p.S2493Y	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2482					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S2482Y(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGCTTCTAAAGAACTCACAAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	115	114					1																	19475106		2203	4300	6503	19347693	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.7445C>A	1.37:g.19475106G>T	ENSP00000364403:p.Ser2482Tyr		19347693	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253096	0.80135	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	T;T;T;T	0.23552	1.91;1.91;1.9;1.92	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.39091	0.1065	L	0.43152	1.355	0.80722	D	1	D	0.61697	0.99	D	0.69142	0.962	T	0.07654	-1.0761	10	0.02654	T	1	.	18.9561	0.92659	0.0:0.0:1.0:0.0	.	2482	Q5T4S7	UBR4_HUMAN	Y	2482;2482;2482;2493;97;1203	ENSP00000364403:S2482Y;ENSP00000364416:S2482Y;ENSP00000364365:S2482Y;ENSP00000364374:S2493Y	ENSP00000364365:S2482Y	S	-	2	0	UBR4	19347693	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.476000	0.97823	2.492000	0.84095	0.305000	0.20034	TCT		0.498	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19475106	G	T	19475106	3	4	61	1	0	0	0	0	1	0	0	0	16944	942	33	2	8334	2	UBR4	1	19475106	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7095	19475106	229775515	76	8061										
UBR4	23352	broad.mit.edu	37	chr1	19478964	19478964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcacctggctagacgtgCgggttgctgcagagaacggt	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19478964C>T	ENST00000375254.3	-	47	6866	c.6839G>A	c.(6838-6840)cGc>cAc	p.R2280H	UBR4_ENST00000375267.2_Missense_Mutation_p.R2280H|UBR4_ENST00000375217.2_Missense_Mutation_p.R2280H|UBR4_ENST00000375226.2_Missense_Mutation_p.R2280H	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2280					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R2280H(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GCTAGACGTGCGGGTTGCTGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	120	120					1																	19478964		2203	4300	6503	19351551	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6839G>A	1.37:g.19478964C>T	ENSP00000364403:p.Arg2280His		19351551	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	31	5.095173	0.94197	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.21062	0.0507	N	0.08118	0	0.80722	D	1	D;D	0.71674	0.998;0.998	P;D	0.72075	0.804;0.976	T	0.27971	-1.0058	10	0.56958	D	0.05	.	19.3135	0.94202	0.0:1.0:0.0:0.0	.	2281;2280	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	H	2280;2280;2280;2280;990;1497	ENSP00000364403:R2280H;ENSP00000364416:R2280H;ENSP00000364365:R2280H;ENSP00000364374:R2280H;ENSP00000404897:R990H	ENSP00000364365:R2280H	R	-	2	0	UBR4	19351551	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.130000	0.77235	2.798000	0.96311	0.650000	0.86243	CGC		0.522	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19478964	C	T	19478964	3	4	61	1	0	0	0	0	1	0	0	0	16944	768	27	1	8952	1	UBR4	1	19478964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3858	19478964	229771657	77	8062										
UBR4	23352	broad.mit.edu	37	chr1	19480410	19480410	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactggcaaagagcaggaGaagtcttactgccaccattg	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19480410G>T	ENST00000375254.3	-	45	6509	c.6482C>A	c.(6481-6483)tCt>tAt	p.S2161Y	UBR4_ENST00000375267.2_Missense_Mutation_p.S2161Y|UBR4_ENST00000375217.2_Missense_Mutation_p.S2161Y|UBR4_ENST00000375226.2_Missense_Mutation_p.S2161Y	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2161					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S2161Y(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGAGCAGGAGAAGTCTTACT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	78	80					1																	19480410		2203	4300	6503	19352997	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6482C>A	1.37:g.19480410G>T	ENSP00000364403:p.Ser2161Tyr		19352997	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	30	5.052116	0.93793	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.25579	1.8;1.8;1.79;1.79	5.31	5.31	0.75309	.	0.063152	0.64402	D	0.000003	T	0.39036	0.1063	L	0.34521	1.04	0.80722	D	1	D;D	0.64830	0.994;0.99	P;D	0.71656	0.805;0.974	T	0.02320	-1.1177	10	0.19147	T	0.46	.	18.1582	0.89700	0.0:0.0:1.0:0.0	.	2162;2161	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	Y	2161;2161;2161;2161;871;1378	ENSP00000364403:S2161Y;ENSP00000364416:S2161Y;ENSP00000364365:S2161Y;ENSP00000364374:S2161Y	ENSP00000364365:S2161Y	S	-	2	0	UBR4	19352997	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.025000	0.93694	2.779000	0.95612	0.591000	0.81541	TCT		0.483	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19480410	G	T	19480410	3	4	61	1	0	0	0	0	1	0	0	0	16944	942	33	2	9317	2	UBR4	1	19480410	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1446	19480410	229770211	78	8063										
UBR4	23352	broad.mit.edu	37	chr1	19488340	19488340	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatgctggttcatgaattCtttctgtgtgatcgtaaaag	9	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19488340C>A	ENST00000375254.3	-	36	5035	c.5008G>T	c.(5008-5010)Gaa>Taa	p.E1670*	UBR4_ENST00000375267.2_Nonsense_Mutation_p.E1670*|UBR4_ENST00000375217.2_Nonsense_Mutation_p.E1670*|UBR4_ENST00000375226.2_Nonsense_Mutation_p.E1670*	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1670					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E1670*(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTCATGAATTCTTTCTGTGTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											88	85	86					1																	19488340		2203	4300	6503	19360927	SO:0001587	stop_gained	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.5008G>T	1.37:g.19488340C>A	ENSP00000364403:p.Glu1670*		19360927	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Nonsense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	37	6.289366	0.97444	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	1670;1670;1670;1670;380;886	.	ENSP00000364365:E1670X	E	-	1	0	UBR4	19360927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.657000	0.67996	2.941000	0.99782	0.655000	0.94253	GAA		0.363	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19488340	C	A	19488340	4	1	61	1	0	0	0	0	0	1	0	0	16944	922	32	2	10827	2	UBR4	1	19488340	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7930	19488340	229762281	79	8064										
UBR4	23352	broad.mit.edu	37	chr1	19525410	19525410	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacaggcccttgattaggaGaatcaagtgtttctgaaaag	11	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19525410G>T	ENST00000375254.3	-	4	418	c.391C>A	c.(391-393)Ctc>Atc	p.L131I	UBR4_ENST00000375267.2_Missense_Mutation_p.L131I|UBR4_ENST00000375217.2_Missense_Mutation_p.L131I|UBR4_ENST00000375226.2_Missense_Mutation_p.L131I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	131					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L131I(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTGATTAGGAGAATCAAGTGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	73	73					1																	19525410		2203	4300	6503	19397997	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.391C>A	1.37:g.19525410G>T	ENSP00000364403:p.Leu131Ile		19397997	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406152	0.62288	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.25749	1.79;1.78;1.78;1.78	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.37972	0.1023	L	0.33485	1.01	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.02512	-1.1148	10	0.27082	T	0.32	.	17.7729	0.88499	0.0:0.0:1.0:0.0	.	131	Q5T4S7	UBR4_HUMAN	I	131	ENSP00000364403:L131I;ENSP00000364416:L131I;ENSP00000364365:L131I;ENSP00000364374:L131I	ENSP00000364365:L131I	L	-	1	0	UBR4	19397997	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	7.968000	0.87980	2.536000	0.85505	0.563000	0.77884	CTC		0.373	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19525410	G	T	19525410	3	4	61	1	0	0	0	0	1	0	0	0	16944	942	33	2	15572	2	UBR4	1	19525410	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37070	19525410	229725211	80	8065										
KIAA0090	23065	broad.mit.edu	37	chr1	19549950	19549950	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggctttcttctgcacagaGgagtgaatgatacgcccagt	11	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19549950G>T	ENST00000477853.1	-	19	2358	c.2316C>A	c.(2314-2316)tcC>tcA	p.S772S	EMC1_ENST00000375208.3_Silent_p.S750S|EMC1_ENST00000375199.3_Silent_p.S771S|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000480380.1_5'Flank	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	772						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)		p.S772S(1)									TCTGCACAGAGGAGTGAATGA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	1											246	208	221					1																	19549950		2203	4300	6503	19422537	SO:0001819	synonymous_variant	23065				CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.2316C>A	1.37:g.19549950G>T			19422537	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	37	CCDS190.1	.	.	.	.	.	.	.	.	.	.	G	8.115	0.779751	0.16120	.	.	ENSG00000127463	ENST00000375197	.	.	.	5.69	2.74	0.32292	.	.	.	.	.	T	0.58221	0.2107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50693	-0.8798	4	.	.	.	-22.0206	8.9505	0.35785	0.0:0.2481:0.3793:0.3726	.	.	.	.	I	506	.	.	L	-	1	0	KIAA0090	19422537	0.445000	0.25657	0.995000	0.50966	0.790000	0.44656	-0.283000	0.08433	0.317000	0.23160	0.462000	0.41574	CTC		0.557	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		T	19549950	G	T	19549950	2	4	61	1	0	0	0	0	0	0	0	1	8174	987	35	2		2	KIAA0090	1	19549950	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24540	19549950	229700671	81	8066										
KIAA0090	23065	broad.mit.edu	37	chr1	19557838	19557838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggactgcaagatggggcGcttcagcactgggggagcta	16	9	1	1	rs116784512	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:19557838G>A	ENST00000477853.1	-	16	1903	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	EMC1_ENST00000375208.3_Missense_Mutation_p.R599C|EMC1_ENST00000375199.3_Missense_Mutation_p.R620C|RP1-43E13.2_ENST00000437898.1_RNA	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	621						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)		p.R621C(1)									AAGATGGGGCGCTTCAGCACT	0.488													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		18955	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	69,4337	62.3+/-99.4	0,69,2134	101	103	102		1861	4.7	1	1	dbSNP_132	102	0,8600		0,0,4300	yes	missense	KIAA0090	NM_015047.1	180	0,69,6434	AA,AG,GG		0.0,1.566,0.5305	possibly-damaging	621/994	19557838	69,12937	2203	4300	6503	19430425	SO:0001583	missense	23065				CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.1861C>T	1.37:g.19557838G>A	ENSP00000420608:p.Arg621Cys		19430425	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	3|3	0.0013736263736263737|0.0013736263736263737	2|2	0.0040650406504065045|0.0040650406504065045	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	21.1|21.1	4.098076|4.098076	0.76870|0.76870	0.01566|0.01566	0.0|0.0	ENSG00000127463|ENSG00000127463	ENST00000375197|ENST00000477853;ENST00000375199;ENST00000375208	.|T;T;T	.|0.24151	.|1.87;1.87;1.87	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	.|0.243072	.|0.41823	.|D	.|0.000803	T|T	0.25082|0.25082	0.0609|0.0609	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.989;0.989;0.999;0.999	.|P;P;P;P	.|0.57776	.|0.827;0.784;0.804;0.642	T|T	0.03121|0.03121	-1.1070|-1.1070	5|10	.|0.37606	.|T	.|0.19	-14.2301|-14.2301	14.792|14.792	0.69848|0.69848	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|599;620;620;621	.|Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.|.;.;.;K0090_HUMAN	V|C	354|621;620;599	.|ENSP00000420608:R621C;ENSP00000364345:R620C;ENSP00000364354:R599C	.|ENSP00000364345:R620C	A|R	-|-	2|1	0|0	KIAA0090|KIAA0090	19430425|19430425	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.965000|6.965000	0.76067|0.76067	2.319000|2.319000	0.78375|0.78375	0.462000|0.462000	0.41574|0.41574	GCG|CGC		0.488	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		A	19557838	G	A	19557838	3	1	61	1	0	0	0	0	1	0	0	0	8174	1087	38	1	1152	1	KIAA0090	1	19557838	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7888	19557838	229692783	82	8067										
OTUD3	23252	broad.mit.edu	37	chr1	20231475	20231475	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggatgaaccaagggaagaGaaatagtaagtccatgacta	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:20231475G>T	ENST00000375120.3	+	6	831	c.830G>T	c.(829-831)aGa>aTa	p.R277I		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	277					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)	p.R277I(2)		breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CAAGGGAAGAGAAATAGTAAG	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	1											61	62	61					1																	20231475		1809	4066	5875	20104062	SO:0001583	missense	23252			AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.830G>T	1.37:g.20231475G>T	ENSP00000364261:p.Arg277Ile		20104062	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	G	8.256	0.810203	0.16537	.	.	ENSG00000169914	ENST00000375120	T	0.23348	1.91	6.06	3.24	0.37175	.	0.536286	0.21772	N	0.069352	T	0.16557	0.0398	L	0.29908	0.895	0.47547	D	0.999453	B	0.06786	0.001	B	0.04013	0.001	T	0.06092	-1.0846	10	0.37606	T	0.19	.	6.6683	0.23054	0.147:0.0:0.7088:0.1442	.	277	Q5T2D3	OTUD3_HUMAN	I	277	ENSP00000364261:R277I	ENSP00000364261:R277I	R	+	2	0	OTUD3	20104062	1.000000	0.71417	0.964000	0.40570	0.178000	0.23041	2.321000	0.43805	0.476000	0.27440	-0.746000	0.03513	AGA		0.323	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			T	20231475	G	T	20231475	3	4	61	1	0	0	0	0	1	0	0	0	11344	942	33	2	852	2	OTUD3	1	20231475	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	673637	20231475	229019146	83	8068										
MUL1	79594	broad.mit.edu	37	chr1	20827771	20827771	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatcgaggggtggaacttCtcatacacagtctctagacc	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:20827771C>A	ENST00000264198.3	-	4	607	c.471G>T	c.(469-471)gaG>gaT	p.E157D		NM_024544.2	NP_078820.2	Q969V5	MUL1_HUMAN	mitochondrial E3 ubiquitin protein ligase 1	157					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|cellular response to exogenous dsRNA (GO:0071360)|mitochondrial fission (GO:0000266)|mitochondrion localization (GO:0051646)|negative regulation of cell growth (GO:0030308)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of innate immune response (GO:0045824)|negative regulation of mitochondrial fusion (GO:0010637)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein sumoylation (GO:0033235)|protein stabilization (GO:0050821)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)	cytoplasm (GO:0005737)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E157D(1)		endometrium(2)|large_intestine(4)|lung(5)	11		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GGTGGAACTTCTCATACACAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	94	94					1																	20827771		2203	4300	6503	20700358	SO:0001583	missense	79594			BC014010	CCDS208.1	1p36.12	2013-01-11	2010-09-17	2008-03-26	ENSG00000090432	ENSG00000090432		"RING-type (C3HC4) zinc fingers"	25762	protein-coding gene	gene with protein product	"ring finger protein 218", "mitochondria-anchored protein ligase", "growth inhibition and death E3 ligase", "mitochondrial ubiquitin ligase activator of NFKB 1"	612037	"chromosome 1 open reading frame 166"	C1orf166		18591963, 12761501, 18213395, 18207745	Standard	NM_024544		Approved	FLJ12875, MULAN, RNF218, MAPL, GIDE	uc001bdi.4	Q969V5	OTTHUMG00000002838	ENST00000264198.3:c.471G>T	1.37:g.20827771C>A	ENSP00000264198:p.Glu157Asp		20700358	B5M497|Q7Z431|Q9H9B5	Missense_Mutation	SNP	ENST00000264198.3	37	CCDS208.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549417	0.65311	.	.	ENSG00000090432	ENST00000264198	T	0.25085	1.82	6.17	6.17	0.99709	.	0.042223	0.85682	D	0.000000	T	0.27205	0.0667	L	0.32530	0.975	0.80722	D	1	D	0.53151	0.958	P	0.46172	0.506	T	0.00438	-1.1739	10	0.26408	T	0.33	-35.5411	18.3732	0.90420	0.0:1.0:0.0:0.0	.	157	Q969V5	MUL1_HUMAN	D	157	ENSP00000264198:E157D	ENSP00000264198:E157D	E	-	3	2	MUL1	20700358	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.739000	0.55075	2.941000	0.99782	0.655000	0.94253	GAG		0.582	MUL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007951.1	NM_024544		A	20827771	C	A	20827771	3	1	61	1	0	0	0	0	1	0	0	0	10014	912	32	2	591	2	MUL1	1	20827771	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	596296	20827771	228422850	84	8069										
KIF17	57576	broad.mit.edu	37	chr1	21009301	21009301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgtctgcgtagcgcttgcGccgcttgtgcttctccttca	10	15	3	0	rs186978787		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21009301G>A	ENST00000247986.2	-	11	2618	c.2308C>T	c.(2308-2310)Cgc>Tgc	p.R770C	KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000375044.1_Missense_Mutation_p.R670C|KIF17_ENST00000400463.3_Missense_Mutation_p.R770C			Q9P2E2	KIF17_HUMAN	kinesin family member 17	770					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.R770C(1)		NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TAGCGCTTGCGCCGCTTGTGC	0.612													G|||	1	0.000199681	0	0	5008	,	,		19923	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	92	79	83		2308,2308	4.8	1	1		83	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KIF17	NM_001122819.1,NM_020816.2	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	770/1029,770/1030	21009301	1,13005	2203	4300	6503	20881888	SO:0001583	missense	57576			AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.2308C>T	1.37:g.21009301G>A	ENSP00000247986:p.Arg770Cys		20881888	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.87	2.664178	0.47572	0.0	1.16E-4	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986;ENST00000321188	T;T;T	0.75704	-0.96;-0.81;-0.81	5.76	4.85	0.62838	.	0.301707	0.17999	U	0.154967	D	0.85673	0.5751	M	0.78344	2.41	0.40039	D	0.975627	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.987;0.995;0.987	D	0.86755	0.1963	10	0.59425	D	0.04	.	13.7204	0.62723	0.0:0.0:0.8461:0.1539	.	770;770;770	B0I1R5;Q9P2E2-3;Q9P2E2	.;.;KIF17_HUMAN	C	670;770;770;151	ENSP00000364184:R670C;ENSP00000383311:R770C;ENSP00000247986:R770C	ENSP00000247986:R770C	R	-	1	0	KIF17	20881888	0.853000	0.29707	0.987000	0.45799	0.103000	0.19146	1.097000	0.30988	1.424000	0.47217	0.563000	0.77884	CGC		0.612	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		A	21009301	G	A	21009301	3	1	61	1	0	0	0	0	1	0	0	0	8300	1087	38	1	801	1	KIF17	1	21009301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	181530	21009301	228241320	85	8070										
HP1BP3	50809	broad.mit.edu	37	chr1	21106929	21106929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccttgagacgtatcagtcGccattttaaataatttctag	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21106929G>A	ENST00000312239.5	-	2	144	c.5C>T	c.(4-6)gCg>gTg	p.A2V	HP1BP3_ENST00000487117.1_5'UTR|HP1BP3_ENST00000375000.1_Missense_Mutation_p.A2V	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	2					nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A2V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		CGTATCAGTCGCCATTTTAAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	73	75					1																	21106929		2203	4300	6503	20979516	SO:0001583	missense	50809			BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.5C>T	1.37:g.21106929G>A	ENSP00000312625:p.Ala2Val		20979516	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	37	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.240317	0.79912	.	.	ENSG00000127483	ENST00000312239;ENST00000438032;ENST00000417710;ENST00000375000;ENST00000414993	T;T	0.51071	0.72;1.74	5.81	4.9	0.64082	.	0.000000	0.64402	D	0.000007	T	0.34250	0.0891	N	0.19112	0.55	0.41343	D	0.987316	P;P	0.50066	0.931;0.569	B;B	0.42062	0.374;0.073	T	0.31081	-0.9956	10	0.87932	D	0	-8.4817	12.6127	0.56560	0.0758:0.0:0.9242:0.0	.	2;2	Q5SSJ5-5;Q5SSJ5	.;HP1B3_HUMAN	V	2	ENSP00000312625:A2V;ENSP00000403039:A2V	ENSP00000312625:A2V	A	-	2	0	HP1BP3	20979516	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.747000	0.62141	2.755000	0.94549	0.650000	0.86243	GCG		0.468	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287		A	21106929	G	A	21106929	3	1	61	1	0	0	0	0	1	0	0	0	7349	1087	38	1	1704	1	HP1BP3	1	21106929	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97628	21106929	228143692	86	8071										
EIF4G3	8672	broad.mit.edu	37	chr1	21191648	21191648	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttctgcttcttctcaaaGacatcatcatctgctttatc	3	12	7	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21191648G>T	ENST00000264211.8	-	15	2756	c.2562C>A	c.(2560-2562)gtC>gtA	p.V854V	EIF4G3_ENST00000400422.1_Silent_p.V854V|EIF4G3_ENST00000374935.3_Silent_p.V574V|EIF4G3_ENST00000536266.1_Silent_p.V458V|EIF4G3_ENST00000537738.1_Silent_p.V344V|EIF4G3_ENST00000602326.1_Silent_p.V860V|EIF4G3_ENST00000374937.3_Silent_p.V860V	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	854	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.|eIF3/EIF4A-binding. {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.V860V(1)|p.V854V(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TCTTCTCAAAGACATCATCAT	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	1											202	183	190					1																	21191648		2203	4300	6503	21064235	SO:0001819	synonymous_variant	8672			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.2562C>A	1.37:g.21191648G>T			21064235	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Silent	SNP	ENST00000264211.8	37	CCDS214.1																																																																																				0.418	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		T	21191648	G	T	21191648	2	4	61	1	0	0	0	0	0	0	0	1	5051	929	33	2		2	EIF4G3	1	21191648	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84719	21191648	228058973	87	8072										
EIF4G3	8672	broad.mit.edu	37	chr1	21212819	21212819	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgatgatctttctgggttCtcttctttggccaggttgag	12	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21212819C>A	ENST00000264211.8	-	13	2325	c.2131G>T	c.(2131-2133)Gaa>Taa	p.E711*	EIF4G3_ENST00000400422.1_Nonsense_Mutation_p.E711*|EIF4G3_ENST00000374935.3_Nonsense_Mutation_p.E431*|EIF4G3_ENST00000536266.1_Nonsense_Mutation_p.E315*|EIF4G3_ENST00000537738.1_Nonsense_Mutation_p.E201*|EIF4G3_ENST00000602326.1_Nonsense_Mutation_p.E717*|EIF4G3_ENST00000374937.3_Nonsense_Mutation_p.E717*	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	711	eIF3/EIF4A-binding. {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.E711*(1)|p.E717*(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TTTCTGGGTTCTCTTCTTTGG	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											195	192	193					1																	21212819		2203	4300	6503	21085406	SO:0001587	stop_gained	8672			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.2131G>T	1.37:g.21212819C>A	ENSP00000264211:p.Glu711*		21085406	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Nonsense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	45	11.990416	0.99625	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	.	.	.	5.2	5.2	0.72013	.	0.130769	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-8.8725	19.1062	0.93296	0.0:1.0:0.0:0.0	.	.	.	.	X	711;907;711;431;201;717;315	.	ENSP00000264211:E711X	E	-	1	0	EIF4G3	21085406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.246000	0.72405	2.571000	0.86741	0.655000	0.94253	GAA		0.413	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		A	21212819	C	A	21212819	4	1	61	1	0	0	0	0	0	1	0	0	5051	922	32	2	2702	2	EIF4G3	1	21212819	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21171	21212819	228037802	88	8073										
EIF4G3	8672	broad.mit.edu	37	chr1	21268658	21268658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaattgtacttcgagcaAcagaagaaacagtggtaggt	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21268658A>G	ENST00000264211.8	-	8	1015	c.821T>C	c.(820-822)gTt>gCt	p.V274A	EIF4G3_ENST00000400422.1_Missense_Mutation_p.V274A|EIF4G3_ENST00000374935.3_Intron|EIF4G3_ENST00000356916.3_Missense_Mutation_p.V285A|EIF4G3_ENST00000544689.1_5'Flank|EIF4G3_ENST00000536266.1_5'UTR|EIF4G3_ENST00000374927.4_Missense_Mutation_p.V274A|EIF4G3_ENST00000374933.3_5'Flank|EIF4G3_ENST00000602326.1_Missense_Mutation_p.V280A|EIF4G3_ENST00000374937.3_Missense_Mutation_p.V280A	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	274					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.V280A(1)|p.V274A(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ACTTCGAGCAACAGAAGAAAC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	1											138	127	131					1																	21268658		2203	4300	6503	21141245	SO:0001583	missense	8672			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.821T>C	1.37:g.21268658A>G	ENSP00000264211:p.Val274Ala		21141245	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	A	11.18	1.561877	0.27915	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374937;ENST00000356916;ENST00000374927;ENST00000537059	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.96	4.83	0.62350	.	1.086740	0.06961	N	0.816444	T	0.10680	0.0261	N	0.08118	0	0.09310	N	0.99999	B;B;B;B;B	0.30605	0.001;0.043;0.287;0.011;0.002	B;B;B;B;B	0.27380	0.007;0.016;0.079;0.009;0.058	T	0.10870	-1.0611	10	0.09084	T	0.74	0.0323	9.2169	0.37353	0.9162:0.0:0.0838:0.0	.	274;469;400;280;274	B4DXR2;Q59GJ0;B1AN89;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	A	274;470;274;280;400;274;285	ENSP00000264211:V274A;ENSP00000383274:V274A;ENSP00000364073:V280A;ENSP00000364062:V274A	ENSP00000264211:V274A	V	-	2	0	EIF4G3	21141245	0.002000	0.14202	0.930000	0.37139	0.577000	0.36160	1.194000	0.32174	2.285000	0.76669	0.533000	0.62120	GTT		0.463	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		G	21268658	A	G	21268658	3	3	61	1	0	0	0	0	1	0	0	0	5051	43	2	4	4032	4	EIF4G3	1	21268658	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	55839	21268658	227981963	89	8074										
ECE1	1889	broad.mit.edu	37	chr1	21563331	21563331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaatctccaggatgatctCggtggcctgaggagatacac	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21563331C>T	ENST00000374893.6	-	12	1470	c.1396G>A	c.(1396-1398)Gag>Aag	p.E466K	ECE1_ENST00000415912.2_Missense_Mutation_p.E450K|ECE1_ENST00000264205.6_Missense_Mutation_p.E463K|ECE1_ENST00000436918.2_Missense_Mutation_p.E466K|ECE1_ENST00000357071.4_Missense_Mutation_p.E454K|ECE1_ENST00000528294.1_5'Flank	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	466					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)	p.E466*(1)|p.E466K(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGGATGATCTCGGTGGCCTGA	0.507																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	1											203	196	198					1																	21563331		2203	4300	6503	21435918	SO:0001583	missense	1889			D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1396G>A	1.37:g.21563331C>T	ENSP00000364028:p.Glu466Lys		21435918	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Missense_Mutation	SNP	ENST00000374893.6	37	CCDS215.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125803	0.37533	.	.	ENSG00000117298	ENST00000415912;ENST00000357071;ENST00000374893;ENST00000436918;ENST00000264205	D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7	5.22	5.22	0.72569	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.145677	0.64402	D	0.000009	T	0.76378	0.3979	L	0.51853	1.615	0.45930	D	0.998766	B;B;B;B;B	0.29481	0.083;0.245;0.135;0.206;0.206	B;B;B;B;B	0.23150	0.044;0.043;0.029;0.026;0.026	T	0.73275	-0.4034	10	0.35671	T	0.21	-37.8026	11.2485	0.49010	0.0:0.9146:0.0:0.0854	.	466;450;466;454;463	B4DKB2;Q2Z2K8;P42892;P42892-2;P42892-4	.;.;ECE1_HUMAN;.;.	K	450;454;466;466;463	ENSP00000405088:E450K;ENSP00000349581:E454K;ENSP00000364028:E466K;ENSP00000388439:E466K;ENSP00000264205:E463K	ENSP00000264205:E463K	E	-	1	0	ECE1	21435918	0.997000	0.39634	0.988000	0.46212	0.353000	0.29299	3.472000	0.53114	2.595000	0.87683	0.561000	0.74099	GAG		0.507	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		T	21563331	C	T	21563331	3	4	61	1	0	0	0	0	1	0	0	0	4900	893	31	1	948	1	ECE1	1	21563331	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294673	21563331	227687290	90	8075										
ECE1	1889	broad.mit.edu	37	chr1	21599382	21599382	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcactgagacacaagcttcGctcaggcacacagaggggga	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21599382G>A	ENST00000374893.6	-	4	377	c.303C>T	c.(301-303)agC>agT	p.S101S	ECE1_ENST00000415912.2_Silent_p.S85S|ECE1_ENST00000264205.6_Silent_p.S98S|ECE1_ENST00000436918.2_Silent_p.S101S|ECE1_ENST00000357071.4_Silent_p.S89S	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	101					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)	p.S101S(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		CACAAGCTTCGCTCAGGCACA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											65	63	63					1																	21599382		2203	4300	6503	21471969	SO:0001819	synonymous_variant	1889			D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.303C>T	1.37:g.21599382G>A			21471969	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	37	CCDS215.1																																																																																				0.607	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		A	21599382	G	A	21599382	2	1	61	1	0	0	0	0	0	0	0	1	4900	1078	38	1		1	ECE1	1	21599382	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36051	21599382	227651239	91	8076										
RAP1GAP	5909	broad.mit.edu	37	chr1	21934721	21934721	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaccttgaaagactcaaaGaagccgccgcccccactgcc	7	17	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21934721G>T	ENST00000374765.4	-	17	1481	c.1281C>A	c.(1279-1281)ttC>ttA	p.F427L	RAP1GAP_ENST00000374761.2_Missense_Mutation_p.F458L|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.F427L|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.F427L|RAP1GAP_ENST00000290101.4_Missense_Mutation_p.F491L	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	427					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)	p.F427L(1)|p.F458L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		AAGACTCAAAGAAGCCGCCGC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	1											55	59	58					1																	21934721		2203	4300	6503	21807308	SO:0001583	missense	5909			BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1281C>A	1.37:g.21934721G>T	ENSP00000363897:p.Phe427Leu		21807308	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	37	CCDS218.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510539	0.85389	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758	D;D;D;D	0.89343	-2.5;-2.47;-2.46;-2.46	4.67	3.75	0.43078	.	0.000000	0.85682	D	0.000000	D	0.90566	0.7043	L	0.41906	1.305	0.58432	D	0.999997	D;P;P;P	0.76494	0.999;0.685;0.603;0.685	D;B;B;B	0.85130	0.997;0.193;0.283;0.193	D	0.89270	0.3604	10	0.48119	T	0.1	-38.9989	10.4411	0.44466	0.0981:0.0:0.9019:0.0	.	427;427;457;427	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	L	491;458;427;427;457;427	ENSP00000290101:F491L;ENSP00000363893:F458L;ENSP00000441661:F427L;ENSP00000363897:F427L	ENSP00000290101:F491L	F	-	3	2	RAP1GAP	21807308	1.000000	0.71417	0.998000	0.56505	0.895000	0.52256	5.354000	0.66040	0.940000	0.37473	0.462000	0.41574	TTC		0.602	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		T	21934721	G	T	21934721	3	4	61	1	0	0	0	0	1	0	0	0	13074	933	33	2	824	2	RAP1GAP	1	21934721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	335339	21934721	227315900	92	8077										
RAP1GAP	5909	broad.mit.edu	37	chr1	21935410	21935410	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcagctttgtcagcaaaAattcctggaactcaggcccc	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:21935410A>C	ENST00000374765.4	-	16	1291	c.1091T>G	c.(1090-1092)tTt>tGt	p.F364C	RAP1GAP_ENST00000374761.2_Missense_Mutation_p.F395C|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.F364C|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.F364C|RAP1GAP_ENST00000290101.4_Missense_Mutation_p.F428C	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	364	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)	p.F364C(1)|p.F395C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TGTCAGCAAAAATTCCTGGAA	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	1											161	148	152					1																	21935410		2203	4300	6503	21807997	SO:0001583	missense	5909			BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1091T>G	1.37:g.21935410A>C	ENSP00000363897:p.Phe364Cys		21807997	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	37	CCDS218.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528372	0.85706	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758	D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05	5.28	5.28	0.74379	Rap/ran-GAP (2);	0.054423	0.85682	D	0.000000	D	0.98748	0.9579	H	0.97465	4.01	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77004	0.966;0.969;0.989;0.981	D	0.99478	1.0947	10	0.87932	D	0	-2.7611	13.153	0.59500	1.0:0.0:0.0:0.0	.	364;364;394;364	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	C	428;395;364;364;394;364	ENSP00000290101:F428C;ENSP00000363893:F395C;ENSP00000441661:F364C;ENSP00000363897:F364C	ENSP00000290101:F428C	F	-	2	0	RAP1GAP	21807997	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.358000	0.79466	2.012000	0.59069	0.496000	0.49642	TTT		0.522	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		C	21935410	A	C	21935410	3	2	61	1	0	0	0	0	1	0	0	0	13074	14	1	4	1018	4	RAP1GAP	1	21935410	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	689	21935410	227315211	93	8078										
LDLRAD2	401944	broad.mit.edu	37	chr1	22139002	22139002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttgctgggggcagccGccctgactgcaactgctttg	13	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22139002G>A	ENST00000344642.2	+	1	245	c.58G>A	c.(58-60)Gcc>Acc	p.A20T	LDLRAD2_ENST00000543870.1_Missense_Mutation_p.A20T	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain containing 2	20						integral component of membrane (GO:0016021)		p.A20T(1)		endometrium(2)|large_intestine(1)|lung(3)	6		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)		GGGGGCAGCCGCCCTGACTGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	42	42					1																	22139002		2203	4300	6503	22011589	SO:0001583	missense	401944			AL590103	CCDS30624.1	1p36.12	2008-02-05	2005-10-07		ENSG00000187942	ENSG00000187942			32071	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 2"				Standard	NM_001013693		Approved		uc001bfg.1	Q5SZI1	OTTHUMG00000002675	ENST00000344642.2:c.58G>A	1.37:g.22139002G>A	ENSP00000340988:p.Ala20Thr		22011589	B9EJB3|Q6ZSN5	Missense_Mutation	SNP	ENST00000344642.2	37	CCDS30624.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247836	0.22880	.	.	ENSG00000187942	ENST00000344642;ENST00000543870	T;T	0.41758	0.99;0.99	4.43	-2.16	0.07080	.	1.211050	0.06262	N	0.694141	T	0.18964	0.0455	N	0.04508	-0.205	0.09310	N	1	B	0.24533	0.105	B	0.12837	0.008	T	0.20706	-1.0267	10	0.18710	T	0.47	-0.0152	9.2999	0.37838	0.5703:0.0:0.4297:0.0	.	20	Q5SZI1	LRAD2_HUMAN	T	20	ENSP00000340988:A20T;ENSP00000444097:A20T	ENSP00000340988:A20T	A	+	1	0	LDLRAD2	22011589	0.000000	0.05858	0.000000	0.03702	0.493000	0.33554	-0.048000	0.11944	-0.399000	0.07668	-0.262000	0.10625	GCC		0.582	LDLRAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007601.1	NM_001013693		A	22139002	G	A	22139002	3	1	61	1	0	0	0	0	1	0	0	0	8728	1087	38	1	60	1	LDLRAD2	1	22139002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203592	22139002	227111619	94	8079										
CELA3A	10136	broad.mit.edu	37	chr1	22333423	22333423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcccagctgggagatgccGtccagctcgcctcactccct	11	18	1	1	rs533686702		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22333423G>A	ENST00000290122.3	+	5	434	c.415G>A	c.(415-417)Gtc>Atc	p.V139I		NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	139	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)	p.V139I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGGAGATGCCGTCCAGCTCGC	0.627													G|||	1	0.000199681	0	0.0014	5008	,	,		17525	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											119	104	109					1																	22333423		2199	4300	6499	22206010	SO:0001583	missense	10136			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"protease E"		"elastase 3A, pancreatic (protease E)", "elastase 3A, pancreatic"	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.415G>A	1.37:g.22333423G>A	ENSP00000290122:p.Val139Ile		22206010	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	.	.	.	.	.	.	.	.	.	.	G	7.848	0.723327	0.15439	.	.	ENSG00000142789	ENST00000290122;ENST00000374661	D	0.90844	-2.74	3.83	3.83	0.44106	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.88862	0.6552	N	0.13299	0.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84607	0.0676	9	0.11182	T	0.66	-73.4051	13.3543	0.60619	0.0:0.0:1.0:0.0	.	139	P09093	CEL3A_HUMAN	I	139;155	ENSP00000290122:V139I	ENSP00000290122:V139I	V	+	1	0	CELA3A	22206010	1.000000	0.71417	0.775000	0.31657	0.129000	0.20672	3.026000	0.49689	1.958000	0.56883	0.400000	0.26472	GTC		0.627	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		A	22333423	G	A	22333423	3	1	61	1	0	0	0	0	1	0	0	0	3219	1145	40	1	433	1	CELA3A	1	22333423	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194421	22333423	226917198	95	8080										
CDC42	998	broad.mit.edu	37	chr1	22417991	22417991	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagaaccgaagaagagccGcaggtgtgtgctgctatgaa	13	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22417991G>A	ENST00000344548.3	+	7	808	c.557G>A	c.(556-558)cGc>cAc	p.R186H	CDC42_ENST00000421089.2_Missense_Mutation_p.R228H|CDC42_ENST00000400259.1_Missense_Mutation_p.R186H	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	186					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)	p.R186H(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		AAGAAGAGCCGCAGGTGTGTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	56	54					1																	22417991		2203	4300	6503	22290578	SO:0001583	missense	998			BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.557G>A	1.37:g.22417991G>A	ENSP00000341072:p.Arg186His		22290578	P21181|P25763|Q7L8R5|Q9UDI2	Missense_Mutation	SNP	ENST00000344548.3	37	CCDS221.1	.	.	.	.	.	.	.	.	.	.	g	13.57	2.275782	0.40294	.	.	ENSG00000070831	ENST00000400259;ENST00000344548;ENST00000421089	T;T;T	0.67865	-0.29;-0.29;0.14	5.22	5.22	0.72569	.	0.170674	0.53938	D	0.000050	T	0.64023	0.2561	L	0.54323	1.7	0.58432	D	0.999997	B;B;B;B	0.20261	0.043;0.028;0.043;0.0	B;B;B;B	0.09377	0.003;0.004;0.003;0.0	T	0.62329	-0.6877	10	0.54805	T	0.06	.	17.3462	0.87310	0.0:0.0:1.0:0.0	.	228;231;228;186	E7ETU3;B4E1U9;B4DMH5;P60953	.;.;.;CDC42_HUMAN	H	186;186;228	ENSP00000383118:R186H;ENSP00000341072:R186H;ENSP00000398592:R228H	ENSP00000341072:R186H	R	+	2	0	CDC42	22290578	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.622000	0.83099	2.443000	0.82685	0.455000	0.32223	CGC		0.443	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		A	22417991	G	A	22417991	3	1	61	1	0	0	0	0	1	0	0	0	3077	1087	38	1	669	1	CDC42	1	22417991	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84568	22417991	226832630	96	8081										
ZBTB40	9923	broad.mit.edu	37	chr1	22816775	22816775	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgttagctgcaaaaatCttctgaccagccttgtaaac	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22816775C>A	ENST00000375647.4	+	2	541	c.334C>A	c.(334-336)Ctt>Att	p.L112I	ZBTB40_ENST00000374651.4_Missense_Mutation_p.L112I|ZBTB40_ENST00000404138.1_Missense_Mutation_p.L112I	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	112					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L112I(1)		endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		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)		CTGCAAAAATCTTCTGACCAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	88	88					1																	22816775		2203	4300	6503	22689362	SO:0001583	missense	9923			AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.334C>A	1.37:g.22816775C>A	ENSP00000364798:p.Leu112Ile		22689362	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.104208	0.76983	.	.	ENSG00000184677	ENST00000404138;ENST00000374649;ENST00000375647;ENST00000400239;ENST00000374651	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	4.8	3.87	0.44632	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.43110	D	0.000619	T	0.67050	0.2852	N	0.16862	0.45	0.23838	N	0.996707	D;D	0.61697	0.987;0.99	P;P	0.61070	0.814;0.883	T	0.57911	-0.7729	10	0.34782	T	0.22	-9.7357	11.5063	0.50468	0.0:0.9103:0.0:0.0897	.	112;112	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	I	112	ENSP00000384527:L112I;ENSP00000364798:L112I;ENSP00000383098:L112I;ENSP00000363782:L112I	ENSP00000363780:L112I	L	+	1	0	ZBTB40	22689362	0.998000	0.40836	0.973000	0.42090	0.980000	0.70556	2.479000	0.45197	2.351000	0.79841	0.591000	0.81541	CTT		0.483	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		A	22816775	C	A	22816775	3	1	61	1	0	0	0	0	1	0	0	0	17581	913	32	2	336	2	ZBTB40	1	22816775	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	398784	22816775	226433846	97	8082										
EPHA8	2046	broad.mit.edu	37	chr1	22902867	22902867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatcaagtttaccctgcGcgactgcaacagcatgcctg	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22902867G>A	ENST00000166244.3	+	3	389	c.317G>A	c.(316-318)cGc>cAc	p.R106H	EPHA8_ENST00000374644.4_Missense_Mutation_p.R106H|EPHA8_ENST00000538803.1_Missense_Mutation_p.R106H	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	106	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.R106H(2)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		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;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTTACCCTGCGCGACTGCAAC	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	1											60	59	59					1																	22902867		2203	4300	6503	22775454	SO:0001583	missense	2046			BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.317G>A	1.37:g.22902867G>A	ENSP00000166244:p.Arg106His		22775454	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.638064	0.87760	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.05855	3.38;3.38;3.38	4.29	4.29	0.51040	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000002	T	0.33440	0.0863	M	0.92317	3.295	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.47381	-0.9122	10	0.87932	D	0	.	15.4668	0.75406	0.0:0.0:1.0:0.0	.	106;106	P29322;P29322-2	EPHA8_HUMAN;.	H	106	ENSP00000166244:R106H;ENSP00000363775:R106H;ENSP00000440274:R106H	ENSP00000166244:R106H	R	+	2	0	EPHA8	22775454	1.000000	0.71417	0.945000	0.38365	0.885000	0.51271	9.657000	0.98554	2.212000	0.71576	0.442000	0.29010	CGC		0.622	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22902867	G	A	22902867	3	1	61	1	0	0	0	0	1	0	0	0	5186	1087	38	1	327	1	EPHA8	1	22902867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86092	22902867	226347754	98	8083										
EPHA8	2046	broad.mit.edu	37	chr1	22915867	22915867	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctggaggctcttcattgcCtttagaaaagtggaacacat	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:22915867C>A	ENST00000166244.3	+	5	1387				EPHA8_ENST00000374644.4_Missense_Mutation_p.L495I|EPHA8_ENST00000538803.1_Missense_Mutation_p.L495I	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.L495I(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		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;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TCTTCATTGCCTTTAGAAAAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											39	43	41					1																	22915867		2197	4290	6487	22788454	SO:0001627	intron_variant	2046			BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1315+168C>A	1.37:g.22915867C>A			22788454	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	C	6.856	0.527156	0.13066	.	.	ENSG00000070886	ENST00000374644;ENST00000538803	T;T	0.01323	5.01;5.01	3.5	-0.845	0.10737	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.09310	N	1	B	0.21905	0.062	B	0.17098	0.017	T	0.48246	-0.9052	7	.	.	.	.	4.2198	0.10552	0.161:0.5375:0.0:0.3015	.	495	P29322-2	.	I	495	ENSP00000363775:L495I;ENSP00000440274:L495I	.	L	+	1	0	EPHA8	22788454	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.791000	0.04599	-0.133000	0.11537	0.491000	0.48974	CTT		0.547	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22915867	C	A	22915867	1	1	61	0	1	0	0	0	0	0	0	0	5186	681	24	2		2	EPHA8	1	22915867	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13000	22915867	226334754	99	8084										
KDM1A	23028	broad.mit.edu	37	chr1	23381623	23381623	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcatggtcttatcaacttCggcatctataagaggataaa	8	8	4	1	rs189014649		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:23381623C>T	ENST00000356634.3	+	5	941	c.792C>T	c.(790-792)ttC>ttT	p.F264F	KDM1A_ENST00000400181.4_Silent_p.F284F|KDM1A_ENST00000542151.1_Silent_p.F284F|RP1-184J9.2_ENST00000427154.1_RNA|MIR4419A_ENST00000583845.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	264	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.F284F(1)		breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TTATCAACTTCGGCATCTATA	0.368													C|||	1	0.000199681	8e-04	0	5008	,	,		13706	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											190	187	188					1																	23381623		2203	4300	6503	23254210	SO:0001819	synonymous_variant	23028			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.792C>T	1.37:g.23381623C>T			23254210	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																				0.368	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		T	23381623	C	T	23381623	2	4	61	1	0	0	0	0	0	0	0	1	8143	883	31	1		1	KDM1A	1	23381623	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	465756	23381623	225868998	100	8085										
ASAP3	55616	broad.mit.edu	37	chr1	23765719	23765719	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttttctgccagactcttcGaattctaaagcccagaggga	8	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:23765719G>A	ENST00000336689.3	-	11	993	c.949C>T	c.(949-951)Cga>Tga	p.R317*	ASAP3_ENST00000495646.1_5'Flank|ASAP3_ENST00000437606.2_Nonsense_Mutation_p.R308*	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	317	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R317*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						CAGACTCTTCGAATTCTAAAG	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											93	75	81					1																	23765719		2203	4300	6503	23638306	SO:0001587	stop_gained	55616			AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.949C>T	1.37:g.23765719G>A	ENSP00000338769:p.Arg317*		23638306	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Nonsense_Mutation	SNP	ENST00000336689.3	37	CCDS235.1	.	.	.	.	.	.	.	.	.	.	G	38	6.713978	0.97784	.	.	ENSG00000088280	ENST00000336689;ENST00000437606	.	.	.	4.94	2.99	0.34606	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8906	0.58069	0.0:0.0:0.7037:0.2963	.	.	.	.	X	317;308	.	ENSP00000338769:R317X	R	-	1	2	ASAP3	23638306	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	3.083000	0.50136	0.756000	0.33013	-0.187000	0.12897	CGA		0.532	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		A	23765719	G	A	23765719	4	1	61	1	0	0	0	0	0	1	0	0	1013	1066	37	1	1822	1	ASAP3	1	23765719	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	384096	23765719	225484902	101	8086										
RPL11	6135	broad.mit.edu	37	chr1	24022387	24022387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggaggccatgcgctggTtccagcagaaggtaaagctg	15	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24022387T>C	ENST00000374550.3	+	5	541	c.496T>C	c.(496-498)Ttc>Ctc	p.F166L	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	166					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.F166L(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		CATGCGCTGGTTCCAGCAGAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	51	55					1																	24022387		2201	4297	6498	23894974	SO:0001583	missense	6135			L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.496T>C	1.37:g.24022387T>C	ENSP00000363676:p.Phe166Leu		23894974	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	37	CCDS238.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905419	0.92107	.	.	ENSG00000142676	ENST00000374550;ENST00000458455	T;T	0.75589	-0.95;-0.95	5.19	5.19	0.71726	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	T	0.76807	0.4039	M	0.68952	2.095	0.80722	D	1	B;B	0.19445	0.036;0.034	B;B	0.35607	0.206;0.142	T	0.73474	-0.3971	10	0.34782	T	0.22	-14.1085	15.0495	0.71854	0.0:0.0:0.0:1.0	.	165;166	P62913-2;P62913	.;RL11_HUMAN	L	166;164	ENSP00000363676:F166L;ENSP00000398888:F164L	ENSP00000363676:F166L	F	+	1	0	RPL11	23894974	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.829000	0.86735	1.962000	0.57031	0.482000	0.46254	TTC		0.493	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		C	24022387	T	C	24022387	3	2	61	1	0	0	0	0	1	0	0	0	13594	1725	60	4	514	4	RPL11	1	24022387	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	256668	24022387	225228234	102	8087										
FUCA1	2517	broad.mit.edu	37	chr1	24180867	24180867	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccgaaatgatttcagattCttctgtaacatcagacaatg	6	8	4	3	rs201499886		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24180867C>A	ENST00000374479.3	-	5	959	c.952G>T	c.(952-954)Gaa>Taa	p.E318*		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	318					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)	p.E318*(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		ATTTCAGATTCTTCTGTAACA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											120	122	121					1																	24180867		2203	4300	6503	24053454	SO:0001587	stop_gained	2517			BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.952G>T	1.37:g.24180867C>A	ENSP00000363603:p.Glu318*		24053454	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Nonsense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	.	.	.	.	.	.	.	.	.	.	C	18.26	3.585463	0.66105	.	.	ENSG00000179163	ENST00000374479;ENST00000374475	.	.	.	4.77	2.81	0.32909	.	0.486350	0.23549	N	0.046990	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-13.6033	9.4182	0.38534	0.1426:0.7822:0.0:0.0752	.	.	.	.	X	318;107	.	ENSP00000363599:E107X	E	-	1	0	FUCA1	24053454	0.001000	0.12720	0.005000	0.12908	0.185000	0.23345	0.737000	0.26144	1.244000	0.43870	0.637000	0.83480	GAA		0.373	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		A	24180867	C	A	24180867	4	1	61	1	0	0	0	0	0	1	0	0	6113	922	32	2	464	2	FUCA1	1	24180867	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158480	24180867	225069754	103	8088										
FUCA1	2517	broad.mit.edu	37	chr1	24181028	24181028	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaacagttctgaccccatCggtcatttactaccacctca	6	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24181028C>T	ENST00000374479.3	-	5	798	c.791G>A	c.(790-792)cGa>cAa	p.R264Q		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	264					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)	p.R264Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		CTGACCCCATCGGTCATTTAC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	105	106					1																	24181028		2203	4300	6503	24053615	SO:0001583	missense	2517			BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.791G>A	1.37:g.24181028C>T	ENSP00000363603:p.Arg264Gln		24053615	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	.	.	.	.	.	.	.	.	.	.	c	33	5.276972	0.95459	.	.	ENSG00000179163	ENST00000374479;ENST00000374475	T	0.70631	-0.5	4.74	4.74	0.60224	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.89058	0.6607	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92464	0.5980	10	0.87932	D	0	-13.9177	17.9954	0.89182	0.0:1.0:0.0:0.0	.	264	P04066	FUCO_HUMAN	Q	264;53	ENSP00000363603:R264Q	ENSP00000363599:R53Q	R	-	2	0	FUCA1	24053615	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.275000	0.78548	2.477000	0.83638	0.632000	0.83419	CGA		0.433	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		T	24181028	C	T	24181028	3	4	61	1	0	0	0	0	1	0	0	0	6113	884	31	1	625	1	FUCA1	1	24181028	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161	24181028	225069593	104	8089										
IL22RA1	58985	broad.mit.edu	37	chr1	24465083	24465083	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcctacgtcttatactcGatgctgtagaccgtgtctgg	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24465083G>A	ENST00000270800.1	-	2	203	c.165C>T	c.(163-165)atC>atT	p.I55I		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	55	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)	p.I55I(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		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)		TCTTATACTCGATGCTGTAGA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											106	101	102					1																	24465083		2203	4300	6503	24337670	SO:0001819	synonymous_variant	58985			AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.165C>T	1.37:g.24465083G>A			24337670	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37	CCDS247.1																																																																																				0.552	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			A	24465083	G	A	24465083	2	1	61	1	0	0	0	0	0	0	0	1	7694	1048	37	1		1	IL22RA1	1	24465083	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	284055	24465083	224785538	105	8090										
C1orf201	90529	broad.mit.edu	37	chr1	24687483	24687483	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacctgggaaaggtggcttCggaggcagaggcgaaggctg	20	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24687483C>T	ENST00000374409.1	-	8	1040	c.786G>A	c.(784-786)ccG>ccA	p.P262P	GRHL3_ENST00000350501.5_Intron|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Silent_p.P215P|STPG1_ENST00000337248.4_Silent_p.P262P|STPG1_ENST00000440416.1_Silent_p.P215P	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	262					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P215P(1)									AAGGTGGCTTCGGAGGCAGAG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											73	69	70					1																	24687483		2203	4300	6503	24560070	SO:0001819	synonymous_variant	90529			BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 2"	615826	"chromosome 1 open reading frame 201"	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.786G>A	1.37:g.24687483C>T			24560070	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Silent	SNP	ENST00000374409.1	37	CCDS55581.1																																																																																				0.517	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122		T	24687483	C	T	24687483	2	4	61	1	0	0	0	0	0	0	0	1	2033	871	31	1		1	C1orf201	1	24687483	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222400	24687483	224563138	106	8091										
NIPAL3	57185	broad.mit.edu	37	chr1	24790531	24790531	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaggtgcctcattgcattCttgggcgtcttcttaatcac	9	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24790531C>A	ENST00000374399.4	+	11	1310	c.942C>A	c.(940-942)ttC>ttA	p.F314L	NIPAL3_ENST00000339255.2_Missense_Mutation_p.F314L|NIPAL3_ENST00000003912.3_Missense_Mutation_p.F232L	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	314						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)	p.F314L(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						TCATTGCATTCTTGGGCGTCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	102	108					1																	24790531		2203	4300	6503	24663118	SO:0001583	missense	57185			BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.942C>A	1.37:g.24790531C>A	ENSP00000363520:p.Phe314Leu		24663118	A2A298|Q6MZT9|Q9BVE6	Missense_Mutation	SNP	ENST00000374399.4	37	CCDS30631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.64|15.64	2.893471|2.893471	0.52121|0.52121	.|.	.|.	ENSG00000001461|ENSG00000001461	ENST00000374399;ENST00000003912;ENST00000339255|ENST00000432012	D;D;D|.	0.87256|.	-2.23;-2.23;-2.23|.	5.95|5.95	5.05|5.05	0.67936|0.67936	.|.	0.041586|.	0.85682|.	N|.	0.000000|.	T|T	0.75882|0.75882	0.3910|0.3910	M|M	0.83384|0.83384	2.64|2.64	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.83275|.	0.996;0.994|.	T|T	0.77925|0.77925	-0.2405|-0.2405	10|5	0.27785|.	T|.	0.31|.	-42.5371|-42.5371	12.2446|12.2446	0.54563|0.54563	0.0:0.8589:0.0:0.1411|0.0:0.8589:0.0:0.1411	.|.	314;314|.	Q6P499;A6NN97|.	NPAL3_HUMAN;.|.	L|Y	314;232;314|126	ENSP00000363520:F314L;ENSP00000003912:F232L;ENSP00000343549:F314L|.	ENSP00000003912:F232L|.	F|S	+|+	3|2	2|0	NIPAL3|NIPAL3	24663118|24663118	0.906000|0.906000	0.30813|0.30813	0.865000|0.865000	0.33974|0.33974	0.044000|0.044000	0.14063|0.14063	1.582000|1.582000	0.36568|0.36568	1.532000|1.532000	0.49169|0.49169	-0.251000|-0.251000	0.11542|0.11542	TTC|TCT		0.507	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448		A	24790531	C	A	24790531	3	1	61	1	0	0	0	0	1	0	0	0	10457	912	32	2	980	2	NIPAL3	1	24790531	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103048	24790531	224460090	107	8092										
SRRM1	10250	broad.mit.edu	37	chr1	24973161	24973161	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctatgtttcatcaggtgGacatgagcaaagtaaatttg	9	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24973161G>T	ENST00000323848.9	+	3	430	c.115G>T	c.(115-117)Gac>Tac	p.D39Y	SRRM1_ENST00000447431.2_Missense_Mutation_p.D39Y|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.D39Y|SRRM1_ENST00000537199.1_5'Flank	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	39	Necessary for DNA and RNA-binding.|Necessary for mRNA 3'-end cleavage and cytoplasmic accumulation.|PWI. {ECO:0000255|PROSITE- ProRule:PRU00627}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.D39Y(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TCATCAGGTGGACATGAGCAA	0.328																																					Ovarian(68;897 1494 3282 17478)											1	Substitution - Missense(1)	large_intestine(1)	1											115	115	115					1																	24973161		2203	4300	6503	24845748	SO:0001583	missense	10250			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.115G>T	1.37:g.24973161G>T	ENSP00000326261:p.Asp39Tyr		24845748	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571909	0.45798	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.57107	0.42;0.42;0.42	5.42	5.42	0.78866	Splicing factor PWI (3);	0.000000	0.64402	D	0.000003	T	0.80412	0.4618	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.84804	0.0786	10	0.87932	D	0	.	19.5679	0.95403	0.0:0.0:1.0:0.0	.	39;39	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	Y	39	ENSP00000326261:D39Y;ENSP00000391430:D39Y;ENSP00000363510:D39Y	ENSP00000326261:D39Y	D	+	1	0	SRRM1	24845748	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.700000	0.98707	2.708000	0.92522	0.650000	0.86243	GAC		0.328	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24973161	G	T	24973161	3	4	61	1	0	0	0	0	1	0	0	0	15207	1174	41	2	125	2	SRRM1	1	24973161	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182630	24973161	224277460	108	8093										
SRRM1	10250	broad.mit.edu	37	chr1	24997927	24997927	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagaaaaagaaggacaaGaaacacaaaaaggataagaa	9	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:24997927G>T	ENST00000323848.9	+	16	2766	c.2451G>T	c.(2449-2451)aaG>aaT	p.K817N	SRRM1_ENST00000447431.2_Missense_Mutation_p.K829N|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.K826N	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	817	Lys-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.K817N(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		agaaggacaagaaacacaaaa	0.403																																					Ovarian(68;897 1494 3282 17478)											1	Substitution - Missense(1)	large_intestine(1)	1											43	42	43					1																	24997927		2203	4300	6503	24870514	SO:0001583	missense	10250			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2451G>T	1.37:g.24997927G>T	ENSP00000326261:p.Lys817Asn		24870514	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353999	0.61293	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.53857	0.6;0.65;0.64	5.81	4.9	0.64082	.	0.000000	0.64402	D	0.000003	T	0.65302	0.2678	L	0.47190	1.495	0.80722	D	1	D;P	0.61080	0.989;0.947	D;D	0.72625	0.978;0.95	T	0.67983	-0.5529	10	0.72032	D	0.01	-2.6228	13.5212	0.61569	0.0755:0.0:0.9245:0.0	.	829;817	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	N	817;829;826	ENSP00000326261:K817N;ENSP00000391430:K829N;ENSP00000363510:K826N	ENSP00000326261:K817N	K	+	3	2	SRRM1	24870514	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.616000	0.61197	1.444000	0.47605	0.650000	0.86243	AAG		0.403	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24997927	G	T	24997927	3	4	61	1	0	0	0	0	1	0	0	0	15207	933	33	2	2513	2	SRRM1	1	24997927	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24766	24997927	224252694	109	8094										
CLIC4	25932	broad.mit.edu	37	chr1	25140685	25140685	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaataagattgaggaatttCttgaagaagtcttatgccct	8	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:25140685C>A	ENST00000374379.4	+	3	480	c.283C>A	c.(283-285)Ctt>Att	p.L95I	CLIC4_ENST00000497755.1_3'UTR	NM_013943.2	NP_039234.1	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	95	Required for insertion into the membrane. {ECO:0000305}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|endothelial cell morphogenesis (GO:0001886)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|keratinocyte differentiation (GO:0030216)|multicellular organism growth (GO:0035264)|negative regulation of cell migration (GO:0030336)|regulation of cytoskeleton organization (GO:0051493)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|vacuolar acidification (GO:0007035)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|microvillus (GO:0005902)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.L95I(1)		large_intestine(3)|lung(2)|skin(1)	6		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)		TGAGGAATTTCTTGAAGAAGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	88	86					1																	25140685		2203	4300	6503	25013272	SO:0001583	missense	25932			AF097330	CCDS256.1	1p	2012-09-26			ENSG00000169504	ENSG00000169504		"Ion channels / Chloride channels : Intracellular"	13518	protein-coding gene	gene with protein product		606536				9139710, 10070163	Standard	NM_013943		Approved	DKFZP566G223, CLIC4L, P64H1, H1, huH1, p64H1	uc001bjo.2	Q9Y696	OTTHUMG00000003327	ENST00000374379.4:c.283C>A	1.37:g.25140685C>A	ENSP00000363500:p.Leu95Ile		25013272	Q9UFW9|Q9UQJ6	Missense_Mutation	SNP	ENST00000374379.4	37	CCDS256.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852197	0.91355	.	.	ENSG00000169504	ENST00000374379;ENST00000444041	T	0.63096	-0.02	5.85	5.85	0.93711	Glutathione S-transferase/chloride channel, C-terminal (1);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.76807	0.4039	L	0.58583	1.82	0.45066	D	0.998084	P;D	0.65815	0.897;0.995	D;D	0.87578	0.97;0.998	T	0.71879	-0.4459	10	0.31617	T	0.26	-13.1949	18.9446	0.92616	0.0:1.0:0.0:0.0	.	75;95	B3KTR3;Q9Y696	.;CLIC4_HUMAN	I	95	ENSP00000363500:L95I	ENSP00000363500:L95I	L	+	1	0	CLIC4	25013272	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.420000	0.80191	2.768000	0.95171	0.655000	0.94253	CTT		0.403	CLIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009332.1	NM_013943		A	25140685	C	A	25140685	3	1	61	1	0	0	0	0	1	0	0	0	3534	913	32	2	293	2	CLIC4	1	25140685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142758	25140685	224109936	110	8095										
RHD	6007	broad.mit.edu	37	chr1	25628087	25628087	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatcgaaaggaagaatgcCgtgttcaacacctactatgc	8	11	1	1	rs367810718		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:25628087C>A	ENST00000328664.4	+	5	866	c.711C>A	c.(709-711)gcC>gcA	p.A237A	RHD_ENST00000357542.4_Silent_p.A237A|RHD_ENST00000417538.2_Silent_p.A237A|RHD_ENST00000454452.2_Silent_p.A237A|RHD_ENST00000342055.5_Silent_p.A237A|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000423810.2_Silent_p.A237A|RHD_ENST00000568195.1_Silent_p.A237A	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	237						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)	p.A237A(1)		breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGAAGAATGCCGTGTTCAACA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	1	GRCh37	CD025467	RHD	D							198	154	170					1																	25628087		2122	3773	5895	25500674	SO:0001819	synonymous_variant	6007			AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"CD molecules", "Blood group antigens"	10009	protein-coding gene	gene with protein product		111680	"Rhesus blood group, D antigen", "Rh blood group, D antigen"	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.711C>A	1.37:g.25628087C>A			25500674	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Silent	SNP	ENST00000328664.4	37	CCDS262.1																																																																																				0.557	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124		A	25628087	C	A	25628087	2	1	61	1	0	0	0	0	0	0	0	1	13364	639	23	2		2	RHD	1	25628087	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	487402	25628087	223622534	111	8096										
TMEM50A	23585	broad.mit.edu	37	chr1	25666998	25666998	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtctggatttctagagggCttgagatgctcagaatgcat	12	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:25666998C>A	ENST00000374358.4	+	2	574	c.21C>A	c.(19-21)ggC>ggA	p.G7G	TMEM50A_ENST00000480937.1_3'UTR|RNU6-1171P_ENST00000516706.1_RNA	NM_014313.3	NP_055128.1	O95807	TM50A_HUMAN	transmembrane protein 50A	7						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.G7G(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;3.47e-27)|Colorectal(126;1.1e-08)|COAD - Colon adenocarcinoma(152;7.48e-07)|STAD - Stomach adenocarcinoma(196;0.00035)|BRCA - Breast invasive adenocarcinoma(304;0.00047)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|GBM - Glioblastoma multiforme(114;0.00106)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.204)		TTCTAGAGGGCTTGAGATGCT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											99	92	94					1																	25666998		2203	4300	6503	25539585	SO:0001819	synonymous_variant	23585			AY071927	CCDS264.1	1p36.11	2008-02-05			ENSG00000183726	ENSG00000183726			30590	protein-coding gene	gene with protein product	"small membrane protein 1"	605348				10938938, 10845894	Standard	NM_014313		Approved	SMP1	uc001bke.3	O95807	OTTHUMG00000007651	ENST00000374358.4:c.21C>A	1.37:g.25666998C>A			25539585		Silent	SNP	ENST00000374358.4	37	CCDS264.1																																																																																				0.373	TMEM50A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020313.1			A	25666998	C	A	25666998	2	1	61	1	0	0	0	0	0	0	0	1	16214	784	28	2		2	TMEM50A	1	25666998	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38911	25666998	223583623	112	8097										
TMEM57	55219	broad.mit.edu	37	chr1	25780777	25780777	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtgtttgcctacagtgtCtctctggatcctctttgttt	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:25780777C>A	ENST00000374343.4	+	4	556	c.377C>A	c.(376-378)tCt>tAt	p.S126Y	TMEM57_ENST00000399763.3_Intron|TMEM57_ENST00000399766.3_Missense_Mutation_p.S126Y|TMEM57_ENST00000470035.1_3'UTR	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	126					brain development (GO:0007420)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|synapse (GO:0045202)		p.S126Y(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		CCTACAGTGTCTCTCTGGATC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											149	139	142					1																	25780777		2203	4300	6503	25653364	SO:0001583	missense	55219			AK001609	CCDS30638.1, CCDS60034.1	1p36.11	2008-02-05			ENSG00000204178	ENSG00000204178			25572	protein-coding gene	gene with protein product		610301				12459264, 15255972	Standard	XM_005245931		Approved	FLJ10747	uc001bkk.3	Q8N5G2	OTTHUMG00000003473	ENST00000374343.4:c.377C>A	1.37:g.25780777C>A	ENSP00000363463:p.Ser126Tyr		25653364	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Missense_Mutation	SNP	ENST00000374343.4	37	CCDS30638.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786425	0.70337	.	.	ENSG00000204178	ENST00000399766;ENST00000374343	T;T	0.76709	-1.04;2.53	6.03	6.03	0.97812	.	0.052309	0.85682	D	0.000000	D	0.88529	0.6461	M	0.75264	2.295	0.80722	D	1	D;D	0.65815	0.994;0.995	D;D	0.77004	0.989;0.953	D	0.88226	0.2900	10	0.66056	D	0.02	-3.5937	19.6124	0.95613	0.0:1.0:0.0:0.0	.	126;126	Q8N5G2-3;Q8N5G2	.;MACOI_HUMAN	Y	126	ENSP00000382668:S126Y;ENSP00000363463:S126Y	ENSP00000363463:S126Y	S	+	2	0	TMEM57	25653364	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.880000	0.98712	0.650000	0.86243	TCT		0.398	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202		A	25780777	C	A	25780777	3	1	61	1	0	0	0	0	1	0	0	0	16223	913	32	2	391	2	TMEM57	1	25780777	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113779	25780777	223469844	113	8098										
LDLRAP1	26119	broad.mit.edu	37	chr1	25889188	25889188	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaagtcgcctttgagttTtggcaggtgtccaaggaagg	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:25889188T>G	ENST00000374338.4	+	5	632	c.513T>G	c.(511-513)ttT>ttG	p.F171L	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	171	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)	p.F171L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		CCTTTGAGTTTTGGCAGGTGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											139	124	129					1																	25889188		2203	4300	6503	25761775	SO:0001583	missense	26119			BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.513T>G	1.37:g.25889188T>G	ENSP00000363458:p.Phe171Leu		25761775	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	37	CCDS30639.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.433226	0.25813	.	.	ENSG00000157978	ENST00000374338	T	0.60797	0.16	5.56	-2.78	0.05859	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.090181	0.85682	N	0.000000	T	0.23014	0.0556	N	0.04090	-0.28	0.50632	D	0.999888	B	0.02656	0.0	B	0.06405	0.002	T	0.37842	-0.9688	10	0.02654	T	1	-0.688	8.3298	0.32180	0.0:0.3884:0.1073:0.5043	.	171	Q5SW96	ARH_HUMAN	L	171	ENSP00000363458:F171L	ENSP00000363458:F171L	F	+	3	2	LDLRAP1	25761775	0.963000	0.33076	0.996000	0.52242	0.997000	0.91878	0.070000	0.14573	-0.232000	0.09811	0.454000	0.30748	TTT		0.577	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627		G	25889188	T	G	25889188	3	3	61	1	0	0	0	0	1	0	0	0	8730	1838	64	4	531	4	LDLRAP1	1	25889188	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	108411	25889188	223361433	114	8099										
MAN1C1	57134	broad.mit.edu	37	chr1	26012982	26012982	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatgcaatggggaaaaacGaactccgtccactaacaaaa	8	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26012982G>A	ENST00000374332.4	+	2	922	c.592G>A	c.(592-594)Gaa>Aaa	p.E198K	MAN1C1_ENST00000263979.3_Missense_Mutation_p.E18K	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	198					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.E198K(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		GGGGAAAAACGAACTCCGTCC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											173	163	166					1																	26012982		2203	4300	6503	25885569	SO:0001583	missense	57134			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.592G>A	1.37:g.26012982G>A	ENSP00000363452:p.Glu198Lys		25885569	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571306	0.86542	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979	T;T	0.76578	-1.03;-1.03	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.93064	0.7792	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95426	0.8512	10	0.87932	D	0	.	14.5703	0.68205	0.0:0.0:1.0:0.0	.	198	Q9NR34	MA1C1_HUMAN	K	198;18;18	ENSP00000363452:E198K;ENSP00000263979:E18K	ENSP00000263979:E18K	E	+	1	0	MAN1C1	25885569	1.000000	0.71417	0.996000	0.52242	0.748000	0.42578	7.203000	0.77864	2.574000	0.86865	0.563000	0.77884	GAA		0.498	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		A	26012982	G	A	26012982	3	1	61	1	0	0	0	0	1	0	0	0	9243	1059	37	1	598	1	MAN1C1	1	26012982	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123794	26012982	223237639	115	8100										
STMN1	3925	broad.mit.edu	37	chr1	26227545	26227545	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagcagggtctttggattCtttgttcttccgcacttctt	9	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26227545C>A	ENST00000399728.1	-	5	775	c.412G>T	c.(412-414)Gaa>Taa	p.E138*	STMN1_ENST00000455785.2_Nonsense_Mutation_p.E138*|STMN1_ENST00000465604.1_5'UTR|STMN1_ENST00000374291.1_Nonsense_Mutation_p.E138*|STMN1_ENST00000357865.2_Nonsense_Mutation_p.E138*|STMN1_ENST00000426559.2_Intron	NM_203401.1	NP_981946.1	P16949	STMN1_HUMAN	stathmin 1	138	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				axonogenesis (GO:0007409)|intracellular signal transduction (GO:0035556)|microtubule depolymerization (GO:0007019)|mitotic spindle organization (GO:0007052)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of cellular component movement (GO:0051272)|response to virus (GO:0009615)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|microtubule (GO:0005874)	signal transducer activity (GO:0004871)|tubulin binding (GO:0015631)	p.E138*(1)		breast(2)|large_intestine(2)|skin(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|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;0.013)|READ - Rectum adenocarcinoma(331;0.0649)		TCTTTGGATTCTTTGTTCTTC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											210	200	204					1																	26227545		2203	4300	6503	26100132	SO:0001587	stop_gained	3925			J04991	CCDS269.1, CCDS44090.1	1p36.11	2011-02-09	2009-04-28	2001-07-13	ENSG00000117632	ENSG00000117632			6510	protein-coding gene	gene with protein product	"oncoprotein 18"	151442	"chromosome 1 open reading frame 215", "stathmin 1/oncoprotein 18"	LAP18, C1orf215		2917975	Standard	NM_005563		Approved	SMN, OP18, PR22, PP19, PP17, Lag, FLJ32206	uc010oev.2	P16949	OTTHUMG00000007389	ENST00000399728.1:c.412G>T	1.37:g.26227545C>A	ENSP00000382633:p.Glu138*		26100132	A2A2D1|B2R4E7|B7Z8N4|D3DPJ5	Nonsense_Mutation	SNP	ENST00000399728.1	37	CCDS269.1	.	.	.	.	.	.	.	.	.	.	C	38	6.965771	0.97967	.	.	ENSG00000117632	ENST00000455785;ENST00000399728;ENST00000357865;ENST00000374291	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.5784	0.95453	0.0:1.0:0.0:0.0	.	.	.	.	X	138	.	ENSP00000350531:E138X	E	-	1	0	STMN1	26100132	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.422000	0.80217	2.710000	0.92621	0.655000	0.94253	GAA		0.413	STMN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019359.1	NM_005563		A	26227545	C	A	26227545	4	1	61	1	0	0	0	0	0	1	0	0	15347	922	32	2	192	2	STMN1	1	26227545	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	214563	26227545	223023076	116	8101										
PAFAH2	5051	broad.mit.edu	37	chr1	26316060	26316060	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatggtctcctctgccttTtggcaggggtagaagagtcg	13	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26316060T>C	ENST00000374282.3	-	3	302	c.123A>G	c.(121-123)caA>caG	p.Q41Q	PAFAH2_ENST00000374284.1_Silent_p.Q41Q|PAFAH2_ENST00000493892.1_Intron	NM_000437.3	NP_000428.2	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2, 40kDa	41					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|phospholipid binding (GO:0005543)	p.Q41Q(1)		NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	9		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCTGCCTTTTGGCAGGGGT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	1											27	25	26					1																	26316060		2202	4300	6502	26188647	SO:0001819	synonymous_variant	5051			D87845	CCDS270.1	1p34.3	2008-09-19	2002-08-29		ENSG00000158006	ENSG00000158006			8579	protein-coding gene	gene with protein product		602344	"platelet-activating factor acetylhydrolase 2 (40kD)"			8955149, 9494101	Standard	NM_000437		Approved	HSD-PLA2	uc001bld.4	Q99487	OTTHUMG00000007437	ENST00000374282.3:c.123A>G	1.37:g.26316060T>C			26188647	D3DPK1|O15458|Q5SY02	Silent	SNP	ENST00000374282.3	37	CCDS270.1																																																																																				0.572	PAFAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019544.1	NM_000437		C	26316060	T	C	26316060	2	2	61	1	0	0	0	0	0	0	0	1	11418	1838	64	4		4	PAFAH2	1	26316060	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	88515	26316060	222934561	117	8102										
TRIM63	84676	broad.mit.edu	37	chr1	26392850	26392850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacgatccatgatcacctCgtggcggcaggtggggcagc	16	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26392850C>T	ENST00000374272.3	-	2	379	c.241G>A	c.(241-243)Gag>Aag	p.E81K	TRIM63_ENST00000483052.1_5'UTR	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	81	Interaction with TTN.				cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E81K(1)		kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		ATGATCACCTCGTGGCGGCAG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	64	70					1																	26392850		2203	4300	6503	26265437	SO:0001583	missense	84676			AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	16007	protein-coding gene	gene with protein product	"muscle-specific RING finger protein 1", "iris ring finger protein", "striated muscle RING zinc finger protein"	606131	"ring finger protein 28", "tripartite motif-containing 63", "tripartite motif containing 63"	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.241G>A	1.37:g.26392850C>T	ENSP00000363390:p.Glu81Lys		26265437	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	.	.	.	.	.	.	.	.	.	.	C	34	5.328726	0.95733	.	.	ENSG00000158022	ENST00000374272	T	0.16897	2.31	5.64	4.73	0.59995	Zinc finger, RING/FYVE/PHD-type (1);	0.045022	0.85682	N	0.000000	T	0.39358	0.1075	M	0.85373	2.75	0.80722	D	1	D	0.64830	0.994	P	0.55112	0.769	T	0.47711	-0.9096	10	0.72032	D	0.01	.	14.1475	0.65360	0.0:0.9273:0.0:0.0727	.	81	Q969Q1	TRI63_HUMAN	K	81	ENSP00000363390:E81K	ENSP00000363390:E81K	E	-	1	0	TRIM63	26265437	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.811000	0.86092	1.389000	0.46526	0.655000	0.94253	GAG		0.597	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588		T	26392850	C	T	26392850	3	4	61	1	0	0	0	0	1	0	0	0	16578	893	31	1	852	1	TRIM63	1	26392850	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76790	26392850	222857771	118	8103										
PDIK1L	149420	broad.mit.edu	37	chr1	26441048	26441048	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatgggatggtgcaaaaGatgtcccacggctctaattc	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26441048G>T	ENST00000374271.4	+	3	536	c.249G>T	c.(247-249)aaG>aaT	p.K83N	PDIK1L_ENST00000374269.1_Missense_Mutation_p.K83N	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	83	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K83N(1)		large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTGCAAAAGATGTCCCACG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	129	130					1																	26441048		2203	4300	6503	26313635	SO:0001583	missense	149420			AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.249G>T	1.37:g.26441048G>T	ENSP00000363389:p.Lys83Asn		26313635	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Missense_Mutation	SNP	ENST00000374271.4	37	CCDS274.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425037	0.62733	.	.	ENSG00000175087	ENST00000444713;ENST00000374271;ENST00000374269	T;T;T	0.63744	0.23;-0.06;-0.06	6.02	5.09	0.68999	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.129855	0.64402	D	0.000003	T	0.59004	0.2162	N	0.25890	0.77	0.26825	N	0.968714	B	0.31256	0.316	P	0.45913	0.497	T	0.58177	-0.7682	10	0.49607	T	0.09	-17.4701	9.7749	0.40612	0.0762:0.1385:0.7853:0.0	.	83	Q8N165	PDK1L_HUMAN	N	83	ENSP00000406510:K83N;ENSP00000363389:K83N;ENSP00000363387:K83N	ENSP00000363387:K83N	K	+	3	2	PDIK1L	26313635	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.159000	0.50731	1.495000	0.48549	0.655000	0.94253	AAG		0.433	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835		T	26441048	G	T	26441048	3	4	61	1	0	0	0	0	1	0	0	0	11704	933	33	2	251	2	PDIK1L	1	26441048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48198	26441048	222809573	119	8104										
CNKSR1	10256	broad.mit.edu	37	chr1	26507226	26507226	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctccaggctacagacagaGaacctgcaaagcctgacaga	10	12	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26507226G>T	ENST00000374253.5	+	3	270	c.231G>T	c.(229-231)gaG>gaT	p.E77D	CNKSR1_ENST00000361530.6_Missense_Mutation_p.E77D|CNKSR1_ENST00000480348.2_3'UTR|CNKSR1_ENST00000531191.1_5'UTR	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	77					Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.E77D(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		TACAGACAGAGAACCTGCAAA	0.602																																					NSCLC(180;1396 2109 28270 30756 34275)											1	Substitution - Missense(1)	large_intestine(1)	1											37	40	39					1																	26507226		2203	4300	6503	26379813	SO:0001583	missense	10256			AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.231G>T	1.37:g.26507226G>T	ENSP00000363371:p.Glu77Asp		26379813	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37		.	.	.	.	.	.	.	.	.	.	G	12.42	1.932174	0.34096	.	.	ENSG00000142675	ENST00000361530;ENST00000422547;ENST00000374253	T;T	0.19394	2.15;2.15	4.93	0.678	0.17969	Sterile alpha motif/pointed domain (1);	0.106535	0.64402	N	0.000007	T	0.15435	0.0372	L	0.46157	1.445	0.80722	D	1	B;B	0.15141	0.012;0.012	B;B	0.12156	0.004;0.007	T	0.06752	-1.0809	10	0.36615	T	0.2	-13.0432	6.3268	0.21248	0.1703:0.3009:0.5288:0.0	.	77;77	Q969H4;Q53GM7	CNKR1_HUMAN;.	D	77	ENSP00000354609:E77D;ENSP00000363371:E77D	ENSP00000354609:E77D	E	+	3	2	CNKSR1	26379813	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	0.855000	0.27805	0.253000	0.21552	0.655000	0.94253	GAG		0.602	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314		T	26507226	G	T	26507226	3	4	61	1	0	0	0	0	1	0	0	0	3612	933	33	2	241	2	CNKSR1	1	26507226	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66178	26507226	222743395	120	8105										
CATSPER4	378807	broad.mit.edu	37	chr1	26517801	26517801	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgggacatgcaggagttCatcactcacatgtacatcaa	9	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26517801C>A	ENST00000456354.2	+	2	304	c.237C>A	c.(235-237)ttC>ttA	p.F79L		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	79					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.F79L(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TGCAGGAGTTCATCACTCACA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	69	75					1																	26517801		2203	4300	6503	26390388	SO:0001583	missense	378807			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.237C>A	1.37:g.26517801C>A	ENSP00000390423:p.Phe79Leu		26390388	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.689529	0.48097	.	.	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97505	-4.41;-4.41	5.54	5.54	0.83059	.	0.115928	0.39146	N	0.001448	D	0.94918	0.8357	L	0.46157	1.445	0.28346	N	0.921111	B	0.24483	0.104	B	0.27608	0.081	D	0.88525	0.3099	10	0.28530	T	0.3	-21.2386	14.9749	0.71264	0.0:1.0:0.0:0.0	.	79	Q7RTX7	CTSR4_HUMAN	L	79	ENSP00000341006:F79L;ENSP00000390423:F79L	ENSP00000341006:F79L	F	+	3	2	CATSPER4	26390388	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	2.739000	0.47409	2.595000	0.87683	0.462000	0.41574	TTC		0.572	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		A	26517801	C	A	26517801	3	1	61	1	0	0	0	0	1	0	0	0	2696	825	29	2	243	2	CATSPER4	1	26517801	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10575	26517801	222732820	121	8106										
CATSPER4	378807	broad.mit.edu	37	chr1	26524225	26524225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtctttatcttgctcttgCggttcttcattaatgaaatc	6	9	5	1	rs144083626	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26524225C>T	ENST00000456354.2	+	4	575	c.508C>T	c.(508-510)Cgg>Tgg	p.R170W		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	170					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.R170W(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGCTCTTGCGGTTCTTCAT	0.542													C|||	2	0.000399361	0	0	5008	,	,		21666	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	105	88	94		508	-0.8	0.9	1	dbSNP_134	94	0,8600		0,0,4300	no	missense	CATSPER4	NM_198137.1	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	170/473	26524225	1,13005	2203	4300	6503	26396812	SO:0001583	missense	378807			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.508C>T	1.37:g.26524225C>T	ENSP00000390423:p.Arg170Trp		26396812	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	17.31	3.357125	0.61293	2.27E-4	0.0	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.98437	-4.93;-4.93	5.1	-0.771	0.11002	Ion transport (1);	0.614157	0.14390	N	0.322563	D	0.93893	0.8046	N	0.08118	0	0.09310	N	0.999999	D	0.56287	0.975	P	0.51229	0.663	D	0.88996	0.3418	10	0.87932	D	0	-15.2581	2.7719	0.05337	0.0885:0.296:0.3237:0.2918	.	170	Q7RTX7	CTSR4_HUMAN	W	170	ENSP00000341006:R170W;ENSP00000390423:R170W	ENSP00000341006:R170W	R	+	1	2	CATSPER4	26396812	0.852000	0.29690	0.882000	0.34594	0.083000	0.17756	0.668000	0.25127	0.130000	0.18549	-0.256000	0.11100	CGG		0.542	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		T	26524225	C	T	26524225	3	4	61	1	0	0	0	0	1	0	0	0	2696	759	27	1	522	1	CATSPER4	1	26524225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6424	26524225	222726396	122	8107										
CCDC21	64793	broad.mit.edu	37	chr1	26603764	26603764	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatatgcccaggacatgggaGaaaactgtgtcacacagtga	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26603764G>T	ENST00000252992.4	+	14	2400	c.2269G>T	c.(2269-2271)Gaa>Taa	p.E757*	SH3BGRL3_ENST00000270792.5_5'Flank|SH3BGRL3_ENST00000319041.6_5'Flank|CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Nonsense_Mutation_p.E706*	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	757						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)		p.E757K(1)|p.E757*(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GGACATGGGAGAAAACTGTGT	0.517																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|skin(1)	1											99	97	98					1																	26603764		2203	4300	6503	26476351	SO:0001587	stop_gained	64793			AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.2269G>T	1.37:g.26603764G>T	ENSP00000252992:p.Glu757*		26476351	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Nonsense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.184806|8.184806	0.98696|0.98696	.|.	.|.	ENSG00000130695|ENSG00000130695	ENST00000453146|ENST00000451429;ENST00000252992	.|.	.|.	.|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.152203|0.152203	0.64402|0.64402	D|D	0.000010|0.000010	T|.	0.82093|.	0.4962|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.83109|.	-0.0124|.	5|.	.|0.87932	.|D	.|0	-7.9417|-7.9417	20.2963|20.2963	0.98556|0.98556	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	D|X	429|706;757	.|.	.|ENSP00000252992:E757X	E|E	+|+	3|1	2|0	CEP85|CEP85	26476351|26476351	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.476000|9.476000	0.97823|0.97823	2.813000|2.813000	0.96785|0.96785	0.655000|0.655000	0.94253|0.94253	GAG|GAA		0.517	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		T	26603764	G	T	26603764	4	4	61	1	0	0	0	0	0	1	0	0	2802	943	33	2	2319	2	CCDC21	1	26603764	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79539	26603764	222646857	123	8108										
UBXN11	91544	broad.mit.edu	37	chr1	26609036	26609036	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgggaatgtgctgaagatCtcaaaggcagaggcatccat	14	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:26609036C>A	ENST00000374222.1	-	16	1781	c.1317G>T	c.(1315-1317)gaG>gaT	p.E439D	UBXN11_ENST00000374217.2_Missense_Mutation_p.E406D|UBXN11_ENST00000357089.4_Missense_Mutation_p.E406D|UBXN11_ENST00000314675.7_Missense_Mutation_p.E319D|UBXN11_ENST00000374223.1_Missense_Mutation_p.E196D|UBXN11_ENST00000374221.3_Missense_Mutation_p.E439D			Q5T124	UBX11_HUMAN	UBX domain protein 11	439	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E439D(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TGCTGAAGATCTCAAAGGCAG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	113	109					1																	26609036		2108	4223	6331	26481623	SO:0001583	missense	91544			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1317G>T	1.37:g.26609036C>A	ENSP00000363339:p.Glu439Asp		26481623	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.915242	0.33815	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.99	1.58	0.23477	UBX (2);	0.162427	0.53938	D	0.000041	T	0.41465	0.1160	L	0.37630	1.12	0.80722	D	1	B;B;B;D	0.76494	0.347;0.347;0.394;0.999	B;B;B;P	0.60886	0.146;0.146;0.168;0.88	T	0.19976	-1.0289	10	0.17832	T	0.49	-29.9228	7.2152	0.25955	0.0:0.6777:0.1445:0.1778	.	406;401;319;439	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	D	319;196;406;439;439;406	ENSP00000324721:E319D;ENSP00000363340:E196D;ENSP00000349601:E406D;ENSP00000363338:E439D;ENSP00000363339:E439D;ENSP00000363334:E406D	ENSP00000324721:E319D	E	-	3	2	UBXN11	26481623	0.985000	0.35326	1.000000	0.80357	0.859000	0.49053	0.019000	0.13444	1.061000	0.40601	0.561000	0.74099	GAG		0.652	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		A	26609036	C	A	26609036	3	1	61	1	0	0	0	0	1	0	0	0	16953	912	32	2	249	2	UBXN11	1	26609036	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5272	26609036	222641585	124	8109										
PIGV	55650	broad.mit.edu	37	chr1	27121172	27121172	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttggcttcctcatgcattCtcaatgccaaggctttttct	7	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27121172C>A	ENST00000374145.1	+	3	1329	c.647C>A	c.(646-648)tCt>tAt	p.S216Y	PIGV_ENST00000078527.4_Missense_Mutation_p.S216Y|PIGV_ENST00000449950.2_Intron	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	216					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.S216Y(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		CTCATGCATTCTCAATGCCAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	97	98					1																	27121172		2203	4300	6503	26993759	SO:0001583	missense	55650			AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.647C>A	1.37:g.27121172C>A	ENSP00000363260:p.Ser216Tyr		26993759	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Missense_Mutation	SNP	ENST00000374145.1	37	CCDS287.1	.	.	.	.	.	.	.	.	.	.	c	7.508	0.654142	0.14580	.	.	ENSG00000060642	ENST00000078527;ENST00000374145	D;D	0.83591	-1.74;-1.74	5.52	4.55	0.56014	.	0.308183	0.36101	N	0.002792	T	0.73148	0.3550	L	0.42487	1.325	0.80722	D	1	B	0.33318	0.408	B	0.33960	0.173	T	0.68769	-0.5321	9	.	.	.	-11.451	5.9267	0.19116	0.1416:0.6483:0.1367:0.0735	.	216	Q9NUD9	PIGV_HUMAN	Y	216	ENSP00000078527:S216Y;ENSP00000363260:S216Y	.	S	+	2	0	PIGV	26993759	0.918000	0.31147	1.000000	0.80357	0.726000	0.41606	1.766000	0.38491	2.602000	0.87976	0.558000	0.71614	TCT		0.527	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		A	27121172	C	A	27121172	3	1	61	1	0	0	0	0	1	0	0	0	11932	913	32	2	653	2	PIGV	1	27121172	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	512136	27121172	222129449	125	8110										
GPATCH3	63906	broad.mit.edu	37	chr1	27226593	27226593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgcgaataagcctctgaGcttgagccaacccccttacc	7	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27226593G>A	ENST00000361720.5	-	1	364	c.341C>T	c.(340-342)gCt>gTt	p.A114V		NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	114							nucleic acid binding (GO:0003676)	p.A114V(1)		endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		AAGCCTCTGAGCTTGAGCCAA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	74	73					1																	27226593		2203	4300	6503	27099180	SO:0001583	missense	63906			BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"G patch domain containing"	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.341C>T	1.37:g.27226593G>A	ENSP00000354645:p.Ala114Val		27099180	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	37	CCDS290.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829237	0.32329	.	.	ENSG00000198746	ENST00000361720;ENST00000536641	T	0.29142	1.58	5.36	5.36	0.76844	.	0.054215	0.85682	D	0.000000	T	0.22898	0.0553	L	0.37630	1.12	0.53005	D	0.999969	P	0.45126	0.851	B	0.37550	0.253	T	0.03139	-1.1068	10	0.13853	T	0.58	-23.0226	15.9531	0.79859	0.0:0.0:1.0:0.0	.	114	Q96I76	GPTC3_HUMAN	V	114	ENSP00000354645:A114V	ENSP00000354645:A114V	A	-	2	0	GPATCH3	27099180	1.000000	0.71417	0.995000	0.50966	0.414000	0.31173	4.189000	0.58358	2.763000	0.94921	0.655000	0.94253	GCT		0.612	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078		A	27226593	G	A	27226593	3	1	61	1	0	0	0	0	1	0	0	0	6612	971	34	3	1264	3	GPATCH3	1	27226593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105421	27226593	222024028	126	8111										
FAM46B	115572	broad.mit.edu	37	chr1	27333166	27333166	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggctccagcggtccgagtCtgtgcacactttcaccagct	11	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27333166C>T	ENST00000289166.5	-	2	712	c.547G>A	c.(547-549)Gac>Aac	p.D183N		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	183								p.D182N(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		CGGTCCGAGTCTGTGCACACT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	133	134					1																	27333166		2203	4300	6503	27205753	SO:0001583	missense	115572			AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.547G>A	1.37:g.27333166C>T	ENSP00000289166:p.Asp183Asn		27205753		Missense_Mutation	SNP	ENST00000289166.5	37	CCDS294.2	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800290	0.90538	.	.	ENSG00000158246	ENST00000289166	T	0.28069	1.63	5.2	5.2	0.72013	Domain of unknown function DUF1693 (1);	0.136427	0.64402	D	0.000003	T	0.56834	0.2012	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.53947	-0.8366	10	0.39692	T	0.17	-41.8921	18.9114	0.92487	0.0:1.0:0.0:0.0	.	183	Q96A09	FA46B_HUMAN	N	183	ENSP00000289166:D183N	ENSP00000289166:D183N	D	-	1	0	FAM46B	27205753	1.000000	0.71417	0.800000	0.32199	0.833000	0.47200	7.647000	0.83462	2.698000	0.92095	0.561000	0.74099	GAC		0.567	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		T	27333166	C	T	27333166	3	4	61	1	0	0	0	0	1	0	0	0	5585	913	32	3	734	3	FAM46B	1	27333166	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106573	27333166	221917455	127	8112										
SLC9A1	6548	broad.mit.edu	37	chr1	27429031	27429031	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacacttcttcacatatttCttattaaaccggttgagcct	5	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27429031C>A	ENST00000263980.3	-	8	2240	c.1665G>T	c.(1663-1665)aaG>aaT	p.K555N	SLC9A1_ENST00000545949.1_Missense_Mutation_p.K216N|SLC9A1_ENST00000490329.1_5'Flank	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	555					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)	p.K555N(1)		central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				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)	TCACATATTTCTTATTAAACC	0.587											OREG0013277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											77	84	82					1																	27429031		2203	4300	6503	27301618	SO:0001583	missense	6548			M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1665G>T	1.37:g.27429031C>A	ENSP00000263980:p.Lys555Asn	794	27301618	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	37	CCDS295.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815905	0.32145	.	.	ENSG00000090020	ENST00000263980;ENST00000374089;ENST00000545949	T;T	0.48522	0.81;1.37	5.04	5.04	0.67666	.	0.046547	0.85682	D	0.000000	T	0.33381	0.0861	L	0.31294	0.92	0.58432	D	0.999999	B	0.24721	0.11	B	0.15870	0.014	T	0.20840	-1.0263	10	0.02654	T	1	.	18.1634	0.89717	0.0:1.0:0.0:0.0	.	555	P19634	SL9A1_HUMAN	N	555;59;216	ENSP00000263980:K555N;ENSP00000445520:K216N	ENSP00000263980:K555N	K	-	3	2	SLC9A1	27301618	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.917000	0.39996	2.623000	0.88846	0.561000	0.74099	AAG		0.587	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		A	27429031	C	A	27429031	3	1	61	1	0	0	0	0	1	0	0	0	14746	912	32	2	802	2	SLC9A1	1	27429031	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95865	27429031	221821590	128	8113										
WDTC1	23038	broad.mit.edu	37	chr1	27609931	27609931	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacacaccgcaaatatcttCtctgtcaaggtgagcaggac	10	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27609931C>A	ENST00000319394.3	+	5	817	c.282C>A	c.(280-282)ttC>ttA	p.F94L	WDTC1_ENST00000361771.3_Missense_Mutation_p.F94L	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	94					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.F94L(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CAAATATCTTCTCTGTCAAGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											66	55	59					1																	27609931		2203	4300	6503	27482518	SO:0001583	missense	23038			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.282C>A	1.37:g.27609931C>A	ENSP00000317971:p.Phe94Leu		27482518	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	C	25.8	4.676655	0.88445	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	T;T	0.58797	0.31;0.31	5.35	4.42	0.53409	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71879	0.3392	M	0.76170	2.325	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.996	T	0.71293	-0.4636	10	0.41790	T	0.15	.	9.0549	0.36399	0.0:0.8091:0.0:0.1909	.	94;94	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	L	94	ENSP00000317971:F94L;ENSP00000355317:F94L	ENSP00000317971:F94L	F	+	3	2	WDTC1	27482518	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.928000	0.48908	1.222000	0.43521	0.655000	0.94253	TTC		0.557	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27609931	C	A	27609931	3	1	61	1	0	0	0	0	1	0	0	0	17382	912	32	2	296	2	WDTC1	1	27609931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180900	27609931	221640690	129	8114										
WDTC1	23038	broad.mit.edu	37	chr1	27630276	27630276	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggatatcaaagaggccaatTtctttggcaggtccgaggcc	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:27630276T>G	ENST00000319394.3	+	14	2168	c.1633T>G	c.(1633-1635)Ttc>Gtc	p.F545V	WDTC1_ENST00000361771.3_Missense_Mutation_p.F544V	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	545					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.F544V(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		AGAGGCCAATTTCTTTGGCAG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	76	76					1																	27630276		2203	4300	6503	27502863	SO:0001583	missense	23038			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.1633T>G	1.37:g.27630276T>G	ENSP00000317971:p.Phe545Val		27502863	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	T	26.0	4.690976	0.88735	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	T;T	0.80653	-1.4;-1.4	4.84	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93377	0.6740	10	0.87932	D	0	.	13.5987	0.62007	0.0:0.0:0.0:1.0	.	545;544	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	V	545;544	ENSP00000317971:F545V;ENSP00000355317:F544V	ENSP00000317971:F545V	F	+	1	0	WDTC1	27502863	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.635000	0.83286	1.809000	0.52856	0.459000	0.35465	TTC		0.557	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		G	27630276	T	G	27630276	3	3	61	1	0	0	0	0	1	0	0	0	17382	1841	64	4	1680	4	WDTC1	1	27630276	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20345	27630276	221620345	130	8115										
PHACTR4	65979	broad.mit.edu	37	chr1	28786740	28786740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttttagaacggaaaataTctatgcgaaagccaagagaa	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:28786740T>C	ENST00000373839.3	+	4	469	c.208T>C	c.(208-210)Tct>Cct	p.S70P	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.S80P	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	70					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)	p.S80P(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ACGGAAAATATCTATGCGAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	80	81					1																	28786740		1833	4076	5909	28659327	SO:0001583	missense	65979			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.208T>C	1.37:g.28786740T>C	ENSP00000362945:p.Ser70Pro		28659327	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.742574	0.89573	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.33865	1.39;1.39	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.61776	0.2374	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.66838	-0.5822	10	0.87932	D	0	-6.5909	14.8061	0.69956	0.0:0.0:0.0:1.0	.	80;70;54	Q8IZ21-2;Q8IZ21;Q8IZ21-3	.;PHAR4_HUMAN;.	P	70;80;69	ENSP00000362945:S70P;ENSP00000362942:S80P	ENSP00000362942:S80P	S	+	1	0	PHACTR4	28659327	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.166000	0.77553	2.101000	0.63845	0.454000	0.30748	TCT		0.378	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		C	28786740	T	C	28786740	3	2	61	1	0	0	0	0	1	0	0	0	11843	1435	50	4	268	4	PHACTR4	1	28786740	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1156464	28786740	220463881	131	8116										
PHACTR4	65979	broad.mit.edu	37	chr1	28792236	28792236	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagcgatgccatgttaaaGaatggccataccacccccat	7	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:28792236G>T	ENST00000373839.3	+	5	573	c.312G>T	c.(310-312)aaG>aaT	p.K104N	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.K114N	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	104					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)	p.K114N(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		CCATGTTAAAGAATGGCCATA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											154	145	147					1																	28792236		1914	4130	6044	28664823	SO:0001583	missense	65979			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.312G>T	1.37:g.28792236G>T	ENSP00000362945:p.Lys104Asn		28664823	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.266769	0.80358	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.35789	1.29;1.29	5.55	3.7	0.42460	.	0.102039	0.64402	D	0.000003	T	0.35941	0.0949	L	0.32530	0.975	0.45250	D	0.998257	D;P;P	0.55800	0.973;0.954;0.928	P;B;P	0.54270	0.747;0.439;0.526	T	0.03898	-1.0994	10	0.22706	T	0.39	-3.1193	9.3965	0.38406	0.1663:0.0:0.8337:0.0	.	114;104;88	Q8IZ21-2;Q8IZ21;Q8IZ21-3	.;PHAR4_HUMAN;.	N	104;114;103	ENSP00000362945:K104N;ENSP00000362942:K114N	ENSP00000362942:K114N	K	+	3	2	PHACTR4	28664823	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	2.342000	0.43992	0.716000	0.32124	0.655000	0.94253	AAG		0.458	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		T	28792236	G	T	28792236	3	4	61	1	0	0	0	0	1	0	0	0	11843	933	33	2	376	2	PHACTR4	1	28792236	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5496	28792236	220458385	132	8117										
RCC1	1104	broad.mit.edu	37	chr1	28862888	28862888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatacagtctgcatggattCggaaggtagggcctttacgt	12	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:28862888C>T	ENST00000373833.6	+	11	1217	c.932C>T	c.(931-933)tCg>tTg	p.S311L	RCC1_ENST00000373831.3_Missense_Mutation_p.S342L|RCC1_ENST00000398958.2_Missense_Mutation_p.S311L|RCC1_ENST00000373832.1_Missense_Mutation_p.S311L			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	311					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.S311L(1)		breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		TGCATGGATTCGGAAGGTAGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											128	130	129					1																	28862888		2203	4300	6503	28735475	SO:0001583	missense	1104			X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.932C>T	1.37:g.28862888C>T	ENSP00000362939:p.Ser311Leu		28735475	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	37	CCDS323.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169631	0.78452	.	.	ENSG00000180198	ENST00000398958;ENST00000373833;ENST00000373832;ENST00000373831;ENST00000411533	T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45	5.8	5.8	0.92144	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.117044	0.64402	D	0.000014	T	0.78830	0.4345	M	0.67625	2.065	0.80722	D	1	P;D;D	0.60575	0.952;0.987;0.988	B;B;B	0.38880	0.099;0.284;0.203	T	0.80872	-0.1188	10	0.42905	T	0.14	-8.6946	18.6252	0.91334	0.0:1.0:0.0:0.0	.	342;328;311	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	L	311;311;311;342;328	ENSP00000381931:S311L;ENSP00000362939:S311L;ENSP00000362938:S311L;ENSP00000362937:S342L;ENSP00000413644:S328L	ENSP00000362937:S342L	S	+	2	0	RCC1	28735475	1.000000	0.71417	0.988000	0.46212	0.966000	0.64601	5.644000	0.67902	2.741000	0.93983	0.655000	0.94253	TCG		0.542	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269		T	28862888	C	T	28862888	3	4	61	1	0	0	0	0	1	0	0	0	13210	893	31	1	1055	1	RCC1	1	28862888	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70652	28862888	220387733	133	8118										
TRNAU1AP	54952	broad.mit.edu	37	chr1	28893924	28893924	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagcgtggcaatccctaaaGcgtgagtcctgcagggaagg	15	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:28893924G>A	ENST00000373830.3	+	6	555	c.529G>A	c.(529-531)Gcg>Acg	p.A177T		NM_017846.4	NP_060316.1	Q9NX07	TSAP1_HUMAN	tRNA selenocysteine 1 associated protein 1	177					selenocysteine incorporation (GO:0001514)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A177T(1)		breast(1)|endometrium(2)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	8						AATCCCTAAAGCGTGAGTCCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											97	94	95					1																	28893924		2203	4300	6503	28766511	SO:0001630	splice_region_variant	54952				CCDS324.1	1p35.3	2013-02-12	2008-09-05	2008-09-05	ENSG00000180098	ENSG00000180098		"RNA binding motif (RRM) containing"	30813	protein-coding gene	gene with protein product			"tRNA selenocysteine associated protein 1"	TRSPAP1		10606267, 16230358	Standard	NM_017846		Approved	SECP43, FLJ20503	uc001bqi.3	Q9NX07	OTTHUMG00000003653	ENST00000373830.3:c.530+1G>A	1.37:g.28893924G>A			28766511	Q86SU7	Missense_Mutation	SNP	ENST00000373830.3	37	CCDS324.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623730	0.46840	.	.	ENSG00000180098	ENST00000373830	T	0.22945	1.93	5.37	5.37	0.77165	Nucleotide-binding, alpha-beta plait (1);	0.462756	0.23670	N	0.045726	T	0.14399	0.0348	N	0.04508	-0.205	0.44515	D	0.997466	B	0.06786	0.001	B	0.06405	0.002	T	0.08576	-1.0715	10	0.38643	T	0.18	.	16.1679	0.81785	0.0:0.0:1.0:0.0	.	177	Q9NX07	TSAP1_HUMAN	T	177	ENSP00000362936:A177T	ENSP00000362936:A177T	A	+	1	0	TRNAU1AP	28766511	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.329000	0.72920	2.672000	0.90937	0.643000	0.83706	GCG		0.567	TRNAU1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010346.1	NM_017846	Missense_Mutation	A	28893924	G	A	28893924	5	1	61	1	0	0	0	0	0	0	1	0	16612	985	34	3	551	3	TRNAU1AP	1	28893924	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31036	28893924	220356697	134	8119										
YTHDF2	51441	broad.mit.edu	37	chr1	29070485	29070485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacgccaagaggaagaagAaagtgttaaaaaggtaaccc	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:29070485A>G	ENST00000373812.3	+	4	2065	c.1703A>G	c.(1702-1704)gAa>gGa	p.E568G	YTHDF2_ENST00000542507.1_Missense_Mutation_p.E568G|YTHDF2_ENST00000541996.1_Missense_Mutation_p.E518G|YTHDF2_ENST00000478283.1_3'UTR	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	568	Interaction with m6A-containing mRNAs.				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)	p.E568G(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAAGAAGAAAGTGTTAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											23	22	22					1																	29070485		1725	3732	5457	28943072	SO:0001583	missense	51441			AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"YTH domain family 2"			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.1703A>G	1.37:g.29070485A>G	ENSP00000362918:p.Glu568Gly		28943072	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Missense_Mutation	SNP	ENST00000373812.3	37	CCDS41296.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172007	0.38315	.	.	ENSG00000198492	ENST00000542507;ENST00000373812;ENST00000541996	T;T;T	0.26223	1.75;1.75;1.75	5.79	5.79	0.91817	.	0.092102	0.64402	D	0.000001	T	0.25827	0.0629	L	0.55834	1.745	0.58432	D	0.999999	B	0.34015	0.435	B	0.26202	0.067	T	0.03863	-1.0997	10	0.62326	D	0.03	-4.0074	15.1126	0.72372	1.0:0.0:0.0:0.0	.	568	Q9Y5A9	YTHD2_HUMAN	G	568;568;518	ENSP00000444660:E568G;ENSP00000362918:E568G;ENSP00000439394:E518G	ENSP00000362918:E568G	E	+	2	0	YTHDF2	28943072	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.241000	0.95402	2.209000	0.71365	0.523000	0.50628	GAA		0.373	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258		G	29070485	A	G	29070485	3	3	61	1	0	0	0	0	1	0	0	0	17539	246	9	4	1717	4	YTHDF2	1	29070485	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	176561	29070485	220180136	135	8120										
PTPRU	10076	broad.mit.edu	37	chr1	29587219	29587219	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcattggcgacgggccGatcgtgcgcaaggagattga	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:29587219G>A	ENST00000345512.3	+	7	1077	c.948G>A	c.(946-948)ccG>ccA	p.P316P	PTPRU_ENST00000373779.3_Silent_p.P316P|PTPRU_ENST00000428026.2_Silent_p.P316P|PTPRU_ENST00000356870.3_Silent_p.P316P|PTPRU_ENST00000460170.2_Silent_p.P316P|PTPRU_ENST00000323874.8_Silent_p.P316P	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	316	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P316P(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GCGACGGGCCGATCGTGCGCA	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	1											76	72	73					1																	29587219		2203	4300	6503	29459806	SO:0001819	synonymous_variant	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.948G>A	1.37:g.29587219G>A			29459806	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Silent	SNP	ENST00000345512.3	37	CCDS334.1																																																																																				0.662	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29587219	G	A	29587219	2	1	61	1	0	0	0	0	0	0	0	1	12850	1045	37	1		1	PTPRU	1	29587219	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	516734	29587219	219663402	136	8121										
PTPRU	10076	broad.mit.edu	37	chr1	29651782	29651782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccacaacttggtggacGttttctttgctgccaaaacc	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:29651782G>A	ENST00000345512.3	+	30	4351	c.4222G>A	c.(4222-4224)Gtt>Att	p.V1408I	PTPRU_ENST00000373779.3_Missense_Mutation_p.V1398I|PTPRU_ENST00000428026.2_Missense_Mutation_p.V1395I|PTPRU_ENST00000356870.3_Missense_Mutation_p.V1404I|PTPRU_ENST00000460170.2_Missense_Mutation_p.V1402I|PTPRU_ENST00000323874.8_Missense_Mutation_p.V1404I	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1408	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V1408I(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CTTGGTGGACGTTTTCTTTGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	103	109					1																	29651782		2203	4300	6503	29524369	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.4222G>A	1.37:g.29651782G>A	ENSP00000334941:p.Val1408Ile		29524369	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.790749	0.31685	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	4.1	3.15	0.36227	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.255680	0.31847	U	0.006970	T	0.70072	0.3182	N	0.25957	0.775	0.43930	D	0.996588	B;B;B;B;B	0.17852	0.02;0.02;0.02;0.024;0.024	B;B;B;B;B	0.19391	0.014;0.014;0.014;0.025;0.025	T	0.63404	-0.6645	9	.	.	.	.	10.056	0.42246	0.1687:0.0:0.8313:0.0	.	1395;1402;1398;1404;1408	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	I	1408;1398;1404;1404;1395;1402	ENSP00000334941:V1408I;ENSP00000362884:V1398I;ENSP00000349333:V1404I;ENSP00000314987:V1404I;ENSP00000392332:V1395I;ENSP00000432906:V1402I	.	V	+	1	0	PTPRU	29524369	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.635000	0.61332	2.097000	0.63578	0.561000	0.74099	GTT		0.587	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			A	29651782	G	A	29651782	3	1	61	1	0	0	0	0	1	0	0	0	12850	1145	40	1	4362	1	PTPRU	1	29651782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64563	29651782	219598839	137	8122										
SDC3	9672	broad.mit.edu	37	chr1	31347355	31347355	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcttcttctggcagctcGaagtctccactgggcccccc	9	17	4	0	rs374946441		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:31347355G>A	ENST00000339394.6	-	4	1125	c.951C>T	c.(949-951)ttC>ttT	p.F317F	SDC3_ENST00000471567.1_5'Flank|SDC3_ENST00000336798.7_Silent_p.F259F	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	317					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.F317F(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGCAGCTCGAAGTCTCCAC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											119	125	123					1																	31347355		2203	4300	6503	31119942	SO:0001819	synonymous_variant	9672			AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"Proteoglycans / Cell Surface : Syndecans"	10660	protein-coding gene	gene with protein product	"syndecan proteoglycan 3"	186357	"syndecan 3 (N-syndecan)"			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.951C>T	1.37:g.31347355G>A			31119942	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																				0.607	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		A	31347355	G	A	31347355	2	1	61	1	0	0	0	0	0	0	0	1	13990	1049	37	1		1	SDC3	1	31347355	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1695573	31347355	217903266	138	8123										
SPOCD1	90853	broad.mit.edu	37	chr1	32259463	32259463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgcagctcttggcggcttCgaaggagcctagcagctcat	12	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32259463C>T	ENST00000360482.2	-	12	2548	c.2419G>A	c.(2419-2421)Gaa>Aaa	p.E807K	SPOCD1_ENST00000373648.2_3'UTR|RP11-84A19.3_ENST00000527035.1_RNA|SPOCD1_ENST00000257100.3_Missense_Mutation_p.E300K|SPOCD1_ENST00000533231.1_Missense_Mutation_p.E807K	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	807					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.E807K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		TTGGCGGCTTCGAAGGAGCCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	128	126					1																	32259463		2203	4300	6503	32032050	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2419G>A	1.37:g.32259463C>T	ENSP00000353670:p.Glu807Lys		32032050	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	c	0.629	-0.817814	0.02776	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231;ENST00000449266	T;T;T;T	0.43688	0.97;1.98;0.94;1.97	4.16	-1.47	0.08772	.	.	.	.	.	T	0.09818	0.0241	N	0.00621	-1.32	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.30736	-0.9968	9	0.02654	T	1	1.7983	5.4059	0.16320	0.0:0.3241:0.1458:0.5301	.	807;243;807	Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;SPOC1_HUMAN	K	300;807;204;243;807;150	ENSP00000257100:E300K;ENSP00000353670:E807K;ENSP00000399778:E243K;ENSP00000435851:E807K	ENSP00000257100:E300K	E	-	1	0	SPOCD1	32032050	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.158000	0.03153	-0.554000	0.06150	-1.849000	0.00571	GAA		0.582	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32259463	C	T	32259463	3	4	61	1	0	0	0	0	1	0	0	0	15117	893	31	1	1251	1	SPOCD1	1	32259463	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	912108	32259463	216991158	139	8124										
SPOCD1	90853	broad.mit.edu	37	chr1	32280414	32280414	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttctgtcacaccctggaGaactcattccaccgtctctg	6	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32280414G>T	ENST00000360482.2	-	2	650	c.521C>A	c.(520-522)tCt>tAt	p.S174Y	SPOCD1_ENST00000373648.2_Missense_Mutation_p.S174Y|SPOCD1_ENST00000257100.3_Intron|SPOCD1_ENST00000533231.1_Missense_Mutation_p.S174Y	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	174					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.S174Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		ACACCCTGGAGAACTCATTCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	67	66					1																	32280414		2203	4300	6503	32053001	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.521C>A	1.37:g.32280414G>T	ENSP00000353670:p.Ser174Tyr		32053001	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030404	0.54790	.	.	ENSG00000134668	ENST00000360482;ENST00000373648;ENST00000533231	T;T;T	0.35236	1.75;1.32;1.75	3.43	2.51	0.30379	.	.	.	.	.	T	0.31420	0.0796	N	0.08118	0	0.09310	N	1	D;D	0.67145	0.996;0.994	P;P	0.60286	0.872;0.748	T	0.08229	-1.0732	9	0.72032	D	0.01	-2.1458	6.637	0.22889	0.1315:0.0:0.8685:0.0	.	174;174	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	Y	174	ENSP00000353670:S174Y;ENSP00000362752:S174Y;ENSP00000435851:S174Y	ENSP00000353670:S174Y	S	-	2	0	SPOCD1	32053001	0.002000	0.14202	0.040000	0.18447	0.461000	0.32589	1.026000	0.30103	1.020000	0.39573	0.655000	0.94253	TCT		0.622	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32280414	G	T	32280414	3	4	61	1	0	0	0	0	1	0	0	0	15117	942	33	2	3189	2	SPOCD1	1	32280414	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20951	32280414	216970207	140	8125										
PTP4A2	8073	broad.mit.edu	37	chr1	32374482	32374482	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcaatgcccattggtatCtctgaagcgtaatcgcatct	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32374482C>A	ENST00000602725.1	-	5	892	c.475G>T	c.(475-477)Gat>Tat	p.D159Y	PTP4A2_ENST00000356536.3_3'UTR|PTP4A2_ENST00000470404.1_3'UTR|PTP4A2_ENST00000457805.2_Missense_Mutation_p.D128Y|RP11-84A19.4_ENST00000602889.1_lincRNA|PTP4A2_ENST00000344035.6_Missense_Mutation_p.D159Y			Q12974	TP4A2_HUMAN	protein tyrosine phosphatase type IVA, member 2	159					peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)	p.D159Y(1)		kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)				CCATTGGTATCTCTGAAGCGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											189	171	177					1																	32374482		2203	4300	6503	32147069	SO:0001583	missense	8073			L48723	CCDS348.1, CCDS53292.1, CCDS59193.1	1p35	2011-06-09			ENSG00000184007	ENSG00000184007		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9635	protein-coding gene	gene with protein product		601584		PTP4A		8661118, 9514946	Standard	NM_080391		Approved	HU-PP-1, PTPCAAX2, OV-1, ptp-IV1a, PRL-2	uc001bty.2	Q12974	OTTHUMG00000003801	ENST00000602725.1:c.475G>T	1.37:g.32374482C>A	ENSP00000473259:p.Asp159Tyr		32147069	A8K9I8|B4DM39|D3DPP0|E9PGJ6|O00649|Q15197|Q15259|Q15260|Q15261|R4GN50	Missense_Mutation	SNP	ENST00000602725.1	37	CCDS348.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827585	0.90955	.	.	ENSG00000184007	ENST00000344035;ENST00000457805	D;D	0.95342	-3.68;-3.67	5.33	5.33	0.75918	.	0.047241	0.85682	D	0.000000	D	0.96090	0.8726	M	0.81942	2.565	0.80722	D	1	P;P	0.36789	0.57;0.547	P;P	0.46339	0.513;0.501	D	0.95922	0.8931	10	0.54805	T	0.06	-43.0073	18.9822	0.92758	0.0:1.0:0.0:0.0	.	128;159	E9PGJ6;Q12974	.;TP4A2_HUMAN	Y	159;128	ENSP00000344909:D159Y;ENSP00000409260:D128Y	ENSP00000344909:D159Y	D	-	1	0	PTP4A2	32147069	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.644000	0.83416	2.663000	0.90544	0.655000	0.94253	GAT		0.413	PTP4A2-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468092.1	NM_080391		A	32374482	C	A	32374482	3	1	61	1	0	0	0	0	1	0	0	0	12806	913	32	2	32	2	PTP4A2	1	32374482	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94068	32374482	216876139	141	8126										
KPNA6	23633	broad.mit.edu	37	chr1	32622505	32622505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagaagctgccatgttcGatagtcttctcatggactct	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32622505G>A	ENST00000373625.3	+	3	283	c.190G>A	c.(190-192)Gat>Aat	p.D64N	KPNA6_ENST00000545542.1_Missense_Mutation_p.D69N|KPNA6_ENST00000537234.1_Missense_Mutation_p.D61N|KPNA6_ENST00000469790.1_3'UTR	NM_012316.4	NP_036448.1	O60684	IMA7_HUMAN	karyopherin alpha 6 (importin alpha 7)	64					maternal process involved in female pregnancy (GO:0060135)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.D64N(1)		large_intestine(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGCCATGTTCGATAGTCTTCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											152	142	146					1																	32622505		2203	4300	6503	32395092	SO:0001583	missense	23633			AF060543	CCDS352.1	1p35.1	2013-02-14			ENSG00000025800	ENSG00000025800		"Importins", "Armadillo repeat containing"	6399	protein-coding gene	gene with protein product		610563				10523667	Standard	NM_012316		Approved	IPOA7, KPNA7, MGC17918, FLJ11249	uc001bug.3	O60684	OTTHUMG00000004333	ENST00000373625.3:c.190G>A	1.37:g.32622505G>A	ENSP00000362728:p.Asp64Asn		32395092	B2RDC7|D3DPP5|Q5VVU3	Missense_Mutation	SNP	ENST00000373625.3	37	CCDS352.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805591	0.70682	.	.	ENSG00000025800	ENST00000373625;ENST00000373617;ENST00000537234;ENST00000545542;ENST00000446515	T;T;T;T	0.32515	1.45;1.45;1.45;2.22	5.39	5.39	0.77823	Importin-alpha, importin-beta-binding domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.044996	0.85682	D	0.000000	T	0.36166	0.0957	M	0.62209	1.925	0.80722	D	1	B;B;B	0.21753	0.06;0.033;0.001	B;B;B	0.17722	0.019;0.013;0.005	T	0.10590	-1.0623	10	0.42905	T	0.14	-13.7165	19.5354	0.95251	0.0:0.0:1.0:0.0	.	69;69;64	F5GYL8;B4DWX3;O60684	.;.;IMA7_HUMAN	N	64;38;61;69;15	ENSP00000362728:D64N;ENSP00000444930:D61N;ENSP00000440609:D69N;ENSP00000415677:D15N	ENSP00000362719:D38N	D	+	1	0	KPNA6	32395092	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	7.952000	0.87827	2.709000	0.92574	0.655000	0.94253	GAT		0.448	KPNA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012527.4	NM_012316		A	32622505	G	A	32622505	3	1	61	1	0	0	0	0	1	0	0	0	8455	1058	37	1	200	1	KPNA6	1	32622505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248023	32622505	216628116	142	8127										
TXLNA	200081	broad.mit.edu	37	chr1	32646878	32646878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggctcagtctggggcccttCgtgatgtctctgaggagctg	15	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32646878C>T	ENST00000373609.1	+	2	486	c.205C>T	c.(205-207)Cgt>Tgt	p.R69C	TXLNA_ENST00000373610.3_Missense_Mutation_p.R69C			P40222	TXLNA_HUMAN	taxilin alpha	69					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|exocytosis (GO:0006887)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	cytokine activity (GO:0005125)|high molecular weight B cell growth factor receptor binding (GO:0030372)	p.R69C(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGGGGCCCTTCGTGATGTCTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											28	32	31					1																	32646878		2202	4300	6502	32419465	SO:0001583	missense	200081			AF516206	CCDS353.1	1p35	2012-02-21			ENSG00000084652	ENSG00000084652			30685	protein-coding gene	gene with protein product		608676				15184072, 14623251	Standard	NM_175852		Approved	DKFZp451J0118	uc001bui.3	P40222	OTTHUMG00000004423	ENST00000373609.1:c.205C>T	1.37:g.32646878C>T	ENSP00000362711:p.Arg69Cys		32419465	D3DPP6|Q5TFJ6|Q66K62|Q86T54|Q86T85|Q86T86|Q86Y86|Q86YW3|Q8N2Y3	Missense_Mutation	SNP	ENST00000373609.1	37	CCDS353.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.853033	0.32699	.	.	ENSG00000084652	ENST00000373610;ENST00000373609	T;T	0.28069	1.63;1.63	4.9	-2.83	0.05769	.	0.695915	0.14078	N	0.342954	T	0.10380	0.0254	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18461	-1.0336	10	0.34782	T	0.22	3.1361	5.1633	0.15073	0.2217:0.3175:0.0:0.4608	.	69	P40222	TXLNA_HUMAN	C	69	ENSP00000362712:R69C;ENSP00000362711:R69C	ENSP00000362711:R69C	R	+	1	0	TXLNA	32419465	0.019000	0.18553	0.133000	0.22050	0.771000	0.43674	-0.165000	0.09968	-0.464000	0.06963	-0.188000	0.12872	CGT		0.567	TXLNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012844.1	NM_175852		T	32646878	C	T	32646878	3	4	61	1	0	0	0	0	1	0	0	0	16827	884	31	1	211	1	TXLNA	1	32646878	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24373	32646878	216603743	143	8128										
LCK	3932	broad.mit.edu	37	chr1	32741530	32741530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggatcgttttcactgtCggtccgggacttcgaccaga	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32741530C>T	ENST00000336890.5	+	7	635	c.497C>T	c.(496-498)tCg>tTg	p.S166L	LCK_ENST00000333070.4_Missense_Mutation_p.S166L|LCK_ENST00000373564.3_Missense_Mutation_p.S224L	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	166	Interaction with PTPRH.|SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)	p.S166L(1)|p.S224L(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	TTTTCACTGTCGGTCCGGGAC	0.542			T	TRB@	T-ALL																																		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	2	Substitution - Missense(2)	large_intestine(2)	1											82	80	81					1																	32741530		2203	4300	6503	32514117	SO:0001583	missense	3932			M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"SH2 domain containing"	6524	protein-coding gene	gene with protein product		153390	"lymphocyte-specific protein tyrosine kinase"			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.497C>T	1.37:g.32741530C>T	ENSP00000337825:p.Ser166Leu		32514117	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Missense_Mutation	SNP	ENST00000336890.5	37	CCDS359.1	.	.	.	.	.	.	.	.	.	.	c	36	5.691188	0.96793	.	.	ENSG00000182866	ENST00000336890;ENST00000495610;ENST00000373557;ENST00000333070;ENST00000436824;ENST00000373564	T;D;D;T;D	0.95788	1.07;-3.81;-3.81;1.07;-3.81	5.47	5.47	0.80525	SH2 motif (5);	0.000000	0.64402	D	0.000012	D	0.99039	0.9671	H	0.99877	4.88	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.996;0.988;0.996	D	0.98832	1.0751	10	0.87932	D	0	.	18.5462	0.91047	0.0:1.0:0.0:0.0	.	210;224;166;166	E7EN21;Q573B4;P06239-3;P06239	.;.;.;LCK_HUMAN	L	166;166;210;166;210;224	ENSP00000337825:S166L;ENSP00000435605:S166L;ENSP00000362658:S210L;ENSP00000328213:S166L;ENSP00000362665:S224L	ENSP00000328213:S166L	S	+	2	0	LCK	32514117	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	7.783000	0.85696	2.764000	0.94973	0.555000	0.69702	TCG		0.542	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356		T	32741530	C	T	32741530	3	4	61	1	0	0	0	0	1	0	0	0	8698	893	31	1	519	1	LCK	1	32741530	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94652	32741530	216509091	144	8129										
TSSK3	81629	broad.mit.edu	37	chr1	32828403	32828403	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttccaaaaaacaccaaaGaaaagtggcaattaaagtta	5	6	0	1	rs145542689		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:32828403G>T	ENST00000373534.3	+	1	606	c.101G>T	c.(100-102)aGa>aTa	p.R34I	FAM229A_ENST00000432622.1_5'Flank|FAM229A_ENST00000415596.1_Intron	NM_052841.3	NP_443073.1	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	34	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R34I(1)		NS(1)|large_intestine(6)|lung(5)|skin(2)|stomach(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)				AAACACCAAAGAAAAGTGGCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	132	129					1																	32828403		2203	4300	6503	32600990	SO:0001583	missense	81629			AF296450	CCDS362.1	1p35-p34	2008-02-05	2005-03-10	2005-03-12	ENSG00000162526	ENSG00000162526			15473	protein-coding gene	gene with protein product		607660	"serine/threonine kinase 22C (spermiogenesis associated)"	STK22C		11597141	Standard	NM_052841		Approved	SPOGA3	uc001bvf.3	Q96PN8	OTTHUMG00000007585	ENST00000373534.3:c.101G>T	1.37:g.32828403G>T	ENSP00000362634:p.Arg34Ile		32600990	Q5TEE5	Missense_Mutation	SNP	ENST00000373534.3	37	CCDS362.1	.	.	.	.	.	.	.	.	.	.	G	8.957	0.969707	0.18659	.	.	ENSG00000162526	ENST00000373534	T	0.66280	-0.2	5.02	4.09	0.47781	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.311959	0.27710	N	0.018169	T	0.51329	0.1668	L	0.45352	1.415	0.80722	D	1	B	0.15473	0.013	B	0.22152	0.038	T	0.48559	-0.9025	10	0.42905	T	0.14	.	7.4961	0.27490	0.0905:0.1698:0.7397:0.0	.	34	Q96PN8	TSSK3_HUMAN	I	34	ENSP00000362634:R34I	ENSP00000362634:R34I	R	+	2	0	TSSK3	32600990	0.949000	0.32298	1.000000	0.80357	0.996000	0.88848	1.015000	0.29963	1.233000	0.43693	0.563000	0.77884	AGA		0.517	TSSK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020049.1			T	32828403	G	T	32828403	3	4	61	1	0	0	0	0	1	0	0	0	16710	942	33	2	103	2	TSSK3	1	32828403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86873	32828403	216422218	145	8130										
ZBTB8A	653121	broad.mit.edu	37	chr1	33059014	33059014	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcaagaaggaagcagttCtccacgttctcacctaagcc	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33059014C>A	ENST00000373510.4	+	3	711	c.482C>A	c.(481-483)tCt>tAt	p.S161Y	RP1-27O5.3_ENST00000480336.1_3'UTR|ZBTB8A_ENST00000316459.4_Missense_Mutation_p.S161Y	NM_001040441.1	NP_001035531.1	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S161Y(1)		cervix(2)|large_intestine(2)|lung(2)|prostate(1)	7						GGAAGCAGTTCTCCACGTTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	68	68					1																	33059014		2203	4300	6503	32831601	SO:0001583	missense	653121			AF548353	CCDS30664.1	1p34.3	2013-01-08	2009-03-25	2009-03-25	ENSG00000160062	ENSG00000160062		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24172	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 8"	ZBTB8		12477932	Standard	NM_001040441		Approved	BOZF1, FLJ90065, ZNF916A	uc001bvn.3	Q96BR9	OTTHUMG00000007855	ENST00000373510.4:c.482C>A	1.37:g.33059014C>A	ENSP00000362609:p.Ser161Tyr		32831601	Q8IUL5|Q8IWR9|Q8N2Y5|Q96BX0	Missense_Mutation	SNP	ENST00000373510.4	37	CCDS30664.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062722	0.55432	.	.	ENSG00000160062	ENST00000373510;ENST00000316459	T;T	0.15372	2.49;2.43	5.41	5.41	0.78517	.	0.393637	0.23738	U	0.045046	T	0.22282	0.0537	N	0.19112	0.55	0.47245	D	0.999364	D;D	0.57571	0.979;0.98	P;P	0.52710	0.707;0.547	T	0.01574	-1.1321	10	0.66056	D	0.02	-12.3393	18.571	0.91135	0.0:1.0:0.0:0.0	.	161;161	Q96BR9;D3DPQ1	ZBT8A_HUMAN;.	Y	161	ENSP00000362609:S161Y;ENSP00000317561:S161Y	ENSP00000317561:S161Y	S	+	2	0	ZBTB8A	32831601	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.639000	0.67868	2.699000	0.92147	0.650000	0.86243	TCT		0.403	ZBTB8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021665.2	NM_144621		A	33059014	C	A	33059014	3	1	61	1	0	0	0	0	1	0	0	0	17595	913	32	2	484	2	ZBTB8A	1	33059014	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230611	33059014	216191607	146	8131										
SYNC	81493	broad.mit.edu	37	chr1	33160583	33160583	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggggtctcagagcctcCttcatttcctggatctcagc	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33160583C>A	ENST00000409190.3	-	2	1574	c.1116G>T	c.(1114-1116)aaG>aaT	p.K372N	SYNC_ENST00000373484.3_Missense_Mutation_p.K372N	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	372	Coil 2.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)	p.K41N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TCAGAGCCTCCTTCATTTCCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	118	118					1																	33160583		2203	4300	6503	32933170	SO:0001583	missense	81493			AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"Intermediate filaments type III"	28897	protein-coding gene	gene with protein product		611750	"syncoilin, intermediate filament 1"	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.1116G>T	1.37:g.33160583C>A	ENSP00000386439:p.Lys372Asn		32933170	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	.	.	.	.	.	.	.	.	.	.	C	14.01	2.406467	0.42715	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.89343	-2.5;-2.5	4.0	0.95	0.19572	Filament (1);	0.268166	0.36665	N	0.002475	D	0.84777	0.5547	N	0.24115	0.695	0.31232	N	0.696208	D;D	0.58268	0.977;0.982	P;P	0.59825	0.787;0.864	T	0.80099	-0.1524	10	0.41790	T	0.15	-16.4699	3.8968	0.09143	0.3312:0.4835:0.0:0.1853	.	372;372	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	N	372	ENSP00000362583:K372N;ENSP00000386439:K372N	ENSP00000362583:K372N	K	-	3	2	SYNC	32933170	0.998000	0.40836	1.000000	0.80357	0.309000	0.27889	0.474000	0.22148	0.277000	0.22141	-0.339000	0.08088	AAG		0.567	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786		A	33160583	C	A	33160583	3	1	61	1	0	0	0	0	1	0	0	0	15482	680	24	2	410	2	SYNC	1	33160583	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101569	33160583	216090038	147	8132										
KIAA1522	57648	broad.mit.edu	37	chr1	33236574	33236574	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctccctcccaagggcctGgcaggtccccctgcttcccc	8	22	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33236574G>T	ENST00000373480.1	+	6	1720	c.1617G>T	c.(1615-1617)ctG>ctT	p.L539L	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000373481.3_Silent_p.L550L|KIAA1522_ENST00000401073.2_Silent_p.L598L	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	539	Pro-rich.							p.L598L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCAAGGGCCTGGCAGGTCCCC	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	1											46	49	48					1																	33236574		1875	4084	5959	33009161	SO:0001819	synonymous_variant	57648			AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.1617G>T	1.37:g.33236574G>T			33009161	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	37	CCDS55588.1																																																																																				0.667	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			T	33236574	G	T	33236574	2	4	61	1	0	0	0	0	0	0	0	1	8259	1335	47	2		2	KIAA1522	1	33236574	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75991	33236574	216014047	148	8133										
YARS	8565	broad.mit.edu	37	chr1	33248102	33248102	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcaacttgttcagtgcGacttcaacagaattcttcag	7	11	4	1	rs201652203		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33248102G>A	ENST00000373477.4	-	9	1853	c.945C>T	c.(943-945)gtC>gtT	p.V315V	YARS_ENST00000469100.1_5'Flank	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	315					apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)	p.V315V(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	TGTTCAGTGCGACTTCAACAG	0.483													G|||	1	0.000199681	0	0	5008	,	,		18590	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											103	99	100					1																	33248102		2203	4300	6503	33020689	SO:0001819	synonymous_variant	8565			U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"Aminoacyl tRNA synthetases / Class I"	12840	protein-coding gene	gene with protein product	"tyrosine tRNA ligase 1, cytoplasmic"	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.945C>T	1.37:g.33248102G>A			33020689	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	37	CCDS368.1																																																																																				0.483	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680		A	33248102	G	A	33248102	2	1	61	1	0	0	0	0	0	0	0	1	17507	1045	37	1		1	YARS	1	33248102	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11528	33248102	216002519	149	8134										
FNDC5	252995	broad.mit.edu	37	chr1	33333804	33333804	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctgcctttgttcttggaGgccatcttctcagcctcacg	10	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33333804G>T	ENST00000373471.3	-	3	462	c.396C>A	c.(394-396)gcC>gcA	p.A132A	FNDC5_ENST00000496770.1_Silent_p.A57A|FNDC5_ENST00000609187.1_Silent_p.A57A	NM_001171940.1|NM_153756.2	NP_001165411.2|NP_715637.2	Q8NAU1	FNDC5_HUMAN	fibronectin type III domain containing 5	132					positive regulation of brown fat cell differentiation (GO:0090336)|response to muscle activity (GO:0014850)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)		p.A57A(1)		breast(1)|large_intestine(1)|lung(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TGTTCTTGGAGGCCATCTTCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											112	117	115					1																	33333804		2203	4300	6503	33106391	SO:0001819	synonymous_variant	252995			AK092102	CCDS369.1, CCDS369.2, CCDS65483.1	1p34.3	2013-10-16			ENSG00000160097	ENSG00000160097		"Fibronectin type III domain containing"	20240	protein-coding gene	gene with protein product	"irisin"	611906				12384288, 22237023, 24120943	Standard	NM_153756		Approved	FRCP2	uc001bwg.3	Q8NAU1	OTTHUMG00000004015	ENST00000373471.3:c.396C>A	1.37:g.33333804G>T			33106391	A6NMC9|D3DPQ6|Q6P6D9|Q7Z676	Silent	SNP	ENST00000373471.3	37																																																																																					0.607	FNDC5-001	KNOWN	non_ATG_start|basic	protein_coding	protein_coding	OTTHUMT00000011467.3	NM_153756		T	33333804	G	T	33333804	2	4	61	1	0	0	0	0	0	0	0	1	5991	987	35	2		2	FNDC5	1	33333804	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85702	33333804	215916817	150	8135										
ZNF362	149076	broad.mit.edu	37	chr1	33764631	33764631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcccccggcatcccggtgcGaatctctctcatctgagccc	9	18	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33764631G>A	ENST00000539719.1	+	9	1417	c.1247G>A	c.(1246-1248)cGa>cAa	p.R416Q	ZNF362_ENST00000373428.5_Missense_Mutation_p.R416Q	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R416Q(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ATCCCGGTGCGAATCTCTCTC	0.672											OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(162;1431 2676 35353 38425)											1	Substitution - Missense(1)	large_intestine(1)	1											55	56	56					1																	33764631		2203	4300	6503	33537218	SO:0001583	missense	149076				CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"Zinc fingers, C2H2-type"	18079	protein-coding gene	gene with protein product	"rotund homolog (Drosophila)"						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.1247G>A	1.37:g.33764631G>A	ENSP00000446335:p.Arg416Gln	842	33537218	Q8WYU4	Missense_Mutation	SNP	ENST00000539719.1	37	CCDS377.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687958	0.88639	.	.	ENSG00000160094	ENST00000539719;ENST00000373428	T;T	0.08634	3.07;3.07	5.3	5.3	0.74995	.	0.492721	0.15128	N	0.279012	T	0.12860	0.0312	N	0.08118	0	0.58432	D	0.999999	D	0.64830	0.994	P	0.61201	0.885	T	0.37820	-0.9689	10	0.66056	D	0.02	-2.099	16.4466	0.83936	0.0:0.0:1.0:0.0	.	416	Q5T0B9	ZN362_HUMAN	Q	416	ENSP00000446335:R416Q;ENSP00000362527:R416Q	ENSP00000362527:R416Q	R	+	2	0	ZNF362	33537218	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.070000	0.64376	2.484000	0.83849	0.655000	0.94253	CGA		0.672	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493		A	33764631	G	A	33764631	3	1	61	1	0	0	0	0	1	0	0	0	17907	1058	37	1	1277	1	ZNF362	1	33764631	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	430827	33764631	215485990	151	8136										
PHC2	1912	broad.mit.edu	37	chr1	33841109	33841109	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtggcacaggcactgctaGatgtatgtgggactggcagc	16	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33841109G>T	ENST00000257118.5	-	1	85	c.32C>A	c.(31-33)tCt>tAt	p.S11Y	PHC2_ENST00000431992.1_Missense_Mutation_p.S11Y|PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000419414.2_Missense_Mutation_p.S11Y	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	11	Ser-rich.				multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S11Y(1)		autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GGCACTGCTAGATGTATGTGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	51	54					1																	33841109		2203	4300	6503	33613696	SO:0001583	missense	1912			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.32C>A	1.37:g.33841109G>T	ENSP00000257118:p.Ser11Tyr		33613696	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105931	0.37145	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.36157	1.68;1.27;1.69	5.39	5.39	0.77823	.	0.485757	0.21497	N	0.073597	T	0.37320	0.0999	L	0.53249	1.67	0.42668	D	0.993506	P;P;P	0.38922	0.651;0.651;0.651	B;B;B	0.37833	0.123;0.259;0.123	T	0.36768	-0.9734	10	0.87932	D	0	-0.5667	14.6558	0.68833	0.0:0.0:1.0:0.0	.	11;11;11	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	Y	11	ENSP00000389436:S11Y;ENSP00000257118:S11Y;ENSP00000391440:S11Y	ENSP00000257118:S11Y	S	-	2	0	PHC2	33613696	1.000000	0.71417	0.011000	0.14972	0.293000	0.27360	5.682000	0.68182	2.517000	0.84864	0.462000	0.41574	TCT		0.642	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		T	33841109	G	T	33841109	3	4	61	1	0	0	0	0	1	0	0	0	11848	942	33	2	2600	2	PHC2	1	33841109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76478	33841109	215409512	152	8137										
ZSCAN20	7579	broad.mit.edu	37	chr1	33960168	33960168	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagccctacaaatgccttGaatgtggaaaaaactttagt	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:33960168G>T	ENST00000361328.3	+	8	2377	c.2224G>T	c.(2224-2226)Gaa>Taa	p.E742*		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	742					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E742*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CAAATGCCTTGAATGTGGAAA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											93	103	100					1																	33960168		2161	4284	6445	33732755	SO:0001587	stop_gained	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.2224G>T	1.37:g.33960168G>T	ENSP00000355053:p.Glu742*		33732755	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Nonsense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	G	36	5.927524	0.97110	.	.	ENSG00000121903	ENST00000326544;ENST00000361328;ENST00000401072	.	.	.	5.9	2.97	0.34412	.	0.309865	0.27526	N	0.018964	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-0.3493	9.6328	0.39789	0.0737:0.268:0.6583:0.0	.	.	.	.	X	742;676;676	.	ENSP00000324450:E742X	E	+	1	0	ZSCAN20	33732755	0.000000	0.05858	0.002000	0.10522	0.697000	0.40408	0.687000	0.25407	0.376000	0.24707	0.561000	0.74099	GAA		0.468	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33960168	G	T	33960168	4	4	61	1	0	0	0	0	0	1	0	0	18271	1291	45	2	2250	2	ZSCAN20	1	33960168	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119059	33960168	215290453	153	8138										
CSMD2	114784	broad.mit.edu	37	chr1	34049245	34049246	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttgactgacttaccatcINSaaaaatctcaaactcatcat							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34049245_34049246insA	ENST00000373381.4	-	47	7412_7413	c.7236_7237insT	c.(7234-7239)tttgatfs	p.D2413fs		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2415	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D2415fs*1(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GACTTACCATCAAAAATCTCAA	0.49																																																1	Insertion - Frameshift(1)	large_intestine(1)	1																																								33821833	SO:0001589	frameshift_variant	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7237dupT	1.37:g.34049250_34049250dupA	ENSP00000362479:p.Asp2413fs		33821832	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Frame_Shift_Ins	INS	ENST00000373381.4	37																																																																																					0.49	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34049246	-	A	34049245	7	5	61	1	0	1	1	0	0	0	0	0	3951	826	29	0	3308	0	CSMD2	1	34049245	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	89077	34049245	215201376	154	8139										
CSMD2	114784	broad.mit.edu	37	chr1	34164401	34164401	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtccggcgctctccactcaGacacagcagctcctcactac	8	18	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34164401G>T	ENST00000373380.1	-	3	716	c.496C>A	c.(496-498)Ctg>Atg	p.L166M	CSMD2_ENST00000373381.4_Missense_Mutation_p.L1293M|CSMD2_ENST00000373388.2_De_novo_Start_InFrame			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1253	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L1253M(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCTCCACTCAGACACAGCAGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	77	78					1																	34164401		2203	4300	6503	33936988	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.496C>A	1.37:g.34164401G>T	ENSP00000362478:p.Leu166Met		33936988	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331838	0.60853	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.66460	-0.21;-0.21	5.76	5.76	0.90799	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000003	T	0.74374	0.3708	L	0.31926	0.97	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.991	D;D;D	0.85130	0.962;0.997;0.959	T	0.67787	-0.5580	10	0.22706	T	0.39	.	19.3155	0.94211	0.0:0.0:1.0:0.0	.	166;1253;1293	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	M	1293;166	ENSP00000362479:L1293M;ENSP00000362478:L166M	ENSP00000241312:L1253M	L	-	1	2	CSMD2	33936988	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.360000	0.59455	2.879000	0.98667	0.650000	0.86243	CTG		0.592	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		T	34164401	G	T	34164401	3	4	61	1	0	0	0	0	1	0	0	0	3951	933	33	2	6890	2	CSMD2	1	34164401	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115156	34164401	215086220	155	8140										
CSMD2	114784	broad.mit.edu	37	chr1	34209162	34209162	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcctctgggtagttgggaGacaggacaaccccagacggg	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34209162G>T	ENST00000373381.4	-	14	2068	c.1892C>A	c.(1891-1893)tCt>tAt	p.S631Y		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	591	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S591Y(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTAGTTGGGAGACAGGACAAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	73	71					1																	34209162		2203	4300	6503	33981749	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.1892C>A	1.37:g.34209162G>T	ENSP00000362479:p.Ser631Tyr		33981749	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	27.5	4.839959	0.91117	.	.	ENSG00000121904	ENST00000373381	T	0.60920	0.15	5.58	5.58	0.84498	CUB (5);	0.000000	0.85682	D	0.000000	D	0.84424	0.5469	H	0.96301	3.8	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.995	D	0.88705	0.3218	10	0.72032	D	0.01	.	18.9334	0.92576	0.0:0.0:1.0:0.0	.	591;631	Q7Z408;E7EUA6	CSMD2_HUMAN;.	Y	631	ENSP00000362479:S631Y	ENSP00000241312:S591Y	S	-	2	0	CSMD2	33981749	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.813000	0.99286	2.782000	0.95742	0.655000	0.94253	TCT		0.572	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34209162	G	T	34209162	3	4	61	1	0	0	0	0	1	0	0	0	3951	942	33	2	8915	2	CSMD2	1	34209162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44761	34209162	215041459	156	8141										
CSMD2	114784	broad.mit.edu	37	chr1	34258031	34258031	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactgcacttacatgtagaGaactgtcttctggtccccat	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34258031G>T	ENST00000338325.1	-	5	779	c.367C>A	c.(367-369)Ctc>Atc	p.L123I	CSMD2_ENST00000373381.4_Missense_Mutation_p.L515I			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	475	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L475I(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TACATGTAGAGAACTGTCTTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											214	170	185					1																	34258031		2203	4300	6503	34030618	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.367C>A	1.37:g.34258031G>T	ENSP00000340311:p.Leu123Ile		34030618	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	37		.	.	.	.	.	.	.	.	.	.	G	15.61	2.883642	0.51908	.	.	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.19250	2.16;2.16	5.2	5.2	0.72013	CUB (5);	0.065037	0.64402	D	0.000006	T	0.31857	0.0810	L	0.38175	1.15	0.80722	D	1	P;P	0.45240	0.854;0.495	P;B	0.56648	0.803;0.217	T	0.00978	-1.1493	10	0.29301	T	0.29	.	16.2961	0.82769	0.0:0.0:1.0:0.0	.	475;515	Q7Z408;E7EUA6	CSMD2_HUMAN;.	I	515;123	ENSP00000362479:L515I;ENSP00000340311:L123I	ENSP00000241312:L475I	L	-	1	0	CSMD2	34030618	1.000000	0.71417	0.989000	0.46669	0.926000	0.56050	5.937000	0.70162	2.466000	0.83321	0.461000	0.40582	CTC		0.562	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896		T	34258031	G	T	34258031	3	4	61	1	0	0	0	0	1	0	0	0	3951	942	33	2	9276	2	CSMD2	1	34258031	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48869	34258031	214992590	157	8142										
HMGB4	127540	broad.mit.edu	37	chr1	34330292	34330292	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtaaacaatgtaatgccaGgaagaagtaccgaatgtcag	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34330292G>T	ENST00000522796.1	+	4	2405	c.500G>T	c.(499-501)aGg>aTg	p.R167M	CSMD2_ENST00000373381.4_Intron|HMGB4_ENST00000425537.1_3'UTR|HMGB4_ENST00000519684.1_Missense_Mutation_p.R167M			Q8WW32	HMGB4_HUMAN	high mobility group box 4	167						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R167M(1)		NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGTAATGCCAGGAAGAAGTAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	71	68					1																	34330292		2203	4300	6503	34102879	SO:0001583	missense	127540				CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.500G>T	1.37:g.34330292G>T	ENSP00000430919:p.Arg167Met		34102879	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	37	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088305	0.36855	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	D;D	0.91521	-2.86;-2.86	5.1	1.87	0.25490	.	0.104471	0.37530	U	0.002043	D	0.88276	0.6393	L	0.58101	1.795	0.09310	N	1	B	0.33379	0.41	B	0.40901	0.343	T	0.80781	-0.1229	10	0.62326	D	0.03	.	6.556	0.22460	0.3359:0.0:0.6641:0.0	.	167	B2R4X7	.	M	167	ENSP00000429214:R167M;ENSP00000430919:R167M	ENSP00000429214:R167M	R	+	2	0	HMGB4	34102879	0.007000	0.16637	0.004000	0.12327	0.034000	0.12701	0.105000	0.15333	0.198000	0.20407	0.609000	0.83330	AGG		0.468	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		T	34330292	G	T	34330292	3	4	61	1	0	0	0	0	1	0	0	0	7249	1000	35	2	502	2	HMGB4	1	34330292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72261	34330292	214920329	158	8143										
C1orf94	84970	broad.mit.edu	37	chr1	34666509	34666509	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgcatcactgaccctgccGcccaagaaacctacatgtcc	6	18	1	2	rs371680483		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:34666509G>A	ENST00000488417.1	+	3	1266	c.1146G>A	c.(1144-1146)ccG>ccA	p.P382P	C1orf94_ENST00000373374.3_Silent_p.P192P	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	382								p.P192P(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				TGACCCTGCCGCCCAAGAAAC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,	0,4406		0,0,2203	58	57	58		1146,576	-11.5	0	1		58	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C1orf94	NM_001134734.1,NM_032884.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	382/599,192/409	34666509	1,13005	2203	4300	6503	34439096	SO:0001819	synonymous_variant	84970			AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1146G>A	1.37:g.34666509G>A			34439096	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																				0.592	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		A	34666509	G	A	34666509	2	1	61	1	0	0	0	0	0	0	0	1	2077	1074	38	1		1	C1orf94	1	34666509	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336217	34666509	214584112	159	8144										
DLGAP3	58512	broad.mit.edu	37	chr1	35365313	35365313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagccagggatggagctcCgggggtggatccggggtggg	22	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35365313C>T	ENST00000373347.1	-	5	1611	c.1343G>A	c.(1342-1344)cGg>cAg	p.R448Q	DLGAP3_ENST00000235180.4_Missense_Mutation_p.R448Q			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	448					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)	p.R448Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				GATGGAGCTCCGGGGGTGGAT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	84	82					1																	35365313		2203	4300	6503	35137900	SO:0001583	missense	58512			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.1343G>A	1.37:g.35365313C>T	ENSP00000362444:p.Arg448Gln		35137900	Q5TDD5|Q9H3X7	Missense_Mutation	SNP	ENST00000373347.1	37	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277690	0.59758	.	.	ENSG00000116544	ENST00000373347;ENST00000235180;ENST00000542913	T;T	0.30714	1.52;1.52	4.84	4.84	0.62591	.	0.126835	0.53938	D	0.000049	T	0.21062	0.0507	L	0.45228	1.405	0.42732	D	0.99371	P	0.49253	0.921	B	0.32211	0.142	T	0.06481	-1.0824	10	0.51188	T	0.08	-14.449	11.5997	0.50995	0.0:0.9183:0.0:0.0817	.	448	O95886	DLGP3_HUMAN	Q	448;448;131	ENSP00000362444:R448Q;ENSP00000235180:R448Q	ENSP00000235180:R448Q	R	-	2	0	DLGAP3	35137900	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.905000	0.56333	2.518000	0.84900	0.563000	0.77884	CGG		0.582	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35365313	C	T	35365313	3	4	61	1	0	0	0	0	1	0	0	0	4572	652	23	1	1628	1	DLGAP3	1	35365313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	698804	35365313	213885308	160	8145										
ZMYM1	79830	broad.mit.edu	37	chr1	35578720	35578720	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaaagacaatatgaaatCtatgaaaataagtgatgaac	6	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35578720C>A	ENST00000373330.1	+	11	1463	c.1289C>A	c.(1288-1290)tCt>tAt	p.S430Y	ZMYM1_ENST00000359858.4_Missense_Mutation_p.S430Y|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	430						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S430Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AATATGAAATCTATGAAAATA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											66	62	63					1																	35578720		1862	4109	5971	35351307	SO:0001583	missense	79830			AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.1289C>A	1.37:g.35578720C>A	ENSP00000362427:p.Ser430Tyr		35351307	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	37	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.736854	0.49045	.	.	ENSG00000197056	ENST00000417119;ENST00000359858;ENST00000373329;ENST00000373330	T;T;T;T	0.25414	1.8;2.5;2.24;2.5	4.69	4.69	0.59074	.	0.277612	0.26428	N	0.024436	T	0.42720	0.1215	L	0.56769	1.78	0.30146	N	0.803486	D;D	0.76494	0.999;0.999	D;D	0.64595	0.927;0.927	T	0.21552	-1.0242	10	0.33940	T	0.23	-13.4706	13.4323	0.61062	0.0:1.0:0.0:0.0	.	411;430	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	Y	430;430;355;430	ENSP00000394233:S430Y;ENSP00000352920:S430Y;ENSP00000362426:S355Y;ENSP00000362427:S430Y	ENSP00000352920:S430Y	S	+	2	0	ZMYM1	35351307	0.994000	0.37717	0.833000	0.33012	0.373000	0.29922	1.863000	0.39459	2.894000	0.99253	0.655000	0.94253	TCT		0.343	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		A	35578720	C	A	35578720	3	1	61	1	0	0	0	0	1	0	0	0	17738	913	32	2	1323	2	ZMYM1	1	35578720	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213407	35578720	213671901	161	8146										
SFPQ	6421	broad.mit.edu	37	chr1	35653593	35653593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggatccatgtagcccattCggctgtaactttcctctctt	7	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35653593C>T	ENST00000357214.5	-	7	1894	c.1796G>A	c.(1795-1797)cGa>cAa	p.R599Q		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	599					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R599Q(1)	SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				GTAGCCCATTCGGCTGTAACT	0.443			T	TFE3	papillary renal cell																																		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	1	Substitution - Missense(1)	large_intestine(1)	1											354	311	326					1																	35653593		2203	4300	6503	35426180	SO:0001583	missense	6421			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1796G>A	1.37:g.35653593C>T	ENSP00000349748:p.Arg599Gln		35426180	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817677	0.90790	.	.	ENSG00000116560	ENST00000357214	T	0.40225	1.04	5.81	5.81	0.92471	.	0.048871	0.85682	D	0.000000	T	0.43433	0.1247	N	0.22421	0.69	0.46678	D	0.99915	D	0.76494	0.999	P	0.53006	0.715	T	0.10291	-1.0636	10	0.21540	T	0.41	-6.5829	20.0656	0.97703	0.0:1.0:0.0:0.0	.	599	P23246	SFPQ_HUMAN	Q	599	ENSP00000349748:R599Q	ENSP00000349748:R599Q	R	-	2	0	SFPQ	35426180	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	7.578000	0.82498	2.752000	0.94435	0.555000	0.69702	CGA		0.443	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35653593	C	T	35653593	3	4	61	1	0	0	0	0	1	0	0	0	14197	884	31	1	343	1	SFPQ	1	35653593	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74873	35653593	213597028	162	8147										
SFPQ	6421	broad.mit.edu	37	chr1	35654859	35654859	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaatttgtcttttgcatCtttcatgtttttttcaactt	3	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35654859C>T	ENST00000357214.5	-	5	1638	c.1540G>A	c.(1540-1542)Gat>Aat	p.D514N		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	514					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.D514N(1)	SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TCTTTTGCATCTTTCATGTTT	0.398			T	TFE3	papillary renal cell																																		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	1	Substitution - Missense(1)	large_intestine(1)	1											209	156	174					1																	35654859		2203	4300	6503	35427446	SO:0001583	missense	6421			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1540G>A	1.37:g.35654859C>T	ENSP00000349748:p.Asp514Asn		35427446	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	C	36	5.719457	0.96839	.	.	ENSG00000116560	ENST00000357214	D	0.92348	-3.02	5.84	5.84	0.93424	.	0.048753	0.85682	D	0.000000	D	0.91878	0.7429	N	0.19112	0.55	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	D	0.92567	0.6063	10	0.59425	D	0.04	-31.2446	20.1346	0.98019	0.0:1.0:0.0:0.0	.	514	P23246	SFPQ_HUMAN	N	514	ENSP00000349748:D514N	ENSP00000349748:D514N	D	-	1	0	SFPQ	35427446	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.724000	0.84798	2.765000	0.95021	0.655000	0.94253	GAT		0.398	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35654859	C	T	35654859	3	4	61	1	0	0	0	0	1	0	0	0	14197	913	32	3	607	3	SFPQ	1	35654859	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1266	35654859	213595762	163	8148										
SFPQ	6421	broad.mit.edu	37	chr1	35656952	35656952	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacactcacaagcttaataAatccgaatcctttgcctttg	4	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35656952A>C	ENST00000357214.5	-	2	1105	c.1007T>G	c.(1006-1008)tTt>tGt	p.F336C		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	336	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.F336C(1)	SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				AAGCTTAATAAATCCGAATCC	0.353			T	TFE3	papillary renal cell																																		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	1	Substitution - Missense(1)	large_intestine(1)	1											85	86	86					1																	35656952		2203	4300	6503	35429539	SO:0001583	missense	6421			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1007T>G	1.37:g.35656952A>C	ENSP00000349748:p.Phe336Cys		35429539	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443109	0.83993	.	.	ENSG00000116560	ENST00000357214	T	0.32988	1.43	5.25	5.25	0.73442	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.71676	0.3368	H	0.98351	4.21	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.83956	0.0319	10	0.87932	D	0	-8.2348	15.1818	0.72965	1.0:0.0:0.0:0.0	.	336	P23246	SFPQ_HUMAN	C	336	ENSP00000349748:F336C	ENSP00000349748:F336C	F	-	2	0	SFPQ	35429539	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.281000	0.95811	1.972000	0.57404	0.455000	0.32223	TTT		0.353	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		C	35656952	A	C	35656952	3	2	61	1	0	0	0	0	1	0	0	0	14197	14	1	4	1152	4	SFPQ	1	35656952	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2093	35656952	213593669	164	8149										
ZMYM4	9202	broad.mit.edu	37	chr1	35790972	35790972	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttccagtttgaacaaaaAagtggtgcagtttttgatga	9	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35790972A>C	ENST00000314607.6	+	2	131	c.51A>C	c.(49-51)aaA>aaC	p.K17N	ZMYM4_ENST00000373297.2_Missense_Mutation_p.K17N	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	17					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K17N(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTGAACAAAAAAGTGGTGCAG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											152	156	155					1																	35790972		2202	4298	6500	35563559	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.51A>C	1.37:g.35790972A>C	ENSP00000322915:p.Lys17Asn		35563559	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.474722	0.63737	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.32023	1.64;1.47	4.53	3.19	0.36642	.	0.479765	0.17252	U	0.181124	T	0.33818	0.0876	N	0.24115	0.695	0.30676	N	0.752846	P	0.51653	0.947	D	0.67231	0.95	T	0.20940	-1.0260	10	0.72032	D	0.01	-2.966	4.5504	0.12108	0.8156:0.0:0.1844:0.0	.	17	Q5VZL5	ZMYM4_HUMAN	N	17	ENSP00000322915:K17N;ENSP00000362394:K17N	ENSP00000322915:K17N	K	+	3	2	ZMYM4	35563559	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.518000	0.45537	1.812000	0.52913	0.377000	0.23210	AAA		0.328	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		C	35790972	A	C	35790972	3	2	61	1	0	0	0	0	1	0	0	0	17741	11	1	4	57	4	ZMYM4	1	35790972	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	134020	35790972	213459649	165	8150										
ZMYM4	9202	broad.mit.edu	37	chr1	35851049	35851049	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattctcttaatagaaatcaGccaaaattacaccgtgtgcg	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35851049G>A	ENST00000314607.6	+	10	1656	c.1576G>A	c.(1576-1578)Gcc>Acc	p.A526T	ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	526					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A526T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ATAGAAATCAGCCAAAATTAC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	78	76					1																	35851049		2203	4300	6503	35623636	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1576G>A	1.37:g.35851049G>A	ENSP00000322915:p.Ala526Thr		35623636	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217039	0.39201	.	.	ENSG00000146463	ENST00000314607	T	0.22134	1.97	5.11	4.19	0.49359	.	0.377489	0.29624	N	0.011626	T	0.22627	0.0546	L	0.48986	1.54	0.80722	D	1	B	0.28783	0.222	B	0.33196	0.159	T	0.03025	-1.1081	10	0.28530	T	0.3	-2.4072	13.7386	0.62833	0.0752:0.0:0.9248:0.0	.	526	Q5VZL5	ZMYM4_HUMAN	T	526	ENSP00000322915:A526T	ENSP00000322915:A526T	A	+	1	0	ZMYM4	35623636	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.038000	0.64177	1.267000	0.44247	0.543000	0.68304	GCC		0.318	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35851049	G	A	35851049	3	1	61	1	0	0	0	0	1	0	0	0	17741	971	34	3	1614	3	ZMYM4	1	35851049	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60077	35851049	213399572	166	8151										
ZMYM4	9202	broad.mit.edu	37	chr1	35884071	35884071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgttggcaagaggaaacGaaatgaagatgatgaggttc	14	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:35884071G>A	ENST00000314607.6	+	29	4417	c.4337G>A	c.(4336-4338)cGa>cAa	p.R1446Q	ZMYM4_ENST00000373297.2_Missense_Mutation_p.R1357Q	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1446					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1446Q(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGAGGAAACGAAATGAAGAT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	1											121	113	116					1																	35884071		2203	4300	6503	35656658	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4337G>A	1.37:g.35884071G>A	ENSP00000322915:p.Arg1446Gln		35656658	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	35	5.584390	0.96578	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25085	1.82;1.85	5.84	5.84	0.93424	.	0.315320	0.33959	N	0.004389	T	0.47525	0.1450	L	0.55481	1.735	0.50313	D	0.999864	D	0.69078	0.997	D	0.63283	0.913	T	0.34800	-0.9814	10	0.72032	D	0.01	-7.1968	20.1381	0.98040	0.0:0.0:1.0:0.0	.	1446	Q5VZL5	ZMYM4_HUMAN	Q	1446;1357	ENSP00000322915:R1446Q;ENSP00000362394:R1357Q	ENSP00000322915:R1446Q	R	+	2	0	ZMYM4	35656658	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.650000	0.67944	2.763000	0.94921	0.650000	0.86243	CGA		0.393	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35884071	G	A	35884071	3	1	61	1	0	0	0	0	1	0	0	0	17741	1058	37	1	4451	1	ZMYM4	1	35884071	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33022	35884071	213366550	167	8152										
CLSPN	63967	broad.mit.edu	37	chr1	36204751	36204751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatacctatgtttttccatCgaaacttcctcattcgccca	4	13	1	1	rs375345515		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36204751C>T	ENST00000318121.3	-	20	3473	c.3416G>A	c.(3415-3417)cGa>cAa	p.R1139Q	RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000466308.1_5'Flank|CLSPN_ENST00000251195.5_Missense_Mutation_p.R1139Q|CLSPN_ENST00000520551.1_Missense_Mutation_p.R1086Q|CLSPN_ENST00000373220.3_Missense_Mutation_p.R1075Q	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1139					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.R1139Q(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTTTTTCCATCGAAACTTCCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG,GLN/ARG	1,4405		0,1,2202	86	80	82		3224,3416	5.9	1	1		82	0,8600		0,0,4300	no	missense,missense	CLSPN	NM_001190481.1,NM_022111.3	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1075/1276,1139/1340	36204751	1,13005	2203	4300	6503	35977338	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3416G>A	1.37:g.36204751C>T	ENSP00000312995:p.Arg1139Gln		35977338	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	C	36	5.693278	0.96793	2.27E-4	0.0	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.39592	1.08;1.07;1.15;1.15	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.71144	-0.4678	10	0.72032	D	0.01	-6.7074	20.3827	0.98937	0.0:1.0:0.0:0.0	.	1075;1139	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Q	1139;1139;1075;1086	ENSP00000251195:R1139Q;ENSP00000312995:R1139Q;ENSP00000362317:R1075Q;ENSP00000428848:R1086Q	ENSP00000251195:R1139Q	R	-	2	0	CLSPN	35977338	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.079000	0.71291	2.823000	0.97156	0.644000	0.83932	CGA		0.478	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		T	36204751	C	T	36204751	3	4	61	1	0	0	0	0	1	0	0	0	3566	884	31	1	627	1	CLSPN	1	36204751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	320680	36204751	213045870	168	8153										
CLSPN	63967	broad.mit.edu	37	chr1	36215115	36215115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcatctgtttctgattttTcttcagtaggaaagtaactg	7	6	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36215115T>C	ENST00000318121.3	-	12	2282	c.2225A>G	c.(2224-2226)gAa>gGa	p.E742G	CLSPN_ENST00000251195.5_Missense_Mutation_p.E742G|CLSPN_ENST00000520551.1_Missense_Mutation_p.E689G|CLSPN_ENST00000373220.3_Missense_Mutation_p.E678G	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	742					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.E742G(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTCTGATTTTTCTTCAGTAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	61	61					1																	36215115		2203	4300	6503	35987702	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.2225A>G	1.37:g.36215115T>C	ENSP00000312995:p.Glu742Gly		35987702	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.988368	0.74589	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.26518	1.73;1.74;1.78;1.81	5.85	5.85	0.93711	.	0.239919	0.42053	D	0.000773	T	0.35038	0.0918	M	0.69823	2.125	0.42109	D	0.99137	B;P	0.38729	0.114;0.644	B;B	0.43623	0.133;0.425	T	0.11108	-1.0601	10	0.13470	T	0.59	-22.6148	16.5479	0.84454	0.0:0.0:0.0:1.0	.	678;742	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	G	742;742;678;689	ENSP00000251195:E742G;ENSP00000312995:E742G;ENSP00000362317:E678G;ENSP00000428848:E689G	ENSP00000251195:E742G	E	-	2	0	CLSPN	35987702	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.251000	0.65438	2.371000	0.80710	0.533000	0.62120	GAA		0.373	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		C	36215115	T	C	36215115	3	2	61	1	0	0	0	0	1	0	0	0	3566	1783	62	4	1850	4	CLSPN	1	36215115	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10364	36215115	213035506	169	8154										
CLSPN	63967	broad.mit.edu	37	chr1	36226481	36226481	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtatttgcagtgtctatGatttctttgtgatggcttga	11	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36226481G>T	ENST00000318121.3	-	8	1098	c.1041C>A	c.(1039-1041)atC>atA	p.I347I	CLSPN_ENST00000251195.5_Silent_p.I347I|CLSPN_ENST00000520551.1_Silent_p.I347I|CLSPN_ENST00000373220.3_Silent_p.I347I	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	347					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.I347I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAGTGTCTATGATTTCTTTGT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											70	70	70					1																	36226481		2147	4266	6413	35999068	SO:0001819	synonymous_variant	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.1041C>A	1.37:g.36226481G>T			35999068	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Silent	SNP	ENST00000318121.3	37	CCDS396.1																																																																																				0.373	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		T	36226481	G	T	36226481	2	4	61	1	0	0	0	0	0	0	0	1	3566	1280	45	2		2	CLSPN	1	36226481	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11366	36226481	213024140	170	8155										
EIF2C4	192670	broad.mit.edu	37	chr1	36282548	36282548	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactgttggaaaaccaattCgactgttagccaatcatttt	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36282548C>T	ENST00000373210.3	+	2	330	c.85C>T	c.(85-87)Cga>Tga	p.R29*		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	29					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)	p.R29*(2)									AAAACCAATTCGACTGTTAGC	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											132	133	133					1																	36282548		2203	4300	6503	36055135	SO:0001587	stop_gained	192670			AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.85C>T	1.37:g.36282548C>T	ENSP00000362306:p.Arg29*		36055135	A7MD27	Nonsense_Mutation	SNP	ENST00000373210.3	37	CCDS397.1	.	.	.	.	.	.	.	.	.	.	C	37	6.398531	0.97533	.	.	ENSG00000134698	ENST00000373210	.	.	.	5.35	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-8.9217	12.9217	0.58237	0.295:0.705:0.0:0.0	.	.	.	.	X	29	.	ENSP00000362306:R29X	R	+	1	2	EIF2C4	36055135	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.009000	0.29886	1.206000	0.43276	0.655000	0.94253	CGA		0.433	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		T	36282548	C	T	36282548	4	4	61	1	0	0	0	0	0	1	0	0	5019	876	31	1	91	1	EIF2C4	1	36282548	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56067	36282548	212968073	171	8156										
EIF2C4	192670	broad.mit.edu	37	chr1	36315852	36315852	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctctgtagtcatgcagGaattcaggtaatttggaagc	10	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36315852G>T	ENST00000373210.3	+	16	2515	c.2270G>T	c.(2269-2271)gGa>gTa	p.G757V	AGO4_ENST00000488778.1_3'UTR	NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	757	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)	p.G757V(1)									AGTCATGCAGGAATTCAGGTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											175	153	161					1																	36315852		2203	4300	6503	36088439	SO:0001583	missense	192670			AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.2270G>T	1.37:g.36315852G>T	ENSP00000362306:p.Gly757Val		36088439	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	37	CCDS397.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085668	0.76642	.	.	ENSG00000134698	ENST00000373210	T	0.30182	1.54	4.82	4.82	0.62117	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.102515	0.64402	D	0.000002	T	0.57592	0.2064	M	0.73430	2.235	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.63466	-0.6631	10	0.87932	D	0	-1.7539	18.2543	0.90014	0.0:0.0:1.0:0.0	.	757	Q9HCK5	AGO4_HUMAN	V	757	ENSP00000362306:G757V	ENSP00000362306:G757V	G	+	2	0	EIF2C4	36088439	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.768000	0.98965	2.361000	0.80049	0.591000	0.81541	GGA		0.423	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		T	36315852	G	T	36315852	3	4	61	1	0	0	0	0	1	0	0	0	5019	1174	41	2	2332	2	EIF2C4	1	36315852	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33304	36315852	212934769	172	8157										
EIF2C1	26523	broad.mit.edu	37	chr1	36358738	36358738	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctggggaagggaaggatcGaatctttaaggtctccatca	12	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36358738G>T	ENST00000373204.4	+	4	584	c.371G>T	c.(370-372)cGa>cTa	p.R124L	AGO1_ENST00000373206.1_Missense_Mutation_p.R49L	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	124					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R124L(1)									GGGAAGGATCGAATCTTTAAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	79	85					1																	36358738		2203	4300	6503	36131325	SO:0001583	missense	26523			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.371G>T	1.37:g.36358738G>T	ENSP00000362300:p.Arg124Leu		36131325	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	37	CCDS398.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993613	0.74703	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.12147	2.72;2.71	5.63	5.63	0.86233	Argonaute/Dicer protein, PAZ (1);	0.000000	0.85682	D	0.000000	T	0.38878	0.1057	M	0.91561	3.22	0.80722	D	1	P	0.46952	0.887	P	0.49528	0.614	T	0.50372	-0.8836	10	0.87932	D	0	-24.8338	19.6727	0.95916	0.0:0.0:1.0:0.0	.	124	Q9UL18	AGO1_HUMAN	L	49;124	ENSP00000362302:R49L;ENSP00000362300:R124L	ENSP00000362300:R124L	R	+	2	0	EIF2C1	36131325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.656000	0.90262	0.591000	0.81541	CGA		0.542	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36358738	G	T	36358738	3	4	61	1	0	0	0	0	1	0	0	0	5016	1058	37	2	385	2	EIF2C1	1	36358738	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42886	36358738	212891883	173	8158										
EIF2C1	26523	broad.mit.edu	37	chr1	36385202	36385202	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctgcgcaccatgtacttCgcttgaaggcagaacgctgt	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36385202C>T	ENST00000373204.4	+	19	2781	c.2568C>T	c.(2566-2568)ttC>ttT	p.F856F	AGO1_ENST00000373206.1_Silent_p.F781F	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	856					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.F856F(1)									CCATGTACTTCGCTTGAAGGC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1											53	51	51					1																	36385202		2203	4300	6503	36157789	SO:0001819	synonymous_variant	26523			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.2568C>T	1.37:g.36385202C>T			36157789	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																				0.592	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36385202	C	T	36385202	2	4	61	1	0	0	0	0	0	0	0	1	5016	883	31	1		1	EIF2C1	1	36385202	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26464	36385202	212865419	174	8159										
EIF2C3	192669	broad.mit.edu	37	chr1	36439109	36439109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaatgatgcttaatatcGatggtaagggaactaaagcc	11	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36439109G>A	ENST00000373191.4	+	5	1004	c.655G>A	c.(655-657)Gat>Aat	p.D219N	AGO3_ENST00000246314.6_Intron|AGO3_ENST00000397828.2_Missense_Mutation_p.D219N|AGO3_ENST00000324350.5_Missense_Mutation_p.D219N	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	219					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)	p.D219N(1)									GCTTAATATCGATGGTAAGGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											195	194	194					1																	36439109		2203	4300	6503	36211696	SO:0001583	missense	192669			AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.655G>A	1.37:g.36439109G>A	ENSP00000362287:p.Asp219Asn		36211696	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	G	35	5.512528	0.96402	.	.	ENSG00000126070	ENST00000324350;ENST00000373191;ENST00000397828	T;T;T	0.26373	1.74;2.17;1.74	5.62	5.62	0.85841	Domain of unknown function DUF1785 (1);	0.000000	0.85682	D	0.000000	T	0.51584	0.1683	M	0.64260	1.97	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.987;0.996	T	0.48906	-0.8993	10	0.62326	D	0.03	.	19.6679	0.95900	0.0:0.0:1.0:0.0	.	219;219	Q9H9G7;Q5TA56	AGO3_HUMAN;.	N	219	ENSP00000317425:D219N;ENSP00000362287:D219N;ENSP00000380928:D219N	ENSP00000317425:D219N	D	+	1	0	EIF2C3	36211696	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	9.869000	0.99810	2.650000	0.89964	0.563000	0.77884	GAT		0.423	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		A	36439109	G	A	36439109	3	1	61	1	0	0	0	0	1	0	0	0	5018	1058	37	1	673	1	EIF2C3	1	36439109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53907	36439109	212811512	175	8160										
ADPRHL2	54936	broad.mit.edu	37	chr1	36558047	36558047	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatggaggagcgtccataCtccagccgcctgaagaagat	13	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36558047C>A	ENST00000373178.4	+	5	756	c.726C>A	c.(724-726)taC>taA	p.Y242*		NM_017825.2	NP_060295.1	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	242						mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(ADP-ribose) glycohydrolase activity (GO:0004649)	p.Y242*(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|pancreas(1)	8		Myeloproliferative disorder(586;0.0393)				AGCGTCCATACTCCAGCCGCC	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											134	136	135					1																	36558047		2203	4300	6503	36330634	SO:0001587	stop_gained	54936			AJ427295	CCDS402.1	1p34.3	2008-02-05			ENSG00000116863	ENSG00000116863			21304	protein-coding gene	gene with protein product		610624				12070318, 16278211	Standard	NM_017825		Approved	ARH3, FLJ20446	uc001bzt.3	Q9NX46	OTTHUMG00000007628	ENST00000373178.4:c.726C>A	1.37:g.36558047C>A	ENSP00000362273:p.Tyr242*		36330634	Q53G94|Q6IAB8|Q9BY47	Nonsense_Mutation	SNP	ENST00000373178.4	37	CCDS402.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247473	0.80024	.	.	ENSG00000116863	ENST00000373178;ENST00000540867;ENST00000543954	.	.	.	5.55	3.68	0.42216	.	0.185047	0.48767	D	0.000168	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7852	8.201	0.31424	0.0:0.7558:0.0:0.2442	.	.	.	.	X	242;162;88	.	ENSP00000362273:Y242X	Y	+	3	2	ADPRHL2	36330634	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	1.196000	0.32198	1.352000	0.45808	0.650000	0.86243	TAC		0.597	ADPRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020199.1	NM_017825		A	36558047	C	A	36558047	4	1	61	1	0	0	0	0	0	1	0	0	333	576	20	2	744	2	ADPRHL2	1	36558047	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118938	36558047	212692574	176	8161										
THRAP3	9967	broad.mit.edu	37	chr1	36748247	36748247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcgttctcgttcattttCgaagtctcggtcccgaagcc	8	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36748247C>T	ENST00000354618.5	+	3	307	c.83C>T	c.(82-84)tCg>tTg	p.S28L	THRAP3_ENST00000469141.2_Missense_Mutation_p.S28L	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	28	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.S28L(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CGTTCATTTTCGAAGTCTCGG	0.463			T	USP6	aneurysmal bone cysts																																Pancreas(129;785 1795 20938 23278 32581)		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	1	Substitution - Missense(1)	large_intestine(1)	1											123	109	114					1																	36748247		2203	4300	6503	36520834	SO:0001583	missense	9967			AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.83C>T	1.37:g.36748247C>T	ENSP00000346634:p.Ser28Leu		36520834	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966000	0.92855	.	.	ENSG00000054118	ENST00000354618;ENST00000469141;ENST00000478853	T;T	0.15718	2.4;2.4	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000008	T	0.40423	0.1116	L	0.55481	1.735	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.03863	-1.0997	10	0.72032	D	0.01	-3.9561	19.3309	0.94288	0.0:1.0:0.0:0.0	.	28	Q9Y2W1	TR150_HUMAN	L	28	ENSP00000346634:S28L;ENSP00000433825:S28L	ENSP00000346634:S28L	S	+	2	0	THRAP3	36520834	0.999000	0.42202	0.995000	0.50966	0.990000	0.78478	5.282000	0.65615	2.880000	0.98712	0.650000	0.86243	TCG		0.463	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		T	36748247	C	T	36748247	3	4	61	1	0	0	0	0	1	0	0	0	15913	893	31	1	85	1	THRAP3	1	36748247	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	190200	36748247	212502374	177	8162										
STK40	83931	broad.mit.edu	37	chr1	36808981	36808981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctcctgggagctatccGcattgctcatttggtcatca	8	13	4	0	rs534849916		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:36808981G>A	ENST00000373129.3	-	11	1479	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V	STK40_ENST00000373132.3_Missense_Mutation_p.A358V|STK40_ENST00000373130.3_Missense_Mutation_p.A363V|STK40_ENST00000359297.2_Missense_Mutation_p.A358V	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	358					glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A358V(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				GGAGCTATCCGCATTGCTCAT	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	1											83	71	75					1																	36808981		2203	4300	6503	36581568	SO:0001583	missense	83931			BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.1073C>T	1.37:g.36808981G>A	ENSP00000362221:p.Ala358Val		36581568	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	.	.	.	.	.	.	.	.	.	.	G	7.014	0.557405	0.13436	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.62941	-0.01;1.99;1.99;-0.01	5.05	4.13	0.48395	Protein kinase-like domain (1);	0.426382	0.27442	N	0.019345	T	0.40094	0.1103	N	0.08118	0	0.09310	N	1	B;B;B	0.16396	0.017;0.0;0.0	B;B;B	0.09377	0.004;0.0;0.0	T	0.17440	-1.0369	10	0.26408	T	0.33	-1.1334	12.2012	0.54326	0.1497:0.0:0.8502:0.0	.	358;363;358	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	V	358;358;363;358	ENSP00000362221:A358V;ENSP00000352245:A358V;ENSP00000362222:A363V;ENSP00000362224:A358V	ENSP00000352245:A358V	A	-	2	0	STK40	36581568	0.963000	0.33076	0.011000	0.14972	0.658000	0.38924	3.387000	0.52501	0.649000	0.30751	-0.797000	0.03246	GCG		0.617	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		A	36808981	G	A	36808981	3	1	61	1	0	0	0	0	1	0	0	0	15346	1087	38	1	242	1	STK40	1	36808981	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60734	36808981	212441640	178	8163										
GRIK3	2899	broad.mit.edu	37	chr1	37270752	37270752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaggacacccgctgccccGccaccacttctccttcatga	6	20	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:37270752G>A	ENST00000373091.3	-	15	2417	c.2401C>T	c.(2401-2403)Cgg>Tgg	p.R801W	GRIK3_ENST00000373093.4_Missense_Mutation_p.R801W	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	801					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.R801W(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CCGCTGCCCCGCCACCACTTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	64	63					1																	37270752		2203	4300	6503	37043339	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.2401C>T	1.37:g.37270752G>A	ENSP00000362183:p.Arg801Trp		37043339	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724256	0.68959	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.11712	2.75;2.75	4.59	1.34	0.21922	Ionotropic glutamate receptor (2);	0.281781	0.33180	N	0.005194	T	0.25158	0.0611	M	0.69823	2.125	0.41159	D	0.986089	D;D	0.76494	0.999;0.999	D;D	0.63703	0.917;0.917	T	0.01436	-1.1355	10	0.87932	D	0	.	9.3998	0.38426	0.0:0.1309:0.4682:0.4009	.	801;801	A9Z1Z8;Q13003	.;GRIK3_HUMAN	W	801	ENSP00000362183:R801W;ENSP00000362185:R801W	ENSP00000362183:R801W	R	-	1	2	GRIK3	37043339	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.088000	0.41663	0.330000	0.23485	0.551000	0.68910	CGG		0.602	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37270752	G	A	37270752	3	1	61	1	0	0	0	0	1	0	0	0	6796	1086	38	1	366	1	GRIK3	1	37270752	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	461771	37270752	211979869	179	8164										
GRIK3	2899	broad.mit.edu	37	chr1	37291299	37291299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattgaggaaggagaagacGctggggttggtgccattggg	20	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:37291299G>A	ENST00000373091.3	-	11	1675	c.1659C>T	c.(1657-1659)agC>agT	p.S553S	GRIK3_ENST00000373093.4_Silent_p.S553S	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	553					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.S553S(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				AGGAGAAGACGCTGGGGTTGG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											125	123	124					1																	37291299		2203	4300	6503	37063886	SO:0001819	synonymous_variant	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1659C>T	1.37:g.37291299G>A			37063886	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																				0.552	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37291299	G	A	37291299	2	1	61	1	0	0	0	0	0	0	0	1	6796	1078	38	1		1	GRIK3	1	37291299	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20547	37291299	211959322	180	8165										
GRIK3	2899	broad.mit.edu	37	chr1	37307417	37307417	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgccgtcctccaccagccGgatctcataggagaaaccaa	8	15	1	1	rs371692662		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:37307417G>A	ENST00000373091.3	-	10	1466	c.1450C>T	c.(1450-1452)Cgg>Tgg	p.R484W	GRIK3_ENST00000373093.4_Missense_Mutation_p.R484W	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	484					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.R484W(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				TCCACCAGCCGGATCTCATAG	0.567													G|||	1	0.000199681	0	0	5008	,	,		21145	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	180	166	171		1450	3.9	1	1		171	0,8600		0,0,4300	no	missense	GRIK3	NM_000831.3	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	484/920	37307417	1,13005	2203	4300	6503	37080004	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1450C>T	1.37:g.37307417G>A	ENSP00000362183:p.Arg484Trp		37080004	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605085	0.66445	2.27E-4	0.0	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.11930	2.73;2.73	4.86	3.94	0.45596	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.41673	0.1169	M	0.89414	3.03	0.42266	D	0.992034	D;D	0.76494	0.999;0.999	D;D	0.64776	0.929;0.929	T	0.55451	-0.8139	10	0.87932	D	0	.	14.8476	0.70272	0.0:0.0:0.8551:0.1449	.	484;484	A9Z1Z8;Q13003	.;GRIK3_HUMAN	W	484	ENSP00000362183:R484W;ENSP00000362185:R484W	ENSP00000362183:R484W	R	-	1	2	GRIK3	37080004	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	5.756000	0.68757	1.155000	0.42497	0.591000	0.81541	CGG		0.567	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37307417	G	A	37307417	3	1	61	1	0	0	0	0	1	0	0	0	6796	1115	39	1	1337	1	GRIK3	1	37307417	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16118	37307417	211943204	181	8166										
RSPO1	284654	broad.mit.edu	37	chr1	38082190	38082190	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcggggttgcgggcgtcGaagtatccaggtgggcagga	19	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:38082190G>A	ENST00000401069.1	-	4	964	c.252C>T	c.(250-252)ttC>ttT	p.F84F	RSPO1_ENST00000373059.1_Silent_p.F57F|RSPO1_ENST00000401071.2_Silent_p.F84F|RSPO1_ENST00000356545.2_Silent_p.F84F|RSPO1_ENST00000401068.1_Silent_p.F84F|RSPO1_ENST00000401070.1_Silent_p.F84F	NM_001242908.1	NP_001229837.1	Q2MKA7	RSPO1_HUMAN	R-spondin 1	84					canonical Wnt signaling pathway (GO:0060070)|male meiosis (GO:0007140)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of gene expression (GO:0010468)|regulation of male germ cell proliferation (GO:2000254)|regulation of receptor internalization (GO:0002090)	extracellular space (GO:0005615)|nucleus (GO:0005634)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.F84F(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGCGGGCGTCGAAGTATCCAG	0.617																																					GBM(122;680 2230 27822 42821)											1	Substitution - coding silent(1)	large_intestine(1)	1											54	58	56					1																	38082190		2024	4173	6197	37854777	SO:0001819	synonymous_variant	284654			AK098225	CCDS41304.1, CCDS55590.1, CCDS55591.1	1p34.2	2014-01-30	2011-06-29		ENSG00000169218	ENSG00000169218		"Endogenous ligands"	21679	protein-coding gene	gene with protein product		609595	"R-spondin homolog (Xenopus laevis)"				Standard	NM_001038633		Approved	FLJ40906, RSPONDIN	uc001cbm.2	Q2MKA7	OTTHUMG00000004321	ENST00000401069.1:c.252C>T	1.37:g.38082190G>A			37854777	A2A420|Q0H8S6|Q14C72|Q5T0F2|Q8N7L5	Silent	SNP	ENST00000401069.1	37	CCDS41304.1																																																																																				0.617	RSPO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012477.2	NM_173640		A	38082190	G	A	38082190	2	1	61	1	0	0	0	0	0	0	0	1	13746	1049	37	1		1	RSPO1	1	38082190	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	774773	38082190	211168431	182	8167										
MTF1	4520	broad.mit.edu	37	chr1	38281185	38281185	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacactgacatgcctcttCttgtttgatgatgatcacag	8	10	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:38281185C>A	ENST00000373036.4	-	11	2025	c.1885G>T	c.(1885-1887)Gaa>Taa	p.E629*		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	629					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.E629*(1)		endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CATGCCTCTTCTTGTTTGATG	0.582																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											57	57	57					1																	38281185		2203	4300	6503	38053772	SO:0001587	stop_gained	4520			BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1885G>T	1.37:g.38281185C>A	ENSP00000362127:p.Glu629*		38053772	B2RAK6|Q96CB1	Nonsense_Mutation	SNP	ENST00000373036.4	37	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	C	38	6.680742	0.97759	.	.	ENSG00000188786	ENST00000373036	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.3748	0.98911	0.0:1.0:0.0:0.0	.	.	.	.	X	629	.	ENSP00000362127:E629X	E	-	1	0	MTF1	38053772	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.408000	0.80041	2.817000	0.96982	0.563000	0.77884	GAA		0.582	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		A	38281185	C	A	38281185	4	1	61	1	0	0	0	0	0	1	0	0	9952	922	32	2	380	2	MTF1	1	38281185	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	198995	38281185	210969436	183	8168										
RRAGC	64121	broad.mit.edu	37	chr1	39318142	39318142	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaatattgaatggtcataGatactagtcagataaaagct	7	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39318142G>T	ENST00000373001.3	-	4	836	c.660C>A	c.(658-660)atC>atA	p.I220I		NM_022157.2	NP_071440.1			Ras-related GTP binding C									p.I220I(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				AATGGTCATAGATACTAGTCA	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	1											105	113	110					1																	39318142		2203	4299	6502	39090729	SO:0001819	synonymous_variant	64121			AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.660C>A	1.37:g.39318142G>T			39090729		Silent	SNP	ENST00000373001.3	37	CCDS430.1																																																																																				0.294	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157		T	39318142	G	T	39318142	2	4	61	1	0	0	0	0	0	0	0	1	13711	932	33	2		2	RRAGC	1	39318142	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1036957	39318142	209932479	184	8169										
RRAGC	64121	broad.mit.edu	37	chr1	39322619	39322619	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatagtcaaaggttgggtCaaaaaagtccatttgcccag	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39322619C>A	ENST00000373001.3	-	2	549	c.373G>T	c.(373-375)Gac>Tac	p.D125Y		NM_022157.2	NP_071440.1			Ras-related GTP binding C									p.D125Y(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				AAGGTTGGGTCAAAAAAGTCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	136	136					1																	39322619		2203	4300	6503	39095206	SO:0001583	missense	64121			AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.373G>T	1.37:g.39322619C>A	ENSP00000362092:p.Asp125Tyr		39095206		Missense_Mutation	SNP	ENST00000373001.3	37	CCDS430.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834806	0.91036	.	.	ENSG00000116954	ENST00000373001	D	0.82803	-1.65	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.93213	0.7838	M	0.89904	3.07	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.79108	0.992;0.978;0.923	D	0.93704	0.7018	10	0.87932	D	0	-22.639	20.2625	0.98452	0.0:1.0:0.0:0.0	.	91;59;125	E7ENI3;D3DPT8;Q9HB90	.;.;RRAGC_HUMAN	Y	125	ENSP00000362092:D125Y	ENSP00000362092:D125Y	D	-	1	0	RRAGC	39095206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.782000	0.95742	0.557000	0.71058	GAC		0.398	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157		A	39322619	C	A	39322619	3	1	61	1	0	0	0	0	1	0	0	0	13711	826	29	2	850	2	RRAGC	1	39322619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4477	39322619	209928002	185	8170										
MYCBP	26292	broad.mit.edu	37	chr1	39332608	39332608	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatacttctctttcatttCggccagttctaggcgaagca	7	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39332608C>T	ENST00000397572.2	-	4	1010	c.211G>A	c.(211-213)Gaa>Aaa	p.E71K	RP5-864K19.4_ENST00000433671.2_RNA|GJA9_ENST00000454994.2_3'UTR|MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000456813.1_RNA	NM_012333.4	NP_036465.2	Q99417	MYCBP_HUMAN	MYC binding protein	71					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.E71K(1)		large_intestine(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)				TCTTTCATTTCGGCCAGTTCT	0.308																																					Esophageal Squamous(155;912 1855 21572 25911 44247)											1	Substitution - Missense(1)	large_intestine(1)	1											59	57	58					1																	39332608		2202	4300	6502	39105195	SO:0001583	missense	26292			AB007191	CCDS431.1	1p33-p32.2	2013-07-09	2013-07-09		ENSG00000214114	ENSG00000214114			7554	protein-coding gene	gene with protein product	"associate of myc-1"	606535	"c-myc binding protein"			9797456	Standard	NM_012333		Approved	AMY-1	uc001ccs.3	Q99417	OTTHUMG00000000484	ENST00000397572.2:c.211G>A	1.37:g.39332608C>T	ENSP00000380702:p.Glu71Lys		39105195	B2R4N0|Q5TA64|Q96HE2	Missense_Mutation	SNP	ENST00000397572.2	37	CCDS431.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.581361	0.86748	.	.	ENSG00000214114	ENST00000397572	.	.	.	5.38	5.38	0.77491	.	0.214786	0.38111	U	0.001809	T	0.45617	0.1351	L	0.29908	0.895	0.80722	D	1	D	0.53619	0.961	B	0.42692	0.395	T	0.38585	-0.9654	9	0.33141	T	0.24	-5.4576	19.127	0.93390	0.0:1.0:0.0:0.0	.	71	Q99417	MYCBP_HUMAN	K	71	.	ENSP00000380702:E71K	E	-	1	0	MYCBP	39105195	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.718000	0.54919	2.511000	0.84671	0.655000	0.94253	GAA		0.308	MYCBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001209.1	NM_012333		T	39332608	C	T	39332608	3	4	61	1	0	0	0	0	1	0	0	0	10047	893	31	1	108	1	MYCBP	1	39332608	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9989	39332608	209918013	186	8171										
GJA9	81025	broad.mit.edu	37	chr1	39340876	39340876	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagaagatgaatttaaacTagggtacactgcagtgtgtg	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39340876T>G	ENST00000360786.3	-	1	1147	c.895A>C	c.(895-897)Agt>Cgt	p.S299R	MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Missense_Mutation_p.S299R|RP5-864K19.4_ENST00000433671.2_RNA|GJA9_ENST00000454994.2_Missense_Mutation_p.S299R|MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|RP5-864K19.4_ENST00000456813.1_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	299					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.S299R(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GAATTTAAACTAGGGTACACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	101	101					1																	39340876		2203	4300	6503	39113463	SO:0001583	missense	81025			AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"Ion channels / Gap junction proteins (connexins)"	19155	protein-coding gene	gene with protein product	"connexin 59"	611923	"gap junction protein, alpha 10, 59kDa"	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.895A>C	1.37:g.39340876T>G	ENSP00000354020:p.Ser299Arg		39113463	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	.	.	.	.	.	.	.	.	.	.	T	9.483	1.098686	0.20552	.	.	ENSG00000131233	ENST00000454994;ENST00000357771;ENST00000360786	D;D;D	0.97665	-4.48;-4.4;-4.4	4.72	-0.249	0.13011	.	2.234430	0.02228	U	0.064609	D	0.91570	0.7337	N	0.19112	0.55	0.09310	N	1	B	0.29805	0.257	B	0.23852	0.049	D	0.86347	0.1708	10	0.17369	T	0.5	.	4.3924	0.11346	0.0:0.2896:0.392:0.3184	.	299	P57773	CXA9_HUMAN	R	299	ENSP00000406846:S299R;ENSP00000350415:S299R;ENSP00000354020:S299R	ENSP00000350415:S299R	S	-	1	0	GJA9	39113463	0.186000	0.23225	0.015000	0.15790	0.208000	0.24298	0.514000	0.22786	0.045000	0.15804	-0.291000	0.09656	AGT		0.388	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772		G	39340876	T	G	39340876	3	3	61	1	0	0	0	0	1	0	0	0	6426	1522	53	4	656	4	GJA9	1	39340876	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8268	39340876	209909745	187	8172										
NDUFS5	4725	broad.mit.edu	37	chr1	39494580	39494580	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcaagatagaatatgatGatttcgtagagtgtttgctt	11	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39494580G>T	ENST00000372969.3	+	2	271	c.184G>T	c.(184-186)Gat>Tat	p.D62Y	NDUFS5_ENST00000372967.3_Missense_Mutation_p.D62Y	NM_004552.2	NP_004543.1	O43920	NDUS5_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH-coenzyme Q reductase)	62					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.D62Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.93e-18)			AGAATATGATGATTTCGTAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	112	114					1																	39494580		2203	4300	6503	39267167	SO:0001583	missense	4725			AF047434	CCDS434.1	1p34.2-p33	2011-07-04	2002-08-29		ENSG00000168653	ENSG00000168653		"Mitochondrial respiratory chain complex / Complex I"	7712	protein-coding gene	gene with protein product	"complex I 51kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 5"	603847	"NADH dehydrogenase (ubiquinone) Fe-S protein 5 (15kD) (NADH-coenzyme Q reductase)"			9763677, 9653160	Standard	NM_004552		Approved	CI-15k	uc001ccy.3	O43920	OTTHUMG00000007497	ENST00000372969.3:c.184G>T	1.37:g.39494580G>T	ENSP00000362060:p.Asp62Tyr		39267167		Missense_Mutation	SNP	ENST00000372969.3	37	CCDS434.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.133494	0.37630	.	.	ENSG00000168653	ENST00000372969;ENST00000372967	D;D	0.83250	-1.7;-1.7	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.83755	0.5323	M	0.70275	2.135	0.80722	D	1	B	0.18968	0.032	B	0.23419	0.046	T	0.80489	-0.1360	10	0.59425	D	0.04	-18.0242	17.3691	0.87371	0.0:0.0:1.0:0.0	.	62	O43920	NDUS5_HUMAN	Y	62	ENSP00000362060:D62Y;ENSP00000362058:D62Y	ENSP00000362058:D62Y	D	+	1	0	NDUFS5	39267167	1.000000	0.71417	0.269000	0.24586	0.252000	0.25951	8.387000	0.90167	2.711000	0.92665	0.655000	0.94253	GAT		0.398	NDUFS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019688.1	NM_004552		T	39494580	G	T	39494580	3	4	61	1	0	0	0	0	1	0	0	0	10326	1290	45	2	186	2	NDUFS5	1	39494580	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153704	39494580	209756041	188	8173										
NDUFS5	4725	broad.mit.edu	37	chr1	39500070	39500070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcctttgacagatgagaCgtgcaggtaccatcaggaag	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39500070C>T	ENST00000372969.3	+	3	310	c.223C>T	c.(223-225)Cgt>Tgt	p.R75C	NDUFS5_ENST00000372967.3_Missense_Mutation_p.R75C	NM_004552.2	NP_004543.1	O43920	NDUS5_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH-coenzyme Q reductase)	75					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R75C(1)		endometrium(1)|kidney(1)|large_intestine(2)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.93e-18)			ACAGATGAGACGTGCAGGTAC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	62	63					1																	39500070		2203	4300	6503	39272657	SO:0001583	missense	4725			AF047434	CCDS434.1	1p34.2-p33	2011-07-04	2002-08-29		ENSG00000168653	ENSG00000168653		"Mitochondrial respiratory chain complex / Complex I"	7712	protein-coding gene	gene with protein product	"complex I 51kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 5"	603847	"NADH dehydrogenase (ubiquinone) Fe-S protein 5 (15kD) (NADH-coenzyme Q reductase)"			9763677, 9653160	Standard	NM_004552		Approved	CI-15k	uc001ccy.3	O43920	OTTHUMG00000007497	ENST00000372969.3:c.223C>T	1.37:g.39500070C>T	ENSP00000362060:p.Arg75Cys		39272657		Missense_Mutation	SNP	ENST00000372969.3	37	CCDS434.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864411	0.32977	.	.	ENSG00000168653	ENST00000372969;ENST00000372967	D;D	0.82893	-1.66;-1.66	5.65	4.72	0.59763	.	0.053612	0.64402	N	0.000001	T	0.80581	0.4650	M	0.69248	2.105	0.54753	D	0.999989	B	0.20671	0.047	B	0.16722	0.016	T	0.77159	-0.2690	10	0.48119	T	0.1	-18.5847	11.509	0.50483	0.3255:0.6745:0.0:0.0	.	75	O43920	NDUS5_HUMAN	C	75	ENSP00000362060:R75C;ENSP00000362058:R75C	ENSP00000362058:R75C	R	+	1	0	NDUFS5	39272657	0.985000	0.35326	0.040000	0.18447	0.016000	0.09150	2.361000	0.44160	1.349000	0.45751	0.655000	0.94253	CGT		0.453	NDUFS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019688.1	NM_004552		T	39500070	C	T	39500070	3	4	61	1	0	0	0	0	1	0	0	0	10326	536	19	1	229	1	NDUFS5	1	39500070	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5490	39500070	209750551	189	8174										
MACF1	23499	broad.mit.edu	37	chr1	39749132	39749132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaatcacttatgtgtcttCgatttatgatgccttcccta	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39749132C>T	ENST00000372915.3	+	8	962	c.875C>T	c.(874-876)tCg>tTg	p.S292L	MACF1_ENST00000317713.7_Missense_Mutation_p.S292L|MACF1_ENST00000361689.2_Missense_Mutation_p.S292L|MACF1_ENST00000545844.1_Missense_Mutation_p.S292L|MACF1_ENST00000567887.1_Missense_Mutation_p.S324L|MACF1_ENST00000564288.1_Missense_Mutation_p.S287L|MACF1_ENST00000539005.1_Missense_Mutation_p.S292L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	292	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S292L(2)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			TATGTGTCTTCGATTTATGAT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	1											170	151	158					1																	39749132		2203	4300	6503	39521719	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.875C>T	1.37:g.39749132C>T	ENSP00000362006:p.Ser292Leu		39521719	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	33	5.220972	0.95139	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65;-3.65;-3.65;-3.65	5.56	5.56	0.83823	.	.	.	.	.	D	0.94231	0.8148	L	0.47078	1.49	0.80722	D	1	B;D	0.64830	0.159;0.994	B;P	0.48873	0.023;0.593	D	0.94724	0.7903	9	0.87932	D	0	.	19.5461	0.95297	0.0:1.0:0.0:0.0	.	292;257	F8W8Q1;Q9UPN3-3	.;.	L	292;292;292;308;292;292;250;441;452	ENSP00000439537:S292L;ENSP00000362006:S292L;ENSP00000354573:S292L;ENSP00000313438:S292L;ENSP00000444364:S292L;ENSP00000435070:S250L;ENSP00000437059:S441L	ENSP00000313438:S292L	S	+	2	0	MACF1	39521719	1.000000	0.71417	0.964000	0.40570	0.977000	0.68977	7.818000	0.86416	2.626000	0.88956	0.585000	0.79938	TCG		0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39749132	C	T	39749132	3	4	61	1	0	0	0	0	1	0	0	0	9174	893	31	1	905	1	MACF1	1	39749132	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	249062	39749132	209501489	190	8175										
MACF1	23499	broad.mit.edu	37	chr1	39759288	39759288	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagccaagagaaattacttCtctgtgagtctagcacagta	8	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39759288C>A	ENST00000372915.3	+	17	2253	c.2166C>A	c.(2164-2166)ttC>ttA	p.F722L	MACF1_ENST00000317713.7_Missense_Mutation_p.F722L|MACF1_ENST00000361689.2_Missense_Mutation_p.F722L|MACF1_ENST00000545844.1_Missense_Mutation_p.F722L|MACF1_ENST00000567887.1_Missense_Mutation_p.F754L|MACF1_ENST00000564288.1_Missense_Mutation_p.F717L|MACF1_ENST00000539005.1_Missense_Mutation_p.F722L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	722					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.F722L(2)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			GAAATTACTTCTCTGTGAGTC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	1											122	109	114					1																	39759288		2203	4300	6503	39531875	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.2166C>A	1.37:g.39759288C>A	ENSP00000362006:p.Phe722Leu		39531875	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	16.81	3.226364	0.58668	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	T;T;T;T;T;T;T	0.65916	-0.18;-0.11;-0.18;-0.18;-0.18;-0.18;-0.18	5.63	4.72	0.59763	.	.	.	.	.	T	0.63034	0.2477	L	0.59436	1.845	0.80722	D	1	B;P	0.41313	0.046;0.745	B;P	0.47376	0.037;0.545	T	0.58912	-0.7552	9	0.20519	T	0.43	.	11.0104	0.47659	0.0:0.8578:0.0:0.1422	.	722;687	F8W8Q1;Q9UPN3-3	.;.	L	722;722;722;722;722;680;871;882	ENSP00000439537:F722L;ENSP00000362006:F722L;ENSP00000354573:F722L;ENSP00000313438:F722L;ENSP00000444364:F722L;ENSP00000435070:F680L;ENSP00000437059:F871L	ENSP00000313438:F722L	F	+	3	2	MACF1	39531875	0.993000	0.37304	1.000000	0.80357	0.984000	0.73092	0.798000	0.27014	1.533000	0.49186	-0.140000	0.14226	TTC		0.468	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39759288	C	A	39759288	3	1	61	1	0	0	0	0	1	0	0	0	9174	912	32	2	2232	2	MACF1	1	39759288	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10156	39759288	209491333	191	8176										
MACF1	23499	broad.mit.edu	37	chr1	39788323	39788323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaaggcctttgtggaatCgcagcagaaatcccctggca	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39788323C>T	ENST00000372915.3	+	31	4175	c.4088C>T	c.(4087-4089)tCg>tTg	p.S1363L	MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.S1363L|MACF1_ENST00000361689.2_Missense_Mutation_p.S1363L|MACF1_ENST00000545844.1_Missense_Mutation_p.S1363L|MACF1_ENST00000567887.1_Missense_Mutation_p.S1395L|MACF1_ENST00000564288.1_Missense_Mutation_p.S1358L|MACF1_ENST00000539005.1_Missense_Mutation_p.S1363L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1363					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S1363L(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			TTTGTGGAATCGCAGCAGAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	122	121					1																	39788323		2203	4300	6503	39560910	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.4088C>T	1.37:g.39788323C>T	ENSP00000362006:p.Ser1363Leu		39560910	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	36	5.815257	0.96982	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262	T;T;T;T;T;T;T	0.63744	-0.03;-0.05;-0.03;-0.06;0.13;1.83;1.83	5.92	5.92	0.95590	.	.	.	.	.	T	0.79516	0.4459	M	0.72894	2.215	0.80722	D	1	D;D;B	0.76494	0.999;0.998;0.254	D;P;B	0.68943	0.961;0.889;0.058	T	0.79776	-0.1661	9	0.72032	D	0.01	.	20.3325	0.98724	0.0:1.0:0.0:0.0	.	1363;1363;1328	F8W8Q1;Q9UPN3-2;Q9UPN3-3	.;.;.	L	1363;1363;1363;1363;1363;1321;1512	ENSP00000439537:S1363L;ENSP00000362006:S1363L;ENSP00000354573:S1363L;ENSP00000313438:S1363L;ENSP00000444364:S1363L;ENSP00000435070:S1321L;ENSP00000437059:S1512L	ENSP00000313438:S1363L	S	+	2	0	MACF1	39560910	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.760000	0.85248	2.805000	0.96524	0.655000	0.94253	TCG		0.463	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39788323	C	T	39788323	3	4	61	1	0	0	0	0	1	0	0	0	9174	893	31	1	4210	1	MACF1	1	39788323	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29035	39788323	209462298	192	8177										
MACF1	23499	broad.mit.edu	37	chr1	39799244	39799244	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgtgaagcttatggagaaGctgaacatgtttcaggggtt	14	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39799244G>A	ENST00000372915.3	+	36	7086	c.6999G>A	c.(6997-6999)aaG>aaA	p.K2333K	MACF1_ENST00000476350.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Silent_p.K768K|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Silent_p.K2365K|MACF1_ENST00000564288.1_Silent_p.K2328K|MACF1_ENST00000539005.1_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	2333					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.K768K(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			TTATGGAGAAGCTGAACATGT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	1											77	78	78					1																	39799244		2203	4300	6503	39571831	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.6999G>A	1.37:g.39799244G>A			39571831	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																					0.403	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39799244	G	A	39799244	2	1	61	1	0	0	0	0	0	0	0	1	9174	962	34	3		3	MACF1	1	39799244	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10921	39799244	209451377	193	8178										
MACF1	23499	broad.mit.edu	37	chr1	39851197	39851197	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaggccctggagatgtctCtctgtccaccagccaagtac	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39851197C>A	ENST00000372915.3	+	56	14042	c.13955C>A	c.(13954-13956)tCt>tAt	p.S4652Y	MACF1_ENST00000317713.7_Missense_Mutation_p.S2585Y|MACF1_ENST00000361689.2_Missense_Mutation_p.S2585Y|MACF1_ENST00000289893.4_Missense_Mutation_p.S3087Y|MACF1_ENST00000545844.1_Missense_Mutation_p.S2585Y|MACF1_ENST00000567887.1_Missense_Mutation_p.S4684Y|MACF1_ENST00000564288.1_Missense_Mutation_p.S4647Y|MACF1_ENST00000539005.1_Missense_Mutation_p.S2564Y			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4652					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S2585Y(1)|p.S3087Y(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			GGAGATGTCTCTCTGTCCACC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	1											61	53	56					1																	39851197		2203	4300	6503	39623784	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13955C>A	1.37:g.39851197C>A	ENSP00000362006:p.Ser4652Tyr		39623784	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	15.84	2.951157	0.53186	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.66815	-0.2;-0.16;-0.2;-0.23;-0.02;0.94	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000010	T	0.79919	0.4529	L	0.51422	1.61	0.80722	D	1	D;P;D	0.76494	0.999;0.886;0.989	D;D;D	0.81914	0.995;0.947;0.923	T	0.78234	-0.2283	10	0.59425	D	0.04	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	4652;2585;2529	Q9UPN3;F8W8Q1;Q9UPN3-3	MACF1_HUMAN;.;.	Y	2585;4652;2585;2585;2564;3087	ENSP00000439537:S2585Y;ENSP00000362006:S4652Y;ENSP00000354573:S2585Y;ENSP00000313438:S2585Y;ENSP00000444364:S2564Y;ENSP00000289893:S3087Y	ENSP00000289893:S3087Y	S	+	2	0	MACF1	39623784	1.000000	0.71417	0.995000	0.50966	0.820000	0.46376	5.452000	0.66638	2.941000	0.99782	0.655000	0.94253	TCT		0.478	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39851197	C	A	39851197	3	1	61	1	0	0	0	0	1	0	0	0	9174	913	32	2	14111	2	MACF1	1	39851197	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51953	39851197	209399424	194	8179										
MACF1	23499	broad.mit.edu	37	chr1	39853455	39853455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagatgaggatggaatcCgggatgagaaggctgggatc	17	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39853455C>T	ENST00000372915.3	+	57	15043	c.14956C>T	c.(14956-14958)Cgg>Tgg	p.R4986W	MACF1_ENST00000317713.7_Missense_Mutation_p.R2919W|MACF1_ENST00000361689.2_Missense_Mutation_p.R2919W|MACF1_ENST00000289893.4_Missense_Mutation_p.R3421W|MACF1_ENST00000545844.1_Missense_Mutation_p.R2919W|MACF1_ENST00000567887.1_Missense_Mutation_p.R5018W|MACF1_ENST00000564288.1_Missense_Mutation_p.R4981W|MACF1_ENST00000539005.1_Missense_Mutation_p.R2898W			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4986					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.R2919W(1)|p.R3421W(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			GGATGGAATCCGGGATGAGAA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	1											62	64	63					1																	39853455		2203	4300	6503	39626042	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.14956C>T	1.37:g.39853455C>T	ENSP00000362006:p.Arg4986Trp		39626042	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.69|15.69	2.908862|2.908862	0.52439|0.52439	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.52295	.|0.67;0.67;0.67;0.67;0.67;0.67	6.17|6.17	5.26|5.26	0.73747|0.73747	.|.	.|0.000000	.|0.56097	.|D	.|0.000027	T|T	0.62588|0.62588	0.2440|0.2440	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.79784	.|0.993;0.982;0.982	T|T	0.65541|0.65541	-0.6143|-0.6143	5|10	.|0.87932	.|D	.|0	.|.	10.3681|10.3681	0.44038|0.44038	0.1358:0.7979:0.0:0.0663|0.1358:0.7979:0.0:0.0663	.|.	.|4986;2919;2863	.|Q9UPN3;F8W8Q1;Q9UPN3-3	.|MACF1_HUMAN;.;.	L|W	2031|2919;4986;2919;2919;2898;3421	.|ENSP00000439537:R2919W;ENSP00000362006:R4986W;ENSP00000354573:R2919W;ENSP00000313438:R2919W;ENSP00000444364:R2898W;ENSP00000289893:R3421W	.|ENSP00000289893:R3421W	P|R	+|+	2|1	0|2	MACF1|MACF1	39626042|39626042	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.933000|0.933000	0.57130|0.57130	2.490000|2.490000	0.45294|0.45294	1.615000|1.615000	0.50252|0.50252	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.493	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39853455	C	T	39853455	3	4	61	1	0	0	0	0	1	0	0	0	9174	643	23	1	15116	1	MACF1	1	39853455	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2258	39853455	209397166	195	8180										
KIAA0754	643314	broad.mit.edu	37	chr1	39877258	39877258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactgctcaggggttagagGgacttgtttcagattcagca	13	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39877258G>A	ENST00000530275.1	+	1	1108	c.913G>A	c.(913-915)Gga>Aga	p.G305R	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	305								p.G305R(1)		central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			GGGGTTAGAGGGACTTGTTTC	0.468											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											168	163	165					1																	39877258		1951	4152	6103	39649845	SO:0001583	missense	643314					1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.913G>A	1.37:g.39877258G>A	ENSP00000431179:p.Gly305Arg	889	39649845	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	G	9.195	1.027048	0.19512	.	.	ENSG00000255103	ENST00000530275	D	0.85629	-2.01	4.41	-2.41	0.06562	.	.	.	.	.	T	0.71508	0.3348	N	0.19112	0.55	0.09310	N	1	B	0.18461	0.028	B	0.19946	0.027	T	0.59952	-0.7357	9	0.87932	D	0	.	6.0916	0.19997	0.3796:0.2264:0.394:0.0	.	305	O94854	K0754_HUMAN	R	305	ENSP00000431179:G305R	ENSP00000431179:G305R	G	+	1	0	RP4-562N20.1	39649845	0.077000	0.21312	0.000000	0.03702	0.009000	0.06853	0.451000	0.21779	-0.328000	0.08539	-0.136000	0.14681	GGA		0.468	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		A	39877258	G	A	39877258	3	1	61	1	0	0	0	0	1	0	0	0	8213	1233	43	3	1323	3	KIAA0754	1	39877258	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23803	39877258	209373363	196	8181										
KIAA0754	643314	broad.mit.edu	37	chr1	39877571	39877571	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattttaataccctggattCttctcaggtgcctaatgctg	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39877571C>A	ENST00000530275.1	+	1	1421	c.1226C>A	c.(1225-1227)tCt>tAt	p.S409Y	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	409								p.S409Y(1)		central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			ACCCTGGATTCTTCTCAGGTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	94	95					1																	39877571		1879	4121	6000	39650158	SO:0001583	missense	643314					1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.1226C>A	1.37:g.39877571C>A	ENSP00000431179:p.Ser409Tyr		39650158	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	C	16.61	3.171192	0.57584	.	.	ENSG00000255103	ENST00000530275	D	0.86865	-2.18	5.2	2.14	0.27477	.	.	.	.	.	D	0.82962	0.5151	N	0.24115	0.695	0.20873	N	0.99984	D	0.55605	0.972	P	0.55222	0.771	T	0.71984	-0.4427	9	0.87932	D	0	.	3.635	0.08146	0.1245:0.4827:0.2926:0.1002	.	409	O94854	K0754_HUMAN	Y	409	ENSP00000431179:S409Y	ENSP00000431179:S409Y	S	+	2	0	RP4-562N20.1	39650158	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.197000	0.32211	0.558000	0.29135	0.655000	0.94253	TCT		0.413	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		A	39877571	C	A	39877571	3	1	61	1	0	0	0	0	1	0	0	0	8213	913	32	2	1636	2	KIAA0754	1	39877571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	313	39877571	209373050	197	8182										
KIAA0754	643314	broad.mit.edu	37	chr1	39880083	39880083	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtatttggcataaaagaGgtgaccagcacagtgctaca	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39880083G>T	ENST00000530275.1	+	1	3933	c.3738G>T	c.(3736-3738)gaG>gaT	p.E1246D	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1246								p.E1246D(1)		central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			GCATAAAAGAGGTGACCAGCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	62	61					1																	39880083		2004	4192	6196	39652670	SO:0001583	missense	643314					1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3738G>T	1.37:g.39880083G>T	ENSP00000431179:p.Glu1246Asp		39652670	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	G	13.82	2.351930	0.41700	.	.	ENSG00000127603;ENSG00000255103	ENST00000482035;ENST00000530275	T;T	0.36699	1.36;1.24	4.8	2.92	0.33932	.	.	.	.	.	T	0.36580	0.0972	N	0.24115	0.695	0.18873	N	0.999983	D	0.60160	0.987	P	0.56916	0.809	T	0.12426	-1.0548	9	0.87932	D	0	.	7.6027	0.28085	0.1981:0.0:0.8019:0.0	.	1246	O94854	K0754_HUMAN	D	4;1246	ENSP00000433104:E4D;ENSP00000431179:E1246D	ENSP00000431179:E1246D	E	+	3	2	MACF1;RP4-562N20.1	39652670	0.286000	0.24305	1.000000	0.80357	0.490000	0.33462	0.230000	0.17852	0.571000	0.29365	0.643000	0.83706	GAG		0.463	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39880083	G	T	39880083	3	4	61	1	0	0	0	0	1	0	0	0	8213	991	35	2	4148	2	KIAA0754	1	39880083	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2512	39880083	209370538	198	8183										
MACF1	23499	broad.mit.edu	37	chr1	39893237	39893237	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcttgctaactcagaacCtgttggcactcagactgcca	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:39893237C>A	ENST00000372915.3	+	61	16529	c.16442C>A	c.(16441-16443)cCt>cAt	p.P5481H	MACF1_ENST00000317713.7_Missense_Mutation_p.P3414H|MACF1_ENST00000361689.2_Missense_Mutation_p.P3414H|MACF1_ENST00000289893.4_Missense_Mutation_p.P3916H|MACF1_ENST00000545844.1_Missense_Mutation_p.P3414H|MACF1_ENST00000567887.1_Missense_Mutation_p.P5513H|MACF1_ENST00000564288.1_Missense_Mutation_p.P5476H|MACF1_ENST00000539005.1_Missense_Mutation_p.P3393H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5481					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.P3414H(1)|p.P3916H(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			AACTCAGAACCTGTTGGCACT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	1											108	112	111					1																	39893237		2203	4300	6503	39665824	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.16442C>A	1.37:g.39893237C>A	ENSP00000362006:p.Pro5481His		39665824	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	25.9	4.682363	0.88542	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893;ENST00000482035	T;T;T;T;T;T;T	0.50813	1.21;1.21;1.21;1.21;1.21;1.21;0.73	5.7	5.7	0.88788	.	0.000000	0.56097	D	0.000021	T	0.71913	0.3396	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	0.999;1.0;0.995	T	0.74044	-0.3791	10	0.72032	D	0.01	.	19.8305	0.96632	0.0:1.0:0.0:0.0	.	5481;3414;3358	Q9UPN3;F8W8Q1;Q9UPN3-3	MACF1_HUMAN;.;.	H	3414;5481;3414;3414;3393;3916;230	ENSP00000439537:P3414H;ENSP00000362006:P5481H;ENSP00000354573:P3414H;ENSP00000313438:P3414H;ENSP00000444364:P3393H;ENSP00000289893:P3916H;ENSP00000433104:P230H	ENSP00000289893:P3916H	P	+	2	0	MACF1	39665824	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.692000	0.91855	0.557000	0.71058	CCT		0.433	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39893237	C	A	39893237	3	1	61	1	0	0	0	0	1	0	0	0	9174	681	24	2	16618	2	MACF1	1	39893237	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13154	39893237	209357384	199	8184										
HEYL	26508	broad.mit.edu	37	chr1	40098379	40098379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggtggacagcggcctgGccatctggctggaaaggaaa	18	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40098379G>A	ENST00000372852.3	-	2	408	c.89C>T	c.(88-90)gCc>gTc	p.A30V	HEYL_ENST00000535435.1_Missense_Mutation_p.A2V|RP1-144F13.3_ENST00000424418.1_RNA	NM_014571.3	NP_055386	Q9NQ87	HEYL_HUMAN	hes-related family bHLH transcription factor with YRPW motif-like	30					atrioventricular valve morphogenesis (GO:0003181)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to BMP stimulus (GO:0071773)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|glomerulus development (GO:0032835)|mesenchymal cell development (GO:0014031)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|pulmonary valve morphogenesis (GO:0003184)|skeletal muscle cell differentiation (GO:0035914)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-1 domain binding (GO:0050683)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A30V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGCGGCCTGGCCATCTGGCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	141	138					1																	40098379		2203	4300	6503	39870966	SO:0001583	missense	26508			BC006087	CCDS439.1	1p34.3	2013-10-17	2013-10-17		ENSG00000163909	ENSG00000163909		"Basic helix-loop-helix proteins"	4882	protein-coding gene	gene with protein product	"hairy/enhancer-of-split related with YRPW motif 3"	609034	"hairy/enhancer-of-split related with YRPW motif-like"			10415358, 10860664	Standard	NM_014571		Approved	bHLHb33, HEY3, HESR3	uc001cdp.3	Q9NQ87	OTTHUMG00000000458	ENST00000372852.3:c.89C>T	1.37:g.40098379G>A	ENSP00000361943:p.Ala30Val		39870966	Q5TG99	Missense_Mutation	SNP	ENST00000372852.3	37	CCDS439.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717827	0.48622	.	.	ENSG00000163909	ENST00000372852;ENST00000535435	T;T	0.60424	0.32;0.19	4.88	4.88	0.63580	.	0.412070	0.24745	N	0.035955	T	0.46927	0.1418	L	0.36672	1.1	0.80722	D	1	B	0.25563	0.129	B	0.23419	0.046	T	0.34775	-0.9815	10	0.16896	T	0.51	-32.3265	15.6176	0.76780	0.0:0.0:1.0:0.0	.	30	Q9NQ87	HEYL_HUMAN	V	30;2	ENSP00000361943:A30V;ENSP00000439071:A2V	ENSP00000361943:A30V	A	-	2	0	HEYL	39870966	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.657000	0.67996	2.632000	0.89209	0.591000	0.81541	GCC		0.607	HEYL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001179.2	NM_014571		A	40098379	G	A	40098379	3	1	61	1	0	0	0	0	1	0	0	0	7101	1203	42	3	913	3	HEYL	1	40098379	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205142	40098379	209152242	200	8185										
TRIT1	54802	broad.mit.edu	37	chr1	40318514	40318514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttttcaagctccacttttCggtcaatcactttctcagtg	5	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40318514C>T	ENST00000316891.5	-	4	463	c.449G>A	c.(448-450)cGa>cAa	p.R150Q	TRIT1_ENST00000545233.1_Intron|TRIT1_ENST00000544981.1_Intron|TRIT1_ENST00000441669.2_Missense_Mutation_p.R70Q|TRIT1_ENST00000491865.1_Intron|TRIT1_ENST00000541099.1_Intron|TRIT1_ENST00000372818.1_Missense_Mutation_p.R150Q|TRIT1_ENST00000537440.1_Intron|TRIT1_ENST00000537223.1_Intron	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	150					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)	p.R150Q(1)		breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CTCCACTTTTCGGTCAATCAC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											257	239	245					1																	40318514		2203	4300	6503	40091101	SO:0001583	missense	54802			AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.449G>A	1.37:g.40318514C>T	ENSP00000321810:p.Arg150Gln		40091101	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Missense_Mutation	SNP	ENST00000316891.5	37	CCDS30681.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361262	0.61403	.	.	ENSG00000043514	ENST00000046894;ENST00000372825;ENST00000441669;ENST00000316891;ENST00000372818	T;T	0.44881	0.91;0.93	5.07	3.15	0.36227	.	0.093792	0.64402	D	0.000001	T	0.46560	0.1399	L	0.39467	1.215	0.80722	D	1	P;P;D	0.76494	0.467;0.476;0.999	B;B;P	0.62740	0.19;0.119;0.906	T	0.23691	-1.0181	10	0.17369	T	0.5	-3.4015	10.1895	0.43017	0.1356:0.7925:0.0:0.0718	.	150;150;70	Q9H3H1;Q9H3H1-4;Q9H3H1-5	MOD5_HUMAN;.;.	Q	150;70;64;150;150	ENSP00000321810:R150Q;ENSP00000361905:R150Q	ENSP00000046894:R150Q	R	-	2	0	TRIT1	40091101	0.990000	0.36364	0.998000	0.56505	0.808000	0.45660	0.951000	0.29135	0.606000	0.29965	0.467000	0.42956	CGA		0.463	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646		T	40318514	C	T	40318514	3	4	61	1	0	0	0	0	1	0	0	0	16600	884	31	1	986	1	TRIT1	1	40318514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220135	40318514	208932107	201	8186										
CAP1	10487	broad.mit.edu	37	chr1	40531973	40531973	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggagttccataccaccgGactggcctggagcaaaacgg	12	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40531973G>A	ENST00000372797.3	+	7	1172	c.611G>A	c.(610-612)gGa>gAa	p.G204E	CAP1_ENST00000340450.3_Missense_Mutation_p.G203E|CAP1_ENST00000372792.2_Missense_Mutation_p.G204E|CAP1_ENST00000372798.1_Missense_Mutation_p.G203E|CAP1_ENST00000372802.1_Missense_Mutation_p.G203E|CAP1_ENST00000372805.3_Missense_Mutation_p.G204E	NM_001105530.1|NM_006367.3	NP_001099000|NP_006358	Q13114	TRAF3_HUMAN	CAP, adenylate cyclase-associated protein 1 (yeast)	0					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G204E(1)		endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	Lung NSC(20;5.03e-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;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CATACCACCGGACTGGCCTGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	73	74					1																	40531973		1922	4112	6034	40304560	SO:0001583	missense	10487			L12168	CCDS41309.1	1p34.3	2010-07-13			ENSG00000131236	ENSG00000131236			20040	protein-coding gene	gene with protein product						1406678, 8761950	Standard	NM_006367		Approved	CAP	uc001cey.4	Q01518	OTTHUMG00000004493	ENST00000372797.3:c.611G>A	1.37:g.40531973G>A	ENSP00000361883:p.Gly204Glu		40304560	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000372797.3	37	CCDS41309.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585911	0.86748	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000414893;ENST00000414281;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805;ENST00000435719;ENST00000372794;ENST00000427843	T;T;T;T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21	4.12	4.12	0.48240	Adenylate cyclase-associated CAP, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.69061	0.3069	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79546	-0.1759	10	0.87932	D	0	-20.3066	15.5427	0.76066	0.0:0.0:1.0:0.0	.	151;204	E7ENY9;Q01518	.;CAP1_HUMAN	E	204;203;55;204;204;181;203;203;204;203;55;204	ENSP00000361883:G204E;ENSP00000361888:G203E;ENSP00000398877:G55E;ENSP00000408561:G204E;ENSP00000361878:G204E;ENSP00000361884:G203E;ENSP00000344832:G203E;ENSP00000361891:G204E;ENSP00000412859:G203E;ENSP00000413656:G204E	ENSP00000344832:G203E	G	+	2	0	CAP1	40304560	1.000000	0.71417	0.984000	0.44739	0.963000	0.63663	9.657000	0.98554	2.145000	0.66743	0.484000	0.47621	GGA		0.493	CAP1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000013109.1	NM_006367		A	40531973	G	A	40531973	3	1	61	1	0	0	0	0	1	0	0	0	2625	1174	41	3	633	3	CAP1	1	40531973	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213459	40531973	208718648	202	8187										
RLF	6018	broad.mit.edu	37	chr1	40702536	40702536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtgtacttactgtcgacGacattttatgtctgcttttc	8	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40702536G>A	ENST00000372771.4	+	8	2189	c.2162G>A	c.(2161-2163)cGa>cAa	p.R721Q		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	721					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R721Q(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TACTGTCGACGACATTTTATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	123	122					1																	40702536		2203	4300	6503	40475123	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.2162G>A	1.37:g.40702536G>A	ENSP00000361857:p.Arg721Gln		40475123	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.712684	0.68730	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.37915	1.17	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.053610	0.64402	D	0.000001	T	0.58779	0.2146	L	0.50333	1.59	0.47037	D	0.999298	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.974	T	0.55134	-0.8188	10	0.72032	D	0.01	-8.4301	20.8794	0.99867	0.0:0.0:1.0:0.0	.	414;721	F5H2M5;Q13129	.;RLF_HUMAN	Q	721;414	ENSP00000361857:R721Q	ENSP00000361857:R721Q	R	+	2	0	RLF	40475123	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	7.544000	0.82117	2.941000	0.99782	0.655000	0.94253	CGA		0.388	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40702536	G	A	40702536	3	1	61	1	0	0	0	0	1	0	0	0	13426	1058	37	1	2192	1	RLF	1	40702536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170563	40702536	208548085	203	8188										
RLF	6018	broad.mit.edu	37	chr1	40702807	40702807	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttggctgtaaaaagttCtattactccaaaattgaata	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40702807C>A	ENST00000372771.4	+	8	2460	c.2433C>A	c.(2431-2433)ttC>ttA	p.F811L		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	811					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.F811L(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			GTAAAAAGTTCTATTACTCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	73	74					1																	40702807		2203	4300	6503	40475394	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.2433C>A	1.37:g.40702807C>A	ENSP00000361857:p.Phe811Leu		40475394	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693453	0.48202	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.14266	2.52	6.13	5.22	0.72569	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.043821	0.85682	D	0.000000	T	0.23886	0.0578	L	0.52266	1.64	0.53005	D	0.99996	P;D	0.67145	0.705;0.996	P;P	0.57620	0.692;0.824	T	0.00041	-1.2231	10	0.41790	T	0.15	-11.1299	11.1476	0.48440	0.0:0.8497:0.0:0.1503	.	504;811	F5H2M5;Q13129	.;RLF_HUMAN	L	811;504	ENSP00000361857:F811L	ENSP00000361857:F811L	F	+	3	2	RLF	40475394	0.725000	0.28048	1.000000	0.80357	0.995000	0.86356	-0.105000	0.10907	2.937000	0.99478	0.650000	0.86243	TTC		0.368	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40702807	C	A	40702807	3	1	61	1	0	0	0	0	1	0	0	0	13426	912	32	2	2463	2	RLF	1	40702807	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271	40702807	208547814	204	8189										
RLF	6018	broad.mit.edu	37	chr1	40705582	40705582	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcatagttcagggcaagaAaacactgtaaaaaatccaac	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40705582A>C	ENST00000372771.4	+	8	5235	c.5208A>C	c.(5206-5208)gaA>gaC	p.E1736D		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1736					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1736D(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			CAGGGCAAGAAAACACTGTAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											48	49	49					1																	40705582		2200	4290	6490	40478169	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.5208A>C	1.37:g.40705582A>C	ENSP00000361857:p.Glu1736Asp		40478169	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	A	7.640	0.680700	0.14907	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.14266	2.52	5.87	4.68	0.58851	.	0.276672	0.39407	N	0.001376	T	0.08313	0.0207	L	0.29908	0.895	0.28757	N	0.901098	B;B	0.14805	0.011;0.006	B;B	0.12156	0.007;0.003	T	0.13548	-1.0505	10	0.27082	T	0.32	-21.2595	3.3689	0.07213	0.6426:0.1428:0.0776:0.137	.	1429;1736	F5H2M5;Q13129	.;RLF_HUMAN	D	1736;1429	ENSP00000361857:E1736D	ENSP00000361857:E1736D	E	+	3	2	RLF	40478169	0.998000	0.40836	1.000000	0.80357	0.951000	0.60555	0.509000	0.22707	2.371000	0.80710	0.533000	0.62120	GAA		0.408	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		C	40705582	A	C	40705582	3	2	61	1	0	0	0	0	1	0	0	0	13426	11	1	4	5238	4	RLF	1	40705582	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2775	40705582	208545039	205	8190										
RLF	6018	broad.mit.edu	37	chr1	40705883	40705883	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccagtgactctacaattCatgagaacctgactgcaatc	6	12	2	3	rs201181495		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40705883C>A	ENST00000372771.4	+	8	5536	c.5509C>A	c.(5509-5511)Cat>Aat	p.H1837N		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1837					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.H1837N(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			CTCTACAATTCATGAGAACCT	0.398													C|||	1	0.000199681	0	0	5008	,	,		20483	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											134	131	132					1																	40705883		2203	4300	6503	40478470	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.5509C>A	1.37:g.40705883C>A	ENSP00000361857:p.His1837Asn		40478470	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	6.976	0.550093	0.13374	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.13901	2.55	5.35	3.42	0.39159	.	0.342769	0.30329	N	0.009861	T	0.10121	0.0248	L	0.29908	0.895	0.27781	N	0.943163	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15636	-1.0430	10	0.38643	T	0.18	-3.1162	10.0787	0.42377	0.1371:0.7895:0.0:0.0734	.	1530;1837	F5H2M5;Q13129	.;RLF_HUMAN	N	1837;1530	ENSP00000361857:H1837N	ENSP00000361857:H1837N	H	+	1	0	RLF	40478470	0.999000	0.42202	1.000000	0.80357	0.965000	0.64279	1.223000	0.32527	0.897000	0.36392	0.655000	0.94253	CAT		0.398	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40705883	C	A	40705883	3	1	61	1	0	0	0	0	1	0	0	0	13426	826	29	2	5539	2	RLF	1	40705883	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	301	40705883	208544738	206	8191										
SMAP2	64744	broad.mit.edu	37	chr1	40878691	40878691	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttaaatcattatagaaaGaaaaagatgacaagtggaaa	8	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40878691G>T	ENST00000539317.1	+	5	359	c.166G>T	c.(166-168)Gaa>Taa	p.E56*		NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2	136	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.E136*(1)		central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			ATTATAGAAAGAAAAAGATGA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											56	57	57					1																	40878691		2203	4300	6503	40651278	SO:0001587	stop_gained	64744			AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"ADP-ribosylation factor GTPase activating proteins"	25082	protein-coding gene	gene with protein product			"stromal membrane-associated protein 1-like", "stromal membrane-associated GTPase-activating protein 2"	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.166G>T	1.37:g.40878691G>T	ENSP00000442835:p.Glu56*		40651278	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Nonsense_Mutation	SNP	ENST00000539317.1	37	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	G	41	8.554656	0.98861	.	.	ENSG00000084070	ENST00000435168;ENST00000372718;ENST00000372708;ENST00000539317	.	.	.	5.5	5.5	0.81552	.	0.244121	0.48286	D	0.000195	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-20.602	17.2513	0.87043	0.0:0.0:1.0:0.0	.	.	.	.	X	136;136;106;56	.	ENSP00000361793:E106X	E	+	1	0	SMAP2	40651278	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.694000	0.74587	2.732000	0.93576	0.650000	0.86243	GAA		0.378	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733		T	40878691	G	T	40878691	4	4	61	1	0	0	0	0	0	1	0	0	14804	943	33	2	424	2	SMAP2	1	40878691	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172808	40878691	208371930	207	8192										
ZNF643	65243	broad.mit.edu	37	chr1	40929056	40929056	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctttctatccatcagaGagtccatactggagtaaaac	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40929056G>T	ENST00000411995.2	+	6	1775	c.1400G>T	c.(1399-1401)aGa>aTa	p.R467I	ZFP69B_ENST00000361584.3_Missense_Mutation_p.R365I|ZFP69B_ENST00000484445.1_3'UTR|RP1-228H13.5_ENST00000565390.1_RNA	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	467					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R365I(1)									ATCCATCAGAGAGTCCATACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	92	92					1																	40929056		2203	4300	6503	40701643	SO:0001583	missense	65243			BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"Zinc fingers, C2H2-type", "-", "-", "-"	28053	protein-coding gene	gene with protein product			"zinc finger protein 643"	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.1400G>T	1.37:g.40929056G>T	ENSP00000399664:p.Arg467Ile		40701643	Q5QPL4	Missense_Mutation	SNP	ENST00000411995.2	37	CCDS452.2	.	.	.	.	.	.	.	.	.	.	.	17.40	3.379401	0.61845	.	.	ENSG00000187801	ENST00000431552;ENST00000411995;ENST00000361584	T;T	0.24908	1.83;1.83	3.14	1.04	0.20106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22551	0.0544	L	0.61036	1.89	0.47374	D	0.999408	B	0.12630	0.006	B	0.08055	0.003	T	0.07252	-1.0782	9	0.59425	D	0.04	.	5.0782	0.14642	0.1249:0.4273:0.4478:0.0	.	467	Q9UJL9	ZN643_HUMAN	I	398;467;365	ENSP00000399664:R467I;ENSP00000354547:R365I	ENSP00000354547:R365I	R	+	2	0	ZNF643	40701643	0.000000	0.05858	0.987000	0.45799	0.998000	0.95712	0.819000	0.27308	0.277000	0.22141	0.655000	0.94253	AGA		0.393	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070		T	40929056	G	T	40929056	3	4	61	1	0	0	0	0	1	0	0	0	18098	942	33	2	1418	2	ZNF643	1	40929056	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50365	40929056	208321565	208	8193										
ZNF642	339559	broad.mit.edu	37	chr1	40947510	40947510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtgacccctggactccCgacagcagaatcccaggtga	11	13	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:40947510C>T	ENST00000372706.1	+	3	1209	c.203C>T	c.(202-204)cCg>cTg	p.P68L	ZFP69_ENST00000372705.3_Missense_Mutation_p.P68L			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	68					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P68L(1)									CCTGGACTCCCGACAGCAGAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	87	89					1																	40947510		2203	4300	6503	40720097	SO:0001583	missense	339559			AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.203C>T	1.37:g.40947510C>T	ENSP00000361791:p.Pro68Leu		40720097	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	37	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.059672	0.00386	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	T;T	0.04275	3.66;3.66	3.55	-7.09	0.01553	.	1.510010	0.04554	N	0.390438	T	0.01800	0.0057	N	0.04805	-0.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41179	-0.9523	10	0.05525	T	0.97	6.4787	5.1678	0.15094	0.1072:0.165:0.1062:0.6216	.	68	Q49AA0	ZN642_HUMAN	L	68	ENSP00000361791:P68L;ENSP00000361790:P68L	ENSP00000361790:P68L	P	+	2	0	ZNF642	40720097	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.865000	0.01649	-2.578000	0.00464	-1.002000	0.02502	CCG		0.483	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		T	40947510	C	T	40947510	3	4	61	1	0	0	0	0	1	0	0	0	18097	652	23	1	209	1	ZNF642	1	40947510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18454	40947510	208303111	209	8194										
KCNQ4	9132	broad.mit.edu	37	chr1	41304024	41304024	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggacctgctgttgggcttCtattcgcgctgcctgcgctc	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:41304024C>A	ENST00000347132.5	+	14	1999	c.1917C>A	c.(1915-1917)ttC>ttA	p.F639L	KCNQ4_ENST00000509682.2_Missense_Mutation_p.F585L|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	639	A-domain (Tetramerization).				inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.F639L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	TGTTGGGCTTCTATTCGCGCT	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	89	88					1																	41304024		2203	4299	6502	41076611	SO:0001583	missense	9132			AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1917C>A	1.37:g.41304024C>A	ENSP00000262916:p.Phe639Leu		41076611	O96025	Missense_Mutation	SNP	ENST00000347132.5	37	CCDS456.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.23|12.23	1.875049|1.875049	0.33162|0.33162	.|.	.|.	ENSG00000117013|ENSG00000117013	ENST00000347132;ENST00000509682|ENST00000443478	D;D|.	0.99563|.	-6.17;-6.17|.	4.79|4.79	4.79|4.79	0.61399|0.61399	Potassium channel, voltage dependent, KCNQ, C-terminal (1);|.	0.138160|.	0.48286|.	D|.	0.000185|.	T|T	0.31389|0.31389	0.0795|0.0795	N|N	0.02315|0.02315	-0.6|-0.6	0.40907|0.40907	D|D	0.984206|0.984206	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.12156|.	0.001;0.007|.	T|T	0.30060|0.30060	-0.9991|-0.9991	10|5	0.31617|.	T|.	0.26|.	-23.3328|-23.3328	15.3194|15.3194	0.74109|0.74109	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	585;639|.	P56696-2;P56696|.	.;KCNQ4_HUMAN|.	L|I	639;585|500	ENSP00000262916:F639L;ENSP00000423756:F585L|.	ENSP00000262916:F639L|.	F|L	+|+	3|1	2|2	KCNQ4|KCNQ4	41076611|41076611	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.928000|0.928000	0.56348|0.56348	2.624000|2.624000	0.46444|0.46444	2.218000|2.218000	0.71995|0.71995	0.313000|0.313000	0.20887|0.20887	TTC|CTA		0.701	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700		A	41304024	C	A	41304024	3	1	61	1	0	0	0	0	1	0	0	0	8106	912	32	2	1971	2	KCNQ4	1	41304024	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	356514	41304024	207946597	210	8195										
SCMH1	22955	broad.mit.edu	37	chr1	41540934	41540934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctttgggaatttcaaaGgttcagctgtcttggatggg	12	6	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:41540934G>T	ENST00000326197.7	-	8	1204	c.905C>A	c.(904-906)cCt>cAt	p.P302H	SCMH1_ENST00000372596.1_Missense_Mutation_p.P241H|SCMH1_ENST00000397171.2_Missense_Mutation_p.P241H|SCMH1_ENST00000372597.1_Missense_Mutation_p.P255H|SCMH1_ENST00000372595.1_Missense_Mutation_p.P241H|SCMH1_ENST00000397174.2_Missense_Mutation_p.P282H|SCMH1_ENST00000402904.2_Missense_Mutation_p.P302H|SCMH1_ENST00000456518.2_Missense_Mutation_p.P144H|SCMH1_ENST00000361191.5_Missense_Mutation_p.P241H|SCMH1_ENST00000337495.5_Missense_Mutation_p.P312H|SCMH1_ENST00000361705.3_Missense_Mutation_p.P255H					sex comb on midleg homolog 1 (Drosophila)									p.P255H(1)|p.P312H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				GAATTTCAAAGGTTCAGCTGT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	1											142	140	141					1																	41540934		2203	4300	6503	41313521	SO:0001583	missense	22955			AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.905C>A	1.37:g.41540934G>T	ENSP00000318094:p.Pro302His		41313521		Missense_Mutation	SNP	ENST00000326197.7	37	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.922353	0.73213	.	.	ENSG00000010803	ENST00000361705;ENST00000456518;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	T;T;T;T;T;T;T;T;T;T;T	0.23950	2.19;1.88;2.18;2.21;2.2;2.2;2.19;2.2;2.2;2.18;2.18	5.29	5.29	0.74685	.	0.310219	0.32244	N	0.006370	T	0.50786	0.1636	M	0.65498	2.005	0.49798	D	0.999828	B;B;D;D	0.89917	0.003;0.005;1.0;1.0	B;B;D;D	0.91635	0.003;0.007;0.999;0.981	T	0.45249	-0.9274	10	0.48119	T	0.1	.	17.8562	0.88764	0.0:0.0:1.0:0.0	.	144;312;255;302	B4DRQ8;Q96GD3-2;Q96GD3-4;Q96GD3	.;.;.;SCMH1_HUMAN	H	255;144;302;282;241;241;255;241;312;241;302	ENSP00000354996:P255H;ENSP00000403974:P144H;ENSP00000386079:P302H;ENSP00000380359:P282H;ENSP00000380356:P241H;ENSP00000354656:P241H;ENSP00000361678:P255H;ENSP00000361677:P241H;ENSP00000337352:P312H;ENSP00000361676:P241H;ENSP00000318094:P302H	ENSP00000318094:P302H	P	-	2	0	SCMH1	41313521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.058000	0.76676	2.640000	0.89533	0.609000	0.83330	CCT		0.517	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			T	41540934	G	T	41540934	3	4	61	1	0	0	0	0	1	0	0	0	13945	1000	35	2	1109	2	SCMH1	1	41540934	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236910	41540934	207709687	211	8196										
SCMH1	22955	broad.mit.edu	37	chr1	41579028	41579028	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagatgtctcgggagtcGaagcggcaccagtagtcaaa	15	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:41579028G>A	ENST00000326197.7	-	7	941	c.642C>T	c.(640-642)ttC>ttT	p.F214F	SCMH1_ENST00000337495.5_Silent_p.F224F|SCMH1_ENST00000361705.3_Silent_p.F167F|SCMH1_ENST00000397174.2_Silent_p.F194F|SCMH1_ENST00000372597.1_Silent_p.F167F|SCMH1_ENST00000361191.5_Silent_p.F153F|SCMH1_ENST00000402904.2_Silent_p.F214F|SCMH1_ENST00000397171.2_Silent_p.F153F|SCMH1_ENST00000372596.1_Silent_p.F153F|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000372595.1_Silent_p.F153F					sex comb on midleg homolog 1 (Drosophila)									p.F167F(1)|p.F224F(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CTCGGGAGTCGAAGCGGCACC	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	1											111	108	109					1																	41579028		2203	4300	6503	41351615	SO:0001819	synonymous_variant	22955			AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.642C>T	1.37:g.41579028G>A			41351615		Silent	SNP	ENST00000326197.7	37	CCDS30688.1																																																																																				0.562	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			A	41579028	G	A	41579028	2	1	61	1	0	0	0	0	0	0	0	1	13945	1049	37	1		1	SCMH1	1	41579028	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38094	41579028	207671593	212	8197										
HIVEP3	59269	broad.mit.edu	37	chr1	41990505	41990505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgctgggcttcttgcagcGaattccacactcctcacaaa	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:41990505G>A	ENST00000372583.1	-	6	6169	c.5284C>T	c.(5284-5286)Cgc>Tgc	p.R1762C	HIVEP3_ENST00000372584.1_Missense_Mutation_p.R1762C|HIVEP3_ENST00000460604.1_Intron|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R1762C|HIVEP3_ENST00000429157.2_Missense_Mutation_p.R1762C	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1762	ZAS2.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1762C(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TTCTTGCAGCGAATTCCACAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											177	140	153					1																	41990505		2203	4300	6503	41763092	SO:0001583	missense	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5284C>T	1.37:g.41990505G>A	ENSP00000361664:p.Arg1762Cys		41763092	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025928	0.93518	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000105	T	0.59555	0.2202	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.65602	-0.6128	10	0.87932	D	0	-18.96	17.7486	0.88428	0.0:0.0:1.0:0.0	.	1762;1762	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	C	1762	ENSP00000361665:R1762C;ENSP00000361664:R1762C;ENSP00000247584:R1762C;ENSP00000410828:R1762C	ENSP00000247584:R1762C	R	-	1	0	HIVEP3	41763092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.601000	0.98297	2.520000	0.84964	0.561000	0.74099	CGC		0.493	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	41990505	G	A	41990505	3	1	61	1	0	0	0	0	1	0	0	0	7209	1058	37	1	1952	1	HIVEP3	1	41990505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	411477	41990505	207260116	213	8198										
HIVEP3	59269	broad.mit.edu	37	chr1	42041223	42041223	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgagtcttaccctccttcGaagattttgatcctcgccgg	8	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:42041223G>A	ENST00000372583.1	-	5	6084	c.5199C>T	c.(5197-5199)ttC>ttT	p.F1733F	HIVEP3_ENST00000372584.1_Silent_p.F1733F|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000247584.5_Silent_p.F1733F|HIVEP3_ENST00000429157.2_Silent_p.F1733F	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1733					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F1733F(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ACCCTCCTTCGAAGATTTTGA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											179	190	186					1																	42041223		2203	4300	6503	41813810	SO:0001819	synonymous_variant	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5199C>T	1.37:g.42041223G>A			41813810	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																				0.552	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	42041223	G	A	42041223	2	1	61	1	0	0	0	0	0	0	0	1	7209	1049	37	1		1	HIVEP3	1	42041223	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50718	42041223	207209398	214	8199										
FOXJ3	22887	broad.mit.edu	37	chr1	42693634	42693634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgtctattgcccagtaggAcccctagaggtaaagaaatt	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:42693634A>G	ENST00000372572.1	-	7	759	c.448T>C	c.(448-450)Tcc>Ccc	p.S150P	FOXJ3_ENST00000361346.1_Missense_Mutation_p.S150P|FOXJ3_ENST00000372573.1_Missense_Mutation_p.S150P|FOXJ3_ENST00000361776.1_Missense_Mutation_p.S150P|FOXJ3_ENST00000545068.1_Missense_Mutation_p.S150P	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	150					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S150P(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCCCAGTAGGACCCCTAGAGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1																																								42466221	SO:0001583	missense	22887			AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"Forkhead boxes"	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.448T>C	1.37:g.42693634A>G	ENSP00000361653:p.Ser150Pro		42466221	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	37	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.264898	0.80358	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886	D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	5.68	5.68	0.88126	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.97955	0.9327	M	0.89840	3.065	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.993	D	0.98853	1.0759	10	0.87932	D	0	.	13.8795	0.63674	1.0:0.0:0.0:0.0	.	150;150	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	P	150	ENSP00000361654:S150P;ENSP00000361653:S150P;ENSP00000354620:S150P;ENSP00000354449:S150P;ENSP00000439044:S150P;ENSP00000393408:S150P	ENSP00000354620:S150P	S	-	1	0	FOXJ3	42466221	1.000000	0.71417	0.972000	0.41901	0.688000	0.40055	7.360000	0.79487	2.153000	0.67306	0.533000	0.62120	TCC		0.388	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		G	42693634	A	G	42693634	3	3	61	1	0	0	0	0	1	0	0	0	6032	275	10	4	1456	4	FOXJ3	1	42693634	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	652411	42693634	206556987	215	8200										
ZMYND12	84217	broad.mit.edu	37	chr1	42902137	42902137	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaactttttaaggtcataGaatatattagccaggtggaa	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:42902137G>A	ENST00000372565.3	-	5	941	c.672C>T	c.(670-672)ttC>ttT	p.F224F	ZMYND12_ENST00000433602.2_Silent_p.F114F|ZMYND12_ENST00000475426.1_5'Flank	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	224						intracellular (GO:0005622)	metal ion binding (GO:0046872)	p.F224F(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TAAGGTCATAGAATATATTAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	1											133	126	128					1																	42902137		2203	4300	6503	42674724	SO:0001819	synonymous_variant	84217			AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"Zinc fingers, MYND-type"	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.672C>T	1.37:g.42902137G>A			42674724	Q5VUS6|Q8TC87|Q96M51	Silent	SNP	ENST00000372565.3	37	CCDS467.1																																																																																				0.448	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257		A	42902137	G	A	42902137	2	1	61	1	0	0	0	0	0	0	0	1	17746	933	33	3		3	ZMYND12	1	42902137	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208503	42902137	206348484	216	8201										
PPCS	79717	broad.mit.edu	37	chr1	42925391	42925391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattgtaattaatcgagctCggaaggctttggaaatttat	9	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:42925391C>T	ENST00000372561.3	+	3	737	c.730C>T	c.(730-732)Cgg>Tgg	p.R244W	PPCS_ENST00000455780.1_Missense_Mutation_p.R71W|PPCS_ENST00000372562.1_Missense_Mutation_p.R71W|PPCS_ENST00000372556.3_3'UTR|PPCS_ENST00000472013.1_3'UTR	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	244					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)	p.R244W(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TAATCGAGCTCGGAAGGCTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	101	102					1																	42925391		1855	4098	5953	42697978	SO:0001583	missense	79717			AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.730C>T	1.37:g.42925391C>T	ENSP00000361642:p.Arg244Trp		42697978	Q3KQT2|Q5VVM0	Missense_Mutation	SNP	ENST00000372561.3	37	CCDS41311.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112146	0.94339	.	.	ENSG00000127125	ENST00000372562;ENST00000455780;ENST00000372561	.	.	.	6.01	6.01	0.97437	DNA/pantothenate metabolism flavoprotein, C-terminal (3);	0.107321	0.64402	D	0.000003	D	0.87313	0.6146	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89663	0.3878	9	0.66056	D	0.02	-7.347	18.015	0.89236	0.0:1.0:0.0:0.0	.	244	Q9HAB8	PPCS_HUMAN	W	71;71;244	.	ENSP00000361642:R244W	R	+	1	2	PPCS	42697978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.404000	0.66344	2.861000	0.98227	0.650000	0.86243	CGG		0.418	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		T	42925391	C	T	42925391	3	4	61	1	0	0	0	0	1	0	0	0	12336	875	31	1	740	1	PPCS	1	42925391	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23254	42925391	206325230	217	8202										
CCDC30	728621	broad.mit.edu	37	chr1	43032078	43032078	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcagctgaaaatgagcttCgatatgaacgagggcagaac	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43032078C>T	ENST00000340612.4	+	5	787	c.787C>T	c.(787-789)Cga>Tga	p.R263*	CCDC30_ENST00000507855.1_Nonsense_Mutation_p.R52*|RNU6-536P_ENST00000363384.1_RNA|CCDC30_ENST00000342022.4_Nonsense_Mutation_p.R263*|CCDC30_ENST00000390640.4_Nonsense_Mutation_p.R52*|CCDC30_ENST00000428554.2_Nonsense_Mutation_p.R263*			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	263						extracellular vesicular exosome (GO:0070062)		p.R263*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						AAATGAGCTTCGATATGAACG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											94	90	91					1																	43032078		2203	4300	6503	42804665	SO:0001587	stop_gained	728621			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.787C>T	1.37:g.43032078C>T	ENSP00000340378:p.Arg263*		42804665	Q14F06|Q5VVM5	Nonsense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.986306	0.93044	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	.	.	.	5.83	4.92	0.64577	.	0.252263	0.39759	N	0.001269	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1432	0.65334	0.1511:0.8489:0.0:0.0	.	.	.	.	X	263;52;263;263;52	.	ENSP00000340378:R263X	R	+	1	2	CCDC30	42804665	0.997000	0.39634	0.999000	0.59377	0.998000	0.95712	1.473000	0.35387	1.455000	0.47813	0.655000	0.94253	CGA		0.408	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		T	43032078	C	T	43032078	4	4	61	1	0	0	0	0	0	1	0	0	2811	876	31	1	805	1	CCDC30	1	43032078	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106687	43032078	206218543	218	8203										
CCDC30	728621	broad.mit.edu	37	chr1	43076721	43076721	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggaagctctacgtgaaGaatatttgcgattattgaag	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43076721G>T	ENST00000340612.4	+	9	1456	c.1456G>T	c.(1456-1458)Gaa>Taa	p.E486*	CCDC30_ENST00000507855.1_Nonsense_Mutation_p.E275*|CCDC30_ENST00000342022.4_Nonsense_Mutation_p.E486*|CCDC30_ENST00000390640.4_Nonsense_Mutation_p.E275*|CCDC30_ENST00000428554.2_Nonsense_Mutation_p.E486*			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	486						extracellular vesicular exosome (GO:0070062)		p.E486*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						TCTACGTGAAGAATATTTGCG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											124	115	118					1																	43076721		2203	4300	6503	42849308	SO:0001587	stop_gained	728621			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1456G>T	1.37:g.43076721G>T	ENSP00000340378:p.Glu486*		42849308	Q14F06|Q5VVM5	Nonsense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.149377	0.37923	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	.	.	.	5.68	2.82	0.32997	.	0.306075	0.37906	N	0.001900	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	7.1413	0.25558	0.2684:0.0:0.7316:0.0	.	.	.	.	X	486;275;486;486;275	.	ENSP00000340378:E486X	E	+	1	0	CCDC30	42849308	0.993000	0.37304	0.060000	0.19600	0.077000	0.17291	0.839000	0.27586	0.757000	0.33036	0.563000	0.77884	GAA		0.363	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		T	43076721	G	T	43076721	4	4	61	1	0	0	0	0	0	1	0	0	2811	943	33	2	1490	2	CCDC30	1	43076721	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44643	43076721	206173900	219	8204										
CCDC30	728621	broad.mit.edu	37	chr1	43111809	43111809	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtttttaaacttagaatCttaaggagtttcctgttcca	6	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43111809C>A	ENST00000340612.4	+	13	1894	c.1894C>A	c.(1894-1896)Ctt>Att	p.L632I	CCDC30_ENST00000507855.1_Missense_Mutation_p.L421I|CCDC30_ENST00000342022.4_Missense_Mutation_p.L632I|CCDC30_ENST00000390640.4_Missense_Mutation_p.L421I|CCDC30_ENST00000428554.2_Missense_Mutation_p.L632I			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	632						extracellular vesicular exosome (GO:0070062)		p.L632I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						AACTTAGAATCTTAAGGAGTt	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											29	30	30					1																	43111809		2203	4299	6502	42884396	SO:0001583	missense	728621			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1894C>A	1.37:g.43111809C>A	ENSP00000340378:p.Leu632Ile		42884396	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	C	6.223	0.409331	0.11812	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.54279	0.58;0.61;0.58;0.58;0.61	1.63	-0.522	0.11928	.	2.530400	0.03167	U	0.170167	T	0.36026	0.0952	L	0.36672	1.1	0.19775	N	0.999954	B;B	0.31730	0.337;0.201	B;B	0.24974	0.057;0.019	T	0.06180	-1.0841	10	0.18276	T	0.48	.	2.8195	0.05467	0.0:0.4932:0.3025:0.2043	.	632;421	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	I	632;421;632;632;421	ENSP00000397035:L632I;ENSP00000426711:L421I;ENSP00000340378:L632I;ENSP00000339280:L632I;ENSP00000375051:L421I	ENSP00000340378:L632I	L	+	1	0	CCDC30	42884396	0.986000	0.35501	0.748000	0.31131	0.233000	0.25261	0.085000	0.14912	-0.130000	0.11599	-0.373000	0.07131	CTT		0.358	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		A	43111809	C	A	43111809	3	1	61	1	0	0	0	0	1	0	0	0	2811	913	32	2	1944	2	CCDC30	1	43111809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35088	43111809	206138812	220	8205										
CCDC30	728621	broad.mit.edu	37	chr1	43111874	43111874	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctctccctccaacaaaGaaacagaaagaaatatacag	5	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43111874G>T	ENST00000340612.4	+	13	1959	c.1959G>T	c.(1957-1959)aaG>aaT	p.K653N	CCDC30_ENST00000507855.1_Missense_Mutation_p.K442N|CCDC30_ENST00000342022.4_Missense_Mutation_p.K653N|CCDC30_ENST00000390640.4_Missense_Mutation_p.K442N|CCDC30_ENST00000428554.2_Missense_Mutation_p.K653N			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	653						extracellular vesicular exosome (GO:0070062)		p.K653N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						ctccaacaaagaaacagaaag	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											43	39	40					1																	43111874		2184	4286	6470	42884461	SO:0001583	missense	728621			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1959G>T	1.37:g.43111874G>T	ENSP00000340378:p.Lys653Asn		42884461	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.045885	0.00398	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	0.427	-0.854	0.10705	.	.	.	.	.	T	0.17066	0.0410	N	0.22421	0.69	0.09310	N	1	P;B	0.42078	0.77;0.0	B;B	0.30251	0.113;0.0	T	0.20140	-1.0284	8	0.12766	T	0.61	.	.	.	.	.	653;442	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	N	653;442;653;653;442	ENSP00000397035:K653N;ENSP00000426711:K442N;ENSP00000340378:K653N;ENSP00000339280:K653N;ENSP00000375051:K442N	ENSP00000340378:K653N	K	+	3	2	CCDC30	42884461	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.316000	0.08071	-0.657000	0.05373	-0.670000	0.03821	AAG		0.418	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		T	43111874	G	T	43111874	3	4	61	1	0	0	0	0	1	0	0	0	2811	933	33	2	2009	2	CCDC30	1	43111874	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65	43111874	206138747	221	8206										
CCDC30	728621	broad.mit.edu	37	chr1	43119620	43119620	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgtgtgttcacagaattCtgaggctggatacataaatg	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43119620C>A	ENST00000340612.4	+	15	2273	c.2273C>A	c.(2272-2274)tCt>tAt	p.S758Y	CCDC30_ENST00000507855.1_Missense_Mutation_p.S547Y|CCDC30_ENST00000342022.4_Missense_Mutation_p.S758Y|CCDC30_ENST00000390640.4_Missense_Mutation_p.S547Y|CCDC30_ENST00000428554.2_Missense_Mutation_p.S758Y			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	758						extracellular vesicular exosome (GO:0070062)		p.S758Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						TCACAGAATTCTGAGGCTGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	76	76					1																	43119620		2203	4300	6503	42892207	SO:0001583	missense	728621			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.2273C>A	1.37:g.43119620C>A	ENSP00000340378:p.Ser758Tyr		42892207	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404045	0.62288	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.53	4.61	0.57282	.	0.102199	0.44097	D	0.000492	T	0.49525	0.1562	L	0.47190	1.495	0.18873	N	0.999981	D;D	0.54047	0.964;0.964	P;P	0.57204	0.815;0.815	T	0.42015	-0.9476	10	0.87932	D	0	.	10.7918	0.46436	0.0:0.9098:0.0:0.0902	.	758;547	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	Y	758;547;758;758;547	ENSP00000397035:S758Y;ENSP00000426711:S547Y;ENSP00000340378:S758Y;ENSP00000339280:S758Y;ENSP00000375051:S547Y	ENSP00000340378:S758Y	S	+	2	0	CCDC30	42892207	0.914000	0.31030	0.887000	0.34795	0.912000	0.54170	1.526000	0.35964	2.597000	0.87782	0.655000	0.94253	TCT		0.408	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		A	43119620	C	A	43119620	3	1	61	1	0	0	0	0	1	0	0	0	2811	913	32	2	2331	2	CCDC30	1	43119620	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7746	43119620	206131001	222	8207										
LEPRE1	64175	broad.mit.edu	37	chr1	43213442	43213442	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataaaagtttccgccatcGaagtccccatttaggtaaag	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43213442G>A	ENST00000296388.5	-	13	1917	c.1866C>T	c.(1864-1866)ttC>ttT	p.F622F	LEPRE1_ENST00000397054.3_Silent_p.F622F|LEPRE1_ENST00000236040.4_Silent_p.F622F|LEPRE1_ENST00000462474.1_5'UTR			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	622	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)	p.F622F(1)		large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TTCCGCCATCGAAGTCCCCAT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											155	154	154					1																	43213442		2203	4300	6503	42986029	SO:0001819	synonymous_variant	64175			AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 1", "growth suppressor 1"	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1866C>T	1.37:g.43213442G>A			42986029	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Silent	SNP	ENST00000296388.5	37	CCDS472.2																																																																																				0.522	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		A	43213442	G	A	43213442	2	1	61	1	0	0	0	0	0	0	0	1	8751	1049	37	1		1	LEPRE1	1	43213442	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93822	43213442	206037179	223	8208										
ERMAP	114625	broad.mit.edu	37	chr1	43302837	43302837	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcctctagacaatcttCtttcagaccatgctaaagaa	4	11	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43302837C>A	ENST00000372517.2	+	7	836	c.592C>A	c.(592-594)Ctt>Att	p.L198I	RP11-342M1.3_ENST00000416809.2_RNA|ERMAP_ENST00000372514.3_Missense_Mutation_p.L198I|ERMAP_ENST00000328249.3_Missense_Mutation_p.L108I|RP11-342M1.3_ENST00000414798.1_RNA|ERMAP_ENST00000487556.1_3'UTR	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	198			Missing (in Sc-3 allele).			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L198I(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGACAATCTTCTTTCAGACCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											146	150	148					1																	43302837		2203	4300	6503	43075424	SO:0001583	missense	114625			AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"Blood group antigens", "Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	15743	protein-coding gene	gene with protein product		609017	"Radin blood group", "Scianna blood group", "erythroblast membrane-associated protein", "erythroblast membrane-associated protein (RD and SC blood groups)"	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.592C>A	1.37:g.43302837C>A	ENSP00000361595:p.Leu198Ile		43075424	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Missense_Mutation	SNP	ENST00000372517.2	37	CCDS475.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691591	0.68271	.	.	ENSG00000164010	ENST00000372517;ENST00000372514;ENST00000328249	T;T;T	0.54071	0.84;0.84;0.59	5.24	5.24	0.73138	.	0.130984	0.33631	N	0.004709	T	0.67239	0.2872	L	0.57536	1.79	0.33816	D	0.628501	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.987	T	0.72427	-0.4297	10	0.33141	T	0.24	.	14.6822	0.69026	0.0:1.0:0.0:0.0	.	259;198	B7Z3C6;Q96PL5	.;ERMAP_HUMAN	I	198;198;108	ENSP00000361595:L198I;ENSP00000361592:L198I;ENSP00000332439:L108I	ENSP00000332439:L108I	L	+	1	0	ERMAP	43075424	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	3.754000	0.55189	2.609000	0.88269	0.563000	0.77884	CTT		0.363	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538		A	43302837	C	A	43302837	3	1	61	1	0	0	0	0	1	0	0	0	5247	913	32	2	610	2	ERMAP	1	43302837	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89395	43302837	205947784	224	8209										
FAM183A	440585	broad.mit.edu	37	chr1	43616459	43616459	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcaccaggaagcccatgtCttggcatgataacctggagg	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43616459C>A	ENST00000335282.4	+	2	161	c.161C>A	c.(160-162)tCt>tAt	p.S54Y	FAM183A_ENST00000409337.1_3'UTR|FAM183A_ENST00000410048.1_Missense_Mutation_p.S26Y	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	54								p.S54Y(2)		kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						AAGCCCATGTCTTGGCATGAT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	1											83	76	78					1																	43616459		1887	4114	6001	43389046	SO:0001583	missense	440585			AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.161C>A	1.37:g.43616459C>A	ENSP00000334415:p.Ser54Tyr		43389046	B7ZBL8	Missense_Mutation	SNP	ENST00000335282.4	37	CCDS44126.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.466049	0.43839	.	.	ENSG00000186973	ENST00000409706;ENST00000410048;ENST00000410025;ENST00000409396;ENST00000335282	.	.	.	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000006	T	0.79287	0.4420	M	0.80847	2.515	0.43522	D	0.995791	D	0.89917	1.0	D	0.87578	0.998	T	0.82246	-0.0552	9	0.87932	D	0	.	13.9061	0.63836	0.0:1.0:0.0:0.0	.	54	A6NL82	F183A_HUMAN	Y	54;26;2;54;54	.	ENSP00000334415:S54Y	S	+	2	0	FAM183A	43389046	0.999000	0.42202	1.000000	0.80357	0.085000	0.17905	2.239000	0.43079	2.420000	0.82092	0.655000	0.94253	TCT		0.478	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376		A	43616459	C	A	43616459	3	1	61	1	0	0	0	0	1	0	0	0	5526	913	32	2	167	2	FAM183A	1	43616459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	313622	43616459	205634162	225	8210										
EBNA1BP2	10969	broad.mit.edu	37	chr1	43632844	43632844	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaacctttctgatatttCttaatagcattcatcatatg	3	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43632844C>A	ENST00000236051.2	-	6	741	c.600G>T	c.(598-600)aaG>aaT	p.K200N	EBNA1BP2_ENST00000431635.2_Missense_Mutation_p.K255N	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	200					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K200N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TCTGATATTTCTTAATAGCAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											217	204	208					1																	43632844		2203	4300	6503	43405431	SO:0001583	missense	10969			U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"EBNA1-binding protein 2"			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.600G>T	1.37:g.43632844C>A	ENSP00000236051:p.Lys200Asn		43405431	Q96A66	Missense_Mutation	SNP	ENST00000236051.2	37	CCDS478.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808085	0.70797	.	.	ENSG00000117395	ENST00000431635;ENST00000236051	T;T	0.53206	0.63;0.63	6.06	4.2	0.49525	.	0.040528	0.85682	D	0.000000	T	0.63988	0.2558	M	0.65677	2.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65236	-0.6217	10	0.87932	D	0	-27.672	9.9447	0.41602	0.0:0.7948:0.0:0.2052	.	200;200	Q6IB29;Q99848	.;EBP2_HUMAN	N	255;200	ENSP00000407323:K255N;ENSP00000236051:K200N	ENSP00000236051:K200N	K	-	3	2	EBNA1BP2	43405431	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	1.688000	0.37690	0.894000	0.36317	0.655000	0.94253	AAG		0.433	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			A	43632844	C	A	43632844	3	1	61	1	0	0	0	0	1	0	0	0	4896	912	32	2	336	2	EBNA1BP2	1	43632844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16385	43632844	205617777	226	8211										
MPL	4352	broad.mit.edu	37	chr1	43818195	43818195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatctctcccagcccaagGccacagtctcagatacctgt	6	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43818195G>A	ENST00000372470.3	+	12	1702	c.1660G>A	c.(1660-1662)Gcc>Acc	p.A554T	RP1-92O14.3_ENST00000424948.1_RNA	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	554					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)	p.A554T(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	CCAGCCCAAGGCCACAGTCTC	0.582			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	1											83	83	83					1																	43818195		2203	4300	6503	43590782	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1660G>A	1.37:g.43818195G>A	ENSP00000361548:p.Ala554Thr		43590782	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	g	12.94	2.089463	0.36855	.	.	ENSG00000117400	ENST00000372470	D	0.82893	-1.66	3.63	2.67	0.31697	.	0.169122	0.24594	U	0.037198	T	0.82185	0.4982	L	0.60455	1.87	0.80722	D	1	D;P	0.56521	0.976;0.932	P;P	0.52598	0.703;0.559	T	0.80082	-0.1531	10	0.39692	T	0.17	-9.4776	7.1618	0.25669	0.1345:0.0:0.8655:0.0	.	547;554	Q308M1;P40238	.;TPOR_HUMAN	T	554	ENSP00000361548:A554T	ENSP00000361548:A554T	A	+	1	0	MPL	43590782	0.990000	0.36364	1.000000	0.80357	0.888000	0.51559	0.632000	0.24583	1.835000	0.53391	0.306000	0.20318	GCC		0.582	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		A	43818195	G	A	43818195	3	1	61	1	0	0	0	0	1	0	0	0	9760	1203	42	3	1706	3	MPL	1	43818195	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185351	43818195	205432426	227	8212										
KIAA0467	23334	broad.mit.edu	37	chr1	43894018	43894018	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatagacatcaccccatttCtccttgcattgtgtggccac	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43894018C>A	ENST00000562955.1	+	27	3856	c.3856C>A	c.(3856-3858)Ctc>Atc	p.L1286I	SZT2_ENST00000372442.1_Missense_Mutation_p.L444I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1343					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.L444I(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CACCCCATTTCTCCTTGCATT	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	1											151	120	130					1																	43894018		2203	4300	6503	43666605	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.3856C>A	1.37:g.43894018C>A	ENSP00000457168:p.Leu1286Ile		43666605	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399179	0.62177	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.54	3.27	0.37495	.	0.078821	0.52532	D	0.000071	T	0.50939	0.1645	L	0.37630	1.12	0.24712	N	0.993192	D	0.89917	1.0	D	0.83275	0.996	T	0.46261	-0.9204	9	0.23891	T	0.37	.	13.3275	0.60467	0.0:0.9106:0.0:0.0894	.	1286	Q5T011-5	.	I	444	.	ENSP00000361519:L444I	L	+	1	0	SZT2	43666605	1.000000	0.71417	0.993000	0.49108	0.869000	0.49853	3.661000	0.54503	0.461000	0.27071	0.655000	0.94253	CTC		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43894018	C	A	43894018	3	1	61	1	0	0	0	0	1	0	0	0	8199	913	32	2	1372	2	KIAA0467	1	43894018	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75823	43894018	205356603	228	8213										
KIAA0467	23334	broad.mit.edu	37	chr1	43895395	43895395	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagaccgaggacctaagCgagcctgagtttcagagcac	12	10	1	3	rs138401303		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43895395C>T	ENST00000562955.1	+	28	4017	c.4017C>T	c.(4015-4017)agC>agT	p.S1339S	SZT2_ENST00000372442.1_Silent_p.S497S	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1396					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.S497S(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						AGGACCTAAGCGAGCCTGAGT	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	1						C		1,4405	2.1+/-5.4	0,1,2202	96	93	94		4017	-5.3	1	1	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	SZT2	NM_015284.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1339/3376	43895395	1,13005	2203	4300	6503	43667982	SO:0001819	synonymous_variant	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.4017C>T	1.37:g.43895395C>T			43667982	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																				0.552	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43895395	C	T	43895395	2	4	61	1	0	0	0	0	0	0	0	1	8199	767	27	1		1	KIAA0467	1	43895395	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1377	43895395	205355226	229	8214										
KIAA0467	23334	broad.mit.edu	37	chr1	43896699	43896699	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtgtgactctggatgtCttcatgctgactttgcccct	9	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43896699C>A	ENST00000562955.1	+	32	4683	c.4683C>A	c.(4681-4683)gtC>gtA	p.V1561V	SZT2_ENST00000372442.1_Silent_p.V719V	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1618					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.V719V(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTCTGGATGTCTTCATGCTGA	0.612																																																2	Substitution - coding silent(2)	large_intestine(2)	1											66	62	63					1																	43896699		2203	4300	6503	43669286	SO:0001819	synonymous_variant	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.4683C>A	1.37:g.43896699C>A			43669286	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																				0.612	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43896699	C	A	43896699	2	1	61	1	0	0	0	0	0	0	0	1	8199	900	32	2		2	KIAA0467	1	43896699	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1304	43896699	205353922	230	8215										
KIAA0467	23334	broad.mit.edu	37	chr1	43904402	43904402	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggatgagctcgtgcgagttCtatgtcggcgcctggatgag	16	9	1	2	rs145034016		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:43904402C>A	ENST00000562955.1	+	46	6370	c.6370C>A	c.(6370-6372)Cta>Ata	p.L2124I	SZT2_ENST00000471177.1_3'UTR|SZT2_ENST00000372442.1_Missense_Mutation_p.L1282I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2181					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.L1282I(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CGTGCGAGTTCTATGTCGGCG	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	1											99	87	91					1																	43904402		2203	4300	6503	43676989	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.6370C>A	1.37:g.43904402C>A	ENSP00000457168:p.Leu2124Ile		43676989	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	14.46	2.540919	0.45280	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000002	T	0.63390	0.2507	L	0.55990	1.75	0.26738	N	0.970441	D	0.89917	1.0	D	0.83275	0.996	T	0.59273	-0.7485	9	0.87932	D	0	.	13.1226	0.59336	0.0:0.9268:0.0:0.0732	.	2124	Q5T011-5	.	I	1282	.	ENSP00000361519:L1282I	L	+	1	2	SZT2	43676989	1.000000	0.71417	1.000000	0.80357	0.232000	0.25224	4.514000	0.60482	2.705000	0.92388	0.655000	0.94253	CTA		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43904402	C	A	43904402	3	1	61	1	0	0	0	0	1	0	0	0	8199	912	32	2	3962	2	KIAA0467	1	43904402	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7703	43904402	205346219	231	8216										
PTPRF	5792	broad.mit.edu	37	chr1	44019609	44019609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccaagctctcagtgctcGaaggtacgtgctagggagac	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:44019609G>A	ENST00000359947.4	+	5	716	c.376G>A	c.(376-378)Gaa>Aaa	p.E126K	PTPRF_ENST00000438120.1_Missense_Mutation_p.E126K|PTPRF_ENST00000372413.3_Missense_Mutation_p.E126K|PTPRF_ENST00000372414.3_Missense_Mutation_p.E126K	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	126					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E116K(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTCAGTGCTCGAAGGTACGTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	88	103					1																	44019609		2203	4300	6503	43792196	SO:0001583	missense	5792			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.376G>A	1.37:g.44019609G>A	ENSP00000353030:p.Glu126Lys		43792196	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031955	0.54790	.	.	ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000437607	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	4.74	4.74	0.60224	Immunoglobulin-like fold (1);	0.000000	0.35349	N	0.003267	T	0.29749	0.0743	L	0.41356	1.27	0.80722	D	1	B;P;P;P	0.46621	0.094;0.881;0.688;0.61	B;B;B;B	0.36608	0.04;0.229;0.039;0.065	T	0.27020	-1.0086	10	0.02654	T	1	.	18.1107	0.89534	0.0:0.0:1.0:0.0	.	126;126;126;126	Q5T020;P10586-2;P10586;Q5T019	.;.;PTPRF_HUMAN;.	K	126	ENSP00000353030:E126K;ENSP00000398822:E126K;ENSP00000361491:E126K;ENSP00000361490:E126K;ENSP00000413306:E126K	ENSP00000353030:E126K	E	+	1	0	PTPRF	43792196	1.000000	0.71417	0.986000	0.45419	0.837000	0.47467	3.894000	0.56250	2.334000	0.79466	0.655000	0.94253	GAA		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			A	44019609	G	A	44019609	3	1	61	1	0	0	0	0	1	0	0	0	12838	1059	37	1	386	1	PTPRF	1	44019609	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115207	44019609	205231012	232	8217										
KDM4A	9682	broad.mit.edu	37	chr1	44169767	44169767	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgaagagcttcccaagaGagtcaaatctagactggtga	12	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:44169767G>T	ENST00000372396.3	+	21	3172	c.3038G>T	c.(3037-3039)aGa>aTa	p.R1013I	KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000453015.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000439057.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	1013					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R1013I(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						CTTCCCAAGAGAGTCAAATCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											223	216	218					1																	44169767		2203	4300	6503	43942354	SO:0001583	missense	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.3038G>T	1.37:g.44169767G>T	ENSP00000361473:p.Arg1013Ile		43942354	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	37	CCDS491.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342063	0.81911	.	.	ENSG00000066135	ENST00000372396	T	0.76709	-1.04	6.08	6.08	0.98989	.	0.038032	0.85682	D	0.000000	D	0.84329	0.5448	M	0.76170	2.325	0.80722	D	1	D	0.57899	0.981	P	0.55161	0.77	D	0.85668	0.1293	10	0.87932	D	0	-18.8086	13.8098	0.63256	0.0695:0.0:0.9305:0.0	.	1013	O75164	KDM4A_HUMAN	I	1013	ENSP00000361473:R1013I	ENSP00000361473:R1013I	R	+	2	0	KDM4A	43942354	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.002000	0.88514	2.894000	0.99253	0.655000	0.94253	AGA		0.468	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		T	44169767	G	T	44169767	3	4	61	1	0	0	0	0	1	0	0	0	8149	942	33	2	3116	2	KDM4A	1	44169767	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	150158	44169767	205080854	233	8218										
ST3GAL3	6487	broad.mit.edu	37	chr1	44365219	44365219	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgctctctgtagactgaaTtcagcaccagtgaaaggctt	9	11	2	3	rs138286395		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:44365219T>C	ENST00000361392.4	+	9	741	c.564T>C	c.(562-564)aaT>aaC	p.N188N	ST3GAL3_ENST00000531993.1_Silent_p.N172N|ST3GAL3_ENST00000372375.2_Silent_p.N242N|ST3GAL3_ENST00000372372.2_Silent_p.N226N|ST3GAL3_ENST00000461375.1_3'UTR|ST3GAL3_ENST00000372362.2_Intron|ST3GAL3_ENST00000545417.1_Intron|ST3GAL3_ENST00000347631.2_Silent_p.N203N|ST3GAL3_ENST00000262915.3_Silent_p.N257N|ST3GAL3_ENST00000335430.6_Intron|ST3GAL3_ENST00000372367.1_Intron|ST3GAL3_ENST00000372366.1_Intron|ST3GAL3_ENST00000533933.1_Silent_p.N188N|ST3GAL3_ENST00000353126.3_Silent_p.N188N|ST3GAL3_ENST00000531816.1_Intron|ST3GAL3_ENST00000372369.1_Silent_p.N188N|ST3GAL3_ENST00000361812.4_Intron|ST3GAL3_ENST00000372365.1_Intron|ST3GAL3_ENST00000528371.1_Intron|ST3GAL3_ENST00000351035.3_Silent_p.N226N|ST3GAL3_ENST00000361746.4_Silent_p.N257N|ST3GAL3_ENST00000372368.2_Silent_p.N242N|ST3GAL3_ENST00000361400.4_Silent_p.N172N|ST3GAL3_ENST00000531451.1_Intron|ST3GAL3_ENST00000330208.2_Intron|ST3GAL3_ENST00000332628.6_Silent_p.N157N|ST3GAL3_ENST00000372377.4_Intron|ST3GAL3_ENST00000372374.2_Silent_p.N157N	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	188					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)	p.N257N(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				GTAGACTGAATTCAGCACCAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1						T	,,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	74	69	71		564,771,609,,564,,726,516,,678	3.1	1	1	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,intron,coding-synonymous	ST3GAL3	NM_006279.2,NM_174963.2,NM_174964.1,NM_174965.1,NM_174966.1,NM_174967.1,NM_174968.2,NM_174969.1,NM_174970.1,NM_174971.2	,,,,,,,,,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	,,,,,,,,,	188/376,257/445,203/391,,188/278,,242/430,172/360,,226/414	44365219	1,13005	2203	4300	6503	44137806	SO:0001819	synonymous_variant	6487			L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"Sialyltransferases"	10866	protein-coding gene	gene with protein product	"ST3Gal III"	606494	"sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)", "mental retardation, non-syndromic, autosomal recessive, 12"	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.564T>C	1.37:g.44365219T>C			44137806	A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Silent	SNP	ENST00000361392.4	37	CCDS492.1																																																																																				0.592	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1	NM_174963		C	44365219	T	C	44365219	2	2	61	1	0	0	0	0	0	0	0	1	15255	1490	52	4		4	ST3GAL3	1	44365219	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	195452	44365219	204885402	234	8219										
ATP6V0B	533	broad.mit.edu	37	chr1	44442883	44442883	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggtcatcgtcgcaattCttcaggtgatgaatcccctt	10	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:44442883C>A	ENST00000472174.2	+	7	979	c.586C>A	c.(586-588)Ctt>Att	p.L196I	ATP6V0B_ENST00000498664.1_Missense_Mutation_p.L149I|B4GALT2_ENST00000434555.2_5'Flank|ATP6V0B_ENST00000236067.4_Missense_Mutation_p.L149I|B4GALT2_ENST00000309519.7_5'Flank|ATP6V0B_ENST00000471859.2_Missense_Mutation_p.L243I|B4GALT2_ENST00000356836.6_5'Flank|ATP6V0B_ENST00000532642.1_Missense_Mutation_p.L196I|B4GALT2_ENST00000372324.1_5'Flank	NM_004047.3	NP_004038.1	Q99437	VATO_HUMAN	ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b	196					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuole (GO:0005773)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)	p.L196I(1)		breast(2)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				CGTCGCAATTCTTCAGGTGAT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	74	72					1																	44442883		2203	4300	6503	44215470	SO:0001583	missense	533			BC000423	CCDS505.1, CCDS41315.1, CCDS72772.1	1p32.3	2010-04-21	2006-01-20	2002-05-10	ENSG00000117410	ENSG00000117410		"ATPases / V-type"	861	protein-coding gene	gene with protein product		603717	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21kD", "ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c''"	ATP6F		9653649	Standard	XM_005270944		Approved	VMA16, HATPL	uc001cld.3	Q99437	OTTHUMG00000008298	ENST00000472174.2:c.586C>A	1.37:g.44442883C>A	ENSP00000431605:p.Leu196Ile		44215470	D3DPY5|Q6IB32	Missense_Mutation	SNP	ENST00000472174.2	37	CCDS505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.982|6.982	0.551156|0.551156	0.13374|0.13374	.|.	.|.	ENSG00000117410|ENSG00000117410	ENST00000440531|ENST00000472174;ENST00000532642;ENST00000236067;ENST00000471859;ENST00000498664	.|T;T;T;T;T	.|0.51817	.|0.69;0.69;0.69;0.69;0.69	4.37|4.37	4.37|4.37	0.52481|0.52481	.|ATPase, F0/V0 complex, subunit C (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.27063|0.27063	0.0663|0.0663	N|N	0.10707|0.10707	0.03|0.03	0.80722|0.80722	D|D	1|1	.|B;B	.|0.27351	.|0.036;0.176	.|B;B	.|0.36666	.|0.047;0.23	T|T	0.11916|0.11916	-1.0568|-1.0568	6|10	0.87932|0.05351	D|T	0|0.99	-10.3698|-10.3698	11.3852|11.3852	0.49780|0.49780	0.0:0.9145:0.0:0.0855|0.0:0.9145:0.0:0.0855	.|.	.|196;196	.|Q99437;E9PNL3	.|VATO_HUMAN;.	L|I	37|196;196;149;243;149	.|ENSP00000431605:L196I;ENSP00000434729:L196I;ENSP00000236067:L149I;ENSP00000432754:L243I;ENSP00000434094:L149I	ENSP00000408413:F37L|ENSP00000236067:L149I	F|L	+|+	3|1	2|0	ATP6V0B|ATP6V0B	44215470|44215470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.900000|0.900000	0.52787|0.52787	2.752000|2.752000	0.47516|0.47516	2.379000|2.379000	0.81126|0.81126	0.655000|0.655000	0.94253|0.94253	TTC|CTT		0.532	ATP6V0B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022854.2	NM_004047		A	44442883	C	A	44442883	3	1	61	1	0	0	0	0	1	0	0	0	1172	913	32	2	612	2	ATP6V0B	1	44442883	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77664	44442883	204807738	235	8220										
ERI3	79033	broad.mit.edu	37	chr1	44804818	44804818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccattgccgccatggatgCgccaaagccgtgggccgcca	12	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:44804818C>T	ENST00000372257.2	-	3	569	c.388G>A	c.(388-390)Gca>Aca	p.A130T	ERI3_ENST00000495828.1_5'UTR|ERI3_ENST00000537474.1_Intron	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	130							exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A130T(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GCCATGGATGCGCCAAAGCCG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	141	138					1																	44804818		2203	4300	6503	44577405	SO:0001583	missense	79033			AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419		"Enhanced RNAi three prime mRNA exonucleases"	17276	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans)", "exoribonuclease 3"	609917	"prion protein interacting protein"	PRNPIP			Standard	XM_005271184		Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.388G>A	1.37:g.44804818C>T	ENSP00000361331:p.Ala130Thr		44577405	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	Missense_Mutation	SNP	ENST00000372257.2	37	CCDS30696.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.546424	0.65198	.	.	ENSG00000117419	ENST00000372257;ENST00000457571	.	.	.	6.07	5.16	0.70880	.	0.239846	0.36740	N	0.002437	T	0.41213	0.1149	N	0.19112	0.55	0.80722	D	1	B;B;B	0.31209	0.012;0.138;0.313	B;B;B	0.20577	0.006;0.026;0.03	T	0.33189	-0.9878	9	0.42905	T	0.14	.	14.4499	0.67376	0.0:0.9301:0.0:0.0699	.	128;52;130	F6UGJ8;B4DN03;O43414	.;.;ERI3_HUMAN	T	130;128	.	ENSP00000361331:A130T	A	-	1	0	ERI3	44577405	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.872000	0.63050	1.586000	0.49944	-0.136000	0.14681	GCA		0.542	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020243.1	NM_024066		T	44804818	C	T	44804818	3	4	61	1	0	0	0	0	1	0	0	0	5242	768	27	1	653	1	ERI3	1	44804818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	361935	44804818	204445803	236	8221										
KIF2C	11004	broad.mit.edu	37	chr1	45223278	45223278	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgaaggtggaaaagcaaCttgttttgcatatggccaga	11	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45223278C>A	ENST00000372224.4	+	11	1141	c.1028C>A	c.(1027-1029)aCt>aAt	p.T343N	KIF2C_ENST00000372218.4_Missense_Mutation_p.T302N|KIF2C_ENST00000493027.1_3'UTR|KIF2C_ENST00000372222.3_Missense_Mutation_p.T230N|RP11-269F19.2_ENST00000440985.1_RNA|RP11-269F19.2_ENST00000428791.1_RNA|KIF2C_ENST00000372217.1_Missense_Mutation_p.T289N	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	343	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)	p.T343N(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					GGAAAAGCAACTTGTTTTGCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	112	114					1																	45223278		2203	4300	6503	44995865	SO:0001583	missense	11004			U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1028C>A	1.37:g.45223278C>A	ENSP00000361298:p.Thr343Asn		44995865	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	.	.	.	.	.	.	.	.	.	.	C	32	5.180411	0.94846	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217	T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2	5.65	5.65	0.86999	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.91994	0.7464	H	0.95504	3.68	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.72075	0.957;0.975;0.976	D	0.93027	0.6445	10	0.59425	D	0.04	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	302;289;343	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	N	302;343;302;230;289	ENSP00000410346:T302N;ENSP00000361298:T343N;ENSP00000361292:T302N;ENSP00000361296:T230N;ENSP00000361291:T289N	ENSP00000361291:T289N	T	+	2	0	KIF2C	44995865	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	ACT		0.502	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845		A	45223278	C	A	45223278	3	1	61	1	0	0	0	0	1	0	0	0	8320	565	20	2	1070	2	KIF2C	1	45223278	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	418460	45223278	204027343	237	8222										
HECTD3	79654	broad.mit.edu	37	chr1	45469395	45469395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggaagactcgggcagcGcgtctgtggtctcgtagctg	16	9	2	1	rs200632297		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45469395G>A	ENST00000372172.4	-	20	2518	c.2447C>T	c.(2446-2448)gCg>gTg	p.A816V	HECTD3_ENST00000372168.3_Missense_Mutation_p.A426V|HECTD3_ENST00000486132.1_5'UTR	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	816	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.A816V(1)|p.A426V(1)|p.A532V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CTCGGGCAGCGCGTCTGTGGT	0.602													G|||	1	0.000199681	0	0	5008	,	,		19899	0		0.001	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	1											62	71	68					1																	45469395		2088	4226	6314	45241982	SO:0001583	missense	79654			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2447C>T	1.37:g.45469395G>A	ENSP00000361245:p.Ala816Val		45241982	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	37	CCDS41318.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	18.11	3.551727	0.65311	.	.	ENSG00000126107	ENST00000372172;ENST00000372168	T;T	0.58652	0.32;0.32	5.74	5.74	0.90152	HECT (4);	0.145674	0.64402	D	0.000008	T	0.47210	0.1433	L	0.41356	1.27	0.52501	D	0.999956	P;P	0.47841	0.796;0.901	B;B	0.38106	0.265;0.254	T	0.49688	-0.8913	10	0.44086	T	0.13	.	13.5904	0.61957	0.0801:0.0:0.9199:0.0	.	816;426	Q5T447;Q5T447-2	HECD3_HUMAN;.	V	816;426	ENSP00000361245:A816V;ENSP00000361241:A426V	ENSP00000361241:A426V	A	-	2	0	HECTD3	45241982	0.785000	0.28726	0.398000	0.26321	0.891000	0.51852	3.064000	0.49986	2.717000	0.92951	0.558000	0.71614	GCG		0.602	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		A	45469395	G	A	45469395	3	1	61	1	0	0	0	0	1	0	0	0	7062	1087	38	1	146	1	HECTD3	1	45469395	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246117	45469395	203781226	238	8223										
HECTD3	79654	broad.mit.edu	37	chr1	45476352	45476352	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccttcctgcagcccgcaGtcgcccaggtgctctgccag	11	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45476352G>A	ENST00000372172.4	-	2	467	c.396C>T	c.(394-396)gaC>gaT	p.D132D	HECTD3_ENST00000372168.3_5'Flank|UROD_ENST00000246337.4_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	132					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.D132D(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GCAGCCCGCAGTCGCCCAGGT	0.716																																																1	Substitution - coding silent(1)	large_intestine(1)	1											8	10	9					1																	45476352		2000	4175	6175	45248939	SO:0001819	synonymous_variant	79654			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.396C>T	1.37:g.45476352G>A			45248939	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	37	CCDS41318.1																																																																																				0.716	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		A	45476352	G	A	45476352	2	1	61	1	0	0	0	0	0	0	0	1	7062	1020	36	3		3	HECTD3	1	45476352	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6957	45476352	203774269	239	8224										
UROD	7389	broad.mit.edu	37	chr1	45479683	45479683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctagtcaccagctgcttCgcatcctcactgatgctctg	9	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45479683C>T	ENST00000246337.4	+	6	696	c.577C>T	c.(577-579)Cgc>Tgc	p.R193C	UROD_ENST00000494399.1_3'UTR|HECTD3_ENST00000372172.4_5'Flank	NM_000374.4	NP_000365.3	P06132	DCUP_HUMAN	uroporphyrinogen decarboxylase	193			R -> P (in FPCT; insoluble protein). {ECO:0000269|PubMed:11719352}.		heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	uroporphyrinogen decarboxylase activity (GO:0004853)	p.R193C(1)		endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					CCAGCTGCTTCGCATCCTCAC	0.557									Porphyria Cutanea Tarda, Type II																																							1	Substitution - Missense(1)	large_intestine(1)	1											97	96	96					1																	45479683		2203	4300	6503	45252270	SO:0001583	missense	7389	Familial Cancer Database	PCT-II	BC001778	CCDS518.1	1p34	2012-10-02			ENSG00000126088	ENSG00000126088	4.1.1.37		12591	protein-coding gene	gene with protein product		613521				3015909, 3460962	Standard	NM_000374		Approved		uc001cna.2	P06132	OTTHUMG00000008949	ENST00000246337.4:c.577C>T	1.37:g.45479683C>T	ENSP00000246337:p.Arg193Cys		45252270	A8K762|Q16863|Q16883|Q53YB8|Q53ZP6|Q6IB28|Q9BUZ0	Missense_Mutation	SNP	ENST00000246337.4	37	CCDS518.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955682	0.53293	.	.	ENSG00000126088	ENST00000246337;ENST00000434478;ENST00000372135	D;D	0.94497	-3.44;-3.44	5.26	1.05	0.20165	Uroporphyrinogen decarboxylase (URO-D) (1);	0.601453	0.18645	N	0.135167	D	0.94512	0.8233	M	0.72353	2.195	0.24283	N	0.9952	D;D	0.58970	0.984;0.958	P;P	0.58970	0.849;0.704	D	0.87318	0.2316	10	0.87932	D	0	-1.1563	2.7308	0.05226	0.1876:0.4398:0.2267:0.146	.	137;193	B4DEM5;P06132	.;DCUP_HUMAN	C	193;172;172	ENSP00000246337:R193C;ENSP00000404489:R172C	ENSP00000246337:R193C	R	+	1	0	UROD	45252270	0.064000	0.20934	0.804000	0.32291	0.825000	0.46686	0.444000	0.21661	0.360000	0.24265	-0.123000	0.14984	CGC		0.557	UROD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024803.1	NM_000374		T	45479683	C	T	45479683	3	4	61	1	0	0	0	0	1	0	0	0	17069	884	31	1	599	1	UROD	1	45479683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3331	45479683	203770938	240	8225										
MUTYH	4595	broad.mit.edu	37	chr1	45797952	45797952	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttgaaatctcctggccgGgctgggtccaccagctgctg	14	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45797952G>T	ENST00000372098.3	-	10	943	c.810C>A	c.(808-810)gcC>gcA	p.A270A	MUTYH_ENST00000355498.2_Silent_p.A245A|MUTYH_ENST00000354383.6_Silent_p.A246A|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528013.2_Silent_p.A259A|MUTYH_ENST00000450313.1_Silent_p.A273A|MUTYH_ENST00000372100.5_Silent_p.A256A|MUTYH_ENST00000456914.2_Silent_p.A245A|MUTYH_ENST00000372104.1_Silent_p.A245A|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000372115.3_Silent_p.A259A|MUTYH_ENST00000372110.3_Silent_p.A260A|MUTYH_ENST00000448481.1_Silent_p.A256A			Q9UIF7	MUTYH_HUMAN	mutY homolog	270					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)	p.A270A(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					CTCCTGGCCGGGCTGGGTCCA	0.612			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																													yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	1	Substitution - coding silent(1)	large_intestine(1)	1											29	31	30					1																	45797952		2203	4300	6503	45570539	SO:0001819	synonymous_variant	4595	Familial Cancer Database	MAP, MYH-associated polyposis	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.810C>A	1.37:g.45797952G>T			45570539	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	37	CCDS520.1																																																																																				0.612	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		T	45797952	G	T	45797952	2	4	61	1	0	0	0	0	0	0	0	1	10023	1219	43	2		2	MUTYH	1	45797952	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	318269	45797952	203452669	241	8226										
MUTYH	4595	broad.mit.edu	37	chr1	45800151	45800151	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgcttcctgtgaccactTcccacggctgctcgtggctt	10	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45800151T>C	ENST00000372098.3	-	2	202	c.69A>G	c.(67-69)ggA>ggG	p.G23G	MUTYH_ENST00000355498.2_Silent_p.G9G|MUTYH_ENST00000354383.6_Silent_p.G9G|MUTYH_ENST00000529984.1_Silent_p.G9G|MUTYH_ENST00000528013.2_Silent_p.G9G|MUTYH_ENST00000450313.1_Silent_p.G23G|MUTYH_ENST00000372100.5_Silent_p.G9G|MUTYH_ENST00000456914.2_Silent_p.G9G|MUTYH_ENST00000372104.1_Silent_p.G9G|MUTYH_ENST00000488731.2_Silent_p.G9G|MUTYH_ENST00000528332.2_Silent_p.G23G|MUTYH_ENST00000531105.1_Silent_p.G9G|MUTYH_ENST00000372115.3_Silent_p.G23G|MUTYH_ENST00000372110.3_Silent_p.G23G|MUTYH_ENST00000448481.1_Silent_p.G9G			Q9UIF7	MUTYH_HUMAN	mutY homolog	23					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)	p.G23G(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TGTGACCACTTCCCACGGCTG	0.537			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																													yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	1	Substitution - coding silent(1)	large_intestine(1)	1											136	107	117					1																	45800151		2203	4300	6503	45572738	SO:0001819	synonymous_variant	4595	Familial Cancer Database	MAP, MYH-associated polyposis	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.69A>G	1.37:g.45800151T>C			45572738	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	37	CCDS520.1																																																																																				0.537	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		C	45800151	T	C	45800151	2	2	61	1	0	0	0	0	0	0	0	1	10023	1770	62	4		4	MUTYH	1	45800151	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2199	45800151	203450470	242	8227										
PRDX1	5052	broad.mit.edu	37	chr1	45981393	45981393	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagttgagtttcttaaattCttctgccctatcactgaaag	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:45981393C>A	ENST00000262746.1	-	3	532	c.193G>T	c.(193-195)Gaa>Taa	p.E65*	PRDX1_ENST00000319248.8_Nonsense_Mutation_p.E65*|PRDX1_ENST00000483583.1_5'UTR|PRDX1_ENST00000372079.1_Intron	NM_002574.3|NM_181696.2	NP_002565.1|NP_859047.1	Q06830	PRDX1_HUMAN	peroxiredoxin 1	65	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|erythrocyte homeostasis (GO:0034101)|hydrogen peroxide catabolic process (GO:0042744)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of NF-kappaB import into nucleus (GO:0042345)|regulation of stress-activated MAPK cascade (GO:0032872)|removal of superoxide radicals (GO:0019430)|retina homeostasis (GO:0001895)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)	heme binding (GO:0020037)|peroxidase activity (GO:0004601)|poly(A) RNA binding (GO:0044822)|thioredoxin peroxidase activity (GO:0008379)	p.E65*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	12	Acute lymphoblastic leukemia(166;0.155)					TTCTTAAATTCTTCTGCCCTA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											114	110	112					1																	45981393		2203	4300	6503	45753980	SO:0001587	stop_gained	5052			BC021683	CCDS522.1	1p34.1	2008-02-05			ENSG00000117450	ENSG00000117450			9352	protein-coding gene	gene with protein product		176763		PAGA		8496166	Standard	NM_181697		Approved	NKEFA	uc021omw.1	Q06830	OTTHUMG00000007738	ENST00000262746.1:c.193G>T	1.37:g.45981393C>A	ENSP00000262746:p.Glu65*		45753980	B5BU26|D3DPZ8|P35703|Q2V576|Q5T154|Q5T155	Nonsense_Mutation	SNP	ENST00000262746.1	37	CCDS522.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774863	0.90108	.	.	ENSG00000117450	ENST00000262746;ENST00000319248;ENST00000447184;ENST00000424390	.	.	.	5.9	5.9	0.94986	.	0.089877	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-16.8716	20.2723	0.98479	0.0:1.0:0.0:0.0	.	.	.	.	X	65	.	ENSP00000262746:E65X	E	-	1	0	PRDX1	45753980	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.499000	0.81566	2.793000	0.96121	0.563000	0.77884	GAA		0.423	PRDX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020845.1	NM_181697		A	45981393	C	A	45981393	4	1	61	1	0	0	0	0	0	1	0	0	12498	922	32	2	422	2	PRDX1	1	45981393	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	181242	45981393	203269228	243	8228										
IPP	3652	broad.mit.edu	37	chr1	46193353	46193353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttactcccagcccacttCgagcctgatgaagtgaagac	9	13	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46193353C>T	ENST00000396478.3	-	5	1100	c.998G>A	c.(997-999)cGa>cAa	p.R333Q		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	333						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.R333Q(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					CAGCCCACTTCGAGCCTGATG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											170	158	163					1																	46193353		2203	4300	6503	45965940	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.998G>A	1.37:g.46193353C>T	ENSP00000379739:p.Arg333Gln		45965940	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	C	36	5.917089	0.97099	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	D;D	0.85773	-2.03;-2.03	5.86	5.86	0.93980	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.93858	0.8035	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93810	0.7109	10	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	333;333	Q9Y573;A2A6V3	IPP_HUMAN;.	Q	333	ENSP00000353024:R333Q;ENSP00000379739:R333Q	ENSP00000353024:R333Q	R	-	2	0	IPP	45965940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.524000	0.81866	2.937000	0.99478	0.650000	0.86243	CGA		0.463	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		T	46193353	C	T	46193353	3	4	61	1	0	0	0	0	1	0	0	0	7821	884	31	1	878	1	IPP	1	46193353	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211960	46193353	203057268	244	8229										
IPP	3652	broad.mit.edu	37	chr1	46206666	46206666	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcttctttttcccaaatCtttcagaatccattgcattg	3	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46206666C>A	ENST00000396478.3	-	3	733	c.631G>T	c.(631-633)Gat>Tat	p.D211Y		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	211						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.D211Y(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TTTCCCAAATCTTTCAGAATC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											169	166	167					1																	46206666		2203	4300	6503	45979253	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.631G>T	1.37:g.46206666C>A	ENSP00000379739:p.Asp211Tyr		45979253	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280990	0.80692	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.72394	-0.65;-0.65	5.17	5.17	0.71159	BTB/Kelch-associated (2);	0.092632	0.64402	D	0.000001	D	0.89815	0.6824	H	0.97077	3.935	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.74348	0.976;0.983	D	0.93118	0.6522	10	0.87932	D	0	.	19.0334	0.92967	0.0:1.0:0.0:0.0	.	211;211	Q9Y573;A2A6V3	IPP_HUMAN;.	Y	211	ENSP00000353024:D211Y;ENSP00000379739:D211Y	ENSP00000353024:D211Y	D	-	1	0	IPP	45979253	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.398000	0.79919	2.577000	0.86979	0.643000	0.83706	GAT		0.378	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		A	46206666	C	A	46206666	3	1	61	1	0	0	0	0	1	0	0	0	7821	913	32	2	1253	2	IPP	1	46206666	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13313	46206666	203043955	245	8230										
IPP	3652	broad.mit.edu	37	chr1	46211843	46211843	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcctgcttcaattcctaGaatcggtacaacatcttttg	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46211843G>T	ENST00000396478.3	-	2	343	c.241C>A	c.(241-243)Cta>Ata	p.L81I		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	81	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.L81I(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TCAATTCCTAGAATCGGTACA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	85	86					1																	46211843		2203	4300	6503	45984430	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.241C>A	1.37:g.46211843G>T	ENSP00000379739:p.Leu81Ile		45984430	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782113	0.31502	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.67345	-0.26;-0.26	5.57	3.68	0.42216	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.320343	0.30076	N	0.010465	T	0.46190	0.1380	L	0.27053	0.805	0.30371	N	0.782859	B;P	0.40534	0.311;0.72	B;B	0.37601	0.222;0.254	T	0.46707	-0.9172	10	0.30854	T	0.27	.	4.6969	0.12808	0.1429:0.1259:0.6146:0.1166	.	81;81	Q9Y573;A2A6V3	IPP_HUMAN;.	I	81	ENSP00000353024:L81I;ENSP00000379739:L81I	ENSP00000353024:L81I	L	-	1	2	IPP	45984430	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.279000	0.33191	1.353000	0.45828	0.655000	0.94253	CTA		0.398	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		T	46211843	G	T	46211843	3	4	61	1	0	0	0	0	1	0	0	0	7821	933	33	2	1647	2	IPP	1	46211843	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5177	46211843	203038778	246	8231										
PIK3R3	8503	broad.mit.edu	37	chr1	46509490	46509490	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgtagggctctgcaaagCcatagccccgagcagtgctg	14	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46509490C>T	ENST00000262741.5	-	10	1930	c.1241G>A	c.(1240-1242)gGc>gAc	p.G414D	PIK3R3_ENST00000420542.1_Missense_Mutation_p.G414D|PIK3R3_ENST00000340332.6_Missense_Mutation_p.G319D|PIK3R3_ENST00000540385.1_Missense_Mutation_p.G460D|RP4-533D7.4_ENST00000450004.1_RNA|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000354242.4_Missense_Mutation_p.G355D|PIK3R3_ENST00000423209.1_Missense_Mutation_p.G355D|PIK3R3_ENST00000372006.1_Missense_Mutation_p.G414D	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	414	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)	p.G414D(1)		endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CTCTGCAAAGCCATAGCCCCG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	110	117					1																	46509490		2203	4300	6503	46282077	SO:0001583	missense	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.1241G>A	1.37:g.46509490C>T	ENSP00000262741:p.Gly414Asp		46282077	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	37	CCDS529.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844359	0.91197	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000354242;ENST00000340332;ENST00000540385;ENST00000423209	D;D;D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	5.77	5.77	0.91146	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.94807	0.8323	M	0.78344	2.41	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.999;1.0;0.995;1.0	D	0.94775	0.7948	10	0.87932	D	0	-3.2593	19.9915	0.97366	0.0:1.0:0.0:0.0	.	460;447;355;414	F6TDL0;Q7Z3W2;Q92569-2;Q92569	.;.;.;P55G_HUMAN	D	414;414;414;355;319;460;355	ENSP00000361075:G414D;ENSP00000262741:G414D;ENSP00000412546:G414D;ENSP00000346188:G355D;ENSP00000342484:G319D;ENSP00000439913:G460D;ENSP00000391431:G355D	ENSP00000262741:G414D	G	-	2	0	PIK3R3	46282077	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.723000	0.93209	0.655000	0.94253	GGC		0.507	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		T	46509490	C	T	46509490	3	4	61	1	0	0	0	0	1	0	0	0	11951	739	26	3	148	3	PIK3R3	1	46509490	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	297647	46509490	202741131	247	8232										
PIK3R3	8503	broad.mit.edu	37	chr1	46511630	46511630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttcttgctactctcacGaattaagaatgcaccatcag	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46511630G>A	ENST00000262741.5	-	9	1836	c.1147C>T	c.(1147-1149)Cgt>Tgt	p.R383C	PIK3R3_ENST00000420542.1_Missense_Mutation_p.R383C|PIK3R3_ENST00000340332.6_Missense_Mutation_p.R288C|PIK3R3_ENST00000540385.1_Missense_Mutation_p.R429C|RP4-533D7.4_ENST00000450004.1_RNA|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000354242.4_Missense_Mutation_p.R324C|PIK3R3_ENST00000423209.1_Missense_Mutation_p.R324C|PIK3R3_ENST00000372006.1_Missense_Mutation_p.R383C	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	383	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)	p.R383C(1)		endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CTACTCTCACGAATTAAGAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											182	170	174					1																	46511630		2203	4300	6503	46284217	SO:0001583	missense	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.1147C>T	1.37:g.46511630G>A	ENSP00000262741:p.Arg383Cys		46284217	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	37	CCDS529.1	.	.	.	.	.	.	.	.	.	.	G	35	5.492234	0.96339	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000354242;ENST00000340332;ENST00000540385;ENST00000423209	D;D;D;D;D;D;D	0.99292	-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7	6.08	6.08	0.98989	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	H	0.99740	4.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.96844	0.9620	10	0.87932	D	0	-6.8398	20.6634	0.99662	0.0:0.0:1.0:0.0	.	429;416;324;383	F6TDL0;Q7Z3W2;Q92569-2;Q92569	.;.;.;P55G_HUMAN	C	383;383;383;324;288;429;324	ENSP00000361075:R383C;ENSP00000262741:R383C;ENSP00000412546:R383C;ENSP00000346188:R324C;ENSP00000342484:R288C;ENSP00000439913:R429C;ENSP00000391431:R324C	ENSP00000262741:R383C	R	-	1	0	PIK3R3	46284217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.894000	0.87336	2.894000	0.99253	0.655000	0.94253	CGT		0.393	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		A	46511630	G	A	46511630	3	1	61	1	0	0	0	0	1	0	0	0	11951	1058	37	1	246	1	PIK3R3	1	46511630	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2140	46511630	202738991	248	8233										
PIK3R3	8503	broad.mit.edu	37	chr1	46521491	46521491	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgttgatctcggatctttCgcagctggatcaggtcaggt	14	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46521491C>T	ENST00000262741.5	-	7	1606	c.917G>A	c.(916-918)cGa>cAa	p.R306Q	PIK3R3_ENST00000420542.1_Missense_Mutation_p.R306Q|PIK3R3_ENST00000340332.6_Intron|PIK3R3_ENST00000540385.1_Missense_Mutation_p.R352Q|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000354242.4_Intron|PIK3R3_ENST00000423209.1_Intron|PIK3R3_ENST00000372006.1_Missense_Mutation_p.R306Q	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	306					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)	p.R306Q(1)		endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	TCGGATCTTTCGCAGCTGGAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											221	201	208					1																	46521491		2203	4300	6503	46294078	SO:0001583	missense	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.917G>A	1.37:g.46521491C>T	ENSP00000262741:p.Arg306Gln		46294078	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	37	CCDS529.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055908	0.76074	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000540385	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.48	4.54	0.55810	.	0.048598	0.85682	D	0.000000	T	0.31606	0.0802	M	0.76002	2.32	0.80722	D	1	B;P;B	0.35807	0.311;0.522;0.171	B;B;B	0.19946	0.01;0.027;0.011	T	0.20306	-1.0279	10	0.41790	T	0.15	.	15.723	0.77728	0.1377:0.8623:0.0:0.0	.	352;339;306	F6TDL0;Q7Z3W2;Q92569	.;.;P55G_HUMAN	Q	306;306;306;352	ENSP00000361075:R306Q;ENSP00000262741:R306Q;ENSP00000412546:R306Q;ENSP00000439913:R352Q	ENSP00000262741:R306Q	R	-	2	0	PIK3R3	46294078	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	1.409000	0.46915	0.650000	0.86243	CGA		0.453	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		T	46521491	C	T	46521491	3	4	61	1	0	0	0	0	1	0	0	0	11951	884	31	1	484	1	PIK3R3	1	46521491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9861	46521491	202729130	249	8234										
TSPAN1	10103	broad.mit.edu	37	chr1	46649988	46649988	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtgggctacttcctcatCgcagccggcgttgtggtctt	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46649988C>T	ENST00000372003.1	+	4	647	c.183C>T	c.(181-183)atC>atT	p.I61I	TSPAN1_ENST00000498443.1_3'UTR	NM_005727.3	NP_005718.2	O60635	TSN1_HUMAN	tetraspanin 1	61					cell migration (GO:0016477)|cell proliferation (GO:0008283)|positive regulation of endocytosis (GO:0045807)|protein stabilization (GO:0050821)|thiamine transmembrane transport (GO:0071934)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.I61I(1)		kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)	Medulloblastoma(700;0.00498)|all_neural(321;0.0212)				ACTTCCTCATCGCAGCCGGCG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	1											183	139	153					1																	46649988		2203	4300	6503	46422575	SO:0001819	synonymous_variant	10103			BC013404	CCDS530.1	1p33	2013-02-14			ENSG00000117472	ENSG00000117472		"Tetraspanins"	20657	protein-coding gene	gene with protein product		613170				9714763, 10719184	Standard	NM_005727		Approved	TSPAN-1, NET-1	uc001cpd.3	O60635	OTTHUMG00000007602	ENST00000372003.1:c.183C>T	1.37:g.46649988C>T			46422575	D3DQ14|O60745|Q5VST0	Silent	SNP	ENST00000372003.1	37	CCDS530.1																																																																																				0.562	TSPAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020135.1	NM_005727		T	46649988	C	T	46649988	2	4	61	1	0	0	0	0	0	0	0	1	16673	874	31	1		1	TSPAN1	1	46649988	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128497	46649988	202600633	250	8235										
C1orf190	541468	broad.mit.edu	37	chr1	46685434	46685434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaccttgaatgagggcatcGaggcagtgcgctggctgttg	16	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:46685434G>A	ENST00000371980.3	+	2	355	c.262G>A	c.(262-264)Gag>Aag	p.E88K	POMGNT1_ENST00000371992.1_5'UTR|POMGNT1_ENST00000396420.3_5'UTR	NM_001013615.2	NP_001013633.1	Q96LR2	LURA1_HUMAN	leucine rich adaptor protein 1	88					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)		p.E88K(1)									TGAGGGCATCGAGGCAGTGCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	64	66					1																	46685434		2203	4300	6503	46458021	SO:0001583	missense	541468			AK057892	CCDS30703.1	1p34.1	2012-02-01	2012-02-01	2012-02-01	ENSG00000171357	ENSG00000171357			32327	protein-coding gene	gene with protein product	"leucine repeat adaptor protein 35a"		"chromosome 1 open reading frame 190"	C1orf190		21048106	Standard	NM_001013615		Approved	FLJ25163, LRAP35a	uc010oma.2	Q96LR2	OTTHUMG00000007605	ENST00000371980.3:c.262G>A	1.37:g.46685434G>A	ENSP00000361048:p.Glu88Lys		46458021		Missense_Mutation	SNP	ENST00000371980.3	37	CCDS30703.1	.	.	.	.	.	.	.	.	.	.	G	36	5.843784	0.97016	.	.	ENSG00000171357	ENST00000371980	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.78285	0.4259	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78687	-0.2107	9	0.87932	D	0	-14.081	20.0956	0.97842	0.0:0.0:1.0:0.0	.	88	Q96LR2	LP35A_HUMAN	K	88	.	ENSP00000361048:E88K	E	+	1	0	C1orf190	46458021	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	9.720000	0.98763	2.746000	0.94184	0.650000	0.86243	GAG		0.602	LURAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020154.1	NM_001013615		A	46685434	G	A	46685434	3	1	61	1	0	0	0	0	1	0	0	0	2029	1059	37	1	268	1	C1orf190	1	46685434	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35446	46685434	202565187	251	8236										
ATPAF1	64756	broad.mit.edu	37	chr1	47119537	47119537	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcaaaatattgctgccaAatctgtacaaaaaagagagg	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47119537A>C	ENST00000371937.4	-	5	596	c.492T>G	c.(490-492)atT>atG	p.I164M	ATPAF1_ENST00000576409.1_Missense_Mutation_p.I187M|ATPAF1_ENST00000532925.1_Missense_Mutation_p.I76M|ATPAF1_ENST00000574428.1_Missense_Mutation_p.I164M|ATPAF1_ENST00000329231.4_Missense_Mutation_p.I187M|ATPAF1_ENST00000542495.1_Missense_Mutation_p.I13M	NM_022745.4	NP_073582.3	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 1	164					protein complex assembly (GO:0006461)	mitochondrion (GO:0005739)		p.I164M(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Acute lymphoblastic leukemia(166;0.155)					ATTGCTGCCAAATCTGTACAA	0.393																																					Melanoma(138;107 1777 21672 30337 52312)											1	Substitution - Missense(1)	large_intestine(1)	1											124	114	117					1																	47119537		2203	4300	6503	46892124	SO:0001583	missense	64756			AK026004	CCDS541.1, CCDS41327.1, CCDS541.2, CCDS41327.2, CCDS57997.1, CCDS57998.1	1p33-p32.3	2012-10-12			ENSG00000123472	ENSG00000123472		"Mitochondrial respiratory chain complex assembly factors"	18803	protein-coding gene	gene with protein product		608917				11410595	Standard	NM_022745		Approved	FLJ22351, Atp11p, ATP11	uc001cqh.4	Q5TC12	OTTHUMG00000007988	ENST00000371937.4:c.492T>G	1.37:g.47119537A>C	ENSP00000361005:p.Ile164Met		46892124	B1AQW7|B7Z7D6|B7Z7I6|Q9H6E3	Missense_Mutation	SNP	ENST00000371937.4	37		.	.	.	.	.	.	.	.	.	.	A	17.77	3.472295	0.63737	.	.	ENSG00000123472	ENST00000371937;ENST00000526821;ENST00000542495;ENST00000329231;ENST00000532925	T	0.59502	0.26	5.8	3.51	0.40186	.	0.104107	0.64402	D	0.000003	T	0.71879	0.3392	M	0.84219	2.685	0.58432	D	0.999996	D;D;D	0.76494	0.989;0.994;0.999	P;P;D	0.72625	0.9;0.879;0.978	T	0.72043	-0.4409	10	0.72032	D	0.01	-7.1469	4.8697	0.13625	0.7071:0.0:0.1536:0.1392	.	76;164;164	B7Z7I6;A8MRA7;Q5TC12	.;.;ATPF1_HUMAN	M	164;78;13;164;76	ENSP00000361005:I164M	ENSP00000330685:I164M	I	-	3	3	ATPAF1	46892124	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.214000	0.32419	1.016000	0.39470	0.528000	0.53228	ATT		0.393	ATPAF1-201	KNOWN	basic	protein_coding	protein_coding		NM_022745		C	47119537	A	C	47119537	3	2	61	1	0	0	0	0	1	0	0	0	1201	10	1	4	514	4	ATPAF1	1	47119537	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	434103	47119537	202131084	252	8237										
CYP4B1	1580	broad.mit.edu	37	chr1	47283832	47283832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctgcgcttttccactgaGaatgcatccaaacgccatcc	6	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47283832G>T	ENST00000271153.4	+	11	1335	c.1299G>T	c.(1297-1299)gaG>gaT	p.E433D	CYP4B1_ENST00000371923.4_Missense_Mutation_p.E434D|CYP4B1_ENST00000371919.4_Missense_Mutation_p.E419D|CYP4B1_ENST00000452782.2_Missense_Mutation_p.E271D			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	433					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.E433D(2)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TTTCCACTGAGAATGCATCCA	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	1											152	140	144					1																	47283832		2203	4300	6503	47056419	SO:0001583	missense	1580			BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1299G>T	1.37:g.47283832G>T	ENSP00000271153:p.Glu433Asp		47056419	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	37	CCDS542.1	.	.	.	.	.	.	.	.	.	.	G	8.705	0.910675	0.17833	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000452782	T;T;T;T	0.80480	-1.38;-1.38;-0.55;-1.38	6.17	3.33	0.38152	.	0.046343	0.85682	N	0.000000	D	0.83760	0.5324	L	0.56280	1.765	0.44149	D	0.99694	D;B;B	0.76494	0.999;0.029;0.035	D;B;B	0.74674	0.984;0.108;0.173	T	0.80482	-0.1363	10	0.46703	T	0.11	.	5.8952	0.18935	0.2729:0.1375:0.5896:0.0	.	419;434;433	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	D	434;433;419;271	ENSP00000360991:E434D;ENSP00000271153:E433D;ENSP00000360987:E419D;ENSP00000400413:E271D	ENSP00000271153:E433D	E	+	3	2	CYP4B1	47056419	1.000000	0.71417	0.974000	0.42286	0.004000	0.04260	1.242000	0.32755	0.493000	0.27837	-0.136000	0.14681	GAG		0.582	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		T	47283832	G	T	47283832	3	4	61	1	0	0	0	0	1	0	0	0	4191	933	33	2	1344	2	CYP4B1	1	47283832	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164295	47283832	201966789	253	8238										
CYP4A11	1579	broad.mit.edu	37	chr1	47407021	47407021	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgccttgatcagcagcaGaagcagaatgagcagggagg	14	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47407021G>T	ENST00000310638.4	-	1	116	c.85C>A	c.(85-87)Ctg>Atg	p.L29M	CYP4A11_ENST00000371904.4_Missense_Mutation_p.L29M|CYP4A11_ENST00000457840.2_De_novo_Start_InFrame|CYP4A11_ENST00000462347.1_Missense_Mutation_p.L29M|CYP4A11_ENST00000371905.1_Missense_Mutation_p.L29M	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	29	Poly-Leu.				arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)	p.L29M(1)		endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	ATCAGCAGCAGAAGCAGAATG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	99	101					1																	47407021		2203	4300	6503	47179608	SO:0001583	missense	1579			L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.85C>A	1.37:g.47407021G>T	ENSP00000311095:p.Leu29Met		47179608	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	37	CCDS543.1	.	.	.	.	.	.	.	.	.	.	-	15.16	2.751885	0.49362	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.73681	-0.77;-0.72;-0.69	4.64	2.75	0.32379	.	0.719601	0.12528	N	0.461057	D	0.82986	0.5156	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79215	-0.1895	10	0.87932	D	0	.	3.978	0.09483	0.2973:0.1788:0.5239:0.0	.	29	Q02928	CP4AB_HUMAN	M	29	ENSP00000311095:L29M;ENSP00000360971:L29M;ENSP00000360972:L29M	ENSP00000311095:L29M	L	-	1	2	CYP4A11	47179608	0.007000	0.16637	0.995000	0.50966	0.704000	0.40688	1.489000	0.35562	0.672000	0.31204	0.644000	0.83932	CTG		0.607	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		T	47407021	G	T	47407021	3	4	61	1	0	0	0	0	1	0	0	0	4189	933	33	2	1522	2	CYP4A11	1	47407021	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123189	47407021	201843600	254	8239										
CYP4X1	260293	broad.mit.edu	37	chr1	47515096	47515096	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtcctctcatttcaggtCtttgaccccttgaggttctc	8	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47515096C>A	ENST00000371901.3	+	11	1525	c.1275C>A	c.(1273-1275)gtC>gtA	p.V425V	CYP4X1_ENST00000538609.1_Silent_p.V424V	NM_178033.1	NP_828847.1	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X, polypeptide 1	425						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.V425V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	17						CATTTCAGGTCTTTGACCCCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											186	187	187					1																	47515096		2203	4300	6503	47287683	SO:0001819	synonymous_variant	260293			AK091806	CCDS544.1	1p33	2008-02-05			ENSG00000186377	ENSG00000186377		"Cytochrome P450s"	20244	protein-coding gene	gene with protein product		614999				12176035	Standard	NM_178033		Approved	MGC40051	uc001cqt.3	Q8N118	OTTHUMG00000008017	ENST00000371901.3:c.1275C>A	1.37:g.47515096C>A			47287683	G3V1U1|Q5VVE5|Q6ZN67|Q8NAZ3	Silent	SNP	ENST00000371901.3	37	CCDS544.1																																																																																				0.443	CYP4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022017.1	NM_178033		A	47515096	C	A	47515096	2	1	61	1	0	0	0	0	0	0	0	1	4199	900	32	2		2	CYP4X1	1	47515096	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108075	47515096	201735525	255	8240										
CYP4Z1	199974	broad.mit.edu	37	chr1	47581250	47581250	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaccacaacccctatttCtgggaagaccctcaggtatg	7	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47581250C>A	ENST00000334194.3	+	10	1254	c.1251C>A	c.(1249-1251)ttC>ttA	p.F417L	CYP4Z1_ENST00000471598.1_3'UTR|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	417						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.F417L(1)		cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						ACCCCTATTTCTGGGAAGACC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	96	99					1																	47581250		2203	4300	6503	47353837	SO:0001583	missense	199974			AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"Cytochrome P450s"	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1251C>A	1.37:g.47581250C>A	ENSP00000334246:p.Phe417Leu		47353837	Q5VVE4	Missense_Mutation	SNP	ENST00000334194.3	37	CCDS545.1	.	.	.	.	.	.	.	.	.	.	c	14.84	2.655473	0.47467	.	.	ENSG00000186160	ENST00000334194	T	0.66638	-0.22	2.7	0.363	0.16118	.	0.201444	0.30809	U	0.008823	T	0.39835	0.1093	N	0.10664	0.02	0.09310	N	0.999993	B	0.20671	0.047	B	0.19148	0.024	T	0.31724	-0.9933	10	0.62326	D	0.03	.	5.9386	0.19179	0.2151:0.575:0.2099:0.0	.	417	Q86W10	CP4Z1_HUMAN	L	417	ENSP00000334246:F417L	ENSP00000334246:F417L	F	+	3	2	CYP4Z1	47353837	0.978000	0.34361	0.152000	0.22495	0.893000	0.52053	1.165000	0.31822	0.322000	0.23283	0.271000	0.19318	TTC		0.443	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		A	47581250	C	A	47581250	3	1	61	1	0	0	0	0	1	0	0	0	4200	912	32	2	1289	2	CYP4Z1	1	47581250	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66154	47581250	201669371	256	8241										
STIL	6491	broad.mit.edu	37	chr1	47735434	47735434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgacttcattattaatatCgacagaaaaattcatgtcct	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47735434C>T	ENST00000360380.3	-	15	2851	c.2488G>A	c.(2488-2490)Gat>Aat	p.D830N	STIL_ENST00000337817.5_Missense_Mutation_p.D830N|STIL_ENST00000243182.6_Missense_Mutation_p.D830N|STIL_ENST00000371877.3_Missense_Mutation_p.D830N|STIL_ENST00000396221.2_Missense_Mutation_p.D830N	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	830					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.D830N(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				TTATTAATATCGACAGAAAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	124	123					1																	47735434		2203	4300	6503	47508021	SO:0001583	missense	6491			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.2488G>A	1.37:g.47735434C>T	ENSP00000353544:p.Asp830Asn		47508021	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.89|12.89	2.073126|2.073126	0.36566|0.36566	.|.	.|.	ENSG00000123473|ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371874;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475|ENST00000436811	T;T;T;T;T;T|.	0.45276|.	2.25;2.25;2.26;2.28;2.25;0.9|.	4.57|4.57	2.65|2.65	0.31530|0.31530	.|.	0.854777|.	0.10835|.	N|.	0.628890|.	T|T	0.38453|0.38453	0.1041|0.1041	L|L	0.48642|0.48642	1.525|1.525	0.24382|0.24382	N|N	0.99479|0.99479	D;P;D;D;D|.	0.56968|.	0.978;0.95;0.978;0.978;0.978|.	P;B;P;P;P|.	0.44597|.	0.454;0.257;0.454;0.454;0.454|.	T|T	0.23868|0.23868	-1.0176|-1.0176	10|5	0.20046|.	T|.	0.44|.	-14.6814|-14.6814	6.1933|6.1933	0.20536|0.20536	0.0:0.6576:0.0:0.3424|0.0:0.6576:0.0:0.3424	.|.	830;783;830;830;830|.	E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468|.	.;.;.;.;STIL_HUMAN|.	N|Q	830;830;169;830;830;830;783|169	ENSP00000353544:D830N;ENSP00000337367:D830N;ENSP00000360944:D830N;ENSP00000379523:D830N;ENSP00000243182:D830N;ENSP00000411664:D783N|.	ENSP00000243182:D830N|.	D|R	-|-	1|2	0|0	STIL|STIL	47508021|47508021	0.705000|0.705000	0.27846|0.27846	0.996000|0.996000	0.52242|0.52242	0.936000|0.936000	0.57629|0.57629	0.706000|0.706000	0.25690|0.25690	1.145000|1.145000	0.42336|0.42336	0.462000|0.462000	0.41574|0.41574	GAT|CGA		0.388	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		T	47735434	C	T	47735434	3	4	61	1	0	0	0	0	1	0	0	0	15321	884	31	1	1394	1	STIL	1	47735434	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154184	47735434	201515187	257	8242										
STIL	6491	broad.mit.edu	37	chr1	47746274	47746274	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtttgctccttgccaaGaatttagcggactatattga	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47746274G>T	ENST00000360380.3	-	13	2219	c.1856C>A	c.(1855-1857)tCt>tAt	p.S619Y	STIL_ENST00000337817.5_Missense_Mutation_p.S619Y|STIL_ENST00000243182.6_Missense_Mutation_p.S619Y|STIL_ENST00000371877.3_Missense_Mutation_p.S619Y|STIL_ENST00000396221.2_Missense_Mutation_p.S619Y	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	619	PIN1-binding. {ECO:0000250}.				cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.S619Y(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				TCCTTGCCAAGAATTTAGCGG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											159	161	161					1																	47746274		2203	4300	6503	47518861	SO:0001583	missense	6491			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.1856C>A	1.37:g.47746274G>T	ENSP00000353544:p.Ser619Tyr		47518861	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.458509	0.43634	.	.	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475	T;T;T;T;T;T	0.52983	1.99;1.99;1.99;1.98;1.99;0.64	5.54	4.44	0.53790	.	0.541442	0.21276	N	0.077237	T	0.52693	0.1750	L	0.32530	0.975	0.35234	D	0.77714	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.998	D;D;D;D;D	0.63381	0.914;0.914;0.914;0.914;0.914	T	0.63014	-0.6731	10	0.72032	D	0.01	-17.2815	10.8053	0.46514	0.0793:0.1344:0.7862:0.0	.	619;572;619;619;619	E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468	.;.;.;.;STIL_HUMAN	Y	619;619;619;619;619;572	ENSP00000353544:S619Y;ENSP00000337367:S619Y;ENSP00000360944:S619Y;ENSP00000379523:S619Y;ENSP00000243182:S619Y;ENSP00000411664:S572Y	ENSP00000243182:S619Y	S	-	2	0	STIL	47518861	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	3.861000	0.56002	2.613000	0.88420	0.650000	0.86243	TCT		0.443	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		T	47746274	G	T	47746274	3	4	61	1	0	0	0	0	1	0	0	0	15321	942	33	2	2034	2	STIL	1	47746274	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10840	47746274	201504347	258	8243										
STIL	6491	broad.mit.edu	37	chr1	47761455	47761455	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattcccaccaatggtagaGaataaaccttgggatcagat	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:47761455G>T	ENST00000360380.3	-	8	1130	c.767C>A	c.(766-768)tCt>tAt	p.S256Y	STIL_ENST00000337817.5_Missense_Mutation_p.S256Y|STIL_ENST00000243182.6_Missense_Mutation_p.S256Y|STIL_ENST00000371877.3_Missense_Mutation_p.S256Y|STIL_ENST00000396221.2_Missense_Mutation_p.S256Y	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	256					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.S256Y(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CAATGGTAGAGAATAAACCTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	108	111					1																	47761455		2203	4298	6501	47534042	SO:0001583	missense	6491			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.767C>A	1.37:g.47761455G>T	ENSP00000353544:p.Ser256Tyr		47534042	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804610	0.70682	.	.	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475	T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74	5.77	5.77	0.91146	.	0.276465	0.40469	N	0.001093	T	0.65048	0.2654	M	0.61703	1.905	0.38761	D	0.954324	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.76071	0.972;0.987;0.972;0.974;0.974	T	0.69038	-0.5251	10	0.72032	D	0.01	-17.4944	13.2196	0.59879	0.0723:0.0:0.9277:0.0	.	256;209;256;256;256	E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468	.;.;.;.;STIL_HUMAN	Y	256;256;256;256;256;209	ENSP00000353544:S256Y;ENSP00000337367:S256Y;ENSP00000360944:S256Y;ENSP00000379523:S256Y;ENSP00000243182:S256Y;ENSP00000411664:S209Y	ENSP00000243182:S256Y	S	-	2	0	STIL	47534042	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.363000	0.52321	2.720000	0.93068	0.557000	0.71058	TCT		0.318	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		T	47761455	G	T	47761455	3	4	61	1	0	0	0	0	1	0	0	0	15321	942	33	2	3143	2	STIL	1	47761455	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15181	47761455	201489166	259	8244										
SLC5A9	200010	broad.mit.edu	37	chr1	48703430	48703430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacagtgggcagctcttcGactacatccaggctgtcacc	9	15	2	0	rs368141578		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:48703430G>A	ENST00000438567.2	+	11	1424	c.1372G>A	c.(1372-1374)Gac>Aac	p.D458N	SLC5A9_ENST00000236495.5_Missense_Mutation_p.D483N|SLC5A9_ENST00000533824.1_Missense_Mutation_p.D479N	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	458					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.D476N(1)		breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GCAGCTCTTCGACTACATCCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ASN/ASP,ASN/ASP	0,4406		0,0,2203	169	132	145		1372,1447	5	1	1		145	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	458/682,483/707	48703430	1,13005	2203	4300	6503	48476017	SO:0001583	missense	200010			BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1372G>A	1.37:g.48703430G>A	ENSP00000401730:p.Asp458Asn		48476017	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	g	17.83	3.484662	0.63962	0.0	1.16E-4	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.88046	-2.33;-2.33;-2.33	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.83529	0.5274	L	0.46819	1.47	0.80722	D	1	B;B;B	0.28933	0.228;0.074;0.074	B;B;B	0.27608	0.081;0.032;0.052	T	0.80151	-0.1502	10	0.27785	T	0.31	.	17.5459	0.87861	0.0:0.0:1.0:0.0	.	479;458;483	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	N	479;458;483	ENSP00000431900:D479N;ENSP00000401730:D458N;ENSP00000236495:D483N	ENSP00000236495:D483N	D	+	1	0	SLC5A9	48476017	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	4.752000	0.62176	2.624000	0.88883	0.651000	0.88453	GAC		0.572	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		A	48703430	G	A	48703430	3	1	61	1	0	0	0	0	1	0	0	0	14709	1058	37	1	1493	1	SLC5A9	1	48703430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	941975	48703430	200547191	260	8245										
SPATA6	54558	broad.mit.edu	37	chr1	48771466	48771466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcattcatacctatactCggggtcactgtcataggcag	8	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:48771466C>T	ENST00000371847.3	-	12	1443	c.1279G>A	c.(1279-1281)Gag>Aag	p.E427K	SPATA6_ENST00000371843.3_Missense_Mutation_p.E411K|SPATA6_ENST00000396199.3_Missense_Mutation_p.E355K	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	427					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.E427K(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TACCTATACTCGGGGTCACTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											175	191	185					1																	48771466		2203	4300	6503	48544053	SO:0001583	missense	54558			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"spermatogenesis-related factor-1"	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.1279G>A	1.37:g.48771466C>T	ENSP00000360913:p.Glu427Lys		48544053	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529376	0.64860	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199	T;T;T	0.14022	2.54;2.66;2.56	4.55	4.55	0.56014	.	0.201069	0.41938	D	0.000783	T	0.21267	0.0512	L	0.34521	1.04	0.33708	D	0.615398	P;D;D	0.76494	0.584;0.995;0.999	B;D;D	0.76575	0.064;0.97;0.988	T	0.01966	-1.1238	10	0.07644	T	0.81	.	13.0003	0.58672	0.0:1.0:0.0:0.0	.	355;411;427	B4DX17;Q9NWH7-2;Q9NWH7	.;.;SPAT6_HUMAN	K	427;411;355	ENSP00000360913:E427K;ENSP00000360909:E411K;ENSP00000379502:E355K	ENSP00000360909:E411K	E	-	1	0	SPATA6	48544053	0.918000	0.31147	0.980000	0.43619	0.983000	0.72400	2.371000	0.44248	2.531000	0.85337	0.467000	0.42956	GAG		0.318	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		T	48771466	C	T	48771466	3	4	61	1	0	0	0	0	1	0	0	0	15052	893	31	1	195	1	SPATA6	1	48771466	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68036	48771466	200479155	261	8246										
SPATA6	54558	broad.mit.edu	37	chr1	48865265	48865265	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcttgatgttctgttttGcagtctgccatgtgattttt	9	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:48865265G>T	ENST00000371847.3	-	7	702	c.538C>A	c.(538-540)Caa>Aaa	p.Q180K	SPATA6_ENST00000371843.3_Missense_Mutation_p.Q180K|SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000396199.3_Missense_Mutation_p.Q108K	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	180					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.Q180K(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GTTCTGTTTTGCAGTCTGCCA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	123	123					1																	48865265		2203	4300	6503	48637852	SO:0001583	missense	54558			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"spermatogenesis-related factor-1"	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.538C>A	1.37:g.48865265G>T	ENSP00000360913:p.Gln180Lys		48637852	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.770229	0.49680	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.47869	2.73;2.73;2.73;0.83	5.04	5.04	0.67666	.	0.407810	0.25750	N	0.028546	T	0.40067	0.1102	L	0.43152	1.355	0.38623	D	0.951196	B;B;B;B	0.34329	0.082;0.449;0.058;0.017	B;B;B;B	0.28638	0.062;0.092;0.034;0.034	T	0.45190	-0.9278	10	0.48119	T	0.1	.	15.6993	0.77533	0.0:0.0:1.0:0.0	.	108;108;180;180	B4DX17;A8MU33;Q9NWH7-2;Q9NWH7	.;.;.;SPAT6_HUMAN	K	180;180;108;21	ENSP00000360913:Q180K;ENSP00000360909:Q180K;ENSP00000379502:Q108K;ENSP00000360907:Q21K	ENSP00000360907:Q21K	Q	-	1	0	SPATA6	48637852	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.118000	0.57884	2.611000	0.88343	0.555000	0.69702	CAA		0.303	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		T	48865265	G	T	48865265	3	4	61	1	0	0	0	0	1	0	0	0	15052	1328	46	2	956	2	SPATA6	1	48865265	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93799	48865265	200385356	262	8247										
BEND5	79656	broad.mit.edu	37	chr1	49224725	49224725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctcctgctggaggtggcGcatctcttcctgttgctgct	12	13	1	0	rs201098567		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:49224725G>A	ENST00000371833.3	-	3	678	c.592C>T	c.(592-594)Cgc>Tgc	p.R198C	BEND5_ENST00000476096.1_5'UTR|AGBL4_ENST00000371839.1_Intron|AGBL4_ENST00000371838.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	198						Golgi apparatus (GO:0005794)		p.R29C(2)		large_intestine(5)|lung(2)|skin(1)	8						TGGAGGTGGCGCATCTCTTCC	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	1						G	CYS/ARG,	0,4406		0,0,2203	98	92	94		592,	4.5	1	1		94	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	BEND5,AGBL4	NM_024603.2,NM_032785.3	180,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	198/422,	49224725	1,13005	2203	4300	6503	48997312	SO:0001583	missense	79656			BC007932	CCDS552.2	1p33	2012-11-22	2008-10-03	2008-10-03	ENSG00000162373	ENSG00000162373		"BEN domain containing"	25668	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 165"	C1orf165		12477932	Standard	NM_024603		Approved	FLJ11588	uc001crx.4	Q7L4P6	OTTHUMG00000008153	ENST00000371833.3:c.592C>T	1.37:g.49224725G>A	ENSP00000360899:p.Arg198Cys		48997312	D3DQ27|Q96A62|Q9HAI3	Missense_Mutation	SNP	ENST00000371833.3	37	CCDS552.2	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788076	0.70337	0.0	1.16E-4	ENSG00000162373	ENST00000371833	.	.	.	5.4	4.47	0.54385	.	0.048307	0.85682	D	0.000000	T	0.42040	0.1185	L	0.29908	0.895	0.58432	D	0.999996	D	0.69078	0.997	B	0.44315	0.446	T	0.24941	-1.0146	8	.	.	.	-20.9454	12.2606	0.54649	0.0:0.0:0.5714:0.4286	.	198	Q7L4P6	BEND5_HUMAN	C	198	.	.	R	-	1	0	BEND5	48997312	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.206000	0.58473	1.376000	0.46267	0.655000	0.94253	CGC		0.587	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603		A	49224725	G	A	49224725	3	1	61	1	0	0	0	0	1	0	0	0	1402	1087	38	1	689	1	BEND5	1	49224725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	359460	49224725	200025896	263	8248										
EPS15	2060	broad.mit.edu	37	chr1	51864705	51864705	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaattctcccacttaccGatgtaatactgctattgttg	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:51864705G>A	ENST00000371733.3	-	20	2147	c.2051C>T	c.(2050-2052)tCg>tTg	p.S684L	EPS15_ENST00000371730.2_Splice_Site_p.S550L|EPS15_ENST00000396122.4_Splice_Site_p.S361L	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	684	15 X 3 AA repeats of D-P-F.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)|p.S684L(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CCCACTTACCGATGTAATACT	0.373			T	MLL	ALL																																		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	3	Whole gene deletion(2)|Substitution - Missense(1)	thyroid(1)|large_intestine(1)|central_nervous_system(1)	1											112	105	108					1																	51864705		2203	4300	6503	51637293	SO:0001630	splice_region_variant	2060			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2052+1C>T	1.37:g.51864705G>A			51637293	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.214472	0.39102	.	.	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000396122	T;T;T	0.17213	2.29;2.29;2.29	5.34	2.43	0.29744	.	.	.	.	.	T	0.14399	0.0348	L	0.43152	1.355	0.36313	D	0.857757	B;B;B	0.22480	0.07;0.066;0.004	B;B;B	0.14578	0.011;0.009;0.004	T	0.08617	-1.0713	9	0.52906	T	0.07	.	9.389	0.38361	0.225:0.0:0.775:0.0	.	550;684;370	B1AUU8;P42566;P42566-2	.;EPS15_HUMAN;.	L	550;684;361	ENSP00000360795:S550L;ENSP00000360798:S684L;ENSP00000379428:S361L	ENSP00000360795:S550L	S	-	2	0	EPS15	51637293	0.681000	0.27614	0.995000	0.50966	0.848000	0.48234	1.640000	0.37186	0.646000	0.30693	0.491000	0.48974	TCG		0.373	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	Missense_Mutation	A	51864705	G	A	51864705	5	1	61	1	0	0	0	0	0	0	1	0	5205	1072	37	1	663	1	EPS15	1	51864705	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2639980	51864705	197385916	264	8249										
EPS15	2060	broad.mit.edu	37	chr1	51871633	51871633	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctggccttcaacatgttCattaaggttggctgtttcac	9	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:51871633C>A	ENST00000371733.3	-	16	1717	c.1621G>T	c.(1621-1623)Gaa>Taa	p.E541*	EPS15_ENST00000371730.2_Intron|EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000396122.4_Nonsense_Mutation_p.E218*	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	541					cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)|p.E541*(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						TCAACATGTTCATTAAGGTTG	0.453			T	MLL	ALL																																		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	3	Whole gene deletion(2)|Substitution - Nonsense(1)	thyroid(1)|large_intestine(1)|central_nervous_system(1)	1											215	182	193					1																	51871633		2203	4300	6503	51644221	SO:0001587	stop_gained	2060			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.1621G>T	1.37:g.51871633C>A	ENSP00000360798:p.Glu541*		51644221	B2R8J7|D3DPJ2|Q5SRH4	Nonsense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	C	38	7.070955	0.98044	.	.	ENSG00000085832	ENST00000371733;ENST00000396122	.	.	.	5.4	5.4	0.78164	.	0.000000	0.32852	N	0.005577	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.3711	0.94488	0.0:1.0:0.0:0.0	.	.	.	.	X	541;218	.	ENSP00000360798:E541X	E	-	1	0	EPS15	51644221	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.102000	0.64572	2.814000	0.96858	0.563000	0.77884	GAA		0.453	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		A	51871633	C	A	51871633	4	1	61	1	0	0	0	0	0	1	0	0	5205	835	29	2	1109	2	EPS15	1	51871633	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6928	51871633	197378988	265	8250										
RAB3B	5865	broad.mit.edu	37	chr1	52442637	52442637	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgatgcccacggtgctaacGaaggctggggtgaacgtgtc	15	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52442637G>A	ENST00000371655.3	-	2	365	c.153C>T	c.(151-153)ttC>ttT	p.F51F		NM_002867.3	NP_002858.2	P20337	RAB3B_HUMAN	RAB3B, member RAS oncogene family	51					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle size (GO:0097494)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.F51F(1)		large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9						CGGTGCTAACGAAGGCTGGGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											174	129	144					1																	52442637		2203	4300	6503	52215225	SO:0001819	synonymous_variant	5865			BC005035	CCDS560.1	1p32-p31	2008-02-05			ENSG00000169213	ENSG00000169213		"RAB, member RAS oncogene"	9778	protein-coding gene	gene with protein product		179510					Standard	NM_002867		Approved		uc001cth.3	P20337	OTTHUMG00000008627	ENST00000371655.3:c.153C>T	1.37:g.52442637G>A			52215225	Q5VUL2|Q9BSI1	Silent	SNP	ENST00000371655.3	37	CCDS560.1																																																																																				0.517	RAB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023816.1	NM_002867		A	52442637	G	A	52442637	2	1	61	1	0	0	0	0	0	0	0	1	12969	1049	37	1		1	RAB3B	1	52442637	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	571004	52442637	196807984	266	8251										
TXNDC12	51060	broad.mit.edu	37	chr1	52490227	52490227	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccccgtcagggctgaaatCttcatctttgggttcctctt	8	13	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52490227C>A	ENST00000371626.4	-	5	1384	c.310G>T	c.(310-312)Gat>Tat	p.D104Y	TXNDC12_ENST00000471493.1_5'UTR	NM_015913.3	NP_056997.1	O95881	TXD12_HUMAN	thioredoxin domain containing 12 (endoplasmic reticulum)	104					cell redox homeostasis (GO:0045454)	endoplasmic reticulum (GO:0005783)	protein-disulfide reductase (glutathione) activity (GO:0019153)	p.D104Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7					Glutathione(DB00143)	GGGCTGAAATCTTCATCTTTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	89	91					1																	52490227		2203	4300	6503	52262815	SO:0001583	missense	51060			AF131758	CCDS561.1	1p32.3	2011-10-19			ENSG00000117862	ENSG00000117862		"Protein disulfide isomerases"	24626	protein-coding gene	gene with protein product	"endoplasmic reticulum thioredoxin superfamily member, 18 kDa", "anterior gradient homolog 1 (Xenopus laevis)", "protein disulfide isomerase family A, member 16"	609448				8619474, 9110174	Standard	NM_015913		Approved	TLP19, ERP18, ERP19, hAG-1, AGR1, PDIA16	uc001cti.4	O95881	OTTHUMG00000008629	ENST00000371626.4:c.310G>T	1.37:g.52490227C>A	ENSP00000360688:p.Asp104Tyr		52262815	B3KQS0|Q5T1T4|Q96H50	Missense_Mutation	SNP	ENST00000371626.4	37	CCDS561.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676810	0.88445	.	.	ENSG00000117862	ENST00000371626	T	0.46451	0.87	5.66	5.66	0.87406	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.159786	0.56097	D	0.000037	T	0.53965	0.1829	L	0.34521	1.04	0.44825	D	0.99783	D	0.61080	0.989	D	0.64877	0.93	T	0.54702	-0.8254	10	0.66056	D	0.02	.	17.9364	0.89013	0.0:1.0:0.0:0.0	.	104	O95881	TXD12_HUMAN	Y	104	ENSP00000360688:D104Y	ENSP00000360688:D104Y	D	-	1	0	TXNDC12	52262815	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.215000	0.72206	2.656000	0.90262	0.655000	0.94253	GAT		0.428	TXNDC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023818.1	NM_015913		A	52490227	C	A	52490227	3	1	61	1	0	0	0	0	1	0	0	0	16833	913	32	2	220	2	TXNDC12	1	52490227	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47590	52490227	196760394	267	8252										
ZFYVE9	9372	broad.mit.edu	37	chr1	52803472	52803472	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtccagattactgcagaGaacatggattccttgaggca	11	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52803472G>T	ENST00000371591.1	+	15	3830	c.3699G>T	c.(3697-3699)gaG>gaT	p.E1233D	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.E1233D|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.E1174D	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1233					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)	p.E1233D(1)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TTACTGCAGAGAACATGGATT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	95	100					1																	52803472		2203	4300	6503	52576060	SO:0001583	missense	9372			AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.3699G>T	1.37:g.52803472G>T	ENSP00000360647:p.Glu1233Asp		52576060	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123326	0.56613	.	.	ENSG00000157077	ENST00000357206;ENST00000287727;ENST00000371591	T;T;T	0.42900	1.02;0.96;0.96	5.54	4.56	0.56223	Domain of unknown function DUF3480 (1);	0.047735	0.85682	D	0.000000	T	0.43523	0.1251	N	0.22421	0.69	0.50467	D	0.999879	B;P	0.52061	0.233;0.95	B;P	0.61940	0.137;0.896	T	0.34551	-0.9824	10	0.87932	D	0	.	7.7054	0.28646	0.1273:0.1577:0.715:0.0	.	1174;1233	O95405-2;O95405	.;ZFYV9_HUMAN	D	1174;1233;1233	ENSP00000349737:E1174D;ENSP00000287727:E1233D;ENSP00000360647:E1233D	ENSP00000287727:E1233D	E	+	3	2	ZFYVE9	52576060	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.590000	0.46154	2.890000	0.99128	0.650000	0.86243	GAG		0.517	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		T	52803472	G	T	52803472	3	4	61	1	0	0	0	0	1	0	0	0	17710	933	33	2	3764	2	ZFYVE9	1	52803472	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	313245	52803472	196447149	268	8253										
ZFYVE9	9372	broad.mit.edu	37	chr1	52810523	52810523	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgactgagcatgttgccaaAgctttttgccttgctctctg	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52810523A>C	ENST00000371591.1	+	17	4154	c.4023A>C	c.(4021-4023)aaA>aaC	p.K1341N	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.K1341N|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.K1282N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1341					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)	p.K1341N(1)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						ATGTTGCCAAAGCTTTTTGCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											166	131	143					1																	52810523		2203	4300	6503	52583111	SO:0001583	missense	9372			AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.4023A>C	1.37:g.52810523A>C	ENSP00000360647:p.Lys1341Asn		52583111	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	18.96	3.733177	0.69189	.	.	ENSG00000157077	ENST00000357206;ENST00000287727;ENST00000371591	T;T;T	0.40756	1.09;1.02;1.02	5.16	3.06	0.35304	Domain of unknown function DUF3480 (1);	0.093882	0.64402	D	0.000001	T	0.51415	0.1673	L	0.54323	1.7	0.40126	D	0.976655	D;P	0.71674	0.998;0.605	D;P	0.66351	0.943;0.449	T	0.50964	-0.8765	10	0.45353	T	0.12	.	7.3022	0.26426	0.3191:0.0:0.6809:0.0	.	1282;1341	O95405-2;O95405	.;ZFYV9_HUMAN	N	1282;1341;1341	ENSP00000349737:K1282N;ENSP00000287727:K1341N;ENSP00000360647:K1341N	ENSP00000287727:K1341N	K	+	3	2	ZFYVE9	52583111	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	0.539000	0.23175	1.387000	0.46486	-0.177000	0.13119	AAA		0.448	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		C	52810523	A	C	52810523	3	2	61	1	0	0	0	0	1	0	0	0	17710	69	3	4	4096	4	ZFYVE9	1	52810523	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7051	52810523	196440098	269	8254										
ORC1L	4998	broad.mit.edu	37	chr1	52854196	52854196	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacacagttctgggtgctCtccttggaaggggcggtgtg	17	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52854196C>T	ENST00000371568.3	-	8	1519	c.1301G>A	c.(1300-1302)aGa>aAa	p.R434K	ORC1_ENST00000371566.1_Missense_Mutation_p.R434K	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	434					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R434K(1)		breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TCTGGGTGCTCTCCTTGGAAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											225	203	210					1																	52854196		2203	4300	6503	52626784	SO:0001583	missense	4998				CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1301G>A	1.37:g.52854196C>T	ENSP00000360623:p.Arg434Lys		52626784	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	C	4.608	0.113058	0.08831	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.39997	1.05;1.05	4.65	2.61	0.31194	.	0.545228	0.23181	N	0.051015	T	0.31606	0.0802	M	0.67953	2.075	0.09310	N	0.999999	B;B	0.16802	0.019;0.007	B;B	0.15052	0.012;0.006	T	0.27640	-1.0068	10	0.07030	T	0.85	-4.3134	5.0959	0.14733	0.0:0.6902:0.0:0.3098	.	434;434	B7Z8H0;Q13415	.;ORC1_HUMAN	K	434	ENSP00000360623:R434K;ENSP00000360621:R434K	ENSP00000360621:R434K	R	-	2	0	ORC1	52626784	0.001000	0.12720	0.006000	0.13384	0.013000	0.08279	0.435000	0.21510	1.201000	0.43203	0.591000	0.81541	AGA		0.488	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		T	52854196	C	T	52854196	3	4	61	1	0	0	0	0	1	0	0	0	11292	913	32	3	1324	3	ORC1L	1	52854196	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43673	52854196	196396425	270	8255										
ORC1L	4998	broad.mit.edu	37	chr1	52859212	52859212	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttctctcctctctaatgtCtatggttttcgaagctgcaa	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52859212C>A	ENST00000371568.3	-	6	1203	c.985G>T	c.(985-987)Gac>Tac	p.D329Y	ORC1_ENST00000371566.1_Missense_Mutation_p.D329Y	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	329					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D329Y(1)		breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TCTCTAATGTCTATGGTTTTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											220	199	206					1																	52859212		2203	4300	6503	52631800	SO:0001583	missense	4998				CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.985G>T	1.37:g.52859212C>A	ENSP00000360623:p.Asp329Tyr		52631800	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	C	9.723	1.160083	0.21454	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.40756	1.02;1.02	4.39	1.44	0.22558	.	1.287320	0.04758	N	0.425818	T	0.28499	0.0705	N	0.22421	0.69	0.09310	N	1	B;B	0.26147	0.143;0.003	B;B	0.18871	0.023;0.006	T	0.27123	-1.0083	10	0.62326	D	0.03	-0.4912	4.3491	0.11146	0.0:0.6121:0.1953:0.1926	.	329;329	B7Z8H0;Q13415	.;ORC1_HUMAN	Y	329	ENSP00000360623:D329Y;ENSP00000360621:D329Y	ENSP00000360621:D329Y	D	-	1	0	ORC1	52631800	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.153000	0.10144	0.338000	0.23692	0.655000	0.94253	GAC		0.458	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		A	52859212	C	A	52859212	3	1	61	1	0	0	0	0	1	0	0	0	11292	913	32	2	1648	2	ORC1L	1	52859212	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5016	52859212	196391409	271	8256										
PRPF38A	84950	broad.mit.edu	37	chr1	52874326	52874326	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttggaacctttgtacaatGactatcgaaaaatcaagagc	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52874326G>A	ENST00000257181.9	+	3	562	c.376G>A	c.(376-378)Gac>Aac	p.D126N	snoU13_ENST00000458879.1_RNA|PRPF38A_ENST00000474048.1_Intron	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	126					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.D126N(1)		cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						TTTGTACAATGACTATCGAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	90	93					1																	52874326		2203	4300	6503	52646914	SO:0001583	missense	84950			AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.376G>A	1.37:g.52874326G>A	ENSP00000257181:p.Asp126Asn		52646914	Q96JW1|Q9BVZ8	Missense_Mutation	SNP	ENST00000257181.9	37	CCDS567.1	.	.	.	.	.	.	.	.	.	.	G	36	5.700546	0.96802	.	.	ENSG00000134748	ENST00000257181	.	.	.	5.37	5.37	0.77165	.	0.086786	0.85682	D	0.000000	D	0.89705	0.6792	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92493	0.6002	9	0.62326	D	0.03	-25.1196	19.1028	0.93281	0.0:0.0:1.0:0.0	.	126	Q8NAV1	PR38A_HUMAN	N	126	.	ENSP00000257181:D126N	D	+	1	0	PRPF38A	52646914	1.000000	0.71417	0.993000	0.49108	0.960000	0.62799	9.722000	0.98770	2.507000	0.84556	0.557000	0.71058	GAC		0.428	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		A	52874326	G	A	52874326	3	1	61	1	0	0	0	0	1	0	0	0	12601	1290	45	3	386	3	PRPF38A	1	52874326	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15114	52874326	196376295	272	8257										
ZCCHC11	23318	broad.mit.edu	37	chr1	52943434	52943434	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttctcttgttaaaatatCttgtatccgtacacatatga	4	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:52943434C>A	ENST00000371544.3	-	12	2231	c.1969G>T	c.(1969-1971)Gat>Tat	p.D657Y	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.D657Y|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	657	PAP-associated 1.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.D657Y(1)		NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GTTAAAATATCTTGTATCCGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	108	107					1																	52943434		2203	4300	6503	52716022	SO:0001583	missense	23318			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1969G>T	1.37:g.52943434C>A	ENSP00000360599:p.Asp657Tyr		52716022	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070409	0.93950	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.72	5.72	0.89469	PAP/25A-associated (1);	0.160682	0.56097	D	0.000037	T	0.80127	0.4566	N	0.19112	0.55	0.80722	D	1	D;D;D	0.63880	0.98;0.993;0.991	P;P;P	0.61070	0.752;0.854;0.883	T	0.82248	-0.0551	10	0.62326	D	0.03	.	19.8631	0.96790	0.0:1.0:0.0:0.0	.	416;657;657	E9PKX1;Q5TAX3-2;Q5TAX3	.;.;TUT4_HUMAN	Y	657;657;586;416	ENSP00000257177:D657Y;ENSP00000360599:D657Y;ENSP00000433486:D586Y;ENSP00000435256:D416Y	ENSP00000257177:D657Y	D	-	1	0	ZCCHC11	52716022	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.291000	0.78721	2.695000	0.91970	0.650000	0.86243	GAT		0.353	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		A	52943434	C	A	52943434	3	1	61	1	0	0	0	0	1	0	0	0	17619	913	32	2	3044	2	ZCCHC11	1	52943434	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69108	52943434	196307187	273	8258										
CPT2	1376	broad.mit.edu	37	chr1	53676514	53676514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttaatgaagtatttaaaGacagcactcagacccctgcc	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:53676514G>T	ENST00000371486.3	+	4	1683	c.1168G>T	c.(1168-1170)Gac>Tac	p.D390Y	RP5-1024G6.2_ENST00000452466.1_RNA	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	390					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)	p.D390Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	AGTATTTAAAGACAGCACTCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											44	42	43					1																	53676514		2203	4300	6503	53449102	SO:0001583	missense	1376			BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"carnitine palmitoyltransferase II"	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1168G>T	1.37:g.53676514G>T	ENSP00000360541:p.Asp390Tyr		53449102	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198650	0.79015	.	.	ENSG00000157184	ENST00000371486	D	0.89415	-2.51	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	D	0.94394	0.8197	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92181	0.5751	10	0.32370	T	0.25	-9.2321	20.4777	0.99188	0.0:0.0:1.0:0.0	.	390	P23786	CPT2_HUMAN	Y	390	ENSP00000360541:D390Y	ENSP00000360541:D390Y	D	+	1	0	CPT2	53449102	1.000000	0.71417	0.996000	0.52242	0.779000	0.44077	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	GAC		0.502	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098		T	53676514	G	T	53676514	3	4	61	1	0	0	0	0	1	0	0	0	3840	942	33	2	1182	2	CPT2	1	53676514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	733080	53676514	195574107	274	8259										
LRP8	7804	broad.mit.edu	37	chr1	53716481	53716481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcttttggtgttcttccGcttccagtttctccagatca	7	12	3	1	rs147172505		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:53716481G>A	ENST00000306052.6	-	17	2658	c.2557C>T	c.(2557-2559)Cgg>Tgg	p.R853W	LRP8_ENST00000371454.2_Missense_Mutation_p.R853W|LRP8_ENST00000347547.2_Missense_Mutation_p.R683W|LRP8_ENST00000354412.3_Missense_Mutation_p.R649W|LRP8_ENST00000465675.1_Missense_Mutation_p.R406W	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	853					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.R853W(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						GTGTTCTTCCGCTTCCAGTTT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											253	215	228					1																	53716481		2203	4300	6503	53489069	SO:0001583	missense	7804			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2557C>T	1.37:g.53716481G>A	ENSP00000303634:p.Arg853Trp		53489069	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504843	0.85176	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.42	4.42	0.53409	.	.	.	.	.	T	0.45115	0.1326	M	0.65975	2.015	0.50632	D	0.999888	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;0.999	P;D;D;P;D;P	0.74674	0.884;0.984;0.963;0.9;0.959;0.884	T	0.44375	-0.9332	9	0.66056	D	0.02	.	16.8378	0.85961	0.0:0.0:0.8627:0.1373	.	406;649;683;853;853;406	B3KU40;Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;.;LRP8_HUMAN;.	W	853;853;406;649;683	ENSP00000303634:R853W;ENSP00000360509:R853W;ENSP00000437009:R406W;ENSP00000346391:R649W;ENSP00000334522:R683W	ENSP00000303634:R853W	R	-	1	2	LRP8	53489069	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.983000	0.56916	2.528000	0.85240	0.563000	0.77884	CGG		0.493	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		A	53716481	G	A	53716481	3	1	61	1	0	0	0	0	1	0	0	0	8992	1086	38	1	346	1	LRP8	1	53716481	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39967	53716481	195534140	275	8260										
GLIS1	148979	broad.mit.edu	37	chr1	54059912	54059912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctcgcccttgcgctggtCgatgtggctcttctcgatgt	12	13	2	0	rs539985102		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54059912C>T	ENST00000312233.2	-	3	1230	c.664G>A	c.(664-666)Gac>Aac	p.D222N		NM_147193.2	NP_671726.2			GLIS family zinc finger 1									p.D222N(1)		endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						TTGCGCTGGTCGATGTGGCTC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	67	75					1																	54059912		2203	4300	6503	53832500	SO:0001583	missense	148979			AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.664G>A	1.37:g.54059912C>T	ENSP00000309653:p.Asp222Asn		53832500		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	.	.	.	.	.	.	.	.	.	.	C	36	5.626807	0.96671	.	.	ENSG00000174332	ENST00000312233	D	0.88664	-2.41	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000020	D	0.88209	0.6375	L	0.53561	1.675	0.80722	D	1	P	0.52692	0.955	B	0.44044	0.439	D	0.87510	0.2439	10	0.35671	T	0.21	.	19.1215	0.93365	0.0:1.0:0.0:0.0	.	222	Q8NBF1	GLIS1_HUMAN	N	222	ENSP00000309653:D222N	ENSP00000309653:D222N	D	-	1	0	GLIS1	53832500	1.000000	0.71417	0.977000	0.42913	0.996000	0.88848	7.818000	0.86416	2.606000	0.88127	0.563000	0.77884	GAC		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	54059912	C	T	54059912	3	4	61	1	0	0	0	0	1	0	0	0	6465	884	31	1	1230	1	GLIS1	1	54059912	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	343431	54059912	195190709	276	8261										
TMEM48	55706	broad.mit.edu	37	chr1	54258947	54258947	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccgttttgacaagaaattCttaatctgagttggaaaaaa	7	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54258947C>A	ENST00000371429.3	-	14	2188	c.1590G>T	c.(1588-1590)aaG>aaT	p.K530N	NDC1_ENST00000537333.1_Missense_Mutation_p.K195N|NDC1_ENST00000234725.8_Missense_Mutation_p.K415N|NDC1_ENST00000540001.1_Intron	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	530					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.K530N(1)									ACAAGAAATTCTTAATCTGAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	106	104					1																	54258947		2203	4300	6503	54031535	SO:0001583	missense	55706			AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"nuclear division cycle 1 homolog (S. cerevisiae)"	610115	"transmembrane protein 48"	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.1590G>T	1.37:g.54258947C>A	ENSP00000360483:p.Lys530Asn		54031535	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Missense_Mutation	SNP	ENST00000371429.3	37	CCDS583.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130341	0.56721	.	.	ENSG00000058804	ENST00000371429;ENST00000360494;ENST00000537333;ENST00000234725	T;T;T	0.45668	0.89;0.89;0.89	4.69	4.69	0.59074	.	0.043135	0.85682	D	0.000000	T	0.50429	0.1615	M	0.64997	1.995	0.80722	D	1	D;D	0.64830	0.994;0.988	P;P	0.62435	0.902;0.88	T	0.45512	-0.9256	10	0.19147	T	0.46	.	6.2253	0.20703	0.0:0.7748:0.0:0.2252	.	490;530	B4DHA3;Q9BTX1	.;NDC1_HUMAN	N	530;413;195;415	ENSP00000360483:K530N;ENSP00000439947:K195N;ENSP00000234725:K415N	ENSP00000234725:K415N	K	-	3	2	TMEM48	54031535	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.207000	0.51106	2.598000	0.87819	0.563000	0.77884	AAG		0.318	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087		A	54258947	C	A	54258947	3	1	61	1	0	0	0	0	1	0	0	0	16211	912	32	2	454	2	TMEM48	1	54258947	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	199035	54258947	194991674	277	8262										
YIPF1	54432	broad.mit.edu	37	chr1	54325753	54325753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattagctggacttggctGcagcaactgtttggtttgga	12	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54325753G>A	ENST00000072644.1	-	10	1241	c.905C>T	c.(904-906)gCa>gTa	p.A302V	YIPF1_ENST00000371399.1_Missense_Mutation_p.A119V|YIPF1_ENST00000539954.1_Missense_Mutation_p.A327V	NM_018982.4	NP_061855.1	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	302						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.A302V(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|skin(1)|urinary_tract(2)	19						GGACTTGGCTGCAGCAACTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	106	109					1																	54325753		2203	4300	6503	54098341	SO:0001583	missense	54432			BC009674	CCDS584.1	1p33-p32.1	2008-02-05			ENSG00000058799	ENSG00000058799		"Yip1 domain family"	25231	protein-coding gene	gene with protein product						12477932	Standard	NM_018982		Approved	DJ167A19.1, FinGER1	uc001cvu.3	Q9Y548	OTTHUMG00000008074	ENST00000072644.1:c.905C>T	1.37:g.54325753G>A	ENSP00000072644:p.Ala302Val		54098341	B2RCM7|D3DQ40|Q9NWJ1	Missense_Mutation	SNP	ENST00000072644.1	37	CCDS584.1	.	.	.	.	.	.	.	.	.	.	G	5.363	0.252155	0.10185	.	.	ENSG00000058799	ENST00000371399;ENST00000072644;ENST00000539954	.	.	.	5.17	2.25	0.28309	.	0.802333	0.11657	N	0.542228	T	0.28234	0.0697	L	0.29908	0.895	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.21245	-1.0251	9	0.19590	T	0.45	-16.9335	8.6839	0.34225	0.3225:0.0:0.6775:0.0	.	302	Q9Y548	YIPF1_HUMAN	V	119;302;327	.	ENSP00000072644:A302V	A	-	2	0	YIPF1	54098341	0.538000	0.26394	0.835000	0.33067	0.567000	0.35839	0.708000	0.25719	0.763000	0.33175	0.655000	0.94253	GCA		0.438	YIPF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022103.5	NM_018982		A	54325753	G	A	54325753	3	1	61	1	0	0	0	0	1	0	0	0	17517	1319	46	3	19	3	YIPF1	1	54325753	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66806	54325753	194924868	278	8263										
YIPF1	54432	broad.mit.edu	37	chr1	54348920	54348920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggtggcatctgggtttgCtgtcagagaagtggctgcat	16	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54348920C>T	ENST00000072644.1	-	4	397	c.61G>A	c.(61-63)Gca>Aca	p.A21T	YIPF1_ENST00000371399.1_5'UTR|YIPF1_ENST00000469457.1_Intron|YIPF1_ENST00000539954.1_Missense_Mutation_p.A46T	NM_018982.4	NP_061855.1	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	21						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.A21T(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|skin(1)|urinary_tract(2)	19						TCTGGGTTTGCTGTCAGAGAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	76	78					1																	54348920		2203	4300	6503	54121508	SO:0001583	missense	54432			BC009674	CCDS584.1	1p33-p32.1	2008-02-05			ENSG00000058799	ENSG00000058799		"Yip1 domain family"	25231	protein-coding gene	gene with protein product						12477932	Standard	NM_018982		Approved	DJ167A19.1, FinGER1	uc001cvu.3	Q9Y548	OTTHUMG00000008074	ENST00000072644.1:c.61G>A	1.37:g.54348920C>T	ENSP00000072644:p.Ala21Thr		54121508	B2RCM7|D3DQ40|Q9NWJ1	Missense_Mutation	SNP	ENST00000072644.1	37	CCDS584.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624020	0.28889	.	.	ENSG00000058799	ENST00000072644;ENST00000539954;ENST00000412288	.	.	.	4.75	4.75	0.60458	.	0.315788	0.33364	N	0.004990	T	0.58793	0.2147	L	0.55481	1.735	0.35909	D	0.83098	B	0.09022	0.002	B	0.09377	0.004	T	0.61893	-0.6969	9	0.31617	T	0.26	-0.2231	17.5527	0.87881	0.0:1.0:0.0:0.0	.	21	Q9Y548	YIPF1_HUMAN	T	21;46;21	.	ENSP00000072644:A21T	A	-	1	0	YIPF1	54121508	1.000000	0.71417	0.972000	0.41901	0.226000	0.24999	2.574000	0.46016	2.463000	0.83235	0.467000	0.42956	GCA		0.448	YIPF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022103.5	NM_018982		T	54348920	C	T	54348920	3	4	61	1	0	0	0	0	1	0	0	0	17517	797	28	3	887	3	YIPF1	1	54348920	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23167	54348920	194901701	279	8264										
DIO1	1733	broad.mit.edu	37	chr1	54360096	54360096	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcagcacccagtatttCtggttcgtcttgaaggtccg	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54360096C>A	ENST00000361921.3	+	1	237	c.213C>A	c.(211-213)ttC>ttA	p.F71L	DIO1_ENST00000534069.1_3'UTR|DIO1_ENST00000525202.1_Intron|DIO1_ENST00000524406.1_5'UTR|DIO1_ENST00000322679.6_Missense_Mutation_p.F71L|DIO1_ENST00000532493.1_Missense_Mutation_p.F71L|DIO1_ENST00000388876.3_Missense_Mutation_p.F71L	NM_000792.5|NM_213593.3	NP_000783.2|NP_998758.1	P49895	IOD1_HUMAN	deiodinase, iodothyronine, type I	71					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)	p.F71L(2)		cervix(1)|endometrium(2)|large_intestine(3)|lung(2)|skin(1)	9						CCCAGTATTTCTGGTTCGTCT	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	1											135	107	116					1																	54360096		2203	4300	6503	54132684	SO:0001583	missense	1733				CCDS30722.1, CCDS41339.1, CCDS41340.1, CCDS53320.1	1p33-p32	2012-03-01			ENSG00000211452	ENSG00000211452	1.97.1.10		2883	protein-coding gene	gene with protein product		147892		TXDI1		8964838	Standard	NM_000792		Approved		uc001cwb.3	P49895	OTTHUMG00000008435	ENST00000361921.3:c.213C>A	1.37:g.54360096C>A	ENSP00000354643:p.Phe71Leu		54132684	Q1RN02|Q3KNP8|Q6Q4C1|Q6Q4C2|Q6Q4C3|Q6Q4C4|Q6Q4C5|Q6Q4C6|Q6Q4C7|Q6Q4C9|Q8WWC6	Missense_Mutation	SNP	ENST00000361921.3	37	CCDS41339.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367542	0.61513	.	.	ENSG00000211452	ENST00000529589;ENST00000361921;ENST00000322679;ENST00000532493;ENST00000388876	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	4.79	1.92	0.25849	.	0.212284	0.42294	D	0.000733	T	0.09905	0.0243	N	0.25485	0.75	0.30003	N	0.815864	B;B;B	0.27625	0.05;0.061;0.183	B;B;B	0.20955	0.032;0.032;0.032	T	0.13737	-1.0498	10	0.27082	T	0.32	.	1.2134	0.01909	0.1462:0.4279:0.1618:0.2642	.	71;71;71	P49895-5;P49895;P49895-4	.;IOD1_HUMAN;.	L	28;71;71;71;71	ENSP00000432797:F28L;ENSP00000354643:F71L;ENSP00000323198:F71L;ENSP00000434758:F71L;ENSP00000373528:F71L	ENSP00000323198:F71L	F	+	3	2	DIO1	54132684	0.999000	0.42202	0.997000	0.53966	0.994000	0.84299	0.502000	0.22594	0.246000	0.21394	0.561000	0.74099	TTC		0.577	DIO1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000023247.3			A	54360096	C	A	54360096	3	1	61	1	0	0	0	0	1	0	0	0	4535	912	32	2	215	2	DIO1	1	54360096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11176	54360096	194890525	280	8265										
CDCP2	200008	broad.mit.edu	37	chr1	54606953	54606953	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataggtgcactcttcattgCcctccacctggaagtccacg	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54606953C>A	ENST00000371330.1	-	3	1428	c.581G>T	c.(580-582)gGc>gTc	p.G194V	RP11-446E24.4_ENST00000525949.1_5'UTR|CDCP2_ENST00000530059.1_5'Flank	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	194	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)		p.G194V(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						CTCTTCATTGCCCTCCACCTG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	68	71					1																	54606953		2203	4300	6503	54379541	SO:0001583	missense	200008				CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.581G>T	1.37:g.54606953C>A	ENSP00000360381:p.Gly194Val		54379541	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	37	CCDS588.2	.	.	.	.	.	.	.	.	.	.	C	16.50	3.142059	0.57044	.	.	ENSG00000157211	ENST00000371330	T	0.18174	2.23	5.04	1.96	0.26148	CUB (5);	0.260219	0.39146	N	0.001456	T	0.20129	0.0484	L	0.45422	1.42	0.33409	D	0.578366	P	0.50710	0.938	P	0.50314	0.637	T	0.22871	-1.0204	10	0.56958	D	0.05	-15.543	9.1527	0.36973	0.0:0.4912:0.4311:0.0777	.	194	Q5VXM1	CDCP2_HUMAN	V	194	ENSP00000360381:G194V	ENSP00000360381:G194V	G	-	2	0	CDCP2	54379541	1.000000	0.71417	0.913000	0.36048	0.882000	0.50991	1.891000	0.39738	0.243000	0.21327	0.561000	0.74099	GGC		0.642	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		A	54606953	C	A	54606953	3	1	61	1	0	0	0	0	1	0	0	0	3100	739	26	2	776	2	CDCP2	1	54606953	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	246857	54606953	194643668	281	8266										
CYB5RL	606495	broad.mit.edu	37	chr1	54644918	54644918	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaaggtcttgaagcaaccGaccagagtgacaaaagtctc	9	10	3	3	rs373797088	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:54644918G>A	ENST00000534324.1	-	5	647	c.648C>T	c.(646-648)gtC>gtT	p.V216V	CYB5RL_ENST00000287899.8_Intron|CYB5RL_ENST00000401046.3_Silent_p.V68V|CYB5RL_ENST00000537208.1_Intron|CYB5RL_ENST00000419823.2_Silent_p.V216V|CYB5RL_ENST00000542737.1_Silent_p.V216V|RP11-446E24.4_ENST00000311841.7_Intron			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	216							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)	p.V216V(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TGAAGCAACCGACCAGAGTGA	0.542													g|||	16	0.00319489	8e-04	0	5008	,	,		21923	0		0	False		,,,				2504	0.0153															1	Substitution - coding silent(1)	large_intestine(1)	1						A		1,3987		0,1,1993	68	73	71		648	-5.8	0.3	1		71	0,8332		0,0,4166	no	coding-synonymous	CYB5RL	NM_001031672.2		0,1,6159	AA,AG,GG		0.0,0.0251,0.0081		216/316	54644918	1,12319	1994	4166	6160	54417506	SO:0001819	synonymous_variant	606495				CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.648C>T	1.37:g.54644918G>A			54417506	B7ZBS4|Q8NF25	Silent	SNP	ENST00000534324.1	37	CCDS44151.1																																																																																				0.542	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672		A	54644918	G	A	54644918	2	1	61	1	0	0	0	0	0	0	0	1	4136	1045	37	1		1	CYB5RL	1	54644918	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37965	54644918	194605703	282	8267										
C1orf175	374977	broad.mit.edu	37	chr1	55119306	55119306	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaatgtagctccagattCtcatgggaccctaatcccag	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:55119306C>A	ENST00000421030.2	+	3	992	c.707C>A	c.(706-708)tCt>tAt	p.S236Y	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.S236Y|MROH7_ENST00000339553.5_Missense_Mutation_p.S236Y|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000472987.1_3'UTR|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S236Y	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	236						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.S236Y(2)									GCTCCAGATTCTCATGGGACC	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	1											60	56	57					1																	55119306		1926	4133	6059	54891894	SO:0001583	missense	374977			AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.707C>A	1.37:g.55119306C>A	ENSP00000396622:p.Ser236Tyr		54891894	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738318	0.30774	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.05319	3.46;3.46;3.46	2.95	1.96	0.26148	.	.	.	.	.	T	0.09642	0.0237	N	0.19112	0.55	0.09310	N	1	P;P;D	0.76494	0.946;0.946;0.999	P;P;P	0.61003	0.654;0.528;0.882	T	0.25916	-1.0118	9	0.87932	D	0	.	7.5704	0.27904	0.0:0.7334:0.2666:0.0	.	236;236;236	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	Y	236	ENSP00000396622:S236Y;ENSP00000343211:S236Y;ENSP00000379044:S236Y	ENSP00000343211:S236Y	S	+	2	0	HEATR8	54891894	0.001000	0.12720	0.001000	0.08648	0.038000	0.13279	1.195000	0.32186	0.751000	0.32900	0.655000	0.94253	TCT		0.458	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		A	55119306	C	A	55119306	3	1	61	1	0	0	0	0	1	0	0	0	2022	913	32	2	709	2	C1orf175	1	55119306	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	474388	55119306	194131315	283	8268										
C1orf175	374977	broad.mit.edu	37	chr1	55172145	55172145	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgccttcatattcctcaGccagagcctggagtatgcca	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:55172145G>C	ENST00000421030.2	+	22	3887	c.3602G>C	c.(3601-3603)aGc>aCc	p.S1201T	MROH7_ENST00000409996.1_Missense_Mutation_p.S769T|MROH7_ENST00000454855.2_Missense_Mutation_p.S719T|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S1201T	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	1201						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.S1198T(1)|p.S1201T(1)									ATATTCCTCAGCCAGAGCCTG	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	1											121	125	124					1																	55172145		1940	4147	6087	54944733	SO:0001583	missense	374977			AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.3602G>C	1.37:g.55172145G>C	ENSP00000396622:p.Ser1201Thr		54944733	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	G	9.473	1.096246	0.20552	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000409996;ENST00000454855;ENST00000371287	T;T;T;T	0.32988	1.43;1.44;1.44;1.44	5.01	1.92	0.25849	Armadillo-like helical (1);Armadillo-type fold (1);	0.367287	0.26421	N	0.024462	T	0.18964	0.0455	L	0.41492	1.28	0.23010	N	0.998432	B;B	0.23937	0.094;0.009	B;B	0.19946	0.027;0.007	T	0.15607	-1.0431	10	0.18710	T	0.47	-4.0294	5.1067	0.14787	0.1821:0.1886:0.6293:0.0	.	1201;1200	Q68CQ1;Q68CQ1-9	HEAT8_HUMAN;.	T	1201;1230;769;719;270	ENSP00000396622:S1201T;ENSP00000387048:S769T;ENSP00000401130:S719T;ENSP00000360336:S270T	ENSP00000360336:S270T	S	+	2	0	HEATR8	54944733	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.962000	0.29280	0.687000	0.31509	0.585000	0.79938	AGC		0.552	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		C	55172145	G	C	55172145	3	2	61	1	0	0	0	0	1	0	0	0	2022	971	34	5	3680	5	C1orf175	1	55172145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52839	55172145	194078476	284	8269										
C1orf177	163747	broad.mit.edu	37	chr1	55277748	55277748	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggacccggcacctacttCttcaaaagcgaccttgagac	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:55277748C>A	ENST00000371273.3	+	6	663	c.648C>A	c.(646-648)ttC>ttA	p.F216L	C1orf177_ENST00000358193.3_Missense_Mutation_p.F216L	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	216								p.F216L(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GCACCTACTTCTTCAAAAGCG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	105	103					1																	55277748		2203	4300	6503	55050336	SO:0001583	missense	163747			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.648C>A	1.37:g.55277748C>A	ENSP00000360320:p.Phe216Leu		55050336	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	C	7.169	0.587296	0.13812	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.19806	2.12;2.12	5.06	1.86	0.25419	.	1.998580	0.02089	N	0.052996	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20438	-1.0275	10	0.36615	T	0.2	-7.5219	3.1041	0.06336	0.1814:0.5452:0.1759:0.0975	.	216;216	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	L	216	ENSP00000350924:F216L;ENSP00000360320:F216L	ENSP00000350924:F216L	F	+	3	2	C1orf177	55050336	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	0.007000	0.13174	0.487000	0.27698	0.462000	0.41574	TTC		0.612	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		A	55277748	C	A	55277748	3	1	61	1	0	0	0	0	1	0	0	0	2023	912	32	2	670	2	C1orf177	1	55277748	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105603	55277748	193972873	285	8270										
C1orf177	163747	broad.mit.edu	37	chr1	55279584	55279584	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttttttctaaacttccccGaaacccgaaaacccctacag	5	14	1	0	rs368171733		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:55279584G>A	ENST00000371273.3	+	7	875	c.860G>A	c.(859-861)cGa>cAa	p.R287Q	C1orf177_ENST00000358193.3_Missense_Mutation_p.R287Q	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	287								p.R287Q(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						AAACTTCCCCGAAACCCGAAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	82	89	87		860,860	5	0.1	1		87	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	287/419,287/415	55279584	1,13005	2203	4300	6503	55052172	SO:0001583	missense	163747			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.860G>A	1.37:g.55279584G>A	ENSP00000360320:p.Arg287Gln		55052172	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.969094	0.34754	0.0	1.16E-4	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.27402	1.67;1.67	4.98	4.98	0.66077	.	0.091434	0.48286	D	0.000182	T	0.44561	0.1299	L	0.43152	1.355	0.22562	N	0.998985	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.26326	-1.0106	10	0.21014	T	0.42	.	13.6147	0.62101	0.0:0.0:1.0:0.0	.	287;287	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	Q	287	ENSP00000350924:R287Q;ENSP00000360320:R287Q	ENSP00000350924:R287Q	R	+	2	0	C1orf177	55052172	0.730000	0.28100	0.081000	0.20488	0.065000	0.16274	2.548000	0.45794	2.588000	0.87417	0.561000	0.74099	CGA		0.483	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		A	55279584	G	A	55279584	3	1	61	1	0	0	0	0	1	0	0	0	2023	1058	37	1	886	1	C1orf177	1	55279584	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1836	55279584	193971037	286	8271										
USP24	23358	broad.mit.edu	37	chr1	55586426	55586426	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatcacaggcaacccggcGaatctgaaattacatgatca	8	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:55586426G>A	ENST00000294383.6	-	38	4350	c.4351C>T	c.(4351-4353)Cgc>Tgc	p.R1451C	USP24_ENST00000407756.1_Missense_Mutation_p.R1291C	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1451					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.R1451C(1)|p.R1368C(1)		breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						GCAACCCGGCGAATCTGAAAT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	1											34	31	32					1																	55586426		1989	4185	6174	55359014	SO:0001583	missense	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.4351C>T	1.37:g.55586426G>A	ENSP00000294383:p.Arg1451Cys		55359014	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889355	0.91889	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.72615	-0.67;-0.67	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.82806	0.5117	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.84563	0.0651	10	0.87932	D	0	.	18.8245	0.92111	0.0:0.0:1.0:0.0	.	1291	B7WPF4	.	C	1451;1291	ENSP00000294383:R1451C;ENSP00000385700:R1291C	ENSP00000294383:R1451C	R	-	1	0	USP24	55359014	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.476000	0.97823	2.456000	0.83038	0.563000	0.77884	CGC		0.433	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55586426	G	A	55586426	3	1	61	1	0	0	0	0	1	0	0	0	17095	1058	37	1	3635	1	USP24	1	55586426	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	306842	55586426	193664195	287	8272										
PRKAA2	5563	broad.mit.edu	37	chr1	57158129	57158129	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcgagacctgaaaccagaGaatgtcctgttggatgcaca	10	10	0	3	rs201580595		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57158129G>A	ENST00000371244.4	+	4	495	c.429G>A	c.(427-429)gaG>gaA	p.E143E		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.E143E(2)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TGAAACCAGAGAATGTCCTGT	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	1											182	171	175					1																	57158129		2203	4300	6503	56930717	SO:0001819	synonymous_variant	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.429G>A	1.37:g.57158129G>A			56930717	Q9H1E8|Q9UD43	Silent	SNP	ENST00000371244.4	37	CCDS605.1																																																																																				0.453	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		A	57158129	G	A	57158129	2	1	61	1	0	0	0	0	0	0	0	1	12528	933	33	3		3	PRKAA2	1	57158129	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1571703	57158129	192092492	288	8273										
PRKAA2	5563	broad.mit.edu	37	chr1	57170075	57170075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtggcatcttggaatccGaagtcagagcaaaccgtatg	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57170075G>A	ENST00000371244.4	+	7	1286	c.1220G>A	c.(1219-1221)cGa>cAa	p.R407Q		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	407			R -> Q (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R407Q(2)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	CTTGGAATCCGAAGTCAGAGC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	1											87	89	88					1																	57170075		2203	4300	6503	56942663	SO:0001583	missense	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.1220G>A	1.37:g.57170075G>A	ENSP00000360290:p.Arg407Gln		56942663	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.152140	0.78001	.	.	ENSG00000162409	ENST00000371244	T	0.80909	-1.43	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.87896	0.6293	L	0.57130	1.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81629	-0.0846	10	0.14656	T	0.56	-11.3992	20.8794	0.99867	0.0:0.0:1.0:0.0	.	407	P54646	AAPK2_HUMAN	Q	407	ENSP00000360290:R407Q	ENSP00000360290:R407Q	R	+	2	0	PRKAA2	56942663	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	CGA		0.413	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		A	57170075	G	A	57170075	3	1	61	1	0	0	0	0	1	0	0	0	12528	1058	37	1	1246	1	PRKAA2	1	57170075	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11946	57170075	192080546	289	8274										
PRKAA2	5563	broad.mit.edu	37	chr1	57171786	57171786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtgaatgcataccatcttCgtgtaagaagaaaaaatcca	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57171786C>T	ENST00000371244.4	+	8	1381	c.1315C>T	c.(1315-1317)Cgt>Tgt	p.R439C		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	439					autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R439C(1)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	ATACCATCTTCGTGTAAGAAG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	76	78					1																	57171786		2203	4300	6503	56944374	SO:0001583	missense	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.1315C>T	1.37:g.57171786C>T	ENSP00000360290:p.Arg439Cys		56944374	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640336	0.67244	.	.	ENSG00000162409	ENST00000371244	T	0.75477	-0.94	5.27	4.31	0.51392	.	0.000000	0.85682	D	0.000000	D	0.87216	0.6122	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.89536	0.3789	10	0.87932	D	0	-17.1395	16.166	0.81757	0.1883:0.8117:0.0:0.0	.	439	P54646	AAPK2_HUMAN	C	439	ENSP00000360290:R439C	ENSP00000360290:R439C	R	+	1	0	PRKAA2	56944374	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.066000	0.30604	2.626000	0.88956	0.462000	0.41574	CGT		0.294	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		T	57171786	C	T	57171786	3	4	61	1	0	0	0	0	1	0	0	0	12528	884	31	1	1345	1	PRKAA2	1	57171786	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1711	57171786	192078835	290	8275										
C1orf168	199920	broad.mit.edu	37	chr1	57258431	57258431	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaagaggtggagcatcaaGattttgaaatttggctcgaa	13	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57258431G>T	ENST00000343433.6	-	2	135	c.55C>A	c.(55-57)Ctt>Att	p.L19I	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	19								p.L19I(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						GGAGCATCAAGATTTTGAAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											141	148	145					1																	57258431		2203	4300	6503	57031019	SO:0001583	missense	199920			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.55C>A	1.37:g.57258431G>T	ENSP00000345972:p.Leu19Ile		57031019	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039504	0.75617	.	.	ENSG00000187889	ENST00000343433	T	0.31769	1.48	4.65	-3.66	0.04489	.	1.125910	0.06777	N	0.784623	T	0.19127	0.0459	L	0.27053	0.805	0.09310	N	1	P;P	0.46142	0.793;0.873	B;B	0.42738	0.396;0.306	T	0.22382	-1.0218	10	0.31617	T	0.26	0.0018	5.0373	0.14441	0.394:0.2719:0.3341:0.0	.	19;19	Q5VWT5-2;Q5VWT5	.;CA168_HUMAN	I	19	ENSP00000345972:L19I	ENSP00000345972:L19I	L	-	1	0	C1orf168	57031019	0.000000	0.05858	0.000000	0.03702	0.836000	0.47400	-0.237000	0.08990	-0.427000	0.07350	0.563000	0.77884	CTT		0.393	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		T	57258431	G	T	57258431	3	4	61	1	0	0	0	0	1	0	0	0	2018	942	33	2	2207	2	C1orf168	1	57258431	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86645	57258431	191992190	291	8276										
C8A	731	broad.mit.edu	37	chr1	57347262	57347262	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctactatggagatgatgaGaaatactttcggaaacccta	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57347262G>T	ENST00000361249.3	+	5	705	c.609G>T	c.(607-609)gaG>gaT	p.E203D		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	203	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)		p.E203D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GAGATGATGAGAAATACTTTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											125	127	126					1																	57347262		2203	4300	6503	57119850	SO:0001583	missense	731			M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.609G>T	1.37:g.57347262G>T	ENSP00000354458:p.Glu203Asp		57119850	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821611	0.50633	.	.	ENSG00000157131	ENST00000361249	D	0.86497	-2.13	5.56	-2.36	0.06663	Membrane attack complex component/perforin (MACPF) domain (1);	0.093821	0.64402	N	0.000001	T	0.71821	0.3385	L	0.42487	1.325	0.53688	D	0.999977	P	0.39157	0.662	B	0.31290	0.127	T	0.58951	-0.7545	10	0.33141	T	0.24	-18.2046	1.82	0.03109	0.2328:0.2209:0.4194:0.127	.	203	P07357	CO8A_HUMAN	D	203	ENSP00000354458:E203D	ENSP00000354458:E203D	E	+	3	2	C8A	57119850	0.998000	0.40836	0.980000	0.43619	0.953000	0.61014	0.455000	0.21843	-0.097000	0.12307	0.655000	0.94253	GAG		0.488	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		T	57347262	G	T	57347262	3	4	61	1	0	0	0	0	1	0	0	0	2422	933	33	2	627	2	C8A	1	57347262	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88831	57347262	191903359	292	8277										
C8B	732	broad.mit.edu	37	chr1	57399055	57399055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagggagcacagtggcagGaactaacttccttctggaac	13	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57399055G>A	ENST00000371237.4	-	10	1571	c.1505C>T	c.(1504-1506)tCc>tTc	p.S502F	C8B_ENST00000543257.1_Missense_Mutation_p.S450F|C8B_ENST00000535057.1_Missense_Mutation_p.S440F	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	502	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)		p.S502F(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ACAGTGGCAGGAACTAACTTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	80	84					1																	57399055		2203	4300	6503	57171643	SO:0001583	missense	732			M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"Complement system"	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1505C>T	1.37:g.57399055G>A	ENSP00000360281:p.Ser502Phe		57171643	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451552	0.63290	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27720	1.82;1.84;1.65	5.07	4.15	0.48705	Membrane attack complex component/perforin (MACPF) domain (1);	0.405216	0.29799	N	0.011164	T	0.44456	0.1294	M	0.76574	2.34	0.53005	D	0.999962	D;D;D	0.63880	0.993;0.993;0.989	P;P;P	0.59487	0.804;0.858;0.726	T	0.26503	-1.0101	10	0.10111	T	0.7	-4.7028	10.8175	0.46585	0.0748:0.1349:0.7902:0.0	.	450;440;502	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	F	502;450;440	ENSP00000360281:S502F;ENSP00000442548:S450F;ENSP00000440113:S440F	ENSP00000360281:S502F	S	-	2	0	C8B	57171643	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	3.992000	0.56980	2.802000	0.96397	0.650000	0.86243	TCC		0.522	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			A	57399055	G	A	57399055	3	1	61	1	0	0	0	0	1	0	0	0	2423	1174	41	3	282	3	C8B	1	57399055	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51793	57399055	191851566	293	8278										
DAB1	1600	broad.mit.edu	37	chr1	57480581	57480581	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtcgatggtgtggtagaAgtcacaggggtcaaattcaa	14	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:57480581A>C	ENST00000371231.1	-	13	1552	c.1518T>G	c.(1516-1518)acT>acG	p.T506T	DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371236.2_Silent_p.T473T|DAB1_ENST00000371234.4_Silent_p.T473T|DAB1_ENST00000414851.2_Silent_p.T455T|DAB1_ENST00000439789.2_Silent_p.T387T|DAB1_ENST00000420954.2_Silent_p.T471T			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	506					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.T473T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						GTGTGGTAGAAGTCACAGGGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											89	82	84					1																	57480581		2203	4300	6503	57253169	SO:0001819	synonymous_variant	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.1518T>G	1.37:g.57480581A>C			57253169	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Silent	SNP	ENST00000371231.1	37																																																																																					0.507	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		C	57480581	A	C	57480581	2	2	61	1	0	0	0	0	0	0	0	1	4223	59	3	4		4	DAB1	1	57480581	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	81526	57480581	191770040	294	8279										
OMA1	115209	broad.mit.edu	37	chr1	58999994	58999994	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcatatcatttttaaattCttccatccactgaaagatta	3	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:58999994C>A	ENST00000371226.3	-	4	852	c.739G>T	c.(739-741)Gaa>Taa	p.E247*	OMA1_ENST00000467063.1_5'UTR|DAB1_ENST00000485760.1_Intron|OMA1_ENST00000358603.2_Nonsense_Mutation_p.E247*	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	247					cristae formation (GO:0042407)|diet induced thermogenesis (GO:0002024)|energy homeostasis (GO:0097009)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrial protein processing (GO:0034982)|negative regulation of mitochondrial fusion (GO:0010637)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.E247*(1)		NS(1)|breast(1)|large_intestine(6)|liver(2)|lung(6)|prostate(1)|skin(1)	18	all_cancers(7;6.54e-05)					TTTTTAAATTCTTCCATCCAC	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											44	44	44					1																	58999994		2203	4300	6503	58772582	SO:0001587	stop_gained	115209			AK091101	CCDS608.1	1p32.2-p32.1	2013-05-03	2013-05-03		ENSG00000162600	ENSG00000162600			29661	protein-coding gene	gene with protein product	"overlapping activity with M-AAA protease", "zinc metallopeptidase OMA1"		"OMA1 zinc metallopeptidase homolog (S. cerevisiae)"			12477932	Standard	NM_145243		Approved	MPRP-1, YKR087C, ZMPOMA1, FLJ33782	uc001cyy.3	Q96E52	OTTHUMG00000010068	ENST00000371226.3:c.739G>T	1.37:g.58999994C>A	ENSP00000360270:p.Glu247*		58772582	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Nonsense_Mutation	SNP	ENST00000371226.3	37	CCDS608.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.62|15.62	2.887603|2.887603	0.52014|0.52014	.|.	.|.	ENSG00000162600|ENSG00000162600	ENST00000358603;ENST00000371226;ENST00000456980;ENST00000419242;ENST00000426139|ENST00000421528	.|.	.|.	.|.	4.66|4.66	3.72|3.72	0.42706|0.42706	.|.	0.168662|.	0.50627|.	D|.	0.000115|.	.|T	.|0.59432	.|0.2193	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.56583	.|-0.7955	.|4	0.40728|.	T|.	0.16|.	-14.4456|-14.4456	9.5703|9.5703	0.39425|0.39425	0.0:0.6529:0.2708:0.0763|0.0:0.6529:0.2708:0.0763	.|.	.|.	.|.	.|.	X|I	247|88	.|.	ENSP00000351417:E247X|.	E|R	-|-	1|2	0|0	OMA1|OMA1	58772582|58772582	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.888000|0.888000	0.51559|0.51559	0.762000|0.762000	0.26503|0.26503	1.268000|1.268000	0.44264|0.44264	0.563000|0.563000	0.77884|0.77884	GAA|AGA		0.323	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243		A	58999994	C	A	58999994	4	1	61	1	0	0	0	0	0	1	0	0	10895	922	32	2	859	2	OMA1	1	58999994	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1519413	58999994	190250627	295	8280										
MYSM1	114803	broad.mit.edu	37	chr1	59142610	59142610	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttaccacatccaaaatTgattgctcctatcaattcga	3	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:59142610T>G	ENST00000472487.1	-	9	1417	c.1378A>C	c.(1378-1380)Aat>Cat	p.N460H	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	460	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.N460H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CATCCAAAATTGATTGCTCCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											135	127	130					1																	59142610		1840	4087	5927	58915198	SO:0001583	missense	114803			AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.1378A>C	1.37:g.59142610T>G	ENSP00000418734:p.Asn460His		58915198	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	37	CCDS41343.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.352510	0.82132	.	.	ENSG00000162601	ENST00000472487	T	0.61742	0.08	5.16	5.16	0.70880	Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);SWIRM (2);	0.000000	0.85682	D	0.000000	T	0.80904	0.4713	M	0.92317	3.295	0.52501	D	0.999958	D	0.71674	0.998	D	0.75484	0.986	D	0.85800	0.1373	10	0.87932	D	0	-25.081	14.3206	0.66484	0.0:0.0:0.0:1.0	.	460	Q5VVJ2	MYSM1_HUMAN	H	460	ENSP00000418734:N460H	ENSP00000418734:N460H	N	-	1	0	MYSM1	58915198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.153000	0.67306	0.477000	0.44152	AAT		0.343	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59142610	T	G	59142610	3	3	61	1	0	0	0	0	1	0	0	0	10131	1812	63	4	1156	4	MYSM1	1	59142610	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	142616	59142610	190108011	296	8281										
MYSM1	114803	broad.mit.edu	37	chr1	59165712	59165712	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgatatccacatccgcctCttcagccgccatgatgggac	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:59165712C>A	ENST00000472487.1	-	1	52	c.13G>T	c.(13-15)Gag>Tag	p.E5*		NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	5					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E5*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					ACATCCGCCTCTTCAGCCGCC	0.692																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											29	37	35					1																	59165712		1920	4121	6041	58938300	SO:0001587	stop_gained	114803			AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.13G>T	1.37:g.59165712C>A	ENSP00000418734:p.Glu5*		58938300	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Nonsense_Mutation	SNP	ENST00000472487.1	37	CCDS41343.1	.	.	.	.	.	.	.	.	.	.	C	37	6.207071	0.97376	.	.	ENSG00000162601	ENST00000472487	.	.	.	4.66	4.66	0.58398	.	0.192351	0.43260	D	0.000584	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-7.8458	13.234	0.59958	0.0:1.0:0.0:0.0	.	.	.	.	X	5	.	ENSP00000418734:E5X	E	-	1	0	MYSM1	58938300	1.000000	0.71417	0.998000	0.56505	0.734000	0.41952	3.926000	0.56491	2.560000	0.86352	0.655000	0.94253	GAG		0.692	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		A	59165712	C	A	59165712	4	1	61	1	0	0	0	0	0	1	0	0	10131	922	32	2	2553	2	MYSM1	1	59165712	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23102	59165712	190084909	297	8282										
C1orf87	127795	broad.mit.edu	37	chr1	60456397	60456397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagagcatattttctcccGaacggaatctgcgcaaggcc	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:60456397G>A	ENST00000371201.3	-	12	1696	c.1589C>T	c.(1588-1590)tCg>tTg	p.S530L	C1orf87_ENST00000395552.1_Missense_Mutation_p.S164L|C1orf87_ENST00000450089.2_Missense_Mutation_p.S301L|C1orf87_ENST00000486478.1_5'UTR	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	530							calcium ion binding (GO:0005509)	p.S530L(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ATTTTCTCCCGAACGGAATCT	0.473																																					NSCLC(75;811 1386 4923 13371 51772)											1	Substitution - Missense(1)	large_intestine(1)	1											215	215	215					1																	60456397		2203	4300	6503	60228985	SO:0001583	missense	127795			AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.1589C>T	1.37:g.60456397G>A	ENSP00000360244:p.Ser530Leu		60228985	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	37	CCDS614.1	.	.	.	.	.	.	.	.	.	.	G	4.683	0.126918	0.08931	.	.	ENSG00000162598	ENST00000371201;ENST00000395552	T;T	0.33438	2.16;1.41	4.62	-2.0	0.07433	.	0.994157	0.08157	N	0.989107	T	0.13628	0.0330	N	0.04959	-0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31110	-0.9955	10	0.27785	T	0.31	-0.2884	8.339	0.32232	0.3012:0.1103:0.5885:0.0	.	530	Q8N0U7	CA087_HUMAN	L	530;164	ENSP00000360244:S530L;ENSP00000378921:S164L	ENSP00000360244:S530L	S	-	2	0	C1orf87	60228985	0.000000	0.05858	0.002000	0.10522	0.466000	0.32739	-0.160000	0.10041	-0.039000	0.13602	-1.305000	0.01319	TCG		0.473	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		A	60456397	G	A	60456397	3	1	61	1	0	0	0	0	1	0	0	0	2070	1059	37	1	55	1	C1orf87	1	60456397	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1290685	60456397	188794224	298	8283										
C1orf87	127795	broad.mit.edu	37	chr1	60466811	60466811	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccattggaggggcaggggCtttcttttcattcttccctg	11	11	3	0	rs61742748	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:60466811C>A	ENST00000371201.3	-	10	1317	c.1210G>T	c.(1210-1212)Gcc>Tcc	p.A404S	C1orf87_ENST00000395552.1_Missense_Mutation_p.A38S|C1orf87_ENST00000450089.2_Missense_Mutation_p.A175S|C1orf87_ENST00000486478.1_5'UTR	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	404							calcium ion binding (GO:0005509)	p.A404S(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						GGGGCAGGGGCTTTCTTTTCA	0.418																																					NSCLC(75;811 1386 4923 13371 51772)											1	Substitution - Missense(1)	large_intestine(1)	1											66	62	64					1																	60466811		2203	4300	6503	60239399	SO:0001583	missense	127795			AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.1210G>T	1.37:g.60466811C>A	ENSP00000360244:p.Ala404Ser		60239399	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	37	CCDS614.1	.	.	.	.	.	.	.	.	.	.	C	8.079	0.771947	0.16051	.	.	ENSG00000162598	ENST00000371201;ENST00000395552;ENST00000450089	T;T	0.31247	2.35;1.5	4.71	-0.0919	0.13658	.	1.137610	0.06639	N	0.760665	T	0.16938	0.0407	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.28650	-1.0037	10	0.29301	T	0.29	0.0774	0.6783	0.00870	0.4038:0.2349:0.2017:0.1596	.	404	Q8N0U7	CA087_HUMAN	S	404;38;175	ENSP00000360244:A404S;ENSP00000378921:A38S	ENSP00000360244:A404S	A	-	1	0	C1orf87	60239399	0.001000	0.12720	0.001000	0.08648	0.052000	0.14988	0.085000	0.14912	-0.104000	0.12154	0.655000	0.94253	GCC		0.418	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		A	60466811	C	A	60466811	3	1	61	1	0	0	0	0	1	0	0	0	2070	797	28	2	442	2	C1orf87	1	60466811	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10414	60466811	188783810	299	8284										
NFIA	4774	broad.mit.edu	37	chr1	61554140	61554140	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaaaggcaagatgcgaaGaattgactgcctccgccagg	12	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:61554140G>T	ENST00000403491.3	+	2	831	c.347G>T	c.(346-348)aGa>aTa	p.R116I	NFIA_ENST00000407417.3_Missense_Mutation_p.R108I|NFIA_ENST00000371185.2_Missense_Mutation_p.R116I|NFIA_ENST00000371191.1_Missense_Mutation_p.R139I|NFIA_ENST00000371189.4_Missense_Mutation_p.R161I|NFIA_ENST00000479364.1_Intron|NFIA_ENST00000371187.3_Missense_Mutation_p.R116I|NFIA_ENST00000485903.2_Missense_Mutation_p.R116I|NFIA_ENST00000371184.2_Missense_Mutation_p.R116I	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	116					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R116I(1)	NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						AAGATGCGAAGAATTGACTGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	122	119					1																	61554140		2203	4300	6503	61326728	SO:0001583	missense	4774			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.347G>T	1.37:g.61554140G>T	ENSP00000384523:p.Arg116Ile		61326728	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Missense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.642410	0.87859	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371185;ENST00000371184;ENST00000371187	T;T;T;T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97;-0.97;-0.97;-0.97	5.87	5.87	0.94306	MAD homology 1, Dwarfin-type (2);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.86916	0.6048	M	0.74647	2.275	0.80722	D	1	D;D;D;D	0.71674	0.998;0.996;0.996;0.984	D;D;D;D	0.76575	0.988;0.985;0.985;0.975	D	0.87201	0.2241	10	0.87932	D	0	-7.8722	20.2032	0.98269	0.0:0.0:1.0:0.0	.	161;139;116;116	F8W8W3;B1AKN8;Q12857;Q12857-2	.;.;NFIA_HUMAN;.	I	139;108;161;116;116;116;116;116	ENSP00000360233:R139I;ENSP00000384680:R108I;ENSP00000360231:R161I;ENSP00000384523:R116I;ENSP00000419785:R116I;ENSP00000360227:R116I;ENSP00000360226:R116I;ENSP00000360229:R116I	ENSP00000360226:R116I	R	+	2	0	NFIA	61326728	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.785000	0.95823	0.650000	0.86243	AGA		0.463	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595		T	61554140	G	T	61554140	3	4	61	1	0	0	0	0	1	0	0	0	10401	942	33	2	499	2	NFIA	1	61554140	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1087329	61554140	187696481	300	8285										
TM2D1	83941	broad.mit.edu	37	chr1	62175007	62175007	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaatgtacttacacatttCggcaagatatgggcttgaaa	9	6	0	2	rs369821446		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62175007C>A	ENST00000606498.1	-	3	361	c.341G>T	c.(340-342)cGa>cTa	p.R114L	TM2D1_ENST00000371177.2_Missense_Mutation_p.R114L|TM2D1_ENST00000294613.5_Missense_Mutation_p.R114L|TM2D1_ENST00000371180.2_Missense_Mutation_p.R176L|TM2D1_ENST00000472989.1_5'UTR			Q9BX74	TM2D1_HUMAN	TM2 domain containing 1	114					apoptotic signaling pathway (GO:0097190)	integral component of plasma membrane (GO:0005887)	beta-amyloid binding (GO:0001540)|G-protein coupled receptor activity (GO:0004930)	p.R176Q(1)|p.R114Q(1)|p.R176L(1)		large_intestine(2)|lung(3)|ovary(1)	6						TTACACATTTCGGCAAGATAT	0.363																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	1											78	74	75					1																	62175007		1840	4083	5923	61947595	SO:0001583	missense	83941			AF353990	CCDS65554.1	1p32.1	2008-02-05			ENSG00000162604	ENSG00000162604			24142	protein-coding gene	gene with protein product		610080				11278849, 12553667	Standard	NM_032027		Approved	BBP	uc001czz.1	Q9BX74	OTTHUMG00000008466	ENST00000606498.1:c.341G>T	1.37:g.62175007C>A	ENSP00000475700:p.Arg114Leu		61947595	A6NDA8	Missense_Mutation	SNP	ENST00000606498.1	37		.	.	.	.	.	.	.	.	.	.	C	24.1	4.488563	0.84854	.	.	ENSG00000162604	ENST00000371180;ENST00000294613;ENST00000371178;ENST00000371177	.	.	.	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000004	T	0.58666	0.2138	L	0.55743	1.74	0.58432	D	0.999995	P	0.45569	0.861	B	0.42738	0.396	T	0.61579	-0.7034	9	0.52906	T	0.07	-10.9907	18.396	0.90499	0.0:1.0:0.0:0.0	.	114	Q9BX74	TM2D1_HUMAN	L	176;114;114;114	.	ENSP00000294613:R114L	R	-	2	0	TM2D1	61947595	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.467000	0.66737	2.882000	0.98803	0.655000	0.94253	CGA		0.363	TM2D1-012	KNOWN	non_canonical_U12|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470779.2	NM_032027		A	62175007	C	A	62175007	3	1	61	1	0	0	0	0	1	0	0	0	16002	884	31	2	298	2	TM2D1	1	62175007	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	620867	62175007	187075614	301	8286										
INADL	10207	broad.mit.edu	37	chr1	62380322	62380322	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagaaccaggacacccaaGaaaagaaagaaaaggtaact	8	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62380322G>T	ENST00000371158.2	+	26	3670	c.3556G>T	c.(3556-3558)Gaa>Taa	p.E1186*	INADL_ENST00000316485.6_Nonsense_Mutation_p.E1186*	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1186					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.E1186*(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GGACACCCAAGAAAAGAAAGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											76	80	79					1																	62380322		2203	4300	6503	62152910	SO:0001587	stop_gained	10207			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3556G>T	1.37:g.62380322G>T	ENSP00000360200:p.Glu1186*		62152910	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Nonsense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	41	8.614343	0.98886	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513	.	.	.	4.69	3.75	0.43078	.	0.912726	0.09394	N	0.808112	.	.	.	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	6.5191	0.22264	0.0969:0.1859:0.7172:0.0	.	.	.	.	X	1186	.	ENSP00000326199:E1186X	E	+	1	0	INADL	62152910	0.053000	0.20554	0.025000	0.17156	0.024000	0.10985	1.935000	0.40173	1.285000	0.44548	0.579000	0.79373	GAA		0.383	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62380322	G	T	62380322	4	4	61	1	0	0	0	0	0	1	0	0	7752	943	33	2	3654	2	INADL	1	62380322	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205315	62380322	186870299	302	8287										
INADL	10207	broad.mit.edu	37	chr1	62582288	62582288	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgattcagggagatcagatCttatctgtgaatggggagga	14	4	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62582288C>A	ENST00000371158.2	+	36	4854	c.4740C>A	c.(4738-4740)atC>atA	p.I1580I	INADL_ENST00000543708.1_Silent_p.I394I	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1580	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.I1580I(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GAGATCAGATCTTATCTGTGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											78	81	80					1																	62582288		1962	4138	6100	62354876	SO:0001819	synonymous_variant	10207			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4740C>A	1.37:g.62582288C>A			62354876	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																				0.488	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62582288	C	A	62582288	2	1	61	1	0	0	0	0	0	0	0	1	7752	903	32	2		2	INADL	1	62582288	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201966	62582288	186668333	303	8288										
L1TD1	54596	broad.mit.edu	37	chr1	62672405	62672405	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttaacagaaactgataaGgacatagctccggtattaga	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62672405G>T	ENST00000498273.1	+	3	400	c.105G>T	c.(103-105)aaG>aaT	p.K35N		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	35								p.K35N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						aaactgataaggacatagctc	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											28	24	25					1																	62672405		2045	3979	6024	62444993	SO:0001583	missense	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.105G>T	1.37:g.62672405G>T	ENSP00000419901:p.Lys35Asn		62444993	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	7.332	0.619068	0.14129	.	.	ENSG00000240563	ENST00000498273	T	0.12879	2.64	1.93	0.999	0.19862	.	.	.	.	.	T	0.07954	0.0199	N	0.14661	0.345	0.09310	N	1	B	0.28026	0.198	B	0.32393	0.145	T	0.35773	-0.9775	9	0.59425	D	0.04	.	4.2957	0.10901	0.2059:0.0:0.7941:0.0	.	35	Q5T7N2	LITD1_HUMAN	N	35	ENSP00000419901:K35N	ENSP00000419901:K35N	K	+	3	2	L1TD1	62444993	0.003000	0.15002	0.003000	0.11579	0.009000	0.06853	0.174000	0.16743	0.378000	0.24764	0.313000	0.20887	AAG		0.333	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		T	62672405	G	T	62672405	3	4	61	1	0	0	0	0	1	0	0	0	8611	991	35	2	107	2	L1TD1	1	62672405	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90117	62672405	186578216	304	8289										
USP1	7398	broad.mit.edu	37	chr1	62911000	62911000	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcctgaagaggacttgggGaagtgtgaaagtgataacac	14	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62911000G>A	ENST00000339950.4	+	6	1964	c.1149G>A	c.(1147-1149)ggG>ggA	p.G383G	USP1_ENST00000371146.1_Silent_p.G383G	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	383	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G383G(1)		breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		AGGACTTGGGGAAGTGTGAAA	0.353																																					Ovarian(122;1846 2315 3982 19504)											1	Substitution - coding silent(1)	large_intestine(1)	1											43	46	45					1																	62911000		2202	4298	6500	62683588	SO:0001819	synonymous_variant	7398				CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"Ubiquitin-specific peptidases"	12607	protein-coding gene	gene with protein product		603478	"ubiquitin specific protease 1"			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.1149G>A	1.37:g.62911000G>A			62683588	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Silent	SNP	ENST00000339950.4	37	CCDS621.1																																																																																				0.353	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415		A	62911000	G	A	62911000	2	1	61	1	0	0	0	0	0	0	0	1	17080	1161	41	3		3	USP1	1	62911000	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	238595	62911000	186339621	305	8290										
DOCK7	85440	broad.mit.edu	37	chr1	62923325	62923325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagttccctttgatactcCttttgatccggcccaattaa	5	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62923325C>A	ENST00000340370.5	-	48	6188	c.6171G>T	c.(6169-6171)aaG>aaT	p.K2057N	DOCK7_ENST00000251157.5_Missense_Mutation_p.K2077N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	2088	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.K2057N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTTGATACTCCTTTTGATCCG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											196	190	192					1																	62923325		2203	4300	6503	62695913	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.6171G>T	1.37:g.62923325C>A	ENSP00000340742:p.Lys2057Asn		62695913	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	4.001866|4.001866	0.74932|0.74932	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000454575|ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	.|T;T	.|0.18960	.|2.18;2.18	5.99|5.99	4.14|4.14	0.48551|0.48551	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.40222	.|0.1108	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;P	.|0.59767	.|0.963;0.975;0.985;0.974;0.986;0.896	.|D;P;P;P;P;P	.|0.64321	.|0.924;0.848;0.888;0.842;0.875;0.802	.|T	.|0.22208	.|-1.0223	.|10	.|0.87932	.|D	.|0	.|.	10.8992|10.8992	0.47040|0.47040	0.0:0.7999:0.0:0.2001|0.0:0.7999:0.0:0.2001	.|.	.|2088;2077;2057;2046;2048;2079	.|Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	.|DOCK7_HUMAN;.;.;.;.;.	X|N	1251|2088;2077;2057;818	.|ENSP00000251157:K2077N;ENSP00000340742:K2057N	.|ENSP00000251157:K2077N	G|K	-|-	1|3	0|2	DOCK7|DOCK7	62695913|62695913	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.387000|1.387000	0.34430|0.34430	0.876000|0.876000	0.35872|0.35872	0.655000|0.655000	0.94253|0.94253	GGA|AAG		0.408	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	62923325	C	A	62923325	3	1	61	1	0	0	0	0	1	0	0	0	4703	680	24	2	166	2	DOCK7	1	62923325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12325	62923325	186327296	306	8291										
DOCK7	85440	broad.mit.edu	37	chr1	62941433	62941433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataaggaaaggcatgagacGtagtcagaatggtcttcctt	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62941433G>A	ENST00000340370.5	-	45	5830	c.5813C>T	c.(5812-5814)aCg>aTg	p.T1938M	DOCK7_ENST00000251157.5_Missense_Mutation_p.T1958M|DOCK7_ENST00000489185.1_5'UTR	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1969	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.T1938M(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						GGCATGAGACGTAGTCAGAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											161	158	159					1																	62941433		2203	4300	6503	62714021	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5813C>T	1.37:g.62941433G>A	ENSP00000340742:p.Thr1938Met		62714021	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.895994	0.91962	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	T;T	0.20598	2.06;2.06	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.61299	0.2336	H	0.94582	3.555	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.994;0.999;0.999;1.0;0.996	T	0.72600	-0.4244	10	0.87932	D	0	.	19.6764	0.95936	0.0:0.0:1.0:0.0	.	1969;1958;1938;1927;1929;1960	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	DOCK7_HUMAN;.;.;.;.;.	M	1969;1958;1938;699	ENSP00000251157:T1958M;ENSP00000340742:T1938M	ENSP00000251157:T1958M	T	-	2	0	DOCK7	62714021	1.000000	0.71417	0.780000	0.31762	0.957000	0.61999	9.869000	0.99810	2.660000	0.90430	0.655000	0.94253	ACG		0.393	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	62941433	G	A	62941433	3	1	61	1	0	0	0	0	1	0	0	0	4703	1145	40	1	536	1	DOCK7	1	62941433	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18108	62941433	186309188	307	8292										
DOCK7	85440	broad.mit.edu	37	chr1	62960062	62960062	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcagcatgattgcttcGttctgagtgcttgcctgcca	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62960062G>A	ENST00000340370.5	-	39	5025	c.5008C>T	c.(5008-5010)Cga>Tga	p.R1670*	DOCK7_ENST00000251157.5_Nonsense_Mutation_p.R1692*	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1701					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.R1670*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TGATTGCTTCGTTCTGAGTGC	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											121	90	100					1																	62960062		2203	4300	6503	62732650	SO:0001587	stop_gained	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5008C>T	1.37:g.62960062G>A	ENSP00000340742:p.Arg1670*		62732650	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Nonsense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	9.863188|9.863188	0.99283|0.99283	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441|ENST00000454575	.|.	.|.	.|.	5.9|5.9	3.82|3.82	0.43975|0.43975	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.62962	.|0.2471	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70781	.|-0.4779	.|3	0.02654|.	T|.	1|.	.|.	13.7953|13.7953	0.63166|0.63166	0.0:0.0:0.5771:0.4229|0.0:0.0:0.5771:0.4229	.|.	.|.	.|.	.|.	X|M	1701;1692;1670;431|863	.|.	ENSP00000251157:R1692X|.	R|T	-|-	1|2	2|0	DOCK7|DOCK7	62732650|62732650	1.000000|1.000000	0.71417|0.71417	0.585000|0.585000	0.28666|0.28666	0.389000|0.389000	0.30415|0.30415	3.195000|3.195000	0.51013|0.51013	1.471000|1.471000	0.48121|0.48121	-0.293000|-0.293000	0.09583|0.09583	CGA|ACG		0.478	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	62960062	G	A	62960062	4	1	61	1	0	0	0	0	0	1	0	0	4703	1153	40	1	1365	1	DOCK7	1	62960062	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18629	62960062	186290559	308	8293										
DOCK7	85440	broad.mit.edu	37	chr1	62979258	62979258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaggtcaagctattcattCgttcaaacacttttttcccc	4	11	3	0	rs368205214		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:62979258C>T	ENST00000340370.5	-	32	4063	c.4046G>A	c.(4045-4047)cGa>cAa	p.R1349Q	DOCK7_ENST00000251157.5_Missense_Mutation_p.R1380Q	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1380					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.R1349Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						GCTATTCATTCGTTCAAACAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	0,4406		0,0,2203	91	86	88		4046	5.6	1	1		88	1,8599	1.2+/-3.3	0,1,4299	no	missense	DOCK7	NM_033407.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1349/2110	62979258	1,13005	2203	4300	6503	62751846	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4046G>A	1.37:g.62979258C>T	ENSP00000340742:p.Arg1349Gln		62751846	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	32	5.115467	0.94339	0.0	1.16E-4	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	T;T	0.01933	4.55;4.55	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.11110	0.0271	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;P	0.69078	0.992;0.994;0.994;0.997;0.988;0.946	P;P;P;P;P;P	0.57548	0.716;0.796;0.713;0.823;0.608;0.507	T	0.00189	-1.1939	10	0.62326	D	0.03	.	19.6914	0.96002	0.0:1.0:0.0:0.0	.	1380;1380;1349;1349;1349;1380	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	DOCK7_HUMAN;.;.;.;.;.	Q	1380;1380;1349;119	ENSP00000251157:R1380Q;ENSP00000340742:R1349Q	ENSP00000251157:R1380Q	R	-	2	0	DOCK7	62751846	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.644000	0.89710	0.563000	0.77884	CGA		0.363	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	62979258	C	T	62979258	3	4	61	1	0	0	0	0	1	0	0	0	4703	884	31	1	2355	1	DOCK7	1	62979258	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19196	62979258	186271363	309	8294										
DOCK7	85440	broad.mit.edu	37	chr1	63018423	63018423	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactcccgatgattgatcGaacttcatcatctggtgacg	8	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63018423G>A	ENST00000340370.5	-	22	2763	c.2746C>T	c.(2746-2748)Cga>Tga	p.R916*	DOCK7_ENST00000251157.5_Nonsense_Mutation_p.R916*	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	916					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.R916*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ATGATTGATCGAACTTCATCA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											103	93	97					1																	63018423		2203	4300	6503	62791011	SO:0001587	stop_gained	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.2746C>T	1.37:g.63018423G>A	ENSP00000340742:p.Arg916*		62791011	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Nonsense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	9.050470|9.050470	0.99048|0.99048	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370|ENST00000454575	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.118551|.	0.64402|.	D|.	0.000015|.	.|T	.|0.63367	.|0.2505	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69510	.|-0.5126	.|3	0.14252|.	T|.	0.57|.	.|.	13.3586|13.3586	0.60642|0.60642	0.0:0.0:0.8424:0.1576|0.0:0.0:0.8424:0.1576	.|.	.|.	.|.	.|.	X|L	916|87	.|.	ENSP00000251157:R916X|.	R|S	-|-	1|2	2|0	DOCK7|DOCK7	62791011|62791011	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.986000|0.986000	0.74619|0.74619	3.948000|3.948000	0.56660|0.56660	2.564000|2.564000	0.86499|0.86499	0.585000|0.585000	0.79938|0.79938	CGA|TCG		0.393	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	63018423	G	A	63018423	4	1	61	1	0	0	0	0	0	1	0	0	4703	1066	37	1	3695	1	DOCK7	1	63018423	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39165	63018423	186232198	310	8295										
DOCK7	85440	broad.mit.edu	37	chr1	63024875	63024875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgaccagagcaaaaaatTtgtcaagataaggatcctaa	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63024875T>G	ENST00000340370.5	-	20	2233	c.2216A>C	c.(2215-2217)aAa>aCa	p.K739T	DOCK7_ENST00000251157.5_Missense_Mutation_p.K739T	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	739					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.K739T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AGCAAAAAATTTGTCAAGATA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	56	57					1																	63024875		2203	4300	6503	62797463	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.2216A>C	1.37:g.63024875T>G	ENSP00000340742:p.Lys739Thr		62797463	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.046632	0.75846	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370	T;T	0.41758	0.99;0.99	4.94	3.82	0.43975	.	0.051657	0.85682	D	0.000000	T	0.51058	0.1652	L	0.41824	1.3	0.58432	D	0.999998	D;D;D;D	0.76494	0.995;0.971;0.998;0.999	D;P;D;D	0.69142	0.962;0.855;0.947;0.959	T	0.48917	-0.8992	10	0.54805	T	0.06	.	10.3386	0.43864	0.0:0.0771:0.0:0.9229	.	739;739;739;739	Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.	T	739	ENSP00000251157:K739T;ENSP00000340742:K739T	ENSP00000251157:K739T	K	-	2	0	DOCK7	62797463	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.134000	0.71689	0.912000	0.36772	0.459000	0.35465	AAA		0.373	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	63024875	T	G	63024875	3	3	61	1	0	0	0	0	1	0	0	0	4703	1841	64	4	4233	4	DOCK7	1	63024875	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6452	63024875	186225746	311	8296										
ANGPTL3	27329	broad.mit.edu	37	chr1	63068014	63068014	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaaaacttcaatgaaacGtgggagaactacaaatatgg	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63068014G>A	ENST00000371129.3	+	5	974	c.894G>A	c.(892-894)acG>acA	p.T298T	ANGPTL3_ENST00000493994.1_3'UTR|DOCK7_ENST00000251157.5_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	298	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)	p.T298T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						TCAATGAAACGTGGGAGAACT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	1											162	160	161					1																	63068014		2203	4300	6503	62840602	SO:0001819	synonymous_variant	27329			AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.894G>A	1.37:g.63068014G>A			62840602	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	37	CCDS622.1																																																																																				0.333	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		A	63068014	G	A	63068014	2	1	61	1	0	0	0	0	0	0	0	1	615	1132	40	1		1	ANGPTL3	1	63068014	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43139	63068014	186182607	312	8297										
ANGPTL3	27329	broad.mit.edu	37	chr1	63069703	63069703	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaatctaattatgttttacGaattgagttggaagactgga	10	4	1	2	rs192778191	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63069703G>A	ENST00000371129.3	+	6	1075	c.995G>A	c.(994-996)cGa>cAa	p.R332Q	ANGPTL3_ENST00000493994.1_3'UTR|DOCK7_ENST00000251157.5_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	332	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)	p.R332Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						TATGTTTTACGAATTGAGTTG	0.318													G|||	2	0.000399361	0	0.0014	5008	,	,		16844	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						G	GLN/ARG,	0,4406		0,0,2203	75	79	78		995,	4.6	1	1		78	1,8593	1.2+/-3.3	0,1,4296	yes	missense,intron	ANGPTL3,DOCK7	NM_014495.2,NM_033407.2	43,	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	332/461,	63069703	1,12999	2203	4297	6500	62842291	SO:0001583	missense	27329			AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.995G>A	1.37:g.63069703G>A	ENSP00000360170:p.Arg332Gln		62842291	A0JLS0|B1ALJ0|B2RCW1	Missense_Mutation	SNP	ENST00000371129.3	37	CCDS622.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.90	3.721182	0.68959	0.0	1.16E-4	ENSG00000132855	ENST00000371129	T	0.80566	-1.39	5.49	4.58	0.56647	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.229780	0.45361	N	0.000377	D	0.86460	0.5938	M	0.87456	2.885	0.37925	D	0.931827	D	0.89917	1.0	D	0.70227	0.968	D	0.87747	0.2589	10	0.49607	T	0.09	.	10.2868	0.43573	0.15:0.0:0.85:0.0	.	332	Q9Y5C1	ANGL3_HUMAN	Q	332	ENSP00000360170:R332Q	ENSP00000360170:R332Q	R	+	2	0	ANGPTL3	62842291	1.000000	0.71417	1.000000	0.80357	0.673000	0.39480	3.773000	0.55333	1.311000	0.45024	0.650000	0.86243	CGA		0.318	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		A	63069703	G	A	63069703	3	1	61	1	0	0	0	0	1	0	0	0	615	1058	37	1	1017	1	ANGPTL3	1	63069703	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1689	63069703	186180918	313	8298										
DOCK7	85440	broad.mit.edu	37	chr1	63099225	63099225	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcacactctccaatgtCtccttgctgtaggacttttt	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63099225C>A	ENST00000340370.5	-	10	1077	c.1060G>T	c.(1060-1062)Gac>Tac	p.D354Y	DOCK7_ENST00000251157.5_Missense_Mutation_p.D354Y|DOCK7_ENST00000404627.2_Missense_Mutation_p.D354Y	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	354					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.D354Y(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TCTCCAATGTCTCCTTGCTGT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											234	229	230					1																	63099225		2203	4300	6503	62871813	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.1060G>T	1.37:g.63099225C>A	ENSP00000340742:p.Asp354Tyr		62871813	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068034	0.76301	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.42900	0.96;0.96;0.96	4.01	4.01	0.46588	.	0.000000	0.85682	D	0.000000	T	0.64505	0.2604	M	0.88775	2.98	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.97110	0.998;1.0;0.993;1.0;0.976	T	0.74399	-0.3678	10	0.87932	D	0	.	16.3272	0.82987	0.0:1.0:0.0:0.0	.	354;354;354;354;354	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	Y	354	ENSP00000251157:D354Y;ENSP00000340742:D354Y;ENSP00000384446:D354Y	ENSP00000251157:D354Y	D	-	1	0	DOCK7	62871813	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.558000	0.82253	2.075000	0.62263	0.555000	0.69702	GAC		0.358	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	63099225	C	A	63099225	3	1	61	1	0	0	0	0	1	0	0	0	4703	913	32	2	5429	2	DOCK7	1	63099225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29522	63099225	186151396	314	8299										
ATG4C	84938	broad.mit.edu	37	chr1	63284707	63284707	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatgctttgaatattgaAaattcagactctgaatcatg	7	7	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63284707A>C	ENST00000317868.4	+	5	633	c.426A>C	c.(424-426)gaA>gaC	p.E142D	ATG4C_ENST00000371120.3_Missense_Mutation_p.E142D	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	142					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.E142D(2)	ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						TGAATATTGAAAATTCAGACT	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	1											63	65	64					1																	63284707		2203	4299	6502	63057295	SO:0001583	missense	84938			AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog C (S. cerevisiae)", "ATG4 autophagy related 4 homolog C (S. cerevisiae)"	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.426A>C	1.37:g.63284707A>C	ENSP00000322159:p.Glu142Asp		63057295	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.254017	0.39896	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000443289;ENST00000540025;ENST00000371118	.	.	.	5.93	1.12	0.20585	.	0.177676	0.52532	D	0.000067	T	0.28732	0.0712	M	0.75777	2.31	0.36548	D	0.871694	B	0.06786	0.001	B	0.12837	0.008	T	0.11867	-1.0570	9	0.12430	T	0.62	-21.2969	5.5083	0.16866	0.4846:0.2489:0.2665:0.0	.	142	Q96DT6	ATG4C_HUMAN	D	142	.	ENSP00000322159:E142D	E	+	3	2	ATG4C	63057295	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.733000	0.26087	0.149000	0.19098	0.533000	0.62120	GAA		0.343	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		C	63284707	A	C	63284707	3	2	61	1	0	0	0	0	1	0	0	0	1099	11	1	4	440	4	ATG4C	1	63284707	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	185482	63284707	185965914	315	8300										
ITGB3BP	23421	broad.mit.edu	37	chr1	63919604	63919604	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacctttgtgaggaagtcCtgtactcttttcaaacagtt	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63919604C>A	ENST00000271002.10	-	7	550	c.469G>T	c.(469-471)Gga>Tga	p.G157*	ITGB3BP_ENST00000461681.1_5'UTR|ITGB3BP_ENST00000371092.3_Nonsense_Mutation_p.G196*|ITGB3BP_ENST00000283568.8_Nonsense_Mutation_p.G157*	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)	157					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.G157*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						TGAGGAAGTCCTGTACTCTTT	0.284																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											109	107	108					1																	63919604		2201	4297	6498	63692192	SO:0001587	stop_gained	23421			U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"centromere protein R"	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.469G>T	1.37:g.63919604C>A	ENSP00000271002:p.Gly157*		63692192	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Nonsense_Mutation	SNP	ENST00000271002.10	37	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.565407	0.27915	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	.	.	.	4.77	1.83	0.25207	.	1.069550	0.07258	N	0.866998	.	.	.	.	.	.	0.34362	D	0.691077	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	0.0771	7.4836	0.27419	0.0:0.7011:0.0:0.2989	.	.	.	.	X	157;196;157	.	ENSP00000271002:G157X	G	-	1	0	ITGB3BP	63692192	0.075000	0.21258	0.011000	0.14972	0.251000	0.25915	0.074000	0.14662	0.675000	0.31264	0.644000	0.83932	GGA		0.284	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288		A	63919604	C	A	63919604	4	1	61	1	0	0	0	0	0	1	0	0	7917	690	24	2	72	2	ITGB3BP	1	63919604	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	634897	63919604	185331017	316	8301										
ITGB3BP	23421	broad.mit.edu	37	chr1	63920611	63920611	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgatttcttctgacaattTctcaacttttgatagcaaca	4	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:63920611T>C	ENST00000271002.10	-	5	364	c.283A>G	c.(283-285)Aaa>Gaa	p.K95E	ITGB3BP_ENST00000461681.1_5'UTR|ITGB3BP_ENST00000371092.3_Missense_Mutation_p.K134E|ITGB3BP_ENST00000283568.8_Missense_Mutation_p.K95E	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)	95					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.K95E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						TCTGACAATTTCTCAACTTTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	66	67					1																	63920611		2198	4296	6494	63693199	SO:0001583	missense	23421			U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"centromere protein R"	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.283A>G	1.37:g.63920611T>C	ENSP00000271002:p.Lys95Glu		63693199	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Missense_Mutation	SNP	ENST00000271002.10	37	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.386327	0.61956	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	T;T;T	0.48201	0.82;0.82;0.82	5.67	4.55	0.56014	.	0.563832	0.17273	N	0.180287	T	0.15392	0.0371	L	0.47716	1.5	0.20196	N	0.999924	B;B;B;B	0.28783	0.091;0.015;0.222;0.111	B;B;B;B	0.24701	0.039;0.012;0.055;0.021	T	0.21999	-1.0229	10	0.07813	T	0.8	-1.3759	9.2361	0.37466	0.0:0.0824:0.0:0.9176	.	95;55;134;95	Q13352-2;D3DQ59;Q13352-5;Q13352	.;.;.;CENPR_HUMAN	E	95;134;95	ENSP00000271002:K95E;ENSP00000360133:K134E;ENSP00000283568:K95E	ENSP00000271002:K95E	K	-	1	0	ITGB3BP	63693199	0.873000	0.30073	0.994000	0.49952	0.652000	0.38707	1.118000	0.31246	0.981000	0.38548	0.528000	0.53228	AAA		0.303	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288		C	63920611	T	C	63920611	3	2	61	1	0	0	0	0	1	0	0	0	7917	1792	62	4	266	4	ITGB3BP	1	63920611	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1007	63920611	185330010	317	8302										
ROR1	4919	broad.mit.edu	37	chr1	64515548	64515548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctatggctctcggctgCggattagaaacctcgacacc	9	14	2	1	rs199925889		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:64515548C>T	ENST00000371079.1	+	3	724	c.349C>T	c.(349-351)Cgg>Tgg	p.R117W	ROR1_ENST00000482426.1_3'UTR|ROR1_ENST00000371080.1_Missense_Mutation_p.R117W	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	117	Ig-like C2-type.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.R117W(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						CTCTCGGCTGCGGATTAGAAA	0.547													C|||	1	0.000199681	0	0	5008	,	,		19236	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											98	103	101					1																	64515548		2203	4300	6503	64288136	SO:0001583	missense	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.349C>T	1.37:g.64515548C>T	ENSP00000360120:p.Arg117Trp		64288136	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.7	4.190507	0.78789	.	.	ENSG00000185483	ENST00000371080;ENST00000371079;ENST00000544776	T;T	0.69306	-0.39;-0.39	5.8	2.85	0.33270	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.38837	N	0.001541	T	0.76033	0.3931	M	0.79343	2.45	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.989;0.998	T	0.80460	-0.1373	10	0.87932	D	0	.	15.2766	0.73745	0.3647:0.6353:0.0:0.0	.	117;117	Q01973;Q66K77	ROR1_HUMAN;.	W	117;117;120	ENSP00000360121:R117W;ENSP00000360120:R117W	ENSP00000360120:R117W	R	+	1	2	ROR1	64288136	0.603000	0.26924	0.977000	0.42913	0.988000	0.76386	0.704000	0.25661	0.328000	0.23435	0.563000	0.77884	CGG		0.547	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		T	64515548	C	T	64515548	3	4	61	1	0	0	0	0	1	0	0	0	13563	759	27	1	359	1	ROR1	1	64515548	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	594937	64515548	184735073	318	8303										
ROR1	4919	broad.mit.edu	37	chr1	64644455	64644455	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaatctcaaaaaccctacAaaattgactcaaagcaagca	3	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:64644455A>C	ENST00000371079.1	+	9	3106	c.2731A>C	c.(2731-2733)Aaa>Caa	p.K911Q	ROR1_ENST00000545203.1_Missense_Mutation_p.K362Q	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	911					peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.K911Q(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						AAAACCCTACAAAATTGACTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	95	96					1																	64644455		2203	4300	6503	64417043	SO:0001583	missense	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.2731A>C	1.37:g.64644455A>C	ENSP00000360120:p.Lys911Gln		64417043	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	.	.	.	.	.	.	.	.	.	.	A	2.860	-0.236265	0.05944	.	.	ENSG00000185483	ENST00000371079;ENST00000544776;ENST00000545203	T;T	0.78246	-0.91;-1.16	5.72	5.72	0.89469	.	0.000000	0.45867	D	0.000327	T	0.46814	0.1412	N	0.08118	0	0.47245	D	0.999367	B	0.17038	0.02	B	0.09377	0.004	T	0.47100	-0.9143	10	0.31617	T	0.26	.	16.2988	0.82793	1.0:0.0:0.0:0.0	.	911	Q01973	ROR1_HUMAN	Q	911;914;362	ENSP00000360120:K911Q;ENSP00000441637:K362Q	ENSP00000360120:K911Q	K	+	1	0	ROR1	64417043	1.000000	0.71417	1.000000	0.80357	0.158000	0.22134	5.997000	0.70646	2.311000	0.77944	0.533000	0.62120	AAA		0.383	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		C	64644455	A	C	64644455	3	2	61	1	0	0	0	0	1	0	0	0	13563	131	5	4	2773	4	ROR1	1	64644455	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	128907	64644455	184606166	319	8304										
CACHD1	57685	broad.mit.edu	37	chr1	65137281	65137281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcacactgtggctgtgAtgggcattgacttcacactc	12	11	1	2	rs74928360		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:65137281A>G	ENST00000371073.2	+	17	2422	c.2422A>G	c.(2422-2424)Atg>Gtg	p.M808V	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.M757V			Q5VU97	CAHD1_HUMAN	cache domain containing 1	808	Cache 2.				calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.M757V(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TGTGGCTGTGATGGGCATTGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											220	192	201					1																	65137281		2203	4300	6503	64909869	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2422A>G	1.37:g.65137281A>G	ENSP00000360113:p.Met808Val		64909869	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	A	8.633	0.894037	0.17613	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.17213	2.29;2.3	6.08	6.08	0.98989	Cache (1);	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.03983	-0.305	0.80722	D	1	P	0.35542	0.508	P	0.51945	0.685	T	0.15435	-1.0437	10	0.02654	T	1	-35.9413	16.6438	0.85155	1.0:0.0:0.0:0.0	.	808	Q5VU97	CAHD1_HUMAN	V	808;757	ENSP00000360113:M808V;ENSP00000290039:M757V	ENSP00000290039:M757V	M	+	1	0	CACHD1	64909869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.550000	0.90675	2.333000	0.79357	0.533000	0.62120	ATG		0.403	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		G	65137281	A	G	65137281	3	3	61	1	0	0	0	0	1	0	0	0	2543	333	12	4	2335	4	CACHD1	1	65137281	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	492826	65137281	184113340	320	8305										
CACHD1	57685	broad.mit.edu	37	chr1	65157009	65157009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttctttttctaggttAcagcaccatgagcccacagg	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:65157009A>G	ENST00000371073.2	+	27	3590	c.3590A>G	c.(3589-3591)tAc>tGc	p.Y1197C	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.Y1146C			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1197					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.Y1146C(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TTTCTAGGTTACAGCACCATG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	83	85					1																	65157009		2203	4300	6503	64929597	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3590A>G	1.37:g.65157009A>G	ENSP00000360113:p.Tyr1197Cys		64929597	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	A	19.03	3.748780	0.69533	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.65178	-0.14;-0.08	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.69205	0.3085	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.74182	-0.3748	10	0.87932	D	0	-28.2494	15.3597	0.74460	1.0:0.0:0.0:0.0	.	1197	Q5VU97	CAHD1_HUMAN	C	1197;1146	ENSP00000360113:Y1197C;ENSP00000290039:Y1146C	ENSP00000290039:Y1146C	Y	+	2	0	CACHD1	64929597	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.850000	0.92190	2.034000	0.60081	0.459000	0.35465	TAC		0.483	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		G	65157009	A	G	65157009	3	3	61	1	0	0	0	0	1	0	0	0	2543	391	14	4	3543	4	CACHD1	1	65157009	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	19728	65157009	184093612	321	8306										
JAK1	3716	broad.mit.edu	37	chr1	65321259	65321259	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgtgcgcaggatctgcttCttgaggtggctcatgaggtc	14	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:65321259C>A	ENST00000342505.4	-	11	1829	c.1581G>T	c.(1579-1581)aaG>aaT	p.K527N		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	527	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.K527N(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGATCTGCTTCTTGAGGTGGC	0.577			Mis		ALL																																		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	1	Substitution - Missense(1)	large_intestine(1)	1											66	69	68					1																	65321259		2092	4218	6310	65093847	SO:0001583	missense	3716			M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1581G>T	1.37:g.65321259C>A	ENSP00000343204:p.Lys527Asn		65093847	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542023	0.65198	.	.	ENSG00000162434	ENST00000342505	T	0.10288	2.89	4.53	4.53	0.55603	SH2 motif (3);	.	.	.	.	T	0.06371	0.0164	L	0.48642	1.525	0.38581	D	0.950182	P	0.44734	0.842	P	0.45343	0.477	T	0.08330	-1.0727	9	0.56958	D	0.05	-7.3002	6.0043	0.19537	0.0:0.7693:0.0:0.2307	.	527	P23458	JAK1_HUMAN	N	527	ENSP00000343204:K527N	ENSP00000343204:K527N	K	-	3	2	JAK1	65093847	0.950000	0.32346	1.000000	0.80357	0.735000	0.41995	0.382000	0.20635	2.519000	0.84933	0.655000	0.94253	AAG		0.577	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65321259	C	A	65321259	3	1	61	1	0	0	0	0	1	0	0	0	7958	912	32	2	1943	2	JAK1	1	65321259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	164250	65321259	183929362	322	8307										
LEPR	3953	broad.mit.edu	37	chr1	66036405	66036405	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcggagtgagcaagataGaaactgctccttatgtgcag	11	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:66036405G>T	ENST00000349533.6	+	4	475	c.290G>T	c.(289-291)aGa>aTa	p.R97I	LEPR_ENST00000371058.1_Missense_Mutation_p.R97I|snoU13_ENST00000459362.1_RNA|LEPR_ENST00000344610.8_Missense_Mutation_p.R97I|LEPR_ENST00000406510.3_5'UTR|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371060.3_Missense_Mutation_p.R97I|LEPR_ENST00000371059.3_Missense_Mutation_p.R97I	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.R97I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GAGCAAGATAGAAACTGCTCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	81	81					1																	66036405		2203	4300	6503	65808993	SO:0001583	missense	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.290G>T	1.37:g.66036405G>T	ENSP00000330393:p.Arg97Ile		65808993	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	G	6.053	0.378052	0.11466	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.55052	0.56;0.58;0.57;0.54;0.56	5.69	2.03	0.26663	.	0.677457	0.15206	N	0.274715	T	0.07369	0.0186	N	0.01352	-0.895	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.09377	0.0;0.0;0.001;0.004	T	0.16453	-1.0402	10	0.36615	T	0.2	-1.6603	2.3012	0.04162	0.598:0.1622:0.0847:0.1551	.	97;97;97;97	P48357-4;P48357;P48357-2;P48357-3	.;LEPR_HUMAN;.;.	I	97	ENSP00000340884:R97I;ENSP00000330393:R97I;ENSP00000360099:R97I;ENSP00000360098:R97I;ENSP00000360097:R97I	ENSP00000340884:R97I	R	+	2	0	LEPR	65808993	0.049000	0.20398	0.793000	0.32043	0.106000	0.19336	-0.050000	0.11904	0.089000	0.17243	-1.394000	0.01149	AGA		0.343	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		T	66036405	G	T	66036405	3	4	61	1	0	0	0	0	1	0	0	0	8750	942	33	2	296	2	LEPR	1	66036405	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	715146	66036405	183214216	323	8308										
LEPR	3953	broad.mit.edu	37	chr1	66102253	66102253	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcttctctagcaaaaattCtccgttgaaggattctttct	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:66102253C>A	ENST00000349533.6	+	20	3238	c.3053C>A	c.(3052-3054)tCt>tAt	p.S1018Y	LEPR_ENST00000406510.3_Missense_Mutation_p.S85Y	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.S1018Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AGCAAAAATTCTCCGTTGAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	71	69					1																	66102253		2202	4297	6499	65874841	SO:0001583	missense	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3053C>A	1.37:g.66102253C>A	ENSP00000330393:p.Ser1018Tyr		65874841	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	C	4.744	0.138366	0.09083	.	.	ENSG00000116678	ENST00000349533;ENST00000406510	T	0.60548	0.18	5.93	3.09	0.35607	.	0.050137	0.85682	D	0.000000	T	0.32675	0.0837	L	0.58101	1.795	0.22366	N	0.999163	B	0.19583	0.037	B	0.21917	0.037	T	0.37596	-0.9699	10	0.66056	D	0.02	-5.9193	8.842	0.35148	0.1236:0.7481:0.0:0.1283	.	1018	P48357	LEPR_HUMAN	Y	1018;85	ENSP00000330393:S1018Y	ENSP00000330393:S1018Y	S	+	2	0	LEPR	65874841	0.135000	0.22499	0.001000	0.08648	0.005000	0.04900	2.793000	0.47845	0.421000	0.25980	-0.840000	0.03056	TCT		0.408	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		A	66102253	C	A	66102253	3	1	61	1	0	0	0	0	1	0	0	0	8750	913	32	2	3353	2	LEPR	1	66102253	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65848	66102253	183148368	324	8309										
LEPR	3953	broad.mit.edu	37	chr1	66102431	66102431	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatgataaaaagtctatCtattatttaggggtcacctc	6	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:66102431C>A	ENST00000349533.6	+	20	3416	c.3231C>A	c.(3229-3231)atC>atA	p.I1077I	LEPR_ENST00000406510.3_Silent_p.I144I	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.I1077I(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AAAAGTCTATCTATTATTTAG	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	1											64	72	69					1																	66102431		2203	4300	6503	65875019	SO:0001819	synonymous_variant	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3231C>A	1.37:g.66102431C>A			65875019	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																				0.398	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		A	66102431	C	A	66102431	2	1	61	1	0	0	0	0	0	0	0	1	8750	903	32	2		2	LEPR	1	66102431	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178	66102431	183148190	325	8310										
PDE4B	5142	broad.mit.edu	37	chr1	66458674	66458674	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaggagcaaatgcatttaGaacttgagcttccgagatta	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:66458674G>A	ENST00000329654.4	+	3	468				PDE4B_ENST00000371049.3_Intron|PDE4B_ENST00000423207.2_Missense_Mutation_p.E29K	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.E29K(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	AATGCATTTAGAACTTGAGCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	102	103					1																	66458674		2203	4300	6503	66231262	SO:0001627	intron_variant	5142			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.281+74156G>A	1.37:g.66458674G>A			66231262	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	37	CCDS632.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909935	0.92107	.	.	ENSG00000184588	ENST00000423207	T	0.69306	-0.39	5.52	5.52	0.82312	.	.	.	.	.	T	0.69682	0.3138	L	0.40543	1.245	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.63734	-0.6570	9	0.32370	T	0.25	.	19.6361	0.95733	0.0:0.0:1.0:0.0	.	34	Q59GM8	.	K	29	ENSP00000392947:E29K	ENSP00000392947:E29K	E	+	1	0	PDE4B	66231262	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.359000	0.79477	2.878000	0.98634	0.650000	0.86243	GAA		0.413	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		A	66458674	G	A	66458674	1	1	61	0	1	0	0	0	0	0	0	0	11671	943	33	3		3	PDE4B	1	66458674	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356243	66458674	182791947	326	8311										
PDE4B	5142	broad.mit.edu	37	chr1	66838105	66838105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagataacaggaactggtAtcagagcatgatacctcaaa	9	7	2	4	rs200211480		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:66838105A>G	ENST00000329654.4	+	17	2142	c.1955A>G	c.(1954-1956)tAt>tGt	p.Y652C	PDE4B_ENST00000371049.3_Missense_Mutation_p.Y652C|PDE4B_ENST00000423207.2_Missense_Mutation_p.Y637C|PDE4B_ENST00000480109.2_Missense_Mutation_p.Y419C|PDE4B_ENST00000371045.5_Missense_Mutation_p.Y480C	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	652					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.Y637C(1)|p.Y652C(1)|p.Y480C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	AGGAACTGGTATCAGAGCATG	0.483																																																3	Substitution - Missense(3)	large_intestine(3)	1											113	104	107					1																	66838105		2203	4300	6503	66610693	SO:0001583	missense	5142			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.1955A>G	1.37:g.66838105A>G	ENSP00000332116:p.Tyr652Cys		66610693	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	37	CCDS632.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.344153	0.82022	.	.	ENSG00000184588	ENST00000329654;ENST00000341517;ENST00000371049;ENST00000423207;ENST00000371045;ENST00000480109	T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.05	5.05	0.67936	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	M	0.84219	2.685	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.996;1.0;0.999;1.0;1.0	D	0.85389	0.1124	10	0.87932	D	0	.	14.9065	0.70724	1.0:0.0:0.0:0.0	.	419;637;522;642;652	A5YW33;Q07343-3;Q13945;Q59GM8;Q07343	.;.;.;.;PDE4B_HUMAN	C	652;652;652;637;480;419	ENSP00000332116:Y652C;ENSP00000342637:Y652C;ENSP00000360088:Y652C;ENSP00000392947:Y637C;ENSP00000360084:Y480C;ENSP00000432592:Y419C	ENSP00000332116:Y652C	Y	+	2	0	PDE4B	66610693	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.029000	0.93718	2.244000	0.73946	0.533000	0.62120	TAT		0.483	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		G	66838105	A	G	66838105	3	3	61	1	0	0	0	0	1	0	0	0	11671	449	16	4	2375	4	PDE4B	1	66838105	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	379431	66838105	182412516	327	8312										
SGIP1	84251	broad.mit.edu	37	chr1	67199489	67199489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtaaacatgccaaatttgAtgactcacctaaagaaagtg	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67199489A>G	ENST00000371037.4	+	21	2034	c.1957A>G	c.(1957-1959)Atg>Gtg	p.M653V	SGIP1_ENST00000371039.1_Missense_Mutation_p.M456V|AL354978.1_ENST00000408728.2_RNA|SGIP1_ENST00000237247.6_Missense_Mutation_p.M684V|SGIP1_ENST00000435165.2_Missense_Mutation_p.M158V|SGIP1_ENST00000371036.3_Missense_Mutation_p.M455V|SGIP1_ENST00000371035.3_Missense_Mutation_p.M443V	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	653	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Necessary and sufficient to mediate interaction with CANX. {ECO:0000250}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)	p.M653V(1)|p.M456V(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						GCCAAATTTGATGACTCACCT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	1											135	131	132					1																	67199489		2203	4300	6503	66972077	SO:0001583	missense	84251			AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.1957A>G	1.37:g.67199489A>G	ENSP00000360076:p.Met653Val		66972077	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	A	13.75	2.329031	0.41197	.	.	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037;ENST00000435165	T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02	6.0	6.0	0.97389	Muniscin C-terminal mu homology domain (1);	0.036257	0.85682	D	0.000000	T	0.14227	0.0344	N	0.04880	-0.145	0.49213	D	0.999765	B;B;B;B;B	0.30634	0.05;0.013;0.166;0.288;0.012	B;B;B;B;B	0.30105	0.089;0.037;0.038;0.111;0.009	T	0.10064	-1.0646	10	0.45353	T	0.12	-18.811	16.5044	0.84266	1.0:0.0:0.0:0.0	.	683;158;255;443;653	A6NEV3;Q6ZV33;B3KR01;B7Z5H8;Q9BQI5	.;.;.;.;SGIP1_HUMAN	V	684;456;443;683;656;455;653;158	ENSP00000237247:M684V;ENSP00000360078:M456V;ENSP00000360074:M443V;ENSP00000360075:M455V;ENSP00000360076:M653V;ENSP00000395525:M158V	ENSP00000237247:M684V	M	+	1	0	SGIP1	66972077	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.295000	0.77249	0.528000	0.53228	ATG		0.353	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		G	67199489	A	G	67199489	3	3	61	1	0	0	0	0	1	0	0	0	14243	333	12	4	2039	4	SGIP1	1	67199489	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	361384	67199489	182051132	328	8313										
WDR78	79819	broad.mit.edu	37	chr1	67306290	67306290	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcctcctccttcttagaTtcttcctctacctcttcatg	2	16	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67306290T>C	ENST00000371026.3	-	9	1411	c.1356A>G	c.(1354-1356)gaA>gaG	p.E452E	WDR78_ENST00000371023.3_Silent_p.E452E|WDR78_ENST00000431318.1_Silent_p.E198E	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	452	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)			p.E452E(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CCTTCTTAGATTCTTCCTCTA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	1											160	162	161					1																	67306290		2203	4300	6503	67078878	SO:0001819	synonymous_variant	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.1356A>G	1.37:g.67306290T>C			67078878	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Silent	SNP	ENST00000371026.3	37	CCDS635.1																																																																																				0.388	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		C	67306290	T	C	67306290	2	2	61	1	0	0	0	0	0	0	0	1	17368	1490	52	4		4	WDR78	1	67306290	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	106801	67306290	181944331	329	8314										
WDR78	79819	broad.mit.edu	37	chr1	67358918	67358918	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtatactctaccttgtaAactgccctaacgtactagga	6	10	1	0	rs112758225		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67358918A>C	ENST00000371026.3	-	3	579	c.524T>G	c.(523-525)tTt>tGt	p.F175C	WDR78_ENST00000371023.3_Missense_Mutation_p.F175C|WDR78_ENST00000371022.3_Missense_Mutation_p.F175C|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	175					hematopoietic progenitor cell differentiation (GO:0002244)			p.F175C(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CTACCTTGTAAACTGCCCTAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	127	125					1																	67358918		2203	4300	6503	67131506	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.524T>G	1.37:g.67358918A>C	ENSP00000360065:p.Phe175Cys		67131506	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.313151	0.60414	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	T;T;T	0.62364	0.03;1.82;0.52	5.29	4.13	0.48395	.	0.100647	0.64402	D	0.000001	T	0.65228	0.2671	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69479	0.964;0.959;0.959	T	0.69767	-0.5056	10	0.87932	D	0	-10.4879	8.3393	0.32235	0.8177:0.0:0.0:0.1823	.	175;175;175	Q5TAD8;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	C	175	ENSP00000360065:F175C;ENSP00000360062:F175C;ENSP00000360061:F175C	ENSP00000360061:F175C	F	-	2	0	WDR78	67131506	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.089000	0.41672	0.918000	0.36919	0.528000	0.53228	TTT		0.313	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		C	67358918	A	C	67358918	3	2	61	1	0	0	0	0	1	0	0	0	17368	14	1	4	2139	4	WDR78	1	67358918	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52628	67358918	181891703	330	8315										
MIER1	57708	broad.mit.edu	37	chr1	67450503	67450503	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtaaacagcaatggaaaaGaaagtccaggttcttctgaa	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67450503G>T	ENST00000355356.3	+	13	1608	c.1459G>T	c.(1459-1461)Gaa>Taa	p.E487*	MIER1_ENST00000401042.3_Intron|MIER1_ENST00000355977.6_Intron|MIER1_ENST00000371018.3_Intron|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000357692.2_Nonsense_Mutation_p.E504*|MIER1_ENST00000401041.1_Nonsense_Mutation_p.E540*|MIER1_ENST00000371016.1_Intron	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	487					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.E487*(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						CAATGGAAAAGAAAGTCCAGG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											69	69	69					1																	67450503		1819	4076	5895	67223091	SO:0001587	stop_gained	57708				CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.1459G>T	1.37:g.67450503G>T	ENSP00000347514:p.Glu487*		67223091	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Nonsense_Mutation	SNP	ENST00000355356.3	37	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	G	37	6.224381	0.97390	.	.	ENSG00000198160	ENST00000371017;ENST00000357692;ENST00000401041;ENST00000355356	.	.	.	5.69	5.69	0.88448	.	0.110433	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.2647	20.205	0.98274	0.0:0.0:1.0:0.0	.	.	.	.	X	508;504;540;487	.	ENSP00000347514:E487X	E	+	1	0	MIER1	67223091	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.079000	0.76829	2.857000	0.98124	0.650000	0.86243	GAA		0.363	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		T	67450503	G	T	67450503	4	4	61	1	0	0	0	0	0	1	0	0	9610	943	33	2	1749	2	MIER1	1	67450503	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91585	67450503	181800118	331	8316										
SLC35D1	23169	broad.mit.edu	37	chr1	67519657	67519657	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatttcgcgggggcttctcCtttaacccgagcatgctgac	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67519657C>A	ENST00000235345.5	-	1	125	c.40G>T	c.(40-42)Gga>Tga	p.G14*	SLC35D1_ENST00000506472.2_5'Flank	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	14					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)	p.G14*(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						GGGGCTTCTCCTTTAACCCGA	0.672																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											46	52	50					1																	67519657		2203	4300	6503	67292245	SO:0001587	stop_gained	23169			AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.40G>T	1.37:g.67519657C>A	ENSP00000235345:p.Gly14*		67292245	A8K185|B7Z3X2|Q52LU5|Q92548	Nonsense_Mutation	SNP	ENST00000235345.5	37	CCDS636.1	.	.	.	.	.	.	.	.	.	.	C	38	7.046336	0.98025	.	.	ENSG00000116704	ENST00000235345	.	.	.	3.41	3.41	0.39046	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-10.2508	12.6981	0.57016	0.0:1.0:0.0:0.0	.	.	.	.	X	14	.	ENSP00000235345:G14X	G	-	1	0	SLC35D1	67292245	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	0.643000	0.24750	1.900000	0.55004	0.462000	0.41574	GGA		0.672	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		A	67519657	C	A	67519657	4	1	61	1	0	0	0	0	0	1	0	0	14618	690	24	2	1075	2	SLC35D1	1	67519657	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69154	67519657	181730964	332	8317										
C1orf141	400757	broad.mit.edu	37	chr1	67581112	67581112	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacttttcaaaattactcTttctaggttcaggctcacat	5	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67581112T>G	ENST00000371007.2	-	5	378	c.269A>C	c.(268-270)aAg>aCg	p.K90T	C1orf141_ENST00000544837.1_Missense_Mutation_p.K90T|C1orf141_ENST00000371006.1_Missense_Mutation_p.K90T	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	90								p.K90T(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						AAAATTACTCTTTCTAGGTTC	0.239																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	50	49					1																	67581112		2191	4272	6463	67353700	SO:0001583	missense	400757			BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.269A>C	1.37:g.67581112T>G	ENSP00000360046:p.Lys90Thr		67353700	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	T	9.094	1.002473	0.19121	.	.	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837;ENST00000371005;ENST00000448166	T;T;T	0.37058	1.22;1.22;1.22	3.94	1.6	0.23607	.	0.772748	0.10543	N	0.662494	T	0.18509	0.0444	L	0.27053	0.805	0.09310	N	1	D	0.63046	0.992	P	0.57152	0.814	T	0.06499	-1.0823	10	0.66056	D	0.02	-1.7688	2.7942	0.05396	0.2214:0.1227:0.0:0.6559	.	90	Q5JVX7	CA141_HUMAN	T	90	ENSP00000360046:K90T;ENSP00000360045:K90T;ENSP00000444018:K90T	ENSP00000360044:K90T	K	-	2	0	C1orf141	67353700	0.001000	0.12720	0.001000	0.08648	0.217000	0.24651	0.337000	0.19841	0.341000	0.23771	-0.333000	0.08304	AAG		0.239	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674		G	67581112	T	G	67581112	3	3	61	1	0	0	0	0	1	0	0	0	2007	1609	56	4	949	4	C1orf141	1	67581112	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	61455	67581112	181669509	333	8318										
C1orf141	400757	broad.mit.edu	37	chr1	67591476	67591476	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgacttgtcttctttgatCtttgatattgccttagacgc	7	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67591476C>A	ENST00000371007.2	-	4	301	c.192G>T	c.(190-192)aaG>aaT	p.K64N	C1orf141_ENST00000544837.1_Missense_Mutation_p.K64N|C1orf141_ENST00000371006.1_Missense_Mutation_p.K64N	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	64								p.K64N(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						CTTCTTTGATCTTTGATATTG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											273	256	262					1																	67591476		2203	4300	6503	67364064	SO:0001583	missense	400757			BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.192G>T	1.37:g.67591476C>A	ENSP00000360046:p.Lys64Asn		67364064	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857639	0.32791	.	.	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000371004;ENST00000544837;ENST00000371005;ENST00000448166;ENST00000371003	T;T;T	0.33654	1.4;1.4;1.4	3.99	0.846	0.18955	.	0.525998	0.15983	N	0.235215	T	0.14141	0.0342	N	0.19112	0.55	0.09310	N	1	D	0.58268	0.982	P	0.54210	0.745	T	0.04991	-1.0913	10	0.72032	D	0.01	-0.0515	2.5464	0.04738	0.1917:0.5153:0.1861:0.1068	.	64	Q5JVX7	CA141_HUMAN	N	64	ENSP00000360046:K64N;ENSP00000360045:K64N;ENSP00000444018:K64N	ENSP00000360042:K64N	K	-	3	2	C1orf141	67364064	0.001000	0.12720	0.000000	0.03702	0.123000	0.20343	0.464000	0.21988	0.195000	0.20347	0.563000	0.77884	AAG		0.343	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674		A	67591476	C	A	67591476	3	1	61	1	0	0	0	0	1	0	0	0	2007	912	32	2	1030	2	C1orf141	1	67591476	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10364	67591476	181659145	334	8319										
SERBP1	26135	broad.mit.edu	37	chr1	67885866	67885866	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacctcttcaacttcattCtccctgtgaaaaggttttca	4	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67885866C>A	ENST00000370995.2	-	6	907	c.822G>T	c.(820-822)gaG>gaT	p.E274D	SERBP1_ENST00000370990.5_Missense_Mutation_p.E268D|SERBP1_ENST00000370994.4_Missense_Mutation_p.E253D|SERBP1_ENST00000484880.1_5'UTR|RNU6-387P_ENST00000411331.1_RNA|SERBP1_ENST00000361219.6_Missense_Mutation_p.E259D			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	274					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)	p.E274D(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						CAACTTCATTCTCCCTGTGAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	94	92					1																	67885866		2203	4300	6503	67658454	SO:0001583	missense	26135			AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.822G>T	1.37:g.67885866C>A	ENSP00000360034:p.Glu274Asp		67658454	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277306	0.59758	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	4.84	-0.66	0.11421	Hyaluronan/mRNA-binding protein (1);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	M	0.62088	1.915	0.58432	D	0.999999	D;D;P;P	0.76494	0.992;0.999;0.604;0.689	D;D;B;P	0.83275	0.989;0.996;0.208;0.676	T	0.53287	-0.8460	10	0.16420	T	0.52	-23.526	11.2134	0.48813	0.0:0.5048:0.0:0.4952	.	316;331;259;274	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	D	253;274;259;268	ENSP00000360033:E253D;ENSP00000360034:E274D;ENSP00000354591:E259D;ENSP00000360029:E268D	ENSP00000354591:E259D	E	-	3	2	SERBP1	67658454	0.951000	0.32395	0.991000	0.47740	0.916000	0.54674	0.151000	0.16283	-0.074000	0.12820	0.460000	0.39030	GAG		0.323	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		A	67885866	C	A	67885866	3	1	61	1	0	0	0	0	1	0	0	0	14112	912	32	2	416	2	SERBP1	1	67885866	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294390	67885866	181364755	335	8320										
SERBP1	26135	broad.mit.edu	37	chr1	67891862	67891862	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacccttttcttcaagtggCttttcgaatcttcgttcacg	6	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:67891862C>T	ENST00000370995.2	-	2	505	c.420G>A	c.(418-420)aaG>aaA	p.K140K	SERBP1_ENST00000370990.5_Silent_p.K140K|SERBP1_ENST00000370994.4_Silent_p.K140K|SERBP1_ENST00000484880.1_5'Flank|SERBP1_ENST00000361219.6_Silent_p.K140K			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	140					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)	p.K140K(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						CTTCAAGTGGCTTTTCGAATC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											189	188	188					1																	67891862		2203	4300	6503	67664450	SO:0001819	synonymous_variant	26135			AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.420G>A	1.37:g.67891862C>T			67664450	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Silent	SNP	ENST00000370995.2	37	CCDS30746.1																																																																																				0.443	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		T	67891862	C	T	67891862	2	4	61	1	0	0	0	0	0	0	0	1	14112	796	28	3		3	SERBP1	1	67891862	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5996	67891862	181358759	336	8321										
RPE65	6121	broad.mit.edu	37	chr1	68903978	68903978	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtaaattggctaaatataaGtaattataaacaaactcaaa	4	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:68903978G>T	ENST00000262340.5	-	10	1073	c.1020C>A	c.(1018-1020)taC>taA	p.Y340*		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	340					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)	p.Y340*(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						CTAAATATAAGTAATTATAAA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											49	52	51					1																	68903978		2203	4300	6503	68676566	SO:0001587	stop_gained	6121			U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1020C>A	1.37:g.68903978G>T	ENSP00000262340:p.Tyr340*		68676566	A8K1L0|Q5T9U3	Nonsense_Mutation	SNP	ENST00000262340.5	37	CCDS643.1	.	.	.	.	.	.	.	.	.	.	G	36	5.919906	0.97105	.	.	ENSG00000116745	ENST00000262340	.	.	.	5.71	2.85	0.33270	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2846	8.5907	0.33686	0.2885:0.0:0.7115:0.0	.	.	.	.	X	340	.	ENSP00000262340:Y340X	Y	-	3	2	RPE65	68676566	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.698000	0.37794	0.779000	0.33543	0.591000	0.81541	TAC		0.338	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		T	68903978	G	T	68903978	4	4	61	1	0	0	0	0	0	1	0	0	13582	1024	36	2	601	2	RPE65	1	68903978	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1012116	68903978	180346643	337	8322										
RPE65	6121	broad.mit.edu	37	chr1	68910339	68910339	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagtaacctctactcctcGaaagtaagaaaaaaacctgt	6	10	2	1	rs61752877		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:68910339G>A	ENST00000262340.5	-	5	423	c.370C>T	c.(370-372)Cga>Tga	p.R124*		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	124					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)	p.R124*(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TCTACTCCTCGAAAGTAAGAA	0.363													G|||	1	0.000199681	8e-04	0	5008	,	,		18235	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	1	GRCh37	CM983760	RPE65	M	rs61752877						56	59	58					1																	68910339		2203	4300	6503	68682927	SO:0001587	stop_gained	6121			U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.370C>T	1.37:g.68910339G>A	ENSP00000262340:p.Arg124*		68682927	A8K1L0|Q5T9U3	Nonsense_Mutation	SNP	ENST00000262340.5	37	CCDS643.1	.	.	.	.	.	.	.	.	.	.	G	35	5.573860	0.96553	.	.	ENSG00000116745	ENST00000262340	.	.	.	5.05	1.88	0.25563	.	0.595355	0.17781	N	0.162247	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-2.5107	14.9632	0.71171	0.0:0.0:0.3727:0.6272	rs61752877	.	.	.	X	124	.	ENSP00000262340:R124X	R	-	1	2	RPE65	68682927	1.000000	0.71417	0.988000	0.46212	0.994000	0.84299	1.775000	0.38584	0.207000	0.20607	0.655000	0.94253	CGA		0.363	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		A	68910339	G	A	68910339	4	1	61	1	0	0	0	0	0	1	0	0	13582	1066	37	1	1271	1	RPE65	1	68910339	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6361	68910339	180340282	338	8323										
DEPDC1	55635	broad.mit.edu	37	chr1	68944921	68944921	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatgatccattaagaaaGaaactaatcttccagcaaga	7	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:68944921G>T	ENST00000456315.2	-	10	2132	c.2018C>A	c.(2017-2019)tCt>tAt	p.S673Y	DEPDC1_ENST00000370966.5_Missense_Mutation_p.S389Y|RP4-694A7.2_ENST00000425820.1_RNA	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	673					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)	p.S389Y(1)|p.S673Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		CATTAAGAAAGAAACTAATCT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	1											89	83	85					1																	68944921		2203	4300	6503	68717509	SO:0001583	missense	55635			AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.2018C>A	1.37:g.68944921G>T	ENSP00000412292:p.Ser673Tyr		68717509	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Missense_Mutation	SNP	ENST00000456315.2	37	CCDS44159.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711253	0.89112	.	.	ENSG00000024526	ENST00000456315;ENST00000370966	T;T	0.54279	0.58;0.58	5.67	5.67	0.87782	Rho GTPase-activating protein domain (1);Rho GTPase activation protein (1);	0.098933	0.64402	D	0.000001	T	0.66867	0.2833	M	0.73598	2.24	0.45366	D	0.998354	D;D	0.89917	0.999;1.0	D;D	0.87578	0.989;0.998	T	0.60203	-0.7309	10	0.23302	T	0.38	-0.0178	19.76	0.96311	0.0:0.0:1.0:0.0	.	673;389	Q5TB30;Q5TB30-2	DEP1A_HUMAN;.	Y	673;389	ENSP00000412292:S673Y;ENSP00000360005:S389Y	ENSP00000360005:S389Y	S	-	2	0	DEPDC1	68717509	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.824000	0.92023	2.670000	0.90874	0.585000	0.79938	TCT		0.353	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025514.2	NM_017779		T	68944921	G	T	68944921	3	4	61	1	0	0	0	0	1	0	0	0	4450	942	33	2	429	2	DEPDC1	1	68944921	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34582	68944921	180305700	339	8324										
LRRC7	57554	broad.mit.edu	37	chr1	70225939	70225939	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgccatgccgatgtttcCgaggtgaagaagaaatcatc	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70225939C>T	ENST00000035383.5	+	1	82	c.52C>T	c.(52-54)Cga>Tga	p.R18*	LRRC7_ENST00000415775.2_5'UTR|LRRC7_ENST00000370958.1_Nonsense_Mutation_p.R56*|LRRC7_ENST00000310961.5_Nonsense_Mutation_p.R23*	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	18						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.R18*(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CCGATGTTTCCGAGGTGAAGA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											55	55	55					1																	70225939		2203	4299	6502	69998527	SO:0001587	stop_gained	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.52C>T	1.37:g.70225939C>T	ENSP00000035383:p.Arg18*		69998527	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Nonsense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	41	9.052384	0.99050	.	.	ENSG00000033122	ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298	.	.	.	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8425	0.92189	0.0:1.0:0.0:0.0	.	.	.	.	X	23;56;18;18	.	ENSP00000035383:R18X	R	+	1	2	LRRC7	69998527	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	CGA		0.463	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70225939	C	T	70225939	4	4	61	1	0	0	0	0	0	1	0	0	9049	644	23	1	54	1	LRRC7	1	70225939	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1281018	70225939	179024682	340	8325										
LRRC7	57554	broad.mit.edu	37	chr1	70504334	70504334	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccaatcccaacaggagtCttagtaatgtcttttctcaa	5	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70504334C>A	ENST00000035383.5	+	19	2743	c.2713C>A	c.(2713-2715)Ctt>Att	p.L905I	LRRC7_ENST00000415775.2_Missense_Mutation_p.L189I|LRRC7_ENST00000310961.5_Missense_Mutation_p.L910I	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	905						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.L905I(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAACAGGAGTCTTAGTAATGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											62	61	61					1																	70504334		2203	4300	6503	70276922	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2713C>A	1.37:g.70504334C>A	ENSP00000035383:p.Leu905Ile		70276922	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.511909	0.27036	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.37752	1.18;1.25;2.35	5.82	5.82	0.92795	.	0.154968	0.44285	D	0.000467	T	0.14098	0.0341	L	0.44542	1.39	0.30817	N	0.738186	B;P;P	0.38078	0.314;0.617;0.483	B;B;B	0.30855	0.075;0.121;0.057	T	0.11299	-1.0593	10	0.21014	T	0.42	.	13.9849	0.64328	0.1513:0.8487:0.0:0.0	.	189;905;905	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	I	910;905;189;728	ENSP00000309245:L910I;ENSP00000035383:L905I;ENSP00000394867:L189I	ENSP00000035383:L905I	L	+	1	0	LRRC7	70276922	1.000000	0.71417	0.999000	0.59377	0.686000	0.39977	4.416000	0.59815	2.762000	0.94881	0.467000	0.42956	CTT		0.418	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70504334	C	A	70504334	3	1	61	1	0	0	0	0	1	0	0	0	9049	913	32	2	2787	2	LRRC7	1	70504334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	278395	70504334	178746287	341	8326										
LRRC7	57554	broad.mit.edu	37	chr1	70505471	70505471	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatagaagctagacggttaGacagggtatgtctggtgttt	13	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70505471G>T	ENST00000035383.5	+	19	3880	c.3850G>T	c.(3850-3852)Gac>Tac	p.D1284Y	LRRC7_ENST00000415775.2_Missense_Mutation_p.D568Y|LRRC7_ENST00000310961.5_Missense_Mutation_p.D1289Y	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1284						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.D1284Y(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TAGACGGTTAGACAGGGTATG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	91	91					1																	70505471		2203	4300	6503	70278059	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3850G>T	1.37:g.70505471G>T	ENSP00000035383:p.Asp1284Tyr		70278059	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.093490	0.56075	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.43688	1.01;0.94;2.01	6.16	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.39489	0.1080	N	0.19112	0.55	0.54753	D	0.999982	D;D;D	0.89917	1.0;0.997;1.0	D;P;D	0.75484	0.986;0.875;0.921	T	0.51180	-0.8738	10	0.87932	D	0	.	14.6377	0.68702	0.0689:0.0:0.9311:0.0	.	568;1284;1284	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	Y	1289;1284;568;1107	ENSP00000309245:D1289Y;ENSP00000035383:D1284Y;ENSP00000394867:D568Y	ENSP00000035383:D1284Y	D	+	1	0	LRRC7	70278059	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.328000	0.96403	1.632000	0.50472	-0.142000	0.14014	GAC		0.448	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70505471	G	T	70505471	3	4	61	1	0	0	0	0	1	0	0	0	9049	942	33	2	3924	2	LRRC7	1	70505471	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1137	70505471	178745150	342	8327										
LRRC7	57554	broad.mit.edu	37	chr1	70541809	70541809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcccaaagccttcagcatcGcagccgggagcagcagccgt	12	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70541809G>A	ENST00000035383.5	+	22	4196	c.4166G>A	c.(4165-4167)cGc>cAc	p.R1389H	LRRC7_ENST00000415775.2_Missense_Mutation_p.R673H|LRRC7_ENST00000310961.5_Missense_Mutation_p.R1347H	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1389						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.R1389H(2)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CTTCAGCATCGCAGCCGGGAG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	1											63	59	61					1																	70541809		2203	4300	6503	70314397	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.4166G>A	1.37:g.70541809G>A	ENSP00000035383:p.Arg1389His		70314397	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323222	0.60634	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.38240	1.15;1.24;2.34	5.86	5.86	0.93980	.	0.061993	0.64402	D	0.000007	T	0.26629	0.0651	L	0.27053	0.805	0.38717	D	0.953366	D;B;B	0.64830	0.994;0.119;0.035	P;B;B	0.52672	0.706;0.027;0.003	T	0.01413	-1.1361	10	0.15952	T	0.53	.	19.1705	0.93575	0.0:0.0:1.0:0.0	.	673;1342;1389	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	H	1347;1389;673;1165	ENSP00000309245:R1347H;ENSP00000035383:R1389H;ENSP00000394867:R673H	ENSP00000035383:R1389H	R	+	2	0	LRRC7	70314397	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.501000	0.81600	2.771000	0.95319	0.650000	0.86243	CGC		0.507	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70541809	G	A	70541809	3	1	61	1	0	0	0	0	1	0	0	0	9049	1087	38	1	4252	1	LRRC7	1	70541809	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36338	70541809	178708812	343	8328										
LRRC40	55631	broad.mit.edu	37	chr1	70618192	70618192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtttattaaaactgagatCgacatcagaaaccatttcct	5	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70618192C>T	ENST00000370952.3	-	12	1442	c.1363G>A	c.(1363-1365)Gat>Aat	p.D455N		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	455						membrane (GO:0016020)		p.D455N(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						AAACTGAGATCGACATCAGAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	73	73					1																	70618192		2203	4292	6495	70390780	SO:0001583	missense	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1363G>A	1.37:g.70618192C>T	ENSP00000359990:p.Asp455Asn		70390780	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	C	5.557	0.287591	0.10513	.	.	ENSG00000066557	ENST00000370952	T	0.54866	0.55	5.45	4.32	0.51571	.	0.043959	0.85682	N	0.000000	T	0.07638	0.0192	N	0.01686	-0.76	0.23351	N	0.997856	B	0.02656	0.0	B	0.01281	0.0	T	0.35943	-0.9768	10	0.06891	T	0.86	.	11.4951	0.50404	0.0:0.071:0.0:0.929	.	455	Q9H9A6	LRC40_HUMAN	N	455	ENSP00000359990:D455N	ENSP00000359990:D455N	D	-	1	0	LRRC40	70390780	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.651000	0.61447	0.894000	0.36317	-0.295000	0.09555	GAT		0.318	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		T	70618192	C	T	70618192	3	4	61	1	0	0	0	0	1	0	0	0	9027	884	31	1	461	1	LRRC40	1	70618192	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76383	70618192	178632429	344	8329										
LRRC40	55631	broad.mit.edu	37	chr1	70639162	70639162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtacctttgatcttgcttCgtagatattttaggacttct	7	7	2	2	rs138941894	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70639162C>T	ENST00000370952.3	-	9	1176	c.1097G>A	c.(1096-1098)cGa>cAa	p.R366Q		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	366						membrane (GO:0016020)		p.R366Q(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GATCTTGCTTCGTAGATATTT	0.318													C|||	4	0.000798722	8e-04	0	5008	,	,		17723	0.002		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	0,4406		0,0,2203	62	62	62		1097	3.8	1	1	dbSNP_134	62	5,8585	4.3+/-15.6	0,5,4290	yes	missense	LRRC40	NM_017768.4	43	0,5,6493	TT,TC,CC		0.0582,0.0,0.0385	benign	366/603	70639162	5,12991	2203	4295	6498	70411750	SO:0001583	missense	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1097G>A	1.37:g.70639162C>T	ENSP00000359990:p.Arg366Gln		70411750	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	1	0.0013192612137203166	C	14.17	2.456399	0.43634	0.0	5.82E-4	ENSG00000066557	ENST00000370952	T	0.36699	1.24	5.64	3.8	0.43715	.	0.101283	0.64402	N	0.000003	T	0.14700	0.0355	M	0.76433	2.335	0.40923	D	0.984325	P	0.34662	0.462	B	0.24269	0.052	T	0.06899	-1.0801	10	0.11794	T	0.64	.	9.5161	0.39106	0.0:0.7819:0.0:0.2181	.	366	Q9H9A6	LRC40_HUMAN	Q	366	ENSP00000359990:R366Q	ENSP00000359990:R366Q	R	-	2	0	LRRC40	70411750	0.999000	0.42202	0.955000	0.39395	0.985000	0.73830	1.760000	0.38430	0.758000	0.33059	-0.254000	0.11334	CGA		0.318	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		T	70639162	C	T	70639162	3	4	61	1	0	0	0	0	1	0	0	0	9027	884	31	1	739	1	LRRC40	1	70639162	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20970	70639162	178611459	345	8330										
LRRC40	55631	broad.mit.edu	37	chr1	70641656	70641656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaatctggttttcacctaCgtgcaattcctacaaaatca	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70641656C>T	ENST00000370952.3	-	7	893	c.814G>A	c.(814-816)Gta>Ata	p.V272I		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	272						membrane (GO:0016020)		p.V272I(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TTTTCACCTACGTGCAATTCC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	92	93					1																	70641656		2203	4299	6502	70414244	SO:0001583	missense	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.814G>A	1.37:g.70641656C>T	ENSP00000359990:p.Val272Ile		70414244	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	C	3.663	-0.069023	0.07228	.	.	ENSG00000066557	ENST00000370952	T	0.53857	0.6	5.53	-2.58	0.06228	.	0.674999	0.14834	N	0.295670	T	0.06325	0.0163	N	0.02334	-0.595	0.22737	N	0.998799	B	0.13594	0.008	B	0.12156	0.007	T	0.31166	-0.9953	10	0.32370	T	0.25	.	1.611	0.02693	0.2138:0.3932:0.2079:0.1851	.	272	Q9H9A6	LRC40_HUMAN	I	272	ENSP00000359990:V272I	ENSP00000359990:V272I	V	-	1	0	LRRC40	70414244	0.704000	0.27836	0.415000	0.26534	0.523000	0.34469	0.546000	0.23284	-0.493000	0.06678	-1.051000	0.02340	GTA		0.313	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		T	70641656	C	T	70641656	3	4	61	1	0	0	0	0	1	0	0	0	9027	536	19	1	1030	1	LRRC40	1	70641656	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2494	70641656	178608965	346	8331										
HHLA3	11147	broad.mit.edu	37	chr1	70820780	70820780	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaacatttactgagcatcTacttcgtgccgtatgtacga	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70820780T>G	ENST00000359875.5	+	1	286	c.146T>G	c.(145-147)cTa>cGa	p.L49R	ANKRD13C_ENST00000370944.4_5'Flank|HHLA3_ENST00000370940.5_Missense_Mutation_p.L49R|HHLA3_ENST00000486110.1_3'UTR|ANKRD13C_ENST00000262346.6_5'Flank|HHLA3_ENST00000432224.1_Missense_Mutation_p.L49R|HHLA3_ENST00000531950.1_Missense_Mutation_p.L49R|HHLA3_ENST00000361764.4_Missense_Mutation_p.L49R	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	49								p.L49R(1)		large_intestine(3)|lung(1)	4						actgagcatctacttcgtgcc	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											107	81	90					1																	70820780		2203	4300	6503	70593368	SO:0001583	missense	11147			AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.146T>G	1.37:g.70820780T>G	ENSP00000352938:p.Leu49Arg		70593368	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Missense_Mutation	SNP	ENST00000359875.5	37	CCDS30753.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.322975	0.41096	.	.	ENSG00000197568	ENST00000361764;ENST00000359875;ENST00000370940;ENST00000531950;ENST00000432224	.	.	.	4.05	2.89	0.33648	.	.	.	.	.	T	0.14960	0.0361	N	0.08118	0	0.09310	N	1	P;P;P	0.50943	0.582;0.94;0.94	B;P;P	0.54100	0.422;0.534;0.742	T	0.05146	-1.0903	8	0.87932	D	0	.	7.7885	0.29106	0.0:0.0:0.2113:0.7887	.	49;49;49	Q9XRX5-2;Q9XRX5-3;Q9XRX5	.;.;HHLA3_HUMAN	R	49	.	ENSP00000352938:L49R	L	+	2	0	HHLA3	70593368	0.001000	0.12720	0.025000	0.17156	0.300000	0.27592	0.151000	0.16283	0.859000	0.35456	0.397000	0.26171	CTA		0.493	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071		G	70820780	T	G	70820780	3	3	61	1	0	0	0	0	1	0	0	0	7117	1522	53	4	148	4	HHLA3	1	70820780	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	179124	70820780	178429841	347	8332										
CTH	1491	broad.mit.edu	37	chr1	70900841	70900841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagagcttgggaggattcGaaagccttgctgagcttccg	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:70900841G>A	ENST00000370938.3	+	10	1177	c.1033G>A	c.(1033-1035)Gaa>Aaa	p.E345K	CTH_ENST00000411986.2_Missense_Mutation_p.E313K|CTH_ENST00000346806.2_Missense_Mutation_p.E301K	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.E345K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GGGAGGATTCGAAAGCCTTGC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	81	82					1																	70900841		2203	4300	6503	70673429	SO:0001583	missense	1491			BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.1033G>A	1.37:g.70900841G>A	ENSP00000359976:p.Glu345Lys		70673429	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	37	CCDS650.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829668	0.91036	.	.	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	D;D;D	0.83419	-1.72;-1.72;-1.72	5.24	5.24	0.73138	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.099858	0.64402	D	0.000002	D	0.88998	0.6590	M	0.64404	1.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.954;0.923;0.996	D	0.89587	0.3825	10	0.87932	D	0	-26.6945	18.8687	0.92303	0.0:0.0:1.0:0.0	.	313;301;345	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	K	313;345;301	ENSP00000413407:E313K;ENSP00000359976:E345K;ENSP00000311554:E301K	ENSP00000311554:E301K	E	+	1	0	CTH	70673429	1.000000	0.71417	0.950000	0.38849	0.758000	0.43043	8.820000	0.92003	2.651000	0.90000	0.650000	0.86243	GAA		0.313	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		A	70900841	G	A	70900841	3	1	61	1	0	0	0	0	1	0	0	0	4015	1059	37	1	1071	1	CTH	1	70900841	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80061	70900841	178349780	348	8333										
PTGER3	5733	broad.mit.edu	37	chr1	71478068	71478068	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggttcagtgaagccaggcGaacagctattaagaagaagt	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:71478068G>T	ENST00000306666.5	-	2	1207	c.997C>A	c.(997-999)Cgc>Agc	p.R333S	PTGER3_ENST00000370932.2_Missense_Mutation_p.R333S|PTGER3_ENST00000351052.5_Missense_Mutation_p.R333S|PTGER3_ENST00000370931.3_Missense_Mutation_p.R333S|PTGER3_ENST00000414819.1_Missense_Mutation_p.R333S|PTGER3_ENST00000354608.5_Missense_Mutation_p.R333S|PTGER3_ENST00000370924.4_Missense_Mutation_p.R333S|PTGER3_ENST00000460330.1_Missense_Mutation_p.R333S|PTGER3_ENST00000356595.4_Missense_Mutation_p.R333S	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	333					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)	p.R333S(1)		endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GAAGCCAGGCGAACAGCTATT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	108	110					1																	71478068		2203	4300	6503	71250656	SO:0001583	missense	5733			X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.997C>A	1.37:g.71478068G>T	ENSP00000302313:p.Arg333Ser		71250656	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	37	CCDS657.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852394	0.91355	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.103731	0.64402	N	0.000002	D	0.85062	0.5611	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.987;0.997;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D;D	0.97110	1.0;1.0;0.878;0.925;1.0;0.999;0.999;1.0	D	0.84641	0.0695	10	0.41790	T	0.15	-25.8093	19.3057	0.94161	0.0:0.0:1.0:0.0	.	333;333;333;333;333;333;333;333	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	S	333	ENSP00000359969:R333S;ENSP00000359970:R333S;ENSP00000280208:R333S;ENSP00000418073:R333S;ENSP00000346624:R333S;ENSP00000349003:R333S;ENSP00000401423:R333S;ENSP00000302313:R333S;ENSP00000359962:R333S	ENSP00000302313:R333S	R	-	1	0	PTGER3	71250656	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.101000	0.94219	2.669000	0.90835	0.491000	0.48974	CGC		0.428	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		T	71478068	G	T	71478068	3	4	61	1	0	0	0	0	1	0	0	0	12779	1058	37	2	490	2	PTGER3	1	71478068	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	577227	71478068	177772553	349	8334										
LRRIQ3	127255	broad.mit.edu	37	chr1	74506922	74506922	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttcatttctttaagtaAattctttctatatttttctg	2	5	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74506922A>C	ENST00000395089.1	-	6	1692	c.1693T>G	c.(1693-1695)Tta>Gta	p.L565V	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.L565V			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	565								p.L565V(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						TCTTTAAGTAAATTCTTTCTA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	39	40					1																	74506922		1791	4052	5843	74279510	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1693T>G	1.37:g.74506922A>C	ENSP00000378524:p.Leu565Val		74279510	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.890893	0.33348	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.18016	2.24;2.24	5.86	3.41	0.39046	.	.	.	.	.	T	0.04318	0.0119	L	0.29908	0.895	0.09310	N	1	P	0.36392	0.551	B	0.33960	0.173	T	0.30563	-0.9974	9	0.72032	D	0.01	.	5.6879	0.17813	0.743:0.1708:0.0862:0.0	.	565	A6PVS8	LRIQ3_HUMAN	V	565	ENSP00000378524:L565V;ENSP00000346414:L565V	ENSP00000346414:L565V	L	-	1	2	LRRIQ3	74279510	0.024000	0.19004	0.072000	0.20136	0.061000	0.15899	0.500000	0.22562	1.148000	0.42385	0.528000	0.53228	TTA		0.294	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		C	74506922	A	C	74506922	3	2	61	1	0	0	0	0	1	0	0	0	9059	11	1	4	189	4	LRRIQ3	1	74506922	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3028854	74506922	174743699	350	8335										
LRRIQ3	127255	broad.mit.edu	37	chr1	74648365	74648365	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccatatactgttaacaaGaacatgtctatatccttttt	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74648365G>T	ENST00000395089.1	-	2	429	c.430C>A	c.(430-432)Ctt>Att	p.L144I	LRRIQ3_ENST00000370909.2_Intron|LRRIQ3_ENST00000370911.3_Missense_Mutation_p.L144I|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.L144I			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	144	LRRCT.							p.L144I(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CTGTTAACAAGAACATGTCTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	116	118					1																	74648365		2203	4298	6501	74420953	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.430C>A	1.37:g.74648365G>T	ENSP00000378524:p.Leu144Ile		74420953	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978909	0.34942	.	.	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000388972;ENST00000370911	T;T;T	0.23348	1.91;1.91;1.91	5.65	1.32	0.21799	.	0.449046	0.20625	N	0.088697	T	0.05318	0.0141	N	0.22421	0.69	0.26022	N	0.98186	P	0.35328	0.495	B	0.31547	0.132	T	0.27706	-1.0066	10	0.38643	T	0.18	.	8.4179	0.32683	0.0:0.4449:0.2883:0.2667	.	144	A6PVS8	LRIQ3_HUMAN	I	144	ENSP00000378524:L144I;ENSP00000346414:L144I;ENSP00000359948:L144I	ENSP00000346414:L144I	L	-	1	0	LRRIQ3	74420953	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.037000	0.30241	0.694000	0.31654	0.650000	0.86243	CTT		0.368	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		T	74648365	G	T	74648365	3	4	61	1	0	0	0	0	1	0	0	0	9059	942	33	2	1468	2	LRRIQ3	1	74648365	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141443	74648365	174602256	351	8336										
FPGT	8790	broad.mit.edu	37	chr1	74671445	74671445	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaatgcttatctacaaaGatgtagaagatatgataact	7	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74671445G>T	ENST00000609362.1	+	4	1751	c.1714G>T	c.(1714-1716)Gat>Tat	p.D572Y	FPGT_ENST00000370894.5_3'UTR|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.D585Y|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000534056.1_Missense_Mutation_p.D318Y|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	572					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.D572Y(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TATCTACAAAGATGTAGAAGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	51	52					1																	74671445		2203	4300	6503	74444033	SO:0001583	missense	8790			AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1714G>T	1.37:g.74671445G>T	ENSP00000476680:p.Asp572Tyr		74444033	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	CCDS663.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.705923	0.30232	.	.	ENSG00000254685	ENST00000370898;ENST00000534056	T;T	0.59906	0.98;0.23	4.83	4.83	0.62350	.	.	.	.	.	T	0.38480	0.1042	L	0.41824	1.3	0.80722	D	1	P;B;B	0.42409	0.779;0.149;0.399	B;B;B	0.36719	0.197;0.061;0.231	T	0.51060	-0.8753	9	0.66056	D	0.02	.	17.9148	0.88945	0.0:0.0:1.0:0.0	.	318;197;572	E9PNQ2;B4E2Y7;O14772	.;.;FPGT_HUMAN	Y	572;318	ENSP00000359935:D572Y;ENSP00000432819:D318Y	ENSP00000359935:D572Y	D	+	1	0	TNNI3K	74444033	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	5.731000	0.68554	2.219000	0.72066	0.563000	0.77884	GAT		0.308	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	74671445	G	T	74671445	3	4	61	1	0	0	0	0	1	0	0	0	6056	942	33	2	1728	2	FPGT	1	74671445	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23080	74671445	174579176	352	8337										
TNNI3K	100526835	broad.mit.edu	37	chr1	74797179	74797179	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctaatgtcaatattcaaGatgcagtttttttcactcca	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74797179G>T	ENST00000370899.3	+	8	830	c.793G>T	c.(793-795)Gat>Tat	p.D265Y	TNNI3K_ENST00000370891.2_Missense_Mutation_p.D265Y|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.D265Y|TNNI3K_ENST00000326637.3_Missense_Mutation_p.D164Y|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.D278Y	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.D164Y(1)									CAATATTCAAGATGCAGTTTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	108	116					1																	74797179		2203	4300	6503	74569767	SO:0001583	missense	51086					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.793G>T	1.37:g.74797179G>T	ENSP00000359936:p.Asp265Tyr		74569767		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.980229	0.74474	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.45	5.45	0.79879	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.50429	0.1615	M	0.90814	3.15	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	T	0.57757	-0.7756	10	0.62326	D	0.03	.	19.0662	0.93113	0.0:0.0:1.0:0.0	.	164;265;265;265	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	Y	265;265;265;265;164	ENSP00000359936:D265Y;ENSP00000359932:D265Y;ENSP00000450895:D265Y;ENSP00000359928:D265Y;ENSP00000322251:D164Y	ENSP00000322251:D164Y	D	+	1	0	RP11-653A5.2;AC093158.1	74569767	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	6.959000	0.76031	2.836000	0.97738	0.655000	0.94253	GAT		0.388	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74797179	G	T	74797179	3	4	61	1	0	0	0	0	1	0	0	0	16368	942	33	2	867	2	TNNI3K	1	74797179	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125734	74797179	174453442	353	8338										
TNNI3K	100526835	broad.mit.edu	37	chr1	74808571	74808571	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcccactccatttctgttCtcgatttggacaccatgata	6	12	2	1	rs201060802		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74808571C>A	ENST00000370899.3	+	10	1068	c.1031C>A	c.(1030-1032)tCt>tAt	p.S344Y	TNNI3K_ENST00000370891.2_Missense_Mutation_p.S344Y|RP11-439H8.4_ENST00000415549.2_RNA|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.S344Y|TNNI3K_ENST00000326637.3_Missense_Mutation_p.S243Y|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.S357Y	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.S243Y(1)									CATTTCTGTTCTCGATTTGGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											192	178	182					1																	74808571		2203	4300	6503	74581159	SO:0001583	missense	51086					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1031C>A	1.37:g.74808571C>A	ENSP00000359936:p.Ser344Tyr		74581159		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	C	17.27	3.345854	0.61073	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.65732	-0.17;-0.17;-0.07;-0.07;-0.17	5.02	4.1	0.47936	Ankyrin repeat-containing domain (4);	0.239804	0.43747	D	0.000522	T	0.69278	0.3093	M	0.89287	3.02	0.37121	D	0.900809	P;P;P;P	0.49783	0.928;0.904;0.904;0.904	P;P;P;P	0.51135	0.544;0.66;0.461;0.461	T	0.79127	-0.1931	10	0.87932	D	0	.	15.4782	0.75501	0.0:0.7393:0.2606:0.0	.	243;344;344;344	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	Y	344;344;344;344;243	ENSP00000359936:S344Y;ENSP00000359932:S344Y;ENSP00000450895:S344Y;ENSP00000359928:S344Y;ENSP00000322251:S243Y	ENSP00000322251:S243Y	S	+	2	0	RP11-653A5.2;AC093158.1	74581159	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	4.339000	0.59322	1.353000	0.45828	-0.172000	0.13284	TCT		0.368	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			A	74808571	C	A	74808571	3	1	61	1	0	0	0	0	1	0	0	0	16368	913	32	2	1113	2	TNNI3K	1	74808571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11392	74808571	174442050	354	8339										
TNNI3K	100526835	broad.mit.edu	37	chr1	74833629	74833629	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccatcacccttggggaaGattaaaagcatgacaaaagg	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74833629G>T	ENST00000370899.3	+	15	1642	c.1605G>T	c.(1603-1605)aaG>aaT	p.K535N	TNNI3K_ENST00000370891.2_Missense_Mutation_p.K535N|RP11-439H8.4_ENST00000415549.2_RNA|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.K535N|TNNI3K_ENST00000326637.3_Missense_Mutation_p.K434N|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.K548N	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.K434N(1)									CCTTGGGGAAGATTAAAAGCA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	69	68					1																	74833629		2203	4298	6501	74606217	SO:0001583	missense	51086					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1605G>T	1.37:g.74833629G>T	ENSP00000359936:p.Lys535Asn		74606217		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	G	18.84	3.709940	0.68730	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000534632;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.75260	-0.92;-0.65;-0.91;-0.91;-0.9	5.9	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	N	0.24115	0.695	0.48236	D	0.999618	P;D;D;D	0.61697	0.956;0.988;0.988;0.99	P;P;P;P	0.58721	0.63;0.844;0.844;0.844	T	0.61402	-0.7070	10	0.23891	T	0.37	.	9.2416	0.37500	0.2142:0.0:0.7858:0.0	.	434;535;535;535	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	N	535;535;156;535;535;434	ENSP00000359936:K535N;ENSP00000359932:K535N;ENSP00000450895:K535N;ENSP00000359928:K535N;ENSP00000322251:K434N	ENSP00000322251:K434N	K	+	3	2	RP11-653A5.2;AC093158.1	74606217	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.228000	0.42981	1.513000	0.48852	0.650000	0.86243	AAG		0.289	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74833629	G	T	74833629	3	4	61	1	0	0	0	0	1	0	0	0	16368	933	33	2	1707	2	TNNI3K	1	74833629	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25058	74833629	174416992	355	8340										
TNNI3K	100526835	broad.mit.edu	37	chr1	74836063	74836063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacacagccaattatacatCgtgacttgaacaggtatttt	7	8	0	3	rs200254775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:74836063C>T	ENST00000370899.3	+	19	2099	c.2062C>T	c.(2062-2064)Cgt>Tgt	p.R688C	TNNI3K_ENST00000370891.2_Missense_Mutation_p.R688C|RP11-439H8.4_ENST00000415549.2_RNA|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.R688C|TNNI3K_ENST00000326637.3_Missense_Mutation_p.R587C|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.R701C	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.R587C(1)									AATTATACATCGTGACTTGAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	90	91					1																	74836063		2203	4299	6502	74608651	SO:0001583	missense	51086					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2062C>T	1.37:g.74836063C>T	ENSP00000359936:p.Arg688Cys		74608651		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	C	21.3	4.131022	0.77549	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637;ENST00000534020	D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.76	4.82	0.62117	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93828	0.8026	M	0.81682	2.555	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.996	D	0.94172	0.7424	10	0.87932	D	0	.	16.2429	0.82424	0.1332:0.8668:0.0:0.0	.	587;688;688;688	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	C	688;688;688;688;587;111	ENSP00000359936:R688C;ENSP00000359932:R688C;ENSP00000450895:R688C;ENSP00000359928:R688C;ENSP00000322251:R587C;ENSP00000434975:R111C	ENSP00000322251:R587C	R	+	1	0	RP11-653A5.2;AC093158.1	74608651	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.584000	0.36589	2.724000	0.93272	0.650000	0.86243	CGT		0.348	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74836063	C	T	74836063	3	4	61	1	0	0	0	0	1	0	0	0	16368	884	31	1	2180	1	TNNI3K	1	74836063	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2434	74836063	174414558	356	8341										
C1orf173	127254	broad.mit.edu	37	chr1	75036861	75036861	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctccttgcaccatatgCtgttgcttctctcgggtttc	7	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75036861C>T	ENST00000326665.5	-	14	4751	c.4533G>A	c.(4531-4533)caG>caA	p.Q1511Q	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1511								p.Q1511Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GCACCATATGCTGTTGCTTCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											191	186	187					1																	75036861		2203	4300	6503	74809449	SO:0001819	synonymous_variant	127254																														ENST00000326665.5:c.4533G>A	1.37:g.75036861C>T			74809449	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	37	CCDS30755.1																																																																																				0.507	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75036861	C	T	75036861	2	4	61	1	0	0	0	0	0	0	0	1	2020	796	28	3		3	C1orf173	1	75036861	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200798	75036861	174213760	357	8342										
C1orf173	127254	broad.mit.edu	37	chr1	75055381	75055381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtgctttcttcccaaaGcttactcttatccttttcct	4	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75055381G>A	ENST00000326665.5	-	12	2328	c.2110C>T	c.(2110-2112)Ctt>Ttt	p.L704F	C1orf173_ENST00000420661.2_Missense_Mutation_p.L507F|RP4-612J11.1_ENST00000416017.1_RNA	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		704	Glu-rich.							p.L704F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TCTTCCCAAAGCTTACTCTTA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											250	240	243					1																	75055381		2203	4300	6503	74827969	SO:0001583	missense	127254																														ENST00000326665.5:c.2110C>T	1.37:g.75055381G>A	ENSP00000322609:p.Leu704Phe		74827969	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	G	8.492	0.862264	0.17178	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.21932	2.49;1.98	5.44	3.53	0.40419	.	.	.	.	.	T	0.10981	0.0268	L	0.34521	1.04	0.21762	N	0.999557	P;P	0.50272	0.846;0.933	P;P	0.50352	0.563;0.638	T	0.08046	-1.0741	9	0.56958	D	0.05	-3.9226	8.9514	0.35792	0.0:0.1624:0.6688:0.1688	.	507;704	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	F	704;507	ENSP00000322609:L704F;ENSP00000398581:L507F	ENSP00000322609:L704F	L	-	1	0	C1orf173	74827969	0.215000	0.23574	0.664000	0.29753	0.024000	0.10985	0.463000	0.21972	0.629000	0.30376	-0.165000	0.13383	CTT		0.478	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75055381	G	A	75055381	3	1	61	1	0	0	0	0	1	0	0	0	2020	971	34	3	2494	3	C1orf173	1	75055381	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18520	75055381	174195240	358	8343										
C1orf173	127254	broad.mit.edu	37	chr1	75112440	75112440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatcatatttagtttatAttctttttcagaaagtattc	3	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75112440A>G	ENST00000326665.5	-	3	372	c.154T>C	c.(154-156)Tat>Cat	p.Y52H		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		52								p.Y52H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TTTAGTTTATATTCTTTTTCA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	1											28	26	26					1																	75112440		2108	4152	6260	74885028	SO:0001583	missense	127254																														ENST00000326665.5:c.154T>C	1.37:g.75112440A>G	ENSP00000322609:p.Tyr52His		74885028	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.985821	0.74589	.	.	ENSG00000178965	ENST00000326665	T	0.20332	2.08	5.71	5.71	0.89125	.	.	.	.	.	T	0.34337	0.0894	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13282	-1.0515	9	0.87932	D	0	-10.4151	14.9681	0.71210	1.0:0.0:0.0:0.0	.	52	Q5RHP9	CA173_HUMAN	H	52	ENSP00000322609:Y52H	ENSP00000322609:Y52H	Y	-	1	0	C1orf173	74885028	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.318000	0.72866	2.179000	0.69175	0.528000	0.53228	TAT		0.284	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			G	75112440	A	G	75112440	3	3	61	1	0	0	0	0	1	0	0	0	2020	449	16	4	4486	4	C1orf173	1	75112440	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	57059	75112440	174138181	359	8344										
CRYZ	1429	broad.mit.edu	37	chr1	75185051	75185051	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctagtgaaaactctgtcAcctttctaggggaagagata	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75185051A>C	ENST00000340866.5	-	4	357	c.270T>G	c.(268-270)ggT>ggG	p.G90G	CRYZ_ENST00000370871.3_Silent_p.G90G|CRYZ_ENST00000370872.3_Intron|CRYZ_ENST00000417775.1_Silent_p.G90G	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	90					protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)	p.G90G(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	AAACTCTGTCACCTTTCTAGG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											67	65	65					1																	75185051		2203	4300	6503	74957639	SO:0001819	synonymous_variant	1429				CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.270T>G	1.37:g.75185051A>C			74957639	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Silent	SNP	ENST00000340866.5	37	CCDS665.1																																																																																				0.373	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1			C	75185051	A	C	75185051	2	2	61	1	0	0	0	0	0	0	0	1	3928	146	6	4		4	CRYZ	1	75185051	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72611	75185051	174065570	360	8345										
SLC44A5	204962	broad.mit.edu	37	chr1	75683626	75683626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataattaaagatccaaatgCtagggatcctgtgtgatatc	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75683626C>A	ENST00000370855.5	-	18	1662	c.1549G>T	c.(1549-1551)Gca>Tca	p.A517S	SLC44A5_ENST00000370859.3_Missense_Mutation_p.A517S|SLC44A5_ENST00000535611.1_Missense_Mutation_p.A387S	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	517					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A517S(1)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GATCCAAATGCTAGGGATCCT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	53	52					1																	75683626		2203	4299	6502	75456214	SO:0001583	missense	204962			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1549G>T	1.37:g.75683626C>A	ENSP00000359892:p.Ala517Ser		75456214	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	37	CCDS667.1	.	.	.	.	.	.	.	.	.	.	C	32	5.110671	0.94292	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535611;ENST00000535790	T;T;T	0.29917	1.55;1.55;1.55	5.93	5.93	0.95920	.	0.105434	0.64402	D	0.000004	T	0.60301	0.2258	M	0.88704	2.975	0.80722	D	1	D;D;D;D;D	0.89917	0.988;0.999;0.998;1.0;0.999	D;D;D;D;D	0.85130	0.989;0.994;0.989;0.997;0.99	T	0.66252	-0.5970	10	0.87932	D	0	-18.1034	20.3261	0.98701	0.0:1.0:0.0:0.0	.	511;556;517;517;556	B7Z5Y4;B7Z470;Q8NCS7;Q8NCS7-2;F5GYS0	.;.;CTL5_HUMAN;.;.	S	517;556;517;387;510	ENSP00000359896:A517S;ENSP00000359892:A517S;ENSP00000443090:A387S	ENSP00000359892:A517S	A	-	1	0	SLC44A5	75456214	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.461000	0.80834	2.814000	0.96858	0.655000	0.94253	GCA		0.289	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		A	75683626	C	A	75683626	3	1	61	1	0	0	0	0	1	0	0	0	14676	797	28	2	749	2	SLC44A5	1	75683626	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	498575	75683626	173566995	361	8346										
SLC44A5	204962	broad.mit.edu	37	chr1	75685020	75685020	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatacaggtacccccgatgtCgccaagaaactgaataaact	7	11	0	2	rs531608712		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:75685020C>T	ENST00000370855.5	-	16	1301	c.1188G>A	c.(1186-1188)gcG>gcA	p.A396A	SLC44A5_ENST00000370859.3_Silent_p.A396A|SLC44A5_ENST00000535611.1_Silent_p.A266A	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	396					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A396A(1)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						CCCCCGATGTCGCCAAGAAAC	0.393													C|||	1	0.000199681	0	0	5008	,	,		17200	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	1											89	83	85					1																	75685020		2203	4300	6503	75457608	SO:0001819	synonymous_variant	204962			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1188G>A	1.37:g.75685020C>T			75457608	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																				0.393	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		T	75685020	C	T	75685020	2	4	61	1	0	0	0	0	0	0	0	1	14676	871	31	1		1	SLC44A5	1	75685020	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1394	75685020	173565601	362	8347										
ACADM	34	broad.mit.edu	37	chr1	76198600	76198600	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaacacacacattccagaGaactgtggtaagctttcttt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:76198600G>T	ENST00000370841.4	+	4	716	c.279G>T	c.(277-279)gaG>gaT	p.E93D	ACADM_ENST00000370834.5_Missense_Mutation_p.E93D|ACADM_ENST00000541113.1_Missense_Mutation_p.E57D|ACADM_ENST00000420607.2_Missense_Mutation_p.E97D|ACADM_ENST00000543667.1_5'UTR	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	93					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)	p.E93D(1)		breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	ACATTCCAGAGAACTGTGGTA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	67	65					1																	76198600		2201	4297	6498	75971188	SO:0001583	missense	34			M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.279G>T	1.37:g.76198600G>T	ENSP00000359878:p.Glu93Asp		75971188	Q5T4U4|Q9NYF1	Missense_Mutation	SNP	ENST00000370841.4	37	CCDS668.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.013721	0.35511	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000420607	D;D;D;D	0.99825	-6.97;-6.97;-6.97;-6.97	5.28	1.14	0.20703	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.102529	0.64402	D	0.000004	D	0.99563	0.9843	M	0.90198	3.095	0.80722	D	1	B;B;P;B;B;B	0.50528	0.064;0.016;0.936;0.268;0.046;0.057	B;B;P;B;B;B	0.53185	0.09;0.083;0.72;0.371;0.099;0.159	D	0.99912	1.1205	10	0.72032	D	0.01	.	7.6362	0.28267	0.5866:0.0:0.4134:0.0	.	57;7;93;93;97;93	B7Z9I1;B4DVE0;E9PJM9;Q5T4U5;P11310-2;P11310	.;.;.;.;.;ACADM_HUMAN	D	93;93;57;97	ENSP00000359878:E93D;ENSP00000359871:E93D;ENSP00000442324:E57D;ENSP00000409612:E97D	ENSP00000359871:E93D	E	+	3	2	ACADM	75971188	1.000000	0.71417	0.970000	0.41538	0.304000	0.27724	1.436000	0.34980	0.181000	0.19994	0.591000	0.81541	GAG		0.323	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			T	76198600	G	T	76198600	3	4	61	1	0	0	0	0	1	0	0	0	113	933	33	2	305	2	ACADM	1	76198600	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	513580	76198600	173052021	363	8348										
ACADM	34	broad.mit.edu	37	chr1	76226906	76226906	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaggttgattctggtcgtCgaaatacctattatgcttct	11	7	2	1	rs148207467		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:76226906C>T	ENST00000370841.4	+	11	1482	c.1045C>T	c.(1045-1047)Cga>Tga	p.R349*	ACADM_ENST00000370834.5_Nonsense_Mutation_p.R382*|ACADM_ENST00000541113.1_Nonsense_Mutation_p.R313*|ACADM_ENST00000481374.1_3'UTR|ACADM_ENST00000420607.2_Nonsense_Mutation_p.R353*|ACADM_ENST00000543667.1_Nonsense_Mutation_p.R160*	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	349					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)	p.R349*(1)		breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	TTCTGGTCGTCGAAATACCTA	0.413													C|||	1	0.000199681	8e-04	0	5008	,	,		16160	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	1	GRCh37	CM940004	ACADM	M	rs148207467	C	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	141	137	138		1045,1057	4.4	1	1	dbSNP_134	138	0,8600		0,0,4300	no	stop-gained,stop-gained	ACADM	NM_000016.4,NM_001127328.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	349/422,353/426	76226906	1,13005	2203	4300	6503	75999494	SO:0001587	stop_gained	34			M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.1045C>T	1.37:g.76226906C>T	ENSP00000359878:p.Arg349*		75999494	Q5T4U4|Q9NYF1	Nonsense_Mutation	SNP	ENST00000370841.4	37	CCDS668.1	.	.	.	.	.	.	.	.	.	.	C	39	7.316268	0.98207	2.27E-4	0.0	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000543667;ENST00000420607	.	.	.	5.3	4.36	0.52297	.	0.052292	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	11.7756	0.51983	0.43:0.57:0.0:0.0	.	.	.	.	X	349;382;313;160;353	.	ENSP00000359871:R382X	R	+	1	2	ACADM	75999494	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	2.507000	0.45442	1.318000	0.45170	0.655000	0.94253	CGA		0.413	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			T	76226906	C	T	76226906	4	4	61	1	0	0	0	0	0	1	0	0	113	876	31	1	1099	1	ACADM	1	76226906	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28306	76226906	173023715	364	8349										
RABGGTB	5876	broad.mit.edu	37	chr1	76257887	76257887	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctattgttgcacaggatttCtggcaattacaagtcagttg	9	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:76257887C>A	ENST00000319942.3	+	7	672	c.601C>A	c.(601-603)Ctg>Atg	p.L201M	RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000535300.1_Missense_Mutation_p.L27M|SNORD45B_ENST00000364617.1_RNA	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	201					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)	p.L201M(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						CACAGGATTTCTGGCAATTAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	63	64					1																	76257887		2203	4300	6503	76030475	SO:0001583	missense	5876			U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.601C>A	1.37:g.76257887C>A	ENSP00000317473:p.Leu201Met		76030475	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772146	0.69992	.	.	ENSG00000137955	ENST00000535300;ENST00000319942;ENST00000370824	T;T	0.69685	-0.42;-0.42	5.58	4.67	0.58626	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.000000	0.85682	D	0.000000	T	0.80149	0.4570	M	0.91090	3.175	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.83275	0.99;0.996	D	0.84080	0.0384	10	0.66056	D	0.02	-23.3431	10.6412	0.45594	0.0:0.8536:0.0:0.1464	.	201;201	Q59GT6;P53611	.;PGTB2_HUMAN	M	27;201;201	ENSP00000440452:L27M;ENSP00000317473:L201M	ENSP00000317473:L201M	L	+	1	2	RABGGTB	76030475	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.697000	0.37784	1.360000	0.45960	0.561000	0.74099	CTG		0.353	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		A	76257887	C	A	76257887	3	1	61	1	0	0	0	0	1	0	0	0	13005	912	32	2	627	2	RABGGTB	1	76257887	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30981	76257887	172992734	365	8350										
ST6GALNAC3	256435	broad.mit.edu	37	chr1	76877856	76877856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggccgcatgaccatgattcGagttgtgtcccataccagcg	11	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:76877856G>A	ENST00000328299.3	+	3	525	c.377G>A	c.(376-378)cGa>cAa	p.R126Q	ST6GALNAC3_ENST00000464140.1_3'UTR	NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	126					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)	p.R126Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						ACCATGATTCGAGTTGTGTCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	124	126					1																	76877856		2203	4300	6503	76650444	SO:0001583	missense	256435				CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"Sialyltransferases"	19343	protein-coding gene	gene with protein product	"ST6GALNAC III"	610133	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.377G>A	1.37:g.76877856G>A	ENSP00000329214:p.Arg126Gln		76650444	Q6PCE0|Q6UX29|Q8N259	Missense_Mutation	SNP	ENST00000328299.3	37	CCDS672.1	.	.	.	.	.	.	.	.	.	.	G	35	5.565048	0.96527	.	.	ENSG00000184005	ENST00000394994;ENST00000328299;ENST00000394993;ENST00000415813	T	0.35048	1.33	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	M	0.86573	2.825	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.992	T	0.67114	-0.5752	10	0.87932	D	0	-14.4154	19.8676	0.96824	0.0:0.0:1.0:0.0	.	61;126;126	B4DM98;Q8NDV1;Q8NDV1-2	.;SIA7C_HUMAN;.	Q	126;126;125;60	ENSP00000329214:R126Q	ENSP00000329214:R126Q	R	+	2	0	ST6GALNAC3	76650444	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.441000	0.97557	2.941000	0.99782	0.655000	0.94253	CGA		0.433	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996		A	76877856	G	A	76877856	3	1	61	1	0	0	0	0	1	0	0	0	15264	1058	37	1	387	1	ST6GALNAC3	1	76877856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	619969	76877856	172372765	366	8351										
ST6GALNAC5	81849	broad.mit.edu	37	chr1	77528888	77528888	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagaataaacctgtgttCtaaggaatgagcatgccaga	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:77528888C>A	ENST00000477717.1	+	5	1243	c.1008C>A	c.(1006-1008)ttC>ttA	p.F336L		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	336					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)	p.F336L(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						AACCTGTGTTCTAAGGAATGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	73	74					1																	77528888		2203	4300	6503	77301476	SO:0001583	missense	81849				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.1008C>A	1.37:g.77528888C>A	ENSP00000417583:p.Phe336Leu		77301476	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	37	CCDS673.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457778	0.63401	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.31510	1.49	5.93	5.0	0.66597	.	0.237399	0.43579	D	0.000544	T	0.10508	0.0257	L	0.36672	1.1	0.47094	D	0.999313	B	0.09022	0.002	B	0.08055	0.003	T	0.08371	-1.0725	10	0.10377	T	0.69	-44.3963	14.275	0.66175	0.0:0.926:0.0:0.074	.	336	Q9BVH7	SIA7E_HUMAN	L	336;246	ENSP00000417583:F336L	ENSP00000406658:F246L	F	+	3	2	ST6GALNAC5	77301476	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	1.224000	0.32539	1.448000	0.47680	0.655000	0.94253	TTC		0.433	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77528888	C	A	77528888	3	1	61	1	0	0	0	0	1	0	0	0	15266	912	32	2	1026	2	ST6GALNAC5	1	77528888	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	651032	77528888	171721733	367	8352										
PIGK	10026	broad.mit.edu	37	chr1	77627340	77627340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgttaggagaataaaatCgttcatacatggatgctcct	8	6	1	1	rs140360373		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:77627340C>T	ENST00000370812.3	-	7	664	c.641G>A	c.(640-642)cGa>cAa	p.R214Q	PIGK_ENST00000478391.1_5'UTR|PIGK_ENST00000445065.1_Missense_Mutation_p.R120Q|PIGK_ENST00000359130.1_Missense_Mutation_p.R214Q|PIGK_ENST00000370813.5_Missense_Mutation_p.R138Q	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	214					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)	p.R214Q(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						AGAATAAAATCGTTCATACAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	109	101	104		641	4.6	1	1	dbSNP_134	104	0,8600		0,0,4300	no	missense	PIGK	NM_005482.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	214/396	77627340	1,13005	2203	4300	6503	77399928	SO:0001583	missense	10026			AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"Phosphatidylinositol glycan anchor biosynthesis"	8965	protein-coding gene	gene with protein product	"GPI transamidase subunit"	605087	"phosphatidylinositol glycan, class K"			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.641G>A	1.37:g.77627340C>T	ENSP00000359848:p.Arg214Gln		77399928	B2R7K3|B4E2M3|O14822|Q5TG77	Missense_Mutation	SNP	ENST00000370812.3	37	CCDS674.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.103317	0.56183	2.27E-4	0.0	ENSG00000142892	ENST00000370812;ENST00000445065;ENST00000370813;ENST00000359130	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.63	4.63	0.57726	.	0.062525	0.64402	D	0.000006	T	0.19967	0.0480	L	0.49350	1.555	0.53688	D	0.999976	B;B;B;B	0.24368	0.094;0.094;0.102;0.063	B;B;B;B	0.21708	0.036;0.036;0.026;0.015	T	0.03493	-1.1031	10	0.17369	T	0.5	-21.0062	11.5412	0.50667	0.0:0.9184:0.0:0.0816	.	138;120;214;214	B4E2M3;B1AK81;A6NEM5;Q92643	.;.;.;GPI8_HUMAN	Q	214;120;138;214	ENSP00000359848:R214Q;ENSP00000388854:R120Q;ENSP00000359849:R138Q;ENSP00000352041:R214Q	ENSP00000352041:R214Q	R	-	2	0	PIGK	77399928	1.000000	0.71417	0.993000	0.49108	0.952000	0.60782	5.580000	0.67464	2.560000	0.86352	0.650000	0.86243	CGA		0.373	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482		T	77627340	C	T	77627340	3	4	61	1	0	0	0	0	1	0	0	0	11921	884	31	1	566	1	PIGK	1	77627340	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98452	77627340	171623281	368	8353										
AK5	26289	broad.mit.edu	37	chr1	77759507	77759507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaactcaaactttccatatCggcggtatgaccggctccct	7	13	1	1	rs371926363		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:77759507C>T	ENST00000354567.2	+	3	540	c.277C>T	c.(277-279)Cgg>Tgg	p.R93W	AK5_ENST00000344720.5_Missense_Mutation_p.R67W|AK5_ENST00000317704.4_Intron	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	93					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)	p.R93W(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						CTTTCCATATCGGCGGTATGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	62	66	64		199,277	5.3	1	1		64	0,8600		0,0,4300	no	missense,missense	AK5	NM_012093.3,NM_174858.2	101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	67/537,93/563	77759507	1,13005	2203	4300	6503	77532095	SO:0001583	missense	26289			AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"Adenylate kinases"	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.277C>T	1.37:g.77759507C>T	ENSP00000346577:p.Arg93Trp		77532095	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Missense_Mutation	SNP	ENST00000354567.2	37	CCDS675.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493657	0.84962	2.27E-4	0.0	ENSG00000154027	ENST00000354567;ENST00000344720;ENST00000478407	T;T;D	0.84873	-0.87;-0.88;-1.91	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.87549	0.6205	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88956	0.3390	10	0.87932	D	0	-0.1	19.2875	0.94084	0.0:1.0:0.0:0.0	.	93	Q9Y6K8	KAD5_HUMAN	W	93;67;67	ENSP00000346577:R93W;ENSP00000341430:R67W;ENSP00000434409:R67W	ENSP00000341430:R67W	R	+	1	2	AK5	77532095	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.799000	0.69101	2.645000	0.89757	0.561000	0.74099	CGG		0.393	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858		T	77759507	C	T	77759507	3	4	61	1	0	0	0	0	1	0	0	0	443	875	31	1	287	1	AK5	1	77759507	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132167	77759507	171491114	369	8354										
ZZZ3	26009	broad.mit.edu	37	chr1	78097917	78097917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggttctcagagtataacGatgttcttgaggttctgata	11	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78097917G>A	ENST00000370801.3	-	5	1598	c.1123C>T	c.(1123-1125)Cgt>Tgt	p.R375C	ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	375					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R375C(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						AGAGTATAACGATGTTCTTGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											132	124	127					1																	78097917		2203	4300	6503	77870505	SO:0001583	missense	26009			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"Zinc fingers, ZZ-type"	24523	protein-coding gene	gene with protein product	"ATAC component 1 homolog (Drosophila)"					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.1123C>T	1.37:g.78097917G>A	ENSP00000359837:p.Arg375Cys		77870505	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	37	CCDS677.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769794	0.49680	.	.	ENSG00000036549	ENST00000370801	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.999	T	0.68961	-0.5271	8	.	.	.	.	12.6925	0.56982	0.0:0.0:0.7268:0.2732	.	375;375;375	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	C	375	.	.	R	-	1	0	ZZZ3	77870505	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	3.491000	0.53252	2.714000	0.92807	0.650000	0.86243	CGT		0.453	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		A	78097917	G	A	78097917	3	1	61	1	0	0	0	0	1	0	0	0	18295	1058	37	1	1632	1	ZZZ3	1	78097917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	338410	78097917	171152704	370	8355										
USP33	23032	broad.mit.edu	37	chr1	78181514	78181514	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaattcataccagagaTtatttagattgtttcggcag	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78181514T>G	ENST00000370793.1	-	19	2397	c.2051A>C	c.(2050-2052)aAt>aCt	p.N684T	USP33_ENST00000370792.3_Missense_Mutation_p.N676T|USP33_ENST00000357428.1_Missense_Mutation_p.N684T|USP33_ENST00000370794.3_Missense_Mutation_p.N653T	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	684	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.N684T(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						ATACCAGAGATTATTTAGATT	0.338																																					Melanoma(152;72 1870 11110 26780 42647)											1	Substitution - Missense(1)	large_intestine(1)	1											86	84	85					1																	78181514		2203	4300	6503	77954102	SO:0001583	missense	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.2051A>C	1.37:g.78181514T>G	ENSP00000359829:p.Asn684Thr		77954102	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.01|17.01	3.278398|3.278398	0.59758|0.59758	.|.	.|.	ENSG00000077254|ENSG00000077254	ENST00000481579|ENST00000370794;ENST00000370793;ENST00000357428;ENST00000370792	.|T;T;T;T	.|0.33216	.|4.02;1.42;1.42;4.02	4.46|4.46	4.46|4.46	0.54185|0.54185	.|Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.|0.207023	.|0.48767	.|D	.|0.000164	T|T	0.28764|0.28764	0.0713|0.0713	M|M	0.63208|0.63208	1.945|1.945	0.51482|0.51482	D|D	0.999925|0.999925	.|P;P;P;P	.|0.41188	.|0.609;0.609;0.661;0.741	.|B;B;P;B	.|0.45913	.|0.363;0.258;0.497;0.388	T|T	0.14783|0.14783	-1.0460|-1.0460	5|10	.|0.72032	.|D	.|0.01	.|.	14.445|14.445	0.67342|0.67342	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|676;653;684;18	.|Q8TEY7-3;Q8TEY7-2;Q8TEY7;Q9Y417	.|.;.;UBP33_HUMAN;.	L|T	289|653;684;684;676	.|ENSP00000359830:N653T;ENSP00000359829:N684T;ENSP00000350009:N684T;ENSP00000359828:N676T	.|ENSP00000350009:N684T	I|N	-|-	1|2	0|0	USP33|USP33	77954102|77954102	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.992000|0.992000	0.81027|0.81027	3.183000|3.183000	0.50918|0.50918	1.952000|1.952000	0.56665|0.56665	0.533000|0.533000	0.62120|0.62120	ATC|AAT		0.338	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		G	78181514	T	G	78181514	3	3	61	1	0	0	0	0	1	0	0	0	17104	1493	52	4	817	4	USP33	1	78181514	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	83597	78181514	171069107	371	8356										
USP33	23032	broad.mit.edu	37	chr1	78207406	78207406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaggaattttttcctgttTcccaagactttcaaaatgag	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78207406T>C	ENST00000370793.1	-	3	416	c.70A>G	c.(70-72)Aaa>Gaa	p.K24E	USP33_ENST00000370792.3_Missense_Mutation_p.K24E|USP33_ENST00000357428.1_Missense_Mutation_p.K24E|USP33_ENST00000528150.1_5'UTR|USP33_ENST00000370794.3_5'UTR	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	24					axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.K24E(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						TTTTCCTGTTTCCCAAGACTT	0.294																																					Melanoma(152;72 1870 11110 26780 42647)											1	Substitution - Missense(1)	large_intestine(1)	1											35	36	36					1																	78207406		2203	4289	6492	77979994	SO:0001583	missense	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.70A>G	1.37:g.78207406T>C	ENSP00000359829:p.Lys24Glu		77979994	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.242901	0.39598	.	.	ENSG00000077254	ENST00000370793;ENST00000357428;ENST00000370792;ENST00000524536;ENST00000530709	T;T;T;T	0.32753	2.96;2.96;2.96;1.44	5.61	4.49	0.54785	.	0.481200	0.17610	N	0.168123	T	0.05227	0.0139	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.01;0.003	B;B	0.10450	0.005;0.002	T	0.21109	-1.0255	10	0.72032	D	0.01	.	3.8548	0.08971	0.134:0.0729:0.1245:0.6687	.	24;24	Q8TEY7-3;Q8TEY7	.;UBP33_HUMAN	E	24	ENSP00000359829:K24E;ENSP00000350009:K24E;ENSP00000359828:K24E;ENSP00000434441:K24E	ENSP00000350009:K24E	K	-	1	0	USP33	77979994	0.026000	0.19158	0.980000	0.43619	0.835000	0.47333	1.674000	0.37544	1.080000	0.41073	0.455000	0.32223	AAA		0.294	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		C	78207406	T	C	78207406	3	2	61	1	0	0	0	0	1	0	0	0	17104	1792	62	4	2862	4	USP33	1	78207406	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	25892	78207406	171043215	372	8357										
FAM73A	374986	broad.mit.edu	37	chr1	78324724	78324724	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagttgaagaaggaaaaatTtactccagagtactgaggta	10	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78324724T>G	ENST00000370791.3	+	9	1130	c.1098T>G	c.(1096-1098)atT>atG	p.I366M	FAM73A_ENST00000443751.2_Missense_Mutation_p.I328M	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	366						integral component of membrane (GO:0016021)		p.I366M(1)		breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		AAGGAAAAATTTACTCCAGAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	94	96					1																	78324724		2203	4300	6503	78097312	SO:0001583	missense	374986				CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.1098T>G	1.37:g.78324724T>G	ENSP00000359827:p.Ile366Met		78097312	Q6MZG0	Missense_Mutation	SNP	ENST00000370791.3	37	CCDS681.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.456594	0.63401	.	.	ENSG00000180488	ENST00000370791;ENST00000443751	T;T	0.28895	1.59;1.59	5.56	2.05	0.26809	.	0.280148	0.38720	N	0.001593	T	0.35653	0.0939	M	0.73217	2.22	0.47511	D	0.999443	P;P;P;P	0.51147	0.879;0.942;0.928;0.942	P;P;P;P	0.60012	0.668;0.867;0.79;0.867	T	0.29305	-1.0016	10	0.87932	D	0	-38.2895	9.5736	0.39442	0.0:0.1969:0.0:0.8031	.	328;366;366;366	F8W7S1;B7ZLZ8;Q8NAN2-2;Q8NAN2	.;.;.;FA73A_HUMAN	M	366;328	ENSP00000359827:I366M;ENSP00000393675:I328M	ENSP00000359827:I366M	I	+	3	3	FAM73A	78097312	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.632000	0.24583	0.935000	0.37341	0.533000	0.62120	ATT		0.378	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		G	78324724	T	G	78324724	3	3	61	1	0	0	0	0	1	0	0	0	5636	1829	64	4	1132	4	FAM73A	1	78324724	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	117318	78324724	170925897	373	8358										
NEXN	91624	broad.mit.edu	37	chr1	78399044	78399044	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggaaaactggaaattaaTtttgaagaattattaaaaca	7	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78399044T>A	ENST00000334785.7	+	10	1315	c.1131T>A	c.(1129-1131)aaT>aaA	p.N377K	NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000457030.1_Missense_Mutation_p.N363K|NEXN_ENST00000330010.8_Missense_Mutation_p.N313K	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)									p.N377K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		TGGAAATTAATTTTGAAGAAT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											29	28	29					1																	78399044		1795	4052	5847	78171632	SO:0001583	missense	91624			AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1131T>A	1.37:g.78399044T>A	ENSP00000333938:p.Asn377Lys		78171632		Missense_Mutation	SNP	ENST00000334785.7	37	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.148727|4.148727	0.78001|0.78001	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000342754|ENST00000401035;ENST00000457030;ENST00000330010;ENST00000334785;ENST00000440324	.|T;T;T;T;T	.|0.76968	.|-1.06;-0.02;-0.16;-0.19;-0.4	5.93|5.93	3.64|3.64	0.41730|0.41730	.|.	.|0.000000	.|0.56097	.|D	.|0.000029	T|T	0.75510|0.75510	0.3859|0.3859	M|M	0.76574|0.76574	2.34|2.34	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.63046	.|0.986;0.992;0.986;0.986	.|D;D;D;D	.|0.69824	.|0.949;0.966;0.926;0.949	T|T	0.76862|0.76862	-0.2802|-0.2802	5|10	.|0.07990	.|T	.|0.79	-26.8768|-26.8768	9.181|9.181	0.37141|0.37141	0.0:0.2033:0.0:0.7967|0.0:0.2033:0.0:0.7967	.|.	.|313;363;377;313	.|D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7	.|.;.;NEXN_HUMAN;.	N|K	277|313;363;313;377;363	.|ENSP00000383814:N313K;ENSP00000388048:N363K;ENSP00000327363:N313K;ENSP00000333938:N377K;ENSP00000411902:N363K	.|ENSP00000327363:N313K	I|N	+|+	2|3	0|2	NEXN|NEXN	78171632|78171632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.039000|3.039000	0.49791|0.49791	0.516000|0.516000	0.28340|0.28340	0.533000|0.533000	0.62120|0.62120	ATT|AAT		0.318	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		A	78399044	T	A	78399044	3	1	61	1	0	0	0	0	1	0	0	0	10386	1490	52	5	1165	5	NEXN	1	78399044	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	74320	78399044	170851577	374	8359										
FUBP1	8880	broad.mit.edu	37	chr1	78433328	78433328	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctttgctgctgatgcatCggtggtaactgtgttccaaa	10	9	0	1	rs375397592		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78433328C>T	ENST00000370768.2	-	4	354	c.273G>A	c.(271-273)ccG>ccA	p.P91P	FUBP1_ENST00000436586.2_Silent_p.P112P|FUBP1_ENST00000370767.1_Silent_p.P91P	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	91					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.P91P(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GCTGATGCATCGGTGGTAACT	0.289			"F, N"		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	1	Substitution - coding silent(1)	large_intestine(1)	1						C		0,4406		0,0,2203	114	105	108		273	-6.1	0.7	1		108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FUBP1	NM_003902.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		91/645	78433328	1,13005	2203	4300	6503	78205916	SO:0001819	synonymous_variant	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.273G>A	1.37:g.78433328C>T			78205916	Q12828	Silent	SNP	ENST00000370768.2	37	CCDS683.1																																																																																				0.289	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		T	78433328	C	T	78433328	2	4	61	1	0	0	0	0	0	0	0	1	6111	871	31	1		1	FUBP1	1	78433328	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34284	78433328	170817293	375	8360										
GIPC2	54810	broad.mit.edu	37	chr1	78546461	78546461	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcccatgtgaaaggaatcGaaaaagaagtgaatgtgtat	11	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78546461G>A	ENST00000370759.3	+	2	536	c.343G>A	c.(343-345)Gaa>Aaa	p.E115K	GIPC2_ENST00000476882.1_3'UTR	NM_017655.4	NP_060125.4	Q8TF65	GIPC2_HUMAN	GIPC PDZ domain containing family, member 2	115						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.E115K(1)		endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)	20						GAAAGGAATCGAAAAAGAAGT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											115	118	117					1																	78546461		2203	4299	6502	78319049	SO:0001583	missense	54810			AB073737	CCDS685.1	1p31.1	2010-05-28			ENSG00000137960	ENSG00000137960			18177	protein-coding gene	gene with protein product	"semaphorin cytoplasmic domain associated protein 2"					11836570	Standard	NM_017655		Approved	FLJ20075, SEMCAP-2	uc001dik.3	Q8TF65	OTTHUMG00000041145	ENST00000370759.3:c.343G>A	1.37:g.78546461G>A	ENSP00000359795:p.Glu115Lys		78319049	Q8IYD3|Q9NXS7	Missense_Mutation	SNP	ENST00000370759.3	37	CCDS685.1	.	.	.	.	.	.	.	.	.	.	A	0.028	-1.352253	0.01256	.	.	ENSG00000137960	ENST00000370759	T	0.39229	1.09	6.16	-0.811	0.10857	PDZ/DHR/GLGF (1);	0.444694	0.26812	N	0.022377	T	0.02047	0.0064	N	0.00308	-1.67	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43956	-0.9359	10	0.02654	T	1	-4.4581	8.4323	0.32766	0.5195:0.2254:0.2551:0.0	.	115	Q8TF65	GIPC2_HUMAN	K	115	ENSP00000359795:E115K	ENSP00000359795:E115K	E	+	1	0	GIPC2	78319049	0.017000	0.18338	0.033000	0.17914	0.116000	0.19942	1.376000	0.34306	-0.258000	0.09446	-0.269000	0.10298	GAA		0.333	GIPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098629.1	NM_017655		A	78546461	G	A	78546461	3	1	61	1	0	0	0	0	1	0	0	0	6413	1059	37	1	349	1	GIPC2	1	78546461	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113133	78546461	170704160	376	8361										
GIPC2	54810	broad.mit.edu	37	chr1	78585115	78585115	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctggaaagtcatcaggaGaaaaaattggttgtggaagg	15	3	2	1	rs140087680		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:78585115G>T	ENST00000370759.3	+	4	839	c.646G>T	c.(646-648)Gaa>Taa	p.E216*		NM_017655.4	NP_060125.4	Q8TF65	GIPC2_HUMAN	GIPC PDZ domain containing family, member 2	216						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.E216*(1)		endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)	20						GTCATCAGGAGAAAAAATTGG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1						G	stop/GLU	0,4406		0,0,2203	126	124	124		646	5.6	0	1	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	GIPC2	NM_017655.4		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		216/316	78585115	1,13005	2203	4300	6503	78357703	SO:0001587	stop_gained	54810			AB073737	CCDS685.1	1p31.1	2010-05-28			ENSG00000137960	ENSG00000137960			18177	protein-coding gene	gene with protein product	"semaphorin cytoplasmic domain associated protein 2"					11836570	Standard	NM_017655		Approved	FLJ20075, SEMCAP-2	uc001dik.3	Q8TF65	OTTHUMG00000041145	ENST00000370759.3:c.646G>T	1.37:g.78585115G>T	ENSP00000359795:p.Glu216*		78357703	Q8IYD3|Q9NXS7	Nonsense_Mutation	SNP	ENST00000370759.3	37	CCDS685.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.372190	0.61624	0.0	1.16E-4	ENSG00000137960	ENST00000370759	.	.	.	5.59	5.59	0.84812	.	0.920867	0.09447	N	0.801029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-10.7946	15.4637	0.75381	0.0:0.0:1.0:0.0	.	.	.	.	X	216	.	ENSP00000359795:E216X	E	+	1	0	GIPC2	78357703	0.176000	0.23096	0.010000	0.14722	0.013000	0.08279	3.330000	0.52068	2.808000	0.96608	0.655000	0.94253	GAA		0.418	GIPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098629.1	NM_017655		T	78585115	G	T	78585115	4	4	61	1	0	0	0	0	0	1	0	0	6413	943	33	2	660	2	GIPC2	1	78585115	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38654	78585115	170665506	377	8362										
IFI44L	10964	broad.mit.edu	37	chr1	79102806	79102806	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcactgtgtggcttatgtCttagacatcaactctattga	7	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:79102806C>A	ENST00000370751.5	+	6	1145	c.966C>A	c.(964-966)gtC>gtA	p.V322V	IFI44L_ENST00000342282.3_Silent_p.V64V|IFI44L_ENST00000476521.1_3'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	322					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)		p.V283V(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						TGGCTTATGTCTTAGACATCA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	1											159	160	160					1																	79102806		2203	4300	6503	78875394	SO:0001819	synonymous_variant	10964			AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.966C>A	1.37:g.79102806C>A			78875394	Q86TE1|Q96B64|Q99984	Silent	SNP	ENST00000370751.5	37	CCDS687.2																																																																																				0.368	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		A	79102806	C	A	79102806	2	1	61	1	0	0	0	0	0	0	0	1	7539	900	32	2		2	IFI44L	1	79102806	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	517691	79102806	170147815	378	8363										
IFI44	10561	broad.mit.edu	37	chr1	79116171	79116171	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactaggactatgtacaccAgaaacactgttttgttgtga	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:79116171A>T	ENST00000370747.4	+	2	376	c.291A>T	c.(289-291)ccA>ccT	p.P97P	IFI44_ENST00000545124.1_Intron|IFI44_ENST00000495254.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	97					response to virus (GO:0009615)	cytoplasm (GO:0005737)		p.P97P(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						TATGTACACCAGAAACACTGT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	92	90					1																	79116171		2203	4300	6503	78888759	SO:0001819	synonymous_variant	10561			D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 5"	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.291A>T	1.37:g.79116171A>T			78888759	B7ZAG3|D3DQ80|Q14496	Silent	SNP	ENST00000370747.4	37	CCDS688.1																																																																																				0.348	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417		T	79116171	A	T	79116171	2	4	61	1	0	0	0	0	0	0	0	1	7538	175	7	5		5	IFI44	1	79116171	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13365	79116171	170134450	379	8364										
IFI44	10561	broad.mit.edu	37	chr1	79116334	79116334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatgaagtttttcgatgcGaaggtaggtttaattagata	10	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:79116334G>A	ENST00000370747.4	+	2	539	c.454G>A	c.(454-456)Gaa>Aaa	p.E152K	IFI44_ENST00000545124.1_Intron|IFI44_ENST00000495254.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	152					response to virus (GO:0009615)	cytoplasm (GO:0005737)		p.E152K(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						TTTTCGATGCGAAGGTAGGTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											38	40	39					1																	79116334		2200	4286	6486	78888922	SO:0001583	missense	10561			D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 5"	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.454G>A	1.37:g.79116334G>A	ENSP00000359783:p.Glu152Lys		78888922	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	37	CCDS688.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857650	0.51376	.	.	ENSG00000137965	ENST00000370747;ENST00000438486	T;T	0.26518	2.79;1.73	3.27	3.27	0.37495	.	0.142017	0.44285	D	0.000465	T	0.26484	0.0647	L	0.35854	1.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70227	0.968;0.957	T	0.02484	-1.1152	10	0.66056	D	0.02	.	10.3025	0.43661	0.0:0.0:1.0:0.0	.	152;152	B7ZB11;Q8TCB0	.;IFI44_HUMAN	K	152;28	ENSP00000359783:E152K;ENSP00000399477:E28K	ENSP00000359783:E152K	E	+	1	0	IFI44	78888922	1.000000	0.71417	1.000000	0.80357	0.286000	0.27126	3.325000	0.52030	2.110000	0.64415	0.467000	0.42956	GAA		0.328	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417		A	79116334	G	A	79116334	3	1	61	1	0	0	0	0	1	0	0	0	7538	1059	37	1	456	1	IFI44	1	79116334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163	79116334	170134287	380	8365										
ELTD1	64123	broad.mit.edu	37	chr1	79392734	79392734	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcagatgatgaaagcaaaGgaccaatactcttataatat	7	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:79392734G>T	ENST00000370742.3	-	8	983	c.920C>A	c.(919-921)cCt>cAt	p.P307H		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	307					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.P307H(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TGAAAGCAAAGGACCAATACT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	67	68					1																	79392734		1804	4078	5882	79165322	SO:0001583	missense	64123			AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.920C>A	1.37:g.79392734G>T	ENSP00000359778:p.Pro307His		79165322	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.367536	0.42003	.	.	ENSG00000162618	ENST00000370742	T	0.09255	3.0	6.02	4.12	0.48240	Domain of unknown function DUF3497 (1);	0.454723	0.26665	N	0.023137	T	0.02848	0.0085	L	0.44542	1.39	0.25325	N	0.989083	B	0.12013	0.005	B	0.19946	0.027	T	0.42361	-0.9456	9	.	.	.	.	6.1918	0.20528	0.0661:0.2534:0.549:0.1315	.	307	Q9HBW9	ELTD1_HUMAN	H	307	ENSP00000359778:P307H	.	P	-	2	0	ELTD1	79165322	1.000000	0.71417	0.997000	0.53966	0.547000	0.35210	3.089000	0.50183	0.846000	0.35142	-0.285000	0.09966	CCT		0.294	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		T	79392734	G	T	79392734	3	4	61	1	0	0	0	0	1	0	0	0	5097	1000	35	2	1184	2	ELTD1	1	79392734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	276400	79392734	169857887	381	8366										
ELTD1	64123	broad.mit.edu	37	chr1	79403526	79403526	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtatcaaactctgtggtCttttggaagctctgggatat	10	6	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:79403526C>A	ENST00000370742.3	-	6	789	c.726G>T	c.(724-726)aaG>aaT	p.K242N		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	242					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.K242N(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		ACTCTGTGGTCTTTTGGAAGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											177	163	167					1																	79403526		1836	4084	5920	79176114	SO:0001583	missense	64123			AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.726G>T	1.37:g.79403526C>A	ENSP00000359778:p.Lys242Asn		79176114	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607127	0.66558	.	.	ENSG00000162618	ENST00000370742	T	0.11063	2.81	5.79	2.94	0.34122	Domain of unknown function DUF3497 (1);	0.187977	0.56097	D	0.000033	T	0.04588	0.0125	L	0.53249	1.67	0.37771	D	0.926681	B	0.21452	0.056	B	0.27076	0.076	T	0.19679	-1.0298	9	.	.	.	.	10.7942	0.46451	0.0:0.797:0.0:0.203	.	242	Q9HBW9	ELTD1_HUMAN	N	242	ENSP00000359778:K242N	.	K	-	3	2	ELTD1	79176114	1.000000	0.71417	0.991000	0.47740	0.897000	0.52465	0.669000	0.25142	0.370000	0.24538	0.557000	0.71058	AAG		0.358	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		A	79403526	C	A	79403526	3	1	61	1	0	0	0	0	1	0	0	0	5097	912	32	2	1386	2	ELTD1	1	79403526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10792	79403526	169847095	382	8367										
LPHN2	23266	broad.mit.edu	37	chr1	82408790	82408790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgccctggactccctatCgtaccgatactttaatagaa	6	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:82408790C>T	ENST00000370728.1	+	8	1180	c.535C>T	c.(535-537)Cgt>Tgt	p.R179C	LPHN2_ENST00000370727.1_Missense_Mutation_p.R179C|LPHN2_ENST00000370723.1_Missense_Mutation_p.R179C|LPHN2_ENST00000359929.3_Missense_Mutation_p.R179C|LPHN2_ENST00000370730.1_Missense_Mutation_p.R179C|LPHN2_ENST00000370715.1_Missense_Mutation_p.R179C|LPHN2_ENST00000319517.6_Missense_Mutation_p.R179C|LPHN2_ENST00000370721.1_Missense_Mutation_p.R183C|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000271029.4_Missense_Mutation_p.R179C|LPHN2_ENST00000335786.5_Missense_Mutation_p.R179C|LPHN2_ENST00000394879.1_Missense_Mutation_p.R179C|LPHN2_ENST00000370713.1_Missense_Mutation_p.R179C|LPHN2_ENST00000370717.2_Missense_Mutation_p.R179C|LPHN2_ENST00000370725.1_Missense_Mutation_p.R179C			O95490	LPHN2_HUMAN	latrophilin 2	179	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.R179C(2)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GACTCCCTATCGTACCGATAC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	1											73	78	77					1																	82408790		2202	4298	6500	82181378	SO:0001583	missense	23266			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.535C>T	1.37:g.82408790C>T	ENSP00000359763:p.Arg179Cys		82181378	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.	.	.	.	.	.	.	.	.	.	C	16.26	3.072310	0.55646	.	.	ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5	5.9	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.94565	0.8249	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.991;0.993	D	0.95695	0.8744	10	0.87932	D	0	.	17.2124	0.86934	0.0:0.8742:0.1258:0.0	.	179;179;179	O95490-3;O95490-4;O95490-2	.;.;.	C	183;179;179;179;179;179;179;179;179;179;179;179;179;179	ENSP00000359756:R183C;ENSP00000359763:R179C;ENSP00000359765:R179C;ENSP00000359762:R179C;ENSP00000359760:R179C;ENSP00000359758:R179C;ENSP00000353006:R179C;ENSP00000359750:R179C;ENSP00000359748:R179C;ENSP00000322270:R179C;ENSP00000359752:R179C;ENSP00000378344:R179C;ENSP00000271029:R179C;ENSP00000337306:R179C	ENSP00000271029:R179C	R	+	1	0	LPHN2	82181378	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	3.893000	0.56243	1.485000	0.48380	0.650000	0.86243	CGT		0.398	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		T	82408790	C	T	82408790	3	4	61	1	0	0	0	0	1	0	0	0	8945	884	31	1	549	1	LPHN2	1	82408790	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3005264	82408790	166841831	383	8368										
LPHN2	23266	broad.mit.edu	37	chr1	82445597	82445597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattgtgcaaaatggtgaaGcattcaaacactttgaaacc	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:82445597G>A	ENST00000370728.1	+	20	3699	c.3054G>A	c.(3052-3054)aaG>aaA	p.K1018K	LPHN2_ENST00000370727.1_Silent_p.K1018K|LPHN2_ENST00000370723.1_Silent_p.K1005K|LPHN2_ENST00000359929.3_Silent_p.K1005K|LPHN2_ENST00000370730.1_Silent_p.K1018K|LPHN2_ENST00000370715.1_Silent_p.K1005K|LPHN2_ENST00000319517.6_Silent_p.K1005K|LPHN2_ENST00000370721.1_Silent_p.K943K|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000271029.4_Silent_p.K1018K|LPHN2_ENST00000335786.5_Silent_p.K1018K|LPHN2_ENST00000394879.1_Silent_p.K1005K|LPHN2_ENST00000370713.1_Silent_p.K1005K|LPHN2_ENST00000370717.2_Silent_p.K1018K|LPHN2_ENST00000370725.1_Silent_p.K1018K			O95490	LPHN2_HUMAN	latrophilin 2	1018					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.K1005K(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		AAATGGTGAAGCATTCAAACA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	1											94	92	93					1																	82445597		2203	4294	6497	82218185	SO:0001819	synonymous_variant	23266			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.3054G>A	1.37:g.82445597G>A			82218185	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Silent	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.971|8.971	0.972981|0.972981	0.18736|0.18736	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000402328|ENST00000449420	.|.	.|.	.|.	5.98|5.98	2.07|2.07	0.26955|0.26955	.|.	.|.	.|.	.|.	.|.	T|T	0.44767|0.44767	0.1309|0.1309	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34453|0.34453	-0.9828|-0.9828	4|4	.|.	.|.	.|.	.|.	10.205|10.205	0.43107|0.43107	0.268:0.0:0.732:0.0|0.268:0.0:0.732:0.0	.|.	.|.	.|.	.|.	T|N	9|886	.|.	.|.	A|S	+|+	1|2	0|0	LPHN2|LPHN2	82218185|82218185	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.948000|0.948000	0.59901|0.59901	2.617000|2.617000	0.46385|0.46385	0.134000|0.134000	0.18681|0.18681	-0.229000|-0.229000	0.12294|0.12294	GCA|AGC		0.284	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		A	82445597	G	A	82445597	2	1	61	1	0	0	0	0	0	0	0	1	8945	962	34	3		3	LPHN2	1	82445597	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36807	82445597	166805024	384	8369										
LPHN2	23266	broad.mit.edu	37	chr1	82456686	82456686	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actataaaagcatgccaaatCttggagctggccatcagctt	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:82456686C>A	ENST00000370728.1	+	25	4882	c.4237C>A	c.(4237-4239)Ctt>Att	p.L1413I	LPHN2_ENST00000370727.1_Missense_Mutation_p.L1385I|LPHN2_ENST00000370723.1_Missense_Mutation_p.L1415I|LPHN2_ENST00000359929.3_Missense_Mutation_p.L1357I|LPHN2_ENST00000370730.1_Missense_Mutation_p.L1370I|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000319517.6_Missense_Mutation_p.L1357I|LPHN2_ENST00000370721.1_Missense_Mutation_p.L1338I|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000271029.4_Missense_Mutation_p.L1385I|LPHN2_ENST00000335786.5_Missense_Mutation_p.L1370I|LPHN2_ENST00000394879.1_Missense_Mutation_p.L1415I|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000370717.2_Missense_Mutation_p.L1428I|LPHN2_ENST00000370725.1_Missense_Mutation_p.L1428I			O95490	LPHN2_HUMAN	latrophilin 2	1413					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.L1357I(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		catgccaaatcttggagctgg	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											50	48	49					1																	82456686		2203	4300	6503	82229274	SO:0001583	missense	23266			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4237C>A	1.37:g.82456686C>A	ENSP00000359763:p.Leu1413Ile		82229274	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.07|14.07	2.425497|2.425497	0.43020|0.43020	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000402328	T;T;T;T;T;T;T;T;T;T;T;T|.	0.80304|.	-1.26;-1.36;-1.34;-1.29;-1.29;-1.19;-1.26;-1.26;-1.29;-1.19;-1.29;-1.34|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.156649|.	0.42053|.	D|.	0.000765|.	T|T	0.67154|0.67154	0.2863|0.2863	L|L	0.60455|0.60455	1.87|1.87	0.47511|0.47511	D|D	0.999449|0.999449	P;D|.	0.62365|.	0.828;0.991|.	P;P|.	0.57283|.	0.54;0.817|.	T|T	0.63247|0.63247	-0.6680|-0.6680	10|5	0.56958|.	D|.	0.05|.	.|.	19.7629|19.7629	0.96329|0.96329	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1357;337|.	O95490-2;B3KVU1|.	.;.|.	I|Y	1338;1413;1370;1385;1428;1415;1357;1357;1428;1415;1385;1370|424	ENSP00000359756:L1338I;ENSP00000359763:L1413I;ENSP00000359765:L1370I;ENSP00000359762:L1385I;ENSP00000359760:L1428I;ENSP00000359758:L1415I;ENSP00000353006:L1357I;ENSP00000322270:L1357I;ENSP00000359752:L1428I;ENSP00000378344:L1415I;ENSP00000271029:L1385I;ENSP00000337306:L1370I|.	ENSP00000271029:L1385I|.	L|S	+|+	1|2	0|0	LPHN2|LPHN2	82229274|82229274	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.908000|0.908000	0.53690|0.53690	3.529000|3.529000	0.53532|0.53532	2.666000|2.666000	0.90696|0.90696	0.561000|0.561000	0.74099|0.74099	CTT|TCT		0.478	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		A	82456686	C	A	82456686	3	1	61	1	0	0	0	0	1	0	0	0	8945	913	32	2	4143	2	LPHN2	1	82456686	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11089	82456686	166793935	385	8370										
RPF1	80135	broad.mit.edu	37	chr1	84945013	84945013	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcgggaagaaaagtctaAaacggaaagccgctgccgaa	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:84945013A>C	ENST00000370654.5	+	1	64	c.49A>C	c.(49-51)Aaa>Caa	p.K17Q	RPF1_ENST00000370656.1_Missense_Mutation_p.K17Q	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	17					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.K17Q(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						GAAAAGTCTAAAACGGAAAGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											27	28	27					1																	84945013		2203	4300	6503	84717601	SO:0001583	missense	80135			AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"RNA processing factor 1", "ribosome production factor 1"		"brix domain containing 5"	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.49A>C	1.37:g.84945013A>C	ENSP00000359688:p.Lys17Gln		84717601	Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	37	CCDS695.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198359	0.58126	.	.	ENSG00000117133	ENST00000370656;ENST00000370654	T;T	0.53423	0.62;1.41	6.17	5.06	0.68205	.	0.200030	0.49916	D	0.000124	T	0.09247	0.0228	N	0.08118	0	0.26905	N	0.967022	B	0.26935	0.164	B	0.22601	0.04	T	0.06607	-1.0817	10	0.22109	T	0.4	-28.3616	5.3222	0.15887	0.7639:0.0:0.2361:0.0	.	17	Q9H9Y2	RPF1_HUMAN	Q	17	ENSP00000359690:K17Q;ENSP00000359688:K17Q	ENSP00000359688:K17Q	K	+	1	0	RPF1	84717601	0.983000	0.35010	0.684000	0.30055	0.691000	0.40173	2.321000	0.43805	2.371000	0.80710	0.533000	0.62120	AAA		0.592	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		C	84945013	A	C	84945013	3	2	61	1	0	0	0	0	1	0	0	0	13583	15	1	4	51	4	RPF1	1	84945013	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2488327	84945013	164305608	386	8371										
RPF1	80135	broad.mit.edu	37	chr1	84961124	84961124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgagcagtgttcgtcttCgtaaagaaattaaggtaagt	10	4	1	2	rs530459635		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:84961124C>T	ENST00000370654.5	+	6	700	c.685C>T	c.(685-687)Cgt>Tgt	p.R229C	GNG5_ENST00000487806.1_5'Flank	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	229	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.R229C(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						TGTTCGTCTTCGTAAAGAAAT	0.308													C|||	1	0.000199681	8e-04	0	5008	,	,		18759	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											59	63	61					1																	84961124		2202	4300	6502	84733712	SO:0001583	missense	80135			AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"RNA processing factor 1", "ribosome production factor 1"		"brix domain containing 5"	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.685C>T	1.37:g.84961124C>T	ENSP00000359688:p.Arg229Cys		84733712	Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	37	CCDS695.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.153079	0.57259	.	.	ENSG00000117133	ENST00000370654	T	0.22134	1.97	5.81	4.88	0.63580	Brix domain (3);Anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.18923	0.0454	M	0.80332	2.49	0.80722	D	1	B	0.23990	0.095	B	0.24701	0.055	T	0.06303	-1.0834	10	0.66056	D	0.02	-6.4412	16.3572	0.83239	0.0:0.8677:0.1323:0.0	.	229	Q9H9Y2	RPF1_HUMAN	C	229	ENSP00000359688:R229C	ENSP00000359688:R229C	R	+	1	0	RPF1	84733712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.694000	0.68272	1.425000	0.47237	0.655000	0.94253	CGT		0.308	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		T	84961124	C	T	84961124	3	4	61	1	0	0	0	0	1	0	0	0	13583	884	31	1	707	1	RPF1	1	84961124	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16111	84961124	164289497	387	8372										
SPATA1	100505741	broad.mit.edu	37	chr1	84991699	84991699	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaggaggaacttggaagaGatcccagtttgttagaaaac	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:84991699G>T	ENST00000370638.2	+	0	752							Q5VX52	SPAT1_HUMAN	spermatogenesis associated 1									p.D185Y(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|prostate(1)	10				Epithelial(280;4.36e-10)|all cancers(265;7.1e-09)|BRCA - Breast invasive adenocarcinoma(282;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(397;0.00286)|KIRC - Kidney renal clear cell carcinoma(1967;0.0111)		ACTTGGAAGAGATCCCAGTTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											34	35	34					1																	84991699		2203	4299	6502	84764287			64173			AF306347		1p22.3	2011-05-24			ENSG00000122432	ENSG00000122432			14682	protein-coding gene	gene with protein product							Standard	XM_005275883		Approved	SP-2	uc021opb.1	Q5VX52	OTTHUMG00000009924		1.37:g.84991699G>T			84764287	A0PJU9|Q0VDJ9|Q0VDK0|Q6P386|Q9HAR4	Missense_Mutation	SNP	ENST00000370638.2	37																																																																																					0.373	SPATA1-007	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000314701.1	NM_022354		T	84991699	G	T	84991699	1	4	61	0	1	0	0	0	0	0	0	0	15037	942	33	2		2	SPATA1	1	84991699	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30575	84991699	164258922	388	8373										
SSX2IP	117178	broad.mit.edu	37	chr1	85113220	85113220	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgccacactccatttttGatttgtacattctcctccaa	4	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85113220G>T	ENST00000342203.3	-	14	2004	c.1741C>A	c.(1741-1743)Caa>Aaa	p.Q581K	SSX2IP_ENST00000437941.2_Missense_Mutation_p.Q554K|SSX2IP_ENST00000605755.1_Missense_Mutation_p.Q554K	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	581					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.Q581K(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CTCCATTTTTGATTTGTACAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											250	202	218					1																	85113220		2203	4300	6503	84885808	SO:0001583	missense	117178				CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1741C>A	1.37:g.85113220G>T	ENSP00000340279:p.Gln581Lys		84885808	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	.	.	.	.	.	.	.	.	.	.	G	12.21	1.868384	0.32977	.	.	ENSG00000117155	ENST00000342203;ENST00000437941	T;T	0.53423	0.63;0.62	5.86	4.95	0.65309	.	0.105176	0.42821	D	0.000645	T	0.16811	0.0404	L	0.44542	1.39	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.08452	-1.0721	10	0.29301	T	0.29	-0.1455	5.4447	0.16529	0.0762:0.1304:0.6414:0.152	.	581;554	Q9Y2D8;B4DFE3	ADIP_HUMAN;.	K	581;554	ENSP00000340279:Q581K;ENSP00000412781:Q554K	ENSP00000340279:Q581K	Q	-	1	0	SSX2IP	84885808	0.371000	0.25056	0.012000	0.15200	0.398000	0.30690	1.750000	0.38329	1.484000	0.48361	0.655000	0.94253	CAA		0.388	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		T	85113220	G	T	85113220	3	4	61	1	0	0	0	0	1	0	0	0	15243	1299	45	2	107	2	SSX2IP	1	85113220	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121521	85113220	164137401	389	8374										
WDR63	126820	broad.mit.edu	37	chr1	85555844	85555844	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatattatccaagagaattCtcagaagaggaaaaagagac	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85555844C>A	ENST00000294664.6	+	8	966	c.786C>A	c.(784-786)ttC>ttA	p.F262L	WDR63_ENST00000370596.1_Intron|WDR63_ENST00000326813.8_Intron	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	262								p.F262L(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		CAAGAGAATTCTCAGAAGAGG	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	48	47					1																	85555844		2200	4288	6488	85328432	SO:0001583	missense	126820				CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.786C>A	1.37:g.85555844C>A	ENSP00000294664:p.Phe262Leu		85328432	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	CCDS702.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.455447	0.26161	.	.	ENSG00000162643	ENST00000294664	T	0.38077	1.16	5.46	3.53	0.40419	.	0.101908	0.64402	D	0.000002	T	0.07098	0.0180	L	0.33245	0.995	0.39226	D	0.963582	B	0.06786	0.001	B	0.09377	0.004	T	0.31558	-0.9939	10	0.02654	T	1	-5.2308	5.3797	0.16183	0.0:0.5902:0.1756:0.2342	.	262	Q8IWG1	WDR63_HUMAN	L	262	ENSP00000294664:F262L	ENSP00000294664:F262L	F	+	3	2	WDR63	85328432	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.715000	0.25822	0.589000	0.29677	0.591000	0.81541	TTC		0.274	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		A	85555844	C	A	85555844	3	1	61	1	0	0	0	0	1	0	0	0	17354	912	32	2	812	2	WDR63	1	85555844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	442624	85555844	163694777	390	8375										
SYDE2	84144	broad.mit.edu	37	chr1	85648420	85648420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgttttcagatccatgTttgctagctttagttgtaag	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85648420T>C	ENST00000341460.5	-	3	1954	c.1905A>G	c.(1903-1905)aaA>aaG	p.K635K		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	635					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.K557K(1)|p.K635K(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		CAGATCCATGTTTGCTAGCTT	0.338																																																2	Substitution - coding silent(2)	large_intestine(2)	1											90	81	84					1																	85648420		1839	4092	5931	85421008	SO:0001819	synonymous_variant	84144			AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1905A>G	1.37:g.85648420T>C			85421008	Q5VT96|Q8NDB8|Q9H8A6	Silent	SNP	ENST00000341460.5	37	CCDS44169.1																																																																																				0.338	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			C	85648420	T	C	85648420	2	2	61	1	0	0	0	0	0	0	0	1	15475	1722	60	4		4	SYDE2	1	85648420	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	92576	85648420	163602201	391	8376										
SYDE2	84144	broad.mit.edu	37	chr1	85656004	85656004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcttcagaacagcagagtCggcctcaccaaaactcaagg	10	12	3	2	rs183800883		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85656004C>T	ENST00000341460.5	-	2	1226	c.1177G>A	c.(1177-1179)Gac>Aac	p.D393N		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	393					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.D315N(1)|p.D393N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		ACAGCAGAGTCGGCCTCACCA	0.468													C|||	1	0.000199681	8e-04	0	5008	,	,		20824	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	1											74	74	74					1																	85656004		2087	4206	6293	85428592	SO:0001583	missense	84144			AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1177G>A	1.37:g.85656004C>T	ENSP00000340594:p.Asp393Asn		85428592	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.011	-1.727394	0.00694	.	.	ENSG00000097096	ENST00000341460	T	0.05925	3.37	6.05	-5.73	0.02398	.	0.627024	0.17470	N	0.173101	T	0.00440	0.0014	N	0.01742	-0.745	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29822	-0.9999	10	0.02654	T	1	.	8.093	0.30811	0.0:0.3118:0.1824:0.5058	.	393;393	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	N	393	ENSP00000340594:D393N	ENSP00000340594:D393N	D	-	1	0	SYDE2	85428592	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.122000	0.10627	-1.292000	0.02366	-1.124000	0.02001	GAC		0.468	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			T	85656004	C	T	85656004	3	4	61	1	0	0	0	0	1	0	0	0	15475	884	31	1	2431	1	SYDE2	1	85656004	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7584	85656004	163594617	392	8377										
SYDE2	84144	broad.mit.edu	37	chr1	85656323	85656323	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatatagccaattgcgtttCtttgaaacagtgatgctgtt	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85656323C>A	ENST00000341460.5	-	2	907	c.858G>T	c.(856-858)aaG>aaT	p.K286N		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	286					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.K208N(1)|p.K286N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AATTGCGTTTCTTTGAAACAG	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	1											164	154	157					1																	85656323		1847	4110	5957	85428911	SO:0001583	missense	84144			AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.858G>T	1.37:g.85656323C>A	ENSP00000340594:p.Lys286Asn		85428911	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.044510	0.75732	.	.	ENSG00000097096	ENST00000341460	T	0.16073	2.37	6.17	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.29817	0.0745	M	0.76002	2.32	0.49213	D	0.999763	D;D	0.89917	0.986;1.0	P;D	0.71656	0.843;0.974	T	0.13045	-1.0524	10	0.87932	D	0	.	13.3838	0.60785	0.0:0.8875:0.0:0.1125	.	286;286	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	N	286	ENSP00000340594:K286N	ENSP00000340594:K286N	K	-	3	2	SYDE2	85428911	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.590000	0.36654	0.949000	0.37715	0.655000	0.94253	AAG		0.388	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			A	85656323	C	A	85656323	3	1	61	1	0	0	0	0	1	0	0	0	15475	912	32	2	2750	2	SYDE2	1	85656323	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	319	85656323	163594298	393	8378										
C1orf52	148423	broad.mit.edu	37	chr1	85718347	85718347	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggttctcctggctctaCtttgcgctttttagaagtat	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:85718347C>A	ENST00000471115.1	-	3	522	c.514G>T	c.(514-516)Gta>Tta	p.V172L	C1orf52_ENST00000294661.4_5'UTR	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	172							poly(A) RNA binding (GO:0044822)	p.V172L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		CCTGGCTCTACTTTGCGCTTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											155	137	143					1																	85718347		2202	4297	6499	85490935	SO:0001583	missense	148423			BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.514G>T	1.37:g.85718347C>A	ENSP00000419417:p.Val172Leu		85490935	B3KX89|Q8TDK5|Q8TDK6	Missense_Mutation	SNP	ENST00000471115.1	37	CCDS703.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.023959	0.35701	.	.	ENSG00000162642	ENST00000471115	.	.	.	5.82	2.69	0.31865	.	0.521283	0.19278	N	0.118233	T	0.20659	0.0497	N	0.21448	0.665	0.80722	D	1	B	0.10296	0.003	B	0.13407	0.009	T	0.05666	-1.0871	9	0.32370	T	0.25	-13.035	6.2983	0.21099	0.0:0.6501:0.0:0.3499	.	172	Q8N6N3	CA052_HUMAN	L	172	.	ENSP00000419417:V172L	V	-	1	0	C1orf52	85490935	0.985000	0.35326	1.000000	0.80357	0.995000	0.86356	-0.018000	0.12568	0.650000	0.30769	0.561000	0.74099	GTA		0.318	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077		A	85718347	C	A	85718347	3	1	61	1	0	0	0	0	1	0	0	0	2050	565	20	2	38	2	C1orf52	1	85718347	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62024	85718347	163532274	394	8379										
ZNHIT6	54680	broad.mit.edu	37	chr1	86123644	86123644	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacttttataaggatctaGttcataatatcttattaata	5	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86123644G>T	ENST00000370574.3	-	9	1391	c.1258C>A	c.(1258-1260)Cta>Ata	p.L420I	ZNHIT6_ENST00000431532.2_Missense_Mutation_p.L381I			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	420					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.L420I(1)		autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						TAAGGATCTAGTTCATAATAT	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	50	49					1																	86123644		2199	4289	6488	85896232	SO:0001583	missense	54680			AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.1258C>A	1.37:g.86123644G>T	ENSP00000359606:p.Leu420Ile		85896232	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	37	CCDS707.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403726	0.62288	.	.	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.58358	0.45;0.34	5.86	3.01	0.34805	.	0.000000	0.64402	D	0.000004	T	0.52273	0.1724	L	0.58354	1.805	0.44241	D	0.997084	D;D	0.76494	0.997;0.999	P;D	0.80764	0.904;0.994	T	0.54721	-0.8251	10	0.54805	T	0.06	-6.8624	7.1909	0.25824	0.1415:0.0:0.7204:0.1381	.	381;420	B4DP13;Q9NWK9	.;BCD1_HUMAN	I	381;420	ENSP00000414344:L381I;ENSP00000359606:L420I	ENSP00000359606:L420I	L	-	1	2	ZNHIT6	85896232	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	1.401000	0.34589	0.494000	0.27859	0.650000	0.86243	CTA		0.254	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		T	86123644	G	T	86123644	3	4	61	1	0	0	0	0	1	0	0	0	18248	1020	36	2	162	2	ZNHIT6	1	86123644	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	405297	86123644	163126977	395	8380										
ZNHIT6	54680	broad.mit.edu	37	chr1	86171989	86171989	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtatgcagttttatctcGaactccattacatgtcagtt	6	8	2	0	rs374783757		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86171989G>A	ENST00000370574.3	-	3	905	c.772C>T	c.(772-774)Cga>Tga	p.R258*	ZNHIT6_ENST00000431532.2_Nonsense_Mutation_p.R219*			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	258					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.R258*(3)		autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						GTTTTATCTCGAACTCCATTA	0.368																																																3	Substitution - Nonsense(3)	large_intestine(3)	1						G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	125	114	118		655,772	3.5	1	1		118	0,8600		0,0,4300	no	stop-gained,stop-gained	ZNHIT6	NM_001170670.1,NM_017953.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	219/432,258/471	86171989	1,13005	2203	4300	6503	85944577	SO:0001587	stop_gained	54680			AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.772C>T	1.37:g.86171989G>A	ENSP00000359606:p.Arg258*		85944577	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Nonsense_Mutation	SNP	ENST00000370574.3	37	CCDS707.1	.	.	.	.	.	.	.	.	.	.	G	38	6.752255	0.97813	2.27E-4	0.0	ENSG00000117174	ENST00000431532;ENST00000370574	.	.	.	5.43	3.49	0.39957	.	0.212842	0.37348	N	0.002123	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.1369	10.4817	0.44698	0.0:0.1126:0.569:0.3183	.	.	.	.	X	219;258	.	ENSP00000359606:R258X	R	-	1	2	ZNHIT6	85944577	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.807000	0.47955	0.729000	0.32403	0.650000	0.86243	CGA		0.368	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		A	86171989	G	A	86171989	4	1	61	1	0	0	0	0	0	1	0	0	18248	1066	37	1	672	1	ZNHIT6	1	86171989	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48345	86171989	163078632	396	8381										
ZNHIT6	54680	broad.mit.edu	37	chr1	86173448	86173448	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctccatgcatcaattcctCttttatgcattgaccaacaa	3	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86173448C>A	ENST00000370574.3	-	1	653	c.520G>T	c.(520-522)Gag>Tag	p.E174*	ZNHIT6_ENST00000431532.2_Nonsense_Mutation_p.E135*			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	174	Glu-rich.				box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.E174*(1)		autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						ATCAATTCCTCTTTTATGCAT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											273	261	265					1																	86173448		2203	4300	6503	85946036	SO:0001587	stop_gained	54680			AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.520G>T	1.37:g.86173448C>A	ENSP00000359606:p.Glu174*		85946036	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Nonsense_Mutation	SNP	ENST00000370574.3	37	CCDS707.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550360	0.86127	.	.	ENSG00000117174	ENST00000431532;ENST00000370574	.	.	.	4.31	-3.66	0.04489	.	0.000000	0.48767	D	0.000172	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-22.5833	6.4705	0.22005	0.0:0.4166:0.3616:0.2217	.	.	.	.	X	135;174	.	ENSP00000359606:E174X	E	-	1	0	ZNHIT6	85946036	0.000000	0.05858	0.032000	0.17829	0.198000	0.23893	-1.081000	0.03403	-0.407000	0.07576	0.491000	0.48974	GAG		0.398	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		A	86173448	C	A	86173448	4	1	61	1	0	0	0	0	0	1	0	0	18248	922	32	2	932	2	ZNHIT6	1	86173448	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1459	86173448	163077173	397	8382										
ODF2L	57489	broad.mit.edu	37	chr1	86820281	86820281	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatactctgcagatttctCtttaaacttaagattgctgt	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86820281C>T	ENST00000359242.3	-	16	1980	c.1699G>A	c.(1699-1701)Gag>Aag	p.E567K	ODF2L_ENST00000524695.1_5'Flank|ODF2L_ENST00000294678.2_Missense_Mutation_p.E551K|ODF2L_ENST00000370566.3_Missense_Mutation_p.E485K|ODF2L_ENST00000317336.7_Missense_Mutation_p.E567K|ODF2L_ENST00000370567.1_Missense_Mutation_p.E538K|ODF2L_ENST00000394731.1_Missense_Mutation_p.E407K	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	567						centrosome (GO:0005813)		p.E538K(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		GCAGATTTCTCTTTAAACTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											139	138	138					1																	86820281		2203	4300	6503	86592869	SO:0001583	missense	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1699G>A	1.37:g.86820281C>T	ENSP00000359600:p.Glu567Lys		86592869	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061394	0.76187	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000462648;ENST00000294678	T;T;T;T;T;T;T;T	0.78246	1.63;1.35;-1.16;1.41;1.41;1.46;0.5;1.38	6.03	5.11	0.69529	.	0.368768	0.31601	N	0.007380	T	0.55305	0.1912	L	0.45698	1.435	0.33892	D	0.637502	P;B;B;B;B	0.35793	0.521;0.174;0.122;0.228;0.228	B;B;B;B;B	0.36244	0.111;0.22;0.081;0.125;0.199	T	0.52859	-0.8519	10	0.16896	T	0.51	-14.945	10.0261	0.42072	0.0:0.8531:0.0:0.1469	.	485;514;538;551;567	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	K	515;485;567;414;567;538;407;74;551	ENSP00000359597:E485K;ENSP00000359600:E567K;ENSP00000433092:E414K;ENSP00000320165:E567K;ENSP00000359598:E538K;ENSP00000378219:E407K;ENSP00000437043:E74K;ENSP00000294678:E551K	ENSP00000294678:E551K	E	-	1	0	ODF2L	86592869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.045000	0.30341	2.861000	0.98227	0.655000	0.94253	GAG		0.363	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			T	86820281	C	T	86820281	3	4	61	1	0	0	0	0	1	0	0	0	10859	922	32	3	356	3	ODF2L	1	86820281	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	646833	86820281	162430340	398	8383										
ODF2L	57489	broad.mit.edu	37	chr1	86824559	86824559	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttactatttcagctgcttCttgcaacttttgtacctgaa	5	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86824559C>A	ENST00000359242.3	-	13	1551	c.1270G>T	c.(1270-1272)Gaa>Taa	p.E424*	ODF2L_ENST00000524695.1_5'UTR|ODF2L_ENST00000294678.2_Nonsense_Mutation_p.E395*|ODF2L_ENST00000370566.3_Nonsense_Mutation_p.E395*|ODF2L_ENST00000317336.7_Nonsense_Mutation_p.E424*|ODF2L_ENST00000370567.1_Nonsense_Mutation_p.E395*|ODF2L_ENST00000394731.1_Nonsense_Mutation_p.E264*	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	424						centrosome (GO:0005813)		p.E395*(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TCAGCTGCTTCTTGCAACTTT	0.239																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											35	35	35					1																	86824559		2185	4265	6450	86597147	SO:0001587	stop_gained	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1270G>T	1.37:g.86824559C>A	ENSP00000359600:p.Glu424*		86597147	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Nonsense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.517813|5.517813	0.96416|0.96416	.|.	.|.	ENSG00000122417|ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000294678;ENST00000479890|ENST00000459999	.|.	.|.	.|.	5.54|5.54	4.43|4.43	0.53597|0.53597	.|.	0.405411|.	0.26931|.	N|.	0.021777|.	.|T	.|0.40694	.|0.1127	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.32613	.|-0.9900	.|3	0.07325|.	T|.	0.83|.	-17.2258|-17.2258	10.1587|10.1587	0.42838|0.42838	0.0:0.8948:0.0:0.1052|0.0:0.8948:0.0:0.1052	.|.	.|.	.|.	.|.	X|N	395;395;424;271;424;395;264;395;225|243	.|.	ENSP00000294678:E395X|.	E|K	-|-	1|3	0|2	ODF2L|ODF2L	86597147|86597147	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	1.632000|1.632000	0.37102|0.37102	2.589000|2.589000	0.87451|0.87451	0.557000|0.557000	0.71058|0.71058	GAA|AAG		0.239	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86824559	C	A	86824559	4	1	61	1	0	0	0	0	0	1	0	0	10859	922	32	2	840	2	ODF2L	1	86824559	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4278	86824559	162426062	399	8384										
ODF2L	57489	broad.mit.edu	37	chr1	86847936	86847936	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatataacctttacatattCtttcaacttatcgttctcgg	3	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86847936C>A	ENST00000359242.3	-	7	894	c.613G>T	c.(613-615)Gaa>Taa	p.E205*	ODF2L_ENST00000294678.2_Nonsense_Mutation_p.E205*|ODF2L_ENST00000370566.3_Nonsense_Mutation_p.E205*|ODF2L_ENST00000317336.7_Nonsense_Mutation_p.E205*|ODF2L_ENST00000370567.1_Nonsense_Mutation_p.E205*|ODF2L_ENST00000394731.1_Nonsense_Mutation_p.E74*	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	205						centrosome (GO:0005813)		p.E205*(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTTACATATTCTTTCAACTTA	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											74	74	74					1																	86847936		2202	4297	6499	86620524	SO:0001587	stop_gained	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.613G>T	1.37:g.86847936C>A	ENSP00000359600:p.Glu205*		86620524	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Nonsense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.609993|4.609993	0.87258|0.87258	.|.	.|.	ENSG00000122417|ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000294678|ENST00000459999	.|.	.|.	.|.	5.4|5.4	4.43|4.43	0.53597|0.53597	.|.	0.691838|.	0.14902|.	N|.	0.291721|.	.|T	.|0.39091	.|0.1065	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.17806	.|-1.0357	.|4	0.06236|0.25106	T|T	0.91|0.35	-5.8712|-5.8712	11.9677|11.9677	0.53044|0.53044	0.1727:0.8273:0.0:0.0|0.1727:0.8273:0.0:0.0	.|.	.|.	.|.	.|.	X|N	205;205;205;81;205;205;74;205|53	.|.	ENSP00000294678:E205X|ENSP00000436849:K53N	E|K	-|-	1|3	0|2	ODF2L|ODF2L	86620524|86620524	0.993000|0.993000	0.37304|0.37304	0.998000|0.998000	0.56505|0.56505	0.043000|0.043000	0.13939|0.13939	1.301000|1.301000	0.33447|0.33447	2.697000|2.697000	0.92050|0.92050	0.557000|0.557000	0.71058|0.71058	GAA|AAG		0.308	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86847936	C	A	86847936	4	1	61	1	0	0	0	0	0	1	0	0	10859	922	32	2	1521	2	ODF2L	1	86847936	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23377	86847936	162402685	400	8385										
ODF2L	57489	broad.mit.edu	37	chr1	86851260	86851260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtcttttcatttagaaTgtcctgcttcaggctaatta	6	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86851260T>C	ENST00000359242.3	-	3	408	c.127A>G	c.(127-129)Att>Gtt	p.I43V	ODF2L_ENST00000294678.2_Missense_Mutation_p.I43V|ODF2L_ENST00000370566.3_Missense_Mutation_p.I43V|ODF2L_ENST00000317336.7_Missense_Mutation_p.I43V|ODF2L_ENST00000370567.1_Missense_Mutation_p.I43V|ODF2L_ENST00000394731.1_Intron	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	43						centrosome (GO:0005813)		p.I43V(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TCATTTAGAATGTCCTGCTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	76	77					1																	86851260		2202	4300	6502	86623848	SO:0001583	missense	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.127A>G	1.37:g.86851260T>C	ENSP00000359600:p.Ile43Val		86623848	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	T	0.288	-0.981595	0.02197	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.21031	2.06;2.04;2.04;2.04;2.03	5.4	-3.36	0.04913	.	0.941874	0.08878	N	0.880490	T	0.02047	0.0064	N	0.04880	-0.145	0.22975	N	0.998487	B;B;B;B;B	0.17465	0.0;0.002;0.0;0.0;0.022	B;B;B;B;B	0.10450	0.001;0.002;0.001;0.002;0.005	T	0.44544	-0.9321	10	0.29301	T	0.29	10.1394	2.309	0.04182	0.1541:0.4161:0.1582:0.2717	.	43;43;43;43;43	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	V	43	ENSP00000359597:I43V;ENSP00000359600:I43V;ENSP00000320165:I43V;ENSP00000359598:I43V;ENSP00000294678:I43V	ENSP00000294678:I43V	I	-	1	0	ODF2L	86623848	0.000000	0.05858	0.010000	0.14722	0.837000	0.47467	-0.060000	0.11712	-0.403000	0.07622	-0.320000	0.08662	ATT		0.353	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			C	86851260	T	C	86851260	3	2	61	1	0	0	0	0	1	0	0	0	10859	1464	51	4	2023	4	ODF2L	1	86851260	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3324	86851260	162399361	401	8386										
ODF2L	57489	broad.mit.edu	37	chr1	86852674	86852674	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaagatggcaaaagagttCttctgaatgacttccatcat	7	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86852674C>A	ENST00000359242.3	-	2	318	c.37G>T	c.(37-39)Gaa>Taa	p.E13*	ODF2L_ENST00000486215.1_Nonsense_Mutation_p.E13*|ODF2L_ENST00000294678.2_Nonsense_Mutation_p.E13*|ODF2L_ENST00000370566.3_Nonsense_Mutation_p.E13*|ODF2L_ENST00000317336.7_Nonsense_Mutation_p.E13*|ODF2L_ENST00000370567.1_Nonsense_Mutation_p.E13*|ODF2L_ENST00000394731.1_5'UTR|ODF2L_ENST00000478286.2_Nonsense_Mutation_p.E13*	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	13						centrosome (GO:0005813)		p.E13*(2)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		CAAAAGAGTTCTTCTGAATGA	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											110	116	114					1																	86852674		2203	4299	6502	86625262	SO:0001587	stop_gained	57489				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.37G>T	1.37:g.86852674C>A	ENSP00000359600:p.Glu13*		86625262	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Nonsense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974777	0.92919	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959;ENST00000478286;ENST00000486215	.	.	.	4.69	3.77	0.43336	.	0.418218	0.20390	N	0.093266	.	.	.	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-4.8939	8.871	0.35316	0.0:0.8942:0.0:0.1058	.	.	.	.	X	13	.	ENSP00000294678:E13X	E	-	1	0	ODF2L	86625262	0.975000	0.34042	0.540000	0.28089	0.644000	0.38419	1.419000	0.34793	1.090000	0.41315	0.557000	0.71058	GAA		0.398	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86852674	C	A	86852674	4	1	61	1	0	0	0	0	0	1	0	0	10859	922	32	2	2117	2	ODF2L	1	86852674	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1414	86852674	162397947	402	8387										
CLCA2	9635	broad.mit.edu	37	chr1	86904649	86904649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtgggcattgccagtttcGacagcaaaggagagatcaga	13	8	1	2	rs55906076	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86904649G>A	ENST00000370565.4	+	7	1225	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	355	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.D355N(2)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TGCCAGTTTCGACAGCAAAGG	0.438																																					Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)											2	Substitution - Missense(2)	large_intestine(2)	1											128	113	118					1																	86904649		2203	4300	6503	86677237	SO:0001583	missense	9635				CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1063G>A	1.37:g.86904649G>A	ENSP00000359596:p.Asp355Asn		86677237	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	G	4.938	0.174189	0.09391	.	.	ENSG00000137975	ENST00000370565	T	0.67171	-0.25	5.92	-2.97	0.05530	von Willebrand factor, type A (3);	0.659654	0.15853	N	0.241412	T	0.16854	0.0405	N	0.17872	0.535	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25572	-1.0128	10	0.13853	T	0.58	-0.648	3.2905	0.06947	0.3835:0.1146:0.3902:0.1117	.	355	Q9UQC9	CLCA2_HUMAN	N	355	ENSP00000359596:D355N	ENSP00000359596:D355N	D	+	1	0	CLCA2	86677237	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.152000	0.16302	-0.807000	0.04393	-0.302000	0.09304	GAC		0.438	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86904649	G	A	86904649	3	1	61	1	0	0	0	0	1	0	0	0	3464	1058	37	1	1089	1	CLCA2	1	86904649	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51975	86904649	162345972	403	8388										
CLCA2	9635	broad.mit.edu	37	chr1	86921087	86921087	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagagattatcttatattGaaaggagttttaacagcaat	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86921087G>T	ENST00000370565.4	+	14	2871	c.2709G>T	c.(2707-2709)ttG>ttT	p.L903F		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	903					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.L903F(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ATCTTATATTGAAAGGAGTTT	0.398																																					Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)											1	Substitution - Missense(1)	large_intestine(1)	1											143	154	150					1																	86921087		2203	4300	6503	86693675	SO:0001583	missense	9635				CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2709G>T	1.37:g.86921087G>T	ENSP00000359596:p.Leu903Phe		86693675	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.253001	0.39797	.	.	ENSG00000137975	ENST00000370565	T	0.03065	4.06	5.62	3.74	0.42951	.	0.607299	0.15487	N	0.259779	T	0.01320	0.0043	L	0.58925	1.835	0.31950	N	0.609783	P	0.44877	0.845	B	0.41619	0.361	T	0.36335	-0.9752	10	0.09590	T	0.72	-4.56	3.3882	0.07280	0.1542:0.1649:0.5589:0.122	.	903	Q9UQC9	CLCA2_HUMAN	F	903	ENSP00000359596:L903F	ENSP00000359596:L903F	L	+	3	2	CLCA2	86693675	0.927000	0.31430	0.998000	0.56505	0.937000	0.57800	0.504000	0.22626	1.393000	0.46605	0.591000	0.81541	TTG		0.398	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86921087	G	T	86921087	3	4	61	1	0	0	0	0	1	0	0	0	3464	1281	45	2	2763	2	CLCA2	1	86921087	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16438	86921087	162329534	404	8389										
CLCA1	1179	broad.mit.edu	37	chr1	86964279	86964279	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacaatggaatccaccaaGacctgaaattaataaggatg	7	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:86964279G>A	ENST00000234701.3	+	14	2489	c.2138G>A	c.(2137-2139)aGa>aAa	p.R713K	CLCA1_ENST00000394711.1_Missense_Mutation_p.R713K			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	713					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)	p.R713K(1)		NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AATCCACCAAGACCTGAAATT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	93	93					1																	86964279		2203	4300	6503	86736867	SO:0001583	missense	1179				CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2138G>A	1.37:g.86964279G>A	ENSP00000234701:p.Arg713Lys		86736867	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	37	CCDS709.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184966	0.38609	.	.	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.02812	4.15;4.15	5.97	1.89	0.25635	.	0.143157	0.45867	D	0.000334	T	0.00695	0.0023	N	0.17922	0.545	0.26945	N	0.966167	B	0.20368	0.044	B	0.21360	0.034	T	0.48768	-0.9006	10	0.27082	T	0.32	-7.7077	8.4115	0.32646	0.1846:0.1156:0.6999:0.0	.	713	A8K7I4	CLCA1_HUMAN	K	713	ENSP00000234701:R713K;ENSP00000378200:R713K	ENSP00000234701:R713K	R	+	2	0	CLCA1	86736867	0.979000	0.34478	0.925000	0.36789	0.701000	0.40568	1.253000	0.32886	0.801000	0.34066	0.655000	0.94253	AGA		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		A	86964279	G	A	86964279	3	1	61	1	0	0	0	0	1	0	0	0	3463	942	33	3	2188	3	CLCA1	1	86964279	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43192	86964279	162286342	405	8390										
CLCA4	22802	broad.mit.edu	37	chr1	87041067	87041067	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgaacccagaaacattaaCtattacagtaacttctcgag	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:87041067C>A	ENST00000370563.3	+	11	1778	c.1736C>A	c.(1735-1737)aCt>aAt	p.T579N	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	579					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)	p.T579N(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		GAAACATTAACTATTACAGTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	74	76					1																	87041067		1871	4103	5974	86813655	SO:0001583	missense	22802			AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"chloride channel, calcium activated, family member 4", "chloride channel regulator 4"			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.1736C>A	1.37:g.87041067C>A	ENSP00000359594:p.Thr579Asn		86813655	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047165	0.75846	.	.	ENSG00000016602	ENST00000370563	T	0.32753	1.44	5.98	5.05	0.67936	Domain of unknown function DUF1973 (1);	0.271361	0.35096	N	0.003452	T	0.46521	0.1397	M	0.71036	2.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.52049	-0.8627	10	0.56958	D	0.05	-31.6027	16.0095	0.80391	0.1358:0.8642:0.0:0.0	.	131;579	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	N	579	ENSP00000359594:T579N	ENSP00000359594:T579N	T	+	2	0	CLCA4	86813655	0.996000	0.38824	0.562000	0.28370	0.990000	0.78478	6.075000	0.71261	1.493000	0.48517	0.655000	0.94253	ACT		0.393	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		A	87041067	C	A	87041067	3	1	61	1	0	0	0	0	1	0	0	0	3465	565	20	2	1778	2	CLCA4	1	87041067	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76788	87041067	162209554	406	8391										
SH3GLB1	51100	broad.mit.edu	37	chr1	87188306	87188306	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaacgtcagccttaaatTttcttactcctttaagaaac	3	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:87188306T>G	ENST00000370558.4	+	4	751	c.427T>G	c.(427-429)Ttt>Gtt	p.F143V	SH3GLB1_ENST00000482504.1_Missense_Mutation_p.F143V|SH3GLB1_ENST00000535010.1_Missense_Mutation_p.F43V	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1	143	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)	p.F143V(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		AGCCTTAAATTTTCTTACTCC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	90	85					1																	87188306		2203	4298	6501	86960894	SO:0001583	missense	51100			AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	10833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 70"	609287	"SH3-domain, GRB2-like, endophilin B1"			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.427T>G	1.37:g.87188306T>G	ENSP00000473267:p.Phe143Val		86960894	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Missense_Mutation	SNP	ENST00000370558.4	37	CCDS710.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.535688	0.64972	.	.	ENSG00000097033	ENST00000212369;ENST00000535010;ENST00000482504	T;T	0.33865	1.39;1.39	5.73	5.73	0.89815	BAR (3);IRSp53/MIM homology domain (IMD) (1);	0.000000	0.85682	D	0.000000	T	0.38772	0.1053	M	0.82056	2.57	0.80722	D	1	B;B;B	0.24426	0.103;0.027;0.078	B;B;B	0.36766	0.038;0.031;0.232	T	0.43877	-0.9364	10	0.72032	D	0.01	0.1558	16.0181	0.80457	0.0:0.0:0.0:1.0	.	43;143;143	B4E182;Q9Y371-2;Q9Y371	.;.;SHLB1_HUMAN	V	143;43;143	ENSP00000441355:F43V;ENSP00000418744:F143V	ENSP00000212369:F143V	F	+	1	0	SH3GLB1	86960894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.915000	0.87484	2.195000	0.70347	0.528000	0.53228	TTT		0.313	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009		G	87188306	T	G	87188306	3	3	61	1	0	0	0	0	1	0	0	0	14290	1841	64	4	441	4	SH3GLB1	1	87188306	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	147239	87188306	162062315	407	8392										
PKN2	5586	broad.mit.edu	37	chr1	89237133	89237133	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgataagtcctcttgaacttCggatggaagaattaaggcat	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89237133C>T	ENST00000370521.3	+	5	1011	c.652C>T	c.(652-654)Cgg>Tgg	p.R218W	PKN2_ENST00000316005.7_Missense_Mutation_p.R218W|PKN2_ENST00000370513.5_Missense_Mutation_p.R218W|PKN2_ENST00000370505.3_Missense_Mutation_p.R61W	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	218					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.R218W(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TCTTGAACTTCGGATGGAAGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	72	74					1																	89237133		1811	4074	5885	89009721	SO:0001583	missense	5586			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.652C>T	1.37:g.89237133C>T	ENSP00000359552:p.Arg218Trp		89009721	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014519	0.75161	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.2	5.2	0.72013	.	0.000000	0.38492	U	0.001676	T	0.45377	0.1339	M	0.88241	2.94	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.992;0.957;0.971	T	0.53251	-0.8465	10	0.87932	D	0	.	13.9901	0.64359	0.1515:0.8485:0.0:0.0	.	218;218;218;218	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	W	218;218;61;218	ENSP00000359552:R218W;ENSP00000317851:R218W;ENSP00000359536:R61W;ENSP00000359544:R218W	ENSP00000317851:R218W	R	+	1	2	PKN2	89009721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.334000	0.59291	2.586000	0.87340	0.655000	0.94253	CGG		0.343	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		T	89237133	C	T	89237133	3	4	61	1	0	0	0	0	1	0	0	0	12011	875	31	1	670	1	PKN2	1	89237133	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2048827	89237133	160013488	408	8393										
PKN2	5586	broad.mit.edu	37	chr1	89237429	89237429	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattaaacgaagtccccaaGaatcatcccaaaagcaggat	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89237429G>T	ENST00000370521.3	+	6	1211	c.852G>T	c.(850-852)aaG>aaT	p.K284N	PKN2_ENST00000316005.7_Missense_Mutation_p.K284N|PKN2_ENST00000370513.5_Missense_Mutation_p.K284N|PKN2_ENST00000370505.3_Missense_Mutation_p.K127N	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	284					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.K284N(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AAGTCCCCAAGAATCATCCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	70	71					1																	89237429		1853	4094	5947	89010017	SO:0001583	missense	5586			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.852G>T	1.37:g.89237429G>T	ENSP00000359552:p.Lys284Asn		89010017	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.731|9.731	1.162398|1.162398	0.21538|0.21538	.|.	.|.	ENSG00000065243|ENSG00000065243	ENST00000436111|ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513	.|T;T;T;T	.|0.23348	.|1.91;1.91;1.91;2.39	5.05|5.05	2.77|2.77	0.32553|0.32553	.|.	.|0.141162	.|0.31472	.|U	.|0.007581	.|T	.|0.12178	.|0.0296	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|B;B;P;P	.|0.51147	.|0.048;0.023;0.638;0.942	.|B;B;P;P	.|0.49999	.|0.143;0.04;0.447;0.628	.|T	.|0.04115	.|-1.0976	.|10	.|0.49607	.|T	.|0.09	.|.	4.2636|4.2636	0.10752|0.10752	0.4846:0.0:0.5154:0.0|0.4846:0.0:0.5154:0.0	.|.	.|284;284;284;284	.|B4DTP5;E7ESL7;Q16513;B1AL79	.|.;.;PKN2_HUMAN;.	X|N	66|284;284;127;284	.|ENSP00000359552:K284N;ENSP00000317851:K284N;ENSP00000359536:K127N;ENSP00000359544:K284N	.|ENSP00000317851:K284N	E|K	+|+	1|3	0|2	PKN2|PKN2	89010017|89010017	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	1.208000|1.208000	0.32345|0.32345	1.267000|1.267000	0.44247|0.44247	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.368	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		T	89237429	G	T	89237429	3	4	61	1	0	0	0	0	1	0	0	0	12011	933	33	2	874	2	PKN2	1	89237429	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	296	89237429	160013192	409	8394										
RBMXL1	494115	broad.mit.edu	37	chr1	89448518	89448518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttgagtagagatcacttCggctgcttgagtaactgtct	10	8	2	3	rs549912567		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89448518C>T	ENST00000321792.5	-	2	1419	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	RBMXL1_ENST00000399794.2_Missense_Mutation_p.R331Q|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000370485.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	331	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R331Q(2)									GAGATCACTTCGGCTGCTTGA	0.517													.|||	1	0.000199681	0	0	5008	,	,		22019	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	1											189	189	189					1																	89448518		2203	4300	6503	89221106	SO:0001583	missense	56267			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"RNA binding motif (RRM) containing"	25073	protein-coding gene	gene with protein product	"kynurenine aminotransferase III"					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.992G>A	1.37:g.89448518C>T	ENSP00000318415:p.Arg331Gln		89221106		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206347	0.58343	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.80566	-1.39;-1.39	1.89	0.913	0.19354	.	0.000000	0.64402	D	0.000001	T	0.53965	0.1829	L	0.55834	1.745	0.29706	N	0.839769	D	0.59767	0.986	B	0.39904	0.313	T	0.51204	-0.8735	10	0.40728	T	0.16	-5.3669	5.8921	0.18919	0.0:0.812:0.0:0.188	.	331	Q96E39	RBMXL_HUMAN	Q	331	ENSP00000318415:R331Q;ENSP00000446099:R331Q	ENSP00000318415:R331Q	R	-	2	0	RBMXL1	89221106	1.000000	0.71417	0.797000	0.32132	0.928000	0.56348	4.995000	0.63908	0.132000	0.18615	0.306000	0.20318	CGA		0.517	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		T	89448518	C	T	89448518	3	4	61	1	0	0	0	0	1	0	0	0	13190	884	31	1	184	1	RBMXL1	1	89448518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211089	89448518	159802103	410	8395										
GBP3	2635	broad.mit.edu	37	chr1	89479939	89479939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaggattttgatcggattCgatgtgtcagctctgtcaca	12	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89479939C>T	ENST00000370481.4	-	5	672	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	199	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.R151Q(1)		breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		TGATCGGATTCGATGTGTCAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	108	114					1																	89479939		2203	4300	6503	89252527	SO:0001583	missense	2635			BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.452G>A	1.37:g.89479939C>T	ENSP00000359512:p.Arg151Gln		89252527	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457772	0.26161	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.61510	0.1	3.98	-0.347	0.12617	Guanylate-binding protein, N-terminal (1);	0.704752	0.13666	N	0.371246	T	0.27489	0.0675	M	0.67625	2.065	0.09310	N	1	P;P	0.48294	0.908;0.809	B;B	0.40864	0.232;0.342	T	0.15752	-1.0426	10	0.23891	T	0.37	.	4.4717	0.11715	0.3027:0.516:0.0:0.1813	.	17;151	F6X827;Q9H0R5	.;GBP3_HUMAN	Q	151	ENSP00000359512:R151Q	ENSP00000235878:R151Q	R	-	2	0	GBP3	89252527	0.000000	0.05858	0.005000	0.12908	0.107000	0.19398	-0.755000	0.04782	-0.151000	0.11176	-0.208000	0.12717	CGA		0.423	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		T	89479939	C	T	89479939	3	4	61	1	0	0	0	0	1	0	0	0	6295	884	31	1	1363	1	GBP3	1	89479939	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31421	89479939	159770682	411	8396										
GBP7	388646	broad.mit.edu	37	chr1	89598020	89598020	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaatttgttctttcagtcGattaatctcttcatttaacg	4	8	5	0	rs376019280		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89598020G>A	ENST00000294671.2	-	11	1867	c.1729C>T	c.(1729-1731)Cga>Tga	p.R577*		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	577						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R577*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TCTTTCAGTCGATTAATCTCT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	1						G	stop/ARG	0,4406		0,0,2203	108	106	107		1729	-1.7	0	1		107	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	GBP7	NM_207398.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		577/639	89598020	1,13005	2203	4300	6503	89370608	SO:0001587	stop_gained	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1729C>T	1.37:g.89598020G>A	ENSP00000294671:p.Arg577*		89370608		Nonsense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078796	0.76528	0.0	1.16E-4	ENSG00000213512	ENST00000294671	.	.	.	4.18	-1.74	0.08056	.	1.808830	0.02588	N	0.099602	.	.	.	.	.	.	0.51767	D	0.999938	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	0.7797	0.01038	0.3111:0.1746:0.3556:0.1587	.	.	.	.	X	577	.	ENSP00000294671:R577X	R	-	1	2	GBP7	89370608	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.043000	0.13971	-0.166000	0.10890	0.563000	0.77884	CGA		0.368	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		A	89598020	G	A	89598020	4	1	61	1	0	0	0	0	0	1	0	0	6299	1066	37	1	191	1	GBP7	1	89598020	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118081	89598020	159652601	412	8397										
GBP7	388646	broad.mit.edu	37	chr1	89630435	89630435	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttccatatcacccaggccCtccgtgtccagaaggatcag	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89630435C>A	ENST00000294671.2	-	3	435	c.297G>T	c.(295-297)gaG>gaT	p.E99D		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	99	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E99D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		CACCCAGGCCCTCCGTGTCCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	92	94					1																	89630435		2203	4300	6503	89403023	SO:0001583	missense	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.297G>T	1.37:g.89630435C>A	ENSP00000294671:p.Glu99Asp		89403023		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863290	0.51482	.	.	ENSG00000213512	ENST00000294671	T	0.64991	-0.13	3.62	-0.819	0.10829	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77685	0.4167	H	0.98818	4.34	0.33597	D	0.601817	D	0.89917	1.0	D	0.91635	0.999	T	0.70995	-0.4720	10	0.87932	D	0	.	4.4516	0.11623	0.158:0.5592:0.0:0.2828	.	99	Q8N8V2	GBP7_HUMAN	D	99	ENSP00000294671:E99D	ENSP00000294671:E99D	E	-	3	2	GBP7	89403023	0.983000	0.35010	0.349000	0.25694	0.667000	0.39255	0.053000	0.14184	-0.274000	0.09232	0.462000	0.41574	GAG		0.458	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		A	89630435	C	A	89630435	3	1	61	1	0	0	0	0	1	0	0	0	6299	680	24	2	1655	2	GBP7	1	89630435	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32415	89630435	159620186	413	8398										
GBP7	388646	broad.mit.edu	37	chr1	89637481	89637481	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggatttgcctgtgcggtaGaggcccacaattgccaccac	11	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89637481G>A	ENST00000294671.2	-	2	276	c.138C>T	c.(136-138)ctC>ctT	p.L46L		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	46	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L46L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		CTGTGCGGTAGAGGCCCACAA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											178	157	164					1																	89637481		2203	4300	6503	89410069	SO:0001819	synonymous_variant	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.138C>T	1.37:g.89637481G>A			89410069		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																				0.502	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		A	89637481	G	A	89637481	2	1	61	1	0	0	0	0	0	0	0	1	6299	929	33	3		3	GBP7	1	89637481	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7046	89637481	159613140	414	8399										
GBP4	115361	broad.mit.edu	37	chr1	89656988	89656988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcagggtcttggtctttGcatgggtgaagatataagaa	12	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89656988G>A	ENST00000355754.6	-	6	969	c.872C>T	c.(871-873)gCa>gTa	p.A291V		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	291	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A291V(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CTTGGTCTTTGCATGGGTGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											129	134	132					1																	89656988		2203	4300	6503	89429576	SO:0001583	missense	115361			AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.872C>T	1.37:g.89656988G>A	ENSP00000359490:p.Ala291Val		89429576	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	G	11.54	1.669371	0.29693	.	.	ENSG00000162654	ENST00000355754	T	0.76448	-1.02	5.18	2.06	0.26882	Guanylate-binding protein, N-terminal (1);	0.733388	0.12912	N	0.428842	T	0.71126	0.3303	M	0.76002	2.32	0.09310	N	1	P	0.39782	0.688	P	0.49708	0.62	T	0.63060	-0.6721	10	0.40728	T	0.16	.	8.1056	0.30883	0.0912:0.4627:0.4461:0.0	.	291	Q96PP9	GBP4_HUMAN	V	291	ENSP00000359490:A291V	ENSP00000359490:A291V	A	-	2	0	GBP4	89429576	0.005000	0.15991	0.007000	0.13788	0.056000	0.15407	1.377000	0.34317	0.344000	0.23847	0.655000	0.94253	GCA		0.418	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941		A	89656988	G	A	89656988	3	1	61	1	0	0	0	0	1	0	0	0	6296	1319	46	3	1074	3	GBP4	1	89656988	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19507	89656988	159593633	415	8400										
GBP5	115362	broad.mit.edu	37	chr1	89732233	89732233	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaacttctgtatacacaGacggggcaaattgaaatttt	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:89732233G>T	ENST00000370459.3	-	6	791	c.664C>A	c.(664-666)Ctg>Atg	p.L222M	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Missense_Mutation_p.L222M			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	222	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.L222M(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TGTATACACAGACGGGGCAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	108	107					1																	89732233		2203	4300	6503	89504821	SO:0001583	missense	115362			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.664C>A	1.37:g.89732233G>T	ENSP00000359488:p.Leu222Met		89504821	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	.	.	.	.	.	.	.	.	.	.	G	9.566	1.119728	0.20877	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.61859	0.07;0.07;0.07	4.45	2.52	0.30459	Guanylate-binding protein, N-terminal (1);	1.846230	0.02456	N	0.086051	T	0.43722	0.1260	M	0.69463	2.115	0.09310	N	1	P	0.44734	0.842	B	0.43990	0.438	T	0.26326	-1.0106	10	0.52906	T	0.07	-0.2797	6.9929	0.24765	0.0939:0.0:0.7173:0.1888	.	222	Q96PP8	GBP5_HUMAN	M	222	ENSP00000340396:L222M;ENSP00000359488:L222M;ENSP00000403010:L222M	ENSP00000340396:L222M	L	-	1	2	GBP5	89504821	0.000000	0.05858	0.113000	0.21522	0.002000	0.02628	0.278000	0.18753	0.775000	0.33450	0.549000	0.68633	CTG		0.343	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		T	89732233	G	T	89732233	3	4	61	1	0	0	0	0	1	0	0	0	6297	933	33	2	1120	2	GBP5	1	89732233	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75245	89732233	159518388	416	8401										
LRRC8C	84230	broad.mit.edu	37	chr1	90179732	90179732	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttccagaaatgtcaccCttgagtctctgcgggatctc	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90179732C>A	ENST00000370454.4	+	3	1858	c.1603C>A	c.(1603-1605)Ctt>Att	p.L535I	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	535					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L535I(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		AAATGTCACCCTTGAGTCTCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	78	78					1																	90179732		2203	4300	6503	89952320	SO:0001583	missense	84230				CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1603C>A	1.37:g.90179732C>A	ENSP00000359483:p.Leu535Ile		89952320	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.833758	0.32421	.	.	ENSG00000171488	ENST00000370454	T	0.27402	1.67	5.56	4.65	0.58169	.	0.057548	0.64402	D	0.000004	T	0.20981	0.0505	L	0.47078	1.49	0.49582	D	0.999808	D	0.58268	0.982	P	0.49451	0.611	T	0.01853	-1.1260	10	0.27082	T	0.32	.	12.4562	0.55706	0.0:0.8613:0.0:0.1387	.	535	Q8TDW0	LRC8C_HUMAN	I	535	ENSP00000359483:L535I	ENSP00000359483:L535I	L	+	1	0	LRRC8C	89952320	0.997000	0.39634	0.998000	0.56505	0.952000	0.60782	3.253000	0.51469	1.495000	0.48549	0.644000	0.83932	CTT		0.468	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		A	90179732	C	A	90179732	3	1	61	1	0	0	0	0	1	0	0	0	9052	681	24	2	1609	2	LRRC8C	1	90179732	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	447499	90179732	159070889	417	8402										
LRRC8D	55144	broad.mit.edu	37	chr1	90399282	90399282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttgtctgagacagcatgcGaagactcagaggaaaacaag	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90399282G>A	ENST00000337338.5	+	3	1062	c.655G>A	c.(655-657)Gaa>Aaa	p.E219K	LRRC8D_ENST00000394593.3_Missense_Mutation_p.E219K	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	219					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E219K(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		GACAGCATGCGAAGACTCAGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	60	60					1																	90399282		2203	4300	6503	90171870	SO:0001583	missense	55144			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.655G>A	1.37:g.90399282G>A	ENSP00000338887:p.Glu219Lys		90171870	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	37	CCDS726.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346078	0.82022	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000441269	T;T;T	0.53423	1.25;1.25;0.62	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.64605	0.2613	M	0.76170	2.325	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.61749	-0.6999	9	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	219	Q7L1W4	LRC8D_HUMAN	K	219	ENSP00000338887:E219K;ENSP00000378093:E219K;ENSP00000405784:E219K	.	E	+	1	0	LRRC8D	90171870	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	GAA		0.448	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90399282	G	A	90399282	3	1	61	1	0	0	0	0	1	0	0	0	9053	1059	37	1	657	1	LRRC8D	1	90399282	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219550	90399282	158851339	418	8403										
LRRC8D	55144	broad.mit.edu	37	chr1	90400781	90400781	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttctctaacaacaagctCgaatccttaccagtggcagt	6	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90400781C>T	ENST00000337338.5	+	3	2561	c.2154C>T	c.(2152-2154)ctC>ctT	p.L718L	LRRC8D_ENST00000394593.3_Silent_p.L718L	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	718					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L718L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		ACAACAAGCTCGAATCCTTAC	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	1											73	76	75					1																	90400781		2202	4300	6502	90173369	SO:0001819	synonymous_variant	55144			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.2154C>T	1.37:g.90400781C>T			90173369	D3DT29|Q6UWB2|Q9NVW3	Silent	SNP	ENST00000337338.5	37	CCDS726.1																																																																																				0.343	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		T	90400781	C	T	90400781	2	4	61	1	0	0	0	0	0	0	0	1	9053	871	31	1		1	LRRC8D	1	90400781	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1499	90400781	158849840	419	8404										
ZNF326	284695	broad.mit.edu	37	chr1	90484307	90484307	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagacaaataatcaaacaGaagtagttaaaataattgaa	5	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90484307G>T	ENST00000340281.4	+	9	1281	c.1138G>T	c.(1138-1140)Gaa>Taa	p.E380*	ZNF326_ENST00000455342.2_Nonsense_Mutation_p.E174*|ZNF326_ENST00000370447.3_Nonsense_Mutation_p.E291*	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	380					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.E380*(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		TAATCAAACAGAAGTAGTTAA	0.234																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											53	60	58					1																	90484307		2197	4285	6482	90256895	SO:0001587	stop_gained	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1138G>T	1.37:g.90484307G>T	ENSP00000340796:p.Glu380*		90256895	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Nonsense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	38	7.021920	0.98010	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	.	.	.	5.56	5.56	0.83823	.	0.196487	0.42172	D	0.000742	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-18.5963	19.1298	0.93400	0.0:0.0:1.0:0.0	.	.	.	.	X	380;380;291;174	.	ENSP00000340796:E380X	E	+	1	0	ZNF326	90256895	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.778000	0.75043	2.620000	0.88729	0.650000	0.86243	GAA		0.234	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90484307	G	T	90484307	4	4	61	1	0	0	0	0	0	1	0	0	17885	943	33	2	1176	2	ZNF326	1	90484307	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83526	90484307	158766314	420	8405										
ZNF326	284695	broad.mit.edu	37	chr1	90492980	90492980	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggagatgaggaggatgAagagaagattgatgaaccta	15	2	0	8			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90492980A>C	ENST00000340281.4	+	12	1612	c.1469A>C	c.(1468-1470)gAa>gCa	p.E490A	ZNF326_ENST00000455342.2_Missense_Mutation_p.E284A|ZNF326_ENST00000370447.3_Missense_Mutation_p.E401A	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	490	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.E490A(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		GAGGAGGATGAAGAGAAGATT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	110	109					1																	90492980		2203	4300	6503	90265568	SO:0001583	missense	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1469A>C	1.37:g.90492980A>C	ENSP00000340796:p.Glu490Ala		90265568	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.491638	0.44249	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.20069	2.1;2.1;2.1	5.54	5.54	0.83059	.	0.119302	0.56097	D	0.000040	T	0.09202	0.0227	L	0.47716	1.5	0.49582	D	0.999807	P;P	0.45348	0.856;0.682	B;B	0.41510	0.359;0.257	T	0.02950	-1.1090	10	0.06494	T	0.89	-6.6663	15.6544	0.77121	1.0:0.0:0.0:0.0	.	490;490	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	A	490;490;401;284	ENSP00000340796:E490A;ENSP00000359476:E401A;ENSP00000403470:E284A	ENSP00000340796:E490A	E	+	2	0	ZNF326	90265568	1.000000	0.71417	0.955000	0.39395	0.681000	0.39784	3.818000	0.55678	2.101000	0.63845	0.482000	0.46254	GAA		0.408	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		C	90492980	A	C	90492980	3	2	61	1	0	0	0	0	1	0	0	0	17885	246	9	4	1519	4	ZNF326	1	90492980	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8673	90492980	158757641	421	8406										
ZNF326	284695	broad.mit.edu	37	chr1	90493069	90493069	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagtagaggaagtggaaGaagtagaggaagtgagagaa	19	0	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90493069G>T	ENST00000340281.4	+	12	1701	c.1558G>T	c.(1558-1560)Gaa>Taa	p.E520*	ZNF326_ENST00000455342.2_Nonsense_Mutation_p.E314*|ZNF326_ENST00000370447.3_Nonsense_Mutation_p.E431*	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	520	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.E520*(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ggaagtggaagaagtagagga	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											72	66	68					1																	90493069		2203	4300	6503	90265657	SO:0001587	stop_gained	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1558G>T	1.37:g.90493069G>T	ENSP00000340796:p.Glu520*		90265657	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Nonsense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	32	5.156240	0.94686	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	.	.	.	4.68	4.68	0.58851	.	1.039550	0.07624	N	0.927539	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-0.4592	11.7591	0.51892	0.0:0.179:0.821:0.0	.	.	.	.	X	520;520;431;314	.	ENSP00000340796:E520X	E	+	1	0	ZNF326	90265657	0.678000	0.27586	0.467000	0.27180	0.338000	0.28826	5.435000	0.66532	2.532000	0.85374	0.491000	0.48974	GAA		0.488	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90493069	G	T	90493069	4	4	61	1	0	0	0	0	0	1	0	0	17885	943	33	2	1608	2	ZNF326	1	90493069	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89	90493069	158757552	422	8407										
ZNF326	284695	broad.mit.edu	37	chr1	90493206	90493206	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagaggaattagaggaagaGacagcaaaggaagaacctgc	14	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:90493206G>T	ENST00000340281.4	+	12	1838	c.1695G>T	c.(1693-1695)gaG>gaT	p.E565D	ZNF326_ENST00000455342.2_Missense_Mutation_p.E359D|ZNF326_ENST00000370447.3_Missense_Mutation_p.E476D	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	565	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)	p.E565D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		tagaggaagagACAGCAAAGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											51	55	54					1																	90493206		2203	4300	6503	90265794	SO:0001583	missense	284695			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1695G>T	1.37:g.90493206G>T	ENSP00000340796:p.Glu565Asp		90265794	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	11.53	1.666518	0.29604	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.49139	0.81;0.79;0.79	3.6	1.3	0.21679	.	0.468781	0.15700	N	0.248963	T	0.08313	0.0207	N	0.08118	0	0.09310	N	1	B;B	0.30511	0.282;0.282	B;B	0.26416	0.069;0.069	T	0.24368	-1.0162	10	0.33141	T	0.24	-7.3519	5.6507	0.17614	0.6051:0.0:0.3949:0.0	.	565;565	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	D	565;565;476;359	ENSP00000340796:E565D;ENSP00000359476:E476D;ENSP00000403470:E359D	ENSP00000340796:E565D	E	+	3	2	ZNF326	90265794	0.615000	0.27026	0.098000	0.21074	0.065000	0.16274	0.300000	0.19156	0.126000	0.18424	-0.381000	0.06696	GAG		0.433	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90493206	G	T	90493206	3	4	61	1	0	0	0	0	1	0	0	0	17885	933	33	2	1745	2	ZNF326	1	90493206	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137	90493206	158757415	423	8408										
ZNF644	84146	broad.mit.edu	37	chr1	91403183	91403183	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatagcagaattcctttCttctcccatccttttatttt	3	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91403183C>A	ENST00000370440.1	-	4	3764	c.3547G>T	c.(3547-3549)Gaa>Taa	p.E1183*	ZNF644_ENST00000337393.5_Nonsense_Mutation_p.E1183*|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	1183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E1183*(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GAATTCCTTTCTTCTCCCATC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											86	88	87					1																	91403183		2203	4299	6502	91175771	SO:0001587	stop_gained	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.3547G>T	1.37:g.91403183C>A	ENSP00000359469:p.Glu1183*		91175771	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Nonsense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	C	42	9.283028	0.99123	.	.	ENSG00000122482	ENST00000370440;ENST00000337393	.	.	.	6.06	6.06	0.98353	.	0.098492	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-20.3988	20.6208	0.99490	0.0:1.0:0.0:0.0	.	.	.	.	X	1183	.	ENSP00000337008:E1183X	E	-	1	0	ZNF644	91175771	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.115000	0.57865	2.882000	0.98803	0.655000	0.94253	GAA		0.358	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91403183	C	A	91403183	4	1	61	1	0	0	0	0	0	1	0	0	18099	922	32	2	448	2	ZNF644	1	91403183	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	909977	91403183	157847438	424	8409										
ZNF644	84146	broad.mit.edu	37	chr1	91404288	91404288	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcactataggtttcatcttCtatggcctgtgtagtgtagt	9	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91404288C>A	ENST00000370440.1	-	3	2840	c.2623G>T	c.(2623-2625)Gaa>Taa	p.E875*	ZNF644_ENST00000337393.5_Nonsense_Mutation_p.E875*|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	875					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E875*(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GTTTCATCTTCTATGGCCTGT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											93	95	94					1																	91404288		2203	4299	6502	91176876	SO:0001587	stop_gained	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2623G>T	1.37:g.91404288C>A	ENSP00000359469:p.Glu875*		91176876	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Nonsense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	C	38	7.037776	0.98021	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	.	.	.	5.45	5.45	0.79879	.	0.262839	0.37483	N	0.002066	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-3.4099	17.4563	0.87608	0.0:1.0:0.0:0.0	.	.	.	.	X	875;875;447	.	ENSP00000337008:E875X	E	-	1	0	ZNF644	91176876	0.999000	0.42202	0.995000	0.50966	0.770000	0.43624	3.422000	0.52749	2.554000	0.86153	0.591000	0.81541	GAA		0.358	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91404288	C	A	91404288	4	1	61	1	0	0	0	0	0	1	0	0	18099	922	32	2	1376	2	ZNF644	1	91404288	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1105	91404288	157846333	425	8410										
ZNF644	84146	broad.mit.edu	37	chr1	91404496	91404496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attactctctttacagctacAcgtctgtgatctttgaagct	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91404496A>G	ENST00000370440.1	-	3	2632	c.2415T>C	c.(2413-2415)cgT>cgC	p.R805R	ZNF644_ENST00000337393.5_Silent_p.R805R|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	805					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R805R(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TTACAGCTACACGTCTGTGAT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	1											69	73	72					1																	91404496		2203	4300	6503	91177084	SO:0001819	synonymous_variant	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2415T>C	1.37:g.91404496A>G			91177084	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																				0.383	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		G	91404496	A	G	91404496	2	3	61	1	0	0	0	0	0	0	0	1	18099	146	6	4		4	ZNF644	1	91404496	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	208	91404496	157846125	426	8411										
ZNF644	84146	broad.mit.edu	37	chr1	91405565	91405565	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgtccacattctctacaaGcatatggccttgggacatta	7	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91405565G>T	ENST00000370440.1	-	3	1563	c.1346C>A	c.(1345-1347)gCt>gAt	p.A449D	ZNF644_ENST00000337393.5_Missense_Mutation_p.A449D|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A449D(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TTCTCTACAAGCATATGGCCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											109	111	110					1																	91405565		2203	4299	6502	91178153	SO:0001583	missense	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.1346C>A	1.37:g.91405565G>T	ENSP00000359469:p.Ala449Asp		91178153	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163856	0.57476	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.78481	-1.18;-1.18	5.82	5.82	0.92795	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.107337	0.64402	D	0.000005	T	0.77758	0.4178	L	0.28740	0.885	0.54753	D	0.99998	D	0.76494	0.999	D	0.87578	0.998	T	0.71758	-0.4496	10	0.18276	T	0.48	-13.814	20.099	0.97865	0.0:0.0:1.0:0.0	.	449	Q9H582	ZN644_HUMAN	D	449;449;21	ENSP00000359469:A449D;ENSP00000337008:A449D	ENSP00000337008:A449D	A	-	2	0	ZNF644	91178153	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.375000	0.79646	2.752000	0.94435	0.655000	0.94253	GCT		0.403	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		T	91405565	G	T	91405565	3	4	61	1	0	0	0	0	1	0	0	0	18099	971	34	2	2653	2	ZNF644	1	91405565	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1069	91405565	157845056	427	8412										
HFM1	164045	broad.mit.edu	37	chr1	91731611	91731611	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaatttgctctttgactCttgaaggggtagcttacttc	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91731611C>A	ENST00000370425.3	-	36	4035	c.3937G>T	c.(3937-3939)Gag>Tag	p.E1313*	HFM1_ENST00000462405.1_Intron|HFM1_ENST00000370424.3_Nonsense_Mutation_p.E992*|HFM1_ENST00000294696.5_Intron	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1313					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.E1313*(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CTCTTTGACTCTTGAAGGGGT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											171	155	160					1																	91731611		1830	4077	5907	91504199	SO:0001587	stop_gained	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3937G>T	1.37:g.91731611C>A	ENSP00000359454:p.Glu1313*		91504199	B1B0B6|Q8N9Q0	Nonsense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	41|41	8.694240|8.694240	0.98918|0.98918	.|.	.|.	ENSG00000162669|ENSG00000162669	ENST00000370425;ENST00000370424|ENST00000430465	.|.	.|.	.|.	5.18|5.18	2.87|2.87	0.33458|0.33458	.|.	0.655088|.	0.14760|.	N|.	0.300045|.	.|T	.|0.38692	.|0.1050	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.33163	.|-0.9879	.|4	0.07990|.	T|.	0.79|.	.|.	5.2351|5.2351	0.15443|0.15443	0.0:0.6984:0.0:0.3016|0.0:0.6984:0.0:0.3016	.|.	.|.	.|.	.|.	X|N	1313;992|524	.|.	ENSP00000359453:E992X|.	E|K	-|-	1|3	0|2	HFM1|HFM1	91504199|91504199	0.992000|0.992000	0.36948|0.36948	0.970000|0.970000	0.41538|0.41538	0.923000|0.923000	0.55619|0.55619	0.474000|0.474000	0.22148|0.22148	1.289000|1.289000	0.44618|0.44618	0.655000|0.655000	0.94253|0.94253	GAG|AAG		0.368	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91731611	C	A	91731611	4	1	61	1	0	0	0	0	0	1	0	0	7104	922	32	2	386	2	HFM1	1	91731611	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	326046	91731611	157519010	428	8413										
HFM1	164045	broad.mit.edu	37	chr1	91784910	91784910	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttgtgtcaaagcaaaatCttgtatgggaatgcatccta	8	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91784910C>T	ENST00000370425.3	-	24	2718	c.2620G>A	c.(2620-2622)Gat>Aat	p.D874N	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.D553N|HFM1_ENST00000294696.5_Missense_Mutation_p.D106N	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	874	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.D874N(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAAGCAAAATCTTGTATGGGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											113	108	109					1																	91784910		2203	4300	6503	91557498	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2620G>A	1.37:g.91784910C>T	ENSP00000359454:p.Asp874Asn		91557498	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371964	0.82573	.	.	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.59906	0.23;0.23;0.23	5.0	5.0	0.66597	Sec63 domain (2);	0.052941	0.85682	D	0.000000	T	0.71341	0.3328	M	0.70787	2.145	0.58432	D	0.999994	D;D;D	0.89917	0.999;0.994;1.0	D;D;D	0.81914	0.974;0.954;0.995	T	0.73852	-0.3852	10	0.59425	D	0.04	.	18.6527	0.91437	0.0:1.0:0.0:0.0	.	553;129;874	A6NGI5;B1B0B5;A2PYH4	.;.;HFM1_HUMAN	N	874;106;553;558	ENSP00000359454:D874N;ENSP00000294696:D106N;ENSP00000359453:D553N	ENSP00000294696:D106N	D	-	1	0	HFM1	91557498	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.776000	0.85560	2.467000	0.83353	0.650000	0.86243	GAT		0.353	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		T	91784910	C	T	91784910	3	4	61	1	0	0	0	0	1	0	0	0	7104	913	32	3	1751	3	HFM1	1	91784910	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53299	91784910	157465711	429	8414										
HFM1	164045	broad.mit.edu	37	chr1	91844664	91844664	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctgaatctcaaatagatCatccattactgtatctccag	5	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91844664C>A	ENST00000370425.3	-	9	1212	c.1114G>T	c.(1114-1116)Gat>Tat	p.D372Y	HFM1_ENST00000370424.3_Missense_Mutation_p.D51Y|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	372	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.D372Y(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TCAAATAGATCATCCATTACT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	84	86					1																	91844664		2203	4299	6502	91617252	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1114G>T	1.37:g.91844664C>A	ENSP00000359454:p.Asp372Tyr		91617252	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534199	0.85812	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421;ENST00000541820	T;T	0.15487	2.42;2.42	5.42	5.42	0.78866	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.40640	U	0.001042	T	0.48003	0.1476	M	0.92268	3.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	T	0.61412	-0.7068	10	0.72032	D	0.01	.	19.2139	0.93768	0.0:1.0:0.0:0.0	.	51;372;372	A6NGI5;B7ZM16;A2PYH4	.;.;HFM1_HUMAN	Y	372;51;56;405	ENSP00000359454:D372Y;ENSP00000359453:D51Y	ENSP00000359450:D56Y	D	-	1	0	HFM1	91617252	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.487000	0.81328	2.534000	0.85438	0.563000	0.77884	GAT		0.308	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91844664	C	A	91844664	3	1	61	1	0	0	0	0	1	0	0	0	7104	826	29	2	3317	2	HFM1	1	91844664	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59754	91844664	157405957	430	8415										
HFM1	164045	broad.mit.edu	37	chr1	91866615	91866615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaaattttccaaagaaaAcaggcaatcatttgatttca	4	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91866615A>G	ENST00000370425.3	-	2	123	c.25T>C	c.(25-27)Ttt>Ctt	p.F9L	HFM1_ENST00000370424.3_5'UTR|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	9					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.F9L(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TCCAAAGAAAACAGGCAATCA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	1											38	41	40					1																	91866615		2201	4288	6489	91639203	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.25T>C	1.37:g.91866615A>G	ENSP00000359454:p.Phe9Leu		91639203	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	A	11.70	1.716884	0.30413	.	.	ENSG00000162669	ENST00000370425;ENST00000541820;ENST00000448819;ENST00000455133	T;T	0.61510	0.1;1.31	5.57	4.43	0.53597	.	.	.	.	.	T	0.17323	0.0416	N	0.12182	0.205	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.08617	-1.0713	9	0.15499	T	0.54	.	9.6835	0.40085	0.8248:0.1752:0.0:0.0	.	9;9	B7ZM16;A2PYH4	.;HFM1_HUMAN	L	9;42;9;9	ENSP00000359454:F9L;ENSP00000409827:F9L	ENSP00000359454:F9L	F	-	1	0	HFM1	91639203	0.985000	0.35326	0.349000	0.25694	0.586000	0.36452	2.976000	0.49289	0.926000	0.37118	0.454000	0.30748	TTT		0.259	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		G	91866615	A	G	91866615	3	3	61	1	0	0	0	0	1	0	0	0	7104	43	2	4	4434	4	HFM1	1	91866615	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	21951	91866615	157384006	431	8416										
CDC7	8317	broad.mit.edu	37	chr1	91977351	91977351	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttaggacattctgaattCtctttcctttcaagaagtac	6	8	3	2	rs375702482		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:91977351C>A	ENST00000428239.1	+	6	702	c.443C>A	c.(442-444)tCt>tAt	p.S148Y	CDC7_ENST00000234626.6_Missense_Mutation_p.S148Y|CDC7_ENST00000430031.2_Missense_Mutation_p.S120Y	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S148Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		ATTCTGAATTCTCTTTCCTTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	89	89					1																	91977351		2203	4297	6500	91749939	SO:0001583	missense	8317			AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.443C>A	1.37:g.91977351C>A	ENSP00000393139:p.Ser148Tyr		91749939	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	37	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696352	0.68386	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239;ENST00000426137	T;T;T;T	0.07021	3.23;3.23;3.23;3.23	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.168127	0.56097	D	0.000039	T	0.19046	0.0457	L	0.53780	1.695	0.48341	D	0.99963	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.982	T	0.00351	-1.1796	10	0.45353	T	0.12	-3.8645	20.0114	0.97452	0.0:1.0:0.0:0.0	.	120;148	B7Z5H7;O00311	.;CDC7_HUMAN	Y	120;148;148;148	ENSP00000407477:S120Y;ENSP00000234626:S148Y;ENSP00000393139:S148Y;ENSP00000398077:S148Y	ENSP00000234626:S148Y	S	+	2	0	CDC7	91749939	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.343000	0.44001	2.732000	0.93576	0.591000	0.81541	TCT		0.303	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		A	91977351	C	A	91977351	3	1	61	1	0	0	0	0	1	0	0	0	3090	913	32	2	461	2	CDC7	1	91977351	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110736	91977351	157273270	432	8417										
TGFBR3	7049	broad.mit.edu	37	chr1	92187527	92187527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaccattattttcaagccGaagatgaaatctattagcca	5	9	2	2	rs41305630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:92187527G>A	ENST00000525962.1	-	7	1121	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	TGFBR3_ENST00000212355.4_Missense_Mutation_p.R354W|TGFBR3_ENST00000370399.2_Missense_Mutation_p.R354W			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	354					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R354W(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		TTTTCAAGCCGAAGATGAAAT	0.383													G|||	1	0.000199681	0	0	5008	,	,		15727	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	81	74	77		1060,1060,1060	0.9	1	1	dbSNP_127	77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	354/851,354/851,354/852	92187527	1,13005	2203	4300	6503	91960115	SO:0001583	missense	7049			L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"Proteoglycans / Cell surface : Other"	11774	protein-coding gene	gene with protein product	"betaglycan proteoglycan"	600742	"transforming growth factor, beta receptor III (betaglycan, 300kDa)"			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.1060C>T	1.37:g.92187527G>A	ENSP00000436127:p.Arg354Trp		91960115	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	12.97	2.097325	0.37048	0.0	1.16E-4	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.33654	1.41;1.4;1.41;1.4	5.25	0.865	0.19074	.	0.556557	0.19317	N	0.117232	T	0.12050	0.0293	L	0.31926	0.97	0.42463	D	0.992799	B;B;B	0.25521	0.035;0.038;0.128	B;B;B	0.19666	0.017;0.023;0.026	T	0.08597	-1.0714	10	0.56958	D	0.05	-8.9521	8.866	0.35286	0.0702:0.0:0.4494:0.4804	rs41305630	354;354;354	A8K5N0;Q03167-2;Q03167	.;.;TGBR3_HUMAN	W	354	ENSP00000212355:R354W;ENSP00000359426:R354W;ENSP00000436127:R354W;ENSP00000432638:R354W	ENSP00000212355:R354W	R	-	1	2	TGFBR3	91960115	0.141000	0.22595	0.999000	0.59377	0.914000	0.54420	1.694000	0.37752	0.671000	0.31185	0.561000	0.74099	CGG		0.383	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		A	92187527	G	A	92187527	3	1	61	1	0	0	0	0	1	0	0	0	15862	1057	37	1	1535	1	TGFBR3	1	92187527	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210176	92187527	157063094	433	8418										
TGFBR3	7049	broad.mit.edu	37	chr1	92193247	92193247	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttcccttaacatcaaaaGatttgatcacccagttgaca	6	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:92193247G>T	ENST00000525962.1	-	6	915	c.854C>A	c.(853-855)tCt>tAt	p.S285Y	TGFBR3_ENST00000212355.4_Missense_Mutation_p.S285Y|TGFBR3_ENST00000468996.2_5'Flank|TGFBR3_ENST00000370399.2_Missense_Mutation_p.S285Y			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	285					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.S285Y(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		AACATCAAAAGATTTGATCAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	89	91					1																	92193247		2203	4300	6503	91965835	SO:0001583	missense	7049			L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"Proteoglycans / Cell surface : Other"	11774	protein-coding gene	gene with protein product	"betaglycan proteoglycan"	600742	"transforming growth factor, beta receptor III (betaglycan, 300kDa)"			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.854C>A	1.37:g.92193247G>T	ENSP00000436127:p.Ser285Tyr		91965835	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.718200	0.89205	.	.	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	6.16	6.16	0.99307	.	0.205159	0.52532	D	0.000063	T	0.55162	0.1903	M	0.62723	1.935	0.54753	D	0.999987	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.75484	0.931;0.986;0.931	T	0.53387	-0.8446	10	0.87932	D	0	-23.5204	20.8598	0.99761	0.0:0.0:1.0:0.0	.	285;285;285	A8K5N0;Q03167-2;Q03167	.;.;TGBR3_HUMAN	Y	285	ENSP00000212355:S285Y;ENSP00000359426:S285Y;ENSP00000436127:S285Y;ENSP00000432638:S285Y	ENSP00000212355:S285Y	S	-	2	0	TGFBR3	91965835	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.135000	0.64777	2.937000	0.99478	0.650000	0.86243	TCT		0.333	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		T	92193247	G	T	92193247	3	4	61	1	0	0	0	0	1	0	0	0	15862	942	33	2	1745	2	TGFBR3	1	92193247	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5720	92193247	157057374	434	8419										
TGFBR3	7049	broad.mit.edu	37	chr1	92195415	92195415	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgtgtacttcctcattCtggggctggctggacatcac	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:92195415C>A	ENST00000525962.1	-	5	745	c.684G>T	c.(682-684)caG>caT	p.Q228H	TGFBR3_ENST00000212355.4_Missense_Mutation_p.Q228H|TGFBR3_ENST00000468996.2_5'UTR|TGFBR3_ENST00000370399.2_Missense_Mutation_p.Q228H			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	228					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.Q228H(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CTTCCTCATTCTGGGGCTGGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											228	197	208					1																	92195415		2203	4300	6503	91968003	SO:0001583	missense	7049			L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"Proteoglycans / Cell surface : Other"	11774	protein-coding gene	gene with protein product	"betaglycan proteoglycan"	600742	"transforming growth factor, beta receptor III (betaglycan, 300kDa)"			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.684G>T	1.37:g.92195415C>A	ENSP00000436127:p.Gln228His		91968003	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	.	.	.	.	.	.	.	.	.	.	C	8.089	0.774135	0.16051	.	.	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.77	1.35	0.21983	.	0.475066	0.26673	N	0.023086	T	0.03520	0.0101	N	0.12746	0.255	0.19300	N	0.999975	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.001	T	0.42565	-0.9444	10	0.11485	T	0.65	-1.191	3.9104	0.09201	0.1118:0.476:0.2438:0.1685	.	228;228;228	A8K5N0;Q03167-2;Q03167	.;.;TGBR3_HUMAN	H	228	ENSP00000212355:Q228H;ENSP00000359426:Q228H;ENSP00000436127:Q228H;ENSP00000432638:Q228H	ENSP00000212355:Q228H	Q	-	3	2	TGFBR3	91968003	0.991000	0.36638	0.582000	0.28627	0.862000	0.49288	0.436000	0.21526	0.342000	0.23796	0.591000	0.81541	CAG		0.458	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		A	92195415	C	A	92195415	3	1	61	1	0	0	0	0	1	0	0	0	15862	912	32	2	1919	2	TGFBR3	1	92195415	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2168	92195415	157055206	435	8420										
BRDT	676	broad.mit.edu	37	chr1	92433778	92433778	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattatctcagatgccacaaGaagagcaagttgtgggtgtt	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:92433778G>T	ENST00000362005.3	+	5	824	c.406G>T	c.(406-408)Gaa>Taa	p.E136*	BRDT_ENST00000370389.2_Nonsense_Mutation_p.E63*|BRDT_ENST00000394530.3_Nonsense_Mutation_p.E90*|BRDT_ENST00000399546.2_Nonsense_Mutation_p.E136*|BRDT_ENST00000402388.1_Nonsense_Mutation_p.E136*	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	136					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)	p.E136*(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		GATGCCACAAGAAGAGCAAGT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											108	111	110					1																	92433778		2203	4300	6503	92206366	SO:0001587	stop_gained	676			AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.406G>T	1.37:g.92433778G>T	ENSP00000354568:p.Glu136*		92206366	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Nonsense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971566	0.92919	.	.	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000423434;ENST00000394530;ENST00000440509;ENST00000427104;ENST00000448194;ENST00000426141;ENST00000552654;ENST00000402388	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.4142	19.7538	0.96281	0.0:0.0:1.0:0.0	.	.	.	.	X	136;63;136;136;136;90;136;136;136;136;63;136	.	ENSP00000354568:E136X	E	+	1	0	BRDT	92206366	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.853000	0.86934	2.690000	0.91761	0.655000	0.94253	GAA		0.373	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		T	92433778	G	T	92433778	4	4	61	1	0	0	0	0	0	1	0	0	1511	943	33	2	416	2	BRDT	1	92433778	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	238363	92433778	156816843	436	8421										
GLMN	11146	broad.mit.edu	37	chr1	92757021	92757021	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaacttttcttttactaTcctctttatctttacacaaa	0	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:92757021T>C	ENST00000370360.3	-	4	320	c.239A>G	c.(238-240)gAt>gGt	p.D80G	GLMN_ENST00000534881.1_Missense_Mutation_p.D80G	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	80					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)	p.D80G(1)		endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		TCTTTTACTATCCTCTTTATC	0.313									Multiple Glomus Tumors (of the Skin), Familial																																							1	Substitution - Missense(1)	large_intestine(1)	1											77	75	76					1																	92757021		2203	4300	6503	92529609	SO:0001583	missense	11146	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.239A>G	1.37:g.92757021T>C	ENSP00000359385:p.Asp80Gly		92529609	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	37	CCDS738.1	.	.	.	.	.	.	.	.	.	.	T	6.664	0.491065	0.12702	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.47528	0.84;0.84	5.86	3.29	0.37713	.	0.281551	0.44285	N	0.000470	T	0.21267	0.0512	L	0.42245	1.32	0.36050	D	0.840713	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.09751	-1.0660	10	0.62326	D	0.03	-0.6685	8.0846	0.30765	0.1286:0.0712:0.0:0.8003	.	80;80	B4DJ85;Q92990	.;GLMN_HUMAN	G	80	ENSP00000359385:D80G;ENSP00000440156:D80G	ENSP00000359385:D80G	D	-	2	0	GLMN	92529609	0.997000	0.39634	0.768000	0.31515	0.012000	0.07955	2.097000	0.41748	1.034000	0.39945	0.482000	0.46254	GAT		0.313	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		C	92757021	T	C	92757021	3	2	61	1	0	0	0	0	1	0	0	0	6468	1435	50	4	1609	4	GLMN	1	92757021	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	323243	92757021	156493600	437	8422										
EVI5	7813	broad.mit.edu	37	chr1	93159368	93159368	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatacttactttttcattTtttttgaattgtatttgact	3	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93159368T>G	ENST00000370331.1	-	9	1229	c.1220A>C	c.(1219-1221)aAa>aCa	p.K407T	EVI5_ENST00000540033.1_Missense_Mutation_p.K407T|EVI5_ENST00000543509.1_Missense_Mutation_p.K407T	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	407	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.K407T(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		CTTTTTCATTTTTTTTGAATT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	85	83					1																	93159368		2202	4296	6498	92931956	SO:0001583	missense	7813			AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1220A>C	1.37:g.93159368T>G	ENSP00000359356:p.Lys407Thr		92931956	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	37	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.236433	0.79800	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509;ENST00000338689	T;T;T	0.06371	3.36;3.36;3.31	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.17874	0.0429	M	0.82193	2.58	0.58432	D	0.999998	D;D	0.69078	0.997;0.996	D;D	0.69142	0.962;0.917	T	0.01363	-1.1374	10	0.41790	T	0.15	-26.0631	15.5716	0.76341	0.0:0.0:0.0:1.0	.	407;407	F5H4R0;O60447	.;EVI5_HUMAN	T	407;407;407;46	ENSP00000359356:K407T;ENSP00000440826:K407T;ENSP00000445019:K407T	ENSP00000345500:K46T	K	-	2	0	EVI5	92931956	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.289000	0.72696	2.072000	0.62099	0.460000	0.39030	AAA		0.318	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		G	93159368	T	G	93159368	3	3	61	1	0	0	0	0	1	0	0	0	5302	1841	64	4	1252	4	EVI5	1	93159368	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	402347	93159368	156091253	438	8423										
RPL5	6125	broad.mit.edu	37	chr1	93306176	93306176	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctatgaaaagaagcccaaGaaagaagttaaaaagaagag	10	4	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93306176G>T	ENST00000370321.3	+	7	864	c.774G>T	c.(772-774)aaG>aaT	p.K258N	SNORA66_ENST00000515986.1_RNA|SNORA66_ENST00000384792.1_RNA	NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	258					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.K258N(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		AGAAGCCCAAGAAAGAAGTTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											85	90	88					1																	93306176		2203	4300	6503	93078764	SO:0001583	missense	6125			U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"L ribosomal proteins"	10360	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 135"	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.774G>T	1.37:g.93306176G>T	ENSP00000359345:p.Lys258Asn		93078764	Q32LZ3|Q53HH6|Q9H3F4	Missense_Mutation	SNP	ENST00000370321.3	37	CCDS741.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297141	0.60086	.	.	ENSG00000122406	ENST00000432788;ENST00000370321	T	0.48836	0.8	5.36	4.45	0.53987	.	0.114107	0.64402	D	0.000016	T	0.60170	0.2248	H	0.94264	3.515	0.80722	D	1	B;B	0.33694	0.421;0.421	P;P	0.44772	0.46;0.46	T	0.69975	-0.4999	10	0.72032	D	0.01	.	14.4608	0.67448	0.0712:0.0:0.9288:0.0	.	258;258	A2RUM7;P46777	.;RL5_HUMAN	N	208;258	ENSP00000359345:K258N	ENSP00000359345:K258N	K	+	3	2	RPL5	93078764	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.134000	0.50538	1.387000	0.46486	0.655000	0.94253	AAG		0.398	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969		T	93306176	G	T	93306176	3	4	61	1	0	0	0	0	1	0	0	0	13634	933	33	2	800	2	RPL5	1	93306176	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146808	93306176	155944445	439	8424										
FAM69A	388650	broad.mit.edu	37	chr1	93312748	93312748	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtatgcttaccttaaagaGactatagaccatttctttaa	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93312748G>T	ENST00000370310.4	-	4	536	c.466C>A	c.(466-468)Ctc>Atc	p.L156I	SNORA51_ENST00000384295.1_RNA	NM_001006605.4|NM_001252269.1|NM_001252271.1	NP_001006606.2|NP_001239198.1|NP_001239200.1	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	156						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.L156I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		ACCTTAAAGAGACTATAGACC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	54	55					1																	93312748		1855	4087	5942	93085336	SO:0001583	missense	388650			AK027146	CCDS44173.1, CCDS72822.1, CCDS72823.1, CCDS72824.1, CCDS72825.1	1p22	2014-06-25			ENSG00000154511	ENSG00000154511			32213	protein-coding gene	gene with protein product		614542				21334309	Standard	NM_001006605		Approved	FLJ23493	uc001dpg.3	Q5T7M9	OTTHUMG00000010894	ENST00000370310.4:c.466C>A	1.37:g.93312748G>T	ENSP00000359333:p.Leu156Ile		93085336	Q6IRV2	Missense_Mutation	SNP	ENST00000370310.4	37	CCDS44173.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865674	0.51588	.	.	ENSG00000154511	ENST00000370310;ENST00000401027	T	0.46451	0.87	5.7	5.7	0.88788	.	0.117488	0.56097	D	0.000021	T	0.19406	0.0466	L	0.36672	1.1	0.41095	D	0.985623	B;B;B	0.28933	0.099;0.164;0.228	B;B;B	0.27796	0.027;0.027;0.083	T	0.03818	-1.1001	10	0.22706	T	0.39	-7.6758	14.0602	0.64795	0.0739:0.0:0.9261:0.0	.	149;156;156	B4E174;Q5T7M9;Q5T7M9-2	.;FA69A_HUMAN;.	I	156	ENSP00000359333:L156I	ENSP00000359333:L156I	L	-	1	0	FAM69A	93085336	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.199000	0.65152	2.711000	0.92665	0.561000	0.74099	CTC		0.358	FAM69A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030046.2	NM_001006605		T	93312748	G	T	93312748	3	4	61	1	0	0	0	0	1	0	0	0	5621	942	33	2	828	2	FAM69A	1	93312748	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6572	93312748	155937873	440	8425										
MTF2	22823	broad.mit.edu	37	chr1	93575840	93575840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcggtctcctttacgtcGaaaccaaaagaccccaacat	6	14	1	1	rs189234488		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93575840G>A	ENST00000370298.4	+	2	348	c.59G>A	c.(58-60)cGa>cAa	p.R20Q	MTF2_ENST00000545708.1_Intron|MTF2_ENST00000540243.1_Intron|MTF2_ENST00000471953.1_3'UTR|MTF2_ENST00000370303.4_Missense_Mutation_p.R20Q	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2	20					chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.R20Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		CCTTTACGTCGAAACCAAAAG	0.433													G|||	1	0.000199681	0	0.0014	5008	,	,		16529	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											120	118	119					1																	93575840		2203	4300	6503	93348428	SO:0001583	missense	22823			AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.59G>A	1.37:g.93575840G>A	ENSP00000359321:p.Arg20Gln		93348428	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Missense_Mutation	SNP	ENST00000370298.4	37	CCDS742.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	14.47	2.544277	0.45280	.	.	ENSG00000143033	ENST00000370298;ENST00000370303	T;T	0.24538	1.86;1.85	5.44	5.44	0.79542	.	0.340379	0.31963	N	0.006797	T	0.06962	0.0177	N	0.13043	0.29	0.80722	D	1	P;P	0.40107	0.499;0.703	B;B	0.23716	0.048;0.044	T	0.13980	-1.0489	10	0.28530	T	0.3	-1.9025	19.2694	0.94003	0.0:0.0:1.0:0.0	.	20;20	B1AKT6;Q9Y483	.;MTF2_HUMAN	Q	20	ENSP00000359321:R20Q;ENSP00000359326:R20Q	ENSP00000359321:R20Q	R	+	2	0	MTF2	93348428	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.932000	0.75869	2.563000	0.86464	0.557000	0.71058	CGA		0.433	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358		A	93575840	G	A	93575840	3	1	61	1	0	0	0	0	1	0	0	0	9953	1058	37	1	65	1	MTF2	1	93575840	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	263092	93575840	155674781	441	8426										
MTF2	22823	broad.mit.edu	37	chr1	93594851	93594851	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggtttatgtctgggaaaGaaataaagaagaagaagcat	11	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93594851G>T	ENST00000370298.4	+	11	1295	c.1006G>T	c.(1006-1008)Gaa>Taa	p.E336*	MTF2_ENST00000545708.1_Nonsense_Mutation_p.E234*|MTF2_ENST00000540243.1_Nonsense_Mutation_p.E234*|MTF2_ENST00000471953.1_3'UTR|MTF2_ENST00000370303.4_Intron	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2	336					chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.E336*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		GTCTGGGAAAGAAATAAAGAA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											65	68	67					1																	93594851		2203	4300	6503	93367439	SO:0001587	stop_gained	22823			AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.1006G>T	1.37:g.93594851G>T	ENSP00000359321:p.Glu336*		93367439	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Nonsense_Mutation	SNP	ENST00000370298.4	37	CCDS742.1	.	.	.	.	.	.	.	.	.	.	G	40	8.293903	0.98747	.	.	ENSG00000143033	ENST00000545708;ENST00000540243;ENST00000370298;ENST00000537953	.	.	.	5.55	5.55	0.83447	.	0.095807	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-10.5793	19.8683	0.96840	0.0:0.0:1.0:0.0	.	.	.	.	X	234;234;336;234	.	ENSP00000359321:E336X	E	+	1	0	MTF2	93367439	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.724000	0.91462	2.753000	0.94483	0.655000	0.94253	GAA		0.328	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358		T	93594851	G	T	93594851	4	4	61	1	0	0	0	0	0	1	0	0	9953	943	33	2	1048	2	MTF2	1	93594851	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19011	93594851	155655770	442	8427										
MTF2	22823	broad.mit.edu	37	chr1	93599333	93599333	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctggcccatatacaagaAaaatgattcaaaaaactgct	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93599333A>C	ENST00000370298.4	+	12	1523	c.1234A>C	c.(1234-1236)Aaa>Caa	p.K412Q	MTF2_ENST00000545708.1_Missense_Mutation_p.K310Q|MTF2_ENST00000540243.1_Missense_Mutation_p.K310Q|MTF2_ENST00000471953.1_3'UTR|MTF2_ENST00000370303.4_Missense_Mutation_p.K355Q	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2	412					chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.K412Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		ATATACAAGAAAAATGATTCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	93	92					1																	93599333		2203	4300	6503	93371921	SO:0001583	missense	22823			AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.1234A>C	1.37:g.93599333A>C	ENSP00000359321:p.Lys412Gln		93371921	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Missense_Mutation	SNP	ENST00000370298.4	37	CCDS742.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.589194	0.28357	.	.	ENSG00000143033	ENST00000545708;ENST00000540243;ENST00000370298;ENST00000370303	T;T;T;T	0.31769	1.48;1.48;1.89;1.89	5.1	5.1	0.69264	.	0.159187	0.56097	D	0.000037	T	0.08758	0.0217	N	0.24115	0.695	0.47065	D	0.999303	P;B;P	0.42735	0.675;0.329;0.788	B;B;B	0.30401	0.099;0.085;0.115	T	0.09552	-1.0669	10	0.24483	T	0.36	-8.914	15.19	0.73035	1.0:0.0:0.0:0.0	.	355;412;310	B1AKT6;Q9Y483;B4DZG1	.;MTF2_HUMAN;.	Q	310;310;412;355	ENSP00000444962:K310Q;ENSP00000443295:K310Q;ENSP00000359321:K412Q;ENSP00000359326:K355Q	ENSP00000359321:K412Q	K	+	1	0	MTF2	93371921	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.797000	0.55514	2.045000	0.60652	0.533000	0.62120	AAA		0.353	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358		C	93599333	A	C	93599333	3	2	61	1	0	0	0	0	1	0	0	0	9953	15	1	4	1280	4	MTF2	1	93599333	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4482	93599333	155651288	443	8428										
TMED5	50999	broad.mit.edu	37	chr1	93621874	93621874	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaggatgtcttccagttTcatatccaatatatctgtgc	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93621874T>C	ENST00000370282.3	-	3	939	c.454A>G	c.(454-456)Aaa>Gaa	p.K152E	TMED5_ENST00000483033.1_5'UTR|TMED5_ENST00000479918.1_Missense_Mutation_p.K152E|TMED5_ENST00000370280.1_Missense_Mutation_p.K152E	NM_016040.4	NP_057124.3	Q9Y3A6	TMED5_HUMAN	transmembrane emp24 protein transport domain containing 5	152					Golgi ribbon formation (GO:0090161)|protein transport (GO:0015031)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K152E(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)		TCTTCCAGTTTCATATCCAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											156	146	149					1																	93621874		2203	4300	6503	93394462	SO:0001583	missense	50999			BC070051	CCDS743.1, CCDS53342.1	1p22.1	2013-09-19			ENSG00000117500	ENSG00000117500			24251	protein-coding gene	gene with protein product						10810093	Standard	NM_016040		Approved	CGI-100	uc001dpn.3	Q9Y3A6	OTTHUMG00000010162	ENST00000370282.3:c.454A>G	1.37:g.93621874T>C	ENSP00000359305:p.Lys152Glu		93394462	B1AKT4|B2R703|D3DT38|Q96AX8	Missense_Mutation	SNP	ENST00000370282.3	37	CCDS743.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.756750	0.89843	.	.	ENSG00000117500	ENST00000370282;ENST00000479918;ENST00000535517;ENST00000370280	T;T;T	0.54279	2.21;2.45;0.58	5.57	4.43	0.53597	GOLD (1);	0.000000	0.85682	D	0.000000	T	0.66694	0.2815	M	0.85710	2.77	0.80722	D	1	D;D	0.89917	1.0;0.967	D;P	0.91635	0.999;0.897	T	0.73477	-0.3970	10	0.87932	D	0	-12.3834	11.9132	0.52751	0.1306:0.0:0.0:0.8694	.	152;152	B1AKT4;Q9Y3A6	.;TMED5_HUMAN	E	152;152;101;152	ENSP00000359305:K152E;ENSP00000418992:K152E;ENSP00000359303:K152E	ENSP00000359303:K152E	K	-	1	0	TMED5	93394462	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	0.918000	0.36919	0.528000	0.53228	AAA		0.333	TMED5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028076.3	NM_016040		C	93621874	T	C	93621874	3	2	61	1	0	0	0	0	1	0	0	0	16046	1792	62	4	296	4	TMED5	1	93621874	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22541	93621874	155628747	444	8429										
CCDC18	343099	broad.mit.edu	37	chr1	93683309	93683309	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaggaaaagaatgaaaaGataaggagtctagaaaccaa	9	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:93683309G>T	ENST00000343253.7	+	14	2344	c.1842G>T	c.(1840-1842)aaG>aaT	p.K614N	CCDC18_ENST00000401026.3_Missense_Mutation_p.K615N|CCDC18_ENST00000557479.1_Missense_Mutation_p.K733N|CCDC18_ENST00000338949.4_Intron|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	614								p.K733N(2)		breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AGAATGAAAAGATAAGGAGTC	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	1											49	47	48					1																	93683309		1814	4076	5890	93455897	SO:0001583	missense	343099					1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1842G>T	1.37:g.93683309G>T	ENSP00000343377:p.Lys614Asn		93455897	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.94|15.94	2.980881|2.980881	0.53827|0.53827	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479|ENST00000370276	T;T;T|.	0.14766|.	2.48;2.48;2.48|.	4.97|4.97	0.86|0.86	0.19042|0.19042	.|.	0.261970|.	0.35013|.	N|.	0.003507|.	T|T	0.36082|0.36082	0.0954|0.0954	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	B|.	0.16802|.	0.019|.	B|.	0.14023|.	0.01|.	T|T	0.21930|0.21930	-1.0231|-1.0231	10|5	0.33940|.	T|.	0.23|.	.|.	4.6191|4.6191	0.12440|0.12440	0.3393:0.2851:0.3756:0.0|0.3393:0.2851:0.3756:0.0	.|.	733|.	G3V388|.	.|.	N|I	614;615;733|668	ENSP00000343377:K614N;ENSP00000383808:K615N;ENSP00000451099:K733N|.	ENSP00000343377:K614N|.	K|R	+|+	3|2	2|0	CCDC18|CCDC18	93455897|93455897	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.986000|0.986000	0.74619|0.74619	0.730000|0.730000	0.26043|0.26043	-0.026000|-0.026000	0.13895|0.13895	-0.165000|-0.165000	0.13383|0.13383	AAG|AGA		0.353	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		T	93683309	G	T	93683309	3	4	61	1	0	0	0	0	1	0	0	0	2800	933	33	2	2253	2	CCDC18	1	93683309	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61435	93683309	155567312	445	8430										
DNTTIP2	30836	broad.mit.edu	37	chr1	94343039	94343039	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaggaagcacaattctaGaaatacctgaaacatgagat	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94343039G>T	ENST00000436063.2	-	2	509	c.452C>A	c.(451-453)tCt>tAt	p.S151Y	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S151Y(1)		NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CACAATTCTAGAAATACCTGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	98	101					1																	94343039		1840	4091	5931	94115627	SO:0001583	missense	30836			AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.452C>A	1.37:g.94343039G>T	ENSP00000411010:p.Ser151Tyr		94115627	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949530	0.73787	.	.	ENSG00000067334	ENST00000436063;ENST00000528680	T	0.41758	0.99	5.23	5.23	0.72850	.	0.103731	0.43579	D	0.000557	T	0.57844	0.2081	M	0.71581	2.175	0.36108	D	0.844627	D	0.89917	1.0	D	0.73380	0.98	T	0.62774	-0.6783	10	0.87932	D	0	.	17.2351	0.86996	0.0:0.0:1.0:0.0	.	151	Q5QJE6	TDIF2_HUMAN	Y	151;158	ENSP00000411010:S151Y	ENSP00000352137:S151Y	S	-	2	0	DNTTIP2	94115627	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.179000	0.71974	2.736000	0.93811	0.644000	0.83932	TCT		0.398	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		T	94343039	G	T	94343039	3	4	61	1	0	0	0	0	1	0	0	0	4693	942	33	2	1842	2	DNTTIP2	1	94343039	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	659730	94343039	154907582	446	8431										
DNTTIP2	30836	broad.mit.edu	37	chr1	94343207	94343207	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcatggtgctcagacacaGaataatttgactctgcctca	7	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94343207G>T	ENST00000436063.2	-	2	341	c.284C>A	c.(283-285)tCt>tAt	p.S95Y	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	95					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S95Y(1)		NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTCAGACACAGAATAATTTGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	92	94					1																	94343207		1917	4124	6041	94115795	SO:0001583	missense	30836			AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.284C>A	1.37:g.94343207G>T	ENSP00000411010:p.Ser95Tyr		94115795	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.387166	0.61956	.	.	ENSG00000067334	ENST00000436063;ENST00000528680	T	0.36157	1.27	4.91	3.99	0.46301	.	0.112747	0.40385	N	0.001111	T	0.43122	0.1233	M	0.71581	2.175	0.25334	N	0.989003	D	0.71674	0.998	D	0.62955	0.909	T	0.37384	-0.9708	10	0.87932	D	0	.	13.5507	0.61730	0.0:0.1743:0.8257:0.0	.	95	Q5QJE6	TDIF2_HUMAN	Y	95;102	ENSP00000411010:S95Y	ENSP00000352137:S95Y	S	-	2	0	DNTTIP2	94115795	1.000000	0.71417	0.981000	0.43875	0.888000	0.51559	4.479000	0.60236	1.267000	0.44247	0.644000	0.83932	TCT		0.453	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		T	94343207	G	T	94343207	3	4	61	1	0	0	0	0	1	0	0	0	4693	942	33	2	2010	2	DNTTIP2	1	94343207	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	94343207	154907414	447	8432										
ABCA4	24	broad.mit.edu	37	chr1	94502739	94502739	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaattccaaaactgctgaGaccaaggtcagccagcgtct	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94502739G>T	ENST00000370225.3	-	25	3861	c.3775C>A	c.(3775-3777)Ctc>Atc	p.L1259I		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1259					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.L1259I(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AAACTGCTGAGACCAAGGTCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	102	101					1																	94502739		2203	4300	6503	94275327	SO:0001583	missense	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3775C>A	1.37:g.94502739G>T	ENSP00000359245:p.Leu1259Ile		94275327	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.963483	0.34659	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	T	0.72942	-0.7	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.43122	0.1233	N	0.20986	0.625	0.80722	D	1	B	0.28233	0.204	B	0.27715	0.082	T	0.46345	-0.9198	10	0.10636	T	0.68	.	19.2914	0.94102	0.0:0.0:1.0:0.0	.	1259	P78363	ABCA4_HUMAN	I	51;1259	ENSP00000359245:L1259I	ENSP00000359245:L1259I	L	-	1	0	ABCA4	94275327	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.376000	0.66178	2.793000	0.96121	0.561000	0.74099	CTC		0.463	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94502739	G	T	94502739	3	4	61	1	0	0	0	0	1	0	0	0	34	942	33	2	3150	2	ABCA4	1	94502739	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159532	94502739	154747882	448	8433										
ABCA4	24	broad.mit.edu	37	chr1	94543389	94543389	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttcagcagtaataccttCttcaccaagctgcctattca	6	13	4	0	rs1800548	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94543389C>A	ENST00000370225.3	-	11	1497	c.1411G>T	c.(1411-1413)Gaa>Taa	p.E471*	ABCA4_ENST00000535735.1_Nonsense_Mutation_p.E471*	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	471			E -> K (in ARMD2 and STGD1; ATP-binding capacity and retinal stimulation as in wild-type; dbSNP:rs1800548). {ECO:0000269|PubMed:10958763}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.E471*(1)|p.E471K(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GTAATACCTTCTTCACCAAGC	0.463																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	1	GRCh37	CM970001	ABCA4	M	rs1800548						162	157	159					1																	94543389		2203	4300	6503	94315977	SO:0001587	stop_gained	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1411G>T	1.37:g.94543389C>A	ENSP00000359245:p.Glu471*		94315977	O15112|O60438|O60915|Q0QD48|Q4LE31	Nonsense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	39	7.569069	0.98365	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	.	.	.	4.94	4.94	0.65067	.	0.252125	0.40554	N	0.001067	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	18.7161	0.91677	0.0:1.0:0.0:0.0	.	.	.	.	X	471	.	ENSP00000359245:E471X	E	-	1	0	ABCA4	94315977	0.855000	0.29742	1.000000	0.80357	0.991000	0.79684	1.629000	0.37071	2.726000	0.93360	0.655000	0.94253	GAA		0.463	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94543389	C	A	94543389	4	1	61	1	0	0	0	0	0	1	0	0	34	922	32	2	5570	2	ABCA4	1	94543389	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40650	94543389	154707232	449	8434										
ABCA4	24	broad.mit.edu	37	chr1	94546039	94546039	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcagaaaacttacttgttCttctgtcataagaatagata	5	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94546039C>A	ENST00000370225.3	-	8	1180	c.1094G>T	c.(1093-1095)aGa>aTa	p.R365I	ABCA4_ENST00000535735.1_Missense_Mutation_p.R365I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	365					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.R365I(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CTTACTTGTTCTTCTGTCATA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											104	109	107					1																	94546039		2203	4300	6503	94318627	SO:0001583	missense	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1094G>T	1.37:g.94546039C>A	ENSP00000359245:p.Arg365Ile		94318627	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846592	0.32606	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.91631	-2.76;-2.88	5.12	2.0	0.26442	.	6.560840	0.00166	N	0.000004	D	0.88276	0.6393	L	0.56769	1.78	0.41207	D	0.986416	B;B	0.18741	0.023;0.03	B;B	0.18263	0.021;0.011	T	0.70051	-0.4978	10	0.56958	D	0.05	.	17.3209	0.87235	0.0:0.3846:0.6154:0.0	.	365;365	F5H6E5;P78363	.;ABCA4_HUMAN	I	365	ENSP00000359245:R365I;ENSP00000437682:R365I	ENSP00000359245:R365I	R	-	2	0	ABCA4	94318627	0.994000	0.37717	1.000000	0.80357	0.912000	0.54170	0.209000	0.17435	0.703000	0.31848	0.650000	0.86243	AGA		0.418	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94546039	C	A	94546039	3	1	61	1	0	0	0	0	1	0	0	0	34	913	32	2	5899	2	ABCA4	1	94546039	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2650	94546039	154704582	450	8435										
ABCA4	24	broad.mit.edu	37	chr1	94564544	94564544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtccgggactccatgagCgaactgcagggagaagaggc	16	10	0	3	rs61748535	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94564544C>T	ENST00000370225.3	-	6	660	c.574G>A	c.(574-576)Gct>Act	p.A192T	ABCA4_ENST00000535735.1_Missense_Mutation_p.A192T	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	192			A -> T (in STGD1).		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.A192T(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		ACTCCATGAGCGAACTGCAGG	0.582													C|||	8	0.00159744	0.0061	0	5008	,	,		18898	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM014807	ABCA4	M	rs61748535	C	THR/ALA	18,4388	26.2+/-53.5	0,18,2185	27	26	26	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574	5.8	1	1	dbSNP_129	26	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ABCA4	NM_000350.2	58	0,19,6484	TT,TC,CC		0.0116,0.4085,0.1461	probably-damaging	192/2274	94564544	19,12987	2203	4300	6503	94337132	SO:0001583	missense	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.574G>A	1.37:g.94564544C>T	ENSP00000359245:p.Ala192Thr		94337132	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	20.7	4.033238	0.75504	0.004085	1.16E-4	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.91124	-2.67;-2.79	5.83	5.83	0.93111	.	0.056355	0.64402	D	0.000001	D	0.85678	0.5752	M	0.64404	1.975	0.58432	D	0.999998	P;D	0.55172	0.744;0.97	B;B	0.41813	0.18;0.367	D	0.84225	0.0463	10	0.20519	T	0.43	.	17.9044	0.88914	0.0:1.0:0.0:0.0	rs61748535	192;192	F5H6E5;P78363	.;ABCA4_HUMAN	T	192	ENSP00000359245:A192T;ENSP00000437682:A192T	ENSP00000359245:A192T	A	-	1	0	ABCA4	94337132	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	7.449000	0.80643	2.757000	0.94681	0.563000	0.77884	GCT		0.582	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94564544	C	T	94564544	3	4	61	1	0	0	0	0	1	0	0	0	34	768	27	1	6427	1	ABCA4	1	94564544	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18505	94564544	154686077	451	8436										
ARHGAP29	9411	broad.mit.edu	37	chr1	94645468	94645468	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggatctcttttgcaaggtCtataaattccttgtacaatc	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94645468C>A	ENST00000260526.6	-	20	2475	c.2293G>T	c.(2293-2295)Gac>Tac	p.D765Y	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	765	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)	p.D765Y(1)		NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TTTGCAAGGTCTATAAATTCC	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											113	109	110					1																	94645468		2202	4293	6495	94418056	SO:0001583	missense	9411				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.2293G>T	1.37:g.94645468C>A	ENSP00000260526:p.Asp765Tyr		94418056	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607017	0.87157	.	.	ENSG00000137962	ENST00000260526	T	0.19669	2.13	6.07	6.07	0.98685	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.40908	D	0.000996	T	0.39145	0.1067	L	0.60067	1.865	0.80722	D	1	D;D	0.76494	0.995;0.999	P;D	0.72982	0.834;0.979	T	0.06789	-1.0807	10	0.72032	D	0.01	-14.1366	20.6439	0.99570	0.0:1.0:0.0:0.0	.	765;765	F8VWZ8;Q52LW3	.;RHG29_HUMAN	Y	765	ENSP00000260526:D765Y	ENSP00000260526:D765Y	D	-	1	0	ARHGAP29	94418056	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.336000	0.79245	2.890000	0.99128	0.650000	0.86243	GAC		0.294	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		A	94645468	C	A	94645468	3	1	61	1	0	0	0	0	1	0	0	0	878	913	32	2	1508	2	ARHGAP29	1	94645468	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80924	94645468	154605153	452	8437										
ARHGAP29	9411	broad.mit.edu	37	chr1	94650597	94650597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaattttccaaacactttCgatgacaaacaaggagacac	5	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:94650597C>T	ENST00000260526.6	-	18	2122	c.1940G>A	c.(1939-1941)cGa>cAa	p.R647Q	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	647					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)	p.R647Q(1)		NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CAAACACTTTCGATGACAAAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											50	51	51					1																	94650597		2202	4300	6502	94423185	SO:0001583	missense	9411				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1940G>A	1.37:g.94650597C>T	ENSP00000260526:p.Arg647Gln		94423185	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.283467	0.59867	.	.	ENSG00000137962	ENST00000260526	D	0.92495	-3.05	5.39	2.11	0.27256	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.382752	0.15801	N	0.243965	T	0.79621	0.4477	L	0.39898	1.24	0.80722	D	1	P;P	0.51791	0.948;0.897	B;B	0.40444	0.176;0.329	T	0.77419	-0.2595	10	0.87932	D	0	-4.049	5.3515	0.16038	0.0:0.4106:0.0:0.5894	.	647;647	F8VWZ8;Q52LW3	.;RHG29_HUMAN	Q	647	ENSP00000260526:R647Q	ENSP00000260526:R647Q	R	-	2	0	ARHGAP29	94423185	1.000000	0.71417	0.990000	0.47175	0.982000	0.71751	4.346000	0.59367	0.641000	0.30601	0.557000	0.71058	CGA		0.353	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		T	94650597	C	T	94650597	3	4	61	1	0	0	0	0	1	0	0	0	878	884	31	1	1869	1	ARHGAP29	1	94650597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5129	94650597	154600024	453	8438										
F3	2152	broad.mit.edu	37	chr1	95005898	95005898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgatttccaagttaaatTatatgctgccacagtatttg	7	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:95005898T>C	ENST00000334047.7	-	2	290	c.127A>G	c.(127-129)Aat>Gat	p.N43D	F3_ENST00000370207.4_Missense_Mutation_p.N43D|F3_ENST00000480356.1_5'UTR	NM_001993.4	NP_001984.1	P13726	TF_HUMAN	coagulation factor III (thromboplastin, tissue factor)	43					activation of blood coagulation via clotting cascade (GO:0002543)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of plasma proteins involved in acute inflammatory response (GO:0002541)|blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|protease binding (GO:0002020)	p.N43D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)	14		all_lung(203;0.00106)|Lung NSC(277;0.00475)		all cancers(265;0.0232)|Epithelial(280;0.121)	Coagulation factor VIIa(DB00036)	CAAGTTAAATTATATGCTGCC	0.368																																					Melanoma(40;358 1339 15970 39161)											1	Substitution - Missense(1)	large_intestine(1)	1											124	125	125					1																	95005898		2203	4300	6503	94778486	SO:0001583	missense	2152			BC011029	CCDS750.1, CCDS53345.1	1p22-p21	2012-10-02			ENSG00000117525	ENSG00000117525		"CD molecules"	3541	protein-coding gene	gene with protein product		134390					Standard	NM_001993		Approved	CD142	uc001dqr.3	P13726	OTTHUMG00000010716	ENST00000334047.7:c.127A>G	1.37:g.95005898T>C	ENSP00000334145:p.Asn43Asp		94778486	D3DT47|Q6FHG2|Q86WH4	Missense_Mutation	SNP	ENST00000334047.7	37	CCDS750.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.516245	0.44763	.	.	ENSG00000117525	ENST00000334047;ENST00000370207	T;T	0.77877	-1.13;-1.13	4.9	3.77	0.43336	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.050335	0.85682	N	0.000000	T	0.70159	0.3192	M	0.82716	2.605	0.38837	D	0.955977	P;P	0.38711	0.643;0.472	B;B	0.41860	0.288;0.368	T	0.72962	-0.4132	10	0.72032	D	0.01	.	7.2499	0.26144	0.0:0.1023:0.0:0.8977	.	43;43	P13726-2;P13726	.;TF_HUMAN	D	43	ENSP00000334145:N43D;ENSP00000359226:N43D	ENSP00000334145:N43D	N	-	1	0	F3	94778486	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	1.888000	0.39708	0.729000	0.32403	0.460000	0.39030	AAT		0.368	F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029593.1	NM_001993		C	95005898	T	C	95005898	3	2	61	1	0	0	0	0	1	0	0	0	5360	1754	61	4	780	4	F3	1	95005898	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	355301	95005898	154244723	454	8439										
SLC44A3	126969	broad.mit.edu	37	chr1	95307663	95307663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtgctggggtttgctatcGtatccacaggcatcacggta	13	10	1	0	rs186467911		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:95307663G>A	ENST00000271227.6	+	8	970	c.868G>A	c.(868-870)Gta>Ata	p.V290I	SLC44A3_ENST00000529450.1_Missense_Mutation_p.V258I|SLC44A3_ENST00000530397.1_3'UTR|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000527077.1_Missense_Mutation_p.V222I|SLC44A3_ENST00000467909.1_Missense_Mutation_p.V242I|SLC44A3_ENST00000446120.2_Missense_Mutation_p.V254I|SLC44A3_ENST00000532427.1_Missense_Mutation_p.V210I	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	290					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V242I(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	GTTTGCTATCGTATCCACAGG	0.443													G|||	1	0.000199681	0	0.0014	5008	,	,		17828	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	145	144	144		868,724	2.7	0	1		144	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SLC44A3	NM_001114106.1,NM_152369.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	290/654,242/606	95307663	1,13005	2203	4300	6503	95080251	SO:0001583	missense	126969			BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.868G>A	1.37:g.95307663G>A	ENSP00000271227:p.Val290Ile		95080251	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	0.892	-0.725154	0.03158	0.0	1.16E-4	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05	5.97	2.71	0.32032	.	0.442572	0.21370	N	0.075646	T	0.01523	0.0049	N	0.03253	-0.375	0.09310	N	1	B;B;B;B;B	0.22800	0.016;0.017;0.016;0.075;0.075	B;B;B;B;B	0.16722	0.012;0.004;0.012;0.016;0.016	T	0.46762	-0.9168	10	0.02654	T	1	-6.8436	4.7945	0.13265	0.3429:0.0:0.5214:0.1357	.	210;254;222;258;290	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	I	254;290;222;258;242;210	ENSP00000389143:V254I;ENSP00000271227:V290I;ENSP00000433641:V222I;ENSP00000431836:V258I;ENSP00000432789:V242I;ENSP00000436661:V210I	ENSP00000271227:V290I	V	+	1	0	SLC44A3	95080251	0.006000	0.16342	0.002000	0.10522	0.010000	0.07245	-0.018000	0.12568	0.650000	0.30769	0.655000	0.94253	GTA		0.443	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		A	95307663	G	A	95307663	3	1	61	1	0	0	0	0	1	0	0	0	14674	1145	40	1	898	1	SLC44A3	1	95307663	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	301765	95307663	153942958	455	8440										
RWDD3	25950	broad.mit.edu	37	chr1	95710051	95710051	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccagaaactggcagtggcAgtgaaaagtgtactttttca	10	7	1	2	rs138509057		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:95710051A>C	ENST00000370202.4	+	2	446	c.370A>C	c.(370-372)Agt>Cgt	p.S124R	RWDD3_ENST00000263893.6_Missense_Mutation_p.S124R|RWDD3_ENST00000495272.1_3'UTR|RWDD3_ENST00000429514.2_Missense_Mutation_p.S109R|RP11-57H12.6_ENST00000604534.1_3'UTR|RP11-57H12.5_ENST00000444665.1_RNA	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	124					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S124R(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		TGGCAGTGGCAGTGAAAAGTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											107	102	104					1																	95710051		1947	4130	6077	95482639	SO:0001583	missense	25950			BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.370A>C	1.37:g.95710051A>C	ENSP00000359221:p.Ser124Arg		95482639	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	37	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	0.534	-0.856386	0.02630	.	.	ENSG00000122481	ENST00000370202;ENST00000429514;ENST00000263893	T;T;T	0.33865	1.39;1.43;1.4	5.38	-5.53	0.02552	.	1.677590	0.02325	N	0.073392	T	0.05456	0.0144	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.16802	0.001;0.001;0.0;0.019;0.0	B;B;B;B;B	0.12156	0.001;0.001;0.0;0.007;0.001	T	0.14811	-1.0459	10	0.18710	T	0.47	0.4062	0.9194	0.01311	0.2608:0.2714:0.1228:0.345	.	109;124;124;109;124	E7ES73;Q9Y3V2;D3DT49;Q9Y3V2-3;Q9Y3V2-2	.;RWDD3_HUMAN;.;.;.	R	124;109;124	ENSP00000359221:S124R;ENSP00000397398:S109R;ENSP00000263893:S124R	ENSP00000263893:S124R	S	+	1	0	RWDD3	95482639	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.566000	0.05922	-0.478000	0.06823	-0.274000	0.10170	AGT		0.438	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485		C	95710051	A	C	95710051	3	2	61	1	0	0	0	0	1	0	0	0	13794	188	7	4	376	4	RWDD3	1	95710051	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	402388	95710051	153540570	456	8441										
PTBP2	58155	broad.mit.edu	37	chr1	97235373	97235373	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagaaactgaagttattgCtttaggcttaccttttggta	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:97235373C>A	ENST00000426398.2	+	4	273	c.230C>A	c.(229-231)gCt>gAt	p.A77D	PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000609116.1_Missense_Mutation_p.A77D|PTBP2_ENST00000541987.1_Missense_Mutation_p.A46D|PTBP2_ENST00000370197.1_Missense_Mutation_p.A77D|PTBP2_ENST00000394184.3_Missense_Mutation_p.A88D|PTBP2_ENST00000370198.1_Missense_Mutation_p.A77D	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	77	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A77D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		GAAGTTATTGCTTTAGGCTTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											113	123	120					1																	97235373		2203	4300	6503	97007961	SO:0001583	missense	58155			AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"RNA binding motif (RRM) containing"	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.230C>A	1.37:g.97235373C>A	ENSP00000412788:p.Ala77Asp		97007961	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Missense_Mutation	SNP	ENST00000426398.2	37	CCDS754.1	.	.	.	.	.	.	.	.	.	.	C	31	5.091190	0.94149	.	.	ENSG00000117569	ENST00000236228;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184;ENST00000541987;ENST00000394176	T;T;T;T;T;T	0.77489	0.89;0.9;0.9;0.88;0.9;-1.1	5.94	5.94	0.96194	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.81408	0.4816	M	0.62209	1.925	0.58432	D	0.999992	P;B;B;B;B;B;P	0.45212	0.853;0.322;0.275;0.425;0.109;0.371;0.797	P;B;B;B;B;B;P	0.52267	0.694;0.202;0.056;0.395;0.094;0.444;0.588	T	0.81839	-0.0748	10	0.66056	D	0.02	-3.2824	20.3736	0.98901	0.0:1.0:0.0:0.0	.	85;88;77;77;77;77;99	B4DSU5;B4DSS8;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3;Q59G43	.;.;.;PTBP2_HUMAN;.;.;.	D	77;77;77;77;88;46;67	ENSP00000236228:A77D;ENSP00000359217:A77D;ENSP00000359216:A77D;ENSP00000412788:A77D;ENSP00000377738:A88D;ENSP00000442475:A46D	ENSP00000236228:A77D	A	+	2	0	PTBP2	97007961	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	5.956000	0.70315	2.820000	0.97059	0.650000	0.86243	GCT		0.358	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1			A	97235373	C	A	97235373	3	1	61	1	0	0	0	0	1	0	0	0	12760	797	28	2	244	2	PTBP2	1	97235373	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1525322	97235373	152015248	457	8442										
DPYD	1806	broad.mit.edu	37	chr1	97544684	97544684	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggtgggcaggtgggtttCtggatcaaactgtatagcct	14	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:97544684C>A	ENST00000370192.3	-	23	3026	c.2926G>T	c.(2926-2928)Gaa>Taa	p.E976*		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	976	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.E976*(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AGGTGGGTTTCTGGATCAAAC	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											172	168	169					1																	97544684		2203	4300	6503	97317272	SO:0001587	stop_gained	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2926G>T	1.37:g.97544684C>A	ENSP00000359211:p.Glu976*		97317272	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Nonsense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	39	7.832616	0.98513	.	.	ENSG00000188641	ENST00000370192	.	.	.	5.46	4.53	0.55603	.	0.113614	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-26.7776	15.1505	0.72692	0.0:0.9286:0.0:0.0714	.	.	.	.	X	976	.	ENSP00000359211:E976X	E	-	1	0	DPYD	97317272	0.998000	0.40836	0.988000	0.46212	0.924000	0.55760	3.894000	0.56250	2.735000	0.93741	0.561000	0.74099	GAA		0.443	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97544684	C	A	97544684	4	1	61	1	0	0	0	0	0	1	0	0	4756	922	32	2	155	2	DPYD	1	97544684	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	309311	97544684	151705937	458	8443										
DPYD	1806	broad.mit.edu	37	chr1	97770900	97770900	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaatcccatcagacctgaGacagtgttggtggctgtaac	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:97770900G>T	ENST00000370192.3	-	18	2314	c.2214C>A	c.(2212-2214)gtC>gtA	p.V738V	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	738					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.V738V(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TCAGACCTGAGACAGTGTTGG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	1											202	170	181					1																	97770900		2203	4300	6503	97543488	SO:0001819	synonymous_variant	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2214C>A	1.37:g.97770900G>T			97543488	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Silent	SNP	ENST00000370192.3	37	CCDS30777.1																																																																																				0.468	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	97770900	G	T	97770900	2	4	61	1	0	0	0	0	0	0	0	1	4756	929	33	2		2	DPYD	1	97770900	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226216	97770900	151479721	459	8444										
DPYD	1806	broad.mit.edu	37	chr1	97981361	97981361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatcattgatgtgctggtgGctggagttgcgctagcaaga	15	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:97981361G>A	ENST00000370192.3	-	13	1761	c.1661C>T	c.(1660-1662)gCc>gTc	p.A554V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	554					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.A554V(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TGTGCTGGTGGCTGGAGTTGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	64	65					1																	97981361		2203	4300	6503	97753949	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1661C>T	1.37:g.97981361G>A	ENSP00000359211:p.Ala554Val		97753949	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397304	0.62177	.	.	ENSG00000188641	ENST00000370192	D	0.85171	-1.95	5.2	5.2	0.72013	Aldolase-type TIM barrel (1);	0.187267	0.49916	D	0.000133	T	0.75079	0.3801	L	0.36672	1.1	0.80722	D	1	B	0.10296	0.003	B	0.18263	0.021	T	0.72308	-0.4332	10	0.62326	D	0.03	-6.0199	19.0953	0.93248	0.0:0.0:1.0:0.0	.	554	Q12882	DPYD_HUMAN	V	554	ENSP00000359211:A554V	ENSP00000359211:A554V	A	-	2	0	DPYD	97753949	1.000000	0.71417	0.899000	0.35326	0.928000	0.56348	9.301000	0.96167	2.595000	0.87683	0.585000	0.79938	GCC		0.413	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97981361	G	A	97981361	3	1	61	1	0	0	0	0	1	0	0	0	4756	1203	42	3	1460	3	DPYD	1	97981361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210461	97981361	151269260	460	8445										
PALMD	54873	broad.mit.edu	37	chr1	100152251	100152251	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttgagaaagagatccaaGatcttgaaaaagctgaactg	11	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100152251G>T	ENST00000263174.4	+	4	646	c.271G>T	c.(271-273)Gat>Tat	p.D91Y	PALMD_ENST00000605497.1_Missense_Mutation_p.D91Y	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	91					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)		p.D91Y(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		AGAGATCCAAGATCTTGAAAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	79	77					1																	100152251		2203	4300	6503	99924839	SO:0001583	missense	54873			AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.271G>T	1.37:g.100152251G>T	ENSP00000263174:p.Asp91Tyr		99924839	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	37	CCDS758.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707519	0.68615	.	.	ENSG00000099260	ENST00000263174	T	0.17370	2.28	5.87	4.96	0.65561	.	0.487637	0.22068	N	0.065064	T	0.11537	0.0281	N	0.22421	0.69	0.35872	D	0.828279	D	0.53885	0.963	P	0.51487	0.671	T	0.03933	-1.0991	10	0.59425	D	0.04	-10.6691	15.2083	0.73198	0.0675:0.0:0.9325:0.0	.	91	Q9NP74	PALMD_HUMAN	Y	91	ENSP00000263174:D91Y	ENSP00000263174:D91Y	D	+	1	0	PALMD	99924839	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.294000	0.43567	1.616000	0.50265	0.655000	0.94253	GAT		0.358	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		T	100152251	G	T	100152251	3	4	61	1	0	0	0	0	1	0	0	0	11442	942	33	2	285	2	PALMD	1	100152251	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2170890	100152251	149098370	461	8446										
FRRS1	391059	broad.mit.edu	37	chr1	100206481	100206481	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccagtagattttatacttCtcaacaactgtgactctgaa	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100206481C>A	ENST00000414213.1	-	6	1045	c.444G>T	c.(442-444)gaG>gaT	p.E148D	FRRS1_ENST00000287474.5_Missense_Mutation_p.E148D			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	148	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)	p.E148D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		TTTTATACTTCTCAACAACTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											157	159	158					1																	100206481		2203	4300	6503	99979069	SO:0001583	missense	391059			AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.444G>T	1.37:g.100206481C>A	ENSP00000393884:p.Glu148Asp		99979069	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	C	10.89	1.479035	0.26511	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.58	4.67	0.58626	.	0.246870	0.40728	N	0.001031	T	0.20170	0.0485	L	0.28400	0.85	0.32154	N	0.583794	P	0.35821	0.523	B	0.37731	0.257	T	0.09729	-1.0661	9	0.45353	T	0.12	-16.6234	9.1069	0.36703	0.0:0.7807:0.0:0.2193	.	148	Q6ZNA5-2	.	D	148	.	ENSP00000287474:E148D	E	-	3	2	FRRS1	99979069	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	1.870000	0.39529	1.364000	0.46038	-0.137000	0.14449	GAG		0.358	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		A	100206481	C	A	100206481	3	1	61	1	0	0	0	0	1	0	0	0	6079	912	32	2	1484	2	FRRS1	1	100206481	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54230	100206481	149044140	462	8447										
AGL	178	broad.mit.edu	37	chr1	100379159	100379159	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagctatttcatgtttcCgaagacccttcagatttaaa	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100379159C>T	ENST00000294724.4	+	30	4504	c.4026C>T	c.(4024-4026)tcC>tcT	p.S1342S	AGL_ENST00000370163.3_Silent_p.S1342S|AGL_ENST00000361915.3_Silent_p.S1342S|AGL_ENST00000370161.2_Silent_p.S1326S|AGL_ENST00000361302.3_Silent_p.S1326S|AGL_ENST00000370165.3_Silent_p.S1342S|AGL_ENST00000361522.4_Silent_p.S1325S	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1342					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)	p.S1342S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TTCATGTTTCCGAAGACCCTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	87	87					1																	100379159		2203	4300	6503	100151747	SO:0001819	synonymous_variant	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.4026C>T	1.37:g.100379159C>T			100151747	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																				0.363	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		T	100379159	C	T	100379159	2	4	61	1	0	0	0	0	0	0	0	1	384	639	23	1		1	AGL	1	100379159	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	172678	100379159	148871462	463	8448										
AGL	178	broad.mit.edu	37	chr1	100382266	100382266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttaaaaatgttctttcccGacattatgttcatcttgaga	7	7	3	1	rs185681971		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100382266G>A	ENST00000294724.4	+	33	4938	c.4460G>A	c.(4459-4461)cGa>cAa	p.R1487Q	AGL_ENST00000370163.3_Missense_Mutation_p.R1487Q|AGL_ENST00000361915.3_Missense_Mutation_p.R1487Q|AGL_ENST00000370161.2_Missense_Mutation_p.R1471Q|AGL_ENST00000361302.3_Missense_Mutation_p.R1471Q|AGL_ENST00000370165.3_Missense_Mutation_p.R1487Q|AGL_ENST00000361522.4_Missense_Mutation_p.R1470Q	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1487			R -> G (in dbSNP:rs12118058).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)	p.R1487Q(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GTTCTTTCCCGACATTATGTT	0.343													G|||	1	0.000199681	0	0	5008	,	,		16809	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											76	79	78					1																	100382266		2203	4300	6503	100154854	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.4460G>A	1.37:g.100382266G>A	ENSP00000294724:p.Arg1487Gln		100154854	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	17.98	3.521963	0.64747	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43	5.89	5.89	0.94794	Six-hairpin glycosidase-like (1);	0.159069	0.56097	N	0.000025	T	0.55065	0.1897	M	0.74647	2.275	0.53005	D	0.999966	B;B;B	0.31581	0.329;0.329;0.211	B;B;B	0.28011	0.075;0.075;0.085	T	0.58651	-0.7599	10	0.13853	T	0.58	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	1470;1471;1487	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	Q	1487;1487;1487;1487;1471;1471;1470	ENSP00000355106:R1487Q;ENSP00000359184:R1487Q;ENSP00000359182:R1487Q;ENSP00000294724:R1487Q;ENSP00000354971:R1471Q;ENSP00000359180:R1471Q;ENSP00000354635:R1470Q	ENSP00000294724:R1487Q	R	+	2	0	AGL	100154854	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.391000	0.73208	2.783000	0.95769	0.655000	0.94253	CGA		0.343	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		A	100382266	G	A	100382266	3	1	61	1	0	0	0	0	1	0	0	0	384	1058	37	1	4655	1	AGL	1	100382266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3107	100382266	148868355	464	8449										
HIAT1	64645	broad.mit.edu	37	chr1	100533593	100533593	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattggagcttatcttggaCgagtatatggggacagcttg	13	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100533593C>T	ENST00000370152.3	+	6	683	c.547C>T	c.(547-549)Cga>Tga	p.R183*	RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	183					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R183*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		TTATCTTGGACGAGTATATGG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											241	226	231					1																	100533593		2203	4300	6503	100306181	SO:0001587	stop_gained	64645			AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.547C>T	1.37:g.100533593C>T	ENSP00000359171:p.Arg183*		100306181	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Nonsense_Mutation	SNP	ENST00000370152.3	37	CCDS763.1	.	.	.	.	.	.	.	.	.	.	C	37	5.994499	0.97184	.	.	ENSG00000156875	ENST00000370152	.	.	.	5.68	5.68	0.88126	.	0.083213	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-19.6079	19.7989	0.96497	0.0:1.0:0.0:0.0	.	.	.	.	X	183	.	ENSP00000359171:R183X	R	+	1	2	HIAT1	100306181	0.998000	0.40836	0.995000	0.50966	0.986000	0.74619	3.637000	0.54324	2.683000	0.91414	0.561000	0.74099	CGA		0.433	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055		T	100533593	C	T	100533593	4	4	61	1	0	0	0	0	0	1	0	0	7118	528	19	1	569	1	HIAT1	1	100533593	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151327	100533593	148717028	465	8450										
SASS6	163786	broad.mit.edu	37	chr1	100586960	100586960	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatttcaaacagcctgcgaGaaatttctttatctccacat	4	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100586960G>T	ENST00000287482.5	-	5	597	c.457C>A	c.(457-459)Ctc>Atc	p.L153I	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	153					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)		p.L153I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		CAGCCTGCGAGAAATTTCTTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	59	58					1																	100586960		2201	4300	6501	100359548	SO:0001583	missense	163786			AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.457C>A	1.37:g.100586960G>T	ENSP00000287482:p.Leu153Ile		100359548	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	37	CCDS764.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736534	0.69304	.	.	ENSG00000156876	ENST00000287482;ENST00000539329	T	0.35048	1.33	5.61	1.05	0.20165	.	0.073764	0.53938	D	0.000050	T	0.44664	0.1304	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44081	-0.9351	10	0.49607	T	0.09	-9.1116	8.0347	0.30486	0.4631:0.0:0.5369:0.0	.	153	Q6UVJ0	SAS6_HUMAN	I	153;126	ENSP00000287482:L153I	ENSP00000287482:L153I	L	-	1	0	SASS6	100359548	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.068000	0.30629	0.398000	0.25338	0.655000	0.94253	CTC		0.303	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		T	100586960	G	T	100586960	3	4	61	1	0	0	0	0	1	0	0	0	13887	942	33	2	1568	2	SASS6	1	100586960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53367	100586960	148663661	466	8451										
RTCD1	8634	broad.mit.edu	37	chr1	100756976	100756976	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggctaaatttattgtgaaGaaatcagaagatgaagaaga	10	3	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:100756976G>T	ENST00000370128.4	+	11	1186	c.1017G>T	c.(1015-1017)aaG>aaT	p.K339N	RTCA_ENST00000260563.4_Missense_Mutation_p.K352N	NM_003729.3	NP_003720.1	O00442	RTCA_HUMAN	RNA 3'-terminal phosphate cyclase	339					RNA processing (GO:0006396)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA-3'-phosphate cyclase activity (GO:0003963)	p.K339N(1)									TTATTGTGAAGAAATCAGAAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	85	81					1																	100756976		2200	4298	6498	100529564	SO:0001583	missense	8634			Y11651	CCDS768.1, CCDS44178.1	1p13.3	2012-03-30	2012-03-30	2012-03-30	ENSG00000137996	ENSG00000137996	6.5.1.4		17981	protein-coding gene	gene with protein product		611286	"RTC domain containing 1", "RNA terminal phosphate cyclase domain 1"	RTCD1		9184239	Standard	NM_003729		Approved	RPC, RTC1	uc001dtd.3	O00442	OTTHUMG00000010920	ENST00000370128.4:c.1017G>T	1.37:g.100756976G>T	ENSP00000359146:p.Lys339Asn		100529564	Q5VVL5|Q5VVL6|Q96E99	Missense_Mutation	SNP	ENST00000370128.4	37	CCDS768.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.748087	0.30955	.	.	ENSG00000137996	ENST00000370128;ENST00000260563	.	.	.	5.74	2.5	0.30297	-terminal phosphate cyclase domain (2);RNA 3&apos (4);-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta (1);-terminal phosphate cyclase (1);	0.306949	0.36303	N	0.002672	T	0.24160	0.0585	L	0.40543	1.245	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.15484	0.005;0.013	T	0.13602	-1.0503	9	0.31617	T	0.26	-13.3176	3.7746	0.08654	0.2535:0.1968:0.5498:0.0	.	352;339	O00442-2;O00442	.;RTC1_HUMAN	N	339;352	.	ENSP00000260563:K352N	K	+	3	2	RTCD1	100529564	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.181000	0.32017	1.436000	0.47453	0.655000	0.94253	AAG		0.368	RTCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030098.2			T	100756976	G	T	100756976	3	4	61	1	0	0	0	0	1	0	0	0	13755	933	33	2	1102	2	RTCD1	1	100756976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170016	100756976	148493645	467	8452										
EXTL2	2135	broad.mit.edu	37	chr1	101343233	101343233	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaaaagtttcaataagaGatctgttctgttgtacgtct	7	5	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:101343233G>T	ENST00000370114.3	-	3	1668	c.232C>A	c.(232-234)Ctc>Atc	p.L78I	EXTL2_ENST00000535414.1_Missense_Mutation_p.L65I|EXTL2_ENST00000370113.3_Missense_Mutation_p.L78I	NM_001033025.2|NM_001261440.1	NP_001028197.1|NP_001248369.1	Q9UBQ6	EXTL2_HUMAN	exostosin-like glycosyltransferase 2	78					heparan sulfate proteoglycan biosynthetic process (GO:0015012)|N-acetylglucosamine metabolic process (GO:0006044)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	alpha-1,4-N-acetylgalactosaminyltransferase activity (GO:0035248)|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.L78I(1)|p.L86I(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	14		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)		TTCAATAAGAGATCTGTTCTG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	1											131	131	131					1																	101343233		2203	4300	6503	101115821	SO:0001583	missense	2135			U76189	CCDS775.1, CCDS72831.1	1p21	2013-03-01	2013-03-01		ENSG00000162694	ENSG00000162694	2.4.1.223	"Exostosin glycosyltransferase family"	3516	protein-coding gene	gene with protein product	"alpha-1,4-N-acteylhexosaminyltransferase"	602411	"exostoses (multiple)-like 2"			9450183, 15831490	Standard	NM_001439		Approved		uc001dtk.2	Q9UBQ6	OTTHUMG00000011814	ENST00000370114.3:c.232C>A	1.37:g.101343233G>T	ENSP00000359132:p.Leu78Ile		101115821	B2R795|D3DT60	Missense_Mutation	SNP	ENST00000370114.3	37	CCDS775.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166935	0.38217	.	.	ENSG00000162694	ENST00000370114;ENST00000370113;ENST00000535414;ENST00000450240;ENST00000416479	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	5.61	5.61	0.85477	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.120577	0.56097	D	0.000027	T	0.64170	0.2574	M	0.62154	1.92	0.47037	D	0.999291	B;B	0.24043	0.096;0.096	B;B	0.37304	0.246;0.246	T	0.57528	-0.7796	10	0.07644	T	0.81	-20.9422	11.0715	0.48006	0.112:0.0:0.888:0.0	.	78;78	Q8N8F1;Q9UBQ6	.;EXTL2_HUMAN	I	78;78;65;86;65	ENSP00000359132:L78I;ENSP00000359131:L78I;ENSP00000444385:L65I;ENSP00000403363:L86I;ENSP00000392255:L65I	ENSP00000359131:L78I	L	-	1	0	EXTL2	101115821	1.000000	0.71417	0.984000	0.44739	0.926000	0.56050	1.917000	0.39996	2.793000	0.96121	0.655000	0.94253	CTC		0.398	EXTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032705.1	NM_001439		T	101343233	G	T	101343233	3	4	61	1	0	0	0	0	1	0	0	0	5339	942	33	2	772	2	EXTL2	1	101343233	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	586257	101343233	147907388	468	8453										
EXTL2	2135	broad.mit.edu	37	chr1	101343377	101343377	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagcaccagctaccagtaAtaatacgaggatgaccacca	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:101343377A>C	ENST00000370114.3	-	3	1524	c.88T>G	c.(88-90)Tta>Gta	p.L30V	EXTL2_ENST00000535414.1_Missense_Mutation_p.L17V|EXTL2_ENST00000370113.3_Missense_Mutation_p.L30V	NM_001033025.2|NM_001261440.1	NP_001028197.1|NP_001248369.1	Q9UBQ6	EXTL2_HUMAN	exostosin-like glycosyltransferase 2	30					heparan sulfate proteoglycan biosynthetic process (GO:0015012)|N-acetylglucosamine metabolic process (GO:0006044)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	alpha-1,4-N-acetylgalactosaminyltransferase activity (GO:0035248)|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.L30V(1)|p.L38V(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	14		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)		GCTACCAGTAATAATACGAGG	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	1											80	69	73					1																	101343377		2203	4300	6503	101115965	SO:0001583	missense	2135			U76189	CCDS775.1, CCDS72831.1	1p21	2013-03-01	2013-03-01		ENSG00000162694	ENSG00000162694	2.4.1.223	"Exostosin glycosyltransferase family"	3516	protein-coding gene	gene with protein product	"alpha-1,4-N-acteylhexosaminyltransferase"	602411	"exostoses (multiple)-like 2"			9450183, 15831490	Standard	NM_001439		Approved		uc001dtk.2	Q9UBQ6	OTTHUMG00000011814	ENST00000370114.3:c.88T>G	1.37:g.101343377A>C	ENSP00000359132:p.Leu30Val		101115965	B2R795|D3DT60	Missense_Mutation	SNP	ENST00000370114.3	37	CCDS775.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.248839	0.39797	.	.	ENSG00000162694	ENST00000370114;ENST00000370113;ENST00000535414;ENST00000450240;ENST00000416479	D;D;D;D;T	0.84070	-1.79;-1.79;-1.79;-1.8;0.3	5.51	2.22	0.28083	.	0.000000	0.85682	D	0.000000	T	0.80470	0.4629	L	0.36672	1.1	0.53688	D	0.999979	D;D	0.69078	0.997;0.997	D;D	0.78314	0.991;0.991	T	0.81286	-0.1001	10	0.72032	D	0.01	-15.4903	10.7109	0.45982	0.2226:0.0:0.7774:0.0	.	30;30	Q8N8F1;Q9UBQ6	.;EXTL2_HUMAN	V	30;30;17;38;17	ENSP00000359132:L30V;ENSP00000359131:L30V;ENSP00000444385:L17V;ENSP00000403363:L38V;ENSP00000392255:L17V	ENSP00000359131:L30V	L	-	1	2	EXTL2	101115965	0.992000	0.36948	0.005000	0.12908	0.038000	0.13279	2.054000	0.41335	0.278000	0.22164	-0.177000	0.13119	TTA		0.453	EXTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032705.1	NM_001439		C	101343377	A	C	101343377	3	2	61	1	0	0	0	0	1	0	0	0	5339	98	4	4	916	4	EXTL2	1	101343377	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	144	101343377	147907244	469	8454										
SLC30A7	148867	broad.mit.edu	37	chr1	101431461	101431461	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattttaagccaaacacataAtatttttactcaggtatgtc	5	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:101431461A>C	ENST00000370112.4	+	10	1257	c.1070A>C	c.(1069-1071)aAt>aCt	p.N357T	SLC30A7_ENST00000357650.4_Missense_Mutation_p.N357T	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	357					cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)	p.N357T(1)		endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		CAAACACATAATATTTTTACT	0.328																																					NSCLC(91;473 1491 3102 16827 21633)											1	Substitution - Missense(1)	large_intestine(1)	1											105	104	104					1																	101431461		2203	4300	6503	101204049	SO:0001583	missense	148867			AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"Solute carriers"	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.1070A>C	1.37:g.101431461A>C	ENSP00000359130:p.Asn357Thr		101204049	B2R949|D3DT61|Q8TCH2	Missense_Mutation	SNP	ENST00000370112.4	37	CCDS776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.12|10.12	1.264279|1.264279	0.23136|0.23136	.|.	.|.	ENSG00000162695|ENSG00000162695	ENST00000370112;ENST00000357650|ENST00000370111	T;T|.	0.63255|.	-0.03;-0.03|.	5.82|5.82	4.68|4.68	0.58851|0.58851	.|.	0.044125|.	0.85682|.	D|.	0.000000|.	T|.	0.42359|.	0.1199|.	L|L	0.41906|0.41906	1.305|1.305	0.80722|0.80722	D|D	1|1	P|.	0.35944|.	0.529|.	B|.	0.31869|.	0.137|.	T|.	0.35251|.	-0.9796|.	10|.	0.28530|.	T|.	0.3|.	-5.2517|-5.2517	11.9523|11.9523	0.52962|0.52962	0.9319:0.0:0.0681:0.0|0.9319:0.0:0.0681:0.0	.|.	357|.	Q8NEW0|.	ZNT7_HUMAN|.	T|Y	357|76	ENSP00000359130:N357T;ENSP00000350278:N357T|.	ENSP00000350278:N357T|.	N|X	+|+	2|3	0|2	SLC30A7|SLC30A7	101204049|101204049	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	5.308000|5.308000	0.65768|0.65768	1.017000|1.017000	0.39495|0.39495	0.533000|0.533000	0.62120|0.62120	AAT|TAA		0.328	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496		C	101431461	A	C	101431461	3	2	61	1	0	0	0	0	1	0	0	0	14597	101	4	4	1108	4	SLC30A7	1	101431461	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	88084	101431461	147819160	470	8455										
DPH5	51611	broad.mit.edu	37	chr1	101487279	101487279	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgcttcttgttccacttCttctctatcagcaacaacca	3	14	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:101487279C>A	ENST00000370109.3	-	3	290	c.178G>T	c.(178-180)Gaa>Taa	p.E60*	DPH5_ENST00000342173.7_Nonsense_Mutation_p.E60*|DPH5_ENST00000370105.3_5'UTR|DPH5_ENST00000488176.1_Nonsense_Mutation_p.E60*	NM_001077394.1|NM_001077395.1|NM_015958.2	NP_001070862.1|NP_001070863.1|NP_057042.2	Q9H2P9	DPH5_HUMAN	diphthamide biosynthesis 5	60					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		diphthine synthase activity (GO:0004164)	p.E60*(1)		endometrium(2)|large_intestine(1)|lung(4)	7		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)		TGTTCCACTTCTTCTCTATCA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											159	148	151					1																	101487279		1861	4114	5975	101259867	SO:0001587	stop_gained	51611			AF132964	CCDS41358.1, CCDS41359.1	1p21.2	2013-05-02	2013-05-02		ENSG00000117543	ENSG00000117543			24270	protein-coding gene	gene with protein product		611075	"DPH5 homolog (S. cerevisiae)"			15485916, 23486472	Standard	NM_015958		Approved	CGI-30	uc001dtt.2	Q9H2P9	OTTHUMG00000010829	ENST00000370109.3:c.178G>T	1.37:g.101487279C>A	ENSP00000359127:p.Glu60*		101259867	A8JZY6|D3DT62|Q9P017|Q9P0I4|Q9Y319	Nonsense_Mutation	SNP	ENST00000370109.3	37	CCDS41358.1	.	.	.	.	.	.	.	.	.	.	C	37	6.632647	0.97722	.	.	ENSG00000117543	ENST00000370109;ENST00000434818;ENST00000422396;ENST00000342173;ENST00000488176	.	.	.	6.02	3.14	0.36123	.	0.255981	0.44285	D	0.000470	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-16.1934	8.6773	0.34187	0.0:0.6789:0.0:0.3211	.	.	.	.	X	60	.	ENSP00000339630:E60X	E	-	1	0	DPH5	101259867	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.385000	0.44371	1.565000	0.49641	0.655000	0.94253	GAA		0.373	DPH5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000029881.1	NM_015958		A	101487279	C	A	101487279	4	1	61	1	0	0	0	0	0	1	0	0	4734	922	32	2	703	2	DPH5	1	101487279	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55818	101487279	147763342	471	8456										
S1PR1	1901	broad.mit.edu	37	chr1	101705491	101705491	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacactctgaccaacaaggaGatgcgtcgggccttcatccg	10	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:101705491G>T	ENST00000305352.6	+	2	1326	c.951G>T	c.(949-951)gaG>gaT	p.E317D		NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	317					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.E317D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						CCAACAAGGAGATGCGTCGGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											192	194	193					1																	101705491		2203	4300	6503	101478079	SO:0001583	missense	1901			M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate", "CD molecules"	3165	protein-coding gene	gene with protein product		601974	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.951G>T	1.37:g.101705491G>T	ENSP00000305416:p.Glu317Asp		101478079	D3DT66|Q9BYY4|Q9NYN8	Missense_Mutation	SNP	ENST00000305352.6	37	CCDS777.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.149689	0.37923	.	.	ENSG00000170989	ENST00000305352;ENST00000424264	T	0.37411	1.2	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.13286	0.0322	L	0.41906	1.305	0.58432	D	0.999999	B	0.15719	0.014	B	0.22880	0.042	T	0.06144	-1.0843	10	0.10902	T	0.67	.	10.3368	0.43854	0.1533:0.0:0.8467:0.0	.	317	P21453	S1PR1_HUMAN	D	317	ENSP00000305416:E317D	ENSP00000305416:E317D	E	+	3	2	S1PR1	101478079	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.755000	0.62198	2.378000	0.81104	0.305000	0.20034	GAG		0.547	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400		T	101705491	G	T	101705491	3	4	61	1	0	0	0	0	1	0	0	0	13830	933	33	2	953	2	S1PR1	1	101705491	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218212	101705491	147545130	472	8457										
OLFM3	118427	broad.mit.edu	37	chr1	102269874	102269874	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccattgttccaggcatagaGagctcgatctcttgcattgt	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:102269874G>T	ENST00000338858.5	-	6	1356	c.1357C>A	c.(1357-1359)Ctc>Atc	p.L453I	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.L433I|OLFM3_ENST00000536598.1_3'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	453	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)		p.L453I(1)|p.L433I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CAGGCATAGAGAGCTCGATCT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	1											200	186	191					1																	102269874		2203	4300	6503	102042462	SO:0001583	missense	118427			AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.1357C>A	1.37:g.102269874G>T	ENSP00000345192:p.Leu453Ile		102042462	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	37		.	.	.	.	.	.	.	.	.	.	G	21.2	4.106751	0.77096	.	.	ENSG00000118733	ENST00000370103;ENST00000338858	D;D	0.95238	-3.65;-3.65	5.77	5.77	0.91146	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.97176	0.9077	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.987	D	0.97034	0.9752	10	0.66056	D	0.02	.	19.9831	0.97336	0.0:0.0:1.0:0.0	.	433;453	Q5T3V6;Q96PB7	.;NOE3_HUMAN	I	433;453	ENSP00000359121:L433I;ENSP00000345192:L453I	ENSP00000345192:L453I	L	-	1	0	OLFM3	102042462	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.476000	0.97823	2.728000	0.93425	0.650000	0.86243	CTC		0.428	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			T	102269874	G	T	102269874	3	4	61	1	0	0	0	0	1	0	0	0	10885	942	33	2	83	2	OLFM3	1	102269874	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	564383	102269874	146980747	473	8458										
COL11A1	1301	broad.mit.edu	37	chr1	103488405	103488405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattcataaaaatcatattCgcctaaatctccatctacca	1	11	4	0	rs372387693		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:103488405C>T	ENST00000370096.3	-	8	1450	c.1138G>A	c.(1138-1140)Gaa>Aaa	p.E380K	COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000353414.4_Missense_Mutation_p.E341K|COL11A1_ENST00000358392.2_Missense_Mutation_p.E392K	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	380	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E392K(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		AAATCATATTCGCCTAAATCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	LYS/GLU,LYS/GLU,LYS/GLU,	0,4406		0,0,2203	75	75	75		1021,1138,1174,	5.4	1	1		75	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,intron	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	56,56,56,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,	341/1768,380/1807,392/1819,	103488405	2,13004	2203	4300	6503	103260993	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1138G>A	1.37:g.103488405C>T	ENSP00000359114:p.Glu380Lys		103260993	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036598	0.54896	0.0	2.33E-4	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000427239	D;T;D;T	0.88664	-2.4;-0.6;-2.41;-0.57	5.41	5.41	0.78517	.	0.055303	0.64402	D	0.000001	D	0.83505	0.5269	M	0.83483	2.645	0.58432	D	0.999995	P;P;P	0.50710	0.938;0.938;0.897	B;B;B	0.36567	0.228;0.228;0.114	D	0.84087	0.0388	10	0.15952	T	0.53	.	17.3759	0.87391	0.0:1.0:0.0:0.0	.	341;392;380	P12107-3;P12107-2;P12107	.;.;COBA1_HUMAN	K	380;392;341;392	ENSP00000359114:E380K;ENSP00000351163:E392K;ENSP00000302551:E341K;ENSP00000408640:E392K	ENSP00000302551:E341K	E	-	1	0	COL11A1	103260993	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	2.984000	0.49353	2.519000	0.84933	0.643000	0.83706	GAA		0.363	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103488405	C	T	103488405	3	4	61	1	0	0	0	0	1	0	0	0	3673	893	31	1	4522	1	COL11A1	1	103488405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1218531	103488405	145762216	474	8459										
COL11A1	1301	broad.mit.edu	37	chr1	103491079	103491079	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtctatacgtattacctCatttgtcccagaaacatgcc	5	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:103491079C>A	ENST00000370096.3	-	7	1300	c.988G>T	c.(988-990)Gag>Tag	p.E330*	COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000353414.4_Nonsense_Mutation_p.E291*|COL11A1_ENST00000358392.2_Nonsense_Mutation_p.E342*	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	330	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E342*(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		CGTATTACCTCATTTGTCCCA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											140	131	134					1																	103491079		2203	4300	6503	103263667	SO:0001587	stop_gained	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.988G>T	1.37:g.103491079C>A	ENSP00000359114:p.Glu330*		103263667	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Nonsense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	36	5.930312	0.97116	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000427239	.	.	.	5.23	5.23	0.72850	.	0.202505	0.41823	D	0.000807	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	19.1629	0.93541	0.0:1.0:0.0:0.0	.	.	.	.	X	330;342;291;342	.	ENSP00000302551:E291X	E	-	1	0	COL11A1	103263667	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	5.562000	0.67346	2.606000	0.88127	0.637000	0.83480	GAG		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103491079	C	A	103491079	4	1	61	1	0	0	0	0	0	1	0	0	3673	835	29	2	4676	2	COL11A1	1	103491079	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2674	103491079	145759542	475	8460										
COL11A1	1301	broad.mit.edu	37	chr1	103540309	103540309	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcattgtcacagttttcttCtccacgctgattgctacccg	6	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:103540309C>A	ENST00000370096.3	-	4	828	c.516G>T	c.(514-516)gaG>gaT	p.E172D	COL11A1_ENST00000512756.1_Missense_Mutation_p.E172D|COL11A1_ENST00000353414.4_Missense_Mutation_p.E172D|COL11A1_ENST00000358392.2_Missense_Mutation_p.E172D	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	172	Laminin G-like.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E172D(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		CAGTTTTCTTCTCCACGCTGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											154	134	140					1																	103540309		2202	4300	6502	103312897	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.516G>T	1.37:g.103540309C>A	ENSP00000359114:p.Glu172Asp		103312897	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	8.558	0.877130	0.17395	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	T;T;T;T;T;T	0.01963	4.53;4.53;4.53;4.53;4.53;4.53	5.73	2.9	0.33743	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.052537	0.85682	D	0.000000	T	0.02193	0.0068	L	0.42245	1.32	0.48341	D	0.999637	D;D;D;D	0.69078	0.997;0.996;0.996;0.997	D;D;D;D	0.79108	0.992;0.987;0.987;0.992	T	0.56980	-0.7889	10	0.11182	T	0.66	.	8.7582	0.34658	0.0:0.7169:0.0:0.2831	.	172;172;172;172	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	D	172;172;172;172;172;99	ENSP00000359114:E172D;ENSP00000351163:E172D;ENSP00000302551:E172D;ENSP00000426533:E172D;ENSP00000408640:E172D;ENSP00000410177:E99D	ENSP00000302551:E172D	E	-	3	2	COL11A1	103312897	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	0.663000	0.25053	0.364000	0.24374	0.650000	0.86243	GAG		0.373	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103540309	C	A	103540309	3	1	61	1	0	0	0	0	1	0	0	0	3673	912	32	2	5317	2	COL11A1	1	103540309	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49230	103540309	145710312	476	8461										
AMY2A	279	broad.mit.edu	37	chr1	104160195	104160195	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattgctcttgaatgtgagCgatatttagctccgaaggga	11	6	1	2	rs182106305	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:104160195C>T	ENST00000414303.2	+	1	197	c.133C>T	c.(133-135)Cga>Tga	p.R45*		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	45					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)	p.R45*(1)		endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	TGAATGTGAGCGATATTTAGC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											265	219	235					1																	104160195		2201	4279	6480	103961718	SO:0001587	stop_gained	279			BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"amylase, alpha 2A; pancreatic"	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.133C>T	1.37:g.104160195C>T	ENSP00000397582:p.Arg45*		103961718	B9EJG1|Q9UBH3	Nonsense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	18.18|18.18	3.566174|3.566174	0.65651|0.65651	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|.	.|.	.|.	3.22|3.22	1.15|1.15	0.20763|0.20763	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.08891|.	0.0220|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.29274|.	-1.0017|.	3|.	.|0.02654	.|T	.|1	.|.	10.7957|10.7957	0.46459|0.46459	0.3439:0.6561:0.0:0.0|0.3439:0.6561:0.0:0.0	.|.	.|.	.|.	.|.	V|X	43|45	.|.	.|ENSP00000377509:R45X	A|R	+|+	2|1	0|2	AMY2A|AMY2A	103961718|103961718	0.999000|0.999000	0.42202|0.42202	0.994000|0.994000	0.49952|0.49952	0.527000|0.527000	0.34593|0.34593	1.964000|1.964000	0.40462|0.40462	0.146000|0.146000	0.19002|0.19002	-0.538000|-0.538000	0.04264|0.04264	GCG|CGA		0.428	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699		T	104160195	C	T	104160195	4	4	61	1	0	0	0	0	0	1	0	0	594	760	27	1	135	1	AMY2A	1	104160195	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	619886	104160195	145090426	477	8462										
NTNG1	22854	broad.mit.edu	37	chr1	107979322	107979322	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgggctcaatccatgatCgttgtaatggctcaggattt	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:107979322C>T	ENST00000370068.1	+	7	2137	c.1291C>T	c.(1291-1293)Cgt>Tgt	p.R431C	NTNG1_ENST00000542803.1_Missense_Mutation_p.R431C|NTNG1_ENST00000370061.3_Missense_Mutation_p.R397C|NTNG1_ENST00000370070.2_Intron|NTNG1_ENST00000370074.4_Intron|NTNG1_ENST00000370073.2_Missense_Mutation_p.R431C|NTNG1_ENST00000370067.1_Intron|NTNG1_ENST00000370071.2_Intron|NTNG1_ENST00000370072.3_Intron|NTNG1_ENST00000370065.1_Intron|NTNG1_ENST00000370066.1_Intron			Q9Y2I2	NTNG1_HUMAN	netrin G1	431	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)		p.R431C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		AATCCATGATCGTTGTAATGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	144	151					1																	107979322		1568	3582	5150	107780845	SO:0001583	missense	22854			AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1291C>T	1.37:g.107979322C>T	ENSP00000359085:p.Arg431Cys		107780845	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	37	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489584	0.84962	.	.	ENSG00000162631	ENST00000370073;ENST00000542803;ENST00000370061;ENST00000370064;ENST00000370062;ENST00000370068	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	6.17	6.17	0.99709	EGF-like, laminin (3);	0.000000	0.64402	D	0.000007	T	0.80121	0.4565	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.63957	0.892;0.92	T	0.79610	-0.1732	10	0.48119	T	0.1	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	397;431	B4DKF0;Q9Y2I2	.;NTNG1_HUMAN	C	431;431;397;234;178;431	ENSP00000359090:R431C;ENSP00000440561:R431C;ENSP00000359078:R397C;ENSP00000359085:R431C	ENSP00000359078:R397C	R	+	1	0	NTNG1	107780845	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.481000	0.81124	2.941000	0.99782	0.655000	0.94253	CGT		0.473	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		T	107979322	C	T	107979322	3	4	61	1	0	0	0	0	1	0	0	0	10735	884	31	1	1447	1	NTNG1	1	107979322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3819127	107979322	141271299	478	8463										
VAV3	10451	broad.mit.edu	37	chr1	108507455	108507455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgggcagcaccttgcaatGgatgagccactgcgcgcact	14	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:108507455G>T	ENST00000370056.4	-	1	311	c.37C>A	c.(37-39)Cat>Aat	p.H13N	VAV3-AS1_ENST00000438318.1_RNA|VAV3_ENST00000527011.1_Missense_Mutation_p.H13N|VAV3_ENST00000371846.4_5'UTR	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	13	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.H13N(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		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)		ACCTTGCAATGGATGAGCCAC	0.716																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	45	49					1																	108507455		2203	4300	6503	108308978	SO:0001583	missense	10451			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.37C>A	1.37:g.108507455G>T	ENSP00000359073:p.His13Asn		108308978	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	G	8.273	0.813768	0.16537	.	.	ENSG00000134215	ENST00000370056;ENST00000527011	T;T	0.58060	0.36;0.36	4.77	4.77	0.60923	Calponin homology domain (5);	0.266237	0.34362	N	0.004027	T	0.10078	0.0247	N	0.00926	-1.1	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.11743	-1.0575	10	0.24483	T	0.36	.	10.6438	0.45608	0.0:0.0:0.6968:0.3032	.	13;13;13	B7ZLR1;E9PQ97;Q9UKW4	.;.;VAV3_HUMAN	N	13	ENSP00000359073:H13N;ENSP00000432540:H13N	ENSP00000359073:H13N	H	-	1	0	VAV3	108308978	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.369000	0.34227	2.228000	0.72767	0.456000	0.33151	CAT		0.716	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108507455	G	T	108507455	3	4	61	1	0	0	0	0	1	0	0	0	17173	1348	47	2	2639	2	VAV3	1	108507455	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	528133	108507455	140743166	479	8464										
SLC25A24	29957	broad.mit.edu	37	chr1	108691003	108691003	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcttcagtaagtaacttCttgtactgtataaacaagtt	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:108691003C>A	ENST00000565488.1	-	7	1047	c.828G>T	c.(826-828)aaG>aaT	p.K276N	SLC25A24_ENST00000370041.4_Missense_Mutation_p.K257N	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	276					ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)	p.K257N(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TAAGTAACTTCTTGTACTGTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											140	129	132					1																	108691003		2203	4300	6503	108492526	SO:0001583	missense	29957			AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"Solute carriers", "EF-hand domain containing"	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.828G>T	1.37:g.108691003C>A	ENSP00000457733:p.Lys276Asn		108492526	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Missense_Mutation	SNP	ENST00000565488.1	37	CCDS41361.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608778	0.66558	.	.	ENSG00000085491	ENST00000264128;ENST00000370041	D	0.83755	-1.76	5.83	5.83	0.93111	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.91202	0.7228	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	D	0.91883	0.5517	10	0.87932	D	0	-31.0486	17.2898	0.87152	0.0:1.0:0.0:0.0	.	276;257	Q6NUK1;Q6NUK1-2	SCMC1_HUMAN;.	N	276;257	ENSP00000359058:K257N	ENSP00000264128:K276N	K	-	3	2	SLC25A24	108492526	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	2.375000	0.44283	2.770000	0.95276	0.655000	0.94253	AAG		0.388	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386		A	108691003	C	A	108691003	3	1	61	1	0	0	0	0	1	0	0	0	14524	912	32	2	621	2	SLC25A24	1	108691003	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	183548	108691003	140559618	480	8465										
SLC25A24	29957	broad.mit.edu	37	chr1	108697624	108697624	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgttcatatgcccagaatTtaacagctgtctcaggagca	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:108697624T>G	ENST00000565488.1	-	6	1022	c.803A>C	c.(802-804)aAa>aCa	p.K268T	SLC25A24_ENST00000370041.4_Missense_Mutation_p.K249T	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	268					ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)	p.K249T(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TGCCCAGAATTTAACAGCTGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	116	118					1																	108697624		2203	4300	6503	108499147	SO:0001583	missense	29957			AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"Solute carriers", "EF-hand domain containing"	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.803A>C	1.37:g.108697624T>G	ENSP00000457733:p.Lys268Thr		108499147	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Missense_Mutation	SNP	ENST00000565488.1	37	CCDS41361.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641367	0.87859	.	.	ENSG00000085491	ENST00000264128;ENST00000370041	T	0.78924	-1.22	5.59	5.59	0.84812	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.83912	0.5357	M	0.67700	2.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.991	D	0.86411	0.1748	10	0.87932	D	0	-26.5396	14.9397	0.70983	0.0:0.0:0.0:1.0	.	268;249	Q6NUK1;Q6NUK1-2	SCMC1_HUMAN;.	T	268;249	ENSP00000359058:K249T	ENSP00000264128:K268T	K	-	2	0	SLC25A24	108499147	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.967000	0.87967	2.121000	0.65114	0.397000	0.26171	AAA		0.383	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386		G	108697624	T	G	108697624	3	3	61	1	0	0	0	0	1	0	0	0	14524	1841	64	4	650	4	SLC25A24	1	108697624	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6621	108697624	140552997	481	8466										
AKNAD1	254268	broad.mit.edu	37	chr1	109366200	109366200	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgttacctttagttggttCtttcctgcaggctcttcggg	11	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109366200C>A	ENST00000370001.3	-	12	2315	c.2047G>T	c.(2047-2049)Gaa>Taa	p.E683*	AKNAD1_ENST00000477908.1_5'Flank|AKNAD1_ENST00000369995.3_Nonsense_Mutation_p.E683*|AKNAD1_ENST00000357393.4_Nonsense_Mutation_p.E390*|AKNAD1_ENST00000369994.1_Nonsense_Mutation_p.E653*	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	683						cytoplasm (GO:0005737)		p.E683*(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TTAGTTGGTTCTTTCCTGCAG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											128	110	116					1																	109366200		2203	4300	6503	109167723	SO:0001587	stop_gained	254268			AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.2047G>T	1.37:g.109366200C>A	ENSP00000359018:p.Glu683*		109167723	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Nonsense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	.	.	.	.	.	.	.	.	.	.	C	14.58	2.578103	0.45902	.	.	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	.	.	.	4.34	1.4	0.22301	.	1.190400	0.06206	N	0.684196	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	0.0052	4.4143	0.11448	0.0:0.6107:0.1862:0.2031	.	.	.	.	X	683;390;653;683	.	ENSP00000349968:E390X	E	-	1	0	AKNAD1	109167723	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.633000	0.24598	0.338000	0.23692	0.561000	0.74099	GAA		0.473	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		A	109366200	C	A	109366200	4	1	61	1	0	0	0	0	0	1	0	0	464	922	32	2	483	2	AKNAD1	1	109366200	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	668576	109366200	139884421	482	8467										
AKNAD1	254268	broad.mit.edu	37	chr1	109391427	109391427	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttttattcttttggaaaAttcttgtacctgcagtgaaa	7	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109391427A>G	ENST00000370001.3	-	5	1460	c.1192T>C	c.(1192-1194)Ttt>Ctt	p.F398L	AKNAD1_ENST00000369995.3_Missense_Mutation_p.F398L|AKNAD1_ENST00000357393.4_Missense_Mutation_p.F105L|AKNAD1_ENST00000369994.1_Missense_Mutation_p.F398L	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	398						cytoplasm (GO:0005737)		p.F398L(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						CTTTTGGAAAATTCTTGTACC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	116	111					1																	109391427		2203	4297	6500	109192950	SO:0001583	missense	254268			AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1192T>C	1.37:g.109391427A>G	ENSP00000359018:p.Phe398Leu		109192950	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	.	.	.	.	.	.	.	.	.	.	A	19.18	3.778217	0.70107	.	.	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.45	4.31	0.51392	.	0.170974	0.42682	D	0.000676	T	0.30572	0.0769	N	0.24115	0.695	0.29914	N	0.823358	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.10245	-1.0638	10	0.66056	D	0.02	-23.9991	10.3672	0.44030	0.9204:0.0:0.0796:0.0	.	105;398	B4DET8;Q5T1N1	.;AKND1_HUMAN	L	398;105;398;398	ENSP00000359018:F398L;ENSP00000349968:F105L;ENSP00000359011:F398L;ENSP00000359012:F398L	ENSP00000349968:F105L	F	-	1	0	AKNAD1	109192950	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.686000	0.54685	2.193000	0.70182	0.533000	0.62120	TTT		0.308	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		G	109391427	A	G	109391427	3	3	61	1	0	0	0	0	1	0	0	0	464	101	4	4	1366	4	AKNAD1	1	109391427	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	25227	109391427	139859194	483	8468										
CLCC1	23155	broad.mit.edu	37	chr1	109486195	109486195	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtacatatgtccacagctCagtagccactaaaaccacga	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109486195C>T	ENST00000369971.2	-	6	733	c.604G>A	c.(604-606)Gag>Aag	p.E202K	CLCC1_ENST00000356970.2_Missense_Mutation_p.E202K|CLCC1_ENST00000369969.2_Intron|CLCC1_ENST00000415331.1_Missense_Mutation_p.E152K|CLCC1_ENST00000302500.4_Intron|CLCC1_ENST00000369968.2_Intron|CLCC1_ENST00000369976.1_Missense_Mutation_p.E202K|CLCC1_ENST00000482889.1_5'UTR|CLCC1_ENST00000369970.3_Missense_Mutation_p.E152K|CLCC1_ENST00000348264.2_Intron|AKNAD1_ENST00000357393.4_Intron	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	202						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)	p.E152K(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		GTCCACAGCTCAGTAGCCACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	99	97					1																	109486195		2203	4300	6503	109287718	SO:0001583	missense	23155			AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"Mid1-related chloride channel (yeast)"					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.604G>A	1.37:g.109486195C>T	ENSP00000358988:p.Glu202Lys		109287718	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096999	0.76870	.	.	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369976;ENST00000369970	T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43	5.26	4.34	0.51931	.	0.218442	0.47455	D	0.000229	T	0.62612	0.2442	M	0.79475	2.455	0.80722	D	1	P;P	0.52842	0.956;0.955	P;P	0.59546	0.859;0.759	T	0.70450	-0.4868	10	0.72032	D	0.01	-28.1997	15.808	0.78531	0.0:0.8632:0.1368:0.0	.	152;202	Q96S66-2;Q96S66	.;CLCC1_HUMAN	K	202;202;152;202;152	ENSP00000349456:E202K;ENSP00000358988:E202K;ENSP00000411591:E152K;ENSP00000358993:E202K;ENSP00000358987:E152K	ENSP00000349456:E202K	E	-	1	0	CLCC1	109287718	0.577000	0.26708	0.920000	0.36463	0.739000	0.42172	1.645000	0.37238	1.319000	0.45190	0.591000	0.81541	GAG		0.393	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127		T	109486195	C	T	109486195	3	4	61	1	0	0	0	0	1	0	0	0	3466	835	29	3	1075	3	CLCC1	1	109486195	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94768	109486195	139764426	484	8469										
WDR47	22911	broad.mit.edu	37	chr1	109524430	109524430	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaaatctaacagtcttatCttgggaaccagatgcaatca	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109524430C>A	ENST00000369962.3	-	13	2545	c.2323G>T	c.(2323-2325)Gat>Tat	p.D775Y	WDR47_ENST00000361054.3_Missense_Mutation_p.D747Y|WDR47_ENST00000400794.3_Missense_Mutation_p.D783Y|WDR47_ENST00000369965.4_Missense_Mutation_p.D776Y|WDR47_ENST00000357672.3_Missense_Mutation_p.D747Y			O94967	WDR47_HUMAN	WD repeat domain 47	775					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.D776Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		ACAGTCTTATCTTGGGAACCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											111	110	110					1																	109524430		2203	4300	6503	109325953	SO:0001583	missense	22911			AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.2323G>T	1.37:g.109524430C>A	ENSP00000358979:p.Asp775Tyr		109325953	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	ENST00000369962.3	37	CCDS44187.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667915	0.88348	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672	D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51	5.4	5.4	0.78164	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.97241	0.9098	H	0.99273	4.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99029	1.0820	10	0.87932	D	0	-13.5098	19.1641	0.93546	0.0:1.0:0.0:0.0	.	747;783;775;776	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	Y	783;775;747;776;747	ENSP00000383599:D783Y;ENSP00000358979:D775Y;ENSP00000354339:D747Y;ENSP00000358982:D776Y;ENSP00000350301:D747Y	ENSP00000350301:D747Y	D	-	1	0	WDR47	109325953	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.532000	0.85374	0.591000	0.81541	GAT		0.368	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		A	109524430	C	A	109524430	3	1	61	1	0	0	0	0	1	0	0	0	17340	913	32	2	448	2	WDR47	1	109524430	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38235	109524430	139726191	485	8470										
C1orf194	127003	broad.mit.edu	37	chr1	109650547	109650547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaatgctaggtacctcgGgatcaaaatagtaggcatcc	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109650547G>A	ENST00000369948.3	-	2	269	c.194C>T	c.(193-195)cCc>cTc	p.P65L	C1orf194_ENST00000369949.4_Missense_Mutation_p.P53L|C1orf194_ENST00000369945.3_Intron			Q5T5A4	CA194_HUMAN	chromosome 1 open reading frame 194	65								p.P53L(1)		large_intestine(2)|lung(2)|ovary(2)	6						AGGTACCTCGGGATCAAAATA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	84	86					1																	109650547		1568	3582	5150	109452070	SO:0001583	missense	127003				CCDS41364.1	1p13.3	2011-03-31			ENSG00000179902	ENSG00000179902			32331	protein-coding gene	gene with protein product							Standard	NM_001122961		Approved		uc009wew.3	Q5T5A4	OTTHUMG00000011735	ENST00000369948.3:c.194C>T	1.37:g.109650547G>A	ENSP00000358964:p.Pro65Leu		109452070	Q5T5A3	Missense_Mutation	SNP	ENST00000369948.3	37		.	.	.	.	.	.	.	.	.	.	g	3.869	-0.028333	0.07589	.	.	ENSG00000179902	ENST00000369949;ENST00000369948	.	.	.	3.93	0.882	0.19172	.	0.649942	0.13547	N	0.379773	T	0.18173	0.0436	M	0.74647	2.275	0.09310	N	1	P;B	0.36535	0.557;0.192	B;B	0.31101	0.124;0.099	T	0.15009	-1.0452	9	0.87932	D	0	-8.4247	4.3693	0.11239	0.2172:0.1846:0.5982:0.0	.	53;65	Q5T5A4-2;Q5T5A4	.;CA194_HUMAN	L	53;65	.	ENSP00000358964:P65L	P	-	2	0	C1orf194	109452070	0.003000	0.15002	0.000000	0.03702	0.020000	0.10135	1.247000	0.32815	0.073000	0.16731	-0.776000	0.03382	CCC		0.488	C1orf194-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000032416.2	NM_001122961		A	109650547	G	A	109650547	3	1	61	1	0	0	0	0	1	0	0	0	2031	1232	43	3	331	3	C1orf194	1	109650547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	126117	109650547	139600074	486	8471										
KIAA1324	57535	broad.mit.edu	37	chr1	109707313	109707313	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccaccgggaactgtacttCgtgagtctgcacacaccccc	9	16	1	1	rs138658561		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109707313C>T	ENST00000369939.3	+	3	650	c.467C>T	c.(466-468)tCg>tTg	p.S156L	KIAA1324_ENST00000529753.1_Splice_Site_p.S156L	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	156					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)	p.S156L(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		AACTGTACTTCGTGAGTCTGC	0.637													C|||	1	0.000199681	8e-04	0	5008	,	,		9269	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	LEU/SER	0,4406		0,0,2203	76	56	63		467	-1.5	0.6	1	dbSNP_134	63	4,8596	3.7+/-12.6	0,4,4296	yes	missense-near-splice	KIAA1324	NM_020775.3	145	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	benign	156/1014	109707313	4,13002	2203	4300	6503	109508836	SO:0001630	splice_region_variant	57535			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.467+1C>T	1.37:g.109707313C>T			109508836	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	16.05	3.013919	0.54468	0.0	4.65E-4	ENSG00000116299	ENST00000531664;ENST00000369939;ENST00000457623;ENST00000529753	T;T;T;T	0.43688	1.56;0.94;0.94;0.94	5.92	-1.51	0.08664	.	1.029680	0.07659	N	0.933379	T	0.12347	0.0300	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.10296	0.003;0.0;0.001;0.001	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.37911	-0.9685	10	0.27082	T	0.32	0.3412	12.3139	0.54944	0.0:0.3531:0.0:0.6469	.	156;156;156;156	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	L	156	ENSP00000431349:S156L;ENSP00000358955:S156L;ENSP00000393964:S156L;ENSP00000434595:S156L	ENSP00000358955:S156L	S	+	2	0	KIAA1324	109508836	0.149000	0.22717	0.577000	0.28562	0.940000	0.58332	0.004000	0.13106	-0.313000	0.08728	0.561000	0.74099	TCG		0.637	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	Missense_Mutation	T	109707313	C	T	109707313	5	4	61	1	0	0	0	0	0	0	1	0	8244	898	31	1	477	1	KIAA1324	1	109707313	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56766	109707313	139543308	487	8472										
KIAA1324	57535	broad.mit.edu	37	chr1	109743433	109743433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccagcagctgacagctgcGccatcatggaaggcgaggat	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109743433G>A	ENST00000369939.3	+	21	3067	c.2884G>A	c.(2884-2886)Gcc>Acc	p.A962T	KIAA1324_ENST00000369938.1_3'UTR|KIAA1324_ENST00000529753.1_Missense_Mutation_p.A875T	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	962					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)	p.A962T(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TGACAGCTGCGCCATCATGGA	0.488											OREG0013630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											106	95	99					1																	109743433		2203	4300	6503	109544956	SO:0001583	missense	57535			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.2884G>A	1.37:g.109743433G>A	ENSP00000358955:p.Ala962Thr	1422	109544956	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	.	.	.	.	.	.	.	.	.	.	G	36	5.852699	0.97030	.	.	ENSG00000116299	ENST00000369939;ENST00000529753	T;T	0.19806	2.12;2.14	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.998;0.998	T	0.31888	-0.9927	10	0.87932	D	0	-31.3648	19.0678	0.93119	0.0:0.0:1.0:0.0	.	962;875;962;962	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	T	962;875	ENSP00000358955:A962T;ENSP00000434595:A875T	ENSP00000358955:A962T	A	+	1	0	KIAA1324	109544956	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.732000	0.98816	2.813000	0.96785	0.655000	0.94253	GCC		0.488	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		A	109743433	G	A	109743433	3	1	61	1	0	0	0	0	1	0	0	0	8244	1087	38	1	2966	1	KIAA1324	1	109743433	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36120	109743433	139507188	488	8473										
SARS	6301	broad.mit.edu	37	chr1	109780386	109780386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcccctttgtgaagcctgCgcccattgagcaggagccat	11	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109780386C>T	ENST00000234677.2	+	11	1496	c.1421C>T	c.(1420-1422)gCg>gTg	p.A474V	SARS_ENST00000468588.1_3'UTR|SARS_ENST00000369923.4_Missense_Mutation_p.A496V	NM_006513.3	NP_006504.2	P49591	SYSC_HUMAN	seryl-tRNA synthetase	474					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|RNA binding (GO:0003723)|serine-tRNA ligase activity (GO:0004828)	p.A474V(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	17		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	GTGAAGCCTGCGCCCATTGAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											128	116	120					1																	109780386		2203	4300	6503	109581909	SO:0001583	missense	6301			BC009390	CCDS795.1	1p13.3	2011-07-01			ENSG00000031698	ENSG00000031698	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	10537	protein-coding gene	gene with protein product	"serine tRNA ligase 1, cytoplasmic"	607529				9431993	Standard	NM_006513		Approved	SERS	uc001dwu.2	P49591	OTTHUMG00000011726	ENST00000234677.2:c.1421C>T	1.37:g.109780386C>T	ENSP00000234677:p.Ala474Val		109581909	B2R6Y9|Q5T5C8|Q9NSE3	Missense_Mutation	SNP	ENST00000234677.2	37	CCDS795.1	.	.	.	.	.	.	.	.	.	.	N	19.95	3.920881	0.73213	.	.	ENSG00000031698	ENST00000234677;ENST00000369923	T;T	0.78126	-1.1;-1.15	6.04	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.67069	0.2854	L	0.51853	1.615	0.80722	D	1	D;P;D;P	0.61697	0.99;0.95;0.973;0.95	P;P;P;B	0.45506	0.483;0.471;0.471;0.353	T	0.69476	-0.5135	10	0.40728	T	0.16	-18.9032	15.1714	0.72875	0.0:0.9319:0.0:0.0681	.	471;474;496;474	Q0VGA5;Q53HA4;Q5T5C7;P49591	.;.;.;SYSC_HUMAN	V	474;496	ENSP00000234677:A474V;ENSP00000358939:A496V	ENSP00000234677:A474V	A	+	2	0	SARS	109581909	1.000000	0.71417	0.847000	0.33407	0.982000	0.71751	7.098000	0.76974	1.586000	0.49944	0.585000	0.79938	GCG		0.517	SARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032394.2	NM_006513		T	109780386	C	T	109780386	3	4	61	1	0	0	0	0	1	0	0	0	13881	768	27	1	1463	1	SARS	1	109780386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36953	109780386	139470235	489	8474										
CELSR2	1952	broad.mit.edu	37	chr1	109803856	109803856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcacctttcgcggcctgcGccagcgtttccacttcaccc	7	19	2	0	rs377639803		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109803856G>A	ENST00000271332.3	+	3	4212	c.4151G>A	c.(4150-4152)cGc>cAc	p.R1384H		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1384	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R1384H(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CGCGGCCTGCGCCAGCGTTTC	0.632																																					NSCLC(158;1285 2011 34800 34852 42084)											1	Substitution - Missense(1)	large_intestine(1)	1						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	57	58	58		4151	4.8	1	1		58	0,8600		0,0,4300	no	missense	CELSR2	NM_001408.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1384/2924	109803856	1,13005	2203	4300	6503	109605379	SO:0001583	missense	1952			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.4151G>A	1.37:g.109803856G>A	ENSP00000271332:p.Arg1384His		109605379	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	G	35	5.591387	0.96590	2.27E-4	0.0	ENSG00000143126	ENST00000271332	T	0.79554	-1.28	4.77	4.77	0.60923	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.89563	0.6751	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90651	0.4582	9	0.62326	D	0.03	.	17.9928	0.89174	0.0:0.0:1.0:0.0	.	1384	Q9HCU4	CELR2_HUMAN	H	1384	ENSP00000271332:R1384H	ENSP00000271332:R1384H	R	+	2	0	CELSR2	109605379	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.635000	0.98437	2.478000	0.83669	0.561000	0.74099	CGC		0.632	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109803856	G	A	109803856	3	1	61	1	0	0	0	0	1	0	0	0	3228	1087	38	1	4161	1	CELSR2	1	109803856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23470	109803856	139446765	490	8475										
CELSR2	1952	broad.mit.edu	37	chr1	109808788	109808788	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtggccccgtacccgcttCgggctgcctgctgctgctcc	13	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109808788C>T	ENST00000271332.3	+	15	6034	c.5973C>T	c.(5971-5973)ttC>ttT	p.F1991F		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1991					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.F1991F(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GTACCCGCTTCGGGCTGCCTG	0.607																																					NSCLC(158;1285 2011 34800 34852 42084)											1	Substitution - coding silent(1)	large_intestine(1)	1											72	64	67					1																	109808788		2203	4300	6503	109610311	SO:0001819	synonymous_variant	1952			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5973C>T	1.37:g.109808788C>T			109610311	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																				0.607	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109808788	C	T	109808788	2	4	61	1	0	0	0	0	0	0	0	1	3228	883	31	1		1	CELSR2	1	109808788	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4932	109808788	139441833	491	8476										
SORT1	6272	broad.mit.edu	37	chr1	109884689	109884689	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatttgctgccagaataGaatagaactgttcctgtccc	7	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:109884689G>T	ENST00000256637.6	-	9	1113	c.1055C>A	c.(1054-1056)tCt>tAt	p.S352Y	SORT1_ENST00000538502.1_Missense_Mutation_p.S215Y	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	352					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)	p.S352Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		TGCCAGAATAGAATAGAACTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	136	142					1																	109884689		2203	4300	6503	109686212	SO:0001583	missense	6272			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.1055C>A	1.37:g.109884689G>T	ENSP00000256637:p.Ser352Tyr		109686212	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	.	.	.	.	.	.	.	.	.	.	g	17.81	3.480007	0.63849	.	.	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.29917	1.55;1.55	6.01	6.01	0.97437	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.32763	0.0840	L	0.42245	1.32	0.80722	D	1	D;D	0.89917	0.975;1.0	P;D	0.97110	0.792;1.0	T	0.04065	-1.0980	10	0.02654	T	1	-16.0378	19.3162	0.94215	0.0:0.0:1.0:0.0	.	215;352	B4DWI3;Q99523	.;SORT_HUMAN	Y	352;215	ENSP00000256637:S352Y;ENSP00000438597:S215Y	ENSP00000256637:S352Y	S	-	2	0	SORT1	109686212	1.000000	0.71417	0.990000	0.47175	0.984000	0.73092	8.748000	0.91615	2.864000	0.98301	0.550000	0.68814	TCT		0.458	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959		T	109884689	G	T	109884689	3	4	61	1	0	0	0	0	1	0	0	0	14972	942	33	2	1488	2	SORT1	1	109884689	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75901	109884689	139365932	492	8477										
CYB561D1	284613	broad.mit.edu	37	chr1	110038434	110038434	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctgaacactccctgttCttcttctgctcccgaaaagc	5	16	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110038434C>T	ENST00000420578.2	+	3	283	c.243C>T	c.(241-243)ttC>ttT	p.F81F	CYB561D1_ENST00000496961.1_3'UTR|CYB561D1_ENST00000310611.4_Missense_Mutation_p.S116F|CYB561D1_ENST00000430195.2_3'UTR|CYB561D1_ENST00000533024.1_Missense_Mutation_p.S37F|CYB561D1_ENST00000528785.1_Silent_p.F81F|CYB561D1_ENST00000369868.3_Silent_p.F103F|CYB561D1_ENST00000393709.3_Silent_p.F24F|CYB561D1_ENST00000527072.1_3'UTR			Q8N8Q1	C56D1_HUMAN	cytochrome b561 family, member D1	81	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.F81F(1)		breast(1)|large_intestine(3)|prostate(1)	5		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0422)|Epithelial(280;0.0655)|all cancers(265;0.0685)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		ACTCCCTGTTCTTCTTCTGCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	1											196	194	195					1																	110038434		2203	4300	6503	109839957	SO:0001819	synonymous_variant	284613			AK096354	CCDS800.1, CCDS44188.1, CCDS44189.1, CCDS44190.1, CCDS44191.1	1p13.2	2013-03-14	2013-03-14		ENSG00000174151	ENSG00000174151		"Cytochrome b genes"	26804	protein-coding gene	gene with protein product			"cytochrome b-561 domain containing 1"			23249217	Standard	NM_182580		Approved	FLJ39035, FLJ44753	uc010ovo.2	Q8N8Q1	OTTHUMG00000011051	ENST00000420578.2:c.243C>T	1.37:g.110038434C>T			109839957	B4DH97|E9PCM8|Q52M36|Q5T6C2|Q5T6C3	Silent	SNP	ENST00000420578.2	37	CCDS800.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.805136	0.50315	.	.	ENSG00000174151	ENST00000533024;ENST00000310611	.	.	.	5.25	4.33	0.51752	.	.	.	.	.	T	0.36054	0.0953	.	.	.	0.80722	D	1	B	0.33448	0.412	B	0.32583	0.148	T	0.46665	-0.9175	7	0.87932	D	0	-28.976	11.5206	0.50549	0.0:0.9149:0.0:0.0851	.	116	Q8N8Q1-2	.	F	37;116	.	ENSP00000309324:S116F	S	+	2	0	CYB561D1	109839957	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	1.938000	0.40203	1.418000	0.47098	0.555000	0.69702	TCT		0.567	CYB561D1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030384.1	NM_182580		T	110038434	C	T	110038434	2	4	61	1	0	0	0	0	0	0	0	1	4126	913	32	3		3	CYB561D1	1	110038434	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153745	110038434	139212187	493	8478										
AMIGO1	57463	broad.mit.edu	37	chr1	110050472	110050472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattgtgcactttcaattCcacagacagtgtctcattga	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110050472C>T	ENST00000369864.4	-	2	1412	c.1063G>A	c.(1063-1065)Gaa>Aaa	p.E355K	AMIGO1_ENST00000369862.1_Missense_Mutation_p.E355K					adhesion molecule with Ig-like domain 1									p.E355K(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0182)|Epithelial(280;0.046)|all cancers(265;0.0492)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		ACTTTCAATTCCACAGACAGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											169	144	152					1																	110050472		2203	4300	6503	109851995	SO:0001583	missense	57463				CCDS30795.1	1p13.3	2013-01-11			ENSG00000181754	ENSG00000181754		"Immunoglobulin superfamily / V-set domain containing"	20824	protein-coding gene	gene with protein product	"amphoterin-induced gene and open reading frame"	615689				12629050	Standard	NM_020703		Approved	AMIGO, KIAA1163	uc001dxx.4	Q86WK6	OTTHUMG00000011653	ENST00000369864.4:c.1063G>A	1.37:g.110050472C>T	ENSP00000358880:p.Glu355Lys		109851995		Missense_Mutation	SNP	ENST00000369864.4	37	CCDS30795.1	.	.	.	.	.	.	.	.	.	.	C	3.057	-0.194190	0.06259	.	.	ENSG00000181754	ENST00000369864;ENST00000369862	T;T	0.65178	-0.14;-0.14	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.318739	0.25294	N	0.031701	T	0.32071	0.0817	L	0.31752	0.955	0.35868	D	0.828022	P	0.41345	0.746	B	0.37144	0.242	T	0.27971	-1.0058	10	0.31617	T	0.26	-13.3151	9.0964	0.36642	0.0:0.7756:0.1486:0.0758	.	355	Q86WK6	AMGO1_HUMAN	K	355	ENSP00000358880:E355K;ENSP00000358878:E355K	ENSP00000358878:E355K	E	-	1	0	AMIGO1	109851995	0.000000	0.05858	1.000000	0.80357	0.941000	0.58515	-0.311000	0.08124	2.941000	0.99782	0.655000	0.94253	GAA		0.507	AMIGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032247.1	NM_020703		T	110050472	C	T	110050472	3	4	61	1	0	0	0	0	1	0	0	0	575	864	30	3	422	3	AMIGO1	1	110050472	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12038	110050472	139200149	494	8479										
GNAT2	2780	broad.mit.edu	37	chr1	110148949	110148949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaaattcaagtctttgaCggaaaacttggtttcaatga	8	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110148949C>T	ENST00000351050.3	-	5	757	c.571G>A	c.(571-573)Gtc>Atc	p.V191I		NM_005272.3	NP_005263.1	P19087	GNAT2_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 2	191					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to light intensity (GO:0009642)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)	p.V191I(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	14		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0422)|Colorectal(144;0.108)|Epithelial(280;0.125)|all cancers(265;0.129)|LUSC - Lung squamous cell carcinoma(189;0.227)		AAGTCTTTGACGGAAAACTTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											145	131	136					1																	110148949		2203	4300	6503	109950472	SO:0001583	missense	2780			BC000233	CCDS803.1	1p13	2013-01-08			ENSG00000134183	ENSG00000134183			4394	protein-coding gene	gene with protein product		139340				8406495	Standard	NM_005272		Approved	ACHM4	uc001dya.3	P19087	OTTHUMG00000011639	ENST00000351050.3:c.571G>A	1.37:g.110148949C>T	ENSP00000251337:p.Val191Ile		109950472		Missense_Mutation	SNP	ENST00000351050.3	37	CCDS803.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.214350	0.58452	.	.	ENSG00000134183	ENST00000351050	D	0.88818	-2.43	5.05	4.13	0.48395	.	0.185160	0.49305	N	0.000153	T	0.62405	0.2425	N	0.05487	-0.04	0.33532	D	0.593706	B	0.25235	0.121	B	0.20184	0.028	T	0.59166	-0.7505	10	0.40728	T	0.16	.	8.7189	0.34428	0.1493:0.7736:0.0:0.0771	.	191	P19087	GNAT2_HUMAN	I	191	ENSP00000251337:V191I	ENSP00000251337:V191I	V	-	1	0	GNAT2	109950472	0.986000	0.35501	0.959000	0.39883	0.986000	0.74619	2.723000	0.47277	1.496000	0.48567	0.655000	0.94253	GTC		0.488	GNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032181.1	NM_005272		T	110148949	C	T	110148949	3	4	61	1	0	0	0	0	1	0	0	0	6532	536	19	1	509	1	GNAT2	1	110148949	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98477	110148949	139101672	495	8480										
GSTM3	2947	broad.mit.edu	37	chr1	110279777	110279777	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagactgtaagtaggcagcGattttctccaaagcctgaaa	9	9	2	2	rs561954445		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110279777G>A	ENST00000540225.1	-	9	904	c.594C>T	c.(592-594)atC>atT	p.I198I	GSTM3_ENST00000256594.3_Silent_p.I198I|GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000361066.2_Silent_p.I198I|RP4-735C1.4_ENST00000431955.1_RNA			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	198	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.I198I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	AGTAGGCAGCGATTTTCTCCA	0.483													G|||	1	0.000199681	0	0	5008	,	,		19336	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											103	95	97					1																	110279777		2203	4300	6503	110081300	SO:0001819	synonymous_variant	2947			BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"Glutathione S-transferases / Soluble"	4635	protein-coding gene	gene with protein product		138390	"glutathione S-transferase M3 (brain)"			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.594C>T	1.37:g.110279777G>A			110081300	O60550|Q96HA3	Silent	SNP	ENST00000540225.1	37	CCDS812.1																																																																																				0.483	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849		A	110279777	G	A	110279777	2	1	61	1	0	0	0	0	0	0	0	1	6860	1048	37	1		1	GSTM3	1	110279777	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130828	110279777	138970844	496	8481										
GSTM3	2947	broad.mit.edu	37	chr1	110280727	110280727	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacgtggtcagagctgtAacagagccttatcagttgtg	11	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110280727A>G	ENST00000540225.1	-	6	668	c.358T>C	c.(358-360)Tac>Cac	p.Y120H	GSTM3_ENST00000256594.3_Missense_Mutation_p.Y120H|GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000361066.2_Missense_Mutation_p.Y120H|RP4-735C1.4_ENST00000431955.1_RNA			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	120	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.Y120H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	TCAGAGCTGTAACAGAGCCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											201	188	192					1																	110280727		2203	4300	6503	110082250	SO:0001583	missense	2947			BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"Glutathione S-transferases / Soluble"	4635	protein-coding gene	gene with protein product		138390	"glutathione S-transferase M3 (brain)"			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.358T>C	1.37:g.110280727A>G	ENSP00000444978:p.Tyr120His		110082250	O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	37	CCDS812.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103466	0.56291	.	.	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.04083	3.71;3.71;3.71	5.26	5.26	0.73747	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.110218	0.64402	D	0.000005	T	0.10465	0.0256	M	0.92507	3.315	0.80722	D	1	B;B;B	0.30605	0.287;0.258;0.287	B;B;B	0.39904	0.131;0.313;0.131	T	0.00183	-1.1945	10	0.66056	D	0.02	-2.1436	14.2885	0.66260	1.0:0.0:0.0:0.0	.	120;126;120	Q6FGJ9;Q59EJ5;P21266	.;.;GSTM3_HUMAN	H	120	ENSP00000444978:Y120H;ENSP00000256594:Y120H;ENSP00000354357:Y120H	ENSP00000256594:Y120H	Y	-	1	0	GSTM3	110082250	1.000000	0.71417	0.997000	0.53966	0.091000	0.18340	5.835000	0.69368	2.198000	0.70561	0.460000	0.39030	TAC		0.443	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849		G	110280727	A	G	110280727	3	3	61	1	0	0	0	0	1	0	0	0	6860	362	13	4	335	4	GSTM3	1	110280727	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	950	110280727	138969894	497	8482										
UBL4B	164153	broad.mit.edu	37	chr1	110655384	110655384	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatgcagcccttggagaaGatggcgctaaaggaggccca	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110655384G>T	ENST00000334179.3	+	1	323	c.228G>T	c.(226-228)aaG>aaT	p.K76N		NM_203412.1	NP_981957.1	Q8N7F7	UBL4B_HUMAN	ubiquitin-like 4B	76	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					cytoplasm (GO:0005737)		p.K76N(1)		endometrium(1)|kidney(1)|large_intestine(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	7		all_cancers(81;1.14e-05)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0236)|all cancers(265;0.0823)|Epithelial(280;0.0917)|Colorectal(144;0.109)|LUSC - Lung squamous cell carcinoma(189;0.134)		CCTTGGAGAAGATGGCGCTAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	76	75					1																	110655384		2203	4300	6503	110456907	SO:0001583	missense	164153				CCDS820.1	1p13.3	2013-09-24			ENSG00000186150	ENSG00000186150			32309	protein-coding gene	gene with protein product		611127				16872915	Standard	NM_203412		Approved	FLJ25690	uc001dzc.3	Q8N7F7	OTTHUMG00000166989	ENST00000334179.3:c.228G>T	1.37:g.110655384G>T	ENSP00000334044:p.Lys76Asn		110456907		Missense_Mutation	SNP	ENST00000334179.3	37	CCDS820.1	.	.	.	.	.	.	.	.	.	.	G	3.900	-0.022134	0.07634	.	.	ENSG00000186150	ENST00000334179	T	0.41065	1.01	4.08	-1.93	0.07594	.	0.460781	0.23123	N	0.051667	T	0.11580	0.0282	M	0.63428	1.95	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.23119	-1.0197	10	0.27785	T	0.31	-21.4569	3.1919	0.06620	0.0892:0.138:0.3052:0.4676	.	76	Q8N7F7	UBL4B_HUMAN	N	76	ENSP00000334044:K76N	ENSP00000334044:K76N	K	+	3	2	UBL4B	110456907	0.386000	0.25180	0.000000	0.03702	0.011000	0.07611	0.516000	0.22817	-0.681000	0.05204	-0.397000	0.06425	AAG		0.577	UBL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392303.1	NM_203412		T	110655384	G	T	110655384	3	4	61	1	0	0	0	0	1	0	0	0	16928	933	33	2	230	2	UBL4B	1	110655384	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	374657	110655384	138595237	498	8483										
SLC6A17	388662	broad.mit.edu	37	chr1	110738257	110738257	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctgttgttcgtccagcgCtccggaaactactttgtcac	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110738257C>T	ENST00000331565.4	+	10	2027	c.1542C>T	c.(1540-1542)cgC>cgT	p.R514R		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	514					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)	p.F511_R514del(1)|p.R514R(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		TCGTCCAGCGCTCCGGAAACT	0.577																																																2	Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|large_intestine(1)	1											106	90	96					1																	110738257		2203	4300	6503	110539780	SO:0001819	synonymous_variant	388662				CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1542C>T	1.37:g.110738257C>T			110539780	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																				0.577	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		T	110738257	C	T	110738257	2	4	61	1	0	0	0	0	0	0	0	1	14717	784	28	3		3	SLC6A17	1	110738257	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82873	110738257	138512364	499	8484										
RBM15	64783	broad.mit.edu	37	chr1	110884473	110884473	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccaagtggctagtagtCttcttgtggagggttcaact	11	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110884473C>A	ENST00000369784.3	+	1	3346	c.2446C>A	c.(2446-2448)Ctt>Att	p.L816I	RBM15_ENST00000602849.1_Missense_Mutation_p.L816I|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000487146.2_Missense_Mutation_p.L816I	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	816	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L816I(1)		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)		GGCTAGTAGTCTTCTTGTGGA	0.517			T	MKL1	acute megakaryocytic leukemia																																		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	1	Substitution - Missense(1)	large_intestine(1)	1											76	75	75					1																	110884473		2203	4300	6503	110685996	SO:0001583	missense	64783			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2446C>A	1.37:g.110884473C>A	ENSP00000358799:p.Leu816Ile		110685996	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629487	0.67015	.	.	ENSG00000162775	ENST00000369784	T	0.24151	1.87	5.25	5.25	0.73442	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	0.360742	0.20188	N	0.097374	T	0.40094	0.1103	M	0.69823	2.125	0.58432	D	0.999992	D;D	0.76494	0.996;0.999	D;D	0.79108	0.992;0.976	T	0.24764	-1.0151	10	0.59425	D	0.04	-8.3374	12.2148	0.54400	0.0:0.9214:0.0:0.0786	.	816;816	Q96T37-3;Q96T37	.;RBM15_HUMAN	I	816	ENSP00000358799:L816I	ENSP00000358799:L816I	L	+	1	0	RBM15	110685996	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.911000	0.63328	2.461000	0.83175	0.655000	0.94253	CTT		0.517	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		A	110884473	C	A	110884473	3	1	61	1	0	0	0	0	1	0	0	0	13153	913	32	2	2448	2	RBM15	1	110884473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146216	110884473	138366148	500	8485										
SLC16A4	9122	broad.mit.edu	37	chr1	110921737	110921737	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaactcttcactttgattTtgtgagactgttaaattttt	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:110921737T>G	ENST00000369779.4	-	6	1017	c.768A>C	c.(766-768)caA>caC	p.Q256H	SLC16A4_ENST00000437429.2_Missense_Mutation_p.Q146H|SLC16A4_ENST00000472422.2_Missense_Mutation_p.Q208H|SLC16A4_ENST00000369781.4_Intron|SLC16A4_ENST00000541986.1_Missense_Mutation_p.Q194H|SLC16A4_ENST00000497687.1_5'UTR	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	256					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.Q256H(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CACTTTGATTTTGTGAGACTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											209	198	202					1																	110921737		2203	4300	6503	110723260	SO:0001583	missense	9122			U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.768A>C	1.37:g.110921737T>G	ENSP00000358794:p.Gln256His		110723260	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	37	CCDS823.1	.	.	.	.	.	.	.	.	.	.	t	15.30	2.794124	0.50102	.	.	ENSG00000168679	ENST00000369779;ENST00000472422;ENST00000437429;ENST00000541986;ENST00000467986	T;T;T;T;T	0.34667	2.46;2.33;1.85;2.46;1.35	5.81	4.67	0.58626	Major facilitator superfamily domain, general substrate transporter (1);	6.744210	0.00166	N	0.000000	T	0.22282	0.0537	N	0.22421	0.69	0.09310	N	1	P;P;P;P	0.52577	0.954;0.836;0.899;0.836	P;P;P;P	0.51229	0.663;0.564;0.537;0.587	T	0.38067	-0.9678	10	0.41790	T	0.15	.	10.7955	0.46457	0.1414:0.0:0.0:0.8586	.	146;194;208;256	E7EPY8;B4DJ67;G3V175;O15374	.;.;.;MOT5_HUMAN	H	256;208;146;194;23	ENSP00000358794:Q256H;ENSP00000432495:Q208H;ENSP00000394790:Q146H;ENSP00000446087:Q194H;ENSP00000435768:Q23H	ENSP00000358794:Q256H	Q	-	3	2	SLC16A4	110723260	0.251000	0.23961	0.460000	0.27093	0.349000	0.29174	1.834000	0.39171	1.004000	0.39156	0.529000	0.55759	CAA		0.408	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		G	110921737	T	G	110921737	3	3	61	1	0	0	0	0	1	0	0	0	14447	1838	64	4	711	4	SLC16A4	1	110921737	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37264	110921737	138328884	501	8486										
KCNA10	3744	broad.mit.edu	37	chr1	111060350	111060350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccttggagtggcgcgagaGcttgaagatgcggaagaccc	15	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111060350G>A	ENST00000369771.2	-	1	1447	c.1060C>T	c.(1060-1062)Ctc>Ttc	p.L354F		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	354					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.L354F(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TGGCGCGAGAGCTTGAAGATG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	118	120					1																	111060350		2203	4300	6503	110861873	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1060C>T	1.37:g.111060350G>A	ENSP00000358786:p.Leu354Phe		110861873		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225062	0.79576	.	.	ENSG00000143105	ENST00000369771	D	0.98150	-4.75	5.63	5.63	0.86233	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98921	0.9634	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99823	1.1048	10	0.87932	D	0	.	18.3064	0.90184	0.0:0.0:1.0:0.0	.	354	Q16322	KCA10_HUMAN	F	354	ENSP00000358786:L354F	ENSP00000358786:L354F	L	-	1	0	KCNA10	110861873	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.865000	0.99609	2.676000	0.91093	0.558000	0.71614	CTC		0.572	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		A	111060350	G	A	111060350	3	1	61	1	0	0	0	0	1	0	0	0	8023	971	34	3	479	3	KCNA10	1	111060350	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138613	111060350	138190271	502	8487										
KCNA10	3744	broad.mit.edu	37	chr1	111060956	111060956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaacattggctgggcgccGaattttcccaccagattggt	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111060956G>A	ENST00000369771.2	-	1	841	c.454C>T	c.(454-456)Cgg>Tgg	p.R152W		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	152					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.R152W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	GCTGGGCGCCGAATTTTCCCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	62	61					1																	111060956		2203	4300	6503	110862479	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.454C>T	1.37:g.111060956G>A	ENSP00000358786:p.Arg152Trp		110862479		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954725	0.53293	.	.	ENSG00000143105	ENST00000369771	T	0.77877	-1.13	5.93	4.96	0.65561	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.88764	0.6525	M	0.92219	3.285	0.48975	D	0.999733	D	0.89917	1.0	D	0.97110	1.0	D	0.90223	0.4273	10	0.87932	D	0	.	12.7042	0.57051	0.0:0.0:0.7221:0.2778	.	152	Q16322	KCA10_HUMAN	W	152	ENSP00000358786:R152W	ENSP00000358786:R152W	R	-	1	2	KCNA10	110862479	0.991000	0.36638	1.000000	0.80357	0.983000	0.72400	1.911000	0.39937	2.797000	0.96272	0.655000	0.94253	CGG		0.458	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		A	111060956	G	A	111060956	3	1	61	1	0	0	0	0	1	0	0	0	8023	1057	37	1	1085	1	KCNA10	1	111060956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	606	111060956	138189665	503	8488										
KCNA2	3737	broad.mit.edu	37	chr1	111146260	111146260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcccccaatggtagtcGgaaccatgtctccatagcct	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111146260G>A	ENST00000485317.1	-	3	1818	c.1145C>T	c.(1144-1146)cCg>cTg	p.P382L	KCNA2_ENST00000316361.4_Missense_Mutation_p.P382L|KCNA2_ENST00000369770.3_Intron|KCNA2_ENST00000525120.1_5'Flank|KCNA2_ENST00000440270.1_Missense_Mutation_p.P382L			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	382					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.P382L(1)		endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	AATGGTAGTCGGAACCATGTC	0.527																																					Pancreas(18;568 735 10587 23710 36357)											1	Substitution - Missense(1)	large_intestine(1)	1											67	68	67					1																	111146260		2203	4300	6503	110947783	SO:0001583	missense	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.1145C>T	1.37:g.111146260G>A	ENSP00000433109:p.Pro382Leu		110947783	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836261	0.71373	.	.	ENSG00000177301	ENST00000485317;ENST00000440270;ENST00000316361	D;D;D	0.98777	-5.13;-5.13;-5.13	5.78	5.78	0.91487	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99729	0.9894	H	0.99914	4.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96987	0.9719	10	0.87932	D	0	.	20.0022	0.97423	0.0:0.0:1.0:0.0	.	382	P16389	KCNA2_HUMAN	L	382	ENSP00000433109:P382L;ENSP00000415257:P382L;ENSP00000314520:P382L	ENSP00000314520:P382L	P	-	2	0	KCNA2	110947783	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	9.807000	0.99171	2.738000	0.93877	0.655000	0.94253	CCG		0.527	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146260	G	A	111146260	3	1	61	1	0	0	0	0	1	0	0	0	8024	1116	39	1	358	1	KCNA2	1	111146260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85304	111146260	138104361	504	8489										
KCNA3	3738	broad.mit.edu	37	chr1	111215852	111215852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgatcaccatatactccGacttactcagagtcgagtta	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111215852G>A	ENST00000369769.2	-	1	1803	c.1580C>T	c.(1579-1581)tCg>tTg	p.S527L		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	527					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)	p.S527L(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	CATATACTCCGACTTACTCAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											101	93	96					1																	111215852		2203	4300	6503	111017375	SO:0001583	missense	3738			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1580C>T	1.37:g.111215852G>A	ENSP00000358784:p.Ser527Leu		111017375	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	37	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561886	0.45590	.	.	ENSG00000177272	ENST00000369769	D	0.97089	-4.24	5.91	5.91	0.95273	.	0.325047	0.29791	U	0.011194	D	0.95705	0.8603	M	0.78456	2.415	0.80722	D	1	B	0.28291	0.206	B	0.20184	0.028	D	0.93609	0.6937	10	0.72032	D	0.01	.	20.2896	0.98541	0.0:0.0:1.0:0.0	.	527	P22001	KCNA3_HUMAN	L	527	ENSP00000358784:S527L	ENSP00000358784:S527L	S	-	2	0	KCNA3	111017375	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.261000	0.72509	2.794000	0.96219	0.655000	0.94253	TCG		0.532	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		A	111215852	G	A	111215852	3	1	61	1	0	0	0	0	1	0	0	0	8025	1059	37	1	151	1	KCNA3	1	111215852	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69592	111215852	138034769	505	8490										
KCNA3	3738	broad.mit.edu	37	chr1	111216437	111216437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaatgatggccacaatgTcgatcaggttcatgatgttt	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111216437T>C	ENST00000369769.2	-	1	1218	c.995A>G	c.(994-996)gAc>gGc	p.D332G		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	332					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)	p.D332G(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	GGCCACAATGTCGATCAGGTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	88	89					1																	111216437		2203	4300	6503	111017960	SO:0001583	missense	3738			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.995A>G	1.37:g.111216437T>C	ENSP00000358784:p.Asp332Gly		111017960	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	37	CCDS828.2	.	.	.	.	.	.	.	.	.	.	T	19.27	3.795482	0.70452	.	.	ENSG00000177272	ENST00000369769	D	0.99388	-5.81	5.37	5.37	0.77165	Ion transport (1);	0.000000	0.85682	U	0.000000	D	0.99750	0.9900	H	0.99425	4.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96805	0.9592	10	0.87932	D	0	.	15.364	0.74507	0.0:0.0:0.0:1.0	.	332	P22001	KCNA3_HUMAN	G	332	ENSP00000358784:D332G	ENSP00000358784:D332G	D	-	2	0	KCNA3	111017960	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	7.947000	0.87758	2.035000	0.60131	0.533000	0.62120	GAC		0.537	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		C	111216437	T	C	111216437	3	2	61	1	0	0	0	0	1	0	0	0	8025	1667	58	4	736	4	KCNA3	1	111216437	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	585	111216437	138034184	506	8491										
CD53	963	broad.mit.edu	37	chr1	111439344	111439344	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcatcttgcccctcagatCgaaaagtggaggtaattttg	10	9	2	1	rs190729207		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111439344C>T	ENST00000271324.5	+	6	605	c.493C>T	c.(493-495)Cga>Tga	p.R165*	CD53_ENST00000429072.2_Intron|CD53_ENST00000497404.1_Intron	NM_000560.3|NM_001040033.1	NP_000551.1|NP_001035122.1	P19397	CD53_HUMAN	CD53 molecule	165					positive regulation of myoblast fusion (GO:1901741)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R165*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	17		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)		CCCCTCAGATCGAAAAGTGGA	0.443													C|||	1	0.000199681	0	0	5008	,	,		20158	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	1											204	188	193					1																	111439344		2203	4300	6503	111240867	SO:0001587	stop_gained	963			BC040693	CCDS829.1	1p13	2013-02-14	2006-03-28		ENSG00000143119	ENSG00000143119		"CD molecules", "Tetraspanins"	1686	protein-coding gene	gene with protein product		151525	"CD53 antigen"	MOX44		8319976	Standard	XM_006711053		Approved	TSPAN25	uc001dzw.3	P19397	OTTHUMG00000048020	ENST00000271324.5:c.493C>T	1.37:g.111439344C>T	ENSP00000271324:p.Arg165*		111240867	B2R905|Q5U0D6	Nonsense_Mutation	SNP	ENST00000271324.5	37	CCDS829.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.92	3.915771	0.73098	.	.	ENSG00000143119	ENST00000271324	.	.	.	5.13	0.562	0.17290	.	2.166060	0.02967	U	0.143950	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	0.9932	0.01461	0.1752:0.4163:0.185:0.2235	.	.	.	.	X	165	.	ENSP00000271324:R165X	R	+	1	2	CD53	111240867	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-0.669000	0.05262	0.118000	0.18165	0.491000	0.48974	CGA		0.443	CD53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032931.1	NM_000560		T	111439344	C	T	111439344	4	4	61	1	0	0	0	0	0	1	0	0	3029	876	31	1	511	1	CD53	1	111439344	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222907	111439344	137811277	507	8492										
C1orf103	55791	broad.mit.edu	37	chr1	111490845	111490845	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctggttttgctgtgactCgtgagaatgttatgttgtga	13	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111490845C>T	ENST00000369763.4	-	4	2436	c.2046G>A	c.(2044-2046)acG>acA	p.T682T	LRIF1_ENST00000494675.1_Silent_p.T146T|LRIF1_ENST00000485275.2_Silent_p.T146T|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	682					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.T682T(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						TGCTGTGACTCGTGAGAATGT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	1											230	215	220					1																	111490845		2203	4300	6503	111292368	SO:0001819	synonymous_variant	55791			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.2046G>A	1.37:g.111490845C>T			111292368	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Silent	SNP	ENST00000369763.4	37	CCDS30800.1																																																																																				0.398	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		T	111490845	C	T	111490845	2	4	61	1	0	0	0	0	0	0	0	1	1983	871	31	1		1	C1orf103	1	111490845	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51501	111490845	137759776	508	8493										
C1orf103	55791	broad.mit.edu	37	chr1	111494469	111494469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taataggcatatttttggatCgcgtcccactaggatcgatg	10	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111494469C>T	ENST00000369763.4	-	2	1427	c.1037G>A	c.(1036-1038)cGa>cAa	p.R346Q	LRIF1_ENST00000494675.1_Intron|LRIF1_ENST00000485275.2_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.R346Q(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						ATTTTTGGATCGCGTCCCACT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											85	89	88					1																	111494469		2203	4300	6503	111295992	SO:0001583	missense	55791			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1037G>A	1.37:g.111494469C>T	ENSP00000358778:p.Arg346Gln		111295992	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	37	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.925972	0.00493	.	.	ENSG00000121931	ENST00000369763	T	0.25579	1.79	5.7	4.58	0.56647	.	0.187793	0.37761	N	0.001947	T	0.02119	0.0066	N	0.01352	-0.895	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	10	0.02654	T	1	-0.0041	9.8151	0.40846	0.0:0.0813:0.0:0.9187	.	346	Q5T3J3	LRIF1_HUMAN	Q	346	ENSP00000358778:R346Q	ENSP00000358778:R346Q	R	-	2	0	LRIF1	111295992	0.994000	0.37717	0.792000	0.32020	0.231000	0.25187	2.466000	0.45084	1.010000	0.39314	-0.312000	0.09012	CGA		0.353	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		T	111494469	C	T	111494469	3	4	61	1	0	0	0	0	1	0	0	0	1983	884	31	1	1284	1	C1orf103	1	111494469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3624	111494469	137756152	509	8494										
C1orf103	55791	broad.mit.edu	37	chr1	111495081	111495081	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcatggtgagtccatcaAttttcacaccatgactctga	7	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111495081A>C	ENST00000369763.4	-	2	815	c.425T>G	c.(424-426)aTt>aGt	p.I142S	LRIF1_ENST00000494675.1_Intron|LRIF1_ENST00000485275.2_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	142					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.I142S(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						GAGTCCATCAATTTTCACACC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	85	83					1																	111495081		2203	4300	6503	111296604	SO:0001583	missense	55791			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.425T>G	1.37:g.111495081A>C	ENSP00000358778:p.Ile142Ser		111296604	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	37	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.798627	0.31777	.	.	ENSG00000121931	ENST00000369763	T	0.26518	1.73	5.65	4.53	0.55603	.	0.489229	0.21086	N	0.080404	T	0.08802	0.0218	N	0.24115	0.695	0.80722	D	1	B	0.30281	0.275	B	0.30646	0.118	T	0.06716	-1.0811	10	0.66056	D	0.02	-2.7797	9.1215	0.36791	0.9145:0.0:0.0855:0.0	.	142	Q5T3J3	LRIF1_HUMAN	S	142	ENSP00000358778:I142S	ENSP00000358778:I142S	I	-	2	0	LRIF1	111296604	0.999000	0.42202	1.000000	0.80357	0.987000	0.75469	2.092000	0.41700	2.159000	0.67721	0.383000	0.25322	ATT		0.378	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		C	111495081	A	C	111495081	3	2	61	1	0	0	0	0	1	0	0	0	1983	101	4	4	1896	4	C1orf103	1	111495081	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	612	111495081	137755540	510	8495										
C1orf103	55791	broad.mit.edu	37	chr1	111495408	111495408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccatccgagccaatcgtcTgaactacttggtacatgcag	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111495408T>C	ENST00000369763.4	-	2	488	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	LRIF1_ENST00000494675.1_5'UTR|LRIF1_ENST00000485275.2_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	33					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.Q33R(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						GCCAATCGTCTGAACTACTTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											44	45	45					1																	111495408		2113	4175	6288	111296931	SO:0001583	missense	55791			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.98A>G	1.37:g.111495408T>C	ENSP00000358778:p.Gln33Arg		111296931	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	37	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	T	15.35	2.806518	0.50421	.	.	ENSG00000121931	ENST00000369763	T	0.28069	1.63	5.52	4.38	0.52667	.	0.184853	0.39020	N	0.001487	T	0.21103	0.0508	L	0.27053	0.805	0.80722	D	1	D	0.55385	0.971	P	0.55455	0.776	T	0.03231	-1.1058	10	0.56958	D	0.05	0.232	10.6745	0.45778	0.0:0.0:0.1675:0.8325	.	33	Q5T3J3	LRIF1_HUMAN	R	33	ENSP00000358778:Q33R	ENSP00000358778:Q33R	Q	-	2	0	LRIF1	111296931	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.545000	0.45769	0.923000	0.37045	0.383000	0.25322	CAG		0.313	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		C	111495408	T	C	111495408	3	2	61	1	0	0	0	0	1	0	0	0	1983	1580	55	4	2223	4	C1orf103	1	111495408	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	327	111495408	137755213	511	8496										
CHI3L2	1117	broad.mit.edu	37	chr1	111773482	111773482	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcatctcatctattcattCgccagcatcgaaaacaacaa	3	13	4	0	rs201031221		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111773482C>T	ENST00000445067.2	+	5	960	c.189C>T	c.(187-189)ttC>ttT	p.F63F	CHI3L2_ENST00000369748.4_Silent_p.F63F|CHI3L2_ENST00000524472.1_5'UTR|CHI3L2_ENST00000466741.1_5'UTR|CHI3L2_ENST00000369744.2_Silent_p.F53F			Q15782	CH3L2_HUMAN	chitinase 3-like 2	63					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.F63F(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		TCTATTCATTCGCCAGCATCG	0.458																																																2	Substitution - coding silent(2)	large_intestine(2)	1											85	74	78					1																	111773482		2203	4300	6503	111575005	SO:0001819	synonymous_variant	1117			U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.189C>T	1.37:g.111773482C>T			111575005	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Silent	SNP	ENST00000445067.2	37	CCDS30802.1	.	.	.	.	.	.	.	.	.	.	C	8.614	0.889849	0.17540	.	.	ENSG00000064886	ENST00000533831	.	.	.	4.09	-1.11	0.09840	.	.	.	.	.	T	0.38799	0.1054	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35699	-0.9778	4	.	.	.	-8.544	8.5256	0.33302	0.0:0.5371:0.0:0.4629	.	.	.	.	L	32	.	.	S	+	2	0	CHI3L2	111575005	0.001000	0.12720	0.009000	0.14445	0.867000	0.49689	-1.416000	0.02467	-0.442000	0.07190	-0.302000	0.09304	TCG		0.458	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000		T	111773482	C	T	111773482	2	4	61	1	0	0	0	0	0	0	0	1	3347	883	31	1		1	CHI3L2	1	111773482	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	278074	111773482	137477139	512	8497										
CHIA	27159	broad.mit.edu	37	chr1	111854963	111854963	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacgagatcaccaccatCgaatggaatgatgtgactct	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111854963C>T	ENST00000369740.1	+	4	310	c.207C>T	c.(205-207)atC>atT	p.I69I	CHIA_ENST00000353665.6_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000343320.6_Silent_p.I69I|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000430615.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	69					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)	p.I69I(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCACCACCATCGAATGGAATG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											124	119	121					1																	111854963		1994	4162	6156	111656486	SO:0001819	synonymous_variant	27159			AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.207C>T	1.37:g.111854963C>T			111656486	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																				0.498	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111854963	C	T	111854963	2	4	61	1	0	0	0	0	0	0	0	1	3348	874	31	1		1	CHIA	1	111854963	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81481	111854963	137395658	513	8498										
OVGP1	5016	broad.mit.edu	37	chr1	111957804	111957804	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggggttatagtcatatttTcacactttccgtggatctca	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:111957804T>G	ENST00000369732.3	-	11	1374	c.1319A>C	c.(1318-1320)gAa>gCa	p.E440A		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	440					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.E440A(1)|p.E504A(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		AGTCATATTTTCACACTTTCC	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	1											88	86	87					1																	111957804		2203	4300	6503	111759327	SO:0001583	missense	5016			U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1319A>C	1.37:g.111957804T>G	ENSP00000358747:p.Glu440Ala		111759327	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.635643	0.29068	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04317	3.65	4.43	3.28	0.37604	.	1.667190	0.03414	N	0.205177	T	0.01940	0.0061	L	0.43923	1.385	0.09310	N	0.999995	B;B	0.25441	0.013;0.126	B;B	0.19946	0.008;0.027	T	0.41716	-0.9493	10	0.37606	T	0.19	-6.9208	8.148	0.31124	0.0:0.0:0.2043:0.7957	.	440;504	Q12889;Q59HH5	OVGP1_HUMAN;.	A	440;504;248	ENSP00000358747:E440A	ENSP00000358743:E504A	E	-	2	0	OVGP1	111759327	0.001000	0.12720	0.009000	0.14445	0.106000	0.19336	0.218000	0.17622	0.998000	0.38996	0.477000	0.44152	GAA		0.502	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		G	111957804	T	G	111957804	3	3	61	1	0	0	0	0	1	0	0	0	11356	1783	62	4	721	4	OVGP1	1	111957804	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	102841	111957804	137292817	514	8499										
RAP1A	5906	broad.mit.edu	37	chr1	112240096	112240096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgccaacagtgtatgctcGaaatcctggatactgcaggg	11	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:112240096G>A	ENST00000369709.3	+	4	339	c.160G>A	c.(160-162)Gaa>Aaa	p.E54K	RAP1A_ENST00000436150.2_Missense_Mutation_p.E54K|RAP1A_ENST00000356415.1_Missense_Mutation_p.E54K|RAP1A_ENST00000545460.1_Missense_Mutation_p.E54K|RAP1A_ENST00000494982.1_3'UTR	NM_002884.2	NP_002875.1	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family	54					activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of vasculogenesis (GO:2001214)|protein transport (GO:0015031)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|guanyl-nucleotide exchange factor complex (GO:0032045)|late endosome (GO:0005770)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.E54K(1)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		GTGTATGCTCGAAATCCTGGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											180	184	183					1																	112240096		2203	4300	6503	112041619	SO:0001583	missense	5906			BC014086	CCDS840.1	1p13.3	2014-05-09			ENSG00000116473	ENSG00000116473			9855	protein-coding gene	gene with protein product		179520				3143720	Standard	XM_006710803		Approved	KREV-1, SMGP21	uc001ebl.3	P62834	OTTHUMG00000011959	ENST00000369709.3:c.160G>A	1.37:g.112240096G>A	ENSP00000358723:p.Glu54Lys		112041619	P10113	Missense_Mutation	SNP	ENST00000369709.3	37	CCDS840.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.649568	0.87958	.	.	ENSG00000116473	ENST00000356415;ENST00000433097;ENST00000369709;ENST00000436150;ENST00000545460	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.33	3.46	0.39613	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.76550	0.4003	M	0.88979	2.995	0.80722	D	1	B	0.33637	0.42	B	0.40636	0.335	T	0.79208	-0.1898	10	0.87932	D	0	.	11.6674	0.51381	0.1455:0.0:0.8545:0.0	.	54	P62834	RAP1A_HUMAN	K	54	ENSP00000348786:E54K;ENSP00000396741:E54K;ENSP00000358723:E54K;ENSP00000394318:E54K;ENSP00000443009:E54K	ENSP00000348786:E54K	E	+	1	0	RAP1A	112041619	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	0.748000	0.32831	0.650000	0.86243	GAA		0.373	RAP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033071.1	NM_002884		A	112240096	G	A	112240096	3	1	61	1	0	0	0	0	1	0	0	0	13072	1059	37	1	170	1	RAP1A	1	112240096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282292	112240096	137010525	515	8500										
DDX20	11218	broad.mit.edu	37	chr1	112303389	112303389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtatcagctacttatcccGaatttttggctaatgctttg	7	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:112303389G>A	ENST00000369702.4	+	5	1362	c.742G>A	c.(742-744)Gaa>Aaa	p.E248K	DDX20_ENST00000475700.1_5'UTR|DDX20_ENST00000536167.1_3'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	248	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)	p.E248K(1)		endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTTATCCCGAATTTTTGGC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	125	126					1																	112303389		2203	4300	6503	112104912	SO:0001583	missense	11218			AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.742G>A	1.37:g.112303389G>A	ENSP00000358716:p.Glu248Lys		112104912	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637888	0.87760	.	.	ENSG00000064703	ENST00000369702	T	0.14516	2.5	4.97	4.97	0.65823	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	N	0.10782	0.045	0.80722	D	1	P	0.42941	0.794	P	0.50192	0.634	T	0.34279	-0.9835	10	0.48119	T	0.1	-17.6876	18.1716	0.89747	0.0:0.0:1.0:0.0	.	248	Q9UHI6	DDX20_HUMAN	K	248	ENSP00000358716:E248K	ENSP00000358716:E248K	E	+	1	0	DDX20	112104912	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.278000	0.95766	2.461000	0.83175	0.491000	0.48974	GAA		0.378	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		A	112303389	G	A	112303389	3	1	61	1	0	0	0	0	1	0	0	0	4354	1059	37	1	760	1	DDX20	1	112303389	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63293	112303389	136947232	516	8501										
KCND3	3752	broad.mit.edu	37	chr1	112323370	112323370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtgcaggtatgcattcGaactgcctgttttggccaca	11	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:112323370G>A	ENST00000315987.2	-	4	1792	c.1313C>T	c.(1312-1314)tCg>tTg	p.S438L	KCND3_ENST00000369697.1_Missense_Mutation_p.S438L|KCND3_ENST00000302127.4_Missense_Mutation_p.S438L	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	438					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.S438L(2)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GTATGCATTCGAACTGCCTGT	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	1											71	55	60					1																	112323370		2203	4300	6503	112124893	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.1313C>T	1.37:g.112323370G>A	ENSP00000319591:p.Ser438Leu		112124893	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.438997	0.63067	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.96913	-4.17;-4.17;-4.17	5.26	5.26	0.73747	.	0.111627	0.64402	D	0.000006	D	0.87613	0.6221	N	0.14661	0.345	0.80722	D	1	B;P	0.37731	0.283;0.607	B;B	0.26094	0.026;0.066	D	0.89543	0.3794	10	0.49607	T	0.09	.	18.4608	0.90737	0.0:0.0:1.0:0.0	.	438;438	Q14D71;Q9UK17	.;KCND3_HUMAN	L	438	ENSP00000358711:S438L;ENSP00000319591:S438L;ENSP00000306923:S438L	ENSP00000306923:S438L	S	-	2	0	KCND3	112124893	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	9.199000	0.95003	2.446000	0.82766	0.655000	0.94253	TCG		0.537	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		A	112323370	G	A	112323370	3	1	61	1	0	0	0	0	1	0	0	0	8041	1059	37	1	674	1	KCND3	1	112323370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19981	112323370	136927251	517	8502										
WNT2B	7482	broad.mit.edu	37	chr1	113057614	113057614	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagtgggcgagggtgccCgagaatggatccgagagtgt	18	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:113057614C>T	ENST00000369684.4	+	2	786	c.301C>T	c.(301-303)Cga>Tga	p.R101*	RP4-671G15.2_ENST00000608357.1_RNA|WNT2B_ENST00000478360.1_3'UTR|WNT2B_ENST00000369686.5_Nonsense_Mutation_p.R82*|WNT2B_ENST00000256640.5_Nonsense_Mutation_p.R9*	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	101					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|chondrocyte differentiation (GO:0002062)|cornea development in camera-type eye (GO:0061303)|forebrain regionalization (GO:0021871)|hematopoietic stem cell proliferation (GO:0071425)|iris morphogenesis (GO:0061072)|lens development in camera-type eye (GO:0002088)|lung induction (GO:0060492)|male gonad development (GO:0008584)|mesenchymal-epithelial cell signaling (GO:0060638)|neuron differentiation (GO:0030182)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.R101R(1)|p.R101*(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|stomach(1)	18	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGAGGGTGCCCGAGAATGGAT	0.607																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1											94	78	83					1																	113057614		2203	4300	6503	112859137	SO:0001587	stop_gained	7482			AB045116	CCDS847.1, CCDS846.1	1p13	2008-07-18			ENSG00000134245	ENSG00000134245		"Wingless-type MMTV integration sites"	12781	protein-coding gene	gene with protein product	"XWNT2, Xenopus, homolog of", "wingless-type MMTV integration site family, member 13"	601968		WNT13		8761309, 10944466	Standard	NM_024494		Approved	XWNT2	uc001ecb.3	Q93097	OTTHUMG00000011157	ENST00000369684.4:c.301C>T	1.37:g.113057614C>T	ENSP00000358698:p.Arg101*		112859137	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Nonsense_Mutation	SNP	ENST00000369684.4	37	CCDS847.1	.	.	.	.	.	.	.	.	.	.	C	37	6.295629	0.97449	.	.	ENSG00000134245	ENST00000256640;ENST00000369686;ENST00000369684	.	.	.	5.3	5.3	0.74995	.	0.054643	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	11.9884	0.53161	0.2897:0.7103:0.0:0.0	.	.	.	.	X	9;82;101	.	ENSP00000256640:R9X	R	+	1	2	WNT2B	112859137	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.417000	0.66423	2.474000	0.83562	0.561000	0.74099	CGA		0.607	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030692.1	NM_004185		T	113057614	C	T	113057614	4	4	61	1	0	0	0	0	0	1	0	0	17427	644	23	1	440	1	WNT2B	1	113057614	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	734244	113057614	136193007	518	8503										
MOV10	4343	broad.mit.edu	37	chr1	113240716	113240716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaacgcttctgccgctggGcgggcctacctcgacaggtg	15	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:113240716G>A	ENST00000413052.2	+	15	2689	c.2299G>A	c.(2299-2301)Gcg>Acg	p.A767T	MOV10_ENST00000369644.1_Missense_Mutation_p.A711T|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000357443.2_Missense_Mutation_p.A767T|MOV10_ENST00000369645.1_Missense_Mutation_p.A767T	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	767					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.A767T(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CTGCCGCTGGGCGGGCCTACC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	73	75					1																	113240716		2203	4300	6503	113042239	SO:0001583	missense	4343			AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2299G>A	1.37:g.113240716G>A	ENSP00000399797:p.Ala767Thr		113042239	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Missense_Mutation	SNP	ENST00000413052.2	37	CCDS853.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946601	0.53186	.	.	ENSG00000155363	ENST00000413052;ENST00000369645;ENST00000369644;ENST00000357443;ENST00000369648	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	5.36	3.42	0.39159	.	0.255560	0.44483	D	0.000460	T	0.45498	0.1345	N	0.13235	0.315	0.80722	D	1	B	0.02656	0.0	B	0.16722	0.016	T	0.30794	-0.9966	10	0.19590	T	0.45	-14.3095	9.7835	0.40662	0.0:0.2874:0.564:0.1486	.	767	Q9HCE1	MOV10_HUMAN	T	767;767;711;767;705	ENSP00000399797:A767T;ENSP00000358659:A767T;ENSP00000358658:A711T;ENSP00000350028:A767T	ENSP00000350028:A767T	A	+	1	0	MOV10	113042239	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	4.676000	0.61627	0.609000	0.30018	0.556000	0.70494	GCG		0.612	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		A	113240716	G	A	113240716	3	1	61	1	0	0	0	0	1	0	0	0	9748	1203	42	3	2353	3	MOV10	1	113240716	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	183102	113240716	136009905	519	8504										
MOV10	4343	broad.mit.edu	37	chr1	113241082	113241082	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgaagtgtgggcgtcatCtccccgtaccggaaacaggt	12	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:113241082C>T	ENST00000413052.2	+	16	2880	c.2490C>T	c.(2488-2490)atC>atT	p.I830I	MOV10_ENST00000369644.1_Silent_p.I774I|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000357443.2_Silent_p.I830I|MOV10_ENST00000369645.1_Silent_p.I830I	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	830					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.I830I(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		TGGGCGTCATCTCCCCGTACC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	1											49	43	45					1																	113241082		2203	4300	6503	113042605	SO:0001819	synonymous_variant	4343			AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2490C>T	1.37:g.113241082C>T			113042605	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																				0.602	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		T	113241082	C	T	113241082	2	4	61	1	0	0	0	0	0	0	0	1	9748	903	32	3		3	MOV10	1	113241082	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366	113241082	136009539	520	8505										
SLC16A1	6566	broad.mit.edu	37	chr1	113456732	113456732	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctgaaataattaggacGacgccacatgcccagtatgt	8	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:113456732G>A	ENST00000538576.1	-	5	2115	c.1284C>T	c.(1282-1284)gtC>gtT	p.V428V	SLC16A1_ENST00000369626.3_Silent_p.V428V	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	428					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.V428V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	TAATTAGGACGACGCCACATG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	1											122	115	117					1																	113456732		2203	4300	6503	113258255	SO:0001819	synonymous_variant	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.1284C>T	1.37:g.113456732G>A			113258255	Q49A45|Q5T8R6|Q9NSJ9	Silent	SNP	ENST00000538576.1	37	CCDS858.1																																																																																				0.378	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		A	113456732	G	A	113456732	2	1	61	1	0	0	0	0	0	0	0	1	14439	1045	37	1		1	SLC16A1	1	113456732	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215650	113456732	135793889	521	8506										
MAGI3	260425	broad.mit.edu	37	chr1	114201773	114201773	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaaaactgaaagttggaGatcatatctctgcagtgaat	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114201773G>T	ENST00000307546.9	+	16	2776	c.2701G>T	c.(2701-2703)Gat>Tat	p.D901Y	MAGI3_ENST00000369615.1_Missense_Mutation_p.D901Y|MAGI3_ENST00000369617.4_Missense_Mutation_p.D926Y|MAGI3_ENST00000369611.4_Missense_Mutation_p.D901Y	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	926	Interaction with LPAR2 and GRIN2B.|PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)	p.D901Y(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	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)		GAAAGTTGGAGATCATATCTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											149	141	144					1																	114201773		2203	4300	6503	114003296	SO:0001583	missense	260425			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2701G>T	1.37:g.114201773G>T	ENSP00000304604:p.Asp901Tyr		114003296	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	37	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	G	32	5.175987	0.94846	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.91290	0.7254	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.92772	0.6233	10	0.87932	D	0	-18.455	20.8794	0.99867	0.0:0.0:1.0:0.0	.	901;901;926	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	Y	926;901;901;901	ENSP00000358630:D926Y;ENSP00000304604:D901Y;ENSP00000358628:D901Y;ENSP00000358624:D901Y	ENSP00000304604:D901Y	D	+	1	0	MAGI3	114003296	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GAT		0.438	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		T	114201773	G	T	114201773	3	4	61	1	0	0	0	0	1	0	0	0	9222	942	33	2	2763	2	MAGI3	1	114201773	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	745041	114201773	135048848	522	8507										
MAGI3	260425	broad.mit.edu	37	chr1	114201835	114201835	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcatgataacattgttcaGctgatcaaagatgctggtgt	9	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114201835G>T	ENST00000307546.9	+	16	2838	c.2763G>T	c.(2761-2763)caG>caT	p.Q921H	MAGI3_ENST00000369615.1_Missense_Mutation_p.Q921H|MAGI3_ENST00000369617.4_Missense_Mutation_p.Q946H|MAGI3_ENST00000369611.4_Missense_Mutation_p.Q921H	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	946	Interaction with LPAR2 and GRIN2B.|PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)	p.Q921H(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	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)		ACATTGTTCAGCTGATCAAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	136	142					1																	114201835		2203	4300	6503	114003358	SO:0001583	missense	260425			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2763G>T	1.37:g.114201835G>T	ENSP00000304604:p.Gln921His		114003358	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	37	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.812047	0.90707	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.41581	0.1165	L	0.35341	1.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.99	T	0.19679	-1.0298	10	0.62326	D	0.03	-21.1146	20.8794	0.99867	0.0:0.0:1.0:0.0	.	921;921;946	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	H	946;921;921;921	ENSP00000358630:Q946H;ENSP00000304604:Q921H;ENSP00000358628:Q921H;ENSP00000358624:Q921H	ENSP00000304604:Q921H	Q	+	3	2	MAGI3	114003358	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.875000	0.56108	2.941000	0.99782	0.655000	0.94253	CAG		0.498	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		T	114201835	G	T	114201835	3	4	61	1	0	0	0	0	1	0	0	0	9222	962	34	2	2825	2	MAGI3	1	114201835	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	114201835	135048786	523	8508										
PHTF1	10745	broad.mit.edu	37	chr1	114253087	114253087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagccaccactcacacccGatctagagccctttaaagga	8	14	2	2	rs572558913	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114253087G>A	ENST00000369604.1	-	11	1541	c.1058C>T	c.(1057-1059)tCg>tTg	p.S353L	PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000357783.2_Missense_Mutation_p.S353L|PHTF1_ENST00000369600.1_Missense_Mutation_p.S300L|PHTF1_ENST00000393357.2_Missense_Mutation_p.S353L|PHTF1_ENST00000369598.1_Missense_Mutation_p.S308L|PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000369596.2_Missense_Mutation_p.S300L			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	353					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S353L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		ACTCACACCCGATCTAGAGCC	0.393													G|||	2	0.000399361	0	0	5008	,	,		15517	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	1											46	48	47					1																	114253087		2203	4300	6503	114054610	SO:0001583	missense	10745			AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.1058C>T	1.37:g.114253087G>A	ENSP00000358617:p.Ser353Leu		114054610	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	37	CCDS861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.048909|4.048909	0.75846|0.75846	.|.	.|.	ENSG00000116793|ENSG00000116793	ENST00000412670|ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783	.|.	.|.	.|.	5.73|5.73	4.83|4.83	0.62350|0.62350	.|.	.|0.259361	.|0.38720	.|N	.|0.001590	T|T	0.41073|0.41073	0.1143|0.1143	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.67145	.|0.931;0.996;0.99	.|B;P;P	.|0.52109	.|0.356;0.69;0.664	T|T	0.35992|0.35992	-0.9766|-0.9766	5|9	.|0.42905	.|T	.|0.14	-10.0345|-10.0345	15.0254|15.0254	0.71667|0.71667	0.0682:0.0:0.9318:0.0|0.0682:0.0:0.9318:0.0	.|.	.|353;108;353	.|Q9UMS5;Q5TCR1;Q9UMS5-2	.|PHTF1_HUMAN;.;.	W|L	109|308;353;300;308;300;353;353	.|.	.|ENSP00000350428:S353L	R|S	-|-	1|2	2|0	PHTF1|PHTF1	114054610|114054610	1.000000|1.000000	0.71417|0.71417	0.409000|0.409000	0.26459|0.26459	0.623000|0.623000	0.37688|0.37688	4.659000|4.659000	0.61504|0.61504	1.452000|1.452000	0.47756|0.47756	-0.126000|-0.126000	0.14955|0.14955	CGG|TCG		0.393	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		A	114253087	G	A	114253087	3	1	61	1	0	0	0	0	1	0	0	0	11893	1059	37	1	1266	1	PHTF1	1	114253087	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51252	114253087	134997534	524	8509										
PHTF1	10745	broad.mit.edu	37	chr1	114267407	114267407	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagatagtctcccaaaaAccaccaataatgggtacaga	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114267407A>G	ENST00000369604.1	-	7	1080	c.597T>C	c.(595-597)ggT>ggC	p.G199G	PHTF1_ENST00000357783.2_Silent_p.G199G|PHTF1_ENST00000369600.1_Silent_p.G146G|PHTF1_ENST00000393357.2_Silent_p.G199G|PHTF1_ENST00000369598.1_Intron|PHTF1_ENST00000447664.2_Silent_p.G199G|PHTF1_ENST00000369596.2_Silent_p.G146G			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	199					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G199G(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		TCTCCCAAAAACCACCAATAA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	1											87	90	89					1																	114267407		2203	4300	6503	114068930	SO:0001819	synonymous_variant	10745			AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.597T>C	1.37:g.114267407A>G			114068930	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Silent	SNP	ENST00000369604.1	37	CCDS861.1																																																																																				0.383	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		G	114267407	A	G	114267407	2	3	61	1	0	0	0	0	0	0	0	1	11893	30	2	4		4	PHTF1	1	114267407	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	14320	114267407	134983214	525	8510										
PTPN22	26191	broad.mit.edu	37	chr1	114375748	114375748	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacctgatttaggacttcGgagttttacactctaaaaga	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114375748G>A	ENST00000359785.5	-	16	2173	c.2038C>T	c.(2038-2040)Cga>Tga	p.R680*	PTPN22_ENST00000525799.1_Nonsense_Mutation_p.R553*|PTPN22_ENST00000420377.2_Nonsense_Mutation_p.R680*|PTPN22_ENST00000528414.1_Nonsense_Mutation_p.R625*|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000538253.1_Nonsense_Mutation_p.R436*	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	680					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)	p.R680*(1)		NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		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)		TTAGGACTTCGGAGTTTTACA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											54	52	52					1																	114375748		2202	4298	6500	114177271	SO:0001587	stop_gained	26191			AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.2038C>T	1.37:g.114375748G>A	ENSP00000352833:p.Arg680*		114177271	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Nonsense_Mutation	SNP	ENST00000359785.5	37	CCDS863.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241160	0.79912	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	.	.	.	5.46	3.36	0.38483	.	0.950261	0.08680	N	0.909584	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5412	0.39252	0.0:0.1438:0.6898:0.1664	.	.	.	.	X	680;625;436;680;553;680	.	ENSP00000346621:R680X	R	-	1	2	PTPN22	114177271	0.087000	0.21565	0.194000	0.23346	0.742000	0.42306	1.844000	0.39269	1.292000	0.44672	0.491000	0.48974	CGA		0.303	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		A	114375748	G	A	114375748	4	1	61	1	0	0	0	0	0	1	0	0	12824	1124	39	1	432	1	PTPN22	1	114375748	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108341	114375748	134874873	526	8511										
BCL2L15	440603	broad.mit.edu	37	chr1	114424443	114424443	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggatggcttggttcccattGatcatacccgtcatggggat	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114424443G>T	ENST00000393316.3	-	3	597	c.426C>A	c.(424-426)atC>atA	p.I142I	BCL2L15_ENST00000471267.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA|BCL2L15_ENST00000393320.3_Intron|BCL2L15_ENST00000488450.1_5'UTR	NM_001010922.2	NP_001010922.1	Q5TBC7	B2L15_HUMAN	BCL2-like 15	142					apoptotic process (GO:0006915)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.I142I(1)		breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)	9	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-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)		GGTTCCCATTGATCATACCCG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											89	83	85					1																	114424443		2203	4300	6503	114225966	SO:0001819	synonymous_variant	440603				CCDS30809.1	1p13.2	2014-03-07			ENSG00000188761	ENSG00000188761			33624	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 178"	C1orf178		12700646, 15961081, 16690252, 17412810	Standard	NM_001010922		Approved	Bfk, FLJ22588	uc001edw.3	Q5TBC7	OTTHUMG00000011940	ENST00000393316.3:c.426C>A	1.37:g.114424443G>T			114225966	A0PJY6|A8K074|I6LA82	Silent	SNP	ENST00000393316.3	37	CCDS30809.1																																																																																				0.502	BCL2L15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033026.2	NM_001010922		T	114424443	G	T	114424443	2	4	61	1	0	0	0	0	0	0	0	1	1374	1280	45	2		2	BCL2L15	1	114424443	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48695	114424443	134826178	527	8512										
HIPK1	204851	broad.mit.edu	37	chr1	114512694	114512694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccctgagtgctctccgagGcaatagtggatccgttttgg	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114512694G>A	ENST00000369558.1	+	14	3120	c.2888G>A	c.(2887-2889)gGc>gAc	p.G963D	HIPK1_ENST00000406344.1_Missense_Mutation_p.G569D|HIPK1_ENST00000369555.2_Missense_Mutation_p.G918D|HIPK1_ENST00000369559.4_Missense_Mutation_p.G963D|HIPK1_ENST00000369553.1_Missense_Mutation_p.G569D|HIPK1_ENST00000340480.4_Missense_Mutation_p.G589D|HIPK1_ENST00000369561.4_Missense_Mutation_p.G929D|HIPK1_ENST00000369554.2_Missense_Mutation_p.G918D|HIPK1_ENST00000426820.2_Missense_Mutation_p.G963D			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	963	Interaction with TP53.|Required for localization to nuclear speckles. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G963D(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-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)		GCTCTCCGAGGCAATAGTGGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											151	151	151					1																	114512694		2203	4300	6503	114314217	SO:0001583	missense	204851			AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.2888G>A	1.37:g.114512694G>A	ENSP00000358571:p.Gly963Asp		114314217	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898643	0.33535	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480;ENST00000369553;ENST00000406344	T;T;T;T;T;T;T;T;T;T	0.51325	0.75;0.71;0.8;0.78;0.78;0.8;0.76;3.81;2.9;2.9	5.95	4.98	0.66077	.	0.000000	0.64402	D	0.000003	T	0.16300	0.0392	N	0.14661	0.345	0.44619	D	0.997594	B;B;B;B	0.33345	0.409;0.156;0.18;0.275	B;B;B;B	0.32022	0.139;0.096;0.034;0.075	T	0.06267	-1.0836	10	0.12430	T	0.62	.	15.9656	0.79968	0.0:0.0:0.8646:0.1354	.	255;569;963;963	E9PCF6;Q86Z02-4;Q86Z02;Q86Z02-2	.;.;HIPK1_HUMAN;.	D	1034;963;963;918;918;963;929;589;569;569	ENSP00000407442:G1034D;ENSP00000358572:G963D;ENSP00000409673:G963D;ENSP00000358567:G918D;ENSP00000358568:G918D;ENSP00000358571:G963D;ENSP00000358574:G929D;ENSP00000340956:G589D;ENSP00000358566:G569D;ENSP00000384960:G569D	ENSP00000340956:G589D	G	+	2	0	HIPK1	114314217	1.000000	0.71417	1.000000	0.80357	0.353000	0.29299	2.304000	0.43655	2.826000	0.97356	0.491000	0.48974	GGC		0.507	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		A	114512694	G	A	114512694	3	1	61	1	0	0	0	0	1	0	0	0	7137	1203	42	3	2956	3	HIPK1	1	114512694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88251	114512694	134737927	528	8513										
OLFML3	56944	broad.mit.edu	37	chr1	114523201	114523201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggccctgggaccaaagGcaagggaagaaggaatgaga	17	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114523201G>A	ENST00000320334.4	+	2	436	c.362G>A	c.(361-363)gGc>gAc	p.G121D	OLFML3_ENST00000369551.1_Missense_Mutation_p.G101D|OLFML3_ENST00000393300.2_Missense_Mutation_p.G101D|OLFML3_ENST00000491700.1_3'UTR	NM_020190.2	NP_064575.1	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3	121					multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)|vesicle (GO:0031982)		p.G121D(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)|urinary_tract(1)	14	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-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)		GGGACCAAAGGCAAGGGAAGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	91	90					1																	114523201		2203	4300	6503	114324724	SO:0001583	missense	56944			AF201945	CCDS870.1, CCDS65618.1, CCDS72839.1	1p13.1	2008-02-05			ENSG00000116774	ENSG00000116774			24956	protein-coding gene	gene with protein product		610088					Standard	NM_001286353		Approved	HNOEL-iso, OLF44	uc001eer.1	Q9NRN5	OTTHUMG00000011980	ENST00000320334.4:c.362G>A	1.37:g.114523201G>A	ENSP00000322273:p.Gly121Asp		114324724	Q53FR1|Q53HV9|Q5SQL6|Q69AX9|Q8NBJ2	Missense_Mutation	SNP	ENST00000320334.4	37	CCDS870.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693423	0.30052	.	.	ENSG00000116774	ENST00000369551;ENST00000320334;ENST00000393300	D;D;D	0.87650	-2.28;-2.19;-2.28	5.59	4.66	0.58398	.	0.427811	0.27787	N	0.017860	T	0.53546	0.1803	N	0.08118	0	0.29710	N	0.839485	B;B	0.23249	0.039;0.082	B;B	0.23574	0.043;0.047	T	0.36089	-0.9762	10	0.12430	T	0.62	.	7.6698	0.28453	0.0967:0.2805:0.6228:0.0	.	101;121	Q9NRN5-2;Q9NRN5	.;OLFL3_HUMAN	D	101;121;101	ENSP00000358564:G101D;ENSP00000322273:G121D;ENSP00000376977:G101D	ENSP00000322273:G121D	G	+	2	0	OLFML3	114324724	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.953000	0.56699	2.629000	0.89072	0.555000	0.69702	GGC		0.502	OLFML3-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033119.1	NM_020190		A	114523201	G	A	114523201	3	1	61	1	0	0	0	0	1	0	0	0	10890	1203	42	3	368	3	OLFML3	1	114523201	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10507	114523201	134727420	529	8514										
SYT6	148281	broad.mit.edu	37	chr1	114682490	114682490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctccttgttcctccaggGcatccagcacagcttccaaa	8	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114682490G>A	ENST00000610222.1	-	2	405	c.259C>T	c.(259-261)Ccc>Tcc	p.P87S	SYT6_ENST00000607941.1_Missense_Mutation_p.P2S|SYT6_ENST00000393296.1_Missense_Mutation_p.P87S|SYT6_ENST00000369547.1_Missense_Mutation_p.P2S|SYT6_ENST00000609117.1_Missense_Mutation_p.P2S			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	87					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.P2S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-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)		TTCCTCCAGGGCATCCAGCAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	71	69					1																	114682490		2203	4300	6503	114484013	SO:0001583	missense	148281				CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.259C>T	1.37:g.114682490G>A	ENSP00000476396:p.Pro87Ser		114484013	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	37		.	.	.	.	.	.	.	.	.	.	g	14.90	2.673502	0.47781	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545;ENST00000425037;ENST00000447981	T;T;T;T;T;T	0.59638	0.25;0.57;0.25;0.57;1.23;0.57	5.66	4.75	0.60458	.	0.290337	0.39615	N	0.001304	T	0.32466	0.0830	N	0.25890	0.77	0.49389	D	0.999782	B	0.26975	0.165	B	0.32090	0.14	T	0.24870	-1.0148	10	0.41790	T	0.15	.	14.522	0.67856	0.0704:0.0:0.9296:0.0	.	87	Q5T7P8	SYT6_HUMAN	S	2;87;2;87;2;2	ENSP00000358560:P2S;ENSP00000376974:P87S;ENSP00000358559:P2S;ENSP00000358558:P87S;ENSP00000412443:P2S;ENSP00000389266:P2S	ENSP00000358558:P87S	P	-	1	0	SYT6	114484013	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	4.074000	0.57577	1.409000	0.46915	0.651000	0.88453	CCC		0.572	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		A	114682490	G	A	114682490	3	1	61	1	0	0	0	0	1	0	0	0	15517	1203	42	3	1297	3	SYT6	1	114682490	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159289	114682490	134568131	530	8515										
TRIM33	51592	broad.mit.edu	37	chr1	114940417	114940417	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtcctgtctgagtagatCtctgtgagtttatcttcaaa	9	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114940417C>A	ENST00000358465.2	-	20	3320	c.3237G>T	c.(3235-3237)gaG>gaT	p.E1079D	TRIM33_ENST00000450349.2_Missense_Mutation_p.E711D|TRIM33_ENST00000369543.2_Missense_Mutation_p.E1062D	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	1079					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E1079D(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		CTGAGTAGATCTCTGTGAGTT	0.453			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	1	Substitution - Missense(1)	large_intestine(1)	1											164	150	155					1																	114940417		2203	4300	6503	114741940	SO:0001583	missense	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.3237G>T	1.37:g.114940417C>A	ENSP00000351250:p.Glu1079Asp		114741940	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.46|13.46	2.244255|2.244255	0.39697|0.39697	.|.	.|.	ENSG00000197323|ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349|ENST00000448034	T;T;T|.	0.20332|.	2.08;2.08;2.08|.	5.3|5.3	5.3|5.3	0.74995|0.74995	Bromodomain (3);|.	0.090754|.	0.85682|.	D|.	0.000000|.	T|T	0.51787|0.51787	0.1695|0.1695	L|L	0.50333|0.50333	1.59|1.59	0.58432|0.58432	D|D	0.999999|0.999999	B;B;P;P|.	0.51791|.	0.259;0.222;0.657;0.948|.	B;B;B;B|.	0.41236|.	0.084;0.129;0.3;0.351|.	T|T	0.49409|0.49409	-0.8943|-0.8943	10|5	0.48119|.	T|.	0.1|.	-12.3833|-12.3833	12.6569|12.6569	0.56791|0.56791	0.0:0.9241:0.0:0.0759|0.0:0.9241:0.0:0.0759	.|.	711;711;1062;1079|.	E7EN20;B3KN30;Q9UPN9-2;Q9UPN9|.	.;.;.;TRI33_HUMAN|.	D|I	1079;1062;711|840	ENSP00000351250:E1079D;ENSP00000358556:E1062D;ENSP00000412077:E711D|.	ENSP00000351250:E1079D|.	E|R	-|-	3|2	2|0	TRIM33|TRIM33	114741940|114741940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.306000|2.306000	0.43673|0.43673	2.646000|2.646000	0.89796|0.89796	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.453	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		A	114940417	C	A	114940417	3	1	61	1	0	0	0	0	1	0	0	0	16547	912	32	2	150	2	TRIM33	1	114940417	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	257927	114940417	134310204	531	8516										
TRIM33	51592	broad.mit.edu	37	chr1	114968214	114968214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatacttgttgttgcatgtGctggagtcgaagctgtgcta	12	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:114968214G>T	ENST00000358465.2	-	9	1635	c.1552C>A	c.(1552-1554)Cac>Aac	p.H518N	TRIM33_ENST00000450349.2_Missense_Mutation_p.H126N|TRIM33_ENST00000369543.2_Missense_Mutation_p.H518N	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	518					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H518N(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		TGTTGCATGTGCTGGAGTCGA	0.448			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	1	Substitution - Missense(1)	large_intestine(1)	1											365	320	335					1																	114968214		2203	4300	6503	114769737	SO:0001583	missense	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.1552C>A	1.37:g.114968214G>T	ENSP00000351250:p.His518Asn		114769737	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.3|26.3	4.727415|4.727415	0.89390|0.89390	.|.	.|.	ENSG00000197323|ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349|ENST00000448034	T;T;T|.	0.78481|.	-0.95;-0.82;-1.18|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.044464|.	0.85682|.	N|.	0.000000|.	T|T	0.67702|0.67702	0.2921|0.2921	M|M	0.64404|0.64404	1.975|1.975	0.80722|0.80722	D|D	1|1	P;P;D;D|.	0.61080|.	0.936;0.936;0.989;0.983|.	P;P;D;D|.	0.72982|.	0.885;0.885;0.979;0.943|.	T|T	0.65701|0.65701	-0.6104|-0.6104	10|5	0.20046|.	T|.	0.44|.	-10.5766|-10.5766	18.9585|18.9585	0.92670|0.92670	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	126;126;518;518|.	E7EN20;B3KN30;Q9UPN9-2;Q9UPN9|.	.;.;.;TRI33_HUMAN|.	N|R	518;518;126|254	ENSP00000351250:H518N;ENSP00000358556:H518N;ENSP00000412077:H126N|.	ENSP00000351250:H518N|.	H|S	-|-	1|3	0|2	TRIM33|TRIM33	114769737|114769737	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.938000|8.938000	0.92943|0.92943	2.554000|2.554000	0.86153|0.86153	0.650000|0.650000	0.86243|0.86243	CAC|AGC		0.448	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		T	114968214	G	T	114968214	3	4	61	1	0	0	0	0	1	0	0	0	16547	1319	46	2	1879	2	TRIM33	1	114968214	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27797	114968214	134282407	532	8517										
DENND2C	163259	broad.mit.edu	37	chr1	115166144	115166144	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacatatgatatcttcataGatattgtcctcagactgtgt	6	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115166144G>T	ENST00000393274.1	-	5	1552	c.927C>A	c.(925-927)atC>atA	p.I309I	DENND2C_ENST00000481894.1_Intron|DENND2C_ENST00000393276.3_Silent_p.I309I|DENND2C_ENST00000393277.1_Silent_p.I309I	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	309					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.I309I(1)		NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-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)		TATCTTCATAGATATTGTCCT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											98	97	97					1																	115166144		2202	4300	6502	114967667	SO:0001819	synonymous_variant	163259				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.927C>A	1.37:g.115166144G>T			114967667	B1AL26|Q5TCX6|Q6P3R3	Silent	SNP	ENST00000393274.1	37	CCDS58018.1																																																																																				0.348	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		T	115166144	G	T	115166144	2	4	61	1	0	0	0	0	0	0	0	1	4441	932	33	2		2	DENND2C	1	115166144	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197930	115166144	134084477	533	8518										
AMPD1	270	broad.mit.edu	37	chr1	115216304	115216304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacactgttccttgccacttCgcacatatcacaggtgctca	7	14	2	0	rs374697989		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115216304C>T	ENST00000520113.2	-	15	2155	c.2140G>A	c.(2140-2142)Gaa>Aaa	p.E714K	AMPD1_ENST00000353928.6_Missense_Mutation_p.E681K|AMPD1_ENST00000369538.3_Missense_Mutation_p.E710K			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	714					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.E681K(1)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	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)	CTTGCCACTTCGCACATATCA	0.433													C|||	1	0.000199681	8e-04	0	5008	,	,		19728	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											103	100	101					1																	115216304		2203	4300	6503	115017827	SO:0001583	missense	270			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.2140G>A	1.37:g.115216304C>T	ENSP00000430075:p.Glu714Lys		115017827	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	35	5.488261	0.96323	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95690	-3.78;-3.78;-3.78	5.93	5.93	0.95920	Adenosine/AMP deaminase (1);	0.103160	0.64402	D	0.000002	D	0.98476	0.9492	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.77557	0.947;0.99	D	0.98858	1.0761	10	0.87932	D	0	-23.8527	20.3368	0.98748	0.0:1.0:0.0:0.0	.	710;681	Q5TF02;P23109	.;AMPD1_HUMAN	K	714;710;681	ENSP00000430075:E714K;ENSP00000358551:E710K;ENSP00000316520:E681K	ENSP00000316520:E681K	E	-	1	0	AMPD1	115017827	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.805000	0.96524	0.655000	0.94253	GAA		0.433	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			T	115216304	C	T	115216304	3	4	61	1	0	0	0	0	1	0	0	0	585	893	31	1	210	1	AMPD1	1	115216304	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50160	115216304	134034317	534	8519										
CSDE1	7812	broad.mit.edu	37	chr1	115266570	115266570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaacactcctcagggggcGaattactttgccagagtaaa	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115266570G>A	ENST00000358528.4	-	16	2233	c.1807C>T	c.(1807-1809)Cgc>Tgc	p.R603C	CSDE1_ENST00000339438.6_Missense_Mutation_p.R572C|CSDE1_ENST00000438362.2_Missense_Mutation_p.R649C|CSDE1_ENST00000261443.5_Missense_Mutation_p.R572C|CSDE1_ENST00000534699.1_Missense_Mutation_p.R603C|CSDE1_ENST00000530886.1_Missense_Mutation_p.R473C|CSDE1_ENST00000369530.1_Missense_Mutation_p.R618C	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	603					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R603C(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-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)		CTCAGGGGGCGAATTACTTTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											181	159	166					1																	115266570		2203	4300	6503	115068093	SO:0001583	missense	7812				CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1807C>T	1.37:g.115266570G>A	ENSP00000351329:p.Arg603Cys		115068093	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.583771	0.65992	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.51432	0.1674	M	0.71036	2.16	0.80722	D	1	B;D;B	0.65815	0.088;0.995;0.01	B;B;B	0.43225	0.007;0.412;0.004	T	0.61831	-0.6982	9	0.87932	D	0	-0.4338	15.581	0.76439	0.0:0.0:0.8623:0.1377	.	618;603;649	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	C	572;649;603;572;473;618;603	.	ENSP00000261443:R572C	R	-	1	0	CSDE1	115068093	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.177000	0.65032	2.941000	0.99782	0.655000	0.94253	CGC		0.418	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		A	115266570	G	A	115266570	3	1	61	1	0	0	0	0	1	0	0	0	3935	1058	37	1	609	1	CSDE1	1	115266570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50266	115266570	133984051	535	8520										
SYCP1	6847	broad.mit.edu	37	chr1	115402409	115402409	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattagaagaaggaatacaaGaaaataaagatttaataaaa	6	1	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115402409G>T	ENST00000369522.3	+	7	742	c.502G>T	c.(502-504)Gaa>Taa	p.E168*	SYCP1_ENST00000369518.1_Nonsense_Mutation_p.E168*	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	168				E -> D (in Ref. 2; BAA22586). {ECO:0000305}.	chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.E168*(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		AGGAATACAAGAAAATAAAGA	0.204																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											9	10	10					1																	115402409		1922	3975	5897	115203932	SO:0001587	stop_gained	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.502G>T	1.37:g.115402409G>T	ENSP00000358535:p.Glu168*		115203932	O14963|Q5VXJ6	Nonsense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	38	7.120366	0.98077	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	.	.	.	4.98	4.98	0.66077	.	0.053608	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-15.9457	17.8515	0.88748	0.0:0.0:1.0:0.0	.	.	.	.	X	168	.	ENSP00000358531:E168X	E	+	1	0	SYCP1	115203932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.195000	0.89723	2.312000	0.78011	0.561000	0.74099	GAA		0.204	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115402409	G	T	115402409	4	4	61	1	0	0	0	0	0	1	0	0	15470	943	33	2	524	2	SYCP1	1	115402409	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135839	115402409	133848212	536	8521										
SYCP1	6847	broad.mit.edu	37	chr1	115430256	115430256	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttacaagattggaaaaAaatgaagatcaattgaaaat	6	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115430256A>C	ENST00000369522.3	+	15	1440	c.1200A>C	c.(1198-1200)aaA>aaC	p.K400N	SYCP1_ENST00000369518.1_Missense_Mutation_p.K400N	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	400				KN -> NY (in Ref. 2; BAA22586). {ECO:0000305}.	chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.K400N(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		GATTGGAAAAAAATGAAGATC	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	1											37	41	40					1																	115430256		2181	4257	6438	115231779	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.1200A>C	1.37:g.115430256A>C	ENSP00000358535:p.Lys400Asn		115231779	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	A	9.745	1.165817	0.21538	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.44482	0.92;0.92;0.92	4.58	3.43	0.39272	.	0.424017	0.26927	N	0.021781	T	0.13756	0.0333	L	0.32530	0.975	0.33998	D	0.649973	B;B	0.17852	0.024;0.024	B;B	0.19391	0.025;0.025	T	0.05321	-1.0892	10	0.33940	T	0.23	-10.1084	7.5026	0.27526	0.8098:0.0:0.0:0.1902	.	400;400	B7ZLS9;Q15431	.;SYCP1_HUMAN	N	400	ENSP00000358535:K400N;ENSP00000410011:K400N;ENSP00000358531:K400N	ENSP00000358531:K400N	K	+	3	2	SYCP1	115231779	1.000000	0.71417	0.999000	0.59377	0.805000	0.45488	2.504000	0.45416	0.753000	0.32945	0.528000	0.53228	AAA		0.259	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		C	115430256	A	C	115430256	3	2	61	1	0	0	0	0	1	0	0	0	15470	11	1	4	1254	4	SYCP1	1	115430256	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	27847	115430256	133820365	537	8522										
SYCP1	6847	broad.mit.edu	37	chr1	115454178	115454178	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaaaagaggttaaagatCtaaaaactgagcttgaaaac	7	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115454178C>A	ENST00000369522.3	+	18	1744	c.1504C>A	c.(1504-1506)Cta>Ata	p.L502I	SYCP1_ENST00000369518.1_Missense_Mutation_p.L502I	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	502				IQLTAITTSEQYYSKEVKDLKTELENEK -> YSYCHYHKW TVLPKRGQRPKLSSKRE (in Ref. 2; BAA22586). {ECO:0000305}.	chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.L502I(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		GGTTAAAGATCTAAAAACTGA	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	67	67					1																	115454178		2202	4288	6490	115255701	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.1504C>A	1.37:g.115454178C>A	ENSP00000358535:p.Leu502Ile		115255701	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841668	0.32513	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.52526	0.66;0.66;0.66	5.6	2.11	0.27256	.	0.382752	0.23750	N	0.044928	T	0.30448	0.0765	M	0.64997	1.995	0.28780	N	0.899885	P;P	0.43750	0.816;0.816	P;P	0.46362	0.514;0.514	T	0.12400	-1.0549	10	0.52906	T	0.07	0.0419	7.6004	0.28073	0.5243:0.3965:0.0:0.0792	.	502;502	B7ZLS9;Q15431	.;SYCP1_HUMAN	I	502	ENSP00000358535:L502I;ENSP00000410011:L502I;ENSP00000358531:L502I	ENSP00000358531:L502I	L	+	1	2	SYCP1	115255701	0.995000	0.38212	0.989000	0.46669	0.548000	0.35241	0.531000	0.23052	0.102000	0.17638	0.585000	0.79938	CTA		0.269	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		A	115454178	C	A	115454178	3	1	61	1	0	0	0	0	1	0	0	0	15470	912	32	2	1570	2	SYCP1	1	115454178	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23922	115454178	133796443	538	8523										
SYCP1	6847	broad.mit.edu	37	chr1	115486998	115486998	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactagaaagtgccaaacaGaaatttggagaaatcacaga	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115486998G>T	ENST00000369522.3	+	24	2205	c.1965G>T	c.(1963-1965)caG>caT	p.Q655H	SYCP1_ENST00000369518.1_Missense_Mutation_p.Q655H	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	655					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.Q655H(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		GTGCCAAACAGAAATTTGGAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	1											39	45	43					1																	115486998		2199	4280	6479	115288521	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.1965G>T	1.37:g.115486998G>T	ENSP00000358535:p.Gln655His		115288521	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.350920	0.41599	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.54675	0.56;0.56;0.56	4.24	-0.722	0.11184	.	0.247253	0.39083	N	0.001473	T	0.37376	0.1001	L	0.51422	1.61	0.27537	N	0.950908	P;P	0.37573	0.6;0.6	P;P	0.49301	0.606;0.606	T	0.42531	-0.9446	10	0.62326	D	0.03	-11.205	8.9172	0.35590	0.5124:0.0:0.4876:0.0	.	655;655	B7ZLS9;Q15431	.;SYCP1_HUMAN	H	655	ENSP00000358535:Q655H;ENSP00000410011:Q655H;ENSP00000358531:Q655H	ENSP00000358531:Q655H	Q	+	3	2	SYCP1	115288521	0.967000	0.33354	0.998000	0.56505	0.704000	0.40688	0.029000	0.13666	-0.096000	0.12329	-0.302000	0.09304	CAG		0.299	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115486998	G	T	115486998	3	4	61	1	0	0	0	0	1	0	0	0	15470	933	33	2	2055	2	SYCP1	1	115486998	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32820	115486998	133763623	539	8524										
SYCP1	6847	broad.mit.edu	37	chr1	115487553	115487553	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagaaagaaattgataagCgatgtcaacataaaatagct	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115487553C>T	ENST00000369522.3	+	25	2344	c.2104C>T	c.(2104-2106)Cga>Tga	p.R702*	SYCP1_ENST00000369518.1_Nonsense_Mutation_p.R702*	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	702					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.R702*(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		AATTGATAAGCGATGTCAACA	0.249																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											39	40	40					1																	115487553		2201	4285	6486	115289076	SO:0001587	stop_gained	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2104C>T	1.37:g.115487553C>T	ENSP00000358535:p.Arg702*		115289076	O14963|Q5VXJ6	Nonsense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	C	36	5.826235	0.96996	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	.	.	.	4.91	3.9	0.45041	.	0.080155	0.50627	D	0.000118	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.3104	15.5178	0.75840	0.1479:0.8521:0.0:0.0	.	.	.	.	X	702	.	ENSP00000358531:R702X	R	+	1	2	SYCP1	115289076	0.995000	0.38212	1.000000	0.80357	0.987000	0.75469	1.957000	0.40392	2.268000	0.75426	0.650000	0.86243	CGA		0.249	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115487553	C	T	115487553	4	4	61	1	0	0	0	0	0	1	0	0	15470	760	27	1	2198	1	SYCP1	1	115487553	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	555	115487553	133763068	540	8525										
SYCP1	6847	broad.mit.edu	37	chr1	115489931	115489931	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcaacttgaaatagaaaGagaagagaaggtaggttttt	12	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:115489931G>T	ENST00000369522.3	+	27	2552	c.2312G>T	c.(2311-2313)aGa>aTa	p.R771I	SYCP1_ENST00000369518.1_Missense_Mutation_p.R771I	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	771					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.R771I(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		GAAATAGAAAGAGAAGAGAAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	65	63					1																	115489931		2203	4293	6496	115291454	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2312G>T	1.37:g.115489931G>T	ENSP00000358535:p.Arg771Ile		115291454	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996108	0.54147	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.51071	0.72;0.72;0.72	5.12	0.656	0.17844	.	0.631633	0.16096	N	0.229806	T	0.15739	0.0379	L	0.43152	1.355	0.32635	N	0.521454	B	0.17268	0.021	B	0.18871	0.023	T	0.03086	-1.1074	10	0.49607	T	0.09	-4.6803	2.1566	0.03814	0.144:0.116:0.4017:0.3383	.	771	Q15431	SYCP1_HUMAN	I	771	ENSP00000358535:R771I;ENSP00000410011:R771I;ENSP00000358531:R771I	ENSP00000358531:R771I	R	+	2	0	SYCP1	115291454	0.989000	0.36119	1.000000	0.80357	0.862000	0.49288	0.009000	0.13219	0.226000	0.20979	0.650000	0.86243	AGA		0.299	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115489931	G	T	115489931	3	4	61	1	0	0	0	0	1	0	0	0	15470	942	33	2	2414	2	SYCP1	1	115489931	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2378	115489931	133760690	541	8526										
CASQ2	845	broad.mit.edu	37	chr1	116275578	116275578	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaagtgttcagctgcttCttcaaaagccttgtagtcta	9	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116275578C>A	ENST00000261448.5	-	5	789	c.550G>T	c.(550-552)Gaa>Taa	p.E184*	CASQ2_ENST00000488931.1_5'Flank|CASQ2_ENST00000456138.2_Nonsense_Mutation_p.E113*	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	184					cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.E184*(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TCAGCTGCTTCTTCAAAAGCC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											108	106	107					1																	116275578		2203	4300	6503	116077101	SO:0001587	stop_gained	845			BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"Protein disulfide isomerases"	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.550G>T	1.37:g.116275578C>A	ENSP00000261448:p.Glu184*		116077101	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Nonsense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	.	.	.	.	.	.	.	.	.	.	C	39	7.864927	0.98531	.	.	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-39.3859	19.7565	0.96296	0.0:1.0:0.0:0.0	.	.	.	.	X	184;113;184	.	ENSP00000261448:E184X	E	-	1	0	CASQ2	116077101	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.553000	0.67287	2.835000	0.97688	0.650000	0.86243	GAA		0.383	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232		A	116275578	C	A	116275578	4	1	61	1	0	0	0	0	0	1	0	0	2687	922	32	2	677	2	CASQ2	1	116275578	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	785647	116275578	132975043	542	8527										
CASQ2	845	broad.mit.edu	37	chr1	116280902	116280902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtagtcttcaatgcgttCgaaggcttggacttccagtt	11	8	2	0	rs375598471		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116280902C>T	ENST00000261448.5	-	4	714	c.475G>A	c.(475-477)Gaa>Aaa	p.E159K	CASQ2_ENST00000456138.2_Intron	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	159					cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.E159K(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TCAATGCGTTCGAAGGCTTGG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	LYS/GLU	0,4406		0,0,2203	244	214	224		475	4.8	1	1		224	2,8598	2.2+/-6.3	0,2,4298	no	missense	CASQ2	NM_001232.3	56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	159/400	116280902	2,13004	2203	4300	6503	116082425	SO:0001583	missense	845			BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"Protein disulfide isomerases"	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.475G>A	1.37:g.116280902C>T	ENSP00000261448:p.Glu159Lys		116082425	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877678	0.72294	0.0	2.33E-4	ENSG00000118729	ENST00000261448;ENST00000446755	T	0.79033	-1.23	5.82	4.85	0.62838	Thioredoxin-like fold (2);	0.097447	0.64402	D	0.000001	T	0.59595	0.2205	M	0.66939	2.045	0.80722	D	1	B	0.26602	0.154	B	0.26614	0.071	T	0.58836	-0.7566	10	0.06236	T	0.91	-30.3587	14.4137	0.67135	0.0:0.8529:0.1471:0.0	.	159	O14958	CASQ2_HUMAN	K	159	ENSP00000261448:E159K	ENSP00000261448:E159K	E	-	1	0	CASQ2	116082425	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.574000	0.53863	2.752000	0.94435	0.655000	0.94253	GAA		0.443	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232		T	116280902	C	T	116280902	3	4	61	1	0	0	0	0	1	0	0	0	2687	893	31	1	756	1	CASQ2	1	116280902	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5324	116280902	132969719	543	8528										
SLC22A15	55356	broad.mit.edu	37	chr1	116563350	116563350	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctttctaggttttgctCttgacatcttatttgcaatt	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116563350C>T	ENST00000369503.4	+	4	572	c.442C>T	c.(442-444)Ctt>Ttt	p.L148F	SLC22A15_ENST00000369502.1_Missense_Mutation_p.L148F	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	148					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.L148F(1)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		AGGTTTTGCTCTTGACATCTT	0.343											OREG0013699	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											122	111	115					1																	116563350		1855	4095	5950	116364873	SO:0001583	missense	55356			AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.442C>T	1.37:g.116563350C>T	ENSP00000358515:p.Leu148Phe	1474	116364873	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	37	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472427	0.43942	.	.	ENSG00000163393	ENST00000369503;ENST00000369502	T;T	0.78246	-1.16;0.07	6.05	5.14	0.70334	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.115058	0.64402	D	0.000014	T	0.57666	0.2069	N	0.21194	0.64	0.44275	D	0.997136	P;P	0.42296	0.568;0.775	B;B	0.42214	0.38;0.334	T	0.59989	-0.7350	10	0.31617	T	0.26	.	14.7748	0.69724	0.0:0.9315:0.0:0.0685	.	148;148	Q8IZD6;Q8IZD6-2	S22AF_HUMAN;.	F	148	ENSP00000358515:L148F;ENSP00000358514:L148F	ENSP00000358514:L148F	L	+	1	0	SLC22A15	116364873	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.066000	0.50002	2.866000	0.98385	0.650000	0.86243	CTT		0.343	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		T	116563350	C	T	116563350	3	4	61	1	0	0	0	0	1	0	0	0	14483	913	32	3	456	3	SLC22A15	1	116563350	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	282448	116563350	132687271	544	8529										
SLC22A15	55356	broad.mit.edu	37	chr1	116569517	116569517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttccctgaattaggatCgattggcggcctgttctttg	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116569517C>T	ENST00000369503.4	+	5	732	c.602C>T	c.(601-603)tCg>tTg	p.S201L	SLC22A15_ENST00000369502.1_Missense_Mutation_p.S201L	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	201					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.S201L(2)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GAATTAGGATCGATTGGCGGC	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	1											224	208	213					1																	116569517		1962	4135	6097	116371040	SO:0001583	missense	55356			AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.602C>T	1.37:g.116569517C>T	ENSP00000358515:p.Ser201Leu		116371040	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	37	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698299	0.68386	.	.	ENSG00000163393	ENST00000369503;ENST00000369502	T;T	0.76316	-1.01;0.11	4.92	4.92	0.64577	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054615	0.85682	D	0.000000	T	0.64427	0.2597	L	0.31845	0.965	0.54753	D	0.999987	P;D	0.54964	0.66;0.969	B;B	0.44085	0.252;0.44	T	0.66404	-0.5932	10	0.38643	T	0.18	.	18.6782	0.91537	0.0:1.0:0.0:0.0	.	201;201	Q8IZD6;Q8IZD6-2	S22AF_HUMAN;.	L	201	ENSP00000358515:S201L;ENSP00000358514:S201L	ENSP00000358514:S201L	S	+	2	0	SLC22A15	116371040	1.000000	0.71417	0.956000	0.39512	0.927000	0.56198	5.400000	0.66320	2.710000	0.92621	0.563000	0.77884	TCG		0.498	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		T	116569517	C	T	116569517	3	4	61	1	0	0	0	0	1	0	0	0	14483	893	31	1	620	1	SLC22A15	1	116569517	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6167	116569517	132681104	545	8530										
ATP1A1	476	broad.mit.edu	37	chr1	116933466	116933466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaattgcaggtctttgtAacagggcagtgtttcaggct	12	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116933466A>G	ENST00000295598.5	+	10	1537	c.1285A>G	c.(1285-1287)Aac>Gac	p.N429D	ATP1A1_ENST00000537345.1_Missense_Mutation_p.N429D|ATP1A1_ENST00000369496.4_Missense_Mutation_p.N398D	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	429					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.N429D(1)		NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	AGGTCTTTGTAACAGGGCAGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											174	166	168					1																	116933466		2203	4300	6503	116734989	SO:0001583	missense	476			D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1285A>G	1.37:g.116933466A>G	ENSP00000295598:p.Asn429Asp		116734989	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	31	5.086812	0.94100	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.84516	-1.86;-1.86;-1.86	5.1	5.1	0.69264	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.088989	0.85682	D	0.000000	D	0.92596	0.7648	M	0.90198	3.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94129	0.7386	10	0.87932	D	0	.	15.0403	0.71785	1.0:0.0:0.0:0.0	.	429;429	F5H3A1;P05023	.;AT1A1_HUMAN	D	429;429;428;398	ENSP00000295598:N429D;ENSP00000445306:N429D;ENSP00000358508:N398D	ENSP00000295598:N429D	N	+	1	0	ATP1A1	116734989	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.130000	0.94437	2.153000	0.67306	0.519000	0.50382	AAC		0.448	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		G	116933466	A	G	116933466	3	3	61	1	0	0	0	0	1	0	0	0	1129	362	13	4	1339	4	ATP1A1	1	116933466	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	363949	116933466	132317155	546	8531										
ATP1A1	476	broad.mit.edu	37	chr1	116943802	116943802	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgccacacagccttcttCgtcagtatcgtggtggtgca	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:116943802C>T	ENST00000295598.5	+	20	3021	c.2769C>T	c.(2767-2769)ttC>ttT	p.F923F	ATP1A1_ENST00000537345.1_Silent_p.F923F|ATP1A1_ENST00000369496.4_Silent_p.F892F	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	923					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.F923F(2)		NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	CAGCCTTCTTCGTCAGTATCG	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	1											91	80	84					1																	116943802		2203	4300	6503	116745325	SO:0001819	synonymous_variant	476			D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2769C>T	1.37:g.116943802C>T			116745325	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Silent	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418198	0.25552	.	.	ENSG00000163399	ENST00000339159	.	.	.	5.1	-4.5	0.03493	.	.	.	.	.	T	0.59500	0.2198	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72080	-0.4398	5	0.66056	D	0.02	.	13.8847	0.63702	0.0:0.2556:0.0:0.7444	.	.	.	.	L	655	.	ENSP00000342827:S655L	S	+	2	0	ATP1A1	116745325	0.102000	0.21896	0.973000	0.42090	0.998000	0.95712	-0.560000	0.05964	-0.728000	0.04882	0.591000	0.81541	TCG		0.507	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		T	116943802	C	T	116943802	2	4	61	1	0	0	0	0	0	0	0	1	1129	883	31	1		1	ATP1A1	1	116943802	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10336	116943802	132306819	547	8532										
CD58	965	broad.mit.edu	37	chr1	117064558	117064558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcacaatacatgttgtaaTtactgctaatggtatgggta	9	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117064558T>G	ENST00000369489.5	-	4	742	c.676A>C	c.(676-678)Att>Ctt	p.I226L	CD58_ENST00000369487.3_Missense_Mutation_p.I226L|CD58_ENST00000457047.2_Missense_Mutation_p.I226L	NM_001779.2	NP_001770.1	P19256	LFA3_HUMAN	CD58 molecule	226					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interferon-gamma (GO:0071346)|cellular response to tumor necrosis factor (GO:0071356)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|positive regulation of interleukin-8 secretion (GO:2000484)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.I226L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		CATGTTGTAATTACTGCTAAT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	75	76					1																	117064558		2197	4298	6495	116866081	SO:0001583	missense	965			BC005930	CCDS888.1, CCDS44199.1	1p13	2008-02-05	2006-03-28		ENSG00000116815	ENSG00000116815		"CD molecules"	1688	protein-coding gene	gene with protein product		153420	"CD58 antigen, (lymphocyte function-associated antigen 3)"	LFA3		9510189	Standard	NM_001144822		Approved		uc001egm.3	P19256	OTTHUMG00000022749	ENST00000369489.5:c.676A>C	1.37:g.117064558T>G	ENSP00000358501:p.Ile226Leu		116866081	A8K7G5|Q5U053|Q6IB65|Q96KI9	Missense_Mutation	SNP	ENST00000369489.5	37	CCDS888.1	.	.	.	.	.	.	.	.	.	.	T	7.315	0.615877	0.14129	.	.	ENSG00000116815	ENST00000369489;ENST00000457047;ENST00000526981;ENST00000369487	T;T;T	0.55930	0.49;0.51;0.84	1.92	-3.85	0.04243	.	5.897520	0.00508	N	0.000163	T	0.11196	0.0273	N	0.24115	0.695	0.09310	N	1	B;B;B	0.32101	0.356;0.229;0.206	B;B;B	0.28139	0.081;0.081;0.086	T	0.03325	-1.1048	10	0.27082	T	0.32	.	0.4243	0.00461	0.1978:0.2962:0.2005:0.3055	.	226;226;226	P19256-3;B1AMW1;P19256	.;.;LFA3_HUMAN	L	226;226;110;226	ENSP00000358501:I226L;ENSP00000409080:I226L;ENSP00000358499:I226L	ENSP00000358499:I226L	I	-	1	0	CD58	116866081	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.026000	0.01434	-1.355000	0.02186	-0.327000	0.08410	ATT		0.289	CD58-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059036.1	NM_001779		G	117064558	T	G	117064558	3	3	61	1	0	0	0	0	1	0	0	0	3031	1493	52	4	92	4	CD58	1	117064558	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	120756	117064558	132186063	548	8533										
IGSF3	3321	broad.mit.edu	37	chr1	117142915	117142915	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgcaagtcaaaggagtcGctgtaggtcacccccggtgt	12	12	2	0	rs376742521		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117142915G>A	ENST00000369486.3	-	7	2442	c.1677C>T	c.(1675-1677)agC>agT	p.S559S	IGSF3_ENST00000318837.6_Silent_p.S579S|IGSF3_ENST00000369483.1_Silent_p.S579S	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	559	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.S559S(1)|p.S579S(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		CAAAGGAGTCGCTGTAGGTCA	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	1						G	,	1,4405	2.1+/-5.4	0,1,2202	27	32	31		1677,1737	-2.3	1	1		31	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	IGSF3	NM_001007237.1,NM_001542.2	,	0,2,6498	AA,AG,GG		0.0116,0.0227,0.0154	,	559/1195,579/1215	117142915	2,12998	2203	4297	6500	116944438	SO:0001819	synonymous_variant	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1677C>T	1.37:g.117142915G>A			116944438	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	CCDS30813.1																																																																																				0.587	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117142915	G	A	117142915	2	1	61	1	0	0	0	0	0	0	0	1	7622	1078	38	1		1	IGSF3	1	117142915	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78357	117142915	132107706	549	8534										
IGSF3	3321	broad.mit.edu	37	chr1	117156487	117156487	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactcggcggcctcgcagtaGaattcgccctggtcagaagg	13	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117156487G>T	ENST00000369486.3	-	4	1497	c.732C>A	c.(730-732)ttC>ttA	p.F244L	IGSF3_ENST00000318837.6_Missense_Mutation_p.F244L|IGSF3_ENST00000369483.1_Missense_Mutation_p.F244L	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	244	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.F244L(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		CCTCGCAGTAGAATTCGCCCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	39	40					1																	117156487		2203	4300	6503	116958010	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.732C>A	1.37:g.117156487G>T	ENSP00000358498:p.Phe244Leu		116958010	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	8.241	0.806934	0.16467	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65549	-0.16;-0.16;-0.16	4.77	4.77	0.60923	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059205	0.64402	D	0.000001	T	0.41259	0.1151	N	0.16307	0.4	0.50813	D	0.999891	P;P	0.46859	0.804;0.885	P;P	0.57548	0.665;0.823	T	0.34453	-0.9828	10	0.10636	T	0.68	-44.5103	8.834	0.35102	0.1002:0.0:0.8998:0.0	.	244;244	O75054;A6NJZ6	IGSF3_HUMAN;.	L	244	ENSP00000358498:F244L;ENSP00000358495:F244L;ENSP00000321184:F244L	ENSP00000321184:F244L	F	-	3	2	IGSF3	116958010	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.102000	0.41796	2.470000	0.83445	0.557000	0.71058	TTC		0.637	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117156487	G	T	117156487	3	4	61	1	0	0	0	0	1	0	0	0	7622	933	33	2	2948	2	IGSF3	1	117156487	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13572	117156487	132094134	550	8535										
PTGFRN	5738	broad.mit.edu	37	chr1	117509565	117509565	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgaaggcgaggcagccaAagcctttctttgctgccgga	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117509565A>C	ENST00000393203.2	+	6	1819	c.1672A>C	c.(1672-1674)Aag>Cag	p.K558Q		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	558	Ig-like C2-type 5.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K558Q(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GAGGCAGCCAAAGCCTTTCTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											40	41	40					1																	117509565		2203	4300	6503	117311088	SO:0001583	missense	5738			AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9601	protein-coding gene	gene with protein product		601204	"prostaglandin F2 receptor negative regulator"			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.1672A>C	1.37:g.117509565A>C	ENSP00000376899:p.Lys558Gln		117311088	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.421068	0.62622	.	.	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.11277	2.79	5.35	4.14	0.48551	Immunoglobulin subtype (1);	0.133789	0.51477	D	0.000091	T	0.02494	0.0076	N	0.16478	0.41	0.38508	D	0.948403	P	0.45240	0.854	P	0.45406	0.479	T	0.41088	-0.9528	10	0.11182	T	0.66	-37.474	5.1848	0.15178	0.726:0.1829:0.0911:0.0	.	558	Q9P2B2	FPRP_HUMAN	Q	558;417	ENSP00000376899:K558Q	ENSP00000376899:K558Q	K	+	1	0	PTGFRN	117311088	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	4.928000	0.63447	2.163000	0.67991	0.528000	0.53228	AAG		0.418	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440		C	117509565	A	C	117509565	3	2	61	1	0	0	0	0	1	0	0	0	12785	15	1	4	1694	4	PTGFRN	1	117509565	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	353078	117509565	131741056	551	8536										
CD101	9398	broad.mit.edu	37	chr1	117544473	117544473	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatgtggcatctttctttCtccttctgagtaagtttcat	6	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117544473C>A	ENST00000256652.4	+	1	92	c.34C>A	c.(34-36)Ctc>Atc	p.L12I	CD101_ENST00000369470.1_Missense_Mutation_p.L12I	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	12					cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.L12I(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATCTTTCTTTCTCCTTCTGAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											294	236	256					1																	117544473		2203	4300	6503	117345996	SO:0001583	missense	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.34C>A	1.37:g.117544473C>A	ENSP00000256652:p.Leu12Ile		117345996	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	C	9.812	1.183356	0.21870	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.04015	3.73;3.73	5.31	4.36	0.52297	Immunoglobulin-like fold (1);	0.463838	0.19912	N	0.103275	T	0.01695	0.0054	L	0.40543	1.245	0.27387	N	0.955254	P	0.42908	0.793	B	0.41202	0.35	T	0.47736	-0.9094	10	0.22109	T	0.4	1.9687	8.4237	0.32716	0.0:0.8877:0.0:0.1123	.	12	Q93033	IGSF2_HUMAN	I	12	ENSP00000256652:L12I;ENSP00000358482:L12I	ENSP00000256652:L12I	L	+	1	0	CD101	117345996	0.988000	0.35896	0.977000	0.42913	0.856000	0.48823	0.722000	0.25925	1.392000	0.46585	0.555000	0.69702	CTC		0.433	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		A	117544473	C	A	117544473	3	1	61	1	0	0	0	0	1	0	0	0	2968	913	32	2	36	2	CD101	1	117544473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34908	117544473	131706148	552	8537										
CD101	9398	broad.mit.edu	37	chr1	117552701	117552701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatacgcagcgggtgcgaagCggagacgtctacgtggagag	17	8	1	2	rs559703299		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117552701C>T	ENST00000256652.4	+	2	331	c.273C>T	c.(271-273)agC>agT	p.S91S	CD101_ENST00000369470.1_Silent_p.S91S	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	91	Ig-like C2-type 1.			S -> G (in Ref. 1; CAA83923). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.S91S(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGGTGCGAAGCGGAGACGTCT	0.532													C|||	1	0.000199681	0	0	5008	,	,		21151	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											95	85	88					1																	117552701		2203	4300	6503	117354224	SO:0001819	synonymous_variant	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.273C>T	1.37:g.117552701C>T			117354224	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																				0.532	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117552701	C	T	117552701	2	4	61	1	0	0	0	0	0	0	0	1	2968	767	27	1		1	CD101	1	117552701	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8228	117552701	131697920	553	8538										
CD101	9398	broad.mit.edu	37	chr1	117556033	117556033	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttttgtttcccagtgaaaGattttcaagtcaacattaca	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117556033G>T	ENST00000256652.4	+	4	905	c.847G>T	c.(847-849)Gat>Tat	p.D283Y	CD101_ENST00000369470.1_Missense_Mutation_p.D283Y	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	283	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.D283Y(2)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCCAGTGAAAGATTTTCAAGT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	1											127	135	132					1																	117556033		2203	4300	6503	117357556	SO:0001583	missense	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.847G>T	1.37:g.117556033G>T	ENSP00000256652:p.Asp283Tyr		117357556	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519223	0.64634	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03831	3.79;3.79	6.06	5.06	0.68205	Immunoglobulin-like (1);	0.463681	0.19944	N	0.102591	T	0.09949	0.0244	M	0.74881	2.28	0.43930	D	0.996581	D	0.76494	0.999	P	0.60789	0.879	T	0.01036	-1.1473	10	0.72032	D	0.01	-5.4844	10.9522	0.47336	0.0927:0.0:0.9073:0.0	.	283	Q93033	IGSF2_HUMAN	Y	283	ENSP00000256652:D283Y;ENSP00000358482:D283Y	ENSP00000256652:D283Y	D	+	1	0	CD101	117357556	0.980000	0.34600	0.996000	0.52242	0.996000	0.88848	1.859000	0.39418	1.411000	0.46957	0.655000	0.94253	GAT		0.478	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117556033	G	T	117556033	3	4	61	1	0	0	0	0	1	0	0	0	2968	942	33	2	861	2	CD101	1	117556033	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3332	117556033	131694588	554	8539										
CD101	9398	broad.mit.edu	37	chr1	117559944	117559944	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcaacacaaggctggaGaaaatggactgggccacctt	12	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117559944G>T	ENST00000256652.4	+	5	1519	c.1461G>T	c.(1459-1461)gaG>gaT	p.E487D	CD101_ENST00000369470.1_Missense_Mutation_p.E487D	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	487	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.E487D(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAAGGCTGGAGAAAATGGACT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	98	102					1																	117559944		2203	4300	6503	117361467	SO:0001583	missense	9398			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1461G>T	1.37:g.117559944G>T	ENSP00000256652:p.Glu487Asp		117361467	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330858	0.41297	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.22539	1.95;1.95	4.62	2.7	0.31948	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.533273	0.18420	N	0.141768	T	0.09905	0.0243	M	0.74258	2.255	0.30320	N	0.787722	B	0.18166	0.026	B	0.18561	0.022	T	0.11690	-1.0577	10	0.48119	T	0.1	-9.3874	6.5166	0.22252	0.0986:0.182:0.7194:0.0	.	487	Q93033	IGSF2_HUMAN	D	487	ENSP00000256652:E487D;ENSP00000358482:E487D	ENSP00000256652:E487D	E	+	3	2	CD101	117361467	1.000000	0.71417	0.988000	0.46212	0.888000	0.51559	1.148000	0.31614	0.640000	0.30582	-0.126000	0.14955	GAG		0.557	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117559944	G	T	117559944	3	4	61	1	0	0	0	0	1	0	0	0	2968	933	33	2	1479	2	CD101	1	117559944	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3911	117559944	131690677	555	8540										
TTF2	8458	broad.mit.edu	37	chr1	117616303	117616303	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgttcttccgatgcattaGaagtaaggcagaggggaaac	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117616303G>T	ENST00000369466.4	+	4	283	c.239G>T	c.(238-240)aGa>aTa	p.R80I		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	80				R -> G (in Ref. 2; AAD49435). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.R80I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		CGATGCATTAGAAGTAAGGCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											154	145	148					1																	117616303		2203	4300	6503	117417826	SO:0001583	missense	8458			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.239G>T	1.37:g.117616303G>T	ENSP00000358478:p.Arg80Ile		117417826	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816603	0.50633	.	.	ENSG00000116830	ENST00000369466	D	0.87256	-2.23	5.24	-1.83	0.07833	.	0.357115	0.20632	N	0.088576	T	0.78227	0.4250	L	0.57536	1.79	0.19775	N	0.999956	P;P	0.48016	0.868;0.904	B;P	0.51355	0.317;0.667	T	0.73062	-0.4101	10	0.72032	D	0.01	-5.0244	5.2832	0.15686	0.5077:0.1538:0.3385:0.0	.	80;80	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	I	80	ENSP00000358478:R80I	ENSP00000358478:R80I	R	+	2	0	TTF2	117417826	0.008000	0.16893	0.062000	0.19696	0.964000	0.63967	0.042000	0.13949	-0.279000	0.09167	0.484000	0.47621	AGA		0.348	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			T	117616303	G	T	117616303	3	4	61	1	0	0	0	0	1	0	0	0	16759	942	33	2	253	2	TTF2	1	117616303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56359	117616303	131634318	556	8541										
TTF2	8458	broad.mit.edu	37	chr1	117632681	117632681	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcaacaaaaaaggtttCtccgttgctctccatttgat	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117632681C>A	ENST00000369466.4	+	14	2391	c.2347C>A	c.(2347-2349)Ctc>Atc	p.L783I		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	783	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.L783I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AAAAAGGTTTCTCCGTTGCTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											109	113	112					1																	117632681		2203	4300	6503	117434204	SO:0001583	missense	8458			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.2347C>A	1.37:g.117632681C>A	ENSP00000358478:p.Leu783Ile		117434204	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.744191	0.89663	.	.	ENSG00000116830	ENST00000369466	D	0.95205	-3.64	5.41	5.41	0.78517	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.35585	N	0.003102	D	0.96617	0.8896	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96633	0.9468	10	0.72032	D	0.01	-15.3937	16.7371	0.85449	0.0:1.0:0.0:0.0	.	783	Q9UNY4	TTF2_HUMAN	I	783	ENSP00000358478:L783I	ENSP00000358478:L783I	L	+	1	0	TTF2	117434204	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	2.799000	0.47892	2.826000	0.97356	0.655000	0.94253	CTC		0.408	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			A	117632681	C	A	117632681	3	1	61	1	0	0	0	0	1	0	0	0	16759	913	32	2	2401	2	TTF2	1	117632681	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16378	117632681	131617940	557	8542										
TTF2	8458	broad.mit.edu	37	chr1	117644078	117644078	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatttggccaaacaagttCtatcagggtctggagaatct	10	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117644078C>A	ENST00000369466.4	+	23	3465	c.3421C>A	c.(3421-3423)Cta>Ata	p.L1141I	TTF2_ENST00000480701.1_3'UTR	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1141	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.L1141I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		CAAACAAGTTCTATCAGGGTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											172	178	176					1																	117644078		2203	4300	6503	117445601	SO:0001583	missense	8458			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3421C>A	1.37:g.117644078C>A	ENSP00000358478:p.Leu1141Ile		117445601	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.548071	0.86022	.	.	ENSG00000116830	ENST00000369466;ENST00000427271	T;T	0.76968	-1.06;-1.06	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.000000	0.31821	N	0.007008	T	0.79868	0.4520	L	0.33710	1.025	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.78745	-0.2084	10	0.44086	T	0.13	-12.2997	17.8168	0.88637	0.0:1.0:0.0:0.0	.	1141	Q9UNY4	TTF2_HUMAN	I	1141;122	ENSP00000358478:L1141I;ENSP00000408111:L122I	ENSP00000358478:L1141I	L	+	1	2	TTF2	117445601	1.000000	0.71417	0.984000	0.44739	0.903000	0.53119	4.524000	0.60552	2.879000	0.98667	0.650000	0.86243	CTA		0.398	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			A	117644078	C	A	117644078	3	1	61	1	0	0	0	0	1	0	0	0	16759	912	32	2	3511	2	TTF2	1	117644078	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11397	117644078	131606543	558	8543										
MAN1A2	10905	broad.mit.edu	37	chr1	117963224	117963224	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtttgaagtcaacattCgatttattggaggcctactt	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:117963224C>A	ENST00000356554.3	+	5	1543	c.808C>A	c.(808-810)Cga>Aga	p.R270R	MAN1A2_ENST00000482811.1_3'UTR	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	270					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.R270R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		AGTCAACATTCGATTTATTGG	0.353																																					Ovarian(33;199 881 8228 13687 31538)											1	Substitution - coding silent(1)	large_intestine(1)	1											128	116	120					1																	117963224		2203	4300	6503	117764747	SO:0001819	synonymous_variant	10905			AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.808C>A	1.37:g.117963224C>A			117764747	Q9H510	Silent	SNP	ENST00000356554.3	37	CCDS895.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562798	0.27915	.	.	ENSG00000198162	ENST00000449370	.	.	.	5.78	4.84	0.62591	.	.	.	.	.	T	0.52058	0.1711	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53865	-0.8378	4	.	.	.	-1.7687	11.9573	0.52988	0.1734:0.8265:0.0:0.0	.	.	.	.	L	2	.	.	F	+	3	2	MAN1A2	117764747	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.273000	0.58914	1.382000	0.46385	0.655000	0.94253	TTC		0.353	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		A	117963224	C	A	117963224	2	1	61	1	0	0	0	0	0	0	0	1	9241	876	31	2		2	MAN1A2	1	117963224	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	319146	117963224	131287397	559	8544										
GDAP2	54834	broad.mit.edu	37	chr1	118454616	118454616	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatctctgatattacttacGaagtgctatgtgtgttgcat	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118454616G>A	ENST00000369443.5	-	5	808	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	GDAP2_ENST00000369442.3_Splice_Site_p.R187C	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	187	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)		p.R187C(2)		kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		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)		TATTACTTACGAAGTGCTATG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	1											100	91	94					1																	118454616		2203	4299	6502	118256139	SO:0001630	splice_region_variant	54834			AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.559+1C>T	1.37:g.118454616G>A			118256139	Q96DZ0	Missense_Mutation	SNP	ENST00000369443.5	37	CCDS897.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984551	0.74474	.	.	ENSG00000196505	ENST00000369443;ENST00000369442	T;T	0.23950	1.88;1.88	5.22	5.22	0.72569	Appr-1-p processing (1);	0.000000	0.85682	D	0.000000	T	0.57403	0.2051	M	0.93106	3.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.67795	-0.5578	9	.	.	.	-9.0828	19.0355	0.92976	0.0:0.0:1.0:0.0	.	187;187	Q9NXN4-2;Q9NXN4	.;GDAP2_HUMAN	C	187	ENSP00000358451:R187C;ENSP00000358450:R187C	.	R	-	1	0	GDAP2	118256139	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.344000	0.65981	2.725000	0.93324	0.644000	0.83932	CGC		0.403	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686	Missense_Mutation	A	118454616	G	A	118454616	5	1	61	1	0	0	0	0	0	0	1	0	6329	1072	37	1	1019	1	GDAP2	1	118454616	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	491392	118454616	130796005	560	8545										
SPAG17	200162	broad.mit.edu	37	chr1	118509244	118509244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatatttgcttccacagGtaggaacagaacctcatgct	9	9	1	1	rs202009513		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118509244G>T	ENST00000336338.5	-	47	6585	c.6520C>A	c.(6520-6522)Cct>Act	p.P2174T		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2174						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.P2174T(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCTTCCACAGGTAGGAACAGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	141	143					1																	118509244		2203	4300	6503	118310767	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.6520C>A	1.37:g.118509244G>T	ENSP00000337804:p.Pro2174Thr		118310767	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205660	0.79127	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.31510	1.49	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000002	T	0.43875	0.1267	L	0.53729	1.69	0.35834	D	0.825508	D	0.89917	1.0	D	0.87578	0.998	T	0.45041	-0.9288	10	0.87932	D	0	.	16.3053	0.82846	0.0:0.0:1.0:0.0	.	2174	Q6Q759	SPG17_HUMAN	T	2174;654	ENSP00000337804:P2174T	ENSP00000337804:P2174T	P	-	1	0	SPAG17	118310767	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.647000	0.67923	2.570000	0.86706	0.655000	0.94253	CCT		0.413	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118509244	G	T	118509244	3	4	61	1	0	0	0	0	1	0	0	0	15018	1261	44	2	159	2	SPAG17	1	118509244	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54628	118509244	130741377	561	8546										
SPAG17	200162	broad.mit.edu	37	chr1	118523901	118523901	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactgccataccttcaggaGattttgttaaattttcagtt	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118523901G>T	ENST00000336338.5	-	43	6061	c.5996C>A	c.(5995-5997)tCt>tAt	p.S1999Y	SPAG17_ENST00000492438.1_5'UTR	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1999						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.S1999Y(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACCTTCAGGAGATTTTGTTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	120	120					1																	118523901		2203	4300	6503	118325424	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5996C>A	1.37:g.118523901G>T	ENSP00000337804:p.Ser1999Tyr		118325424	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.119600	0.37436	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.20200	2.09	4.68	2.8	0.32819	.	1.528690	0.03417	N	0.205701	T	0.09202	0.0227	L	0.50333	1.59	0.09310	N	1	P	0.36183	0.542	B	0.34452	0.183	T	0.33317	-0.9873	10	0.72032	D	0.01	.	6.9684	0.24635	0.2092:0.0:0.7908:0.0	.	1999	Q6Q759	SPG17_HUMAN	Y	1999;479	ENSP00000337804:S1999Y	ENSP00000337804:S1999Y	S	-	2	0	SPAG17	118325424	0.185000	0.23213	0.002000	0.10522	0.002000	0.02628	2.777000	0.47717	0.582000	0.29556	-0.142000	0.14014	TCT		0.398	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118523901	G	T	118523901	3	4	61	1	0	0	0	0	1	0	0	0	15018	942	33	2	699	2	SPAG17	1	118523901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14657	118523901	130726720	562	8547										
SPAG17	200162	broad.mit.edu	37	chr1	118530471	118530471	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattacctcgttttgtctatCttttctttccagcgttttga	5	9	3	1	rs115088568	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118530471C>A	ENST00000336338.5	-	40	5720	c.5655G>T	c.(5653-5655)aaG>aaT	p.K1885N		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1885						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.K1885N(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTTTGTCTATCTTTTCTTTCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											181	162	169					1																	118530471		2203	4300	6503	118331994	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5655G>T	1.37:g.118530471C>A	ENSP00000337804:p.Lys1885Asn		118331994	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403296	0.25291	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.20881	2.04	3.77	0.864	0.19068	.	0.491288	0.21853	N	0.068153	T	0.06872	0.0175	M	0.68317	2.08	0.21020	N	0.999807	B	0.28552	0.215	B	0.23419	0.046	T	0.23904	-1.0175	10	0.48119	T	0.1	.	3.2931	0.06956	0.2049:0.5744:0.0:0.2207	.	1885	Q6Q759	SPG17_HUMAN	N	1885;365	ENSP00000337804:K1885N	ENSP00000337804:K1885N	K	-	3	2	SPAG17	118331994	0.772000	0.28567	0.312000	0.25196	0.297000	0.27493	1.000000	0.29770	0.198000	0.20407	0.655000	0.94253	AAG		0.413	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118530471	C	A	118530471	3	1	61	1	0	0	0	0	1	0	0	0	15018	912	32	2	1052	2	SPAG17	1	118530471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6570	118530471	130720150	563	8548										
SPAG17	200162	broad.mit.edu	37	chr1	118535239	118535239	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcaaaggcctttccaaatCtgagtaccaaacggaggtcc	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118535239C>T	ENST00000336338.5	-	36	5276	c.5211G>A	c.(5209-5211)caG>caA	p.Q1737Q		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1737						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.Q1737Q(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTTTCCAAATCTGAGTACCAA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	1											72	73	72					1																	118535239		2203	4300	6503	118336762	SO:0001819	synonymous_variant	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5211G>A	1.37:g.118535239C>T			118336762	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																				0.423	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118535239	C	T	118535239	2	4	61	1	0	0	0	0	0	0	0	1	15018	912	32	3		3	SPAG17	1	118535239	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4768	118535239	130715382	564	8549										
SPAG17	200162	broad.mit.edu	37	chr1	118558638	118558638	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggataacaatggggtcaagtCtgctattctttctaatcctt	8	8	4	0	rs371694375		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118558638C>A	ENST00000336338.5	-	29	4302	c.4237G>T	c.(4237-4239)Gac>Tac	p.D1413Y		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1413						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.D1413Y(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGGGTCAAGTCTGCTATTCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											163	175	171					1																	118558638		2203	4300	6503	118360161	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4237G>T	1.37:g.118558638C>A	ENSP00000337804:p.Asp1413Tyr		118360161	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.241435	0.22711	.	.	ENSG00000155761	ENST00000336338	T	0.19938	2.11	4.85	2.94	0.34122	.	0.599784	0.17659	N	0.166386	T	0.20820	0.0501	L	0.56769	1.78	0.09310	N	1	D	0.71674	0.998	P	0.61477	0.889	T	0.04693	-1.0933	10	0.72032	D	0.01	.	8.8126	0.34976	0.0:0.8162:0.0:0.1838	.	1413	Q6Q759	SPG17_HUMAN	Y	1413	ENSP00000337804:D1413Y	ENSP00000337804:D1413Y	D	-	1	0	SPAG17	118360161	0.180000	0.23148	0.007000	0.13788	0.101000	0.19017	0.765000	0.26546	0.441000	0.26529	0.305000	0.20034	GAC		0.408	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118558638	C	A	118558638	3	1	61	1	0	0	0	0	1	0	0	0	15018	913	32	2	2514	2	SPAG17	1	118558638	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23399	118558638	130691983	565	8550										
SPAG17	200162	broad.mit.edu	37	chr1	118584644	118584644	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgctcctcttctgctaatcGatgttgctcttctttccatg	7	13	4	0	rs201253941		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118584644G>A	ENST00000336338.5	-	21	2901	c.2836C>T	c.(2836-2838)Cga>Tga	p.R946*		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	946						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.R946*(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCTGCTAATCGATGTTGCTCT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											180	172	175					1																	118584644		2203	4300	6503	118386167	SO:0001587	stop_gained	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2836C>T	1.37:g.118584644G>A	ENSP00000337804:p.Arg946*		118386167	Q8NAZ1|Q9NT21	Nonsense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	39	7.812121	0.98504	.	.	ENSG00000155761	ENST00000336338	.	.	.	5.36	2.34	0.29019	.	0.136940	0.49916	D	0.000140	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4587	0.61214	0.0:0.0:0.442:0.558	.	.	.	.	X	946	.	ENSP00000337804:R946X	R	-	1	2	SPAG17	118386167	0.029000	0.19370	0.881000	0.34555	0.854000	0.48673	0.901000	0.28445	0.286000	0.22352	-0.188000	0.12872	CGA		0.368	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118584644	G	A	118584644	4	1	61	1	0	0	0	0	0	1	0	0	15018	1066	37	1	3947	1	SPAG17	1	118584644	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26006	118584644	130665977	566	8551										
SPAG17	200162	broad.mit.edu	37	chr1	118598485	118598485	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattcctgatatatagcttCttcttttgtaatccaatctt	4	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:118598485C>A	ENST00000336338.5	-	19	2658	c.2593G>T	c.(2593-2595)Gaa>Taa	p.E865*		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	865						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.E865*(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TATATAGCTTCTTCTTTTGTA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											114	117	116					1																	118598485		2203	4298	6501	118400008	SO:0001587	stop_gained	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2593G>T	1.37:g.118598485C>A	ENSP00000337804:p.Glu865*		118400008	Q8NAZ1|Q9NT21	Nonsense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	36	5.872205	0.97049	.	.	ENSG00000155761	ENST00000336338	.	.	.	5.35	5.35	0.76521	.	0.045994	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.0834	0.81020	0.0:1.0:0.0:0.0	.	.	.	.	X	865	.	ENSP00000337804:E865X	E	-	1	0	SPAG17	118400008	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	3.881000	0.56152	2.784000	0.95788	0.585000	0.79938	GAA		0.338	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118598485	C	A	118598485	4	1	61	1	0	0	0	0	0	1	0	0	15018	922	32	2	4198	2	SPAG17	1	118598485	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13841	118598485	130652136	567	8552										
TBX15	6913	broad.mit.edu	37	chr1	119456754	119456754	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgtttctcccagaatCtctgaatcctttagcaaaag	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:119456754C>A	ENST00000369429.3	-	6	919	c.910G>T	c.(910-912)Gat>Tat	p.D304Y	TBX15_ENST00000207157.3_Missense_Mutation_p.D198Y			Q96SF7	TBX15_HUMAN	T-box 15	304					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.D198Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		CTCCCAGAATCTCTGAATCCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	120	121					1																	119456754		2203	4300	6503	119258277	SO:0001583	missense	6913			AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"T-boxes"	11594	protein-coding gene	gene with protein product		604127	"T-box 14"	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.910G>T	1.37:g.119456754C>A	ENSP00000358437:p.Asp304Tyr		119258277	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		.	.	.	.	.	.	.	.	.	.	C	23.8	4.462091	0.84425	.	.	ENSG00000092607	ENST00000344218;ENST00000207157;ENST00000369429	D;D	0.90620	-2.7;-2.7	5.68	5.68	0.88126	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97065	0.9041	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97799	1.0243	10	0.87932	D	0	.	19.8002	0.96504	0.0:1.0:0.0:0.0	.	304	Q96SF7	TBX15_HUMAN	Y	68;198;304	ENSP00000207157:D198Y;ENSP00000358437:D304Y	ENSP00000207157:D198Y	D	-	1	0	TBX15	119258277	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.465000	0.80898	2.674000	0.91012	0.655000	0.94253	GAT		0.383	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		A	119456754	C	A	119456754	3	1	61	1	0	0	0	0	1	0	0	0	15691	913	32	2	910	2	TBX15	1	119456754	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	858269	119456754	129793867	568	8553										
WARS2	10352	broad.mit.edu	37	chr1	119619219	119619219	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccggaaaatactcgcttCttgctgtctttctggaacaa	8	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:119619219C>A	ENST00000235521.4	-	2	128	c.102G>T	c.(100-102)aaG>aaT	p.K34N	WARS2_ENST00000537870.1_5'UTR|WARS2_ENST00000369426.5_Missense_Mutation_p.K34N	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	34					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)	p.K34N(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	ATACTCGCTTCTTGCTGTCTT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	1											117	129	125					1																	119619219		2203	4300	6503	119420742	SO:0001583	missense	10352			BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"Aminoacyl tRNA synthetases / Class I"	12730	protein-coding gene	gene with protein product	"tryptophan tRNA ligase 2, mitochondrial"	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.102G>T	1.37:g.119619219C>A	ENSP00000235521:p.Lys34Asn		119420742	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Missense_Mutation	SNP	ENST00000235521.4	37	CCDS900.1	.	.	.	.	.	.	.	.	.	.	C	7.123	0.578384	0.13686	.	.	ENSG00000116874	ENST00000369426;ENST00000235521	T;T	0.52754	0.65;0.65	5.78	-0.797	0.10909	.	1.240190	0.05185	N	0.502157	T	0.18841	0.0452	L	0.41079	1.255	0.09310	N	0.999999	B;B;B;B	0.23377	0.084;0.023;0.002;0.023	B;B;B;B	0.22152	0.022;0.038;0.016;0.038	T	0.40213	-0.9575	10	0.59425	D	0.04	-0.3613	6.7756	0.23619	0.1113:0.5031:0.0:0.3856	.	34;34;34;34	B7Z448;B7Z6G7;Q9UGM6;B1ALR1	.;.;SYWM_HUMAN;.	N	34	ENSP00000358434:K34N;ENSP00000235521:K34N	ENSP00000235521:K34N	K	-	3	2	WARS2	119420742	0.000000	0.05858	0.000000	0.03702	0.654000	0.38779	0.131000	0.15870	0.153000	0.19213	0.591000	0.81541	AAG		0.448	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836		A	119619219	C	A	119619219	3	1	61	1	0	0	0	0	1	0	0	0	17290	912	32	2	1029	2	WARS2	1	119619219	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162465	119619219	129631402	569	8554										
HSD3B2	3284	broad.mit.edu	37	chr1	119965219	119965219	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtggaccggcacaaggaGaccctgaagtccaagactca	11	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:119965219G>T	ENST00000543831.1	+	4	1344	c.1095G>T	c.(1093-1095)gaG>gaT	p.E365D	HSD3B2_ENST00000369416.3_Missense_Mutation_p.E365D	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	365					androgen biosynthetic process (GO:0006702)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.E365D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	GGCACAAGGAGACCCTGAAGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											41	38	39					1																	119965219		2203	4300	6503	119766742	SO:0001583	missense	3284			BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5218	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 2"	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.1095G>T	1.37:g.119965219G>T	ENSP00000445122:p.Glu365Asp		119766742	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	.	.	.	.	.	.	.	.	.	.	-	8.944	0.966483	0.18659	.	.	ENSG00000203859	ENST00000543831;ENST00000369416	T;T	0.70869	-0.52;-0.52	4.05	2.1	0.27182	.	0.451094	0.24750	N	0.035909	T	0.47967	0.1474	M	0.69823	2.125	0.09310	N	1	B	0.24368	0.102	B	0.24394	0.053	T	0.45026	-0.9289	9	.	.	.	-16.7288	9.4021	0.38440	0.1832:0.0:0.8168:0.0	.	365	P26439	3BHS2_HUMAN	D	365	ENSP00000445122:E365D;ENSP00000358424:E365D	.	E	+	3	2	HSD3B2	119766742	0.015000	0.18098	0.023000	0.16930	0.687000	0.40016	1.025000	0.30090	0.709000	0.31976	0.298000	0.19748	GAG		0.512	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198		T	119965219	G	T	119965219	3	4	61	1	0	0	0	0	1	0	0	0	7412	933	33	2	1105	2	HSD3B2	1	119965219	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346000	119965219	129285402	570	8555										
HSD3B1	3283	broad.mit.edu	37	chr1	120050165	120050165	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagaggatcatccgcctCttggtgaaggagaaggagct	15	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120050165C>T	ENST00000369413.3	+	2	211	c.66C>T	c.(64-66)ctC>ctT	p.L22L	HSD3B1_ENST00000235547.6_Silent_p.L24L|HSD3B1_ENST00000528909.1_Silent_p.L22L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	22					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.L22L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	TCATCCGCCTCTTGGTGAAGG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											133	117	122					1																	120050165		2203	4300	6503	119851688	SO:0001819	synonymous_variant	3283			S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5217	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 1"	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.66C>T	1.37:g.120050165C>T			119851688	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																				0.522	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		T	120050165	C	T	120050165	2	4	61	1	0	0	0	0	0	0	0	1	7411	900	32	3		3	HSD3B1	1	120050165	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84946	120050165	129200456	571	8556										
ZNF697	90874	broad.mit.edu	37	chr1	120165628	120165628	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaggtgcgagttacgcccGaagcccttcccgcactcgcg	11	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120165628G>A	ENST00000421812.2	-	3	1457	c.1338C>T	c.(1336-1338)ttC>ttT	p.F446F		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	446					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F37F(1)		ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		AGTTACGCCCGAAGCCCTTCC	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	1											18	21	20					1																	120165628		2187	4293	6480	119967151	SO:0001819	synonymous_variant	90874			AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"Zinc fingers, C2H2-type"	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.1338C>T	1.37:g.120165628G>A			119967151	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																				0.667	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		A	120165628	G	A	120165628	2	1	61	1	0	0	0	0	0	0	0	1	18139	1049	37	1		1	ZNF697	1	120165628	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115463	120165628	129084993	572	8557										
HMGCS2	3158	broad.mit.edu	37	chr1	120311388	120311388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgggctactgggagcaggCgagcaggtgtgagggaggtt	22	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120311388C>T	ENST00000369406.3	-	1	129	c.80G>A	c.(79-81)cGc>cAc	p.R27H	HMGCS2_ENST00000544913.2_Missense_Mutation_p.R27H	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	27					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)	p.R27H(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TGGGAGCAGGCGAGCAGGTGT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	81	84					1																	120311388		2203	4300	6503	120112911	SO:0001583	missense	3158			BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.80G>A	1.37:g.120311388C>T	ENSP00000358414:p.Arg27His		120112911	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	37	CCDS905.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118236	0.37339	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.90732	-2.72;-2.48	4.32	0.072	0.14385	.	0.678764	0.13000	N	0.421716	T	0.56187	0.1968	N	0.12182	0.205	0.09310	N	0.99999	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.51020	-0.8758	10	0.12103	T	0.63	-10.1781	3.569	0.07910	0.1779:0.5183:0.0:0.3038	.	27;27	B7Z8R3;P54868	.;HMCS2_HUMAN	H	27	ENSP00000358414:R27H;ENSP00000439495:R27H	ENSP00000358414:R27H	R	-	2	0	HMGCS2	120112911	0.026000	0.19158	0.028000	0.17463	0.641000	0.38312	-0.099000	0.11007	-0.084000	0.12595	0.491000	0.48974	CGC		0.502	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		T	120311388	C	T	120311388	3	4	61	1	0	0	0	0	1	0	0	0	7254	768	27	1	1482	1	HMGCS2	1	120311388	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145760	120311388	128939233	573	8558										
REG4	83998	broad.mit.edu	37	chr1	120342483	120342483	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccgtaagactgacactcGagctatgtacaaggagaggt	11	8	0	3	rs587636387	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120342483G>A	ENST00000354219.1	-	5	607	c.168C>T	c.(166-168)ctC>ctT	p.L56L	REG4_ENST00000256585.5_Silent_p.L56L|REG4_ENST00000530654.1_Silent_p.L56L	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	56	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)	p.L56L(1)		central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		ACTGACACTCGAGCTATGTAC	0.512													G|||	3	0.000599042	0	0	5008	,	,		21107	0.003		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											180	169	173					1																	120342483		2203	4300	6503	120144006	SO:0001819	synonymous_variant	83998			AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"regenerating gene type IV", " gastrointestinal secretory protein"	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.168C>T	1.37:g.120342483G>A			120144006	Q8NER6|Q8NER7	Silent	SNP	ENST00000354219.1	37	CCDS906.1																																																																																				0.512	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044		A	120342483	G	A	120342483	2	1	61	1	0	0	0	0	0	0	0	1	13251	1045	37	1		1	REG4	1	120342483	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31095	120342483	128908138	574	8559										
ADAM30	11085	broad.mit.edu	37	chr1	120438019	120438019	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatccagcatattctagaGaacacacttttccaaacgac	5	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120438019G>T	ENST00000369400.1	-	1	1099	c.941C>A	c.(940-942)tCt>tAt	p.S314Y		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	314	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S314Y(2)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		ATATTCTAGAGAACACACTTT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	1											83	83	83					1																	120438019		2203	4300	6503	120239542	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.941C>A	1.37:g.120438019G>T	ENSP00000358407:p.Ser314Tyr		120239542	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902868	0.33628	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.12039	2.72	4.78	-5.62	0.02481	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	3.802300	0.01458	U	0.015758	T	0.05502	0.0145	L	0.49126	1.545	0.09310	N	1	B	0.19935	0.04	B	0.29663	0.105	T	0.49390	-0.8945	10	0.59425	D	0.04	.	8.7689	0.34719	0.0:0.4524:0.1803:0.3673	.	314	Q9UKF2	ADA30_HUMAN	Y	314	ENSP00000358407:S314Y	ENSP00000358407:S314Y	S	-	2	0	ADAM30	120239542	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.708000	0.05035	-0.734000	0.04843	0.563000	0.77884	TCT		0.403	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		T	120438019	G	T	120438019	3	4	61	1	0	0	0	0	1	0	0	0	248	942	33	2	1435	2	ADAM30	1	120438019	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95536	120438019	128812602	575	8560										
ADAM30	11085	broad.mit.edu	37	chr1	120438101	120438101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccaatctgatgacaggcGagcatttaatacactttttt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120438101G>A	ENST00000369400.1	-	1	1017	c.859C>T	c.(859-861)Cgc>Tgc	p.R287C		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	287	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R287C(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		GATGACAGGCGAGCATTTAAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											40	44	43					1																	120438101		2202	4300	6502	120239624	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.859C>T	1.37:g.120438101G>A	ENSP00000358407:p.Arg287Cys		120239624	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689446	0.48097	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.66995	-0.24	4.96	2.94	0.34122	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.644830	0.12530	U	0.460901	T	0.71022	0.3291	M	0.88031	2.925	0.09310	N	1	P	0.51791	0.948	P	0.55161	0.77	T	0.63014	-0.6731	10	0.87932	D	0	.	10.3305	0.43820	0.0:0.0:0.6079:0.3921	.	287	Q9UKF2	ADA30_HUMAN	C	287	ENSP00000358407:R287C	ENSP00000358407:R287C	R	-	1	0	ADAM30	120239624	0.000000	0.05858	0.011000	0.14972	0.010000	0.07245	0.527000	0.22987	1.008000	0.39264	0.563000	0.77884	CGC		0.343	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		A	120438101	G	A	120438101	3	1	61	1	0	0	0	0	1	0	0	0	248	1058	37	1	1517	1	ADAM30	1	120438101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82	120438101	128812520	576	8561										
NOTCH2	4853	broad.mit.edu	37	chr1	120459239	120459239	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatggtctgtgatgtctcGattggcaaaatggtctaaca	10	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:120459239G>A	ENST00000256646.2	-	34	6325	c.6106C>T	c.(6106-6108)Cga>Tga	p.R2036*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2036					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.R2036*(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTGATGTCTCGATTGGCAAAA	0.527			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Nonsense(1)	large_intestine(1)	1											70	63	65					1																	120459239		2203	4300	6503	120260762	SO:0001587	stop_gained	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.6106C>T	1.37:g.120459239G>A	ENSP00000256646:p.Arg2036*		120260762	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	47	13.242336	0.99729	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.84	5.84	0.93424	.	0.000000	0.33938	U	0.004416	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1228	0.93371	0.0:0.0:1.0:0.0	.	.	.	.	X	2036	.	ENSP00000256646:R2036X	R	-	1	2	NOTCH2	120260762	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	5.528000	0.67129	2.765000	0.95021	0.655000	0.94253	CGA		0.527	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120459239	G	A	120459239	4	1	61	1	0	0	0	0	0	1	0	0	10579	1066	37	1	1313	1	NOTCH2	1	120459239	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21138	120459239	128791382	577	8562										
PDE4DIP	9659	broad.mit.edu	37	chr1	145075756	145075756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggactgaggggttcgcgtcGcgtccccggaccggtaaggc	18	12	0	1	rs587728009		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145075756G>A	ENST00000530740.1	-	1	145	c.107C>T	c.(106-108)gCg>gTg	p.A36V	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A36V|PDE4DIP_ENST00000369345.4_Missense_Mutation_p.A36V|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.A36V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.A36V(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGTTCGCGTCGCGTCCCCGGA	0.726			T	PDGFRB	MPD																																		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	1	Substitution - Missense(1)	large_intestine(1)	1											42	54	50					1																	145075756		2203	4298	6501	143787113	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.107C>T	1.37:g.145075756G>A	ENSP00000435654:p.Ala36Val		143787113	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	37		.	.	.	.	.	.	.	.	.	.	G	13.39	2.222121	0.39300	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.08807	4.75;4.75;3.05	3.4	1.23	0.21249	.	.	.	.	.	T	0.01387	0.0045	N	0.14661	0.345	0.09310	N	1	P;P	0.43352	0.78;0.804	B;B	0.34038	0.174;0.039	T	0.48163	-0.9059	9	0.38643	T	0.18	.	9.1142	0.36746	0.0:0.4981:0.5019:0.0	.	36;36	Q5TB27;E9PJ64	.;.	V	36	ENSP00000435654:A36V;ENSP00000358366:A36V;ENSP00000358354:A36V	ENSP00000358351:A36V	A	-	2	0	PDE4DIP	143787113	0.002000	0.14202	0.003000	0.11579	0.004000	0.04260	0.069000	0.14552	0.723000	0.32274	-0.416000	0.06073	GCG		0.726	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		A	145075756	G	A	145075756	3	1	61	1	0	0	0	0	1	0	0	0	11674	1087	38	1	8705	1	PDE4DIP	1	145075756	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24616517	145075756	104174865	578	8563										
SEC22B	9554	broad.mit.edu	37	chr1	145115872	145115872	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgttaatagtgtatgtcCgattctggtggctgtgaaat	11	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145115872C>T	ENST00000453618.1	+	0	958							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)						ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											AGTGTATGTCCGATTCTGGTG	0.418																																																0			1											212	211	211					1																	145115872		1998	4184	6182	143827229			9554			AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380				10700	protein-coding gene	gene with protein product		604029	"SEC22, vesicle trafficking protein (S. cerevisiae)-like 1", "SEC22 vesicle trafficking protein-like 1 (S. cerevisiae)", "SEC22 vesicle trafficking protein homolog B (S. cerevisiae)"	SEC22L1		9094723, 16354670	Standard	NM_004892		Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745		1.37:g.145115872C>T			143827229	A8K1G0	Nonsense_Mutation	SNP	ENST00000453618.1	37																																																																																					0.418	SEC22B-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000038523.5	NM_004892		T	145115872	C	T	145115872	1	4	61	0	1	0	0	0	0	0	0	0	14026	644	23	1		1	SEC22B	1	145115872	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40116	145115872	104134749	579	8564										
NOTCH2NL	388677	broad.mit.edu	37	chr1	145281451	145281451	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactgtggccaaccagttCtcctgcaaatgcctcacagg	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145281451C>T	ENST00000369340.3	+	5	825	c.381C>T	c.(379-381)ttC>ttT	p.F127F	RP11-458D21.5_ENST00000468030.1_Silent_p.F127F|NOTCH2NL_ENST00000344859.3_Silent_p.F127F|NOTCH2NL_ENST00000362074.6_Silent_p.F127F			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	127	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.F127F(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CCAACCAGTTCTCCTGCAAAT	0.522																																																2	Substitution - coding silent(2)	large_intestine(2)	1																																								143992808	SO:0001819	synonymous_variant	388677				CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"Notch homolog 2 (Drosophila) N-terminal like"			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.381C>T	1.37:g.145281451C>T			143992808	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Silent	SNP	ENST00000369340.3	37	CCDS909.1																																																																																				0.522	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458		T	145281451	C	T	145281451	2	4	61	1	0	0	0	0	0	0	0	1	10580	912	32	3		3	NOTCH2NL	1	145281451	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165579	145281451	103969170	580	8565										
HFE2	148738	broad.mit.edu	37	chr1	145415515	145415515	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcggtacatggcatcgaaGacctgatgatccagcacaac	11	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145415515G>T	ENST00000336751.5	+	3	572	c.334G>T	c.(334-336)Gac>Tac	p.D112Y	HFE2_ENST00000475797.1_Intron|HFE2_ENST00000497365.1_Intron|HFE2_ENST00000357836.5_5'UTR	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN	hemochromatosis type 2 (juvenile)	112					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|iron ion homeostasis (GO:0055072)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.D112Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGGCATCGAAGACCTGATGAT	0.731																																																1	Substitution - Missense(1)	large_intestine(1)	1											36	39	38					1																	145415515		2203	4298	6501	144126872	SO:0001583	missense	148738			AY372521	CCDS72877.1, CCDS72878.1, CCDS72879.1	1q21.2	2014-06-26			ENSG00000168509	ENSG00000168509			4887	protein-coding gene	gene with protein product	"repulsive guidance molecule c"	608374				10205270, 14647275	Standard	NM_213653		Approved	JH, HFE2A, RGMC, HJV, hemojuvelin, haemojuvelin	uc001eni.2	Q6ZVN8	OTTHUMG00000013748	ENST00000336751.5:c.334G>T	1.37:g.145415515G>T	ENSP00000337014:p.Asp112Tyr		144126872	B1ALI7|Q2PQ63|Q6IMF6|Q8NAH2|Q8WVJ5	Missense_Mutation	SNP	ENST00000336751.5	37	CCDS910.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898046	0.91962	.	.	ENSG00000168509	ENST00000336751	D	0.97731	-4.51	4.72	4.72	0.59763	Repulsive guidance molecule, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98277	0.9429	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98342	1.0539	10	0.48119	T	0.1	-20.4887	15.2193	0.73299	0.0:0.0:1.0:0.0	.	112	Q6ZVN8	RGMC_HUMAN	Y	112	ENSP00000337014:D112Y	ENSP00000337014:D112Y	D	+	1	0	HFE2	144126872	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.430000	0.90283	2.442000	0.82660	0.558000	0.71614	GAC		0.731	HFE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038527.1	NM_145277		T	145415515	G	T	145415515	3	4	61	1	0	0	0	0	1	0	0	0	7103	942	33	2	340	2	HFE2	1	145415515	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134064	145415515	103835106	581	8566										
LIX1L	128077	broad.mit.edu	37	chr1	145492276	145492276	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccggaggagtgctgcaaaGattgcgctaatgaattctgt	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145492276G>T	ENST00000369308.3	+	3	572	c.498G>T	c.(496-498)aaG>aaT	p.K166N	RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000366105.2_RNA|RP11-315I20.1_ENST00000437207.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	166								p.K166N(1)		large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GTGCTGCAAAGATTGCGCTAA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	100	100					1																	145492276		2203	4300	6503	144203633	SO:0001583	missense	128077			AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.498G>T	1.37:g.145492276G>T	ENSP00000358314:p.Lys166Asn		144203633	Q6AI36	Missense_Mutation	SNP	ENST00000369308.3	37	CCDS915.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.229981	0.79688	.	.	ENSG00000152022	ENST00000369308;ENST00000449167	T	0.64991	-0.13	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.75428	0.3848	M	0.76838	2.35	0.54753	D	0.999989	D	0.89917	1.0	D	0.91635	0.999	T	0.78588	-0.2146	10	0.87932	D	0	-32.9431	15.5426	0.76066	0.0:0.0:1.0:0.0	.	166	Q8IVB5	LIX1L_HUMAN	N	166;113	ENSP00000358314:K166N	ENSP00000358314:K166N	K	+	3	2	LIX1L	144203633	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.778000	0.47726	2.611000	0.88343	0.563000	0.77884	AAG		0.458	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		T	145492276	G	T	145492276	3	4	61	1	0	0	0	0	1	0	0	0	8856	933	33	2	508	2	LIX1L	1	145492276	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76761	145492276	103758345	582	8567										
LIX1L	128077	broad.mit.edu	37	chr1	145498745	145498745	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttgtgctggctgctggGcagttgggcaatatgcattc	13	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145498745G>A	ENST00000369308.3	+	6	1055	c.981G>A	c.(979-981)ggG>ggA	p.G327G	RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	327								p.G327G(1)		large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGGCTGCTGGGCAGTTGGGCA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											46	45	45					1																	145498745		2203	4300	6503	144210102	SO:0001819	synonymous_variant	128077			AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.981G>A	1.37:g.145498745G>A			144210102	Q6AI36	Silent	SNP	ENST00000369308.3	37	CCDS915.1																																																																																				0.517	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		A	145498745	G	A	145498745	2	1	61	1	0	0	0	0	0	0	0	1	8856	1190	42	3		3	LIX1L	1	145498745	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6469	145498745	103751876	583	8568										
ITGA10	8515	broad.mit.edu	37	chr1	145538015	145538015	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgctagagtttgagttTagctgctcctctctcctgag	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145538015T>G	ENST00000369304.3	+	22	2869	c.2694T>G	c.(2692-2694)ttT>ttG	p.F898L	ITGA10_ENST00000539363.1_Missense_Mutation_p.F755L|ITGA10_ENST00000538811.1_Missense_Mutation_p.F767L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	898					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.F898L(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGTTTGAGTTTAGCTGCTCCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											220	205	210					1																	145538015		2203	4300	6503	144249372	SO:0001583	missense	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2694T>G	1.37:g.145538015T>G	ENSP00000358310:p.Phe898Leu		144249372	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394118	0.83011	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.43688	0.94;0.94;0.94	5.71	-1.22	0.09494	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.38558	0.1045	L	0.58810	1.83	0.46654	D	0.999141	P;P;D;P	0.76494	0.907;0.907;0.999;0.924	P;P;D;P	0.80764	0.747;0.664;0.994;0.823	T	0.39502	-0.9611	10	0.56958	D	0.05	.	4.923	0.13880	0.1685:0.48:0.0:0.3515	.	864;767;755;898	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	L	898;864;755;767	ENSP00000358310:F898L;ENSP00000439894:F755L;ENSP00000440011:F767L	ENSP00000358310:F898L	F	+	3	2	ITGA10	144249372	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.661000	0.37408	0.060000	0.16281	0.533000	0.62120	TTT		0.522	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		G	145538015	T	G	145538015	3	3	61	1	0	0	0	0	1	0	0	0	7894	1751	61	4	2780	4	ITGA10	1	145538015	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	39270	145538015	103712606	584	8569										
ITGA10	8515	broad.mit.edu	37	chr1	145538748	145538748	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaccctgcaccgctatgaGgttcacccatatgggaccct	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145538748G>T	ENST00000369304.3	+	24	3034	c.2859G>T	c.(2857-2859)gaG>gaT	p.E953D	ITGA10_ENST00000539363.1_Missense_Mutation_p.E810D|ITGA10_ENST00000538811.1_Missense_Mutation_p.E822D|RP11-315I20.3_ENST00000415065.2_RNA	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	953					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.E953D(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ACCGCTATGAGGTTCACCCAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	66	70					1																	145538748		2203	4300	6503	144250105	SO:0001583	missense	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2859G>T	1.37:g.145538748G>T	ENSP00000358310:p.Glu953Asp		144250105	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466441	0.43839	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.46063	0.88;0.88;0.88	5.44	0.409	0.16382	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	L	0.57536	1.79	0.46874	D	0.999235	P;P;D;P	0.76494	0.603;0.907;0.999;0.655	B;P;D;P	0.83275	0.399;0.615;0.996;0.534	T	0.26087	-1.0113	10	0.24483	T	0.36	.	8.9246	0.35632	0.3892:0.0:0.6108:0.0	.	919;822;810;953	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	D	953;919;810;822	ENSP00000358310:E953D;ENSP00000439894:E810D;ENSP00000440011:E822D	ENSP00000358310:E953D	E	+	3	2	ITGA10	144250105	1.000000	0.71417	0.996000	0.52242	0.890000	0.51754	1.271000	0.33098	-0.062000	0.13088	-0.140000	0.14226	GAG		0.537	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		T	145538748	G	T	145538748	3	4	61	1	0	0	0	0	1	0	0	0	7894	991	35	2	2953	2	ITGA10	1	145538748	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	733	145538748	103711873	585	8570										
ANKRD35	148741	broad.mit.edu	37	chr1	145561582	145561582	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaaggtcccaaccagaaGaacaggggccaccccagagc	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145561582G>A	ENST00000355594.4	+	10	1357	c.1270G>A	c.(1270-1272)Gaa>Aaa	p.E424K		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	424								p.E424K(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCAACCAGAAGAACAGGGGCC	0.552																																					Melanoma(9;127 754 22988 51047)											1	Substitution - Missense(1)	large_intestine(1)	1											58	69	65					1																	145561582		2203	4300	6503	144272939	SO:0001583	missense	148741			AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1270G>A	1.37:g.145561582G>A	ENSP00000347802:p.Glu424Lys		144272939	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	6.172	0.399827	0.11696	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.67345	-0.26	5.63	2.64	0.31445	.	0.396851	0.21411	N	0.074972	T	0.31857	0.0810	L	0.51422	1.61	0.09310	N	0.999997	B	0.09022	0.002	B	0.10450	0.005	T	0.27226	-1.0080	10	0.11182	T	0.66	-4.4324	8.3572	0.32338	0.0809:0.2922:0.6269:0.0	.	424	Q8N283	ANR35_HUMAN	K	333;424	ENSP00000347802:E424K	ENSP00000347802:E424K	E	+	1	0	ANKRD35	144272939	0.936000	0.31750	0.014000	0.15608	0.189000	0.23516	2.495000	0.45337	0.381000	0.24851	0.655000	0.94253	GAA		0.552	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145561582	G	A	145561582	3	1	61	1	0	0	0	0	1	0	0	0	664	943	33	3	1308	3	ANKRD35	1	145561582	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22834	145561582	103689039	586	8571										
ANKRD35	148741	broad.mit.edu	37	chr1	145562160	145562160	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggacagctggagaaggaGatgtcagtactgagactgag	16	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145562160G>T	ENST00000355594.4	+	10	1935	c.1848G>T	c.(1846-1848)gaG>gaT	p.E616D		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	616								p.E616D(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGGAGAAGGAGATGTCAGTAC	0.597																																					Melanoma(9;127 754 22988 51047)											1	Substitution - Missense(1)	large_intestine(1)	1											44	50	48					1																	145562160		2203	4300	6503	144273517	SO:0001583	missense	148741			AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1848G>T	1.37:g.145562160G>T	ENSP00000347802:p.Glu616Asp		144273517	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.937014	0.34189	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.54071	0.59	4.73	2.76	0.32466	.	0.000000	0.48286	D	0.000190	T	0.53626	0.1808	M	0.70595	2.14	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.53535	-0.8425	10	0.36615	T	0.2	-27.9395	6.6501	0.22957	0.2315:0.0:0.7685:0.0	.	616	Q8N283	ANR35_HUMAN	D	525;616	ENSP00000347802:E616D	ENSP00000347802:E616D	E	+	3	2	ANKRD35	144273517	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	2.783000	0.47766	0.537000	0.28751	-0.345000	0.07892	GAG		0.597	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145562160	G	T	145562160	3	4	61	1	0	0	0	0	1	0	0	0	664	933	33	2	1886	2	ANKRD35	1	145562160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	578	145562160	103688461	587	8572										
CD160	11126	broad.mit.edu	37	chr1	145704139	145704139	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatggtgaacatcaactgaGatgatatttcaccaacacca	6	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:145704139G>T	ENST00000369288.2	-	4	495	c.278C>A	c.(277-279)tCt>tAt	p.S93Y	CD160_ENST00000401557.3_Missense_Mutation_p.S93Y|CD160_ENST00000235933.6_Missense_Mutation_p.S93Y|CD160_ENST00000369290.1_Intron	NM_007053.2	NP_008984.1	O95971	BY55_HUMAN	CD160 molecule	93	Ig-like V-type.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|defense response to Gram-negative bacterium (GO:0050829)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	MHC class I receptor activity (GO:0032393)|receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.S93Y(1)		endometrium(3)|large_intestine(2)|lung(2)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			CATCAACTGAGATGATATTTC	0.488																																					Colon(182;1122 1999 4065 44014 53024)											1	Substitution - Missense(1)	large_intestine(1)	1											128	116	120					1																	145704139		2203	4300	6503	144415496	SO:0001583	missense	11126			AF060981	CCDS72861.1	1q21.2	2011-01-25	2006-03-28		ENSG00000117281	ENSG00000117281		"CD molecules"	17013	protein-coding gene	gene with protein product		604463	"CD160 antigen"			9743336, 9973372	Standard	NM_007053		Approved	BY55, NK1, NK28	uc001eol.1	O95971	OTTHUMG00000013749	ENST00000369288.2:c.278C>A	1.37:g.145704139G>T	ENSP00000358294:p.Ser93Tyr		144415496		Missense_Mutation	SNP	ENST00000369288.2	37	CCDS923.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.833512	0.32421	.	.	ENSG00000117281	ENST00000235933;ENST00000369288;ENST00000401557	T;T;T	0.03496	3.91;3.91;3.91	4.34	4.34	0.51931	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.189889	0.26248	N	0.025464	T	0.04407	0.0121	L	0.32530	0.975	0.21105	N	0.999783	D	0.76494	0.999	D	0.64237	0.923	T	0.20273	-1.0280	10	0.87932	D	0	-4.1596	12.2039	0.54340	0.0:0.0:1.0:0.0	.	93	O95971	BY55_HUMAN	Y	93	ENSP00000235933:S93Y;ENSP00000358294:S93Y;ENSP00000385199:S93Y	ENSP00000235933:S93Y	S	-	2	0	CD160	144415496	0.005000	0.15991	0.615000	0.29064	0.023000	0.10783	1.515000	0.35845	2.245000	0.73994	0.563000	0.77884	TCT		0.488	CD160-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038532.2	NM_007053		T	145704139	G	T	145704139	3	4	61	1	0	0	0	0	1	0	0	0	2972	942	33	2	279	2	CD160	1	145704139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141979	145704139	103546482	588	8573										
FMO5	2330	broad.mit.edu	37	chr1	146673043	146673043	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaagccagaaatgatacGatttggcaggtcatcattta	8	9	2	2	rs143729816		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:146673043G>T	ENST00000254090.4	-	7	1262	c.874C>A	c.(874-876)Cgt>Agt	p.R292S	RP11-337C18.8_ENST00000607149.1_RNA|RP11-337C18.10_ENST00000606856.1_RNA|FMO5_ENST00000441068.2_Missense_Mutation_p.R292S|FMO5_ENST00000369272.3_Intron|RP11-337C18.8_ENST00000606757.1_RNA	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5	292						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.R292S(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	25	all_hematologic(923;0.0487)					GAAATGATACGATTTGGCAGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	71	71					1																	146673043		2203	4300	6503	145139667	SO:0001583	missense	2330			Z47553	CCDS926.1, CCDS44209.1, CCDS44210.1	1q21.1	2011-08-04			ENSG00000131781	ENSG00000131781			3773	protein-coding gene	gene with protein product		603957				8786146, 9119381	Standard	NM_001461		Approved		uc001epi.2	P49326	OTTHUMG00000014607	ENST00000254090.4:c.874C>A	1.37:g.146673043G>T	ENSP00000254090:p.Arg292Ser		145139667	B2RBG1|C9JJD1|Q8IV22	Missense_Mutation	SNP	ENST00000254090.4	37	CCDS926.1	.	.	.	.	.	.	.	.	.	.	.	18.45	3.626805	0.66901	.	.	ENSG00000131781	ENST00000441068;ENST00000254090	T;T	0.53640	0.61;0.61	6.17	3.03	0.35002	.	0.000000	0.85682	D	0.000000	T	0.49795	0.1578	M	0.74258	2.255	0.80722	D	1	P;D	0.53885	0.661;0.963	P;P	0.60345	0.657;0.873	T	0.52102	-0.8620	9	.	.	.	-2.5869	9.1547	0.36985	0.1453:0.0:0.7265:0.1282	.	292;292	P49326;C9JJD1	FMO5_HUMAN;.	S	292	ENSP00000416011:R292S;ENSP00000254090:R292S	.	R	-	1	0	FMO5	145139667	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.116000	0.41930	0.946000	0.37632	0.655000	0.94253	CGT		0.448	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	NM_001461		T	146673043	G	T	146673043	3	4	61	1	0	0	0	0	1	0	0	0	5977	1058	37	2	882	2	FMO5	1	146673043	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	968904	146673043	102577578	589	8574										
CHD1L	9557	broad.mit.edu	37	chr1	146736083	146736083	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatttatgtatttgagttCtcagtagtcttcagtctcct	6	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:146736083C>T	ENST00000369258.4	+	7	599	c.579C>T	c.(577-579)ttC>ttT	p.F193F	CHD1L_ENST00000369259.3_Intron|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Silent_p.F193F	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	193	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)	p.F193F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					TATTTGAGTTCTCAGTAGTCT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											42	38	40					1																	146736083		2202	4297	6499	145202707	SO:0001819	synonymous_variant	9557			AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.579C>T	1.37:g.146736083C>T			145202707	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	37	CCDS927.1																																																																																				0.433	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		T	146736083	C	T	146736083	2	4	61	1	0	0	0	0	0	0	0	1	3330	912	32	3		3	CHD1L	1	146736083	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63040	146736083	102514538	590	8575										
CHD1L	9557	broad.mit.edu	37	chr1	146766156	146766156	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggtatggtactgagcgaCttattcggaaacatctggct	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:146766156C>A	ENST00000369258.4	+	22	2592	c.2572C>A	c.(2572-2574)Ctt>Att	p.L858I	CHD1L_ENST00000369259.3_Missense_Mutation_p.L654I|CHD1L_ENST00000361293.5_Missense_Mutation_p.L577I|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Missense_Mutation_p.L764I	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	858	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)	p.L858I(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					TACTGAGCGACTTATTCGGAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											281	241	255					1																	146766156		2203	4300	6503	145232780	SO:0001583	missense	9557			AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2572C>A	1.37:g.146766156C>A	ENSP00000358262:p.Leu858Ile		145232780	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.658417	0.88154	.	.	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.7	5.7	0.88788	Appr-1-p processing (1);	0.000000	0.85682	D	0.000000	T	0.48572	0.1507	L	0.41356	1.27	0.58432	D	0.999998	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.87578	0.971;0.998;0.931	T	0.49615	-0.8921	10	0.72032	D	0.01	.	15.3248	0.74150	0.0:1.0:0.0:0.0	.	764;654;858	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	I	764;654;858;577	ENSP00000389031:L764I;ENSP00000358263:L654I;ENSP00000358262:L858I;ENSP00000355100:L577I	ENSP00000355100:L577I	L	+	1	0	CHD1L	145232780	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.796000	0.75145	2.696000	0.92011	0.655000	0.94253	CTT		0.428	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		A	146766156	C	A	146766156	3	1	61	1	0	0	0	0	1	0	0	0	3330	565	20	2	2658	2	CHD1L	1	146766156	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30073	146766156	102484465	591	8576										
BCL9	607	broad.mit.edu	37	chr1	147084858	147084858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatacccctaaagcactccCtggcccaggtgggagcatgg	11	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:147084858C>T	ENST00000234739.3	+	5	970	c.230C>T	c.(229-231)cCt>cTt	p.P77L	BCL9_ENST00000473292.1_Intron	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	77					canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.P77L(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					AAAGCACTCCCTGGCCCAGGT	0.582			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	1	Substitution - Missense(1)	large_intestine(1)	1											33	35	34					1																	147084858		2203	4300	6503	145551482	SO:0001583	missense	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.230C>T	1.37:g.147084858C>T	ENSP00000234739:p.Pro77Leu		145551482	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444605	0.43429	.	.	ENSG00000116128	ENST00000234739	T	0.54866	0.55	5.4	5.4	0.78164	.	0.207564	0.43110	D	0.000612	T	0.25195	0.0612	N	0.22421	0.69	0.49483	D	0.999793	B	0.33694	0.421	B	0.27500	0.08	T	0.22487	-1.0215	10	0.62326	D	0.03	-3.0873	14.2315	0.65895	0.149:0.851:0.0:0.0	.	77	O00512	BCL9_HUMAN	L	77	ENSP00000234739:P77L	ENSP00000234739:P77L	P	+	2	0	BCL9	145551482	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	3.757000	0.55212	2.797000	0.96272	0.655000	0.94253	CCT		0.582	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		T	147084858	C	T	147084858	3	4	61	1	0	0	0	0	1	0	0	0	1382	681	24	3	236	3	BCL9	1	147084858	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	318702	147084858	102165763	592	8577										
BCL9	607	broad.mit.edu	37	chr1	147090704	147090704	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccaaccaggaccagaattCttcccagaataccagactgc	8	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:147090704C>A	ENST00000234739.3	+	8	1483	c.743C>A	c.(742-744)tCt>tAt	p.S248Y		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	248	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.S248Y(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GACCAGAATTCTTCCCAGAAT	0.582			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	1	Substitution - Missense(1)	large_intestine(1)	1											93	100	97					1																	147090704		2203	4300	6503	145557328	SO:0001583	missense	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.743C>A	1.37:g.147090704C>A	ENSP00000234739:p.Ser248Tyr		145557328	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.715490	0.48622	.	.	ENSG00000116128	ENST00000234739	T	0.66815	-0.23	5.46	5.46	0.80206	.	0.167126	0.52532	D	0.000071	T	0.31857	0.0810	N	0.08118	0	0.31492	N	0.665893	B;B	0.25169	0.119;0.119	B;B	0.21360	0.034;0.034	T	0.32613	-0.9900	10	0.56958	D	0.05	-9.1365	14.3604	0.66768	0.1477:0.8522:0.0:0.0	.	248;248	Q1JQ81;O00512	.;BCL9_HUMAN	Y	248	ENSP00000234739:S248Y	ENSP00000234739:S248Y	S	+	2	0	BCL9	145557328	0.998000	0.40836	0.957000	0.39632	0.983000	0.72400	2.748000	0.47483	2.840000	0.97914	0.655000	0.94253	TCT		0.582	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		A	147090704	C	A	147090704	3	1	61	1	0	0	0	0	1	0	0	0	1382	913	32	2	761	2	BCL9	1	147090704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5846	147090704	102159917	593	8578										
GJA8	2703	broad.mit.edu	37	chr1	147380238	147380238	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggatgagcaatccgacttCgtgtgcaacacccagcagcc	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:147380238C>T	ENST00000369235.1	+	1	156	c.156C>T	c.(154-156)ttC>ttT	p.F52F	GJA8_ENST00000240986.4_Silent_p.F52F			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	52					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)	p.F52F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					AATCCGACTTCGTGTGCAACA	0.592																																					Melanoma(76;1255 1795 8195 52096)											1	Substitution - coding silent(1)	large_intestine(1)	1											131	106	114					1																	147380238		2203	4300	6503	145846862	SO:0001819	synonymous_variant	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.156C>T	1.37:g.147380238C>T			145846862	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																				0.592	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380238	C	T	147380238	2	4	61	1	0	0	0	0	0	0	0	1	6425	883	31	1		1	GJA8	1	147380238	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289534	147380238	101870383	594	8579										
NBPF15	284565	broad.mit.edu	37	chr1	148594465	148594465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcactggatagatgttattCgactccgtcaatgtactttg	8	9	2	1	rs200949130		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:148594465C>T	ENST00000369187.3	+	19	2327	c.1838C>T	c.(1837-1839)tCg>tTg	p.S613L	NBPF15_ENST00000442702.2_Missense_Mutation_p.S613L	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	613	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S613L(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					AGATGTTATTCGACTCCGTCA	0.458													.|||	1	0.000199681	0	0	5008	,	,		21856	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											203	262	242					1																	148594465		2203	4299	6502	146861089	SO:0001583	missense	284565			BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"neuroblastoma breakpoint family"	28791	protein-coding gene	gene with protein product		610414, 614005	"neuroblastoma breakpoint family, member 16"	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1838C>T	1.37:g.148594465C>T	ENSP00000358188:p.Ser613Leu		146861089	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	8.926	0.962258	0.18583	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.06849	3.25;3.25	0.502	-0.754	0.11065	DUF1220 (2);	.	.	.	.	T	0.03305	0.0096	L	0.28274	0.84	0.09310	N	1	D	0.76494	0.999	D	0.79784	0.993	T	0.12785	-1.0534	8	0.02654	T	1	.	.	.	.	.	613	Q8N660	NBPFF_HUMAN	L	613	ENSP00000416864:S613L;ENSP00000358188:S613L	ENSP00000358188:S613L	S	+	2	0	NBPF15	146861089	0.208000	0.23494	0.001000	0.08648	0.003000	0.03518	-1.514000	0.02254	-0.279000	0.09167	0.377000	0.23210	TCG		0.458	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638		T	148594465	C	T	148594465	3	4	61	1	0	0	0	0	1	0	0	0	10226	893	31	1	1896	1	NBPF15	1	148594465	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1214227	148594465	100656156	595	8580										
OTUD7B	56957	broad.mit.edu	37	chr1	149916639	149916639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtgagtttttcttcttcTtctccagtgtctcagtgccg	8	11	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:149916639T>A	ENST00000369135.4	-	12	1943	c.1649A>T	c.(1648-1650)aAg>aTg	p.K550M		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	550					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.K550M(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TTTCTTCTTCTTCTCCAGTGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											85	91	89					1																	149916639		2010	4196	6206	148183263	SO:0001583	missense	56957			AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.1649A>T	1.37:g.149916639T>A	ENSP00000358131:p.Lys550Met		148183263	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.776826	0.70107	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.39787	1.06	4.99	4.99	0.66335	.	0.112114	0.64402	D	0.000012	T	0.47783	0.1464	L	0.51422	1.61	0.52099	D	0.999941	D	0.89917	1.0	D	0.80764	0.994	T	0.43180	-0.9407	9	.	.	.	-24.5599	14.0274	0.64594	0.0:0.0:0.0:1.0	.	550	Q6GQQ9	OTU7B_HUMAN	M	550	ENSP00000358131:K550M	.	K	-	2	0	OTUD7B	148183263	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.150000	0.71801	2.101000	0.63845	0.455000	0.32223	AAG		0.577	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		A	149916639	T	A	149916639	3	1	61	1	0	0	0	0	1	0	0	0	11350	1609	56	5	886	5	OTUD7B	1	149916639	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1322174	149916639	99333982	596	8581										
RPRD2	23248	broad.mit.edu	37	chr1	150413428	150413428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctctaagtctgtagaacGaatctttaaaatctgggaag	9	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150413428G>A	ENST00000369068.4	+	3	369	c.365G>A	c.(364-366)cGa>cAa	p.R122Q	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.R122Q|RPRD2_ENST00000539519.1_Missense_Mutation_p.R122Q|RPRD2_ENST00000369067.3_Missense_Mutation_p.R122Q	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	122	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.R122Q(2)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TCTGTAGAACGAATCTTTAAA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	1											48	46	47					1																	150413428		1798	4057	5855	148680052	SO:0001583	missense	23248			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.365G>A	1.37:g.150413428G>A	ENSP00000358064:p.Arg122Gln		148680052	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	G	31	5.101775	0.94245	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369067;ENST00000369068	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.33	4.4	0.53042	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);Domain of unknown function DUF618 (1);	0.052014	0.64402	D	0.000001	T	0.67401	0.2889	M	0.89095	3.005	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.87578	0.998;0.998;0.905	T	0.76828	-0.2815	10	0.87932	D	0	-5.1549	15.3747	0.74596	0.0:0.0:0.8595:0.1405	.	122;122;122	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	Q	122	ENSP00000383785:R122Q;ENSP00000445482:R122Q;ENSP00000358063:R122Q;ENSP00000358064:R122Q	ENSP00000358063:R122Q	R	+	2	0	RPRD2	148680052	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.133000	0.94460	1.444000	0.47605	0.650000	0.86243	CGA		0.333	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		A	150413428	G	A	150413428	3	1	61	1	0	0	0	0	1	0	0	0	13654	1058	37	1	375	1	RPRD2	1	150413428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	496789	150413428	98837193	597	8582										
RPRD2	23248	broad.mit.edu	37	chr1	150443901	150443901	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagttctacccagatacttCtttccaagaagatgaggatt	7	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150443901C>A	ENST00000369068.4	+	11	2481	c.2477C>A	c.(2476-2478)tCt>tAt	p.S826Y	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.S800Y|RPRD2_ENST00000539519.1_Missense_Mutation_p.S800Y	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	826	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.S826Y(2)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CCAGATACTTCTTTCCAAGAA	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	1											49	46	47					1																	150443901		1876	4107	5983	148710525	SO:0001583	missense	23248			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.2477C>A	1.37:g.150443901C>A	ENSP00000358064:p.Ser826Tyr		148710525	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193253	0.58017	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.57436	0.41;0.4;0.42	5.0	5.0	0.66597	.	0.071813	0.56097	D	0.000039	T	0.50922	0.1644	N	0.24115	0.695	0.35003	D	0.756135	D;D;D	0.69078	0.99;0.995;0.997	P;P;D	0.63793	0.723;0.829;0.918	T	0.59521	-0.7439	10	0.87932	D	0	-12.4642	18.5409	0.91027	0.0:1.0:0.0:0.0	.	800;826;800	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	Y	800;800;826	ENSP00000383785:S800Y;ENSP00000445482:S800Y;ENSP00000358064:S826Y	ENSP00000358064:S826Y	S	+	2	0	RPRD2	148710525	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.163000	0.64948	2.608000	0.88229	0.650000	0.86243	TCT		0.463	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		A	150443901	C	A	150443901	3	1	61	1	0	0	0	0	1	0	0	0	13654	913	32	2	2519	2	RPRD2	1	150443901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30473	150443901	98806720	598	8583										
TARS2	80222	broad.mit.edu	37	chr1	150463184	150463184	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggcttttaccatgatttCttcctgggaaaggagaggtg	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150463184C>A	ENST00000369064.3	+	4	529	c.495C>A	c.(493-495)ttC>ttA	p.F165L	TARS2_ENST00000606933.1_Missense_Mutation_p.F165L|TARS2_ENST00000369054.2_Missense_Mutation_p.F165L|TARS2_ENST00000438568.2_Intron	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	165					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)	p.F165L(1)		cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	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;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	ACCATGATTTCTTCCTGGGAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	118	118					1																	150463184		2203	4300	6503	148729808	SO:0001583	missense	80222			BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.495C>A	1.37:g.150463184C>A	ENSP00000358060:p.Phe165Leu		148729808	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	37	CCDS952.1	.	.	.	.	.	.	.	.	.	.	C	2.167	-0.390711	0.04932	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	T;T	0.12465	2.68;2.68	5.23	3.22	0.36961	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.206732	0.43747	D	0.000525	T	0.08044	0.0201	M	0.88775	2.98	0.80722	D	1	B;B	0.26195	0.144;0.087	B;B	0.18263	0.014;0.021	T	0.04386	-1.0955	10	0.25106	T	0.35	-9.1272	5.3627	0.16098	0.15:0.6327:0.1323:0.085	.	165;165	Q9H9V2;Q9BW92	.;SYTM_HUMAN	L	165;165;33;33	ENSP00000358050:F165L;ENSP00000358060:F165L	ENSP00000358047:F33L	F	+	3	2	TARS2	148729808	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	1.679000	0.37597	1.418000	0.47098	0.563000	0.77884	TTC		0.507	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		A	150463184	C	A	150463184	3	1	61	1	0	0	0	0	1	0	0	0	15599	912	32	2	509	2	TARS2	1	150463184	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19283	150463184	98787437	599	8584										
ADAMTSL4	54507	broad.mit.edu	37	chr1	150526360	150526360	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccaggtagcagggagacGccctgatccttttccttcgg	11	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150526360G>A	ENST00000369038.2	+	4	1094	c.893G>A	c.(892-894)cGc>cAc	p.R298H	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.R298H|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.R298H|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.R298H|MIR4257_ENST00000581735.1_RNA|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	298					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)	p.R298H(1)		breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	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)			GCAGGGAGACGCCCTGATCCT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	1											36	35	35					1																	150526360		2203	4300	6503	148792984	SO:0001583	missense	54507			BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.893G>A	1.37:g.150526360G>A	ENSP00000358034:p.Arg298His		148792984	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582035	0.28180	.	.	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.62232	0.13;0.04;0.32;0.04	4.97	-9.94	0.00449	.	.	.	.	.	T	0.08714	0.0216	N	0.01874	-0.695	0.09310	N	1	B;B;B;B	0.09022	0.002;0.001;0.001;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.21793	-1.0235	9	0.11794	T	0.64	.	9.5669	0.39405	0.3375:0.4791:0.1835:0.0	.	298;298;298;298	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	H	298	ENSP00000358037:R298H;ENSP00000271643:R298H;ENSP00000358035:R298H;ENSP00000358034:R298H	ENSP00000271643:R298H	R	+	2	0	ADAMTSL4	148792984	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-1.927000	0.01561	-1.827000	0.01204	-1.022000	0.02435	CGC		0.677	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150526360	G	A	150526360	3	1	61	1	0	0	0	0	1	0	0	0	277	1087	38	1	907	1	ADAMTSL4	1	150526360	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63176	150526360	98724261	600	8585										
ENSA	2029	broad.mit.edu	37	chr1	150601923	150601923	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggtctcctccgcagggttCtcttcttcttgtttctggga	10	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150601923C>A	ENST00000369014.5	-	1	149	c.24G>T	c.(22-24)gaG>gaT	p.E8D	ENSA_ENST00000361532.5_5'Flank|ENSA_ENST00000513281.1_5'Flank|ENSA_ENST00000271690.8_Missense_Mutation_p.E8D|ENSA_ENST00000354702.3_5'Flank|ENSA_ENST00000361631.5_5'Flank|ENSA_ENST00000356527.5_Missense_Mutation_p.E8D|ENSA_ENST00000339643.5_Missense_Mutation_p.E8D|ENSA_ENST00000369009.3_Missense_Mutation_p.E8D|ENSA_ENST00000503345.1_Missense_Mutation_p.E8D|ENSA_ENST00000362052.7_Missense_Mutation_p.E8D|ENSA_ENST00000369016.4_Missense_Mutation_p.E8D|ENSA_ENST00000503241.1_Missense_Mutation_p.E8D			O43768	ENSA_HUMAN	endosulfine alpha	8					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)	p.E8D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|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;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			CCGCAGGGTTCTCTTCTTCTT	0.662																																					Esophageal Squamous(188;763 2078 3002 3411 26027)											1	Substitution - Missense(1)	large_intestine(1)	1											61	63	63					1																	150601923		2203	4300	6503	148868547	SO:0001583	missense	2029			X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420			3360	protein-coding gene	gene with protein product		603061				9653196	Standard	NM_004436		Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369014.5:c.24G>T	1.37:g.150601923C>A	ENSP00000358010:p.Glu8Asp		148868547	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	Missense_Mutation	SNP	ENST00000369014.5	37	CCDS958.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126996	0.37533	.	.	ENSG00000143420	ENST00000369016;ENST00000369014;ENST00000369009;ENST00000339643;ENST00000271690;ENST00000356527;ENST00000502246;ENST00000503345;ENST00000503241;ENST00000362052	T	0.45276	0.9	5.78	2.41	0.29592	.	0.219631	0.39274	N	0.001407	T	0.09468	0.0233	N	0.20986	0.625	0.29221	N	0.873938	B;B;B;B;B	0.30146	0.022;0.27;0.002;0.0;0.004	B;B;B;B;B	0.28139	0.011;0.086;0.004;0.0;0.009	T	0.16808	-1.0390	10	0.27082	T	0.32	.	5.3893	0.16236	0.0:0.5639:0.1535:0.2826	.	8;8;8;8;8	A6NMQ3;O43768-8;E9PB69;O43768;O43768-3	.;.;.;ENSA_HUMAN;.	D	8	ENSP00000358012:E8D	ENSP00000271690:E8D	E	-	3	2	ENSA	148868547	0.976000	0.34144	1.000000	0.80357	0.603000	0.37013	-0.098000	0.11024	0.774000	0.33427	0.460000	0.39030	GAG		0.662	ENSA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084720.2	NM_207042		A	150601923	C	A	150601923	3	1	61	1	0	0	0	0	1	0	0	0	5149	912	32	2	597	2	ENSA	1	150601923	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75563	150601923	98648698	601	8586										
GOLPH3L	55204	broad.mit.edu	37	chr1	150621053	150621053	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacactatcttgaagttttTtcactagtcgctgtttctct	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150621053T>G	ENST00000271732.3	-	5	646	c.602A>C	c.(601-603)aAa>aCa	p.K201T	GOLPH3L_ENST00000540514.1_Missense_Mutation_p.K157T	NM_018178.5	NP_060648.2	Q9H4A5	GLP3L_HUMAN	golgi phosphoprotein 3-like	201					Golgi organization (GO:0007030)|positive regulation of protein secretion (GO:0050714)	Golgi membrane (GO:0000139)|trans-Golgi network membrane (GO:0032588)	phosphatidylinositol-4-phosphate binding (GO:0070273)	p.K201T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|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;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTGAAGTTTTTTCACTAGTCG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											97	93	94					1																	150621053		2203	4300	6503	148887677	SO:0001583	missense	55204			AJ296153	CCDS966.1	1q21	2008-02-05			ENSG00000143457	ENSG00000143457			24882	protein-coding gene	gene with protein product		612208					Standard	NM_018178		Approved	GPP34R	uc001evj.2	Q9H4A5	OTTHUMG00000035009	ENST00000271732.3:c.602A>C	1.37:g.150621053T>G	ENSP00000271732:p.Lys201Thr		148887677	B1AN09|B7Z6N3|Q9NVK0	Missense_Mutation	SNP	ENST00000271732.3	37	CCDS966.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.586001	0.66105	.	.	ENSG00000143457	ENST00000271732;ENST00000369003;ENST00000540514;ENST00000427665	.	.	.	5.44	4.3	0.51218	.	0.127744	0.51477	D	0.000082	T	0.69124	0.3076	M	0.82630	2.6	0.51482	D	0.999928	P;B	0.50156	0.932;0.155	P;B	0.58013	0.831;0.359	T	0.73849	-0.3853	9	0.62326	D	0.03	-22.787	10.2523	0.43377	0.0:0.088:0.0:0.912	.	157;201	F5H4M3;Q9H4A5	.;GLP3L_HUMAN	T	201;223;157;223	.	ENSP00000271732:K201T	K	-	2	0	GOLPH3L	148887677	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.116000	0.50399	2.285000	0.76669	0.533000	0.62120	AAA		0.453	GOLPH3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084734.1	NM_018178		G	150621053	T	G	150621053	3	3	61	1	0	0	0	0	1	0	0	0	6589	1841	64	4	259	4	GOLPH3L	1	150621053	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19130	150621053	98629568	602	8587										
ARNT	405	broad.mit.edu	37	chr1	150812072	150812072	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtaccatatctgacagttCtgtgatgtaggctgtcatct	11	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150812072C>A	ENST00000358595.5	-	6	531	c.331G>T	c.(331-333)Gaa>Taa	p.E111*	ARNT_ENST00000505755.1_Nonsense_Mutation_p.E96*|ARNT_ENST00000354396.2_Nonsense_Mutation_p.E111*|ARNT_ENST00000515192.1_Nonsense_Mutation_p.E102*	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	111	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.E111*(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCTGACAGTTCTGTGATGTAG	0.507			T	ETV6	AML																																		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	1	Substitution - Nonsense(1)	large_intestine(1)	1											195	171	179					1																	150812072		2203	4300	6503	149078696	SO:0001587	stop_gained	405			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.331G>T	1.37:g.150812072C>A	ENSP00000351407:p.Glu111*		149078696	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Nonsense_Mutation	SNP	ENST00000358595.5	37	CCDS970.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331361	0.95733	.	.	ENSG00000143437	ENST00000358595;ENST00000368975;ENST00000354396;ENST00000515192;ENST00000394700;ENST00000505755	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	111;111;111;102;95;96	.	ENSP00000346372:E111X	E	-	1	0	ARNT	149078696	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GAA		0.507	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			A	150812072	C	A	150812072	4	1	61	1	0	0	0	0	0	1	0	0	966	922	32	2	2106	2	ARNT	1	150812072	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191019	150812072	98438549	603	8588										
FAM63A	55793	broad.mit.edu	37	chr1	150974949	150974949	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtctgctggctcccgttCtctagcctccccatcagcat	8	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:150974949C>A	ENST00000361936.5	-	3	1099	c.145G>T	c.(145-147)Gaa>Taa	p.E49*	FAM63A_ENST00000493834.2_Intron|FAM63A_ENST00000312210.5_Intron|FAM63A_ENST00000361738.6_Nonsense_Mutation_p.E97*|FAM63A_ENST00000470877.1_Intron	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	49						extracellular vesicular exosome (GO:0070062)		p.E49*(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	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)			GGCTCCCGTTCTCTAGCCTCC	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											113	104	107					1																	150974949		2203	4300	6503	149241573	SO:0001587	stop_gained	55793			BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.145G>T	1.37:g.150974949C>A	ENSP00000354814:p.Glu49*		149241573	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Nonsense_Mutation	SNP	ENST00000361936.5	37	CCDS976.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831201	0.71258	.	.	ENSG00000143409	ENST00000361936;ENST00000361738	.	.	.	5.18	3.25	0.37280	.	0.984348	0.08290	N	0.968620	.	.	.	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-4.846	7.5497	0.27788	0.0:0.597:0.3167:0.0863	.	.	.	.	X	49;97	.	ENSP00000354669:E97X	E	-	1	0	FAM63A	149241573	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	0.346000	0.19997	0.703000	0.31848	0.655000	0.94253	GAA		0.587	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379		A	150974949	C	A	150974949	4	1	61	1	0	0	0	0	0	1	0	0	5615	922	32	2	1300	2	FAM63A	1	150974949	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162877	150974949	98275672	604	8589										
PRUNE	58497	broad.mit.edu	37	chr1	151006395	151006395	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacccaggtctctcgaaaGaaacttctgcccctgctcca	6	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151006395G>T	ENST00000271620.3	+	8	1203	c.1047G>T	c.(1045-1047)aaG>aaT	p.K349N	PRUNE_ENST00000368934.1_Missense_Mutation_p.K114N|PRUNE_ENST00000368936.1_Missense_Mutation_p.K167N|PRUNE_ENST00000368935.1_Missense_Mutation_p.K64N|PRUNE_ENST00000368937.1_Missense_Mutation_p.K114N|BNIPL_ENST00000295294.7_5'Flank|PRUNE_ENST00000271619.8_Missense_Mutation_p.K137N|BNIPL_ENST00000368931.3_5'Flank	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	349						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)	p.K349N(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	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)			TCTCTCGAAAGAAACTTCTGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											129	122	124					1																	151006395		2203	4300	6503	149273019	SO:0001583	missense	58497			U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"prune homolog (Drosophila)"			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.1047G>T	1.37:g.151006395G>T	ENSP00000271620:p.Lys349Asn		149273019	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	37	CCDS977.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626129	0.66901	.	.	ENSG00000143363	ENST00000271620;ENST00000302413;ENST00000271619;ENST00000368937;ENST00000431193;ENST00000368936;ENST00000368935;ENST00000368934	T;T;T;T;T;T;T	0.66815	0.55;0.18;0.16;-0.23;0.39;0.54;0.16	5.35	4.39	0.52855	DHHA2 (1);	0.000000	0.85682	D	0.000000	T	0.72606	0.3481	M	0.79258	2.445	0.40652	D	0.98204	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.75744	-0.3210	9	.	.	.	-20.9474	7.64	0.28288	0.1968:0.0:0.8032:0.0	.	137;349	E9PCU1;Q86TP1	.;PRUNE_HUMAN	N	349;282;137;114;114;167;64;114	ENSP00000271620:K349N;ENSP00000271619:K137N;ENSP00000357933:K114N;ENSP00000392632:K114N;ENSP00000357932:K167N;ENSP00000357931:K64N;ENSP00000357930:K114N	.	K	+	3	2	PRUNE	149273019	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.271000	0.51608	1.534000	0.49203	-0.345000	0.07892	AAG		0.552	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		T	151006395	G	T	151006395	3	4	61	1	0	0	0	0	1	0	0	0	12674	933	33	2	1077	2	PRUNE	1	151006395	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31446	151006395	98244226	605	8590										
MLLT11	10962	broad.mit.edu	37	chr1	151039824	151039824	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccacctacaaggtcaaaGacagcagcgttggcaaaatg	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151039824G>T	ENST00000368921.3	+	2	2926	c.124G>T	c.(124-126)Gac>Tac	p.D42Y	CDC42SE1_ENST00000439374.2_Intron	NM_006818.3	NP_006809.1	Q13015	AF1Q_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	42					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of apoptotic process (GO:0043065)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of transcription, DNA-templated (GO:0045893)	intracellular (GO:0005622)		p.D42Y(1)		upper_aerodigestive_tract(1)	1	Lung SC(34;0.00471)|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)			CAAGGTCAAAGACAGCAGCGT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	118	118					1																	151039824		2203	4300	6503	149306448	SO:0001583	missense	10962			BC006471	CCDS982.1	1q21	2008-02-05			ENSG00000213190	ENSG00000213190			16997	protein-coding gene	gene with protein product	"ALL1 fused gene from chromosome 1q"	604684				7833468	Standard	NM_006818		Approved	AF1Q	uc001ewq.3	Q13015	OTTHUMG00000035160	ENST00000368921.3:c.124G>T	1.37:g.151039824G>T	ENSP00000357917:p.Asp42Tyr		149306448		Missense_Mutation	SNP	ENST00000368921.3	37	CCDS982.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282018	0.40394	.	.	ENSG00000213190	ENST00000368921	.	.	.	5.96	1.85	0.25348	.	0.830389	0.10197	U	0.703921	T	0.23249	0.0562	.	.	.	0.09310	N	1	P	0.40875	0.731	B	0.44224	0.444	T	0.13442	-1.0509	8	0.62326	D	0.03	-0.7062	8.59	0.33682	0.3496:0.0:0.6504:0.0	.	42	Q13015	AF1Q_HUMAN	Y	42	.	ENSP00000357917:D42Y	D	+	1	0	MLLT11	149306448	0.936000	0.31750	0.191000	0.23289	0.560000	0.35617	1.854000	0.39368	0.356000	0.24157	0.655000	0.94253	GAC		0.522	MLLT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085103.1	NM_006818		T	151039824	G	T	151039824	3	4	61	1	0	0	0	0	1	0	0	0	9657	942	33	2	126	2	MLLT11	1	151039824	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33429	151039824	98210797	606	8591										
MLLT11	10962	broad.mit.edu	37	chr1	151039956	151039956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccagcatccactccttcGaactggacttgctctaaggc	8	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151039956G>A	ENST00000368921.3	+	2	3058	c.256G>A	c.(256-258)Gaa>Aaa	p.E86K	CDC42SE1_ENST00000439374.2_Intron	NM_006818.3	NP_006809.1	Q13015	AF1Q_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11	86					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of apoptotic process (GO:0043065)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of transcription, DNA-templated (GO:0045893)	intracellular (GO:0005622)		p.E86K(1)		upper_aerodigestive_tract(1)	1	Lung SC(34;0.00471)|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)			CCACTCCTTCGAACTGGACTT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											135	128	130					1																	151039956		2203	4300	6503	149306580	SO:0001583	missense	10962			BC006471	CCDS982.1	1q21	2008-02-05			ENSG00000213190	ENSG00000213190			16997	protein-coding gene	gene with protein product	"ALL1 fused gene from chromosome 1q"	604684				7833468	Standard	NM_006818		Approved	AF1Q	uc001ewq.3	Q13015	OTTHUMG00000035160	ENST00000368921.3:c.256G>A	1.37:g.151039956G>A	ENSP00000357917:p.Glu86Lys		149306580		Missense_Mutation	SNP	ENST00000368921.3	37	CCDS982.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914358	0.92178	.	.	ENSG00000213190	ENST00000368921	.	.	.	6.17	6.17	0.99709	.	0.201158	0.30547	U	0.009381	T	0.42063	0.1186	.	.	.	0.41598	D	0.988836	P	0.49253	0.921	B	0.37144	0.242	T	0.51426	-0.8707	8	0.59425	D	0.04	-1.1821	19.4432	0.94831	0.0:0.0:1.0:0.0	.	86	Q13015	AF1Q_HUMAN	K	86	.	ENSP00000357917:E86K	E	+	1	0	MLLT11	149306580	1.000000	0.71417	0.892000	0.35008	0.951000	0.60555	6.110000	0.71535	2.941000	0.99782	0.655000	0.94253	GAA		0.512	MLLT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085103.1	NM_006818		A	151039956	G	A	151039956	3	1	61	1	0	0	0	0	1	0	0	0	9657	1059	37	1	258	1	MLLT11	1	151039956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132	151039956	98210665	607	8592										
GABPB2	126626	broad.mit.edu	37	chr1	151065706	151065706	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaaggacatgctgaagatGacagctttgcattgggccac	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151065706G>T	ENST00000368918.3	+	4	646	c.315G>T	c.(313-315)atG>atT	p.M105I	GABPB2_ENST00000368917.1_Missense_Mutation_p.M105I|GABPB2_ENST00000368916.1_Missense_Mutation_p.M105I	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	105					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)	p.M105I(1)		breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		TGCTGAAGATGACAGCTTTGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											150	143	145					1																	151065706		2203	4300	6503	149332330	SO:0001583	missense	126626				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"Ankyrin repeat domain containing"	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.315G>T	1.37:g.151065706G>T	ENSP00000357914:p.Met105Ile		149332330	B1AVJ8|D3DV14|Q8NAR5	Missense_Mutation	SNP	ENST00000368918.3	37	CCDS983.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.883545	0.91740	.	.	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000446567;ENST00000368916	T;T;T	0.64438	-0.1;-0.1;-0.1	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.036820	0.85682	D	0.000000	T	0.61060	0.2317	N	0.25789	0.76	0.80722	D	1	D;D;D;D	0.89917	0.996;0.988;0.976;1.0	D;D;D;D	0.87578	0.993;0.984;0.947;0.998	T	0.57596	-0.7784	10	0.28530	T	0.3	-3.034	17.4152	0.87498	0.0:0.0:1.0:0.0	.	121;105;105;105	B4DXA3;Q5SZG2;B2R924;Q8TAK5	.;.;.;GABP2_HUMAN	I	105;105;121;105	ENSP00000357914:M105I;ENSP00000357913:M105I;ENSP00000357912:M105I	ENSP00000357912:M105I	M	+	3	0	GABPB2	149332330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.593000	0.82686	2.695000	0.91970	0.561000	0.74099	ATG		0.433	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618		T	151065706	G	T	151065706	3	4	61	1	0	0	0	0	1	0	0	0	6178	1290	45	2	325	2	GABPB2	1	151065706	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25750	151065706	98184915	608	8593										
POGZ	23126	broad.mit.edu	37	chr1	151378291	151378291	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgccgcagcatgaaacGcacagcccactcataggaga	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151378291G>A	ENST00000271715.2	-	19	3534	c.3220C>T	c.(3220-3222)Cgt>Tgt	p.R1074C	POGZ_ENST00000361398.3_Missense_Mutation_p.R1021C|POGZ_ENST00000409503.1_Missense_Mutation_p.R1065C|POGZ_ENST00000368863.2_Missense_Mutation_p.R979C|POGZ_ENST00000531094.1_Missense_Mutation_p.R1012C|POGZ_ENST00000540984.1_Missense_Mutation_p.R436C|POGZ_ENST00000491586.1_Missense_Mutation_p.R1030C|POGZ_ENST00000392723.1_Missense_Mutation_p.R1021C	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	1074	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1074C(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AGCATGAAACGCACAGCCCAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	74	76					1																	151378291		2203	4300	6503	149644915	SO:0001583	missense	23126			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.3220C>T	1.37:g.151378291G>A	ENSP00000271715:p.Arg1074Cys		149644915	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.683336	0.47991	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586	T;T;T;T;T;T;T;T	0.29917	5.55;5.57;5.55;5.49;5.56;5.55;1.55;5.03	5.97	4.98	0.66077	Homeodomain-related (1);Pogo transposase / Cenp-B / PDC2, DNA-binding HTH domain (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000003	T	0.29389	0.0732	N	0.14661	0.345	0.46185	D	0.998911	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.81914	0.981;0.981;0.995;0.995;0.992;0.981	T	0.20840	-1.0263	10	0.87932	D	0	-14.0145	14.9763	0.71277	0.0:0.0:0.7837:0.2163	.	1012;1065;979;1030;1021;1074	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	C	1021;1074;1021;979;1065;1012;436;1030	ENSP00000376484:R1021C;ENSP00000271715:R1074C;ENSP00000354467:R1021C;ENSP00000357856:R979C;ENSP00000386836:R1065C;ENSP00000431259:R1012C;ENSP00000443547:R436C;ENSP00000418408:R1030C	ENSP00000271715:R1074C	R	-	1	0	POGZ	149644915	0.745000	0.28261	1.000000	0.80357	0.999000	0.98932	0.459000	0.21908	2.828000	0.97474	0.655000	0.94253	CGT		0.522	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151378291	G	A	151378291	3	1	61	1	0	0	0	0	1	0	0	0	12217	1087	38	1	1016	1	POGZ	1	151378291	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	312585	151378291	97872330	609	8594										
POGZ	23126	broad.mit.edu	37	chr1	151400746	151400746	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactgtgggacggtgcttcGaatggtaagagtggccggga	19	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151400746G>A	ENST00000271715.2	-	6	1026	c.712C>T	c.(712-714)Cga>Tga	p.R238*	POGZ_ENST00000361398.3_Nonsense_Mutation_p.R185*|POGZ_ENST00000409503.1_Nonsense_Mutation_p.R238*|POGZ_ENST00000368863.2_Nonsense_Mutation_p.R143*|POGZ_ENST00000531094.1_Nonsense_Mutation_p.R185*|POGZ_ENST00000540984.1_Intron|POGZ_ENST00000491586.1_Nonsense_Mutation_p.R185*|POGZ_ENST00000392723.1_Nonsense_Mutation_p.R185*	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	238					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R238*(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			ACGGTGCTTCGAATGGTAAGA	0.602																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											294	280	284					1																	151400746		2203	4300	6503	149667370	SO:0001587	stop_gained	23126			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.712C>T	1.37:g.151400746G>A	ENSP00000271715:p.Arg238*		149667370	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Nonsense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	39	7.337810	0.98221	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000437847	.	.	.	5.17	3.26	0.37387	.	0.000000	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5588	12.8644	0.57932	0.0:0.0:0.5814:0.4186	.	.	.	.	X	185;238;185;143;238;185;185;238	.	ENSP00000271715:R238X	R	-	1	2	POGZ	149667370	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.294000	0.43567	0.721000	0.32231	0.563000	0.77884	CGA		0.602	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151400746	G	A	151400746	4	1	61	1	0	0	0	0	0	1	0	0	12217	1066	37	1	3590	1	POGZ	1	151400746	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22455	151400746	97849875	610	8595										
THEM4	117145	broad.mit.edu	37	chr1	151860784	151860784	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagattggcagtcatgacGattcccccagccatcattgc	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:151860784G>A	ENST00000368814.3	-	4	871	c.522C>T	c.(520-522)atC>atT	p.I174I	THEM4_ENST00000477437.1_5'UTR	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	174					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)	p.I174I(1)		endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CAGTCATGACGATTCCCCCAG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	1											113	99	104					1																	151860784		2203	4300	6503	150127408	SO:0001819	synonymous_variant	117145			AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"C-terminal modulator protein"	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.522C>T	1.37:g.151860784G>A			150127408	B2RBX2|Q96KR2	Silent	SNP	ENST00000368814.3	37	CCDS1006.1																																																																																				0.413	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055		A	151860784	G	A	151860784	2	1	61	1	0	0	0	0	0	0	0	1	15897	1048	37	1		1	THEM4	1	151860784	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	460038	151860784	97389837	611	8596										
TCHHL1	126637	broad.mit.edu	37	chr1	152059163	152059163	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttcctggttcttgagtgTcaaacattctacagacatcc	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152059163T>C	ENST00000368806.1	-	3	1059	c.995A>G	c.(994-996)gAc>gGc	p.D332G		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	332							calcium ion binding (GO:0005509)	p.D332G(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TTCTTGAGTGTCAAACATTCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											238	222	227					1																	152059163		2203	4300	6503	150325787	SO:0001583	missense	126637				CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.995A>G	1.37:g.152059163T>C	ENSP00000357796:p.Asp332Gly		150325787	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	12.45	1.941539	0.34283	.	.	ENSG00000182898	ENST00000368806	T	0.27557	1.66	4.94	3.79	0.43588	.	0.796012	0.10466	N	0.671389	T	0.08537	0.0212	L	0.36672	1.1	0.09310	N	1	P	0.38978	0.652	B	0.33254	0.16	T	0.18840	-1.0324	10	0.27785	T	0.31	-0.8694	8.1491	0.31130	0.1791:0.0:0.0:0.8209	.	332	Q5QJ38	TCHL1_HUMAN	G	332	ENSP00000357796:D332G	ENSP00000357796:D332G	D	-	2	0	TCHHL1	150325787	0.043000	0.20138	0.010000	0.14722	0.005000	0.04900	1.552000	0.36244	0.831000	0.34780	0.524000	0.50904	GAC		0.463	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		C	152059163	T	C	152059163	3	2	61	1	0	0	0	0	1	0	0	0	15740	1667	58	4	1723	4	TCHHL1	1	152059163	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	198379	152059163	97191458	612	8597										
HRNR	388697	broad.mit.edu	37	chr1	152192657	152192657	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaggagtgacctgagccaGatccatgctgagtgtaacca	13	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152192657G>T	ENST00000368801.2	-	3	1523	c.1448C>A	c.(1447-1449)tCt>tAt	p.S483Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	483					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S483Y(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCTGAGCCAGATCCATGCTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											287	270	276					1																	152192657		2203	4300	6503	150459281	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1448C>A	1.37:g.152192657G>T	ENSP00000357791:p.Ser483Tyr		150459281	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	7.319	0.616540	0.14129	.	.	ENSG00000197915	ENST00000368801	T	0.01787	4.64	3.79	2.85	0.33270	.	.	.	.	.	T	0.00468	0.0015	N	0.24115	0.695	0.19300	N	0.99998	P	0.41673	0.759	B	0.32805	0.153	T	0.50898	-0.8773	9	0.34782	T	0.22	.	8.3074	0.32051	0.0:0.0:0.7636:0.2364	.	483	Q86YZ3	HORN_HUMAN	Y	483	ENSP00000357791:S483Y	ENSP00000357791:S483Y	S	-	2	0	HRNR	150459281	0.000000	0.05858	0.187000	0.23214	0.007000	0.05969	0.083000	0.14871	0.774000	0.33427	0.499000	0.49734	TCT		0.547	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152192657	G	T	152192657	3	4	61	1	0	0	0	0	1	0	0	0	7380	942	33	2	7108	2	HRNR	1	152192657	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133494	152192657	97057964	613	8598										
HRNR	388697	broad.mit.edu	37	chr1	152193008	152193008	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaggagtgacctgagccaGaaccatgcttactatagcca	10	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152193008G>T	ENST00000368801.2	-	3	1172	c.1097C>A	c.(1096-1098)tCt>tAt	p.S366Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	366					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S366Y(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCTGAGCCAGAACCATGCTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											166	155	159					1																	152193008		2203	4300	6503	150459632	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1097C>A	1.37:g.152193008G>T	ENSP00000357791:p.Ser366Tyr		150459632	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	g	5.781	0.328487	0.10956	.	.	ENSG00000197915	ENST00000368801	T	0.06933	3.24	4.72	-1.81	0.07882	.	.	.	.	.	T	0.02012	0.0063	N	0.24115	0.695	0.09310	N	1	D	0.54964	0.969	P	0.50754	0.649	T	0.24154	-1.0168	9	0.23891	T	0.37	.	1.7213	0.02912	0.231:0.2516:0.3883:0.1291	.	366	Q86YZ3	HORN_HUMAN	Y	366	ENSP00000357791:S366Y	ENSP00000357791:S366Y	S	-	2	0	HRNR	150459632	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.113000	0.10774	-0.562000	0.06086	-1.021000	0.02439	TCT		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152193008	G	T	152193008	3	4	61	1	0	0	0	0	1	0	0	0	7380	942	33	2	7459	2	HRNR	1	152193008	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	351	152193008	97057613	614	8599										
FLG	2312	broad.mit.edu	37	chr1	152275590	152275590	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgaccatgttccttagcGgtactagagtctgactgtac	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152275590G>T	ENST00000368799.1	-	3	11807	c.11772C>A	c.(11770-11772)acC>acA	p.T3924T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3924	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.T3924T(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTCCTTAGCGGTACTAGAGT	0.488									Ichthyosis																																							1	Substitution - coding silent(1)	large_intestine(1)	1											123	120	121					1																	152275590		2203	4300	6503	150542214	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11772C>A	1.37:g.152275590G>T			150542214	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.488	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152275590	G	T	152275590	2	4	61	1	0	0	0	0	0	0	0	1	5941	1103	39	2		2	FLG	1	152275590	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82582	152275590	96975031	615	8600										
FLG	2312	broad.mit.edu	37	chr1	152276236	152276236	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcacctggtagaggaaaGaccctgaacgtccagacctt	10	12	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152276236G>T	ENST00000368799.1	-	3	11161	c.11126C>A	c.(11125-11127)tCt>tAt	p.S3709Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3709	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S3709Y(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGAGGAAAGACCCTGAACG	0.612									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											133	139	137					1																	152276236		2203	4297	6500	150542860	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11126C>A	1.37:g.152276236G>T	ENSP00000357789:p.Ser3709Tyr		150542860	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	8.403	0.842337	0.16963	.	.	ENSG00000143631	ENST00000368799	T	0.02369	4.32	1.96	1.96	0.26148	.	.	.	.	.	T	0.04407	0.0121	M	0.64997	1.995	0.09310	N	1	D	0.69078	0.997	D	0.69824	0.966	T	0.39121	-0.9629	9	0.45353	T	0.12	.	7.5083	0.27558	0.0:0.0:1.0:0.0	.	3709	P20930	FILA_HUMAN	Y	3709	ENSP00000357789:S3709Y	ENSP00000357789:S3709Y	S	-	2	0	FLG	150542860	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.096000	0.15147	1.427000	0.47276	0.552000	0.68991	TCT		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152276236	G	T	152276236	3	4	61	1	0	0	0	0	1	0	0	0	5941	942	33	2	1063	2	FLG	1	152276236	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	646	152276236	96974385	616	8601										
FLG	2312	broad.mit.edu	37	chr1	152276563	152276563	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaattctctgcatgatgaGtgcctgattgtctggagctc	12	8	2	3	rs149031473		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152276563G>A	ENST00000368799.1	-	3	10834	c.10799C>T	c.(10798-10800)aCt>aTt	p.T3600I	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3600	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.T3600I(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCATGATGAGTGCCTGATTG	0.562									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											171	193	186					1																	152276563		2203	4298	6501	150543187	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10799C>T	1.37:g.152276563G>A	ENSP00000357789:p.Thr3600Ile		150543187	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	8.831	0.939870	0.18281	.	.	ENSG00000143631	ENST00000368799	T	0.01767	4.65	2.96	1.79	0.24919	.	.	.	.	.	T	0.02342	0.0072	M	0.68317	2.08	0.09310	N	1	D	0.67145	0.996	D	0.63793	0.918	T	0.45190	-0.9278	9	0.42905	T	0.14	.	6.7349	0.23403	0.0:0.0:0.5393:0.4607	.	3600	P20930	FILA_HUMAN	I	3600	ENSP00000357789:T3600I	ENSP00000357789:T3600I	T	-	2	0	FLG	150543187	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.087000	0.14958	0.257000	0.21650	0.502000	0.49764	ACT		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152276563	G	A	152276563	3	1	61	1	0	0	0	0	1	0	0	0	5941	1029	36	3	1390	3	FLG	1	152276563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	327	152276563	96974058	617	8602										
FLG	2312	broad.mit.edu	37	chr1	152280009	152280009	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcttgggacgttgagtgCctggagctgtctcgtgcctg	14	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152280009C>T	ENST00000368799.1	-	3	7388	c.7353G>A	c.(7351-7353)agG>agA	p.R2451R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2451	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R2451R(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGTTGAGTGCCTGGAGCTGT	0.577									Ichthyosis																																							1	Substitution - coding silent(1)	large_intestine(1)	1											332	304	313					1																	152280009		2203	4300	6503	150546633	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7353G>A	1.37:g.152280009C>T			150546633	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152280009	C	T	152280009	2	4	61	1	0	0	0	0	0	0	0	1	5941	738	26	3		3	FLG	1	152280009	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3446	152280009	96970612	618	8603										
FLG	2312	broad.mit.edu	37	chr1	152283355	152283355	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctgtccatgagaggaaGactctgtgtgatgagtgcct	13	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152283355G>A	ENST00000368799.1	-	3	4042	c.4007C>T	c.(4006-4008)tCt>tTt	p.S1336F	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1336	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1336F(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGAGAGGAAGACTCTGTGTG	0.547									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											318	306	310					1																	152283355		2203	4300	6503	150549979	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4007C>T	1.37:g.152283355G>A	ENSP00000357789:p.Ser1336Phe		150549979	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	8.655	0.899174	0.17686	.	.	ENSG00000143631	ENST00000368799	T	0.01854	4.6	2.24	2.24	0.28232	.	.	.	.	.	T	0.00552	0.0018	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.20955	0.032	T	0.49303	-0.8954	9	0.59425	D	0.04	.	8.0038	0.30313	0.0:0.0:1.0:0.0	.	1336	P20930	FILA_HUMAN	F	1336	ENSP00000357789:S1336F	ENSP00000357789:S1336F	S	-	2	0	FLG	150549979	0.001000	0.12720	0.001000	0.08648	0.014000	0.08584	0.220000	0.17660	1.269000	0.44280	0.456000	0.33151	TCT		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152283355	G	A	152283355	3	1	61	1	0	0	0	0	1	0	0	0	5941	942	33	3	8182	3	FLG	1	152283355	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3346	152283355	96967266	619	8604										
FLG	2312	broad.mit.edu	37	chr1	152284522	152284522	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcactgtcactgtcctggCtaacactggatccctggcgc	9	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152284522C>T	ENST00000368799.1	-	3	2875	c.2840G>A	c.(2839-2841)aGc>aAc	p.S947N	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	947	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S947N(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTGTCCTGGCTAACACTGGA	0.552									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											332	301	311					1																	152284522		2203	4300	6503	150551146	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2840G>A	1.37:g.152284522C>T	ENSP00000357789:p.Ser947Asn		150551146	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	9.753	1.168044	0.21621	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.20881	2.04	4.07	4.07	0.47477	.	.	.	.	.	T	0.28764	0.0713	M	0.69823	2.125	0.09310	N	1	D	0.89917	1.0	D	0.74674	0.984	T	0.05484	-1.0882	9	0.31617	T	0.26	.	11.8487	0.52399	0.0:1.0:0.0:0.0	.	947	P20930	FILA_HUMAN	N	947;154	ENSP00000357789:S947N	ENSP00000357789:S947N	S	-	2	0	FLG	150551146	0.000000	0.05858	0.006000	0.13384	0.020000	0.10135	0.445000	0.21677	1.832000	0.53329	0.473000	0.43528	AGC		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152284522	C	T	152284522	3	4	61	1	0	0	0	0	1	0	0	0	5941	797	28	3	9349	3	FLG	1	152284522	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1167	152284522	96966099	620	8605										
FLG	2312	broad.mit.edu	37	chr1	152284696	152284696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttctgcttgcacttctgGatcctgactgcccacgggag	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152284696G>A	ENST00000368799.1	-	3	2701	c.2666C>T	c.(2665-2667)tCc>tTc	p.S889F	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	889	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S889F(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCACTTCTGGATCCTGACTG	0.557									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											366	358	361					1																	152284696		2203	4300	6503	150551320	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2666C>T	1.37:g.152284696G>A	ENSP00000357789:p.Ser889Phe		150551320	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	2.948	-0.217329	0.06101	.	.	ENSG00000143631	ENST00000368799	T	0.03801	3.8	2.61	1.67	0.24075	.	.	.	.	.	T	0.02304	0.0071	M	0.77820	2.39	0.09310	N	1	B	0.30973	0.302	B	0.19946	0.027	T	0.35649	-0.9780	9	0.66056	D	0.02	.	6.5119	0.22226	0.0:0.0:0.7126:0.2874	.	889	P20930	FILA_HUMAN	F	889	ENSP00000357789:S889F	ENSP00000357789:S889F	S	-	2	0	FLG	150551320	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	1.576000	0.36504	0.315000	0.23110	-0.492000	0.04666	TCC		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152284696	G	A	152284696	3	1	61	1	0	0	0	0	1	0	0	0	5941	1174	41	3	9523	3	FLG	1	152284696	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	174	152284696	96965925	621	8606										
FLG	2312	broad.mit.edu	37	chr1	152287809	152287809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttaccttcaggatttgccGaaattccttttccagaagtt	6	10	2	1	rs138819199		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152287809G>A	ENST00000368799.1	-	2	159	c.124C>T	c.(124-126)Cgg>Tgg	p.R42W	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	42	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R42W(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGGATTTGCCGAAATTCCTTT	0.333									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	171	177	175		124	0.9	0	1	dbSNP_134	175	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	42/4062	152287809	1,13005	2203	4300	6503	150554433	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.124C>T	1.37:g.152287809G>A	ENSP00000357789:p.Arg42Trp		150554433	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413968	0.25465	2.27E-4	0.0	ENSG00000143631	ENST00000368799	T	0.10005	2.92	5.2	0.907	0.19321	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.11452	0.0279	M	0.68317	2.08	0.09310	N	1	D	0.89917	1.0	D	0.75484	0.986	T	0.12734	-1.0536	9	0.72032	D	0.01	-3.2577	1.2855	0.02049	0.1964:0.1744:0.4494:0.1798	.	42	P20930	FILA_HUMAN	W	42	ENSP00000357789:R42W	ENSP00000357789:R42W	R	-	1	2	FLG	150554433	0.041000	0.20044	0.001000	0.08648	0.004000	0.04260	0.868000	0.27982	0.343000	0.23821	-0.261000	0.10672	CGG		0.333	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152287809	G	A	152287809	3	1	61	1	0	0	0	0	1	0	0	0	5941	1057	37	1	12069	1	FLG	1	152287809	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3113	152287809	96962812	622	8607										
FLG2	388698	broad.mit.edu	37	chr1	152323117	152323117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagttgcttgtttgcagtgCtgtctgttgaccatgaaagg	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152323117C>T	ENST00000388718.5	-	3	7217	c.7145G>A	c.(7144-7146)aGc>aAc	p.S2382N	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2382					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S2382N(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTTGCAGTGCTGTCTGTTGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	141	143					1																	152323117		2203	4300	6503	150589741	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.7145G>A	1.37:g.152323117C>T	ENSP00000373370:p.Ser2382Asn		150589741	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	6.339	0.430656	0.12045	.	.	ENSG00000143520	ENST00000388718	T	0.22134	1.97	4.14	-2.41	0.06562	.	.	.	.	.	T	0.01800	0.0057	N	0.08118	0	0.09310	N	1	P	0.35011	0.48	B	0.27887	0.084	T	0.40794	-0.9544	9	0.20046	T	0.44	0.4129	2.5967	0.04855	0.4963:0.2574:0.1452:0.1011	.	2382	Q5D862	FILA2_HUMAN	N	2382	ENSP00000373370:S2382N	ENSP00000373370:S2382N	S	-	2	0	FLG2	150589741	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.504000	0.00964	-0.159000	0.11021	0.460000	0.39030	AGC		0.413	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152323117	C	T	152323117	3	4	61	1	0	0	0	0	1	0	0	0	5942	797	28	3	34	3	FLG2	1	152323117	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35308	152323117	96927504	623	8608										
FLG2	388698	broad.mit.edu	37	chr1	152323873	152323873	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgactctccatgttgagatCtggcttggccataagtgtgt	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152323873C>A	ENST00000388718.5	-	3	6461	c.6389G>T	c.(6388-6390)aGa>aTa	p.R2130I	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2130					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R2130I(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTTGAGATCTGGCTTGGCC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											449	415	427					1																	152323873		2203	4300	6503	150590497	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6389G>T	1.37:g.152323873C>A	ENSP00000373370:p.Arg2130Ile		150590497	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.709175	0.30322	.	.	ENSG00000143520	ENST00000388718	T	0.03801	3.8	4.5	2.63	0.31362	.	.	.	.	.	T	0.04588	0.0125	L	0.44542	1.39	0.09310	N	1	D	0.67145	0.996	D	0.66716	0.946	T	0.38757	-0.9646	9	0.35671	T	0.21	2.2173	6.8053	0.23774	0.0:0.7891:0.0:0.2109	.	2130	Q5D862	FILA2_HUMAN	I	2130	ENSP00000373370:R2130I	ENSP00000373370:R2130I	R	-	2	0	FLG2	150590497	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.090000	0.15025	0.644000	0.30656	0.551000	0.68910	AGA		0.522	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152323873	C	A	152323873	3	1	61	1	0	0	0	0	1	0	0	0	5942	913	32	2	790	2	FLG2	1	152323873	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	756	152323873	96926748	624	8609										
FLG2	388698	broad.mit.edu	37	chr1	152325189	152325189	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccatgagtagttccatgTctctcaggaactatggattc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152325189T>C	ENST00000388718.5	-	3	5145	c.5073A>G	c.(5071-5073)agA>agG	p.R1691R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1691					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R1691R(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TAGTTCCATGTCTCTCAGGAA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											411	358	376					1																	152325189		2203	4300	6503	150591813	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5073A>G	1.37:g.152325189T>C			150591813	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.488	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		C	152325189	T	C	152325189	2	2	61	1	0	0	0	0	0	0	0	1	5942	1664	58	4		4	FLG2	1	152325189	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1316	152325189	96925432	625	8610										
FLG2	388698	broad.mit.edu	37	chr1	152325310	152325310	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggactcactgtggctaGatctctgtcttccagttgtc	9	12	3	1	rs188198910		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152325310G>T	ENST00000388718.5	-	3	5024	c.4952C>A	c.(4951-4953)tCt>tAt	p.S1651Y	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1651					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1651Y(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTGTGGCTAGATCTCTGTCT	0.512													G|||	1	0.000199681	0	0	5008	,	,		26792	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	TYR/SER	1,4405	2.1+/-5.4	0,1,2202	429	382	398		4952	1.4	0	1		398	0,8600		0,0,4300	no	missense	FLG2	NM_001014342.2	144	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	benign	1651/2392	152325310	1,13005	2203	4300	6503	150591934	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4952C>A	1.37:g.152325310G>T	ENSP00000373370:p.Ser1651Tyr		150591934	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.901	1.206774	0.22205	2.27E-4	0.0	ENSG00000143520	ENST00000388718	T	0.35421	1.31	4.56	1.43	0.22495	.	.	.	.	.	T	0.21509	0.0518	L	0.48986	1.54	0.09310	N	1	D	0.59357	0.985	P	0.50970	0.655	T	0.05632	-1.0873	9	0.62326	D	0.03	0.1094	5.648	0.17600	0.0952:0.0:0.5627:0.3421	.	1651	Q5D862	FILA2_HUMAN	Y	1651	ENSP00000373370:S1651Y	ENSP00000373370:S1651Y	S	-	2	0	FLG2	150591934	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.484000	0.22308	0.098000	0.17522	0.549000	0.68633	TCT		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152325310	G	T	152325310	3	4	61	1	0	0	0	0	1	0	0	0	5942	942	33	2	2227	2	FLG2	1	152325310	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121	152325310	96925311	626	8611										
FLG2	388698	broad.mit.edu	37	chr1	152325407	152325407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctatctgtccatgagtagTtccgtgtctctcatgaactg	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152325407T>C	ENST00000388718.5	-	3	4927	c.4855A>G	c.(4855-4857)Act>Gct	p.T1619A	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1619					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.T1619A(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCATGAGTAGTTCCGTGTCTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											395	345	362					1																	152325407		2203	4300	6503	150592031	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4855A>G	1.37:g.152325407T>C	ENSP00000373370:p.Thr1619Ala		150592031	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.282571	0.23392	.	.	ENSG00000143520	ENST00000388718	T	0.50277	0.75	3.81	-4.83	0.03161	.	.	.	.	.	T	0.13457	0.0326	L	0.55481	1.735	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.22312	-1.0220	9	0.28530	T	0.3	-0.0389	1.2502	0.01980	0.1456:0.3012:0.1484:0.4047	.	1619	Q5D862	FILA2_HUMAN	A	1619	ENSP00000373370:T1619A	ENSP00000373370:T1619A	T	-	1	0	FLG2	150592031	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.579000	0.05834	-0.651000	0.05415	-0.712000	0.03635	ACT		0.517	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		C	152325407	T	C	152325407	3	2	61	1	0	0	0	0	1	0	0	0	5942	1725	60	4	2324	4	FLG2	1	152325407	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	97	152325407	96925214	627	8612										
FLG2	388698	broad.mit.edu	37	chr1	152325885	152325885	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtgtctcccatgaactgtGgatcctgactctccatgttg	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152325885G>A	ENST00000388718.5	-	3	4449	c.4377C>T	c.(4375-4377)tcC>tcT	p.S1459S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1459					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1459S(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGAACTGTGGATCCTGACT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											419	373	388					1																	152325885		2203	4300	6503	150592509	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4377C>T	1.37:g.152325885G>A			150592509	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.502	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152325885	G	A	152325885	2	1	61	1	0	0	0	0	0	0	0	1	5942	1335	47	3		3	FLG2	1	152325885	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	478	152325885	96924736	628	8613										
FLG2	388698	broad.mit.edu	37	chr1	152326848	152326848	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgctgtgcaaagccagaGgatttacctgtgcctgaccc	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152326848G>T	ENST00000388718.5	-	3	3486	c.3414C>A	c.(3412-3414)tcC>tcA	p.S1138S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1138	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1138S(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAAAGCCAGAGGATTTACCTG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	1											210	199	203					1																	152326848		2203	4300	6503	150593472	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3414C>A	1.37:g.152326848G>T			150593472	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.532	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152326848	G	T	152326848	2	4	61	1	0	0	0	0	0	0	0	1	5942	987	35	2		2	FLG2	1	152326848	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	963	152326848	96923773	629	8614										
FLG2	388698	broad.mit.edu	37	chr1	152329216	152329216	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatcctctctgactatagGactgactacaggggttagac	9	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152329216G>T	ENST00000388718.5	-	3	1118	c.1046C>A	c.(1045-1047)tCc>tAc	p.S349Y	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	349	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S349Y(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGACTATAGGACTGACTACA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											143	134	137					1																	152329216		2203	4300	6503	150595840	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1046C>A	1.37:g.152329216G>T	ENSP00000373370:p.Ser349Tyr		150595840	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413975	0.25465	.	.	ENSG00000143520	ENST00000388718	T	0.18657	2.2	4.16	4.16	0.48862	.	.	.	.	.	T	0.27169	0.0666	L	0.59436	1.845	0.29923	N	0.822557	D	0.89917	1.0	D	0.78314	0.991	T	0.01630	-1.1308	9	0.28530	T	0.3	-1.1968	12.251	0.54597	0.0:0.0:1.0:0.0	.	349	Q5D862	FILA2_HUMAN	Y	349	ENSP00000373370:S349Y	ENSP00000373370:S349Y	S	-	2	0	FLG2	150595840	.	.	0.975000	0.42487	0.289000	0.27227	.	.	2.600000	0.87896	0.650000	0.86243	TCC		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152329216	G	T	152329216	3	4	61	1	0	0	0	0	1	0	0	0	5942	1174	41	2	6133	2	FLG2	1	152329216	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2368	152329216	96921405	630	8615										
KPRP	448834	broad.mit.edu	37	chr1	152732987	152732987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacccatatataacagtcGctgtcctcgccgccccattt	6	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152732987G>A	ENST00000606109.1	+	1	951	c.923G>A	c.(922-924)cGc>cAc	p.R308H	KPRP_ENST00000368773.1_Missense_Mutation_p.R308H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	308	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.R308H(1)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TATAACAGTCGCTGTCCTCGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											48	49	49					1																	152732987		2203	4300	6503	150999611	SO:0001583	missense	448834			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.923G>A	1.37:g.152732987G>A	ENSP00000475216:p.Arg308His		150999611		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	1.075	-0.668801	0.03403	.	.	ENSG00000203786	ENST00000368773	T	0.11495	2.77	5.3	1.04	0.20106	.	0.994182	0.08158	N	0.988958	T	0.01222	0.0040	N	0.04508	-0.205	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.49041	-0.8980	10	0.18276	T	0.48	-0.2085	6.8297	0.23902	0.4812:0.0:0.5188:0.0	.	308	Q5T749	KPRP_HUMAN	H	308	ENSP00000357762:R308H	ENSP00000357762:R308H	R	+	2	0	KPRP	150999611	0.001000	0.12720	0.013000	0.15412	0.087000	0.18053	0.493000	0.22451	-0.004000	0.14419	-0.379000	0.06801	CGC		0.597	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152732987	G	A	152732987	3	1	61	1	0	0	0	0	1	0	0	0	8457	1087	38	1	925	1	KPRP	1	152732987	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	403771	152732987	96517634	631	8616										
LCE1A	353131	broad.mit.edu	37	chr1	152800004	152800004	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcccaagtgcacccccaAgtgccctcccaagtgcccca	6	22	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:152800004A>C	ENST00000335123.2	+	1	56	c.56A>C	c.(55-57)aAg>aCg	p.K19T		NM_178348.2	NP_848125.1	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	19	Cys-rich.				keratinization (GO:0031424)			p.K19T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	8	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			tgcacccccaagtgccctccc	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											51	59	56					1																	152800004		2203	4300	6503	151066628	SO:0001583	missense	353131				CCDS1028.1	1q21.3	2011-01-28			ENSG00000186844	ENSG00000186844		"Late cornified envelopes"	29459	protein-coding gene	gene with protein product		612603				11698679	Standard	NM_178348		Approved	LEP1	uc010pdw.2	Q5T7P2	OTTHUMG00000012447	ENST00000335123.2:c.56A>C	1.37:g.152800004A>C	ENSP00000334869:p.Lys19Thr		151066628		Missense_Mutation	SNP	ENST00000335123.2	37	CCDS1028.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.385907	0.25031	.	.	ENSG00000186844	ENST00000368766;ENST00000335123	T;T	0.04454	3.62;3.62	4.18	3.0	0.34707	.	0.000000	0.35772	N	0.002981	T	0.03305	0.0096	M	0.83774	2.66	0.21627	N	0.999618	P	0.37330	0.59	B	0.37451	0.25	T	0.24977	-1.0145	10	0.87932	D	0	.	6.8826	0.24181	0.7944:0.0:0.0:0.2056	.	19	Q5T7P2	LCE1A_HUMAN	T	19	ENSP00000357755:K19T;ENSP00000334869:K19T	ENSP00000334869:K19T	K	+	2	0	LCE1A	151066628	0.982000	0.34865	0.990000	0.47175	0.993000	0.82548	2.263000	0.43293	0.718000	0.32166	0.456000	0.33151	AAG		0.627	LCE1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034660.2	NM_178348		C	152800004	A	C	152800004	3	2	61	1	0	0	0	0	1	0	0	0	8681	72	3	4	58	4	LCE1A	1	152800004	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	67017	152800004	96450617	632	8617										
PGLYRP4	57115	broad.mit.edu	37	chr1	153315577	153315577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgttacctttcttagtgCcaaagaaggcaaagcccagg	9	10	1	1	rs374415659|rs386635578		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:153315577C>T	ENST00000359650.5	-	5	525	c.461G>A	c.(460-462)gGc>gAc	p.G154D	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.G150D|PGLYRP4_ENST00000490266.1_5'Flank	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	154					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.G154D(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTTCTTAGTGCCAAAGAAGGC	0.488													C|||	1	0.000199681	0	0	5008	,	,		20480	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						C	ASP/GLY	1,4405	2.1+/-5.4	0,1,2202	156	123	134		461	4.7	1	1		134	0,8600		0,0,4300	no	missense	PGLYRP4	NM_020393.2	94	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	154/374	153315577	1,13005	2203	4300	6503	151582201	SO:0001583	missense	57115			AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.461G>A	1.37:g.153315577C>T	ENSP00000352672:p.Gly154Asp		151582201	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.406139	0.62288	2.27E-4	0.0	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.70869	-0.52;-0.52	4.71	4.71	0.59529	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.000000	0.47455	D	0.000225	D	0.87285	0.6139	H	0.97415	4	0.35351	D	0.787383	D;D	0.89917	0.999;1.0	D;D	0.76071	0.978;0.987	D	0.91352	0.5105	10	0.87932	D	0	-8.6536	13.0053	0.58701	0.0:1.0:0.0:0.0	.	150;154	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	D	150;154	ENSP00000357728:G150D;ENSP00000352672:G154D	ENSP00000352672:G154D	G	-	2	0	PGLYRP4	151582201	0.545000	0.26449	0.978000	0.43139	0.644000	0.38419	3.888000	0.56204	2.427000	0.82271	0.655000	0.94253	GGC		0.488	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		T	153315577	C	T	153315577	3	4	61	1	0	0	0	0	1	0	0	0	11827	739	26	3	680	3	PGLYRP4	1	153315577	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	515573	153315577	95935044	633	8618										
C1orf77	26097	broad.mit.edu	37	chr1	153610824	153610824	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagtgaatattcgggcttCgatgcagcaacaacagcagc	11	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:153610824C>T	ENST00000368694.3	+	3	431	c.119C>T	c.(118-120)tCg>tTg	p.S40L	CHTOP_ENST00000495554.1_3'UTR|CHTOP_ENST00000368690.3_Missense_Mutation_p.S40L|CHTOP_ENST00000403433.1_Missense_Mutation_p.S40L|CHTOP_ENST00000368687.1_Missense_Mutation_p.S15L|CHTOP_ENST00000368686.1_5'UTR	NM_001206612.1|NM_015607.3	NP_001193541.1|NP_056422.2	Q9Y3Y2	CHTOP_HUMAN	chromatin target of PRMT1	40					mRNA export from nucleus (GO:0006406)|positive regulation of ATPase activity (GO:0032781)|positive regulation of helicase activity (GO:0051096)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|transcription export complex (GO:0000346)	poly(A) RNA binding (GO:0044822)	p.S40L(1)		endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(6)	13						ATTCGGGCTTCGATGCAGCAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	77	77					1																	153610824		2203	4300	6503	151877448	SO:0001583	missense	26097				CCDS1048.1, CCDS72917.1, CCDS72918.1	1q21.3	2011-03-24	2011-03-24	2011-03-24	ENSG00000160679	ENSG00000160679			24511	protein-coding gene	gene with protein product	"small protein rich in arginine and glycine", "Friend of Prmt1"	614206	"chromosome 1 open reading frame 77"	C1orf77		19254951	Standard	NM_015607		Approved	DKFZP547E1010, SRAG, FOP	uc001fcn.2	Q9Y3Y2	OTTHUMG00000037052	ENST00000368694.3:c.119C>T	1.37:g.153610824C>T	ENSP00000357683:p.Ser40Leu		151877448	D3DV55|Q0VAQ8|Q2VPI9|Q5T7Y8|Q5T7Y9|Q5T7Z0|Q6NSM4|Q6PB28|Q8WYT9|Q9BUC5|Q9H034|Q9H2L0	Missense_Mutation	SNP	ENST00000368694.3	37	CCDS1048.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.825129	0.71143	.	.	ENSG00000160679	ENST00000368694;ENST00000403433;ENST00000368690;ENST00000368687	D;D	0.91011	-2.77;-2.77	5.5	5.5	0.81552	.	0.050729	0.85682	D	0.000000	T	0.81559	0.4848	L	0.36672	1.1	0.54753	D	0.999982	B;B;B	0.32968	0.025;0.392;0.272	B;B;B	0.25884	0.026;0.064;0.029	D	0.83580	0.0117	10	0.72032	D	0.01	.	16.94	0.86215	0.0:1.0:0.0:0.0	.	40;40;40	Q9Y3Y2-4;Q9Y3Y2-3;Q9Y3Y2	.;.;CHTOP_HUMAN	L	40;40;40;15	ENSP00000385228:S40L;ENSP00000357679:S40L	ENSP00000357676:S15L	S	+	2	0	CHTOP	151877448	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.390000	0.79816	2.861000	0.98227	0.655000	0.94253	TCG		0.438	CHTOP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089967.1	NM_015607		T	153610824	C	T	153610824	3	4	61	1	0	0	0	0	1	0	0	0	2065	893	31	1	125	1	C1orf77	1	153610824	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	295247	153610824	95639797	634	8619										
SLC27A3	11000	broad.mit.edu	37	chr1	153749017	153749017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggagtccctggagccgGacctgcccgccctgagagcc	13	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:153749017G>A	ENST00000368661.3	+	2	897	c.832G>A	c.(832-834)Gac>Aac	p.D278N	SLC27A3_ENST00000484014.1_3'UTR|SLC27A3_ENST00000271857.2_Missense_Mutation_p.D359N	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	278					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)	p.D278N(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCTGGAGCCGGACCTGCCCGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	81	77					1																	153749017		2203	4300	6503	152015641	SO:0001583	missense	11000			BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.832G>A	1.37:g.153749017G>A	ENSP00000357650:p.Asp278Asn		152015641	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453687	0.63290	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.10477	2.87;2.87	4.68	4.68	0.58851	AMP-dependent synthetase/ligase (1);	0.136051	0.49305	D	0.000147	T	0.12561	0.0305	L	0.49778	1.585	0.27543	N	0.95075	D	0.58268	0.982	D	0.64410	0.925	T	0.07233	-1.0783	10	0.25106	T	0.35	-33.3469	12.9581	0.58442	0.0:0.0:1.0:0.0	.	278	Q5K4L6	S27A3_HUMAN	N	359;278	ENSP00000271857:D359N;ENSP00000357650:D278N	ENSP00000271857:D359N	D	+	1	0	SLC27A3	152015641	0.623000	0.27094	0.998000	0.56505	0.917000	0.54804	1.166000	0.31834	2.440000	0.82611	0.491000	0.48974	GAC		0.622	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		A	153749017	G	A	153749017	3	1	61	1	0	0	0	0	1	0	0	0	14564	1174	41	3	838	3	SLC27A3	1	153749017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138193	153749017	95501604	635	8620										
NUP210L	91181	broad.mit.edu	37	chr1	154029322	154029322	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagttgatgtgtattttCttcccatcttgtccttggca	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154029322C>A	ENST00000368559.3	-	23	3280	c.3209G>T	c.(3208-3210)aGa>aTa	p.R1070I	NUP210L_ENST00000271854.3_Missense_Mutation_p.R1070I|NUP210L_ENST00000368553.1_Missense_Mutation_p.R3I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1070					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)		p.R1070K(1)|p.R1070I(1)		NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TGTGTATTTTCTTCCCATCTT	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	1											157	143	147					1																	154029322		1875	4116	5991	152295946	SO:0001583	missense	91181			AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.3209G>T	1.37:g.154029322C>A	ENSP00000357547:p.Arg1070Ile		152295946	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658051	0.47467	.	.	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.29655	3.34;1.56;3.1	4.95	4.02	0.46733	.	0.086330	0.50627	D	0.000112	T	0.18257	0.0438	M	0.64997	1.995	0.45295	D	0.998292	P;P	0.46395	0.877;0.8	B;B	0.42462	0.216;0.388	T	0.02625	-1.1132	10	0.48119	T	0.1	-32.6142	8.5269	0.33311	0.0:0.7627:0.1531:0.0842	.	1070;1070	E7EP56;Q5VU65	.;P210L_HUMAN	I	1070;3;1070	ENSP00000357547:R1070I;ENSP00000357541:R3I;ENSP00000271854:R1070I	ENSP00000271854:R1070I	R	-	2	0	NUP210L	152295946	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	2.189000	0.42621	1.268000	0.44264	0.650000	0.86243	AGA		0.378	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	154029322	C	A	154029322	3	1	61	1	0	0	0	0	1	0	0	0	10792	913	32	2	2529	2	NUP210L	1	154029322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280305	154029322	95221299	636	8621										
UBAP2L	9898	broad.mit.edu	37	chr1	154241244	154241244	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggatagcagtcctttgaGaaacaaggttttcattccgg	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154241244G>A	ENST00000361546.2	+	25	3024	c.2982G>A	c.(2980-2982)gaG>gaA	p.E994E	UBAP2L_ENST00000484819.1_3'UTR|UBAP2L_ENST00000428931.1_Silent_p.E994E|UBAP2L_ENST00000271877.7_Silent_p.E1004E			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	994					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.E490E(1)|p.E994E(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGTCCTTTGAGAAACAAGGTT	0.537																																																2	Substitution - coding silent(2)	large_intestine(2)	1											144	135	138					1																	154241244		2203	4300	6503	152507868	SO:0001819	synonymous_variant	9898			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.2982G>A	1.37:g.154241244G>A			152507868	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Silent	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	G	2.762	-0.257696	0.05791	.	.	ENSG00000143569	ENST00000433615;ENST00000428595	T;T	0.40476	1.03;1.03	5.34	4.36	0.52297	.	0.060929	0.64402	D	0.000005	T	0.47948	0.1473	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49670	-0.8915	7	0.59425	D	0.04	-6.9403	14.1973	0.65679	0.0:0.1508:0.8492:0.0	.	.	.	.	K	325;273	ENSP00000407672:E325K;ENSP00000398609:E273K	ENSP00000398609:E273K	E	+	1	0	UBAP2L	152507868	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.469000	0.45110	2.486000	0.83907	0.557000	0.71058	GAA		0.537	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		A	154241244	G	A	154241244	2	1	61	1	0	0	0	0	0	0	0	1	16878	933	33	3		3	UBAP2L	1	154241244	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211922	154241244	95009377	637	8622										
ATP8B2	57198	broad.mit.edu	37	chr1	154304153	154304153	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaataaccagtttgtggCggtaagggacagggtacccc	13	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154304153C>T	ENST00000368489.3	+	7	536	c.536C>T	c.(535-537)gCg>gTg	p.A179V	ATP8B2_ENST00000368487.3_Splice_Site_p.A146V|ATP8B2_ENST00000426445.1_3'UTR|ATP8B2_ENST00000341822.2_Splice_Site_p.A165V	NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	165					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.A179V(1)	IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CAGTTTGTGGCGGTAAGGGAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	110	113					1																	154304153		2203	4300	6503	152570777	SO:0001630	splice_region_variant	57198			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.537+1C>T	1.37:g.154304153C>T			152570777	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.414644	0.83449	.	.	ENSG00000143515	ENST00000368487;ENST00000368489;ENST00000341822	D;D;D	0.88509	-2.39;-2.39;-2.39	5.14	5.14	0.70334	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.060792	0.64402	D	0.000004	D	0.87521	0.6198	M	0.74546	2.27	0.80722	D	1	P;P;P	0.49253	0.921;0.774;0.469	B;B;B	0.43018	0.405;0.244;0.075	D	0.89274	0.3607	10	0.59425	D	0.04	.	17.782	0.88527	0.0:1.0:0.0:0.0	.	165;179;146	P98198;P98198-3;P98198-4	AT8B2_HUMAN;.;.	V	146;179;165	ENSP00000357472:A146V;ENSP00000357475:A179V;ENSP00000340448:A165V	ENSP00000340448:A165V	A	+	2	0	ATP8B2	152570777	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.601000	0.82783	2.676000	0.91093	0.561000	0.74099	GCG		0.473	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	Missense_Mutation	T	154304153	C	T	154304153	5	4	61	1	0	0	0	0	0	0	1	0	1196	782	27	1	562	1	ATP8B2	1	154304153	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62909	154304153	94946468	638	8623										
ATP8B2	57198	broad.mit.edu	37	chr1	154307027	154307027	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcagaacaaagttcaaaaGaacgagtatcgatcgcctaa	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154307027G>A	ENST00000368489.3	+	11	896	c.896G>A	c.(895-897)aGa>aAa	p.R299K	ATP8B2_ENST00000368487.3_Missense_Mutation_p.R266K|ATP8B2_ENST00000426445.1_3'UTR|ATP8B2_ENST00000341822.2_Missense_Mutation_p.R285K	NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	285					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R299K(1)	IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AAGTTCAAAAGAACGAGTATC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											103	95	98					1																	154307027		2203	4300	6503	152573651	SO:0001583	missense	57198			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.896G>A	1.37:g.154307027G>A	ENSP00000357475:p.Arg299Lys		152573651	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	35	5.526657	0.96431	.	.	ENSG00000143515	ENST00000368487;ENST00000368489;ENST00000341822	D;T;T	0.90444	-2.67;-0.83;-0.83	4.86	4.86	0.63082	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95262	0.8463	M	0.86740	2.835	0.51012	D	0.999908	D;D;P	0.76494	0.999;0.998;0.849	D;D;P	0.85130	0.997;0.97;0.55	D	0.94864	0.8024	10	0.48119	T	0.1	.	16.7414	0.85460	0.0:0.0:1.0:0.0	.	285;299;266	P98198;P98198-3;P98198-4	AT8B2_HUMAN;.;.	K	266;299;285	ENSP00000357472:R266K;ENSP00000357475:R299K;ENSP00000340448:R285K	ENSP00000340448:R285K	R	+	2	0	ATP8B2	152573651	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.591000	0.74090	2.526000	0.85167	0.591000	0.81541	AGA		0.537	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		A	154307027	G	A	154307027	3	1	61	1	0	0	0	0	1	0	0	0	1196	942	33	3	938	3	ATP8B2	1	154307027	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2874	154307027	94943594	639	8624										
ATP8B2	57198	broad.mit.edu	37	chr1	154310016	154310016	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgcccatttcactctatGtcaggtatgtgccttctctg	8	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154310016G>A	ENST00000368489.3	+	12	1129	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I	RNU7-57P_ENST00000459540.1_RNA|ATP8B2_ENST00000368487.3_Missense_Mutation_p.V344I|ATP8B2_ENST00000426445.1_3'UTR|ATP8B2_ENST00000341822.2_Missense_Mutation_p.V363I	NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	363					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V377I(1)	IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTCACTCTATGTCAGGTATGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											336	289	305					1																	154310016		2203	4300	6503	152576640	SO:0001583	missense	57198			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1129G>A	1.37:g.154310016G>A	ENSP00000357475:p.Val377Ile		152576640	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349237	0.61183	.	.	ENSG00000143515	ENST00000368487;ENST00000368489;ENST00000341822	D;D;D	0.90676	-2.71;-2.71;-2.71	5.41	5.41	0.78517	ATPase, P-type, ATPase-associated domain (1);	0.146245	0.45361	D	0.000361	D	0.93471	0.7917	M	0.63208	1.945	0.80722	D	1	D;D;P	0.64830	0.974;0.994;0.634	D;D;P	0.64687	0.913;0.928;0.616	D	0.93656	0.6977	10	0.87932	D	0	.	17.9338	0.89006	0.0:0.0:1.0:0.0	.	363;377;344	P98198;P98198-3;P98198-4	AT8B2_HUMAN;.;.	I	344;377;363	ENSP00000357472:V344I;ENSP00000357475:V377I;ENSP00000340448:V363I	ENSP00000340448:V363I	V	+	1	0	ATP8B2	152576640	1.000000	0.71417	0.998000	0.56505	0.305000	0.27757	9.581000	0.98210	2.815000	0.96918	0.561000	0.74099	GTC		0.507	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		A	154310016	G	A	154310016	3	1	61	1	0	0	0	0	1	0	0	0	1196	1377	48	3	1175	3	ATP8B2	1	154310016	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2989	154310016	94940605	640	8625										
ATP8B2	57198	broad.mit.edu	37	chr1	154315769	154315769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacatccgcaagcggatgtCggtcataggtgaggccaggc	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154315769C>T	ENST00000368489.3	+	16	1733	c.1733C>T	c.(1732-1734)tCg>tTg	p.S578L		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	564					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.S578L(1)	IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AAGCGGATGTCGGTCATAGGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											35	32	33					1																	154315769		2203	4300	6503	152582393	SO:0001583	missense	57198			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1733C>T	1.37:g.154315769C>T	ENSP00000357475:p.Ser578Leu		152582393	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	C	35	5.544638	0.96488	.	.	ENSG00000143515	ENST00000368489	D	0.84873	-1.91	5.65	5.65	0.86999	.	0.065425	0.64402	D	0.000006	D	0.95943	0.8679	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97011	0.9736	10	0.87932	D	0	.	18.891	0.92403	0.0:1.0:0.0:0.0	.	578	P98198-3	.	L	578	ENSP00000357475:S578L	ENSP00000357475:S578L	S	+	2	0	ATP8B2	152582393	1.000000	0.71417	0.970000	0.41538	0.987000	0.75469	5.845000	0.69437	2.941000	0.99782	0.655000	0.94253	TCG		0.577	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		T	154315769	C	T	154315769	3	4	61	1	0	0	0	0	1	0	0	0	1196	893	31	1	1925	1	ATP8B2	1	154315769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5753	154315769	94934852	641	8626										
SHE	126669	broad.mit.edu	37	chr1	154461806	154461806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagagccttcaccagggGatctttggaaccccgtcgtc	12	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154461806G>A	ENST00000304760.2	-	3	831	c.745C>T	c.(745-747)Ccc>Tcc	p.P249S		NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	249								p.P249S(1)		breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTCACCAGGGGATCTTTGGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	68	65					1																	154461806		2203	4300	6503	152728430	SO:0001583	missense	126669			AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.745C>T	1.37:g.154461806G>A	ENSP00000307369:p.Pro249Ser		152728430	Q8TEQ5	Missense_Mutation	SNP	ENST00000304760.2	37	CCDS30877.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475970	0.44044	.	.	ENSG00000169291	ENST00000304760	T	0.28895	1.59	5.17	5.17	0.71159	.	0.277762	0.36200	N	0.002735	T	0.11793	0.0287	L	0.39633	1.23	0.30271	N	0.792298	P	0.48764	0.915	B	0.42386	0.386	T	0.08889	-1.0700	10	0.09338	T	0.73	-1.8722	12.8567	0.57890	0.0:0.0:0.837:0.163	.	249	Q5VZ18	SHE_HUMAN	S	249	ENSP00000307369:P249S	ENSP00000307369:P249S	P	-	1	0	SHE	152728430	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	6.061000	0.71148	2.864000	0.98301	0.549000	0.68633	CCC		0.488	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		A	154461806	G	A	154461806	3	1	61	1	0	0	0	0	1	0	0	0	14313	1174	41	3	758	3	SHE	1	154461806	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146037	154461806	94788815	642	8627										
TDRD10	126668	broad.mit.edu	37	chr1	154517335	154517335	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattgattttggacagttgGccaccatccctgtgcagtct	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154517335G>A	ENST00000368480.3	+	11	947	c.862G>A	c.(862-864)Gcc>Acc	p.A288T	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.A288T			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	288	Tudor.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.A288T(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGGACAGTTGGCCACCATCCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											227	193	205					1																	154517335		2203	4300	6503	152783959	SO:0001583	missense	126668			AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.862G>A	1.37:g.154517335G>A	ENSP00000357465:p.Ala288Thr		152783959	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	37	CCDS41406.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.272924	0.40194	.	.	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.08896	3.04;3.04	4.17	2.2	0.27929	Maternal tudor protein (1);	0.119176	0.34725	N	0.003734	T	0.04497	0.0123	L	0.32530	0.975	0.21527	N	0.99966	P;P	0.52316	0.952;0.873	P;B	0.54460	0.753;0.441	T	0.24190	-1.0167	10	0.72032	D	0.01	-12.3446	6.0593	0.19828	0.1078:0.1891:0.7031:0.0	.	288;288	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	T	288	ENSP00000357467:A288T;ENSP00000357465:A288T	ENSP00000357465:A288T	A	+	1	0	TDRD10	152783959	0.021000	0.18746	0.244000	0.24202	0.117000	0.20001	0.111000	0.15458	0.367000	0.24454	0.557000	0.71058	GCC		0.542	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		A	154517335	G	A	154517335	3	1	61	1	0	0	0	0	1	0	0	0	15770	1203	42	3	900	3	TDRD10	1	154517335	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55529	154517335	94733286	643	8628										
CHRNB2	1141	broad.mit.edu	37	chr1	154543823	154543823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaccatgaagttccgttCgtggacctacgaccgcacag	10	14	0	1	rs75760566	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154543823C>T	ENST00000368476.3	+	5	788	c.524C>T	c.(523-525)tCg>tTg	p.S175L		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	175					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.S175L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	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)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	AAGTTCCGTTCGTGGACCTAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	108	118					1																	154543823		2203	4300	6503	152810447	SO:0001583	missense	1141			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.524C>T	1.37:g.154543823C>T	ENSP00000357461:p.Ser175Leu		152810447	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	37	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.760191	0.89932	.	.	ENSG00000160716	ENST00000368476	D	0.86497	-2.13	4.38	4.38	0.52667	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97362	0.9970	10	0.87932	D	0	.	16.7273	0.85426	0.0:1.0:0.0:0.0	.	175	P17787	ACHB2_HUMAN	L	175	ENSP00000357461:S175L	ENSP00000357461:S175L	S	+	2	0	CHRNB2	152810447	1.000000	0.71417	0.974000	0.42286	0.949000	0.60115	7.616000	0.83018	2.238000	0.73509	0.563000	0.77884	TCG		0.552	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		T	154543823	C	T	154543823	3	4	61	1	0	0	0	0	1	0	0	0	3397	893	31	1	542	1	CHRNB2	1	154543823	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26488	154543823	94706798	644	8629										
CHRNB2	1141	broad.mit.edu	37	chr1	154544157	154544157	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgctcatctccaagatCgtgcctcccacctccctcga	6	19	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154544157C>T	ENST00000368476.3	+	5	1122	c.858C>T	c.(856-858)atC>atT	p.I286I		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	286					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.I286I(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	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)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TCTCCAAGATCGTGCCTCCCA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											220	164	183					1																	154544157		2203	4300	6503	152810781	SO:0001819	synonymous_variant	1141			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.858C>T	1.37:g.154544157C>T			152810781	Q9UEH9	Silent	SNP	ENST00000368476.3	37	CCDS1070.1																																																																																				0.582	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		T	154544157	C	T	154544157	2	4	61	1	0	0	0	0	0	0	0	1	3397	874	31	1		1	CHRNB2	1	154544157	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	334	154544157	94706464	645	8630										
ADAR	103	broad.mit.edu	37	chr1	154574376	154574376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccaagcctgagctgagaCtgcaataaaaggctcaagaa	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154574376C>T	ENST00000368474.4	-	2	941	c.742G>A	c.(742-744)Gtc>Atc	p.V248I	ADAR_ENST00000292205.5_Missense_Mutation_p.V291I|ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'Flank	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	248					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.V248I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TGAGCTGAGACTGCAATAAAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											115	119	117					1																	154574376		2203	4300	6503	152841000	SO:0001583	missense	103			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.742G>A	1.37:g.154574376C>T	ENSP00000357459:p.Val248Ile		152841000	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	C	8.101	0.776636	0.16120	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.11495	2.77;2.79;2.78	2.09	-0.364	0.12553	.	3.791260	0.02764	U	0.118893	T	0.02807	0.0084	L	0.39898	1.24	0.09310	N	1	P;P;B	0.40834	0.73;0.73;0.043	B;B;B	0.38020	0.263;0.263;0.003	T	0.29150	-1.0021	10	0.38643	T	0.18	.	2.8284	0.05491	0.0:0.4922:0.3034:0.2043	.	248;248;248	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	I	291;248;243	ENSP00000292205:V291I;ENSP00000357459:V248I;ENSP00000431794:V243I	ENSP00000292205:V291I	V	-	1	0	ADAR	152841000	0.472000	0.25870	0.055000	0.19348	0.112000	0.19704	-0.026000	0.12392	0.188000	0.20168	0.491000	0.48974	GTC		0.517	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		T	154574376	C	T	154574376	3	4	61	1	0	0	0	0	1	0	0	0	281	565	20	3	2994	3	ADAR	1	154574376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30219	154574376	94676245	646	8631										
ADAR	103	broad.mit.edu	37	chr1	154574713	154574713	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgttcctgatcttggtaGatactcagttcctggaaatg	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154574713G>T	ENST00000368474.4	-	2	604	c.405C>A	c.(403-405)atC>atA	p.I135I	ADAR_ENST00000292205.5_Silent_p.I178I|ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'UTR	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	135					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.I135I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GATCTTGGTAGATACTCAGTT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	1											66	68	68					1																	154574713		2203	4300	6503	152841337	SO:0001819	synonymous_variant	103			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.405C>A	1.37:g.154574713G>T			152841337	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																				0.522	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		T	154574713	G	T	154574713	2	4	61	1	0	0	0	0	0	0	0	1	281	932	33	2		2	ADAR	1	154574713	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	337	154574713	94675908	647	8632										
KCNN3	3782	broad.mit.edu	37	chr1	154842176	154842176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctggctctggagttgggCgagctgagacaggggatgcg	21	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:154842176C>T	ENST00000271915.4	-	1	580	c.265G>A	c.(265-267)Gcc>Acc	p.A89T	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	94	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.A89T(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	TGGAGTTGGGCGAGCTGAGAC	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	1											27	19	22					1																	154842176		2191	4280	6471	153108800	SO:0001583	missense	3782			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.265G>A	1.37:g.154842176C>T	ENSP00000271915:p.Ala89Thr		153108800	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	C	9.444	1.088706	0.20390	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	D	0.95171	-3.63	4.82	-0.862	0.10673	.	1.056700	0.07450	N	0.898802	T	0.74688	0.3749	N	0.14661	0.345	0.22873	N	0.998629	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.65417	-0.6173	10	0.13108	T	0.6	-3.2171	8.8886	0.35418	0.0:0.4964:0.0:0.5036	.	95;94	Q6JXY2;Q9UGI6	.;KCNN3_HUMAN	T	89;184	ENSP00000271915:A89T	ENSP00000271915:A89T	A	-	1	0	KCNN3	153108800	0.957000	0.32711	0.974000	0.42286	0.994000	0.84299	0.172000	0.16704	-0.021000	0.14009	0.563000	0.77884	GCC		0.687	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842176	C	T	154842176	3	4	61	1	0	0	0	0	1	0	0	0	8101	768	27	1	1984	1	KCNN3	1	154842176	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	267463	154842176	94408445	648	8633										
DCST2	127579	broad.mit.edu	37	chr1	155003054	155003054	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcattgagatccacagaGaagtggtgggtggctgtcat	16	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155003054G>T	ENST00000368424.3	-	6	931	c.873C>A	c.(871-873)ttC>ttA	p.F291L	DCST2_ENST00000295536.5_Missense_Mutation_p.F291L	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	291						integral component of membrane (GO:0016021)		p.F291L(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	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)			GATCCACAGAGAAGTGGTGGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	57	65					1																	155003054		2203	4300	6503	153269678	SO:0001583	missense	127579			AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.873C>A	1.37:g.155003054G>T	ENSP00000357409:p.Phe291Leu		153269678	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	G	17.32	3.360497	0.61403	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.25749	1.78;1.84	5.08	5.08	0.68730	.	0.065598	0.64402	D	0.000011	T	0.10208	0.0250	L	0.34521	1.04	0.35289	D	0.782025	B	0.21225	0.053	B	0.20184	0.028	T	0.07966	-1.0745	10	0.20519	T	0.43	-31.4202	15.741	0.77894	0.0:0.0:1.0:0.0	.	291	Q5T1A1	DCST2_HUMAN	L	291	ENSP00000357409:F291L;ENSP00000295536:F291L	ENSP00000295536:F291L	F	-	3	2	DCST2	153269678	0.986000	0.35501	1.000000	0.80357	0.989000	0.77384	1.551000	0.36233	2.531000	0.85337	0.655000	0.94253	TTC		0.607	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		T	155003054	G	T	155003054	3	4	61	1	0	0	0	0	1	0	0	0	4309	933	33	2	1488	2	DCST2	1	155003054	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160878	155003054	94247567	649	8634										
DCST1	149095	broad.mit.edu	37	chr1	155015221	155015221	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcaccagtgatggaggtTtggtgccgcaatcgcatccc	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155015221T>G	ENST00000295542.1	+	9	999	c.903T>G	c.(901-903)gtT>gtG	p.V301V	DCST1_ENST00000392480.1_Silent_p.V301V|DCST1_ENST00000368419.2_Silent_p.V301V|RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000423025.2_Silent_p.V276V	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	301						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.V301V(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TGATGGAGGTTTGGTGCCGCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	1											113	95	101					1																	155015221		2203	4300	6503	153281845	SO:0001819	synonymous_variant	149095			AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.903T>G	1.37:g.155015221T>G			153281845	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	37	CCDS1083.1																																																																																				0.597	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		G	155015221	T	G	155015221	2	3	61	1	0	0	0	0	0	0	0	1	4308	1828	64	4		4	DCST1	1	155015221	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12167	155015221	94235400	650	8635										
ADAM15	8751	broad.mit.edu	37	chr1	155028558	155028558	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccagctgtctttcagttCttccggcccctgaatgtacg	9	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155028558C>A	ENST00000356955.2	+	9	848	c.747C>A	c.(745-747)ttC>ttA	p.F249L	ADAM15_ENST00000449910.2_Missense_Mutation_p.F249L|ADAM15_ENST00000368410.2_Intron|ADAM15_ENST00000360674.4_Missense_Mutation_p.F249L|ADAM15_ENST00000359280.4_Missense_Mutation_p.F249L|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000447332.3_Missense_Mutation_p.F233L|ADAM15_ENST00000531455.1_Missense_Mutation_p.F259L|ADAM15_ENST00000271836.6_Missense_Mutation_p.F249L|ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000368412.3_Missense_Mutation_p.F249L|ADAM15_ENST00000355956.2_Missense_Mutation_p.F249L	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	249	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.F249L(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TCTTTCAGTTCTTCCGGCCCC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	64	64					1																	155028558		2203	4300	6503	153295182	SO:0001583	missense	8751			U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"ADAM metallopeptidase domain containing"	193	protein-coding gene	gene with protein product	"metargidin"	605548	"a disintegrin and metalloproteinase domain 15 (metargidin)"			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.747C>A	1.37:g.155028558C>A	ENSP00000349436:p.Phe249Leu		153295182	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.622743	0.87460	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000271836;ENST00000531455	T;T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08;0.08	4.84	4.84	0.62591	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.43747	D	0.000540	T	0.50480	0.1618	N	0.21545	0.675	0.80722	D	1	D;D;D;D;P;D;D;D;B;D	0.76494	0.999;0.999;0.997;0.998;0.868;0.998;0.998;0.998;0.207;0.999	D;D;D;D;P;D;D;D;B;D	0.85130	0.976;0.976;0.983;0.995;0.848;0.96;0.96;0.971;0.316;0.997	T	0.55655	-0.8107	10	0.49607	T	0.09	.	8.9483	0.35773	0.0:0.9012:0.0:0.0988	.	259;266;233;249;249;249;249;249;249;249	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	L	249;249;249;249;249;249;249;259	ENSP00000349436:F249L;ENSP00000403843:F249L;ENSP00000352226:F249L;ENSP00000353892:F249L;ENSP00000357397:F249L;ENSP00000348227:F249L;ENSP00000271836:F249L;ENSP00000432927:F259L	ENSP00000271836:F249L	F	+	3	2	ADAM15	153295182	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	0.883000	0.28200	2.498000	0.84270	0.462000	0.41574	TTC		0.627	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		A	155028558	C	A	155028558	3	1	61	1	0	0	0	0	1	0	0	0	237	912	32	2	781	2	ADAM15	1	155028558	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13337	155028558	94222063	651	8636										
ADAM15	8751	broad.mit.edu	37	chr1	155030608	155030608	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgggcgcaaccccagtggCagttatgtgtcctgcacccc	12	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155030608C>T	ENST00000356955.2	+	14	1799	c.1698C>T	c.(1696-1698)ggC>ggT	p.G566G	ADAM15_ENST00000449910.2_Silent_p.G566G|ADAM15_ENST00000368410.2_Silent_p.G272G|ADAM15_ENST00000360674.4_Silent_p.G566G|ADAM15_ENST00000359280.4_Silent_p.G566G|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000447332.3_Silent_p.G550G|ADAM15_ENST00000531455.1_Silent_p.G576G|ADAM15_ENST00000271836.6_Silent_p.G566G|ADAM15_ENST00000368413.1_Silent_p.G272G|ADAM15_ENST00000368412.3_Silent_p.G566G|ADAM15_ENST00000355956.2_Silent_p.G566G	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	566	Cys-rich.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.G566G(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			ACCCCAGTGGCAGTTATGTGT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											53	59	57					1																	155030608		2203	4300	6503	153297232	SO:0001819	synonymous_variant	8751			U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"ADAM metallopeptidase domain containing"	193	protein-coding gene	gene with protein product	"metargidin"	605548	"a disintegrin and metalloproteinase domain 15 (metargidin)"			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1698C>T	1.37:g.155030608C>T			153297232	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Silent	SNP	ENST00000356955.2	37	CCDS1087.1																																																																																				0.582	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		T	155030608	C	T	155030608	2	4	61	1	0	0	0	0	0	0	0	1	237	697	25	3		3	ADAM15	1	155030608	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2050	155030608	94220013	652	8637										
THBS3	7059	broad.mit.edu	37	chr1	155170942	155170942	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttggtctgggtagccatcGatgtctgtgtcagtcccaca	12	11	3	0	rs148689308		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155170942G>A	ENST00000368378.3	-	12	1403	c.1383C>T	c.(1381-1383)atC>atT	p.I461I	RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000430312.1_RNA|THBS3_ENST00000457183.2_Silent_p.I341I|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541576.1_Intron|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000486260.1_5'UTR	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	461					bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.I461I(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)			GGTAGCCATCGATGTCTGTGT	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		20631	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		3,4403	6.2+/-15.9	0,3,2200	236	192	207		1383	-5.7	0.8	1	dbSNP_134	207	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	THBS3	NM_007112.3		0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308		461/957	155170942	4,13002	2203	4300	6503	153437566	SO:0001819	synonymous_variant	7059			L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1383C>T	1.37:g.155170942G>A			153437566	B1AVR8|B4DQ20|Q8WV34	Silent	SNP	ENST00000368378.3	37	CCDS1099.1																																																																																				0.592	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155170942	G	A	155170942	2	1	61	1	0	0	0	0	0	0	0	1	15894	1048	37	1		1	THBS3	1	155170942	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140334	155170942	94079679	653	8638										
HCN3	57657	broad.mit.edu	37	chr1	155252554	155252554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgggccctacgcatcgttCgcttcaccaagatcctaagc	8	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155252554C>T	ENST00000368358.3	+	2	639	c.631C>T	c.(631-633)Cgc>Tgc	p.R211C	HCN3_ENST00000496230.1_3'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	211					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.R211C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	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)			ACGCATCGTTCGCTTCACCAA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	53	57					1																	155252554		2203	4300	6503	153519178	SO:0001583	missense	57657			AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.631C>T	1.37:g.155252554C>T	ENSP00000357342:p.Arg211Cys		153519178	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Missense_Mutation	SNP	ENST00000368358.3	37	CCDS1108.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171975	0.78452	.	.	ENSG00000143630	ENST00000368358	D	0.98792	-5.14	4.97	4.03	0.46877	Ion transport (1);	0.000000	0.48767	D	0.000172	D	0.99061	0.9678	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99804	1.1037	10	0.87932	D	0	.	10.3674	0.44033	0.3705:0.6295:0.0:0.0	.	211	Q9P1Z3	HCN3_HUMAN	C	211	ENSP00000357342:R211C	ENSP00000357342:R211C	R	+	1	0	HCN3	153519178	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.606000	0.61126	1.396000	0.46663	0.591000	0.81541	CGC		0.602	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		T	155252554	C	T	155252554	3	4	61	1	0	0	0	0	1	0	0	0	7019	884	31	1	637	1	HCN3	1	155252554	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81612	155252554	93998067	654	8639										
PKLR	5313	broad.mit.edu	37	chr1	155264362	155264362	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgacggcagccacgtcGctggctttccgcacaaagga	12	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155264362G>A	ENST00000342741.4	-	6	914	c.876C>T	c.(874-876)agC>agT	p.S292S	PKLR_ENST00000392414.3_Silent_p.S261S	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	292					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.S292S(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CAGCCACGTCGCTGGCTTTCC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	1											91	80	84					1																	155264362		2203	4300	6503	153530986	SO:0001819	synonymous_variant	5313			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.876C>T	1.37:g.155264362G>A			153530986	O75758|P11973	Silent	SNP	ENST00000342741.4	37	CCDS1109.1																																																																																				0.612	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		A	155264362	G	A	155264362	2	1	61	1	0	0	0	0	0	0	0	1	12007	1078	38	1		1	PKLR	1	155264362	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11808	155264362	93986259	655	8640										
PKLR	5313	broad.mit.edu	37	chr1	155265465	155265465	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtcccgcacctcgtgggaGccgtgggagaagttgagtcg	16	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155265465G>A	ENST00000342741.4	-	3	404	c.366C>T	c.(364-366)ggC>ggT	p.G122G	PKLR_ENST00000392414.3_Silent_p.G91G	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	122					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.G122G(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CCTCGTGGGAGCCGTGGGAGA	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	1											87	72	77					1																	155265465		2203	4300	6503	153532089	SO:0001819	synonymous_variant	5313			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.366C>T	1.37:g.155265465G>A			153532089	O75758|P11973	Silent	SNP	ENST00000342741.4	37	CCDS1109.1																																																																																				0.657	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		A	155265465	G	A	155265465	2	1	61	1	0	0	0	0	0	0	0	1	12007	958	34	3		3	PKLR	1	155265465	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1103	155265465	93985156	656	8641										
RUSC1	23623	broad.mit.edu	37	chr1	155298025	155298025	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgagatgccttctcctcaGgagcttgaggcctcagcacc	10	16	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155298025G>A	ENST00000368352.5	+	9	2650	c.2499G>A	c.(2497-2499)caG>caA	p.Q833Q	RUSC1_ENST00000292254.4_Silent_p.Q364Q|RUSC1_ENST00000462780.1_3'UTR|RUSC1_ENST00000368354.3_Silent_p.Q727Q|RUSC1_ENST00000368349.4_Silent_p.Q364Q|RUSC1_ENST00000368347.4_Silent_p.Q423Q	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	833					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)	p.Q364Q(1)|p.Q727Q(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	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)			CTTCTCCTCAGGAGCTTGAGG	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	1											94	91	92					1																	155298025		2203	4300	6503	153564649	SO:0001819	synonymous_variant	23623			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.2499G>A	1.37:g.155298025G>A			153564649	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																				0.547	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			A	155298025	G	A	155298025	2	1	61	1	0	0	0	0	0	0	0	1	13787	991	35	3		3	RUSC1	1	155298025	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32560	155298025	93952596	657	8642										
ASH1L	55870	broad.mit.edu	37	chr1	155340671	155340671	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacctttttcctcagctcGaaatcgttctagacattgca	5	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155340671G>A	ENST00000368346.3	-	11	7090	c.6451C>T	c.(6451-6453)Cga>Tga	p.R2151*	ASH1L_ENST00000392403.3_Nonsense_Mutation_p.R2146*			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2151	Catalytic domain.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R2146*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCCTCAGCTCGAAATCGTTCT	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											163	166	165					1																	155340671		2203	4300	6503	153607295	SO:0001587	stop_gained	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.6451C>T	1.37:g.155340671G>A	ENSP00000357330:p.Arg2151*		153607295	Q59GP1|Q5T714|Q5T715|Q9P2C7	Nonsense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	G	51	18.596542	0.99907	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	.	.	.	5.4	4.45	0.53987	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1163	0.72404	0.0:0.0:0.8578:0.1422	.	.	.	.	X	2151;2146	.	ENSP00000357330:R2151X	R	-	1	2	ASH1L	153607295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.718000	0.68455	2.548000	0.85928	0.650000	0.86243	CGA		0.493	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155340671	G	A	155340671	4	1	61	1	0	0	0	0	0	1	0	0	1042	1066	37	1	2530	1	ASH1L	1	155340671	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42646	155340671	93909950	658	8643										
ASH1L	55870	broad.mit.edu	37	chr1	155348173	155348173	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaggggtttgacatcaacGtagacatcttgaaaagaaag	11	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155348173G>A	ENST00000368346.3	-	10	6885	c.6246C>T	c.(6244-6246)taC>taT	p.Y2082Y	ASH1L_ENST00000392403.3_Silent_p.Y2077Y			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2082	Catalytic domain.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.Y2077Y(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGACATCAACGTAGACATCTT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	1											141	138	139					1																	155348173		2203	4300	6503	153614797	SO:0001819	synonymous_variant	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.6246C>T	1.37:g.155348173G>A			153614797	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																					0.403	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155348173	G	A	155348173	2	1	61	1	0	0	0	0	0	0	0	1	1042	1140	40	1		1	ASH1L	1	155348173	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7502	155348173	93902448	659	8644										
ASH1L	55870	broad.mit.edu	37	chr1	155348300	155348300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaagttactcacttgaacGaattttcttatatagtggga	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155348300G>A	ENST00000368346.3	-	9	6871	c.6232C>T	c.(6232-6234)Cgt>Tgt	p.R2078C	ASH1L_ENST00000392403.3_Missense_Mutation_p.R2073C			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2078	Catalytic domain.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R2073C(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCACTTGAACGAATTTTCTTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	60	60					1																	155348300		2203	4300	6503	153614924	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.6232C>T	1.37:g.155348300G>A	ENSP00000357330:p.Arg2078Cys		153614924	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	G	21.2	4.119196	0.77323	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	T;T	0.80824	-1.42;-1.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.69196	0.3084	M	0.69358	2.11	0.80722	D	1	B;B	0.31893	0.234;0.345	B;B	0.19946	0.012;0.027	T	0.73701	-0.3900	10	0.87932	D	0	.	12.8982	0.58111	0.0746:0.0:0.9254:0.0	.	2078;2073	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	C	2078;2073	ENSP00000357330:R2078C;ENSP00000376204:R2073C	ENSP00000357330:R2078C	R	-	1	0	ASH1L	153614924	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.770000	0.55310	2.941000	0.99782	0.655000	0.94253	CGT		0.343	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155348300	G	A	155348300	3	1	61	1	0	0	0	0	1	0	0	0	1042	1058	37	1	2757	1	ASH1L	1	155348300	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127	155348300	93902321	660	8645										
ASH1L	55870	broad.mit.edu	37	chr1	155449710	155449710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcattttatttattttgCggataattgttttcattaat	4	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155449710C>T	ENST00000368346.3	-	3	3590	c.2951G>A	c.(2950-2952)cGc>cAc	p.R984H	ASH1L_ENST00000392403.3_Missense_Mutation_p.R984H			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	984					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R984H(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			ATTTATTTTGCGGATAATTGT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	51	51					1																	155449710		2202	4296	6498	153716334	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2951G>A	1.37:g.155449710C>T	ENSP00000357330:p.Arg984His		153716334	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	16.66	3.185918	0.57909	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.90385	-2.66;-2.66	5.16	5.16	0.70880	.	0.062767	0.64402	D	0.000003	D	0.86928	0.6051	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.60236	0.747;0.871	D	0.90344	0.4361	10	0.66056	D	0.02	.	18.4468	0.90686	0.0:1.0:0.0:0.0	.	984;984	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	H	984	ENSP00000357330:R984H;ENSP00000376204:R984H	ENSP00000357330:R984H	R	-	2	0	ASH1L	153716334	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.932000	0.70121	2.699000	0.92147	0.650000	0.86243	CGC		0.318	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155449710	C	T	155449710	3	4	61	1	0	0	0	0	1	0	0	0	1042	768	27	1	6047	1	ASH1L	1	155449710	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101410	155449710	93800911	661	8646										
YY1AP1	55249	broad.mit.edu	37	chr1	155649246	155649246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttgaggctcagccacacGctcctcctcttctgggccat	9	16	3	1	rs550862847		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155649246G>A	ENST00000295566.4	-	4	300	c.277C>T	c.(277-279)Cgt>Tgt	p.R93C	YY1AP1_ENST00000404643.1_Missense_Mutation_p.R27C|YY1AP1_ENST00000347088.5_Missense_Mutation_p.R27C|YY1AP1_ENST00000359205.5_Missense_Mutation_p.R16C|YY1AP1_ENST00000535662.1_5'Flank|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000407221.1_Missense_Mutation_p.R16C|YY1AP1_ENST00000405763.3_Missense_Mutation_p.R165C|YY1AP1_ENST00000368340.5_Missense_Mutation_p.R165C|YY1AP1_ENST00000368339.5_Missense_Mutation_p.R165C|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000476093.1_5'UTR|YY1AP1_ENST00000311573.5_Missense_Mutation_p.R16C|YY1AP1_ENST00000355499.4_Missense_Mutation_p.R27C|YY1AP1_ENST00000438245.2_Missense_Mutation_p.R27C|YY1AP1_ENST00000368330.2_Missense_Mutation_p.R27C|YY1AP1_ENST00000361831.5_Missense_Mutation_p.R16C	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	93					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R93C(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TCAGCCACACGCTCCTCCTCT	0.483													G|||	1	0.000199681	0	0	5008	,	,		19797	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											144	119	128					1																	155649246		2203	4300	6503	153915870	SO:0001583	missense	55249			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.277C>T	1.37:g.155649246G>A	ENSP00000295566:p.Arg93Cys		153915870	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	G	7.194	0.592040	0.13812	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000405763;ENST00000438245;ENST00000443231;ENST00000454523	T;T;T;T;T;T;T;T;T;T;T	0.24723	1.89;1.87;1.89;1.87;1.89;1.84;1.85;1.87;1.89;1.88;1.84	3.18	2.13	0.27403	.	0.698583	0.14375	N	0.323540	T	0.14874	0.0359	L	0.56769	1.78	0.30588	N	0.761821	B;B;D;B;B;B;B	0.61080	0.011;0.015;0.989;0.084;0.001;0.005;0.031	B;B;P;B;B;B;B	0.47573	0.006;0.006;0.55;0.016;0.001;0.0;0.004	T	0.03795	-1.1003	10	0.39692	T	0.17	.	7.2751	0.26279	0.0:0.0:0.5748:0.4252	.	27;93;165;165;93;27;165	B4DZQ4;B4DQQ0;B4DMP2;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	C	16;27;16;27;16;165;93;27;16;27;165;165;27;16;27	ENSP00000352134:R16C;ENSP00000347686:R27C;ENSP00000311138:R16C;ENSP00000316079:R27C;ENSP00000355298:R16C;ENSP00000357324:R165C;ENSP00000295566:R93C;ENSP00000357314:R27C;ENSP00000385791:R16C;ENSP00000385390:R27C;ENSP00000357323:R165C	ENSP00000295566:R93C	R	-	1	0	YY1AP1	153915870	0.006000	0.16342	0.990000	0.47175	0.464000	0.32679	1.627000	0.37050	1.589000	0.49982	0.305000	0.20034	CGT		0.483	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		A	155649246	G	A	155649246	3	1	61	1	0	0	0	0	1	0	0	0	17548	1087	38	1	2205	1	YY1AP1	1	155649246	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199536	155649246	93601375	662	8647										
GON4L	54856	broad.mit.edu	37	chr1	155722014	155722014	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctctcttgagtgtctggTttcccggacacatgtcttct	8	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155722014T>C	ENST00000368331.1	-	30	6258	c.6210A>G	c.(6208-6210)aaA>aaG	p.K2070K	GON4L_ENST00000437809.1_Silent_p.K2069K|GON4L_ENST00000271883.5_Silent_p.K2069K	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	2070					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K2070K(1)|p.K2069K(1)		NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GAGTGTCTGGTTTCCCGGACA	0.527																																																2	Substitution - coding silent(2)	large_intestine(2)	1											46	47	47					1																	155722014		1892	4100	5992	153988638	SO:0001819	synonymous_variant	54856			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.6210A>G	1.37:g.155722014T>C			153988638	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	37																																																																																					0.527	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		C	155722014	T	C	155722014	2	2	61	1	0	0	0	0	0	0	0	1	6592	1722	60	4		4	GON4L	1	155722014	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	72768	155722014	93528607	663	8648										
GON4L	54856	broad.mit.edu	37	chr1	155735543	155735543	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggttctaggccctgaaaggCattttccccatcagccacag	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155735543C>A	ENST00000368331.1	-	21	3769	c.3721G>T	c.(3721-3723)Gcc>Tcc	p.A1241S	GON4L_ENST00000437809.1_Missense_Mutation_p.A1241S|GON4L_ENST00000271883.5_Missense_Mutation_p.A1241S|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000361040.5_Missense_Mutation_p.A1241S	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1241					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A1241S(3)		NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCCTGAAAGGCATTTTCCCCA	0.502																																																3	Substitution - Missense(3)	large_intestine(3)	1											75	78	77					1																	155735543		2203	4298	6501	154002167	SO:0001583	missense	54856			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.3721G>T	1.37:g.155735543C>A	ENSP00000357315:p.Ala1241Ser		154002167	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	C	10.62	1.401282	0.25291	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000361040	T;T;T;T	0.14391	2.81;2.81;2.81;2.51	5.08	3.08	0.35506	.	0.351848	0.27210	N	0.020411	T	0.03305	0.0096	L	0.50333	1.59	0.26123	N	0.980523	B;P;B;P	0.38335	0.427;0.627;0.41;0.545	B;B;B;B	0.32980	0.082;0.156;0.064;0.136	T	0.34625	-0.9821	10	0.20046	T	0.44	.	5.5444	0.17055	0.1645:0.6494:0.0:0.1861	.	1241;437;1241;1241	Q3T8J9-2;Q1ED43;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	S	1241	ENSP00000396117:A1241S;ENSP00000357315:A1241S;ENSP00000271883:A1241S;ENSP00000354322:A1241S	ENSP00000271883:A1241S	A	-	1	0	GON4L	154002167	0.709000	0.27886	0.995000	0.50966	0.300000	0.27592	0.040000	0.13905	1.379000	0.46325	0.650000	0.86243	GCC		0.502	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155735543	C	A	155735543	3	1	61	1	0	0	0	0	1	0	0	0	6592	710	25	2	3166	2	GON4L	1	155735543	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13529	155735543	93515078	664	8649										
GON4L	54856	broad.mit.edu	37	chr1	155796652	155796652	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaatgaagagtccaccatCttctatctcttcctcaggtt	7	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155796652C>A	ENST00000368331.1	-	3	721	c.673G>T	c.(673-675)Gat>Tat	p.D225Y	GON4L_ENST00000437809.1_Missense_Mutation_p.D225Y|GON4L_ENST00000271883.5_Missense_Mutation_p.D225Y|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000361040.5_Missense_Mutation_p.D225Y	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	225					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D225Y(1)		NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AGTCCACCATCTTCTATCTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	113	114					1																	155796652		2203	4300	6503	154063276	SO:0001583	missense	54856			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.673G>T	1.37:g.155796652C>A	ENSP00000357315:p.Asp225Tyr		154063276	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	C	18.73	3.686827	0.68157	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.14893	2.66;2.67;2.66;2.47	4.69	4.69	0.59074	.	0.268177	0.29021	N	0.013392	T	0.20495	0.0493	L	0.34521	1.04	0.33459	D	0.584713	P;D;P;P	0.89917	0.874;1.0;0.769;0.852	P;D;B;P	0.91635	0.667;0.999;0.332;0.533	T	0.01175	-1.1428	10	0.72032	D	0.01	.	13.3018	0.60330	0.0:1.0:0.0:0.0	.	225;225;225;225	A4PB68;Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	Y	225	ENSP00000396117:D225Y;ENSP00000357315:D225Y;ENSP00000271883:D225Y;ENSP00000354322:D225Y	ENSP00000271883:D225Y	D	-	1	0	GON4L	154063276	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	3.586000	0.53950	2.605000	0.88082	0.491000	0.48974	GAT		0.408	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155796652	C	A	155796652	3	1	61	1	0	0	0	0	1	0	0	0	6592	913	32	2	6286	2	GON4L	1	155796652	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61109	155796652	93453969	665	8650										
RIT1	6016	broad.mit.edu	37	chr1	155870193	155870193	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcttcaagttactgaatCtttcttcttccggaatggtg	7	9	5	1	rs545031201		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155870193C>A	ENST00000368323.3	-	6	850	c.646G>T	c.(646-648)Gat>Tat	p.D216Y	RIT1_ENST00000368322.3_Missense_Mutation_p.D233Y|RIT1_ENST00000539040.1_Missense_Mutation_p.D180Y	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	216					GTP catabolic process (GO:0006184)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)	p.D216Y(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			GTTACTGAATCTTTCTTCTTC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											232	237	236					1																	155870193		2203	4300	6503	154136817	SO:0001583	missense	6016			AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622			10023	protein-coding gene	gene with protein product	"Ric-like, expressed in many tissues", "GTP-binding protein Roc1"	609591	"Ric (Drosophila)-like, expressed in many tissues"	RIT		8824319, 8918462	Standard	NM_006912		Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.646G>T	1.37:g.155870193C>A	ENSP00000357306:p.Asp216Tyr		154136817	B4DQE8|O00646|O00720|Q5VY89|Q5VY90	Missense_Mutation	SNP	ENST00000368323.3	37	CCDS1123.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.527626	0.44969	.	.	ENSG00000143622	ENST00000368323;ENST00000539040;ENST00000368322	T;T;T	0.68624	-0.33;0.12;-0.34	5.13	5.13	0.70059	.	0.143694	0.46442	D	0.000295	T	0.32224	0.0822	N	0.08118	0	0.51012	D	0.999905	B	0.23854	0.092	B	0.14578	0.011	T	0.39663	-0.9603	10	0.87932	D	0	.	12.7597	0.57356	0.0:0.9204:0.0:0.0795	.	216	Q92963	RIT1_HUMAN	Y	216;180;233	ENSP00000357306:D216Y;ENSP00000441950:D180Y;ENSP00000357305:D233Y	ENSP00000357305:D233Y	D	-	1	0	RIT1	154136817	0.992000	0.36948	0.789000	0.31954	0.977000	0.68977	2.993000	0.49425	2.665000	0.90641	0.591000	0.81541	GAT		0.423	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	NM_006912		A	155870193	C	A	155870193	3	1	61	1	0	0	0	0	1	0	0	0	13423	913	32	2	17	2	RIT1	1	155870193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73541	155870193	93380428	666	8651										
KIAA0907	22889	broad.mit.edu	37	chr1	155895603	155895603	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtacagcatgttctagaCccacaaataatttatcttga	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:155895603C>T	ENST00000368321.3	-	7	736	c.713G>A	c.(712-714)gGt>gAt	p.G238D	KIAA0907_ENST00000368320.3_Missense_Mutation_p.G238D|KIAA0907_ENST00000482337.1_5'UTR|SCARNA4_ENST00000516999.1_RNA|KIAA0907_ENST00000368319.3_Missense_Mutation_p.G238D	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	238							RNA binding (GO:0003723)	p.G238D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			ATGTTCTAGACCCACAAATAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											66	63	64					1																	155895603		2203	4300	6503	154162227	SO:0001583	missense	22889			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.713G>A	1.37:g.155895603C>T	ENSP00000357304:p.Gly238Asp		154162227	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	37	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511291	0.85389	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	T;T;T	0.42513	0.97;0.97;0.97	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.51568	0.1682	L	0.48935	1.535	0.80722	D	1	D;D;D	0.76494	0.999;0.99;0.996	D;P;P	0.70935	0.971;0.87;0.87	T	0.44298	-0.9337	10	0.45353	T	0.12	-9.8406	19.3789	0.94523	0.0:1.0:0.0:0.0	.	238;238;238	Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;K0907_HUMAN	D	238	ENSP00000357304:G238D;ENSP00000357303:G238D;ENSP00000357302:G238D	ENSP00000357302:G238D	G	-	2	0	KIAA0907	154162227	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.484000	0.81180	2.664000	0.90586	0.650000	0.86243	GGT		0.363	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		T	155895603	C	T	155895603	3	4	61	1	0	0	0	0	1	0	0	0	8220	507	18	3	1163	3	KIAA0907	1	155895603	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25410	155895603	93355018	667	8652										
ROBLD3	28956	broad.mit.edu	37	chr1	156025082	156025082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataacgagggatcactgctgGcctactctggttacggggac	13	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156025082G>T	ENST00000368305.4	+	2	235	c.97G>T	c.(97-99)Gcc>Tcc	p.A33S	LAMTOR2_ENST00000368302.3_Missense_Mutation_p.A33S|UBQLN4_ENST00000472638.1_5'Flank|LAMTOR2_ENST00000368304.5_Missense_Mutation_p.A33S|UBQLN4_ENST00000368309.3_5'Flank|LAMTOR2_ENST00000489664.1_3'UTR	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	33					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)		p.A33S(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						ATCACTGCTGGCCTACTCTGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	114	112					1																	156025082		2203	4300	6503	154291706	SO:0001583	missense	28956			BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"mitogen activated protein binding protein interacting protein", "MAPKSP1 adaptor protein", "endosomal adaptor protein"	610389	"roadblock domain containing 3"	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.97G>T	1.37:g.156025082G>T	ENSP00000357288:p.Ala33Ser		154291706	Q5VY97|Q5VY98|Q5VY99	Missense_Mutation	SNP	ENST00000368305.4	37	CCDS1128.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.924262	0.92319	.	.	ENSG00000116586	ENST00000368305;ENST00000368304;ENST00000368302	T;T;T	0.27402	1.67;1.67;1.67	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.32496	0.0831	L	0.53561	1.675	0.80722	D	1	B;B	0.30104	0.052;0.268	B;P	0.44561	0.122;0.453	T	0.08146	-1.0736	10	0.37606	T	0.19	-11.2792	18.4132	0.90559	0.0:0.0:1.0:0.0	.	33;33	Q5VY98;Q9Y2Q5	.;LTOR2_HUMAN	S	33	ENSP00000357288:A33S;ENSP00000357287:A33S;ENSP00000357285:A33S	ENSP00000357285:A33S	A	+	1	0	LAMTOR2	154291706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.174000	0.94824	2.687000	0.91594	0.655000	0.94253	GCC		0.592	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1	NM_014017		T	156025082	G	T	156025082	3	4	61	1	0	0	0	0	1	0	0	0	13549	1203	42	2	103	2	ROBLD3	1	156025082	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129479	156025082	93225539	668	8653										
MEX3A	92312	broad.mit.edu	37	chr1	156047000	156047000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggctatcgattgctgcgtCggggctccccgccaggaagt	15	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156047000C>T	ENST00000532414.2	-	2	927	c.928G>A	c.(928-930)Gac>Aac	p.D310N	AL355388.1_ENST00000410679.1_RNA|MEX3A_ENST00000442784.1_5'UTR	NM_001093725.1	NP_001087194.1	A1L020	MEX3A_HUMAN	mex-3 RNA binding family member A	310						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D429N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	Hepatocellular(266;0.158)|all_neural(408;0.195)					ATTGCTGCGTCGGGGCTCCCC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	82	78					1																	156047000		2049	4189	6238	154313624	SO:0001583	missense	92312			AK024097	CCDS53377.1	1q22	2013-09-24	2013-08-21	2007-07-18	ENSG00000254726	ENSG00000254726		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	33482	protein-coding gene	gene with protein product		611007	"ring finger and KH domain containing 4", "mex-3 homolog A (C. elegans)"	RKHD4		17267406	Standard	NM_001093725		Approved		uc001fnd.4	A1L020	OTTHUMG00000017465	ENST00000532414.2:c.928G>A	1.37:g.156047000C>T	ENSP00000432845:p.Asp310Asn		154313624		Missense_Mutation	SNP	ENST00000532414.2	37	CCDS53377.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.253876	0.22965	.	.	ENSG00000254726	ENST00000532414	T	0.59083	0.29	5.59	5.59	0.84812	.	0.280305	0.33553	N	0.004796	T	0.39306	0.1073	L	0.42245	1.32	0.39167	D	0.962521	B	0.22480	0.07	B	0.08055	0.003	T	0.27773	-1.0064	10	0.45353	T	0.12	.	18.1563	0.89692	0.0:1.0:0.0:0.0	.	310	A1L020	MEX3A_HUMAN	N	310	ENSP00000432845:D310N	ENSP00000432845:D310N	D	-	1	0	MEX3A	154313624	0.999000	0.42202	0.974000	0.42286	0.058000	0.15608	3.441000	0.52893	2.637000	0.89404	0.313000	0.20887	GAC		0.657	MEX3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046218.3	NM_001093725		T	156047000	C	T	156047000	3	4	61	1	0	0	0	0	1	0	0	0	9539	884	31	1	638	1	MEX3A	1	156047000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21918	156047000	93203621	669	8654										
C1orf85	112770	broad.mit.edu	37	chr1	156265400	156265401	+	Frame_Shift_Ins	INS	-	-	C													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggggctgggggcacagtgINScccccaaccccaggtgcact					rs368515457		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156265400_156265401insC	ENST00000362007.1	-	1	62_63	c.36_37insG	c.(34-39)gggcacfs	p.H13fs	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	13					intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.H13fs*36(1)		breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					GGGGCACAGTGCCCCCAACCCC	0.649																																																1	Insertion - Frameshift(1)	large_intestine(1)	1																																								154532025	SO:0001589	frameshift_variant	112770			BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"kidney lysosomal membrane protein"					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.37dupG	1.37:g.156265405_156265405dupC	ENSP00000354553:p.His13fs		154532024	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Frame_Shift_Ins	INS	ENST00000362007.1	37	CCDS1139.1																																																																																				0.649	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580		C	156265401	-	C	156265400	7	5	61	1	0	1	1	0	0	0	0	0	2068	1319	46	0	1207	0	C1orf85	1	156265400	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	218400	156265400	92985221	670	8655										
RHBG	57127	broad.mit.edu	37	chr1	156354578	156354578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccttccaggtgcctggcGagcatgaggataaagcccag	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156354578G>A	ENST00000368249.1	+	10	1357	c.1319G>A	c.(1318-1320)cGa>cAa	p.R440Q	RHBG_ENST00000255013.3_Missense_Mutation_p.R371Q|RHBG_ENST00000400992.2_Missense_Mutation_p.R408Q|RHBG_ENST00000368246.2_Missense_Mutation_p.E439K|RHBG_ENST00000494874.1_3'UTR	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	440					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.R440Q(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GGTGCCTGGCGAGCATGAGGA	0.602											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											48	56	53					1																	156354578		2001	4156	6157	154621202	SO:0001583	missense	57127			AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"Solute carriers"	14572	protein-coding gene	gene with protein product		607079	"Rhesus blood group, B glycoprotein"			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.1319G>A	1.37:g.156354578G>A	ENSP00000357232:p.Arg440Gln	1777	154621202	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.561|9.561	1.118492|1.118492	0.20877|0.20877	.|.	.|.	ENSG00000132677|ENSG00000132677	ENST00000368246|ENST00000368249;ENST00000400992;ENST00000255013	T|T;T;T	0.19532|0.24538	2.14|2.04;1.85;1.87	5.55|5.55	2.46|2.46	0.29980|0.29980	.|.	.|0.567013	.|0.17914	.|N	.|0.157760	T|T	0.02649|0.02649	0.0080|0.0080	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|P;B	.|0.39071	.|0.658;0.305	.|B;B	.|0.26310	.|0.068;0.031	T|T	0.40117|0.40117	-0.9580|-0.9580	7|10	0.54805|0.16896	T|T	0.06|0.51	-15.2438|-15.2438	8.5837|8.5837	0.33644|0.33644	0.0:0.3185:0.5169:0.1646|0.0:0.3185:0.5169:0.1646	.|.	.|408;477	.|Q9H310-3;Q5SZW5	.|.;.	K|Q	439|440;408;371	ENSP00000357229:E439K|ENSP00000357232:R440Q;ENSP00000383777:R408Q;ENSP00000255013:R371Q	ENSP00000357229:E439K|ENSP00000255013:R371Q	E|R	+|+	1|2	0|0	RHBG|RHBG	154621202|154621202	0.176000|0.176000	0.23096|0.23096	0.046000|0.046000	0.18839|0.18839	0.117000|0.117000	0.20001|0.20001	2.039000|2.039000	0.41193|0.41193	0.702000|0.702000	0.31825|0.31825	-0.225000|-0.225000	0.12378|0.12378	GAG|CGA		0.602	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395		A	156354578	G	A	156354578	3	1	61	1	0	0	0	0	1	0	0	0	13361	1059	37	1	1357	1	RHBG	1	156354578	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89178	156354578	92896043	671	8656										
IQGAP3	128239	broad.mit.edu	37	chr1	156521881	156521881	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaatttcagcagggcatcGaagtaactggcagtggggtg	15	8	1	0	rs377601754		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156521881G>A	ENST00000361170.2	-	14	1465	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	485					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)	p.F485F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCAGGGCATCGAAGTAACTGG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	85	69	74		1455	-0.5	1	1		74	0,8600		0,0,4300	no	coding-synonymous	IQGAP3	NM_178229.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		485/1632	156521881	1,13005	2203	4300	6503	154788505	SO:0001819	synonymous_variant	128239			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1455C>T	1.37:g.156521881G>A			154788505	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																				0.542	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		A	156521881	G	A	156521881	2	1	61	1	0	0	0	0	0	0	0	1	7837	1049	37	1		1	IQGAP3	1	156521881	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167303	156521881	92728740	672	8657										
BCAN	63827	broad.mit.edu	37	chr1	156622065	156622065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacacaatccatggtaccGcccacggggttctcagaaga	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156622065G>A	ENST00000329117.5	+	8	1659	c.1323G>A	c.(1321-1323)ccG>ccA	p.P441P	BCAN_ENST00000361588.5_Silent_p.P441P|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	441	Glu-rich.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.P441P(1)		cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCATGGTACCGCCCACGGGGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	1											58	57	57					1																	156622065		2203	4299	6502	154888689	SO:0001819	synonymous_variant	63827			BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1323G>A	1.37:g.156622065G>A			154888689	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																				0.493	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156622065	G	A	156622065	2	1	61	1	0	0	0	0	0	0	0	1	1346	1074	38	1		1	BCAN	1	156622065	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100184	156622065	92628556	673	8658										
NES	10763	broad.mit.edu	37	chr1	156640514	156640514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctcttcccaggcagctCggagaactctgtccccagac	9	16	3	2	rs529267878		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156640514C>T	ENST00000368223.3	-	4	3598	c.3466G>A	c.(3466-3468)Gag>Aag	p.E1156K		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1156	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)	p.E1156K(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCAGGCAGCTCGGAGAACTCT	0.632													C|||	1	0.000199681	0	0	5008	,	,		15982	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											62	66	65					1																	156640514		2203	4300	6503	154907138	SO:0001583	missense	10763			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3466G>A	1.37:g.156640514C>T	ENSP00000357206:p.Glu1156Lys		154907138	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	7.847	0.723201	0.15439	.	.	ENSG00000132688	ENST00000368223	D	0.86030	-2.06	3.48	-1.05	0.10036	.	.	.	.	.	T	0.53867	0.1823	L	0.36672	1.1	0.09310	N	1	P	0.38370	0.628	B	0.24394	0.053	T	0.42965	-0.9420	9	0.66056	D	0.02	.	6.21	0.20623	0.0:0.5665:0.1868:0.2467	.	1156	P48681	NEST_HUMAN	K	1156	ENSP00000357206:E1156K	ENSP00000357206:E1156K	E	-	1	0	NES	154907138	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.175000	0.03102	-0.443000	0.07180	-0.391000	0.06502	GAG		0.632	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156640514	C	T	156640514	3	4	61	1	0	0	0	0	1	0	0	0	10368	893	31	1	1403	1	NES	1	156640514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18449	156640514	92610107	674	8659										
SH2D2A	9047	broad.mit.edu	37	chr1	156779563	156779563	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcttccaaagtttgattCttcggtcctcagggaaagtc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156779563C>A	ENST00000368199.3	-	6	757	c.604G>T	c.(604-606)Gaa>Taa	p.E202*	SH2D2A_ENST00000368198.3_Nonsense_Mutation_p.E184*|SH2D2A_ENST00000392306.2_Nonsense_Mutation_p.E212*	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A	202	Pro-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)	p.E202Q(1)|p.E202*(1)|p.E212Q(1)		endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAGTTTGATTCTTCGGTCCTC	0.587																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	lung(2)|large_intestine(1)	1											143	135	137					1																	156779563		2203	4300	6503	155046187	SO:0001587	stop_gained	9047			AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"SH2 domain containing"	10821	protein-coding gene	gene with protein product	"T lymphocyte specific adaptor protein", "T cell specific adapter protein TSAd", "T cell specific adpater protein TSAd"	604514	"SH2 domain protein 2A"			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.604G>T	1.37:g.156779563C>A	ENSP00000357182:p.Glu202*		155046187	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Nonsense_Mutation	SNP	ENST00000368199.3	37	CCDS1159.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624844	0.28889	.	.	ENSG00000027869	ENST00000368199;ENST00000368198;ENST00000392306	.	.	.	3.76	1.77	0.24775	.	3.070300	0.00760	N	0.001128	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-0.0061	5.0318	0.14413	0.0:0.6621:0.2155:0.1224	.	.	.	.	X	202;184;212	.	ENSP00000357181:E184X	E	-	1	0	SH2D2A	155046187	0.359000	0.24955	0.050000	0.19076	0.079000	0.17450	0.510000	0.22723	0.332000	0.23536	0.555000	0.69702	GAA		0.587	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975		A	156779563	C	A	156779563	4	1	61	1	0	0	0	0	0	1	0	0	14269	922	32	2	577	2	SH2D2A	1	156779563	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139049	156779563	92471058	675	8660										
INSRR	3645	broad.mit.edu	37	chr1	156816326	156816326	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacctgcaggcagcgttcGgaggtagacgatgggactct	14	11	1	1	rs552398222		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156816326G>A	ENST00000368195.3	-	8	2191	c.1795C>T	c.(1795-1797)Cga>Tga	p.R599*	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	599	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R599*(2)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGCAGCGTTCGGAGGTAGACG	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		19882	0		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(2)	1											102	74	83					1																	156816326		2203	4300	6503	155082950	SO:0001587	stop_gained	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1795C>T	1.37:g.156816326G>A	ENSP00000357178:p.Arg599*		155082950	O60724|Q5VZS3	Nonsense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	43	10.414319	0.99401	.	.	ENSG00000027644	ENST00000368195	.	.	.	5.35	3.49	0.39957	.	0.186794	0.26450	N	0.024318	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3176	0.32111	0.0814:0.0:0.7628:0.1557	.	.	.	.	X	599	.	ENSP00000357178:R599X	R	-	1	2	INSRR	155082950	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.556000	0.73932	0.829000	0.34733	-0.152000	0.13540	CGA		0.577	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156816326	G	A	156816326	4	1	61	1	0	0	0	0	0	1	0	0	7795	1124	39	1	2157	1	INSRR	1	156816326	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36763	156816326	92434295	676	8661										
ARHGEF11	9826	broad.mit.edu	37	chr1	156911187	156911187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcagctcctcaggttcaGgttcaccatggaacacgtct	10	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:156911187G>T	ENST00000361409.2	-	34	4113	c.3371C>A	c.(3370-3372)cCt>cAt	p.P1124H	ARHGEF11_ENST00000315174.8_Missense_Mutation_p.P540H|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.P1164H|ARHGEF11_ENST00000487682.1_5'UTR	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1124					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P1164H(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTCAGGTTCAGGTTCACCATG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	93	96					1																	156911187		2203	4300	6503	155177811	SO:0001583	missense	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3371C>A	1.37:g.156911187G>T	ENSP00000354644:p.Pro1124His		155177811	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.682722	0.29872	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.65364	-0.15;-0.15;-0.05	4.61	2.43	0.29744	.	0.871688	0.09800	N	0.754221	T	0.35422	0.0931	N	0.19112	0.55	0.09310	N	1	P;P;P	0.42993	0.797;0.694;0.797	P;B;B	0.47470	0.548;0.243;0.424	T	0.23583	-1.0184	10	0.72032	D	0.01	0.0125	7.4696	0.27340	0.0:0.2873:0.5378:0.1749	.	540;1124;1164	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	H	1164;1124;540	ENSP00000357177:P1164H;ENSP00000354644:P1124H;ENSP00000313470:P540H	ENSP00000313470:P540H	P	-	2	0	ARHGEF11	155177811	0.094000	0.21725	0.001000	0.08648	0.027000	0.11550	1.779000	0.38624	0.460000	0.27045	0.462000	0.41574	CCT		0.547	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156911187	G	T	156911187	3	4	61	1	0	0	0	0	1	0	0	0	896	1000	35	2	1225	2	ARHGEF11	1	156911187	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94861	156911187	92339434	677	8662										
ETV3	2117	broad.mit.edu	37	chr1	157103953	157103953	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggcatcaccagcttgttGaagttaaatttataggtaaa	9	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157103953G>T	ENST00000368192.4	-	4	415	c.351C>A	c.(349-351)ttC>ttA	p.F117L	ETV3_ENST00000460850.1_5'Flank|ETV3_ENST00000326786.4_Missense_Mutation_p.F117L	NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	117					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.F117L(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				CCAGCTTGTTGAAGTTAAATT	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	1											166	149	154					1																	157103953		2203	4300	6503	155370577	SO:0001583	missense	2117			BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.351C>A	1.37:g.157103953G>T	ENSP00000357175:p.Phe117Leu		155370577	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	ENST00000368192.4	37	CCDS44250.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.166555	0.57476	.	.	ENSG00000117036	ENST00000368192;ENST00000326786	T;T	0.55760	0.5;0.5	6.17	3.34	0.38264	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (2);	0.183156	0.37761	N	0.001959	T	0.51787	0.1695	L	0.52364	1.645	0.49483	D	0.999797	B;D	0.55605	0.033;0.972	B;D	0.64687	0.036;0.928	T	0.56300	-0.8002	10	0.72032	D	0.01	.	10.8377	0.46696	0.2057:0.0:0.7943:0.0	.	117;117	P41162-2;P41162	.;ETV3_HUMAN	L	117	ENSP00000357175:F117L;ENSP00000327316:F117L	ENSP00000327316:F117L	F	-	3	2	ETV3	155370577	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.036000	0.57304	0.497000	0.27926	-0.150000	0.13652	TTC		0.333	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		T	157103953	G	T	157103953	3	4	61	1	0	0	0	0	1	0	0	0	5292	1281	45	2	1227	2	ETV3	1	157103953	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192766	157103953	92146668	678	8663										
FCRL5	83416	broad.mit.edu	37	chr1	157508987	157508987	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaagctgatggccactcCtcctgcagagttggccgacc	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157508987C>A	ENST00000361835.3	-	7	1448	c.1291G>T	c.(1291-1293)Gga>Tga	p.G431*	FCRL5_ENST00000356953.4_Nonsense_Mutation_p.G431*|FCRL5_ENST00000368190.3_Nonsense_Mutation_p.G431*|FCRL5_ENST00000368191.3_Nonsense_Mutation_p.G346*|FCRL5_ENST00000368189.3_Nonsense_Mutation_p.G431*	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	431	Ig-like C2-type 4.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.G431*(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ATGGCCACTCCTCCTGCAGAG	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											77	65	69					1																	157508987		2203	4300	6503	155775611	SO:0001587	stop_gained	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1291G>T	1.37:g.157508987C>A	ENSP00000354691:p.Gly431*		155775611	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Nonsense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251598	0.80135	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	.	.	.	3.17	-3.58	0.04597	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	8.281	0.31900	0.0:0.3625:0.0:0.6375	.	.	.	.	X	431;431;431;346;431	.	ENSP00000349434:G431X	G	-	1	0	FCRL5	155775611	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.631000	0.00871	-0.988000	0.03489	0.462000	0.41574	GGA		0.572	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157508987	C	A	157508987	4	1	61	1	0	0	0	0	0	1	0	0	5817	690	24	2	1686	2	FCRL5	1	157508987	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	405034	157508987	91741634	679	8664										
FCRL3	115352	broad.mit.edu	37	chr1	157648642	157648642	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgaatagaggactgtaAgttcctggtagaaaaaaaca	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157648642A>C	ENST00000368184.3	-	15	2354	c.2063T>G	c.(2062-2064)cTt>cGt	p.L688R	FCRL3_ENST00000473231.1_5'UTR|FCRL3_ENST00000368186.5_Missense_Mutation_p.L688R	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	688						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L688R(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					GAGGACTGTAAGTTCCTGGTA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	111	113					1																	157648642		2203	4300	6503	155915266	SO:0001583	missense	115352			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.2063T>G	1.37:g.157648642A>C	ENSP00000357167:p.Leu688Arg		155915266	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607011	0.28623	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.48836	0.81;0.8	3.75	0.582	0.17412	.	4.901340	0.00799	N	0.001404	T	0.20414	0.0491	L	0.29908	0.895	0.09310	N	1	B;P;P	0.47677	0.205;0.899;0.893	B;P;B	0.45881	0.013;0.496;0.396	T	0.05801	-1.0863	10	0.52906	T	0.07	.	2.4877	0.04602	0.289:0.0:0.4803:0.2307	.	688;593;688	Q96P31;D3DVD1;Q96P31-6	FCRL3_HUMAN;.;.	R	688	ENSP00000357169:L688R;ENSP00000357167:L688R	ENSP00000292392:L688R	L	-	2	0	FCRL3	155915266	0.000000	0.05858	0.082000	0.20525	0.024000	0.10985	0.090000	0.15025	0.106000	0.17784	-0.336000	0.08194	CTT		0.463	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		C	157648642	A	C	157648642	3	2	61	1	0	0	0	0	1	0	0	0	5815	72	3	4	145	4	FCRL3	1	157648642	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	139655	157648642	91601979	680	8665										
FCRL3	115352	broad.mit.edu	37	chr1	157665845	157665845	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacttctcacggtgactcGaatccacgtgctgaggatgg	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157665845G>A	ENST00000368184.3	-	7	1408	c.1117C>T	c.(1117-1119)Cga>Tga	p.R373*	FCRL3_ENST00000473231.1_5'UTR|RP11-367J7.3_ENST00000453692.1_RNA|FCRL3_ENST00000368186.5_Nonsense_Mutation_p.R373*	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	373						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R373*(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ACGGTGACTCGAATCCACGTG	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											112	99	104					1																	157665845		2203	4300	6503	155932469	SO:0001587	stop_gained	115352			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.1117C>T	1.37:g.157665845G>A	ENSP00000357167:p.Arg373*		155932469	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Nonsense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926830	0.92319	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	.	.	.	5.67	-0.271	0.12922	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	4.7954	0.13270	0.0:0.2127:0.3156:0.4717	.	.	.	.	X	373	.	ENSP00000292392:R373X	R	-	1	2	FCRL3	155932469	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.199000	0.09491	-0.143000	0.11334	-0.262000	0.10625	CGA		0.517	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		A	157665845	G	A	157665845	4	1	61	1	0	0	0	0	0	1	0	0	5815	1066	37	1	1123	1	FCRL3	1	157665845	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17203	157665845	91584776	681	8666										
FCRL3	115352	broad.mit.edu	37	chr1	157666947	157666947	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactctgtacacgtatctgaGatctcaggctcctttttttg	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157666947G>T	ENST00000368184.3	-	6	1118	c.827C>A	c.(826-828)tCt>tAt	p.S276Y	FCRL3_ENST00000473231.1_5'UTR|RP11-367J7.3_ENST00000453692.1_RNA|FCRL3_ENST00000368186.5_Missense_Mutation_p.S276Y	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	276						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S276Y(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ACGTATCTGAGATCTCAGGCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											97	82	87					1																	157666947		2203	4300	6503	155933571	SO:0001583	missense	115352			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.827C>A	1.37:g.157666947G>T	ENSP00000357167:p.Ser276Tyr		155933571	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.793299	0.50102	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.10960	2.82;2.82	5.85	-0.112	0.13572	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.593500	0.01630	N	0.023519	T	0.18383	0.0441	M	0.88640	2.97	0.09310	N	1	D;P	0.54964	0.969;0.82	P;P	0.61132	0.862;0.884	T	0.02301	-1.1180	10	0.66056	D	0.02	.	4.811	0.13344	0.3805:0.0:0.4749:0.1445	.	276;276	Q96P31;Q96P31-6	FCRL3_HUMAN;.	Y	276	ENSP00000357169:S276Y;ENSP00000357167:S276Y	ENSP00000292392:S276Y	S	-	2	0	FCRL3	155933571	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.056000	0.14256	0.077000	0.16863	0.491000	0.48974	TCT		0.537	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		T	157666947	G	T	157666947	3	4	61	1	0	0	0	0	1	0	0	0	5815	942	33	2	1417	2	FCRL3	1	157666947	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1102	157666947	91583674	682	8667										
FCRL2	79368	broad.mit.edu	37	chr1	157739665	157739665	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatacttgctctgcacgtGaatctgggattggaggctct	12	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157739665G>T	ENST00000361516.3	-	4	634	c.586C>A	c.(586-588)Cac>Aac	p.H196N	FCRL2_ENST00000392274.3_Missense_Mutation_p.H196N|FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000469986.1_5'Flank	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	196					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.H196N(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTCTGCACGTGAATCTGGGAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	81	81					1																	157739665		2203	4300	6503	156006289	SO:0001583	missense	79368			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.586C>A	1.37:g.157739665G>T	ENSP00000355157:p.His196Asn		156006289	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	G	1.208	-0.630444	0.03610	.	.	ENSG00000132704	ENST00000361516;ENST00000392274	T;T	0.11385	2.78;2.78	4.03	2.11	0.27256	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.497730	0.04581	N	0.395039	T	0.02767	0.0083	L	0.43598	1.365	0.09310	N	1	B;B;B	0.16396	0.017;0.004;0.015	B;B;B	0.16722	0.016;0.007;0.007	T	0.42982	-0.9419	10	0.15066	T	0.55	.	5.263	0.15584	0.1149:0.2221:0.6631:0.0	.	196;196;196	B4E0W2;B4DVJ9;Q96LA5	.;.;FCRL2_HUMAN	N	196	ENSP00000355157:H196N;ENSP00000376100:H196N	ENSP00000355157:H196N	H	-	1	0	FCRL2	156006289	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-0.009000	0.12765	0.629000	0.30376	0.655000	0.94253	CAC		0.478	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		T	157739665	G	T	157739665	3	4	61	1	0	0	0	0	1	0	0	0	5814	1290	45	2	976	2	FCRL2	1	157739665	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72718	157739665	91510956	683	8668										
FCRL2	79368	broad.mit.edu	37	chr1	157740375	157740375	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaagccatcttctgaattTtccagttctgttctccctgg	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157740375T>G	ENST00000361516.3	-	3	182	c.134A>C	c.(133-135)aAa>aCa	p.K45T	FCRL2_ENST00000392274.3_Missense_Mutation_p.K45T|FCRL2_ENST00000368181.4_Missense_Mutation_p.K45T|FCRL2_ENST00000469986.1_5'Flank	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	45	Ig-like C2-type 1.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.K45T(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTTCTGAATTTTCCAGTTCTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	67	67					1																	157740375		2203	4300	6503	156006999	SO:0001583	missense	79368			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.134A>C	1.37:g.157740375T>G	ENSP00000355157:p.Lys45Thr		156006999	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	T	8.077	0.771631	0.16051	.	.	ENSG00000132704	ENST00000292389;ENST00000361516;ENST00000368181;ENST00000392274	T;T;T	0.10960	2.82;2.82;2.82	4.33	-3.33	0.04958	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	4.471960	0.01053	U	0.004507	T	0.05227	0.0139	L	0.34521	1.04	0.09310	N	1	B;P;P;B	0.43662	0.001;0.814;0.782;0.036	B;P;P;B	0.46172	0.008;0.484;0.506;0.05	T	0.34925	-0.9809	10	0.72032	D	0.01	.	10.7881	0.46417	0.0:0.6106:0.0:0.3894	.	45;45;45;45	B4E0W2;B4DVJ9;Q96LA5-5;Q96LA5	.;.;.;FCRL2_HUMAN	T	45	ENSP00000355157:K45T;ENSP00000357163:K45T;ENSP00000376100:K45T	ENSP00000292389:K45T	K	-	2	0	FCRL2	156006999	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.835000	0.01692	-0.537000	0.06290	-0.263000	0.10527	AAA		0.428	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		G	157740375	T	G	157740375	3	3	61	1	0	0	0	0	1	0	0	0	5814	1841	64	4	1432	4	FCRL2	1	157740375	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	710	157740375	91510246	684	8669										
CD5L	922	broad.mit.edu	37	chr1	157803134	157803134	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccatagcatttccggtctCtgaaggagggagagagggac	16	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157803134C>A	ENST00000368174.4	-	5	983	c.887G>T	c.(886-888)aGa>aTa	p.R296I	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	296	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.R296I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TTTCCGGTCTCTGAAGGAGGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	117	116					1																	157803134		2203	4300	6503	156069758	SO:0001583	missense	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.887G>T	1.37:g.157803134C>A	ENSP00000357156:p.Arg296Ile		156069758	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	C	2.748	-0.260692	0.05791	.	.	ENSG00000073754	ENST00000368174	T	0.36157	1.27	4.84	1.14	0.20703	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	3.435030	0.00792	N	0.001352	T	0.10380	0.0254	N	0.16478	0.41	0.09310	N	1	B	0.22276	0.067	B	0.27380	0.079	T	0.20940	-1.0260	10	0.38643	T	0.18	.	7.6731	0.28470	0.0:0.2904:0.0:0.7096	.	296	O43866	CD5L_HUMAN	I	296	ENSP00000357156:R296I	ENSP00000357156:R296I	R	-	2	0	CD5L	156069758	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.868000	0.04236	0.323000	0.23307	-0.294000	0.09567	AGA		0.577	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157803134	C	A	157803134	3	1	61	1	0	0	0	0	1	0	0	0	3033	913	32	2	164	2	CD5L	1	157803134	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62759	157803134	91447487	685	8670										
CD5L	922	broad.mit.edu	37	chr1	157805906	157805906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccacccgcccttcacagCggtggaggccccccaccagc	9	22	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:157805906C>T	ENST00000368174.4	-	3	191	c.95G>A	c.(94-96)cGc>cAc	p.R32H	CD5L_ENST00000484609.1_5'UTR	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	32	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.R32H(3)|p.R32P(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CCCTTCACAGCGGTGGAGGCC	0.622																																																4	Substitution - Missense(4)	urinary_tract(1)|large_intestine(1)|lung(1)|endometrium(1)	1											43	46	45					1																	157805906		2203	4300	6503	156072530	SO:0001583	missense	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.95G>A	1.37:g.157805906C>T	ENSP00000357156:p.Arg32His		156072530	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256784	0.39896	.	.	ENSG00000073754	ENST00000368174	T	0.36340	1.26	4.85	1.9	0.25705	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.150671	0.31312	N	0.007862	T	0.11281	0.0275	L	0.43598	1.365	0.26669	N	0.971761	P	0.50819	0.939	B	0.39027	0.288	T	0.10567	-1.0624	10	0.40728	T	0.16	.	7.7613	0.28955	0.0:0.709:0.0:0.291	.	32	O43866	CD5L_HUMAN	H	32	ENSP00000357156:R32H	ENSP00000357156:R32H	R	-	2	0	CD5L	156072530	0.000000	0.05858	0.569000	0.28460	0.331000	0.28603	-0.759000	0.04761	0.221000	0.20879	0.563000	0.77884	CGC		0.622	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		T	157805906	C	T	157805906	3	4	61	1	0	0	0	0	1	0	0	0	3033	768	27	1	964	1	CD5L	1	157805906	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2772	157805906	91444715	686	8671										
CD1D	912	broad.mit.edu	37	chr1	158152678	158152678	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggatacagtgaagcccaaGgcctggctgtcccgtggccc	13	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158152678G>T	ENST00000368171.3	+	5	1117	c.618G>T	c.(616-618)aaG>aaT	p.K206N		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	206	Ig-like.				antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)	p.K206N(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					TGAAGCCCAAGGCCTGGCTGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	77	76					1																	158152678		2203	4300	6503	156419302	SO:0001583	missense	912			BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1637	protein-coding gene	gene with protein product		188410	"CD1D antigen, d polypeptide", "CD1d antigen"			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.618G>T	1.37:g.158152678G>T	ENSP00000357153:p.Lys206Asn		156419302	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Missense_Mutation	SNP	ENST00000368171.3	37	CCDS1173.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306373	0.40795	.	.	ENSG00000158473	ENST00000368171	T	0.01665	4.7	5.18	1.73	0.24493	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);	1.182760	0.06173	N	0.678094	T	0.00845	0.0028	M	0.64260	1.97	0.21984	N	0.99943	B	0.32753	0.383	B	0.20955	0.032	T	0.46247	-0.9205	10	0.87932	D	0	-2.0586	5.9386	0.19179	0.3721:0.0:0.6279:0.0	.	206	P15813	CD1D_HUMAN	N	206	ENSP00000357153:K206N	ENSP00000357153:K206N	K	+	3	2	CD1D	156419302	0.531000	0.26338	0.684000	0.30055	0.991000	0.79684	0.145000	0.16157	0.672000	0.31204	0.655000	0.94253	AAG		0.547	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		T	158152678	G	T	158152678	3	4	61	1	0	0	0	0	1	0	0	0	2983	991	35	2	632	2	CD1D	1	158152678	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346772	158152678	91097943	687	8672										
CD1A	909	broad.mit.edu	37	chr1	158224912	158224912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccatgtcacctggatcGcatccttttacaaccattcc	4	16	1	0	rs140904380		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158224912G>A	ENST00000289429.5	+	2	630	c.97G>A	c.(97-99)Gca>Aca	p.A33T		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	33					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.A33T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	CACCTGGATCGCATCCTTTTA	0.468													G|||	1	0.000199681	8e-04	0	5008	,	,		20436	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	THR/ALA	0,4406		0,0,2203	137	115	123		97	-0.8	0	1	dbSNP_134	123	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CD1A	NM_001763.2	58	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	benign	33/328	158224912	5,13001	2203	4300	6503	156491536	SO:0001583	missense	909			M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.97G>A	1.37:g.158224912G>A	ENSP00000289429:p.Ala33Thr		156491536	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	37	CCDS1174.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	10.67	1.414423	0.25465	0.0	5.81E-4	ENSG00000158477	ENST00000289429	T	0.18174	2.23	4.54	-0.785	0.10950	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.826170	0.03768	N	0.259261	T	0.02267	0.0070	N	0.04203	-0.255	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.41502	-0.9505	10	0.51188	T	0.08	-0.0225	4.9472	0.13994	0.3014:0.0:0.3237:0.3748	.	33	P06126	CD1A_HUMAN	T	33	ENSP00000289429:A33T	ENSP00000289429:A33T	A	+	1	0	CD1A	156491536	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.636000	0.05465	-0.297000	0.08934	-1.810000	0.00614	GCA		0.468	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		A	158224912	G	A	158224912	3	1	61	1	0	0	0	0	1	0	0	0	2980	1087	38	1	103	1	CD1A	1	158224912	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72234	158224912	91025709	688	8673										
CD1C	911	broad.mit.edu	37	chr1	158261186	158261186	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcaagtcaagattactcGaaatgtaagttcaatcatct	6	8	4	1	rs116022586		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158261186G>A	ENST00000368170.3	+	2	603	c.324G>A	c.(322-324)tcG>tcA	p.S108S		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	108					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)	p.S108S(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					AAGATTACTCGAAATGTAAGT	0.358													G|||	1	0.000199681	0	0	5008	,	,		20470	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											79	78	78					1																	158261186		2203	4300	6503	156527810	SO:0001819	synonymous_variant	911			M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.324G>A	1.37:g.158261186G>A			156527810	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Silent	SNP	ENST00000368170.3	37	CCDS1175.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	-	1.194	-0.634396	0.03584	.	.	ENSG00000158481	ENST00000443761	.	.	.	3.52	-7.03	0.01584	.	.	.	.	.	T	0.04048	0.0113	.	.	.	0.20403	N	0.999906	.	.	.	.	.	.	T	0.09509	-1.0671	4	.	.	.	.	1.9632	0.03390	0.1547:0.1239:0.3972:0.3242	.	.	.	.	K	43	.	.	E	+	1	0	CD1C	156527810	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.544000	0.00019	-5.865000	0.00008	-2.289000	0.00267	GAA		0.358	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		A	158261186	G	A	158261186	2	1	61	1	0	0	0	0	0	0	0	1	2982	1045	37	1		1	CD1C	1	158261186	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36274	158261186	90989435	689	8674										
OR10T2	128360	broad.mit.edu	37	chr1	158368620	158368620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataggatatgagaattaacaGaaaaggcaccataattacca	7	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158368620G>T	ENST00000334438.1	-	1	636	c.637C>A	c.(637-639)Ctg>Atg	p.L213M		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L213M(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					AGAATTAACAGAAAAGGCACC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	59	59					1																	158368620		2203	4300	6503	156635244	SO:0001583	missense	128360			AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"GPCR / Class A : Olfactory receptors"	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.637C>A	1.37:g.158368620G>T	ENSP00000334115:p.Leu213Met		156635244	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.826096	0.32237	.	.	ENSG00000186306	ENST00000334438	T	0.44083	0.93	4.57	-0.0451	0.13853	GPCR, rhodopsin-like superfamily (1);	0.499688	0.14898	N	0.291971	T	0.15132	0.0365	L	0.41415	1.275	0.09310	N	1	B	0.26547	0.152	B	0.36766	0.232	T	0.36841	-0.9731	10	0.30078	T	0.28	.	5.4465	0.16537	0.0785:0.3909:0.397:0.1335	.	213	Q8NGX3	O10T2_HUMAN	M	213	ENSP00000334115:L213M	ENSP00000334115:L213M	L	-	1	2	OR10T2	156635244	0.000000	0.05858	0.013000	0.15412	0.804000	0.45430	-2.783000	0.00772	0.119000	0.18210	0.655000	0.94253	CTG		0.468	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		T	158368620	G	T	158368620	3	4	61	1	0	0	0	0	1	0	0	0	10950	933	33	2	309	2	OR10T2	1	158368620	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107434	158368620	90882001	690	8675										
OR10R2	343406	broad.mit.edu	37	chr1	158449677	158449677	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggagtgcatgccccaaAttcttatattcacatacctg	6	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158449677A>C	ENST00000368152.1	+	1	10	c.10A>C	c.(10-12)Att>Ctt	p.I4L	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I4L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					CATGCCCCAAATTCTTATATT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	128	128					1																	158449677		2203	4300	6503	156716301	SO:0001583	missense	343406			AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"GPCR / Class A : Olfactory receptors"	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.10A>C	1.37:g.158449677A>C	ENSP00000357134:p.Ile4Leu		156716301	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	a	0.097	-1.157534	0.01686	.	.	ENSG00000198965	ENST00000368152	T	0.00000	9.95	3.88	-7.09	0.01553	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08659	-1.0711	9	0.21014	T	0.42	.	1.2959	0.02070	0.2197:0.3055:0.0953:0.3795	.	4	Q8NGX6	O10R2_HUMAN	L	4	ENSP00000357134:I4L	ENSP00000357134:I4L	I	+	1	0	OR10R2	156716301	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.446000	0.06837	-1.088000	0.03077	-0.403000	0.06358	ATT		0.423	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472		C	158449677	A	C	158449677	3	2	61	1	0	0	0	0	1	0	0	0	10948	101	4	4	12	4	OR10R2	1	158449677	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	81057	158449677	90800944	691	8676										
OR6Y1	391112	broad.mit.edu	37	chr1	158517671	158517671	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgactgtgacataccacatCtccaggaaggagaggtggct	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158517671C>A	ENST00000302617.3	-	1	224	c.225G>T	c.(223-225)gaG>gaT	p.E75D		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E75D(1)		NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					CATACCACATCTCCAGGAAGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	93	95					1																	158517671		2202	4300	6502	156784295	SO:0001583	missense	391112			BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.225G>T	1.37:g.158517671C>A	ENSP00000304807:p.Glu75Asp		156784295	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.527128	0.44969	.	.	ENSG00000197532	ENST00000302617	T	0.00008	9.61	4.91	2.04	0.26737	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000703	T	0.00039	0.0001	N	0.21097	0.63	0.27702	N	0.945764	D	0.89917	1.0	D	0.83275	0.996	T	0.32824	-0.9892	10	0.02654	T	1	.	5.0082	0.14298	0.0:0.5015:0.2428:0.2557	.	75	Q8NGX8	OR6Y1_HUMAN	D	75	ENSP00000304807:E75D	ENSP00000304807:E75D	E	-	3	2	OR6Y1	156784295	0.001000	0.12720	1.000000	0.80357	0.979000	0.70002	-0.905000	0.04075	0.359000	0.24239	-0.244000	0.11960	GAG		0.453	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		A	158517671	C	A	158517671	3	1	61	1	0	0	0	0	1	0	0	0	11244	912	32	2	754	2	OR6Y1	1	158517671	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67994	158517671	90732950	692	8677										
OR10Z1	128368	broad.mit.edu	37	chr1	158576933	158576933	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctctgctgaggggcagaaGaaggccttctccacttgtgc	12	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158576933G>T	ENST00000361284.1	+	1	705	c.705G>T	c.(703-705)aaG>aaT	p.K235N		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K235N(1)		endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AGGGGCAGAAGAAGGCCTTCT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											171	172	172					1																	158576933		2203	4300	6503	156843557	SO:0001583	missense	128368			AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.705G>T	1.37:g.158576933G>T	ENSP00000354707:p.Lys235Asn		156843557	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.724975	0.48833	.	.	ENSG00000198967	ENST00000361284	T	0.00137	8.68	5.25	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.225081	0.24786	N	0.035604	T	0.00073	0.0002	M	0.66939	2.045	0.23243	N	0.998052	P	0.34615	0.459	B	0.37650	0.255	T	0.05599	-1.0875	10	0.59425	D	0.04	.	6.0585	0.19824	0.516:0.0:0.484:0.0	.	235	Q8NGY1	O10Z1_HUMAN	N	235	ENSP00000354707:K235N	ENSP00000354707:K235N	K	+	3	2	OR10Z1	156843557	0.006000	0.16342	0.929000	0.37066	0.978000	0.69477	0.031000	0.13710	0.638000	0.30545	0.650000	0.86243	AAG		0.512	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576933	G	T	158576933	3	4	61	1	0	0	0	0	1	0	0	0	10954	933	33	2	707	2	OR10Z1	1	158576933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59262	158576933	90673688	693	8678										
SPTA1	6708	broad.mit.edu	37	chr1	158609681	158609681	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagagccagaactcaaaGtcccggatgcttgtgttgaa	11	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158609681G>A	ENST00000368147.4	-	34	5034	c.4854C>T	c.(4852-4854)gaC>gaT	p.D1618D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1618					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.D1618D(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGAACTCAAAGTCCCGGATGC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											186	175	179					1																	158609681		1906	4117	6023	156876305	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4854C>T	1.37:g.158609681G>A			156876305	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158609681	G	A	158609681	2	1	61	1	0	0	0	0	0	0	0	1	15155	1020	36	3		3	SPTA1	1	158609681	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32748	158609681	90640940	694	8679										
SPTA1	6708	broad.mit.edu	37	chr1	158622424	158622424	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtctgcgttcttctgcccGatccaagagggagcggtatc	12	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158622424G>A	ENST00000368147.4	-	23	3388	c.3208C>T	c.(3208-3210)Cgg>Tgg	p.R1070W		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1070					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R1070W(1)|p.R1070R(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTTCTGCCCGATCCAAGAGG	0.428																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	1											91	84	86					1																	158622424		1871	4102	5973	156889048	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3208C>T	1.37:g.158622424G>A	ENSP00000357129:p.Arg1070Trp		156889048	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883448	0.33255	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.67523	-0.27;-0.27	5.3	2.21	0.28008	.	0.000000	0.29745	N	0.011301	T	0.65471	0.2694	L	0.51422	1.61	0.30771	N	0.742984	D	0.76494	0.999	D	0.68765	0.96	T	0.64228	-0.6457	10	0.52906	T	0.07	.	13.4118	0.60946	0.0:0.0:0.438:0.562	.	1070	P02549	SPTA1_HUMAN	W	1070	ENSP00000357130:R1070W;ENSP00000357129:R1070W	ENSP00000357129:R1070W	R	-	1	2	SPTA1	156889048	0.713000	0.27926	0.411000	0.26484	0.056000	0.15407	0.736000	0.26130	0.768000	0.33290	-0.182000	0.12963	CGG		0.428	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158622424	G	A	158622424	3	1	61	1	0	0	0	0	1	0	0	0	15155	1057	37	1	4171	1	SPTA1	1	158622424	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12743	158622424	90628197	695	8680										
SPTA1	6708	broad.mit.edu	37	chr1	158623165	158623165	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggccagtcttctgacataGacagctgggacaatgccctg	12	11	2	2	rs371406234		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158623165G>T	ENST00000368147.4	-	22	3267	c.3087C>A	c.(3085-3087)gtC>gtA	p.V1029V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1029	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.V1029V(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCTGACATAGACAGCTGGGA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											95	96	96					1																	158623165		2042	4179	6221	156889789	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3087C>A	1.37:g.158623165G>T			156889789	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.552	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158623165	G	T	158623165	2	4	61	1	0	0	0	0	0	0	0	1	15155	929	33	2		2	SPTA1	1	158623165	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	741	158623165	90627456	696	8681										
SPTA1	6708	broad.mit.edu	37	chr1	158639215	158639215	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccttgtaatcttcatcatCtgccaactttttcttcttgt	3	11	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158639215C>A	ENST00000368147.4	-	14	1996	c.1816G>T	c.(1816-1818)Gat>Tat	p.D606Y		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	606					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.D606Y(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTTCATCATCTGCCAACTTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											285	268	273					1																	158639215		1918	4136	6054	156905839	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1816G>T	1.37:g.158639215C>A	ENSP00000357129:p.Asp606Tyr		156905839	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536711	0.65085	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51071	0.72;0.72	4.72	4.72	0.59763	.	0.000000	0.33309	N	0.005054	T	0.46171	0.1379	L	0.47716	1.5	0.40352	D	0.979146	D	0.61697	0.99	D	0.64506	0.926	T	0.51116	-0.8746	10	0.66056	D	0.02	.	7.2763	0.26286	0.0:0.8222:0.0:0.1778	.	606	P02549	SPTA1_HUMAN	Y	606	ENSP00000357130:D606Y;ENSP00000357129:D606Y	ENSP00000357129:D606Y	D	-	1	0	SPTA1	156905839	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.220000	0.65267	2.618000	0.88619	0.655000	0.94253	GAT		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158639215	C	A	158639215	3	1	61	1	0	0	0	0	1	0	0	0	15155	913	32	2	5599	2	SPTA1	1	158639215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16050	158639215	90611406	697	8682										
OR6K2	81448	broad.mit.edu	37	chr1	158670073	158670073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagagggctgcatatggCcaggtagtggtcaaaggcca	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158670073C>T	ENST00000359610.2	-	1	413	c.370G>A	c.(370-372)Gcc>Acc	p.A124T		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A124T(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					CTGCATATGGCCAGGTAGTGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	105	109					1																	158670073		2203	4300	6503	156936697	SO:0001583	missense	81448			BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.370G>A	1.37:g.158670073C>T	ENSP00000352626:p.Ala124Thr		156936697	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238812	0.79800	.	.	ENSG00000196171	ENST00000359610	T	0.01947	4.54	4.7	4.7	0.59300	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38005	N	0.001850	T	0.13970	0.0338	H	0.96142	3.775	0.40301	D	0.978616	D	0.76494	0.999	D	0.65987	0.94	T	0.10474	-1.0628	10	0.87932	D	0	-10.1739	16.574	0.84632	0.0:1.0:0.0:0.0	.	124	Q8NGY2	OR6K2_HUMAN	T	124	ENSP00000352626:A124T	ENSP00000352626:A124T	A	-	1	0	OR6K2	156936697	0.996000	0.38824	1.000000	0.80357	0.908000	0.53690	3.493000	0.53266	2.413000	0.81919	0.650000	0.86243	GCC		0.473	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		T	158670073	C	T	158670073	3	4	61	1	0	0	0	0	1	0	0	0	11233	739	26	3	608	3	OR6K2	1	158670073	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30858	158670073	90580548	698	8683										
OR6K6	128371	broad.mit.edu	37	chr1	158724992	158724992	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggctgcctcctgcagatGtactttttccactcacttgg	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158724992G>T	ENST00000368144.2	+	1	483	c.387G>T	c.(385-387)atG>atT	p.M129I		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M129I(1)		endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					TCCTGCAGATGTACTTTTTCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	75	76					1																	158724992		2203	4300	6503	156991616	SO:0001583	missense	128371			BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.387G>T	1.37:g.158724992G>T	ENSP00000357126:p.Met129Ile		156991616	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	37	CCDS30904.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.523541	0.27299	.	.	ENSG00000180433	ENST00000368144	T	0.02015	4.5	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000055	T	0.00967	0.0032	L	0.37750	1.13	0.35695	D	0.815136	B	0.32245	0.361	B	0.28784	0.094	T	0.56914	-0.7900	10	0.39692	T	0.17	-24.6507	9.3473	0.38115	0.0:0.1548:0.6848:0.1604	.	129	Q8NGW6	OR6K6_HUMAN	I	129	ENSP00000357126:M129I	ENSP00000357126:M129I	M	+	3	0	OR6K6	156991616	0.994000	0.37717	1.000000	0.80357	0.907000	0.53573	0.805000	0.27112	2.848000	0.98002	0.655000	0.94253	ATG		0.502	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		T	158724992	G	T	158724992	3	4	61	1	0	0	0	0	1	0	0	0	11235	1377	48	2	389	2	OR6K6	1	158724992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54919	158724992	90525629	699	8684										
OR6N1	128372	broad.mit.edu	37	chr1	158735886	158735886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttataacaaaatctactaggAcatttatagacgtatcagtg	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158735886A>G	ENST00000335094.2	-	1	606	c.587T>C	c.(586-588)gTc>gCc	p.V196A		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V196A(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					ATCTACTAGGACATTTATAGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	111	109					1																	158735886		2203	4300	6503	157002510	SO:0001583	missense	128372			BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"GPCR / Class A : Olfactory receptors"	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.587T>C	1.37:g.158735886A>G	ENSP00000335535:p.Val196Ala		157002510	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	.	.	.	.	.	.	.	.	.	.	A	12.09	1.834464	0.32421	.	.	ENSG00000197403	ENST00000335094	T	0.00069	8.77	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.170242	0.27917	N	0.017321	T	0.00073	0.0002	N	0.12853	0.265	0.09310	N	0.999999	P	0.52170	0.951	P	0.53035	0.716	T	0.02179	-1.1200	10	0.54805	T	0.06	-18.139	7.7837	0.29080	0.8143:0.0:0.0:0.1857	.	196	Q8NGY5	OR6N1_HUMAN	A	196	ENSP00000335535:V196A	ENSP00000335535:V196A	V	-	2	0	OR6N1	157002510	0.000000	0.05858	0.982000	0.44146	0.922000	0.55478	0.662000	0.25038	1.986000	0.57962	0.533000	0.62120	GTC		0.473	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		G	158735886	A	G	158735886	3	3	61	1	0	0	0	0	1	0	0	0	11237	275	10	4	354	4	OR6N1	1	158735886	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10894	158735886	90514735	700	8685										
MNDA	4332	broad.mit.edu	37	chr1	158815417	158815417	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggcaggtggatgcaagaaGaaatgttccccaaaacgacc	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158815417G>T	ENST00000368141.4	+	5	872	c.611G>T	c.(610-612)aGa>aTa	p.R204I		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	204	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R204I(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					GATGCAAGAAGAAATGTTCCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	60	61					1																	158815417		2203	4300	6503	157082041	SO:0001583	missense	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.611G>T	1.37:g.158815417G>T	ENSP00000357123:p.Arg204Ile		157082041		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721419	0.30503	.	.	ENSG00000163563	ENST00000368141	T	0.05649	3.41	4.0	-1.32	0.09201	HIN-200/IF120x (1);Nucleic acid-binding, OB-fold (1);	1.451250	0.04590	N	0.396665	T	0.02848	0.0085	L	0.61218	1.895	0.09310	N	1	D	0.57899	0.981	B	0.42692	0.395	T	0.34179	-0.9839	10	0.52906	T	0.07	0.0617	4.0355	0.09727	0.4293:0.179:0.3917:0.0	.	204	P41218	MNDA_HUMAN	I	204	ENSP00000357123:R204I	ENSP00000357123:R204I	R	+	2	0	MNDA	157082041	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.958000	0.03857	-0.128000	0.11641	-0.176000	0.13171	AGA		0.483	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		T	158815417	G	T	158815417	3	4	61	1	0	0	0	0	1	0	0	0	9706	942	33	2	625	2	MNDA	1	158815417	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79531	158815417	90435204	701	8686										
MNDA	4332	broad.mit.edu	37	chr1	158817691	158817691	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaactggtgtgtggaagTcacagcttcatcaaggtggg	14	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158817691T>G	ENST00000368141.4	+	6	1422	c.1161T>G	c.(1159-1161)agT>agG	p.S387R		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	387	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S387R(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TGTGTGGAAGTCACAGCTTCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	112	114					1																	158817691		2203	4300	6503	157084315	SO:0001583	missense	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.1161T>G	1.37:g.158817691T>G	ENSP00000357123:p.Ser387Arg		157084315		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	T	5.736	0.320205	0.10845	.	.	ENSG00000163563	ENST00000368141	T	0.21031	2.03	3.76	-3.92	0.04155	HIN-200/IF120x (1);Nucleic acid-binding, OB-fold (1);	3.387390	0.01384	N	0.013026	T	0.01489	0.0048	N	0.01576	-0.805	0.09310	N	1	B	0.30179	0.271	B	0.20767	0.031	T	0.20273	-1.0280	10	0.16420	T	0.52	4.3861	5.4577	0.16600	0.0:0.1931:0.4842:0.3227	.	387	P41218	MNDA_HUMAN	R	387	ENSP00000357123:S387R	ENSP00000357123:S387R	S	+	3	2	MNDA	157084315	0.000000	0.05858	0.002000	0.10522	0.381000	0.30169	-1.114000	0.03293	-0.943000	0.03691	0.460000	0.39030	AGT		0.433	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		G	158817691	T	G	158817691	3	3	61	1	0	0	0	0	1	0	0	0	9706	1664	58	4	1179	4	MNDA	1	158817691	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2274	158817691	90432930	702	8687										
PYHIN1	149628	broad.mit.edu	37	chr1	158912050	158912050	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtgaatgaagcctcttCtgtatctgaagctggtcctg	12	8	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158912050C>T	ENST00000368140.1	+	5	1108	c.863C>T	c.(862-864)tCt>tTt	p.S288F	PYHIN1_ENST00000392252.3_Missense_Mutation_p.S279F|PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Missense_Mutation_p.S279F|PYHIN1_ENST00000392254.2_Missense_Mutation_p.S288F	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	288	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)		p.S288F(1)		breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					GAAGCCTCTTCTGTATCTGAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	48	48					1																	158912050		2203	4299	6502	157178674	SO:0001583	missense	149628			AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.863C>T	1.37:g.158912050C>T	ENSP00000357122:p.Ser288Phe		157178674	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043373	0.36085	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.15952	2.38;2.38;2.38;2.38	2.85	-2.63	0.06133	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.14013	0.0339	M	0.69358	2.11	0.09310	N	1	D;P;D;D	0.63046	0.982;0.933;0.982;0.992	P;P;P;D	0.64506	0.852;0.846;0.852;0.926	T	0.09487	-1.0672	9	0.72032	D	0.01	.	0.4942	0.00569	0.194:0.3484:0.1914:0.2663	.	279;288;279;288	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	F	288;279;288;279	ENSP00000357122:S288F;ENSP00000357120:S279F;ENSP00000376083:S288F;ENSP00000376082:S279F	ENSP00000357120:S279F	S	+	2	0	PYHIN1	157178674	0.000000	0.05858	0.001000	0.08648	0.216000	0.24613	-1.164000	0.03135	-0.285000	0.09089	-0.150000	0.13652	TCT		0.348	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		T	158912050	C	T	158912050	3	4	61	1	0	0	0	0	1	0	0	0	12902	913	32	3	877	3	PYHIN1	1	158912050	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94359	158912050	90338571	703	8688										
PYHIN1	149628	broad.mit.edu	37	chr1	158913597	158913597	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaattgtaaataggaaGacgacaatctatgaaattca	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:158913597G>T	ENST00000368140.1	+	6	1265	c.1020G>T	c.(1018-1020)aaG>aaT	p.K340N	PYHIN1_ENST00000392252.3_Missense_Mutation_p.K331N|PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Missense_Mutation_p.K331N|PYHIN1_ENST00000392254.2_Missense_Mutation_p.K340N	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	340	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)		p.K340N(1)		breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					TAAATAGGAAGACGACAATCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	67	66					1																	158913597		2203	4300	6503	157180221	SO:0001583	missense	149628			AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1020G>T	1.37:g.158913597G>T	ENSP00000357122:p.Lys340Asn		157180221	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.729472	0.30684	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	3.13	-2.57	0.06248	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.12774	0.0310	L	0.47716	1.5	0.09310	N	1	D;D;D;D	0.89917	1.0;0.982;1.0;1.0	D;P;D;D	0.80764	0.993;0.905;0.993;0.994	T	0.07385	-1.0775	9	0.44086	T	0.13	.	4.3417	0.11113	0.5214:0.2099:0.2688:0.0	.	331;340;331;340	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	N	340;331;340;331	ENSP00000357122:K340N;ENSP00000357120:K331N;ENSP00000376083:K340N;ENSP00000376082:K331N	ENSP00000357120:K331N	K	+	3	2	PYHIN1	157180221	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.121000	0.00595	-0.466000	0.06943	-0.211000	0.12701	AAG		0.348	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		T	158913597	G	T	158913597	3	4	61	1	0	0	0	0	1	0	0	0	12902	933	33	2	1038	2	PYHIN1	1	158913597	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1547	158913597	90337024	704	8689										
CADM3	57863	broad.mit.edu	37	chr1	159163717	159163717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccttcactgtcagcagctCggtgacattccaggttaccc	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159163717C>T	ENST00000368125.4	+	5	735	c.578C>T	c.(577-579)tCg>tTg	p.S193L	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Missense_Mutation_p.S227L	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	193	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.S227L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					GTCAGCAGCTCGGTGACATTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	92	97					1																	159163717		2203	4300	6503	157430341	SO:0001583	missense	57863			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.578C>T	1.37:g.159163717C>T	ENSP00000357107:p.Ser193Leu		157430341	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337201	0.60963	.	.	ENSG00000162706	ENST00000368124;ENST00000368125	T;T	0.76060	-0.99;-0.99	5.14	5.14	0.70334	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.283931	0.29692	N	0.011445	T	0.44829	0.1312	L	0.28556	0.865	0.30557	N	0.764842	P;P	0.48162	0.905;0.906	P;B	0.44623	0.455;0.24	T	0.38265	-0.9669	10	0.08599	T	0.76	.	9.4974	0.38997	0.0:0.907:0.0:0.093	.	193;227	Q8N126;Q8N126-2	CADM3_HUMAN;.	L	227;193	ENSP00000357106:S227L;ENSP00000357107:S193L	ENSP00000357106:S227L	S	+	2	0	CADM3	157430341	0.734000	0.28142	0.999000	0.59377	0.990000	0.78478	1.174000	0.31932	2.666000	0.90696	0.655000	0.94253	TCG		0.522	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		T	159163717	C	T	159163717	3	4	61	1	0	0	0	0	1	0	0	0	2574	893	31	1	702	1	CADM3	1	159163717	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	250120	159163717	90086904	705	8690										
CADM3	57863	broad.mit.edu	37	chr1	159163822	159163822	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccacctctcaacgcattgAagttttatgtatgtcatggg	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159163822A>C	ENST00000368125.4	+	5	840	c.683A>C	c.(682-684)gAa>gCa	p.E228A	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Missense_Mutation_p.E262A	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	228	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.E262A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					CAACGCATTGAAGTTTTATGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											103	102	102					1																	159163822		2203	4300	6503	157430446	SO:0001583	missense	57863			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.683A>C	1.37:g.159163822A>C	ENSP00000357107:p.Glu228Ala		157430446	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043362	0.75732	.	.	ENSG00000162706	ENST00000368124;ENST00000368125	D;D	0.86366	-2.11;-2.11	5.03	5.03	0.67393	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.268994	0.37623	N	0.002018	T	0.77096	0.4080	L	0.56199	1.76	0.42043	D	0.991089	B;B	0.29590	0.25;0.119	B;B	0.26202	0.061;0.067	T	0.78828	-0.2050	10	0.46703	T	0.11	.	12.764	0.57380	1.0:0.0:0.0:0.0	.	228;262	Q8N126;Q8N126-2	CADM3_HUMAN;.	A	262;228	ENSP00000357106:E262A;ENSP00000357107:E228A	ENSP00000357106:E262A	E	+	2	0	CADM3	157430446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.402000	0.44521	2.108000	0.64289	0.533000	0.62120	GAA		0.493	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		C	159163822	A	C	159163822	3	2	61	1	0	0	0	0	1	0	0	0	2574	246	9	4	807	4	CADM3	1	159163822	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	105	159163822	90086799	706	8691										
CADM3	57863	broad.mit.edu	37	chr1	159169596	159169596	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgccatcatcggtgggatCgtggctttcattgtcttcct	10	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159169596C>T	ENST00000368125.4	+	8	1165	c.1008C>T	c.(1006-1008)atC>atT	p.I336I	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000497636.1_3'UTR|CTA-134P22.2_ENST00000609696.1_RNA|CADM3_ENST00000368124.4_Silent_p.I370I	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	336					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.I370I(3)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					TCGGTGGGATCGTGGCTTTCA	0.557																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	1											176	139	151					1																	159169596		2203	4300	6503	157436220	SO:0001819	synonymous_variant	57863			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.1008C>T	1.37:g.159169596C>T			157436220	Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																				0.557	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		T	159169596	C	T	159169596	2	4	61	1	0	0	0	0	0	0	0	1	2574	874	31	1		1	CADM3	1	159169596	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5774	159169596	90081025	707	8692										
FCER1A	2205	broad.mit.edu	37	chr1	159275907	159275907	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatggtgaagctctcaagtActggtatgagaaccacaaca	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159275907A>G	ENST00000368115.1	+	5	560	c.461A>G	c.(460-462)tAc>tGc	p.Y154C	FCER1A_ENST00000368114.1_Missense_Mutation_p.Y121C	NM_002001.3	NP_001992.1	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide	154	Ig-like 2.				activation of JUN kinase activity (GO:0007257)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leukotriene biosynthetic process (GO:0019370)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of type I hypersensitivity (GO:0001812)|serotonin secretion (GO:0001820)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)	p.Y154C(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(19)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	GCTCTCAAGTACTGGTATGAG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											183	160	168					1																	159275907		2203	4300	6503	157542531	SO:0001583	missense	2205			BC015195	CCDS1184.1	1q23	2013-01-11			ENSG00000179639	ENSG00000179639		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3609	protein-coding gene	gene with protein product		147140		FCE1A		8245459	Standard	NM_002001		Approved		uc001ftq.3	P12319	OTTHUMG00000037176	ENST00000368115.1:c.461A>G	1.37:g.159275907A>G	ENSP00000357097:p.Tyr154Cys		157542531		Missense_Mutation	SNP	ENST00000368115.1	37	CCDS1184.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.842965	0.51057	.	.	ENSG00000179639	ENST00000368115;ENST00000368114	T;T	0.09723	2.95;2.95	4.78	2.39	0.29439	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.254059	0.28354	N	0.015659	T	0.18718	0.0449	M	0.85630	2.765	0.30546	N	0.765964	D	0.89917	1.0	D	0.79108	0.992	T	0.03684	-1.1013	10	0.87932	D	0	.	7.3907	0.26909	0.6497:0.0:0.0:0.3503	.	154	P12319	FCERA_HUMAN	C	154;121	ENSP00000357097:Y154C;ENSP00000357096:Y121C	ENSP00000357096:Y121C	Y	+	2	0	FCER1A	157542531	0.851000	0.29673	0.100000	0.21137	0.959000	0.62525	1.185000	0.32065	0.299000	0.22661	0.528000	0.53228	TAC		0.493	FCER1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090328.2	NM_002001		G	159275907	A	G	159275907	3	3	61	1	0	0	0	0	1	0	0	0	5793	391	14	4	475	4	FCER1A	1	159275907	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	106311	159275907	89974714	708	8693										
FCRL6	343413	broad.mit.edu	37	chr1	159784039	159784039	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaagggaaagatgaaggTgttgtctactctgtggtgca	14	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159784039T>G	ENST00000368106.3	+	8	1105	c.1104T>G	c.(1102-1104)ggT>ggG	p.G368G	FCRL6_ENST00000321935.6_Silent_p.G375G|FCRL6_ENST00000339348.5_Silent_p.G368G|FCRL6_ENST00000392235.3_Silent_p.G273G	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	368						external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.G368G(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					AAGATGAAGGTGTTGTCTACT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											205	182	190					1																	159784039		2203	4300	6503	158050663	SO:0001819	synonymous_variant	343413			AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.1104T>G	1.37:g.159784039T>G			158050663	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Silent	SNP	ENST00000368106.3	37	CCDS30912.1																																																																																				0.458	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310		G	159784039	T	G	159784039	2	3	61	1	0	0	0	0	0	0	0	1	5818	1683	59	4		4	FCRL6	1	159784039	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	508132	159784039	89466582	709	8694										
CCDC19	25790	broad.mit.edu	37	chr1	159846360	159846360	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctaccgaagaatcctctcGaactcatcccggtcccgttg	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159846360G>A	ENST00000368099.4	-	10	1402	c.1338C>T	c.(1336-1338)ttC>ttT	p.F446F	CCDC19_ENST00000476696.1_5'UTR|CCDC19_ENST00000426543.2_Silent_p.F361F	NM_012337.2	NP_036469.2												p.F446F(1)		endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			GAATCCTCTCGAACTCATCCC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	81	82					1																	159846360		2203	4300	6503	158112984	SO:0001819	synonymous_variant	25790																														ENST00000368099.4:c.1338C>T	1.37:g.159846360G>A			158112984		Silent	SNP	ENST00000368099.4	37	CCDS30914.1																																																																																				0.532	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			A	159846360	G	A	159846360	2	1	61	1	0	0	0	0	0	0	0	1	2801	1049	37	1		1	CCDC19	1	159846360	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62321	159846360	89404261	710	8695										
CCDC19	25790	broad.mit.edu	37	chr1	159847190	159847190	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatggccctcaagcgtgcGatctccttctctttctccct	7	16	4	0	rs373151220		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159847190G>A	ENST00000368099.4	-	9	1171	c.1107C>T	c.(1105-1107)atC>atT	p.I369I	CCDC19_ENST00000476696.1_5'UTR|CCDC19_ENST00000426543.2_Silent_p.I284I	NM_012337.2	NP_036469.2												p.I369I(1)		endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			TCAAGCGTGCGATCTCCTTCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	310	253	272		1107	-3.7	0.7	1		272	0,8600		0,0,4300	no	coding-synonymous	CCDC19	NM_012337.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		369/552	159847190	1,13005	2203	4300	6503	158113814	SO:0001819	synonymous_variant	25790																														ENST00000368099.4:c.1107C>T	1.37:g.159847190G>A			158113814		Silent	SNP	ENST00000368099.4	37	CCDS30914.1																																																																																				0.542	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			A	159847190	G	A	159847190	2	1	61	1	0	0	0	0	0	0	0	1	2801	1048	37	1		1	CCDC19	1	159847190	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	830	159847190	89403431	711	8696										
TAGLN2	8407	broad.mit.edu	37	chr1	159889569	159889569	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatggtggaggcctggatCttctttactggggcctgccc	14	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159889569C>A	ENST00000368097.4	-	3	547	c.237G>T	c.(235-237)aaG>aaT	p.K79N	TAGLN2_ENST00000368096.1_Missense_Mutation_p.K100N|TAGLN2_ENST00000478033.1_5'UTR|TAGLN2_ENST00000320307.4_Missense_Mutation_p.K79N	NM_001277223.1|NM_003564.1	NP_001264152.1|NP_003555.1	P37802	TAGL2_HUMAN	transgelin 2	79	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)		p.K79N(1)		endometrium(1)|large_intestine(2)|lung(6)	9	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGCCTGGATCTTCTTTACTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											193	180	185					1																	159889569		2203	4300	6503	158156193	SO:0001583	missense	8407			D21261	CCDS1189.1, CCDS60314.1	1q21-q25	2008-07-18			ENSG00000158710	ENSG00000158710			11554	protein-coding gene	gene with protein product	"SM22-alpha homolog"	604634				9693045	Standard	NM_001277223		Approved	KIAA0120, HA1756	uc031pqu.1	P37802	OTTHUMG00000022793	ENST00000368097.4:c.237G>T	1.37:g.159889569C>A	ENSP00000357077:p.Lys79Asn		158156193	E9KL39|Q5JRQ6|Q5JRQ7|Q6FGI1|Q9BUH5|Q9H4P0	Missense_Mutation	SNP	ENST00000368097.4	37	CCDS1189.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.670859	0.67814	.	.	ENSG00000158710	ENST00000368097;ENST00000368096;ENST00000320307;ENST00000397334	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.09	5.09	0.68999	Calponin homology domain (5);	0.000000	0.41823	U	0.000802	T	0.76926	0.4056	M	0.93763	3.455	0.52501	D	0.999951	P	0.47350	0.894	P	0.59424	0.857	T	0.82049	-0.0650	9	.	.	.	-30.4484	9.9096	0.41397	0.0:0.9064:0.0:0.0936	.	79	P37802	TAGL2_HUMAN	N	79;100;79;79	ENSP00000357077:K79N;ENSP00000357076:K100N;ENSP00000357075:K79N;ENSP00000412429:K79N	.	K	-	3	2	TAGLN2	158156193	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.576000	0.23744	2.525000	0.85131	0.655000	0.94253	AAG		0.532	TAGLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059105.1	NM_003564		A	159889569	C	A	159889569	3	1	61	1	0	0	0	0	1	0	0	0	15578	912	32	2	374	2	TAGLN2	1	159889569	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42379	159889569	89361052	712	8697										
IGSF9	57549	broad.mit.edu	37	chr1	159897978	159897978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcaccacatgctcccttCggggccatctctcagggcca	9	17	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:159897978C>T	ENST00000368094.1	-	19	3397	c.3200G>A	c.(3199-3201)cGa>cAa	p.R1067Q	IGSF9_ENST00000361509.3_Missense_Mutation_p.R1051Q|TAGLN2_ENST00000368097.4_5'Flank|TAGLN2_ENST00000478033.1_5'Flank|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	1067					dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.R1051Q(1)		central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGCTCCCTTCGGGGCCATCT	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	72	74					1																	159897978		2198	4294	6492	158164602	SO:0001583	missense	57549			AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.3200G>A	1.37:g.159897978C>T	ENSP00000357073:p.Arg1067Gln		158164602		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112171	0.77210	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.73152	-0.72;-0.65	3.63	3.63	0.41609	.	0.000000	0.29266	U	0.012654	T	0.63558	0.2521	N	0.24115	0.695	0.37788	D	0.927261	D;D	0.89917	0.981;1.0	P;D	0.74023	0.551;0.982	T	0.64525	-0.6387	9	.	.	.	-5.1441	12.8415	0.57805	0.0:1.0:0.0:0.0	.	1067;605	Q9P2J2;C9JI81	TUTLA_HUMAN;.	Q	1051;1067;605	ENSP00000355049:R1051Q;ENSP00000357073:R1067Q	.	R	-	2	0	IGSF9	158164602	0.982000	0.34865	0.996000	0.52242	0.941000	0.58515	2.978000	0.49305	1.852000	0.53769	0.563000	0.77884	CGA		0.667	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159897978	C	T	159897978	3	4	61	1	0	0	0	0	1	0	0	0	7626	884	31	1	351	1	IGSF9	1	159897978	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8409	159897978	89352643	713	8698										
PIGM	93183	broad.mit.edu	37	chr1	160000274	160000274	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacactagtcatatttgattCtctctgtcaggggttcttct	7	9	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160000274C>A	ENST00000368090.2	-	1	1509	c.1256G>T	c.(1255-1257)aGa>aTa	p.R419I		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	419					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.R419I(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ATATTTGATTCTCTCTGTCAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	133	129					1																	160000274		2203	4300	6503	158266898	SO:0001583	missense	93183			AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.1256G>T	1.37:g.160000274C>A	ENSP00000357069:p.Arg419Ile		158266898		Missense_Mutation	SNP	ENST00000368090.2	37	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952659	0.34471	.	.	ENSG00000143315	ENST00000368090	T	0.47869	0.83	4.45	2.41	0.29592	.	0.259954	0.37304	N	0.002157	T	0.18299	0.0439	L	0.48642	1.525	0.47374	D	0.999407	B	0.20671	0.047	B	0.21360	0.034	T	0.05131	-1.0904	9	.	.	.	-20.3242	5.4785	0.16710	0.0:0.7432:0.0:0.2568	.	419	Q9H3S5	PIGM_HUMAN	I	419	ENSP00000357069:R419I	.	R	-	2	0	PIGM	158266898	0.983000	0.35010	0.931000	0.37212	0.647000	0.38526	1.354000	0.34056	1.072000	0.40860	0.462000	0.41574	AGA		0.368	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		A	160000274	C	A	160000274	3	1	61	1	0	0	0	0	1	0	0	0	11923	913	32	2	19	2	PIGM	1	160000274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102296	160000274	89250347	714	8699										
PIGM	93183	broad.mit.edu	37	chr1	160000978	160000978	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatgggaaggatgtaagtCactggatatatcttcatatg	11	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160000978C>A	ENST00000368090.2	-	1	805	c.552G>T	c.(550-552)gtG>gtT	p.V184V		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	184					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.V184V(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGATGTAAGTCACTGGATATA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											126	125	126					1																	160000978		2203	4300	6503	158267602	SO:0001819	synonymous_variant	93183			AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.552G>T	1.37:g.160000978C>A			158267602		Silent	SNP	ENST00000368090.2	37	CCDS1192.1																																																																																				0.488	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		A	160000978	C	A	160000978	2	1	61	1	0	0	0	0	0	0	0	1	11923	813	29	2		2	PIGM	1	160000978	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	704	160000978	89249643	715	8700										
PIGM	93183	broad.mit.edu	37	chr1	160001428	160001428	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtcctggaagacgccataGaaaaccagggcgactctggc	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160001428G>T	ENST00000368090.2	-	1	355	c.102C>A	c.(100-102)ttC>ttA	p.F34L		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	34					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.F34L(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGACGCCATAGAAAACCAGGG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	78	77					1																	160001428		2203	4300	6503	158268052	SO:0001583	missense	93183			AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.102C>A	1.37:g.160001428G>T	ENSP00000357069:p.Phe34Leu		158268052		Missense_Mutation	SNP	ENST00000368090.2	37	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	G	5.501	0.277474	0.10403	.	.	ENSG00000143315	ENST00000368090	T	0.37584	1.19	5.03	2.0	0.26442	.	0.447701	0.23676	N	0.045679	T	0.04003	0.0112	N	0.02296	-0.605	0.31898	N	0.616309	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	9	.	.	.	-4.9934	8.2388	0.31645	0.0:0.3275:0.5032:0.1693	.	34	Q9H3S5	PIGM_HUMAN	L	34	ENSP00000357069:F34L	.	F	-	3	2	PIGM	158268052	0.997000	0.39634	0.951000	0.38953	0.987000	0.75469	0.908000	0.28545	0.254000	0.21573	0.561000	0.74099	TTC		0.627	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		T	160001428	G	T	160001428	3	4	61	1	0	0	0	0	1	0	0	0	11923	933	33	2	1173	2	PIGM	1	160001428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	450	160001428	89249193	716	8701										
ATP1A2	477	broad.mit.edu	37	chr1	160099959	160099959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaagggggccccagagcGcattctggaccggtgctcca	15	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160099959G>A	ENST00000361216.3	+	12	1618	c.1529G>A	c.(1528-1530)cGc>cAc	p.R510H	ATP1A2_ENST00000392233.3_Missense_Mutation_p.R510H	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	510					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.R510H(2)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	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)			GCCCCAGAGCGCATTCTGGAC	0.592																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	1											78	77	78					1																	160099959		2203	4300	6503	158366583	SO:0001583	missense	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1529G>A	1.37:g.160099959G>A	ENSP00000354490:p.Arg510His		158366583	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.119607|5.119607	0.94385|0.94385	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000447527|ENST00000361216;ENST00000392233;ENST00000435866	.|T;T	.|0.80480	.|-1.38;-1.38	4.61|4.61	4.61|4.61	0.57282|0.57282	.|ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88422|0.88422	0.6432|0.6432	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.999	D|D	0.90211|0.90211	0.4264|0.4264	5|10	.|0.87932	.|D	.|0	.|.	16.564|16.564	0.84574|0.84574	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|510;410;510	.|B1AKY9;F5GXJ7;P50993	.|.;.;AT1A2_HUMAN	T|H	221|510;510;213	.|ENSP00000354490:R510H;ENSP00000376066:R510H	.|ENSP00000354490:R510H	A|R	+|+	1|2	0|0	ATP1A2|ATP1A2	158366583|158366583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.852000|9.852000	0.99516|0.99516	2.283000|2.283000	0.76528|0.76528	0.511000|0.511000	0.50034|0.50034	GCA|CGC		0.592	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160099959	G	A	160099959	3	1	61	1	0	0	0	0	1	0	0	0	1130	1087	38	1	1575	1	ATP1A2	1	160099959	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98531	160099959	89150662	717	8702										
ATP1A2	477	broad.mit.edu	37	chr1	160105338	160105338	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtctctaagcaggcagccGacatgatcctgctggatgac	11	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160105338G>A	ENST00000361216.3	+	16	2319	c.2230G>A	c.(2230-2232)Gac>Aac	p.D744N	ATP1A2_ENST00000392233.3_Missense_Mutation_p.D744N	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	744					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.D744N(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	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)			GCAGGCAGCCGACATGATCCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											140	104	116					1																	160105338		2203	4297	6500	158371962	SO:0001583	missense	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2230G>A	1.37:g.160105338G>A	ENSP00000354490:p.Asp744Asn		158371962	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.945628	0.92593	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866	D;D	0.99382	-5.8;-5.8	4.31	4.31	0.51392	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99339	0.9768	M	0.91459	3.21	0.80722	D	1	D;D	0.67145	0.996;0.993	P;P	0.56563	0.801;0.638	D	0.98776	1.0730	10	0.87932	D	0	.	16.0832	0.81020	0.0:0.0:1.0:0.0	.	644;744	F5GXJ7;P50993	.;AT1A2_HUMAN	N	744;744;447	ENSP00000354490:D744N;ENSP00000376066:D744N	ENSP00000354490:D744N	D	+	1	0	ATP1A2	158371962	1.000000	0.71417	0.995000	0.50966	0.837000	0.47467	9.593000	0.98250	2.383000	0.81215	0.561000	0.74099	GAC		0.582	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105338	G	A	160105338	3	1	61	1	0	0	0	0	1	0	0	0	1130	1058	37	1	2292	1	ATP1A2	1	160105338	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5379	160105338	89145283	718	8703										
ATP1A2	477	broad.mit.edu	37	chr1	160105639	160105639	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccccacaggccgcctgatCtttgacaacttgaagaaatc	7	14	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160105639C>A	ENST00000361216.3	+	17	2384	c.2295C>A	c.(2293-2295)atC>atA	p.I765I	ATP1A2_ENST00000392233.3_Silent_p.I765I	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	765					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.I765I(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	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)			GCCGCCTGATCTTTGACAACT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											145	128	134					1																	160105639		2203	4300	6503	158372263	SO:0001819	synonymous_variant	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2295C>A	1.37:g.160105639C>A			158372263	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	C	9.663	1.144776	0.21288	.	.	ENSG00000018625	ENST00000447527	.	.	.	4.38	3.47	0.39725	.	.	.	.	.	T	0.47192	0.1432	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45352	-0.9267	4	.	.	.	.	9.8154	0.40849	0.0:0.9017:0.0:0.0983	.	.	.	.	Y	476	.	.	S	+	2	0	ATP1A2	158372263	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.553000	0.45837	1.194000	0.43101	0.555000	0.69702	TCT		0.577	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105639	C	A	160105639	2	1	61	1	0	0	0	0	0	0	0	1	1130	903	32	2		2	ATP1A2	1	160105639	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	301	160105639	89144982	719	8704										
ATP1A2	477	broad.mit.edu	37	chr1	160109516	160109516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcatgggtgtagccctccGcatgtacccgctcaagtgag	13	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160109516G>A	ENST00000361216.3	+	21	3016	c.2927G>A	c.(2926-2928)cGc>cAc	p.R976H	ATP1A2_ENST00000392233.3_Missense_Mutation_p.R976H	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	976					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.R976H(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	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)			GTAGCCCTCCGCATGTACCCG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	80	83					1																	160109516		2203	4300	6503	158376140	SO:0001583	missense	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2927G>A	1.37:g.160109516G>A	ENSP00000354490:p.Arg976His		158376140	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.90|19.90	3.912101|3.912101	0.72983|0.72983	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000447527|ENST00000361216;ENST00000392233;ENST00000435866	.|D;D	.|0.88586	.|-2.4;-2.4	4.37|4.37	4.37|4.37	0.52481|0.52481	.|ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92987|0.92987	0.7768|0.7768	M|M	0.87269|0.87269	2.87|2.87	0.80722|0.80722	D|D	1|1	.|B;D	.|0.76494	.|0.089;0.999	.|B;P	.|0.59703	.|0.027;0.862	D|D	0.93665|0.93665	0.6985|0.6985	5|10	.|0.62326	.|D	.|0.03	.|.	14.8061|14.8061	0.69956|0.69956	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|876;976	.|F5GXJ7;P50993	.|.;AT1A2_HUMAN	T|H	670|976;976;679	.|ENSP00000354490:R976H;ENSP00000376066:R976H	.|ENSP00000354490:R976H	A|R	+|+	1|2	0|0	ATP1A2|ATP1A2	158376140|158376140	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.769000|7.769000	0.85360|0.85360	2.420000|2.420000	0.82092|0.82092	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160109516	G	A	160109516	3	1	61	1	0	0	0	0	1	0	0	0	1130	1087	38	1	3009	1	ATP1A2	1	160109516	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3877	160109516	89141105	720	8705										
ATP1A2	477	broad.mit.edu	37	chr1	160109746	160109746	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatctatgatgaggtccgAaagctcatcctgcggcggta	11	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160109746A>G	ENST00000361216.3	+	22	3095	c.3006A>G	c.(3004-3006)cgA>cgG	p.R1002R	ATP1A2_ENST00000392233.3_Silent_p.R991R	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	1002					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.R1002R(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	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)			ATGAGGTCCGAAAGCTCATCC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											138	124	129					1																	160109746		2203	4300	6503	158376370	SO:0001819	synonymous_variant	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.3006A>G	1.37:g.160109746A>G			158376370	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	8.700	0.909568	0.17833	.	.	ENSG00000018625	ENST00000447527	.	.	.	4.37	-8.75	0.00834	.	.	.	.	.	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63866	-0.6540	4	.	.	.	.	12.018	0.53326	0.1523:0.377:0.4708:0.0	.	.	.	.	G	696	.	.	E	+	2	0	ATP1A2	158376370	0.000000	0.05858	0.128000	0.21923	0.965000	0.64279	-3.501000	0.00450	-3.561000	0.00141	-0.316000	0.08728	GAA		0.582	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		G	160109746	A	G	160109746	2	3	61	1	0	0	0	0	0	0	0	1	1130	233	9	4		4	ATP1A2	1	160109746	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	230	160109746	89140875	721	8706										
ATP1A4	480	broad.mit.edu	37	chr1	160128855	160128855	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaagaggtggtgttgggaGacctggtggaaatcaagggt	17	4	1	2	rs146292275		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160128855G>T	ENST00000368081.4	+	5	1060	c.589G>T	c.(589-591)Gac>Tac	p.D197Y		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	197					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.D197Y(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGTGTTGGGAGACCTGGTGGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	TYR/ASP	1,4405	2.1+/-5.4	0,1,2202	141	124	130		589	4.8	1	1	dbSNP_134	130	0,8600		0,0,4300	no	missense	ATP1A4	NM_144699.3	160	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging	197/1030	160128855	1,13005	2203	4300	6503	158395479	SO:0001583	missense	480			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.589G>T	1.37:g.160128855G>T	ENSP00000357060:p.Asp197Tyr		158395479	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031809	0.54790	2.27E-4	0.0	ENSG00000132681	ENST00000368081	D	0.97598	-4.45	4.85	4.85	0.62838	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	H	0.99956	5.05	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97894	1.0299	10	0.87932	D	0	.	15.8419	0.78852	0.0:0.0:1.0:0.0	.	197	Q13733	AT1A4_HUMAN	Y	197	ENSP00000357060:D197Y	ENSP00000357060:D197Y	D	+	1	0	ATP1A4	158395479	1.000000	0.71417	0.999000	0.59377	0.061000	0.15899	9.869000	0.99810	2.399000	0.81585	0.555000	0.69702	GAC		0.493	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		T	160128855	G	T	160128855	3	4	61	1	0	0	0	0	1	0	0	0	1132	942	33	2	607	2	ATP1A4	1	160128855	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19109	160128855	89121766	722	8707										
ATP1A4	480	broad.mit.edu	37	chr1	160134055	160134055	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacctatcgctgctgagatCgaacacttcatccatctgat	6	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160134055C>T	ENST00000368081.4	+	7	1359	c.888C>T	c.(886-888)atC>atT	p.I296I		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	296					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.I296I(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTGCTGAGATCGAACACTTCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	1											274	218	237					1																	160134055		2203	4300	6503	158400679	SO:0001819	synonymous_variant	480			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.888C>T	1.37:g.160134055C>T			158400679	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																				0.542	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		T	160134055	C	T	160134055	2	4	61	1	0	0	0	0	0	0	0	1	1132	874	31	1		1	ATP1A4	1	160134055	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5200	160134055	89116566	723	8708										
ATP1A4	480	broad.mit.edu	37	chr1	160141112	160141112	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggtgctccggagaggatCttggagttttgttctacctt	13	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160141112C>A	ENST00000368081.4	+	11	2034	c.1563C>A	c.(1561-1563)atC>atA	p.I521I		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	521					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.I521I(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CGGAGAGGATCTTGGAGTTTT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											133	126	128					1																	160141112		2203	4300	6503	158407736	SO:0001819	synonymous_variant	480			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1563C>A	1.37:g.160141112C>A			158407736	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																				0.507	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160141112	C	A	160141112	2	1	61	1	0	0	0	0	0	0	0	1	1132	903	32	2		2	ATP1A4	1	160141112	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7057	160141112	89109509	724	8709										
ATP1A4	480	broad.mit.edu	37	chr1	160145907	160145907	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatctttgacaacctgaaGaaatccatcatgtacaccct	5	12	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160145907G>T	ENST00000368081.4	+	16	2808	c.2337G>T	c.(2335-2337)aaG>aaT	p.K779N	ATP1A4_ENST00000418334.1_3'UTR|ATP1A4_ENST00000470705.1_5'Flank	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	779					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.K779N(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ACAACCTGAAGAAATCCATCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											238	219	225					1																	160145907		2203	4300	6503	158412531	SO:0001583	missense	480			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.2337G>T	1.37:g.160145907G>T	ENSP00000357060:p.Lys779Asn		158412531	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668738	0.88348	.	.	ENSG00000132681	ENST00000368081	D	0.98474	-4.95	4.47	4.47	0.54385	ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99269	0.9745	H	0.95884	3.735	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98779	1.0731	10	0.87932	D	0	.	15.05	0.71862	0.0:0.0:1.0:0.0	.	779	Q13733	AT1A4_HUMAN	N	779	ENSP00000357060:K779N	ENSP00000357060:K779N	K	+	3	2	ATP1A4	158412531	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.657000	0.98554	2.476000	0.83614	0.555000	0.69702	AAG		0.557	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		T	160145907	G	T	160145907	3	4	61	1	0	0	0	0	1	0	0	0	1132	933	33	2	2399	2	ATP1A4	1	160145907	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4795	160145907	89104714	725	8710										
CASQ1	844	broad.mit.edu	37	chr1	160164904	160164904	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggctacttcaagagcaaaGactcagagcgtgggtaaccc	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160164904G>T	ENST00000368078.3	+	4	764	c.568G>T	c.(568-570)Gac>Tac	p.D190Y	CASQ1_ENST00000368079.3_Missense_Mutation_p.D184Y			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	190					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)	p.D184Y(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CAAGAGCAAAGACTCAGAGCG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	120	126					1																	160164904		2203	4300	6503	158431528	SO:0001583	missense	844			S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"Protein disulfide isomerases"	1512	protein-coding gene	gene with protein product	"calsequestrin 1, fast-twitch, skeletal muscle", "calmitine"	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.568G>T	1.37:g.160164904G>T	ENSP00000357057:p.Asp190Tyr		158431528	B1AKZ2|B2R863|Q8TBW7	Missense_Mutation	SNP	ENST00000368078.3	37	CCDS1198.2	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679219	0.68042	.	.	ENSG00000143318	ENST00000368079;ENST00000368078;ENST00000441151	T;T	0.77358	-1.09;-1.09	4.24	4.24	0.50183	Thioredoxin-like fold (2);	0.165039	0.53938	D	0.000057	T	0.80613	0.4656	L	0.52011	1.625	0.46149	D	0.998899	D	0.76494	0.999	D	0.63957	0.92	T	0.83277	-0.0040	10	0.87932	D	0	.	15.9216	0.79580	0.0:0.0:1.0:0.0	.	190	P31415	CASQ1_HUMAN	Y	184;190;105	ENSP00000357058:D184Y;ENSP00000357057:D190Y	ENSP00000357057:D190Y	D	+	1	0	CASQ1	158431528	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.349000	0.79799	0.557000	0.71058	GAC		0.532	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231		T	160164904	G	T	160164904	3	4	61	1	0	0	0	0	1	0	0	0	2686	942	33	2	582	2	CASQ1	1	160164904	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18997	160164904	89085717	726	8711										
CASQ1	844	broad.mit.edu	37	chr1	160168502	160168502	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatccacattgtggccttCgcagaggaagctgatcctgg	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160168502C>T	ENST00000368078.3	+	8	1060	c.864C>T	c.(862-864)ttC>ttT	p.F288F	CASQ1_ENST00000467691.1_Silent_p.F9F|CASQ1_ENST00000368079.3_Silent_p.F282F			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	288					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)	p.F282F(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTGTGGCCTTCGCAGAGGAAG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	1											106	103	104					1																	160168502		2203	4300	6503	158435126	SO:0001819	synonymous_variant	844			S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"Protein disulfide isomerases"	1512	protein-coding gene	gene with protein product	"calsequestrin 1, fast-twitch, skeletal muscle", "calmitine"	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.864C>T	1.37:g.160168502C>T			158435126	B1AKZ2|B2R863|Q8TBW7	Silent	SNP	ENST00000368078.3	37	CCDS1198.2																																																																																				0.532	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231		T	160168502	C	T	160168502	2	4	61	1	0	0	0	0	0	0	0	1	2686	883	31	1		1	CASQ1	1	160168502	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3598	160168502	89082119	727	8712										
DCAF8	50717	broad.mit.edu	37	chr1	160187498	160187498	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccccaggttctcgccagcGctgtggatgggaaaggcttg	14	11	1	0	rs371987013		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160187498G>A	ENST00000368073.3	-	14	2112	c.1678C>T	c.(1678-1680)Cgc>Tgc	p.R560C	DCAF8_ENST00000326837.2_Splice_Site_p.R560C|DCAF8_ENST00000368074.1_Splice_Site_p.R560C|DCAF8_ENST00000556710.1_Splice_Site_p.R714C|DCAF8_ENST00000608310.1_Splice_Site_p.R714C			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	560					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R560C(1)		cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						TCTCGCCAGCGCTGTGGATGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											66	67	66					1																	160187498		2203	4300	6503	158454122	SO:0001630	splice_region_variant	50717			AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24891	protein-coding gene	gene with protein product		615820	"WD repeat domain 42A"	WDR42A		11401431	Standard	NM_015726		Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000368073.3:c.1678-1C>T	1.37:g.160187498G>A			158454122	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	Missense_Mutation	SNP	ENST00000368073.3	37	CCDS1200.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844275	0.51164	.	.	ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465	ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000540855;ENST00000556710	T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.18;-0.18	5.23	5.23	0.72850	.	0.309917	0.21839	U	0.068353	T	0.55337	0.1914	M	0.64997	1.995	0.53688	D	0.999979	D;P	0.59767	0.986;0.916	B;B	0.43123	0.409;0.232	T	0.63559	-0.6610	10	0.56958	D	0.05	-6.1442	12.7642	0.57383	0.0:0.0:0.8358:0.1642	.	714;560	G3V3G9;Q5TAQ9	.;DCAF8_HUMAN	C	560;560;560;714;541;714	ENSP00000357052:R560C;ENSP00000318227:R560C;ENSP00000357053:R560C;ENSP00000451989:R714C;ENSP00000451235:R714C	ENSP00000318227:R560C	R	-	1	0	RP11-574F21.3;DCAF8	158454122	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.563000	0.45922	2.721000	0.93114	0.655000	0.94253	CGC		0.567	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726	Missense_Mutation	A	160187498	G	A	160187498	5	1	61	1	0	0	0	0	0	0	1	0	4282	1101	38	1	119	1	DCAF8	1	160187498	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18996	160187498	89063123	728	8713										
COPA	1314	broad.mit.edu	37	chr1	160293311	160293311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagcccagtttactccacGatcgtgaccctgtagaaaag	10	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160293311G>A	ENST00000241704.7	-	8	845	c.616C>T	c.(616-618)Cgt>Tgt	p.R206C	Y_RNA_ENST00000365208.1_RNA|COPA_ENST00000368069.3_Missense_Mutation_p.R206C	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	206					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)	p.R206C(1)		central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTTACTCCACGATCGTGACCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	76	80					1																	160293311		2203	4300	6503	158559935	SO:0001583	missense	1314			U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.616C>T	1.37:g.160293311G>A	ENSP00000241704:p.Arg206Cys		158559935	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	37	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310940	0.81358	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.60548	0.18;0.18	4.88	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	L	0.49699	1.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.987	T	0.69587	-0.5105	10	0.87932	D	0	-10.6841	16.8089	0.85713	0.0:0.0:1.0:0.0	.	206;206	P53621;P53621-2	COPA_HUMAN;.	C	206	ENSP00000357048:R206C;ENSP00000241704:R206C	ENSP00000241704:R206C	R	-	1	0	COPA	158559935	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.096000	0.76960	2.538000	0.85594	0.650000	0.86243	CGT		0.438	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		A	160293311	G	A	160293311	3	1	61	1	0	0	0	0	1	0	0	0	3733	1058	37	1	3189	1	COPA	1	160293311	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105813	160293311	88957310	729	8714										
SLAMF6	114836	broad.mit.edu	37	chr1	160456959	160456959	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctaggtgtccagatttCtgtttcctgtaaaaagaatc	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160456959C>A	ENST00000368057.3	-	7	946	c.886G>T	c.(886-888)Gaa>Taa	p.E296*	SLAMF6_ENST00000368055.1_Nonsense_Mutation_p.E185*|SLAMF6_ENST00000368059.3_Nonsense_Mutation_p.E295*			Q96DU3	SLAF6_HUMAN	SLAM family member 6	296						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.E295*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(4)	22	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			GTCCAGATTTCTGTTTCCTGT	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											126	130	129					1																	160456959		2203	4300	6503	158723583	SO:0001587	stop_gained	114836			AL832854	CCDS1205.1, CCDS53393.1, CCDS53394.1	1q23.1	2013-01-29			ENSG00000162739	ENSG00000162739		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21392	protein-coding gene	gene with protein product		606446				11489943	Standard	NM_052931		Approved	KALI, NTBA, KALIb, Ly108, SF2000, NTB-A, CD352	uc001fwe.2	Q96DU3	OTTHUMG00000022729	ENST00000368057.3:c.886G>T	1.37:g.160456959C>A	ENSP00000357036:p.Glu296*		158723583	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Nonsense_Mutation	SNP	ENST00000368057.3	37	CCDS53394.1	.	.	.	.	.	.	.	.	.	.	C	9.078	0.998569	0.19121	.	.	ENSG00000162739	ENST00000368059;ENST00000368057;ENST00000368055	.	.	.	3.82	-5.36	0.02689	.	2.128600	0.02234	N	0.065173	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	0.7983	6.7255	0.23355	0.1366:0.2134:0.0:0.6501	.	.	.	.	X	295;296;185	.	ENSP00000357034:E185X	E	-	1	0	SLAMF6	158723583	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.297000	0.08276	-1.277000	0.02411	0.563000	0.77884	GAA		0.333	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		A	160456959	C	A	160456959	4	1	61	1	0	0	0	0	0	1	0	0	14405	922	32	2	120	2	SLAMF6	1	160456959	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163648	160456959	88793662	730	8715										
SLAMF6	114836	broad.mit.edu	37	chr1	160460017	160460017	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttcgctgagtagacaaaGatagggaatctgaaaaataa	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160460017G>T	ENST00000368057.3	-	5	827	c.767C>A	c.(766-768)tCt>tAt	p.S256Y	SLAMF6_ENST00000368055.1_Missense_Mutation_p.S145Y|SLAMF6_ENST00000368059.3_Missense_Mutation_p.S256Y			Q96DU3	SLAF6_HUMAN	SLAM family member 6	256						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.S256Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(4)	22	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			AGTAGACAAAGATAGGGAATC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											111	116	115					1																	160460017		2203	4300	6503	158726641	SO:0001583	missense	114836			AL832854	CCDS1205.1, CCDS53393.1, CCDS53394.1	1q23.1	2013-01-29			ENSG00000162739	ENSG00000162739		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21392	protein-coding gene	gene with protein product		606446				11489943	Standard	NM_052931		Approved	KALI, NTBA, KALIb, Ly108, SF2000, NTB-A, CD352	uc001fwe.2	Q96DU3	OTTHUMG00000022729	ENST00000368057.3:c.767C>A	1.37:g.160460017G>T	ENSP00000357036:p.Ser256Tyr		158726641	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Missense_Mutation	SNP	ENST00000368057.3	37	CCDS53394.1	.	.	.	.	.	.	.	.	.	.	G	1.719	-0.497167	0.04291	.	.	ENSG00000162739	ENST00000368059;ENST00000368057;ENST00000368055	T;T;T	0.41065	1.01;1.01;1.01	3.56	-7.12	0.01537	.	6.669670	0.00166	N	0.000001	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.20671	0.0;0.028;0.047;0.006;0.006	B;B;B;B;B	0.18263	0.0;0.009;0.021;0.006;0.006	T	0.06661	-1.0814	10	0.59425	D	0.04	4.1188	3.0542	0.06179	0.0903:0.3066:0.3037:0.2994	.	145;145;207;256;256	B7Z6A7;Q5TAS6;B4E1U5;Q96DU3;B2R8X8	.;.;.;SLAF6_HUMAN;.	Y	256;256;145	ENSP00000357038:S256Y;ENSP00000357036:S256Y;ENSP00000357034:S145Y	ENSP00000357034:S145Y	S	-	2	0	SLAMF6	158726641	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.170000	0.01268	-3.010000	0.00273	-1.142000	0.01873	TCT		0.483	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		T	160460017	G	T	160460017	3	4	61	1	0	0	0	0	1	0	0	0	14405	942	33	2	247	2	SLAMF6	1	160460017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3058	160460017	88790604	731	8716										
SLAMF6	114836	broad.mit.edu	37	chr1	160460919	160460919	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggcaggctgttaccttcGcaaagcttctgggcagagac	13	10	1	2	rs145888090	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160460919G>A	ENST00000368057.3	-	3	702	c.642C>T	c.(640-642)tgC>tgT	p.C214C	SLAMF6_ENST00000368055.1_Silent_p.C103C|SLAMF6_ENST00000368059.3_Silent_p.C214C			Q96DU3	SLAF6_HUMAN	SLAM family member 6	214						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.C214C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(4)	22	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			TGTTACCTTCGCAAAGCTTCT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,,,	0,4406		0,0,2203	76	78	77		642,495,309,642	-3.3	0	1	dbSNP_134	77	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLAMF6	NM_001184714.1,NM_001184715.1,NM_001184716.1,NM_052931.4	,,,	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	,,,	214/333,165/283,103/222,214/332	160460919	7,12999	2203	4300	6503	158727543	SO:0001819	synonymous_variant	114836			AL832854	CCDS1205.1, CCDS53393.1, CCDS53394.1	1q23.1	2013-01-29			ENSG00000162739	ENSG00000162739		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21392	protein-coding gene	gene with protein product		606446				11489943	Standard	NM_052931		Approved	KALI, NTBA, KALIb, Ly108, SF2000, NTB-A, CD352	uc001fwe.2	Q96DU3	OTTHUMG00000022729	ENST00000368057.3:c.642C>T	1.37:g.160460919G>A			158727543	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Silent	SNP	ENST00000368057.3	37	CCDS53394.1																																																																																				0.512	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		A	160460919	G	A	160460919	2	1	61	1	0	0	0	0	0	0	0	1	14405	1079	38	1		1	SLAMF6	1	160460919	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	902	160460919	88789702	732	8717										
SLAMF6	114836	broad.mit.edu	37	chr1	160461173	160461173	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaacttgtatgttcctcaGttgtcctgtttgcagaaaaa	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160461173G>T	ENST00000368057.3	-	3	448	c.388C>A	c.(388-390)Ctg>Atg	p.L130M	SLAMF6_ENST00000368055.1_Missense_Mutation_p.L19M|SLAMF6_ENST00000368059.3_Missense_Mutation_p.L130M			Q96DU3	SLAF6_HUMAN	SLAM family member 6	130						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.L130M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(4)	22	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			ATGTTCCTCAGTTGTCCTGTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	81	82					1																	160461173		2203	4300	6503	158727797	SO:0001583	missense	114836			AL832854	CCDS1205.1, CCDS53393.1, CCDS53394.1	1q23.1	2013-01-29			ENSG00000162739	ENSG00000162739		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21392	protein-coding gene	gene with protein product		606446				11489943	Standard	NM_052931		Approved	KALI, NTBA, KALIb, Ly108, SF2000, NTB-A, CD352	uc001fwe.2	Q96DU3	OTTHUMG00000022729	ENST00000368057.3:c.388C>A	1.37:g.160461173G>T	ENSP00000357036:p.Leu130Met		158727797	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Missense_Mutation	SNP	ENST00000368057.3	37	CCDS53394.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374347	0.42105	.	.	ENSG00000162739	ENST00000368059;ENST00000368057;ENST00000368055	T;T;T	0.26660	2.43;2.43;1.72	4.37	3.45	0.39498	Immunoglobulin-like fold (1);	0.084555	0.47093	D	0.000249	T	0.43700	0.1259	M	0.90977	3.165	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;0.998;1.0;1.0;0.999;0.999	T	0.39603	-0.9606	10	0.72032	D	0.01	-16.2418	9.8955	0.41316	0.0:0.0:0.7973:0.2027	.	19;19;81;130;130;130	B7Z6A7;Q5TAS6;B4E1U5;Q96DU3-2;Q96DU3;B2R8X8	.;.;.;.;SLAF6_HUMAN;.	M	130;130;19	ENSP00000357038:L130M;ENSP00000357036:L130M;ENSP00000357034:L19M	ENSP00000357034:L19M	L	-	1	2	SLAMF6	158727797	0.518000	0.26234	0.024000	0.17045	0.095000	0.18619	2.700000	0.47085	1.181000	0.42912	0.655000	0.94253	CTG		0.403	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		T	160461173	G	T	160461173	3	4	61	1	0	0	0	0	1	0	0	0	14405	1020	36	2	634	2	SLAMF6	1	160461173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	254	160461173	88789448	733	8718										
CD84	8832	broad.mit.edu	37	chr1	160523189	160523189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtcttctcttgaacaaacGgaacaaaaacactgaagaca	6	9	2	3	rs111581582		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160523189G>T	ENST00000311224.4	-	4	805	c.739C>A	c.(739-741)Cgt>Agt	p.R247S	RP11-528G1.2_ENST00000446952.1_RNA|CD84_ENST00000368054.3_Missense_Mutation_p.R247S|CD84_ENST00000368047.3_5'Flank|CD84_ENST00000534968.1_Missense_Mutation_p.R133S|CD84_ENST00000368051.3_Missense_Mutation_p.R247S|CD84_ENST00000368048.3_Missense_Mutation_p.R247S	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	247					blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R247S(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TTGAACAAACGGAACAAAAAC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	88	88					1																	160523189		2203	4300	6503	158789813	SO:0001583	missense	8832			AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1704	protein-coding gene	gene with protein product		604513	"CD84 antigen (leukocyte antigen)", "CD84 molecule "			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.739C>A	1.37:g.160523189G>T	ENSP00000312367:p.Arg247Ser		158789813	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	37	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772565	0.31411	.	.	ENSG00000066294	ENST00000534968;ENST00000368054;ENST00000368048;ENST00000311224;ENST00000368051;ENST00000360056	T;T;T;T;T;T	0.63096	2.42;0.12;0.19;0.21;1.18;-0.02	4.93	1.02	0.19986	.	2.441840	0.02033	U	0.048661	T	0.28896	0.0717	L	0.34521	1.04	0.09310	N	1	B;P;P;B;B;P	0.37573	0.369;0.6;0.6;0.072;0.035;0.468	B;B;B;B;B;B	0.37346	0.091;0.247;0.168;0.025;0.034;0.168	T	0.09885	-1.0654	10	0.22109	T	0.4	4.5478	6.7197	0.23323	0.3772:0.0:0.6228:0.0	.	247;247;133;247;247;247	Q9UIB8-5;Q9UIB8-4;Q9UIB8-7;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;.;.;SLAF5_HUMAN;.;.	S	133;247;247;247;247;247	ENSP00000442845:R133S;ENSP00000357033:R247S;ENSP00000357027:R247S;ENSP00000312367:R247S;ENSP00000357030:R247S;ENSP00000353163:R247S	ENSP00000312367:R247S	R	-	1	0	CD84	158789813	0.001000	0.12720	0.000000	0.03702	0.162000	0.22319	0.363000	0.20301	0.095000	0.17434	0.650000	0.86243	CGT		0.463	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874		T	160523189	G	T	160523189	3	4	61	1	0	0	0	0	1	0	0	0	3048	1116	39	2	318	2	CD84	1	160523189	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62016	160523189	88727432	734	8719										
SLAMF1	6504	broad.mit.edu	37	chr1	160582285	160582285	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatgcctcacctggacaGactctgggacaggctctgtg	13	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160582285G>T	ENST00000302035.6	-	6	1299	c.950C>A	c.(949-951)tCt>tAt	p.S317Y	SLAMF1_ENST00000235739.5_Missense_Mutation_p.S287Y|SLAMF1_ENST00000538290.1_3'UTR	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	317					lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.S317Y(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			CACCTGGACAGACTCTGGGAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											54	51	52					1																	160582285		2203	4300	6503	158848909	SO:0001583	missense	6504			U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.950C>A	1.37:g.160582285G>T	ENSP00000306190:p.Ser317Tyr		158848909	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	G	9.803	1.181176	0.21787	.	.	ENSG00000117090	ENST00000302035;ENST00000235739	T;T	0.46819	0.86;0.86	4.18	3.26	0.37387	.	0.763645	0.11973	N	0.511603	T	0.22666	0.0547	L	0.36672	1.1	0.20873	N	0.999837	P	0.44877	0.845	B	0.40782	0.34	T	0.04621	-1.0938	10	0.72032	D	0.01	-31.9671	10.1934	0.43041	0.0:0.2015:0.7985:0.0	.	317	Q13291	SLAF1_HUMAN	Y	317;287	ENSP00000306190:S317Y;ENSP00000235739:S287Y	ENSP00000235739:S287Y	S	-	2	0	SLAMF1	158848909	0.702000	0.27816	0.017000	0.16124	0.053000	0.15095	3.699000	0.54778	1.332000	0.45431	-0.165000	0.13383	TCT		0.488	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			T	160582285	G	T	160582285	3	4	61	1	0	0	0	0	1	0	0	0	14404	942	33	2	65	2	SLAMF1	1	160582285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59096	160582285	88668336	735	8720										
SLAMF1	6504	broad.mit.edu	37	chr1	160607239	160607239	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttttgttcatgctcttatTtatcctttcatatgtcaggg	7	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160607239T>G	ENST00000302035.6	-	2	506	c.157A>C	c.(157-159)Aat>Cat	p.N53H	SLAMF1_ENST00000235739.5_Missense_Mutation_p.N53H|SLAMF1_ENST00000355199.3_Missense_Mutation_p.N53H|SLAMF1_ENST00000538290.1_Missense_Mutation_p.N53H	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	53	Ig-like V-type.				lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.N53H(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ATGCTCTTATTTATCCTTTCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											139	108	119					1																	160607239		2203	4300	6503	158873863	SO:0001583	missense	6504			U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.157A>C	1.37:g.160607239T>G	ENSP00000306190:p.Asn53His		158873863	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.725216	0.48833	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	4.19	4.19	0.49359	Signaling lymphocytic activation molecule, N-terminal (2);	0.591047	0.15229	N	0.273515	T	0.44180	0.1281	L	0.39898	1.24	0.09310	N	1	D;D	0.76494	0.999;0.998	D;D	0.70227	0.968;0.935	T	0.24083	-1.0170	10	0.56958	D	0.05	-16.2659	9.9337	0.41539	0.0:0.0:0.0:1.0	.	53;53	B4E2E4;Q13291	.;SLAF1_HUMAN	H	53	ENSP00000306190:N53H;ENSP00000235739:N53H;ENSP00000438406:N53H;ENSP00000347333:N53H	ENSP00000235739:N53H	N	-	1	0	SLAMF1	158873863	0.002000	0.14202	0.090000	0.20809	0.681000	0.39784	0.945000	0.29056	2.117000	0.64856	0.402000	0.26972	AAT		0.478	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			G	160607239	T	G	160607239	3	3	61	1	0	0	0	0	1	0	0	0	14404	1841	64	4	874	4	SLAMF1	1	160607239	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24954	160607239	88643382	736	8721										
F11R	50848	broad.mit.edu	37	chr1	160970814	160970814	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagaagcaactcacctgtGatcttgttattatagcaaac	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:160970814G>T	ENST00000368026.6	-	3	511	c.237C>A	c.(235-237)atC>atA	p.I79I	F11R_ENST00000537746.1_Silent_p.I79I|F11R_ENST00000472573.1_5'UTR|F11R_ENST00000289779.3_3'UTR	NM_016946.4	NP_058642.1	Q9Y624	JAM1_HUMAN	F11 receptor	79	Ig-like V-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.I79I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)	12	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)			ACTCACCTGTGATCTTGTTAT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											112	100	104					1																	160970814		2203	4300	6503	159237438	SO:0001819	synonymous_variant	50848			AF111713	CCDS1213.1	1q21.2-q21.3	2013-01-29	2003-02-07	2003-02-14	ENSG00000158769	ENSG00000158769		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14685	protein-coding gene	gene with protein product		605721	"junctional adhesion molecule 1"	JAM1		10395639, 7646439	Standard	NM_016946		Approved	PAM-1, JCAM, JAM-1, JAM-A, JAMA, CD321	uc009wtt.3	Q9Y624	OTTHUMG00000028602	ENST00000368026.6:c.237C>A	1.37:g.160970814G>T			159237438	B7Z941	Silent	SNP	ENST00000368026.6	37	CCDS1213.1																																																																																				0.498	F11R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071458.3	NM_016946		T	160970814	G	T	160970814	2	4	61	1	0	0	0	0	0	0	0	1	5351	1280	45	2		2	F11R	1	160970814	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	363575	160970814	88279807	737	8722										
ARHGAP30	257106	broad.mit.edu	37	chr1	161018732	161018732	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggcttcccccagcctcCcctctatcctcactggcctt	5	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161018732C>T	ENST00000368013.3	-	12	2399	c.2079G>A	c.(2077-2079)ggG>ggA	p.G693G	USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368016.3_Intron|ARHGAP30_ENST00000368015.1_Silent_p.G516G|USF1_ENST00000435396.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	693	Glu-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)	p.G693G(1)		breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCCCAGCCTCCCCTCTATCCT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	1											186	193	191					1																	161018732		2203	4300	6503	159285356	SO:0001819	synonymous_variant	257106			AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.2079G>A	1.37:g.161018732C>T			159285356	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																				0.557	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161018732	C	T	161018732	2	4	61	1	0	0	0	0	0	0	0	1	879	610	22	3		3	ARHGAP30	1	161018732	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47918	161018732	88231889	738	8723										
NIT1	4817	broad.mit.edu	37	chr1	161088609	161088609	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaggcctcctcacagattCctgtcccttctgtgtcctgg	8	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161088609C>T	ENST00000368009.2	+	2	112	c.36C>T	c.(34-36)ttC>ttT	p.F12F	NIT1_ENST00000496861.1_3'UTR|PFDN2_ENST00000468311.1_5'Flank|DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000392190.5_5'UTR|NIT1_ENST00000368007.4_Intron|PFDN2_ENST00000368010.3_5'Flank|NIT1_ENST00000368008.1_Silent_p.F12F	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	12					nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)	p.F12F(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CTCACAGATTCCTGTCCCTTC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											169	142	151					1																	161088609		2203	4300	6503	159355233	SO:0001819	synonymous_variant	4817			AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.36C>T	1.37:g.161088609C>T			159355233	B1AQP3|D3DVF4|O76091	Silent	SNP	ENST00000368009.2	37	CCDS1218.1																																																																																				0.502	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			T	161088609	C	T	161088609	2	4	61	1	0	0	0	0	0	0	0	1	10464	854	30	3		3	NIT1	1	161088609	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69877	161088609	88162012	739	8724										
DEDD	9191	broad.mit.edu	37	chr1	161092144	161092144	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgaggtaggtgagctcagaGaacttgatgtcacagatgat	13	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161092144G>T	ENST00000368006.3	-	6	964	c.750C>A	c.(748-750)ttC>ttA	p.F250L	DEDD_ENST00000545495.1_Missense_Mutation_p.F250L|DEDD_ENST00000489249.1_5'UTR|DEDD_ENST00000368005.1_Missense_Mutation_p.F280L|DEDD_ENST00000458050.2_Missense_Mutation_p.F250L|DEDD_ENST00000490843.2_Missense_Mutation_p.F250L|DEDD_ENST00000392188.1_Missense_Mutation_p.F280L|NIT1_ENST00000368008.1_Intron	NM_032998.2	NP_127491.1	O75618	DEDD_HUMAN	death effector domain containing	250					decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)	p.F250L(1)		cervix(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|skin(1)	10	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGAGCTCAGAGAACTTGATGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											152	140	144					1																	161092144		2203	4300	6503	159358768	SO:0001583	missense	9191			AF043733	CCDS1219.1	1q23.1	2008-02-05	2002-01-14		ENSG00000158796	ENSG00000158796			2755	protein-coding gene	gene with protein product		606841	"death effector domain-containing"			9774341, 9832420	Standard	XM_005245597		Approved	DEFT, FLDED1, CASP8IP1, KE05, DEDD1	uc001fxz.3	O75618	OTTHUMG00000033104	ENST00000368006.3:c.750C>A	1.37:g.161092144G>T	ENSP00000356985:p.Phe250Leu		159358768	D3DVF5|O60737	Missense_Mutation	SNP	ENST00000368006.3	37	CCDS1219.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676174	0.67928	.	.	ENSG00000158796	ENST00000368006;ENST00000392188;ENST00000545495;ENST00000458050;ENST00000541906;ENST00000368005;ENST00000535389	.	.	.	5.27	3.42	0.39159	.	0.000000	0.85682	D	0.000000	T	0.62672	0.2447	M	0.68952	2.095	0.58432	D	0.999999	D;D;D	0.76494	0.996;0.999;0.993	D;D;D	0.79784	0.986;0.993;0.935	T	0.67189	-0.5733	9	0.87932	D	0	.	10.0705	0.42330	0.1631:0.0:0.8369:0.0	.	207;280;250	B4DKM1;B1AQP5;O75618	.;.;DEDD_HUMAN	L	250;280;250;250;250;280;207	.	ENSP00000356984:F280L	F	-	3	2	DEDD	159358768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.530000	0.67141	0.803000	0.34113	-0.137000	0.14449	TTC		0.512	DEDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080582.1	NM_004216		T	161092144	G	T	161092144	3	4	61	1	0	0	0	0	1	0	0	0	4390	933	33	2	210	2	DEDD	1	161092144	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3535	161092144	88158477	740	8725										
B4GALT3	8703	broad.mit.edu	37	chr1	161145843	161145843	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggccgctccagcagcctcCgcaacatcctgggggtgaga	13	14	0	1	rs375294931		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161145843C>T	ENST00000319769.5	-	3	230	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Missense_Mutation_p.R3Q|B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	3					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.R3Q(1)		cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	CAGCAGCCTCCGCAACATCCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	40	41	41		8,8,8	4.5	1	1		41	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	3/394,3/394,3/394	161145843	1,13005	2203	4300	6503	159412467	SO:0001583	missense	8703			BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"Beta 4-glycosyltransferases"	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.8G>A	1.37:g.161145843C>T	ENSP00000320965:p.Arg3Gln		159412467	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604358	0.87157	0.0	1.16E-4	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000541560;ENST00000310413;ENST00000367998;ENST00000367997	T;T	0.52057	0.68;0.68	5.49	4.52	0.55395	.	0.434742	0.24815	N	0.035365	T	0.29158	0.0725	N	0.19112	0.55	0.40091	D	0.976259	D;D	0.65815	0.988;0.995	B;P	0.48952	0.411;0.596	T	0.06092	-1.0846	10	0.42905	T	0.14	-12.918	14.0074	0.64473	0.152:0.8479:0.0:0.0	.	3;3	B3KPV4;O60512	.;B4GT3_HUMAN	Q	3	ENSP00000320965:R3Q;ENSP00000356977:R3Q	ENSP00000308551:R3Q	R	-	2	0	B4GALT3	159412467	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.266000	0.65525	2.570000	0.86706	0.557000	0.71058	CGG		0.617	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779		T	161145843	C	T	161145843	3	4	61	1	0	0	0	0	1	0	0	0	1273	652	23	1	1197	1	B4GALT3	1	161145843	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53699	161145843	88104778	741	8726										
ADAMTS4	9507	broad.mit.edu	37	chr1	161167952	161167952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtggagttcagccccccGatattgtaacacgcctaaca	10	12	1	0	rs546291574		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161167952G>A	ENST00000367996.5	-	1	894	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W	ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Missense_Mutation_p.R156W|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	156					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)	p.R156W(2)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	TCAGCCCCCCGATATTGTAAC	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	1											57	58	58					1																	161167952		2203	4300	6503	159434576	SO:0001583	missense	9507			AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.466C>T	1.37:g.161167952G>A	ENSP00000356975:p.Arg156Trp		159434576	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.401656	0.42613	.	.	ENSG00000158859	ENST00000367996;ENST00000367995	T;T	0.06449	3.3;3.3	5.44	4.5	0.54988	Peptidase M12B, propeptide (1);	0.244243	0.27773	N	0.017910	T	0.09202	0.0227	L	0.52573	1.65	0.31738	N	0.636143	D;D	0.76494	0.999;0.999	P;P	0.61658	0.877;0.892	T	0.01512	-1.1336	10	0.66056	D	0.02	.	14.1608	0.65446	0.0:0.0:0.8486:0.1514	.	156;156	Q5VTW1;O75173	.;ATS4_HUMAN	W	156	ENSP00000356975:R156W;ENSP00000356974:R156W	ENSP00000356974:R156W	R	-	1	2	ADAMTS4	159434576	0.797000	0.28877	0.018000	0.16275	0.446000	0.32137	2.515000	0.45512	1.230000	0.43646	0.491000	0.48974	CGG		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		A	161167952	G	A	161167952	3	1	61	1	0	0	0	0	1	0	0	0	268	1057	37	1	2083	1	ADAMTS4	1	161167952	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22109	161167952	88082669	742	8727										
NDUFS2	4720	broad.mit.edu	37	chr1	161179284	161179284	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcacagtgctgtttggaGaaatcacacgtttgttgaac	9	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161179284G>T	ENST00000367993.3	+	6	974	c.526G>T	c.(526-528)Gaa>Taa	p.E176*	NDUFS2_ENST00000476409.2_Nonsense_Mutation_p.E78*|NDUFS2_ENST00000392179.4_Nonsense_Mutation_p.E176*	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	176					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)	p.E176*(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	GCTGTTTGGAGAAATCACACG	0.522											OREG0013941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	1											90	78	82					1																	161179284		2203	4300	6503	159445908	SO:0001587	stop_gained	4720			BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.526G>T	1.37:g.161179284G>T	ENSP00000356972:p.Glu176*	1814	159445908	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Nonsense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	.	.	.	.	.	.	.	.	.	.	G	38	6.677258	0.97755	.	.	ENSG00000158864	ENST00000367993;ENST00000392179;ENST00000476409	.	.	.	5.15	5.15	0.70609	.	0.108901	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.5462	0.87863	0.0:0.0:1.0:0.0	.	.	.	.	X	176;176;78	.	ENSP00000356972:E176X	E	+	1	0	NDUFS2	159445908	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.709000	0.91379	2.654000	0.90174	0.655000	0.94253	GAA		0.522	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		T	161179284	G	T	161179284	4	4	61	1	0	0	0	0	0	1	0	0	10323	943	33	2	544	2	NDUFS2	1	161179284	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11332	161179284	88071337	743	8728										
NDUFS2	4720	broad.mit.edu	37	chr1	161180119	161180119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaacaataggatctggcGaaatcggacaattgacattg	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161180119G>A	ENST00000367993.3	+	9	1254	c.806G>A	c.(805-807)cGa>cAa	p.R269Q	NDUFS2_ENST00000476409.2_Missense_Mutation_p.R171Q|NDUFS2_ENST00000465923.1_3'UTR|NDUFS2_ENST00000392179.4_Missense_Mutation_p.R269Q	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	269					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)	p.R269Q(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	AGGATCTGGCGAAATCGGACA	0.428											OREG0013941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											137	123	128					1																	161180119		2203	4300	6503	159446743	SO:0001583	missense	4720			BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.806G>A	1.37:g.161180119G>A	ENSP00000356972:p.Arg269Gln	1814	159446743	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163577	0.57476	.	.	ENSG00000158864	ENST00000367993;ENST00000392179;ENST00000476409	D;D;D	0.87966	-2.32;-2.32;-2.32	5.29	3.23	0.37069	NADH-quinone oxidoreductase, subunit D (1);	0.491311	0.21033	N	0.081316	T	0.68339	0.2990	L	0.38175	1.15	0.37233	D	0.905767	B;B;B;B	0.13145	0.007;0.002;0.002;0.002	B;B;B;B	0.19946	0.027;0.005;0.002;0.003	T	0.61352	-0.7080	9	0.62326	D	0.03	.	7.3489	0.26678	0.2864:0.0:0.7136:0.0	.	218;171;269;269	B7Z792;B7Z9L2;Q53HG2;O75306	.;.;.;NDUS2_HUMAN	Q	269;269;171	ENSP00000356972:R269Q;ENSP00000376018:R269Q;ENSP00000446447:R171Q	ENSP00000356972:R269Q	R	+	2	0	NDUFS2	159446743	1.000000	0.71417	0.917000	0.36280	0.975000	0.68041	2.409000	0.44583	0.674000	0.31244	0.655000	0.94253	CGA		0.428	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		A	161180119	G	A	161180119	3	1	61	1	0	0	0	0	1	0	0	0	10323	1058	37	1	836	1	NDUFS2	1	161180119	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	835	161180119	88070502	744	8729										
NR1I3	9970	broad.mit.edu	37	chr1	161200917	161200917	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgctcaccaggagagaaGagggccatggcagccaagag	16	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161200917G>T	ENST00000367982.4	-	7	968	c.813C>A	c.(811-813)ctC>ctA	p.L271L	NR1I3_ENST00000505005.1_Intron|NR1I3_ENST00000367979.2_Silent_p.L271L|NR1I3_ENST00000412844.2_Silent_p.L242L|NR1I3_ENST00000367985.3_Intron|NR1I3_ENST00000367984.4_Intron|NR1I3_ENST00000511748.1_Intron|NR1I3_ENST00000506209.1_Silent_p.L238L|NR1I3_ENST00000512372.1_Intron|NR1I3_ENST00000511944.1_Intron|NR1I3_ENST00000367981.3_Silent_p.L238L|NR1I3_ENST00000504010.1_Intron|NR1I3_ENST00000508387.1_Intron|NR1I3_ENST00000508740.1_Silent_p.L238L|NR1I3_ENST00000367983.4_Silent_p.L267L|NR1I3_ENST00000511676.1_Silent_p.L238L|NR1I3_ENST00000479324.1_5'UTR|NR1I3_ENST00000437437.2_Silent_p.L238L|NR1I3_ENST00000428574.2_Silent_p.L267L|NR1I3_ENST00000367980.2_Silent_p.L271L|NR1I3_ENST00000442691.2_Silent_p.L271L|NR1I3_ENST00000502985.1_Intron|NR1I3_ENST00000515621.1_Silent_p.L192L			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	271					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.L267L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CAGGAGAGAAGAGGGCCATGG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	1											50	52	51					1																	161200917		2203	4300	6503	159467541	SO:0001819	synonymous_variant	9970			Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"Nuclear hormone receptors"	7969	protein-coding gene	gene with protein product	"constitutive androstane receptor"	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.813C>A	1.37:g.161200917G>T			159467541	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Silent	SNP	ENST00000367982.4	37	CCDS41430.1																																																																																				0.537	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			T	161200917	G	T	161200917	2	4	61	1	0	0	0	0	0	0	0	1	10652	929	33	2		2	NR1I3	1	161200917	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20798	161200917	88049704	745	8730										
NR1I3	9970	broad.mit.edu	37	chr1	161206282	161206282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagccctcacaagtcagcGcattaaagtggtagcctgtg	11	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161206282G>A	ENST00000367982.4	-	2	229	c.74C>T	c.(73-75)gCg>gTg	p.A25V	NR1I3_ENST00000505005.1_Missense_Mutation_p.A25V|NR1I3_ENST00000367979.2_Missense_Mutation_p.A25V|NR1I3_ENST00000515452.1_Missense_Mutation_p.A25V|NR1I3_ENST00000412844.2_Intron|NR1I3_ENST00000367985.3_Missense_Mutation_p.A25V|NR1I3_ENST00000367984.4_Missense_Mutation_p.A25V|NR1I3_ENST00000511748.1_Intron|NR1I3_ENST00000506209.1_Intron|NR1I3_ENST00000512372.1_Intron|NR1I3_ENST00000511944.1_Missense_Mutation_p.A25V|NR1I3_ENST00000367981.3_Intron|NR1I3_ENST00000504010.1_Intron|NR1I3_ENST00000508387.1_Intron|NR1I3_ENST00000508740.1_Intron|NR1I3_ENST00000367983.4_Missense_Mutation_p.A25V|NR1I3_ENST00000511676.1_Intron|NR1I3_ENST00000437437.2_Intron|NR1I3_ENST00000428574.2_Missense_Mutation_p.A25V|NR1I3_ENST00000367980.2_Missense_Mutation_p.A25V|NR1I3_ENST00000442691.2_Missense_Mutation_p.A25V|NR1I3_ENST00000502985.1_Missense_Mutation_p.A25V|NR1I3_ENST00000515621.1_Intron			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	25					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.A25V(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			ACAAGTCAGCGCATTAAAGTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											182	163	169					1																	161206282		2203	4300	6503	159472906	SO:0001583	missense	9970			Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"Nuclear hormone receptors"	7969	protein-coding gene	gene with protein product	"constitutive androstane receptor"	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.74C>T	1.37:g.161206282G>A	ENSP00000356961:p.Ala25Val		159472906	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	37	CCDS41430.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807780	0.50421	.	.	ENSG00000143257	ENST00000367983;ENST00000367980;ENST00000442691;ENST00000428574;ENST00000505005;ENST00000367982;ENST00000502985;ENST00000511944;ENST00000367984;ENST00000367985;ENST00000367979;ENST00000515452	D;D;D;D;D;D;D;D;D;D;D;D	0.96522	-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04	5.44	5.44	0.79542	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.153402	0.56097	D	0.000021	D	0.91613	0.7350	N	0.11724	0.165	0.42474	D	0.992833	D;D;D;D;P;D;D;D;P;D	0.89917	0.999;0.97;0.993;0.987;0.951;0.986;1.0;0.982;0.741;1.0	D;P;P;D;P;P;D;P;B;D	0.91635	0.954;0.784;0.62;0.924;0.692;0.895;0.999;0.631;0.416;0.998	D	0.87326	0.2321	9	0.06099	T	0.92	.	10.0637	0.42290	0.0885:0.0:0.9115:0.0	.	25;25;25;25;25;25;25;25;25;25	B7Z8R7;Q6GZ85;E9PHC8;Q0VAC9;F1D8Q1;Q14994;E9PC13;Q6GZ72;Q4U0F0;E9PB75	.;.;.;.;.;NR1I3_HUMAN;.;.;.;.	V	25	ENSP00000356962:A25V;ENSP00000356959:A25V;ENSP00000406493:A25V;ENSP00000412672:A25V;ENSP00000424934:A25V;ENSP00000356961:A25V;ENSP00000421374:A25V;ENSP00000426292:A25V;ENSP00000356963:A25V;ENSP00000356965:A25V;ENSP00000356958:A25V;ENSP00000427034:A25V	ENSP00000356958:A25V	A	-	2	0	NR1I3	159472906	1.000000	0.71417	0.993000	0.49108	0.396000	0.30629	3.806000	0.55583	2.837000	0.97791	0.655000	0.94253	GCG		0.532	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			A	161206282	G	A	161206282	3	1	61	1	0	0	0	0	1	0	0	0	10652	1087	38	1	1126	1	NR1I3	1	161206282	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5365	161206282	88044339	746	8731										
MPZ	4359	broad.mit.edu	37	chr1	161276520	161276520	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcaaagacatacagcgtGacctgagaggtcttgcccac	9	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161276520G>A	ENST00000533357.1	-	3	492	c.426C>T	c.(424-426)gtC>gtT	p.V142V	MPZ_ENST00000491222.2_5'UTR|MPZ_ENST00000360451.6_Silent_p.V152V|MPZ_ENST00000526189.1_Intron|MPZ_ENST00000336559.4_Silent_p.V142V	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	142	Ig-like V-type.				cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.V152V(1)		central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			CATACAGCGTGACCTGAGAGG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											203	169	181					1																	161276520		2203	4300	6503	159543144	SO:0001819	synonymous_variant	4359			BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"Immunoglobulin superfamily / V-set domain containing"	7225	protein-coding gene	gene with protein product		159440	"Charcot-Marie-Tooth neuropathy 1B"	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.426C>T	1.37:g.161276520G>A			159543144	Q16072|Q5VTH4|Q92677|Q9BR67	Silent	SNP	ENST00000533357.1	37	CCDS1229.2																																																																																				0.502	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530		A	161276520	G	A	161276520	2	1	61	1	0	0	0	0	0	0	0	1	9778	1277	45	3		3	MPZ	1	161276520	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70238	161276520	87974101	747	8732										
FCGR2C	2214	broad.mit.edu	37	chr1	161559543	161559543	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccaacaacaatgacagcGgggagtacacgtgccagact	12	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161559543G>A	ENST00000540048.1	-	2	94				FCGR2B_ENST00000367960.5_Intron|FCGR2C_ENST00000473530.2_RNA|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367962.4_Intron|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2C_ENST00000466542.2_RNA			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CAATGACAGCGGGGAGTACAC	0.597																																																0			1											35	35	35					1																	161559543		2151	4133	6284	159826167	SO:0001627	intron_variant	9103			BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+40614C>T	1.37:g.161559543G>A			159826167	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37																																																																																					0.597	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569		A	161559543	G	A	161559543	1	1	61	0	1	0	0	0	0	0	0	0	5802	1116	39	1		1	FCGR2C	1	161559543	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283023	161559543	87691078	748	8733										
FCRLB	127943	broad.mit.edu	37	chr1	161693282	161693282	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctccagcccatcagcactCtctggtatttgggccaccta	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161693282C>T	ENST00000367948.2	+	5	393	c.178C>T	c.(178-180)Ctc>Ttc	p.L60F	FCRLB_ENST00000392158.1_Missense_Mutation_p.L60F|FCRLB_ENST00000336830.5_Missense_Mutation_p.L60F|FCRLB_ENST00000367946.3_Missense_Mutation_p.L60F|FCRLB_ENST00000367944.3_Missense_Mutation_p.L53F|FCRLB_ENST00000367945.1_Missense_Mutation_p.L53F			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	60	Ig-like C2-type 1.				negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)		p.L60F(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CATCAGCACTCTCTGGTATTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	124	126					1																	161693282		2203	4300	6503	159959906	SO:0001583	missense	127943			AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26431	protein-coding gene	gene with protein product		609251	"Fc receptor-like and mucin-like 2"	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.178C>T	1.37:g.161693282C>T	ENSP00000356925:p.Leu60Phe		159959906	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	37	CCDS30927.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.224544	0.58668	.	.	ENSG00000162746	ENST00000367948;ENST00000367946;ENST00000367945;ENST00000336830;ENST00000367944;ENST00000392158	T;T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68;2.68	5.76	3.58	0.41010	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.44902	D	0.000416	T	0.13072	0.0317	L	0.38175	1.15	0.31341	N	0.683638	D;P;D;P;P	0.89917	0.998;0.859;1.0;0.859;0.747	P;B;D;B;B	0.74674	0.862;0.36;0.984;0.36;0.397	T	0.01814	-1.1268	10	0.62326	D	0.03	.	8.7067	0.34358	0.0:0.8027:0.0:0.1973	.	53;53;60;60;60	Q6BAA4-3;Q6BAA4-5;Q6BAA4-2;Q6BAA4-4;Q6BAA4	.;.;.;.;FCRLB_HUMAN	F	60;60;53;60;53;60	ENSP00000356925:L60F;ENSP00000356923:L60F;ENSP00000356922:L53F;ENSP00000338598:L60F;ENSP00000356921:L53F;ENSP00000375999:L60F	ENSP00000338598:L60F	L	+	1	0	FCRLB	159959906	0.973000	0.33851	0.993000	0.49108	0.995000	0.86356	1.464000	0.35288	1.429000	0.47314	0.655000	0.94253	CTC		0.557	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		T	161693282	C	T	161693282	3	4	61	1	0	0	0	0	1	0	0	0	5820	913	32	3	188	3	FCRLB	1	161693282	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133739	161693282	87557339	749	8734										
ATF6	22926	broad.mit.edu	37	chr1	161753848	161753848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttattcagtctcgtctcctCggtcagtggactcttattct	8	11	6	0	rs150872316		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161753848C>T	ENST00000367942.3	+	4	383	c.316C>T	c.(316-318)Cgg>Tgg	p.R106W		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	106	Transcription activation.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.R106W(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	CTCGTCTCCTCGGTCAGTGGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TRP/ARG	0,4406		0,0,2203	160	154	156		316	4.8	1	1	dbSNP_134	156	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ATF6	NM_007348.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	106/671	161753848	1,13005	2203	4300	6503	160020472	SO:0001583	missense	22926			AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.316C>T	1.37:g.161753848C>T	ENSP00000356919:p.Arg106Trp		160020472	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	16.32	3.090696	0.55968	0.0	1.16E-4	ENSG00000118217	ENST00000367942	T	0.14766	2.48	5.72	4.79	0.61399	.	0.669254	0.15042	N	0.283801	T	0.05181	0.0138	L	0.29908	0.895	0.22562	N	0.99899	P;D	0.56968	0.926;0.978	B;B	0.40410	0.153;0.328	T	0.17018	-1.0383	9	0.66056	D	0.02	-3.0892	12.6162	0.56578	0.0:0.8337:0.1663:0.0	.	106;107	P18850;Q59H30	ATF6A_HUMAN;.	W	106	ENSP00000356919:R106W	ENSP00000356919:R106W	R	+	1	2	ATF6	160020472	0.366000	0.25014	0.993000	0.49108	0.985000	0.73830	0.854000	0.27791	1.374000	0.46228	0.655000	0.94253	CGG		0.398	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		T	161753848	C	T	161753848	3	4	61	1	0	0	0	0	1	0	0	0	1085	875	31	1	330	1	ATF6	1	161753848	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60566	161753848	87496773	750	8735										
ATF6	22926	broad.mit.edu	37	chr1	161928323	161928323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcctccatatcaaaagttCgtcagttcctccttacctcc	4	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161928323C>T	ENST00000367942.3	+	16	1959	c.1892C>T	c.(1891-1893)tCg>tTg	p.S631L		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	631					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.S631L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	ATCAAAAGTTCGTCAGTTCCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											185	144	158					1																	161928323		2203	4300	6503	160194947	SO:0001583	missense	22926			AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1892C>T	1.37:g.161928323C>T	ENSP00000356919:p.Ser631Leu		160194947	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	.	.	.	.	.	.	.	.	.	.	C	33	5.226069	0.95173	.	.	ENSG00000118217	ENST00000367942	T	0.19806	2.12	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.39809	0.1092	M	0.71036	2.16	0.47341	D	0.999391	D	0.89917	1.0	D	0.80764	0.994	T	0.25433	-1.0132	9	0.87932	D	0	-9.4663	17.2159	0.86944	0.0:1.0:0.0:0.0	.	631	P18850	ATF6A_HUMAN	L	631	ENSP00000356919:S631L	ENSP00000356919:S631L	S	+	2	0	ATF6	160194947	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	6.470000	0.73558	2.657000	0.90304	0.650000	0.86243	TCG		0.517	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		T	161928323	C	T	161928323	3	4	61	1	0	0	0	0	1	0	0	0	1085	893	31	1	1954	1	ATF6	1	161928323	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174475	161928323	87322298	751	8736										
OLFML2B	25903	broad.mit.edu	37	chr1	161953493	161953493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagatgacatggtaagtgAcctggtggccattgtcccag	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:161953493A>G	ENST00000294794.3	-	8	2648	c.2225T>C	c.(2224-2226)gTc>gCc	p.V742A	OLFML2B_ENST00000367938.1_Missense_Mutation_p.V225A|OLFML2B_ENST00000367940.2_Missense_Mutation_p.V743A	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	742	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.V742A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			ATGGTAAGTGACCTGGTGGCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											204	180	188					1																	161953493		2203	4300	6503	160220117	SO:0001583	missense	25903			BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.2225T>C	1.37:g.161953493A>G	ENSP00000294794:p.Val742Ala		160220117	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	37	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178726	0.78564	.	.	ENSG00000162745	ENST00000294794;ENST00000367940;ENST00000367938	D;D;D	0.92647	-3.08;-3.08;-3.08	5.3	5.3	0.74995	Olfactomedin-like (3);	.	.	.	.	D	0.95752	0.8618	M	0.89353	3.025	0.42683	D	0.993550	D;D	0.76494	0.997;0.999	D;D	0.71414	0.973;0.973	D	0.96713	0.9527	8	0.87932	D	0	.	13.4819	0.61340	1.0:0.0:0.0:0.0	.	743;742	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	A	742;743;225	ENSP00000294794:V742A;ENSP00000356917:V743A;ENSP00000356915:V225A	ENSP00000294794:V742A	V	-	2	0	OLFML2B	160220117	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.153000	0.94687	2.116000	0.64780	0.533000	0.62120	GTC		0.547	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		G	161953493	A	G	161953493	3	3	61	1	0	0	0	0	1	0	0	0	10889	275	10	4	31	4	OLFML2B	1	161953493	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	25170	161953493	87297128	752	8737										
NOS1AP	9722	broad.mit.edu	37	chr1	162257186	162257186	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagtgagcattatggtttCagtggatggagtgaaagtga	15	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:162257186C>A	ENST00000361897.5	+	3	632	c.230C>A	c.(229-231)tCa>tAa	p.S77*	NOS1AP_ENST00000530878.1_Nonsense_Mutation_p.S77*	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	77	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)	p.S77*(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			ATTATGGTTTCAGTGGATGGA	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											143	140	141					1																	162257186		2203	4300	6503	160523810	SO:0001587	stop_gained	9722			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.230C>A	1.37:g.162257186C>A	ENSP00000355133:p.Ser77*		160523810	B7ZLF5|O43564|Q3T551|Q5VU95	Nonsense_Mutation	SNP	ENST00000361897.5	37	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	C	40	8.245702	0.98724	.	.	ENSG00000198929	ENST00000530878;ENST00000361897	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1378	0.81497	0.0:1.0:0.0:0.0	.	.	.	.	X	77	.	ENSP00000355133:S77X	S	+	2	0	NOS1AP	160523810	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.546000	0.73887	2.460000	0.83146	0.655000	0.94253	TCA		0.413	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		A	162257186	C	A	162257186	4	1	61	1	0	0	0	0	0	1	0	0	10573	838	29	2	240	2	NOS1AP	1	162257186	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	303693	162257186	86993435	753	8738										
UHMK1	127933	broad.mit.edu	37	chr1	162469778	162469778	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtttacaatccacttttCtccaaatgtgccatcacgct	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:162469778C>A	ENST00000489294.1	+	2	460	c.302C>A	c.(301-303)tCt>tAt	p.S101Y	UHMK1_ENST00000538489.1_Missense_Mutation_p.S101Y|UHMK1_ENST00000545294.1_Missense_Mutation_p.S27Y|UHMK1_ENST00000282169.8_3'UTR	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	101	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)	p.S101Y(1)		endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			ATCCACTTTTCTCCAAATGTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											197	180	185					1																	162469778		2203	4300	6503	160736402	SO:0001583	missense	127933			BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"RNA binding motif (RRM) containing"	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.302C>A	1.37:g.162469778C>A	ENSP00000420270:p.Ser101Tyr		160736402	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689306	0.68271	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.66099	-0.19;2.01;2.01	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.184155	0.49305	D	0.000155	T	0.44644	0.1303	L	0.29908	0.895	.	.	.	P;P;P	0.49447	0.804;0.837;0.924	B;B;P	0.44772	0.26;0.377;0.46	T	0.48917	-0.8992	9	0.42905	T	0.14	-4.0587	16.4617	0.84056	0.0:1.0:0.0:0.0	.	101;101;27	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	Y	27;101;101	ENSP00000441226:S27Y;ENSP00000446416:S101Y;ENSP00000420270:S101Y	ENSP00000420270:S101Y	S	+	2	0	UHMK1	160736402	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.834000	0.55798	2.739000	0.93911	0.655000	0.94253	TCT		0.383	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866		A	162469778	C	A	162469778	3	1	61	1	0	0	0	0	1	0	0	0	17006	913	32	2	358	2	UHMK1	1	162469778	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212592	162469778	86780843	754	8739										
DDR2	4921	broad.mit.edu	37	chr1	162724618	162724618	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggatggcactcgctggatCtcttggcggaaccgtcatgg	15	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:162724618C>T	ENST00000367922.3	+	6	828	c.390C>T	c.(388-390)atC>atT	p.I130I	DDR2_ENST00000367921.3_Silent_p.I130I	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	130	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.I130I(1)		central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	CTCGCTGGATCTCTTGGCGGA	0.532																																					NSCLC(161;314 2006 8283 19651 23192)											1	Substitution - coding silent(1)	large_intestine(1)	1											91	74	79					1																	162724618		2203	4300	6503	160991242	SO:0001819	synonymous_variant	4921			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.390C>T	1.37:g.162724618C>T			160991242	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																				0.532	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		T	162724618	C	T	162724618	2	4	61	1	0	0	0	0	0	0	0	1	4343	903	32	3		3	DDR2	1	162724618	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	254840	162724618	86526003	755	8740										
RGS4	5999	broad.mit.edu	37	chr1	163038728	163038728	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcagatcttggaccatgTataatatgatgcttctaatc	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163038728T>C	ENST00000367909.6	+	0	0				RGS4_ENST00000367908.4_5'Flank|RGS4_ENST00000421743.2_Missense_Mutation_p.Y2H|RGS4_ENST00000531057.1_5'Flank|RGS4_ENST00000527809.1_5'Flank	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4						inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.Y2H(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						TTGGACCATGTATAATATGAT	0.458																																					Ovarian(76;1257 1738 3039 6086)											1	Substitution - Missense(1)	large_intestine(1)	1											62	63	63					1																	163038728		1967	4164	6131	161305352	SO:0001631	upstream_gene_variant	5999			BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417		1.37:g.163038728T>C	Exception_encountered		161305352	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	37	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.477958	0.26511	.	.	ENSG00000117152	ENST00000421743	T	0.58940	0.3	4.2	-2.68	0.06041	.	.	.	.	.	T	0.10208	0.0250	N	0.08118	0	0.30974	N	0.7227589999999999	B	0.33637	0.42	B	0.23716	0.048	T	0.14200	-1.0481	8	0.87932	D	0	.	0.8476	0.01165	0.1672:0.3057:0.1714:0.3558	.	2	A7XA59	.	H	2	ENSP00000397181:Y2H	ENSP00000397181:Y2H	Y	+	1	0	RGS4	161305352	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.107000	0.03316	-0.630000	0.05567	0.460000	0.39030	TAT		0.458	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		C	163038728	T	C	163038728	1	2	61	0	1	0	0	0	0	0	0	0	13344	1638	57	4		4	RGS4	1	163038728	5'Flank	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	314110	163038728	86211893	756	8741										
RGS5	8490	broad.mit.edu	37	chr1	163138119	163138119	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccaactgagtctggcttCtggaggagaattcccaactt	9	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163138119C>A	ENST00000313961.5	-	2	361	c.84G>T	c.(82-84)caG>caT	p.Q28H	RGS5_ENST00000534288.1_5'UTR|RGS5_ENST00000367903.3_Missense_Mutation_p.Q48H|RGS5_ENST00000530507.1_Missense_Mutation_p.Q28H|RGS5_ENST00000527988.1_Intron|RP11-267N12.1_ENST00000415437.1_RNA	NM_001254749.1|NM_003617.3	NP_001241678.1|NP_003608.1	O15539	RGS5_HUMAN	regulator of G-protein signaling 5	28					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.Q28H(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20			LUSC - Lung squamous cell carcinoma(543;0.187)			AGTCTGGCTTCTGGAGGAGAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											203	194	197					1																	163138119		2203	4300	6503	161404743	SO:0001583	missense	8490			AF030108	CCDS1244.1, CCDS55652.1, CCDS58041.1	1q23.1	2008-02-05	2007-08-14		ENSG00000143248	ENSG00000143248		"Regulators of G-protein signaling"	10001	protein-coding gene	gene with protein product		603276	"regulator of G-protein signalling 5"			9747037	Standard	NM_003617		Approved		uc021pdt.1	O15539	OTTHUMG00000034441	ENST00000313961.5:c.84G>T	1.37:g.163138119C>A	ENSP00000319308:p.Gln28His		161404743	E9PMP5|Q53XA9|Q599J0	Missense_Mutation	SNP	ENST00000313961.5	37	CCDS1244.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195372	0.58126	.	.	ENSG00000143248	ENST00000313961;ENST00000367903;ENST00000530507	T;T;T	0.56941	0.52;0.43;0.52	5.79	4.88	0.63580	.	0.113910	0.64402	D	0.000009	T	0.31765	0.0807	M	0.64630	1.985	0.44366	D	0.997261	B	0.27679	0.185	B	0.26310	0.068	T	0.20140	-1.0284	9	0.22706	T	0.39	.	12.6809	0.56922	0.0:0.9202:0.0:0.0798	.	28	O15539	RGS5_HUMAN	H	28;48;28	ENSP00000319308:Q28H;ENSP00000356879:Q48H;ENSP00000433001:Q28H	ENSP00000319308:Q28H	Q	-	3	2	RGS5	161404743	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.866000	0.48420	1.455000	0.47813	0.557000	0.71058	CAG		0.448	RGS5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083264.1	NM_003617		A	163138119	C	A	163138119	3	1	61	1	0	0	0	0	1	0	0	0	13345	912	32	2	477	2	RGS5	1	163138119	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99391	163138119	86112502	757	8742										
NUF2	83540	broad.mit.edu	37	chr1	163295940	163295940	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggtaaaaacctcaccaaGaatgatctttatccaaatcc	5	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163295940G>T	ENST00000271452.3	+	2	378	c.99G>T	c.(97-99)aaG>aaT	p.K33N	NUF2_ENST00000524800.1_Missense_Mutation_p.K33N|NUF2_ENST00000490881.1_3'UTR|NUF2_ENST00000367900.3_Missense_Mutation_p.K33N	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	33	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.K33N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					ACCTCACCAAGAATGATCTTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	116	116					1																	163295940		2203	4300	6503	161562564	SO:0001583	missense	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.99G>T	1.37:g.163295940G>T	ENSP00000271452:p.Lys33Asn		161562564	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608752	0.66558	.	.	ENSG00000143228	ENST00000534289;ENST00000450453;ENST00000524800;ENST00000442820;ENST00000367900;ENST00000271452	T;T;T	0.35236	1.37;1.32;1.32	5.68	3.83	0.44106	.	0.000000	0.85682	D	0.000000	T	0.37376	0.1001	M	0.63843	1.955	0.50632	D	0.999888	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.998	T	0.28522	-1.0041	9	0.25751	T	0.34	-29.2521	8.2218	0.31545	0.2438:0.0:0.7562:0.0	.	33;33;33	E9PQC4;Q9BZD4;B1AQT4	.;NUF2_HUMAN;.	N	33	ENSP00000436888:K33N;ENSP00000356875:K33N;ENSP00000271452:K33N	ENSP00000271452:K33N	K	+	3	2	NUF2	161562564	1.000000	0.71417	0.999000	0.59377	0.892000	0.51952	1.739000	0.38217	0.891000	0.36235	0.650000	0.86243	AAG		0.368	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		T	163295940	G	T	163295940	3	4	61	1	0	0	0	0	1	0	0	0	10778	933	33	2	101	2	NUF2	1	163295940	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157821	163295940	85954681	758	8743										
NUF2	83540	broad.mit.edu	37	chr1	163313567	163313567	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttgaaagaaatacaagaGagtttgaaaacaaaaattgt	7	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163313567G>T	ENST00000271452.3	+	10	993	c.714G>T	c.(712-714)gaG>gaT	p.E238D	NUF2_ENST00000524800.1_Missense_Mutation_p.E238D|NUF2_ENST00000367900.3_Missense_Mutation_p.E238D	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	238	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.E238D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					AAATACAAGAGAGTTTGAAAA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											24	27	26					1																	163313567		2139	4264	6403	161580191	SO:0001583	missense	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.714G>T	1.37:g.163313567G>T	ENSP00000271452:p.Glu238Asp		161580191	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	9.585	1.124502	0.20959	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.33865	1.4;1.39;1.39	4.83	-1.03	0.10102	.	0.481398	0.24499	N	0.037997	T	0.03959	0.0111	N	0.08118	0	0.34727	D	0.729342	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.003	T	0.35724	-0.9777	9	0.20046	T	0.44	-5.3096	2.3635	0.04313	0.2699:0.419:0.2:0.111	.	238;238	E9PQC4;Q9BZD4	.;NUF2_HUMAN	D	238	ENSP00000436888:E238D;ENSP00000356875:E238D;ENSP00000271452:E238D	ENSP00000271452:E238D	E	+	3	2	NUF2	161580191	0.926000	0.31397	0.841000	0.33234	0.957000	0.61999	-0.016000	0.12613	-0.273000	0.09246	0.585000	0.79938	GAG		0.289	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		T	163313567	G	T	163313567	3	4	61	1	0	0	0	0	1	0	0	0	10778	933	33	2	748	2	NUF2	1	163313567	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17627	163313567	85937054	759	8744										
NUF2	83540	broad.mit.edu	37	chr1	163315501	163315501	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatatgaaatctatggaGactcagttgactgcctgcct	9	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163315501G>T	ENST00000271452.3	+	11	1120	c.841G>T	c.(841-843)Gac>Tac	p.D281Y	NUF2_ENST00000524800.1_Intron|NUF2_ENST00000367900.3_Missense_Mutation_p.D281Y	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	281	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.D281Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					AATCTATGGAGACTCAGTTGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	108	109					1																	163315501		2203	4300	6503	161582125	SO:0001583	missense	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.841G>T	1.37:g.163315501G>T	ENSP00000271452:p.Asp281Tyr		161582125	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.056790	0.55325	.	.	ENSG00000143228	ENST00000367900;ENST00000271452	T;T	0.34275	1.37;1.37	4.88	4.88	0.63580	.	0.138617	0.64402	D	0.000004	T	0.46464	0.1394	L	0.56769	1.78	0.46927	D	0.999251	D	0.89917	1.0	D	0.91635	0.999	T	0.47315	-0.9127	9	0.54805	T	0.06	-21.8775	13.4109	0.60942	0.0:0.0:1.0:0.0	.	281	Q9BZD4	NUF2_HUMAN	Y	281	ENSP00000356875:D281Y;ENSP00000271452:D281Y	ENSP00000271452:D281Y	D	+	1	0	NUF2	161582125	1.000000	0.71417	0.987000	0.45799	0.508000	0.34012	5.239000	0.65371	2.518000	0.84900	0.591000	0.81541	GAC		0.358	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		T	163315501	G	T	163315501	3	4	61	1	0	0	0	0	1	0	0	0	10778	942	33	2	879	2	NUF2	1	163315501	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1934	163315501	85935120	760	8745										
NUF2	83540	broad.mit.edu	37	chr1	163317623	163317623	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaagactgaagaaaattCgttcaaaagactgatgattg	9	4	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:163317623C>T	ENST00000271452.3	+	12	1298	c.1019C>T	c.(1018-1020)tCg>tTg	p.S340L	NUF2_ENST00000524800.1_Missense_Mutation_p.S293L|NUF2_ENST00000367900.3_Missense_Mutation_p.S340L	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	340	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.S340L(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					GAAGAAAATTCGTTCAAAAGA	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	1											80	82	81					1																	163317623		2203	4300	6503	161584247	SO:0001583	missense	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.1019C>T	1.37:g.163317623C>T	ENSP00000271452:p.Ser340Leu		161584247	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201709	0.79015	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.33438	1.41;1.52;1.52	6.03	5.11	0.69529	.	0.200321	0.45606	N	0.000343	T	0.21590	0.0520	L	0.51422	1.61	0.34261	D	0.679949	D;D	0.63046	0.992;0.992	P;P	0.48063	0.565;0.565	T	0.02144	-1.1206	9	0.27082	T	0.32	-6.7455	12.874	0.57980	0.0:0.9225:0.0:0.0775	.	293;340	E9PQC4;Q9BZD4	.;NUF2_HUMAN	L	293;340;340	ENSP00000436888:S293L;ENSP00000356875:S340L;ENSP00000271452:S340L	ENSP00000271452:S340L	S	+	2	0	NUF2	161584247	0.907000	0.30839	0.866000	0.34008	0.995000	0.86356	1.953000	0.40352	2.854000	0.98071	0.655000	0.94253	TCG		0.338	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		T	163317623	C	T	163317623	3	4	61	1	0	0	0	0	1	0	0	0	10778	893	31	1	1061	1	NUF2	1	163317623	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2122	163317623	85932998	761	8746										
RXRG	6258	broad.mit.edu	37	chr1	165379964	165379964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaagcaaaatgacctggtcCtccaaggtgaggtcagagaa	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:165379964C>A	ENST00000359842.5	-	6	1190	c.888G>T	c.(886-888)gaG>gaT	p.E296D	RXRG_ENST00000470566.1_5'Flank	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	296	Ligand-binding. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E296D(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	TGACCTGGTCCTCCAAGGTGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	80	83					1																	165379964		2203	4300	6503	163646588	SO:0001583	missense	6258			U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"Nuclear hormone receptors"	10479	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 3"	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.888G>T	1.37:g.165379964C>A	ENSP00000352900:p.Glu296Asp		163646588	A6NIP1|Q6IBU7	Missense_Mutation	SNP	ENST00000359842.5	37	CCDS1248.1	.	.	.	.	.	.	.	.	.	.	C	3.015	-0.203017	0.06219	.	.	ENSG00000143171	ENST00000359842	T	0.70164	-0.46	5.1	0.951	0.19579	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.049918	0.85682	D	0.000000	T	0.17109	0.0411	N	0.12746	0.255	0.45704	D	0.998611	B	0.11235	0.004	B	0.14023	0.01	T	0.18147	-1.0346	9	0.02654	T	1	.	8.1327	0.31037	0.0:0.5527:0.0:0.4473	.	296	P48443	RXRG_HUMAN	D	296	ENSP00000352900:E296D	ENSP00000352900:E296D	E	-	3	2	RXRG	163646588	0.996000	0.38824	1.000000	0.80357	0.980000	0.70556	0.358000	0.20216	0.336000	0.23639	-0.253000	0.11424	GAG		0.473	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917		A	165379964	C	A	165379964	3	1	61	1	0	0	0	0	1	0	0	0	13802	680	24	2	523	2	RXRG	1	165379964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2062341	165379964	83870657	762	8747										
MAEL	84944	broad.mit.edu	37	chr1	166974588	166974588	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccctctaagacttggattCgaagcctcctagatgtggcc	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:166974588C>T	ENST00000367872.4	+	8	1043	c.799C>T	c.(799-801)Cga>Tga	p.R267*	RNA5SP65_ENST00000363166.1_RNA|MAEL_ENST00000491055.1_3'UTR|MAEL_ENST00000367870.2_Nonsense_Mutation_p.R236*	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	267					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)	p.R267*(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						GACTTGGATTCGAAGCCTCCT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											86	91	89					1																	166974588		2203	4300	6503	165241212	SO:0001587	stop_gained	84944			AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.799C>T	1.37:g.166974588C>T	ENSP00000356846:p.Arg267*		165241212	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Nonsense_Mutation	SNP	ENST00000367872.4	37	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	C	36	5.675685	0.96764	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	.	.	.	5.66	4.75	0.60458	.	0.391386	0.22093	N	0.064721	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	8.9472	0.35767	0.0:0.8307:0.0:0.1693	.	.	.	.	X	267;236;236	.	ENSP00000356844:R236X	R	+	1	2	MAEL	165241212	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.366000	0.34193	1.388000	0.46506	0.591000	0.81541	CGA		0.408	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		T	166974588	C	T	166974588	4	4	61	1	0	0	0	0	0	1	0	0	9184	876	31	1	829	1	MAEL	1	166974588	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1594624	166974588	82276033	763	8748										
DUSP27	92235	broad.mit.edu	37	chr1	167097350	167097350	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggacacctcctcctaccaCgaggcaaatggcaactctgt	8	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:167097350C>T	ENST00000361200.2	+	6	3148	c.2982C>T	c.(2980-2982)caC>caT	p.H994H	DUSP27_ENST00000443333.1_Silent_p.H994H|DUSP27_ENST00000271385.5_Silent_p.H994H|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	994	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.H994H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CCTCCTACCACGAGGCAAATG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	1											84	79	81					1																	167097350		2203	4300	6503	165363974	SO:0001819	synonymous_variant	92235			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2982C>T	1.37:g.167097350C>T			165363974	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	CCDS30932.1																																																																																				0.517	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167097350	C	T	167097350	2	4	61	1	0	0	0	0	0	0	0	1	4835	535	19	1		1	DUSP27	1	167097350	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122762	167097350	82153271	764	8749										
RCSD1	92241	broad.mit.edu	37	chr1	167663470	167663470	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgtgcgatctaggcccagCgaggcagaggaggtgcctgt	18	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:167663470C>T	ENST00000367854.3	+	5	736	c.405C>T	c.(403-405)agC>agT	p.S135S	RCSD1_ENST00000537350.1_Silent_p.S105S	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	135					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)	p.S135S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					CTAGGCCCAGCGAGGCAGAGG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	1											63	59	60					1																	167663470		2203	4300	6503	165930094	SO:0001819	synonymous_variant	92241			BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.405C>T	1.37:g.167663470C>T			165930094	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Silent	SNP	ENST00000367854.3	37	CCDS1263.1																																																																																				0.587	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		T	167663470	C	T	167663470	2	4	61	1	0	0	0	0	0	0	0	1	13222	767	27	1		1	RCSD1	1	167663470	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	566120	167663470	81587151	765	8750										
MPZL1	9019	broad.mit.edu	37	chr1	167741682	167741682	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaaaaaccctcctgacatCgttgtccagcctggacacat	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:167741682C>T	ENST00000359523.2	+	3	631	c.429C>T	c.(427-429)atC>atT	p.I143I	MPZL1_ENST00000392121.3_Intron|MPZL1_ENST00000474859.1_Silent_p.I143I	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	143	Ig-like V-type.				cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)	p.I143I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					CTCCTGACATCGTTGTCCAGC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	1											118	103	108					1																	167741682		2203	4300	6503	166008306	SO:0001819	synonymous_variant	9019			AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"Immunoglobulin superfamily / V-set domain containing"	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.429C>T	1.37:g.167741682C>T			166008306	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Silent	SNP	ENST00000359523.2	37	CCDS1264.1																																																																																				0.398	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569		T	167741682	C	T	167741682	2	4	61	1	0	0	0	0	0	0	0	1	9779	874	31	1		1	MPZL1	1	167741682	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78212	167741682	81508939	766	8751										
ADCY10	55811	broad.mit.edu	37	chr1	167787447	167787447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggttcttcttggcaaaaGatttttagctctattggaaa	8	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:167787447G>T	ENST00000367851.4	-	31	4529	c.4345C>A	c.(4345-4347)Ctt>Att	p.L1449I	ADCY10_ENST00000367848.1_Missense_Mutation_p.L1357I|ADCY10_ENST00000545172.1_Missense_Mutation_p.L1296I|RP1-313L4.3_ENST00000451545.1_RNA	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1449					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.L1449I(1)|p.L1449V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CTTGGCAAAAGATTTTTAGCT	0.373																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											105	102	103					1																	167787447		2203	4300	6503	166054071	SO:0001583	missense	55811			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.4345C>A	1.37:g.167787447G>T	ENSP00000356825:p.Leu1449Ile		166054071	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235709	0.39498	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.37411	1.2;1.21;1.21	5.63	1.62	0.23740	.	0.000000	0.38897	N	0.001535	T	0.40570	0.1122	M	0.69823	2.125	0.28603	N	0.909054	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.36212	-0.9757	8	.	.	.	-12.431	8.3238	0.32145	0.3266:0.0:0.6734:0.0	.	1357;1449	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	I	1296;1449;1357	ENSP00000441992:L1296I;ENSP00000356825:L1449I;ENSP00000356822:L1357I	.	L	-	1	0	ADCY10	166054071	0.310000	0.24527	0.002000	0.10522	0.052000	0.14988	1.155000	0.31700	0.319000	0.23209	0.655000	0.94253	CTT		0.373	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167787447	G	T	167787447	3	4	61	1	0	0	0	0	1	0	0	0	293	942	33	2	499	2	ADCY10	1	167787447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45765	167787447	81463174	767	8752										
DCAF6	55827	broad.mit.edu	37	chr1	167962640	167962640	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaagatgatacagcacgaGaacttaaaactccttctgcg	8	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:167962640G>T	ENST00000312263.6	+	7	1069	c.865G>T	c.(865-867)Gaa>Taa	p.E289*	DCAF6_ENST00000432587.2_Nonsense_Mutation_p.E258*|DCAF6_ENST00000367840.3_Nonsense_Mutation_p.E289*|DCAF6_ENST00000367843.3_Nonsense_Mutation_p.E289*	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	289					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.E289*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TACAGCACGAGAACTTAAAAC	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											69	69	69					1																	167962640		2203	4299	6502	166229264	SO:0001587	stop_gained	55827			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.865G>T	1.37:g.167962640G>T	ENSP00000311949:p.Glu289*		166229264	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Nonsense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	33	5.257770	0.95368	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	18.051	0.89349	0.0:0.0:1.0:0.0	.	.	.	.	X	289;258;289;289	.	ENSP00000311949:E289X	E	+	1	0	DCAF6	166229264	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.199000	0.77831	2.325000	0.78763	0.454000	0.30748	GAA		0.453	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		T	167962640	G	T	167962640	4	4	61	1	0	0	0	0	0	1	0	0	4280	943	33	2	891	2	DCAF6	1	167962640	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	175193	167962640	81287981	768	8753										
DCAF6	55827	broad.mit.edu	37	chr1	168034954	168034954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgataatcatgtggtaAactgcctgcagccacatccg	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:168034954A>G	ENST00000312263.6	+	16	2497	c.2293A>G	c.(2293-2295)Aac>Gac	p.N765D	DCAF6_ENST00000432587.2_Missense_Mutation_p.N825D|DCAF6_ENST00000367840.3_Missense_Mutation_p.N856D|DCAF6_ENST00000367843.3_Missense_Mutation_p.N785D	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	765					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.N785D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TCATGTGGTAAACTGCCTGCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	72	73					1																	168034954		2203	4300	6503	166301578	SO:0001583	missense	55827			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2293A>G	1.37:g.168034954A>G	ENSP00000311949:p.Asn765Asp		166301578	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928512	0.92389	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	5.41	5.41	0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83986	0.5373	H	0.96889	3.9	0.47862	D	0.999531	D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;0.999	D;D;D;D;D	0.97110	0.997;1.0;0.999;0.999;0.998	D	0.89655	0.3872	9	0.87932	D	0	.	15.7437	0.77922	1.0:0.0:0.0:0.0	.	825;438;856;765;785	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	D	785;825;765;856	ENSP00000356817:N785D;ENSP00000396238:N825D;ENSP00000311949:N765D;ENSP00000356814:N856D	ENSP00000311949:N765D	N	+	1	0	DCAF6	166301578	1.000000	0.71417	0.943000	0.38184	0.976000	0.68499	8.740000	0.91579	2.184000	0.69523	0.459000	0.35465	AAC		0.413	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		G	168034954	A	G	168034954	3	3	61	1	0	0	0	0	1	0	0	0	4280	14	1	4	2419	4	DCAF6	1	168034954	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72314	168034954	81215667	769	8754										
DCAF6	55827	broad.mit.edu	37	chr1	168037611	168037611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaggttataactcgaaacGaactcatgctggaagaaact	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:168037611G>A	ENST00000312263.6	+	18	2632	c.2428G>A	c.(2428-2430)Gaa>Aaa	p.E810K	DCAF6_ENST00000432587.2_Missense_Mutation_p.E870K|DCAF6_ENST00000367840.3_Missense_Mutation_p.E901K|DCAF6_ENST00000367843.3_Missense_Mutation_p.E830K	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	810					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.E830K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						AACTCGAAACGAACTCATGCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	104	107					1																	168037611		2203	4300	6503	166304235	SO:0001583	missense	55827			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2428G>A	1.37:g.168037611G>A	ENSP00000311949:p.Glu810Lys		166304235	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.259650	0.80246	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	D;T;D;D	0.81908	-1.54;0.23;-1.55;-1.55	5.81	5.81	0.92471	.	0.105207	0.64402	D	0.000005	T	0.76378	0.3979	L	0.61218	1.895	0.45025	D	0.998041	B;P;P;B;B	0.49307	0.358;0.86;0.922;0.15;0.267	B;B;B;B;B	0.39339	0.066;0.297;0.266;0.052;0.132	T	0.77247	-0.2658	9	0.33940	T	0.23	.	20.0912	0.97820	0.0:0.0:1.0:0.0	.	870;483;901;810;830	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	K	830;870;810;901	ENSP00000356817:E830K;ENSP00000396238:E870K;ENSP00000311949:E810K;ENSP00000356814:E901K	ENSP00000311949:E810K	E	+	1	0	DCAF6	166304235	1.000000	0.71417	0.909000	0.35828	0.319000	0.28217	9.234000	0.95347	2.746000	0.94184	0.591000	0.81541	GAA		0.378	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		A	168037611	G	A	168037611	3	1	61	1	0	0	0	0	1	0	0	0	4280	1059	37	1	2562	1	DCAF6	1	168037611	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2657	168037611	81213010	770	8755										
GPR161	23432	broad.mit.edu	37	chr1	168065845	168065845	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcacatgcccagtagttCtttgcgaactgtcttgttcc	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:168065845C>A	ENST00000367838.1	-	5	1313	c.1000G>T	c.(1000-1002)Gaa>Taa	p.E334*	GPR161_ENST00000367836.1_Nonsense_Mutation_p.E202*|GPR161_ENST00000367835.1_Nonsense_Mutation_p.E334*|GPR161_ENST00000546300.1_Nonsense_Mutation_p.E220*|GPR161_ENST00000361697.2_Nonsense_Mutation_p.E334*|GPR161_ENST00000271357.5_Nonsense_Mutation_p.E334*|GPR161_ENST00000539777.1_Nonsense_Mutation_p.E256*|GPR161_ENST00000537209.1_Nonsense_Mutation_p.E354*	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	334					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)	p.E334*(1)		breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					CCCAGTAGTTCTTTGCGAACT	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											84	85	84					1																	168065845		2203	4300	6503	166332469	SO:0001587	stop_gained	23432			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1000G>T	1.37:g.168065845C>A	ENSP00000356812:p.Glu334*		166332469	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Nonsense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	C	43	9.923824	0.99297	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	.	.	.	5.61	4.7	0.59300	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-21.0204	14.2282	0.65873	0.0:0.9275:0.0:0.0725	.	.	.	.	X	334;334;202;334;220;256;354;334	.	ENSP00000271357:E334X	E	-	1	0	GPR161	166332469	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	7.637000	0.83313	1.500000	0.48636	0.655000	0.94253	GAA		0.552	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		A	168065845	C	A	168065845	4	1	61	1	0	0	0	0	0	1	0	0	6685	922	32	2	605	2	GPR161	1	168065845	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28234	168065845	81184776	771	8756										
TBX19	9095	broad.mit.edu	37	chr1	168274276	168274276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcttttccaatccagatgGagtgtgcacagcaggaaact	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:168274276G>A	ENST00000367821.3	+	6	809	c.758G>A	c.(757-759)gGa>gAa	p.G253E		NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	253					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G253E(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					AATCCAGATGGAGTGTGCACA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											156	142	147					1																	168274276		2203	4300	6503	166540900	SO:0001583	missense	9095			AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.758G>A	1.37:g.168274276G>A	ENSP00000356795:p.Gly253Glu		166540900	Q52M53	Missense_Mutation	SNP	ENST00000367821.3	37	CCDS1272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.528|9.528	1.110169|1.110169	0.20714|0.20714	.|.	.|.	ENSG00000143178|ENSG00000143178	ENST00000367821|ENST00000441464	D|.	0.82893|.	-1.66|.	5.62|5.62	4.69|4.69	0.59074|0.59074	.|.	0.687680|.	0.14499|.	N|.	0.315849|.	T|.	0.30135|.	0.0755|.	N|N	0.22421|0.22421	0.69|0.69	.|.	.|.	.|.	P|.	0.37781|.	0.608|.	B|.	0.32624|.	0.149|.	T|.	0.11324|.	-1.0592|.	9|.	0.30078|.	T|.	0.28|.	.|.	11.907|11.907	0.52717|0.52717	0.0:0.3038:0.6962:0.0|0.0:0.3038:0.6962:0.0	.|.	253|.	O60806|.	TBX19_HUMAN|.	E|X	253|85	ENSP00000356795:G253E|.	ENSP00000356795:G253E|.	G|W	+|+	2|3	0|0	TBX19|TBX19	166540900|166540900	0.459000|0.459000	0.25768|0.25768	0.139000|0.139000	0.22197|0.22197	0.039000|0.039000	0.13416|0.13416	4.409000|4.409000	0.59768|0.59768	2.642000|2.642000	0.89623|0.89623	0.655000|0.655000	0.94253|0.94253	GGA|TGG		0.522	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		A	168274276	G	A	168274276	3	1	61	1	0	0	0	0	1	0	0	0	15693	1174	41	3	780	3	TBX19	1	168274276	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208431	168274276	80976345	772	8757										
TBX19	9095	broad.mit.edu	37	chr1	168282180	168282180	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtggcctcgcatcccttCgcgggctggggtggcccagg	17	14	0	0	rs370679374		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:168282180C>T	ENST00000367821.3	+	8	1338	c.1287C>T	c.(1285-1287)ttC>ttT	p.F429F	TBX19_ENST00000465440.1_3'UTR	NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	429					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F429F(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					CGCATCCCTTCGCGGGCTGGG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		1,4405	2.1+/-5.4	0,1,2202	43	45	44		1287	0.5	0	1		44	0,8600		0,0,4300	no	coding-synonymous	TBX19	NM_005149.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		429/449	168282180	1,13005	2203	4300	6503	166548804	SO:0001819	synonymous_variant	9095			AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.1287C>T	1.37:g.168282180C>T			166548804	Q52M53	Silent	SNP	ENST00000367821.3	37	CCDS1272.1	.	.	.	.	.	.	.	.	.	.	C	0.205	-1.041276	0.02013	2.27E-4	0.0	ENSG00000143178	ENST00000431969;ENST00000441464	.	.	.	5.53	0.488	0.16848	.	.	.	.	.	T	0.18800	0.0451	.	.	.	.	.	.	.	.	.	.	.	.	T	0.14227	-1.0480	3	.	.	.	.	5.6207	0.17455	0.0:0.5836:0.1325:0.2839	.	.	.	.	C	299;262	.	.	R	+	1	0	TBX19	166548804	0.008000	0.16893	0.025000	0.17156	0.119000	0.20118	-0.193000	0.09573	-0.156000	0.11079	-1.084000	0.02203	CGC		0.622	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		T	168282180	C	T	168282180	2	4	61	1	0	0	0	0	0	0	0	1	15693	883	31	1		1	TBX19	1	168282180	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7904	168282180	80968441	773	8758										
NME7	29922	broad.mit.edu	37	chr1	169292359	169292359	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataattgttttcttacttttCtttcctactgcccagctggc	5	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169292359C>T	ENST00000367811.3	-	3	530	c.274G>A	c.(274-276)Gaa>Aaa	p.E92K	NME7_ENST00000472647.1_Missense_Mutation_p.E56K|NME7_ENST00000469474.1_5'UTR|RP4-800F24.1_ENST00000432081.1_RNA	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	92					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.E92K(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					TCTTACTTTTCTTTCCTACTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	71	70					1																	169292359		2203	4300	6503	167558983	SO:0001583	missense	29922			AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.274G>A	1.37:g.169292359C>T	ENSP00000356785:p.Glu92Lys		167558983	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Missense_Mutation	SNP	ENST00000367811.3	37	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	C	33	5.196626	0.94960	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	T;T	0.64991	-0.13;-0.13	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.81673	0.4872	M	0.91140	3.18	0.46654	D	0.999144	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.98	D	0.85554	0.1223	9	0.66056	D	0.02	.	18.3471	0.90326	0.0:1.0:0.0:0.0	.	96;92	Q59GR0;Q9Y5B8	.;NDK7_HUMAN	K	56;92	ENSP00000433341:E56K;ENSP00000356785:E92K	ENSP00000356785:E92K	E	-	1	0	NME7	167558983	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.322000	0.65852	2.495000	0.84180	0.655000	0.94253	GAA		0.358	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		T	169292359	C	T	169292359	3	4	61	1	0	0	0	0	1	0	0	0	10527	922	32	3	896	3	NME7	1	169292359	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1010179	169292359	79958262	774	8759										
BLZF1	8548	broad.mit.edu	37	chr1	169347574	169347574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgttctcttctaggtaaatCgtgagttaaaaaagttactg	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169347574C>T	ENST00000367808.3	+	4	898	c.475C>T	c.(475-477)Cgt>Tgt	p.R159C	BLZF1_ENST00000329281.2_Missense_Mutation_p.R159C			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	159					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)	p.R159C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					CTAGGTAAATCGTGAGTTAAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	123	123					1																	169347574		2203	4300	6503	167614198	SO:0001583	missense	8548			U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.475C>T	1.37:g.169347574C>T	ENSP00000356782:p.Arg159Cys		167614198	O15298|Q5T531|Q5T533|Q9GZX4	Missense_Mutation	SNP	ENST00000367808.3	37	CCDS1278.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849993	0.91277	.	.	ENSG00000117475	ENST00000367808;ENST00000329281;ENST00000426663	T;T;T	0.13538	2.58;2.58;2.58	5.91	5.91	0.95273	.	0.047245	0.85682	D	0.000000	T	0.22322	0.0538	M	0.66939	2.045	0.50632	D	0.999882	D;D	0.76494	0.999;0.999	P;P	0.52758	0.708;0.708	T	0.00577	-1.1662	9	0.62326	D	0.03	-22.0183	20.2985	0.98592	0.0:1.0:0.0:0.0	.	159;159	A8K6R0;Q9H2G9	.;GO45_HUMAN	C	159	ENSP00000356782:R159C;ENSP00000327541:R159C;ENSP00000404408:R159C	ENSP00000327541:R159C	R	+	1	0	BLZF1	167614198	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.417000	0.66423	2.793000	0.96121	0.655000	0.94253	CGT		0.333	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666		T	169347574	C	T	169347574	3	4	61	1	0	0	0	0	1	0	0	0	1454	884	31	1	485	1	BLZF1	1	169347574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55215	169347574	79903047	775	8760										
C1orf114	57821	broad.mit.edu	37	chr1	169364415	169364416	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagcttgttgctctgccaINSttttttccatccgtttcctt							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169364415_169364416insT	ENST00000367806.3	-	6	1551_1552	c.1399_1400insA	c.(1399-1401)atgfs	p.M467fs	BLZF1_ENST00000329281.2_Intron|CCDC181_ENST00000367805.3_Frame_Shift_Ins_p.M466fs|CCDC181_ENST00000545005.1_Frame_Shift_Ins_p.M466fs	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	467						nucleus (GO:0005634)		p.M466fs*12(1)									TTGCTCTGCCATTTTTTCCATC	0.406																																																1	Insertion - Frameshift(1)	large_intestine(1)	1																																								167631040	SO:0001589	frameshift_variant	57821			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1400dupA	1.37:g.169364421_169364421dupT	ENSP00000356780:p.Met467fs		167631039	O60780|Q53FD5|Q5TID9|Q8TC48	Frame_Shift_Ins	INS	ENST00000367806.3	37																																																																																					0.406	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		T	169364416	-	T	169364415	7	5	61	1	0	1	1	0	0	0	0	0	1993	217	8	0	133	0	C1orf114	1	169364415	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	16841	169364415	79886206	776	8761										
C1orf114	57821	broad.mit.edu	37	chr1	169388388	169388388	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttcttctatttttcGtcgctcttcctagtaaaaga	4	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169388388G>A	ENST00000367806.3	-	4	1230	c.1078C>T	c.(1078-1080)Cga>Tga	p.R360*	CCDC181_ENST00000367805.3_Nonsense_Mutation_p.R360*|CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000545005.1_Nonsense_Mutation_p.R360*	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	360						nucleus (GO:0005634)		p.R360*(1)									TCTATTTTTCGTCGCTCTTCC	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											55	51	53					1																	169388388		2203	4299	6502	167655012	SO:0001587	stop_gained	57821			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1078C>T	1.37:g.169388388G>A	ENSP00000356780:p.Arg360*		167655012	O60780|Q53FD5|Q5TID9|Q8TC48	Nonsense_Mutation	SNP	ENST00000367806.3	37		.	.	.	.	.	.	.	.	.	.	G	37	6.129063	0.97310	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005	.	.	.	6.16	4.18	0.49190	.	0.363514	0.30210	N	0.010143	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.3997	14.8251	0.70104	0.0:0.0:0.4826:0.5173	.	.	.	.	X	360	.	ENSP00000356779:R360X	R	-	1	2	C1orf114	167655012	0.630000	0.27155	0.984000	0.44739	0.994000	0.84299	1.131000	0.31406	0.766000	0.33244	0.650000	0.86243	CGA		0.303	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		A	169388388	G	A	169388388	4	1	61	1	0	0	0	0	0	1	0	0	1993	1153	40	1	460	1	C1orf114	1	169388388	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23973	169388388	79862233	777	8762										
F5	2153	broad.mit.edu	37	chr1	169484782	169484782	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacatttcagaggacagaGacttgcagccctgtgttata	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169484782G>A	ENST00000367797.3	-	24	6629	c.6428C>T	c.(6427-6429)tCt>tTt	p.S2143F	F5_ENST00000367796.3_Missense_Mutation_p.S2148F	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	2143	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.S2143F(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AGAGGACAGAGACTTGCAGCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											176	163	167					1																	169484782		2203	4300	6503	167751406	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.6428C>T	1.37:g.169484782G>A	ENSP00000356771:p.Ser2143Phe		167751406	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265901	0.59540	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98419	-4.92;-4.92	5.61	4.69	0.59074	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.055341	0.85682	D	0.000000	D	0.98124	0.9381	M	0.64997	1.995	0.43271	D	0.995227	D	0.63046	0.992	P	0.61275	0.886	D	0.98720	1.0708	9	0.87932	D	0	-19.2838	16.1449	0.81559	0.0:0.1341:0.8659:0.0	.	2143	P12259	FA5_HUMAN	F	2143;2148	ENSP00000356771:S2143F;ENSP00000356770:S2148F	ENSP00000356770:S2148F	S	-	2	0	F5	167751406	1.000000	0.71417	0.933000	0.37362	0.839000	0.47603	5.221000	0.65272	1.346000	0.45694	-0.499000	0.04595	TCT		0.413	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169484782	G	A	169484782	3	1	61	1	0	0	0	0	1	0	0	0	5361	942	33	3	254	3	F5	1	169484782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96394	169484782	79765839	778	8763										
F5	2153	broad.mit.edu	37	chr1	169509667	169509667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagttgatgtttgtcctaAcatcagttttgtaggggtca	12	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169509667A>G	ENST00000367797.3	-	13	4862	c.4661T>C	c.(4660-4662)gTt>gCt	p.V1554A	F5_ENST00000367796.3_Missense_Mutation_p.V1559A	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1554	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.V1554A(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTTTGTCCTAACATCAGTTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	99	101					1																	169509667		2203	4300	6503	167776291	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4661T>C	1.37:g.169509667A>G	ENSP00000356771:p.Val1554Ala		167776291	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	A	3.460	-0.110218	0.06924	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.33438	1.41;1.41	5.93	-6.93	0.01638	.	2.039210	0.01392	N	0.013274	T	0.04998	0.0134	N	0.19112	0.55	0.23813	N	0.996778	B	0.18610	0.029	B	0.18263	0.021	T	0.16600	-1.0397	9	0.21540	T	0.41	2.1569	4.8507	0.13535	0.2276:0.2113:0.4654:0.0957	.	1554	P12259	FA5_HUMAN	A	1554;1559	ENSP00000356771:V1554A;ENSP00000356770:V1559A	ENSP00000356770:V1559A	V	-	2	0	F5	167776291	0.000000	0.05858	0.000000	0.03702	0.762000	0.43233	0.140000	0.16056	-0.780000	0.04553	-0.353000	0.07706	GTT		0.418	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		G	169509667	A	G	169509667	3	3	61	1	0	0	0	0	1	0	0	0	5361	43	2	4	2065	4	F5	1	169509667	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24885	169509667	79740954	779	8764										
F5	2153	broad.mit.edu	37	chr1	169521894	169521894	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtgaaggactcatcttcGtactgtgtgtacataacttt	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169521894G>A	ENST00000367797.3	-	8	1398	c.1197C>T	c.(1195-1197)taC>taT	p.Y399Y	F5_ENST00000546081.1_Silent_p.Y262Y|F5_ENST00000367796.3_Silent_p.Y399Y	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	399	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.Y399Y(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	ACTCATCTTCGTACTGTGTGT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	1											168	172	171					1																	169521894		2203	4300	6503	167788518	SO:0001819	synonymous_variant	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1197C>T	1.37:g.169521894G>A			167788518	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																				0.353	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169521894	G	A	169521894	2	1	61	1	0	0	0	0	0	0	0	1	5361	1140	40	1		1	F5	1	169521894	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12227	169521894	79728727	780	8765										
F5	2153	broad.mit.edu	37	chr1	169524516	169524516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgtgccgcctctgctcaCgagttattttcttaagattc	7	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169524516C>T	ENST00000367797.3	-	7	1223	c.1022G>A	c.(1021-1023)cGt>cAt	p.R341H	F5_ENST00000546081.1_Missense_Mutation_p.R204H|F5_ENST00000367796.3_Missense_Mutation_p.R341H	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	341					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.R341H(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CCTCTGCTCACGAGTTATTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											135	125	128					1																	169524516		2203	4300	6503	167791140	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1022G>A	1.37:g.169524516C>T	ENSP00000356771:p.Arg341His		167791140	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.353033	0.41700	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98807	-5.15;-5.15;-5.15	5.69	1.47	0.22746	.	1.246990	0.05314	N	0.525382	D	0.95714	0.8606	M	0.67953	2.075	0.30642	N	0.756336	D	0.55385	0.971	P	0.45232	0.474	D	0.89532	0.3786	9	0.36615	T	0.2	-0.2281	5.0161	0.14337	0.5725:0.2292:0.1121:0.0861	.	341	P12259	FA5_HUMAN	H	341;341;204	ENSP00000356771:R341H;ENSP00000356770:R341H;ENSP00000439664:R204H	ENSP00000356770:R341H	R	-	2	0	F5	167791140	0.000000	0.05858	0.000000	0.03702	0.684000	0.39900	0.248000	0.18198	0.022000	0.15160	-0.195000	0.12781	CGT		0.428	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		T	169524516	C	T	169524516	3	4	61	1	0	0	0	0	1	0	0	0	5361	536	19	1	5728	1	F5	1	169524516	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2622	169524516	79726105	781	8766										
F5	2153	broad.mit.edu	37	chr1	169526043	169526043	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgaatggagaataattCtggccccgagctcattccca	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169526043C>A	ENST00000367797.3	-	6	994	c.793G>T	c.(793-795)Gaa>Taa	p.E265*	F5_ENST00000546081.1_Nonsense_Mutation_p.E128*|F5_ENST00000367796.3_Nonsense_Mutation_p.E265*	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	265	F5/8 type A 1.|Plastocyanin-like 2.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.E265*(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GAGAATAATTCTGGCCCCGAG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											110	90	96					1																	169526043		2203	4300	6503	167792667	SO:0001587	stop_gained	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.793G>T	1.37:g.169526043C>A	ENSP00000356771:p.Glu265*		167792667	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Nonsense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	40	8.257626	0.98729	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.3163	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	265;265;128	.	ENSP00000356770:E265X	E	-	1	0	F5	167792667	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.456000	0.80751	2.890000	0.99128	0.650000	0.86243	GAA		0.483	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169526043	C	A	169526043	4	1	61	1	0	0	0	0	0	1	0	0	5361	922	32	2	5961	2	F5	1	169526043	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1527	169526043	79724578	782	8767										
SELP	6403	broad.mit.edu	37	chr1	169565302	169565302	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcccggatgatgcctacaGtacatggttccctgcccagg	11	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169565302G>A	ENST00000263686.6	-	12	1999	c.1962C>T	c.(1960-1962)taC>taT	p.Y654Y	SELP_ENST00000367792.2_Silent_p.Y470Y|SELP_ENST00000367794.2_Silent_p.Y592Y|SELP_ENST00000458599.2_Silent_p.Y470Y|SELP_ENST00000367788.2_Silent_p.Y592Y|SELP_ENST00000367793.2_Silent_p.Y592Y|SELP_ENST00000367791.2_Silent_p.Y468Y|SELP_ENST00000367786.2_Silent_p.Y592Y	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	654	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)	p.Y654Y(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	GATGCCTACAGTACATGGTTC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											256	254	255					1																	169565302		2203	4300	6503	167831926	SO:0001819	synonymous_variant	6403			BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"CD molecules"	10721	protein-coding gene	gene with protein product		173610	"selectin P (granule membrane protein 140kD, antigen CD62)"	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.1962C>T	1.37:g.169565302G>A			167831926	Q5R344|Q8IVD1	Silent	SNP	ENST00000263686.6	37	CCDS1282.1																																																																																				0.498	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005		A	169565302	G	A	169565302	2	1	61	1	0	0	0	0	0	0	0	1	14056	1024	36	3		3	SELP	1	169565302	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39259	169565302	79685319	783	8768										
SELP	6403	broad.mit.edu	37	chr1	169582864	169582864	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaatccagggtaacaggaGcaggtgtagttcccgatggt	14	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169582864G>T	ENST00000263686.6	-	4	586	c.549C>A	c.(547-549)tgC>tgA	p.C183*	SELP_ENST00000367792.2_Nonsense_Mutation_p.C183*|SELP_ENST00000367794.2_Nonsense_Mutation_p.C183*|SELP_ENST00000458599.2_Nonsense_Mutation_p.C183*|SELP_ENST00000367788.2_Nonsense_Mutation_p.C183*|SELP_ENST00000367793.2_Nonsense_Mutation_p.C183*|SELP_ENST00000367791.2_Nonsense_Mutation_p.C183*|SELP_ENST00000367786.2_Nonsense_Mutation_p.C183*	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	183	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)	p.C183*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	GGTAACAGGAGCAGGTGTAGT	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											135	118	123					1																	169582864		2203	4300	6503	167849488	SO:0001587	stop_gained	6403			BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"CD molecules"	10721	protein-coding gene	gene with protein product		173610	"selectin P (granule membrane protein 140kD, antigen CD62)"	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.549C>A	1.37:g.169582864G>T	ENSP00000263686:p.Cys183*		167849488	Q5R344|Q8IVD1	Nonsense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.952576|5.952576	0.97139|0.97139	.|.	.|.	ENSG00000174175|ENSG00000174175	ENST00000367795;ENST00000367790;ENST00000426706;ENST00000367789;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367792;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599|ENST00000446728	.|.	.|.	.|.	5.14|5.14	3.26|3.26	0.37387|0.37387	.|.	0.107749|.	0.42420|.	D|.	0.000704|.	.|T	.|0.33904	.|0.0879	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.14531	.|-1.0469	.|3	0.02654|.	T|.	1|.	-25.9235|-25.9235	8.5426|8.5426	0.33402|0.33402	0.2422:0.0:0.7578:0.0|0.2422:0.0:0.7578:0.0	.|.	.|.	.|.	.|.	X|I	183;183;182;183;183;183;183;183;183;183;183;183;168|183	.|.	ENSP00000263686:C183X|.	C|L	-|-	3|1	2|0	SELP|SELP	167849488|167849488	0.625000|0.625000	0.27111|0.27111	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.475000|0.475000	0.22164|0.22164	0.849000|0.849000	0.35215|0.35215	0.655000|0.655000	0.94253|0.94253	TGC|CTC		0.473	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005		T	169582864	G	T	169582864	4	4	61	1	0	0	0	0	0	1	0	0	14056	963	34	2	1995	2	SELP	1	169582864	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17562	169582864	79667757	784	8769										
SELL	6402	broad.mit.edu	37	chr1	169670782	169670782	+	Frame_Shift_Del	DEL	G	G	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgccactggaatgaagaGggggttataatcaccctcct							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169670782delG	ENST00000236147.4	-	7	1199	c.1039delC	c.(1039-1041)ctcfs	p.L347fs	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	334					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)	p.L334fs*25(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					GGAATGAAGAGGGGGTTATAA	0.398																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											49	46	47					1																	169670782		1859	4097	5956	167937406	SO:0001589	frameshift_variant	6402			M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.1039delC	1.37:g.169670782delG	ENSP00000236147:p.Leu347fs		167937406	B2R6Q8|P15023|Q9UJ43	Frame_Shift_Del	DEL	ENST00000236147.4	37	CCDS53427.1																																																																																				0.398	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		-	169670782	G	-	169670782	7	5	61	1	0	1	0	1	0	0	0	0	14053	1000	35	0	130	0	SELL	1	169670782	Frame_Shift_Del	DEL	G	TCGA-AG-A002-01A-01W-A00K-09	87918	169670782	79579839	785	8770										
SELL	6402	broad.mit.edu	37	chr1	169672447	169672447	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagatgattcacaaatggTtttcttcttcccaattaact	4	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169672447T>C	ENST00000236147.4	-	6	1100	c.940A>G	c.(940-942)Acc>Gcc	p.T314A	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	301	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)	p.T301A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					TCACAAATGGTTTTCTTCTTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	91	94					1																	169672447		1894	4122	6016	167939071	SO:0001583	missense	6402			M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.940A>G	1.37:g.169672447T>C	ENSP00000236147:p.Thr314Ala		167939071	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	.	.	.	.	.	.	.	.	.	.	T	0.661	-0.805692	0.02819	.	.	ENSG00000188404	ENST00000236147	T	0.63255	-0.03	4.59	3.47	0.39725	Complement control module (2);Sushi/SCR/CCP (3);	0.233634	0.29972	N	0.010734	T	0.33000	0.0848	L	0.56199	1.76	0.09310	N	1	B;B	0.18013	0.025;0.018	B;B	0.23419	0.046;0.021	T	0.20974	-1.0259	10	0.22109	T	0.4	-7.7541	8.3131	0.32084	0.0:0.0949:0.0:0.9051	.	314;301	Q8WW79;P14151	.;LYAM1_HUMAN	A	314	ENSP00000236147:T314A	ENSP00000236147:T314A	T	-	1	0	SELL	167939071	0.003000	0.15002	0.020000	0.16555	0.129000	0.20672	0.560000	0.23500	0.906000	0.36621	0.528000	0.53228	ACC		0.433	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		C	169672447	T	C	169672447	3	2	61	1	0	0	0	0	1	0	0	0	14053	1725	60	4	233	4	SELL	1	169672447	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1665	169672447	79578174	786	8771										
SELL	6402	broad.mit.edu	37	chr1	169677664	169677664	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcagtcctccttgttcttCttgttgttgggctcaccatc	8	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169677664C>A	ENST00000236147.4	-	3	565	c.405G>T	c.(403-405)aaG>aaT	p.K135N	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	122	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)	p.K122N(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					CCTTGTTCTTCTTGTTGTTGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	97	97					1																	169677664		2051	4220	6271	167944288	SO:0001583	missense	6402			M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.405G>T	1.37:g.169677664C>A	ENSP00000236147:p.Lys135Asn		167944288	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.551268	0.65311	.	.	ENSG00000188404	ENST00000236147	T	0.18174	2.23	5.71	3.51	0.40186	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.111838	0.39341	N	0.001397	T	0.22820	0.0551	M	0.64404	1.975	0.40832	D	0.98359	D;D	0.65815	0.995;0.995	D;P	0.63793	0.918;0.891	T	0.01697	-1.1293	10	0.62326	D	0.03	-15.2473	10.3627	0.44003	0.0:0.78:0.0:0.22	.	135;122	Q8WW79;P14151	.;LYAM1_HUMAN	N	135	ENSP00000236147:K135N	ENSP00000236147:K135N	K	-	3	2	SELL	167944288	0.574000	0.26684	0.972000	0.41901	0.906000	0.53458	1.203000	0.32284	1.418000	0.47098	0.650000	0.86243	AAG		0.478	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		A	169677664	C	A	169677664	3	1	61	1	0	0	0	0	1	0	0	0	14053	912	32	2	780	2	SELL	1	169677664	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5217	169677664	79572957	787	8772										
SELE	6401	broad.mit.edu	37	chr1	169695870	169695870	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatttccgaagccagaggaGaaatggtgctaatgtcagga	13	7	1	2	rs5355	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169695870G>T	ENST00000333360.7	-	11	1862	c.1723C>A	c.(1723-1725)Ctc>Atc	p.L575I	SELE_ENST00000367782.4_Missense_Mutation_p.L512I|SELE_ENST00000367775.1_Missense_Mutation_p.L450I|SELE_ENST00000367776.1_Missense_Mutation_p.L512I|SELE_ENST00000367777.1_Missense_Mutation_p.L512I|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367781.4_Missense_Mutation_p.L512I|SELE_ENST00000367774.1_Missense_Mutation_p.L449I|SELE_ENST00000367779.4_Missense_Mutation_p.L449I|SELE_ENST00000367780.4_Missense_Mutation_p.L450I	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	575			L -> F (in dbSNP:rs5355). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:10982036, ECO:0000269|PubMed:8557254, ECO:0000269|Ref.4}.		actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.L575I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	AGCCAGAGGAGAAATGGTGCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM961269	SELE	M	rs5355						85	72	76					1																	169695870		2203	4300	6503	167962494	SO:0001583	missense	6401			M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1723C>A	1.37:g.169695870G>T	ENSP00000331736:p.Leu575Ile		167962494	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	G	9.973	1.225973	0.22542	.	.	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.23147	1.93;1.92;2.02;1.95;1.95;1.92;2.02;1.93;1.95	5.52	4.6	0.57074	.	0.263488	0.20200	N	0.097120	T	0.11836	0.0288	L	0.58669	1.825	0.20703	N	0.999865	B	0.21821	0.061	B	0.21708	0.036	T	0.12863	-1.0531	10	0.31617	T	0.26	-14.6227	11.9311	0.52847	0.0:0.0:0.827:0.173	.	575	P16581	LYAM2_HUMAN	I	512;512;450;449;575;512;450;512;449	ENSP00000356755:L512I;ENSP00000356756:L512I;ENSP00000356754:L450I;ENSP00000356753:L449I;ENSP00000331736:L575I;ENSP00000356751:L512I;ENSP00000356749:L450I;ENSP00000356750:L512I;ENSP00000356748:L449I	ENSP00000331736:L575I	L	-	1	0	SELE	167962494	1.000000	0.71417	0.982000	0.44146	0.103000	0.19146	2.279000	0.43435	1.303000	0.44873	0.650000	0.86243	CTC		0.418	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		T	169695870	G	T	169695870	3	4	61	1	0	0	0	0	1	0	0	0	14050	942	33	2	121	2	SELE	1	169695870	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18206	169695870	79554751	788	8773										
C1orf156	92342	broad.mit.edu	37	chr1	169761966	169761966	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaatggtttctgaggtgaGaatgagatcatattttacaa	10	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169761966G>T	ENST00000310392.4	-	2	1224	c.871C>A	c.(871-873)Ctc>Atc	p.L291I	C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000286031.6_5'Flank|C1orf112_ENST00000498289.1_Intron|C1orf112_ENST00000456684.1_5'Flank|METTL18_ENST00000303469.2_Missense_Mutation_p.L291I|C1orf112_ENST00000359326.4_5'Flank	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	291						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)	p.L291I(1)		kidney(1)|large_intestine(3)|lung(4)	8						TCTGAGGTGAGAATGAGATCA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	60	59					1																	169761966		2203	4300	6503	168028590	SO:0001583	missense	92342			AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"histidine protein methyltransferase 1"	615255	"chromosome 1 open reading frame 156"	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.871C>A	1.37:g.169761966G>T	ENSP00000307975:p.Leu291Ile		168028590	B2R9T5	Missense_Mutation	SNP	ENST00000310392.4	37	CCDS1284.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766426	0.69878	.	.	ENSG00000171806	ENST00000310392;ENST00000303469	T;T	0.12039	2.72;2.72	6.17	6.17	0.99709	.	0.087235	0.52532	D	0.000076	T	0.25005	0.0607	L	0.56199	1.76	0.48901	D	0.999724	D	0.56746	0.977	D	0.67382	0.951	T	0.00066	-1.2144	10	0.34782	T	0.22	-15.719	19.4432	0.94831	0.0:0.0:1.0:0.0	.	291	O95568	MET18_HUMAN	I	291	ENSP00000307975:L291I;ENSP00000307077:L291I	ENSP00000307077:L291I	L	-	1	0	METTL18	168028590	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.198000	0.65147	2.941000	0.99782	0.655000	0.94253	CTC		0.338	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418		T	169761966	G	T	169761966	3	4	61	1	0	0	0	0	1	0	0	0	2012	942	33	2	251	2	C1orf156	1	169761966	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66096	169761966	79488655	789	8774										
C1orf112	55732	broad.mit.edu	37	chr1	169771776	169771776	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacagactgtgaaattattCgatgacatgatgtatgaatt	8	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169771776C>T	ENST00000286031.6	+	4	781	c.81C>T	c.(79-81)ttC>ttT	p.F27F	C1orf112_ENST00000413811.2_5'UTR|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000456684.1_Silent_p.F85F|C1orf112_ENST00000359326.4_Silent_p.F27F	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	27								p.F27F(1)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGAAATTATTCGATGACATGA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	1											61	65	64					1																	169771776		2203	4298	6501	168038400	SO:0001819	synonymous_variant	55732			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.81C>T	1.37:g.169771776C>T			168038400	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																				0.328	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		T	169771776	C	T	169771776	2	4	61	1	0	0	0	0	0	0	0	1	1991	883	31	1		1	C1orf112	1	169771776	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9810	169771776	79478845	790	8775										
C1orf112	55732	broad.mit.edu	37	chr1	169773343	169773343	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggtttgcatggacccttTagtagatgacaatgatgata	10	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169773343T>G	ENST00000286031.6	+	6	1140	c.440T>G	c.(439-441)tTa>tGa	p.L147*	C1orf112_ENST00000413811.2_Nonsense_Mutation_p.L118*|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000456684.1_Nonsense_Mutation_p.L205*|C1orf112_ENST00000359326.4_Nonsense_Mutation_p.L147*	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	147								p.L147*(1)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATGGACCCTTTAGTAGATGAC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											133	133	133					1																	169773343		2203	4300	6503	168039967	SO:0001587	stop_gained	55732			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.440T>G	1.37:g.169773343T>G	ENSP00000286031:p.Leu147*		168039967	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Nonsense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	T	38	6.939392	0.97948	.	.	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000456684;ENST00000286031	.	.	.	4.99	-0.331	0.12679	.	1.209150	0.05479	N	0.554407	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	1.1434	5.9663	0.19326	0.0:0.4359:0.1427:0.4214	.	.	.	.	X	118;147;205;147	.	ENSP00000286031:L147X	L	+	2	0	C1orf112	168039967	0.019000	0.18553	0.010000	0.14722	0.688000	0.40055	0.555000	0.23422	-0.168000	0.10853	-1.139000	0.01908	TTA		0.358	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		G	169773343	T	G	169773343	4	3	61	1	0	0	0	0	0	1	0	0	1991	1764	61	4	454	4	C1orf112	1	169773343	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1567	169773343	79477278	791	8776										
SCYL3	57147	broad.mit.edu	37	chr1	169825010	169825010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggcgtgctgccagaaaaGaaacatttagggaatatgct	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169825010G>T	ENST00000367770.1	-	11	1448	c.1401C>A	c.(1399-1401)ttC>ttA	p.F467L	SCYL3_ENST00000367771.6_Intron|SCYL3_ENST00000367772.4_Missense_Mutation_p.F467L			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	467					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.F467L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGCCAGAAAAGAAACATTTAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	86	88					1																	169825010		2203	4300	6503	168091634	SO:0001583	missense	57147			BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.1401C>A	1.37:g.169825010G>T	ENSP00000356744:p.Phe467Leu		168091634	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	37	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.345390	0.24426	.	.	ENSG00000000457	ENST00000367772;ENST00000367770	T;T	0.12672	2.66;2.66	3.28	1.31	0.21738	.	2.650200	0.00721	N	0.000884	T	0.01627	0.0052	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	10	0.11485	T	0.65	-0.5301	3.8343	0.08888	0.1307:0.0:0.61:0.2593	.	467	Q8IZE3	PACE1_HUMAN	L	467	ENSP00000356746:F467L;ENSP00000356744:F467L	ENSP00000356744:F467L	F	-	3	2	SCYL3	168091634	0.008000	0.16893	0.021000	0.16686	0.810000	0.45777	0.843000	0.27640	0.362000	0.24319	0.557000	0.71058	TTC		0.403	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		T	169825010	G	T	169825010	3	4	61	1	0	0	0	0	1	0	0	0	13986	933	33	2	839	2	SCYL3	1	169825010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51667	169825010	79425611	792	8777										
SCYL3	57147	broad.mit.edu	37	chr1	169847945	169847945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttagcaagcaagggtgacGaagtgtcttcaaatgcttta	10	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:169847945G>A	ENST00000367770.1	-	2	228	c.181C>T	c.(181-183)Cgt>Tgt	p.R61C	SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367771.6_Missense_Mutation_p.R61C|SCYL3_ENST00000367772.4_Missense_Mutation_p.R61C			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	61	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.R61C(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CAAGGGTGACGAAGTGTCTTC	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	1											101	101	101					1																	169847945		2203	4300	6503	168114569	SO:0001583	missense	57147			BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.181C>T	1.37:g.169847945G>A	ENSP00000356744:p.Arg61Cys		168114569	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	37	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293913	0.81025	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770;ENST00000423670	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88840	0.6546	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90729	0.4641	9	.	.	.	-15.4784	19.0922	0.93231	0.0:0.0:1.0:0.0	.	61;61	Q8IZE3-2;Q8IZE3	.;PACE1_HUMAN	C	61	ENSP00000356746:R61C;ENSP00000356745:R61C;ENSP00000356744:R61C;ENSP00000407993:R61C	.	R	-	1	0	SCYL3	168114569	1.000000	0.71417	0.985000	0.45067	0.993000	0.82548	5.630000	0.67805	2.668000	0.90789	0.563000	0.77884	CGT		0.408	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		A	169847945	G	A	169847945	3	1	61	1	0	0	0	0	1	0	0	0	13986	1058	37	1	2095	1	SCYL3	1	169847945	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22935	169847945	79402676	793	8778										
C1orf129	80133	broad.mit.edu	37	chr1	170955788	170955788	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcacctgatgataaaatCgcatctgatgcagcatccat	6	11	3	3	rs374921240		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:170955788C>T	ENST00000367758.3	+	10	915	c.816C>T	c.(814-816)atC>atT	p.I272I	MROH9_ENST00000367759.4_Silent_p.I272I	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	272								p.I272I(1)									ATGATAAAATCGCATCTGATG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	1											162	147	152					1																	170955788		1987	4178	6165	169222412	SO:0001819	synonymous_variant	80133			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.816C>T	1.37:g.170955788C>T			169222412	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																				0.453	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		T	170955788	C	T	170955788	2	4	61	1	0	0	0	0	0	0	0	1	2002	874	31	1		1	C1orf129	1	170955788	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1107843	170955788	78294833	794	8779										
FMO3	2328	broad.mit.edu	37	chr1	171076911	171076911	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaaaaagaatcggctgtCtttgatgctgtaatggtttg	12	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171076911C>A	ENST00000367755.4	+	4	528	c.417C>A	c.(415-417)gtC>gtA	p.V139V	FMO3_ENST00000538429.1_Silent_p.V76V|FMO3_ENST00000542847.1_Silent_p.V119V|FMO3_ENST00000392085.2_Silent_p.V139V	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	139					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.V139V(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	AATCGGCTGTCTTTGATGCTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	1											149	149	149					1																	171076911		2203	4300	6503	169343535	SO:0001819	synonymous_variant	2328			BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.417C>A	1.37:g.171076911C>A			169343535	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	37	CCDS1292.1																																																																																				0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		A	171076911	C	A	171076911	2	1	61	1	0	0	0	0	0	0	0	1	5975	900	32	2		2	FMO3	1	171076911	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121123	171076911	78173710	795	8780										
FMO3	2328	broad.mit.edu	37	chr1	171086513	171086513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacttcagaagccttgcttCtttttccattggctgaagct	8	10	2	3	rs28363595	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171086513C>A	ENST00000367755.4	+	9	1641	c.1530C>A	c.(1528-1530)ttC>ttA	p.F510L	FMO3_ENST00000538429.1_Missense_Mutation_p.F447L|FMO3_ENST00000542847.1_Missense_Mutation_p.F490L|FMO3_ENST00000392085.2_Missense_Mutation_p.F510L	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	510					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.F510L(2)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	AGCCTTGCTTCTTTTTCCATT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	1											162	149	154					1																	171086513		2203	4300	6503	169353137	SO:0001583	missense	2328			BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.1530C>A	1.37:g.171086513C>A	ENSP00000356729:p.Phe510Leu		169353137	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	C	4.809	0.150351	0.09185	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	4.55	-9.11	0.00711	.	1.099820	0.07088	N	0.838315	T	0.04227	0.0117	N	0.01188	-0.97	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.0	T	0.31336	-0.9947	10	0.11182	T	0.66	0.2722	12.843	0.57813	0.3976:0.4944:0.108:0.0	.	447;490;510	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	L	510;510;490;447	ENSP00000356729:F510L;ENSP00000375935:F510L;ENSP00000444073:F490L;ENSP00000439500:F447L	ENSP00000356729:F510L	F	+	3	2	FMO3	169353137	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.627000	0.00874	-2.996000	0.00278	-1.113000	0.02065	TTC		0.468	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		A	171086513	C	A	171086513	3	1	61	1	0	0	0	0	1	0	0	0	5975	912	32	2	1560	2	FMO3	1	171086513	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9602	171086513	78164108	796	8781										
FMO2	2327	broad.mit.edu	37	chr1	171174589	171174589	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcaacaggatatagtttCtcttttcccttccttgaaga	6	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171174589C>A	ENST00000209929.7	+	7	1157	c.999C>A	c.(997-999)ttC>ttA	p.F333L	RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.F333L|FMO2_ENST00000529935.1_3'UTR			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	332					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.F333L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GATATAGTTTCTCTTTTCCCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	97	98					1																	171174589		2203	4300	6503	169441213	SO:0001583	missense	2327			BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.999C>A	1.37:g.171174589C>A	ENSP00000209929:p.Phe333Leu		169441213	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801667	0.50315	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.61392	0.11;0.11	5.67	1.03	0.20045	.	0.145939	0.64402	D	0.000006	T	0.41511	0.1162	M	0.64676	1.99	0.09310	N	1	B	0.31290	0.318	B	0.42361	0.385	T	0.46303	-0.9201	10	0.56958	D	0.05	-6.418	8.3692	0.32404	0.0:0.4738:0.0:0.5262	.	333	Q99518	FMO2_HUMAN	L	333	ENSP00000209929:F333L;ENSP00000405905:F333L	ENSP00000209929:F333L	F	+	3	2	FMO2	169441213	0.000000	0.05858	0.771000	0.31576	0.994000	0.84299	-0.115000	0.10741	0.295000	0.22570	0.655000	0.94253	TTC		0.403	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		A	171174589	C	A	171174589	3	1	61	1	0	0	0	0	1	0	0	0	5974	912	32	2	1021	2	FMO2	1	171174589	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88076	171174589	78076032	797	8782										
FMO1	2326	broad.mit.edu	37	chr1	171236711	171236711	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaaggcagagccagtctCtacaagtctgtggtttccaa	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171236711C>A	ENST00000354841.4	+	2	293	c.162C>A	c.(160-162)ctC>ctA	p.L54L	FMO1_ENST00000367750.3_Silent_p.L54L|FMO1_ENST00000402921.2_Intron|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	54					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.L54L(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GAGCCAGTCTCTACAAGTCTG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											167	147	154					1																	171236711		2203	4300	6503	169503335	SO:0001819	synonymous_variant	2326			M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.162C>A	1.37:g.171236711C>A			169503335	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																				0.433	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		A	171236711	C	A	171236711	2	1	61	1	0	0	0	0	0	0	0	1	5973	900	32	2		2	FMO1	1	171236711	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62122	171236711	78013910	798	8783										
FMO4	2329	broad.mit.edu	37	chr1	171288976	171288976	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcataccatggccaagaaAgttgcagtgattggagctgg	14	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171288976A>C	ENST00000367749.3	+	3	342	c.12A>C	c.(10-12)aaA>aaC	p.K4N		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	4					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.K4N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TGGCCAAGAAAGTTGCAGTGA	0.453																																					Pancreas(24;816 862 7754 7993 32832)											1	Substitution - Missense(1)	large_intestine(1)	1											161	143	149					1																	171288976		2203	4300	6503	169555600	SO:0001583	missense	2329			BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.12A>C	1.37:g.171288976A>C	ENSP00000356723:p.Lys4Asn		169555600	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.160163	0.38119	.	.	ENSG00000076258	ENST00000367749	T	0.61392	0.11	5.18	1.34	0.21922	.	0.173576	0.52532	D	0.000079	T	0.41880	0.1178	M	0.62209	1.925	0.37195	D	0.904118	B	0.30236	0.274	B	0.43413	0.419	T	0.43278	-0.9401	10	0.62326	D	0.03	-6.5952	3.5686	0.07909	0.5655:0.0:0.1583:0.2762	.	4	P31512	FMO4_HUMAN	N	4	ENSP00000356723:K4N	ENSP00000356723:K4N	K	+	3	2	FMO4	169555600	0.002000	0.14202	0.962000	0.40283	0.915000	0.54546	-0.430000	0.06973	-0.032000	0.13758	0.528000	0.53228	AAA		0.453	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		C	171288976	A	C	171288976	3	2	61	1	0	0	0	0	1	0	0	0	5976	69	3	4	14	4	FMO4	1	171288976	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52265	171288976	77961645	799	8784										
FMO4	2329	broad.mit.edu	37	chr1	171293410	171293410	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcactggacatttcctgaAtccccatttacctttggaag	7	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171293410A>G	ENST00000367749.3	+	5	785	c.455A>G	c.(454-456)aAt>aGt	p.N152S	FMO4_ENST00000462992.1_3'UTR	NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	152					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.N152S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CATTTCCTGAATCCCCATTTA	0.443																																					Pancreas(24;816 862 7754 7993 32832)											1	Substitution - Missense(1)	large_intestine(1)	1											487	465	473					1																	171293410		2203	4300	6503	169560034	SO:0001583	missense	2329			BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.455A>G	1.37:g.171293410A>G	ENSP00000356723:p.Asn152Ser		169560034	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.587034	0.28268	.	.	ENSG00000076258	ENST00000367749	T	0.57436	0.4	5.93	-6.01	0.02199	.	0.467195	0.25355	N	0.031261	T	0.09423	0.0232	N	0.20574	0.59	0.20638	N	0.999879	B	0.15719	0.014	B	0.20184	0.028	T	0.38178	-0.9673	10	0.07175	T	0.84	-6.8292	10.1045	0.42524	0.4014:0.1089:0.4897:0.0	.	152	P31512	FMO4_HUMAN	S	152	ENSP00000356723:N152S	ENSP00000356723:N152S	N	+	2	0	FMO4	169560034	0.002000	0.14202	0.023000	0.16930	0.670000	0.39368	1.280000	0.33202	-1.558000	0.01690	-0.250000	0.11733	AAT		0.443	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		G	171293410	A	G	171293410	3	3	61	1	0	0	0	0	1	0	0	0	5976	101	4	4	465	4	FMO4	1	171293410	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4434	171293410	77957211	800	8785										
FMO4	2329	broad.mit.edu	37	chr1	171310701	171310701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttttctttggaccatgtaCtccttatcagtaccgcctca	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171310701C>A	ENST00000367749.3	+	10	1730	c.1400C>A	c.(1399-1401)aCt>aAt	p.T467N		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	467					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.T467N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GGACCATGTACTCCTTATCAG	0.493																																					Pancreas(24;816 862 7754 7993 32832)											1	Substitution - Missense(1)	large_intestine(1)	1											119	101	107					1																	171310701		2203	4300	6503	169577325	SO:0001583	missense	2329			BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1400C>A	1.37:g.171310701C>A	ENSP00000356723:p.Thr467Asn		169577325	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706924	0.48412	.	.	ENSG00000076258	ENST00000367749	T	0.54071	0.59	5.52	3.5	0.40072	.	0.160935	0.56097	D	0.000038	T	0.39759	0.1090	M	0.69185	2.1	0.43246	D	0.99516	P	0.36483	0.555	B	0.37387	0.248	T	0.47459	-0.9116	10	0.46703	T	0.11	-13.7724	14.8735	0.70478	0.0:0.5954:0.4046:0.0	.	467	P31512	FMO4_HUMAN	N	467	ENSP00000356723:T467N	ENSP00000356723:T467N	T	+	2	0	FMO4	169577325	0.892000	0.30473	0.997000	0.53966	0.831000	0.47069	1.966000	0.40481	1.287000	0.44583	0.655000	0.94253	ACT		0.493	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		A	171310701	C	A	171310701	3	1	61	1	0	0	0	0	1	0	0	0	5976	565	20	2	1430	2	FMO4	1	171310701	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17291	171310701	77939920	801	8786										
BAT2L2	23215	broad.mit.edu	37	chr1	171510545	171510545	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagcctgataatcatgttCgaatagataatagactgcta	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171510545C>T	ENST00000338920.4	+	16	4171	c.3934C>T	c.(3934-3936)Cga>Tga	p.R1312*	PRRC2C_ENST00000392078.3_Nonsense_Mutation_p.R1314*|PRRC2C_ENST00000426496.2_Nonsense_Mutation_p.R1312*|PRRC2C_ENST00000367742.3_Nonsense_Mutation_p.R1314*	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1312					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.R1314*(1)									TAATCATGTTCGAATAGATAA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											51	52	52					1																	171510545		2203	4300	6503	169777169	SO:0001587	stop_gained	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.3934C>T	1.37:g.171510545C>T	ENSP00000343629:p.Arg1312*		169777169	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Nonsense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	44	11.132231	0.99520	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.	.	.	5.51	3.58	0.41010	.	0.000000	0.38164	N	0.001793	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7063	0.40218	0.2982:0.5727:0.1291:0.0	.	.	.	.	X	1314;1313;1312;1314;1312;1069	.	ENSP00000343629:R1312X	R	+	1	2	PRRC2C	169777169	0.991000	0.36638	1.000000	0.80357	0.933000	0.57130	1.317000	0.33631	0.639000	0.30564	0.563000	0.77884	CGA		0.413	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171510545	C	T	171510545	4	4	61	1	0	0	0	0	0	1	0	0	1322	876	31	1	3992	1	BAT2L2	1	171510545	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	199844	171510545	77740076	802	8787										
MYOC	4653	broad.mit.edu	37	chr1	171621527	171621527	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttgggtgctgctgtctctCtgtaagttatggatgactga	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171621527C>T	ENST00000037502.6	-	1	296	c.225G>A	c.(223-225)caG>caA	p.Q75Q		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	75					bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)	p.Q75Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TGCTGTCTCTCTGTAAGTTAT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	1											129	101	110					1																	171621527		2203	4300	6503	169888150	SO:0001819	synonymous_variant	4653			BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.225G>A	1.37:g.171621527C>T			169888150	B2RD84|O00620|Q7Z6Q9	Silent	SNP	ENST00000037502.6	37	CCDS1297.1																																																																																				0.572	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		T	171621527	C	T	171621527	2	4	61	1	0	0	0	0	0	0	0	1	10116	912	32	3		3	MYOC	1	171621527	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110982	171621527	77629094	803	8788										
VAMP4	8674	broad.mit.edu	37	chr1	171678834	171678834	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgccaccacatttgccttcGaagttgtttggatctgttgc	9	11	1	0	rs577477919		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171678834G>A	ENST00000236192.7	-	6	702	c.316C>T	c.(316-318)Cga>Tga	p.R106*	VAMP4_ENST00000415773.1_Nonsense_Mutation_p.R105*|VAMP4_ENST00000482519.1_5'UTR|VAMP4_ENST00000367740.2_Nonsense_Mutation_p.R105*	NM_001185127.1|NM_003762.4	NP_001172056.1|NP_003753.2	O75379	VAMP4_HUMAN	vesicle-associated membrane protein 4	106	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				Golgi to plasma membrane protein transport (GO:0043001)|regulation of Golgi to plasma membrane protein transport (GO:0042996)|SNARE complex assembly (GO:0035493)	cell surface (GO:0009986)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|SNARE complex (GO:0031201)|trans-Golgi network (GO:0005802)		p.R106*(1)		large_intestine(4)	4	all_cancers(6;1.42e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					ATTTGCCTTCGAAGTTGTTTG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											191	162	172					1																	171678834		2203	4300	6503	169945457	SO:0001587	stop_gained	8674			AF044310	CCDS1298.1, CCDS53430.1	1q24-q25	2013-02-13			ENSG00000117533	ENSG00000117533		"Vesicle-associated membrane proteins"	12645	protein-coding gene	gene with protein product		606909				9553086	Standard	NM_003762		Approved		uc001ghx.2	O75379	OTTHUMG00000034788	ENST00000236192.7:c.316C>T	1.37:g.171678834G>A	ENSP00000236192:p.Arg106*		169945457	A2IDD8|Q96IY9|Q96J20|Q9UEL7	Nonsense_Mutation	SNP	ENST00000236192.7	37	CCDS1298.1	.	.	.	.	.	.	.	.	.	.	G	39	7.459897	0.98299	.	.	ENSG00000117533	ENST00000236192;ENST00000415773;ENST00000367740	.	.	.	5.46	5.46	0.80206	.	0.069919	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9128	0.58189	0.0:0.0:0.8376:0.1624	.	.	.	.	X	106;105;105	.	ENSP00000236192:R106X	R	-	1	2	VAMP4	169945457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.560000	0.67332	2.565000	0.86533	0.650000	0.86243	CGA		0.393	VAMP4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000304033.2	NM_003762		A	171678834	G	A	171678834	4	1	61	1	0	0	0	0	0	1	0	0	17155	1066	37	1	121	1	VAMP4	1	171678834	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57307	171678834	77571787	804	8789										
METTL13	51603	broad.mit.edu	37	chr1	171753612	171753612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccactgtgaaaccatcgCgggacaatcattttgcgatt	9	12	1	1	rs202234390		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:171753612C>T	ENST00000361735.3	+	2	1152	c.886C>T	c.(886-888)Cgg>Tgg	p.R296W	METTL13_ENST00000362019.3_Missense_Mutation_p.R210W|METTL13_ENST00000458517.1_Missense_Mutation_p.R295W|METTL13_ENST00000367737.5_Intron	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	296							methyltransferase activity (GO:0008168)	p.R296W(2)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GAAACCATCGCGGGACAATCA	0.622													C|||	1	0.000199681	0	0	5008	,	,		15300	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	1																																								170020235	SO:0001583	missense	51603			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"KIAA0859"	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.886C>T	1.37:g.171753612C>T	ENSP00000354920:p.Arg296Trp		170020235	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	17.83	3.486189	0.63962	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000361735	T;T;T	0.32023	2.21;1.47;2.21	5.33	0.624	0.17659	.	0.123265	0.52532	D	0.000069	T	0.29355	0.0731	L	0.51422	1.61	0.44275	D	0.997133	D;D	0.89917	0.999;1.0	P;D	0.68483	0.818;0.958	T	0.04320	-1.0960	9	.	.	.	-6.5228	9.767	0.40567	0.324:0.5973:0.0:0.0787	.	295;296	B4E2X3;Q8N6R0	.;MTL13_HUMAN	W	295;210;296	ENSP00000401955:R295W;ENSP00000355393:R210W;ENSP00000354920:R296W	.	R	+	1	2	METTL13	170020235	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.267000	0.43329	0.148000	0.19059	-0.136000	0.14681	CGG		0.622	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955		T	171753612	C	T	171753612	3	4	61	1	0	0	0	0	1	0	0	0	9527	759	27	1	892	1	METTL13	1	171753612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74778	171753612	77497009	805	8790										
DNM3	26052	broad.mit.edu	37	chr1	172011179	172011179	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatttgctgtggactttgaGaagagaattgaagggtcagg	14	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172011179G>T	ENST00000355305.5	+	8	1180	c.1023G>T	c.(1021-1023)gaG>gaT	p.E341D	DNM3_ENST00000367731.1_Missense_Mutation_p.E341D|DNM3_ENST00000520906.1_Missense_Mutation_p.E341D|DNM3_ENST00000367733.2_Missense_Mutation_p.E341D|DNM3_ENST00000358155.4_Missense_Mutation_p.E341D			Q9UQ16	DYN3_HUMAN	dynamin 3	341					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E341D(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TGGACTTTGAGAAGAGAATTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											146	141	142					1																	172011179		1835	4082	5917	170277802	SO:0001583	missense	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1023G>T	1.37:g.172011179G>T	ENSP00000347457:p.Glu341Asp		170277802	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		.	.	.	.	.	.	.	.	.	.	G	13.80	2.344578	0.41498	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	5.65	4.73	0.59995	.	0.103853	0.64402	D	0.000005	T	0.50616	0.1626	L	0.49640	1.575	0.51767	D	0.999939	B;B;B;B	0.20368	0.004;0.044;0.01;0.009	B;B;B;B	0.18561	0.02;0.019;0.019;0.022	T	0.50849	-0.8779	10	0.22706	T	0.39	.	10.4407	0.44464	0.1587:0.0:0.8413:0.0	.	341;341;341;341	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	D	341;341;341;341;341;341;231	ENSP00000350876:E341D;ENSP00000356707:E341D;ENSP00000347457:E341D;ENSP00000356705:E341D;ENSP00000429701:E341D;ENSP00000429416:E231D	ENSP00000347457:E341D	E	+	3	2	DNM3	170277802	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.827000	0.39102	1.383000	0.46405	0.491000	0.48974	GAG		0.383	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		T	172011179	G	T	172011179	3	4	61	1	0	0	0	0	1	0	0	0	4684	933	33	2	1053	2	DNM3	1	172011179	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	257567	172011179	77239442	806	8791										
DNM3	26052	broad.mit.edu	37	chr1	172051028	172051028	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaccaaccatgaagacttCattggcttcgcaaagtacgt	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172051028C>A	ENST00000355305.5	+	12	1636	c.1479C>A	c.(1477-1479)ttC>ttA	p.F493L	DNM3_ENST00000367731.1_Missense_Mutation_p.F493L|DNM3_ENST00000520906.1_Missense_Mutation_p.F493L|DNM3_ENST00000367733.2_Missense_Mutation_p.F493L|DNM3_ENST00000358155.4_Missense_Mutation_p.F493L			Q9UQ16	DYN3_HUMAN	dynamin 3	493					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F493L(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ATGAAGACTTCATTGGCTTCG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	145	147					1																	172051028		1918	4139	6057	170317651	SO:0001583	missense	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1479C>A	1.37:g.172051028C>A	ENSP00000347457:p.Phe493Leu		170317651	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		.	.	.	.	.	.	.	.	.	.	C	25.7	4.669454	0.88348	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28;-1.28	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.88175	0.6366	M	0.77313	2.365	0.54753	D	0.999987	D;D;D;D	0.89917	1.0;0.994;0.999;1.0	D;P;D;D	0.97110	1.0;0.858;0.986;1.0	D	0.88849	0.3318	10	0.87932	D	0	.	15.6157	0.76767	0.0:1.0:0.0:0.0	.	493;493;493;493	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	L	493;493;493;493;493;493;383	ENSP00000350876:F493L;ENSP00000356707:F493L;ENSP00000347457:F493L;ENSP00000356705:F493L;ENSP00000429701:F493L;ENSP00000429416:F383L	ENSP00000347457:F493L	F	+	3	2	DNM3	170317651	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.199000	0.42715	2.832000	0.97577	0.655000	0.94253	TTC		0.373	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		A	172051028	C	A	172051028	3	1	61	1	0	0	0	0	1	0	0	0	4684	825	29	2	1525	2	DNM3	1	172051028	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39849	172051028	77199593	807	8792										
DNM3	26052	broad.mit.edu	37	chr1	172061997	172061997	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtcaggttcacaagaaAaccacagttggaaatcaggt	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172061997A>C	ENST00000355305.5	+	13	1684	c.1527A>C	c.(1525-1527)aaA>aaC	p.K509N	DNM3_ENST00000367731.1_Missense_Mutation_p.K509N|DNM3_ENST00000520906.1_Missense_Mutation_p.K509N|DNM3_ENST00000367733.2_Missense_Mutation_p.K509N|DNM3_ENST00000358155.4_Missense_Mutation_p.K509N			Q9UQ16	DYN3_HUMAN	dynamin 3	509					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.K509N(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TTCACAAGAAAACCACAGTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	67	68					1																	172061997		1859	4085	5944	170328620	SO:0001583	missense	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1527A>C	1.37:g.172061997A>C	ENSP00000347457:p.Lys509Asn		170328620	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		.	.	.	.	.	.	.	.	.	.	A	13.64	2.298645	0.40694	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	D;D;D;D;D;D	0.94232	-3.23;-3.07;-3.27;-3.24;-3.38;-3.05	5.92	3.3	0.37823	.	0.821584	0.11539	N	0.553955	D	0.84570	0.5501	L	0.41236	1.265	0.44214	D	0.997045	B;B;B;B	0.22541	0.003;0.033;0.071;0.003	B;B;B;B	0.26614	0.022;0.071;0.071;0.013	T	0.81406	-0.0947	10	0.54805	T	0.06	.	9.178	0.37123	0.8333:0.0:0.1667:0.0	.	509;509;509;509	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	N	509;509;509;509;509;509;399	ENSP00000350876:K509N;ENSP00000356707:K509N;ENSP00000347457:K509N;ENSP00000356705:K509N;ENSP00000429701:K509N;ENSP00000429416:K399N	ENSP00000347457:K509N	K	+	3	2	DNM3	170328620	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.135000	0.57997	1.077000	0.40990	-0.361000	0.07541	AAA		0.368	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		C	172061997	A	C	172061997	3	2	61	1	0	0	0	0	1	0	0	0	4684	11	1	4	1577	4	DNM3	1	172061997	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10969	172061997	77188624	808	8793										
C1orf9	51430	broad.mit.edu	37	chr1	172558077	172558077	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccctggtttgagtcagaGacacaaatattttgcagtga	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172558077G>A	ENST00000263688.3	+	18	2055	c.1836G>A	c.(1834-1836)gaG>gaA	p.E612E	SUCO_ENST00000367723.4_Silent_p.E763E|SUCO_ENST00000608151.1_Silent_p.E764E|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	612					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.E612E(1)|p.E764E(1)									TTGAGTCAGAGACACAAATAT	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	1											103	102	102					1																	172558077		2203	4300	6503	170824700	SO:0001819	synonymous_variant	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1836G>A	1.37:g.172558077G>A			170824700	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																				0.413	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		A	172558077	G	A	172558077	2	1	61	1	0	0	0	0	0	0	0	1	2073	933	33	3		3	C1orf9	1	172558077	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	496080	172558077	76692544	809	8794										
C1orf9	51430	broad.mit.edu	37	chr1	172558636	172558636	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctatgaaacaaataaaGttaatgagttaatggataat	6	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172558636G>T	ENST00000263688.3	+	18	2614	c.2395G>T	c.(2395-2397)Gtt>Ttt	p.V799F	SUCO_ENST00000367723.4_Missense_Mutation_p.V950F|SUCO_ENST00000608151.1_Missense_Mutation_p.V951F|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	799					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.V799F(1)|p.V951F(1)									AACAAATAAAGTTAATGAGTT	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	1											32	34	33					1																	172558636		2190	4282	6472	170825259	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2395G>T	1.37:g.172558636G>T	ENSP00000263688:p.Val799Phe		170825259	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	0.564	-0.843929	0.02671	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	4.78	0.365	0.16131	.	1.306880	0.05313	N	0.525253	T	0.12347	0.0300	L	0.40543	1.245	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.0	B;B;B	0.08055	0.003;0.002;0.001	T	0.23440	-1.0188	9	0.42905	T	0.14	-0.0086	1.448	0.02368	0.2621:0.3478:0.2586:0.1315	.	799;951;799	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	F	951;799	.	ENSP00000263688:V799F	V	+	1	0	C1orf9	170825259	0.000000	0.05858	0.014000	0.15608	0.175000	0.22909	0.068000	0.14531	0.075000	0.16796	-0.140000	0.14226	GTT		0.333	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172558636	G	T	172558636	3	4	61	1	0	0	0	0	1	0	0	0	2073	1029	36	2	2465	2	C1orf9	1	172558636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	559	172558636	76691985	810	8795										
C1orf9	51430	broad.mit.edu	37	chr1	172558897	172558897	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttacagaggacagctacaGatttttatgctgaattgcaa	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172558897G>T	ENST00000263688.3	+	18	2875	c.2656G>T	c.(2656-2658)Gat>Tat	p.D886Y	SUCO_ENST00000367723.4_Missense_Mutation_p.D1037Y|SUCO_ENST00000608151.1_Missense_Mutation_p.D1038Y|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	886					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.D1038Y(1)|p.D886Y(1)									GACAGCTACAGATTTTTATGC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	1											90	93	92					1																	172558897		2200	4296	6496	170825520	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2656G>T	1.37:g.172558897G>T	ENSP00000263688:p.Asp886Tyr		170825520	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.089001	0.76756	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.29	5.29	0.74685	.	0.044149	0.85682	D	0.000000	T	0.74966	0.3786	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78137	-0.2321	9	0.87932	D	0	-21.0784	17.492	0.87707	0.0:0.0:1.0:0.0	.	886;1038;886	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	Y	1038;886	.	ENSP00000263688:D886Y	D	+	1	0	C1orf9	170825520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.400000	0.97290	2.460000	0.83146	0.655000	0.94253	GAT		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172558897	G	T	172558897	3	4	61	1	0	0	0	0	1	0	0	0	2073	942	33	2	2726	2	C1orf9	1	172558897	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	261	172558897	76691724	811	8796										
C1orf9	51430	broad.mit.edu	37	chr1	172560200	172560200	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagaatacttcaagaataGcagaggagcaggttggtttc	11	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172560200G>T	ENST00000263688.3	+	19	3121	c.2902G>T	c.(2902-2904)Gca>Tca	p.A968S	SUCO_ENST00000367723.4_Missense_Mutation_p.A1119S|SUCO_ENST00000608151.1_Missense_Mutation_p.A1120S|SUCO_ENST00000610051.1_Missense_Mutation_p.A597S	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	968					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.A968S(1)|p.A1120S(1)									TTCAAGAATAGCAGAGGAGCA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	1											95	97	96					1																	172560200		2203	4300	6503	170826823	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2902G>T	1.37:g.172560200G>T	ENSP00000263688:p.Ala968Ser		170826823	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.188111	0.78789	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	T;T	0.40476	1.03;1.03	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.57932	0.2087	M	0.74258	2.255	0.80722	D	1	D;D;D;D	0.76494	0.999;0.962;0.994;0.982	D;P;P;P	0.66196	0.942;0.534;0.757;0.773	T	0.59123	-0.7513	10	0.52906	T	0.07	-17.1602	18.1275	0.89590	0.0:0.0:1.0:0.0	.	597;968;1120;968	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	S	1120;968	ENSP00000356696:A1120S;ENSP00000263688:A968S	ENSP00000263688:A968S	A	+	1	0	C1orf9	170826823	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.323000	0.96364	2.616000	0.88540	0.650000	0.86243	GCA		0.333	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172560200	G	T	172560200	3	4	61	1	0	0	0	0	1	0	0	0	2073	971	34	2	2976	2	C1orf9	1	172560200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1303	172560200	76690421	812	8797										
C1orf9	51430	broad.mit.edu	37	chr1	172571855	172571855	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgtttctcttcctatgatGatatgaatttgaaaagaaga	9	4	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:172571855G>T	ENST00000263688.3	+	22	3412	c.3193G>T	c.(3193-3195)Gat>Tat	p.D1065Y	SUCO_ENST00000367723.4_Missense_Mutation_p.D1216Y|SUCO_ENST00000608151.1_Missense_Mutation_p.D1217Y|SUCO_ENST00000610051.1_Missense_Mutation_p.D694Y	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1065					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.D1217Y(1)|p.D1065Y(1)									TTCCTATGATGATATGAATTT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	1											222	223	223					1																	172571855		2203	4300	6503	170838478	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3193G>T	1.37:g.172571855G>T	ENSP00000263688:p.Asp1065Tyr		170838478	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962932	0.74016	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.84	5.84	0.93424	.	0.043062	0.85682	D	0.000000	T	0.76111	0.3942	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.998;0.999	T	0.77544	-0.2548	9	0.87932	D	0	-21.7605	18.6944	0.91594	0.0:0.0:1.0:0.0	.	694;1065;1217;1065	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	Y	1217;1065	.	ENSP00000263688:D1065Y	D	+	1	0	C1orf9	170838478	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.437000	0.90302	2.751000	0.94390	0.655000	0.94253	GAT		0.338	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172571855	G	T	172571855	3	4	61	1	0	0	0	0	1	0	0	0	2073	1290	45	2	3279	2	C1orf9	1	172571855	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11655	172571855	76678766	813	8798										
SLC9A11	284525	broad.mit.edu	37	chr1	173502869	173502869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagatatcaatgattccaAtaaccaggataaaaaattcc	4	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173502869A>G	ENST00000367714.3	-	17	2464	c.2042T>C	c.(2041-2043)aTt>aCt	p.I681T	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_3'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	681	Ion transport-like. {ECO:0000250}.				sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.I681T(1)									AATGATTCCAATAACCAGGAT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	60	57					1																	173502869		2202	4295	6497	171769492	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.2042T>C	1.37:g.173502869A>G	ENSP00000356687:p.Ile681Thr		171769492	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	1.595	-0.528122	0.04112	.	.	ENSG00000162753	ENST00000367714	D	0.97480	-4.4	5.26	2.78	0.32641	Ion transport (1);	1.831980	0.02557	N	0.096329	D	0.85665	0.5749	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.80863	-0.1192	10	0.48119	T	0.1	-0.6316	4.2694	0.10778	0.7301:0.0:0.0942:0.1756	.	681	Q5TAH2	S9A11_HUMAN	T	681	ENSP00000356687:I681T	ENSP00000356687:I681T	I	-	2	0	SLC9A11	171769492	0.027000	0.19231	0.016000	0.15963	0.002000	0.02628	1.280000	0.33202	0.956000	0.37904	0.528000	0.53228	ATT		0.284	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		G	173502869	A	G	173502869	3	3	61	1	0	0	0	0	1	0	0	0	14748	101	4	4	1380	4	SLC9A11	1	173502869	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	931014	173502869	75747752	814	8799										
SLC9A11	284525	broad.mit.edu	37	chr1	173505010	173505010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctatacaatattccaaGaaagttaaaacatttttaaa	2	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173505010G>T	ENST00000367714.3	-	15	2156	c.1734C>A	c.(1732-1734)ttC>ttA	p.F578L	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Intron	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	578					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.F578L(1)									AATATTCCAAGAAAGTTAAAA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	1											30	36	34					1																	173505010		2143	4195	6338	171771633	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1734C>A	1.37:g.173505010G>T	ENSP00000356687:p.Phe578Leu		171771633	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	G	1.013	-0.687321	0.03328	.	.	ENSG00000162753	ENST00000367714	T	0.04275	3.66	5.81	2.48	0.30137	.	0.605739	0.15672	N	0.250356	T	0.00967	0.0032	L	0.36672	1.1	0.09310	N	1	B	0.22346	0.068	B	0.15484	0.013	T	0.47898	-0.9081	10	0.11485	T	0.65	-5.8685	3.7288	0.08485	0.2435:0.2051:0.5513:0.0	.	578	Q5TAH2	S9A11_HUMAN	L	578	ENSP00000356687:F578L	ENSP00000356687:F578L	F	-	3	2	SLC9A11	171771633	0.739000	0.28196	0.234000	0.24042	0.083000	0.17756	1.040000	0.30278	0.747000	0.32809	0.603000	0.83216	TTC		0.259	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173505010	G	T	173505010	3	4	61	1	0	0	0	0	1	0	0	0	14748	933	33	2	1696	2	SLC9A11	1	173505010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2141	173505010	75745611	815	8800										
KLHL20	27252	broad.mit.edu	37	chr1	173685202	173685202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggaaggaaagccaatgcGcaggtaggcatttaggaaga	14	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173685202G>A	ENST00000209884.4	+	2	156	c.20G>A	c.(19-21)cGc>cAc	p.R7H	KLHL20_ENST00000546011.1_Silent_p.A9A|KLHL20_ENST00000493170.1_3'UTR	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	7					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)	p.R7H(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						AAGCCAATGCGCAGGTAGGCA	0.338																																					GBM(159;862 2695 6559 23041)											1	Substitution - Missense(1)	large_intestine(1)	1											146	136	140					1																	173685202		2203	4300	6503	171951825	SO:0001583	missense	27252			AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"Kelch-like", "BTB/POZ domain containing"	25056	protein-coding gene	gene with protein product			"kelch-like 20 (Drosophila)"			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.20G>A	1.37:g.173685202G>A	ENSP00000209884:p.Arg7His		171951825	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	37	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398910	0.83120	.	.	ENSG00000076321	ENST00000209884	T	0.69806	-0.43	5.3	5.3	0.74995	.	0.727185	0.14156	N	0.337718	T	0.60779	0.2295	N	0.14661	0.345	0.80722	D	1	D;D	0.65815	0.995;0.976	D;P	0.69479	0.964;0.522	T	0.64058	-0.6496	10	0.45353	T	0.12	.	14.816	0.70034	0.0:0.0:1.0:0.0	.	7;7	Q9BS75;Q9Y2M5	.;KLH20_HUMAN	H	7	ENSP00000209884:R7H	ENSP00000209884:R7H	R	+	2	0	KLHL20	171951825	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.841000	0.62824	2.616000	0.88540	0.655000	0.94253	CGC		0.338	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		A	173685202	G	A	173685202	3	1	61	1	0	0	0	0	1	0	0	0	8396	1087	38	1	22	1	KLHL20	1	173685202	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180192	173685202	75565419	816	8801										
CENPL	91687	broad.mit.edu	37	chr1	173776547	173776547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caataaaagcattgagaagtCtagaatactctttgagatta	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173776547C>A	ENST00000345664.6	-	3	491	c.278G>T	c.(277-279)aGa>aTa	p.R93I	Y_RNA_ENST00000516548.1_RNA|CENPL_ENST00000356198.2_Missense_Mutation_p.R93I|CENPL_ENST00000367710.3_Missense_Mutation_p.R93I	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	93					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)		p.R93I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						ATTGAGAAGTCTAGAATACTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											60	65	63					1																	173776547		2203	4300	6503	172043170	SO:0001583	missense	91687			BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.278G>T	1.37:g.173776547C>A	ENSP00000323543:p.Arg93Ile		172043170	Q5TEL5|Q96ND4	Missense_Mutation	SNP	ENST00000345664.6	37	CCDS30938.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939640	0.52972	.	.	ENSG00000120334	ENST00000356198;ENST00000345664;ENST00000367710	T;T;T	0.55760	1.08;0.5;0.5	5.63	2.45	0.29901	.	0.203175	0.49916	D	0.000138	T	0.32704	0.0838	L	0.53249	1.67	0.58432	D	0.999996	P;B	0.45474	0.859;0.314	B;B	0.40009	0.316;0.284	T	0.25467	-1.0131	10	0.87932	D	0	-1.7003	12.2682	0.54691	0.0:0.8317:0.0:0.1683	.	93;93	Q8N0S6-2;Q8N0S6	.;CENPL_HUMAN	I	93	ENSP00000348527:R93I;ENSP00000323543:R93I;ENSP00000356683:R93I	ENSP00000323543:R93I	R	-	2	0	CENPL	172043170	0.970000	0.33590	1.000000	0.80357	0.978000	0.69477	0.695000	0.25527	0.261000	0.21753	0.655000	0.94253	AGA		0.358	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		A	173776547	C	A	173776547	3	1	61	1	0	0	0	0	1	0	0	0	3242	913	32	2	910	2	CENPL	1	173776547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91345	173776547	75474074	817	8802										
DARS2	55157	broad.mit.edu	37	chr1	173797501	173797501	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttggtcctaagagatttCgatgggcttgttcaagttat	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173797501C>T	ENST00000361951.4	+	3	985	c.258C>T	c.(256-258)ttC>ttT	p.F86F	DARS2_ENST00000239457.5_5'UTR	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	86					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.F86F(1)		breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	TAAGAGATTTCGATGGGCTTG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	1											100	100	100					1																	173797501		2203	4300	6503	172064124	SO:0001819	synonymous_variant	55157			AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	25538	protein-coding gene	gene with protein product	"aspartate tRNA ligase 2, mitochondrial"	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.258C>T	1.37:g.173797501C>T			172064124		Silent	SNP	ENST00000361951.4	37	CCDS1311.1																																																																																				0.373	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122		T	173797501	C	T	173797501	2	4	61	1	0	0	0	0	0	0	0	1	4248	883	31	1		1	DARS2	1	173797501	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20954	173797501	75453120	818	8803										
DARS2	55157	broad.mit.edu	37	chr1	173822638	173822638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcccagagagctggaatCggcccaccacccatttactg	8	14	0	1	rs146122206		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:173822638C>T	ENST00000361951.4	+	14	2223	c.1496C>T	c.(1495-1497)tCg>tTg	p.S499L	DARS2_ENST00000239457.5_Missense_Mutation_p.S81L|DARS2_ENST00000471476.1_3'UTR	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	499					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.S499L(1)		breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	GAGCTGGAATCGGCCCACCAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	87	87					1																	173822638		2203	4300	6503	172089261	SO:0001583	missense	55157			AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	25538	protein-coding gene	gene with protein product	"aspartate tRNA ligase 2, mitochondrial"	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.1496C>T	1.37:g.173822638C>T	ENSP00000355086:p.Ser499Leu		172089261		Missense_Mutation	SNP	ENST00000361951.4	37	CCDS1311.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816641	0.90790	.	.	ENSG00000117593	ENST00000361951;ENST00000239457	D;D	0.92149	-1.78;-2.98	5.38	4.45	0.53987	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.063272	0.64402	D	0.000003	D	0.96046	0.8712	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96921	0.9674	10	0.87932	D	0	-13.5637	14.9191	0.70822	0.0:0.8558:0.1442:0.0	.	499	Q6PI48	SYDM_HUMAN	L	499;81	ENSP00000355086:S499L;ENSP00000239457:S81L	ENSP00000239457:S81L	S	+	2	0	DARS2	172089261	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.603000	0.82811	1.236000	0.43740	0.591000	0.81541	TCG		0.507	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122		T	173822638	C	T	173822638	3	4	61	1	0	0	0	0	1	0	0	0	4248	893	31	1	1550	1	DARS2	1	173822638	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25137	173822638	75427983	819	8804										
RABGAP1L	9910	broad.mit.edu	37	chr1	174274198	174274198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagcgagagtctgacaaGgaggaaccagtcactcctac	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:174274198G>T	ENST00000251507.4	+	11	1572	c.1398G>T	c.(1396-1398)aaG>aaT	p.K466N	RABGAP1L_ENST00000357444.6_Missense_Mutation_p.K429N|RABGAP1L_ENST00000367689.3_Missense_Mutation_p.K113N	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0								p.K466N(1)		NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						AGTCTGACAAGGAGGAACCAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	78	82					1																	174274198		2203	4300	6503	172540821	SO:0001583	missense	9910			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.1398G>T	1.37:g.174274198G>T	ENSP00000251507:p.Lys466Asn		172540821	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	37	CCDS1314.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.157405	0.38119	.	.	ENSG00000152061	ENST00000357444;ENST00000367689;ENST00000251507;ENST00000457696;ENST00000367692	T;T;T	0.44881	0.91;3.5;0.93	5.33	0.206	0.15208	.	0.188770	0.46145	D	0.000304	T	0.26738	0.0654	L	0.36672	1.1	0.80722	D	1	P;B;B;B;P	0.37276	0.514;0.327;0.177;0.177;0.589	B;B;B;B;B	0.35813	0.151;0.045;0.093;0.093;0.211	T	0.03315	-1.1049	10	0.24483	T	0.36	.	8.1102	0.30909	0.4221:0.0:0.5779:0.0	.	478;113;466;466;429	B7WPG6;Q5JZA9;F1LJ00;Q5R372;Q5R372-2	.;.;.;RBG1L_HUMAN;.	N	429;113;466;478;478	ENSP00000350027:K429N;ENSP00000251507:K466N;ENSP00000403136:K478N	ENSP00000251507:K466N	K	+	3	2	RABGAP1L	172540821	0.886000	0.30341	0.995000	0.50966	0.996000	0.88848	-0.325000	0.07976	-0.009000	0.14296	0.655000	0.94253	AAG		0.448	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765		T	174274198	G	T	174274198	3	4	61	1	0	0	0	0	1	0	0	0	13002	991	35	2	1436	2	RABGAP1L	1	174274198	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	451560	174274198	74976423	820	8805										
CACYBP	27101	broad.mit.edu	37	chr1	174979150	174979150	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggagacgatgatatgaagCgaaccattaataaagcctgg	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:174979150C>T	ENST00000367679.2	+	6	1070	c.622C>T	c.(622-624)Cga>Tga	p.R208*	CACYBP_ENST00000367681.2_Nonsense_Mutation_p.R165*|MRPS14_ENST00000498253.1_5'Flank|CACYBP_ENST00000405362.1_Nonsense_Mutation_p.R165*	NM_014412.2	NP_055227.1	Q9HB71	CYBP_HUMAN	calcyclin binding protein	208	Interaction with S100A6. {ECO:0000250}.|Interaction with SKP1.|SGS. {ECO:0000255|PROSITE- ProRule:PRU00386}.				aging (GO:0007568)|cardiac muscle cell differentiation (GO:0055007)|cellular response to calcium ion (GO:0071277)|negative regulation of cell death (GO:0060548)|positive regulation of DNA replication (GO:0045740)|response to growth hormone (GO:0060416)	beta-catenin destruction complex (GO:0030877)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.R208*(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	11						TGATATGAAGCGAACCATTAA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											98	95	96					1																	174979150		2203	4300	6503	173245773	SO:0001587	stop_gained	27101			BC022352	CCDS1315.1, CCDS30942.1	1q24-q25	2008-02-05			ENSG00000116161	ENSG00000116161			30423	protein-coding gene	gene with protein product		606186				11389839, 12421809	Standard	XM_005245092		Approved	SIP, S100A6BP	uc001gkj.1	Q9HB71	OTTHUMG00000034941	ENST00000367679.2:c.622C>T	1.37:g.174979150C>T	ENSP00000356652:p.Arg208*		173245773	B2ZWH2|B3KSF1|O60666|Q5R370|Q5R371	Nonsense_Mutation	SNP	ENST00000367679.2	37	CCDS1315.1	.	.	.	.	.	.	.	.	.	.	C	38	6.700454	0.97772	.	.	ENSG00000116161	ENST00000367681;ENST00000450101;ENST00000367679;ENST00000405362	.	.	.	5.89	3.88	0.44766	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.4319	16.5609	0.84566	0.3408:0.6592:0.0:0.0	.	.	.	.	X	165;181;208;165	.	ENSP00000356652:R208X	R	+	1	2	CACYBP	173245773	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.898000	0.39809	0.845000	0.35118	-1.357000	0.01221	CGA		0.393	CACYBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084583.3	NM_014412		T	174979150	C	T	174979150	4	4	61	1	0	0	0	0	0	1	0	0	2570	760	27	1	644	1	CACYBP	1	174979150	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	704952	174979150	74271471	821	8806										
TNN	63923	broad.mit.edu	37	chr1	175046851	175046851	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacgccacagaaggactgCgagttggcaggcagtgtcca	14	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175046851C>T	ENST00000239462.4	+	2	410	c.297C>T	c.(295-297)tgC>tgT	p.C99C		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	99					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.C99C(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		AGAAGGACTGCGAGTTGGCAG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											57	55	56					1																	175046851		2203	4300	6503	173313474	SO:0001819	synonymous_variant	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.297C>T	1.37:g.175046851C>T			173313474	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																				0.607	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175046851	C	T	175046851	2	4	61	1	0	0	0	0	0	0	0	1	16362	776	27	1		1	TNN	1	175046851	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67701	175046851	74203770	822	8807										
TNN	63923	broad.mit.edu	37	chr1	175052929	175052929	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtgacagatgagactgaGaactcccttgacgtggagtg	15	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175052929G>T	ENST00000239462.4	+	5	1205	c.1092G>T	c.(1090-1092)gaG>gaT	p.E364D		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	364	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.E364D(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ATGAGACTGAGAACTCCCTTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	84	89					1																	175052929		2203	4300	6503	173319552	SO:0001583	missense	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1092G>T	1.37:g.175052929G>T	ENSP00000239462:p.Glu364Asp		173319552	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267026	0.40095	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.57752	0.38	5.28	2.42	0.29668	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.051579	0.85682	D	0.000000	T	0.59459	0.2195	L	0.49699	1.58	0.25914	N	0.983191	D;P	0.67145	0.996;0.872	D;P	0.66716	0.946;0.781	T	0.48536	-0.9027	10	0.35671	T	0.21	.	8.2076	0.31465	0.3093:0.0:0.6907:0.0	.	364;364	B3KXB6;Q9UQP3	.;TENN_HUMAN	D	364	ENSP00000239462:E364D	ENSP00000239462:E364D	E	+	3	2	TNN	173319552	0.010000	0.17322	0.121000	0.21740	0.346000	0.29079	0.275000	0.18698	0.619000	0.30197	-0.216000	0.12614	GAG		0.557	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175052929	G	T	175052929	3	4	61	1	0	0	0	0	1	0	0	0	16362	933	33	2	1106	2	TNN	1	175052929	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6078	175052929	74197692	823	8808										
TNN	63923	broad.mit.edu	37	chr1	175054543	175054543	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctgcttgtttccaggtCtgcacccggggactgagtat	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175054543C>T	ENST00000239462.4	+	6	1350	c.1237C>T	c.(1237-1239)Ctg>Ttg	p.L413L		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	413	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.L413L(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GTTTCCAGGTCTGCACCCGGG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	1											52	46	48					1																	175054543		2203	4300	6503	173321166	SO:0001819	synonymous_variant	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1237C>T	1.37:g.175054543C>T			173321166	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																				0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175054543	C	T	175054543	2	4	61	1	0	0	0	0	0	0	0	1	16362	912	32	3		3	TNN	1	175054543	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1614	175054543	74196078	824	8809										
TNR	7143	broad.mit.edu	37	chr1	175299265	175299265	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaggtttctgctgtcctcGacagagaacctgtcgtagga	11	10	1	1	rs377731803		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175299265G>A	ENST00000367674.2	-	21	4446	c.3738C>T	c.(3736-3738)gtC>gtT	p.V1246V	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Silent_p.V1246V			Q92752	TENR_HUMAN	tenascin R	1246	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.V1246V(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGCTGTCCTCGACAGAGAACC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	84	70	75		3738	-6.2	0.4	1		75	0,8600		0,0,4300	no	coding-synonymous	TNR	NM_003285.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1246/1359	175299265	1,13005	2203	4300	6503	173565888	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3738C>T	1.37:g.175299265G>A			173565888	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.582	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175299265	G	A	175299265	2	1	61	1	0	0	0	0	0	0	0	1	16377	1045	37	1		1	TNR	1	175299265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244722	175299265	73951356	825	8810										
TNR	7143	broad.mit.edu	37	chr1	175328855	175328855	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtagcaatcagatccacaGggttgtccatggctgaaaca	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175328855G>T	ENST00000367674.2	-	15	3575	c.2867C>A	c.(2866-2868)cCt>cAt	p.P956H	TNR_ENST00000263525.2_Missense_Mutation_p.P956H			Q92752	TENR_HUMAN	tenascin R	956	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.P956H(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CAGATCCACAGGGTTGTCCAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	83	88					1																	175328855		2203	4300	6503	173595478	SO:0001583	missense	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2867C>A	1.37:g.175328855G>T	ENSP00000356646:p.Pro956His		173595478	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778199	0.90195	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.79940	-1.32;-1.32	5.85	5.85	0.93711	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.91848	0.7420	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92565	0.6061	10	0.87932	D	0	.	19.76	0.96311	0.0:0.0:1.0:0.0	.	956	Q92752	TENR_HUMAN	H	956;956;866	ENSP00000356646:P956H;ENSP00000263525:P956H	ENSP00000263525:P956H	P	-	2	0	TNR	173595478	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.143000	0.94623	2.753000	0.94483	0.655000	0.94253	CCT		0.473	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		T	175328855	G	T	175328855	3	4	61	1	0	0	0	0	1	0	0	0	16377	1000	35	2	1245	2	TNR	1	175328855	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29590	175328855	73921766	826	8811										
TNR	7143	broad.mit.edu	37	chr1	175331866	175331866	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgctgttgaggctgatttcGtattcggtagctgggttcag	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175331866G>A	ENST00000367674.2	-	14	3495	c.2787C>T	c.(2785-2787)taC>taT	p.Y929Y	TNR_ENST00000263525.2_Silent_p.Y929Y			Q92752	TENR_HUMAN	tenascin R	929	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.Y929Y(2)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GGCTGATTTCGTATTCGGTAG	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	1											218	185	196					1																	175331866		2203	4300	6503	173598489	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2787C>T	1.37:g.175331866G>A			173598489	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.532	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175331866	G	A	175331866	2	1	61	1	0	0	0	0	0	0	0	1	16377	1140	40	1		1	TNR	1	175331866	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3011	175331866	73918755	827	8812										
TNR	7143	broad.mit.edu	37	chr1	175355352	175355352	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttcaaaagaatgaaatcGactttggctcgagggggaat	11	5	1	2	rs375626142		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175355352G>A	ENST00000367674.2	-	8	2301	c.1593C>T	c.(1591-1593)gtC>gtT	p.V531V	TNR_ENST00000263525.2_Silent_p.V531V			Q92752	TENR_HUMAN	tenascin R	531	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.V531V(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GAATGAAATCGACTTTGGCTC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		0,4406		0,0,2203	31	36	34		1593	-8.3	0.7	1		34	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TNR	NM_003285.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		531/1359	175355352	4,13002	2203	4300	6503	173621975	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1593C>T	1.37:g.175355352G>A			173621975	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.577	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175355352	G	A	175355352	2	1	61	1	0	0	0	0	0	0	0	1	16377	1045	37	1		1	TNR	1	175355352	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23486	175355352	73895269	828	8813										
TNR	7143	broad.mit.edu	37	chr1	175375428	175375428	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccctctccagcatctcGatccggctcagcagctcctg	7	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:175375428G>A	ENST00000367674.2	-	3	1131	c.423C>T	c.(421-423)atC>atT	p.I141I	TNR_ENST00000263525.2_Silent_p.I141I			Q92752	TENR_HUMAN	tenascin R	141					associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.I141I(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCAGCATCTCGATCCGGCTCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	1											140	123	129					1																	175375428		2203	4300	6503	173642051	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.423C>T	1.37:g.175375428G>A			173642051	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	8.664	0.901242	0.17760	.	.	ENSG00000116147	ENST00000422274	.	.	.	5.24	-5.95	0.02241	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.2574	0.04059	0.4861:0.0979:0.2199:0.1961	.	.	.	.	X	25	.	.	R	-	1	2	TNR	173642051	0.669000	0.27502	0.426000	0.26672	0.874000	0.50279	-0.091000	0.11146	-1.106000	0.03008	-1.083000	0.02208	CGA		0.597	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175375428	G	A	175375428	2	1	61	1	0	0	0	0	0	0	0	1	16377	1048	37	1		1	TNR	1	175375428	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20076	175375428	73875193	829	8814										
RFWD2	64326	broad.mit.edu	37	chr1	176132982	176132982	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagtggtccaatttgaacCtcttttcctcaaatctttgc	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:176132982C>A	ENST00000367669.3	-	4	1125	c.611G>T	c.(610-612)aGg>aTg	p.R204M	RFWD2_ENST00000308769.8_Missense_Mutation_p.R204M	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	204					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)	p.R204M(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CAATTTGAACCTCTTTTCCTC	0.269																																					Ovarian(134;1413 1765 5706 35534 51541)											1	Substitution - Missense(1)	large_intestine(1)	1											54	53	53					1																	176132982		2203	4294	6497	174399605	SO:0001583	missense	64326			AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.611G>T	1.37:g.176132982C>A	ENSP00000356641:p.Arg204Met		174399605	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	37	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182575	0.78677	.	.	ENSG00000143207	ENST00000367669;ENST00000367666;ENST00000308769;ENST00000498306;ENST00000436424	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	5.1	5.1	0.69264	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.32255	0.0823	L	0.50333	1.59	0.80722	D	1	P;D;P	0.61697	0.931;0.99;0.88	P;D;P	0.69142	0.56;0.962;0.84	T	0.01228	-1.1412	10	0.45353	T	0.12	-14.6798	18.1145	0.89546	0.0:1.0:0.0:0.0	.	204;204;204	Q8NHY2-2;Q8NHY2;Q504W6	.;RFWD2_HUMAN;.	M	204;59;204;63;204	ENSP00000356641:R204M;ENSP00000356638:R59M;ENSP00000310943:R204M;ENSP00000433810:R63M	ENSP00000310943:R204M	R	-	2	0	RFWD2	174399605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.920000	0.63390	2.350000	0.79820	0.591000	0.81541	AGG		0.269	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		A	176132982	C	A	176132982	3	1	61	1	0	0	0	0	1	0	0	0	13297	681	24	2	1652	2	RFWD2	1	176132982	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	757554	176132982	73117639	830	8815										
PAPPA2	60676	broad.mit.edu	37	chr1	176659600	176659600	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgttttgttttctgttaaGaatacatgggggcctttgag	11	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:176659600G>A	ENST00000367662.3	+	5	3595				PAPPA2_ENST00000367661.3_Missense_Mutation_p.R822K	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2						bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R822K(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TTTCTGTTAAGAATACATGGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											48	47	47					1																	176659600		1875	4104	5979	174926223	SO:0001627	intron_variant	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.2431+34G>A	1.37:g.176659600G>A			174926223	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.537133	0.27475	.	.	ENSG00000116183	ENST00000367661	T	0.30448	1.53	5.19	3.26	0.37387	.	.	.	.	.	T	0.17662	0.0424	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.26052	-1.0114	7	.	.	.	.	7.0513	0.25075	0.0937:0.1748:0.7315:0.0	.	822	A9Z1Y8	.	K	822	ENSP00000356633:R822K	.	R	+	2	0	PAPPA2	174926223	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.035000	0.13797	0.649000	0.30751	0.462000	0.41574	AGA		0.488	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176659600	G	A	176659600	1	1	61	0	1	0	0	0	0	0	0	0	11464	942	33	3		3	PAPPA2	1	176659600	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	526618	176659600	72591021	831	8816										
PAPPA2	60676	broad.mit.edu	37	chr1	176709326	176709326	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaggggcagaatcatcaggGacagaggtacaaacttccct	12	10	2	2	rs371355700		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:176709326G>T	ENST00000367662.3	+	14	5309	c.4145G>T	c.(4144-4146)gGa>gTa	p.G1382V		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1382					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.G1382V(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						AATCATCAGGGACAGAGGTAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	67	68					1																	176709326		1966	4158	6124	174975949	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4145G>T	1.37:g.176709326G>T	ENSP00000356634:p.Gly1382Val		174975949	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696627	0.30142	.	.	ENSG00000116183	ENST00000367662	T	0.01629	4.72	5.91	1.94	0.25998	.	1.101770	0.06730	N	0.776460	T	0.02688	0.0081	M	0.63843	1.955	0.80722	D	1	B	0.28783	0.222	B	0.18871	0.023	T	0.36187	-0.9758	10	0.42905	T	0.14	-1.5173	6.4213	0.21746	0.2069:0.2403:0.5528:0.0	.	1382	Q9BXP8	PAPP2_HUMAN	V	1382	ENSP00000356634:G1382V	ENSP00000356634:G1382V	G	+	2	0	PAPPA2	174975949	0.984000	0.35163	1.000000	0.80357	0.807000	0.45602	0.431000	0.21444	0.403000	0.25479	-0.150000	0.13652	GGA		0.473	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176709326	G	T	176709326	3	4	61	1	0	0	0	0	1	0	0	0	11464	1174	41	2	4248	2	PAPPA2	1	176709326	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49726	176709326	72541295	832	8817										
FAM5B	57795	broad.mit.edu	37	chr1	177242646	177242646	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgagaccaggaccggtcCtctgggctgcagcaactatg	12	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177242646C>A	ENST00000361539.4	+	5	1004	c.692C>A	c.(691-693)cCt>cAt	p.P231H	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	231	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.P231H(1)									AGGACCGGTCCTCTGGGCTGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	82	85					1																	177242646		2203	4300	6503	175509269	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.692C>A	1.37:g.177242646C>A	ENSP00000354481:p.Pro231His		175509269	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977098	0.92982	.	.	ENSG00000198797	ENST00000361539	T	0.22336	1.96	5.24	5.24	0.73138	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.983;0.997	T	0.52646	-0.8548	10	0.87932	D	0	-13.2285	18.4376	0.90652	0.0:1.0:0.0:0.0	.	126;231	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	H	231	ENSP00000354481:P231H	ENSP00000354481:P231H	P	+	2	0	FAM5B	175509269	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.711000	0.84669	2.459000	0.83118	0.655000	0.94253	CCT		0.493	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177242646	C	A	177242646	3	1	61	1	0	0	0	0	1	0	0	0	5612	681	24	2	706	2	FAM5B	1	177242646	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	533320	177242646	72007975	833	8818										
FAM5B	57795	broad.mit.edu	37	chr1	177247890	177247890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctctgcaagcgctgccatCgccagcctcgcttccgcctg	9	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177247890C>T	ENST00000361539.4	+	7	1516	c.1204C>T	c.(1204-1206)Cgc>Tgc	p.R402C	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	402					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.R402C(2)									GCGCTGCCATCGCCAGCCTCG	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	1											53	55	54					1																	177247890		2203	4300	6503	175514513	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1204C>T	1.37:g.177247890C>T	ENSP00000354481:p.Arg402Cys		175514513	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607974	0.66558	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15372	2.43	5.39	3.36	0.38483	.	0.230912	0.38436	N	0.001681	T	0.26521	0.0648	L	0.44542	1.39	0.33909	D	0.639466	B;D;B	0.89917	0.038;1.0;0.029	B;P;B	0.62184	0.017;0.899;0.003	T	0.35201	-0.9798	10	0.72032	D	0.01	-26.6843	7.9241	0.29863	0.2778:0.6323:0.0:0.09	.	152;297;402	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	C	152;402	ENSP00000354481:R402C	ENSP00000354481:R402C	R	+	1	0	FAM5B	175514513	0.943000	0.32029	0.997000	0.53966	0.983000	0.72400	2.108000	0.41854	1.278000	0.44430	0.655000	0.94253	CGC		0.617	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		T	177247890	C	T	177247890	3	4	61	1	0	0	0	0	1	0	0	0	5612	884	31	1	1226	1	FAM5B	1	177247890	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5244	177247890	72002731	834	8819										
FAM5B	57795	broad.mit.edu	37	chr1	177250109	177250109	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgggggcagccactctgaGagctggttcatgcctgtgaa	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177250109G>A	ENST00000361539.4	+	8	2109	c.1797G>A	c.(1795-1797)gaG>gaA	p.E599E	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	599					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.E599E(1)									GCCACTCTGAGAGCTGGTTCA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											58	57	57					1																	177250109		2203	4300	6503	175516732	SO:0001819	synonymous_variant	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1797G>A	1.37:g.177250109G>A			175516732	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	37	CCDS1320.1																																																																																				0.552	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250109	G	A	177250109	2	1	61	1	0	0	0	0	0	0	0	1	5612	933	33	3		3	FAM5B	1	177250109	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2219	177250109	72000512	835	8820										
FAM5B	57795	broad.mit.edu	37	chr1	177250258	177250258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgtttacctacggagccGaatcaagtccctggatgaca	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177250258G>A	ENST00000361539.4	+	8	2258	c.1946G>A	c.(1945-1947)cGa>cAa	p.R649Q	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	649					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.R649Q(2)									CTACGGAGCCGAATCAAGTCC	0.463																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											62	61	61					1																	177250258		2203	4300	6503	175516881	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1946G>A	1.37:g.177250258G>A	ENSP00000354481:p.Arg649Gln		175516881	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.190002	0.78789	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.17691	2.26	5.16	5.16	0.70880	.	0.062133	0.64402	D	0.000004	T	0.42787	0.1218	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.988	T	0.34700	-0.9818	10	0.72032	D	0.01	-7.2313	18.2239	0.89910	0.0:0.0:1.0:0.0	.	544;649	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	Q	402;649	ENSP00000354481:R649Q	ENSP00000354481:R649Q	R	+	2	0	FAM5B	175516881	1.000000	0.71417	0.988000	0.46212	0.746000	0.42486	9.726000	0.98782	2.391000	0.81399	0.313000	0.20887	CGA		0.463	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250258	G	A	177250258	3	1	61	1	0	0	0	0	1	0	0	0	5612	1058	37	1	1972	1	FAM5B	1	177250258	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149	177250258	72000363	836	8821										
FAM5B	57795	broad.mit.edu	37	chr1	177250535	177250535	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtccgacttgaccttttCtcctgcttgctccggcatcg	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177250535C>A	ENST00000361539.4	+	8	2535	c.2223C>A	c.(2221-2223)ttC>ttA	p.F741L	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	741					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.F741L(1)									TTGACCTTTTCTCCTGCTTGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	79	82					1																	177250535		2203	4300	6503	175517158	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.2223C>A	1.37:g.177250535C>A	ENSP00000354481:p.Phe741Leu		175517158	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076228	0.55646	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.17854	2.25	5.05	0.955	0.19602	.	0.000000	0.85682	D	0.000000	T	0.34803	0.0910	M	0.69823	2.125	0.58432	D	0.999997	D;D	0.76494	0.999;0.993	D;D	0.80764	0.994;0.956	T	0.02519	-1.1147	10	0.38643	T	0.18	-23.0026	10.1966	0.43058	0.0:0.7265:0.0:0.2735	.	636;741	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	L	494;741	ENSP00000354481:F741L	ENSP00000354481:F741L	F	+	3	2	FAM5B	175517158	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	0.937000	0.28951	0.164000	0.19529	0.313000	0.20887	TTC		0.552	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250535	C	A	177250535	3	1	61	1	0	0	0	0	1	0	0	0	5612	912	32	2	2249	2	FAM5B	1	177250535	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	277	177250535	72000086	837	8822										
SEC16B	89866	broad.mit.edu	37	chr1	177928080	177928080	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctttctgctggcaaaaCgtcataatatccaccttatg	7	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:177928080C>T	ENST00000308284.6	-	9	1118	c.1029G>A	c.(1027-1029)acG>acA	p.T343T	SEC16B_ENST00000464631.2_Silent_p.T344T|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	343					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)		p.T344T(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GCTGGCAAAACGTCATAATAT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1											62	60	60					1																	177928080		1911	4132	6043	176194703	SO:0001819	synonymous_variant	89866			AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.1029G>A	1.37:g.177928080C>T			176194703	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																				0.502	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		T	177928080	C	T	177928080	2	4	61	1	0	0	0	0	0	0	0	1	14024	523	19	1		1	SEC16B	1	177928080	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	677545	177928080	71322541	838	8823										
RALGPS2	55103	broad.mit.edu	37	chr1	178802660	178802660	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactatataagtagcttaaaGatgacaccttgcattcccta	6	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:178802660G>T	ENST00000367635.3	+	8	920	c.582G>T	c.(580-582)aaG>aaT	p.K194N	RALGPS2_ENST00000367634.2_Missense_Mutation_p.K194N	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	194	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.K194N(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						GTAGCTTAAAGATGACACCTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											144	139	141					1																	178802660		2203	4292	6495	177069283	SO:0001583	missense	55103			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.582G>T	1.37:g.178802660G>T	ENSP00000356607:p.Lys194Asn		177069283	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	37	CCDS1325.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107667	0.56291	.	.	ENSG00000116191	ENST00000367635;ENST00000367634;ENST00000324778	T;T;T	0.29142	1.58;1.58;1.58	6.01	6.01	0.97437	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.077693	0.85682	D	0.000000	T	0.33527	0.0866	L	0.41236	1.265	0.51233	D	0.999919	P;P	0.45902	0.868;0.868	P;P	0.51453	0.67;0.67	T	0.01966	-1.1238	10	0.09338	T	0.73	.	13.3441	0.60561	0.0723:0.0:0.9277:0.0	.	194;194	B7Z7B1;Q86X27	.;RGPS2_HUMAN	N	194;194;159	ENSP00000356607:K194N;ENSP00000356606:K194N;ENSP00000313613:K159N	ENSP00000313613:K159N	K	+	3	2	RALGPS2	177069283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.251000	0.43187	2.861000	0.98227	0.650000	0.86243	AAG		0.303	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		T	178802660	G	T	178802660	3	4	61	1	0	0	0	0	1	0	0	0	13055	933	33	2	608	2	RALGPS2	1	178802660	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	874580	178802660	70447961	839	8824										
ANGPTL1	9068	broad.mit.edu	37	chr1	178834689	178834689	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgatcatgtctttaatggTacttgcatcttgccccttgg	10	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:178834689T>C	ENST00000234816.2	-	3	670	c.223A>G	c.(223-225)Acc>Gcc	p.T75A	RALGPS2_ENST00000367634.2_Intron|RALGPS2_ENST00000367635.3_Intron|ANGPTL1_ENST00000367629.1_Missense_Mutation_p.T75A	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	75					transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)	p.T75A(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						TCTTTAATGGTACTTGCATCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											302	223	250					1																	178834689		2203	4300	6503	177101312	SO:0001583	missense	9068			AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"Fibrinogen C domain containing"	489	protein-coding gene	gene with protein product	"angioarrestin"	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.223A>G	1.37:g.178834689T>C	ENSP00000234816:p.Thr75Ala		177101312	Q5T5Z5	Missense_Mutation	SNP	ENST00000234816.2	37	CCDS1327.1	.	.	.	.	.	.	.	.	.	.	T	4.032	0.003399	0.07866	.	.	ENSG00000116194	ENST00000234816;ENST00000367629;ENST00000415564;ENST00000444255	T;T	0.53640	0.61;0.61	5.52	1.85	0.25348	.	0.467342	0.25668	N	0.029092	T	0.27098	0.0664	N	0.19112	0.55	0.21782	N	0.999544	B	0.06786	0.001	B	0.12156	0.007	T	0.20140	-1.0284	10	0.15066	T	0.55	.	8.2488	0.31704	0.0:0.2287:0.0:0.7713	.	75	O95841	ANGL1_HUMAN	A	75;75;39;75	ENSP00000234816:T75A;ENSP00000356601:T75A	ENSP00000234816:T75A	T	-	1	0	ANGPTL1	177101312	0.978000	0.34361	0.612000	0.29024	0.975000	0.68041	0.670000	0.25157	0.068000	0.16574	0.454000	0.30748	ACC		0.463	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673		C	178834689	T	C	178834689	3	2	61	1	0	0	0	0	1	0	0	0	613	1638	57	4	1268	4	ANGPTL1	1	178834689	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32029	178834689	70415932	840	8825										
TOR3A	64222	broad.mit.edu	37	chr1	179064252	179064252	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaagaagagacactggatGaaatagcccagatgatggtg	12	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179064252G>T	ENST00000367627.3	+	6	1845	c.1093G>T	c.(1093-1095)Gaa>Taa	p.E365*	TOR3A_ENST00000352445.6_Intron	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	365					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E365*(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						GACACTGGATGAAATAGCCCA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											174	167	169					1																	179064252		2203	4300	6503	177330875	SO:0001587	stop_gained	64222			BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"ATP-dependant interferon responsive"	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.1093G>T	1.37:g.179064252G>T	ENSP00000356599:p.Glu365*		177330875	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Nonsense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	G	39	7.699119	0.98441	.	.	ENSG00000186283	ENST00000367627	.	.	.	5.91	2.46	0.29980	.	0.332562	0.34906	N	0.003596	.	.	.	.	.	.	0.42059	D	0.991151	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-2.4396	3.6602	0.08236	0.1632:0.2447:0.4762:0.1159	.	.	.	.	X	365	.	ENSP00000356599:E365X	E	+	1	0	TOR3A	177330875	1.000000	0.71417	0.028000	0.17463	0.222000	0.24845	3.666000	0.54540	0.757000	0.33036	0.655000	0.94253	GAA		0.507	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371		T	179064252	G	T	179064252	4	4	61	1	0	0	0	0	0	1	0	0	16416	1291	45	2	1115	2	TOR3A	1	179064252	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229563	179064252	70186369	841	8826										
ABL2	27	broad.mit.edu	37	chr1	179087822	179087822	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctcttctcggttgcattCtcggaggtaatccagcaaat	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179087822C>A	ENST00000502732.1	-	7	1326	c.1123G>T	c.(1123-1125)Gaa>Taa	p.E375*	ABL2_ENST00000367623.4_Nonsense_Mutation_p.E354*|ABL2_ENST00000512653.1_Nonsense_Mutation_p.E360*|ABL2_ENST00000392043.3_Nonsense_Mutation_p.E354*|ABL2_ENST00000511413.1_Nonsense_Mutation_p.E375*|ABL2_ENST00000344730.3_Nonsense_Mutation_p.E360*|ABL2_ENST00000408940.3_Nonsense_Mutation_p.E339*|ABL2_ENST00000504405.1_Nonsense_Mutation_p.E339*|ABL2_ENST00000507173.1_Nonsense_Mutation_p.E354*	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)	p.E339*(1)		breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	CGGTTGCATTCTCGGAGGTAA	0.428			T	ETV6	AML																																		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	1	Substitution - Nonsense(1)	large_intestine(1)	1											182	157	165					1																	179087822		2203	4300	6503	177354445	SO:0001587	stop_gained	27			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1123G>T	1.37:g.179087822C>A	ENSP00000427562:p.Glu375*		177354445	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Nonsense_Mutation	SNP	ENST00000502732.1	37	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	C	37	6.009085	0.97195	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413;ENST00000392043	.	.	.	4.92	4.92	0.64577	.	0.000000	0.53938	D	0.000059	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.4674	0.87637	0.0:1.0:0.0:0.0	.	.	.	.	X	375;339;360;360;339;354;354;375;354	.	ENSP00000339209:E360X	E	-	1	0	ABL2	177354445	1.000000	0.71417	0.956000	0.39512	0.994000	0.84299	7.776000	0.85560	2.434000	0.82447	0.655000	0.94253	GAA		0.428	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		A	179087822	C	A	179087822	4	1	61	1	0	0	0	0	0	1	0	0	93	922	32	2	2494	2	ABL2	1	179087822	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23570	179087822	70162799	842	8827										
C1orf125	126859	broad.mit.edu	37	chr1	179460808	179460808	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatgatataggagttgcgCgattggagctagatgcgatt	13	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179460808C>T	ENST00000367618.3	+	19	2614	c.2227C>T	c.(2227-2229)Cga>Tga	p.R743*		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	743								p.R743*(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AGGAGTTGCGCGATTGGAGCT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											168	162	164					1																	179460808		2203	4300	6503	177727431	SO:0001587	stop_gained	126859			BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2227C>T	1.37:g.179460808C>T	ENSP00000356590:p.Arg743*		177727431	Q6AWB2|Q96LJ3|Q96M01	Nonsense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888720	0.91814	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	.	.	.	5.5	-2.1	0.07210	.	1.326530	0.05005	N	0.469855	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-4.0432	7.941	0.29959	0.2199:0.5028:0.2773:0.0	.	.	.	.	X	743;701;677	.	ENSP00000353471:R701X	R	+	1	2	AXDND1	177727431	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	-0.030000	0.12308	-0.660000	0.05352	0.591000	0.81541	CGA		0.413	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		T	179460808	C	T	179460808	4	4	61	1	0	0	0	0	0	1	0	0	1999	760	27	1	2297	1	C1orf125	1	179460808	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	372986	179460808	69789813	843	8828										
C1orf125	126859	broad.mit.edu	37	chr1	179503004	179503004	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaattgaacatatgcaggaGaagttactgtaagtatgagt	11	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179503004G>T	ENST00000367618.3	+	24	3177	c.2790G>T	c.(2788-2790)gaG>gaT	p.E930D		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	930	Glu-rich.							p.E930D(2)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						ATATGCAGGAGAAGTTACTGT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	1											136	125	129					1																	179503004		2203	4300	6503	177769627	SO:0001583	missense	126859			BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2790G>T	1.37:g.179503004G>T	ENSP00000356590:p.Glu930Asp		177769627	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	3.110	-0.182758	0.06340	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.26223	1.75;1.75	4.5	0.211	0.15236	.	0.687725	0.13486	N	0.384326	T	0.12944	0.0314	L	0.27053	0.805	0.38036	D	0.935301	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.20638	-1.0269	10	0.18276	T	0.48	-0.6102	3.1584	0.06512	0.0937:0.3066:0.4191:0.1806	.	814;930	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	D	930;814;790	ENSP00000356590:E930D;ENSP00000391716:E790D	ENSP00000353471:E814D	E	+	3	2	AXDND1	177769627	0.005000	0.15991	0.828000	0.32881	0.294000	0.27393	-0.121000	0.10643	-0.044000	0.13491	-0.976000	0.02587	GAG		0.403	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		T	179503004	G	T	179503004	3	4	61	1	0	0	0	0	1	0	0	0	1999	933	33	2	2880	2	C1orf125	1	179503004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42196	179503004	69747617	844	8829										
NPHS2	7827	broad.mit.edu	37	chr1	179526313	179526313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagaggcattttccattCggtagtagcaaatggcatct	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179526313C>T	ENST00000367615.4	-	5	655	c.587G>A	c.(586-588)cGa>cAa	p.R196Q	NPHS2_ENST00000367616.4_Intron	NM_014625.2	NP_055440.1	Q9NP85	PODO_HUMAN	nephrosis 2, idiopathic, steroid-resistant (podocin)	196					actin cytoskeleton reorganization (GO:0031532)|excretion (GO:0007588)|metanephric glomerular visceral epithelial cell development (GO:0072249)	cell-cell junction (GO:0005911)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)		p.R196Q(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	20						ATTTTCCATTCGGTAGTAGCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM021649	NPHS2	M							136	117	123					1																	179526313		2203	4300	6503	177792936	SO:0001583	missense	7827			AJ279254	CCDS1331.1, CCDS72988.1	1q25-q31	2014-06-27			ENSG00000116218	ENSG00000116218			13394	protein-coding gene	gene with protein product		604766				8589695, 10742096	Standard	XM_005245483		Approved	SRN1, PDCN	uc001gmq.4	Q9NP85	OTTHUMG00000035252	ENST00000367615.4:c.587G>A	1.37:g.179526313C>T	ENSP00000356587:p.Arg196Gln		177792936	B1AM32|B1AM33|Q8N6Q5	Missense_Mutation	SNP	ENST00000367615.4	37	CCDS1331.1	.	.	.	.	.	.	.	.	.	.	C	34	5.398396	0.96030	.	.	ENSG00000116218	ENST00000367615	D	0.95377	-3.69	5.78	5.78	0.91487	.	0.069580	0.64402	D	0.000018	D	0.96030	0.8707	L	0.55481	1.735	0.80722	D	1	P	0.47191	0.891	P	0.51945	0.685	D	0.96157	0.9112	10	0.72032	D	0.01	-10.1255	18.5762	0.91155	0.0:1.0:0.0:0.0	.	196	Q9NP85	PODO_HUMAN	Q	196	ENSP00000356587:R196Q	ENSP00000356587:R196Q	R	-	2	0	NPHS2	177792936	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.507000	0.60434	2.749000	0.94314	0.655000	0.94253	CGA		0.428	NPHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085283.1			T	179526313	C	T	179526313	3	4	61	1	0	0	0	0	1	0	0	0	10614	884	31	1	580	1	NPHS2	1	179526313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23309	179526313	69724308	845	8830										
TDRD5	163589	broad.mit.edu	37	chr1	179621199	179621199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgagctcaaccctttagCtttatacacgacatccagtg	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179621199C>T	ENST00000367614.1	+	13	2386	c.2027C>T	c.(2026-2028)gCt>gTt	p.A676V	TDRD5_ENST00000444136.1_Missense_Mutation_p.A676V|TDRD5_ENST00000294848.8_Missense_Mutation_p.A676V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	676					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)		p.A676V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AACCCTTTAGCTTTATACACG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	82	84					1																	179621199		2203	4300	6503	177887822	SO:0001583	missense	163589			AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2027C>T	1.37:g.179621199C>T	ENSP00000356586:p.Ala676Val		177887822	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833399	0.71258	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.38401	2.61;2.61;2.78;1.14	5.56	4.64	0.57946	.	0.692979	0.13632	N	0.373608	T	0.45796	0.1360	L	0.60455	1.87	0.33379	D	0.574579	D;P	0.53745	0.962;0.871	P;B	0.51170	0.661;0.376	T	0.56232	-0.8013	10	0.36615	T	0.2	-0.5054	12.9089	0.58169	0.1626:0.8374:0.0:0.0	.	676;676	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	676;676;676;132	ENSP00000356586:A676V;ENSP00000294848:A676V;ENSP00000406052:A676V;ENSP00000410744:A132V	ENSP00000294848:A676V	A	+	2	0	TDRD5	177887822	0.996000	0.38824	1.000000	0.80357	0.969000	0.65631	0.759000	0.26461	1.334000	0.45468	0.650000	0.86243	GCT		0.403	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179621199	C	T	179621199	3	4	61	1	0	0	0	0	1	0	0	0	15772	797	28	3	2073	3	TDRD5	1	179621199	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94886	179621199	69629422	846	8831										
FAM163A	148753	broad.mit.edu	37	chr1	179783254	179783254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggcagcaccccagagttAcccggtgacctggccaggct	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179783254A>G	ENST00000341785.4	+	5	830	c.434A>G	c.(433-435)tAc>tGc	p.Y145C	RP11-12M5.3_ENST00000453051.1_RNA|RP11-12M5.3_ENST00000415218.1_RNA	NM_173509.2	NP_775780.1	Q96GL9	F163A_HUMAN	family with sequence similarity 163, member A	145						integral component of membrane (GO:0016021)		p.Y145C(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)	15						CCCCAGAGTTACCCGGTGACC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											63	72	69					1																	179783254		2203	4300	6503	178049877	SO:0001583	missense	148753			BC009382	CCDS1333.1	1q25.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000143340	ENSG00000143340			28274	protein-coding gene	gene with protein product		611727	"chromosome 1 open reading frame 76"	C1orf76		12477932	Standard	NM_173509		Approved	MGC16664	uc001gnj.3	Q96GL9	OTTHUMG00000035262	ENST00000341785.4:c.434A>G	1.37:g.179783254A>G	ENSP00000354891:p.Tyr145Cys		178049877	A8K8R7	Missense_Mutation	SNP	ENST00000341785.4	37	CCDS1333.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.033565	0.35893	.	.	ENSG00000143340	ENST00000341785	.	.	.	4.67	2.1	0.27182	.	0.301825	0.31897	N	0.006898	T	0.41627	0.1167	L	0.36672	1.1	0.28529	N	0.91266	D	0.61697	0.99	P	0.53313	0.723	T	0.32481	-0.9905	9	0.59425	D	0.04	-19.0441	10.0085	0.41972	0.6514:0.0:0.0:0.3486	.	145	Q96GL9	F163A_HUMAN	C	145	.	ENSP00000354891:Y145C	Y	+	2	0	FAM163A	178049877	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	2.556000	0.45862	0.729000	0.32403	-0.490000	0.04691	TAC		0.597	FAM163A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085300.1	NM_173509		G	179783254	A	G	179783254	3	3	61	1	0	0	0	0	1	0	0	0	5492	391	14	4	440	4	FAM163A	1	179783254	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	162055	179783254	69467367	847	8832										
CEP350	9857	broad.mit.edu	37	chr1	179966252	179966252	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggttgttaatgttgataaCtcagtaacagcaaaagtcag	9	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:179966252C>T	ENST00000367607.3	+	6	1378	c.960C>T	c.(958-960)aaC>aaT	p.N320N		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	320					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.N320N(2)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						ATGTTGATAACTCAGTAACAG	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	1											120	131	128					1																	179966252		2203	4300	6503	178232875	SO:0001819	synonymous_variant	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.960C>T	1.37:g.179966252C>T			178232875	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1																																																																																				0.428	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	179966252	C	T	179966252	2	4	61	1	0	0	0	0	0	0	0	1	3260	564	20	3		3	CEP350	1	179966252	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	182998	179966252	69284369	848	8833										
CEP350	9857	broad.mit.edu	37	chr1	180061964	180061964	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgccactagtagaattCttgatatgtcagatggcaag	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180061964C>T	ENST00000367607.3	+	34	7142	c.6724C>T	c.(6724-6726)Ctt>Ttt	p.L2242F	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2242					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L2242F(2)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TAGTAGAATTCTTGATATGTC	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	1											17	17	17					1																	180061964		2195	4291	6486	178328587	SO:0001583	missense	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.6724C>T	1.37:g.180061964C>T	ENSP00000356579:p.Leu2242Phe		178328587	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.009|0.009	-1.858811|-1.858811	0.00558|0.00558	.|.	.|.	ENSG00000135837|ENSG00000135837	ENST00000367607|ENST00000429851	T|.	0.57107|.	0.42|.	5.73|5.73	2.7|2.7	0.31948|0.31948	.|.	0.597834|.	0.13812|.	N|.	0.361049|.	T|T	0.25901|0.25901	0.0631|0.0631	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.18745|0.18745	-1.0327|-1.0327	9|5	.|.	.|.	.|.	.|.	6.7945|6.7945	0.23717|0.23717	0.0:0.6079:0.0:0.3921|0.0:0.6079:0.0:0.3921	.|.	2242;2242|.	E7EU22;Q5VT06|.	.;CE350_HUMAN|.	F|F	2242|416	ENSP00000356579:L2242F|.	.|.	L|S	+|+	1|2	0|0	CEP350|CEP350	178328587|178328587	0.000000|0.000000	0.05858|0.05858	0.528000|0.528000	0.27938|0.27938	0.047000|0.047000	0.14425|0.14425	0.126000|0.126000	0.15769|0.15769	0.905000|0.905000	0.36596|0.36596	0.655000|0.655000	0.94253|0.94253	CTT|TCT		0.323	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180061964	C	T	180061964	3	4	61	1	0	0	0	0	1	0	0	0	3260	913	32	3	6854	3	CEP350	1	180061964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95712	180061964	69188657	849	8834										
CEP350	9857	broad.mit.edu	37	chr1	180080232	180080232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggatctttgagaccctgaTcaaagatactattgatgttc	9	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180080232T>C	ENST00000367607.3	+	38	9708	c.9290T>C	c.(9289-9291)aTc>aCc	p.I3097T	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	3097					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.I3097T(2)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GAGACCCTGATCAAAGATACT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	1											121	103	109					1																	180080232		2203	4300	6503	178346855	SO:0001583	missense	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.9290T>C	1.37:g.180080232T>C	ENSP00000356579:p.Ile3097Thr		178346855	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979070	0.74360	.	.	ENSG00000135837	ENST00000367607;ENST00000417046	T	0.62105	0.05	6.05	6.05	0.98169	.	0.000000	0.49916	D	0.000131	T	0.78253	0.4254	M	0.72118	2.19	0.53005	D	0.999967	D;D	0.65815	0.993;0.995	D;D	0.72338	0.977;0.975	T	0.78056	-0.2353	9	.	.	.	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	3097;3097	E7EU22;Q5VT06	.;CE350_HUMAN	T	3097;561	ENSP00000356579:I3097T	.	I	+	2	0	CEP350	178346855	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.970000	0.70431	2.320000	0.78422	0.528000	0.53228	ATC		0.453	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180080232	T	C	180080232	3	2	61	1	0	0	0	0	1	0	0	0	3260	1435	50	4	9436	4	CEP350	1	180080232	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18268	180080232	69170389	850	8835										
LHX4	89884	broad.mit.edu	37	chr1	180243490	180243490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccccagtctccatcctccAtatcgtccctgccatcccac	3	22	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180243490A>G	ENST00000263726.2	+	6	1193	c.949A>G	c.(949-951)Ata>Gta	p.I317V	RP5-1180C10.2_ENST00000415414.1_RNA|RP5-1180C10.2_ENST00000440959.2_RNA	NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	317					medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.I317V(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						TCCATCCTCCATATCGTCCCT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											190	166	174					1																	180243490		2203	4300	6503	178510113	SO:0001583	missense	89884			AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"Homeoboxes / LIM class"	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	ENST00000263726.2:c.949A>G	1.37:g.180243490A>G	ENSP00000263726:p.Ile317Val		178510113	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Missense_Mutation	SNP	ENST00000263726.2	37	CCDS1338.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568749	0.28003	.	.	ENSG00000121454	ENST00000263726	D	0.87729	-2.29	5.68	4.35	0.52113	.	0.049202	0.85682	D	0.000000	D	0.82508	0.5052	L	0.51422	1.61	0.50632	D	0.999888	B	0.18968	0.032	B	0.20184	0.028	T	0.78247	-0.2278	10	0.32370	T	0.25	.	11.2789	0.49181	0.9148:0.0:0.0852:0.0	.	317	Q969G2	LHX4_HUMAN	V	317	ENSP00000263726:I317V	ENSP00000263726:I317V	I	+	1	0	LHX4	178510113	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.262000	0.43285	2.151000	0.67156	0.533000	0.62120	ATA		0.542	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343		G	180243490	A	G	180243490	3	3	61	1	0	0	0	0	1	0	0	0	8796	217	8	4	971	4	LHX4	1	180243490	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	163258	180243490	69007131	851	8836										
XPR1	9213	broad.mit.edu	37	chr1	180780600	180780600	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtggaatattcattgtaCtgaatattacccttgtgctt	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180780600C>A	ENST00000367590.4	+	7	937	c.739C>A	c.(739-741)Ctg>Atg	p.L247M	XPR1_ENST00000367589.3_Missense_Mutation_p.L247M	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	247					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.L247M(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						ATTCATTGTACTGAATATTAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											162	144	150					1																	180780600		2203	4300	6503	179047223	SO:0001583	missense	9213			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.739C>A	1.37:g.180780600C>A	ENSP00000356562:p.Leu247Met		179047223	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496506	0.64186	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.55930	0.49	5.4	2.42	0.29668	.	0.000000	0.85682	D	0.000000	T	0.63721	0.2535	M	0.78285	2.405	0.80722	D	1	P;P	0.51449	0.945;0.632	P;B	0.57152	0.814;0.41	T	0.61997	-0.6947	10	0.54805	T	0.06	-6.6507	8.0584	0.30619	0.0:0.6615:0.0:0.3385	.	247;247	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	M	247	ENSP00000356562:L247M	ENSP00000356561:L247M	L	+	1	2	XPR1	179047223	0.981000	0.34729	0.997000	0.53966	0.953000	0.61014	0.644000	0.24766	0.289000	0.22422	-0.150000	0.13652	CTG		0.368	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		A	180780600	C	A	180780600	3	1	61	1	0	0	0	0	1	0	0	0	17491	564	20	2	765	2	XPR1	1	180780600	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	537110	180780600	68470021	852	8837										
XPR1	9213	broad.mit.edu	37	chr1	180794048	180794048	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctttgaacttaatccgaGaagcaatttgtctcatcaac	5	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180794048G>T	ENST00000367590.4	+	8	1121	c.923G>T	c.(922-924)aGa>aTa	p.R308I	XPR1_ENST00000367589.3_Missense_Mutation_p.R308I|AL590085.1_ENST00000579998.1_RNA	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	308					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.R308I(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CTTAATCCGAGAAGCAATTTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	121	124					1																	180794048		2203	4300	6503	179060671	SO:0001583	missense	9213			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.923G>T	1.37:g.180794048G>T	ENSP00000356562:p.Arg308Ile		179060671	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.954902	0.92726	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T;T	0.46451	0.87;0.87	5.65	5.65	0.86999	EXS, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72112	0.3420	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77186	-0.2680	10	0.87932	D	0	-10.6426	19.315	0.94208	0.0:0.0:1.0:0.0	.	308;308	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	I	308	ENSP00000356562:R308I;ENSP00000356561:R308I	ENSP00000356561:R308I	R	+	2	0	XPR1	179060671	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	9.283000	0.95860	2.665000	0.90641	0.650000	0.86243	AGA		0.383	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		T	180794048	G	T	180794048	3	4	61	1	0	0	0	0	1	0	0	0	17491	942	33	2	953	2	XPR1	1	180794048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13448	180794048	68456573	853	8838										
XPR1	9213	broad.mit.edu	37	chr1	180832953	180832953	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatggactggggtctcttCgataagaatgctggagagaa	14	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180832953C>T	ENST00000367590.4	+	12	1809	c.1611C>T	c.(1609-1611)ttC>ttT	p.F537F	XPR1_ENST00000367589.3_Silent_p.F472F	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	537	EXS. {ECO:0000255|PROSITE- ProRule:PRU00712}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.F537F(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						GGGGTCTCTTCGATAAGAATG	0.408																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	1											142	139	140					1																	180832953		2203	4300	6503	179099576	SO:0001819	synonymous_variant	9213			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1611C>T	1.37:g.180832953C>T			179099576	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																				0.408	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		T	180832953	C	T	180832953	2	4	61	1	0	0	0	0	0	0	0	1	17491	883	31	1		1	XPR1	1	180832953	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38905	180832953	68417668	854	8839										
XPR1	9213	broad.mit.edu	37	chr1	180849378	180849378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgaaaccgccagaagaatCggtcatggaagtacaaccag	10	10	1	2	rs200954931		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:180849378C>T	ENST00000367590.4	+	14	2173	c.1975C>T	c.(1975-1977)Cgg>Tgg	p.R659W	XPR1_ENST00000367589.3_Missense_Mutation_p.R594W	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	659					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.R659W(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CCAGAAGAATCGGTCATGGAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											158	149	152					1																	180849378		2203	4300	6503	179116001	SO:0001583	missense	9213			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1975C>T	1.37:g.180849378C>T	ENSP00000356562:p.Arg659Trp		179116001	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132725	0.77662	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.48522	0.81	5.86	4.89	0.63831	.	0.106321	0.64402	D	0.000002	T	0.54415	0.1857	L	0.36672	1.1	0.24507	N	0.994223	D;D	0.69078	0.997;0.99	P;P	0.61132	0.877;0.884	T	0.49485	-0.8935	10	0.72032	D	0.01	-14.8572	13.559	0.61777	0.2558:0.7442:0.0:0.0	.	594;659	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	W	659;594	ENSP00000356562:R659W	ENSP00000356561:R594W	R	+	1	2	XPR1	179116001	1.000000	0.71417	0.995000	0.50966	0.876000	0.50452	3.635000	0.54309	2.777000	0.95525	0.591000	0.81541	CGG		0.522	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		T	180849378	C	T	180849378	3	4	61	1	0	0	0	0	1	0	0	0	17491	875	31	1	2029	1	XPR1	1	180849378	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16425	180849378	68401243	855	8840										
MR1	3140	broad.mit.edu	37	chr1	181021489	181021489	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatggatgaaaaacggggaAgaaattgtccaagaaattga	11	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181021489A>C	ENST00000367580.5	+	4	728	c.723A>C	c.(721-723)gaA>gaC	p.E241D	MR1_ENST00000438435.2_Intron|MR1_ENST00000282990.6_Intron|MR1_ENST00000434571.2_Intron|MR1_ENST00000367579.3_Missense_Mutation_p.E196D	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	241	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)	p.E241D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	AAAACGGGGAAGAAATTGTCC	0.448																																					Colon(174;1412 1962 45296 46549 47110)											1	Substitution - Missense(1)	large_intestine(1)	1											65	67	67					1																	181021489		2203	4300	6503	179288112	SO:0001583	missense	3140			AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.723A>C	1.37:g.181021489A>C	ENSP00000356552:p.Glu241Asp		179288112	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	37	CCDS1342.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.224228	0.58668	.	.	ENSG00000153029	ENST00000367580;ENST00000367579	T;T	0.03152	4.03;4.03	4.19	4.19	0.49359	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.233360	0.30528	N	0.009425	T	0.17109	0.0411	M	0.80422	2.495	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.79108	0.986;0.992	T	0.00305	-1.1831	10	0.87932	D	0	.	11.2783	0.49180	1.0:0.0:0.0:0.0	.	196;241	Q95460-2;Q95460	.;HMR1_HUMAN	D	241;196	ENSP00000356552:E241D;ENSP00000356551:E196D	ENSP00000356551:E196D	E	+	3	2	MR1	179288112	0.998000	0.40836	0.999000	0.59377	0.803000	0.45373	2.478000	0.45189	1.763000	0.52060	0.533000	0.62120	GAA		0.448	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531		C	181021489	A	C	181021489	3	2	61	1	0	0	0	0	1	0	0	0	9782	69	3	4	737	4	MR1	1	181021489	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	172111	181021489	68229132	856	8841										
CACNA1E	777	broad.mit.edu	37	chr1	181453006	181453006	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggccgcctacaagcagacGaaagcacagagggcgcggac	15	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181453006G>A	ENST00000367573.2	+	1	126	c.126G>A	c.(124-126)acG>acA	p.T42T	CACNA1E_ENST00000367570.1_Silent_p.T42T|CACNA1E_ENST00000360108.3_Silent_p.T42T|CACNA1E_ENST00000526775.1_Silent_p.T42T|CACNA1E_ENST00000358338.5_5'UTR|CACNA1E_ENST00000357570.5_5'UTR|CACNA1E_ENST00000367567.4_5'UTR	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	42					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.T42T(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ACAAGCAGACGAAAGCACAGA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	1											64	72	69					1																	181453006		1892	4097	5989	179719629	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.126G>A	1.37:g.181453006G>A			179719629	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.622	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181453006	G	A	181453006	2	1	61	1	0	0	0	0	0	0	0	1	2548	1045	37	1		1	CACNA1E	1	181453006	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	431517	181453006	67797615	857	8842										
CACNA1E	777	broad.mit.edu	37	chr1	181453096	181453096	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagatccctgttcatcttCggagaagataacattgtcag	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181453096C>T	ENST00000367573.2	+	1	216	c.216C>T	c.(214-216)ttC>ttT	p.F72F	CACNA1E_ENST00000367570.1_Silent_p.F72F|CACNA1E_ENST00000360108.3_Silent_p.F72F|CACNA1E_ENST00000526775.1_Silent_p.F72F|CACNA1E_ENST00000358338.5_Silent_p.F23F|CACNA1E_ENST00000357570.5_Silent_p.F23F|CACNA1E_ENST00000367567.4_5'UTR	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	72					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.F72F(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGTTCATCTTCGGAGAAGATA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1											169	173	172					1																	181453096		1913	4133	6046	179719719	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.216C>T	1.37:g.181453096C>T			179719719	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.498	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181453096	C	T	181453096	2	4	61	1	0	0	0	0	0	0	0	1	2548	883	31	1		1	CACNA1E	1	181453096	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90	181453096	67797525	858	8843										
CACNA1E	777	broad.mit.edu	37	chr1	181724430	181724430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcaacatactcattgtgTacaagctcttcatgttcatc	4	11	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181724430T>C	ENST00000367573.2	+	28	3886	c.3886T>C	c.(3886-3888)Tac>Cac	p.Y1296H	CACNA1E_ENST00000367570.1_Missense_Mutation_p.Y1296H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.Y1277H|CACNA1E_ENST00000526775.1_Missense_Mutation_p.Y1277H|CACNA1E_ENST00000358338.5_Missense_Mutation_p.Y1228H|CACNA1E_ENST00000357570.5_Missense_Mutation_p.Y1247H|CACNA1E_ENST00000367567.4_Missense_Mutation_p.Y903H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1296					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.Y1296H(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ACTCATTGTGTACAAGCTCTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											221	208	212					1																	181724430		2028	4210	6238	179991053	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3886T>C	1.37:g.181724430T>C	ENSP00000356545:p.Tyr1296His		179991053	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686920	0.88639	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02	5.29	5.29	0.74685	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99026	0.9667	M	0.88906	2.99	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.83275	0.969;0.995;0.996	D	0.99679	1.0998	10	0.87932	D	0	.	14.8849	0.70560	0.0:0.0:0.0:1.0	.	1277;1296;1296	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	H	1296;1277;1247;1228;903;1277;1296	ENSP00000356542:Y1296H;ENSP00000434814:Y1277H;ENSP00000350183:Y1247H;ENSP00000351101:Y1228H;ENSP00000356539:Y903H;ENSP00000353222:Y1277H;ENSP00000356545:Y1296H	ENSP00000350183:Y1247H	Y	+	1	0	CACNA1E	179991053	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.894000	0.87336	1.998000	0.58463	0.528000	0.53228	TAC		0.478	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181724430	T	C	181724430	3	2	61	1	0	0	0	0	1	0	0	0	2548	1638	57	4	3996	4	CACNA1E	1	181724430	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	271334	181724430	67526191	859	8844										
CACNA1E	777	broad.mit.edu	37	chr1	181754849	181754849	+	Splice_Site	DEL	A	A	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttccctctttttacccagAaaaatgcccccatgttccag							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181754849delA	ENST00000367573.2	+	43	5680	c.5680delA	c.(5680-5682)aaa>aa	p.K1894fs	CACNA1E_ENST00000367570.1_Splice_Site_p.K1894fs|CACNA1E_ENST00000360108.3_Splice_Site_p.K1875fs|CACNA1E_ENST00000526775.1_Splice_Site_p.K1875fs|CACNA1E_ENST00000358338.5_Splice_Site_p.K1826fs|CACNA1E_ENST00000357570.5_Splice_Site_p.K1845fs|CACNA1E_ENST00000367567.4_Splice_Site_p.K1501fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1894					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.N1895fs*35(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TTTTACCCAGAAAAATGCCCC	0.458																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											136	135	135					1																	181754849		1876	4101	5977	180021472	SO:0001630	splice_region_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5680-1A>-	1.37:g.181754849delA			180021472	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	37	CCDS55664.1																																																																																				0.458	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Frame_Shift_Del	-	181754849	A	-	181754849	8	5	61	1	0	1	0	1	0	0	1	0	2548	260	9	0	5850	0	CACNA1E	1	181754849	Splice_Site	DEL	A	TCGA-AG-A002-01A-01W-A00K-09	30419	181754849	67495772	860	8845										
CACNA1E	777	broad.mit.edu	37	chr1	181759605	181759605	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccggagtggatacccttcGatgagtccactctctcccca	10	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:181759605G>T	ENST00000367573.2	+	44	5811	c.5811G>T	c.(5809-5811)tcG>tcT	p.S1937S	CACNA1E_ENST00000367570.1_Silent_p.S1937S|CACNA1E_ENST00000360108.3_Silent_p.S1918S|CACNA1E_ENST00000526775.1_Silent_p.S1918S|CACNA1E_ENST00000358338.5_Silent_p.S1869S|CACNA1E_ENST00000357570.5_Silent_p.S1888S|CACNA1E_ENST00000367567.4_Silent_p.S1544S	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1937					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.S1937S(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GATACCCTTCGATGAGTCCAC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	1											83	91	89					1																	181759605		1934	4123	6057	180026228	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5811G>T	1.37:g.181759605G>T			180026228	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.532	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181759605	G	T	181759605	2	4	61	1	0	0	0	0	0	0	0	1	2548	1045	37	2		2	CACNA1E	1	181759605	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4756	181759605	67491016	861	8846										
NPL	80896	broad.mit.edu	37	chr1	182775327	182775327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgagcgtctcagagcgtCgccaggttgcagaggagtgg	16	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:182775327C>T	ENST00000367553.1	+	4	234	c.190C>T	c.(190-192)Cgc>Tgc	p.R64C	NPL_ENST00000367554.3_5'UTR|NPL_ENST00000367550.2_Missense_Mutation_p.R64C|NPL_ENST00000258317.2_Missense_Mutation_p.R64C|NPL_ENST00000367552.2_Missense_Mutation_p.R64C|NPL_ENST00000463899.1_3'UTR|NPL_ENST00000367555.1_Missense_Mutation_p.R64C	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	64					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)	p.R64C(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						CTCAGAGCGTCGCCAGGTTGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	116	116					1																	182775327		2203	4300	6503	181041950	SO:0001583	missense	80896			AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 1 (E. coli)"	611412	"chromosome 1 open reading frame 13"	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.190C>T	1.37:g.182775327C>T	ENSP00000356524:p.Arg64Cys		181041950	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Missense_Mutation	SNP	ENST00000367553.1	37	CCDS1350.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431700	0.43122	.	.	ENSG00000135838	ENST00000367555;ENST00000367553;ENST00000367552;ENST00000258317;ENST00000367550	D;D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63;-3.63	5.26	3.35	0.38373	Aldolase-type TIM barrel (1);	0.298563	0.34906	N	0.003586	D	0.88768	0.6526	L	0.38175	1.15	0.40845	D	0.983702	B;B;B	0.17268	0.021;0.003;0.007	B;B;B	0.12156	0.004;0.001;0.007	T	0.81816	-0.0759	10	0.48119	T	0.1	-10.0271	4.6888	0.12771	0.1706:0.6414:0.0:0.188	.	64;64;64	Q9BXD5-4;Q9BXD5;Q9BXD5-3	.;NPL_HUMAN;.	C	64	ENSP00000356526:R64C;ENSP00000356524:R64C;ENSP00000356523:R64C;ENSP00000258317:R64C;ENSP00000356521:R64C	ENSP00000258317:R64C	R	+	1	0	NPL	181041950	1.000000	0.71417	0.717000	0.30585	0.907000	0.53573	1.694000	0.37752	0.576000	0.29452	0.563000	0.77884	CGC		0.522	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		T	182775327	C	T	182775327	3	4	61	1	0	0	0	0	1	0	0	0	10616	884	31	1	200	1	NPL	1	182775327	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1015722	182775327	66475294	862	8847										
DHX9	1660	broad.mit.edu	37	chr1	182841579	182841579	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatgttttgtgaatatttCttcaattgccccatcattga	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:182841579C>A	ENST00000367549.3	+	15	1775	c.1665C>A	c.(1663-1665)ttC>ttA	p.F555L		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	555	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)	p.F555L(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GTGAATATTTCTTCAATTGCC	0.398																																					Colon(69;210 1162 3697 13559 39565)											1	Substitution - Missense(1)	large_intestine(1)	1											221	188	198					1																	182841579		1854	4093	5947	181108202	SO:0001583	missense	1660			L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1665C>A	1.37:g.182841579C>A	ENSP00000356520:p.Phe555Leu		181108202	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.979006	0.92982	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.35605	1.3	6.08	6.08	0.98989	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.49847	0.1581	M	0.71920	2.185	0.80722	D	1	P	0.43662	0.814	P	0.45794	0.493	T	0.48547	-0.9026	10	0.59425	D	0.04	.	20.2825	0.98528	0.0:1.0:0.0:0.0	.	555	Q08211	DHX9_HUMAN	L	555	ENSP00000356520:F555L	ENSP00000356520:F555L	F	+	3	2	DHX9	181108202	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.439000	0.52878	2.894000	0.99253	0.591000	0.81541	TTC		0.398	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182841579	C	A	182841579	3	1	61	1	0	0	0	0	1	0	0	0	4527	912	32	2	1719	2	DHX9	1	182841579	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66252	182841579	66409042	863	8848										
C1orf14	81626	broad.mit.edu	37	chr1	182908441	182908441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctgatactcaatgagctCgacacgtttgtttttatatt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:182908441C>T	ENST00000367547.3	-	5	1182	c.946G>A	c.(946-948)Gag>Aag	p.E316K	SHCBP1L_ENST00000423786.1_Missense_Mutation_p.E197K|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	388								p.E316K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TCAATGAGCTCGACACGTTTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	83	85					1																	182908441		2203	4300	6503	181175064	SO:0001583	missense	81626			AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.946G>A	1.37:g.182908441C>T	ENSP00000356518:p.Glu316Lys		181175064	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.150910	0.57151	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.45276	0.9;0.93	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000028	T	0.56819	0.2011	L	0.56769	1.78	0.41741	D	0.989612	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.972;0.994;0.988	T	0.51545	-0.8692	10	0.11485	T	0.65	-21.274	15.1536	0.72723	0.0:1.0:0.0:0.0	.	388;197;316	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	K	316;385;197	ENSP00000356518:E316K;ENSP00000397308:E197K	ENSP00000287709:E385K	E	-	1	0	SHCBP1L	181175064	0.997000	0.39634	0.917000	0.36280	0.696000	0.40369	4.591000	0.61019	2.311000	0.77944	0.563000	0.77884	GAG		0.373	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182908441	C	T	182908441	3	4	61	1	0	0	0	0	1	0	0	0	2006	893	31	1	1039	1	C1orf14	1	182908441	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66862	182908441	66342180	864	8849										
C1orf14	81626	broad.mit.edu	37	chr1	182909616	182909616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaatgttggaagaaaagggCtcagcaacagaaacagtaac	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:182909616C>T	ENST00000367547.3	-	3	854	c.618G>A	c.(616-618)gaG>gaA	p.E206E	SHCBP1L_ENST00000423786.1_Silent_p.E87E|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	278								p.E206E(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						AAGAAAAGGGCTCAGCAACAG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	1											72	71	71					1																	182909616		2203	4300	6503	181176239	SO:0001819	synonymous_variant	81626			AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.618G>A	1.37:g.182909616C>T			181176239	Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	37	CCDS30955.1																																																																																				0.368	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182909616	C	T	182909616	2	4	61	1	0	0	0	0	0	0	0	1	2006	796	28	3		3	C1orf14	1	182909616	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1175	182909616	66341005	865	8850										
LAMC1	3915	broad.mit.edu	37	chr1	183086019	183086019	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctacagtgtttattctatCtcctctacctttcagattgg	7	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183086019C>A	ENST00000258341.4	+	8	1802	c.1545C>A	c.(1543-1545)atC>atA	p.I515I		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	515	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.I515I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TTTATTCTATCTCCTCTACCT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	1											109	105	106					1																	183086019		2203	4300	6503	181352642	SO:0001819	synonymous_variant	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1545C>A	1.37:g.183086019C>A			181352642	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																				0.388	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183086019	C	A	183086019	2	1	61	1	0	0	0	0	0	0	0	1	8636	903	32	2		2	LAMC1	1	183086019	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	176403	183086019	66164602	866	8851										
LAMC1	3915	broad.mit.edu	37	chr1	183087279	183087279	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtgggacatacagtgagaGaagtaagttatgatataatt	11	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183087279G>T	ENST00000258341.4	+	11	2245	c.1988G>T	c.(1987-1989)aGa>aTa	p.R663I		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	663	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.R663I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TACAGTGAGAGAAGTAAGTTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											80	84	83					1																	183087279		2203	4300	6503	181353902	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1988G>T	1.37:g.183087279G>T	ENSP00000258341:p.Arg663Ile		181353902	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.369082	0.82463	.	.	ENSG00000135862	ENST00000258341	T	0.37058	1.22	5.0	5.0	0.66597	Laminin B type IV (2);Laminin B, subgroup (1);	0.050042	0.85682	D	0.000000	T	0.54191	0.1843	L	0.52364	1.645	0.80722	D	1	D	0.63880	0.993	D	0.67103	0.949	T	0.51647	-0.8679	10	0.41790	T	0.15	.	18.3307	0.90268	0.0:0.0:1.0:0.0	.	663	P11047	LAMC1_HUMAN	I	663	ENSP00000258341:R663I	ENSP00000258341:R663I	R	+	2	0	LAMC1	181353902	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.999000	0.49473	2.317000	0.78254	0.650000	0.86243	AGA		0.353	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183087279	G	T	183087279	3	4	61	1	0	0	0	0	1	0	0	0	8636	942	33	2	2030	2	LAMC1	1	183087279	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1260	183087279	66163342	867	8852										
LAMC1	3915	broad.mit.edu	37	chr1	183097840	183097840	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatagactaaaggaagcaGagagggaagttatggacctc	14	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183097840G>A	ENST00000258341.4	+	18	3492	c.3235G>A	c.(3235-3237)Gag>Aag	p.E1079K	LAMC1_ENST00000466964.1_3'UTR	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1079	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.E1079K(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AAAGGAAGCAGAGAGGGAAGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											141	117	125					1																	183097840		2203	4300	6503	181364463	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.3235G>A	1.37:g.183097840G>A	ENSP00000258341:p.Glu1079Lys		181364463	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420804	0.83559	.	.	ENSG00000135862	ENST00000258341	T	0.36699	1.24	5.81	4.88	0.63580	.	0.260859	0.42964	D	0.000622	T	0.40222	0.1108	M	0.63843	1.955	0.80722	D	1	B	0.24258	0.1	B	0.24541	0.054	T	0.31081	-0.9956	10	0.59425	D	0.04	.	16.7187	0.85404	0.0:0.1296:0.8704:0.0	.	1079	P11047	LAMC1_HUMAN	K	1079	ENSP00000258341:E1079K	ENSP00000258341:E1079K	E	+	1	0	LAMC1	181364463	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.193000	0.77780	1.425000	0.47237	0.655000	0.94253	GAG		0.468	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183097840	G	A	183097840	3	1	61	1	0	0	0	0	1	0	0	0	8636	943	33	3	3305	3	LAMC1	1	183097840	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10561	183097840	66152781	868	8853										
LAMC1	3915	broad.mit.edu	37	chr1	183101654	183101654	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcaaacagcatttgagaTtgaagagcttaataggaagt	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183101654T>G	ENST00000258341.4	+	21	3943	c.3686T>G	c.(3685-3687)aTt>aGt	p.I1229S		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1229	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.I1229S(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GCATTTGAGATTGAAGAGCTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	121	124					1																	183101654		2203	4300	6503	181368277	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.3686T>G	1.37:g.183101654T>G	ENSP00000258341:p.Ile1229Ser		181368277	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.393248	0.83011	.	.	ENSG00000135862	ENST00000258341	T	0.22134	1.97	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.44329	0.1288	M	0.73962	2.25	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.45891	-0.9230	10	0.87932	D	0	.	15.3599	0.74464	0.0:0.0:0.0:1.0	.	1229	P11047	LAMC1_HUMAN	S	1229	ENSP00000258341:I1229S	ENSP00000258341:I1229S	I	+	2	0	LAMC1	181368277	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.402000	0.79972	2.112000	0.64535	0.533000	0.62120	ATT		0.403	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		G	183101654	T	G	183101654	3	3	61	1	0	0	0	0	1	0	0	0	8636	1493	52	4	3768	4	LAMC1	1	183101654	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3814	183101654	66148967	869	8854										
LAMC1	3915	broad.mit.edu	37	chr1	183106903	183106903	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcaactgcaggaagcaGaaaaagagctaaagagaaaa	11	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183106903G>T	ENST00000258341.4	+	26	4671	c.4414G>T	c.(4414-4416)Gaa>Taa	p.E1472*	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1472	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.E1472*(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GCAGGAAGCAGAAAAAGAGCT	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											89	85	86					1																	183106903		2203	4300	6503	181373526	SO:0001587	stop_gained	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4414G>T	1.37:g.183106903G>T	ENSP00000258341:p.Glu1472*		181373526	Q5VYE7	Nonsense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	46	12.402667	0.99664	.	.	ENSG00000135862	ENST00000258341	.	.	.	5.64	5.64	0.86602	.	0.095731	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.7095	0.96089	0.0:0.0:1.0:0.0	.	.	.	.	X	1472	.	ENSP00000258341:E1472X	E	+	1	0	LAMC1	181373526	1.000000	0.71417	0.987000	0.45799	0.993000	0.82548	8.810000	0.91950	2.647000	0.89833	0.655000	0.94253	GAA		0.428	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183106903	G	T	183106903	4	4	61	1	0	0	0	0	0	1	0	0	8636	943	33	2	4516	2	LAMC1	1	183106903	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5249	183106903	66143718	870	8855										
LAMC2	3918	broad.mit.edu	37	chr1	183187559	183187559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtgacccagctggcatcGcagggccctgtgacgcgggc	15	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183187559G>A	ENST00000264144.4	+	4	504	c.439G>A	c.(439-441)Gca>Aca	p.A147T	LAMC2_ENST00000493293.1_Missense_Mutation_p.A147T	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	147	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.A147T(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCTGGCATCGCAGGGCCCTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											36	37	37					1																	183187559		2203	4300	6503	181454182	SO:0001583	missense	3918			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.439G>A	1.37:g.183187559G>A	ENSP00000264144:p.Ala147Thr		181454182	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	G	3.809	-0.040159	0.07497	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.61274	0.12;0.12	5.26	0.274	0.15654	EGF-like, laminin (3);Growth factor, receptor (1);	2.153060	0.02522	N	0.092689	T	0.26159	0.0638	N	0.02275	-0.615	0.09310	N	1	B;B	0.15719	0.004;0.014	B;B	0.06405	0.002;0.001	T	0.34551	-0.9824	10	0.02654	T	1	.	3.4714	0.07569	0.2549:0.0:0.2778:0.4673	.	147;147	Q13753;Q13753-2	LAMC2_HUMAN;.	T	147	ENSP00000432063:A147T;ENSP00000264144:A147T	ENSP00000264144:A147T	A	+	1	0	LAMC2	181454182	0.001000	0.12720	0.010000	0.14722	0.992000	0.81027	-0.271000	0.08572	-0.205000	0.10219	0.655000	0.94253	GCA		0.522	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183187559	G	A	183187559	3	1	61	1	0	0	0	0	1	0	0	0	8637	1087	38	1	453	1	LAMC2	1	183187559	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80656	183187559	66063062	871	8856										
LAMC2	3918	broad.mit.edu	37	chr1	183195871	183195871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgaccctgatttcagccCgccctgtctctggagcccca	9	16	2	2	rs552102778		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183195871C>T	ENST00000264144.4	+	9	1170	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	LAMC2_ENST00000493293.1_Missense_Mutation_p.R369C	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	369	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.R369C(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GATTTCAGCCCGCCCTGTCTC	0.498													C|||	1	0.000199681	8e-04	0	5008	,	,		20652	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											133	136	135					1																	183195871		2203	4300	6503	181462494	SO:0001583	missense	3918			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.1105C>T	1.37:g.183195871C>T	ENSP00000264144:p.Arg369Cys		181462494	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059345	0.76074	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.40476	1.03;1.03	5.39	5.39	0.77823	Laminin B type IV (2);Laminin B, subgroup (1);Growth factor, receptor (1);	0.082729	0.52532	D	0.000075	T	0.62011	0.2393	L	0.55213	1.73	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.988;0.982	T	0.62020	-0.6942	10	0.54805	T	0.06	.	19.1486	0.93479	0.0:1.0:0.0:0.0	.	369;369;369	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	C	369	ENSP00000432063:R369C;ENSP00000264144:R369C	ENSP00000264144:R369C	R	+	1	0	LAMC2	181462494	0.967000	0.33354	1.000000	0.80357	0.715000	0.41141	4.207000	0.58480	2.512000	0.84698	0.549000	0.68633	CGC		0.498	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		T	183195871	C	T	183195871	3	4	61	1	0	0	0	0	1	0	0	0	8637	652	23	1	1139	1	LAMC2	1	183195871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8312	183195871	66054750	872	8857										
LAMC2	3918	broad.mit.edu	37	chr1	183209467	183209467	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgataccagagccaagaAcgctggggttacaatccaag	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183209467A>G	ENST00000264144.4	+	22	3334	c.3269A>G	c.(3268-3270)aAc>aGc	p.N1090S	LAMC2_ENST00000461729.1_3'UTR|LAMC2_ENST00000493293.1_Missense_Mutation_p.N1090S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	1090	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.N1090S(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGAGCCAAGAACGCTGGGGTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	106	113					1																	183209467		2203	4300	6503	181476090	SO:0001583	missense	3918			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.3269A>G	1.37:g.183209467A>G	ENSP00000264144:p.Asn1090Ser		181476090	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	A	0.834	-0.744359	0.03065	.	.	ENSG00000058085	ENST00000493293;ENST00000264144	T;T	0.76709	2.52;-1.04	5.59	2.11	0.27256	.	0.557133	0.19288	N	0.117999	T	0.57888	0.2084	N	0.22421	0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.0;0.002	T	0.34900	-0.9810	10	0.10111	T	0.7	.	7.5436	0.27753	0.6654:0.0:0.3346:0.0	.	1090;1090;1090	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	S	1090	ENSP00000432063:N1090S;ENSP00000264144:N1090S	ENSP00000264144:N1090S	N	+	2	0	LAMC2	181476090	0.923000	0.31300	0.258000	0.24420	0.054000	0.15201	0.603000	0.24149	0.429000	0.26202	0.533000	0.62120	AAC		0.473	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		G	183209467	A	G	183209467	3	3	61	1	0	0	0	0	1	0	0	0	8637	43	2	4	3355	4	LAMC2	1	183209467	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13596	183209467	66041154	873	8858										
NMNAT2	23057	broad.mit.edu	37	chr1	183262892	183262892	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatcccgccaatcacaataAaccttccagttttgtgcaga	5	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183262892A>C	ENST00000287713.6	-	2	456	c.122T>G	c.(121-123)tTt>tGt	p.F41C	NMNAT2_ENST00000294868.4_Missense_Mutation_p.F36C	NM_015039.3	NP_055854.1	Q9BZQ4	NMNA2_HUMAN	nicotinamide nucleotide adenylyltransferase 2	41					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|late endosome (GO:0005770)|synapse (GO:0045202)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)	p.F41C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(7)|skin(2)	18						AATCACAATAAACCTTCCAGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											104	94	98					1																	183262892		2203	4300	6503	181529515	SO:0001583	missense	23057			AF288395	CCDS1353.1, CCDS1354.1	1q25	2008-02-05	2003-04-30	2003-05-02	ENSG00000157064	ENSG00000157064			16789	protein-coding gene	gene with protein product		608701	"chromosome 1 open reading frame 15"	C1orf15		11318611, 12359228	Standard	NM_015039		Approved	KIAA0479, PNAT2	uc001gqc.2	Q9BZQ4	OTTHUMG00000035519	ENST00000287713.6:c.122T>G	1.37:g.183262892A>C	ENSP00000287713:p.Phe41Cys		181529515	O75067|Q5T1Q3|Q8WU99|Q96QW1	Missense_Mutation	SNP	ENST00000287713.6	37	CCDS1353.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.545430	0.65198	.	.	ENSG00000157064	ENST00000287713;ENST00000294868	D;D	0.96685	-4.09;-4.09	5.9	5.9	0.94986	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.052992	0.85682	D	0.000000	D	0.96972	0.9011	L	0.43923	1.385	0.80722	D	1	B;D	0.76494	0.411;0.999	B;D	0.79108	0.096;0.992	D	0.97329	0.9949	10	0.54805	T	0.06	-17.5391	15.1562	0.72743	1.0:0.0:0.0:0.0	.	41;36	Q9BZQ4;Q9BZQ4-2	NMNA2_HUMAN;.	C	41;36	ENSP00000287713:F41C;ENSP00000294868:F36C	ENSP00000287713:F41C	F	-	2	0	NMNAT2	181529515	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.120000	0.89581	2.251000	0.74343	0.528000	0.53228	TTT		0.463	NMNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086255.1			C	183262892	A	C	183262892	3	2	61	1	0	0	0	0	1	0	0	0	10530	14	1	4	841	4	NMNAT2	1	183262892	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	53425	183262892	65987729	874	8859										
SMG7	9887	broad.mit.edu	37	chr1	183519916	183519916	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagccagccagtctcctcAttcctctaacccaagcagcc	5	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183519916A>G	ENST00000347615.2	+	20	3133	c.3014A>G	c.(3013-3015)cAt>cGt	p.H1005R	SMG7_ENST00000367537.3_Missense_Mutation_p.H1038R|SMG7_ENST00000515829.2_Missense_Mutation_p.H959R|SMG7_ENST00000508461.1_Missense_Mutation_p.H1013R|SMG7_ENST00000507469.1_Missense_Mutation_p.H1009R|SMG7_ENST00000456731.2_Missense_Mutation_p.H917R	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	1005	Ser-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.H1005R(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CAGTCTCCTCATTCCTCTAAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	118	120					1																	183519916		2203	4300	6503	181786539	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.3014A>G	1.37:g.183519916A>G	ENSP00000340766:p.His1005Arg		181786539	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390046	0.82902	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.33654	1.44;1.47;1.41;1.52;1.4;1.41	5.45	5.45	0.79879	.	0.098510	0.64402	D	0.000001	T	0.48241	0.1489	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D	0.63880	0.993;0.993;0.989;0.993;0.993	D;D;D;D;D	0.75020	0.977;0.977;0.985;0.977;0.977	T	0.44620	-0.9316	10	0.45353	T	0.12	-15.178	15.8223	0.78667	1.0:0.0:0.0:0.0	.	1013;917;959;1005;1009	E9PCI0;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;SMG7_HUMAN;.	R	917;1038;1013;1005;1009;959	ENSP00000407629:H917R;ENSP00000356507:H1038R;ENSP00000426915:H1013R;ENSP00000340766:H1005R;ENSP00000425133:H1009R;ENSP00000421358:H959R	ENSP00000340766:H1005R	H	+	2	0	SMG7	181786539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.451000	0.90343	2.188000	0.69820	0.528000	0.53228	CAT		0.423	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		G	183519916	A	G	183519916	3	3	61	1	0	0	0	0	1	0	0	0	14835	217	8	4	3246	4	SMG7	1	183519916	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	257024	183519916	65730705	875	8860										
APOBEC4	403314	broad.mit.edu	37	chr1	183617469	183617469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaaaaataaatactaaGagtgatgcctggatacgtaa	9	5	0	3	rs189818313		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183617469G>T	ENST00000308641.4	-	2	719	c.448C>A	c.(448-450)Ctt>Att	p.L150I	APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000304685.4_Intron|RGL1_ENST00000536277.1_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	150					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.L150I(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						TAAATACTAAGAGTGATGCCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	106	104					1																	183617469		2203	4300	6503	181884092	SO:0001583	missense	403314			BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"Apolipoprotein B mRNA editing enzymes"	32152	protein-coding gene	gene with protein product		609908	"chromosome 1 open reading frame 169"	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.448C>A	1.37:g.183617469G>T	ENSP00000310622:p.Leu150Ile		181884092	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821159	0.50633	.	.	ENSG00000173627	ENST00000308641	T	0.72051	-0.62	5.0	4.05	0.47172	APOBEC-like, N-terminal (1);	0.000000	0.51477	D	0.000090	T	0.72676	0.3490	L	0.34521	1.04	0.34579	D	0.714243	D	0.55385	0.971	P	0.57548	0.823	T	0.81675	-0.0825	10	0.87932	D	0	-16.6803	14.0276	0.64594	0.0:0.0:0.8474:0.1526	.	150	Q8WW27	ABEC4_HUMAN	I	150	ENSP00000310622:L150I	ENSP00000310622:L150I	L	-	1	0	APOBEC4	181884092	1.000000	0.71417	0.954000	0.39281	0.547000	0.35210	4.436000	0.59948	1.046000	0.40249	0.655000	0.94253	CTT		0.458	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454		T	183617469	G	T	183617469	3	4	61	1	0	0	0	0	1	0	0	0	796	942	33	2	659	2	APOBEC4	1	183617469	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97553	183617469	65633152	876	8861										
RGL1	23179	broad.mit.edu	37	chr1	183853909	183853909	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggctgcatttggtctcGaagggataagaaggaaaaca	13	7	1	1	rs141178460		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183853909G>A	ENST00000360851.3	+	7	966	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	RGL1_ENST00000539189.1_Missense_Mutation_p.R263Q|RGL1_ENST00000304685.4_Missense_Mutation_p.R298Q|RGL1_ENST00000536277.1_Missense_Mutation_p.R261Q			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	263	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.R298Q(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						ATTTGGTCTCGAAGGGATAAG	0.463													G|||	1	0.000199681	0	0	5008	,	,		19209	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	GLN/ARG	0,4406		0,0,2203	141	119	126		893	-6	0.5	1	dbSNP_134	126	1,8599	1.2+/-3.3	0,1,4299	no	missense	RGL1	NM_015149.3	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	298/804	183853909	1,13005	2203	4300	6503	182120532	SO:0001583	missense	23179			AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.788G>A	1.37:g.183853909G>A	ENSP00000354097:p.Arg263Gln		182120532	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	G	5.588	0.293350	0.10567	0.0	1.16E-4	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000543395;ENST00000360851;ENST00000539189	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.26	-6.01	0.02199	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.583469	0.18200	N	0.148545	T	0.10208	0.0250	N	0.03608	-0.345	0.26494	N	0.974891	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.0;0.002;0.001;0.001	T	0.27938	-1.0059	10	0.02654	T	1	.	16.8486	0.85987	0.7052:0.0:0.2948:0.0	.	263;261;68;263;298	F5H6U6;B7Z2W5;F5H3C3;Q9NZL6;Q5SXQ6	.;.;.;RGL1_HUMAN;.	Q	298;298;261;68;263;263	ENSP00000303192:R298Q;ENSP00000356501:R298Q;ENSP00000438662:R261Q;ENSP00000354097:R263Q;ENSP00000437355:R263Q	ENSP00000303192:R298Q	R	+	2	0	RGL1	182120532	0.801000	0.28930	0.456000	0.27044	0.994000	0.84299	0.168000	0.16622	-1.128000	0.02922	-0.145000	0.13849	CGA		0.463	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		A	183853909	G	A	183853909	3	1	61	1	0	0	0	0	1	0	0	0	13313	1058	37	1	919	1	RGL1	1	183853909	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236440	183853909	65396712	877	8862										
RGL1	23179	broad.mit.edu	37	chr1	183869368	183869368	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccttcaggactacatcGaggtgagttccatgtgggtg	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183869368G>A	ENST00000360851.3	+	11	1493	c.1315G>A	c.(1315-1317)Gag>Aag	p.E439K	RGL1_ENST00000539189.1_Intron|RGL1_ENST00000304685.4_Missense_Mutation_p.E474K|RGL1_ENST00000536277.1_Missense_Mutation_p.E437K			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	439	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.E474K(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						GGACTACATCGAGGTGAGTTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											160	108	126					1																	183869368		2203	4300	6503	182135991	SO:0001583	missense	23179			AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1315G>A	1.37:g.183869368G>A	ENSP00000354097:p.Glu439Lys		182135991	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	G	18.92	3.724736	0.68959	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000543395;ENST00000360851	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.08	4.16	0.48862	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.50257	0.1605	L	0.52266	1.64	0.80722	D	1	D;D;D;D	0.76494	0.999;0.971;0.999;0.999	D;P;D;D	0.81914	0.995;0.55;0.995;0.995	T	0.41233	-0.9520	10	0.14252	T	0.57	.	14.6875	0.69059	0.0:0.0:0.8535:0.1464	.	437;244;439;474	B7Z2W5;F5H3C3;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	K	474;474;437;244;439	ENSP00000303192:E474K;ENSP00000356501:E474K;ENSP00000438662:E437K;ENSP00000354097:E439K	ENSP00000303192:E474K	E	+	1	0	RGL1	182135991	1.000000	0.71417	0.968000	0.41197	0.660000	0.38997	8.969000	0.93411	1.344000	0.45657	0.655000	0.94253	GAG		0.512	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		A	183869368	G	A	183869368	3	1	61	1	0	0	0	0	1	0	0	0	13313	1059	37	1	1462	1	RGL1	1	183869368	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15459	183869368	65381253	878	8863										
RGL1	23179	broad.mit.edu	37	chr1	183895347	183895347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaacaagtgaaactgcGtagccggaccagcttgacgt	13	9	0	3	rs200168009		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:183895347G>A	ENST00000360851.3	+	18	2406	c.2228G>A	c.(2227-2229)cGt>cAt	p.R743H	RGL1_ENST00000539189.1_Missense_Mutation_p.R714H|RGL1_ENST00000304685.4_Missense_Mutation_p.R778H|RGL1_ENST00000536277.1_Missense_Mutation_p.R741H			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	743					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.R778H(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						GTGAAACTGCGTAGCCGGACC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	HIS/ARG	0,4406		0,0,2203	92	87	88		2333	4.4	0.4	1		88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RGL1	NM_015149.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	778/804	183895347	1,13005	2203	4300	6503	182161970	SO:0001583	missense	23179			AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.2228G>A	1.37:g.183895347G>A	ENSP00000354097:p.Arg743His		182161970	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	G	21.6	4.170126	0.78452	0.0	1.16E-4	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.50277	0.76;0.76;0.77;0.77;0.75	5.37	4.45	0.53987	.	0.167388	0.52532	D	0.000065	T	0.54013	0.1832	L	0.27053	0.805	0.58432	D	0.999992	D;D;D;D	0.76494	0.999;0.983;0.983;0.983	D;P;P;P	0.72625	0.978;0.635;0.513;0.513	T	0.57219	-0.7849	10	0.59425	D	0.04	.	12.6926	0.56982	0.0:0.0:0.8346:0.1654	.	714;741;743;778	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	H	778;778;741;743;714	ENSP00000303192:R778H;ENSP00000356501:R778H;ENSP00000438662:R741H;ENSP00000354097:R743H;ENSP00000437355:R714H	ENSP00000303192:R778H	R	+	2	0	RGL1	182161970	1.000000	0.71417	0.358000	0.25811	0.882000	0.50991	7.051000	0.76627	1.354000	0.45846	0.650000	0.86243	CGT		0.498	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		A	183895347	G	A	183895347	3	1	61	1	0	0	0	0	1	0	0	0	13313	1145	40	1	2403	1	RGL1	1	183895347	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25979	183895347	65355274	879	8864										
TSEN15	116461	broad.mit.edu	37	chr1	184041968	184041968	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttttccagaatatttCtcttagaagatgacatccat	4	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:184041968C>A	ENST00000361641.1	+	5	582	c.503C>A	c.(502-504)tCt>tAt	p.S168Y	TSEN15_ENST00000423085.2_Missense_Mutation_p.L121I|TSEN15_ENST00000533373.1_Missense_Mutation_p.F133L	NM_052965.2	NP_443197.1	Q8WW01	SEN15_HUMAN	TSEN15 tRNA splicing endonuclease subunit	168					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)	tRNA-intron endonuclease activity (GO:0000213)	p.S168Y(1)		breast(1)|kidney(3)|large_intestine(2)|lung(2)	8						CAGAATATTTCTCTTAGAAGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	78	78					1																	184041968		2202	4298	6500	182308591	SO:0001583	missense	116461			AF288394	CCDS1361.1, CCDS44286.1, CCDS72993.1	1q25	2013-08-06	2013-08-06	2008-06-12	ENSG00000198860	ENSG00000198860		"tRNA splicing endonuclease subunits"	16791	protein-coding gene	gene with protein product		608756	"chromosome 1 open reading frame 19", "tRNA splicing endonuclease 15 homolog (S. cerevisiae)"	C1orf19		11318611, 17166513	Standard	XM_006711148		Approved		uc001gqt.4	Q8WW01	OTTHUMG00000035461	ENST00000361641.1:c.503C>A	1.37:g.184041968C>A	ENSP00000355299:p.Ser168Tyr		182308591	B4DKP0|Q9BZQ5	Missense_Mutation	SNP	ENST00000361641.1	37	CCDS1361.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.71|13.71|13.71	2.317697|2.317697|2.317697	0.40996|0.40996|0.40996	.|.|.	.|.|.	ENSG00000198860|ENSG00000198860|ENSG00000198860	ENST00000533373|ENST00000423085|ENST00000361641	T|T|T	0.28255|0.32515|0.36340	1.62|1.45|1.26	4.88|4.88|4.88	3.96|3.96|3.96	0.45880|0.45880|0.45880	.|.|.	.|.|0.382368	.|.|0.26601	.|.|N	.|.|0.023475	T|T|T	0.25232|0.25232|0.25232	0.0613|0.0613|0.0613	.|.|.	.|.|.	.|.|.	0.21105|0.21105|0.21105	N|N|N	0.999787|0.999787|0.999787	.|B|P	.|0.22604|0.44090	.|0.072|0.826	.|B|B	.|0.20384|0.38712	.|0.029|0.28	T|T|T	0.18935|0.18935|0.18935	-1.0321|-1.0321|-1.0321	6|8|9	0.87932|0.52906|0.48119	D|T|T	0|0.07|0.1	-9.7901|-9.7901|-9.7901	8.173|8.173|8.173	0.31266|0.31266|0.31266	0.0:0.895:0.0:0.105|0.0:0.895:0.0:0.105|0.0:0.895:0.0:0.105	.|.|.	.|121|168	.|B4DKP0|Q8WW01	.|.|SEN15_HUMAN	L|I|Y	133|121|168	ENSP00000436996:F133L|ENSP00000402002:L121I|ENSP00000355299:S168Y	ENSP00000436996:F133L|ENSP00000402002:L121I|ENSP00000355299:S168Y	F|L|S	+|+|+	3|1|2	2|0|0	TSEN15|TSEN15|TSEN15	182308591|182308591|182308591	0.991000|0.991000|0.991000	0.36638|0.36638|0.36638	0.992000|0.992000|0.992000	0.48379|0.48379|0.48379	0.871000|0.871000|0.871000	0.50021|0.50021|0.50021	1.945000|1.945000|1.945000	0.40273|0.40273|0.40273	2.631000|2.631000|2.631000	0.89168|0.89168|0.89168	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTC|TCT		0.308	TSEN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086132.1			A	184041968	C	A	184041968	3	1	61	1	0	0	0	0	1	0	0	0	16651	913	32	2	521	2	TSEN15	1	184041968	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146621	184041968	65208653	880	8865										
EDEM3	80267	broad.mit.edu	37	chr1	184675862	184675862	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcctctttgtatcagtgcGatttttcccatcactgcctc	6	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:184675862G>A	ENST00000318130.8	-	18	2384	c.2118C>T	c.(2116-2118)atC>atT	p.I706I	EDEM3_ENST00000367512.3_Silent_p.I663I|EDEM3_ENST00000466392.1_5'UTR	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	706	PA.				cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.I663I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GTATCAGTGCGATTTTTCCCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											171	122	139					1																	184675862		2203	4300	6503	182942485	SO:0001819	synonymous_variant	80267			AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.2118C>T	1.37:g.184675862G>A			182942485	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Silent	SNP	ENST00000318130.8	37	CCDS1363.2																																																																																				0.433	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		A	184675862	G	A	184675862	2	1	61	1	0	0	0	0	0	0	0	1	4924	1048	37	1		1	EDEM3	1	184675862	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	633894	184675862	64574759	881	8866										
RNF2	6045	broad.mit.edu	37	chr1	185056762	185056762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtttatatgagttacaacGaacacctcaggtaatgacta	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185056762G>A	ENST00000367510.3	+	2	365	c.77G>A	c.(76-78)cGa>cAa	p.R26Q	RNF2_ENST00000367509.4_Missense_Mutation_p.R26Q	NM_007212.3	NP_009143.1	Q99496	RING2_HUMAN	ring finger protein 2	26	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R26Q(1)		breast(3)|endometrium(2)|large_intestine(4)|lung(3)|skin(2)	14		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)		GAGTTACAACGAACACCTCAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	99	101					1																	185056762		2203	4300	6503	183323385	SO:0001583	missense	6045			BC012583, Y10571	CCDS1365.1	1q25.3	2013-01-09			ENSG00000121481	ENSG00000121481		"RING-type (C3HC4) zinc fingers"	10061	protein-coding gene	gene with protein product		608985				11513855	Standard	XM_005245413		Approved	BAP-1, BAP1, DING, HIPI3, RING1B, RING2	uc001grc.1	Q99496	OTTHUMG00000035391	ENST00000367510.3:c.77G>A	1.37:g.185056762G>A	ENSP00000356480:p.Arg26Gln		183323385	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000367510.3	37	CCDS1365.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239350	0.79800	.	.	ENSG00000121481	ENST00000367510;ENST00000367509;ENST00000453650	T;T	0.21932	1.98;1.98	4.97	4.05	0.47172	.	0.000000	0.85682	D	0.000000	T	0.37785	0.1016	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.70716	0.97;0.583	T	0.18272	-1.0342	10	0.87932	D	0	-1.1738	13.3428	0.60555	0.0773:0.0:0.9226:0.0	.	26;26	B3KRH1;Q99496	.;RING2_HUMAN	Q	26	ENSP00000356480:R26Q;ENSP00000400722:R26Q	ENSP00000356479:R26Q	R	+	2	0	RNF2	183323385	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.990000	0.93510	1.218000	0.43458	0.591000	0.81541	CGA		0.383	RNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085793.1	NM_007212		A	185056762	G	A	185056762	3	1	61	1	0	0	0	0	1	0	0	0	13509	1058	37	1	79	1	RNF2	1	185056762	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	380900	185056762	64193859	882	8867										
RNF2	6045	broad.mit.edu	37	chr1	185069002	185069002	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttagctttagaagaacttCgaagcaaaggtgaatcaaac	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185069002C>T	ENST00000367510.3	+	6	1105	c.817C>T	c.(817-819)Cga>Tga	p.R273*	RNF2_ENST00000367509.4_Nonsense_Mutation_p.R201*	NM_007212.3	NP_009143.1	Q99496	RING2_HUMAN	ring finger protein 2	273					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R273*(1)		breast(3)|endometrium(2)|large_intestine(4)|lung(3)|skin(2)	14		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)		AGAAGAACTTCGAAGCAAAGG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											93	93	93					1																	185069002		2203	4300	6503	183335625	SO:0001587	stop_gained	6045			BC012583, Y10571	CCDS1365.1	1q25.3	2013-01-09			ENSG00000121481	ENSG00000121481		"RING-type (C3HC4) zinc fingers"	10061	protein-coding gene	gene with protein product		608985				11513855	Standard	XM_005245413		Approved	BAP-1, BAP1, DING, HIPI3, RING1B, RING2	uc001grc.1	Q99496	OTTHUMG00000035391	ENST00000367510.3:c.817C>T	1.37:g.185069002C>T	ENSP00000356480:p.Arg273*		183335625	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000367510.3	37	CCDS1365.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.879195	0.91740	.	.	ENSG00000121481	ENST00000367510;ENST00000367509	.	.	.	5.83	4.9	0.64082	.	0.051265	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	0.3111	16.2201	0.82254	0.1339:0.8661:0.0:0.0	.	.	.	.	X	273;201	.	ENSP00000356479:R201X	R	+	1	2	RNF2	183335625	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.403000	0.44530	1.429000	0.47314	0.650000	0.86243	CGA		0.393	RNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085793.1	NM_007212		T	185069002	C	T	185069002	4	4	61	1	0	0	0	0	0	1	0	0	13509	876	31	1	835	1	RNF2	1	185069002	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12240	185069002	64181619	883	8868										
C1orf25	81627	broad.mit.edu	37	chr1	185094192	185094192	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccaaaccatggtgaagaGattcaaatagcattcttttg	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185094192G>T	ENST00000367506.5	-	12	1911	c.1643C>A	c.(1642-1644)tCt>tAt	p.S548Y	TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	548	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.				adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)	p.S548Y(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						ATGGTGAAGAGATTCAAATAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	99	99					1																	185094192		2203	4300	6503	183360815	SO:0001583	missense	81627			AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.1643C>A	1.37:g.185094192G>T	ENSP00000356476:p.Ser548Tyr		183360815	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Missense_Mutation	SNP	ENST00000367506.5	37	CCDS1366.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162678	0.57368	.	.	ENSG00000121486	ENST00000367506;ENST00000458395	.	.	.	4.91	3.99	0.46301	.	0.103999	0.64402	D	0.000003	T	0.62502	0.2433	L	0.39898	1.24	0.80722	D	1	D	0.62365	0.991	P	0.57776	0.827	T	0.59883	-0.7370	9	0.29301	T	0.29	-10.5337	15.6427	0.77020	0.0:0.1377:0.8623:0.0	.	548	Q7Z2T5	TRM1L_HUMAN	Y	548;172	.	ENSP00000356476:S548Y	S	-	2	0	TRMT1L	183360815	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	6.551000	0.73909	1.180000	0.42898	0.585000	0.79938	TCT		0.348	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		T	185094192	G	T	185094192	3	4	61	1	0	0	0	0	1	0	0	0	2040	942	33	2	574	2	C1orf25	1	185094192	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25190	185094192	64156429	884	8869										
C1orf26	54823	broad.mit.edu	37	chr1	185143877	185143877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttagagacaattctgaaAaatgtgtcttagagaaatgg	9	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185143877A>G	ENST00000367500.4	+	5	763	c.598A>G	c.(598-600)Aaa>Gaa	p.K200E	SWT1_ENST00000367501.3_Missense_Mutation_p.K200E	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	200								p.K200E(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CAATTCTGAAAAATGTGTCTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											45	51	49					1																	185143877		2195	4294	6489	183410500	SO:0001583	missense	54823			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.598A>G	1.37:g.185143877A>G	ENSP00000356470:p.Lys200Glu		183410500	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.297430	0.23650	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.21191	2.02;2.02	5.46	2.67	0.31697	.	0.401227	0.23910	N	0.043360	T	0.12347	0.0300	L	0.41710	1.295	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.38845	-0.9642	10	0.07482	T	0.82	.	4.7308	0.12964	0.5269:0.3427:0.1304:0.0	.	200	Q5T5J6	SWT1_HUMAN	E	200	ENSP00000356471:K200E;ENSP00000356470:K200E	ENSP00000356470:K200E	K	+	1	0	SWT1	183410500	0.954000	0.32549	0.838000	0.33150	0.639000	0.38242	1.090000	0.30902	0.213000	0.20722	0.374000	0.22700	AAA		0.343	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		G	185143877	A	G	185143877	3	3	61	1	0	0	0	0	1	0	0	0	2041	15	1	4	612	4	C1orf26	1	185143877	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	49685	185143877	64106744	885	8870										
C1orf26	54823	broad.mit.edu	37	chr1	185175836	185175836	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggttggctgtatttggatTagttatggaaaagaacttgc	12	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185175836T>G	ENST00000367500.4	+	13	2078	c.1913T>G	c.(1912-1914)tTa>tGa	p.L638*	SWT1_ENST00000367501.3_Nonsense_Mutation_p.L638*	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	638			L -> F (in dbSNP:rs2295950).					p.L638*(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GTATTTGGATTAGTTATGGAA	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											71	74	73					1																	185175836		2202	4294	6496	183442459	SO:0001587	stop_gained	54823			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1913T>G	1.37:g.185175836T>G	ENSP00000356470:p.Leu638*		183442459	Q8NEK9|Q9BZQ7|Q9NXQ0	Nonsense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	T	39	7.407702	0.98265	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	.	.	.	5.83	5.83	0.93111	.	0.370207	0.25481	N	0.030377	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5559	0.45117	0.1439:0.0:0.0:0.8561	.	.	.	.	X	638	.	ENSP00000356470:L638X	L	+	2	0	SWT1	183442459	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	1.440000	0.35024	2.226000	0.72624	0.482000	0.46254	TTA		0.318	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		G	185175836	T	G	185175836	4	3	61	1	0	0	0	0	0	1	0	0	2041	1764	61	4	1959	4	C1orf26	1	185175836	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31959	185175836	64074785	886	8871										
C1orf26	54823	broad.mit.edu	37	chr1	185191084	185191084	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagaaatcactgttttctCgagttctcatcttccccaac	4	13	5	1	rs374079943	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185191084C>T	ENST00000367500.4	+	15	2390	c.2225C>T	c.(2224-2226)tCg>tTg	p.S742L	SWT1_ENST00000367501.3_Missense_Mutation_p.S742L	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	742								p.S742L(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						ACTGTTTTCTCGAGTTCTCAT	0.378													C|||	2	0.000399361	0.0015	0	5008	,	,		17525	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	160	169	166		2225,2225	2.8	0	1		166	0,8600		0,0,4300	no	missense,missense	SWT1	NM_017673.6,NM_001105518.1	145,145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	742/901,742/901	185191084	1,13005	2203	4300	6503	183457707	SO:0001583	missense	54823			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2225C>T	1.37:g.185191084C>T	ENSP00000356470:p.Ser742Leu		183457707	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	C	0.930	-0.712905	0.03206	2.27E-4	0.0	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.17528	2.27;2.27	5.43	2.77	0.32553	.	0.932048	0.09017	N	0.860683	T	0.07143	0.0181	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.38908	-0.9639	10	0.12103	T	0.63	.	8.2078	0.31465	0.0:0.6888:0.0:0.3112	.	742	Q5T5J6	SWT1_HUMAN	L	742	ENSP00000356471:S742L;ENSP00000356470:S742L	ENSP00000356470:S742L	S	+	2	0	SWT1	183457707	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.748000	0.26305	0.931000	0.37242	0.591000	0.81541	TCG		0.378	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		T	185191084	C	T	185191084	3	4	61	1	0	0	0	0	1	0	0	0	2041	893	31	1	2279	1	C1orf26	1	185191084	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15248	185191084	64059537	887	8872										
C1orf26	54823	broad.mit.edu	37	chr1	185245771	185245771	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttactgcccaggaaatTtatgattgtgtttctcagac	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185245771T>G	ENST00000367500.4	+	18	2709	c.2544T>G	c.(2542-2544)atT>atG	p.I848M	SWT1_ENST00000367501.3_Missense_Mutation_p.I848M	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	848								p.I848M(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CCCAGGAAATTTATGATTGTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	67	64					1																	185245771		2202	4293	6495	183512394	SO:0001583	missense	54823			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2544T>G	1.37:g.185245771T>G	ENSP00000356470:p.Ile848Met		183512394	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.157443	0.38119	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.42513	0.97;0.97	5.98	2.37	0.29283	.	0.328436	0.29767	N	0.011256	T	0.18923	0.0454	N	0.08118	0	0.19300	N	0.999972	B	0.12013	0.005	B	0.11329	0.006	T	0.16041	-1.0416	10	0.72032	D	0.01	.	2.5206	0.04679	0.1434:0.0821:0.1732:0.6012	.	848	Q5T5J6	SWT1_HUMAN	M	848	ENSP00000356471:I848M;ENSP00000356470:I848M	ENSP00000356470:I848M	I	+	3	3	SWT1	183512394	0.995000	0.38212	0.994000	0.49952	0.970000	0.65996	-0.008000	0.12788	0.153000	0.19213	0.528000	0.53228	ATT		0.303	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		G	185245771	T	G	185245771	3	3	61	1	0	0	0	0	1	0	0	0	2041	1829	64	4	2610	4	C1orf26	1	185245771	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	54687	185245771	64004850	888	8873										
IVNS1ABP	10625	broad.mit.edu	37	chr1	185267182	185267182	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgttaaaactggaaaatCtttgtataggggctccattc	8	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185267182C>A	ENST00000367498.3	-	15	2536	c.1914G>T	c.(1912-1914)aaG>aaT	p.K638N	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.K420N	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	638					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)		p.K638N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						ACTGGAAAATCTTTGTATAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											95	101	99					1																	185267182		2203	4300	6503	183533805	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1914G>T	1.37:g.185267182C>A	ENSP00000356468:p.Lys638Asn		183533805	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911286	0.33721	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.77358	-1.09;-0.6	5.37	4.44	0.53790	.	0.400085	0.30667	N	0.009140	T	0.63438	0.2511	N	0.24115	0.695	0.37522	D	0.917578	B;B	0.16396	0.002;0.017	B;B	0.19666	0.004;0.026	T	0.65051	-0.6262	10	0.66056	D	0.02	.	8.2079	0.31467	0.0:0.7209:0.1531:0.126	.	420;638	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	N	638;420	ENSP00000356468:K638N;ENSP00000375864:K420N	ENSP00000356468:K638N	K	-	3	2	IVNS1ABP	183533805	0.963000	0.33076	1.000000	0.80357	0.991000	0.79684	0.070000	0.14573	2.673000	0.90976	0.557000	0.71058	AAG		0.393	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		A	185267182	C	A	185267182	3	1	61	1	0	0	0	0	1	0	0	0	7951	912	32	2	18	2	IVNS1ABP	1	185267182	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21411	185267182	63983439	889	8874										
IVNS1ABP	10625	broad.mit.edu	37	chr1	185269663	185269663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattatagcattcgactgttCgaagacattcctctctgtta	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185269663C>T	ENST00000367498.3	-	11	1770	c.1148G>A	c.(1147-1149)cGa>cAa	p.R383Q	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.R165Q	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	383					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)		p.R383Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						TTCGACTGTTCGAAGACATTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	129	128					1																	185269663		2203	4300	6503	183536286	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1148G>A	1.37:g.185269663C>T	ENSP00000356468:p.Arg383Gln		183536286	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	c	25.8	4.676711	0.88445	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.78481	-1.18;-1.18	5.76	4.86	0.63082	Galactose oxidase, beta-propeller (1);	0.051731	0.85682	N	0.000000	T	0.81716	0.4881	L	0.37697	1.125	0.58432	D	0.999997	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65874	0.939;0.936;0.919	T	0.82057	-0.0646	10	0.45353	T	0.12	.	15.0675	0.72008	0.0:0.9322:0.0:0.0678	.	165;84;383	A8MVR0;Q6MZF3;Q9Y6Y0	.;.;NS1BP_HUMAN	Q	383;165	ENSP00000356468:R383Q;ENSP00000375864:R165Q	ENSP00000356468:R383Q	R	-	2	0	IVNS1ABP	183536286	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.966000	0.70395	1.443000	0.47586	-0.119000	0.15052	CGA		0.398	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		T	185269663	C	T	185269663	3	4	61	1	0	0	0	0	1	0	0	0	7951	884	31	1	800	1	IVNS1ABP	1	185269663	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2481	185269663	63980958	890	8875										
IVNS1ABP	10625	broad.mit.edu	37	chr1	185277942	185277942	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatactctacctgctttactCgatccatcttcagctttttt	4	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185277942C>T	ENST00000367498.3	-	5	969	c.347G>A	c.(346-348)cGa>cAa	p.R116Q	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_5'UTR|IVNS1ABP_ENST00000367497.1_Missense_Mutation_p.R116Q	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	116					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)		p.R116Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						CTGCTTTACTCGATCCATCTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	164	166					1																	185277942		2203	4300	6503	183544565	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.347G>A	1.37:g.185277942C>T	ENSP00000356468:p.Arg116Gln		183544565	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	31	5.083854	0.94050	.	.	ENSG00000116679	ENST00000367498;ENST00000367497	T;T	0.68903	-0.36;-0.36	5.88	5.88	0.94601	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.80752	0.4683	M	0.62154	1.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76200	-0.3046	10	0.32370	T	0.25	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	116	Q9Y6Y0	NS1BP_HUMAN	Q	116	ENSP00000356468:R116Q;ENSP00000356467:R116Q	ENSP00000356467:R116Q	R	-	2	0	IVNS1ABP	183544565	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.711000	0.84669	2.789000	0.95967	0.591000	0.81541	CGA		0.303	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		T	185277942	C	T	185277942	3	4	61	1	0	0	0	0	1	0	0	0	7951	884	31	1	1625	1	IVNS1ABP	1	185277942	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8279	185277942	63972679	891	8876										
HMCN1	83872	broad.mit.edu	37	chr1	185947090	185947090	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttccatcagccaactaaGaacaggagctctctttattt	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:185947090G>T	ENST00000271588.4	+	16	2772	c.2543G>T	c.(2542-2544)aGa>aTa	p.R848I	HMCN1_ENST00000485744.1_3'UTR|HMCN1_ENST00000367492.2_Missense_Mutation_p.R848I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	848	Ig-like C2-type 5.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R848I(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGCCAACTAAGAACAGGAGCT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	92	91					1																	185947090		2203	4300	6503	184213713	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.2543G>T	1.37:g.185947090G>T	ENSP00000271588:p.Arg848Ile		184213713	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.589381	0.66105	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67523	-0.27;-0.27	5.89	0.476	0.16779	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.342530	0.35525	N	0.003145	T	0.64249	0.2581	N	0.25825	0.765	0.43364	D	0.995449	P;D	0.89917	0.899;1.0	P;D	0.85130	0.509;0.997	T	0.58323	-0.7656	10	0.31617	T	0.26	.	6.0392	0.19724	0.2683:0.3463:0.3854:0.0	.	232;848	Q96RW7-3;Q96RW7	.;HMCN1_HUMAN	I	848	ENSP00000271588:R848I;ENSP00000356462:R848I	ENSP00000271588:R848I	R	+	2	0	HMCN1	184213713	1.000000	0.71417	0.961000	0.40146	0.995000	0.86356	1.551000	0.36233	0.096000	0.17463	-0.140000	0.14226	AGA		0.318	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	185947090	G	T	185947090	3	4	61	1	0	0	0	0	1	0	0	0	7241	942	33	2	2605	2	HMCN1	1	185947090	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	669148	185947090	63303531	892	8877										
HMCN1	83872	broad.mit.edu	37	chr1	186023026	186023026	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaggcaattacaaatttCaattgctgaaaagtctgatg	10	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186023026C>A	ENST00000271588.4	+	44	6999	c.6770C>A	c.(6769-6771)tCa>tAa	p.S2257*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.S2257*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2257	Ig-like C2-type 20.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S2257*(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTACAAATTTCAATTGCTGAA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											95	96	96					1																	186023026		2203	4300	6503	184289649	SO:0001587	stop_gained	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.6770C>A	1.37:g.186023026C>A	ENSP00000271588:p.Ser2257*		184289649	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	48	14.611578	0.99803	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	4.77	4.77	0.60923	.	0.123332	0.56097	D	0.000022	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	11.6566	0.51322	0.0:0.9174:0.0:0.0826	.	.	.	.	X	2257	.	ENSP00000271588:S2257X	S	+	2	0	HMCN1	184289649	1.000000	0.71417	0.949000	0.38748	0.634000	0.38068	4.720000	0.61944	2.349000	0.79799	0.404000	0.27445	TCA		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186023026	C	A	186023026	4	1	61	1	0	0	0	0	0	1	0	0	7241	838	29	2	6944	2	HMCN1	1	186023026	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75936	186023026	63227595	893	8878										
HMCN1	83872	broad.mit.edu	37	chr1	186088326	186088326	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttttcatttttaggagCaattgaaatacttgccaccc	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186088326C>T	ENST00000271588.4	+	78	12081	c.11852C>T	c.(11851-11853)gCa>gTa	p.A3951V	HMCN1_ENST00000367492.2_Missense_Mutation_p.A3951V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3951	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.A3951V(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTTTTAGGAGCAATTGAAATA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	75	76					1																	186088326		2203	4300	6503	184354949	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11852C>T	1.37:g.186088326C>T	ENSP00000271588:p.Ala3951Val		184354949	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.866374	0.51588	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67171	-0.25;-0.25	5.44	5.44	0.79542	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.350254	0.33496	N	0.004859	T	0.52224	0.1721	L	0.31157	0.91	0.09310	N	0.999998	P	0.44946	0.846	B	0.41946	0.371	T	0.47983	-0.9074	10	0.23891	T	0.37	.	9.2806	0.37727	0.0:0.7773:0.1464:0.0763	.	3951	Q96RW7	HMCN1_HUMAN	V	3951	ENSP00000271588:A3951V;ENSP00000356462:A3951V	ENSP00000271588:A3951V	A	+	2	0	HMCN1	184354949	0.027000	0.19231	0.982000	0.44146	0.978000	0.69477	2.525000	0.45598	2.563000	0.86464	0.585000	0.79938	GCA		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186088326	C	T	186088326	3	4	61	1	0	0	0	0	1	0	0	0	7241	710	25	3	12162	3	HMCN1	1	186088326	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65300	186088326	63162295	894	8879										
HMCN1	83872	broad.mit.edu	37	chr1	186097328	186097328	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacttcctggagacgtgtCattaaataaaggagaacagc	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186097328C>A	ENST00000271588.4	+	83	13038	c.12809C>A	c.(12808-12810)tCa>tAa	p.S4270*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.S4270*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4270	Ig-like C2-type 42.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S4270*(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGAGACGTGTCATTAAATAAA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											117	105	109					1																	186097328		2203	4300	6503	184363951	SO:0001587	stop_gained	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12809C>A	1.37:g.186097328C>A	ENSP00000271588:p.Ser4270*		184363951	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	55	24.041056	0.99958	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.36	5.36	0.76844	.	0.171002	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3837	0.60783	0.0:0.9244:0.0:0.0756	.	.	.	.	X	4270	.	ENSP00000271588:S4270X	S	+	2	0	HMCN1	184363951	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.757000	0.68766	2.502000	0.84385	0.585000	0.79938	TCA		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186097328	C	A	186097328	4	1	61	1	0	0	0	0	0	1	0	0	7241	838	29	2	13139	2	HMCN1	1	186097328	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9002	186097328	63153293	895	8880										
HMCN1	83872	broad.mit.edu	37	chr1	186106697	186106697	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtggaaaaggcatccaAaagaggagtcgtctgtgcaa	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186106697A>C	ENST00000271588.4	+	88	13879	c.13650A>C	c.(13648-13650)caA>caC	p.Q4550H	HMCN1_ENST00000367492.2_Missense_Mutation_p.Q4550H	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4550	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.Q4550H(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGGCATCCAAAAGAGGAGTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	71	71					1																	186106697		2203	4300	6503	184373320	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13650A>C	1.37:g.186106697A>C	ENSP00000271588:p.Gln4550His		184373320	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	19.76	3.887612	0.72410	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.57752	0.38;0.38	5.78	-2.49	0.06403	.	0.000000	0.85682	D	0.000000	T	0.67173	0.2865	M	0.79011	2.435	0.48288	D	0.999625	D	0.89917	1.0	D	0.91635	0.999	T	0.65471	-0.6160	10	0.52906	T	0.07	.	11.8055	0.52152	0.5454:0.0:0.4546:0.0	.	4550	Q96RW7	HMCN1_HUMAN	H	4550	ENSP00000271588:Q4550H;ENSP00000356462:Q4550H	ENSP00000271588:Q4550H	Q	+	3	2	HMCN1	184373320	0.988000	0.35896	0.930000	0.37139	0.974000	0.67602	0.198000	0.17217	-0.840000	0.04206	-0.417000	0.06048	CAA		0.478	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186106697	A	C	186106697	3	2	61	1	0	0	0	0	1	0	0	0	7241	11	1	4	14000	4	HMCN1	1	186106697	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9369	186106697	63143924	896	8881										
HMCN1	83872	broad.mit.edu	37	chr1	186134248	186134248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctctgtggtaggagatCgcagtaatcagtgcccctcc	10	13	2	1	rs536109375		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186134248C>T	ENST00000271588.4	+	98	15491	c.15262C>T	c.(15262-15264)Cgc>Tgc	p.R5088C	HMCN1_ENST00000367492.2_Missense_Mutation_p.R5088C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5088	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R5088C(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGTAGGAGATCGCAGTAATCA	0.433													C|||	1	0.000199681	0	0	5008	,	,		19640	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											162	157	159					1																	186134248		2203	4300	6503	184400871	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15262C>T	1.37:g.186134248C>T	ENSP00000271588:p.Arg5088Cys		184400871	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038807	0.75617	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.64991	-0.12;-0.13	5.27	4.23	0.50019	G2 nidogen/fibulin G2F (1);	0.157320	0.53938	D	0.000044	T	0.64316	0.2587	L	0.36672	1.1	0.58432	D	0.99999	D	0.76494	0.999	P	0.56088	0.791	T	0.66168	-0.5991	10	0.54805	T	0.06	.	13.7068	0.62644	0.1983:0.8017:0.0:0.0	.	5088	Q96RW7	HMCN1_HUMAN	C	5088	ENSP00000271588:R5088C;ENSP00000356462:R5088C	ENSP00000271588:R5088C	R	+	1	0	HMCN1	184400871	0.964000	0.33143	0.999000	0.59377	0.996000	0.88848	2.531000	0.45650	2.621000	0.88768	0.655000	0.94253	CGC		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186134248	C	T	186134248	3	4	61	1	0	0	0	0	1	0	0	0	7241	884	31	1	15652	1	HMCN1	1	186134248	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27551	186134248	63116373	897	8882										
PRG4	10216	broad.mit.edu	37	chr1	186270758	186270758	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccgctgctttgagtccttCgagagagggagggagtgtga	18	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186270758C>T	ENST00000445192.2	+	4	279	c.234C>T	c.(232-234)ttC>ttT	p.F78F	PRG4_ENST00000367484.3_Silent_p.F37F|PRG4_ENST00000367485.4_Silent_p.F78F|PRG4_ENST00000367486.3_Silent_p.F78F|PRG4_ENST00000367483.4_Silent_p.F37F	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	78	SMB 2. {ECO:0000255|PROSITE- ProRule:PRU00350}.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.F78F(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TTGAGTCCTTCGAGAGAGGGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	1											144	132	136					1																	186270758		2203	4300	6503	184537381	SO:0001819	synonymous_variant	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.234C>T	1.37:g.186270758C>T			184537381	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																				0.478	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		T	186270758	C	T	186270758	2	4	61	1	0	0	0	0	0	0	0	1	12515	883	31	1		1	PRG4	1	186270758	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136510	186270758	62979863	898	8883										
PRG4	10216	broad.mit.edu	37	chr1	186280685	186280685	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcagcgctttcaacagcTaaatataagaactggcctga	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186280685T>G	ENST00000445192.2	+	10	3795	c.3750T>G	c.(3748-3750)gcT>gcG	p.A1250A	PRG4_ENST00000367484.3_Silent_p.A779A|PRG4_ENST00000367485.4_Silent_p.A1157A|PRG4_ENST00000367486.3_Silent_p.A1207A|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Silent_p.A1209A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1250					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.A1250A(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TTTCAACAGCTAAATATAAGA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	1											72	79	77					1																	186280685		2203	4300	6503	184547308	SO:0001819	synonymous_variant	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3750T>G	1.37:g.186280685T>G			184547308	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																				0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186280685	T	G	186280685	2	3	61	1	0	0	0	0	0	0	0	1	12515	1509	53	4		4	PRG4	1	186280685	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9927	186280685	62969936	899	8884										
TPR	7175	broad.mit.edu	37	chr1	186291462	186291462	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacttactgaattgcttcaGcaaatccatcagtacgatgt	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186291462G>T	ENST00000367478.4	-	45	6745	c.6449C>A	c.(6448-6450)gCt>gAt	p.A2150D		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2150					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.A2137D(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		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)		AATTGCTTCAGCAAATCCATC	0.328			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Missense(1)	large_intestine(1)	1											90	84	85					1																	186291462		1867	4105	5972	184558085	SO:0001583	missense	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.6449C>A	1.37:g.186291462G>T	ENSP00000356448:p.Ala2150Asp		184558085	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466337	0.43839	.	.	ENSG00000047410	ENST00000367478	T	0.25912	1.77	5.43	4.51	0.55191	.	0.056069	0.64402	D	0.000001	T	0.26666	0.0652	L	0.60455	1.87	0.47819	D	0.999525	B	0.02656	0.0	B	0.06405	0.002	T	0.06661	-1.0814	10	0.15952	T	0.53	.	16.2304	0.82332	0.0:0.1331:0.8669:0.0	.	2150	P12270	TPR_HUMAN	D	2150	ENSP00000356448:A2150D	ENSP00000356448:A2150D	A	-	2	0	TPR	184558085	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.913000	0.56394	1.268000	0.44264	0.650000	0.86243	GCT		0.328	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186291462	G	T	186291462	3	4	61	1	0	0	0	0	1	0	0	0	16456	971	34	2	670	2	TPR	1	186291462	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10777	186291462	62959159	900	8885										
TPR	7175	broad.mit.edu	37	chr1	186312586	186312586	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacctagtttcagcaatttCtttttctcgtcgtataaatc	4	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186312586C>A	ENST00000367478.4	-	27	3918	c.3622G>T	c.(3622-3624)Gaa>Taa	p.E1208*		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1208					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.E1209*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		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)		TCAGCAATTTCTTTTTCTCGT	0.348			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Nonsense(1)	large_intestine(1)	1											82	76	78					1																	186312586		1876	4103	5979	184579209	SO:0001587	stop_gained	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3622G>T	1.37:g.186312586C>A	ENSP00000356448:p.Glu1208*		184579209	Q15655|Q5SWY0|Q99968	Nonsense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	45	11.841169	0.99609	.	.	ENSG00000047410	ENST00000367478	.	.	.	5.05	5.05	0.67936	.	0.153299	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.4082	0.90542	0.0:1.0:0.0:0.0	.	.	.	.	X	1208	.	ENSP00000356448:E1208X	E	-	1	0	TPR	184579209	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.725000	0.68507	2.362000	0.80069	0.549000	0.68633	GAA		0.348	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186312586	C	A	186312586	4	1	61	1	0	0	0	0	0	1	0	0	16456	922	32	2	3569	2	TPR	1	186312586	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21124	186312586	62938035	901	8886										
TPR	7175	broad.mit.edu	37	chr1	186313687	186313687	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctctctcatacttattCtgagcttccacagctatttt	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186313687C>A	ENST00000367478.4	-	25	3533	c.3237G>T	c.(3235-3237)caG>caT	p.Q1079H		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1079					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.Q1080H(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		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)		CATACTTATTCTGAGCTTCCA	0.383			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Missense(1)	large_intestine(1)	1											112	103	106					1																	186313687		1896	4123	6019	184580310	SO:0001583	missense	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3237G>T	1.37:g.186313687C>A	ENSP00000356448:p.Gln1079His		184580310	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.588436	0.66105	.	.	ENSG00000047410	ENST00000367478	T	0.33438	1.41	5.42	4.51	0.55191	Tetratricopeptide, MLP1/MLP2-like (1);	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	M	0.73962	2.25	0.51482	D	0.999928	D	0.76494	0.999	D	0.87578	0.998	T	0.58679	-0.7594	10	0.54805	T	0.06	.	14.0065	0.64468	0.0:0.927:0.0:0.073	.	1079	P12270	TPR_HUMAN	H	1079	ENSP00000356448:Q1079H	ENSP00000356448:Q1079H	Q	-	3	2	TPR	184580310	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.709000	0.25734	1.295000	0.44724	0.555000	0.69702	CAG		0.383	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186313687	C	A	186313687	3	1	61	1	0	0	0	0	1	0	0	0	16456	912	32	2	3962	2	TPR	1	186313687	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1101	186313687	62936934	902	8887										
TPR	7175	broad.mit.edu	37	chr1	186324609	186324609	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcaaatctgtaacttgttCttgaagtttctcaagctgct	7	9	3	1	rs554995748		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186324609C>A	ENST00000367478.4	-	17	2400	c.2104G>T	c.(2104-2106)Gaa>Taa	p.E702*	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	702					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.E703*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		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)		GTAACTTGTTCTTGAAGTTTC	0.294			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Nonsense(1)	large_intestine(1)	1											134	122	125					1																	186324609		1799	4066	5865	184591232	SO:0001587	stop_gained	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2104G>T	1.37:g.186324609C>A	ENSP00000356448:p.Glu702*		184591232	Q15655|Q5SWY0|Q99968	Nonsense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	42	9.301186	0.99130	.	.	ENSG00000047410	ENST00000367478	.	.	.	5.11	4.2	0.49525	.	0.452778	0.24755	N	0.035867	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	13.8197	0.63313	0.0:0.9256:0.0:0.0744	.	.	.	.	X	702	.	ENSP00000356448:E702X	E	-	1	0	TPR	184591232	1.000000	0.71417	0.988000	0.46212	0.963000	0.63663	5.678000	0.68153	1.297000	0.44761	0.591000	0.81541	GAA		0.294	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186324609	C	A	186324609	4	1	61	1	0	0	0	0	0	1	0	0	16456	922	32	2	5127	2	TPR	1	186324609	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10922	186324609	62926012	903	8888										
TPR	7175	broad.mit.edu	37	chr1	186327736	186327736	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctctctcaagtacagatGattgcttgttggctttatca	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186327736G>T	ENST00000367478.4	-	13	1732	c.1436C>A	c.(1435-1437)tCa>tAa	p.S479*	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	479	Necessary for association to the NPC.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.S480*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		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)		AAGTACAGATGATTGCTTGTT	0.318			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Nonsense(1)	large_intestine(1)	1											203	185	191					1																	186327736		1890	4126	6016	184594359	SO:0001587	stop_gained	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1436C>A	1.37:g.186327736G>T	ENSP00000356448:p.Ser479*		184594359	Q15655|Q5SWY0|Q99968	Nonsense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	41	8.652887	0.98901	.	.	ENSG00000047410	ENST00000367478	.	.	.	5.24	5.24	0.73138	.	0.139770	0.49916	D	0.000134	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	18.8241	0.92109	0.0:0.0:1.0:0.0	.	.	.	.	X	479	.	ENSP00000356448:S479X	S	-	2	0	TPR	184594359	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.593000	0.82686	2.469000	0.83416	0.650000	0.86243	TCA		0.318	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186327736	G	T	186327736	4	4	61	1	0	0	0	0	0	1	0	0	16456	1294	45	2	5811	2	TPR	1	186327736	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3127	186327736	62922885	904	8889										
PTGS2	5743	broad.mit.edu	37	chr1	186645252	186645252	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagttctgggtcaaatttCagtttgaagtgatagccact	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186645252C>T	ENST00000367468.5	-	8	1171	c.1035G>A	c.(1033-1035)ctG>ctA	p.L345L	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	345					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.L345L(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GGTCAAATTTCAGTTTGAAGT	0.353																																																2	Substitution - coding silent(2)	large_intestine(2)	1											129	131	130					1																	186645252		2203	4300	6503	184911875	SO:0001819	synonymous_variant	5743			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1035G>A	1.37:g.186645252C>T			184911875	A8K802|Q16876	Silent	SNP	ENST00000367468.5	37	CCDS1371.1																																																																																				0.353	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		T	186645252	C	T	186645252	2	4	61	1	0	0	0	0	0	0	0	1	12791	813	29	3		3	PTGS2	1	186645252	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	317516	186645252	62605369	905	8890										
PTGS2	5743	broad.mit.edu	37	chr1	186646898	186646898	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgagccctggggatcaggGatgaactttcttcttagaag	12	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186646898G>T	ENST00000367468.5	-	5	658	c.522C>A	c.(520-522)atC>atA	p.I174I	PTGS2_ENST00000490885.2_5'UTR|RP5-973M2.2_ENST00000608917.1_lincRNA	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	174					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.I174I(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GGGGATCAGGGATGAACTTTC	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	1											104	104	104					1																	186646898		2203	4300	6503	184913521	SO:0001819	synonymous_variant	5743			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.522C>A	1.37:g.186646898G>T			184913521	A8K802|Q16876	Silent	SNP	ENST00000367468.5	37	CCDS1371.1																																																																																				0.413	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		T	186646898	G	T	186646898	2	4	61	1	0	0	0	0	0	0	0	1	12791	1164	41	2		2	PTGS2	1	186646898	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1646	186646898	62603723	906	8891										
PLA2G4A	5321	broad.mit.edu	37	chr1	186919851	186919851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtgatgatgaatcacacGaacccaaaggtgagtgagcc	11	9	1	5	rs200911298	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:186919851G>A	ENST00000367466.3	+	13	1479	c.1327G>A	c.(1327-1329)Gaa>Aaa	p.E443K	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.E383K	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	443	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.E443K(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TGAATCACACGAACCCAAAGG	0.393													G|||	2	0.000399361	8e-04	0	5008	,	,		15506	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	1											60	57	58					1																	186919851		2203	4300	6503	185186474	SO:0001583	missense	5321			M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.1327G>A	1.37:g.186919851G>A	ENSP00000356436:p.Glu443Lys		185186474	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	9.145	1.014773	0.19355	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.10960	2.82;2.82	6.07	6.07	0.98685	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.411866	0.30979	N	0.008488	T	0.04543	0.0124	N	0.02539	-0.55	0.28325	N	0.922033	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.26326	-1.0106	10	0.06625	T	0.88	-6.5997	15.8546	0.78968	0.0:0.1446:0.8554:0.0	.	383;443	E7EU42;P47712	.;PA24A_HUMAN	K	443;383	ENSP00000356436:E443K;ENSP00000406892:E383K	ENSP00000356436:E443K	E	+	1	0	PLA2G4A	185186474	0.844000	0.29557	0.967000	0.41034	0.489000	0.33432	2.286000	0.43496	2.885000	0.99019	0.655000	0.94253	GAA		0.393	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		A	186919851	G	A	186919851	3	1	61	1	0	0	0	0	1	0	0	0	12032	1059	37	1	1373	1	PLA2G4A	1	186919851	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272953	186919851	62330770	907	8892										
FAM5C	339479	broad.mit.edu	37	chr1	190203515	190203515	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacataccttgcaactgaatCttattctcaggactctgaac	5	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:190203515C>A	ENST00000367462.3	-	5	942	c.711G>T	c.(709-711)aaG>aaT	p.K237N	BRINP3_ENST00000534846.1_Missense_Mutation_p.K135N	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	237	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.K237N(1)									GCAACTGAATCTTATTCTCAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											111	102	105					1																	190203515		2203	4300	6503	188470138	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.711G>T	1.37:g.190203515C>A	ENSP00000356432:p.Lys237Asn		188470138	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795924	0.50208	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.25250	2.06;1.81	5.87	4.95	0.65309	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.47691	0.1459	M	0.69358	2.11	0.54753	D	0.999989	D;D	0.76494	0.999;0.998	D;D	0.78314	0.991;0.981	T	0.49476	-0.8936	10	0.87932	D	0	.	11.9139	0.52755	0.0:0.9145:0.0:0.0855	.	135;237	B7Z260;Q76B58	.;FAM5C_HUMAN	N	237;135	ENSP00000356432:K237N;ENSP00000438022:K135N	ENSP00000356432:K237N	K	-	3	2	FAM5C	188470138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.984000	0.40658	1.455000	0.47813	0.650000	0.86243	AAG		0.378	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190203515	C	A	190203515	3	1	61	1	0	0	0	0	1	0	0	0	5613	912	32	2	1605	2	FAM5C	1	190203515	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3283664	190203515	59047106	908	8893										
FAM5C	339479	broad.mit.edu	37	chr1	190250796	190250796	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagtcttatgttgcggaaGaattcaggggcaagaggcag	14	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:190250796G>T	ENST00000367462.3	-	3	552	c.321C>A	c.(319-321)ttC>ttA	p.F107L	RP11-547I7.1_ENST00000452178.1_RNA|BRINP3_ENST00000534846.1_Intron	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	107	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.F107L(1)									TGTTGCGGAAGAATTCAGGGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	84	85					1																	190250796		2203	4300	6503	188517419	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.321C>A	1.37:g.190250796G>T	ENSP00000356432:p.Phe107Leu		188517419	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.013540	0.93346	.	.	ENSG00000162670	ENST00000367462	D	0.89552	-2.53	5.88	4.96	0.65561	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.85682	D	0.000000	D	0.93019	0.7778	M	0.71581	2.175	0.80722	D	1	D	0.57257	0.979	D	0.71414	0.973	D	0.93010	0.6431	10	0.87932	D	0	.	12.0373	0.53433	0.0826:0.0:0.9174:0.0	.	107	Q76B58	FAM5C_HUMAN	L	107	ENSP00000356432:F107L	ENSP00000356432:F107L	F	-	3	2	FAM5C	188517419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.437000	0.52863	2.787000	0.95880	0.585000	0.79938	TTC		0.433	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190250796	G	T	190250796	3	4	61	1	0	0	0	0	1	0	0	0	5613	933	33	2	2003	2	FAM5C	1	190250796	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47281	190250796	58999825	909	8894										
RGS13	6003	broad.mit.edu	37	chr1	192628481	192628481	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcagattaacattgacaGttcgacaagagagactatca	7	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:192628481G>T	ENST00000391995.2	+	7	596	c.308G>T	c.(307-309)aGt>aTt	p.S103I	RGS13_ENST00000482095.1_3'UTR|RGS13_ENST00000543215.1_Missense_Mutation_p.S103I	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	103	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.S103I(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						AACATTGACAGTTCGACAAGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	85	92					1																	192628481		2203	4300	6503	190895104	SO:0001583	missense	6003			AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"Regulators of G-protein signaling"	9995	protein-coding gene	gene with protein product		607190	"regulator of G-protein signalling 13"			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.308G>T	1.37:g.192628481G>T	ENSP00000375853:p.Ser103Ile		190895104	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434448	0.25813	.	.	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.02103	4.45;4.45	5.69	3.82	0.43975	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.343203	0.37715	N	0.001978	T	0.12860	0.0312	M	0.86268	2.805	0.28424	N	0.917575	D	0.69078	0.997	D	0.69307	0.963	T	0.02398	-1.1165	10	0.54805	T	0.06	.	13.2925	0.60278	0.1468:0.0:0.8532:0.0	.	103	O14921	RGS13_HUMAN	I	103	ENSP00000375853:S103I;ENSP00000442837:S103I	ENSP00000375853:S103I	S	+	2	0	RGS13	190895104	0.580000	0.26733	0.858000	0.33744	0.499000	0.33736	1.004000	0.29822	0.359000	0.24239	-1.094000	0.02160	AGT		0.343	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927		T	192628481	G	T	192628481	3	4	61	1	0	0	0	0	1	0	0	0	13333	1029	36	2	322	2	RGS13	1	192628481	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2377685	192628481	56622140	910	8895										
RGS2	5997	broad.mit.edu	37	chr1	192780207	192780207	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacttcaaaaaaaccaaatCaccccaaaagctgtcctcaa	3	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:192780207C>A	ENST00000235382.5	+	4	402	c.371C>A	c.(370-372)tCa>tAa	p.S124*		NM_002923.3	NP_002914.1	P41220	RGS2_HUMAN	regulator of G-protein signaling 2	124	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				brown fat cell differentiation (GO:0050873)|cell cycle (GO:0007049)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phospholipase activity (GO:0010519)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of microtubule polymerization (GO:0031116)|regulation of adrenergic receptor signaling pathway (GO:0071877)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of translation (GO:0006417)|relaxation of cardiac muscle (GO:0055119)|relaxation of vascular smooth muscle (GO:0060087)|spermatogenesis (GO:0007283)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.S124*(1)		large_intestine(3)|lung(1)|urinary_tract(1)	5						AAAACCAAATCACCCCAAAAG	0.383																																					Pancreas(71;51 2183 4981)											1	Substitution - Nonsense(1)	large_intestine(1)	1											115	122	120					1																	192780207		2203	4300	6503	191046830	SO:0001587	stop_gained	5997			L13463	CCDS1377.1	1q31	2014-06-19	2014-06-19		ENSG00000116741	ENSG00000116741		"Regulators of G-protein signaling", "Endogenous ligands"	9998	protein-coding gene	gene with protein product		600861	"regulator of G-protein signalling 2, 24kD", "regulator of G-protein signalling 2, 24kDa", "regulator of G-protein signaling 2, 24kDa"	G0S8		8179820	Standard	NM_002923		Approved		uc001gsl.3	P41220	OTTHUMG00000035600	ENST00000235382.5:c.371C>A	1.37:g.192780207C>A	ENSP00000235382:p.Ser124*		191046830	Q6I9U5	Nonsense_Mutation	SNP	ENST00000235382.5	37	CCDS1377.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.462241	0.84425	.	.	ENSG00000116741	ENST00000235382	.	.	.	5.0	5.0	0.66597	.	0.057580	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.872	0.86042	0.0:1.0:0.0:0.0	.	.	.	.	X	124	.	ENSP00000235382:S124X	S	+	2	0	RGS2	191046830	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.026000	0.70873	2.311000	0.77944	0.563000	0.77884	TCA		0.383	RGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086396.1	NM_002923		A	192780207	C	A	192780207	4	1	61	1	0	0	0	0	0	1	0	0	13339	838	29	2	385	2	RGS2	1	192780207	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151726	192780207	56470414	911	8896										
TROVE2	6738	broad.mit.edu	37	chr1	193038240	193038240	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagaagcagatagccaattCtcaggatggatatgtatggc	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:193038240C>A	ENST00000367446.3	+	2	266	c.56C>A	c.(55-57)tCt>tAt	p.S19Y	TROVE2_ENST00000367441.1_Missense_Mutation_p.S19Y|TROVE2_ENST00000367444.3_Missense_Mutation_p.S19Y|TROVE2_ENST00000367443.1_Missense_Mutation_p.S19Y|TROVE2_ENST00000460715.2_Intron|TROVE2_ENST00000432079.1_Intron|TROVE2_ENST00000367445.3_Missense_Mutation_p.S19Y|TROVE2_ENST00000400968.2_Missense_Mutation_p.S19Y|TROVE2_ENST00000416058.2_5'UTR	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	19	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)	p.S19Y(1)		biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						ATAGCCAATTCTCAGGATGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	98	100					1																	193038240		1929	4131	6060	191304863	SO:0001583	missense	6738			BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.56C>A	1.37:g.193038240C>A	ENSP00000356416:p.Ser19Tyr		191304863	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	37	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441199	0.63067	.	.	ENSG00000116747	ENST00000400968;ENST00000415442;ENST00000506303;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T;T;T	0.15487	2.51;2.42;2.42;2.51;2.51;2.51;2.51;2.51	5.33	4.41	0.53225	TROVE (2);	0.061072	0.64402	D	0.000002	T	0.40448	0.1117	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.76494	0.994;0.994;0.999;0.997	P;P;D;D	0.67103	0.877;0.877;0.949;0.914	T	0.36672	-0.9738	10	0.62326	D	0.03	-10.4852	15.7145	0.77658	0.0:0.7424:0.2576:0.0	.	19;19;19;19	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	Y	19	ENSP00000383752:S19Y;ENSP00000401176:S19Y;ENSP00000425296:S19Y;ENSP00000356416:S19Y;ENSP00000356413:S19Y;ENSP00000356415:S19Y;ENSP00000356414:S19Y;ENSP00000356411:S19Y	ENSP00000356411:S19Y	S	+	2	0	TROVE2	191304863	1.000000	0.71417	0.980000	0.43619	0.984000	0.73092	4.752000	0.62176	1.233000	0.43693	0.557000	0.71058	TCT		0.378	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		A	193038240	C	A	193038240	3	1	61	1	0	0	0	0	1	0	0	0	16616	913	32	2	58	2	TROVE2	1	193038240	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258033	193038240	56212381	912	8897										
TROVE2	6738	broad.mit.edu	37	chr1	193046097	193046097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaaacttacaagacaggtCatggtctcagagggaaactg	11	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:193046097C>A	ENST00000367446.3	+	5	1213	c.1003C>A	c.(1003-1005)Cat>Aat	p.H335N	TROVE2_ENST00000367441.1_Missense_Mutation_p.H335N|TROVE2_ENST00000367444.3_Missense_Mutation_p.H335N|TROVE2_ENST00000367443.1_Missense_Mutation_p.H335N|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000432079.1_Missense_Mutation_p.H60N|TROVE2_ENST00000367445.3_Missense_Mutation_p.H335N|TROVE2_ENST00000400968.2_Missense_Mutation_p.H335N|TROVE2_ENST00000416058.2_Missense_Mutation_p.H60N	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	335	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)	p.H335N(1)		biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						CAAGACAGGTCATGGTCTCAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	81	83					1																	193046097		1883	4103	5986	191312720	SO:0001583	missense	6738			BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.1003C>A	1.37:g.193046097C>A	ENSP00000356416:p.His335Asn		191312720	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	37	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894290	0.72639	.	.	ENSG00000116747	ENST00000400968;ENST00000416058;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56;2.56;2.56	5.81	5.81	0.92471	TROVE (2);	0.047372	0.85682	D	0.000000	T	0.20618	0.0496	M	0.72894	2.215	0.54753	D	0.999983	B;B;P;P	0.37015	0.021;0.011;0.578;0.553	B;B;B;B	0.37144	0.014;0.014;0.174;0.242	T	0.04242	-1.0966	10	0.16420	T	0.52	-17.7185	20.1409	0.98058	0.0:1.0:0.0:0.0	.	335;335;335;335	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	N	335;60;335;335;335;335;335	ENSP00000383752:H335N;ENSP00000411421:H60N;ENSP00000356416:H335N;ENSP00000356413:H335N;ENSP00000356415:H335N;ENSP00000356414:H335N;ENSP00000356411:H335N	ENSP00000356411:H335N	H	+	1	0	TROVE2	191312720	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.550000	0.53691	2.768000	0.95171	0.644000	0.83932	CAT		0.333	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		A	193046097	C	A	193046097	3	1	61	1	0	0	0	0	1	0	0	0	16616	826	29	2	1017	2	TROVE2	1	193046097	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7857	193046097	56204524	913	8898										
GLRX2	51022	broad.mit.edu	37	chr1	193065766	193065766	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtataaacatcactgaaattCtttcctcttactttttttta	2	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:193065766C>A	ENST00000367439.3	-	4	532	c.484G>T	c.(484-486)Gaa>Taa	p.E162*	GLRX2_ENST00000367440.3_Nonsense_Mutation_p.E163*|GLRX2_ENST00000472197.1_5'Flank	NM_197962.2	NP_932066.1	Q9NS18	GLRX2_HUMAN	glutaredoxin 2	162					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|DNA protection (GO:0042262)|glutathione metabolic process (GO:0006749)|protein folding (GO:0006457)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|response to hydrogen peroxide (GO:0042542)|response to organic substance (GO:0010033)|response to redox state (GO:0051775)|response to temperature stimulus (GO:0009266)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|arsenate reductase (glutaredoxin) activity (GO:0008794)|electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|metal ion binding (GO:0046872)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)	p.E163*(1)		breast(1)|large_intestine(1)|lung(3)	5					Glutathione(DB00143)	CACTGAAATTCTTTCCTCTTA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											54	55	54					1																	193065766		2202	4300	6502	191332389	SO:0001587	stop_gained	51022			AF132495	CCDS1380.1, CCDS1381.1	1q31.2	2012-09-20			ENSG00000023572	ENSG00000023572			16065	protein-coding gene	gene with protein product	"bA101E13.1 (GRX2 glutaredoxin (thioltransferase) 2)"	606820				11297543	Standard	NM_016066		Approved	GRX2, bA101E13.1	uc001gsz.2	Q9NS18	OTTHUMG00000035677	ENST00000367439.3:c.484G>T	1.37:g.193065766C>A	ENSP00000356409:p.Glu162*		191332389	Q3LR69|Q7L1N7|Q96JC0|Q9Y3D4	Nonsense_Mutation	SNP	ENST00000367439.3	37	CCDS1381.1	.	.	.	.	.	.	.	.	.	.	C	35	5.581864	0.96578	.	.	ENSG00000023572	ENST00000367439;ENST00000367440	.	.	.	5.47	3.57	0.40892	.	2.537240	0.00961	N	0.003116	.	.	.	.	.	.	0.25192	N	0.990124	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-2.4256	5.2862	0.15702	0.1559:0.6296:0.1366:0.0778	.	.	.	.	X	162;163	.	ENSP00000356409:E162X	E	-	1	0	GLRX2	191332389	0.930000	0.31532	0.068000	0.19968	0.898000	0.52572	1.599000	0.36751	0.651000	0.30788	0.561000	0.74099	GAA		0.323	GLRX2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086699.1	NM_016066		A	193065766	C	A	193065766	4	1	61	1	0	0	0	0	0	1	0	0	6480	922	32	2	14	2	GLRX2	1	193065766	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19669	193065766	56184855	914	8899										
KCNT2	343450	broad.mit.edu	37	chr1	196309545	196309545	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctggacacattgctttttCtctgctggtcttggttttta	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196309545C>A	ENST00000294725.9	-	16	2624	c.1709G>T	c.(1708-1710)aGa>aTa	p.R570I	KCNT2_ENST00000609185.1_Missense_Mutation_p.R520I|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Missense_Mutation_p.R520I|KCNT2_ENST00000367433.5_Missense_Mutation_p.R570I|KCNT2_ENST00000451324.2_Missense_Mutation_p.R181I			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	570					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.R570I(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						ATTGCTTTTTCTCTGCTGGTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	111	114					1																	196309545		2203	4300	6503	194576168	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1709G>T	1.37:g.196309545C>A	ENSP00000294725:p.Arg570Ile		194576168	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.253651	0.39797	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000535608;ENST00000451324;ENST00000294725	T;T;T;T	0.31510	2.22;2.24;1.49;2.47	5.84	2.85	0.33270	.	0.162631	0.43747	D	0.000523	T	0.28366	0.0701	L	0.54323	1.7	0.40959	D	0.984605	B;B;B;B;B	0.34372	0.158;0.012;0.059;0.451;0.158	B;B;B;B;B	0.38428	0.048;0.041;0.15;0.273;0.048	T	0.04153	-1.0973	10	0.38643	T	0.18	-11.6251	6.8685	0.24106	0.0:0.596:0.0:0.404	.	570;552;570;520;570	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	I	570;520;391;181;570	ENSP00000356403:R570I;ENSP00000356401:R520I;ENSP00000405474:R181I;ENSP00000294725:R570I	ENSP00000294725:R570I	R	-	2	0	KCNT2	194576168	0.906000	0.30813	0.999000	0.59377	0.819000	0.46315	1.163000	0.31798	0.293000	0.22520	-0.143000	0.13931	AGA		0.343	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		A	196309545	C	A	196309545	3	1	61	1	0	0	0	0	1	0	0	0	8113	913	32	2	1750	2	KCNT2	1	196309545	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3243779	196309545	52941076	915	8900										
CFH	3075	broad.mit.edu	37	chr1	196648807	196648807	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcctatatctcagaagaTtatttataaggagaatgaac	6	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196648807T>G	ENST00000359637.2	+	5	544	c.482T>G	c.(481-483)aTt>aGt	p.I161S	CFH_ENST00000367429.4_Missense_Mutation_p.I225S|CFH_ENST00000439155.2_Missense_Mutation_p.I225S			P08603	CFAH_HUMAN	complement factor H	225	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.I225S(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TCTCAGAAGATTATTTATAAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	61	60					1																	196648807		2203	4298	6501	194915430	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.482T>G	1.37:g.196648807T>G	ENSP00000352658:p.Ile161Ser		194915430	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000359637.2	37		.	.	.	.	.	.	.	.	.	.	T	5.020	0.189393	0.09547	.	.	ENSG00000000971	ENST00000367429;ENST00000439155;ENST00000391986;ENST00000359637	T;T;T	0.62639	0.01;0.01;0.01	5.99	-12.0	0.00017	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.28433	0.0703	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.16396	0.001;0.017;0.003;0.004	B;B;B;B	0.19391	0.001;0.025;0.0;0.001	T	0.15636	-1.0430	9	0.08179	T	0.78	.	10.5628	0.45154	0.1079:0.6182:0.1972:0.0767	.	161;225;225;225	Q5TFM2;P08603-2;P08603;F8WDX4	.;.;CFAH_HUMAN;.	S	225;225;225;161	ENSP00000356399:I225S;ENSP00000402656:I225S;ENSP00000352658:I161S	ENSP00000352658:I161S	I	+	2	0	CFH	194915430	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-3.536000	0.00438	-2.827000	0.00341	-1.560000	0.00886	ATT		0.323	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		G	196648807	T	G	196648807	3	3	61	1	0	0	0	0	1	0	0	0	3289	1493	52	4	696	4	CFH	1	196648807	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	339262	196648807	52601814	916	8901										
CFH	3075	broad.mit.edu	37	chr1	196659244	196659244	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atataatcaaaatcatggaaGaaagtttgtacagggtaaat	8	3	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196659244G>T	ENST00000359637.2	+	8	1081	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	CFH_ENST00000367429.4_Missense_Mutation_p.R404I|CFH_ENST00000439155.2_Missense_Mutation_p.R404I			P08603	CFAH_HUMAN	complement factor H	404	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.R404I(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AATCATGGAAGAAAGTTTGTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	59	59					1																	196659244		2203	4300	6503	194925867	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.1019G>T	1.37:g.196659244G>T	ENSP00000352658:p.Arg340Ile		194925867	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000359637.2	37		.	.	.	.	.	.	.	.	.	.	G	14.41	2.528103	0.44969	.	.	ENSG00000000971	ENST00000367429;ENST00000439155;ENST00000391986;ENST00000359637	T;T;T	0.64991	-0.13;-0.13;-0.13	4.69	-9.38	0.00623	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.61751	0.2372	L	0.49513	1.565	0.09310	N	1	D;P;P;P	0.65815	0.995;0.945;0.931;0.702	D;P;P;B	0.65233	0.933;0.674;0.655;0.437	T	0.64609	-0.6367	9	0.37606	T	0.19	.	4.9411	0.13965	0.55:0.2385:0.1313:0.0802	.	340;404;404;404	Q5TFM2;P08603-2;P08603;F8WDX4	.;.;CFAH_HUMAN;.	I	404;404;404;340	ENSP00000356399:R404I;ENSP00000402656:R404I;ENSP00000352658:R340I	ENSP00000352658:R340I	R	+	2	0	CFH	194925867	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.743000	0.00797	-3.522000	0.00147	-0.136000	0.14681	AGA		0.353	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		T	196659244	G	T	196659244	3	4	61	1	0	0	0	0	1	0	0	0	3289	942	33	2	1245	2	CFH	1	196659244	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10437	196659244	52591377	917	8902										
CFH	3075	broad.mit.edu	37	chr1	196695703	196695703	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtggtggaatattattgCaatcctagatttctaatgaa	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196695703C>T	ENST00000367429.4	+	13	2217	c.1977C>T	c.(1975-1977)tgC>tgT	p.C659C		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	659	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.C659C(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AATATTATTGCAATCCTAGAT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											101	106	104					1																	196695703		2203	4298	6501	194962326	SO:0001819	synonymous_variant	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.1977C>T	1.37:g.196695703C>T			194962326	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																				0.348	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196695703	C	T	196695703	2	4	61	1	0	0	0	0	0	0	0	1	3289	718	25	3		3	CFH	1	196695703	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36459	196695703	52554918	918	8903										
CFH	3075	broad.mit.edu	37	chr1	196709779	196709779	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatctccacctgagatttCtcatggtgttgtagctcaca	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196709779C>A	ENST00000367429.4	+	18	3053	c.2813C>A	c.(2812-2814)tCt>tAt	p.S938Y		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	938	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.S938Y(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						CCTGAGATTTCTCATGGTGTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	117	118					1																	196709779		2203	4300	6503	194976402	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2813C>A	1.37:g.196709779C>A	ENSP00000356399:p.Ser938Tyr		194976402	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	16.23	3.065212	0.55432	.	.	ENSG00000000971	ENST00000367429	T	0.66815	-0.23	6.16	-6.7	0.01766	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.47377	0.1442	N	0.25380	0.74	0.09310	N	1	B	0.18741	0.03	B	0.17722	0.019	T	0.44726	-0.9309	9	0.54805	T	0.06	.	9.0334	0.36273	0.6733:0.1792:0.0863:0.0613	.	938	P08603	CFAH_HUMAN	Y	938	ENSP00000356399:S938Y	ENSP00000356399:S938Y	S	+	2	0	CFH	194976402	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.042000	0.01414	-0.665000	0.05317	-0.271000	0.10264	TCT		0.338	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		A	196709779	C	A	196709779	3	1	61	1	0	0	0	0	1	0	0	0	3289	913	32	2	2901	2	CFH	1	196709779	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14076	196709779	52540842	919	8904										
CFH	3075	broad.mit.edu	37	chr1	196714960	196714960	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttagattctacaggaaaAtgtgggccccctccacctat	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196714960A>T	ENST00000367429.4	+	21	3564	c.3324A>T	c.(3322-3324)aaA>aaT	p.K1108N		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1108	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.K1108N(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						CTACAGGAAAATGTGGGCCCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											160	152	155					1																	196714960		2203	4300	6503	194981583	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3324A>T	1.37:g.196714960A>T	ENSP00000356399:p.Lys1108Asn		194981583	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	14.19	2.462827	0.43736	.	.	ENSG00000000971	ENST00000367429	T	0.32515	1.45	4.77	0.958	0.19619	Complement control module (1);Sushi/SCR/CCP (1);	.	.	.	.	T	0.22742	0.0549	M	0.72118	2.19	0.80722	D	1	P	0.38195	0.622	B	0.29598	0.104	T	0.08911	-1.0699	9	0.16896	T	0.51	.	6.1711	0.20418	0.5286:0.3184:0.0:0.153	.	1108	P08603	CFAH_HUMAN	N	1108	ENSP00000356399:K1108N	ENSP00000356399:K1108N	K	+	3	2	CFH	194981583	1.000000	0.71417	0.980000	0.43619	0.358000	0.29455	1.173000	0.31920	-0.021000	0.14009	0.449000	0.29647	AAA		0.403	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196714960	A	T	196714960	3	4	61	1	0	0	0	0	1	0	0	0	3289	98	4	5	3424	5	CFH	1	196714960	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5181	196714960	52535661	920	8905										
CFH	3075	broad.mit.edu	37	chr1	196716272	196716272	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatcccgagaaattatggaAaattataacatagcattaag	6	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196716272A>C	ENST00000367429.4	+	22	3765	c.3525A>C	c.(3523-3525)gaA>gaC	p.E1175D		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1175	Sushi 20. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.E1175D(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AAATTATGGAAAATTATAACA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	105	104					1																	196716272		2203	4298	6501	194982895	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3525A>C	1.37:g.196716272A>C	ENSP00000356399:p.Glu1175Asp		194982895	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	13.15	2.150969	0.38021	.	.	ENSG00000000971	ENST00000367429	D	0.83914	-1.78	4.48	-0.989	0.10242	Complement control module (1);Sushi/SCR/CCP (1);	.	.	.	.	T	0.75317	0.3833	L	0.54323	1.7	0.09310	N	1	P	0.38148	0.62	B	0.44108	0.441	T	0.61227	-0.7105	9	0.16420	T	0.52	.	0.2339	0.00184	0.2874:0.1502:0.1897:0.3727	.	1175	P08603	CFAH_HUMAN	D	1175	ENSP00000356399:E1175D	ENSP00000356399:E1175D	E	+	3	2	CFH	194982895	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.139000	0.03213	-0.044000	0.13491	0.454000	0.30748	GAA		0.333	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		C	196716272	A	C	196716272	3	2	61	1	0	0	0	0	1	0	0	0	3289	11	1	4	3629	4	CFH	1	196716272	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1312	196716272	52534349	921	8906										
CFH	3075	broad.mit.edu	37	chr1	196716339	196716339	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagaacaggtgaatcagttGaatttgtgtgtaaacgggga	14	4	1	3	rs121913063		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196716339G>T	ENST00000367429.4	+	22	3832	c.3592G>T	c.(3592-3594)Gaa>Taa	p.E1198*		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1198	Sushi 20. {ECO:0000255|PROSITE- ProRule:PRU00302}.		E -> A (in AHUS1). {ECO:0000269|PubMed:14583443}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.E1198*(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TGAATCAGTTGAATTTGTGTG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	1	GRCh37	CM060895|CM070672	CFH	M	rs121913063						249	223	232					1																	196716339		2203	4300	6503	194982962	SO:0001587	stop_gained	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3592G>T	1.37:g.196716339G>T	ENSP00000356399:p.Glu1198*		194982962	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Nonsense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	37	6.295108	0.97449	.	.	ENSG00000000971	ENST00000367429	.	.	.	4.35	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	11.7776	0.51995	0.0:0.1778:0.8222:0.0	.	.	.	.	X	1198	.	ENSP00000356399:E1198X	E	+	1	0	CFH	194982962	0.999000	0.42202	0.974000	0.42286	0.007000	0.05969	3.600000	0.54052	1.196000	0.43129	-0.485000	0.04761	GAA		0.398	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196716339	G	T	196716339	4	4	61	1	0	0	0	0	0	1	0	0	3289	1291	45	2	3696	2	CFH	1	196716339	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67	196716339	52534282	922	8907										
CFHR4	3080	broad.mit.edu	37	chr1	196857310	196857310	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatcaatgtcattctgacCttgtgggtttcctgtgctaa	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196857310C>T	ENST00000367421.3	+	2	135				CFHR4_ENST00000608469.1_Intron|CFHR4_ENST00000367416.2_Silent_p.T10T|CFHR4_ENST00000367418.2_Silent_p.T10T|CFHR4_ENST00000251424.4_Silent_p.T10T			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)		p.T10T(2)		large_intestine(2)|ovary(1)|skin(3)	6						TCATTCTGACCTTGTGGGTTT	0.348																																																2	Substitution - coding silent(2)	large_intestine(2)	1											147	141	143					1																	196857310		2201	4299	6500	195123933	SO:0001627	intron_variant	10877			X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"Complement system"	4890	protein-coding gene	gene with protein product		600889	"H factor (complement)-like 3"	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367421.3:c.59-61275C>T	1.37:g.196857310C>T			195123933	Q14310|Q5T9T1	Silent	SNP	ENST00000367421.3	37																																																																																					0.348	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666		T	196857310	C	T	196857310	1	4	61	0	1	0	0	0	0	0	0	0	3293	668	24	3		3	CFHR4	1	196857310	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140971	196857310	52393311	923	8908										
CFHR2	3080	broad.mit.edu	37	chr1	196927075	196927075	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaatggagacattacttCattcctgttgtcagtatatg	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:196927075C>T	ENST00000367415.5	+	4	585	c.485C>T	c.(484-486)tCa>tTa	p.S162L	CFHR2_ENST00000367421.3_Missense_Mutation_p.S162L|CFHR2_ENST00000496448.1_3'UTR|CFHR2_ENST00000476712.2_Missense_Mutation_p.S146L	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	162	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)		p.S162L(1)		large_intestine(2)|ovary(1)|skin(3)	6						GACATTACTTCATTCCTGTTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											156	142	147					1																	196927075		2203	4300	6503	195193698	SO:0001583	missense	3080			X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"Complement system"	4890	protein-coding gene	gene with protein product		600889	"H factor (complement)-like 3"	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.485C>T	1.37:g.196927075C>T	ENSP00000356385:p.Ser162Leu		195193698	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	.	.	.	.	.	.	.	.	.	.	.	14.22	2.470180	0.43839	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	T;T	0.46063	0.88;0.88	4.25	4.25	0.50352	Complement control module (2);Sushi/SCR/CCP (3);	0.320980	0.17426	N	0.174644	T	0.43456	0.1248	M	0.63428	1.95	0.09310	N	1	P	0.44241	0.829	B	0.41466	0.358	T	0.39099	-0.9630	10	0.42905	T	0.14	.	14.1516	0.65389	0.0:1.0:0.0:0.0	.	162	P36980	FHR2_HUMAN	L	162	ENSP00000356391:S162L;ENSP00000356385:S162L	ENSP00000356385:S162L	S	+	2	0	CFHR2	195193698	0.007000	0.16637	0.013000	0.15412	0.175000	0.22909	1.790000	0.38734	1.881000	0.54492	0.514000	0.50259	TCA		0.378	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666		T	196927075	C	T	196927075	3	4	61	1	0	0	0	0	1	0	0	0	3291	838	29	3	499	3	CFHR2	1	196927075	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69765	196927075	52323546	924	8909										
F13B	2165	broad.mit.edu	37	chr1	197029565	197029565	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatcagatccacttagatAataattttcatgacagaaaa	4	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197029565A>C	ENST00000367412.1	-	5	779	c.736T>G	c.(736-738)Tat>Gat	p.Y246D		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	246	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)		p.Y246D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						CCACTTAGATAATAATTTTCA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	77	75					1																	197029565		2203	4294	6497	195296188	SO:0001583	missense	2165			M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.736T>G	1.37:g.197029565A>C	ENSP00000356382:p.Tyr246Asp		195296188	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960896	0.53400	.	.	ENSG00000143278	ENST00000367412	T	0.64803	-0.12	5.76	-2.22	0.06952	Complement control module (2);Sushi/SCR/CCP (3);	0.608641	0.12564	N	0.457931	T	0.47930	0.1472	N	0.17764	0.52	0.27429	N	0.954051	P	0.37594	0.601	P	0.45558	0.485	T	0.47381	-0.9122	10	0.40728	T	0.16	.	6.8894	0.24220	0.5123:0.0:0.3775:0.1102	.	246	P05160	F13B_HUMAN	D	246	ENSP00000356382:Y246D	ENSP00000356382:Y246D	Y	-	1	0	F13B	195296188	0.209000	0.23505	0.908000	0.35775	0.980000	0.70556	0.137000	0.15995	-0.579000	0.05952	-0.297000	0.09499	TAT		0.313	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		C	197029565	A	C	197029565	3	2	61	1	0	0	0	0	1	0	0	0	5354	362	13	4	1281	4	F13B	1	197029565	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	102490	197029565	52221056	925	8910										
ASPM	259266	broad.mit.edu	37	chr1	197070153	197070153	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaagcagcctgaatagttCgtacagatttctgaactgct	8	8	1	3	rs202193200	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197070153C>T	ENST00000367409.4	-	18	8484	c.8228G>A	c.(8227-8229)cGa>cAa	p.R2743Q	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2743	IQ 31. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.R2743Q(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CTGAATAGTTCGTACAGATTT	0.333													C|||	4	0.000798722	0.0015	0	5008	,	,		19139	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											39	42	41					1																	197070153		2201	4296	6497	195336776	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8228G>A	1.37:g.197070153C>T	ENSP00000356379:p.Arg2743Gln		195336776	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.98	2.698761	0.48307	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.56444	0.46	4.5	-4.82	0.03171	.	1.293920	0.05622	N	0.580062	T	0.50103	0.1596	N	0.25890	0.77	0.09310	N	1	D;D	0.71674	0.998;0.981	D;P	0.70227	0.968;0.797	T	0.49615	-0.8921	10	0.37606	T	0.19	.	2.8073	0.05431	0.4442:0.1838:0.2834:0.0886	.	729;2743	E7EQ84;Q8IZT6	.;ASPM_HUMAN	Q	2743;729	ENSP00000356379:R2743Q	ENSP00000356376:R729Q	R	-	2	0	ASPM	195336776	0.000000	0.05858	0.000000	0.03702	0.826000	0.46750	0.321000	0.19558	-0.507000	0.06549	0.462000	0.41574	CGA		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197070153	C	T	197070153	3	4	61	1	0	0	0	0	1	0	0	0	1057	884	31	1	2249	1	ASPM	1	197070153	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40588	197070153	52180468	926	8911										
ASPM	259266	broad.mit.edu	37	chr1	197094013	197094013	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatacctgaaaagcaaacGctattttccaaagcaacctg	5	10	0	1	rs550484483		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197094013G>A	ENST00000367409.4	-	12	3411	c.3155C>T	c.(3154-3156)gCg>gTg	p.A1052V	ASPM_ENST00000367408.1_Missense_Mutation_p.A302V|ASPM_ENST00000294732.7_Missense_Mutation_p.A1052V	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1052	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.A1052V(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AAAAGCAAACGCTATTTTCCA	0.279													G|||	1	0.000199681	0	0	5008	,	,		14705	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											143	153	149					1																	197094013		2203	4299	6502	195360636	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3155C>T	1.37:g.197094013G>A	ENSP00000356379:p.Ala1052Val		195360636	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689073	0.29962	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.60299	0.2;0.2;0.2	5.54	2.63	0.31362	Calponin homology domain (4);	0.261022	0.32802	N	0.005637	T	0.22205	0.0535	N	0.02142	-0.665	0.29596	N	0.848031	B;B	0.18610	0.029;0.017	B;B	0.12837	0.008;0.006	T	0.31861	-0.9928	10	0.02654	T	1	.	7.3367	0.26613	0.4253:0.0:0.5747:0.0	.	1052;1052	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	V	1052;1052;302	ENSP00000356379:A1052V;ENSP00000294732:A1052V;ENSP00000356378:A302V	ENSP00000294732:A1052V	A	-	2	0	ASPM	195360636	0.991000	0.36638	0.539000	0.28077	0.867000	0.49689	1.580000	0.36547	0.826000	0.34661	0.557000	0.71058	GCG		0.279	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197094013	G	A	197094013	3	1	61	1	0	0	0	0	1	0	0	0	1057	1087	38	1	7346	1	ASPM	1	197094013	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23860	197094013	52156608	927	8912										
ASPM	259266	broad.mit.edu	37	chr1	197111714	197111714	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttacctcgtttttataactCttagatttacttaatattgg	5	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197111714C>A	ENST00000367409.4	-	3	1924	c.1668G>T	c.(1666-1668)aaG>aaT	p.K556N	ASPM_ENST00000294732.7_Missense_Mutation_p.K556N	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	556					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.K556N(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTTTATAACTCTTAGATTTAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											92	98	96					1																	197111714		2203	4299	6502	195378337	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1668G>T	1.37:g.197111714C>A	ENSP00000356379:p.Lys556Asn		195378337	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.209627	0.58343	.	.	ENSG00000066279	ENST00000367409;ENST00000294732	T;T	0.59502	0.26;1.54	5.56	-1.48	0.08745	.	0.819993	0.11184	N	0.590692	T	0.46092	0.1375	M	0.63843	1.955	0.09310	N	1	B;P	0.34462	0.013;0.454	B;B	0.29663	0.007;0.105	T	0.29731	-1.0002	10	0.33940	T	0.23	.	6.682	0.23125	0.0:0.4985:0.2343:0.2672	.	556;556	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	N	556	ENSP00000356379:K556N;ENSP00000294732:K556N	ENSP00000294732:K556N	K	-	3	2	ASPM	195378337	0.000000	0.05858	0.000000	0.03702	0.896000	0.52359	-0.763000	0.04740	-0.121000	0.11787	-0.233000	0.12211	AAG		0.348	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197111714	C	A	197111714	3	1	61	1	0	0	0	0	1	0	0	0	1057	912	32	2	8869	2	ASPM	1	197111714	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17701	197111714	52138907	928	8913										
ZBTB41	360023	broad.mit.edu	37	chr1	197150125	197150125	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataattcttcacctttctcGtactgattttccacagataa	4	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197150125G>A	ENST00000367405.4	-	5	1737	c.1669C>T	c.(1669-1671)Cga>Tga	p.R557*	ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	557					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R557*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						CACCTTTCTCGTACTGATTTT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											174	157	163					1																	197150125		2203	4300	6503	195416748	SO:0001587	stop_gained	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.1669C>T	1.37:g.197150125G>A	ENSP00000356375:p.Arg557*		195416748	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Nonsense_Mutation	SNP	ENST00000367405.4	37	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	G	38	6.678037	0.97755	.	.	ENSG00000177888	ENST00000367405	.	.	.	5.66	2.12	0.27331	.	0.000000	0.37261	N	0.002179	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8055	0.63227	0.0:0.0:0.2894:0.7106	.	.	.	.	X	557	.	ENSP00000356375:R557X	R	-	1	2	ZBTB41	195416748	0.993000	0.37304	0.999000	0.59377	0.996000	0.88848	2.286000	0.43496	0.769000	0.33313	0.585000	0.79938	CGA		0.343	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		A	197150125	G	A	197150125	4	1	61	1	0	0	0	0	0	1	0	0	17582	1153	40	1	1084	1	ZBTB41	1	197150125	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38411	197150125	52100496	929	8914										
ZBTB41	360023	broad.mit.edu	37	chr1	197169589	197169589	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagatttgaagtaaccttTctcctcttcttcattgcagt	5	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197169589T>C	ENST00000367405.4	-	1	83	c.15A>G	c.(13-15)agA>agG	p.R5R	ZBTB41_ENST00000467322.1_5'UTR|CRB1_ENST00000535699.1_5'Flank	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	5					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R5R(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						AAGTAACCTTTCTCCTCTTCT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	1											62	64	63					1																	197169589		2203	4300	6503	195436212	SO:0001819	synonymous_variant	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.15A>G	1.37:g.197169589T>C			195436212	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Silent	SNP	ENST00000367405.4	37	CCDS30960.1																																																																																				0.358	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		C	197169589	T	C	197169589	2	2	61	1	0	0	0	0	0	0	0	1	17582	1780	62	4		4	ZBTB41	1	197169589	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19464	197169589	52081032	930	8915										
CRB1	23418	broad.mit.edu	37	chr1	197404377	197404377	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagcaatttctcaaaatCtctaccaattcagtggtcac	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197404377C>A	ENST00000367400.3	+	9	3519	c.3384C>A	c.(3382-3384)atC>atA	p.I1128I	CRB1_ENST00000367399.2_Silent_p.I1016I|CRB1_ENST00000544212.1_Silent_p.I609I|CRB1_ENST00000535699.1_Silent_p.I1104I|CRB1_ENST00000367397.1_Silent_p.I509I|RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000538660.1_Intron	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1128	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I1128I(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TTCTCAAAATCTCTACCAATT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	1											87	85	85					1																	197404377		2203	4300	6503	195671000	SO:0001819	synonymous_variant	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3384C>A	1.37:g.197404377C>A			195671000	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	37	CCDS1390.1																																																																																				0.388	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197404377	C	A	197404377	2	1	61	1	0	0	0	0	0	0	0	1	3854	903	32	2		2	CRB1	1	197404377	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	234788	197404377	51846244	931	8916										
DENND1B	163486	broad.mit.edu	37	chr1	197480859	197480859	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaaaaaatctactaaccGtaggtttgtaatcaatgtca	5	6	3	0	rs200671323		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197480859G>A								CRB1 (33274 upstream) : DENND1B (40525 downstream)														p.T169M(1)									TCTACTAACCGTAGGTTTGTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	MET/THR	0,4406		0,0,2203	48	48	48		1814	5.7	1	1		48	2,8590	2.2+/-6.3	0,2,4294	no	missense-near-splice	DENND1B	NM_001195215.1	81	0,2,6497	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	605/776	197480859	2,12996	2203	4296	6499	195747482	SO:0001628	intergenic_variant	163486																															1.37:g.197480859G>A			195747482		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	G	18.37	3.608480	0.66558	0.0	2.33E-4	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.33438	1.41	5.7	5.7	0.88788	.	0.510093	0.17058	U	0.188674	T	0.37517	0.1006	L	0.58101	1.795	0.80722	D	1	D	0.56968	0.978	P	0.51833	0.681	T	0.04065	-1.0980	10	0.23302	T	0.38	.	8.9392	0.35720	0.0735:0.0:0.7772:0.1492	.	605	Q6P3S1-5	.	M	245;605;585	ENSP00000375839:T245M	ENSP00000375839:T245M	T	-	2	0	DENND1B	195747482	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.207000	0.32333	2.690000	0.91761	0.650000	0.86243	ACG	0	0.363									A	197480859	G	A	197480859	1	1	61	0	1	0	0	0	0	0	0	0	4438	1159	40	1		1	DENND1B	1	197480859	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76482	197480859	51769762	932	8917										
LHX9	56956	broad.mit.edu	37	chr1	197887035	197887035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcacgggatctccggaGgccacatccaaggcatcatg	10	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197887035G>T	ENST00000367387.4	+	1	507	c.82G>T	c.(82-84)Ggc>Tgc	p.G28C	LHX9_ENST00000337020.2_Missense_Mutation_p.G28C|LHX9_ENST00000606127.1_3'UTR|LHX9_ENST00000561173.1_Missense_Mutation_p.G34C|LHX9_ENST00000367390.3_Missense_Mutation_p.G19C|LHX9_ENST00000367391.1_Missense_Mutation_p.G19C	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	28					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.G28C(1)		endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						GATCTCCGGAGGCCACATCCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	99	99					1																	197887035		2203	4300	6503	196153658	SO:0001583	missense	56956			AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.82G>T	1.37:g.197887035G>T	ENSP00000356357:p.Gly28Cys		196153658	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	ENST00000367387.4	37	CCDS1393.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677982	0.88445	.	.	ENSG00000143355	ENST00000367391;ENST00000367390;ENST00000367388;ENST00000337020;ENST00000367387	T;D;T;D	0.88586	0.59;-2.37;0.48;-2.4	5.06	5.06	0.68205	.	0.051108	0.85682	D	0.000000	D	0.90810	0.7114	L	0.46157	1.445	0.52099	D	0.999949	P;P;D	0.54047	0.939;0.922;0.964	P;P;P	0.55345	0.599;0.774;0.774	D	0.91457	0.5186	10	0.59425	D	0.04	.	17.7666	0.88480	0.0:0.0:1.0:0.0	.	28;19;19	Q9NQ69;Q9NQ69-3;Q9NQ69-2	LHX9_HUMAN;.;.	C	19;19;71;28;28	ENSP00000356361:G19C;ENSP00000356360:G19C;ENSP00000337969:G28C;ENSP00000356357:G28C	ENSP00000337969:G28C	G	+	1	0	LHX9	196153658	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.128000	0.94424	2.506000	0.84524	0.655000	0.94253	GGC		0.612	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		T	197887035	G	T	197887035	3	4	61	1	0	0	0	0	1	0	0	0	8800	1000	35	2	116	2	LHX9	1	197887035	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	406176	197887035	51363586	933	8918										
LHX9	56956	broad.mit.edu	37	chr1	197890683	197890683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctggcggccaagagcggCggcctggccctgccttactt	15	14	0	1	rs375826024		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:197890683C>T	ENST00000367387.4	+	3	1052	c.627C>T	c.(625-627)ggC>ggT	p.G209G	LHX9_ENST00000337020.2_Silent_p.G209G|LHX9_ENST00000561173.1_Silent_p.G215G|LHX9_ENST00000367390.3_Silent_p.G200G|LHX9_ENST00000367391.1_Silent_p.G200G	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	209					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.G209G(2)|p.G200G(2)		endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CCAAGAGCGGCGGCCTGGCCC	0.637																																																4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	1											33	33	33					1																	197890683		2203	4300	6503	196157306	SO:0001819	synonymous_variant	56956			AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.627C>T	1.37:g.197890683C>T			196157306	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	ENST00000367387.4	37	CCDS1393.1																																																																																				0.637	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		T	197890683	C	T	197890683	2	4	61	1	0	0	0	0	0	0	0	1	8800	755	27	1		1	LHX9	1	197890683	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3648	197890683	51359938	934	8919										
NEK7	140609	broad.mit.edu	37	chr1	198248097	198248097	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacagatataaaaccagcTaatgtgttcattacagccac	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:198248097T>C	ENST00000367385.4	+	7	837	c.495T>C	c.(493-495)gcT>gcC	p.A165A	NEK7_ENST00000538004.1_Silent_p.A165A	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A165A(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						TAAAACCAGCTAATGTGTTCA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	1											79	80	80					1																	198248097		2203	4300	6503	196514720	SO:0001819	synonymous_variant	140609			AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.495T>C	1.37:g.198248097T>C			196514720	A6NGT8	Silent	SNP	ENST00000367385.4	37	CCDS1394.1																																																																																				0.368	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		C	198248097	T	C	198248097	2	2	61	1	0	0	0	0	0	0	0	1	10360	1509	53	4		4	NEK7	1	198248097	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	357414	198248097	51002524	935	8920										
PTPRC	5788	broad.mit.edu	37	chr1	198668734	198668734	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaccttcccacgcacgcaGactcgcagacgccctctgct	7	20	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:198668734G>T	ENST00000367376.2	+	5	505	c.334G>T	c.(334-336)Gac>Tac	p.D112Y	PTPRC_ENST00000594404.1_Intron|PTPRC_ENST00000391970.3_3'UTR|PTPRC_ENST00000352140.3_Missense_Mutation_p.D112Y|PTPRC_ENST00000442510.2_Missense_Mutation_p.D114Y|PTPRC_ENST00000348564.6_Intron	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	112					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D112Y(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CACGCACGCAGACTCGCAGAC	0.527											OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											116	119	118					1																	198668734		2203	4300	6503	196935357	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.334G>T	1.37:g.198668734G>T	ENSP00000356346:p.Asp112Tyr	2100	196935357	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	15.34	2.804346	0.50315	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000271610;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000418674	T	0.03152	4.03	5.21	2.8	0.32819	.	0.747332	0.11864	N	0.522044	T	0.11750	0.0286	L	0.59436	1.845	0.09310	N	0.999992	D;D;D;D;D;D	0.71674	0.998;0.991;0.995;0.995;0.976;0.976	D;P;P;P;P;P	0.65443	0.935;0.818;0.887;0.887;0.556;0.556	T	0.17501	-1.0367	10	0.87932	D	0	.	6.836	0.23937	0.2831:0.0:0.7169:0.0	.	48;48;48;153;112;112	F5GXZ3;B4DSZ5;Q5T9M4;Q6Q1P2;E9PC28;P08575	.;.;.;.;.;PTPRC_HUMAN	Y	114;48;112;112;153;46;112;46;112	ENSP00000193532:D112Y	ENSP00000271610:D153Y	D	+	1	0	PTPRC	196935357	0.001000	0.12720	0.241000	0.24154	0.645000	0.38454	0.708000	0.25719	0.292000	0.22492	0.455000	0.32223	GAC		0.527	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198668734	G	T	198668734	3	4	61	1	0	0	0	0	1	0	0	0	12834	942	33	2	359	2	PTPRC	1	198668734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420637	198668734	50581887	936	8921										
PTPRC	5788	broad.mit.edu	37	chr1	198711004	198711004	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctcttgactagaaaaaaGaaaaagcaactggaagagag	9	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:198711004G>T	ENST00000367376.2	+	24	2575	c.2404G>T	c.(2404-2406)Gaa>Taa	p.E802*	PTPRC_ENST00000594404.1_Nonsense_Mutation_p.E641*|PTPRC_ENST00000352140.3_Nonsense_Mutation_p.E754*|PTPRC_ENST00000442510.2_Nonsense_Mutation_p.E804*|PTPRC_ENST00000348564.6_Nonsense_Mutation_p.E643*	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	802	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E802*(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CTAGAAAAAAGAAAAAGCAAC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											35	36	35					1																	198711004		2203	4300	6503	196977627	SO:0001587	stop_gained	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2404G>T	1.37:g.198711004G>T	ENSP00000356346:p.Glu802*		196977627	A8K7W6|Q16614|Q9H0Y6	Nonsense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	40	8.203037	0.98704	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	.	.	.	5.95	5.95	0.96441	.	0.000000	0.49916	D	0.000128	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	20.3854	0.98941	0.0:0.0:1.0:0.0	.	.	.	.	X	804;754;802;641	.	ENSP00000306782:E641X	E	+	1	0	PTPRC	196977627	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	5.099000	0.64554	2.825000	0.97269	0.655000	0.94253	GAA		0.413	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198711004	G	T	198711004	4	4	61	1	0	0	0	0	0	1	0	0	12834	943	33	2	2505	2	PTPRC	1	198711004	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42270	198711004	50539617	937	8922										
PTPRC	5788	broad.mit.edu	37	chr1	198721845	198721845	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaaaaacttccccagaaGaattcctctgaagggaacaa	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:198721845G>T	ENST00000367376.2	+	31	3618	c.3447G>T	c.(3445-3447)aaG>aaT	p.K1149N	PTPRC_ENST00000594404.1_Missense_Mutation_p.K988N|PTPRC_ENST00000352140.3_Missense_Mutation_p.K1101N|PTPRC_ENST00000442510.2_Missense_Mutation_p.K1151N|PTPRC_ENST00000348564.6_Missense_Mutation_p.K990N	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1149	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.K1149N(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						TTCCCCAGAAGAATTCCTCTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	72	72					1																	198721845		2203	4299	6502	196988468	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3447G>T	1.37:g.198721845G>T	ENSP00000356346:p.Lys1149Asn		196988468	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	11.64	1.699128	0.30142	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	T	0.14022	2.54	5.41	-2.95	0.05564	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.834296	0.10354	N	0.684788	T	0.19644	0.0472	L	0.38733	1.17	0.09310	N	1	D;D;D	0.63880	0.988;0.993;0.988	P;D;P	0.67900	0.902;0.954;0.902	T	0.16748	-1.0392	10	0.59425	D	0.04	.	5.8275	0.18562	0.6484:0.0:0.1642:0.1875	.	990;1101;1149	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	N	1151;1101;1149;988	ENSP00000193532:K1101N	ENSP00000306782:K988N	K	+	3	2	PTPRC	196988468	0.432000	0.25554	0.000000	0.03702	0.022000	0.10575	0.833000	0.27504	-0.371000	0.08004	-0.145000	0.13849	AAG		0.433	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198721845	G	T	198721845	3	4	61	1	0	0	0	0	1	0	0	0	12834	933	33	2	3576	2	PTPRC	1	198721845	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10841	198721845	50528776	938	8923										
PTPRC	5788	broad.mit.edu	37	chr1	198725110	198725110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaagtaaagaaaaacaacCatcaagaagataaaattgaa	6	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:198725110C>A	ENST00000367376.2	+	33	3886	c.3715C>A	c.(3715-3717)Cat>Aat	p.H1239N	PTPRC_ENST00000594404.1_Missense_Mutation_p.H1078N|PTPRC_ENST00000352140.3_Missense_Mutation_p.H1191N|PTPRC_ENST00000442510.2_Missense_Mutation_p.H1241N|PTPRC_ENST00000348564.6_Missense_Mutation_p.H1080N	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1239					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.H1239N(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GAAAAACAACCATCAAGAAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	100	99					1																	198725110		2203	4300	6503	196991733	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3715C>A	1.37:g.198725110C>A	ENSP00000356346:p.His1239Asn		196991733	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	1.457	-0.563385	0.03939	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	T	0.02301	4.35	5.7	-1.7	0.08159	.	1.130980	0.06723	N	0.775166	T	0.01870	0.0059	N	0.05383	-0.06	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.47649	-0.9101	10	0.15952	T	0.53	.	19.5182	0.95174	0.291:0.709:0.0:0.0	.	1080;1191;1239	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	N	1241;1191;1239;1078	ENSP00000193532:H1191N	ENSP00000306782:H1078N	H	+	1	0	PTPRC	196991733	0.000000	0.05858	0.000000	0.03702	0.418000	0.31294	-0.211000	0.09332	-0.130000	0.11599	-0.474000	0.04947	CAT		0.388	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198725110	C	A	198725110	3	1	61	1	0	0	0	0	1	0	0	0	12834	594	21	2	3852	2	PTPRC	1	198725110	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3265	198725110	50525511	939	8924										
ZNF281	23528	broad.mit.edu	37	chr1	200377217	200377217	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggtaaatatcttcttttCtttgaaaactgcatggcatc	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200377217C>A	ENST00000294740.3	-	2	1741	c.1617G>T	c.(1615-1617)aaG>aaT	p.K539N	ZNF281_ENST00000367352.3_Missense_Mutation_p.K503N|ZNF281_ENST00000367353.1_Missense_Mutation_p.K539N	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	539					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.K539N(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						ATCTTCTTTTCTTTGAAAACT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	80	80					1																	200377217		2203	4300	6503	198643840	SO:0001583	missense	23528			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.1617G>T	1.37:g.200377217C>A	ENSP00000294740:p.Lys539Asn		198643840	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	37	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.301045	0.40694	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.59906	0.23;0.23;0.23	5.48	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	M	0.71036	2.16	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.74494	-0.3647	10	0.72032	D	0.01	-17.2303	10.1478	0.42774	0.0:0.8492:0.0:0.1508	.	503;539	A6NF48;Q9Y2X9	.;ZN281_HUMAN	N	539;539;503;244	ENSP00000294740:K539N;ENSP00000356322:K539N;ENSP00000356321:K503N	ENSP00000294740:K539N	K	-	3	2	ZNF281	198643840	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.678000	0.37586	1.305000	0.44909	0.650000	0.86243	AAG		0.403	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		A	200377217	C	A	200377217	3	1	61	1	0	0	0	0	1	0	0	0	17857	912	32	2	1074	2	ZNF281	1	200377217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1652107	200377217	48873404	940	8925										
ZNF281	23528	broad.mit.edu	37	chr1	200378004	200378004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaatgaggacatgtctcCgcaggtgataggagcttcgg	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200378004C>T	ENST00000294740.3	-	2	954	c.830G>A	c.(829-831)cGg>cAg	p.R277Q	ZNF281_ENST00000367352.3_Missense_Mutation_p.R241Q|ZNF281_ENST00000367353.1_Missense_Mutation_p.R277Q	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	277					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.R277Q(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						GACATGTCTCCGCAGGTGATA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	78	79					1																	200378004		2203	4300	6503	198644627	SO:0001583	missense	23528			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.830G>A	1.37:g.200378004C>T	ENSP00000294740:p.Arg277Gln		198644627	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	37	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.135016	0.56828	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352	T;T;T	0.04275	3.66;3.66;3.66	5.64	5.64	0.86602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.08223	0.0205	N	0.12422	0.21	0.58432	D	0.999996	D;D	0.67145	0.996;0.996	P;P	0.60286	0.827;0.872	T	0.54403	-0.8299	10	0.11485	T	0.65	-15.1359	19.715	0.96113	0.0:1.0:0.0:0.0	.	241;277	A6NF48;Q9Y2X9	.;ZN281_HUMAN	Q	277;277;241	ENSP00000294740:R277Q;ENSP00000356322:R277Q;ENSP00000356321:R241Q	ENSP00000294740:R277Q	R	-	2	0	ZNF281	198644627	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.953000	0.70290	2.644000	0.89710	0.655000	0.94253	CGG		0.458	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		T	200378004	C	T	200378004	3	4	61	1	0	0	0	0	1	0	0	0	17857	652	23	1	1861	1	ZNF281	1	200378004	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	787	200378004	48872617	941	8926										
KIF14	9928	broad.mit.edu	37	chr1	200524573	200524573	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcattagttttcatttCtttggtaacctatagagaat	7	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200524573C>A	ENST00000367350.4	-	28	4801	c.4363G>T	c.(4363-4365)Gaa>Taa	p.E1455*		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1455	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.E1455*(1)|p.E1455Q(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GTTTTCATTTCTTTGGTAACC	0.264																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|breast(1)	1											53	57	55					1																	200524573		2199	4282	6481	198791196	SO:0001587	stop_gained	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4363G>T	1.37:g.200524573C>A	ENSP00000356319:p.Glu1455*		198791196	Q14CI8|Q4G0A5|Q5T1W3	Nonsense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	C	45	11.675202	0.99590	.	.	ENSG00000118193	ENST00000367350	.	.	.	4.97	2.94	0.34122	.	0.768392	0.12153	N	0.494681	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	9.2363	0.37468	0.0:0.1542:0.6824:0.1634	.	.	.	.	X	1455	.	ENSP00000356319:E1455X	E	-	1	0	KIF14	198791196	0.913000	0.31002	0.763000	0.31416	0.857000	0.48899	2.785000	0.47782	1.301000	0.44836	-0.165000	0.13383	GAA		0.264	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		A	200524573	C	A	200524573	4	1	61	1	0	0	0	0	0	1	0	0	8297	922	32	2	595	2	KIF14	1	200524573	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146569	200524573	48726048	942	8927										
KIF14	9928	broad.mit.edu	37	chr1	200534701	200534701	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatcataactctgtccaAaaaaatctaacgaagaacca	3	11	4	1	rs577782006		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200534701A>C	ENST00000367350.4	-	24	4196	c.3758T>G	c.(3757-3759)tTt>tGt	p.F1253C		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1253	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.F1253C(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						ACTCTGTCCAAAAAAATCTAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											59	60	60					1																	200534701		2201	4300	6501	198801324	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3758T>G	1.37:g.200534701A>C	ENSP00000356319:p.Phe1253Cys		198801324	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935578	0.52866	.	.	ENSG00000118193	ENST00000367350	T	0.73363	-0.74	5.57	5.57	0.84162	.	0.155169	0.44097	D	0.000491	T	0.58637	0.2136	N	0.08118	0	0.21553	N	0.999646	B	0.29805	0.257	B	0.30179	0.112	T	0.59925	-0.7362	10	0.87932	D	0	.	15.7225	0.77724	1.0:0.0:0.0:0.0	.	1253	Q15058	KIF14_HUMAN	C	1253	ENSP00000356319:F1253C	ENSP00000356319:F1253C	F	-	2	0	KIF14	198801324	1.000000	0.71417	0.552000	0.28243	0.952000	0.60782	6.783000	0.75078	2.117000	0.64856	0.482000	0.46254	TTT		0.333	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200534701	A	C	200534701	3	2	61	1	0	0	0	0	1	0	0	0	8297	14	1	4	1216	4	KIF14	1	200534701	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10128	200534701	48715920	943	8928										
KIF14	9928	broad.mit.edu	37	chr1	200573037	200573037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagatctattaggttaattCgacttgttattctgtgatcg	8	7	2	2	rs373895990		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200573037C>T	ENST00000367350.4	-	9	2231	c.1793G>A	c.(1792-1794)cGa>cAa	p.R598Q		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	598	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.R598Q(3)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TAGGTTAATTCGACTTGTTAT	0.368																																																3	Substitution - Missense(3)	large_intestine(3)	1											127	119	122					1																	200573037		2203	4300	6503	198839660	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.1793G>A	1.37:g.200573037C>T	ENSP00000356319:p.Arg598Gln		198839660	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473371	0.84640	.	.	ENSG00000118193	ENST00000367350	T	0.74737	-0.87	5.31	5.31	0.75309	Kinesin, motor domain (5);Kinesin, motor region, conserved site (1);	0.056634	0.64402	D	0.000001	T	0.78084	0.4228	L	0.31578	0.945	0.50813	D	0.999896	D	0.89917	1.0	D	0.72982	0.979	T	0.79446	-0.1800	10	0.59425	D	0.04	.	12.7829	0.57487	0.0:0.9144:0.0:0.0856	.	598	Q15058	KIF14_HUMAN	Q	598	ENSP00000356319:R598Q	ENSP00000356319:R598Q	R	-	2	0	KIF14	198839660	1.000000	0.71417	0.977000	0.42913	0.497000	0.33675	5.709000	0.68384	2.481000	0.83766	0.585000	0.79938	CGA		0.368	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		T	200573037	C	T	200573037	3	4	61	1	0	0	0	0	1	0	0	0	8297	884	31	1	3241	1	KIF14	1	200573037	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38336	200573037	48677584	944	8929										
KIF14	9928	broad.mit.edu	37	chr1	200574488	200574488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataccagtagcagcagtagCtctttgtttatttcccaatt	6	10	1	0	rs371145728		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200574488C>T	ENST00000367350.4	-	8	2107	c.1669G>A	c.(1669-1671)Gct>Act	p.A557T		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	557	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.A557T(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GCAGCAGTAGCTCTTTGTTTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	THR/ALA	0,4406		0,0,2203	93	100	97		1669	5.4	0.1	1		97	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIF14	NM_014875.2	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	557/1649	200574488	1,13005	2203	4300	6503	198841111	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.1669G>A	1.37:g.200574488C>T	ENSP00000356319:p.Ala557Thr		198841111	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114458	0.77210	0.0	1.16E-4	ENSG00000118193	ENST00000367350	T	0.74526	-0.85	5.45	5.45	0.79879	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	N	0.04203	-0.255	0.80722	D	1	P	0.40578	0.722	P	0.49953	0.627	T	0.68010	-0.5522	10	0.27082	T	0.32	.	19.2887	0.94090	0.0:1.0:0.0:0.0	.	557	Q15058	KIF14_HUMAN	T	557	ENSP00000356319:A557T	ENSP00000356319:A557T	A	-	1	0	KIF14	198841111	1.000000	0.71417	0.114000	0.21550	0.963000	0.63663	7.429000	0.80309	2.535000	0.85469	0.650000	0.86243	GCT		0.368	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		T	200574488	C	T	200574488	3	4	61	1	0	0	0	0	1	0	0	0	8297	797	28	3	3369	3	KIF14	1	200574488	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1451	200574488	48676133	945	8930										
KIF14	9928	broad.mit.edu	37	chr1	200578009	200578009	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaccagaaggtcgtgaatTttttcattatatacttcaaa	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200578009T>G	ENST00000367350.4	-	5	1941	c.1503A>C	c.(1501-1503)aaA>aaC	p.K501N		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	501	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.K501N(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GGTCGTGAATTTTTTCATTAT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	51	50					1																	200578009		2200	4289	6489	198844632	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.1503A>C	1.37:g.200578009T>G	ENSP00000356319:p.Lys501Asn		198844632	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917373	0.73098	.	.	ENSG00000118193	ENST00000367350	T	0.75821	-0.97	5.47	4.35	0.52113	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.81278	0.4789	L	0.56769	1.78	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	T	0.82165	-0.0592	10	0.87932	D	0	.	8.1537	0.31156	0.0:0.1512:0.0:0.8488	.	501	Q15058	KIF14_HUMAN	N	501	ENSP00000356319:K501N	ENSP00000356319:K501N	K	-	3	2	KIF14	198844632	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.552000	0.36244	2.072000	0.62099	0.528000	0.53228	AAA		0.284	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		G	200578009	T	G	200578009	3	3	61	1	0	0	0	0	1	0	0	0	8297	1838	64	4	3547	4	KIF14	1	200578009	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3521	200578009	48672612	946	8931										
DDX59	83479	broad.mit.edu	37	chr1	200635470	200635470	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaacttgtagaagatgtttCgctttacactccaaactaca	5	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200635470C>T	ENST00000331314.6	-	2	612	c.399G>A	c.(397-399)gcG>gcA	p.A133A	DDX59_ENST00000367348.3_Silent_p.A133A|DDX59_ENST00000447706.2_Silent_p.A133A	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	133						cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.A133A(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						GAAGATGTTTCGCTTTACACT	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	1											101	101	101					1																	200635470		2203	4300	6503	198902093	SO:0001819	synonymous_variant	83479			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.399G>A	1.37:g.200635470C>T			198902093	Q6PJL2|Q8IVW3|Q9H0W3	Silent	SNP	ENST00000331314.6	37	CCDS30964.1																																																																																				0.438	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		T	200635470	C	T	200635470	2	4	61	1	0	0	0	0	0	0	0	1	4382	871	31	1		1	DDX59	1	200635470	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57461	200635470	48615151	947	8932										
CAMSAP1L1	23271	broad.mit.edu	37	chr1	200776524	200776524	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcacatttggccatgatCgataccctcatgatggctta	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:200776524C>T	ENST00000236925.4	+	3	469	c.420C>T	c.(418-420)atC>atT	p.I140I	CAMSAP2_ENST00000413307.2_Silent_p.I140I|CAMSAP2_ENST00000358823.2_Silent_p.I140I			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	140					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)	p.I140I(1)									TGGCCATGATCGATACCCTCA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	1											88	81	83					1																	200776524		2203	4300	6503	199043147	SO:0001819	synonymous_variant	23271			AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.420C>T	1.37:g.200776524C>T			199043147	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	37																																																																																					0.318	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200776524	C	T	200776524	2	4	61	1	0	0	0	0	0	0	0	1	2618	874	31	1		1	CAMSAP1L1	1	200776524	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	141054	200776524	48474097	948	8933										
CACNA1S	779	broad.mit.edu	37	chr1	201009832	201009832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatctccacacagggtttgCtgtggggtcctgtatgcaag	13	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201009832C>A	ENST00000362061.3	-	42	5370	c.5144G>T	c.(5143-5145)aGc>aTc	p.S1715I	RP11-168O16.2_ENST00000415359.1_RNA|CACNA1S_ENST00000367338.3_Missense_Mutation_p.S1696I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1715					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S1715I(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACAGGGTTTGCTGTGGGGTCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	39	40					1																	201009832		2203	4300	6503	199276455	SO:0001583	missense	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.5144G>T	1.37:g.201009832C>A	ENSP00000355192:p.Ser1715Ile		199276455	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	10.17	1.277716	0.23307	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96136	-3.92;-3.84	4.79	2.77	0.32553	.	449.682000	0.00166	N	0.000000	D	0.90776	0.7104	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.80231	-0.1468	10	0.22706	T	0.39	.	5.7317	0.18042	0.0:0.6923:0.1992:0.1085	.	1715	Q13698	CAC1S_HUMAN	I	1715;1696	ENSP00000355192:S1715I;ENSP00000356307:S1696I	ENSP00000355192:S1715I	S	-	2	0	CACNA1S	199276455	0.000000	0.05858	0.027000	0.17364	0.004000	0.04260	0.123000	0.15708	1.007000	0.39238	0.585000	0.79938	AGC		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201009832	C	A	201009832	3	1	61	1	0	0	0	0	1	0	0	0	2553	797	28	2	489	2	CACNA1S	1	201009832	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233308	201009832	48240789	949	8934										
CACNA1S	779	broad.mit.edu	37	chr1	201052428	201052428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacttccagcgaaagatgcGgttccactgcctccaatgtc	9	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201052428G>A	ENST00000362061.3	-	10	1481	c.1255C>T	c.(1255-1257)Cgc>Tgc	p.R419C	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R419C	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	419					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R419C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGAAAGATGCGGTTCCACTGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											192	158	170					1																	201052428		2203	4300	6503	199319051	SO:0001583	missense	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1255C>T	1.37:g.201052428G>A	ENSP00000355192:p.Arg419Cys		199319051	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790457	0.90367	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96967	-4.19;-4.09	4.59	4.59	0.56863	.	0.105688	0.64402	D	0.000003	D	0.98457	0.9486	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.66847	0.947	D	0.99808	1.1039	10	0.87932	D	0	.	17.7262	0.88366	0.0:0.0:1.0:0.0	.	419	Q13698	CAC1S_HUMAN	C	419	ENSP00000355192:R419C;ENSP00000356307:R419C	ENSP00000355192:R419C	R	-	1	0	CACNA1S	199319051	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.705000	0.98719	2.232000	0.73038	0.643000	0.83706	CGC		0.542	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201052428	G	A	201052428	3	1	61	1	0	0	0	0	1	0	0	0	2553	1116	39	1	4506	1	CACNA1S	1	201052428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42596	201052428	48198193	950	8935										
CACNA1S	779	broad.mit.edu	37	chr1	201063114	201063114	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcatggcggcttcaatCgagaagacaatgaggaagaa	11	7	3	4	rs201012916		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201063114C>T	ENST00000362061.3	-	3	520	c.294G>A	c.(292-294)tcG>tcA	p.S98S	CACNA1S_ENST00000367338.3_Silent_p.S98S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	98					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S98S(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGGCTTCAATCGAGAAGACAA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	86	86					1																	201063114		2203	4300	6503	199329737	SO:0001819	synonymous_variant	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.294G>A	1.37:g.201063114C>T			199329737	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																				0.527	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201063114	C	T	201063114	2	4	61	1	0	0	0	0	0	0	0	1	2553	871	31	1		1	CACNA1S	1	201063114	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10686	201063114	48187507	951	8936										
PKP1	5317	broad.mit.edu	37	chr1	201297899	201297899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctttgcagcaaggtttcGataggaacatgctgggaacc	11	10	0	0	rs201180970		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201297899G>A	ENST00000352845.3	+	14	2179	c.2179G>A	c.(2179-2181)Gat>Aat	p.D727N	PKP1_ENST00000367324.3_Missense_Mutation_p.D706N|PKP1_ENST00000263946.3_Missense_Mutation_p.D727N			Q13835	PKP1_HUMAN	plakophilin 1	727					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)	p.D706N(1)		NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GCAAGGTTTCGATAGGAACAT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											175	166	169					1																	201297899		2203	4300	6503	199564522	SO:0001583	missense	5317			X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.2179G>A	1.37:g.201297899G>A	ENSP00000295597:p.Asp727Asn		199564522	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233932	0.58886	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.73047	-0.71;-0.59;-0.59	4.28	3.36	0.38483	.	0.374093	0.27275	N	0.020115	T	0.53610	0.1807	L	0.27053	0.805	0.33040	D	0.531273	P;P;P	0.40107	0.608;0.614;0.703	B;B;B	0.34301	0.179;0.168;0.115	T	0.62845	-0.6768	10	0.33940	T	0.23	-16.165	12.4696	0.55779	0.083:0.0:0.917:0.0	.	314;706;727	Q14BN3;Q13835-2;Q13835	.;.;PKP1_HUMAN	N	706;727;727	ENSP00000356293:D706N;ENSP00000263946:D727N;ENSP00000295597:D727N	ENSP00000263946:D727N	D	+	1	0	PKP1	199564522	1.000000	0.71417	0.375000	0.26029	0.910000	0.53928	4.636000	0.61339	0.906000	0.36621	0.511000	0.50034	GAT		0.527	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201297899	G	A	201297899	3	1	61	1	0	0	0	0	1	0	0	0	12015	1058	37	1	2233	1	PKP1	1	201297899	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	234785	201297899	47952722	952	8937										
LAD1	3898	broad.mit.edu	37	chr1	201355818	201355818	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcttctctgagctgtttCttttctctgacactgctatc	5	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201355818C>A	ENST00000391967.2	-	3	972	c.671G>T	c.(670-672)aGa>aTa	p.R224I	LAD1_ENST00000367313.3_Missense_Mutation_p.R238I	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	224	8 X SEK repeats.					basement membrane (GO:0005604)	structural molecule activity (GO:0005198)	p.R224I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TGAGCTGTTTCTTTTCTCTGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											101	111	108					1																	201355818		2203	4300	6503	199622441	SO:0001583	missense	3898			U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.671G>T	1.37:g.201355818C>A	ENSP00000375829:p.Arg224Ile		199622441	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118295	0.37339	.	.	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.12774	2.65;2.66	4.86	-1.43	0.08884	.	0.957919	0.08702	N	0.906343	T	0.07369	0.0186	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.29432	0.244;0.218	B;B	0.31101	0.022;0.124	T	0.40664	-0.9551	10	0.32370	T	0.25	-0.3712	2.8269	0.05488	0.2789:0.3566:0.2742:0.0902	.	238;224	E9PDI4;O00515	.;LAD1_HUMAN	I	224;238	ENSP00000375829:R224I;ENSP00000356282:R238I	ENSP00000356282:R238I	R	-	2	0	LAD1	199622441	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.761000	0.04751	0.027000	0.15297	0.609000	0.83330	AGA		0.502	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558		A	201355818	C	A	201355818	3	1	61	1	0	0	0	0	1	0	0	0	8621	913	32	2	914	2	LAD1	1	201355818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57919	201355818	47894803	953	8938										
LMOD1	25802	broad.mit.edu	37	chr1	201868488	201868488	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagctggtgagagtgaattCttcaggttctccatgataag	12	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201868488C>A	ENST00000367288.4	-	2	1899	c.1653G>T	c.(1651-1653)aaG>aaT	p.K551N	RP11-307B6.3_ENST00000458139.1_RNA|RP11-307B6.3_ENST00000414927.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	551					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.K551N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						AGAGTGAATTCTTCAGGTTCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											25	28	27					1																	201868488		1853	4089	5942	200135111	SO:0001583	missense	25802			X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.1653G>T	1.37:g.201868488C>A	ENSP00000356257:p.Lys551Asn		200135111	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522630	0.64747	.	.	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.83163	-1.69	4.97	4.97	0.65823	.	0.344301	0.21073	N	0.080631	T	0.80854	0.4703	L	0.57536	1.79	0.42535	D	0.99305	P;P	0.44429	0.835;0.835	B;B	0.43445	0.329;0.42	T	0.82768	-0.0294	10	0.72032	D	0.01	-27.6942	9.3686	0.38239	0.0:0.902:0.0:0.098	.	500;551	B4E3S9;P29536	.;LMOD1_HUMAN	N	551;551;500	ENSP00000356257:K551N	ENSP00000356257:K551N	K	-	3	2	LMOD1	200135111	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.205000	0.51090	2.253000	0.74438	0.655000	0.94253	AAG		0.582	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2			A	201868488	C	A	201868488	3	1	61	1	0	0	0	0	1	0	0	0	8880	912	32	2	157	2	LMOD1	1	201868488	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	512670	201868488	47382133	954	8939										
RNPEP	6051	broad.mit.edu	37	chr1	201966452	201966452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgcttctcggcaggtatgActtgctcttcatgccaccgt	9	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:201966452A>G	ENST00000295640.4	+	5	903	c.860A>G	c.(859-861)gAc>gGc	p.D287G	RP11-465N4.5_ENST00000608886.1_RNA|RNPEP_ENST00000367286.3_Missense_Mutation_p.D248G|RP11-465N4.4_ENST00000415582.1_RNA|RP11-465N4.4_ENST00000419190.1_RNA|RNPEP_ENST00000471105.1_3'UTR	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	287					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.D287G(1)		breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		GGCAGGTATGACTTGCTCTTC	0.587																																					GBM(19;39 479 7473 13131 19462)											1	Substitution - Missense(1)	large_intestine(1)	1											78	78	78					1																	201966452		2203	4300	6503	200233075	SO:0001583	missense	6051			BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.860A>G	1.37:g.201966452A>G	ENSP00000295640:p.Asp287Gly		200233075	Q9BVM9|Q9H1D4|Q9NPT7	Missense_Mutation	SNP	ENST00000295640.4	37	CCDS1418.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289513	0.59976	.	.	ENSG00000176393	ENST00000295640;ENST00000367286;ENST00000447312;ENST00000449524	T;T;T;T	0.03635	3.86;3.86;3.86;3.86	5.1	5.1	0.69264	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	H	0.95470	3.675	0.80722	D	1	P;P	0.47409	0.895;0.895	P;P	0.61328	0.766;0.887	T	0.19031	-1.0318	10	0.87932	D	0	-32.3081	13.8782	0.63667	1.0:0.0:0.0:0.0	.	295;287	Q7RU04;Q9H4A4	.;AMPB_HUMAN	G	287;248;156;33	ENSP00000295640:D287G;ENSP00000356255:D248G;ENSP00000389602:D156G;ENSP00000407614:D33G	ENSP00000295640:D287G	D	+	2	0	RNPEP	200233075	1.000000	0.71417	0.927000	0.36925	0.811000	0.45836	8.862000	0.92283	1.914000	0.55421	0.523000	0.50628	GAC		0.587	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		G	201966452	A	G	201966452	3	3	61	1	0	0	0	0	1	0	0	0	13546	275	10	4	878	4	RNPEP	1	201966452	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	97964	201966452	47284169	955	8940										
PTPN7	5778	broad.mit.edu	37	chr1	202127249	202127249	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccccaatttcttaccaaGaattcttcttccagttgctt	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202127249G>T	ENST00000308986.5	-	3	433	c.303C>A	c.(301-303)ttC>ttA	p.F101L	PTPN7_ENST00000367279.4_Missense_Mutation_p.F140L|PTPN7_ENST00000544762.1_5'UTR|PTPN7_ENST00000309017.3_Missense_Mutation_p.F206L|PTPN7_ENST00000492977.1_5'UTR|PTPN7_ENST00000543735.1_Intron			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7	101	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)	p.F140L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						TTCTTACCAAGAATTCTTCTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	51	52					1																	202127249		2203	4300	6503	200393872	SO:0001583	missense	5778			BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931	ENST00000308986.5:c.303C>A	1.37:g.202127249G>T	ENSP00000311133:p.Phe101Leu		200393872	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.49|18.49	3.635535|3.635535	0.67130|0.67130	.|.	.|.	ENSG00000143851|ENSG00000143851	ENST00000367279;ENST00000309017;ENST00000308986;ENST00000477554;ENST00000476061;ENST00000467283;ENST00000464870;ENST00000486116;ENST00000492451|ENST00000435759	T;T;T;T;T;T;T;T;T|.	0.62639|.	2.16;2.16;2.16;2.16;2.03;2.03;2.03;1.27;0.01|.	5.03|5.03	0.983|0.983	0.19767|0.19767	Protein-tyrosine phosphatase, receptor/non-receptor type (2);|.	0.000000|.	0.64402|.	D|.	0.000008|.	T|T	0.75466|0.75466	0.3853|0.3853	M|M	0.87617|0.87617	2.895|2.895	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0;1.0|.	D;D;D;D;D|.	0.81914|.	0.991;0.949;0.983;0.988;0.995|.	T|T	0.77950|0.77950	-0.2395|-0.2395	10|6	0.87932|0.87932	D|D	0|0	.|.	10.3183|10.3183	0.43751|0.43751	0.3907:0.0:0.6093:0.0|0.3907:0.0:0.6093:0.0	.|.	175;49;53;101;140|.	B4DZD9;B4DVF0;Q8NFX3;P35236;P35236-2|.	.;.;.;PTN7_HUMAN;.|.	L|I	140;206;101;182;100;101;101;101;101|108	ENSP00000356248:F140L;ENSP00000309116:F206L;ENSP00000311133:F101L;ENSP00000418416:F182L;ENSP00000419993:F100L;ENSP00000418837:F101L;ENSP00000420434:F101L;ENSP00000417350:F101L;ENSP00000417410:F101L|.	ENSP00000311133:F101L|ENSP00000406042:L108I	F|L	-|-	3|1	2|0	PTPN7|PTPN7	200393872|200393872	0.159000|0.159000	0.22864|0.22864	0.893000|0.893000	0.35052|0.35052	0.872000|0.872000	0.50106|0.50106	0.470000|0.470000	0.22084|0.22084	0.516000|0.516000	0.28340|0.28340	0.462000|0.462000	0.41574|0.41574	TTC|CTT		0.602	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832		T	202127249	G	T	202127249	3	4	61	1	0	0	0	0	1	0	0	0	12830	933	33	2	811	2	PTPN7	1	202127249	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160797	202127249	47123372	956	8941										
PPP1R12B	4660	broad.mit.edu	37	chr1	202409840	202409840	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttattttacaggagagaGaaaacaaaagctatattagt	7	3	0	2	rs112006906|rs567694055	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202409840G>T	ENST00000608999.1	+	11	1618	c.1465G>T	c.(1465-1467)Gaa>Taa	p.E489*	PPP1R12B_ENST00000336894.4_Nonsense_Mutation_p.E489*|RP11-175B9.2_ENST00000602961.1_RNA	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	489					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)	p.E489*(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			ACAGGAGAGAGAAAACAAAAG	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											102	103	102					1																	202409840		2203	4300	6503	200676463	SO:0001587	stop_gained	4660			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1465G>T	1.37:g.202409840G>T	ENSP00000476755:p.Glu489*		200676463	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Nonsense_Mutation	SNP	ENST00000608999.1	37	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	G	40	8.048857	0.98627	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	.	.	.	5.96	5.05	0.67936	.	0.163581	0.43416	D	0.000580	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	14.7832	0.69781	0.0695:0.0:0.9305:0.0	.	.	.	.	X	489	.	ENSP00000337897:E489X	E	+	1	0	PPP1R12B	200676463	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.412000	0.73303	1.524000	0.49035	0.655000	0.94253	GAA		0.348	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		T	202409840	G	T	202409840	4	4	61	1	0	0	0	0	0	1	0	0	12389	943	33	2	1597	2	PPP1R12B	1	202409840	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282591	202409840	46840781	957	8942										
PPP1R12B	4660	broad.mit.edu	37	chr1	202464749	202464749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctaagaggctgtccatccGagagaggaggcggcccaagg	15	11	1	2	rs3817221		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202464749G>A	ENST00000608999.1	+	17	2540	c.2387G>A	c.(2386-2388)cGa>cAa	p.R796Q	PPP1R12B_ENST00000336894.4_Missense_Mutation_p.R796Q|PPP1R12B_ENST00000367270.4_Missense_Mutation_p.R22Q|PPP1R12B_ENST00000391959.3_Missense_Mutation_p.R22Q|PPP1R12B_ENST00000290419.5_3'UTR	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	796					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)	p.R796Q(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTGTCCATCCGAGAGAGGAGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	91	91					1																	202464749		2203	4300	6503	200731372	SO:0001583	missense	4660			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2387G>A	1.37:g.202464749G>A	ENSP00000476755:p.Arg796Gln		200731372	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	37	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	G	32	5.129886	0.94473	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000391959;ENST00000367270	T;T;T;T	0.51817	1.02;1.03;0.7;0.69	5.55	5.55	0.83447	.	0.000000	0.56097	D	0.000025	T	0.63733	0.2536	L	0.52206	1.635	0.46260	D	0.998951	D;D;D	0.89917	0.98;1.0;1.0	P;D;D	0.79108	0.664;0.992;0.968	T	0.61676	-0.7014	10	0.49607	T	0.09	.	16.7828	0.85567	0.0:0.0:1.0:0.0	rs3817221;rs3817221	22;796;796	O60237-3;O60237;F8W8M3	.;MYPT2_HUMAN;.	Q	796;796;22;22	ENSP00000384496:R796Q;ENSP00000337897:R796Q;ENSP00000375821:R22Q;ENSP00000356239:R22Q	ENSP00000337897:R796Q	R	+	2	0	PPP1R12B	200731372	1.000000	0.71417	0.902000	0.35471	0.663000	0.39108	6.869000	0.75521	2.768000	0.95171	0.655000	0.94253	CGA		0.463	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		A	202464749	G	A	202464749	3	1	61	1	0	0	0	0	1	0	0	0	12389	1058	37	1	2543	1	PPP1R12B	1	202464749	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54909	202464749	46785872	958	8943										
SYT2	127833	broad.mit.edu	37	chr1	202571113	202571113	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacctctccaatgatgtCatgtttggagaagcggtcaa	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202571113C>A	ENST00000367267.1	-	6	898	c.706G>T	c.(706-708)Gac>Tac	p.D236Y	RP11-569A11.1_ENST00000428573.1_RNA|SYT2_ENST00000367268.4_Missense_Mutation_p.D236Y	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	236	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)	p.D236Y(1)		NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	CCAATGATGTCATGTTTGGAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											174	158	163					1																	202571113		2203	4300	6503	200837736	SO:0001583	missense	127833			AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.706G>T	1.37:g.202571113C>A	ENSP00000356236:p.Asp236Tyr		200837736	Q496K5|Q8NBE5	Missense_Mutation	SNP	ENST00000367267.1	37	CCDS1427.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829939	0.91036	.	.	ENSG00000143858	ENST00000367268;ENST00000367267	T;T	0.72394	-0.65;-0.65	5.45	5.45	0.79879	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.85682	D	0.000000	D	0.89639	0.6773	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.92700	0.6174	10	0.87932	D	0	.	18.9002	0.92439	0.0:1.0:0.0:0.0	.	236	Q8N9I0	SYT2_HUMAN	Y	236	ENSP00000356237:D236Y;ENSP00000356236:D236Y	ENSP00000356236:D236Y	D	-	1	0	SYT2	200837736	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.794000	0.85869	2.558000	0.86282	0.563000	0.77884	GAC		0.547	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		A	202571113	C	A	202571113	3	1	61	1	0	0	0	0	1	0	0	0	15513	826	29	2	569	2	SYT2	1	202571113	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106364	202571113	46679508	959	8944										
SYT2	127833	broad.mit.edu	37	chr1	202571575	202571575	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttggtctcatatttcttCttcttgtcaggaaggaggaa	9	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202571575C>A	ENST00000367267.1	-	5	756	c.564G>T	c.(562-564)aaG>aaT	p.K188N	RP11-569A11.1_ENST00000428573.1_RNA|SYT2_ENST00000367268.4_Missense_Mutation_p.K188N	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	188	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)	p.K188N(1)		NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	CATATTTCTTCTTCTTGTCAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											136	127	130					1																	202571575		2203	4300	6503	200838198	SO:0001583	missense	127833			AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.564G>T	1.37:g.202571575C>A	ENSP00000356236:p.Lys188Asn		200838198	Q496K5|Q8NBE5	Missense_Mutation	SNP	ENST00000367267.1	37	CCDS1427.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621651	0.87460	.	.	ENSG00000143858	ENST00000367268;ENST00000367267	T;T	0.70399	-0.48;-0.48	5.58	5.58	0.84498	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	L	0.58583	1.82	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.81816	-0.0759	10	0.87932	D	0	.	12.5398	0.56163	0.0:0.9231:0.0:0.0769	.	188	Q8N9I0	SYT2_HUMAN	N	188	ENSP00000356237:K188N;ENSP00000356236:K188N	ENSP00000356236:K188N	K	-	3	2	SYT2	200838198	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.360000	0.52299	2.626000	0.88956	0.655000	0.94253	AAG		0.532	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		A	202571575	C	A	202571575	3	1	61	1	0	0	0	0	1	0	0	0	15513	912	32	2	715	2	SYT2	1	202571575	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	462	202571575	46679046	960	8945										
RABIF	5877	broad.mit.edu	37	chr1	202850139	202850139	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcgttccaaggccacataGaaactgttcttgtcatctag	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202850139G>T	ENST00000367262.3	-	2	375	c.339C>A	c.(337-339)ttC>ttA	p.F113L		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	113					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)	p.F113L(1)		large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			AGGCCACATAGAAACTGTTCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	107	111					1																	202850139		2203	4300	6503	201116762	SO:0001583	missense	5877			S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.339C>A	1.37:g.202850139G>T	ENSP00000356231:p.Phe113Leu		201116762	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	37	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375801	0.82682	.	.	ENSG00000183155	ENST00000367262	.	.	.	5.81	3.93	0.45458	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.000000	0.85682	D	0.000000	T	0.76990	0.4065	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.77064	-0.2726	9	0.39692	T	0.17	-41.698	9.9876	0.41852	0.2111:0.0:0.7889:0.0	.	113	P47224	MSS4_HUMAN	L	113	.	ENSP00000356231:F113L	F	-	3	2	RABIF	201116762	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.863000	0.48396	1.477000	0.48234	-0.258000	0.10820	TTC		0.493	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1			T	202850139	G	T	202850139	3	4	61	1	0	0	0	0	1	0	0	0	13006	933	33	2	36	2	RABIF	1	202850139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	278564	202850139	46400482	961	8946										
ADIPOR1	51094	broad.mit.edu	37	chr1	202911345	202911345	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccaagtcccaggaacacGcctgaacagaacagacataa	8	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202911345G>A	ENST00000340990.5	-	7	1105	c.807C>T	c.(805-807)ggC>ggT	p.G269G	ADIPOR1_ENST00000436244.1_Splice_Site_p.G269G	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	269					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|hormone-mediated signaling pathway (GO:0009755)|leptin-mediated signaling pathway (GO:0033210)|negative regulation of cell growth (GO:0030308)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of JAK-STAT cascade (GO:0046427)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)	p.G269G(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(75;0.141)			CCAGGAACACGCCTGAACAGA	0.507																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	1											61	58	59					1																	202911345		2203	4300	6503	201177968	SO:0001630	splice_region_variant	51094				CCDS1430.1	1q32.1	2012-08-22			ENSG00000159346	ENSG00000159346		"GPCR / Unclassified : Adiponectin receptors"	24040	protein-coding gene	gene with protein product		607945				12802337	Standard	XM_006711360		Approved	PAQR1, ACDCR1	uc001gyq.5	Q96A54	OTTHUMG00000041391	ENST00000340990.5:c.806-1C>T	1.37:g.202911345G>A			201177968	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Silent	SNP	ENST00000340990.5	37	CCDS1430.1																																																																																				0.507	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999	Silent	A	202911345	G	A	202911345	5	1	61	1	0	0	0	0	0	0	1	0	318	1101	38	1	328	1	ADIPOR1	1	202911345	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61206	202911345	46339276	962	8947										
CYB5R1	51706	broad.mit.edu	37	chr1	202932233	202932233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaaccagagcttaaagcGattgggatagcgggcctgca	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:202932233G>A	ENST00000367249.4	-	8	780	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C	CYB5R1_ENST00000497655.1_5'UTR	NM_016243.2	NP_057327.2	Q9UHQ9	NB5R1_HUMAN	cytochrome b5 reductase 1	236					sterol biosynthetic process (GO:0016126)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)	p.R236C(1)		breast(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(75;0.141)		Flavin adenine dinucleotide(DB03147)	AGCTTAAAGCGATTGGGATAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	117	119					1																	202932233		2203	4300	6503	201198856	SO:0001583	missense	51706			AF169481	CCDS1431.1	1q32.1	2011-04-08		2005-07-13	ENSG00000159348	ENSG00000159348	1.6.2.2		13397	protein-coding gene	gene with protein product		608341	"NAD(P)H:quinone oxidoreductase type 3, polypeptide A2"	NQO3A2		12975309, 10611283	Standard	NM_016243		Approved	humb5R2	uc001gyt.2	Q9UHQ9	OTTHUMG00000041387	ENST00000367249.4:c.706C>T	1.37:g.202932233G>A	ENSP00000356218:p.Arg236Cys		201198856	A0PK21|B2R8E0|O95329|Q53F73|Q8NCL5|Q9UHJ1	Missense_Mutation	SNP	ENST00000367249.4	37	CCDS1431.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333924	0.81801	.	.	ENSG00000159348	ENST00000367249	D	0.95307	-3.67	5.98	5.98	0.97165	Oxidoreductase FAD/NAD(P)-binding (1);	0.000000	0.85682	D	0.000000	D	0.97331	0.9127	H	0.98542	4.26	0.80722	D	1	P	0.44260	0.83	B	0.44133	0.442	D	0.98333	1.0534	10	0.87932	D	0	-3.4644	17.9305	0.88996	0.0:0.0:1.0:0.0	.	236	Q9UHQ9	NB5R1_HUMAN	C	236	ENSP00000356218:R236C	ENSP00000356218:R236C	R	-	1	0	CYB5R1	201198856	0.900000	0.30661	0.955000	0.39395	0.950000	0.60333	4.154000	0.58125	2.837000	0.97791	0.591000	0.81541	CGC		0.483	CYB5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099155.1	NM_016243		A	202932233	G	A	202932233	3	1	61	1	0	0	0	0	1	0	0	0	4132	1058	37	1	219	1	CYB5R1	1	202932233	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20888	202932233	46318388	963	8948										
PPFIA4	8497	broad.mit.edu	37	chr1	203037706	203037706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccctggacgagaacttcGaccacaacacactggccctg	10	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203037706G>A	ENST00000447715.2	+	32	3649	c.3208G>A	c.(3208-3210)Gac>Aac	p.D1070N	PPFIA4_ENST00000272198.6_Missense_Mutation_p.D586N|PPFIA4_ENST00000295706.4_Missense_Mutation_p.D577N|PPFIA4_ENST00000414050.2_Missense_Mutation_p.D799N|PPFIA4_ENST00000367240.2_Missense_Mutation_p.D1071N|PPFIA4_ENST00000599966.1_Missense_Mutation_p.D577N			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1070	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.D1216N(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CGAGAACTTCGACCACAACAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											66	67	67					1																	203037706		2080	4205	6285	201304329	SO:0001583	missense	8497			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.3208G>A	1.37:g.203037706G>A	ENSP00000402576:p.Asp1070Asn		201304329	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	G	34	5.366628	0.95900	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88	3.59	3.59	0.41128	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (1);Sterile alpha motif, type 2 (1);	0.000000	0.42964	U	0.000631	D	0.89347	0.6689	M	0.66439	2.03	0.58432	D	0.999999	B;D;P;D;D	0.62365	0.099;0.991;0.647;0.989;0.991	B;P;B;P;P	0.57548	0.061;0.799;0.143;0.729;0.823	D	0.91240	0.5021	10	0.87932	D	0	-20.253	15.7465	0.77949	0.0:0.0:1.0:0.0	.	799;1070;272;577;586	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	N	1071;1070;577;799;586	ENSP00000356209:D1071N;ENSP00000402576:D1070N;ENSP00000295706:D577N;ENSP00000400379:D799N;ENSP00000272198:D586N	ENSP00000272198:D586N	D	+	1	0	PPFIA4	201304329	1.000000	0.71417	0.994000	0.49952	0.902000	0.53008	9.522000	0.98032	2.010000	0.58986	0.555000	0.69702	GAC		0.562	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203037706	G	A	203037706	3	1	61	1	0	0	0	0	1	0	0	0	12343	1058	37	1	1810	1	PPFIA4	1	203037706	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105473	203037706	46212915	964	8949										
MYOG	4656	broad.mit.edu	37	chr1	203054999	203054999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgctcgtagcctggtggttCgaagccctggaggtggacag	16	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203054999C>T	ENST00000241651.4	-	1	165	c.91G>A	c.(91-93)Gaa>Aaa	p.E31K		NM_002479.5	NP_002470.2	P15173	MYOG_HUMAN	myogenin (myogenic factor 4)	31					cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lithium ion (GO:0071285)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|negative regulation of cell proliferation (GO:0008285)|ossification (GO:0001503)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of muscle atrophy (GO:0014737)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myoblast fusion (GO:1901739)|regulation of satellite cell proliferation (GO:0014842)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|skeletal muscle fiber development (GO:0048741)|skeletal muscle tissue development (GO:0007519)|striated muscle atrophy (GO:0014891)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E31K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|urinary_tract(1)	12						CCTGGTGGTTCGAAGCCCTGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											50	47	48					1																	203054999		2203	4300	6503	201321622	SO:0001583	missense	4656			BC053899	CCDS1433.1	1q31-q41	2013-05-21			ENSG00000122180	ENSG00000122180		"Basic helix-loop-helix proteins"	7612	protein-coding gene	gene with protein product		159980		MYF4		10329008	Standard	NM_002479		Approved	bHLHc3	uc001gzd.4	P15173	OTTHUMG00000042127	ENST00000241651.4:c.91G>A	1.37:g.203054999C>T	ENSP00000241651:p.Glu31Lys		201321622	Q53XW6	Missense_Mutation	SNP	ENST00000241651.4	37	CCDS1433.1	.	.	.	.	.	.	.	.	.	.	c	26.8	4.774527	0.90108	.	.	ENSG00000122180	ENST00000241651	T	0.80214	-1.35	5.68	5.68	0.88126	Myogenic basic muscle-specific protein (2);	0.401828	0.27654	N	0.018407	T	0.78672	0.4320	M	0.74258	2.255	0.58432	D	0.999994	B	0.33612	0.419	B	0.27170	0.077	T	0.79926	-0.1597	10	0.66056	D	0.02	.	13.0541	0.58969	0.0:0.9267:0.0:0.0733	.	31	P15173	MYOG_HUMAN	K	31	ENSP00000241651:E31K	ENSP00000241651:E31K	E	-	1	0	MYOG	201321622	1.000000	0.71417	0.997000	0.53966	0.915000	0.54546	5.539000	0.67199	2.679000	0.91253	0.558000	0.71614	GAA		0.637	MYOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100279.1	NM_002479		T	203054999	C	T	203054999	3	4	61	1	0	0	0	0	1	0	0	0	10120	893	31	1	595	1	MYOG	1	203054999	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17293	203054999	46195622	965	8950										
ADORA1	134	broad.mit.edu	37	chr1	203098042	203098042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcgccctggtctctgtgCccgggaacgtgctggtgatc	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203098042C>T	ENST00000367236.4	+	2	994	c.73C>T	c.(73-75)Ccc>Tcc	p.P25S	ADORA1_ENST00000337894.4_Missense_Mutation_p.P25S|ADORA1_ENST00000367235.1_Missense_Mutation_p.P25S|ADORA1_ENST00000309502.3_Missense_Mutation_p.P25S|RP11-335O13.7_ENST00000421055.1_RNA	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	25					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)	p.P25S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	GGTCTCTGTGCCCGGGAACGT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	1											169	126	141					1																	203098042		2203	4300	6503	201364665	SO:0001583	missense	134			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.73C>T	1.37:g.203098042C>T	ENSP00000356205:p.Pro25Ser		201364665	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.634110	0.47049	.	.	ENSG00000163485	ENST00000309502;ENST00000367236;ENST00000337894;ENST00000367235	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.05	5.05	0.67936	.	0.288318	0.40144	N	0.001174	T	0.23492	0.0568	N	0.02334	-0.595	0.40609	D	0.981657	P;B	0.45531	0.86;0.013	P;B	0.45343	0.477;0.017	T	0.38757	-0.9646	10	0.48119	T	0.1	-17.5135	18.4106	0.90549	0.0:1.0:0.0:0.0	.	58;25	B7Z379;P30542	.;AA1R_HUMAN	S	25	ENSP00000308549:P25S;ENSP00000356205:P25S;ENSP00000338435:P25S;ENSP00000356204:P25S	ENSP00000308549:P25S	P	+	1	0	ADORA1	201364665	0.997000	0.39634	0.986000	0.45419	0.936000	0.57629	1.630000	0.37081	2.338000	0.79540	0.603000	0.83216	CCC		0.652	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		T	203098042	C	T	203098042	3	4	61	1	0	0	0	0	1	0	0	0	326	739	26	3	75	3	ADORA1	1	203098042	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43043	203098042	46152579	966	8951										
CHI3L1	1116	broad.mit.edu	37	chr1	203151867	203151867	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggagactcactgggatatCttggcaatgtcatagctgct	11	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203151867C>A	ENST00000255409.3	-	6	704	c.579G>T	c.(577-579)aaG>aaT	p.K193N		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	193					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.K193N(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						ACTGGGATATCTTGGCAATGT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											117	104	108					1																	203151867		2203	4300	6503	201418490	SO:0001583	missense	1116			BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.579G>T	1.37:g.203151867C>A	ENSP00000255409:p.Lys193Asn		201418490	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.231|8.231	0.804593|0.804593	0.16467|0.16467	.|.	.|.	ENSG00000133048|ENSG00000133048	ENST00000404436|ENST00000255409	.|T	.|0.05996	.|3.36	5.4|5.4	2.43|2.43	0.29744|0.29744	.|Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.778290	.|0.11283	.|N	.|0.580061	T|T	0.04861|0.04861	0.0131|0.0131	L|L	0.35341|0.35341	1.055|1.055	0.23016|0.23016	N|N	0.998422|0.998422	.|B	.|0.33883	.|0.43	.|B	.|0.29862	.|0.108	T|T	0.36792|0.36792	-0.9733|-0.9733	5|10	.|0.54805	.|T	.|0.06	-7.1391|-7.1391	4.5981|4.5981	0.12340|0.12340	0.0:0.5925:0.1839:0.2236|0.0:0.5925:0.1839:0.2236	.|.	.|193	.|P36222	.|CH3L1_HUMAN	Y|N	23|193	.|ENSP00000255409:K193N	.|ENSP00000255409:K193N	D|K	-|-	1|3	0|2	CHI3L1|CHI3L1	201418490|201418490	0.760000|0.760000	0.28428|0.28428	0.019000|0.019000	0.16419|0.16419	0.237000|0.237000	0.25408|0.25408	0.277000|0.277000	0.18734|0.18734	1.229000|1.229000	0.43630|0.43630	0.561000|0.561000	0.74099|0.74099	GAT|AAG		0.567	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276		A	203151867	C	A	203151867	3	1	61	1	0	0	0	0	1	0	0	0	3346	912	32	2	592	2	CHI3L1	1	203151867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53825	203151867	46098754	967	8952										
CHIT1	1118	broad.mit.edu	37	chr1	203192283	203192283	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcgattttgtccacctcGtatccagcatccacataggt	9	12	0	0	rs114168492	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203192283G>A	ENST00000367229.1	-	6	619	c.585C>T	c.(583-585)taC>taT	p.Y195Y	CHIT1_ENST00000255427.3_Silent_p.Y176Y|CHIT1_ENST00000484834.1_Intron|CHIT1_ENST00000535569.1_Silent_p.Y186Y	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	195					chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)	p.Y195Y(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						TGTCCACCTCGTATCCAGCAT	0.577													G|||	8	0.00159744	0.0045	0	5008	,	,		20758	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		35,4371	38.4+/-70.7	0,35,2168	145	137	139		585	-8.2	0	1	dbSNP_132	139	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	CHIT1	NM_003465.2		0,44,6459	AA,AG,GG		0.1047,0.7944,0.3383		195/467	203192283	44,12962	2203	4300	6503	201458906	SO:0001819	synonymous_variant	1118			U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.585C>T	1.37:g.203192283G>A			201458906	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Silent	SNP	ENST00000367229.1	37	CCDS1436.1																																																																																				0.577	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465		A	203192283	G	A	203192283	2	1	61	1	0	0	0	0	0	0	0	1	3352	1140	40	1		1	CHIT1	1	203192283	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40416	203192283	46058338	968	8953										
FMOD	2331	broad.mit.edu	37	chr1	203316631	203316631	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctatcggggacggtgtaGacattgttgtgctccatgta	13	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203316631G>T	ENST00000354955.4	-	2	1231	c.768C>A	c.(766-768)gtC>gtA	p.V256V	FMOD_ENST00000493296.1_Intron	NM_002023.4	NP_002014.2	Q06828	FMOD_HUMAN	fibromodulin	256					carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor complex assembly (GO:0007181)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.V256V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	17			BRCA - Breast invasive adenocarcinoma(75;0.171)			GGACGGTGTAGACATTGTTGT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	1											104	100	101					1																	203316631		2203	4300	6503	201583254	SO:0001819	synonymous_variant	2331			U05291	CCDS30976.1	1q32	2008-02-05			ENSG00000122176	ENSG00000122176		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3774	protein-coding gene	gene with protein product	"fibromodulin proteoglycan"	600245				7851907	Standard	NM_002023		Approved	SLRR2E	uc001gzr.3	Q06828	OTTHUMG00000035910	ENST00000354955.4:c.768C>A	1.37:g.203316631G>T			201583254	Q15331|Q8IV47	Silent	SNP	ENST00000354955.4	37	CCDS30976.1																																																																																				0.567	FMOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087472.1	NM_002023		T	203316631	G	T	203316631	2	4	61	1	0	0	0	0	0	0	0	1	5978	929	33	2		2	FMOD	1	203316631	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	124348	203316631	45933990	969	8954										
PRELP	5549	broad.mit.edu	37	chr1	203452712	203452712	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgcgatggattaacctgGacaacaaccgaatccgcaag	10	12	0	0	rs574411918		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203452712G>T	ENST00000343110.2	+	2	527	c.400G>T	c.(400-402)Gac>Tac	p.D134Y		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	134					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.D134Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			GATTAACCTGGACAACAACCG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	87	88					1																	203452712		2203	4300	6503	201719335	SO:0001583	missense	5549			BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	9357	protein-coding gene	gene with protein product	"prolargin proteoglycan"	601914	"proline arginine-rich end leucine-rich repeat protein"				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.400G>T	1.37:g.203452712G>T	ENSP00000343924:p.Asp134Tyr		201719335	Q6FG38	Missense_Mutation	SNP	ENST00000343110.2	37	CCDS1438.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.346727	0.61073	.	.	ENSG00000188783	ENST00000343110	T	0.57752	0.38	4.71	4.71	0.59529	.	0.190722	0.46145	D	0.000317	T	0.53932	0.1827	L	0.27944	0.81	0.51482	D	0.999929	D	0.61080	0.989	P	0.61201	0.885	T	0.44772	-0.9306	10	0.09843	T	0.71	-16.2896	16.2483	0.82460	0.0:0.0:1.0:0.0	.	134	P51888	PRELP_HUMAN	Y	134	ENSP00000343924:D134Y	ENSP00000343924:D134Y	D	+	1	0	PRELP	201719335	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.088000	0.71371	2.165000	0.68154	0.462000	0.41574	GAC		0.557	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725		T	203452712	G	T	203452712	3	4	61	1	0	0	0	0	1	0	0	0	12507	1174	41	2	402	2	PRELP	1	203452712	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136081	203452712	45797909	970	8955										
OPTC	26254	broad.mit.edu	37	chr1	203467859	203467859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggttcctctgtgtattgcGatgacattgacctagaggac	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203467859G>A	ENST00000367222.2	+	4	537	c.421G>A	c.(421-423)Gat>Aat	p.D141N		NM_014359.3	NP_055174.1	Q9UBM4	OPT_HUMAN	opticin	141	LRRNT.				negative regulation of angiogenesis (GO:0016525)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.D141N(1)		breast(1)|cervix(1)|kidney(5)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.109)			TGTGTATTGCGATGACATTGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											167	129	142					1																	203467859		2203	4300	6503	201734482	SO:0001583	missense	26254			AF161702	CCDS1439.1	1q31	2008-02-05			ENSG00000188770	ENSG00000188770			8158	protein-coding gene	gene with protein product	"oculoglycan"	605127				10636917	Standard	NM_014359		Approved		uc001gzu.1	Q9UBM4	OTTHUMG00000036100	ENST00000367222.2:c.421G>A	1.37:g.203467859G>A	ENSP00000356191:p.Asp141Asn		201734482	Q5T2G4	Missense_Mutation	SNP	ENST00000367222.2	37	CCDS1439.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527220	0.85706	.	.	ENSG00000188770	ENST00000367222	T	0.02446	4.29	4.85	3.94	0.45596	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	M	0.77820	2.39	0.53688	D	0.999976	D	0.71674	0.998	P	0.58391	0.838	T	0.00775	-1.1571	10	0.72032	D	0.01	-17.5731	11.7228	0.51691	0.0861:0.0:0.9139:0.0	.	141	Q9UBM4	OPT_HUMAN	N	141	ENSP00000356191:D141N	ENSP00000356191:D141N	D	+	1	0	OPTC	201734482	1.000000	0.71417	0.078000	0.20375	0.878000	0.50629	5.453000	0.66645	1.263000	0.44181	0.561000	0.74099	GAT		0.562	OPTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087964.1	NM_014359		A	203467859	G	A	203467859	3	1	61	1	0	0	0	0	1	0	0	0	10919	1058	37	1	431	1	OPTC	1	203467859	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15147	203467859	45782762	971	8956										
ATP2B4	493	broad.mit.edu	37	chr1	203671198	203671198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaggagtccctgaaaatCgcaacaaaggtaacctctcc	7	12	1	1	rs141117629		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203671198C>T	ENST00000357681.5	+	7	2051	c.928C>T	c.(928-930)Cgc>Tgc	p.R310C	ATP2B4_ENST00000391954.2_Missense_Mutation_p.R310C|ATP2B4_ENST00000367219.3_Intron|ATP2B4_ENST00000341360.2_Missense_Mutation_p.R310C|ATP2B4_ENST00000367218.3_Missense_Mutation_p.R310C	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	310					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.R310C(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CCCTGAAAATCGCAACAAAGG	0.433											OREG0014124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1						C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	136	132	133		928,928	5.7	1	1	dbSNP_134	133	0,8600		0,0,4300	no	missense,missense	ATP2B4	NM_001001396.2,NM_001684.4	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	310/1171,310/1206	203671198	1,13005	2203	4300	6503	201937821	SO:0001583	missense	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.928C>T	1.37:g.203671198C>T	ENSP00000350310:p.Arg310Cys	2138	201937821	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	37	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.493980	0.64186	2.27E-4	0.0	ENSG00000058668	ENST00000357681;ENST00000367218;ENST00000391954;ENST00000341360	D;D;D;D	0.93307	-3.19;-3.2;-3.18;-3.2	5.65	5.65	0.86999	ATPase, P-type, ATPase-associated domain (1);	.	.	.	.	D	0.92424	0.7595	N	0.08118	0	0.80722	D	1	B;B;D	0.89917	0.044;0.043;1.0	B;B;D	0.65773	0.027;0.008;0.938	D	0.94031	0.7301	9	0.56958	D	0.05	-9.5457	18.4987	0.90874	0.0:1.0:0.0:0.0	.	310;310;310	P23634;P23634-6;B1APW5	AT2B4_HUMAN;.;.	C	310	ENSP00000350310:R310C;ENSP00000356187:R310C;ENSP00000375816:R310C;ENSP00000340930:R310C	ENSP00000340930:R310C	R	+	1	0	ATP2B4	201937821	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.130000	0.77235	2.673000	0.90976	0.557000	0.71058	CGC		0.433	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		T	203671198	C	T	203671198	3	4	61	1	0	0	0	0	1	0	0	0	1143	884	31	1	950	1	ATP2B4	1	203671198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203339	203671198	45579423	972	8957										
ATP2B4	493	broad.mit.edu	37	chr1	203672838	203672838	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaacagccaggagggaatCgacaatgaggaaaaggacaa	12	8	1	1	rs576322841		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203672838C>T	ENST00000357681.5	+	8	2119	c.996C>T	c.(994-996)atC>atT	p.I332I	ATP2B4_ENST00000391954.2_Silent_p.I332I|ATP2B4_ENST00000367219.3_Silent_p.I320I|ATP2B4_ENST00000341360.2_Silent_p.I332I|ATP2B4_ENST00000367218.3_Silent_p.I332I	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	332					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.I332I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AGGAGGGAATCGACAATGAGG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	1											109	100	103					1																	203672838		2203	4300	6503	201939461	SO:0001819	synonymous_variant	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.996C>T	1.37:g.203672838C>T			201939461	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Silent	SNP	ENST00000357681.5	37	CCDS1440.1																																																																																				0.532	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		T	203672838	C	T	203672838	2	4	61	1	0	0	0	0	0	0	0	1	1143	874	31	1		1	ATP2B4	1	203672838	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1640	203672838	45577783	973	8958										
ATP2B4	493	broad.mit.edu	37	chr1	203676208	203676208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaactttgtgataaatCgcagaccatggctccctgag	9	10	0	4	rs376933890		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203676208C>T	ENST00000357681.5	+	9	2294	c.1171C>T	c.(1171-1173)Cgc>Tgc	p.R391C	ATP2B4_ENST00000391954.2_Missense_Mutation_p.R391C|ATP2B4_ENST00000367219.3_Missense_Mutation_p.R379C|ATP2B4_ENST00000341360.2_Missense_Mutation_p.R391C|ATP2B4_ENST00000367218.3_Missense_Mutation_p.R391C	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	391					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.R391C(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGTGATAAATCGCAGACCATG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	155	124	135		1171,1171	0.6	0	1		135	0,8600		0,0,4300	no	missense,missense	ATP2B4	NM_001001396.2,NM_001684.4	180,180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	391/1171,391/1206	203676208	2,13004	2203	4300	6503	201942831	SO:0001583	missense	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.1171C>T	1.37:g.203676208C>T	ENSP00000350310:p.Arg391Cys		201942831	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	37	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.914446	0.33815	4.54E-4	0.0	ENSG00000058668	ENST00000357681;ENST00000367218;ENST00000367219;ENST00000391954;ENST00000341360	D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45	6.17	0.562	0.17290	ATPase, P-type, ATPase-associated domain (1);	0.850395	0.10134	N	0.711704	D	0.92277	0.7550	M	0.62088	1.915	0.20403	N	0.99991	D;D;D	0.63046	0.992;0.961;0.99	P;B;P	0.53549	0.729;0.319;0.536	D	0.86530	0.1821	10	0.66056	D	0.02	-0.1077	21.9586	0.99964	0.0:0.3231:0.6769:0.0	.	391;391;391	P23634;P23634-6;B1APW5	AT2B4_HUMAN;.;.	C	391;391;379;391;391	ENSP00000350310:R391C;ENSP00000356187:R391C;ENSP00000356188:R379C;ENSP00000375816:R391C;ENSP00000340930:R391C	ENSP00000340930:R391C	R	+	1	0	ATP2B4	201942831	0.000000	0.05858	0.001000	0.08648	0.092000	0.18411	-0.477000	0.06583	0.121000	0.18284	-0.176000	0.13171	CGC		0.468	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		T	203676208	C	T	203676208	3	4	61	1	0	0	0	0	1	0	0	0	1143	884	31	1	1201	1	ATP2B4	1	203676208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3370	203676208	45574413	974	8959										
ATP2B4	493	broad.mit.edu	37	chr1	203702501	203702501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccccaccacttctgttCctgctgtttcatctcctcct	3	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203702501C>T	ENST00000341360.2	+	20	3857	c.3460C>T	c.(3460-3462)Cct>Tct	p.P1154S	ATP2B4_ENST00000357681.5_Intron|ATP2B4_ENST00000391954.2_Missense_Mutation_p.P1118S|ATP2B4_ENST00000367219.3_Missense_Mutation_p.P1142S|ATP2B4_ENST00000367218.3_Missense_Mutation_p.P1154S			P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	0					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.P1154S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CACTTCTGTTCCTGCTGTTTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											190	158	169					1																	203702501		2203	4300	6503	201969124	SO:0001583	missense	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000341360.2:c.3460C>T	1.37:g.203702501C>T	ENSP00000340930:p.Pro1154Ser		201969124	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000341360.2	37	CCDS30977.1	.	.	.	.	.	.	.	.	.	.	C	0.037	-1.303694	0.01353	.	.	ENSG00000058668	ENST00000367218;ENST00000367219;ENST00000391954;ENST00000341360	D;D;D;D	0.92397	-3.01;-3.0;-3.03;-3.01	3.67	-0.589	0.11683	.	.	.	.	.	T	0.77280	0.4107	N	0.04508	-0.205	0.21553	N	0.999642	B	0.02656	0.0	B	0.04013	0.001	T	0.62358	-0.6871	9	0.02654	T	1	.	10.3567	0.43969	0.0:0.4487:0.4194:0.1319	.	1154	B1APW5	.	S	1154;1142;1118;1154	ENSP00000356187:P1154S;ENSP00000356188:P1142S;ENSP00000375816:P1118S;ENSP00000340930:P1154S	ENSP00000340930:P1154S	P	+	1	0	ATP2B4	201969124	1.000000	0.71417	0.839000	0.33178	0.460000	0.32559	3.421000	0.52742	-0.091000	0.12440	-1.291000	0.01355	CCT		0.448	ATP2B4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087463.1	NM_001001396		T	203702501	C	T	203702501	3	4	61	1	0	0	0	0	1	0	0	0	1143	855	30	3	3538	3	ATP2B4	1	203702501	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26293	203702501	45548120	975	8960										
LAX1	54900	broad.mit.edu	37	chr1	203743523	203743523	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcagcagatcccagtgGaagccagcagcaggctgaga	13	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203743523G>A	ENST00000442561.2	+	5	1301	c.911G>A	c.(910-912)gGa>gAa	p.G304E	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Missense_Mutation_p.G288E	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	304					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)	p.G304E(1)		central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GATCCCAGTGGAAGCCAGCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											80	76	77					1																	203743523		2203	4300	6503	202010146	SO:0001583	missense	54900			AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"LAT-like membrane associated protein", "linker for activation of x cells"					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.911G>A	1.37:g.203743523G>A	ENSP00000406970:p.Gly304Glu		202010146	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	37	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845785	0.32606	.	.	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	4.79	3.86	0.44501	.	0.833616	0.10640	N	0.651165	T	0.22781	0.0550	N	0.16656	0.425	0.09310	N	1	P;P	0.35107	0.484;0.484	B;B	0.35655	0.207;0.207	T	0.12785	-1.0534	9	0.17369	T	0.5	-1.2747	9.5358	0.39222	0.0978:0.0:0.9022:0.0	.	288;304	B7Z744;Q8IWV1	.;LAX1_HUMAN	E	304;288	.	ENSP00000356186:G288E	G	+	2	0	LAX1	202010146	0.001000	0.12720	0.002000	0.10522	0.460000	0.32559	0.828000	0.27435	1.341000	0.45600	0.655000	0.94253	GGA		0.517	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773		A	203743523	G	A	203743523	3	1	61	1	0	0	0	0	1	0	0	0	8670	1174	41	3	974	3	LAX1	1	203743523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41022	203743523	45507098	976	8961										
ZC3H11A	9877	broad.mit.edu	37	chr1	203807188	203807188	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacattgacaaaacaccaaaGaaaggtacctgtgttcttac	6	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:203807188G>T	ENST00000545588.1	+	10	4796	c.969G>T	c.(967-969)aaG>aaT	p.K323N	ZC3H11A_ENST00000367210.1_Missense_Mutation_p.K323N|ZC3H11A_ENST00000367212.3_Missense_Mutation_p.K323N|ZC3H11A_ENST00000332127.4_Missense_Mutation_p.K323N|ZC3H11A_ENST00000367214.1_Missense_Mutation_p.K323N	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	323					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.K323N(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AAACACCAAAGAAAGGTACCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	89	94					1																	203807188		2203	4300	6503	202073811	SO:0001583	missense	9877				CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.969G>T	1.37:g.203807188G>T	ENSP00000438527:p.Lys323Asn		202073811	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000545588.1	37	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011497	0.75046	.	.	ENSG00000058673	ENST00000453771;ENST00000367214;ENST00000537080;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.75	4.84	0.62591	.	0.519008	0.23378	N	0.048830	T	0.58779	0.2146	M	0.65498	2.005	0.37236	D	0.905918	D	0.59357	0.985	P	0.59171	0.853	T	0.61778	-0.6993	10	0.24483	T	0.36	-17.993	11.0117	0.47667	0.0857:0.0:0.9143:0.0	.	323	O75152	ZC11A_HUMAN	N	323;323;269;323;323;323;323	ENSP00000356183:K323N;ENSP00000356181:K323N;ENSP00000333253:K323N;ENSP00000438527:K323N;ENSP00000356179:K323N	ENSP00000333253:K323N	K	+	3	2	ZC3H11A	202073811	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.502000	0.45398	1.580000	0.49851	0.650000	0.86243	AAG		0.398	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		T	203807188	G	T	203807188	3	4	61	1	0	0	0	0	1	0	0	0	17599	933	33	2	1003	2	ZC3H11A	1	203807188	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63665	203807188	45443433	977	8962										
SOX13	9580	broad.mit.edu	37	chr1	204095205	204095205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaccggtacagcgaggaCgaggactcggagggcgaaga	17	8	0	1	rs200693347		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204095205C>T	ENST00000367204.1	+	14	1921	c.1812C>T	c.(1810-1812)gaC>gaT	p.D604D		NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	604					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D604D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			ACAGCGAGGACGAGGACTCGG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	1											140	177	164					1																	204095205		2184	4270	6454	202361828	SO:0001819	synonymous_variant	9580				CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"SRY (sex determining region Y)-boxes"	11192	protein-coding gene	gene with protein product	"islet cell antibody 12", "SRY-related HMG-box gene 13", "type 1 diabetes autoantigen", "SRY-box 13"	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.1812C>T	1.37:g.204095205C>T			202361828	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Silent	SNP	ENST00000367204.1	37	CCDS44299.1																																																																																				0.627	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686		T	204095205	C	T	204095205	2	4	61	1	0	0	0	0	0	0	0	1	14981	535	19	1		1	SOX13	1	204095205	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	288017	204095205	45155416	978	8963										
ETNK2	55224	broad.mit.edu	37	chr1	204109170	204109170	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcccctctcacctgcaaaCtcattgaaatggttgccaat	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204109170C>T	ENST00000367202.4	-	5	1011	c.861G>A	c.(859-861)gaG>gaA	p.E287E	RP11-74C13.3_ENST00000433869.1_RNA|ETNK2_ENST00000367199.2_Silent_p.E218E|ETNK2_ENST00000367197.1_5'UTR|ETNK2_ENST00000477125.1_5'UTR|ETNK2_ENST00000367201.3_Silent_p.E287E|ETNK2_ENST00000367198.2_Silent_p.E109E	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	287					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)	p.E287E(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CACCTGCAAACTCATTGAAAT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											170	143	152					1																	204109170		2203	4300	6503	202375793	SO:0001819	synonymous_variant	55224			AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.861G>A	1.37:g.204109170C>T			202375793	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Silent	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	C	9.552	1.116073	0.20795	.	.	ENSG00000143845	ENST00000422072	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	T	0.63498	0.2516	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61676	-0.7014	4	.	.	.	-11.0304	11.4456	0.50120	0.0:0.9161:0.0:0.0839	.	.	.	.	N	50	.	.	S	-	2	0	ETNK2	202375793	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.495000	0.35627	2.525000	0.85131	0.650000	0.86243	AGT		0.443	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		T	204109170	C	T	204109170	2	4	61	1	0	0	0	0	0	0	0	1	5287	564	20	3		3	ETNK2	1	204109170	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13965	204109170	45141451	979	8964										
REN	5972	broad.mit.edu	37	chr1	204124205	204124205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaactctgtgtagaactttCggatgaaggtggcccccagg	12	10	1	2	rs371478505		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204124205C>T	ENST00000272190.8	-	10	1188	c.1160G>A	c.(1159-1161)cGa>cAa	p.R387Q	REN_ENST00000367195.2_Missense_Mutation_p.R384Q|ETNK2_ENST00000367199.2_5'Flank	NM_000537.3	NP_000528.1	P00797	RENI_HUMAN	renin	387					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cell maturation (GO:0048469)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|drinking behavior (GO:0042756)|hormone-mediated signaling pathway (GO:0009755)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mesonephros development (GO:0001823)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of MAPK cascade (GO:0043408)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cAMP (GO:0051591)|response to cGMP (GO:0070305)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|peptidase activity (GO:0008233)|receptor binding (GO:0005102)	p.R387Q(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(4)|urinary_tract(1)	19	all_cancers(21;0.00965)|Breast(84;0.116)|all_epithelial(62;0.157)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)		Aliskiren(DB01258)|Remikiren(DB00212)	GTAGAACTTTCGGATGAAGGT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	0,4406		0,0,2203	80	74	76		1160	5	1	1		76	1,8599		0,1,4299	no	missense	REN	NM_000537.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	387/407	204124205	1,13005	2203	4300	6503	202390828	SO:0001583	missense	5972			BC047752	CCDS30981.1	1q32	2008-02-05			ENSG00000143839	ENSG00000143839	3.4.23.15		9958	protein-coding gene	gene with protein product		179820					Standard	NM_000537		Approved		uc001haq.2	P00797	OTTHUMG00000036059	ENST00000272190.8:c.1160G>A	1.37:g.204124205C>T	ENSP00000272190:p.Arg387Gln		202390828	Q6FI38|Q6T5C2	Missense_Mutation	SNP	ENST00000272190.8	37	CCDS30981.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045818	0.75846	0.0	1.16E-4	ENSG00000143839	ENST00000367195;ENST00000545733;ENST00000272190	T;T	0.60797	0.16;0.16	5.03	5.03	0.67393	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.111183	0.64402	D	0.000014	T	0.61565	0.2357	M	0.64170	1.965	0.34330	D	0.687574	D	0.60160	0.987	P	0.45377	0.478	T	0.76247	-0.3029	10	0.72032	D	0.01	.	18.3198	0.90234	0.0:1.0:0.0:0.0	.	387	P00797	RENI_HUMAN	Q	384;306;387	ENSP00000356163:R384Q;ENSP00000272190:R387Q	ENSP00000272190:R387Q	R	-	2	0	REN	202390828	1.000000	0.71417	0.999000	0.59377	0.751000	0.42716	3.862000	0.56009	2.487000	0.83934	0.591000	0.81541	CGA		0.607	REN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087891.1	NM_000537		T	204124205	C	T	204124205	3	4	61	1	0	0	0	0	1	0	0	0	13261	884	31	1	64	1	REN	1	204124205	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15035	204124205	45126416	980	8965										
REN	5972	broad.mit.edu	37	chr1	204125321	204125321	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacatcaaacagcctcttCttggctcccaaggcctccat	5	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204125321C>A	ENST00000272190.8	-	8	973	c.945G>T	c.(943-945)aaG>aaT	p.K315N	REN_ENST00000367195.2_Missense_Mutation_p.K312N	NM_000537.3	NP_000528.1	P00797	RENI_HUMAN	renin	315					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cell maturation (GO:0048469)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|drinking behavior (GO:0042756)|hormone-mediated signaling pathway (GO:0009755)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mesonephros development (GO:0001823)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of MAPK cascade (GO:0043408)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cAMP (GO:0051591)|response to cGMP (GO:0070305)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|peptidase activity (GO:0008233)|receptor binding (GO:0005102)	p.K315N(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(4)|urinary_tract(1)	19	all_cancers(21;0.00965)|Breast(84;0.116)|all_epithelial(62;0.157)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)		Aliskiren(DB01258)|Remikiren(DB00212)	ACAGCCTCTTCTTGGCTCCCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											223	217	219					1																	204125321		2203	4300	6503	202391944	SO:0001583	missense	5972			BC047752	CCDS30981.1	1q32	2008-02-05			ENSG00000143839	ENSG00000143839	3.4.23.15		9958	protein-coding gene	gene with protein product		179820					Standard	NM_000537		Approved		uc001haq.2	P00797	OTTHUMG00000036059	ENST00000272190.8:c.945G>T	1.37:g.204125321C>A	ENSP00000272190:p.Lys315Asn		202391944	Q6FI38|Q6T5C2	Missense_Mutation	SNP	ENST00000272190.8	37	CCDS30981.1	.	.	.	.	.	.	.	.	.	.	C	2.664	-0.279115	0.05642	.	.	ENSG00000143839	ENST00000367195;ENST00000545733;ENST00000272190	T;T	0.58506	0.33;0.33	4.43	2.5	0.30297	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.802668	0.12134	N	0.496501	T	0.45034	0.1322	L	0.41710	1.295	0.26659	N	0.971955	B	0.18166	0.026	B	0.17979	0.02	T	0.31668	-0.9935	10	0.27082	T	0.32	.	7.5537	0.27812	0.0:0.7905:0.0:0.2095	.	315	P00797	RENI_HUMAN	N	312;234;315	ENSP00000356163:K312N;ENSP00000272190:K315N	ENSP00000272190:K315N	K	-	3	2	REN	202391944	0.961000	0.32948	0.997000	0.53966	0.369000	0.29798	0.144000	0.16135	0.404000	0.25506	0.462000	0.41574	AAG		0.562	REN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087891.1	NM_000537		A	204125321	C	A	204125321	3	1	61	1	0	0	0	0	1	0	0	0	13261	912	32	2	287	2	REN	1	204125321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1116	204125321	45125300	981	8966										
REN	5972	broad.mit.edu	37	chr1	204131291	204131291	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattctcttgaggaagatCctggcccagggtggaggaag	16	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204131291C>T	ENST00000272190.8	-	2	127	c.99G>A	c.(97-99)cgG>cgA	p.R33R	REN_ENST00000367195.2_Splice_Site_p.R33R	NM_000537.3	NP_000528.1	P00797	RENI_HUMAN	renin	33			R -> W (in dbSNP:rs11571098).		angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cell maturation (GO:0048469)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|drinking behavior (GO:0042756)|hormone-mediated signaling pathway (GO:0009755)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mesonephros development (GO:0001823)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of MAPK cascade (GO:0043408)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cAMP (GO:0051591)|response to cGMP (GO:0070305)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|peptidase activity (GO:0008233)|receptor binding (GO:0005102)	p.R33R(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(4)|urinary_tract(1)	19	all_cancers(21;0.00965)|Breast(84;0.116)|all_epithelial(62;0.157)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)		Aliskiren(DB01258)|Remikiren(DB00212)	TGAGGAAGATCCTGGCCCAGG	0.547											OREG0014128	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	1											96	82	87					1																	204131291		2203	4300	6503	202397914	SO:0001630	splice_region_variant	5972			BC047752	CCDS30981.1	1q32	2008-02-05			ENSG00000143839	ENSG00000143839	3.4.23.15		9958	protein-coding gene	gene with protein product		179820					Standard	NM_000537		Approved		uc001haq.2	P00797	OTTHUMG00000036059	ENST00000272190.8:c.99-1G>A	1.37:g.204131291C>T		2142	202397914	Q6FI38|Q6T5C2	Silent	SNP	ENST00000272190.8	37	CCDS30981.1																																																																																				0.547	REN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087891.1	NM_000537	Silent	T	204131291	C	T	204131291	5	4	61	1	0	0	0	0	0	0	1	0	13261	869	30	3	1157	3	REN	1	204131291	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5970	204131291	45119330	982	8967										
PPP1R15B	84919	broad.mit.edu	37	chr1	204379885	204379885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttcagcaaataggataCcacactgaaattgtctatgc	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204379885C>T	ENST00000367188.4	-	1	1034	c.655G>A	c.(655-657)Gta>Ata	p.V219I	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	219					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)	p.V219I(1)		breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			AAATAGGATACCACACTGAAA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	118	119					1																	204379885		2203	4300	6503	202646508	SO:0001583	missense	84919			AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.655G>A	1.37:g.204379885C>T	ENSP00000356156:p.Val219Ile		202646508	Q53GQ4|Q658M2|Q6P156|Q96SN1	Missense_Mutation	SNP	ENST00000367188.4	37	CCDS1445.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.979676	0.53827	.	.	ENSG00000158615	ENST00000367188;ENST00000543650	T	0.23754	1.89	5.4	3.54	0.40534	Protein phosphatase 1, regulatory subunit 15B, N-terminal (1);	0.207947	0.31392	N	0.007724	T	0.29028	0.0721	M	0.61703	1.905	0.24644	N	0.993559	B	0.24618	0.107	B	0.33690	0.168	T	0.30650	-0.9971	10	0.87932	D	0	-7.4566	8.3387	0.32230	0.0:0.8184:0.0:0.1816	.	219	Q5SWA1	PR15B_HUMAN	I	219;129	ENSP00000356156:V219I	ENSP00000356156:V219I	V	-	1	0	PPP1R15B	202646508	0.895000	0.30542	0.572000	0.28498	0.278000	0.26855	2.560000	0.45896	0.651000	0.30788	0.655000	0.94253	GTA		0.498	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		T	204379885	C	T	204379885	3	4	61	1	0	0	0	0	1	0	0	0	12398	507	18	3	1494	3	PPP1R15B	1	204379885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	248594	204379885	44870736	983	8968										
PIK3C2B	5287	broad.mit.edu	37	chr1	204394013	204394013	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacttcgagatcccagggcGaaccagccggtcttctcctg	11	14	2	2	rs577562908		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204394013G>A	ENST00000367187.3	-	34	5428	c.4872C>T	c.(4870-4872)ttC>ttT	p.F1624F	PIK3C2B_ENST00000424712.2_Silent_p.F1596F|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1624					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.F1624F(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			ATCCCAGGGCGAACCAGCCGG	0.642													G|||	1	0.000199681	0	0	5008	,	,		17201	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	1											63	57	59					1																	204394013		2203	4300	6503	202660636	SO:0001819	synonymous_variant	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4872C>T	1.37:g.204394013G>A			202660636	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																				0.642	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		A	204394013	G	A	204394013	2	1	61	1	0	0	0	0	0	0	0	1	11941	1049	37	1		1	PIK3C2B	1	204394013	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14128	204394013	44856608	984	8969										
PIK3C2B	5287	broad.mit.edu	37	chr1	204401413	204401413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcttgagagtgtgtgttCgggaggcaaaggagagggtc	18	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204401413C>T	ENST00000367187.3	-	28	4626	c.4070G>A	c.(4069-4071)cGa>cAa	p.R1357Q	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R1329Q|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1357					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R1357Q(1)|p.R1357L(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			AGTGTGTGTTCGGGAGGCAAA	0.502																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											124	120	121					1																	204401413		2203	4300	6503	202668036	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4070G>A	1.37:g.204401413C>T	ENSP00000356155:p.Arg1357Gln		202668036	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	c	19.80	3.895587	0.72639	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.61158	0.13;0.29	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.61961	0.2389	L	0.42686	1.345	0.35678	D	0.81385	P;D	0.71674	0.582;0.998	B;P	0.55999	0.18;0.789	T	0.65425	-0.6171	10	0.31617	T	0.26	.	13.4575	0.61208	0.0:0.9282:0.0:0.0718	.	1329;1357	F5GWN5;O00750	.;P3C2B_HUMAN	Q	1357;1329	ENSP00000356155:R1357Q;ENSP00000400561:R1329Q	ENSP00000356155:R1357Q	R	-	2	0	PIK3C2B	202668036	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	2.790000	0.47821	2.891000	0.99171	0.651000	0.88453	CGA		0.502	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		T	204401413	C	T	204401413	3	4	61	1	0	0	0	0	1	0	0	0	11941	884	31	1	862	1	PIK3C2B	1	204401413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7400	204401413	44849208	985	8970										
PIK3C2B	5287	broad.mit.edu	37	chr1	204433727	204433727	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggatgtcagagccagatCgaaggctgtacaggaagaaa	13	7	1	3	rs2271416	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204433727C>T	ENST00000367187.3	-	5	1596	c.1040G>A	c.(1039-1041)cGa>cAa	p.R347Q	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R347Q	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	347					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R347Q(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			AGAGCCAGATCGAAGGCTGTA	0.517													C|||	2	0.000399361	0	0	5008	,	,		21001	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	0,4406		0,0,2203	93	93	93		1040	5.2	0.4	1	dbSNP_100	93	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PIK3C2B	NM_002646.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	347/1635	204433727	1,13005	2203	4300	6503	202700350	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1040G>A	1.37:g.204433727C>T	ENSP00000356155:p.Arg347Gln		202700350	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	26.1	4.702449	0.88924	0.0	1.16E-4	ENSG00000133056	ENST00000367187;ENST00000424712;ENST00000438854;ENST00000367184	T;T	0.69926	-0.27;-0.44	5.24	5.24	0.73138	.	0.222120	0.29631	N	0.011613	T	0.78059	0.4224	L	0.50333	1.59	0.37830	D	0.928707	D;D	0.89917	1.0;0.997	D;D	0.80764	0.994;0.968	T	0.81178	-0.1051	10	0.72032	D	0.01	.	16.7749	0.85548	0.0:1.0:0.0:0.0	rs2271416;rs2271416	347;347	F5GWN5;O00750	.;P3C2B_HUMAN	Q	347;347;125;125	ENSP00000356155:R347Q;ENSP00000400561:R347Q	ENSP00000356152:R125Q	R	-	2	0	PIK3C2B	202700350	0.992000	0.36948	0.412000	0.26496	0.893000	0.52053	5.131000	0.64751	2.723000	0.93209	0.655000	0.94253	CGA		0.517	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		T	204433727	C	T	204433727	3	4	61	1	0	0	0	0	1	0	0	0	11941	884	31	1	3984	1	PIK3C2B	1	204433727	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32314	204433727	44816894	986	8971										
MDM4	4194	broad.mit.edu	37	chr1	204518437	204518437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattgtcgaagaaccatttCggctcctgtcgttagaccta	9	10	0	3	rs201947927		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204518437C>T	ENST00000367182.3	+	11	1262	c.1100C>T	c.(1099-1101)tCg>tTg	p.S367L	MDM4_ENST00000454264.2_Missense_Mutation_p.S317L|MDM4_ENST00000391947.2_3'UTR|MDM4_ENST00000463049.1_3'UTR|MDM4_ENST00000367183.3_Missense_Mutation_p.S41L|MDM4_ENST00000507825.2_Intron	NM_001204171.1|NM_001278516.1|NM_001278517.1|NM_001278518.1|NM_001278519.1|NM_002393.4	NP_001191100.1|NP_001265445.1|NP_001265446.1|NP_001265447.1|NP_001265448.1|NP_002384.2	O15151	MDM4_HUMAN	MDM4, p53 regulator	367					cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|G0 to G1 transition (GO:0045023)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|zinc ion binding (GO:0008270)	p.S367L(2)		central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			AGAACCATTTCGGCTCCTGTC	0.408			A		"GBM, bladder, retinoblastoma"								C|||	1	0.000199681	0	0.0014	5008	,	,		22943	0		0	False		,,,				2504	0						Dom	yes		1	1q32	4194	Mdm4 p53 binding protein homolog		M	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	1											139	137	138					1																	204518437		2203	4300	6503	202785060	SO:0001583	missense	4194			AF007111	CCDS1447.1, CCDS55674.1, CCDS55675.1, CCDS60396.1, CCDS73007.1, CCDS73008.1, CCDS73009.1	1q32	2014-03-03	2014-03-03		ENSG00000198625	ENSG00000198625			6974	protein-coding gene	gene with protein product		602704	"mouse double minute 4, human homolog of; p53-binding protein", "Mdm4, transformed 3T3 cell double minute 4, p53 binding protein (mouse)", "Mdm4 p53 binding protein homolog (mouse)"			9226370, 14660608	Standard	NM_002393		Approved	MDMX, HDMX	uc001hba.3	O15151	OTTHUMG00000035877	ENST00000367182.3:c.1100C>T	1.37:g.204518437C>T	ENSP00000356150:p.Ser367Leu		202785060	Q2M2Y2|Q32SL2|Q6GS18|Q8IV83	Missense_Mutation	SNP	ENST00000367182.3	37	CCDS1447.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	34	5.345498	0.95807	.	.	ENSG00000198625	ENST00000367182;ENST00000454264;ENST00000367183;ENST00000444261	T;T;T;T	0.50813	2.86;2.86;0.73;2.86	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67382	0.932;0.951	T	0.61922	-0.6963	10	0.62326	D	0.03	-11.2631	20.4745	0.99168	0.0:1.0:0.0:0.0	.	367;317	O15151;Q2M2Y2	MDM4_HUMAN;.	L	367;317;41;145	ENSP00000356150:S367L;ENSP00000396840:S317L;ENSP00000356151:S41L;ENSP00000395254:S145L	ENSP00000356150:S367L	S	+	2	0	MDM4	202785060	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.461000	0.80834	2.941000	0.99782	0.655000	0.94253	TCG		0.408	MDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087415.2	NM_002393		T	204518437	C	T	204518437	3	4	61	1	0	0	0	0	1	0	0	0	9444	893	31	1	1138	1	MDM4	1	204518437	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84710	204518437	44732184	987	8972										
NFASC	23114	broad.mit.edu	37	chr1	204913519	204913519	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtcttggcggagccatcGaaattcctatggatcgtgag	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204913519G>A	ENST00000401399.1	+	2	275	c.76G>A	c.(76-78)Gaa>Aaa	p.E26K	NFASC_ENST00000367171.4_Missense_Mutation_p.E26K|NFASC_ENST00000367172.4_Missense_Mutation_p.E26K|NFASC_ENST00000339876.6_Missense_Mutation_p.E26K|NFASC_ENST00000513543.1_Missense_Mutation_p.E26K|NFASC_ENST00000367170.4_Missense_Mutation_p.E26K|NFASC_ENST00000360049.4_Missense_Mutation_p.E26K|NFASC_ENST00000404076.1_Missense_Mutation_p.E26K|NFASC_ENST00000338515.6_Missense_Mutation_p.E26K|NFASC_ENST00000403080.1_Missense_Mutation_p.E26K|NFASC_ENST00000539706.1_Missense_Mutation_p.E26K|NFASC_ENST00000404907.1_Missense_Mutation_p.E26K|NFASC_ENST00000367169.4_Missense_Mutation_p.E26K|NFASC_ENST00000338586.6_Missense_Mutation_p.E26K			O94856	NFASC_HUMAN	neurofascin	26					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.E26K(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CGGAGCCATCGAAATTCCTAT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	48	49					1																	204913519		2203	4300	6503	203180142	SO:0001583	missense	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.76G>A	1.37:g.204913519G>A	ENSP00000385637:p.Glu26Lys		203180142	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742638	0.69418	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;T;T	0.85171	-0.14;-0.18;-0.12;-0.12;-0.09;-0.12;-0.04;-0.02;-0.09;-0.56;-0.57;-0.15;-0.09;-1.95;-0.04;-0.02;-0.11	5.33	5.33	0.75918	.	0.000000	0.42821	D	0.000656	T	0.77232	0.4100	N	0.08118	0	0.46609	D	0.999128	B;B;P;D;B;B	0.56746	0.029;0.0;0.945;0.977;0.001;0.021	B;B;P;P;B;B	0.47528	0.029;0.0;0.449;0.549;0.003;0.01	T	0.81417	-0.0942	10	0.54805	T	0.06	.	15.8689	0.79091	0.0:0.0:1.0:0.0	.	26;26;128;26;26;26	O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.	K	26;26;26;26;26;26;26;26;26;26;26;26;26;26;26;26;26;2	ENSP00000356140:E26K;ENSP00000356139:E26K;ENSP00000356138:E26K;ENSP00000342128:E26K;ENSP00000344786:E26K;ENSP00000343509:E26K;ENSP00000438614:E26K;ENSP00000353154:E26K;ENSP00000356137:E26K;ENSP00000412161:E26K;ENSP00000384875:E26K;ENSP00000385676:E26K;ENSP00000385637:E26K;ENSP00000427586:E26K;ENSP00000384061:E26K;ENSP00000425908:E26K;ENSP00000415031:E2K	ENSP00000295776:E26K	E	+	1	0	NFASC	203180142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.712000	0.68407	2.779000	0.95612	0.561000	0.74099	GAA		0.597	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204913519	G	A	204913519	3	1	61	1	0	0	0	0	1	0	0	0	10390	1059	37	1	78	1	NFASC	1	204913519	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	395082	204913519	44337102	988	8973										
NFASC	23114	broad.mit.edu	37	chr1	204923410	204923410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccctggtgattgacttcCgcagtggcgggcggccggag	18	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:204923410C>T	ENST00000401399.1	+	5	509	c.310C>T	c.(310-312)Cgc>Tgc	p.R104C	NFASC_ENST00000367171.4_Missense_Mutation_p.R104C|NFASC_ENST00000367172.4_Missense_Mutation_p.R104C|NFASC_ENST00000339876.6_Missense_Mutation_p.R104C|NFASC_ENST00000513543.1_Missense_Mutation_p.R98C|NFASC_ENST00000367170.4_Missense_Mutation_p.R104C|NFASC_ENST00000360049.4_Missense_Mutation_p.R98C|NFASC_ENST00000404076.1_Missense_Mutation_p.R98C|NFASC_ENST00000338515.6_Missense_Mutation_p.R104C|NFASC_ENST00000403080.1_Missense_Mutation_p.R104C|NFASC_ENST00000539706.1_Missense_Mutation_p.R98C|NFASC_ENST00000404907.1_Missense_Mutation_p.R98C|NFASC_ENST00000367169.4_Missense_Mutation_p.R104C|NFASC_ENST00000338586.6_Missense_Mutation_p.R104C			O94856	NFASC_HUMAN	neurofascin	104	Ig-like C2-type 1.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.R98C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GATTGACTTCCGCAGTGGCGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	54	53					1																	204923410		2203	4300	6503	203190033	SO:0001583	missense	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.310C>T	1.37:g.204923410C>T	ENSP00000385637:p.Arg104Cys		203190033	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827836	0.90955	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;T;T	0.95885	-0.21;-0.27;-0.19;-0.2;-0.2;-0.2;-0.12;-0.1;-0.18;-0.73;-0.66;-0.23;-0.2;-3.84;-0.12;-0.1;-0.11	5.37	5.37	0.77165	.	0.115488	0.39210	N	0.001437	D	0.96109	0.8732	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D	0.71674	0.993;0.988;0.98;0.998;0.992;0.997	P;B;P;P;P;P	0.55965	0.509;0.435;0.663;0.788;0.674;0.745	D	0.95298	0.8401	10	0.37606	T	0.19	.	18.6966	0.91603	0.0:1.0:0.0:0.0	.	98;98;200;104;98;104	O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.	C	104;104;104;104;104;104;98;98;98;104;104;104;98;104;104;98;98;74	ENSP00000356140:R104C;ENSP00000356139:R104C;ENSP00000356138:R104C;ENSP00000342128:R104C;ENSP00000344786:R104C;ENSP00000343509:R104C;ENSP00000438614:R98C;ENSP00000353154:R98C;ENSP00000356137:R104C;ENSP00000412161:R104C;ENSP00000384875:R104C;ENSP00000385676:R98C;ENSP00000385637:R104C;ENSP00000427586:R104C;ENSP00000384061:R98C;ENSP00000425908:R98C;ENSP00000415031:R74C	ENSP00000295776:R98C	R	+	1	0	NFASC	203190033	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.634000	0.54302	2.516000	0.84829	0.655000	0.94253	CGC		0.592	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204923410	C	T	204923410	3	4	61	1	0	0	0	0	1	0	0	0	10390	652	23	1	324	1	NFASC	1	204923410	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9891	204923410	44327211	989	8974										
CNTN2	6900	broad.mit.edu	37	chr1	205028276	205028276	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgacggacgggcgtcacttCgtgtcccagaccacagggaa	13	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:205028276C>T	ENST00000331830.4	+	6	836	c.552C>T	c.(550-552)ttC>ttT	p.F184F		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	184	Ig-like C2-type 2.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)	p.F184F(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GGCGTCACTTCGTGTCCCAGA	0.582																																					Melanoma(183;2548 2817 37099 41192)											1	Substitution - coding silent(1)	large_intestine(1)	1											75	64	68					1																	205028276		2203	4300	6503	203294899	SO:0001819	synonymous_variant	6900			X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.552C>T	1.37:g.205028276C>T			203294899	P78432|Q5T054	Silent	SNP	ENST00000331830.4	37	CCDS1449.1																																																																																				0.582	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		T	205028276	C	T	205028276	2	4	61	1	0	0	0	0	0	0	0	1	3647	883	31	1		1	CNTN2	1	205028276	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104866	205028276	44222345	990	8975										
CNTN2	6900	broad.mit.edu	37	chr1	205031103	205031103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctacagtgcgctggctgCggaacggggagcctctggcc	17	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:205031103C>T	ENST00000331830.4	+	9	1368	c.1084C>T	c.(1084-1086)Cgg>Tgg	p.R362W	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	362	Ig-like C2-type 4.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)	p.R362W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCGCTGGCTGCGGAACGGGGA	0.642											OREG0014144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Melanoma(183;2548 2817 37099 41192)											1	Substitution - Missense(1)	large_intestine(1)	1											18	21	20					1																	205031103		2200	4294	6494	203297726	SO:0001583	missense	6900			X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1084C>T	1.37:g.205031103C>T	ENSP00000330633:p.Arg362Trp	2149	203297726	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479028	0.84747	.	.	ENSG00000184144	ENST00000331830	D	0.83506	-1.73	5.16	3.17	0.36434	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47852	D	0.000205	D	0.90487	0.7020	M	0.83312	2.635	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.71656	0.974;0.96;0.974	D	0.90652	0.4583	10	0.72032	D	0.01	.	13.2951	0.60292	0.2975:0.7025:0.0:0.0	.	362;362;253	A1L3A3;Q02246;Q68DA2	.;CNTN2_HUMAN;.	W	362	ENSP00000330633:R362W	ENSP00000330633:R362W	R	+	1	2	CNTN2	203297726	0.972000	0.33761	0.999000	0.59377	0.993000	0.82548	2.272000	0.43373	0.478000	0.27488	0.557000	0.71058	CGG		0.642	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		T	205031103	C	T	205031103	3	4	61	1	0	0	0	0	1	0	0	0	3647	759	27	1	1114	1	CNTN2	1	205031103	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2827	205031103	44219518	991	8976										
DSTYK	25778	broad.mit.edu	37	chr1	205129252	205129252	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggacccacctcatatagtGaaattccaaagccagatcat	6	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:205129252G>T	ENST00000367162.3	-	8	2125	c.2095C>A	c.(2095-2097)Cac>Aac	p.H699N	DSTYK_ENST00000367161.3_Missense_Mutation_p.H699N|DSTYK_ENST00000367160.4_Intron	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	699	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.H160N(1)|p.H699N(1)		breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						CTCATATAGTGAAATTCCAAA	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	1											146	148	148					1																	205129252		2203	4300	6503	203395875	SO:0001583	missense	25778			AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.2095C>A	1.37:g.205129252G>T	ENSP00000356130:p.His699Asn		203395875	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	37	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	G	32	5.131311	0.94473	.	.	ENSG00000133059	ENST00000367161;ENST00000367162	T;T	0.64260	-0.09;-0.09	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65893	0.2735	N	0.13168	0.305	0.80722	D	1	D;D;P	0.58620	0.983;0.978;0.529	P;D;B	0.63488	0.592;0.915;0.407	T	0.71041	-0.4707	10	0.62326	D	0.03	-19.8715	19.1782	0.93612	0.0:0.0:1.0:0.0	.	160;699;699	Q6XUX3-4;Q6XUX3-2;Q6XUX3	.;.;DUSTY_HUMAN	N	699	ENSP00000356129:H699N;ENSP00000356130:H699N	ENSP00000356129:H699N	H	-	1	0	DSTYK	203395875	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.437000	0.97535	2.641000	0.89580	0.563000	0.77884	CAC		0.463	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		T	205129252	G	T	205129252	3	4	61	1	0	0	0	0	1	0	0	0	4796	1290	45	2	718	2	DSTYK	1	205129252	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98149	205129252	44121369	992	8977										
ELK4	2005	broad.mit.edu	37	chr1	205589034	205589034	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtgtataaattctggatTtgcttaaaagggcaaataaa	9	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:205589034T>G	ENST00000357992.4	-	3	1420				ELK4_ENST00000289703.4_Missense_Mutation_p.Q380H|ELK4_ENST00000468523.1_5'Flank	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)	p.Q380H(1)	SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			AATTCTGGATTTGCTTAAAAG	0.383			T	SLC45A3	prostate																																		Dom	yes		1	1q32	2005	"ELK4, ETS-domain protein (SRF accessory protein 1)"		E	1	Substitution - Missense(1)	large_intestine(1)	1											62	64	64					1																	205589034		2203	4300	6503	203855657	SO:0001627	intron_variant	2005			M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+59A>C	1.37:g.205589034T>G			203855657	P28323|Q6GSJ2	Missense_Mutation	SNP	ENST00000357992.4	37	CCDS1456.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.619141	0.28801	.	.	ENSG00000158711	ENST00000289703	T	0.32753	1.44	5.66	-9.3	0.00649	.	.	.	.	.	T	0.14700	0.0355	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36187	-0.9758	8	0.87932	D	0	.	1.3284	0.02130	0.2021:0.3306:0.1976:0.2697	.	380	P28324-2	.	H	380	ENSP00000289703:Q380H	ENSP00000289703:Q380H	Q	-	3	2	ELK4	203855657	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.022000	0.12480	-1.317000	0.02292	-0.313000	0.08912	CAA		0.383	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795		G	205589034	T	G	205589034	1	3	61	0	1	0	0	0	0	0	0	0	5074	1838	64	4		4	ELK4	1	205589034	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	459782	205589034	43661587	993	8978										
NUCKS1	64710	broad.mit.edu	37	chr1	205698728	205698728	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagattcctgaaactgtgaGtaatcaacaaccttcctatt	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:205698728G>T	ENST00000367142.4	-	2	341	c.39C>A	c.(37-39)taC>taA	p.Y13*	SNORA72_ENST00000365074.1_RNA	NM_022731.4	NP_073568.2	Q9H1E3	NUCKS_HUMAN	nuclear casein kinase and cyclin-dependent kinase substrate 1	13						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.Y13*(1)		endometrium(4)|large_intestine(1)|lung(9)	14	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			GAAACTGTGAGTAATCAACAA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											146	154	151					1																	205698728		2203	4300	6503	203965351	SO:0001587	stop_gained	64710				CCDS30987.1	1q32.1	2008-02-05			ENSG00000069275	ENSG00000069275			29923	protein-coding gene	gene with protein product		611912				11298763	Standard	NM_022731		Approved	NUCKS	uc001hdb.3	Q9H1E3	OTTHUMG00000035996	ENST00000367142.4:c.39C>A	1.37:g.205698728G>T	ENSP00000356110:p.Tyr13*		203965351	Q54AC0|Q5PXE7|Q9H1D6|Q9H723	Nonsense_Mutation	SNP	ENST00000367142.4	37	CCDS30987.1	.	.	.	.	.	.	.	.	.	.	G	37	6.138350	0.97315	.	.	ENSG00000069275	ENST00000367142;ENST00000264531	.	.	.	5.36	1.46	0.22682	.	0.055129	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.383	9.4799	0.38895	0.5717:0.0:0.4283:0.0	.	.	.	.	X	13;25	.	ENSP00000264531:Y25X	Y	-	3	2	NUCKS1	203965351	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	1.043000	0.30316	-0.007000	0.14345	-0.242000	0.12053	TAC		0.333	NUCKS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087729.1	NM_022731		T	205698728	G	T	205698728	4	4	61	1	0	0	0	0	0	1	0	0	10751	1024	36	2	716	2	NUCKS1	1	205698728	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109694	205698728	43551893	994	8979										
IKBKE	9641	broad.mit.edu	37	chr1	206648290	206648290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggagagccctgagaatgCctttgggctgcctgaggatg	16	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:206648290C>T	ENST00000367120.3	+	5	684	c.311C>T	c.(310-312)gCc>gTc	p.A104V	IKBKE_ENST00000537984.1_Missense_Mutation_p.A19V|IKBKE_ENST00000463979.1_3'UTR	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)	p.A104V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					CCTGAGAATGCCTTTGGGCTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	1											187	138	155					1																	206648290		2203	4300	6503	204714913	SO:0001583	missense	9641			AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.311C>T	1.37:g.206648290C>T	ENSP00000356087:p.Ala104Val		204714913	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.900746	0.92035	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.66460	-0.21;-0.21	5.23	5.23	0.72850	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.061016	0.64402	D	0.000004	T	0.76572	0.4006	M	0.65975	2.015	0.54753	D	0.999985	P;P	0.51653	0.919;0.947	P;P	0.54174	0.686;0.744	T	0.78919	-0.2014	10	0.59425	D	0.04	0.8967	18.3958	0.90497	0.0:1.0:0.0:0.0	.	19;104	Q3B754;Q14164	.;IKKE_HUMAN	V	104;19	ENSP00000356087:A104V;ENSP00000444529:A19V	ENSP00000356087:A104V	A	+	2	0	IKBKE	204714913	1.000000	0.71417	0.647000	0.29507	0.637000	0.38172	7.739000	0.84976	2.440000	0.82611	0.561000	0.74099	GCC		0.637	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			T	206648290	C	T	206648290	3	4	61	1	0	0	0	0	1	0	0	0	7633	739	26	3	321	3	IKBKE	1	206648290	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	949562	206648290	42602331	995	8980										
IKBKE	9641	broad.mit.edu	37	chr1	206651575	206651575	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccaagtgctggggcttCgaccagttctttgcggagac	14	11	1	1	rs144754298		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:206651575C>T	ENST00000367120.3	+	9	1258	c.885C>T	c.(883-885)ttC>ttT	p.F295F	IKBKE_ENST00000537984.1_Silent_p.F210F	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	295	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)	p.F295F(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GCTGGGGCTTCGACCAGTTCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1							,,	1,4405	2.1+/-5.4	0,1,2202	129	106	114		630,885,885	-0.1	1	1	dbSNP_134	114	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	210/632,295/658,295/717	206651575	1,13005	2203	4300	6503	204718198	SO:0001819	synonymous_variant	9641			AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.885C>T	1.37:g.206651575C>T			204718198	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																				0.607	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			T	206651575	C	T	206651575	2	4	61	1	0	0	0	0	0	0	0	1	7633	883	31	1		1	IKBKE	1	206651575	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3285	206651575	42599046	996	8981										
LGTN	1939	broad.mit.edu	37	chr1	206776509	206776509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcactgagatctgctgaatCcagggccagtggagcaatgg	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:206776509C>T	ENST00000271764.2	-	6	788	c.580G>A	c.(580-582)Gat>Aat	p.D194N	EIF2D_ENST00000367114.3_Intron	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	194					formation of translation preinitiation complex (GO:0001731)|intracellular protein transport (GO:0006886)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor activity (GO:0004872)|translation initiation factor activity (GO:0003743)	p.D194N(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						TCTGCTGAATCCAGGGCCAGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	118	121					1																	206776509		2203	4300	6503	204843132	SO:0001583	missense	1939			BC001585	CCDS1465.1, CCDS55680.1	1q32.1	2014-05-06	2011-01-19	2011-01-19	ENSG00000143486	ENSG00000143486			6583	protein-coding gene	gene with protein product		613709				20566627	Standard	NM_001201478		Approved	LGTN	uc001heh.2	P41214	OTTHUMG00000184619	ENST00000271764.2:c.580G>A	1.37:g.206776509C>T	ENSP00000271764:p.Asp194Asn		204843132	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Missense_Mutation	SNP	ENST00000271764.2	37	CCDS1465.1	.	.	.	.	.	.	.	.	.	.	C	9.429	1.085125	0.20390	.	.	ENSG00000143486	ENST00000271764;ENST00000367111;ENST00000437518	T;T	0.42513	0.97;0.97	5.99	4.15	0.48705	.	0.419944	0.30076	N	0.010463	T	0.23094	0.0558	N	0.14661	0.345	0.20873	N	0.999831	B	0.02656	0.0	B	0.04013	0.001	T	0.18053	-1.0349	10	0.16420	T	0.52	-27.3009	9.4	0.38426	0.0:0.8376:0.0:0.1624	.	194	P41214	EIF2D_HUMAN	N	194;166;166	ENSP00000271764:D194N;ENSP00000394685:D166N	ENSP00000271764:D194N	D	-	1	0	EIF2D	204843132	0.031000	0.19500	0.176000	0.23000	0.120000	0.20174	0.710000	0.25748	0.883000	0.36040	-0.137000	0.14449	GAT		0.537	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893		T	206776509	C	T	206776509	3	4	61	1	0	0	0	0	1	0	0	0	8783	855	30	3	1214	3	LGTN	1	206776509	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124934	206776509	42474112	997	8982										
IL10	3586	broad.mit.edu	37	chr1	206944288	206944288	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcctgagggtcttcaggttCtcccccagggagttcacatg	12	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:206944288C>A	ENST00000423557.1	-	3	400	c.342G>T	c.(340-342)gaG>gaT	p.E114D	IL10_ENST00000471071.1_5'UTR	NM_000572.2	NP_000563.1	P22301	IL10_HUMAN	interleukin 10	114					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|defense response to bacterium (GO:0042742)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|leukocyte chemotaxis (GO:0030595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of chronic inflammatory response to antigenic stimulus (GO:0002875)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interferon-alpha biosynthetic process (GO:0045355)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of myeloid dendritic cell activation (GO:0030886)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor biosynthetic process (GO:0032800)|regulation of gene expression (GO:0010468)|regulation of isotype switching (GO:0045191)|regulation of sensory perception of pain (GO:0051930)|response to activity (GO:0014823)|response to carbon monoxide (GO:0034465)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to inactivity (GO:0014854)|response to insulin (GO:0032868)|response to molecule of bacterial origin (GO:0002237)|type 2 immune response (GO:0042092)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-10 receptor binding (GO:0005141)	p.E114D(1)		endometrium(1)|large_intestine(6)|lung(4)|prostate(1)	12	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TCTTCAGGTTCTCCCCCAGGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											141	134	137					1																	206944288		2203	4300	6503	205010911	SO:0001583	missense	3586			M57627	CCDS1467.1	1q31-q32	2011-07-14			ENSG00000136634	ENSG00000136634		"Interleukins and interleukin receptors"	5962	protein-coding gene	gene with protein product	"cytokine synthesis inhibitory factor", "T-cell growth inhibitory factor"	124092				9162098	Standard	NM_000572		Approved	CSIF, TGIF, IL10A, IL-10	uc001hen.1	P22301	OTTHUMG00000036386	ENST00000423557.1:c.342G>T	1.37:g.206944288C>A	ENSP00000412237:p.Glu114Asp		205010911		Missense_Mutation	SNP	ENST00000423557.1	37	CCDS1467.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.324172	0.24080	.	.	ENSG00000136634	ENST00000423557	T	0.70631	-0.5	5.99	-12.0	0.00017	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.380589	0.32386	N	0.006179	T	0.75309	0.3832	M	0.81341	2.54	0.20975	N	0.999811	D	0.57257	0.979	D	0.70935	0.971	T	0.74328	-0.3701	10	0.45353	T	0.12	-15.3671	11.2206	0.48853	0.0:0.538:0.2578:0.2042	.	114	P22301	IL10_HUMAN	D	114	ENSP00000412237:E114D	ENSP00000412237:E114D	E	-	3	2	IL10	205010911	0.624000	0.27102	0.464000	0.27143	0.022000	0.10575	-0.714000	0.05002	-1.620000	0.01564	-1.202000	0.01658	GAG		0.537	IL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088564.3	NM_000572		A	206944288	C	A	206944288	3	1	61	1	0	0	0	0	1	0	0	0	7640	912	32	2	206	2	IL10	1	206944288	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	167779	206944288	42306333	998	8983										
FAIM3	9214	broad.mit.edu	37	chr1	207085260	207085260	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgggggaggagtggtgAactggagggaccttgcccct	20	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207085260A>C	ENST00000367091.3	-	4	668	c.525T>G	c.(523-525)gtT>gtG	p.V175V	FAIM3_ENST00000528654.1_Intron|FAIM3_ENST00000420007.2_Silent_p.V175V|FAIM3_ENST00000442471.2_Silent_p.V63V	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	175					cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.V175V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					AGGAGTGGTGAACTGGAGGGA	0.537											OREG0014185	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	1											148	150	149					1																	207085260		2203	4300	6503	205151883	SO:0001819	synonymous_variant	9214			AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.525T>G	1.37:g.207085260A>C		2164	205151883	A8K7J2|B7Z6Z0|D9MWM3	Silent	SNP	ENST00000367091.3	37	CCDS1473.1																																																																																				0.537	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		C	207085260	A	C	207085260	2	2	61	1	0	0	0	0	0	0	0	1	5393	233	9	4		4	FAIM3	1	207085260	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	140972	207085260	42165361	999	8984										
FAIM3	9214	broad.mit.edu	37	chr1	207087225	207087225	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccactaggaacagattCttgcgtgggtattgcttcag	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207087225C>A	ENST00000367091.3	-	2	395	c.252G>T	c.(250-252)aaG>aaT	p.K84N	FAIM3_ENST00000528654.1_Intron|FAIM3_ENST00000420007.2_Missense_Mutation_p.K84N|FAIM3_ENST00000442471.2_Intron	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	84	Ig-like.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.K84N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					GGAACAGATTCTTGCGTGGGT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											140	129	133					1																	207087225		2203	4300	6503	205153848	SO:0001583	missense	9214			AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.252G>T	1.37:g.207087225C>A	ENSP00000356058:p.Lys84Asn		205153848	A8K7J2|B7Z6Z0|D9MWM3	Missense_Mutation	SNP	ENST00000367091.3	37	CCDS1473.1	.	.	.	.	.	.	.	.	.	.	C	8.025	0.760426	0.15914	.	.	ENSG00000162894	ENST00000367091;ENST00000420007;ENST00000525793;ENST00000529560;ENST00000530505	T;T;T;T;T	0.04234	3.67;3.67;3.67;3.67;3.67	5.28	4.36	0.52297	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.863268	0.10018	N	0.726323	T	0.03608	0.0103	N	0.15975	0.35	0.09310	N	1	B	0.25272	0.122	B	0.24155	0.051	T	0.42481	-0.9449	10	0.10377	T	0.69	-5.1729	12.0666	0.53592	0.0:0.8271:0.1729:0.0	.	84	O60667	FAIM3_HUMAN	N	84;84;84;84;115	ENSP00000356058:K84N;ENSP00000403356:K84N;ENSP00000432936:K84N;ENSP00000437331:K84N;ENSP00000436316:K115N	ENSP00000356058:K84N	K	-	3	2	FAIM3	205153848	0.000000	0.05858	0.004000	0.12327	0.566000	0.35808	0.186000	0.16978	1.217000	0.43442	0.655000	0.94253	AAG		0.522	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		A	207087225	C	A	207087225	3	1	61	1	0	0	0	0	1	0	0	0	5393	912	32	2	948	2	FAIM3	1	207087225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1965	207087225	42163396	1000	8985										
PIGR	5284	broad.mit.edu	37	chr1	207110752	207110752	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctcaggtcttcataaaCcagctcgggctcgggcttta	10	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207110752C>T	ENST00000356495.4	-	4	916	c.733G>A	c.(733-735)Gtt>Att	p.V245I		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	245					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.V245I(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TCTTCATAAACCAGCTCGGGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											58	57	57					1																	207110752		2203	4300	6503	205177375	SO:0001583	missense	5284				CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.733G>A	1.37:g.207110752C>T	ENSP00000348888:p.Val245Ile		205177375	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	9.115	1.007569	0.19199	.	.	ENSG00000162896	ENST00000356495	T	0.04917	3.53	5.79	-7.71	0.01254	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.925858	0.09145	N	0.842387	T	0.04634	0.0126	L	0.52905	1.665	0.09310	N	1	B	0.34103	0.437	B	0.29176	0.099	T	0.27365	-1.0076	10	0.17369	T	0.5	-20.169	7.814	0.29247	0.0845:0.1565:0.5762:0.1828	.	245	P01833	PIGR_HUMAN	I	245	ENSP00000348888:V245I	ENSP00000348888:V245I	V	-	1	0	PIGR	205177375	0.047000	0.20315	0.059000	0.19551	0.331000	0.28603	-0.542000	0.06091	-1.283000	0.02393	0.655000	0.94253	GTT		0.552	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		T	207110752	C	T	207110752	3	4	61	1	0	0	0	0	1	0	0	0	11928	507	18	3	1593	3	PIGR	1	207110752	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23527	207110752	42139869	1001	8986										
FCAMR	83953	broad.mit.edu	37	chr1	207135887	207135887	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagccttgagcccttcaatGaatttggagctgcagacaga	10	11	1	4	rs375632066		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207135887G>T	ENST00000324852.4	-	5	797	c.323C>A	c.(322-324)tCa>tAa	p.S108*	FCAMR_ENST00000450945.2_Nonsense_Mutation_p.S108*|FCAMR_ENST00000486178.1_5'Flank|FCAMR_ENST00000400962.3_Nonsense_Mutation_p.S108*	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	63	Ig-like V-type.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S84*(1)|p.S108*(1)		endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						GCCCTTCAATGAATTTGGAGC	0.527																																					Ovarian(199;1883 2142 16966 44409 45154)											2	Substitution - Nonsense(2)	large_intestine(2)	1											14	15	15					1																	207135887		1568	3581	5149	205202510	SO:0001587	stop_gained	83953			AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.323C>A	1.37:g.207135887G>T	ENSP00000316491:p.Ser108*		205202510	Q32M82|Q8WWV5|Q96SA2	Nonsense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	G	33	5.257480	0.95368	.	.	ENSG00000162897	ENST00000400962;ENST00000324852;ENST00000450945;ENST00000367087	.	.	.	5.32	3.44	0.39384	.	0.458067	0.20202	N	0.097076	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-3.7154	7.33	0.26577	0.0904:0.1698:0.7397:0.0	.	.	.	.	X	108;108;108;84	.	ENSP00000316491:S108X	S	-	2	0	FCAMR	205202510	0.284000	0.24287	0.001000	0.08648	0.359000	0.29487	4.788000	0.62439	0.626000	0.30322	-0.175000	0.13238	TCA		0.527	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		T	207135887	G	T	207135887	4	4	61	1	0	0	0	0	0	1	0	0	5791	1294	45	2	1426	2	FCAMR	1	207135887	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25135	207135887	42114734	1002	8987										
C1orf116	79098	broad.mit.edu	37	chr1	207196615	207196615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctttctcaggctctggcGcaagcctccccggttctcca	9	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207196615G>A	ENST00000359470.5	-	4	743	c.494C>T	c.(493-495)gCg>gTg	p.A165V	C1orf116_ENST00000461135.2_5'UTR	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	165						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.A165V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					AGGCTCTGGCGCAAGCCTCCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											52	55	54					1																	207196615		2203	4300	6503	205263238	SO:0001583	missense	79098				CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"specifically androgen-regulated gene"	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.494C>T	1.37:g.207196615G>A	ENSP00000352447:p.Ala165Val		205263238	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	37	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	G	0.735	-0.778549	0.02929	.	.	ENSG00000182795	ENST00000359470	T	0.07216	3.21	4.63	-9.26	0.00662	.	2.900000	0.00926	N	0.002643	T	0.02727	0.0082	N	0.08118	0	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	10	0.02654	T	1	5.5891	3.5676	0.07905	0.3928:0.1123:0.3851:0.1098	.	165	Q9BW04	SARG_HUMAN	V	165	ENSP00000352447:A165V	ENSP00000352447:A165V	A	-	2	0	C1orf116	205263238	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.150000	0.10189	-2.334000	0.00630	-2.759000	0.00122	GCG		0.597	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115		A	207196615	G	A	207196615	3	1	61	1	0	0	0	0	1	0	0	0	1995	1087	38	1	1315	1	C1orf116	1	207196615	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60728	207196615	42054006	1003	8988										
PFKFB2	5208	broad.mit.edu	37	chr1	207228092	207228092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcttcctcagaacagaaCaacaacagctatgaaaccaa	5	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207228092C>T	ENST00000367080.3	+	2	154	c.30C>T	c.(28-30)aaC>aaT	p.N10N	PFKFB2_ENST00000367079.2_Silent_p.N10N|PFKFB2_ENST00000411990.2_5'UTR|YOD1_ENST00000391927.1_5'Flank|YOD1_ENST00000367084.1_5'Flank|PFKFB2_ENST00000545806.1_5'UTR	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	10	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)	p.N10N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					CAGAACAGAACAACAACAGCT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1											65	60	62					1																	207228092		2203	4300	6503	205294715	SO:0001819	synonymous_variant	5208				CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.30C>T	1.37:g.207228092C>T			205294715	O60824|Q5VVQ3|Q5VVQ4|Q9H3P1	Silent	SNP	ENST00000367080.3	37	CCDS31004.1																																																																																				0.433	PFKFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087838.1			T	207228092	C	T	207228092	2	4	61	1	0	0	0	0	0	0	0	1	11792	477	17	3		3	PFKFB2	1	207228092	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31477	207228092	42022529	1004	8989										
C4BPA	722	broad.mit.edu	37	chr1	207297310	207297310	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtcgttgtgaagtccaaGatagaggagttggctggagt	15	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207297310G>T	ENST00000367070.3	+	5	666	c.472G>T	c.(472-474)Gat>Tat	p.D158Y		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	158	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.D158Y(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TGAAGTCCAAGATAGAGGAGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	72	72					1																	207297310		2203	4300	6503	205363933	SO:0001583	missense	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.472G>T	1.37:g.207297310G>T	ENSP00000356037:p.Asp158Tyr		205363933	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.122706	0.56613	.	.	ENSG00000123838	ENST00000367070	T	0.25414	1.8	5.9	4.04	0.47022	Complement control module (2);Sushi/SCR/CCP (3);	0.507164	0.19563	N	0.111296	T	0.52435	0.1734	M	0.87456	2.885	0.09310	N	0.999999	D	0.76494	0.999	D	0.75484	0.986	T	0.47649	-0.9101	10	0.72032	D	0.01	.	8.7244	0.34460	0.1706:0.0:0.8294:0.0	.	158	P04003	C4BPA_HUMAN	Y	158	ENSP00000356037:D158Y	ENSP00000356037:D158Y	D	+	1	0	C4BPA	205363933	0.356000	0.24930	0.020000	0.16555	0.149000	0.21700	2.156000	0.42310	0.842000	0.35045	0.650000	0.86243	GAT		0.348	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207297310	G	T	207297310	3	4	61	1	0	0	0	0	1	0	0	0	2255	942	33	2	486	2	C4BPA	1	207297310	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69218	207297310	41953311	1005	8990										
CR2	1380	broad.mit.edu	37	chr1	207640078	207640078	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatatttcaataaatattCttcttgccctgagcccatag	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207640078C>A	ENST00000367058.3	+	2	455	c.266C>A	c.(265-267)tCt>tAt	p.S89Y	CR2_ENST00000367057.3_Missense_Mutation_p.S89Y|CR2_ENST00000458541.2_Missense_Mutation_p.S89Y|CR2_ENST00000367059.3_Missense_Mutation_p.S89Y	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	89	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.S89Y(1)		NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						AATAAATATTCTTCTTGCCCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	87	87					1																	207640078		2203	4300	6503	205706701	SO:0001583	missense	1380			M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.266C>A	1.37:g.207640078C>A	ENSP00000356025:p.Ser89Tyr		205706701	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.567218	0.45694	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79	5.0	3.11	0.35812	Complement control module (1);Sushi/SCR/CCP (1);	.	.	.	.	T	0.81235	0.4780	M	0.68593	2.085	0.09310	N	1	D;D;D	0.76494	0.979;0.996;0.999	P;D;D	0.69824	0.827;0.925;0.966	T	0.67550	-0.5642	9	0.29301	T	0.29	.	7.9038	0.29750	0.0:0.8114:0.0:0.1886	.	89;89;89	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	Y	89	ENSP00000356025:S89Y;ENSP00000356024:S89Y;ENSP00000356026:S89Y;ENSP00000404222:S89Y	ENSP00000356024:S89Y	S	+	2	0	CR2	205706701	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	1.889000	0.39718	0.685000	0.31468	0.655000	0.94253	TCT		0.398	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207640078	C	A	207640078	3	1	61	1	0	0	0	0	1	0	0	0	3848	913	32	2	272	2	CR2	1	207640078	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	342768	207640078	41610543	1006	8991										
CR1	1378	broad.mit.edu	37	chr1	207741233	207741233	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggaaaacctctggaagtCtttccctttggaaaagcagt	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207741233C>A	ENST00000367049.4	+	25	4017	c.4017C>A	c.(4015-4017)gtC>gtA	p.V1339V	CR1_ENST00000367051.1_Silent_p.V889V|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367053.1_Silent_p.V889V|CR1_ENST00000400960.2_Silent_p.V889V|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Intron	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	889	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.V894V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CTCTGGAAGTCTTTCCCTTTG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	1											139	157	151					1																	207741233		1810	4097	5907	205807856	SO:0001819	synonymous_variant	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4017C>A	1.37:g.207741233C>A			205807856	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1																																																																																				0.463	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207741233	C	A	207741233	2	1	61	1	0	0	0	0	0	0	0	1	3846	900	32	2		2	CR1	1	207741233	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101155	207741233	41509388	1007	8992										
CR1	1378	broad.mit.edu	37	chr1	207741297	207741297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacagagggacgagcttcGacctcattggagagagcacc	13	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207741297G>A	ENST00000367049.4	+	25	4081	c.4081G>A	c.(4081-4083)Gac>Aac	p.D1361N	CR1_ENST00000367051.1_Missense_Mutation_p.D911N|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367053.1_Missense_Mutation_p.D911N|CR1_ENST00000400960.2_Missense_Mutation_p.D911N|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Intron	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	911	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.D916N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GACGAGCTTCGACCTCATTGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	111	105					1																	207741297		1821	4085	5906	205807920	SO:0001583	missense	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4081G>A	1.37:g.207741297G>A	ENSP00000356016:p.Asp1361Asn		205807920	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	g	1.023	-0.684229	0.03353	.	.	ENSG00000203710	ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	2.73	-4.85	0.03142	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.03871	0.0109	N	0.01086	-1.025	0.09310	N	1	B;B;B;P	0.35208	0.039;0.056;0.01;0.49	B;B;B;B	0.22152	0.038;0.011;0.004;0.038	T	0.38993	-0.9635	9	0.17832	T	0.49	.	5.0844	0.14675	0.6589:0.1668:0.1743:0.0	.	911;461;911;1361	Q5SR44;E9PQN4;P17927;E9PDY4	.;.;CR1_HUMAN;.	N	911;911;911;1361	ENSP00000356018:D911N;ENSP00000356020:D911N;ENSP00000383744:D911N;ENSP00000356016:D1361N	ENSP00000356016:D1361N	D	+	1	0	CR1	205807920	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	0.144000	0.16135	-0.956000	0.03631	-1.536000	0.00914	GAC		0.542	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207741297	G	A	207741297	3	1	61	1	0	0	0	0	1	0	0	0	3846	1058	37	1	4179	1	CR1	1	207741297	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64	207741297	41509324	1008	8993										
CR1	1378	broad.mit.edu	37	chr1	207753667	207753667	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctgggcaggaagtgttCtacagctgtgagcctggcta	13	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207753667C>A	ENST00000367049.4	+	30	5019	c.5019C>A	c.(5017-5019)ttC>ttA	p.F1673L	CR1_ENST00000367051.1_Missense_Mutation_p.F1223L|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367053.1_Missense_Mutation_p.F1223L|CR1_ENST00000400960.2_Missense_Mutation_p.F1223L|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Missense_Mutation_p.F1223L	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1223	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.F1228L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AGGAAGTGTTCTACAGCTGTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											125	128	127					1																	207753667		1985	4176	6161	205820290	SO:0001583	missense	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.5019C>A	1.37:g.207753667C>A	ENSP00000356016:p.Phe1673Leu		205820290	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	3.815	-0.038936	0.07497	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.38	2.45	0.29901	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.42810	0.1219	N	0.25825	0.765	0.23056	N	0.998361	B;B;B	0.17667	0.023;0.002;0.011	B;B;B	0.21546	0.035;0.003;0.017	T	0.28618	-1.0038	9	0.11485	T	0.65	.	5.7418	0.18098	0.1911:0.705:0.0:0.1039	.	1223;1223;1673	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	L	1223;1223;1223;1223;773;1673	ENSP00000356019:F1223L;ENSP00000356018:F1223L;ENSP00000356020:F1223L;ENSP00000383744:F1223L;ENSP00000436139:F773L;ENSP00000356016:F1673L	ENSP00000356016:F1673L	F	+	3	2	CR1	205820290	0.268000	0.24133	0.794000	0.32065	0.638000	0.38207	0.244000	0.18124	0.386000	0.24997	0.655000	0.94253	TTC		0.582	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207753667	C	A	207753667	3	1	61	1	0	0	0	0	1	0	0	0	3846	912	32	2	5137	2	CR1	1	207753667	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12370	207753667	41496954	1009	8994										
CR1	1378	broad.mit.edu	37	chr1	207791444	207791444	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccacccaagatccaaaaCgggcattacattggaggaca	8	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207791444C>T	ENST00000367049.4	+	42	6918	c.6918C>T	c.(6916-6918)aaC>aaT	p.N2306N	CR1_ENST00000367051.1_Silent_p.N1856N|CR1_ENST00000367053.1_Silent_p.N1856N|CR1_ENST00000400960.2_Silent_p.N1856N|CR1_ENST00000367052.1_Silent_p.N1856N	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1856					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.N1861N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AGATCCAAAACGGGCATTACA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											113	109	110					1																	207791444		1960	4157	6117	205858067	SO:0001819	synonymous_variant	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6918C>T	1.37:g.207791444C>T			205858067	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	4.034	0.003899	0.07866	.	.	ENSG00000203710	ENST00000529814	.	.	.	4.07	-5.8	0.02347	.	.	.	.	.	T	0.25269	0.0614	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.30794	-0.9966	4	.	.	.	.	6.4242	0.21760	0.1275:0.2794:0.0:0.5931	.	.	.	.	M	479	.	.	T	+	2	0	CR1	205858067	0.001000	0.12720	0.001000	0.08648	0.147000	0.21601	-2.115000	0.01328	-1.243000	0.02519	-0.251000	0.11542	ACG		0.438	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207791444	C	T	207791444	2	4	61	1	0	0	0	0	0	0	0	1	3846	535	19	1		1	CR1	1	207791444	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37777	207791444	41459177	1010	8995										
CD46	4179	broad.mit.edu	37	chr1	207940416	207940416	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatatcaggatttggaaaAaaattttactacaaagcaac	6	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207940416A>C	ENST00000358170.2	+	6	888	c.732A>C	c.(730-732)aaA>aaC	p.K244N	CD46_ENST00000441839.2_Missense_Mutation_p.K244N|CD46_ENST00000361067.1_Missense_Mutation_p.K244N|CD46_ENST00000354848.1_Missense_Mutation_p.K244N|CD46_ENST00000367041.1_Missense_Mutation_p.K244N|CD46_ENST00000480003.1_Missense_Mutation_p.K244N|CD46_ENST00000322875.4_Missense_Mutation_p.K244N|CD46_ENST00000367047.1_Missense_Mutation_p.K181N|CD46_ENST00000322918.5_Missense_Mutation_p.K244N|CD46_ENST00000367042.1_Missense_Mutation_p.K244N|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000360212.2_Missense_Mutation_p.K244N|CD46_ENST00000357714.1_Missense_Mutation_p.K244N	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	244	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)	p.K244N(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						GATTTGGAAAAAAATTTTACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	71	70					1																	207940416		2203	4300	6503	206007039	SO:0001583	missense	4179			BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.732A>C	1.37:g.207940416A>C	ENSP00000350893:p.Lys244Asn		206007039	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	37	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.843570	0.51057	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.14	-3.24	0.05094	Complement control module (2);Sushi/SCR/CCP (3);	1.157720	0.06572	N	0.748798	T	0.52565	0.1742	N	0.11106	0.095	0.09310	N	1	P;B;P;P;B;D;P;P;P;P;P;D;D;D	0.61080	0.871;0.275;0.921;0.932;0.275;0.987;0.932;0.93;0.871;0.923;0.871;0.967;0.967;0.989	B;B;B;P;B;P;P;P;B;P;B;P;P;P	0.62014	0.321;0.085;0.445;0.666;0.085;0.834;0.469;0.599;0.321;0.522;0.321;0.639;0.639;0.897	T	0.49204	-0.8964	10	0.28530	T	0.3	.	5.5474	0.17071	0.2933:0.3156:0.3912:0.0	.	244;244;244;244;244;244;244;244;244;244;244;244;244;244	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	N	244;244;244;244;244;244;244;181;244;244;244;244	ENSP00000350893:K244N;ENSP00000346912:K244N;ENSP00000314664:K244N;ENSP00000356009:K244N;ENSP00000356008:K244N;ENSP00000350346:K244N;ENSP00000313875:K244N;ENSP00000356014:K181N;ENSP00000413543:K244N;ENSP00000354358:K244N;ENSP00000353342:K244N;ENSP00000418471:K244N	ENSP00000313875:K244N	K	+	3	2	CD46	206007039	0.000000	0.05858	0.000000	0.03702	0.316000	0.28119	-0.326000	0.07965	-0.319000	0.08652	0.533000	0.62120	AAA		0.368	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		C	207940416	A	C	207940416	3	2	61	1	0	0	0	0	1	0	0	0	3024	11	1	4	754	4	CD46	1	207940416	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	148972	207940416	41310205	1011	8996										
CD46	4179	broad.mit.edu	37	chr1	207958995	207958995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtaatttgtgttgtcccGtacagatatcttcaaaggag	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:207958995G>A	ENST00000358170.2	+	12	1251	c.1095G>A	c.(1093-1095)ccG>ccA	p.P365P	CD46_ENST00000441839.2_Intron|CD46_ENST00000361067.1_Silent_p.P351P|CD46_ENST00000354848.1_Silent_p.P350P|CD46_ENST00000367041.1_Silent_p.P335P|CD46_ENST00000480003.1_Silent_p.P336P|CD46_ENST00000322875.4_Silent_p.P365P|CD46_ENST00000367047.1_Silent_p.P302P|CD46_ENST00000322918.5_Intron|CD46_ENST00000367042.1_Silent_p.P350P|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000360212.2_Silent_p.P321P|CD46_ENST00000357714.1_Silent_p.P335P	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	365					adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)	p.P365P(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						GTGTTGTCCCGTACAGATATC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											237	239	238					1																	207958995		2203	4300	6503	206025618	SO:0001819	synonymous_variant	4179			BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.1095G>A	1.37:g.207958995G>A			206025618	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Silent	SNP	ENST00000358170.2	37	CCDS1485.1																																																																																				0.348	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		A	207958995	G	A	207958995	2	1	61	1	0	0	0	0	0	0	0	1	3024	1132	40	1		1	CD46	1	207958995	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18579	207958995	41291626	1012	8997										
PLXNA2	5362	broad.mit.edu	37	chr1	208234146	208234146	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgccatggatggtcactcGcgtccctccttccggcggtc	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:208234146G>A	ENST00000367033.3	-	13	3380	c.2623C>T	c.(2623-2625)Cga>Tga	p.R875*		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	875	IPT/TIG 1.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R875*(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		ATGGTCACTCGCGTCCCTCCT	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											59	55	56					1																	208234146		2203	4300	6503	206300769	SO:0001587	stop_gained	5362			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2623C>T	1.37:g.208234146G>A	ENSP00000356000:p.Arg875*		206300769	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Nonsense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	47	13.437591	0.99742	.	.	ENSG00000076356	ENST00000367033	.	.	.	4.75	4.75	0.60458	.	0.056265	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.151	0.54050	0.0:0.0:0.7092:0.2908	.	.	.	.	X	875	.	ENSP00000356000:R875X	R	-	1	2	PLXNA2	206300769	0.953000	0.32496	0.995000	0.50966	0.961000	0.63080	1.656000	0.37355	2.200000	0.70718	0.655000	0.94253	CGA		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208234146	G	A	208234146	4	1	61	1	0	0	0	0	0	1	0	0	12151	1095	38	1	3141	1	PLXNA2	1	208234146	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	275151	208234146	41016475	1013	8998										
CAMK1G	57172	broad.mit.edu	37	chr1	209778899	209778899	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtttctggtggggagctCtttgaccggatcctggagcg	16	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:209778899C>A	ENST00000009105.1	+	5	560	c.315C>A	c.(313-315)ctC>ctA	p.L105L	CAMK1G_ENST00000361322.2_Silent_p.L105L			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.L105L(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		GTGGGGAGCTCTTTGACCGGA	0.498																																					Ovarian(163;530 1939 9680 28669 48710)											1	Substitution - coding silent(1)	large_intestine(1)	1											136	132	134					1																	209778899		2203	4300	6503	207845522	SO:0001819	synonymous_variant	57172				CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.315C>A	1.37:g.209778899C>A			207845522	Q86UH5|Q9Y3J7	Silent	SNP	ENST00000009105.1	37	CCDS1486.1																																																																																				0.498	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		A	209778899	C	A	209778899	2	1	61	1	0	0	0	0	0	0	0	1	2604	900	32	2		2	CAMK1G	1	209778899	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1544753	209778899	39471722	1014	8999										
CAMK1G	57172	broad.mit.edu	37	chr1	209782394	209782394	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagatcaaggagggctaCtatgagtttgagtctccatt	12	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:209782394C>A	ENST00000009105.1	+	8	950	c.705C>A	c.(703-705)taC>taA	p.Y235*	CAMK1G_ENST00000361322.2_Nonsense_Mutation_p.Y235*|CAMK1G_ENST00000494990.1_3'UTR			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	235	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.Y235*(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		AGGAGGGCTACTATGAGTTTG	0.493																																					Ovarian(163;530 1939 9680 28669 48710)											1	Substitution - Nonsense(1)	large_intestine(1)	1											172	156	161					1																	209782394		2203	4300	6503	207849017	SO:0001587	stop_gained	57172				CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.705C>A	1.37:g.209782394C>A	ENSP00000009105:p.Tyr235*		207849017	Q86UH5|Q9Y3J7	Nonsense_Mutation	SNP	ENST00000009105.1	37	CCDS1486.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.482870|5.482870	0.96307|0.96307	.|.	.|.	ENSG00000008118|ENSG00000008118	ENST00000423146|ENST00000009105;ENST00000361322	T|.	0.64991|.	-0.13|.	5.48|5.48	1.98|1.98	0.26296|0.26296	.|.	.|0.136420	.|0.33875	.|N	.|0.004476	T|.	0.41003|.	0.1140|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.48502|.	-0.9030|.	5|.	0.87932|0.31617	D|T	0|0.26	.|.	6.5874|6.5874	0.22628|0.22628	0.1279:0.6329:0.0:0.2392|0.1279:0.6329:0.0:0.2392	.|.	.|.	.|.	.|.	N|X	210|235	ENSP00000392173:T210N|.	ENSP00000392173:T210N|ENSP00000009105:Y235X	T|Y	+|+	2|3	0|2	CAMK1G|CAMK1G	207849017|207849017	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	0.670000|0.670000	0.25157|0.25157	0.630000|0.630000	0.30394|0.30394	-0.367000|-0.367000	0.07326|0.07326	ACT|TAC		0.493	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		A	209782394	C	A	209782394	4	1	61	1	0	0	0	0	0	1	0	0	2604	576	20	2	731	2	CAMK1G	1	209782394	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3495	209782394	39468227	1015	9000										
G0S2	50486	broad.mit.edu	37	chr1	209849137	209849137	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagcgtgctggccctcttCggcgtggtgctcggcctgat	16	13	1	1	rs199631971		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:209849137C>T	ENST00000367029.4	+	2	270	c.108C>T	c.(106-108)ttC>ttT	p.F36F	RP1-28O10.1_ENST00000445272.1_RNA|RP1-28O10.1_ENST00000441672.1_RNA	NM_015714.3	NP_056529.1	P27469	G0S2_HUMAN	G0/G1 switch 2	36					cellular lipid metabolic process (GO:0044255)|extrinsic apoptotic signaling pathway (GO:0097191)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|small molecule metabolic process (GO:0044281)	lipid particle (GO:0005811)|mitochondrion (GO:0005739)		p.F36F(1)		large_intestine(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.041)		TGGCCCTCTTCGGCGTGGTGC	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		17190	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											43	34	37					1																	209849137		2203	4299	6502	207915760	SO:0001819	synonymous_variant	50486				CCDS1488.1	1q32.2	2014-04-22	2014-04-22		ENSG00000123689	ENSG00000123689			30229	protein-coding gene	gene with protein product	"putative lymphocyte G0/G1 switch gene"	614447	"G0/G1switch 2"			1930693, 10645953	Standard	NM_015714		Approved		uc001hhi.4	P27469	OTTHUMG00000036479	ENST00000367029.4:c.108C>T	1.37:g.209849137C>T			207915760	Q6FGC8	Silent	SNP	ENST00000367029.4	37	CCDS1488.1																																																																																				0.682	G0S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088732.1	NM_015714		T	209849137	C	T	209849137	2	4	61	1	0	0	0	0	0	0	0	1	6158	883	31	1		1	G0S2	1	209849137	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66743	209849137	39401484	1016	9001										
TRAF3IP3	80342	broad.mit.edu	37	chr1	209946308	209946308	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagggacagcttaatgaaGacaaactgaaggggaaactg	12	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:209946308G>T	ENST00000367024.1	+	9	1234	c.718G>T	c.(718-720)Gac>Tac	p.D240Y	TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.D240Y|TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.D220Y|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.D220Y|TRAF3IP3_ENST00000367023.1_5'UTR|TRAF3IP3_ENST00000477431.1_5'UTR|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.D220Y			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	240						integral component of membrane (GO:0016021)		p.D220Y(1)		breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		GCTTAATGAAGACAAACTGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	93	96					1																	209946308		2203	4300	6503	208012931	SO:0001583	missense	80342				CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.718G>T	1.37:g.209946308G>T	ENSP00000355991:p.Asp240Tyr		208012931	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	37	CCDS1490.2	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064908	0.55432	.	.	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.72615	-0.4;-0.67;-0.59;-0.67;-0.59	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.84101	0.5398	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77004	0.988;0.983;0.989;0.983	D	0.85912	0.1441	10	0.87932	D	0	-5.4293	17.6886	0.88263	0.0:0.0:1.0:0.0	.	240;220;240;220	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	Y	220;240;223;220;240;220	ENSP00000383743:D220Y;ENSP00000355992:D240Y;ENSP00000355993:D220Y;ENSP00000355991:D240Y;ENSP00000010338:D220Y	ENSP00000010338:D220Y	D	+	1	0	TRAF3IP3	208012931	1.000000	0.71417	1.000000	0.80357	0.392000	0.30506	5.709000	0.68384	2.514000	0.84764	0.462000	0.41574	GAC		0.418	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2			T	209946308	G	T	209946308	3	4	61	1	0	0	0	0	1	0	0	0	16482	942	33	2	744	2	TRAF3IP3	1	209946308	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97171	209946308	39304313	1017	9002										
C1orf74	148304	broad.mit.edu	37	chr1	209956321	209956321	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactctctgggacactaaaaGaatagagcaggattgggggt	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:209956321G>T	ENST00000294811.1	-	2	915	c.659C>A	c.(658-660)tCt>tAt	p.S220Y		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	220								p.S220Y(1)		endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GACACTAAAAGAATAGAGCAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	88	85					1																	209956321		2203	4300	6503	208022944	SO:0001583	missense	148304			AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.659C>A	1.37:g.209956321G>T	ENSP00000294811:p.Ser220Tyr		208022944		Missense_Mutation	SNP	ENST00000294811.1	37	CCDS1491.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683102	0.88542	.	.	ENSG00000162757	ENST00000294811	T	0.62788	0.0	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.80380	0.4612	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82092	-0.0628	10	0.87932	D	0	-22.676	19.4121	0.94679	0.0:0.0:1.0:0.0	.	220	Q96LT6	CA074_HUMAN	Y	220	ENSP00000294811:S220Y	ENSP00000294811:S220Y	S	-	2	0	C1orf74	208022944	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.059000	0.93902	2.595000	0.87683	0.655000	0.94253	TCT		0.498	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485		T	209956321	G	T	209956321	3	4	61	1	0	0	0	0	1	0	0	0	2064	942	33	2	154	2	C1orf74	1	209956321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10013	209956321	39294300	1018	9003										
C1orf107	27042	broad.mit.edu	37	chr1	210001487	210001487	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagaaacatcttcgagatTtcggcgaggagcatcccttc	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210001487T>G	ENST00000491415.2	+	1	136	c.79T>G	c.(79-81)Ttc>Gtc	p.F27V		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	27					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.F27V(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						TCTTCGAGATTTCGGCGAGGA	0.557											OREG0014221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											67	63	64					1																	210001487		2203	4300	6503	208068110	SO:0001583	missense	27042			BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.79T>G	1.37:g.210001487T>G	ENSP00000419005:p.Phe27Val	2187	208068110	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	37	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736715	0.89482	.	.	ENSG00000117597	ENST00000491415	T	0.48201	0.82	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.66528	0.2798	M	0.68593	2.085	0.53688	D	0.999978	D	0.76494	0.999	D	0.80764	0.994	T	0.69727	-0.5067	10	0.62326	D	0.03	-20.9733	14.7946	0.69868	0.0:0.0:0.0:1.0	.	27	Q68CQ4	DIEXF_HUMAN	V	27	ENSP00000419005:F27V	ENSP00000419005:F27V	F	+	1	0	DIEXF	208068110	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.343000	0.65976	1.967000	0.57214	0.533000	0.62120	TTC		0.557	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		G	210001487	T	G	210001487	3	3	61	1	0	0	0	0	1	0	0	0	1987	1841	64	4	81	4	C1orf107	1	210001487	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	45166	210001487	39249134	1019	9004										
C1orf107	27042	broad.mit.edu	37	chr1	210006604	210006604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacatcacaaacatcccccGaagagttcacagatgcaaaa	6	13	2	2	rs538401701	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210006604G>A	ENST00000491415.2	+	4	520	c.463G>A	c.(463-465)Gaa>Aaa	p.E155K		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	155	Glu-rich.				multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E155K(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AACATCCCCCGAAGAGTTCAC	0.453													G|||	3	0.000599042	0	0	5008	,	,		17460	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	1											98	89	92					1																	210006604		2203	4300	6503	208073227	SO:0001583	missense	27042			BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.463G>A	1.37:g.210006604G>A	ENSP00000419005:p.Glu155Lys		208073227	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	37	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.749238	0.30955	.	.	ENSG00000117597	ENST00000491415	T	0.51817	0.69	5.68	3.82	0.43975	.	0.311270	0.39274	N	0.001418	T	0.33847	0.0877	L	0.53249	1.67	0.30988	N	0.721683	P	0.46457	0.878	B	0.33521	0.165	T	0.38950	-0.9637	10	0.09084	T	0.74	-8.7707	12.0825	0.53680	0.1385:0.0:0.8615:0.0	.	155	Q68CQ4	DIEXF_HUMAN	K	155	ENSP00000419005:E155K	ENSP00000419005:E155K	E	+	1	0	DIEXF	208073227	1.000000	0.71417	0.065000	0.19835	0.052000	0.14988	4.927000	0.63440	0.772000	0.33382	0.650000	0.86243	GAA		0.453	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		A	210006604	G	A	210006604	3	1	61	1	0	0	0	0	1	0	0	0	1987	1059	37	1	477	1	C1orf107	1	210006604	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5117	210006604	39244017	1020	9005										
SYT14	255928	broad.mit.edu	37	chr1	210194557	210194557	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatacagtcctctatcgGcagagtatgatggatacagt	10	7	1	3	rs148481999	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210194557G>A	ENST00000472886.1	+	4	414	c.400G>A	c.(400-402)Gca>Aca	p.A134T	SYT14_ENST00000399639.2_Missense_Mutation_p.A134T|SYT14_ENST00000367019.1_Missense_Mutation_p.A134T|SYT14_ENST00000537238.1_Missense_Mutation_p.A96T|SYT14_ENST00000422431.1_Missense_Mutation_p.A179T|SYT14_ENST00000367015.1_Missense_Mutation_p.A96T|SYT14_ENST00000534859.1_Missense_Mutation_p.A134T|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	134					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)	p.A134T(1)		endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		TCCTCTATCGGCAGAGTATGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	121	110	113		535,400,535,400	5.2	1	1	dbSNP_134	113	0,8600		0,0,4300	yes	missense,missense,missense,missense	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	58,58,58,58	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	179/620,134/575,179/601,134/556	210194557	4,13002	2203	4300	6503	208261180	SO:0001583	missense	255928			AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.400G>A	1.37:g.210194557G>A	ENSP00000418901:p.Ala134Thr		208261180	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	37	CCDS31014.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249089	0.80024	9.08E-4	0.0	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000399639;ENST00000537238;ENST00000367019;ENST00000472886;ENST00000367015	T;T;T;T;T;T;T	0.18338	3.34;3.2;2.22;3.47;3.21;3.46;3.47	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	L	0.54323	1.7	0.80722	D	1	P;P;D;P	0.67145	0.915;0.915;0.996;0.774	B;B;D;B	0.77557	0.217;0.23;0.99;0.389	T	0.02844	-1.1103	10	0.39692	T	0.17	-12.9934	18.9756	0.92735	0.0:0.0:1.0:0.0	.	162;134;134;179	A1L3Y1;Q8NB59;Q8NB59-6;F5H426	.;SYT14_HUMAN;.;.	T	179;134;134;96;134;134;96	ENSP00000389039:A179T;ENSP00000442891:A134T;ENSP00000445837:A134T;ENSP00000437423:A96T;ENSP00000355986:A134T;ENSP00000418901:A134T;ENSP00000355982:A96T	ENSP00000355982:A96T	A	+	1	0	SYT14	208261180	1.000000	0.71417	0.966000	0.40874	0.860000	0.49131	8.054000	0.89451	2.571000	0.86741	0.650000	0.86243	GCA		0.393	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		A	210194557	G	A	210194557	3	1	61	1	0	0	0	0	1	0	0	0	15509	1203	42	3	553	3	SYT14	1	210194557	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187953	210194557	39056064	1021	9006										
SYT14	255928	broad.mit.edu	37	chr1	210273383	210273383	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagctcaaggatcatcttcGcagcttcctaaaccttttga	6	12	4	1	rs370207388		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210273383G>A	ENST00000472886.1	+	6	755	c.741G>A	c.(739-741)tcG>tcA	p.S247S	SYT14_ENST00000399639.2_Silent_p.S247S|SYT14_ENST00000367019.1_Silent_p.S247S|SYT14_ENST00000537238.1_Silent_p.S209S|SYT14_ENST00000422431.1_Silent_p.S292S|SYT14_ENST00000367015.1_Silent_p.S209S|SYT14_ENST00000534859.1_Silent_p.S247S|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	247					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)	p.S247S(1)		endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		GATCATCTTCGCAGCTTCCTA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,,,	1,4405	2.1+/-5.4	0,1,2202	53	51	51		876,741,876,741	2.2	1	1		51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	292/620,247/575,292/601,247/556	210273383	1,13005	2203	4300	6503	208340006	SO:0001819	synonymous_variant	255928			AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.741G>A	1.37:g.210273383G>A			208340006	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	37	CCDS31014.1																																																																																				0.348	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		A	210273383	G	A	210273383	2	1	61	1	0	0	0	0	0	0	0	1	15509	1074	38	1		1	SYT14	1	210273383	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78826	210273383	38977238	1022	9007										
HHAT	55733	broad.mit.edu	37	chr1	210796900	210796900	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccccacaagctcgccgtCgattccacgctgcccttgct	7	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210796900C>T	ENST00000367010.1	+	11	1503	c.1276C>T	c.(1276-1278)Cga>Tga	p.R426*	HHAT_ENST00000308852.6_Nonsense_Mutation_p.R381*|HHAT_ENST00000545154.1_Nonsense_Mutation_p.R427*|HHAT_ENST00000391905.3_Nonsense_Mutation_p.R426*|HHAT_ENST00000537898.1_Nonsense_Mutation_p.R361*|HHAT_ENST00000261458.3_Nonsense_Mutation_p.R426*|HHAT_ENST00000413764.2_Nonsense_Mutation_p.R426*|HHAT_ENST00000545781.1_Nonsense_Mutation_p.R363*|HHAT_ENST00000541565.1_Nonsense_Mutation_p.R289*|HHAT_ENST00000367009.1_Nonsense_Mutation_p.R116*	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	426					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)	p.R426*(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		AGCTCGCCGTCGATTCCACGC	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											287	267	274					1																	210796900		2203	4300	6503	208863523	SO:0001587	stop_gained	55733			AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.1276C>T	1.37:g.210796900C>T	ENSP00000355977:p.Arg426*		208863523	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Nonsense_Mutation	SNP	ENST00000367010.1	37	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	C	37	5.991240	0.97179	.	.	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000367009	.	.	.	5.87	4.96	0.65561	.	0.070853	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-12.052	13.7417	0.62852	0.1541:0.8458:0.0:0.0	.	.	.	.	X	426;289;427;361;426;363;426;381;426;116	.	ENSP00000261458:R426X	R	+	1	2	HHAT	208863523	0.970000	0.33590	0.109000	0.21407	0.003000	0.03518	2.636000	0.46545	1.475000	0.48197	-0.175000	0.13238	CGA		0.512	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		T	210796900	C	T	210796900	4	4	61	1	0	0	0	0	0	1	0	0	7110	876	31	1	1412	1	HHAT	1	210796900	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	523517	210796900	38453721	1023	9008										
KCNH1	3756	broad.mit.edu	37	chr1	210856886	210856886	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgccaggatgggactccGatcctggggactcctggcct	13	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210856886G>A	ENST00000271751.4	-	11	2734	c.2707C>T	c.(2707-2709)Cgg>Tgg	p.R903W	KCNH1_ENST00000367007.4_Missense_Mutation_p.R876W			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	903					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.R903W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ATGGGACTCCGATCCTGGGGA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	57	59					1																	210856886		2203	4300	6503	208923509	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2707C>T	1.37:g.210856886G>A	ENSP00000271751:p.Arg903Trp		208923509	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.850855	0.51270	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99014	-5.31;-5.33	4.93	2.99	0.34606	.	0.056524	0.64402	D	0.000001	D	0.97860	0.9297	L	0.46157	1.445	0.49798	D	0.999822	D;D	0.61697	0.975;0.99	P;P	0.48571	0.582;0.462	D	0.96541	0.9400	10	0.72032	D	0.01	.	13.7222	0.62735	0.0:0.0:0.7199:0.2801	.	876;903	Q14CL3;O95259	.;KCNH1_HUMAN	W	903;876	ENSP00000271751:R903W;ENSP00000355974:R876W	ENSP00000271751:R903W	R	-	1	2	KCNH1	208923509	1.000000	0.71417	0.998000	0.56505	0.378000	0.30076	4.346000	0.59367	0.453000	0.26858	0.561000	0.74099	CGG		0.607	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	210856886	G	A	210856886	3	1	61	1	0	0	0	0	1	0	0	0	8052	1057	37	1	266	1	KCNH1	1	210856886	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59986	210856886	38393735	1024	9009										
KCNH1	3756	broad.mit.edu	37	chr1	210857205	210857205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcctggaaggatacgggCgtggcaggactctcacgcac	15	12	1	0	rs138875472		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210857205C>T	ENST00000271751.4	-	11	2415	c.2388G>A	c.(2386-2388)acG>acA	p.T796T	KCNH1_ENST00000367007.4_Silent_p.T769T			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	796					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.T796T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		AGGATACGGGCGTGGCAGGAC	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C	,	0,4406		0,0,2203	57	55	56		2307,2388	-1.3	1	1	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KCNH1	NM_002238.3,NM_172362.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	769/963,796/990	210857205	1,13005	2203	4300	6503	208923828	SO:0001819	synonymous_variant	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2388G>A	1.37:g.210857205C>T			208923828	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	37	CCDS1496.1																																																																																				0.667	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210857205	C	T	210857205	2	4	61	1	0	0	0	0	0	0	0	1	8052	755	27	1		1	KCNH1	1	210857205	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	319	210857205	38393416	1025	9010										
KCNH1	3756	broad.mit.edu	37	chr1	210857360	210857360	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggcctctttctgctgtcGgaatctctggaagaggcgcc	12	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:210857360G>A	ENST00000271751.4	-	11	2260	c.2233C>T	c.(2233-2235)Cga>Tga	p.R745*	KCNH1_ENST00000367007.4_Nonsense_Mutation_p.R718*			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	745	Calmodulin-binding.				myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.R745*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TTCTGCTGTCGGAATCTCTGG	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											38	42	41					1																	210857360		2203	4300	6503	208923983	SO:0001587	stop_gained	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2233C>T	1.37:g.210857360G>A	ENSP00000271751:p.Arg745*		208923983	B1AQ26|O76035|Q14CL3	Nonsense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	38	7.113523	0.98074	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	.	.	.	4.62	4.62	0.57501	.	0.062938	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0384	0.47816	0.0:0.0:0.6727:0.3273	.	.	.	.	X	745;718	.	ENSP00000271751:R745X	R	-	1	2	KCNH1	208923983	1.000000	0.71417	0.999000	0.59377	0.912000	0.54170	4.726000	0.61986	2.120000	0.65058	0.561000	0.74099	CGA		0.592	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	210857360	G	A	210857360	4	1	61	1	0	0	0	0	0	1	0	0	8052	1124	39	1	740	1	KCNH1	1	210857360	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155	210857360	38393261	1026	9011										
KCNH1	3756	broad.mit.edu	37	chr1	211093327	211093327	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcacagcagctccatattCaatgtagtggtccagcttac	8	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211093327C>A	ENST00000271751.4	-	7	1144	c.1117G>T	c.(1117-1119)Gaa>Taa	p.E373*	KCNH1_ENST00000367007.4_Nonsense_Mutation_p.E346*			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	373					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.E373*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		GCTCCATATTCAATGTAGTGG	0.557																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											119	119	119					1																	211093327		2203	4300	6503	209159950	SO:0001587	stop_gained	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1117G>T	1.37:g.211093327C>A	ENSP00000271751:p.Glu373*		209159950	B1AQ26|O76035|Q14CL3	Nonsense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	40	8.319735	0.98757	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	18.8072	0.92041	0.0:1.0:0.0:0.0	.	.	.	.	X	373;346	.	ENSP00000271751:E373X	E	-	1	0	KCNH1	209159950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.538000	0.82048	2.691000	0.91804	0.655000	0.94253	GAA		0.557	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	211093327	C	A	211093327	4	1	61	1	0	0	0	0	0	1	0	0	8052	835	29	2	1872	2	KCNH1	1	211093327	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235967	211093327	38157294	1027	9012										
KCNH1	3756	broad.mit.edu	37	chr1	211280669	211280669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaaatccatcattgctgtAcacaataggccagtccacta	6	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211280669A>G	ENST00000271751.4	-	2	157	c.130T>C	c.(130-132)Tac>Cac	p.Y44H	KCNH1_ENST00000367007.4_Missense_Mutation_p.Y44H			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	44	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.Y44H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TCATTGCTGTACACAATAGGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											137	137	137					1																	211280669		2203	4300	6503	209347292	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.130T>C	1.37:g.211280669A>G	ENSP00000271751:p.Tyr44His		209347292	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517731	0.85495	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99663	-6.33;-6.33	5.62	5.62	0.85841	PAS (3);PAS fold (1);	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97543	1.0087	10	0.87932	D	0	.	15.0199	0.71621	1.0:0.0:0.0:0.0	.	44;44	Q14CL3;O95259	.;KCNH1_HUMAN	H	44	ENSP00000271751:Y44H;ENSP00000355974:Y44H	ENSP00000271751:Y44H	Y	-	1	0	KCNH1	209347292	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.915000	0.92740	2.129000	0.65627	0.533000	0.62120	TAC		0.408	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		G	211280669	A	G	211280669	3	3	61	1	0	0	0	0	1	0	0	0	8052	391	14	4	2879	4	KCNH1	1	211280669	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	187342	211280669	37969952	1028	9013										
TRAF5	7188	broad.mit.edu	37	chr1	211542888	211542888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaaggagttcaagcagtTtgcacagttgtttggcaaaa	11	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211542888T>C	ENST00000261464.5	+	9	938	c.884T>C	c.(883-885)tTt>tCt	p.F295S	TRAF5_ENST00000427925.2_Missense_Mutation_p.F189S|TRAF5_ENST00000367004.3_Missense_Mutation_p.F295S|TRAF5_ENST00000336184.2_Missense_Mutation_p.F295S	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	295					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F295S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TTCAAGCAGTTTGCACAGTTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	129	129					1																	211542888		2203	4300	6503	209609511	SO:0001583	missense	7188			AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.884T>C	1.37:g.211542888T>C	ENSP00000261464:p.Phe295Ser		209609511	B4DIS9|B4E0A2|Q6FHY1	Missense_Mutation	SNP	ENST00000261464.5	37	CCDS1497.1	.	.	.	.	.	.	.	.	.	.	T	3.235	-0.156613	0.06544	.	.	ENSG00000082512	ENST00000336184;ENST00000427925;ENST00000261464;ENST00000367004	T;D;T;T	0.82711	2.14;-1.64;2.14;2.14	4.12	2.97	0.34412	.	0.987960	0.08268	N	0.971882	T	0.78149	0.4238	L	0.50333	1.59	0.26050	N	0.981497	B;B;B	0.22604	0.045;0.034;0.072	B;B;B	0.23852	0.049;0.03;0.042	T	0.60747	-0.7202	10	0.21540	T	0.41	-14.0971	9.1492	0.36953	0.2886:0.0:0.0:0.7114	.	189;306;295	F5H1P7;B4E0A2;O00463	.;.;TRAF5_HUMAN	S	295;189;295;295	ENSP00000336825:F295S;ENSP00000389891:F189S;ENSP00000261464:F295S;ENSP00000355971:F295S	ENSP00000261464:F295S	F	+	2	0	TRAF5	209609511	1.000000	0.71417	0.990000	0.47175	0.424000	0.31475	2.425000	0.44723	0.454000	0.26884	-0.991000	0.02546	TTT		0.393	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		C	211542888	T	C	211542888	3	2	61	1	0	0	0	0	1	0	0	0	16484	1841	64	4	914	4	TRAF5	1	211542888	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	262219	211542888	37707733	1029	9014										
TRAF5	7188	broad.mit.edu	37	chr1	211545787	211545787	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgaggagagtttgactcaCtgttgcagtggccattcagg	14	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211545787C>A	ENST00000261464.5	+	11	1471	c.1417C>A	c.(1417-1419)Ctg>Atg	p.L473M	TRAF5_ENST00000427925.2_Missense_Mutation_p.L367M|TRAF5_ENST00000367004.3_Missense_Mutation_p.L473M|TRAF5_ENST00000336184.2_Missense_Mutation_p.L473M	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	473	Interaction with EIF2AK2/PKR.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L473M(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		GTTTGACTCACTGTTGCAGTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											107	96	100					1																	211545787		2203	4300	6503	209612410	SO:0001583	missense	7188			AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.1417C>A	1.37:g.211545787C>A	ENSP00000261464:p.Leu473Met		209612410	B4DIS9|B4E0A2|Q6FHY1	Missense_Mutation	SNP	ENST00000261464.5	37	CCDS1497.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195644	0.58126	.	.	ENSG00000082512	ENST00000336184;ENST00000427925;ENST00000261464;ENST00000367004	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.51	1.0	0.19881	TRAF-type (1);TRAF-like (1);MATH (3);	0.158198	0.44688	D	0.000432	T	0.63570	0.2522	M	0.91300	3.195	0.38485	D	0.947824	D;D;D	0.76494	0.999;0.997;0.994	D;D;D	0.71414	0.969;0.973;0.952	T	0.64715	-0.6342	10	0.66056	D	0.02	-14.0361	5.6523	0.17622	0.127:0.5437:0.0:0.3293	.	367;484;473	F5H1P7;B4E0A2;O00463	.;.;TRAF5_HUMAN	M	473;367;473;473	ENSP00000336825:L473M;ENSP00000389891:L367M;ENSP00000261464:L473M;ENSP00000355971:L473M	ENSP00000261464:L473M	L	+	1	2	TRAF5	209612410	0.072000	0.21174	0.994000	0.49952	0.994000	0.84299	0.522000	0.22909	0.383000	0.24910	-0.143000	0.13931	CTG		0.532	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		A	211545787	C	A	211545787	3	1	61	1	0	0	0	0	1	0	0	0	16484	564	20	2	1455	2	TRAF5	1	211545787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2899	211545787	37704834	1030	9015										
NEK2	4751	broad.mit.edu	37	chr1	211846853	211846853	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaataaggtgtgccaacaAatgtttttgcaaaactcgtg	9	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211846853A>C	ENST00000366999.4	-	3	665	c.527T>G	c.(526-528)tTt>tGt	p.F176C	NEK2_ENST00000366998.3_Missense_Mutation_p.F176C|NEK2_ENST00000540251.1_Missense_Mutation_p.F133C|NEK2_ENST00000462283.1_5'Flank|RP11-122M14.1_ENST00000415202.1_RNA	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)	p.F176C(1)		breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TGTGCCAACAAATGTTTTTGC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	1											70	73	72					1																	211846853		2203	4300	6503	209913476	SO:0001583	missense	4751			U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.527T>G	1.37:g.211846853A>C	ENSP00000355966:p.Phe176Cys		209913476	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184952	0.78677	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.42131	1.73;0.98;1.73	5.23	5.23	0.72850	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	L	0.46670	1.46	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.74023	0.969;0.982;0.969	T	0.51212	-0.8734	10	0.29301	T	0.29	.	15.4096	0.74908	1.0:0.0:0.0:0.0	.	176;176;176	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	C	176;133;176	ENSP00000355966:F176C;ENSP00000440237:F133C;ENSP00000355965:F176C	ENSP00000355965:F176C	F	-	2	0	NEK2	209913476	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.079000	0.76829	2.095000	0.63458	0.460000	0.39030	TTT		0.343	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		C	211846853	A	C	211846853	3	2	61	1	0	0	0	0	1	0	0	0	10355	14	1	4	834	4	NEK2	1	211846853	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	301066	211846853	37403768	1031	9016										
LPGAT1	9926	broad.mit.edu	37	chr1	211952346	211952346	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagctttgggataagctatCgttgtatctattatccactg	8	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:211952346C>T	ENST00000366997.4	-	6	994	c.768G>A	c.(766-768)acG>acA	p.T256T	LPGAT1_ENST00000366996.1_Silent_p.T256T	NM_014873.2	NP_055688.1	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1	256					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring acyl groups (GO:0016746)	p.T256T(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)		GATAAGCTATCGTTGTATCTA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	1											165	169	168					1																	211952346		2203	4300	6503	210018969	SO:0001819	synonymous_variant	9926			D86960	CCDS31018.1	1q32.3	2008-05-14	2004-11-25	2004-11-26	ENSG00000123684	ENSG00000123684			28985	protein-coding gene	gene with protein product		610473	"family with sequence similarity 34, member A"	FAM34A		9039502, 15485873	Standard	NM_014873		Approved	KIAA0205, FAM34A1, NET8	uc001hiv.3	Q92604	OTTHUMG00000037120	ENST00000366997.4:c.768G>A	1.37:g.211952346C>T			210018969	Q53YL2	Silent	SNP	ENST00000366997.4	37	CCDS31018.1																																																																																				0.338	LPGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090150.1	NM_014873		T	211952346	C	T	211952346	2	4	61	1	0	0	0	0	0	0	0	1	8943	871	31	1		1	LPGAT1	1	211952346	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105493	211952346	37298275	1032	9017										
INTS7	25896	broad.mit.edu	37	chr1	212148535	212148535	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcaatccctttgtgataGaattttaaagattcagcaat	7	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212148535G>T	ENST00000366994.3	-	13	1892	c.1788C>A	c.(1786-1788)ttC>ttA	p.F596L	INTS7_ENST00000366992.3_Missense_Mutation_p.F596L|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.F596L|INTS7_ENST00000440600.2_Missense_Mutation_p.F547L	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	596					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)		p.F596L(1)		NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		CTTTGTGATAGAATTTTAAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	67	68					1																	212148535		2203	4300	6503	210215158	SO:0001583	missense	25896			AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.1788C>A	1.37:g.212148535G>T	ENSP00000355961:p.Phe596Leu		210215158	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.711850	0.30322	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.64438	1.15;1.17;1.16;-0.1	6.06	6.06	0.98353	.	0.138414	0.64402	D	0.000003	T	0.28962	0.0719	N	0.01048	-1.04	0.43304	D	0.995306	B;B;B;B	0.21606	0.058;0.058;0.058;0.058	B;B;B;B	0.18561	0.022;0.022;0.022;0.022	T	0.40289	-0.9571	10	0.10111	T	0.7	-14.5861	11.0773	0.48038	0.0672:0.0:0.8025:0.1303	.	547;596;596;596	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	L	596;596;596;547	ENSP00000355961:F596L;ENSP00000355960:F596L;ENSP00000355959:F596L;ENSP00000388908:F547L	ENSP00000355959:F596L	F	-	3	2	INTS7	210215158	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.527000	0.45615	2.882000	0.98803	0.655000	0.94253	TTC		0.378	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		T	212148535	G	T	212148535	3	4	61	1	0	0	0	0	1	0	0	0	7804	933	33	2	1132	2	INTS7	1	212148535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196189	212148535	37102086	1033	9018										
PPP2R5A	5525	broad.mit.edu	37	chr1	212530531	212530531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattgtacttctggaataaCgaatatattcttagtttgat	7	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212530531C>T	ENST00000261461.2	+	11	1705	c.1131C>T	c.(1129-1131)aaC>aaT	p.N377N	RP11-384C4.2_ENST00000447949.1_RNA|PPP2R5A_ENST00000537030.3_Silent_p.N320N	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	377					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)	p.N377N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		TCTGGAATAACGAATATATTC	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	1											92	93	93					1																	212530531		2202	4298	6500	210597154	SO:0001819	synonymous_variant	5525			BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9309	protein-coding gene	gene with protein product		601643	"protein phosphatase 2, regulatory subunit B (B56), alpha isoform", "protein phosphatase 2, regulatory subunit B', alpha isoform"			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.1131C>T	1.37:g.212530531C>T			210597154	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Silent	SNP	ENST00000261461.2	37	CCDS1503.1																																																																																				0.318	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243		T	212530531	C	T	212530531	2	4	61	1	0	0	0	0	0	0	0	1	12426	535	19	1		1	PPP2R5A	1	212530531	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	381996	212530531	36720090	1034	9019										
TMEM206	55248	broad.mit.edu	37	chr1	212548612	212548612	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcactttttttggcagctgGcctctggtcaatgtagttaa	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212548612G>T	ENST00000261455.4	-	7	951	c.814C>A	c.(814-816)Cca>Aca	p.P272T	TMEM206_ENST00000535273.1_Missense_Mutation_p.P333T	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	272						cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.P272T(1)		breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TTGGCAGCTGGCCTCTGGTCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	73	74					1																	212548612		2203	4300	6503	210615235	SO:0001583	missense	55248			AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.814C>A	1.37:g.212548612G>T	ENSP00000261455:p.Pro272Thr		210615235	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908235	0.52333	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	6.08	6.08	0.98989	.	0.225461	0.47455	D	0.000233	T	0.36054	0.0953	N	0.19112	0.55	0.45852	D	0.998714	P;B	0.35793	0.521;0.275	B;B	0.34652	0.187;0.067	T	0.18178	-1.0345	9	0.32370	T	0.25	-26.3648	10.505	0.44828	0.0:0.1195:0.7003:0.1802	.	333;272	B7Z4D6;Q9H813	.;TM206_HUMAN	T	272;333	.	ENSP00000261455:P272T	P	-	1	0	TMEM206	210615235	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	4.134000	0.57990	2.894000	0.99253	0.591000	0.81541	CCA		0.438	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		T	212548612	G	T	212548612	3	4	61	1	0	0	0	0	1	0	0	0	16170	1203	42	2	246	2	TMEM206	1	212548612	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18081	212548612	36702009	1035	9020										
NENF	29937	broad.mit.edu	37	chr1	212619266	212619266	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcggctacactgcccggaGaattctcaatgaggatggca	12	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212619266G>T	ENST00000366988.3	+	4	494	c.437G>T	c.(436-438)aGa>aTa	p.R146I	NENF_ENST00000473900.1_3'UTR	NM_013349.4	NP_037481.1	Q9UMX5	NENF_HUMAN	neudesin neurotrophic factor	146					positive regulation of MAPK cascade (GO:0043410)	extracellular space (GO:0005615)	heme binding (GO:0020037)|metal ion binding (GO:0046872)	p.R146I(1)		endometrium(1)|kidney(1)|large_intestine(2)	4				all cancers(67;0.00967)|OV - Ovarian serous cystadenocarcinoma(81;0.0108)|GBM - Glioblastoma multiforme(131;0.0325)|Epithelial(68;0.132)		ACTGCCCGGAGAATTCTCAAT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											118	112	114					1																	212619266		2203	4300	6503	210685889	SO:0001583	missense	29937				CCDS1505.1	1q32.3	2011-07-05	2011-07-05		ENSG00000117691	ENSG00000117691			30384	protein-coding gene	gene with protein product	"neudesin"	611874	"neuron derived neurotrophic factor"			9771976, 15605373	Standard	NM_013349		Approved	CIR2, SCIRP10, SPUF	uc001hjd.3	Q9UMX5	OTTHUMG00000036744	ENST00000366988.3:c.437G>T	1.37:g.212619266G>T	ENSP00000355955:p.Arg146Ile		210685889	A1KYQ8|Q53FZ6|Q5TM90	Missense_Mutation	SNP	ENST00000366988.3	37	CCDS1505.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852290	0.91355	.	.	ENSG00000117691	ENST00000366988	T	0.79352	-1.26	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.88036	0.6329	M	0.75447	2.3	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.88966	0.3397	10	0.62326	D	0.03	-4.8993	18.7286	0.91724	0.0:0.0:1.0:0.0	.	146	Q9UMX5	NENF_HUMAN	I	146	ENSP00000355955:R146I	ENSP00000355955:R146I	R	+	2	0	NENF	210685889	1.000000	0.71417	0.199000	0.23439	0.943000	0.58893	9.451000	0.97610	2.490000	0.84030	0.585000	0.79938	AGA		0.547	NENF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089291.1	NM_013349		T	212619266	G	T	212619266	3	4	61	1	0	0	0	0	1	0	0	0	10366	942	33	2	451	2	NENF	1	212619266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70654	212619266	36631355	1036	9021										
FAM71A	149647	broad.mit.edu	37	chr1	212798608	212798608	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaggtttgtacggatctCtgttcaagaccatgagaaac	10	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212798608C>A	ENST00000294829.3	+	1	820	c.389C>A	c.(388-390)tCt>tAt	p.S130Y	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	130						nucleus (GO:0005634)		p.S130Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		GTACGGATCTCTGTTCAAGAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											97	101	100					1																	212798608		2203	4300	6503	210865231	SO:0001583	missense	149647				CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.389C>A	1.37:g.212798608C>A	ENSP00000294829:p.Ser130Tyr		210865231	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087165	0.36855	.	.	ENSG00000162771	ENST00000294829	T	0.18810	2.19	4.53	4.53	0.55603	.	0.092777	0.44902	D	0.000401	T	0.40815	0.1132	L	0.58302	1.8	0.24318	N	0.995053	D	0.89917	1.0	D	0.77004	0.989	T	0.11251	-1.0595	10	0.56958	D	0.05	-16.0992	13.0067	0.58710	0.0:1.0:0.0:0.0	.	130	Q8IYT1	FA71A_HUMAN	Y	130	ENSP00000294829:S130Y	ENSP00000294829:S130Y	S	+	2	0	FAM71A	210865231	0.959000	0.32827	0.294000	0.24946	0.141000	0.21300	2.268000	0.43338	2.521000	0.84997	0.557000	0.71058	TCT		0.522	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		A	212798608	C	A	212798608	3	1	61	1	0	0	0	0	1	0	0	0	5626	913	32	2	391	2	FAM71A	1	212798608	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179342	212798608	36452013	1037	9022										
FAM71A	149647	broad.mit.edu	37	chr1	212798955	212798955	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaggggagggactccaaAatgactttaacaaacccact	10	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:212798955A>C	ENST00000294829.3	+	1	1167	c.736A>C	c.(736-738)Aat>Cat	p.N246H	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	246						nucleus (GO:0005634)		p.N246H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		GGGACTCCAAAATGACTTTAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	112	109					1																	212798955		2203	4300	6503	210865578	SO:0001583	missense	149647				CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.736A>C	1.37:g.212798955A>C	ENSP00000294829:p.Asn246His		210865578	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	A	3.848	-0.032474	0.07543	.	.	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03386	3.95	4.12	-5.71	0.02413	.	3.363500	0.01189	N	0.007282	T	0.00845	0.0028	N	0.00260	-1.75	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46119	-0.9214	10	0.02654	T	1	1.4717	4.4207	0.11479	0.5143:0.1693:0.0:0.3165	.	246	Q8IYT1	FA71A_HUMAN	H	246;21	ENSP00000294829:N246H	ENSP00000294829:N246H	N	+	1	0	FAM71A	210865578	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.467000	0.06664	-0.947000	0.03673	-0.232000	0.12228	AAT		0.527	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		C	212798955	A	C	212798955	3	2	61	1	0	0	0	0	1	0	0	0	5626	14	1	4	738	4	FAM71A	1	212798955	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	347	212798955	36451666	1038	9023										
FLVCR1	28982	broad.mit.edu	37	chr1	213032521	213032521	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttgtgccaccgccgtgCtgggcaatcaggtaagtact	12	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:213032521C>A	ENST00000366971.4	+	1	925	c.727C>A	c.(727-729)Ctg>Atg	p.L243M	FLVCR1-AS1_ENST00000356684.3_lincRNA	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	243					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)	p.L243M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		CACCGCCGTGCTGGGCAATCA	0.557																																					Esophageal Squamous(199;2235 2952 19233 26256)											1	Substitution - Missense(1)	large_intestine(1)	1											69	73	72					1																	213032521		2203	4300	6503	211099144	SO:0001583	missense	28982			AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.727C>A	1.37:g.213032521C>A	ENSP00000355938:p.Leu243Met		211099144	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	37	CCDS1510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.67|18.67	3.673768|3.673768	0.67928|0.67928	.|.	.|.	ENSG00000162769|ENSG00000162769	ENST00000419102|ENST00000366971	.|D	.|0.92199	.|-2.99	5.21|5.21	3.33|3.33	0.38152|0.38152	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.92545	.|0.7632	L|L	0.41710|0.41710	1.295|1.295	0.53688|0.53688	D|D	0.999978|0.999978	.|D	.|0.76494	.|0.999	.|D	.|0.72982	.|0.979	.|D	.|0.89340	.|0.3653	.|10	.|0.28530	.|T	.|0.3	-18.0741|-18.0741	10.8263|10.8263	0.46633|0.46633	0.0:0.845:0.0:0.155|0.0:0.845:0.0:0.155	.|.	.|243	.|Q9Y5Y0	.|FLVC1_HUMAN	X|M	88|243	.|ENSP00000355938:L243M	.|ENSP00000355938:L243M	C|L	+|+	3|1	2|2	FLVCR1|FLVCR1	211099144|211099144	0.336000|0.336000	0.24757|0.24757	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.249000|0.249000	0.18216|0.18216	0.568000|0.568000	0.29311|0.29311	0.655000|0.655000	0.94253|0.94253	TGC|CTG		0.557	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053		A	213032521	C	A	213032521	3	1	61	1	0	0	0	0	1	0	0	0	5964	796	28	2	729	2	FLVCR1	1	213032521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233566	213032521	36218100	1039	9024										
RPS6KC1	26750	broad.mit.edu	37	chr1	213414441	213414441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaagactgaagggaatgGtgttgatacaaaagctatta	11	4	0	4	rs144668404	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:213414441G>A	ENST00000366960.3	+	11	1772	c.1622G>A	c.(1621-1623)gGt>gAt	p.G541D	RPS6KC1_ENST00000543354.1_Missense_Mutation_p.G244D|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.G329D|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.G529D|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	541					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.G541D(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAAGGGAATGGTGTTGATACA	0.448													G|||	3	0.000599042	0.0023	0	5008	,	,		20495	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	ASP/GLY,ASP/GLY	4,4402	8.1+/-20.4	0,4,2199	42	42	42		1586,1622	0.2	0	1	dbSNP_134	42	0,8600		0,0,4300	yes	missense,missense	RPS6KC1	NM_001136138.1,NM_012424.3	94,94	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	benign,benign	529/1055,541/1067	213414441	4,13002	2203	4300	6503	211481064	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1622G>A	1.37:g.213414441G>A	ENSP00000355927:p.Gly541Asp		211481064	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	1.089	-0.664583	0.03428	9.08E-4	0.0	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.38077	1.56;1.58;1.58;1.16	4.71	0.236	0.15471	.	0.816078	0.11293	N	0.579068	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.17899	-1.0354	10	0.38643	T	0.18	-21.276	4.7296	0.12957	0.31:0.1535:0.5365:0.0	.	329;541;529	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	D	329;541;529;244	ENSP00000442306:G329D;ENSP00000355927:G541D;ENSP00000355926:G529D;ENSP00000439282:G244D	ENSP00000355926:G529D	G	+	2	0	RPS6KC1	211481064	0.394000	0.25246	0.000000	0.03702	0.603000	0.37013	0.326000	0.19646	-0.274000	0.09232	-0.378000	0.06908	GGT		0.448	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		A	213414441	G	A	213414441	3	1	61	1	0	0	0	0	1	0	0	0	13695	1261	44	3	1664	3	RPS6KC1	1	213414441	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	381920	213414441	35836180	1040	9025										
RPS6KC1	26750	broad.mit.edu	37	chr1	213414619	213414619	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatagccccatggaattCtttaggatagacagtaagga	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:213414619C>A	ENST00000366960.3	+	11	1950	c.1800C>A	c.(1798-1800)ttC>ttA	p.F600L	RPS6KC1_ENST00000543354.1_Missense_Mutation_p.F303L|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.F388L|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.F588L|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	600					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.F600L(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		CCATGGAATTCTTTAGGATAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	45	44					1																	213414619		2203	4299	6502	211481242	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1800C>A	1.37:g.213414619C>A	ENSP00000355927:p.Phe600Leu		211481242	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	7.838	0.721258	0.15372	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.43688	1.31;1.37;1.38;0.94	5.39	3.54	0.40534	.	0.101101	0.64402	D	0.000002	T	0.25791	0.0628	L	0.34521	1.04	0.42629	D	0.993371	B;B;B	0.14805	0.011;0.007;0.007	B;B;B	0.19148	0.024;0.012;0.012	T	0.06643	-1.0815	10	0.13470	T	0.59	-18.929	5.0496	0.14501	0.1465:0.6294:0.0:0.2241	.	388;600;588	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	L	388;600;588;303	ENSP00000442306:F388L;ENSP00000355927:F600L;ENSP00000355926:F588L;ENSP00000439282:F303L	ENSP00000355926:F588L	F	+	3	2	RPS6KC1	211481242	0.961000	0.32948	1.000000	0.80357	0.981000	0.71138	0.096000	0.15147	0.665000	0.31066	-0.262000	0.10625	TTC		0.408	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		A	213414619	C	A	213414619	3	1	61	1	0	0	0	0	1	0	0	0	13695	912	32	2	1842	2	RPS6KC1	1	213414619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178	213414619	35836002	1041	9026										
RPS6KC1	26750	broad.mit.edu	37	chr1	213415476	213415476	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggaaatacatcagatttTtgaggaccttgataaaaaat	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:213415476T>G	ENST00000366960.3	+	11	2807	c.2657T>G	c.(2656-2658)tTt>tGt	p.F886C	RPS6KC1_ENST00000543354.1_Missense_Mutation_p.F589C|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.F674C|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.F874C|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	886	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.F886C(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		CATCAGATTTTTGAGGACCTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	100	99					1																	213415476		2203	4300	6503	211482099	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2657T>G	1.37:g.213415476T>G	ENSP00000355927:p.Phe886Cys		211482099	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.450842	0.63290	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049386	0.85682	D	0.000000	T	0.80347	0.4606	M	0.62154	1.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.81947	-0.0700	10	0.72032	D	0.01	-33.0577	16.3483	0.83171	0.0:0.0:0.0:1.0	.	674;886;874	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	C	674;886;874;589	ENSP00000442306:F674C;ENSP00000355927:F886C;ENSP00000355926:F874C;ENSP00000439282:F589C	ENSP00000355926:F874C	F	+	2	0	RPS6KC1	211482099	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.303000	0.78871	2.254000	0.74563	0.533000	0.62120	TTT		0.433	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		G	213415476	T	G	213415476	3	3	61	1	0	0	0	0	1	0	0	0	13695	1841	64	4	2699	4	RPS6KC1	1	213415476	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	857	213415476	35835145	1042	9027										
PTPN14	5784	broad.mit.edu	37	chr1	214625243	214625243	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaatttgtccagatgtttCttcagaggtttctccagctc	9	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214625243C>A	ENST00000366956.5	-	3	443	c.249G>T	c.(247-249)aaG>aaT	p.K83N	PTPN14_ENST00000543945.1_Missense_Mutation_p.K83N	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	83	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.K83N(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CCAGATGTTTCTTCAGAGGTT	0.458																																					Colon(92;557 1424 24372 34121 40073)											1	Substitution - Missense(1)	large_intestine(1)	1											111	108	109					1																	214625243		2203	4300	6503	212691866	SO:0001583	missense	5784			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.249G>T	1.37:g.214625243C>A	ENSP00000355923:p.Lys83Asn		212691866	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.330754	0.81690	.	.	ENSG00000152104	ENST00000366956;ENST00000543945	T;T	0.77750	-1.12;-1.12	5.45	5.45	0.79879	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	D	0.85340	0.5674	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86232	0.1638	10	0.72032	D	0.01	.	13.5559	0.61759	0.0:0.9253:0.0:0.0747	.	83	Q15678	PTN14_HUMAN	N	83	ENSP00000355923:K83N;ENSP00000443330:K83N	ENSP00000355923:K83N	K	-	3	2	PTPN14	212691866	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.776000	0.68924	2.565000	0.86533	0.555000	0.69702	AAG		0.458	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214625243	C	A	214625243	3	1	61	1	0	0	0	0	1	0	0	0	12818	912	32	2	3382	2	PTPN14	1	214625243	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1209767	214625243	34625378	1043	9028										
CENPF	1063	broad.mit.edu	37	chr1	214814402	214814402	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaccttaagtgcccttgaGaacaaggaaaaagagctgca	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214814402G>T	ENST00000366955.3	+	12	2889	c.2721G>T	c.(2719-2721)gaG>gaT	p.E907D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E907D(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GTGCCCTTGAGAACAAGGAAA	0.393																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											73	77	76					1																	214814402		2203	4300	6503	212881025	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.2721G>T	1.37:g.214814402G>T	ENSP00000355922:p.Glu907Asp		212881025	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.551684	0.45487	.	.	ENSG00000117724	ENST00000366955	T	0.04234	3.67	5.19	2.14	0.27477	.	0.216636	0.23232	N	0.050442	T	0.10981	0.0268	.	.	.	0.30602	N	0.760455	D	0.67145	0.996	P	0.60012	0.867	T	0.04593	-1.0940	9	0.30854	T	0.27	.	8.5933	0.33701	0.3298:0.0:0.6702:0.0	.	907	P49454	CENPF_HUMAN	D	907	ENSP00000355922:E907D	ENSP00000355922:E907D	E	+	3	2	CENPF	212881025	0.990000	0.36364	0.995000	0.50966	0.903000	0.53119	0.683000	0.25349	0.622000	0.30249	0.609000	0.83330	GAG		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214814402	G	T	214814402	3	4	61	1	0	0	0	0	1	0	0	0	3237	933	33	2	2763	2	CENPF	1	214814402	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189159	214814402	34436219	1044	9029										
CENPF	1063	broad.mit.edu	37	chr1	214815587	214815587	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgaacaagctgaatgaGctagagaaaatatgtgaaat	9	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214815587G>T	ENST00000366955.3	+	12	4074	c.3906G>T	c.(3904-3906)gaG>gaT	p.E1302D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E1302D(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGCTGAATGAGCTAGAGAAAA	0.393																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											71	70	71					1																	214815587		2203	4300	6503	212882210	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3906G>T	1.37:g.214815587G>T	ENSP00000355922:p.Glu1302Asp		212882210	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135227	0.37728	.	.	ENSG00000117724	ENST00000366955	T	0.23950	1.88	4.77	-1.46	0.08800	.	0.435743	0.16923	N	0.193999	T	0.30039	0.0752	.	.	.	0.09310	N	1	D	0.67145	0.996	P	0.58266	0.836	T	0.17137	-1.0379	9	0.28530	T	0.3	.	6.1235	0.20165	0.4391:0.0:0.4364:0.1245	.	1302	P49454	CENPF_HUMAN	D	1302	ENSP00000355922:E1302D	ENSP00000355922:E1302D	E	+	3	2	CENPF	212882210	0.986000	0.35501	0.002000	0.10522	0.763000	0.43281	0.281000	0.18810	-0.170000	0.10816	0.511000	0.50034	GAG		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214815587	G	T	214815587	3	4	61	1	0	0	0	0	1	0	0	0	3237	962	34	2	3948	2	CENPF	1	214815587	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1185	214815587	34435034	1045	9030										
CENPF	1063	broad.mit.edu	37	chr1	214816319	214816319	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaccccttcggccccagcGaagggtgttgaagagcttga	13	11	0	3	rs564882822		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214816319G>A	ENST00000366955.3	+	12	4806	c.4638G>A	c.(4636-4638)gcG>gcA	p.A1546A		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1642	2 X 96 AA approximate tandem repeats.		Missing. {ECO:0000269|PubMed:7651420}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.A1546A(2)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CGGCCCCAGCGAAGGGTGTTG	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		20317	0		0	False		,,,				2504	0				Colon(80;575 1284 11000 14801 43496)											2	Substitution - coding silent(2)	large_intestine(2)	1											43	46	45					1																	214816319		2203	4300	6503	212882942	SO:0001819	synonymous_variant	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.4638G>A	1.37:g.214816319G>A			212882942	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.493	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		A	214816319	G	A	214816319	2	1	61	1	0	0	0	0	0	0	0	1	3237	1045	37	1		1	CENPF	1	214816319	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	732	214816319	34434302	1046	9031										
CENPF	1063	broad.mit.edu	37	chr1	214830332	214830332	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagatcaaagaactgaaaGaaactcttgaagaaaaaacc	7	7	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214830332G>T	ENST00000366955.3	+	18	8710	c.8542G>T	c.(8542-8544)Gaa>Taa	p.E2848*		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2944	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E2848*(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAACTGAAAGAAACTCTTGA	0.368																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - Nonsense(1)	large_intestine(1)	1											81	80	81					1																	214830332		2203	4300	6503	212896955	SO:0001587	stop_gained	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8542G>T	1.37:g.214830332G>T	ENSP00000355922:p.Glu2848*		212896955	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	48	14.805713	0.99810	.	.	ENSG00000117724	ENST00000366955	.	.	.	5.23	5.23	0.72850	.	0.000000	0.33938	N	0.004410	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	14.7485	0.69508	0.0:0.1442:0.8558:0.0	.	.	.	.	X	2848	.	ENSP00000355922:E2848X	E	+	1	0	CENPF	212896955	1.000000	0.71417	0.987000	0.45799	0.041000	0.13682	3.675000	0.54605	2.608000	0.88229	0.561000	0.74099	GAA		0.368	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214830332	G	T	214830332	4	4	61	1	0	0	0	0	0	1	0	0	3237	943	33	2	8608	2	CENPF	1	214830332	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14013	214830332	34420289	1047	9032										
CENPF	1063	broad.mit.edu	37	chr1	214832361	214832361	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaacagctggtggcagcaGatcacaaaaggtaaactact	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:214832361G>T	ENST00000366955.3	+	19	9299	c.9131G>T	c.(9130-9132)aGa>aTa	p.R3044I		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	3140	Sufficient for centromere localization.|Sufficient for nuclear localization.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.R3044I(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGTGGCAGCAGATCACAAAAG	0.512											OREG0014250	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(80;575 1284 11000 14801 43496)											1	Substitution - Missense(1)	large_intestine(1)	1											69	68	68					1																	214832361		2203	4300	6503	212898984	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.9131G>T	1.37:g.214832361G>T	ENSP00000355922:p.Arg3044Ile	2224	212898984	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835030	0.71373	.	.	ENSG00000117724	ENST00000366955	T	0.04603	3.59	5.63	3.75	0.43078	.	0.000000	0.40144	N	0.001177	T	0.12135	0.0295	M	0.63843	1.955	0.42212	D	0.991819	D	0.57899	0.981	P	0.57371	0.819	T	0.00885	-1.1527	10	0.87932	D	0	.	7.3279	0.26566	0.3537:0.0:0.6463:0.0	.	3140	P49454	CENPF_HUMAN	I	3044	ENSP00000355922:R3044I	ENSP00000355922:R3044I	R	+	2	0	CENPF	212898984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.063000	0.49978	1.382000	0.46385	0.655000	0.94253	AGA		0.512	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214832361	G	T	214832361	3	4	61	1	0	0	0	0	1	0	0	0	3237	942	33	2	9201	2	CENPF	1	214832361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2029	214832361	34418260	1048	9033										
KCNK2	3776	broad.mit.edu	37	chr1	215342568	215342568	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacatctcaccacgcacaGaaggcggcaaaatattctgt	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215342568G>T	ENST00000444842.2	+	4	652	c.502G>T	c.(502-504)Gaa>Taa	p.E168*	KCNK2_ENST00000391894.2_Nonsense_Mutation_p.E153*|KCNK2_ENST00000391895.2_Nonsense_Mutation_p.E164*	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	168					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)	p.E153*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	ACCACGCACAGAAGGCGGCAA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											143	146	145					1																	215342568		2203	4300	6503	213409191	SO:0001587	stop_gained	3776			AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.502G>T	1.37:g.215342568G>T	ENSP00000394033:p.Glu168*		213409191	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Nonsense_Mutation	SNP	ENST00000444842.2	37	CCDS41467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.603176|4.603176	0.87157|0.87157	.|.	.|.	ENSG00000082482|ENSG00000082482	ENST00000391895;ENST00000478774;ENST00000391894;ENST00000444842;ENST00000457122|ENST00000366948	.|.	.|.	.|.	6.16|6.16	5.2|5.2	0.72013|0.72013	.|.	0.178111|.	0.64402|.	D|.	0.000009|.	.|T	.|0.60818	.|0.2298	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71155	.|-0.4675	.|4	0.11182|0.66056	T|D	0.66|0.02	.|.	10.3881|10.3881	0.44152|0.44152	0.0724:0.2191:0.7084:0.0|0.0724:0.2191:0.7084:0.0	.|.	.|.	.|.	.|.	X|H	164;112;153;168;112|124	.|.	ENSP00000375764:E153X|ENSP00000355915:Q124H	E|Q	+|+	1|3	0|2	KCNK2|KCNK2	213409191|213409191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	4.355000|4.355000	0.59424|0.59424	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GAA|CAG		0.363	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		T	215342568	G	T	215342568	4	4	61	1	0	0	0	0	0	1	0	0	8087	943	33	2	559	2	KCNK2	1	215342568	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	510207	215342568	33908053	1049	9034										
KCTD3	51133	broad.mit.edu	37	chr1	215751367	215751367	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggcttctcttatgtgaaGaattggagcgttcctcttgt	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215751367G>T	ENST00000259154.4	+	6	634	c.340G>T	c.(340-342)Gaa>Taa	p.E114*		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	114					protein homooligomerization (GO:0051260)			p.E114*(2)		breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		CTTATGTGAAGAATTGGAGCG	0.343																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											183	181	182					1																	215751367		2203	4300	6503	213817990	SO:0001587	stop_gained	51133			AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"potassium channel tetramerisation domain containing 3"			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.340G>T	1.37:g.215751367G>T	ENSP00000259154:p.Glu114*		213817990	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Nonsense_Mutation	SNP	ENST00000259154.4	37	CCDS1515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.492127|5.492127	0.96339|0.96339	.|.	.|.	ENSG00000136636|ENSG00000136636	ENST00000259154;ENST00000366945|ENST00000448333	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80025	.|0.4548	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77710	.|-0.2486	.|3	0.51188|.	T|.	0.08|.	-34.8986|-34.8986	20.0591|20.0591	0.97667|0.97667	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	114|86	.|.	ENSP00000259154:E114X|.	E|R	+|+	1|2	0|0	KCTD3|KCTD3	213817990|213817990	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.995000|0.995000	0.86356|0.86356	9.404000|9.404000	0.97306|0.97306	2.739000|2.739000	0.93911|0.93911	0.491000|0.491000	0.48974|0.48974	GAA|AGA		0.343	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		T	215751367	G	T	215751367	4	4	61	1	0	0	0	0	0	1	0	0	8131	943	33	2	362	2	KCTD3	1	215751367	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	408799	215751367	33499254	1050	9035										
USH2A	7399	broad.mit.edu	37	chr1	215812548	215812548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcgtcttaacacttccttCgtcagtcgtgcagatgacct	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215812548C>T	ENST00000307340.3	-	69	15387	c.15001G>A	c.(15001-15003)Gaa>Aaa	p.E5001K	USH2A_ENST00000366943.2_Missense_Mutation_p.E5001K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5001					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.E5001K(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACACTTCCTTCGTCAGTCGTG	0.408										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											194	195	195					1																	215812548		2203	4300	6503	213879171	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15001G>A	1.37:g.215812548C>T	ENSP00000305941:p.Glu5001Lys		213879171	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	1.794	-0.478722	0.04414	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.12465	2.69;2.68	5.2	1.24	0.21308	Fibronectin, type III (1);	0.428384	0.17015	U	0.190330	T	0.11623	0.0283	L	0.60455	1.87	0.22354	N	0.999178	B	0.25312	0.123	B	0.12837	0.008	T	0.25984	-1.0116	10	0.26408	T	0.33	.	6.6613	0.23016	0.0:0.6599:0.1332:0.2069	.	5001	O75445	USH2A_HUMAN	K	5001	ENSP00000305941:E5001K;ENSP00000355910:E5001K	ENSP00000305941:E5001K	E	-	1	0	USH2A	213879171	0.052000	0.20516	0.229000	0.23960	0.028000	0.11728	0.310000	0.19356	0.204000	0.20548	-0.121000	0.15023	GAA		0.408	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215812548	C	T	215812548	3	4	61	1	0	0	0	0	1	0	0	0	17076	893	31	1	623	1	USH2A	1	215812548	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61181	215812548	33438073	1051	9036										
USH2A	7399	broad.mit.edu	37	chr1	215848533	215848533	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctgaattccaagtgtaGattttatattcacactgcgt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215848533G>T	ENST00000307340.3	-	63	13106	c.12720C>A	c.(12718-12720)atC>atA	p.I4240I	USH2A_ENST00000366943.2_Silent_p.I4240I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4240	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.I4240I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCCAAGTGTAGATTTTATATT	0.418										HNSCC(13;0.011)																																						1	Substitution - coding silent(1)	large_intestine(1)	1											100	95	97					1																	215848533		2203	4300	6503	213915156	SO:0001819	synonymous_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12720C>A	1.37:g.215848533G>T			213915156	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.418	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215848533	G	T	215848533	2	4	61	1	0	0	0	0	0	0	0	1	17076	932	33	2		2	USH2A	1	215848533	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35985	215848533	33402088	1052	9037										
USH2A	7399	broad.mit.edu	37	chr1	215848859	215848859	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctctggtgcaggcctccaGggtcagtgtgtagagagtga	16	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215848859G>A	ENST00000307340.3	-	63	12780	c.12394C>T	c.(12394-12396)Ctg>Ttg	p.L4132L	USH2A_ENST00000366943.2_Silent_p.L4132L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4132	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.L4132L(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAGGCCTCCAGGGTCAGTGTG	0.562										HNSCC(13;0.011)																																						1	Substitution - coding silent(1)	large_intestine(1)	1											51	51	51					1																	215848859		2203	4300	6503	213915482	SO:0001819	synonymous_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12394C>T	1.37:g.215848859G>A			213915482	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.562	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215848859	G	A	215848859	2	1	61	1	0	0	0	0	0	0	0	1	17076	991	35	3		3	USH2A	1	215848859	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	326	215848859	33401762	1053	9038										
USH2A	7399	broad.mit.edu	37	chr1	215953270	215953270	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctggtactctttaatgacGccgtttgatttctcagggac	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215953270G>A	ENST00000307340.3	-	55	11240	c.10854C>T	c.(10852-10854)ggC>ggT	p.G3618G	USH2A_ENST00000366943.2_Silent_p.G3618G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3618	Fibronectin type-III 21. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.G3618G(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTTAATGACGCCGTTTGATT	0.517										HNSCC(13;0.011)																																						1	Substitution - coding silent(1)	large_intestine(1)	1											184	146	159					1																	215953270		2203	4300	6503	214019893	SO:0001819	synonymous_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.10854C>T	1.37:g.215953270G>A			214019893	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.517	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215953270	G	A	215953270	2	1	61	1	0	0	0	0	0	0	0	1	17076	1074	38	1		1	USH2A	1	215953270	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104411	215953270	33297351	1054	9039										
USH2A	7399	broad.mit.edu	37	chr1	215987117	215987117	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacccagagcagcactgatGatttggttgtgcctcctgta	10	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:215987117G>T	ENST00000307340.3	-	49	10086	c.9700C>A	c.(9700-9702)Cat>Aat	p.H3234N	USH2A_ENST00000366943.2_Missense_Mutation_p.H3234N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3234					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.H3234N(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAGCACTGATGATTTGGTTGT	0.443										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											136	126	129					1																	215987117		2203	4300	6503	214053740	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9700C>A	1.37:g.215987117G>T	ENSP00000305941:p.His3234Asn		214053740	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.761478	0.49468	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13538	2.58;2.58	5.8	2.49	0.30216	Fibronectin, type III (2);	0.169432	0.27473	U	0.019210	T	0.18087	0.0434	M	0.66506	2.035	0.09310	N	0.999999	P	0.47106	0.89	B	0.43413	0.419	T	0.08351	-1.0726	10	0.72032	D	0.01	.	11.3589	0.49632	0.2805:0.0:0.7195:0.0	.	3234	O75445	USH2A_HUMAN	N	3234	ENSP00000305941:H3234N;ENSP00000355910:H3234N	ENSP00000305941:H3234N	H	-	1	0	USH2A	214053740	0.860000	0.29831	0.001000	0.08648	0.022000	0.10575	1.308000	0.33528	0.806000	0.34183	-0.229000	0.12294	CAT		0.443	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215987117	G	T	215987117	3	4	61	1	0	0	0	0	1	0	0	0	17076	1290	45	2	6004	2	USH2A	1	215987117	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33847	215987117	33263504	1055	9040										
USH2A	7399	broad.mit.edu	37	chr1	216251574	216251574	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacacttgctgatatgaaaGagccttcctttttaataatg	6	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216251574G>T	ENST00000307340.3	-	27	5815	c.5429C>A	c.(5428-5430)tCt>tAt	p.S1810Y	RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.S1810Y	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1810	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.S1810Y(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGATATGAAAGAGCCTTCCTT	0.438										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											166	169	168					1																	216251574		2203	4300	6503	214318197	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5429C>A	1.37:g.216251574G>T	ENSP00000305941:p.Ser1810Tyr		214318197	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316491	0.81469	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.78707	-1.2;-1.2	5.01	5.01	0.66863	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.42821	D	0.000644	D	0.83519	0.5272	M	0.68317	2.08	0.20703	N	0.999865	P	0.49253	0.921	P	0.55222	0.771	T	0.75587	-0.3266	10	0.21540	T	0.41	.	18.3099	0.90195	0.0:0.0:1.0:0.0	.	1810	O75445	USH2A_HUMAN	Y	1810	ENSP00000305941:S1810Y;ENSP00000355910:S1810Y	ENSP00000305941:S1810Y	S	-	2	0	USH2A	214318197	1.000000	0.71417	0.006000	0.13384	0.760000	0.43138	5.767000	0.68850	2.338000	0.79540	0.650000	0.86243	TCT		0.438	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216251574	G	T	216251574	3	4	61	1	0	0	0	0	1	0	0	0	17076	942	33	2	10363	2	USH2A	1	216251574	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	264457	216251574	32999047	1056	9041										
USH2A	7399	broad.mit.edu	37	chr1	216348705	216348705	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagctggtagagatgactCtctcctttccagctgatata	9	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216348705C>A	ENST00000307340.3	-	21	4902	c.4516G>T	c.(4516-4518)Gag>Tag	p.E1506*	USH2A_ENST00000366942.3_Nonsense_Mutation_p.E1506*|USH2A_ENST00000366943.2_Nonsense_Mutation_p.E1506*	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1506					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.E1506*(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGAGATGACTCTCTCCTTTCC	0.443										HNSCC(13;0.011)																																						1	Substitution - Nonsense(1)	large_intestine(1)	1											124	104	111					1																	216348705		2203	4300	6503	214415328	SO:0001587	stop_gained	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4516G>T	1.37:g.216348705C>A	ENSP00000305941:p.Glu1506*		214415328	Q5VVM9|Q6S362|Q9NS27	Nonsense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	45	11.343749	0.99549	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	.	.	.	5.49	3.59	0.41128	.	0.729565	0.11606	U	0.547312	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	11.7063	0.51599	0.0:0.8083:0.1238:0.0678	.	.	.	.	X	1506	.	ENSP00000305941:E1506X	E	-	1	0	USH2A	214415328	0.307000	0.24500	0.453000	0.27007	0.588000	0.36517	2.431000	0.44775	0.648000	0.30732	0.544000	0.68410	GAG		0.443	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216348705	C	A	216348705	4	1	61	1	0	0	0	0	0	1	0	0	17076	922	32	2	11314	2	USH2A	1	216348705	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97131	216348705	32901916	1057	9042										
USH2A	7399	broad.mit.edu	37	chr1	216465643	216465643	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgcattgacaaggtttacAattgaaagcgtaaacttgat	9	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216465643A>G	ENST00000307340.3	-	10	2100	c.1714T>C	c.(1714-1716)Tgt>Cgt	p.C572R	USH2A_ENST00000366942.3_Missense_Mutation_p.C572R|USH2A_ENST00000366943.2_Missense_Mutation_p.C572R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	572	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.C572R(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAAGGTTTACAATTGAAAGCG	0.418										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											112	104	107					1																	216465643		2203	4300	6503	214532266	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1714T>C	1.37:g.216465643A>G	ENSP00000305941:p.Cys572Arg		214532266	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.627086	0.66901	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;D;D	0.95307	-3.67;-3.67;-3.67	4.81	4.81	0.61882	EGF-like, laminin (2);	0.000000	0.46145	U	0.000317	D	0.98239	0.9417	H	0.97587	4.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.99533	1.0961	10	0.87932	D	0	.	14.3867	0.66949	1.0:0.0:0.0:0.0	.	572;572	O75445-2;O75445	.;USH2A_HUMAN	R	572	ENSP00000305941:C572R;ENSP00000355910:C572R;ENSP00000355909:C572R	ENSP00000305941:C572R	C	-	1	0	USH2A	214532266	1.000000	0.71417	0.385000	0.26158	0.880000	0.50808	8.241000	0.89816	1.810000	0.52873	0.383000	0.25322	TGT		0.418	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216465643	A	G	216465643	3	3	61	1	0	0	0	0	1	0	0	0	17076	130	5	4	14160	4	USH2A	1	216465643	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116938	216465643	32784978	1058	9043										
USH2A	7399	broad.mit.edu	37	chr1	216595308	216595308	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaaaaataaaacttgcaGaattgctatgggcgttagga	9	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216595308G>T	ENST00000307340.3	-	2	757	c.371C>A	c.(370-372)tCt>tAt	p.S124Y	USH2A_ENST00000366942.3_Missense_Mutation_p.S124Y|USH2A_ENST00000366943.2_Missense_Mutation_p.S124Y	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	124					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.S124Y(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AAAACTTGCAGAATTGCTATG	0.453										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											99	95	96					1																	216595308		2203	4300	6503	214661931	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.371C>A	1.37:g.216595308G>T	ENSP00000305941:p.Ser124Tyr		214661931	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191486	0.78902	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.65364	-0.15;-0.15;-0.15	5.42	5.42	0.78866	Concanavalin A-like lectin/glucanase (1);	0.373747	0.19379	U	0.115701	T	0.68970	0.3059	L	0.54323	1.7	0.09310	N	0.999997	P;P	0.43885	0.785;0.82	P;P	0.52189	0.509;0.692	T	0.64550	-0.6381	10	0.72032	D	0.01	.	13.4996	0.61447	0.0749:0.0:0.9251:0.0	.	124;124	O75445-2;O75445	.;USH2A_HUMAN	Y	124	ENSP00000305941:S124Y;ENSP00000355910:S124Y;ENSP00000355909:S124Y	ENSP00000305941:S124Y	S	-	2	0	USH2A	214661931	0.985000	0.35326	0.019000	0.16419	0.687000	0.40016	5.973000	0.70456	2.543000	0.85770	0.591000	0.81541	TCT		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216595308	G	T	216595308	3	4	61	1	0	0	0	0	1	0	0	0	17076	942	33	2	15535	2	USH2A	1	216595308	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129665	216595308	32655313	1059	9044										
USH2A	7399	broad.mit.edu	37	chr1	216595573	216595573	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctccagccttgggaaaaGacctcgtgactcagtcaagg	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216595573G>T	ENST00000307340.3	-	2	492	c.106C>A	c.(106-108)Ctt>Att	p.L36I	USH2A_ENST00000366942.3_Missense_Mutation_p.L36I|USH2A_ENST00000366943.2_Missense_Mutation_p.L36I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	36					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.L36I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTGGGAAAAGACCTCGTGAC	0.463										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											81	85	84					1																	216595573		2203	4300	6503	214662196	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.106C>A	1.37:g.216595573G>T	ENSP00000305941:p.Leu36Ile		214662196	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	9.354	1.066352	0.20067	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.19938	2.56;2.55;2.11	5.27	3.34	0.38264	.	0.547947	0.13118	U	0.412430	T	0.18383	0.0441	L	0.56769	1.78	0.09310	N	0.999995	B;P	0.35077	0.418;0.483	B;B	0.27076	0.076;0.051	T	0.12656	-1.0539	10	0.19147	T	0.46	.	10.5486	0.45074	0.0727:0.1338:0.7935:0.0	.	36;36	O75445-2;O75445	.;USH2A_HUMAN	I	36	ENSP00000305941:L36I;ENSP00000355910:L36I;ENSP00000355909:L36I	ENSP00000305941:L36I	L	-	1	0	USH2A	214662196	0.998000	0.40836	0.286000	0.24833	0.783000	0.44284	2.448000	0.44926	0.568000	0.29311	0.591000	0.81541	CTT		0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216595573	G	T	216595573	3	4	61	1	0	0	0	0	1	0	0	0	17076	942	33	2	15800	2	USH2A	1	216595573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	265	216595573	32655048	1060	9045										
ESRRG	2104	broad.mit.edu	37	chr1	216741392	216741392	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgttctccgcatctatcCtgcgcttgtacttctgccga	9	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:216741392C>A	ENST00000408911.3	-	4	791	c.638G>T	c.(637-639)aGg>aTg	p.R213M	ESRRG_ENST00000463665.1_Missense_Mutation_p.R151M|ESRRG_ENST00000487276.1_Missense_Mutation_p.R190M|ESRRG_ENST00000493603.1_Missense_Mutation_p.R190M|ESRRG_ENST00000366938.2_Missense_Mutation_p.R190M|ESRRG_ENST00000366937.1_Missense_Mutation_p.R218M|ESRRG_ENST00000366940.2_Missense_Mutation_p.R190M|ESRRG_ENST00000361395.2_Missense_Mutation_p.R190M|ESRRG_ENST00000359162.2_Missense_Mutation_p.R190M|ESRRG_ENST00000493748.1_Missense_Mutation_p.R190M|ESRRG_ENST00000361525.3_Missense_Mutation_p.R190M|ESRRG_ENST00000360012.3_Missense_Mutation_p.R190M|ESRRG_ENST00000391890.3_Missense_Mutation_p.R190M	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	213					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R213M(1)		endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CGCATCTATCCTGCGCTTGTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											187	155	166					1																	216741392		2203	4300	6503	214808015	SO:0001583	missense	2104			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.638G>T	1.37:g.216741392C>A	ENSP00000386171:p.Arg213Met		214808015	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289300	0.80914	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;T;D;D;D	0.94280	-3.33;-3.33;-3.37;-3.34;-3.33;-3.33;-3.33;-3.33;-3.33;-3.39;0.45;-3.33;-3.33;-3.17	5.5	5.5	0.81552	Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);	0.044496	0.85682	D	0.000000	D	0.96984	0.9015	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;0.994;0.99	D;D;D	0.77004	0.989;0.989;0.962	D	0.97265	0.9907	10	0.72032	D	0.01	.	19.3869	0.94560	0.0:1.0:0.0:0.0	.	151;218;213	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	M	190;190;218;213;190;190;190;190;190;190;151;190;190;190;190	ENSP00000355225:R190M;ENSP00000355907:R190M;ENSP00000355904:R218M;ENSP00000386171:R213M;ENSP00000352077:R190M;ENSP00000354584:R190M;ENSP00000355905:R190M;ENSP00000353108:R190M;ENSP00000419594:R190M;ENSP00000375761:R190M;ENSP00000418629:R151M;ENSP00000419155:R190M;ENSP00000417374:R190M;ENSP00000419514:R190M	ENSP00000346386:R190M	R	-	2	0	ESRRG	214808015	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.578000	0.87016	0.650000	0.86243	AGG		0.522	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		A	216741392	C	A	216741392	3	1	61	1	0	0	0	0	1	0	0	0	5275	681	24	2	754	2	ESRRG	1	216741392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145819	216741392	32509229	1061	9046										
SPATA17	128153	broad.mit.edu	37	chr1	217947761	217947761	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaaagcctttaacacaccGaagacctaaagttaagcaga	8	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:217947761G>A	ENST00000366933.4	+	7	660	c.605G>A	c.(604-606)cGa>cAa	p.R202Q		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	202						cytoplasm (GO:0005737)		p.R202Q(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TTAACACACCGAAGACCTAAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	100	102					1																	217947761		2203	4300	6503	216014384	SO:0001583	missense	128153			AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.605G>A	1.37:g.217947761G>A	ENSP00000355900:p.Arg202Gln		216014384	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	G	6.810	0.518481	0.13005	.	.	ENSG00000162814	ENST00000366933	T	0.44482	0.92	4.9	-9.81	0.00487	.	1.471100	0.04379	N	0.360393	T	0.25195	0.0612	N	0.21142	0.635	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.30060	-0.9991	10	0.18710	T	0.47	-7.5571	12.5108	0.56005	0.5995:0.2108:0.1898:0.0	.	202	Q96L03	SPT17_HUMAN	Q	202	ENSP00000355900:R202Q	ENSP00000355900:R202Q	R	+	2	0	SPATA17	216014384	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-3.202000	0.00560	-4.029000	0.00080	-1.008000	0.02478	CGA		0.438	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		A	217947761	G	A	217947761	3	1	61	1	0	0	0	0	1	0	0	0	15041	1058	37	1	631	1	SPATA17	1	217947761	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1206369	217947761	31302860	1062	9047										
TGFB2	7042	broad.mit.edu	37	chr1	218578555	218578555	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctacttcagaattgttCgatttgacgtctcagcaatg	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:218578555C>T	ENST00000366930.4	+	2	858	c.391C>T	c.(391-393)Cga>Tga	p.R131*	TGFB2_ENST00000366929.4_Nonsense_Mutation_p.R159*	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	131					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R131*(1)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		CAGAATTGTTCGATTTGACGT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											231	223	226					1																	218578555		2203	4300	6503	216645178	SO:0001587	stop_gained	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.391C>T	1.37:g.218578555C>T	ENSP00000355897:p.Arg131*		216645178	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Nonsense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	C	40	8.300258	0.98750	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	.	.	.	5.09	2.99	0.34606	.	0.292022	0.31936	N	0.006822	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2887	0.54807	0.4335:0.5665:0.0:0.0	.	.	.	.	X	131;159	.	ENSP00000355896:R159X	R	+	1	2	TGFB2	216645178	0.983000	0.35010	0.996000	0.52242	0.940000	0.58332	2.945000	0.49043	1.096000	0.41439	0.650000	0.86243	CGA		0.418	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		T	218578555	C	T	218578555	4	4	61	1	0	0	0	0	0	1	0	0	15857	876	31	1	485	1	TGFB2	1	218578555	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	630794	218578555	30672066	1063	9048										
TGFB2	7042	broad.mit.edu	37	chr1	218607427	218607427	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttttcccctccagattCtcaagtccaaagatttaaca	3	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:218607427C>A	ENST00000366930.4	+	3	981	c.514C>A	c.(514-516)Ctc>Atc	p.L172I	TGFB2_ENST00000366929.4_Missense_Mutation_p.L200I	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	172					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.L172I(1)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		CCTCCAGATTCTCAAGTCCAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											207	223	217					1																	218607427		2203	4300	6503	216674050	SO:0001583	missense	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.514C>A	1.37:g.218607427C>A	ENSP00000355897:p.Leu172Ile		216674050	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.187259	0.78789	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.68181	-0.31;-0.31	5.91	5.91	0.95273	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67325	0.2881	L	0.49571	1.57	0.54753	D	0.999987	B;B	0.27013	0.166;0.013	B;B	0.38327	0.271;0.043	T	0.62407	-0.6861	10	0.33940	T	0.23	.	15.3903	0.74739	0.0:0.9319:0.0:0.0681	.	200;172	P61812-2;P61812	.;TGFB2_HUMAN	I	172;200	ENSP00000355897:L172I;ENSP00000355896:L200I	ENSP00000355896:L200I	L	+	1	0	TGFB2	216674050	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	1.844000	0.39269	2.808000	0.96608	0.655000	0.94253	CTC		0.413	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		A	218607427	C	A	218607427	3	1	61	1	0	0	0	0	1	0	0	0	15857	913	32	2	612	2	TGFB2	1	218607427	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28872	218607427	30643194	1064	9049										
TGFB2	7042	broad.mit.edu	37	chr1	218614675	218614675	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattgaacagctttctaatAtgattgtaaagtcttgcaaa	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:218614675A>G	ENST00000366930.4	+	7	1683	c.1216A>G	c.(1216-1218)Atg>Gtg	p.M406V	TGFB2_ENST00000479322.1_3'UTR|TGFB2_ENST00000366929.4_Missense_Mutation_p.M434V	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	406					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.M406V(1)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCTTTCTAATATGATTGTAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	93	94					1																	218614675		2203	4300	6503	216681298	SO:0001583	missense	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.1216A>G	1.37:g.218614675A>G	ENSP00000355897:p.Met406Val		216681298	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831509	0.71258	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.74526	-0.85;-0.85	5.91	5.91	0.95273	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89846	0.6833	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.92352	0.5890	10	0.87932	D	0	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	434;406	P61812-2;P61812	.;TGFB2_HUMAN	V	406;434	ENSP00000355897:M406V;ENSP00000355896:M434V	ENSP00000355896:M434V	M	+	1	0	TGFB2	216681298	1.000000	0.71417	0.930000	0.37139	0.979000	0.70002	9.339000	0.96797	2.254000	0.74563	0.533000	0.62120	ATG		0.388	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		G	218614675	A	G	218614675	3	3	61	1	0	0	0	0	1	0	0	0	15857	449	16	4	1330	4	TGFB2	1	218614675	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7248	218614675	30635946	1065	9050										
EPRS	2058	broad.mit.edu	37	chr1	220142238	220142238	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagttcacagagtggtttGaaggggatgcaaaggctttt	14	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:220142238G>T	ENST00000366923.3	-	32	4718	c.4449C>A	c.(4447-4449)ttC>ttA	p.F1483L	EPRS_ENST00000468487.1_5'UTR	NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1483	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)	p.F1483L(1)		breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AGAGTGGTTTGAAGGGGATGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	103	105					1																	220142238		2203	4300	6503	218208861	SO:0001583	missense	2058			X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.4449C>A	1.37:g.220142238G>T	ENSP00000355890:p.Phe1483Leu		218208861	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	G	33	5.206901	0.95033	.	.	ENSG00000136628	ENST00000366923	T	0.08008	3.14	5.66	5.66	0.87406	Prolyl-tRNA synthetase, class II, C-terminal (3);Prolyl-tRNA synthetase, class II (1);	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	M	0.62088	1.915	0.80722	D	1	P	0.49447	0.924	P	0.50754	0.649	T	0.00067	-1.2143	10	0.46703	T	0.11	-16.6413	19.7525	0.96273	0.0:0.0:1.0:0.0	.	1483	P07814	SYEP_HUMAN	L	1483	ENSP00000355890:F1483L	ENSP00000355890:F1483L	F	-	3	2	EPRS	218208861	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.782000	0.68973	2.669000	0.90835	0.591000	0.81541	TTC		0.458	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		T	220142238	G	T	220142238	3	4	61	1	0	0	0	0	1	0	0	0	5204	1281	45	2	93	2	EPRS	1	220142238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1527563	220142238	29108383	1066	9051										
MARK1	4139	broad.mit.edu	37	chr1	220808816	220808816	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcagtcccctgctcacctGaaggtccagagaagtatctc	8	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:220808816G>T	ENST00000366917.4	+	12	1487	c.1221G>T	c.(1219-1221)ctG>ctT	p.L407L	MARK1_ENST00000402574.1_Silent_p.L272L|MARK1_ENST00000366918.4_Silent_p.L385L					MAP/microtubule affinity-regulating kinase 1									p.L407L(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		CTGCTCACCTGAAGGTCCAGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	1											81	76	77					1																	220808816		2203	4300	6503	218875439	SO:0001819	synonymous_variant	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1221G>T	1.37:g.220808816G>T			218875439		Silent	SNP	ENST00000366917.4	37	CCDS31029.2																																																																																				0.488	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220808816	G	T	220808816	2	4	61	1	0	0	0	0	0	0	0	1	9342	1277	45	2		2	MARK1	1	220808816	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	666578	220808816	28441805	1067	9052										
MARK1	4139	broad.mit.edu	37	chr1	220826690	220826690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcacatccaaatttgttCgcaggtcagtaccaatgtac	6	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:220826690C>T	ENST00000366917.4	+	16	2250	c.1984C>T	c.(1984-1986)Cgc>Tgc	p.R662C	MARK1_ENST00000402574.1_Missense_Mutation_p.R527C|MARK1_ENST00000366918.4_Missense_Mutation_p.R640C					MAP/microtubule affinity-regulating kinase 1									p.R662C(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		CAAATTTGTTCGCAGGTCAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	58	58					1																	220826690		2203	4300	6503	218893313	SO:0001583	missense	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1984C>T	1.37:g.220826690C>T	ENSP00000355884:p.Arg662Cys		218893313		Missense_Mutation	SNP	ENST00000366917.4	37	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	C	31	5.079435	0.94050	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.57595	0.95;0.95;0.39	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.77498	0.4139	M	0.87827	2.91	0.49687	D	0.999813	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76575	0.97;0.961;0.985;0.988	T	0.81739	-0.0795	10	0.87932	D	0	.	19.0367	0.92982	0.0:1.0:0.0:0.0	.	662;527;662;640	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	C	527;640;662	ENSP00000386017:R527C;ENSP00000355885:R640C;ENSP00000355884:R662C	ENSP00000355884:R662C	R	+	1	0	MARK1	218893313	1.000000	0.71417	0.978000	0.43139	0.983000	0.72400	7.578000	0.82498	2.506000	0.84524	0.462000	0.41574	CGC		0.373	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220826690	C	T	220826690	3	4	61	1	0	0	0	0	1	0	0	0	9342	884	31	1	2046	1	MARK1	1	220826690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17874	220826690	28423931	1068	9053										
HLX	3142	broad.mit.edu	37	chr1	221054679	221054679	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaaactcgaacccaagaAattcagttcagcatcagttc	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:221054679A>C	ENST00000366903.6	+	2	2237	c.736A>C	c.(736-738)Aat>Cat	p.N246H	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_5'UTR	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	246					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.N246H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		GAACCCAAGAAATTCAGTTCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	86	86					1																	221054679		2203	4300	6503	219121302	SO:0001583	missense	3142			BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"Homeoboxes / ANTP class : NKL subclass"	4978	protein-coding gene	gene with protein product		142995	"H2.0 (Drosophila)-like homeo box 1", "H2.0-like homeobox 1 (Drosophila)", "H2.0-like homeobox 1"	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.736A>C	1.37:g.221054679A>C	ENSP00000355870:p.Asn246His		219121302	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.685670	0.47991	.	.	ENSG00000136630	ENST00000366903	T	0.35605	1.3	5.82	5.82	0.92795	.	0.177095	0.36972	N	0.002311	T	0.22166	0.0534	N	0.08118	0	0.80722	D	1	B	0.17852	0.024	B	0.10450	0.005	T	0.05716	-1.0868	10	0.30854	T	0.27	-15.5678	15.8434	0.78868	1.0:0.0:0.0:0.0	.	246	Q14774	HLX_HUMAN	H	246	ENSP00000355870:N246H	ENSP00000355870:N246H	N	+	1	0	HLX	219121302	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	6.467000	0.73547	2.224000	0.72417	0.459000	0.35465	AAT		0.522	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		C	221054679	A	C	221054679	3	2	61	1	0	0	0	0	1	0	0	0	7237	14	1	4	742	4	HLX	1	221054679	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	227989	221054679	28195942	1069	9054										
HLX	3142	broad.mit.edu	37	chr1	221055525	221055525	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtccctatgctgtgctcacGaaggacaccatgccgcagac	11	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:221055525G>A	ENST00000366903.6	+	3	2293	c.792G>A	c.(790-792)acG>acA	p.T264T	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_Silent_p.T50T	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	264					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.T264T(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CTGTGCTCACGAAGGACACCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											51	42	45					1																	221055525		2203	4300	6503	219122148	SO:0001819	synonymous_variant	3142			BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"Homeoboxes / ANTP class : NKL subclass"	4978	protein-coding gene	gene with protein product		142995	"H2.0 (Drosophila)-like homeo box 1", "H2.0-like homeobox 1 (Drosophila)", "H2.0-like homeobox 1"	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.792G>A	1.37:g.221055525G>A			219122148	B2R8A8|Q15988|Q59HE7|Q9NZ75	Silent	SNP	ENST00000366903.6	37	CCDS1527.1																																																																																				0.577	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		A	221055525	G	A	221055525	2	1	61	1	0	0	0	0	0	0	0	1	7237	1045	37	1		1	HLX	1	221055525	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	846	221055525	28195096	1070	9055										
MIA3	375056	broad.mit.edu	37	chr1	222801630	222801630	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatccaacagataaagagcaGaattcaaatgaagaggacaa	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:222801630G>T	ENST00000344922.5	+	4	1093	c.1068G>T	c.(1066-1068)caG>caT	p.Q356H	MIA3_ENST00000344507.1_Missense_Mutation_p.Q356H|MIA3_ENST00000344441.6_Missense_Mutation_p.Q356H|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	356					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.Q356H(2)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		ATAAAGAGCAGAATTCAAATG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	1											79	74	76					1																	222801630		1836	4096	5932	220868253	SO:0001583	missense	375056				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1068G>T	1.37:g.222801630G>T	ENSP00000340900:p.Gln356His		220868253	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210395	0.39003	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000344507	T;T;T	0.43294	0.95;0.95;1.46	5.19	3.32	0.38043	.	.	.	.	.	T	0.43590	0.1254	L	0.53249	1.67	0.09310	N	1	P;P	0.50528	0.936;0.845	P;P	0.50378	0.639;0.459	T	0.28427	-1.0044	9	0.49607	T	0.09	.	4.6794	0.12727	0.2434:0.0:0.5679:0.1887	.	356;356	Q5JRA6-2;Q5JRA6	.;MIA3_HUMAN	H	356	ENSP00000340900:Q356H;ENSP00000340587:Q356H;ENSP00000341348:Q356H	ENSP00000325973:Q356H	Q	+	3	2	MIA3	220868253	0.022000	0.18835	0.005000	0.12908	0.137000	0.21094	0.681000	0.25320	0.683000	0.31428	-0.459000	0.05422	CAG		0.398	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222801630	G	T	222801630	3	4	61	1	0	0	0	0	1	0	0	0	9595	933	33	2	1082	2	MIA3	1	222801630	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1746105	222801630	26448991	1071	9056										
MIA3	375056	broad.mit.edu	37	chr1	222824036	222824036	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatatgattctctctgatGaagcaattaaatataaggta	6	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:222824036G>T	ENST00000344922.5	+	10	3806	c.3781G>T	c.(3781-3783)Gaa>Taa	p.E1261*	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Nonsense_Mutation_p.E139*|MIA3_ENST00000344441.6_Nonsense_Mutation_p.E1261*	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1261					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.E1261*(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TCTCTCTGATGAAGCAATTAA	0.264																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											72	81	78					1																	222824036		1798	4043	5841	220890659	SO:0001587	stop_gained	375056				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3781G>T	1.37:g.222824036G>T	ENSP00000340900:p.Glu1261*		220890659	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Nonsense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.520083|7.520083	0.98335|0.98335	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471|ENST00000354906	.|.	.|.	.|.	5.39|5.39	4.47|4.47	0.54385|0.54385	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.52906|.	T|.	0.07|.	.|.	12.2719|12.2719	0.54710|0.54710	0.0787:0.0:0.9213:0.0|0.0787:0.0:0.9213:0.0	.|.	.|.	.|.	.|.	X|L	1261;1261;1261;139;139|843	.|.	ENSP00000284471:E139X|.	E|X	+|+	1|2	0|2	MIA3|MIA3	220890659|220890659	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.598000|2.598000	0.46223|0.46223	1.391000|1.391000	0.46566|0.46566	0.655000|0.655000	0.94253|0.94253	GAA|TGA		0.264	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222824036	G	T	222824036	4	4	61	1	0	0	0	0	0	1	0	0	9595	1291	45	2	3819	2	MIA3	1	222824036	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22406	222824036	26426585	1072	9057										
MIA3	375056	broad.mit.edu	37	chr1	222828095	222828095	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggcagaaagtggagattCtgaatgagctctatcagcag	13	6	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:222828095C>A	ENST00000344922.5	+	18	4592	c.4567C>A	c.(4567-4569)Ctg>Atg	p.L1523M	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Missense_Mutation_p.L401M|MIA3_ENST00000344441.6_Missense_Mutation_p.L1523M	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1523					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.L1523M(1)|p.L1523L(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AGTGGAGATTCTGAATGAGCT	0.393																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1											106	101	102					1																	222828095		1949	4149	6098	220894718	SO:0001583	missense	375056				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.4567C>A	1.37:g.222828095C>A	ENSP00000340900:p.Leu1523Met		220894718	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.492617	0.64074	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471	T;T;T	0.52526	1.09;1.09;0.66	5.46	4.56	0.56223	.	.	.	.	.	T	0.51244	0.1663	N	0.20530	0.585	0.42107	D	0.99136	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.45906	-0.9229	9	0.18710	T	0.47	.	14.5378	0.67973	0.0:0.9291:0.0:0.0709	.	401;1523	Q5JRA6-4;Q5JRA6	.;MIA3_HUMAN	M	1523;1523;1464;401;401	ENSP00000340900:L1523M;ENSP00000340587:L1523M;ENSP00000345866:L401M	ENSP00000284471:L401M	L	+	1	2	MIA3	220894718	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	4.517000	0.60503	1.447000	0.47661	0.655000	0.94253	CTG		0.393	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		A	222828095	C	A	222828095	3	1	61	1	0	0	0	0	1	0	0	0	9595	912	32	2	4637	2	MIA3	1	222828095	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4059	222828095	26422526	1073	9058										
DISP1	84976	broad.mit.edu	37	chr1	223177026	223177026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcgtcccatccttttgagCgttatgatgctgaatacaaa	9	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223177026C>T	ENST00000284476.6	+	8	2451	c.2287C>T	c.(2287-2289)Cgt>Tgt	p.R763C		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	763					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.R763C(3)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		TCCTTTTGAGCGTTATGATGC	0.483																																																3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	1											81	78	79					1																	223177026		2203	4300	6503	221243649	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2287C>T	1.37:g.223177026C>T	ENSP00000284476:p.Arg763Cys		221243649	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.292790	0.80914	.	.	ENSG00000154309	ENST00000284476	D	0.94000	-3.33	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.96312	0.8797	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96198	0.9143	10	0.72032	D	0.01	-31.3579	20.0016	0.97412	0.0:1.0:0.0:0.0	.	763	Q96F81	DISP1_HUMAN	C	763	ENSP00000284476:R763C	ENSP00000284476:R763C	R	+	1	0	DISP1	221243649	1.000000	0.71417	0.671000	0.29857	0.981000	0.71138	7.776000	0.85560	2.802000	0.96397	0.655000	0.94253	CGT		0.483	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		T	223177026	C	T	223177026	3	4	61	1	0	0	0	0	1	0	0	0	4550	768	27	1	2313	1	DISP1	1	223177026	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	348931	223177026	26073595	1074	9059										
DISP1	84976	broad.mit.edu	37	chr1	223179126	223179126	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagaatgaaccaaaagtcCtatttaatcatttaatgggg	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223179126C>A	ENST00000284476.6	+	8	4551	c.4387C>A	c.(4387-4389)Cta>Ata	p.L1463I		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1463					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.L1463I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		ACCAAAAGTCCTATTTAATCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	81	81					1																	223179126		2203	4300	6503	221245749	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.4387C>A	1.37:g.223179126C>A	ENSP00000284476:p.Leu1463Ile		221245749	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	0.111	-1.138664	0.01742	.	.	ENSG00000154309	ENST00000284476	D	0.91686	-2.89	5.52	-11.0	0.00169	.	1.421560	0.04366	N	0.358270	T	0.76926	0.4056	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.66476	-0.5914	10	0.09084	T	0.74	-0.1608	12.7814	0.57479	0.15:0.6697:0.1071:0.0732	.	1463	Q96F81	DISP1_HUMAN	I	1463	ENSP00000284476:L1463I	ENSP00000284476:L1463I	L	+	1	2	DISP1	221245749	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.151000	0.03175	-3.709000	0.00117	-1.139000	0.01908	CTA		0.438	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		A	223179126	C	A	223179126	3	1	61	1	0	0	0	0	1	0	0	0	4550	680	24	2	4413	2	DISP1	1	223179126	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2100	223179126	26071495	1075	9060										
TLR5	7100	broad.mit.edu	37	chr1	223285062	223285062	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaagtagagaatatctaGattttctagcctgttttctg	9	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223285062G>T	ENST00000540964.1	-	4	1773	c.1312C>A	c.(1312-1314)Cta>Ata	p.L438I	TLR5_ENST00000342210.6_Missense_Mutation_p.L438I			O60602	TLR5_HUMAN	toll-like receptor 5	438			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)	p.L438I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AGAATATCTAGATTTTCTAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	83	82					1																	223285062		2203	4300	6503	221351685	SO:0001583	missense	7100				CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1312C>A	1.37:g.223285062G>T	ENSP00000440643:p.Leu438Ile		221351685	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	G	9.071	0.997020	0.19043	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.26373	1.74;1.74;1.74	5.59	1.58	0.23477	.	0.225469	0.37906	N	0.001893	T	0.42381	0.1200	M	0.83483	2.645	0.23010	N	0.998434	B	0.32604	0.377	P	0.49665	0.618	T	0.44112	-0.9349	10	0.87932	D	0	.	5.4359	0.16480	0.2769:0.0:0.5829:0.1402	.	438	O60602	TLR5_HUMAN	I	438	ENSP00000440643:L438I;ENSP00000355846:L438I;ENSP00000340089:L438I	ENSP00000340089:L438I	L	-	1	2	TLR5	221351685	0.000000	0.05858	0.051000	0.19133	0.026000	0.11368	-0.573000	0.05874	0.283000	0.22279	-1.069000	0.02264	CTA		0.408	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		T	223285062	G	T	223285062	3	4	61	1	0	0	0	0	1	0	0	0	15993	933	33	2	1268	2	TLR5	1	223285062	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105936	223285062	25965559	1076	9061										
SUSD4	55061	broad.mit.edu	37	chr1	223441994	223441994	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgttatgaatctcagcatCttcgatttgagggatacggc	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223441994C>T	ENST00000343846.3	-	3	1018	c.385G>A	c.(385-387)Gat>Aat	p.D129N	SUSD4_ENST00000344029.6_Missense_Mutation_p.D129N|SUSD4_ENST00000484758.2_Missense_Mutation_p.D58N|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366878.4_Missense_Mutation_p.D129N|SUSD4_ENST00000454695.2_5'UTR|SUSD4_ENST00000494793.2_Missense_Mutation_p.D129N			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	129	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.D129N(2)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		ATCTCAGCATCTTCGATTTGA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	1											191	164	173					1																	223441994		2203	4300	6503	221508617	SO:0001583	missense	55061			AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.385G>A	1.37:g.223441994C>T	ENSP00000344219:p.Asp129Asn		221508617	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.094065	0.56075	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000271787;ENST00000344029	T;T;T	0.61627	0.09;0.09;0.09	5.91	5.91	0.95273	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.49916	D	0.000130	T	0.66799	0.2826	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	0.999;0.998;1.0	D;D;D	0.91635	0.993;0.991;0.999	T	0.56786	-0.7921	10	0.10636	T	0.68	-19.2668	19.2811	0.94053	0.0:1.0:0.0:0.0	.	58;129;129	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	N	129;129;58;129;129	ENSP00000344219:D129N;ENSP00000355843:D129N;ENSP00000339926:D129N	ENSP00000271787:D129N	D	-	1	0	SUSD4	221508617	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.924000	0.70054	2.802000	0.96397	0.650000	0.86243	GAT		0.393	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		T	223441994	C	T	223441994	3	4	61	1	0	0	0	0	1	0	0	0	15449	913	32	3	1264	3	SUSD4	1	223441994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156932	223441994	25808627	1077	9062										
C1orf65	164127	broad.mit.edu	37	chr1	223568657	223568657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatggtactagaggcccagCtccgtgcctgtcagcagaac	12	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223568657C>T	ENST00000366875.3	+	1	1943	c.1840C>T	c.(1840-1842)Ctc>Ttc	p.L614F		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		614								p.L614F(1)|p.H393Y(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		AGAGGCCCAGCTCCGTGCCTG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	1											44	44	44					1																	223568657		2203	4298	6501	221635280	SO:0001583	missense	164127																														ENST00000366875.3:c.1840C>T	1.37:g.223568657C>T	ENSP00000355840:p.Leu614Phe		221635280	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.383146	0.42207	.	.	ENSG00000178395	ENST00000366875	T	0.29142	1.58	5.35	1.24	0.21308	.	.	.	.	.	T	0.11879	0.0289	N	0.12182	0.205	0.37108	D	0.900212	B	0.32031	0.352	B	0.27262	0.078	T	0.18681	-1.0329	9	0.21014	T	0.42	.	2.431	0.04471	0.134:0.4089:0.2915:0.1656	.	614	Q8N715	CA065_HUMAN	F	614	ENSP00000355840:L614F	ENSP00000355840:L614F	L	+	1	0	C1orf65	221635280	0.000000	0.05858	0.227000	0.23927	0.232000	0.25224	-0.064000	0.11636	0.219000	0.20840	0.655000	0.94253	CTC		0.557	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223568657	C	T	223568657	3	4	61	1	0	0	0	0	1	0	0	0	2061	797	28	3	1842	3	C1orf65	1	223568657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	126663	223568657	25681964	1078	9063										
CAPN2	824	broad.mit.edu	37	chr1	223934750	223934750	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgccaccactgagggcttCgaagacttcaccggaggcat	13	12	1	2	rs139316104		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223934750C>T	ENST00000295006.5	+	5	921	c.612C>T	c.(610-612)ttC>ttT	p.F204F	CAPN2_ENST00000433674.2_Silent_p.F126F	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	204	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.F204F(2)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CTGAGGGCTTCGAAGACTTCA	0.532													C|||	1	0.000199681	0	0	5008	,	,		18452	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	1						C	,	0,4406		0,0,2203	124	118	120		378,612	-4.9	1	1	dbSNP_134	120	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	CAPN2	NM_001146068.1,NM_001748.4	,	0,8,6495	TT,TC,CC		0.093,0.0,0.0615	,	126/623,204/701	223934750	8,12998	2203	4300	6503	222001373	SO:0001819	synonymous_variant	824			J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.612C>T	1.37:g.223934750C>T			222001373	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Silent	SNP	ENST00000295006.5	37	CCDS31035.1																																																																																				0.532	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		T	223934750	C	T	223934750	2	4	61	1	0	0	0	0	0	0	0	1	2633	883	31	1		1	CAPN2	1	223934750	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366093	223934750	25315871	1079	9064										
TP53BP2	7159	broad.mit.edu	37	chr1	223968574	223968574	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggccaagctcctttgtCttggtttaattcttgggtac	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:223968574C>A	ENST00000343537.7	-	18	3677	c.3386G>T	c.(3385-3387)aGa>aTa	p.R1129I	TP53BP2_ENST00000391878.2_Missense_Mutation_p.R1000I|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Missense_Mutation_p.R362I	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	1123					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.R1000I(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GCTCCTTTGTCTTGGTTTAAT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	92	92					1																	223968574		2203	4300	6503	222035197	SO:0001583	missense	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.3386G>T	1.37:g.223968574C>A	ENSP00000341957:p.Arg1129Ile		222035197	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	C	34	5.353193	0.95830	.	.	ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879	T;T;T	0.60424	0.19;0.37;0.37	5.48	5.48	0.80851	Src homology-3 domain (1);	0.043510	0.85682	D	0.000000	T	0.74756	0.3758	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.996	T	0.76005	-0.3117	10	0.87932	D	0	.	19.7152	0.96115	0.0:1.0:0.0:0.0	.	1129;1123	B4DG66;Q13625	.;ASPP2_HUMAN	I	1000;1129;362	ENSP00000375750:R1000I;ENSP00000341957:R1129I;ENSP00000375751:R362I	ENSP00000341957:R1129I	R	-	2	0	TP53BP2	222035197	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.733000	0.93635	0.591000	0.81541	AGA		0.303	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223968574	C	A	223968574	3	1	61	1	0	0	0	0	1	0	0	0	16424	913	32	2	22	2	TP53BP2	1	223968574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33824	223968574	25282047	1080	9065										
NVL	4931	broad.mit.edu	37	chr1	224495758	224495758	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtccaagaaaaaactgtCtttctttacacttggggttt	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:224495758C>A	ENST00000281701.6	-	6	809	c.550G>T	c.(550-552)Gac>Tac	p.D184Y	NVL_ENST00000469075.1_Intron|RNU6-1008P_ENST00000384160.1_RNA|NVL_ENST00000482491.1_Intron|NVL_ENST00000340871.4_Intron|NVL_ENST00000391875.2_Missense_Mutation_p.D78Y|NVL_ENST00000361463.3_Missense_Mutation_p.D78Y	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	184						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.D184Y(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		AAAAAACTGTCTTTCTTTACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	119	119					1																	224495758		2203	4300	6503	222562381	SO:0001583	missense	4931			U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.550G>T	1.37:g.224495758C>A	ENSP00000281701:p.Asp184Tyr		222562381	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	37	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509398	0.44660	.	.	ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000361463;ENST00000492281;ENST00000436927	D;D;D	0.95482	-3.51;-3.59;-3.72	5.53	5.53	0.82687	.	0.607085	0.17369	N	0.176729	D	0.93291	0.7862	L	0.27053	0.805	0.26347	N	0.977268	P	0.52842	0.956	P	0.48030	0.564	D	0.88927	0.3370	10	0.72032	D	0.01	-5.3817	15.318	0.74095	0.0:0.8606:0.1394:0.0	.	184	O15381	NVL_HUMAN	Y	184;78;78;89;80	ENSP00000281701:D184Y;ENSP00000375747:D78Y;ENSP00000354779:D78Y	ENSP00000281701:D184Y	D	-	1	0	NVL	222562381	0.892000	0.30473	0.248000	0.24265	0.613000	0.37349	0.896000	0.28377	2.753000	0.94483	0.655000	0.94253	GAC		0.393	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224495758	C	A	224495758	3	1	61	1	0	0	0	0	1	0	0	0	10811	913	32	2	2092	2	NVL	1	224495758	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	527184	224495758	24754863	1081	9066										
CNIH3	149111	broad.mit.edu	37	chr1	224868687	224868687	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgatgagttaaggacaGattttaagagccccatagac	9	8	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:224868687G>T	ENST00000272133.3	+	2	991	c.109G>T	c.(109-111)Gat>Tat	p.D37Y		NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3	37					intracellular signal transduction (GO:0035556)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|postsynaptic membrane (GO:0045211)	channel regulator activity (GO:0016247)	p.D37Y(1)		large_intestine(5)|lung(4)	9	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		GTTAAGGACAGATTTTAAGAG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											142	138	139					1																	224868687		2203	4300	6503	222935310	SO:0001583	missense	149111			AF070524	CCDS1544.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143786	ENSG00000143786			26802	protein-coding gene	gene with protein product			"cornichon homolog 3 (Drosophila)"			8619474, 9110174	Standard	NM_152495		Approved	FLJ38993, CNIH-3	uc001hos.1	Q8TBE1	OTTHUMG00000037634	ENST00000272133.3:c.109G>T	1.37:g.224868687G>T	ENSP00000272133:p.Asp37Tyr		222935310		Missense_Mutation	SNP	ENST00000272133.3	37	CCDS1544.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979604	0.74360	.	.	ENSG00000143786	ENST00000272133	T	0.72282	-0.64	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.84561	0.5499	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.86301	0.1680	10	0.87932	D	0	0.9572	18.0599	0.89373	0.0:0.0:1.0:0.0	.	37	Q8TBE1	CNIH3_HUMAN	Y	37	ENSP00000272133:D37Y	ENSP00000272133:D37Y	D	+	1	0	CNIH3	222935310	1.000000	0.71417	0.960000	0.40013	0.775000	0.43874	6.690000	0.74567	2.573000	0.86826	0.643000	0.83706	GAT		0.493	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091752.2	NM_152495		T	224868687	G	T	224868687	3	4	61	1	0	0	0	0	1	0	0	0	3610	942	33	2	115	2	CNIH3	1	224868687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	372929	224868687	24381934	1082	9067										
CNIH3	149111	broad.mit.edu	37	chr1	224872519	224872519	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaacggttgaggaacatcGagcgcatctgcttccttctg	13	10	2	1	rs374139283		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:224872519G>A	ENST00000272133.3	+	3	1054	c.172G>A	c.(172-174)Gag>Aag	p.E58K		NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3	58					intracellular signal transduction (GO:0035556)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|postsynaptic membrane (GO:0045211)	channel regulator activity (GO:0016247)	p.E58K(1)		large_intestine(5)|lung(4)	9	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		GAGGAACATCGAGCGCATCTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											203	163	177					1																	224872519		2203	4300	6503	222939142	SO:0001583	missense	149111			AF070524	CCDS1544.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143786	ENSG00000143786			26802	protein-coding gene	gene with protein product			"cornichon homolog 3 (Drosophila)"			8619474, 9110174	Standard	NM_152495		Approved	FLJ38993, CNIH-3	uc001hos.1	Q8TBE1	OTTHUMG00000037634	ENST00000272133.3:c.172G>A	1.37:g.224872519G>A	ENSP00000272133:p.Glu58Lys		222939142		Missense_Mutation	SNP	ENST00000272133.3	37	CCDS1544.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909028	0.72868	.	.	ENSG00000143786	ENST00000272133	.	.	.	4.49	4.49	0.54785	.	0.000000	0.85682	U	0.000000	T	0.61751	0.2372	N	0.22421	0.69	0.49687	D	0.999815	D	0.89917	1.0	D	0.67548	0.952	T	0.62048	-0.6936	9	0.34782	T	0.22	-8.3074	15.9805	0.80105	0.0:0.0:1.0:0.0	.	58	Q8TBE1	CNIH3_HUMAN	K	58	.	ENSP00000272133:E58K	E	+	1	0	CNIH3	222939142	1.000000	0.71417	0.959000	0.39883	0.986000	0.74619	6.605000	0.74155	2.063000	0.61619	0.551000	0.68910	GAG		0.532	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091752.2	NM_152495		A	224872519	G	A	224872519	3	1	61	1	0	0	0	0	1	0	0	0	3610	1059	37	1	182	1	CNIH3	1	224872519	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3832	224872519	24378102	1083	9068										
LBR	3930	broad.mit.edu	37	chr1	225591070	225591070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcccaagccacgccgtAtttcttcttacagtggtact	6	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:225591070A>G	ENST00000338179.2	-	14	1908	c.1783T>C	c.(1783-1785)Tac>Cac	p.Y595H	LBR_ENST00000272163.4_Missense_Mutation_p.Y595H	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	595					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)	p.Y595H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		GCCACGCCGTATTTCTTCTTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	111	113					1																	225591070		2203	4300	6503	223657693	SO:0001583	missense	3930			L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1783T>C	1.37:g.225591070A>G	ENSP00000339883:p.Tyr595His		223657693	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	37	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331602	0.81690	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.99264	-5.65;-5.65	6.17	6.17	0.99709	Sterol reductase, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99471	0.9812	M	0.90145	3.09	0.80722	D	1	D	0.64830	0.994	D	0.64595	0.927	D	0.98586	1.0652	10	0.62326	D	0.03	-21.7758	16.8222	0.85835	1.0:0.0:0.0:0.0	.	595	Q14739	LBR_HUMAN	H	595	ENSP00000272163:Y595H;ENSP00000339883:Y595H	ENSP00000272163:Y595H	Y	-	1	0	LBR	223657693	1.000000	0.71417	0.900000	0.35374	0.487000	0.33371	9.189000	0.94928	2.371000	0.80710	0.533000	0.62120	TAC		0.423	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		G	225591070	A	G	225591070	3	3	61	1	0	0	0	0	1	0	0	0	8674	449	16	4	68	4	LBR	1	225591070	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	718551	225591070	23659551	1084	9069										
ENAH	55740	broad.mit.edu	37	chr1	225686082	225686082	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttttagctttgttaattCttttctcatttcatctaaaa	2	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:225686082C>A	ENST00000366844.3	-	14	2156	c.1705G>T	c.(1705-1707)Gaa>Taa	p.E569*	ENAH_ENST00000366843.2_Nonsense_Mutation_p.E548*|ENAH_ENST00000284563.6_Nonsense_Mutation_p.E795*	NM_001008493.1|NM_018212.4	NP_001008493.1|NP_060682.2	Q8N8S7	ENAH_HUMAN	enabled homolog (Drosophila)	569	EVH2 block C.|EVH2.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|intracellular transport (GO:0046907)|neural tube closure (GO:0001843)|T cell receptor signaling pathway (GO:0050852)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)|synapse (GO:0045202)	WW domain binding (GO:0050699)	p.E569*(1)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		TTTGTTAATTCTTTTCTCATT	0.254																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											62	60	60					1																	225686082		2202	4291	6493	223752705	SO:0001587	stop_gained	55740			AK001635	CCDS31040.1, CCDS31041.1	1q32.2	2013-08-06			ENSG00000154380	ENSG00000154380			18271	protein-coding gene	gene with protein product	"mammalian enabled"	609061				1420303	Standard	XM_005273182		Approved	FLJ10773, NDPP1, MENA	uc001hpc.1	Q8N8S7	OTTHUMG00000037742	ENST00000366844.3:c.1705G>T	1.37:g.225686082C>A	ENSP00000355809:p.Glu569*		223752705	D0PQI2|Q502W5|Q5T5M7|Q5VTQ9|Q5VTR0|Q9NVF3|Q9UFB8	Nonsense_Mutation	SNP	ENST00000366844.3	37	CCDS31041.1	.	.	.	.	.	.	.	.	.	.	C	38	6.845073	0.97881	.	.	ENSG00000154380	ENST00000366844;ENST00000366843;ENST00000284563;ENST00000538194	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-17.0267	20.0185	0.97487	0.0:1.0:0.0:0.0	.	.	.	.	X	569;548;795;510	.	ENSP00000284563:E795X	E	-	1	0	ENAH	223752705	1.000000	0.71417	0.998000	0.56505	0.234000	0.25298	6.711000	0.74675	2.809000	0.96659	0.467000	0.42956	GAA		0.254	ENAH-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357426.2	NM_018212		A	225686082	C	A	225686082	4	1	61	1	0	0	0	0	0	1	0	0	5124	922	32	2	78	2	ENAH	1	225686082	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95012	225686082	23564539	1085	9070										
TMEM63A	9725	broad.mit.edu	37	chr1	226040394	226040394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgatgggacaagtgatgCtgtaggccacgatgacagtg	15	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:226040394C>T	ENST00000366835.3	-	20	2144	c.1874G>A	c.(1873-1875)aGc>aAc	p.S625N		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	625					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)	p.S625N(1)		breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					ACAAGTGATGCTGTAGGCCAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											185	120	142					1																	226040394		2203	4300	6503	224107017	SO:0001583	missense	9725				CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"KIAA0792"	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.1874G>A	1.37:g.226040394C>T	ENSP00000355800:p.Ser625Asn		224107017	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300902	0.95601	.	.	ENSG00000196187	ENST00000366835	T	0.43688	0.94	5.27	5.27	0.74061	Domain of unknown function DUF221 (1);	0.000000	0.85682	D	0.000000	T	0.71728	0.3374	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78084	-0.2342	10	0.87932	D	0	-42.1077	18.8876	0.92385	0.0:1.0:0.0:0.0	.	625	O94886	TM63A_HUMAN	N	625	ENSP00000355800:S625N	ENSP00000355800:S625N	S	-	2	0	TMEM63A	224107017	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.701000	0.84566	2.459000	0.83118	0.563000	0.77884	AGC		0.572	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		T	226040394	C	T	226040394	3	4	61	1	0	0	0	0	1	0	0	0	16229	797	28	3	569	3	TMEM63A	1	226040394	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	354312	226040394	23210227	1086	9071										
C1orf55	163859	broad.mit.edu	37	chr1	226173203	226173203	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtgaacgccaataaatCtatagtttccttatcaataa	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:226173203C>A	ENST00000272091.7	-	7	1174	c.1156G>T	c.(1156-1158)Gat>Tat	p.D386Y		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	386								p.D374Y(1)									GCCAATAAATCTATAGTTTCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	64	65					1																	226173203		1855	4089	5944	224239826	SO:0001583	missense	163859			BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.1156G>T	1.37:g.226173203C>A	ENSP00000272091:p.Asp386Tyr		224239826	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	37	CCDS41473.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107411	0.77096	.	.	ENSG00000143751	ENST00000272091;ENST00000366818;ENST00000366817	T;T	0.63744	-0.02;-0.06	5.31	3.42	0.39159	.	0.149237	0.56097	D	0.000024	T	0.80884	0.4709	M	0.90542	3.125	0.58432	D	0.999995	D	0.89917	1.0	D	0.81914	0.995	D	0.84354	0.0534	10	0.87932	D	0	-23.4396	11.902	0.52688	0.0:0.8562:0.0:0.1438	.	386	Q6IQ49	CA055_HUMAN	Y	386;374;291	ENSP00000272091:D386Y;ENSP00000355782:D291Y	ENSP00000272091:D386Y	D	-	1	0	C1orf55	224239826	1.000000	0.71417	0.113000	0.21522	0.585000	0.36419	4.339000	0.59322	1.240000	0.43803	0.591000	0.81541	GAT		0.398	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		A	226173203	C	A	226173203	3	1	61	1	0	0	0	0	1	0	0	0	2053	913	32	2	203	2	C1orf55	1	226173203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132809	226173203	23077418	1087	9072										
C1orf55	163859	broad.mit.edu	37	chr1	226175634	226175634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcctgcagtttggcaacgGcaacgttttccctttcttca	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:226175634G>A	ENST00000272091.7	-	6	1115	c.1097C>T	c.(1096-1098)gCc>gTc	p.A366V		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	366								p.A354V(1)									TTTGGCAACGGCAACGTTTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											159	156	157					1																	226175634		1944	4144	6088	224242257	SO:0001583	missense	163859			BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.1097C>T	1.37:g.226175634G>A	ENSP00000272091:p.Ala366Val		224242257	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	37	CCDS41473.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.357156	0.41801	.	.	ENSG00000143751	ENST00000272091;ENST00000366818;ENST00000366817	T;T	0.46451	0.88;0.87	5.72	4.8	0.61643	.	0.435728	0.25981	N	0.027074	T	0.32010	0.0815	L	0.36672	1.1	0.09310	N	1	P;P	0.37276	0.589;0.454	B;B	0.32677	0.15;0.037	T	0.13710	-1.0499	10	0.30854	T	0.27	-1.6115	14.4935	0.67667	0.0:0.1464:0.8536:0.0	.	354;366	Q6IQ49-2;Q6IQ49	.;CA055_HUMAN	V	366;354;271	ENSP00000272091:A366V;ENSP00000355782:A271V	ENSP00000272091:A366V	A	-	2	0	C1orf55	224242257	0.093000	0.21703	0.002000	0.10522	0.003000	0.03518	2.466000	0.45084	1.549000	0.49425	0.650000	0.86243	GCC		0.463	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		A	226175634	G	A	226175634	3	1	61	1	0	0	0	0	1	0	0	0	2053	1203	42	3	266	3	C1orf55	1	226175634	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2431	226175634	23074987	1088	9073										
ACBD3	64746	broad.mit.edu	37	chr1	226349248	226349248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacttttgctgctccaaccGaagcctttcttcttctatcc	4	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:226349248G>A	ENST00000366812.5	-	4	766	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	ACBD3_ENST00000464927.1_5'UTR	NM_022735.3	NP_073572.2	Q9H3P7	GCP60_HUMAN	acyl-CoA binding domain containing 3	238	Arg-rich.|Glu-rich.				steroid biosynthetic process (GO:0006694)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)	p.R238W(1)		breast(2)|endometrium(3)|large_intestine(5)|lung(7)|skin(1)|urinary_tract(2)	20	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		TGCTCCAACCGAAGcctttct	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	129	135					1																	226349248		2202	4300	6502	224415871	SO:0001583	missense	64746			AB043587	CCDS1551.1	1q41	2013-10-16	2010-04-30	2003-11-12	ENSG00000182827	ENSG00000182827		"A-kinase anchor proteins"	15453	protein-coding gene	gene with protein product	"PBR- and PKA-associated protein 7"	606809	"golgi complex associated protein 1, 60kDa", "acyl-Coenzyme A binding domain containing 3"	GOLPH1, GOCAP1		12692076, 20150326	Standard	NM_022735		Approved	GCP60, PAP7	uc001hpy.3	Q9H3P7	OTTHUMG00000037560	ENST00000366812.5:c.712C>T	1.37:g.226349248G>A	ENSP00000355777:p.Arg238Trp		224415871	B2RB29|Q5VTJ0|Q6P9F1|Q8IZC5|Q8N4D6|Q9H6U3	Missense_Mutation	SNP	ENST00000366812.5	37	CCDS1551.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221398	0.79464	.	.	ENSG00000182827	ENST00000366812	T	0.44482	0.92	4.84	4.84	0.62591	.	0.054894	0.85682	D	0.000000	T	0.65954	0.2741	M	0.79805	2.47	0.58432	D	0.999998	D	0.89917	1.0	D	0.75020	0.985	T	0.70872	-0.4754	10	0.87932	D	0	-12.1984	15.5056	0.75739	0.0:0.0:1.0:0.0	.	238	Q9H3P7	GCP60_HUMAN	W	238	ENSP00000355777:R238W	ENSP00000355777:R238W	R	-	1	2	ACBD3	224415871	0.992000	0.36948	0.998000	0.56505	0.921000	0.55340	2.423000	0.44705	2.602000	0.87976	0.563000	0.77884	CGG		0.408	ACBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091528.1	NM_022735		A	226349248	G	A	226349248	3	1	61	1	0	0	0	0	1	0	0	0	123	1057	37	1	894	1	ACBD3	1	226349248	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173614	226349248	22901373	1089	9074										
LIN9	286826	broad.mit.edu	37	chr1	226453952	226453952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggagtataatgtaaccGtggtggggtcataaaaaatc	13	4	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:226453952G>A	ENST00000328205.5	-	9	1491	c.946C>T	c.(946-948)Cgg>Tgg	p.R316W	LIN9_ENST00000481685.1_Missense_Mutation_p.R281W|LIN9_ENST00000366801.1_Missense_Mutation_p.R265W	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	300					DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)		p.R316W(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		TAATGTAACCGTGGTGGGGTC	0.343																																					Ovarian(197;1696 2974 11248 14117)											1	Substitution - Missense(1)	large_intestine(1)	1											67	66	67					1																	226453952		2203	4300	6503	224520575	SO:0001583	missense	286826			AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"TUDOR gene similar", "rb related pathway actor"	609375	"lin-9 homolog (C. elegans)"			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.946C>T	1.37:g.226453952G>A	ENSP00000329102:p.Arg316Trp		224520575	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012231	0.75046	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.83	5.83	0.93111	.	0.051200	0.85682	D	0.000000	T	0.78679	0.4321	M	0.64404	1.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.928;0.952;0.998	T	0.77456	-0.2581	9	0.52906	T	0.07	.	20.1218	0.97964	0.0:0.0:1.0:0.0	.	281;300;450	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	W	276;316;371;265;281;450	.	ENSP00000329102:R316W	R	-	1	2	LIN9	224520575	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.725000	0.68507	2.763000	0.94921	0.561000	0.74099	CGG		0.343	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083		A	226453952	G	A	226453952	3	1	61	1	0	0	0	0	1	0	0	0	8837	1144	40	1	758	1	LIN9	1	226453952	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104704	226453952	22796669	1090	9075										
CABC1	56997	broad.mit.edu	37	chr1	227152993	227152993	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactcattctctgccatggGctttcagcgaaggttcttcc	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227152993G>A	ENST00000366779.1	+	8	3241	c.470G>A	c.(469-471)gGc>gAc	p.G157D	ADCK3_ENST00000366778.1_Missense_Mutation_p.G105D|ADCK3_ENST00000478406.1_Intron|ADCK3_ENST00000433743.2_5'Flank|ADCK3_ENST00000458507.2_Intron|ADCK3_ENST00000366777.3_Missense_Mutation_p.G157D			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	157					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G157D(1)		endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						TCTGCCATGGGCTTTCAGCGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	1											38	42	41					1																	227152993		2202	4300	6502	225219616	SO:0001583	missense	56997			AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.470G>A	1.37:g.227152993G>A	ENSP00000355741:p.Gly157Asp		225219616	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	37	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589789	0.46214	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000366775;ENST00000405743	T;T;T;T;T	0.75260	-0.64;-0.64;-0.64;-0.81;-0.92	5.77	4.83	0.62350	.	0.915258	0.09604	N	0.779861	T	0.70185	0.3195	L	0.56769	1.78	0.36921	D	0.891394	B	0.22983	0.078	B	0.18263	0.021	T	0.69243	-0.5196	10	0.56958	D	0.05	-11.3085	8.7547	0.34639	0.0767:0.0:0.7722:0.151	.	157	Q8NI60	ADCK3_HUMAN	D	157;105;157;82;2;108	ENSP00000355741:G157D;ENSP00000355740:G105D;ENSP00000355739:G157D;ENSP00000355738:G82D;ENSP00000355737:G2D	ENSP00000355737:G2D	G	+	2	0	ADCK3	225219616	0.022000	0.18835	0.099000	0.21106	0.079000	0.17450	1.004000	0.29822	2.740000	0.93945	0.557000	0.71058	GGC		0.632	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		A	227152993	G	A	227152993	3	1	61	1	0	0	0	0	1	0	0	0	2533	1203	42	3	476	3	CABC1	1	227152993	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	699041	227152993	22097628	1091	9076										
CDC42BPA	8476	broad.mit.edu	37	chr1	227279657	227279657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcgttcatattgttgtTtgaactcactttcaaattcc	4	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227279657T>C	ENST00000366769.3	-	16	3576	c.2285A>G	c.(2284-2286)aAa>aGa	p.K762R	CDC42BPA_ENST00000366765.3_Missense_Mutation_p.K762R|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.K762R|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.K762R|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.K762R|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.K762R|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.K681R	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)									p.K681R(1)|p.K762R(1)		NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				ATATTGTTGTTTGAACTCACT	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	1											186	175	179					1																	227279657		2200	4297	6497	225346280	SO:0001583	missense	8476			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.2285A>G	1.37:g.227279657T>C	ENSP00000355731:p.Lys762Arg		225346280		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.046247	0.75846	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.67698	-0.21;-0.28;-0.22;-0.22;-0.21;-0.18;-0.2	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.74038	0.3664	L	0.43152	1.355	0.47737	D	0.999501	D;B;D;B;B	0.76494	0.999;0.335;0.998;0.096;0.044	D;B;D;B;B	0.85130	0.996;0.19;0.997;0.073;0.061	T	0.69285	-0.5185	10	0.17369	T	0.5	.	15.1634	0.72801	0.0:0.0:0.0:1.0	.	762;762;681;762;762	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-2	.;.;.;.;.	R	762;681;762;762;762;26;762;762	ENSP00000355731:K762R;ENSP00000355729:K681R;ENSP00000335341:K762R;ENSP00000355728:K762R;ENSP00000355726:K762R;ENSP00000443275:K762R;ENSP00000355727:K762R	ENSP00000335341:K762R	K	-	2	0	CDC42BPA	225346280	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	6.911000	0.75746	2.053000	0.61076	0.455000	0.32223	AAA		0.303	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227279657	T	C	227279657	3	2	61	1	0	0	0	0	1	0	0	0	3078	1841	64	4	2958	4	CDC42BPA	1	227279657	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	126664	227279657	21970964	1092	9077										
CDC42BPA	8476	broad.mit.edu	37	chr1	227307536	227307536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctctttcttgttgtaacGttttgatttgtttttcataa	5	6	3	1	rs375379778		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227307536G>A	ENST00000366769.3	-	12	2907	c.1616C>T	c.(1615-1617)aCg>aTg	p.T539M	CDC42BPA_ENST00000366765.3_Missense_Mutation_p.T539M|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.T539M|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.T539M|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.T539M|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.T539M|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.T539M	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)									p.T539M(2)		NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TTGTTGTAACGTTTTGATTTG	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	1											120	120	120					1																	227307536		2202	4299	6501	225374159	SO:0001583	missense	8476			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.1616C>T	1.37:g.227307536G>A	ENSP00000355731:p.Thr539Met		225374159		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586441	0.28268	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.67523	-0.22;-0.2;-0.22;-0.22;-0.27;-0.23;-0.22	5.66	1.17	0.20885	.	0.945848	0.08979	N	0.866154	T	0.51346	0.1669	N	0.19112	0.55	0.20764	N	0.999855	B;B;B;B	0.16603	0.003;0.007;0.018;0.001	B;B;B;B	0.17098	0.003;0.011;0.017;0.006	T	0.42899	-0.9424	10	0.45353	T	0.12	.	10.5588	0.45133	0.3565:0.0:0.6434:0.0	.	539;539;539;539	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5	.;.;.;.	M	539	ENSP00000355731:T539M;ENSP00000355729:T539M;ENSP00000335341:T539M;ENSP00000355728:T539M;ENSP00000355726:T539M;ENSP00000443275:T539M;ENSP00000355727:T539M	ENSP00000335341:T539M	T	-	2	0	CDC42BPA	225374159	0.001000	0.12720	0.318000	0.25279	0.966000	0.64601	0.414000	0.21164	0.330000	0.23485	-0.145000	0.13849	ACG		0.303	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		A	227307536	G	A	227307536	3	1	61	1	0	0	0	0	1	0	0	0	3078	1145	40	1	3643	1	CDC42BPA	1	227307536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27879	227307536	21943085	1093	9078										
ZNF678	339500	broad.mit.edu	37	chr1	227842252	227842252	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaaatctttcaatgtattGaatgtggcagaaattttagc	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227842252G>T	ENST00000343776.5	+	4	646	c.301G>T	c.(301-303)Gaa>Taa	p.E101*	ZNF678_ENST00000397097.3_Nonsense_Mutation_p.E156*|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E101*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TCAATGTATTGAATGTGGCAG	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											76	81	79					1																	227842252		2203	4300	6503	225908875	SO:0001587	stop_gained	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.301G>T	1.37:g.227842252G>T	ENSP00000344828:p.Glu101*		225908875	Q8IVQ9	Nonsense_Mutation	SNP	ENST00000343776.5	37		.	.	.	.	.	.	.	.	.	.	G	8.624	0.892199	0.17613	.	.	ENSG00000181450	ENST00000343776;ENST00000397097;ENST00000440339	.	.	.	1.15	-1.13	0.09775	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	5.5152	0.16902	0.3747:0.0:0.6253:0.0	.	.	.	.	X	101;156;156	.	ENSP00000344828:E101X	E	+	1	0	ZNF678	225908875	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.382000	0.20635	-0.375000	0.07955	-0.216000	0.12614	GAA		0.358	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		T	227842252	G	T	227842252	4	4	61	1	0	0	0	0	0	1	0	0	18124	1291	45	2	480	2	ZNF678	1	227842252	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	534716	227842252	21408369	1094	9079										
ZNF678	339500	broad.mit.edu	37	chr1	227842889	227842889	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccttactcgtcataaaaGaattcatactggagaaaaac	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227842889G>T	ENST00000343776.5	+	4	1283	c.938G>T	c.(937-939)aGa>aTa	p.R313I	ZNF678_ENST00000397097.3_Missense_Mutation_p.R368I|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R313I(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				CGTCATAAAAGAATTCATACT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	1											45	50	49					1																	227842889		2203	4298	6501	225909512	SO:0001583	missense	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.938G>T	1.37:g.227842889G>T	ENSP00000344828:p.Arg313Ile		225909512	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		.	.	.	.	.	.	.	.	.	.	G	10.03	1.239663	0.22711	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.02446	4.29;4.29	1.62	-1.34	0.09143	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	L	0.61036	1.89	0.37593	D	0.920247	P	0.41910	0.764	P	0.51918	0.684	T	0.49351	-0.8949	9	0.33141	T	0.24	.	3.7708	0.08640	0.2008:0.2548:0.5444:0.0	.	313	Q5SXM1	ZN678_HUMAN	I	313;368	ENSP00000344828:R313I;ENSP00000440403:R368I	ENSP00000344828:R313I	R	+	2	0	ZNF678	225909512	0.001000	0.12720	0.022000	0.16811	0.173000	0.22820	1.022000	0.30052	-0.037000	0.13646	0.603000	0.83216	AGA		0.388	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		T	227842889	G	T	227842889	3	4	61	1	0	0	0	0	1	0	0	0	18124	942	33	2	1117	2	ZNF678	1	227842889	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	637	227842889	21407732	1095	9080										
ZNF678	339500	broad.mit.edu	37	chr1	227843057	227843057	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacctcactcagcataaaaGaattcatactggagagaaac	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227843057G>T	ENST00000343776.5	+	4	1451	c.1106G>T	c.(1105-1107)aGa>aTa	p.R369I	ZNF678_ENST00000397097.3_Missense_Mutation_p.R424I|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	369					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R369I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				CAGCATAAAAGAATTCATACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											34	38	36					1																	227843057		2199	4295	6494	225909680	SO:0001583	missense	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1106G>T	1.37:g.227843057G>T	ENSP00000344828:p.Arg369Ile		225909680	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		.	.	.	.	.	.	.	.	.	.	G	7.832	0.720050	0.15372	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.24908	1.83;1.83	1.5	0.462	0.16695	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26557	0.0649	L	0.50333	1.59	0.45108	D	0.998124	P	0.40180	0.705	P	0.47346	0.544	T	0.03957	-1.0989	9	0.33141	T	0.24	.	6.2127	0.20638	0.1959:0.0:0.8041:0.0	.	369	Q5SXM1	ZN678_HUMAN	I	369;424	ENSP00000344828:R369I;ENSP00000440403:R424I	ENSP00000344828:R369I	R	+	2	0	ZNF678	225909680	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.192000	0.09587	-0.085000	0.12573	-0.283000	0.09986	AGA		0.388	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		T	227843057	G	T	227843057	3	4	61	1	0	0	0	0	1	0	0	0	18124	942	33	2	1285	2	ZNF678	1	227843057	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	227843057	21407564	1096	9081										
ZNF678	339500	broad.mit.edu	37	chr1	227843241	227843241	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagaattcatactggagaGaaaccctacaaatgtaaaga	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227843241G>T	ENST00000343776.5	+	4	1635	c.1290G>T	c.(1288-1290)gaG>gaT	p.E430D	ZNF678_ENST00000397097.3_Missense_Mutation_p.E485D|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E430D(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				ATACTGGAGAGAAACCCTACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											34	39	37					1																	227843241		2198	4293	6491	225909864	SO:0001583	missense	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1290G>T	1.37:g.227843241G>T	ENSP00000344828:p.Glu430Asp		225909864	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		.	.	.	.	.	.	.	.	.	.	G	13.25	2.180270	0.38511	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.26810	1.71;1.71	1.63	0.596	0.17496	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36826	0.0981	L	0.43701	1.375	0.28635	N	0.907452	D	0.67145	0.996	D	0.79108	0.992	T	0.19647	-1.0299	9	0.66056	D	0.02	.	6.3896	0.21579	0.1897:0.0:0.8103:0.0	.	430	Q5SXM1	ZN678_HUMAN	D	430;485	ENSP00000344828:E430D;ENSP00000440403:E485D	ENSP00000344828:E430D	E	+	3	2	ZNF678	225909864	1.000000	0.71417	0.094000	0.20943	0.032000	0.12392	2.109000	0.41863	-0.039000	0.13602	-0.208000	0.12717	GAG		0.368	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		T	227843241	G	T	227843241	3	4	61	1	0	0	0	0	1	0	0	0	18124	933	33	2	1469	2	ZNF678	1	227843241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184	227843241	21407380	1097	9082										
ZNF678	339500	broad.mit.edu	37	chr1	227843477	227843477	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccatagtaagtataagaGaatttatactggagaggaac	9	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227843477G>T	ENST00000343776.5	+	4	1871	c.1526G>T	c.(1525-1527)aGa>aTa	p.R509I	ZNF678_ENST00000397097.3_Missense_Mutation_p.R564I|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R509I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				AAGTATAAGAGAATTTATACT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											44	48	46					1																	227843477		2201	4295	6496	225910100	SO:0001583	missense	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1526G>T	1.37:g.227843477G>T	ENSP00000344828:p.Arg509Ile		225910100	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		.	.	.	.	.	.	.	.	.	.	G	2.717	-0.267535	0.05754	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.32753	1.44;1.44	1.08	-0.225	0.13111	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23532	0.0569	L	0.51914	1.62	0.38354	D	0.944418	B	0.17667	0.023	B	0.13407	0.009	T	0.05131	-1.0904	9	0.40728	T	0.16	.	6.2192	0.20671	0.0:0.0:0.701:0.299	.	509	Q5SXM1	ZN678_HUMAN	I	509;564	ENSP00000344828:R509I;ENSP00000440403:R564I	ENSP00000344828:R509I	R	+	2	0	ZNF678	225910100	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.682000	0.05185	-0.523000	0.06409	-0.530000	0.04314	AGA		0.323	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		T	227843477	G	T	227843477	3	4	61	1	0	0	0	0	1	0	0	0	18124	942	33	2	1705	2	ZNF678	1	227843477	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236	227843477	21407144	1098	9083										
SNAP47	116841	broad.mit.edu	37	chr1	227947156	227947156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcaagaacctcttcccccGcagagaagagctgctcagtc	10	15	2	3	rs183802543		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:227947156G>A	ENST00000366759.4	+	3	1507	c.1093G>A	c.(1093-1095)Gca>Aca	p.A365T	SNAP47_ENST00000366760.1_Missense_Mutation_p.A123T|SNAP47_ENST00000315781.5_Missense_Mutation_p.A365T	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	365					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.A365T(1)		endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CTCTTCCCCCGCAGAGAAGAG	0.517													G|||	1	0.000199681	0	0	5008	,	,		20427	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	THR/ALA	0,4406		0,0,2203	115	118	117		1093	1.1	0	1		117	1,8599	1.2+/-3.3	0,1,4299	no	missense	SNAP47	NM_053052.3	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	365/465	227947156	1,13005	2203	4300	6503	226013779	SO:0001583	missense	116841			AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 142"	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.1093G>A	1.37:g.227947156G>A	ENSP00000355721:p.Ala365Thr		226013779	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	5.504|5.504	0.277926|0.277926	0.10403|0.10403	0.0|0.0	1.16E-4|1.16E-4	ENSG00000143740|ENSG00000143740	ENST00000366760;ENST00000366759;ENST00000315781|ENST00000418653;ENST00000426344	T;T;T|.	0.45668|.	0.89;2.2;2.18|.	5.04|5.04	1.08|1.08	0.20341|0.20341	.|.	0.734758|.	0.13883|.	N|.	0.356219|.	T|T	0.45438|0.45438	0.1342|0.1342	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.33379|.	0.001;0.196;0.41;0.41;0.196|.	B;B;B;B;B|.	0.25140|.	0.005;0.008;0.058;0.049;0.011|.	T|T	0.35724|0.35724	-0.9777|-0.9777	10|5	0.14656|.	T|.	0.56|.	-15.4879|-15.4879	7.4981|7.4981	0.27500|0.27500	0.445:0.0:0.555:0.0|0.445:0.0:0.555:0.0	.|.	123;365;177;365;123|.	Q5SQN1-3;Q5SQN1;Q5TBZ4;Q5SQN1-2;Q5SQN1-4|.	.;SNP47_HUMAN;.;.;.|.	T|H	123;365;365|177;356	ENSP00000355722:A123T;ENSP00000355721:A365T;ENSP00000314157:A365T|.	ENSP00000314157:A365T|.	A|R	+|+	1|2	0|0	SNAP47|SNAP47	226013779|226013779	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.011000|0.011000	0.07611|0.07611	0.327000|0.327000	0.19663|0.19663	0.045000|0.045000	0.15804|0.15804	0.561000|0.561000	0.74099|0.74099	GCA|CGC		0.517	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052		A	227947156	G	A	227947156	3	1	61	1	0	0	0	0	1	0	0	0	14869	1087	38	1	1103	1	SNAP47	1	227947156	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103679	227947156	21303465	1099	9084										
OBSCN	84033	broad.mit.edu	37	chr1	228433136	228433136	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaagggggtgtttgcgaaGgagcagtcagtgcataatga	15	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228433136G>T	ENST00000422127.1	+	12	3548	c.3504G>T	c.(3502-3504)aaG>aaT	p.K1168N	OBSCN_ENST00000570156.2_Missense_Mutation_p.K1260N|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.K1168N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1168	Ig-like 12.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.K1168N(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGTTTGCGAAGGAGCAGTCAG	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	1											72	71	72					1																	228433136		2047	4197	6244	226499759	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3504G>T	1.37:g.228433136G>T	ENSP00000409493:p.Lys1168Asn		226499759	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	6.207	0.406381	0.11754	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.63417	0.36;-0.04	4.2	4.2	0.49525	Immunoglobulin-like (1);	0.068087	0.64402	D	0.000020	T	0.54271	0.1848	N	0.17474	0.49	0.80722	D	1	D;B	0.64830	0.994;0.075	D;B	0.63703	0.917;0.01	T	0.54289	-0.8316	10	0.20519	T	0.43	.	3.5628	0.07889	0.0942:0.2423:0.5115:0.1519	.	1168;1168	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	N	1168	ENSP00000284548:K1168N;ENSP00000409493:K1168N	ENSP00000284548:K1168N	K	+	3	2	OBSCN	226499759	1.000000	0.71417	0.878000	0.34440	0.231000	0.25187	1.109000	0.31135	1.887000	0.54652	0.306000	0.20318	AAG		0.582	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228433136	G	T	228433136	3	4	61	1	0	0	0	0	1	0	0	0	10843	991	35	2	3546	2	OBSCN	1	228433136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	485980	228433136	20817485	1100	9085										
OBSCN	84033	broad.mit.edu	37	chr1	228433244	228433244	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtggtacaaggacgggaaGaagctgagctccagctcaaa	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228433244G>T	ENST00000422127.1	+	12	3656	c.3612G>T	c.(3610-3612)aaG>aaT	p.K1204N	OBSCN_ENST00000570156.2_Missense_Mutation_p.K1296N|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.K1204N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1204	Ig-like 12.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.K1204N(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGACGGGAAGAAGCTGAGCT	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	1											100	98	99					1																	228433244		2091	4209	6300	226499867	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3612G>T	1.37:g.228433244G>T	ENSP00000409493:p.Lys1204Asn		226499867	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	9.920	1.211990	0.22289	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.68624	-0.34;-0.34	4.63	3.71	0.42584	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.58969	1.84	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	T	0.70601	-0.4827	10	0.31617	T	0.26	.	6.9777	0.24686	0.2631:0.0:0.7369:0.0	.	1204;1204	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	N	1204	ENSP00000284548:K1204N;ENSP00000409493:K1204N	ENSP00000284548:K1204N	K	+	3	2	OBSCN	226499867	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	2.195000	0.42677	2.144000	0.66660	0.306000	0.20318	AAG		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228433244	G	T	228433244	3	4	61	1	0	0	0	0	1	0	0	0	10843	933	33	2	3654	2	OBSCN	1	228433244	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108	228433244	20817377	1101	9086										
OBSCN	84033	broad.mit.edu	37	chr1	228476379	228476379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaagagagcatagaagggGccacagccacgctgcggtgt	14	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228476379G>A	ENST00000422127.1	+	38	10173	c.10129G>A	c.(10129-10131)Gcc>Acc	p.A3377T	OBSCN_ENST00000366709.4_Missense_Mutation_p.A496T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A496T|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3377T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A3806T|OBSCN_ENST00000359599.6_Missense_Mutation_p.A2224T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3377	Ig-like 34.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.A3660T(1)|p.A3431T(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATAGAAGGGGCCACAGCCAC	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	1											77	83	81					1																	228476379		2060	4203	6263	226543002	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10129G>A	1.37:g.228476379G>A	ENSP00000409493:p.Ala3377Thr		226543002	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085168	0.36758	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41	4.97	-3.07	0.05363	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.047850	0.07651	N	0.931844	T	0.39517	0.1081	N	0.13371	0.34	0.09310	N	1	B;B	0.16603	0.009;0.018	B;B	0.21546	0.035;0.006	T	0.19224	-1.0312	10	0.14656	T	0.56	.	1.2792	0.02037	0.3178:0.1023:0.3706:0.2093	.	3377;3377	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	3377;3377;496;496;2224	ENSP00000284548:A3377T;ENSP00000409493:A3377T;ENSP00000355668:A496T;ENSP00000355670:A496T;ENSP00000352613:A2224T	ENSP00000284548:A3377T	A	+	1	0	OBSCN	226543002	0.000000	0.05858	0.102000	0.21198	0.097000	0.18754	-0.689000	0.05144	-0.704000	0.05042	0.491000	0.48974	GCC		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228476379	G	A	228476379	3	1	61	1	0	0	0	0	1	0	0	0	10843	1203	42	3	10275	3	OBSCN	1	228476379	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43135	228476379	20774242	1102	9087										
OBSCN	84033	broad.mit.edu	37	chr1	228505603	228505603	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttccccagcagagccaccGaagcctgtgcctccccagcc	9	19	0	1	rs565920635		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228505603G>A	ENST00000422127.1	+	53	13904	c.13860G>A	c.(13858-13860)ccG>ccA	p.P4620P	OBSCN_ENST00000366709.4_Silent_p.P1739P|OBSCN_ENST00000366707.4_Silent_p.P2254P|OBSCN_ENST00000284548.11_Silent_p.P4620P|OBSCN_ENST00000570156.2_Silent_p.P5577P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4620					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.P5202P(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGAGCCACCGAAGCCTGTGC	0.667													g|||	1	0.000199681	0	0	5008	,	,		17253	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	1											21	25	24					1																	228505603		2037	4173	6210	226572226	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13860G>A	1.37:g.228505603G>A			226572226	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																				0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228505603	G	A	228505603	2	1	61	1	0	0	0	0	0	0	0	1	10843	1045	37	1		1	OBSCN	1	228505603	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29224	228505603	20745018	1103	9088										
OBSCN	84033	broad.mit.edu	37	chr1	228509314	228509314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgtgtcgtggccagcaaGgcagatgtgcgagcccgctg	17	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228509314G>T	ENST00000422127.1	+	55	14816	c.14772G>T	c.(14770-14772)aaG>aaT	p.K4924N	OBSCN_ENST00000366709.4_Missense_Mutation_p.K2043N|OBSCN_ENST00000366707.4_Missense_Mutation_p.K2558N|OBSCN_ENST00000284548.11_Missense_Mutation_p.K4924N|OBSCN_ENST00000570156.2_Missense_Mutation_p.K5881N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4924	Ig-like 48.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.K5506N(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGCCAGCAAGGCAGATGTGC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											34	39	37					1																	228509314		2179	4268	6447	226575937	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.14772G>T	1.37:g.228509314G>T	ENSP00000409493:p.Lys4924Asn		226575937	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799482	0.50208	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.34	4.41	0.53225	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.64000	0.2559	N	0.20574	0.59	0.39192	D	0.962988	D;D	0.67145	0.996;0.986	P;P	0.60345	0.873;0.799	T	0.68127	-0.5491	10	0.62326	D	0.03	.	8.7351	0.34523	0.2453:0.0:0.7547:0.0	.	4924;4924	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	N	4924;4924;2558;2043	ENSP00000284548:K4924N;ENSP00000409493:K4924N;ENSP00000355668:K2558N;ENSP00000355670:K2043N	ENSP00000284548:K4924N	K	+	3	2	OBSCN	226575937	1.000000	0.71417	0.912000	0.35992	0.179000	0.23085	2.624000	0.46444	1.236000	0.43740	0.655000	0.94253	AAG		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228509314	G	T	228509314	3	4	61	1	0	0	0	0	1	0	0	0	10843	991	35	2	14986	2	OBSCN	1	228509314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3711	228509314	20741307	1104	9089										
OBSCN	84033	broad.mit.edu	37	chr1	228538555	228538555	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacagtcccaccacggttCgtgaacaaggtccgggcctc	10	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228538555C>T	ENST00000422127.1	+	77	18374	c.18330C>T	c.(18328-18330)ttC>ttT	p.F6110F	OBSCN_ENST00000366709.4_Silent_p.F3229F|OBSCN_ENST00000366707.4_Silent_p.F3744F|OBSCN_ENST00000284548.11_Silent_p.F6110F|OBSCN_ENST00000570156.2_Silent_p.F7067F	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6110	Ig-like 53.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.F6692F(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CACCACGGTTCGTGAACAAGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	1											43	47	46					1																	228538555		1932	4136	6068	226605178	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18330C>T	1.37:g.228538555C>T			226605178	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	7.228	0.598707	0.13939	.	.	ENSG00000154358	ENST00000441106	.	.	.	5.58	2.09	0.27110	.	.	.	.	.	T	0.57388	0.2050	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50303	-0.8844	4	.	.	.	.	8.4842	0.33061	0.0:0.2273:0.0:0.7727	.	.	.	.	C	727	.	.	R	+	1	0	OBSCN	226605178	1.000000	0.71417	0.999000	0.59377	0.004000	0.04260	0.896000	0.28377	0.428000	0.26173	-0.339000	0.08088	CGT		0.582	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228538555	C	T	228538555	2	4	61	1	0	0	0	0	0	0	0	1	10843	883	31	1		1	OBSCN	1	228538555	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29241	228538555	20712066	1105	9090										
OBSCN	84033	broad.mit.edu	37	chr1	228556554	228556554	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagttcgtctcccccgaGatcatccagcagaaccctgt	8	16	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:228556554G>T	ENST00000422127.1	+	89	19943	c.19899G>T	c.(19897-19899)gaG>gaT	p.E6633D	OBSCN_ENST00000366707.4_Missense_Mutation_p.E4267D|OBSCN_ENST00000570156.2_Missense_Mutation_p.E7590D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6633	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.E7215D(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCTCCCCCGAGATCATCCAGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	105	104					1																	228556554		2004	4171	6175	226623177	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.19899G>T	1.37:g.228556554G>T	ENSP00000409493:p.Glu6633Asp		226623177	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.56|14.56	2.572716|2.572716	0.45798|0.45798	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.74737	.|-0.87;-0.87	4.64|4.64	1.48|1.48	0.22813|0.22813	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|.	.|.	.|.	.|.	D|D	0.88235|0.88235	0.6382|0.6382	H|H	0.97158|0.97158	3.95|3.95	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.72075	.|0.976	D|D	0.86000|0.86000	0.1494|0.1494	5|9	.|0.87932	.|D	.|0	.|.	7.0897|7.0897	0.25277|0.25277	0.4874:0.0:0.5126:0.0|0.4874:0.0:0.5126:0.0	.|.	.|6633	.|Q5VST9	.|OBSCN_HUMAN	Y|D	1250|6633;4267	.|ENSP00000409493:E6633D;ENSP00000355668:E4267D	.|ENSP00000355668:E4267D	D|E	+|+	1|3	0|2	OBSCN|OBSCN	226623177|226623177	1.000000|1.000000	0.71417|0.71417	0.803000|0.803000	0.32268|0.32268	0.325000|0.325000	0.28411|0.28411	1.893000|1.893000	0.39758|0.39758	0.214000|0.214000	0.20742|0.20742	-1.598000|-1.598000	0.00824|0.00824	GAT|GAG		0.582	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228556554	G	T	228556554	3	4	61	1	0	0	0	0	1	0	0	0	10843	933	33	2	21459	2	OBSCN	1	228556554	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17999	228556554	20694067	1106	9091										
ACTA1	58	broad.mit.edu	37	chr1	229567634	229567634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaggtggtctcgtgaatgCccgccgactccatacctggg	13	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229567634C>T	ENST00000366684.3	-	6	926	c.824G>A	c.(823-825)gGc>gAc	p.G275D	ACTA1_ENST00000366683.2_Missense_Mutation_p.G187D	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	275					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)	p.G275D(1)		endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				CTCGTGAATGCCCGCCGACTC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	105	109					1																	229567634		2203	4300	6503	227634257	SO:0001583	missense	58			J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"nemaline myopathy type 3"	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.824G>A	1.37:g.229567634C>T	ENSP00000355645:p.Gly275Asp		227634257	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	37	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.352885	0.41700	.	.	ENSG00000143632	ENST00000366684;ENST00000308794;ENST00000366683;ENST00000366682	D;D	0.97352	-4.35;-4.35	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.99309	0.9758	H	0.99811	4.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98117	1.0423	10	0.87932	D	0	.	17.2969	0.87172	0.0:1.0:0.0:0.0	.	275	P68133	ACTS_HUMAN	D	275;185;187;240	ENSP00000355645:G275D;ENSP00000355644:G187D	ENSP00000312351:G185D	G	-	2	0	ACTA1	227634257	1.000000	0.71417	0.997000	0.53966	0.374000	0.29953	7.602000	0.82796	2.304000	0.77564	0.563000	0.77884	GGC		0.677	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		T	229567634	C	T	229567634	3	4	61	1	0	0	0	0	1	0	0	0	191	739	26	3	317	3	ACTA1	1	229567634	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1011080	229567634	19682987	1107	9092										
NUP133	55746	broad.mit.edu	37	chr1	229634011	229634011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagctctcaggtatcaaccGaattagttggcttcctgatg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229634011G>A	ENST00000261396.3	-	6	782	c.691C>T	c.(691-693)Cgg>Tgg	p.R231W	NUP133_ENST00000537506.1_Missense_Mutation_p.R215W	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	231					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.R231W(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GGTATCAACCGAATTAGTTGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	70	70					1																	229634011		2203	4300	6503	227700634	SO:0001583	missense	55746				CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.691C>T	1.37:g.229634011G>A	ENSP00000261396:p.Arg231Trp		227700634	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444469	0.63178	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.44881	0.91;0.91;0.91	5.71	4.8	0.61643	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.63519	-0.6619	10	0.37606	T	0.19	-11.2303	16.1184	0.81324	0.0:0.0:0.8651:0.1349	.	231	Q8WUM0	NU133_HUMAN	W	231;231;231;215	ENSP00000261396:R231W;ENSP00000355640:R231W;ENSP00000443496:R215W	ENSP00000261396:R231W	R	-	1	2	NUP133	227700634	1.000000	0.71417	0.456000	0.27044	0.598000	0.36846	3.815000	0.55651	1.405000	0.46838	0.650000	0.86243	CGG		0.398	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		A	229634011	G	A	229634011	3	1	61	1	0	0	0	0	1	0	0	0	10785	1057	37	1	2863	1	NUP133	1	229634011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66377	229634011	19616610	1108	9093										
URB2	9816	broad.mit.edu	37	chr1	229770932	229770932	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagcaggtcaacccaaGacgtgcctttggggatgtga	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229770932G>T	ENST00000258243.2	+	4	708	c.572G>T	c.(571-573)aGa>aTa	p.R191I		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	191						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R191I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						GTCAACCCAAGACGTGCCTTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											68	60	62					1																	229770932		2203	4300	6503	227837555	SO:0001583	missense	9816			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.572G>T	1.37:g.229770932G>T	ENSP00000258243:p.Arg191Ile		227837555	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439254	0.43326	.	.	ENSG00000135763	ENST00000258243	T	0.10192	2.9	5.68	2.54	0.30619	.	0.233607	0.47093	D	0.000241	T	0.11067	0.0270	L	0.51422	1.61	0.30927	N	0.727333	P	0.49961	0.93	P	0.44732	0.459	T	0.09185	-1.0686	9	.	.	.	-8.9912	6.2545	0.20865	0.6623:0.0:0.3377:0.0	.	191	Q14146	URB2_HUMAN	I	191	ENSP00000258243:R191I	.	R	+	2	0	URB2	227837555	0.862000	0.29867	0.059000	0.19551	0.775000	0.43874	2.975000	0.49281	0.368000	0.24481	0.650000	0.86243	AGA		0.607	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229770932	G	T	229770932	3	4	61	1	0	0	0	0	1	0	0	0	17065	942	33	2	582	2	URB2	1	229770932	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136921	229770932	19479689	1109	9094										
URB2	9816	broad.mit.edu	37	chr1	229771492	229771492	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatctacaacatcgctgccGacagaattcggcacgaagag	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229771492G>A	ENST00000258243.2	+	4	1268	c.1132G>A	c.(1132-1134)Gac>Aac	p.D378N		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	378						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.D378N(2)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CATCGCTGCCGACAGAATTCG	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	1											56	56	56					1																	229771492		2203	4300	6503	227838115	SO:0001583	missense	9816			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.1132G>A	1.37:g.229771492G>A	ENSP00000258243:p.Asp378Asn		227838115	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.528408	0.64860	.	.	ENSG00000135763	ENST00000258243	T	0.54279	0.58	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.71879	0.3392	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71048	-0.4705	9	.	.	.	-25.0062	19.1348	0.93422	0.0:0.0:1.0:0.0	.	378	Q14146	URB2_HUMAN	N	378	ENSP00000258243:D378N	.	D	+	1	0	URB2	227838115	1.000000	0.71417	0.174000	0.22961	0.056000	0.15407	9.238000	0.95380	2.601000	0.87937	0.650000	0.86243	GAC		0.527	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229771492	G	A	229771492	3	1	61	1	0	0	0	0	1	0	0	0	17065	1058	37	1	1142	1	URB2	1	229771492	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	560	229771492	19479129	1110	9095										
URB2	9816	broad.mit.edu	37	chr1	229771734	229771734	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttattcgtactgtcttccaGacttatgccaaactccgaca	5	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229771734G>T	ENST00000258243.2	+	4	1510	c.1374G>T	c.(1372-1374)caG>caT	p.Q458H		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	458						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.Q458H(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CTGTCTTCCAGACTTATGCCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											106	116	113					1																	229771734		2203	4300	6503	227838357	SO:0001583	missense	9816			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.1374G>T	1.37:g.229771734G>T	ENSP00000258243:p.Gln458His		227838357	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732017	0.48939	.	.	ENSG00000135763	ENST00000258243	T	0.36157	1.27	5.35	4.44	0.53790	.	0.056903	0.64402	D	0.000001	T	0.31734	0.0806	M	0.66939	2.045	0.53005	D	0.999966	P	0.47106	0.89	B	0.35278	0.199	T	0.17776	-1.0358	9	.	.	.	-21.2738	10.755	0.46232	0.0713:0.1315:0.7971:0.0	.	458	Q14146	URB2_HUMAN	H	458	ENSP00000258243:Q458H	.	Q	+	3	2	URB2	227838357	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	1.835000	0.39181	1.418000	0.47098	0.650000	0.86243	CAG		0.547	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229771734	G	T	229771734	3	4	61	1	0	0	0	0	1	0	0	0	17065	933	33	2	1384	2	URB2	1	229771734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	242	229771734	19478887	1111	9096										
URB2	9816	broad.mit.edu	37	chr1	229779337	229779337	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcatttgggagccttgtTcacccaaatgttagaggttg	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:229779337T>C	ENST00000258243.2	+	5	3828	c.3692T>C	c.(3691-3693)tTc>tCc	p.F1231S		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1231						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.F1231S(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						GGAGCCTTGTTCACCCAAATG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											164	153	157					1																	229779337		2203	4300	6503	227845960	SO:0001583	missense	9816			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3692T>C	1.37:g.229779337T>C	ENSP00000258243:p.Phe1231Ser		227845960	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.983160	0.34942	.	.	ENSG00000135763	ENST00000258243	T	0.32023	1.47	5.36	5.36	0.76844	.	0.518798	0.22239	N	0.062703	T	0.24044	0.0582	L	0.27053	0.805	0.09310	N	1	P	0.44578	0.838	B	0.41813	0.367	T	0.11372	-1.0590	9	.	.	.	-11.9915	13.0077	0.58715	0.0:0.0:0.0:1.0	.	1231	Q14146	URB2_HUMAN	S	1231	ENSP00000258243:F1231S	.	F	+	2	0	URB2	227845960	0.407000	0.25352	0.032000	0.17829	0.281000	0.26958	3.527000	0.53517	2.153000	0.67306	0.528000	0.53228	TTC		0.463	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		C	229779337	T	C	229779337	3	2	61	1	0	0	0	0	1	0	0	0	17065	1783	62	4	3706	4	URB2	1	229779337	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7603	229779337	19471284	1112	9097										
GALNT2	2590	broad.mit.edu	37	chr1	230372166	230372166	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatgactacagcaatgatCgtgagtactgacactgattt	10	7	0	5	rs537078461		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:230372166C>T	ENST00000366672.4	+	5	613	c.541C>T	c.(541-543)Cct>Tct	p.P181S	GALNT2_ENST00000543760.1_Splice_Site_p.P143S|GALNT2_ENST00000541865.1_Splice_Site_p.P91S	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	181	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.P181S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CAGCAATGATCGTGAGTACTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	76	77					1																	230372166		2203	4300	6503	228438789	SO:0001630	splice_region_variant	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.541+1C>T	1.37:g.230372166C>T			228438789	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730859	0.48939	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000541865	T;T;T	0.61510	0.1;0.1;0.1	5.54	5.54	0.83059	Glycosyl transferase, family 2 (1);	0.290613	0.38217	N	0.001778	T	0.50154	0.1599	L	0.61218	1.895	0.58432	D	0.999999	P;B	0.36616	0.561;0.193	B;B	0.24155	0.051;0.019	T	0.53308	-0.8457	10	0.38643	T	0.18	.	13.9496	0.64109	0.0:0.8476:0.1524:0.0	.	181;143	Q10471;G3V1S6	GALT2_HUMAN;.	S	143;181;91	ENSP00000445017:P143S;ENSP00000355632:P181S;ENSP00000444346:P91S	ENSP00000355632:P181S	P	+	1	0	GALNT2	228438789	0.997000	0.39634	0.999000	0.59377	0.973000	0.67179	1.438000	0.35002	2.607000	0.88179	0.655000	0.94253	CCT		0.448	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	Missense_Mutation	T	230372166	C	T	230372166	5	4	61	1	0	0	0	0	0	0	1	0	6233	898	31	1	559	1	GALNT2	1	230372166	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	592829	230372166	18878455	1113	9098										
AGT	183	broad.mit.edu	37	chr1	230846407	230846407	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaggtatgaaggtggggtCtttgggcttcccggcattgg	17	7	1	1	rs374540090		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:230846407C>A	ENST00000366667.4	-	2	404	c.190G>T	c.(190-192)Gac>Tac	p.D64Y	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	64					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)	p.D64Y(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AAGGTGGGGTCTTTGGGCTTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	TYR/ASP	1,4405	2.1+/-5.4	0,1,2202	95	95	95		190	4.3	0	1		95	0,8600		0,0,4300	no	missense	AGT	NM_000029.3	160	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging	64/486	230846407	1,13005	2203	4300	6503	228913030	SO:0001583	missense	183			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.190G>T	1.37:g.230846407C>A	ENSP00000355627:p.Asp64Tyr		228913030	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	C	9.999	1.232950	0.22626	2.27E-4	0.0	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.88509	-2.39	5.19	4.27	0.50696	Serpin domain (1);	0.452064	0.25222	N	0.032235	D	0.86037	0.5837	L	0.51422	1.61	0.09310	N	1	D;D	0.59357	0.985;0.982	B;P	0.44359	0.321;0.447	T	0.79850	-0.1629	10	0.72032	D	0.01	.	10.4632	0.44592	0.0:0.7914:0.1355:0.0731	.	64;64	B2R5S1;P01019	.;ANGT_HUMAN	Y	64	ENSP00000355627:D64Y	ENSP00000355627:D64Y	D	-	1	0	AGT	228913030	0.003000	0.15002	0.019000	0.16419	0.010000	0.07245	1.237000	0.32695	1.290000	0.44636	0.561000	0.74099	GAC		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		A	230846407	C	A	230846407	3	1	61	1	0	0	0	0	1	0	0	0	399	913	32	2	1283	2	AGT	1	230846407	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	474241	230846407	18404214	1114	9099										
TTC13	79573	broad.mit.edu	37	chr1	231060654	231060654	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtgtcttcccattcattcGaactttcgagttggtccatg	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231060654G>A	ENST00000366661.4	-	14	1661	c.1654C>T	c.(1654-1656)Cga>Tga	p.R552*	TTC13_ENST00000366662.4_Nonsense_Mutation_p.R499*|TTC13_ENST00000414259.1_Nonsense_Mutation_p.R499*	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	552								p.R552*(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		CCATTCATTCGAACTTTCGAG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											216	176	189					1																	231060654		2203	4300	6503	229127277	SO:0001587	stop_gained	79573				CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.1654C>T	1.37:g.231060654G>A	ENSP00000355621:p.Arg552*		229127277	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Nonsense_Mutation	SNP	ENST00000366661.4	37	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	G	40	8.176742	0.98691	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	-29.1504	19.106	0.93294	0.0:0.0:1.0:0.0	.	.	.	.	X	552;499;499	.	ENSP00000355621:R552X	R	-	1	2	TTC13	229127277	1.000000	0.71417	0.960000	0.40013	0.797000	0.45037	9.813000	0.99286	2.576000	0.86940	0.655000	0.94253	CGA		0.438	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		A	231060654	G	A	231060654	4	1	61	1	0	0	0	0	0	1	0	0	16720	1066	37	1	968	1	TTC13	1	231060654	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214247	231060654	18189967	1115	9100										
TTC13	79573	broad.mit.edu	37	chr1	231097001	231097001	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaggagtcacagggtgatGatcccttgggttcgcagtct	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231097001G>T	ENST00000366661.4	-	2	327	c.320C>A	c.(319-321)tCa>tAa	p.S107*	TTC13_ENST00000366662.4_Nonsense_Mutation_p.S107*|TTC13_ENST00000414259.1_Nonsense_Mutation_p.S107*	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	107								p.S107*(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		ACAGGGTGATGATCCCTTGGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											124	114	117					1																	231097001		2203	4300	6503	229163624	SO:0001587	stop_gained	79573				CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.320C>A	1.37:g.231097001G>T	ENSP00000355621:p.Ser107*		229163624	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Nonsense_Mutation	SNP	ENST00000366661.4	37	CCDS1588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.138002|5.138002	0.94517|0.94517	.|.	.|.	ENSG00000143643|ENSG00000143643	ENST00000522821|ENST00000366661;ENST00000366662;ENST00000414259	.|.	.|.	.|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.432330	.|0.24985	.|N	.|0.034024	T|.	0.44540|.	0.1298|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.39663|.	-0.9603|.	3|.	.|0.02654	.|T	.|1	-13.0404|-13.0404	17.6627|17.6627	0.88196|0.88196	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	N|X	96|107	.|.	.|ENSP00000355621:S107X	H|S	-|-	1|2	0|0	TTC13|TTC13	229163624|229163624	1.000000|1.000000	0.71417|0.71417	0.502000|0.502000	0.27614|0.27614	0.840000|0.840000	0.47671|0.47671	4.550000|4.550000	0.60733|0.60733	2.463000|2.463000	0.83235|0.83235	0.557000|0.557000	0.71058|0.71058	CAT|TCA		0.423	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		T	231097001	G	T	231097001	4	4	61	1	0	0	0	0	0	1	0	0	16720	1294	45	2	2350	2	TTC13	1	231097001	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36347	231097001	18153620	1116	9101										
TRIM67	440730	broad.mit.edu	37	chr1	231342418	231342418	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtgtacgtcggtaaggaGactttgtgtaccatcgacgg	14	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231342418G>T	ENST00000366653.5	+	7	1701	c.1701G>T	c.(1699-1701)gaG>gaT	p.E567D	TRIM67_ENST00000444294.3_Missense_Mutation_p.E565D|TRIM67_ENST00000366652.2_Missense_Mutation_p.E567D|TRIM67_ENST00000449018.3_Missense_Mutation_p.E505D			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	567	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.E567D(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TCGGTAAGGAGACTTTGTGTA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	81	79					1																	231342418		2045	4218	6263	229409041	SO:0001583	missense	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1701G>T	1.37:g.231342418G>T	ENSP00000355613:p.Glu567Asp		229409041	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.997362	0.54147	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.5	5.5	0.81552	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41442	0.1159	N	0.25957	0.775	0.58432	D	0.999999	B	0.11235	0.004	B	0.23574	0.047	T	0.20140	-1.0284	10	0.35671	T	0.21	.	13.037	0.58877	0.0739:0.0:0.9261:0.0	.	567	Q6ZTA4	TRI67_HUMAN	D	565;567;505;567	ENSP00000412124:E565D;ENSP00000355612:E567D;ENSP00000400163:E505D;ENSP00000355613:E567D	ENSP00000355612:E567D	E	+	3	2	TRIM67	229409041	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.765000	0.62271	2.741000	0.93983	0.655000	0.94253	GAG		0.488	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231342418	G	T	231342418	3	4	61	1	0	0	0	0	1	0	0	0	16580	933	33	2	1727	2	TRIM67	1	231342418	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	245417	231342418	17908203	1117	9102										
TRIM67	440730	broad.mit.edu	37	chr1	231344821	231344821	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgcgttctccaagggcGtgcactactgggagctgcac	13	13	1	0	rs370765650		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231344821G>A	ENST00000366653.5	+	8	1948	c.1948G>A	c.(1948-1950)Gtg>Atg	p.V650M	TRIM67_ENST00000444294.3_Missense_Mutation_p.V648M|TRIM67_ENST00000366652.2_Missense_Mutation_p.V650M|TRIM67_ENST00000449018.3_Missense_Mutation_p.V588M			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	650	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.V650M(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				CTCCAAGGGCGTGCACTACTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	MET/VAL	0,4366		0,0,2183	92	102	99		1948	4.8	0.1	1		99	1,8571	1.2+/-3.3	0,1,4285	no	missense	TRIM67	NM_001004342.3	21	0,1,6468	AA,AG,GG		0.0117,0.0,0.0077	possibly-damaging	650/784	231344821	1,12937	2183	4286	6469	229411444	SO:0001583	missense	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1948G>A	1.37:g.231344821G>A	ENSP00000355613:p.Val650Met		229411444	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.787675	0.49997	0.0	1.17E-4	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.73	4.82	0.62117	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.509696	0.21287	N	0.077059	T	0.81460	0.4827	M	0.86343	2.81	0.24960	N	0.991739	D	0.63046	0.992	D	0.65773	0.938	T	0.74210	-0.3739	10	0.45353	T	0.12	.	11.2457	0.48996	0.1403:0.0:0.8597:0.0	.	650	Q6ZTA4	TRI67_HUMAN	M	648;650;588;650	ENSP00000412124:V648M;ENSP00000355612:V650M;ENSP00000400163:V588M;ENSP00000355613:V650M	ENSP00000355612:V650M	V	+	1	0	TRIM67	229411444	0.991000	0.36638	0.071000	0.20095	0.139000	0.21198	3.412000	0.52679	1.555000	0.49500	0.655000	0.94253	GTG		0.617	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		A	231344821	G	A	231344821	3	1	61	1	0	0	0	0	1	0	0	0	16580	1145	40	1	1978	1	TRIM67	1	231344821	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2403	231344821	17905800	1118	9103										
C1orf131	8443	broad.mit.edu	37	chr1	231374790	231374790	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagttccttgaagaagctcGaagcgctcttcctctggcct	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231374790G>A	ENST00000366647.4	+	0	0				C1orf131_ENST00000366649.2_Missense_Mutation_p.S88L|C1orf131_ENST00000366651.3_Missense_Mutation_p.S88L|C1orf131_ENST00000318906.2_Missense_Mutation_p.S88L|C1orf131_ENST00000471936.1_5'UTR|GNPAT_ENST00000366646.3_5'Flank	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)	p.S88L(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				GAAGAAGCTCGAAGCGCTCTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											75	72	73					1																	231374790		2203	4300	6503	229441413	SO:0001631	upstream_gene_variant	128061			AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024		1.37:g.231374790G>A	Exception_encountered		229441413	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	G	4.089	0.014442	0.07959	.	.	ENSG00000143633	ENST00000366649;ENST00000318906;ENST00000366651;ENST00000366648;ENST00000451322	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.24	2.36	0.29203	.	0.556835	0.18352	N	0.143855	T	0.10723	0.0262	L	0.35723	1.085	0.09310	N	1	B;B;B;B;B	0.28667	0.03;0.219;0.017;0.017;0.017	B;B;B;B;B	0.22880	0.007;0.042;0.004;0.007;0.004	T	0.19128	-1.0315	10	0.37606	T	0.19	-6.9819	4.4599	0.11661	0.1802:0.0:0.642:0.1778	.	88;88;88;88;88	B4E0F7;Q8NDD1-4;Q8NDD1;Q8NDD1-3;Q8NDD1-2	.;.;CA131_HUMAN;.;.	L	88;88;88;78;71	ENSP00000355609:S88L;ENSP00000321341:S88L;ENSP00000355611:S88L;ENSP00000401677:S71L	ENSP00000321341:S88L	S	-	2	0	C1orf131	229441413	0.411000	0.25384	0.063000	0.19743	0.003000	0.03518	0.732000	0.26072	0.886000	0.36113	-0.137000	0.14449	TCG		0.547	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			A	231374790	G	A	231374790	1	1	61	0	1	0	0	0	0	0	0	0	2004	1059	37	1		1	C1orf131	1	231374790	5'Flank	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29969	231374790	17875831	1119	9104										
EGLN1	54583	broad.mit.edu	37	chr1	231506425	231506425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgccttctggaaaaattCgaagtatacctccacttacc	5	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231506425C>T	ENST00000366641.3	-	3	4186	c.1031G>A	c.(1030-1032)cGa>cAa	p.R344Q	EGLN1_ENST00000476717.1_5'UTR	NM_022051.2	NP_071334.1			egl-9 family hypoxia-inducible factor 1									p.R344Q(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	16		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)				TGGAAAAATTCGAAGTATACC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	108	108					1																	231506425		2203	4300	6503	229573048	SO:0001583	missense	54583			AJ310543	CCDS1595.1	1q42.1	2013-08-21	2013-08-21	2001-08-24	ENSG00000135766	ENSG00000135766		"Zinc fingers, MYND-type"	1232	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 2"	606425	"EGL nine (C.elegans) homolog 1", "egl nine homolog 1 (C. elegans)"	C1orf12		11056053	Standard	NM_022051		Approved	SM-20, PHD2, ZMYND6, HIFPH2	uc001huv.2	Q9GZT9	OTTHUMG00000038027	ENST00000366641.3:c.1031G>A	1.37:g.231506425C>T	ENSP00000355601:p.Arg344Gln		229573048		Missense_Mutation	SNP	ENST00000366641.3	37	CCDS1595.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917973	0.92249	.	.	ENSG00000135766	ENST00000366641	T	0.59083	0.29	5.73	5.73	0.89815	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.74966	0.3786	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.63877	0.919	T	0.71170	-0.4671	10	0.30854	T	0.27	-4.6704	19.9155	0.97058	0.0:1.0:0.0:0.0	.	344	Q9GZT9	EGLN1_HUMAN	Q	344	ENSP00000355601:R344Q	ENSP00000355601:R344Q	R	-	2	0	EGLN1	229573048	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.008000	0.70739	2.699000	0.92147	0.650000	0.86243	CGA		0.393	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051		T	231506425	C	T	231506425	3	4	61	1	0	0	0	0	1	0	0	0	4979	884	31	1	261	1	EGLN1	1	231506425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131635	231506425	17744196	1120	9105										
DISC1	27185	broad.mit.edu	37	chr1	231830420	231830420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggctcctccagttctctgGatccctcactggctggctgt	10	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231830420G>A	ENST00000602281.1	+	2	969	c.916G>A	c.(916-918)Gat>Aat	p.D306N	DISC1_ENST00000366636.4_Missense_Mutation_p.D306N|DISC1_ENST00000366633.3_Missense_Mutation_p.D306N|DISC1_ENST00000539444.1_Missense_Mutation_p.D306N|DISC1_ENST00000439617.2_Missense_Mutation_p.D306N|DISC1_ENST00000317586.4_Missense_Mutation_p.D306N|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000535983.1_Missense_Mutation_p.D306N|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000537876.1_Missense_Mutation_p.D306N|DISC1_ENST00000366637.3_5'UTR	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	306	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)		p.D306N(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				CAGTTCTCTGGATCCCTCACT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	57	57					1																	231830420		2203	4300	6503	229897043	SO:0001583	missense	27185			AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.916G>A	1.37:g.231830420G>A	ENSP00000473425:p.Asp306Asn		229897043	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006796	0.54361	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944;ENST00000366632	T;T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	4.94	2.94	0.34122	.	0.337382	0.33110	N	0.005280	T	0.40372	0.1114	L	0.58101	1.795	0.09310	N	1	P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;P;D;D	0.67145	0.557;0.976;0.996;0.993;0.976;0.974;0.976;0.976;0.976;0.976;0.981;0.996;0.996;0.976;0.977;0.933;0.988;0.977;0.933;0.976;0.962	B;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P	0.60236	0.277;0.677;0.866;0.784;0.677;0.796;0.743;0.743;0.677;0.743;0.813;0.871;0.871;0.677;0.787;0.544;0.844;0.787;0.544;0.677;0.628	T	0.20874	-1.0262	10	0.45353	T	0.12	-0.6843	12.4158	0.55492	0.0:0.4001:0.5999:0.0	.	306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306;306	C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;A7E2W8;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;.	N	306;306;306;306;306;306;306;306;306;306;306;306;157	ENSP00000403888:D306N;ENSP00000320784:D306N;ENSP00000355596:D306N;ENSP00000443996:D306N;ENSP00000440909:D306N;ENSP00000355593:D306N;ENSP00000440953:D306N;ENSP00000295051:D306N;ENSP00000441193:D306N	ENSP00000295051:D306N	D	+	1	0	DISC1	229897043	0.045000	0.20229	0.000000	0.03702	0.022000	0.10575	2.674000	0.46867	0.545000	0.28902	0.561000	0.74099	GAT		0.617	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		A	231830420	G	A	231830420	3	1	61	1	0	0	0	0	1	0	0	0	4549	1174	41	3	922	3	DISC1	1	231830420	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	323995	231830420	17420201	1121	9106										
DISC1	27185	broad.mit.edu	37	chr1	231885698	231885698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttacaacaaagattagaaGacctggaacaagagaaaatc	8	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:231885698G>T	ENST00000602281.1	+	4	1197	c.1144G>T	c.(1144-1146)Gac>Tac	p.D382Y	DISC1_ENST00000366636.4_Missense_Mutation_p.D382Y|DISC1_ENST00000366633.3_Missense_Mutation_p.D382Y|DISC1_ENST00000539444.1_Missense_Mutation_p.D382Y|DISC1_ENST00000439617.2_Missense_Mutation_p.D382Y|DISC1_ENST00000602873.1_Missense_Mutation_p.D32Y|DISC1_ENST00000535983.1_Missense_Mutation_p.D382Y|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000537876.1_Missense_Mutation_p.D382Y|DISC1_ENST00000366637.3_5'UTR	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	382	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)		p.D382Y(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				AAGATTAGAAGACCTGGAACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											102	100	101					1																	231885698		2203	4300	6503	229952321	SO:0001583	missense	27185			AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1144G>T	1.37:g.231885698G>T	ENSP00000473425:p.Asp382Tyr		229952321	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	.	18.56	3.649651	0.67358	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.15372	2.88;2.7;2.69;2.45;2.88;2.46;2.46;2.43	4.75	3.76	0.43208	.	0.358789	0.27595	N	0.018674	T	0.25195	0.0612	L	0.34521	1.04	0.23739	N	0.996973	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.999;0.997;0.998;0.999;0.999;0.998;0.998;0.999;0.995;0.999;0.999;0.998;0.999;0.999;0.998;0.998;0.998;0.998;0.998	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D	0.70487	0.946;0.912;0.969;0.947;0.969;0.935;0.911;0.969;0.874;0.947;0.947;0.911;0.947;0.947;0.946;0.911;0.946;0.911;0.911	T	0.02042	-1.1224	10	0.87932	D	0	-8.5446	7.0498	0.25067	0.1251:0.0:0.8749:0.0	.	414;382;414;382;382;382;382;382;32;382;382;382;382;382;382;382;382;382;382	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	Y	382;382;382;414;382;382;382;382;382;382;382	ENSP00000403888:D382Y;ENSP00000355596:D382Y;ENSP00000443996:D382Y;ENSP00000440909:D382Y;ENSP00000355593:D382Y;ENSP00000440953:D382Y;ENSP00000295051:D382Y;ENSP00000441193:D382Y	ENSP00000295051:D382Y	D	+	1	0	DISC1	229952321	0.997000	0.39634	1.000000	0.80357	0.960000	0.62799	2.116000	0.41930	2.442000	0.82660	0.655000	0.94253	GAC		0.458	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		T	231885698	G	T	231885698	3	4	61	1	0	0	0	0	1	0	0	0	4549	942	33	2	1517	2	DISC1	1	231885698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55278	231885698	17364923	1122	9107										
SIPA1L2	57568	broad.mit.edu	37	chr1	232551265	232551265	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcccgtgcagcatccacGaggtgggtccaatctaaccc	10	14	1	0	rs202017607		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:232551265G>A	ENST00000366630.1	-	18	5095	c.4737C>T	c.(4735-4737)ctC>ctT	p.L1579L	SIPA1L2_ENST00000262861.4_Silent_p.L1579L|SIPA1L2_ENST00000308942.4_Silent_p.L653L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1579					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.L1579L(2)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CAGCATCCACGAGGTGGGTCC	0.582																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	1											93	106	102					1																	232551265		1960	4165	6125	230617888	SO:0001819	synonymous_variant	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4737C>T	1.37:g.232551265G>A			230617888	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																				0.582	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232551265	G	A	232551265	2	1	61	1	0	0	0	0	0	0	0	1	14367	1045	37	1		1	SIPA1L2	1	232551265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	665567	232551265	16699356	1123	9108										
SIPA1L2	57568	broad.mit.edu	37	chr1	232564165	232564165	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtcactaacctttcttcGcccctcctccactaaggggc	6	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:232564165G>A	ENST00000366630.1	-	16	4760	c.4402C>T	c.(4402-4404)Cga>Tga	p.R1468*	SIPA1L2_ENST00000262861.4_Nonsense_Mutation_p.R1468*|SIPA1L2_ENST00000308942.4_Nonsense_Mutation_p.R542*			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1468					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.R1468*(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				ACCTTTCTTCGCCCCTCCTCC	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											79	71	73					1																	232564165		1842	4098	5940	230630788	SO:0001587	stop_gained	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4402C>T	1.37:g.232564165G>A	ENSP00000355589:p.Arg1468*		230630788	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Nonsense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	47	13.120571	0.99721	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	.	.	.	5.86	0.894	0.19242	.	0.415283	0.25570	N	0.029769	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.9461	10.0101	0.41981	0.0975:0.0:0.3444:0.5581	.	.	.	.	X	1468;1468;542	.	ENSP00000262861:R1468X	R	-	1	2	SIPA1L2	230630788	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	2.673000	0.46858	0.470000	0.27294	-0.262000	0.10625	CGA		0.403	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232564165	G	A	232564165	4	1	61	1	0	0	0	0	0	1	0	0	14367	1095	38	1	794	1	SIPA1L2	1	232564165	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12900	232564165	16686456	1124	9109										
SIPA1L2	57568	broad.mit.edu	37	chr1	232649848	232649848	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccctccagtctcatttCtaaagtaaggacaactaagg	6	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:232649848C>A	ENST00000366630.1	-	2	1596	c.1238G>T	c.(1237-1239)aGa>aTa	p.R413I	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R413I			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	413					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.R413I(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AGTCTCATTTCTAAAGTAAGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											160	155	157					1																	232649848		1959	4146	6105	230716471	SO:0001583	missense	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1238G>T	1.37:g.232649848C>A	ENSP00000355589:p.Arg413Ile		230716471	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678482	0.88542	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.86432	-2.12;-2.12	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.94377	0.8192	M	0.87456	2.885	0.80722	D	1	D	0.71674	0.998	D	0.71870	0.975	D	0.94664	0.7851	10	0.72032	D	0.01	-28.7966	19.3561	0.94414	0.0:1.0:0.0:0.0	.	413	Q9P2F8	SI1L2_HUMAN	I	413	ENSP00000355589:R413I;ENSP00000262861:R413I	ENSP00000262861:R413I	R	-	2	0	SIPA1L2	230716471	1.000000	0.71417	0.758000	0.31321	0.993000	0.82548	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	AGA		0.517	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232649848	C	A	232649848	3	1	61	1	0	0	0	0	1	0	0	0	14367	913	32	2	4014	2	SIPA1L2	1	232649848	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85683	232649848	16600773	1125	9110										
KIAA1383	54627	broad.mit.edu	37	chr1	232942625	232942625	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaactataaggaagataAatattctgaaaagagcagtg	9	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:232942625A>C	ENST00000418460.1	+	1	1983	c.1856A>C	c.(1855-1857)aAa>aCa	p.K619T		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	477					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)	p.K619T(2)									AAGGAAGATAAATATTCTGAA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	1											25	25	25					1																	232942625		1836	4094	5930	231009248	SO:0001583	missense	54627			AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1856A>C	1.37:g.232942625A>C	ENSP00000403208:p.Lys619Thr		231009248	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	.	.	.	.	.	.	.	.	.	.	A	0.685	-0.796615	0.02862	.	.	ENSG00000212916	ENST00000418460	.	.	.	5.24	-1.38	0.09027	.	0.645821	0.12677	U	0.448287	T	0.33089	0.0851	M	0.63428	1.95	0.09310	N	1	B	0.17667	0.023	B	0.17433	0.018	T	0.35992	-0.9766	9	0.59425	D	0.04	-2.8639	2.553	0.04753	0.1785:0.4238:0.241:0.1567	.	477	Q9P2G4	K1383_HUMAN	T	619	.	ENSP00000403208:K619T	K	+	2	0	KIAA1383	231009248	0.000000	0.05858	0.001000	0.08648	0.051000	0.14879	-0.615000	0.05597	-0.272000	0.09259	0.533000	0.62120	AAA		0.393	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		C	232942625	A	C	232942625	3	2	61	1	0	0	0	0	1	0	0	0	8249	14	1	4	1858	4	KIAA1383	1	232942625	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	292777	232942625	16307996	1126	9111										
PCNXL2	80003	broad.mit.edu	37	chr1	233152693	233152693	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttccgtgcacagtgttGaatccattctagataaacat	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:233152693G>T	ENST00000258229.9	-	27	5047	c.4813C>A	c.(4813-4815)Caa>Aaa	p.Q1605K	PCNXL2_ENST00000344698.2_Missense_Mutation_p.Q257K	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1605						integral component of membrane (GO:0016021)		p.Q1605K(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GCACAGTGTTGAATCCATTCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											103	100	101					1																	233152693		1959	4172	6131	231219316	SO:0001583	missense	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4813C>A	1.37:g.233152693G>T	ENSP00000258229:p.Gln1605Lys		231219316	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531808	0.85706	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.22539	1.95;3.06	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.40498	0.1119	L	0.38649	1.16	0.80722	D	1	P;D	0.71674	0.902;0.998	P;D	0.77557	0.616;0.99	T	0.12682	-1.0538	10	0.87932	D	0	.	20.0471	0.97613	0.0:0.0:1.0:0.0	.	1605;257	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	K	257;1605	ENSP00000340759:Q257K;ENSP00000258229:Q1605K	ENSP00000258229:Q1605K	Q	-	1	0	PCNXL2	231219316	1.000000	0.71417	0.990000	0.47175	0.612000	0.37316	9.324000	0.96373	2.731000	0.93534	0.655000	0.94253	CAA		0.438	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		T	233152693	G	T	233152693	3	4	61	1	0	0	0	0	1	0	0	0	11623	1299	45	2	1632	2	PCNXL2	1	233152693	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210068	233152693	16097928	1127	9112										
PCNXL2	80003	broad.mit.edu	37	chr1	233161102	233161102	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctctgtcctcctcgtcGccctccatgatggcttctac	7	18	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:233161102G>A	ENST00000258229.9	-	26	4629	c.4395C>T	c.(4393-4395)ggC>ggT	p.G1465G	PCNXL2_ENST00000344698.2_Silent_p.G117G	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1465						integral component of membrane (GO:0016021)		p.G1465G(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CCTCCTCGTCGCCCTCCATGA	0.567											OREG0014326	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	1											75	83	80					1																	233161102		2182	4275	6457	231227725	SO:0001819	synonymous_variant	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4395C>T	1.37:g.233161102G>A		2363	231227725	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																				0.567	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233161102	G	A	233161102	2	1	61	1	0	0	0	0	0	0	0	1	11623	1074	38	1		1	PCNXL2	1	233161102	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8409	233161102	16089519	1128	9113										
KIAA1804	84451	broad.mit.edu	37	chr1	233490632	233490632	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcgtttgccttaattctcGaacagttgactgctattgaa	7	9	1	2	rs550700262		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:233490632G>A	ENST00000366624.3	+	4	1447	c.1186G>A	c.(1186-1188)Gaa>Aaa	p.E396K	MLK4_ENST00000366623.3_Missense_Mutation_p.E396K	NM_032435.2	NP_115811.2												p.E396K(1)									CTTAATTCTCGAACAGTTGAC	0.383													G|||	1	0.000199681	0	0	5008	,	,		18748	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											149	141	144					1																	233490632		2203	4300	6503	231557255	SO:0001583	missense	84451																														ENST00000366624.3:c.1186G>A	1.37:g.233490632G>A	ENSP00000355583:p.Glu396Lys		231557255		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	4.432	0.080016	0.08533	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.89050	-2.46;-2.46	5.22	2.25	0.28309	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.214607	0.40302	N	0.001125	T	0.72479	0.3465	N	0.11106	0.095	0.80722	D	1	B;B	0.23937	0.094;0.001	B;B	0.18561	0.022;0.002	T	0.61168	-0.7117	10	0.06494	T	0.89	.	9.2703	0.37668	0.0768:0.3482:0.5751:0.0	.	396;396	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	K	396	ENSP00000355582:E396K;ENSP00000355583:E396K	ENSP00000355582:E396K	E	+	1	0	RP5-862P8.2	231557255	1.000000	0.71417	0.586000	0.28679	0.462000	0.32619	4.433000	0.59929	0.302000	0.22762	0.655000	0.94253	GAA		0.383	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			A	233490632	G	A	233490632	3	1	61	1	0	0	0	0	1	0	0	0	8280	1059	37	1	1200	1	KIAA1804	1	233490632	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	329530	233490632	15759989	1129	9114										
KIAA1804	84451	broad.mit.edu	37	chr1	233514916	233514916	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaaagaaaacggagtcaGctctgtatgggtgcaccgtc	13	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:233514916G>T	ENST00000366624.3	+	9	2425	c.2164G>T	c.(2164-2166)Gct>Tct	p.A722S	MLK4_ENST00000366622.1_Missense_Mutation_p.A168S	NM_032435.2	NP_115811.2												p.A722S(1)									AACGGAGTCAGCTCTGTATGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	78	76					1																	233514916		2203	4300	6503	231581539	SO:0001583	missense	84451																														ENST00000366624.3:c.2164G>T	1.37:g.233514916G>T	ENSP00000355583:p.Ala722Ser		231581539		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509673	0.64522	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.39997	1.05;1.05	4.94	4.94	0.65067	.	0.079076	0.53938	D	0.000060	T	0.63628	0.2527	M	0.65975	2.015	0.44660	D	0.997643	D;P	0.76494	0.999;0.945	D;P	0.71656	0.974;0.65	T	0.66204	-0.5982	10	0.62326	D	0.03	.	18.3695	0.90402	0.0:0.0:1.0:0.0	.	169;722	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	S	722;168	ENSP00000355583:A722S;ENSP00000355581:A168S	ENSP00000355581:A168S	A	+	1	0	RP5-862P8.2	231581539	1.000000	0.71417	0.103000	0.21229	0.013000	0.08279	6.445000	0.73456	2.570000	0.86706	0.650000	0.86243	GCT		0.552	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233514916	G	T	233514916	3	4	61	1	0	0	0	0	1	0	0	0	8280	971	34	2	2198	2	KIAA1804	1	233514916	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24284	233514916	15735705	1130	9115										
SLC35F3	148641	broad.mit.edu	37	chr1	234367368	234367368	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgaccttcaggaagttCgacgcgcccttcaccctcac	8	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:234367368C>T	ENST00000366617.3	+	2	510	c.282C>T	c.(280-282)ttC>ttT	p.F94F	SLC35F3_ENST00000366618.3_Silent_p.F163F			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	94					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)		p.F163F(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			TCAGGAAGTTCGACGCGCCCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	1											173	149	157					1																	234367368		2203	4300	6503	232433991	SO:0001819	synonymous_variant	148641				CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"Solute carriers"	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366617.3:c.282C>T	1.37:g.234367368C>T			232433991	Q5TDD6|Q8N9C9	Silent	SNP	ENST00000366617.3	37																																																																																					0.587	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	NM_173508		T	234367368	C	T	234367368	2	4	61	1	0	0	0	0	0	0	0	1	14627	883	31	1		1	SLC35F3	1	234367368	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	852452	234367368	14883253	1131	9116										
RBM34	23029	broad.mit.edu	37	chr1	235324364	235324364	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccggcggactcccgcgaacGccgtcgtcaggattctctct	11	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235324364G>A	ENST00000408888.3	-	2	302	c.72C>T	c.(70-72)ggC>ggT	p.G24G	RBM34_ENST00000366606.3_Silent_p.G19G			P42696	RBM34_HUMAN	RNA binding motif protein 34	24						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G24G(1)		central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			TCCCGCGAACGCCGTCGTCAG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	1											40	48	46					1																	235324364		2073	4188	6261	233390987	SO:0001819	synonymous_variant	23029				CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.72C>T	1.37:g.235324364G>A			233390987	A8K8J7|Q8N2Z8|Q9H5A1	Silent	SNP	ENST00000408888.3	37	CCDS41477.2																																																																																				0.612	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235324364	G	A	235324364	2	1	61	1	0	0	0	0	0	0	0	1	13168	1074	38	1		1	RBM34	1	235324364	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	956996	235324364	13926257	1132	9117										
ARID4B	51742	broad.mit.edu	37	chr1	235388051	235388051	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttgtacaattgctgaaGaaagttctccctttcttctg	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235388051G>T	ENST00000264183.3	-	12	1434	c.937C>A	c.(937-939)Ctt>Att	p.L313I	ARID4B_ENST00000349213.3_Missense_Mutation_p.L313I|ARID4B_ENST00000366603.2_Missense_Mutation_p.L313I	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	313	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.|Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L313I(2)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			AATTGCTGAAGAAAGTTCTCC	0.269																																																2	Substitution - Missense(2)	large_intestine(2)	1											52	53	53					1																	235388051		2200	4292	6492	233454674	SO:0001583	missense	51742			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"-"	15550	protein-coding gene	gene with protein product		609696	"retinoblastoma binding protein 1-like 1", "AT rich interactive domain 4B (RBP1- like)"	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.937C>A	1.37:g.235388051G>T	ENSP00000264183:p.Leu313Ile		233454674	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411615	0.83340	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.45	5.45	0.79879	ARID/BRIGHT DNA-binding domain (5);	0.056505	0.64402	D	0.000001	T	0.79811	0.4510	L	0.52905	1.665	0.80722	D	1	D;D;D	0.71674	0.998;0.996;0.996	D;D;D	0.80764	0.99;0.994;0.973	T	0.80079	-0.1532	10	0.62326	D	0.03	-11.0695	19.6409	0.95757	0.0:0.0:1.0:0.0	.	313;313;313	Q4LE39-3;Q4LE39-2;Q4LE39	.;.;ARI4B_HUMAN	I	313	ENSP00000264184:L313I;ENSP00000355562:L313I;ENSP00000264183:L313I;ENSP00000391497:L313I	ENSP00000264183:L313I	L	-	1	0	ARID4B	233454674	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	7.341000	0.79300	2.717000	0.92951	0.650000	0.86243	CTT		0.269	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		T	235388051	G	T	235388051	3	4	61	1	0	0	0	0	1	0	0	0	920	942	33	2	3053	2	ARID4B	1	235388051	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63687	235388051	13862570	1133	9118										
GGPS1	9453	broad.mit.edu	37	chr1	235505820	235505820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatctgacagagggaaaGttctcatttcctactattca	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235505820G>T	ENST00000282841.5	+	4	868	c.636G>T	c.(634-636)aaG>aaT	p.K212N	GGPS1_ENST00000358966.2_Missense_Mutation_p.K212N|GGPS1_ENST00000391855.2_Missense_Mutation_p.K158N|GGPS1_ENST00000488594.1_Missense_Mutation_p.K212N|GGPS1_ENST00000476121.1_Missense_Mutation_p.K212N			O95749	GGPPS_HUMAN	geranylgeranyl diphosphate synthase 1	212					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|geranylgeranyl diphosphate biosynthetic process (GO:0033386)|isoprenoid metabolic process (GO:0006720)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	dimethylallyltranstransferase activity (GO:0004161)|farnesyltranstransferase activity (GO:0004311)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)	p.K212N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;1.39e-05)		Zoledronate(DB00399)	CAGAGGGAAAGTTCTCATTTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	86	84					1																	235505820		2203	4300	6503	233572443	SO:0001583	missense	9453			AB016043	CCDS1604.1	1q43	2010-04-27			ENSG00000152904	ENSG00000152904	2.5.1.1, 2.5.1.10, 2.5.1.29		4249	protein-coding gene	gene with protein product		606982				9741684, 10101267	Standard	NR_036605		Approved	GGPPS1	uc001hwv.3	O95749	OTTHUMG00000037963	ENST00000282841.5:c.636G>T	1.37:g.235505820G>T	ENSP00000282841:p.Lys212Asn		233572443	A8MVQ8|Q5T2C8|Q6NW19	Missense_Mutation	SNP	ENST00000282841.5	37	CCDS1604.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628163	0.66901	.	.	ENSG00000152904	ENST00000488594;ENST00000471812;ENST00000358966;ENST00000282841;ENST00000391855;ENST00000476121;ENST00000497327	T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	6.17	1.13	0.20643	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	D	0.87661	0.6233	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85269	0.1055	10	0.87932	D	0	-18.2081	7.5513	0.27798	0.2424:0.1093:0.6483:0.0	.	212	O95749	GGPPS_HUMAN	N	212;212;212;212;158;212;212	ENSP00000418690:K212N;ENSP00000417772:K212N;ENSP00000351852:K212N;ENSP00000282841:K212N;ENSP00000375728:K158N;ENSP00000420183:K212N;ENSP00000417865:K212N	ENSP00000282841:K212N	K	+	3	2	GGPS1	233572443	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	2.474000	0.45154	-0.027000	0.13873	0.655000	0.94253	AAG		0.368	GGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092656.1	NM_004837		T	235505820	G	T	235505820	3	4	61	1	0	0	0	0	1	0	0	0	6380	1020	36	2	646	2	GGPS1	1	235505820	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117769	235505820	13744801	1134	9119										
GNG4	2786	broad.mit.edu	37	chr1	235715441	235715441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaagaacttcttctcgcGaaaggggttttctgatgcag	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235715441G>A	ENST00000366598.4	-	3	411	c.196C>T	c.(196-198)Cgc>Tgc	p.R66C	GNG4_ENST00000391854.2_Missense_Mutation_p.R66C|GNG4_ENST00000366597.1_Missense_Mutation_p.R66C|GNG4_ENST00000450593.1_Missense_Mutation_p.R66C|GNG4_ENST00000484517.1_5'UTR			P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein), gamma 4	66					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell growth (GO:0030308)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)	p.R66C(2)		NS(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			TTCTTCTCGCGAAAGGGGTTT	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	1											166	164	165					1																	235715441		2203	4300	6503	233782064	SO:0001583	missense	2786			BC022485	CCDS1607.1	1q42.3	2008-02-05			ENSG00000168243	ENSG00000168243			4407	protein-coding gene	gene with protein product		604388				7665596	Standard	NM_001098721		Approved		uc001hxh.4	P50150	OTTHUMG00000040740	ENST00000366598.4:c.196C>T	1.37:g.235715441G>A	ENSP00000355557:p.Arg66Cys		233782064		Missense_Mutation	SNP	ENST00000366598.4	37	CCDS1607.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.651009	0.67472	.	.	ENSG00000168243	ENST00000450593;ENST00000391854;ENST00000366598;ENST00000366597	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.75	2.66	0.31614	G-protein gamma domain (5);	0.000000	0.64402	D	0.000001	T	0.48750	0.1517	.	.	.	0.44825	D	0.997832	D	0.89917	1.0	D	0.69824	0.966	T	0.56147	-0.8027	9	0.87932	D	0	-14.4191	12.4754	0.55809	0.0:0.0:0.5693:0.4307	.	66	P50150	GBG4_HUMAN	C	66	ENSP00000398629:R66C;ENSP00000375727:R66C;ENSP00000355557:R66C;ENSP00000355556:R66C	ENSP00000355556:R66C	R	-	1	0	GNG4	233782064	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.563000	0.45922	1.177000	0.42855	0.561000	0.74099	CGC		0.517	GNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097906.1	NM_004485		A	235715441	G	A	235715441	3	1	61	1	0	0	0	0	1	0	0	0	6549	1058	37	1	35	1	GNG4	1	235715441	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	209621	235715441	13535180	1135	9120										
LYST	1130	broad.mit.edu	37	chr1	235826273	235826273	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgctaaggaaggaataGaacattggctgtttcaagcg	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235826273G>T	ENST00000389794.3	-	53	11547	c.11373C>A	c.(11371-11373)ttC>ttA	p.F3791L	LYST_ENST00000389793.2_Missense_Mutation_p.F3791L|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3791					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.F3791L(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GGAAGGAATAGAACATTGGCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	134	133					1																	235826273		2203	4300	6503	233892896	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.11373C>A	1.37:g.235826273G>T	ENSP00000374444:p.Phe3791Leu		233892896	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	35	5.570407	0.96540	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.62941	-0.01;-0.01	5.87	5.87	0.94306	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73753	0.3627	L	0.59436	1.845	0.80722	D	1	D	0.54397	0.966	P	0.57283	0.817	T	0.69525	-0.5122	10	0.35671	T	0.21	.	20.2033	0.98269	0.0:0.0:1.0:0.0	.	3791	Q99698	LYST_HUMAN	L	3791	ENSP00000374444:F3791L;ENSP00000374443:F3791L	ENSP00000374443:F3791L	F	-	3	2	LYST	233892896	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.573000	0.67417	2.779000	0.95612	0.655000	0.94253	TTC		0.468	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235826273	G	T	235826273	3	4	61	1	0	0	0	0	1	0	0	0	9158	933	33	2	36	2	LYST	1	235826273	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110832	235826273	13424348	1136	9121										
LYST	1130	broad.mit.edu	37	chr1	235972610	235972610	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaatgagaatattcacatCgtctgtgcctttttcttgta	6	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235972610C>T	ENST00000389794.3	-	5	1682	c.1508G>A	c.(1507-1509)cGa>cAa	p.R503Q	LYST_ENST00000389793.2_Missense_Mutation_p.R503Q|LYST_ENST00000536965.1_Missense_Mutation_p.R503Q			Q99698	LYST_HUMAN	lysosomal trafficking regulator	503					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.R503Q(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATATTCACATCGTCTGTGCCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	111	111					1																	235972610		2203	4300	6503	234039233	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.1508G>A	1.37:g.235972610C>T	ENSP00000374444:p.Arg503Gln		234039233	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502589	0.85176	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.15372	2.43;2.43;2.43	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.42562	0.1208	M	0.64997	1.995	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.21895	-1.0232	10	0.66056	D	0.02	.	19.2976	0.94129	0.0:1.0:0.0:0.0	.	503;503	Q99698-3;Q99698	.;LYST_HUMAN	Q	503	ENSP00000374444:R503Q;ENSP00000374443:R503Q;ENSP00000438315:R503Q	ENSP00000374443:R503Q	R	-	2	0	LYST	234039233	1.000000	0.71417	0.651000	0.29564	0.945000	0.59286	7.487000	0.81328	2.547000	0.85894	0.650000	0.86243	CGA		0.368	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235972610	C	T	235972610	3	4	61	1	0	0	0	0	1	0	0	0	9158	884	31	1	10093	1	LYST	1	235972610	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146337	235972610	13278011	1137	9122										
LYST	1130	broad.mit.edu	37	chr1	235972904	235972904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatctgaagaactccttccAaaagctcaggtaaaagaagg	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235972904A>G	ENST00000389794.3	-	5	1388	c.1214T>C	c.(1213-1215)tTg>tCg	p.L405S	LYST_ENST00000389793.2_Missense_Mutation_p.L405S|LYST_ENST00000536965.1_Missense_Mutation_p.L405S			Q99698	LYST_HUMAN	lysosomal trafficking regulator	405					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.L405S(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AACTCCTTCCAAAAGCTCAGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											95	100	98					1																	235972904		2203	4300	6503	234039527	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.1214T>C	1.37:g.235972904A>G	ENSP00000374444:p.Leu405Ser		234039527	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	18.82	3.706093	0.68615	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.72505	-0.66;-0.66;2.51	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	D	0.82337	0.5015	M	0.64997	1.995	0.53005	D	0.99996	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.941	D	0.84334	0.0523	10	0.87932	D	0	.	15.7025	0.77552	1.0:0.0:0.0:0.0	.	405;405	Q99698-3;Q99698	.;LYST_HUMAN	S	405	ENSP00000374444:L405S;ENSP00000374443:L405S;ENSP00000438315:L405S	ENSP00000374443:L405S	L	-	2	0	LYST	234039527	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.111000	0.64477	0.482000	0.46254	TTG		0.408	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235972904	A	G	235972904	3	3	61	1	0	0	0	0	1	0	0	0	9158	131	5	4	10387	4	LYST	1	235972904	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	294	235972904	13277717	1138	9123										
LYST	1130	broad.mit.edu	37	chr1	235973133	235973133	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaagatgcaacactgttcGaaagagcatcctttgaatca	8	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235973133G>A	ENST00000389794.3	-	5	1159	c.985C>T	c.(985-987)Cga>Tga	p.R329*	LYST_ENST00000389793.2_Nonsense_Mutation_p.R329*|LYST_ENST00000536965.1_Nonsense_Mutation_p.R329*			Q99698	LYST_HUMAN	lysosomal trafficking regulator	329					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.R329R(1)|p.R329*(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AACACTGTTCGAAAGAGCATC	0.438																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1											46	44	45					1																	235973133		2203	4300	6503	234039756	SO:0001587	stop_gained	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.985C>T	1.37:g.235973133G>A	ENSP00000374444:p.Arg329*		234039756	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Nonsense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	39	7.905411	0.98554	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	.	.	.	5.49	2.35	0.29111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.3614	0.38197	0.0679:0.0:0.5627:0.3693	.	.	.	.	X	329	.	ENSP00000374443:R329X	R	-	1	2	LYST	234039756	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.688000	0.54699	0.747000	0.32809	0.655000	0.94253	CGA		0.438	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235973133	G	A	235973133	4	1	61	1	0	0	0	0	0	1	0	0	9158	1066	37	1	10616	1	LYST	1	235973133	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229	235973133	13277488	1139	9124										
LYST	1130	broad.mit.edu	37	chr1	235973720	235973720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacatttacttttgcagaaAcctgactagacagggcactt	7	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:235973720A>G	ENST00000389794.3	-	5	572	c.398T>C	c.(397-399)gTt>gCt	p.V133A	LYST_ENST00000389793.2_Missense_Mutation_p.V133A|LYST_ENST00000536965.1_Missense_Mutation_p.V133A			Q99698	LYST_HUMAN	lysosomal trafficking regulator	133					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.V133A(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTTTGCAGAAACCTGACTAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	89	88					1																	235973720		2203	4300	6503	234040343	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.398T>C	1.37:g.235973720A>G	ENSP00000374444:p.Val133Ala		234040343	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	1.483	-0.556731	0.03967	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.12672	2.66;2.66;2.66	5.8	3.31	0.37934	.	0.546063	0.20143	N	0.098323	T	0.09818	0.0241	L	0.44542	1.39	0.23113	N	0.998272	B;B	0.28233	0.204;0.0	B;B	0.30401	0.115;0.001	T	0.25984	-1.0116	10	0.33940	T	0.23	.	0.4985	0.00576	0.4422:0.2033:0.1596:0.195	.	133;133	Q99698-3;Q99698	.;LYST_HUMAN	A	133	ENSP00000374444:V133A;ENSP00000374443:V133A;ENSP00000438315:V133A	ENSP00000374443:V133A	V	-	2	0	LYST	234040343	0.233000	0.23772	1.000000	0.80357	0.957000	0.61999	1.439000	0.35013	0.996000	0.38943	0.460000	0.39030	GTT		0.398	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235973720	A	G	235973720	3	3	61	1	0	0	0	0	1	0	0	0	9158	43	2	4	11203	4	LYST	1	235973720	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	587	235973720	13276901	1140	9125										
NID1	4811	broad.mit.edu	37	chr1	236141260	236141260	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcataggtgggtgcagccGccattgttcactgagcagta	13	9	1	1	rs373795201		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236141260G>A	ENST00000264187.6	-	20	3733	c.3651C>T	c.(3649-3651)ggC>ggT	p.G1217G	NID1_ENST00000366595.3_Silent_p.G1084G	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1217	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.G1217G(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGGTGCAGCCGCCATTGTTCA	0.512													G|||	1	0.000199681	0	0	5008	,	,		16734	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	1						G		0,4406		0,0,2203	76	75	75		3651	-11.4	0.2	1		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NID1	NM_002508.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1217/1248	236141260	1,13005	2203	4300	6503	234207883	SO:0001819	synonymous_variant	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3651C>T	1.37:g.236141260G>A			234207883	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																				0.512	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236141260	G	A	236141260	2	1	61	1	0	0	0	0	0	0	0	1	10445	1074	38	1		1	NID1	1	236141260	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167540	236141260	13109361	1141	9126										
NID1	4811	broad.mit.edu	37	chr1	236143893	236143893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatcctccggttcgtgccGtccatgtaggaagtttcaat	11	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236143893G>A	ENST00000264187.6	-	17	3370	c.3288C>T	c.(3286-3288)gaC>gaT	p.D1096D	NID1_ENST00000366595.3_Silent_p.D963D	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1096					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.D1096D(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGTTCGTGCCGTCCATGTAGG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	1											95	89	91					1																	236143893		2203	4300	6503	234210516	SO:0001819	synonymous_variant	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3288C>T	1.37:g.236143893G>A			234210516	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																				0.512	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236143893	G	A	236143893	2	1	61	1	0	0	0	0	0	0	0	1	10445	1136	40	1		1	NID1	1	236143893	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2633	236143893	13106728	1142	9127										
NID1	4811	broad.mit.edu	37	chr1	236157131	236157131	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcgcccccgctgccccgaGaatgtgttctcgctcgtgct	11	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236157131G>T	ENST00000264187.6	-	13	2651	c.2569C>A	c.(2569-2571)Ctc>Atc	p.L857I	NID1_ENST00000366595.3_Missense_Mutation_p.L724I	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	857	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.L857I(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GCTGCCCCGAGAATGTGTTCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											32	33	33					1																	236157131		2203	4300	6503	234223754	SO:0001583	missense	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2569C>A	1.37:g.236157131G>T	ENSP00000264187:p.Leu857Ile		234223754	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957676	0.53400	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.68479	-0.33;-0.33	5.56	4.64	0.57946	Thyroglobulin type-1 (3);	0.124031	0.56097	D	0.000040	T	0.72779	0.3503	M	0.81942	2.565	0.20074	N	0.999935	D;B	0.61697	0.99;0.368	P;B	0.50617	0.646;0.199	T	0.69431	-0.5147	10	0.66056	D	0.02	.	9.7067	0.40220	0.1513:0.0:0.8487:0.0	.	724;857	P14543-2;P14543	.;NID1_HUMAN	I	857;724	ENSP00000264187:L857I;ENSP00000355554:L724I	ENSP00000264187:L857I	L	-	1	0	NID1	234223754	0.931000	0.31567	0.976000	0.42696	0.539000	0.34962	1.104000	0.31074	2.608000	0.88229	0.455000	0.32223	CTC		0.627	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		T	236157131	G	T	236157131	3	4	61	1	0	0	0	0	1	0	0	0	10445	942	33	2	1206	2	NID1	1	236157131	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13238	236157131	13093490	1143	9128										
NID1	4811	broad.mit.edu	37	chr1	236189352	236189352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaaggtgatggtctggcGccactggtaagtgtagatgc	16	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236189352G>A	ENST00000264187.6	-	8	1910	c.1828C>T	c.(1828-1830)Cgc>Tgc	p.R610C	NID1_ENST00000366595.3_Missense_Mutation_p.R610C	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	610	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.R610C(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	ATGGTCTGGCGCCACTGGTAA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	116	119					1																	236189352		2203	4300	6503	234255975	SO:0001583	missense	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.1828C>T	1.37:g.236189352G>A	ENSP00000264187:p.Arg610Cys		234255975	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002803	0.74932	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.32515	1.45;1.45	5.02	4.04	0.47022	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.053961	0.64402	D	0.000001	T	0.52725	0.1752	M	0.69823	2.125	0.48830	D	0.999715	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.981	T	0.55964	-0.8057	10	0.72032	D	0.01	.	13.3515	0.60605	0.0:0.0:0.7446:0.2554	.	610;610	P14543-2;P14543	.;NID1_HUMAN	C	610	ENSP00000264187:R610C;ENSP00000355554:R610C	ENSP00000264187:R610C	R	-	1	0	NID1	234255975	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.611000	0.54132	2.600000	0.87896	0.655000	0.94253	CGC		0.612	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236189352	G	A	236189352	3	1	61	1	0	0	0	0	1	0	0	0	10445	1087	38	1	1967	1	NID1	1	236189352	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32221	236189352	13061269	1144	9129										
GPR137B	7107	broad.mit.edu	37	chr1	236368476	236368476	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtcccagatcttatttCtttgacaaccctcgaagata	5	11	3	3	rs373821559		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236368476C>T	ENST00000366592.3	+	6	1108	c.1017C>T	c.(1015-1017)ttC>ttT	p.F339F	GPR137B_ENST00000477559.1_3'UTR	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	339						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)		p.F339F(1)		endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			GATCTTATTTCTTTGACAACC	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	1											210	207	208					1																	236368476		2203	4300	6503	234435099	SO:0001819	synonymous_variant	7107			AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.1017C>T	1.37:g.236368476C>T			234435099	Q53EK7|Q5TAE6|Q6FHI3	Silent	SNP	ENST00000366592.3	37	CCDS1609.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.402929	0.25291	.	.	ENSG00000077585	ENST00000454895	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	T	0.65428	0.2690	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62397	-0.6863	4	.	.	.	-37.3962	13.1354	0.59405	0.0:0.9265:0.0:0.0735	.	.	.	.	F	203	.	.	S	+	2	0	GPR137B	234435099	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.305000	0.43664	2.798000	0.96311	0.650000	0.86243	TCT		0.468	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		T	236368476	C	T	236368476	2	4	61	1	0	0	0	0	0	0	0	1	6666	912	32	3		3	GPR137B	1	236368476	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179124	236368476	12882145	1145	9130										
ERO1LB	56605	broad.mit.edu	37	chr1	236384168	236384168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagcaactatttcctgtCgggtgagttggaagccttta	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236384168C>T	ENST00000354619.5	-	15	1508	c.1307G>A	c.(1306-1308)cGa>cAa	p.R436Q	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	436					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)	p.R436Q(1)		NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TATTTCCTGTCGGGTGAGTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	93	92					1																	236384168		2203	4300	6503	234450791	SO:0001583	missense	56605			AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.1307G>A	1.37:g.236384168C>T	ENSP00000346635:p.Arg436Gln		234450791	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	C	30	5.054482	0.93793	.	.	ENSG00000086619	ENST00000354619;ENST00000264181	T;T	0.56776	0.44;0.44	5.12	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.76962	0.4061	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82502	-0.0425	10	0.72032	D	0.01	-11.9086	13.9587	0.64166	0.0:0.9248:0.0:0.0752	.	436	Q86YB8	ERO1B_HUMAN	Q	436;161	ENSP00000346635:R436Q;ENSP00000264181:R161Q	ENSP00000264181:R161Q	R	-	2	0	ERO1LB	234450791	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.650000	0.67944	2.397000	0.81536	0.579000	0.79373	CGA		0.368	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		T	236384168	C	T	236384168	3	4	61	1	0	0	0	0	1	0	0	0	5253	884	31	1	104	1	ERO1LB	1	236384168	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15692	236384168	12866453	1146	9131										
ERO1LB	56605	broad.mit.edu	37	chr1	236385268	236385268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtcacatccaacacagtCcattatacgggagatattct	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236385268C>T	ENST00000354619.5	-	14	1366	c.1165G>A	c.(1165-1167)Gac>Aac	p.D389N		NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	389					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)	p.D389N(2)		NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	CCAACACAGTCCATTATACGG	0.343																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	1											105	103	104					1																	236385268		2203	4300	6503	234451891	SO:0001583	missense	56605			AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.1165G>A	1.37:g.236385268C>T	ENSP00000346635:p.Asp389Asn		234451891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	C	36	5.734211	0.96865	.	.	ENSG00000086619	ENST00000354619;ENST00000264181	T;T	0.58506	0.33;0.33	5.79	5.79	0.91817	.	0.044204	0.85682	D	0.000000	T	0.79293	0.4421	M	0.82323	2.585	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.79072	-0.1953	10	0.48119	T	0.1	-23.0621	20.0275	0.97527	0.0:1.0:0.0:0.0	.	389	Q86YB8	ERO1B_HUMAN	N	389;114	ENSP00000346635:D389N;ENSP00000264181:D114N	ENSP00000264181:D114N	D	-	1	0	ERO1LB	234451891	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.422000	0.80217	2.737000	0.93849	0.650000	0.86243	GAC		0.343	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		T	236385268	C	T	236385268	3	4	61	1	0	0	0	0	1	0	0	0	5253	855	30	3	250	3	ERO1LB	1	236385268	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1100	236385268	12865353	1147	9132										
ERO1LB	56605	broad.mit.edu	37	chr1	236399589	236399589	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagttacttgaaacagttCtcttcatagatgctgttcca	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236399589C>A	ENST00000354619.5	-	7	816	c.615G>T	c.(613-615)gaG>gaT	p.E205D	ERO1LB_ENST00000327333.8_3'UTR	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	205					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)	p.E205D(1)		NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TGAAACAGTTCTCTTCATAGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											144	148	146					1																	236399589		2203	4300	6503	234466212	SO:0001583	missense	56605			AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.615G>T	1.37:g.236399589C>A	ENSP00000346635:p.Glu205Asp		234466212	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065947	0.76187	.	.	ENSG00000086619	ENST00000354619	T	0.57436	0.4	5.55	0.7	0.18099	.	0.000000	0.85682	D	0.000000	T	0.71443	0.3340	M	0.90650	3.135	0.80722	D	1	D	0.64830	0.994	D	0.65443	0.935	T	0.71790	-0.4486	10	0.87932	D	0	-27.5676	9.1773	0.37120	0.0:0.2801:0.0:0.7199	.	205	Q86YB8	ERO1B_HUMAN	D	205	ENSP00000346635:E205D	ENSP00000346635:E205D	E	-	3	2	ERO1LB	234466212	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	0.585000	0.23879	-0.125000	0.11703	-0.471000	0.05019	GAG		0.537	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		A	236399589	C	A	236399589	3	1	61	1	0	0	0	0	1	0	0	0	5253	912	32	2	828	2	ERO1LB	1	236399589	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14321	236399589	12851032	1148	9133										
LGALS8	3964	broad.mit.edu	37	chr1	236711312	236711312	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtatcctttcctttcagAtgataatttattgtgatgtt	6	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236711312A>G	ENST00000366584.4	+	10	1371	c.805A>G	c.(805-807)Atg>Gtg	p.M269V	LGALS8_ENST00000526634.1_Splice_Site_p.M269V|LGALS8_ENST00000341872.6_Splice_Site_p.M269V|LGALS8_ENST00000525042.1_Splice_Site_p.M252V|LGALS8_ENST00000352231.2_Splice_Site_p.M311V|LGALS8_ENST00000526589.1_Splice_Site_p.M311V|LGALS8_ENST00000416919.2_Splice_Site_p.M252V|LGALS8_ENST00000527974.1_Splice_Site_p.M311V|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000450372.2_Splice_Site_p.M311V|LGALS8_ENST00000323938.6_Splice_Site_p.M242V	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	269	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.M311V(1)		kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTCCTTTCAGATGATAATTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											109	103	105					1																	236711312		2203	4300	6503	234777935	SO:0001630	splice_region_variant	3964			X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"Lectins, galactoside-binding"	6569	protein-coding gene	gene with protein product	"galectin 8"	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.805-1A>G	1.37:g.236711312A>G			234777935	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.515218	0.44763	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63;3.63;3.63;3.63;3.63;3.63	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.152098	0.64402	D	0.000015	T	0.04272	0.0118	L	0.28054	0.825	0.46241	D	0.998949	B;B;B	0.31581	0.329;0.073;0.329	B;B;B	0.31869	0.094;0.135;0.137	T	0.54173	-0.8333	9	.	.	.	-15.1152	11.4418	0.50100	0.8076:0.1924:0.0:0.0	.	252;269;311	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	V	311;311;311;269;311;269;310;252;242;269;252	ENSP00000431398:M311V;ENSP00000309576:M311V;ENSP00000435460:M311V;ENSP00000342139:M269V;ENSP00000408657:M311V;ENSP00000355543:M269V;ENSP00000410843:M252V;ENSP00000434860:M242V;ENSP00000437040:M269V;ENSP00000431884:M252V	.	M	+	1	0	LGALS8	234777935	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.144000	0.58057	2.212000	0.71576	0.528000	0.53228	ATG		0.363	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499	Missense_Mutation	G	236711312	A	G	236711312	5	3	61	1	0	0	0	0	0	0	1	0	8770	347	12	4	969	4	LGALS8	1	236711312	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	311723	236711312	12539309	1149	9134										
HEATR1	55127	broad.mit.edu	37	chr1	236750713	236750713	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacataccattctccattCtttgaaagttctgctctttg	4	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236750713C>A	ENST00000366582.3	-	14	1818	c.1704G>T	c.(1702-1704)aaG>aaT	p.K568N	HEATR1_ENST00000366581.2_Missense_Mutation_p.K568N	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	568					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.K568N(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ATTCTCCATTCTTTGAAAGTT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	1											43	41	42					1																	236750713		2200	4289	6489	234817336	SO:0001583	missense	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1704G>T	1.37:g.236750713C>A	ENSP00000355541:p.Lys568Asn		234817336	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880858	0.51801	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.64991	-0.13;0.69	5.58	2.6	0.31112	Armadillo-like helical (1);Armadillo-type fold (1);	0.297452	0.32769	N	0.005668	T	0.47488	0.1448	L	0.36672	1.1	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30149	-0.9988	10	0.44086	T	0.13	.	7.3438	0.26652	0.0:0.6151:0.0:0.3849	.	568	Q9H583	HEAT1_HUMAN	N	568	ENSP00000355541:K568N;ENSP00000355540:K568N	ENSP00000355540:K568N	K	-	3	2	HEATR1	234817336	0.997000	0.39634	0.967000	0.41034	0.745000	0.42441	0.596000	0.24044	0.248000	0.21435	-0.136000	0.14681	AAG		0.294	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		A	236750713	C	A	236750713	3	1	61	1	0	0	0	0	1	0	0	0	7048	912	32	2	4858	2	HEATR1	1	236750713	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39401	236750713	12499908	1150	9135										
HEATR1	55127	broad.mit.edu	37	chr1	236766479	236766479	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgaatcaaccactccaGacacttctgtgctggcttaa	7	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:236766479G>T	ENST00000366582.3	-	3	454	c.340C>A	c.(340-342)Ctg>Atg	p.L114M	HEATR1_ENST00000366579.1_Missense_Mutation_p.L114M|HEATR1_ENST00000366581.2_Missense_Mutation_p.L114M	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	114					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.L114M(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			AACCACTCCAGACACTTCTGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	110	114					1																	236766479		2203	4300	6503	234833102	SO:0001583	missense	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.340C>A	1.37:g.236766479G>T	ENSP00000355541:p.Leu114Met		234833102	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312654	0.40895	.	.	ENSG00000119285	ENST00000366582;ENST00000366581;ENST00000366579	T;T;T	0.54279	0.58;0.58;0.58	5.29	4.38	0.52667	.	0.243774	0.35525	N	0.003153	T	0.64659	0.2618	M	0.78344	2.41	0.47276	D	0.999376	D	0.59767	0.986	P	0.52627	0.704	T	0.70350	-0.4896	10	0.62326	D	0.03	.	13.8584	0.63545	0.0738:0.0:0.9262:0.0	.	114	Q9H583	HEAT1_HUMAN	M	114	ENSP00000355541:L114M;ENSP00000355540:L114M;ENSP00000355538:L114M	ENSP00000355538:L114M	L	-	1	2	HEATR1	234833102	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	3.379000	0.52440	1.239000	0.43787	-0.251000	0.11542	CTG		0.353	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236766479	G	T	236766479	3	4	61	1	0	0	0	0	1	0	0	0	7048	933	33	2	6266	2	HEATR1	1	236766479	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15766	236766479	12484142	1151	9136										
RYR2	6262	broad.mit.edu	37	chr1	237532885	237532885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacggacatgccatattgCtgcgccattcctatagtggc	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237532885C>T	ENST00000366574.2	+	6	678	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	RYR2_ENST00000360064.6_Silent_p.L119L|RYR2_ENST00000542537.1_Silent_p.L105L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	121	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.L119L(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGCCATATTGCTGCGCCATTC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											150	125	133					1																	237532885		1968	4155	6123	235599508	SO:0001819	synonymous_variant	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.361C>T	1.37:g.237532885C>T			235599508	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.458	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237532885	C	T	237532885	2	4	61	1	0	0	0	0	0	0	0	1	13806	796	28	3		3	RYR2	1	237532885	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	766406	237532885	11717736	1152	9137										
RYR2	6262	broad.mit.edu	37	chr1	237675032	237675032	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacccatgcctggtggagttCtccaagctgcctgaacagga	11	13	1	1	rs4336838		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237675032C>A	ENST00000366574.2	+	24	3080	c.2763C>A	c.(2761-2763)ttC>ttA	p.F921L	RYR2_ENST00000360064.6_Missense_Mutation_p.F919L|RYR2_ENST00000542537.1_Missense_Mutation_p.F905L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	921	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.F919L(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGGTGGAGTTCTCCAAGCTGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	56	56					1																	237675032		1902	4127	6029	235741655	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2763C>A	1.37:g.237675032C>A	ENSP00000355533:p.Phe921Leu		235741655	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.272060	0.80469	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.93076	-3.16;-3.16;-3.16	5.44	3.57	0.40892	Ryanodine receptor Ryr (1);	0.000000	0.64402	D	0.000002	D	0.94905	0.8353	M	0.86953	2.85	0.80722	D	1	P	0.48911	0.917	P	0.51016	0.656	D	0.94732	0.7910	10	0.87932	D	0	.	9.8224	0.40891	0.0:0.7826:0.0:0.2174	.	921	Q92736	RYR2_HUMAN	L	921;919;905	ENSP00000355533:F921L;ENSP00000353174:F919L;ENSP00000443798:F905L	ENSP00000353174:F919L	F	+	3	2	RYR2	235741655	0.981000	0.34729	1.000000	0.80357	0.997000	0.91878	0.517000	0.22832	1.297000	0.44761	0.655000	0.94253	TTC		0.443	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237675032	C	A	237675032	3	1	61	1	0	0	0	0	1	0	0	0	13806	912	32	2	2857	2	RYR2	1	237675032	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142147	237675032	11575589	1153	9138										
RYR2	6262	broad.mit.edu	37	chr1	237756882	237756882	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggctttgacttggacaGagttcgcacagtaacagtta	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237756882G>T	ENST00000366574.2	+	33	4699	c.4382G>T	c.(4381-4383)aGa>aTa	p.R1461I	RYR2_ENST00000360064.6_Missense_Mutation_p.R1459I|RYR2_ENST00000542537.1_Missense_Mutation_p.R1445I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1461	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.R1459I(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GACTTGGACAGAGTTCGCACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	89	92					1																	237756882		1900	4119	6019	235823505	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4382G>T	1.37:g.237756882G>T	ENSP00000355533:p.Arg1461Ile		235823505	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819784	0.71028	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.60424	0.19;0.19;0.19	4.9	3.99	0.46301	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.242826	0.33732	N	0.004609	T	0.39410	0.1077	N	0.19112	0.55	0.80722	D	1	P	0.39601	0.68	B	0.35607	0.206	T	0.40905	-0.9538	10	0.72032	D	0.01	.	9.7796	0.40640	0.1572:0.0:0.8428:0.0	.	1461	Q92736	RYR2_HUMAN	I	1461;1459;1445	ENSP00000355533:R1461I;ENSP00000353174:R1459I;ENSP00000443798:R1445I	ENSP00000353174:R1459I	R	+	2	0	RYR2	235823505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.282000	0.58971	1.265000	0.44215	0.650000	0.86243	AGA		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237756882	G	T	237756882	3	4	61	1	0	0	0	0	1	0	0	0	13806	942	33	2	4512	2	RYR2	1	237756882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81850	237756882	11493739	1154	9139										
RYR2	6262	broad.mit.edu	37	chr1	237780692	237780692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagctccaagacaatcaacGtttccgatacaacgaagtca	6	11	2	1	rs373600053		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237780692G>A	ENST00000366574.2	+	38	6139	c.5822G>A	c.(5821-5823)cGt>cAt	p.R1941H	RYR2_ENST00000360064.6_Missense_Mutation_p.R1939H|RYR2_ENST00000542537.1_Missense_Mutation_p.R1925H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1941	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.R1939H(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GACAATCAACGTTTCCGATAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	HIS/ARG	0,3966		0,0,1983	101	93	95		5822	5.4	1	1		95	1,8371		0,1,4185	no	missense	RYR2	NM_001035.2	29	0,1,6168	AA,AG,GG		0.0119,0.0,0.0081	probably-damaging	1941/4968	237780692	1,12337	1983	4186	6169	235847315	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5822G>A	1.37:g.237780692G>A	ENSP00000355533:p.Arg1941His		235847315	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346932	0.82022	0.0	1.19E-4	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.73681	-0.77;-0.77;-0.77	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000005	D	0.84492	0.5484	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.69479	0.964	D	0.84132	0.0412	10	0.46703	T	0.11	.	19.1627	0.93541	0.0:0.0:1.0:0.0	.	1941	Q92736	RYR2_HUMAN	H	1941;1939;1925	ENSP00000355533:R1941H;ENSP00000353174:R1939H;ENSP00000443798:R1925H	ENSP00000353174:R1939H	R	+	2	0	RYR2	235847315	0.960000	0.32886	0.963000	0.40424	0.982000	0.71751	4.064000	0.57506	2.517000	0.84864	0.650000	0.86243	CGT		0.473	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237780692	G	A	237780692	3	1	61	1	0	0	0	0	1	0	0	0	13806	1145	40	1	5972	1	RYR2	1	237780692	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23810	237780692	11469929	1155	9140										
RYR2	6262	broad.mit.edu	37	chr1	237895389	237895389	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagatgaaggcactaagaGagttgatcctctacatcagc	10	8	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237895389G>T	ENST00000366574.2	+	78	11296	c.10979G>T	c.(10978-10980)aGa>aTa	p.R3660I	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.R3658I|RYR2_ENST00000542537.1_Missense_Mutation_p.R3644I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3660					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.R3658I(2)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGCACTAAGAGAGTTGATCCT	0.398																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	1											110	108	109					1																	237895389		1851	4085	5936	235962012	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10979G>T	1.37:g.237895389G>T	ENSP00000355533:p.Arg3660Ile		235962012	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.310528	0.40895	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96587	-4.06;-4.04;-4.06	5.62	2.27	0.28462	.	0.215362	0.31636	N	0.007317	D	0.90195	0.6935	N	0.14661	0.345	0.80722	D	1	P;P	0.44344	0.833;0.698	B;B	0.41271	0.352;0.156	D	0.87856	0.2661	10	0.66056	D	0.02	-11.2005	7.7813	0.29066	0.2126:0.1252:0.6621:0.0	.	615;3660	B4DGV4;Q92736	.;RYR2_HUMAN	I	3660;3658;3644;615	ENSP00000355533:R3660I;ENSP00000353174:R3658I;ENSP00000443798:R3644I	ENSP00000353174:R3658I	R	+	2	0	RYR2	235962012	1.000000	0.71417	0.995000	0.50966	0.669000	0.39330	3.984000	0.56923	0.734000	0.32515	0.655000	0.94253	AGA		0.398	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237895389	G	T	237895389	3	4	61	1	0	0	0	0	1	0	0	0	13806	942	33	2	11289	2	RYR2	1	237895389	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114697	237895389	11355232	1156	9141										
RYR2	6262	broad.mit.edu	37	chr1	237947717	237947717	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggggccgaggatggctttCttctccattctgacggtcag	13	11	4	1	rs373606009	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:237947717C>A	ENST00000366574.2	+	90	13022	c.12705C>A	c.(12703-12705)ttC>ttA	p.F4235L	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.F4241L|RYR2_ENST00000542537.1_Missense_Mutation_p.F4219L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4235					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.F4233L(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGATGGCTTTCTTCTCCATTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											56	62	60					1																	237947717		1968	4149	6117	236014340	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12705C>A	1.37:g.237947717C>A	ENSP00000355533:p.Phe4235Leu		236014340	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	1.126	-0.653753	0.03480	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96522	-4.04;-4.04;-4.04	5.11	4.12	0.48240	.	0.163221	0.38959	N	0.001502	D	0.88955	0.6578	N	0.05306	-0.075	0.80722	D	1	B;B	0.13594	0.008;0.001	B;B	0.10450	0.005;0.001	D	0.84305	0.0507	10	0.23891	T	0.37	.	11.6494	0.51279	0.0:0.8615:0.0:0.1385	.	1209;4235	B4DGV4;Q92736	.;RYR2_HUMAN	L	4235;4241;4219;1209	ENSP00000355533:F4235L;ENSP00000353174:F4241L;ENSP00000443798:F4219L	ENSP00000353174:F4241L	F	+	3	2	RYR2	236014340	0.998000	0.40836	0.999000	0.59377	0.021000	0.10359	1.201000	0.32259	2.657000	0.90304	0.655000	0.94253	TTC		0.542	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237947717	C	A	237947717	3	1	61	1	0	0	0	0	1	0	0	0	13806	912	32	2	13063	2	RYR2	1	237947717	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52328	237947717	11302904	1157	9142										
ZP4	57829	broad.mit.edu	37	chr1	238050102	238050102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcacgagtgacagagccacGgctcccatttttcacatccc	8	15	2	2	rs367738455		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:238050102G>A	ENST00000366570.4	-	6	966	c.808C>T	c.(808-810)Cgt>Tgt	p.R270C	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	270	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)	p.R270C(1)		breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACAGAGCCACGGCTCCCATTT	0.483																																					NSCLC(166;160 2029 11600 18754 19936)											1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	0,4406		0,0,2203	173	157	163		808	-0.9	0	1		163	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZP4	NM_021186.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	270/541	238050102	1,13005	2203	4300	6503	236116725	SO:0001583	missense	57829			U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.808C>T	1.37:g.238050102G>A	ENSP00000355529:p.Arg270Cys		236116725	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632956	0.47049	0.0	1.16E-4	ENSG00000116996	ENST00000366570	D	0.82433	-1.61	4.96	-0.865	0.10662	Zona pellucida sperm-binding protein (3);	0.666723	0.13728	N	0.366904	T	0.81230	0.4779	L	0.61218	1.895	0.09310	N	1	D	0.58970	0.984	P	0.52386	0.697	T	0.69989	-0.4995	10	0.45353	T	0.12	-0.2781	3.3005	0.06982	0.0861:0.3789:0.2562:0.2789	.	270	Q12836	ZP4_HUMAN	C	270	ENSP00000355529:R270C	ENSP00000355529:R270C	R	-	1	0	ZP4	236116725	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.221000	0.17680	-0.133000	0.11537	-0.152000	0.13540	CGT		0.483	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			A	238050102	G	A	238050102	3	1	61	1	0	0	0	0	1	0	0	0	18257	1116	39	1	842	1	ZP4	1	238050102	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102385	238050102	11200519	1158	9143										
ZP4	57829	broad.mit.edu	37	chr1	238051678	238051678	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtttccatagtagcagGaattcacctcttcagagcta	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:238051678G>T	ENST00000366570.4	-	4	691	c.533C>A	c.(532-534)tCc>tAc	p.S178Y	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	178	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)	p.S178F(1)|p.S178Y(1)		breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ATAGTAGCAGGAATTCACCTC	0.507																																					NSCLC(166;160 2029 11600 18754 19936)											2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	1											129	109	116					1																	238051678		2203	4300	6503	236118301	SO:0001583	missense	57829			U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.533C>A	1.37:g.238051678G>T	ENSP00000355529:p.Ser178Tyr		236118301	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	G	3.652	-0.071393	0.07228	.	.	ENSG00000116996	ENST00000366570	T	0.54479	0.57	4.98	3.1	0.35709	P-type trefoil (5);	0.445538	0.23993	N	0.042554	T	0.33876	0.0878	N	0.25890	0.77	0.24084	N	0.995933	B	0.14805	0.011	B	0.27608	0.081	T	0.30268	-0.9984	10	0.02654	T	1	-10.9002	9.1251	0.36810	0.1792:0.0:0.8208:0.0	.	178	Q12836	ZP4_HUMAN	Y	178	ENSP00000355529:S178Y	ENSP00000355529:S178Y	S	-	2	0	ZP4	236118301	0.993000	0.37304	0.762000	0.31397	0.144000	0.21451	2.701000	0.47094	0.493000	0.27837	0.655000	0.94253	TCC		0.507	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238051678	G	T	238051678	3	4	61	1	0	0	0	0	1	0	0	0	18257	1174	41	2	1125	2	ZP4	1	238051678	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1576	238051678	11198943	1159	9144										
RGS7	6000	broad.mit.edu	37	chr1	240966210	240966210	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaaaccagtacctttttCtttgcctgtagaagctcctg	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:240966210C>A	ENST00000407727.1	-	15	1352	c.1353G>T	c.(1351-1353)aaG>aaT	p.K451N	RGS7_ENST00000348120.2_Missense_Mutation_p.K398N|RGS7_ENST00000366562.4_Missense_Mutation_p.K451N|RGS7_ENST00000331110.7_Missense_Mutation_p.K425N|RGS7_ENST00000446183.2_Missense_Mutation_p.K367N|RGS7_ENST00000366564.1_Missense_Mutation_p.K451N|RGS7_ENST00000366563.1_Missense_Mutation_p.K451N|RGS7_ENST00000366565.1_Missense_Mutation_p.K451N|RGS7_ENST00000401882.1_Missense_Mutation_p.K398N			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	451					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.K451N(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GTACCTTTTTCTTTGCCTGTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	134	130					1																	240966210		2203	4300	6503	239032833	SO:0001583	missense	6000			BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1353G>T	1.37:g.240966210C>A	ENSP00000384428:p.Lys451Asn		239032833	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	37		.	.	.	.	.	.	.	.	.	.	C	20.8	4.054397	0.75960	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.35048	1.46;1.49;1.46;1.45;1.33;1.45;1.46;1.46;1.49;1.45	6.04	6.04	0.98038	.	0.090164	0.85682	D	0.000000	T	0.40448	0.1117	N	0.19112	0.55	0.58432	D	0.999999	P;P;D;P;D;P;P	0.59357	0.749;0.749;0.985;0.837;0.975;0.523;0.749	B;B;P;P;P;B;B	0.60473	0.412;0.434;0.856;0.617;0.875;0.433;0.412	T	0.12578	-1.0542	10	0.40728	T	0.16	.	12.8339	0.57761	0.0:0.9264:0.0:0.0736	.	367;425;398;451;451;451;451	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	N	425;451;451;451;282;398;367;451;451;398	ENSP00000331485:K425N;ENSP00000355523:K451N;ENSP00000355522:K451N;ENSP00000355521:K451N;ENSP00000404399:K282N;ENSP00000341242:K398N;ENSP00000390138:K367N;ENSP00000355520:K451N;ENSP00000384428:K451N;ENSP00000385508:K398N	ENSP00000331485:K425N	K	-	3	2	RGS7	239032833	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.959000	0.63666	2.873000	0.98535	0.563000	0.77884	AAG		0.363	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		A	240966210	C	A	240966210	3	1	61	1	0	0	0	0	1	0	0	0	13347	912	32	2	122	2	RGS7	1	240966210	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2914532	240966210	8284411	1160	9145										
RGS7	6000	broad.mit.edu	37	chr1	240978044	240978044	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttttgacatttttaaccGatgtctatctaactgtattt	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:240978044G>A	ENST00000407727.1	-	11	816	c.817C>T	c.(817-819)Cgg>Tgg	p.R273W	RGS7_ENST00000348120.2_Missense_Mutation_p.R220W|RGS7_ENST00000366562.4_Missense_Mutation_p.R273W|RGS7_ENST00000331110.7_Missense_Mutation_p.R247W|RGS7_ENST00000446183.2_Missense_Mutation_p.R189W|RGS7_ENST00000366564.1_Missense_Mutation_p.R273W|RGS7_ENST00000366563.1_Missense_Mutation_p.R273W|RGS7_ENST00000366565.1_Missense_Mutation_p.R273W|RGS7_ENST00000401882.1_Missense_Mutation_p.R220W			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	273	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.R273W(2)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			ATTTTTAACCGATGTCTATCT	0.289																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	1											111	115	113					1																	240978044		2203	4298	6501	239044667	SO:0001583	missense	6000			BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.817C>T	1.37:g.240978044G>A	ENSP00000384428:p.Arg273Trp		239044667	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	37		.	.	.	.	.	.	.	.	.	.	G	21.4	4.140656	0.77775	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37	6.06	6.06	0.98353	G-protein gamma domain (4);	0.000000	0.85682	D	0.000000	T	0.49712	0.1573	L	0.50333	1.59	0.58432	D	0.999993	D;D;D;D;D;P;D	0.89917	0.997;0.999;0.999;0.997;1.0;0.473;0.999	P;D;D;D;D;B;D	0.70016	0.892;0.93;0.944;0.913;0.963;0.118;0.967	T	0.41431	-0.9509	10	0.40728	T	0.16	-13.0511	9.3859	0.38342	0.0723:0.0:0.7831:0.1446	.	189;247;220;273;273;273;273	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	W	247;273;273;273;104;220;189;273;273;220	ENSP00000331485:R247W;ENSP00000355523:R273W;ENSP00000355522:R273W;ENSP00000355521:R273W;ENSP00000404399:R104W;ENSP00000341242:R220W;ENSP00000390138:R189W;ENSP00000355520:R273W;ENSP00000384428:R273W;ENSP00000385508:R220W	ENSP00000331485:R247W	R	-	1	2	RGS7	239044667	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.069000	0.57541	2.882000	0.98803	0.655000	0.94253	CGG		0.289	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		A	240978044	G	A	240978044	3	1	61	1	0	0	0	0	1	0	0	0	13347	1057	37	1	674	1	RGS7	1	240978044	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11834	240978044	8272577	1161	9146										
FH	2271	broad.mit.edu	37	chr1	241669400	241669400	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccagctgcgagctcataGattcttggcatggcagcttt	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241669400G>T	ENST00000366560.3	-	6	845	c.807C>A	c.(805-807)atC>atA	p.I269I		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	269					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)	p.I269I(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		CGAGCTCATAGATTCTTGGCA	0.378			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	1	Substitution - coding silent(1)	large_intestine(1)	1											107	107	107					1																	241669400		2203	4300	6503	239736023	SO:0001819	synonymous_variant	2271	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.807C>A	1.37:g.241669400G>T			239736023	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																				0.378	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		T	241669400	G	T	241669400	2	4	61	1	0	0	0	0	0	0	0	1	5894	932	33	2		2	FH	1	241669400	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	691356	241669400	7581221	1162	9147										
FH	2271	broad.mit.edu	37	chr1	241675354	241675354	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaattgctctattgctaatGacttcatttacattcatatt	3	8	4	1	rs202061330		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241675354G>A	ENST00000366560.3	-	4	506	c.468C>T	c.(466-468)gtC>gtT	p.V156V	FH_ENST00000493477.1_5'Flank	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	156					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)	p.V156V(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TATTGCTAATGACTTCATTTA	0.393			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	1	Substitution - coding silent(1)	large_intestine(1)	1											215	194	201					1																	241675354		2203	4300	6503	239741977	SO:0001819	synonymous_variant	2271	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.468C>T	1.37:g.241675354G>A			239741977	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																				0.393	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241675354	G	A	241675354	2	1	61	1	0	0	0	0	0	0	0	1	5894	1277	45	3		3	FH	1	241675354	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5954	241675354	7575267	1163	9148										
KMO	8564	broad.mit.edu	37	chr1	241750008	241750008	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagactgcttggtatttgatGagttaatggataaattcagt	10	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241750008G>A	ENST00000366559.4	+	11	1296	c.985G>A	c.(985-987)Gag>Aag	p.E329K	KMO_ENST00000366558.3_Missense_Mutation_p.E329K|KMO_ENST00000366557.4_Missense_Mutation_p.E329K	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)									p.E329K(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			GGTATTTGATGAGTTAATGGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											124	123	123					1																	241750008		2203	4300	6503	239816631	SO:0001583	missense	8564			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.985G>A	1.37:g.241750008G>A	ENSP00000355517:p.Glu329Lys		239816631		Missense_Mutation	SNP	ENST00000366559.4	37	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	G	35	5.591903	0.96590	.	.	ENSG00000117009	ENST00000366559;ENST00000366558;ENST00000366557	T;T;T	0.46451	0.87;0.87;0.87	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.65657	0.2712	M	0.78285	2.405	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.996	D;D;D	0.68483	0.958;0.934;0.929	T	0.66312	-0.5955	10	0.62326	D	0.03	.	16.3795	0.83443	0.0:0.0:1.0:0.0	.	329;329;329	O15229;A8K693;O15229-2	KMO_HUMAN;.;.	K	329	ENSP00000355517:E329K;ENSP00000355516:E329K;ENSP00000355515:E329K	ENSP00000355515:E329K	E	+	1	0	KMO	239816631	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.106000	0.89555	2.941000	0.99782	0.655000	0.94253	GAG		0.313	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679		A	241750008	G	A	241750008	3	1	61	1	0	0	0	0	1	0	0	0	8445	1291	45	3	1027	3	KMO	1	241750008	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74654	241750008	7500613	1164	9149										
KMO	8564	broad.mit.edu	37	chr1	241752099	241752099	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatcccagatgatcacgcGatttcagacctatccatgta	7	11	2	4	rs566876281		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241752099G>A	ENST00000366559.4	+	12	1376	c.1065G>A	c.(1063-1065)gcG>gcA	p.A355A	KMO_ENST00000366558.3_Silent_p.A355A|KMO_ENST00000366557.4_Silent_p.A355A	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)									p.A355A(3)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			ATGATCACGCGATTTCAGACC	0.363																																																3	Substitution - coding silent(3)	large_intestine(3)	1											182	168	173					1																	241752099		2203	4300	6503	239818722	SO:0001819	synonymous_variant	8564			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.1065G>A	1.37:g.241752099G>A			239818722		Silent	SNP	ENST00000366559.4	37	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	G	1.302	-0.604681	0.03717	.	.	ENSG00000117009	ENST00000366555	.	.	.	6.06	-8.99	0.00751	.	.	.	.	.	T	0.46190	0.1380	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53528	-0.8426	4	.	.	.	.	7.579	0.27952	0.3432:0.3067:0.3501:0.0	.	.	.	.	N	41	.	.	D	+	1	0	KMO	239818722	0.000000	0.05858	0.279000	0.24732	0.059000	0.15707	-5.767000	0.00099	-1.532000	0.01747	-1.619000	0.00793	GAT		0.363	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679		A	241752099	G	A	241752099	2	1	61	1	0	0	0	0	0	0	0	1	8445	1045	37	1		1	KMO	1	241752099	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2091	241752099	7498522	1165	9150										
WDR64	128025	broad.mit.edu	37	chr1	241901737	241901737	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccagggaggaccaggaGacatgcagatttactctatg	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241901737G>A	ENST00000366552.2	+	10	1444	c.1237G>A	c.(1237-1239)Gac>Aac	p.D413N	WDR64_ENST00000437684.2_Missense_Mutation_p.D413N	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	413								p.D133N(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			AGGACCAGGAGACATGCAGAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											125	117	120					1																	241901737		2203	4300	6503	239968360	SO:0001583	missense	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1237G>A	1.37:g.241901737G>A	ENSP00000355510:p.Asp413Asn		239968360	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	G	26.6	4.754556	0.89843	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.46451	1.0;1.04;0.87	5.95	5.95	0.96441	.	0.246636	0.36268	N	0.002683	T	0.56247	0.1972	L	0.46157	1.445	0.40865	D	0.983862	D	0.76494	0.999	D	0.64144	0.922	T	0.49143	-0.8970	10	0.35671	T	0.21	-28.0715	17.2915	0.87158	0.0:0.0:1.0:0.0	.	133	D1MPS4	.	N	413;413;184	ENSP00000355510:D413N;ENSP00000402446:D413N;ENSP00000406656:D184N	ENSP00000355510:D413N	D	+	1	0	WDR64	239968360	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.849000	0.69465	2.817000	0.96982	0.563000	0.77884	GAC		0.398	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241901737	G	A	241901737	3	1	61	1	0	0	0	0	1	0	0	0	17355	942	33	3	1275	3	WDR64	1	241901737	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149638	241901737	7348884	1166	9151										
WDR64	128025	broad.mit.edu	37	chr1	241946640	241946640	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaagtaatctatgtagaaGaaaaacaagtggtacttact	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241946640G>T	ENST00000366552.2	+	22	2839	c.2632G>T	c.(2632-2634)Gaa>Taa	p.E878*	WDR64_ENST00000437684.2_Nonsense_Mutation_p.E711*	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	878								p.E431*(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			CTATGTAGAAGAAAAACAAGT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											76	74	75					1																	241946640		2203	4300	6503	240013263	SO:0001587	stop_gained	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2632G>T	1.37:g.241946640G>T	ENSP00000355510:p.Glu878*		240013263	B1ANT0|Q7Z573|Q96LY9	Nonsense_Mutation	SNP	ENST00000366552.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.759542|8.759542	0.98943|0.98943	.|.	.|.	ENSG00000162843|ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635|ENST00000425826	.|.	.|.	.|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.793281|.	0.11828|.	N|.	0.525520|.	.|T	.|0.73776	.|0.3630	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72510	.|-0.4271	.|3	0.56958|.	D|.	0.05|.	-0.8861|-0.8861	17.0121|17.0121	0.86409|0.86409	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	878;711;482|356	.|.	ENSP00000355510:E878X|.	E|K	+|+	1|3	0|2	WDR64|WDR64	240013263|240013263	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.829000|0.829000	0.46940|0.46940	3.891000|3.891000	0.56227|0.56227	2.767000|2.767000	0.95098|0.95098	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.413	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241946640	G	T	241946640	4	4	61	1	0	0	0	0	0	1	0	0	17355	943	33	2	2718	2	WDR64	1	241946640	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44903	241946640	7303981	1167	9152										
WDR64	128025	broad.mit.edu	37	chr1	241964454	241964455	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccacgaagaagaagtttgINSaaaaaaaatttagtcccaca							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:241964454_241964455insA	ENST00000366552.2	+	27	3390_3391	c.3183_3184insA	c.(3184-3186)aaafs	p.K1062fs	WDR64_ENST00000437684.2_Frame_Shift_Ins_p.K895fs	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	1062								p.N617fs*>19(1)|p.N1064fs*>19(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GAAGAAGTTTGAAAAAAAATTT	0.381																																																2	Insertion - Frameshift(2)	large_intestine(2)	1																																								240031078	SO:0001589	frameshift_variant	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.3191dupA	1.37:g.241964462_241964462dupA	ENSP00000355510:p.Lys1062fs		240031077	B1ANT0|Q7Z573|Q96LY9	Frame_Shift_Ins	INS	ENST00000366552.2	37																																																																																					0.381	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241964455	-	A	241964454	7	5	61	1	0	1	1	0	0	0	0	0	17355	1281	45	0	3289	0	WDR64	1	241964454	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	17814	241964454	7286167	1168	9153										
PLD5	200150	broad.mit.edu	37	chr1	242263996	242263996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgctccatctgtcaccAtgtacttgttgcgatttaac	7	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:242263996A>G	ENST00000536534.2	-	9	1569	c.1328T>C	c.(1327-1329)aTg>aCg	p.M443T	PLD5_ENST00000427495.1_Missense_Mutation_p.M381T|PLD5_ENST00000442594.2_Missense_Mutation_p.M351T			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	443	PLD phosphodiesterase 2.					integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.M351T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			ATCTGTCACCATGTACTTGTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											239	199	213					1																	242263996		2203	4300	6503	240330619	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1328T>C	1.37:g.242263996A>G	ENSP00000440896:p.Met443Thr		240330619	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	A	14.38	2.518336	0.44763	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.25085	1.82;1.82;1.82	5.64	4.47	0.54385	Phospholipase D/Transphosphatidylase (1);	0.078359	0.85682	D	0.000000	T	0.28995	0.0720	M	0.77712	2.385	0.46167	D	0.998903	P;P;P	0.41848	0.763;0.651;0.763	B;B;B	0.36608	0.229;0.115;0.124	T	0.24333	-1.0163	10	0.87932	D	0	-22.0619	10.5932	0.45321	0.8572:0.0:0.0:0.1428	.	351;443;381	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	T	381;351;443	ENSP00000401285:M381T;ENSP00000414188:M351T;ENSP00000440896:M443T	ENSP00000401285:M381T	M	-	2	0	PLD5	240330619	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.843000	0.69424	2.153000	0.67306	0.528000	0.53228	ATG		0.453	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		G	242263996	A	G	242263996	3	3	61	1	0	0	0	0	1	0	0	0	12080	217	8	4	290	4	PLD5	1	242263996	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	299542	242263996	6986625	1169	9154										
CEP170	9859	broad.mit.edu	37	chr1	243329107	243329107	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagctgcctaagtgaagtaGggttttattatctccaccag	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:243329107G>T	ENST00000366542.1	-	13	2206	c.2155C>A	c.(2155-2157)Cta>Ata	p.L719I	CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.L621I|CEP170_ENST00000366544.1_Missense_Mutation_p.L621I	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	719						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.L719I(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			AAGTGAAGTAGGGTTTTATTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											141	130	133					1																	243329107		1830	4076	5906	241395730	SO:0001583	missense	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2155C>A	1.37:g.243329107G>T	ENSP00000355500:p.Leu719Ile		241395730	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	G	0.701	-0.790903	0.02884	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543	T;T;T	0.45276	0.94;0.91;0.9	5.01	4.1	0.47936	.	0.361869	0.23360	N	0.049033	T	0.21631	0.0521	N	0.14661	0.345	0.09310	N	0.999999	P;P;P;P	0.39862	0.692;0.545;0.545;0.593	B;B;B;B	0.35114	0.167;0.107;0.196;0.098	T	0.07177	-1.0786	10	0.37606	T	0.19	-0.2483	6.6337	0.22872	0.2863:0.0:0.7137:0.0	.	682;621;621;719	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.;.;.;CE170_HUMAN	I	719;621;621	ENSP00000355500:L719I;ENSP00000355502:L621I;ENSP00000355501:L621I	ENSP00000355500:L719I	L	-	1	2	CEP170	241395730	0.697000	0.27767	0.040000	0.18447	0.216000	0.24613	2.004000	0.40854	1.116000	0.41820	-0.350000	0.07774	CTA		0.388	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		T	243329107	G	T	243329107	3	4	61	1	0	0	0	0	1	0	0	0	3256	991	35	2	2661	2	CEP170	1	243329107	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1065111	243329107	5921514	1170	9155										
CEP170	9859	broad.mit.edu	37	chr1	243354730	243354730	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttggttccctacagaaaGgaaaaagtacttcttcattt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:243354730G>T	ENST00000366542.1	-	8	749	c.698C>A	c.(697-699)cCt>cAt	p.P233H	CEP170_ENST00000366543.1_Missense_Mutation_p.P233H|CEP170_ENST00000366544.1_Missense_Mutation_p.P233H	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	233						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.P233H(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CCTACAGAAAGGAAAAAGTAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											18	15	16					1																	243354730		1760	4009	5769	241421353	SO:0001583	missense	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.698C>A	1.37:g.243354730G>T	ENSP00000355500:p.Pro233His		241421353	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.66|17.66	3.445249|3.445249	0.63178|0.63178	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081	.|T;T;T	.|0.29397	.|1.57;1.57;1.57	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	.|0.381500	.|0.28653	.|N	.|0.014598	T|T	0.46367|0.46367	0.1389|0.1389	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.997;0.999	.|D;D;P	.|0.77004	.|0.989;0.983;0.864	T|T	0.38001|0.38001	-0.9681|-0.9681	5|10	.|0.54805	.|T	.|0.06	-15.2249|-15.2249	11.5908|11.5908	0.50945|0.50945	0.0814:0.0:0.9186:0.0|0.0814:0.0:0.9186:0.0	.|.	.|233;233;233	.|Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;CE170_HUMAN	I|H	135|233;233;233;131	.|ENSP00000355500:P233H;ENSP00000355502:P233H;ENSP00000355501:P233H	.|ENSP00000355500:P233H	L|P	-|-	1|2	0|0	CEP170|CEP170	241421353|241421353	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.588000|3.588000	0.53964|0.53964	2.282000|2.282000	0.76494|0.76494	0.455000|0.455000	0.32223|0.32223	CTT|CCT		0.358	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		T	243354730	G	T	243354730	3	4	61	1	0	0	0	0	1	0	0	0	3256	1000	35	2	4138	2	CEP170	1	243354730	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25623	243354730	5895891	1171	9156										
CEP170	9859	broad.mit.edu	37	chr1	243363931	243363931	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgcagatttggataattCtgattctgaagatttttggg	10	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:243363931C>A	ENST00000366542.1	-	6	436	c.385G>T	c.(385-387)Gaa>Taa	p.E129*	CEP170_ENST00000366543.1_Nonsense_Mutation_p.E129*|CEP170_ENST00000366544.1_Nonsense_Mutation_p.E129*	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	129						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.E129*(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TTGGATAATTCTGATTCTGAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											5	4	4					1																	243363931		1652	3724	5376	241430554	SO:0001587	stop_gained	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.385G>T	1.37:g.243363931C>A	ENSP00000355500:p.Glu129*		241430554	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Nonsense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.66|17.66	3.443603|3.443603	0.63067|0.63067	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081;ENST00000522191|ENST00000336415	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.139948|.	0.49305|.	D|.	0.000147|.	.|T	.|0.74465	.|0.3720	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73864	.|-0.3848	.|4	0.23302|.	T|.	0.38|.	-20.0422|-20.0422	18.5737|18.5737	0.91147|0.91147	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|H	129;129;129;27;129|30	.|.	ENSP00000355500:E129X|.	E|Q	-|-	1|3	0|2	CEP170|CEP170	241430554|241430554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	2.974000|2.974000	0.49272|0.49272	2.469000|2.469000	0.83416|0.83416	0.555000|0.555000	0.69702|0.69702	GAA|CAG		0.373	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243363931	C	A	243363931	4	1	61	1	0	0	0	0	0	1	0	0	3256	922	32	2	4459	2	CEP170	1	243363931	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9201	243363931	5886690	1172	9157										
SDCCAG8	10806	broad.mit.edu	37	chr1	243471469	243471469	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatatgcagaccatcgaaAgactggttaagtaagtatgc	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:243471469A>C	ENST00000366541.3	+	8	1037	c.919A>C	c.(919-921)Aga>Cga	p.R307R	SDCCAG8_ENST00000391846.1_Silent_p.R307R|SDCCAG8_ENST00000355875.4_Silent_p.R264R|SDCCAG8_ENST00000343783.6_Silent_p.R162R	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	307	Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)		p.R307R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		GACCATCGAAAGACTGGTTAA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	1											209	178	189					1																	243471469		2203	4300	6503	241538092	SO:0001819	synonymous_variant	10806			AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.919A>C	1.37:g.243471469A>C			241538092	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																				0.418	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		C	243471469	A	C	243471469	2	2	61	1	0	0	0	0	0	0	0	1	13996	64	3	4		4	SDCCAG8	1	243471469	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	107538	243471469	5779152	1173	9158										
AKT3	10000	broad.mit.edu	37	chr1	243809199	243809199	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttattattttctacctttCttttatgatgggttgtagag	8	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:243809199C>A	ENST00000366539.1	-	5	625	c.425G>T	c.(424-426)aGa>aTa	p.R142I	AKT3_ENST00000263826.5_Missense_Mutation_p.R142I|AKT3_ENST00000336199.5_Missense_Mutation_p.R142I|AKT3_ENST00000366540.1_Missense_Mutation_p.R142I			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	142					mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R142I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TTCTACCTTTCTTTTATGATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											182	182	182					1																	243809199		2203	4300	6503	241875822	SO:0001583	missense	10000			AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.425G>T	1.37:g.243809199C>A	ENSP00000355497:p.Arg142Ile		241875822	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Missense_Mutation	SNP	ENST00000366539.1	37	CCDS31077.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.335386	0.60853	.	.	ENSG00000117020	ENST00000336199;ENST00000366540;ENST00000366539;ENST00000263826	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.24	5.24	0.73138	Protein kinase-like domain (1);	0.052296	0.85682	D	0.000000	T	0.25158	0.0611	N	0.08118	0	0.80722	D	1	B;B	0.12630	0.002;0.006	B;B	0.16289	0.007;0.015	T	0.08146	-1.0736	10	0.87932	D	0	.	12.2184	0.54420	0.0:0.9222:0.0:0.0778	.	142;142	Q9Y243;Q9Y243-2	AKT3_HUMAN;.	I	142	ENSP00000336943:R142I;ENSP00000355498:R142I;ENSP00000355497:R142I;ENSP00000263826:R142I	ENSP00000263826:R142I	R	-	2	0	AKT3	241875822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.636000	0.54317	2.442000	0.82660	0.591000	0.81541	AGA		0.373	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690		A	243809199	C	A	243809199	3	1	61	1	0	0	0	0	1	0	0	0	481	913	32	2	1102	2	AKT3	1	243809199	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	337730	243809199	5441422	1174	9159										
ADSS	159	broad.mit.edu	37	chr1	244574618	244574618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctcatcttcaataaatCgaacatagttttgtgcatta	6	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:244574618C>T	ENST00000366535.3	-	12	1605	c.1289G>A	c.(1288-1290)cGa>cAa	p.R430Q	RP11-518L10.5_ENST00000417765.1_RNA	NM_001126.3	NP_001117.2			adenylosuccinate synthase									p.R430Q(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			TTCAATAAATCGAACATAGTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											138	134	135					1																	244574618		2203	4299	6502	242641241	SO:0001583	missense	159			BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.1289G>A	1.37:g.244574618C>T	ENSP00000355493:p.Arg430Gln		242641241		Missense_Mutation	SNP	ENST00000366535.3	37	CCDS1624.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660347	0.47572	.	.	ENSG00000035687	ENST00000366535;ENST00000449326	T	0.41758	0.99	5.81	2.57	0.30868	.	0.222912	0.47852	D	0.000210	T	0.28797	0.0714	L	0.37507	1.11	0.54753	D	0.999983	B	0.27264	0.173	B	0.15870	0.014	T	0.16247	-1.0409	10	0.49607	T	0.09	-8.9745	9.0199	0.36193	0.1251:0.7304:0.0:0.1445	.	430	P30520	PURA2_HUMAN	Q	430;409	ENSP00000355493:R430Q	ENSP00000355493:R430Q	R	-	2	0	ADSS	242641241	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	3.065000	0.49994	1.455000	0.47813	0.650000	0.86243	CGA		0.318	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		T	244574618	C	T	244574618	3	4	61	1	0	0	0	0	1	0	0	0	347	884	31	1	89	1	ADSS	1	244574618	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	765419	244574618	4676003	1175	9160										
C1orf101	257044	broad.mit.edu	37	chr1	244724243	244724243	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaacagtgggtttcccaaGactttacattagatgcccct	7	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:244724243G>T	ENST00000366534.4	+	10	1357	c.1303G>T	c.(1303-1305)Gac>Tac	p.D435Y	C1orf101_ENST00000366531.3_Missense_Mutation_p.D284Y|C1orf101_ENST00000366533.4_Missense_Mutation_p.D435Y|C1orf101_ENST00000473875.1_3'UTR	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	435						CatSper complex (GO:0036128)		p.D435H(2)|p.D435Y(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			GGTTTCCCAAGACTTTACATT	0.358																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	1											126	127	127					1																	244724243		2203	4300	6503	242790866	SO:0001583	missense	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.1303G>T	1.37:g.244724243G>T	ENSP00000355492:p.Asp435Tyr		242790866	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	37	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148030	0.37923	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042;ENST00000366531	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	5.08	5.08	0.68730	.	0.288330	0.29321	N	0.012485	T	0.53753	0.1816	L	0.54323	1.7	0.27802	N	0.942469	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.68765	0.941;0.96;0.96	T	0.50566	-0.8813	10	0.87932	D	0	.	14.3098	0.66407	0.0:0.0:1.0:0.0	.	355;435;435	B1AQM6;Q5SY80;Q5SY80-2	.;CA101_HUMAN;.	Y	435;435;435;355;284	ENSP00000355492:D435Y;ENSP00000355491:D435Y;ENSP00000395796:D355Y;ENSP00000355489:D284Y	ENSP00000355489:D284Y	D	+	1	0	C1orf101	242790866	1.000000	0.71417	0.985000	0.45067	0.009000	0.06853	1.714000	0.37961	2.508000	0.84585	0.655000	0.94253	GAC		0.358	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		T	244724243	G	T	244724243	3	4	61	1	0	0	0	0	1	0	0	0	1982	942	33	2	1341	2	C1orf101	1	244724243	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149625	244724243	4526378	1176	9161										
PPPDE1	51029	broad.mit.edu	37	chr1	244855279	244855279	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggcaatgcttatcattTaatgcataaaaactgcaatc	5	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:244855279T>G	ENST00000302550.11	+	4	687	c.308T>G	c.(307-309)tTa>tGa	p.L103*	DESI2_ENST00000263831.7_Nonsense_Mutation_p.L70*	NM_016076.3	NP_057160.2	Q9BSY9	DESI2_HUMAN	desumoylating isopeptidase 2	103	PPPDE peptidase.					cytoplasm (GO:0005737)	peptidase activity (GO:0008233)	p.L103*(1)									GCTTATCATTTAATGCATAAA	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											62	67	65					1																	244855279		2203	4291	6494	242921902	SO:0001587	stop_gained	51029			AK025651	CCDS1626.1, CCDS73055.1	1q44	2012-05-16	2012-05-16	2012-05-16	ENSG00000121644	ENSG00000121644			24264	protein-coding gene	gene with protein product		614638	"chromosome 1 open reading frame 121", "family with sequence similarity 152, member A", "PPPDE peptidase domain containing 1"	C1orf121, FAM152A, PPPDE1		10810093, 22370726	Standard	XM_005273154		Approved	CGI-146, FLJ21998	uc001iao.3	Q9BSY9	OTTHUMG00000040398	ENST00000302550.11:c.308T>G	1.37:g.244855279T>G	ENSP00000306528:p.Leu103*		242921902	B1APK6|Q5VVC6|Q9NYS2|Q9Y3E4	Nonsense_Mutation	SNP	ENST00000302550.11	37	CCDS1626.1	.	.	.	.	.	.	.	.	.	.	T	35	5.471082	0.96274	.	.	ENSG00000121644	ENST00000302550;ENST00000263831	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	.	.	.	X	103;70	.	ENSP00000263831:L70X	L	+	2	0	PPPDE1	242921902	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.668000	0.83897	2.291000	0.77112	0.533000	0.62120	TTA		0.318	DESI2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097168.1	NM_016076		G	244855279	T	G	244855279	4	3	61	1	0	0	0	0	0	1	0	0	12442	1764	61	4	322	4	PPPDE1	1	244855279	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	131036	244855279	4395342	1177	9162										
PPPDE1	51029	broad.mit.edu	37	chr1	244868861	244868861	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttctcttctgtagattCtttgtgggaaagagattcct	8	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:244868861C>A	ENST00000302550.11	+	5	734	c.355C>A	c.(355-357)Ctt>Att	p.L119I	DESI2_ENST00000263831.7_Missense_Mutation_p.L86I	NM_016076.3	NP_057160.2	Q9BSY9	DESI2_HUMAN	desumoylating isopeptidase 2	119	PPPDE peptidase.					cytoplasm (GO:0005737)	peptidase activity (GO:0008233)	p.L119I(1)									TCTGTAGATTCTTTGTGGGAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	97	95					1																	244868861		2203	4300	6503	242935484	SO:0001583	missense	51029			AK025651	CCDS1626.1, CCDS73055.1	1q44	2012-05-16	2012-05-16	2012-05-16	ENSG00000121644	ENSG00000121644			24264	protein-coding gene	gene with protein product		614638	"chromosome 1 open reading frame 121", "family with sequence similarity 152, member A", "PPPDE peptidase domain containing 1"	C1orf121, FAM152A, PPPDE1		10810093, 22370726	Standard	XM_005273154		Approved	CGI-146, FLJ21998	uc001iao.3	Q9BSY9	OTTHUMG00000040398	ENST00000302550.11:c.355C>A	1.37:g.244868861C>A	ENSP00000306528:p.Leu119Ile		242935484	B1APK6|Q5VVC6|Q9NYS2|Q9Y3E4	Missense_Mutation	SNP	ENST00000302550.11	37	CCDS1626.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.794453	0.70452	.	.	ENSG00000121644	ENST00000302550;ENST00000263831	.	.	.	6.16	6.16	0.99307	Domain of unknown function DUF862, eukaryotic (1);	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	M	0.88704	2.975	0.58432	D	0.999999	D;D	0.62365	0.988;0.991	D;D	0.68353	0.944;0.957	D	0.86149	0.1586	9	0.66056	D	0.02	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	86;119	Q9BSY9-2;Q9BSY9	.;PPDE1_HUMAN	I	119;86	.	ENSP00000263831:L86I	L	+	1	0	PPPDE1	242935484	0.998000	0.40836	0.996000	0.52242	0.806000	0.45545	3.258000	0.51507	2.937000	0.99478	0.650000	0.86243	CTT		0.522	DESI2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097168.1	NM_016076		A	244868861	C	A	244868861	3	1	61	1	0	0	0	0	1	0	0	0	12442	913	32	2	373	2	PPPDE1	1	244868861	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13582	244868861	4381760	1178	9163										
SMYD3	64754	broad.mit.edu	37	chr1	246091253	246091253	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctctcccacctcgatgtCtcggactgctcgcagtaaga	8	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:246091253C>T	ENST00000388985.4	-	7	681	c.682G>A	c.(682-684)Gac>Aac	p.D228N	SMYD3_ENST00000490107.1_Missense_Mutation_p.D169N|SMYD3_ENST00000541742.1_Missense_Mutation_p.D169N|SMYD3_ENST00000366517.1_5'UTR			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	228	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)	p.D169N(1)		breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		ACCTCGATGTCTCGGACTGCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	71	73					1																	246091253		2203	4300	6503	244157876	SO:0001583	missense	64754			AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	15513	protein-coding gene	gene with protein product		608783	"zinc finger, MYND domain containing 1"	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.682G>A	1.37:g.246091253C>T	ENSP00000373637:p.Asp228Asn		244157876	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	.	.	.	.	.	.	.	.	.	.	C	9.881	1.201468	0.22121	.	.	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985;ENST00000391836	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.66	4.74	0.60224	SET domain (3);	0.417225	0.27941	N	0.017238	T	0.76983	0.4064	L	0.43701	1.375	0.40486	D	0.980493	B;B	0.06786	0.001;0.0	B;B	0.11329	0.004;0.006	T	0.71279	-0.4640	10	0.23302	T	0.38	-18.2689	15.0019	0.71479	0.0:0.9306:0.0:0.0694	.	228;39	Q9H7B4;B3KN46	SMYD3_HUMAN;.	N	169;169;58;228;39	ENSP00000444184:D169N;ENSP00000419184:D169N;ENSP00000373637:D228N;ENSP00000375712:D39N	ENSP00000373637:D228N	D	-	1	0	SMYD3	244157876	0.993000	0.37304	0.289000	0.24876	0.103000	0.19146	3.313000	0.51935	2.656000	0.90262	0.655000	0.94253	GAC		0.517	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		T	246091253	C	T	246091253	3	4	61	1	0	0	0	0	1	0	0	0	14860	913	32	3	628	3	SMYD3	1	246091253	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1222392	246091253	3159368	1179	9164										
SMYD3	64754	broad.mit.edu	37	chr1	246493821	246493821	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtaaagcttctctgattCtgaaggtgctccatccatct	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:246493821C>A	ENST00000388985.4	-	4	354	c.355G>T	c.(355-357)Gaa>Taa	p.E119*	SMYD3_ENST00000490107.1_Nonsense_Mutation_p.E60*|SMYD3_ENST00000403792.3_Nonsense_Mutation_p.E119*|SMYD3_ENST00000541742.1_Nonsense_Mutation_p.E60*			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	119	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)	p.E60*(1)		breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		TTCTCTGATTCTGAAGGTGCT	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											70	74	73					1																	246493821		2203	4299	6502	244560444	SO:0001587	stop_gained	64754			AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	15513	protein-coding gene	gene with protein product		608783	"zinc finger, MYND domain containing 1"	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.355G>T	1.37:g.246493821C>A	ENSP00000373637:p.Glu119*		244560444	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Nonsense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.641517	0.87859	.	.	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000388985;ENST00000453676;ENST00000403792;ENST00000455277	.	.	.	5.33	4.35	0.52113	.	0.521212	0.18582	N	0.136990	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-15.8061	12.1752	0.54182	0.0:0.7451:0.2549:0.0	.	.	.	.	X	60;60;119;60;119;60	.	ENSP00000373637:E119X	E	-	1	0	SMYD3	244560444	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	1.989000	0.40707	2.663000	0.90544	0.650000	0.86243	GAA		0.338	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		A	246493821	C	A	246493821	4	1	61	1	0	0	0	0	0	1	0	0	14860	922	32	2	967	2	SMYD3	1	246493821	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402568	246493821	2756800	1180	9165										
TFB2M	64216	broad.mit.edu	37	chr1	246729180	246729180	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttggttttcccaaataGatttgcgccagggtctcagc	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:246729180G>T	ENST00000366514.4	-	1	446	c.261C>A	c.(259-261)atC>atA	p.I87I	TFB2M_ENST00000544618.1_Silent_p.I87I|CNST_ENST00000366512.3_5'Flank|CNST_ENST00000366513.4_5'Flank	NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	87					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)	p.I87I(1)		breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			TTCCCAAATAGATTTGCGCCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	1											86	89	88					1																	246729180		2203	4300	6503	244795803	SO:0001819	synonymous_variant	64216			AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.261C>A	1.37:g.246729180G>T			244795803	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																				0.473	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366		T	246729180	G	T	246729180	2	4	61	1	0	0	0	0	0	0	0	1	15833	932	33	2		2	TFB2M	1	246729180	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	235359	246729180	2521441	1181	9166										
CNST	163882	broad.mit.edu	37	chr1	246784781	246784781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaagaaaaagtactaagcGcagtcacatatgctgttgat	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:246784781G>A	ENST00000366513.4	+	3	699	c.430G>A	c.(430-432)Gca>Aca	p.A144T	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Missense_Mutation_p.A144T	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	144					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)	p.A144T(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AGTACTAAGCGCAGTCACATA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	1											203	209	207					1																	246784781		2203	4300	6503	244851404	SO:0001583	missense	163882			AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.430G>A	1.37:g.246784781G>A	ENSP00000355470:p.Ala144Thr		244851404	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.783110	0.31593	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.19105	2.18;2.17	5.46	4.44	0.53790	.	0.799329	0.11228	N	0.585928	T	0.11965	0.0291	L	0.39898	1.24	0.32098	N	0.590941	P;P	0.38978	0.652;0.652	B;B	0.26517	0.07;0.07	T	0.03993	-1.0986	10	0.16420	T	0.52	-1.9637	5.18	0.15156	0.1993:0.0:0.8007:0.0	.	144;144	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	T	144	ENSP00000355470:A144T;ENSP00000355469:A144T	ENSP00000355469:A144T	A	+	1	0	CNST	244851404	0.035000	0.19736	0.031000	0.17742	0.130000	0.20726	0.977000	0.29475	2.551000	0.86045	0.655000	0.94253	GCA		0.393	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		A	246784781	G	A	246784781	3	1	61	1	0	0	0	0	1	0	0	0	3640	1087	38	1	436	1	CNST	1	246784781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55601	246784781	2465840	1182	9167										
ZNF670	93474	broad.mit.edu	37	chr1	247201111	247201111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagtatgcgttctttcatgTattcccaagtaagtggaacg	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247201111T>C	ENST00000366503.2	-	4	968	c.810A>G	c.(808-810)atA>atG	p.I270M		NM_001204220.1|NM_033213.4	NP_001191149.1|NP_149990.1	Q9BS34	ZN670_HUMAN	zinc finger protein 670	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I270M(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17	all_cancers(71;4.01e-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;0.00427)			TTCTTTCATGTATTCCCAAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	120	120					1																	247201111		2203	4300	6503	245267734	SO:0001583	missense	93474				CCDS31087.1	1q44	2013-01-08			ENSG00000135747	ENSG00000135747		"Zinc fingers, C2H2-type", "-"	28167	protein-coding gene	gene with protein product						12477932	Standard	NM_033213		Approved	MGC12466	uc001icd.2	Q9BS34	OTTHUMG00000040868	ENST00000366503.2:c.810A>G	1.37:g.247201111T>C	ENSP00000355459:p.Ile270Met		245267734		Missense_Mutation	SNP	ENST00000366503.2	37	CCDS31087.1	.	.	.	.	.	.	.	.	.	.	T	1.011	-0.687986	0.03328	.	.	ENSG00000135747	ENST00000366503	T	0.07567	3.18	0.641	0.641	0.17759	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05868	0.0153	L	0.28400	0.85	0.19575	N	0.999965	B	0.31383	0.321	B	0.33568	0.166	T	0.39210	-0.9625	9	0.41790	T	0.15	.	2.6854	0.05106	0.0:0.3462:0.0:0.6538	.	270	Q9BS34	ZN670_HUMAN	M	270	ENSP00000355459:I270M	ENSP00000355459:I270M	I	-	3	3	ZNF670	245267734	0.000000	0.05858	0.014000	0.15608	0.070000	0.16714	-5.228000	0.00139	0.508000	0.28173	0.383000	0.25322	ATA		0.423	ZNF670-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098183.3	NM_033213		C	247201111	T	C	247201111	3	2	61	1	0	0	0	0	1	0	0	0	18116	1628	57	4	363	4	ZNF670	1	247201111	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	416330	247201111	2049510	1183	9168										
NLRP3	114548	broad.mit.edu	37	chr1	247586591	247586591	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaggaagacagcattgaaGaggagtggatgggtttactg	16	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247586591G>T	ENST00000336119.3	+	2	1089	c.343G>T	c.(343-345)Gag>Tag	p.E115*	NLRP3_ENST00000366497.2_Nonsense_Mutation_p.E115*|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000348069.2_Nonsense_Mutation_p.E115*|NLRP3_ENST00000391827.2_Nonsense_Mutation_p.E115*|NLRP3_ENST00000391828.3_Nonsense_Mutation_p.E115*|NLRP3_ENST00000366496.2_Nonsense_Mutation_p.E115*	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	115					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.E115*(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CAGCATTGAAGAGGAGTGGAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											213	209	211					1																	247586591		2203	4300	6503	245653214	SO:0001587	stop_gained	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.343G>T	1.37:g.247586591G>T	ENSP00000337383:p.Glu115*		245653214	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Nonsense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	G	39	7.906537	0.98554	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	.	.	.	4.1	4.1	0.47936	.	0.000000	0.47852	D	0.000217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	12.1447	0.54016	0.0:0.0:1.0:0.0	.	.	.	.	X	115	.	ENSP00000337383:E115X	E	+	1	0	NLRP3	245653214	0.998000	0.40836	0.943000	0.38184	0.114000	0.19823	3.110000	0.50352	2.587000	0.87381	0.655000	0.94253	GAG		0.408	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247586591	G	T	247586591	4	4	61	1	0	0	0	0	0	1	0	0	10509	943	33	2	349	2	NLRP3	1	247586591	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	385480	247586591	1664030	1184	9169										
NLRP3	114548	broad.mit.edu	37	chr1	247599321	247599321	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtcaggatcttgcatcaGtattgagcaccagccattcc	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247599321G>T	ENST00000336119.3	+	6	3294	c.2548G>T	c.(2548-2550)Gta>Tta	p.V850L	NLRP3_ENST00000366497.2_Intron|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000391827.2_Missense_Mutation_p.V793L|NLRP3_ENST00000391828.3_Missense_Mutation_p.V850L|NLRP3_ENST00000366496.2_Intron	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	850					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.V850L(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TCTTGCATCAGTATTGAGCAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	108	116					1																	247599321		2203	4300	6503	245665944	SO:0001583	missense	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2548G>T	1.37:g.247599321G>T	ENSP00000337383:p.Val850Leu		245665944	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	g	11.80	1.748031	0.30955	.	.	ENSG00000162711	ENST00000391828;ENST00000336119;ENST00000391827	T;T;T	0.42900	0.96;0.96;0.96	3.78	2.87	0.33458	.	0.000000	0.32836	N	0.005583	T	0.35189	0.0923	L	0.45470	1.425	0.37748	D	0.925869	B;B;P	0.45428	0.141;0.333;0.858	B;B;B	0.43386	0.029;0.142;0.418	T	0.29305	-1.0016	10	0.45353	T	0.12	.	7.4138	0.27032	0.1172:0.0:0.8828:0.0	.	830;793;850	B7ZKS9;Q96P20-4;Q96P20	.;.;NALP3_HUMAN	L	850;850;793	ENSP00000375704:V850L;ENSP00000337383:V850L;ENSP00000375703:V793L	ENSP00000337383:V850L	V	+	1	0	NLRP3	245665944	0.305000	0.24481	0.012000	0.15200	0.002000	0.02628	3.740000	0.55082	1.190000	0.43042	0.536000	0.68110	GTA		0.502	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247599321	G	T	247599321	3	4	61	1	0	0	0	0	1	0	0	0	10509	1029	36	2	2570	2	NLRP3	1	247599321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12730	247599321	1651300	1185	9170										
NLRP3	114548	broad.mit.edu	37	chr1	247599390	247599390	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgggagactcaggagtcGcaattttatgtgaaaaagcc	11	8	1	2	rs201867582		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247599390G>A	ENST00000336119.3	+	6	3363	c.2617G>A	c.(2617-2619)Gca>Aca	p.A873T	NLRP3_ENST00000366497.2_Intron|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000391827.2_Missense_Mutation_p.A816T|NLRP3_ENST00000391828.3_Missense_Mutation_p.A873T|NLRP3_ENST00000366496.2_Intron	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	873					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.A873T(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CTCAGGAGTCGCAATTTTATG	0.463													G|||	1	0.000199681	0	0	5008	,	,		20472	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						G	THR/ALA,,THR/ALA,THR/ALA,	1,4405	2.1+/-5.4	0,1,2202	101	94	96		2617,,2446,2617,	-1.8	0	1		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron,missense,missense,intron	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	58,,58,58,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,,benign,benign,	873/1037,,816/980,873/1037,	247599390	2,13004	2203	4300	6503	245666013	SO:0001583	missense	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2617G>A	1.37:g.247599390G>A	ENSP00000337383:p.Ala873Thr		245666013	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	g	6.439	0.449065	0.12223	2.27E-4	1.16E-4	ENSG00000162711	ENST00000391828;ENST00000336119;ENST00000391827	T;T;T	0.48522	0.81;0.81;0.81	3.63	-1.75	0.08031	.	1.009950	0.07976	N	0.984869	T	0.25044	0.0608	N	0.12182	0.205	0.09310	N	1	B;B;B	0.17667	0.0;0.002;0.023	B;B;B	0.13407	0.0;0.001;0.009	T	0.17592	-1.0364	10	0.39692	T	0.17	.	4.2389	0.10638	0.4427:0.1842:0.3731:0.0	.	853;816;873	B7ZKS9;Q96P20-4;Q96P20	.;.;NALP3_HUMAN	T	873;873;816	ENSP00000375704:A873T;ENSP00000337383:A873T;ENSP00000375703:A816T	ENSP00000337383:A873T	A	+	1	0	NLRP3	245666013	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.043000	0.13971	-0.335000	0.08451	-0.331000	0.08364	GCA		0.463	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247599390	G	A	247599390	3	1	61	1	0	0	0	0	1	0	0	0	10509	1087	38	1	2639	1	NLRP3	1	247599390	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69	247599390	1651231	1186	9171										
OR2B11	127623	broad.mit.edu	37	chr1	247614710	247614710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagcggtgtcagcacacGacagcttgatcacggccggc	12	14	3	1	rs534641794		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247614710G>A	ENST00000318749.6	-	1	598	c.575C>T	c.(574-576)tCg>tTg	p.S192L		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S192L(1)		endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-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)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GTCAGCACACGACAGCTTGAT	0.557													G|||	1	0.000199681	0	0	5008	,	,		20350	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											61	62	62					1																	247614710		2203	4300	6503	245681333	SO:0001583	missense	127623				CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.575C>T	1.37:g.247614710G>A	ENSP00000325682:p.Ser192Leu		245681333	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.778280	0.31502	.	.	ENSG00000177535	ENST00000318749	T	0.00291	8.27	5.09	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	1.018430	0.07864	N	0.966747	T	0.00496	0.0016	M	0.89601	3.045	0.09310	N	1	P	0.46578	0.88	B	0.41894	0.369	T	0.53683	-0.8404	10	0.87932	D	0	.	13.7998	0.63192	0.0:0.1544:0.8456:0.0	.	192	Q5JQS5	OR2BB_HUMAN	L	192	ENSP00000325682:S192L	ENSP00000325682:S192L	S	-	2	0	OR2B11	245681333	0.004000	0.15560	0.386000	0.26170	0.013000	0.08279	1.437000	0.34991	1.512000	0.48834	0.643000	0.83706	TCG		0.557	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		A	247614710	G	A	247614710	3	1	61	1	0	0	0	0	1	0	0	0	11019	1059	37	1	381	1	OR2B11	1	247614710	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15320	247614710	1635911	1187	9172										
OR2G3	81469	broad.mit.edu	37	chr1	247769041	247769041	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcatcatctcatatctgGatccccctcttcatacccca	2	16	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247769041G>T	ENST00000320002.2	+	1	186	c.154G>T	c.(154-156)Gat>Tat	p.D52Y	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D52Y(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	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;0.017)			CTCATATCTGGATCCCCCTCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1											269	263	265					1																	247769041		2203	4300	6503	245835664	SO:0001583	missense	81469			BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"GPCR / Class A : Olfactory receptors"	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.154G>T	1.37:g.247769041G>T	ENSP00000326301:p.Asp52Tyr		245835664	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814650	0.32053	.	.	ENSG00000177476	ENST00000320002	T	0.02974	4.09	3.57	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	0.195513	0.23680	N	0.045640	T	0.21387	0.0515	H	0.98701	4.305	0.09310	N	1	D	0.89917	1.0	D	0.69142	0.962	T	0.12477	-1.0546	10	0.72032	D	0.01	.	5.8438	0.18652	0.112:0.0:0.6927:0.1953	.	52	Q8NGZ4	OR2G3_HUMAN	Y	52	ENSP00000326301:D52Y	ENSP00000326301:D52Y	D	+	1	0	OR2G3	245835664	0.000000	0.05858	0.210000	0.23637	0.050000	0.14768	0.041000	0.13927	0.828000	0.34709	-0.544000	0.04233	GAT		0.448	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1			T	247769041	G	T	247769041	3	4	61	1	0	0	0	0	1	0	0	0	11030	1174	41	2	156	2	OR2G3	1	247769041	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154331	247769041	1481580	1188	9173										
OR2G3	81469	broad.mit.edu	37	chr1	247769458	247769458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcaagttggcttgtgtgGacaccactgtcaatgaattg	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247769458G>A	ENST00000320002.2	+	1	603	c.571G>A	c.(571-573)Gac>Aac	p.D191N	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D191N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	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;0.017)			GGCTTGTGTGGACACCACTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											234	202	213					1																	247769458		2203	4300	6503	245836081	SO:0001583	missense	81469			BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"GPCR / Class A : Olfactory receptors"	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.571G>A	1.37:g.247769458G>A	ENSP00000326301:p.Asp191Asn		245836081	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.183206	0.57800	.	.	ENSG00000177476	ENST00000320002	T	0.00231	8.49	3.52	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38381	U	0.001703	T	0.00300	0.0009	L	0.60067	1.865	0.09310	N	1	P	0.46578	0.88	P	0.53006	0.715	T	0.47045	-0.9147	10	0.46703	T	0.11	.	9.9601	0.41691	0.0:0.0:0.7956:0.2044	.	191	Q8NGZ4	OR2G3_HUMAN	N	191	ENSP00000326301:D191N	ENSP00000326301:D191N	D	+	1	0	OR2G3	245836081	0.999000	0.42202	0.627000	0.29227	0.908000	0.53690	2.982000	0.49337	0.762000	0.33152	0.386000	0.25728	GAC		0.438	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1			A	247769458	G	A	247769458	3	1	61	1	0	0	0	0	1	0	0	0	11030	1174	41	3	573	3	OR2G3	1	247769458	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	417	247769458	1481163	1189	9174										
OR6F1	343169	broad.mit.edu	37	chr1	247875554	247875554	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatggcacgggggccacaGaaggacaggccactgatgag	16	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247875554G>A	ENST00000302084.2	-	1	551	c.504C>T	c.(502-504)ttC>ttT	p.F168F	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F168F(1)		breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	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)			GGGGGCCACAGAAGGACAGGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	1											78	87	84					1																	247875554		2203	4300	6503	245942177	SO:0001819	synonymous_variant	343169			BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.504C>T	1.37:g.247875554G>A			245942177	B2RNV6|Q6IF02|Q96R39	Silent	SNP	ENST00000302084.2	37	CCDS31095.1																																																																																				0.597	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		A	247875554	G	A	247875554	2	1	61	1	0	0	0	0	0	0	0	1	11232	933	33	3		3	OR6F1	1	247875554	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	106096	247875554	1375067	1190	9175										
OR1C1	26188	broad.mit.edu	37	chr1	247921178	247921178	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggattgagatcacagaaGaaatgatggatgatattgga	13	2	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:247921178G>T	ENST00000408896.2	-	1	804	c.531C>A	c.(529-531)ttC>ttA	p.F177L		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	177					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F177L(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	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)			GATCACAGAAGAAATGATGGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											64	64	64					1																	247921178		2112	4244	6356	245987801	SO:0001583	missense	26188			X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"GPCR / Class A : Olfactory receptors"	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.531C>A	1.37:g.247921178G>T	ENSP00000386138:p.Phe177Leu		245987801	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Missense_Mutation	SNP	ENST00000408896.2	37	CCDS41481.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.402072	0.62288	.	.	ENSG00000221888	ENST00000408896	T	0.00346	8.01	3.19	1.23	0.21249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00815	0.0027	M	0.88241	2.94	0.22489	N	0.999051	D	0.89917	1.0	D	0.91635	0.999	T	0.43245	-0.9403	9	0.87932	D	0	.	6.5202	0.22271	0.3249:0.0:0.6751:0.0	.	177	Q15619	OR1C1_HUMAN	L	177	ENSP00000386138:F177L	ENSP00000386138:F177L	F	-	3	2	OR1C1	245987801	0.095000	0.21747	0.999000	0.59377	0.992000	0.81027	0.475000	0.22164	0.187000	0.20147	0.580000	0.79431	TTC		0.488	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1			T	247921178	G	T	247921178	3	4	61	1	0	0	0	0	1	0	0	0	10983	933	33	2	415	2	OR1C1	1	247921178	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45624	247921178	1329443	1191	9176										
TRIM58	25893	broad.mit.edu	37	chr1	248028063	248028063	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtttgagaagcatcgtggCtttctggcccaggaggagca	15	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248028063C>A	ENST00000366481.3	+	3	621	c.573C>A	c.(571-573)ggC>ggA	p.G191G		NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	191						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.G191G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	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)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AGCATCGTGGCTTTCTGGCCC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	1											65	53	57					1																	248028063		2203	4300	6503	246094686	SO:0001819	synonymous_variant	25893			AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.573C>A	1.37:g.248028063C>A			246094686	Q6B0H9	Silent	SNP	ENST00000366481.3	37	CCDS1636.1																																																																																				0.617	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		A	248028063	C	A	248028063	2	1	61	1	0	0	0	0	0	0	0	1	16571	784	28	2		2	TRIM58	1	248028063	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106885	248028063	1222558	1192	9177										
OR2T8	343172	broad.mit.edu	37	chr1	248084956	248084956	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtccccttttccctcatcCtgtcctcctatggtctcatc	5	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248084956C>A	ENST00000319968.4	+	1	637	c.637C>A	c.(637-639)Ctg>Atg	p.L213M		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L213M(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TTCCCTCATCCTGTCCTCCTA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											4	4	4					1																	248084956		1794	3640	5434	246151579	SO:0001583	missense	343172				CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"GPCR / Class A : Olfactory receptors"	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.637C>A	1.37:g.248084956C>A	ENSP00000326225:p.Leu213Met		246151579		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903315	0.33628	.	.	ENSG00000177462	ENST00000319968	T	0.00269	8.37	3.56	0.484	0.16825	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29280	U	0.012616	T	0.00300	0.0009	L	0.52011	1.625	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.52968	-0.8504	10	0.48119	T	0.1	.	3.1081	0.06348	0.2804:0.4013:0.0:0.3183	.	213	A6NH00	OR2T8_HUMAN	M	213	ENSP00000326225:L213M	ENSP00000326225:L213M	L	+	1	2	OR2T8	246151579	0.000000	0.05858	0.020000	0.16555	0.195000	0.23768	-1.956000	0.01522	0.214000	0.20742	0.404000	0.27445	CTG		0.547	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522		A	248084956	C	A	248084956	3	1	61	1	0	0	0	0	1	0	0	0	11061	680	24	2	639	2	OR2T8	1	248084956	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56893	248084956	1165665	1193	9178										
OR2L8	391190	broad.mit.edu	37	chr1	248112400	248112400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccattgttcctaagatgGcatctgattttctgcatgga	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248112400G>A	ENST00000357191.3	+	1	241	c.241G>A	c.(241-243)Gca>Aca	p.A81T	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A81T(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	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;0.0152)			TCCTAAGATGGCATCTGATTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											296	262	273					1																	248112400		2203	4297	6500	246179023	SO:0001583	missense	391190			BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.241G>A	1.37:g.248112400G>A	ENSP00000349719:p.Ala81Thr		246179023	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	G	9.525	1.109210	0.20714	.	.	ENSG00000196936	ENST00000357191	T	0.00344	8.02	1.64	0.388	0.16264	GPCR, rhodopsin-like superfamily (1);	1.380920	0.05644	U	0.583995	T	0.00271	0.0008	M	0.61703	1.905	0.09310	N	1	B	0.15719	0.014	B	0.16722	0.016	T	0.46359	-0.9197	10	0.41790	T	0.15	.	2.1751	0.03860	0.257:0.0:0.2758:0.4672	.	81	Q8NGY9	OR2L8_HUMAN	T	81	ENSP00000349719:A81T	ENSP00000349719:A81T	A	+	1	0	OR2L8	246179023	0.000000	0.05858	0.380000	0.26093	0.147000	0.21601	-2.039000	0.01418	0.905000	0.36596	0.479000	0.44913	GCA		0.443	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112400	G	A	248112400	3	1	61	1	0	0	0	0	1	0	0	0	11040	1203	42	3	243	3	OR2L8	1	248112400	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27444	248112400	1138221	1194	9179										
OR2L2	26246	broad.mit.edu	37	chr1	248201717	248201717	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgattcttctcatctttTtggacatccatctccacaca	3	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248201717T>G	ENST00000366479.2	+	1	244	c.148T>G	c.(148-150)Ttg>Gtg	p.L50V	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L50V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TCTCATCTTTTTGGACATCCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											286	269	275					1																	248201717		2203	4300	6503	246268340	SO:0001583	missense	26246			X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"GPCR / Class A : Olfactory receptors"	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.148T>G	1.37:g.248201717T>G	ENSP00000355435:p.Leu50Val		246268340	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	4.562	0.104327	0.08731	.	.	ENSG00000203663	ENST00000366479	T	0.02944	4.1	2.09	-3.5	0.04710	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02649	0.0080	L	0.56124	1.755	0.09310	N	1	B	0.10296	0.003	B	0.14578	0.011	T	0.47328	-0.9126	9	0.22706	T	0.39	.	2.757	0.05295	0.3332:0.2197:0.0:0.447	.	50	Q8NH16	OR2L2_HUMAN	V	50	ENSP00000355435:L50V	ENSP00000355435:L50V	L	+	1	2	OR2L2	246268340	0.000000	0.05858	0.015000	0.15790	0.112000	0.19704	-5.507000	0.00117	-0.295000	0.08960	0.163000	0.16589	TTG		0.383	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		G	248201717	T	G	248201717	3	3	61	1	0	0	0	0	1	0	0	0	11038	1838	64	4	150	4	OR2L2	1	248201717	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	89317	248201717	1048904	1195	9180										
OR2L13	284521	broad.mit.edu	37	chr1	248262824	248262824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatgattcacctcatccaCgtggatcctcgtctccacac	6	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248262824C>T	ENST00000358120.2	+	2	292	c.147C>T	c.(145-147)caC>caT	p.H49H	OR2L13_ENST00000366478.2_Silent_p.H49H			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H49H(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			ACCTCATCCACGTGGATCCTC	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	1											225	211	216					1																	248262824		2203	4300	6503	246329447	SO:0001819	synonymous_variant	284521			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.147C>T	1.37:g.248262824C>T			246329447	Q5VUR5	Silent	SNP	ENST00000358120.2	37	CCDS1637.1																																																																																				0.502	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		T	248262824	C	T	248262824	2	4	61	1	0	0	0	0	0	0	0	1	11037	535	19	1		1	OR2L13	1	248262824	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61107	248262824	987797	1196	9181										
OR2L13	284521	broad.mit.edu	37	chr1	248263467	248263467	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatcttcggcccaggaatCtccgctcaccagctgaagac	8	16	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248263467C>A	ENST00000358120.2	+	2	935	c.790C>A	c.(790-792)Ctc>Atc	p.L264I	OR2L13_ENST00000366478.2_Missense_Mutation_p.L264I			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L264I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			GCCCAGGAATCTCCGCTCACC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											119	118	118					1																	248263467		2203	4300	6503	246330090	SO:0001583	missense	284521			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.790C>A	1.37:g.248263467C>A	ENSP00000350836:p.Leu264Ile		246330090	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	C	3.641	-0.073628	0.07184	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00042	8.84;8.84	4.21	-0.155	0.13395	GPCR, rhodopsin-like superfamily (1);	0.207905	0.22233	N	0.062800	T	0.00109	0.0003	L	0.33245	0.995	0.09310	N	1	B	0.20261	0.043	B	0.33196	0.159	T	0.41805	-0.9488	10	0.56958	D	0.05	.	1.1183	0.01719	0.2503:0.3243:0.2543:0.171	.	264	Q8N349	OR2LD_HUMAN	I	264	ENSP00000355434:L264I;ENSP00000350836:L264I	ENSP00000350836:L264I	L	+	1	0	OR2L13	246330090	0.000000	0.05858	0.001000	0.08648	0.092000	0.18411	-0.896000	0.04114	0.081000	0.16988	-0.749000	0.03505	CTC		0.468	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		A	248263467	C	A	248263467	3	1	61	1	0	0	0	0	1	0	0	0	11037	913	32	2	792	2	OR2L13	1	248263467	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	643	248263467	987154	1197	9182										
OR2M5	127059	broad.mit.edu	37	chr1	248308859	248308859	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatacaccaatctcatgaGacccaaaatttgtggactta	6	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248308859G>T	ENST00000366476.1	+	1	410	c.410G>T	c.(409-411)aGa>aTa	p.R137I		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R137I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			AATCTCATGAGACCCAAAATT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											269	269	269					1																	248308859		2203	4300	6503	246375482	SO:0001583	missense	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.410G>T	1.37:g.248308859G>T	ENSP00000355432:p.Arg137Ile		246375482		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	9.360	1.067850	0.20067	.	.	ENSG00000162727	ENST00000366476	T	0.38560	1.13	2.9	0.667	0.17907	GPCR, rhodopsin-like superfamily (1);	0.856574	0.09546	U	0.787603	T	0.41282	0.1152	M	0.73962	2.25	0.09310	N	1	B	0.20164	0.042	B	0.23716	0.048	T	0.48822	-0.9001	10	0.87932	D	0	.	5.3781	0.16176	0.2124:0.1839:0.6037:0.0	.	137	A3KFT3	OR2M5_HUMAN	I	137	ENSP00000355432:R137I	ENSP00000355432:R137I	R	+	2	0	OR2M5	246375482	0.000000	0.05858	0.007000	0.13788	0.036000	0.12997	-1.759000	0.01808	1.316000	0.45131	0.492000	0.49549	AGA		0.453	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		T	248308859	G	T	248308859	3	4	61	1	0	0	0	0	1	0	0	0	11044	942	33	2	412	2	OR2M5	1	248308859	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45392	248308859	941762	1198	9183										
OR2M5	127059	broad.mit.edu	37	chr1	248308950	248308950	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcgacattttccttctcCtactgtgggtctcgggaaat	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248308950C>A	ENST00000366476.1	+	1	501	c.501C>A	c.(499-501)tcC>tcA	p.S167S		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S167S(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			TTTCCTTCTCCTACTGTGGGT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											278	262	267					1																	248308950		2203	4300	6503	246375573	SO:0001819	synonymous_variant	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.501C>A	1.37:g.248308950C>A			246375573		Silent	SNP	ENST00000366476.1	37	CCDS31105.1																																																																																				0.438	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		A	248308950	C	A	248308950	2	1	61	1	0	0	0	0	0	0	0	1	11044	668	24	2		2	OR2M5	1	248308950	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91	248308950	941671	1199	9184										
OR2M3	127062	broad.mit.edu	37	chr1	248366709	248366709	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttggctctgagtgctttCttttggctgttatggcttat	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248366709C>A	ENST00000456743.1	+	1	378	c.340C>A	c.(340-342)Ctt>Att	p.L114I		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L114I(1)		endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TGAGTGCTTTCTTTTGGCTGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											240	246	244					1																	248366709		2203	4300	6503	246433332	SO:0001583	missense	127062				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.340C>A	1.37:g.248366709C>A	ENSP00000389625:p.Leu114Ile		246433332	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103019	0.37145	.	.	ENSG00000228198	ENST00000456743	T	0.00585	6.39	2.36	-0.0859	0.13684	GPCR, rhodopsin-like superfamily (1);	0.000000	0.27113	U	0.020866	T	0.01976	0.0062	M	0.75264	2.295	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.21008	-1.0258	10	0.72032	D	0.01	.	9.8843	0.41253	0.358:0.642:0.0:0.0	.	114	Q8NG83	OR2M3_HUMAN	I	114	ENSP00000389625:L114I	ENSP00000389625:L114I	L	+	1	0	OR2M3	246433332	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-4.446000	0.00232	0.296000	0.22592	0.405000	0.27470	CTT		0.453	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		A	248366709	C	A	248366709	3	1	61	1	0	0	0	0	1	0	0	0	11042	913	32	2	342	2	OR2M3	1	248366709	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57759	248366709	883912	1200	9185										
OR2M3	127062	broad.mit.edu	37	chr1	248367165	248367165	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatacggcccacatctgatCgctccccaacacaggacaag	7	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248367165C>T	ENST00000456743.1	+	1	834	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R266C(1)		endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CACATCTGATCGCTCCCCAAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	1											189	172	178					1																	248367165		2203	4300	6503	246433788	SO:0001583	missense	127062				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.796C>T	1.37:g.248367165C>T	ENSP00000389625:p.Arg266Cys		246433788	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841787	0.32513	.	.	ENSG00000228198	ENST00000456743	T	0.00137	8.68	2.54	0.382	0.16234	GPCR, rhodopsin-like superfamily (1);	1.645920	0.04293	U	0.345971	T	0.00328	0.0010	M	0.67700	2.07	0.09310	N	1	D	0.64830	0.994	P	0.61070	0.883	T	0.45920	-0.9228	10	0.72032	D	0.01	.	2.0929	0.03660	0.4734:0.2597:0.1569:0.11	.	266	Q8NG83	OR2M3_HUMAN	C	266	ENSP00000389625:R266C	ENSP00000389625:R266C	R	+	1	0	OR2M3	246433788	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.663000	0.01968	-0.032000	0.13758	-0.746000	0.03513	CGC		0.507	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		T	248367165	C	T	248367165	3	4	61	1	0	0	0	0	1	0	0	0	11042	884	31	1	798	1	OR2M3	1	248367165	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	456	248367165	883456	1201	9186										
OR2M7	391196	broad.mit.edu	37	chr1	248487080	248487080	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcataggagaatgatgaGatgtgggctgaatgcacatg	14	6	0	4	rs199675516		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248487080G>T	ENST00000317965.2	-	1	819	c.791C>A	c.(790-792)tCt>tAt	p.S264Y		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S264Y(1)		breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGAATGATGAGATGTGGGCTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											158	143	148					1																	248487080		2203	4300	6503	246553703	SO:0001583	missense	391196			BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"GPCR / Class A : Olfactory receptors"	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.791C>A	1.37:g.248487080G>T	ENSP00000324557:p.Ser264Tyr		246553703	B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	G	3.896	-0.022961	0.07634	.	.	ENSG00000177186	ENST00000317965	T	0.00274	8.35	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.575794	0.13102	U	0.413710	T	0.00845	0.0028	H	0.94582	3.555	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.31251	-0.9950	10	0.87932	D	0	.	8.5476	0.33430	0.0:0.2407:0.7593:0.0	.	264	Q8NG81	OR2M7_HUMAN	Y	264	ENSP00000324557:S264Y	ENSP00000324557:S264Y	S	-	2	0	OR2M7	246553703	0.001000	0.12720	0.018000	0.16275	0.010000	0.07245	0.573000	0.23699	0.850000	0.35239	0.194000	0.17425	TCT		0.478	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		T	248487080	G	T	248487080	3	4	61	1	0	0	0	0	1	0	0	0	11045	942	33	2	150	2	OR2M7	1	248487080	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119915	248487080	763541	1202	9187										
OR2T6	254879	broad.mit.edu	37	chr1	248551559	248551559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctcggtggtgactgcatCctacaccaggattctcatca	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248551559C>T	ENST00000355728.2	+	1	650	c.650C>T	c.(649-651)tCc>tTc	p.S217F		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S217F(1)		endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGACTGCATCCTACACCAGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											300	230	254					1																	248551559		2203	4300	6503	246618182	SO:0001583	missense	254879			AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.650C>T	1.37:g.248551559C>T	ENSP00000347965:p.Ser217Phe		246618182	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417359	0.42918	.	.	ENSG00000198104	ENST00000355728	T	0.42513	0.97	4.13	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000453	T	0.72053	0.3413	H	0.95151	3.63	0.36621	D	0.875743	D	0.89917	1.0	D	0.83275	0.996	T	0.82770	-0.0293	10	0.87932	D	0	.	11.2441	0.48987	0.0:0.9086:0.0:0.0914	.	217	Q8NHC8	OR2T6_HUMAN	F	217	ENSP00000347965:S217F	ENSP00000347965:S217F	S	+	2	0	OR2T6	246618182	1.000000	0.71417	0.713000	0.30519	0.267000	0.26476	6.674000	0.74487	2.295000	0.77249	0.643000	0.83706	TCC		0.522	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		T	248551559	C	T	248551559	3	4	61	1	0	0	0	0	1	0	0	0	11060	855	30	3	652	3	OR2T6	1	248551559	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64479	248551559	699062	1203	9188										
OR2T1	26696	broad.mit.edu	37	chr1	248569430	248569430	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaagatattaccttatatCggcacaactgtaggatcaat	8	7	1	1	rs145103744		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248569430C>T	ENST00000366474.1	+	1	135	c.135C>T	c.(133-135)atC>atT	p.I45I		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I45I(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TACCTTATATCGGCACAACTG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	1						C		0,4406		0,0,2203	151	149	150		135	-0.8	0	1	dbSNP_134	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	OR2T1	NM_030904.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		45/370	248569430	2,13004	2203	4300	6503	246636053	SO:0001819	synonymous_variant	26696			U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"GPCR / Class A : Olfactory receptors"	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.135C>T	1.37:g.248569430C>T			246636053	Q6IEZ9	Silent	SNP	ENST00000366474.1	37	CCDS31115.1																																																																																				0.378	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			T	248569430	C	T	248569430	2	4	61	1	0	0	0	0	0	0	0	1	11047	874	31	1		1	OR2T1	1	248569430	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17871	248569430	681191	1204	9189										
OR2G6	391211	broad.mit.edu	37	chr1	248685811	248685811	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccacttttaaaccccatTatctacactctgagaaacaa	2	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248685811T>C	ENST00000343414.4	+	1	896	c.864T>C	c.(862-864)atT>atC	p.I288I		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I288I(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TAAACCCCATTATCTACACTC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	1											67	70	69					1																	248685811		2203	4300	6503	246752434	SO:0001819	synonymous_variant	391211				CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.864T>C	1.37:g.248685811T>C			246752434	B2RP33	Silent	SNP	ENST00000343414.4	37	CCDS31119.1																																																																																				0.443	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		C	248685811	T	C	248685811	2	2	61	1	0	0	0	0	0	0	0	1	11031	1742	61	4		4	OR2G6	1	248685811	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	116381	248685811	564810	1205	9190										
OR2T34	127068	broad.mit.edu	37	chr1	248737422	248737422	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaccatgatgggggtgaGaagcatgaggatgcagcaca	16	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248737422G>A	ENST00000328782.2	-	1	658	c.637C>T	c.(637-639)Ctc>Ttc	p.L213F		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L213F(1)|p.L213I(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGGGGGTGAGAAGCATGAGG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	1											198	212	208					1																	248737422		2113	4300	6413	246804045	SO:0001583	missense	127068			BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.637C>T	1.37:g.248737422G>A	ENSP00000330904:p.Leu213Phe		246804045	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	12.97	2.096423	0.36952	.	.	ENSG00000183310	ENST00000328782	T	0.39056	1.1	2.37	0.0232	0.14136	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.48926	0.1527	L	0.61387	1.9	0.09310	N	1	D	0.56287	0.975	P	0.58130	0.833	T	0.35822	-0.9773	9	0.66056	D	0.02	.	3.6116	0.08062	0.2543:0.0:0.5517:0.194	.	213	Q8NGX1	O2T34_HUMAN	F	213	ENSP00000330904:L213F	ENSP00000330904:L213F	L	-	1	0	OR2T34	246804045	0.001000	0.12720	0.076000	0.20297	0.110000	0.19582	0.210000	0.17455	0.208000	0.20626	0.123000	0.15791	CTC		0.557	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		A	248737422	G	A	248737422	3	1	61	1	0	0	0	0	1	0	0	0	11056	942	33	3	323	3	OR2T34	1	248737422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51611	248737422	513199	1206	9191										
OR2T34	127068	broad.mit.edu	37	chr1	248737750	248737750	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtggaagaacatctggatCccacagcctgacggggaaat	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248737750C>T	ENST00000328782.2	-	1	330	c.309G>A	c.(307-309)ggG>ggA	p.G103G		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G103G(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACATCTGGATCCCACAGCCTG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	1											97	88	91					1																	248737750		2157	4270	6427	246804373	SO:0001819	synonymous_variant	127068			BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.309G>A	1.37:g.248737750C>T			246804373	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	37	CCDS31120.1																																																																																				0.552	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		T	248737750	C	T	248737750	2	4	61	1	0	0	0	0	0	0	0	1	11056	842	30	3		3	OR2T34	1	248737750	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	328	248737750	512871	1207	9192										
OR2T10	127069	broad.mit.edu	37	chr1	248756259	248756259	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaggatgacatcatatCtttctcaggagtttggtagg	11	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:248756259C>A	ENST00000330500.2	-	1	841	c.811G>T	c.(811-813)Gat>Tat	p.D271Y	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271Y(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GACATCATATCTTTCTCAGGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											57	63	61					1																	248756259		2046	4232	6278	246822882	SO:0001583	missense	127069				CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"GPCR / Class A : Olfactory receptors"	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.811G>T	1.37:g.248756259C>A	ENSP00000329210:p.Asp271Tyr		246822882	B2RNK7	Missense_Mutation	SNP	ENST00000330500.2	37	CCDS31121.1	.	.	.	.	.	.	.	.	.	.	.	4.275	0.050142	0.08243	.	.	ENSG00000184022	ENST00000330500	T	0.00256	8.42	2.35	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00754	0.0025	H	0.96239	3.79	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.33471	-0.9867	9	0.87932	D	0	.	6.7622	0.23546	0.0:0.8459:0.0:0.1541	.	271	Q8NGZ9	O2T10_HUMAN	Y	271	ENSP00000329210:D271Y	ENSP00000329210:D271Y	D	-	1	0	OR2T10	246822882	0.000000	0.05858	0.590000	0.28732	0.005000	0.04900	0.217000	0.17603	1.123000	0.41961	0.447000	0.29281	GAT		0.423	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097139.1	NM_001004693		A	248756259	C	A	248756259	3	1	61	1	0	0	0	0	1	0	0	0	11048	913	32	2	130	2	OR2T10	1	248756259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18509	248756259	494362	1208	9193										
ZNF692	55657	broad.mit.edu	37	chr1	249150502	249150502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgctcatctggggaggagCtgtaggtccataagctggca	14	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr1:249150502C>T	ENST00000306601.4	-	6	810	c.644G>A	c.(643-645)aGc>aAc	p.S215N	ZNF692_ENST00000366469.5_Missense_Mutation_p.S215N|ZNF692_ENST00000451251.1_Missense_Mutation_p.S220N|ZNF692_ENST00000427146.1_Intron|ZNF692_ENST00000468455.1_5'UTR|AL672294.1_ENST00000417047.1_RNA|ZNF692_ENST00000366471.3_Intron	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S215N(1)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TGGGGAGGAGCTGTAGGTCCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											190	159	170					1																	249150502		2203	4300	6503	247117125	SO:0001583	missense	55657			BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163		"Zinc fingers, C2H2-type"	26049	protein-coding gene	gene with protein product						12477932	Standard	NM_001136036		Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.644G>A	1.37:g.249150502C>T	ENSP00000305483:p.Ser215Asn		247117125	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	Missense_Mutation	SNP	ENST00000306601.4	37	CCDS31127.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607499	0.66558	.	.	ENSG00000171163	ENST00000306601;ENST00000366469;ENST00000451251	T;T;T	0.07800	3.17;3.21;3.16	4.72	4.72	0.59763	.	0.429783	0.24492	N	0.038045	T	0.12561	0.0305	L	0.46157	1.445	0.80722	D	1	P;P	0.51057	0.941;0.941	P;P	0.49597	0.616;0.616	T	0.09751	-1.0660	10	0.19147	T	0.46	-9.053	13.3852	0.60791	0.0:1.0:0.0:0.0	.	220;215	B4DXZ0;Q9BU19	.;ZN692_HUMAN	N	215;215;220	ENSP00000305483:S215N;ENSP00000355425:S215N;ENSP00000391200:S220N	ENSP00000305483:S215N	S	-	2	0	ZNF692	247117125	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.666000	0.54540	2.626000	0.88956	0.462000	0.41574	AGC		0.547	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097298.1	NM_017865		T	249150502	C	T	249150502	3	4	61	1	0	0	0	0	1	0	0	0	18136	797	28	3	943	3	ZNF692	1	249150502	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	394243	249150502	100119	1209	9194										
TMEM18	129787	broad.mit.edu	37	chr2	669830	669830	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatccccctggagtcgaaaTactggtatttcgaaaataat	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:669830T>C	ENST00000281017.3	-	4	347	c.254A>G	c.(253-255)tAt>tGt	p.Y85C	TMEM18_ENST00000405941.3_Missense_Mutation_p.Y88C|TMEM18_ENST00000355654.2_Missense_Mutation_p.Y72C	NM_152834.2	NP_690047.2	Q96B42	TMM18_HUMAN	transmembrane protein 18	85					cell migration (GO:0016477)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)	p.Y85C(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)	10	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		GGAGTCGAAATACTGGTATTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	62	62					2																	669830		2203	4300	6503	659830	SO:0001583	missense	129787			AL137269	CCDS33141.1	2p25.3	2008-02-05			ENSG00000151353	ENSG00000151353			25257	protein-coding gene	gene with protein product		613220				12477932	Standard	NM_152834		Approved	DKFZp434C1714	uc002qwl.3	Q96B42	OTTHUMG00000151381	ENST00000281017.3:c.254A>G	2.37:g.669830T>C	ENSP00000281017:p.Tyr85Cys		659830	D6W4X9|Q8N5H2|Q9NTH3	Missense_Mutation	SNP	ENST00000281017.3	37	CCDS33141.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.050590	0.55218	.	.	ENSG00000151353	ENST00000281017;ENST00000355654;ENST00000405941	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.82393	0.5027	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86103	0.1557	9	0.87932	D	0	-14.1017	12.4143	0.55483	0.0:0.0:0.0:1.0	.	85	Q96B42	TMM18_HUMAN	C	85;72;88	.	ENSP00000281017:Y85C	Y	-	2	0	TMEM18	659830	1.000000	0.71417	0.996000	0.52242	0.254000	0.26022	6.597000	0.74118	2.185000	0.69588	0.449000	0.29647	TAT		0.358	TMEM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322427.1	NM_152834		C	669830	T	C	669830	3	2	61	1	0	0	0	0	1	0	0	0	16137	1406	49	4	176	4	TMEM18	2	669830	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09		669830	242529543	1210	9195										
SNTG2	54221	broad.mit.edu	37	chr2	1094066	1094066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagcacaacgtccctgtcGtcatatcaaaaatattcgaa	6	11	2	1	rs200509062		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1094066G>A	ENST00000308624.5	+	4	424	c.295G>A	c.(295-297)Gtc>Atc	p.V99I	SNTG2_ENST00000407292.1_Intron	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	99	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.V99I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CGTCCCTGTCGTCATATCAAA	0.378													G|||	1	0.000199681	0	0	5008	,	,		18356	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											114	108	109					2																	1094066		1879	4107	5986	1084066	SO:0001583	missense	54221			AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.295G>A	2.37:g.1094066G>A	ENSP00000311837:p.Val99Ile		1084066	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.78	3.696372	0.68386	.	.	ENSG00000172554	ENST00000308624	T	0.27720	1.65	4.42	4.42	0.53409	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.42086	0.1187	L	0.28054	0.825	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.39881	-0.9592	10	0.56958	D	0.05	.	14.8075	0.69968	0.0:0.0:1.0:0.0	.	99	Q9NY99	SNTG2_HUMAN	I	99	ENSP00000311837:V99I	ENSP00000311837:V99I	V	+	1	0	SNTG2	1084066	1.000000	0.71417	0.997000	0.53966	0.432000	0.31715	7.431000	0.80335	1.967000	0.57214	0.563000	0.77884	GTC		0.378	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		A	1094066	G	A	1094066	3	1	61	1	0	0	0	0	1	0	0	0	14912	1145	40	1	309	1	SNTG2	2	1094066	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	424236	1094066	242105307	1211	9196										
SNTG2	54221	broad.mit.edu	37	chr2	1251191	1251191	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagcactgaagggcccgtcCttctacgttttcagcactcc	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1251191C>A	ENST00000308624.5	+	12	1110	c.981C>A	c.(979-981)tcC>tcA	p.S327S	SNTG2_ENST00000407292.1_Silent_p.S200S	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	327	PH.				central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.S327S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		AGGGCCCGTCCTTCTACGTTT	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	2											63	62	62					2																	1251191		2003	4190	6193	1233742	SO:0001819	synonymous_variant	54221			AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.981C>A	2.37:g.1251191C>A			1233742	Q05AH5	Silent	SNP	ENST00000308624.5	37	CCDS46220.1																																																																																				0.537	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		A	1251191	C	A	1251191	2	1	61	1	0	0	0	0	0	0	0	1	14912	668	24	2		2	SNTG2	2	1251191	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157125	1251191	241948182	1212	9197										
TPO	7173	broad.mit.edu	37	chr2	1499800	1499800	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgtcttcacggatgcacaGaggcgtgagctggagaagca	14	10	2	3	rs200234204		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1499800G>T	ENST00000345913.4	+	12	2137	c.2046G>T	c.(2044-2046)caG>caT	p.Q682H	TPO_ENST00000382198.1_Missense_Mutation_p.Q509H|TPO_ENST00000346956.3_Missense_Mutation_p.Q682H|TPO_ENST00000337415.3_Missense_Mutation_p.Q682H|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Missense_Mutation_p.Q625H|TPO_ENST00000329066.4_Missense_Mutation_p.Q682H|TPO_ENST00000349624.3_Missense_Mutation_p.Q509H	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	682					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.Q682H(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CGGATGCACAGAGGCGTGAGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	62	67					2																	1499800		2203	4300	6503	1478807	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2046G>T	2.37:g.1499800G>T	ENSP00000318820:p.Gln682His		1478807	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.50|11.50	1.656104|1.656104	0.29425|0.29425	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607|ENST00000446278	T;T;T;T;T;T;T;T;T|.	0.71817|.	-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6|.	4.52|4.52	2.61|2.61	0.31194|0.31194	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82504|0.82504	0.5051|0.5051	H|H	0.97611|0.97611	4.04|4.04	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.998;1.0;1.0|.	T|T	0.83021|0.83021	-0.0167|-0.0167	10|5	0.87932|.	D|.	0|.	-37.6232|-37.6232	6.8225|6.8225	0.23864|0.23864	0.3517:0.0:0.6483:0.0|0.3517:0.0:0.6483:0.0	.|.	682;509;625;682|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	H|I	682;682;682;509;682;625;509;611;156|157	ENSP00000337263:Q682H;ENSP00000318820:Q682H;ENSP00000263886:Q682H;ENSP00000332044:Q509H;ENSP00000329869:Q682H;ENSP00000371636:Q625H;ENSP00000371633:Q509H;ENSP00000405788:Q611H;ENSP00000419461:Q156H|.	ENSP00000329869:Q682H|.	Q|R	+|+	3|2	2|0	TPO|TPO	1478807|1478807	1.000000|1.000000	0.71417|0.71417	0.178000|0.178000	0.23040|0.23040	0.048000|0.048000	0.14542|0.14542	1.917000|1.917000	0.39996|0.39996	0.991000|0.991000	0.38814|0.38814	0.561000|0.561000	0.74099|0.74099	CAG|AGA		0.582	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1499800	G	T	1499800	3	4	61	1	0	0	0	0	1	0	0	0	16450	933	33	2	2088	2	TPO	2	1499800	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248609	1499800	241699573	1213	9198										
PXDN	7837	broad.mit.edu	37	chr2	1651996	1651997	+	Missense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatctcatttttcaggtcctCgaacgtgtgtgccgccgata					rs199680670		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1651996_1651997CG>TA	ENST00000252804.4	-	17	3605_3606	c.3555_3556CG>TA	c.(3553-3558)ttCGag>ttTAag	p.E1186K		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1186					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.F1185>?(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TTCAGGTCCTCGAACGTGTGTG	0.569																																																1	Complex(1)	large_intestine(1)	2																																								1631004	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3555_3556delinsTA	2.37:g.1651996_1651997delinsTA	ENSP00000252804:p.Glu1186Lys		1631003	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	DNP	ENST00000252804.4	37	CCDS46221.1																																																																																				0.569	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		TA	1651997	CG	TA	1651996	3	4	61	1	0	0	0	0	1	0	0	0	12884	893	31	1	911	1	PXDN	2	1651996	Missense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	152196	1651996	241547377	1214	9199										
PXDN	7837	broad.mit.edu	37	chr2	1653138	1653138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcgggtgtgacggtctccGtcccgatcagggtggtggac	17	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1653138G>A	ENST00000252804.4	-	17	2464	c.2414C>T	c.(2413-2415)aCg>aTg	p.T805M		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	805					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.T805M(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GACGGTCTCCGTCCCGATCAG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	73	69					2																	1653138		2159	4253	6412	1632145	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2414C>T	2.37:g.1653138G>A	ENSP00000252804:p.Thr805Met		1632145	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915582	0.52546	.	.	ENSG00000130508	ENST00000252804	T	0.69435	-0.4	5.33	5.33	0.75918	.	0.110977	0.64402	D	0.000010	D	0.84257	0.5432	M	0.87328	2.875	0.58432	D	0.999999	D	0.76494	0.999	D	0.66716	0.946	D	0.86779	0.1978	10	0.87932	D	0	-18.5012	19.4361	0.94796	0.0:0.0:1.0:0.0	.	805	Q92626	PXDN_HUMAN	M	805	ENSP00000252804:T805M	ENSP00000252804:T805M	T	-	2	0	PXDN	1632145	1.000000	0.71417	0.008000	0.14137	0.101000	0.19017	9.717000	0.98755	2.661000	0.90470	0.558000	0.71614	ACG		0.652	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1653138	G	A	1653138	3	1	61	1	0	0	0	0	1	0	0	0	12884	1145	40	1	2053	1	PXDN	2	1653138	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1142	1653138	241546235	1215	9200										
PXDN	7837	broad.mit.edu	37	chr2	1657475	1657475	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgtccgttcaaagatttCtcccgcccgtgcctgttcaa	7	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1657475C>A	ENST00000252804.4	-	16	2079	c.2029G>T	c.(2029-2031)Gaa>Taa	p.E677*		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	677					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.E677*(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TCAAAGATTTCTCCCGCCCGT	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											73	76	75					2																	1657475		2018	4179	6197	1636482	SO:0001587	stop_gained	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2029G>T	2.37:g.1657475C>A	ENSP00000252804:p.Glu677*		1636482	A8QM65|D6W4Y0|Q4KMG2	Nonsense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.765651|6.765651	0.97821|0.97821	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000433670|ENST00000252804	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.77432|.	0.4129|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.80264|.	-0.1455|.	4|.	.|0.66056	.|D	.|0.02	-41.5373|-41.5373	18.6167|18.6167	0.91305|0.91305	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	672|677	.|.	.|ENSP00000252804:E677X	E|E	-|-	3|1	2|0	PXDN|PXDN	1636482|1636482	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.215000|0.215000	0.24574|0.24574	7.644000|7.644000	0.83416|0.83416	2.468000|2.468000	0.83385|0.83385	0.585000|0.585000	0.79938|0.79938	GAG|GAA		0.512	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1657475	C	A	1657475	4	1	61	1	0	0	0	0	0	1	0	0	12884	922	32	2	2442	2	PXDN	2	1657475	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4337	1657475	241541898	1216	9201										
MYT1L	23040	broad.mit.edu	37	chr2	1795758	1795758	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagtcacgtaagcatcaaAattttgttcattgattggat	8	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1795758A>C	ENST00000399161.2	-	25	4189	c.3442T>G	c.(3442-3444)Ttt>Gtt	p.F1148V	MYT1L_ENST00000407844.1_Missense_Mutation_p.F146V|MYT1L_ENST00000428368.2_Missense_Mutation_p.F1146V	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1148					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.F1148V(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TAAGCATCAAAATTTTGTTCA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	70	73					2																	1795758		1824	4083	5907	1774765	SO:0001583	missense	23040			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3442T>G	2.37:g.1795758A>C	ENSP00000382114:p.Phe1148Val		1774765	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	A	21.1	4.103331	0.76983	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000407844;ENST00000428368	T;T	0.55413	0.52;0.52	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.69780	0.3149	M	0.73962	2.25	0.80722	D	1	P;D;D	0.67145	0.844;0.996;0.991	B;P;P	0.60012	0.366;0.867;0.73	T	0.72456	-0.4288	10	0.54805	T	0.06	-13.8934	16.3275	0.82990	1.0:0.0:0.0:0.0	.	146;1148;1146	Q9UL68-3;Q9UL68;Q9UL68-4	.;MYT1L_HUMAN;.	V	1148;1094;146;1146	ENSP00000382114:F1148V;ENSP00000396103:F1146V	ENSP00000295067:F1094V	F	-	1	0	MYT1L	1774765	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.251000	0.95483	2.266000	0.75297	0.529000	0.55759	TTT		0.294	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		C	1795758	A	C	1795758	3	2	61	1	0	0	0	0	1	0	0	0	10137	14	1	4	122	4	MYT1L	2	1795758	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	138283	1795758	241403615	1217	9202										
MYT1L	23040	broad.mit.edu	37	chr2	1843011	1843011	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccgtcttgaccgacttcCaggagaactgggagccattc	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1843011C>A	ENST00000399161.2	-	21	3737	c.2990G>T	c.(2989-2991)tGg>tTg	p.W997L	MYT1L_ENST00000471668.1_5'UTR|MYT1L_ENST00000428368.2_Missense_Mutation_p.W995L|MYT1L_ENST00000407844.1_5'UTR	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	997					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.W997L(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GACCGACTTCCAGGAGAACTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											37	44	41					2																	1843011		2034	4186	6220	1822018	SO:0001583	missense	23040			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2990G>T	2.37:g.1843011C>A	ENSP00000382114:p.Trp997Leu		1822018	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	C	34	5.352917	0.95830	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000399157;ENST00000428368	T;T	0.46063	0.88;0.88	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	L	0.61036	1.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.63238	-0.6682	10	0.51188	T	0.08	-25.4149	19.5365	0.95255	0.0:1.0:0.0:0.0	.	997;995	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	L	997;943;51;995	ENSP00000382114:W997L;ENSP00000396103:W995L	ENSP00000295067:W943L	W	-	2	0	MYT1L	1822018	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.755000	0.85180	2.618000	0.88619	0.563000	0.77884	TGG		0.647	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1843011	C	A	1843011	3	1	61	1	0	0	0	0	1	0	0	0	10137	595	21	2	590	2	MYT1L	2	1843011	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47253	1843011	241356362	1218	9203										
MYT1L	23040	broad.mit.edu	37	chr2	1855434	1855434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgatgagaagcataattgCcggtgatatgtccagaacca	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:1855434C>T	ENST00000399161.2	-	19	3500	c.2753G>A	c.(2752-2754)gGc>gAc	p.G918D	MYT1L_ENST00000428368.2_Missense_Mutation_p.G916D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	918					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G918D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		AGCATAATTGCCGGTGATATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											117	114	115					2																	1855434		1942	4176	6118	1834441	SO:0001583	missense	23040			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2753G>A	2.37:g.1855434C>T	ENSP00000382114:p.Gly918Asp		1834441	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	C	20.1	3.932066	0.73442	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.72615	-0.67;-0.65	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.87176	0.6112	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88953	0.3388	10	0.66056	D	0.02	-45.0511	16.934	0.86198	0.0:1.0:0.0:0.0	.	918;916	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	D	918;864;916	ENSP00000382114:G918D;ENSP00000396103:G916D	ENSP00000295067:G864D	G	-	2	0	MYT1L	1834441	1.000000	0.71417	0.999000	0.59377	0.510000	0.34073	5.513000	0.67037	2.731000	0.93534	0.557000	0.71058	GGC		0.423	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1855434	C	T	1855434	3	4	61	1	0	0	0	0	1	0	0	0	10137	739	26	3	835	3	MYT1L	2	1855434	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12423	1855434	241343939	1219	9204										
TTC15	51112	broad.mit.edu	37	chr2	3405575	3405575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttaaagacttgatgcttCgctttctgggtgaaaaagct	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:3405575C>T	ENST00000324266.5	+	3	1270	c.1075C>T	c.(1075-1077)Cgc>Tgc	p.R359C	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.R359C	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	359					vesicle-mediated transport (GO:0016192)			p.R359C(1)									CTTGATGCTTCGCTTTCTGGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											164	162	163					2																	3405575		2203	4300	6503	3384582	SO:0001583	missense	51112			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1075C>T	2.37:g.3405575C>T	ENSP00000324318:p.Arg359Cys		3384582	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.794064	0.50102	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.53423	0.62;0.62	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.68742	0.3034	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.989;0.991	T	0.71636	-0.4533	10	0.72032	D	0.01	.	17.7305	0.88376	0.0:1.0:0.0:0.0	.	342;359	E7ENL7;Q8WVT3	.;TPC12_HUMAN	C	359;342;359	ENSP00000371544:R359C;ENSP00000324318:R359C	ENSP00000303612:R342C	R	+	1	0	TTC15	3384582	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.869000	0.75521	2.605000	0.88082	0.655000	0.94253	CGC		0.393	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		T	3405575	C	T	3405575	3	4	61	1	0	0	0	0	1	0	0	0	16722	884	31	1	1081	1	TTC15	2	3405575	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1550141	3405575	239793798	1220	9205										
ALLC	55821	broad.mit.edu	37	chr2	3743375	3743375	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactgcaactgaccccaaaGaacctgcagacctagtggcc	10	14	0	3	rs372781677		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:3743375G>T	ENST00000252505.3	+	8	742	c.580G>T	c.(580-582)Gaa>Taa	p.E194*	ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	213					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)	p.E194*(1)		breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		TGACCCCAAAGAACCTGCAGA	0.428										HNSCC(21;0.051)																																						1	Substitution - Nonsense(1)	large_intestine(1)	2						G	stop/GLU	0,3790		0,0,1895	97	97	97		580	5.4	0.1	2		97	1,8203		0,1,4101	no	stop-gained	ALLC	NM_018436.3		0,1,5996	TT,TG,GG		0.0122,0.0,0.0083		194/392	3743375	1,11993	1895	4102	5997	3721250	SO:0001587	stop_gained	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.580G>T	2.37:g.3743375G>T	ENSP00000252505:p.Glu194*		3721250	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Nonsense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	G	37	6.434736	0.97564	0.0	1.22E-4	ENSG00000151360	ENST00000252505	.	.	.	5.42	5.42	0.78866	.	0.256882	0.44097	D	0.000488	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-27.592	16.7056	0.85371	0.0:0.0:1.0:0.0	.	.	.	.	X	194	.	ENSP00000252505:E194X	E	+	1	0	ALLC	3721250	1.000000	0.71417	0.139000	0.22197	0.619000	0.37552	4.199000	0.58426	2.554000	0.86153	0.561000	0.74099	GAA		0.428	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			T	3743375	G	T	3743375	4	4	61	1	0	0	0	0	0	1	0	0	534	943	33	2	606	2	ALLC	2	3743375	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	337800	3743375	239455998	1221	9206										
CMPK2	129607	broad.mit.edu	37	chr2	7001396	7001396	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccaaagagtaaaaagctCttctaatgatagttggttca	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:7001396C>A	ENST00000256722.5	-	3	910	c.911G>T	c.(910-912)aGa>aTa	p.R304I	CMPK2_ENST00000458098.1_Missense_Mutation_p.R304I|CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000404168.1_Missense_Mutation_p.R304I	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	304					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)	p.R304I(1)		large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GTAAAAAGCTCTTCTAATGAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											117	107	110					2																	7001396		1898	4117	6015	6918847	SO:0001583	missense	129607				CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"cytidylate kinase 2"	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.911G>T	2.37:g.7001396C>A	ENSP00000256722:p.Arg304Ile		6918847	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	37	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	C	32	5.121787	0.94385	.	.	ENSG00000134326	ENST00000458098;ENST00000256722;ENST00000404168	D;D;D	0.94092	-3.35;-3.35;-3.35	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.97111	0.9056	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97509	1.0065	10	0.72032	D	0.01	-11.3612	19.2026	0.93717	0.0:1.0:0.0:0.0	.	304;304	Q5EBM0-3;Q5EBM0	.;CMPK2_HUMAN	I	304	ENSP00000396385:R304I;ENSP00000256722:R304I;ENSP00000384915:R304I	ENSP00000256722:R304I	R	-	2	0	CMPK2	6918847	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.124000	0.77185	2.535000	0.85469	0.563000	0.77884	AGA		0.418	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315		A	7001396	C	A	7001396	3	1	61	1	0	0	0	0	1	0	0	0	3587	913	32	2	450	2	CMPK2	2	7001396	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3258021	7001396	236197977	1222	9207										
RNF144A	9781	broad.mit.edu	37	chr2	7154894	7154894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagatataaaaagctacaaTttgaaagaggtaggtgcctg	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:7154894T>A	ENST00000320892.6	+	5	734	c.292T>A	c.(292-294)Ttt>Att	p.F98I	RNF144A_ENST00000467276.1_Intron	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	98					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.F98I(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		AAAGCTACAATTTGAAAGAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	109	108					2																	7154894		2203	4300	6503	7072345	SO:0001583	missense	9781			D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"RING-type (C3HC4) zinc fingers"	20457	protein-coding gene	gene with protein product			"ring finger protein 144"	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.292T>A	2.37:g.7154894T>A	ENSP00000321330:p.Phe98Ile		7072345	D6W4Y6|Q585H5	Missense_Mutation	SNP	ENST00000320892.6	37	CCDS1657.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.2|21.2	4.111505|4.111505	0.77210|0.77210	.|.	.|.	ENSG00000151692|ENSG00000151692	ENST00000320892;ENST00000427092|ENST00000432850	T|.	0.80480|.	-1.38|.	5.52|5.52	4.37|4.37	0.52481|0.52481	Zinc finger, C6HC-type (2);|.	0.131604|.	0.64402|.	D|.	0.000001|.	T|T	0.59972|0.59972	0.2233|0.2233	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	B|.	0.26445|.	0.149|.	B|.	0.28385|.	0.089|.	T|T	0.56282|0.56282	-0.8005|-0.8005	10|5	0.28530|.	T|.	0.3|.	.|.	11.3655|11.3655	0.49668|0.49668	0.0:0.0708:0.0:0.9292|0.0:0.0708:0.0:0.9292	.|.	98|.	P50876|.	R144A_HUMAN|.	I|K	98|93	ENSP00000321330:F98I|.	ENSP00000321330:F98I|.	F|N	+|+	1|3	0|2	RNF144A|RNF144A	7072345|7072345	1.000000|1.000000	0.71417|0.71417	0.934000|0.934000	0.37439|0.37439	0.986000|0.986000	0.74619|0.74619	7.218000|7.218000	0.77991|0.77991	1.038000|1.038000	0.40049|0.40049	0.533000|0.533000	0.62120|0.62120	TTT|AAT		0.373	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	NM_014746		A	7154894	T	A	7154894	3	1	61	1	0	0	0	0	1	0	0	0	13482	1493	52	5	302	5	RNF144A	2	7154894	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	153498	7154894	236044479	1223	9208										
KIDINS220	57498	broad.mit.edu	37	chr2	8871684	8871684	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgacctttcggaagatttCttgcctgggagaagcttact	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:8871684C>A	ENST00000256707.3	-	30	4663	c.4482G>T	c.(4480-4482)aaG>aaT	p.K1494N	KIDINS220_ENST00000418530.1_Missense_Mutation_p.K1395N|KIDINS220_ENST00000427284.1_Missense_Mutation_p.K1475N|KIDINS220_ENST00000473731.1_Missense_Mutation_p.K1475N	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1494					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.K1494N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CGGAAGATTTCTTGCCTGGGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	56	55					2																	8871684		1882	4102	5984	8789135	SO:0001583	missense	57498			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4482G>T	2.37:g.8871684C>A	ENSP00000256707:p.Lys1494Asn		8789135	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.743746	0.49151	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.69435	-0.4;-0.39;-0.36;-0.39	5.92	4.12	0.48240	.	0.629622	0.18325	N	0.144676	T	0.60792	0.2296	N	0.24115	0.695	0.36468	D	0.867084	B;B;P	0.49090	0.127;0.078;0.919	B;B;P	0.49561	0.135;0.083;0.615	T	0.68205	-0.5470	10	0.72032	D	0.01	.	11.9321	0.52853	0.0:0.8119:0.1225:0.0656	.	1395;1494;348	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	N	1494;1475;1395;1475	ENSP00000256707:K1494N;ENSP00000411849:K1475N;ENSP00000414923:K1395N;ENSP00000418974:K1475N	ENSP00000256707:K1494N	K	-	3	2	KIDINS220	8789135	1.000000	0.71417	0.981000	0.43875	0.911000	0.54048	3.826000	0.55738	0.831000	0.34780	0.655000	0.94253	AAG		0.483	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		A	8871684	C	A	8871684	3	1	61	1	0	0	0	0	1	0	0	0	8292	912	32	2	837	2	KIDINS220	2	8871684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1716790	8871684	234327689	1224	9209										
MBOAT2	129642	broad.mit.edu	37	chr2	9000883	9000883	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaatgaaataatgtctaaaGttatttctcatctgaaataa	4	5	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:9000883G>T	ENST00000305997.3	-	12	1395	c.1197C>A	c.(1195-1197)aaC>aaA	p.N399K	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	399					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.N399K(1)	MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AATGTCTAAAGTTATTTCTCA	0.299																																					Ovarian(194;1699 3813 22401)											1	Substitution - Missense(1)	large_intestine(1)	2											49	47	48					2																	9000883		2203	4292	6495	8918334	SO:0001583	missense	129642			BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.1197C>A	2.37:g.9000883G>T	ENSP00000302177:p.Asn399Lys		8918334	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234276	0.58886	.	.	ENSG00000143797	ENST00000305997	T	0.72282	-0.64	5.96	3.18	0.36537	.	0.041338	0.85682	N	0.000000	T	0.75184	0.3815	L	0.58810	1.83	0.51767	D	0.999939	D	0.63046	0.992	D	0.66351	0.943	T	0.70215	-0.4933	10	0.34782	T	0.22	-23.8809	5.4193	0.16392	0.3165:0.0:0.5538:0.1298	.	399	Q6ZWT7	MBOA2_HUMAN	K	399	ENSP00000302177:N399K	ENSP00000302177:N399K	N	-	3	2	MBOAT2	8918334	1.000000	0.71417	0.634000	0.29324	0.954000	0.61252	2.169000	0.42434	0.408000	0.25621	-0.182000	0.12963	AAC		0.299	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		T	9000883	G	T	9000883	3	4	61	1	0	0	0	0	1	0	0	0	9387	1020	36	2	373	2	MBOAT2	2	9000883	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129199	9000883	234198490	1225	9210										
MBOAT2	129642	broad.mit.edu	37	chr2	9098719	9098719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttgaatgtagataagttCgaaaccaaatggctgctagc	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:9098719C>T	ENST00000305997.3	-	2	326	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	43					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R43Q(2)	MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TAGATAAGTTCGAAACCAAAT	0.358																																					Ovarian(194;1699 3813 22401)											2	Substitution - Missense(2)	large_intestine(2)	2											70	71	71					2																	9098719		2203	4300	6503	9016170	SO:0001583	missense	129642			BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.128G>A	2.37:g.9098719C>T	ENSP00000302177:p.Arg43Gln		9016170	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041664	0.93685	.	.	ENSG00000143797	ENST00000305997	T	0.12465	2.68	6.03	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.55774	-0.8088	10	0.72032	D	0.01	-4.7565	17.4628	0.87624	0.0:0.8759:0.1241:0.0	.	43;43	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	Q	43	ENSP00000302177:R43Q	ENSP00000302177:R43Q	R	-	2	0	MBOAT2	9016170	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.409000	0.80053	1.547000	0.49401	0.655000	0.94253	CGA		0.358	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		T	9098719	C	T	9098719	3	4	61	1	0	0	0	0	1	0	0	0	9387	884	31	1	1482	1	MBOAT2	2	9098719	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97836	9098719	234100654	1226	9211										
CPSF3	51692	broad.mit.edu	37	chr2	9593094	9593094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaggccagcgggtctcagGaatacttgttaaaagaaact	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:9593094G>T	ENST00000238112.3	+	12	1654	c.1448G>T	c.(1447-1449)gGa>gTa	p.G483V	CPSF3_ENST00000460593.1_Missense_Mutation_p.G446V	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	483					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.G483V(1)		NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	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)		CGGGTCTCAGGAATACTTGTT	0.348																																					Colon(194;1259 2048 3845 5218 19985)											1	Substitution - Missense(1)	large_intestine(1)	2											55	53	54					2																	9593094		2203	4299	6502	9510545	SO:0001583	missense	51692			AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"cleavage and polyadenylation specific factor 3, 73kD subunit"			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.1448G>T	2.37:g.9593094G>T	ENSP00000238112:p.Gly483Val		9510545	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	37	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.864412	0.91511	.	.	ENSG00000119203	ENST00000238112;ENST00000540142;ENST00000427001;ENST00000460593	T;T	0.69306	-0.39;-0.36	5.87	5.87	0.94306	-end-processing endonuclease polyadenylation factor C-term (1);Pre-mRNA 3&apos (1);	0.114776	0.64402	D	0.000018	D	0.86234	0.5884	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87947	0.2721	10	0.87932	D	0	-16.2305	20.2181	0.98305	0.0:0.0:1.0:0.0	.	434;483	E7ER23;Q9UKF6	.;CPSF3_HUMAN	V	483;205;434;446	ENSP00000238112:G483V;ENSP00000418957:G446V	ENSP00000238112:G483V	G	+	2	0	CPSF3	9510545	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.658000	0.98594	2.785000	0.95823	0.655000	0.94253	GGA		0.348	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		T	9593094	G	T	9593094	3	4	61	1	0	0	0	0	1	0	0	0	3832	1174	41	2	1494	2	CPSF3	2	9593094	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	494375	9593094	233606279	1227	9212										
ADAM17	6868	broad.mit.edu	37	chr2	9666362	9666362	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagctcttcttttcactcGatgaacaagctctaatatga	6	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:9666362G>A	ENST00000310823.3	-	6	813	c.631C>T	c.(631-633)Cga>Tga	p.R211*	ADAM17_ENST00000497134.1_Nonsense_Mutation_p.R211*	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	211					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)	p.R211*(1)		breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CTTTTCACTCGATGAACAAGC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											144	127	133					2																	9666362		2203	4300	6503	9583813	SO:0001587	stop_gained	6868			U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.631C>T	2.37:g.9666362G>A	ENSP00000309968:p.Arg211*		9583813	O60226	Nonsense_Mutation	SNP	ENST00000310823.3	37	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	G	38	6.709999	0.97780	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	.	.	.	5.35	5.35	0.76521	.	0.114561	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4198	0.94716	0.0:0.0:1.0:0.0	.	.	.	.	X	211	.	ENSP00000309968:R211X	R	-	1	2	ADAM17	9583813	1.000000	0.71417	0.711000	0.30485	0.983000	0.72400	5.358000	0.66064	2.665000	0.90641	0.585000	0.79938	CGA		0.358	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			A	9666362	G	A	9666362	4	1	61	1	0	0	0	0	0	1	0	0	238	1066	37	1	1899	1	ADAM17	2	9666362	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73268	9666362	233533011	1228	9213										
GRHL1	29841	broad.mit.edu	37	chr2	10101455	10101455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagcgggtggtggttttcGatcggaatctcaatactgac	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:10101455G>A	ENST00000324907.9	+	4	695	c.559G>A	c.(559-561)Gat>Aat	p.D187N	GRHL1_ENST00000324883.5_Silent_p.S23S|GRHL1_ENST00000405379.2_Missense_Mutation_p.D187N	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	187					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S23S(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		GGTGGTTTTCGATCGGAATCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	2											123	118	120					2																	10101455		2203	4300	6503	10018906	SO:0001583	missense	29841			AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.559G>A	2.37:g.10101455G>A	ENSP00000324693:p.Asp187Asn		10018906	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	G	29.5	5.013654	0.93404	.	.	ENSG00000134317	ENST00000405379;ENST00000324907	T;T	0.12147	2.71;2.71	5.5	5.5	0.81552	.	0.043088	0.85682	D	0.000000	T	0.19525	0.0469	L	0.60455	1.87	0.80722	D	1	P	0.51351	0.944	B	0.41174	0.349	T	0.01574	-1.1321	10	0.72032	D	0.01	.	19.3932	0.94594	0.0:0.0:1.0:0.0	.	187	Q9NZI5	GRHL1_HUMAN	N	187	ENSP00000384209:D187N;ENSP00000324693:D187N	ENSP00000324693:D187N	D	+	1	0	GRHL1	10018906	1.000000	0.71417	0.996000	0.52242	0.802000	0.45316	9.188000	0.94921	2.594000	0.87642	0.563000	0.77884	GAT		0.542	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10101455	G	A	10101455	3	1	61	1	0	0	0	0	1	0	0	0	6784	1058	37	1	573	1	GRHL1	2	10101455	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	435093	10101455	233097918	1229	9214										
GRHL1	29841	broad.mit.edu	37	chr2	10104084	10104084	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggagacagtaccatgacGtacctgaacaaaggccagtt	10	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:10104084G>A	ENST00000324907.9	+	6	952	c.816G>A	c.(814-816)acG>acA	p.T272T	GRHL1_ENST00000324883.5_Silent_p.T83T|GRHL1_ENST00000405379.2_Silent_p.T272T	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	272					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T83T(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		GTACCATGACGTACCTGAACA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											155	129	138					2																	10104084		2203	4300	6503	10021535	SO:0001819	synonymous_variant	29841			AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.816G>A	2.37:g.10104084G>A			10021535	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	37	CCDS33144.2																																																																																				0.443	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10104084	G	A	10104084	2	1	61	1	0	0	0	0	0	0	0	1	6784	1132	40	1		1	GRHL1	2	10104084	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2629	10104084	233095289	1230	9215										
HPCAL1	3241	broad.mit.edu	37	chr2	10566860	10566860	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccctgcaggcaaactgtcCttggaagaattcatcagagg	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:10566860C>A	ENST00000381765.3	+	6	1021	c.495C>A	c.(493-495)tcC>tcA	p.S165S	HPCAL1_ENST00000307845.3_Silent_p.S165S	NM_134421.2	NP_602293.1	P37235	HPCL1_HUMAN	hippocalcin-like 1	165	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S165S(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		GCAAACTGTCCTTGGAAGAAT	0.577																																					Pancreas(70;1384 1800 31595 46836)											1	Substitution - coding silent(1)	large_intestine(1)	2											135	136	136					2																	10566860		2203	4300	6503	10484311	SO:0001819	synonymous_variant	3241				CCDS1671.1	2p25.1	2013-01-10			ENSG00000115756	ENSG00000115756		"EF-hand domain containing"	5145	protein-coding gene	gene with protein product	"visinin-like protein 3", "calcium-binding protein BDR-1"	600207				8038222, 14739275	Standard	NM_002149		Approved	BDR1, HLP2, VILIP-3	uc031rnq.1	P37235	OTTHUMG00000090451	ENST00000381765.3:c.495C>A	2.37:g.10566860C>A			10484311	Q969S5	Silent	SNP	ENST00000381765.3	37	CCDS1671.1																																																																																				0.577	HPCAL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206898.1	NM_002149		A	10566860	C	A	10566860	2	1	61	1	0	0	0	0	0	0	0	1	7351	668	24	2		2	HPCAL1	2	10566860	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	462776	10566860	232632513	1231	9216										
ODC1	4953	broad.mit.edu	37	chr2	10584280	10584280	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcactatcaaaagtcatCatctggactccattattagc	4	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:10584280C>A	ENST00000234111.4	-	5	900	c.390G>T	c.(388-390)atG>atT	p.M130I	ODC1_ENST00000405333.1_Missense_Mutation_p.M130I|SNORA80B_ENST00000383906.1_RNA|ODC1_ENST00000446285.1_5'UTR	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	130					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)	p.M130I(1)		NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	CAAAAGTCATCATCTGGACTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											205	215	212					2																	10584280		2203	4300	6503	10501731	SO:0001583	missense	4953				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.390G>T	2.37:g.10584280C>A	ENSP00000234111:p.Met130Ile		10501731	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	37	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290428	0.59976	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000537630	T;T	0.39406	1.08;1.08	5.37	5.37	0.77165	Orn/DAP/Arg decarboxylase 2, N-terminal (1);	0.036104	0.85682	D	0.000000	T	0.31482	0.0798	N	0.17082	0.46	0.58432	D	0.999999	B	0.06786	0.001	B	0.12156	0.007	T	0.04915	-1.0918	10	0.30078	T	0.28	.	19.1175	0.93348	0.0:1.0:0.0:0.0	.	130	P11926	DCOR_HUMAN	I	130;130;1	ENSP00000234111:M130I;ENSP00000385333:M130I	ENSP00000234111:M130I	M	-	3	0	ODC1	10501731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.929000	0.70096	2.508000	0.84585	0.655000	0.94253	ATG		0.433	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			A	10584280	C	A	10584280	3	1	61	1	0	0	0	0	1	0	0	0	10856	826	29	2	1027	2	ODC1	2	10584280	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17420	10584280	232615093	1232	9217										
PQLC3	130814	broad.mit.edu	37	chr2	11304376	11304376	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgcagaagtggatcataGacctggccatggtaagtatt	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11304376G>T	ENST00000295083.3	+	4	518	c.343G>T	c.(343-345)Gac>Tac	p.D115Y	PQLC3_ENST00000402361.1_Missense_Mutation_p.D115Y|PQLC3_ENST00000476787.1_Intron|PQLC3_ENST00000441908.2_Missense_Mutation_p.D115Y	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	115						integral component of membrane (GO:0016021)		p.D115Y(1)		kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		GTGGATCATAGACCTGGCCAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											180	137	152					2																	11304376		2203	4300	6503	11221827	SO:0001583	missense	130814			BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 22"	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.343G>T	2.37:g.11304376G>T	ENSP00000295083:p.Asp115Tyr		11221827	B2R8K1|B4DWA4	Missense_Mutation	SNP	ENST00000295083.3	37	CCDS1679.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153522	0.78114	.	.	ENSG00000162976	ENST00000445402;ENST00000295083;ENST00000441908;ENST00000402361	D;T;D;D	0.91996	-2.24;-0.63;-2.24;-2.95	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.96056	0.8715	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.985;0.999	D	0.95792	0.8825	10	0.52906	T	0.07	-21.8814	16.697	0.85338	0.0:0.0:1.0:0.0	.	115;115	B4DWA4;Q8N755	.;PQLC3_HUMAN	Y	138;115;115;115	ENSP00000410430:D138Y;ENSP00000295083:D115Y;ENSP00000406148:D115Y;ENSP00000384129:D115Y	ENSP00000295083:D115Y	D	+	1	0	PQLC3	11221827	1.000000	0.71417	0.992000	0.48379	0.922000	0.55478	7.804000	0.85993	2.669000	0.90835	0.561000	0.74099	GAC		0.418	PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391		T	11304376	G	T	11304376	3	4	61	1	0	0	0	0	1	0	0	0	12454	942	33	2	357	2	PQLC3	2	11304376	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	720096	11304376	231894997	1233	9218										
ROCK2	9475	broad.mit.edu	37	chr2	11334443	11334443	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttcactgtcatagaaaaGaatcttcttactgcttacaa	5	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11334443G>A	ENST00000315872.6	-	29	3995	c.3547C>T	c.(3547-3549)Ctt>Ttt	p.L1183F	ROCK2_ENST00000401753.1_Missense_Mutation_p.L940F	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	1183	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.L1183F(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TCATAGAAAAGAATCTTCTTA	0.254																																																2	Substitution - Missense(2)	large_intestine(2)	2											85	83	84					2																	11334443		1794	4040	5834	11251894	SO:0001583	missense	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.3547C>T	2.37:g.11334443G>A	ENSP00000317985:p.Leu1183Phe		11251894	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749802	0.89753	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.77489	-1.1;-1.1	5.81	5.81	0.92471	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.73385	0.3580	N	0.25426	0.745	0.80722	D	1	P	0.43701	0.815	P	0.47015	0.534	T	0.67562	-0.5639	10	0.13470	T	0.59	.	20.0755	0.97742	0.0:0.0:1.0:0.0	.	1183	O75116	ROCK2_HUMAN	F	1183;940;541	ENSP00000317985:L1183F;ENSP00000385509:L940F	ENSP00000317985:L1183F	L	-	1	0	ROCK2	11251894	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.864000	0.99589	2.749000	0.94314	0.460000	0.39030	CTT		0.254	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11334443	G	A	11334443	3	1	61	1	0	0	0	0	1	0	0	0	13555	942	33	3	639	3	ROCK2	2	11334443	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30067	11334443	231864930	1234	9219										
ROCK2	9475	broad.mit.edu	37	chr2	11338840	11338840	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaatttgttatttaattCttctttctcatttgcaagat	3	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11338840C>A	ENST00000315872.6	-	24	3419	c.2971G>T	c.(2971-2973)Gaa>Taa	p.E991*	ROCK2_ENST00000401753.1_Nonsense_Mutation_p.E748*	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	991	RHOA binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.E991*(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TTATTTAATTCTTCTTTCTCA	0.284																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											61	56	58					2																	11338840		1807	4065	5872	11256291	SO:0001587	stop_gained	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2971G>T	2.37:g.11338840C>A	ENSP00000317985:p.Glu991*		11256291	Q53QZ0|Q53SJ7|Q9UQN5	Nonsense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	C	45	11.991441	0.99625	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	.	.	.	5.5	5.5	0.81552	.	0.047611	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	19.3897	0.94576	0.0:1.0:0.0:0.0	.	.	.	.	X	991;748;349	.	ENSP00000317985:E991X	E	-	1	0	ROCK2	11256291	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.477000	0.81069	2.591000	0.87537	0.591000	0.81541	GAA		0.284	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11338840	C	A	11338840	4	1	61	1	0	0	0	0	0	1	0	0	13555	922	32	2	1235	2	ROCK2	2	11338840	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4397	11338840	231860533	1235	9220										
ROCK2	9475	broad.mit.edu	37	chr2	11342198	11342198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagaaatactgttctgcttCgagctgatcctggagctctt	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11342198C>T	ENST00000315872.6	-	21	3047	c.2599G>A	c.(2599-2601)Gaa>Aaa	p.E867K	ROCK2_ENST00000401753.1_Missense_Mutation_p.E624K	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	867					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.E867K(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TGTTCTGCTTCGAGCTGATCC	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	2											203	183	190					2																	11342198		1882	4120	6002	11259649	SO:0001583	missense	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2599G>A	2.37:g.11342198C>T	ENSP00000317985:p.Glu867Lys		11259649	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	C	36	5.827035	0.96996	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.67865	-0.29;0.6	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.83220	0.5207	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.81413	-0.0944	10	0.38643	T	0.18	.	20.0749	0.97738	0.0:1.0:0.0:0.0	.	867	O75116	ROCK2_HUMAN	K	867;624;225	ENSP00000317985:E867K;ENSP00000385509:E624K	ENSP00000317985:E867K	E	-	1	0	ROCK2	11259649	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.818000	0.86416	2.759000	0.94783	0.591000	0.81541	GAA		0.353	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			T	11342198	C	T	11342198	3	4	61	1	0	0	0	0	1	0	0	0	13555	893	31	1	1619	1	ROCK2	2	11342198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3358	11342198	231857175	1236	9221										
ROCK2	9475	broad.mit.edu	37	chr2	11351874	11351874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttatctgctagtcgtgcCtttgtggccttatgttcagc	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11351874C>A	ENST00000315872.6	-	18	2584	c.2136G>T	c.(2134-2136)aaG>aaT	p.K712N	ROCK2_ENST00000401753.1_Missense_Mutation_p.K469N	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	712	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.K712N(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CTAGTCGTGCCTTTGTGGCCT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	2											234	210	218					2																	11351874		1888	4107	5995	11269325	SO:0001583	missense	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2136G>T	2.37:g.11351874C>A	ENSP00000317985:p.Lys712Asn		11269325	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037555	0.75617	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.64438	-0.1;0.93	5.85	4.73	0.59995	.	0.047909	0.85682	D	0.000000	T	0.68412	0.2998	M	0.70275	2.135	0.53688	D	0.999973	D	0.52996	0.957	P	0.52823	0.71	T	0.67719	-0.5598	10	0.39692	T	0.17	.	9.6935	0.40143	0.0:0.0841:0.0:0.9159	.	712	O75116	ROCK2_HUMAN	N	712;469;70	ENSP00000317985:K712N;ENSP00000385509:K469N	ENSP00000317985:K712N	K	-	3	2	ROCK2	11269325	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.560000	0.36331	1.090000	0.41315	0.655000	0.94253	AAG		0.373	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11351874	C	A	11351874	3	1	61	1	0	0	0	0	1	0	0	0	13555	680	24	2	2094	2	ROCK2	2	11351874	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9676	11351874	231847499	1237	9222										
GREB1	9687	broad.mit.edu	37	chr2	11716645	11716645	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaccaaaggacctttaatCtgttggaaaggctcaggtga	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11716645C>A	ENST00000381486.2	+	5	921	c.621C>A	c.(619-621)atC>atA	p.I207I	GREB1_ENST00000263834.5_Silent_p.I207I|GREB1_ENST00000381483.2_Silent_p.I207I|GREB1_ENST00000389825.3_Silent_p.I97I|GREB1_ENST00000234142.5_Silent_p.I207I	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	207						integral component of membrane (GO:0016021)		p.I207I(3)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GACCTTTAATCTGTTGGAAAG	0.517																																					Ovarian(39;850 945 2785 23371 33093)											3	Substitution - coding silent(3)	large_intestine(3)	2											95	89	91					2																	11716645		2203	4300	6503	11634096	SO:0001819	synonymous_variant	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.621C>A	2.37:g.11716645C>A			11634096	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																				0.517	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11716645	C	A	11716645	2	1	61	1	0	0	0	0	0	0	0	1	6781	903	32	2		2	GREB1	2	11716645	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	364771	11716645	231482728	1238	9223										
GREB1	9687	broad.mit.edu	37	chr2	11733113	11733113	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgacagcgtgcacgtcatCgagtgtgcttactccctggc	11	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11733113C>T	ENST00000381486.2	+	11	1857	c.1557C>T	c.(1555-1557)atC>atT	p.I519I	GREB1_ENST00000234142.5_Silent_p.I519I	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	519						integral component of membrane (GO:0016021)		p.I519I(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TGCACGTCATCGAGTGTGCTT	0.682																																					Ovarian(39;850 945 2785 23371 33093)											1	Substitution - coding silent(1)	large_intestine(1)	2											20	21	21					2																	11733113		2100	4217	6317	11650564	SO:0001819	synonymous_variant	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1557C>T	2.37:g.11733113C>T			11650564	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																				0.682	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11733113	C	T	11733113	2	4	61	1	0	0	0	0	0	0	0	1	6781	874	31	1		1	GREB1	2	11733113	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16468	11733113	231466260	1239	9224										
GREB1	9687	broad.mit.edu	37	chr2	11774263	11774263	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccttggagcagggagttCtcctggtcggaaaggaacgt	14	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11774263C>A	ENST00000381486.2	+	29	5298	c.4998C>A	c.(4996-4998)ttC>ttA	p.F1666L	GREB1_ENST00000234142.5_Missense_Mutation_p.F1666L|GREB1_ENST00000396123.1_Missense_Mutation_p.F664L	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1666						integral component of membrane (GO:0016021)		p.F1666L(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCAGGGAGTTCTCCTGGTCGG	0.612																																					Ovarian(39;850 945 2785 23371 33093)											1	Substitution - Missense(1)	large_intestine(1)	2											86	93	90					2																	11774263		2133	4248	6381	11691714	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4998C>A	2.37:g.11774263C>A	ENSP00000370896:p.Phe1666Leu		11691714	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	5.356	0.250904	0.10130	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.40225	1.04;1.04;1.04	5.01	-5.5	0.02576	.	0.489617	0.23055	N	0.052441	T	0.22205	0.0535	N	0.22421	0.69	0.09310	N	0.999992	B	0.02656	0.0	B	0.04013	0.001	T	0.27938	-1.0059	10	0.11182	T	0.66	-14.1994	14.8684	0.70434	0.0:0.312:0.0:0.688	.	1666	Q4ZG55	GREB1_HUMAN	L	1666;1666;664	ENSP00000370896:F1666L;ENSP00000234142:F1666L;ENSP00000379429:F664L	ENSP00000234142:F1666L	F	+	3	2	GREB1	11691714	0.057000	0.20700	0.240000	0.24138	0.777000	0.43975	-0.257000	0.08745	-0.945000	0.03681	-0.379000	0.06801	TTC		0.612	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11774263	C	A	11774263	3	1	61	1	0	0	0	0	1	0	0	0	6781	912	32	2	5216	2	GREB1	2	11774263	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41150	11774263	231425110	1240	9225										
NTSR2	23620	broad.mit.edu	37	chr2	11802178	11802178	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctggcctccctggataaaGgtcttcttccatacgatgaa	8	12	2	1	rs138433349		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11802178G>T	ENST00000306928.5	-	2	847	c.813C>A	c.(811-813)acC>acA	p.T271T		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	271					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.T271T(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CCTGGATAAAGGTCTTCTTCC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	2											75	82	80					2																	11802178		2203	4300	6503	11719629	SO:0001819	synonymous_variant	23620			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.813C>A	2.37:g.11802178G>T			11719629	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	37	CCDS1681.1																																																																																				0.607	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			T	11802178	G	T	11802178	2	4	61	1	0	0	0	0	0	0	0	1	10742	987	35	2		2	NTSR2	2	11802178	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27915	11802178	231397195	1241	9226										
LPIN1	23175	broad.mit.edu	37	chr2	11925046	11925046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactcgcaaaacatgcaagcGacaacggagcccggtcagcc	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:11925046G>A	ENST00000256720.2	+	9	1378	c.1285G>A	c.(1285-1287)Gac>Aac	p.D429N	LPIN1_ENST00000404113.2_5'Flank|LPIN1_ENST00000396099.1_Missense_Mutation_p.D471N|LPIN1_ENST00000396097.1_Missense_Mutation_p.D159N|LPIN1_ENST00000449576.2_Missense_Mutation_p.D514N|LPIN1_ENST00000425416.2_Missense_Mutation_p.D435N	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	429					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.D429N(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ACATGCAAGCGACAACGGAGC	0.642											OREG0014445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											46	48	47					2																	11925046		2203	4300	6503	11842497	SO:0001583	missense	23175			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1285G>A	2.37:g.11925046G>A	ENSP00000256720:p.Asp429Asn	675	11842497	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	36	5.955177	0.97145	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	5.68	5.68	0.88126	.	0.141559	0.64402	D	0.000007	T	0.67040	0.2851	L	0.47716	1.5	0.80722	D	1	P;P	0.51351	0.873;0.944	P;B	0.45449	0.481;0.349	T	0.67197	-0.5731	10	0.42905	T	0.14	-39.0641	19.798	0.96494	0.0:0.0:1.0:0.0	.	514;429	F5GY24;Q14693	.;LPIN1_HUMAN	N	514;471;435;429;159	ENSP00000397908:D514N;ENSP00000379406:D471N;ENSP00000401522:D435N;ENSP00000256720:D429N;ENSP00000379404:D159N	ENSP00000256720:D429N	D	+	1	0	LPIN1	11842497	1.000000	0.71417	0.787000	0.31911	0.506000	0.33950	7.232000	0.78116	2.677000	0.91161	0.563000	0.77884	GAC		0.642	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		A	11925046	G	A	11925046	3	1	61	1	0	0	0	0	1	0	0	0	8947	1058	37	1	1315	1	LPIN1	2	11925046	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122868	11925046	231274327	1242	9227										
TRIB2	28951	broad.mit.edu	37	chr2	12863671	12863671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaattcatctttaaggacGaagagaggtaggtctcatcc	11	7	3	1	rs546825227		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:12863671G>A	ENST00000405331.3	+	2	626	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	TRIB2_ENST00000381465.2_Missense_Mutation_p.E50K|TRIB2_ENST00000155926.4_Missense_Mutation_p.E186K					tribbles pseudokinase 2									p.E186K(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTTTAAGGACGAAGAGAGGTA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											40	43	42					2																	12863671		2203	4299	6502	12781122	SO:0001583	missense	28951			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000405331.3:c.556G>A	2.37:g.12863671G>A	ENSP00000384260:p.Glu186Lys		12781122		Missense_Mutation	SNP	ENST00000405331.3	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.181458	0.78677	.	.	ENSG00000071575	ENST00000155926;ENST00000381465;ENST00000405331	T;T;T	0.64438	-0.1;-0.1;-0.1	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.133960	0.64402	D	0.000002	T	0.44912	0.1316	N	0.13299	0.325	0.80722	D	1	B	0.24618	0.107	B	0.21708	0.036	T	0.41305	-0.9516	10	0.07813	T	0.8	-15.1376	18.6653	0.91488	0.0:0.0:1.0:0.0	.	186	Q92519	TRIB2_HUMAN	K	186;50;186	ENSP00000155926:E186K;ENSP00000370874:E50K;ENSP00000384260:E186K	ENSP00000155926:E186K	E	+	1	0	TRIB2	12781122	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	9.869000	0.99810	2.656000	0.90262	0.655000	0.94253	GAA		0.532	TRIB2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000323585.1	NM_021643		A	12863671	G	A	12863671	3	1	61	1	0	0	0	0	1	0	0	0	16523	1059	37	1	562	1	TRIB2	2	12863671	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	938625	12863671	230335702	1243	9228										
TRIB2	28951	broad.mit.edu	37	chr2	12880833	12880833	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacagattttagcgtctcGaattcagcatatggtgctaa	8	8	3	1	rs369596172		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:12880833G>A	ENST00000155926.4	+	3	2364	c.945G>A	c.(943-945)tcG>tcA	p.S315S	TRIB2_ENST00000381465.2_Silent_p.S179S	NM_021643.3	NP_067675.1			tribbles pseudokinase 2									p.S315S(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTAGCGTCTCGAATTCAGCAT	0.522													G|||	1	0.000199681	0	0	5008	,	,		19471	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	2						G		0,4406		0,0,2203	75	72	73		945	-3.5	1	2		73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRIB2	NM_021643.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		315/344	12880833	1,13005	2203	4300	6503	12798284	SO:0001819	synonymous_variant	28951			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000155926.4:c.945G>A	2.37:g.12880833G>A			12798284		Silent	SNP	ENST00000155926.4	37	CCDS1683.1																																																																																				0.522	TRIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207114.2	NM_021643		A	12880833	G	A	12880833	2	1	61	1	0	0	0	0	0	0	0	1	16523	1045	37	1		1	TRIB2	2	12880833	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17162	12880833	230318540	1244	9229										
NBAS	51594	broad.mit.edu	37	chr2	15468417	15468417	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtagttccgatttgatatGcaccaccacatttttgcccc	6	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:15468417G>A	ENST00000281513.5	-	37	4392	c.4367C>T	c.(4366-4368)gCa>gTa	p.A1456V	NBAS_ENST00000441750.1_Missense_Mutation_p.A1336V	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1456					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.A1456V(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						GATTTGATATGCACCACCACA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											164	150	155					2																	15468417		2203	4300	6503	15385868	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.4367C>T	2.37:g.15468417G>A	ENSP00000281513:p.Ala1456Val		15385868	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.367|8.367	0.834424|0.834424	0.16820|0.16820	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513|ENST00000442506	T;T|.	0.10288|.	2.89;3.06|.	5.45|5.45	1.09|1.09	0.20402|0.20402	.|.	0.686003|.	0.16185|.	N|.	0.225680|.	T|T	0.17662|0.17662	0.0424|0.0424	N|N	0.11201|0.11201	0.11|0.11	0.09310|0.09310	N|N	1|1	B;B|.	0.20052|.	0.041;0.0|.	B;B|.	0.19391|.	0.025;0.001|.	T|T	0.27536|0.27536	-1.0071|-1.0071	10|5	0.87932|.	D|.	0|.	.|.	6.5682|6.5682	0.22523|0.22523	0.4883:0.0:0.5117:0.0|0.4883:0.0:0.5117:0.0	.|.	1336;1456|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	V|Y	1336;1456|504	ENSP00000413201:A1336V;ENSP00000281513:A1456V|.	ENSP00000281513:A1456V|.	A|H	-|-	2|1	0|0	NBAS|NBAS	15385868|15385868	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	1.009000|1.009000	0.29886|0.29886	0.373000|0.373000	0.24621|0.24621	-0.150000|-0.150000	0.13652|0.13652	GCA|CAT		0.378	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15468417	G	A	15468417	3	1	61	1	0	0	0	0	1	0	0	0	10216	1319	46	3	2812	3	NBAS	2	15468417	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2587584	15468417	227730956	1245	9230										
NBAS	51594	broad.mit.edu	37	chr2	15618355	15618356	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtagaactcacctttgaINSttttttttctcttctcagta							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:15618355_15618356insT	ENST00000281513.5	-	13	1166_1167	c.1141_1142insA	c.(1141-1143)atcfs	p.I381fs	NBAS_ENST00000441750.1_Frame_Shift_Ins_p.I381fs	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	381					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.I381fs*4(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTCACCTTTGATTTTTTTTCTC	0.317																																																1	Insertion - Frameshift(1)	large_intestine(1)	2																																								15535807	SO:0001589	frameshift_variant	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1142dupA	2.37:g.15618363_15618363dupT	ENSP00000281513:p.Ile381fs		15535806	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Frame_Shift_Ins	INS	ENST00000281513.5	37	CCDS1685.1																																																																																				0.317	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15618356	-	T	15618355	7	5	61	1	0	1	1	0	0	0	0	0	10216	333	12	0	6133	0	NBAS	2	15618355	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	149938	15618355	227581018	1246	9231										
MYCN	4613	broad.mit.edu	37	chr2	16082286	16082286	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctacccggacgaagatGacttctacttcggcggcccc	10	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:16082286G>T	ENST00000281043.3	+	2	397	c.100G>T	c.(100-102)Gac>Tac	p.D34Y	MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000453400.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	34					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D34Y(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GGACGAAGATGACTTCTACTT	0.637			A		neuroblastoma																																		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	1	Substitution - Missense(1)	large_intestine(1)	2											46	49	48					2																	16082286		2203	4300	6503	15999737	SO:0001583	missense	4613			BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.100G>T	2.37:g.16082286G>T	ENSP00000281043:p.Asp34Tyr		15999737	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	37	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205363	0.79127	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	T	0.24723	1.84	3.22	3.22	0.36961	Transcription regulator Myc, N-terminal (1);	0.082006	0.46442	U	0.000281	T	0.54287	0.1849	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65668	-0.6112	10	0.87932	D	0	-7.9728	14.78	0.69760	0.0:0.0:1.0:0.0	.	34	P04198	MYCN_HUMAN	Y	34	ENSP00000281043:D34Y	ENSP00000281043:D34Y	D	+	1	0	MYCN	15999737	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.548000	0.98103	1.522000	0.49001	0.561000	0.74099	GAC		0.637	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		T	16082286	G	T	16082286	3	4	61	1	0	0	0	0	1	0	0	0	10051	1290	45	2	102	2	MYCN	2	16082286	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	463931	16082286	227117087	1247	9232										
MYCN	4613	broad.mit.edu	37	chr2	16085942	16085942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctaagagcttgagcccccGaaactctgactcggaggaca	12	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:16085942G>A	ENST00000281043.3	+	3	1415	c.1118G>A	c.(1117-1119)cGa>cAa	p.R373Q		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	373					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R373Q(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TTGAGCCCCCGAAACTCTGAC	0.597			A		neuroblastoma																																		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	1	Substitution - Missense(1)	large_intestine(1)	2											50	53	52					2																	16085942		2203	4300	6503	16003393	SO:0001583	missense	4613			BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.1118G>A	2.37:g.16085942G>A	ENSP00000281043:p.Arg373Gln		16003393	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	37	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	G	31	5.062475	0.93898	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	D	0.81579	-1.51	4.99	4.99	0.66335	.	1.466510	0.04383	N	0.361122	D	0.89681	0.6785	L	0.58669	1.825	0.58432	D	0.999999	D	0.89917	1.0	D	0.63957	0.92	T	0.80427	-0.1387	10	0.87932	D	0	-1.189	18.6563	0.91455	0.0:0.0:1.0:0.0	.	373	P04198	MYCN_HUMAN	Q	373;291	ENSP00000281043:R373Q	ENSP00000281043:R373Q	R	+	2	0	MYCN	16003393	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.792000	0.99085	2.505000	0.84491	0.655000	0.94253	CGA		0.597	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		A	16085942	G	A	16085942	3	1	61	1	0	0	0	0	1	0	0	0	10051	1058	37	1	1124	1	MYCN	2	16085942	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3656	16085942	227113431	1248	9233										
RAD51AP2	729475	broad.mit.edu	37	chr2	17697126	17697126	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttttctatcttagtatCtttgtgaacttggcaactat	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:17697126C>A	ENST00000399080.2	-	1	2580	c.2557G>T	c.(2557-2559)Gat>Tat	p.D853Y		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	853								p.D853Y(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ATCTTAGTATCTTTGTGAACT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											48	46	46					2																	17697126		1810	4067	5877	17560607	SO:0001583	missense	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.2557G>T	2.37:g.17697126C>A	ENSP00000382030:p.Asp853Tyr		17560607		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	C	8.964	0.971180	0.18659	.	.	ENSG00000214842	ENST00000399080	T	0.26957	1.7	5.05	1.1	0.20463	.	.	.	.	.	T	0.28896	0.0717	L	0.27053	0.805	0.09310	N	0.999999	D	0.57571	0.98	P	0.59948	0.866	T	0.11227	-1.0596	9	0.59425	D	0.04	-1.0327	6.3895	0.21579	0.0:0.558:0.2759:0.1661	.	853	Q09MP3	R51A2_HUMAN	Y	853	ENSP00000382030:D853Y	ENSP00000382030:D853Y	D	-	1	0	RAD51AP2	17560607	0.000000	0.05858	0.007000	0.13788	0.061000	0.15899	0.133000	0.15912	0.237000	0.21200	0.655000	0.94253	GAT		0.299	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		A	17697126	C	A	17697126	3	1	61	1	0	0	0	0	1	0	0	0	13024	913	32	2	934	2	RAD51AP2	2	17697126	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1611184	17697126	225502247	1249	9234										
RAD51AP2	729475	broad.mit.edu	37	chr2	17697924	17697924	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtcaaagttattgagcaAaaaagctatgttagttttca	8	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:17697924A>C	ENST00000399080.2	-	1	1782	c.1759T>G	c.(1759-1761)Ttg>Gtg	p.L587V		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	587								p.L587V(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTATTGAGCAAAAAAGCTATG	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	2											20	20	20					2																	17697924		1773	3993	5766	17561405	SO:0001583	missense	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.1759T>G	2.37:g.17697924A>C	ENSP00000382030:p.Leu587Val		17561405		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.704096	0.48412	.	.	ENSG00000214842	ENST00000399080	T	0.28454	1.61	3.74	-0.62	0.11567	.	.	.	.	.	T	0.19685	0.0473	L	0.27053	0.805	0.09310	N	1	P	0.37330	0.59	B	0.40410	0.328	T	0.22661	-1.0210	9	0.87932	D	0	0.9681	2.1806	0.03873	0.5905:0.1592:0.0957:0.1546	.	587	Q09MP3	R51A2_HUMAN	V	587	ENSP00000382030:L587V	ENSP00000382030:L587V	L	-	1	2	RAD51AP2	17561405	0.001000	0.12720	0.005000	0.12908	0.560000	0.35617	0.428000	0.21395	0.111000	0.17947	0.383000	0.25322	TTG		0.254	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		C	17697924	A	C	17697924	3	2	61	1	0	0	0	0	1	0	0	0	13024	11	1	4	1732	4	RAD51AP2	2	17697924	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	798	17697924	225501449	1250	9235										
RAD51AP2	729475	broad.mit.edu	37	chr2	17698599	17698599	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgaaattctttctagagtCtcttacattacactggatac	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:17698599C>T	ENST00000399080.2	-	1	1107	c.1084G>A	c.(1084-1086)Gac>Aac	p.D362N		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	362								p.D362N(2)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTCTAGAGTCTCTTACATTA	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	2											55	54	54					2																	17698599		1824	4082	5906	17562080	SO:0001583	missense	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.1084G>A	2.37:g.17698599C>T	ENSP00000382030:p.Asp362Asn		17562080		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	C	0.040	-1.289051	0.01387	.	.	ENSG00000214842	ENST00000399080	T	0.25414	1.8	4.57	-1.29	0.09288	.	.	.	.	.	T	0.11965	0.0291	N	0.17082	0.46	0.09310	N	1	B	0.20780	0.048	B	0.24541	0.054	T	0.31586	-0.9938	9	0.30078	T	0.28	3.6165	1.669	0.02808	0.2099:0.2515:0.3617:0.1769	.	362	Q09MP3	R51A2_HUMAN	N	362	ENSP00000382030:D362N	ENSP00000382030:D362N	D	-	1	0	RAD51AP2	17562080	0.000000	0.05858	0.004000	0.12327	0.088000	0.18126	-0.991000	0.03728	-0.058000	0.13177	0.655000	0.94253	GAC		0.378	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		T	17698599	C	T	17698599	3	4	61	1	0	0	0	0	1	0	0	0	13024	913	32	3	2407	3	RAD51AP2	2	17698599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	675	17698599	225500774	1251	9236										
RAD51AP2	729475	broad.mit.edu	37	chr2	17699489	17699489	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagggtctaggggacaacTcccagactttttccgcctca	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:17699489T>C	ENST00000399080.2	-	1	217	c.194A>G	c.(193-195)gAg>gGg	p.E65G		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	65								p.E65G(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGGGGACAACTCCCAGACTTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	80	79					2																	17699489		1889	4108	5997	17562970	SO:0001583	missense	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.194A>G	2.37:g.17699489T>C	ENSP00000382030:p.Glu65Gly		17562970		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	T	13.36	2.213618	0.39102	.	.	ENSG00000214842	ENST00000399080	T	0.37058	1.22	3.72	-0.187	0.13268	.	.	.	.	.	T	0.28134	0.0694	L	0.27053	0.805	0.09310	N	1	D	0.57571	0.98	P	0.49085	0.6	T	0.14868	-1.0457	9	0.72032	D	0.01	-6.7555	4.5229	0.11968	0.0:0.1111:0.3992:0.4897	.	65	Q09MP3	R51A2_HUMAN	G	65	ENSP00000382030:E65G	ENSP00000382030:E65G	E	-	2	0	RAD51AP2	17562970	0.917000	0.31117	0.260000	0.24451	0.136000	0.21042	0.552000	0.23376	-0.026000	0.13895	0.482000	0.46254	GAG		0.537	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		C	17699489	T	C	17699489	3	2	61	1	0	0	0	0	1	0	0	0	13024	1551	54	4	3297	4	RAD51AP2	2	17699489	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	890	17699489	225499884	1252	9237										
NT5C1B	93034	broad.mit.edu	37	chr2	18765849	18765849	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcccagtaggcagcctcGtagtcgtcctcgtcctcccg	11	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:18765849G>A	ENST00000359846.2	-	5	911	c.834C>T	c.(832-834)taC>taT	p.Y278Y	RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000600945.1_Silent_p.Y278Y|NT5C1B_ENST00000460052.1_5'Flank|NT5C1B-RDH14_ENST00000532967.1_Silent_p.Y278Y|NT5C1B_ENST00000304081.4_Silent_p.Y218Y	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	278					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.Y278Y(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				AGGCAGCCTCGTAGTCGTCCT	0.697																																																1	Substitution - coding silent(1)	large_intestine(1)	2											17	19	18					2																	18765849		2201	4300	6501	18629330	SO:0001819	synonymous_variant	93034			AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.834C>T	2.37:g.18765849G>A			18629330	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Silent	SNP	ENST00000359846.2	37	CCDS33150.1																																																																																				0.697	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			A	18765849	G	A	18765849	2	1	61	1	0	0	0	0	0	0	0	1	10717	1140	40	1		1	NT5C1B	2	18765849	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1066360	18765849	224433524	1253	9238										
SDC1	6382	broad.mit.edu	37	chr2	20405120	20405120	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctgcacctgagccggaGaagttgtcagagtcatcccc	10	14	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:20405120G>T	ENST00000254351.4	-	2	376	c.132C>A	c.(130-132)ttC>ttA	p.F44L	SDC1_ENST00000381150.1_Missense_Mutation_p.F44L|SDC1_ENST00000482879.1_5'UTR|SDC1_ENST00000403076.1_Missense_Mutation_p.F44L	NM_002997.4	NP_002988	P18827	SDC1_HUMAN	syndecan 1	44					canonical Wnt signaling pathway (GO:0060070)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|myoblast development (GO:0048627)|odontogenesis (GO:0042476)|phototransduction, visible light (GO:0007603)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to toxic substance (GO:0009636)|retinoid metabolic process (GO:0001523)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|striated muscle cell development (GO:0055002)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein C-terminus binding (GO:0008022)	p.F44L(1)		NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2)	21	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		CTGAGCCGGAGAAGTTGTCAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	92	91					2																	20405120		2203	4300	6503	20268601	SO:0001583	missense	6382			AJ551176	CCDS1697.1	2p24.1	2008-02-05			ENSG00000115884	ENSG00000115884		"CD molecules", "Proteoglycans / Cell Surface : Syndecans"	10658	protein-coding gene	gene with protein product	"syndecan proteoglycan 1"	186355		SDC			Standard	XM_005262621		Approved	CD138, syndecan, SYND1	uc002rdo.1	P18827	OTTHUMG00000090751	ENST00000254351.4:c.132C>A	2.37:g.20405120G>T	ENSP00000254351:p.Phe44Leu		20268601	D6W523|Q53QV0|Q546D3|Q96HB7	Missense_Mutation	SNP	ENST00000254351.4	37	CCDS1697.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179798	0.57800	.	.	ENSG00000115884	ENST00000254351;ENST00000381150;ENST00000403076;ENST00000429035	T;T;T;T	0.63913	1.98;1.98;-0.0;-0.07	4.46	1.63	0.23807	.	0.000000	0.56097	D	0.000034	T	0.74344	0.3704	M	0.73598	2.24	0.37142	D	0.901773	D;P	0.71674	0.998;0.934	D;P	0.83275	0.996;0.856	T	0.76080	-0.3090	10	0.87932	D	0	-20.8761	8.4761	0.33014	0.2726:0.0:0.7274:0.0	.	44;44	E9PHH3;P18827	.;SDC1_HUMAN	L	44;44;44;52	ENSP00000254351:F44L;ENSP00000370542:F44L;ENSP00000384613:F44L;ENSP00000400773:F52L	ENSP00000254351:F44L	F	-	3	2	SDC1	20268601	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	1.417000	0.34770	0.210000	0.20664	0.462000	0.41574	TTC		0.537	SDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207495.1	NM_001006946		T	20405120	G	T	20405120	3	4	61	1	0	0	0	0	1	0	0	0	13988	933	33	2	816	2	SDC1	2	20405120	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1639271	20405120	222794253	1254	9239										
PUM2	23369	broad.mit.edu	37	chr2	20453751	20453751	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcagcacgggaggcatgAgtaacacacttttctactac	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:20453751A>G	ENST00000361078.2	-	19	2923	c.2901T>C	c.(2899-2901)acT>acC	p.T967T	PUM2_ENST00000319801.5_Silent_p.T888T|PUM2_ENST00000536417.1_Silent_p.T909T|PUM2_ENST00000403432.1_Silent_p.T965T|PUM2_ENST00000338086.5_Silent_p.T965T			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	967	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)	p.T965T(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGAGGCATGAGTAACACACT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	2											122	109	114					2																	20453751		2203	4300	6503	20317232	SO:0001819	synonymous_variant	23369			AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.2901T>C	2.37:g.20453751A>G			20317232	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	37																																																																																					0.378	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		G	20453751	A	G	20453751	2	3	61	1	0	0	0	0	0	0	0	1	12863	291	11	4		4	PUM2	2	20453751	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	48631	20453751	222745622	1255	9240										
PUM2	23369	broad.mit.edu	37	chr2	20490475	20490475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttgctgctgcagctgccGcaagtgattctgcttgctgc	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:20490475G>A	ENST00000361078.2	-	9	1251	c.1229C>T	c.(1228-1230)gCg>gTg	p.A410V	PUM2_ENST00000319801.5_Missense_Mutation_p.A410V|PUM2_ENST00000536417.1_Missense_Mutation_p.A354V|PUM2_ENST00000403432.1_Missense_Mutation_p.A410V|PUM2_ENST00000338086.5_Missense_Mutation_p.A410V			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	410	Ala-rich.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)	p.A410V(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCAGCTGCCGCAAGTGATTC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	58	59					2																	20490475		2203	4300	6503	20353956	SO:0001583	missense	23369			AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1229C>T	2.37:g.20490475G>A	ENSP00000354370:p.Ala410Val		20353956	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	G	7.551	0.662800	0.14645	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.19394	2.19;2.39;2.47;2.15;2.19;2.19	5.02	5.02	0.67125	.	0.157934	0.40554	U	0.001077	T	0.16300	0.0392	N	0.19112	0.55	0.53688	D	0.999974	B;B;B	0.15473	0.002;0.005;0.013	B;B;B	0.11329	0.004;0.001;0.006	T	0.05937	-1.0855	10	0.25106	T	0.35	-8.7157	18.703	0.91627	0.0:0.0:1.0:0.0	.	354;410;410	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	V	410;410;410;301;410;354	ENSP00000338173:A410V;ENSP00000354370:A410V;ENSP00000326746:A410V;ENSP00000409905:A301V;ENSP00000385992:A410V;ENSP00000440093:A354V	ENSP00000326746:A410V	A	-	2	0	PUM2	20353956	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.193000	0.65120	2.499000	0.84300	0.591000	0.81541	GCG		0.468	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		A	20490475	G	A	20490475	3	1	61	1	0	0	0	0	1	0	0	0	12863	1087	38	1	2013	1	PUM2	2	20490475	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36724	20490475	222708898	1256	9241										
PUM2	23369	broad.mit.edu	37	chr2	20508242	20508242	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaacaagtggtttattagCtgtaggattaggaagaggcc	12	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:20508242C>A	ENST00000361078.2	-	5	644	c.622G>T	c.(622-624)Gct>Tct	p.A208S	PUM2_ENST00000319801.5_Missense_Mutation_p.A208S|PUM2_ENST00000536417.1_Missense_Mutation_p.A152S|PUM2_ENST00000403432.1_Missense_Mutation_p.A208S|PUM2_ENST00000420234.1_5'UTR|PUM2_ENST00000338086.5_Missense_Mutation_p.A208S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	208	Interaction with SNAPIN.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)	p.A208S(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTTTATTAGCTGTAGGATTA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	78	77					2																	20508242		2203	4300	6503	20371723	SO:0001583	missense	23369			AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.622G>T	2.37:g.20508242C>A	ENSP00000354370:p.Ala208Ser		20371723	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	C	13.38	2.219705	0.39201	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417;ENST00000442400	T;T;T;T;T;T	0.17691	2.28;2.54;2.53;2.26;2.28;2.28	6.07	2.04	0.26737	.	0.541209	0.22812	N	0.055327	T	0.06005	0.0156	N	0.03608	-0.345	0.28293	N	0.923471	B;B;B	0.13594	0.0;0.008;0.002	B;B;B	0.14023	0.001;0.01;0.002	T	0.34378	-0.9831	10	0.22109	T	0.4	-0.0334	5.2574	0.15553	0.126:0.523:0.0:0.351	.	152;208;208	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	S	208;208;208;99;208;152;208	ENSP00000338173:A208S;ENSP00000354370:A208S;ENSP00000326746:A208S;ENSP00000409905:A99S;ENSP00000385992:A208S;ENSP00000440093:A152S	ENSP00000326746:A208S	A	-	1	0	PUM2	20371723	0.965000	0.33210	0.997000	0.53966	0.995000	0.86356	0.241000	0.18065	0.085000	0.17107	-0.145000	0.13849	GCT		0.458	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		A	20508242	C	A	20508242	3	1	61	1	0	0	0	0	1	0	0	0	12863	797	28	2	2636	2	PUM2	2	20508242	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17767	20508242	222691131	1257	9242										
C2orf43	60526	broad.mit.edu	37	chr2	20939875	20939875	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaacatagagaacatatcGaaaccagcacaaaagtggag	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:20939875G>A	ENST00000237822.3	-	5	638	c.559C>T	c.(559-561)Cga>Tga	p.R187*	C2orf43_ENST00000381090.3_Nonsense_Mutation_p.R187*|C2orf43_ENST00000403006.2_Nonsense_Mutation_p.R57*|C2orf43_ENST00000541941.1_Nonsense_Mutation_p.R57*|C2orf43_ENST00000440866.2_Intron|C2orf43_ENST00000435420.2_Nonsense_Mutation_p.R139*	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	187								p.R187*(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAACATATCGAAACCAGCAC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											118	115	116					2																	20939875		2203	4300	6503	20803356	SO:0001587	stop_gained	60526			AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.559C>T	2.37:g.20939875G>A	ENSP00000237822:p.Arg187*		20803356	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Nonsense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	.	.	.	.	.	.	.	.	.	.	G	39	7.554306	0.98355	.	.	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000541941;ENST00000432947;ENST00000412261	.	.	.	5.61	4.72	0.59763	.	0.056018	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-7.6822	13.8478	0.63479	0.0:0.0:0.8457:0.1542	.	.	.	.	X	57;187;187;139;57;57;139	.	ENSP00000237822:R187X	R	-	1	2	C2orf43	20803356	1.000000	0.71417	0.950000	0.38849	0.978000	0.69477	3.868000	0.56055	1.472000	0.48140	0.650000	0.86243	CGA		0.418	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		A	20939875	G	A	20939875	4	1	61	1	0	0	0	0	0	1	0	0	2173	1066	37	1	430	1	C2orf43	2	20939875	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	431633	20939875	222259498	1258	9243										
APOB	338	broad.mit.edu	37	chr2	21228262	21228262	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgaaacactttttggaagCgtgaactgggacacagttaa	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21228262C>T	ENST00000233242.1	-	26	11605	c.11478G>A	c.(11476-11478)acG>acA	p.T3826T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3826					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.T3826T(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTTGGAAGCGTGAACTGGG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	2											156	148	151					2																	21228262		2203	4300	6503	21081767	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11478G>A	2.37:g.21228262C>T			21081767	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21228262	C	T	21228262	2	4	61	1	0	0	0	0	0	0	0	1	785	755	27	1		1	APOB	2	21228262	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	288387	21228262	221971111	1259	9244										
APOB	338	broad.mit.edu	37	chr2	21229227	21229227	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgaatattcccgagaaaGaaccgaacccttgacatctc	6	13	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21229227G>T	ENST00000233242.1	-	26	10640	c.10513C>A	c.(10513-10515)Ctt>Att	p.L3505I		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3505	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.L3505I(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCCGAGAAAGAACCGAACCC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	106	105					2																	21229227		2203	4300	6503	21082732	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10513C>A	2.37:g.21229227G>T	ENSP00000233242:p.Leu3505Ile		21082732	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	4.178	0.031670	0.08101	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.80480	-1.38	5.67	1.87	0.25490	.	0.847968	0.10288	N	0.692735	T	0.75852	0.3906	M	0.62723	1.935	0.37791	D	0.927356	B	0.26708	0.157	B	0.26094	0.066	T	0.68503	-0.5391	10	0.56958	D	0.05	.	6.2093	0.20619	0.2968:0.1253:0.578:0.0	.	3505	P04114	APOB_HUMAN	I	3505	ENSP00000233242:L3505I	ENSP00000233242:L3505I	L	-	1	0	APOB	21082732	0.002000	0.14202	0.277000	0.24703	0.025000	0.11179	-0.069000	0.11542	0.063000	0.16370	-0.137000	0.14449	CTT		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21229227	G	T	21229227	3	4	61	1	0	0	0	0	1	0	0	0	785	942	33	2	3194	2	APOB	2	21229227	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	965	21229227	221970146	1260	9245										
APOB	338	broad.mit.edu	37	chr2	21230633	21230633	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgggctgaaaagaaaagaGaatttttcaaagttccaata	9	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21230633G>T	ENST00000233242.1	-	26	9234	c.9107C>A	c.(9106-9108)tCt>tAt	p.S3036Y		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3036					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.S3036Y(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAGAAAAGAGAATTTTTCAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	54	52					2																	21230633		2203	4299	6502	21084138	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9107C>A	2.37:g.21230633G>T	ENSP00000233242:p.Ser3036Tyr		21084138	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784583	0.49997	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.39406	1.08	5.87	5.87	0.94306	.	0.224693	0.32175	N	0.006479	T	0.61949	0.2388	M	0.73962	2.25	0.80722	D	1	D	0.67145	0.996	P	0.61800	0.894	T	0.64812	-0.6319	10	0.87932	D	0	.	14.8744	0.70483	0.0:0.0:0.8228:0.1772	.	3036	P04114	APOB_HUMAN	Y	3036	ENSP00000233242:S3036Y	ENSP00000233242:S3036Y	S	-	2	0	APOB	21084138	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	3.728000	0.54991	2.780000	0.95670	0.655000	0.94253	TCT		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21230633	G	T	21230633	3	4	61	1	0	0	0	0	1	0	0	0	785	942	33	2	4600	2	APOB	2	21230633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1406	21230633	221968740	1261	9246										
APOB	338	broad.mit.edu	37	chr2	21233605	21233605	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattcttggggcttctcaacGgcatctctcatctctaaagc	7	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21233605G>T	ENST00000233242.1	-	26	6262	c.6135C>A	c.(6133-6135)gcC>gcA	p.A2045A		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2045	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.A2045A(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTTCTCAACGGCATCTCTCA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	2											99	107	104					2																	21233605		2203	4300	6503	21087110	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6135C>A	2.37:g.21233605G>T			21087110	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21233605	G	T	21233605	2	4	61	1	0	0	0	0	0	0	0	1	785	1103	39	2		2	APOB	2	21233605	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2972	21233605	221965768	1262	9247										
APOB	338	broad.mit.edu	37	chr2	21234124	21234124	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggctgaagccagcccagcGatgtctgtgttgagccgatg	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21234124G>A	ENST00000233242.1	-	26	5743	c.5616C>T	c.(5614-5616)atC>atT	p.I1872I		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1872					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.I1872I(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGCCCAGCGATGTCTGTGT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											122	115	117					2																	21234124		2203	4300	6503	21087629	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5616C>T	2.37:g.21234124G>A			21087629	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21234124	G	A	21234124	2	1	61	1	0	0	0	0	0	0	0	1	785	1048	37	1		1	APOB	2	21234124	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	519	21234124	221965249	1263	9248										
APOB	338	broad.mit.edu	37	chr2	21236251	21236251	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagggacttggaactctcGagatggcagatggaatccca	13	8	1	2	rs121918383		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21236251G>A	ENST00000233242.1	-	25	4124	c.3997C>T	c.(3997-3999)Cga>Tga	p.R1333*		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1333					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R1333*(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGAACTCTCGAGATGGCAGA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	2	GRCh37	CM880006	APOB	M	rs121918383						137	134	135					2																	21236251		2203	4300	6503	21089756	SO:0001587	stop_gained	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3997C>T	2.37:g.21236251G>A	ENSP00000233242:p.Arg1333*		21089756	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	39	7.824761	0.98510	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	.	.	.	5.53	3.6	0.41247	.	0.595809	0.15923	N	0.238037	.	.	.	.	.	.	0.20074	A	6.40381e-05	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0713	0.64861	0.0:0.0:0.6221:0.3778	.	.	.	.	X	1333	.	ENSP00000233242:R1333X	R	-	1	2	APOB	21089756	0.018000	0.18449	0.308000	0.25141	0.146000	0.21551	1.074000	0.30703	1.438000	0.47492	0.563000	0.77884	CGA		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21236251	G	A	21236251	4	1	61	1	0	0	0	0	0	1	0	0	785	1066	37	1	9714	1	APOB	2	21236251	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2127	21236251	221963122	1264	9249										
APOB	338	broad.mit.edu	37	chr2	21251356	21251356	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataagataggcagccagtcGcttatctcccggagaagcat	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21251356G>A	ENST00000233242.1	-	13	1799	c.1672C>T	c.(1672-1674)Cga>Tga	p.R558*	APOB_ENST00000399256.4_Nonsense_Mutation_p.R558*	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	558	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R558*(1)|p.R558R(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGCCAGTCGCTTATCTCCC	0.448																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	2											118	113	115					2																	21251356		2203	4300	6503	21104861	SO:0001587	stop_gained	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1672C>T	2.37:g.21251356G>A	ENSP00000233242:p.Arg558*		21104861	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	40	8.018009	0.98613	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	.	.	.	5.69	3.83	0.44106	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9372	0.64032	0.0:0.0:0.5904:0.4096	.	.	.	.	X	558	.	ENSP00000233242:R558X	R	-	1	2	APOB	21104861	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.327000	0.59247	0.819000	0.34492	0.655000	0.94253	CGA		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21251356	G	A	21251356	4	1	61	1	0	0	0	0	0	1	0	0	785	1095	38	1	12087	1	APOB	2	21251356	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15105	21251356	221948017	1265	9250										
APOB	338	broad.mit.edu	37	chr2	21265342	21265342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggtgcttgaatcgggtcGcatcttctaacgtggggaga	16	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:21265342G>A	ENST00000233242.1	-	3	255	c.128C>T	c.(127-129)gCg>gTg	p.A43V	APOB_ENST00000399256.4_Missense_Mutation_p.A43V	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	43	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.A43V(2)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATCGGGTCGCATCTTCTAA	0.517											OREG0014485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	2											121	104	110					2																	21265342		2203	4300	6503	21118847	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.128C>T	2.37:g.21265342G>A	ENSP00000233242:p.Ala43Val	747	21118847	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460587	0.63513	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.05649	5.67;3.41	5.18	5.18	0.71444	.	0.315283	0.26959	N	0.021631	T	0.12092	0.0294	L	0.36672	1.1	0.33807	D	0.627409	D	0.65815	0.995	P	0.51193	0.662	T	0.01488	-1.1342	10	0.72032	D	0.01	.	18.3477	0.90327	0.0:0.0:1.0:0.0	.	43	P04114	APOB_HUMAN	V	43	ENSP00000233242:A43V;ENSP00000382200:A43V	ENSP00000233242:A43V	A	-	2	0	APOB	21118847	0.991000	0.36638	0.798000	0.32154	0.215000	0.24574	4.627000	0.61276	2.793000	0.96121	0.655000	0.94253	GCG		0.517	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21265342	G	A	21265342	3	1	61	1	0	0	0	0	1	0	0	0	785	1087	38	1	13671	1	APOB	2	21265342	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13986	21265342	221934031	1266	9251										
ATAD2B	54454	broad.mit.edu	37	chr2	23977597	23977597	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttccaggcttgtcgtttTtgcctgctctaaaattaatt	7	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:23977597T>G	ENST00000238789.5	-	26	4469	c.4126A>C	c.(4126-4128)Aaa>Caa	p.K1376Q	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1376						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.K1376Q(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGTCGTTTTTGCCTGCTCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	93	92					2																	23977597		1831	4074	5905	23831101	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.4126A>C	2.37:g.23977597T>G	ENSP00000238789:p.Lys1376Gln		23831101	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.655|3.655	-0.070676|-0.070676	0.07228|0.07228	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000238789;ENST00000546030|ENST00000381024	D|.	0.91464|.	-2.85|.	5.39|5.39	4.16|4.16	0.48862|0.48862	.|.	0.314890|.	0.26349|.	N|.	0.024884|.	T|T	0.20981|0.20981	0.0505|0.0505	N|N	0.05441|0.05441	-0.05|-0.05	0.25046|0.25046	N|N	0.991162|0.991162	B;B|.	0.14012|.	0.005;0.009|.	B;B|.	0.13407|.	0.004;0.009|.	T|T	0.13683|0.13683	-1.0500|-1.0500	10|5	0.12766|.	T|.	0.61|.	.|.	11.0804|11.0804	0.48057|0.48057	0.0:0.0:0.1533:0.8467|0.0:0.0:0.1533:0.8467	.|.	1376;1371|.	Q9ULI0;Q9ULI0-2|.	ATD2B_HUMAN;.|.	Q|H	1376;544|651	ENSP00000238789:K1376Q|.	ENSP00000238789:K1376Q|.	K|Q	-|-	1|3	0|2	ATAD2B|ATAD2B	23831101|23831101	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.806000|0.806000	0.45545|0.45545	3.297000|3.297000	0.51810|0.51810	2.191000|2.191000	0.70037|0.70037	0.528000|0.528000	0.53228|0.53228	AAA|CAA		0.388	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		G	23977597	T	G	23977597	3	3	61	1	0	0	0	0	1	0	0	0	1073	1850	64	4	262	4	ATAD2B	2	23977597	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2712255	23977597	219221776	1267	9252										
ATAD2B	54454	broad.mit.edu	37	chr2	24046131	24046131	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtagtttagagtaccttCttttttgtcactctggctaa	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24046131C>A	ENST00000238789.5	-	16	2471	c.2128G>T	c.(2128-2130)Gaa>Taa	p.E710*	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	710						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.E710*(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGTACCTTCTTTTTTGTCA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											52	47	49					2																	24046131		1836	4082	5918	23899635	SO:0001587	stop_gained	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2128G>T	2.37:g.24046131C>A	ENSP00000238789:p.Glu710*		23899635	B9ZVQ5|Q6ZNA6|Q8N9E7	Nonsense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	40	8.283822	0.98742	.	.	ENSG00000119778	ENST00000238789	.	.	.	4.88	4.88	0.63580	.	1.077550	0.07191	N	0.855801	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	18.4005	0.90514	0.0:1.0:0.0:0.0	.	.	.	.	X	710	.	ENSP00000238789:E710X	E	-	1	0	ATAD2B	23899635	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	3.445000	0.52921	2.433000	0.82419	0.561000	0.74099	GAA		0.328	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24046131	C	A	24046131	4	1	61	1	0	0	0	0	0	1	0	0	1073	922	32	2	2300	2	ATAD2B	2	24046131	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68534	24046131	219153242	1268	9253										
ATAD2B	54454	broad.mit.edu	37	chr2	24051805	24051805	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatctgtaagatgtgttttCttgcctaagatgaaaagcac	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24051805C>A	ENST00000238789.5	-	15	2076	c.1733G>T	c.(1732-1734)aGa>aTa	p.R578I	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	578						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.R578I(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGTGTTTTCTTGCCTAAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											99	93	95					2																	24051805		1832	4082	5914	23905309	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1733G>T	2.37:g.24051805C>A	ENSP00000238789:p.Arg578Ile		23905309	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053573	0.93793	.	.	ENSG00000119778	ENST00000238789;ENST00000458510	D;D	0.95518	-3.73;-3.31	4.7	4.7	0.59300	.	.	.	.	.	D	0.97071	0.9043	M	0.90369	3.11	0.80722	D	1	D	0.53312	0.959	P	0.49361	0.608	D	0.98160	1.0446	9	0.87932	D	0	.	18.5316	0.90995	0.0:1.0:0.0:0.0	.	578	Q9ULI0	ATD2B_HUMAN	I	578;16	ENSP00000238789:R578I;ENSP00000392764:R16I	ENSP00000238789:R578I	R	-	2	0	ATAD2B	23905309	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.730000	0.84881	2.551000	0.86045	0.650000	0.86243	AGA		0.353	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24051805	C	A	24051805	3	1	61	1	0	0	0	0	1	0	0	0	1073	913	32	2	2699	2	ATAD2B	2	24051805	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5674	24051805	219147568	1269	9254										
ATAD2B	54454	broad.mit.edu	37	chr2	24103529	24103529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattggaggtgcttggtatCgatccactgtttttctctgt	10	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24103529C>T	ENST00000238789.5	-	7	1224	c.881G>A	c.(880-882)cGa>cAa	p.R294Q		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	294						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.R294Q(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTGGTATCGATCCACTGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											167	148	154					2																	24103529		1866	4099	5965	23957033	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.881G>A	2.37:g.24103529C>T	ENSP00000238789:p.Arg294Gln		23957033	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.805413	0.90623	.	.	ENSG00000119778	ENST00000238789;ENST00000442596;ENST00000439915	D;T	0.92397	-3.03;0.73	5.02	5.02	0.67125	.	.	.	.	.	D	0.95089	0.8409	M	0.64997	1.995	0.50171	D	0.999853	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.922	D	0.93250	0.6634	9	0.24483	T	0.36	.	18.7355	0.91753	0.0:1.0:0.0:0.0	.	308;294	C9JG15;Q9ULI0	.;ATD2B_HUMAN	Q	294;146;308	ENSP00000238789:R294Q;ENSP00000403177:R308Q	ENSP00000238789:R294Q	R	-	2	0	ATAD2B	23957033	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.708000	0.74660	2.514000	0.84764	0.650000	0.86243	CGA		0.368	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		T	24103529	C	T	24103529	3	4	61	1	0	0	0	0	1	0	0	0	1073	884	31	1	3583	1	ATAD2B	2	24103529	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51724	24103529	219095844	1270	9255										
ATAD2B	54454	broad.mit.edu	37	chr2	24110750	24110750	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggttcacactttcaaatCtgtttttcctggaacgacaa	6	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24110750C>A	ENST00000238789.5	-	4	867	c.524G>T	c.(523-525)aGa>aTa	p.R175I		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	175						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.R175I(1)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACTTTCAAATCTGTTTTTCCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											139	139	139					2																	24110750		1856	4084	5940	23964254	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.524G>T	2.37:g.24110750C>A	ENSP00000238789:p.Arg175Ile		23964254	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657430	0.67586	.	.	ENSG00000119778	ENST00000238789;ENST00000442596;ENST00000439915	D;T	0.94138	-3.36;0.45	4.36	4.36	0.52297	.	.	.	.	.	D	0.93154	0.7820	M	0.66939	2.045	0.52501	D	0.999959	P;P	0.42010	0.673;0.768	B;B	0.43018	0.405;0.277	D	0.93907	0.7193	9	0.54805	T	0.06	.	17.2634	0.87078	0.0:1.0:0.0:0.0	.	175;175	C9JG15;Q9ULI0	.;ATD2B_HUMAN	I	175;13;175	ENSP00000238789:R175I;ENSP00000403177:R175I	ENSP00000238789:R175I	R	-	2	0	ATAD2B	23964254	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.727000	0.61993	2.154000	0.67381	0.563000	0.77884	AGA		0.373	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24110750	C	A	24110750	3	1	61	1	0	0	0	0	1	0	0	0	1073	913	32	2	3952	2	ATAD2B	2	24110750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7221	24110750	219088623	1271	9256										
C2orf44	80304	broad.mit.edu	37	chr2	24261280	24261280	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagtagatcaaaattataTtacaagtgttggaagccact	8	6	1	2	rs376816524		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24261280T>G	ENST00000295148.4	-	2	1142	c.1085A>C	c.(1084-1086)aAt>aCt	p.N362T	C2orf44_ENST00000406895.3_Missense_Mutation_p.N362T	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	362								p.N362T(1)	C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAATTATATTACAAGTGTT	0.398			T	ALK	NSCLC																																		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	1	Substitution - Missense(1)	large_intestine(1)	2											51	55	54					2																	24261280		2202	4292	6494	24114784	SO:0001583	missense	80304			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.1085A>C	2.37:g.24261280T>G	ENSP00000295148:p.Asn362Thr		24114784	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.388115	0.61956	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.49432	0.78;0.78	5.38	2.99	0.34606	WD40/YVTN repeat-like-containing domain (1);	0.177231	0.64402	D	0.000014	T	0.57051	0.2027	M	0.74258	2.255	0.42369	D	0.992446	D;D	0.64830	0.983;0.994	P;P	0.54544	0.755;0.755	T	0.58440	-0.7636	10	0.72032	D	0.01	-23.86	8.0819	0.30750	0.0:0.2219:0.0:0.7781	.	362;362	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	T	362	ENSP00000295148:N362T;ENSP00000385816:N362T	ENSP00000295148:N362T	N	-	2	0	C2orf44	24114784	1.000000	0.71417	0.004000	0.12327	0.940000	0.58332	3.259000	0.51515	0.448000	0.26722	0.533000	0.62120	AAT		0.398	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		G	24261280	T	G	24261280	3	3	61	1	0	0	0	0	1	0	0	0	2174	1493	52	4	1092	4	C2orf44	2	24261280	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	150530	24261280	218938093	1272	9257										
SF3B14	51639	broad.mit.edu	37	chr2	24291225	24291225	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacaaaaccacaaggtatCtgttacaaacattgaatccc	5	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24291225C>A	ENST00000233468.4	-	3	467	c.254G>T	c.(253-255)aGa>aTa	p.R85I		NM_016047.3	NP_057131.1												p.R85I(1)		NS(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAAGGTATCTGTTACAAAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	116	121					2																	24291225		2203	4300	6503	24144729	SO:0001583	missense	51639																														ENST00000233468.4:c.254G>T	2.37:g.24291225C>A	ENSP00000233468:p.Arg85Ile		24144729		Missense_Mutation	SNP	ENST00000233468.4	37	CCDS1707.1	.	.	.	.	.	.	.	.	.	.	C	34	5.312069	0.95655	.	.	ENSG00000115128	ENST00000233468	T	0.21031	2.03	5.05	5.05	0.67936	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.65270	0.2675	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79603	-0.1735	10	0.87932	D	0	-26.1176	19.279	0.94044	0.0:1.0:0.0:0.0	.	85	Q9Y3B4	PM14_HUMAN	I	85	ENSP00000233468:R85I	ENSP00000233468:R85I	R	-	2	0	AC008073.5	24144729	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.737000	0.84957	2.729000	0.93468	0.650000	0.86243	AGA		0.408	SF3B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246826.1			A	24291225	C	A	24291225	3	1	61	1	0	0	0	0	1	0	0	0	14187	913	32	2	131	2	SF3B14	2	24291225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29945	24291225	218908148	1273	9258										
C2orf84	653140	broad.mit.edu	37	chr2	24413339	24413339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagagaaaaagacggccGacctaagtcaggctgcgttt	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24413339G>A	ENST00000295150.3	+	6	546	c.460G>A	c.(460-462)Gac>Aac	p.D154N		NM_001040710.1	NP_001035800.1	Q86W67	F228A_HUMAN	family with sequence similarity 228, member A	154								p.D154N(1)									AAAGACGGCCGACCTAAGTCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	50	50					2																	24413339		1880	4100	5980	24266843	SO:0001583	missense	653140				CCDS42659.1	2p23.3	2012-07-04	2012-07-04	2012-07-04	ENSG00000186453	ENSG00000186453			34418	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 84"	C2orf84			Standard	NM_001040710		Approved	FLJ30851	uc002rfc.3	Q86W67	OTTHUMG00000151903	ENST00000295150.3:c.460G>A	2.37:g.24413339G>A	ENSP00000295150:p.Asp154Asn		24266843		Missense_Mutation	SNP	ENST00000295150.3	37	CCDS42659.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362046	0.41902	.	.	ENSG00000186453	ENST00000295150;ENST00000415196	T;T	0.47528	0.86;0.84	3.64	0.854	0.19007	.	0.356629	0.20561	N	0.089907	T	0.18759	0.0450	N	0.04959	-0.14	0.09310	N	1	B	0.27791	0.189	B	0.20184	0.028	T	0.17715	-1.0360	10	0.15952	T	0.53	3.0656	5.4725	0.16678	0.3768:0.0:0.6232:0.0	.	154	Q86W67	CB084_HUMAN	N	154;55	ENSP00000295150:D154N;ENSP00000416595:D55N	ENSP00000295150:D154N	D	+	1	0	C2orf84	24266843	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.410000	0.21098	0.166000	0.19597	-0.143000	0.13931	GAC		0.458	FAM228A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324342.1	NM_001040710		A	24413339	G	A	24413339	3	1	61	1	0	0	0	0	1	0	0	0	2205	1058	37	1	478	1	C2orf84	2	24413339	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122114	24413339	218786034	1274	9259										
ITSN2	50618	broad.mit.edu	37	chr2	24498709	24498709	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgtgtgttgtaggtttCtctcagttcctaaggagaaa	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24498709C>A	ENST00000355123.4	-	18	2397	c.1954G>T	c.(1954-1956)Gaa>Taa	p.E652*	ITSN2_ENST00000361999.3_Nonsense_Mutation_p.E625*|ITSN2_ENST00000406921.3_Nonsense_Mutation_p.E652*|SCARNA21_ENST00000515996.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	652					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.E651*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGTAGGTTTCTCTCAGTTCC	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											125	119	121					2																	24498709		2203	4300	6503	24352213	SO:0001587	stop_gained	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1954G>T	2.37:g.24498709C>A	ENSP00000347244:p.Glu652*		24352213	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Nonsense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	41	8.940039	0.99010	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000406921	.	.	.	5.69	4.82	0.62117	.	0.187754	0.24525	U	0.037762	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.0114	0.71552	0.0:0.9316:0.0:0.0683	.	.	.	.	X	625;652;625;652	.	ENSP00000347244:E652X	E	-	1	0	ITSN2	24352213	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.455000	0.52993	1.555000	0.49500	0.650000	0.86243	GAA		0.318	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		A	24498709	C	A	24498709	4	1	61	1	0	0	0	0	0	1	0	0	7948	922	32	2	3282	2	ITSN2	2	24498709	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85370	24498709	218700664	1275	9260										
ITSN2	50618	broad.mit.edu	37	chr2	24521590	24521590	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtttaacctgacaatttCttcttgttctctattctttt	4	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24521590C>A	ENST00000355123.4	-	13	1881	c.1438G>T	c.(1438-1440)Gaa>Taa	p.E480*	ITSN2_ENST00000361999.3_Nonsense_Mutation_p.E480*|ITSN2_ENST00000406921.3_Nonsense_Mutation_p.E480*	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	480					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.E479*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGACAATTTCTTCTTGTTCT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											157	155	156					2																	24521590		2203	4300	6503	24375094	SO:0001587	stop_gained	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1438G>T	2.37:g.24521590C>A	ENSP00000347244:p.Glu480*		24375094	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Nonsense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	40	8.055304	0.98632	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	.	.	.	5.24	5.24	0.73138	.	0.186790	0.24666	U	0.036598	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	19.1951	0.93684	0.0:1.0:0.0:0.0	.	.	.	.	X	480;480;480;504;480;505	.	ENSP00000347244:E480X	E	-	1	0	ITSN2	24375094	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.366000	0.59492	2.628000	0.89032	0.484000	0.47621	GAA		0.388	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		A	24521590	C	A	24521590	4	1	61	1	0	0	0	0	0	1	0	0	7948	922	32	2	3818	2	ITSN2	2	24521590	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22881	24521590	218677783	1276	9261										
ITSN2	50618	broad.mit.edu	37	chr2	24526719	24526719	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgactgaagaagggcatttCtagcttgaaaacctgattaa	9	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24526719C>A	ENST00000355123.4	-	9	1249	c.806G>T	c.(805-807)aGa>aTa	p.R269I	ITSN2_ENST00000361999.3_Missense_Mutation_p.R269I|ITSN2_ENST00000406921.3_Missense_Mutation_p.R269I	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	269	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.R268I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGGGCATTTCTAGCTTGAAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	88	87					2																	24526719		2203	4300	6503	24380223	SO:0001583	missense	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.806G>T	2.37:g.24526719C>A	ENSP00000347244:p.Arg269Ile		24380223	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288918	0.80914	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.81	4.81	0.61882	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.40385	U	0.001111	T	0.54334	0.1852	M	0.75884	2.315	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.992;0.992;0.992;0.997	T	0.57271	-0.7840	10	0.87932	D	0	.	12.8407	0.57800	0.0:0.9212:0.0:0.0788	.	269;269;269;269	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	I	269;269;269;293;269;294	ENSP00000354561:R269I;ENSP00000347244:R269I;ENSP00000370250:R269I;ENSP00000384499:R269I;ENSP00000391224:R294I	ENSP00000347244:R269I	R	-	2	0	ITSN2	24380223	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.298000	0.59067	2.674000	0.91012	0.491000	0.48974	AGA		0.303	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		A	24526719	C	A	24526719	3	1	61	1	0	0	0	0	1	0	0	0	7948	913	32	2	4466	2	ITSN2	2	24526719	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5129	24526719	218672654	1277	9262										
NCOA1	8648	broad.mit.edu	37	chr2	24962316	24962316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctagttgatacaccaaaatCggcaagctatcttaaaccag	6	10	2	1	rs138247764		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:24962316C>T	ENST00000406961.1	+	18	3869	c.3217C>T	c.(3217-3219)Cgg>Tgg	p.R1073W	NCOA1_ENST00000407230.1_Missense_Mutation_p.R922W|NCOA1_ENST00000405141.1_Missense_Mutation_p.R1073W|NCOA1_ENST00000538539.1_Missense_Mutation_p.R1073W|NCOA1_ENST00000348332.3_Missense_Mutation_p.R1073W|NCOA1_ENST00000288599.5_Missense_Mutation_p.R1073W|NCOA1_ENST00000395856.3_Missense_Mutation_p.R1073W			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1073	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.R1073W(3)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACACCAAAATCGGCAAGCTAT	0.368			T	PAX3	alveolar rhadomyosarcoma																																		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	3	Substitution - Missense(3)	large_intestine(2)|skin(1)	2											129	119	123					2																	24962316		2203	4300	6503	24815820	SO:0001583	missense	8648			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3217C>T	2.37:g.24962316C>T	ENSP00000385216:p.Arg1073Trp		24815820	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308010	0.81247	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.77	4.88	0.63580	.	0.058137	0.64402	D	0.000002	T	0.71736	0.3375	M	0.75085	2.285	0.80722	D	1	D;D;D;D	0.69078	0.997;0.995;0.997;0.995	P;P;P;P	0.56474	0.799;0.635;0.799;0.635	T	0.77197	-0.2676	10	0.87932	D	0	.	16.6848	0.85302	0.0:0.87:0.13:0.0	.	1073;1073;1073;922	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	W	1073;1073;922;1073;1073;1073;1073	ENSP00000385216:R1073W;ENSP00000385097:R1073W;ENSP00000385195:R922W;ENSP00000444039:R1073W;ENSP00000320940:R1073W;ENSP00000288599:R1073W;ENSP00000379197:R1073W	ENSP00000288599:R1073W	R	+	1	2	NCOA1	24815820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.002000	0.57053	1.543000	0.49345	0.655000	0.94253	CGG		0.368	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24962316	C	T	24962316	3	4	61	1	0	0	0	0	1	0	0	0	10259	875	31	1	3271	1	NCOA1	2	24962316	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	435597	24962316	218237057	1278	9263										
C2orf79	391356	broad.mit.edu	37	chr2	25016120	25016120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctaccagtgcgcccgccgGccaggagaacggagcttgtg	15	14	0	1	rs545737721	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25016120G>A	ENST00000328379.5	-	1	131	c.127C>T	c.(127-129)Ccg>Tcg	p.P43S	PTRHD1_ENST00000487316.1_5'Flank|CENPO_ENST00000260662.1_5'Flank|CENPO_ENST00000380834.2_5'UTR|CENPO_ENST00000473706.1_5'UTR	NM_001013663.1	NP_001013685.1	Q6GMV3	PTRD1_HUMAN	peptidyl-tRNA hydrolase domain containing 1	43						extracellular vesicular exosome (GO:0070062)	aminoacyl-tRNA hydrolase activity (GO:0004045)	p.P43S(1)		autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|skin(1)	6						GCGCCCGCCGGCCAGGAGAAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	65	63					2																	25016120		2203	4300	6503	24869624	SO:0001583	missense	391356				CCDS33156.1	2p23.3	2011-05-09	2011-05-09	2011-05-09	ENSG00000184924	ENSG00000184924			33782	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 79"	C2orf79		12477932	Standard	NM_001013663		Approved	LOC391356	uc002rfm.3	Q6GMV3	OTTHUMG00000151978	ENST00000328379.5:c.127C>T	2.37:g.25016120G>A	ENSP00000330389:p.Pro43Ser		24869624		Missense_Mutation	SNP	ENST00000328379.5	37	CCDS33156.1	.	.	.	.	.	.	.	.	.	.	G	36	5.697887	0.96802	.	.	ENSG00000184924	ENST00000328379	T	0.09538	2.97	6.06	6.06	0.98353	Peptidyl-tRNA hydrolase II domain (2);	0.111999	0.64402	D	0.000008	T	0.30103	0.0754	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.00039	-1.2239	10	0.54805	T	0.06	.	19.3923	0.94587	0.0:0.0:1.0:0.0	.	43	Q6GMV3	PTRD1_HUMAN	S	43	ENSP00000330389:P43S	ENSP00000330389:P43S	P	-	1	0	PTRHD1	24869624	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	8.308000	0.89966	2.882000	0.98803	0.655000	0.94253	CCG		0.647	PTRHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324626.3	NM_001013663		A	25016120	G	A	25016120	3	1	61	1	0	0	0	0	1	0	0	0	2202	1203	42	3	303	3	C2orf79	2	25016120	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53804	25016120	218183253	1279	9264										
CENPO	79172	broad.mit.edu	37	chr2	25039527	25039527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcttagagtgactttgcaGccctcctgactgggcccttg	10	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25039527G>T	ENST00000380834.2	+	6	1032	c.607G>T	c.(607-609)Gcc>Tcc	p.A203S	CENPO_ENST00000395845.2_Intron|CENPO_ENST00000260662.1_Missense_Mutation_p.A203S|CENPO_ENST00000473706.1_Missense_Mutation_p.A197S			Q9BU64	CENPO_HUMAN	centromere protein O	203					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A203S(1)		breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TGACTTTGCAGCCCTCCTGAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											357	366	363					2																	25039527		2203	4300	6503	24893031	SO:0001583	missense	79172			AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092			28152	protein-coding gene	gene with protein product		611504				16622420, 16622419	Standard	NM_024322		Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.607G>T	2.37:g.25039527G>T	ENSP00000370214:p.Ala203Ser		24893031	B2RDC0|D6W536|Q53T55|Q96JV3	Missense_Mutation	SNP	ENST00000380834.2	37	CCDS1714.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167913	0.57476	.	.	ENSG00000138092	ENST00000380834;ENST00000473706;ENST00000260662	T;T;T	0.42131	0.98;0.99;0.98	6.08	4.25	0.50352	.	0.518099	0.18416	N	0.141888	T	0.36054	0.0953	L	0.60455	1.87	0.24003	N	0.996208	P;B	0.35872	0.525;0.39	B;B	0.33454	0.164;0.079	T	0.13602	-1.0503	10	0.21014	T	0.42	-12.9614	10.7335	0.46111	0.068:0.0:0.7994:0.1326	.	197;203	Q9BU64-2;Q9BU64	.;CENPO_HUMAN	S	203;197;203	ENSP00000370214:A203S;ENSP00000417787:A197S;ENSP00000260662:A203S	ENSP00000260662:A203S	A	+	1	0	CENPO	24893031	0.216000	0.23585	0.942000	0.38095	0.990000	0.78478	2.461000	0.45040	0.868000	0.35678	0.655000	0.94253	GCC		0.488	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246856.2	NM_024322		T	25039527	G	T	25039527	3	4	61	1	0	0	0	0	1	0	0	0	3245	971	34	2	625	2	CENPO	2	25039527	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23407	25039527	218159846	1280	9265										
DNMT3A	1788	broad.mit.edu	37	chr2	25458668	25458668	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctttatggagtttgacctCgtagtaatggtcctcacttt	9	8	1	1	rs138445723	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25458668C>T	ENST00000264709.3	-	22	2842	c.2505G>A	c.(2503-2505)acG>acA	p.T835T	DNMT3A_ENST00000321117.5_Silent_p.T835T|DNMT3A_ENST00000380746.4_Silent_p.T646T|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000402667.1_Silent_p.T612T	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	835	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.T835T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTTTGACCTCGTAGTAATGG	0.443			"Mis, F, N, S"		AML																																		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - coding silent(1)	large_intestine(1)	2						C	,,	1,4405	2.1+/-5.4	0,1,2202	175	158	164		2505,1938,2505	-5.8	0.9	2	dbSNP_134	164	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,	835/913,646/724,835/913	25458668	2,13004	2203	4300	6503	25312172	SO:0001819	synonymous_variant	1788				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2505G>A	2.37:g.25458668C>T			25312172	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	37	CCDS33157.1																																																																																				0.443	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25458668	C	T	25458668	2	4	61	1	0	0	0	0	0	0	0	1	4687	871	31	1		1	DNMT3A	2	25458668	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	419141	25458668	217740705	1281	9266										
DNMT3A	1788	broad.mit.edu	37	chr2	25462057	25462057	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgtgcagctgacacttCtttggcatcaatcatcacag	8	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25462057C>A	ENST00000264709.3	-	20	2687	c.2350G>T	c.(2350-2352)Gaa>Taa	p.E784*	DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.E784*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.E595*|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.E561*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	784	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.E784*(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGACACTTCTTTGGCATCA	0.577			"Mis, F, N, S"		AML																																		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Nonsense(1)	large_intestine(1)	2											69	62	64					2																	25462057		2203	4300	6503	25315561	SO:0001587	stop_gained	1788				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2350G>T	2.37:g.25462057C>A	ENSP00000264709:p.Glu784*		25315561	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	40	8.458116	0.98820	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.46	4.58	0.56647	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-6.9598	12.2239	0.54449	0.0:0.917:0.0:0.083	.	.	.	.	X	595;784;784;561	.	ENSP00000264709:E784X	E	-	1	0	DNMT3A	25315561	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.201000	0.51059	1.317000	0.45149	0.561000	0.74099	GAA		0.577	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		A	25462057	C	A	25462057	4	1	61	1	0	0	0	0	0	1	0	0	4687	922	32	2	404	2	DNMT3A	2	25462057	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3389	25462057	217737316	1282	9267										
DTNB	1838	broad.mit.edu	37	chr2	25861939	25861939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttctgtaagttgatagtCgtatgacatcaaaattctga	8	6	3	3	rs189303418	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25861939C>T	ENST00000406818.3	-	3	341	c.92G>A	c.(91-93)cGa>cAa	p.R31Q	DTNB_ENST00000288642.8_Missense_Mutation_p.R31Q|DTNB_ENST00000407186.1_Missense_Mutation_p.R31Q|DTNB_ENST00000405222.1_Missense_Mutation_p.R31Q|DTNB_ENST00000407038.3_Missense_Mutation_p.R31Q|DTNB_ENST00000472690.1_5'UTR|DTNB_ENST00000545439.1_5'UTR|DTNB_ENST00000496972.2_5'UTR|DTNB_ENST00000404103.3_Missense_Mutation_p.R31Q|DTNB_ENST00000407661.3_Missense_Mutation_p.R31Q	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	31						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R31Q(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTTGATAGTCGTATGACATC	0.373													C|||	2	0.000399361	0	0	5008	,	,		19914	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,3721		0,1,1860	78	75	76		92,92,92,92,92	6	1	2		76	4,8212		0,4,4104	yes	missense,missense,missense,missense,missense	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	43,43,43,43,43	0,5,5964	TT,TC,CC		0.0487,0.0269,0.0419	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	31/628,31/598,31/568,31/610,31/561	25861939	5,11933	1861	4108	5969	25715443	SO:0001583	missense	1838			AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.92G>A	2.37:g.25861939C>T	ENSP00000384084:p.Arg31Gln		25715443	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	37	CCDS46237.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	34	5.333103	0.95758	2.69E-4	4.87E-4	ENSG00000138101	ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000303659;ENST00000349996	T;T;T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	5.96	5.96	0.96718	EF-hand domain, type 1 (1);	0.084351	0.56097	D	0.000026	D	0.86912	0.6047	M	0.88570	2.965	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.996;1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;D;D;D;D	0.83275	0.989;0.947;0.996;0.974;0.987;0.976;0.939;0.964	D	0.88524	0.3098	10	0.87932	D	0	-7.4068	17.1412	0.86754	0.0:1.0:0.0:0.0	.	31;31;31;31;31;31;31;31	O60941-3;B7Z6A9;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941	.;.;.;.;.;.;.;DTNB_HUMAN	Q	31	ENSP00000384084:R31Q;ENSP00000385482:R31Q;ENSP00000385193:R31Q;ENSP00000384767:R31Q;ENSP00000384787:R31Q;ENSP00000385784:R31Q;ENSP00000288642:R31Q;ENSP00000306529:R31Q;ENSP00000340957:R31Q	ENSP00000288642:R31Q	R	-	2	0	DTNB	25715443	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.479000	0.73600	2.832000	0.97577	0.655000	0.94253	CGA		0.373	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		T	25861939	C	T	25861939	3	4	61	1	0	0	0	0	1	0	0	0	4800	884	31	1	1863	1	DTNB	2	25861939	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	399882	25861939	217337434	1283	9268										
ASXL2	55252	broad.mit.edu	37	chr2	25965541	25965541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctagctaagcaatcactgGtagatagagtttccctgctg	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:25965541G>A	ENST00000435504.4	-	13	3958	c.3665C>T	c.(3664-3666)aCc>aTc	p.T1222I	ASXL2_ENST00000404843.1_Missense_Mutation_p.T705I|ASXL2_ENST00000272341.4_Missense_Mutation_p.T705I|ASXL2_ENST00000336112.4_Missense_Mutation_p.T1194I			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	1222					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)	p.T1222I(1)|p.T705I(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAATCACTGGTAGATAGAGT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	2											91	87	88					2																	25965541		1954	4156	6110	25819045	SO:0001583	missense	55252					2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.3665C>T	2.37:g.25965541G>A	ENSP00000391447:p.Thr1222Ile		25819045	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		.	.	.	.	.	.	.	.	.	.	G	7.656	0.683956	0.14907	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	6.01	1.93	0.25924	.	0.762727	0.13351	N	0.394390	T	0.19446	0.0467	M	0.65975	2.015	0.09310	N	1	B;B	0.29432	0.244;0.006	B;B	0.29176	0.099;0.005	T	0.26052	-1.0114	10	0.27785	T	0.31	-4.0539	4.3539	0.11169	0.0737:0.2433:0.433:0.25	.	705;1222	Q76L83-2;Q76L83	.;ASXL2_HUMAN	I	1222;1194;705;705	ENSP00000391447:T1222I;ENSP00000337250:T1194I;ENSP00000383920:T705I;ENSP00000272341:T705I	ENSP00000272341:T705I	T	-	2	0	ASXL2	25819045	0.036000	0.19791	0.125000	0.21846	0.810000	0.45777	0.387000	0.20718	0.066000	0.16515	0.650000	0.86243	ACC		0.473	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		A	25965541	G	A	25965541	3	1	61	1	0	0	0	0	1	0	0	0	1068	1261	44	3	646	3	ASXL2	2	25965541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103602	25965541	217233832	1284	9269										
HADHA	3030	broad.mit.edu	37	chr2	26432731	26432731	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccatcaaggcctttgattCtttggtcattacaagctctc	6	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:26432731C>A	ENST00000380649.3	-	11	1132	c.1003G>T	c.(1003-1005)Gaa>Taa	p.E335*		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	335					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)	p.E335*(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCTTTGATTCTTTGGTCATT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											108	110	110					2																	26432731		2203	4300	6503	26286235	SO:0001587	stop_gained	3030			D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1003G>T	2.37:g.26432731C>A	ENSP00000370023:p.Glu335*		26286235	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Nonsense_Mutation	SNP	ENST00000380649.3	37	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	C	39	7.430239	0.98279	.	.	ENSG00000084754	ENST00000380649	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-32.5237	19.1882	0.93653	0.0:1.0:0.0:0.0	.	.	.	.	X	335	.	ENSP00000370023:E335X	E	-	1	0	HADHA	26286235	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.783000	0.85696	2.879000	0.98667	0.650000	0.86243	GAA		0.398	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		A	26432731	C	A	26432731	4	1	61	1	0	0	0	0	0	1	0	0	6964	922	32	2	1328	2	HADHA	2	26432731	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	467190	26432731	216766642	1285	9270										
EPT1	85465	broad.mit.edu	37	chr2	26607835	26607835	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttttccagaagctataAaaataacaccttgaaactca	3	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:26607835A>T	ENST00000260585.7	+	8	859	c.740A>T	c.(739-741)aAa>aTa	p.K247I		NM_033505.2	NP_277040.1	Q9C0D9	EPT1_HUMAN	ethanolaminephosphotransferase 1 (CDP-ethanolamine-specific)	247					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)	p.K247I(1)									AGAAGCTATAAAAATAACACC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											95	87	89					2																	26607835		1809	4069	5878	26461339	SO:0001583	missense	85465				CCDS46240.1	2p23.3	2012-03-01			ENSG00000138018	ENSG00000138018	2.7.8.1		29361	protein-coding gene	gene with protein product	"selenoprotein I"	607915				11214970, 17132865	Standard	NM_033505		Approved	KIAA1724, SELI, SEPI	uc021veu.1	Q9C0D9	OTTHUMG00000151931	ENST00000260585.7:c.740A>T	2.37:g.26607835A>T	ENSP00000260585:p.Lys247Ile		26461339	Q63ZE3	Missense_Mutation	SNP	ENST00000260585.7	37	CCDS46240.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999818	0.54147	.	.	ENSG00000138018	ENST00000260585;ENST00000447170	T	0.51325	0.71	5.97	1.16	0.20824	.	0.101188	0.64402	D	0.000005	T	0.44685	0.1305	M	0.79805	2.47	0.42975	D	0.994441	P	0.34864	0.473	B	0.34991	0.193	T	0.33137	-0.9880	10	0.22706	T	0.39	-25.1497	8.9112	0.35555	0.6423:0.0:0.3577:0.0	.	247	Q9C0D9	EPT1_HUMAN	I	247;123	ENSP00000260585:K247I	ENSP00000260585:K247I	K	+	2	0	EPT1	26461339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.789000	0.47813	0.515000	0.28320	0.528000	0.53228	AAA		0.308	EPT1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000324484.3	NM_033505.2		T	26607835	A	T	26607835	3	4	61	1	0	0	0	0	1	0	0	0	5212	14	1	5	770	5	EPT1	2	26607835	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	175104	26607835	216591538	1286	9271										
OTOF	9381	broad.mit.edu	37	chr2	26683797	26683797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcttttgcttgaagatggAcacgaggggcacgtccacct	13	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:26683797A>G	ENST00000272371.2	-	44	5761	c.5635T>C	c.(5635-5637)Tcc>Ccc	p.S1879P	OTOF_ENST00000403946.3_Missense_Mutation_p.S1879P|OTOF_ENST00000402415.3_Missense_Mutation_p.S1189P|OTOF_ENST00000339598.3_Missense_Mutation_p.S1112P|OTOF_ENST00000338581.6_Missense_Mutation_p.S1112P	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1879					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.S1879P(1)|p.S1112P(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGAAGATGGACACGAGGGGC	0.642																																					GBM(102;732 1451 20652 24062 31372)											2	Substitution - Missense(2)	large_intestine(2)	2											84	68	73					2																	26683797		2203	4300	6503	26537301	SO:0001583	missense	9381			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.5635T>C	2.37:g.26683797A>G	ENSP00000272371:p.Ser1879Pro		26537301	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	a	23.8	4.461147	0.84317	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32	4.54	4.54	0.55810	C2 calcium/lipid-binding domain, CaLB (1);	0.114352	0.64402	N	0.000008	D	0.91171	0.7219	M	0.92169	3.28	0.80722	D	1	D;D;D;D	0.71674	0.996;0.995;0.998;0.995	D;D;D;D	0.70716	0.914;0.97;0.961;0.97	D	0.93072	0.6483	10	0.72032	D	0.01	-23.6919	13.5678	0.61828	1.0:0.0:0.0:0.0	.	1879;1112;1189;1112	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	P	1112;1112;1189;1879;1879	ENSP00000345137:S1112P;ENSP00000344521:S1112P;ENSP00000383906:S1189P;ENSP00000272371:S1879P;ENSP00000385255:S1879P	ENSP00000272371:S1879P	S	-	1	0	OTOF	26537301	1.000000	0.71417	0.999000	0.59377	0.912000	0.54170	9.336000	0.96533	1.688000	0.51068	0.375000	0.23000	TCC		0.642	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			G	26683797	A	G	26683797	3	3	61	1	0	0	0	0	1	0	0	0	11334	275	10	4	555	4	OTOF	2	26683797	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	75962	26683797	216515576	1287	9272										
KCNK3	3777	broad.mit.edu	37	chr2	26950926	26950926	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacgtggccttcagcttCgtctacatccttacgggcct	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:26950926C>T	ENST00000302909.3	+	2	800	c.675C>T	c.(673-675)ttC>ttT	p.F225F		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	225					brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)	p.F225F(1)		endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	CCTTCAGCTTCGTCTACATCC	0.632																																					GBM(80;1457 1631 27100 45946)											1	Substitution - coding silent(1)	large_intestine(1)	2											84	66	72					2																	26950926		2203	4300	6503	26804430	SO:0001819	synonymous_variant	3777			AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6278	protein-coding gene	gene with protein product		603220				9312005, 9721223, 16382106	Standard	NM_002246		Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.675C>T	2.37:g.26950926C>T			26804430	Q53SU2	Silent	SNP	ENST00000302909.3	37	CCDS1727.1																																																																																				0.632	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		T	26950926	C	T	26950926	2	4	61	1	0	0	0	0	0	0	0	1	8088	883	31	1		1	KCNK3	2	26950926	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	267129	26950926	216248447	1288	9273										
TMEM214	54867	broad.mit.edu	37	chr2	27260521	27260521	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcatacctacttcccttCtttcctgtccagagccaccc	4	19	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27260521C>A	ENST00000238788.9	+	9	1165	c.1103C>A	c.(1102-1104)tCt>tAt	p.S368Y	TMEM214_ENST00000404032.3_Missense_Mutation_p.S323Y	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	368					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S368Y(1)		kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TACTTCCCTTCTTTCCTGTCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											115	116	116					2																	27260521		1942	4143	6085	27114025	SO:0001583	missense	54867				CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1103C>A	2.37:g.27260521C>A	ENSP00000238788:p.Ser368Tyr		27114025	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.8|27.8	4.861203|4.861203	0.91433|0.91433	.|.	.|.	ENSG00000119777|ENSG00000119777	ENST00000425720|ENST00000238788;ENST00000404032;ENST00000537397	.|T;T	.|0.50277	.|0.75;0.75	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69646|0.69646	0.3134|0.3134	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.81914	.|0.995;0.995	T|T	0.71328|0.71328	-0.4626|-0.4626	5|10	.|0.62326	.|D	.|0.03	-20.9244|-20.9244	17.5913|17.5913	0.87997|0.87997	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|323;368	.|Q6NUQ4-2;Q6NUQ4	.|.;TM214_HUMAN	I|Y	127|368;323;108	.|ENSP00000238788:S368Y;ENSP00000384417:S323Y	.|ENSP00000238788:S368Y	L|S	+|+	1|2	0|0	TMEM214|TMEM214	27114025|27114025	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	7.298000|7.298000	0.78815|0.78815	2.700000|2.700000	0.92200|0.92200	0.561000|0.561000	0.74099|0.74099	CTT|TCT		0.572	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		A	27260521	C	A	27260521	3	1	61	1	0	0	0	0	1	0	0	0	16176	913	32	2	1137	2	TMEM214	2	27260521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	309595	27260521	215938852	1289	9274										
C2orf28	51374	broad.mit.edu	37	chr2	27439464	27439464	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtttgtgctgatggtttCcatggatacaagtgtatgcg	13	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27439464C>A	ENST00000606999.1	+	6	619	c.561C>A	c.(559-561)ttC>ttA	p.F187L	ATRAID_ENST00000380171.3_Missense_Mutation_p.F242L|CAD_ENST00000403525.1_5'Flank|CAD_ENST00000264705.4_5'Flank|ATRAID_ENST00000405489.3_Missense_Mutation_p.F129L	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor	187	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.F242L(1)									CTGATGGTTTCCATGGATACA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											378	362	367					2																	27439464		2203	4300	6503	27292968	SO:0001583	missense	51374			BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405	ENST00000606999.1:c.561C>A	2.37:g.27439464C>A	ENSP00000476080:p.Phe187Leu		27292968	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Missense_Mutation	SNP	ENST00000606999.1	37		.	.	.	.	.	.	.	.	.	.	C	19.19	3.779955	0.70222	.	.	ENSG00000138085	ENST00000380171;ENST00000405489	D;T	0.87179	-2.22;0.71	5.67	2.77	0.32553	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.091955	0.85682	D	0.000000	D	0.91300	0.7257	M	0.76328	2.33	0.42692	D	0.993583	D;D	0.71674	0.996;0.998	D;D	0.77557	0.99;0.987	D	0.90114	0.4194	10	0.72032	D	0.01	-21.1804	7.8445	0.29419	0.0:0.7189:0.0:0.2811	.	187;242	Q6UW56;Q6UW56-3	APR3_HUMAN;.	L	242;129	ENSP00000369518:F242L;ENSP00000384033:F129L	ENSP00000369518:F242L	F	+	3	2	C2orf28	27292968	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	0.946000	0.29069	0.690000	0.31570	-0.367000	0.07326	TTC		0.463	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		A	27439464	C	A	27439464	3	1	61	1	0	0	0	0	1	0	0	0	2166	854	30	2	748	2	C2orf28	2	27439464	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178943	27439464	215759909	1290	9275										
CAD	790	broad.mit.edu	37	chr2	27465748	27465748	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaccctccaggaggaattCgagagcattgaggaggcgct	13	11	1	2	rs141620726		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27465748C>T	ENST00000403525.1	+	41	6342	c.6198C>T	c.(6196-6198)ttC>ttT	p.F2066F	CAD_ENST00000264705.4_Silent_p.F2129F			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.F2129F(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGAGGAATTCGAGAGCATTG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C		1,4405	2.1+/-5.4	0,1,2202	56	54	55		6387	-1.2	1	2	dbSNP_134	55	0,8600		0,0,4300	no	coding-synonymous	CAD	NM_004341.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		2129/2226	27465748	1,13005	2203	4300	6503	27319252	SO:0001819	synonymous_variant	790			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.6198C>T	2.37:g.27465748C>T			27319252	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	C	9.172	1.021441	0.19433	2.27E-4	0.0	ENSG00000084774	ENST00000428460	.	.	.	5.28	-1.2	0.09554	.	.	.	.	.	T	0.55321	0.1913	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50110	-0.8866	4	.	.	.	-23.4525	9.6319	0.39785	0.0:0.3906:0.0:0.6094	.	.	.	.	L	197	.	.	S	+	2	0	CAD	27319252	0.432000	0.25554	0.996000	0.52242	0.958000	0.62258	-0.378000	0.07446	-0.213000	0.10094	-0.424000	0.05967	TCG		0.577	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			T	27465748	C	T	27465748	2	4	61	1	0	0	0	0	0	0	0	1	2571	883	31	1		1	CAD	2	27465748	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26284	27465748	215733625	1291	9276										
GTF3C2	2976	broad.mit.edu	37	chr2	27565880	27565880	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttggattgatctaagaGaccaggaaccagtggggctg	16	6	1	2	rs147615647	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27565880G>T	ENST00000359541.2	-	3	811	c.382C>A	c.(382-384)Ctc>Atc	p.L128I	AC109828.1_ENST00000589853.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000588707.1_RNA|GTF3C2_ENST00000264720.3_Missense_Mutation_p.L128I|AC109828.1_ENST00000589232.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	128					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)		p.L128I(1)		central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGATCTAAGAGACCAGGAACC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	99	101					2																	27565880		2203	4300	6503	27419384	SO:0001583	missense	2976			D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.382C>A	2.37:g.27565880G>T	ENSP00000352536:p.Leu128Ile		27419384	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	37	CCDS1749.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089363	0.36855	.	.	ENSG00000115207	ENST00000359541;ENST00000264720;ENST00000457748	T;T	0.73681	-0.77;-0.77	5.31	4.43	0.53597	.	0.301944	0.27176	N	0.020561	T	0.59128	0.2171	N	0.19112	0.55	0.31093	N	0.710634	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.003	T	0.59968	-0.7354	10	0.41790	T	0.15	-6.6888	11.3264	0.49450	0.0:0.0:0.8194:0.1806	.	128;128;128	Q8WUA4-2;Q8WUA4;Q53QN0	.;TF3C2_HUMAN;.	I	128	ENSP00000352536:L128I;ENSP00000264720:L128I	ENSP00000264720:L128I	L	-	1	0	GTF3C2	27419384	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.703000	0.47110	1.466000	0.48025	0.563000	0.77884	CTC		0.547	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			T	27565880	G	T	27565880	3	4	61	1	0	0	0	0	1	0	0	0	6894	942	33	2	2421	2	GTF3C2	2	27565880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100132	27565880	215633493	1292	9277										
SNX17	9784	broad.mit.edu	37	chr2	27596794	27596794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcaacgggcagaaagttCtggtcaacgtgctaacttca	10	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27596794C>A	ENST00000233575.2	+	5	610	c.388C>A	c.(388-390)Ctg>Atg	p.L130M	SNX17_ENST00000537606.1_Missense_Mutation_p.L105M|SNX17_ENST00000542478.1_5'UTR|SNX17_ENST00000543024.1_5'UTR	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	130	FERM-like.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)	p.L130M(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGAAAGTTCTGGTCAACGT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											129	109	116					2																	27596794		2203	4300	6503	27450298	SO:0001583	missense	9784			D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"Sorting nexins"	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.388C>A	2.37:g.27596794C>A	ENSP00000233575:p.Leu130Met		27450298	B4DQM7|Q53HN7|Q6IAS3	Missense_Mutation	SNP	ENST00000233575.2	37	CCDS1750.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.515827	0.27123	.	.	ENSG00000115234	ENST00000233575;ENST00000537606	T;T	0.74947	-0.89;-0.89	5.2	3.37	0.38596	Ras-association (1);	0.620984	0.16471	N	0.212977	T	0.53498	0.1800	L	0.27053	0.805	0.80722	D	1	P;P;B;P	0.50066	0.931;0.804;0.064;0.726	B;B;B;B	0.37198	0.243;0.135;0.007;0.188	T	0.52193	-0.8608	10	0.52906	T	0.07	-3.5356	3.4704	0.07565	0.267:0.5037:0.1442:0.0851	.	105;118;110;130	B4DQM7;B4DTB8;B4DQ37;Q15036	.;.;.;SNX17_HUMAN	M	130;105	ENSP00000233575:L130M;ENSP00000439208:L105M	ENSP00000233575:L130M	L	+	1	2	SNX17	27450298	0.998000	0.40836	0.990000	0.47175	0.643000	0.38383	1.758000	0.38410	0.744000	0.32741	0.561000	0.74099	CTG		0.567	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748		A	27596794	C	A	27596794	3	1	61	1	0	0	0	0	1	0	0	0	14925	912	32	2	406	2	SNX17	2	27596794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30914	27596794	215602579	1293	9278										
C2orf16	84226	broad.mit.edu	37	chr2	27799768	27799768	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatggggagcaaactccaaGaacaaattatcaaatcatgg	8	7	2	1	rs368950997		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27799768G>A	ENST00000408964.2	+	1	380	c.329G>A	c.(328-330)aGa>aAa	p.R110K		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	110						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.R110K(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CAAACTCCAAGAACAAATTAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	54	55					2																	27799768		1852	4104	5956	27653272	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.329G>A	2.37:g.27799768G>A	ENSP00000386190:p.Arg110Lys		27653272	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	0.056	-1.235977	0.01505	.	.	ENSG00000221843	ENST00000408964	T	0.05139	3.49	3.74	-0.29	0.12847	.	.	.	.	.	T	0.02418	0.0074	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48559	-0.9025	9	0.08837	T	0.75	.	8.5773	0.33605	0.3964:0.0:0.6036:0.0	.	110	Q68DN1	CB016_HUMAN	K	110	ENSP00000386190:R110K	ENSP00000386190:R110K	R	+	2	0	C2orf16	27653272	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.264000	0.08658	-0.376000	0.07943	-1.598000	0.00824	AGA		0.408	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27799768	G	A	27799768	3	1	61	1	0	0	0	0	1	0	0	0	2163	942	33	3	331	3	C2orf16	2	27799768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202974	27799768	215399605	1294	9279										
C2orf16	84226	broad.mit.edu	37	chr2	27800094	27800094	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtaagggatcaaggctcaAaattcttaggattaactcca	9	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27800094A>C	ENST00000408964.2	+	1	706	c.655A>C	c.(655-657)Aaa>Caa	p.K219Q		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	219						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.K219Q(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TCAAGGCTCAAAATTCTTAGG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	48	49					2																	27800094		1872	4102	5974	27653598	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.655A>C	2.37:g.27800094A>C	ENSP00000386190:p.Lys219Gln		27653598	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.393526	0.62066	.	.	ENSG00000221843	ENST00000408964	T	0.09163	3.01	4.02	1.35	0.21983	.	.	.	.	.	T	0.07279	0.0184	N	0.24115	0.695	0.19575	N	0.999961	B	0.33044	0.395	B	0.35655	0.207	T	0.36114	-0.9761	9	0.45353	T	0.12	.	4.1921	0.10426	0.6808:0.206:0.1132:0.0	.	219	Q68DN1	CB016_HUMAN	Q	219	ENSP00000386190:K219Q	ENSP00000386190:K219Q	K	+	1	0	C2orf16	27653598	0.001000	0.12720	0.081000	0.20488	0.288000	0.27193	0.076000	0.14712	0.151000	0.19162	0.460000	0.39030	AAA		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27800094	A	C	27800094	3	2	61	1	0	0	0	0	1	0	0	0	2163	15	1	4	657	4	C2orf16	2	27800094	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	326	27800094	215399279	1295	9280										
C2orf16	84226	broad.mit.edu	37	chr2	27800558	27800558	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcaggagtgcaggtagaGaaaactttgcaattaacccc	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27800558G>T	ENST00000408964.2	+	1	1170	c.1119G>T	c.(1117-1119)gaG>gaT	p.E373D		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	373						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.E373D(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TGCAGGTAGAGAAAACTTTGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	61	62					2																	27800558		1906	4122	6028	27654062	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1119G>T	2.37:g.27800558G>T	ENSP00000386190:p.Glu373Asp		27654062	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	8.889	0.953574	0.18431	.	.	ENSG00000221843	ENST00000408964	T	0.05513	3.43	3.36	1.41	0.22369	.	.	.	.	.	T	0.02688	0.0081	N	0.14661	0.345	0.09310	N	1	P	0.46512	0.879	B	0.37144	0.242	T	0.36841	-0.9731	9	0.17369	T	0.5	.	3.2933	0.06957	0.1426:0.0:0.5971:0.2602	.	373	Q68DN1	CB016_HUMAN	D	373	ENSP00000386190:E373D	ENSP00000386190:E373D	E	+	3	2	C2orf16	27654062	0.001000	0.12720	0.001000	0.08648	0.014000	0.08584	0.077000	0.14738	0.670000	0.31165	0.563000	0.77884	GAG		0.463	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27800558	G	T	27800558	3	4	61	1	0	0	0	0	1	0	0	0	2163	933	33	2	1121	2	C2orf16	2	27800558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	464	27800558	215398815	1296	9281										
C2orf16	84226	broad.mit.edu	37	chr2	27801327	27801327	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcaggaattgaagcaataAattgtgtggatttacttcca	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27801327A>C	ENST00000408964.2	+	1	1939	c.1888A>C	c.(1888-1890)Aat>Cat	p.N630H		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	630						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.N630H(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TGAAGCAATAAATTGTGTGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	77	78					2																	27801327		1871	4109	5980	27654831	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1888A>C	2.37:g.27801327A>C	ENSP00000386190:p.Asn630His		27654831	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	8.139	0.784770	0.16189	.	.	ENSG00000221843	ENST00000408964	T	0.05580	3.42	4.42	0.563	0.17296	.	.	.	.	.	T	0.05318	0.0141	N	0.14661	0.345	0.09310	N	1	D	0.55605	0.972	P	0.47941	0.562	T	0.39542	-0.9609	9	0.66056	D	0.02	.	6.454	0.21920	0.4378:0.0:0.5622:0.0	.	630	Q68DN1	CB016_HUMAN	H	630	ENSP00000386190:N630H	ENSP00000386190:N630H	N	+	1	0	C2orf16	27654831	0.001000	0.12720	0.000000	0.03702	0.035000	0.12851	0.173000	0.16724	-0.018000	0.14079	-0.366000	0.07423	AAT		0.408	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27801327	A	C	27801327	3	2	61	1	0	0	0	0	1	0	0	0	2163	14	1	4	1890	4	C2orf16	2	27801327	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	769	27801327	215398046	1297	9282										
C2orf16	84226	broad.mit.edu	37	chr2	27802467	27802467	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttcaatggtatatcccaaGaagtcattcaacatatgcct	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27802467G>A	ENST00000408964.2	+	1	3079	c.3028G>A	c.(3028-3030)Gaa>Aaa	p.E1010K	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1010						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.E1010K(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TATATCCCAAGAAGTCATTCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	97	97					2																	27802467		2066	4223	6289	27655971	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3028G>A	2.37:g.27802467G>A	ENSP00000386190:p.Glu1010Lys		27655971	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	8.666	0.901800	0.17760	.	.	ENSG00000221843	ENST00000408964	T	0.05382	3.45	4.96	4.06	0.47325	.	.	.	.	.	T	0.06416	0.0165	N	0.08118	0	0.09310	N	0.99999	P	0.50156	0.932	P	0.53450	0.726	T	0.42816	-0.9429	9	0.25106	T	0.35	.	9.482	0.38906	0.099:0.0:0.901:0.0	.	1010	Q68DN1	CB016_HUMAN	K	1010	ENSP00000386190:E1010K	ENSP00000386190:E1010K	E	+	1	0	C2orf16	27655971	0.988000	0.35896	0.933000	0.37362	0.056000	0.15407	1.621000	0.36986	2.583000	0.87209	0.467000	0.42956	GAA		0.438	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27802467	G	A	27802467	3	1	61	1	0	0	0	0	1	0	0	0	2163	943	33	3	3030	3	C2orf16	2	27802467	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1140	27802467	215396906	1298	9283										
C2orf16	84226	broad.mit.edu	37	chr2	27803332	27803332	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatcaccaagcgacttaGaaaacacagaaagttctaca	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27803332G>T	ENST00000408964.2	+	1	3944	c.3893G>T	c.(3892-3894)aGa>aTa	p.R1298I	ZNF512_ENST00000355467.4_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000556601.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1298						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.R1298I(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AAGCGACTTAGAAAACACAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	78	79					2																	27803332		1833	4091	5924	27656836	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3893G>T	2.37:g.27803332G>T	ENSP00000386190:p.Arg1298Ile		27656836	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.236112	0.22626	.	.	ENSG00000221843	ENST00000408964	T	0.55413	0.52	5.31	2.49	0.30216	.	.	.	.	.	T	0.54598	0.1868	N	0.24115	0.695	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.39781	-0.9597	9	0.66056	D	0.02	.	7.4688	0.27336	0.2813:0.0:0.7187:0.0	.	1298	Q68DN1	CB016_HUMAN	I	1298	ENSP00000386190:R1298I	ENSP00000386190:R1298I	R	+	2	0	C2orf16	27656836	0.019000	0.18553	0.008000	0.14137	0.039000	0.13416	0.406000	0.21032	0.605000	0.29947	0.563000	0.77884	AGA		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27803332	G	T	27803332	3	4	61	1	0	0	0	0	1	0	0	0	2163	942	33	2	3895	2	C2orf16	2	27803332	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	865	27803332	215396041	1299	9284										
C2orf16	84226	broad.mit.edu	37	chr2	27804682	27804682	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcacagtccctctgagaGaagacatcacagtccctctg	7	15	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27804682G>T	ENST00000408964.2	+	1	5294	c.5243G>T	c.(5242-5244)aGa>aTa	p.R1748I	ZNF512_ENST00000355467.4_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000556601.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1748	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.R1748I(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CCCTCTGAGAGAAGACATCAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	2											193	196	195					2																	27804682		1918	4142	6060	27658186	SO:0001583	missense	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5243G>T	2.37:g.27804682G>T	ENSP00000386190:p.Arg1748Ile		27658186	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.999573	0.35320	.	.	ENSG00000221843	ENST00000408964	T	0.05996	3.36	3.63	0.729	0.18266	.	.	.	.	.	T	0.10294	0.0252	L	0.61218	1.895	0.09310	N	1	P	0.38300	0.626	P	0.44696	0.458	T	0.21415	-1.0246	9	0.62326	D	0.03	.	5.3286	0.15920	0.2052:0.1697:0.6251:0.0	.	1748	Q68DN1	CB016_HUMAN	I	1748	ENSP00000386190:R1748I	ENSP00000386190:R1748I	R	+	2	0	C2orf16	27658186	0.005000	0.15991	0.000000	0.03702	0.003000	0.03518	0.762000	0.26503	0.126000	0.18424	0.462000	0.41574	AGA		0.552	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27804682	G	T	27804682	3	4	61	1	0	0	0	0	1	0	0	0	2163	942	33	2	5245	2	C2orf16	2	27804682	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1350	27804682	215394691	1300	9285										
ZNF512	84450	broad.mit.edu	37	chr2	27844028	27844028	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcctctctaggactggttCgttgtaaacccaacaacaac	7	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27844028C>T	ENST00000355467.4	+	14	1487	c.1404C>T	c.(1402-1404)ttC>ttT	p.F468F	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000413371.2_Silent_p.F391F|ZNF512_ENST00000416005.2_Silent_p.F439F|ZNF512_ENST00000379717.1_Silent_p.F467F|ZNF512_ENST00000556601.1_Silent_p.F337F	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	468					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F468F(2)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					AGGACTGGTTCGTTGTAAACC	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	2											52	54	53					2																	27844028		2203	4300	6503	27697532	SO:0001819	synonymous_variant	84450			AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"Zinc fingers, C2H2-type"	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.1404C>T	2.37:g.27844028C>T			27697532	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Silent	SNP	ENST00000355467.4	37	CCDS1758.1																																																																																				0.418	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434		T	27844028	C	T	27844028	2	4	61	1	0	0	0	0	0	0	0	1	17995	883	31	1		1	ZNF512	2	27844028	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39346	27844028	215355345	1301	9286										
SLC4A1AP	22950	broad.mit.edu	37	chr2	27887296	27887296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgacggagaatgcgacaGcaacgggccgggcttctacc	13	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:27887296G>A	ENST00000326019.6	+	1	959	c.677G>A	c.(676-678)aGc>aAc	p.S226N	SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000404798.2_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	226	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S226N(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					GAATGCGACAGCAACGGGCCG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	71	70					2																	27887296		2203	4300	6503	27740800	SO:0001583	missense	22950				CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"lung cancer oncogene 3"	602655	"solute carrier family 4 (anion exchanger), member 1, adapter protein"			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.677G>A	2.37:g.27887296G>A	ENSP00000323837:p.Ser226Asn		27740800	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	37	CCDS33166.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387185	0.25031	.	.	ENSG00000163798	ENST00000326019	T	0.32272	1.46	4.27	1.24	0.21308	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.482646	0.21791	N	0.069062	T	0.16642	0.0400	N	0.16656	0.425	0.09310	N	1	B	0.26602	0.154	B	0.31101	0.124	T	0.23154	-1.0196	10	0.24483	T	0.36	-0.7038	7.3489	0.26678	0.1774:0.1519:0.6707:0.0	.	226	Q9BWU0	NADAP_HUMAN	N	226	ENSP00000323837:S226N	ENSP00000323837:S226N	S	+	2	0	SLC4A1AP	27740800	0.999000	0.42202	0.431000	0.26735	0.455000	0.32408	1.959000	0.40412	0.426000	0.26116	0.555000	0.69702	AGC		0.612	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158		A	27887296	G	A	27887296	3	1	61	1	0	0	0	0	1	0	0	0	14690	971	34	3	679	3	SLC4A1AP	2	27887296	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43268	27887296	215312077	1302	9287										
FOSL2	2355	broad.mit.edu	37	chr2	28627119	28627119	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcgctcgcacccctacaGccccctgccgggcctggcct	9	23	0	0	rs199613963		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:28627119G>T	ENST00000264716.4	+	2	1111	c.248G>T	c.(247-249)aGc>aTc	p.S83I	FOSL2_ENST00000460736.1_3'UTR|FOSL2_ENST00000379619.1_Missense_Mutation_p.S58I|FOSL2_ENST00000545753.1_Missense_Mutation_p.S44I	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	83					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S83I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					CACCCCTACAGCCCCCTGCCG	0.637													G|||	1	0.000199681	0	0	5008	,	,		16772	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											120	112	115					2																	28627119		2203	4300	6503	28480623	SO:0001583	missense	2355				CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.248G>T	2.37:g.28627119G>T	ENSP00000264716:p.Ser83Ile		28480623	B2RD58|B3KP27|B4DYV4|Q6FG46	Missense_Mutation	SNP	ENST00000264716.4	37	CCDS1766.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	29.7	5.028052	0.93518	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000436647;ENST00000545753	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.32	5.32	0.75619	.	0.040810	0.85682	D	0.000000	T	0.56499	0.1989	M	0.61703	1.905	0.47547	D	0.99945	D	0.61697	0.99	P	0.54664	0.758	T	0.55134	-0.8188	10	0.40728	T	0.16	-18.3961	18.9807	0.92754	0.0:0.0:1.0:0.0	.	83	P15408	FOSL2_HUMAN	I	58;83;44;44	ENSP00000368939:S58I;ENSP00000264716:S83I;ENSP00000396497:S44I;ENSP00000439303:S44I	ENSP00000264716:S83I	S	+	2	0	FOSL2	28480623	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.212000	0.65225	2.485000	0.83878	0.563000	0.77884	AGC		0.637	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		T	28627119	G	T	28627119	3	4	61	1	0	0	0	0	1	0	0	0	6007	971	34	2	254	2	FOSL2	2	28627119	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	739823	28627119	214572254	1303	9288										
SPDYA	245711	broad.mit.edu	37	chr2	29038968	29038968	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagatcacatcagcctaaaAagcccattactctgaagcgt	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29038968A>C	ENST00000334056.5	+	3	277	c.88A>C	c.(88-90)Aag>Cag	p.K30Q	SPDYA_ENST00000462832.1_3'UTR|SPDYA_ENST00000379579.4_Missense_Mutation_p.K30Q	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A									p.K30Q(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					TCAGCCTAAAAAGCCCATTAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	119	121					2																	29038968		2203	4300	6503	28892472	SO:0001583	missense	245711			AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"Speedy homologs"	30613	protein-coding gene	gene with protein product		614029	"speedy homolog 1 (Drosophila)", "speedy homolog A (Xenopus laevis)"	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000334056.5:c.88A>C	2.37:g.29038968A>C	ENSP00000335628:p.Lys30Gln		28892472		Missense_Mutation	SNP	ENST00000334056.5	37	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103647	0.56291	.	.	ENSG00000163806	ENST00000379579;ENST00000334056;ENST00000449210	.	.	.	5.04	5.04	0.67666	.	0.102208	0.38778	U	0.001572	T	0.54806	0.1881	L	0.34521	1.04	0.38522	D	0.948744	D;D	0.64830	0.994;0.993	P;P	0.57057	0.723;0.812	T	0.59941	-0.7359	9	0.51188	T	0.08	-35.5016	11.7213	0.51683	0.8525:0.1475:0.0:0.0	.	30;30	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	Q	30	.	ENSP00000335628:K30Q	K	+	1	0	SPDYA	28892472	1.000000	0.71417	0.988000	0.46212	0.434000	0.31775	3.275000	0.51639	2.023000	0.59567	0.533000	0.62120	AAG		0.378	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	NM_182756		C	29038968	A	C	29038968	3	2	61	1	0	0	0	0	1	0	0	0	15066	15	1	4	90	4	SPDYA	2	29038968	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	411849	29038968	214160405	1304	9289										
FAM179A	165186	broad.mit.edu	37	chr2	29225513	29225513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgatgcctctcatccagaGcatccctaccacccctgagg	8	18	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29225513G>T	ENST00000379558.4	+	5	890	c.539G>T	c.(538-540)aGc>aTc	p.S180I	FAM179A_ENST00000403861.2_Missense_Mutation_p.S180I	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	180								p.S180I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CTCATCCAGAGCATCCCTACC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	2											30	37	34					2																	29225513		1995	4161	6156	29079017	SO:0001583	missense	165186			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.539G>T	2.37:g.29225513G>T	ENSP00000368876:p.Ser180Ile		29079017	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315389	0.60524	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.19250	2.49;2.16	5.03	5.03	0.67393	.	.	.	.	.	T	0.34774	0.0909	L	0.32530	0.975	0.30304	N	0.789202	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.963	T	0.12319	-1.0552	9	0.46703	T	0.11	.	13.87	0.63612	0.0:0.0:1.0:0.0	.	180;180	F8W8E4;Q6ZUX3	.;F179A_HUMAN	I	180	ENSP00000368876:S180I;ENSP00000384699:S180I	ENSP00000368876:S180I	S	+	2	0	FAM179A	29079017	1.000000	0.71417	1.000000	0.80357	0.418000	0.31294	3.649000	0.54417	2.319000	0.78375	0.555000	0.69702	AGC		0.662	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29225513	G	T	29225513	3	4	61	1	0	0	0	0	1	0	0	0	5521	971	34	2	553	2	FAM179A	2	29225513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186545	29225513	213973860	1305	9290										
C2orf71	388939	broad.mit.edu	37	chr2	29293989	29293989	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtgcggtggggaagttcGccgctttgtggtgggtgggc	21	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29293989G>A	ENST00000331664.5	-	1	3138	c.3139C>T	c.(3139-3141)Cga>Tga	p.R1047*		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1047	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.R1047*(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGGGAAGTTCGCCGCTTTGTG	0.672																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											38	46	43					2																	29293989		1956	4106	6062	29147493	SO:0001587	stop_gained	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3139C>T	2.37:g.29293989G>A	ENSP00000332809:p.Arg1047*		29147493		Nonsense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	G	37	6.623926	0.97714	.	.	ENSG00000179270	ENST00000331664	.	.	.	4.84	0.0147	0.14101	.	3.446140	0.00481	N	0.000133	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	8.0497	6.7037	0.23238	0.0767:0.2515:0.5608:0.1111	.	.	.	.	X	1047	.	ENSP00000332809:R1047X	R	-	1	2	C2orf71	29147493	0.238000	0.23825	0.000000	0.03702	0.001000	0.01503	0.757000	0.26433	0.046000	0.15833	0.313000	0.20887	CGA		0.672	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29293989	G	A	29293989	4	1	61	1	0	0	0	0	0	1	0	0	2197	1095	38	1	735	1	C2orf71	2	29293989	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68476	29293989	213905384	1306	9291										
C2orf71	388939	broad.mit.edu	37	chr2	29296526	29296526	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatggatgatgcacagaAttgcttcatatttggagagg	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29296526A>C	ENST00000331664.5	-	1	601	c.602T>G	c.(601-603)aTt>aGt	p.I201S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	201			I -> F (in RP54; induces proteasomal degradation). {ECO:0000269|PubMed:20398886}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.I201S(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GATGCACAGAATTGCTTCATA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	89	88					2																	29296526		2041	4195	6236	29150030	SO:0001583	missense	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.602T>G	2.37:g.29296526A>C	ENSP00000332809:p.Ile201Ser		29150030		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.129393	0.56721	.	.	ENSG00000179270	ENST00000331664	T	0.31769	1.48	5.52	5.52	0.82312	.	0.431994	0.23477	N	0.047754	T	0.50820	0.1638	L	0.58101	1.795	0.18873	N	0.999987	D	0.67145	0.996	D	0.64410	0.925	T	0.48222	-0.9054	10	0.87932	D	0	-2.1054	15.6464	0.77055	1.0:0.0:0.0:0.0	.	201	A6NGG8	CB071_HUMAN	S	201	ENSP00000332809:I201S	ENSP00000332809:I201S	I	-	2	0	C2orf71	29150030	0.972000	0.33761	0.003000	0.11579	0.924000	0.55760	9.095000	0.94175	2.102000	0.63906	0.459000	0.35465	ATT		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		C	29296526	A	C	29296526	3	2	61	1	0	0	0	0	1	0	0	0	2197	101	4	4	3272	4	C2orf71	2	29296526	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2537	29296526	213902847	1307	9292										
C2orf71	388939	broad.mit.edu	37	chr2	29296871	29296871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtccttccatatctttcCttttgcctgaagcaggatct	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29296871C>T	ENST00000331664.5	-	1	256	c.257G>A	c.(256-258)aGg>aAg	p.R86K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	86					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.R86K(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CATATCTTTCCTTTTGCCTGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	2											212	196	201					2																	29296871		1930	4145	6075	29150375	SO:0001583	missense	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.257G>A	2.37:g.29296871C>T	ENSP00000332809:p.Arg86Lys		29150375		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	0.558	-0.846381	0.02671	.	.	ENSG00000179270	ENST00000331664	T	0.18016	2.24	4.51	1.69	0.24217	.	1.369090	0.04594	N	0.397232	T	0.07188	0.0182	N	0.04508	-0.205	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.30679	-0.9970	10	0.02654	T	1	-0.3305	6.0593	0.19828	0.0:0.5739:0.1317:0.2943	.	86	A6NGG8	CB071_HUMAN	K	86	ENSP00000332809:R86K	ENSP00000332809:R86K	R	-	2	0	C2orf71	29150375	0.000000	0.05858	0.000000	0.03702	0.838000	0.47535	0.103000	0.15292	0.046000	0.15833	0.561000	0.74099	AGG		0.512	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		T	29296871	C	T	29296871	3	4	61	1	0	0	0	0	1	0	0	0	2197	681	24	3	3617	3	C2orf71	2	29296871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	345	29296871	213902502	1308	9293										
ALK	238	broad.mit.edu	37	chr2	29416201	29416201	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccctgttgctggtagccGtaattgacattcccacaagg	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29416201G>A	ENST00000389048.3	-	29	5658	c.4752C>T	c.(4750-4752)taC>taT	p.Y1584Y	ALK_ENST00000431873.1_Silent_p.Y414Y	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1584					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y1584Y(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GCTGGTAGCCGTAATTGACAT	0.537			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - coding silent(1)	large_intestine(1)	2											77	75	76					2																	29416201		2203	4300	6503	29269705	SO:0001819	synonymous_variant	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4752C>T	2.37:g.29416201G>A			29269705	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.537	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29416201	G	A	29416201	2	1	61	1	0	0	0	0	0	0	0	1	525	1140	40	1		1	ALK	2	29416201	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119330	29416201	213783172	1309	9294										
ALK	238	broad.mit.edu	37	chr2	29543728	29543728	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcttcaaagttgcagtAaaaacccacaggcagtttcc	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29543728A>C	ENST00000389048.3	-	7	2341	c.1435T>G	c.(1435-1437)Tac>Gac	p.Y479D	ALK_ENST00000431873.1_Intron|ALK_ENST00000498037.1_5'Flank	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	479	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y479D(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	AAGTTGCAGTAAAAACCCACA	0.512			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - Missense(1)	large_intestine(1)	2											174	160	165					2																	29543728		2203	4300	6503	29397232	SO:0001583	missense	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1435T>G	2.37:g.29543728A>C	ENSP00000373700:p.Tyr479Asp		29397232	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559767	0.45590	.	.	ENSG00000171094	ENST00000389048	T	0.01838	4.61	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);MAM domain (1);	0.000000	0.43747	D	0.000530	T	0.10380	0.0254	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.01643	-1.1305	9	.	.	.	.	14.1373	0.65295	1.0:0.0:0.0:0.0	.	479	Q9UM73	ALK_HUMAN	D	479	ENSP00000373700:Y479D	.	Y	-	1	0	ALK	29397232	1.000000	0.71417	0.998000	0.56505	0.031000	0.12232	5.371000	0.66150	2.333000	0.79357	0.533000	0.62120	TAC		0.512	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	29543728	A	C	29543728	3	2	61	1	0	0	0	0	1	0	0	0	525	362	13	4	3519	4	ALK	2	29543728	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	127527	29543728	213655645	1310	9295										
ALK	238	broad.mit.edu	37	chr2	29606605	29606605	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagattcagataccttcactGcagttcttcagggcaaagaa	8	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29606605G>A	ENST00000389048.3	-	5	2181	c.1275C>T	c.(1273-1275)tgC>tgT	p.C425C	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	425	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.C425C(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TACCTTCACTGCAGTTCTTCA	0.507			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	1	Substitution - coding silent(1)	large_intestine(1)	2											107	91	97					2																	29606605		2203	4300	6503	29460109	SO:0001819	synonymous_variant	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1275C>T	2.37:g.29606605G>A			29460109	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.507	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29606605	G	A	29606605	2	1	61	1	0	0	0	0	0	0	0	1	525	1311	46	3		3	ALK	2	29606605	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62877	29606605	213592768	1311	9296										
ALK	238	broad.mit.edu	37	chr2	29606679	29606679	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtattccagggccactcGaaatgggttgtctggacgcc	13	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:29606679G>A	ENST00000389048.3	-	5	2107	c.1201C>T	c.(1201-1203)Cga>Tga	p.R401*	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	401	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R401*(3)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	AGGGCCACTCGAAATGGGTTG	0.483			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	3	Substitution - Nonsense(3)	large_intestine(2)|ovary(1)	2											120	113	115					2																	29606679		2203	4300	6503	29460183	SO:0001587	stop_gained	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1201C>T	2.37:g.29606679G>A	ENSP00000373700:p.Arg401*		29460183	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Nonsense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	G	46	12.444284	0.99668	.	.	ENSG00000171094	ENST00000389048	.	.	.	6.02	6.02	0.97574	.	0.000000	0.29980	N	0.010702	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6932	0.88275	0.0:0.0:1.0:0.0	.	.	.	.	X	401	.	.	R	-	1	2	ALK	29460183	1.000000	0.71417	0.998000	0.56505	0.459000	0.32528	4.361000	0.59461	2.857000	0.98124	0.650000	0.86243	CGA		0.483	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29606679	G	A	29606679	4	1	61	1	0	0	0	0	0	1	0	0	525	1066	37	1	3761	1	ALK	2	29606679	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74	29606679	213592694	1312	9297										
LCLAT1	253558	broad.mit.edu	37	chr2	30863380	30863380	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttataatcaccattgtaatCtttgtgctgcaagagagaat	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:30863380C>A	ENST00000309052.4	+	7	1349	c.1140C>A	c.(1138-1140)atC>atA	p.I380I	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000379509.3_Silent_p.I342I|LCLAT1_ENST00000540623.1_Silent_p.I342I	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	380					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.I380I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						CCATTGTAATCTTTGTGCTGC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	2											139	136	137					2																	30863380		2203	4300	6503	30716884	SO:0001819	synonymous_variant	253558			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.1140C>A	2.37:g.30863380C>A			30716884	A6H8Z7|Q8N1Q7	Silent	SNP	ENST00000309052.4	37	CCDS1772.1																																																																																				0.368	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		A	30863380	C	A	30863380	2	1	61	1	0	0	0	0	0	0	0	1	8699	903	32	2		2	LCLAT1	2	30863380	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1256701	30863380	212335993	1313	9298										
CAPN13	92291	broad.mit.edu	37	chr2	30955362	30955362	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggggaagctgaccctgccGacgctgtcgctgtacctgag	14	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:30955362G>A	ENST00000295055.8	-	20	2045	c.1869C>T	c.(1867-1869)gtC>gtT	p.V623V	CAPN13_ENST00000534090.2_Silent_p.V623V	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	623					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.V623V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TGACCCTGCCGACGCTGTCGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	2											28	32	31					2																	30955362		2103	4220	6323	30808866	SO:0001819	synonymous_variant	92291				CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1869C>T	2.37:g.30955362G>A			30808866	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	37	CCDS46252.1																																																																																				0.597	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		A	30955362	G	A	30955362	2	1	61	1	0	0	0	0	0	0	0	1	2632	1045	37	1		1	CAPN13	2	30955362	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91982	30955362	212244011	1314	9299										
EHD3	30845	broad.mit.edu	37	chr2	31483759	31483759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccctgcgcaagctcaacGacctcatcaaaagggccagg	10	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:31483759G>A	ENST00000322054.5	+	4	1171	c.886G>A	c.(886-888)Gac>Aac	p.D296N	EHD3_ENST00000541626.1_Intron	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	296					blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.D296N(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					CAAGCTCAACGACCTCATCAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	58	57					2																	31483759		2203	4300	6503	31337263	SO:0001583	missense	30845			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"EF-hand domain containing"	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.886G>A	2.37:g.31483759G>A	ENSP00000327116:p.Asp296Asn		31337263	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345420	0.82022	.	.	ENSG00000013016	ENST00000322054	D	0.96011	-3.88	4.77	4.77	0.60923	.	0.092366	0.64402	D	0.000001	D	0.98065	0.9362	M	0.92649	3.33	0.80722	D	1	D	0.71674	0.998	D	0.64144	0.922	D	0.98808	1.0742	10	0.59425	D	0.04	-37.3948	17.9928	0.89174	0.0:0.0:1.0:0.0	.	296	Q9NZN3	EHD3_HUMAN	N	296	ENSP00000327116:D296N	ENSP00000327116:D296N	D	+	1	0	EHD3	31337263	1.000000	0.71417	0.990000	0.47175	0.963000	0.63663	9.657000	0.98554	2.478000	0.83669	0.561000	0.74099	GAC		0.617	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600		A	31483759	G	A	31483759	3	1	61	1	0	0	0	0	1	0	0	0	4990	1058	37	1	900	1	EHD3	2	31483759	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	528397	31483759	211715614	1315	9300										
SRD5A2	0	broad.mit.edu	37	chr2	31754441	31754441	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcaaatgcaagtgctgGgagggaccaagtggccaggg	16	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:31754441G>T	ENST00000435713.1	+	0	255				SRD5A2_ENST00000405650.1_RNA																							GCAAGTGCTGGGAGGGACCAA	0.473																																																0			2											74	73	73					2																	31754441		1927	4132	6059	31607945			6716																															2.37:g.31754441G>T			31607945		Missense_Mutation	SNP	ENST00000435713.1	37																																																																																					0.473	AL133247.2-001	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000325125.1			T	31754441	G	T	31754441	1	4	61	0	1	0	0	0	0	0	0	0	15178	1232	43	2		2	SRD5A2	2	31754441	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	270682	31754441	211444932	1316	9301										
MEMO1	51072	broad.mit.edu	37	chr2	32093524	32093524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataattcaaaaacgaaaaaCtcatattcattccattcttc	1	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32093524C>T	ENST00000295065.5	-	9	1109	c.800G>A	c.(799-801)aGt>aAt	p.S267N	MEMO1_ENST00000490459.1_5'UTR|MEMO1_ENST00000404530.1_Missense_Mutation_p.S267N|DPY30_ENST00000446765.1_5'UTR|MEMO1_ENST00000426310.2_Missense_Mutation_p.S244N|MEMO1_ENST00000379383.3_Missense_Mutation_p.S270N	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	267					regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.S267N(1)		NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					AAACGAAAAACTCATATTCAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											25	24	24					2																	32093524		2203	4300	6503	31947028	SO:0001583	missense	51072			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.800G>A	2.37:g.32093524C>T	ENSP00000295065:p.Ser267Asn		31947028	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Missense_Mutation	SNP	ENST00000295065.5	37	CCDS1776.1	.	.	.	.	.	.	.	.	.	.	C	8.784	0.928902	0.18131	.	.	ENSG00000162959	ENST00000295065;ENST00000379383;ENST00000404530;ENST00000426310	.	.	.	5.23	5.23	0.72850	.	0.038439	0.85682	D	0.000000	T	0.42426	0.1202	N	0.13235	0.315	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.22871	-1.0204	9	0.20046	T	0.44	-0.856	18.7757	0.91911	0.0:1.0:0.0:0.0	.	244;267	Q9Y316-2;Q9Y316	.;MEMO1_HUMAN	N	267;270;267;244	.	ENSP00000295065:S267N	S	-	2	0	MEMO1	31947028	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.642000	0.61383	2.608000	0.88229	0.650000	0.86243	AGT		0.418	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955		T	32093524	C	T	32093524	3	4	61	1	0	0	0	0	1	0	0	0	9501	565	20	3	97	3	MEMO1	2	32093524	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	339083	32093524	211105849	1317	9302										
MEMO1	51072	broad.mit.edu	37	chr2	32094968	32094968	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatagtattatggtatttCttcaagtaattgctaaaaga	6	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32094968C>A	ENST00000295065.5	-	8	1020	c.711G>T	c.(709-711)aaG>aaT	p.K237N	MEMO1_ENST00000490459.1_5'UTR|MEMO1_ENST00000404530.1_Missense_Mutation_p.K237N|DPY30_ENST00000446765.1_5'UTR|MEMO1_ENST00000426310.2_Missense_Mutation_p.K214N|MEMO1_ENST00000379383.3_Missense_Mutation_p.K240N	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	237					regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.K237N(1)		NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					TATGGTATTTCTTCAAGTAAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	75	75					2																	32094968		2202	4290	6492	31948472	SO:0001583	missense	51072			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.711G>T	2.37:g.32094968C>A	ENSP00000295065:p.Lys237Asn		31948472	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Missense_Mutation	SNP	ENST00000295065.5	37	CCDS1776.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448660	0.84101	.	.	ENSG00000162959	ENST00000295065;ENST00000379383;ENST00000404530;ENST00000426310	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.74199	0.3685	M	0.64997	1.995	0.80722	D	1	B;D	0.64830	0.089;0.994	B;P	0.58970	0.198;0.849	T	0.77024	-0.2741	9	0.59425	D	0.04	-14.2427	17.8705	0.88810	0.0:1.0:0.0:0.0	.	214;237	Q9Y316-2;Q9Y316	.;MEMO1_HUMAN	N	237;240;237;214	.	ENSP00000295065:K237N	K	-	3	2	MEMO1	31948472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.936000	0.70153	2.389000	0.81357	0.585000	0.79938	AAG		0.294	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955		A	32094968	C	A	32094968	3	1	61	1	0	0	0	0	1	0	0	0	9501	912	32	2	190	2	MEMO1	2	32094968	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1444	32094968	211104405	1318	9303										
SPAST	6683	broad.mit.edu	37	chr2	32379455	32379455	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatctagatgagaaatattCgattatctgacttcactgaa	6	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32379455C>T	ENST00000315285.3	+	17	1866	c.1741C>T	c.(1741-1743)Cga>Tga	p.R581*	SPAST_ENST00000345662.1_Nonsense_Mutation_p.R549*	NM_014946.3	NP_055761.2			spastin									p.R581*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GAGAAATATTCGATTATCTGA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	2	GRCh37	CM051998	SPAST	M							79	80	79					2																	32379455		2203	4300	6503	32232959	SO:0001587	stop_gained	6683			AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1741C>T	2.37:g.32379455C>T	ENSP00000320885:p.Arg581*		32232959		Nonsense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	C	36	5.766269	0.96914	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	.	.	.	5.63	4.76	0.60689	.	0.390481	0.26935	N	0.021750	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-2.6781	7.9564	0.30045	0.2544:0.6666:0.0:0.0791	.	.	.	.	X	549;581	.	ENSP00000320885:R581X	R	+	1	2	SPAST	32232959	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.304000	0.51866	1.513000	0.48852	0.563000	0.77884	CGA		0.353	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		T	32379455	C	T	32379455	4	4	61	1	0	0	0	0	0	1	0	0	15036	876	31	1	1807	1	SPAST	2	32379455	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	284487	32379455	210819918	1319	9304										
SLC30A6	55676	broad.mit.edu	37	chr2	32445306	32445306	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcagtgcatgtaagaattCgacgagatgccaatgaacaa	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32445306C>T	ENST00000282587.5	+	14	947	c.910C>T	c.(910-912)Cga>Tga	p.R304*	SLC30A6_ENST00000357055.3_Nonsense_Mutation_p.R107*|SLC30A6_ENST00000406369.1_Nonsense_Mutation_p.R230*|SLC30A6_ENST00000538303.1_Nonsense_Mutation_p.R275*|SLC30A6_ENST00000379343.2_Nonsense_Mutation_p.R344*|SLC30A6_ENST00000435660.1_Nonsense_Mutation_p.R281*	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	304					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)	p.R304*(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TGTAAGAATTCGACGAGATGC	0.353																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											94	81	85					2																	32445306		2203	4300	6503	32298810	SO:0001587	stop_gained	55676			AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.910C>T	2.37:g.32445306C>T	ENSP00000282587:p.Arg304*		32298810	A5YM45|B7Z901|Q8N5C9|Q96NC3	Nonsense_Mutation	SNP	ENST00000282587.5	37	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824978	0.90955	.	.	ENSG00000152683	ENST00000379343;ENST00000282587;ENST00000435660;ENST00000538303;ENST00000357055;ENST00000406369	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3124	14.3706	0.66836	0.1481:0.8519:0.0:0.0	.	.	.	.	X	344;304;281;275;107;230	.	ENSP00000282587:R304X	R	+	1	2	SLC30A6	32298810	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.407000	0.66363	2.702000	0.92279	0.591000	0.81541	CGA		0.353	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			T	32445306	C	T	32445306	4	4	61	1	0	0	0	0	0	1	0	0	14596	876	31	1	964	1	SLC30A6	2	32445306	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65851	32445306	210754067	1320	9305										
NLRC4	58484	broad.mit.edu	37	chr2	32474873	32474873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcagcctgaggcttgtgGcagagctgaatattttcccc	11	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32474873G>A	ENST00000404025.2	-	5	2548	c.2060C>T	c.(2059-2061)gCc>gTc	p.A687V	NLRC4_ENST00000360906.5_Missense_Mutation_p.A687V|NLRC4_ENST00000402280.1_Missense_Mutation_p.A687V|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	687					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.A687V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GAGGCTTGTGGCAGAGCTGAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	79	80					2																	32474873		2203	4300	6503	32328377	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2060C>T	2.37:g.32474873G>A	ENSP00000385090:p.Ala687Val		32328377	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002108	0.35320	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.52754	0.65;0.65;0.65	3.4	2.51	0.30379	.	0.000000	0.40222	N	0.001142	T	0.44414	0.1292	L	0.29908	0.895	0.31833	N	0.624548	D	0.58268	0.982	P	0.52031	0.688	T	0.58126	-0.7691	9	0.42905	T	0.14	-11.764	12.2969	0.54852	0.0:0.1739:0.8261:0.0	.	687	Q9NPP4	NLRC4_HUMAN	V	687	ENSP00000354159:A687V;ENSP00000385428:A687V;ENSP00000385090:A687V	ENSP00000354159:A687V	A	-	2	0	NLRC4	32328377	0.863000	0.29885	0.451000	0.26982	0.223000	0.24884	3.441000	0.52893	0.996000	0.38943	0.543000	0.68304	GCC		0.463	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		A	32474873	G	A	32474873	3	1	61	1	0	0	0	0	1	0	0	0	10500	1203	42	3	1038	3	NLRC4	2	32474873	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29567	32474873	210724500	1321	9306										
NLRC4	58484	broad.mit.edu	37	chr2	32475708	32475708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggacacatcctgcagttCgaaatcaaacttgtgggaga	11	9	1	1	rs144123569		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32475708C>T	ENST00000404025.2	-	5	1713	c.1225G>A	c.(1225-1227)Gaa>Aaa	p.E409K	NLRC4_ENST00000360906.5_Missense_Mutation_p.E409K|NLRC4_ENST00000402280.1_Missense_Mutation_p.E409K|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	409	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.|Winged-helix domain (WHD). {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.E409K(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TCCTGCAGTTCGAAATCAAAC	0.473													C|||	1	0.000199681	8e-04	0	5008	,	,		22313	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											55	57	57					2																	32475708		2203	4300	6503	32329212	SO:0001583	missense	58484			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1225G>A	2.37:g.32475708C>T	ENSP00000385090:p.Glu409Lys		32329212	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.006	-2.077324	0.00375	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.10860	2.83;2.83;2.83	2.97	-1.66	0.08265	.	1.102920	0.07138	N	0.846839	T	0.09069	0.0224	L	0.44542	1.39	0.23192	N	0.998144	B	0.09022	0.002	B	0.04013	0.001	T	0.40156	-0.9578	9	0.27082	T	0.32	.	6.1007	0.20045	0.0:0.3531:0.3734:0.2735	.	409	Q9NPP4	NLRC4_HUMAN	K	409	ENSP00000354159:E409K;ENSP00000385428:E409K;ENSP00000385090:E409K	ENSP00000354159:E409K	E	-	1	0	NLRC4	32329212	0.030000	0.19436	0.003000	0.11579	0.006000	0.05464	-0.681000	0.05191	-0.970000	0.03569	-2.441000	0.00211	GAA		0.473	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		T	32475708	C	T	32475708	3	4	61	1	0	0	0	0	1	0	0	0	10500	893	31	1	1873	1	NLRC4	2	32475708	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	835	32475708	210723665	1322	9307										
BIRC6	57448	broad.mit.edu	37	chr2	32640364	32640364	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactgttccacagattattGaaatggagctggatagtcag	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32640364G>T	ENST00000421745.2	+	10	2139	c.2005G>T	c.(2005-2007)Gaa>Taa	p.E669*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	669					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.E669*(1)|p.E641*(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ACAGATTATTGAAATGGAGCT	0.408																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Nonsense(2)	large_intestine(2)	2											87	82	83					2																	32640364		2203	4300	6503	32493868	SO:0001587	stop_gained	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2005G>T	2.37:g.32640364G>T	ENSP00000393596:p.Glu669*		32493868	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	39	7.839206	0.98519	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.8856	0.96911	0.0:0.0:1.0:0.0	.	.	.	.	X	669	.	ENSP00000393596:E669X	E	+	1	0	BIRC6	32493868	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.506000	0.97992	2.771000	0.95319	0.650000	0.86243	GAA		0.408	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32640364	G	T	32640364	4	4	61	1	0	0	0	0	0	1	0	0	1439	1291	45	2	2043	2	BIRC6	2	32640364	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164656	32640364	210559009	1323	9308										
BIRC6	57448	broad.mit.edu	37	chr2	32667430	32667430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacctactttcaaaaacacGaaaatttctgtcagacatcg	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32667430G>A	ENST00000421745.2	+	19	4279	c.4145G>A	c.(4144-4146)cGa>cAa	p.R1382Q		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1382					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.R1354Q(1)|p.R1382Q(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCAAAAACACGAAAATTTCTG	0.403																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Missense(2)	large_intestine(2)	2											105	100	102					2																	32667430		2203	4300	6503	32520934	SO:0001583	missense	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4145G>A	2.37:g.32667430G>A	ENSP00000393596:p.Arg1382Gln		32520934	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561874	0.45590	.	.	ENSG00000115760	ENST00000421745	T	0.72942	-0.7	5.21	5.21	0.72293	.	0.086182	0.47093	D	0.000253	T	0.48132	0.1483	N	0.04355	-0.22	0.49130	D	0.999752	B	0.21147	0.052	B	0.10450	0.005	T	0.50499	-0.8821	10	0.07175	T	0.84	.	18.7528	0.91821	0.0:0.0:1.0:0.0	.	1382	Q9NR09	BIRC6_HUMAN	Q	1382	ENSP00000393596:R1382Q	ENSP00000393596:R1382Q	R	+	2	0	BIRC6	32520934	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.541000	0.82084	2.413000	0.81919	0.650000	0.86243	CGA		0.403	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32667430	G	A	32667430	3	1	61	1	0	0	0	0	1	0	0	0	1439	1058	37	1	4219	1	BIRC6	2	32667430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27066	32667430	210531943	1324	9309										
BIRC6	57448	broad.mit.edu	37	chr2	32726811	32726811	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacatctcactaaacatgaAaactttcatggtgggttgga	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32726811A>C	ENST00000421745.2	+	47	9197	c.9063A>C	c.(9061-9063)gaA>gaC	p.E3021D		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3021					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.E2993D(1)|p.E3021D(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTAAACATGAAAACTTTCATG	0.398																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Missense(2)	large_intestine(2)	2											103	103	103					2																	32726811		2203	4300	6503	32580315	SO:0001583	missense	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9063A>C	2.37:g.32726811A>C	ENSP00000393596:p.Glu3021Asp		32580315	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	14.27	2.485244	0.44147	.	.	ENSG00000115760	ENST00000421745	T	0.75938	-0.98	5.78	-0.0533	0.13818	.	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	L	0.38531	1.155	0.44454	D	0.997389	D	0.58970	0.984	D	0.68192	0.956	T	0.69899	-0.5020	10	0.32370	T	0.25	.	12.0394	0.53444	0.5517:0.0:0.4483:0.0	.	3021	Q9NR09	BIRC6_HUMAN	D	3021	ENSP00000393596:E3021D	ENSP00000393596:E3021D	E	+	3	2	BIRC6	32580315	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.282000	0.33226	-0.230000	0.09840	0.460000	0.39030	GAA		0.398	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32726811	A	C	32726811	3	2	61	1	0	0	0	0	1	0	0	0	1439	11	1	4	9249	4	BIRC6	2	32726811	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	59381	32726811	210472562	1325	9310										
BIRC6	57448	broad.mit.edu	37	chr2	32750029	32750029	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaaaccatgaagagaaaGaaaaagttaaagcggaaaat	9	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32750029G>T	ENST00000421745.2	+	58	11832	c.11698G>T	c.(11698-11700)Gaa>Taa	p.E3900*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3900					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.E3872*(1)|p.E3900*(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGAAGAGAAAGAAAAAGTTAA	0.294																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - Nonsense(2)	large_intestine(2)	2											38	41	40					2																	32750029		2196	4281	6477	32603533	SO:0001587	stop_gained	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.11698G>T	2.37:g.32750029G>T	ENSP00000393596:p.Glu3900*		32603533	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	54	23.129291	0.99953	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.31	5.31	0.75309	.	0.107942	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	19.3339	0.94307	0.0:0.0:1.0:0.0	.	.	.	.	X	3900	.	ENSP00000393596:E3900X	E	+	1	0	BIRC6	32603533	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.375000	0.97178	2.629000	0.89072	0.655000	0.94253	GAA		0.294	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32750029	G	T	32750029	4	4	61	1	0	0	0	0	0	1	0	0	1439	943	33	2	11928	2	BIRC6	2	32750029	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23218	32750029	210449344	1326	9311										
BIRC6	57448	broad.mit.edu	37	chr2	32770897	32770897	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagccaccattccccacgAgttccaaactctagcgtgaa	7	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32770897A>G	ENST00000421745.2	+	63	12914	c.12780A>G	c.(12778-12780)cgA>cgG	p.R4260R		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4260					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.R4232R(1)|p.R4260R(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATTCCCCACGAGTTCCAAACT	0.388																																					Pancreas(94;175 1509 16028 18060 45422)											2	Substitution - coding silent(2)	large_intestine(2)	2											137	115	122					2																	32770897		2203	4300	6503	32624401	SO:0001819	synonymous_variant	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.12780A>G	2.37:g.32770897A>G			32624401	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																				0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32770897	A	G	32770897	2	3	61	1	0	0	0	0	0	0	0	1	1439	291	11	4		4	BIRC6	2	32770897	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	20868	32770897	210428476	1327	9312										
TTC27	55622	broad.mit.edu	37	chr2	32983489	32983489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcccggtaccgcagtgctcGtgctcagcgctccaaagccc	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:32983489G>A	ENST00000317907.4	+	13	1814	c.1583G>A	c.(1582-1584)cGt>cAt	p.R528H		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	528								p.R528H(2)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						CGCAGTGCTCGTGCTCAGCGC	0.498																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	2											115	107	110					2																	32983489		2203	4300	6503	32836993	SO:0001583	missense	55622			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1583G>A	2.37:g.32983489G>A	ENSP00000313953:p.Arg528His		32836993	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682304	0.88542	.	.	ENSG00000018699	ENST00000317907	T	0.65178	-0.14	5.86	5.86	0.93980	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.107046	0.56097	D	0.000021	D	0.84097	0.5397	M	0.90870	3.155	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.85928	0.1450	10	0.56958	D	0.05	-15.4191	20.1772	0.98182	0.0:0.0:1.0:0.0	.	528	Q6P3X3	TTC27_HUMAN	H	528	ENSP00000313953:R528H	ENSP00000313953:R528H	R	+	2	0	TTC27	32836993	1.000000	0.71417	0.062000	0.19696	0.495000	0.33615	9.869000	0.99810	2.778000	0.95560	0.655000	0.94253	CGT		0.498	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		A	32983489	G	A	32983489	3	1	61	1	0	0	0	0	1	0	0	0	16735	1145	40	1	1633	1	TTC27	2	32983489	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	212592	32983489	210215884	1328	9313										
TTC27	55622	broad.mit.edu	37	chr2	33037571	33037571	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttctttctccttcctcagGcattccagtgcctctcaaag	6	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33037571G>A	ENST00000317907.4	+	18	2428	c.2197G>A	c.(2197-2199)Gca>Aca	p.A733T		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	733								p.A733T(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						CCTTCCTCAGGCATTCCAGTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	101	102					2																	33037571		2203	4300	6503	32891075	SO:0001630	splice_region_variant	55622			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2197-1G>A	2.37:g.33037571G>A			32891075	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440868	0.83993	.	.	ENSG00000018699	ENST00000317907	T	0.75050	-0.9	5.18	5.18	0.71444	.	1.369420	0.05020	N	0.472617	T	0.81083	0.4749	M	0.71036	2.16	0.54753	D	0.999987	P	0.51933	0.949	P	0.47673	0.554	T	0.72616	-0.4239	9	.	.	.	-11.5087	14.5053	0.67748	0.0:0.0:0.8439:0.1561	.	733	Q6P3X3	TTC27_HUMAN	T	733	ENSP00000313953:A733T	.	A	+	1	0	TTC27	32891075	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.729000	0.62008	2.413000	0.81919	0.561000	0.74099	GCA		0.383	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	Missense_Mutation	A	33037571	G	A	33037571	5	1	61	1	0	0	0	0	0	0	1	0	16735	1217	42	3	2267	3	TTC27	2	33037571	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54082	33037571	210161802	1329	9314										
TTC27	55622	broad.mit.edu	37	chr2	33042581	33042581	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagctgtacaaatgctttCttctgttcgactcaatttac	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33042581C>A	ENST00000317907.4	+	19	2597	c.2366C>A	c.(2365-2367)tCt>tAt	p.S789Y		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	789								p.S789Y(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						CAAATGCTTTCTTCTGTTCGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	118	122					2																	33042581		2203	4300	6503	32896085	SO:0001583	missense	55622			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2366C>A	2.37:g.33042581C>A	ENSP00000313953:p.Ser789Tyr		32896085	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100355	0.56183	.	.	ENSG00000018699	ENST00000317907	T	0.60299	0.2	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.70692	0.3253	M	0.64567	1.98	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.64377	-0.6422	10	0.02654	T	1	-16.4288	19.4334	0.94781	0.0:1.0:0.0:0.0	.	789	Q6P3X3	TTC27_HUMAN	Y	789	ENSP00000313953:S789Y	ENSP00000313953:S789Y	S	+	2	0	TTC27	32896085	1.000000	0.71417	0.924000	0.36721	0.053000	0.15095	6.197000	0.72100	2.664000	0.90586	0.591000	0.81541	TCT		0.353	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		A	33042581	C	A	33042581	3	1	61	1	0	0	0	0	1	0	0	0	16735	913	32	2	2440	2	TTC27	2	33042581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5010	33042581	210156792	1330	9315										
LTBP1	4052	broad.mit.edu	37	chr2	33526597	33526597	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgctcatagacattgatGaatgccagcaccgtcatctc	7	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33526597G>T	ENST00000404816.2	+	22	3720	c.3367G>T	c.(3367-3369)Gaa>Taa	p.E1123*	LTBP1_ENST00000390003.4_Nonsense_Mutation_p.E798*|LTBP1_ENST00000402934.1_Nonsense_Mutation_p.E744*|LTBP1_ENST00000404525.1_Nonsense_Mutation_p.E744*|LTBP1_ENST00000498013.1_3'UTR|LTBP1_ENST00000354476.3_Nonsense_Mutation_p.E1124*|LTBP1_ENST00000407925.1_Nonsense_Mutation_p.E797*|LTBP1_ENST00000418533.2_Nonsense_Mutation_p.E797*|LTBP1_ENST00000272273.5_Nonsense_Mutation_p.E63*			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1123	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.E1124*(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGACATTGATGAATGCCAGCA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											153	146	149					2																	33526597		2203	4300	6503	33380101	SO:0001587	stop_gained	4052				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3367G>T	2.37:g.33526597G>T	ENSP00000386043:p.Glu1123*		33380101	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Nonsense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.301568|8.301568	0.98750|0.98750	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669|ENST00000415140	.|.	.|.	.|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74215	.|0.3687	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73088	.|-0.4093	.|3	0.87932|.	D|.	0|.	.|.	17.8642|17.8642	0.88791|0.88791	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1123;1124;798;797;744;744;797;63;1|84	.|.	ENSP00000272273:E63X|.	E|M	+|+	1|3	0|0	LTBP1|LTBP1	33380101|33380101	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.093000|0.093000	0.18481|0.18481	7.813000|7.813000	0.86123|0.86123	2.508000|2.508000	0.84585|0.84585	0.563000|0.563000	0.77884|0.77884	GAA|ATG		0.443	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33526597	G	T	33526597	4	4	61	1	0	0	0	0	0	1	0	0	9102	1291	45	2	3508	2	LTBP1	2	33526597	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	484016	33526597	209672776	1331	9316										
RASGRP3	25780	broad.mit.edu	37	chr2	33745064	33745064	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaatgaatttcgattaaaGatctgctacttcatgaggta	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33745064G>T	ENST00000403687.3	+	5	959	c.219G>T	c.(217-219)aaG>aaT	p.K73N	RASGRP3_ENST00000407811.1_Missense_Mutation_p.K73N|RASGRP3_ENST00000402538.3_Missense_Mutation_p.K73N	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	73	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.K73N(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					TTCGATTAAAGATCTGCTACT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											99	100	99					2																	33745064		1825	4081	5906	33598568	SO:0001583	missense	25780			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.219G>T	2.37:g.33745064G>T	ENSP00000384192:p.Lys73Asn		33598568	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984722	0.74474	.	.	ENSG00000152689	ENST00000402538;ENST00000437184;ENST00000403687;ENST00000442390;ENST00000444784;ENST00000423159;ENST00000407811	T;T;T;T;T;T;T	0.51325	0.71;1.35;0.71;1.5;1.35;1.35;0.71	6.17	5.3	0.74995	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.101413	0.64402	D	0.000004	T	0.53834	0.1821	M	0.71036	2.16	0.44289	D	0.997152	P;P	0.38677	0.642;0.642	P;P	0.45276	0.475;0.475	T	0.58967	-0.7542	10	0.87932	D	0	-15.7218	10.0361	0.42129	0.1884:0.0:0.8116:0.0	.	73;73	D6W583;Q8IV61	.;GRP3_HUMAN	N	73	ENSP00000385886:K73N;ENSP00000393866:K73N;ENSP00000384192:K73N;ENSP00000405648:K73N;ENSP00000400602:K73N;ENSP00000388139:K73N;ENSP00000383917:K73N	ENSP00000385886:K73N	K	+	3	2	RASGRP3	33598568	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.816000	0.55658	1.632000	0.50472	0.655000	0.94253	AAG		0.383	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		T	33745064	G	T	33745064	3	4	61	1	0	0	0	0	1	0	0	0	13113	933	33	2	229	2	RASGRP3	2	33745064	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218467	33745064	209454309	1332	9317										
RASGRP3	25780	broad.mit.edu	37	chr2	33747055	33747055	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatgagaagagtcacacaGaggaaaaaagtatccaagaa	11	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33747055G>T	ENST00000403687.3	+	7	1142	c.402G>T	c.(400-402)caG>caT	p.Q134H	RASGRP3_ENST00000407811.1_Missense_Mutation_p.Q134H|RASGRP3_ENST00000402538.3_Missense_Mutation_p.Q134H	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	134					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.Q134H(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GAGTCACACAGAGGAAAAAAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											129	125	126					2																	33747055		1876	4104	5980	33600559	SO:0001583	missense	25780			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.402G>T	2.37:g.33747055G>T	ENSP00000384192:p.Gln134His		33600559	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.871668	0.72065	.	.	ENSG00000152689	ENST00000402538;ENST00000437184;ENST00000403687;ENST00000407811	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	6.03	5.16	0.70880	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.50034	0.1592	M	0.62723	1.935	0.47341	D	0.999399	D;D	0.71674	0.998;0.998	D;D	0.72075	0.976;0.976	T	0.48614	-0.9020	10	0.46703	T	0.11	-16.5548	11.6098	0.51053	0.1845:0.0:0.8155:0.0	.	134;134	D6W583;Q8IV61	.;GRP3_HUMAN	H	134	ENSP00000385886:Q134H;ENSP00000393866:Q134H;ENSP00000384192:Q134H;ENSP00000383917:Q134H	ENSP00000385886:Q134H	Q	+	3	2	RASGRP3	33600559	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.127000	0.57944	1.569000	0.49696	0.557000	0.71058	CAG		0.428	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		T	33747055	G	T	33747055	3	4	61	1	0	0	0	0	1	0	0	0	13113	933	33	2	420	2	RASGRP3	2	33747055	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1991	33747055	209452318	1333	9318										
RASGRP3	25780	broad.mit.edu	37	chr2	33774812	33774812	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttctgcgaacactgtgcGggatttgtaagtctgttttc	10	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:33774812G>A	ENST00000403687.3	+	14	2276	c.1536G>A	c.(1534-1536)gcG>gcA	p.A512A	RASGRP3_ENST00000407811.1_Silent_p.A511A|RASGRP3_ENST00000402538.3_Silent_p.A512A	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	512					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.A512A(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					AACACTGTGCGGGATTTGTAA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	2											171	149	156					2																	33774812		1872	4102	5974	33628316	SO:0001819	synonymous_variant	25780			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1536G>A	2.37:g.33774812G>A			33628316	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	37	CCDS46256.1																																																																																				0.378	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		A	33774812	G	A	33774812	2	1	61	1	0	0	0	0	0	0	0	1	13113	1103	39	1		1	RASGRP3	2	33774812	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27757	33774812	209424561	1334	9319										
CRIM1	51232	broad.mit.edu	37	chr2	36740790	36740790	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaggagagctggcacgaTgggtgccgggaatgctactg	17	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:36740790T>C	ENST00000280527.2	+	11	2239	c.1872T>C	c.(1870-1872)gaT>gaC	p.D624D	RP11-78I14.1_ENST00000609765.1_RNA	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	624	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D624D(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GCTGGCACGATGGGTGCCGGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2											91	87	88					2																	36740790		2203	4300	6503	36594294	SO:0001819	synonymous_variant	51232			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.1872T>C	2.37:g.36740790T>C			36594294	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	37	CCDS1783.1																																																																																				0.582	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		C	36740790	T	C	36740790	2	2	61	1	0	0	0	0	0	0	0	1	3879	1461	51	4		4	CRIM1	2	36740790	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2965978	36740790	206458583	1335	9320										
CRIM1	51232	broad.mit.edu	37	chr2	36749383	36749383	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatagcgtaattagctgtttCtctgagtcctgcccttctgt	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:36749383C>A	ENST00000280527.2	+	13	2722	c.2355C>A	c.(2353-2355)ttC>ttA	p.F785L		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	785	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F785L(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TTAGCTGTTTCTCTGAGTCCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											198	179	185					2																	36749383		2203	4300	6503	36602887	SO:0001583	missense	51232			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.2355C>A	2.37:g.36749383C>A	ENSP00000280527:p.Phe785Leu		36602887	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436941	0.62955	.	.	ENSG00000150938	ENST00000280527;ENST00000413985	T;T	0.71103	-0.54;-0.54	5.66	4.78	0.61160	von Willebrand factor, type C (4);	0.262756	0.38381	N	0.001711	T	0.60183	0.2249	L	0.35854	1.095	0.33256	D	0.559079	B	0.28439	0.212	B	0.32465	0.146	T	0.62431	-0.6856	10	0.14656	T	0.56	-17.2404	13.1261	0.59356	0.0:0.9237:0.0:0.0763	.	785	Q9NZV1	CRIM1_HUMAN	L	785;147	ENSP00000280527:F785L;ENSP00000403120:F147L	ENSP00000280527:F785L	F	+	3	2	CRIM1	36602887	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.365000	0.52335	2.662000	0.90505	0.557000	0.71058	TTC		0.458	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		A	36749383	C	A	36749383	3	1	61	1	0	0	0	0	1	0	0	0	3879	912	32	2	2405	2	CRIM1	2	36749383	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8593	36749383	206449990	1336	9321										
CRIM1	51232	broad.mit.edu	37	chr2	36774281	36774281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcagaagaaacagtggatAccactgctttgctggtatcg	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:36774281A>G	ENST00000280527.2	+	16	3268	c.2901A>G	c.(2899-2901)atA>atG	p.I967M	AC007401.2_ENST00000406220.1_Intron	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	967					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.I967M(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				AACAGTGGATACCACTGCTTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											91	91	91					2																	36774281		2203	4300	6503	36627785	SO:0001583	missense	51232			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.2901A>G	2.37:g.36774281A>G	ENSP00000280527:p.Ile967Met		36627785	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.649603	0.67358	.	.	ENSG00000150938	ENST00000280527	T	0.05199	3.48	5.8	-3.79	0.04320	.	0.227892	0.43579	D	0.000551	T	0.04048	0.0113	L	0.29908	0.895	0.34294	D	0.683552	P	0.38250	0.624	B	0.41088	0.347	T	0.36986	-0.9725	10	0.48119	T	0.1	-0.9629	2.6984	0.05141	0.3235:0.3129:0.0623:0.3013	.	967	Q9NZV1	CRIM1_HUMAN	M	967	ENSP00000280527:I967M	ENSP00000280527:I967M	I	+	3	3	CRIM1	36627785	0.936000	0.31750	0.920000	0.36463	0.999000	0.98932	-0.020000	0.12525	-0.461000	0.06993	0.533000	0.62120	ATA		0.368	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		G	36774281	A	G	36774281	3	3	61	1	0	0	0	0	1	0	0	0	3879	381	14	4	2963	4	CRIM1	2	36774281	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24898	36774281	206425092	1337	9322										
FEZ2	9637	broad.mit.edu	37	chr2	36805790	36805790	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccattctgagagctgccatTttttagtttctttttctttt	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:36805790T>G	ENST00000405912.3	-	5	852	c.853A>C	c.(853-855)Aat>Cat	p.N285H	FEZ2_ENST00000305852.7_Missense_Mutation_p.N114H|FEZ2_ENST00000379245.4_Missense_Mutation_p.N285H	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	285					axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165)			p.N285H(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	7		all_hematologic(82;0.21)				GAGCTGCCATTTTTTAGTTTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											115	114	114					2																	36805790		1863	4104	5967	36659294	SO:0001583	missense	9637			U60061	CCDS46257.1, CCDS46258.1	2p21	2008-05-15			ENSG00000171055	ENSG00000171055			3660	protein-coding gene	gene with protein product		604826				9096408	Standard	NM_005102		Approved		uc002rpg.2	Q9UHY8	OTTHUMG00000152148	ENST00000405912.3:c.853A>C	2.37:g.36805790T>G	ENSP00000385112:p.Asn285His		36659294	Q5EBN3|Q76LN0|Q99690	Missense_Mutation	SNP	ENST00000405912.3	37	CCDS46257.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.83|17.83	3.486633|3.486633	0.63962|0.63962	.|.	.|.	ENSG00000171055|ENSG00000171055	ENST00000441005|ENST00000379245;ENST00000305852;ENST00000405912;ENST00000357996	T|T;T;T;T	0.34472|0.30981	1.36|1.51;1.51;1.51;1.51	6.04|6.04	4.9|4.9	0.64082|0.64082	.|.	.|0.169341	.|0.64402	.|D	.|0.000005	T|T	0.40595|0.40595	0.1123|0.1123	L|L	0.43152|0.43152	1.355|1.355	0.32628|0.32628	N|N	0.522374|0.522374	.|P;P;P;P	.|0.50617	.|0.937;0.564;0.883;0.896	.|P;P;P;P	.|0.56398	.|0.628;0.797;0.632;0.776	T|T	0.54443|0.54443	-0.8293|-0.8293	7|10	0.72032|0.59425	D|D	0.01|0.04	-21.4915|-21.4915	11.3652|11.3652	0.49668|0.49668	0.0:0.0701:0.0:0.9299|0.0:0.0701:0.0:0.9299	.|.	.|285;285;285;114	.|G3V0F5;Q9UHY8;Q9UHY8-2;Q7Z674	.|.;FEZ2_HUMAN;.;.	T|H	86|285;114;285;184	ENSP00000415325:K86T|ENSP00000368547:N285H;ENSP00000305843:N114H;ENSP00000385112:N285H;ENSP00000350685:N184H	ENSP00000415325:K86T|ENSP00000305843:N114H	K|N	-|-	2|1	0|0	FEZ2|FEZ2	36659294|36659294	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.962000|0.962000	0.63368|0.63368	4.849000|4.849000	0.62882|0.62882	1.118000|1.118000	0.41863|0.41863	0.460000|0.460000	0.39030|0.39030	AAA|AAT		0.393	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1			G	36805790	T	G	36805790	3	3	61	1	0	0	0	0	1	0	0	0	5843	1841	64	4	309	4	FEZ2	2	36805790	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31509	36805790	206393583	1338	9323										
VIT	5212	broad.mit.edu	37	chr2	36970386	36970386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctactccagtgtgtgtggcGctgccgtacacaggtgagtg	14	11	0	1	rs202044807		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:36970386G>A	ENST00000389975.3	+	4	564	c.262G>A	c.(262-264)Gct>Act	p.A88T	VIT_ENST00000404084.1_Missense_Mutation_p.A66T|VIT_ENST00000497382.1_De_novo_Start_OutOfFrame|VIT_ENST00000457137.2_Missense_Mutation_p.A88T|VIT_ENST00000379242.3_Missense_Mutation_p.A88T|VIT_ENST00000401530.1_Missense_Mutation_p.A88T|VIT_ENST00000379241.3_Missense_Mutation_p.A88T	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	88	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)	p.A88T(2)		autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TGTGTGTGGCGCTGCCGTACA	0.493													G|||	1	0.000199681	0	0	5008	,	,		18355	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	104	90	94		262,262,262,262,262	4.8	0.1	2		94	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_001177972.1,NM_053276.3	58,58,58,58,58	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	88/679,88/658,88/657,88/204,88/694	36970386	3,13003	2203	4300	6503	36823890	SO:0001583	missense	5212			AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.262G>A	2.37:g.36970386G>A	ENSP00000374625:p.Ala88Thr		36823890	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189433	0.57909	0.0	3.49E-4	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81;-3.81;-3.81	4.78	4.78	0.61160	LCCL (5);	0.110901	0.64402	D	0.000009	D	0.97548	0.9197	M	0.80508	2.5	0.58432	D	0.999995	D;D;D;D;D;D	0.89917	1.0;0.998;0.996;0.998;0.998;1.0	D;D;P;D;P;D	0.74674	0.979;0.943;0.81;0.943;0.906;0.984	D	0.98344	1.0540	10	0.87932	D	0	-15.7685	16.3882	0.83523	0.0:0.0:1.0:0.0	.	88;88;88;88;88;88	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	T	88;88;88;88;66;88;88	ENSP00000368544:A88T;ENSP00000374625:A88T;ENSP00000393561:A88T;ENSP00000384154:A66T;ENSP00000368543:A88T;ENSP00000385658:A88T	ENSP00000368543:A88T	A	+	1	0	VIT	36823890	1.000000	0.71417	0.108000	0.21378	0.012000	0.07955	7.260000	0.78391	2.363000	0.80096	0.655000	0.94253	GCT		0.493	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				A	36970386	G	A	36970386	3	1	61	1	0	0	0	0	1	0	0	0	17211	1087	38	1	272	1	VIT	2	36970386	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164596	36970386	206228987	1339	9324										
VIT	5212	broad.mit.edu	37	chr2	37041341	37041341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggagtgatcacctatgCgataggcgttgcctgggctg	14	10	1	1	rs141772569		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37041341C>T	ENST00000389975.3	+	15	2176	c.1874C>T	c.(1873-1875)gCg>gTg	p.A625V	VIT_ENST00000404084.1_Missense_Mutation_p.A577V|VIT_ENST00000497382.1_Missense_Mutation_p.A294V|VIT_ENST00000379242.3_Missense_Mutation_p.A640V|VIT_ENST00000401530.1_Missense_Mutation_p.A604V|VIT_ENST00000379241.3_Missense_Mutation_p.A603V	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	625	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)	p.A640V(1)		autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				ATCACCTATGCGATAGGCGTT	0.517													C|||	1	0.000199681	8e-04	0	5008	,	,		19642	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	4,4402	9.9+/-24.2	0,4,2199	103	88	93		1874,1811,1808,1919	5.5	0.9	2	dbSNP_134	93	0,8600		0,0,4300	yes	missense,missense,missense,missense	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	64,64,64,64	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	625/679,604/658,603/657,640/694	37041341	4,13002	2203	4300	6503	36894845	SO:0001583	missense	5212			AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1874C>T	2.37:g.37041341C>T	ENSP00000374625:p.Ala625Val		36894845	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	33	5.247811	0.95305	9.08E-4	0.0	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95;-1.95	5.52	5.52	0.82312	von Willebrand factor, type A (3);	0.346379	0.34200	N	0.004177	D	0.90184	0.6932	M	0.71871	2.18	0.58432	D	0.999996	D;D;D;D	0.60160	0.987;0.984;0.987;0.984	P;P;P;P	0.57679	0.825;0.732;0.825;0.732	D	0.87853	0.2659	10	0.27082	T	0.32	-16.8856	19.4602	0.94914	0.0:1.0:0.0:0.0	.	604;603;625;640	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	V	640;625;294;577;603;604	ENSP00000368544:A640V;ENSP00000374625:A625V;ENSP00000417874:A294V;ENSP00000384154:A577V;ENSP00000368543:A603V;ENSP00000385658:A604V	ENSP00000368543:A603V	A	+	2	0	VIT	36894845	1.000000	0.71417	0.931000	0.37212	0.730000	0.41778	7.786000	0.85741	2.590000	0.87494	0.655000	0.94253	GCG		0.517	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				T	37041341	C	T	37041341	3	4	61	1	0	0	0	0	1	0	0	0	17211	768	27	1	2102	1	VIT	2	37041341	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70955	37041341	206158032	1340	9325										
VIT	5212	broad.mit.edu	37	chr2	37041403	37041403	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccactcaccccgccagaGaccactccttctttgtggac	7	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37041403G>T	ENST00000389975.3	+	15	2238	c.1936G>T	c.(1936-1938)Gac>Tac	p.D646Y	VIT_ENST00000404084.1_Missense_Mutation_p.D598Y|VIT_ENST00000497382.1_Missense_Mutation_p.D315Y|VIT_ENST00000379242.3_Missense_Mutation_p.D661Y|VIT_ENST00000401530.1_Missense_Mutation_p.D625Y|VIT_ENST00000379241.3_Missense_Mutation_p.D624Y	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	646	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)	p.D661Y(1)		autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				CCCCGCCAGAGACCACTCCTT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	109	116					2																	37041403		2203	4300	6503	36894907	SO:0001583	missense	5212			AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1936G>T	2.37:g.37041403G>T	ENSP00000374625:p.Asp646Tyr		36894907	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453727	0.84209	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.52	5.52	0.82312	von Willebrand factor, type A (3);	0.147481	0.64402	D	0.000011	D	0.91085	0.7194	M	0.82716	2.605	0.50813	D	0.999895	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.74348	0.983;0.982;0.983;0.983	D	0.92064	0.5659	10	0.87932	D	0	-28.1577	14.3161	0.66452	0.0:0.0:0.8517:0.1483	.	625;624;646;661	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	Y	661;646;315;598;624;625	ENSP00000368544:D661Y;ENSP00000374625:D646Y;ENSP00000417874:D315Y;ENSP00000384154:D598Y;ENSP00000368543:D624Y;ENSP00000385658:D625Y	ENSP00000368543:D624Y	D	+	1	0	VIT	36894907	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	4.764000	0.62264	2.590000	0.87494	0.655000	0.94253	GAC		0.522	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				T	37041403	G	T	37041403	3	4	61	1	0	0	0	0	1	0	0	0	17211	942	33	2	2164	2	VIT	2	37041403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	37041403	206157970	1341	9326										
HEATR5B	54497	broad.mit.edu	37	chr2	37208731	37208731	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgctcgcttggcttgctcGaacggcagtttctagacgca	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37208731G>A	ENST00000233099.5	-	36	6213	c.6118C>T	c.(6118-6120)Cga>Tga	p.R2040*	HEATR5B_ENST00000354531.2_Nonsense_Mutation_p.R1951*	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	2040						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.R2040*(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TGGCTTGCTCGAACGGCAGTT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											70	74	72					2																	37208731		2203	4300	6503	37062235	SO:0001587	stop_gained	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.6118C>T	2.37:g.37208731G>A	ENSP00000233099:p.Arg2040*		37062235	B5MDU8|Q7Z3B2|Q9NVL7	Nonsense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	46	12.271283	0.99652	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	.	.	.	5.61	2.61	0.31194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.46167	D	0.998903	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3798	14.9817	0.71316	0.0:0.0:0.5486:0.4514	.	.	.	.	X	2040;1951	.	ENSP00000233099:R2040X	R	-	1	2	HEATR5B	37062235	0.984000	0.35163	1.000000	0.80357	0.899000	0.52679	1.497000	0.35649	0.814000	0.34374	0.655000	0.94253	CGA		0.453	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37208731	G	A	37208731	4	1	61	1	0	0	0	0	0	1	0	0	7053	1066	37	1	101	1	HEATR5B	2	37208731	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167328	37208731	205990642	1342	9327										
HEATR5B	54497	broad.mit.edu	37	chr2	37268422	37268422	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcctagatacaacatctcGagccgatttcaacctgaaaa	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37268422G>A	ENST00000233099.5	-	19	2805	c.2710C>T	c.(2710-2712)Cga>Tga	p.R904*	HEATR5B_ENST00000354531.2_Nonsense_Mutation_p.R904*	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	904						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.R904*(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ACAACATCTCGAGCCGATTTC	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											123	110	115					2																	37268422		2203	4300	6503	37121926	SO:0001587	stop_gained	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2710C>T	2.37:g.37268422G>A	ENSP00000233099:p.Arg904*		37121926	B5MDU8|Q7Z3B2|Q9NVL7	Nonsense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	41	8.696621	0.98918	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.7461	15.0449	0.71819	0.0:0.0:0.8573:0.1427	.	.	.	.	X	904	.	ENSP00000233099:R904X	R	-	1	2	HEATR5B	37121926	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.658000	0.74407	2.569000	0.86673	0.655000	0.94253	CGA		0.388	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37268422	G	A	37268422	4	1	61	1	0	0	0	0	0	1	0	0	7053	1066	37	1	3577	1	HEATR5B	2	37268422	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59691	37268422	205930951	1343	9328										
SULT6B1	391365	broad.mit.edu	37	chr2	37406711	37406712	+	Nonsense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgtatctttagggtttCgaaatatcaccaatatctag					rs11569744|rs147099571	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37406711_37406712CG>TA	ENST00000535679.1	-	4	417_418	c.418_419CG>TA	c.(418-420)CGa>TAa	p.R140*	SULT6B1_ENST00000407963.1_Nonsense_Mutation_p.R102*|SULT6B1_ENST00000260637.3_Nonsense_Mutation_p.R102*|SULT6B1_ENST00000379149.2_Intron			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	140						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)	p.R102>?(1)|p.R102Q(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				TTTAGGGTTTCGAAATATCACC	0.361																																																2	Substitution - Missense(1)|Complex(1)	large_intestine(1)|lung(1)	2																																								37260216	SO:0001587	stop_gained	391365			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"Sulfotransferases, cytosolic"	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.418_419delinsTA	2.37:g.37406711_37406712delinsTA	ENSP00000444081:p.Arg140*		37260215	B2RTS7	Nonsense_Mutation	DNP	ENST00000535679.1	37																																																																																					0.361	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		TA	37406712	CG	TA	37406711	4	4	61	1	0	0	0	0	0	1	0	0	15423	884	31	1	508	1	SULT6B1	2	37406711	Nonsense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	138289	37406711	205792662	1344	9329										
CEBPZ	10153	broad.mit.edu	37	chr2	37447545	37447545	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctttttgagttcccaaaGacttgtattttcagctccac	5	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37447545G>T	ENST00000234170.5	-	5	2282	c.2137C>A	c.(2137-2139)Ctt>Att	p.L713I		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	713					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L713I(1)		breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				AGTTCCCAAAGACTTGTATTT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	2											44	45	45					2																	37447545		2203	4300	6503	37301049	SO:0001583	missense	10153			M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2137C>A	2.37:g.37447545G>T	ENSP00000234170:p.Leu713Ile		37301049	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.358849	0.41801	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.29917	1.55	5.6	3.69	0.42338	Armadillo-type fold (1);CCAAT-binding factor (1);	0.060912	0.64402	D	0.000003	T	0.44265	0.1285	M	0.88570	2.965	0.44247	D	0.997095	P	0.42556	0.783	P	0.44518	0.452	T	0.48456	-0.9034	10	0.87932	D	0	.	9.5356	0.39220	0.2393:0.0:0.7607:0.0	.	713	Q03701	CEBPZ_HUMAN	I	713	ENSP00000234170:L713I	ENSP00000234170:L713I	L	-	1	0	CEBPZ	37301049	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.794000	0.47853	0.632000	0.30432	0.650000	0.86243	CTT		0.274	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		T	37447545	G	T	37447545	3	4	61	1	0	0	0	0	1	0	0	0	3210	942	33	2	1075	2	CEBPZ	2	37447545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40834	37447545	205751828	1345	9330										
PRKD3	23683	broad.mit.edu	37	chr2	37518061	37518061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagagcatctcaccacagTaatcacagaaagtaggagct	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37518061T>C	ENST00000379066.1	-	4	1271	c.509A>G	c.(508-510)tAc>tGc	p.Y170C	PRKD3_ENST00000234179.2_Missense_Mutation_p.Y170C			O94806	KPCD3_HUMAN	protein kinase D3	170					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)	p.Y170C(2)		breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CTCACCACAGTAATCACAGAA	0.373																																					Melanoma(80;621 1355 8613 11814 51767)											2	Substitution - Missense(2)	large_intestine(2)	2											157	152	154					2																	37518061		2203	4300	6503	37371565	SO:0001583	missense	23683			AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.509A>G	2.37:g.37518061T>C	ENSP00000368356:p.Tyr170Cys		37371565	D6W587|Q53TR7|Q8NEL8	Missense_Mutation	SNP	ENST00000379066.1	37	CCDS1789.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.015057	0.75161	.	.	ENSG00000115825	ENST00000379066;ENST00000234179;ENST00000443187	D;D;D	0.93189	-3.18;-3.18;-3.18	4.84	4.84	0.62591	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.070514	0.64402	D	0.000016	D	0.95262	0.8463	L	0.60012	1.86	0.58432	D	0.999993	D;D	0.67145	0.995;0.996	D;D	0.64687	0.917;0.928	D	0.95629	0.8688	10	0.66056	D	0.02	-20.0606	14.7407	0.69451	0.0:0.0:0.0:1.0	.	170;170	O94806-2;O94806	.;KPCD3_HUMAN	C	170;170;66	ENSP00000368356:Y170C;ENSP00000234179:Y170C;ENSP00000401839:Y66C	ENSP00000234179:Y170C	Y	-	2	0	PRKD3	37371565	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.997000	0.88414	1.932000	0.55993	0.533000	0.62120	TAC		0.373	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		C	37518061	T	C	37518061	3	2	61	1	0	0	0	0	1	0	0	0	12554	1638	57	4	2227	4	PRKD3	2	37518061	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	70516	37518061	205681312	1346	9331										
QPCT	25797	broad.mit.edu	37	chr2	37596913	37596913	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagccaggtggttcgaaaGacttcaagcaattggtaagc	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:37596913G>T	ENST00000338415.3	+	5	967	c.809G>T	c.(808-810)aGa>aTa	p.R270I	QPCT_ENST00000537448.1_Missense_Mutation_p.R221I	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	270					cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.R270I(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				TGGTTCGAAAGACTTCAAGCA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	92	92					2																	37596913		2203	4300	6503	37450417	SO:0001583	missense	25797			X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"glutaminyl cyclase"	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.809G>T	2.37:g.37596913G>T	ENSP00000344829:p.Arg270Ile		37450417	Q16770|Q3KRG6|Q53TR4	Missense_Mutation	SNP	ENST00000338415.3	37	CCDS1790.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.217626	0.58560	.	.	ENSG00000115828	ENST00000338415;ENST00000404976;ENST00000537448;ENST00000444022	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.24	5.24	0.73138	Peptidase M28 (1);	0.118119	0.64402	D	0.000009	T	0.54208	0.1844	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	T	0.62647	-0.6810	10	0.72032	D	0.01	-23.8759	18.8415	0.92186	0.0:0.0:1.0:0.0	.	221;270	Q16769-2;Q16769	.;QPCT_HUMAN	I	270;221;221;35	ENSP00000344829:R270I;ENSP00000385391:R221I;ENSP00000441606:R221I;ENSP00000389227:R35I	ENSP00000344829:R270I	R	+	2	0	QPCT	37450417	1.000000	0.71417	0.951000	0.38953	0.029000	0.11900	8.679000	0.91220	2.442000	0.82660	0.591000	0.81541	AGA		0.338	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2			T	37596913	G	T	37596913	3	4	61	1	0	0	0	0	1	0	0	0	12911	942	33	2	827	2	QPCT	2	37596913	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78852	37596913	205602460	1347	9332										
FAM82A1	151393	broad.mit.edu	37	chr2	38216720	38216720	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctatgtatctgagtttgaGggtttacaaaacaaaatcaa	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:38216720G>T	ENST00000406384.1	+	6	1022	c.828G>T	c.(826-828)gaG>gaT	p.E276D	RMDN2_ENST00000417700.2_Missense_Mutation_p.E131D|RMDN2_ENST00000407257.1_Missense_Mutation_p.E454D|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000234195.3_Missense_Mutation_p.E454D|RMDN2_ENST00000354545.2_Missense_Mutation_p.E276D	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2	276						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)		p.E454D(1)									CTGAGTTTGAGGGTTTACAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											179	161	167					2																	38216720		2203	4300	6503	38070224	SO:0001583	missense	151393			AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"family with sequence similarity 82, member A1"	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.828G>T	2.37:g.38216720G>T	ENSP00000386004:p.Glu276Asp		38070224	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Missense_Mutation	SNP	ENST00000406384.1	37	CCDS54351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.37|13.37	2.217960|2.217960	0.39201|0.39201	.|.	.|.	ENSG00000115841|ENSG00000115841	ENST00000354545;ENST00000406384;ENST00000407257;ENST00000417700;ENST00000234195;ENST00000442857|ENST00000425641	T;T;T;T;T;T|.	0.54675|.	0.56;0.56;0.56;0.56;0.56;0.56|.	5.8|5.8	2.05|2.05	0.26809|0.26809	.|.	0.190168|.	0.45126|.	D|.	0.000381|.	T|T	0.46328|0.46328	0.1387|0.1387	L|L	0.55103|0.55103	1.725|1.725	0.30259|0.30259	N|N	0.793356|0.793356	B;B;B;B|.	0.28584|.	0.216;0.062;0.032;0.062|.	B;B;B;B|.	0.36845|.	0.234;0.093;0.031;0.093|.	T|T	0.45963|0.45963	-0.9225|-0.9225	10|5	0.49607|.	T|.	0.09|.	-10.3783|-10.3783	7.1915|7.1915	0.25828|0.25828	0.4177:0.0:0.5823:0.0|0.4177:0.0:0.5823:0.0	.|.	454;131;276;131|.	Q96LZ7-2;Q96LZ7-4;Q96LZ7;Q96LZ7-3|.	.;.;RMD2_HUMAN;.|.	D|W	276;276;454;131;454;131|11	ENSP00000346549:E276D;ENSP00000386004:E276D;ENSP00000385049:E454D;ENSP00000392977:E131D;ENSP00000234195:E454D;ENSP00000416367:E131D|.	ENSP00000234195:E454D|.	E|G	+|+	3|1	2|0	FAM82A1|FAM82A1	38070224|38070224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	0.377000|0.377000	0.20552|0.20552	0.388000|0.388000	0.25054|0.25054	0.650000|0.650000	0.86243|0.86243	GAG|GGG		0.338	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713		T	38216720	G	T	38216720	3	4	61	1	0	0	0	0	1	0	0	0	5649	991	35	2	1840	2	FAM82A1	2	38216720	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	619807	38216720	204982653	1348	9333										
FAM82A1	151393	broad.mit.edu	37	chr2	38224620	38224620	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtttggaaaaataccatCttcaactgtacaagaagctt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:38224620C>A	ENST00000406384.1	+	8	1201	c.1007C>A	c.(1006-1008)tCt>tAt	p.S336Y	RMDN2_ENST00000417700.2_Missense_Mutation_p.S191Y|RMDN2_ENST00000407257.1_Missense_Mutation_p.S514Y|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000234195.3_Missense_Mutation_p.S514Y|RMDN2_ENST00000354545.2_Missense_Mutation_p.S336Y	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2	336						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)		p.S514Y(1)									AAAATACCATCTTCAACTGTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	130	130					2																	38224620		2203	4300	6503	38078124	SO:0001583	missense	151393			AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"family with sequence similarity 82, member A1"	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.1007C>A	2.37:g.38224620C>A	ENSP00000386004:p.Ser336Tyr		38078124	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Missense_Mutation	SNP	ENST00000406384.1	37	CCDS54351.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243517	0.39697	.	.	ENSG00000115841	ENST00000354545;ENST00000406384;ENST00000407257;ENST00000417700;ENST00000234195;ENST00000442857	T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69	5.82	4.93	0.64822	Tetratricopeptide-like helical (1);	0.329374	0.30695	N	0.009076	T	0.53481	0.1799	M	0.76170	2.325	0.31708	N	0.639825	P;B;B;B	0.37423	0.594;0.016;0.016;0.009	B;B;B;B	0.40565	0.333;0.014;0.014;0.014	T	0.66976	-0.5787	10	0.72032	D	0.01	-7.744	14.2835	0.66228	0.1493:0.8507:0.0:0.0	.	514;191;336;191	Q96LZ7-2;Q96LZ7-4;Q96LZ7;Q96LZ7-3	.;.;RMD2_HUMAN;.	Y	336;336;514;191;514;191	ENSP00000346549:S336Y;ENSP00000386004:S336Y;ENSP00000385049:S514Y;ENSP00000392977:S191Y;ENSP00000234195:S514Y;ENSP00000416367:S191Y	ENSP00000234195:S514Y	S	+	2	0	FAM82A1	38078124	1.000000	0.71417	0.910000	0.35882	0.853000	0.48598	2.667000	0.46808	1.437000	0.47472	0.655000	0.94253	TCT		0.373	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713		A	38224620	C	A	38224620	3	1	61	1	0	0	0	0	1	0	0	0	5649	913	32	2	2027	2	FAM82A1	2	38224620	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7900	38224620	204974753	1349	9334										
CYP1B1	1545	broad.mit.edu	37	chr2	38298077	38298077	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgcatcttagaaagttCttcgccaatgcaccgccttt	7	12	2	1	rs72549374		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:38298077C>A	ENST00000260630.3	-	3	1821	c.1420G>T	c.(1420-1422)Gaa>Taa	p.E474*	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Nonsense_Mutation_p.E474*	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	474					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.E474*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	TTAGAAAGTTCTTCGCCAATG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											74	74	74					2																	38298077		2203	4300	6503	38151581	SO:0001587	stop_gained	1545			U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"Cytochrome P450s"	2597	protein-coding gene	gene with protein product		601771	"cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1420G>T	2.37:g.38298077C>A	ENSP00000260630:p.Glu474*		38151581	Q5TZW8|Q93089|Q9H316	Nonsense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	.	.	.	.	.	.	.	.	.	.	C	37	6.167172	0.97343	.	.	ENSG00000138061	ENST00000260630;ENST00000407341	.	.	.	5.95	5.08	0.68730	.	0.046997	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	13.1458	0.59461	0.0:0.9229:0.0:0.0771	.	.	.	.	X	474	.	ENSP00000260630:E474X	E	-	1	0	CYP1B1	38151581	0.991000	0.36638	0.528000	0.27938	0.172000	0.22775	2.300000	0.43620	1.526000	0.49068	0.655000	0.94253	GAA		0.473	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		A	38298077	C	A	38298077	4	1	61	1	0	0	0	0	0	1	0	0	4157	922	32	2	215	2	CYP1B1	2	38298077	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73457	38298077	204901296	1350	9335										
ATL2	64225	broad.mit.edu	37	chr2	38540386	38540386	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaatcaaaaacattaatgtCtatacacagaaaaaataaaa	3	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:38540386C>T	ENST00000378954.4	-	7	713		c.e7-1		ATL2_ENST00000332337.4_Splice_Site|ATL2_ENST00000539122.1_Splice_Site|ATL2_ENST00000406122.1_Splice_Site|ATL2_ENST00000452935.2_Splice_Site|ATL2_ENST00000402054.1_Splice_Site|ATL2_ENST00000419554.2_Splice_Site|ATL2_ENST00000546051.1_Splice_Site	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2						endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.?(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						ACATTAATGTCTATACACAGA	0.294																																																1	Unknown(1)	large_intestine(1)	2											61	56	58					2																	38540386		2202	4300	6502	38393890	SO:0001630	splice_region_variant	64225				CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"ADP-ribosylation factor-like 6 interacting protein 2"	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.712-1G>A	2.37:g.38540386C>T			38393890	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Splice_Site	SNP	ENST00000378954.4	37	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511039	0.85389	.	.	ENSG00000119787	ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130;ENST00000443098	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9865	0.92773	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATL2	38393890	1.000000	0.71417	0.996000	0.52242	0.882000	0.50991	7.666000	0.83877	2.724000	0.93272	0.561000	0.74099	.		0.294	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	Intron	T	38540386	C	T	38540386	5	4	61	1	0	0	0	0	0	0	1	0	1108	927	32	3	1180	3	ATL2	2	38540386	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	242309	38540386	204658987	1351	9336										
SFRS7	6432	broad.mit.edu	37	chr2	38976794	38976794	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtctatcaaaacgtgatCtccgaggcatgcctgtcgat	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:38976794C>T	ENST00000313117.6	-	3	500	c.263G>A	c.(262-264)aGa>aAa	p.R88K	SRSF7_ENST00000446327.2_Missense_Mutation_p.R88K|SRSF7_ENST00000409276.1_Missense_Mutation_p.R88K|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	88	Sufficiernt for interaction with NXF1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R88K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						AAAACGTGATCTCCGAGGCAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	96	99					2																	38976794		2203	4300	6503	38830298	SO:0001583	missense	6432			L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"Zinc fingers, CCHC domain containing", "Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10789	protein-coding gene	gene with protein product	"SR splicing factor 7"	600572	"splicing factor, arginine/serine-rich 7 (35kD)", "splicing factor, arginine/serine-rich 7, 35kDa"	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.263G>A	2.37:g.38976794C>T	ENSP00000325905:p.Arg88Lys		38830298	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	37	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.495210	0.44352	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	T;T;T	0.74842	-0.88;-0.88;-0.88	5.93	5.93	0.95920	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.64402	D	0.000001	T	0.61862	0.2381	N	0.20685	0.6	0.43417	D	0.995569	B;B	0.31680	0.335;0.138	B;B	0.30943	0.122;0.057	T	0.58640	-0.7601	10	0.10902	T	0.67	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	88;88	G5E9M3;Q16629	.;SRSF7_HUMAN	K	88	ENSP00000325905:R88K;ENSP00000402264:R88K;ENSP00000386806:R88K	ENSP00000325905:R88K	R	-	2	0	SRSF7	38830298	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.661000	0.54503	2.805000	0.96524	0.655000	0.94253	AGA		0.413	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		T	38976794	C	T	38976794	3	4	61	1	0	0	0	0	1	0	0	0	14219	913	32	3	477	3	SFRS7	2	38976794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	436408	38976794	204222579	1352	9337										
DHX57	90957	broad.mit.edu	37	chr2	39025560	39025560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgatcaagttcgcaacGaagctcctttaccagttcag	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39025560G>A	ENST00000295373.6	-	24	4168	c.4042C>T	c.(4042-4044)Cgt>Tgt	p.R1348C		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1348							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1348C(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				AGTTCGCAACGAAGCTCCTTT	0.438																																					Melanoma(191;1090 2095 4375 23729 47341)											1	Substitution - Missense(1)	large_intestine(1)	2											107	97	101					2																	39025560		2203	4300	6503	38879064	SO:0001583	missense	90957			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.4042C>T	2.37:g.39025560G>A	ENSP00000295373:p.Arg1348Cys		38879064	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.4|23.4	4.407876|4.407876	0.83340|0.83340	.|.	.|.	ENSG00000163214|ENSG00000163214	ENST00000295373|ENST00000452978	T|.	0.09538|.	2.97|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.52532|.	D|.	0.000066|.	D|D	0.86226|0.86226	0.5882|0.5882	M|M	0.91818|0.91818	3.245|3.245	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	D|D	0.88655|0.88655	0.3185|0.3185	10|5	0.87932|.	D|.	0|.	.|.	19.192|19.192	0.93671|0.93671	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1348;695|.	Q6P158;Q59G60|.	DHX57_HUMAN;.|.	C|L	1348|626	ENSP00000295373:R1348C|.	ENSP00000295373:R1348C|.	R|S	-|-	1|2	0|0	DHX57|DHX57	38879064|38879064	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.827000|0.827000	0.46813|0.46813	7.403000|7.403000	0.79983|0.79983	2.716000|2.716000	0.92895|0.92895	0.650000|0.650000	0.86243|0.86243	CGT|TCG		0.438	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		A	39025560	G	A	39025560	3	1	61	1	0	0	0	0	1	0	0	0	4524	1058	37	1	122	1	DHX57	2	39025560	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48766	39025560	204173813	1353	9338										
DHX57	90957	broad.mit.edu	37	chr2	39033813	39033813	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagtactggtcttctgaAattttccttctgggcttttc	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39033813A>C	ENST00000295373.6	-	22	3830	c.3704T>G	c.(3703-3705)tTt>tGt	p.F1235C		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1235							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F1235C(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GGTCTTCTGAAATTTTCCTTC	0.358																																					Melanoma(191;1090 2095 4375 23729 47341)											1	Substitution - Missense(1)	large_intestine(1)	2											123	113	117					2																	39033813		2203	4300	6503	38887317	SO:0001583	missense	90957			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3704T>G	2.37:g.39033813A>C	ENSP00000295373:p.Phe1235Cys		38887317	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.424673	0.62733	.	.	ENSG00000163214	ENST00000295373	T	0.02974	4.09	5.37	2.74	0.32292	Domain of unknown function DUF1605 (1);	0.112412	0.40385	N	0.001113	T	0.11324	0.0276	M	0.79926	2.475	0.41589	D	0.988783	D	0.71674	0.998	D	0.63113	0.911	T	0.00603	-1.1649	10	0.62326	D	0.03	.	8.98	0.35959	0.7144:0.0:0.0:0.2856	.	1235	Q6P158	DHX57_HUMAN	C	1235	ENSP00000295373:F1235C	ENSP00000295373:F1235C	F	-	2	0	DHX57	38887317	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	3.098000	0.50259	2.042000	0.60477	0.379000	0.24179	TTT		0.358	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39033813	A	C	39033813	3	2	61	1	0	0	0	0	1	0	0	0	4524	14	1	4	468	4	DHX57	2	39033813	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8253	39033813	204165560	1354	9339										
DHX57	90957	broad.mit.edu	37	chr2	39088341	39088341	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatatacgacaggttccGaagtttccgcaaatgtcaag	9	8	1	1	rs369485938		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39088341G>A	ENST00000295373.6	-	5	1337	c.1211C>T	c.(1210-1212)tCg>tTg	p.S404L	DHX57_ENST00000479345.2_5'UTR|AC018693.6_ENST00000442829.1_RNA	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	404							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S404L(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GACAGGTTCCGAAGTTTCCGC	0.418																																					Melanoma(191;1090 2095 4375 23729 47341)											1	Substitution - Missense(1)	large_intestine(1)	2						G	LEU/SER	0,4406		0,0,2203	87	89	88		1211	5.7	1	2		88	1,8599	1.2+/-3.3	0,1,4299	no	missense	DHX57	NM_198963.1	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	404/1387	39088341	1,13005	2203	4300	6503	38941845	SO:0001583	missense	90957			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.1211C>T	2.37:g.39088341G>A	ENSP00000295373:p.Ser404Leu		38941845	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939968	0.52972	0.0	1.16E-4	ENSG00000163214	ENST00000295373;ENST00000355320	T	0.24151	1.87	5.67	5.67	0.87782	Ubiquitin-conjugating enzyme/RWD-like (1);RWD domain (1);	0.689880	0.12600	N	0.454833	T	0.25158	0.0611	L	0.40543	1.245	0.28468	N	0.91555	P;B	0.49185	0.92;0.433	B;B	0.43445	0.42;0.195	T	0.16958	-1.0385	10	0.87932	D	0	.	9.8217	0.40887	0.0:0.1246:0.6848:0.1907	.	404;404	Q6P158-2;Q6P158	.;DHX57_HUMAN	L	404;302	ENSP00000295373:S404L	ENSP00000295373:S404L	S	-	2	0	DHX57	38941845	0.015000	0.18098	0.982000	0.44146	0.810000	0.45777	1.551000	0.36233	2.677000	0.91161	0.655000	0.94253	TCG		0.418	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		A	39088341	G	A	39088341	3	1	61	1	0	0	0	0	1	0	0	0	4524	1059	37	1	3029	1	DHX57	2	39088341	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54528	39088341	204111032	1355	9340										
SOS1	6654	broad.mit.edu	37	chr2	39213270	39213270	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccaaagggggaggttggaGatgtagtggtgagcttgaga	19	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39213270G>T	ENST00000426016.1	-	24	3783	c.3697C>A	c.(3697-3699)Ctc>Atc	p.L1233I	SOS1_ENST00000395038.2_Missense_Mutation_p.L1218I|SOS1_ENST00000402219.2_Missense_Mutation_p.L1233I			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1233					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1233I(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				GGAGGTTGGAGATGTAGTGGT	0.522									Noonan syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	2											143	149	147					2																	39213270		2203	4300	6503	39066774	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3697C>A	2.37:g.39213270G>T	ENSP00000387784:p.Leu1233Ile		39066774	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220519	0.79464	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038	T;T;T	0.78126	-1.05;-1.05;-1.15	5.8	5.8	0.92144	.	0.134989	0.50627	D	0.000109	D	0.85531	0.5718	L	0.52573	1.65	0.80722	D	1	D	0.63880	0.993	D	0.67548	0.952	D	0.84701	0.0728	10	0.51188	T	0.08	.	20.0586	0.97663	0.0:0.0:1.0:0.0	.	1233	Q07889	SOS1_HUMAN	I	1233;1233;950;1218	ENSP00000387784:L1233I;ENSP00000384675:L1233I;ENSP00000378479:L1218I	ENSP00000378479:L1218I	L	-	1	0	SOS1	39066774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.610000	0.90902	2.741000	0.93983	0.650000	0.86243	CTC		0.522	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39213270	G	T	39213270	3	4	61	1	0	0	0	0	1	0	0	0	14973	942	33	2	308	2	SOS1	2	39213270	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	124929	39213270	203986103	1356	9341										
MAP4K3	8491	broad.mit.edu	37	chr2	39552677	39552677	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcaggatcatcatcatcGaaatcatggtaagtggaatg	9	8	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39552677G>A	ENST00000263881.3	-	12	1224	c.900C>T	c.(898-900)ttC>ttT	p.F300F	MAP4K3_ENST00000536018.1_5'UTR|MAP4K3_ENST00000437545.1_Silent_p.F237F|MAP4K3_ENST00000341681.5_Silent_p.F300F|RP11-449G16.1_ENST00000609671.1_RNA	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	300					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.F300F(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CATCATCATCGAAATCATGGT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											102	98	99					2																	39552677		2203	4300	6503	39406181	SO:0001819	synonymous_variant	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.900C>T	2.37:g.39552677G>A			39406181	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	37	CCDS1803.1																																																																																				0.358	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		A	39552677	G	A	39552677	2	1	61	1	0	0	0	0	0	0	0	1	9291	1049	37	1		1	MAP4K3	2	39552677	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	339407	39552677	203646696	1357	9342										
TMEM178	130733	broad.mit.edu	37	chr2	39931316	39931316	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccaagaccatacagcaaGatgagtggcacctgcttcgt	9	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39931316G>T	ENST00000281961.2	+	2	552	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	TMEM178A_ENST00000482239.1_3'UTR	NM_152390.2	NP_689603.2	Q8NBL3	T178A_HUMAN	transmembrane protein 178A	166						integral component of membrane (GO:0016021)		p.D166Y(1)									CATACAGCAAGATGAGTGGCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	80	83					2																	39931316		2203	4300	6503	39784820	SO:0001583	missense	130733			BC029530	CCDS1804.1	2p22.1	2012-06-29	2012-06-29	2012-06-29	ENSG00000152154	ENSG00000152154			28517	protein-coding gene	gene with protein product			"transmembrane protein 178"	TMEM178		12975309	Standard	NM_001167959		Approved	MGC33926	uc002rrt.3	Q8NBL3	OTTHUMG00000128591	ENST00000281961.2:c.496G>T	2.37:g.39931316G>T	ENSP00000281961:p.Asp166Tyr		39784820	Q6UWI6|Q8N6N4	Missense_Mutation	SNP	ENST00000281961.2	37	CCDS1804.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358265	0.82243	.	.	ENSG00000152154	ENST00000281961	T	0.55413	0.52	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.72028	0.3410	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71328	-0.4626	9	.	.	.	-8.5976	17.2112	0.86930	0.0:0.0:1.0:0.0	.	166	Q8NBL3	TM178_HUMAN	Y	166	ENSP00000281961:D166Y	.	D	+	1	0	TMEM178	39784820	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.431000	0.90285	2.653000	0.90120	0.655000	0.94253	GAT		0.473	TMEM178A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250445.2	NM_152390		T	39931316	G	T	39931316	3	4	61	1	0	0	0	0	1	0	0	0	16134	942	33	2	502	2	TMEM178	2	39931316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	378639	39931316	203268057	1358	9343										
TMEM178	130733	broad.mit.edu	37	chr2	39944352	39944352	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtttattagccggaccaaGattgcacagctaaagtctgg	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39944352G>T	ENST00000281961.2	+	4	911	c.855G>T	c.(853-855)aaG>aaT	p.K285N	TMEM178A_ENST00000482239.1_3'UTR	NM_152390.2	NP_689603.2	Q8NBL3	T178A_HUMAN	transmembrane protein 178A	285						integral component of membrane (GO:0016021)		p.K285N(1)									GCCGGACCAAGATTGCACAGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	126	130					2																	39944352		2203	4300	6503	39797856	SO:0001583	missense	130733			BC029530	CCDS1804.1	2p22.1	2012-06-29	2012-06-29	2012-06-29	ENSG00000152154	ENSG00000152154			28517	protein-coding gene	gene with protein product			"transmembrane protein 178"	TMEM178		12975309	Standard	NM_001167959		Approved	MGC33926	uc002rrt.3	Q8NBL3	OTTHUMG00000128591	ENST00000281961.2:c.855G>T	2.37:g.39944352G>T	ENSP00000281961:p.Lys285Asn		39797856	Q6UWI6|Q8N6N4	Missense_Mutation	SNP	ENST00000281961.2	37	CCDS1804.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653964	0.47362	.	.	ENSG00000152154	ENST00000281961	T	0.50548	0.74	5.91	5.91	0.95273	.	0.258350	0.38897	N	0.001538	T	0.28234	0.0697	N	0.08118	0	0.48452	D	0.999652	P	0.38978	0.652	B	0.33960	0.173	T	0.11179	-1.0598	9	.	.	.	-10.0119	17.7923	0.88558	0.0:0.0:1.0:0.0	.	285	Q8NBL3	TM178_HUMAN	N	285	ENSP00000281961:K285N	.	K	+	3	2	TMEM178	39797856	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	3.830000	0.55768	2.793000	0.96121	0.655000	0.94253	AAG		0.542	TMEM178A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250445.2	NM_152390		T	39944352	G	T	39944352	3	4	61	1	0	0	0	0	1	0	0	0	16134	933	33	2	869	2	TMEM178	2	39944352	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13036	39944352	203255021	1359	9344										
THUMPD2	80745	broad.mit.edu	37	chr2	39997145	39997145	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggttatcatctctctgaGaaagtttttccttttttgca	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:39997145G>T	ENST00000505747.1	-	3	404	c.377C>A	c.(376-378)tCt>tAt	p.S126Y	THUMPD2_ENST00000454352.2_Missense_Mutation_p.S96Y|THUMPD2_ENST00000403537.3_5'UTR|THUMPD2_ENST00000260619.6_Missense_Mutation_p.S96Y	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	126							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.S96Y(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				ATCTCTCTGAGAAAGTTTTTC	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	55	55					2																	39997145		2201	4294	6495	39850649	SO:0001583	missense	80745			AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.377C>A	2.37:g.39997145G>T	ENSP00000423933:p.Ser126Tyr		39850649	A8K7I7|Q53TT8|Q53TV0	Missense_Mutation	SNP	ENST00000505747.1	37	CCDS1805.2	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282823	0.40394	.	.	ENSG00000138050	ENST00000505747;ENST00000260619;ENST00000454352	.	.	.	5.71	4.84	0.62591	.	0.611001	0.17676	N	0.165800	T	0.51856	0.1699	L	0.59436	1.845	0.27207	N	0.960028	P;D;D	0.61080	0.923;0.989;0.981	P;P;P	0.55667	0.657;0.781;0.781	T	0.46925	-0.9156	8	.	.	.	.	10.833	0.46671	0.0866:0.0:0.9134:0.0	.	96;33;126	E7EUG5;B4DP37;Q9BTF0	.;.;THUM2_HUMAN	Y	126;96;96	.	.	S	-	2	0	THUMPD2	39850649	0.938000	0.31826	0.630000	0.29268	0.165000	0.22458	2.615000	0.46368	1.409000	0.46915	0.650000	0.86243	TCT		0.303	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264		T	39997145	G	T	39997145	3	4	61	1	0	0	0	0	1	0	0	0	15922	942	33	2	1166	2	THUMPD2	2	39997145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52793	39997145	203202228	1360	9345										
SLC8A1	6546	broad.mit.edu	37	chr2	40656512	40656512	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaccagagcaccatctaaGaaattttcaacatgagaatt	6	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:40656512G>T	ENST00000403092.1	-	2	942	c.909C>A	c.(907-909)ttC>ttA	p.F303L	SLC8A1_ENST00000542024.1_Missense_Mutation_p.F303L|SLC8A1_ENST00000542756.1_Missense_Mutation_p.F303L|SLC8A1_ENST00000405269.1_Missense_Mutation_p.F303L|SLC8A1_ENST00000406785.2_Missense_Mutation_p.F303L|SLC8A1_ENST00000408028.2_Missense_Mutation_p.F303L|SLC8A1_ENST00000332839.4_Missense_Mutation_p.F303L|SLC8A1_ENST00000406391.2_Missense_Mutation_p.F303L|SLC8A1_ENST00000405901.3_Missense_Mutation_p.F303L|SLC8A1_ENST00000402441.1_Missense_Mutation_p.F303L			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	303					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.F303L(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CACCATCTAAGAAATTTTCAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											139	146	144					2																	40656512		2203	4300	6503	40510016	SO:0001583	missense	6546				CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.909C>A	2.37:g.40656512G>T	ENSP00000384763:p.Phe303Leu		40510016	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898345	0.33535	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.26810	1.72;1.75;1.75;1.75;1.72;1.72;1.75;1.71;1.72;1.72	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	N	0.25144	0.715	0.80722	D	1	B;D;B;B;B	0.57257	0.023;0.979;0.016;0.193;0.061	B;D;B;B;B	0.75484	0.098;0.986;0.082;0.066;0.081	T	0.04678	-1.0934	10	0.09338	T	0.73	.	11.211	0.48797	0.0823:0.0:0.9177:0.0	.	303;303;303;303;303	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	L	303	ENSP00000383886:F303L;ENSP00000440727:F303L;ENSP00000384763:F303L;ENSP00000385678:F303L;ENSP00000385188:F303L;ENSP00000385535:F303L;ENSP00000332931:F303L;ENSP00000384908:F303L;ENSP00000385811:F303L;ENSP00000443515:F303L	ENSP00000332931:F303L	F	-	3	2	SLC8A1	40510016	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.383000	0.52471	2.832000	0.97577	0.655000	0.94253	TTC		0.443	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40656512	G	T	40656512	3	4	61	1	0	0	0	0	1	0	0	0	14743	933	33	2	2160	2	SLC8A1	2	40656512	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	659367	40656512	202542861	1361	9346										
MTA3	57504	broad.mit.edu	37	chr2	42931347	42931347	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaagcagcaaaccaaatCccaaccaaatatccactagt	4	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:42931347C>T	ENST00000405094.1	+	12	1039	c.1039C>T	c.(1039-1041)Ccc>Tcc	p.P347S	MTA3_ENST00000406652.1_Missense_Mutation_p.P290S|MTA3_ENST00000472767.1_3'UTR|MTA3_ENST00000406911.1_Missense_Mutation_p.P346S|MTA3_ENST00000405592.1_Missense_Mutation_p.P290S|MTA3_ENST00000407270.3_Missense_Mutation_p.P347S			Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	347						intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P347S(1)		endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						CAAACCAAATCCCAACCAAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											68	65	66					2																	42931347		1887	4105	5992	42784851	SO:0001583	missense	57504			AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935		"GATA zinc finger domain containing"	23784	protein-coding gene	gene with protein product		609050	"metastasis associated gene family, member 3"			12705869, 14613024	Standard	NM_001282755		Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000405094.1:c.1039C>T	2.37:g.42931347C>T	ENSP00000385823:p.Pro347Ser		42784851	Q9NSP2|Q9ULF4	Missense_Mutation	SNP	ENST00000405094.1	37		.	.	.	.	.	.	.	.	.	.	C	17.81	3.480408	0.63849	.	.	ENSG00000057935	ENST00000405592;ENST00000406652;ENST00000407270;ENST00000282366;ENST00000406911;ENST00000405094	T;T;T;T;T	0.50001	0.76;0.76;0.84;0.83;0.79	5.6	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.72399	0.3455	M	0.85373	2.75	0.58432	D	0.999995	D;D;P	0.89917	1.0;1.0;0.866	D;D;P	0.83275	0.996;0.996;0.566	T	0.78411	-0.2214	10	0.72032	D	0.01	-15.0189	16.3774	0.83410	0.0:0.868:0.132:0.0	.	346;347;290	E7EQY4;Q9BTC8-2;D6W5A2	.;.;.	S	290;290;347;347;346;347	ENSP00000383973:P290S;ENSP00000384249:P290S;ENSP00000385045:P347S;ENSP00000385241:P346S;ENSP00000385823:P347S	ENSP00000282366:P347S	P	+	1	0	MTA3	42784851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.557000	0.82243	1.319000	0.45190	0.563000	0.77884	CCC		0.408	MTA3-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318159.1	NM_020744		T	42931347	C	T	42931347	3	4	61	1	0	0	0	0	1	0	0	0	9940	855	30	3	1085	3	MTA3	2	42931347	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2274835	42931347	200268026	1362	9347										
THADA	63892	broad.mit.edu	37	chr2	43798992	43798992	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaagcaagcctaatgtatCtatccttacctaaaaaacat	3	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:43798992C>A	ENST00000405006.4	-	13	2269	c.1918G>T	c.(1918-1920)Gat>Tat	p.D640Y	THADA_ENST00000404790.1_Missense_Mutation_p.D640Y|THADA_ENST00000415080.2_Missense_Mutation_p.D350Y|THADA_ENST00000330266.7_Missense_Mutation_p.D350Y|THADA_ENST00000405975.2_Missense_Mutation_p.D640Y|THADA_ENST00000403856.1_Missense_Mutation_p.D640Y|THADA_ENST00000402360.2_Missense_Mutation_p.D640Y	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	640								p.D640Y(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CCTAATGTATCTATCCTTACC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	110	109					2																	43798992		1847	4094	5941	43652496	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.1918G>T	2.37:g.43798992C>A	ENSP00000385995:p.Asp640Tyr		43652496	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.229361	0.79688	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;1.18;1.18;1.42	5.16	5.16	0.70880	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80088	0.4559	M	0.73598	2.24	0.54753	D	0.999989	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;0.998;0.998	T	0.82303	-0.0524	10	0.87932	D	0	.	19.0152	0.92890	0.0:1.0:0.0:0.0	.	640;640;640;350;640	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	Y	350;640;640;350;640;640;640;640	ENSP00000331105:D350Y;ENSP00000386088:D640Y;ENSP00000416048:D350Y;ENSP00000385995:D640Y;ENSP00000385441:D640Y;ENSP00000384266:D640Y;ENSP00000385469:D640Y	ENSP00000331105:D350Y	D	-	1	0	THADA	43652496	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	7.325000	0.79124	2.563000	0.86464	0.591000	0.81541	GAT		0.323	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		A	43798992	C	A	43798992	3	1	61	1	0	0	0	0	1	0	0	0	15879	913	32	2	4047	2	THADA	2	43798992	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	867645	43798992	199400381	1363	9348										
THADA	63892	broad.mit.edu	37	chr2	43804357	43804357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggacactggtgcagtccaCtgaacgaagcagcacactgc	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:43804357C>T	ENST00000405006.4	-	10	1192	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	THADA_ENST00000404790.1_Missense_Mutation_p.V281M|THADA_ENST00000415080.2_De_novo_Start_InFrame|THADA_ENST00000330266.7_5'Flank|THADA_ENST00000405975.2_Missense_Mutation_p.V281M|THADA_ENST00000403856.1_Missense_Mutation_p.V281M|THADA_ENST00000402360.2_Missense_Mutation_p.V281M	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	281								p.V281M(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GTGCAGTCCACTGAACGAAGC	0.443											OREG0014580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											24	25	25					2																	43804357		1965	4152	6117	43657861	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.841G>A	2.37:g.43804357C>T	ENSP00000385995:p.Val281Met	919	43657861	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.981962	0.74474	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T	0.34472	2.82;2.82;1.4;1.4;1.36	5.28	4.37	0.52481	.	0.413650	0.23924	N	0.043205	T	0.47266	0.1436	M	0.61703	1.905	0.80722	D	1	D;P;D;P	0.55800	0.968;0.928;0.973;0.933	P;P;P;P	0.59171	0.819;0.772;0.853;0.596	T	0.41124	-0.9526	10	0.45353	T	0.12	-4.3772	6.975	0.24670	0.1297:0.6735:0.1256:0.0713	.	281;281;281;281	B5MC89;Q8IY32;Q6YHU6-5;Q6YHU6	.;.;.;THADA_HUMAN	M	281	ENSP00000386088:V281M;ENSP00000385995:V281M;ENSP00000385441:V281M;ENSP00000384266:V281M;ENSP00000385469:V281M	ENSP00000349464:V281M	V	-	1	0	THADA	43657861	0.022000	0.18835	0.861000	0.33841	0.466000	0.32739	1.295000	0.33377	2.464000	0.83262	0.561000	0.74099	GTG		0.443	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		T	43804357	C	T	43804357	3	4	61	1	0	0	0	0	1	0	0	0	15879	565	20	3	5136	3	THADA	2	43804357	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5365	43804357	199395016	1364	9349										
THADA	63892	broad.mit.edu	37	chr2	43818076	43818076	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccatttttatctgctttCtccagcagaggcacaatcta	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:43818076C>A	ENST00000405006.4	-	4	540	c.189G>T	c.(187-189)gaG>gaT	p.E63D	THADA_ENST00000404790.1_Missense_Mutation_p.E63D|THADA_ENST00000415080.2_5'UTR|THADA_ENST00000405975.2_Missense_Mutation_p.E63D|THADA_ENST00000403856.1_Missense_Mutation_p.E63D|THADA_ENST00000402360.2_Missense_Mutation_p.E63D	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	63			E -> G (in dbSNP:rs10210191).					p.E63D(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TATCTGCTTTCTCCAGCAGAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	71	72					2																	43818076		1816	4073	5889	43671580	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.189G>T	2.37:g.43818076C>A	ENSP00000385995:p.Glu63Asp		43671580	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499236	0.64298	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T	0.35236	2.76;2.76;1.35;1.35;1.32	5.21	4.34	0.51931	.	0.213634	0.38837	N	0.001547	T	0.50497	0.1619	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.67145	0.99;0.976;0.996;0.958	P;P;P;P	0.62089	0.829;0.652;0.898;0.45	T	0.47407	-0.9120	10	0.38643	T	0.18	.	12.3086	0.54915	0.0:0.9219:0.0:0.0781	.	63;63;63;63	B5MC89;Q8IY32;Q6YHU6-5;Q6YHU6	.;.;.;THADA_HUMAN	D	63	ENSP00000386088:E63D;ENSP00000385995:E63D;ENSP00000385441:E63D;ENSP00000384266:E63D;ENSP00000385469:E63D	ENSP00000349464:E63D	E	-	3	2	THADA	43671580	0.998000	0.40836	1.000000	0.80357	0.777000	0.43975	0.288000	0.18939	1.432000	0.47375	0.655000	0.94253	GAG		0.323	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		A	43818076	C	A	43818076	3	1	61	1	0	0	0	0	1	0	0	0	15879	912	32	2	5812	2	THADA	2	43818076	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13719	43818076	199381297	1365	9350										
PLEKHH2	130271	broad.mit.edu	37	chr2	43919744	43919744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtgtcaagatctggagtCgctaatacaggaaaaagatg	11	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:43919744C>T	ENST00000282406.4	+	4	388	c.278C>T	c.(277-279)tCg>tTg	p.S93L		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	93					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)	p.S93L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GATCTGGAGTCGCTAATACAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	94	92					2																	43919744		2203	4300	6503	43773248	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.278C>T	2.37:g.43919744C>T	ENSP00000282406:p.Ser93Leu		43773248	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	C	9.790	1.177545	0.21787	.	.	ENSG00000152527	ENST00000282406	T	0.51817	0.69	5.24	1.1	0.20463	.	0.377447	0.28322	N	0.015775	T	0.33760	0.0874	L	0.43152	1.355	0.09310	N	1	B;B	0.23735	0.014;0.09	B;B	0.22601	0.001;0.04	T	0.17961	-1.0352	10	0.40728	T	0.16	-1.7573	6.0633	0.19850	0.0:0.4697:0.1293:0.401	.	93;93	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	L	93	ENSP00000282406:S93L	ENSP00000282406:S93L	S	+	2	0	PLEKHH2	43773248	0.021000	0.18746	0.095000	0.20976	0.840000	0.47671	0.316000	0.19469	0.613000	0.30089	-0.251000	0.11542	TCG		0.338	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43919744	C	T	43919744	3	4	61	1	0	0	0	0	1	0	0	0	12108	893	31	1	288	1	PLEKHH2	2	43919744	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101668	43919744	199279629	1366	9351										
ABCG5	64240	broad.mit.edu	37	chr2	44040324	44040324	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacaagagctggaataaaTgaatacaaaatcagaaagtt	8	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44040324T>G	ENST00000260645.1	-	13	2026	c.1887A>C	c.(1885-1887)tcA>tcC	p.S629S	ABCG5_ENST00000543989.1_Silent_p.S234S|ABCG5_ENST00000405322.1_Silent_p.S458S	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	629	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)	p.S629S(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CTGGAATAAATGAATACAAAA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											97	96	96					2																	44040324		2203	4300	6503	43893828	SO:0001819	synonymous_variant	64240			T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1887A>C	2.37:g.44040324T>G			43893828	Q2T9G2|Q96QZ2|Q96QZ3	Silent	SNP	ENST00000260645.1	37	CCDS1814.1																																																																																				0.383	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		G	44040324	T	G	44040324	2	3	61	1	0	0	0	0	0	0	0	1	71	1451	51	4		4	ABCG5	2	44040324	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	120580	44040324	199159049	1367	9352										
LRPPRC	10128	broad.mit.edu	37	chr2	44115746	44115746	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcctggttatttcaagaaGagttttccctcaattttctt	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44115746G>T	ENST00000260665.7	-	38	4235	c.4178C>A	c.(4177-4179)tCt>tAt	p.S1393Y		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1393	RNA-binding.				mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.S1393Y(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ATTTCAAGAAGAGTTTTCCCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	90	89					2																	44115746		2203	4299	6502	43969250	SO:0001583	missense	10128			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.4178C>A	2.37:g.44115746G>T	ENSP00000260665:p.Ser1393Tyr		43969250	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301404	0.40694	.	.	ENSG00000138095	ENST00000260665	T	0.57107	0.42	5.75	2.97	0.34412	.	0.701585	0.14273	N	0.330034	T	0.35970	0.0950	L	0.43152	1.355	0.09310	N	1	P	0.37864	0.61	B	0.24701	0.055	T	0.29640	-1.0005	10	0.62326	D	0.03	-14.4087	5.5607	0.17142	0.1515:0.0:0.5649:0.2836	.	1393	P42704	LPPRC_HUMAN	Y	1393	ENSP00000260665:S1393Y	ENSP00000260665:S1393Y	S	-	2	0	LRPPRC	43969250	0.032000	0.19561	0.002000	0.10522	0.004000	0.04260	0.993000	0.29680	0.775000	0.33450	0.655000	0.94253	TCT		0.328	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		T	44115746	G	T	44115746	3	4	61	1	0	0	0	0	1	0	0	0	8994	942	33	2	10	2	LRPPRC	2	44115746	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75422	44115746	199083627	1368	9353										
LRPPRC	10128	broad.mit.edu	37	chr2	44170992	44170992	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgttgtatctttgataaGaacatccttctctttcatct	6	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44170992G>A	ENST00000260665.7	-	23	2395	c.2338C>T	c.(2338-2340)Ctt>Ttt	p.L780F		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	780					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L780F(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TCTTTGATAAGAACATCCTTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											117	116	117					2																	44170992		2203	4300	6503	44024496	SO:0001583	missense	10128			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2338C>T	2.37:g.44170992G>A	ENSP00000260665:p.Leu780Phe		44024496	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	G	7.998	0.754746	0.15778	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	T	0.56103	0.48	6.16	4.31	0.51392	.	0.583803	0.18628	N	0.135675	T	0.47691	0.1459	L	0.51422	1.61	0.80722	D	1	B;B	0.34103	0.005;0.437	B;B	0.35353	0.009;0.201	T	0.32587	-0.9901	10	0.09590	T	0.72	-0.6534	17.0992	0.86644	0.0:0.2631:0.7369:0.0	.	680;780	F5H4J6;P42704	.;LPPRC_HUMAN	F	680;780	ENSP00000260665:L780F	ENSP00000260665:L780F	L	-	1	0	LRPPRC	44024496	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.637000	0.24659	0.861000	0.35504	0.650000	0.86243	CTT		0.373	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		A	44170992	G	A	44170992	3	1	61	1	0	0	0	0	1	0	0	0	8994	942	33	3	1910	3	LRPPRC	2	44170992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55246	44170992	199028381	1369	9354										
PPM1B	5495	broad.mit.edu	37	chr2	44445125	44445125	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagattatggagaagtctggCgaggaaggaatgcctgatct	15	5	2	3	rs150223863	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44445125C>T	ENST00000282412.4	+	4	1396	c.984C>T	c.(982-984)ggC>ggT	p.G328G	PPM1B_ENST00000378540.4_3'UTR|PPM1B_ENST00000345249.4_Silent_p.G41G|PPM1B_ENST00000409432.3_Silent_p.G328G|PPM1B_ENST00000378551.2_Silent_p.G328G	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	328					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.G328G(1)		kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				AGAAGTCTGGCGAGGAAGGAA	0.418													C|||	2	0.000399361	0	0	5008	,	,		15270	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C	,,,	0,4406		0,0,2203	77	80	79		984,984,984,123	-4.3	1	2	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPM1B	NM_001033557.1,NM_002706.4,NM_177968.2,NM_177969.2	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	328/381,328/480,328/388,41/193	44445125	1,13005	2203	4300	6503	44298629	SO:0001819	synonymous_variant	5495			AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.984C>T	2.37:g.44445125C>T			44298629	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Silent	SNP	ENST00000282412.4	37	CCDS1817.1																																																																																				0.418	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		T	44445125	C	T	44445125	2	4	61	1	0	0	0	0	0	0	0	1	12370	755	27	1		1	PPM1B	2	44445125	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274133	44445125	198754248	1370	9355										
PREPL	9581	broad.mit.edu	37	chr2	44565627	44565627	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctcttcattgtaaaaaAtaaatcccaattcataattg	2	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44565627A>C	ENST00000409936.1	-	8	1455	c.1018T>G	c.(1018-1020)Ttt>Gtt	p.F340V	PREPL_ENST00000260648.6_Missense_Mutation_p.F340V|PREPL_ENST00000409957.1_Missense_Mutation_p.F251V|PREPL_ENST00000378511.3_Intron|PREPL_ENST00000541738.1_Missense_Mutation_p.F251V|PREPL_ENST00000378520.3_Missense_Mutation_p.F340V|PREPL_ENST00000409272.1_Missense_Mutation_p.F340V|PREPL_ENST00000409411.1_Missense_Mutation_p.F251V|PREPL_ENST00000410081.1_Missense_Mutation_p.F340V	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	340						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.F340V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ATTGTAAAAAATAAATCCCAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	75	77					2																	44565627		2203	4300	6503	44419131	SO:0001583	missense	9581			AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.1018T>G	2.37:g.44565627A>C	ENSP00000386543:p.Phe340Val		44419131	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	A	2.227	-0.377066	0.05000	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520	T;T;T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28	5.35	2.88	0.33553	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.249687	0.39909	N	0.001233	T	0.08268	0.0206	N	0.00413	-1.525	0.27108	N	0.962442	B;B	0.23185	0.003;0.081	B;B	0.20184	0.001;0.028	T	0.30794	-0.9966	10	0.13470	T	0.59	-20.5314	6.1325	0.20213	0.4827:0.3853:0.0:0.1321	.	340;340	Q4J6C6-2;Q4J6C6	.;PPCEL_HUMAN	V	251;251;251;340;340;340;340;340	ENSP00000439626:F251V;ENSP00000387095:F251V;ENSP00000387241:F251V;ENSP00000386543:F340V;ENSP00000260648:F340V;ENSP00000386909:F340V;ENSP00000386509:F340V;ENSP00000367781:F340V	ENSP00000260648:F340V	F	-	1	0	PREPL	44419131	0.960000	0.32886	0.999000	0.59377	0.889000	0.51656	2.240000	0.43088	2.021000	0.59480	0.533000	0.62120	TTT		0.363	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		C	44565627	A	C	44565627	3	2	61	1	0	0	0	0	1	0	0	0	12509	101	4	4	1197	4	PREPL	2	44565627	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	120502	44565627	198633746	1371	9356										
PREPL	9581	broad.mit.edu	37	chr2	44586653	44586653	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccttacatgagaagctccGacttgggatgtttcttgcta	9	9	1	1	rs202213424		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:44586653G>A	ENST00000409936.1	-	2	639	c.202C>T	c.(202-204)Cgg>Tgg	p.R68W	PREPL_ENST00000260648.6_Missense_Mutation_p.R68W|CAMKMT_ENST00000378494.3_5'Flank|CAMKMT_ENST00000402247.1_5'Flank|PREPL_ENST00000409957.1_Intron|PREPL_ENST00000378511.3_Missense_Mutation_p.R68W|PREPL_ENST00000541738.1_Intron|CAMKMT_ENST00000403853.3_5'Flank|PREPL_ENST00000378520.3_Missense_Mutation_p.R68W|PREPL_ENST00000409272.1_Missense_Mutation_p.R68W|CAMKMT_ENST00000407131.1_5'Flank|PREPL_ENST00000540817.1_Intron|PREPL_ENST00000409411.1_Intron|PREPL_ENST00000410081.1_Missense_Mutation_p.R68W	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	68						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.R68W(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GAGAAGCTCCGACTTGGGATG	0.303													G|||	1	0.000199681	0	0	5008	,	,		18038	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											138	140	139					2																	44586653		2203	4300	6503	44440157	SO:0001583	missense	9581			AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.202C>T	2.37:g.44586653G>A	ENSP00000386543:p.Arg68Trp		44440157	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.12	3.553825	0.65425	.	.	ENSG00000138078	ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511;ENST00000438314	.	.	.	5.27	4.38	0.52667	.	0.251803	0.28409	N	0.015459	T	0.51176	0.1659	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.995;0.997;0.976	T	0.59215	-0.7496	9	0.66056	D	0.02	-13.6207	11.022	0.47724	0.0:0.0:0.8148:0.1852	.	68;68;68	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	W	68	.	ENSP00000260648:R68W	R	-	1	2	PREPL	44440157	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.781000	0.38644	1.407000	0.46875	0.655000	0.94253	CGG		0.303	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		A	44586653	G	A	44586653	3	1	61	1	0	0	0	0	1	0	0	0	12509	1057	37	1	2037	1	PREPL	2	44586653	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21026	44586653	198612720	1372	9357										
SIX2	10736	broad.mit.edu	37	chr2	45235844	45235844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactcgcgcagcacgctgcGactcttttccttgaagcagt	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:45235844G>A	ENST00000303077.6	-	1	725	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	136					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|kidney development (GO:0001822)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesenchymal stem cell proliferation (GO:0097168)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|middle ear morphogenesis (GO:0042474)|nephron development (GO:0072006)|nephron morphogenesis (GO:0072028)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus (GO:0006606)|regulation of branching involved in ureteric bud morphogenesis (GO:0090189)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R136C(1)		endometrium(6)|large_intestine(3)|lung(8)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGCACGCTGCGACTCTTTTCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	59	57					2																	45235844		2203	4300	6503	45089348	SO:0001583	missense	10736			AF136939	CCDS1822.1	2p21	2011-06-20	2007-07-13		ENSG00000170577	ENSG00000170577		"Homeoboxes / SINE class"	10888	protein-coding gene	gene with protein product		604994	"sine oculis homeobox (Drosophila) homolog 2", "sine oculis homeobox homolog 2 (Drosophila)"				Standard	NM_016932		Approved		uc002ruo.3	Q9NPC8	OTTHUMG00000152421	ENST00000303077.6:c.406C>T	2.37:g.45235844G>A	ENSP00000304502:p.Arg136Cys		45089348	Q9BXH7	Missense_Mutation	SNP	ENST00000303077.6	37	CCDS1822.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488359	0.84854	.	.	ENSG00000170577	ENST00000303077	D	0.96232	-3.95	5.19	5.19	0.71726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98764	0.9584	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99755	1.1019	10	0.87932	D	0	-32.1445	18.33	0.90265	0.0:0.0:1.0:0.0	.	136;136	Q8TBA2;Q9NPC8	.;SIX2_HUMAN	C	136	ENSP00000304502:R136C	ENSP00000304502:R136C	R	-	1	0	SIX2	45089348	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.509000	0.53386	2.413000	0.81919	0.462000	0.41574	CGC		0.667	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2			A	45235844	G	A	45235844	3	1	61	1	0	0	0	0	1	0	0	0	14384	1058	37	1	477	1	SIX2	2	45235844	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	649191	45235844	197963529	1373	9358										
SRBD1	55133	broad.mit.edu	37	chr2	45774717	45774717	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcggaagccttgtccacaAtgcaagtaaaccacatcagt	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:45774717A>C	ENST00000263736.4	-	13	1772	c.1710T>G	c.(1708-1710)caT>caG	p.H570Q	SRBD1_ENST00000535761.1_Missense_Mutation_p.H89Q	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	570					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)	p.H570Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			CTTGTCCACAATGCAAGTAAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											65	64	65					2																	45774717		2203	4299	6502	45628221	SO:0001583	missense	55133			AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.1710T>G	2.37:g.45774717A>C	ENSP00000263736:p.His570Gln		45628221	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	37	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	A	18.83	3.707797	0.68615	.	.	ENSG00000068784	ENST00000263736;ENST00000535761	T;T	0.46451	0.87;0.87	5.54	1.91	0.25777	YqgF/RNase H-like domain (2);	0.000000	0.85682	D	0.000000	T	0.62233	0.2411	M	0.87682	2.9	0.41085	D	0.98555	D	0.76494	0.999	D	0.66196	0.942	T	0.62464	-0.6849	10	0.72032	D	0.01	.	8.2251	0.31564	0.6987:0.0:0.3013:0.0	.	570	Q8N5C6	SRBD1_HUMAN	Q	570;89	ENSP00000263736:H570Q;ENSP00000441272:H89Q	ENSP00000263736:H570Q	H	-	3	2	SRBD1	45628221	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.569000	0.36428	0.084000	0.17077	0.533000	0.62120	CAT		0.318	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45774717	A	C	45774717	3	2	61	1	0	0	0	0	1	0	0	0	15172	98	4	4	1313	4	SRBD1	2	45774717	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	538873	45774717	197424656	1374	9359										
SRBD1	55133	broad.mit.edu	37	chr2	45832558	45832558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcctggacctgtactttcGctcttcttggcaatgatgac	8	12	2	2	rs113207448	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:45832558G>A	ENST00000263736.4	-	2	85	c.23C>T	c.(22-24)gCg>gTg	p.A8V		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	8					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)	p.A8V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			CTGTACTTTCGCTCTTCTTGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	168	166	167		23	4.7	1	2	dbSNP_132	167	2,8598	2.2+/-6.3	0,2,4298	no	missense	SRBD1	NM_018079.4	64	0,5,6498	AA,AG,GG		0.0233,0.0681,0.0384	benign	8/996	45832558	5,13001	2203	4300	6503	45686062	SO:0001583	missense	55133			AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.23C>T	2.37:g.45832558G>A	ENSP00000263736:p.Ala8Val		45686062	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	37	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068235	0.36470	6.81E-4	2.33E-4	ENSG00000068784	ENST00000263736	T	0.26810	1.71	5.58	4.69	0.59074	.	0.336216	0.25494	N	0.030292	T	0.13628	0.0330	N	0.12746	0.255	0.80722	D	1	B	0.19445	0.036	B	0.10450	0.005	T	0.10132	-1.0643	10	0.18276	T	0.48	.	10.8543	0.46789	0.0883:0.0:0.9117:0.0	.	8	Q8N5C6	SRBD1_HUMAN	V	8	ENSP00000263736:A8V	ENSP00000263736:A8V	A	-	2	0	SRBD1	45686062	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	2.605000	0.46283	1.342000	0.45619	0.655000	0.94253	GCG		0.358	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		A	45832558	G	A	45832558	3	1	61	1	0	0	0	0	1	0	0	0	15172	1087	38	1	3044	1	SRBD1	2	45832558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57841	45832558	197366815	1375	9360										
PRKCE	5581	broad.mit.edu	37	chr2	45879282	45879282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagatcaaaatctgcgagGccgtgagcttgaagcccaca	10	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:45879282G>A	ENST00000306156.3	+	1	370	c.43G>A	c.(43-45)Gcc>Acc	p.A15T		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	15	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)	p.A15T(1)	MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	AATCTGCGAGGCCGTGAGCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											41	45	44					2																	45879282		2202	4299	6501	45732786	SO:0001583	missense	5581				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.43G>A	2.37:g.45879282G>A	ENSP00000306124:p.Ala15Thr		45732786	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	37	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	35	5.558753	0.96514	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.25414	1.8;1.8	4.71	4.71	0.59529	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.069396	0.56097	D	0.000033	T	0.61974	0.2390	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74300	-0.3710	10	0.87932	D	0	.	17.673	0.88224	0.0:0.0:1.0:0.0	.	15	Q02156	KPCE_HUMAN	T	15	ENSP00000394574:A15T;ENSP00000306124:A15T	ENSP00000306124:A15T	A	+	1	0	PRKCE	45732786	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.766000	0.98957	2.152000	0.67230	0.561000	0.74099	GCC		0.622	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			A	45879282	G	A	45879282	3	1	61	1	0	0	0	0	1	0	0	0	12545	1203	42	3	45	3	PRKCE	2	45879282	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46724	45879282	197320091	1376	9361										
PRKCE	5581	broad.mit.edu	37	chr2	46207445	46207445	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatttgcagtctgcacctgCgtggtccacaagcggtgcca	11	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:46207445C>T	ENST00000306156.3	+	5	945	c.618C>T	c.(616-618)tgC>tgT	p.C206C		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	206					activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)	p.C206C(1)	MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	TCTGCACCTGCGTGGTCCACA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	2											70	67	68					2																	46207445		1824	3811	5635	46060949	SO:0001819	synonymous_variant	5581				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.618C>T	2.37:g.46207445C>T			46060949	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Silent	SNP	ENST00000306156.3	37	CCDS1824.1																																																																																				0.527	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			T	46207445	C	T	46207445	2	4	61	1	0	0	0	0	0	0	0	1	12545	776	27	1		1	PRKCE	2	46207445	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	328163	46207445	196991928	1377	9362										
MSH2	4436	broad.mit.edu	37	chr2	47639556	47639556	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttctttcaaaatagataAttcaaagaggaggaattctg	7	4	4	2	rs267607929|rs63751602		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:47639556A>C	ENST00000233146.2	+	4	872	c.649A>C	c.(649-651)Att>Ctt	p.I217L	MSH2_ENST00000543555.1_Missense_Mutation_p.I151L|MSH2_ENST00000406134.1_Missense_Mutation_p.I217L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	217					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)|p.I217L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAAATAGATAATTCAAAGAGG	0.303			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	4	Whole gene deletion(2)|Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)	2											37	39	38					2																	47639556		2202	4300	6502	47493060	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.649A>C	2.37:g.47639556A>C	ENSP00000233146:p.Ile217Leu		47493060	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	A	3.647	-0.072248	0.07228	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792;ENST00000413880	D;D;D	0.85484	-1.99;-1.99;-1.99	5.3	2.91	0.33838	DNA mismatch repair protein MutS, connector (1);	0.196466	0.44483	D	0.000443	T	0.63674	0.2531	N	0.05414	-0.055	0.38098	D	0.937179	B;B;B;B	0.06786	0.001;0.0;0.0;0.001	B;B;B;B	0.15484	0.005;0.001;0.003;0.013	T	0.52616	-0.8552	10	0.08599	T	0.76	-7.169	5.2615	0.15576	0.6498:0.1465:0.2037:0.0	.	151;217;217;217	B4E2Z2;E7EQQ1;E9PHA6;P43246	.;.;.;MSH2_HUMAN	L	217;151;217;217;217;217;217;217;53	ENSP00000233146:I217L;ENSP00000442697:I151L;ENSP00000384199:I217L	ENSP00000233146:I217L	I	+	1	0	MSH2	47493060	1.000000	0.71417	1.000000	0.80357	0.081000	0.17604	3.258000	0.51507	0.852000	0.35287	0.456000	0.33151	ATT		0.303	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			C	47639556	A	C	47639556	3	2	61	1	0	0	0	0	1	0	0	0	9900	101	4	4	663	4	MSH2	2	47639556	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1432111	47639556	195559817	1378	9363										
MSH2	4436	broad.mit.edu	37	chr2	47656939	47656939	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggcagactttacaagaaGatttacttcgtcgattccca	8	9	0	4	rs193922372		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:47656939G>T	ENST00000233146.2	+	7	1358	c.1135G>T	c.(1135-1137)Gat>Tat	p.D379Y	MSH2_ENST00000543555.1_Missense_Mutation_p.D313Y|MSH2_ENST00000406134.1_Missense_Mutation_p.D379Y	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	379					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)|p.D379Y(1)|p.E378del(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTTACAAGAAGATTTACTTCG	0.328			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	6	Whole gene deletion(2)|Unknown(2)|Substitution - Missense(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|endometrium(1)	2											82	81	81					2																	47656939		2203	4300	6503	47510443	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1135G>T	2.37:g.47656939G>T	ENSP00000233146:p.Asp379Tyr		47510443	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	g	25.1	4.598247	0.87055	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000422810;ENST00000413880	D;D;D	0.90504	-2.68;-2.68;-2.68	5.59	5.59	0.84812	DNA mismatch repair protein MutS, core (3);	0.000000	0.85682	D	0.000000	D	0.95335	0.8486	M	0.77313	2.365	0.80722	D	1	D;D;P	0.76494	0.998;0.999;0.899	D;D;D	0.68621	0.959;0.959;0.918	D	0.95468	0.8549	10	0.87932	D	0	-13.467	19.5819	0.95471	0.0:0.0:1.0:0.0	.	313;379;379	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	Y	379;313;379;379;379;379;379;29;165	ENSP00000233146:D379Y;ENSP00000442697:D313Y;ENSP00000384199:D379Y	ENSP00000233146:D379Y	D	+	1	0	MSH2	47510443	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.923000	0.92808	2.631000	0.89168	0.651000	0.88453	GAT		0.328	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			T	47656939	G	T	47656939	3	4	61	1	0	0	0	0	1	0	0	0	9900	942	33	2	1161	2	MSH2	2	47656939	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17383	47656939	195542434	1379	9364										
MSH2	4436	broad.mit.edu	37	chr2	47657021	47657021	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacttacaagattgttaccGactctatcagggtataaatc	6	8	2	1	rs146567853	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:47657021G>A	ENST00000233146.2	+	7	1440	c.1217G>A	c.(1216-1218)cGa>cAa	p.R406Q	MSH2_ENST00000543555.1_Missense_Mutation_p.R340Q|MSH2_ENST00000406134.1_Missense_Mutation_p.R406Q	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	406					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)|p.R406Q(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATTGTTACCGACTCTATCAG	0.363			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	5	Whole gene deletion(2)|Unknown(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)	2							GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	83	77	79		1217	4.6	1	2	dbSNP_134	79	0,8600		0,0,4300	no	missense	MSH2	NM_000251.1	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	406/935	47657021	1,13005	2203	4300	6503	47510525	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1217G>A	2.37:g.47657021G>A	ENSP00000233146:p.Arg406Gln		47510525	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.05|18.05	3.537076|3.537076	0.65085|0.65085	2.27E-4|2.27E-4	0.0|0.0	ENSG00000095002|ENSG00000095002	ENST00000448533|ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000422810;ENST00000413880	.|D;D;D	.|0.90324	.|-2.65;-2.65;-2.65	5.45|5.45	4.57|4.57	0.56435|0.56435	.|DNA mismatch repair protein MutS, core (3);	.|0.056207	.|0.64402	.|N	.|0.000001	D|D	0.89392|0.89392	0.6702|0.6702	M|M	0.81179|0.81179	2.53|2.53	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.32467	.|0.051;0.372;0.067	.|B;B;B	.|0.27608	.|0.026;0.043;0.081	D|D	0.88356|0.88356	0.2984|0.2984	6|10	0.66056|0.62326	D|D	0.02|0.03	-0.6071|-0.6071	11.2565|11.2565	0.49056|0.49056	0.1469:0.0:0.8531:0.0|0.1469:0.0:0.8531:0.0	.|.	.|340;406;406	.|B4E2Z2;E9PHA6;P43246	.|.;.;MSH2_HUMAN	N|Q	406|406;340;406;406;406;406;56;192	.|ENSP00000233146:R406Q;ENSP00000442697:R340Q;ENSP00000384199:R406Q	ENSP00000415023:D406N|ENSP00000233146:R406Q	D|R	+|+	1|2	0|0	MSH2|MSH2	47510525|47510525	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.991000|0.991000	0.79684|0.79684	5.919000|5.919000	0.70005|0.70005	1.317000|1.317000	0.45149|0.45149	0.651000|0.651000	0.88453|0.88453	GAC|CGA		0.363	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			A	47657021	G	A	47657021	3	1	61	1	0	0	0	0	1	0	0	0	9900	1058	37	1	1243	1	MSH2	2	47657021	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82	47657021	195542352	1380	9365										
MSH6	2956	broad.mit.edu	37	chr2	48026932	48026932	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaggaaatctctcaaagGaaactaaaacaattctaaag	5	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48026932G>T	ENST00000234420.5	+	4	1962	c.1810G>T	c.(1810-1812)Gaa>Taa	p.E604*	MSH6_ENST00000540021.1_Nonsense_Mutation_p.E474*|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Nonsense_Mutation_p.E302*	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	604					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)|p.E604*(1)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTCTCAAAGGAAACTAAAAC	0.408			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	3	Whole gene deletion(2)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	2											69	72	71					2																	48026932		2201	4299	6500	47880436	SO:0001587	stop_gained	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.1810G>T	2.37:g.48026932G>T	ENSP00000234420:p.Glu604*		47880436	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Nonsense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	G	39	7.566572	0.98361	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	.	.	.	5.25	5.25	0.73442	.	0.210963	0.49305	D	0.000160	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-2.5414	18.8489	0.92218	0.0:0.0:1.0:0.0	.	.	.	.	X	604;602;474;302	.	ENSP00000234420:E604X	E	+	1	0	MSH6	47880436	1.000000	0.71417	0.323000	0.25347	0.021000	0.10359	9.794000	0.99096	2.468000	0.83385	0.585000	0.79938	GAA		0.408	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		T	48026932	G	T	48026932	4	4	61	1	0	0	0	0	0	1	0	0	9904	1175	41	2	1824	2	MSH6	2	48026932	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	369911	48026932	195172441	1381	9366										
MSH6	2956	broad.mit.edu	37	chr2	48027990	48027990	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcctcctggaatacctagaGaaacagcgcaacagaattgg	10	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48027990G>T	ENST00000234420.5	+	4	3020	c.2868G>T	c.(2866-2868)gaG>gaT	p.E956D	MSH6_ENST00000540021.1_Missense_Mutation_p.E826D|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.E654D	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	956					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)|p.E956D(1)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AATACCTAGAGAAACAGCGCA	0.448			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	3	Whole gene deletion(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	2											44	45	45					2																	48027990		2203	4300	6503	47881494	SO:0001583	missense	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2868G>T	2.37:g.48027990G>T	ENSP00000234420:p.Glu956Asp		47881494	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	G	1.904	-0.452321	0.04540	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.90069	-2.61;-2.61;-2.61	5.61	3.74	0.42951	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.157767	0.56097	N	0.000039	T	0.68742	0.3034	N	0.03209	-0.39	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.006;0.004;0.001	T	0.55761	-0.8090	10	0.09084	T	0.74	-13.333	3.9452	0.09346	0.0764:0.2248:0.4523:0.2465	.	826;956;956	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	D	956;954;826;654	ENSP00000234420:E956D;ENSP00000446475:E826D;ENSP00000438580:E654D	ENSP00000234420:E956D	E	+	3	2	MSH6	47881494	0.826000	0.29277	1.000000	0.80357	0.993000	0.82548	-0.093000	0.11111	0.665000	0.31066	0.563000	0.77884	GAG		0.448	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		T	48027990	G	T	48027990	3	4	61	1	0	0	0	0	1	0	0	0	9904	933	33	2	2882	2	MSH6	2	48027990	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1058	48027990	195171383	1382	9367										
FOXN2	3344	broad.mit.edu	37	chr2	48589787	48589787	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtttgtttttcagtggttCtttatcacctcactatttaa	5	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48589787C>A	ENST00000340553.3	+	5	905	c.644C>A	c.(643-645)tCt>tAt	p.S215Y		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	215					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S215Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			TTCAGTGGTTCTTTATCACCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	112	115					2																	48589787		2203	4300	6503	48443291	SO:0001583	missense	3344				CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.644C>A	2.37:g.48589787C>A	ENSP00000343633:p.Ser215Tyr		48443291	Q15769|Q6P4Q2	Missense_Mutation	SNP	ENST00000340553.3	37	CCDS1838.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691290	0.48097	.	.	ENSG00000170802	ENST00000413569;ENST00000304367;ENST00000340553	D;D	0.95307	-3.67;-3.52	5.6	4.72	0.59763	.	0.192799	0.47455	D	0.000233	D	0.92469	0.7609	L	0.47190	1.495	0.28737	N	0.902163	P	0.37864	0.61	B	0.38106	0.265	D	0.88949	0.3385	10	0.87932	D	0	.	16.1356	0.81487	0.0:0.866:0.134:0.0	.	215	P32314	FOXN2_HUMAN	Y	215;124;215	ENSP00000388486:S215Y;ENSP00000343633:S215Y	ENSP00000305685:S124Y	S	+	2	0	FOXN2	48443291	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	4.704000	0.61831	1.352000	0.45808	0.650000	0.86243	TCT		0.383	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		A	48589787	C	A	48589787	3	1	61	1	0	0	0	0	1	0	0	0	6039	913	32	2	654	2	FOXN2	2	48589787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	561797	48589787	194609586	1383	9368										
KLRAQ1	129285	broad.mit.edu	37	chr2	48692642	48692642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttaaagctgaagatgcGagatattgctgggcaggccc	12	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48692642G>A	ENST00000294952.8	+	9	915	c.758G>A	c.(757-759)cGa>cAa	p.R253Q	PPP1R21_ENST00000449090.2_Missense_Mutation_p.R253Q|PPP1R21_ENST00000281394.4_Missense_Mutation_p.R253Q	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	253						membrane (GO:0016020)	phosphatase binding (GO:0019902)	p.R253L(2)|p.R253Q(1)		endometrium(2)|kidney(4)|lung(9)	15						CTGAAGATGCGAGATATTGCT	0.358																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	2											100	99	99					2																	48692642		2203	4300	6503	48546146	SO:0001583	missense	129285			AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30595	protein-coding gene	gene with protein product			"coiled-coil domain containing 128", "KLRAQ motif containing 1"	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.758G>A	2.37:g.48692642G>A	ENSP00000294952:p.Arg253Gln		48546146	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Missense_Mutation	SNP	ENST00000294952.8	37	CCDS46278.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389820	0.82902	.	.	ENSG00000162869	ENST00000281394;ENST00000294952;ENST00000449090	.	.	.	5.24	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.73528	0.3598	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;0.999	D;D;D;P;P	0.87578	0.998;0.992;0.997;0.806;0.896	T	0.69720	-0.5069	9	0.17832	T	0.49	-13.0447	15.1118	0.72362	0.0:0.0:0.8571:0.1429	.	253;253;253;253;253	E1B6W7;Q6ZMI0;Q6ZMI0-2;Q6ZMI0-3;Q6ZMI0-4	.;PPR21_HUMAN;.;.;.	Q	253	.	ENSP00000281394:R253Q	R	+	2	0	KLRAQ1	48546146	1.000000	0.71417	0.978000	0.43139	0.837000	0.47467	7.489000	0.81451	1.183000	0.42943	-0.188000	0.12872	CGA		0.358	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994		A	48692642	G	A	48692642	3	1	61	1	0	0	0	0	1	0	0	0	8434	1058	37	1	792	1	KLRAQ1	2	48692642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102855	48692642	194506731	1384	9369										
STON1	11037	broad.mit.edu	37	chr2	48808528	48808528	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtttgtctatgcactgTctatgtgctgaagaaaatgc	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48808528T>C	ENST00000406226.1	+	3	951	c.756T>C	c.(754-756)tgT>tgC	p.C252C	STON1-GTF2A1L_ENST00000309827.2_Silent_p.C252C|STON1_ENST00000404752.1_Silent_p.C252C|STON1-GTF2A1L_ENST00000402114.2_Silent_p.C252C|STON1-GTF2A1L_ENST00000394751.3_Silent_p.C252C|STON1-GTF2A1L_ENST00000405008.1_Silent_p.C252C|STON1-GTF2A1L_ENST00000394754.1_Silent_p.C252C|STON1_ENST00000309835.3_Silent_p.C252C	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	252					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.C252C(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTATGCACTGTCTATGTGCTG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	2											94	84	87					2																	48808528		2203	4300	6503	48662032	SO:0001819	synonymous_variant	286749			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.756T>C	2.37:g.48808528T>C			48662032	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																				0.433	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		C	48808528	T	C	48808528	2	2	61	1	0	0	0	0	0	0	0	1	15355	1673	58	4		4	STON1	2	48808528	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	115886	48808528	194390845	1385	9370										
STON1	11037	broad.mit.edu	37	chr2	48818859	48818859	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaagaaattccctctgaTtggtatccatttgctactgt	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48818859T>C	ENST00000406226.1	+	4	2193	c.1998T>C	c.(1996-1998)gaT>gaC	p.D666D	STON1-GTF2A1L_ENST00000309827.2_Silent_p.D666D|STON1_ENST00000404752.1_Silent_p.D666D|STON1-GTF2A1L_ENST00000402114.2_Silent_p.D666D|STON1-GTF2A1L_ENST00000394751.3_Silent_p.D666D|STON1-GTF2A1L_ENST00000405008.1_Silent_p.D666D|STON1-GTF2A1L_ENST00000394754.1_Silent_p.D666D|STON1_ENST00000309835.3_Silent_p.D666D	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	666	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.D666D(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCCCTCTGATTGGTATCCAT	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	2											182	175	177					2																	48818859		2203	4300	6503	48672363	SO:0001819	synonymous_variant	286749			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1998T>C	2.37:g.48818859T>C			48672363	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																				0.453	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		C	48818859	T	C	48818859	2	2	61	1	0	0	0	0	0	0	0	1	15355	1490	52	4		4	STON1	2	48818859	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10331	48818859	194380514	1386	9371										
GTF2A1L	11036	broad.mit.edu	37	chr2	48848080	48848080	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaggaacaagttttaaaaGacttgaagcaggtttgtagc	11	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48848080G>T	ENST00000403751.3	+	2	149	c.112G>T	c.(112-114)Gac>Tac	p.D38Y	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.D742Y|GTF2A1L_ENST00000430487.2_Intron|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.D742Y|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.D742Y|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.D742Y|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.D742Y|GTF2A1L_ENST00000468326.1_3'UTR	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	38					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.D742N(1)|p.D742Y(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGTTTTAAAAGACTTGAAGCA	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	2											54	54	54					2																	48848080		2203	4298	6501	48701584	SO:0001583	missense	286749			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.112G>T	2.37:g.48848080G>T	ENSP00000384597:p.Asp38Tyr		48701584	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400046	0.62177	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000403751	T;T;T;T;T;T;T	0.56444	0.46;0.46;0.46;0.46;0.46;0.46;0.46	4.7	4.7	0.59300	Transcription factor IIA, alpha subunit, N-terminal (1);Transcription factor IIA, helical (1);	0.129372	0.51477	D	0.000100	T	0.69522	0.3120	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	0.966;1.0;1.0;0.999	P;D;D;D	0.81914	0.641;0.989;0.995;0.969	T	0.72494	-0.4276	10	0.87932	D	0	.	12.6651	0.56837	0.0834:0.0:0.9166:0.0	.	742;742;38;742	A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;TF2AY_HUMAN;.	Y	742;742;742;742;742;37;38;38	ENSP00000385499:D742Y;ENSP00000385701:D742Y;ENSP00000378236:D742Y;ENSP00000311493:D742Y;ENSP00000378234:D742Y;ENSP00000396702:D38Y;ENSP00000384597:D38Y	ENSP00000384597:D38Y	D	+	1	0	STON1-GTF2A1L;GTF2A1L	48701584	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.149000	0.71795	2.611000	0.88343	0.561000	0.74099	GAC		0.328	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		T	48848080	G	T	48848080	3	4	61	1	0	0	0	0	1	0	0	0	6874	942	33	2	118	2	GTF2A1L	2	48848080	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29221	48848080	194351293	1387	9372										
GTF2A1L	11036	broad.mit.edu	37	chr2	48873757	48873757	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcttcaagcaactactgAaaaatcacagagaattgaaa	6	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48873757A>G	ENST00000403751.3	+	6	591	c.554A>G	c.(553-555)gAa>gGa	p.E185G	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.E889G|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.E151G|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.E889G|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.E842G|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.E889G|LHCGR_ENST00000420913.3_Intron|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.E889G	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	185					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.E889G(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCAACTACTGAAAAATCACAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	88	88					2																	48873757		2203	4300	6503	48727261	SO:0001583	missense	286749			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.554A>G	2.37:g.48873757A>G	ENSP00000384597:p.Glu185Gly		48727261	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.907920	0.72868	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000448460;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T;T	0.52526	2.83;2.82;2.83;2.83;3.02;1.03;0.66	5.29	4.11	0.48088	.	0.392324	0.23782	N	0.044614	T	0.66645	0.2810	M	0.78049	2.395	0.58432	D	0.999999	D;B;D;D;P	0.89917	1.0;0.437;0.967;0.999;0.626	D;B;P;D;B	0.85130	0.997;0.115;0.69;0.979;0.34	T	0.68435	-0.5409	10	0.72032	D	0.01	.	10.0412	0.42160	0.8306:0.1693:0.0:0.0	.	151;842;889;185;889	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	G	889;889;889;889;842;184;151;194;151;185	ENSP00000385499:E889G;ENSP00000385701:E889G;ENSP00000378236:E889G;ENSP00000311493:E889G;ENSP00000378234:E842G;ENSP00000412645:E151G;ENSP00000396702:E194G	ENSP00000384597:E185G	E	+	2	0	STON1-GTF2A1L;GTF2A1L	48727261	1.000000	0.71417	0.125000	0.21846	0.975000	0.68041	3.528000	0.53524	0.987000	0.38709	0.482000	0.46254	GAA		0.418	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		G	48873757	A	G	48873757	3	3	61	1	0	0	0	0	1	0	0	0	6874	246	9	4	576	4	GTF2A1L	2	48873757	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	25677	48873757	194325616	1388	9373										
GTF2A1L	11036	broad.mit.edu	37	chr2	48897095	48897095	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacagtagtgataatgaaGaccctcaagtaaacattgta	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:48897095G>T	ENST00000403751.3	+	7	1250	c.1213G>T	c.(1213-1215)Gac>Tac	p.D405Y	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.D1109Y|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.D371Y|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.D1109Y|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.D1062Y|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.D1109Y|LHCGR_ENST00000420913.3_5'Flank|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.D1109Y	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	405					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.D1109Y(2)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGATAATGAAGACCCTCAAGT	0.373																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	2											74	78	77					2																	48897095		2203	4300	6503	48750599	SO:0001583	missense	286749			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.1213G>T	2.37:g.48897095G>T	ENSP00000384597:p.Asp405Tyr		48750599	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.450396	0.43531	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000430487;ENST00000403751;ENST00000508440	T;T;T;T;T	0.13196	2.61;2.62;2.61;2.61;2.77	5.5	5.5	0.81552	.	0.194584	0.44097	D	0.000489	T	0.42494	0.1205	M	0.84082	2.675	0.80722	D	1	D;D;D;D;D	0.76494	0.993;0.998;0.999;0.984;0.996	D;P;D;D;D	0.71184	0.911;0.888;0.966;0.914;0.972	T	0.41413	-0.9510	10	0.87932	D	0	.	17.9581	0.89075	0.0:0.0:1.0:0.0	.	371;1062;1109;405;1109	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	Y	1109;1109;1109;1109;1062;404;371;405;54	ENSP00000385499:D1109Y;ENSP00000385701:D1109Y;ENSP00000378236:D1109Y;ENSP00000311493:D1109Y;ENSP00000378234:D1062Y	ENSP00000384597:D405Y	D	+	1	0	STON1-GTF2A1L;GTF2A1L	48750599	1.000000	0.71417	0.988000	0.46212	0.130000	0.20726	7.046000	0.76592	2.584000	0.87258	0.561000	0.74099	GAC		0.373	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		T	48897095	G	T	48897095	3	4	61	1	0	0	0	0	1	0	0	0	6874	942	33	2	1239	2	GTF2A1L	2	48897095	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23338	48897095	194302278	1389	9374										
FSHR	2492	broad.mit.edu	37	chr2	49191105	49191105	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaattggatgaagctcagaGctagaaaaatacaaaaagaa	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:49191105G>A	ENST00000406846.2	-	10	974	c.855C>T	c.(853-855)atC>atT	p.I285I	FSHR_ENST00000541117.1_Splice_Site_p.I21I|FSHR_ENST00000304421.4_Splice_Site_p.I259I|FSHR_ENST00000346173.3_Splice_Site_p.L223L	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	285					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)	p.I285I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		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)|Suramin(DB04786)|Urofollitropin(DB00094)	GAAGCTCAGAGCTAGAAAAAT	0.378									Gonadal Dysgenesis, 46 XX																																							1	Substitution - coding silent(1)	large_intestine(1)	2											72	71	71					2																	49191105		2202	4300	6502	49044609	SO:0001630	splice_region_variant	2492	Familial Cancer Database			CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.855-1C>T	2.37:g.49191105G>A			49044609	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Silent	SNP	ENST00000406846.2	37	CCDS1843.1																																																																																				0.378	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		Silent	A	49191105	G	A	49191105	5	1	61	1	0	0	0	0	0	0	1	0	6092	985	34	3	1236	3	FSHR	2	49191105	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	294010	49191105	194008268	1390	9375										
NRXN1	9378	broad.mit.edu	37	chr2	50779858	50779858	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccatctagcatctcaatAgcaaagaagtccacctttat	6	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:50779858A>G	ENST00000406316.2	-	9	3102	c.1626T>C	c.(1624-1626)gcT>gcC	p.A542A	NRXN1_ENST00000406859.3_Silent_p.A542A|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000402717.3_Silent_p.A534A|NRXN1_ENST00000401669.2_Silent_p.A542A|NRXN1_ENST00000405472.3_Silent_p.A534A|NRXN1_ENST00000404971.1_Silent_p.A582A	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	542	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.A542A(1)|p.A583A(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCATCTCAATAGCAAAGAAGT	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	2											170	156	161					2																	50779858		1913	4119	6032	50633362	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1626T>C	2.37:g.50779858A>G			50633362	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.448	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			G	50779858	A	G	50779858	2	3	61	1	0	0	0	0	0	0	0	1	10696	407	15	4		4	NRXN1	2	50779858	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1588753	50779858	192419515	1391	9376										
ASB3	100302652	broad.mit.edu	37	chr2	53941710	53941710	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtaagtggtattaacaagTccaagattctataaatacac	6	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:53941710T>G	ENST00000263634.3	-	7	925	c.791A>C	c.(790-792)gAc>gCc	p.D264A	ASB3_ENST00000406625.2_Missense_Mutation_p.D299A|GPR75-ASB3_ENST00000406687.1_Missense_Mutation_p.D191A|GPR75-ASB3_ENST00000394717.2_Missense_Mutation_p.D191A|GPR75-ASB3_ENST00000482829.1_5'UTR|GPR75-ASB3_ENST00000352846.3_Missense_Mutation_p.D302A|ASB3_ENST00000498475.2_5'UTR	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough									p.D264A(1)									TATTAACAAGTCCAAGATTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	84	84					2																	53941710		2203	4300	6503	53795214	SO:0001583	missense	51130				CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.791A>C	2.37:g.53941710T>G	ENSP00000263634:p.Asp264Ala		53795214		Missense_Mutation	SNP	ENST00000263634.3	37	CCDS1846.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.378046	0.42105	.	.	ENSG00000115239	ENST00000263634;ENST00000406625;ENST00000406687;ENST00000394717;ENST00000352846;ENST00000446049	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	6.02	6.02	0.97574	Ankyrin repeat-containing domain (4);	0.372798	0.33591	N	0.004757	T	0.62539	0.2436	L	0.39245	1.2	0.30502	N	0.770254	P;B;B	0.38395	0.629;0.126;0.075	B;B;B	0.44315	0.446;0.08;0.055	T	0.68918	-0.5282	9	0.51188	T	0.08	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	181;299;264	B4DZX6;Q2TAI4;Q9Y575	.;.;ASB3_HUMAN	A	264;299;191;191;302;181	ENSP00000263634:D264A;ENSP00000385085:D299A;ENSP00000384728:D191A;ENSP00000378206:D191A;ENSP00000313756:D302A	ENSP00000263634:D264A	D	-	2	0	ASB3	53795214	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.582000	0.36568	2.311000	0.77944	0.533000	0.62120	GAC		0.373	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3			G	53941710	T	G	53941710	3	3	61	1	0	0	0	0	1	0	0	0	1025	1667	58	4	781	4	ASB3	2	53941710	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3161852	53941710	189257663	1392	9377										
ERLEC1	27248	broad.mit.edu	37	chr2	54045093	54045093	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgaaaatggacttctttCtctccccaactaaaggatat	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54045093C>A	ENST00000185150.4	+	14	1570	c.1439C>A	c.(1438-1440)tCt>tAt	p.S480Y	ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ERLEC1_ENST00000378239.5_Missense_Mutation_p.S426Y|ERLEC1_ENST00000405123.3_Missense_Mutation_p.S454Y|ASB3_ENST00000498475.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	480					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)	p.S480Y(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						GGACTTCTTTCTCTCCCCAAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	111	110					2																	54045093		2203	4298	6501	53898597	SO:0001583	missense	27248			AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"erlectin 1"	611229	"chromosome 2 open reading frame 30"	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.1439C>A	2.37:g.54045093C>A	ENSP00000185150:p.Ser480Tyr		53898597	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	37	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.766167	0.49574	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	T;T	0.48201	0.86;0.82	5.99	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	.	.	.	0.30477	N	0.772752	P;P;P	0.40794	0.651;0.686;0.729	B;B;B	0.42555	0.391;0.234;0.386	T	0.53514	-0.8428	9	0.72032	D	0.01	-7.3783	11.5161	0.50522	0.0:0.8611:0.0:0.1389	.	426;454;480	Q96DZ1-2;B5MC72;Q96DZ1	.;.;ERLEC_HUMAN	Y	454;480;426	ENSP00000385629:S454Y;ENSP00000185150:S480Y	ENSP00000185150:S480Y	S	+	2	0	ERLEC1	53898597	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.395000	0.66291	0.875000	0.35847	-0.140000	0.14226	TCT		0.358	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701		A	54045093	C	A	54045093	3	1	61	1	0	0	0	0	1	0	0	0	5244	913	32	2	1493	2	ERLEC1	2	54045093	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103383	54045093	189154280	1393	9378										
PSME4	23198	broad.mit.edu	37	chr2	54114518	54114518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcaatttctccagaattCgagcagtaaactcagggaca	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54114518C>T	ENST00000404125.1	-	40	4662	c.4607G>A	c.(4606-4608)cGa>cAa	p.R1536Q	PSME4_ENST00000476586.1_5'Flank|PSME4_ENST00000421748.2_Missense_Mutation_p.R680Q	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1536					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.R1422Q(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CTCCAGAATTCGAGCAGTAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	115	118					2																	54114518		2203	4300	6503	53968022	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.4607G>A	2.37:g.54114518C>T	ENSP00000384211:p.Arg1536Gln		53968022	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737910	0.89573	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.64803	-0.12;-0.12	5.33	5.33	0.75918	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67154	0.2863	L	0.57536	1.79	0.80722	D	1	P;D;D;D	0.62365	0.868;0.991;0.991;0.987	B;P;P;B	0.51229	0.294;0.663;0.663;0.351	T	0.61946	-0.6958	10	0.13108	T	0.6	-3.9897	19.3798	0.94527	0.0:1.0:0.0:0.0	.	911;680;680;1536	Q14997-2;Q14997-3;F8WB44;Q14997	.;.;.;PSME4_HUMAN	Q	680;1536	ENSP00000410830:R680Q;ENSP00000384211:R1536Q	ENSP00000384211:R1536Q	R	-	2	0	PSME4	53968022	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.715000	0.84713	2.644000	0.89710	0.655000	0.94253	CGA		0.393	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		T	54114518	C	T	54114518	3	4	61	1	0	0	0	0	1	0	0	0	12743	884	31	1	952	1	PSME4	2	54114518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69425	54114518	189084855	1394	9379										
PSME4	23198	broad.mit.edu	37	chr2	54120830	54120830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaaagaggcaaaaacgtCgtggattaaacttatctttt	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54120830C>T	ENST00000404125.1	-	35	4074	c.4019G>A	c.(4018-4020)cGa>cAa	p.R1340Q	PSME4_ENST00000421748.2_Missense_Mutation_p.R484Q	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1340					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.R1226Q(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GCAAAAACGTCGTGGATTAAA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	84	81					2																	54120830		2202	4297	6499	53974334	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.4019G>A	2.37:g.54120830C>T	ENSP00000384211:p.Arg1340Gln		53974334	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	C	33	5.247654	0.95305	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.22336	1.96;1.96	5.56	5.56	0.83823	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.40498	0.1119	M	0.63428	1.95	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.978	P;P;B	0.61940	0.634;0.896;0.351	T	0.07966	-1.0745	10	0.12103	T	0.63	.	19.5336	0.95240	0.0:1.0:0.0:0.0	.	715;484;1340	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	Q	484;1340	ENSP00000410830:R484Q;ENSP00000384211:R1340Q	ENSP00000384211:R1340Q	R	-	2	0	PSME4	53974334	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.861000	0.69553	2.637000	0.89404	0.455000	0.32223	CGA		0.279	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		T	54120830	C	T	54120830	3	4	61	1	0	0	0	0	1	0	0	0	12743	884	31	1	1560	1	PSME4	2	54120830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6312	54120830	189078543	1395	9380										
PSME4	23198	broad.mit.edu	37	chr2	54127071	54127071	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaattccttccttaattttTtctgggctaagcaatatctg	5	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54127071T>G	ENST00000404125.1	-	29	3424	c.3369A>C	c.(3367-3369)gaA>gaC	p.E1123D	PSME4_ENST00000421748.2_Missense_Mutation_p.E267D	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1123					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.E1009D(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CCTTAATTTTTTCTGGGCTAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											186	188	187					2																	54127071		2203	4300	6503	53980575	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3369A>C	2.37:g.54127071T>G	ENSP00000384211:p.Glu1123Asp		53980575	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096786	0.56075	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.26067	1.78;1.76	5.63	-1.02	0.10135	Armadillo-type fold (1);	0.049718	0.85682	D	0.000000	T	0.16896	0.0406	L	0.55481	1.735	0.41164	D	0.986114	B;B;B	0.18310	0.027;0.026;0.004	B;B;B	0.16289	0.009;0.015;0.004	T	0.06862	-1.0803	10	0.29301	T	0.29	.	2.6651	0.05041	0.1105:0.1823:0.1141:0.5931	.	498;267;1123	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	D	267;1123	ENSP00000410830:E267D;ENSP00000384211:E1123D	ENSP00000384211:E1123D	E	-	3	2	PSME4	53980575	0.994000	0.37717	0.986000	0.45419	0.964000	0.63967	0.071000	0.14594	0.054000	0.16065	0.533000	0.62120	GAA		0.343	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54127071	T	G	54127071	3	3	61	1	0	0	0	0	1	0	0	0	12743	1838	64	4	2234	4	PSME4	2	54127071	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6241	54127071	189072302	1396	9381										
PSME4	23198	broad.mit.edu	37	chr2	54131204	54131204	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgtctatcaggccttaaGaactccaaaaccaagggaat	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54131204G>T	ENST00000404125.1	-	27	3088	c.3033C>A	c.(3031-3033)ttC>ttA	p.F1011L	PSME4_ENST00000421748.2_Missense_Mutation_p.F155L	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1011					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.F897L(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CAGGCCTTAAGAACTCCAAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											115	117	116					2																	54131204		2203	4300	6503	53984708	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3033C>A	2.37:g.54131204G>T	ENSP00000384211:p.Phe1011Leu		53984708	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	G	9.563	1.119056	0.20877	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.60424	0.19;0.19	5.7	1.91	0.25777	Armadillo-like helical (1);Armadillo-type fold (1);	0.051026	0.85682	D	0.000000	T	0.28896	0.0717	N	0.04203	-0.255	0.54753	D	0.999984	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.06499	-1.0823	10	0.11182	T	0.66	.	10.1985	0.43069	0.322:0.0:0.678:0.0	.	386;155;1011	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	L	155;1011	ENSP00000410830:F155L;ENSP00000384211:F1011L	ENSP00000384211:F1011L	F	-	3	2	PSME4	53984708	0.990000	0.36364	0.999000	0.59377	0.993000	0.82548	0.190000	0.17057	0.766000	0.33244	-0.136000	0.14681	TTC		0.378	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		T	54131204	G	T	54131204	3	4	61	1	0	0	0	0	1	0	0	0	12743	933	33	2	2578	2	PSME4	2	54131204	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4133	54131204	189068169	1397	9382										
PSME4	23198	broad.mit.edu	37	chr2	54135500	54135500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaagttgaagcttttccatCgggagtcaaattcatgcttg	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54135500C>T	ENST00000404125.1	-	24	2796	c.2741G>A	c.(2740-2742)cGa>cAa	p.R914Q	PSME4_ENST00000421748.2_Missense_Mutation_p.R58Q	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	914					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.R800Q(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GCTTTTCCATCGGGAGTCAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											57	57	57					2																	54135500		2203	4298	6501	53989004	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2741G>A	2.37:g.54135500C>T	ENSP00000384211:p.Arg914Gln		53989004	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070342	0.76301	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.13657	2.57;2.57	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	L	0.45352	1.415	0.80722	D	1	D;D;P	0.89917	0.96;1.0;0.868	P;D;B	0.72338	0.527;0.977;0.143	T	0.02654	-1.1128	10	0.11182	T	0.66	.	19.0819	0.93186	0.0:1.0:0.0:0.0	.	289;58;914	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	Q	58;914	ENSP00000410830:R58Q;ENSP00000384211:R914Q	ENSP00000384211:R914Q	R	-	2	0	PSME4	53989004	1.000000	0.71417	0.989000	0.46669	0.988000	0.76386	7.818000	0.86416	2.486000	0.83907	0.655000	0.94253	CGA		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		T	54135500	C	T	54135500	3	4	61	1	0	0	0	0	1	0	0	0	12743	884	31	1	2882	1	PSME4	2	54135500	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4296	54135500	189063873	1398	9383										
SPTBN1	6711	broad.mit.edu	37	chr2	54873343	54873343	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctccagaccctccagaaaGaaatccaggggcaccagcct	8	17	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:54873343G>T	ENST00000356805.4	+	23	4878	c.4597G>T	c.(4597-4599)Gaa>Taa	p.E1533*	SPTBN1_ENST00000333896.5_Nonsense_Mutation_p.E1520*	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1533					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.E1533*(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CCTCCAGAAAGAAATCCAGGG	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											100	110	107					2																	54873343		2203	4300	6503	54726847	SO:0001587	stop_gained	6711				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.4597G>T	2.37:g.54873343G>T	ENSP00000349259:p.Glu1533*		54726847	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Nonsense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	48	14.058704	0.99777	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5596	0.99324	0.0:0.0:1.0:0.0	.	.	.	.	X	1533;1520	.	ENSP00000334156:E1520X	E	+	1	0	SPTBN1	54726847	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	9.769000	0.98969	2.868000	0.98415	0.555000	0.69702	GAA		0.527	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54873343	G	T	54873343	4	4	61	1	0	0	0	0	0	1	0	0	15158	943	33	2	4796	2	SPTBN1	2	54873343	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	737843	54873343	188326030	1399	9384										
RTN4	57142	broad.mit.edu	37	chr2	55252757	55252757	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatctgcaaaggaattttCtcctttttgctcaatgttga	6	9	3	1	rs151330533		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55252757C>A	ENST00000337526.6	-	3	2721	c.2478G>T	c.(2476-2478)gaG>gaT	p.E826D	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.E620D|RTN4_ENST00000404909.1_Missense_Mutation_p.E620D|RTN4_ENST00000354474.6_Missense_Mutation_p.E594D|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Missense_Mutation_p.E620D|RTN4_ENST00000357376.3_Missense_Mutation_p.E620D	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	826					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.E620D(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						AAGGAATTTTCTCCTTTTTGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	82	82					2																	55252757		2203	4300	6503	55106261	SO:0001583	missense	57142			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.2478G>T	2.37:g.55252757C>A	ENSP00000337838:p.Glu826Asp		55106261	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	C	9.844	1.191805	0.21954	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.24908	1.84;1.84;1.83;1.84;1.84;1.89	5.45	3.56	0.40772	.	0.231244	0.44483	D	0.000458	T	0.18923	0.0454	L	0.56769	1.78	0.29050	N	0.884554	P	0.37636	0.603	B	0.28385	0.089	T	0.16778	-1.0391	10	0.42905	T	0.14	-5.5058	5.8923	0.18919	0.1381:0.632:0.0:0.2299	.	826	Q9NQC3	RTN4_HUMAN	D	620;620;826;620;620;594	ENSP00000384471:E620D;ENSP00000349944:E620D;ENSP00000337838:E826D;ENSP00000378109:E620D;ENSP00000385650:E620D;ENSP00000346465:E594D	ENSP00000337838:E826D	E	-	3	2	RTN4	55106261	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.675000	0.25232	1.184000	0.42957	-0.345000	0.07892	GAG		0.358	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			A	55252757	C	A	55252757	3	1	61	1	0	0	0	0	1	0	0	0	13765	912	32	2	1166	2	RTN4	2	55252757	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	379414	55252757	187946616	1400	9385										
RTN4	57142	broad.mit.edu	37	chr2	55252835	55252835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgagcttaaaagattcCaaatatggctttcctccctc	5	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55252835C>A	ENST00000337526.6	-	3	2643	c.2400G>T	c.(2398-2400)ttG>ttT	p.L800F	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.L594F|RTN4_ENST00000404909.1_Missense_Mutation_p.L594F|RTN4_ENST00000354474.6_Missense_Mutation_p.L568F|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Missense_Mutation_p.L594F|RTN4_ENST00000357376.3_Missense_Mutation_p.L594F	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	800					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.L594F(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						TAAAAGATTCCAAATATGGCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											88	88	88					2																	55252835		2203	4300	6503	55106339	SO:0001583	missense	57142			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.2400G>T	2.37:g.55252835C>A	ENSP00000337838:p.Leu800Phe		55106339	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434727	0.43224	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.30981	1.53;1.53;1.51;1.53;1.53;1.6	5.45	3.44	0.39384	.	0.000000	0.50627	D	0.000103	T	0.50480	0.1618	M	0.71581	2.175	0.40254	D	0.978109	D	0.76494	0.999	D	0.85130	0.997	T	0.49995	-0.8879	10	0.72032	D	0.01	-7.478	8.6826	0.34218	0.0:0.7456:0.0:0.2544	.	800	Q9NQC3	RTN4_HUMAN	F	594;594;800;594;594;568	ENSP00000384471:L594F;ENSP00000349944:L594F;ENSP00000337838:L800F;ENSP00000378109:L594F;ENSP00000385650:L594F;ENSP00000346465:L568F	ENSP00000337838:L800F	L	-	3	2	RTN4	55106339	0.993000	0.37304	1.000000	0.80357	0.960000	0.62799	0.128000	0.15810	0.509000	0.28195	0.655000	0.94253	TTG		0.368	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			A	55252835	C	A	55252835	3	1	61	1	0	0	0	0	1	0	0	0	13765	593	21	2	1244	2	RTN4	2	55252835	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78	55252835	187946538	1401	9386										
RTN4	57142	broad.mit.edu	37	chr2	55254501	55254501	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtattcatgttctttgaaaGaagcggctgagagaggagac	14	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55254501G>T	ENST00000337526.6	-	3	977	c.734C>A	c.(733-735)tCt>tAt	p.S245Y	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.S39Y|RTN4_ENST00000404909.1_Missense_Mutation_p.S39Y|RTN4_ENST00000354474.6_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Missense_Mutation_p.S39Y|RTN4_ENST00000357376.3_Missense_Mutation_p.S39Y	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	245					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.S39Y(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						TTCTTTGAAAGAAGCGGCTGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	73	72					2																	55254501		2203	4300	6503	55108005	SO:0001583	missense	57142			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.734C>A	2.37:g.55254501G>T	ENSP00000337838:p.Ser245Tyr		55108005	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826625	0.71143	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000427710	T;T;T;T;T	0.23754	1.89;1.89;2.25;1.89;1.89	6.02	6.02	0.97574	.	0.615249	0.16136	N	0.227948	T	0.39306	0.1073	L	0.59436	1.845	0.80722	D	1	D	0.56521	0.976	P	0.47744	0.556	T	0.18903	-1.0322	10	0.72032	D	0.01	-1.7326	20.547	0.99278	0.0:0.0:1.0:0.0	.	245	Q9NQC3	RTN4_HUMAN	Y	39;39;245;39;39;39	ENSP00000384471:S39Y;ENSP00000349944:S39Y;ENSP00000337838:S245Y;ENSP00000378109:S39Y;ENSP00000385650:S39Y	ENSP00000337838:S245Y	S	-	2	0	RTN4	55108005	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.778000	0.75043	2.850000	0.98022	0.650000	0.86243	TCT		0.443	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			T	55254501	G	T	55254501	3	4	61	1	0	0	0	0	1	0	0	0	13765	942	33	2	2910	2	RTN4	2	55254501	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1666	55254501	187944872	1402	9387										
C2orf63	130162	broad.mit.edu	37	chr2	55444966	55444966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgcttcaagttggattgTtcttttcctgtaatatacca	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55444966T>C	ENST00000401408.1	-	4	691	c.346A>G	c.(346-348)Aca>Gca	p.T116A	CLHC1_ENST00000494539.1_Intron|AC012358.7_ENST00000366153.2_RNA|CLHC1_ENST00000407122.1_Missense_Mutation_p.T116A|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_5'UTR	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	116								p.T116A(2)									AGTTGGATTGTTCTTTTCCTG	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	2											110	103	105					2																	55444966		2203	4299	6502	55298470	SO:0001583	missense	130162				CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 63"	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.346A>G	2.37:g.55444966T>C	ENSP00000384869:p.Thr116Ala		55298470	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	T	0.929	-0.713221	0.03206	.	.	ENSG00000162994	ENST00000407122;ENST00000401408	T;T	0.14640	2.49;2.49	5.96	2.21	0.28008	.	0.987148	0.08251	N	0.974541	T	0.07863	0.0197	N	0.20766	0.605	0.58432	D	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.29701	-1.0003	10	0.02654	T	1	-0.018	8.81	0.34961	0.0:0.3399:0.0:0.6601	.	116	Q8NHS4	CB063_HUMAN	A	116	ENSP00000385778:T116A;ENSP00000384869:T116A	ENSP00000384869:T116A	T	-	1	0	C2orf63	55298470	0.095000	0.21747	0.279000	0.24732	0.953000	0.61014	0.215000	0.17562	0.475000	0.27415	0.533000	0.62120	ACA		0.368	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		C	55444966	T	C	55444966	3	2	61	1	0	0	0	0	1	0	0	0	2188	1725	60	4	1454	4	C2orf63	2	55444966	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	190465	55444966	187754407	1403	9388										
CCDC88A	55704	broad.mit.edu	37	chr2	55536322	55536322	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggaggagatgggtcataaAatttgtattgatccataatt	10	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55536322A>C	ENST00000436346.1	-	24	4989	c.4148T>G	c.(4147-4149)tTt>tGt	p.F1383C	CCDC88A_ENST00000336838.6_Missense_Mutation_p.F1382C|CCDC88A_ENST00000422883.2_Missense_Mutation_p.F6C|CCDC88A_ENST00000413716.2_Missense_Mutation_p.F1382C|AC012358.8_ENST00000366287.4_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.F1383C	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1383					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.F1383C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						TGGGTCATAAAATTTGTATTG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	47	47					2																	55536322		2197	4284	6481	55389826	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4148T>G	2.37:g.55536322A>C	ENSP00000410608:p.Phe1383Cys		55389826	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	21.9|21.9|21.9	4.218355|4.218355|4.218355	0.79464|0.79464|0.79464	.|.|.	.|.|.	ENSG00000115355|ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000444458|ENST00000456975	T;T;T;T;T;T|.|.	0.58652|.|.	0.32;0.32;0.32;0.32;0.32;0.32|.|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|0.000000|.	0.49916|0.49916|.	U|U|.	0.000140|0.000140|.	T|T|T	0.72859|0.72859|0.72859	0.3513|0.3513|0.3513	M|M|M	0.65498|0.65498|0.65498	2.005|2.005|2.005	0.37516|0.37516|0.37516	D|D|D	0.917333|0.917333|0.917333	P;D;D;D;D;P;D|.|.	0.89917|.|.	0.884;1.0;1.0;1.0;1.0;0.849;1.0|.|.	P;D;D;D;D;P;D|.|.	0.91635|.|.	0.465;0.998;0.974;0.999;0.984;0.523;0.984|.|.	T|T|T	0.75611|0.75611|0.75611	-0.3258|-0.3258|-0.3258	10|7|5	0.66056|0.87932|.	D|D|.	0.02|0|.	-17.7153|-17.7153|-17.7153	16.2055|16.2055|16.2055	0.82126|0.82126|0.82126	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	1382;1383;1328;6;1383;1382;1382|.|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.|.	.;.;.;.;GRDN_HUMAN;.;.|.|.	C|V|M	1382;1383;1383;6;428;1382;558|8|363	ENSP00000338728:F1382C;ENSP00000263630:F1383C;ENSP00000410608:F1383C;ENSP00000390012:F428C;ENSP00000404431:F1382C;ENSP00000405080:F558C|.|.	ENSP00000263630:F1383C|ENSP00000413401:F8V|.	F|F|I	-|-|-	2|1|3	0|0|3	CCDC88A|CCDC88A|CCDC88A	55389826|55389826|55389826	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.991000|0.991000|0.991000	0.79684|0.79684|0.79684	9.210000|9.210000|9.210000	0.95106|0.95106|0.95106	2.226000|2.226000|2.226000	0.72624|0.72624|0.72624	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	TTT|TTT|ATT		0.289	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55536322	A	C	55536322	3	2	61	1	0	0	0	0	1	0	0	0	2869	14	1	4	1503	4	CCDC88A	2	55536322	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	91356	55536322	187663051	1404	9389										
CCDC88A	55704	broad.mit.edu	37	chr2	55544773	55544773	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccatgtttagagataaGagattcatactctgaagcct	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55544773G>T	ENST00000436346.1	-	20	4370	c.3529C>A	c.(3529-3531)Ctt>Att	p.L1177I	CCDC88A_ENST00000336838.6_Missense_Mutation_p.L1176I|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000608103.1_RNA|CCDC88A_ENST00000413716.2_Missense_Mutation_p.L1176I|AC012358.8_ENST00000599352.1_RNA|AC012358.8_ENST00000366287.4_RNA|AC012358.8_ENST00000599475.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.L1177I|AC012358.8_ENST00000594078.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1177					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.L1177I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						TTAGAGATAAGAGATTCATAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											68	72	71					2																	55544773		2203	4300	6503	55398277	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.3529C>A	2.37:g.55544773G>T	ENSP00000410608:p.Leu1177Ile		55398277	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.135981|5.135981	0.94517|0.94517	.|.	.|.	ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000456975	T;T;T;T;T;T|.	0.64991|.	1.4;1.63;1.65;-0.13;1.43;0.52|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.41938|.	U|.	0.000792|.	D|D	0.83339|0.83339	0.5233|0.5233	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.998;0.999;0.999;0.998;1.0;0.999|.	D;D;D;D;D;D|.	0.87578|.	0.947;0.993;0.996;0.947;0.998;0.997|.	D|D	0.83994|0.83994	0.0339|0.0339	10|6	0.62326|0.59425	D|D	0.03|0.04	-4.8031|-4.8031	20.3172|20.3172	0.98658|0.98658	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1176;1177;1122;1177;1176;1176|.	B7ZM78;Q3V6T2-2;D6W5D1;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.	.;.;.;GRDN_HUMAN;.;.|.	I|Y	1176;1177;1177;222;1176;352|157	ENSP00000338728:L1176I;ENSP00000263630:L1177I;ENSP00000410608:L1177I;ENSP00000390012:L222I;ENSP00000404431:L1176I;ENSP00000405080:L352I|.	ENSP00000263630:L1177I|ENSP00000415267:S157Y	L|S	-|-	1|2	0|0	CCDC88A|CCDC88A	55398277|55398277	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.578000|9.578000	0.98200|0.98200	2.801000|2.801000	0.96364|0.96364	0.650000|0.650000	0.86243|0.86243	CTT|TCT		0.378	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		T	55544773	G	T	55544773	3	4	61	1	0	0	0	0	1	0	0	0	2869	942	33	2	2138	2	CCDC88A	2	55544773	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8451	55544773	187654600	1405	9390										
CCDC104	112942	broad.mit.edu	37	chr2	55756108	55756108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcagctgcaagccattcGaataattcaagagagaaatg	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55756108G>A	ENST00000349456.4	+	4	525	c.377G>A	c.(376-378)cGa>cAa	p.R126Q	CCDC104_ENST00000406691.3_Missense_Mutation_p.R126Q|CCDC104_ENST00000407816.3_Missense_Mutation_p.R126Q|CCDC104_ENST00000339012.3_Missense_Mutation_p.R151Q|CCDC104_ENST00000403007.3_Missense_Mutation_p.R126Q			Q96G28	CFA36_HUMAN		126								p.R126Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAAGCCATTCGAATAATTCAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	55	55					2																	55756108		2203	4300	6503	55609612	SO:0001583	missense	112942																														ENST00000349456.4:c.377G>A	2.37:g.55756108G>A	ENSP00000295117:p.Arg126Gln		55609612	Q53SF0|Q53ST9|Q6UY34	Missense_Mutation	SNP	ENST00000349456.4	37	CCDS1854.2	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829275	0.71258	.	.	ENSG00000163001	ENST00000339012;ENST00000406691;ENST00000349456;ENST00000407816;ENST00000403007	T;T;T;T;T	0.30714	2.22;1.52;2.24;2.29;1.52	6.17	5.3	0.74995	.	0.058328	0.64402	D	0.000002	T	0.28034	0.0691	L	0.34521	1.04	0.48236	D	0.999614	P;D	0.58620	0.874;0.983	B;B	0.44315	0.117;0.446	T	0.02070	-1.1219	10	0.33141	T	0.24	.	15.327	0.74172	0.0663:0.0:0.9337:0.0	.	126;151	Q96G28;Q96G28-2	CC104_HUMAN;.	Q	151;126;126;126;126	ENSP00000342699:R151Q;ENSP00000385400:R126Q;ENSP00000295117:R126Q;ENSP00000385376:R126Q;ENSP00000385972:R126Q	ENSP00000342699:R151Q	R	+	2	0	CCDC104	55609612	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.873000	0.63057	1.620000	0.50308	0.655000	0.94253	CGA		0.333	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2			A	55756108	G	A	55756108	3	1	61	1	0	0	0	0	1	0	0	0	2745	1058	37	1	391	1	CCDC104	2	55756108	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211335	55756108	187443265	1406	9391										
SMEK2	57223	broad.mit.edu	37	chr2	55825950	55825951	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttggaacagctgcaatagINSttttttaatatagccttcat							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55825950_55825951insT	ENST00000345102.5	-	4	823_824	c.522_523insA	c.(520-525)aaactafs	p.L175fs	SMEK2_ENST00000407823.3_Frame_Shift_Ins_p.L175fs|SMEK2_ENST00000272313.5_Frame_Shift_Ins_p.L175fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	175					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)		p.L175fs*15(1)		kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCTGCAATAGTTTTTTAATAT	0.401																																																1	Insertion - Frameshift(1)	large_intestine(1)	2																																								55679455	SO:0001589	frameshift_variant	57223			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.523dupA	2.37:g.55825956_55825956dupT	ENSP00000339769:p.Leu175fs		55679454	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Ins	INS	ENST00000345102.5	37	CCDS46289.1																																																																																				0.401	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		T	55825951	-	T	55825950	7	5	61	1	0	1	1	0	0	0	0	0	14831	1020	36	0	2082	0	SMEK2	2	55825950	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	69842	55825950	187373423	1407	9392										
SMEK2	57223	broad.mit.edu	37	chr2	55844384	55844384	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccattgccggtcttcgttcAgggtatagaccttcactcgc	9	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55844384A>G	ENST00000345102.5	-	1	339	c.38T>C	c.(37-39)cTg>cCg	p.L13P	SMEK2_ENST00000407823.3_Missense_Mutation_p.L13P|SMEK2_ENST00000272313.5_Missense_Mutation_p.L13P|RP11-554J4.1_ENST00000608113.1_RNA|SMEK2_ENST00000477749.1_5'UTR	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	13	WH1.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)		p.L13P(1)		kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GTCTTCGTTCAGGGTATAGAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	62	66					2																	55844384		2203	4300	6503	55697888	SO:0001583	missense	57223			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.38T>C	2.37:g.55844384A>G	ENSP00000339769:p.Leu13Pro		55697888	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	37	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.980761	0.92982	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.45276	0.9;0.9;0.9	5.06	5.06	0.68205	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.73674	0.3617	H	0.94385	3.53	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.967;0.976	T	0.82230	-0.0560	10	0.87932	D	0	-3.4817	14.9772	0.71283	1.0:0.0:0.0:0.0	.	13;13;13	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3	.;P4R3B_HUMAN;.	P	13	ENSP00000272313:L13P;ENSP00000385912:L13P;ENSP00000339769:L13P	ENSP00000272313:L13P	L	-	2	0	SMEK2	55697888	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	8.761000	0.91691	2.130000	0.65690	0.459000	0.35465	CTG		0.647	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55844384	A	G	55844384	3	3	61	1	0	0	0	0	1	0	0	0	14831	188	7	4	2579	4	SMEK2	2	55844384	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18434	55844384	187354989	1408	9393										
PNPT1	87178	broad.mit.edu	37	chr2	55872499	55872499	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacctacaacaggtccatTttcttttctagatgctcgag	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55872499T>G	ENST00000447944.2	-	22	1893	c.1807A>C	c.(1807-1809)Aat>Cat	p.N603H		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	603					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)	p.N603H(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACAGGTCCATTTTCTTTTCTA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	95	97					2																	55872499		2203	4300	6503	55726003	SO:0001583	missense	87178			BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1807A>C	2.37:g.55872499T>G	ENSP00000400646:p.Asn603His		55726003	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957743	0.73902	.	.	ENSG00000138035	ENST00000447944	T	0.63096	-0.02	5.66	5.66	0.87406	.	0.047736	0.85682	D	0.000000	T	0.59742	0.2216	N	0.25890	0.77	0.46416	D	0.999035	P	0.40376	0.715	P	0.48921	0.595	T	0.56390	-0.7987	10	0.25106	T	0.35	-8.7895	15.8851	0.79241	0.0:0.0:0.0:1.0	.	603	Q8TCS8	PNPT1_HUMAN	H	603	ENSP00000400646:N603H	ENSP00000393953:N603H	N	-	1	0	PNPT1	55726003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.644000	0.83416	2.156000	0.67533	0.528000	0.53228	AAT		0.418	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		G	55872499	T	G	55872499	3	3	61	1	0	0	0	0	1	0	0	0	12204	1841	64	4	572	4	PNPT1	2	55872499	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	28115	55872499	187326874	1409	9394										
PNPT1	87178	broad.mit.edu	37	chr2	55900192	55900192	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcctgctgtaaaatgttCtctgcagaggcttccaacat	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55900192C>A	ENST00000447944.2	-	9	788	c.702G>T	c.(700-702)gaG>gaT	p.E234D		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	234					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)	p.E234D(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GTAAAATGTTCTCTGCAGAGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	81	78					2																	55900192		2203	4300	6503	55753696	SO:0001583	missense	87178			BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.702G>T	2.37:g.55900192C>A	ENSP00000400646:p.Glu234Asp		55753696	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.839107	0.32513	.	.	ENSG00000138035	ENST00000447944	T	0.41065	1.01	5.67	-1.66	0.08265	Exoribonuclease, phosphorolytic domain 2 (2);	0.054221	0.64402	N	0.000001	T	0.15825	0.0381	N	0.05078	-0.115	0.44603	D	0.99757	B	0.12630	0.006	B	0.16289	0.015	T	0.15150	-1.0447	10	0.11485	T	0.65	-6.712	8.0781	0.30729	0.0:0.3492:0.1105:0.5403	.	234	Q8TCS8	PNPT1_HUMAN	D	234	ENSP00000400646:E234D	ENSP00000386075:E234D	E	-	3	2	PNPT1	55753696	0.905000	0.30787	0.992000	0.48379	0.997000	0.91878	0.037000	0.13840	-0.263000	0.09378	0.655000	0.94253	GAG		0.358	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		A	55900192	C	A	55900192	3	1	61	1	0	0	0	0	1	0	0	0	12204	912	32	2	1729	2	PNPT1	2	55900192	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27693	55900192	187299181	1410	9395										
PNPT1	87178	broad.mit.edu	37	chr2	55906867	55906867	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaatttaaagtactagaaGacatttcttttcttgttggg	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:55906867G>T	ENST00000447944.2	-	8	715	c.629C>A	c.(628-630)tCt>tAt	p.S210Y		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	210					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)	p.S210Y(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGTACTAGAAGACATTTCTTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	119	118					2																	55906867		2201	4299	6500	55760371	SO:0001583	missense	87178			BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.629C>A	2.37:g.55906867G>T	ENSP00000400646:p.Ser210Tyr		55760371	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.915653	0.73098	.	.	ENSG00000138035	ENST00000447944	T	0.50277	0.75	5.0	5.0	0.66597	Exoribonuclease, phosphorolytic domain 2 (2);	0.341607	0.31167	N	0.008137	T	0.58949	0.2158	M	0.62088	1.915	0.49798	D	0.999821	P	0.36660	0.564	P	0.46419	0.516	T	0.63382	-0.6650	10	0.87932	D	0	-11.5326	18.3432	0.90313	0.0:0.0:1.0:0.0	.	210	Q8TCS8	PNPT1_HUMAN	Y	210	ENSP00000400646:S210Y	ENSP00000386075:S210Y	S	-	2	0	PNPT1	55760371	1.000000	0.71417	0.987000	0.45799	0.969000	0.65631	4.827000	0.62723	2.517000	0.84864	0.549000	0.68633	TCT		0.323	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		T	55906867	G	T	55906867	3	4	61	1	0	0	0	0	1	0	0	0	12204	942	33	2	1806	2	PNPT1	2	55906867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6675	55906867	187292506	1411	9396										
VRK2	7444	broad.mit.edu	37	chr2	58312046	58312046	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatggcccgttattttcaGaacttaaattttatcagaga	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:58312046G>T	ENST00000435505.2	+	7	962	c.217G>T	c.(217-219)Gaa>Taa	p.E73*	VRK2_ENST00000440705.2_Nonsense_Mutation_p.E50*|VRK2_ENST00000340157.4_Nonsense_Mutation_p.E73*|VRK2_ENST00000412104.2_Nonsense_Mutation_p.E73*|VRK2_ENST00000417641.2_Nonsense_Mutation_p.E73*			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	73	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E73Q(1)|p.E73*(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						GTTATTTTCAGAACTTAAATT	0.279																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	2											19	20	19					2																	58312046		2181	4269	6450	58165550	SO:0001587	stop_gained	7444			AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.217G>T	2.37:g.58312046G>T	ENSP00000408002:p.Glu73*		58165550	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Nonsense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	g	34	5.343043	0.95783	.	.	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000423109;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705;ENST00000428021	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-29.6085	18.95	0.92638	0.0:0.0:1.0:0.0	.	.	.	.	X	73;73;73;73;73;73;50;78	.	ENSP00000342381:E73X	E	+	1	0	VRK2	58165550	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.952000	0.87827	2.775000	0.95449	0.586000	0.80456	GAA		0.279	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		T	58312046	G	T	58312046	4	4	61	1	0	0	0	0	0	1	0	0	17260	943	33	2	227	2	VRK2	2	58312046	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2405179	58312046	184887327	1412	9397										
FANCL	55120	broad.mit.edu	37	chr2	58388666	58388666	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattttttacctcatataaGcatatttgatggaaaggttg	7	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:58388666G>A	ENST00000233741.4	-	12	1047	c.1011C>T	c.(1009-1011)tgC>tgT	p.C337C	FANCL_ENST00000402135.3_Silent_p.C342C|FANCL_ENST00000403676.1_Silent_p.C220C|FANCL_ENST00000403295.3_Silent_p.C309C	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	337					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C337C(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						CCTCATATAAGCATATTTGAT	0.333								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - coding silent(1)	large_intestine(1)	2											81	86	84					2																	58388666		2202	4298	6500	58242170	SO:0001819	synonymous_variant	55120	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"Zinc fingers, PHD-type", "Fanconi anemia, complementation groups"	20748	protein-coding gene	gene with protein product		608111	"PHD finger protein 9"	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.1011C>T	2.37:g.58388666G>A			58242170	Q6GU60	Silent	SNP	ENST00000233741.4	37	CCDS1860.1																																																																																				0.333	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		A	58388666	G	A	58388666	2	1	61	1	0	0	0	0	0	0	0	1	5689	963	34	3		3	FANCL	2	58388666	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76620	58388666	184810707	1413	9398										
BCL11A	53335	broad.mit.edu	37	chr2	60679729	60679729	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagaacttaagggctctcGagcttccatccgaaaactgc	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:60679729G>A	ENST00000359629.5	-	5	999	c.703C>T	c.(703-705)Cga>Tga	p.R235*	BCL11A_ENST00000537768.1_Missense_Mutation_p.S437L|BCL11A_ENST00000538214.1_Nonsense_Mutation_p.R785*|BCL11A_ENST00000356842.4_Missense_Mutation_p.S768L	NM_138559.1	NP_612569.1	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	0					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)	p.S768L(1)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AAGGGCTCTCGAGCTTCCATC	0.557			T	IGH@	B-CLL																																		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	1	Substitution - Missense(1)	large_intestine(1)	2											87	93	91					2																	60679729		2203	4300	6503	60533233	SO:0001587	stop_gained	53335			AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000359629.5:c.703C>T	2.37:g.60679729G>A	ENSP00000352648:p.Arg235*		60533233	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Nonsense_Mutation	SNP	ENST00000359629.5	37	CCDS46295.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.299358|6.299358	0.97453|0.97453	.|.	.|.	ENSG00000119866|ENSG00000119866	ENST00000359629;ENST00000538214|ENST00000356842;ENST00000378117;ENST00000537768	.|T;T	.|0.08370	.|3.1;3.23	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|.	.|.	.|.	.|.	.|T	.|0.09862	.|0.0242	.|.	.|.	.|.	0.31928|0.31928	N|N	0.612505|0.612505	.|B;B	.|0.28208	.|0.08;0.203	.|B;B	.|0.15052	.|0.012;0.012	.|T	.|0.03278	.|-1.1053	.|8	0.07325|0.87932	T|D	0.83|0	.|.	18.5018|18.5018	0.90884|0.90884	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|437;768	.|B4DT16;D9YZV9	.|.;.	X|L	235;785|768;793;437	.|ENSP00000349300:S768L;ENSP00000443712:S437L	ENSP00000352648:R235X|ENSP00000349300:S768L	R|S	-|-	1|2	2|0	BCL11A|BCL11A	60533233|60533233	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.069000|6.069000	0.71209|0.71209	2.810000|2.810000	0.96702|0.96702	0.650000|0.650000	0.86243|0.86243	CGA|TCG		0.557	BCL11A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325349.2	NM_022893		A	60679729	G	A	60679729	4	1	61	1	0	0	0	0	0	1	0	0	1364	1068	37	1	32	1	BCL11A	2	60679729	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2291063	60679729	182519644	1414	9399										
PAPOLG	64895	broad.mit.edu	37	chr2	60996020	60996020	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaagatggcattagaaacTtaagagtaagtatcctctgg	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:60996020T>G	ENST00000238714.3	+	5	682	c.433T>G	c.(433-435)Tta>Gta	p.L145V		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	145					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.L145V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			CATTAGAAACTTAAGAGTAAG	0.289																																					GBM(183;1497 2932 21839 46797)											1	Substitution - Missense(1)	large_intestine(1)	2											34	36	35					2																	60996020		2200	4292	6492	60849524	SO:0001583	missense	64895			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.433T>G	2.37:g.60996020T>G	ENSP00000238714:p.Leu145Val		60849524	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812436	0.50527	.	.	ENSG00000115421	ENST00000238714	.	.	.	5.61	3.23	0.37069	Nucleotidyl transferase domain (1);Poly(A) polymerase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	M	0.65677	2.01	0.51767	D	0.999936	P	0.38745	0.645	P	0.55545	0.778	T	0.69957	-0.5004	9	0.72032	D	0.01	-21.8176	8.1563	0.31171	0.0:0.2363:0.0:0.7637	.	145	Q9BWT3	PAPOG_HUMAN	V	145	.	ENSP00000238714:L145V	L	+	1	2	PAPOLG	60849524	0.999000	0.42202	0.998000	0.56505	0.990000	0.78478	3.260000	0.51523	0.422000	0.26005	0.402000	0.26972	TTA		0.289	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		G	60996020	T	G	60996020	3	3	61	1	0	0	0	0	1	0	0	0	11462	1606	56	4	451	4	PAPOLG	2	60996020	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	316291	60996020	182203353	1415	9400										
PAPOLG	64895	broad.mit.edu	37	chr2	61024275	61024275	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtcatcaaaaattccattCgactgacccttaatcggtaa	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61024275C>T	ENST00000238714.3	+	22	2440	c.2191C>T	c.(2191-2193)Cga>Tga	p.R731*		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	731					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.R731*(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			AAATTCCATTCGACTGACCCT	0.398																																					GBM(183;1497 2932 21839 46797)											1	Substitution - Nonsense(1)	large_intestine(1)	2											127	114	118					2																	61024275		2203	4300	6503	60877779	SO:0001587	stop_gained	64895			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.2191C>T	2.37:g.61024275C>T	ENSP00000238714:p.Arg731*		60877779	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Nonsense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156349	0.78114	.	.	ENSG00000115421	ENST00000238714;ENST00000378104;ENST00000412217	.	.	.	5.64	3.68	0.42216	.	0.158262	0.53938	D	0.000051	.	.	.	.	.	.	0.44352	D	0.997241	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.4719	13.9315	0.63998	0.373:0.627:0.0:0.0	.	.	.	.	X	731;398;377	.	ENSP00000238714:R731X	R	+	1	2	PAPOLG	60877779	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.887000	0.56197	1.460000	0.47911	0.591000	0.81541	CGA		0.398	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		T	61024275	C	T	61024275	4	4	61	1	0	0	0	0	0	1	0	0	11462	876	31	1	2277	1	PAPOLG	2	61024275	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28255	61024275	182175098	1416	9401										
PUS10	150962	broad.mit.edu	37	chr2	61187580	61187580	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattaattcttccactgaaGattccagcttcctttctcca	3	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61187580G>T	ENST00000316752.6	-	11	1208	c.947C>A	c.(946-948)tCt>tAt	p.S316Y	PUS10_ENST00000407787.1_Missense_Mutation_p.S316Y	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	316	RNA binding forefinger loop. {ECO:0000255}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.S316Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TTCCACTGAAGATTCCAGCTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	135	134					2																	61187580		2203	4300	6503	61041084	SO:0001583	missense	150962			AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.947C>A	2.37:g.61187580G>T	ENSP00000326003:p.Ser316Tyr		61041084	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.985137	0.74474	.	.	ENSG00000162927	ENST00000316752;ENST00000407787	T;T	0.47177	0.85;0.85	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.66973	0.2844	M	0.66378	2.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.62445	-0.6853	10	0.27785	T	0.31	-12.7691	19.0383	0.92987	0.0:0.0:1.0:0.0	.	316;316	A8K6R4;Q3MIT2	.;PUS10_HUMAN	Y	316	ENSP00000326003:S316Y;ENSP00000386074:S316Y	ENSP00000326003:S316Y	S	-	2	0	PUS10	61041084	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.783000	0.75078	2.507000	0.84556	0.455000	0.32223	TCT		0.333	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		T	61187580	G	T	61187580	3	4	61	1	0	0	0	0	1	0	0	0	12868	942	33	2	674	2	PUS10	2	61187580	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163305	61187580	182011793	1417	9402										
PUS10	150962	broad.mit.edu	37	chr2	61189977	61189977	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacttaaggaaatcctcttCctttatcttattcaaggctt	4	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61189977C>A	ENST00000316752.6	-	9	1033	c.772G>T	c.(772-774)Gaa>Taa	p.E258*	PUS10_ENST00000407787.1_Nonsense_Mutation_p.E258*	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	258					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.E258*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			AAATCCTCTTCCTTTATCTTA	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											66	62	64					2																	61189977		2196	4295	6491	61043481	SO:0001587	stop_gained	150962			AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.772G>T	2.37:g.61189977C>A	ENSP00000326003:p.Glu258*		61043481	Q5JPJ5|Q96MI8	Nonsense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	C	36	5.864136	0.97043	.	.	ENSG00000162927	ENST00000316752;ENST00000407787	.	.	.	5.46	5.46	0.80206	.	0.102234	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	1.1293	19.6784	0.95946	0.0:1.0:0.0:0.0	.	.	.	.	X	258	.	ENSP00000326003:E258X	E	-	1	0	PUS10	61043481	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.829000	0.75314	2.724000	0.93272	0.585000	0.79938	GAA		0.308	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		A	61189977	C	A	61189977	4	1	61	1	0	0	0	0	0	1	0	0	12868	864	30	2	857	2	PUS10	2	61189977	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2397	61189977	182009396	1418	9403										
PUS10	150962	broad.mit.edu	37	chr2	61235931	61235931	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcacagaattcttgaaGaattcctaggcatacattac	5	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61235931G>T	ENST00000316752.6	-	3	607	c.346C>A	c.(346-348)Ctt>Att	p.L116I	PUS10_ENST00000407787.1_Missense_Mutation_p.L116I	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	116					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.L116I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			AATTCTTGAAGAATTCCTAGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											50	52	52					2																	61235931		2202	4299	6501	61089435	SO:0001583	missense	150962			AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.346C>A	2.37:g.61235931G>T	ENSP00000326003:p.Leu116Ile		61089435	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535626	0.85812	.	.	ENSG00000162927	ENST00000316752;ENST00000407787;ENST00000421319	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.84415	0.5467	M	0.88775	2.98	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.86972	0.2098	9	0.66056	D	0.02	-15.619	16.8502	0.85992	0.0:0.0:1.0:0.0	.	116	Q3MIT2	PUS10_HUMAN	I	116	.	ENSP00000326003:L116I	L	-	1	0	PUS10	61089435	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.107000	0.71517	2.583000	0.87209	0.591000	0.81541	CTT		0.323	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		T	61235931	G	T	61235931	3	4	61	1	0	0	0	0	1	0	0	0	12868	942	33	2	1307	2	PUS10	2	61235931	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45954	61235931	181963442	1419	9404										
PEX13	5194	broad.mit.edu	37	chr2	61275624	61275624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaacaacaacccaaagtgCgtggttggcttctggctagc	11	11	1	1	rs376720470		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61275624C>T	ENST00000295030.5	+	4	969	c.931C>T	c.(931-933)Cgt>Tgt	p.R311C		NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	311	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)		p.R311C(1)		endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			ACCCAAAGTGCGTGGTTGGCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG	0,4406		0,0,2203	57	61	60		931	6	1	2		60	1,8599	1.2+/-3.3	0,1,4299	no	missense	PEX13	NM_002618.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	311/404	61275624	1,13005	2203	4300	6503	61129128	SO:0001583	missense	5194			U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"peroxisome biogenesis factor 13"			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.931C>T	2.37:g.61275624C>T	ENSP00000295030:p.Arg311Cys		61129128	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	37	CCDS1866.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.877208	0.91664	0.0	1.16E-4	ENSG00000162928	ENST00000295030	T	0.48201	0.82	5.96	5.96	0.96718	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.73837	0.3638	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.75673	-0.3236	10	0.72032	D	0.01	-11.1913	20.4082	0.99013	0.0:1.0:0.0:0.0	.	311	Q92968	PEX13_HUMAN	C	311	ENSP00000295030:R311C	ENSP00000295030:R311C	R	+	1	0	PEX13	61129128	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.724000	0.68500	2.814000	0.96858	0.655000	0.94253	CGT		0.388	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		T	61275624	C	T	61275624	3	4	61	1	0	0	0	0	1	0	0	0	11772	768	27	1	945	1	PEX13	2	61275624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39693	61275624	181923749	1420	9405										
USP34	9736	broad.mit.edu	37	chr2	61415279	61415279	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccagatatccttgtgacGacatggattgtagattcaat	9	7	1	3	rs375982399		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61415279G>A	ENST00000398571.2	-	80	10675	c.10599C>T	c.(10597-10599)gtC>gtT	p.V3533V	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3533					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.V3533V(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TCCTTGTGACGACATGGATTG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		0,3864		0,0,1932	67	64	65		10599	4.7	1	2		65	2,8272		0,2,4135	no	coding-synonymous	USP34	NM_014709.3		0,2,6067	AA,AG,GG		0.0242,0.0,0.0165		3533/3547	61415279	2,12136	1932	4137	6069	61268783	SO:0001819	synonymous_variant	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.10599C>T	2.37:g.61415279G>A			61268783	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	.	3.033	-0.199147	0.06219	0.0	2.42E-4	ENSG00000115464	ENST00000411912	.	.	.	5.52	4.65	0.58169	.	.	.	.	.	T	0.73055	0.3538	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73382	-0.4000	4	.	.	.	.	16.9441	0.86226	0.0:0.8718:0.1282:0.0	.	.	.	.	C	1210	.	.	R	-	1	0	USP34	61268783	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.524000	0.35942	1.472000	0.48140	-0.197000	0.12766	CGT		0.443	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61415279	G	A	61415279	2	1	61	1	0	0	0	0	0	0	0	1	17105	1045	37	1		1	USP34	2	61415279	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139655	61415279	181784094	1421	9406										
USP34	9736	broad.mit.edu	37	chr2	61441528	61441528	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcagaaagtttaggctgGaaaaggttccacaaatccat	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61441528G>A	ENST00000398571.2	-	68	8425	c.8349C>T	c.(8347-8349)ttC>ttT	p.F2783F	USP34_ENST00000472689.1_Intron	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2783					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.F2783F(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GTTTAGGCTGGAAAAGGTTCC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	2											89	85	86					2																	61441528		1866	4102	5968	61295032	SO:0001819	synonymous_variant	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.8349C>T	2.37:g.61441528G>A			61295032	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	6.058	0.379080	0.11466	.	.	ENSG00000115464	ENST00000411912	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	T	0.76622	0.4013	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74259	-0.3723	4	.	.	.	.	20.0108	0.97448	0.0:0.0:1.0:0.0	.	.	.	.	S	543	.	.	P	-	1	0	USP34	61295032	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.835000	0.99442	2.738000	0.93877	0.591000	0.81541	CCA		0.378	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61441528	G	A	61441528	2	1	61	1	0	0	0	0	0	0	0	1	17105	1165	41	3		3	USP34	2	61441528	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26249	61441528	181757845	1422	9407										
USP34	9736	broad.mit.edu	37	chr2	61454211	61454211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacatttcacctttctgatCgagactgttcaaccaaaaga	5	10	3	3	rs371000877		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61454211C>T	ENST00000398571.2	-	62	7662	c.7586G>A	c.(7585-7587)cGa>cAa	p.R2529Q		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2529					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R2529Q(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CCTTTCTGATCGAGACTGTTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	GLN/ARG	0,3694		0,0,1847	110	97	101		7586	5.3	1	2		101	1,8171		0,1,4085	no	missense	USP34	NM_014709.3	43	0,1,5932	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	2529/3547	61454211	1,11865	1847	4086	5933	61307715	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.7586G>A	2.37:g.61454211C>T	ENSP00000381577:p.Arg2529Gln		61307715	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	36	5.644478	0.96704	0.0	1.22E-4	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.05513	3.77;3.43	5.29	5.29	0.74685	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.10981	0.0268	L	0.59436	1.845	0.80722	D	1	P	0.47409	0.895	B	0.40940	0.344	T	0.02053	-1.1222	10	0.62326	D	0.03	.	18.9386	0.92597	0.0:1.0:0.0:0.0	.	2529	Q70CQ2	UBP34_HUMAN	Q	2377;2377;2529;807	ENSP00000381577:R2529Q;ENSP00000410559:R807Q	ENSP00000263989:R2377Q	R	-	2	0	USP34	61307715	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.745000	0.85046	2.478000	0.83669	0.650000	0.86243	CGA		0.348	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61454211	C	T	61454211	3	4	61	1	0	0	0	0	1	0	0	0	17105	884	31	1	3130	1	USP34	2	61454211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12683	61454211	181745162	1423	9408										
USP34	9736	broad.mit.edu	37	chr2	61472346	61472346	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctgaataaaacttaccGtcatctctccaccaaaacat	2	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61472346G>A	ENST00000398571.2	-	51	6702	c.6626C>T	c.(6625-6627)aCg>aTg	p.T2209M		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2209	USP.				positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.T2209M(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AAAACTTACCGTCATCTCTCC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											112	102	105					2																	61472346		1836	4094	5930	61325850	SO:0001630	splice_region_variant	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.6627+1C>T	2.37:g.61472346G>A			61325850	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747939	0.89663	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.05580	3.42;3.42	5.34	5.34	0.76211	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.14442	0.0349	L	0.44542	1.39	0.80722	D	1	B	0.34349	0.45	P	0.47573	0.55	T	0.06899	-1.0801	10	0.32370	T	0.25	.	19.391	0.94583	0.0:0.0:1.0:0.0	.	2209	Q70CQ2	UBP34_HUMAN	M	2057;2057;2209;487	ENSP00000381577:T2209M;ENSP00000410559:T487M	ENSP00000263989:T2057M	T	-	2	0	USP34	61325850	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.619000	0.98369	2.657000	0.90304	0.585000	0.79938	ACG		0.323	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		Missense_Mutation	A	61472346	G	A	61472346	5	1	61	1	0	0	0	0	0	0	1	0	17105	1159	40	1	4134	1	USP34	2	61472346	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18135	61472346	181727027	1424	9409										
USP34	9736	broad.mit.edu	37	chr2	61505526	61505526	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacatcaaattttaccttCgaatacagtcagccaaatgt	4	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61505526C>T	ENST00000398571.2	-	40	5385	c.5309G>A	c.(5308-5310)cGa>cAa	p.R1770Q		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1770					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R1770Q(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATTTTACCTTCGAATACAGTC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	2											52	47	48					2																	61505526		1802	4078	5880	61359030	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5309G>A	2.37:g.61505526C>T	ENSP00000381577:p.Arg1770Gln		61359030	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612969	0.46631	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.03860	3.93;3.78	5.22	5.22	0.72569	.	0.067743	0.56097	D	0.000033	T	0.03220	0.0094	N	0.08118	0	0.42745	D	0.993757	B	0.28082	0.2	B	0.23018	0.043	T	0.57476	-0.7805	10	0.18710	T	0.47	.	16.9682	0.86291	0.0:1.0:0.0:0.0	.	1770	Q70CQ2	UBP34_HUMAN	Q	1618;1618;1770;48	ENSP00000381577:R1770Q;ENSP00000410559:R48Q	ENSP00000263989:R1618Q	R	-	2	0	USP34	61359030	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	5.331000	0.65905	2.440000	0.82611	0.467000	0.42956	CGA		0.279	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61505526	C	T	61505526	3	4	61	1	0	0	0	0	1	0	0	0	17105	884	31	1	5495	1	USP34	2	61505526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33180	61505526	181693847	1425	9410										
USP34	9736	broad.mit.edu	37	chr2	61539018	61539018	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaataccagtgccttcaatTtgccactgtctcagatgata	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61539018T>G	ENST00000398571.2	-	26	3646	c.3570A>C	c.(3568-3570)caA>caC	p.Q1190H		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1190					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Q1190H(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TGCCTTCAATTTGCCACTGTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	78	80					2																	61539018		1915	4114	6029	61392522	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3570A>C	2.37:g.61539018T>G	ENSP00000381577:p.Gln1190His		61392522	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360454	0.61403	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.03580	3.88	5.28	0.985	0.19779	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	L	0.44542	1.39	0.46609	D	0.999128	D	0.57571	0.98	D	0.66979	0.948	T	0.01657	-1.1302	10	0.62326	D	0.03	.	9.897	0.41324	0.0:0.3186:0.0:0.6814	.	1190	Q70CQ2	UBP34_HUMAN	H	1038;1038;1190	ENSP00000381577:Q1190H	ENSP00000263989:Q1038H	Q	-	3	2	USP34	61392522	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	0.858000	0.27845	-0.002000	0.14469	0.477000	0.44152	CAA		0.398	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			G	61539018	T	G	61539018	3	3	61	1	0	0	0	0	1	0	0	0	17105	1838	64	4	7290	4	USP34	2	61539018	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33492	61539018	181660355	1426	9411										
USP34	9736	broad.mit.edu	37	chr2	61546367	61546367	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatgttgatctttacttcGaacttgatttaaaaaccaat	5	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61546367G>A	ENST00000398571.2	-	22	3185	c.3109C>T	c.(3109-3111)Cga>Tga	p.R1037*		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1037					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R1037*(3)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TCTTTACTTCGAACTTGATTT	0.333																																																3	Substitution - Nonsense(3)	large_intestine(3)	2											125	115	118					2																	61546367		1862	4089	5951	61399871	SO:0001587	stop_gained	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3109C>T	2.37:g.61546367G>A	ENSP00000381577:p.Arg1037*		61399871	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Nonsense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	43	9.842842	0.99277	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9987	0.97401	0.0:0.0:1.0:0.0	.	.	.	.	X	885;885;1037	.	ENSP00000263989:R885X	R	-	1	2	USP34	61399871	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.519000	0.73768	2.738000	0.93877	0.591000	0.81541	CGA		0.333	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61546367	G	A	61546367	4	1	61	1	0	0	0	0	0	1	0	0	17105	1066	37	1	7767	1	USP34	2	61546367	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7349	61546367	181653006	1427	9412										
USP34	9736	broad.mit.edu	37	chr2	61566607	61566607	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttattaatccttcagaaaGattaacctataaaaaatgta	3	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61566607G>T	ENST00000398571.2	-	18	2699	c.2623C>A	c.(2623-2625)Ctt>Att	p.L875I		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	875					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.L875I(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CCTTCAGAAAGATTAACCTAT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	2											48	42	44					2																	61566607		1783	4054	5837	61420111	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.2623C>A	2.37:g.61566607G>T	ENSP00000381577:p.Leu875Ile		61420111	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	31	5.081639	0.94050	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.04970	3.52	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	L	0.57536	1.79	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.00438	-1.1739	10	0.26408	T	0.33	.	19.6641	0.95886	0.0:0.0:1.0:0.0	.	875	Q70CQ2	UBP34_HUMAN	I	723;723;875	ENSP00000381577:L875I	ENSP00000263989:L723I	L	-	1	0	USP34	61420111	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.993000	0.88291	2.653000	0.90120	0.460000	0.39030	CTT		0.289	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61566607	G	T	61566607	3	4	61	1	0	0	0	0	1	0	0	0	17105	942	33	2	8269	2	USP34	2	61566607	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20240	61566607	181632766	1428	9413										
XPO1	7514	broad.mit.edu	37	chr2	61721179	61721179	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattcaagacaaattttaaaGatttcagtttcttctacttc	3	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:61721179G>T	ENST00000401558.2	-	12	1822	c.1095C>A	c.(1093-1095)atC>atA	p.I365I	XPO1_ENST00000404992.2_Silent_p.I365I|XPO1_ENST00000406957.1_Silent_p.I365I	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	365	Interaction with Ran and nuclear export complex formation.|Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)	p.I365I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AAATTTTAAAGATTTCAGTTT	0.358			Mis		CLL																																	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	1	Substitution - coding silent(1)	large_intestine(1)	2											102	109	107					2																	61721179		2203	4300	6503	61574683	SO:0001819	synonymous_variant	7514			Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.1095C>A	2.37:g.61721179G>T			61574683	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Silent	SNP	ENST00000401558.2	37	CCDS33205.1																																																																																				0.358	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		T	61721179	G	T	61721179	2	4	61	1	0	0	0	0	0	0	0	1	17485	932	33	2		2	XPO1	2	61721179	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154572	61721179	181478194	1429	9414										
FAM161A	84140	broad.mit.edu	37	chr2	62063155	62063155	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaacacaacctgagcaactCtttcaaatagcagtggcctc	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:62063155C>A	ENST00000405894.3	-	4	1774	c.1673G>T	c.(1672-1674)aGa>aTa	p.R558I	FAM161A_ENST00000404929.1_Missense_Mutation_p.R614I	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	558					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)		p.R558I(1)|p.R449I(1)|p.R558K(1)|p.R449K(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CTGAGCAACTCTTTCAAATAG	0.308																																																4	Substitution - Missense(4)	large_intestine(2)|pancreas(2)	2											176	177	177					2																	62063155		1800	4067	5867	61916659	SO:0001583	missense	84140				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1673G>T	2.37:g.62063155C>A	ENSP00000385893:p.Arg558Ile		61916659	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502160	0.64298	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.23147	2.08;1.92	5.34	4.47	0.54385	.	0.072294	0.56097	U	0.000030	T	0.48059	0.1479	M	0.76328	2.33	0.52099	D	0.999944	D;D	0.89917	0.999;1.0	D;D	0.73380	0.964;0.98	T	0.47535	-0.9110	10	0.52906	T	0.07	-1.5634	10.924	0.47182	0.0:0.8472:0.0:0.1528	.	558;614	Q3B820;Q3B820-3	F161A_HUMAN;.	I	614;558	ENSP00000385158:R614I;ENSP00000385893:R558I	ENSP00000385158:R614I	R	-	2	0	FAM161A	61916659	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	2.305000	0.43664	1.264000	0.44198	-0.140000	0.14226	AGA		0.308	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62063155	C	A	62063155	3	1	61	1	0	0	0	0	1	0	0	0	5488	913	32	2	321	2	FAM161A	2	62063155	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	341976	62063155	181136218	1430	9415										
FAM161A	84140	broad.mit.edu	37	chr2	62066799	62066799	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactgttaagagttttggaGacttgtgttctgagaggtgt	13	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:62066799G>A	ENST00000405894.3	-	3	1441	c.1340C>T	c.(1339-1341)tCt>tTt	p.S447F	FAM161A_ENST00000404929.1_Missense_Mutation_p.S447F	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	447					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)		p.S338F(1)|p.S447F(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GAGTTTTGGAGACTTGTGTTC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	2											126	112	116					2																	62066799		1868	4102	5970	61920303	SO:0001583	missense	84140				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1340C>T	2.37:g.62066799G>A	ENSP00000385893:p.Ser447Phe		61920303	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	G	1.444	-0.566814	0.03910	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.23147	1.92;1.92	5.19	-10.4	0.00318	.	2.126740	0.01162	N	0.006679	T	0.09949	0.0244	N	0.05383	-0.06	0.09310	N	1	B;B	0.16166	0.016;0.004	B;B	0.16722	0.016;0.005	T	0.11518	-1.0584	10	0.09590	T	0.72	-21.5296	7.4306	0.27126	0.143:0.0753:0.1435:0.6383	.	447;447	Q3B820;Q3B820-3	F161A_HUMAN;.	F	447	ENSP00000385158:S447F;ENSP00000385893:S447F	ENSP00000385158:S447F	S	-	2	0	FAM161A	61920303	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.757000	0.04772	-3.347000	0.00182	-1.012000	0.02466	TCT		0.403	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62066799	G	A	62066799	3	1	61	1	0	0	0	0	1	0	0	0	5488	942	33	3	658	3	FAM161A	2	62066799	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3644	62066799	181132574	1431	9416										
FAM161A	84140	broad.mit.edu	37	chr2	62067353	62067353	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgctttatgtaccatttcGatatctgatttagatttcat	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:62067353G>A	ENST00000405894.3	-	3	887	c.786C>T	c.(784-786)atC>atT	p.I262I	FAM161A_ENST00000404929.1_Silent_p.I262I	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	262					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)		p.I153I(1)|p.I262I(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GTACCATTTCGATATCTGATT	0.393																																																2	Substitution - coding silent(2)	large_intestine(2)	2											194	170	177					2																	62067353		1820	4086	5906	61920857	SO:0001819	synonymous_variant	84140				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.786C>T	2.37:g.62067353G>A			61920857	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																				0.393	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62067353	G	A	62067353	2	1	61	1	0	0	0	0	0	0	0	1	5488	1048	37	1		1	FAM161A	2	62067353	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	554	62067353	181132020	1432	9417										
EHBP1	23301	broad.mit.edu	37	chr2	63058227	63058227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcaatttagatgacttcGaagaagataatgaagatgat	10	3	0	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:63058227G>A	ENST00000263991.5	+	7	1050	c.568G>A	c.(568-570)Gaa>Aaa	p.E190K	AC007098.1_ENST00000452397.1_RNA|EHBP1_ENST00000405289.1_Missense_Mutation_p.E190K|EHBP1_ENST00000431489.1_Missense_Mutation_p.E190K|EHBP1_ENST00000405015.3_Missense_Mutation_p.E190K|EHBP1_ENST00000354487.3_Missense_Mutation_p.E190K	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	190						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.E190K(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGATGACTTCGAAGAAGATAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											115	105	108					2																	63058227		2203	4300	6503	62911731	SO:0001583	missense	23301			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.568G>A	2.37:g.63058227G>A	ENSP00000263991:p.Glu190Lys		62911731	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	G	36	5.640263	0.96693	.	.	ENSG00000115504	ENST00000405015;ENST00000449820;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T;T	0.75154	-0.91;0.85;0.81;-0.91;-0.9;-0.91;-0.91	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.84745	0.5540	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.965;0.991	D	0.83610	0.0133	10	0.52906	T	0.07	.	20.3967	0.98985	0.0:0.0:1.0:0.0	.	190;190;190	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	K	190;70;190;190;190;190;190	ENSP00000384143:E190K;ENSP00000399609:E70K;ENSP00000384829:E190K;ENSP00000403783:E190K;ENSP00000263991:E190K;ENSP00000346482:E190K;ENSP00000385524:E190K	ENSP00000263991:E190K	E	+	1	0	EHBP1	62911731	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.416000	0.97383	2.829000	0.97493	0.655000	0.94253	GAA		0.338	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		A	63058227	G	A	63058227	3	1	61	1	0	0	0	0	1	0	0	0	4986	1059	37	1	590	1	EHBP1	2	63058227	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	990874	63058227	180141146	1433	9418										
OTX1	5013	broad.mit.edu	37	chr2	63283029	63283029	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccgtagctgcaggcgccGccaccgcagcagcctcttat	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:63283029G>A	ENST00000282549.2	+	5	919	c.643G>A	c.(643-645)Gcc>Acc	p.A215T	OTX1_ENST00000366671.3_Missense_Mutation_p.A215T	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	215					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A215T(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					TGCAGGCGCCGCCACCGCAGC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	2											20	22	21					2																	63283029		2200	4295	6495	63136533	SO:0001583	missense	5013				CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.643G>A	2.37:g.63283029G>A	ENSP00000282549:p.Ala215Thr		63136533	A6NHA2|B3KTJ4|Q53TG6	Missense_Mutation	SNP	ENST00000282549.2	37	CCDS1873.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527835	0.44969	.	.	ENSG00000115507	ENST00000366671;ENST00000282549	D;D	0.90844	-2.74;-2.74	3.47	3.47	0.39725	Transcription factor Otx, C-terminal (1);	0.322027	0.24628	N	0.036902	D	0.83746	0.5321	L	0.36672	1.1	0.40165	D	0.977118	B	0.19817	0.039	B	0.09377	0.004	T	0.79356	-0.1837	10	0.26408	T	0.33	.	10.5954	0.45333	0.0:0.0:1.0:0.0	.	215	P32242	OTX1_HUMAN	T	215	ENSP00000355631:A215T;ENSP00000282549:A215T	ENSP00000282549:A215T	A	+	1	0	OTX1	63136533	0.997000	0.39634	0.997000	0.53966	0.957000	0.61999	2.605000	0.46283	1.920000	0.55613	0.462000	0.41574	GCC		0.677	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			A	63283029	G	A	63283029	3	1	61	1	0	0	0	0	1	0	0	0	11351	1087	38	1	653	1	OTX1	2	63283029	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	224802	63283029	179916344	1434	9419										
C2orf86	51057	broad.mit.edu	37	chr2	63401881	63401881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagggagggaggttatctgGaaatgagtcttctccttgag	15	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:63401881G>A	ENST00000272321.7	-	15	2529	c.2002C>T	c.(2002-2004)Cca>Tca	p.P668S	WDPCP_ENST00000398544.3_Missense_Mutation_p.P509S|WDPCP_ENST00000409199.1_Missense_Mutation_p.P476S|WDPCP_ENST00000409120.1_Missense_Mutation_p.P476S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	668					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.P668S(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						AGGTTATCTGGAAATGAGTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											155	143	147					2																	63401881		1863	4100	5963	63255385	SO:0001583	missense	51057				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.2002C>T	2.37:g.63401881G>A	ENSP00000272321:p.Pro668Ser		63255385	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.183736	0.38609	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544	T;T;T;T	0.76709	-1.04;-0.45;-0.45;-0.45	5.29	4.4	0.53042	.	0.497073	0.16717	N	0.202402	T	0.70789	0.3264	L	0.32530	0.975	0.80722	D	1	B;B	0.30634	0.19;0.288	B;B	0.36244	0.11;0.22	T	0.69606	-0.5100	10	0.59425	D	0.04	-0.2098	11.2467	0.49002	0.0:0.0:0.817:0.183	.	668;509	O95876;O95876-3	FRITZ_HUMAN;.	S	668;476;476;509	ENSP00000272321:P668S;ENSP00000386592:P476S;ENSP00000386769:P476S;ENSP00000381552:P509S	ENSP00000272321:P668S	P	-	1	0	WDPCP	63255385	0.944000	0.32072	0.996000	0.52242	0.927000	0.56198	0.658000	0.24979	1.222000	0.43521	0.508000	0.49915	CCA		0.423	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		A	63401881	G	A	63401881	3	1	61	1	0	0	0	0	1	0	0	0	2207	1174	41	3	254	3	C2orf86	2	63401881	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118852	63401881	179797492	1435	9420										
C2orf86	51057	broad.mit.edu	37	chr2	63631593	63631593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtaacattcctgcagcagCtgatggcctttgactttagt	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:63631593C>T	ENST00000272321.7	-	10	1552	c.1025G>A	c.(1024-1026)aGc>aAc	p.S342N	WDPCP_ENST00000409199.1_Missense_Mutation_p.S150N|WDPCP_ENST00000409562.3_Missense_Mutation_p.S342N|WDPCP_ENST00000398544.3_Missense_Mutation_p.S183N|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409120.1_Missense_Mutation_p.S150N	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	342					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.S342N(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						CCTGCAGCAGCTGATGGCCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	121	122					2																	63631593		1982	4171	6153	63485097	SO:0001583	missense	51057				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.1025G>A	2.37:g.63631593C>T	ENSP00000272321:p.Ser342Asn		63485097	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945353	0.73672	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);	0.101090	0.64402	D	0.000001	T	0.73760	0.3628	M	0.76002	2.32	0.45076	D	0.998094	P;D;P;B	0.89917	0.728;1.0;0.854;0.244	B;D;P;B	0.74348	0.397;0.983;0.505;0.155	T	0.74077	-0.3781	10	0.54805	T	0.06	-11.295	19.8499	0.96734	0.0:1.0:0.0:0.0	.	150;342;342;183	E9PFG9;O95876-2;O95876;O95876-3	.;.;FRITZ_HUMAN;.	N	342;150;150;183;342	ENSP00000272321:S342N;ENSP00000386592:S150N;ENSP00000386769:S150N;ENSP00000381552:S183N;ENSP00000387222:S342N	ENSP00000272321:S342N	S	-	2	0	WDPCP	63485097	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.122000	0.57910	2.779000	0.95612	0.591000	0.81541	AGC		0.443	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		T	63631593	C	T	63631593	3	4	61	1	0	0	0	0	1	0	0	0	2207	797	28	3	1251	3	C2orf86	2	63631593	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	229712	63631593	179567780	1436	9421										
C2orf86	51057	broad.mit.edu	37	chr2	63664615	63664615	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcagaagactccatcttCttggtaaactgaataaaaca	5	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:63664615C>T	ENST00000272321.7	-	8	1100	c.573G>A	c.(571-573)aaG>aaA	p.K191K	WDPCP_ENST00000409199.1_5'UTR|WDPCP_ENST00000409562.3_Silent_p.K191K|WDPCP_ENST00000398544.3_Silent_p.K32K|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409120.1_5'UTR	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	191					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.K191K(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						ACTCCATCTTCTTGGTAAACT	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	2											49	48	48					2																	63664615		1790	4042	5832	63518119	SO:0001819	synonymous_variant	51057				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.573G>A	2.37:g.63664615C>T			63518119	Q53RW4|Q7Z2Z3	Silent	SNP	ENST00000272321.7	37	CCDS42688.1																																																																																				0.279	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		T	63664615	C	T	63664615	2	4	61	1	0	0	0	0	0	0	0	1	2207	912	32	3		3	C2orf86	2	63664615	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33022	63664615	179534758	1437	9422										
UGP2	7360	broad.mit.edu	37	chr2	64111204	64111204	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaatcattgtcgtgtgaaAatctacactttcaatcaaag	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:64111204A>C	ENST00000337130.5	+	5	1028	c.552A>C	c.(550-552)aaA>aaC	p.K184N	ACA59_ENST00000515966.1_RNA|UGP2_ENST00000445915.2_Missense_Mutation_p.K193N|UGP2_ENST00000467648.2_Missense_Mutation_p.K173N|UGP2_ENST00000394417.2_Missense_Mutation_p.K173N|UGP2_ENST00000487469.1_3'UTR	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	184					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)	p.K184N(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						GTCGTGTGAAAATCTACACTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	77	77					2																	64111204		2203	4299	6502	63964708	SO:0001583	missense	7360				CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.552A>C	2.37:g.64111204A>C	ENSP00000338703:p.Lys184Asn		63964708	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	37	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.359379	0.41801	.	.	ENSG00000169764	ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915;ENST00000491621	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.72	5.72	0.89469	.	0.040435	0.85682	D	0.000000	T	0.16300	0.0392	L	0.46885	1.475	0.58432	D	0.999999	B;B	0.14012	0.009;0.009	B;B	0.21151	0.033;0.022	T	0.04522	-1.0945	10	0.40728	T	0.16	-44.1392	9.1549	0.36988	0.8588:0.0:0.1412:0.0	.	193;184	E7EUC7;Q16851	.;UGPA_HUMAN	N	173;173;184;193;173	ENSP00000377939:K173N;ENSP00000420793:K173N;ENSP00000338703:K184N;ENSP00000411803:K193N;ENSP00000420342:K173N	ENSP00000338703:K184N	K	+	3	2	UGP2	63964708	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.430000	0.34914	2.183000	0.69458	0.533000	0.62120	AAA		0.333	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		C	64111204	A	C	64111204	3	2	61	1	0	0	0	0	1	0	0	0	16983	11	1	4	570	4	UGP2	2	64111204	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	446589	64111204	179088169	1438	9423										
UGP2	7360	broad.mit.edu	37	chr2	64112910	64112910	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgtctaacatagataatCtgggtgccacagtggatctg	11	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:64112910C>A	ENST00000337130.5	+	6	1239	c.763C>A	c.(763-765)Ctg>Atg	p.L255M	ACA59_ENST00000515966.1_RNA|UGP2_ENST00000445915.2_Missense_Mutation_p.L264M|UGP2_ENST00000467648.2_Missense_Mutation_p.L244M|UGP2_ENST00000394417.2_Missense_Mutation_p.L244M|UGP2_ENST00000487469.1_3'UTR	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	255					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)	p.L255M(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						CATAGATAATCTGGGTGCCAC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											126	127	127					2																	64112910		2203	4300	6503	63966414	SO:0001583	missense	7360				CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.763C>A	2.37:g.64112910C>A	ENSP00000338703:p.Leu255Met		63966414	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	37	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697888	0.68386	.	.	ENSG00000169764	ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.8	2.67	0.31697	.	0.000000	0.85682	D	0.000000	T	0.55353	0.1915	M	0.66560	2.04	0.80722	D	1	D;D	0.58268	0.982;0.982	D;P	0.63192	0.912;0.902	T	0.55970	-0.8056	10	0.62326	D	0.03	-37.3379	9.0806	0.36550	0.0:0.6581:0.0:0.3419	.	264;255	E7EUC7;Q16851	.;UGPA_HUMAN	M	244;244;255;264	ENSP00000377939:L244M;ENSP00000420793:L244M;ENSP00000338703:L255M;ENSP00000411803:L264M	ENSP00000338703:L255M	L	+	1	2	UGP2	63966414	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.613000	0.46351	0.814000	0.34374	-0.136000	0.14681	CTG		0.383	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		A	64112910	C	A	64112910	3	1	61	1	0	0	0	0	1	0	0	0	16983	912	32	2	785	2	UGP2	2	64112910	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1706	64112910	179086463	1439	9424										
VPS54	51542	broad.mit.edu	37	chr2	64176173	64176173	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagttaaaacacatacctCttctaaaacttgacagtcat	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:64176173C>A	ENST00000272322.4	-	8	1289	c.1135G>T	c.(1135-1137)Gag>Tag	p.E379*	VPS54_ENST00000409558.4_Nonsense_Mutation_p.E367*|VPS54_ENST00000354504.3_Nonsense_Mutation_p.E262*			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	379					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)		p.E379*(1)		endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						ACACATACCTCTTCTAAAACT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											94	89	91					2																	64176173		2202	4297	6499	64029677	SO:0001587	stop_gained	51542			AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1135G>T	2.37:g.64176173C>A	ENSP00000272322:p.Glu379*		64029677	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Nonsense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	C	42	9.753894	0.99255	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	.	.	.	5.23	5.23	0.72850	.	0.047978	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	19.1696	0.93572	0.0:1.0:0.0:0.0	.	.	.	.	X	262;379;367;367;379	.	ENSP00000272322:E379X	E	-	1	0	VPS54	64029677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.172000	0.58243	2.592000	0.87571	0.655000	0.94253	GAG		0.313	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		A	64176173	C	A	64176173	4	1	61	1	0	0	0	0	0	1	0	0	17256	922	32	2	1862	2	VPS54	2	64176173	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63263	64176173	179023200	1440	9425										
PELI1	57162	broad.mit.edu	37	chr2	64322274	64322274	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcgtgctgcattgatttcCtgtcttaaagcttctaaatg	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:64322274C>T	ENST00000358912.4	-	7	1261	c.819G>A	c.(817-819)caG>caA	p.Q273Q		NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	273					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.Q273Q(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						CATTGATTTCCTGTCTTAAAG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	2											110	104	106					2																	64322274		2203	4300	6503	64175778	SO:0001819	synonymous_variant	57162				CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"Pellino homologs"	8827	protein-coding gene	gene with protein product		614797	"pellino (Drosophila) homolog 1", "pellino homolog 1 (Drosophila)"			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.819G>A	2.37:g.64322274C>T			64175778	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																				0.458	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651		T	64322274	C	T	64322274	2	4	61	1	0	0	0	0	0	0	0	1	11752	680	24	3		3	PELI1	2	64322274	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146101	64322274	178877099	1441	9426										
AFTPH	54812	broad.mit.edu	37	chr2	64778628	64778628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggagccagacatcattcGaatgtactcttcatccccac	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:64778628G>A	ENST00000422803.1	+	2	334	c.20G>A	c.(19-21)cGa>cAa	p.R7Q	AFTPH_ENST00000409933.1_Missense_Mutation_p.R7Q|AFTPH_ENST00000238855.7_Missense_Mutation_p.R7Q|AFTPH_ENST00000238856.4_Missense_Mutation_p.R7Q|AFTPH_ENST00000409183.1_5'Flank			Q6ULP2	AFTIN_HUMAN	aftiphilin	7					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)	p.R7Q(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GACATCATTCGAATGTACTCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											83	88	87					2																	64778628		2198	4300	6498	64632132	SO:0001583	missense	54812			AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.20G>A	2.37:g.64778628G>A	ENSP00000397726:p.Arg7Gln		64632132	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	37		.	.	.	.	.	.	.	.	.	.	G	13.96	2.392675	0.42410	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.63	4.76	0.60689	.	0.082377	0.48286	N	0.000183	T	0.24736	0.0600	M	0.74258	2.255	0.47994	D	0.999562	P;P;P;P	0.43352	0.804;0.804;0.804;0.804	B;B;B;B	0.33750	0.11;0.169;0.169;0.11	T	0.18053	-1.0349	10	0.87932	D	0	-2.2079	14.8785	0.70513	0.0689:0.0:0.9311:0.0	.	7;7;7;7	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	Q	7	ENSP00000238856:R7Q;ENSP00000397726:R7Q;ENSP00000238855:R7Q;ENSP00000387071:R7Q	ENSP00000238855:R7Q	R	+	2	0	AFTPH	64632132	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.291000	0.72719	1.529000	0.49120	0.655000	0.94253	CGA		0.378	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		A	64778628	G	A	64778628	3	1	61	1	0	0	0	0	1	0	0	0	364	1058	37	1	22	1	AFTPH	2	64778628	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	456354	64778628	178420745	1442	9427										
CEP68	23177	broad.mit.edu	37	chr2	65309732	65309732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctggagagccacgcagatCgcctgtatgactctatcttg	11	11	2	3	rs141590287		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:65309732C>T	ENST00000377990.2	+	6	2370	c.2167C>T	c.(2167-2169)Cgc>Tgc	p.R723C	RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000260569.4_Missense_Mutation_p.R586C|CEP68_ENST00000546106.1_3'UTR	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	723					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.R723C(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						CCACGCAGATCGCCTGTATGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG	0,4406		0,0,2203	162	150	154		2167	4.7	0.3	2	dbSNP_134	154	1,8599	1.2+/-3.3	0,1,4299	no	missense	CEP68	NM_015147.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	723/758	65309732	1,13005	2203	4300	6503	65163236	SO:0001583	missense	23177			BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2167C>T	2.37:g.65309732C>T	ENSP00000367229:p.Arg723Cys		65163236	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313609	0.81358	0.0	1.16E-4	ENSG00000011523	ENST00000377990;ENST00000260569	T;T	0.19669	2.13;2.24	5.61	4.73	0.59995	.	0.782790	0.11788	N	0.529517	T	0.40272	0.1110	L	0.56769	1.78	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	P;P	0.56700	0.804;0.804	T	0.24190	-1.0167	10	0.87932	D	0	-2.846	16.5739	0.84632	0.0:0.8694:0.1306:0.0	.	723;586	Q76N32;Q76N32-2	CEP68_HUMAN;.	C	723;586	ENSP00000367229:R723C;ENSP00000260569:R586C	ENSP00000260569:R586C	R	+	1	0	CEP68	65163236	0.949000	0.32298	0.271000	0.24616	0.986000	0.74619	3.934000	0.56553	1.363000	0.46019	0.561000	0.74099	CGC		0.498	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		T	65309732	C	T	65309732	3	4	61	1	0	0	0	0	1	0	0	0	3264	884	31	1	2185	1	CEP68	2	65309732	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	531104	65309732	177889641	1443	9428										
CEP68	23177	broad.mit.edu	37	chr2	65309814	65309814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaagcccatggcggcaaTggagcacccatgtgaagggg	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:65309814T>C	ENST00000377990.2	+	6	2452	c.2249T>C	c.(2248-2250)aTg>aCg	p.M750T	RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000260569.4_Missense_Mutation_p.M613T	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	750					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.M750T(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						ATGGCGGCAATGGAGCACCCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	102	103					2																	65309814		2203	4300	6503	65163318	SO:0001583	missense	23177			BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2249T>C	2.37:g.65309814T>C	ENSP00000367229:p.Met750Thr		65163318	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	T	9.701	1.154471	0.21371	.	.	ENSG00000011523	ENST00000377990;ENST00000260569	T;T	0.13089	2.63;2.62	5.0	-2.73	0.05950	.	3.212500	0.01076	N	0.004918	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35699	-0.9778	10	0.87932	D	0	3.0625	1.6063	0.02684	0.2633:0.4049:0.1858:0.146	.	750;613	Q76N32;Q76N32-2	CEP68_HUMAN;.	T	750;613	ENSP00000367229:M750T;ENSP00000260569:M613T	ENSP00000260569:M613T	M	+	2	0	CEP68	65163318	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.057000	0.11768	-0.294000	0.08973	-0.527000	0.04329	ATG		0.522	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		C	65309814	T	C	65309814	3	2	61	1	0	0	0	0	1	0	0	0	3264	1464	51	4	2267	4	CEP68	2	65309814	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	82	65309814	177889559	1444	9429										
ACTR2	10097	broad.mit.edu	37	chr2	65467088	65467088	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccaaagtgggaaacattGaaatcaaggtaatattttat	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:65467088G>T	ENST00000260641.5	+	2	308	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	ACTR2_ENST00000476840.1_3'UTR|ACTR2_ENST00000377982.4_Nonsense_Mutation_p.E51*|ACTR2_ENST00000542850.1_5'UTR	NM_005722.3	NP_005713.1	P61160	ARP2_HUMAN	ARP2 actin-related protein 2 homolog (yeast)	51					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)	p.E51*(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	12						GGGAAACATTGAAATCAAGGT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											55	54	55					2																	65467088		2203	4299	6502	65320592	SO:0001587	stop_gained	10097			AF006082	CCDS1881.1, CCDS46307.1	2p14	2008-05-20	2001-11-28		ENSG00000138071	ENSG00000138071			169	protein-coding gene	gene with protein product		604221	"ARP2 (actin-related protein 2, yeast) homolog"			9230079	Standard	NM_001005386		Approved	ARP2	uc002sdp.3	P61160	OTTHUMG00000129540	ENST00000260641.5:c.151G>T	2.37:g.65467088G>T	ENSP00000260641:p.Glu51*		65320592	B2RCP5|D6W5F4|E9PF41|O15142|Q96C82	Nonsense_Mutation	SNP	ENST00000260641.5	37	CCDS1881.1	.	.	.	.	.	.	.	.	.	.	G	38	6.865130	0.97897	.	.	ENSG00000138071	ENST00000260641;ENST00000377982	.	.	.	5.87	5.87	0.94306	.	0.000000	0.34853	U	0.003633	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-23.7224	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	X	51	.	ENSP00000260641:E51X	E	+	1	0	ACTR2	65320592	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	GAA		0.323	ACTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251730.1	NM_001005386		T	65467088	G	T	65467088	4	4	61	1	0	0	0	0	0	1	0	0	211	1291	45	2	157	2	ACTR2	2	65467088	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157274	65467088	177732285	1445	9430										
SPRED2	200734	broad.mit.edu	37	chr2	65541002	65541002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcctccttccgccgccgcGacttgccccgggagggctgc	13	19	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:65541002G>A	ENST00000356388.4	-	6	1079	c.890C>T	c.(889-891)tCg>tTg	p.S297L	SPRED2_ENST00000443619.2_Missense_Mutation_p.S294L|SPRED2_ENST00000474228.1_5'Flank	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	297					inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.S297L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						CCGCCGCCGCGACTTGCCCCG	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	2											44	50	48					2																	65541002		2202	4298	6500	65394506	SO:0001583	missense	200734			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.890C>T	2.37:g.65541002G>A	ENSP00000348753:p.Ser297Leu		65394506	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949414	0.53186	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315;ENST00000421087	T;T;T;T	0.78003	-1.14;-1.13;-1.14;-0.14	5.75	3.81	0.43845	.	0.287715	0.33110	N	0.005275	T	0.76637	0.4015	M	0.71581	2.175	0.36141	D	0.846799	B;B	0.13145	0.007;0.006	B;B	0.06405	0.002;0.002	T	0.78927	-0.2011	10	0.48119	T	0.1	-7.7818	15.7879	0.78322	0.0:0.2573:0.7427:0.0	.	294;297	E9PEP0;Q7Z698	.;SPRE2_HUMAN	L	297;294;312;179	ENSP00000348753:S297L;ENSP00000393697:S294L;ENSP00000390595:S312L;ENSP00000407627:S179L	ENSP00000348753:S297L	S	-	2	0	SPRED2	65394506	1.000000	0.71417	0.982000	0.44146	0.944000	0.59088	2.893000	0.48633	1.395000	0.46643	0.655000	0.94253	TCG		0.677	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			A	65541002	G	A	65541002	3	1	61	1	0	0	0	0	1	0	0	0	15132	1059	37	1	370	1	SPRED2	2	65541002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73914	65541002	177658371	1446	9431										
SPRED2	200734	broad.mit.edu	37	chr2	65541250	65541250	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccgggggttgatgcgcacGatctcctcgtcgtcgtccgg	14	14	1	1	rs151327457		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:65541250G>A	ENST00000356388.4	-	6	831	c.642C>T	c.(640-642)atC>atT	p.I214I	SPRED2_ENST00000443619.2_Silent_p.I211I|SPRED2_ENST00000474228.1_5'Flank	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	214	KBD. {ECO:0000255|PROSITE- ProRule:PRU00821}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.I214I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TGATGCGCACGATCTCCTCGT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	2											45	43	44					2																	65541250		2203	4300	6503	65394754	SO:0001819	synonymous_variant	200734			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.642C>T	2.37:g.65541250G>A			65394754	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Silent	SNP	ENST00000356388.4	37	CCDS33211.1																																																																																				0.622	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			A	65541250	G	A	65541250	2	1	61	1	0	0	0	0	0	0	0	1	15132	1048	37	1		1	SPRED2	2	65541250	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248	65541250	177658123	1447	9432										
ETAA1	54465	broad.mit.edu	37	chr2	67630947	67630947	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgcatttactacaagtgAttttgaggatgattgggaaa	11	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:67630947A>T	ENST00000272342.5	+	5	1263	c.1133A>T	c.(1132-1134)gAt>gTt	p.D378V	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	378						cytoplasm (GO:0005737)		p.D378V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						ACTACAAGTGATTTTGAGGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	91	90					2																	67630947		2203	4297	6500	67484451	SO:0001583	missense	54465			AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1133A>T	2.37:g.67630947A>T	ENSP00000272342:p.Asp378Val		67484451	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.033525	0.54896	.	.	ENSG00000143971	ENST00000272342	T	0.35973	1.28	5.77	4.63	0.57726	.	0.052545	0.64402	D	0.000001	T	0.58090	0.2098	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.60915	-0.7168	10	0.87932	D	0	-30.5644	10.7691	0.46312	0.9262:0.0:0.0738:0.0	.	378	Q9NY74	ETAA1_HUMAN	V	378	ENSP00000272342:D378V	ENSP00000272342:D378V	D	+	2	0	ETAA1	67484451	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.698000	0.54771	1.022000	0.39626	0.533000	0.62120	GAT		0.368	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		T	67630947	A	T	67630947	3	4	61	1	0	0	0	0	1	0	0	0	5280	333	12	5	1151	5	ETAA1	2	67630947	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2089697	67630947	175568426	1448	9433										
ETAA1	54465	broad.mit.edu	37	chr2	67631578	67631578	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccctcatttgccaatgaAattattaaagcatgtcatca	5	9	3	1	rs61737411	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:67631578A>C	ENST00000272342.5	+	5	1894	c.1764A>C	c.(1762-1764)gaA>gaC	p.E588D	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	588						cytoplasm (GO:0005737)		p.E588D(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TTGCCAATGAAATTATTAAAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	97	95					2																	67631578		2203	4300	6503	67485082	SO:0001583	missense	54465			AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1764A>C	2.37:g.67631578A>C	ENSP00000272342:p.Glu588Asp		67485082	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.550417	0.45383	.	.	ENSG00000143971	ENST00000272342	T	0.30981	1.51	5.83	4.67	0.58626	.	0.065091	0.64402	D	0.000006	T	0.35682	0.0940	L	0.43152	1.355	0.32486	N	0.540871	D	0.65815	0.995	P	0.59288	0.855	T	0.47129	-0.9141	10	0.34782	T	0.22	-33.8915	3.9521	0.09374	0.6564:0.1096:0.1279:0.1061	.	588	Q9NY74	ETAA1_HUMAN	D	588	ENSP00000272342:E588D	ENSP00000272342:E588D	E	+	3	2	ETAA1	67485082	1.000000	0.71417	0.990000	0.47175	0.705000	0.40729	1.126000	0.31344	0.462000	0.27095	-1.139000	0.01908	GAA		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		C	67631578	A	C	67631578	3	2	61	1	0	0	0	0	1	0	0	0	5280	11	1	4	1782	4	ETAA1	2	67631578	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	631	67631578	175567795	1449	9434										
ETAA1	54465	broad.mit.edu	37	chr2	67631731	67631731	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagaaagtatatgtgagatCaataataattccgaacatgg	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:67631731C>A	ENST00000272342.5	+	5	2047	c.1917C>A	c.(1915-1917)atC>atA	p.I639I	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	639						cytoplasm (GO:0005737)		p.I639I(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TATGTGAGATCAATAATAATT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	2											108	112	111					2																	67631731		2202	4300	6502	67485235	SO:0001819	synonymous_variant	54465			AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1917C>A	2.37:g.67631731C>A			67485235	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																				0.343	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		A	67631731	C	A	67631731	2	1	61	1	0	0	0	0	0	0	0	1	5280	816	29	2		2	ETAA1	2	67631731	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153	67631731	175567642	1450	9435										
FBXO48	554251	broad.mit.edu	37	chr2	68692121	68692121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagccctgcacagactccGaatgtccagctgactgaaaa	9	12	0	4	rs150942426	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:68692121G>A	ENST00000377957.3	-	3	564	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	APLF_ENST00000303795.4_5'Flank	NM_001024680.1	NP_001019851.1	Q5FWF7	FBX48_HUMAN	F-box protein 48	53	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.							p.R53W(1)		endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						CACAGACTCCGAATGTCCAGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	116	116					2																	68692121		2203	4300	6503	68545625	SO:0001583	missense	554251			BC089423	CCDS33213.1	2p13.3	2011-03-09			ENSG00000204923	ENSG00000204923		"F-boxes /  "other""	33857	protein-coding gene	gene with protein product							Standard	XM_005264407		Approved		uc002seo.3	Q5FWF7	OTTHUMG00000152585	ENST00000377957.3:c.157C>T	2.37:g.68692121G>A	ENSP00000367193:p.Arg53Trp		68545625		Missense_Mutation	SNP	ENST00000377957.3	37	CCDS33213.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.715447	0.30413	.	.	ENSG00000204923	ENST00000377957	T	0.52526	0.66	6.07	4.26	0.50523	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	1.478860	0.03526	N	0.221691	T	0.58595	0.2133	M	0.85777	2.775	0.21762	N	0.99955	B	0.14012	0.009	B	0.08055	0.003	T	0.50474	-0.8824	10	0.72032	D	0.01	0.8263	10.7575	0.46245	0.0661:0.2439:0.69:0.0	.	53	Q5FWF7	FBX48_HUMAN	W	53	ENSP00000367193:R53W	ENSP00000367193:R53W	R	-	1	2	FBXO48	68545625	0.001000	0.12720	0.226000	0.23910	0.032000	0.12392	1.037000	0.30241	0.886000	0.36113	-0.165000	0.13383	CGG		0.418	FBXO48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326900.2	NM_001024680		A	68692121	G	A	68692121	3	1	61	1	0	0	0	0	1	0	0	0	5776	1057	37	1	318	1	FBXO48	2	68692121	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1060390	68692121	174507252	1451	9436										
APLF	200558	broad.mit.edu	37	chr2	68717383	68717383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggcaggtggtcagctgcGaatcaaaccggtaaatatgt	14	7	2	0	rs150464758	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:68717383G>A	ENST00000303795.4	+	2	329	c.158G>A	c.(157-159)cGa>cAa	p.R53Q		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	53	FHA-like.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.R53Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGTCAGCTGCGAATCAAACCG	0.373													G|||	2	0.000399361	0.0015	0	5008	,	,		17875	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	84	85	85		158	5.9	1	2	dbSNP_134	85	0,8600		0,0,4300	no	missense	APLF	NM_173545.2	43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	53/512	68717383	2,13004	2203	4300	6503	68570887	SO:0001583	missense	200558			BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.158G>A	2.37:g.68717383G>A	ENSP00000307004:p.Arg53Gln		68570887	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	.	.	.	.	.	.	.	.	.	.	g	27.2	4.812522	0.90707	4.54E-4	0.0	ENSG00000169621	ENST00000303795	T	0.22945	1.93	5.93	5.93	0.95920	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	T	0.50051	0.1593	M	0.66939	2.045	0.40220	D	0.977729	D	0.89917	1.0	D	0.87578	0.998	T	0.43163	-0.9408	10	0.49607	T	0.09	.	15.841	0.78845	0.0:0.0:1.0:0.0	.	53	Q8IW19	APLF_HUMAN	Q	53	ENSP00000307004:R53Q	ENSP00000307004:R53Q	R	+	2	0	APLF	68570887	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.289000	0.51747	2.814000	0.96858	0.655000	0.94253	CGA		0.373	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		A	68717383	G	A	68717383	3	1	61	1	0	0	0	0	1	0	0	0	776	1058	37	1	164	1	APLF	2	68717383	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25262	68717383	174481990	1452	9437										
APLF	200558	broad.mit.edu	37	chr2	68794511	68794511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatagaatatagacataataCgcttccaggtaagtaagttt	8	5	0	2	rs199832884		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:68794511C>T	ENST00000303795.4	+	9	1496	c.1325C>T	c.(1324-1326)aCg>aTg	p.T442M	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	442					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.T442M(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AGACATAATACGCTTCCAGGT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	57	56					2																	68794511		2201	4300	6501	68648015	SO:0001583	missense	200558			BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1325C>T	2.37:g.68794511C>T	ENSP00000307004:p.Thr442Met		68648015	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	.	.	.	.	.	.	.	.	.	.	C	8.618	0.890722	0.17613	.	.	ENSG00000169621	ENST00000303795	T	0.22945	1.93	4.99	-0.169	0.13339	Zinc finger, C2H2, APLF-like (1);	0.728970	0.13325	N	0.396330	T	0.13884	0.0336	L	0.36672	1.1	0.09310	N	1	B	0.34313	0.448	B	0.25884	0.064	T	0.14476	-1.0471	10	0.44086	T	0.13	.	3.6139	0.08070	0.1688:0.4668:0.0:0.3644	.	442	Q8IW19	APLF_HUMAN	M	442	ENSP00000307004:T442M	ENSP00000307004:T442M	T	+	2	0	APLF	68648015	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-0.797000	0.04570	0.101000	0.17610	-0.224000	0.12420	ACG		0.284	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		T	68794511	C	T	68794511	3	4	61	1	0	0	0	0	1	0	0	0	776	536	19	1	1359	1	APLF	2	68794511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77128	68794511	174404862	1453	9438										
PROKR1	10887	broad.mit.edu	37	chr2	68882441	68882441	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttctacggcttcaccatCgtgcgcgacttcttccccac	6	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:68882441C>T	ENST00000303786.3	+	3	1335	c.915C>T	c.(913-915)atC>atT	p.I305I	PROKR1_ENST00000394342.2_Silent_p.I305I			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	305					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.I305I(1)		endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GCTTCACCATCGTGCGCGACT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2											142	107	119					2																	68882441		2203	4300	6503	68735945	SO:0001819	synonymous_variant	10887			AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"GPCR / Class A : Prokineticin receptors"	4524	protein-coding gene	gene with protein product		607122	"G protein-coupled receptor 73"	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.915C>T	2.37:g.68882441C>T			68735945	A5JUU2|Q53QT9|Q8NFJ7	Silent	SNP	ENST00000303786.3	37	CCDS1889.1																																																																																				0.582	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			T	68882441	C	T	68882441	2	4	61	1	0	0	0	0	0	0	0	1	12586	874	31	1		1	PROKR1	2	68882441	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87930	68882441	174316932	1454	9439										
ARHGAP25	9938	broad.mit.edu	37	chr2	69040538	69040538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgggcagctcacgaatgCggatgaggcaaaggtttgca	15	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69040538C>T	ENST00000295381.3	+	6	1210	c.791C>T	c.(790-792)gCg>gTg	p.A264V	ARHGAP25_ENST00000409030.3_Missense_Mutation_p.A257V|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.A258V|ARHGAP25_ENST00000497079.1_Missense_Mutation_p.A258V|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.A265V|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.A225V|ARHGAP25_ENST00000544262.1_Missense_Mutation_p.A239V	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	264	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.A258V(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTCACGAATGCGGATGAGGCA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	89	95					2																	69040538		2203	4300	6503	68894042	SO:0001583	missense	9938			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.791C>T	2.37:g.69040538C>T	ENSP00000295381:p.Ala264Val		68894042	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.571|7.571	0.666696|0.666696	0.14710|0.14710	.|.	.|.	ENSG00000163219|ENSG00000163219	ENST00000544262;ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533|ENST00000497259	T;T;T;T;T;T;T|.	0.19806|.	2.12;2.18;2.18;2.18;2.18;2.18;2.18|.	5.85|5.85	3.95|3.95	0.45737|0.45737	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);|.	0.363698|.	0.30940|.	N|.	0.008566|.	T|T	0.19644|0.19644	0.0472|0.0472	N|N	0.14661|0.14661	0.345|0.345	0.28093|0.28093	N|N	0.931739|0.931739	B;B;B;B;B;B;B|.	0.23937|.	0.02;0.094;0.035;0.086;0.086;0.093;0.012|.	B;B;B;B;B;B;B|.	0.21708|.	0.011;0.036;0.006;0.006;0.006;0.011;0.009|.	T|T	0.13683|0.13683	-1.0500|-1.0500	10|5	0.28530|.	T|.	0.3|.	.|.	4.1188|4.1188	0.10095|0.10095	0.168:0.5993:0.0:0.2327|0.168:0.5993:0.0:0.2327	.|.	225;239;265;258;257;258;264|.	E9PFQ7;B7Z8K7;P42331-4;G5E9G2;P42331-3;P42331-2;P42331|.	.;.;.;.;.;.;RHG25_HUMAN|.	V|W	239;264;265;225;257;258;258;258;249|124	ENSP00000439917:A239V;ENSP00000295381:A264V;ENSP00000386911:A265V;ENSP00000420583:A225V;ENSP00000386863:A257V;ENSP00000386241:A258V;ENSP00000417139:A258V|.	ENSP00000295381:A264V|.	A|R	+|+	2|1	0|2	ARHGAP25|ARHGAP25	68894042|68894042	0.574000|0.574000	0.26684|0.26684	0.984000|0.984000	0.44739|0.44739	0.017000|0.017000	0.09413|0.09413	2.118000|2.118000	0.41949|0.41949	1.477000|1.477000	0.48234|0.48234	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.527	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		T	69040538	C	T	69040538	3	4	61	1	0	0	0	0	1	0	0	0	874	768	27	1	856	1	ARHGAP25	2	69040538	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158097	69040538	174158835	1455	9440										
ARHGAP25	9938	broad.mit.edu	37	chr2	69045084	69045084	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactgtgattggtgtgaatCtcatcaggtcgaaggtcgaa	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69045084C>A	ENST00000295381.3	+	8	1377	c.958C>A	c.(958-960)Ctc>Atc	p.L320I	ARHGAP25_ENST00000409030.3_Missense_Mutation_p.L313I|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.L314I|ARHGAP25_ENST00000497079.1_Missense_Mutation_p.L314I|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.L321I|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.L281I|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.L14I	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	320	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.L314I(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TGGTGTGAATCTCATCAGGTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											176	159	164					2																	69045084		2203	4300	6503	68898588	SO:0001583	missense	9938			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.958C>A	2.37:g.69045084C>A	ENSP00000295381:p.Leu320Ile		68898588	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	C	11.35	1.612146	0.28712	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533;ENST00000479844	T;T;T;T;T;T;T	0.58940	0.3;2.13;2.13;0.3;2.13;2.13;1.29	5.32	5.32	0.75619	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.47948	0.1473	N	0.12182	0.205	0.80722	D	1	P;P;P;P;P;B	0.52842	0.793;0.956;0.956;0.956;0.944;0.035	B;P;P;P;B;B	0.49085	0.268;0.6;0.6;0.6;0.341;0.084	T	0.38308	-0.9667	10	0.18710	T	0.47	.	18.1728	0.89752	0.0:1.0:0.0:0.0	.	281;321;314;313;314;320	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331-2;P42331	.;.;.;.;.;RHG25_HUMAN	I	320;321;281;313;314;314;314;305;14	ENSP00000295381:L320I;ENSP00000386911:L321I;ENSP00000420583:L281I;ENSP00000386863:L313I;ENSP00000386241:L314I;ENSP00000417139:L314I;ENSP00000417467:L14I	ENSP00000295381:L320I	L	+	1	0	ARHGAP25	68898588	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.453000	0.44970	2.777000	0.95525	0.650000	0.86243	CTC		0.473	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		A	69045084	C	A	69045084	3	1	61	1	0	0	0	0	1	0	0	0	874	913	32	2	1031	2	ARHGAP25	2	69045084	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4546	69045084	174154289	1456	9441										
ARHGAP25	9938	broad.mit.edu	37	chr2	69049681	69049681	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatctttaaaaatgaattCtggtcgccttcctcagaggc	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69049681C>T	ENST00000295381.3	+	10	1826	c.1407C>T	c.(1405-1407)ttC>ttT	p.F469F	ARHGAP25_ENST00000409030.3_Silent_p.F462F|ARHGAP25_ENST00000409220.1_Silent_p.F463F|ARHGAP25_ENST00000409202.3_Silent_p.F470F|ARHGAP25_ENST00000467265.1_Silent_p.F430F|ARHGAP25_ENST00000479844.1_Silent_p.F163F	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	469					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.F463F(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						AAAATGAATTCTGGTCGCCTT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	2											85	87	86					2																	69049681		2203	4300	6503	68903185	SO:0001819	synonymous_variant	9938			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1407C>T	2.37:g.69049681C>T			68903185	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	C	9.600	1.128534	0.21041	.	.	ENSG00000163219	ENST00000497259	.	.	.	5.38	4.51	0.55191	.	.	.	.	.	T	0.55737	0.1939	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53885	-0.8375	4	.	.	.	.	6.1131	0.20112	0.0:0.6781:0.1556:0.1663	.	.	.	.	F	329	.	.	S	+	2	0	ARHGAP25	68903185	0.991000	0.36638	1.000000	0.80357	0.985000	0.73830	0.116000	0.15561	1.399000	0.46721	0.557000	0.71058	TCT		0.488	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		T	69049681	C	T	69049681	2	4	61	1	0	0	0	0	0	0	0	1	874	912	32	3		3	ARHGAP25	2	69049681	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4597	69049681	174149692	1457	9442										
GKN1	56287	broad.mit.edu	37	chr2	69201798	69201798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcctctgtccactgctttCgtgaagacaagatgaagttc	8	11	1	4	rs141746794		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69201798C>T	ENST00000377938.2	+	1	94	c.31C>T	c.(31-33)Cgt>Tgt	p.R11C		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	11					digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)		p.R11C(1)		breast(2)|large_intestine(4)|lung(5)	11						CCACTGCTTTCGTGAAGACAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG	0,4406		0,0,2203	173	154	161		31	-1.6	0.1	2	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	GKN1	NM_019617.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	11/200	69201798	1,13005	2203	4300	6503	69055302	SO:0001583	missense	56287			AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"BRICHOS domain containing"	23217	protein-coding gene	gene with protein product	"BRICHOS domain containing 1"	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.31C>T	2.37:g.69201798C>T	ENSP00000367172:p.Arg11Cys		69055302	Q8IUA9	Missense_Mutation	SNP	ENST00000377938.2	37	CCDS1891.2	.	.	.	.	.	.	.	.	.	.	C	8.210	0.800099	0.16397	0.0	1.16E-4	ENSG00000169605	ENST00000377938	T	0.48522	0.81	5.35	-1.6	0.08426	.	1.119980	0.06955	N	0.815227	T	0.24122	0.0584	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.23655	-1.0182	10	0.48119	T	0.1	0.0244	9.0111	0.36142	0.0:0.3346:0.4654:0.2001	.	11	Q9NS71	GKN1_HUMAN	C	11	ENSP00000367172:R11C	ENSP00000367172:R11C	R	+	1	0	GKN1	69055302	0.000000	0.05858	0.114000	0.21550	0.559000	0.35586	-0.230000	0.09083	-0.154000	0.11118	-0.982000	0.02568	CGT		0.413	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617		T	69201798	C	T	69201798	3	4	61	1	0	0	0	0	1	0	0	0	6444	884	31	1	33	1	GKN1	2	69201798	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152117	69201798	173997575	1458	9443										
GFPT1	2673	broad.mit.edu	37	chr2	69586437	69586437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtagttggtgatgattCcattgtgaataacgataaat	9	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69586437C>T	ENST00000357308.4	-	5	549	c.371G>A	c.(370-372)gGa>gAa	p.G124E	GFPT1_ENST00000361060.5_Missense_Mutation_p.G124E	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1	124	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|circadian regulation of gene expression (GO:0032922)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glucosamine biosynthetic process (GO:0006042)|glutamine metabolic process (GO:0006541)|negative regulation of glycogen biosynthetic process (GO:0045719)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|protein N-linked glycosylation via asparagine (GO:0018279)|response to sucrose (GO:0009744)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.G124E(1)		endometrium(1)|large_intestine(3)|lung(5)|skin(3)	12						GGTGATGATTCCATTGTGAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	78	75					2																	69586437		2203	4300	6503	69439941	SO:0001583	missense	2673				CCDS33216.1, CCDS58713.1	2p13	2014-09-17	2010-05-11		ENSG00000198380	ENSG00000198380	2.6.1.16		4241	protein-coding gene	gene with protein product		138292	"glutamine-fructose-6-phosphate transaminase 1"	GFPT		1460020	Standard	NM_002056		Approved	GFAT, GFA, GFAT1	uc002sfi.2	Q06210	OTTHUMG00000152666	ENST00000357308.4:c.371G>A	2.37:g.69586437C>T	ENSP00000349860:p.Gly124Glu		69439941	Q53QE6|Q9BXF8	Missense_Mutation	SNP	ENST00000357308.4	37	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776825	0.90195	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	D;D	0.97575	-4.44;-4.44	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.99230	0.9732	H	0.99582	4.64	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.98472	1.0601	10	0.87932	D	0	-18.8729	17.1804	0.86853	0.0:1.0:0.0:0.0	.	124	Q06210-2	.	E	124	ENSP00000349860:G124E;ENSP00000354347:G124E	ENSP00000349860:G124E	G	-	2	0	GFPT1	69439941	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.320000	0.79064	2.699000	0.92147	0.563000	0.77884	GGA		0.333	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	69586437	C	T	69586437	3	4	61	1	0	0	0	0	1	0	0	0	6365	855	30	3	1734	3	GFPT1	2	69586437	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	384639	69586437	173612936	1459	9444										
AAK1	22848	broad.mit.edu	37	chr2	69732794	69732794	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgagcctccaagcttctCgggatgtttgcctggagaga	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69732794C>T	ENST00000409085.4	-	16	2552	c.2176G>A	c.(2176-2178)Gag>Aag	p.E726K	AAK1_ENST00000406297.3_Missense_Mutation_p.E726K|AAK1_ENST00000409068.1_Intron	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	726					endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)	p.E726K(2)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CCAAGCTTCTCGGGATGTTTG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	2											62	63	63					2																	69732794		1906	4113	6019	69586298	SO:0001583	missense	22848			AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.2176G>A	2.37:g.69732794C>T	ENSP00000386456:p.Glu726Lys		69586298	Q4ZFZ3|Q53RX6|Q9UPV4	Missense_Mutation	SNP	ENST00000409085.4	37	CCDS1893.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029298	0.75504	.	.	ENSG00000115977	ENST00000409085;ENST00000406297	T;T	0.32753	1.44;1.44	5.67	5.67	0.87782	.	0.165937	0.51477	D	0.000088	T	0.37812	0.1017	L	0.34521	1.04	0.54753	D	0.999984	P;P;D	0.69078	0.649;0.761;0.997	B;B;P	0.54026	0.06;0.128;0.74	T	0.02064	-1.1220	10	0.29301	T	0.29	-23.7129	18.3583	0.90365	0.0:1.0:0.0:0.0	.	726;726;726	B7ZLC4;Q2M2I8-2;Q2M2I8	.;.;AAK1_HUMAN	K	726	ENSP00000386456:E726K;ENSP00000385181:E726K	ENSP00000385181:E726K	E	-	1	0	AAK1	69586298	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.225000	0.65294	2.675000	0.91044	0.655000	0.94253	GAG		0.488	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		T	69732794	C	T	69732794	3	4	61	1	0	0	0	0	1	0	0	0	16	893	31	1	737	1	AAK1	2	69732794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146357	69732794	173466579	1460	9445										
AAK1	22848	broad.mit.edu	37	chr2	69769766	69769766	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtaaagcctgtttgcagGcgctggttcatcaggtttac	11	9	3	0	rs367688452		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:69769766G>A	ENST00000409085.4	-	5	799	c.423C>T	c.(421-423)cgC>cgT	p.R141R	AAK1_ENST00000406297.3_Silent_p.R141R|AAK1_ENST00000470281.1_5'UTR|AAK1_ENST00000409068.1_Silent_p.R141R	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	141	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)	p.R141R(2)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CTGTTTGCAGGCGCTGGTTCA	0.473																																																2	Substitution - coding silent(2)	large_intestine(2)	2											137	139	139					2																	69769766		1911	4137	6048	69623270	SO:0001819	synonymous_variant	22848			AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.423C>T	2.37:g.69769766G>A			69623270	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																				0.473	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		A	69769766	G	A	69769766	2	1	61	1	0	0	0	0	0	0	0	1	16	1190	42	3		3	AAK1	2	69769766	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36972	69769766	173429607	1461	9446										
GMCL1	64395	broad.mit.edu	37	chr2	70076860	70076860	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaacagatgtctggttttCtaaacagaggaaaggtaggc	12	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:70076860C>A	ENST00000282570.3	+	8	1171	c.920C>A	c.(919-921)tCt>tAt	p.S307Y		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	307					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)		p.S307Y(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						GTCTGGTTTTCTAAACAGAGG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											73	75	75					2																	70076860		2203	4299	6502	69930364	SO:0001583	missense	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.920C>A	2.37:g.70076860C>A	ENSP00000282570:p.Ser307Tyr		69930364	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	37	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	C	5.690	0.311841	0.10789	.	.	ENSG00000087338	ENST00000282570	T	0.56776	0.44	5.56	5.56	0.83823	.	0.054264	0.85682	D	0.000000	T	0.37785	0.1016	L	0.27053	0.805	0.40082	D	0.976146	B	0.12013	0.005	B	0.11329	0.006	T	0.28490	-1.0042	10	0.02654	T	1	-13.067	17.0154	0.86418	0.0:1.0:0.0:0.0	.	307	Q96IK5	GMCL1_HUMAN	Y	307	ENSP00000282570:S307Y	ENSP00000282570:S307Y	S	+	2	0	GMCL1	69930364	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	4.257000	0.58816	2.605000	0.88082	0.655000	0.94253	TCT		0.318	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		A	70076860	C	A	70076860	3	1	61	1	0	0	0	0	1	0	0	0	6505	913	32	2	950	2	GMCL1	2	70076860	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	307094	70076860	173122513	1462	9447										
MXD1	4084	broad.mit.edu	37	chr2	70162550	70162550	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttggacccgaatcaagtCgacacactacgttgagttta	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:70162550C>T	ENST00000264444.2	+	4	531	c.271C>T	c.(271-273)Cga>Tga	p.R91*	MXD1_ENST00000540449.1_Nonsense_Mutation_p.R81*	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	91	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)	p.R91*(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						CGAATCAAGTCGACACACTAC	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											120	101	107					2																	70162550		2203	4300	6503	70016054	SO:0001587	stop_gained	4084				CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.271C>T	2.37:g.70162550C>T	ENSP00000264444:p.Arg91*		70016054	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Nonsense_Mutation	SNP	ENST00000264444.2	37	CCDS1896.1	.	.	.	.	.	.	.	.	.	.	C	37	6.511282	0.97624	.	.	ENSG00000059728	ENST00000435990;ENST00000264444;ENST00000540449	.	.	.	5.94	5.06	0.68205	.	0.053582	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.6773	0.56901	0.4027:0.5973:0.0:0.0	.	.	.	.	X	59;91;81	.	ENSP00000264444:R91X	R	+	1	2	MXD1	70016054	0.028000	0.19301	0.982000	0.44146	0.980000	0.70556	0.220000	0.17660	1.514000	0.48869	0.555000	0.69702	CGA		0.448	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357		T	70162550	C	T	70162550	4	4	61	1	0	0	0	0	0	1	0	0	10029	876	31	1	285	1	MXD1	2	70162550	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85690	70162550	173036823	1463	9448										
PCBP1	5093	broad.mit.edu	37	chr2	70314922	70314922	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaaatgtgactctcaccaTtcggcttcttatgcacggaa	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:70314922T>A	ENST00000303577.5	+	1	338	c.47T>A	c.(46-48)aTt>aAt	p.I16N	PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	16	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.I16N(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						ACTCTCACCATTCGGCTTCTT	0.562																																					Colon(85;1146 1307 3484 18706 25380)											1	Substitution - Missense(1)	large_intestine(1)	2											101	102	102					2																	70314922		2203	4300	6503	70168426	SO:0001583	missense	5093				CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.47T>A	2.37:g.70314922T>A	ENSP00000305556:p.Ile16Asn		70168426	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	37	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	T	19.14	3.770039	0.69992	.	.	ENSG00000169564	ENST00000303577	T	0.32753	1.44	4.03	4.03	0.46877	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	M	0.91510	3.215	0.80722	D	1	D	0.63880	0.993	D	0.72982	0.979	T	0.69628	-0.5094	10	0.87932	D	0	.	11.6121	0.51066	0.0:0.0:0.0:1.0	.	16	Q15365	PCBP1_HUMAN	N	16	ENSP00000305556:I16N	ENSP00000305556:I16N	I	+	2	0	PCBP1	70168426	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.788000	0.69020	2.066000	0.61787	0.529000	0.55759	ATT		0.562	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70314922	T	A	70314922	3	1	61	1	0	0	0	0	1	0	0	0	11531	1493	52	5	49	5	PCBP1	2	70314922	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	152372	70314922	172884451	1464	9449										
TIA1	7072	broad.mit.edu	37	chr2	70443341	70443341	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaaaaaccatccctaccGaacaaatgaatatcctttat	2	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:70443341G>A	ENST00000433529.2	-	10	973	c.763C>T	c.(763-765)Cgg>Tgg	p.R255W	TIA1_ENST00000445587.1_Splice_Site_p.R244C|TIA1_ENST00000415783.2_Splice_Site_p.R244W|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000482876.1_5'UTR|TIA1_ENST00000282574.4_Splice_Site_p.R255W	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	255	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)	p.R255W(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						CATCCCTACCGAACAAATGAA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	2											33	32	33					2																	70443341		2203	4297	6500	70296845	SO:0001630	splice_region_variant	7072				CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001		"RNA binding motif (RRM) containing"	11802	protein-coding gene	gene with protein product	"T-cell-restricted intracellular antigen-1", "nucleolysin TIA-1 isoform p40"	603518	"TIA1 cytotoxic granule-associated RNA-binding protein"			8176212, 12486009	Standard	NM_022173		Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000433529.2:c.764+1C>T	2.37:g.70443341G>A			70296845	Q53SS9	Missense_Mutation	SNP	ENST00000433529.2	37	CCDS1901.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.87|16.87	3.243330|3.243330	0.58995|0.58995	.|.	.|.	ENSG00000116001|ENSG00000116001	ENST00000445587|ENST00000433529;ENST00000415783;ENST00000477807;ENST00000282574;ENST00000454815	T|T;T;T;T	0.17370|0.17370	2.28|2.28;2.28;2.28;2.28	5.22|5.22	4.33|4.33	0.51752|0.51752	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.168057|0.168057	0.53938|0.53938	D|D	0.000059|0.000059	T|T	0.42787|0.42787	0.1218|0.1218	M|M	0.77103|0.77103	2.36|2.36	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.44802|0.44802	-0.9304|-0.9304	8|10	0.87932|0.66056	D|D	0|0.02	-20.7668|-20.7668	13.9211|13.9211	0.63933|0.63933	0.0:0.0:0.8465:0.1535|0.0:0.0:0.8465:0.1535	.|.	.|244;255	.|P31483-2;P31483	.|.;TIA1_HUMAN	C|W	244|255;244;333;255;26	ENSP00000399567:R244C|ENSP00000401371:R255W;ENSP00000404023:R244W;ENSP00000282574:R255W;ENSP00000402263:R26W	ENSP00000399567:R244C|ENSP00000282574:R255W	R|R	-|-	1|1	0|2	TIA1|TIA1	70296845|70296845	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.697000|0.697000	0.40408|0.40408	2.368000|2.368000	0.44222|0.44222	1.404000|1.404000	0.46819|0.46819	0.491000|0.491000	0.48974|0.48974	CGT|CGG		0.284	TIA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251842.2	NM_022037	Missense_Mutation	A	70443341	G	A	70443341	5	1	61	1	0	0	0	0	0	0	1	0	15926	1072	37	1	413	1	TIA1	2	70443341	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128419	70443341	172756032	1465	9450										
CD207	50489	broad.mit.edu	37	chr2	71060161	71060161	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtacttccagccttgaGaaaccacctgtagaatatca	7	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71060161G>T	ENST00000410009.3	-	4	632	c.587C>A	c.(586-588)tCt>tAt	p.S196Y		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	196					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)	p.S196Y(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						CCAGCCTTGAGAAACCACCTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	66	67					2																	71060161		1877	4111	5988	70913669	SO:0001583	missense	50489			AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.587C>A	2.37:g.71060161G>T	ENSP00000386378:p.Ser196Tyr		70913669		Missense_Mutation	SNP	ENST00000410009.3	37		.	.	.	.	.	.	.	.	.	.	G	0.030	-1.343279	0.01277	.	.	ENSG00000116031	ENST00000410009	T	0.18016	2.24	5.35	2.47	0.30058	C-type lectin fold (1);C-type lectin (1);	0.274240	0.26450	N	0.024308	T	0.16041	0.0386	M	0.65975	2.015	0.09310	N	1	B	0.29085	0.232	B	0.24006	0.05	T	0.19063	-1.0317	10	0.62326	D	0.03	.	5.5051	0.16850	0.1767:0.0:0.6608:0.1625	.	196	Q9UJ71	CLC4K_HUMAN	Y	196	ENSP00000386378:S196Y	ENSP00000386378:S196Y	S	-	2	0	CD207	70913669	0.384000	0.25164	0.360000	0.25837	0.733000	0.41908	2.269000	0.43346	0.717000	0.32145	0.655000	0.94253	TCT		0.448	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		T	71060161	G	T	71060161	3	4	61	1	0	0	0	0	1	0	0	0	2989	942	33	2	411	2	CD207	2	71060161	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	616820	71060161	172139212	1466	9451										
VAX2	25806	broad.mit.edu	37	chr2	71159962	71159962	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagcagagacctggagaaGcgggcgtcctcctcagcctc	13	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71159962G>A	ENST00000234392.2	+	3	533	c.501G>A	c.(499-501)aaG>aaA	p.K167K	snoU13_ENST00000459218.1_RNA	NM_012476.2	NP_036608.1	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	167					axonogenesis (GO:0007409)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic eye morphogenesis (GO:0048048)|forebrain development (GO:0030900)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K167K(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	7						ACCTGGAGAAGCGGGCGTCCT	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	2											43	47	46					2																	71159962		2203	4300	6503	71013470	SO:0001819	synonymous_variant	25806			Y17791	CCDS1911.1	2p13.3	2011-06-20			ENSG00000116035	ENSG00000116035		"Homeoboxes / ANTP class : NKL subclass"	12661	protein-coding gene	gene with protein product		604295				10485894	Standard	NM_012476		Approved	DRES93	uc002shh.3	Q9UIW0	OTTHUMG00000129714	ENST00000234392.2:c.501G>A	2.37:g.71159962G>A			71013470	Q53Y33	Silent	SNP	ENST00000234392.2	37	CCDS1911.1																																																																																				0.647	VAX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251923.1			A	71159962	G	A	71159962	2	1	61	1	0	0	0	0	0	0	0	1	17175	962	34	3		3	VAX2	2	71159962	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99801	71159962	172039411	1467	9452										
ANKRD53	79998	broad.mit.edu	37	chr2	71211329	71211329	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcctatggcaggacatttCtctactatcagactgtggat	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71211329C>A	ENST00000360589.3	+	6	937				ANKRD53_ENST00000272421.6_Missense_Mutation_p.S327Y|ANKRD53_ENST00000457410.1_Intron|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000441349.1_Missense_Mutation_p.S238Y	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53									p.S327Y(1)		endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CAGGACATTTCTCTACTATCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											144	133	137					2																	71211329		2203	4300	6503	71064837	SO:0001627	intron_variant	79998			BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"Ankyrin repeat domain containing"	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.904-412C>A	2.37:g.71211329C>A			71064837	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067224	0.36470	.	.	ENSG00000144031	ENST00000272421;ENST00000441349	T;T	0.74632	-0.59;-0.86	3.96	3.96	0.45880	.	.	.	.	.	D	0.82889	0.5135	.	.	.	0.52501	D	0.999951	D;D	0.76494	0.998;0.999	P;D	0.64237	0.84;0.923	D	0.83994	0.0339	8	0.59425	D	0.04	.	11.7906	0.52068	0.0:1.0:0.0:0.0	.	238;327	C9JQK2;Q8N9V6-2	.;.	Y	327;238	ENSP00000272421:S327Y;ENSP00000388883:S238Y	ENSP00000272421:S327Y	S	+	2	0	ANKRD53	71064837	0.003000	0.15002	0.071000	0.20095	0.008000	0.06430	0.290000	0.18975	2.499000	0.84300	0.563000	0.77884	TCT		0.483	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933		A	71211329	C	A	71211329	1	1	61	0	1	0	0	0	0	0	0	0	679	913	32	2		2	ANKRD53	2	71211329	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51367	71211329	171988044	1468	9453										
MCEE	84693	broad.mit.edu	37	chr2	71351592	71351592	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgacccaggttccacacaGaacctgtcacttgatccaag	8	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71351592G>T	ENST00000244217.5	-	2	139	c.122C>A	c.(121-123)tCt>tAt	p.S41Y	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	41					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)	p.S41Y(1)		kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GTTCCACACAGAACCTGTCAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											114	123	120					2																	71351592		2203	4300	6503	71205100	SO:0001583	missense	84693			AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"glyoxalase domain containing 2"	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.122C>A	2.37:g.71351592G>T	ENSP00000244217:p.Ser41Tyr		71205100	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.185660	0.38609	.	.	ENSG00000124370	ENST00000244217	T	0.65549	-0.16	5.33	1.25	0.21368	.	0.769218	0.12686	N	0.447558	T	0.44912	0.1316	L	0.39898	1.24	0.09310	N	1	P	0.47604	0.898	B	0.36766	0.232	T	0.32375	-0.9909	10	0.52906	T	0.07	-5.5935	5.3569	0.16065	0.0767:0.244:0.5446:0.1347	.	41	Q96PE7	MCEE_HUMAN	Y	41	ENSP00000244217:S41Y	ENSP00000244217:S41Y	S	-	2	0	MCEE	71205100	0.999000	0.42202	0.000000	0.03702	0.032000	0.12392	3.710000	0.54860	0.018000	0.15052	0.650000	0.86243	TCT		0.468	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601		T	71351592	G	T	71351592	3	4	61	1	0	0	0	0	1	0	0	0	9407	942	33	2	416	2	MCEE	2	71351592	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140263	71351592	171847781	1469	9454										
ZNF638	27332	broad.mit.edu	37	chr2	71650056	71650056	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtactcccagcattcaaacaGaaactttggtacagcaggaa	8	10	1	1	rs4130106		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71650056G>T	ENST00000409544.1	+	22	4042	c.3412G>T	c.(3412-3414)Gaa>Taa	p.E1138*	ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Nonsense_Mutation_p.E78*|ZNF638_ENST00000264447.4_Nonsense_Mutation_p.E1138*	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1138	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E1138*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CATTCAAACAGAAACTTTGGT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											97	95	96					2																	71650056		2203	4300	6503	71503564	SO:0001587	stop_gained	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3412G>T	2.37:g.71650056G>T	ENSP00000386433:p.Glu1138*		71503564	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Nonsense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	46	12.665327	0.99687	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	.	.	.	5.54	4.65	0.58169	.	0.104719	0.42682	D	0.000678	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-10.6596	9.6204	0.39719	0.0933:0.0:0.9067:0.0	.	.	.	.	X	717;1138;1138;78;78	.	ENSP00000264447:E1138X	E	+	1	0	ZNF638	71503564	0.999000	0.42202	0.995000	0.50966	0.342000	0.28953	3.465000	0.53064	2.764000	0.94973	0.655000	0.94253	GAA		0.413	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71650056	G	T	71650056	4	4	61	1	0	0	0	0	0	1	0	0	18094	943	33	2	3494	2	ZNF638	2	71650056	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298464	71650056	171549317	1470	9455										
ZNF638	27332	broad.mit.edu	37	chr2	71650501	71650501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgtgacgttagtaccagGaattcccactggggatgaga	12	7	0	2	rs370324872		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71650501G>A	ENST00000409544.1	+	22	4487	c.3857G>A	c.(3856-3858)gGa>gAa	p.G1286E	ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Missense_Mutation_p.G226E|ZNF638_ENST00000264447.4_Missense_Mutation_p.G1286E	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1286	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.G1286E(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTAGTACCAGGAATTCCCACT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	53	53					2																	71650501		2203	4298	6501	71504009	SO:0001583	missense	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3857G>A	2.37:g.71650501G>A	ENSP00000386433:p.Gly1286Glu		71504009	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	5.369	0.253349	0.10185	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.33438	1.45;1.45;1.41	5.49	2.74	0.32292	.	0.499782	0.20538	N	0.090368	T	0.22166	0.0534	L	0.34521	1.04	0.09310	N	0.999998	B;B;P	0.48589	0.044;0.01;0.912	B;B;P	0.47673	0.021;0.012;0.554	T	0.10636	-1.0621	10	0.05351	T	0.99	-2.8481	7.9263	0.29876	0.2482:0.0:0.7518:0.0	.	1286;1286;1286	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	E	865;1286;1286;226;226	ENSP00000264447:G1286E;ENSP00000386433:G1286E;ENSP00000386813:G226E	ENSP00000264447:G1286E	G	+	2	0	ZNF638	71504009	0.029000	0.19370	0.002000	0.10522	0.005000	0.04900	0.766000	0.26560	0.381000	0.24851	-0.251000	0.11542	GGA		0.363	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71650501	G	A	71650501	3	1	61	1	0	0	0	0	1	0	0	0	18094	1174	41	3	3939	3	ZNF638	2	71650501	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	445	71650501	171548872	1471	9456										
ZNF638	27332	broad.mit.edu	37	chr2	71654054	71654054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttggtaactgtggatgaAattggagaagtggaagagct	15	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71654054A>G	ENST00000409544.1	+	24	5685	c.5055A>G	c.(5053-5055)gaA>gaG	p.E1685E	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Silent_p.E625E|ZNF638_ENST00000264447.4_Silent_p.E1685E	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1685					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E1685E(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CTGTGGATGAAATTGGAGAAG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	2											101	102	102					2																	71654054		2203	4300	6503	71507562	SO:0001819	synonymous_variant	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5055A>G	2.37:g.71654054A>G			71507562	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																				0.403	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71654054	A	G	71654054	2	3	61	1	0	0	0	0	0	0	0	1	18094	11	1	4		4	ZNF638	2	71654054	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3553	71654054	171545319	1472	9457										
DYSF	8291	broad.mit.edu	37	chr2	71883306	71883306	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaggtctatgacacacaGctggagaatgtggaggcctt	14	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71883306G>T	ENST00000258104.3	+	42	4801	c.4524G>T	c.(4522-4524)caG>caT	p.Q1508H	DYSF_ENST00000409366.1_Missense_Mutation_p.Q1530H|DYSF_ENST00000409762.1_Missense_Mutation_p.Q1525H|DYSF_ENST00000409744.1_Missense_Mutation_p.Q1516H|DYSF_ENST00000394120.2_Missense_Mutation_p.Q1509H|DYSF_ENST00000410041.1_Missense_Mutation_p.Q1526H|DYSF_ENST00000409582.3_Missense_Mutation_p.Q1546H|DYSF_ENST00000409651.1_Missense_Mutation_p.Q1540H|DYSF_ENST00000410020.3_Missense_Mutation_p.Q1547H|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Missense_Mutation_p.Q1539H|DYSF_ENST00000429174.2_Missense_Mutation_p.Q1529H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1508					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.Q1508H(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						ATGACACACAGCTGGAGAATG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2											160	160	160					2																	71883306		2203	4300	6503	71736814	SO:0001583	missense	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4524G>T	2.37:g.71883306G>T	ENSP00000258104:p.Gln1508His		71736814	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750327	0.49257	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.64;-1.64;-1.65;-1.65;-1.65;-1.64;-1.64;-1.64;-1.65	5.54	-4.15	0.03881	.	0.644414	0.16613	N	0.206840	T	0.72645	0.3486	N	0.22421	0.69	0.27733	N	0.944741	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.29253	0.239;0.238;0.238;0.238;0.238;0.13;0.13;0.13;0.065;0.238;0.065;0.065;0.143;0.238;0.153	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.38264	0.212;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.269;0.139	T	0.66060	-0.6017	10	0.66056	D	0.02	-0.0742	11.5042	0.50456	0.1735:0.1218:0.7048:0.0	.	272;1540;1547;1530;1495;1526;1516;1525;1515;1539;1546;1529;1494;1509;1508	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	1539;1525;1546;1529;1508;1540;1509;1516;1530;1547;1526	ENSP00000407046:Q1539H;ENSP00000387137:Q1525H;ENSP00000386547:Q1546H;ENSP00000398305:Q1529H;ENSP00000258104:Q1508H;ENSP00000386683:Q1540H;ENSP00000377678:Q1509H;ENSP00000386285:Q1516H;ENSP00000386512:Q1530H;ENSP00000386881:Q1547H;ENSP00000386617:Q1526H	ENSP00000258104:Q1508H	Q	+	3	2	DYSF	71736814	0.988000	0.35896	0.443000	0.26883	0.994000	0.84299	0.328000	0.19681	-0.760000	0.04677	-0.290000	0.09829	CAG		0.502	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71883306	G	T	71883306	3	4	61	1	0	0	0	0	1	0	0	0	4870	962	34	2	4949	2	DYSF	2	71883306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229252	71883306	171316067	1473	9458										
DYSF	8291	broad.mit.edu	37	chr2	71896785	71896785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacagacgtgcattatcGttccctgggaggtgaaggca	13	8	0	3	rs143939123	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:71896785G>A	ENST00000258104.3	+	50	5853	c.5576G>A	c.(5575-5577)cGt>cAt	p.R1859H	DYSF_ENST00000409366.1_Missense_Mutation_p.R1881H|DYSF_ENST00000409762.1_Missense_Mutation_p.R1876H|DYSF_ENST00000409744.1_Missense_Mutation_p.R1867H|DYSF_ENST00000394120.2_Missense_Mutation_p.R1860H|DYSF_ENST00000410041.1_Missense_Mutation_p.R1877H|DYSF_ENST00000409582.3_Missense_Mutation_p.R1897H|DYSF_ENST00000409651.1_Missense_Mutation_p.R1891H|DYSF_ENST00000410020.3_Missense_Mutation_p.R1898H|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Missense_Mutation_p.R1890H|DYSF_ENST00000429174.2_Missense_Mutation_p.R1880H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1859	C2 7. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R1859H(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GTGCATTATCGTTCCCTGGGA	0.438													G|||	2	0.000399361	0.0015	0	5008	,	,		23536	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	219	182	194		5579,5534,5597,5639,5669,5627,5690,5672,5642,5600,5630,5537,5693,5576	4.9	1	2	dbSNP_134	194	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	29,29,29,29,29,29,29,29,29,29,29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1860/2082,1845/2067,1866/2088,1880/2102,1890/2112,1876/2098,1897/2119,1891/2113,1881/2103,1867/2089,1877/2099,1846/2068,1898/2120,1859/2081	71896785	1,13005	2203	4300	6503	71750293	SO:0001583	missense	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5576G>A	2.37:g.71896785G>A	ENSP00000258104:p.Arg1859His		71750293	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831448	0.91036	0.0	1.16E-4	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	4.87	4.87	0.63330	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.098372	0.64402	D	0.000003	D	0.95294	0.8473	M	0.84433	2.695	0.52099	D	0.999946	D;D;D;D;D;D;D;D;D;D;D;P;D;D;D	0.89917	0.999;0.999;0.999;0.996;0.996;1.0;1.0;1.0;0.977;0.999;0.973;0.614;0.996;0.996;0.999	D;P;D;P;P;D;D;D;P;D;P;B;P;P;D	0.72338	0.967;0.897;0.91;0.897;0.852;0.977;0.977;0.977;0.476;0.938;0.606;0.228;0.897;0.897;0.938	D	0.94569	0.7769	10	0.40728	T	0.16	-26.1585	15.8904	0.79293	0.0:0.0:1.0:0.0	.	623;1891;1898;1881;1846;1877;1867;1876;1866;1890;1897;1880;1845;1860;1859	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	1890;1876;1897;1880;1859;1891;1860;1867;1881;1898;1877	ENSP00000407046:R1890H;ENSP00000387137:R1876H;ENSP00000386547:R1897H;ENSP00000398305:R1880H;ENSP00000258104:R1859H;ENSP00000386683:R1891H;ENSP00000377678:R1860H;ENSP00000386285:R1867H;ENSP00000386512:R1881H;ENSP00000386881:R1898H;ENSP00000386617:R1877H	ENSP00000258104:R1859H	R	+	2	0	DYSF	71750293	1.000000	0.71417	0.990000	0.47175	0.912000	0.54170	9.492000	0.97957	2.698000	0.92095	0.655000	0.94253	CGT		0.438	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71896785	G	A	71896785	3	1	61	1	0	0	0	0	1	0	0	0	4870	1145	40	1	6033	1	DYSF	2	71896785	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13479	71896785	171302588	1474	9459										
EXOC6B	23233	broad.mit.edu	37	chr2	72742224	72742224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgttttcgcctctgttttCggtagtaattctcaaatgtt	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:72742224C>T	ENST00000272427.6	-	9	1077	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	EXOC6B_ENST00000410104.1_Missense_Mutation_p.R316Q	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	316					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)		p.R316Q(1)		breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						CCTCTGTTTTCGGTAGTAATT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	77	77					2																	72742224		1860	4096	5956	72595732	SO:0001583	missense	23233			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.947G>A	2.37:g.72742224C>T	ENSP00000272427:p.Arg316Gln		72595732	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	37	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	C	35	5.538349	0.96460	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.32272	1.46;1.46	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.60521	0.2275	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.78314	0.921;0.991	T	0.62081	-0.6929	10	0.33940	T	0.23	.	17.0845	0.86608	0.0:1.0:0.0:0.0	.	316;316	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	Q	316	ENSP00000272427:R316Q;ENSP00000386698:R316Q	ENSP00000272427:R316Q	R	-	2	0	EXOC6B	72595732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.513000	0.81739	2.601000	0.87937	0.650000	0.86243	CGA		0.383	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		T	72742224	C	T	72742224	3	4	61	1	0	0	0	0	1	0	0	0	5322	884	31	1	1544	1	EXOC6B	2	72742224	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	845439	72742224	170457149	1475	9460										
SFXN5	94097	broad.mit.edu	37	chr2	73215392	73215392	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgcaggtcttacctacaGcagggaacggcacaaacctc	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73215392G>T	ENST00000272433.2	-	10	750	c.620C>A	c.(619-621)gCt>gAt	p.A207D	SFXN5_ENST00000474528.1_5'UTR|SFXN5_ENST00000410065.1_Missense_Mutation_p.A207D	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	207					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)	p.A207D(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						CTTACCTACAGCAGGGAACGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	2											111	96	101					2																	73215392		2203	4300	6503	73068900	SO:0001583	missense	94097			AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"Sideroflexins"	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.620C>A	2.37:g.73215392G>T	ENSP00000272433:p.Ala207Asp		73068900	A8K116|Q494Y3|Q53T29	Missense_Mutation	SNP	ENST00000272433.2	37	CCDS1922.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.7|28.7	4.943420|4.943420	0.92593|0.92593	.|.	.|.	ENSG00000144040|ENSG00000144040	ENST00000272433;ENST00000410065|ENST00000411783	T;T|.	0.55760|.	0.5;0.5|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.105878|.	0.64402|.	D|.	0.000005|.	D|.	0.87350|.	0.6155|.	H|H	0.95712|0.95712	3.71|3.71	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.997|.	D;D|.	0.87578|.	0.998;0.956|.	D|.	0.90733|.	0.4644|.	10|.	0.87932|.	D|.	0|.	-14.892|-14.892	17.0322|17.0322	0.86464|0.86464	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	207;207|.	B8ZZJ6;Q8TD22|.	.;SFXN5_HUMAN|.	D|X	207|196	ENSP00000272433:A207D;ENSP00000387076:A207D|.	ENSP00000272433:A207D|.	A|C	-|-	2|3	0|2	SFXN5|SFXN5	73068900|73068900	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.946000|7.946000	0.87746|0.87746	2.699000|2.699000	0.92147|0.92147	0.591000|0.591000	0.81541|0.81541	GCT|TGC		0.557	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579		T	73215392	G	T	73215392	3	4	61	1	0	0	0	0	1	0	0	0	14235	971	34	2	422	2	SFXN5	2	73215392	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	473168	73215392	169983981	1476	9461										
SMYD5	10322	broad.mit.edu	37	chr2	73452017	73452017	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacagttgtgtgcccaatGcagagacctcctttccagaa	8	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73452017G>T	ENST00000389501.4	+	11	1009	c.964G>T	c.(964-966)Gca>Tca	p.A322S		NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	322	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.A206S(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						TGTGCCCAATGCAGAGACCTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											128	110	116					2																	73452017		2203	4300	6503	73305525	SO:0001583	missense	10322			U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.964G>T	2.37:g.73452017G>T	ENSP00000374152:p.Ala322Ser		73305525	D6W5H3|Q13558	Missense_Mutation	SNP	ENST00000389501.4	37	CCDS33221.2	.	.	.	.	.	.	.	.	.	.	G	31	5.096453	0.94197	.	.	ENSG00000135632	ENST00000389501	D	0.83075	-1.68	5.06	5.06	0.68205	SET domain (3);	0.051795	0.85682	D	0.000000	D	0.90407	0.6997	M	0.77103	2.36	0.80722	D	1	D	0.69078	0.997	D	0.64877	0.93	D	0.90686	0.4609	10	0.56958	D	0.05	-9.555	17.5337	0.87822	0.0:0.0:1.0:0.0	.	322	Q6GMV2	SMYD5_HUMAN	S	322	ENSP00000374152:A322S	ENSP00000374152:A322S	A	+	1	0	SMYD5	73305525	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.542000	0.98086	2.813000	0.96785	0.655000	0.94253	GCA		0.483	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		T	73452017	G	T	73452017	3	4	61	1	0	0	0	0	1	0	0	0	14862	1319	46	2	1006	2	SMYD5	2	73452017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236625	73452017	169747356	1477	9462										
SMYD5	10322	broad.mit.edu	37	chr2	73452805	73452805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcagcgggagcgcagccGccacagccgccacaagatcc	12	17	1	1	rs139106271		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73452805G>A	ENST00000389501.4	+	12	1127	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	PRADC1_ENST00000480093.1_5'Flank	NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	361							metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.R245H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						GAGCGCAGCCGCCACAGCCGC	0.562													G|||	1	0.000199681	8e-04	0	5008	,	,		14647	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	87	104	98		1082	4.9	1	2	dbSNP_134	98	0,8600		0,0,4300	yes	missense	SMYD5	NM_006062.2	29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	possibly-damaging	361/419	73452805	3,13003	2203	4300	6503	73306313	SO:0001583	missense	10322			U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.1082G>A	2.37:g.73452805G>A	ENSP00000374152:p.Arg361His		73306313	D6W5H3|Q13558	Missense_Mutation	SNP	ENST00000389501.4	37	CCDS33221.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	34	5.337107	0.95758	6.81E-4	0.0	ENSG00000135632	ENST00000389501	T	0.56611	0.45	4.86	4.86	0.63082	.	0.060009	0.64402	D	0.000004	T	0.63390	0.2507	M	0.78456	2.415	0.80722	D	1	D	0.65815	0.995	P	0.51945	0.685	T	0.61004	-0.7150	10	0.16896	T	0.51	-10.7965	17.0836	0.86604	0.0:0.0:1.0:0.0	.	361	Q6GMV2	SMYD5_HUMAN	H	361	ENSP00000374152:R361H	ENSP00000374152:R361H	R	+	2	0	SMYD5	73306313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.516000	0.98017	2.704000	0.92352	0.655000	0.94253	CGC		0.562	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		A	73452805	G	A	73452805	3	1	61	1	0	0	0	0	1	0	0	0	14862	1087	38	1	1128	1	SMYD5	2	73452805	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	788	73452805	169746568	1478	9463										
ALMS1	7840	broad.mit.edu	37	chr2	73679174	73679174	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggaccagctgaccagaaGactggaataaacatcctgcc	9	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73679174G>A	ENST00000264448.6	+	8	5628	c.5517G>A	c.(5515-5517)aaG>aaA	p.K1839K	ALMS1_ENST00000377715.1_Silent_p.K1839K|ALMS1_ENST00000409009.1_Silent_p.K1797K	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1839	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.K1839K(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTGACCAGAAGACTGGAATAA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	2											82	78	79					2																	73679174		1845	4099	5944	73532682	SO:0001819	synonymous_variant	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.5517G>A	2.37:g.73679174G>A			73532682	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																				0.448	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73679174	G	A	73679174	2	1	61	1	0	0	0	0	0	0	0	1	535	933	33	3		3	ALMS1	2	73679174	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226369	73679174	169520199	1479	9464										
ALMS1	7840	broad.mit.edu	37	chr2	73680193	73680193	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagctgatcaaattaccgGattacaaacagttccctctg	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73680193G>T	ENST00000264448.6	+	8	6647	c.6536G>T	c.(6535-6537)gGa>gTa	p.G2179V	ALMS1_ENST00000377715.1_Missense_Mutation_p.G2179V|ALMS1_ENST00000409009.1_Missense_Mutation_p.G2137V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2179	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.G2179V(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CAAATTACCGGATTACAAACA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											83	77	79					2																	73680193		1870	4101	5971	73533701	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6536G>T	2.37:g.73680193G>T	ENSP00000264448:p.Gly2179Val		73533701	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	2.943	-0.218557	0.06101	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.17054	3.17;3.17;2.3	5.46	0.112	0.14623	.	0.602091	0.14982	N	0.287172	T	0.10981	0.0268	N	0.25890	0.77	0.19300	N	0.99997	B;B;B	0.32302	0.078;0.242;0.363	B;B;B	0.36378	0.069;0.161;0.223	T	0.23940	-1.0174	10	0.66056	D	0.02	.	3.7002	0.08379	0.2802:0.0:0.3166:0.4032	.	2179;2137;2179	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	V	2137;2179;2179	ENSP00000386627:G2137V;ENSP00000264448:G2179V;ENSP00000366944:G2179V	ENSP00000264448:G2179V	G	+	2	0	ALMS1	73533701	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.057000	0.11768	-0.112000	0.11979	-0.140000	0.14226	GGA		0.378	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73680193	G	T	73680193	3	4	61	1	0	0	0	0	1	0	0	0	535	1174	41	2	6566	2	ALMS1	2	73680193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1019	73680193	169519180	1480	9465										
ALMS1	7840	broad.mit.edu	37	chr2	73716882	73716882	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacatccacaactagataGacacccttgtgctttcagat	6	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73716882G>T	ENST00000264448.6	+	10	7904	c.7793G>T	c.(7792-7794)aGa>aTa	p.R2598I	ALMS1_ENST00000409009.1_Missense_Mutation_p.R2556I|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2598					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.R2598I(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CAACTAGATAGACACCCTTGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	89	90					2																	73716882		1941	4129	6070	73570390	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7793G>T	2.37:g.73716882G>T	ENSP00000264448:p.Arg2598Ile		73570390	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	4.632	0.117555	0.08881	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.06371	3.31;3.31	4.45	0.611	0.17586	.	1.013620	0.07890	N	0.971091	T	0.04003	0.0112	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43940	-0.9360	10	0.72032	D	0.01	.	3.7056	0.08400	0.3065:0.187:0.5065:0.0	.	2598;2556;2598	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	I	2556;2598	ENSP00000386627:R2556I;ENSP00000264448:R2598I	ENSP00000264448:R2598I	R	+	2	0	ALMS1	73570390	0.001000	0.12720	0.000000	0.03702	0.034000	0.12701	0.352000	0.20113	0.091000	0.17302	0.650000	0.86243	AGA		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73716882	G	T	73716882	3	4	61	1	0	0	0	0	1	0	0	0	535	942	33	2	7831	2	ALMS1	2	73716882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36689	73716882	169482491	1481	9466										
ALMS1	7840	broad.mit.edu	37	chr2	73718420	73718420	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctgtagcacaggatcaaGaatctttaggttttctagga	9	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73718420G>T	ENST00000264448.6	+	10	9442	c.9331G>T	c.(9331-9333)Gaa>Taa	p.E3111*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.E3069*|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3111					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E3111*(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						ACAGGATCAAGAATCTTTAGG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											101	96	97					2																	73718420		1861	4094	5955	73571928	SO:0001587	stop_gained	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.9331G>T	2.37:g.73718420G>T	ENSP00000264448:p.Glu3111*		73571928	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	51	17.391595	0.99885	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	.	.	.	4.12	4.12	0.48240	.	0.000000	0.47093	D	0.000248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	12.1941	0.54288	0.0:0.0:1.0:0.0	.	.	.	.	X	3069;3111	.	ENSP00000264448:E3111X	E	+	1	0	ALMS1	73571928	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.534000	0.36051	2.617000	0.88574	0.580000	0.79431	GAA		0.388	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73718420	G	T	73718420	4	4	61	1	0	0	0	0	0	1	0	0	535	943	33	2	9369	2	ALMS1	2	73718420	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1538	73718420	169480953	1482	9467										
ALMS1	7840	broad.mit.edu	37	chr2	73829360	73829360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatctcccgctctggggagCggataaagcgcctgaagtta	12	11	3	1	rs569696567		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73829360C>T	ENST00000264448.6	+	20	12271	c.12160C>T	c.(12160-12162)Cgg>Tgg	p.R4054W	ALMS1_ENST00000409009.1_Missense_Mutation_p.R4012W|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4054	ALMS motif.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.R4054W(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTCTGGGGAGCGGATAAAGCG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	52	50					2																	73829360		2202	4300	6502	73682868	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12160C>T	2.37:g.73829360C>T	ENSP00000264448:p.Arg4054Trp		73682868	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940292	0.73557	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.33865	1.39;1.39	5.38	3.53	0.40419	.	0.000000	0.64402	D	0.000003	T	0.50633	0.1627	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50346	-0.8839	10	0.87932	D	0	.	11.3515	0.49589	0.4817:0.5183:0.0:0.0	.	4012;4054	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	W	4012;4054	ENSP00000386627:R4012W;ENSP00000264448:R4054W	ENSP00000264448:R4054W	R	+	1	2	ALMS1	73682868	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	1.533000	0.36040	0.779000	0.33543	0.655000	0.94253	CGG		0.478	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73829360	C	T	73829360	3	4	61	1	0	0	0	0	1	0	0	0	535	759	27	1	12238	1	ALMS1	2	73829360	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110940	73829360	169370013	1483	9468										
DUSP11	8446	broad.mit.edu	37	chr2	73993721	73993721	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacactggaattccaattCcttaaagagaatattttcca	6	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73993721C>A	ENST00000272444.3	-	8	800	c.759G>T	c.(757-759)aaG>aaT	p.K253N	DUSP11_ENST00000480948.1_Intron	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	206					peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)	p.K206N(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						AATTCCAATTCCTTAAAGAGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	84	84					2																	73993721		2203	4300	6503	73847229	SO:0001630	splice_region_variant	8446			AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.759-1G>T	2.37:g.73993721C>A			73847229	B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	37	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	C	10.11	1.260412	0.23051	.	.	ENSG00000144048	ENST00000272444	.	.	.	4.82	3.93	0.45458	.	0.386777	0.30949	N	0.008560	T	0.45074	0.1324	L	0.56769	1.78	0.58432	D	0.999997	P	0.44627	0.839	B	0.38106	0.265	T	0.45366	-0.9266	9	0.45353	T	0.12	.	9.4518	0.38731	0.0:0.9019:0.0:0.0981	.	206	O75319	DUS11_HUMAN	N	253	.	ENSP00000272444:K253N	K	-	3	2	DUSP11	73847229	0.988000	0.35896	0.351000	0.25721	0.206000	0.24218	1.784000	0.38674	1.376000	0.46267	0.563000	0.77884	AAG		0.348	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3		Missense_Mutation	A	73993721	C	A	73993721	5	1	61	1	0	0	0	0	0	0	1	0	4822	869	30	2	382	2	DUSP11	2	73993721	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	164361	73993721	169205652	1484	9469										
DUSP11	8446	broad.mit.edu	37	chr2	73996446	73996446	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtacagtggacaccaataAgtttatctataaaaagaaaa	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:73996446A>C	ENST00000272444.3	-	5	622	c.581T>G	c.(580-582)cTt>cGt	p.L194R	DUSP11_ENST00000443070.1_Missense_Mutation_p.L194R|DUSP11_ENST00000377706.4_Missense_Mutation_p.L147R|DUSP11_ENST00000480948.1_5'UTR	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	147	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)	p.L147R(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						GACACCAATAAGTTTATCTAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											83	86	85					2																	73996446		2203	4300	6503	73849954	SO:0001583	missense	8446			AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.581T>G	2.37:g.73996446A>C	ENSP00000272444:p.Leu194Arg		73849954	B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	37	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923681	0.73213	.	.	ENSG00000144048	ENST00000272444;ENST00000443070;ENST00000377706	D;D;D	0.84873	-1.91;-1.91;-1.91	4.8	4.8	0.61643	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	M	0.84846	2.72	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.99	D	0.93234	0.6620	10	0.72032	D	0.01	-9.0045	12.6347	0.56677	1.0:0.0:0.0:0.0	.	194;147	C9JYA6;O75319	.;DUS11_HUMAN	R	194;194;147	ENSP00000272444:L194R;ENSP00000413444:L194R;ENSP00000366935:L147R	ENSP00000272444:L194R	L	-	2	0	DUSP11	73849954	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.927000	0.75840	2.144000	0.66660	0.528000	0.53228	CTT		0.363	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3			C	73996446	A	C	73996446	3	2	61	1	0	0	0	0	1	0	0	0	4822	72	3	4	572	4	DUSP11	2	73996446	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2725	73996446	169202927	1485	9470										
DUSP11	8446	broad.mit.edu	37	chr2	74000985	74000985	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgaatttaaaaatagtCtcatcatcaggcacttgatg	7	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74000985C>A	ENST00000272444.3	-	4	557	c.516G>T	c.(514-516)gaG>gaT	p.E172D	DUSP11_ENST00000443070.1_Missense_Mutation_p.E172D|DUSP11_ENST00000377706.4_Missense_Mutation_p.E125D|DUSP11_ENST00000480948.1_5'UTR	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	125	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)	p.E125D(2)		breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						TAAAAATAGTCTCATCATCAG	0.308																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											98	107	104					2																	74000985		2203	4299	6502	73854493	SO:0001583	missense	8446			AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.516G>T	2.37:g.74000985C>A	ENSP00000272444:p.Glu172Asp		73854493	B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	37	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	C	9.328	1.059747	0.19987	.	.	ENSG00000144048	ENST00000272444;ENST00000443070;ENST00000377706;ENST00000452812	D;D;D	0.85484	-1.99;-1.99;-1.99	4.95	1.85	0.25348	Dual specificity phosphatase, catalytic domain (1);	0.679638	0.14418	N	0.320843	T	0.68869	0.3048	N	0.20401	0.57	0.32517	N	0.536784	B;B	0.13145	0.007;0.0	B;B	0.10450	0.005;0.002	T	0.58896	-0.7555	10	0.05833	T	0.94	-0.0053	7.9804	0.30181	0.0:0.1491:0.3399:0.511	.	172;125	C9JYA6;O75319	.;DUS11_HUMAN	D	172;172;125;123	ENSP00000272444:E172D;ENSP00000413444:E172D;ENSP00000366935:E125D	ENSP00000272444:E172D	E	-	3	2	DUSP11	73854493	0.002000	0.14202	0.993000	0.49108	0.695000	0.40330	-0.457000	0.06745	0.237000	0.21200	-0.165000	0.13383	GAG		0.308	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3			A	74000985	C	A	74000985	3	1	61	1	0	0	0	0	1	0	0	0	4822	912	32	2	641	2	DUSP11	2	74000985	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4539	74000985	169198388	1486	9471										
C2orf78	388960	broad.mit.edu	37	chr2	74043283	74043283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcactcgggaaaaagatcGatatgaaaactggattctct	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74043283G>A	ENST00000409561.1	+	3	2054	c.1933G>A	c.(1933-1935)Gat>Aat	p.D645N		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	645								p.D615N(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						GAAAAAGATCGATATGAAAAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	56	55					2																	74043283		1872	4101	5973	73896791	SO:0001583	missense	388960			AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.1933G>A	2.37:g.74043283G>A	ENSP00000387124:p.Asp645Asn		73896791		Missense_Mutation	SNP	ENST00000409561.1	37	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105067	0.37145	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.48522	0.81	4.9	2.96	0.34315	.	0.602207	0.14612	N	0.308955	T	0.59032	0.2164	M	0.65975	2.015	0.09310	N	1	D	0.76494	0.999	P	0.62649	0.905	T	0.46233	-0.9206	10	0.62326	D	0.03	-5.4529	6.307	0.21145	0.1011:0.187:0.7119:0.0	.	645	A6NCI8	CB078_HUMAN	N	645;615	ENSP00000387124:D645N	ENSP00000340692:D615N	D	+	1	0	C2orf78	73896791	0.297000	0.24408	0.014000	0.15608	0.000000	0.00434	2.360000	0.44151	1.209000	0.43321	-0.251000	0.11542	GAT		0.507	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		A	74043283	G	A	74043283	3	1	61	1	0	0	0	0	1	0	0	0	2201	1058	37	1	1943	1	C2orf78	2	74043283	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42298	74043283	169156090	1487	9472										
TET3	200424	broad.mit.edu	37	chr2	74328397	74328397	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccagtgggggctgttcccCggtgaggggcagcaggcagc	20	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74328397C>T	ENST00000409262.3	+	9	4077	c.4077C>T	c.(4075-4077)ccC>ccT	p.P1359P		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1359					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.P636P(1)|p.P1359P(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGCTGTTCCCCGGTGAGGGGC	0.657																																																2	Substitution - coding silent(2)	large_intestine(2)	2											20	24	23					2																	74328397		1890	4105	5995	74181905	SO:0001819	synonymous_variant	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.4077C>T	2.37:g.74328397C>T			74181905	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																				0.657	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74328397	C	T	74328397	2	4	61	1	0	0	0	0	0	0	0	1	15810	639	23	1		1	TET3	2	74328397	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	285114	74328397	168870976	1488	9473										
BOLA3	388962	broad.mit.edu	37	chr2	74362773	74362773	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatgcatctctttgatttCttcttttagtgcctaagtaa	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74362773C>A	ENST00000327428.5	-	4	390	c.271G>T	c.(271-273)Gaa>Taa	p.E91*	BOLA3_ENST00000295326.4_Missense_Mutation_p.R61I	NM_212552.2	NP_997717.2	Q53S33	BOLA3_HUMAN	bolA family member 3	91						extracellular region (GO:0005576)		p.E91*(1)		large_intestine(1)|lung(1)	2						TCTTTGATTTCTTCTTTTAGT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											207	178	188					2																	74362773		2203	4300	6503	74216281	SO:0001587	stop_gained	388962			BC017744	CCDS33224.1, CCDS33225.1	2p13.1	2013-09-02	2013-09-02		ENSG00000163170	ENSG00000163170			24415	protein-coding gene	gene with protein product		613183	"bolA-like 3 (E. coli)", "bolA homolog 3 (E. coli)"			14718656	Standard	NM_001035505		Approved		uc002skc.1	Q53S33	OTTHUMG00000152834	ENST00000327428.5:c.271G>T	2.37:g.74362773C>A	ENSP00000331369:p.Glu91*		74216281	G3XAB0	Nonsense_Mutation	SNP	ENST00000327428.5	37	CCDS33225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.565259|5.565259	0.96527|0.96527	.|.	.|.	ENSG00000163170|ENSG00000163170	ENST00000327428|ENST00000295326	.|.	.|.	.|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79251	.|0.4414	.|.	.|.	.|.	0.46096|0.46096	D|D	0.998865|0.998865	.|D	.|0.76494	.|0.999	.|D	.|0.74023	.|0.982	.|T	.|0.81413	.|-0.0944	.|7	0.62326|0.87932	D|D	0.03|0	-14.6026|-14.6026	16.3832|16.3832	0.83489|0.83489	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|61	.|G3XAB0	.|.	X|I	91|61	.|.	ENSP00000331369:E91X|ENSP00000295326:R61I	E|R	-|-	1|2	0|0	BOLA3|BOLA3	74216281|74216281	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	5.594000|5.594000	0.67557|0.67557	2.804000|2.804000	0.96469|0.96469	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.413	BOLA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328207.2	NM_212552		A	74362773	C	A	74362773	4	1	61	1	0	0	0	0	0	1	0	0	1489	922	32	2	127	2	BOLA3	2	74362773	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34376	74362773	168836600	1489	9474										
MOBKL1B	55233	broad.mit.edu	37	chr2	74394224	74394224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatgttgatctggttaaaGaaatccacagctgcagagat	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74394224G>T	ENST00000396049.4	-	3	385	c.192C>A	c.(190-192)ttC>ttA	p.F64L	MOB1A_ENST00000497054.1_5'UTR|MOB1A_ENST00000409969.2_Missense_Mutation_p.F64L	NM_018221.3	NP_060691.2	Q9H8S9	MOB1A_HUMAN	MOB kinase activator 1A	64					hippo signaling (GO:0035329)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)	p.F64L(1)									TCTGGTTAAAGAAATCCACAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	98	99					2																	74394224		1875	4140	6015	74247732	SO:0001583	missense	55233				CCDS46340.1	2p13.1	2011-09-28	2011-09-28	2011-09-27	ENSG00000114978	ENSG00000114978		"MOB kinase activators"	16015	protein-coding gene	gene with protein product		609281	"chromosome 2 open reading frame 6", "MOB1, Mps One Binder kinase activator-like 1B (yeast)", "MOB1 Mps One Binder homolog A (yeast)"	C2orf6, MOBK1B, MOBKL1B		11319234, 20624913	Standard	NM_018221		Approved	FLJ10788, MOB1, FLJ11595, Mob4B, Mats1	uc002skh.4	Q9H8S9	OTTHUMG00000152833	ENST00000396049.4:c.192C>A	2.37:g.74394224G>T	ENSP00000379364:p.Phe64Leu		74247732	Q53S34|Q9H3T5|Q9HAI0|Q9NVE2	Missense_Mutation	SNP	ENST00000396049.4	37	CCDS46340.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342679	0.82022	.	.	ENSG00000114978	ENST00000396049;ENST00000409969	.	.	.	5.12	4.23	0.50019	.	0.106928	0.64402	D	0.000004	T	0.78566	0.4303	M	0.83603	2.65	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.80476	-0.1366	9	0.62326	D	0.03	.	11.7436	0.51807	0.0874:0.0:0.9126:0.0	.	64;64	Q9H8S9-2;Q9H8S9	.;MOB1A_HUMAN	L	64	.	ENSP00000379364:F64L	F	-	3	2	MOBKL1B	74247732	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.182000	0.50910	2.652000	0.90054	0.650000	0.86243	TTC		0.383	MOB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328200.2	NM_018221		T	74394224	G	T	74394224	3	4	61	1	0	0	0	0	1	0	0	0	9713	933	33	2	474	2	MOBKL1B	2	74394224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31451	74394224	168805149	1490	9475										
DCTN1	1639	broad.mit.edu	37	chr2	74589243	74589243	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggctccagggcgctgaGatactgtctccttgaggacc	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74589243G>T	ENST00000361874.3	-	31	3952	c.3635C>A	c.(3634-3636)tCt>tAt	p.S1212Y	DCTN1_ENST00000409567.3_Missense_Mutation_p.S1187Y|RP11-287D1.3_ENST00000451608.2_Missense_Mutation_p.S125Y|DCTN1_ENST00000409868.1_Missense_Mutation_p.S1190Y|DCTN1_ENST00000394003.3_Missense_Mutation_p.S1205Y|DCTN1_ENST00000407639.2_Missense_Mutation_p.S1078Y|DCTN1_ENST00000409240.1_Missense_Mutation_p.S1170Y|DCTN1_ENST00000409438.1_Missense_Mutation_p.S1073Y	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1212					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)	p.S1212Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						AGGGCGCTGAGATACTGTCTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											112	92	99					2																	74589243		2203	4300	6503	74442751	SO:0001583	missense	1639				CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.3635C>A	2.37:g.74589243G>T	ENSP00000354791:p.Ser1212Tyr		74442751	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615998	0.46631	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.78816	-0.78;-0.97;-0.79;-0.79;-1.21;-0.97;-0.99	5.24	4.36	0.52297	.	0.177801	0.27240	N	0.020274	T	0.63581	0.2523	N	0.19112	0.55	0.09310	N	1	P;P;P;P;P;P;B	0.43633	0.61;0.61;0.553;0.813;0.573;0.681;0.108	B;B;B;B;B;B;B	0.40009	0.086;0.125;0.102;0.316;0.23;0.206;0.026	T	0.59568	-0.7430	10	0.72032	D	0.01	-2.8228	9.6494	0.39888	0.1689:0.0:0.8311:0.0	.	1187;1170;1212;1205;1078;1073;1195	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	Y	1212;1205;1195;1078;1073;1170;1190;1187	ENSP00000354791:S1212Y;ENSP00000377571:S1205Y;ENSP00000384844:S1078Y;ENSP00000387270:S1073Y;ENSP00000386406:S1170Y;ENSP00000387327:S1190Y;ENSP00000386843:S1187Y	ENSP00000354791:S1212Y	S	-	2	0	DCTN1	74442751	0.074000	0.21230	0.918000	0.36340	0.992000	0.81027	1.717000	0.37991	1.206000	0.43276	0.491000	0.48974	TCT		0.572	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74589243	G	T	74589243	3	4	61	1	0	0	0	0	1	0	0	0	4312	942	33	2	209	2	DCTN1	2	74589243	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	195019	74589243	168610130	1491	9476										
DCTN1	1639	broad.mit.edu	37	chr2	74595229	74595229	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcacttagttcaaacttCtcctgggcctgcttccggat	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74595229C>A	ENST00000361874.3	-	17	2201	c.1884G>T	c.(1882-1884)gaG>gaT	p.E628D	DCTN1_ENST00000409567.3_Missense_Mutation_p.E608D|DCTN1_ENST00000409868.1_Missense_Mutation_p.E611D|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.E621D|DCTN1_ENST00000407639.2_Missense_Mutation_p.E494D|DCTN1_ENST00000409240.1_Missense_Mutation_p.E591D|DCTN1_ENST00000409438.1_Missense_Mutation_p.E494D	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	628					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)	p.E628D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						GTTCAAACTTCTCCTGGGCCT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	2											27	27	27					2																	74595229		2202	4299	6501	74448737	SO:0001583	missense	1639				CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1884G>T	2.37:g.74595229C>A	ENSP00000354791:p.Glu628Asp		74448737	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.945312	0.53079	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.25	3.47	0.39725	.	0.000000	0.43747	D	0.000532	D	0.87597	0.6217	L	0.42744	1.35	0.58432	D	0.999999	B;P;D;B;B;D	0.63046	0.267;0.752;0.992;0.096;0.068;0.99	B;P;D;B;B;D	0.74348	0.216;0.485;0.983;0.147;0.048;0.971	D	0.85224	0.1028	10	0.38643	T	0.18	-12.3531	10.8657	0.46853	0.0:0.8448:0.0:0.1552	.	608;591;628;621;494;494	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	D	628;621;611;494;494;591;611;608	ENSP00000354791:E628D;ENSP00000377571:E621D;ENSP00000384844:E494D;ENSP00000387270:E494D;ENSP00000386406:E591D;ENSP00000387327:E611D;ENSP00000386843:E608D	ENSP00000354791:E628D	E	-	3	2	DCTN1	74448737	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.528000	0.45624	0.791000	0.33826	-0.140000	0.14226	GAG		0.562	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		A	74595229	C	A	74595229	3	1	61	1	0	0	0	0	1	0	0	0	4312	912	32	2	2016	2	DCTN1	2	74595229	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5986	74595229	168604144	1492	9477										
RTKN	84058	broad.mit.edu	37	chr2	74655826	74655826	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagctgccagacggcaacAcacgctaccataaaggggca	11	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74655826A>G	ENST00000348227.4	+	0	1147				RTKN_ENST00000233330.6_Missense_Mutation_p.C247R|RTKN_ENST00000272430.5_Missense_Mutation_p.C297R|RTKN_ENST00000305557.5_Missense_Mutation_p.C284R	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54									p.C297R(1)		breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						AGACGGCAACACACGCTACCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											37	35	36					2																	74655826		2203	4300	6503	74509334	SO:0001628	intergenic_variant	6242			AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"WD repeat domain containing"	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951		2.37:g.74655826A>G			74509334	D6W5I3|Q53H85|Q86V45	Missense_Mutation	SNP	ENST00000348227.4	37	CCDS1940.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.457647	0.63401	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.37411	1.22;1.2;1.22	5.54	4.37	0.52481	.	0.100354	0.64402	D	0.000001	T	0.54727	0.1876	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.53655	-0.8408	10	0.15499	T	0.54	.	10.9432	0.47285	0.8426:0.1574:0.0:0.0	.	297;284	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	R	284;297;247	ENSP00000305298:C284R;ENSP00000272430:C297R;ENSP00000233330:C247R	ENSP00000233330:C247R	C	-	1	0	RTKN	74509334	1.000000	0.71417	0.989000	0.46669	0.728000	0.41692	8.231000	0.89794	0.925000	0.37094	-0.316000	0.08728	TGT		0.632	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118		G	74655826	A	G	74655826	1	3	61	0	1	0	0	0	0	0	0	0	13759	159	6	4		4	RTKN	2	74655826	IGR	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	60597	74655826	168543547	1493	9478										
RTKN	6242	broad.mit.edu	37	chr2	74655978	74655978	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcacacacatacttaccatGactggcaagggtgaggtcat	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74655978G>T	ENST00000233330.6	-	7	1014	c.697C>A	c.(697-699)Cat>Aat	p.H233N	RTKN_ENST00000272430.5_Missense_Mutation_p.H283N|RTKN_ENST00000305557.5_Missense_Mutation_p.H270N	NM_001015056.1	NP_001015056.1			rhotekin									p.H270N(1)|p.H283N(1)		endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						TACTTACCATGACTGGCAAGG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	2											135	95	109					2																	74655978		2203	4300	6503	74509486	SO:0001583	missense	6242			AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.697C>A	2.37:g.74655978G>T	ENSP00000233330:p.His233Asn		74509486		Missense_Mutation	SNP	ENST00000233330.6	37	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	G	5.991	0.366802	0.11352	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.26518	1.73;1.74;1.74	5.55	4.59	0.56863	.	0.306760	0.33477	N	0.004864	T	0.08492	0.0211	N	0.00960	-1.095	0.38149	D	0.938691	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.21211	-1.0252	10	0.27785	T	0.31	.	10.2842	0.43558	0.0:0.0:0.6752:0.3248	.	283;270	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	N	270;283;233	ENSP00000305298:H270N;ENSP00000272430:H283N;ENSP00000233330:H233N	ENSP00000233330:H233N	H	-	1	0	RTKN	74509486	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.756000	0.62205	2.634000	0.89283	0.561000	0.74099	CAT		0.557	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		T	74655978	G	T	74655978	3	4	61	1	0	0	0	0	1	0	0	0	13759	1290	45	2	868	2	RTKN	2	74655978	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152	74655978	168543395	1494	9479										
RTKN	6242	broad.mit.edu	37	chr2	74666701	74666701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggctgagtgccatctgccGaatgtagagcatattcaggt	12	9	2	2	rs191801087		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74666701G>A	ENST00000305557.5	-	2	634	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W	RTKN_ENST00000233330.6_Intron|RTKN_ENST00000272430.5_Intron|RTKN_ENST00000484453.1_Intron	NM_033046.2	NP_149035.1			rhotekin									p.R17W(1)		endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						GCCATCTGCCGAATGTAGAGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2											185	145	158					2																	74666701		2203	4300	6503	74520209	SO:0001583	missense	6242			AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000305557.5:c.49C>T	2.37:g.74666701G>A	ENSP00000305298:p.Arg17Trp		74520209		Missense_Mutation	SNP	ENST00000305557.5	37	CCDS1941.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	24.1	4.494945	0.85069	.	.	ENSG00000114993	ENST00000305557	T	0.38560	1.13	4.81	4.81	0.61882	.	.	.	.	.	T	0.65575	0.2704	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70204	-0.4936	8	0.87932	D	0	.	15.4186	0.74991	0.0:0.0:1.0:0.0	.	17	Q9BST9-2	.	W	17	ENSP00000305298:R17W	ENSP00000305298:R17W	R	-	1	2	RTKN	74520209	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.253000	0.65452	2.511000	0.84671	0.462000	0.41574	CGG		0.587	RTKN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252217.4	NM_001015055		A	74666701	G	A	74666701	3	1	61	1	0	0	0	0	1	0	0	0	13759	1057	37	1	1651	1	RTKN	2	74666701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10723	74666701	168532672	1495	9480										
WBP1	23559	broad.mit.edu	37	chr2	74687164	74687164	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctttccctaccggttcaCtgcttgaccttcgtgagtga	9	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74687164C>T	ENST00000233615.2	+	3	611	c.337C>T	c.(337-339)Ctg>Ttg	p.L113L	WBP1_ENST00000409737.1_Silent_p.L110L|WBP1_ENST00000494741.1_3'UTR|MOGS_ENST00000462443.1_5'Flank|WBP1_ENST00000393972.3_Silent_p.L147L	NM_012477.3	NP_036609.1	Q96G27	WBP1_HUMAN	WW domain binding protein 1	113							WW domain binding (GO:0050699)	p.L113L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	8						TACCGGTTCACTGCTTGACCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	2											88	89	88					2																	74687164		2203	4300	6503	74540672	SO:0001819	synonymous_variant	23559			U79457	CCDS1943.1	2p12	2012-04-20			ENSG00000239779	ENSG00000239779			12737	protein-coding gene	gene with protein product		606961				7644498	Standard	NM_012477		Approved	WBP-1	uc002slj.2	Q96G27	OTTHUMG00000129958	ENST00000233615.2:c.337C>T	2.37:g.74687164C>T			74540672	B2RE02|O95637	Silent	SNP	ENST00000233615.2	37	CCDS1943.1																																																																																				0.542	WBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252221.2	NM_012477		T	74687164	C	T	74687164	2	4	61	1	0	0	0	0	0	0	0	1	17297	564	20	3		3	WBP1	2	74687164	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20463	74687164	168512209	1496	9481										
MRPL53	116540	broad.mit.edu	37	chr2	74699728	74699728	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtttttctcgaagggacaGaactgaacccgaacctgttt	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74699728G>T	ENST00000258105.7	-	1	721	c.60C>A	c.(58-60)ttC>ttA	p.F20L	MRPL53_ENST00000409710.1_Missense_Mutation_p.F20L	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	20						mitochondrion (GO:0005739)|ribosome (GO:0005840)		p.F20L(1)		central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						CGAAGGGACAGAACTGAACCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	98	102					2																	74699728		2203	4300	6503	74553236	SO:0001583	missense	116540			BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"Mitochondrial ribosomal proteins / large subunits"	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.60C>A	2.37:g.74699728G>T	ENSP00000258105:p.Phe20Leu		74553236		Missense_Mutation	SNP	ENST00000258105.7	37	CCDS1944.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181002	0.57800	.	.	ENSG00000204822	ENST00000258105;ENST00000409710	T;T	0.66460	0.22;-0.21	5.2	1.43	0.22495	.	0.000000	0.85682	D	0.000000	T	0.72795	0.3505	M	0.78637	2.42	0.80722	D	1	P	0.49783	0.928	P	0.56916	0.809	T	0.69495	-0.5130	10	0.72032	D	0.01	-32.0689	4.6231	0.12465	0.2572:0.1599:0.5829:0.0	.	20	Q96EL3	RM53_HUMAN	L	20	ENSP00000258105:F20L;ENSP00000386920:F20L	ENSP00000258105:F20L	F	-	3	2	MRPL53	74553236	1.000000	0.71417	0.979000	0.43373	0.010000	0.07245	0.424000	0.21330	0.078000	0.16900	-0.150000	0.13652	TTC		0.597	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050		T	74699728	G	T	74699728	3	4	61	1	0	0	0	0	1	0	0	0	9847	933	33	2	290	2	MRPL53	2	74699728	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12564	74699728	168499645	1497	9482										
TTC31	64427	broad.mit.edu	37	chr2	74717830	74717830	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggctgaggaggagcgcatGaaacagaaagcagagaaaaa	15	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74717830G>T	ENST00000233623.5	+	5	517	c.510G>T	c.(508-510)atG>atT	p.M170I	TTC31_ENST00000410003.1_Missense_Mutation_p.M170I|TTC31_ENST00000442235.2_Missense_Mutation_p.M26I|TTC31_ENST00000463189.1_3'UTR	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	170								p.M170I(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						AGGAGCGCATGAAACAGAAAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											50	52	51					2																	74717830		2001	4179	6180	74571338	SO:0001583	missense	64427			AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"Tetratricopeptide (TTC) repeat domain containing"	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.510G>T	2.37:g.74717830G>T	ENSP00000233623:p.Met170Ile		74571338	Q4KN40|Q53FD4|Q9H9F7	Missense_Mutation	SNP	ENST00000233623.5	37	CCDS42701.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.247681	0.39697	.	.	ENSG00000115282	ENST00000545977;ENST00000410003;ENST00000441635;ENST00000442235;ENST00000233623	T;T;T	0.57752	1.55;0.94;0.38	4.7	1.9	0.25705	.	0.572237	0.15640	N	0.251947	T	0.39358	0.1075	L	0.45581	1.43	0.09310	N	1	B;B;B;B	0.10296	0.003;0.0;0.0;0.003	B;B;B;B	0.08055	0.003;0.001;0.001;0.002	T	0.19844	-1.0293	10	0.22706	T	0.39	.	6.0794	0.19933	0.3152:0.0:0.6848:0.0	.	26;140;170;99	B4DZV1;Q86XF2;Q49AM3;F5H175	.;.;TTC31_HUMAN;.	I	99;170;170;26;170	ENSP00000387213:M170I;ENSP00000416823:M26I;ENSP00000233623:M170I	ENSP00000233623:M170I	M	+	3	0	TTC31	74571338	0.405000	0.25336	0.663000	0.29738	0.996000	0.88848	0.476000	0.22180	0.699000	0.31761	0.561000	0.74099	ATG		0.537	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492		T	74717830	G	T	74717830	3	4	61	1	0	0	0	0	1	0	0	0	16740	1290	45	2	528	2	TTC31	2	74717830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18102	74717830	168481543	1498	9483										
AUP1	165545	broad.mit.edu	37	chr2	74755126	74755126	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttggcgatgaacaggacGaagccacctgcaaagaaaca	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74755126G>A	ENST00000404568.3	-	0	0				AUP1_ENST00000377526.3_Missense_Mutation_p.R227C|HTRA2_ENST00000352222.3_5'Flank|HTRA2_ENST00000258080.3_5'Flank|DQX1_ENST00000393951.2_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.R227C(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TGAACAGGACGAAGCCACCTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	111	110					2																	74755126		1976	4167	6143	74608634	SO:0001631	upstream_gene_variant	550			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		2.37:g.74755126G>A	Exception_encountered		74608634	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630767	0.46944	.	.	ENSG00000115307	ENST00000377526;ENST00000258081;ENST00000412627	D	0.93488	-3.23	4.9	4.9	0.64082	.	0.552015	0.18698	N	0.133668	D	0.83830	0.5339	N	0.08118	0	0.25282	N	0.989427	P;P;P	0.46327	0.876;0.705;0.77	B;B;B	0.39152	0.183;0.01;0.292	T	0.78663	-0.2116	10	0.72032	D	0.01	1.282	9.0626	0.36444	0.0973:0.0:0.9027:0.0	.	284;293;227	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	C	227;291;229	ENSP00000366748:R227C	ENSP00000258081:R291C	R	-	1	0	AUP1	74608634	1.000000	0.71417	0.869000	0.34112	0.987000	0.75469	6.093000	0.71422	2.552000	0.86080	0.563000	0.77884	CGT		0.577	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		A	74755126	G	A	74755126	1	1	61	0	1	0	0	0	0	0	0	0	1221	1058	37	1		1	AUP1	2	74755126	5'Flank	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37296	74755126	168444247	1499	9484										
LOXL3	84695	broad.mit.edu	37	chr2	74761232	74761232	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagactccaggtacctggaGaatgtagtttcctggcttca	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74761232G>T	ENST00000264094.3	-	12	2142	c.2071C>A	c.(2071-2073)Ctc>Atc	p.L691I	LOXL3_ENST00000393937.2_Missense_Mutation_p.L546I|LOXL3_ENST00000409249.1_Missense_Mutation_p.L409I|LOXL3_ENST00000409549.1_Missense_Mutation_p.L635I|LOXL3_ENST00000409986.1_Missense_Mutation_p.L546I	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	691	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.L691I(1)		endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						GGTACCTGGAGAATGTAGTTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	84	85					2																	74761232		2203	4300	6503	74614740	SO:0001583	missense	84695			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.2071C>A	2.37:g.74761232G>T	ENSP00000264094:p.Leu691Ile		74614740	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966544	0.53507	.	.	ENSG00000115318	ENST00000264094;ENST00000409249;ENST00000393937;ENST00000409549;ENST00000409986	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	4.6	4.6	0.57074	.	0.159891	0.43110	D	0.000601	T	0.44891	0.1315	L	0.41906	1.305	0.46749	D	0.999188	P;D;P;P	0.61080	0.94;0.989;0.815;0.77	P;D;P;B	0.64877	0.605;0.93;0.542;0.298	T	0.30268	-0.9984	10	0.51188	T	0.08	.	8.8127	0.34976	0.1016:0.0:0.8984:0.0	.	546;635;546;691	B9A025;E7END4;Q6IPL7;P58215	.;.;.;LOXL3_HUMAN	I	691;409;546;635;546	ENSP00000264094:L691I;ENSP00000387103:L409I;ENSP00000377512:L546I;ENSP00000386696:L635I;ENSP00000386545:L546I	ENSP00000264094:L691I	L	-	1	0	LOXL3	74614740	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	1.626000	0.37039	2.541000	0.85698	0.563000	0.77884	CTC		0.517	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		T	74761232	G	T	74761232	3	4	61	1	0	0	0	0	1	0	0	0	8930	942	33	2	202	2	LOXL3	2	74761232	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6106	74761232	168438141	1500	9485										
LOXL3	84695	broad.mit.edu	37	chr2	74779731	74779731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacagcagcagcccccaggGgctccactgccagacactga	11	17	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74779731G>A	ENST00000264094.3	-	2	102	c.31C>T	c.(31-33)Ccc>Tcc	p.P11S	DOK1_ENST00000409429.1_Intron|LOXL3_ENST00000393937.2_Missense_Mutation_p.P11S|LOXL3_ENST00000484369.1_5'UTR|LOXL3_ENST00000409249.1_Missense_Mutation_p.P11S|DOK1_ENST00000233668.5_5'Flank|DOK1_ENST00000340004.6_5'Flank|LOXL3_ENST00000409549.1_Missense_Mutation_p.P11S|LOXL3_ENST00000409986.1_Missense_Mutation_p.P11S	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	11					epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.P11S(1)|p.P11T(1)		endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						AGCCCCCAGGGGCTCCACTGC	0.642																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	2											8	8	8					2																	74779731		2163	4232	6395	74633239	SO:0001583	missense	84695			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.31C>T	2.37:g.74779731G>A	ENSP00000264094:p.Pro11Ser		74633239	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	G	8.148	0.786645	0.16189	.	.	ENSG00000115318	ENST00000264094;ENST00000409249;ENST00000393937;ENST00000409549;ENST00000409986;ENST00000413469	T;T;T;T;T;T	0.01240	5.23;5.13;5.21;5.26;5.2;5.12	4.67	2.82	0.32997	.	0.931417	0.08916	N	0.875110	T	0.01489	0.0048	L	0.27053	0.805	0.58432	D	0.999998	B;B;B;B	0.13594	0.002;0.008;0.002;0.008	B;B;B;B	0.09377	0.004;0.004;0.004;0.004	T	0.49925	-0.8887	10	0.42905	T	0.14	.	7.4117	0.27021	0.0:0.1743:0.6203:0.2055	.	11;11;11;11	B9A025;E7END4;Q6IPL7;P58215	.;.;.;LOXL3_HUMAN	S	11	ENSP00000264094:P11S;ENSP00000387103:P11S;ENSP00000377512:P11S;ENSP00000386696:P11S;ENSP00000386545:P11S;ENSP00000398260:P11S	ENSP00000264094:P11S	P	-	1	0	LOXL3	74633239	0.006000	0.16342	0.237000	0.24090	0.866000	0.49608	0.081000	0.14823	0.549000	0.28973	-0.485000	0.04761	CCC		0.642	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		A	74779731	G	A	74779731	3	1	61	1	0	0	0	0	1	0	0	0	8930	1232	43	3	2282	3	LOXL3	2	74779731	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18499	74779731	168419642	1501	9486										
DOK1	1796	broad.mit.edu	37	chr2	74782767	74782767	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgccctggagatgctggaGaactccttgtacagccctac	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74782767G>T	ENST00000233668.5	+	3	1095	c.426G>T	c.(424-426)gaG>gaT	p.E142D	DOK1_ENST00000409429.1_Missense_Mutation_p.E3D|M1AP_ENST00000464686.1_5'Flank|LOXL3_ENST00000393937.2_5'Flank|LOXL3_ENST00000484369.1_5'Flank|DOK1_ENST00000480318.1_3'UTR|LOXL3_ENST00000409249.1_5'Flank|DOK1_ENST00000340004.6_Missense_Mutation_p.E142D|LOXL3_ENST00000409549.1_5'Flank|LOXL3_ENST00000264094.3_5'Flank|LOXL3_ENST00000409986.1_5'Flank	NM_001381.3	NP_001372.1	Q99704	DOK1_HUMAN	docking protein 1, 62kDa (downstream of tyrosine kinase 1)	142					cell surface receptor signaling pathway (GO:0007166)|insulin receptor signaling pathway (GO:0008286)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor signaling protein activity (GO:0005057)	p.E142D(1)		endometrium(3)|large_intestine(2)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						AGATGCTGGAGAACTCCTTGT	0.577																																					Esophageal Squamous(36;520 860 12502 33616 51270)											1	Substitution - Missense(1)	large_intestine(1)	2											53	53	53					2																	74782767		2203	4300	6503	74636275	SO:0001583	missense	1796			U70987	CCDS1954.1, CCDS56125.1	2p13	2008-05-21	2002-08-29		ENSG00000115325	ENSG00000115325			2990	protein-coding gene	gene with protein product		602919	"docking protein 1, 62kD (downstream of tyrosine kinase 1)"			9008160, 9790776, 15546884	Standard	NM_001381		Approved	p62dok	uc002sms.3	Q99704	OTTHUMG00000129956	ENST00000233668.5:c.426G>T	2.37:g.74782767G>T	ENSP00000233668:p.Glu142Asp		74636275	O43204|Q53TY2|Q9UHG6	Missense_Mutation	SNP	ENST00000233668.5	37	CCDS1954.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.339973	0.81911	.	.	ENSG00000115325	ENST00000409429;ENST00000233668;ENST00000340004	D;D	0.82619	-1.63;-1.63	4.8	4.8	0.61643	.	0.119003	0.56097	D	0.000039	D	0.84502	0.5486	L	0.35593	1.075	0.34692	D	0.725834	D;D	0.58970	0.984;0.984	D;D	0.68192	0.956;0.956	D	0.85087	0.0949	10	0.25106	T	0.35	-32.6186	13.235	0.59965	0.0:0.0:1.0:0.0	.	131;142	B4DJN1;Q99704	.;DOK1_HUMAN	D	3;142;142	ENSP00000387016:E3D;ENSP00000233668:E142D	ENSP00000233668:E142D	E	+	3	2	DOK1	74636275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.665000	0.54532	2.503000	0.84419	0.561000	0.74099	GAG		0.577	DOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252218.3	NM_001381		T	74782767	G	T	74782767	3	4	61	1	0	0	0	0	1	0	0	0	4707	933	33	2	436	2	DOK1	2	74782767	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3036	74782767	168416606	1502	9487										
SEMA4F	10505	broad.mit.edu	37	chr2	74900869	74900869	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatgaagatggagacgacGaaatctacttcttctttacg	11	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:74900869G>A	ENST00000357877.2	+	7	885	c.736G>A	c.(736-738)Gaa>Aaa	p.E246K	SEMA4F_ENST00000339773.5_Intron	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	246	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.E246K(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TGGAGACGACGAAATCTACTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											93	96	95					2																	74900869		2203	4300	6503	74754377	SO:0001583	missense	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.736G>A	2.37:g.74900869G>A	ENSP00000350547:p.Glu246Lys		74754377	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.408905	0.25378	.	.	ENSG00000135622	ENST00000357877	T	0.08282	3.11	4.79	3.9	0.45041	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.272209	0.30762	N	0.008927	T	0.02970	0.0088	N	0.11313	0.125	0.80722	D	1	B	0.28880	0.226	B	0.19148	0.024	T	0.32929	-0.9888	10	0.02654	T	1	.	6.3284	0.21257	0.094:0.0:0.7212:0.1848	.	246	O95754	SEM4F_HUMAN	K	246	ENSP00000350547:E246K	ENSP00000350547:E246K	E	+	1	0	SEMA4F	74754377	1.000000	0.71417	0.159000	0.22649	0.990000	0.78478	5.247000	0.65416	1.128000	0.42052	0.462000	0.41574	GAA		0.572	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74900869	G	A	74900869	3	1	61	1	0	0	0	0	1	0	0	0	14072	1059	37	1	762	1	SEMA4F	2	74900869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118102	74900869	168298504	1503	9488										
C2orf3	6936	broad.mit.edu	37	chr2	75893095	75893095	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatgtgcagactgcaataAaaactgaatgaagttttcta	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:75893095A>C	ENST00000321027.3	-	16	2321	c.2188T>G	c.(2188-2190)Tta>Gta	p.L730V	MRPL19_ENST00000358788.6_Intron|GCFC2_ENST00000409857.3_Missense_Mutation_p.L692V|MRPL19_ENST00000409374.1_Intron|GCFC2_ENST00000541687.1_3'UTR	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	730					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.L730V(1)									GACTGCAATAAAAACTGAATG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	83	82					2																	75893095		2203	4300	6503	75746603	SO:0001583	missense	6936			AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.2188T>G	2.37:g.75893095A>C	ENSP00000318690:p.Leu730Val		75746603	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.817665	0.71028	.	.	ENSG00000005436	ENST00000321027;ENST00000409857;ENST00000427862	T;T;T	0.60548	1.67;1.73;0.18	5.04	5.04	0.67666	.	0.067454	0.64402	D	0.000018	T	0.72439	0.3460	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.73385	-0.3999	9	.	.	.	-14.2054	11.7362	0.51767	1.0:0.0:0.0:0.0	.	730	P16383	GCF_HUMAN	V	730;692;148	ENSP00000318690:L730V;ENSP00000386552:L692V;ENSP00000409340:L148V	.	L	-	1	2	C2orf3	75746603	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.171000	0.42453	2.199000	0.70637	0.528000	0.53228	TTA		0.338	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		C	75893095	A	C	75893095	3	2	61	1	0	0	0	0	1	0	0	0	2168	11	1	4	165	4	C2orf3	2	75893095	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	992226	75893095	167306278	1504	9489										
LRRTM4	80059	broad.mit.edu	37	chr2	76975878	76975878	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgacctggcgatggtggcGatgaagctgtggtctcggcc	17	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:76975878G>A	ENST00000409093.1	-	4	2052	c.1716C>T	c.(1714-1716)atC>atT	p.I572I	LRRTM4_ENST00000409911.1_Silent_p.I573I|LRRTM4_ENST00000409884.1_Silent_p.I572I			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	572					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.I572I(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		CGATGGTGGCGATGAAGCTGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	2											148	137	140					2																	76975878		1568	3582	5150	76829386	SO:0001819	synonymous_variant	80059			AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.1716C>T	2.37:g.76975878G>A			76829386	Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	37	CCDS46346.1																																																																																				0.617	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		A	76975878	G	A	76975878	2	1	61	1	0	0	0	0	0	0	0	1	9071	1048	37	1		1	LRRTM4	2	76975878	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1082783	76975878	166223495	1505	9490										
LRRTM4	80059	broad.mit.edu	37	chr2	77746887	77746887	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccatcacatctgcagttCtttgggcaagctctctgagc	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:77746887C>A	ENST00000409093.1	-	3	444	c.108G>T	c.(106-108)aaG>aaT	p.K36N	LRRTM4_ENST00000409088.3_Missense_Mutation_p.K36N|LRRTM4_ENST00000409911.1_Missense_Mutation_p.K37N|LRRTM4_ENST00000409282.1_Missense_Mutation_p.K37N|LRRTM4_ENST00000409884.1_Missense_Mutation_p.K36N			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	36	LRRNT.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.K36N(2)		autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		ATCTGCAGTTCTTTGGGCAAG	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	2											87	84	85					2																	77746887		2024	4181	6205	77600395	SO:0001583	missense	80059			AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.108G>T	2.37:g.77746887C>A	ENSP00000386357:p.Lys36Asn		77600395	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	C	9.618	1.133041	0.21041	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63	5.72	3.93	0.45458	Leucine-rich repeat-containing N-terminal (1);	0.291867	0.38605	N	0.001622	T	0.04182	0.0116	L	0.27053	0.805	0.45330	D	0.998321	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.12837	0.001;0.002;0.008	T	0.45101	-0.9284	10	0.26408	T	0.33	.	11.1213	0.48291	0.0:0.8497:0.0:0.1503	.	37;36;36	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	N	37;36;36;36;37	ENSP00000387228:K37N;ENSP00000387297:K36N;ENSP00000386357:K36N;ENSP00000386236:K36N;ENSP00000386286:K37N	ENSP00000386236:K36N	K	-	3	2	LRRTM4	77600395	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.634000	0.37123	0.781000	0.33589	0.655000	0.94253	AAG		0.468	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		A	77746887	C	A	77746887	3	1	61	1	0	0	0	0	1	0	0	0	9071	912	32	2	1678	2	LRRTM4	2	77746887	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	771009	77746887	165452486	1506	9491										
REG1A	5967	broad.mit.edu	37	chr2	79349136	79349136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattgccagaacatgaattCgggcaacctggtgtctgtgc	11	10	1	2	rs200969301	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:79349136C>T	ENST00000233735.1	+	4	309	c.206C>T	c.(205-207)tCg>tTg	p.S69L		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	69	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)	p.S69L(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(26)|prostate(1)|upper_aerodigestive_tract(1)	39						AACATGAATTCGGGCAACCTG	0.527													C|||	2	0.000399361	0	0	5008	,	,		19825	0		0.002	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|NS(1)	2											132	124	127					2																	79349136		2203	4300	6503	79202644	SO:0001583	missense	5967				CCDS1964.1	2p12	2008-09-04	2008-06-04		ENSG00000115386	ENSG00000115386			9951	protein-coding gene	gene with protein product	"pancreatic stone protein", "pancreatic thread protein"	167770	"regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein)"	REG		2332435, 8333731	Standard	NM_002909		Approved	PSP, PTP, PSPS, PSPS1	uc002snz.3	P05451	OTTHUMG00000130016	ENST00000233735.1:c.206C>T	2.37:g.79349136C>T	ENSP00000233735:p.Ser69Leu		79202644	P11379|Q4ZG28	Missense_Mutation	SNP	ENST00000233735.1	37	CCDS1964.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	11.79	1.743269	0.30865	.	.	ENSG00000115386	ENST00000233735	T	0.08720	3.06	3.51	2.58	0.30949	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.31797	N	0.007047	T	0.13713	0.0332	M	0.88031	2.925	0.09310	N	1	B	0.24426	0.103	B	0.16289	0.015	T	0.14615	-1.0466	10	0.56958	D	0.05	.	7.9852	0.30207	0.2439:0.7561:0.0:0.0	.	69	P05451	REG1A_HUMAN	L	69	ENSP00000233735:S69L	ENSP00000233735:S69L	S	+	2	0	REG1A	79202644	0.001000	0.12720	0.046000	0.18839	0.963000	0.63663	0.456000	0.21859	0.759000	0.33084	0.563000	0.77884	TCG		0.527	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252289.1	NM_002909		T	79349136	C	T	79349136	3	4	61	1	0	0	0	0	1	0	0	0	13247	893	31	1	216	1	REG1A	2	79349136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1602249	79349136	163850237	1507	9492										
LRRTM1	347730	broad.mit.edu	37	chr2	80529644	80529644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaaggagaagatgaggGccatggtgcccgtgaccacc	16	9	0	5	rs556319399		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:80529644G>A	ENST00000295057.3	-	2	1957	c.1301C>T	c.(1300-1302)gCc>gTc	p.A434V	CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.A434V	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	434					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.A434V(2)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						GAAGATGAGGGCCATGGTGCC	0.622										HNSCC(69;0.2)																																						2	Substitution - Missense(2)	large_intestine(2)	2											97	85	89					2																	80529644		2203	4300	6503	80383155	SO:0001583	missense	347730			AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1301C>T	2.37:g.80529644G>A	ENSP00000295057:p.Ala434Val		80383155	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283387	0.80803	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.59906	0.23;0.23	5.18	5.18	0.71444	.	0.000000	0.64402	U	0.000001	T	0.74275	0.3695	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.73607	-0.3929	9	.	.	.	.	18.6948	0.91596	0.0:0.0:1.0:0.0	.	434	Q86UE6	LRRT1_HUMAN	V	434	ENSP00000295057:A434V;ENSP00000386646:A434V	.	A	-	2	0	LRRTM1	80383155	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.864000	0.99589	2.383000	0.81215	0.561000	0.74099	GCC		0.622	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80529644	G	A	80529644	3	1	61	1	0	0	0	0	1	0	0	0	9068	1203	42	3	271	3	LRRTM1	2	80529644	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1180508	80529644	162669729	1508	9493										
LRRTM1	347730	broad.mit.edu	37	chr2	80530141	80530141	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatggggctccatgtactcGatctcgttgcccgacaagtc	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:80530141G>A	ENST00000295057.3	-	2	1460	c.804C>T	c.(802-804)atC>atT	p.I268I	CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron|LRRTM1_ENST00000409148.1_Silent_p.I268I	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	268					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.I268I(2)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CCATGTACTCGATCTCGTTGC	0.597										HNSCC(69;0.2)																																						2	Substitution - coding silent(2)	large_intestine(2)	2											80	79	79					2																	80530141		2203	4300	6503	80383652	SO:0001819	synonymous_variant	347730			AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.804C>T	2.37:g.80530141G>A			80383652	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																				0.597	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80530141	G	A	80530141	2	1	61	1	0	0	0	0	0	0	0	1	9068	1048	37	1		1	LRRTM1	2	80530141	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	497	80530141	162669232	1509	9494										
SUCLG1	8802	broad.mit.edu	37	chr2	84658638	84658638	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacccaaacttactgaattAtgttgcttcaaaaattctgc	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:84658638A>G	ENST00000393868.2	-	7	1029	c.819T>C	c.(817-819)caT>caC	p.H273H	SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	273					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)	p.H273H(1)		kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	TTACTGAATTATGTTGCTTCA	0.333																																					Ovarian(48;203 1101 37206 40305 50790)											1	Substitution - coding silent(1)	large_intestine(1)	2											112	112	112					2																	84658638		2202	4300	6502	84512149	SO:0001819	synonymous_variant	8802			Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"succinate-CoA ligase, GDP-forming, alpha subunit"			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.819T>C	2.37:g.84658638A>G			84512149	Q9BWB0|Q9UNP6	Silent	SNP	ENST00000393868.2	37	CCDS1967.2																																																																																				0.333	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2	NM_003849		G	84658638	A	G	84658638	2	3	61	1	0	0	0	0	0	0	0	1	15403	446	16	4		4	SUCLG1	2	84658638	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4128497	84658638	158540735	1510	9495										
SUCLG1	8802	broad.mit.edu	37	chr2	84658709	84658709	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaatcaatatgatgccttCtgtggcagaatcgttcaaaa	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:84658709C>A	ENST00000393868.2	-	7	958	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	250					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)	p.E250*(1)		kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	ATGATGCCTTCTGTGGCAGAA	0.353																																					Ovarian(48;203 1101 37206 40305 50790)											1	Substitution - Nonsense(1)	large_intestine(1)	2											121	120	120					2																	84658709		2203	4300	6503	84512220	SO:0001587	stop_gained	8802			Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"succinate-CoA ligase, GDP-forming, alpha subunit"			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.748G>T	2.37:g.84658709C>A	ENSP00000377446:p.Glu250*		84512220	Q9BWB0|Q9UNP6	Nonsense_Mutation	SNP	ENST00000393868.2	37	CCDS1967.2	.	.	.	.	.	.	.	.	.	.	C	38	7.281323	0.98186	.	.	ENSG00000163541	ENST00000393868	.	.	.	6.17	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-10.9795	15.2546	0.73576	0.0:0.8591:0.1409:0.0	.	.	.	.	X	250	.	ENSP00000377446:E250X	E	-	1	0	SUCLG1	84512220	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	6.005000	0.70716	1.587000	0.49959	0.655000	0.94253	GAA		0.353	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2	NM_003849		A	84658709	C	A	84658709	4	1	61	1	0	0	0	0	0	1	0	0	15403	922	32	2	304	2	SUCLG1	2	84658709	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71	84658709	158540664	1511	9496										
DNAH6	1768	broad.mit.edu	37	chr2	84800693	84800693	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtcttgatttacaagctCttaaacttcaggaacctggt	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:84800693C>A	ENST00000237449.6	+	11	1914	c.1906C>A	c.(1906-1908)Ctt>Att	p.L636I	DNAH6_ENST00000389394.3_Missense_Mutation_p.L636I|DNAH6_ENST00000398278.2_Missense_Mutation_p.L636I			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	636	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L215I(1)|p.L636I(1)		NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTACAAGCTCTTAAACTTCA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	2											97	108	104					2																	84800693		2203	4300	6503	84654204	SO:0001583	missense	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1906C>A	2.37:g.84800693C>A	ENSP00000237449:p.Leu636Ile		84654204	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	8.992	0.977930	0.18812	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.25250	1.81;1.93;1.81	4.95	4.06	0.47325	.	0.000000	0.43416	D	0.000573	T	0.22205	0.0535	L	0.40543	1.245	0.30641	N	0.756498	B;P	0.45474	0.011;0.859	B;P	0.46253	0.007;0.509	T	0.04078	-1.0979	10	0.19590	T	0.45	.	7.8325	0.29351	0.1576:0.7561:0.0:0.0863	.	636;215	Q9C0G6;Q9C0G6-3	DYH6_HUMAN;.	I	636	ENSP00000374045:L636I;ENSP00000381326:L636I;ENSP00000237449:L636I	ENSP00000237449:L636I	L	+	1	0	DNAH6	84654204	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.968000	0.40500	2.272000	0.75746	0.491000	0.48974	CTT		0.363	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84800693	C	A	84800693	3	1	61	1	0	0	0	0	1	0	0	0	4616	913	32	2	1948	2	DNAH6	2	84800693	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	141984	84800693	158398680	1512	9497										
TGOLN2	10618	broad.mit.edu	37	chr2	85553925	85553925	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctctgaagacttaacttcCtcctgcgggggagaaatgag	13	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:85553925C>T	ENST00000409232.3	-	2	991	c.930G>A	c.(928-930)gaG>gaA	p.E310E	TGOLN2_ENST00000377386.3_Silent_p.E310E|TGOLN2_ENST00000282120.2_Silent_p.E154E|TGOLN2_ENST00000398263.2_Silent_p.E252E|TGOLN2_ENST00000444342.2_Silent_p.E310E|TGOLN2_ENST00000409015.1_Silent_p.E310E			O43493	TGON2_HUMAN	trans-golgi network protein 2	310						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)		p.E310E(1)									ACTTAACTTCCTCCTGCGGGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	2											53	50	51					2																	85553925		1892	4121	6013	85407436	SO:0001819	synonymous_variant	10618			AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.930G>A	2.37:g.85553925C>T			85407436	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Silent	SNP	ENST00000409232.3	37	CCDS56126.1																																																																																				0.517	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		T	85553925	C	T	85553925	2	4	61	1	0	0	0	0	0	0	0	1	15875	680	24	3		3	TGOLN2	2	85553925	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	753232	85553925	157645448	1513	9498										
ELMOD3	84173	broad.mit.edu	37	chr2	85617484	85617484	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactggttttggctgcagttCttccccatccacactttctc	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:85617484C>A	ENST00000409890.2	+	13	1610				ELMOD3_ENST00000409013.3_Intron|ELMOD3_ENST00000315658.7_Missense_Mutation_p.L347I|ELMOD3_ENST00000393852.4_Intron|ELMOD3_ENST00000409344.3_Intron|ELMOD3_ENST00000490508.1_Intron			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3						phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.L347I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						GGCTGCAGTTCTTCCCCATCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											184	177	180					2																	85617484		2203	4300	6503	85470995	SO:0001627	intron_variant	84173			AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"RNA binding motif (RRM) containing"	26158	protein-coding gene	gene with protein product		615427	"RNA binding motif protein 29", "RNA binding motif and ELMO/CED-12 domain 1", "deafness, autosomal recessive 88"	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.943+96C>A	2.37:g.85617484C>A			85470995	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Missense_Mutation	SNP	ENST00000409890.2	37	CCDS46352.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.470381	0.26423	.	.	ENSG00000115459	ENST00000315658	T	0.37584	1.19	4.34	1.52	0.23074	.	1.837580	0.03207	U	0.175599	T	0.22399	0.0540	.	.	.	0.09310	N	1	B	0.33238	0.403	B	0.25405	0.06	T	0.14896	-1.0456	8	.	.	.	0.2746	6.0666	0.19866	0.0:0.6573:0.0:0.3427	.	347	Q96FG2-6	.	I	347	ENSP00000318264:L347I	.	L	+	1	0	ELMOD3	85470995	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.785000	0.26830	0.008000	0.14787	-0.218000	0.12543	CTT		0.537	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213		A	85617484	C	A	85617484	1	1	61	0	1	0	0	0	0	0	0	0	5083	913	32	2		2	ELMOD3	2	85617484	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63559	85617484	157581889	1514	9499										
GGCX	2677	broad.mit.edu	37	chr2	85778164	85778164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagggctaggtgatgtcGtatacaccttatggtactca	11	7	1	2	rs187605466	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:85778164G>A	ENST00000233838.4	-	13	1852	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	GGCX_ENST00000430215.3_Missense_Mutation_p.T534M|GGCX_ENST00000473665.1_5'Flank	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	591					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)	p.T591M(1)		endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	AGGTGATGTCGTATACACCTT	0.448													G|||	3	0.000599042	0.0023	0	5008	,	,		20879	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2	GRCh37	CM064016	GGCX	M	rs187605466						174	156	162					2																	85778164		2203	4300	6503	85631675	SO:0001583	missense	2677				CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1772C>T	2.37:g.85778164G>A	ENSP00000233838:p.Thr591Met		85631675	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	20.4	3.990709	0.74589	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.85861	-2.04;-2.04	5.53	5.53	0.82687	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);	0.000000	0.85682	D	0.000000	D	0.91005	0.7171	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.982;0.98	D	0.92121	0.5704	10	0.87932	D	0	-13.0388	17.3142	0.87218	0.0:0.0:1.0:0.0	.	534;407;591	E9PEE1;B4DQW4;P38435	.;.;VKGC_HUMAN	M	591;534	ENSP00000233838:T591M;ENSP00000408045:T534M	ENSP00000233838:T591M	T	-	2	0	GGCX	85631675	1.000000	0.71417	0.547000	0.28179	0.518000	0.34316	8.948000	0.93006	2.763000	0.94921	0.561000	0.74099	ACG		0.448	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		A	85778164	G	A	85778164	3	1	61	1	0	0	0	0	1	0	0	0	6376	1145	40	1	516	1	GGCX	2	85778164	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160680	85778164	157421209	1515	9500										
GGCX	2677	broad.mit.edu	37	chr2	85780363	85780363	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctacaaacctgggtgaGaaaatgagaatagggcagga	13	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:85780363G>T	ENST00000233838.4	-	8	1227	c.1147C>A	c.(1147-1149)Ctc>Atc	p.L383I	GGCX_ENST00000430215.3_Missense_Mutation_p.L326I|GGCX_ENST00000473665.1_5'UTR	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	383					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)	p.L383I(1)		endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	ACCTGGGTGAGAAAATGAGAA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	2											112	125	121					2																	85780363		2203	4300	6503	85633874	SO:0001583	missense	2677				CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1147C>A	2.37:g.85780363G>T	ENSP00000233838:p.Leu383Ile		85633874	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	G	0.505	-0.869011	0.02570	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.91631	-2.88;-2.88	5.64	4.68	0.58851	.	0.184635	0.46442	D	0.000298	T	0.72645	0.3486	N	0.00670	-1.27	0.38906	D	0.957423	B;B;B	0.12013	0.003;0.001;0.005	B;B;B	0.17979	0.01;0.003;0.02	T	0.73023	-0.4113	10	0.02654	T	1	-23.249	12.5756	0.56362	0.0:0.0:0.7619:0.2381	.	326;222;383	E9PEE1;B4DQW4;P38435	.;.;VKGC_HUMAN	I	383;326	ENSP00000233838:L383I;ENSP00000408045:L326I	ENSP00000233838:L383I	L	-	1	0	GGCX	85633874	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	5.065000	0.64344	2.657000	0.90304	0.655000	0.94253	CTC		0.547	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85780363	G	T	85780363	3	4	61	1	0	0	0	0	1	0	0	0	6376	942	33	2	1161	2	GGCX	2	85780363	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2199	85780363	157419010	1516	9501										
SFTPB	6439	broad.mit.edu	37	chr2	85892767	85892767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgcctggagggccccggGcagcacagggaggacgagct	17	14	0	0	rs138274558		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:85892767G>A	ENST00000519937.2	-	5	563	c.544C>T	c.(544-546)Ccc>Tcc	p.P182S	SFTPB_ENST00000393822.3_Missense_Mutation_p.P194S|SFTPB_ENST00000409383.1_Missense_Mutation_p.P194S|SFTPB_ENST00000342375.3_Missense_Mutation_p.P182S			P07988	PSPB_HUMAN	surfactant protein B	182					organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)		p.P182S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						AGGGCCCCGGGCAGCACAGGG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2							SER/PRO,SER/PRO	1,4403	2.1+/-5.4	0,1,2201	40	44	43		580,580	3.9	0.5	2	dbSNP_134	43	0,8600		0,0,4300	no	missense,missense	SFTPB	NM_000542.3,NM_198843.2	74,74	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	194/394,194/394	85892767	1,13003	2202	4300	6502	85746278	SO:0001583	missense	6439			J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"surfactant, pulmonary-associated protein B"	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.544C>T	2.37:g.85892767G>A	ENSP00000428719:p.Pro182Ser		85746278	Q96R04	Missense_Mutation	SNP	ENST00000519937.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.79|14.79	2.641910|2.641910	0.47153|0.47153	2.27E-4|2.27E-4	0.0|0.0	ENSG00000168878|ENSG00000168878	ENST00000428225|ENST00000519937;ENST00000393822;ENST00000342375;ENST00000409383;ENST00000441838	.|T;T;T;T	.|0.70399	.|0.56;-0.31;-0.48;-0.31	4.84|4.84	3.9|3.9	0.45041|0.45041	.|.	.|0.150101	.|0.30667	.|N	.|0.009132	T|T	0.70535|0.70535	0.3235|0.3235	M|M	0.68317|0.68317	2.08|2.08	0.19945|0.19945	N|N	0.999948|0.999948	.|D;P	.|0.54772	.|0.968;0.824	.|P;B	.|0.48704	.|0.587;0.276	T|T	0.63269|0.63269	-0.6675|-0.6675	5|10	.|0.34782	.|T	.|0.22	-3.4787|-3.4787	9.5689|9.5689	0.39416|0.39416	0.0:0.0:0.7909:0.2091|0.0:0.0:0.7909:0.2091	.|.	.|194;182	.|D6W5L6;P07988	.|.;PSPB_HUMAN	V|S	178|184;194;182;194;150	.|ENSP00000428719:P184S;ENSP00000377409:P194S;ENSP00000345161:P182S;ENSP00000386346:P194S	.|ENSP00000345161:P182S	A|P	-|-	2|1	0|0	SFTPB|SFTPB	85746278|85746278	0.087000|0.087000	0.21565|0.21565	0.538000|0.538000	0.28064|0.28064	0.277000|0.277000	0.26821|0.26821	1.102000|1.102000	0.31050|0.31050	2.242000|2.242000	0.73789|0.73789	0.556000|0.556000	0.70494|0.70494	GCC|CCC		0.667	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843		A	85892767	G	A	85892767	3	1	61	1	0	0	0	0	1	0	0	0	14228	1203	42	3	625	3	SFTPB	2	85892767	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112404	85892767	157306606	1517	9502										
ST3GAL5	8869	broad.mit.edu	37	chr2	86071630	86071630	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgttttggctgcagtggGattttttctgccacctgctt	10	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86071630G>A	ENST00000377332.3	-	6	1005	c.897C>T	c.(895-897)atC>atT	p.I299I	ST3GAL5_ENST00000393805.1_Silent_p.I271I|ST3GAL5_ENST00000393808.3_Silent_p.I276I	NM_003896.3	NP_003887.3	Q9UNP4	SIAT9_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	299					carbohydrate metabolic process (GO:0005975)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	lactosylceramide alpha-2,3-sialyltransferase activity (GO:0047291)|neolactotetraosylceramide alpha-2,3-sialyltransferase activity (GO:0004513)|sialyltransferase activity (GO:0008373)	p.I299I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15						GCTGCAGTGGGATTTTTTCTG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	2											90	88	89					2																	86071630		2203	4300	6503	85925141	SO:0001819	synonymous_variant	8869			AB018356	CCDS1986.2, CCDS42705.1	2p11.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000115525	ENSG00000115525	2.4.99.9	"Sialyltransferases"	10872	protein-coding gene	gene with protein product		604402	"sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase; GM3 synthase)"	SIAT9		9822625	Standard	NM_003896		Approved	ST3GalV, SIATGM3S	uc002sqq.1	Q9UNP4	OTTHUMG00000130171	ENST00000377332.3:c.897C>T	2.37:g.86071630G>A			85925141	B3KM82|D6W5L9|O94902|Q53QU1|Q6NZX4|Q6YFL1	Silent	SNP	ENST00000377332.3	37	CCDS1986.2																																																																																				0.458	ST3GAL5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252486.1	NM_003896		A	86071630	G	A	86071630	2	1	61	1	0	0	0	0	0	0	0	1	15257	1164	41	3		3	ST3GAL5	2	86071630	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178863	86071630	157127743	1518	9503										
POLR1A	25885	broad.mit.edu	37	chr2	86327141	86327141	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggagctcaatgtggcccaGgtgcccagaacagttgctga	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86327141G>T	ENST00000263857.6	-	2	610	c.232C>A	c.(232-234)Ctg>Atg	p.L78M	POLR1A_ENST00000409681.1_Missense_Mutation_p.L78M			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	78					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.L78M(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ATGTGGCCCAGGTGCCCAGAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	95	93					2																	86327141		2039	4187	6226	86180652	SO:0001583	missense	25885			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.232C>A	2.37:g.86327141G>T	ENSP00000263857:p.Leu78Met		86180652	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354417	0.24512	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.19669	2.13;2.13	5.78	3.04	0.35103	RNA polymerase Rpb1, domain 1 (1);	0.139981	0.49916	D	0.000139	T	0.16896	0.0406	L	0.32530	0.975	0.40580	D	0.981382	B;B	0.31879	0.073;0.344	B;B	0.35688	0.05;0.208	T	0.06463	-1.0825	10	0.34782	T	0.22	-15.5589	9.9487	0.41626	0.2929:0.0:0.7071:0.0	.	78;78	B9ZVN9;O95602	.;RPA1_HUMAN	M	78	ENSP00000263857:L78M;ENSP00000386300:L78M	ENSP00000263857:L78M	L	-	1	2	POLR1A	86180652	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	2.233000	0.43027	0.383000	0.24910	0.563000	0.77884	CTG		0.557	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		T	86327141	G	T	86327141	3	4	61	1	0	0	0	0	1	0	0	0	12240	991	35	2	5062	2	POLR1A	2	86327141	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	255511	86327141	156872232	1519	9504										
PTCD3	55037	broad.mit.edu	37	chr2	86362002	86362002	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgctgctgatatcaaatCtgcgtatgaaagccaaccca	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86362002C>A	ENST00000254630.7	+	21	1736	c.1670C>A	c.(1669-1671)tCt>tAt	p.S557Y	SNORD94_ENST00000386037.1_RNA	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	557					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)	p.S557Y(1)		NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						GATATCAAATCTGCGTATGAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	144	142					2																	86362002		2203	4300	6503	86215513	SO:0001583	missense	55037				CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.1670C>A	2.37:g.86362002C>A	ENSP00000254630:p.Ser557Tyr		86215513	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352967	0.24512	.	.	ENSG00000132300	ENST00000254630	T	0.34072	1.38	5.71	4.8	0.61643	.	0.453411	0.26761	N	0.022635	T	0.38665	0.1049	L	0.55743	1.74	0.36435	D	0.865145	P;B	0.39443	0.674;0.372	B;B	0.40165	0.321;0.1	T	0.51028	-0.8757	10	0.52906	T	0.07	-17.6877	16.0796	0.80995	0.1345:0.8655:0.0:0.0	.	148;557	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	Y	557	ENSP00000254630:S557Y	ENSP00000254630:S557Y	S	+	2	0	PTCD3	86215513	0.941000	0.31946	0.382000	0.26119	0.124000	0.20399	1.646000	0.37249	2.688000	0.91661	0.655000	0.94253	TCT		0.468	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		A	86362002	C	A	86362002	3	1	61	1	0	0	0	0	1	0	0	0	12763	913	32	2	1752	2	PTCD3	2	86362002	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34861	86362002	156837371	1520	9505										
IMMT	10989	broad.mit.edu	37	chr2	86371720	86371720	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacaagctatttctggtttCatcaatcattgctacccttc	5	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86371720C>A	ENST00000410111.3	-	15	2335	c.1948G>T	c.(1948-1950)Gaa>Taa	p.E650*	IMMT_ENST00000442664.2_Nonsense_Mutation_p.E649*|IMMT_ENST00000449247.2_Nonsense_Mutation_p.E639*|IMMT_ENST00000254636.5_Nonsense_Mutation_p.E551*|IMMT_ENST00000409051.2_Nonsense_Mutation_p.E603*	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	650					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.E650*(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTTCTGGTTTCATCAATCATT	0.537																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											123	119	120					2																	86371720		1884	4118	6002	86225231	SO:0001587	stop_gained	10989			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1948G>T	2.37:g.86371720C>A	ENSP00000387262:p.Glu650*		86225231	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Nonsense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.938483|4.938483	0.92526|0.92526	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715|ENST00000419070	.|.	.|.	.|.	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.66056|.	D|.	0.02|.	-20.6593|-20.6593	19.3809|19.3809	0.94532|0.94532	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	551;639;650;649;603;639;618;264;551|504	.|.	ENSP00000254636:E551X|.	E|X	-|-	1|2	0|2	IMMT|IMMT	86225231|86225231	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.456000|0.456000	0.32438|0.32438	7.651000|7.651000	0.83577|0.83577	2.816000|2.816000	0.96949|0.96949	0.644000|0.644000	0.83932|0.83932	GAA|TGA		0.537	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86371720	C	A	86371720	4	1	61	1	0	0	0	0	0	1	0	0	7739	835	29	2	332	2	IMMT	2	86371720	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9718	86371720	156827653	1521	9506										
IMMT	10989	broad.mit.edu	37	chr2	86373206	86373206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactctgaacagcctgttCgattcctctgagtctggcat	8	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86373206C>T	ENST00000410111.3	-	14	2035	c.1648G>A	c.(1648-1650)Gaa>Aaa	p.E550K	IMMT_ENST00000442664.2_Missense_Mutation_p.E549K|IMMT_ENST00000449247.2_Missense_Mutation_p.E539K|IMMT_ENST00000254636.5_Missense_Mutation_p.E451K|IMMT_ENST00000409051.2_Missense_Mutation_p.E503K	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	550					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.E550K(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ACAGCCTGTTCGATTCCTCTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	51	52					2																	86373206		1829	4078	5907	86226717	SO:0001583	missense	10989			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1648G>A	2.37:g.86373206C>T	ENSP00000387262:p.Glu550Lys		86226717	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.471610|5.471610	0.96274|0.96274	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000409715|ENST00000419070	T;T;T;T;T|.	0.37584|.	1.19;1.19;1.19;1.19;1.19|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78780|0.78780	0.4337|0.4337	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	1.0;0.998;0.998;0.996;1.0;0.998|.	T|T	0.77357|0.77357	-0.2618|-0.2618	10|5	0.39692|.	T|.	0.17|.	-23.3027|-23.3027	20.1438|20.1438	0.98071|0.98071	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	503;538;452;539;518;550|.	B9A067;B4DKR1;B4DS66;Q16891-2;Q16891-3;Q16891|.	.;.;.;.;.;IMMT_HUMAN|.	K|Q	451;539;550;549;503;539;518;451|404	ENSP00000254636:E451K;ENSP00000396899:E539K;ENSP00000387262:E550K;ENSP00000407788:E549K;ENSP00000387227:E503K|.	ENSP00000254636:E451K|.	E|R	-|-	1|2	0|0	IMMT|IMMT	86226717|86226717	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.055000|7.055000	0.76656|0.76656	2.768000|2.768000	0.95171|0.95171	0.650000|0.650000	0.86243|0.86243	GAA|CGA		0.358	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		T	86373206	C	T	86373206	3	4	61	1	0	0	0	0	1	0	0	0	7739	893	31	1	636	1	IMMT	2	86373206	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1486	86373206	156826167	1522	9507										
MRPL35	51318	broad.mit.edu	37	chr2	86434405	86434405	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaccgtgaaagctgtcatCgataggtttcttcgacttca	9	9	3	2	rs374724139		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86434405C>T	ENST00000337109.4	+	3	367	c.333C>T	c.(331-333)atC>atT	p.I111I	MRPL35_ENST00000409180.1_Silent_p.I111I|MRPL35_ENST00000605125.1_Intron|MRPL35_ENST00000254644.8_Silent_p.I111I	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	111					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)	p.I111I(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						AAGCTGTCATCGATAGGTTTC	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	0,4406		0,0,2203	100	93	95		333,333	4.2	1	2		95	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	MRPL35	NM_016622.3,NM_145644.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	111/189,111/171	86434405	3,13003	2203	4300	6503	86287916	SO:0001819	synonymous_variant	51318			AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"Mitochondrial ribosomal proteins / large subunits"	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.333C>T	2.37:g.86434405C>T			86287916	A6NKV6|B2RB93|Q658U7|Q8WWA2	Silent	SNP	ENST00000337109.4	37	CCDS1988.1																																																																																				0.483	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622		T	86434405	C	T	86434405	2	4	61	1	0	0	0	0	0	0	0	1	9828	874	31	1		1	MRPL35	2	86434405	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61199	86434405	156764968	1523	9508										
KDM3A	55818	broad.mit.edu	37	chr2	86693919	86693919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtagaaccttcagctttaGcttgccgatcacagaattta	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86693919G>T	ENST00000409556.1	+	11	1797	c.1432G>T	c.(1432-1434)Gct>Tct	p.A478S	KDM3A_ENST00000542128.1_Missense_Mutation_p.A426S|KDM3A_ENST00000312912.5_Missense_Mutation_p.A478S|KDM3A_ENST00000409064.1_Missense_Mutation_p.A478S|KDM3A_ENST00000485171.1_Intron			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	478					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.A478S(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						TTCAGCTTTAGCTTGCCGATC	0.383																																					NSCLC(96;1150 1523 6936 46253 49736)											1	Substitution - Missense(1)	large_intestine(1)	2											50	52	52					2																	86693919		2203	4300	6503	86547430	SO:0001583	missense	55818			AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1432G>T	2.37:g.86693919G>T	ENSP00000386660:p.Ala478Ser		86547430	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	G	3.872	-0.027790	0.07589	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.09	2.24	0.28232	.	0.692003	0.13569	N	0.378239	T	0.19565	0.0470	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.11329	0.001;0.006	T	0.25398	-1.0133	10	0.10377	T	0.69	.	8.6886	0.34254	0.2569:0.0:0.7431:0.0	.	426;478	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	478;478;478;478;426	ENSP00000386660:A478S;ENSP00000323659:A478S;ENSP00000386516:A478S;ENSP00000438324:A426S	ENSP00000323659:A478S	A	+	1	0	KDM3A	86547430	0.002000	0.14202	0.989000	0.46669	0.958000	0.62258	0.788000	0.26872	0.645000	0.30675	0.563000	0.77884	GCT		0.383	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		T	86693919	G	T	86693919	3	4	61	1	0	0	0	0	1	0	0	0	8147	971	34	2	1466	2	KDM3A	2	86693919	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259514	86693919	156505454	1524	9509										
RNF103	7844	broad.mit.edu	37	chr2	86831930	86831930	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaggaaataattaatagaGaattatatgtccctaaagtg	8	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:86831930G>T	ENST00000237455.4	-	4	2062	c.1094C>A	c.(1093-1095)tCt>tAt	p.S365Y	CHMP3_ENST00000439940.2_Intron|RNF103_ENST00000477307.1_5'UTR|AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000426549.1_RNA|AC015971.2_ENST00000439077.1_RNA|AC015971.2_ENST00000424788.1_RNA|RNF103-CHMP3_ENST00000604011.1_Intron	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	365					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S365Y(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						AATTAATAGAGAATTATATGT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											59	67	64					2																	86831930		2201	4299	6500	86685441	SO:0001583	missense	7844			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.1094C>A	2.37:g.86831930G>T	ENSP00000237455:p.Ser365Tyr		86685441	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Missense_Mutation	SNP	ENST00000237455.4	37	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.603143	0.66445	.	.	ENSG00000239305	ENST00000237455	T	0.47177	0.85	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.67202	0.2868	L	0.60455	1.87	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.68078	-0.5504	10	0.62326	D	0.03	-18.1452	19.3733	0.94498	0.0:0.0:1.0:0.0	.	365	O00237	RN103_HUMAN	Y	365	ENSP00000237455:S365Y	ENSP00000237455:S365Y	S	-	2	0	RNF103	86685441	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.220000	0.78008	2.584000	0.87258	0.460000	0.39030	TCT		0.333	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		T	86831930	G	T	86831930	3	4	61	1	0	0	0	0	1	0	0	0	13460	942	33	2	967	2	RNF103	2	86831930	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138011	86831930	156367443	1525	9510										
KRCC1	51315	broad.mit.edu	37	chr2	88328068	88328068	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaagagtcatatgtcttCtttgaatgcttcattaggtt	8	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:88328068C>A	ENST00000347055.3	-	4	408	c.15G>T	c.(13-15)aaG>aaT	p.K5N		NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN	lysine-rich coiled-coil 1	5								p.K5N(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						CATATGTCTTCTTTGAATGCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											30	33	32					2																	88328068		2202	4298	6500	88109183	SO:0001583	missense	51315			AF208845	CCDS2000.1	2p11.2	2008-02-05			ENSG00000172086	ENSG00000172086			28039	protein-coding gene	gene with protein product						12477932	Standard	XM_005264360		Approved	FLJ22333	uc002sso.1	Q9NPI7	OTTHUMG00000130315	ENST00000347055.3:c.15G>T	2.37:g.88328068C>A	ENSP00000340083:p.Lys5Asn		88109183	Q3B7J7	Missense_Mutation	SNP	ENST00000347055.3	37	CCDS2000.1	.	.	.	.	.	.	.	.	.	.	.	11.52	1.662257	0.29515	.	.	ENSG00000172086	ENST00000347055	T	0.37235	1.21	5.62	3.78	0.43462	.	0.614043	0.15851	N	0.241537	T	0.32285	0.0824	L	0.52206	1.635	0.33443	D	0.58266	B	0.24368	0.102	B	0.24155	0.051	T	0.37150	-0.9718	10	0.48119	T	0.1	.	9.1156	0.36755	0.0:0.7636:0.154:0.0824	.	5	Q9NPI7	KRCC1_HUMAN	N	5	ENSP00000340083:K5N	ENSP00000340083:K5N	K	-	3	2	KRCC1	88109183	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	1.063000	0.30567	0.691000	0.31592	0.655000	0.94253	AAG		0.363	KRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252664.1	NM_016618		A	88328068	C	A	88328068	3	1	61	1	0	0	0	0	1	0	0	0	8462	912	32	2	768	2	KRCC1	2	88328068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1496138	88328068	154871305	1526	9511										
SMYD1	150572	broad.mit.edu	37	chr2	88387501	88387501	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggggaggaggagcagaaGgacctgcgggtggacgtgga	21	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:88387501G>T	ENST00000419482.2	+	3	520	c.435G>T	c.(433-435)aaG>aaT	p.K145N	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Missense_Mutation_p.K145N	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	145	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.K145N(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						AGGAGCAGAAGGACCTGCGGG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	94	105					2																	88387501		2203	4300	6503	88168616	SO:0001583	missense	150572			AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.435G>T	2.37:g.88387501G>T	ENSP00000393453:p.Lys145Asn		88168616	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	37	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513290	0.64522	.	.	ENSG00000115593	ENST00000419482;ENST00000444564	D;D	0.81996	-1.56;-1.56	4.82	3.93	0.45458	SET domain (2);	0.205916	0.52532	D	0.000077	T	0.76111	0.3942	N	0.19112	0.55	0.80722	D	1	D	0.56521	0.976	P	0.51918	0.684	T	0.73049	-0.4105	10	0.33141	T	0.24	-22.2131	8.6334	0.33933	0.0826:0.1512:0.7661:0.0	.	145	Q8NB12	SMYD1_HUMAN	N	145	ENSP00000393453:K145N;ENSP00000407888:K145N	ENSP00000393453:K145N	K	+	3	2	SMYD1	88168616	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.941000	0.40233	1.127000	0.42034	0.561000	0.74099	AAG		0.627	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		T	88387501	G	T	88387501	3	4	61	1	0	0	0	0	1	0	0	0	14858	991	35	2	445	2	SMYD1	2	88387501	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59433	88387501	154811872	1527	9512										
SMYD1	150572	broad.mit.edu	37	chr2	88387588	88387588	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacatctcgcacatcttCggagtggtaggccccctgcg	11	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:88387588C>T	ENST00000419482.2	+	3	607	c.522C>T	c.(520-522)ttC>ttT	p.F174F	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.F174F	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	174	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.F174F(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CGCACATCTTCGGAGTGGTAG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	2											101	62	75					2																	88387588		2203	4300	6503	88168703	SO:0001819	synonymous_variant	150572			AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.522C>T	2.37:g.88387588C>T			88168703	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																				0.597	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		T	88387588	C	T	88387588	2	4	61	1	0	0	0	0	0	0	0	1	14858	883	31	1		1	SMYD1	2	88387588	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87	88387588	154811785	1528	9513										
EIF2AK3	9451	broad.mit.edu	37	chr2	88913369	88913369	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgctgataattactaatGacctgtaaatattaaaaata	5	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:88913369G>A	ENST00000303236.3	-	2	612	c.311C>T	c.(310-312)tCa>tTa	p.S104L	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	104					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)	p.S104L(1)		ovary(3)	3						AATTACTAATGACCTGtaaat	0.383																																					GBM(138;671 1851 16235 39058 45249)											1	Substitution - Missense(1)	large_intestine(1)	2											61	56	57					2																	88913369		2203	4300	6503	88694484	SO:0001583	missense	9451			AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.311C>T	2.37:g.88913369G>A	ENSP00000307235:p.Ser104Leu		88694484	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.534394	0.85812	.	.	ENSG00000172071	ENST00000303236	T	0.73681	-0.77	5.38	5.38	0.77491	Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.82268	0.5000	M	0.74258	2.255	0.50632	D	0.999887	D	0.56521	0.976	P	0.52481	0.7	T	0.83247	-0.0055	10	0.48119	T	0.1	-12.5106	19.1382	0.93436	0.0:0.0:1.0:0.0	.	104	Q9NZJ5	E2AK3_HUMAN	L	104	ENSP00000307235:S104L	ENSP00000307235:S104L	S	-	2	0	EIF2AK3	88694484	1.000000	0.71417	0.959000	0.39883	0.604000	0.37047	7.387000	0.79785	2.507000	0.84556	0.655000	0.94253	TCA		0.383	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		A	88913369	G	A	88913369	3	1	61	1	0	0	0	0	1	0	0	0	5009	1294	45	3	3103	3	EIF2AK3	2	88913369	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	525781	88913369	154286004	1529	9514										
RPIA	22934	broad.mit.edu	37	chr2	88999564	88999564	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatctgaacctcgtctgTattcccacttccttccaggt	7	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:88999564T>C	ENST00000283646.4	+	3	439	c.384T>C	c.(382-384)tgT>tgC	p.C128C		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	128					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)	p.C128C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				ACCTCGTCTGTATTCCCACTT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	2											175	165	168					2																	88999564		1925	4141	6066	88780679	SO:0001819	synonymous_variant	22934			L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"ribose 5-phosphate epimerase"	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.384T>C	2.37:g.88999564T>C			88780679	Q541P9|Q96BJ6	Silent	SNP	ENST00000283646.4	37	CCDS2004.2																																																																																				0.463	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			C	88999564	T	C	88999564	2	2	61	1	0	0	0	0	0	0	0	1	13590	1644	57	4		4	RPIA	2	88999564	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	86195	88999564	154199809	1530	9515										
ADRA2B	151	broad.mit.edu	37	chr2	96781139	96781139	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttctccccagtggacttCgagtgtccgttgacctctct	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96781139C>T	ENST00000409345.3	-	1	845	c.750G>A	c.(748-750)tcG>tcA	p.S250S		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	250					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)	p.S250S(1)		endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CAGTGGACTTCGAGTGTCCGT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	2											21	23	23					2																	96781139		1880	4119	5999	96144866	SO:0001819	synonymous_variant	151			M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.750G>A	2.37:g.96781139C>T			96144866	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																				0.652	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			T	96781139	C	T	96781139	2	4	61	1	0	0	0	0	0	0	0	1	338	871	31	1		1	ADRA2B	2	96781139	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7781575	96781139	146418234	1531	9516										
ASTL	431705	broad.mit.edu	37	chr2	96789618	96789618	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacatccccttgaaatgatTtctaggtacacagccccctg	8	13	1	2	rs577986927		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96789618T>G	ENST00000342380.2	-	9	1266	c.1267A>C	c.(1267-1269)Aat>Cat	p.N423H		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)									p.N423H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						TTGAAATGATTTCTAGGTACA	0.582													T|||	1	0.000199681	0	0.0014	5008	,	,		20133	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											68	75	73					2																	96789618		2203	4300	6503	96153345	SO:0001583	missense	431705			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.1267A>C	2.37:g.96789618T>G	ENSP00000343674:p.Asn423His		96153345		Missense_Mutation	SNP	ENST00000342380.2	37	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	T	6.768	0.510603	0.12883	.	.	ENSG00000188886	ENST00000342380	T	0.64618	-0.11	4.44	0.706	0.18133	.	0.634518	0.13400	N	0.390698	T	0.38931	0.1059	N	0.08118	0	0.09310	N	1	B	0.28512	0.214	B	0.31751	0.135	T	0.34204	-0.9838	10	0.66056	D	0.02	-0.0632	5.8422	0.18639	0.0:0.3956:0.0:0.6044	.	423	Q6HA08	ASTL_HUMAN	H	423	ENSP00000343674:N423H	ENSP00000343674:N423H	N	-	1	0	ASTL	96153345	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.291000	0.08343	0.279000	0.22186	0.454000	0.30748	AAT		0.582	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			G	96789618	T	G	96789618	3	3	61	1	0	0	0	0	1	0	0	0	1064	1841	64	4	31	4	ASTL	2	96789618	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8479	96789618	146409755	1532	9517										
ASTL	431705	broad.mit.edu	37	chr2	96795838	96795838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaggagtagtcatagggCgtcagcatgttgctgctctg	14	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96795838C>T	ENST00000342380.2	-	7	683	c.684G>A	c.(682-684)acG>acA	p.T228T		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)									p.T228T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						AGTCATAGGGCGTCAGCATGT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	2											138	141	140					2																	96795838		2203	4300	6503	96159565	SO:0001819	synonymous_variant	431705			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.684G>A	2.37:g.96795838C>T			96159565		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																				0.478	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			T	96795838	C	T	96795838	2	4	61	1	0	0	0	0	0	0	0	1	1064	755	27	1		1	ASTL	2	96795838	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6220	96795838	146403535	1533	9518										
ASTL	431705	broad.mit.edu	37	chr2	96798409	96798409	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttctggagacacgtgggCgccagggagaccacctgcat	13	14	1	2	rs369122887		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96798409C>T	ENST00000342380.2	-	6	506	c.507G>A	c.(505-507)gcG>gcA	p.A169A		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)									p.A169A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GACACGTGGGCGCCAGGGAGA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	2						T		1,4405	2.1+/-5.4	0,1,2202	75	77	76		507	-4.4	0.6	2		76	0,8600		0,0,4300	no	coding-synonymous	ASTL	NM_001002036.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		169/432	96798409	1,13005	2203	4300	6503	96162136	SO:0001819	synonymous_variant	431705			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.507G>A	2.37:g.96798409C>T			96162136		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																				0.642	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			T	96798409	C	T	96798409	2	4	61	1	0	0	0	0	0	0	0	1	1064	755	27	1		1	ASTL	2	96798409	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2571	96798409	146400964	1534	9519										
ASTL	431705	broad.mit.edu	37	chr2	96799217	96799217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtcctgataggtgacaaaCctgatgcacgtggaacgttc	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96799217C>T	ENST00000342380.2	-	5	401	c.402G>A	c.(400-402)agG>agA	p.R134R		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)									p.R134R(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						AGGTGACAAACCTGATGCACG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	2											104	92	96					2																	96799217		2203	4300	6503	96162944	SO:0001819	synonymous_variant	431705			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.402G>A	2.37:g.96799217C>T			96162944		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																				0.572	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			T	96799217	C	T	96799217	2	4	61	1	0	0	0	0	0	0	0	1	1064	506	18	3		3	ASTL	2	96799217	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	808	96799217	146400156	1535	9520										
SNRNP200	23020	broad.mit.edu	37	chr2	96943648	96943648	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgacgtgcggatcattgAacttagggttattcagcttg	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96943648A>C	ENST00000323853.5	-	40	5728	c.5651T>G	c.(5650-5652)tTc>tGc	p.F1884C	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1884	SEC63 2.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.F1884C(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CGGATCATTGAACTTAGGGTT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											127	134	132					2																	96943648		2203	4300	6503	96307375	SO:0001583	missense	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5651T>G	2.37:g.96943648A>C	ENSP00000317123:p.Phe1884Cys		96307375	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371896	0.42003	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	T	0.60672	0.17	4.91	4.91	0.64330	Sec63 domain (3);	0.053010	0.85682	D	0.000000	T	0.63861	0.2547	M	0.87617	2.895	0.80722	D	1	B	0.14805	0.011	B	0.19391	0.025	T	0.65459	-0.6163	10	0.48119	T	0.1	-18.6376	13.9519	0.64123	1.0:0.0:0.0:0.0	.	1884	O75643	U520_HUMAN	C	1884;343;467	ENSP00000317123:F1884C	ENSP00000317123:F1884C	F	-	2	0	SNRNP200	96307375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.923000	0.75817	2.183000	0.69458	0.533000	0.62120	TTC		0.507	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		C	96943648	A	C	96943648	3	2	61	1	0	0	0	0	1	0	0	0	14889	246	9	4	783	4	SNRNP200	2	96943648	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	144431	96943648	146255725	1536	9521										
SNRNP200	23020	broad.mit.edu	37	chr2	96962701	96962701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagcagcagattctcatcCgtctcaagggcagcacggta	10	13	2	1	rs142142479		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96962701C>T	ENST00000323853.5	-	12	1562	c.1485G>A	c.(1483-1485)acG>acA	p.T495T	SNRNP200_ENST00000349783.5_Silent_p.T495T	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	495	Helicase ATP-binding 1. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.T495T(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GATTCTCATCCGTCTCAAGGG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C		1,4405	2.1+/-5.4	0,1,2202	73	66	69		1485	-9.5	1	2	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous	SNRNP200	NM_014014.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		495/2137	96962701	1,13005	2203	4300	6503	96326428	SO:0001819	synonymous_variant	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.1485G>A	2.37:g.96962701C>T			96326428	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																				0.493	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		T	96962701	C	T	96962701	2	4	61	1	0	0	0	0	0	0	0	1	14889	639	23	1		1	SNRNP200	2	96962701	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19053	96962701	146236672	1537	9522										
ITPRIPL1	150771	broad.mit.edu	37	chr2	96992559	96992559	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagtttgaagagagaaagCgagccgctgagcagaggcag	17	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:96992559C>T	ENST00000439118.2	+	3	441	c.190C>T	c.(190-192)Cga>Tga	p.R64*	ITPRIPL1_ENST00000361124.4_Nonsense_Mutation_p.R72*|ITPRIPL1_ENST00000542887.1_Nonsense_Mutation_p.R56*|ITPRIPL1_ENST00000536814.1_Nonsense_Mutation_p.R56*	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	64						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R72*(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AGAGAGAAAGCGAGCCGCTGA	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											88	91	90					2																	96992559		2203	4300	6503	96356286	SO:0001587	stop_gained	150771				CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"KIAA1754-like", "inositol 1,4,5-triphosphate receptor interacting protein-like 1"	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.190C>T	2.37:g.96992559C>T	ENSP00000389308:p.Arg64*		96356286	F5H1L8|Q8NE61	Nonsense_Mutation	SNP	ENST00000439118.2	37	CCDS46360.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146563	0.94603	.	.	ENSG00000198885	ENST00000420176;ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	.	.	.	5.23	3.35	0.38373	.	0.747693	0.10353	N	0.684833	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.2575	9.2863	0.37760	0.1428:0.7787:0.0:0.0785	.	.	.	.	X	56;56;64;72;56	.	ENSP00000355121:R72X	R	+	1	2	ITPRIPL1	96356286	0.004000	0.15560	0.021000	0.16686	0.776000	0.43924	0.302000	0.19192	1.155000	0.42497	0.655000	0.94253	CGA		0.552	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495		T	96992559	C	T	96992559	4	4	61	1	0	0	0	0	0	1	0	0	7945	760	27	1	230	1	ITPRIPL1	2	96992559	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29858	96992559	146206814	1538	9523										
KIAA1310	55683	broad.mit.edu	37	chr2	97275281	97275281	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtcaacccttctgatttCttctttgctttgcttattct	5	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:97275281C>A	ENST00000431828.1	-	12	1414	c.1338G>T	c.(1336-1338)aaG>aaT	p.K446N	KANSL3_ENST00000441706.2_Missense_Mutation_p.K359N|KANSL3_ENST00000440133.1_Missense_Mutation_p.K240N|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000599854.1_Missense_Mutation_p.K359N			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	446					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.K446N(1)									CTTCTGATTTCTTCTTTGCTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											359	356	357					2																	97275281		1906	4124	6030	96639008	SO:0001583	missense	55683			BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1338G>T	2.37:g.97275281C>A	ENSP00000396749:p.Lys446Asn		96639008	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	37	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.122174	0.77436	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000441706;ENST00000440133;ENST00000444759	T;T	0.54866	0.58;0.55	5.2	4.33	0.51752	.	0.089923	0.85682	D	0.000000	T	0.61299	0.2336	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.71674	0.998;0.994;0.998;0.997	P;P;P;P	0.62184	0.852;0.76;0.876;0.899	T	0.62817	-0.6774	10	0.59425	D	0.04	.	11.5096	0.50486	0.0:0.9125:0.0:0.0875	.	240;446;359;334	B4E1W4;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.;.	N	359;334;446;359;240;240	ENSP00000396749:K446N;ENSP00000406207:K240N	ENSP00000346144:K359N	K	-	3	2	KIAA1310	96639008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.635000	0.61332	1.192000	0.43071	0.655000	0.94253	AAG		0.383	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		A	97275281	C	A	97275281	3	1	61	1	0	0	0	0	1	0	0	0	8243	912	32	2	1338	2	KIAA1310	2	97275281	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	282722	97275281	145924092	1539	9524										
ANKRD36B	57730	broad.mit.edu	37	chr2	98167926	98167926	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcattaccttcaaggctgGttttttctgagaagacactg	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98167926G>T	ENST00000443455.1	-	0	1401							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TTCAAGGCTGGTTTTTTCTGA	0.318																																																0			2											56	53	54					2																	98167926		1820	4003	5823	97534358			57730			AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98167926G>T			97534358	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																					0.318	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		T	98167926	G	T	98167926	1	4	61	0	1	0	0	0	0	0	0	0	666	1261	44	2		2	ANKRD36B	2	98167926	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	892645	98167926	145031447	1540	9525										
VWA3B	200403	broad.mit.edu	37	chr2	98732199	98732199	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagagcagaagatggcaGagtatacaatgtaagtcaga	11	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98732199G>T	ENST00000477737.1	+	3	485	c.281G>T	c.(280-282)aGa>aTa	p.R94I	VWA3B_ENST00000451075.2_Nonsense_Mutation_p.E28*|VWA3B_ENST00000435344.1_Missense_Mutation_p.R94I	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	94								p.R94I(1)		NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GAAGATGGCAGAGTATACAAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											84	81	82					2																	98732199		2133	4260	6393	98098631	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.281G>T	2.37:g.98732199G>T	ENSP00000417955:p.Arg94Ile		98098631	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.106338|6.106338	0.97286|0.97286	.|.	.|.	ENSG00000168658|ENSG00000168658	ENST00000451075|ENST00000435344;ENST00000477737	.|T;T	.|0.39056	.|1.1;1.1	5.53|5.53	0.115|0.115	0.14643|0.14643	.|.	.|0.570028	.|0.16734	.|N	.|0.201739	.|T	.|0.24624	.|0.0597	L|L	0.35414|0.35414	1.06|1.06	0.80722|0.80722	A|A	1|1	.|P;B	.|0.43885	.|0.82;0.046	.|B;B	.|0.36719	.|0.231;0.047	.|T	.|0.25363	.|-1.0134	.|9	0.05620|0.42905	T|T	0.96|0.14	.|.	6.3008|6.3008	0.21111|0.21111	0.265:0.514:0.221:0.0|0.265:0.514:0.221:0.0	.|.	.|94;94	.|Q502W6;Q502W6-8	.|VWA3B_HUMAN;.	X|I	28|94	.|ENSP00000401959:R94I;ENSP00000417955:R94I	ENSP00000389463:E28X|ENSP00000411168:R94I	E|R	+|+	1|2	0|0	VWA3B|VWA3B	98098631|98098631	0.213000|0.213000	0.23551|0.23551	0.086000|0.086000	0.20670|0.20670	0.994000|0.994000	0.84299|0.84299	0.090000|0.090000	0.15025|0.15025	0.262000|0.262000	0.21774|0.21774	0.563000|0.563000	0.77884|0.77884	GAG|AGA		0.493	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98732199	G	T	98732199	3	4	61	1	0	0	0	0	1	0	0	0	17281	942	33	2	287	2	VWA3B	2	98732199	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	564273	98732199	144467174	1541	9526										
VWA3B	200403	broad.mit.edu	37	chr2	98834347	98834347	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaggtcaaacgttttcaGgaaattcctatttataccat	6	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98834347G>T	ENST00000477737.1	+	14	2079	c.1875G>T	c.(1873-1875)caG>caT	p.Q625H		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	625	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.							p.Q625H(1)		NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AACGTTTTCAGGAAATTCCTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											97	88	91					2																	98834347		1836	4083	5919	98200779	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1875G>T	2.37:g.98834347G>T	ENSP00000417955:p.Gln625His		98200779	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.25|15.25	2.777368|2.777368	0.49786|0.49786	.|.	.|.	ENSG00000168658|ENSG00000168658	ENST00000473149|ENST00000477737	.|T	.|0.08458	.|3.09	5.77|5.77	3.87|3.87	0.44632|0.44632	.|von Willebrand factor, type A (3);	.|0.480379	.|0.18852	.|N	.|0.129380	.|T	.|0.11836	.|0.0288	N|N	0.20986|0.20986	0.625|0.625	0.80722|0.80722	D|D	1|1	.|D;P;P;D	.|0.71674	.|0.998;0.856;0.728;0.995	.|D;B;B;D	.|0.67382	.|0.951;0.376;0.189;0.912	.|T	.|0.22556	.|-1.0213	.|10	.|0.32370	.|T	.|0.25	.|.	5.2486|5.2486	0.15510|0.15510	0.1746:0.1707:0.6547:0.0|0.1746:0.1707:0.6547:0.0	.|.	.|17;625;625;625	.|Q502W6-5;Q502W6;Q502W6-8;Q502W6-6	.|.;VWA3B_HUMAN;.;.	X|H	36|625	.|ENSP00000417955:Q625H	.|ENSP00000417955:Q625H	G|Q	+|+	1|3	0|2	VWA3B|VWA3B	98200779|98200779	0.127000|0.127000	0.22367|0.22367	1.000000|1.000000	0.80357|0.80357	0.587000|0.587000	0.36485|0.36485	0.166000|0.166000	0.16583|0.16583	1.440000|1.440000	0.47531|0.47531	0.655000|0.655000	0.94253|0.94253	GGA|CAG		0.393	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98834347	G	T	98834347	3	4	61	1	0	0	0	0	1	0	0	0	17281	991	35	2	1925	2	VWA3B	2	98834347	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102148	98834347	144365026	1542	9527										
VWA3B	200403	broad.mit.edu	37	chr2	98846644	98846644	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcctttcagatcaaaaggTtcagaaaaagaaagtccttc	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98846644T>C	ENST00000477737.1	+	16	2486	c.2282T>C	c.(2281-2283)gTt>gCt	p.V761A		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	761								p.V761A(1)		NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GATCAAAAGGTTCAGAAAAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	81	84					2																	98846644		1833	4100	5933	98213076	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2282T>C	2.37:g.98846644T>C	ENSP00000417955:p.Val761Ala		98213076	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.425986	0.25726	.	.	ENSG00000168658	ENST00000477737	T	0.05580	3.42	4.29	-3.34	0.04943	.	2.099500	0.02258	N	0.067330	T	0.03915	0.0110	N	0.22421	0.69	0.09310	N	0.999997	B;B;B;B	0.13145	0.006;0.001;0.001;0.007	B;B;B;B	0.14023	0.004;0.003;0.001;0.01	T	0.38112	-0.9676	10	0.02654	T	1	.	6.1025	0.20055	0.0:0.4949:0.1726:0.3326	.	153;761;761;761	Q502W6-5;Q502W6;Q502W6-8;Q502W6-6	.;VWA3B_HUMAN;.;.	A	761	ENSP00000417955:V761A	ENSP00000417955:V761A	V	+	2	0	VWA3B	98213076	0.177000	0.23109	0.194000	0.23346	0.239000	0.25481	-0.545000	0.06069	-0.712000	0.04988	-0.619000	0.04042	GTT		0.413	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		C	98846644	T	C	98846644	3	2	61	1	0	0	0	0	1	0	0	0	17281	1725	60	4	2340	4	VWA3B	2	98846644	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12297	98846644	144352729	1543	9528										
VWA3B	200403	broad.mit.edu	37	chr2	98853051	98853051	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttagttcttcagatgtgtCttcagaaaactggctgaaga	9	7	5	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98853051C>A	ENST00000477737.1	+	19	2735	c.2531C>A	c.(2530-2532)tCt>tAt	p.S844Y		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	844								p.S844Y(1)		NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TCAGATGTGTCTTCAGAAAAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	107	107					2																	98853051		1943	4151	6094	98219483	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2531C>A	2.37:g.98853051C>A	ENSP00000417955:p.Ser844Tyr		98219483	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.107897	0.56291	.	.	ENSG00000168658	ENST00000477737	T	0.09163	3.01	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000009	T	0.30978	0.0782	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.998;1.0	D;D;D;D	0.91635	0.971;0.979;0.962;0.999	T	0.01977	-1.1236	10	0.87932	D	0	.	17.2494	0.87038	0.0:1.0:0.0:0.0	.	236;844;844;844	Q502W6-5;Q502W6;Q502W6-8;Q502W6-6	.;VWA3B_HUMAN;.;.	Y	844	ENSP00000417955:S844Y	ENSP00000417955:S844Y	S	+	2	0	VWA3B	98219483	1.000000	0.71417	0.700000	0.30305	0.522000	0.34438	4.962000	0.63687	2.429000	0.82318	0.591000	0.81541	TCT		0.438	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98853051	C	A	98853051	3	1	61	1	0	0	0	0	1	0	0	0	17281	913	32	2	2601	2	VWA3B	2	98853051	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6407	98853051	144346322	1544	9529										
CNGA3	1261	broad.mit.edu	37	chr2	98986517	98986517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcagaccgagatctcaatCgcgctgaaaatggcctcagc	9	14	3	3	rs149069990		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:98986517C>T	ENST00000272602.2	+	1	118	c.79C>T	c.(79-81)Cgc>Tgc	p.R27C	CNGA3_ENST00000393504.1_Missense_Mutation_p.R27C|CNGA3_ENST00000436404.2_Missense_Mutation_p.R27C			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	27					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.R27C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGATCTCAATCGCGCTGAAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	131	108	116		79,79	-6	0	2	dbSNP_134	116	0,8600		0,0,4300	no	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	27/677,27/695	98986517	1,13005	2203	4300	6503	98352949	SO:0001583	missense	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.79C>T	2.37:g.98986517C>T	ENSP00000272602:p.Arg27Cys		98352949	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	37	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	C	9.588	1.125328	0.20959	2.27E-4	0.0	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602	D;D;D	0.97731	-4.51;-4.45;-4.51	4.2	-5.98	0.02220	.	.	.	.	.	D	0.91540	0.7328	N	0.17474	0.49	0.09310	N	1	B;B	0.14438	0.003;0.01	B;B	0.04013	0.0;0.001	T	0.82528	-0.0412	9	0.49607	T	0.09	.	5.3574	0.16069	0.2518:0.1951:0.0:0.5531	.	27;27	Q4VAP7;Q16281	.;CNGA3_HUMAN	C	27	ENSP00000377140:R27C;ENSP00000410070:R27C;ENSP00000272602:R27C	ENSP00000272602:R27C	R	+	1	0	CNGA3	98352949	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.285000	0.08410	-1.149000	0.02843	-0.783000	0.03347	CGC		0.502	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	98986517	C	T	98986517	3	4	61	1	0	0	0	0	1	0	0	0	3604	884	31	1	81	1	CNGA3	2	98986517	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133466	98986517	144212856	1545	9530										
INPP4A	3631	broad.mit.edu	37	chr2	99169414	99169414	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggccttgagaggacactCgccatcttggcagacaaggt	12	11	1	2	rs137960574	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:99169414C>T	ENST00000523221.1	+	13	1344	c.1344C>T	c.(1342-1344)ctC>ctT	p.L448L	INPP4A_ENST00000409540.3_Silent_p.L448L|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Silent_p.L448L|INPP4A_ENST00000074304.5_Silent_p.L448L|INPP4A_ENST00000409851.3_Silent_p.L443L|INPP4A_ENST00000545415.1_Silent_p.L448L			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	448					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.L448L(2)		breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						AGAGGACACTCGCCATCTTGG	0.577													C|||	2	0.000399361	0	0.0014	5008	,	,		21217	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	2						C	,,,	0,4012		0,0,2006	37	37	37		1344,1329,1344,1344	-10.1	0	2	dbSNP_134	37	2,8330		0,2,4164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	0,2,6170	TT,TC,CC		0.024,0.0,0.0162	,,,	448/978,443/973,448/955,448/939	99169414	2,12342	2006	4166	6172	98535846	SO:0001819	synonymous_variant	3631			U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"inositol polyphosphate-4-phosphatase, type I, 107kD"	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1344C>T	2.37:g.99169414C>T			98535846	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																				0.577	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566		T	99169414	C	T	99169414	2	4	61	1	0	0	0	0	0	0	0	1	7773	871	31	1		1	INPP4A	2	99169414	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	182897	99169414	144029959	1546	9531										
INPP4A	3631	broad.mit.edu	37	chr2	99203982	99203982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgaagaatgttggaagtCgcaaatatgcatttaattcc	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:99203982C>T	ENST00000523221.1	+	24	2845	c.2845C>T	c.(2845-2847)Cgc>Tgc	p.R949C	INPP4A_ENST00000409463.1_Missense_Mutation_p.R278C|INPP4A_ENST00000409016.4_Missense_Mutation_p.R910C|INPP4A_ENST00000074304.5_Missense_Mutation_p.R949C|INPP4A_ENST00000409851.3_Missense_Mutation_p.R944C|INPP4A_ENST00000545415.1_Missense_Mutation_p.R910C			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	949					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.R949C(1)		breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						TGTTGGAAGTCGCAAATATGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	86	87					2																	99203982		1866	4085	5951	98570414	SO:0001583	missense	3631			U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"inositol polyphosphate-4-phosphatase, type I, 107kD"	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.2845C>T	2.37:g.99203982C>T	ENSP00000427722:p.Arg949Cys		98570414	O15326|Q13187|Q53TD8|Q8TC02	Missense_Mutation	SNP	ENST00000523221.1	37	CCDS46369.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248318	0.95305	.	.	ENSG00000040933	ENST00000409016;ENST00000409851;ENST00000409463;ENST00000074304;ENST00000545415;ENST00000523221	T;T;T;T;T;T	0.50277	1.62;1.96;0.75;1.96;1.62;1.96	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.71796	0.3382	M	0.80982	2.52	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.995;0.975;0.999;0.999	T	0.74526	-0.3636	10	0.72032	D	0.01	-22.8426	18.4048	0.90532	0.0:1.0:0.0:0.0	.	910;278;949;944	Q96PE3-2;B8ZZB2;Q96PE3;Q96PE3-3	.;.;INP4A_HUMAN;.	C	910;944;278;949;910;949	ENSP00000386704:R910C;ENSP00000386777:R944C;ENSP00000386329:R278C;ENSP00000074304:R949C;ENSP00000442149:R910C;ENSP00000427722:R949C	ENSP00000074304:R949C	R	+	1	0	INPP4A	98570414	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.818000	0.69236	2.824000	0.97209	0.655000	0.94253	CGC		0.423	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566		T	99203982	C	T	99203982	3	4	61	1	0	0	0	0	1	0	0	0	7773	884	31	1	3124	1	INPP4A	2	99203982	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34568	99203982	143995391	1547	9532										
C2orf15	80705	broad.mit.edu	37	chr2	99767156	99767156	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttatttcaaaacaccaaGaaaataagattagaagacac	5	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:99767156G>T	ENST00000393483.3	-	1	225				C2ORF15_ENST00000302513.2_Missense_Mutation_p.K79N|C2ORF15_ENST00000409684.1_Missense_Mutation_p.K79N	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.K79N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						AAAACACCAAGAAAATAAGAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											73	75	75					2																	99767156		2203	4300	6503	99133588	SO:0001627	intron_variant	150590			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.619+3999C>A	2.37:g.99767156G>T			99133588	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.294693	0.40594	.	.	ENSG00000241962	ENST00000302513;ENST00000409684	.	.	.	4.89	2.88	0.33553	.	.	.	.	.	T	0.29093	0.0723	N	0.08118	0	0.80722	D	1	B	0.28552	0.215	B	0.30179	0.112	T	0.16424	-1.0403	8	0.87932	D	0	-4.5683	4.4966	0.11840	0.1166:0.0:0.6608:0.2226	.	79	Q8WU43	CB015_HUMAN	N	79	.	ENSP00000302202:K79N	K	+	3	2	C2orf15	99133588	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	0.667000	0.25112	1.222000	0.43521	0.462000	0.41574	AAG		0.388	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		T	99767156	G	T	99767156	1	4	61	0	1	0	0	0	0	0	0	0	2162	933	33	2		2	C2orf15	2	99767156	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	563174	99767156	143432217	1548	9533										
LIPT1	51601	broad.mit.edu	37	chr2	99778797	99778797	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccaaaaaaaagtatgataGaatggaaaatctgaaattaa	6	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:99778797G>T	ENST00000393473.2	+	3	601	c.377G>T	c.(376-378)aGa>aTa	p.R126I	LIPT1_ENST00000340066.1_Missense_Mutation_p.R126I|LIPT1_ENST00000393477.3_Missense_Mutation_p.R126I|MRPL30_ENST00000410042.1_Intron|LIPT1_ENST00000393471.2_Missense_Mutation_p.R126I|LIPT1_ENST00000393474.3_Missense_Mutation_p.R126I	NM_001204830.1|NM_015929.3	NP_001191759.1|NP_057013.1	Q9Y234	LIPT_HUMAN	lipoyltransferase 1	126	BPL/LPL catalytic. {ECO:0000255|PROSITE- ProRule:PRU01067}.				cellular protein modification process (GO:0006464)|lipid metabolic process (GO:0006629)|protein lipoylation (GO:0009249)	mitochondrion (GO:0005739)	transferase activity, transferring acyl groups (GO:0016746)	p.R126I(1)		large_intestine(6)|lung(1)	7					Lipoic Acid(DB00166)	AAGTATGATAGAATGGAAAAT	0.393																																					GBM(84;665 1268 21657 25485 30647)											1	Substitution - Missense(1)	large_intestine(1)	2											50	50	50					2																	99778797		2203	4300	6503	99145229	SO:0001583	missense	51601			AB017566	CCDS2039.1	2q11.2	2010-11-25			ENSG00000144182	ENSG00000144182	2.3.1.181		29569	protein-coding gene	gene with protein product		610284				10103005	Standard	NM_145197		Approved	MGC12290, MGC13378	uc002szq.4	Q9Y234	OTTHUMG00000130640	ENST00000393473.2:c.377G>T	2.37:g.99778797G>T	ENSP00000377115:p.Arg126Ile		99145229	Q4ZFZ1	Missense_Mutation	SNP	ENST00000393473.2	37	CCDS2039.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513855	0.85389	.	.	ENSG00000144182	ENST00000393473;ENST00000393477;ENST00000393474;ENST00000340066;ENST00000393471;ENST00000449211;ENST00000434566	D;D;D;D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32;-3.32;-3.32;-3.32	4.9	4.9	0.64082	Biotin/lipoate A/B protein ligase (1);	0.000000	0.85682	D	0.000000	D	0.96065	0.8718	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.96071	0.9046	10	0.56958	D	0.05	-2.0447	17.2441	0.87022	0.0:0.0:1.0:0.0	.	126	Q9Y234	LIPT_HUMAN	I	126	ENSP00000377115:R126I;ENSP00000377118:R126I;ENSP00000377116:R126I;ENSP00000342071:R126I;ENSP00000377114:R126I;ENSP00000387387:R126I;ENSP00000393591:R126I	ENSP00000342071:R126I	R	+	2	0	LIPT1	99145229	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.595000	0.98260	2.553000	0.86117	0.650000	0.86243	AGA		0.393	LIPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253128.1	NM_015929		T	99778797	G	T	99778797	3	4	61	1	0	0	0	0	1	0	0	0	8853	942	33	2	379	2	LIPT1	2	99778797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11641	99778797	143420576	1549	9534										
LIPT1	51601	broad.mit.edu	37	chr2	99779515	99779515	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagtaaatggaatattctCtgtgaaaaaattaagggaat	8	3	1	1	rs148385959		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:99779515C>T	ENST00000393473.2	+	3	1319	c.1095C>T	c.(1093-1095)ctC>ctT	p.L365L	LIPT1_ENST00000340066.1_Silent_p.L365L|LIPT1_ENST00000393477.3_Silent_p.L365L|MRPL30_ENST00000410042.1_Intron|LIPT1_ENST00000393471.2_Silent_p.L365L|LIPT1_ENST00000393474.3_Silent_p.L365L	NM_001204830.1|NM_015929.3	NP_001191759.1|NP_057013.1	Q9Y234	LIPT_HUMAN	lipoyltransferase 1	365					cellular protein modification process (GO:0006464)|lipid metabolic process (GO:0006629)|protein lipoylation (GO:0009249)	mitochondrion (GO:0005739)	transferase activity, transferring acyl groups (GO:0016746)	p.L365L(1)		large_intestine(6)|lung(1)	7					Lipoic Acid(DB00166)	GGAATATTCTCTGTGAAAAAA	0.303																																					GBM(84;665 1268 21657 25485 30647)											1	Substitution - coding silent(1)	large_intestine(1)	2											40	39	39					2																	99779515		1977	4184	6161	99145947	SO:0001819	synonymous_variant	51601			AB017566	CCDS2039.1	2q11.2	2010-11-25			ENSG00000144182	ENSG00000144182	2.3.1.181		29569	protein-coding gene	gene with protein product		610284				10103005	Standard	NM_145197		Approved	MGC12290, MGC13378	uc002szq.4	Q9Y234	OTTHUMG00000130640	ENST00000393473.2:c.1095C>T	2.37:g.99779515C>T			99145947	Q4ZFZ1	Silent	SNP	ENST00000393473.2	37	CCDS2039.1																																																																																				0.303	LIPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253128.1	NM_015929		T	99779515	C	T	99779515	2	4	61	1	0	0	0	0	0	0	0	1	8853	900	32	3		3	LIPT1	2	99779515	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	718	99779515	143419858	1550	9535										
EIF5B	9669	broad.mit.edu	37	chr2	100006294	100006294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcgagcaaaggctattatTgtagaatttgcacagcaggt	12	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100006294T>C	ENST00000289371.6	+	15	2587	c.2385T>C	c.(2383-2385)atT>atC	p.I795I		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	795	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.I795I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGCTATTATTGTAGAATTTG	0.353																																					Colon(162;2388 2567 2705 3444)											1	Substitution - coding silent(1)	large_intestine(1)	2											82	77	78					2																	100006294		1822	4084	5906	99372726	SO:0001819	synonymous_variant	9669			AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.2385T>C	2.37:g.100006294T>C			99372726	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																				0.353	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		C	100006294	T	C	100006294	2	2	61	1	0	0	0	0	0	0	0	1	5057	1800	63	4		4	EIF5B	2	100006294	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	226779	100006294	143193079	1551	9536										
REV1	51455	broad.mit.edu	37	chr2	100022947	100022947	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaactgattcacgtgaatCccaacctagaacccagaata	5	13	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100022947C>A	ENST00000258428.3	-	16	2682	c.2454G>T	c.(2452-2454)ggG>ggT	p.G818G	REV1_ENST00000465835.1_5'UTR|RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000393445.3_Silent_p.G817G	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	818					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.G818G(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCACGTGAATCCCAACCTAGA	0.418								Direct reversal of damage																																								1	Substitution - coding silent(1)	large_intestine(1)	2											61	62	62					2																	100022947		2203	4300	6503	99389379	SO:0001819	synonymous_variant	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.2454G>T	2.37:g.100022947C>A			99389379	O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	CCDS2045.1																																																																																				0.418	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100022947	C	A	100022947	2	1	61	1	0	0	0	0	0	0	0	1	13276	842	30	2		2	REV1	2	100022947	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16653	100022947	143176426	1552	9537										
REV1	51455	broad.mit.edu	37	chr2	100027203	100027203	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccaaattttgcagtttCtacaggagccccaggctttc	8	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100027203C>A	ENST00000258428.3	-	14	2527	c.2299G>T	c.(2299-2301)Gaa>Taa	p.E767*	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Nonsense_Mutation_p.E766*	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	767					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.E767*(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTTGCAGTTTCTACAGGAGCC	0.403								Direct reversal of damage																																								1	Substitution - Nonsense(1)	large_intestine(1)	2											119	114	116					2																	100027203		2203	4300	6503	99393635	SO:0001587	stop_gained	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.2299G>T	2.37:g.100027203C>A	ENSP00000258428:p.Glu767*		99393635	O95941|Q53SI7|Q9C0J4|Q9NUP2	Nonsense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	43	9.910501	0.99293	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	19.0357	0.92976	0.0:1.0:0.0:0.0	.	.	.	.	X	766;767	.	ENSP00000258428:E767X	E	-	1	0	REV1	99393635	1.000000	0.71417	0.833000	0.33012	0.962000	0.63368	7.347000	0.79356	2.559000	0.86315	0.650000	0.86243	GAA		0.403	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100027203	C	A	100027203	4	1	61	1	0	0	0	0	0	1	0	0	13276	922	32	2	1496	2	REV1	2	100027203	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4256	100027203	143172170	1553	9538										
REV1	51455	broad.mit.edu	37	chr2	100038009	100038009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtctttgatttccatacGaacagcatttgcaaattcat	6	9	2	1	rs560500168		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100038009G>A	ENST00000258428.3	-	11	2011	c.1783C>T	c.(1783-1785)Cgt>Tgt	p.R595C	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.R594C	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	595	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.R595C(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ATTTCCATACGAACAGCATTT	0.398								Direct reversal of damage																																								1	Substitution - Missense(1)	large_intestine(1)	2											193	176	182					2																	100038009		2203	4300	6503	99404441	SO:0001583	missense	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1783C>T	2.37:g.100038009G>A	ENSP00000258428:p.Arg595Cys		99404441	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629831	0.87660	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.80304	-1.36;-1.36	5.59	5.59	0.84812	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.000000	0.85682	D	0.000000	D	0.92548	0.7633	M	0.92459	3.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93799	0.7099	10	0.87932	D	0	.	19.5763	0.95446	0.0:0.0:1.0:0.0	.	595;594	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	C	594;595	ENSP00000377091:R594C;ENSP00000258428:R595C	ENSP00000258428:R595C	R	-	1	0	REV1	99404441	1.000000	0.71417	0.943000	0.38184	0.991000	0.79684	6.765000	0.74965	2.646000	0.89796	0.655000	0.94253	CGT		0.398	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100038009	G	A	100038009	3	1	61	1	0	0	0	0	1	0	0	0	13276	1058	37	1	2024	1	REV1	2	100038009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10806	100038009	143161364	1554	9539										
AFF3	3899	broad.mit.edu	37	chr2	100343547	100343547	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaaacttacgatgtattCgatgtgccactgtctggact	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100343547C>T	ENST00000409236.2	-	9	1195	c.1083G>A	c.(1081-1083)tcG>tcA	p.S361S	AFF3_ENST00000356421.2_Silent_p.S386S|AFF3_ENST00000317233.4_Silent_p.S361S|AFF3_ENST00000409579.1_Silent_p.S386S			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	361					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.S386S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ACGATGTATTCGATGTGCCAC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	2											84	82	83					2																	100343547		2203	4300	6503	99709979	SO:0001819	synonymous_variant	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1083G>A	2.37:g.100343547C>T			99709979	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																				0.348	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		T	100343547	C	T	100343547	2	4	61	1	0	0	0	0	0	0	0	1	358	871	31	1		1	AFF3	2	100343547	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	305538	100343547	142855826	1555	9540										
AFF3	3899	broad.mit.edu	37	chr2	100623208	100623208	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcacgctggtttccgaagaCgacttcagcttaggagactc	11	11	1	2	rs371774868		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:100623208C>T	ENST00000409236.2	-	5	871	c.759G>A	c.(757-759)tcG>tcA	p.S253S	AFF3_ENST00000356421.2_Silent_p.S278S|AFF3_ENST00000317233.4_Silent_p.S253S|AFF3_ENST00000409579.1_Silent_p.S278S			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	253					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.S278S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TTTCCGAAGACGACTTCAGCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	3,4403	6.2+/-15.9	0,3,2200	69	65	66		834,759	-11.1	0	2		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	AFF3	NM_001025108.1,NM_002285.2	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	278/1252,253/1227	100623208	3,13003	2203	4300	6503	99989640	SO:0001819	synonymous_variant	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.759G>A	2.37:g.100623208C>T			99989640	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																				0.582	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		T	100623208	C	T	100623208	2	4	61	1	0	0	0	0	0	0	0	1	358	523	19	1		1	AFF3	2	100623208	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279661	100623208	142576165	1556	9541										
CHST10	9486	broad.mit.edu	37	chr2	101010210	101010210	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataagtctttcgaagggatCtcttacaataaaaaacttga	6	6	2	1	rs368455898		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:101010210C>A	ENST00000264249.3	-	7	953	c.568G>T	c.(568-570)Gat>Tat	p.D190Y	CHST10_ENST00000542617.1_Missense_Mutation_p.D238Y|CHST10_ENST00000409701.1_Missense_Mutation_p.D190Y	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	190					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)	p.D190Y(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						TCGAAGGGATCTCTTACAATA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											50	55	53					2																	101010210		2203	4300	6503	100376642	SO:0001583	missense	9486			BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.568G>T	2.37:g.101010210C>A	ENSP00000264249:p.Asp190Tyr		100376642	Q53T18	Missense_Mutation	SNP	ENST00000264249.3	37	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.869513	0.91587	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701	T;T;T	0.79352	1.25;-1.26;1.25	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.89825	0.6827	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89753	0.3941	10	0.72032	D	0.01	-28.288	20.6208	0.99490	0.0:1.0:0.0:0.0	.	190	O43529	CHSTA_HUMAN	Y	190;238;190	ENSP00000264249:D190Y;ENSP00000438869:D238Y;ENSP00000387309:D190Y	ENSP00000264249:D190Y	D	-	1	0	CHST10	100376642	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	7.625000	0.83145	2.882000	0.98803	0.655000	0.94253	GAT		0.423	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		A	101010210	C	A	101010210	3	1	61	1	0	0	0	0	1	0	0	0	3404	913	32	2	506	2	CHST10	2	101010210	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	387002	101010210	142189163	1557	9542										
MAP4K4	9448	broad.mit.edu	37	chr2	102441865	102441865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactcaaagaagactggatcGcttacatctccagagaaatc	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102441865G>A	ENST00000347699.4	+	5	391	c.391G>A	c.(391-393)Gct>Act	p.A131T	MAP4K4_ENST00000350198.4_Missense_Mutation_p.A131T|MAP4K4_ENST00000413150.2_Missense_Mutation_p.A131T|MAP4K4_ENST00000456652.1_Missense_Mutation_p.A131T|MAP4K4_ENST00000302217.5_Missense_Mutation_p.A131T|MAP4K4_ENST00000350878.4_Missense_Mutation_p.A111T|MAP4K4_ENST00000324219.4_Missense_Mutation_p.A131T|MAP4K4_ENST00000425019.1_Missense_Mutation_p.A131T	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.A131T(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AGACTGGATCGCTTACATCTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											98	98	98					2																	102441865		1939	4146	6085	101808297	SO:0001583	missense	9448			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.391G>A	2.37:g.102441865G>A	ENSP00000314363:p.Ala131Thr		101808297	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.940131	0.92526	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T;T;T	0.65732	1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;-0.17	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80793	0.4691	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.997;1.0;0.997;0.982;0.996;0.995;0.995;0.995;0.992;0.992	T	0.81448	-0.0928	10	0.87932	D	0	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	111;131;111;131;131;131;131;131;131;131	B7Z388;B7Z3V5;E7ESS2;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;.;M4K4_HUMAN;.;.;.;.	T	131;131;131;131;131;131;131;93;111	ENSP00000392830:A131T;ENSP00000313644:A131T;ENSP00000281111:A131T;ENSP00000303600:A131T;ENSP00000389752:A131T;ENSP00000387370:A131T;ENSP00000314363:A131T;ENSP00000409720:A93T;ENSP00000343658:A111T	ENSP00000303600:A131T	A	+	1	0	MAP4K4	101808297	1.000000	0.71417	0.914000	0.36105	0.979000	0.70002	9.813000	0.99286	2.783000	0.95769	0.655000	0.94253	GCT		0.488	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		A	102441865	G	A	102441865	3	1	61	1	0	0	0	0	1	0	0	0	9292	1087	38	1	409	1	MAP4K4	2	102441865	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1431655	102441865	140757508	1558	9543										
MAP4K4	9448	broad.mit.edu	37	chr2	102503559	102503559	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctttgcagtcatttggaGaattggtacataagccatta	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102503559G>T	ENST00000347699.4	+	27	3196	c.3196G>T	c.(3196-3198)Gaa>Taa	p.E1066*	MAP4K4_ENST00000350198.4_Nonsense_Mutation_p.E985*|MAP4K4_ENST00000413150.2_Nonsense_Mutation_p.E981*|MAP4K4_ENST00000456652.1_Nonsense_Mutation_p.E865*|MAP4K4_ENST00000302217.5_Nonsense_Mutation_p.E869*|MAP4K4_ENST00000350878.4_Nonsense_Mutation_p.E1106*|MAP4K4_ENST00000324219.4_Nonsense_Mutation_p.E1147*|MAP4K4_ENST00000425019.1_Nonsense_Mutation_p.E1099*	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	1066	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.E1147*(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GTCATTTGGAGAATTGGTACA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											60	57	58					2																	102503559		1889	4124	6013	101869991	SO:0001587	stop_gained	9448			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.3196G>T	2.37:g.102503559G>T	ENSP00000314363:p.Glu1066*		101869991	O75172|Q9NST7	Nonsense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.487624|7.487624	0.98316|0.98316	.|.	.|.	ENSG00000071054|ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878|ENST00000421882	.|.	.|.	.|.	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	0.123345|.	0.53938|.	D|.	0.000046|.	.|T	.|0.74520	.|0.3727	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74064	.|-0.3785	.|3	0.66056|.	D|.	0.02|.	.|.	18.4585|18.4585	0.90729|0.90729	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1099;1147;985;869;981;865;1066;997;1106|882	.|.	ENSP00000303600:E869X|.	E|R	+|+	1|2	0|0	MAP4K4|MAP4K4	101869991|101869991	1.000000|1.000000	0.71417|0.71417	0.663000|0.663000	0.29738|0.29738	0.991000|0.991000	0.79684|0.79684	9.869000|9.869000	0.99810|0.99810	2.352000|2.352000	0.79861|0.79861	0.557000|0.557000	0.71058|0.71058	GAA|AGA		0.423	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		T	102503559	G	T	102503559	4	4	61	1	0	0	0	0	0	1	0	0	9292	943	33	2	3553	2	MAP4K4	2	102503559	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61694	102503559	140695814	1559	9544										
IL1R2	7850	broad.mit.edu	37	chr2	102632479	102632479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacctgagtgaattcacccGtgacaaaactgacgtgaaga	10	9	1	7	rs143112573		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102632479G>A	ENST00000332549.3	+	4	708	c.479G>A	c.(478-480)cGt>cAt	p.R160H	IL1R2_ENST00000393414.2_Missense_Mutation_p.R160H|IL1R2_ENST00000441002.1_Missense_Mutation_p.R160H	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	160	Ig-like C2-type 2.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R160H(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						GAATTCACCCGTGACAAAACT	0.388																																					Pancreas(106;189 1628 2302 5133 12295)											1	Substitution - Missense(1)	large_intestine(1)	2						G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	66	63	64		479,479	-4.2	0	2	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	IL1R2	NM_004633.3,NM_173343.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	160/399,160/399	102632479	1,13005	2203	4300	6503	101998911	SO:0001583	missense	7850			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.479G>A	2.37:g.102632479G>A	ENSP00000330959:p.Arg160His		101998911	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648989	0.47362	0.0	1.16E-4	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000457817;ENST00000441002	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.53	-4.17	0.03857	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.713730	0.02589	N	0.099709	T	0.61035	0.2315	N	0.17082	0.46	0.09310	N	1	B	0.17038	0.02	B	0.06405	0.002	T	0.50533	-0.8817	10	0.44086	T	0.13	.	6.9654	0.24619	0.5597:0.2593:0.181:0.0	.	160	P27930	IL1R2_HUMAN	H	160	ENSP00000330959:R160H;ENSP00000377066:R160H;ENSP00000408415:R160H;ENSP00000414611:R160H	ENSP00000330959:R160H	R	+	2	0	IL1R2	101998911	0.000000	0.05858	0.000000	0.03702	0.980000	0.70556	-1.514000	0.02254	-0.453000	0.07076	0.655000	0.94253	CGT		0.388	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		A	102632479	G	A	102632479	3	1	61	1	0	0	0	0	1	0	0	0	7680	1145	40	1	489	1	IL1R2	2	102632479	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128920	102632479	140566894	1560	9545										
IL1R2	7850	broad.mit.edu	37	chr2	102638706	102638706	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaagaccatatcagcttCtctgggtaaggcccacaagg	9	13	3	1	rs199970902		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102638706C>A	ENST00000332549.3	+	6	975	c.746C>A	c.(745-747)tCt>tAt	p.S249Y	IL1R2_ENST00000393414.2_Missense_Mutation_p.S249Y|IL1R2_ENST00000441002.1_Missense_Mutation_p.S249Y	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	249	Ig-like C2-type 3.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.S249Y(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						ATATCAGCTTCTCTGGGTAAG	0.502																																					Pancreas(106;189 1628 2302 5133 12295)											1	Substitution - Missense(1)	large_intestine(1)	2											150	146	147					2																	102638706		2203	4300	6503	102005138	SO:0001583	missense	7850			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.746C>A	2.37:g.102638706C>A	ENSP00000330959:p.Ser249Tyr		102005138	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.251353	0.59212	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000441002	T;T;T	0.14391	2.51;2.51;2.51	6.17	5.29	0.74685	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.161907	0.40908	D	0.000985	T	0.32041	0.0816	M	0.62723	1.935	0.19575	N	0.999969	D	0.76494	0.999	D	0.65233	0.933	T	0.11941	-1.0567	10	0.72032	D	0.01	.	12.9168	0.58211	0.1622:0.8378:0.0:0.0	.	249	P27930	IL1R2_HUMAN	Y	249	ENSP00000330959:S249Y;ENSP00000377066:S249Y;ENSP00000414611:S249Y	ENSP00000330959:S249Y	S	+	2	0	IL1R2	102005138	0.991000	0.36638	0.187000	0.23214	0.122000	0.20287	4.026000	0.57232	1.602000	0.50124	0.655000	0.94253	TCT		0.502	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		A	102638706	C	A	102638706	3	1	61	1	0	0	0	0	1	0	0	0	7680	913	32	2	764	2	IL1R2	2	102638706	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6227	102638706	140560667	1561	9546										
IL1R1	3554	broad.mit.edu	37	chr2	102793014	102793014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgagaaaatgccagaatCgattaaattcattaagcaga	7	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102793014C>T	ENST00000410023.1	+	12	1823	c.1505C>T	c.(1504-1506)tCg>tTg	p.S502L	IL1R1_ENST00000233946.3_Missense_Mutation_p.S502L|IL1R1_ENST00000424272.1_3'UTR|IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409929.1_Missense_Mutation_p.S471L|AC007271.3_ENST00000428188.1_RNA			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	502	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.S502L(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATGCCAGAATCGATTAAATTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	68	68					2																	102793014		2203	4300	6503	102159446	SO:0001583	missense	3554			M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1505C>T	2.37:g.102793014C>T	ENSP00000386380:p.Ser502Leu		102159446	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368480	0.82463	.	.	ENSG00000115594	ENST00000409929;ENST00000410023;ENST00000233946	T;T;T	0.09163	3.01;3.01;3.01	5.61	5.61	0.85477	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.053759	0.85682	D	0.000000	T	0.34193	0.0889	M	0.66506	2.035	0.46131	D	0.998888	D;D	0.89917	0.999;1.0	D;D	0.74348	0.983;0.983	T	0.01920	-1.1247	10	0.87932	D	0	.	19.6512	0.95812	0.0:1.0:0.0:0.0	.	471;502	B8ZZW4;P14778	.;IL1R1_HUMAN	L	471;502;502	ENSP00000386776:S471L;ENSP00000386380:S502L;ENSP00000233946:S502L	ENSP00000233946:S502L	S	+	2	0	IL1R1	102159446	1.000000	0.71417	0.996000	0.52242	0.667000	0.39255	5.650000	0.67944	2.646000	0.89796	0.563000	0.77884	TCG		0.433	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			T	102793014	C	T	102793014	3	4	61	1	0	0	0	0	1	0	0	0	7679	893	31	1	1543	1	IL1R1	2	102793014	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154308	102793014	140406359	1562	9547										
IL1RL2	8808	broad.mit.edu	37	chr2	102849559	102849559	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatataagttgtttatattCggcagagatgaattccctgg	11	5	0	2	rs377736284		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102849559C>T	ENST00000264257.2	+	10	1398	c.1272C>T	c.(1270-1272)ttC>ttT	p.F424F	IL1RL2_ENST00000441515.2_Silent_p.F306F|IL1RL2_ENST00000539491.1_Silent_p.F424F|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	424	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)	p.F424F(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TGTTTATATTCGGCAGAGATG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C		0,4406		0,0,2203	94	92	93		1272	1.1	1	2		93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IL1RL2	NM_003854.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		424/576	102849559	1,13005	2203	4300	6503	102215991	SO:0001819	synonymous_variant	8808			U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1272C>T	2.37:g.102849559C>T			102215991	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Silent	SNP	ENST00000264257.2	37	CCDS2056.1																																																																																				0.453	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		T	102849559	C	T	102849559	2	4	61	1	0	0	0	0	0	0	0	1	7685	883	31	1		1	IL1RL2	2	102849559	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56545	102849559	140349814	1563	9548										
IL1RL2	8808	broad.mit.edu	37	chr2	102851532	102851532	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattgagctggagaaaatCgaggactacacagtcatgcc	10	10	2	2	rs200453765		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102851532C>T	ENST00000264257.2	+	11	1599	c.1473C>T	c.(1471-1473)atC>atT	p.I491I	IL1RL2_ENST00000441515.2_Silent_p.I373I|IL1RL2_ENST00000539491.1_Silent_p.I491I|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	491	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)	p.I491I(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TGGAGAAAATCGAGGACTACA	0.498													C|||	1	0.000199681	8e-04	0	5008	,	,		21332	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											163	139	147					2																	102851532		2203	4300	6503	102217964	SO:0001819	synonymous_variant	8808			U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1473C>T	2.37:g.102851532C>T			102217964	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Silent	SNP	ENST00000264257.2	37	CCDS2056.1																																																																																				0.498	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		T	102851532	C	T	102851532	2	4	61	1	0	0	0	0	0	0	0	1	7685	874	31	1		1	IL1RL2	2	102851532	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1973	102851532	140347841	1564	9549										
IL1RL1	9173	broad.mit.edu	37	chr2	102956625	102956625	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaatcagattgcaatgttCcagattatttgatgtattca	6	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:102956625C>A	ENST00000233954.1	+	4	611	c.340C>A	c.(340-342)Cca>Aca	p.P114T	IL1RL1_ENST00000409584.1_Missense_Mutation_p.P114T|IL1RL1_ENST00000311734.2_Missense_Mutation_p.P114T|IL1RL1_ENST00000473175.1_3'UTR|IL1RL1_ENST00000404917.2_5'UTR|IL1RL1_ENST00000393393.3_Missense_Mutation_p.P114T	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	114	Ig-like C2-type 2.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)	p.P114T(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						TTGCAATGTTCCAGATTATTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	73	73					2																	102956625		2203	4298	6501	102323057	SO:0001583	missense	9173			D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5998	protein-coding gene	gene with protein product	"homolog of mouse growth stimulation-expressed"	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.340C>A	2.37:g.102956625C>A	ENSP00000233954:p.Pro114Thr		102323057	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725959	0.69074	.	.	ENSG00000115602	ENST00000233954;ENST00000393393;ENST00000311734;ENST00000409584	T;T;T;T	0.78003	-0.16;2.09;-1.14;2.18	5.22	4.34	0.51931	Immunoglobulin-like (1);	1.958180	0.02740	N	0.116228	D	0.88980	0.6585	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.974	T	0.73297	-0.4027	10	0.31617	T	0.26	.	9.8715	0.41177	0.0:0.9056:0.0:0.0944	.	114;114	Q01638-2;Q01638	.;ILRL1_HUMAN	T	114	ENSP00000233954:P114T;ENSP00000377052:P114T;ENSP00000310371:P114T;ENSP00000386618:P114T	ENSP00000233954:P114T	P	+	1	0	IL1RL1	102323057	0.799000	0.28903	0.617000	0.29091	0.318000	0.28184	2.069000	0.41481	1.187000	0.43000	0.563000	0.77884	CCA		0.343	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232		A	102956625	C	A	102956625	3	1	61	1	0	0	0	0	1	0	0	0	7684	855	30	2	350	2	IL1RL1	2	102956625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105093	102956625	140242748	1565	9550										
IL18R1	8809	broad.mit.edu	37	chr2	103003385	103003385	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatattggtgaaagcaatCtaaatgttttatataattgc	6	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:103003385C>A	ENST00000409599.1	+	9	1230	c.874C>A	c.(874-876)Cta>Ata	p.L292I	IL18R1_ENST00000233957.1_Missense_Mutation_p.L292I			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	292	Ig-like C2-type 3.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.L292I(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TGAAAGCAATCTAAATGTTTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											88	92	91					2																	103003385		2203	4300	6503	102369817	SO:0001583	missense	8809			U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.874C>A	2.37:g.103003385C>A	ENSP00000387211:p.Leu292Ile		102369817	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.823506	0.32237	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957	T;T;T	0.03301	3.98;3.98;3.98	4.54	1.67	0.24075	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.141766	0.32106	N	0.006574	T	0.09686	0.0238	M	0.78637	2.42	0.37377	D	0.911868	D;D	0.57899	0.981;0.981	P;P	0.56514	0.8;0.8	T	0.08576	-1.0715	10	0.54805	T	0.06	.	3.362	0.07190	0.2057:0.5807:0.0:0.2136	.	292;292	B7ZKV7;Q13478	.;IL18R_HUMAN	I	292	ENSP00000386663:L292I;ENSP00000387211:L292I;ENSP00000233957:L292I	ENSP00000233957:L292I	L	+	1	2	IL18R1	102369817	0.960000	0.32886	0.359000	0.25824	0.023000	0.10783	0.720000	0.25896	0.622000	0.30249	0.462000	0.41574	CTA		0.388	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		A	103003385	C	A	103003385	3	1	61	1	0	0	0	0	1	0	0	0	7668	912	32	2	900	2	IL18R1	2	103003385	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46760	103003385	140195988	1566	9551										
IL18RAP	8807	broad.mit.edu	37	chr2	103068314	103068314	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtcaatggacccagtatCtttgaactacaagcagcagt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:103068314C>A	ENST00000264260.2	+	12	2062	c.1473C>A	c.(1471-1473)atC>atA	p.I491I	IL18RAP_ENST00000409369.1_Silent_p.I349I	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	491	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.I491I(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						GACCCAGTATCTTTGAACTAC	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											131	134	133					2																	103068314		2203	4300	6503	102434746	SO:0001819	synonymous_variant	8807			AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1473C>A	2.37:g.103068314C>A			102434746	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Silent	SNP	ENST00000264260.2	37	CCDS2061.1																																																																																				0.383	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		A	103068314	C	A	103068314	2	1	61	1	0	0	0	0	0	0	0	1	7669	903	32	2		2	IL18RAP	2	103068314	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64929	103068314	140131059	1567	9552										
MFSD9	84804	broad.mit.edu	37	chr2	103335029	103335029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccccgagaggagaggggcGatgatgcggcccactgcagt	16	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:103335029G>A	ENST00000258436.5	-	6	1318	c.1275C>T	c.(1273-1275)atC>atT	p.I425I	MFSD9_ENST00000496253.1_5'Flank	NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	425					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.I425I(1)		breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						GGAGAGGGGCGATGATGCGGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	2											24	28	27					2																	103335029		2203	4299	6502	102701461	SO:0001819	synonymous_variant	84804				CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.1275C>T	2.37:g.103335029G>A			102701461	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																				0.647	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		A	103335029	G	A	103335029	2	1	61	1	0	0	0	0	0	0	0	1	9569	1048	37	1		1	MFSD9	2	103335029	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	266715	103335029	139864344	1568	9553										
GPR45	11250	broad.mit.edu	37	chr2	105858422	105858422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgcacccctcaggatctCcttggccatagtgatgctgc	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:105858422C>T	ENST00000258456.1	+	1	223	c.107C>T	c.(106-108)tCc>tTc	p.S36F		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S36F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						CTCAGGATCTCCTTGGCCATA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	116	119					2																	105858422		2203	4300	6503	105224854	SO:0001583	missense	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.107C>T	2.37:g.105858422C>T	ENSP00000258456:p.Ser36Phe		105224854	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	C	2.387	-0.340674	0.05243	.	.	ENSG00000135973	ENST00000258456	T	0.35048	1.33	5.6	2.36	0.29203	.	0.429953	0.24231	N	0.040351	T	0.17066	0.0410	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22347	-1.0219	10	0.09843	T	0.71	-25.9393	4.8489	0.13528	0.0:0.5134:0.1887:0.2979	.	36	Q9Y5Y3	GPR45_HUMAN	F	36	ENSP00000258456:S36F	ENSP00000258456:S36F	S	+	2	0	GPR45	105224854	0.000000	0.05858	0.068000	0.19968	0.025000	0.11179	0.064000	0.14437	0.705000	0.31890	-0.379000	0.06801	TCC		0.602	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		T	105858422	C	T	105858422	3	4	61	1	0	0	0	0	1	0	0	0	6716	855	30	3	109	3	GPR45	2	105858422	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2523393	105858422	137340951	1569	9554										
GPR45	11250	broad.mit.edu	37	chr2	105858752	105858752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggacaagctgaacccgcGcagggccaaggtgatcatcg	13	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:105858752G>A	ENST00000258456.1	+	1	553	c.437G>A	c.(436-438)cGc>cAc	p.R146H		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R146H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						CTGAACCCGCGCAGGGCCAAG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	2											43	41	42					2																	105858752		2203	4300	6503	105225184	SO:0001583	missense	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.437G>A	2.37:g.105858752G>A	ENSP00000258456:p.Arg146His		105225184	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	G	8.606	0.887929	0.17540	.	.	ENSG00000135973	ENST00000258456	T	0.42513	0.97	5.04	4.16	0.48862	GPCR, rhodopsin-like superfamily (1);	0.140424	0.46145	D	0.000301	T	0.27241	0.0668	L	0.39085	1.19	0.25947	N	0.982799	B	0.02656	0.0	B	0.06405	0.002	T	0.19224	-1.0312	10	0.12766	T	0.61	-18.5465	6.6289	0.22845	0.3166:0.0:0.6834:0.0	.	146	Q9Y5Y3	GPR45_HUMAN	H	146	ENSP00000258456:R146H	ENSP00000258456:R146H	R	+	2	0	GPR45	105225184	0.453000	0.25721	0.104000	0.21259	0.990000	0.78478	3.870000	0.56070	1.125000	0.41998	0.462000	0.41574	CGC		0.657	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		A	105858752	G	A	105858752	3	1	61	1	0	0	0	0	1	0	0	0	6716	1087	38	1	439	1	GPR45	2	105858752	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	330	105858752	137340621	1570	9555										
FHL2	2274	broad.mit.edu	37	chr2	105977855	105977855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtcgttatgccactgcCgttcctcaaaggagatgtat	10	10	1	1	rs188279857	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:105977855C>T	ENST00000409807.1	-	6	1059	c.725G>A	c.(724-726)cGg>cAg	p.R242Q	AC012360.6_ENST00000457290.2_RNA|FHL2_ENST00000358129.4_Missense_Mutation_p.R242Q|FHL2_ENST00000344213.4_Missense_Mutation_p.R352Q|FHL2_ENST00000336660.5_3'UTR|FHL2_ENST00000408995.1_Missense_Mutation_p.R242Q|FHL2_ENST00000322142.8_Missense_Mutation_p.R242Q|FHL2_ENST00000393353.3_Missense_Mutation_p.R242Q|FHL2_ENST00000393352.3_Missense_Mutation_p.R242Q|FHL2_ENST00000409177.1_Missense_Mutation_p.R358Q			Q14192	FHL2_HUMAN	four and a half LIM domains 2	242	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R242Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						ATGCCACTGCCGTTCCTCAAA	0.493													C|||	2	0.000399361	0	0	5008	,	,		20494	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											118	99	106					2																	105977855		2203	4300	6503	105344287	SO:0001583	missense	2274				CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.725G>A	2.37:g.105977855C>T	ENSP00000386665:p.Arg242Gln		105344287	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Missense_Mutation	SNP	ENST00000409807.1	37	CCDS2070.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	23.1	4.379171	0.82682	.	.	ENSG00000115641	ENST00000409177;ENST00000344213;ENST00000393353;ENST00000393352;ENST00000322142;ENST00000358129;ENST00000409807;ENST00000408995	D;D;D;D;D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25	5.48	4.6	0.57074	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.90212	0.6940	L	0.59436	1.845	0.80722	D	1	D;P;D;D	0.61080	0.989;0.94;0.98;0.989	P;P;P;P	0.60415	0.805;0.529;0.874;0.805	D	0.88879	0.3338	10	0.32370	T	0.25	.	14.5791	0.68274	0.0:0.9294:0.0:0.0706	.	242;242;352;242	Q6I9R8;Q2I5I4;Q2XQU9;Q14192	.;.;.;FHL2_HUMAN	Q	242;352;242;242;242;242;242;242	ENSP00000386892:R242Q;ENSP00000344266:R352Q;ENSP00000377021:R242Q;ENSP00000377020:R242Q;ENSP00000322909:R242Q;ENSP00000350846:R242Q;ENSP00000386665:R242Q;ENSP00000386633:R242Q	ENSP00000322909:R242Q	R	-	2	0	FHL2	105344287	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	7.729000	0.84864	1.439000	0.47511	0.650000	0.86243	CGG		0.493	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1			T	105977855	C	T	105977855	3	4	61	1	0	0	0	0	1	0	0	0	5898	652	23	1	118	1	FHL2	2	105977855	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119103	105977855	137221518	1571	9556										
UXS1	80146	broad.mit.edu	37	chr2	106761723	106761723	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatccagtgctccacgtttCtcttcctgcccgtgaagaaa	8	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:106761723C>A	ENST00000409501.3	-	6	437	c.380G>T	c.(379-381)aGa>aTa	p.R127I	UXS1_ENST00000428048.2_Intron|UXS1_ENST00000479621.1_5'UTR|UXS1_ENST00000283148.7_Missense_Mutation_p.R132I|UXS1_ENST00000540130.1_Missense_Mutation_p.R70I			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	127					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)	p.R132I(1)|p.R127I(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						CTCCACGTTTCTCTTCCTGCC	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	2											104	104	104					2																	106761723		2028	4172	6200	106128155	SO:0001583	missense	80146			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	17729	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 6E, member 12"	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.380G>T	2.37:g.106761723C>A	ENSP00000387019:p.Arg127Ile		106128155	Q8NBX3|Q9H5C2	Missense_Mutation	SNP	ENST00000409501.3	37	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785905	0.90282	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000457835	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.84	5.84	0.93424	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90024	0.6885	L	0.35542	1.07	0.80722	D	1	P;P	0.44478	0.836;0.739	B;B	0.37888	0.169;0.26	D	0.90878	0.4751	10	0.66056	D	0.02	-9.9009	20.1381	0.98040	0.0:1.0:0.0:0.0	.	132;127	Q8NBZ7-2;Q8NBZ7	.;UXS1_HUMAN	I	132;70;127;70	ENSP00000283148:R132I;ENSP00000438265:R70I;ENSP00000387019:R127I;ENSP00000399316:R70I	ENSP00000283148:R132I	R	-	2	0	UXS1	106128155	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	7.456000	0.80751	2.763000	0.94921	0.650000	0.86243	AGA		0.537	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3		A	106761723	C	A	106761723	3	1	61	1	0	0	0	0	1	0	0	0	17149	913	32	2	922	2	UXS1	2	106761723	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	783868	106761723	136437650	1572	9557										
SLC5A7	60482	broad.mit.edu	37	chr2	108609438	108609438	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttttaggtggcctgttCtttgcaaaacctatgcgttc	8	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:108609438C>A	ENST00000264047.2	+	4	579	c.303C>A	c.(301-303)ttC>ttA	p.F101L	SLC5A7_ENST00000540517.1_5'UTR|SLC5A7_ENST00000409059.1_Missense_Mutation_p.F101L	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	101					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)	p.F101L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GTGGCCTGTTCTTTGCAAAAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											130	134	133					2																	108609438		2203	4300	6503	107975870	SO:0001583	missense	60482			AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.303C>A	2.37:g.108609438C>A	ENSP00000264047:p.Phe101Leu		107975870	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	37	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.680537	0.47886	.	.	ENSG00000115665	ENST00000409059;ENST00000264047	D;D	0.84660	-1.88;-1.88	6.16	0.674	0.17946	.	0.044401	0.85682	D	0.000000	T	0.75406	0.3845	L	0.32530	0.975	0.80722	D	1	B	0.27316	0.175	B	0.33339	0.162	T	0.61787	-0.6991	10	0.25106	T	0.35	-20.7315	8.3349	0.32208	0.0:0.3047:0.0:0.6953	.	101	Q9GZV3	SC5A7_HUMAN	L	101	ENSP00000387346:F101L;ENSP00000264047:F101L	ENSP00000264047:F101L	F	+	3	2	SLC5A7	107975870	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.856000	0.27818	0.171000	0.19730	0.650000	0.86243	TTC		0.378	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108609438	C	A	108609438	3	1	61	1	0	0	0	0	1	0	0	0	14707	912	32	2	313	2	SLC5A7	2	108609438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1847715	108609438	134589935	1573	9558										
GCC2	9648	broad.mit.edu	37	chr2	109086652	109086652	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgtgaggcaagtgaaaaGaacatccagaagaaatatga	10	5	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109086652G>T	ENST00000309863.6	+	6	1581	c.867G>T	c.(865-867)aaG>aaT	p.K289N	GCC2_ENST00000485546.1_3'UTR	NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	289					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)	p.K289N(1)		breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						CAAGTGAAAAGAACATCCAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	125	122					2																	109086652		2203	4299	6502	108453084	SO:0001583	missense	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.867G>T	2.37:g.109086652G>T	ENSP00000307939:p.Lys289Asn		108453084	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	2.929	-0.221522	0.06061	.	.	ENSG00000135968	ENST00000435553;ENST00000309863;ENST00000409896;ENST00000393318	T	0.33865	1.39	5.21	3.32	0.38043	.	0.376436	0.26620	N	0.023380	T	0.20251	0.0487	L	0.27053	0.805	0.09310	N	0.999991	B	0.06786	0.001	B	0.04013	0.001	T	0.10660	-1.0620	10	0.23302	T	0.38	.	4.6153	0.12422	0.14:0.0:0.4992:0.3608	.	289	Q8IWJ2	GCC2_HUMAN	N	289;289;252;34	ENSP00000307939:K289N	ENSP00000307939:K289N	K	+	3	2	GCC2	108453084	0.894000	0.30519	0.123000	0.21794	0.506000	0.33950	1.201000	0.32259	1.275000	0.44379	0.467000	0.42956	AAG		0.353	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109086652	G	T	109086652	3	4	61	1	0	0	0	0	1	0	0	0	6306	933	33	2	889	2	GCC2	2	109086652	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	477214	109086652	134112721	1574	9559										
GCC2	9648	broad.mit.edu	37	chr2	109088435	109088435	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttttaattcaagttgaaGaagtatctcaaacatgtagc	6	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109088435G>T	ENST00000309863.6	+	6	3364	c.2650G>T	c.(2650-2652)Gaa>Taa	p.E884*		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	884					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)	p.E884*(1)		breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						TCAAGTTGAAGAAGTATCTCA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											31	34	33					2																	109088435		2199	4292	6491	108454867	SO:0001587	stop_gained	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2650G>T	2.37:g.109088435G>T	ENSP00000307939:p.Glu884*		108454867	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Nonsense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	39	7.797904	0.98495	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	.	.	.	5.45	5.45	0.79879	.	0.137625	0.49305	D	0.000148	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	12.9469	0.58376	0.0744:0.0:0.9256:0.0	.	.	.	.	X	884;847;628	.	ENSP00000307939:E884X	E	+	1	0	GCC2	108454867	1.000000	0.71417	0.993000	0.49108	0.755000	0.42902	4.754000	0.62191	2.728000	0.93425	0.650000	0.86243	GAA		0.313	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109088435	G	T	109088435	4	4	61	1	0	0	0	0	0	1	0	0	6306	943	33	2	2672	2	GCC2	2	109088435	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1783	109088435	134110938	1575	9560										
GCC2	9648	broad.mit.edu	37	chr2	109116158	109116158	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttcctgttataaatacGatgttgcagctcagccctga	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109116158G>A	ENST00000309863.6	+	22	5646	c.4932G>A	c.(4930-4932)acG>acA	p.T1644T		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1644	GRIP. {ECO:0000255|PROSITE- ProRule:PRU00250}.|Mediates interaction with RAB9A.				Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)	p.T1644T(1)		breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						TTATAAATACGATGTTGCAGC	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											79	81	80					2																	109116158		2200	4278	6478	108482590	SO:0001819	synonymous_variant	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4932G>A	2.37:g.109116158G>A			108482590	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																				0.423	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		A	109116158	G	A	109116158	2	1	61	1	0	0	0	0	0	0	0	1	6306	1045	37	1		1	GCC2	2	109116158	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27723	109116158	134083215	1576	9561										
RANBP2	5903	broad.mit.edu	37	chr2	109369470	109369470	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagggcagcggtcttaattCtttttatgatcaacgagaat	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109369470C>A	ENST00000283195.6	+	13	1898	c.1772C>A	c.(1771-1773)tCt>tAt	p.S591Y		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	591					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S591Y(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GGTCTTAATTCTTTTTATGAT	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	2											20	20	20					2																	109369470		1869	4053	5922	108735902	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1772C>A	2.37:g.109369470C>A	ENSP00000283195:p.Ser591Tyr		108735902	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.918403	0.73098	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.32272	1.46	4.33	4.33	0.51752	.	.	.	.	.	T	0.54919	0.1888	M	0.67953	2.075	0.45097	D	0.998113	D	0.89917	1.0	D	0.85130	0.997	T	0.60667	-0.7218	9	0.87932	D	0	-17.4731	17.3743	0.87387	0.0:1.0:0.0:0.0	.	591	P49792	RBP2_HUMAN	Y	591	ENSP00000283195:S591Y	ENSP00000283195:S591Y	S	+	2	0	RANBP2	108735902	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.367000	0.66127	2.388000	0.81334	0.650000	0.86243	TCT		0.328	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		A	109369470	C	A	109369470	3	1	61	1	0	0	0	0	1	0	0	0	13065	913	32	2	1822	2	RANBP2	2	109369470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253312	109369470	133829903	1577	9562										
RANBP2	5903	broad.mit.edu	37	chr2	109379749	109379749	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcatatttatgcctatccGcaacagatgcacacaccgcc	6	15	0	1	rs542711340	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109379749G>A	ENST00000283195.6	+	20	2880	c.2754G>A	c.(2752-2754)ccG>ccA	p.P918P		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	918					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.P918P(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATGCCTATCCGCAACAGATGC	0.453													g|||	3	0.000599042	0	0	5008	,	,		19150	0		0	False		,,,				2504	0.0031															2	Substitution - coding silent(2)	large_intestine(2)	2											98	91	93					2																	109379749		2203	4300	6503	108746181	SO:0001819	synonymous_variant	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2754G>A	2.37:g.109379749G>A			108746181	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																				0.453	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		A	109379749	G	A	109379749	2	1	61	1	0	0	0	0	0	0	0	1	13065	1074	38	1		1	RANBP2	2	109379749	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10279	109379749	133819624	1578	9563										
RANBP2	5903	broad.mit.edu	37	chr2	109380686	109380686	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaaacatctggtaaaattCgccttctaatgagacgagag	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109380686C>T	ENST00000283195.6	+	20	3817	c.3691C>T	c.(3691-3693)Cgc>Tgc	p.R1231C		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1231	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R1231C(4)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGGTAAAATTCGCCTTCTAAT	0.383																																																4	Substitution - Missense(4)	large_intestine(4)	2											72	73	72					2																	109380686		2203	4300	6503	108747118	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3691C>T	2.37:g.109380686C>T	ENSP00000283195:p.Arg1231Cys		108747118	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132503	0.77662	.	.	ENSG00000153201	ENST00000283195	T	0.66638	-0.22	5.45	5.45	0.79879	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	D	0.89015	0.6595	H	0.97440	4.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92728	0.6197	9	0.87932	D	0	-10.0827	19.3035	0.94153	0.0:1.0:0.0:0.0	.	1231	P49792	RBP2_HUMAN	C	1231	ENSP00000283195:R1231C	ENSP00000283195:R1231C	R	+	1	0	RANBP2	108747118	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.814000	0.86154	2.535000	0.85469	0.650000	0.86243	CGC		0.383	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109380686	C	T	109380686	3	4	61	1	0	0	0	0	1	0	0	0	13065	884	31	1	3769	1	RANBP2	2	109380686	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	937	109380686	133818687	1579	9564										
RANBP2	5903	broad.mit.edu	37	chr2	109380930	109380930	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagccccaggaacaaatgTagccatggcgtcaaatcagg	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109380930T>C	ENST00000283195.6	+	20	4061	c.3935T>C	c.(3934-3936)gTa>gCa	p.V1312A		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1312					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.V1312A(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GGAACAAATGTAGCCATGGCG	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	2											64	66	65					2																	109380930		2202	4299	6501	108747362	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3935T>C	2.37:g.109380930T>C	ENSP00000283195:p.Val1312Ala		108747362	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	2.752	-0.259913	0.05791	.	.	ENSG00000153201	ENST00000283195	T	0.26810	1.71	5.37	-1.13	0.09775	.	.	.	.	.	T	0.11750	0.0286	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	9	0.27785	T	0.31	0.9687	5.9581	0.19286	0.0:0.363:0.1781:0.4589	.	1312	P49792	RBP2_HUMAN	A	1312	ENSP00000283195:V1312A	ENSP00000283195:V1312A	V	+	2	0	RANBP2	108747362	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	-0.879000	0.04188	-0.192000	0.10432	0.528000	0.53228	GTA		0.393	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109380930	T	C	109380930	3	2	61	1	0	0	0	0	1	0	0	0	13065	1638	57	4	4013	4	RANBP2	2	109380930	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	244	109380930	133818443	1580	9565										
RANBP2	5903	broad.mit.edu	37	chr2	109382902	109382902	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaagaccccaatttcaaGggattttcaggtgctggaga	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109382902G>T	ENST00000283195.6	+	20	6033	c.5907G>T	c.(5905-5907)aaG>aaT	p.K1969N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1969					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K1969N(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CCAATTTCAAGGGATTTTCAG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	2											63	76	72					2																	109382902		1991	3965	5956	108749334	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.5907G>T	2.37:g.109382902G>T	ENSP00000283195:p.Lys1969Asn		108749334	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068498	0.36470	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.29397	1.57	5.75	1.45	0.22620	.	.	.	.	.	T	0.41213	0.1149	M	0.66939	2.045	0.27496	N	0.952146	D	0.63880	0.993	P	0.53954	0.738	T	0.24190	-1.0167	9	0.54805	T	0.06	-24.7365	8.0476	0.30559	0.5186:0.0:0.4814:0.0	.	1969	P49792	RBP2_HUMAN	N	993;1969	ENSP00000283195:K1969N	ENSP00000283195:K1969N	K	+	3	2	RANBP2	108749334	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	1.369000	0.34227	0.367000	0.24454	0.557000	0.71058	AAG		0.378	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109382902	G	T	109382902	3	4	61	1	0	0	0	0	1	0	0	0	13065	991	35	2	5985	2	RANBP2	2	109382902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1972	109382902	133816471	1581	9566										
RANBP2	5903	broad.mit.edu	37	chr2	109382974	109382974	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaataaagcaaacacttcCggtgactttgagaaagatga	9	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109382974C>T	ENST00000283195.6	+	20	6105	c.5979C>T	c.(5977-5979)tcC>tcT	p.S1993S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1993					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S1993S(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CAAACACTTCCGGTGACTTTG	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	2																																								108749406	SO:0001819	synonymous_variant	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.5979C>T	2.37:g.109382974C>T			108749406	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																				0.388	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109382974	C	T	109382974	2	4	61	1	0	0	0	0	0	0	0	1	13065	639	23	1		1	RANBP2	2	109382974	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72	109382974	133816399	1582	9567										
RANBP2	5903	broad.mit.edu	37	chr2	109384127	109384127	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgagaagggaccaagtaTtaaaactttgtgccaatcac	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109384127T>G	ENST00000283195.6	+	20	7258	c.7132T>G	c.(7132-7134)Tta>Gta	p.L2378V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2378	RanBD1 3. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.L2378V(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GGACCAAGTATTAAAACTTTG	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	2											72	83	79					2																	109384127		2114	4079	6193	108750559	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7132T>G	2.37:g.109384127T>G	ENSP00000283195:p.Leu2378Val		108750559	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637627	0.47049	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.53206	0.63	5.47	3.1	0.35709	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.69548	0.3123	M	0.92077	3.27	0.28840	N	0.896647	D	0.60575	0.988	D	0.64776	0.929	T	0.62807	-0.6776	9	0.48119	T	0.1	-19.5036	6.7994	0.23742	0.0:0.2758:0.0:0.7242	.	2378	P49792	RBP2_HUMAN	V	1402;2378	ENSP00000283195:L2378V	ENSP00000283195:L2378V	L	+	1	2	RANBP2	108750559	0.994000	0.37717	0.926000	0.36857	0.928000	0.56348	2.662000	0.46766	1.026000	0.39733	0.254000	0.18369	TTA		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109384127	T	G	109384127	3	3	61	1	0	0	0	0	1	0	0	0	13065	1490	52	4	7210	4	RANBP2	2	109384127	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1153	109384127	133815246	1583	9568										
RANBP2	5903	broad.mit.edu	37	chr2	109384299	109384299	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagactcgtttaagaaaaTttttgatgaagcaaaaacag	8	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109384299T>G	ENST00000283195.6	+	20	7430	c.7304T>G	c.(7303-7305)aTt>aGt	p.I2435S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2435	RanBD1 3. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.I2435S(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TTTAAGAAAATTTTTGATGAA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	2											49	56	54					2																	109384299		1380	2844	4224	108750731	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7304T>G	2.37:g.109384299T>G	ENSP00000283195:p.Ile2435Ser		108750731	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.303015	0.23736	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.42513	0.97	5.47	5.47	0.80525	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.41926	0.1180	L	0.37850	1.14	0.27381	N	0.955413	P	0.43169	0.8	P	0.53266	0.722	T	0.23261	-1.0193	9	0.11794	T	0.64	-17.7937	7.7825	0.29072	0.0:0.0722:0.1389:0.7889	.	2435	P49792	RBP2_HUMAN	S	1459;2435	ENSP00000283195:I2435S	ENSP00000283195:I2435S	I	+	2	0	RANBP2	108750731	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.014000	0.57145	2.209000	0.71365	0.254000	0.18369	ATT		0.398	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109384299	T	G	109384299	3	3	61	1	0	0	0	0	1	0	0	0	13065	1493	52	4	7382	4	RANBP2	2	109384299	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	172	109384299	133815074	1584	9569										
CCDC138	165055	broad.mit.edu	37	chr2	109404505	109404505	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtatgatttttcaaatttTtatcagtctaagtataagag	6	3	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:109404505T>G	ENST00000295124.4	+	2	171	c.111T>G	c.(109-111)ttT>ttG	p.F37L	CCDC138_ENST00000412964.2_Missense_Mutation_p.F37L|CCDC138_ENST00000470608.1_3'UTR	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	37								p.F37L(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TTTCAAATTTTTATCAGTCTA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											22	25	24					2																	109404505		2159	4290	6449	108770937	SO:0001583	missense	165055			AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.111T>G	2.37:g.109404505T>G	ENSP00000295124:p.Phe37Leu		108770937	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-2.013712	0.00422	.	.	ENSG00000163006	ENST00000412964;ENST00000295124	D;D	0.90385	-2.66;-2.66	3.88	3.88	0.44766	.	0.735663	0.12345	N	0.477123	D	0.83138	0.5189	L	0.44542	1.39	0.20196	N	0.99993	B;B	0.28291	0.206;0.026	B;B	0.24394	0.053;0.015	T	0.68595	-0.5367	10	0.09590	T	0.72	-0.0232	6.7753	0.23617	0.2084:0.0:0.0:0.7916	.	37;37	Q96M89-2;Q96M89	.;CC138_HUMAN	L	37	ENSP00000411800:F37L;ENSP00000295124:F37L	ENSP00000295124:F37L	F	+	3	2	CCDC138	108770937	0.998000	0.40836	0.770000	0.31555	0.007000	0.05969	2.806000	0.47947	1.975000	0.57531	0.533000	0.62120	TTT		0.294	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		G	109404505	T	G	109404505	3	3	61	1	0	0	0	0	1	0	0	0	2778	1838	64	4	117	4	CCDC138	2	109404505	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20206	109404505	133794868	1585	9570										
SEPT10	151011	broad.mit.edu	37	chr2	110303730	110303730	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagagaaagcaattatttCttcttccaaaagtcttctct	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:110303730C>A	ENST00000397712.2	-	10	1624	c.1246G>T	c.(1246-1248)Gaa>Taa	p.E416*	SEPT10_ENST00000545389.1_Nonsense_Mutation_p.E249*|SEPT10_ENST00000397714.2_Nonsense_Mutation_p.E393*|SEPT10_ENST00000468616.1_5'UTR|SEPT10_ENST00000437928.1_Nonsense_Mutation_p.E401*|SEPT10_ENST00000334001.6_Nonsense_Mutation_p.E283*|SEPT10_ENST00000415095.1_Nonsense_Mutation_p.E416*|SEPT10_ENST00000356688.4_Nonsense_Mutation_p.E416*	NM_144710.3	NP_653311.1	Q9P0V9	SEP10_HUMAN	septin 10	416					cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.E393*(2)		breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						GCAATTATTTCTTCTTCCAAA	0.423											OREG0014878	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Nonsense(2)	large_intestine(2)	2											104	104	104					2																	110303730		1855	4080	5935	109661019	SO:0001587	stop_gained	151011			AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522		"Septins"	14349	protein-coding gene	gene with protein product	"sept1-like"	611737				12711328	Standard	NM_144710		Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000397712.2:c.1246G>T	2.37:g.110303730C>A	ENSP00000380824:p.Glu416*	1426	109661019	B3KRQ9|Q86VP5|Q9HAH6	Nonsense_Mutation	SNP	ENST00000397712.2	37	CCDS46383.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.651836	0.67472	.	.	ENSG00000186522	ENST00000356688;ENST00000397712;ENST00000397714;ENST00000334001;ENST00000437928;ENST00000545389;ENST00000415095	.	.	.	5.87	5.87	0.94306	.	0.161766	0.42548	D	0.000689	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.0453	0.93018	0.0:1.0:0.0:0.0	.	.	.	.	X	416;416;393;283;401;249;416	.	ENSP00000334234:E283X	E	-	1	0	SEPT10	109661019	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	6.953000	0.75995	2.797000	0.96272	0.650000	0.86243	GAA		0.423	SEPT10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337804.1	NM_144710		A	110303730	C	A	110303730	4	1	61	1	0	0	0	0	0	1	0	0	14097	922	32	2	126	2	SEPT10	2	110303730	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	899225	110303730	132895643	1586	9571										
SEPT10	151011	broad.mit.edu	37	chr2	110325453	110325453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggaactggtatatctggAcgccattgctgaccaattca	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:110325453A>G	ENST00000397712.2	-	6	1079	c.701T>C	c.(700-702)gTc>gCc	p.V234A	SEPT10_ENST00000545389.1_Missense_Mutation_p.V67A|SEPT10_ENST00000397714.2_Missense_Mutation_p.V211A|SEPT10_ENST00000468616.1_5'Flank|SEPT10_ENST00000437928.1_Missense_Mutation_p.V219A|SEPT10_ENST00000334001.6_Missense_Mutation_p.V101A|SEPT10_ENST00000415095.1_Missense_Mutation_p.V234A|SEPT10_ENST00000356688.4_Missense_Mutation_p.V234A	NM_144710.3	NP_653311.1	Q9P0V9	SEP10_HUMAN	septin 10	234	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.V211A(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						GTATATCTGGACGCCATTGCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	116	119					2																	110325453		1979	4182	6161	109682742	SO:0001583	missense	151011			AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522		"Septins"	14349	protein-coding gene	gene with protein product	"sept1-like"	611737				12711328	Standard	NM_144710		Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000397712.2:c.701T>C	2.37:g.110325453A>G	ENSP00000380824:p.Val234Ala		109682742	B3KRQ9|Q86VP5|Q9HAH6	Missense_Mutation	SNP	ENST00000397712.2	37	CCDS46383.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680226	0.88542	.	.	ENSG00000186522	ENST00000352314;ENST00000356688;ENST00000397712;ENST00000397714;ENST00000334001;ENST00000437928;ENST00000545389;ENST00000415095;ENST00000493445;ENST00000423520	T;T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57	5.77	4.62	0.57501	.	0.179884	0.37483	N	0.002061	T	0.76716	0.4026	H	0.94964	3.605	0.52099	D	0.999949	P;D;P;P;P;D	0.60160	0.609;0.958;0.956;0.929;0.554;0.987	P;P;P;P;B;P	0.61874	0.524;0.747;0.79;0.791;0.389;0.895	T	0.82325	-0.0513	10	0.87932	D	0	.	11.8468	0.52389	0.9316:0.0:0.0684:0.0	.	101;67;234;234;211;234	B7Z371;B7Z277;A8K7M3;B5ME97;Q9P0V9-3;Q9P0V9	.;.;.;.;.;SEP10_HUMAN	A	192;234;234;211;101;219;67;234;41;67	ENSP00000349116:V234A;ENSP00000380824:V234A;ENSP00000380826:V211A;ENSP00000334234:V101A;ENSP00000407790:V219A;ENSP00000439364:V67A;ENSP00000396728:V234A;ENSP00000445707:V41A;ENSP00000416597:V67A	ENSP00000334234:V101A	V	-	2	0	SEPT10	109682742	1.000000	0.71417	0.959000	0.39883	0.936000	0.57629	8.780000	0.91799	1.111000	0.41721	0.533000	0.62120	GTC		0.398	SEPT10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337804.1	NM_144710		G	110325453	A	G	110325453	3	3	61	1	0	0	0	0	1	0	0	0	14097	275	10	4	687	4	SEPT10	2	110325453	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	21723	110325453	132873920	1587	9572										
NPHP1	4867	broad.mit.edu	37	chr2	110926031	110926031	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcataaaccaagactaacctCtaggtaggttctgggaacaa	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:110926031C>A	ENST00000393272.3	-	6	719	c.622G>T	c.(622-624)Gag>Tag	p.E208*	NPHP1_ENST00000316534.4_Nonsense_Mutation_p.E208*|NPHP1_ENST00000355301.4_Nonsense_Mutation_p.E146*|NPHP1_ENST00000445609.2_Nonsense_Mutation_p.E208*|NPHP1_ENST00000417665.1_Nonsense_Mutation_p.E208*	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	208	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.E208*(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						AGACTAACCTCTAGGTAGGTT	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											132	133	132					2																	110926031		2203	4300	6503	110283320	SO:0001587	stop_gained	4867			AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.622G>T	2.37:g.110926031C>A	ENSP00000376953:p.Glu208*		110283320	O14837	Nonsense_Mutation	SNP	ENST00000393272.3	37	CCDS46385.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.649267	0.67358	.	.	ENSG00000144061	ENST00000316534;ENST00000445609;ENST00000393272;ENST00000355301;ENST00000417665	.	.	.	5.41	4.54	0.55810	.	0.228513	0.43579	D	0.000546	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-20.6403	7.6624	0.28410	0.0:0.7464:0.1655:0.0882	.	.	.	.	X	208;208;208;146;208	.	ENSP00000313169:E208X	E	-	1	0	NPHP1	110283320	0.970000	0.33590	0.997000	0.53966	0.277000	0.26821	0.797000	0.26999	1.285000	0.44548	0.563000	0.77884	GAG		0.363	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		A	110926031	C	A	110926031	4	1	61	1	0	0	0	0	0	1	0	0	10610	922	32	2	1639	2	NPHP1	2	110926031	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	600578	110926031	132273342	1588	9573										
ACOXL	55289	broad.mit.edu	37	chr2	111556225	111556225	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtgtgaaaatgcggagaaGatgtatattggaaatgccat	12	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:111556225G>T	ENST00000389811.4	+	6	608	c.384G>T	c.(382-384)aaG>aaT	p.K128N	ACOXL_ENST00000439055.1_Missense_Mutation_p.K128N|ACOXL_ENST00000340561.4_Missense_Mutation_p.K128N			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	128					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)	p.K128N(1)		kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						ATGCGGAGAAGATGTATATTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											147	139	141					2																	111556225		1919	4138	6057	111272696	SO:0001583	missense	55289				CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"acyl-Coenzyme A oxidase-like"				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.384G>T	2.37:g.111556225G>T	ENSP00000374461:p.Lys128Asn		111272696	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		.	.	.	.	.	.	.	.	.	.	G	14.98	2.697975	0.48307	.	.	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000340561	D;D;D	0.99695	-6.43;-6.43;-6.43	5.22	5.22	0.72569	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.000000	0.64402	D	0.000001	D	0.99880	0.9943	H	0.99712	4.72	0.42590	D	0.99324	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.96187	0.9135	10	0.87932	D	0	-36.6461	16.2818	0.82694	0.0:0.0:1.0:0.0	.	128;128;128	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	N	128	ENSP00000374461:K128N;ENSP00000407761:K128N;ENSP00000343717:K128N	ENSP00000343717:K128N	K	+	3	2	ACOXL	111272696	1.000000	0.71417	1.000000	0.80357	0.164000	0.22412	1.975000	0.40569	2.438000	0.82558	0.650000	0.86243	AAG		0.438	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		T	111556225	G	T	111556225	3	4	61	1	0	0	0	0	1	0	0	0	161	933	33	2	402	2	ACOXL	2	111556225	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	630194	111556225	131643148	1589	9574										
ANAPC1	64682	broad.mit.edu	37	chr2	112552462	112552462	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgagagagatactattttCtcttataatctgtcaatata	5	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:112552462C>T	ENST00000341068.3	-	35	5078	c.4306G>A	c.(4306-4308)Gaa>Aaa	p.E1436K		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1436					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.E1436K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						ATACTATTTTCTCTTATAATC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											6	5	5					2																	112552462		1843	3890	5733	112268933	SO:0001583	missense	64682			AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4306G>A	2.37:g.112552462C>T	ENSP00000339109:p.Glu1436Lys		112268933	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.18|12.18	1.859311|1.859311	0.32884|0.32884	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	T|T	0.27256|0.26957	1.68|1.7	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.156567|.	0.26631|.	U|.	0.023301|.	T|T	0.31513|0.31513	0.0799|0.0799	L|L	0.29908|0.29908	0.895|0.895	0.58432|0.58432	D|D	0.999994|0.999994	B|.	0.15930|.	0.015|.	B|.	0.14023|.	0.01|.	T|T	0.01621|0.01621	-1.1310|-1.1310	10|6	0.08599|.	T|.	0.76|.	-17.8806|-17.8806	18.7416|18.7416	0.91775|0.91775	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1436|.	Q9H1A4|.	APC1_HUMAN|.	K|K	1436|970	ENSP00000339109:E1436K|ENSP00000396695:R970K	ENSP00000339109:E1436K|.	E|R	-|-	1|2	0|0	ANAPC1|ANAPC1	112268933|112268933	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.575000|5.575000	0.67430|0.67430	2.513000|2.513000	0.84729|0.84729	0.563000|0.563000	0.77884|0.77884	GAA|AGA		0.308	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		T	112552462	C	T	112552462	3	4	61	1	0	0	0	0	1	0	0	0	598	922	32	3	1584	3	ANAPC1	2	112552462	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	996237	112552462	130646911	1590	9575										
MERTK	10461	broad.mit.edu	37	chr2	112751865	112751865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttggccagaatggcagccGagctcggatctctgttcaag	13	10	2	1	rs202242962		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:112751865G>A	ENST00000295408.4	+	9	1591	c.1334G>A	c.(1333-1335)cGa>cAa	p.R445Q	MERTK_ENST00000409780.1_Missense_Mutation_p.R269Q|MERTK_ENST00000421804.2_Missense_Mutation_p.R445Q			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	445	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R445Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						AATGGCAGCCGAGCTCGGATC	0.527													G|||	1	0.000199681	0	0	5008	,	,		18673	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											119	117	118					2																	112751865		2203	4300	6503	112468336	SO:0001583	missense	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1334G>A	2.37:g.112751865G>A	ENSP00000295408:p.Arg445Gln		112468336	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	1.851	-0.464991	0.04476	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780	T;T;T	0.53206	0.63;0.63;0.63	4.95	-9.89	0.00464	Fibronectin, type III (3);Immunoglobulin-like fold (1);	2.361860	0.02365	N	0.077284	T	0.26846	0.0657	N	0.20685	0.6	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.12837	-1.0532	10	0.12103	T	0.63	0.0	10.0875	0.42428	0.2231:0.0:0.6026:0.1742	.	445	Q12866	MERTK_HUMAN	Q	445;445;40;269	ENSP00000295408:R445Q;ENSP00000389152:R445Q;ENSP00000387277:R269Q	ENSP00000295408:R445Q	R	+	2	0	MERTK	112468336	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-3.075000	0.00616	-2.863000	0.00326	-1.423000	0.01107	CGA		0.527	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			A	112751865	G	A	112751865	3	1	61	1	0	0	0	0	1	0	0	0	9509	1058	37	1	1368	1	MERTK	2	112751865	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199403	112751865	130447508	1591	9576										
FBLN7	129804	broad.mit.edu	37	chr2	112917277	112917277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcagcaaacagcagctcCtctcggccatccgccagctg	9	17	2	0	rs140000827		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:112917277C>A	ENST00000331203.2	+	2	371	c.100C>A	c.(100-102)Ctc>Atc	p.L34I	FBLN7_ENST00000409903.1_Missense_Mutation_p.L34I|FBLN7_ENST00000409450.3_Missense_Mutation_p.L34I|FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409667.3_Missense_Mutation_p.L34I	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	34					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.L34I(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						ACAGCAGCTCCTCTCGGCCAT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	2											48	48	48					2																	112917277		2203	4300	6503	112633748	SO:0001583	missense	129804				CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.100C>A	2.37:g.112917277C>A	ENSP00000331411:p.Leu34Ile		112633748	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	37	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250344	0.59212	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409667;ENST00000409450	D;T;T;T	0.81499	-1.5;-1.43;1.32;-1.48	5.48	4.6	0.57074	.	0.071355	0.64402	D	0.000019	T	0.79753	0.4500	M	0.64997	1.995	0.39145	D	0.962115	P;D;B;B	0.52996	0.952;0.957;0.005;0.129	P;B;B;B	0.45310	0.476;0.439;0.006;0.043	T	0.79347	-0.1841	10	0.27082	T	0.32	-41.4108	14.6821	0.69026	0.1466:0.8534:0.0:0.0	.	34;34;34;34	Q53RD9-4;Q53RD9-2;Q53RD9;B8ZZC1	.;.;FBLN7_HUMAN;.	I	34	ENSP00000331411:L34I;ENSP00000386295:L34I;ENSP00000386822:L34I;ENSP00000387000:L34I	ENSP00000331411:L34I	L	+	1	0	FBLN7	112633748	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.759000	0.55227	1.315000	0.45114	-0.270000	0.10280	CTC		0.612	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		A	112917277	C	A	112917277	3	1	61	1	0	0	0	0	1	0	0	0	5720	681	24	2	106	2	FBLN7	2	112917277	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165412	112917277	130282096	1592	9577										
FBLN7	129804	broad.mit.edu	37	chr2	112922646	112922646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagtacttagtggatcacGaagtccattttacctgcaac	8	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:112922646G>A	ENST00000331203.2	+	3	575	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K	FBLN7_ENST00000409903.1_Missense_Mutation_p.E102K|FBLN7_ENST00000409450.3_Missense_Mutation_p.E102K|FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409667.3_Missense_Mutation_p.E102K	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	102	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.E102K(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						AGTGGATCACGAAGTCCATTT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	86	87					2																	112922646		2203	4300	6503	112639117	SO:0001583	missense	129804				CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.304G>A	2.37:g.112922646G>A	ENSP00000331411:p.Glu102Lys		112639117	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	37	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	G	35	5.427845	0.96131	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409667;ENST00000409450	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	5.6	5.6	0.85130	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.72843	0.3511	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.994;0.998;1.0;0.999	T	0.65463	-0.6162	10	0.06625	T	0.88	-17.8603	18.3917	0.90485	0.0:0.0:1.0:0.0	.	102;102;102;102	Q53RD9-4;Q53RD9-2;Q53RD9;B8ZZC1	.;.;FBLN7_HUMAN;.	K	102	ENSP00000331411:E102K;ENSP00000386295:E102K;ENSP00000386822:E102K;ENSP00000387000:E102K	ENSP00000331411:E102K	E	+	1	0	FBLN7	112639117	1.000000	0.71417	0.957000	0.39632	0.909000	0.53808	8.303000	0.89955	2.649000	0.89929	0.655000	0.94253	GAA		0.577	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		A	112922646	G	A	112922646	3	1	61	1	0	0	0	0	1	0	0	0	5720	1059	37	1	314	1	FBLN7	2	112922646	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5369	112922646	130276727	1593	9578										
ZC3H6	376940	broad.mit.edu	37	chr2	113069447	113069447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgccgaagaaaatcaaacGaaaagaacgtgggggaagaa	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113069447G>A	ENST00000409871.1	+	5	1081	c.680G>A	c.(679-681)cGa>cAa	p.R227Q	ZC3H6_ENST00000343936.4_Missense_Mutation_p.R227Q	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	227							metal ion binding (GO:0046872)	p.R227Q(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AAAATCAAACGAAAAGAACGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	77	76					2																	113069447		1837	4084	5921	112785918	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.680G>A	2.37:g.113069447G>A	ENSP00000386764:p.Arg227Gln		112785918	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437117	0.83885	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15718	2.4;2.4	4.98	4.98	0.66077	.	0.414610	0.23752	N	0.044912	T	0.29028	0.0721	M	0.71581	2.175	0.33744	D	0.619769	D	0.62365	0.991	P	0.51895	0.683	T	0.44847	-0.9301	10	0.49607	T	0.09	-11.0204	10.8063	0.46520	0.0887:0.0:0.9113:0.0	.	227	P61129	ZC3H6_HUMAN	Q	227;227;204	ENSP00000386764:R227Q;ENSP00000340298:R227Q	ENSP00000340298:R227Q	R	+	2	0	ZC3H6	112785918	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.071000	0.57556	2.473000	0.83533	0.462000	0.41574	CGA		0.368	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		A	113069447	G	A	113069447	3	1	61	1	0	0	0	0	1	0	0	0	17610	1058	37	1	698	1	ZC3H6	2	113069447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146801	113069447	130129926	1594	9579										
ZC3H6	376940	broad.mit.edu	37	chr2	113089379	113089379	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaggagctaaattaggaGatcctagactacaaaaaaat	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113089379G>T	ENST00000409871.1	+	12	3285	c.2884G>T	c.(2884-2886)Gat>Tat	p.D962Y	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Missense_Mutation_p.D962Y	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	962							metal ion binding (GO:0046872)	p.D962Y(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TAAATTAGGAGATCCTAGACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	67	69					2																	113089379		1855	4092	5947	112805850	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2884G>T	2.37:g.113089379G>T	ENSP00000386764:p.Asp962Tyr		112805850	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806658	0.70682	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.18960	2.18;2.18	5.79	5.79	0.91817	.	0.485469	0.23779	N	0.044659	T	0.51787	0.1695	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52426	-0.8577	10	0.87932	D	0	-21.298	20.0401	0.97581	0.0:0.0:1.0:0.0	.	962	P61129	ZC3H6_HUMAN	Y	962	ENSP00000386764:D962Y;ENSP00000340298:D962Y	ENSP00000340298:D962Y	D	+	1	0	ZC3H6	112805850	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.972000	0.70448	2.716000	0.92895	0.591000	0.81541	GAT		0.408	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		T	113089379	G	T	113089379	3	4	61	1	0	0	0	0	1	0	0	0	17610	942	33	2	2930	2	ZC3H6	2	113089379	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19932	113089379	130109994	1595	9580										
POLR1B	84172	broad.mit.edu	37	chr2	113332763	113332763	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttcatcttctcagaggaGaactcggccttagaatactt	7	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113332763G>T	ENST00000263331.5	+	15	3445	c.2865G>T	c.(2863-2865)gaG>gaT	p.E955D	POLR1B_ENST00000417433.2_Missense_Mutation_p.E899D|POLR1B_ENST00000541869.1_Missense_Mutation_p.E993D|POLR1B_ENST00000537335.1_Missense_Mutation_p.E744D|POLR1B_ENST00000409894.3_Missense_Mutation_p.E772D	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	955					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.E955D(1)		breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						TCTCAGAGGAGAACTCGGCCT	0.488																																					Ovarian(16;256 576 9537 23969 41147)											1	Substitution - Missense(1)	large_intestine(1)	2											98	102	101					2																	113332763		2203	4300	6503	113049234	SO:0001583	missense	84172			AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.2865G>T	2.37:g.113332763G>T	ENSP00000263331:p.Glu955Asp		113049234	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557114	0.27827	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433;ENST00000536096	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.59	5.59	0.84812	DNA-directed RNA polymerase, subunit 2, domain 6 (2);	0.140757	0.64402	D	0.000007	T	0.51770	0.1694	N	0.11427	0.14	0.51482	D	0.999926	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.08055	0.002;0.003;0.001;0.003	T	0.50189	-0.8857	10	0.07482	T	0.82	-25.1426	11.8098	0.52175	0.081:0.0:0.919:0.0	.	993;772;899;955	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	D	955;993;772;744;899;314	ENSP00000263331:E955D;ENSP00000444136:E993D;ENSP00000387143:E772D;ENSP00000437914:E744D;ENSP00000405358:E899D	ENSP00000263331:E955D	E	+	3	2	POLR1B	113049234	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.185000	0.50934	2.622000	0.88805	0.563000	0.77884	GAG		0.488	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		T	113332763	G	T	113332763	3	4	61	1	0	0	0	0	1	0	0	0	12241	933	33	2	2923	2	POLR1B	2	113332763	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	243384	113332763	129866610	1596	9581										
CKAP2L	150468	broad.mit.edu	37	chr2	113498583	113498583	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaaagagtcagaagtaatCcctgtgtatgtaagatcatg	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113498583C>T	ENST00000302450.6	-	8	1902	c.1824G>A	c.(1822-1824)ggG>ggA	p.G608G	NT5DC4_ENST00000327581.4_Intron|CKAP2L_ENST00000541405.1_Splice_Site_p.G443G	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	608						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.G608G(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						CAGAAGTAATCCCTGTGTATG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	2											131	120	123					2																	113498583		2203	4300	6503	113215054	SO:0001630	splice_region_variant	150468			AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1823-1G>A	2.37:g.113498583C>T			113215054	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Silent	SNP	ENST00000302450.6	37	CCDS2100.1																																																																																				0.343	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	Silent	T	113498583	C	T	113498583	5	4	61	1	0	0	0	0	0	0	1	0	3449	869	30	3	421	3	CKAP2L	2	113498583	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165820	113498583	129700790	1597	9582										
CKAP2L	150468	broad.mit.edu	37	chr2	113509978	113509978	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttcctttattacttttcTttttgttttaagttccatag	3	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113509978T>A	ENST00000302450.6	-	5	1546	c.1468A>T	c.(1468-1470)Aga>Tga	p.R490*	CKAP2L_ENST00000541405.1_Nonsense_Mutation_p.R325*	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	490						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R490*(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						ATTACTTTTCTTTTTGTTTTA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											100	101	101					2																	113509978		2202	4299	6501	113226449	SO:0001587	stop_gained	150468			AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1468A>T	2.37:g.113509978T>A	ENSP00000305204:p.Arg490*		113226449	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Nonsense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	T	33	5.273185	0.95429	.	.	ENSG00000169607	ENST00000541405;ENST00000302450	.	.	.	5.51	5.51	0.81932	.	0.485095	0.23309	N	0.049591	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.3616	13.5607	0.61788	0.0:0.0:0.0:1.0	.	.	.	.	X	325;490	.	ENSP00000305204:R490X	R	-	1	2	CKAP2L	113226449	1.000000	0.71417	0.996000	0.52242	0.117000	0.20001	4.498000	0.60373	2.093000	0.63338	0.477000	0.44152	AGA		0.333	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		A	113509978	T	A	113509978	4	1	61	1	0	0	0	0	0	1	0	0	3449	1617	56	5	789	5	CKAP2L	2	113509978	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11395	113509978	129689395	1598	9583										
IL1B	3553	broad.mit.edu	37	chr2	113591100	113591100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagtggtggtcggagattCgtagctggatgccgccatcc	15	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113591100C>T	ENST00000263341.2	-	4	362	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	IL1B_ENST00000491056.1_5'UTR	NM_000576.2	NP_000567.1	P01584	IL1B_HUMAN	interleukin 1, beta	51					activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular response to drug (GO:0035690)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to organic substance (GO:0071310)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|embryo implantation (GO:0007566)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|hyaluronan biosynthetic process (GO:0030213)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-1 beta production (GO:0032611)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|monocyte aggregation (GO:0070487)|negative regulation of adiponectin secretion (GO:0070164)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of MAP kinase activity (GO:0043407)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion molecule production (GO:0060355)|positive regulation of cell division (GO:0051781)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myosin light chain kinase activity (GO:0035505)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell mediated immunity (GO:0002711)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein kinase B signaling (GO:0043491)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of insulin secretion (GO:0050796)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|sequestering of triglyceride (GO:0030730)|signal transduction (GO:0007165)|smooth muscle adaptation (GO:0014805)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	cytokine activity (GO:0005125)|interleukin-1 receptor binding (GO:0005149)|protein domain specific binding (GO:0019904)	p.R51Q(1)		breast(2)|central_nervous_system(1)|large_intestine(1)|lung(8)	12					Canakinumab(DB06168)|Gallium nitrate(DB05260)|Minocycline(DB01017)|Rilonacept(DB06372)	GTCGGAGATTCGTAGCTGGAT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	94	96					2																	113591100		2203	4300	6503	113307571	SO:0001583	missense	3553			M15330	CCDS2102.1	2q14	2014-01-30			ENSG00000125538	ENSG00000125538		"Interleukins and interleukin receptors", "Endogenous ligands"	5992	protein-coding gene	gene with protein product		147720				2954882, 2989698	Standard	NM_000576		Approved	IL1F2, IL-1B, IL1-BETA	uc002tii.1	P01584	OTTHUMG00000131344	ENST00000263341.2:c.152G>A	2.37:g.113591100C>T	ENSP00000263341:p.Arg51Gln		113307571	Q53X59|Q53XX2|Q7M4S7|Q7RU01|Q96HE5|Q9UCT6	Missense_Mutation	SNP	ENST00000263341.2	37	CCDS2102.1	.	.	.	.	.	.	.	.	.	.	C	1.023	-0.684356	0.03353	.	.	ENSG00000125538	ENST00000263341;ENST00000418817;ENST00000432018;ENST00000416750	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	4.72	0.872	0.19113	Interleukin-1 propeptide (1);	0.810801	0.11915	N	0.517278	T	0.09774	0.0240	N	0.00395	-1.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.35025	-0.9805	10	0.02654	T	1	-0.5004	6.853	0.24024	0.0:0.2849:0.0:0.7151	.	51	P01584	IL1B_HUMAN	Q	51	ENSP00000263341:R51Q;ENSP00000407219:R51Q;ENSP00000409680:R51Q;ENSP00000400854:R51Q	ENSP00000263341:R51Q	R	-	2	0	IL1B	113307571	0.040000	0.19996	0.031000	0.17742	0.013000	0.08279	0.695000	0.25527	0.067000	0.16545	-1.300000	0.01332	CGA		0.627	IL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254125.2	NM_000576		T	113591100	C	T	113591100	3	4	61	1	0	0	0	0	1	0	0	0	7672	884	31	1	673	1	IL1B	2	113591100	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81122	113591100	129608273	1599	9584										
IL1F5	26525	broad.mit.edu	37	chr2	113818507	113818507	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctgcatgcagggaaggtCattaaaggttggtgatgaaa	16	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:113818507C>A	ENST00000393200.2	+	3	269	c.108C>A	c.(106-108)gtC>gtA	p.V36V	IL36RN_ENST00000346807.3_Silent_p.V36V	NM_012275.2	NP_036407.1	Q9UBH0	I36RA_HUMAN	interleukin 36 receptor antagonist	36					antifungal humoral response (GO:0019732)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of interferon-gamma secretion (GO:1902714)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)	extracellular space (GO:0005615)	interleukin-1 receptor antagonist activity (GO:0005152)	p.V36V(1)		large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CAGGGAAGGTCATTAAAGGTT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	2											96	83	88					2																	113818507		2203	4300	6503	113534978	SO:0001819	synonymous_variant	26525			AF201830	CCDS2111.1	2q14	2014-09-17	2011-06-06	2011-06-06	ENSG00000136695	ENSG00000136695		"Interleukins and interleukin receptors"	15561	protein-coding gene	gene with protein product	"family of interleukin 1-delta", "interleukin-1 receptor antagonist homolog 1", "interleukin-1 HY1", "IL-1 related protein 3"	605507	"interleukin 1 family, member 5 (delta)"	IL1F5		10625660, 10512743, 11574262	Standard	NM_012275		Approved	FIL1, FIL1(DELTA), FIL1D, IL1HY1, IL1RP3, IL1L1, IL-1F5, IL36RA, MGC29840	uc002tit.3	Q9UBH0	OTTHUMG00000131337	ENST00000393200.2:c.108C>A	2.37:g.113818507C>A			113534978	A8K2I4|Q56AT9|Q7RTZ6	Silent	SNP	ENST00000393200.2	37	CCDS2111.1																																																																																				0.478	IL36RN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330729.1	NM_173170		A	113818507	C	A	113818507	2	1	61	1	0	0	0	0	0	0	0	1	7674	813	29	2		2	IL1F5	2	113818507	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	227407	113818507	129380866	1600	9585										
FOXD4L1	200350	broad.mit.edu	37	chr2	114257173	114257173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcccccctactcgtacatcGcgctcatcaccatggccatc	6	19	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:114257173G>A	ENST00000306507.5	+	1	513	c.340G>A	c.(340-342)Gcg>Acg	p.A114T		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	114					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A114T(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						CTCGTACATCGCGCTCATCAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											32	44	40					2																	114257173		2198	4273	6471	113973643	SO:0001583	missense	200350			AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.340G>A	2.37:g.114257173G>A	ENSP00000302756:p.Ala114Thr		113973643	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	19.25	3.791138	0.70452	.	.	ENSG00000184492	ENST00000306507	D	0.95554	-3.74	2.85	2.85	0.33270	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);Transcription factor, fork head, conserved site (1);	0.000000	0.33631	U	0.004718	D	0.96580	0.8884	M	0.63843	1.955	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.96435	0.9322	10	0.87932	D	0	.	11.4865	0.50356	0.0:0.0:1.0:0.0	.	114	Q9NU39	FX4L1_HUMAN	T	114	ENSP00000302756:A114T	ENSP00000302756:A114T	A	+	1	0	FOXD4L1	113973643	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	5.902000	0.69869	1.602000	0.50124	0.184000	0.17185	GCG		0.647	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184		A	114257173	G	A	114257173	3	1	61	1	0	0	0	0	1	0	0	0	6019	1087	38	1	342	1	FOXD4L1	2	114257173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	438666	114257173	128942200	1601	9586										
RABL2A	11159	broad.mit.edu	37	chr2	114398567	114398567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcccatgcatcgtggtgGccaataaaattgatggtggg	13	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:114398567G>A	ENST00000393167.3	+	6	619	c.394G>A	c.(394-396)Gcc>Acc	p.A132T	RABL2A_ENST00000478880.1_3'UTR|RABL2A_ENST00000393166.3_Missense_Mutation_p.A132T|RABL2A_ENST00000376439.3_Intron|RABL2A_ENST00000409875.1_Missense_Mutation_p.A132T|RABL2A_ENST00000393165.3_Missense_Mutation_p.A132T|RABL2A_ENST00000409842.1_Intron	NM_013412.2	NP_038198.1	Q9UBK7	RBL2A_HUMAN	RAB, member of RAS oncogene family-like 2A	132					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A132T(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|stomach(3)	9						CATCGTGGTGGCCAATAAAAT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											39	38	39					2																	114398567		2200	4279	6479	114115037	SO:0001583	missense	11159				CCDS2118.1	2q13	2014-05-09			ENSG00000144134	ENSG00000144134		"RAB, member RAS oncogene"	9799	protein-coding gene	gene with protein product		605412				10444334	Standard	NM_007082		Approved		uc010flb.3	Q9UBK7	OTTHUMG00000047828	ENST00000393167.3:c.394G>A	2.37:g.114398567G>A	ENSP00000376872:p.Ala132Thr		114115037	B7ZBD6|Q9NU37	Missense_Mutation	SNP	ENST00000393167.3	37	CCDS2118.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.155510	0.57259	.	.	ENSG00000144134	ENST00000393167;ENST00000393165;ENST00000393166;ENST00000409875	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	3.14	3.14	0.36123	Small GTP-binding protein domain (1);	0.045684	0.85682	D	0.000000	D	0.89511	0.6736	H	0.95574	3.69	0.80722	D	1	D;D;D	0.59767	0.977;0.986;0.977	P;P;P	0.61722	0.893;0.838;0.893	D	0.92227	0.5789	10	0.87932	D	0	-11.3908	12.5625	0.56291	0.0:0.0:1.0:0.0	.	132;132;132	Q6IC14;A0AUY0;Q9UBK7	.;.;RBL2A_HUMAN	T	132	ENSP00000376872:A132T;ENSP00000376870:A132T;ENSP00000376871:A132T;ENSP00000387229:A132T	ENSP00000376870:A132T	A	+	1	0	RABL2A	114115037	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	8.564000	0.90726	1.721000	0.51461	0.505000	0.49811	GCC		0.532	RABL2A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000109047.2			A	114398567	G	A	114398567	3	1	61	1	0	0	0	0	1	0	0	0	13007	1203	42	3	412	3	RABL2A	2	114398567	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141394	114398567	128800806	1602	9587										
SLC35F5	80255	broad.mit.edu	37	chr2	114483038	114483038	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actactttattgggaaactcGaagtcctcaaatccagtata	6	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:114483038G>A	ENST00000245680.2	-	12	1580	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC35F5_ENST00000470204.2_5'UTR	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	389					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.F389F(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						TGGGAAACTCGAAGTCCTCAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											92	90	91					2																	114483038		2203	4299	6502	114199508	SO:0001819	synonymous_variant	80255			AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.1167C>T	2.37:g.114483038G>A			114199508	Q9H6P8|Q9H7D8	Silent	SNP	ENST00000245680.2	37	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	G	9.429	1.085117	0.20390	.	.	ENSG00000115084	ENST00000447673	.	.	.	6.07	-0.653	0.11447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.6138	10.8914	0.46998	0.5617:0.0:0.4383:0.0	.	.	.	.	X	152	.	.	R	-	1	2	SLC35F5	114199508	0.990000	0.36364	0.998000	0.56505	0.995000	0.86356	0.450000	0.21762	-0.101000	0.12219	-0.345000	0.07892	CGA		0.358	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		A	114483038	G	A	114483038	2	1	61	1	0	0	0	0	0	0	0	1	14629	1049	37	1		1	SLC35F5	2	114483038	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84471	114483038	128716335	1603	9588										
SLC35F5	80255	broad.mit.edu	37	chr2	114492240	114492240	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatactgcagcaaggattaaGgtaaaaagtcctatgaggag	11	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:114492240G>T	ENST00000245680.2	-	9	1256	c.843C>A	c.(841-843)acC>acA	p.T281T		NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	281	EamA.				transport (GO:0006810)	integral component of membrane (GO:0016021)		p.T281T(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						CAAGGATTAAGGTAAAAAGTC	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	2											58	59	59					2																	114492240		2202	4297	6499	114208710	SO:0001819	synonymous_variant	80255			AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.843C>A	2.37:g.114492240G>T			114208710	Q9H6P8|Q9H7D8	Silent	SNP	ENST00000245680.2	37	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	G	9.259	1.042831	0.19748	.	.	ENSG00000115084	ENST00000447673	.	.	.	5.62	0.516	0.17019	.	.	.	.	.	T	0.50343	0.1610	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35226	-0.9797	4	.	.	.	-9.5952	4.6379	0.12534	0.344:0.0:0.4233:0.2327	.	.	.	.	I	31	.	.	L	-	1	0	SLC35F5	114208710	0.871000	0.30034	0.999000	0.59377	0.998000	0.95712	-0.074000	0.11450	0.093000	0.17368	0.655000	0.94253	CTT		0.299	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		T	114492240	G	T	114492240	2	4	61	1	0	0	0	0	0	0	0	1	14629	987	35	2		2	SLC35F5	2	114492240	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9202	114492240	128707133	1604	9589										
ACTR3	10096	broad.mit.edu	37	chr2	114714966	114714966	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaagtatgccacaccaaAaaggattatgaagaaattgg	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:114714966A>C	ENST00000263238.2	+	12	1511	c.1191A>C	c.(1189-1191)aaA>aaC	p.K397N	ACTR3_ENST00000536059.1_Missense_Mutation_p.K335N|ACTR3_ENST00000535589.2_Missense_Mutation_p.K346N	NM_001277140.1|NM_005721.3	NP_001264069.1|NP_005712.1	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog (yeast)	397					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron differentiation (GO:0045666)|regulation of myosin II filament organization (GO:0043519)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|spindle localization (GO:0051653)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|hemidesmosome (GO:0030056)|lamellipodium (GO:0030027)|membrane (GO:0016020)|podosome (GO:0002102)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)	p.K397N(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(2)	15						GCCACACCAAAAAGGATTATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											128	120	122					2																	114714966		2203	4300	6503	114431436	SO:0001583	missense	10096			AF006083	CCDS33277.1, CCDS63000.1	2q14.1	2010-07-20	2001-11-28		ENSG00000115091	ENSG00000115091			170	protein-coding gene	gene with protein product		604222	"ARP3 (actin-related protein 3, yeast) homolog"			9230079	Standard	NM_005721		Approved	ARP3	uc002tkx.2	P61158	OTTHUMG00000153497	ENST00000263238.2:c.1191A>C	2.37:g.114714966A>C	ENSP00000263238:p.Lys397Asn		114431436	P32391|Q53QM2	Missense_Mutation	SNP	ENST00000263238.2	37	CCDS33277.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180351	0.57800	.	.	ENSG00000115091	ENST00000263238;ENST00000536059;ENST00000544784;ENST00000535589	D;D;D	0.96774	-4.12;-4.12;-4.12	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98498	0.9499	H	0.96365	3.81	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.99044	1.0825	10	0.87932	D	0	-9.9318	9.3712	0.38254	0.9203:0.0:0.0797:0.0	.	335;397	F5H3P5;P61158	.;ARP3_HUMAN	N	397;335;268;346	ENSP00000263238:K397N;ENSP00000445257:K335N;ENSP00000444987:K346N	ENSP00000263238:K397N	K	+	3	2	ACTR3	114431436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.053000	0.49901	2.087000	0.62958	0.533000	0.62120	AAA		0.358	ACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331366.2	NM_005721		C	114714966	A	C	114714966	3	2	61	1	0	0	0	0	1	0	0	0	212	11	1	4	1237	4	ACTR3	2	114714966	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	222726	114714966	128484407	1605	9590										
DPP10	57628	broad.mit.edu	37	chr2	116283510	116283510	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagacattcagtttcaccaGatttaaaatatgtccttctg	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:116283510G>T	ENST00000410059.1	+	5	883	c.403G>T	c.(403-405)Gat>Tat	p.D135Y	DPP10_ENST00000393147.2_Missense_Mutation_p.D139Y|DPP10_ENST00000310323.8_Missense_Mutation_p.D128Y|DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000409163.1_Missense_Mutation_p.D85Y	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	135						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.D128Y(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGTTTCACCAGATTTAAAATA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	100	101					2																	116283510		2203	4300	6503	115999980	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.403G>T	2.37:g.116283510G>T	ENSP00000386565:p.Asp135Tyr		115999980	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.910027	0.72983	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000419287;ENST00000476155	T;T;D;T;T;D	0.98120	0.72;0.72;-4.73;0.72;0.72;-4.73	4.99	4.99	0.66335	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.126462	0.51477	D	0.000089	D	0.99048	0.9674	H	0.94847	3.59	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.995;0.98;0.997;0.997	D	0.99267	1.0892	10	0.87932	D	0	-29.0934	15.5937	0.76562	0.0:0.0:1.0:0.0	.	128;139;131;135	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	Y	135;85;131;139;128;85;85	ENSP00000386565:D135Y;ENSP00000387038:D85Y;ENSP00000376854:D131Y;ENSP00000376855:D139Y;ENSP00000309066:D128Y;ENSP00000402499:D85Y	ENSP00000309066:D128Y	D	+	1	0	DPP10	115999980	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.715000	0.74697	2.578000	0.87016	0.563000	0.77884	GAT		0.313	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116283510	G	T	116283510	3	4	61	1	0	0	0	0	1	0	0	0	4738	942	33	2	592	2	DPP10	2	116283510	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1568544	116283510	126915863	1606	9591										
DPP10	57628	broad.mit.edu	37	chr2	116594286	116594286	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatgttcatggcttgaaaGaagaaaatatattaataatt	6	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:116594286G>T	ENST00000410059.1	+	24	2626	c.2146G>T	c.(2146-2148)Gaa>Taa	p.E716*	DPP10_ENST00000393147.2_Nonsense_Mutation_p.E720*|DPP10_ENST00000310323.8_Nonsense_Mutation_p.E709*|DPP10_ENST00000409163.1_Nonsense_Mutation_p.E666*	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	716						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.E709*(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TGGCTTGAAAGAAGAAAATAT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											79	96	91					2																	116594286		2203	4300	6503	116310756	SO:0001587	stop_gained	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.2146G>T	2.37:g.116594286G>T	ENSP00000386565:p.Glu716*		116310756	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Nonsense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	40	8.287367	0.98742	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	.	.	.	5.15	5.15	0.70609	.	0.106581	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-19.4675	17.7899	0.88548	0.0:0.0:1.0:0.0	.	.	.	.	X	716;666;720;709	.	ENSP00000309066:E709X	E	+	1	0	DPP10	116310756	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.177000	0.71961	2.667000	0.90743	0.561000	0.74099	GAA		0.313	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116594286	G	T	116594286	4	4	61	1	0	0	0	0	0	1	0	0	4738	943	33	2	2411	2	DPP10	2	116594286	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	310776	116594286	126605087	1607	9592										
DDX18	8886	broad.mit.edu	37	chr2	118582211	118582211	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagacctggcaaggatttCtctgaaaaaggagccattgt	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:118582211C>A	ENST00000263239.2	+	8	1261	c.1133C>A	c.(1132-1134)tCt>tAt	p.S378Y		NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	378	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.S378Y(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCAAGGATTTCTCTGAAAAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											128	128	128					2																	118582211		2203	4300	6503	118298681	SO:0001583	missense	8886			X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.1133C>A	2.37:g.118582211C>A	ENSP00000263239:p.Ser378Tyr		118298681	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	37	CCDS2120.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090393	0.94149	.	.	ENSG00000088205	ENST00000263239;ENST00000539346;ENST00000415038	T;T	0.04454	3.62;3.62	4.71	4.71	0.59529	DEAD-like helicase (2);	1.022150	0.07739	N	0.946487	T	0.07503	0.0189	N	0.16862	0.45	0.80722	D	1	P	0.51147	0.942	P	0.46362	0.514	T	0.52961	-0.8505	10	0.87932	D	0	.	18.223	0.89907	0.0:1.0:0.0:0.0	.	378	Q9NVP1	DDX18_HUMAN	Y	378;117;61	ENSP00000263239:S378Y;ENSP00000415604:S61Y	ENSP00000263239:S378Y	S	+	2	0	DDX18	118298681	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	7.125000	0.77193	2.618000	0.88619	0.563000	0.77884	TCT		0.393	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		A	118582211	C	A	118582211	3	1	61	1	0	0	0	0	1	0	0	0	4351	913	32	2	1163	2	DDX18	2	118582211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1987925	118582211	124617162	1608	9593										
CCDC93	54520	broad.mit.edu	37	chr2	118706917	118706917	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttggatcagctttggattCtatcttctcgagggctgctt	10	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:118706917C>A	ENST00000376300.2	-	14	1260	c.1123G>T	c.(1123-1125)Gaa>Taa	p.E375*	CCDC93_ENST00000460781.1_5'Flank|CCDC93_ENST00000319432.5_Nonsense_Mutation_p.E374*	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	375								p.E375*(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						GCTTTGGATTCTATCTTCTCG	0.418																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											244	209	221					2																	118706917		2203	4300	6503	118423387	SO:0001587	stop_gained	54520			BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.1123G>T	2.37:g.118706917C>A	ENSP00000365477:p.Glu375*		118423387	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Nonsense_Mutation	SNP	ENST00000376300.2	37	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	C	39	7.324537	0.98214	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-22.5054	17.5969	0.88014	0.0:1.0:0.0:0.0	.	.	.	.	X	375;374	.	ENSP00000324135:E374X	E	-	1	0	CCDC93	118423387	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.820000	0.62671	2.824000	0.97209	0.655000	0.94253	GAA		0.418	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		A	118706917	C	A	118706917	4	1	61	1	0	0	0	0	0	1	0	0	2878	922	32	2	816	2	CCDC93	2	118706917	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124706	118706917	124492456	1609	9594										
MARCO	8685	broad.mit.edu	37	chr2	119699895	119699895	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgagaaataagaaaattCtcaaggaggacgagctcttg	10	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:119699895C>A	ENST00000327097.4	+	1	154	c.19C>A	c.(19-21)Ctc>Atc	p.L7I	MARCO_ENST00000541757.1_5'UTR	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	7					apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)	p.L7I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						TAAGAAAATTCTCAAGGAGGA	0.443																																					GBM(8;18 374 7467 11269 32796)											1	Substitution - Missense(1)	large_intestine(1)	2											73	74	73					2																	119699895		2203	4300	6503	119416365	SO:0001583	missense	8685			AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.19C>A	2.37:g.119699895C>A	ENSP00000318916:p.Leu7Ile		119416365	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	C	7.421	0.636651	0.14386	.	.	ENSG00000019169	ENST00000327097;ENST00000410021	D	0.91843	-2.92	4.95	1.22	0.21188	.	0.171960	0.26224	N	0.025604	D	0.86489	0.5945	L	0.29908	0.895	0.29334	N	0.866518	P	0.52842	0.956	P	0.48166	0.569	T	0.80533	-0.1340	9	.	.	.	.	6.515	0.22242	0.0:0.6133:0.0:0.3867	.	7	Q9UEW3	MARCO_HUMAN	I	7	ENSP00000318916:L7I	.	L	+	1	0	MARCO	119416365	0.077000	0.21312	0.105000	0.21289	0.657000	0.38888	-0.126000	0.10563	0.386000	0.24997	0.563000	0.77884	CTC		0.443	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		A	119699895	C	A	119699895	3	1	61	1	0	0	0	0	1	0	0	0	9341	913	32	2	21	2	MARCO	2	119699895	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	992978	119699895	123499478	1610	9595										
MARCO	8685	broad.mit.edu	37	chr2	119750794	119750794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggacaatttgcgatgaCgagtggcaaaattctgatgc	14	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:119750794C>T	ENST00000327097.4	+	16	1482	c.1347C>T	c.(1345-1347)gaC>gaT	p.D449D	MARCO_ENST00000541757.1_Silent_p.D371D	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	449	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)	p.D449D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						TTTGCGATGACGAGTGGCAAA	0.527																																					GBM(8;18 374 7467 11269 32796)											1	Substitution - coding silent(1)	large_intestine(1)	2											184	174	177					2																	119750794		2203	4300	6503	119467264	SO:0001819	synonymous_variant	8685			AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.1347C>T	2.37:g.119750794C>T			119467264	B4DW79|Q9Y5S3	Silent	SNP	ENST00000327097.4	37	CCDS2124.1																																																																																				0.527	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		T	119750794	C	T	119750794	2	4	61	1	0	0	0	0	0	0	0	1	9341	535	19	1		1	MARCO	2	119750794	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50899	119750794	123448579	1611	9596										
PCDP1	200373	broad.mit.edu	37	chr2	120362779	120362779	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaccagggcactgaaatTtcaaaaacgagacagatgaa	10	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120362779T>C	ENST00000413369.3	+	11	1134	c.1047T>C	c.(1045-1047)atT>atC	p.I349I	PCDP1_ENST00000597189.1_3'UTR|PCDP1_ENST00000602047.1_Silent_p.I63I	NM_001271049.1	NP_001257978												p.I63I(1)				Colorectal(110;0.196)					GCACTGAAATTTCAAAAACGA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	2											66	69	68					2																	120362779		2203	4300	6503	120079249	SO:0001819	synonymous_variant	200373																														ENST00000413369.3:c.1047T>C	2.37:g.120362779T>C			120079249		Silent	SNP	ENST00000413369.3	37	CCDS33282.2																																																																																				0.388	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			C	120362779	T	C	120362779	2	2	61	1	0	0	0	0	0	0	0	1	11603	1829	64	4		4	PCDP1	2	120362779	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	611985	120362779	122836594	1612	9597										
PCDP1	200373	broad.mit.edu	37	chr2	120385248	120385248	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcgaatttcttcaaattCttcctgaggcggatcagtca	10	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120385248C>A	ENST00000413369.3	+	16	1623	c.1536C>A	c.(1534-1536)ttC>ttA	p.F512L	PCDP1_ENST00000597189.1_3'UTR|PCDP1_ENST00000602047.1_Missense_Mutation_p.F226L	NM_001271049.1	NP_001257978												p.F226L(1)				Colorectal(110;0.196)					TCTTCAAATTCTTCCTGAGGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	121	118					2																	120385248		2203	4300	6503	120101718	SO:0001583	missense	200373																														ENST00000413369.3:c.1536C>A	2.37:g.120385248C>A	ENSP00000393222:p.Phe512Leu		120101718		Missense_Mutation	SNP	ENST00000413369.3	37	CCDS33282.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	2.942|2.942	-0.218569|-0.218569	0.06101|0.06101	.|.	.|.	ENSG00000163075|ENSG00000163075	ENST00000295220;ENST00000413369|ENST00000443972;ENST00000413057	T|.	0.29397|.	1.57|.	4.18|4.18	-0.818|-0.818	0.10833|0.10833	.|.	2.861720|.	0.00969|.	N|.	0.003203|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.26643|0.26643	-1.0097|-1.0097	10|5	0.15499|.	T|.	0.54|.	4.4754|4.4754	4.1907|4.1907	0.10419|0.10419	0.0:0.4463:0.169:0.3847|0.0:0.4463:0.169:0.3847	.|.	356;512|.	Q4G0U5-3;Q4G0U5|.	.;PCDP1_HUMAN|.	L|Y	226;512|71;60	ENSP00000393222:F512L|.	ENSP00000295220:F226L|.	F|S	+|+	3|2	2|0	AC069154.2|AC069154.2	120101718|120101718	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.131000|0.131000	0.15870|0.15870	-0.174000|-0.174000	0.10743|0.10743	-0.119000|-0.119000	0.15052|0.15052	TTC|TCT		0.468	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			A	120385248	C	A	120385248	3	1	61	1	0	0	0	0	1	0	0	0	11603	912	32	2	708	2	PCDP1	2	120385248	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22469	120385248	122814125	1613	9598										
TMEM177	80775	broad.mit.edu	37	chr2	120438602	120438602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggccagccagctccgctccCtccacagctgcagagcctct	10	19	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120438602C>A	ENST00000424086.1	+	2	646	c.173C>A	c.(172-174)cCt>cAt	p.P58H	TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000401466.1_Missense_Mutation_p.P58H|TMEM177_ENST00000409951.1_Missense_Mutation_p.P58H|TMEM177_ENST00000272521.6_Missense_Mutation_p.P58H	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	58						integral component of membrane (GO:0016021)		p.P58H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	13	Colorectal(110;0.196)					GCTCCGCTCCCTCCACAGCTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	2											121	123	122					2																	120438602		2203	4300	6503	120155072	SO:0001583	missense	80775			BC004404	CCDS2128.1	2q14.2	2008-02-05			ENSG00000144120	ENSG00000144120			28143	protein-coding gene	gene with protein product						12477932	Standard	NM_001105198		Approved	MGC10993	uc002tmc.1	Q53S58	OTTHUMG00000153312	ENST00000424086.1:c.173C>A	2.37:g.120438602C>A	ENSP00000402661:p.Pro58His		120155072	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	37	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987855	0.35036	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000445518;ENST00000409951;ENST00000415646	T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22	4.48	3.6	0.41247	.	0.308940	0.36303	N	0.002671	T	0.14227	0.0344	L	0.40543	1.245	0.09310	N	1	B;P	0.36249	0.412;0.545	B;B	0.38194	0.128;0.267	T	0.14337	-1.0476	10	0.72032	D	0.01	-3.5286	6.343	0.21332	0.0:0.7128:0.1867:0.1004	.	58;58	B8ZZT5;Q53S58	.;TM177_HUMAN	H	58	ENSP00000385966:P58H;ENSP00000402661:P58H;ENSP00000272521:P58H;ENSP00000405898:P58H;ENSP00000386430:P58H	ENSP00000272521:P58H	P	+	2	0	TMEM177	120155072	0.077000	0.21312	0.030000	0.17652	0.412000	0.31113	3.603000	0.54074	1.258000	0.44101	0.549000	0.68633	CCT		0.582	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		A	120438602	C	A	120438602	3	1	61	1	0	0	0	0	1	0	0	0	16133	681	24	2	175	2	TMEM177	2	120438602	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53354	120438602	122760771	1614	9599										
PTPN4	5775	broad.mit.edu	37	chr2	120640090	120640090	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattattagctgaacttggaGactacgatcagtcagagaac	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120640090G>T	ENST00000263708.2	+	8	1249	c.478G>T	c.(478-480)Gac>Tac	p.D160Y		NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	160	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.D160Y(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	TGAACTTGGAGACTACGATCA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											26	26	26					2																	120640090		2187	4283	6470	120356560	SO:0001583	missense	5775				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.478G>T	2.37:g.120640090G>T	ENSP00000263708:p.Asp160Tyr		120356560	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.954686	0.73902	.	.	ENSG00000088179	ENST00000263708	T	0.80214	-1.35	5.73	4.85	0.62838	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.045054	0.85682	D	0.000000	D	0.93706	0.7989	H	0.98507	4.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95888	0.8904	10	0.87932	D	0	.	14.8363	0.70187	0.0691:0.0:0.9309:0.0	.	160	P29074	PTN4_HUMAN	Y	160	ENSP00000263708:D160Y	ENSP00000263708:D160Y	D	+	1	0	PTPN4	120356560	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.246000	0.78247	1.430000	0.47334	0.591000	0.81541	GAC		0.299	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			T	120640090	G	T	120640090	3	4	61	1	0	0	0	0	1	0	0	0	12827	942	33	2	504	2	PTPN4	2	120640090	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	201488	120640090	122559283	1615	9600										
PTPN4	5775	broad.mit.edu	37	chr2	120723143	120723143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatggagtccctgatgattCgagtgactttctagattttg	10	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120723143C>T	ENST00000263708.2	+	25	3251	c.2480C>T	c.(2479-2481)tCg>tTg	p.S827L	PTPN4_ENST00000544261.1_Missense_Mutation_p.S460L	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	827	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.S827L(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	CCTGATGATTCGAGTGACTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											157	137	143					2																	120723143		2203	4300	6503	120439613	SO:0001583	missense	5775				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2480C>T	2.37:g.120723143C>T	ENSP00000263708:p.Ser827Leu		120439613	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.013547	0.93346	.	.	ENSG00000088179	ENST00000263708;ENST00000544261	T;T	0.12672	2.66;2.66	5.62	5.62	0.85841	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	L	0.54863	1.705	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.01334	-1.1382	10	0.56958	D	0.05	.	19.6764	0.95936	0.0:1.0:0.0:0.0	.	827	P29074	PTN4_HUMAN	L	827;460	ENSP00000263708:S827L;ENSP00000445841:S460L	ENSP00000263708:S827L	S	+	2	0	PTPN4	120439613	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.625000	0.83145	2.660000	0.90430	0.655000	0.94253	TCG		0.428	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			T	120723143	C	T	120723143	3	4	61	1	0	0	0	0	1	0	0	0	12827	893	31	1	2574	1	PTPN4	2	120723143	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83053	120723143	122476230	1616	9601										
EPB41L5	57669	broad.mit.edu	37	chr2	120833065	120833065	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttaggtatttatttgttCttcagttaaaacaagatatt	5	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:120833065C>A	ENST00000263713.5	+	6	635	c.421C>A	c.(421-423)Ctt>Att	p.L141I	EPB41L5_ENST00000443902.2_Missense_Mutation_p.L141I|EPB41L5_ENST00000452780.1_Missense_Mutation_p.L141I|EPB41L5_ENST00000443124.1_Missense_Mutation_p.L141I|EPB41L5_ENST00000331393.4_Missense_Mutation_p.L141I	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	141	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)		p.L141I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						TTTATTTGTTCTTCAGTTAAA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	2											97	97	97					2																	120833065		2201	4291	6492	120549535	SO:0001583	missense	57669			AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.421C>A	2.37:g.120833065C>A	ENSP00000263713:p.Leu141Ile		120549535	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	37	CCDS2130.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550232	0.86127	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28	4.73	4.73	0.59995	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.64402	D	0.000010	D	0.93779	0.8011	H	0.97829	4.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.999	D	0.96291	0.9214	10	0.87932	D	0	.	17.6568	0.88180	0.0:1.0:0.0:0.0	.	141;141;141	Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;E41L5_HUMAN	I	141	ENSP00000263713:L141I;ENSP00000393856:L141I;ENSP00000329687:L141I;ENSP00000393722:L141I;ENSP00000390439:L141I	ENSP00000263713:L141I	L	+	1	0	EPB41L5	120549535	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.685000	0.46959	2.313000	0.78055	0.555000	0.69702	CTT		0.284	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		A	120833065	C	A	120833065	3	1	61	1	0	0	0	0	1	0	0	0	5170	913	32	2	439	2	EPB41L5	2	120833065	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109922	120833065	122366308	1617	9602										
RALB	5899	broad.mit.edu	37	chr2	121047164	121047164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaacaccttagggaacagaTtctccgtgtgaaggctgaag	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:121047164T>C	ENST00000272519.5	+	4	602	c.332T>C	c.(331-333)aTt>aCt	p.I111T	RALB_ENST00000474855.2_Missense_Mutation_p.I133T|RALB_ENST00000404963.3_Missense_Mutation_p.I132T|RALB_ENST00000470417.1_3'UTR|RALB_ENST00000420510.1_Missense_Mutation_p.I111T	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	111					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.I111T(1)		endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				AGGGAACAGATTCTCCGTGTG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	138	133					2																	121047164		2203	4300	6503	120763634	SO:0001583	missense	5899				CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"ras related GTP binding protein B"	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.332T>C	2.37:g.121047164T>C	ENSP00000272519:p.Ile111Thr		120763634	B4E040|Q53T32|Q6ZS74	Missense_Mutation	SNP	ENST00000272519.5	37	CCDS2131.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.604203	0.87157	.	.	ENSG00000144118	ENST00000447591;ENST00000474855;ENST00000272519;ENST00000420510;ENST00000404963;ENST00000412383;ENST00000449649	T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	5.4	5.4	0.78164	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92172	0.7518	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.87578	0.998;0.998;0.998	D	0.94090	0.7352	10	0.87932	D	0	.	15.5811	0.76439	0.0:0.0:0.0:1.0	.	133;132;111	B4E040;Q6ZS74;P11234	.;.;RALB_HUMAN	T	133;133;111;111;132;111;111	ENSP00000402866:I133T;ENSP00000438764:I133T;ENSP00000272519:I111T;ENSP00000414224:I111T;ENSP00000384328:I132T;ENSP00000398162:I111T;ENSP00000407062:I111T	ENSP00000272519:I111T	I	+	2	0	RALB	120763634	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.719000	0.84751	2.270000	0.75569	0.459000	0.35465	ATT		0.463	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881		C	121047164	T	C	121047164	3	2	61	1	0	0	0	0	1	0	0	0	13048	1493	52	4	342	4	RALB	2	121047164	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	214099	121047164	122152209	1618	9603										
RALB	5899	broad.mit.edu	37	chr2	121050803	121050803	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaaagcagcaagaacaaGaaaagttttaaagaaagatg	9	3	0	5	rs148881695		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:121050803G>T	ENST00000272519.5	+	5	858	c.588G>T	c.(586-588)aaG>aaT	p.K196N	RALB_ENST00000474855.2_Missense_Mutation_p.K218N|RALB_ENST00000404963.3_Missense_Mutation_p.K217N|RALB_ENST00000470417.1_3'UTR|RALB_ENST00000420510.1_Missense_Mutation_p.K196N	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	196					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.K196N(1)		endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				GCAAGAACAAGAAAAGTTTTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	106	107					2																	121050803		2203	4300	6503	120767273	SO:0001583	missense	5899				CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"ras related GTP binding protein B"	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.588G>T	2.37:g.121050803G>T	ENSP00000272519:p.Lys196Asn		120767273	B4E040|Q53T32|Q6ZS74	Missense_Mutation	SNP	ENST00000272519.5	37	CCDS2131.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.585168	0.66105	.	.	ENSG00000144118	ENST00000474855;ENST00000272519;ENST00000420510;ENST00000404963	T;T;T;T	0.66099	-0.19;-0.18;-0.18;0.26	5.75	5.75	0.90469	.	0.062072	0.64402	D	0.000007	T	0.66086	0.2754	L	0.51914	1.62	0.80722	D	1	P;D;P	0.56968	0.791;0.978;0.671	B;P;B	0.53146	0.255;0.719;0.188	T	0.63571	-0.6607	10	0.35671	T	0.21	.	13.1859	0.59680	0.0726:0.0:0.9274:0.0	.	218;217;196	B4E040;Q6ZS74;P11234	.;.;RALB_HUMAN	N	218;196;196;217	ENSP00000438764:K218N;ENSP00000272519:K196N;ENSP00000414224:K196N;ENSP00000384328:K217N	ENSP00000272519:K196N	K	+	3	2	RALB	120767273	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.342000	0.65970	2.719000	0.93026	0.655000	0.94253	AAG		0.433	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881		T	121050803	G	T	121050803	3	4	61	1	0	0	0	0	1	0	0	0	13048	933	33	2	602	2	RALB	2	121050803	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3639	121050803	122148570	1619	9604										
CLASP1	23332	broad.mit.edu	37	chr2	122120867	122120867	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactcttaacgccagtgctcGaattgaatgctagaatacaa	7	9	1	2	rs145127425	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:122120867G>A	ENST00000263710.4	-	37	4476	c.4087C>T	c.(4087-4089)Cga>Tga	p.R1363*	CLASP1_ENST00000455322.2_Nonsense_Mutation_p.R1319*|CLASP1_ENST00000545861.1_Nonsense_Mutation_p.R1070*|CLASP1_ENST00000541859.1_Nonsense_Mutation_p.R1080*|CLASP1_ENST00000541377.1_Nonsense_Mutation_p.R1302*|CLASP1_ENST00000409078.3_Nonsense_Mutation_p.R1296*|CLASP1_ENST00000397587.3_Nonsense_Mutation_p.R1303*	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1363	Interaction with CLIP2. {ECO:0000250}.|Interaction with PHLDB2 and RSN.|Localization to kinetochores.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)	p.R1363*(2)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					GCCAGTGCTCGAATTGAATGC	0.468																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											71	65	67					2																	122120867		1960	4154	6114	121837337	SO:0001587	stop_gained	23332			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.4087C>T	2.37:g.122120867G>A	ENSP00000263710:p.Arg1363*		121837337	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Nonsense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	G	44	11.084874	0.99513	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	.	.	.	5.34	5.34	0.76211	.	0.057652	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.1363	14.2001	0.65696	0.0:0.0:0.8145:0.1855	.	.	.	.	X	1363;1319;1303;1302;1080;1296;1070	.	ENSP00000263710:R1363X	R	-	1	2	CLASP1	121837337	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	4.912000	0.63335	2.659000	0.90383	0.563000	0.77884	CGA		0.468	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		A	122120867	G	A	122120867	4	1	61	1	0	0	0	0	0	1	0	0	3460	1066	37	1	545	1	CLASP1	2	122120867	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1070064	122120867	121078506	1620	9605										
CNTNAP5	129684	broad.mit.edu	37	chr2	125192138	125192138	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgatgagtactctcaaaGatgtgatctccctgaagttc	9	8	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:125192138G>T	ENST00000431078.1	+	5	971	c.607G>T	c.(607-609)Gat>Tat	p.D203Y		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	203	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.D203Y(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TACTCTCAAAGATGTGATCTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											122	117	119					2																	125192138		2017	4200	6217	124908608	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.607G>T	2.37:g.125192138G>T	ENSP00000399013:p.Asp203Tyr		124908608	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575651	0.86645	.	.	ENSG00000155052	ENST00000431078	T	0.79352	-1.26	5.48	5.48	0.80851	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	0.000000	0.49305	D	0.000156	D	0.84129	0.5404	M	0.91196	3.185	0.80722	D	1	P	0.47677	0.899	B	0.42282	0.382	D	0.88542	0.3110	10	0.87932	D	0	.	18.3591	0.90368	0.0:0.0:1.0:0.0	.	203	Q8WYK1	CNTP5_HUMAN	Y	203	ENSP00000399013:D203Y	ENSP00000399013:D203Y	D	+	1	0	CNTNAP5	124908608	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.687000	0.98667	2.576000	0.86940	0.655000	0.94253	GAT		0.493	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125192138	G	T	125192138	3	4	61	1	0	0	0	0	1	0	0	0	3656	942	33	2	625	2	CNTNAP5	2	125192138	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3071271	125192138	118007235	1621	9606										
CNTNAP5	129684	broad.mit.edu	37	chr2	125204385	125204385	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgccaccctgggcagcctCctggatgaccagcactggca	11	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:125204385C>A	ENST00000431078.1	+	6	1153	c.789C>A	c.(787-789)ctC>ctA	p.L263L		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	263	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.L263L(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGGGCAGCCTCCTGGATGACC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	2											60	64	63					2																	125204385		2152	4278	6430	124920855	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.789C>A	2.37:g.125204385C>A			124920855	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.617	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125204385	C	A	125204385	2	1	61	1	0	0	0	0	0	0	0	1	3656	842	30	2		2	CNTNAP5	2	125204385	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12247	125204385	117994988	1622	9607										
CNTNAP5	129684	broad.mit.edu	37	chr2	125521709	125521709	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcattaaagacttcattCgactcgaaataagctgtaag	8	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:125521709C>T	ENST00000431078.1	+	16	2879	c.2515C>T	c.(2515-2517)Cga>Tga	p.R839*		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	839	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.R839*(2)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGACTTCATTCGACTCGAAAT	0.373																																																2	Substitution - Nonsense(2)	large_intestine(1)|kidney(1)	2											106	101	103					2																	125521709		1832	4081	5913	125238179	SO:0001587	stop_gained	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2515C>T	2.37:g.125521709C>T	ENSP00000399013:p.Arg839*		125238179	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Nonsense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	44	10.565196	0.99428	.	.	ENSG00000155052	ENST00000431078	.	.	.	5.75	4.86	0.63082	.	0.000000	0.40385	N	0.001103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9074	0.58160	0.2953:0.7047:0.0:0.0	.	.	.	.	X	839	.	ENSP00000399013:R839X	R	+	1	2	CNTNAP5	125238179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.880000	0.48530	1.398000	0.46701	0.655000	0.94253	CGA		0.373	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125521709	C	T	125521709	4	4	61	1	0	0	0	0	0	1	0	0	3656	876	31	1	2577	1	CNTNAP5	2	125521709	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	317324	125521709	117677664	1623	9608										
ERCC3	2071	broad.mit.edu	37	chr2	128044365	128044365	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgctcggcctcccaggacCttttggtggtgtggcccagc	13	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128044365C>A	ENST00000285398.2	-	8	1350	c.1256G>T	c.(1255-1257)aGg>aTg	p.R419M	ERCC3_ENST00000493187.2_Missense_Mutation_p.R355M	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	419	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)	p.R419M(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTCCCAGGACCTTTTGGTGGT	0.597			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	1	Substitution - Missense(1)	large_intestine(1)	2											110	104	106					2																	128044365		2203	4300	6503	127760835	SO:0001583	missense	2071	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.1256G>T	2.37:g.128044365C>A	ENSP00000285398:p.Arg419Met		127760835	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	37	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005539	0.93287	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.76186	-1.0;-1.0	5.26	5.26	0.73747	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	H	0.94582	3.555	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.92785	0.6243	10	0.87932	D	0	-31.5627	19.2242	0.93812	0.0:1.0:0.0:0.0	.	419	P19447	ERCC3_HUMAN	M	419;355	ENSP00000285398:R419M;ENSP00000444796:R355M	ENSP00000285398:R419M	R	-	2	0	ERCC3	127760835	1.000000	0.71417	0.997000	0.53966	0.799000	0.45148	7.776000	0.85560	2.605000	0.88082	0.655000	0.94253	AGG		0.597	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		A	128044365	C	A	128044365	3	1	61	1	0	0	0	0	1	0	0	0	5227	681	24	2	1124	2	ERCC3	2	128044365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2522656	128044365	115155008	1624	9609										
MAP3K2	10746	broad.mit.edu	37	chr2	128081548	128081548	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcctccttttccaaatttCtcaaagatagggttatcata	5	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128081548C>A	ENST00000409947.1	-	11	1050	c.768G>T	c.(766-768)gaG>gaT	p.E256D	MAP3K2_ENST00000344908.5_Missense_Mutation_p.E256D			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	256					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.E256D(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	TTCCAAATTTCTCAAAGATAG	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	2											65	57	59					2																	128081548		1792	4046	5838	127798018	SO:0001583	missense	10746			AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.768G>T	2.37:g.128081548C>A	ENSP00000387246:p.Glu256Asp		127798018	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	37	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	C	7.931	0.740720	0.15642	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.38077	1.16;1.16	4.85	3.01	0.34805	.	0.054771	0.64402	N	0.000001	T	0.15609	0.0376	N	0.14661	0.345	0.49915	D	0.999839	B	0.06786	0.001	B	0.06405	0.002	T	0.09818	-1.0657	10	0.06891	T	0.86	.	5.3613	0.16089	0.1475:0.6336:0.1424:0.0765	.	256	Q9Y2U5	M3K2_HUMAN	D	256	ENSP00000387246:E256D;ENSP00000343463:E256D	ENSP00000343463:E256D	E	-	3	2	MAP3K2	127798018	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.424000	0.44714	0.614000	0.30107	0.555000	0.69702	GAG		0.274	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		A	128081548	C	A	128081548	3	1	61	1	0	0	0	0	1	0	0	0	9280	912	32	2	1119	2	MAP3K2	2	128081548	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37183	128081548	115117825	1625	9610										
MYO7B	4648	broad.mit.edu	37	chr2	128317302	128317302	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactgctgactcaggatgtCggggttcaggctggtaagaa	15	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128317302C>T	ENST00000409816.2	+	1	37	c.5C>T	c.(4-6)tCg>tTg	p.S2L	MYO7B_ENST00000428314.1_Missense_Mutation_p.S2L|MYO7B_ENST00000389524.4_Missense_Mutation_p.S2L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	2						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S2L(2)		breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CTCAGGATGTCGGGGTTCAGG	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	2											140	151	147					2																	128317302		2053	4192	6245	128033772	SO:0001583	missense	4648				CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.5C>T	2.37:g.128317302C>T	ENSP00000386461:p.Ser2Leu		128033772	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	C	1.997	-0.430414	0.04669	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87729	-2.28;-2.29;-2.29	3.87	2.03	0.26663	.	.	.	.	.	T	0.70902	0.3277	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.08055	0.003	T	0.59075	-0.7522	9	0.36615	T	0.2	.	5.3124	0.15837	0.0:0.7423:0.0:0.2577	.	2	Q6PIF6	MYO7B_HUMAN	L	2	ENSP00000374175:S2L;ENSP00000415090:S2L;ENSP00000386461:S2L	ENSP00000374175:S2L	S	+	2	0	MYO7B	128033772	0.031000	0.19500	0.399000	0.26333	0.058000	0.15608	0.225000	0.17757	0.932000	0.37266	-0.142000	0.14014	TCG		0.502	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128317302	C	T	128317302	3	4	61	1	0	0	0	0	1	0	0	0	10113	893	31	1	7	1	MYO7B	2	128317302	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235754	128317302	114882071	1626	9611										
WDR33	55339	broad.mit.edu	37	chr2	128466446	128466446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagggcggggagtatcacGaaaatgttcatgacctggcc	13	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128466446G>A	ENST00000322313.4	-	21	3744	c.3586C>T	c.(3586-3588)Cgt>Tgt	p.R1196C		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1196					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1196C(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GGAGTATCACGAAAATGTTCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	50	51					2																	128466446		2203	4300	6503	128182916	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3586C>T	2.37:g.128466446G>A	ENSP00000325377:p.Arg1196Cys		128182916	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969087	0.74131	.	.	ENSG00000136709	ENST00000322313	D	0.91945	-2.94	5.56	5.56	0.83823	.	0.070560	0.56097	D	0.000030	D	0.86822	0.6025	N	0.19112	0.55	0.80722	D	1	D	0.61697	0.99	B	0.40659	0.336	D	0.89092	0.3483	10	0.66056	D	0.02	-9.5501	18.5233	0.90962	0.0:0.0:1.0:0.0	.	1196	Q9C0J8	WDR33_HUMAN	C	1196	ENSP00000325377:R1196C	ENSP00000325377:R1196C	R	-	1	0	WDR33	128182916	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.663000	0.61532	2.640000	0.89533	0.655000	0.94253	CGT		0.517	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128466446	G	A	128466446	3	1	61	1	0	0	0	0	1	0	0	0	17327	1058	37	1	432	1	WDR33	2	128466446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149144	128466446	114732927	1627	9612										
WDR33	55339	broad.mit.edu	37	chr2	128471176	128471176	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttcttctctgcgccctcGaaaacgtgggtcctcgggat	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128471176G>A	ENST00000322313.4	-	18	3447	c.3289C>T	c.(3289-3291)Cga>Tga	p.R1097*		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1097					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1097*(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTGCGCCCTCGAAAACGTGGG	0.602																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											121	127	125					2																	128471176		2203	4300	6503	128187646	SO:0001587	stop_gained	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3289C>T	2.37:g.128471176G>A	ENSP00000325377:p.Arg1097*		128187646	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Nonsense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	42	9.524565	0.99195	.	.	ENSG00000136709	ENST00000322313	.	.	.	5.81	4.85	0.62838	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.9399	17.6121	0.88056	0.0:0.0:0.8683:0.1317	.	.	.	.	X	1097	.	ENSP00000325377:R1097X	R	-	1	2	WDR33	128187646	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	4.210000	0.58500	2.738000	0.93877	0.655000	0.94253	CGA		0.602	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128471176	G	A	128471176	4	1	61	1	0	0	0	0	0	1	0	0	17327	1066	37	1	741	1	WDR33	2	128471176	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4730	128471176	114728197	1628	9613										
WDR33	55339	broad.mit.edu	37	chr2	128528479	128528479	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatcaggtcgcttataaAacagctgtcgaggtgcctgg	11	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128528479A>C	ENST00000322313.4	-	2	235	c.77T>G	c.(76-78)tTt>tGt	p.F26C	WDR33_ENST00000393006.1_Missense_Mutation_p.F26C|WDR33_ENST00000409658.3_Missense_Mutation_p.F26C	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	26					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.F26C(2)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TCGCTTATAAAACAGCTGTCG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	2											117	111	113					2																	128528479		2203	4300	6503	128244949	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.77T>G	2.37:g.128528479A>C	ENSP00000325377:p.Phe26Cys		128244949	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.633573	0.67015	.	.	ENSG00000136709	ENST00000322313;ENST00000393006;ENST00000409658;ENST00000408998	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.64216	0.2578	L	0.36672	1.1	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.77557	0.987;0.981;0.99	T	0.67341	-0.5695	10	0.72032	D	0.01	-6.8121	15.6889	0.77434	1.0:0.0:0.0:0.0	.	26;26;26	Q9C0J8-2;Q6NUQ0;Q9C0J8	.;.;WDR33_HUMAN	C	26	ENSP00000325377:F26C;ENSP00000376730:F26C;ENSP00000387186:F26C;ENSP00000386861:F26C	ENSP00000325377:F26C	F	-	2	0	WDR33	128244949	1.000000	0.71417	0.971000	0.41717	0.975000	0.68041	9.199000	0.95003	2.113000	0.64589	0.482000	0.46254	TTT		0.433	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		C	128528479	A	C	128528479	3	2	61	1	0	0	0	0	1	0	0	0	17327	14	1	4	4426	4	WDR33	2	128528479	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	57303	128528479	114670894	1629	9614										
SAP130	79595	broad.mit.edu	37	chr2	128772380	128772380	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttgcaagtcgttacctcGaggtaaatgagaagctccaa	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128772380G>A	ENST00000259235.3	-	5	823	c.694C>T	c.(694-696)Cga>Tga	p.R232*	SAP130_ENST00000357702.5_Nonsense_Mutation_p.R232*|SAP130_ENST00000259234.6_Nonsense_Mutation_p.R206*	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	232					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.R232*(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TCGTTACCTCGAGGTAAATGA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											97	92	93					2																	128772380		2203	4300	6503	128488850	SO:0001587	stop_gained	79595			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"sin3A-associated protein, 130kDa"			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.694C>T	2.37:g.128772380G>A	ENSP00000259235:p.Arg232*		128488850	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Nonsense_Mutation	SNP	ENST00000259235.3	37	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	G	34	5.370088	0.95900	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234;ENST00000424298	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3887	0.74726	0.0:0.0:0.8608:0.1392	.	.	.	.	X	232;232;206;206	.	ENSP00000259234:R206X	R	-	1	2	SAP130	128488850	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.422000	0.52749	2.894000	0.99253	0.655000	0.94253	CGA		0.403	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		A	128772380	G	A	128772380	4	1	61	1	0	0	0	0	0	1	0	0	13868	1066	37	1	2625	1	SAP130	2	128772380	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	243901	128772380	114426993	1630	9615										
UGGT1	56886	broad.mit.edu	37	chr2	128896367	128896367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagtggctgttcttagaGcatataattatgttgcccaa	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128896367G>A	ENST00000259253.6	+	16	1707	c.1660G>A	c.(1660-1662)Gca>Aca	p.A554T	UGGT1_ENST00000375990.3_Missense_Mutation_p.A530T	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	554					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.A554T(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TGTTCTTAGAGCATATAATTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											158	148	151					2																	128896367		2203	4300	6503	128612837	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1660G>A	2.37:g.128896367G>A	ENSP00000259253:p.Ala554Thr		128612837	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.459768	0.63401	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.01474	4.85;4.85	4.86	4.86	0.63082	.	0.156358	0.56097	D	0.000028	T	0.03434	0.0099	M	0.64676	1.99	0.58432	D	0.999995	B;B	0.21225	0.025;0.053	B;B	0.25405	0.047;0.06	T	0.40021	-0.9585	10	0.49607	T	0.09	.	13.7028	0.62620	0.0771:0.0:0.9229:0.0	.	530;554	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	T	530;554	ENSP00000365158:A530T;ENSP00000259253:A554T	ENSP00000259253:A554T	A	+	1	0	UGGT1	128612837	1.000000	0.71417	0.996000	0.52242	0.901000	0.52897	6.929000	0.75852	2.409000	0.81822	0.650000	0.86243	GCA		0.378	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		A	128896367	G	A	128896367	3	1	61	1	0	0	0	0	1	0	0	0	16981	971	34	3	1722	3	UGGT1	2	128896367	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123987	128896367	114303006	1631	9616										
UGGT1	56886	broad.mit.edu	37	chr2	128918826	128918826	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatctcatattcaacagcttCgggtagaagaagatgtgtaa	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128918826C>T	ENST00000259253.6	+	25	2856	c.2809C>T	c.(2809-2811)Cgg>Tgg	p.R937W	UGGT1_ENST00000375990.3_Missense_Mutation_p.R913W	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	937					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.R937W(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TCAACAGCTTCGGGTAGAAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	94	93					2																	128918826		2203	4300	6503	128635296	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.2809C>T	2.37:g.128918826C>T	ENSP00000259253:p.Arg937Trp		128635296	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.549996	0.65311	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.08896	3.04;3.04	5.86	5.86	0.93980	.	0.180390	0.49305	D	0.000152	T	0.13543	0.0328	L	0.40543	1.245	0.42510	D	0.992968	P;P	0.49862	0.901;0.929	P;B	0.51229	0.663;0.394	T	0.01504	-1.1338	9	.	.	.	.	13.9617	0.64185	0.0:0.8044:0.1956:0.0	.	913;937	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	W	913;937	ENSP00000365158:R913W;ENSP00000259253:R937W	.	R	+	1	2	UGGT1	128635296	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.315000	0.51951	2.777000	0.95525	0.655000	0.94253	CGG		0.358	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		T	128918826	C	T	128918826	3	4	61	1	0	0	0	0	1	0	0	0	16981	875	31	1	2907	1	UGGT1	2	128918826	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22459	128918826	114280547	1632	9617										
UGGT1	56886	broad.mit.edu	37	chr2	128928834	128928834	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttatgaactgccaatccaAactttctgacatgcctttaa	4	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128928834A>C	ENST00000259253.6	+	28	3127	c.3080A>C	c.(3079-3081)aAa>aCa	p.K1027T	UGGT1_ENST00000375990.3_Missense_Mutation_p.K1003T	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1027					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.K1027T(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TGCCAATCCAAACTTTCTGAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											91	89	90					2																	128928834		2203	4300	6503	128645304	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.3080A>C	2.37:g.128928834A>C	ENSP00000259253:p.Lys1027Thr		128645304	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.118308	0.77323	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.32023	1.47;1.47	5.53	5.53	0.82687	.	0.046788	0.85682	D	0.000000	T	0.40171	0.1106	M	0.82323	2.585	0.80722	D	1	B;B	0.14805	0.002;0.011	B;B	0.21151	0.013;0.033	T	0.27365	-1.0076	9	.	.	.	.	15.3255	0.74157	1.0:0.0:0.0:0.0	.	1003;1027	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	T	1003;1027	ENSP00000365158:K1003T;ENSP00000259253:K1027T	.	K	+	2	0	UGGT1	128645304	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.589000	0.67523	2.108000	0.64289	0.528000	0.53228	AAA		0.333	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		C	128928834	A	C	128928834	3	2	61	1	0	0	0	0	1	0	0	0	16981	14	1	4	3190	4	UGGT1	2	128928834	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10008	128928834	114270539	1633	9618										
UGGT1	56886	broad.mit.edu	37	chr2	128931419	128931419	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggaaggtcattgctacgAcatcaccacaggccagcctc	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:128931419A>C	ENST00000259253.6	+	30	3406	c.3359A>C	c.(3358-3360)gAc>gCc	p.D1120A	UGGT1_ENST00000375990.3_Missense_Mutation_p.D1096A	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1120					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.D1120A(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CATTGCTACGACATCACCACA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											138	118	125					2																	128931419		2203	4300	6503	128647889	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.3359A>C	2.37:g.128931419A>C	ENSP00000259253:p.Asp1120Ala		128647889	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.562610	0.86335	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.46063	0.88;0.88	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.69324	0.3098	M	0.92219	3.285	0.80722	D	1	D	0.54601	0.967	P	0.59221	0.854	T	0.78006	-0.2373	9	.	.	.	.	15.8249	0.78690	1.0:0.0:0.0:0.0	.	1120	Q9NYU2	UGGG1_HUMAN	A	1096;1120	ENSP00000365158:D1096A;ENSP00000259253:D1120A	.	D	+	2	0	UGGT1	128647889	1.000000	0.71417	0.991000	0.47740	0.817000	0.46193	8.425000	0.90270	2.194000	0.70268	0.533000	0.62120	GAC		0.493	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		C	128931419	A	C	128931419	3	2	61	1	0	0	0	0	1	0	0	0	16981	275	10	4	3477	4	UGGT1	2	128931419	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2585	128931419	114267954	1634	9619										
POTEF	728378	broad.mit.edu	37	chr2	130877719	130877719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccatgaaggcactgtcatCgtagtctccccaagcgccca	8	16	2	1	rs376091861	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:130877719C>T	ENST00000409914.2	-	3	769	c.370G>A	c.(370-372)Gat>Aat	p.D124N	POTEF_ENST00000360967.5_Missense_Mutation_p.D124N|POTEF_ENST00000361163.4_Missense_Mutation_p.D124N|POTEF_ENST00000357462.5_Missense_Mutation_p.D124N	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	124					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.D124N(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCACTGTCATCGTAGTCTCCC	0.577													.|||	4	0.000798722	0.003	0	5008	,	,		17097	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2						C	ASN/ASP	4,4398		0,4,2197	80	96	90		370	-1.2	0	2		90	1,8597		0,1,4298	no	missense	POTEF	NM_001099771.2	23	0,5,6495	TT,TC,CC		0.0116,0.0909,0.0385	benign	124/1076	130877719	5,12995	2201	4299	6500	130594189	SO:0001583	missense	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.370G>A	2.37:g.130877719C>T	ENSP00000386786:p.Asp124Asn		130594189	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	11.10	1.540657	0.27563	9.09E-4	1.16E-4	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.77098	-1.07;-1.07;1.75;1.73	0.619	-1.16	0.09678	.	.	.	.	.	T	0.61949	0.2388	L	0.58101	1.795	0.09310	N	1	P	0.52463	0.953	B	0.29267	0.1	T	0.56335	-0.7996	8	0.87932	D	0	.	.	.	.	.	124	A5A3E0	POTEF_HUMAN	N	124	ENSP00000350052:D124N;ENSP00000386786:D124N;ENSP00000354232:D124N;ENSP00000355012:D124N	ENSP00000350052:D124N	D	-	1	0	POTEF	130594189	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.497000	0.02289	-0.409000	0.07553	0.162000	0.16502	GAT		0.577	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		T	130877719	C	T	130877719	3	4	61	1	0	0	0	0	1	0	0	0	12296	884	31	1	2917	1	POTEF	2	130877719	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1946300	130877719	112321654	1635	9620										
CCDC74B	91409	broad.mit.edu	37	chr2	130897938	130897938	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgttagaggcctctgctttCtcctttctgaaacagtcatt	8	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:130897938C>A	ENST00000310463.6	-	5	827	c.690G>T	c.(688-690)gaG>gaT	p.E230D	CCDC74B_ENST00000392984.3_Missense_Mutation_p.E332D|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Missense_Mutation_p.E164D	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	230								p.E230D(1)		endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CCTCTGCTTTCTCCTTTCTGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	87	84					2																	130897938		2203	4300	6503	130614408	SO:0001583	missense	91409				CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.690G>T	2.37:g.130897938C>A	ENSP00000308873:p.Glu230Asp		130614408	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	37	CCDS2155.1	.	.	.	.	.	.	.	.	.	.	.	9.863	1.196766	0.22037	.	.	ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984	T;T;T	0.28895	1.72;1.67;1.59	2.5	-2.71	0.05986	.	0.233058	0.20849	U	0.084570	T	0.35653	0.0939	M	0.67953	2.075	0.09310	N	1	D;D;D	0.64830	0.994;0.969;0.99	P;P;P	0.54664	0.583;0.533;0.758	T	0.23904	-1.0175	10	0.36615	T	0.2	.	6.4458	0.21875	0.0:0.5103:0.0:0.4897	.	332;164;230	E7ESC5;Q96LY2-2;Q96LY2	.;.;CC74B_HUMAN	D	164;230;332	ENSP00000386294:E164D;ENSP00000308873:E230D;ENSP00000376710:E332D	ENSP00000308873:E230D	E	-	3	2	CCDC74B	130614408	0.000000	0.05858	0.039000	0.18376	0.060000	0.15804	-0.140000	0.10342	-0.707000	0.05022	0.298000	0.19748	GAG		0.632	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		A	130897938	C	A	130897938	3	1	61	1	0	0	0	0	1	0	0	0	2854	912	32	2	468	2	CCDC74B	2	130897938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20219	130897938	112301435	1636	9621										
TUBA3E	112714	broad.mit.edu	37	chr2	130952791	130952791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcctgtaggtccctgtgCgcacttcatctgcaaaagag	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:130952791C>T	ENST00000312988.7	-	3	336	c.236G>A	c.(235-237)cGc>cAc	p.R79H		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	79					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R79H(1)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGTCCCTGTGCGCACTTCATC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	2											129	130	130					2																	130952791		2203	4300	6503	130669261	SO:0001583	missense	112714			BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"Tubulins"	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.236G>A	2.37:g.130952791C>T	ENSP00000318197:p.Arg79His		130669261		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	c	16.54	3.151791	0.57151	.	.	ENSG00000152086	ENST00000312988	T	0.69806	-0.43	2.99	2.99	0.34606	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.49916	U	0.000129	T	0.76828	0.4042	H	0.94964	3.605	0.48087	D	0.999587	P	0.43938	0.822	P	0.44447	0.45	D	0.83764	0.0216	10	0.87932	D	0	.	11.7436	0.51807	0.0:1.0:0.0:0.0	.	79	Q6PEY2	TBA3E_HUMAN	H	79	ENSP00000318197:R79H	ENSP00000318197:R79H	R	-	2	0	TUBA3E	130669261	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.470000	0.73558	1.683000	0.51011	0.455000	0.32223	CGC		0.512	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312		T	130952791	C	T	130952791	3	4	61	1	0	0	0	0	1	0	0	0	16788	768	27	1	1128	1	TUBA3E	2	130952791	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54853	130952791	112246582	1637	9622										
ARHGEF4	50649	broad.mit.edu	37	chr2	131688757	131688757	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggctggagaagacacagaGaaagaagttgcagaagcagg	16	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:131688757G>T	ENST00000326016.5	+	3	746	c.227G>T	c.(226-228)aGa>aTa	p.R76I	ARHGEF4_ENST00000392953.3_Missense_Mutation_p.R76I|ARHGEF4_ENST00000409359.1_Missense_Mutation_p.R932I|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.R76I|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.R76I|SCARNA4_ENST00000517020.2_RNA|ARHGEF4_ENST00000428230.2_Missense_Mutation_p.R76I	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	76	ABR (APC-binding region) domain.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.R76I(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		AAGACACAGAGAAAGAAGTTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											38	32	34					2																	131688757		2203	4300	6503	131405227	SO:0001583	missense	50649			AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.227G>T	2.37:g.131688757G>T	ENSP00000316845:p.Arg76Ile		131405227	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	37	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.276343	0.40294	.	.	ENSG00000136002	ENST00000409359;ENST00000326016;ENST00000392953;ENST00000438985;ENST00000428230;ENST00000525839;ENST00000409303	T;T;T;T;T;T;T	0.73789	0.62;-0.49;-0.61;0.67;0.68;-0.61;-0.78	4.72	3.7	0.42460	.	.	.	.	.	T	0.75019	0.3793	L	0.34521	1.04	0.49687	D	0.999813	P;D;P;P	0.76494	0.917;0.999;0.95;0.917	B;D;P;B	0.74023	0.445;0.982;0.648;0.445	T	0.75505	-0.3294	9	0.87932	D	0	.	5.0624	0.14564	0.1948:0.0:0.8052:0.0	.	76;932;76;76	E9PEM0;E7EV07;Q9NR80-4;Q9NR80	.;.;.;ARHG4_HUMAN	I	932;76;76;256;76;76;76	ENSP00000386794:R932I;ENSP00000316845:R76I;ENSP00000376680:R76I;ENSP00000389661:R256I;ENSP00000398455:R76I;ENSP00000432267:R76I;ENSP00000387285:R76I	ENSP00000316845:R76I	R	+	2	0	ARHGEF4	131405227	0.891000	0.30450	0.880000	0.34516	0.545000	0.35147	1.083000	0.30815	2.151000	0.67156	0.467000	0.42956	AGA		0.597	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			T	131688757	G	T	131688757	3	4	61	1	0	0	0	0	1	0	0	0	908	942	33	2	229	2	ARHGEF4	2	131688757	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	735966	131688757	111510616	1638	9623										
POTEE	445582	broad.mit.edu	37	chr2	131976095	131976095	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctacagggagagcggcaaGagcaacgtgggcacttctgg	16	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:131976095G>T	ENST00000356920.5	+	1	214	c.120G>T	c.(118-120)aaG>aaT	p.K40N	POTEE_ENST00000358087.5_Missense_Mutation_p.K40N|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	40					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K40N(2)									AGAGCGGCAAGAGCAACGTGG	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	2											132	153	146					2																	131976095		2189	4298	6487	131692565	SO:0001583	missense	445582			AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.120G>T	2.37:g.131976095G>T	ENSP00000439189:p.Lys40Asn		131692565	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	7.124	0.578560	0.13686	.	.	ENSG00000188219	ENST00000356920;ENST00000358087	T;T	0.80393	-1.37;1.25	0.1	0.1	0.14510	.	.	.	.	.	T	0.70141	0.3190	L	0.27053	0.805	0.09310	N	1	P	0.39094	0.659	B	0.42959	0.403	T	0.61574	-0.7035	8	0.87932	D	0	.	.	.	.	.	40	Q6S8J3	POTEE_HUMAN	N	40	ENSP00000439189:K40N;ENSP00000443049:K40N	ENSP00000439189:K40N	K	+	3	2	AC131180.1	131692565	0.015000	0.18098	0.043000	0.18650	0.043000	0.13939	0.240000	0.18042	0.170000	0.19704	0.173000	0.16961	AAG		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		T	131976095	G	T	131976095	3	4	61	1	0	0	0	0	1	0	0	0	12295	933	33	2	122	2	POTEE	2	131976095	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	287338	131976095	111223278	1639	9624										
TUBA3D	113457	broad.mit.edu	37	chr2	132237994	132237994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccatcacagcctccctgcGatttgatggggccctgaatg	10	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:132237994G>A	ENST00000321253.6	+	4	835	c.728G>A	c.(727-729)cGa>cAa	p.R243Q		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	243					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R243Q(2)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GCCTCCCTGCGATTTGATGGG	0.567																																					Ovarian(137;2059 2432 35543 39401)											2	Substitution - Missense(2)	large_intestine(2)	2											87	119	109					2																	132237994		1982	4281	6263	131954464	SO:0001583	missense	113457			K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"Tubulins"	24071	protein-coding gene	gene with protein product	"alpha-tubulin isotype H2-alpha"					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.728G>A	2.37:g.132237994G>A	ENSP00000326042:p.Arg243Gln		131954464	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	g	7.395	0.631548	0.14322	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	T	0.74209	-0.82	2.24	-1.18	0.09617	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.44688	U	0.000440	D	0.83792	0.5331	M	0.91249	3.19	0.31925	N	0.612915	D	0.89917	1.0	D	0.70016	0.967	T	0.79952	-0.1586	10	0.72032	D	0.01	.	4.0589	0.09829	0.2665:0.1951:0.5383:0.0	.	243	Q13748	TBA3C_HUMAN	Q	243	ENSP00000326042:R243Q	ENSP00000326042:R243Q	R	+	2	0	TUBA3D	131954464	0.879000	0.30193	0.614000	0.29051	0.020000	0.10135	3.620000	0.54203	-0.518000	0.06452	-1.031000	0.02408	CGA		0.567	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132237994	G	A	132237994	3	1	61	1	0	0	0	0	1	0	0	0	16787	1058	37	1	742	1	TUBA3D	2	132237994	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	261899	132237994	110961379	1640	9625										
NCKAP5	344148	broad.mit.edu	37	chr2	133538652	133538652	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttggtacttccatatcGgctttgattttcatgttttt	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:133538652G>A	ENST00000409261.1	-	15	5395	c.5022C>T	c.(5020-5022)gcC>gcT	p.A1674A	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.A1674A|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1674								p.A1674A(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTTCCATATCGGCTTTGATTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											93	93	93					2																	133538652		1899	4117	6016	133255122	SO:0001819	synonymous_variant	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.5022C>T	2.37:g.133538652G>A			133255122	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				0.473	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133538652	G	A	133538652	2	1	61	1	0	0	0	0	0	0	0	1	10254	1103	39	1		1	NCKAP5	2	133538652	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1300658	133538652	109660721	1641	9626										
NCKAP5	344148	broad.mit.edu	37	chr2	133538725	133538725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgagacaggagccctgaGaactgccctttaacacattc	9	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:133538725G>T	ENST00000409261.1	-	15	5322	c.4949C>A	c.(4948-4950)tCt>tAt	p.S1650Y	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.S1650Y|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1650								p.S1650Y(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GGAGCCCTGAGAACTGCCCTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											114	116	115					2																	133538725		1925	4134	6059	133255195	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4949C>A	2.37:g.133538725G>T	ENSP00000387128:p.Ser1650Tyr		133255195	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970680	0.53614	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.12672	2.66;2.66	5.35	5.35	0.76521	.	0.000000	0.32190	U	0.006448	T	0.27900	0.0687	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01102	-1.1451	10	0.72032	D	0.01	.	17.4224	0.87518	0.0:0.0:1.0:0.0	.	1650	O14513	NCKP5_HUMAN	Y	1650	ENSP00000387128:S1650Y;ENSP00000380603:S1650Y	ENSP00000380603:S1650Y	S	-	2	0	NCKAP5	133255195	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	5.359000	0.66074	2.780000	0.95670	0.655000	0.94253	TCT		0.448	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133538725	G	T	133538725	3	4	61	1	0	0	0	0	1	0	0	0	10254	942	33	2	804	2	NCKAP5	2	133538725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73	133538725	109660648	1642	9627										
NCKAP5	344148	broad.mit.edu	37	chr2	133539774	133539774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaaaccccaagacttttGcatctttcttttctactttg	3	12	3	1	rs376182292		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:133539774G>A	ENST00000409261.1	-	14	4983	c.4610C>T	c.(4609-4611)gCa>gTa	p.A1537V	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.A1537V|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1537								p.A1537V(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CAAGACTTTTGCATCTTTCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	VAL/ALA,	0,3638		0,0,1819	93	95	94		4610,	3.5	0	2		94	1,8173		0,1,4086	no	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	64,	0,1,5905	AA,AG,GG		0.0122,0.0,0.0085	benign,	1537/1910,	133539774	1,11811	1819	4087	5906	133256244	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4610C>T	2.37:g.133539774G>A	ENSP00000387128:p.Ala1537Val		133256244	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	9.045	0.990726	0.18966	0.0	1.22E-4	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10005	2.92;2.92	5.33	3.55	0.40652	.	0.433798	0.16675	U	0.204201	T	0.07413	0.0187	L	0.27053	0.805	0.09310	N	0.999993	B	0.17268	0.021	B	0.18263	0.021	T	0.34800	-0.9814	10	0.28530	T	0.3	.	6.9482	0.24530	0.1523:0.1423:0.7054:0.0	.	1537	O14513	NCKP5_HUMAN	V	1537	ENSP00000387128:A1537V;ENSP00000380603:A1537V	ENSP00000380603:A1537V	A	-	2	0	NCKAP5	133256244	0.222000	0.23652	0.020000	0.16555	0.977000	0.68977	1.185000	0.32065	0.842000	0.35045	0.591000	0.81541	GCA		0.393	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133539774	G	A	133539774	3	1	61	1	0	0	0	0	1	0	0	0	10254	1319	46	3	1147	3	NCKAP5	2	133539774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1049	133539774	109659599	1643	9628										
NCKAP5	344148	broad.mit.edu	37	chr2	133540974	133540974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcagtcctttctcatgaGcactttgacaaccatgaggg	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:133540974G>T	ENST00000409261.1	-	14	3783	c.3410C>A	c.(3409-3411)gCt>gAt	p.A1137D	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.A1137D|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1137								p.A1137D(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TTTCTCATGAGCACTTTGACA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2											134	136	136					2																	133540974		2052	4203	6255	133257444	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3410C>A	2.37:g.133540974G>T	ENSP00000387128:p.Ala1137Asp		133257444	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021177	0.35701	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10099	2.91;2.91	5.26	3.45	0.39498	.	2.130700	0.03081	U	0.158536	T	0.07143	0.0181	N	0.08118	0	0.80722	D	1	B	0.34015	0.435	B	0.30572	0.117	T	0.15009	-1.0452	10	0.28530	T	0.3	.	9.4106	0.38489	0.0754:0.1432:0.7813:0.0	.	1137	O14513	NCKP5_HUMAN	D	1137	ENSP00000387128:A1137D;ENSP00000380603:A1137D	ENSP00000380603:A1137D	A	-	2	0	NCKAP5	133257444	0.985000	0.35326	0.403000	0.26384	0.480000	0.33159	2.070000	0.41491	0.783000	0.33636	0.650000	0.86243	GCT		0.498	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133540974	G	T	133540974	3	4	61	1	0	0	0	0	1	0	0	0	10254	971	34	2	2347	2	NCKAP5	2	133540974	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1200	133540974	109658399	1644	9629										
NCKAP5	344148	broad.mit.edu	37	chr2	133542399	133542399	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcacacattcttctgaaGaagtcctttttacaactctt	4	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:133542399G>T	ENST00000409261.1	-	14	2358	c.1985C>A	c.(1984-1986)tCt>tAt	p.S662Y	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.S662Y|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	662								p.S662Y(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TTCTTCTGAAGAAGTCCTTTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											112	110	111					2																	133542399		1879	4106	5985	133258869	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.1985C>A	2.37:g.133542399G>T	ENSP00000387128:p.Ser662Tyr		133258869	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	g	18.76	3.692704	0.68271	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.45668	0.89;0.89	5.64	5.64	0.86602	.	0.000000	0.38492	U	0.001662	T	0.55816	0.1944	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.56001	-0.8051	10	0.87932	D	0	.	18.0682	0.89397	0.0:0.0:1.0:0.0	.	662	O14513	NCKP5_HUMAN	Y	662	ENSP00000387128:S662Y;ENSP00000380603:S662Y	ENSP00000380603:S662Y	S	-	2	0	NCKAP5	133258869	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.728000	0.62000	2.937000	0.99478	0.651000	0.88453	TCT		0.448	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133542399	G	T	133542399	3	4	61	1	0	0	0	0	1	0	0	0	10254	942	33	2	3772	2	NCKAP5	2	133542399	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1425	133542399	109656974	1645	9630										
CCNT2	905	broad.mit.edu	37	chr2	135710248	135710248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaaatattggagaaaacGcctaataggttgaagaagat	9	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135710248G>A	ENST00000264157.5	+	8	771	c.741G>A	c.(739-741)acG>acA	p.T247T	CCNT2_ENST00000295238.6_Silent_p.T247T|CCNT2_ENST00000537343.1_Silent_p.T72T	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	247					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T247T(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		TGGAGAAAACGCCTAATAGGT	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	2											78	83	82					2																	135710248		2203	4300	6503	135426718	SO:0001819	synonymous_variant	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.741G>A	2.37:g.135710248G>A			135426718	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Silent	SNP	ENST00000264157.5	37	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	G	7.698	0.692541	0.15039	.	.	ENSG00000082258	ENST00000452521;ENST00000438691	.	.	.	5.7	-2.26	0.06867	.	.	.	.	.	T	0.40119	0.1104	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30937	-0.9961	4	.	.	.	.	2.5371	0.04716	0.4427:0.0904:0.3064:0.1605	.	.	.	.	T	70;38	.	.	A	+	1	0	CCNT2	135426718	0.001000	0.12720	0.991000	0.47740	0.854000	0.48673	-1.478000	0.02329	-0.143000	0.11334	0.650000	0.86243	GCC		0.308	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		A	135710248	G	A	135710248	2	1	61	1	0	0	0	0	0	0	0	1	2941	1074	38	1		1	CCNT2	2	135710248	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2167849	135710248	107489125	1646	9631										
CCNT2	905	broad.mit.edu	37	chr2	135711329	135711329	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataattcctcagaaaatgtCtttagataaatatagagaaa	5	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135711329C>A	ENST00000264157.5	+	9	1334	c.1304C>A	c.(1303-1305)tCt>tAt	p.S435Y	CCNT2_ENST00000295238.6_Missense_Mutation_p.S435Y|CCNT2_ENST00000537343.1_Missense_Mutation_p.S260Y	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	435					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S435Y(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CAGAAAATGTCTTTAGATAAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	50	49					2																	135711329		2197	4299	6496	135427799	SO:0001583	missense	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1304C>A	2.37:g.135711329C>A	ENSP00000264157:p.Ser435Tyr		135427799	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	37	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.266648	0.59540	.	.	ENSG00000082258	ENST00000537343;ENST00000295238;ENST00000264157	T;T	0.39229	1.09;1.14	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.66247	0.2770	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	0.99;1.0;1.0	D;D;D	0.74023	0.912;0.959;0.982	T	0.67821	-0.5571	10	0.87932	D	0	.	19.8769	0.96880	0.0:1.0:0.0:0.0	.	260;435;435	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	Y	260;435;435	ENSP00000295238:S435Y;ENSP00000264157:S435Y	ENSP00000264157:S435Y	S	+	2	0	CCNT2	135427799	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.192000	0.77771	2.712000	0.92718	0.650000	0.86243	TCT		0.388	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		A	135711329	C	A	135711329	3	1	61	1	0	0	0	0	1	0	0	0	2941	913	32	2	1338	2	CCNT2	2	135711329	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1081	135711329	107488044	1647	9632										
YSK4	80122	broad.mit.edu	37	chr2	135738854	135738854	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcaatggcccaaaacggtTtataatactagagattgagc	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135738854T>G	ENST00000375845.3	-	9	3487	c.3457A>C	c.(3457-3459)Aac>Cac	p.N1153H	MAP3K19_ENST00000392918.3_Missense_Mutation_p.N287H|MAP3K19_ENST00000392915.1_3'UTR|MAP3K19_ENST00000358371.4_Missense_Mutation_p.N1040H|MAP3K19_ENST00000375844.3_Missense_Mutation_p.N335H|MAP3K19_ENST00000315513.3_Missense_Mutation_p.N14H|MAP3K19_ENST00000392917.3_Missense_Mutation_p.N285H	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1153	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.N1153H(1)|p.N505H(1)									CCAAAACGGTTTATAATACTA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	2											120	118	119					2																	135738854		2203	4300	6503	135455324	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3457A>C	2.37:g.135738854T>G	ENSP00000365005:p.Asn1153His		135455324	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	T	10.98	1.503299	0.26949	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000437365;ENST00000315513	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.75	5.75	0.90469	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.126714	0.35739	N	0.003019	T	0.41534	0.1163	N	0.10707	0.03	0.20196	N	0.999926	B;B;P;B;P	0.39480	0.158;0.452;0.675;0.417;0.507	B;B;B;B;B	0.37550	0.071;0.228;0.087;0.087;0.253	T	0.42172	-0.9467	10	0.49607	T	0.09	.	11.2765	0.49170	0.0:0.0:0.1524:0.8476	.	285;1040;287;335;1153	B7ZMH9;Q56UN5-3;Q56UN5-4;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	H	1153;1040;335;287;285;543;14	ENSP00000365005:N1153H;ENSP00000351140:N1040H;ENSP00000365004:N335H;ENSP00000376650:N287H;ENSP00000376649:N285H;ENSP00000392827:N543H;ENSP00000321160:N14H	ENSP00000321160:N14H	N	-	1	0	YSK4	135455324	0.980000	0.34600	1.000000	0.80357	0.754000	0.42855	0.611000	0.24268	2.192000	0.70111	0.460000	0.39030	AAC		0.423	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		G	135738854	T	G	135738854	3	3	61	1	0	0	0	0	1	0	0	0	17535	1841	64	4	537	4	YSK4	2	135738854	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27525	135738854	107460519	1648	9633										
YSK4	80122	broad.mit.edu	37	chr2	135741333	135741333	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattttcagaaaatatcttCttttcatttgagatgagaaa	5	5	4	3	rs557761734		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135741333C>A	ENST00000375845.3	-	8	3165	c.3135G>T	c.(3133-3135)aaG>aaT	p.K1045N	MAP3K19_ENST00000392918.3_Missense_Mutation_p.K227N|MAP3K19_ENST00000392915.1_Missense_Mutation_p.K1062N|MAP3K19_ENST00000358371.4_Missense_Mutation_p.K932N|MAP3K19_ENST00000375844.3_Missense_Mutation_p.K227N|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1045							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K1045N(1)|p.K397N(1)									AAAATATCTTCTTTTCATTTG	0.393													C|||	1	0.000199681	0	0.0014	5008	,	,		14179	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											98	99	99					2																	135741333		2203	4300	6503	135457803	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3135G>T	2.37:g.135741333C>A	ENSP00000365005:p.Lys1045Asn		135457803	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	7.876	0.729169	0.15507	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392915;ENST00000437365	T;T;T;T;T;T	0.74106	-0.6;-0.59;-0.53;-0.81;1.66;-0.72	5.39	2.5	0.30297	Protein kinase-like domain (1);	0.121115	0.37261	N	0.002165	T	0.68531	0.3011	L	0.60455	1.87	0.58432	D	0.999999	B;B;B;B;B	0.32382	0.169;0.005;0.368;0.005;0.105	B;B;B;B;B	0.36845	0.063;0.011;0.234;0.011;0.028	T	0.64024	-0.6504	10	0.56958	D	0.05	.	6.8407	0.23961	0.4809:0.4372:0.0:0.0818	.	932;227;1062;227;1045	Q56UN5-3;Q56UN5-4;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	N	1045;932;227;227;1062;435	ENSP00000365005:K1045N;ENSP00000351140:K932N;ENSP00000365004:K227N;ENSP00000376650:K227N;ENSP00000376647:K1062N;ENSP00000392827:K435N	ENSP00000351140:K932N	K	-	3	2	YSK4	135457803	0.764000	0.28473	0.997000	0.53966	0.104000	0.19210	0.694000	0.25512	0.349000	0.23975	0.549000	0.68633	AAG		0.393	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		A	135741333	C	A	135741333	3	1	61	1	0	0	0	0	1	0	0	0	17535	912	32	2	863	2	YSK4	2	135741333	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2479	135741333	107458040	1649	9634										
YSK4	80122	broad.mit.edu	37	chr2	135744284	135744284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcatttcatatgtgtttTtttctgagaaagtcttgttc	9	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135744284T>C	ENST00000375845.3	-	7	2188	c.2158A>G	c.(2158-2160)Aaa>Gaa	p.K720E	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.K737E|MAP3K19_ENST00000358371.4_Missense_Mutation_p.K607E|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	720							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K72E(1)|p.K720E(1)									ATATGTGTTTTTTTCTGAGAA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	2											107	107	107					2																	135744284		2203	4300	6503	135460754	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2158A>G	2.37:g.135744284T>C	ENSP00000365005:p.Lys720Glu		135460754	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	T	8.666	0.901708	0.17760	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.74106	-0.72;-0.7;1.64;-0.81	5.67	5.67	0.87782	.	0.226096	0.31484	N	0.007571	T	0.66268	0.2772	L	0.29908	0.895	0.80722	D	1	B;P;B	0.41848	0.112;0.763;0.068	B;B;B	0.42361	0.079;0.385;0.036	T	0.69727	-0.5067	10	0.56958	D	0.05	.	11.8581	0.52451	0.0:0.0:0.1458:0.8542	.	607;737;720	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	E	720;607;737;110	ENSP00000365005:K720E;ENSP00000351140:K607E;ENSP00000376647:K737E;ENSP00000392827:K110E	ENSP00000351140:K607E	K	-	1	0	YSK4	135460754	1.000000	0.71417	1.000000	0.80357	0.086000	0.17979	2.495000	0.45337	2.155000	0.67459	0.459000	0.35465	AAA		0.383	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		C	135744284	T	C	135744284	3	2	61	1	0	0	0	0	1	0	0	0	17535	1850	64	4	1844	4	YSK4	2	135744284	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2951	135744284	107455089	1650	9635										
YSK4	80122	broad.mit.edu	37	chr2	135745456	135745456	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctcaaaagacaccaaaGactgccctttttcaaagtga	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135745456G>T	ENST00000375845.3	-	7	1016	c.986C>A	c.(985-987)tCt>tAt	p.S329Y	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.S346Y|MAP3K19_ENST00000358371.4_Missense_Mutation_p.S216Y|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	329							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S329Y(1)									AGACACCAAAGACTGCCCTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	66	65					2																	135745456		2203	4300	6503	135461926	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.986C>A	2.37:g.135745456G>T	ENSP00000365005:p.Ser329Tyr		135461926	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	G	7.911	0.736418	0.15574	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.72394	-0.65;-0.63;1.71	4.67	1.7	0.24286	.	0.196285	0.25361	N	0.031227	T	0.60612	0.2282	L	0.46157	1.445	0.09310	N	0.999999	P;P;P	0.43701	0.688;0.815;0.561	B;B;B	0.43701	0.246;0.428;0.125	T	0.51521	-0.8695	10	0.40728	T	0.16	.	4.9567	0.14044	0.2433:0.2973:0.4594:0.0	.	216;346;329	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	Y	329;216;346	ENSP00000365005:S329Y;ENSP00000351140:S216Y;ENSP00000376647:S346Y	ENSP00000351140:S216Y	S	-	2	0	YSK4	135461926	0.001000	0.12720	0.002000	0.10522	0.108000	0.19459	0.659000	0.24994	0.524000	0.28502	0.637000	0.83480	TCT		0.403	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		T	135745456	G	T	135745456	3	4	61	1	0	0	0	0	1	0	0	0	17535	942	33	2	3016	2	YSK4	2	135745456	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1172	135745456	107453917	1651	9636										
YSK4	80122	broad.mit.edu	37	chr2	135745735	135745735	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgagacttggaatgtttCtttctttttcttttggaaac	8	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135745735C>A	ENST00000375845.3	-	7	737	c.707G>T	c.(706-708)aGa>aTa	p.R236I	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.R253I|MAP3K19_ENST00000358371.4_Missense_Mutation_p.R123I|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	236							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R236I(1)									TGGAATGTTTCTTTCTTTTTC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	113	108					2																	135745735		2203	4300	6503	135462205	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.707G>T	2.37:g.135745735C>A	ENSP00000365005:p.Arg236Ile		135462205	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	5.540	0.284522	0.10513	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.72942	-0.7;-0.69;1.65	4.96	0.796	0.18648	.	0.313760	0.23076	N	0.052210	T	0.58337	0.2115	L	0.35854	1.095	0.19300	N	0.999977	P;P;P	0.49358	0.85;0.923;0.766	B;P;B	0.45276	0.395;0.475;0.222	T	0.53975	-0.8362	10	0.87932	D	0	.	5.2682	0.15611	0.1295:0.5583:0.0:0.3122	.	123;253;236	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	I	236;123;253	ENSP00000365005:R236I;ENSP00000351140:R123I;ENSP00000376647:R253I	ENSP00000351140:R123I	R	-	2	0	YSK4	135462205	0.000000	0.05858	0.002000	0.10522	0.027000	0.11550	-0.045000	0.12003	-0.032000	0.13758	0.557000	0.71058	AGA		0.468	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		A	135745735	C	A	135745735	3	1	61	1	0	0	0	0	1	0	0	0	17535	913	32	2	3295	2	YSK4	2	135745735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279	135745735	107453638	1652	9637										
RAB3GAP1	22930	broad.mit.edu	37	chr2	135851207	135851207	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgttccacaatctatgcaAgatttgctgggtatgaataa	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135851207A>C	ENST00000264158.8	+	5	349	c.306A>C	c.(304-306)caA>caC	p.Q102H	RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.Q102H|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.Q58H	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	102					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.Q102H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		AATCTATGCAAGATTTGCTGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											195	181	186					2																	135851207		2203	4300	6503	135567677	SO:0001583	missense	22930			D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.306A>C	2.37:g.135851207A>C	ENSP00000264158:p.Gln102His		135567677	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824147	0.50739	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.46451	0.89;0.87;0.89	5.63	1.98	0.26296	.	0.000000	0.85682	D	0.000000	T	0.31513	0.0799	L	0.51422	1.61	0.42704	D	0.993625	P;B	0.37955	0.612;0.303	B;B	0.37091	0.241;0.241	T	0.05550	-1.0878	10	0.16896	T	0.51	-17.2886	8.3479	0.32284	0.5982:0.0:0.4018:0.0	.	102;102	C9J837;Q15042	.;RB3GP_HUMAN	H	102;58;102	ENSP00000264158:Q102H;ENSP00000444306:Q58H;ENSP00000411418:Q102H	ENSP00000264158:Q102H	Q	+	3	2	RAB3GAP1	135567677	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.972000	0.29409	0.491000	0.27793	0.533000	0.62120	CAA		0.353	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		C	135851207	A	C	135851207	3	2	61	1	0	0	0	0	1	0	0	0	12972	69	3	4	324	4	RAB3GAP1	2	135851207	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	105472	135851207	107348166	1653	9638										
RAB3GAP1	22930	broad.mit.edu	37	chr2	135872890	135872890	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcgaaatggttcatcttaGaaaagtgccaaatcagtaca	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135872890G>T	ENST00000264158.8	+	7	630	c.587G>T	c.(586-588)aGa>aTa	p.R196I	RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.R196I|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.R152I	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	196					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.R196I(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		GTTCATCTTAGAAAAGTGCCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											157	140	146					2																	135872890		2203	4300	6503	135589360	SO:0001583	missense	22930			D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.587G>T	2.37:g.135872890G>T	ENSP00000264158:p.Arg196Ile		135589360	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.929588	0.92389	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.51325	0.71;0.72;0.71	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.51346	0.1669	L	0.55481	1.735	0.80722	D	1	P;P	0.49961	0.93;0.93	P;P	0.45506	0.483;0.483	T	0.57329	-0.7830	10	0.59425	D	0.04	-1.5292	18.6179	0.91310	0.0:0.0:1.0:0.0	.	196;196	C9J837;Q15042	.;RB3GP_HUMAN	I	196;152;196	ENSP00000264158:R196I;ENSP00000444306:R152I;ENSP00000411418:R196I	ENSP00000264158:R196I	R	+	2	0	RAB3GAP1	135589360	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.764000	0.85297	2.482000	0.83794	0.650000	0.86243	AGA		0.403	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		T	135872890	G	T	135872890	3	4	61	1	0	0	0	0	1	0	0	0	12972	942	33	2	613	2	RAB3GAP1	2	135872890	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21683	135872890	107326483	1654	9639										
ZRANB3	84083	broad.mit.edu	37	chr2	135965372	135965372	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggactgtgtatggatttaGaaatgggacacaggctccat	12	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:135965372G>T	ENST00000264159.6	-	19	2757	c.2641C>A	c.(2641-2643)Cta>Ata	p.L881I	ZRANB3_ENST00000536680.1_Missense_Mutation_p.L879I|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000401392.1_Missense_Mutation_p.L879I	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	881					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)	p.L344I(1)|p.L881I(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		TATGGATTTAGAAATGGGACA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	2											75	70	71					2																	135965372		1903	4130	6033	135681842	SO:0001583	missense	84083			AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2641C>A	2.37:g.135965372G>T	ENSP00000264159:p.Leu881Ile		135681842	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.276135	0.40294	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.91011	-2.77;-2.77;-2.75	6.03	5.15	0.70609	.	0.483859	0.19460	N	0.113720	D	0.90290	0.6963	M	0.73962	2.25	0.22446	N	0.999093	B;B	0.26400	0.148;0.145	B;B	0.29598	0.053;0.104	D	0.83591	0.0123	10	0.51188	T	0.08	-20.0611	13.3259	0.60459	0.0733:0.0:0.9267:0.0	.	881;879	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	I	344;344;879;881;879	ENSP00000383979:L879I;ENSP00000264159:L881I;ENSP00000441320:L879I	ENSP00000264159:L881I	L	-	1	2	ZRANB3	135681842	0.021000	0.18746	0.130000	0.21974	0.135000	0.20990	0.980000	0.29513	1.563000	0.49615	-0.140000	0.14226	CTA		0.388	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		T	135965372	G	T	135965372	3	4	61	1	0	0	0	0	1	0	0	0	18263	933	33	2	610	2	ZRANB3	2	135965372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92482	135965372	107234001	1655	9640										
R3HDM1	23518	broad.mit.edu	37	chr2	136374262	136374262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaaagttaaagctagttCggagccttgcagtgtgtgaa	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136374262C>T	ENST00000264160.4	+	5	608	c.238C>T	c.(238-240)Cgg>Tgg	p.R80W	R3HDM1_ENST00000409478.1_Intron|R3HDM1_ENST00000410054.1_Intron|R3HDM1_ENST00000329971.3_Intron|R3HDM1_ENST00000409606.1_Missense_Mutation_p.R80W	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	80							poly(A) RNA binding (GO:0044822)	p.R80W(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		AAAGCTAGTTCGGAGCCTTGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	50	51					2																	136374262		2203	4300	6503	136090732	SO:0001583	missense	23518			D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.238C>T	2.37:g.136374262C>T	ENSP00000264160:p.Arg80Trp		136090732	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154337	0.78114	.	.	ENSG00000048991	ENST00000264160;ENST00000409606	T;T	0.56444	0.48;0.46	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.72894	2.215	0.80722	D	1	D;D	0.65815	0.995;0.995	P;P	0.50231	0.635;0.635	T	0.67133	-0.5747	10	0.87932	D	0	-11.9555	14.6469	0.68767	0.1455:0.8545:0.0:0.0	.	80;80	E9PBB4;Q15032	.;R3HD1_HUMAN	W	80	ENSP00000264160:R80W;ENSP00000387010:R80W	ENSP00000264160:R80W	R	+	1	2	R3HDM1	136090732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.023000	0.76437	2.689000	0.91719	0.585000	0.79938	CGG		0.393	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136374262	C	T	136374262	3	4	61	1	0	0	0	0	1	0	0	0	12924	875	31	1	248	1	R3HDM1	2	136374262	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	408890	136374262	106825111	1656	9641										
R3HDM1	23518	broad.mit.edu	37	chr2	136396663	136396663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgatagttctggaagcaGcaaaagcataggcaggcttt	13	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136396663G>T	ENST00000264160.4	+	14	1560	c.1190G>T	c.(1189-1191)aGc>aTc	p.S397I	R3HDM1_ENST00000443537.2_3'UTR|R3HDM1_ENST00000409478.1_Missense_Mutation_p.S353I|R3HDM1_ENST00000410054.1_Missense_Mutation_p.S341I|R3HDM1_ENST00000329971.3_Missense_Mutation_p.S353I|R3HDM1_ENST00000409606.1_Missense_Mutation_p.S397I	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	397							poly(A) RNA binding (GO:0044822)	p.S397I(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		TCTGGAAGCAGCAAAAGCATA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											77	84	82					2																	136396663		2202	4300	6502	136113133	SO:0001583	missense	23518			D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.1190G>T	2.37:g.136396663G>T	ENSP00000264160:p.Ser397Ile		136113133	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.75|18.75	3.690775|3.690775	0.68271|0.68271	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000441871;ENST00000429703;ENST00000425804|ENST00000422577;ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606	.|T;T;T;T;T	.|0.33654	.|1.42;1.4;1.42;1.4;1.4	5.31|5.31	4.4|4.4	0.53042|0.53042	.|.	.|0.035497	.|0.85682	.|D	.|0.000000	T|T	0.51839|0.51839	0.1698|0.1698	L|L	0.50333|0.50333	1.59|1.59	0.33876|0.33876	D|D	0.635557|0.635557	.|P;D;D;D	.|0.71674	.|0.937;0.997;0.998;0.998	.|P;P;D;D	.|0.78314	.|0.735;0.895;0.991;0.991	T|T	0.63060|0.63060	-0.6721|-0.6721	5|10	.|0.38643	.|T	.|0.18	-1.1046|-1.1046	13.116|13.116	0.59299|0.59299	0.0806:0.0:0.9194:0.0|0.0806:0.0:0.9194:0.0	.|.	.|353;397;341;397	.|G5E9G8;E9PBB4;E9PG42;Q15032	.|.;.;.;R3HD1_HUMAN	H|I	88;85;65|353;353;397;353;341;397	.|ENSP00000386457:S353I;ENSP00000264160:S397I;ENSP00000331396:S353I;ENSP00000386877:S341I;ENSP00000387010:S397I	.|ENSP00000264160:S397I	Q|S	+|+	3|2	2|0	R3HDM1|R3HDM1	136113133|136113133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.939000|4.939000	0.63526|0.63526	1.163000|1.163000	0.42636|0.42636	0.655000|0.655000	0.94253|0.94253	CAG|AGC		0.418	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136396663	G	T	136396663	3	4	61	1	0	0	0	0	1	0	0	0	12924	971	34	2	1236	2	R3HDM1	2	136396663	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22401	136396663	106802710	1657	9642										
LCT	3938	broad.mit.edu	37	chr2	136545931	136545931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcaattcctgttggcttCgttgtgttttcccttgctta	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136545931C>T	ENST00000264162.2	-	17	5757	c.5747G>A	c.(5746-5748)cGa>cAa	p.R1916Q		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1916					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.R1916Q(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTGTTGGCTTCGTTGTGTTTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											243	231	235					2																	136545931		2203	4300	6503	136262401	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.5747G>A	2.37:g.136545931C>T	ENSP00000264162:p.Arg1916Gln		136262401	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	8.337	0.827887	0.16749	.	.	ENSG00000115850	ENST00000264162	T	0.26660	1.72	5.64	1.82	0.25136	.	0.737088	0.12638	N	0.451587	T	0.09555	0.0235	N	0.03608	-0.345	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.36768	-0.9734	10	0.20046	T	0.44	0.0586	5.3304	0.15930	0.0724:0.2707:0.5186:0.1383	.	1916	P09848	LPH_HUMAN	Q	1916	ENSP00000264162:R1916Q	ENSP00000264162:R1916Q	R	-	2	0	LCT	136262401	0.000000	0.05858	0.004000	0.12327	0.030000	0.12068	0.400000	0.20932	0.052000	0.16007	-0.796000	0.03273	CGA		0.463	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136545931	C	T	136545931	3	4	61	1	0	0	0	0	1	0	0	0	8715	884	31	1	40	1	LCT	2	136545931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149268	136545931	106653442	1658	9643										
LCT	3938	broad.mit.edu	37	chr2	136566282	136566282	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttttgtgctgcacgattCtggagtagtacgtgttgagg	15	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136566282C>A	ENST00000264162.2	-	8	3645	c.3635G>T	c.(3634-3636)aGa>aTa	p.R1212I	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1212	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.R1212I(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTGCACGATTCTGGAGTAGTA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	2											205	175	185					2																	136566282		2203	4300	6503	136282752	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.3635G>T	2.37:g.136566282C>A	ENSP00000264162:p.Arg1212Ile		136282752	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	7.784	0.710079	0.15239	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.33654	1.4	5.76	0.0582	0.14326	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.342024	0.35291	N	0.003317	T	0.25494	0.0620	L	0.29908	0.895	0.26718	N	0.970838	B	0.30727	0.292	B	0.38500	0.275	T	0.17228	-1.0376	10	0.52906	T	0.07	-2.5035	4.8827	0.13688	0.1466:0.3758:0.0:0.4776	rs35564057	1212	P09848	LPH_HUMAN	I	1212;644	ENSP00000264162:R1212I	ENSP00000264162:R1212I	R	-	2	0	LCT	136282752	0.000000	0.05858	0.001000	0.08648	0.317000	0.28152	-0.151000	0.10175	0.053000	0.16036	-0.253000	0.11424	AGA		0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136566282	C	A	136566282	3	1	61	1	0	0	0	0	1	0	0	0	8715	913	32	2	2188	2	LCT	2	136566282	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20351	136566282	106633091	1659	9644										
LCT	3938	broad.mit.edu	37	chr2	136567502	136567502	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaaccagaagggccttcGaagccatcaatgagggaacg	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136567502G>A	ENST00000264162.2	-	8	2425	c.2415C>T	c.(2413-2415)ttC>ttT	p.F805F	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	805	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.F805F(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AAGGGCCTTCGAAGCCATCAA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	2																																								136283972	SO:0001819	synonymous_variant	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2415C>T	2.37:g.136567502G>A			136283972	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.448	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136567502	G	A	136567502	2	1	61	1	0	0	0	0	0	0	0	1	8715	1049	37	1		1	LCT	2	136567502	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1220	136567502	106631871	1660	9645										
LCT	3938	broad.mit.edu	37	chr2	136594269	136594269	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccgaaggagtggaaggcGaatgtggcatagtcggcgaa	16	8	0	0	rs201744785		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136594269G>A	ENST00000264162.2	-	1	481	c.471C>T	c.(469-471)ttC>ttT	p.F157F		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	157	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.F157F(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGTGGAAGGCGAATGTGGCAT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2											106	94	98					2																	136594269		2203	4300	6503	136310739	SO:0001819	synonymous_variant	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.471C>T	2.37:g.136594269G>A			136310739	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136594269	G	A	136594269	2	1	61	1	0	0	0	0	0	0	0	1	8715	1049	37	1		1	LCT	2	136594269	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26767	136594269	106605104	1661	9646										
MCM6	4175	broad.mit.edu	37	chr2	136614333	136614333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaaggataaagaagagatCgaatcgggacatgatgggag	14	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:136614333C>T	ENST00000264156.2	-	11	1651	c.1591G>A	c.(1591-1593)Gat>Aat	p.D531N	MCM6_ENST00000492091.1_Intron	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	531	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)	p.D531N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		AAGAAGAGATCGAATCGGGAC	0.408																																					Ovarian(196;141 2104 8848 24991 25939)											1	Substitution - Missense(1)	large_intestine(1)	2											134	130	132					2																	136614333		2203	4300	6503	136330803	SO:0001583	missense	4175				CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"MIS5 homolog (S.pombe)"	601806	"minichromosome maintenance deficient (mis5, S. pombe) 6", "MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)", "minichromosome maintenance deficient 6 homolog (S. cerevisiae)"				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.1591G>A	2.37:g.136614333C>T	ENSP00000264156:p.Asp531Asn		136330803	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	37	CCDS2179.1	.	.	.	.	.	.	.	.	.	.	C	35	5.452722	0.96223	.	.	ENSG00000076003	ENST00000264156	T	0.18174	2.23	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.66567	0.2802	H	0.99697	4.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82808	-0.0274	10	0.87932	D	0	-24.4756	19.9601	0.97247	0.0:1.0:0.0:0.0	.	531	Q14566	MCM6_HUMAN	N	531	ENSP00000264156:D531N	ENSP00000264156:D531N	D	-	1	0	MCM6	136330803	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.683000	0.84093	2.720000	0.93068	0.655000	0.94253	GAT		0.408	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		T	136614333	C	T	136614333	3	4	61	1	0	0	0	0	1	0	0	0	9421	884	31	1	902	1	MCM6	2	136614333	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20064	136614333	106585040	1662	9647										
THSD7B	80731	broad.mit.edu	37	chr2	137814327	137814327	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggttgcaaatgaaatatgCgaacactttgcccttcagcc	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:137814327C>T	ENST00000409968.1	+	3	655	c.477C>T	c.(475-477)tgC>tgT	p.C159C	THSD7B_ENST00000272643.3_Silent_p.C159C|THSD7B_ENST00000543459.1_Silent_p.C18C|THSD7B_ENST00000413152.2_Silent_p.C128C			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	159	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.C159C(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATGAAATATGCGAACACTTTG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	2											143	147	146					2																	137814327		2030	4184	6214	137530797	SO:0001819	synonymous_variant	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.477C>T	2.37:g.137814327C>T			137530797		Silent	SNP	ENST00000409968.1	37																																																																																					0.522	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	137814327	C	T	137814327	2	4	61	1	0	0	0	0	0	0	0	1	15919	776	27	1		1	THSD7B	2	137814327	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1199994	137814327	105385046	1663	9648										
THSD7B	80731	broad.mit.edu	37	chr2	137917830	137917830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgggacccgccccgttgCcctctcagctctgcaatatc	10	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:137917830C>T	ENST00000409968.1	+	6	1595	c.1417C>T	c.(1417-1419)Ccc>Tcc	p.P473S	THSD7B_ENST00000272643.3_Missense_Mutation_p.P473S|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000485379.1_3'UTR|THSD7B_ENST00000413152.2_Missense_Mutation_p.P442S			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	473	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.P473S(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CGCCCCGTTGCCCTCTCAGCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											170	168	169					2																	137917830		2022	4173	6195	137634300	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1417C>T	2.37:g.137917830C>T	ENSP00000387145:p.Pro473Ser		137634300		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	4.534	0.099194	0.08681	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.59502	0.26;0.26;0.26	5.96	2.76	0.32466	.	0.192472	0.56097	D	0.000039	T	0.25044	0.0608	N	0.01438	-0.865	0.35270	D	0.78041	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.20739	-1.0266	10	0.09590	T	0.72	.	11.1064	0.48205	0.1078:0.2224:0.6698:0.0	.	473;442	Q9C0I4;C9JKN6	THS7B_HUMAN;.	S	473;473;442	ENSP00000387145:P473S;ENSP00000272643:P473S;ENSP00000413841:P442S	ENSP00000272643:P473S	P	+	1	0	THSD7B	137634300	0.065000	0.20965	0.710000	0.30468	0.029000	0.11900	0.291000	0.18994	0.853000	0.35312	-0.171000	0.13296	CCC		0.517	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	137917830	C	T	137917830	3	4	61	1	0	0	0	0	1	0	0	0	15919	739	26	3	1342	3	THSD7B	2	137917830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103503	137917830	105281543	1664	9649										
THSD7B	80731	broad.mit.edu	37	chr2	138000044	138000044	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgtccagattctactcGacctgaaactgtgcgcccct	8	14	1	3	rs76693568	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:138000044G>A	ENST00000409968.1	+	10	2346	c.2168G>A	c.(2167-2169)cGa>cAa	p.R723Q	THSD7B_ENST00000272643.3_Missense_Mutation_p.R723Q|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Missense_Mutation_p.R692Q			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	723	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.R723Q(2)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		GATTCTACTCGACCTGAAACT	0.458													G|||	21	0.00419329	0	0	5008	,	,		19203	0.0208		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	2											138	130	133					2																	138000044		1958	4140	6098	137716514	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2168G>A	2.37:g.138000044G>A	ENSP00000387145:p.Arg723Gln		137716514		Missense_Mutation	SNP	ENST00000409968.1	37		15	0.006868131868131868	0	0.0	0	0.0	15	0.026223776223776224	0	0.0	G	22.5	4.303943	0.81136	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.61627	0.09;0.09;0.09	5.78	5.78	0.91487	.	0.052700	0.85682	D	0.000000	T	0.53834	0.1821	M	0.67517	2.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.65034	-0.6266	10	0.40728	T	0.16	.	20.0124	0.97464	0.0:0.0:1.0:0.0	.	723;692	Q9C0I4;C9JKN6	THS7B_HUMAN;.	Q	723;723;692	ENSP00000387145:R723Q;ENSP00000272643:R723Q;ENSP00000413841:R692Q	ENSP00000272643:R723Q	R	+	2	0	THSD7B	137716514	1.000000	0.71417	0.964000	0.40570	0.189000	0.23516	9.230000	0.95299	2.749000	0.94314	0.655000	0.94253	CGA		0.458	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		A	138000044	G	A	138000044	3	1	61	1	0	0	0	0	1	0	0	0	15919	1058	37	1	2109	1	THSD7B	2	138000044	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82214	138000044	105199329	1665	9650										
LRP1B	53353	broad.mit.edu	37	chr2	141055480	141055480	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgacaaaaatcctcacaGactgtcttaccacagtttgg	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141055480G>T	ENST00000389484.3	-	84	13835	c.12864C>A	c.(12862-12864)gtC>gtA	p.V4288V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4288	EGF-like 19. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.V4288V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AATCCTCACAGACTGTCTTAC	0.468										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - coding silent(1)	large_intestine(1)	2											127	131	130					2																	141055480		2203	4300	6503	140771950	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12864C>A	2.37:g.141055480G>T			140771950	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.304345	0.23736	.	.	ENSG00000168702	ENST00000437977;ENST00000442974	.	.	.	6.08	4.25	0.50352	.	.	.	.	.	T	0.54464	0.1860	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50482	-0.8823	4	.	.	.	.	5.1534	0.15021	0.1299:0.1185:0.6289:0.1226	.	.	.	.	Y	520;20	.	.	S	-	2	0	LRP1B	140771950	0.801000	0.28930	1.000000	0.80357	0.978000	0.69477	-0.107000	0.10873	0.869000	0.35703	0.655000	0.94253	TCT		0.468	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141055480	G	T	141055480	2	4	61	1	0	0	0	0	0	0	0	1	8984	929	33	2		2	LRP1B	2	141055480	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3055436	141055480	102143893	1666	9651										
LRP1B	53353	broad.mit.edu	37	chr2	141081480	141081480	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatctagttgtttataacGatgagatatcaaaacacctt	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141081480G>A	ENST00000389484.3	-	81	13467	c.12496C>T	c.(12496-12498)Cgt>Tgt	p.R4166C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4166					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.R4166C(2)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		TGTTTATAACGATGAGATATC	0.244										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											50	57	55					2																	141081480		2201	4288	6489	140797950	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12496C>T	2.37:g.141081480G>A	ENSP00000374135:p.Arg4166Cys		140797950	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.576837	0.86645	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91464	-2.85	5.37	5.37	0.77165	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000001	D	0.92335	0.7568	M	0.61703	1.905	0.58432	D	0.999999	D	0.71674	0.998	P	0.50791	0.65	D	0.92577	0.6071	10	0.56958	D	0.05	.	19.4645	0.94932	0.0:0.0:1.0:0.0	.	4166	Q9NZR2	LRP1B_HUMAN	C	4166;4104	ENSP00000374135:R4166C	ENSP00000374135:R4166C	R	-	1	0	LRP1B	140797950	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.363000	0.97131	2.679000	0.91253	0.655000	0.94253	CGT		0.244	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141081480	G	A	141081480	3	1	61	1	0	0	0	0	1	0	0	0	8984	1058	37	1	1347	1	LRP1B	2	141081480	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26000	141081480	102117893	1667	9652										
LRP1B	53353	broad.mit.edu	37	chr2	141122262	141122262	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcttcatcagagttgtctCcacagtcgtcctctccatca	8	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141122262C>A	ENST00000389484.3	-	72	12070	c.11099G>T	c.(11098-11100)gGa>gTa	p.G3700V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3700	LDL-receptor class A 30. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.G3700V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AGAGTTGTCTCCACAGTCGTC	0.408										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											111	109	110					2																	141122262		2203	4299	6502	140838732	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.11099G>T	2.37:g.141122262C>A	ENSP00000374135:p.Gly3700Val		140838732	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.643641	0.87859	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95482	-3.72	5.58	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.97414	0.9154	M	0.81179	2.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97041	0.9757	10	0.35671	T	0.21	.	14.8134	0.70013	0.0:0.9304:0.0:0.0696	.	3700	Q9NZR2	LRP1B_HUMAN	V	3700;3638	ENSP00000374135:G3700V	ENSP00000374135:G3700V	G	-	2	0	LRP1B	140838732	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.705000	0.68355	1.500000	0.48636	0.655000	0.94253	GGA		0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141122262	C	A	141122262	3	1	61	1	0	0	0	0	1	0	0	0	8984	855	30	2	2780	2	LRP1B	2	141122262	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40782	141122262	102077111	1668	9653										
LRP1B	53353	broad.mit.edu	37	chr2	141267580	141267580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtcggggcacgcaggcaCgagagccctggcagctgaac	15	12	0	2	rs143765896	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141267580C>T	ENST00000389484.3	-	52	9286	c.8315G>A	c.(8314-8316)cGt>cAt	p.R2772H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2772	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.R2772H(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CACGCAGGCACGAGAGCCCTG	0.512										TSP Lung(27;0.18)			T|||	3	0.000599042	0.0015	0	5008	,	,		19641	0		0.001	False		,,,				2504	0				Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2						T	HIS/ARG	4,4402	825.9+/-416.6	0,4,2199	125	114	118		8315	0	0.8	2	dbSNP_134	118	0,8600		0,0,4300	yes	missense	LRP1B	NM_018557.2	29	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	2772/4600	141267580	4,13002	2203	4300	6503	140984050	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8315G>A	2.37:g.141267580C>T	ENSP00000374135:p.Arg2772His		140984050	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	7.156	0.584653	0.13749	9.08E-4	0.0	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.41758	0.99	6.17	0.0293	0.14162	.	0.148373	0.46145	N	0.000303	T	0.18002	0.0432	N	0.04820	-0.15	0.19775	N	0.999956	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	10	0.12766	T	0.61	.	11.0651	0.47970	0.0:0.3639:0.0:0.6361	.	2772	Q9NZR2	LRP1B_HUMAN	H	2772;2710	ENSP00000374135:R2772H	ENSP00000374135:R2772H	R	-	2	0	LRP1B	140984050	1.000000	0.71417	0.845000	0.33349	0.948000	0.59901	1.239000	0.32719	-0.221000	0.09973	-0.254000	0.11334	CGT		0.512	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141267580	C	T	141267580	3	4	61	1	0	0	0	0	1	0	0	0	8984	536	19	1	5644	1	LRP1B	2	141267580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145318	141267580	101931793	1669	9654										
LRP1B	53353	broad.mit.edu	37	chr2	141283846	141283846	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatctgcacaatctatgttCtggttgcatcgtgctgatct	9	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141283846C>A	ENST00000389484.3	-	48	8807	c.7836G>T	c.(7834-7836)caG>caT	p.Q2612H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2612	LDL-receptor class A 13. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.Q2612H(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AATCTATGTTCTGGTTGCATC	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											164	141	149					2																	141283846		2203	4300	6503	141000316	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7836G>T	2.37:g.141283846C>A	ENSP00000374135:p.Gln2612His		141000316	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.440408	0.63067	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95554	-3.74	5.08	3.93	0.45458	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.94118	0.8114	N	0.17922	0.545	0.47862	D	0.999536	D	0.76494	0.999	D	0.87578	0.998	D	0.91502	0.5220	10	0.28530	T	0.3	.	8.5839	0.33646	0.0:0.7936:0.0:0.2064	.	2612	Q9NZR2	LRP1B_HUMAN	H	2612;2550	ENSP00000374135:Q2612H	ENSP00000374135:Q2612H	Q	-	3	2	LRP1B	141000316	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.797000	0.55514	1.134000	0.42165	0.650000	0.86243	CAG		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141283846	C	A	141283846	3	1	61	1	0	0	0	0	1	0	0	0	8984	912	32	2	6139	2	LRP1B	2	141283846	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16266	141283846	101915527	1670	9655										
LRP1B	53353	broad.mit.edu	37	chr2	141291605	141291605	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacctttacaatctaattCatcagagttgtctccgcagt	5	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141291605C>T	ENST00000389484.3	-	47	8718	c.7747G>A	c.(7747-7749)Gaa>Aaa	p.E2583K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2583	LDL-receptor class A 12. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.E2583K(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CAATCTAATTCATCAGAGTTG	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											118	112	114					2																	141291605		2203	4300	6503	141008075	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7747G>A	2.37:g.141291605C>T	ENSP00000374135:p.Glu2583Lys		141008075	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553193	0.96501	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97924	-4.61	5.42	5.42	0.78866	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.99348	0.9771	H	0.98426	4.23	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.98446	1.0589	10	0.66056	D	0.02	.	19.5918	0.95518	0.0:1.0:0.0:0.0	.	2583	Q9NZR2	LRP1B_HUMAN	K	2583;2521	ENSP00000374135:E2583K	ENSP00000374135:E2583K	E	-	1	0	LRP1B	141008075	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.399000	0.79935	2.700000	0.92200	0.563000	0.77884	GAA		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141291605	C	T	141291605	3	4	61	1	0	0	0	0	1	0	0	0	8984	835	29	3	6232	3	LRP1B	2	141291605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7759	141291605	101907768	1671	9656										
LRP1B	53353	broad.mit.edu	37	chr2	141359089	141359089	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgatgacagcttccctgtCaaatgctccaggccgagtct	11	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141359089C>T	ENST00000389484.3	-	42	7890	c.6919G>A	c.(6919-6921)Gac>Aac	p.D2307N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2307					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.D2307N(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		GCTTCCCTGTCAAATGCTCCA	0.468										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											154	128	137					2																	141359089		2203	4300	6503	141075559	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6919G>A	2.37:g.141359089C>T	ENSP00000374135:p.Asp2307Asn		141075559	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	9.533	1.111268	0.20714	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91180	-2.8	5.04	1.97	0.26223	Six-bladed beta-propeller, TolB-like (1);	0.466272	0.22246	N	0.062610	T	0.70587	0.3241	N	0.02916	-0.46	0.23975	N	0.996299	B	0.02656	0.0	B	0.01281	0.0	T	0.57917	-0.7728	10	0.11485	T	0.65	.	3.967	0.09436	0.0:0.32:0.4746:0.2054	.	2307	Q9NZR2	LRP1B_HUMAN	N	2307;2245	ENSP00000374135:D2307N	ENSP00000374135:D2307N	D	-	1	0	LRP1B	141075559	0.781000	0.28676	0.486000	0.27416	0.959000	0.62525	0.256000	0.18351	1.206000	0.43276	0.561000	0.74099	GAC		0.468	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141359089	C	T	141359089	3	4	61	1	0	0	0	0	1	0	0	0	8984	826	29	3	7080	3	LRP1B	2	141359089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67484	141359089	101840284	1672	9657										
LRP1B	53353	broad.mit.edu	37	chr2	141607890	141607890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgcataaagaagaaattTtttcatttctaaaaaagaaa	4	4	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141607890T>C	ENST00000389484.3	-	29	5691	c.4720A>G	c.(4720-4722)Aaa>Gaa	p.K1574E		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1574					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.K1574E(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AGAAGAAATTTTTTCATTTCT	0.294										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											37	36	36					2																	141607890		2202	4300	6502	141324360	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4720A>G	2.37:g.141607890T>C	ENSP00000374135:p.Lys1574Glu		141324360	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	17.04	3.288061	0.59976	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.92595	-2.54;-3.07	5.32	5.32	0.75619	.	0.072807	0.53938	U	0.000049	D	0.83681	0.5307	L	0.32530	0.975	0.38275	D	0.942259	B;P	0.43094	0.021;0.799	B;B	0.32762	0.013;0.152	D	0.84576	0.0658	10	0.06099	T	0.92	.	15.2914	0.73868	0.0:0.0:0.0:1.0	.	757;1574	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	E	1574;1512;719	ENSP00000374135:K1574E;ENSP00000413239:K719E	ENSP00000374135:K1574E	K	-	1	0	LRP1B	141324360	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	6.012000	0.70767	2.032000	0.59987	0.260000	0.18958	AAA		0.294	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141607890	T	C	141607890	3	2	61	1	0	0	0	0	1	0	0	0	8984	1850	64	4	9331	4	LRP1B	2	141607890	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	248801	141607890	101591483	1673	9658										
LRP1B	53353	broad.mit.edu	37	chr2	141641429	141641429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccctggggtgttccatggCtcctgctattagtgtagttc	13	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141641429C>T	ENST00000389484.3	-	25	5097	c.4126G>A	c.(4126-4128)Gcc>Acc	p.A1376T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1376					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.A1376T(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		TGTTCCATGGCTCCTGCTATT	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											160	159	159					2																	141641429		2203	4300	6503	141357899	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4126G>A	2.37:g.141641429C>T	ENSP00000374135:p.Ala1376Thr		141357899	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170213	0.57584	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.96200	-3.94;-3.94	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.143679	0.46758	D	0.000278	D	0.92374	0.7580	N	0.14661	0.345	0.41736	D	0.989584	B;P	0.43231	0.387;0.801	P;B	0.44921	0.464;0.438	D	0.92069	0.5663	10	0.38643	T	0.18	.	20.0553	0.97649	0.0:1.0:0.0:0.0	.	559;1376	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	T	1376;1314;521	ENSP00000374135:A1376T;ENSP00000413239:A521T	ENSP00000374135:A1376T	A	-	1	0	LRP1B	141357899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.707000	0.84623	2.803000	0.96430	0.655000	0.94253	GCC		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141641429	C	T	141641429	3	4	61	1	0	0	0	0	1	0	0	0	8984	797	28	3	9941	3	LRP1B	2	141641429	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33539	141641429	101557944	1674	9659										
LRP1B	53353	broad.mit.edu	37	chr2	141747188	141747188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggggatgcagcgattatTctggcatttaaactgatcat	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141747188T>C	ENST00000389484.3	-	17	3654	c.2683A>G	c.(2683-2685)Aat>Gat	p.N895D	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	895	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.N895D(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CAGCGATTATTCTGGCATTTA	0.398										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											126	118	121					2																	141747188		2203	4300	6503	141463658	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2683A>G	2.37:g.141747188T>C	ENSP00000374135:p.Asn895Asp		141463658	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	35	5.435274	0.96150	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91464	-2.85	5.69	5.69	0.88448	.	0.062767	0.64402	U	0.000007	D	0.89438	0.6715	L	0.53617	1.68	0.50039	D	0.999849	P	0.47484	0.896	B	0.43301	0.415	D	0.89853	0.4011	10	0.49607	T	0.09	.	16.2484	0.82467	0.0:0.0:0.0:1.0	.	895	Q9NZR2	LRP1B_HUMAN	D	895;833	ENSP00000374135:N895D	ENSP00000374135:N895D	N	-	1	0	LRP1B	141463658	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.947000	0.87758	2.291000	0.77112	0.533000	0.62120	AAT		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141747188	T	C	141747188	3	2	61	1	0	0	0	0	1	0	0	0	8984	1783	62	4	11416	4	LRP1B	2	141747188	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	105759	141747188	101452185	1675	9660										
LRP1B	53353	broad.mit.edu	37	chr2	141986974	141986974	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctcaattgtttcaaaatTtgcaattaatagtataggtg	6	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:141986974T>G	ENST00000389484.3	-	6	1599	c.628A>C	c.(628-630)Aat>Cat	p.N210H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	210					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.N210H(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		GTTTCAAAATTTGCAATTAAT	0.294										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											32	35	34					2																	141986974		2196	4281	6477	141703444	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.628A>C	2.37:g.141986974T>G	ENSP00000374135:p.Asn210His		141703444	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.908571	0.52439	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91407	-2.84	4.87	4.87	0.63330	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.236010	0.35870	U	0.002940	D	0.87928	0.6301	L	0.57536	1.79	0.26118	N	0.980593	P	0.36733	0.567	B	0.33521	0.165	T	0.82729	-0.0313	10	0.49607	T	0.09	.	14.1588	0.65434	0.0:0.0:0.0:1.0	.	210	Q9NZR2	LRP1B_HUMAN	H	210;148	ENSP00000374135:N210H	ENSP00000374135:N210H	N	-	1	0	LRP1B	141703444	1.000000	0.71417	0.997000	0.53966	0.372000	0.29890	4.409000	0.59768	1.838000	0.53458	0.477000	0.44152	AAT		0.294	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141986974	T	G	141986974	3	3	61	1	0	0	0	0	1	0	0	0	8984	1841	64	4	13515	4	LRP1B	2	141986974	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	239786	141986974	101212399	1676	9661										
KYNU	8942	broad.mit.edu	37	chr2	143712407	143712407	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaagaaatagccctaatGaatgctttgactgtaaattt	8	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:143712407G>T	ENST00000264170.4	+	5	660	c.402G>T	c.(400-402)atG>atT	p.M134I	KYNU_ENST00000375773.2_Missense_Mutation_p.M134I|KYNU_ENST00000409512.1_Missense_Mutation_p.M134I	NM_003937.2	NP_003928.1			kynureninase									p.M134I(1)		large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TAGCCCTAATGAATGCTTTGA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	112	109					2																	143712407		2203	4298	6501	143428877	SO:0001583	missense	8942			U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.402G>T	2.37:g.143712407G>T	ENSP00000264170:p.Met134Ile		143428877		Missense_Mutation	SNP	ENST00000264170.4	37	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547345	0.86022	.	.	ENSG00000115919	ENST00000264170;ENST00000375773;ENST00000409512	D;D;D	0.85702	-2.02;-2.02;-2.02	5.72	4.84	0.62591	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.94098	0.8108	M	0.93898	3.47	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.77004	0.989;0.987	D	0.95542	0.8613	10	0.87932	D	0	.	15.2033	0.73157	0.0678:0.0:0.9322:0.0	.	134;134	Q16719;Q9BVW3	KYNU_HUMAN;.	I	134	ENSP00000264170:M134I;ENSP00000364928:M134I;ENSP00000386731:M134I	ENSP00000264170:M134I	M	+	3	0	KYNU	143428877	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.995000	0.93534	1.554000	0.49487	0.650000	0.86243	ATG		0.294	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998		T	143712407	G	T	143712407	3	4	61	1	0	0	0	0	1	0	0	0	8609	1290	45	2	416	2	KYNU	2	143712407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1725433	143712407	99486966	1677	9662										
ZEB2	9839	broad.mit.edu	37	chr2	145155875	145155875	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtctctttacctgaaatCcttgtttccgctggtacttt	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:145155875C>T	ENST00000558170.2	-	8	4063	c.2879G>A	c.(2878-2880)gGa>gAa	p.G960E	ZEB2_ENST00000303660.4_Missense_Mutation_p.G960E|ZEB2_ENST00000409487.3_Missense_Mutation_p.G960E|ZEB2_ENST00000539609.3_Missense_Mutation_p.G936E	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	960					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.G960E(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		TACCTGAAATCCTTGTTTCCG	0.388																																					Melanoma(33;1235 1264 5755 16332)											1	Substitution - Missense(1)	large_intestine(1)	2											82	80	81					2																	145155875		2203	4300	6503	144872345	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.2879G>A	2.37:g.145155875C>T	ENSP00000454157:p.Gly960Glu		144872345	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023747	0.54683	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487	T;T;T	0.14640	2.5;2.49;2.49	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.38772	0.1053	M	0.61703	1.905	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.997;0.997	D;D;D;D	0.97110	1.0;0.96;0.942;0.942	T	0.03268	-1.1054	10	0.72032	D	0.01	-1.9384	20.1374	0.98035	0.0:1.0:0.0:0.0	.	936;825;959;960	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	E	936;960;960	ENSP00000443792:G936E;ENSP00000302501:G960E;ENSP00000386854:G960E	ENSP00000302501:G960E	G	-	2	0	ZEB2	144872345	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.089000	0.71384	2.763000	0.94921	0.563000	0.77884	GGA		0.388	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		T	145155875	C	T	145155875	3	4	61	1	0	0	0	0	1	0	0	0	17663	855	30	3	777	3	ZEB2	2	145155875	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1443468	145155875	98043498	1678	9663										
ZEB2	9839	broad.mit.edu	37	chr2	145157797	145157797	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaggaaccagaatgggaGaaacgtttcttgcagtttgg	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:145157797G>T	ENST00000558170.2	-	8	2141	c.957C>A	c.(955-957)ttC>ttA	p.F319L	ZEB2_ENST00000303660.4_Missense_Mutation_p.F319L|ZEB2_ENST00000409487.3_Missense_Mutation_p.F319L|ZEB2_ENST00000539609.3_Missense_Mutation_p.F295L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	319					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.F319L(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CAGAATGGGAGAAACGTTTCT	0.368																																					Melanoma(33;1235 1264 5755 16332)											1	Substitution - Missense(1)	large_intestine(1)	2	GRCh37	CI072628	ZEB2	I							48	51	50					2																	145157797		2203	4300	6503	144874267	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.957C>A	2.37:g.145157797G>T	ENSP00000454157:p.Phe319Leu		144874267	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.345550	0.61073	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.69708	0.3141	M	0.82433	2.59	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.979;0.985	D;D;D;D	0.85130	0.997;0.996;0.982;0.977	T	0.73994	-0.3807	10	0.87932	D	0	-8.4777	19.4311	0.94768	0.0:0.0:1.0:0.0	.	295;184;318;319	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	L	314;295;319;319;319;319	ENSP00000443792:F295L;ENSP00000302501:F319L;ENSP00000386854:F319L;ENSP00000395496:F319L;ENSP00000376601:F319L	ENSP00000302501:F319L	F	-	3	2	ZEB2	144874267	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.488000	0.66869	2.590000	0.87494	0.563000	0.77884	TTC		0.368	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		T	145157797	G	T	145157797	3	4	61	1	0	0	0	0	1	0	0	0	17663	933	33	2	2699	2	ZEB2	2	145157797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1922	145157797	98041576	1679	9664										
ACVR2A	92	broad.mit.edu	37	chr2	148672871	148672871	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaagcccagttgcttaacGaatatgtggctgtcaaaata	10	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:148672871G>T	ENST00000241416.7	+	5	1276	c.640G>T	c.(640-642)Gaa>Taa	p.E214*	ACVR2A_ENST00000404590.1_Nonsense_Mutation_p.E214*|ACVR2A_ENST00000535787.1_Nonsense_Mutation_p.E106*	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.E214*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GTTGCTTAACGAATATGTGGC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											131	134	133					2																	148672871		2203	4299	6502	148389341	SO:0001587	stop_gained	92				CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.640G>T	2.37:g.148672871G>T	ENSP00000241416:p.Glu214*		148389341	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Nonsense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	43	10.119343	0.99340	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	.	.	.	5.92	5.92	0.95590	.	0.087632	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	.	.	.	X	214;106;214	.	ENSP00000241416:E214X	E	+	1	0	ACVR2A	148389341	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.822000	0.97130	0.650000	0.86243	GAA		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		T	148672871	G	T	148672871	4	4	61	1	0	0	0	0	0	1	0	0	223	1059	37	2	658	2	ACVR2A	2	148672871	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3515074	148672871	94526502	1680	9665										
ACVR2A	92	broad.mit.edu	37	chr2	148684829	148684829	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgttgactttcctcccaaaGaatctagtctatgatggttg	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:148684829G>T	ENST00000241416.7	+	11	2164	c.1528G>T	c.(1528-1530)Gaa>Taa	p.E510*	ACVR2A_ENST00000404590.1_Nonsense_Mutation_p.E510*|ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000535787.1_Nonsense_Mutation_p.E402*	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	510					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.E510*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TCCTCCCAAAGAATCTAGTCT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											79	71	74					2																	148684829		2203	4300	6503	148401299	SO:0001587	stop_gained	92				CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1528G>T	2.37:g.148684829G>T	ENSP00000241416:p.Glu510*		148401299	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Nonsense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	42	9.683793	0.99238	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	.	.	.	5.88	5.88	0.94601	.	0.098491	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.2187	0.98312	0.0:0.0:1.0:0.0	.	.	.	.	X	510;402;510	.	ENSP00000241416:E510X	E	+	1	0	ACVR2A	148401299	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.780000	0.95670	0.655000	0.94253	GAA		0.398	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		T	148684829	G	T	148684829	4	4	61	1	0	0	0	0	0	1	0	0	223	943	33	2	1570	2	ACVR2A	2	148684829	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11958	148684829	94514544	1681	9666										
MBD5	55777	broad.mit.edu	37	chr2	149247393	149247393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaattcaagaggggctCggctgcccaagaatctagac	13	9	2	4	rs558876535		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149247393C>T	ENST00000407073.1	+	12	4490	c.3493C>T	c.(3493-3495)Cgg>Tgg	p.R1165W	MBD5_ENST00000404807.1_Missense_Mutation_p.R1398W	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1165					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R1165W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AAGAGGGGCTCGGCTGCCCAA	0.473													C|||	1	0.000199681	0	0	5008	,	,		20438	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	2											67	73	71					2																	149247393		2203	4300	6503	148963863	SO:0001583	missense	55777			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3493C>T	2.37:g.149247393C>T	ENSP00000386049:p.Arg1165Trp		148963863	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.348928	0.61183	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.55413	0.54;0.52	6.08	6.08	0.98989	.	0.000000	0.56097	D	0.000025	T	0.62877	0.2464	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65952	-0.6043	10	0.87932	D	0	-6.446	20.6634	0.99662	0.0:1.0:0.0:0.0	.	1398;1165	E9PHH0;Q9P267	.;MBD5_HUMAN	W	1165;1398	ENSP00000386049:R1165W;ENSP00000384672:R1398W	ENSP00000384672:R1398W	R	+	1	2	MBD5	148963863	0.731000	0.28111	0.999000	0.59377	0.987000	0.75469	1.310000	0.33551	2.894000	0.99253	0.655000	0.94253	CGG		0.473	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			T	149247393	C	T	149247393	3	4	61	1	0	0	0	0	1	0	0	0	9377	875	31	1	3519	1	MBD5	2	149247393	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	562564	149247393	93951980	1682	9667										
KIF5C	3800	broad.mit.edu	37	chr2	149679726	149679726	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagggaagccatatgtcttCgacagagtgctacctcccaa	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149679726C>T	ENST00000435030.1	+	2	515	c.147C>T	c.(145-147)ttC>ttT	p.F49F				O60282	KIF5C_HUMAN	kinesin family member 5C	49	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.F49F(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CATATGTCTTCGACAGAGTGC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											85	82	83					2																	149679726		1869	4122	5991	149396196	SO:0001819	synonymous_variant	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.147C>T	2.37:g.149679726C>T			149396196	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																					0.393	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149679726	C	T	149679726	2	4	61	1	0	0	0	0	0	0	0	1	8328	883	31	1		1	KIF5C	2	149679726	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	432333	149679726	93519647	1683	9668										
KIF5C	3800	broad.mit.edu	37	chr2	149803434	149803434	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaatgaacacagctctaGaagtcacagtatcttcctga	7	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149803434G>T	ENST00000435030.1	+	8	979	c.611G>T	c.(610-612)aGa>aTa	p.R204I	KIF5C_ENST00000414838.2_Missense_Mutation_p.R109I|KIF5C_ENST00000397413.1_5'Flank			O60282	KIF5C_HUMAN	kinesin family member 5C	204	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R204I(1)|p.R107I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CACAGCTCTAGAAGTCACAGT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	2											93	85	87					2																	149803434		1831	4097	5928	149511680	SO:0001583	missense	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.611G>T	2.37:g.149803434G>T	ENSP00000393379:p.Arg204Ile		149511680	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.355823	0.95854	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436	D;D	0.87571	-2.27;-2.27	5.64	5.64	0.86602	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93958	0.7238	9	0.87932	D	0	.	19.8946	0.96949	0.0:0.0:1.0:0.0	.	204	O60282	KIF5C_HUMAN	I	204;109;107	ENSP00000393379:R204I;ENSP00000410115:R109I	ENSP00000334176:R107I	R	+	2	0	KIF5C	149511680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.937000	0.99478	0.650000	0.86243	AGA		0.348	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149803434	G	T	149803434	3	4	61	1	0	0	0	0	1	0	0	0	8328	942	33	2	563	2	KIF5C	2	149803434	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123708	149803434	93395939	1684	9669										
KIF5C	3800	broad.mit.edu	37	chr2	149806389	149806389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagggagctgttcttgacGaagctaaaaatatcaataag	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149806389G>A	ENST00000435030.1	+	9	1119	c.751G>A	c.(751-753)Gaa>Aaa	p.E251K	KIF5C_ENST00000414838.2_Missense_Mutation_p.E156K|KIF5C_ENST00000397413.1_Missense_Mutation_p.E19K|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	251	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E154K(1)|p.E251K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TGTTCTTGACGAAGCTAAAAA	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	2											106	103	104					2																	149806389		1923	4141	6064	149514635	SO:0001583	missense	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.751G>A	2.37:g.149806389G>A	ENSP00000393379:p.Glu251Lys		149514635	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.495491	0.96355	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.85088	-1.94;-1.94;-1.94	5.65	5.65	0.86999	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.93048	0.7787	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93046	0.6461	9	0.87932	D	0	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	251	O60282	KIF5C_HUMAN	K	251;156;154;19	ENSP00000393379:E251K;ENSP00000410115:E156K;ENSP00000380560:E19K	ENSP00000334176:E154K	E	+	1	0	KIF5C	149514635	1.000000	0.71417	0.982000	0.44146	0.756000	0.42949	9.657000	0.98554	2.941000	0.99782	0.655000	0.94253	GAA		0.443	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149806389	G	A	149806389	3	1	61	1	0	0	0	0	1	0	0	0	8328	1059	37	1	707	1	KIF5C	2	149806389	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2955	149806389	93392984	1685	9670										
KIF5C	3800	broad.mit.edu	37	chr2	149818509	149818509	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaccatcaagaatacagtCtctgtgaacctagaactgac	7	10	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149818509C>A	ENST00000435030.1	+	11	1361	c.993C>A	c.(991-993)gtC>gtA	p.V331V	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.V99V|KIF5C_ENST00000414838.2_Silent_p.V236V			O60282	KIF5C_HUMAN	kinesin family member 5C	331					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.V234V(2)|p.V331V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		AGAATACAGTCTCTGTGAACC	0.353																																																3	Substitution - coding silent(3)	large_intestine(3)	2											112	103	106					2																	149818509		1826	4091	5917	149526755	SO:0001819	synonymous_variant	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.993C>A	2.37:g.149818509C>A			149526755	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																					0.353	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149818509	C	A	149818509	2	1	61	1	0	0	0	0	0	0	0	1	8328	900	32	2		2	KIF5C	2	149818509	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12120	149818509	93380864	1686	9671										
KIF5C	3800	broad.mit.edu	37	chr2	149837920	149837920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatacaggaggagctgacaCgtctccagattgaaaatgag	12	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149837920C>T	ENST00000435030.1	+	14	1782	c.1414C>T	c.(1414-1416)Cgt>Tgt	p.R472C	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Missense_Mutation_p.R240C|KIF5C_ENST00000414838.2_Missense_Mutation_p.R377C			O60282	KIF5C_HUMAN	kinesin family member 5C	472					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R375C(1)|p.R472C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GGAGCTGACACGTCTCCAGAT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	2											51	51	51					2																	149837920		2061	4249	6310	149546166	SO:0001583	missense	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1414C>T	2.37:g.149837920C>T	ENSP00000393379:p.Arg472Cys		149546166	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	C	29.5	5.012170	0.93346	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.82167	-1.58;-1.58;-1.58	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.91723	0.7383	.	.	.	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76575	0.915;0.988	D	0.92205	0.5771	9	0.87932	D	0	.	19.3716	0.94490	0.0:1.0:0.0:0.0	.	472;38	O60282;Q3LIE3	KIF5C_HUMAN;.	C	472;377;375;240	ENSP00000393379:R472C;ENSP00000410115:R377C;ENSP00000380560:R240C	ENSP00000334176:R375C	R	+	1	0	KIF5C	149546166	1.000000	0.71417	0.976000	0.42696	0.994000	0.84299	7.619000	0.83057	2.805000	0.96524	0.655000	0.94253	CGT		0.453	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149837920	C	T	149837920	3	4	61	1	0	0	0	0	1	0	0	0	8328	536	19	1	1390	1	KIF5C	2	149837920	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19411	149837920	93361453	1687	9672										
KIF5C	3800	broad.mit.edu	37	chr2	149840214	149840214	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaaagggcaactgagatCctgaatttgctgttgaaaga	11	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149840214C>A	ENST00000435030.1	+	15	2018	c.1650C>A	c.(1648-1650)atC>atA	p.I550I	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.I318I|KIF5C_ENST00000414838.2_Silent_p.I455I			O60282	KIF5C_HUMAN	kinesin family member 5C	550					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.I453I(1)|p.I550I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CAACTGAGATCCTGAATTTGC	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	2											85	85	85					2																	149840214		1894	4130	6024	149548460	SO:0001819	synonymous_variant	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1650C>A	2.37:g.149840214C>A			149548460	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																					0.438	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149840214	C	A	149840214	2	1	61	1	0	0	0	0	0	0	0	1	8328	845	30	2		2	KIF5C	2	149840214	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2294	149840214	93359159	1688	9673										
KIF5C	3800	broad.mit.edu	37	chr2	149864533	149864533	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcccagaagcagaaaatTtccttcttggagaataacct	8	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:149864533T>G	ENST00000435030.1	+	23	2870	c.2502T>G	c.(2500-2502)atT>atG	p.I834M	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Missense_Mutation_p.I602M|KIF5C_ENST00000414838.2_Missense_Mutation_p.I739M			O60282	KIF5C_HUMAN	kinesin family member 5C	834					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.I834M(1)|p.I737M(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		AGCAGAAAATTTCCTTCTTGG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	2											72	78	76					2																	149864533		1946	4143	6089	149572779	SO:0001583	missense	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2502T>G	2.37:g.149864533T>G	ENSP00000393379:p.Ile834Met		149572779	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	T	16.78	3.217427	0.58560	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.92446	-3.04;-3.04;-3.04	5.58	0.252	0.15545	.	0.000000	0.85682	D	0.000000	D	0.94847	0.8335	.	.	.	0.40461	D	0.980241	D;D	0.89917	0.995;1.0	D;D	0.78314	0.916;0.991	D	0.92928	0.6361	8	.	.	.	.	10.7888	0.46422	0.0:0.4784:0.0:0.5216	.	834;142	O60282;Q59GB8	KIF5C_HUMAN;.	M	834;739;737;602	ENSP00000393379:I834M;ENSP00000410115:I739M;ENSP00000380560:I602M	.	I	+	3	3	KIF5C	149572779	0.986000	0.35501	0.997000	0.53966	0.984000	0.73092	0.192000	0.17096	-0.173000	0.10761	0.460000	0.39030	ATT		0.547	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		G	149864533	T	G	149864533	3	3	61	1	0	0	0	0	1	0	0	0	8328	1829	64	4	2514	4	KIF5C	2	149864533	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24319	149864533	93334840	1689	9674										
LYPD6	130574	broad.mit.edu	37	chr2	150294316	150294316	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgagacttcacagtgaaaGacattatctacctccatcct	5	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:150294316G>T	ENST00000334166.4	+	2	351	c.94G>T	c.(94-96)Gac>Tac	p.D32Y	LYPD6_ENST00000409381.1_Missense_Mutation_p.D32Y	NM_194317.3	NP_919298.1	Q86Y78	LYPD6_HUMAN	LY6/PLAUR domain containing 6	32						extracellular region (GO:0005576)		p.D32Y(1)		large_intestine(1)|lung(4)	5				BRCA - Breast invasive adenocarcinoma(221;0.0667)		CACAGTGAAAGACATTATCTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											101	93	96					2																	150294316		2203	4300	6503	150002562	SO:0001583	missense	130574			BC047013	CCDS2188.1	2q23.2	2008-02-05			ENSG00000187123	ENSG00000187123			28751	protein-coding gene	gene with protein product		613359				12477932	Standard	NM_001195685		Approved	MGC52057	uc021vqt.1	Q86Y78	OTTHUMG00000131852	ENST00000334166.4:c.94G>T	2.37:g.150294316G>T	ENSP00000334463:p.Asp32Tyr		150002562	B3KWC0|Q4G121|Q53TR3|Q659B1	Missense_Mutation	SNP	ENST00000334166.4	37	CCDS2188.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261635	0.80358	.	.	ENSG00000187123	ENST00000409381;ENST00000334166;ENST00000414420	T;T;T	0.27890	1.64;1.64;1.64	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.54208	0.1844	M	0.65975	2.015	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	T	0.53711	-0.8400	10	0.59425	D	0.04	-8.5246	17.1582	0.86797	0.0:0.0:1.0:0.0	.	32	Q86Y78	LYPD6_HUMAN	Y	32	ENSP00000386413:D32Y;ENSP00000334463:D32Y;ENSP00000392286:D32Y	ENSP00000334463:D32Y	D	+	1	0	LYPD6	150002562	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.863000	0.87023	2.650000	0.89964	0.585000	0.79938	GAC		0.483	LYPD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254800.2	NM_194317		T	150294316	G	T	150294316	3	4	61	1	0	0	0	0	1	0	0	0	9144	942	33	2	96	2	LYPD6	2	150294316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	429783	150294316	92905057	1690	9675										
RND3	390	broad.mit.edu	37	chr2	151331453	151331453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaatcagcacagcatccGaatcagggtaagagaggggg	14	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:151331453G>A	ENST00000375734.2	-	3	533	c.284C>T	c.(283-285)tCg>tTg	p.S95L	RND3_ENST00000263895.4_Missense_Mutation_p.S95L|RND3_ENST00000472416.1_5'UTR|RND3_ENST00000409557.1_5'UTR	NM_001254738.1	NP_001241667.1	P61587	RND3_HUMAN	Rho family GTPase 3	95					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.S95L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.106)		CACAGCATCCGAATCAGGGTA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	94	95					2																	151331453		2203	4300	6503	151039699	SO:0001583	missense	390				CCDS2190.1	2q23.3	2008-02-05	2005-01-24	2005-01-27	ENSG00000115963	ENSG00000115963			671	protein-coding gene	gene with protein product		602924	"ras homolog gene family, member E"	ARHE		8649376	Standard	NM_001254738		Approved	RhoE, Rho8	uc002txe.3	P61587	OTTHUMG00000131859	ENST00000375734.2:c.284C>T	2.37:g.151331453G>A	ENSP00000364886:p.Ser95Leu		151039699	D3DP95|P52199	Missense_Mutation	SNP	ENST00000375734.2	37	CCDS2190.1	.	.	.	.	.	.	.	.	.	.	G	36	5.655655	0.96724	.	.	ENSG00000115963	ENST00000375734;ENST00000263895;ENST00000439275;ENST00000454202	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	6.02	6.02	0.97574	Small GTP-binding protein domain (1);	0.053071	0.85682	D	0.000000	D	0.84005	0.5377	M	0.90705	3.14	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.997	P;P;P	0.59115	0.852;0.814;0.814	D	0.86453	0.1774	10	0.87932	D	0	-3.7159	19.5289	0.95219	0.0:0.0:1.0:0.0	.	95;95;95	B2R838;D3DP96;P61587	.;.;RND3_HUMAN	L	95	ENSP00000364886:S95L;ENSP00000263895:S95L;ENSP00000395997:S95L;ENSP00000411950:S95L	ENSP00000263895:S95L	S	-	2	0	RND3	151039699	1.000000	0.71417	0.836000	0.33094	0.889000	0.51656	9.751000	0.98889	2.865000	0.98341	0.655000	0.94253	TCG		0.463	RND3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254809.1	NM_005168		A	151331453	G	A	151331453	3	1	61	1	0	0	0	0	1	0	0	0	13458	1059	37	1	462	1	RND3	2	151331453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1037137	151331453	91867920	1691	9676										
NMI	9111	broad.mit.edu	37	chr2	152127279	152127279	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacttctccacctccattCtttgcccgttgaaagtgaat	5	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152127279C>A	ENST00000243346.5	-	8	1322	c.852G>T	c.(850-852)aaG>aaT	p.K284N		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	284					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)	p.K284N(1)		endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		CACCTCCATTCTTTGCCCGTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											184	172	176					2																	152127279		2203	4300	6503	151835525	SO:0001583	missense	9111			U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.852G>T	2.37:g.152127279C>A	ENSP00000243346:p.Lys284Asn		151835525	B5BU69|Q53TI8|Q9BVE5	Missense_Mutation	SNP	ENST00000243346.5	37	CCDS2192.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314992	0.23908	.	.	ENSG00000123609	ENST00000243346	T	0.51071	0.72	5.26	0.526	0.17078	Nmi/IFP 35 (1);	0.373716	0.30126	N	0.010349	T	0.27241	0.0668	L	0.33710	1.025	0.18873	N	0.999983	B	0.13145	0.007	B	0.14023	0.01	T	0.08868	-1.0701	10	0.20046	T	0.44	-11.8808	2.9092	0.05731	0.1951:0.4343:0.0:0.3706	.	284	Q13287	NMI_HUMAN	N	284	ENSP00000243346:K284N	ENSP00000243346:K284N	K	-	3	2	NMI	151835525	0.173000	0.23056	0.953000	0.39169	0.908000	0.53690	-0.073000	0.11468	0.175000	0.19841	0.591000	0.81541	AAG		0.388	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688		A	152127279	C	A	152127279	3	1	61	1	0	0	0	0	1	0	0	0	10528	912	32	2	75	2	NMI	2	152127279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	795826	152127279	91072094	1692	9677										
RIF1	55183	broad.mit.edu	37	chr2	152319839	152319839	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaaaagcaaagcaaagaGaagggactttttcaaaatct	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152319839G>T	ENST00000243326.5	+	29	4288	c.3805G>T	c.(3805-3807)Gaa>Taa	p.E1269*	RIF1_ENST00000444746.2_Nonsense_Mutation_p.E1269*|RIF1_ENST00000453091.2_Nonsense_Mutation_p.E1269*|RIF1_ENST00000430328.2_Nonsense_Mutation_p.E1269*|RIF1_ENST00000428287.2_Nonsense_Mutation_p.E1269*			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.E1269*(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		AAAGCAAAGAGAAGGGACTTT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											75	85	82					2																	152319839		2203	4297	6500	152028085	SO:0001587	stop_gained	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3805G>T	2.37:g.152319839G>T	ENSP00000243326:p.Glu1269*		152028085	A0AVS0|Q9NS16	Nonsense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	G	40	8.161676	0.98683	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	.	.	.	5.33	3.45	0.39498	.	0.743939	0.13411	N	0.389849	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-13.1687	5.1314	0.14913	0.0788:0.1462:0.6235:0.1515	.	.	.	.	X	1269	.	ENSP00000243326:E1269X	E	+	1	0	RIF1	152028085	1.000000	0.71417	0.955000	0.39395	0.639000	0.38242	2.689000	0.46993	0.563000	0.29222	0.563000	0.77884	GAA		0.358	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152319839	G	T	152319839	4	4	61	1	0	0	0	0	0	1	0	0	13396	943	33	2	3919	2	RIF1	2	152319839	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192560	152319839	90879534	1693	9678										
RIF1	55183	broad.mit.edu	37	chr2	152320140	152320140	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaatgctgtattattggAaactaatactgtagaggaga	11	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152320140A>C	ENST00000243326.5	+	29	4589	c.4106A>C	c.(4105-4107)gAa>gCa	p.E1369A	RIF1_ENST00000444746.2_Missense_Mutation_p.E1369A|RIF1_ENST00000453091.2_Missense_Mutation_p.E1369A|RIF1_ENST00000430328.2_Missense_Mutation_p.E1369A|RIF1_ENST00000428287.2_Missense_Mutation_p.E1369A			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.E1369A(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GTATTATTGGAAACTAATACT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	69	67					2																	152320140		2200	4300	6500	152028386	SO:0001583	missense	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.4106A>C	2.37:g.152320140A>C	ENSP00000243326:p.Glu1369Ala		152028386	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.209124	0.39003	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.14	5.14	0.70334	.	0.298852	0.35805	N	0.002977	T	0.28267	0.0698	L	0.50333	1.59	0.80722	D	1	B;B	0.33637	0.349;0.42	B;B	0.28465	0.056;0.09	T	0.07195	-1.0785	10	0.48119	T	0.1	-7.2597	13.9392	0.64043	1.0:0.0:0.0:0.0	.	1369;1369	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	A	1369	ENSP00000390181:E1369A;ENSP00000414615:E1369A;ENSP00000415691:E1369A;ENSP00000243326:E1369A;ENSP00000416123:E1369A	ENSP00000243326:E1369A	E	+	2	0	RIF1	152028386	0.770000	0.28543	0.476000	0.27291	0.044000	0.14063	1.025000	0.30090	1.953000	0.56701	0.455000	0.32223	GAA		0.348	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			C	152320140	A	C	152320140	3	2	61	1	0	0	0	0	1	0	0	0	13396	246	9	4	4220	4	RIF1	2	152320140	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	301	152320140	90879233	1694	9679										
RIF1	55183	broad.mit.edu	37	chr2	152320827	152320827	+	Frame_Shift_Del	DEL	A	A	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggaatgtataaaagctgAaaatcagtcacatgattata							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152320827delA	ENST00000243326.5	+	29	5276	c.4793delA	c.(4792-4794)gaafs	p.E1598fs	RIF1_ENST00000444746.2_Frame_Shift_Del_p.E1598fs|RIF1_ENST00000453091.2_Frame_Shift_Del_p.E1598fs|RIF1_ENST00000430328.2_Frame_Shift_Del_p.E1598fs|RIF1_ENST00000428287.2_Frame_Shift_Del_p.E1598fs			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.N1599fs*14(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATAAAAGCTGAAAATCAGTCA	0.328																																																1	Deletion - Frameshift(1)	large_intestine(1)	2											60	59	59					2																	152320827		2203	4300	6503	152029073	SO:0001589	frameshift_variant	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.4793delA	2.37:g.152320827delA	ENSP00000243326:p.Glu1598fs		152029073	A0AVS0|Q9NS16	Frame_Shift_Del	DEL	ENST00000243326.5	37	CCDS2194.1																																																																																				0.328	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			-	152320827	A	-	152320827	7	5	61	1	0	1	0	1	0	0	0	0	13396	246	9	0	4907	0	RIF1	2	152320827	Frame_Shift_Del	DEL	A	TCGA-AG-A002-01A-01W-A00K-09	687	152320827	90878546	1695	9680										
NEB	4703	broad.mit.edu	37	chr2	152349881	152349881	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataccgagctaatgttttCttggttgcgcttagctctct	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152349881C>A	ENST00000172853.10	-	143	19330	c.19183G>T	c.(19183-19185)Gaa>Taa	p.E6395*	NEB_ENST00000397336.2_Nonsense_Mutation_p.E226*|NEB_ENST00000603639.1_Nonsense_Mutation_p.E8251*|RIF1_ENST00000457745.1_Intron|NEB_ENST00000409198.1_Nonsense_Mutation_p.E6395*|NEB_ENST00000427231.2_Nonsense_Mutation_p.E8251*|NEB_ENST00000509223.2_Nonsense_Mutation_p.E164*|NEB_ENST00000397345.3_Nonsense_Mutation_p.E8251*|NEB_ENST00000604864.1_Nonsense_Mutation_p.E8251*|NEB_ENST00000498015.2_Intron			P20929	NEBU_HUMAN	nebulin	6395					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E6395*(1)|p.E6395K(1)|p.E8251K(1)|p.E8251*(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTAATGTTTTCTTGGTTGCGC	0.383																																																4	Substitution - Nonsense(2)|Substitution - Missense(2)	urinary_tract(2)|large_intestine(2)	2											121	109	113					2																	152349881		1848	4101	5949	152058127	SO:0001587	stop_gained	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.19183G>T	2.37:g.152349881C>A	ENSP00000172853:p.Glu6395*		152058127	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Nonsense_Mutation	SNP	ENST00000172853.10	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	23.9|23.9|23.9	4.468360|4.468360|4.468360	0.84533|0.84533|0.84533	.|.|.	.|.|.	ENSG00000183091|ENSG00000183091|ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000397336;ENST00000509223|ENST00000397337|ENST00000421461	.|.|.	.|.|.	.|.|.	5.98|5.98|5.98	5.09|5.09|5.09	0.68999|0.68999|0.68999	.|.|.	0.454150|.|.	0.23658|.|.	N|.|.	0.045858|.|.	.|T|T	.|0.73009|0.73009	.|0.3532|0.3532	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.74359|0.74359	.|-0.3691|-0.3691	.|3|3	0.45353|.|.	T|.|.	0.12|.|.	.|.|.	16.8063|16.8063|16.8063	0.85706|0.85706|0.85706	0.0:0.8709:0.1291:0.0|0.0:0.8709:0.1291:0.0|0.0:0.8709:0.1291:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	6395;8251;8251;6395;226;164|384|396	.|.|.	ENSP00000172853:E6395X|.|.	E|K|R	-|-|-	1|3|2	0|2|0	NEB|NEB|NEB	152058127|152058127|152058127	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	3.332000|3.332000|3.332000	0.52083|0.52083|0.52083	1.513000|1.513000|1.513000	0.48852|0.48852|0.48852	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|AAG|AGA		0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152349881	C	A	152349881	4	1	61	1	0	0	0	0	0	1	0	0	10333	922	32	2	854	2	NEB	2	152349881	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29054	152349881	90849492	1696	9681										
NEB	4703	broad.mit.edu	37	chr2	152350697	152350697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctaatgttttcttgattgCgtttgactctctgcatctca	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152350697C>T	ENST00000172853.10	-	141	19136	c.18989G>A	c.(18988-18990)cGc>cAc	p.R6330H	NEB_ENST00000397336.2_Missense_Mutation_p.R161H|NEB_ENST00000603639.1_Missense_Mutation_p.R8186H|RIF1_ENST00000457745.1_Intron|NEB_ENST00000409198.1_Missense_Mutation_p.R6330H|NEB_ENST00000427231.2_Missense_Mutation_p.R8186H|NEB_ENST00000509223.2_Missense_Mutation_p.R130H|NEB_ENST00000397345.3_Missense_Mutation_p.R8186H|NEB_ENST00000604864.1_Missense_Mutation_p.R8186H|NEB_ENST00000498015.2_Intron			P20929	NEBU_HUMAN	nebulin	6330					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.R6330H(1)|p.R8186H(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCTTGATTGCGTTTGACTCT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	2											114	95	101					2																	152350697		1880	4112	5992	152058943	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18989G>A	2.37:g.152350697C>T	ENSP00000172853:p.Arg6330His		152058943	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.29|14.29	2.491768|2.491768	0.44249|0.44249	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000397337;ENST00000434685|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000397336;ENST00000509223	.|T;T;T;T;T;T;T	.|0.46819	.|0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.82|5.82	4.94|4.94	0.65067|0.65067	.|.	.|0.000000	.|0.64402	.|D	.|0.000014	T|T	0.65228|0.65228	0.2671|0.2671	M|M	0.71581|0.71581	2.175|2.175	0.21064|0.21064	N|N	0.999796|0.999796	.|P;B;B;B;B;D	.|0.89917	.|0.894;0.104;0.009;0.1;0.004;1.0	.|B;B;B;B;B;D	.|0.91635	.|0.36;0.059;0.005;0.024;0.002;0.999	T|T	0.59679|0.59679	-0.7409|-0.7409	5|10	.|0.19590	.|T	.|0.45	.|.	14.4962|14.4962	0.67688|0.67688	0.0:0.929:0.0:0.071|0.0:0.929:0.0:0.071	.|.	.|130;161;130;6330;2730;8186	.|B7Z6B9;B7Z6P9;B7Z6N8;P20929;Q14215;F8WCL5	.|.;.;.;NEBU_HUMAN;.;.	T|H	320;489|6330;8186;8186;2348;2730;6330;161;130	.|ENSP00000386259:R6330H;ENSP00000380505:R8186H;ENSP00000416578:R8186H;ENSP00000410961:R2730H;ENSP00000172853:R6330H;ENSP00000380497:R161H;ENSP00000427083:R130H	.|ENSP00000172853:R6330H	A|R	-|-	1|2	0|0	NEB|NEB	152058943|152058943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.693000|1.693000	0.37742|0.37742	1.456000|1.456000	0.47831|0.47831	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.438	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152350697	C	T	152350697	3	4	61	1	0	0	0	0	1	0	0	0	10333	768	27	1	1056	1	NEB	2	152350697	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	816	152350697	90848676	1697	9682										
NEB	4703	broad.mit.edu	37	chr2	152375525	152375525	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacatgattcatgatcagaGactccttcatgtcagtcacg	9	10	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152375525G>T	ENST00000172853.10	-	127	17693	c.17546C>A	c.(17545-17547)tCt>tAt	p.S5849Y	NEB_ENST00000603639.1_Missense_Mutation_p.S7550Y|NEB_ENST00000409198.1_Missense_Mutation_p.S5849Y|NEB_ENST00000427231.2_Missense_Mutation_p.S7550Y|NEB_ENST00000397345.3_Missense_Mutation_p.S7550Y|NEB_ENST00000604864.1_Missense_Mutation_p.S7550Y			P20929	NEBU_HUMAN	nebulin	5849					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.S5849Y(1)|p.S7550Y(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CATGATCAGAGACTCCTTCAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2											152	142	145					2																	152375525		1903	4111	6014	152083771	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17546C>A	2.37:g.152375525G>T	ENSP00000172853:p.Ser5849Tyr		152083771	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.168388|5.168388	0.94768|0.94768	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000434685|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.|T;T;T;T;T	.|0.50277	.|3.26;3.26;3.26;0.75;3.26	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71584|0.71584	0.3357|0.3357	M|M	0.74258|0.74258	2.255|2.255	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.998	.|D;D;D	.|0.91635	.|0.998;0.999;0.972	T|T	0.71586|0.71586	-0.4548|-0.4548	5|10	.|0.66056	.|D	.|0.02	.|.	20.5568|20.5568	0.99304|0.99304	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|5849;7550;2280	.|P20929;F8WCP0;Q14215	.|NEBU_HUMAN;.;.	I|Y	173|5849;7550;7550;1898;2280;5849	.|ENSP00000386259:S5849Y;ENSP00000380505:S7550Y;ENSP00000416578:S7550Y;ENSP00000410961:S2280Y;ENSP00000172853:S5849Y	.|ENSP00000172853:S5849Y	L|S	-|-	1|2	0|0	NEB|NEB	152083771|152083771	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	9.869000|9.869000	0.99810|0.99810	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	CTC|TCT		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152375525	G	T	152375525	3	4	61	1	0	0	0	0	1	0	0	0	10333	942	33	2	3040	2	NEB	2	152375525	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24828	152375525	90823848	1698	9683										
NEB	4703	broad.mit.edu	37	chr2	152376261	152376261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcttgcccttttctttatCgaaattttctcggtatttaa	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152376261C>T	ENST00000172853.10	-	126	17545	c.17398G>A	c.(17398-17400)Gat>Aat	p.D5800N	NEB_ENST00000603639.1_Missense_Mutation_p.D7501N|NEB_ENST00000409198.1_Missense_Mutation_p.D5800N|NEB_ENST00000427231.2_Missense_Mutation_p.D7501N|NEB_ENST00000397345.3_Missense_Mutation_p.D7501N|NEB_ENST00000604864.1_Missense_Mutation_p.D7501N			P20929	NEBU_HUMAN	nebulin	5800					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.D5800N(1)|p.D7501N(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTTTCTTTATCGAAATTTTCT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	2											261	227	237					2																	152376261		1829	4079	5908	152084507	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17398G>A	2.37:g.152376261C>T	ENSP00000172853:p.Asp5800Asn		152084507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	14.09	2.430596	0.43122	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	6.16	3.01	0.34805	.	0.399718	0.31323	N	0.007858	T	0.35711	0.0941	L	0.59436	1.845	0.80722	D	1	B;B;B	0.17852	0.014;0.008;0.024	B;B;B	0.19946	0.027;0.012;0.016	T	0.09443	-1.0674	10	0.28530	T	0.3	.	7.8698	0.29558	0.2215:0.6721:0.0:0.1064	.	5800;7501;2231	P20929;F8WCP0;Q14215	NEBU_HUMAN;.;.	N	5800;7501;7501;1849;2231;5800	ENSP00000386259:D5800N;ENSP00000380505:D7501N;ENSP00000416578:D7501N;ENSP00000410961:D2231N;ENSP00000172853:D5800N	ENSP00000172853:D5800N	D	-	1	0	NEB	152084507	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	1.324000	0.33712	0.303000	0.22785	0.650000	0.86243	GAT		0.353	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152376261	C	T	152376261	3	4	61	1	0	0	0	0	1	0	0	0	10333	884	31	1	3192	1	NEB	2	152376261	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	736	152376261	90823112	1699	9684										
NEB	4703	broad.mit.edu	37	chr2	152380919	152380919	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccttgcggtgcttggctCtgtactccacctgaatcaga	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152380919C>A	ENST00000172853.10	-	125	17429	c.17282G>T	c.(17281-17283)aGa>aTa	p.R5761I	NEB_ENST00000603639.1_Missense_Mutation_p.R7462I|NEB_ENST00000409198.1_Missense_Mutation_p.R5761I|NEB_ENST00000427231.2_Missense_Mutation_p.R7462I|NEB_ENST00000397345.3_Missense_Mutation_p.R7462I|NEB_ENST00000604864.1_Missense_Mutation_p.R7462I			P20929	NEBU_HUMAN	nebulin	5761					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.R5761I(1)|p.R7462I(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTGCTTGGCTCTGTACTCCAC	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	2											129	124	126					2																	152380919		2074	4220	6294	152089165	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17282G>T	2.37:g.152380919C>A	ENSP00000172853:p.Arg5761Ile		152089165	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.89|17.89	3.500696|3.500696	0.64298|0.64298	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000434685|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.|T;T;T;T;T	.|0.55930	.|0.49;0.65;0.65;0.49;0.49	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.044560	.|0.85682	.|D	.|0.000000	.|T	.|0.57755	.|0.2075	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.99;0.997;0.994	.|D;D;P	.|0.69479	.|0.953;0.964;0.908	.|T	.|0.60747	.|-0.7202	.|10	.|0.87932	.|D	.|0	.|.	7.8249|7.8249	0.29309|0.29309	0.0:0.8119:0.0:0.1881|0.0:0.8119:0.0:0.1881	.|.	.|5761;7462;2192	.|P20929;F8WCP0;Q14215	.|NEBU_HUMAN;.;.	X|I	85|5761;7462;7462;1810;2192;5761	.|ENSP00000386259:R5761I;ENSP00000380505:R7462I;ENSP00000416578:R7462I;ENSP00000410961:R2192I;ENSP00000172853:R5761I	.|ENSP00000172853:R5761I	E|R	-|-	1|2	0|0	NEB|NEB	152089165|152089165	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.279000|0.279000	0.26890|0.26890	4.870000|4.870000	0.63035|0.63035	2.813000|2.813000	0.96785|0.96785	0.655000|0.655000	0.94253|0.94253	GAG|AGA		0.537	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152380919	C	A	152380919	3	1	61	1	0	0	0	0	1	0	0	0	10333	913	32	2	3312	2	NEB	2	152380919	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4658	152380919	90818454	1700	9685										
NEB	4703	broad.mit.edu	37	chr2	152381773	152381773	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttctccttgacaaacttCtttttgtaatttgtctaaat	3	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152381773C>A	ENST00000172853.10	-	123	17220	c.17073G>T	c.(17071-17073)aaG>aaT	p.K5691N	NEB_ENST00000603639.1_Missense_Mutation_p.K7392N|NEB_ENST00000409198.1_Missense_Mutation_p.K5691N|NEB_ENST00000427231.2_Missense_Mutation_p.K7392N|NEB_ENST00000397345.3_Missense_Mutation_p.K7392N|NEB_ENST00000604864.1_Missense_Mutation_p.K7392N			P20929	NEBU_HUMAN	nebulin	5691					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.K7392N(1)|p.K5691N(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGACAAACTTCTTTTTGTAAT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	2											111	101	104					2																	152381773		1842	4090	5932	152090019	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17073G>T	2.37:g.152381773C>A	ENSP00000172853:p.Lys5691Asn		152090019	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.942733|3.942733	0.73672|0.73672	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853|ENST00000434685	T;T;T;T;T|.	0.52754|.	0.65;0.65;0.65;0.65;0.65|.	6.06|6.06	5.19|5.19	0.71726|0.71726	.|.	0.217653|.	0.48286|.	D|.	0.000186|.	T|T	0.51568|0.51568	0.1682|0.1682	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D;D|.	0.65815|.	0.974;0.967;0.995|.	P;P;P|.	0.60415|.	0.777;0.839;0.874|.	T|T	0.48055|0.48055	-0.9068|-0.9068	10|5	0.54805|.	T|.	0.06|.	.|.	11.379|11.379	0.49746|0.49746	0.0:0.8625:0.0:0.1375|0.0:0.8625:0.0:0.1375	.|.	5691;7392;2122|.	P20929;F8WCP0;Q14215|.	NEBU_HUMAN;.;.|.	N|I	5691;7392;7392;1740;2122;5691|15	ENSP00000386259:K5691N;ENSP00000380505:K7392N;ENSP00000416578:K7392N;ENSP00000410961:K2122N;ENSP00000172853:K5691N|.	ENSP00000172853:K5691N|.	K|R	-|-	3|2	2|0	NEB|NEB	152090019|152090019	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.229000|3.229000	0.51278|0.51278	1.571000|1.571000	0.49722|0.49722	0.655000|0.655000	0.94253|0.94253	AAG|AGA		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152381773	C	A	152381773	3	1	61	1	0	0	0	0	1	0	0	0	10333	912	32	2	3529	2	NEB	2	152381773	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	854	152381773	90817600	1701	9686										
NEB	4703	broad.mit.edu	37	chr2	152390743	152390743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacctgactgatctggtCgcctgcggtcttagccagca	11	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152390743C>T	ENST00000172853.10	-	115	16447	c.16300G>A	c.(16300-16302)Gac>Aac	p.D5434N	NEB_ENST00000603639.1_Intron|NEB_ENST00000409198.1_Missense_Mutation_p.D5434N|NEB_ENST00000427231.2_Missense_Mutation_p.D7135N|NEB_ENST00000397345.3_Intron|NEB_ENST00000604864.1_Missense_Mutation_p.D7135N			P20929	NEBU_HUMAN	nebulin	5434					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.D5434N(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGATCTGGTCGCCTGCGGTC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	2											173	177	176					2																	152390743		1995	4179	6174	152098989	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16300G>A	2.37:g.152390743C>T	ENSP00000172853:p.Asp5434Asn		152098989	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	13.03	2.116240	0.37339	.	.	ENSG00000183091	ENST00000409198;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	6.03	4.24	0.50183	.	0.332419	0.34700	N	0.003748	T	0.19565	0.0470	N	0.02865	-0.47	0.80722	D	1	B;P	0.49185	0.316;0.92	B;B	0.38264	0.146;0.269	T	0.04115	-1.0976	10	0.14656	T	0.56	.	10.7381	0.46137	0.0:0.782:0.0:0.218	.	5434;1865	P20929;Q14215	NEBU_HUMAN;.	N	5434;7135;1483;1865;5434	ENSP00000386259:D5434N;ENSP00000416578:D7135N;ENSP00000410961:D1865N;ENSP00000172853:D5434N	ENSP00000172853:D5434N	D	-	1	0	NEB	152098989	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.271000	0.51608	0.884000	0.36064	0.655000	0.94253	GAC		0.527	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152390743	C	T	152390743	3	4	61	1	0	0	0	0	1	0	0	0	10333	884	31	1	4443	1	NEB	2	152390743	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8970	152390743	90808630	1702	9687										
NEB	4703	broad.mit.edu	37	chr2	152419150	152419150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagatctcctgggcgtttCggacgcgtataacattgggt	12	9	2	1	rs575958060		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152419150C>T	ENST00000172853.10	-	92	13910	c.13763G>A	c.(13762-13764)cGa>cAa	p.R4588Q	NEB_ENST00000603639.1_Missense_Mutation_p.R6289Q|NEB_ENST00000409198.1_Missense_Mutation_p.R4588Q|NEB_ENST00000427231.2_Missense_Mutation_p.R6289Q|NEB_ENST00000397345.3_Missense_Mutation_p.R6289Q|NEB_ENST00000604864.1_Missense_Mutation_p.R6289Q			P20929	NEBU_HUMAN	nebulin	4588					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.R4588Q(2)|p.R6289Q(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGGGCGTTTCGGACGCGTAT	0.517													C|||	1	0.000199681	0	0	5008	,	,		16629	0		0	False		,,,				2504	0.001															4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	2											82	79	80					2																	152419150		2035	4168	6203	152127396	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.13763G>A	2.37:g.152419150C>T	ENSP00000172853:p.Arg4588Gln		152127396	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	18.59	3.657176	0.67586	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.74	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.67915	0.2944	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;0.992	D;P	0.91635	0.999;0.874	T	0.71237	-0.4652	10	0.66056	D	0.02	.	13.0088	0.58720	0.0:0.8684:0.0:0.1316	.	4588;1019	P20929;Q14215	NEBU_HUMAN;.	Q	4588;6289;6289;637;1019;4588	ENSP00000386259:R4588Q;ENSP00000380505:R6289Q;ENSP00000416578:R6289Q;ENSP00000410961:R1019Q;ENSP00000172853:R4588Q	ENSP00000172853:R4588Q	R	-	2	0	NEB	152127396	0.996000	0.38824	0.052000	0.19188	0.263000	0.26337	2.099000	0.41767	0.900000	0.36469	0.563000	0.77884	CGA		0.517	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152419150	C	T	152419150	3	4	61	1	0	0	0	0	1	0	0	0	10333	884	31	1	7072	1	NEB	2	152419150	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28407	152419150	90780223	1703	9688										
NEB	4703	broad.mit.edu	37	chr2	152423966	152423966	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaacataatgacctttttGcttcacatgttcagctttgt	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152423966G>A	ENST00000172853.10	-	86	12916	c.12769C>T	c.(12769-12771)Caa>Taa	p.Q4257*	NEB_ENST00000603639.1_Nonsense_Mutation_p.Q5958*|NEB_ENST00000409198.1_Nonsense_Mutation_p.Q4257*|NEB_ENST00000427231.2_Nonsense_Mutation_p.Q5958*|NEB_ENST00000397345.3_Nonsense_Mutation_p.Q5958*|NEB_ENST00000604864.1_Nonsense_Mutation_p.Q5958*			P20929	NEBU_HUMAN	nebulin	4257					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.Q5958*(1)|p.Q4257*(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGACCTTTTTGCTTCACATGT	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											88	77	81					2																	152423966		1940	4151	6091	152132212	SO:0001587	stop_gained	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.12769C>T	2.37:g.152423966G>A	ENSP00000172853:p.Gln4257*		152132212	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Nonsense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	55	23.750573	0.99957	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	20.2885	0.98538	0.0:0.0:1.0:0.0	.	.	.	.	X	4257;5958;5958;306;688;4257	.	ENSP00000172853:Q4257X	Q	-	1	0	NEB	152132212	1.000000	0.71417	0.978000	0.43139	0.947000	0.59692	7.876000	0.87215	2.791000	0.96007	0.650000	0.86243	CAA		0.433	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152423966	G	A	152423966	4	1	61	1	0	0	0	0	0	1	0	0	10333	1328	46	3	8090	3	NEB	2	152423966	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4816	152423966	90775407	1704	9689										
NEB	4703	broad.mit.edu	37	chr2	152472613	152472613	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggactcttccaaagcaagtTtatagagtttctgtagaaaa	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152472613T>G	ENST00000172853.10	-	72	10610	c.10463A>C	c.(10462-10464)aAa>aCa	p.K3488T	NEB_ENST00000603639.1_Missense_Mutation_p.K3731T|NEB_ENST00000409198.1_Missense_Mutation_p.K3488T|NEB_ENST00000427231.2_Missense_Mutation_p.K3731T|NEB_ENST00000397345.3_Missense_Mutation_p.K3731T|NEB_ENST00000604864.1_Missense_Mutation_p.K3731T			P20929	NEBU_HUMAN	nebulin	3488					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.K3488T(1)|p.K3731T(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CAAAGCAAGTTTATAGAGTTT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	2											51	52	51					2																	152472613		1835	4076	5911	152180859	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.10463A>C	2.37:g.152472613T>G	ENSP00000172853:p.Lys3488Thr		152180859	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	18.32	3.598058	0.66332	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.25	4.08	0.47627	.	0.351121	0.28784	N	0.014147	T	0.66470	0.2792	M	0.77616	2.38	0.80722	D	1	B	0.15473	0.013	B	0.23018	0.043	T	0.68146	-0.5486	10	0.54805	T	0.06	.	10.7863	0.46407	0.0:0.0806:0.0:0.9194	.	3488	P20929	NEBU_HUMAN	T	3488;3731;3731;3488	ENSP00000386259:K3488T;ENSP00000380505:K3731T;ENSP00000416578:K3731T;ENSP00000172853:K3488T	ENSP00000172853:K3488T	K	-	2	0	NEB	152180859	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.490000	0.45294	2.104000	0.64026	0.528000	0.53228	AAA		0.373	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152472613	T	G	152472613	3	3	61	1	0	0	0	0	1	0	0	0	10333	1841	64	4	14922	4	NEB	2	152472613	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	48647	152472613	90726760	1705	9690										
NEB	4703	broad.mit.edu	37	chr2	152501066	152501066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccttttctcttcagctcCtcataacccattcggtagag	5	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152501066C>A	ENST00000172853.10	-	56	7707	c.7560G>T	c.(7558-7560)gaG>gaT	p.E2520D	NEB_ENST00000603639.1_Missense_Mutation_p.E2520D|NEB_ENST00000409198.1_Missense_Mutation_p.E2520D|NEB_ENST00000427231.2_Missense_Mutation_p.E2520D|NEB_ENST00000397345.3_Missense_Mutation_p.E2520D|NEB_ENST00000604864.1_Missense_Mutation_p.E2520D			P20929	NEBU_HUMAN	nebulin	2520					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E2520D(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTTCAGCTCCTCATAACCCA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	2											141	131	135					2																	152501066		1841	4094	5935	152209312	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7560G>T	2.37:g.152501066C>A	ENSP00000172853:p.Glu2520Asp		152209312	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	17.14	3.312230	0.60414	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.4	1.58	0.23477	.	0.000000	0.85682	D	0.000000	T	0.68320	0.2988	M	0.73372	2.23	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.62826	-0.6772	10	0.22706	T	0.39	.	8.7017	0.34329	0.0:0.4762:0.0:0.5238	.	2520	P20929	NEBU_HUMAN	D	2520	ENSP00000386259:E2520D;ENSP00000380505:E2520D;ENSP00000416578:E2520D;ENSP00000172853:E2520D	ENSP00000172853:E2520D	E	-	3	2	NEB	152209312	0.078000	0.21339	0.999000	0.59377	0.997000	0.91878	-0.258000	0.08733	0.077000	0.16863	0.557000	0.71058	GAG		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152501066	C	A	152501066	3	1	61	1	0	0	0	0	1	0	0	0	10333	680	24	2	18634	2	NEB	2	152501066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28453	152501066	90698307	1706	9691										
NEB	4703	broad.mit.edu	37	chr2	152502747	152502747	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaagcttctctataaagtCtctaaaataagaaataataa	3	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152502747C>T	ENST00000172853.10	-	55	7580	c.7433G>A	c.(7432-7434)aGa>aAa	p.R2478K	NEB_ENST00000603639.1_Splice_Site_p.R2478K|NEB_ENST00000409198.1_Splice_Site_p.R2478K|NEB_ENST00000427231.2_Splice_Site_p.R2478K|NEB_ENST00000397345.3_Splice_Site_p.R2478K|NEB_ENST00000604864.1_Splice_Site_p.R2478K			P20929	NEBU_HUMAN	nebulin	2478					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.R2478K(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTATAAAGTCTCTAAAATAA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	2											56	51	53					2																	152502747		1812	4090	5902	152210993	SO:0001630	splice_region_variant	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7432-1G>A	2.37:g.152502747C>T			152210993	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	10.37	1.331371	0.24167	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.6	3.78	0.43462	.	0.302133	0.36034	N	0.002833	T	0.31544	0.0800	L	0.58810	1.83	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.13710	-1.0499	10	0.05525	T	0.97	.	7.9938	0.30256	0.2883:0.6381:0.0:0.0736	.	2478	P20929	NEBU_HUMAN	K	2478	ENSP00000386259:R2478K;ENSP00000380505:R2478K;ENSP00000416578:R2478K;ENSP00000172853:R2478K	ENSP00000172853:R2478K	R	-	2	0	NEB	152210993	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.046000	0.30354	0.816000	0.34421	0.655000	0.94253	AGA		0.333	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Missense_Mutation	T	152502747	C	T	152502747	5	4	61	1	0	0	0	0	0	0	1	0	10333	927	32	3	18765	3	NEB	2	152502747	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1681	152502747	90696626	1707	9692										
NEB	4703	broad.mit.edu	37	chr2	152518760	152518760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttcttttcactaataatCtccatggctttcttgttttt	3	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152518760C>A	ENST00000172853.10	-	46	6006	c.5859G>T	c.(5857-5859)gaG>gaT	p.E1953D	NEB_ENST00000603639.1_Missense_Mutation_p.E1953D|NEB_ENST00000409198.1_Missense_Mutation_p.E1953D|NEB_ENST00000427231.2_Missense_Mutation_p.E1953D|NEB_ENST00000397345.3_Missense_Mutation_p.E1953D|NEB_ENST00000604864.1_Missense_Mutation_p.E1953D			P20929	NEBU_HUMAN	nebulin	1953					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E1953D(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CACTAATAATCTCCATGGCTT	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	2											114	110	111					2																	152518760		1885	4096	5981	152227006	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.5859G>T	2.37:g.152518760C>A	ENSP00000172853:p.Glu1953Asp		152227006	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	16.79	3.219378	0.58560	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.08458	3.15;3.35;3.35;3.09	5.75	3.6	0.41247	.	0.118078	0.64402	D	0.000012	T	0.14270	0.0345	L	0.48935	1.535	0.80722	D	1	P	0.50528	0.936	P	0.54706	0.759	T	0.02244	-1.1189	10	0.36615	T	0.2	.	9.9	0.41342	0.0:0.7623:0.0:0.2377	.	1953	P20929	NEBU_HUMAN	D	1953	ENSP00000386259:E1953D;ENSP00000380505:E1953D;ENSP00000416578:E1953D;ENSP00000172853:E1953D	ENSP00000172853:E1953D	E	-	3	2	NEB	152227006	0.172000	0.23043	1.000000	0.80357	0.998000	0.95712	-0.335000	0.07873	1.570000	0.49709	0.650000	0.86243	GAG		0.458	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152518760	C	A	152518760	3	1	61	1	0	0	0	0	1	0	0	0	10333	912	32	2	20375	2	NEB	2	152518760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16013	152518760	90680613	1708	9693										
NEB	4703	broad.mit.edu	37	chr2	152554088	152554088	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttctgcagaacagtatcGagcttgaatttgggggtctc	12	7	2	2	rs371658494		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152554088G>A	ENST00000172853.10	-	14	1374	c.1227C>T	c.(1225-1227)ctC>ctT	p.L409L	NEB_ENST00000603639.1_Silent_p.L409L|NEB_ENST00000409198.1_Silent_p.L409L|NEB_ENST00000427231.2_Silent_p.L409L|NEB_ENST00000397345.3_Silent_p.L409L|NEB_ENST00000604864.1_Silent_p.L409L			P20929	NEBU_HUMAN	nebulin	409					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.L409L(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GAACAGTATCGAGCTTGAATT	0.328																																																2	Substitution - coding silent(2)	large_intestine(2)	2						G	,,	0,3660		0,0,1830	138	134	135		1227,1227,1227	-5.2	0.7	2		135	1,8173		0,1,4086	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,1,5916	AA,AG,GG		0.0122,0.0,0.0085	,,	409/8526,409/8526,409/6670	152554088	1,11833	1830	4087	5917	152262334	SO:0001819	synonymous_variant	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.1227C>T	2.37:g.152554088G>A			152262334	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.328	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152554088	G	A	152554088	2	1	61	1	0	0	0	0	0	0	0	1	10333	1045	37	1		1	NEB	2	152554088	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35328	152554088	90645285	1709	9694										
NEB	4703	broad.mit.edu	37	chr2	152566209	152566209	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttttttattcattttataCtctggtgtttcggtctgcat	7	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152566209C>A	ENST00000172853.10	-	12	1143	c.996G>T	c.(994-996)gaG>gaT	p.E332D	NEB_ENST00000603639.1_Missense_Mutation_p.E332D|NEB_ENST00000409198.1_Missense_Mutation_p.E332D|NEB_ENST00000427231.2_Missense_Mutation_p.E332D|NEB_ENST00000397345.3_Missense_Mutation_p.E332D|NEB_ENST00000604864.1_Missense_Mutation_p.E332D			P20929	NEBU_HUMAN	nebulin	332					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E332D(2)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCATTTTATACTCTGGTGTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	2											97	85	89					2																	152566209		1824	4075	5899	152274455	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.996G>T	2.37:g.152566209C>A	ENSP00000172853:p.Glu332Asp		152274455	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	14.39	2.521711	0.44866	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000536533	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.54	2.34	0.29019	.	0.197064	0.44097	D	0.000493	T	0.43166	0.1235	N	0.24115	0.695	0.80722	D	1	D	0.60160	0.987	P	0.59288	0.855	T	0.14008	-1.0488	10	0.18276	T	0.48	.	9.202	0.37265	0.0:0.6225:0.0:0.3775	.	332	P20929	NEBU_HUMAN	D	332;332;332;332;58	ENSP00000386259:E332D;ENSP00000380505:E332D;ENSP00000416578:E332D;ENSP00000172853:E332D	ENSP00000172853:E332D	E	-	3	2	NEB	152274455	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.702000	0.25631	0.722000	0.32252	0.655000	0.94253	GAG		0.378	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152566209	C	A	152566209	3	1	61	1	0	0	0	0	1	0	0	0	10333	564	20	2	25374	2	NEB	2	152566209	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12121	152566209	90633164	1710	9695										
ARL5A	26225	broad.mit.edu	37	chr2	152663435	152663435	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgctacagtcatgcattCtttaacatcttgtttattag	5	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:152663435C>A	ENST00000295087.8	-	5	702	c.391G>T	c.(391-393)Gaa>Taa	p.E131*	ARL5A_ENST00000428992.2_Nonsense_Mutation_p.E94*	NM_001037174.1|NM_012097.3	NP_001032251.1|NP_036229.1	Q9Y689	ARL5A_HUMAN	ADP-ribosylation factor-like 5A	131					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)	p.E131*(2)		breast(1)|large_intestine(2)|liver(1)|lung(2)	6				BRCA - Breast invasive adenocarcinoma(221;0.153)		GTCATGCATTCTTTAACATCT	0.373																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											94	85	88					2																	152663435		2203	4300	6503	152371681	SO:0001587	stop_gained	26225			AF100740	CCDS2195.1, CCDS46425.1	2q23.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000162980	ENSG00000162980		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	696	protein-coding gene	gene with protein product		608960	"ADP-ribosylation factor-like 5"	ARL5			Standard	NM_012097		Approved		uc002txx.1	Q9Y689	OTTHUMG00000131887	ENST00000295087.8:c.391G>T	2.37:g.152663435C>A	ENSP00000295087:p.Glu131*		152371681	Q580I5	Nonsense_Mutation	SNP	ENST00000295087.8	37	CCDS2195.1	.	.	.	.	.	.	.	.	.	.	C	36	5.605948	0.96626	.	.	ENSG00000162980	ENST00000295087;ENST00000452215;ENST00000428992	.	.	.	5.6	4.66	0.58398	.	0.150635	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-12.98	15.954	0.79865	0.0:0.8651:0.1349:0.0	.	.	.	.	X	131;94;94	.	ENSP00000295087:E131X	E	-	1	0	ARL5A	152371681	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.041000	0.70988	2.640000	0.89533	0.561000	0.74099	GAA		0.373	ARL5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254837.1			A	152663435	C	A	152663435	4	1	61	1	0	0	0	0	0	1	0	0	940	922	32	2	156	2	ARL5A	2	152663435	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97226	152663435	90535938	1711	9696										
STAM2	10254	broad.mit.edu	37	chr2	153006733	153006733	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtagtgttgtactcattCgtggctttttctataaaata	7	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:153006733C>T	ENST00000263904.4	-	2	400	c.51G>A	c.(49-51)acG>acA	p.T17T	STAM2_ENST00000465460.1_5'Flank	NM_005843.4	NP_005834.4	O75886	STAM2_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	17	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T17T(1)		endometrium(3)|large_intestine(4)|lung(8)|ovary(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.22)		TGTACTCATTCGTGGCTTTTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	2											131	110	117					2																	153006733		2203	4299	6502	152714979	SO:0001819	synonymous_variant	10254			AF042274	CCDS2196.1	2q23.3	2009-04-29			ENSG00000115145	ENSG00000115145			11358	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	606244				10899310, 10993906	Standard	NM_005843		Approved	Hbp	uc002tyc.4	O75886	OTTHUMG00000131885	ENST00000263904.4:c.51G>A	2.37:g.153006733C>T			152714979	A8K8A0|D3DPA1|Q7LDQ0|Q9UF58	Silent	SNP	ENST00000263904.4	37	CCDS2196.1																																																																																				0.363	STAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254835.2	NM_005843		T	153006733	C	T	153006733	2	4	61	1	0	0	0	0	0	0	0	1	15288	871	31	1		1	STAM2	2	153006733	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	343298	153006733	90192640	1712	9697										
FMNL2	114793	broad.mit.edu	37	chr2	153405596	153405596	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaactggaaatttctttgaGaactaaccacattgggtaag	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:153405596G>T	ENST00000288670.9	+	4	711	c.344G>T	c.(343-345)aGa>aTa	p.R115I		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	115	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.R115I(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						ATTTCTTTGAGAACTAACCAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											67	63	64					2																	153405596		1814	4074	5888	153113842	SO:0001583	missense	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.344G>T	2.37:g.153405596G>T	ENSP00000288670:p.Arg115Ile		153113842	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250234	0.80024	.	.	ENSG00000157827	ENST00000288670	D	0.90324	-2.65	5.86	5.86	0.93980	.	0.105395	0.64402	D	0.000002	D	0.96562	0.8878	M	0.91459	3.21	0.80722	D	1	D	0.64830	0.994	D	0.74348	0.983	D	0.96559	0.9414	10	0.87932	D	0	.	20.1581	0.98126	0.0:0.0:1.0:0.0	.	115	Q96PY5-3	.	I	115	ENSP00000288670:R115I	ENSP00000288670:R115I	R	+	2	0	FMNL2	153113842	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	8.709000	0.91379	2.937000	0.99478	0.650000	0.86243	AGA		0.343	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		T	153405596	G	T	153405596	3	4	61	1	0	0	0	0	1	0	0	0	5971	942	33	2	358	2	FMNL2	2	153405596	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	398863	153405596	89793777	1713	9698										
FMNL2	114793	broad.mit.edu	37	chr2	153482066	153482066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgaaattgatgatgagcGaattctggaggtatttttct	10	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:153482066G>A	ENST00000475377.2	+	3	277	c.77G>A	c.(76-78)cGa>cAa	p.R26Q	FMNL2_ENST00000288670.9_Missense_Mutation_p.R651Q|FMNL2_ENST00000497192.1_3'UTR			Q96PY5	FMNL2_HUMAN	formin-like 2	651	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.R651Q(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						GATGATGAGCGAATTCTGGAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	111	113					2																	153482066		1856	4092	5948	153190312	SO:0001583	missense	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000475377.2:c.77G>A	2.37:g.153482066G>A	ENSP00000418959:p.Arg26Gln		153190312	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000475377.2	37		.	.	.	.	.	.	.	.	.	.	G	20.5	3.994758	0.74703	.	.	ENSG00000157827	ENST00000288670;ENST00000421344;ENST00000475377	T;T	0.16324	2.35;2.35	6.17	6.17	0.99709	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.19685	0.0473	L	0.28014	0.82	0.80722	D	1	D;B;B	0.53745	0.962;0.069;0.255	P;B;B	0.45881	0.496;0.041;0.057	T	0.00253	-1.1875	10	0.40728	T	0.16	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	651;132;651	Q96PY5;Q6ZN96;Q96PY5-3	FMNL2_HUMAN;.;.	Q	651;132;26	ENSP00000288670:R651Q;ENSP00000418959:R26Q	ENSP00000288670:R651Q	R	+	2	0	FMNL2	153190312	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.785000	0.75089	2.941000	0.99782	0.655000	0.94253	CGA		0.438	FMNL2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333583.3	NM_052905		A	153482066	G	A	153482066	3	1	61	1	0	0	0	0	1	0	0	0	5971	1058	37	1	2014	1	FMNL2	2	153482066	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76470	153482066	89717307	1714	9699										
PRPF40A	55660	broad.mit.edu	37	chr2	153515506	153515506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttcttatgcttttttgActttttataacttctctctg	3	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:153515506A>G	ENST00000410080.1	-	24	3065	c.2524T>C	c.(2524-2526)Tca>Cca	p.S842P		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	869					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S738P(1)|p.S869P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TGCTTTTTTGACTTTTTATAA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	2											47	48	48					2																	153515506		1804	4066	5870	153223752	SO:0001583	missense	55660			AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.2524T>C	2.37:g.153515506A>G	ENSP00000386458:p.Ser842Pro		153223752	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.054466	0.55218	.	.	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961	T	0.35789	1.29	5.25	5.25	0.73442	.	0.188358	0.48767	D	0.000168	T	0.36826	0.0981	L	0.53249	1.67	0.54753	D	0.999982	P;P	0.49783	0.928;0.928	P;P	0.44811	0.461;0.461	T	0.19778	-1.0295	10	0.48119	T	0.1	-0.5388	10.6996	0.45920	0.8576:0.0:0.0:0.1424	.	869;842	O75400;E9PFS0	PR40A_HUMAN;.	P	842;851;738;793	ENSP00000386458:S842P	ENSP00000348770:S851P	S	-	1	0	PRPF40A	153223752	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	6.075000	0.71261	2.130000	0.65690	0.456000	0.33151	TCA		0.323	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		G	153515506	A	G	153515506	3	3	61	1	0	0	0	0	1	0	0	0	12605	275	10	4	280	4	PRPF40A	2	153515506	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33440	153515506	89683867	1715	9700										
PRPF40A	55660	broad.mit.edu	37	chr2	153527834	153527834	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatcttcatagatttcaaGacgatcacgttctgatattg	6	8	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:153527834G>T	ENST00000410080.1	-	14	1973	c.1432C>A	c.(1432-1434)Ctt>Att	p.L478I		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	505	FF 2.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L505I(1)|p.L374I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TAGATTTCAAGACGATCACGT	0.269																																																2	Substitution - Missense(2)	large_intestine(2)	2											98	99	99					2																	153527834		1796	4064	5860	153236080	SO:0001583	missense	55660			AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.1432C>A	2.37:g.153527834G>T	ENSP00000386458:p.Leu478Ile		153236080	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477087	0.84640	.	.	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961	T	0.34275	1.37	5.41	4.53	0.55603	FF domain (4);	0.000000	0.85682	D	0.000000	T	0.44644	0.1303	N	0.22421	0.69	0.53005	D	0.99996	D;D	0.63046	0.992;0.992	P;D	0.67725	0.814;0.953	T	0.48468	-0.9033	10	0.72032	D	0.01	-10.5526	14.1767	0.65546	0.0725:0.0:0.9275:0.0	.	505;478	O75400;E9PFS0	PR40A_HUMAN;.	I	478;487;374;425	ENSP00000386458:L478I	ENSP00000348770:L487I	L	-	1	0	PRPF40A	153236080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.542000	0.67218	1.413000	0.46997	0.591000	0.81541	CTT		0.269	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		T	153527834	G	T	153527834	3	4	61	1	0	0	0	0	1	0	0	0	12605	942	33	2	1412	2	PRPF40A	2	153527834	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12328	153527834	89671539	1716	9701										
NR4A2	4929	broad.mit.edu	37	chr2	157185044	157185044	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcatttttttgcactgtgCgctgcaaaaggagacaatat	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:157185044C>T	ENST00000339562.4	-	4	1228	c.866G>A	c.(865-867)cGc>cAc	p.R289H	NR4A2_ENST00000409572.1_Splice_Site_p.R289H|NR4A2_ENST00000539077.1_Splice_Site_p.R300H|NR4A2_ENST00000409108.2_Splice_Site_p.R289H|NR4A2_ENST00000429376.1_Splice_Site_p.R226H|NR4A2_ENST00000426264.1_Splice_Site_p.R226H	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	289					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R289H(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TTGCACTGTGCGCTGCAAAAG	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	2											66	66	66					2																	157185044		2203	4300	6503	156893290	SO:0001630	splice_region_variant	4929			X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.865-1G>A	2.37:g.157185044C>T			156893290	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.365293	0.82463	.	.	ENSG00000153234	ENST00000339562;ENST00000426264;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000429376	D;D;D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	6.17	6.17	0.99709	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.99884	4.89	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96830	0.9610	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	289	P43354	NR4A2_HUMAN	H	289;226;289;300;289;226	ENSP00000344479:R289H;ENSP00000389986:R226H;ENSP00000386747:R289H;ENSP00000444925:R300H;ENSP00000386993:R289H;ENSP00000410952:R226H	ENSP00000344479:R289H	R	-	2	0	NR4A2	156893290	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CGC		0.418	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		Missense_Mutation	T	157185044	C	T	157185044	5	4	61	1	0	0	0	0	0	0	1	0	10664	782	27	1	950	1	NR4A2	2	157185044	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3657210	157185044	86014329	1717	9702										
GPD2	2820	broad.mit.edu	37	chr2	157425919	157425919	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatggcagaagataccataAatgctgctgtcaaaactcat	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:157425919A>C	ENST00000310454.6	+	11	1717	c.1345A>C	c.(1345-1347)Aat>Cat	p.N449H	GPD2_ENST00000540309.1_Intron|GPD2_ENST00000409674.1_Missense_Mutation_p.N449H|GPD2_ENST00000409125.4_Missense_Mutation_p.N222H|GPD2_ENST00000438166.2_Missense_Mutation_p.N449H	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	449					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)	p.N449H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						AGATACCATAAATGCTGCTGT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	77	77					2																	157425919		2203	4300	6503	157134165	SO:0001583	missense	2820				CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.1345A>C	2.37:g.157425919A>C	ENSP00000308610:p.Asn449His		157134165	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.749117	0.49257	.	.	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000409674	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.78	-0.949	0.10376	.	0.129759	0.64402	D	0.000002	T	0.45135	0.1327	M	0.68952	2.095	0.31156	N	0.70488	B	0.09022	0.002	B	0.22601	0.04	T	0.45760	-0.9239	10	0.87932	D	0	.	6.063	0.19848	0.2685:0.0:0.5635:0.168	.	449	P43304	GPDM_HUMAN	H	449;222;449;449	ENSP00000308610:N449H;ENSP00000386484:N222H;ENSP00000409708:N449H;ENSP00000386425:N449H	ENSP00000308610:N449H	N	+	1	0	GPD2	157134165	1.000000	0.71417	0.111000	0.21465	0.998000	0.95712	2.849000	0.48286	-0.143000	0.11334	0.528000	0.53228	AAT		0.393	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			C	157425919	A	C	157425919	3	2	61	1	0	0	0	0	1	0	0	0	6626	14	1	4	1383	4	GPD2	2	157425919	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	240875	157425919	85773454	1718	9703										
GALNT5	11227	broad.mit.edu	37	chr2	158114861	158114861	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggggcatggggcaaagaGaatgttagaaaaactgagga	15	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158114861G>T	ENST00000259056.4	+	1	752	c.267G>T	c.(265-267)gaG>gaT	p.E89D		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	89					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.E89D(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GGGGCAAAGAGAATGTTAGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	118	117					2																	158114861		2203	4300	6503	157823107	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.267G>T	2.37:g.158114861G>T	ENSP00000259056:p.Glu89Asp		157823107	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579645	0.86645	.	.	ENSG00000136542	ENST00000259056	T	0.60797	0.16	5.51	4.62	0.57501	.	1.158020	0.06288	N	0.698697	T	0.54143	0.1840	L	0.36672	1.1	0.33076	D	0.535949	B	0.21225	0.053	B	0.20184	0.028	T	0.53236	-0.8467	10	0.87932	D	0	.	13.8542	0.63515	0.0:0.1535:0.8465:0.0	.	89	Q7Z7M9	GALT5_HUMAN	D	89	ENSP00000259056:E89D	ENSP00000259056:E89D	E	+	3	2	GALNT5	157823107	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.452000	0.44961	1.431000	0.47355	0.655000	0.94253	GAG		0.478	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		T	158114861	G	T	158114861	3	4	61	1	0	0	0	0	1	0	0	0	6236	933	33	2	269	2	GALNT5	2	158114861	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	688942	158114861	85084512	1719	9704										
GALNT5	11227	broad.mit.edu	37	chr2	158115166	158115166	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagtacacatgggacgtgTcagtttaaaacaggagcccc	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158115166T>C	ENST00000259056.4	+	1	1057	c.572T>C	c.(571-573)gTc>gCc	p.V191A		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	191					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.V191A(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						ATGGGACGTGTCAGTTTAAAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	53	52					2																	158115166		2203	4300	6503	157823412	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.572T>C	2.37:g.158115166T>C	ENSP00000259056:p.Val191Ala		157823412	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020348	0.35606	.	.	ENSG00000136542	ENST00000259056	T	0.58210	0.35	4.83	-1.85	0.07784	.	5.342070	0.00166	N	0.000009	T	0.38081	0.1027	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34477	-0.9827	10	0.66056	D	0.02	.	5.1345	0.14928	0.0:0.382:0.3346:0.2834	.	191	Q7Z7M9	GALT5_HUMAN	A	191	ENSP00000259056:V191A	ENSP00000259056:V191A	V	+	2	0	GALNT5	157823412	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.118000	0.10692	-0.155000	0.11098	-0.313000	0.08912	GTC		0.473	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		C	158115166	T	C	158115166	3	2	61	1	0	0	0	0	1	0	0	0	6236	1667	58	4	574	4	GALNT5	2	158115166	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	305	158115166	85084207	1720	9705										
GALNT5	11227	broad.mit.edu	37	chr2	158115886	158115886	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaattgatgtgacactttCtccaagggaccccaaagctc	8	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158115886C>A	ENST00000259056.4	+	1	1777	c.1292C>A	c.(1291-1293)tCt>tAt	p.S431Y		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	431					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.S431Y(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GTGACACTTTCTCCAAGGGAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											73	72	72					2																	158115886		2203	4300	6503	157824132	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1292C>A	2.37:g.158115886C>A	ENSP00000259056:p.Ser431Tyr		157824132	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487938	0.84854	.	.	ENSG00000136542	ENST00000259056	T	0.59224	0.28	6.05	6.05	0.98169	.	0.889887	0.09869	N	0.745178	T	0.69314	0.3097	L	0.50333	1.59	0.39389	D	0.966396	D	0.67145	0.996	P	0.56700	0.804	T	0.66268	-0.5966	10	0.66056	D	0.02	.	16.4622	0.84064	0.0:0.8689:0.1311:0.0	.	431	Q7Z7M9	GALT5_HUMAN	Y	431	ENSP00000259056:S431Y	ENSP00000259056:S431Y	S	+	2	0	GALNT5	157824132	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	1.677000	0.37576	2.878000	0.98634	0.650000	0.86243	TCT		0.488	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		A	158115886	C	A	158115886	3	1	61	1	0	0	0	0	1	0	0	0	6236	913	32	2	1294	2	GALNT5	2	158115886	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	720	158115886	85083487	1721	9706										
GALNT5	11227	broad.mit.edu	37	chr2	158157217	158157217	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggtggtgaaattgagatCattccctgctcccgagtggg	14	8	1	2	rs201738512		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158157217C>A	ENST00000259056.4	+	7	2630	c.2145C>A	c.(2143-2145)atC>atA	p.I715I	RN7SKP281_ENST00000410472.1_RNA	NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	715	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.I715I(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						AAATTGAGATCATTCCCTGCT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	2											151	148	149					2																	158157217		2203	4300	6503	157865463	SO:0001819	synonymous_variant	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.2145C>A	2.37:g.158157217C>A			157865463	A5PKZ1|Q9UGK7|Q9UHL6	Silent	SNP	ENST00000259056.4	37	CCDS2203.1																																																																																				0.438	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		A	158157217	C	A	158157217	2	1	61	1	0	0	0	0	0	0	0	1	6236	816	29	2		2	GALNT5	2	158157217	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41331	158157217	85042156	1722	9707										
ACVR1C	130399	broad.mit.edu	37	chr2	158397681	158397681	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcgtttgaaggactcaaaGatattcacattcattgtatc	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158397681G>T	ENST00000243349.8	-	7	1506	c.1146C>A	c.(1144-1146)atC>atA	p.I382I	ACVR1C_ENST00000335450.7_Silent_p.I302I|ACVR1C_ENST00000409680.3_Silent_p.I332I|ACVR1C_ENST00000348328.5_Silent_p.I225I	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC									p.I382I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						AGGACTCAAAGATATTCACAT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											144	145	144					2																	158397681		2203	4300	6503	158105927	SO:0001819	synonymous_variant	130399			BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.1146C>A	2.37:g.158397681G>T			158105927		Silent	SNP	ENST00000243349.8	37	CCDS2205.1																																																																																				0.383	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		T	158397681	G	T	158397681	2	4	61	1	0	0	0	0	0	0	0	1	222	932	33	2		2	ACVR1C	2	158397681	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	240464	158397681	84801692	1723	9708										
ACVR1C	130399	broad.mit.edu	37	chr2	158399351	158399351	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatattctttgattttatgtCtcgatgagcaatagcaggtt	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158399351C>A	ENST00000243349.8	-	6	1327	c.967G>T	c.(967-969)Gac>Tac	p.D323Y	ACVR1C_ENST00000335450.7_Missense_Mutation_p.D243Y|ACVR1C_ENST00000409680.3_Missense_Mutation_p.D273Y|ACVR1C_ENST00000348328.5_Missense_Mutation_p.D166Y	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC									p.D323Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						GATTTTATGTCTCGATGAGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											165	153	157					2																	158399351		2203	4300	6503	158107597	SO:0001583	missense	130399			BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.967G>T	2.37:g.158399351C>A	ENSP00000243349:p.Asp323Tyr		158107597		Missense_Mutation	SNP	ENST00000243349.8	37	CCDS2205.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817640	0.90790	.	.	ENSG00000123612	ENST00000243349;ENST00000409680;ENST00000348328;ENST00000335450	D;D;D;D	0.93076	-3.16;-3.16;-3.16;-3.16	5.77	5.77	0.91146	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000057	D	0.98333	0.9447	H	0.98612	4.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98991	1.0808	10	0.87932	D	0	.	19.9422	0.97170	0.0:1.0:0.0:0.0	.	166;243;323	Q8NER5-2;Q8NER5-3;Q8NER5	.;.;ACV1C_HUMAN	Y	323;273;166;243	ENSP00000243349:D323Y;ENSP00000387168:D273Y;ENSP00000335139:D166Y;ENSP00000335178:D243Y	ENSP00000243349:D323Y	D	-	1	0	ACVR1C	158107597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.890000	0.99128	0.650000	0.86243	GAC		0.373	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		A	158399351	C	A	158399351	3	1	61	1	0	0	0	0	1	0	0	0	222	913	32	2	530	2	ACVR1C	2	158399351	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1670	158399351	84800022	1724	9709										
ACVR1	90	broad.mit.edu	37	chr2	158622630	158622630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgaagatagtcgtacaacGatcccatttcatgataatgt	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:158622630G>A	ENST00000263640.3	-	8	1298	c.869C>T	c.(868-870)tCg>tTg	p.S290L	ACVR1_ENST00000409283.2_Missense_Mutation_p.S290L|ACVR1_ENST00000410057.2_Missense_Mutation_p.S290L|ACVR1_ENST00000434821.1_Missense_Mutation_p.S290L	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.S290L(2)		endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	GTCGTACAACGATCCCATTTC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2											105	93	97					2																	158622630		2203	4300	6503	158330876	SO:0001583	missense	90				CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.869C>T	2.37:g.158622630G>A	ENSP00000263640:p.Ser290Leu		158330876		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	G	35	5.549165	0.96488	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	D;D;D;D	0.95103	-3.61;-3.61;-3.61;-3.61	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98105	0.9375	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98264	1.0500	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	290	Q04771	ACVR1_HUMAN	L	290	ENSP00000263640:S290L;ENSP00000387273:S290L;ENSP00000405004:S290L;ENSP00000387127:S290L	ENSP00000263640:S290L	S	-	2	0	ACVR1	158330876	1.000000	0.71417	0.967000	0.41034	0.979000	0.70002	7.922000	0.87538	2.941000	0.99782	0.655000	0.94253	TCG		0.413	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		A	158622630	G	A	158622630	3	1	61	1	0	0	0	0	1	0	0	0	220	1059	37	1	676	1	ACVR1	2	158622630	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223279	158622630	84576743	1725	9710										
PKP4	8502	broad.mit.edu	37	chr2	159459596	159459596	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttagctcaactgagaagtCatttccttggagatcaacag	8	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:159459596C>A	ENST00000389759.3	+	4	372	c.260C>A	c.(259-261)tCa>tAa	p.S87*	PKP4_ENST00000389757.3_Nonsense_Mutation_p.S87*	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	87					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)		p.S87*(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						ACTGAGAAGTCATTTCCTTGG	0.269										HNSCC(62;0.18)																																						1	Substitution - Nonsense(1)	large_intestine(1)	2											42	51	48					2																	159459596		2188	4276	6464	159167842	SO:0001587	stop_gained	8502			X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.260C>A	2.37:g.159459596C>A	ENSP00000374409:p.Ser87*		159167842	Q86W91	Nonsense_Mutation	SNP	ENST00000389759.3	37	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	36	5.947250	0.97134	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	.	.	.	5.58	5.58	0.84498	.	0.280723	0.35870	N	0.002924	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2382	15.4147	0.74956	0.0:1.0:0.0:0.0	.	.	.	.	X	87	.	ENSP00000374407:S87X	S	+	2	0	PKP4	159167842	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.152000	0.58111	2.792000	0.96026	0.555000	0.69702	TCA		0.269	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159459596	C	A	159459596	4	1	61	1	0	0	0	0	0	1	0	0	12018	838	29	2	270	2	PKP4	2	159459596	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	836966	159459596	83739777	1726	9711										
PKP4	8502	broad.mit.edu	37	chr2	159537101	159537101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacagtatggactgaaatCgaccacaaattatgtagact	7	8	0	2	rs199647676		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:159537101C>T	ENST00000389759.3	+	22	3603	c.3491C>T	c.(3490-3492)tCg>tTg	p.S1164L	PKP4_ENST00000389757.3_Missense_Mutation_p.S1121L|AC005042.4_ENST00000442666.1_RNA|AC005042.4_ENST00000342892.4_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	1164					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)		p.S1164L(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						GGACTGAAATCGACCACAAAT	0.418										HNSCC(62;0.18)			C|||	1	0.000199681	0	0	5008	,	,		18242	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											131	131	131					2																	159537101		2203	4300	6503	159245347	SO:0001583	missense	8502			X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.3491C>T	2.37:g.159537101C>T	ENSP00000374409:p.Ser1164Leu		159245347	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	37	CCDS33305.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.50	3.636819	0.67130	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	D;T	0.81996	-1.56;-1.39	5.49	5.49	0.81192	.	0.249150	0.35495	N	0.003179	T	0.79661	0.4484	L	0.29908	0.895	0.80722	D	1	D;D;D	0.57899	0.967;0.981;0.967	B;P;B	0.44696	0.242;0.458;0.242	T	0.82833	-0.0262	10	0.87932	D	0	-6.9202	19.7433	0.96241	0.0:1.0:0.0:0.0	.	1119;1121;1164	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	L	1121;1164	ENSP00000374407:S1121L;ENSP00000374409:S1164L	ENSP00000374407:S1121L	S	+	2	0	PKP4	159245347	1.000000	0.71417	0.966000	0.40874	0.986000	0.74619	7.445000	0.80570	2.733000	0.93635	0.655000	0.94253	TCG		0.418	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			T	159537101	C	T	159537101	3	4	61	1	0	0	0	0	1	0	0	0	12018	893	31	1	3573	1	PKP4	2	159537101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77505	159537101	83662272	1727	9712										
TANC1	85461	broad.mit.edu	37	chr2	160075828	160075828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacgcccctcatggtggctgCttgtgaagggcacttgagca	14	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160075828C>T	ENST00000263635.6	+	21	3695	c.3458C>T	c.(3457-3459)gCt>gTt	p.A1153V	TANC1_ENST00000454300.1_Missense_Mutation_p.A1047V	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1153					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)		p.A1153V(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						ATGGTGGCTGCTTGTGAAGGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											121	126	125					2																	160075828		2009	4178	6187	159784074	SO:0001583	missense	85461			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3458C>T	2.37:g.160075828C>T	ENSP00000263635:p.Ala1153Val		159784074	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	C	36	5.975178	0.97162	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.70516	-0.04;-0.49	5.49	5.49	0.81192	Ankyrin repeat-containing domain (4);	0.182250	0.47455	D	0.000222	T	0.73845	0.3639	N	0.20845	0.615	0.80722	D	1	P;P;D	0.63046	0.86;0.638;0.992	B;B;P	0.61275	0.404;0.154;0.886	T	0.78048	-0.2356	10	0.87932	D	0	.	19.0001	0.92830	0.0:1.0:0.0:0.0	.	1145;1047;1153	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	V	1047;1153	ENSP00000396339:A1047V;ENSP00000263635:A1153V	ENSP00000263635:A1153V	A	+	2	0	TANC1	159784074	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.069000	0.71209	2.578000	0.87016	0.655000	0.94253	GCT		0.507	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160075828	C	T	160075828	3	4	61	1	0	0	0	0	1	0	0	0	15583	797	28	3	3532	3	TANC1	2	160075828	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	538727	160075828	83123545	1728	9713										
TANC1	85461	broad.mit.edu	37	chr2	160085307	160085307	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttcttgtcgacaccagGactttggcatggcagaggaa	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160085307G>A	ENST00000263635.6	+	26	4288	c.4051G>A	c.(4051-4053)Gac>Aac	p.D1351N	TANC1_ENST00000454300.1_Splice_Site_p.D1245N	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1351					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)		p.D1351N(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TCGACACCAGGACTTTGGCAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2											159	157	158					2																	160085307		2002	4173	6175	159793553	SO:0001630	splice_region_variant	85461			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4051-1G>A	2.37:g.160085307G>A			159793553	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	G	35	5.597474	0.96602	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.74209	-0.82;-0.82	5.28	5.28	0.74379	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.81336	0.4801	L	0.37750	1.13	0.80722	D	1	D;P	0.89917	1.0;0.927	D;P	0.91635	0.999;0.888	T	0.79165	-0.1916	9	.	.	.	.	19.2808	0.94052	0.0:0.0:1.0:0.0	.	1343;1351	B9EK39;Q9C0D5	.;TANC1_HUMAN	N	1245;1351	ENSP00000396339:D1245N;ENSP00000263635:D1351N	.	D	+	1	0	TANC1	159793553	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.813000	0.99286	2.623000	0.88846	0.655000	0.94253	GAC		0.498	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		Missense_Mutation	A	160085307	G	A	160085307	5	1	61	1	0	0	0	0	0	0	1	0	15583	1188	41	3	4145	3	TANC1	2	160085307	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9479	160085307	83114066	1729	9714										
WDSUB1	151525	broad.mit.edu	37	chr2	160092547	160092547	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaatatcaacaattttaCttttggtgtgtctccagcca	5	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160092547C>A	ENST00000409990.3	-	11	1684	c.1428G>T	c.(1426-1428)aaG>aaT	p.K476N	WDSUB1_ENST00000359774.4_Missense_Mutation_p.K476N|WDSUB1_ENST00000392796.3_Missense_Mutation_p.K476N|WDSUB1_ENST00000409124.1_Missense_Mutation_p.K429N|WDSUB1_ENST00000358147.4_Missense_Mutation_p.K384N	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	476	U-box.						ubiquitin-protein transferase activity (GO:0004842)	p.K476N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						AACAATTTTACTTTTGGTGTG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	69	69					2																	160092547		2203	4300	6503	159800793	SO:0001583	missense	151525			AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"WD repeat domain containing", "Sterile alpha motif (SAM) domain containing", "U-box domain containing"	26697	protein-coding gene	gene with protein product			"WD repeat and SAM domain containing 1", "WD repeat, SAM and U-box domain containing 1"	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.1428G>T	2.37:g.160092547C>A	ENSP00000387078:p.Lys476Asn		159800793	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331259	0.41297	.	.	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	T;T;T;T;T	0.59906	0.6;0.23;0.6;0.6;0.57	6.17	2.53	0.30540	U box domain (1);	0.169946	0.41097	D	0.000949	T	0.43612	0.1255	L	0.36672	1.1	0.29006	N	0.88719	B;B;B	0.14438	0.01;0.003;0.003	B;B;B	0.19391	0.025;0.019;0.019	T	0.41413	-0.9510	10	0.87932	D	0	.	5.877	0.18834	0.0:0.1544:0.1393:0.7063	.	384;429;476	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	N	476;384;476;476;429	ENSP00000352820:K476N;ENSP00000350866:K384N;ENSP00000376545:K476N;ENSP00000387078:K476N;ENSP00000386891:K429N	ENSP00000350866:K384N	K	-	3	2	WDSUB1	159800793	0.623000	0.27094	1.000000	0.80357	0.154000	0.21943	0.824000	0.27379	0.198000	0.20407	-0.175000	0.13238	AAG		0.323	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		A	160092547	C	A	160092547	3	1	61	1	0	0	0	0	1	0	0	0	17381	564	20	2	6	2	WDSUB1	2	160092547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7240	160092547	83106826	1730	9715										
BAZ2B	29994	broad.mit.edu	37	chr2	160206398	160206398	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagggtgttcgtggcaaaaGactaaaccattgtctattct	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160206398G>T	ENST00000392783.2	-	28	5179	c.4684C>A	c.(4684-4686)Ctt>Att	p.L1562I	BAZ2B_ENST00000392782.1_Missense_Mutation_p.L1526I|BAZ2B_ENST00000355831.2_Missense_Mutation_p.L1528I|BAZ2B_ENST00000343439.5_Missense_Mutation_p.L1462I	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1562					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1562I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CGTGGCAAAAGACTAAACCAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											194	192	193					2																	160206398		2105	4227	6332	159914644	SO:0001583	missense	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4684C>A	2.37:g.160206398G>T	ENSP00000376534:p.Leu1562Ile		159914644	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152665	0.38021	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.68479	-0.33;-0.26;-0.33;-0.28	6.17	5.29	0.74685	.	0.000000	0.33553	U	0.004788	T	0.80717	0.4676	M	0.72894	2.215	0.53688	D	0.999974	D;D	0.71674	0.998;0.998	D;D	0.83275	0.996;0.994	T	0.81575	-0.0870	10	0.48119	T	0.1	-8.7007	15.4602	0.75349	0.066:0.0:0.934:0.0	.	1526;1562	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	I	1526;1562;1528;1462	ENSP00000376533:L1526I;ENSP00000376534:L1562I;ENSP00000348087:L1528I;ENSP00000339670:L1462I	ENSP00000339670:L1462I	L	-	1	0	BAZ2B	159914644	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.422000	0.80217	1.616000	0.50265	0.655000	0.94253	CTT		0.448	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160206398	G	T	160206398	3	4	61	1	0	0	0	0	1	0	0	0	1333	942	33	2	1862	2	BAZ2B	2	160206398	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113851	160206398	82992975	1731	9716										
BAZ2B	29994	broad.mit.edu	37	chr2	160241704	160241704	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgccagttcattgatcagGaaagccaggactgaagcttt	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160241704G>T	ENST00000392783.2	-	23	4143	c.3648C>A	c.(3646-3648)ttC>ttA	p.F1216L	BAZ2B_ENST00000392782.1_Missense_Mutation_p.F1180L|AC008277.1_ENST00000420020.1_RNA|BAZ2B_ENST00000355831.2_Missense_Mutation_p.F1182L|BAZ2B_ENST00000343439.5_Missense_Mutation_p.F1116L	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.F1216L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CATTGATCAGGAAAGCCAGGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											134	131	132					2																	160241704		1903	4135	6038	159949950	SO:0001583	missense	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.3648C>A	2.37:g.160241704G>T	ENSP00000376534:p.Phe1216Leu		159949950	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447351	0.84101	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.62941	0.05;0.08;0.05;-0.01	5.75	1.91	0.25777	.	0.000000	0.38548	U	0.001644	T	0.73241	0.3562	M	0.74467	2.265	0.50467	D	0.999872	B;D	0.71674	0.037;0.998	B;D	0.73380	0.024;0.98	T	0.70912	-0.4743	10	0.59425	D	0.04	-2.7574	7.2237	0.26003	0.2579:0.1145:0.6276:0.0	.	1180;1216	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	L	1180;1216;1182;1116	ENSP00000376533:F1180L;ENSP00000376534:F1216L;ENSP00000348087:F1182L;ENSP00000339670:F1116L	ENSP00000339670:F1116L	F	-	3	2	BAZ2B	159949950	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.829000	0.39121	0.341000	0.23771	0.655000	0.94253	TTC		0.438	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160241704	G	T	160241704	3	4	61	1	0	0	0	0	1	0	0	0	1333	1165	41	2	2918	2	BAZ2B	2	160241704	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35306	160241704	82957669	1732	9717										
BAZ2B	29994	broad.mit.edu	37	chr2	160268930	160268930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggaggtcgacctttccGacgtctcatcctggattcct	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160268930G>A	ENST00000392783.2	-	14	3088	c.2593C>T	c.(2593-2595)Cgg>Tgg	p.R865W	BAZ2B_ENST00000392782.1_Missense_Mutation_p.R829W|BAZ2B_ENST00000355831.2_Missense_Mutation_p.R831W|BAZ2B_ENST00000343439.5_Missense_Mutation_p.R765W	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	865	Arg-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R865W(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CGACCTTTCCGACGTCTCATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											254	228	236					2																	160268930		1956	4148	6104	159977176	SO:0001583	missense	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2593C>T	2.37:g.160268930G>A	ENSP00000376534:p.Arg865Trp		159977176	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	19.19	3.778851	0.70107	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;D	0.86366	0.16;0.23;0.16;-2.11	5.56	5.56	0.83823	.	0.000000	0.35378	U	0.003248	D	0.89308	0.6678	L	0.29908	0.895	0.58432	D	0.999995	P;P;D;P	0.89917	0.523;0.477;1.0;0.53	B;B;D;B	0.79108	0.089;0.106;0.992;0.069	D	0.90178	0.4240	10	0.72032	D	0.01	-8.3128	14.3697	0.66830	0.0:0.0:0.852:0.148	.	669;765;829;865	Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;BAZ2B_HUMAN	W	829;865;831;765	ENSP00000376533:R829W;ENSP00000376534:R865W;ENSP00000348087:R831W;ENSP00000339670:R765W	ENSP00000339670:R765W	R	-	1	2	BAZ2B	159977176	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.388000	0.59633	2.605000	0.88082	0.557000	0.71058	CGG		0.453	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160268930	G	A	160268930	3	1	61	1	0	0	0	0	1	0	0	0	1333	1057	37	1	4009	1	BAZ2B	2	160268930	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27226	160268930	82930443	1733	9718										
LY75	4065	broad.mit.edu	37	chr2	160661611	160661611	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcactccttgtgcatatcGaactgatgagaaacccgcca	7	12	1	2	rs139579850		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160661611G>A	ENST00000263636.4	-	35	5140	c.5113C>T	c.(5113-5115)Cga>Tga	p.R1705*	LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron|LY75_ENST00000554112.1_Intron	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1705					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R1705*(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TGTGCATATCGAACTGATGAG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	2						G	,,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	90	85	87		,,5113	5.7	1	2	dbSNP_134	87	0,8600		0,0,4300	no	intron,intron,stop-gained	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	,,1705/1723	160661611	1,13005	2203	4300	6503	160369857	SO:0001587	stop_gained	4065			AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.5113C>T	2.37:g.160661611G>A	ENSP00000263636:p.Arg1705*		160369857	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Nonsense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	41	8.903613	0.98996	2.27E-4	0.0	ENSG00000054219	ENST00000263636	.	.	.	5.66	5.66	0.87406	.	0.709223	0.10881	U	0.623853	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6706	0.85266	0.0:0.0:1.0:0.0	.	.	.	.	X	1705	.	ENSP00000263636:R1705X	R	-	1	2	LY75	160369857	1.000000	0.71417	1.000000	0.80357	0.195000	0.23768	5.563000	0.67352	2.690000	0.91761	0.655000	0.94253	CGA		0.398	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160661611	G	A	160661611	4	1	61	1	0	0	0	0	0	1	0	0	9129	1066	37	1	59	1	LY75	2	160661611	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	392681	160661611	82537762	1734	9719										
LY75	4065	broad.mit.edu	37	chr2	160676304	160676304	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcttcaataactttaaaGgtttgaatatcccagaagcc	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160676304G>T	ENST00000263636.4	-	29	4113	c.4086C>A	c.(4084-4086)acC>acA	p.T1362T	LY75_ENST00000553424.1_Silent_p.T1362T|LY75-CD302_ENST00000504764.1_Silent_p.T1362T|LY75-CD302_ENST00000505052.1_Silent_p.T1362T|LY75_ENST00000554112.1_Silent_p.T1362T	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1362	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.T1362T(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TAACTTTAAAGGTTTGAATAT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	2											83	90	88					2																	160676304		2203	4300	6503	160384550	SO:0001819	synonymous_variant	4065			AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4086C>A	2.37:g.160676304G>T			160384550	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																				0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160676304	G	T	160676304	2	4	61	1	0	0	0	0	0	0	0	1	9129	987	35	2		2	LY75	2	160676304	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14693	160676304	82523069	1735	9720										
PLA2R1	22925	broad.mit.edu	37	chr2	160806201	160806201	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgttgctgtcggcaaaaacGcagtcaccaaggagggagga	14	10	1	0	rs374812046		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160806201G>A	ENST00000283243.7	-	25	3833	c.3627C>T	c.(3625-3627)tgC>tgT	p.C1209C	PLA2R1_ENST00000392771.1_Silent_p.C1209C	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1209	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)	p.C1209C(1)	PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CGGCAAAAACGCAGTCACCAA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G	,,	0,4406		0,0,2203	86	81	83		3627,3627,3627	0.6	1	2		83	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	1209/1325,1209/1462,1209/1464	160806201	2,13004	2203	4300	6503	160514447	SO:0001819	synonymous_variant	22925			U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3627C>T	2.37:g.160806201G>A			160514447	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																				0.478	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			A	160806201	G	A	160806201	2	1	61	1	0	0	0	0	0	0	0	1	12041	1079	38	1		1	PLA2R1	2	160806201	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129897	160806201	82393172	1736	9721										
PLA2R1	22925	broad.mit.edu	37	chr2	160832605	160832605	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttgctgtggatgaattCttgctcatgtgcagaatgaa	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160832605C>A	ENST00000283243.7	-	17	2775	c.2569G>T	c.(2569-2571)Gaa>Taa	p.E857*	PLA2R1_ENST00000392771.1_Nonsense_Mutation_p.E857*	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	857	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)	p.E857*(1)|p.E857K(1)	PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						TGGATGAATTCTTGCTCATGT	0.423																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|skin(1)	2											161	150	154					2																	160832605		2203	4300	6503	160540851	SO:0001587	stop_gained	22925			U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.2569G>T	2.37:g.160832605C>A	ENSP00000283243:p.Glu857*		160540851	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Nonsense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	C	40	8.310297	0.98754	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	.	.	.	5.18	5.18	0.71444	.	0.299112	0.37623	N	0.002020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	17.8206	0.88649	0.0:1.0:0.0:0.0	.	.	.	.	X	857	.	ENSP00000283243:E857X	E	-	1	0	PLA2R1	160540851	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	3.449000	0.52950	2.560000	0.86352	0.561000	0.74099	GAA		0.423	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			A	160832605	C	A	160832605	4	1	61	1	0	0	0	0	0	1	0	0	12041	922	32	2	1886	2	PLA2R1	2	160832605	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26404	160832605	82366768	1737	9722										
PLA2R1	22925	broad.mit.edu	37	chr2	160901352	160901352	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccacttatgaatatacttCcgtgaggccaccactgtgtt	7	11	0	2	rs267598938		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:160901352C>T	ENST00000283243.7	-	2	632	c.426G>A	c.(424-426)cgG>cgA	p.R142R	PLA2R1_ENST00000392771.1_Silent_p.R142R	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	142	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		R -> Q (in dbSNP:rs12327936).		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)	p.R142R(1)	PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GAATATACTTCCGTGAGGCCA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	2											77	80	79					2																	160901352		2203	4300	6503	160609598	SO:0001819	synonymous_variant	22925			U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.426G>A	2.37:g.160901352C>T			160609598	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																				0.468	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160901352	C	T	160901352	2	4	61	1	0	0	0	0	0	0	0	1	12041	842	30	3		3	PLA2R1	2	160901352	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68747	160901352	82298021	1738	9723										
TANK	10010	broad.mit.edu	37	chr2	162087536	162087536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaacagataaacaagaagCgctgtttaagcctcaggcta	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162087536C>T	ENST00000392749.2	+	7	814	c.575C>T	c.(574-576)gCg>gTg	p.A192V	TANK_ENST00000405852.1_Missense_Mutation_p.A192V|TANK_ENST00000259075.2_Missense_Mutation_p.A192V|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000402568.1_Intron|AC009299.2_ENST00000445372.1_RNA|TANK_ENST00000406287.1_Intron	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	192					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.A192V(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						AAACAAGAAGCGCTGTTTAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	61	62					2																	162087536		2203	4300	6503	161795782	SO:0001583	missense	10010			U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.575C>T	2.37:g.162087536C>T	ENSP00000376505:p.Ala192Val		161795782	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.	.	.	.	.	.	.	.	.	.	C	5.480	0.273540	0.10403	.	.	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623	T;T;T;T	0.32753	1.88;1.88;1.44;1.46	5.78	-1.47	0.08772	.	0.499035	0.23123	N	0.051672	T	0.10508	0.0257	N	0.08118	0	0.31671	N	0.644309	B	0.12013	0.005	B	0.06405	0.002	T	0.21793	-1.0235	10	0.15952	T	0.53	-0.0219	4.2335	0.10615	0.3811:0.2845:0.0:0.3344	.	192	Q92844	TANK_HUMAN	V	192;192;192;83	ENSP00000259075:A192V;ENSP00000376505:A192V;ENSP00000385487:A192V;ENSP00000412556:A83V	ENSP00000259075:A192V	A	+	2	0	TANK	161795782	0.507000	0.26146	0.460000	0.27093	0.174000	0.22865	0.196000	0.17176	-0.052000	0.13311	-0.186000	0.12905	GCG		0.438	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		T	162087536	C	T	162087536	3	4	61	1	0	0	0	0	1	0	0	0	15585	768	27	1	630	1	TANK	2	162087536	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1186184	162087536	81111837	1739	9724										
TANK	10010	broad.mit.edu	37	chr2	162087872	162087872	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagctatacaaaaccttaAaacaactgacaaaacaaagc	3	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162087872A>C	ENST00000392749.2	+	7	1150	c.911A>C	c.(910-912)aAa>aCa	p.K304T	TANK_ENST00000405852.1_Missense_Mutation_p.K304T|TANK_ENST00000259075.2_Missense_Mutation_p.K304T|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000402568.1_Intron|AC009299.2_ENST00000445372.1_RNA|TANK_ENST00000406287.1_Intron	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	304					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.K304T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CAAAACCTTAAAACAACTGAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											95	95	95					2																	162087872		2203	4300	6503	161796118	SO:0001583	missense	10010			U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.911A>C	2.37:g.162087872A>C	ENSP00000376505:p.Lys304Thr		161796118	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.	.	.	.	.	.	.	.	.	.	A	9.892	1.204558	0.22205	.	.	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623;ENST00000439442	T;T;T;T;T	0.35048	1.79;1.79;1.33;1.35;1.84	5.58	4.35	0.52113	.	0.230481	0.37809	N	0.001932	T	0.25975	0.0633	L	0.43152	1.355	0.80722	D	1	B	0.21071	0.051	B	0.14023	0.01	T	0.08166	-1.0735	10	0.23891	T	0.37	-15.4339	6.8538	0.24030	0.6344:0.2461:0.0:0.1194	.	304	Q92844	TANK_HUMAN	T	304;304;304;195;59	ENSP00000259075:K304T;ENSP00000376505:K304T;ENSP00000385487:K304T;ENSP00000412556:K195T;ENSP00000387439:K59T	ENSP00000259075:K304T	K	+	2	0	TANK	161796118	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	1.309000	0.33539	2.250000	0.74265	0.482000	0.46254	AAA		0.398	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		C	162087872	A	C	162087872	3	2	61	1	0	0	0	0	1	0	0	0	15585	14	1	4	966	4	TANK	2	162087872	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	336	162087872	81111501	1740	9725										
TBR1	10716	broad.mit.edu	37	chr2	162274716	162274716	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttctttctctaggaaaTcgggtctatatgcatccgga	9	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162274716T>C	ENST00000389554.3	+	3	1169	c.852T>C	c.(850-852)aaT>aaC	p.N284N	TBR1_ENST00000410035.1_5'UTR	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	284					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N284N(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						CTCTAGGAAATCGGGTCTATA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											55	58	57					2																	162274716		2203	4300	6503	161982962	SO:0001819	synonymous_variant	10716			U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"T-boxes"	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.852T>C	2.37:g.162274716T>C			161982962	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	37	CCDS33310.1																																																																																				0.473	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593		C	162274716	T	C	162274716	2	2	61	1	0	0	0	0	0	0	0	1	15686	1432	50	4		4	TBR1	2	162274716	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	186844	162274716	80924657	1741	9726										
SLC4A10	57282	broad.mit.edu	37	chr2	162696337	162696337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagtttattcttggaaccGaggatgatgacgaggaacac	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162696337G>A	ENST00000446997.1	+	4	409	c.316G>A	c.(316-318)Gag>Aag	p.E106K	SLC4A10_ENST00000375514.5_Missense_Mutation_p.E117K|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000415876.2_Missense_Mutation_p.E106K|SLC4A10_ENST00000421911.1_Missense_Mutation_p.E106K|SLC4A10_ENST00000535165.1_Missense_Mutation_p.E106K|SLC4A10_ENST00000272716.5_Missense_Mutation_p.E106K	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	106					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)	p.E106K(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	TCTTGGAACCGAGGATGATGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	121	122					2																	162696337		2086	4236	6322	162404583	SO:0001583	missense	57282				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.316G>A	2.37:g.162696337G>A	ENSP00000393066:p.Glu106Lys		162404583	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	37	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	G	36	5.817536	0.96982	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000535165;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T;T	0.80393	-1.34;-1.34;0.42;-1.35;-1.37;-1.37	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.90570	0.7044	M	0.82823	2.61	0.80722	D	1	D;P;D;D	0.89917	1.0;0.78;1.0;0.99	D;B;D;P	0.74674	0.984;0.277;0.984;0.715	D	0.90231	0.4279	10	0.48119	T	0.1	.	19.616	0.95634	0.0:0.0:1.0:0.0	.	117;106;106;106	F8W675;E7EW28;Q6U841-2;Q6U841	.;.;.;S4A10_HUMAN	K	117;106;106;106;106;106;106;106	ENSP00000364664:E117K;ENSP00000395797:E106K;ENSP00000437527:E106K;ENSP00000272716:E106K;ENSP00000393066:E106K;ENSP00000404486:E106K	ENSP00000272716:E106K	E	+	1	0	SLC4A10	162404583	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.670000	0.98625	2.646000	0.89796	0.650000	0.86243	GAG		0.453	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		A	162696337	G	A	162696337	3	1	61	1	0	0	0	0	1	0	0	0	14688	1059	37	1	415	1	SLC4A10	2	162696337	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	421621	162696337	80503036	1742	9727										
SLC4A10	57282	broad.mit.edu	37	chr2	162760617	162760617	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttagcatcttttctatttCtctactgcgcgtgtatgtct	7	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162760617C>A	ENST00000446997.1	+	13	1639	c.1546C>A	c.(1546-1548)Ctc>Atc	p.L516I	SLC4A10_ENST00000375514.5_Missense_Mutation_p.L497I|SLC4A10_ENST00000415876.2_Missense_Mutation_p.L486I|SLC4A10_ENST00000421911.1_Missense_Mutation_p.L516I|SLC4A10_ENST00000535165.1_3'UTR|SLC4A10_ENST00000272716.5_Missense_Mutation_p.L486I	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	516					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)	p.L486I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	TTTTCTATTTCTCTACTGCGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	70	71					2																	162760617		1882	4154	6036	162468863	SO:0001583	missense	57282				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.1546C>A	2.37:g.162760617C>A	ENSP00000393066:p.Leu516Ile		162468863	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	37	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251416	0.59212	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14	5.65	5.65	0.86999	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81791	0.4897	L	0.45137	1.4	0.80722	D	1	D;D;P	0.63046	0.992;0.992;0.522	D;D;B	0.66716	0.946;0.946;0.433	T	0.74337	-0.3698	10	0.02654	T	1	.	19.7176	0.96129	0.0:1.0:0.0:0.0	.	497;486;516	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	I	497;486;486;485;516;516;515	ENSP00000364664:L497I;ENSP00000395797:L486I;ENSP00000272716:L486I;ENSP00000393066:L516I;ENSP00000404486:L516I	ENSP00000272716:L486I	L	+	1	0	SLC4A10	162468863	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	2.670000	0.90874	0.563000	0.77884	CTC		0.423	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		A	162760617	C	A	162760617	3	1	61	1	0	0	0	0	1	0	0	0	14688	913	32	2	1681	2	SLC4A10	2	162760617	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64280	162760617	80438756	1743	9728										
SLC4A10	57282	broad.mit.edu	37	chr2	162820806	162820806	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcaagagctgctattgtCtttcccatgatggtatgaaa	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:162820806C>A	ENST00000446997.1	+	22	3117	c.3024C>A	c.(3022-3024)gtC>gtA	p.V1008V	SLC4A10_ENST00000375514.5_Silent_p.V989V|SLC4A10_ENST00000415876.2_Silent_p.V978V|SLC4A10_ENST00000421911.1_Silent_p.V1008V|SLC4A10_ENST00000272716.5_Silent_p.V978V	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	1008				V -> A (in Ref. 3; BAH11596). {ECO:0000305}.	bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)	p.V978V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	CTGCTATTGTCTTTCCCATGA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	2											103	93	96					2																	162820806		1845	4093	5938	162529052	SO:0001819	synonymous_variant	57282				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.3024C>A	2.37:g.162820806C>A			162529052	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	37	CCDS54411.1																																																																																				0.378	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		A	162820806	C	A	162820806	2	1	61	1	0	0	0	0	0	0	0	1	14688	900	32	2		2	SLC4A10	2	162820806	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60189	162820806	80378567	1744	9729										
FAP	2191	broad.mit.edu	37	chr2	163029724	163029724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctgctcttgccatcacaGttgaattctggaaaagagaa	8	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163029724G>T	ENST00000188790.4	-	24	2249	c.2042C>A	c.(2041-2043)aCt>aAt	p.T681N	FAP_ENST00000443424.1_Missense_Mutation_p.T656N|AC007750.5_ENST00000418968.3_RNA	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha									p.T681N(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TGCCATCACAGTTGAATTCTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	99	99					2																	163029724		2203	4300	6503	162737970	SO:0001583	missense	2191			U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.2042C>A	2.37:g.163029724G>T	ENSP00000188790:p.Thr681Asn		162737970		Missense_Mutation	SNP	ENST00000188790.4	37	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745037	0.69418	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.39997	1.05;1.05	5.62	5.62	0.85841	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.047437	0.85682	D	0.000000	T	0.49167	0.1541	N	0.16656	0.425	0.80722	D	1	B;B;D	0.54772	0.41;0.168;0.968	B;B;D	0.63283	0.241;0.234;0.913	T	0.47497	-0.9113	10	0.42905	T	0.14	-24.1704	20.024	0.97514	0.0:0.0:1.0:0.0	.	656;160;681	B4DLR2;Q12884-2;Q12884	.;.;SEPR_HUMAN	N	681;656	ENSP00000188790:T681N;ENSP00000411391:T656N	ENSP00000188790:T681N	T	-	2	0	FAP	162737970	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.995000	0.93534	2.809000	0.96659	0.655000	0.94253	ACT		0.348	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			T	163029724	G	T	163029724	3	4	61	1	0	0	0	0	1	0	0	0	5692	1029	36	2	252	2	FAP	2	163029724	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208918	163029724	80169649	1745	9730										
KCNH7	90134	broad.mit.edu	37	chr2	163279902	163279902	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctggaaatattcttcaaGacgttgcctcagagggttgg	13	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163279902G>T	ENST00000332142.5	-	9	2197	c.2098C>A	c.(2098-2100)Ctt>Att	p.L700I	KCNH7_ENST00000328032.4_Missense_Mutation_p.L693I	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	700					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.L700I(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TATTCTTCAAGACGTTGCCTC	0.453																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	large_intestine(1)	2											253	235	242					2																	163279902		2203	4300	6503	162988148	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2098C>A	2.37:g.163279902G>T	ENSP00000331727:p.Leu700Ile		162988148	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	G	32	5.168623	0.94768	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.96041	-3.89;-3.89	5.95	5.95	0.96441	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.97161	0.9072	L	0.52905	1.665	0.80722	D	1	D;D	0.89917	1.0;0.974	D;P	0.85130	0.997;0.841	D	0.96595	0.9440	10	0.48119	T	0.1	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	693;700	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	I	700;693	ENSP00000331727:L700I;ENSP00000333781:L693I	ENSP00000333781:L693I	L	-	1	0	KCNH7	162988148	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.729000	0.74775	2.824000	0.97209	0.655000	0.94253	CTT		0.453	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		T	163279902	G	T	163279902	3	4	61	1	0	0	0	0	1	0	0	0	8058	942	33	2	1590	2	KCNH7	2	163279902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	250178	163279902	79919471	1746	9731										
KCNH7	90134	broad.mit.edu	37	chr2	163291772	163291772	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttaggagacacattcccGaatcctacactggttaaact	8	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163291772G>A	ENST00000332142.5	-	8	1989	c.1890C>T	c.(1888-1890)ttC>ttT	p.F630F	KCNH7_ENST00000328032.4_Silent_p.F623F	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	630					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.F630F(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	ACACATTCCCGAATCCTACAC	0.383																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - coding silent(1)	large_intestine(1)	2											170	156	161					2																	163291772		2203	4300	6503	163000018	SO:0001819	synonymous_variant	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1890C>T	2.37:g.163291772G>A			163000018	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	CCDS2219.1																																																																																				0.383	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163291772	G	A	163291772	2	1	61	1	0	0	0	0	0	0	0	1	8058	1049	37	1		1	KCNH7	2	163291772	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11870	163291772	79907601	1747	9732										
KCNH7	90134	broad.mit.edu	37	chr2	163292002	163292002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaaagatgcacattaagaGcattagaacagcagcgccat	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163292002G>T	ENST00000332142.5	-	8	1759	c.1660C>A	c.(1660-1662)Ctc>Atc	p.L554I	KCNH7_ENST00000328032.4_Missense_Mutation_p.L547I	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	554					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.L554I(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CACATTAAGAGCATTAGAACA	0.473																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	large_intestine(1)	2											90	85	87					2																	163292002		2203	4300	6503	163000248	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1660C>A	2.37:g.163292002G>T	ENSP00000331727:p.Leu554Ile		163000248	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.955747	0.92726	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.98474	-4.95;-4.95	5.9	5.9	0.94986	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98620	0.9538	M	0.66506	2.035	0.80722	D	1	D;P	0.89917	1.0;0.933	D;P	0.91635	0.999;0.718	D	0.99063	1.0831	10	0.87932	D	0	.	14.4259	0.67215	0.0698:0.0:0.9302:0.0	.	547;554	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	I	554;547	ENSP00000331727:L554I;ENSP00000333781:L547I	ENSP00000333781:L547I	L	-	1	0	KCNH7	163000248	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.687000	0.68219	2.788000	0.95919	0.650000	0.86243	CTC		0.473	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		T	163292002	G	T	163292002	3	4	61	1	0	0	0	0	1	0	0	0	8058	971	34	2	2032	2	KCNH7	2	163292002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	230	163292002	79907371	1748	9733										
KCNH7	90134	broad.mit.edu	37	chr2	163693250	163693250	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggcacagttctgcactCtggcatttgcaatgataaat	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163693250C>A	ENST00000332142.5	-	2	203	c.104G>T	c.(103-105)aGa>aTa	p.R35I	KCNH7_ENST00000328032.4_Missense_Mutation_p.R35I	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	35					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.R35I(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GTTCTGCACTCTGGCATTTGC	0.403																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	large_intestine(1)	2											63	57	59					2																	163693250		2203	4300	6503	163401496	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.104G>T	2.37:g.163693250C>A	ENSP00000331727:p.Arg35Ile		163401496	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172520	0.94807	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.99619	-5.13;-6.28	6.08	6.08	0.98989	PAS (1);	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	M	0.83774	2.66	0.80722	D	1	P;P	0.52842	0.956;0.956	P;D	0.67231	0.79;0.95	D	0.98378	1.0557	10	0.87932	D	0	.	19.6516	0.95815	0.0:1.0:0.0:0.0	.	35;35	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	I	35	ENSP00000331727:R35I;ENSP00000333781:R35I	ENSP00000333781:R35I	R	-	2	0	KCNH7	163401496	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.894000	0.99253	0.655000	0.94253	AGA		0.403	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163693250	C	A	163693250	3	1	61	1	0	0	0	0	1	0	0	0	8058	913	32	2	3612	2	KCNH7	2	163693250	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	401248	163693250	79506123	1749	9734										
KCNH7	90134	broad.mit.edu	37	chr2	163694963	163694963	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaacttactttgcccttcAaatttccgaatgatggtccc	6	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:163694963A>C	ENST00000332142.5	-	1	165	c.66T>G	c.(64-66)ttT>ttG	p.F22L	KCNH7_ENST00000328032.4_Missense_Mutation_p.F22L	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	22					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.F22L(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TTTGCCCTTCAAATTTCCGAA	0.567																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	large_intestine(1)	2											160	136	144					2																	163694963		2203	4300	6503	163403209	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.66T>G	2.37:g.163694963A>C	ENSP00000331727:p.Phe22Leu		163403209	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636460	0.47049	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.99598	-5.14;-6.26	5.44	4.3	0.51218	PAS (1);	0.000000	0.85682	D	0.000000	D	0.99441	0.9802	M	0.77406	2.37	0.42035	D	0.991045	D;B	0.64830	0.994;0.002	D;B	0.71870	0.975;0.011	D	0.98576	1.0648	10	0.72032	D	0.01	.	10.0117	0.41990	0.9209:0.0:0.0791:0.0	.	22;22	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	L	22	ENSP00000331727:F22L;ENSP00000333781:F22L	ENSP00000333781:F22L	F	-	3	2	KCNH7	163403209	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.037000	0.41174	2.062000	0.61559	0.377000	0.23210	TTT		0.567	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		C	163694963	A	C	163694963	3	2	61	1	0	0	0	0	1	0	0	0	8058	127	5	4	3654	4	KCNH7	2	163694963	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1713	163694963	79504410	1750	9735										
GRB14	2888	broad.mit.edu	37	chr2	165353991	165353991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctaccagggaattctctgAtatacttctctggaaaaaag	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165353991A>G	ENST00000263915.3	-	10	1652	c.1114T>C	c.(1114-1116)Tca>Cca	p.S372P	GRB14_ENST00000543549.1_Missense_Mutation_p.S285P|GRB14_ENST00000497306.1_5'Flank	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	372					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.S372P(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						GAATTCTCTGATATACTTCTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	70	70					2																	165353991		2203	4300	6503	165062237	SO:0001583	missense	2888				CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.1114T>C	2.37:g.165353991A>G	ENSP00000263915:p.Ser372Pro		165062237	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.691297	0.88735	.	.	ENSG00000115290	ENST00000263915;ENST00000543549;ENST00000446413	T;T;T	0.41400	1.51;1.6;1.0	5.71	5.71	0.89125	BPS (Between PH and SH2) domain (1);	0.000000	0.85682	D	0.000000	T	0.66587	0.2804	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.71130	-0.4682	10	0.87932	D	0	-8.5627	15.9883	0.80179	1.0:0.0:0.0:0.0	.	285;372	B7Z7F9;Q14449	.;GRB14_HUMAN	P	372;285;327	ENSP00000263915:S372P;ENSP00000443699:S285P;ENSP00000416786:S327P	ENSP00000263915:S372P	S	-	1	0	GRB14	165062237	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.313000	0.96297	2.172000	0.68678	0.533000	0.62120	TCA		0.353	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			G	165353991	A	G	165353991	3	3	61	1	0	0	0	0	1	0	0	0	6778	333	12	4	528	4	GRB14	2	165353991	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1659028	165353991	77845382	1751	9736										
GRB14	2888	broad.mit.edu	37	chr2	165383583	165383583	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaaagtatagtttgttttCttcttctatcccccagttgg	6	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165383583C>A	ENST00000263915.3	-	4	1082	c.544G>T	c.(544-546)Gaa>Taa	p.E182*	GRB14_ENST00000543549.1_Nonsense_Mutation_p.E95*	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	182	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.E182*(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						AGTTTGTTTTCTTCTTCTATC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											104	103	104					2																	165383583		2202	4295	6497	165091829	SO:0001587	stop_gained	2888				CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.544G>T	2.37:g.165383583C>A	ENSP00000263915:p.Glu182*		165091829	B7Z7F9|Q7Z6I1	Nonsense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	C	37	6.635167	0.97722	.	.	ENSG00000115290	ENST00000263915;ENST00000543549;ENST00000446413;ENST00000424693	.	.	.	5.84	5.84	0.93424	.	0.242338	0.48767	D	0.000173	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-9.6295	20.139	0.98050	0.0:1.0:0.0:0.0	.	.	.	.	X	182;95;137;124	.	ENSP00000263915:E182X	E	-	1	0	GRB14	165091829	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.640000	0.83355	2.764000	0.94973	0.655000	0.94253	GAA		0.328	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			A	165383583	C	A	165383583	4	1	61	1	0	0	0	0	0	1	0	0	6778	922	32	2	1122	2	GRB14	2	165383583	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29592	165383583	77815790	1752	9737										
COBLL1	22837	broad.mit.edu	37	chr2	165551820	165551820	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtaagaagcagtggaattTttgtcaatcctatctacagg	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165551820T>G	ENST00000392717.2	-	13	2314	c.2310A>C	c.(2308-2310)aaA>aaC	p.K770N	COBLL1_ENST00000194871.6_Missense_Mutation_p.K799N|COBLL1_ENST00000409184.3_Missense_Mutation_p.K732N|COBLL1_ENST00000375458.2_Missense_Mutation_p.K694N|COBLL1_ENST00000342193.4_Missense_Mutation_p.K732N			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	770						extracellular vesicular exosome (GO:0070062)		p.K732N(2)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CAGTGGAATTTTTGTCAATCC	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	2											160	160	160					2																	165551820		2203	4300	6503	165260066	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2310A>C	2.37:g.165551820T>G	ENSP00000376478:p.Lys770Asn		165260066	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	T	14.77	2.635279	0.47049	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.03	3.66	0.41972	.	0.072732	0.64402	D	0.000018	T	0.68504	0.3008	L	0.58101	1.795	0.37042	D	0.897206	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.76575	0.988;0.988;0.974	T	0.71715	-0.4509	9	0.72032	D	0.01	-12.774	8.414	0.32659	0.0:0.0686:0.1328:0.7986	.	770;799;732	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	N	694;732;732;770;799	.	ENSP00000194871:K799N	K	-	3	2	COBLL1	165260066	0.997000	0.39634	0.766000	0.31476	0.291000	0.27294	1.827000	0.39102	0.519000	0.28406	0.455000	0.32223	AAA		0.378	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		G	165551820	T	G	165551820	3	3	61	1	0	0	0	0	1	0	0	0	3660	1838	64	4	1316	4	COBLL1	2	165551820	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	168237	165551820	77647553	1753	9738										
COBLL1	22837	broad.mit.edu	37	chr2	165552275	165552275	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaccttctacattgatttCtgttttcttcactccatttt	2	11	4	1	rs554340557	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165552275C>A	ENST00000392717.2	-	13	1859	c.1855G>T	c.(1855-1857)Gaa>Taa	p.E619*	COBLL1_ENST00000194871.6_Nonsense_Mutation_p.E648*|COBLL1_ENST00000409184.3_Nonsense_Mutation_p.E581*|COBLL1_ENST00000375458.2_Nonsense_Mutation_p.E543*|COBLL1_ENST00000342193.4_Nonsense_Mutation_p.E581*			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	619						extracellular vesicular exosome (GO:0070062)		p.E581*(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						ACATTGATTTCTGTTTTCTTC	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											148	135	139					2																	165552275		2203	4300	6503	165260521	SO:0001587	stop_gained	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1855G>T	2.37:g.165552275C>A	ENSP00000376478:p.Glu619*		165260521	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Nonsense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	C	36	5.781320	0.96929	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.43	5.43	0.79202	.	0.393509	0.25912	N	0.027498	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-9.6741	18.2479	0.89993	0.0:1.0:0.0:0.0	.	.	.	.	X	543;581;581;619;648	.	ENSP00000194871:E648X	E	-	1	0	COBLL1	165260521	0.984000	0.35163	0.968000	0.41197	0.042000	0.13812	1.091000	0.30915	2.558000	0.86282	0.655000	0.94253	GAA		0.318	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165552275	C	A	165552275	4	1	61	1	0	0	0	0	0	1	0	0	3660	922	32	2	1771	2	COBLL1	2	165552275	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455	165552275	77647098	1754	9739										
SLC38A11	151258	broad.mit.edu	37	chr2	165772438	165772438	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacataaccccgaccgcttgAatggcattgggctttgcaaa	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165772438A>G	ENST00000409149.3	-	7	786	c.495T>C	c.(493-495)atT>atC	p.I165I	SLC38A11_ENST00000303735.4_Silent_p.I143I|SLC38A11_ENST00000409058.1_Silent_p.I196I|SLC38A11_ENST00000493887.1_5'UTR|SLC38A11_ENST00000409662.1_Silent_p.I165I	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	165					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.I143I(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						CGACCGCTTGAATGGCATTGG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	2											208	224	218					2																	165772438		2203	4300	6503	165480684	SO:0001819	synonymous_variant	151258				CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"Solute carriers"	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.495T>C	2.37:g.165772438A>G			165480684	B4DF99|Q8N887	Silent	SNP	ENST00000409149.3	37	CCDS56142.1																																																																																				0.373	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512		G	165772438	A	G	165772438	2	3	61	1	0	0	0	0	0	0	0	1	14640	242	9	4		4	SLC38A11	2	165772438	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	220163	165772438	77426935	1755	9740										
SCN3A	6328	broad.mit.edu	37	chr2	165969469	165969469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccataagcaacccatttgaGaagcatttccagaatgaata	6	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165969469G>T	ENST00000360093.3	-	21	4260	c.3769C>A	c.(3769-3771)Ctc>Atc	p.L1257I	SCN3A_ENST00000283254.7_Missense_Mutation_p.L1257I|SCN3A_ENST00000409101.3_Missense_Mutation_p.L1208I	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1257					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.L1257I(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACCCATTTGAGAAGCATTTCC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											189	208	202					2																	165969469		2203	4296	6499	165677715	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.3769C>A	2.37:g.165969469G>T	ENSP00000353206:p.Leu1257Ile		165677715	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	G	20.6	4.017173	0.75161	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.98849	-5.18;-5.18;-5.18;-5.18	5.88	5.88	0.94601	Ion transport (1);	0.000000	0.52532	D	0.000076	D	0.98425	0.9476	L	0.42245	1.32	0.80722	D	1	D;D;D;D;D	0.89917	0.99;0.997;0.998;0.998;1.0	D;D;D;D;D	0.91635	0.945;0.992;0.99;0.99;0.999	D	0.97774	1.0228	10	0.36615	T	0.2	.	13.8521	0.63504	0.0783:0.0:0.9217:0.0	.	1257;1208;1208;1208;1257	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	I	1257;1257;1208;1208	ENSP00000353206:L1257I;ENSP00000283254:L1257I;ENSP00000386726:L1208I;ENSP00000403348:L1208I	ENSP00000283254:L1257I	L	-	1	0	SCN3A	165677715	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	4.467000	0.60155	2.789000	0.95967	0.591000	0.81541	CTC		0.333	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		T	165969469	G	T	165969469	3	4	61	1	0	0	0	0	1	0	0	0	13955	942	33	2	2265	2	SCN3A	2	165969469	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197031	165969469	77229904	1756	9741										
SCN3A	6328	broad.mit.edu	37	chr2	165994619	165994619	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggacatttctgtctagattCttcaagttctggagggacaa	10	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:165994619C>A	ENST00000360093.3	-	15	2652	c.2161G>T	c.(2161-2163)Gaa>Taa	p.E721*	SCN3A_ENST00000283254.7_Nonsense_Mutation_p.E721*|SCN3A_ENST00000409101.3_Nonsense_Mutation_p.E672*	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	721					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E721*(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTCTAGATTCTTCAAGTTCT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											67	68	68					2																	165994619		2203	4299	6502	165702865	SO:0001587	stop_gained	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2161G>T	2.37:g.165994619C>A	ENSP00000353206:p.Glu721*		165702865	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Nonsense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	45	11.730589	0.99596	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	.	.	.	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.3431	0.98773	0.0:1.0:0.0:0.0	.	.	.	.	X	721;721;672;672	.	ENSP00000283254:E721X	E	-	1	0	SCN3A	165702865	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	2.880000	0.98712	0.650000	0.86243	GAA		0.343	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		A	165994619	C	A	165994619	4	1	61	1	0	0	0	0	0	1	0	0	13955	922	32	2	3897	2	SCN3A	2	165994619	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25150	165994619	77204754	1757	9742										
SCN2A	6326	broad.mit.edu	37	chr2	166165920	166165920	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttgagaacattcagagttCtccgagcattgaaaacaatt	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166165920C>T	ENST00000375437.2	+	6	954	c.664C>T	c.(664-666)Ctc>Ttc	p.L222F	SCN2A_ENST00000357398.3_Intron|SCN2A_ENST00000283256.6_Missense_Mutation_p.L222F|SCN2A_ENST00000375427.2_Intron	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	222					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.L222F(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATTCAGAGTTCTCCGAGCATT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	93	97					2																	166165920		2203	4299	6502	165874166	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.664C>T	2.37:g.166165920C>T	ENSP00000364586:p.Leu222Phe		165874166	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552756	0.65425	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000283256	D;D;D	0.99042	-5.36;-5.36;-5.36	5.58	5.58	0.84498	Ion transport (1);	.	.	.	.	D	0.99396	0.9787	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99016	1.0816	9	0.87932	D	0	.	18.1063	0.89521	0.0:1.0:0.0:0.0	.	222	Q99250	SCN2A_HUMAN	F	222	ENSP00000406454:L222F;ENSP00000364586:L222F;ENSP00000283256:L222F	ENSP00000283256:L222F	L	+	1	0	SCN2A	165874166	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.052000	0.71080	2.789000	0.95967	0.655000	0.94253	CTC		0.448	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166165920	C	T	166165920	3	4	61	1	0	0	0	0	1	0	0	0	13953	913	32	3	778	3	SCN2A	2	166165920	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171301	166165920	77033453	1758	9743										
SCN2A	6326	broad.mit.edu	37	chr2	166201227	166201227	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttggtaagagctacaaaGaatgtgtctgcaagatttcc	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166201227G>T	ENST00000375437.2	+	16	3015	c.2725G>T	c.(2725-2727)Gaa>Taa	p.E909*	SCN2A_ENST00000357398.3_Nonsense_Mutation_p.E909*|SCN2A_ENST00000283256.6_Nonsense_Mutation_p.E909*|SCN2A_ENST00000375427.2_Nonsense_Mutation_p.E909*	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	909					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E909*(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGCTACAAAGAATGTGTCTG	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											192	178	183					2																	166201227		2203	4300	6503	165909473	SO:0001587	stop_gained	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.2725G>T	2.37:g.166201227G>T	ENSP00000364586:p.Glu909*		165909473	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Nonsense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	42	9.415077	0.99164	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	.	.	.	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.9329	0.97127	0.0:0.0:1.0:0.0	.	.	.	.	X	909	.	ENSP00000283256:E909X	E	+	1	0	SCN2A	165909473	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.779000	0.85648	2.714000	0.92807	0.650000	0.86243	GAA		0.488	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166201227	G	T	166201227	4	4	61	1	0	0	0	0	0	1	0	0	13953	943	33	2	2879	2	SCN2A	2	166201227	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35307	166201227	76998146	1759	9744										
SCN2A	6326	broad.mit.edu	37	chr2	166210777	166210777	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccactgatgatgataacGaaatgaataatctccagatt	7	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166210777G>A	ENST00000375437.2	+	17	3285	c.2995G>A	c.(2995-2997)Gaa>Aaa	p.E999K	SCN2A_ENST00000357398.3_Missense_Mutation_p.E999K|SCN2A_ENST00000283256.6_Missense_Mutation_p.E999K|SCN2A_ENST00000375427.2_Missense_Mutation_p.E999K	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	999			E -> K (in EIEE11; the disease progresses to West syndrome). {ECO:0000269|PubMed:23935176}.		intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E999K(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGATGATAACGAAATGAATAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											161	166	165					2																	166210777		2203	4300	6503	165919023	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.2995G>A	2.37:g.166210777G>A	ENSP00000364586:p.Glu999Lys		165919023	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294606	0.95546	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.69	5.69	0.88448	Sodium ion transport-associated (1);	0.000000	0.64402	D	0.000001	D	0.95294	0.8473	M	0.91920	3.255	0.80722	D	1	D;D	0.55800	0.971;0.973	P;P	0.59012	0.567;0.85	D	0.95786	0.8821	10	0.87932	D	0	.	19.8068	0.96534	0.0:0.0:1.0:0.0	.	999;999	Q99250-2;Q99250	.;SCN2A_HUMAN	K	999	ENSP00000364586:E999K;ENSP00000349973:E999K;ENSP00000283256:E999K;ENSP00000364576:E999K	ENSP00000283256:E999K	E	+	1	0	SCN2A	165919023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.864000	0.99589	2.658000	0.90341	0.655000	0.94253	GAA		0.388	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		A	166210777	G	A	166210777	3	1	61	1	0	0	0	0	1	0	0	0	13953	1059	37	1	3153	1	SCN2A	2	166210777	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9550	166210777	76988596	1760	9745										
SCN2A	6326	broad.mit.edu	37	chr2	166211175	166211175	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcagatatggaggaaagCaaagaggtaaaaatgtttaa	12	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166211175C>T	ENST00000375437.2	+	17	3683	c.3393C>T	c.(3391-3393)agC>agT	p.S1131S	SCN2A_ENST00000357398.3_Silent_p.S1131S|SCN2A_ENST00000283256.6_Silent_p.S1131S|SCN2A_ENST00000375427.2_Silent_p.S1131S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1131					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.S1131S(2)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGAGGAAAGCAAAGAGGTAA	0.338																																																2	Substitution - coding silent(2)	large_intestine(2)	2											45	46	46					2																	166211175		2197	4299	6496	165919421	SO:0001819	synonymous_variant	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3393C>T	2.37:g.166211175C>T			165919421	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																				0.338	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166211175	C	T	166211175	2	4	61	1	0	0	0	0	0	0	0	1	13953	709	25	3		3	SCN2A	2	166211175	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	398	166211175	76988198	1761	9746										
SCN2A	6326	broad.mit.edu	37	chr2	166245139	166245139	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgttgattttctacagGaatgtttctggctgaactga	9	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166245139G>A	ENST00000375437.2	+	27	5113	c.4823G>A	c.(4822-4824)gGa>gAa	p.G1608E	SCN2A_ENST00000357398.3_Splice_Site_p.G1608E|SCN2A_ENST00000283256.6_Splice_Site_p.G1608E|SCN2A_ENST00000375427.2_Splice_Site_p.G1608E	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1608					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G1608E(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTTCTACAGGAATGTTTCTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											62	64	63					2																	166245139		2203	4300	6503	165953385	SO:0001630	splice_region_variant	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.4823-1G>A	2.37:g.166245139G>A			165953385	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.666617	0.47677	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.98264	-4.83;-4.83;-4.83;-4.83	5.6	5.6	0.85130	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.98635	0.9543	L	0.58302	1.8	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	D	0.98683	1.0693	9	.	.	.	.	20.039	0.97573	0.0:0.0:1.0:0.0	.	1608;1608	Q99250-2;Q99250	.;SCN2A_HUMAN	E	1608	ENSP00000364586:G1608E;ENSP00000349973:G1608E;ENSP00000283256:G1608E;ENSP00000364576:G1608E	.	G	+	2	0	SCN2A	165953385	1.000000	0.71417	0.944000	0.38274	0.534000	0.34807	9.842000	0.99487	2.808000	0.96608	0.552000	0.68991	GGA		0.358	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	Missense_Mutation	A	166245139	G	A	166245139	5	1	61	1	0	0	0	0	0	0	1	0	13953	1188	41	3	5021	3	SCN2A	2	166245139	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33964	166245139	76954234	1762	9747										
SCN2A	6326	broad.mit.edu	37	chr2	166245220	166245220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtcttgccaggattggccGaatcctacgtctgatcaaag	10	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166245220G>A	ENST00000375437.2	+	27	5194	c.4904G>A	c.(4903-4905)cGa>cAa	p.R1635Q	SCN2A_ENST00000357398.3_Missense_Mutation_p.R1635Q|SCN2A_ENST00000283256.6_Missense_Mutation_p.R1635Q|SCN2A_ENST00000375427.2_Missense_Mutation_p.R1635Q	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1635					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R1635Q(2)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGATTGGCCGAATCCTACGT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	2											110	110	110					2																	166245220		2203	4297	6500	165953466	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.4904G>A	2.37:g.166245220G>A	ENSP00000364586:p.Arg1635Gln		165953466	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652866	0.67472	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.99607	-6.27;-6.27;-6.27;-6.27	5.49	5.49	0.81192	Ion transport (1);	0.085395	0.47093	D	0.000260	D	0.99792	0.9912	H	0.98388	4.22	0.80722	D	1	D;B	0.63880	0.993;0.332	P;B	0.59487	0.858;0.106	D	0.97143	0.9826	10	0.87932	D	0	.	19.8035	0.96518	0.0:0.0:1.0:0.0	.	1635;1635	Q99250-2;Q99250	.;SCN2A_HUMAN	Q	1635	ENSP00000364586:R1635Q;ENSP00000349973:R1635Q;ENSP00000283256:R1635Q;ENSP00000364576:R1635Q	ENSP00000283256:R1635Q	R	+	2	0	SCN2A	165953466	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.844000	0.99494	2.751000	0.94390	0.552000	0.68991	CGA		0.468	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		A	166245220	G	A	166245220	3	1	61	1	0	0	0	0	1	0	0	0	13953	1058	37	1	5102	1	SCN2A	2	166245220	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81	166245220	76954153	1763	9748										
CSRNP3	80034	broad.mit.edu	37	chr2	166535777	166535777	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcacgaaagccatgcaaaGaatgcttctttttatgccaa	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166535777G>T	ENST00000342316.4	+	5	1544	c.1272G>T	c.(1270-1272)aaG>aaT	p.K424N	CSRNP3_ENST00000314499.7_Missense_Mutation_p.K424N|CSRNP3_ENST00000409420.1_Missense_Mutation_p.K456N	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	424					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K424N(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						GCCATGCAAAGAATGCTTCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											135	136	135					2																	166535777		2203	4300	6503	166244023	SO:0001583	missense	80034			AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1272G>T	2.37:g.166535777G>T	ENSP00000344042:p.Lys424Asn		166244023	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	37	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	G	9.294	1.051373	0.19827	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.79	1.89	0.25635	.	0.100864	0.64402	D	0.000001	T	0.26882	0.0658	N	0.19112	0.55	0.36785	D	0.88454	B	0.27229	0.172	B	0.20955	0.032	T	0.14035	-1.0487	10	0.18710	T	0.47	-27.032	9.2263	0.37410	0.6902:0.0:0.3098:0.0	.	424	Q8WYN3	CSRN3_HUMAN	N	424;431;424;424;456	ENSP00000412081:K424N;ENSP00000318258:K424N;ENSP00000344042:K424N;ENSP00000387195:K456N	ENSP00000318258:K424N	K	+	3	2	CSRNP3	166244023	0.995000	0.38212	0.467000	0.27180	0.950000	0.60333	0.569000	0.23638	0.071000	0.16664	-0.345000	0.07892	AAG		0.443	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		T	166535777	G	T	166535777	3	4	61	1	0	0	0	0	1	0	0	0	3971	933	33	2	1286	2	CSRNP3	2	166535777	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	290557	166535777	76663596	1764	9749										
TTC21B	79809	broad.mit.edu	37	chr2	166740370	166740370	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttgctgattgaatgtaAatatcagcaagtagcagcca	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166740370A>C	ENST00000243344.7	-	26	3755	c.3618T>G	c.(3616-3618)atT>atG	p.I1206M	TTC21B_ENST00000536175.1_Missense_Mutation_p.I144M	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1206					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)		p.I1206M(1)		breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						ATTGAATGTAAATATCAGCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											135	134	135					2																	166740370		2203	4300	6503	166448616	SO:0001583	missense	79809			AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.3618T>G	2.37:g.166740370A>C	ENSP00000243344:p.Ile1206Met		166448616	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425495	0.62733	.	.	ENSG00000123607	ENST00000536175;ENST00000243344	T;T	0.39592	1.07;1.07	5.48	4.24	0.50183	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.47581	0.1453	M	0.74467	2.265	0.58432	D	0.999996	P	0.46277	0.875	P	0.45428	0.48	T	0.55438	-0.8141	10	0.72032	D	0.01	-24.5206	11.0613	0.47948	0.7939:0.0:0.0:0.2061	.	1206	Q7Z4L5	TT21B_HUMAN	M	144;1206	ENSP00000438692:I144M;ENSP00000243344:I1206M	ENSP00000243344:I1206M	I	-	3	3	TTC21B	166448616	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.465000	0.35299	2.202000	0.70862	0.477000	0.44152	ATT		0.393	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		C	166740370	A	C	166740370	3	2	61	1	0	0	0	0	1	0	0	0	16728	10	1	4	348	4	TTC21B	2	166740370	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	204593	166740370	76459003	1765	9750										
SCN1A	6323	broad.mit.edu	37	chr2	166892609	166892609	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaagtcttccgtgtttaaAttttcaaagtcagattctcc	5	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166892609A>T	ENST00000303395.4	-	16	3377	c.3378T>A	c.(3376-3378)aaT>aaA	p.N1126K	AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.N1115K|SCN1A_ENST00000409050.1_Missense_Mutation_p.N1098K|AC010127.3_ENST00000597623.1_RNA|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.N1126K			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1126					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.N1115K(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCGTGTTTAAATTTTCAAAGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											159	161	161					2																	166892609		2203	4300	6503	166600855	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3378T>A	2.37:g.166892609A>T	ENSP00000303540:p.Asn1126Lys		166600855	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.449846	0.43531	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	5.44	1.63	0.23807	Sodium ion transport-associated (1);	0.000000	0.85682	D	0.000000	D	0.88250	0.6386	M	0.90759	3.145	0.42832	D	0.994025	B;P;P	0.47841	0.181;0.901;0.8	B;P;P	0.48571	0.125;0.582;0.561	D	0.85460	0.1166	10	0.42905	T	0.14	.	8.8173	0.35004	0.7641:0.0:0.2359:0.0	.	1115;1098;1126	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	K	1126;1126;1115;1098	ENSP00000407030:N1126K;ENSP00000303540:N1126K;ENSP00000364554:N1115K;ENSP00000386312:N1098K	ENSP00000303540:N1126K	N	-	3	2	SCN1A	166600855	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.521000	0.22893	0.093000	0.17368	-0.408000	0.06270	AAT		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166892609	A	T	166892609	3	4	61	1	0	0	0	0	1	0	0	0	13951	98	4	5	2695	5	SCN1A	2	166892609	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	152239	166892609	76306764	1766	9751										
SCN1A	6323	broad.mit.edu	37	chr2	166897865	166897865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaaatgggtccatcacaAccaggttgacaacatgtttc	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166897865A>G	ENST00000303395.4	-	13	2290	c.2291T>C	c.(2290-2292)gTt>gCt	p.V764A	AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.V753A|SCN1A_ENST00000409050.1_Missense_Mutation_p.V736A|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.V764A			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	764					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.V753A(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTCCATCACAACCAGGTTGAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	112	114					2																	166897865		2203	4300	6503	166606111	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2291T>C	2.37:g.166897865A>G	ENSP00000303540:p.Val764Ala		166606111	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379188	0.61735	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96685	-4.09;-4.09;-4.05;-4.01	5.54	5.54	0.83059	.	0.216367	0.32785	N	0.005657	D	0.95996	0.8696	M	0.80332	2.49	0.47862	D	0.999533	B;B;B	0.21606	0.058;0.034;0.017	B;B;B	0.21917	0.037;0.016;0.009	D	0.94405	0.7626	10	0.87932	D	0	.	15.9597	0.79918	1.0:0.0:0.0:0.0	.	753;736;764	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	A	764;764;753;736	ENSP00000407030:V764A;ENSP00000303540:V764A;ENSP00000364554:V753A;ENSP00000386312:V736A	ENSP00000303540:V764A	V	-	2	0	SCN1A	166606111	0.999000	0.42202	0.982000	0.44146	0.860000	0.49131	9.284000	0.95882	2.226000	0.72624	0.482000	0.46254	GTT		0.408	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166897865	A	G	166897865	3	3	61	1	0	0	0	0	1	0	0	0	13951	43	2	4	3794	4	SCN1A	2	166897865	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5256	166897865	76301508	1767	9752										
SCN1A	6323	broad.mit.edu	37	chr2	166898859	166898859	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcgttgcctttgggaagGatcttctagaaagtccatgg	12	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166898859G>T	ENST00000303395.4	-	12	2118	c.2119C>A	c.(2119-2121)Cct>Act	p.P707T	AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.P696T|SCN1A_ENST00000409050.1_Missense_Mutation_p.P679T|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.P707T			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	707					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.P696T(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTTGGGAAGGATCTTCTAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2	GRCh37	CI065852	SCN1A	I							154	146	149					2																	166898859		2203	4300	6503	166607105	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2119C>A	2.37:g.166898859G>T	ENSP00000303540:p.Pro707Thr		166607105	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313250	0.60414	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.91237	-2.81;-2.81;-2.81;-2.81	5.82	5.82	0.92795	Domain of unknown function DUF3451 (1);	0.000000	0.64402	D	0.000003	D	0.91713	0.7380	M	0.65677	2.01	0.53688	D	0.999976	B;B;B	0.29766	0.06;0.186;0.256	B;B;B	0.37091	0.046;0.077;0.241	D	0.89507	0.3768	10	0.51188	T	0.08	.	20.1092	0.97906	0.0:0.0:1.0:0.0	.	696;679;707	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	T	707;707;696;679	ENSP00000407030:P707T;ENSP00000303540:P707T;ENSP00000364554:P696T;ENSP00000386312:P679T	ENSP00000303540:P707T	P	-	1	0	SCN1A	166607105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.086000	0.76885	2.745000	0.94114	0.655000	0.94253	CCT		0.358	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166898859	G	T	166898859	3	4	61	1	0	0	0	0	1	0	0	0	13951	1174	41	2	3970	2	SCN1A	2	166898859	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	994	166898859	76300514	1768	9753										
SCN1A	6323	broad.mit.edu	37	chr2	166901651	166901651	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtcctcagattcagattTttggaattcatcctcatctt	6	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166901651T>G	ENST00000303395.4	-	10	1563	c.1564A>C	c.(1564-1566)Aaa>Caa	p.K522Q	AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.K522Q|SCN1A_ENST00000409050.1_Missense_Mutation_p.K522Q|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.K522Q			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	522					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.K522Q(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GATTCAGATTTTTGGAATTCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											241	239	240					2																	166901651		2203	4300	6503	166609897	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1564A>C	2.37:g.166901651T>G	ENSP00000303540:p.Lys522Gln		166609897	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059555	0.76074	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02	6.17	6.17	0.99709	Domain of unknown function DUF3451 (1);	0.000000	0.64402	D	0.000001	D	0.91429	0.7295	M	0.70595	2.14	0.46113	D	0.99887	B;B;B	0.31769	0.013;0.002;0.339	B;B;B	0.29353	0.018;0.024;0.101	D	0.90365	0.4376	10	0.62326	D	0.03	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	522;522;522	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	Q	522	ENSP00000407030:K522Q;ENSP00000303540:K522Q;ENSP00000364554:K522Q;ENSP00000386312:K522Q	ENSP00000303540:K522Q	K	-	1	0	SCN1A	166609897	1.000000	0.71417	0.943000	0.38184	0.988000	0.76386	4.832000	0.62759	2.371000	0.80710	0.533000	0.62120	AAA		0.443	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166901651	T	G	166901651	3	3	61	1	0	0	0	0	1	0	0	0	13951	1850	64	4	4533	4	SCN1A	2	166901651	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2792	166901651	76297722	1769	9754										
SCN1A	6323	broad.mit.edu	37	chr2	166915079	166915079	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcacttgaaaaaggataTgaatgtaccaaaatcttaat	5	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:166915079T>C	ENST00000303395.4	-	2	383		c.e2+1		AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Splice_Site|SCN1A_ENST00000409050.1_Splice_Site|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Splice_Site_p.S128S			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit						adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.?(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAAAAGGATATGAATGTACCA	0.338																																																1	Unknown(1)	large_intestine(1)	2											57	60	59					2																	166915079		2203	4299	6502	166623325	SO:0001630	splice_region_variant	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.383+1A>G	2.37:g.166915079T>C			166623325	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Splice_Site	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.372854	0.82573	.	.	ENSG00000144285	ENST00000303395;ENST00000375405;ENST00000409050	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7387	0.69437	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCN1A	166623325	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.773000	0.85462	2.130000	0.65690	0.482000	0.46254	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	Intron	C	166915079	T	C	166915079	5	2	61	1	0	0	0	0	0	0	1	0	13951	1478	51	4	5745	4	SCN1A	2	166915079	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	13428	166915079	76284294	1770	9755										
SCN9A	6335	broad.mit.edu	37	chr2	167055217	167055217	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgctgtctttccctttgtCttccttttctgttctgtctt	5	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167055217C>A	ENST00000409435.1	-	26	5931	c.5932G>T	c.(5932-5934)Gac>Tac	p.D1978Y	SCN9A_ENST00000409672.1_Missense_Mutation_p.D1967Y|SCN9A_ENST00000303354.6_Missense_Mutation_p.D1979Y|SCN9A_ENST00000375387.4_Missense_Mutation_p.D1979Y|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1978					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.D1967Y(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCCCTTTGTCTTCCTTTTCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	100	102					2																	167055217		1906	4127	6033	166763463	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.5932G>T	2.37:g.167055217C>A	ENSP00000386330:p.Asp1978Tyr		166763463	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533645	0.27387	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.96232	-3.93;-3.95;-3.95;-3.95	5.86	4.04	0.47022	.	0.090341	0.48286	D	0.000194	D	0.95664	0.8590	M	0.75447	2.3	0.42855	D	0.994095	B	0.24092	0.097	B	0.26693	0.072	D	0.93216	0.6604	10	0.59425	D	0.04	.	16.3649	0.83317	0.0:0.7509:0.2491:0.0	.	1967	E7EUN6	.	Y	1967;1979;1979;1978	ENSP00000386306:D1967Y;ENSP00000364536:D1979Y;ENSP00000304748:D1979Y;ENSP00000386330:D1978Y	ENSP00000304748:D1979Y	D	-	1	0	SCN9A	166763463	0.999000	0.42202	1.000000	0.80357	0.952000	0.60782	0.776000	0.26704	0.800000	0.34041	0.591000	0.81541	GAC		0.348	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167055217	C	A	167055217	3	1	61	1	0	0	0	0	1	0	0	0	13962	913	32	2	38	2	SCN9A	2	167055217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140138	167055217	76144156	1771	9756										
SCN9A	6335	broad.mit.edu	37	chr2	167060500	167060500	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaaccacaaaatcaaaaAtattccatcctacagtgaag	3	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167060500A>C	ENST00000409435.1	-	25	4738	c.4739T>G	c.(4738-4740)aTt>aGt	p.I1580S	SCN9A_ENST00000409672.1_Missense_Mutation_p.I1569S|SCN9A_ENST00000303354.6_Missense_Mutation_p.I1581S|SCN9A_ENST00000375387.4_Missense_Mutation_p.I1581S|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1580					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.I1569S(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAAATCAAAAATATTCCATCC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											50	48	49					2																	167060500		2091	4266	6357	166768746	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4739T>G	2.37:g.167060500A>C	ENSP00000386330:p.Ile1580Ser		166768746	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032639	0.75504	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98876	-5.2;-5.2;-5.2;-5.2	4.47	4.47	0.54385	.	0.075143	0.53938	D	0.000048	D	0.99257	0.9741	M	0.92169	3.28	0.48288	D	0.999624	D	0.71674	0.998	D	0.79108	0.992	D	0.99023	1.0818	10	0.87932	D	0	.	14.0598	0.64793	1.0:0.0:0.0:0.0	.	1569	E7EUN6	.	S	1569;1581;1581;1580	ENSP00000386306:I1569S;ENSP00000364536:I1581S;ENSP00000304748:I1581S;ENSP00000386330:I1580S	ENSP00000304748:I1581S	I	-	2	0	SCN9A	166768746	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.247000	0.95444	1.794000	0.52575	0.374000	0.22700	ATT		0.308	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		C	167060500	A	C	167060500	3	2	61	1	0	0	0	0	1	0	0	0	13962	101	4	4	1235	4	SCN9A	2	167060500	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5283	167060500	76138873	1772	9757										
SCN9A	6335	broad.mit.edu	37	chr2	167133603	167133603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactctccacacagcacgcGgaacacaatcaggaaggagt	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167133603G>A	ENST00000409435.1	-	15	2763	c.2764C>T	c.(2764-2766)Cgc>Tgc	p.R922C	SCN9A_ENST00000409672.1_Missense_Mutation_p.R911C|SCN9A_ENST00000303354.6_Missense_Mutation_p.R923C|SCN9A_ENST00000375387.4_Missense_Mutation_p.R923C|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	922					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.R911C(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CACAGCACGCGGAACACAATC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											198	189	192					2																	167133603		2203	4297	6500	166841849	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.2764C>T	2.37:g.167133603G>A	ENSP00000386330:p.Arg922Cys		166841849	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827439	0.90955	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98901	-5.22;-5.22;-5.22;-5.22	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000003	D	0.99591	0.9852	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97715	1.0193	10	0.87932	D	0	.	20.096	0.97843	0.0:0.0:1.0:0.0	.	911	E7EUN6	.	C	911;923;923;922	ENSP00000386306:R911C;ENSP00000364536:R923C;ENSP00000304748:R923C;ENSP00000386330:R922C	ENSP00000304748:R923C	R	-	1	0	SCN9A	166841849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.518000	0.67068	2.819000	0.97034	0.650000	0.86243	CGC		0.488	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167133603	G	A	167133603	3	1	61	1	0	0	0	0	1	0	0	0	13962	1116	39	1	3250	1	SCN9A	2	167133603	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73103	167133603	76065770	1773	9758										
SCN9A	6335	broad.mit.edu	37	chr2	167141202	167141202	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttctgctctcattgtctcCaaaaatgctgtgctcatcat	5	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167141202C>A	ENST00000409435.1	-	11	1734	c.1735G>T	c.(1735-1737)Gga>Tga	p.G579*	SCN9A_ENST00000409672.1_Nonsense_Mutation_p.G579*|SCN9A_ENST00000303354.6_Nonsense_Mutation_p.G580*|SCN9A_ENST00000375387.4_Nonsense_Mutation_p.G580*|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	579					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.G579*(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCATTGTCTCCAAAAATGCTG	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											100	104	103					2																	167141202		2075	4230	6305	166849448	SO:0001587	stop_gained	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1735G>T	2.37:g.167141202C>A	ENSP00000386330:p.Gly579*		166849448	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Nonsense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	37	6.106978	0.97291	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	.	.	.	5.64	5.64	0.86602	.	0.094242	0.47093	D	0.000254	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	20.0585	0.97663	0.0:1.0:0.0:0.0	.	.	.	.	X	579;580;580;579;444;444	.	ENSP00000304748:G580X	G	-	1	0	SCN9A	166849448	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.445000	0.80570	2.812000	0.96745	0.557000	0.71058	GGA		0.502	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167141202	C	A	167141202	4	1	61	1	0	0	0	0	0	1	0	0	13962	603	21	2	4262	2	SCN9A	2	167141202	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7599	167141202	76058171	1774	9759										
SCN9A	6335	broad.mit.edu	37	chr2	167143018	167143018	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttttctttcttctgtttCttctttctttagcactttta	2	9	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167143018C>A	ENST00000409435.1	-	10	1429	c.1430G>T	c.(1429-1431)aGa>aTa	p.R477I	SCN9A_ENST00000409672.1_Missense_Mutation_p.R477I|SCN9A_ENST00000303354.6_Missense_Mutation_p.R478I|SCN9A_ENST00000375387.4_Missense_Mutation_p.R478I|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	477					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.R477I(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTTCTGTTTCTTCTTTCTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	52	53					2																	167143018		1817	4080	5897	166851264	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1430G>T	2.37:g.167143018C>A	ENSP00000386330:p.Arg477Ile		166851264	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592994	0.86953	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94;-2.94	5.86	4.01	0.46588	Domain of unknown function DUF3451 (1);	0.174418	0.38778	N	0.001567	D	0.95277	0.8468	M	0.91561	3.22	0.80722	D	1	P;P;D	0.54964	0.784;0.566;0.969	P;P;P	0.54889	0.763;0.507;0.703	D	0.95536	0.8608	10	0.72032	D	0.01	.	11.1693	0.48563	0.1279:0.8056:0.0:0.0665	.	477;477;478	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	I	477;478;478;477;342;342	ENSP00000386306:R477I;ENSP00000364536:R478I;ENSP00000304748:R478I;ENSP00000386330:R477I;ENSP00000413212:R342I;ENSP00000393141:R342I	ENSP00000304748:R478I	R	-	2	0	SCN9A	166851264	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.923000	0.63412	1.491000	0.48482	0.585000	0.79938	AGA		0.403	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167143018	C	A	167143018	3	1	61	1	0	0	0	0	1	0	0	0	13962	913	32	2	4571	2	SCN9A	2	167143018	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1816	167143018	76056355	1775	9760										
SCN9A	6335	broad.mit.edu	37	chr2	167149858	167149858	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttctgccaattttcacAcaggtgtacccctctggaca	9	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167149858A>G	ENST00000409435.1	-	8	989	c.990T>C	c.(988-990)tgT>tgC	p.C330C	SCN9A_ENST00000409672.1_Silent_p.C330C|SCN9A_ENST00000303354.6_Silent_p.C331C|SCN9A_ENST00000375387.4_Silent_p.C331C|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	330					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.C330C(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAATTTTCACACAGGTGTACC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											57	59	58					2																	167149858		2004	4216	6220	166858104	SO:0001819	synonymous_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.990T>C	2.37:g.167149858A>G			166858104	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																				0.443	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		G	167149858	A	G	167149858	2	3	61	1	0	0	0	0	0	0	0	1	13962	157	6	4		4	SCN9A	2	167149858	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6840	167149858	76049515	1776	9761										
SCN7A	6332	broad.mit.edu	37	chr2	167262860	167262860	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatattgcaacttgaaaaaGacagagcatactgttgccaa	7	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167262860G>T	ENST00000409855.1	-	25	4405	c.4279C>A	c.(4279-4281)Ctt>Att	p.L1427I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1427					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.L1427I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	ACTTGAAAAAGACAGAGCATA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											183	176	178					2																	167262860		1896	4142	6038	166971106	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4279C>A	2.37:g.167262860G>T	ENSP00000386796:p.Leu1427Ile		166971106		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.246446	0.39697	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.97598	-4.45	5.14	3.26	0.37387	Ion transport (1);	0.239589	0.29424	N	0.012194	D	0.96012	0.8701	M	0.87456	2.885	0.35030	D	0.758669	B	0.26120	0.142	B	0.26693	0.072	D	0.95516	0.8590	10	0.87932	D	0	.	6.0142	0.19592	0.0892:0.0:0.5238:0.387	.	1427	Q01118	SCN7A_HUMAN	I	1427	ENSP00000386796:L1427I	ENSP00000259060:L1427I	L	-	1	0	SCN7A	166971106	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	4.474000	0.60203	0.795000	0.33922	-0.282000	0.10007	CTT		0.363	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167262860	G	T	167262860	3	4	61	1	0	0	0	0	1	0	0	0	13960	942	33	2	773	2	SCN7A	2	167262860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113002	167262860	75936513	1777	9762										
SCN7A	6332	broad.mit.edu	37	chr2	167333982	167333982	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatactcacattttttttCttgtagtaatatgggtccac	5	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167333982C>A	ENST00000409855.1	-	2	351	c.225G>T	c.(223-225)aaG>aaT	p.K75N		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	75					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K75N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CATTTTTTTTCTTGTAGTAAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											20	17	18					2																	167333982		1763	3971	5734	167042228	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.225G>T	2.37:g.167333982C>A	ENSP00000386796:p.Lys75Asn		167042228		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.727880	0.00694	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98090	-4.07;-4.1;-4.71	4.17	-0.184	0.13280	.	0.589164	0.14795	N	0.297997	D	0.91418	0.7292	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.79748	-0.1673	10	0.02654	T	1	.	0.7587	0.01003	0.3787:0.2185:0.2223:0.1806	.	75	Q01118	SCN7A_HUMAN	N	75	ENSP00000386796:K75N;ENSP00000413699:K75N;ENSP00000403846:K75N	ENSP00000259060:K75N	K	-	3	2	SCN7A	167042228	0.006000	0.16342	0.235000	0.24058	0.861000	0.49209	0.015000	0.13355	-0.145000	0.11294	0.655000	0.94253	AAG		0.308	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167333982	C	A	167333982	3	1	61	1	0	0	0	0	1	0	0	0	13960	912	32	2	4919	2	SCN7A	2	167333982	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71122	167333982	75865391	1778	9763										
XIRP2	129446	broad.mit.edu	37	chr2	167760391	167760391	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaacaaaccagctgagtaCggtggaaaggtaaggagcca	14	7	0	1	rs368478393		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:167760391C>T	ENST00000409728.1	+	2	488	c.399C>T	c.(397-399)taC>taT	p.Y133Y	XIRP2_ENST00000409756.2_Silent_p.Y133Y|XIRP2_ENST00000295237.9_Silent_p.Y133Y|XIRP2_ENST00000420519.1_Silent_p.Y133Y|XIRP2_ENST00000409195.1_Silent_p.Y133Y|XIRP2_ENST00000409043.1_Silent_p.Y133Y	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.Y133Y(2)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CAGCTGAGTACGGTGGAAAGG	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	2						C	,,	0,3912		0,0,1956	108	109	109		399,399,399	-7.9	0	2		109	1,8329		0,1,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_152381.5	,,	0,1,6120	TT,TC,CC		0.012,0.0,0.0082	,,	133/939,133/972,133/3550	167760391	1,12241	1956	4165	6121	167468637	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.399C>T	2.37:g.167760391C>T			167468637	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409728.1	37	CCDS56143.1																																																																																				0.478	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		T	167760391	C	T	167760391	2	4	61	1	0	0	0	0	0	0	0	1	17470	547	19	1		1	XIRP2	2	167760391	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426409	167760391	75438982	1779	9764										
XIRP2	129446	broad.mit.edu	37	chr2	168096454	168096454	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtccaaagtacagaaaatTgatgttcatggaacagaaat	10	5	1	3	rs547800851		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168096454T>G	ENST00000409728.1	+	7	1136	c.1047T>G	c.(1045-1047)atT>atG	p.I349M	XIRP2_ENST00000409605.1_Missense_Mutation_p.I94M|XIRP2_ENST00000420519.1_Missense_Mutation_p.I349M|XIRP2_ENST00000409273.1_Missense_Mutation_p.I94M|XIRP2_ENST00000409195.1_Missense_Mutation_p.I316M|XIRP2_ENST00000409043.1_Missense_Mutation_p.I316M|XIRP2_ENST00000295237.9_Missense_Mutation_p.I316M|XIRP2_ENST00000409756.2_Missense_Mutation_p.I316M	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	141					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.I316M(1)|p.I349M(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TACAGAAAATTGATGTTCATG	0.398													T|||	1	0.000199681	0	0	5008	,	,		15978	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											92	92	92					2																	168096454		1869	4105	5974	167804700	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1047T>G	2.37:g.168096454T>G	ENSP00000386619:p.Ile349Met		167804700	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	T	8.471	0.857560	0.17106	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237;ENST00000409273;ENST00000409605	T;T;T;T;T;T;T;T	0.77877	-1.12;-1.13;4.2;-1.12;-1.13;4.2;4.21;-1.1	5.9	2.21	0.28008	.	1.038600	0.07567	N	0.917926	T	0.67674	0.2918	L	0.48642	1.525	0.19775	N	0.999953	B;B;B;B;B	0.28820	0.029;0.184;0.224;0.065;0.065	B;B;B;B;B	0.24848	0.006;0.041;0.056;0.015;0.015	T	0.58306	-0.7659	10	0.59425	D	0.04	0.0724	2.0589	0.03587	0.1551:0.0858:0.192:0.5671	.	141;316;349;141;94	A4UGR9;A4UGR9-4;A4UGR9-6;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.;.;.	M	316;349;316;316;349;316;94;94	ENSP00000386454:I316M;ENSP00000386619:I349M;ENSP00000386840:I316M;ENSP00000386724:I316M;ENSP00000415541:I349M;ENSP00000295237:I316M;ENSP00000387255:I94M;ENSP00000386981:I94M	ENSP00000295237:I316M	I	+	3	3	XIRP2	167804700	0.015000	0.18098	0.619000	0.29118	0.073000	0.16967	-0.296000	0.08287	0.455000	0.26910	0.528000	0.53228	ATT		0.398	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		G	168096454	T	G	168096454	3	3	61	1	0	0	0	0	1	0	0	0	17470	1800	63	4	966	4	XIRP2	2	168096454	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	336063	168096454	75102919	1780	9765										
XIRP2	129446	broad.mit.edu	37	chr2	168100268	168100268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacaaagatatcacagaaaTtaaagttgtccgaggaatat	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168100268T>G	ENST00000409195.1	+	9	2455	c.2366T>G	c.(2365-2367)aTt>aGt	p.I789S	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.I567S|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.I789S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	614					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.I789S(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATCACAGAAATTAAAGTTGTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	66	67					2																	168100268		1853	4096	5949	167808514	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2366T>G	2.37:g.168100268T>G	ENSP00000386840:p.Ile789Ser		167808514	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.410507	0.62399	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03496	3.91;3.91;3.91	5.92	5.92	0.95590	.	0.177135	0.49916	D	0.000134	T	0.13970	0.0338	L	0.59436	1.845	0.46044	D	0.998836	D;D;D	0.67145	0.993;0.996;0.996	P;P;D	0.65010	0.796;0.9;0.931	T	0.01386	-1.1368	10	0.35671	T	0.21	-18.8251	16.3636	0.83296	0.0:0.0:0.0:1.0	.	614;614;567	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	789;789;567	ENSP00000386840:I789S;ENSP00000295237:I789S;ENSP00000387255:I567S	ENSP00000295237:I789S	I	+	2	0	XIRP2	167808514	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.692000	0.84203	2.267000	0.75376	0.528000	0.53228	ATT		0.403	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168100268	T	G	168100268	3	3	61	1	0	0	0	0	1	0	0	0	17470	1493	52	4	2396	4	XIRP2	2	168100268	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3814	168100268	75099105	1781	9766										
XIRP2	129446	broad.mit.edu	37	chr2	168102574	168102574	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattaaagaaaccttagaaGatctctactctcaaaaagtt	5	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168102574G>T	ENST00000409195.1	+	9	4761	c.4672G>T	c.(4672-4674)Gat>Tat	p.D1558Y	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.D1336Y|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.D1558Y|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1383					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.D1558Y(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACCTTAGAAGATCTCTACTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	49	50					2																	168102574		1818	4076	5894	167810820	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4672G>T	2.37:g.168102574G>T	ENSP00000386840:p.Asp1558Tyr		167810820	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457052	0.43634	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02525	4.26;4.26;4.26	5.56	4.68	0.58851	.	0.155915	0.56097	D	0.000034	T	0.03871	0.0109	N	0.14661	0.345	0.41908	D	0.990458	P;D;P	0.56035	0.956;0.974;0.846	P;P;P	0.51135	0.459;0.66;0.568	T	0.60419	-0.7267	10	0.44086	T	0.13	-4.1944	13.1091	0.59263	0.0784:0.0:0.9216:0.0	.	1383;1383;1336	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Y	1558;1558;1336	ENSP00000386840:D1558Y;ENSP00000295237:D1558Y;ENSP00000387255:D1336Y	ENSP00000295237:D1558Y	D	+	1	0	XIRP2	167810820	1.000000	0.71417	0.669000	0.29828	0.960000	0.62799	4.602000	0.61098	1.360000	0.45960	0.563000	0.77884	GAT		0.363	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168102574	G	T	168102574	3	4	61	1	0	0	0	0	1	0	0	0	17470	942	33	2	4702	2	XIRP2	2	168102574	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2306	168102574	75096799	1782	9767										
XIRP2	129446	broad.mit.edu	37	chr2	168103732	168103732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggtacataaagaaggtGtaataaaaaaagatgctaaa	9	2	0	3	rs374129597		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168103732G>A	ENST00000409195.1	+	9	5919	c.5830G>A	c.(5830-5832)Gta>Ata	p.V1944I	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.V1722I|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.V1944I|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1769					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.V1944I(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TAAAGAAGGTGTAATAAAAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	43	44					2																	168103732		1842	4102	5944	167811978	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5830G>A	2.37:g.168103732G>A	ENSP00000386840:p.Val1944Ile		167811978	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.477762	0.00011	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02197	4.4;4.4;4.4	4.66	-4.66	0.03329	.	1.318270	0.04834	N	0.439297	T	0.01387	0.0045	N	0.16307	0.4	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.001;0.004;0.002	T	0.48127	-0.9062	10	0.05351	T	0.99	0.9339	7.9051	0.29757	0.5964:0.0:0.2936:0.11	.	1769;1769;1722	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	I	1944;1944;1722	ENSP00000386840:V1944I;ENSP00000295237:V1944I;ENSP00000387255:V1722I	ENSP00000295237:V1944I	V	+	1	0	XIRP2	167811978	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.227000	0.17795	-0.880000	0.03997	-1.131000	0.01979	GTA		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168103732	G	A	168103732	3	1	61	1	0	0	0	0	1	0	0	0	17470	1377	48	3	5860	3	XIRP2	2	168103732	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1158	168103732	75095641	1783	9768										
XIRP2	129446	broad.mit.edu	37	chr2	168104924	168104924	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggctgaatttgaaagttTtccaggcctccctcttcctc	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168104924T>G	ENST00000409195.1	+	9	7111	c.7022T>G	c.(7021-7023)tTt>tGt	p.F2341C	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.F2119C|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.F2341C|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2166					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.F2341C(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTTGAAAGTTTTCCAGGCCTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	139	139					2																	168104924		1876	4104	5980	167813170	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7022T>G	2.37:g.168104924T>G	ENSP00000386840:p.Phe2341Cys		167813170	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.465946	0.26335	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03717	3.83;3.83;3.83	5.95	4.77	0.60923	.	0.257134	0.36409	N	0.002618	T	0.05960	0.0155	L	0.56769	1.78	0.20196	N	0.999928	B;B;B	0.24368	0.028;0.047;0.102	B;B;B	0.24155	0.014;0.032;0.051	T	0.19976	-1.0289	10	0.41790	T	0.15	-0.4949	12.3216	0.54987	0.0:0.0:0.1417:0.8583	.	2166;2166;2119	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	C	2341;2341;2119	ENSP00000386840:F2341C;ENSP00000295237:F2341C;ENSP00000387255:F2119C	ENSP00000295237:F2341C	F	+	2	0	XIRP2	167813170	0.970000	0.33590	0.757000	0.31301	0.657000	0.38888	4.060000	0.57477	1.043000	0.40175	0.533000	0.62120	TTT		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168104924	T	G	168104924	3	3	61	1	0	0	0	0	1	0	0	0	17470	1841	64	4	7052	4	XIRP2	2	168104924	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1192	168104924	75094449	1784	9769										
XIRP2	129446	broad.mit.edu	37	chr2	168105757	168105757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggctctcaaagtaatgctCggatactaggagtgtgttct	11	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168105757C>T	ENST00000409195.1	+	9	7944	c.7855C>T	c.(7855-7857)Cgg>Tgg	p.R2619W	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R2397W|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R2619W|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2444					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.R2619W(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGTAATGCTCGGATACTAGG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	86	87					2																	168105757		1906	4118	6024	167814003	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7855C>T	2.37:g.168105757C>T	ENSP00000386840:p.Arg2619Trp		167814003	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.495941	0.64186	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02631	4.22;4.22;4.22	5.71	4.81	0.61882	.	0.649429	0.15717	N	0.248095	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	D;D;P	0.57257	0.964;0.979;0.85	B;B;B	0.43123	0.232;0.409;0.409	T	0.49986	-0.8880	10	0.59425	D	0.04	0.0084	13.3963	0.60856	0.0:0.7945:0.2055:0.0	.	2444;2444;2397	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	W	2619;2619;2397;33	ENSP00000386840:R2619W;ENSP00000295237:R2619W;ENSP00000387255:R2397W	ENSP00000295237:R2619W	R	+	1	2	XIRP2	167814003	0.001000	0.12720	0.214000	0.23707	0.750000	0.42670	0.484000	0.22308	1.303000	0.44873	0.655000	0.94253	CGG		0.463	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168105757	C	T	168105757	3	4	61	1	0	0	0	0	1	0	0	0	17470	875	31	1	7885	1	XIRP2	2	168105757	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	833	168105757	75093616	1785	9770										
XIRP2	129446	broad.mit.edu	37	chr2	168106437	168106437	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaacacgaacatctgaaGaataaatcagcaccaaaggt	7	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168106437G>T	ENST00000409195.1	+	9	8624	c.8535G>T	c.(8533-8535)aaG>aaT	p.K2845N	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.K2623N|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.K2845N|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2670					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.K2845N(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACATCTGAAGAATAAATCAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	106	107					2																	168106437		1868	4105	5973	167814683	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8535G>T	2.37:g.168106437G>T	ENSP00000386840:p.Lys2845Asn		167814683	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	5.683	0.310668	0.10733	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02890	4.12;4.12;4.13	4.43	0.269	0.15631	.	0.830760	0.10785	N	0.634440	T	0.02193	0.0068	L	0.34521	1.04	0.09310	N	1	B;B;B	0.32160	0.244;0.358;0.358	B;B;B	0.30782	0.056;0.12;0.12	T	0.46148	-0.9212	10	0.35671	T	0.21	0.6126	1.9597	0.03384	0.164:0.13:0.4453:0.2607	.	2670;2670;2623	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2845;2845;2623;259	ENSP00000386840:K2845N;ENSP00000295237:K2845N;ENSP00000387255:K2623N	ENSP00000295237:K2845N	K	+	3	2	XIRP2	167814683	0.001000	0.12720	0.000000	0.03702	0.131000	0.20780	0.109000	0.15417	-0.021000	0.14009	0.655000	0.94253	AAG		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168106437	G	T	168106437	3	4	61	1	0	0	0	0	1	0	0	0	17470	933	33	2	8565	2	XIRP2	2	168106437	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	680	168106437	75092936	1786	9771										
XIRP2	129446	broad.mit.edu	37	chr2	168106743	168106743	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttaaatatagtggaattCttgagaaaacgtgaagaact	9	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168106743C>A	ENST00000409195.1	+	9	8930	c.8841C>A	c.(8839-8841)ttC>ttA	p.F2947L	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.F2725L|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.F2947L|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2772					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.F2947L(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TAGTGGAATTCTTGAGAAAAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											91	89	90					2																	168106743		1831	4082	5913	167814989	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8841C>A	2.37:g.168106743C>A	ENSP00000386840:p.Phe2947Leu		167814989	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.373616	0.42105	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02525	4.26;4.26;4.26	6.02	5.09	0.68999	.	0.457165	0.22842	N	0.054969	T	0.04182	0.0116	M	0.62723	1.935	0.30530	N	0.767505	B;B;B	0.24823	0.068;0.112;0.112	B;B;B	0.18561	0.01;0.022;0.022	T	0.08371	-1.0725	10	0.27082	T	0.32	-2.1736	9.5464	0.39284	0.0:0.8272:0.0:0.1728	.	2772;2772;2725	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	L	2947;2947;2725;361	ENSP00000386840:F2947L;ENSP00000295237:F2947L;ENSP00000387255:F2725L	ENSP00000295237:F2947L	F	+	3	2	XIRP2	167814989	0.170000	0.23016	0.999000	0.59377	0.974000	0.67602	0.171000	0.16685	1.426000	0.47256	0.655000	0.94253	TTC		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168106743	C	A	168106743	3	1	61	1	0	0	0	0	1	0	0	0	17470	912	32	2	8871	2	XIRP2	2	168106743	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	306	168106743	75092630	1787	9772										
XIRP2	129446	broad.mit.edu	37	chr2	168108198	168108198	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagtcaaattgttgagtcGaagatgaaaacctcttcatc	9	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:168108198G>A	ENST00000409195.1	+	9	10385	c.10296G>A	c.(10294-10296)tcG>tcA	p.S3432S	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.S3210S|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Silent_p.S3432S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3257					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.S3432S(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGTTGAGTCGAAGATGAAAA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	2											69	68	68					2																	168108198		1900	4119	6019	167816444	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10296G>A	2.37:g.168108198G>A			167816444	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																				0.448	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168108198	G	A	168108198	2	1	61	1	0	0	0	0	0	0	0	1	17470	1045	37	1		1	XIRP2	2	168108198	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1455	168108198	75091175	1788	9773										
LASS6	253782	broad.mit.edu	37	chr2	169551547	169551547	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgttttctcagttcactGatatcaaaagaaaggtaaga	8	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169551547G>T	ENST00000305747.6	+	6	1182	c.595G>T	c.(595-597)Gat>Tat	p.D199Y	CERS6_ENST00000392687.4_Missense_Mutation_p.D199Y	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	199	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.D199Y(1)									TCAGTTCACTGATATCAAAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											214	182	193					2																	169551547		2203	4300	6503	169259793	SO:0001583	missense	253782			BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"Homeoboxes / CERS class"	23826	protein-coding gene	gene with protein product		615336	"LAG1 longevity assurance homolog 6 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 6"	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.595G>T	2.37:g.169551547G>T	ENSP00000306579:p.Asp199Tyr		169259793	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239249	0.79800	.	.	ENSG00000172292	ENST00000305747;ENST00000392687	D;D	0.85171	-1.95;-1.95	5.51	5.51	0.81932	TRAM/LAG1/CLN8 homology domain (3);	0.000000	0.85682	D	0.000000	D	0.94961	0.8370	H	0.95816	3.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96175	0.9126	10	0.87932	D	0	-33.0729	18.1779	0.89767	0.0:0.0:1.0:0.0	.	199;199	Q32M63;Q6ZMG9	.;CERS6_HUMAN	Y	199	ENSP00000306579:D199Y;ENSP00000376453:D199Y	ENSP00000306579:D199Y	D	+	1	0	CERS6	169259793	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	8.281000	0.89905	2.582000	0.87167	0.655000	0.94253	GAT		0.413	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		T	169551547	G	T	169551547	3	4	61	1	0	0	0	0	1	0	0	0	8665	1290	45	2	617	2	LASS6	2	169551547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1443349	169551547	73647826	1789	9774										
LASS6	253782	broad.mit.edu	37	chr2	169571515	169571515	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttctttcctcaaggactTtggcattatgttcctgcacc	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169571515T>G	ENST00000305747.6	+	7	1201	c.614T>G	c.(613-615)tTt>tGt	p.F205C	CERS6_ENST00000392687.4_Missense_Mutation_p.F205C	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	205	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.F205C(1)									CTCAAGGACTTTGGCATTATG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											292	273	280					2																	169571515		2203	4300	6503	169279761	SO:0001583	missense	253782			BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"Homeoboxes / CERS class"	23826	protein-coding gene	gene with protein product		615336	"LAG1 longevity assurance homolog 6 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 6"	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.614T>G	2.37:g.169571515T>G	ENSP00000306579:p.Phe205Cys		169279761	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.668471	0.67814	.	.	ENSG00000172292	ENST00000305747;ENST00000392687	D;D	0.86562	-2.14;-2.14	5.35	5.35	0.76521	TRAM/LAG1/CLN8 homology domain (3);	0.000000	0.85682	D	0.000000	D	0.95677	0.8594	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.97031	0.9750	10	0.87932	D	0	-30.1858	14.3041	0.66373	0.0:0.0:0.0:1.0	.	205;205	Q32M63;Q6ZMG9	.;CERS6_HUMAN	C	205	ENSP00000306579:F205C;ENSP00000376453:F205C	ENSP00000306579:F205C	F	+	2	0	CERS6	169279761	1.000000	0.71417	0.996000	0.52242	0.542000	0.35054	7.450000	0.80656	2.018000	0.59344	0.533000	0.62120	TTT		0.398	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		G	169571515	T	G	169571515	3	3	61	1	0	0	0	0	1	0	0	0	8665	1841	64	4	640	4	LASS6	2	169571515	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19968	169571515	73627858	1790	9775										
NOSTRIN	115677	broad.mit.edu	37	chr2	169721373	169721373	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattatacacgagaaaaaaGaaggaggatggtggtttgga	14	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169721373G>T	ENST00000317647.7	+	16	1643	c.1414G>T	c.(1414-1416)Gaa>Taa	p.E472*	NOSTRIN_ENST00000397206.2_Nonsense_Mutation_p.E394*|NOSTRIN_ENST00000445023.2_Nonsense_Mutation_p.E394*|NOSTRIN_ENST00000397209.2_Nonsense_Mutation_p.E444*|NOSTRIN_ENST00000421711.2_Nonsense_Mutation_p.E444*|NOSTRIN_ENST00000444448.2_Nonsense_Mutation_p.E529*|NOSTRIN_ENST00000458381.2_Nonsense_Mutation_p.E529*	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	472	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)	p.E529*(1)|p.E472*(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						CGAGAAAAAAGAAGGAGGATG	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											140	127	131					2																	169721373		1863	4105	5968	169429619	SO:0001587	stop_gained	115677			AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"nitric oxide synthase trafficker"			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.1414G>T	2.37:g.169721373G>T	ENSP00000318921:p.Glu472*		169429619	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Nonsense_Mutation	SNP	ENST00000317647.7	37	CCDS42771.1	.	.	.	.	.	.	.	.	.	.	G	41	8.614156	0.98886	.	.	ENSG00000163072	ENST00000458381;ENST00000444448;ENST00000317647;ENST00000445023;ENST00000397206;ENST00000397209;ENST00000421711	.	.	.	4.96	4.07	0.47477	.	0.576772	0.18337	N	0.144313	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-14.2349	11.4263	0.50012	0.0925:0.0:0.9075:0.0	.	.	.	.	X	529;529;472;394;394;444;444	.	ENSP00000318921:E472X	E	+	1	0	NOSTRIN	169429619	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.002000	0.49496	2.446000	0.82766	0.557000	0.71058	GAA		0.423	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946		T	169721373	G	T	169721373	4	4	61	1	0	0	0	0	0	1	0	0	10577	943	33	2	1651	2	NOSTRIN	2	169721373	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149858	169721373	73478000	1791	9776										
G6PC2	57818	broad.mit.edu	37	chr2	169758968	169758968	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacaggatattatttggtCatcgaccttactggtgggtc	10	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169758968C>A	ENST00000375363.3	+	2	324	c.232C>A	c.(232-234)Cat>Aat	p.H78N	SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000429379.2_Missense_Mutation_p.H78N|G6PC2_ENST00000421979.1_Intron	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	78					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.H78N(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						ATTATTTGGTCATCGACCTTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	81	82					2																	169758968		2203	4300	6503	169467214	SO:0001583	missense	57818			AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"islet specific glucose 6 phosphatase catalytic subunit related protein"	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.232C>A	2.37:g.169758968C>A	ENSP00000364512:p.His78Asn		169467214	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	ENST00000375363.3	37	CCDS2230.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.280361	0.59758	.	.	ENSG00000152254	ENST00000375363;ENST00000429379	T;T	0.74421	-0.84;-0.84	5.58	4.71	0.59529	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.146099	0.45361	D	0.000371	T	0.70107	0.3186	L	0.46157	1.445	0.80722	D	1	B;P	0.38677	0.425;0.642	B;B	0.37508	0.252;0.252	T	0.72584	-0.4249	10	0.56958	D	0.05	0.2432	16.679	0.85287	0.0:0.8702:0.1298:0.0	.	78;78	E9PAX2;Q9NQR9	.;G6PC2_HUMAN	N	78	ENSP00000364512:H78N;ENSP00000396939:H78N	ENSP00000364512:H78N	H	+	1	0	G6PC2	169467214	0.996000	0.38824	1.000000	0.80357	0.993000	0.82548	2.375000	0.44283	1.359000	0.45940	-0.127000	0.14921	CAT		0.333	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176		A	169758968	C	A	169758968	3	1	61	1	0	0	0	0	1	0	0	0	6163	826	29	2	238	2	G6PC2	2	169758968	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37595	169758968	73440405	1792	9777										
ABCB11	8647	broad.mit.edu	37	chr2	169801156	169801156	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagcaagtcttgttgtcaAtgctccagggctatttctga	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169801156A>C	ENST00000263817.6	-	21	2693	c.2569T>G	c.(2569-2571)Ttg>Gtg	p.L857V		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	857	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.L857V(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CTTGTTGTCAATGCTCCAGGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											189	177	181					2																	169801156		1900	4130	6030	169509402	SO:0001583	missense	8647			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.2569T>G	2.37:g.169801156A>C	ENSP00000263817:p.Leu857Val		169509402	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.242538	0.58995	.	.	ENSG00000073734	ENST00000263817	D	0.93604	-3.25	5.74	0.858	0.19030	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96090	0.8726	M	0.85710	2.77	0.58432	D	0.999996	D;D	0.89917	1.0;0.997	D;D	0.79108	0.992;0.97	D	0.94960	0.8107	10	0.87932	D	0	.	10.8844	0.46957	0.3855:0.0:0.6145:0.0	.	299;857	B4DZQ8;O95342	.;ABCBB_HUMAN	V	857	ENSP00000263817:L857V	ENSP00000263817:L857V	L	-	1	2	ABCB11	169509402	0.699000	0.27786	0.871000	0.34182	0.892000	0.51952	0.976000	0.29462	0.050000	0.15949	-1.117000	0.02048	TTG		0.448	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		C	169801156	A	C	169801156	3	2	61	1	0	0	0	0	1	0	0	0	42	98	4	4	1428	4	ABCB11	2	169801156	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	42188	169801156	73398217	1793	9778										
ABCB11	8647	broad.mit.edu	37	chr2	169850337	169850337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagatggtcgaggtcatgcGctgaatgaaaagggccattt	13	7	1	3	rs199841445		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:169850337G>A	ENST00000263817.6	-	8	791	c.667C>T	c.(667-669)Cgc>Tgc	p.R223C		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	223	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.R223C(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	GAGGTCATGCGCTGAATGAAA	0.408													G|||	1	0.000199681	0	0	5008	,	,		20006	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	CYS/ARG	1,3785		0,1,1892	54	52	53		667	4.7	1	2		53	0,8212		0,0,4106	yes	missense	ABCB11	NM_003742.2	180	0,1,5998	AA,AG,GG		0.0,0.0264,0.0083	probably-damaging	223/1322	169850337	1,11997	1893	4106	5999	169558583	SO:0001583	missense	8647			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.667C>T	2.37:g.169850337G>A	ENSP00000263817:p.Arg223Cys		169558583	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.48	3.134778	0.56828	2.64E-4	0.0	ENSG00000073734	ENST00000263817	D	0.89617	-2.54	5.56	4.65	0.58169	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.094015	0.64402	D	0.000001	D	0.87962	0.6310	N	0.21194	0.64	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.85948	0.1462	10	0.38643	T	0.18	-5.9104	7.6409	0.28292	0.0871:0.0:0.7522:0.1607	.	223	O95342	ABCBB_HUMAN	C	223	ENSP00000263817:R223C	ENSP00000263817:R223C	R	-	1	0	ABCB11	169558583	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.907000	0.39897	1.242000	0.43836	0.650000	0.86243	CGC		0.408	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		A	169850337	G	A	169850337	3	1	61	1	0	0	0	0	1	0	0	0	42	1087	38	1	3382	1	ABCB11	2	169850337	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49181	169850337	73349036	1794	9779										
LRP2	4036	broad.mit.edu	37	chr2	170009420	170009420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagttggggatgtaggcaCgtttgatagcaccaaaccta	11	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170009420C>T	ENST00000263816.3	-	67	12635	c.12350G>A	c.(12349-12351)cGt>cAt	p.R4117H		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4117					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R4117H(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GATGTAGGCACGTTTGATAGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											245	241	242					2																	170009420		2203	4300	6503	169717666	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12350G>A	2.37:g.170009420C>T	ENSP00000263816:p.Arg4117His		169717666	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.603582	0.96626	.	.	ENSG00000081479	ENST00000263816	D	0.90261	-2.64	5.59	5.59	0.84812	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.102136	0.64402	D	0.000002	D	0.95614	0.8574	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	P	0.59115	0.852	D	0.95648	0.8704	10	0.62326	D	0.03	.	19.9507	0.97198	0.0:1.0:0.0:0.0	.	4117	P98164	LRP2_HUMAN	H	4117	ENSP00000263816:R4117H	ENSP00000263816:R4117H	R	-	2	0	LRP2	169717666	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.772000	0.85439	2.763000	0.94921	0.655000	0.94253	CGT		0.478	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170009420	C	T	170009420	3	4	61	1	0	0	0	0	1	0	0	0	8985	536	19	1	1669	1	LRP2	2	170009420	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159083	170009420	73189953	1795	9780										
LRP2	4036	broad.mit.edu	37	chr2	170025143	170025143	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacatggtttttgcattcGaacatagtagcctggcagta	9	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170025143G>A	ENST00000263816.3	-	61	11826	c.11541C>T	c.(11539-11541)ttC>ttT	p.F3847F		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3847	LDL-receptor class A 34. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.F3847F(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTTTGCATTCGAACATAGTAG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	2											98	89	92					2																	170025143		2203	4300	6503	169733389	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11541C>T	2.37:g.170025143G>A			169733389	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	9.741	1.164966	0.21538	.	.	ENSG00000081479	ENST00000536293	.	.	.	5.82	-6.33	0.01988	.	.	.	.	.	T	0.62048	0.2396	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63812	-0.6552	5	0.23891	T	0.37	.	17.3947	0.87442	0.8962:0.0:0.1038:0.0	.	.	.	.	L	512	.	ENSP00000438157:S512L	S	-	2	0	LRP2	169733389	0.971000	0.33674	0.855000	0.33649	0.823000	0.46562	0.340000	0.19892	-1.073000	0.03137	-0.367000	0.07326	TCG		0.428	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170025143	G	A	170025143	2	1	61	1	0	0	0	0	0	0	0	1	8985	1049	37	1		1	LRP2	2	170025143	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15723	170025143	73174230	1796	9781										
LRP2	4036	broad.mit.edu	37	chr2	170026299	170026299	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgtccacttgtacactGaaaatattcaggatggcagg	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170026299G>T	ENST00000263816.3	-	60	11695	c.11410C>A	c.(11410-11412)Cag>Aag	p.Q3804K		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3804	LDL-receptor class A 33. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.Q3804K(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CTTGTACACTGAAAATATTCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											144	120	128					2																	170026299		2203	4300	6503	169734545	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11410C>A	2.37:g.170026299G>T	ENSP00000263816:p.Gln3804Lys		169734545	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	36	5.658978	0.96734	.	.	ENSG00000081479	ENST00000263816	D	0.95622	-3.76	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.96269	0.8783	L	0.33245	0.995	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.94411	0.7632	10	0.27082	T	0.32	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	3804	P98164	LRP2_HUMAN	K	3804	ENSP00000263816:Q3804K	ENSP00000263816:Q3804K	Q	-	1	0	LRP2	169734545	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.624000	0.98398	2.941000	0.99782	0.655000	0.94253	CAG		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170026299	G	T	170026299	3	4	61	1	0	0	0	0	1	0	0	0	8985	1299	45	2	2637	2	LRP2	2	170026299	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1156	170026299	73173074	1797	9782										
LRP2	4036	broad.mit.edu	37	chr2	170030522	170030522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcggccattagcacaccGaaactggcccggccggcagg	14	15	0	0	rs373064113		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170030522G>A	ENST00000263816.3	-	56	11206	c.10921C>T	c.(10921-10923)Cgg>Tgg	p.R3641W		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3641	LDL-receptor class A 29. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R3641W(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTAGCACACCGAAACTGGCCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	TRP/ARG	0,4406		0,0,2203	77	70	72		10921	4.2	0.2	2		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP2	NM_004525.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3641/4656	170030522	1,13005	2203	4300	6503	169738768	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10921C>T	2.37:g.170030522G>A	ENSP00000263816:p.Arg3641Trp		169738768	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223463	0.39300	0.0	1.16E-4	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.96334	-3.98	5.31	4.16	0.48862	.	0.447170	0.27035	N	0.021248	D	0.97139	0.9065	M	0.75447	2.3	0.30469	N	0.773517	D	0.76494	0.999	P	0.60345	0.873	D	0.95081	0.8213	10	0.72032	D	0.01	.	11.3482	0.49573	0.0:0.0:0.3044:0.6956	.	3641	P98164	LRP2_HUMAN	W	3641;336	ENSP00000263816:R3641W	ENSP00000263816:R3641W	R	-	1	2	LRP2	169738768	0.949000	0.32298	0.185000	0.23176	0.018000	0.09664	2.170000	0.42443	0.884000	0.36064	-0.280000	0.10049	CGG		0.537	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170030522	G	A	170030522	3	1	61	1	0	0	0	0	1	0	0	0	8985	1057	37	1	3142	1	LRP2	2	170030522	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4223	170030522	73168851	1798	9783										
LRP2	4036	broad.mit.edu	37	chr2	170077010	170077010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattggaaagccaactccaaGagctgtcccatcattggcaa	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170077010G>T	ENST00000263816.3	-	34	5887	c.5602C>A	c.(5602-5604)Ctt>Att	p.L1868I		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1868					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.L1868I(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCAACTCCAAGAGCTGTCCCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	129	134					2																	170077010		2203	4300	6503	169785256	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5602C>A	2.37:g.170077010G>T	ENSP00000263816:p.Leu1868Ile		169785256	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028165	0.35797	.	.	ENSG00000081479	ENST00000263816	D	0.89485	-2.52	5.87	1.75	0.24633	Six-bladed beta-propeller, TolB-like (1);	0.591766	0.18723	N	0.132941	T	0.82213	0.4988	M	0.68952	2.095	0.09310	N	0.999999	P	0.36222	0.544	B	0.30495	0.116	T	0.71034	-0.4709	10	0.35671	T	0.21	.	2.7631	0.05312	0.134:0.1127:0.3583:0.395	.	1868	P98164	LRP2_HUMAN	I	1868	ENSP00000263816:L1868I	ENSP00000263816:L1868I	L	-	1	0	LRP2	169785256	0.993000	0.37304	0.164000	0.22755	0.945000	0.59286	2.547000	0.45786	0.340000	0.23745	0.650000	0.86243	CTT		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170077010	G	T	170077010	3	4	61	1	0	0	0	0	1	0	0	0	8985	942	33	2	8549	2	LRP2	2	170077010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46488	170077010	73122363	1799	9784										
LRP2	4036	broad.mit.edu	37	chr2	170090062	170090062	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagtccagtacacagagtCttcaaagagagttagggcat	11	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170090062C>A	ENST00000263816.3	-	30	5242	c.4957G>T	c.(4957-4959)Gac>Tac	p.D1653Y		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1653					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.D1653Y(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TACACAGAGTCTTCAAAGAGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	65	67					2																	170090062		2203	4300	6503	169798308	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.4957G>T	2.37:g.170090062C>A	ENSP00000263816:p.Asp1653Tyr		169798308	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558161	0.65538	.	.	ENSG00000081479	ENST00000263816	D	0.92099	-2.97	5.16	5.16	0.70880	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.092419	0.64402	D	0.000001	D	0.97476	0.9174	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.65684	0.937	D	0.98718	1.0707	10	0.87932	D	0	.	19.018	0.92902	0.0:1.0:0.0:0.0	.	1653	P98164	LRP2_HUMAN	Y	1653	ENSP00000263816:D1653Y	ENSP00000263816:D1653Y	D	-	1	0	LRP2	169798308	1.000000	0.71417	0.995000	0.50966	0.074000	0.17049	7.750000	0.85110	2.573000	0.86826	0.557000	0.71058	GAC		0.478	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170090062	C	A	170090062	3	1	61	1	0	0	0	0	1	0	0	0	8985	913	32	2	9210	2	LRP2	2	170090062	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13052	170090062	73109311	1800	9785										
LRP2	4036	broad.mit.edu	37	chr2	170150730	170150730	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagcacgagggatacactCtccattgccacatgaaaact	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170150730C>T	ENST00000263816.3	-	6	865	c.580G>A	c.(580-582)Gag>Aag	p.E194K	LRP2_ENST00000443831.1_Missense_Mutation_p.E194K	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	194	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.E194K(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGGATACACTCTCCATTGCCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											172	144	154					2																	170150730		2203	4300	6503	169858976	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.580G>A	2.37:g.170150730C>T	ENSP00000263816:p.Glu194Lys		169858976	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	7.980	0.751031	0.15778	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.95482	-3.72;-3.72	5.58	1.59	0.23543	.	0.780131	0.12219	N	0.488581	D	0.89111	0.6622	N	0.16098	0.37	0.38717	D	0.953367	B;P	0.38395	0.098;0.629	B;B	0.40982	0.173;0.345	T	0.81141	-0.1068	9	.	.	.	.	6.8216	0.23861	0.1232:0.5735:0.2377:0.0655	.	194;194	E9PC35;P98164	.;LRP2_HUMAN	K	194	ENSP00000263816:E194K;ENSP00000409813:E194K	.	E	-	1	0	LRP2	169858976	0.951000	0.32395	0.028000	0.17463	0.036000	0.12997	0.586000	0.23894	0.066000	0.16515	-0.176000	0.13171	GAG		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170150730	C	T	170150730	3	4	61	1	0	0	0	0	1	0	0	0	8985	922	32	3	13683	3	LRP2	2	170150730	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60668	170150730	73048643	1801	9786										
KBTBD10	10324	broad.mit.edu	37	chr2	170366315	170366315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagcgggaacttgcagaGgaactgcggctttaccaatc	11	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170366315G>T	ENST00000284669.1	+	1	104	c.27G>T	c.(25-27)gaG>gaT	p.E9D	RP11-724O16.1_ENST00000513963.1_Intron|BBS5_ENST00000554017.1_Intron	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	9					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.E9D(1)									AACTTGCAGAGGAACTGCGGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	91	89					2																	170366315		2203	4300	6503	170074561	SO:0001583	missense	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.27G>T	2.37:g.170366315G>T	ENSP00000284669:p.Glu9Asp		170074561	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	37	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.402635	0.25291	.	.	ENSG00000239474	ENST00000284669	T	0.73258	-0.73	5.03	5.03	0.67393	BTB/POZ fold (1);	0.049205	0.85682	D	0.000000	T	0.55673	0.1935	L	0.35288	1.05	0.47905	D	0.999548	B	0.20988	0.05	B	0.23574	0.047	T	0.51849	-0.8653	10	0.25751	T	0.34	.	6.6872	0.23152	0.1319:0.0:0.71:0.1581	.	9	O60662	KBTBA_HUMAN	D	9	ENSP00000284669:E9D	ENSP00000284669:E9D	E	+	3	2	KBTBD10	170074561	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.314000	0.43743	2.323000	0.78572	0.585000	0.79938	GAG		0.478	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		T	170366315	G	T	170366315	3	4	61	1	0	0	0	0	1	0	0	0	8011	991	35	2	29	2	KBTBD10	2	170366315	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215585	170366315	72833058	1802	9787										
KBTBD10	10324	broad.mit.edu	37	chr2	170366494	170366494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatctgaaattgatgaggCgaaaaaaaaggaggtagtgc	12	3	1	3	rs151212497		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170366494C>T	ENST00000284669.1	+	1	283	c.206C>T	c.(205-207)gCg>gTg	p.A69V	RP11-724O16.1_ENST00000513963.1_Intron|BBS5_ENST00000554017.1_Intron	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	69	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.A69V(1)									ATTGATGAGGCGAAAAAAAAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	VAL/ALA	4,4402	8.1+/-20.4	0,4,2199	147	146	146		206	-8	0.3	2	dbSNP_134	146	0,8600		0,0,4300	no	missense	KBTBD10	NM_006063.2	64	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	69/607	170366494	4,13002	2203	4300	6503	170074740	SO:0001583	missense	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.206C>T	2.37:g.170366494C>T	ENSP00000284669:p.Ala69Val		170074740	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	37	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133833	0.37630	9.08E-4	0.0	ENSG00000239474	ENST00000284669	T	0.71698	-0.59	5.17	-8.03	0.01114	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.336995	0.33980	N	0.004372	T	0.56108	0.1963	L	0.58810	1.83	0.20703	N	0.999863	B	0.27594	0.182	B	0.28916	0.096	T	0.42666	-0.9438	10	0.56958	D	0.05	.	7.0064	0.24838	0.405:0.4496:0.0599:0.0855	.	69	O60662	KBTBA_HUMAN	V	69	ENSP00000284669:A69V	ENSP00000284669:A69V	A	+	2	0	KBTBD10	170074740	1.000000	0.71417	0.315000	0.25238	0.898000	0.52572	3.337000	0.52120	-1.967000	0.01008	-0.291000	0.09656	GCG		0.388	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		T	170366494	C	T	170366494	3	4	61	1	0	0	0	0	1	0	0	0	8011	768	27	1	208	1	KBTBD10	2	170366494	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179	170366494	72832879	1803	9788										
KBTBD10	10324	broad.mit.edu	37	chr2	170367161	170367161	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatttacttcctggttaCctgaatgacattcccaggca	8	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170367161C>A	ENST00000284669.1	+	1	950	c.873C>A	c.(871-873)taC>taA	p.Y291*	RP11-724O16.1_ENST00000513963.1_Intron|BBS5_ENST00000554017.1_Intron	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	291					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.Y291*(1)									TTCCTGGTTACCTGAATGACA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											143	145	144					2																	170367161		2203	4300	6503	170075407	SO:0001587	stop_gained	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.873C>A	2.37:g.170367161C>A	ENSP00000284669:p.Tyr291*		170075407	Q53R42	Nonsense_Mutation	SNP	ENST00000284669.1	37	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313054	0.95655	.	.	ENSG00000239474	ENST00000284669	.	.	.	5.32	4.44	0.53790	.	0.053841	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4217	0.32705	0.0:0.7659:0.0:0.2341	.	.	.	.	X	291	.	ENSP00000284669:Y291X	Y	+	3	2	KBTBD10	170075407	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.243000	0.32767	1.242000	0.43836	0.467000	0.42956	TAC		0.473	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		A	170367161	C	A	170367161	4	1	61	1	0	0	0	0	0	1	0	0	8011	518	18	2	875	2	KBTBD10	2	170367161	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	667	170367161	72832212	1804	9789										
KBTBD10	10324	broad.mit.edu	37	chr2	170371087	170371087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatatgtttttttcagctcGatagcatagcatctgaatgg	8	6	2	1	rs190032295		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170371087G>A	ENST00000284669.1	+	2	1191	c.1114G>A	c.(1114-1116)Gat>Aat	p.D372N	KLHL41_ENST00000463400.1_3'UTR|RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.D310N|BBS5_ENST00000554017.1_Missense_Mutation_p.D310N	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	372					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.D372N(1)									TTTTCAGCTCGATAGCATAGC	0.393													G|||	1	0.000199681	8e-04	0	5008	,	,		18518	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											71	70	70					2																	170371087		2203	4300	6503	170079333	SO:0001583	missense	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1114G>A	2.37:g.170371087G>A	ENSP00000284669:p.Asp372Asn		170079333	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	37	CCDS2234.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.27	3.587628	0.66105	.	.	ENSG00000163093;ENSG00000251569;ENSG00000239474	ENST00000554017;ENST00000513963;ENST00000284669	T;T;T	0.71341	-0.56;-0.56;-0.56	5.72	5.72	0.89469	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.83238	0.5211	M	0.67397	2.05	0.80722	D	1	P;D	0.76494	0.664;0.999	B;D	0.71870	0.195;0.975	T	0.80997	-0.1132	10	0.41790	T	0.15	-1.3808	20.2406	0.98372	0.0:0.0:1.0:0.0	.	310;372	E9PBE3;O60662	.;KBTBA_HUMAN	N	310;310;372	ENSP00000452313:D310N;ENSP00000424363:D310N;ENSP00000284669:D372N	ENSP00000284669:D372N	D	+	1	0	BBS5;RP11-724O16.1;KBTBD10	170079333	1.000000	0.71417	0.998000	0.56505	0.158000	0.22134	7.871000	0.87180	2.857000	0.98124	0.650000	0.86243	GAT		0.393	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		A	170371087	G	A	170371087	3	1	61	1	0	0	0	0	1	0	0	0	8011	1058	37	1	1120	1	KBTBD10	2	170371087	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3926	170371087	72828286	1805	9790										
FASTKD1	79675	broad.mit.edu	37	chr2	170402869	170402869	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgctgtaaagtagcaatCatttcttcaagaagtgactc	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170402869C>A	ENST00000453153.2	-	8	1906	c.1560G>T	c.(1558-1560)atG>atT	p.M520I	FASTKD1_ENST00000453929.2_Missense_Mutation_p.M520I	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	520					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.M520I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AAGTAGCAATCATTTCTTCAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	88	89					2																	170402869		2203	4300	6503	170111115	SO:0001583	missense	79675			AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1560G>T	2.37:g.170402869C>A	ENSP00000400513:p.Met520Ile		170111115	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	C	3.854	-0.031327	0.07543	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.16457	2.34;2.34	4.57	-7.67	0.01272	.	0.569606	0.20222	N	0.096662	T	0.05777	0.0151	N	0.22421	0.69	0.09310	N	1	B;B	0.20052	0.041;0.024	B;B	0.10450	0.005;0.002	T	0.27054	-1.0085	10	0.17832	T	0.49	-14.7619	1.6611	0.02792	0.2934:0.1348:0.3659:0.2058	.	520;520	Q53R41-2;Q53R41	.;FAKD1_HUMAN	I	520	ENSP00000400513:M520I;ENSP00000403229:M520I	ENSP00000400513:M520I	M	-	3	0	FASTKD1	170111115	0.003000	0.15002	0.000000	0.03702	0.006000	0.05464	-0.635000	0.05471	-1.531000	0.01749	-0.302000	0.09304	ATG		0.368	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170402869	C	A	170402869	3	1	61	1	0	0	0	0	1	0	0	0	5704	826	29	2	1015	2	FASTKD1	2	170402869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31782	170402869	72796504	1806	9791										
C2orf77	129881	broad.mit.edu	37	chr2	170531499	170531499	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatttgtctttctgcctCtatttcttcatcacgcttct	4	11	7	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170531499C>A	ENST00000447353.1	-	3	451	c.346G>T	c.(346-348)Gag>Tag	p.E116*		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	116								p.E110*(1)									CTTTCTGCCTCTATTTCTTCA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											61	53	56					2																	170531499		1812	4063	5875	170239745	SO:0001587	stop_gained	129881			BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"hypothetical LOC129881"		"chromosome 2 open reading frame 77"	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.346G>T	2.37:g.170531499C>A	ENSP00000391504:p.Glu116*		170239745	Q6PJF6	Nonsense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166646	0.78339	.	.	ENSG00000154479	ENST00000447353;ENST00000421028;ENST00000419478	.	.	.	6.03	5.15	0.70609	.	0.153481	0.42172	U	0.000751	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	14.727	0.69351	0.0:0.9313:0.0:0.0686	.	.	.	.	X	116;17;92	.	ENSP00000408143:E92X	E	-	1	0	C2orf77	170239745	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	4.549000	0.60726	2.861000	0.98227	0.655000	0.94253	GAG		0.303	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		A	170531499	C	A	170531499	4	1	61	1	0	0	0	0	0	1	0	0	2200	922	32	2	1340	2	C2orf77	2	170531499	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128630	170531499	72667874	1807	9792										
KLHL23	151230	broad.mit.edu	37	chr2	170592252	170592252	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagccttaggccttcaaaGaagctgcctgctcaccgaaa	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170592252G>T	ENST00000392647.2	+	2	972	c.728G>T	c.(727-729)aGa>aTa	p.R243I	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Missense_Mutation_p.R243I	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	243								p.R243I(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						GGCCTTCAAAGAAGCTGCCTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	66	65					2																	170592252		2203	4300	6503	170300498	SO:0001583	missense	151230			BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.728G>T	2.37:g.170592252G>T	ENSP00000376419:p.Arg243Ile		170300498	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	37	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.478080	0.44044	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	T;T;T	0.70516	-0.48;-0.48;-0.49	5.81	5.81	0.92471	.	0.183555	0.64402	D	0.000019	T	0.48874	0.1524	N	0.08118	0	0.33203	D	0.552387	B	0.14012	0.009	B	0.14578	0.011	T	0.55823	-0.8080	9	0.66056	D	0.02	.	7.6139	0.28145	0.1933:0.0:0.8067:0.0	.	243	Q8NBE8	KLH23_HUMAN	I	243;243;64	ENSP00000272797:R243I;ENSP00000376419:R243I;ENSP00000394732:R64I	ENSP00000272797:R243I	R	+	2	0	KLHL23	170300498	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.241000	0.65384	2.738000	0.93877	0.655000	0.94253	AGA		0.398	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		T	170592252	G	T	170592252	3	4	61	1	0	0	0	0	1	0	0	0	8399	942	33	2	730	2	KLHL23	2	170592252	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60753	170592252	72607121	1808	9793										
METTL5	29081	broad.mit.edu	37	chr2	170669011	170669011	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgctggcaggtcatatcGaagttctgtaaaacaaaagc	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170669011G>A	ENST00000260953.5	-	6	863	c.547C>T	c.(547-549)Cga>Tga	p.R183*	METTL5_ENST00000409965.1_Nonsense_Mutation_p.R183*|METTL5_ENST00000410097.1_Nonsense_Mutation_p.R183*|METTL5_ENST00000409837.1_Nonsense_Mutation_p.R183*|METTL5_ENST00000308099.3_Nonsense_Mutation_p.R138*|METTL5_ENST00000392640.2_Nonsense_Mutation_p.R183*|METTL5_ENST00000409340.1_Nonsense_Mutation_p.R84*	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	183							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)	p.R183*(1)		breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						AGGTCATATCGAAGTTCTGTA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											126	129	128					2																	170669011		2203	4300	6503	170377257	SO:0001587	stop_gained	29081			AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.547C>T	2.37:g.170669011G>A	ENSP00000260953:p.Arg183*		170377257	D3DPC9|Q9NVX1	Nonsense_Mutation	SNP	ENST00000260953.5	37	CCDS33320.1	.	.	.	.	.	.	.	.	.	.	G	37	6.290675	0.97449	.	.	ENSG00000138382	ENST00000409837;ENST00000409340;ENST00000260953;ENST00000409965;ENST00000392640;ENST00000308099;ENST00000410097;ENST00000538491	.	.	.	5.54	3.64	0.41730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.494	14.2564	0.66055	0.0:0.0:0.4563:0.5437	.	.	.	.	X	183;84;183;183;183;138;183;39	.	ENSP00000260953:R183X	R	-	1	2	METTL5	170377257	0.979000	0.34478	0.998000	0.56505	0.997000	0.91878	1.289000	0.33307	0.589000	0.29677	0.591000	0.81541	CGA		0.373	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168		A	170669011	G	A	170669011	4	1	61	1	0	0	0	0	0	1	0	0	9533	1066	37	1	90	1	METTL5	2	170669011	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76759	170669011	72530362	1809	9794										
METTL5	29081	broad.mit.edu	37	chr2	170677648	170677648	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattcataattactgtatcGaatgacttggacattctgtt	8	6	2	1	rs373339746		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170677648G>A	ENST00000260953.5	-	3	676	c.360C>T	c.(358-360)ttC>ttT	p.F120F	METTL5_ENST00000409965.1_Silent_p.F120F|METTL5_ENST00000410097.1_Silent_p.F120F|METTL5_ENST00000409837.1_Silent_p.F120F|METTL5_ENST00000308099.3_Silent_p.F120F|METTL5_ENST00000392640.2_Silent_p.F120F|METTL5_ENST00000409340.1_Intron	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	120							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)	p.F120F(2)		breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						TTACTGTATCGAATGACTTGG	0.303																																																2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	2						G		0,4406		0,0,2203	103	103	103		360	3.8	1	2		103	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	METTL5	NM_014168.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		120/210	170677648	2,13004	2203	4300	6503	170385894	SO:0001819	synonymous_variant	29081			AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.360C>T	2.37:g.170677648G>A			170385894	D3DPC9|Q9NVX1	Silent	SNP	ENST00000260953.5	37	CCDS33320.1	.	.	.	.	.	.	.	.	.	.	G	9.178	1.022876	0.19433	0.0	2.33E-4	ENSG00000138382	ENST00000540464;ENST00000442181	.	.	.	5.04	3.81	0.43845	.	.	.	.	.	T	0.58119	0.2100	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53373	-0.8448	4	.	.	.	-2.7061	8.2197	0.31534	0.8422:0.0:0.1578:0.0	.	.	.	.	L	120;31	.	.	S	-	2	0	METTL5	170385894	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.675000	0.54605	0.854000	0.35336	-0.290000	0.09829	TCG		0.303	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168		A	170677648	G	A	170677648	2	1	61	1	0	0	0	0	0	0	0	1	9533	1049	37	1		1	METTL5	2	170677648	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8637	170677648	72521725	1810	9795										
UBR3	130507	broad.mit.edu	37	chr2	170857922	170857922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcttacatggaatcattaCgggtaagttgattgcaaaaa	8	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:170857922C>T	ENST00000272793.5	+	27	4077	c.4027C>T	c.(4027-4029)Cgg>Tgg	p.R1343W	UBR3_ENST00000418381.1_Missense_Mutation_p.R1343W|UBR3_ENST00000392631.1_Missense_Mutation_p.R164W			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1343					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R196W(1)|p.R1343W(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						GGAATCATTACGGGTAAGTTG	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	2											98	93	95					2																	170857922		2203	4299	6502	170566168	SO:0001583	missense	130507			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4027C>T	2.37:g.170857922C>T	ENSP00000272793:p.Arg1343Trp		170566168	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	c	14.66	2.600256	0.46423	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681	T;T;T;T	0.64803	-0.12;-0.12;-0.12;0.67	5.05	4.16	0.48862	Zinc finger, RING/FYVE/PHD-type (1);	0.054772	0.64402	D	0.000001	T	0.51924	0.1703	L	0.41236	1.265	0.41529	D	0.988447	B;B;B	0.25105	0.008;0.012;0.118	B;B;B	0.14578	0.003;0.008;0.011	T	0.56854	-0.7910	10	0.66056	D	0.02	.	13.2413	0.59997	0.0:0.9225:0.0:0.0775	.	1343;164;1343	Q6ZT12;Q6ZT12-2;E7EVK3	UBR3_HUMAN;.;.	W	1343;1343;1343;164;14	ENSP00000272793:R1343W;ENSP00000396068:R1343W;ENSP00000376408:R164W;ENSP00000389097:R14W	ENSP00000272793:R1343W	R	+	1	2	UBR3	170566168	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.698000	0.37794	2.518000	0.84900	0.298000	0.19748	CGG		0.338	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		T	170857922	C	T	170857922	3	4	61	1	0	0	0	0	1	0	0	0	16943	527	19	1	4133	1	UBR3	2	170857922	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180274	170857922	72341451	1811	9796										
MYO3B	140469	broad.mit.edu	37	chr2	171070963	171070963	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcggttggatgaagcaatGatctcatacatcttgtacgg	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171070963G>T	ENST00000408978.4	+	4	539	c.396G>T	c.(394-396)atG>atT	p.M132I	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Missense_Mutation_p.M141I|MYO3B_ENST00000409044.3_Missense_Mutation_p.M132I	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.M132I(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ATGAAGCAATGATCTCATACA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											99	94	95					2																	171070963		1957	4156	6113	170779209	SO:0001583	missense	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.396G>T	2.37:g.171070963G>T	ENSP00000386213:p.Met132Ile		170779209	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.37|10.37	1.332403|1.332403	0.24167|0.24167	.|.	.|.	ENSG00000071909|ENSG00000071909	ENST00000442690|ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	.|T;T;T;T	.|0.64618	.|-0.11;-0.11;-0.11;-0.11	5.41|5.41	3.33|3.33	0.38152|0.38152	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.725862	.|0.14305	.|N	.|0.328027	T|T	0.32436|0.32436	0.0829|0.0829	N|N	0.03084|0.03084	-0.415|-0.415	0.28187|0.28187	N|N	0.927921|0.927921	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.001;0.0;0.0;0.0	T|T	0.14643|0.14643	-1.0465|-1.0465	5|10	.|0.15066	.|T	.|0.55	.|.	7.0749|7.0749	0.25199|0.25199	0.1665:0.285:0.5484:0.0|0.1665:0.285:0.5484:0.0	.|.	.|132;132;132;132	.|Q8WXR4-5;B7ZM71;Q8WXR4-4;Q8WXR4	.|.;.;.;MYO3B_HUMAN	Y|I	132|132;132;131;141;141	.|ENSP00000386497:M132I;ENSP00000386213:M132I;ENSP00000446237:M141I;ENSP00000335100:M141I	.|ENSP00000314213:M131I	D|M	+|+	1|3	0|0	MYO3B|MYO3B	170779209|170779209	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	0.772000|0.772000	0.26647|0.26647	2.549000|2.549000	0.85964|0.85964	0.650000|0.650000	0.86243|0.86243	GAT|ATG		0.493	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171070963	G	T	171070963	3	4	61	1	0	0	0	0	1	0	0	0	10107	1290	45	2	410	2	MYO3B	2	171070963	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213041	171070963	72128410	1812	9797										
MYO3B	140469	broad.mit.edu	37	chr2	171248043	171248043	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcaggagagagaaaaatTttcatatattttactatatt	5	3	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171248043T>G	ENST00000408978.4	+	15	1734	c.1591T>G	c.(1591-1593)Ttt>Gtt	p.F531V	MYO3B_ENST00000334231.6_Missense_Mutation_p.F540V|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.F531V	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	531	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.F531V(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						AGAGAAAAATTTTCATATATT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											22	23	23					2																	171248043		1774	4045	5819	170956289	SO:0001583	missense	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1591T>G	2.37:g.171248043T>G	ENSP00000386213:p.Phe531Val		170956289	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.631939	0.87660	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	6.17	6.17	0.99709	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.92391	0.7585	H	0.96691	3.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	D	0.94648	0.7836	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	531;531;531	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	V	531;531;530;540;540	ENSP00000386497:F531V;ENSP00000386213:F531V;ENSP00000446237:F540V;ENSP00000335100:F540V	ENSP00000314213:F530V	F	+	1	0	MYO3B	170956289	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.499000	0.81566	2.371000	0.80710	0.533000	0.62120	TTT		0.343	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			G	171248043	T	G	171248043	3	3	61	1	0	0	0	0	1	0	0	0	10107	1841	64	4	1649	4	MYO3B	2	171248043	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	177080	171248043	71951330	1813	9798										
MYO3B	140469	broad.mit.edu	37	chr2	171248960	171248960	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcttacagaagacaattCgaagcaattcagcattgctt	8	8	2	2	rs369862213	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171248960C>T	ENST00000408978.4	+	16	1889	c.1746C>T	c.(1744-1746)ttC>ttT	p.F582F	MYO3B_ENST00000334231.6_Silent_p.F591F|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.F582F	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	582	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.F582F(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GAAGACAATTCGAAGCAATTC	0.398													C|||	2	0.000399361	0	0	5008	,	,		22538	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	2											114	104	107					2																	171248960		1920	4127	6047	170957206	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1746C>T	2.37:g.171248960C>T			170957206	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																				0.398	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171248960	C	T	171248960	2	4	61	1	0	0	0	0	0	0	0	1	10107	883	31	1		1	MYO3B	2	171248960	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	917	171248960	71950413	1814	9799										
MYO3B	140469	broad.mit.edu	37	chr2	171258191	171258191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacactcctgcagccagacGaaaacatatggcaagttcct	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171258191G>A	ENST00000408978.4	+	18	2262	c.2119G>A	c.(2119-2121)Gaa>Aaa	p.E707K	MYO3B_ENST00000334231.6_Missense_Mutation_p.E716K|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.E707K	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	707	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.E707K(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GCAGCCAGACGAAAACATATG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	44	45					2																	171258191		1947	4144	6091	170966437	SO:0001583	missense	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2119G>A	2.37:g.171258191G>A	ENSP00000386213:p.Glu707Lys		170966437	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	A	8.068	0.769706	0.15983	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	5.92	5.92	0.95590	Myosin head, motor domain (2);	0.323419	0.40554	N	0.001063	T	0.35941	0.0949	N	0.00677	-1.265	0.19300	N	0.999979	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.23547	-1.0185	10	0.06757	T	0.87	.	12.1441	0.54014	0.9334:0.0:0.0666:0.0	.	707;707;707	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	K	707;707;706;716;716	ENSP00000386497:E707K;ENSP00000386213:E707K;ENSP00000446237:E716K;ENSP00000335100:E716K	ENSP00000314213:E706K	E	+	1	0	MYO3B	170966437	1.000000	0.71417	0.996000	0.52242	0.873000	0.50193	4.512000	0.60469	1.077000	0.40990	-0.254000	0.11334	GAA		0.527	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171258191	G	A	171258191	3	1	61	1	0	0	0	0	1	0	0	0	10107	1059	37	1	2189	1	MYO3B	2	171258191	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9231	171258191	71941182	1815	9800										
MYO3B	140469	broad.mit.edu	37	chr2	171259412	171259412	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatatctttggattcgagaaTtttcagagaaattcatttga	8	4	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171259412T>A	ENST00000408978.4	+	19	2327	c.2184T>A	c.(2182-2184)aaT>aaA	p.N728K	MYO3B_ENST00000334231.6_Missense_Mutation_p.N737K|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.N728K	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	728	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.N728K(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GATTCGAGAATTTTCAGAGAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											130	120	123					2																	171259412		1861	4101	5962	170967658	SO:0001583	missense	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2184T>A	2.37:g.171259412T>A	ENSP00000386213:p.Asn728Lys		170967658	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.159853	0.57368	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	6.02	2.27	0.28462	Myosin head, motor domain (3);	0.077058	0.85682	D	0.000000	D	0.91771	0.7397	M	0.79011	2.435	0.39490	D	0.96802	D;B;P	0.67145	0.996;0.243;0.809	D;B;P	0.64595	0.927;0.167;0.589	D	0.90882	0.4754	10	0.51188	T	0.08	.	12.8328	0.57756	0.0:0.8866:0.0:0.1134	.	728;728;728	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	K	728;728;727;737;737	ENSP00000386497:N728K;ENSP00000386213:N728K;ENSP00000446237:N737K;ENSP00000335100:N737K	ENSP00000314213:N727K	N	+	3	2	MYO3B	170967658	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.378000	0.34328	0.116000	0.18110	0.533000	0.62120	AAT		0.413	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171259412	T	A	171259412	3	1	61	1	0	0	0	0	1	0	0	0	10107	1490	52	5	2258	5	MYO3B	2	171259412	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1221	171259412	71939961	1816	9801										
GAD1	2571	broad.mit.edu	37	chr2	171702049	171702049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacatgtacagcatcatggCtgctcgctacaagtacttcc	7	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171702049C>T	ENST00000358196.3	+	8	1335	c.785C>T	c.(784-786)gCt>gTt	p.A262V		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	262					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.A262V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						AGCATCATGGCTGCTCGCTAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											116	115	116					2																	171702049		2203	4300	6503	171410295	SO:0001583	missense	2571				CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.785C>T	2.37:g.171702049C>T	ENSP00000350928:p.Ala262Val		171410295	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.620056	0.28801	.	.	ENSG00000128683	ENST00000358196	T	0.62364	0.03	5.67	5.67	0.87782	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.152563	0.64402	D	0.000011	T	0.40645	0.1125	N	0.05124	-0.11	0.80722	D	1	B	0.15473	0.013	B	0.12156	0.007	T	0.44050	-0.9353	10	0.02654	T	1	-11.7753	19.7657	0.96340	0.0:1.0:0.0:0.0	.	262	Q99259	DCE1_HUMAN	V	262	ENSP00000350928:A262V	ENSP00000350928:A262V	A	+	2	0	GAD1	171410295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.590000	0.67530	2.649000	0.89929	0.655000	0.94253	GCT		0.507	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171702049	C	T	171702049	3	4	61	1	0	0	0	0	1	0	0	0	6198	797	28	3	852	3	GAD1	2	171702049	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	442637	171702049	71497324	1817	9802										
GORASP2	26003	broad.mit.edu	37	chr2	171811171	171811171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttatagcctaggatgtgGcattggatatggttatttgc	11	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171811171G>A	ENST00000234160.4	+	6	1393	c.578G>A	c.(577-579)gGc>gAc	p.G193D	GORASP2_ENST00000493692.1_Intron|GORASP2_ENST00000452526.2_Missense_Mutation_p.G205D	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	193					mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G193D(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						CTAGGATGTGGCATTGGATAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	104	105					2																	171811171		2203	4300	6503	171519417	SO:0001583	missense	26003				CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.578G>A	2.37:g.171811171G>A	ENSP00000234160:p.Gly193Asp		171519417	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	37	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.098758	0.76870	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.46451	0.9;0.87	5.84	5.84	0.93424	.	0.049198	0.85682	D	0.000000	T	0.37625	0.1010	L	0.31065	0.9	0.80722	D	1	B;B;P	0.42518	0.414;0.414;0.782	B;B;B	0.43018	0.204;0.204;0.405	T	0.04017	-1.0984	10	0.21540	T	0.41	-12.0031	18.333	0.90277	0.0:0.0:1.0:0.0	.	149;205;193	B4DNR1;B4DKT0;Q9H8Y8	.;.;GORS2_HUMAN	D	193;205	ENSP00000234160:G193D;ENSP00000410208:G205D	ENSP00000234160:G193D	G	+	2	0	GORASP2	171519417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.721000	0.84768	2.762000	0.94881	0.551000	0.68910	GGC		0.403	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			A	171811171	G	A	171811171	3	1	61	1	0	0	0	0	1	0	0	0	6596	1203	42	3	600	3	GORASP2	2	171811171	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109122	171811171	71388202	1818	9803										
TLK1	9874	broad.mit.edu	37	chr2	171850438	171850438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaatcgatcttcttttCgatatgccaaacagcgtctt	5	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171850438C>T	ENST00000431350.2	-	21	2557	c.2153G>A	c.(2152-2154)cGa>cAa	p.R718Q	TLK1_ENST00000442919.2_Missense_Mutation_p.R670Q|TLK1_ENST00000434911.2_Missense_Mutation_p.R622Q|TLK1_ENST00000360843.3_Missense_Mutation_p.R739Q|TLK1_ENST00000521943.1_Missense_Mutation_p.R670Q			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	718	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R670Q(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						ATCTTCTTTTCGATATGCCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											134	120	125					2																	171850438		2203	4300	6503	171558684	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.2153G>A	2.37:g.171850438C>T	ENSP00000411099:p.Arg718Gln		171558684	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.873091	0.51695	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.71	5.71	0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063919	0.64402	D	0.000014	T	0.24005	0.0581	N	0.16743	0.435	0.80722	D	1	P;P;P	0.51537	0.941;0.946;0.875	P;B;B	0.45195	0.473;0.342;0.269	T	0.03315	-1.1049	10	0.87932	D	0	-20.8556	19.845	0.96705	0.0:1.0:0.0:0.0	.	622;739;718	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	Q	670;718;739;670;622	ENSP00000402165:R670Q;ENSP00000411099:R718Q;ENSP00000354089:R739Q;ENSP00000428113:R670Q;ENSP00000409222:R622Q	ENSP00000354089:R739Q	R	-	2	0	TLK1	171558684	1.000000	0.71417	1.000000	0.80357	0.017000	0.09413	7.818000	0.86416	2.698000	0.92095	0.650000	0.86243	CGA		0.393	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		T	171850438	C	T	171850438	3	4	61	1	0	0	0	0	1	0	0	0	15982	884	31	1	151	1	TLK1	2	171850438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39267	171850438	71348935	1819	9804										
TLK1	9874	broad.mit.edu	37	chr2	171863327	171863327	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgtatctgtatccaaggaGaaataatcatagagtttaac	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171863327G>T	ENST00000431350.2	-	16	1985	c.1581C>A	c.(1579-1581)ttC>ttA	p.F527L	TLK1_ENST00000442919.2_Missense_Mutation_p.F479L|TLK1_ENST00000434911.2_Missense_Mutation_p.F431L|TLK1_ENST00000360843.3_Missense_Mutation_p.F548L|TLK1_ENST00000521943.1_Missense_Mutation_p.F479L			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	527	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F527L(1)|p.F479L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TATCCAAGGAGAAATAATCAT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	2											108	116	114					2																	171863327		2203	4297	6500	171571573	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1581C>A	2.37:g.171863327G>T	ENSP00000411099:p.Phe527Leu		171571573	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.421428	0.62622	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	4.95	4.06	0.47325	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	L	0.41236	1.265	0.80722	D	1	D;D;D	0.76494	0.985;0.994;0.999	D;D;D	0.91635	0.914;0.919;0.999	T	0.09378	-1.0677	10	0.49607	T	0.09	.	8.3235	0.32142	0.2399:0.0:0.7601:0.0	.	431;548;527	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	L	479;527;548;479;431	ENSP00000402165:F479L;ENSP00000411099:F527L;ENSP00000354089:F548L;ENSP00000428113:F479L;ENSP00000409222:F431L	ENSP00000354089:F548L	F	-	3	2	TLK1	171571573	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.822000	0.39052	1.232000	0.43678	0.454000	0.30748	TTC		0.348	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		T	171863327	G	T	171863327	3	4	61	1	0	0	0	0	1	0	0	0	15982	933	33	2	743	2	TLK1	2	171863327	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12889	171863327	71336046	1820	9805										
TLK1	9874	broad.mit.edu	37	chr2	171906331	171906331	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatgactaacttcacaaGattctgaaatgcaaaaccat	5	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171906331G>A	ENST00000431350.2	-	10	1377	c.973C>T	c.(973-975)Ctt>Ttt	p.L325F	TLK1_ENST00000442919.2_Missense_Mutation_p.L277F|TLK1_ENST00000434911.2_Missense_Mutation_p.L229F|TLK1_ENST00000360843.3_Missense_Mutation_p.L346F|TLK1_ENST00000521943.1_Missense_Mutation_p.L277F			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	325					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L277F(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						AACTTCACAAGATTCTGAAAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	103	105					2																	171906331		2203	4300	6503	171614577	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.973C>T	2.37:g.171906331G>A	ENSP00000411099:p.Leu325Phe		171614577	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516951	0.85495	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.70164	-0.42;-0.46;-0.42;-0.42;-0.39	5.72	5.72	0.89469	.	0.060456	0.64402	D	0.000002	D	0.85305	0.5666	M	0.86651	2.83	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.98;0.991;0.999	D	0.86680	0.1916	10	0.87932	D	0	-16.0099	20.2504	0.98404	0.0:0.0:1.0:0.0	.	229;346;325	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	F	277;325;346;277;229	ENSP00000402165:L277F;ENSP00000411099:L325F;ENSP00000354089:L346F;ENSP00000428113:L277F;ENSP00000409222:L229F	ENSP00000354089:L346F	L	-	1	0	TLK1	171614577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.875000	0.87205	2.850000	0.98022	0.650000	0.86243	CTT		0.343	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		A	171906331	G	A	171906331	3	1	61	1	0	0	0	0	1	0	0	0	15982	942	33	3	1375	3	TLK1	2	171906331	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43004	171906331	71293042	1821	9806										
TLK1	9874	broad.mit.edu	37	chr2	171906585	171906585	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagcctaccttttcaataaGaagtttcttgctcattgata	5	8	3	2	rs564665685		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:171906585G>A	ENST00000431350.2	-	9	1236	c.832C>T	c.(832-834)Ctt>Ttt	p.L278F	TLK1_ENST00000442919.2_Missense_Mutation_p.L230F|TLK1_ENST00000434911.2_Missense_Mutation_p.L182F|TLK1_ENST00000360843.3_Missense_Mutation_p.L299F|TLK1_ENST00000521943.1_Missense_Mutation_p.L230F			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	278					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L230F(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTTTCAATAAGAAGTTTCTTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	103	105					2																	171906585		2201	4299	6500	171614831	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.832C>T	2.37:g.171906585G>A	ENSP00000411099:p.Leu278Phe		171614831	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003547	0.74932	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.74315	-0.76;-0.83;-0.75;-0.76;-0.68	6.03	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.87184	0.6114	M	0.86864	2.845	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.998;0.999	D	0.88617	0.3160	10	0.87932	D	0	-21.3314	13.885	0.63704	0.123:0.0:0.877:0.0	.	182;299;278	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	F	230;278;299;230;182	ENSP00000402165:L230F;ENSP00000411099:L278F;ENSP00000354089:L299F;ENSP00000428113:L230F;ENSP00000409222:L182F	ENSP00000354089:L299F	L	-	1	0	TLK1	171614831	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.755000	0.68750	2.854000	0.98071	0.655000	0.94253	CTT		0.313	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		A	171906585	G	A	171906585	3	1	61	1	0	0	0	0	1	0	0	0	15982	942	33	3	1520	3	TLK1	2	171906585	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	254	171906585	71292788	1822	9807										
DCAF17	80067	broad.mit.edu	37	chr2	172333405	172333405	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaatagaaaataatagttCtcagcatcagatctctgaag	7	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172333405C>A	ENST00000375255.3	+	11	1454	c.1127C>A	c.(1126-1128)tCt>tAt	p.S376Y	DCAF17_ENST00000468592.1_3'UTR|DCAF17_ENST00000539783.1_Intron	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	376					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.S376Y(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						AATAATAGTTCTCAGCATCAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	76	75					2																	172333405		2203	4300	6503	172041651	SO:0001583	missense	80067			AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"DDB1 and CUL4 associated factors"	25784	protein-coding gene	gene with protein product	"Woodhouse-Sakati syndrome"	612515	"chromosome 2 open reading frame 37"	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.1127C>A	2.37:g.172333405C>A	ENSP00000364404:p.Ser376Tyr		172041651	B2RTW5|Q53TN3|Q9H908	Missense_Mutation	SNP	ENST00000375255.3	37	CCDS2243.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.721|0.721	-0.783455|-0.783455	0.02907|0.02907	.|.	.|.	ENSG00000115827|ENSG00000115827	ENST00000339506;ENST00000431110|ENST00000375255;ENST00000429466	.|T	.|0.48201	.|0.82	5.55|5.55	1.33|1.33	0.21861|0.21861	.|.	.|0.919351	.|0.09484	.|N	.|0.795959	T|T	0.22044|0.22044	0.0531|0.0531	N|N	0.16478|0.16478	0.41|0.41	0.21256|0.21256	N|N	0.999745|0.999745	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.27673|0.27673	-1.0067|-1.0067	5|10	.|0.02654	.|T	.|1	-0.2733|-0.2733	1.3583|1.3583	0.02186|0.02186	0.238:0.3853:0.2081:0.1687|0.238:0.3853:0.2081:0.1687	.|.	.|376	.|Q5H9S7	.|DCA17_HUMAN	I|Y	127;78|376;126	.|ENSP00000364404:S376Y	.|ENSP00000364404:S376Y	L|S	+|+	1|2	0|0	DCAF17|DCAF17	172041651|172041651	0.903000|0.903000	0.30736|0.30736	0.989000|0.989000	0.46669|0.46669	0.975000|0.975000	0.68041|0.68041	1.139000|1.139000	0.31504|0.31504	-0.059000|-0.059000	0.13154|0.13154	-0.317000|-0.317000	0.08691|0.08691	CTC|TCT		0.343	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000		A	172333405	C	A	172333405	3	1	61	1	0	0	0	0	1	0	0	0	4275	913	32	2	1169	2	DCAF17	2	172333405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426820	172333405	70865968	1823	9808										
CYBRD1	79901	broad.mit.edu	37	chr2	172398157	172398157	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcctgatgaaatccatcCatgcagggttaaatgcagtt	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172398157C>A	ENST00000321348.4	+	2	454	c.256C>A	c.(256-258)Cat>Aat	p.H86N	CYBRD1_ENST00000468308.1_3'UTR|CYBRD1_ENST00000409484.1_Missense_Mutation_p.H28N|CYBRD1_ENST00000375252.3_Intron	NM_024843.3	NP_079119.3	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1	86	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				cellular iron ion homeostasis (GO:0006879)|response to iron ion (GO:0010039)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|oxidoreductase activity, oxidizing metal ions (GO:0016722)	p.H86N(1)		endometrium(1)|kidney(1)|large_intestine(3)|liver(2)|lung(3)	10						GAAATCCATCCATGCAGGGTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											172	157	162					2																	172398157		2203	4300	6503	172106403	SO:0001583	missense	79901			AK027115	CCDS2244.1, CCDS46449.1, CCDS58736.1	2q31	2013-03-14			ENSG00000071967	ENSG00000071967		"Cytochrome b genes"	20797	protein-coding gene	gene with protein product	"ferric-chelate reductase 3", "cytochrome b561 family, member A2"	605745				11230685	Standard	NM_001127383		Approved	DCYTB, FLJ23462, FRRS3, CYB561A2	uc002ugy.4	Q53TN4	OTTHUMG00000132260	ENST00000321348.4:c.256C>A	2.37:g.172398157C>A	ENSP00000319141:p.His86Asn		172106403	B2RE79|B4DWD7|Q6KC16|Q6KC17|Q6P147|Q6ZR51|Q9H0Q8|Q9H5G5	Missense_Mutation	SNP	ENST00000321348.4	37	CCDS2244.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408356	0.83340	.	.	ENSG00000071967	ENST00000409484;ENST00000321348;ENST00000445146	D;D;D	0.83673	-1.75;-1.75;-1.75	5.38	5.38	0.77491	Cytochrome b561, eukaryote (1);Cytochrome b561/ferric reductase transmembrane (2);	0.000000	0.85682	D	0.000000	D	0.94381	0.8193	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95909	0.8921	10	0.87932	D	0	-13.982	19.1378	0.93435	0.0:1.0:0.0:0.0	.	86	Q53TN4	CYBR1_HUMAN	N	28;86;47	ENSP00000386739:H28N;ENSP00000319141:H86N;ENSP00000402242:H47N	ENSP00000319141:H86N	H	+	1	0	CYBRD1	172106403	1.000000	0.71417	0.999000	0.59377	0.423000	0.31445	7.757000	0.85209	2.521000	0.84997	0.650000	0.86243	CAT		0.443	CYBRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255344.2	NM_024843		A	172398157	C	A	172398157	3	1	61	1	0	0	0	0	1	0	0	0	4140	594	21	2	262	2	CYBRD1	2	172398157	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64752	172398157	70801216	1824	9809										
DYNC1I2	1781	broad.mit.edu	37	chr2	172584373	172584373	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcaaaatttcatccaaatCttgttgttggtggtacatat	7	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172584373C>A	ENST00000397119.3	+	12	1206	c.1039C>A	c.(1039-1041)Ctt>Att	p.L347I	DYNC1I2_ENST00000534253.2_Missense_Mutation_p.L347I|DYNC1I2_ENST00000409453.1_Missense_Mutation_p.L347I|DYNC1I2_ENST00000263811.4_Missense_Mutation_p.L341I|DYNC1I2_ENST00000508530.1_Missense_Mutation_p.L321I|DYNC1I2_ENST00000358002.6_Missense_Mutation_p.L339I|DYNC1I2_ENST00000410079.3_Missense_Mutation_p.L339I|DYNC1I2_ENST00000340296.4_Missense_Mutation_p.L321I|DYNC1I2_ENST00000409317.1_Missense_Mutation_p.L341I|DYNC1I2_ENST00000409773.1_Missense_Mutation_p.L347I|DYNC1I2_ENST00000409197.1_Missense_Mutation_p.L321I	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	347					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)	p.L347I(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			TCATCCAAATCTTGTTGTTGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	75	77					2																	172584373		1868	4113	5981	172292619	SO:0001583	missense	1781			AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"Cytoplasmic dyneins", "WD repeat domain containing"	2964	protein-coding gene	gene with protein product		603331	"dynein, cytoplasmic, intermediate polypeptide 2"	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.1039C>A	2.37:g.172584373C>A	ENSP00000380308:p.Leu347Ile		172292619	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	Missense_Mutation	SNP	ENST00000397119.3	37	CCDS46450.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685154	0.47991	.	.	ENSG00000077380	ENST00000340296;ENST00000534253;ENST00000263811;ENST00000397119;ENST00000410079;ENST00000508530;ENST00000409197;ENST00000409317;ENST00000409773;ENST00000409453;ENST00000358002	T;T;T;T;T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53	6.01	4.23	0.50019	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.061356	0.64402	D	0.000003	T	0.39989	0.1099	M	0.70903	2.155	0.58432	D	0.999991	B;P;P;P;P;P	0.50943	0.043;0.94;0.742;0.742;0.742;0.894	B;B;P;P;P;P	0.48425	0.034;0.303;0.577;0.577;0.577;0.476	T	0.26018	-1.0115	10	0.49607	T	0.09	-12.9809	11.0199	0.47711	0.0:0.7518:0.0:0.2482	.	70;339;341;321;321;347	B4DX93;B7ZA04;Q13409-2;Q13409-6;Q13409-3;Q13409	.;.;.;.;.;DC1I2_HUMAN	I	321;347;341;347;339;321;321;341;347;347;339	ENSP00000339430:L321I;ENSP00000433791:L347I;ENSP00000263811:L341I;ENSP00000380308:L347I;ENSP00000386522:L339I;ENSP00000423339:L321I;ENSP00000386397:L321I;ENSP00000386591:L341I;ENSP00000386415:L347I;ENSP00000386886:L347I;ENSP00000350692:L339I	ENSP00000263811:L341I	L	+	1	0	DYNC1I2	172292619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.221000	0.42917	0.884000	0.36064	0.650000	0.86243	CTT		0.393	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378		A	172584373	C	A	172584373	3	1	61	1	0	0	0	0	1	0	0	0	4854	913	32	2	1081	2	DYNC1I2	2	172584373	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	186216	172584373	70615000	1825	9810										
SLC25A12	8604	broad.mit.edu	37	chr2	172700943	172700943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttatgcccaaaatgcagtCggataaattcacaatcccag	8	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172700943C>T	ENST00000422440.2	-	5	438	c.401G>A	c.(400-402)cGa>cAa	p.R134Q	SLC25A12_ENST00000392592.4_Missense_Mutation_p.R27Q|SLC25A12_ENST00000472748.1_5'UTR	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	134	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)	p.R134Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	AAAATGCAGTCGGATAAATTC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	133	130					2																	172700943		2203	4300	6503	172409189	SO:0001583	missense	8604			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.401G>A	2.37:g.172700943C>T	ENSP00000388658:p.Arg134Gln		172409189	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.679187	0.29783	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.77620	-1.11;-1.1	5.8	5.8	0.92144	EF-hand-like domain (1);	0.063732	0.64402	D	0.000007	T	0.65873	0.2733	N	0.16233	0.39	0.58432	D	0.99999	B;B	0.23806	0.091;0.04	B;B	0.13407	0.009;0.009	T	0.59573	-0.7429	10	0.22109	T	0.4	-7.1792	20.0706	0.97721	0.0:1.0:0.0:0.0	.	27;134	B3KR64;O75746	.;CMC1_HUMAN	Q	134;27	ENSP00000388658:R134Q;ENSP00000376371:R27Q	ENSP00000376371:R27Q	R	-	2	0	SLC25A12	172409189	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.927000	0.63440	2.744000	0.94065	0.655000	0.94253	CGA		0.333	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		T	172700943	C	T	172700943	3	4	61	1	0	0	0	0	1	0	0	0	14511	884	31	1	1691	1	SLC25A12	2	172700943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116570	172700943	70498430	1826	9811										
HAT1	8520	broad.mit.edu	37	chr2	172782063	172782063	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggatttggtgctatggaGaaatttttggtagaatataa	11	1	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172782063G>T	ENST00000264108.4	+	2	60	c.24G>T	c.(22-24)gaG>gaT	p.E8D	HAT1_ENST00000392584.1_5'UTR|SLC25A12_ENST00000472748.1_Intron	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	8					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)	p.E8D(1)		breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GTGCTATGGAGAAATTTTTGG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											94	97	96					2																	172782063		2203	4300	6503	172490309	SO:0001583	missense	8520			AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.24G>T	2.37:g.172782063G>T	ENSP00000264108:p.Glu8Asp		172490309	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Missense_Mutation	SNP	ENST00000264108.4	37	CCDS2245.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641283	0.47153	.	.	ENSG00000128708	ENST00000264108	.	.	.	5.88	2.76	0.32466	.	0.253697	0.32918	N	0.005493	T	0.55321	0.1913	L	0.40543	1.245	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.55496	-0.8132	9	0.87932	D	0	-25.5205	5.6699	0.17717	0.3645:0.0:0.6355:0.0	.	8	O14929	HAT1_HUMAN	D	8	.	ENSP00000264108:E8D	E	+	3	2	HAT1	172490309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.922000	0.28734	0.825000	0.34637	0.655000	0.94253	GAG		0.343	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		T	172782063	G	T	172782063	3	4	61	1	0	0	0	0	1	0	0	0	6985	933	33	2	30	2	HAT1	2	172782063	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81120	172782063	70417310	1827	9812										
HAT1	8520	broad.mit.edu	37	chr2	172821966	172821966	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagttgatttcaagccattCggaaccttacttcataccta	6	10	2	1	rs533334266		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:172821966C>T	ENST00000264108.4	+	5	453	c.417C>T	c.(415-417)ttC>ttT	p.F139F	HAT1_ENST00000392584.1_Silent_p.F54F|SLC25A12_ENST00000472748.1_Intron	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	139					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)	p.F139F(1)		breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TCAAGCCATTCGGAACCTTAC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	2											70	70	70					2																	172821966		2203	4300	6503	172530212	SO:0001819	synonymous_variant	8520			AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.417C>T	2.37:g.172821966C>T			172530212	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Silent	SNP	ENST00000264108.4	37	CCDS2245.1																																																																																				0.348	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		T	172821966	C	T	172821966	2	4	61	1	0	0	0	0	0	0	0	1	6985	883	31	1		1	HAT1	2	172821966	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39903	172821966	70377407	1828	9813										
ITGA6	3655	broad.mit.edu	37	chr2	173333961	173333961	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatctcaggattgaagacGatatggatgggggagattgg	16	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:173333961G>T	ENST00000264106.6	+	4	699	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	ITGA6_ENST00000409532.1_Missense_Mutation_p.D52Y|ITGA6_ENST00000375221.2_Missense_Mutation_p.D166Y|ITGA6_ENST00000343713.4_Missense_Mutation_p.D166Y|ITGA6_ENST00000264107.7_Missense_Mutation_p.D166Y|ITGA6_ENST00000409080.1_Missense_Mutation_p.D166Y			P23229	ITA6_HUMAN	integrin, alpha 6	166					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.D166N(1)|p.D166Y(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			GATTGAAGACGATATGGATGG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	2											179	172	174					2																	173333961		2203	4300	6503	173042207	SO:0001583	missense	3655				CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.496G>T	2.37:g.173333961G>T	ENSP00000264106:p.Asp166Tyr		173042207	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.983076	0.74474	.	.	ENSG00000091409	ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	6.17	6.17	0.99709	.	0.199493	0.52532	D	0.000078	T	0.52517	0.1739	M	0.77820	2.39	0.80722	D	1	B;B;B	0.31026	0.304;0.056;0.056	B;B;B	0.32677	0.15;0.15;0.118	T	0.53676	-0.8405	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	166;166;166	P23229-4;G5E9H1;P23229-2	.;.;.	Y	52;52;166;166;166;166;166;166;166	ENSP00000413470:D52Y;ENSP00000386614:D52Y;ENSP00000264107:D166Y;ENSP00000264106:D166Y;ENSP00000364369:D166Y;ENSP00000341078:D166Y;ENSP00000386896:D166Y;ENSP00000406694:D166Y;ENSP00000394169:D166Y	ENSP00000264106:D166Y	D	+	1	0	ITGA6	173042207	1.000000	0.71417	0.976000	0.42696	0.962000	0.63368	6.695000	0.74593	2.941000	0.99782	0.655000	0.94253	GAT		0.458	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				T	173333961	G	T	173333961	3	4	61	1	0	0	0	0	1	0	0	0	7901	1058	37	2	510	2	ITGA6	2	173333961	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	511995	173333961	69865412	1829	9814										
ITGA6	3655	broad.mit.edu	37	chr2	173356032	173356032	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtctcttattttgcgctcGaggttatggaacagcacatt	10	9	1	0	rs61757097	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:173356032G>A	ENST00000264106.6	+	23	3182	c.2979G>A	c.(2977-2979)tcG>tcA	p.S993S	ITGA6_ENST00000409532.1_Silent_p.S835S|ITGA6_ENST00000375221.2_Silent_p.S993S|ITGA6_ENST00000343713.4_Silent_p.S949S|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Silent_p.S954S|ITGA6_ENST00000409080.1_Silent_p.S954S			P23229	ITA6_HUMAN	integrin, alpha 6	993					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.S954S(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TTTTGCGCTCGAGGTTATGGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	2											137	134	135					2																	173356032		2203	4300	6503	173064278	SO:0001819	synonymous_variant	3655				CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2979G>A	2.37:g.173356032G>A			173064278	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	37																																																																																					0.488	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				A	173356032	G	A	173356032	2	1	61	1	0	0	0	0	0	0	0	1	7901	1045	37	1		1	ITGA6	2	173356032	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22071	173356032	69843341	1830	9815										
PDK1	5163	broad.mit.edu	37	chr2	173460578	173460578	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtcaacagactcaataGaaagactcccagtgtataac	6	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:173460578G>T	ENST00000282077.3	+	11	1374	c.1192G>T	c.(1192-1194)Gaa>Taa	p.E398*	PDK1_ENST00000392571.2_Nonsense_Mutation_p.E418*|PDK1_ENST00000410055.1_Nonsense_Mutation_p.E398*|PDK1_ENST00000544863.1_Nonsense_Mutation_p.E243*|PDK1_ENST00000543905.1_Nonsense_Mutation_p.E322*			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	398					cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.E398*(1)		central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			AGACTCAATAGAAAGACTCCC	0.413									Autosomal Dominant Polycystic Kidney Disease																																							1	Substitution - Nonsense(1)	large_intestine(1)	2											62	58	60					2																	173460578		2203	4300	6503	173168824	SO:0001587	stop_gained	5163	Familial Cancer Database	ADPKD	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"pyruvate dehydrogenase kinase, isoenzyme 1"			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.1192G>T	2.37:g.173460578G>T	ENSP00000282077:p.Glu398*		173168824	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Nonsense_Mutation	SNP	ENST00000282077.3	37	CCDS2250.1	.	.	.	.	.	.	.	.	.	.	G	33	5.197320	0.94960	.	.	ENSG00000152256	ENST00000543905;ENST00000544863;ENST00000282077;ENST00000392571;ENST00000410055	.	.	.	5.94	5.94	0.96194	.	0.091706	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-22.2097	20.3736	0.98901	0.0:0.0:1.0:0.0	.	.	.	.	X	322;243;398;418;398	.	ENSP00000282077:E398X	E	+	1	0	PDK1	173168824	1.000000	0.71417	0.988000	0.46212	0.412000	0.31113	9.741000	0.98843	2.820000	0.97059	0.650000	0.86243	GAA		0.413	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610		T	173460578	G	T	173460578	4	4	61	1	0	0	0	0	0	1	0	0	11706	943	33	2	1234	2	PDK1	2	173460578	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104546	173460578	69738795	1831	9816										
ZAK	51776	broad.mit.edu	37	chr2	174034590	174034590	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagttttatggagtaattCttgaacctcccaactatggc	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:174034590C>A	ENST00000375213.3	+	3	295	c.217C>A	c.(217-219)Ctt>Att	p.L73I	MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000338983.3_Missense_Mutation_p.L73I|MLTK_ENST00000431503.2_De_novo_Start_OutOfFrame|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000409176.2_Missense_Mutation_p.L73I|MLTK_ENST00000539448.1_Missense_Mutation_p.L73I|MLK7-AS1_ENST00000422703.1_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		73	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)	p.L73I(2)									TGGAGTAATTCTTGAACCTCC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	2											140	137	138					2																	174034590		2203	4300	6503	173742836	SO:0001583	missense	51776																														ENST00000375213.3:c.217C>A	2.37:g.174034590C>A	ENSP00000364361:p.Leu73Ile		173742836	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117980	0.37339	.	.	ENSG00000091436	ENST00000539448;ENST00000409176;ENST00000338983;ENST00000375213;ENST00000422149	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	5.67	5.67	0.87782	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117867	0.64402	D	0.000020	T	0.66829	0.2829	N	0.08118	0	0.80722	D	1	B;B;B;B	0.13145	0.001;0.007;0.002;0.001	B;B;B;B	0.16722	0.004;0.016;0.007;0.003	T	0.62685	-0.6802	10	0.12430	T	0.62	.	14.242	0.65963	0.1866:0.8133:0.0:0.0	.	73;73;73;73	Q9NYL2-2;Q9NYL2;D4Q8H0;Q9NYL2-3	.;MLTK_HUMAN;.;.	I	73	ENSP00000439414:L73I;ENSP00000387259:L73I;ENSP00000340257:L73I;ENSP00000364361:L73I;ENSP00000411923:L73I	ENSP00000340257:L73I	L	+	1	0	AC013461.1	173742836	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.827000	0.48112	2.663000	0.90544	0.557000	0.71058	CTT		0.338	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			A	174034590	C	A	174034590	3	1	61	1	0	0	0	0	1	0	0	0	17552	913	32	2	223	2	ZAK	2	174034590	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	574012	174034590	69164783	1832	9817										
ZAK	51776	broad.mit.edu	37	chr2	174055770	174055770	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattcctgttttctcagatCtgtgactttggtgcctctcg	9	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:174055770C>A	ENST00000375213.3	+	7	525	c.447C>A	c.(445-447)atC>atA	p.I149I	MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000338983.3_Silent_p.I149I|MLTK_ENST00000431503.2_Silent_p.I48I|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000409176.2_Silent_p.I149I|MLTK_ENST00000539448.1_Silent_p.I149I|MLK7-AS1_ENST00000422703.1_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		149	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)	p.I149I(2)									TTTCTCAGATCTGTGACTTTG	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	2											174	165	168					2																	174055770		2203	4300	6503	173764016	SO:0001819	synonymous_variant	51776																														ENST00000375213.3:c.447C>A	2.37:g.174055770C>A			173764016	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Silent	SNP	ENST00000375213.3	37	CCDS42777.1																																																																																				0.388	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			A	174055770	C	A	174055770	2	1	61	1	0	0	0	0	0	0	0	1	17552	903	32	2		2	ZAK	2	174055770	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21180	174055770	69143603	1833	9818										
ZAK	51776	broad.mit.edu	37	chr2	174086134	174086134	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaattcttccaaaaccacatCtaagagaagggggaagaaag	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:174086134C>A	ENST00000375213.3	+	11	1065				MLTK_ENST00000431503.2_Missense_Mutation_p.S314Y|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Intron|MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000338983.3_Missense_Mutation_p.S415Y|MLTK_ENST00000539448.1_Missense_Mutation_p.S415Y	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN							activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)	p.S415Y(1)									AAAACCACATCTAAGAGAAGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											95	94	94					2																	174086134		2203	4300	6503	173794380	SO:0001627	intron_variant	51776																														ENST00000375213.3:c.987+4156C>A	2.37:g.174086134C>A			173794380	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487867	0.64074	.	.	ENSG00000091436	ENST00000539448;ENST00000338983;ENST00000431503	T;T;D	0.83335	-1.24;-1.24;-1.71	5.89	5.0	0.66597	.	.	.	.	.	T	0.76040	0.3932	N	0.14661	0.345	0.28542	N	0.912034	B;P	0.50943	0.34;0.94	B;P	0.44860	0.121;0.462	T	0.73228	-0.4049	9	0.87932	D	0	.	16.7161	0.85397	0.0:0.8664:0.1336:0.0	.	415;415	A8K710;D4Q8H0	.;.	Y	415;415;314	ENSP00000439414:S415Y;ENSP00000340257:S415Y;ENSP00000399787:S314Y	ENSP00000340257:S415Y	S	+	2	0	AC013461.1	173794380	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.991000	0.49409	1.458000	0.47871	0.655000	0.94253	TCT		0.458	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			A	174086134	C	A	174086134	1	1	61	0	1	0	0	0	0	0	0	0	17552	913	32	2		2	ZAK	2	174086134	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30364	174086134	69113239	1834	9819										
SP3	6670	broad.mit.edu	37	chr2	174820423	174820423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcccaaagaatctagatCgacactattgattggtacaa	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:174820423C>T	ENST00000310015.6	-	4	1347	c.817G>A	c.(817-819)Gat>Aat	p.D273N	SP3_ENST00000483084.1_5'Flank|SP3_ENST00000455789.2_Missense_Mutation_p.D220N|SP3_ENST00000418194.2_Missense_Mutation_p.D205N	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	273					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.D273N(1)	EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			GAATCTAGATCGACACTATTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											89	87	88					2																	174820423		2203	4300	6503	174528669	SO:0001583	missense	6670			M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.817G>A	2.37:g.174820423C>T	ENSP00000310301:p.Asp273Asn		174528669	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.982119	0.53827	.	.	ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194	T;T;T	0.05139	3.49;3.49;3.49	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.20901	0.0503	L	0.53249	1.67	0.80722	D	1	D;P;D	0.89917	1.0;0.921;1.0	D;B;D	0.83275	0.99;0.137;0.996	T	0.03852	-1.0998	10	0.13470	T	0.59	.	20.062	0.97678	0.0:1.0:0.0:0.0	.	270;273;220	B7ZLN9;Q02447;Q02447-6	.;SP3_HUMAN;.	N	273;220;205	ENSP00000310301:D273N;ENSP00000388903:D220N;ENSP00000406140:D205N	ENSP00000310301:D273N	D	-	1	0	SP3	174528669	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.461000	0.80834	2.730000	0.93505	0.563000	0.77884	GAT		0.438	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		T	174820423	C	T	174820423	3	4	61	1	0	0	0	0	1	0	0	0	15002	884	31	1	1544	1	SP3	2	174820423	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	734289	174820423	68378950	1835	9820										
GPR155	151556	broad.mit.edu	37	chr2	175309901	175309901	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccataaacaactggaaaGattctgtaaagaaaggagaa	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175309901G>T	ENST00000392552.2	-	13	2255	c.2017C>A	c.(2017-2019)Ctt>Att	p.L673I	GPR155_ENST00000392551.2_Missense_Mutation_p.L673I|GPR155_ENST00000295500.4_Missense_Mutation_p.L673I|GPR155_ENST00000459996.1_5'UTR	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	673					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L673I(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						CAACTGGAAAGATTCTGTAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											39	40	40					2																	175309901		2203	4300	6503	175018147	SO:0001583	missense	151556			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.2017C>A	2.37:g.175309901G>T	ENSP00000376335:p.Leu673Ile		175018147	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	37	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996517	0.35226	.	.	ENSG00000163328	ENST00000392552;ENST00000510236;ENST00000392551;ENST00000295500	T;T;T	0.57752	0.38;0.38;0.38	5.54	4.67	0.58626	.	0.116810	0.64402	N	0.000012	T	0.43456	0.1248	L	0.43923	1.385	0.47183	D	0.999349	B;B	0.25048	0.117;0.013	B;B	0.23018	0.043;0.03	T	0.36890	-0.9729	10	0.48119	T	0.1	-13.0178	10.023	0.42055	0.0724:0.1374:0.7902:0.0	.	153;673	F5H464;Q7Z3F1	.;GP155_HUMAN	I	673;153;673;673	ENSP00000376335:L673I;ENSP00000376334:L673I;ENSP00000295500:L673I	ENSP00000295500:L673I	L	-	1	0	GPR155	175018147	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	3.849000	0.55910	1.356000	0.45884	0.551000	0.68910	CTT		0.343	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		T	175309901	G	T	175309901	3	4	61	1	0	0	0	0	1	0	0	0	6680	942	33	2	611	2	GPR155	2	175309901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	489478	175309901	67889472	1836	9821										
GPR155	151556	broad.mit.edu	37	chr2	175333667	175333667	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaggctgacaatacttatAtcaaaactaacattctggat	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175333667A>G	ENST00000392552.2	-	5	1393	c.1155T>C	c.(1153-1155)gaT>gaC	p.D385D	GPR155_ENST00000392551.2_Silent_p.D385D|GPR155_ENST00000295500.4_Silent_p.D385D	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	385					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D385D(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						CAATACTTATATCAAAACTAA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											189	176	181					2																	175333667		2203	4300	6503	175041913	SO:0001819	synonymous_variant	151556			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1155T>C	2.37:g.175333667A>G			175041913	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Silent	SNP	ENST00000392552.2	37	CCDS2259.1																																																																																				0.423	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		G	175333667	A	G	175333667	2	3	61	1	0	0	0	0	0	0	0	1	6680	446	16	4		4	GPR155	2	175333667	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	23766	175333667	67865706	1837	9822										
GPR155	151556	broad.mit.edu	37	chr2	175337936	175337936	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggagtccgagtcccacaAtttttattttattttgagaa	8	7	0	1	rs61735115	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175337936A>C	ENST00000392552.2	-	3	855	c.617T>G	c.(616-618)aTt>aGt	p.I206S	GPR155_ENST00000392551.2_Missense_Mutation_p.I206S|GPR155_ENST00000295500.4_Missense_Mutation_p.I206S	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	206					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.I206S(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						GAGTCCCACAATTTTTATTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											45	49	48					2																	175337936		2202	4299	6501	175046182	SO:0001583	missense	151556			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.617T>G	2.37:g.175337936A>C	ENSP00000376335:p.Ile206Ser		175046182	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	37	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399016	0.62177	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.47528	0.84;0.84;0.84	5.54	5.54	0.83059	.	0.045228	0.85682	D	0.000000	T	0.38401	0.1039	N	0.16903	0.455	0.80722	D	1	P	0.49635	0.926	P	0.44772	0.46	T	0.36915	-0.9728	10	0.54805	T	0.06	-17.7487	15.6788	0.77352	1.0:0.0:0.0:0.0	.	206	Q7Z3F1	GP155_HUMAN	S	206	ENSP00000376335:I206S;ENSP00000376334:I206S;ENSP00000295500:I206S	ENSP00000295500:I206S	I	-	2	0	GPR155	175046182	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.696000	0.91302	2.084000	0.62774	0.533000	0.62120	ATT		0.358	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		C	175337936	A	C	175337936	3	2	61	1	0	0	0	0	1	0	0	0	6680	101	4	4	2051	4	GPR155	2	175337936	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4269	175337936	67861437	1838	9823										
WIPF1	7456	broad.mit.edu	37	chr2	175436460	175436460	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctcactgggcgggggaGgaagaggacctgaacgtcct	16	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175436460G>T	ENST00000392547.2	-	5	1172	c.1073C>A	c.(1072-1074)cCt>cAt	p.P358H	AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Missense_Mutation_p.P358H|WIPF1_ENST00000272746.5_Missense_Mutation_p.P358H|WIPF1_ENST00000392546.2_Missense_Mutation_p.P358H|WIPF1_ENST00000467149.1_5'Flank|WIPF1_ENST00000359761.3_Missense_Mutation_p.P358H|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000409891.1_Missense_Mutation_p.P358H	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	358	Pro-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.P358H(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						GGGCGGGGGAGGAAGAGGACC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	70	69					2																	175436460		2203	4300	6503	175144706	SO:0001583	missense	7456			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1073C>A	2.37:g.175436460G>T	ENSP00000376330:p.Pro358His		175144706	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269133	0.40095	.	.	ENSG00000115935	ENST00000392547;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891;ENST00000409415	T;T;T;T;T;T	0.61274	0.84;0.82;0.84;0.84;0.59;0.12	4.85	3.97	0.46021	.	0.174971	0.51477	D	0.000093	T	0.74824	0.3767	M	0.80746	2.51	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.70935	0.971;0.963;0.971;0.936	T	0.78074	-0.2346	10	0.72032	D	0.01	.	12.6233	0.56616	0.0815:0.0:0.9185:0.0	.	358;358;358;358	O43516-3;E9PB87;O43516-2;O43516	.;.;.;WIPF1_HUMAN	H	358	ENSP00000376330:P358H;ENSP00000272746:P358H;ENSP00000352802:P358H;ENSP00000376329:P358H;ENSP00000386431:P358H;ENSP00000387150:P358H	ENSP00000272746:P358H	P	-	2	0	WIPF1	175144706	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	8.522000	0.90573	1.044000	0.40200	-0.310000	0.09108	CCT		0.617	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		T	175436460	G	T	175436460	3	4	61	1	0	0	0	0	1	0	0	0	17407	1000	35	2	454	2	WIPF1	2	175436460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98524	175436460	67762913	1839	9824										
WIPF1	7456	broad.mit.edu	37	chr2	175450269	175450269	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagtgcaaacgtcgggggCggcgggggtgctggaggggg	23	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175450269C>T	ENST00000392547.2	-	2	132	c.33G>A	c.(31-33)ccG>ccA	p.P11P	AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000410117.1_Silent_p.P11P|WIPF1_ENST00000409415.3_Silent_p.P11P|WIPF1_ENST00000272746.5_Silent_p.P11P|AC010894.5_ENST00000454203.1_RNA|WIPF1_ENST00000392546.2_Silent_p.P11P|WIPF1_ENST00000359761.3_Silent_p.P11P|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000409891.1_Silent_p.P11P	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	11	Poly-Pro.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.P11P(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						ACGTCGGGGGCGGCGGGGGTG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	2											27	30	29					2																	175450269		2203	4300	6503	175158515	SO:0001819	synonymous_variant	7456			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.33G>A	2.37:g.175450269C>T			175158515	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Silent	SNP	ENST00000392547.2	37	CCDS2260.1																																																																																				0.493	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		T	175450269	C	T	175450269	2	4	61	1	0	0	0	0	0	0	0	1	17407	755	27	1		1	WIPF1	2	175450269	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13809	175450269	67749104	1840	9825										
CHRNA1	1134	broad.mit.edu	37	chr2	175624274	175624274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccacgacctggcggtggTcttccactggccgcaccacg	11	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175624274T>C	ENST00000261007.5	-	2	197	c.131A>G	c.(130-132)gAc>gGc	p.D44G	AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Missense_Mutation_p.D44G|CHRNA1_ENST00000409323.1_Missense_Mutation_p.D44G|CHRNA1_ENST00000348749.5_Missense_Mutation_p.D44G|CHRNA1_ENST00000409219.1_Missense_Mutation_p.D44G	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	44					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)	p.D44G(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	CTGGCGGTGGTCTTCCACTGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2											128	125	126					2																	175624274		2203	4300	6503	175332520	SO:0001583	missense	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.131A>G	2.37:g.175624274T>C	ENSP00000261007:p.Asp44Gly		175332520	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.383971	0.82792	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	5.91	5.91	0.95273	Neurotransmitter-gated ion-channel ligand-binding (3);	0.154081	0.64402	D	0.000013	T	0.76933	0.4057	L	0.45470	1.425	0.36011	D	0.838067	B;B;B	0.29270	0.083;0.033;0.24	B;B;B	0.39935	0.064;0.074;0.314	T	0.81684	-0.0821	10	0.87932	D	0	.	12.2232	0.54445	0.0:0.0:0.1419:0.8581	.	44;44;44	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	G	44	ENSP00000261008:D44G;ENSP00000261007:D44G;ENSP00000387026:D44G;ENSP00000386611:D44G;ENSP00000386684:D44G	ENSP00000261007:D44G	D	-	2	0	CHRNA1	175332520	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.145000	0.71769	2.263000	0.75096	0.379000	0.24179	GAC		0.602	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			C	175624274	T	C	175624274	3	2	61	1	0	0	0	0	1	0	0	0	3387	1667	58	4	1353	4	CHRNA1	2	175624274	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	174005	175624274	67575099	1841	9826										
ATF2	1386	broad.mit.edu	37	chr2	175957926	175957926	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccttttttcatcaggatCttcgttagctgctcttctcc	5	13	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:175957926C>A	ENST00000264110.2	-	12	1346	c.1048G>T	c.(1048-1050)Gat>Tat	p.D350Y	ATF2_ENST00000409437.1_Missense_Mutation_p.D234Y|ATF2_ENST00000426833.3_Missense_Mutation_p.D332Y|ATF2_ENST00000345739.5_Missense_Mutation_p.D292Y|ATF2_ENST00000392543.2_Intron|ATF2_ENST00000538946.1_Missense_Mutation_p.D332Y|ATF2_ENST00000409635.1_Missense_Mutation_p.D292Y|ATF2_ENST00000409499.1_Intron|ATF2_ENST00000392544.1_Missense_Mutation_p.D350Y|ATF2_ENST00000487334.2_3'UTR	NM_001256090.1|NM_001256091.1|NM_001880.3	NP_001243019.1|NP_001243020.1|NP_001871.2	P15336	ATF2_HUMAN	activating transcription factor 2	350					adipose tissue development (GO:0060612)|cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|fat cell differentiation (GO:0045444)|histone acetylation (GO:0016573)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|outflow tract morphogenesis (GO:0003151)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta2 production (GO:0032915)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	cAMP response element binding (GO:0035497)|cAMP response element binding protein binding (GO:0008140)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.D350Y(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.125)		Pseudoephedrine(DB00852)	TCATCAGGATCTTCGTTAGCT	0.423																																					Pancreas(17;87 705 4534 15538 30988)											1	Substitution - Missense(1)	large_intestine(1)	2											106	97	100					2																	175957926		2203	4300	6503	175666172	SO:0001583	missense	1386			X15875	CCDS2262.1, CCDS58737.1, CCDS58738.1, CCDS58739.1	2q32	2013-01-10			ENSG00000115966	ENSG00000115966		"basic leucine zipper proteins"	784	protein-coding gene	gene with protein product		123811	"cAMP responsive element binding protein 2"	CREB2		1833307, 1838349	Standard	NM_001880		Approved	TREB7, CRE-BP1, HB16	uc002ujl.4	P15336	OTTHUMG00000132424	ENST00000264110.2:c.1048G>T	2.37:g.175957926C>A	ENSP00000264110:p.Asp350Tyr		175666172	A1L3Z2|A4D7U4|A4D7U5|A4D7V1|D3DPE9|G8JLM5|Q13000|Q3B7B7|Q4ZFU9|Q53RY2|Q8TAR1|Q96JT8	Missense_Mutation	SNP	ENST00000264110.2	37	CCDS2262.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.301440|4.301440	0.81136|0.81136	.|.	.|.	ENSG00000115966|ENSG00000115966	ENST00000264110;ENST00000345739;ENST00000542046;ENST00000409437;ENST00000409635;ENST00000392544;ENST00000426833;ENST00000538946|ENST00000435004	D;T;T;T;D;D;T|.	0.81908|.	-1.55;0.01;-0.9;0.01;-1.55;-1.52;-1.06|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Basic-leucine zipper (bZIP) transcription factor (1);|.	0.049534|.	0.85682|.	D|.	0.000000|.	D|D	0.85733|0.85733	0.5765|0.5765	M|M	0.90369|0.90369	3.11|3.11	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;0.996|.	D;D;D;P|.	0.79108|.	0.922;0.99;0.992;0.832|.	D|D	0.87593|0.87593	0.2492|0.2492	10|5	0.87932|.	D|.	0|.	-51.7631|-51.7631	19.7806|19.7806	0.96414|0.96414	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	332;327;292;350|.	A4D7U4;B3KY57;Q3B7B7;P15336|.	.;.;.;ATF2_HUMAN|.	Y|N	350;292;327;234;292;350;332;332|178	ENSP00000264110:D350Y;ENSP00000340576:D292Y;ENSP00000386326:D234Y;ENSP00000387093:D292Y;ENSP00000376327:D350Y;ENSP00000407911:D332Y;ENSP00000437952:D332Y|.	ENSP00000264110:D350Y|.	D|K	-|-	1|3	0|2	ATF2|ATF2	175666172|175666172	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.725000|5.725000	0.68507|0.68507	2.669000|2.669000	0.90835|0.90835	0.650000|0.650000	0.86243|0.86243	GAT|AAG		0.423	ATF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255562.1	NM_001880		A	175957926	C	A	175957926	3	1	61	1	0	0	0	0	1	0	0	0	1081	913	32	2	481	2	ATF2	2	175957926	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	333652	175957926	67241447	1842	9827										
KIAA1715	80856	broad.mit.edu	37	chr2	176835501	176835501	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttaacttactatttttttCctctgggattttaaatcatc	4	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:176835501C>A	ENST00000272748.4	-	6	595	c.348G>T	c.(346-348)agG>agT	p.R116S	KIAA1715_ENST00000535310.1_Missense_Mutation_p.R41S|KIAA1715_ENST00000544803.1_Missense_Mutation_p.R116S	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	116					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.R116S(1)		endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			CTATTTTTTTCCTCTGGGATT	0.234																																																1	Substitution - Missense(1)	large_intestine(1)	2											9	9	9					2																	176835501		1998	4102	6100	176543747	SO:0001583	missense	80856			AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"lunapark", "limb and neural patterns"	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.348G>T	2.37:g.176835501C>A	ENSP00000272748:p.Arg116Ser		176543747	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Missense_Mutation	SNP	ENST00000272748.4	37	CCDS33332.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678874	0.47886	.	.	ENSG00000144320	ENST00000272748;ENST00000536291;ENST00000544803;ENST00000535310;ENST00000392540	.	.	.	4.96	4.96	0.65561	.	0.087235	0.85682	D	0.000000	T	0.44265	0.1285	L	0.34521	1.04	0.34813	D	0.737934	B;B;P;B	0.35328	0.43;0.139;0.495;0.031	B;B;B;B	0.33960	0.173;0.055;0.077;0.034	T	0.62096	-0.6926	9	0.87932	D	0	-1.781	16.0512	0.80763	0.0:1.0:0.0:0.0	.	118;116;113;116	F5H2Y7;B7ZLA8;B7ZLA9;Q9C0E8	.;.;.;LNP_HUMAN	S	116;118;116;41;111	.	ENSP00000272748:R116S	R	-	3	2	KIAA1715	176543747	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.503000	0.53340	2.450000	0.82876	0.591000	0.81541	AGG		0.234	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834		A	176835501	C	A	176835501	3	1	61	1	0	0	0	0	1	0	0	0	8275	854	30	2	970	2	KIAA1715	2	176835501	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	877575	176835501	66363872	1843	9828										
KIAA1715	80856	broad.mit.edu	37	chr2	176857128	176857128	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatttttttccctaaattCttccaatgcttgaatttcct	3	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:176857128C>A	ENST00000272748.4	-	4	335	c.88G>T	c.(88-90)Gaa>Taa	p.E30*	KIAA1715_ENST00000535310.1_5'UTR|KIAA1715_ENST00000544803.1_Nonsense_Mutation_p.E30*|KIAA1715_ENST00000466445.1_5'Flank	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	30					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.E30*(1)		endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			TCCCTAAATTCTTCCAATGCT	0.259																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											65	69	68					2																	176857128		2201	4297	6498	176565374	SO:0001587	stop_gained	80856			AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"lunapark", "limb and neural patterns"	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.88G>T	2.37:g.176857128C>A	ENSP00000272748:p.Glu30*		176565374	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Nonsense_Mutation	SNP	ENST00000272748.4	37	CCDS33332.1	.	.	.	.	.	.	.	.	.	.	C	35	5.539442	0.96474	.	.	ENSG00000144320	ENST00000272748;ENST00000544803;ENST00000392540;ENST00000445472	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.7002	19.005	0.92846	0.0:1.0:0.0:0.0	.	.	.	.	X	30;30;25;30	.	ENSP00000272748:E30X	E	-	1	0	KIAA1715	176565374	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.270000	0.78493	2.592000	0.87571	0.460000	0.39030	GAA		0.259	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834		A	176857128	C	A	176857128	4	1	61	1	0	0	0	0	0	1	0	0	8275	922	32	2	1238	2	KIAA1715	2	176857128	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21627	176857128	66342245	1844	9829										
HOXD9	3235	broad.mit.edu	37	chr2	176988747	176988747	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccagacgcttgagctggaGaaagaattcctcttcaacat	8	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:176988747G>T	ENST00000249499.6	+	2	1312	c.903G>T	c.(901-903)gaG>gaT	p.E301D	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	301					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E291D(1)		endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TTGAGCTGGAGAAAGAATTCC	0.547																																					GBM(47;924 952 7959 9248 12176)											1	Substitution - Missense(1)	large_intestine(1)	2											96	107	104					2																	176988747		2203	4300	6503	176696993	SO:0001583	missense	3235				CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"Homeoboxes / ANTP class : HOXL subclass"	5140	protein-coding gene	gene with protein product		142982	"homeo box D9"	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.903G>T	2.37:g.176988747G>T	ENSP00000249499:p.Glu301Asp		176696993	Q86ST1	Missense_Mutation	SNP	ENST00000249499.6	37	CCDS2267.2	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631965	0.67015	.	.	ENSG00000128709	ENST00000249499	D	0.97791	-4.54	5.6	4.61	0.57282	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.98998	0.9658	H	0.98388	4.22	0.50467	D	0.999878	P	0.51351	0.944	D	0.74674	0.984	D	0.99164	1.0862	10	0.87932	D	0	.	4.4831	0.11776	0.2823:0.0:0.7177:0.0	.	301	P28356	HXD9_HUMAN	D	301	ENSP00000249499:E301D	ENSP00000249499:E301D	E	+	3	2	HOXD9	176696993	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.776000	0.47709	2.637000	0.89404	0.650000	0.86243	GAG		0.547	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			T	176988747	G	T	176988747	3	4	61	1	0	0	0	0	1	0	0	0	7347	933	33	2	909	2	HOXD9	2	176988747	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131619	176988747	66210626	1845	9830										
HOXD9	3235	broad.mit.edu	37	chr2	176988882	176988882	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaaaaagatgagcaaggaGaaatgccccaaaggagactg	12	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:176988882G>T	ENST00000249499.6	+	2	1447	c.1038G>T	c.(1036-1038)gaG>gaT	p.E346D	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	346					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E336D(1)		endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TGAGCAAGGAGAAATGCCCCA	0.527																																					GBM(47;924 952 7959 9248 12176)											1	Substitution - Missense(1)	large_intestine(1)	2											64	78	73					2																	176988882		2203	4300	6503	176697128	SO:0001583	missense	3235				CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"Homeoboxes / ANTP class : HOXL subclass"	5140	protein-coding gene	gene with protein product		142982	"homeo box D9"	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.1038G>T	2.37:g.176988882G>T	ENSP00000249499:p.Glu346Asp		176697128	Q86ST1	Missense_Mutation	SNP	ENST00000249499.6	37	CCDS2267.2	.	.	.	.	.	.	.	.	.	.	G	9.895	1.205215	0.22205	.	.	ENSG00000128709	ENST00000249499	D	0.93953	-3.32	5.7	4.63	0.57726	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.231848	0.30293	N	0.009951	D	0.86431	0.5931	N	0.21324	0.655	0.43896	D	0.996523	P	0.37636	0.603	B	0.34489	0.184	D	0.84578	0.0659	10	0.18710	T	0.47	.	14.3623	0.66782	0.0849:0.0:0.9151:0.0	.	346	P28356	HXD9_HUMAN	D	346	ENSP00000249499:E346D	ENSP00000249499:E346D	E	+	3	2	HOXD9	176697128	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.253000	0.51469	2.694000	0.91930	0.650000	0.86243	GAG		0.527	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			T	176988882	G	T	176988882	3	4	61	1	0	0	0	0	1	0	0	0	7347	933	33	2	1044	2	HOXD9	2	176988882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135	176988882	66210491	1846	9831										
HOXD3	3232	broad.mit.edu	37	chr2	177036549	177036549	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgctggccacgtggcctaCtccggccagctgccgccagt	13	18	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:177036549C>A	ENST00000468418.3	+	4	2936	c.846C>A	c.(844-846)taC>taA	p.Y282*	HOXD3_ENST00000410016.1_Nonsense_Mutation_p.Y282*|HOXD-AS1_ENST00000416928.2_RNA|HOXD3_ENST00000249440.3_Nonsense_Mutation_p.Y282*			P31249	HXD3_HUMAN	homeobox D3	282					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y282*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		ACGTGGCCTACTCCGGCCAGC	0.697																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											13	15	15					2																	177036549		2192	4281	6473	176744795	SO:0001587	stop_gained	3232				CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"Homeoboxes / ANTP class : HOXL subclass"	5137	protein-coding gene	gene with protein product		142980	"homeo box D3"	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.846C>A	2.37:g.177036549C>A	ENSP00000424734:p.Tyr282*		176744795	Q99955|Q9BSC5	Nonsense_Mutation	SNP	ENST00000468418.3	37	CCDS2270.1	.	.	.	.	.	.	.	.	.	.	C	37	6.392700	0.97529	.	.	ENSG00000128652	ENST00000468418;ENST00000410016;ENST00000249440	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8689	0.52509	0.0:0.9203:0.0:0.0797	.	.	.	.	X	282	.	ENSP00000249440:Y282X	Y	+	3	2	HOXD3	176744795	1.000000	0.71417	0.991000	0.47740	0.907000	0.53573	1.333000	0.33816	2.606000	0.88127	0.561000	0.74099	TAC		0.697	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4			A	177036549	C	A	177036549	4	1	61	1	0	0	0	0	0	1	0	0	7344	576	20	2	852	2	HOXD3	2	177036549	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47667	177036549	66162824	1847	9832										
HOXD1	3231	broad.mit.edu	37	chr2	177054839	177054839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtttatcaagaaccccgGcagcccttctcagtcccaag	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:177054839G>A	ENST00000331462.4	+	2	1179	c.956G>A	c.(955-957)gGc>gAc	p.G319D	HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000413969.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	319					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G319D(1)		kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		AAGAACCCCGGCAGCCCTTCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	52	50					2																	177054839		2203	4300	6503	176763085	SO:0001583	missense	3231				CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.956G>A	2.37:g.177054839G>A	ENSP00000328598:p.Gly319Asp		176763085	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	G	9.270	1.045482	0.19748	.	.	ENSG00000128645	ENST00000331462	D	0.90563	-2.69	5.84	3.82	0.43975	.	0.438581	0.19175	N	0.120824	T	0.80549	0.4644	N	0.24115	0.695	0.25270	N	0.989528	B;B	0.24823	0.112;0.112	B;B	0.22386	0.039;0.039	T	0.64659	-0.6355	10	0.18710	T	0.47	.	5.8289	0.18568	0.1533:0.568:0.2787:0.0	.	319;319	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	D	319	ENSP00000328598:G319D	ENSP00000328598:G319D	G	+	2	0	HOXD1	176763085	0.001000	0.12720	0.069000	0.20011	0.174000	0.22865	0.411000	0.21115	0.694000	0.31654	0.655000	0.94253	GGC		0.582	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			A	177054839	G	A	177054839	3	1	61	1	0	0	0	0	1	0	0	0	7339	1203	42	3	962	3	HOXD1	2	177054839	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18290	177054839	66144534	1848	9833										
HNRNPA3	220988	broad.mit.edu	37	chr2	178081235	178081235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaaaaaaatttagttcaGaaataccacactattaatgg	5	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178081235G>T	ENST00000392524.2	+	5	795	c.558G>T	c.(556-558)caG>caT	p.Q186H	HNRNPA3_ENST00000411529.2_Missense_Mutation_p.Q164H|HNRNPA3_ENST00000435711.1_Missense_Mutation_p.Q186H			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	186	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Q186H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						ATTTAGTTCAGAAATACCACA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											51	55	54					2																	178081235		2203	4300	6503	177789481	SO:0001583	missense	220988			AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"RNA binding motif (RRM) containing"	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.558G>T	2.37:g.178081235G>T	ENSP00000376309:p.Gln186His		177789481	D3DPF4|Q53RW7|Q6URK5	Missense_Mutation	SNP	ENST00000392524.2	37	CCDS2273.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116460	0.56505	.	.	ENSG00000170144	ENST00000392524;ENST00000411529;ENST00000416446;ENST00000420139;ENST00000435711	T;T;T	0.74209	-0.82;-0.82;-0.82	3.99	3.99	0.46301	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.41001	D	0.000973	T	0.76793	0.4037	L	0.33624	1.015	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.69142	0.962;0.922	T	0.76583	-0.2906	10	0.46703	T	0.11	.	11.3241	0.49438	0.0893:0.0:0.9107:0.0	.	164;186	B4DDB6;P51991	.;ROA3_HUMAN	H	186;164;164;164;186	ENSP00000376309:Q186H;ENSP00000408487:Q164H;ENSP00000416340:Q186H	ENSP00000376309:Q186H	Q	+	3	2	HNRNPA3	177789481	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.499000	0.60380	2.251000	0.74343	0.563000	0.77884	CAG		0.338	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247		T	178081235	G	T	178081235	3	4	61	1	0	0	0	0	1	0	0	0	7281	933	33	2	576	2	HNRNPA3	2	178081235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1026396	178081235	65118138	1849	9834										
NFE2L2	4780	broad.mit.edu	37	chr2	178095799	178095799	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttttctgcaattctgaGcagccactttattcttaccc	4	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178095799G>A	ENST00000397062.3	-	5	2086	c.1532C>T	c.(1531-1533)gCt>gTt	p.A511V	NFE2L2_ENST00000464747.1_Missense_Mutation_p.A495V|NFE2L2_ENST00000397063.4_Missense_Mutation_p.A495V|NFE2L2_ENST00000446151.2_Missense_Mutation_p.A488V	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	511	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A511V(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GCAATTCTGAGCAGCCACTTT	0.348			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																													Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	1	Substitution - Missense(1)	large_intestine(1)	2											128	112	117					2																	178095799		1826	4080	5906	177804045	SO:0001583	missense	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.1532C>T	2.37:g.178095799G>A	ENSP00000380252:p.Ala511Val		177804045	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.607003	0.87157	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627	T;T;T;D	0.95342	0.03;0.03;0.03;-3.68	5.95	5.95	0.96441	Basic-leucine zipper (bZIP) transcription factor (3);Eukaryotic transcription factor, Skn-1-like, DNA-binding (2);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.98178	0.9398	M	0.93763	3.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98510	1.0618	10	0.87932	D	0	-14.4011	20.3747	0.98911	0.0:0.0:1.0:0.0	.	488;511	E9PGJ7;Q16236	.;NF2L2_HUMAN	V	495;511;488;239	ENSP00000380253:A495V;ENSP00000380252:A511V;ENSP00000411575:A488V;ENSP00000391590:A239V	ENSP00000380252:A511V	A	-	2	0	NFE2L2	177804045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.817000	0.96982	0.563000	0.77884	GCT		0.348	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178095799	G	A	178095799	3	1	61	1	0	0	0	0	1	0	0	0	10399	971	34	3	289	3	NFE2L2	2	178095799	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14564	178095799	65103574	1850	9835										
NFE2L2	4780	broad.mit.edu	37	chr2	178096193	178096193	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggggcactatctagctCttccacttcagaatcactga	7	13	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178096193C>A	ENST00000397062.3	-	5	1692	c.1138G>T	c.(1138-1140)Gag>Tag	p.E380*	NFE2L2_ENST00000464747.1_Nonsense_Mutation_p.E364*|NFE2L2_ENST00000397063.4_Nonsense_Mutation_p.E364*|NFE2L2_ENST00000446151.2_Nonsense_Mutation_p.E357*	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	380					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E380*(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CTATCTAGCTCTTCCACTTCA	0.478			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																													Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	1	Substitution - Nonsense(1)	large_intestine(1)	2											152	152	152					2																	178096193		2181	4296	6477	177804439	SO:0001587	stop_gained	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.1138G>T	2.37:g.178096193C>A	ENSP00000380252:p.Glu380*		177804439	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Nonsense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694598	0.88830	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627	.	.	.	5.83	5.83	0.93111	.	0.135056	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-16.5333	20.1374	0.98035	0.0:1.0:0.0:0.0	.	.	.	.	X	364;380;357;108	.	ENSP00000380252:E380X	E	-	1	0	NFE2L2	177804439	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.274000	0.78538	2.763000	0.94921	0.563000	0.77884	GAG		0.478	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178096193	C	A	178096193	4	1	61	1	0	0	0	0	0	1	0	0	10399	922	32	2	683	2	NFE2L2	2	178096193	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	394	178096193	65103180	1851	9836										
NFE2L2	4780	broad.mit.edu	37	chr2	178098009	178098009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaaacgggaatgtctgcGccaaaagctgcatgcagtca	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178098009G>A	ENST00000397062.3	-	3	925	c.371C>T	c.(370-372)gCg>gTg	p.A124V	NFE2L2_ENST00000423513.1_Missense_Mutation_p.A108V|NFE2L2_ENST00000464747.1_Missense_Mutation_p.A108V|NFE2L2_ENST00000397063.4_Missense_Mutation_p.A108V|NFE2L2_ENST00000446151.2_Missense_Mutation_p.A108V	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	124					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A124V(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GAATGTCTGCGCCAAAAGCTG	0.358			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																													Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	1	Substitution - Missense(1)	large_intestine(1)	2											108	97	100					2																	178098009		1856	4122	5978	177806255	SO:0001583	missense	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.371C>T	2.37:g.178098009G>A	ENSP00000380252:p.Ala124Val		177806255	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630822	0.87660	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44	5.65	4.75	0.60458	.	0.148276	0.64402	D	0.000011	T	0.39835	0.1093	M	0.81497	2.545	0.49582	D	0.999803	D;P;D	0.53151	0.958;0.949;0.958	B;P;B	0.44623	0.267;0.455;0.267	T	0.44636	-0.9315	10	0.56958	D	0.05	.	11.4261	0.50012	0.0:0.1363:0.7221:0.1416	.	108;108;124	E9PGJ7;C9JFL6;Q16236	.;.;NF2L2_HUMAN	V	108;124;108;108;108;108	ENSP00000380253:A108V;ENSP00000380252:A124V;ENSP00000411575:A108V;ENSP00000400073:A108V;ENSP00000412191:A108V;ENSP00000410015:A108V	ENSP00000380252:A124V	A	-	2	0	NFE2L2	177806255	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.021000	0.70832	1.338000	0.45544	0.491000	0.48974	GCG		0.358	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098009	G	A	178098009	3	1	61	1	0	0	0	0	1	0	0	0	10399	1087	38	1	1458	1	NFE2L2	2	178098009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1816	178098009	65101364	1852	9837										
AGPS	8540	broad.mit.edu	37	chr2	178301756	178301756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggaaggaatgtttgagcGaattcctgatatagttttat	11	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178301756G>A	ENST00000264167.4	+	5	757	c.611G>A	c.(610-612)cGa>cAa	p.R204Q	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	204	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)	p.R204Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			ATGTTTGAGCGAATTCCTGAT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	132	130					2																	178301756		2203	4300	6503	178010002	SO:0001583	missense	8540			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.611G>A	2.37:g.178301756G>A	ENSP00000264167:p.Arg204Gln		178010002	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.871480	0.91587	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	D	0.82526	-1.62	5.52	4.64	0.57946	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (2);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.89735	0.3929	10	0.72032	D	0.01	.	14.2952	0.66308	0.0719:0.0:0.9281:0.0	.	204	O00116	ADAS_HUMAN	Q	204;74	ENSP00000264167:R204Q	ENSP00000264167:R204Q	R	+	2	0	AGPS	178010002	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.468000	0.90393	1.315000	0.45114	0.655000	0.94253	CGA		0.303	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			A	178301756	G	A	178301756	3	1	61	1	0	0	0	0	1	0	0	0	394	1058	37	1	629	1	AGPS	2	178301756	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203747	178301756	64897617	1853	9838										
TTC30B	150737	broad.mit.edu	37	chr2	178415849	178415849	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaagagttcctatcaccAaattcacaatgcagagatgg	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178415849A>T	ENST00000408939.3	-	1	1893	c.1643T>A	c.(1642-1644)tTg>tAg	p.L548*		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	548					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.L548*(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			TCCTATCACCAAATTCACAAT	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											209	221	217					2																	178415849		2203	4300	6503	178124095	SO:0001587	stop_gained	150737			AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	26425	protein-coding gene	gene with protein product						12477932	Standard	NM_152517		Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.1643T>A	2.37:g.178415849A>T	ENSP00000386181:p.Leu548*		178124095	Q63HQ1|Q96NE6	Nonsense_Mutation	SNP	ENST00000408939.3	37	CCDS42784.1	.	.	.	.	.	.	.	.	.	.	A	38	6.880855	0.97908	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9246	0.70866	1.0:0.0:0.0:0.0	.	.	.	.	X	501;548	.	ENSP00000386181:L548X	L	-	2	0	TTC30B	178124095	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.673000	0.91186	2.160000	0.67779	0.533000	0.62120	TTG		0.393	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334193.2	NM_152517		T	178415849	A	T	178415849	4	4	61	1	0	0	0	0	0	1	0	0	16739	131	5	5	358	5	TTC30B	2	178415849	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	114093	178415849	64783524	1854	9839										
TTC30B	150737	broad.mit.edu	37	chr2	178416144	178416144	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgttacagaattccacagAtttgcggaagatcttttcca	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178416144A>C	ENST00000408939.3	-	1	1598	c.1348T>G	c.(1348-1350)Tct>Gct	p.S450A		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	450					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.S450A(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			AATTCCACAGATTTGCGGAAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											323	331	328					2																	178416144		2203	4300	6503	178124390	SO:0001583	missense	150737			AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	26425	protein-coding gene	gene with protein product						12477932	Standard	NM_152517		Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.1348T>G	2.37:g.178416144A>C	ENSP00000386181:p.Ser450Ala		178124390	Q63HQ1|Q96NE6	Missense_Mutation	SNP	ENST00000408939.3	37	CCDS42784.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.806673	0.50421	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	T	0.25749	1.78	4.53	4.53	0.55603	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	M	0.80422	2.495	0.80722	D	1	P	0.45044	0.849	P	0.45639	0.488	T	0.28870	-1.0030	10	0.27785	T	0.31	.	14.305	0.66380	1.0:0.0:0.0:0.0	.	450	Q8N4P2	TT30B_HUMAN	A	403;450	ENSP00000386181:S450A	ENSP00000386181:S450A	S	-	1	0	TTC30B	178124390	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	8.936000	0.92931	2.032000	0.59987	0.533000	0.62120	TCT		0.388	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334193.2	NM_152517		C	178416144	A	C	178416144	3	2	61	1	0	0	0	0	1	0	0	0	16739	333	12	4	653	4	TTC30B	2	178416144	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	295	178416144	64783229	1855	9840										
TTC30A	92104	broad.mit.edu	37	chr2	178482356	178482356	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggcatctaagaagtcataGagatagggtgtgaggaactt	14	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178482356G>A	ENST00000355689.5	-	1	1338	c.1074C>T	c.(1072-1074)ctC>ctT	p.L358L	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	358					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.L358L(1)		autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AGAAGTCATAGAGATAGGGTG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											122	128	126					2																	178482356		2203	4300	6503	178190602	SO:0001819	synonymous_variant	92104			AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"Tetratricopeptide (TTC) repeat domain containing"	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.1074C>T	2.37:g.178482356G>A			178190602	A8K8N0|Q8IVP2	Silent	SNP	ENST00000355689.5	37	CCDS2276.1																																																																																				0.473	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275		A	178482356	G	A	178482356	2	1	61	1	0	0	0	0	0	0	0	1	16738	929	33	3		3	TTC30A	2	178482356	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66212	178482356	64717017	1856	9841										
PDE11A	50940	broad.mit.edu	37	chr2	178681637	178681637	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgccaagtccacaaaaGatgacaaaagcctaggaaag	9	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178681637G>T	ENST00000286063.6	-	9	1973	c.1656C>A	c.(1654-1656)atC>atA	p.I552I	PDE11A_ENST00000409504.1_Silent_p.I194I|PDE11A_ENST00000389683.3_Silent_p.I108I|PDE11A_ENST00000358450.4_Silent_p.I302I|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000449286.2_Silent_p.I194I	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	552	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.I552I(1)|p.I302I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GTCCACAAAAGATGACAAAAG	0.423									Primary Pigmented Nodular Adrenocortical Disease, Familial																																							2	Substitution - coding silent(2)	large_intestine(2)	2											106	98	101					2																	178681637		2203	4300	6503	178389883	SO:0001819	synonymous_variant	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1656C>A	2.37:g.178681637G>T			178389883	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1																																																																																				0.423	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			T	178681637	G	T	178681637	2	4	61	1	0	0	0	0	0	0	0	1	11662	932	33	2		2	PDE11A	2	178681637	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199281	178681637	64517736	1857	9842										
PDE11A	50940	broad.mit.edu	37	chr2	178705092	178705092	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcggagtatgatgatttCtccatgctttctttgaaact	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178705092C>A	ENST00000286063.6	-	6	1703	c.1386G>T	c.(1384-1386)gaG>gaT	p.E462D	PDE11A_ENST00000409504.1_Missense_Mutation_p.E104D|PDE11A_ENST00000389683.3_Missense_Mutation_p.E18D|PDE11A_ENST00000358450.4_Missense_Mutation_p.E212D|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000449286.2_Missense_Mutation_p.E104D	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	462	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.E212D(1)|p.E462D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ATGATGATTTCTCCATGCTTT	0.423									Primary Pigmented Nodular Adrenocortical Disease, Familial																																							2	Substitution - Missense(2)	large_intestine(2)	2											110	106	107					2																	178705092		2203	4300	6503	178413338	SO:0001583	missense	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1386G>T	2.37:g.178705092C>A	ENSP00000286063:p.Glu462Asp		178413338	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.39|13.39	2.224118|2.224118	0.39300|0.39300	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000433879	T;T;T;T;T|.	0.73575|.	-0.22;-0.22;-0.22;-0.76;-0.22|.	5.69|5.69	4.81|4.81	0.61882|0.61882	GAF (2);|.	0.156322|.	0.64402|.	D|.	0.000016|.	T|T	0.53367|0.53367	0.1792|0.1792	L|L	0.28740|0.28740	0.885|0.885	0.80722|0.80722	D|D	1|1	B;B|.	0.11235|.	0.003;0.004|.	B;B|.	0.13407|.	0.006;0.009|.	T|T	0.45789|0.45789	-0.9237|-0.9237	10|5	0.27785|.	T|.	0.31|.	.|.	13.2396|13.2396	0.59989|0.59989	0.0:0.8711:0.0:0.1289|0.0:0.8711:0.0:0.1289	.|.	212;462|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	D|I	462;212;104;18;104|101	ENSP00000286063:E462D;ENSP00000351232:E212D;ENSP00000386539:E104D;ENSP00000374333:E18D;ENSP00000390599:E104D|.	ENSP00000286063:E462D|.	E|R	-|-	3|2	2|0	PDE11A|PDE11A	178413338|178413338	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.948000|0.948000	0.59901|0.59901	1.634000|1.634000	0.37123|0.37123	2.696000|2.696000	0.92011|0.92011	0.467000|0.467000	0.42956|0.42956	GAG|AGA		0.423	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178705092	C	A	178705092	3	1	61	1	0	0	0	0	1	0	0	0	11662	912	32	2	1475	2	PDE11A	2	178705092	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23455	178705092	64494281	1858	9843										
PDE11A	50940	broad.mit.edu	37	chr2	178936595	178936595	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagatggcacttgtagtcGatggctgtagggggataccg	15	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178936595G>A	ENST00000286063.6	-	1	887	c.570C>T	c.(568-570)atC>atT	p.I190I	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	190					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.I190I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ACTTGTAGTCGATGGCTGTAG	0.517									Primary Pigmented Nodular Adrenocortical Disease, Familial																																							1	Substitution - coding silent(1)	large_intestine(1)	2											99	92	95					2																	178936595		2203	4300	6503	178644841	SO:0001819	synonymous_variant	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.570C>T	2.37:g.178936595G>A			178644841	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1																																																																																				0.517	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178936595	G	A	178936595	2	1	61	1	0	0	0	0	0	0	0	1	11662	1048	37	1		1	PDE11A	2	178936595	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231503	178936595	64262778	1859	9844										
RBM45	129831	broad.mit.edu	37	chr2	178988278	178988278	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttcagtattttaatgtaGcatcagctatttatgcaaaa	7	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:178988278G>A	ENST00000286070.5	+	6	975	c.883G>A	c.(883-885)Gca>Aca	p.A295T		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	297					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A295T(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TTTTAATGTAGCATCAGCTAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	100	102					2																	178988278		2203	4300	6503	178696524	SO:0001583	missense	129831			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"RNA binding motif (RRM) containing"	24468	protein-coding gene	gene with protein product	"developmentally regulated RNA binding protein 1"	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.883G>A	2.37:g.178988278G>A	ENSP00000286070:p.Ala295Thr		178696524	Q6NYL0|Q8NFC9	Missense_Mutation	SNP	ENST00000286070.5	37	CCDS33335.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.185144	0.57909	.	.	ENSG00000155636	ENST00000286070	T	0.06449	3.3	4.86	3.97	0.46021	.	0.108677	0.64402	D	0.000007	T	0.10380	0.0254	L	0.43152	1.355	0.39801	D	0.972574	D	0.58620	0.983	P	0.54544	0.755	T	0.33904	-0.9850	10	0.16896	T	0.51	-15.8997	9.691	0.40127	0.0:0.1537:0.6869:0.1594	.	295	Q8IUH3-3	.	T	295	ENSP00000286070:A295T	ENSP00000286070:A295T	A	+	1	0	RBM45	178696524	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.056000	0.76662	1.157000	0.42530	0.460000	0.39030	GCA		0.368	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		A	178988278	G	A	178988278	3	1	61	1	0	0	0	0	1	0	0	0	13176	971	34	3	905	3	RBM45	2	178988278	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51683	178988278	64211095	1860	9845										
OSBPL6	114880	broad.mit.edu	37	chr2	179247226	179247226	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgttgcagacaatatttCtcggcaaagtatgcatcatt	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179247226C>T	ENST00000190611.4	+	16	1989	c.1613C>T	c.(1612-1614)tCt>tTt	p.S538F	OSBPL6_ENST00000392505.2_Missense_Mutation_p.S563F|OSBPL6_ENST00000409631.1_Missense_Mutation_p.S502F|OSBPL6_ENST00000357080.4_Missense_Mutation_p.S471F|OSBPL6_ENST00000315022.2_Missense_Mutation_p.S542F|OSBPL6_ENST00000359685.3_Missense_Mutation_p.S502F|OSBPL6_ENST00000409045.3_Missense_Mutation_p.S507F	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	538					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.S538F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			GACAATATTTCTCGGCAAAGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	108	112					2																	179247226		2203	4300	6503	178955472	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1613C>T	2.37:g.179247226C>T	ENSP00000190611:p.Ser538Phe		178955472	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.029222	0.93518	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.13089	2.64;2.65;2.62;2.65;2.65;2.65;2.64	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.30572	0.0769	L	0.44542	1.39	0.80722	D	1	D;D;P;D;D;D	0.76494	0.957;0.998;0.935;0.998;0.996;0.999	P;D;P;D;P;D	0.83275	0.865;0.958;0.796;0.958;0.823;0.996	T	0.01208	-1.1418	10	0.13853	T	0.58	-16.2973	20.3932	0.98965	0.0:1.0:0.0:0.0	.	507;542;502;563;538;471	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	F	563;502;471;507;538;502;542	ENSP00000376293:S563F;ENSP00000352713:S502F;ENSP00000349591:S471F;ENSP00000387248:S507F;ENSP00000190611:S538F;ENSP00000386885:S502F;ENSP00000318723:S542F	ENSP00000190611:S538F	S	+	2	0	OSBPL6	178955472	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.516000	0.60496	2.824000	0.97209	0.655000	0.94253	TCT		0.428	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		T	179247226	C	T	179247226	3	4	61	1	0	0	0	0	1	0	0	0	11312	913	32	3	1789	3	OSBPL6	2	179247226	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258948	179247226	63952147	1861	9846										
PRKRA	8575	broad.mit.edu	37	chr2	179309179	179309179	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaataggattaagctggttCtttggttgcttggaagggtc	13	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179309179C>A	ENST00000325748.4	-	4	566	c.366G>T	c.(364-366)aaG>aaT	p.K122N	PRKRA_ENST00000438687.3_Missense_Mutation_p.K9N|PRKRA_ENST00000432031.2_Missense_Mutation_p.K111N|PRKRA_ENST00000470200.1_5'Flank|PRKRA_ENST00000487082.1_Missense_Mutation_p.K97N	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	122	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.K122N(2)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			TAAGCTGGTTCTTTGGTTGCT	0.353																																					Melanoma(200;68 3001 23825 48764)											2	Substitution - Missense(2)	large_intestine(2)	2											99	102	101					2																	179309179		2203	4300	6503	179017425	SO:0001583	missense	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.366G>T	2.37:g.179309179C>A	ENSP00000318176:p.Lys122Asn		179017425	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010122	0.54361	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	T;T;T;T	0.73897	-0.79;-0.69;-0.78;-0.78	6.07	6.07	0.98685	.	0.446573	0.24623	N	0.036951	T	0.69106	0.3074	L	0.42744	1.35	0.39895	D	0.973828	B;B	0.13594	0.008;0.002	B;B	0.11329	0.002;0.006	T	0.62539	-0.6833	10	0.30078	T	0.28	.	17.5607	0.87906	0.0:1.0:0.0:0.0	.	122;111	O75569;O75569-2	PRKRA_HUMAN;.	N	122;9;97;111	ENSP00000318176:K122N;ENSP00000398980:K9N;ENSP00000430604:K97N;ENSP00000393883:K111N	ENSP00000318176:K122N	K	-	3	2	PRKRA	179017425	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.458000	0.45014	2.884000	0.98904	0.655000	0.94253	AAG		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690		A	179309179	C	A	179309179	3	1	61	1	0	0	0	0	1	0	0	0	12558	912	32	2	595	2	PRKRA	2	179309179	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61953	179309179	63890194	1862	9847										
PLEKHA3	65977	broad.mit.edu	37	chr2	179358692	179358692	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatttgttcaccatgatgaGaatcattcatctcctagtgc	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179358692G>T	ENST00000234453.5	+	4	828	c.426G>T	c.(424-426)gaG>gaT	p.E142D	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	142						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)	p.E142D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			ACCATGATGAGAATCATTCAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											142	132	135					2																	179358692		2203	4300	6503	179066938	SO:0001583	missense	65977			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.426G>T	2.37:g.179358692G>T	ENSP00000234453:p.Glu142Asp		179066938	Q4ZG69|Q86TQ1|Q9NXT3	Missense_Mutation	SNP	ENST00000234453.5	37	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.147312	0.37923	.	.	ENSG00000116095	ENST00000234453	T	0.13901	2.55	5.83	4.91	0.64330	.	0.278011	0.41194	D	0.000934	T	0.10294	0.0252	N	0.16478	0.41	0.49798	D	0.999824	B	0.02656	0.0	B	0.04013	0.001	T	0.21143	-1.0254	10	0.21014	T	0.42	-0.9437	18.5871	0.91194	0.0:0.1266:0.8734:0.0	.	142	Q9HB20	PKHA3_HUMAN	D	142	ENSP00000234453:E142D	ENSP00000234453:E142D	E	+	3	2	PLEKHA3	179066938	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	2.734000	0.47368	2.755000	0.94549	0.650000	0.86243	GAG		0.443	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		T	179358692	G	T	179358692	3	4	61	1	0	0	0	0	1	0	0	0	12088	933	33	2	440	2	PLEKHA3	2	179358692	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49513	179358692	63840681	1863	9848										
TTN	7273	broad.mit.edu	37	chr2	179397979	179397979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtttcttgtacctcaggcGttccacttgtaggtgagcct	10	11	2	1	rs72629785	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179397979G>A	ENST00000591111.1	-	308	98664	c.98440C>T	c.(98440-98442)Cgc>Tgc	p.R32814C	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R25390C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R31887C|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R25515C|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R25582C|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R34455C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32814					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R25582C(1)|p.R25515C(1)|p.R25390C(1)|p.R31885C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACCTCAGGCGTTCCACTTGT	0.478													G|||	16	0.00319489	0.0121	0	5008	,	,		22770	0		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	2						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	37,3917		1,35,1941	98	94	96		76168,95659,76543,76744	5.8	1	2	dbSNP_130	96	0,8294		0,0,4147	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	180,180,180,180	1,35,6088	AA,AG,GG		0.0,0.9358,0.3021	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25390/26927,31887/33424,25515/27052,25582/27119	179397979	37,12211	1977	4147	6124	179106225	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.98440C>T	2.37:g.179397979G>A	ENSP00000465570:p.Arg32814Cys		179106225	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	17.93	3.509228	0.64522	0.009358	0.0	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64618	-0.11;0.1;0.08;0.07	5.78	5.78	0.91487	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57814	0.2079	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;P;P;P	0.57846	0.828;0.828;0.828;0.828	T	0.67650	-0.5616	9	0.87932	D	0	.	19.6001	0.95559	0.0:0.0:1.0:0.0	.	25390;25515;25582;32814	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	31887;25390;25582;25515;25387	ENSP00000343764:R31887C;ENSP00000434586:R25390C;ENSP00000340554:R25582C;ENSP00000352154:R25515C	ENSP00000340554:R25582C	R	-	1	0	TTN	179106225	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	7.832000	0.86757	2.745000	0.94114	0.555000	0.69702	CGC		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179397979	G	A	179397979	3	1	61	1	0	0	0	0	1	0	0	0	16775	1145	40	1	4636	1	TTN	2	179397979	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39287	179397979	63801394	1864	9849										
TTN	7273	broad.mit.edu	37	chr2	179400455	179400455	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagatcttgtcctttctgCcaggtgatcacaggatctgg	11	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179400455C>T	ENST00000591111.1	-	308	96188	c.95964G>A	c.(95962-95964)tgG>tgA	p.W31988*	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.W24564*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.W31061*|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.W24689*|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.W24756*|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.W33629*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31988	Ig-like 142.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.W31059*(1)|p.W24689*(1)|p.W24756*(1)|p.W24564*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCCTTTCTGCCAGGTGATCA	0.453																																																4	Substitution - Nonsense(4)	large_intestine(4)	2											122	123	123					2																	179400455		1963	4163	6126	179108701	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95964G>A	2.37:g.179400455C>T	ENSP00000465570:p.Trp31988*		179108701	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	70	111.601612	0.99998	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.319	0.94229	0.0:1.0:0.0:0.0	.	.	.	.	X	31061;24564;24756;24689;24561	.	ENSP00000340554:W24756X	W	-	3	0	TTN	179108701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.640000	0.89533	0.563000	0.77884	TGG		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179400455	C	T	179400455	4	4	61	1	0	0	0	0	0	1	0	0	16775	740	26	3	7112	3	TTN	2	179400455	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2476	179400455	63798918	1865	9850										
TTN	7273	broad.mit.edu	37	chr2	179403940	179403940	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagaactcttggttacatCgagtacttctggaggattgc	10	8	2	1	rs267599023		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179403940C>T	ENST00000591111.1	-	303	94023	c.93799G>A	c.(93799-93801)Gat>Aat	p.D31267N	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D23843N|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D30340N|TTN-AS1_ENST00000415561.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D23968N|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D24035N|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D32908N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31267	Fibronectin type-III 128. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D23968N(1)|p.D30338N(1)|p.D23843N(1)|p.D24035N(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGTTACATCGAGTACTTCT	0.443																																																4	Substitution - Missense(4)	large_intestine(4)	2											117	107	110					2																	179403940		1929	4122	6051	179112186	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93799G>A	2.37:g.179403940C>T	ENSP00000465570:p.Asp31267Asn		179112186	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	25.8	4.679912	0.88542	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	6.17	6.17	0.99709	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70675	0.3251	L	0.49455	1.56	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.69577	-0.5108	9	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	23843;23968;24035;31267	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	30340;23843;24035;23968;23840	ENSP00000343764:D30340N;ENSP00000434586:D23843N;ENSP00000340554:D24035N;ENSP00000352154:D23968N	ENSP00000340554:D24035N	D	-	1	0	TTN	179112186	1.000000	0.71417	0.973000	0.42090	0.995000	0.86356	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GAT		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179403940	C	T	179403940	3	4	61	1	0	0	0	0	1	0	0	0	16775	884	31	1	9297	1	TTN	2	179403940	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3485	179403940	63795433	1866	9851										
TTN	7273	broad.mit.edu	37	chr2	179404446	179404446	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgtagacagccttcttGccacatttattttccagaac	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179404446G>A	ENST00000591111.1	-	302	93647	c.93423C>T	c.(93421-93423)ggC>ggT	p.G31141G	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Silent_p.G23717G|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.G30214G|TTN-AS1_ENST00000415561.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.G23842G|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342175.6_Silent_p.G23909G|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Silent_p.G32782G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31141	Ig-like 139.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G23842G(1)|p.G23909G(1)|p.G23717G(1)|p.G30212G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCCTTCTTGCCACATTTAT	0.478																																																4	Substitution - coding silent(4)	large_intestine(4)	2											122	112	115					2																	179404446		1985	4162	6147	179112692	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93423C>T	2.37:g.179404446G>A			179112692	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179404446	G	A	179404446	2	1	61	1	0	0	0	0	0	0	0	1	16775	1306	46	3		3	TTN	2	179404446	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	506	179404446	63794927	1867	9852										
TTN	7273	broad.mit.edu	37	chr2	179404590	179404590	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttggtccatttacatatTgggaatggttttcctttgat	8	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179404590T>C	ENST00000591111.1	-	302	93503	c.93279A>G	c.(93277-93279)ccA>ccG	p.P31093P	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Silent_p.P23669P|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.P30166P|TTN-AS1_ENST00000415561.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.P23794P|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342175.6_Silent_p.P23861P|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Silent_p.P32734P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31093	Ig-like 139.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P23794P(1)|p.P30164P(1)|p.P23669P(1)|p.P23861P(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTACATATTGGGAATGGTT	0.418																																																4	Substitution - coding silent(4)	large_intestine(4)	2											136	127	130					2																	179404590		1986	4174	6160	179112836	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93279A>G	2.37:g.179404590T>C			179112836	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179404590	T	C	179404590	2	2	61	1	0	0	0	0	0	0	0	1	16775	1799	63	4		4	TTN	2	179404590	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	144	179404590	63794783	1868	9853										
TTN	7273	broad.mit.edu	37	chr2	179407003	179407003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacttacggatgctgctgcGacactctatgacctcagact	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179407003G>A	ENST00000591111.1	-	299	92781	c.92557C>T	c.(92557-92559)Cgc>Tgc	p.R30853C	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R23429C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R29926C|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R23554C|TTN_ENST00000342175.6_Missense_Mutation_p.R23621C|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R32494C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30853	Fibronectin type-III 124. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R29924C(1)|p.R23429C(1)|p.R23621C(1)|p.R23554C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGCTGCTGCGACACTCTATG	0.463																																																4	Substitution - Missense(4)	large_intestine(4)	2											48	46	47					2																	179407003		2038	4190	6228	179115249	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.92557C>T	2.37:g.179407003G>A	ENSP00000465570:p.Arg30853Cys		179115249	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	26.1	4.707743	0.89018	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65364	-0.15;0.04;0.01;0.01	6.17	5.25	0.73442	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.57621	0.2066	L	0.27053	0.805	0.52501	D	0.999959	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;P;P;P	0.50490	0.642;0.642;0.642;0.642	T	0.61192	-0.7112	9	0.87932	D	0	.	12.7826	0.57485	0.0:0.0:0.6932:0.3068	.	23429;23554;23621;30853	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	29926;23429;23621;23554;23426	ENSP00000343764:R29926C;ENSP00000434586:R23429C;ENSP00000340554:R23621C;ENSP00000352154:R23554C	ENSP00000340554:R23621C	R	-	1	0	TTN	179115249	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.635000	0.74295	2.941000	0.99782	0.655000	0.94253	CGC		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179407003	G	A	179407003	3	1	61	1	0	0	0	0	1	0	0	0	16775	1058	37	1	10555	1	TTN	2	179407003	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2413	179407003	63792370	1869	9854										
TTN	7273	broad.mit.edu	37	chr2	179408940	179408940	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaatacctattctttccaCgggctcaatttcagcaattg	5	10	3	0	rs191786700	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179408940C>T	ENST00000591111.1	-	295	91317	c.91093G>A	c.(91093-91095)Gtg>Atg	p.V30365M	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V22941M|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V29438M|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V23066M|TTN_ENST00000342175.6_Missense_Mutation_p.V23133M|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V32006M|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30365	Fibronectin type-III 121. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V22941M(1)|p.V23133M(1)|p.V29436M(1)|p.V23066M(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTCTTTCCACGGGCTCAATT	0.383													C|||	5	0.000998403	0.003	0.0014	5008	,	,		22493	0		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	2						C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	5,3679		0,5,1837	75	73	74		69397,69196,88312,68821	5.2	0.9	2		74	3,8169		0,3,4083	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	21,21,21,21	0,8,5920	TT,TC,CC		0.0367,0.1357,0.0675	benign,benign,benign,benign	23133/27119,23066/27052,29438/33424,22941/26927	179408940	8,11848	1842	4086	5928	179117186	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.91093G>A	2.37:g.179408940C>T	ENSP00000465570:p.Val30365Met		179117186	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	9.930	1.214635	0.22289	0.001357	3.67E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63255	-0.03;0.22;0.2;0.19	6.04	5.16	0.70880	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.48960	0.1529	L	0.47716	1.5	0.45690	D	0.9986	B;B;B;B	0.23735	0.09;0.09;0.09;0.09	B;B;B;B	0.16289	0.015;0.015;0.015;0.015	T	0.54715	-0.8252	9	0.87932	D	0	.	15.6058	0.76668	0.0:0.9342:0.0:0.0658	.	22941;23066;23133;30365	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	29438;22941;23133;23066;22938	ENSP00000343764:V29438M;ENSP00000434586:V22941M;ENSP00000340554:V23133M;ENSP00000352154:V23066M	ENSP00000340554:V23133M	V	-	1	0	TTN	179117186	0.939000	0.31865	0.918000	0.36340	0.208000	0.24298	1.896000	0.39789	1.572000	0.49736	0.561000	0.74099	GTG		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179408940	C	T	179408940	3	4	61	1	0	0	0	0	1	0	0	0	16775	536	19	1	12035	1	TTN	2	179408940	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1937	179408940	63790433	1870	9855										
TTN	7273	broad.mit.edu	37	chr2	179412259	179412259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgactttaatttgagtgCgcttgacactggaattgaca	11	6	0	4	rs577262832		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179412259C>T	ENST00000591111.1	-	289	89395	c.89171G>A	c.(89170-89172)cGc>cAc	p.R29724H	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R22300H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R28797H|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R22425H|TTN_ENST00000342175.6_Missense_Mutation_p.R22492H|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R31365H|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29724	Fibronectin type-III 116. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R22425H(1)|p.R28795H(1)|p.R22492H(1)|p.R22300H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTTGAGTGCGCTTGACACT	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											74	72	73					2																	179412259		1894	4117	6011	179120505	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.89171G>A	2.37:g.179412259C>T	ENSP00000465570:p.Arg29724His		179120505	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	20.6	4.011315	0.75046	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72653	0.3487	M	0.64997	1.995	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.73052	-0.4104	9	0.87932	D	0	.	20.3081	0.98638	0.0:1.0:0.0:0.0	.	22300;22425;22492;29724	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	28797;22300;22492;22425;22297	ENSP00000343764:R28797H;ENSP00000434586:R22300H;ENSP00000340554:R22492H;ENSP00000352154:R22425H	ENSP00000340554:R22492H	R	-	2	0	TTN	179120505	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.795000	0.96236	0.655000	0.94253	CGC		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179412259	C	T	179412259	3	4	61	1	0	0	0	0	1	0	0	0	16775	768	27	1	13981	1	TTN	2	179412259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3319	179412259	63787114	1871	9856										
TTN	7273	broad.mit.edu	37	chr2	179412379	179412379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccccatgacaggacacacGattcagctgagacagatgag	10	12	1	4	rs143679526	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179412379G>A	ENST00000591111.1	-	289	89275	c.89051C>T	c.(89050-89052)tCg>tTg	p.S29684L	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S22260L|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S28757L|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S22385L|TTN_ENST00000342175.6_Missense_Mutation_p.S22452L|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S31325L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29684	Fibronectin type-III 116. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S22260L(1)|p.S22385L(1)|p.S22452L(1)|p.S28755L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGGACACACGATTCAGCTGA	0.468													G|||	2	0.000399361	0.0015	0	5008	,	,		20061	0		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	2											137	134	135					2																	179412379		1950	4149	6099	179120625	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.89051C>T	2.37:g.179412379G>A	ENSP00000465570:p.Ser29684Leu		179120625	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	16.05	3.012360	0.54468	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84732	0.5537	M	0.91818	3.245	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.87012	0.2123	9	0.87932	D	0	.	20.3081	0.98638	0.0:0.0:1.0:0.0	.	22260;22385;22452;29684	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	28757;22260;22452;22385;22257	ENSP00000343764:S28757L;ENSP00000434586:S22260L;ENSP00000340554:S22452L;ENSP00000352154:S22385L	ENSP00000340554:S22452L	S	-	2	0	TTN	179120625	1.000000	0.71417	0.997000	0.53966	0.669000	0.39330	7.876000	0.87215	2.795000	0.96236	0.655000	0.94253	TCG		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179412379	G	A	179412379	3	1	61	1	0	0	0	0	1	0	0	0	16775	1059	37	1	14101	1	TTN	2	179412379	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120	179412379	63786994	1872	9857										
TTN	7273	broad.mit.edu	37	chr2	179413522	179413522	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggtaggcaatgaagaggCgaatactggccccagctcta	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179413522C>T	ENST00000591111.1	-	289	88132	c.87908G>A	c.(87907-87909)cGc>cAc	p.R29303H	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R21879H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R28376H|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R22004H|TTN_ENST00000342175.6_Missense_Mutation_p.R22071H|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R30944H|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29303	Ig-like 134.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R22004H(1)|p.R22071H(1)|p.R21879H(1)|p.R28374H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATGAAGAGGCGAATACTGGC	0.468																																																4	Substitution - Missense(4)	large_intestine(4)	2											122	118	119					2																	179413522		1959	4145	6104	179121768	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.87908G>A	2.37:g.179413522C>T	ENSP00000465570:p.Arg29303His		179121768	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.43	2.830078	0.50845	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.97	4.97	0.65823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.48370	0.1496	M	0.76002	2.32	0.39008	D	0.959486	B;B;B;B	0.27140	0.169;0.169;0.169;0.169	B;B;B;B	0.24701	0.032;0.032;0.032;0.055	T	0.56366	-0.7991	9	0.87932	D	0	.	18.6009	0.91247	0.0:1.0:0.0:0.0	.	21879;22004;22071;29303	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	28376;21879;22071;22004;21876	ENSP00000343764:R28376H;ENSP00000434586:R21879H;ENSP00000340554:R22071H;ENSP00000352154:R22004H	ENSP00000340554:R22071H	R	-	2	0	TTN	179121768	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.762000	0.38451	2.457000	0.83068	0.557000	0.71058	CGC		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179413522	C	T	179413522	3	4	61	1	0	0	0	0	1	0	0	0	16775	768	27	1	15244	1	TTN	2	179413522	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1143	179413522	63785851	1873	9858										
TTN	7273	broad.mit.edu	37	chr2	179417092	179417092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttcagttttactgaagcGaacaaattcactttctttca	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179417092G>A	ENST00000591111.1	-	285	85836	c.85612C>T	c.(85612-85614)Cgc>Tgc	p.R28538C	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R21114C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R27611C|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R21239C|TTN_ENST00000342175.6_Missense_Mutation_p.R21306C|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R30179C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28538	Ig-like 132.		R -> H. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R21306C(1)|p.R21114C(1)|p.R21239C(1)|p.R27609C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTACTGAAGCGAACAAATTCA	0.383																																																4	Substitution - Missense(4)	large_intestine(4)	2											88	83	84					2																	179417092		1883	4098	5981	179125338	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.85612C>T	2.37:g.179417092G>A	ENSP00000465570:p.Arg28538Cys		179125338	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.44	2.237741	0.39598	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.76	5.76	0.90799	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79707	0.4492	M	0.64170	1.965	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.80464	-0.1371	9	0.87932	D	0	.	15.0877	0.72167	0.0:0.0:0.8583:0.1417	.	21114;21239;21306;28538	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	27611;21114;21306;21239;21111	ENSP00000343764:R27611C;ENSP00000434586:R21114C;ENSP00000340554:R21306C;ENSP00000352154:R21239C	ENSP00000340554:R21306C	R	-	1	0	TTN	179125338	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	5.565000	0.67365	2.882000	0.98803	0.655000	0.94253	CGC		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179417092	G	A	179417092	3	1	61	1	0	0	0	0	1	0	0	0	16775	1058	37	1	17556	1	TTN	2	179417092	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3570	179417092	63782281	1874	9859										
TTN	7273	broad.mit.edu	37	chr2	179417917	179417917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattttcctgtatcattgcGagtaacttgaggaatggtga	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179417917G>A	ENST00000591111.1	-	285	85011	c.84787C>T	c.(84787-84789)Cgc>Tgc	p.R28263C	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R20839C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R27336C|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R20964C|TTN_ENST00000342175.6_Missense_Mutation_p.R21031C|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R29904C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28263	Ig-like 131.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R20839C(1)|p.R20964C(1)|p.R21031C(1)|p.R27334C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATCATTGCGAGTAACTTGA	0.403																																																4	Substitution - Missense(4)	large_intestine(4)	2											171	167	168					2																	179417917		1935	4128	6063	179126163	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.84787C>T	2.37:g.179417917G>A	ENSP00000465570:p.Arg28263Cys		179126163	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	14.68	2.608316	0.46527	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.39	4.46	0.54185	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78013	0.4217	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.86666	0.1907	9	0.87932	D	0	.	16.0479	0.80734	0.0:0.0:0.8657:0.1343	.	20839;20964;21031;28263	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	27336;20839;21031;20964;20836	ENSP00000343764:R27336C;ENSP00000434586:R20839C;ENSP00000340554:R21031C;ENSP00000352154:R20964C	ENSP00000340554:R21031C	R	-	1	0	TTN	179126163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.877000	0.56123	2.677000	0.91161	0.655000	0.94253	CGC		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179417917	G	A	179417917	3	1	61	1	0	0	0	0	1	0	0	0	16775	1058	37	1	18381	1	TTN	2	179417917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	825	179417917	63781456	1875	9860										
TTN	7273	broad.mit.edu	37	chr2	179419339	179419339	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacaccatagaccacacaaCgcggcttgtctcacgctttt	7	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179419339C>T	ENST00000591111.1	-	282	84036	c.83812G>A	c.(83812-83814)Gtt>Att	p.V27938I	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V20514I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V27011I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V20639I|TTN_ENST00000342175.6_Missense_Mutation_p.V20706I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V29579I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27938	Fibronectin type-III 103. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V20639I(1)|p.V27009I(1)|p.V20514I(1)|p.V20706I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACCACACAACGCGGCTTGTC	0.468																																																4	Substitution - Missense(4)	large_intestine(4)	2											98	100	100					2																	179419339		2037	4192	6229	179127585	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83812G>A	2.37:g.179419339C>T	ENSP00000465570:p.Val27938Ile		179127585	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.48	2.847101	0.51164	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.66	5.66	0.87406	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.40767	0.1130	N	0.25332	0.735	0.50039	D	0.999841	P;P;P;P	0.47841	0.901;0.901;0.901;0.768	B;B;B;B	0.34385	0.181;0.181;0.181;0.12	T	0.50039	-0.8874	9	0.87932	D	0	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	20514;20639;20706;27938	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	27011;20514;20706;20639;20511	ENSP00000343764:V27011I;ENSP00000434586:V20514I;ENSP00000340554:V20706I;ENSP00000352154:V20639I	ENSP00000340554:V20706I	V	-	1	0	TTN	179127585	1.000000	0.71417	0.540000	0.28089	0.955000	0.61496	4.400000	0.59709	2.826000	0.97356	0.655000	0.94253	GTT		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179419339	C	T	179419339	3	4	61	1	0	0	0	0	1	0	0	0	16775	536	19	1	19368	1	TTN	2	179419339	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1422	179419339	63780034	1876	9861										
TTN	7273	broad.mit.edu	37	chr2	179422773	179422773	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaacactttctttgagaTtgatggtcaggttctcagca	9	8	3	2	rs375374455		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179422773T>G	ENST00000591111.1	-	278	82609	c.82385A>C	c.(82384-82386)aAt>aCt	p.N27462T	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N20038T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N26535T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N20163T|TTN_ENST00000342175.6_Missense_Mutation_p.N20230T|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N29103T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27462					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.N26533T(1)|p.N20230T(1)|p.N20163T(1)|p.N20038T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTTTGAGATTGATGGTCAG	0.433																																																4	Substitution - Missense(4)	large_intestine(4)	2											121	117	118					2																	179422773		1897	4120	6017	179131019	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.82385A>C	2.37:g.179422773T>G	ENSP00000465570:p.Asn27462Thr		179131019	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.71	2.319470	0.41096	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.63	5.63	0.86233	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.40670	0.1126	N	0.01874	-0.695	0.38022	D	0.934881	B;B;B;B	0.22080	0.064;0.064;0.064;0.064	B;B;B;B	0.24848	0.031;0.031;0.056;0.056	T	0.49615	-0.8921	9	0.87932	D	0	.	16.1297	0.81418	0.0:0.0:0.0:1.0	.	20038;20163;20230;27462	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	26535;20038;20230;20163;20035	ENSP00000343764:N26535T;ENSP00000434586:N20038T;ENSP00000340554:N20230T;ENSP00000352154:N20163T	ENSP00000340554:N20230T	N	-	2	0	TTN	179131019	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	2.590000	0.46154	2.270000	0.75569	0.460000	0.39030	AAT		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179422773	T	G	179422773	3	3	61	1	0	0	0	0	1	0	0	0	16775	1493	52	4	20811	4	TTN	2	179422773	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3434	179422773	63776600	1877	9862										
TTN	7273	broad.mit.edu	37	chr2	179424881	179424881	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcttgcctgagtccacaaTtttgggtttggatggaggag	14	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179424881T>A	ENST00000591111.1	-	276	81279	c.81055A>T	c.(81055-81057)Att>Ttt	p.I27019F	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I19595F|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I26092F|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I19720F|TTN_ENST00000342175.6_Missense_Mutation_p.I19787F|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I28660F|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27019	Fibronectin type-III 97. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.I26090F(1)|p.I19595F(1)|p.I19787F(1)|p.I19720F(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGTCCACAATTTTGGGTTTG	0.453																																																4	Substitution - Missense(4)	large_intestine(4)	2											107	104	105					2																	179424881		1897	4111	6008	179133127	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81055A>T	2.37:g.179424881T>A	ENSP00000465570:p.Ile27019Phe		179133127	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.47	2.245631	0.39697	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	6.17	1.06	0.20224	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59142	0.2172	M	0.76574	2.34	0.54753	D	0.999988	P;P;P;P	0.38582	0.638;0.638;0.638;0.638	P;P;P;P	0.47015	0.534;0.534;0.534;0.534	T	0.60047	-0.7339	9	0.87932	D	0	.	10.0984	0.42488	0.0:0.2487:0.0:0.7513	.	19595;19720;19787;27019	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	26092;19595;19787;19720;19592	ENSP00000343764:I26092F;ENSP00000434586:I19595F;ENSP00000340554:I19787F;ENSP00000352154:I19720F	ENSP00000340554:I19787F	I	-	1	0	TTN	179133127	1.000000	0.71417	0.922000	0.36590	0.985000	0.73830	1.824000	0.39072	-0.040000	0.13580	0.533000	0.62120	ATT		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179424881	T	A	179424881	3	1	61	1	0	0	0	0	1	0	0	0	16775	1493	52	5	22149	5	TTN	2	179424881	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2108	179424881	63774492	1878	9863										
TTN	7273	broad.mit.edu	37	chr2	179425230	179425230	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtaaatggatctagtgcCtttatagctacactctctag	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179425230C>A	ENST00000591111.1	-	276	80930	c.80706G>T	c.(80704-80706)aaG>aaT	p.K26902N	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K19478N|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K25975N|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K19603N|TTN_ENST00000342175.6_Missense_Mutation_p.K19670N|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K28543N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26902	Fibronectin type-III 95. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K19670N(1)|p.K19478N(1)|p.K25973N(1)|p.K19603N(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATCTAGTGCCTTTATAGCTA	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	2											74	71	72					2																	179425230		1875	4104	5979	179133476	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.80706G>T	2.37:g.179425230C>A	ENSP00000465570:p.Lys26902Asn		179133476	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.52	1.372701	0.24857	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63913	-0.07;0.18;0.15;0.14	5.88	4.08	0.47627	Fibronectin, type III (3);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.61400	0.2344	M	0.71581	2.175	0.45066	D	0.99808	P;P;P;P	0.50272	0.933;0.933;0.933;0.883	P;P;P;B	0.44860	0.462;0.462;0.462;0.299	T	0.63431	-0.6639	9	0.87932	D	0	.	7.3855	0.26880	0.0:0.6414:0.0:0.3586	.	19478;19603;19670;26902	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	25975;19478;19670;19603;19475	ENSP00000343764:K25975N;ENSP00000434586:K19478N;ENSP00000340554:K19670N;ENSP00000352154:K19603N	ENSP00000340554:K19670N	K	-	3	2	TTN	179133476	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.259000	0.32956	0.812000	0.34326	-0.136000	0.14681	AAG		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179425230	C	A	179425230	3	1	61	1	0	0	0	0	1	0	0	0	16775	680	24	2	22498	2	TTN	2	179425230	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	349	179425230	63774143	1879	9864										
TTN	7273	broad.mit.edu	37	chr2	179425834	179425834	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taactataataggcccagtgGattcagatggctcactaact	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179425834G>A	ENST00000591111.1	-	276	80326	c.80102C>T	c.(80101-80103)tCc>tTc	p.S26701F	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S19277F|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S25774F|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S19402F|TTN_ENST00000342175.6_Missense_Mutation_p.S19469F|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S28342F|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26701	Fibronectin type-III 94. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S25772F(1)|p.S19277F(1)|p.S19469F(1)|p.S19402F(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGCCCAGTGGATTCAGATGG	0.418																																																4	Substitution - Missense(4)	large_intestine(4)	2											106	105	105					2																	179425834		1911	4110	6021	179134080	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.80102C>T	2.37:g.179425834G>A	ENSP00000465570:p.Ser26701Phe		179134080	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.40	1.627335	0.28978	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.84	4.95	0.65309	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.64560	0.2609	M	0.84156	2.68	0.38089	D	0.936916	P;P;P;P	0.50272	0.933;0.933;0.933;0.883	P;P;P;P	0.48030	0.564;0.564;0.564;0.467	T	0.75280	-0.3373	9	0.87932	D	0	.	15.3196	0.74112	0.0677:0.0:0.9323:0.0	.	19277;19402;19469;26701	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	25774;19277;19469;19402;19275	ENSP00000343764:S25774F;ENSP00000434586:S19277F;ENSP00000340554:S19469F;ENSP00000352154:S19402F	ENSP00000340554:S19469F	S	-	2	0	TTN	179134080	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.973000	0.56845	1.449000	0.47699	0.561000	0.74099	TCC		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179425834	G	A	179425834	3	1	61	1	0	0	0	0	1	0	0	0	16775	1174	41	3	23102	3	TTN	2	179425834	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	604	179425834	63773539	1880	9865										
TTN	7273	broad.mit.edu	37	chr2	179426797	179426797	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgaagcttccttaataGatagtgatgttacagtcttt	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179426797G>T	ENST00000591111.1	-	276	79363	c.79139C>A	c.(79138-79140)tCt>tAt	p.S26380Y	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S18956Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S25453Y|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S19081Y|TTN_ENST00000342175.6_Missense_Mutation_p.S19148Y|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S28021Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26380	Ig-like 127.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S19148Y(1)|p.S19081Y(1)|p.S25451Y(1)|p.S18956Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCCTTAATAGATAGTGATGT	0.368																																																4	Substitution - Missense(4)	large_intestine(4)	2											43	45	44					2																	179426797		1874	4098	5972	179135043	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.79139C>A	2.37:g.179426797G>T	ENSP00000465570:p.Ser26380Tyr		179135043	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	6.885	0.532829	0.13127	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	6.05	2.85	0.33270	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53722	0.1814	N	0.17278	0.47	0.09310	N	1	B;B;B;B	0.30793	0.295;0.295;0.295;0.065	B;B;B;B	0.34452	0.104;0.104;0.183;0.12	T	0.53092	-0.8487	9	0.87932	D	0	.	13.0288	0.58831	0.2052:0.0:0.7948:0.0	.	18956;19081;19148;26380	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	25453;18956;19148;19081;18954	ENSP00000343764:S25453Y;ENSP00000434586:S18956Y;ENSP00000340554:S19148Y;ENSP00000352154:S19081Y	ENSP00000340554:S19148Y	S	-	2	0	TTN	179135043	0.000000	0.05858	0.089000	0.20774	0.991000	0.79684	1.097000	0.30988	0.880000	0.35969	0.650000	0.86243	TCT		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179426797	G	T	179426797	3	4	61	1	0	0	0	0	1	0	0	0	16775	942	33	2	24065	2	TTN	2	179426797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	963	179426797	63772576	1881	9866										
TTN	7273	broad.mit.edu	37	chr2	179427757	179427757	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacttcgggttctggtcgaCctttgatagtgacaaataag	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179427757C>G	ENST00000591111.1	-	276	78403	c.78179G>C	c.(78178-78180)gGt>gCt	p.G26060A	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G18636A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G25133A|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G18761A|TTN_ENST00000342175.6_Missense_Mutation_p.G18828A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G27701A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26060	Ig-like 126.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G18828A(1)|p.G25131A(1)|p.G18761A(1)|p.G18636A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGGTCGACCTTTGATAGT	0.458																																																4	Substitution - Missense(4)	large_intestine(4)	2											150	147	148					2																	179427757		1939	4129	6068	179136003	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78179G>C	2.37:g.179427757C>G	ENSP00000465570:p.Gly26060Ala		179136003	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.53	2.860613	0.51482	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	6.04	6.04	0.98038	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91334	0.7267	M	0.91196	3.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.92039	0.5639	9	0.87932	D	0	.	20.5792	0.99380	0.0:1.0:0.0:0.0	.	18636;18761;18828;26060	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	25133;18636;18828;18761;18634	ENSP00000343764:G25133A;ENSP00000434586:G18636A;ENSP00000340554:G18828A;ENSP00000352154:G18761A	ENSP00000340554:G18828A	G	-	2	0	TTN	179136003	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.873000	0.98535	0.561000	0.74099	GGT		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179427757	C	G	179427757	3	3	61	1	0	0	0	0	1	0	0	0	16775	507	18	5	25025	5	TTN	2	179427757	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	960	179427757	63771616	1882	9867										
TTN	7273	broad.mit.edu	37	chr2	179428976	179428976	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacggatgtcggcttcaaGaacaaaagtctctcctgcat	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179428976G>T	ENST00000591111.1	-	276	77184	c.76960C>A	c.(76960-76962)Ctt>Att	p.L25654I	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L18230I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L24727I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L18355I|TTN_ENST00000342175.6_Missense_Mutation_p.L18422I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L27295I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25654	Ig-like 125.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L18230I(1)|p.L24725I(1)|p.L18422I(1)|p.L18355I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCGGCTTCAAGAACAAAAGTC	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	2											153	152	152					2																	179428976		1906	4123	6029	179137222	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76960C>A	2.37:g.179428976G>T	ENSP00000465570:p.Leu25654Ile		179137222	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.15	2.151089	0.38021	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	6.07	6.07	0.98685	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67757	0.2927	L	0.28458	0.855	0.50467	D	0.999874	B;B;B;B	0.32409	0.37;0.37;0.37;0.198	B;B;B;B	0.30316	0.114;0.114;0.114;0.114	T	0.67821	-0.5571	9	0.87932	D	0	.	20.6452	0.99591	0.0:0.0:1.0:0.0	.	18230;18355;18422;25654	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	24727;18230;18422;18355;18228	ENSP00000343764:L24727I;ENSP00000434586:L18230I;ENSP00000340554:L18422I;ENSP00000352154:L18355I	ENSP00000340554:L18422I	L	-	1	0	TTN	179137222	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.072000	0.71238	2.885000	0.99019	0.650000	0.86243	CTT		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179428976	G	T	179428976	3	4	61	1	0	0	0	0	1	0	0	0	16775	942	33	2	26244	2	TTN	2	179428976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1219	179428976	63770397	1883	9868										
TTN	7273	broad.mit.edu	37	chr2	179430354	179430354	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagtaacaactgcattacaGactttggattcagccacaat	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179430354G>T	ENST00000591111.1	-	276	75806	c.75582C>A	c.(75580-75582)gtC>gtA	p.V25194V	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.V17770V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.V24267V|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.V17895V|TTN_ENST00000342175.6_Silent_p.V17962V|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Silent_p.V26835V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25194	Fibronectin type-III 83. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V17962V(1)|p.V24265V(1)|p.V17770V(1)|p.V17895V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCATTACAGACTTTGGATT	0.443																																																4	Substitution - coding silent(4)	large_intestine(4)	2											192	188	189					2																	179430354		1918	4146	6064	179138600	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.75582C>A	2.37:g.179430354G>T			179138600	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179430354	G	T	179430354	2	4	61	1	0	0	0	0	0	0	0	1	16775	929	33	2		2	TTN	2	179430354	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1378	179430354	63769019	1884	9869										
TTN	7273	broad.mit.edu	37	chr2	179431305	179431305	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctactacatatcccaagatCtcactgccgccatcatagat	4	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179431305C>A	ENST00000591111.1	-	276	74855	c.74631G>T	c.(74629-74631)gaG>gaT	p.E24877D	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E17453D|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E23950D|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E17578D|TTN_ENST00000342175.6_Missense_Mutation_p.E17645D|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E26518D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24877	Fibronectin type-III 81. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E23948D(1)|p.E17453D(1)|p.E17578D(1)|p.E17645D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCCCAAGATCTCACTGCCGC	0.428																																																4	Substitution - Missense(4)	large_intestine(4)	2											169	171	170					2																	179431305		1882	4107	5989	179139551	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74631G>T	2.37:g.179431305C>A	ENSP00000465570:p.Glu24877Asp		179139551	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	9.921	1.212122	0.22289	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.78	0.69	0.18039	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.25975	0.0633	N	0.25789	0.76	0.26121	N	0.980553	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.09377	0.004;0.004;0.004;0.003	T	0.25293	-1.0136	9	0.87932	D	0	.	3.5814	0.07955	0.4329:0.3142:0.0:0.2529	.	17453;17578;17645;24877	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	23950;17453;17645;17578;17451	ENSP00000343764:E23950D;ENSP00000434586:E17453D;ENSP00000340554:E17645D;ENSP00000352154:E17578D	ENSP00000340554:E17645D	E	-	3	2	TTN	179139551	0.893000	0.30496	0.998000	0.56505	0.902000	0.53008	-0.019000	0.12546	0.315000	0.23110	0.561000	0.74099	GAG		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179431305	C	A	179431305	3	1	61	1	0	0	0	0	1	0	0	0	16775	912	32	2	28573	2	TTN	2	179431305	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	951	179431305	63768068	1885	9870										
TTN	7273	broad.mit.edu	37	chr2	179431523	179431523	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttaatcctgtcactcttaGacgcaaatctgtaatgcggc	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179431523G>T	ENST00000591111.1	-	276	74637	c.74413C>A	c.(74413-74415)Cta>Ata	p.L24805I	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L17381I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L23878I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L17506I|TTN_ENST00000342175.6_Missense_Mutation_p.L17573I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L26446I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24805	Fibronectin type-III 80. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L17381I(1)|p.L17506I(1)|p.L23876I(1)|p.L17573I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACTCTTAGACGCAAATCT	0.403																																																4	Substitution - Missense(4)	large_intestine(4)	2											76	76	76					2																	179431523		1863	4109	5972	179139769	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74413C>A	2.37:g.179431523G>T	ENSP00000465570:p.Leu24805Ile		179139769	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	8.919	0.960597	0.18583	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.75	1.38	0.22167	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45316	0.1336	L	0.42245	1.32	0.28400	N	0.918691	B;B;B;P	0.43578	0.124;0.124;0.124;0.811	B;B;B;B	0.42386	0.074;0.074;0.133;0.386	T	0.40059	-0.9583	9	0.87932	D	0	.	8.5254	0.33302	0.5337:0.0:0.4663:0.0	.	17381;17506;17573;24805	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	23878;17381;17573;17506;17379	ENSP00000343764:L23878I;ENSP00000434586:L17381I;ENSP00000340554:L17573I;ENSP00000352154:L17506I	ENSP00000340554:L17573I	L	-	1	2	TTN	179139769	1.000000	0.71417	0.215000	0.23724	0.871000	0.50021	3.932000	0.56537	0.346000	0.23899	-0.291000	0.09656	CTA		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179431523	G	T	179431523	3	4	61	1	0	0	0	0	1	0	0	0	16775	933	33	2	28791	2	TTN	2	179431523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218	179431523	63767850	1886	9871										
TTN	7273	broad.mit.edu	37	chr2	179431901	179431901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcaacaacatagtgagAaatgtcactgccaccatctt	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179431901A>G	ENST00000591111.1	-	276	74259	c.74035T>C	c.(74035-74037)Tct>Cct	p.S24679P	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S17255P|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S23752P|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S17380P|TTN_ENST00000342175.6_Missense_Mutation_p.S17447P|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S26320P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24679	Fibronectin type-III 79. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S23750P(1)|p.S17255P(1)|p.S17447P(1)|p.S17380P(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATAGTGAGAAATGTCACTG	0.453																																																4	Substitution - Missense(4)	large_intestine(4)	2											110	111	110					2																	179431901		1904	4113	6017	179140147	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74035T>C	2.37:g.179431901A>G	ENSP00000465570:p.Ser24679Pro		179140147	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	11.96	1.795206	0.31777	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	5.52	4.34	0.51931	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76863	0.4047	M	0.90814	3.15	0.44316	D	0.997199	D;D;D;D	0.62365	0.991;0.991;0.991;0.983	P;P;P;P	0.62089	0.898;0.898;0.898;0.857	T	0.80520	-0.1346	9	0.87932	D	0	.	11.6256	0.51142	0.9292:0.0:0.0708:0.0	.	17255;17380;17447;24679	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	23752;17255;17447;17380;17253	ENSP00000343764:S23752P;ENSP00000434586:S17255P;ENSP00000340554:S17447P;ENSP00000352154:S17380P	ENSP00000340554:S17447P	S	-	1	0	TTN	179140147	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.365000	0.79537	0.876000	0.35872	0.379000	0.24179	TCT		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179431901	A	G	179431901	3	3	61	1	0	0	0	0	1	0	0	0	16775	246	9	4	29169	4	TTN	2	179431901	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	378	179431901	63767472	1887	9872										
TTN	7273	broad.mit.edu	37	chr2	179432012	179432012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtcctggtctatctaataCttttacatttactgggaatg	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179432012C>A	ENST00000591111.1	-	276	74148	c.73924G>T	c.(73924-73926)Gta>Tta	p.V24642L	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V17218L|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V23715L|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V17343L|TTN_ENST00000342175.6_Missense_Mutation_p.V17410L|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V26283L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24642					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V17410L(1)|p.V23713L(1)|p.V17218L(1)|p.V17343L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTATCTAATACTTTTACATTT	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	2											158	163	162					2																	179432012		1838	4079	5917	179140258	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73924G>T	2.37:g.179432012C>A	ENSP00000465570:p.Val24642Leu		179140258	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.01	2.707055	0.48412	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.65	5.65	0.86999	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91872	0.7427	H	0.95004	3.61	0.80722	D	1	D;D;D;D	0.69078	0.997;0.994;0.994;0.997	D;D;D;D	0.80764	0.994;0.978;0.978;0.994	D	0.93582	0.6913	9	0.87932	D	0	.	19.7238	0.96153	0.0:1.0:0.0:0.0	.	17218;17343;17410;24642	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	23715;17218;17410;17343;17216	ENSP00000343764:V23715L;ENSP00000434586:V17218L;ENSP00000340554:V17410L;ENSP00000352154:V17343L	ENSP00000340554:V17410L	V	-	1	0	TTN	179140258	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.770000	0.85390	2.649000	0.89929	0.561000	0.74099	GTA		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179432012	C	A	179432012	3	1	61	1	0	0	0	0	1	0	0	0	16775	565	20	2	29280	2	TTN	2	179432012	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111	179432012	63767361	1888	9873										
TTN	7273	broad.mit.edu	37	chr2	179432768	179432768	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacaaaatactgtttctttCttttctctccaggtggtaac	5	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179432768C>A	ENST00000591111.1	-	276	73392	c.73168G>T	c.(73168-73170)Gaa>Taa	p.E24390*	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.E16966*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.E23463*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.E17091*|TTN_ENST00000342175.6_Nonsense_Mutation_p.E17158*|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.E26031*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24390	Fibronectin type-III 77. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E17091*(1)|p.E23461*(1)|p.E17158*(1)|p.E16966*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGTTTCTTTCTTTTCTCTCC	0.408																																																4	Substitution - Nonsense(4)	large_intestine(4)	2											96	88	91					2																	179432768		1871	4104	5975	179141014	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73168G>T	2.37:g.179432768C>A	ENSP00000465570:p.Glu24390*		179141014	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	63	78.280969	0.99993	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.71	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.8823	0.70542	0.0:0.9307:0.0:0.0693	.	.	.	.	X	23463;16966;17158;17091;16964	.	ENSP00000340554:E17158X	E	-	1	0	TTN	179141014	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	1.400000	0.46741	0.650000	0.86243	GAA		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179432768	C	A	179432768	4	1	61	1	0	0	0	0	0	1	0	0	16775	922	32	2	30036	2	TTN	2	179432768	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	756	179432768	63766605	1889	9874										
TTN	7273	broad.mit.edu	37	chr2	179433487	179433487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaattaccagatctttgGcaactattggaactgcaagg	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179433487G>A	ENST00000591111.1	-	276	72673	c.72449C>T	c.(72448-72450)gCc>gTc	p.A24150V	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A16726V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A23223V|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A16851V|TTN_ENST00000342175.6_Missense_Mutation_p.A16918V|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A25791V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24150	Fibronectin type-III 75. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A16851V(1)|p.A16726V(1)|p.A23221V(1)|p.A16918V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGATCTTTGGCAACTATTGG	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											79	74	76					2																	179433487		1886	4104	5990	179141733	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72449C>T	2.37:g.179433487G>A	ENSP00000465570:p.Ala24150Val		179141733	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.87	2.367291	0.41902	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.84	4.95	0.65309	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.47691	0.1459	L	0.48642	1.525	0.58432	D	0.999994	B;B;B;B	0.24882	0.113;0.113;0.113;0.103	B;B;B;B	0.13407	0.009;0.009;0.009;0.006	T	0.47302	-0.9128	9	0.87932	D	0	.	15.3189	0.74105	0.0679:0.0:0.9321:0.0	.	16726;16851;16918;24150	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	23223;16726;16918;16851;16724	ENSP00000343764:A23223V;ENSP00000434586:A16726V;ENSP00000340554:A16918V;ENSP00000352154:A16851V	ENSP00000340554:A16918V	A	-	2	0	TTN	179141733	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.030000	0.88816	1.435000	0.47434	0.655000	0.94253	GCC		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179433487	G	A	179433487	3	1	61	1	0	0	0	0	1	0	0	0	16775	1203	42	3	30755	3	TTN	2	179433487	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	719	179433487	63765886	1890	9875										
TTN	7273	broad.mit.edu	37	chr2	179445069	179445069	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcactttcacaacaatgGtatattcctttttaccacag	4	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179445069G>A	ENST00000591111.1	-	267	62338	c.62114C>T	c.(62113-62115)aCc>aTc	p.T20705I	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T13281I|TTN-AS1_ENST00000592600.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T19778I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T13406I|TTN_ENST00000342175.6_Missense_Mutation_p.T13473I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T22346I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20705					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T13473I(1)|p.T19776I(1)|p.T13406I(1)|p.T13281I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACAACAATGGTATATTCCTT	0.299																																																4	Substitution - Missense(4)	large_intestine(4)	2											175	160	165					2																	179445069		1832	4081	5913	179153315	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.62114C>T	2.37:g.179445069G>A	ENSP00000465570:p.Thr20705Ile		179153315	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.16	2.153921	0.38021	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.69	5.69	0.88448	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78541	0.4299	M	0.78285	2.405	0.80722	D	1	P;P;P;P	0.51537	0.946;0.946;0.946;0.946	P;P;P;P	0.51974	0.566;0.566;0.566;0.686	T	0.81202	-0.1040	9	0.87932	D	0	.	19.7982	0.96494	0.0:0.0:1.0:0.0	.	13281;13406;13473;20705	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	19778;13281;13473;13406;13279	ENSP00000343764:T19778I;ENSP00000434586:T13281I;ENSP00000340554:T13473I;ENSP00000352154:T13406I	ENSP00000340554:T13473I	T	-	2	0	TTN	179153315	1.000000	0.71417	0.923000	0.36655	0.813000	0.45954	9.799000	0.99117	2.675000	0.91044	0.563000	0.77884	ACC		0.299	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179445069	G	A	179445069	3	1	61	1	0	0	0	0	1	0	0	0	16775	1261	44	3	41126	3	TTN	2	179445069	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11582	179445069	63754304	1891	9876										
TTN	7273	broad.mit.edu	37	chr2	179449091	179449091	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatagattctgaatgaataCtcaagaccttctacaaggcc	7	10	3	4	rs397517660	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179449091C>T	ENST00000591111.1	-	261	60488	c.60264G>A	c.(60262-60264)gaG>gaA	p.E20088E	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.E12664E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.E19161E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.E12789E|TTN_ENST00000342175.6_Silent_p.E12856E|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Silent_p.E21729E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20088	Fibronectin type-III 45. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E19159E(1)|p.E12856E(1)|p.E12664E(1)|p.E12789E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAATGAATACTCAAGACCTT	0.448													C|||	2	0.000399361	0	0	5008	,	,		19421	0		0	False		,,,				2504	0.002															4	Substitution - coding silent(4)	large_intestine(4)	2											115	113	114					2																	179449091		1918	4132	6050	179157337	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.60264G>A	2.37:g.179449091C>T			179157337	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179449091	C	T	179449091	2	4	61	1	0	0	0	0	0	0	0	1	16775	564	20	3		3	TTN	2	179449091	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4022	179449091	63750282	1892	9877										
TTN	7273	broad.mit.edu	37	chr2	179454575	179454575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggttggccttgattaatCgtttagtgacatctgatgca	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179454575C>T	ENST00000591111.1	-	254	57178	c.56954G>A	c.(56953-56955)cGa>cAa	p.R18985Q	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R11561Q|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R18058Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R11686Q|TTN_ENST00000342175.6_Missense_Mutation_p.R11753Q|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R20626Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18985	Fibronectin type-III 37. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R18056Q(1)|p.R11686Q(1)|p.R11753Q(1)|p.R11561Q(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTGATTAATCGTTTAGTGAC	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	2											178	162	167					2																	179454575		1862	4100	5962	179162821	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.56954G>A	2.37:g.179454575C>T	ENSP00000465570:p.Arg18985Gln		179162821	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.30	2.792013	0.50102	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	6.1	6.1	0.99115	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67316	0.2880	L	0.37466	1.105	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.67193	-0.5732	9	0.87932	D	0	.	20.7146	0.99709	0.0:1.0:0.0:0.0	.	11561;11686;11753;18985	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	18058;11561;11753;11686;11559	ENSP00000343764:R18058Q;ENSP00000434586:R11561Q;ENSP00000340554:R11753Q;ENSP00000352154:R11686Q	ENSP00000340554:R11753Q	R	-	2	0	TTN	179162821	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.992000	0.70609	2.902000	0.99343	0.650000	0.86243	CGA		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179454575	C	T	179454575	3	4	61	1	0	0	0	0	1	0	0	0	16775	884	31	1	46338	1	TTN	2	179454575	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5484	179454575	63744798	1893	9878										
TTN	7273	broad.mit.edu	37	chr2	179455319	179455319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttgtctttcagtttaGgattaataggtggtccaggt	11	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179455319G>A	ENST00000591111.1	-	254	56434	c.56210C>T	c.(56209-56211)cCt>cTt	p.P18737L	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P11313L|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P17810L|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P11438L|TTN_ENST00000342175.6_Missense_Mutation_p.P11505L|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P20378L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18737	Fibronectin type-III 36. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P11313L(1)|p.P11505L(1)|p.P11438L(1)|p.P17808L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCAGTTTAGGATTAATAGG	0.453																																																4	Substitution - Missense(4)	large_intestine(4)	2											98	98	98					2																	179455319		1897	4111	6008	179163565	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.56210C>T	2.37:g.179455319G>A	ENSP00000465570:p.Pro18737Leu		179163565	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.63	2.293535	0.40594	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.11	6.11	0.99139	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56156	0.1966	L	0.28192	0.835	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.57057	-0.7876	9	0.87932	D	0	.	20.7342	0.99715	0.0:0.0:1.0:0.0	.	11313;11438;11505;18737	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	17810;11313;11505;11438;11311	ENSP00000343764:P17810L;ENSP00000434586:P11313L;ENSP00000340554:P11505L;ENSP00000352154:P11438L	ENSP00000340554:P11505L	P	-	2	0	TTN	179163565	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.728000	0.98792	2.906000	0.99361	0.655000	0.94253	CCT		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179455319	G	A	179455319	3	1	61	1	0	0	0	0	1	0	0	0	16775	1000	35	3	47082	3	TTN	2	179455319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	744	179455319	63744054	1894	9879										
TTN	7273	broad.mit.edu	37	chr2	179457237	179457237	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactggagtcacatcaattCttgctttagttggagcatct	8	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179457237C>T	ENST00000591111.1	-	251	54796	c.54572G>A	c.(54571-54573)aGa>aAa	p.R18191K	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R10767K|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R17264K|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R10892K|TTN_ENST00000342175.6_Missense_Mutation_p.R10959K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R19832K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18191	Ig-like 105.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R10959K(1)|p.R17262K(1)|p.R10767K(1)|p.R10892K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACATCAATTCTTGCTTTAGT	0.403																																																4	Substitution - Missense(4)	large_intestine(4)	2											295	273	280					2																	179457237		1901	4118	6019	179165483	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.54572G>A	2.37:g.179457237C>T	ENSP00000465570:p.Arg18191Lys		179165483	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.24	1.879675	0.33162	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	6.03	1.69	0.24217	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.34571	0.0902	L	0.39245	1.2	0.21256	N	0.999744	B;B;B;B	0.12013	0.005;0.005;0.005;0.005	B;B;B;B	0.15870	0.014;0.014;0.014;0.014	T	0.34551	-0.9824	9	0.87932	D	0	.	3.4919	0.07641	0.0:0.3071:0.2092:0.4837	.	10767;10892;10959;18191	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	17264;10767;10959;10892;10765	ENSP00000343764:R17264K;ENSP00000434586:R10767K;ENSP00000340554:R10959K;ENSP00000352154:R10892K	ENSP00000340554:R10959K	R	-	2	0	TTN	179165483	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.745000	0.47459	0.427000	0.26145	0.557000	0.71058	AGA		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179457237	C	T	179457237	3	4	61	1	0	0	0	0	1	0	0	0	16775	913	32	3	48732	3	TTN	2	179457237	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1918	179457237	63742136	1895	9880										
TTN	7273	broad.mit.edu	37	chr2	179457755	179457755	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggctgccaagttagatcGactgaattgcatgttgtatc	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179457755G>A	ENST00000591111.1	-	250	54392	c.54168C>T	c.(54166-54168)gtC>gtT	p.V18056V	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.V10632V|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.V17129V|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.V10757V|TTN_ENST00000342175.6_Silent_p.V10824V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Silent_p.V19697V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18056	Fibronectin type-III 31. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V17127V(1)|p.V10632V(1)|p.V10757V(1)|p.V10824V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTTAGATCGACTGAATTGC	0.393																																																4	Substitution - coding silent(4)	large_intestine(4)	2											125	121	122					2																	179457755		1908	4136	6044	179166001	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.54168C>T	2.37:g.179457755G>A			179166001	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179457755	G	A	179457755	2	1	61	1	0	0	0	0	0	0	0	1	16775	1045	37	1		1	TTN	2	179457755	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	518	179457755	63741618	1896	9881										
TTN	7273	broad.mit.edu	37	chr2	179458544	179458544	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagagataaccatgtaatCtttggtcacctcatcaaaac	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179458544C>A	ENST00000591111.1	-	248	53784	c.53560G>T	c.(53560-53562)Gat>Tat	p.D17854Y	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D10430Y|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D16927Y|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D10555Y|TTN_ENST00000342175.6_Missense_Mutation_p.D10622Y|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D19495Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17854	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D10555Y(1)|p.D16925Y(1)|p.D10430Y(1)|p.D10622Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCATGTAATCTTTGGTCACC	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	2											56	53	54					2																	179458544		1842	4089	5931	179166790	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53560G>T	2.37:g.179458544C>A	ENSP00000465570:p.Asp17854Tyr		179166790	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.72	2.320391	0.41096	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	5.86	5.86	0.93980	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79992	0.4542	M	0.91612	3.225	0.44104	D	0.996875	P;P;P;P	0.45474	0.859;0.859;0.859;0.859	P;P;P;P	0.55455	0.641;0.641;0.776;0.776	T	0.82682	-0.0336	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	10430;10555;10622;17854	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	16927;10430;10622;10555;10428	ENSP00000343764:D16927Y;ENSP00000434586:D10430Y;ENSP00000340554:D10622Y;ENSP00000352154:D10555Y	ENSP00000340554:D10622Y	D	-	1	0	TTN	179166790	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.871000	0.56077	2.937000	0.99478	0.650000	0.86243	GAT		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179458544	C	A	179458544	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	49756	2	TTN	2	179458544	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	789	179458544	63740829	1897	9882										
TTN	7273	broad.mit.edu	37	chr2	179462764	179462764	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcacaacaagctttgttcCtctcacttctttatctttac	3	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179462764C>A	ENST00000591111.1	-	243	52434	c.52210G>T	c.(52210-52212)Gga>Tga	p.G17404*	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.G9980*|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.G16477*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.G10105*|TTN_ENST00000342175.6_Nonsense_Mutation_p.G10172*|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.G19045*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17404	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G16475*(1)|p.G9980*(1)|p.G10105*(1)|p.G10172*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCTTTGTTCCTCTCACTTCT	0.388																																																4	Substitution - Nonsense(4)	large_intestine(4)	2											230	226	227					2																	179462764		1833	4088	5921	179171009	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.52210G>T	2.37:g.179462764C>A	ENSP00000465570:p.Gly17404*		179171009	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	60	49.352308	0.99987	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	16477;9980;10172;10105;9978	.	ENSP00000340554:G10172X	G	-	1	0	TTN	179171009	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.686000	0.84128	2.941000	0.99782	0.655000	0.94253	GGA		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179462764	C	A	179462764	4	1	61	1	0	0	0	0	0	1	0	0	16775	690	24	2	50840	2	TTN	2	179462764	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4220	179462764	63736609	1898	9883										
TTN	7273	broad.mit.edu	37	chr2	179463639	179463639	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgataggatctcggttaactCtcttccatctctttgaagtg	8	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179463639C>A	ENST00000591111.1	-	241	52099	c.51875G>T	c.(51874-51876)aGa>aTa	p.R17292I	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R9868I|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R16365I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R9993I|TTN_ENST00000342175.6_Missense_Mutation_p.R10060I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R18933I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17292	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R9993I(1)|p.R10060I(1)|p.R9868I(1)|p.R16363I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCGGTTAACTCTCTTCCATCT	0.443																																																4	Substitution - Missense(4)	large_intestine(4)	2											110	108	109					2																	179463639		1880	4116	5996	179171884	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51875G>T	2.37:g.179463639C>A	ENSP00000465570:p.Arg17292Ile		179171884	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.72	3.202523	0.58234	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.98	5.98	0.97165	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71178	0.3309	L	0.55990	1.75	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.71020	-0.4713	9	0.87932	D	0	.	20.4561	0.99145	0.0:1.0:0.0:0.0	.	9868;9993;10060;17292	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	16365;9868;10060;9993;9866	ENSP00000343764:R16365I;ENSP00000434586:R9868I;ENSP00000340554:R10060I;ENSP00000352154:R9993I	ENSP00000340554:R10060I	R	-	2	0	TTN	179171884	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.922000	0.63404	2.843000	0.97960	0.650000	0.86243	AGA		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179463639	C	A	179463639	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	51183	2	TTN	2	179463639	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	875	179463639	63735734	1899	9884										
TTN	7273	broad.mit.edu	37	chr2	179469984	179469984	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccttaactttgatagtgtCtcctcgaacactcagacgca	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179469984C>A	ENST00000591111.1	-	230	49221	c.48997G>T	c.(48997-48999)Gac>Tac	p.D16333Y	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D8909Y|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D15406Y|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D9034Y|TTN_ENST00000342175.6_Missense_Mutation_p.D9101Y|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D17974Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16333	Ig-like 100.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D9101Y(1)|p.D8909Y(1)|p.D15406Y(1)|p.D9034Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGATAGTGTCTCCTCGAACA	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											31	30	30					2																	179469984		1885	4097	5982	179178229	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48997G>T	2.37:g.179469984C>A	ENSP00000465570:p.Asp16333Tyr		179178229	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.22	2.470604	0.43942	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.69251	0.3090	M	0.80847	2.515	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.72107	-0.4390	9	0.87932	D	0	.	19.9346	0.97133	0.0:1.0:0.0:0.0	.	8909;9034;9101;16333	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	15406;8909;9101;9034;8909	ENSP00000343764:D15406Y;ENSP00000434586:D8909Y;ENSP00000340554:D9101Y;ENSP00000352154:D9034Y	ENSP00000340554:D9101Y	D	-	1	0	TTN	179178229	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.371000	0.34250	2.712000	0.92718	0.563000	0.77884	GAC		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179469984	C	A	179469984	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	54105	2	TTN	2	179469984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6345	179469984	63729389	1900	9885										
TTN	7273	broad.mit.edu	37	chr2	179471809	179471809	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggccacagccaaacttgttCttggcaataacacggaactt	9	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179471809C>A	ENST00000591111.1	-	228	48821	c.48597G>T	c.(48595-48597)aaG>aaT	p.K16199N	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K8775N|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K15272N|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K8900N|TTN_ENST00000342175.6_Missense_Mutation_p.K8967N|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K17840N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16199	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K8775N(1)|p.K8967N(1)|p.K8900N(1)|p.K15272N(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAACTTGTTCTTGGCAATAA	0.403																																																4	Substitution - Missense(4)	large_intestine(4)	2											179	173	175					2																	179471809		1892	4118	6010	179180054	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48597G>T	2.37:g.179471809C>A	ENSP00000465570:p.Lys16199Asn		179180054	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.63	1.404359	0.25378	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.35	4.47	0.54385	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.62073	0.2398	L	0.42581	1.335	0.45621	D	0.998552	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.72982	0.961;0.961;0.961;0.979	T	0.64123	-0.6481	9	0.87932	D	0	.	10.0066	0.41961	0.0:0.8466:0.0:0.1534	.	8775;8900;8967;16199	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	15272;8775;8967;8900;8775	ENSP00000343764:K15272N;ENSP00000434586:K8775N;ENSP00000340554:K8967N;ENSP00000352154:K8900N	ENSP00000340554:K8967N	K	-	3	2	TTN	179180054	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.152000	0.42272	1.258000	0.44101	0.561000	0.74099	AAG		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179471809	C	A	179471809	3	1	61	1	0	0	0	0	1	0	0	0	16775	912	32	2	54513	2	TTN	2	179471809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1825	179471809	63727564	1901	9886										
TTN	7273	broad.mit.edu	37	chr2	179471993	179471993	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagttaagtagacacattTttctgtttgttacaacaggt	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179471993T>G	ENST00000591111.1	-	228	48637	c.48413A>C	c.(48412-48414)aAa>aCa	p.K16138T	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K8714T|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K15211T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K8839T|TTN_ENST00000342175.6_Missense_Mutation_p.K8906T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K17779T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16138	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K8714T(1)|p.K15211T(1)|p.K8906T(1)|p.K8839T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAGACACATTTTTCTGTTTGT	0.363																																																4	Substitution - Missense(4)	large_intestine(4)	2											107	99	102					2																	179471993		1854	4093	5947	179180238	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48413A>C	2.37:g.179471993T>G	ENSP00000465570:p.Lys16138Thr		179180238	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.18	2.161602	0.38119	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.99	5.99	0.97316	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.52075	0.1712	N	0.11000	0.08	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.62412	-0.6860	9	0.87932	D	0	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	8714;8839;8906;16138	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	15211;8714;8906;8839;8714	ENSP00000343764:K15211T;ENSP00000434586:K8714T;ENSP00000340554:K8906T;ENSP00000352154:K8839T	ENSP00000340554:K8906T	K	-	2	0	TTN	179180238	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.991000	0.88244	2.291000	0.77112	0.533000	0.62120	AAA		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179471993	T	G	179471993	3	3	61	1	0	0	0	0	1	0	0	0	16775	1841	64	4	54697	4	TTN	2	179471993	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	184	179471993	63727380	1902	9887										
TTN	7273	broad.mit.edu	37	chr2	179474276	179474276	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcacttctaggcttgttCtcagaatgactttgggggca	11	8	3	2	rs370986897		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179474276C>A	ENST00000591111.1	-	223	47062	c.46838G>T	c.(46837-46839)aGa>aTa	p.R15613I	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R8189I|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R14686I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R8314I|TTN_ENST00000342175.6_Missense_Mutation_p.R8381I|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R17254I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15613	Ig-like 98.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R8189I(1)|p.R14686I(1)|p.R8314I(1)|p.R8381I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAGGCTTGTTCTCAGAATGAC	0.323																																																4	Substitution - Missense(4)	large_intestine(4)	2											112	106	108					2																	179474276		1854	4099	5953	179182521	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46838G>T	2.37:g.179474276C>A	ENSP00000465570:p.Arg15613Ile		179182521	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.95	1.790148	0.31685	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63255	-0.03;0.22;0.19;0.18	5.85	4.05	0.47172	Immunoglobulin subtype (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.55369	0.1916	L	0.51422	1.61	0.41040	D	0.98522	B;B;B;B	0.21381	0.055;0.055;0.055;0.055	B;B;B;B	0.27170	0.041;0.041;0.077;0.077	T	0.54788	-0.8241	9	0.87932	D	0	.	7.8608	0.29509	0.0:0.6203:0.2272:0.1526	.	8189;8314;8381;15613	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	14686;8189;8381;8314;8189	ENSP00000343764:R14686I;ENSP00000434586:R8189I;ENSP00000340554:R8381I;ENSP00000352154:R8314I	ENSP00000340554:R8381I	R	-	2	0	TTN	179182521	0.340000	0.24792	1.000000	0.80357	0.997000	0.91878	-0.131000	0.10482	0.796000	0.33947	0.655000	0.94253	AGA		0.323	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179474276	C	A	179474276	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	56292	2	TTN	2	179474276	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2283	179474276	63725097	1903	9888										
TTN	7273	broad.mit.edu	37	chr2	179476863	179476863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtcacatcaaccactgCcagggcgtagggtggtccag	12	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179476863C>T	ENST00000591111.1	-	217	45576	c.45352G>A	c.(45352-45354)Gca>Aca	p.A15118T	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A7694T|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A14191T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A7819T|TTN_ENST00000342175.6_Missense_Mutation_p.A7886T|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A16759T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15118	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A7886T(1)|p.A7819T(1)|p.A14191T(1)|p.A7694T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAACCACTGCCAGGGCGTAG	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											83	74	77					2																	179476863		1882	4099	5981	179185108	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45352G>A	2.37:g.179476863C>T	ENSP00000465570:p.Ala15118Thr		179185108	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.94	1.492370	0.26774	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	6.17	-8.11	0.01082	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.21062	0.0507	N	0.01410	-0.885	0.09310	N	0.999992	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.001;0.002;0.002	T	0.41034	-0.9531	9	0.87932	D	0	.	11.5412	0.50667	0.0873:0.4905:0.0:0.4221	.	7694;7819;7886;15118	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	14191;7694;7886;7819;7694	ENSP00000343764:A14191T;ENSP00000434586:A7694T;ENSP00000340554:A7886T;ENSP00000352154:A7819T	ENSP00000340554:A7886T	A	-	1	0	TTN	179185108	0.000000	0.05858	0.338000	0.25549	0.890000	0.51754	-0.334000	0.07883	-1.308000	0.02318	-0.136000	0.14681	GCA		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179476863	C	T	179476863	3	4	61	1	0	0	0	0	1	0	0	0	16775	739	26	3	57802	3	TTN	2	179476863	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2587	179476863	63722510	1904	9889										
TTN	7273	broad.mit.edu	37	chr2	179478881	179478881	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtactctttattggggattaAtttggtggccttgaagtttg	12	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179478881A>T	ENST00000591111.1	-	212	44544	c.44320T>A	c.(44320-44322)Tta>Ata	p.L14774I	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L7350I|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L13847I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L7475I|TTN_ENST00000342175.6_Missense_Mutation_p.L7542I|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L16415I|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14774	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L7350I(1)|p.L7475I(1)|p.L7542I(1)|p.L13847I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGGGATTAATTTGGTGGCC	0.428																																																4	Substitution - Missense(4)	large_intestine(4)	2											158	148	151					2																	179478881		1921	4131	6052	179187126	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44320T>A	2.37:g.179478881A>T	ENSP00000465570:p.Leu14774Ile		179187126	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.22	2.171957	0.38315	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86	6.07	6.07	0.98685	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94311	0.8172	H	0.96576	3.845	0.40706	D	0.982523	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.95322	0.8421	9	0.87932	D	0	.	8.8507	0.35199	0.8615:0.0:0.1385:0.0	.	7350;7475;7542;14774	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	13847;7350;7542;7475;7350	ENSP00000343764:L13847I;ENSP00000434586:L7350I;ENSP00000340554:L7542I;ENSP00000352154:L7475I	ENSP00000340554:L7542I	L	-	1	2	TTN	179187126	0.937000	0.31787	1.000000	0.80357	0.887000	0.51463	1.820000	0.39032	2.326000	0.78906	0.533000	0.62120	TTA		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179478881	A	T	179478881	3	4	61	1	0	0	0	0	1	0	0	0	16775	98	4	5	58854	5	TTN	2	179478881	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2018	179478881	63720492	1905	9890										
TTN	7273	broad.mit.edu	37	chr2	179481881	179481881	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggtgagaggaccaagaatTtcagatggatctgaaacacc	12	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179481881T>A	ENST00000591111.1	-	205	43142	c.42918A>T	c.(42916-42918)gaA>gaT	p.E14306D	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E6882D|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E13379D|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E7007D|TTN_ENST00000342175.6_Missense_Mutation_p.E7074D|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E15947D|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14306	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E13379D(1)|p.E7007D(1)|p.E6882D(1)|p.E7074D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACCAAGAATTTCAGATGGAT	0.353																																																4	Substitution - Missense(4)	large_intestine(4)	2											67	62	64					2																	179481881		1849	4092	5941	179190126	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42918A>T	2.37:g.179481881T>A	ENSP00000465570:p.Glu14306Asp		179190126	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	10.55	1.380390	0.24944	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.76	1.32	0.21799	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.28532	0.0706	L	0.33710	1.025	0.33643	D	0.607449	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.25950	-1.0117	9	0.87932	D	0	.	5.4503	0.16560	0.1498:0.3009:0.0:0.5493	.	6882;7007;7074;14306	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	13379;6882;7074;7007;6882	ENSP00000343764:E13379D;ENSP00000434586:E6882D;ENSP00000340554:E7074D;ENSP00000352154:E7007D	ENSP00000340554:E7074D	E	-	3	2	TTN	179190126	0.993000	0.37304	1.000000	0.80357	0.993000	0.82548	0.359000	0.20233	0.309000	0.22966	-0.256000	0.11100	GAA		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179481881	T	A	179481881	3	1	61	1	0	0	0	0	1	0	0	0	16775	1838	64	5	60284	5	TTN	2	179481881	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3000	179481881	63717492	1906	9891										
TTN	7273	broad.mit.edu	37	chr2	179482566	179482566	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttttccaactccaattcGattttgggctctcactcgga	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179482566G>A	ENST00000591111.1	-	203	42813	c.42589C>T	c.(42589-42591)Cga>Tga	p.R14197*	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.R6773*|TTN_ENST00000342992.6_Nonsense_Mutation_p.R13270*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R6898*|TTN_ENST00000342175.6_Nonsense_Mutation_p.R6965*|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R15838*|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14197	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R6965*(1)|p.R6773*(1)|p.R13270*(1)|p.R6898*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTCCAATTCGATTTTGGGCT	0.453																																																4	Substitution - Nonsense(4)	large_intestine(4)	2											168	159	162					2																	179482566		1961	4158	6119	179190811	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42589C>T	2.37:g.179482566G>A	ENSP00000465570:p.Arg14197*		179190811	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	58	33.214130	0.99981	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.63	1.43	0.22495	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.1415	0.81528	0.0:0.0:0.4471:0.5529	.	.	.	.	X	13270;6773;6965;6898;6773	.	ENSP00000340554:R6965X	R	-	1	2	TTN	179190811	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	1.250000	0.32850	0.369000	0.24510	-0.169000	0.13324	CGA		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179482566	G	A	179482566	4	1	61	1	0	0	0	0	0	1	0	0	16775	1066	37	1	60621	1	TTN	2	179482566	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	685	179482566	63716807	1907	9892										
TTN	7273	broad.mit.edu	37	chr2	179484735	179484735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccacaaaaagtctagcaCgagacttcctgtcttctacc	5	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179484735C>T	ENST00000591111.1	-	199	41710	c.41486G>A	c.(41485-41487)cGt>cAt	p.R13829H	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R6405H|TTN_ENST00000342992.6_Missense_Mutation_p.R12902H|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R6530H|TTN_ENST00000342175.6_Missense_Mutation_p.R6597H|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R15470H|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13829	Ig-like 94.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R6405H(1)|p.R12902H(1)|p.R6530H(1)|p.R6597H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTCTAGCACGAGACTTCCT	0.308																																																4	Substitution - Missense(4)	large_intestine(4)	2											98	90	92					2																	179484735		1832	4102	5934	179192980	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.41486G>A	2.37:g.179484735C>T	ENSP00000465570:p.Arg13829His		179192980	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.50	2.850568	0.51270	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.73	5.73	0.89815	Immunoglobulin subtype (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.85932	0.5812	L	0.47078	1.49	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.86061	0.1532	9	0.87932	D	0	.	20.2886	0.98538	0.0:1.0:0.0:0.0	.	6405;6530;6597;13829	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	12902;6405;6597;6530;6405	ENSP00000343764:R12902H;ENSP00000434586:R6405H;ENSP00000340554:R6597H;ENSP00000352154:R6530H	ENSP00000340554:R6597H	R	-	2	0	TTN	179192980	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	7.718000	0.84743	2.882000	0.98803	0.655000	0.94253	CGT		0.308	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179484735	C	T	179484735	3	4	61	1	0	0	0	0	1	0	0	0	16775	536	19	1	61740	1	TTN	2	179484735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2169	179484735	63714638	1908	9893										
TTN	7273	broad.mit.edu	37	chr2	179516230	179516230	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccaccagaggcaccttcTtttcaggaacaacctccttg	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179516230T>G	ENST00000591111.1	-	162	35200	c.34976A>C	c.(34975-34977)aAg>aCg	p.K11659T	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K10732T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K13166T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11659	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K10732T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGCACCTTCTTTTCAGGAAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											65	63	63					2																	179516230		1836	4081	5917	179224475	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.34976A>C	2.37:g.179516230T>G	ENSP00000465570:p.Lys11659Thr		179224475	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.33|16.33	3.092979|3.092979	0.56075|0.56075	.|.	.|.	ENSG00000155657|ENSG00000155657	ENST00000426232|ENST00000342992;ENST00000429997;ENST00000446966	.|D;D	.|0.81579	.|-1.51;-1.51	5.22|5.22	5.22|5.22	0.72569|0.72569	.|Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.|.	.|.	.|.	.|.	D|D	0.84683|0.84683	0.5526|0.5526	M|M	0.71871|0.71871	2.18|2.18	0.80722|0.80722	D|D	1|1	.|P	.|0.42078	.|0.77	.|P	.|0.48598	.|0.583	D|D	0.86825|0.86825	0.2007|0.2007	5|9	.|0.87932	.|D	.|0	.|.	15.3938|15.3938	0.74774|0.74774	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|11659	.|Q8WZ42	.|TITIN_HUMAN	N|T	6|10732;5;5	.|ENSP00000343764:K10732T;ENSP00000408004:K5T	.|ENSP00000343764:K10732T	K|K	-|-	3|2	2|0	TTN|TTN	179224475|179224475	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.691000|2.691000	0.47010|0.47010	2.094000|2.094000	0.63399|0.63399	0.528000|0.528000	0.53228|0.53228	AAA|AAG		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179516230	T	G	179516230	3	3	61	1	0	0	0	0	1	0	0	0	16775	1609	56	4	68398	4	TTN	2	179516230	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31495	179516230	63683143	1909	9894										
TTN	7273	broad.mit.edu	37	chr2	179516427	179516427	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcaggttttttggcaacGacagcaggtgctttcttttc	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179516427G>A	ENST00000591111.1	-	161	35132	c.34908C>T	c.(34906-34908)gtC>gtT	p.V11636V	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.V10709V|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Silent_p.V13143V|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11636	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V10709V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTGGCAACGACAGCAGGTG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											123	114	117					2																	179516427		1870	4103	5973	179224672	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.34908C>T	2.37:g.179516427G>A			179224672	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179516427	G	A	179516427	2	1	61	1	0	0	0	0	0	0	0	1	16775	1045	37	1		1	TTN	2	179516427	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197	179516427	63682946	1910	9895										
TTN	7273	broad.mit.edu	37	chr2	179535881	179535881	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttggagggatgattttCtcagatatctcaggcccttc	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179535881C>A	ENST00000591111.1	-	152	34346	c.34122G>T	c.(34120-34122)gaG>gaT	p.E11374D	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E10447D|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E11748D|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11374	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E50D(1)|p.E10447D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATGATTTTCTCAGATATCT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	2											109	95	99					2																	179535881		1792	4062	5854	179244126	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.34122G>T	2.37:g.179535881C>A	ENSP00000465570:p.Glu11374Asp		179244126	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.70|15.70	2.909563|2.909563	0.52439|0.52439	.|.	.|.	ENSG00000155657|ENSG00000155657	ENST00000342992;ENST00000541862|ENST00000448510	T|.	0.65732|.	-0.17|.	5.93|5.93	5.05|5.05	0.67936|0.67936	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);|.	.|.	.|.	.|.	.|.	T|.	0.39462|.	0.1079|.	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	B|.	0.19200|.	0.034|.	B|.	0.16722|.	0.016|.	T|.	0.18085|.	-1.0348|.	9|.	0.87932|0.11794	D|T	0|0.64	.|.	9.3537|9.3537	0.38153|0.38153	0.0:0.7799:0.0:0.2201|0.0:0.7799:0.0:0.2201	.|.	11374|.	Q8WZ42|.	TITIN_HUMAN|.	D|X	10447;50|106	ENSP00000343764:E10447D|.	ENSP00000343764:E10447D|ENSP00000399176:E106X	E|E	-|-	3|1	2|0	TTN|TTN	179244126|179244126	0.649000|0.649000	0.27322|0.27322	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.310000|0.310000	0.19356|0.19356	1.510000|1.510000	0.48803|0.48803	0.563000|0.563000	0.77884|0.77884	GAG|GAA		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179535881	C	A	179535881	3	1	61	1	0	0	0	0	1	0	0	0	16775	912	32	2	69292	2	TTN	2	179535881	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19454	179535881	63663492	1911	9896										
TTN	7273	broad.mit.edu	37	chr2	179542573	179542573	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcttcaggaacaatttCttcttcaaatagaacttcct	3	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179542573C>A	ENST00000591111.1	-	144	33339	c.33115G>T	c.(33115-33117)Gaa>Taa	p.E11039*	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.E10112*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.E11356*|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	10179	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E10112*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGAACAATTTCTTCTTCAAAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											88	87	87					2																	179542573		1838	4083	5921	179250818	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.33115G>T	2.37:g.179542573C>A	ENSP00000465570:p.Glu11039*		179250818	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	60	47.406482	0.99987	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.9098	0.19020	0.141:0.648:0.1364:0.0746	.	.	.	.	X	10112	.	ENSP00000343764:E10112X	E	-	1	0	TTN	179250818	0.074000	0.21230	1.000000	0.80357	0.390000	0.30446	0.500000	0.22562	2.878000	0.98634	0.650000	0.86243	GAA		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179542573	C	A	179542573	4	1	61	1	0	0	0	0	0	1	0	0	16775	922	32	2	70331	2	TTN	2	179542573	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6692	179542573	63656800	1912	9897										
TTN	7273	broad.mit.edu	37	chr2	179547473	179547473	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttcatactcccgctcctcGtattcttcatattggtcata	5	13	4	0	rs369046627		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179547473G>A	ENST00000591111.1	-	133	32318	c.32094C>T	c.(32092-32094)taC>taT	p.Y10698Y	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.Y9771Y|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Silent_p.Y11015Y|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Y9771Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCGCTCCTCGTATTCTTCAT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	2											304	284	290					2																	179547473		1881	4099	5980	179255718	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32094C>T	2.37:g.179547473G>A			179255718	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179547473	G	A	179547473	2	1	61	1	0	0	0	0	0	0	0	1	16775	1140	40	1		1	TTN	2	179547473	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4900	179547473	63651900	1913	9898										
TTN	7273	broad.mit.edu	37	chr2	179550274	179550274	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcagcttccactctcttaGaaataatgtgcagcttttct	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179550274G>T	ENST00000591111.1	-	126	31636	c.31412C>A	c.(31411-31413)tCt>tAt	p.S10471Y	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S9544Y|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S10788Y|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S9544F(2)|p.S9544Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACTCTCTTAGAAATAATGTG	0.358																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	2											105	101	102					2																	179550274		1903	4119	6022	179258519	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.31412C>A	2.37:g.179550274G>T	ENSP00000465570:p.Ser10471Tyr		179258519	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	14.92	2.679047	0.47886	.	.	ENSG00000155657	ENST00000342992	T	0.66280	-0.2	5.95	5.95	0.96441	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.54415	0.1857	N	0.22421	0.69	0.80722	D	1	B	0.31009	0.303	B	0.33890	0.172	T	0.56565	-0.7958	9	0.87932	D	0	.	18.5737	0.91147	0.0:0.0:1.0:0.0	.	10471	Q8WZ42	TITIN_HUMAN	Y	9544	ENSP00000343764:S9544Y	ENSP00000343764:S9544Y	S	-	2	0	TTN	179258519	1.000000	0.71417	0.555000	0.28281	0.971000	0.66376	4.816000	0.62642	2.824000	0.97209	0.655000	0.94253	TCT		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179550274	G	T	179550274	3	4	61	1	0	0	0	0	1	0	0	0	16775	942	33	2	72106	2	TTN	2	179550274	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2801	179550274	63649099	1914	9899										
TTN	7273	broad.mit.edu	37	chr2	179571337	179571337	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgtccctaatctccagtTttgcttcatcgcctttttgg	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179571337T>G	ENST00000591111.1	-	100	28537	c.28313A>C	c.(28312-28314)aAa>aCa	p.K9438T	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K8511T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.K9755T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13534	Ig-like 77.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K8511T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATCTCCAGTTTTGCTTCATC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											182	178	179					2																	179571337		1909	4134	6043	179279582	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.28313A>C	2.37:g.179571337T>G	ENSP00000465570:p.Lys9438Thr		179279582	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	15.60	2.881035	0.51801	.	.	ENSG00000155657	ENST00000342992	T	0.63096	-0.02	6.1	6.1	0.99115	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61726	0.2370	N	0.04508	-0.205	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.72779	-0.4190	9	0.87932	D	0	.	16.686	0.85306	0.0:0.0:0.0:1.0	.	9438	Q8WZ42	TITIN_HUMAN	T	8511	ENSP00000343764:K8511T	ENSP00000343764:K8511T	K	-	2	0	TTN	179279582	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	4.072000	0.57563	2.340000	0.79590	0.528000	0.53228	AAA		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179571337	T	G	179571337	3	3	61	1	0	0	0	0	1	0	0	0	16775	1841	64	4	75309	4	TTN	2	179571337	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	21063	179571337	63628036	1915	9900										
TTN	7273	broad.mit.edu	37	chr2	179571633	179571633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgacacaaaaaagagtCttccatctaccgcagctttc	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179571633C>A	ENST00000591111.1	-	99	28363	c.28139G>T	c.(28138-28140)aGa>aTa	p.R9380I	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R8453I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.R9697I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13480	Ig-like 77.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R8453I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAAAAGAGTCTTCCATCTAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	52	53					2																	179571633		1864	4107	5971	179279878	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.28139G>T	2.37:g.179571633C>A	ENSP00000465570:p.Arg9380Ile		179279878	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.37	2.215723	0.39102	.	.	ENSG00000155657	ENST00000342992	T	0.61158	0.13	6.16	2.1	0.27182	Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.40247	0.1109	N	0.19112	0.55	0.80722	D	1	B	0.18863	0.031	B	0.17098	0.017	T	0.18398	-1.0338	9	0.87932	D	0	.	8.7796	0.34783	0.0:0.2599:0.0:0.7401	.	9380	Q8WZ42	TITIN_HUMAN	I	8453	ENSP00000343764:R8453I	ENSP00000343764:R8453I	R	-	2	0	TTN	179279878	0.997000	0.39634	0.704000	0.30370	0.617000	0.37484	1.819000	0.39022	0.118000	0.18165	0.650000	0.86243	AGA		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179571633	C	A	179571633	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	75487	2	TTN	2	179571633	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296	179571633	63627740	1916	9901										
TTN	7273	broad.mit.edu	37	chr2	179575504	179575504	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taactaatctggtactttccGccacttcgtatttctctgct	5	12	2	0	rs375083775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179575504G>A	ENST00000591111.1	-	96	27593	c.27369C>T	c.(27367-27369)ggC>ggT	p.G9123G	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.G8196G|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.G9440G|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13254	Ig-like 74.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G8196G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTACTTTCCGCCACTTCGTA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G	,,,	1,3979		0,1,1989	148	143	144		,24588,,	-12.3	0.4	2		144	0,8340		0,0,4170	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6159	AA,AG,GG		0.0,0.0251,0.0081	,,,	,8196/33424,,	179575504	1,12319	1990	4170	6160	179283749	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27369C>T	2.37:g.179575504G>A			179283749	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179575504	G	A	179575504	2	1	61	1	0	0	0	0	0	0	0	1	16775	1074	38	1		1	TTN	2	179575504	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3871	179575504	63623869	1917	9902										
TTN	7273	broad.mit.edu	37	chr2	179577163	179577163	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggattgccgatttttcagtCgtagttatattacacctctg	8	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179577163C>T	ENST00000591111.1	-	93	26759	c.26535G>A	c.(26533-26535)acG>acA	p.T8845T	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.T7918T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.T9162T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12994	Ig-like 71.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T7918T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTTTCAGTCGTAGTTATAT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	2											105	105	105					2																	179577163		1850	4106	5956	179285408	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.26535G>A	2.37:g.179577163C>T			179285408	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179577163	C	T	179577163	2	4	61	1	0	0	0	0	0	0	0	1	16775	871	31	1		1	TTN	2	179577163	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1659	179577163	63622210	1918	9903										
TTN	7273	broad.mit.edu	37	chr2	179579140	179579140	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggttgcaatgttttctgaAtaagaaatccatatgttgtc	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179579140A>C	ENST00000591111.1	-	89	25634	c.25410T>G	c.(25408-25410)taT>taG	p.Y8470*	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y7543*|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y8787*|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12638	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Y7543*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTTTTCTGAATAAGAAATCC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											92	86	88					2																	179579140		1855	4092	5947	179287385	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25410T>G	2.37:g.179579140A>C	ENSP00000465570:p.Tyr8470*		179287385	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	59	36.354107	0.99983	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.96	0.534	0.17127	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.0105	0.47659	0.6826:0.0:0.3174:0.0	.	.	.	.	X	7543	.	ENSP00000343764:Y7543X	Y	-	3	2	TTN	179287385	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	2.259000	0.43259	-0.129000	0.11620	0.533000	0.62120	TAT		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179579140	A	C	179579140	4	2	61	1	0	0	0	0	0	1	0	0	16775	108	4	4	78256	4	TTN	2	179579140	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1977	179579140	63620233	1919	9904										
TTN	7273	broad.mit.edu	37	chr2	179579257	179579257	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgaacttctttaccaacGacagtagatatgtcactgag	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179579257G>A	ENST00000591111.1	-	89	25517	c.25293C>T	c.(25291-25293)gtC>gtT	p.V8431V	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.V7504V|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.V8748V|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12602	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V7504V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTACCAACGACAGTAGATA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											56	50	52					2																	179579257		1852	4107	5959	179287502	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25293C>T	2.37:g.179579257G>A			179287502	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179579257	G	A	179579257	2	1	61	1	0	0	0	0	0	0	0	1	16775	1045	37	1		1	TTN	2	179579257	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117	179579257	63620116	1920	9905										
TTN	7273	broad.mit.edu	37	chr2	179584460	179584460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccatctttgaaccacttgGctgagagttctggtgttcca	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179584460G>A	ENST00000591111.1	-	80	23032	c.22808C>T	c.(22807-22809)gCc>gTc	p.A7603V	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.A6676V|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.A7920V|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13153	Ig-like 58.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A6676V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAACCACTTGGCTGAGAGTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											131	122	125					2																	179584460		1894	4112	6006	179292705	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22808C>T	2.37:g.179584460G>A	ENSP00000465570:p.Ala7603Val		179292705	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	9.670	1.146562	0.21288	.	.	ENSG00000155657	ENST00000342992	T	0.54279	0.58	6.08	3.24	0.37175	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23249	0.0562	N	0.00652	-1.29	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.26849	-1.0091	9	0.87932	D	0	.	11.0696	0.47995	0.2065:0.0:0.7935:0.0	.	7603	Q8WZ42	TITIN_HUMAN	V	6676	ENSP00000343764:A6676V	ENSP00000343764:A6676V	A	-	2	0	TTN	179292705	0.152000	0.22762	0.996000	0.52242	0.848000	0.48234	1.699000	0.37804	0.409000	0.25649	0.655000	0.94253	GCC		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179584460	G	A	179584460	3	1	61	1	0	0	0	0	1	0	0	0	16775	1203	42	3	80894	3	TTN	2	179584460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5203	179584460	63614913	1921	9906										
TTN	7273	broad.mit.edu	37	chr2	179585317	179585317	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgggggagttcccgaaatTtcacattggagaatcacatc	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179585317T>C	ENST00000591111.1	-	78	22445	c.22221A>G	c.(22219-22221)gaA>gaG	p.E7407E	RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.E6480E|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.E7724E|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12967	Ig-like 56.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E6480E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCCCGAAATTTCACATTGGA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											54	48	50					2																	179585317		1806	4070	5876	179293562	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22221A>G	2.37:g.179585317T>C			179293562	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179585317	T	C	179585317	2	2	61	1	0	0	0	0	0	0	0	1	16775	1838	64	4		4	TTN	2	179585317	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	857	179585317	63614056	1922	9907										
TTN	7273	broad.mit.edu	37	chr2	179588030	179588030	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagaatgatcacttaatCtcttcaaaaatgcagctggt	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179588030C>A	ENST00000591111.1	-	73	20977	c.20753G>T	c.(20752-20754)aGa>aTa	p.R6918I	RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R5991I|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.R7235I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12506	Ig-like 51.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R5991I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCACTTAATCTCTTCAAAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	81	82					2																	179588030		1880	4116	5996	179296275	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.20753G>T	2.37:g.179588030C>A	ENSP00000465570:p.Arg6918Ile		179296275	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	8.899	0.955886	0.18507	.	.	ENSG00000155657	ENST00000342992	T	0.65916	-0.18	6.06	2.43	0.29744	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57548	0.2061	L	0.54323	1.7	0.58432	D	0.999998	B	0.30793	0.295	B	0.35655	0.207	T	0.55082	-0.8196	9	0.87932	D	0	.	9.0315	0.36262	0.0:0.2207:0.0:0.7793	.	6918	Q8WZ42	TITIN_HUMAN	I	5991	ENSP00000343764:R5991I	ENSP00000343764:R5991I	R	-	2	0	TTN	179296275	0.973000	0.33851	0.839000	0.33178	0.983000	0.72400	1.789000	0.38724	0.175000	0.19841	-0.312000	0.09012	AGA		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179588030	C	A	179588030	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	82977	2	TTN	2	179588030	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2713	179588030	63611343	1923	9908										
TTN	7273	broad.mit.edu	37	chr2	179593325	179593325	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcattactgactgaattCtaaaactggccacgttattt	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179593325C>A	ENST00000591111.1	-	64	18601	c.18377G>T	c.(18376-18378)aGa>aTa	p.R6126I	RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R5199I|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.R6443I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12913	Ig-like 42.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R5199I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACTGAATTCTAAAACTGGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	60	62					2																	179593325		1870	4112	5982	179301570	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.18377G>T	2.37:g.179593325C>A	ENSP00000465570:p.Arg6126Ile		179301570	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.62	1.993149	0.35131	.	.	ENSG00000155657	ENST00000342992	T	0.67865	-0.29	5.63	5.63	0.86233	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73385	0.3580	L	0.28556	0.865	0.80722	D	1	D	0.67145	0.996	P	0.62298	0.9	T	0.75602	-0.3261	9	0.87932	D	0	.	20.0572	0.97657	0.0:1.0:0.0:0.0	.	6126	Q8WZ42	TITIN_HUMAN	I	5199	ENSP00000343764:R5199I	ENSP00000343764:R5199I	R	-	2	0	TTN	179301570	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.202000	0.58446	2.826000	0.97356	0.655000	0.94253	AGA		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179593325	C	A	179593325	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	85389	2	TTN	2	179593325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5295	179593325	63606048	1924	9909										
TTN	7273	broad.mit.edu	37	chr2	179596553	179596553	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcctgaatgaaagtcttAtactttctaccacttcgcag	6	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179596553A>G	ENST00000591111.1	-	56	16322	c.16098T>C	c.(16096-16098)taT>taC	p.Y5366Y	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.Y4439Y|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Silent_p.Y5683Y|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12186	Ig-like 34.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Y4439Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAAAGTCTTATACTTTCTAC	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	2											125	129	128					2																	179596553		1998	4170	6168	179304798	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16098T>C	2.37:g.179596553A>G			179304798	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179596553	A	G	179596553	2	3	61	1	0	0	0	0	0	0	0	1	16775	456	16	4		4	TTN	2	179596553	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3228	179596553	63602820	1925	9910										
TTN	7273	broad.mit.edu	37	chr2	179597238	179597238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacatgtgtacgtgcccGaatcagaggtttttactaaa	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179597238G>A	ENST00000591111.1	-	54	15823	c.15599C>T	c.(15598-15600)tCg>tTg	p.S5200L	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.S4273L|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S5517L|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12567	Ig-like 32.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S4273L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTACGTGCCCGAATCAGAGGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	53	54					2																	179597238		1875	4111	5986	179305483	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.15599C>T	2.37:g.179597238G>A	ENSP00000465570:p.Ser5200Leu		179305483	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.72	1.722543	0.30503	.	.	ENSG00000155657	ENST00000342992	T	0.69306	-0.39	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.83783	0.5329	M	0.87328	2.875	0.80722	D	1	D	0.71674	0.998	P	0.60415	0.874	D	0.85095	0.0954	9	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	5200	Q8WZ42	TITIN_HUMAN	L	4273	ENSP00000343764:S4273L	ENSP00000343764:S4273L	S	-	2	0	TTN	179305483	1.000000	0.71417	0.999000	0.59377	0.659000	0.38960	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	TCG		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179597238	G	A	179597238	3	1	61	1	0	0	0	0	1	0	0	0	16775	1059	37	1	88207	1	TTN	2	179597238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	685	179597238	63602135	1926	9911										
TTN	7273	broad.mit.edu	37	chr2	179597332	179597332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaccagctctttgttgcCcttaaaccatctgattgtga	7	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179597332C>T	ENST00000591111.1	-	54	15729	c.15505G>A	c.(15505-15507)Ggc>Agc	p.G5169S	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G4242S|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G5486S|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12536	Ig-like 32.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G4242S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTTGTTGCCCTTAAACCAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											67	65	65					2																	179597332		1870	4112	5982	179305577	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.15505G>A	2.37:g.179597332C>T	ENSP00000465570:p.Gly5169Ser		179305577	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	17.37	3.371504	0.61624	.	.	ENSG00000155657	ENST00000342992	T	0.44881	0.91	6.06	6.06	0.98353	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53546	0.1803	M	0.75884	2.315	0.80722	D	1	B	0.31752	0.338	B	0.37015	0.239	T	0.54669	-0.8259	9	0.87932	D	0	.	20.6208	0.99490	0.0:1.0:0.0:0.0	.	5169	Q8WZ42	TITIN_HUMAN	S	4242	ENSP00000343764:G4242S	ENSP00000343764:G4242S	G	-	1	0	TTN	179305577	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	GGC		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179597332	C	T	179597332	3	4	61	1	0	0	0	0	1	0	0	0	16775	623	22	3	88301	3	TTN	2	179597332	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94	179597332	63602041	1927	9912										
TTN	7273	broad.mit.edu	37	chr2	179602934	179602934	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagatatactttgaagatCgaatagaacacttgtcactc	8	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179602934C>T	ENST00000591111.1	-	47	13519	c.13295G>A	c.(13294-13296)cGa>cAa	p.R4432Q	TTN_ENST00000460472.2_Missense_Mutation_p.R4386Q|TTN_ENST00000342992.6_Missense_Mutation_p.R3505Q|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R4511Q|TTN_ENST00000342175.6_Missense_Mutation_p.R4578Q|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R4749Q|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12188	Ig-like 24.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R4386Q(1)|p.R3505Q(1)|p.R4511Q(1)|p.R4578Q(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTGAAGATCGAATAGAACA	0.463																																																4	Substitution - Missense(4)	large_intestine(4)	2											65	62	63					2																	179602934		1865	4110	5975	179311179	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.13295G>A	2.37:g.179602934C>T	ENSP00000465570:p.Arg4432Gln		179311179	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.50	2.553503	0.45487	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.67	4.79	0.61399	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54598	0.1868	.	.	.	0.20196	N	0.999925	B;B;B;B	0.19817	0.01;0.01;0.039;0.01	B;B;B;B	0.10450	0.003;0.003;0.005;0.003	T	0.47535	-0.9110	8	0.87932	D	0	.	8.6128	0.33813	0.0:0.7862:0.0:0.2138	.	4386;4511;4578;4432	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	3505;4386;4578;4511;4386	ENSP00000343764:R3505Q;ENSP00000434586:R4386Q;ENSP00000340554:R4578Q;ENSP00000352154:R4511Q	ENSP00000340554:R4578Q	R	-	2	0	TTN	179311179	0.914000	0.31030	1.000000	0.80357	0.911000	0.54048	1.639000	0.37176	2.689000	0.91719	0.462000	0.41574	CGA		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179602934	C	T	179602934	3	4	61	1	0	0	0	0	1	0	0	0	16775	884	31	1	90539	1	TTN	2	179602934	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5602	179602934	63596439	1928	9913										
TTN	7273	broad.mit.edu	37	chr2	179604479	179604479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttggctccttgctgaattCtaggaccctcagctgttagg	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179604479C>A	ENST00000591111.1	-	46	12754	c.12530G>T	c.(12529-12531)aGa>aTa	p.R4177I	TTN_ENST00000460472.2_Missense_Mutation_p.R4131I|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R4256I|TTN_ENST00000342175.6_Missense_Mutation_p.R4323I|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R4494I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R4256I(1)|p.R4323I(1)|p.R4131I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGCTGAATTCTAGGACCCTC	0.388																																																3	Substitution - Missense(3)	large_intestine(3)	2											189	187	188					2																	179604479		1856	4102	5958	179312724	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12530G>T	2.37:g.179604479C>A	ENSP00000465570:p.Arg4177Ile		179312724	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	3.278	-0.147579	0.06627	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.65549	-0.08;-0.16;-0.16	5.44	3.63	0.41609	.	.	.	.	.	T	0.53562	0.1804	L	0.43152	1.355	0.09310	N	1	B;B;B	0.16166	0.016;0.016;0.016	B;B;B	0.17098	0.017;0.017;0.017	T	0.51655	-0.8678	9	0.87932	D	0	.	9.183	0.37154	0.0:0.7049:0.0:0.2951	.	4131;4256;4323	D3DPF9;E7EQE6;E7ET18	.;.;.	I	4131;4323;4256;4131	ENSP00000434586:R4131I;ENSP00000340554:R4323I;ENSP00000352154:R4256I	ENSP00000340554:R4323I	R	-	2	0	TTN	179312724	0.005000	0.15991	0.031000	0.17742	0.265000	0.26407	1.841000	0.39240	1.314000	0.45095	-0.150000	0.13652	AGA		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179604479	C	A	179604479	3	1	61	1	0	0	0	0	1	0	0	0	16775	913	32	2	91308	2	TTN	2	179604479	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1545	179604479	63594894	1929	9914										
TTN	7273	broad.mit.edu	37	chr2	179605373	179605373	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagaggctcaactgttaatGaattaatttgttctatggac	8	6	3	2	rs370912401		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179605373G>T	ENST00000591111.1	-	46	11860	c.11636C>A	c.(11635-11637)tCa>tAa	p.S3879*	TTN_ENST00000460472.2_Nonsense_Mutation_p.S3833*|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.S3958*|TTN_ENST00000342175.6_Nonsense_Mutation_p.S4025*|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.S4196*|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S4025*(1)|p.S3833*(1)|p.S3958*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTGTTAATGAATTAATTTG	0.393																																																3	Substitution - Nonsense(3)	large_intestine(3)	2						G	stop/SER,,stop/SER,stop/SER	0,3694		0,0,1847	83	80	81		11498,,11873,12074	3.4	0.1	2		81	1,8183		0,1,4091	no	stop-gained,intron,stop-gained,stop-gained	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,5938	TT,TG,GG		0.0122,0.0,0.0084	,,,	3833/26927,,3958/27052,4025/27119	179605373	1,11877	1847	4092	5939	179313618	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11636C>A	2.37:g.179605373G>T	ENSP00000465570:p.Ser3879*		179313618	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	51	18.341181	0.99903	0.0	1.22E-4	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.51	3.39	0.38822	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	1.7031	0.02876	0.2283:0.1235:0.4477:0.2004	.	.	.	.	X	3833;4025;3958;3833	.	ENSP00000340554:S4025X	S	-	2	0	TTN	179313618	0.000000	0.05858	0.108000	0.21378	0.032000	0.12392	0.316000	0.19469	1.344000	0.45657	0.655000	0.94253	TCA		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179605373	G	T	179605373	4	4	61	1	0	0	0	0	0	1	0	0	16775	1294	45	2	92202	2	TTN	2	179605373	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	894	179605373	63594000	1930	9915										
TTN	7273	broad.mit.edu	37	chr2	179606070	179606070	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaacagtaggggcaggctCtccaaccactgtgtactcaa	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179606070C>A	ENST00000591111.1	-	46	11163	c.10939G>T	c.(10939-10941)Gag>Tag	p.E3647*	TTN_ENST00000460472.2_Nonsense_Mutation_p.E3601*|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.E3726*|TTN_ENST00000342175.6_Nonsense_Mutation_p.E3793*|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.E3964*|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13953	Ig-like 22.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E3793*(1)|p.E3601*(1)|p.E3726*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGGCAGGCTCTCCAACCACT	0.453																																																3	Substitution - Nonsense(3)	large_intestine(3)	2											128	126	126					2																	179606070		1932	4139	6071	179314315	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10939G>T	2.37:g.179606070C>A	ENSP00000465570:p.Glu3647*		179314315	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	53	20.953359	0.99935	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.87	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.3318	0.43827	0.0:0.7959:0.0:0.204	.	.	.	.	X	3601;3793;3726;3601	.	ENSP00000340554:E3793X	E	-	1	0	TTN	179314315	0.991000	0.36638	0.993000	0.49108	0.941000	0.58515	2.770000	0.47662	1.627000	0.50400	0.655000	0.94253	GAG		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179606070	C	A	179606070	4	1	61	1	0	0	0	0	0	1	0	0	16775	922	32	2	92899	2	TTN	2	179606070	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	697	179606070	63593303	1931	9916										
TTN	7273	broad.mit.edu	37	chr2	179612317	179612317	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacttcttccacctccattGaagtgattgattcactctgg	6	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179612317G>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.S4937L|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S4937L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACCTCCATTGAAGTGATTGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	124	127					2																	179612317		2203	4300	6503	179320562	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+5533C>T	2.37:g.179612317G>A			179320562	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	17.24	3.338254	0.60963	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.64085	-0.08	5.79	4.91	0.64330	.	.	.	.	.	T	0.53367	0.1792	L	0.50333	1.59	0.80722	D	1	B	0.20671	0.047	B	0.18263	0.021	T	0.49409	-0.8943	9	0.30854	T	0.27	.	9.6569	0.39932	0.0706:0.0:0.7889:0.1405	.	4937	Q8WZ42-6	.	L	4937;251	ENSP00000354117:S4937L	ENSP00000304714:S251L	S	-	2	0	TTN	179320562	0.999000	0.42202	0.856000	0.33681	0.858000	0.48976	3.534000	0.53568	1.443000	0.47586	0.655000	0.94253	TCA		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179612317	G	A	179612317	1	1	61	0	1	0	0	0	0	0	0	0	16775	1294	45	3		3	TTN	2	179612317	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6247	179612317	63587056	1932	9917										
TTN	7273	broad.mit.edu	37	chr2	179612744	179612744	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcccaccatcctgctttgGaaatgctgccaactctggtt	8	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179612744G>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.P4795S|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P4795S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCTGCTTTGGAAATGCTGCC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	53	56					2																	179612744		2203	4300	6503	179320989	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+5106C>T	2.37:g.179612744G>A			179320989	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	9.614	1.131983	0.21041	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.55234	0.53	5.59	0.113	0.14631	.	.	.	.	.	T	0.29684	0.0741	N	0.08118	0	0.09310	N	0.999999	B	0.10296	0.003	B	0.11329	0.006	T	0.25398	-1.0133	9	0.66056	D	0.02	.	7.0918	0.25287	0.0697:0.355:0.4651:0.1102	.	4795	Q8WZ42-6	.	S	4795;109	ENSP00000354117:P4795S	ENSP00000304714:P109S	P	-	1	0	TTN	179320989	0.059000	0.20769	0.001000	0.08648	0.025000	0.11179	0.321000	0.19558	0.278000	0.22164	0.585000	0.79938	CCA		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179612744	G	A	179612744	1	1	61	0	1	0	0	0	0	0	0	0	16775	1174	41	3		3	TTN	2	179612744	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	427	179612744	63586629	1933	9918										
TTN	7273	broad.mit.edu	37	chr2	179613321	179613321	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggatgttggattttaaaAtaagcttcttctggttgacc	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179613321A>G	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Silent_p.Y4602Y|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Y4602Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATTTTAAAATAAGCTTCTT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	2											124	134	131					2																	179613321		2203	4299	6502	179321566	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+4529T>C	2.37:g.179613321A>G			179321566	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179613321	A	G	179613321	1	3	61	0	1	0	0	0	0	0	0	0	16775	108	4	4		4	TTN	2	179613321	Intron	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	577	179613321	63586052	1934	9919										
TTN	7273	broad.mit.edu	37	chr2	179613961	179613961	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatttctttcttaatagtgAcatcactgaaatcatcaaca	3	8	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179613961A>G	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.V4389A|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V4389A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTAATAGTGACATCACTGAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	61	60					2																	179613961		2200	4295	6495	179322206	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+3889T>C	2.37:g.179613961A>G			179322206	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.61	2.288267	0.40494	.	.	ENSG00000155657	ENST00000360870	T	0.61158	0.13	5.23	-2.38	0.06622	.	.	.	.	.	T	0.33000	0.0848	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16719	-1.0393	9	0.18276	T	0.48	.	2.8024	0.05418	0.3504:0.1271:0.3984:0.1241	.	4389	Q8WZ42-6	.	A	4389	ENSP00000354117:V4389A	ENSP00000354117:V4389A	V	-	2	0	TTN	179322206	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.062000	0.11674	-0.464000	0.06963	0.460000	0.39030	GTC		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179613961	A	G	179613961	1	3	61	0	1	0	0	0	0	0	0	0	16775	275	10	4		4	TTN	2	179613961	Intron	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	640	179613961	63585412	1935	9920										
TTN	7273	broad.mit.edu	37	chr2	179614844	179614844	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggaaagcaattctgtgtCtccagagggaggaactggtg	14	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179614844C>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.D4095Y|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D4095Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTCTGTGTCTCCAGAGGGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											77	73	74					2																	179614844		2203	4299	6502	179323089	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+3006G>T	2.37:g.179614844C>A			179323089	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.88	2.070824	0.36566	.	.	ENSG00000155657	ENST00000360870	T	0.58506	0.33	5.54	4.66	0.58398	.	.	.	.	.	T	0.54255	0.1847	N	0.24115	0.695	0.80722	D	1	P	0.51537	0.946	P	0.55161	0.77	T	0.57394	-0.7819	9	0.59425	D	0.04	.	9.4577	0.38764	0.1424:0.7857:0.0:0.0719	.	4095	Q8WZ42-6	.	Y	4095	ENSP00000354117:D4095Y	ENSP00000354117:D4095Y	D	-	1	0	TTN	179323089	1.000000	0.71417	0.237000	0.24090	0.109000	0.19521	2.013000	0.40942	1.476000	0.48215	0.655000	0.94253	GAC		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179614844	C	A	179614844	1	1	61	0	1	0	0	0	0	0	0	0	16775	913	32	2		2	TTN	2	179614844	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	883	179614844	63584529	1936	9921										
TTN	7273	broad.mit.edu	37	chr2	179615267	179615267	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtcaccttcataaacttCttgagattcaatttcttgaa	4	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179615267C>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Nonsense_Mutation_p.E3954*|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E3954*(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCATAAACTTCTTGAGATTCA	0.368																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											37	38	37					2																	179615267		2203	4296	6499	179323512	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+2583G>T	2.37:g.179615267C>A			179323512	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	53	21.328997	0.99939	.	.	ENSG00000155657	ENST00000360870	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	19.861	0.96785	0.0:1.0:0.0:0.0	.	.	.	.	X	3954	.	ENSP00000354117:E3954X	E	-	1	0	TTN	179323512	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	2.769000	0.47654	2.767000	0.95098	0.655000	0.94253	GAA		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179615267	C	A	179615267	1	1	61	0	1	0	0	0	0	0	0	0	16775	922	32	2		2	TTN	2	179615267	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	423	179615267	63584106	1937	9922										
TTN	7273	broad.mit.edu	37	chr2	179615666	179615666	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcaccatataaatggtCttttggtagactttccttta	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179615666C>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.D3821Y|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D3821Y(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATAAATGGTCTTTTGGTAGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	114	111					2																	179615666		2201	4296	6497	179323911	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+2184G>T	2.37:g.179615666C>A			179323911	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	23.7	4.447606	0.84101	.	.	ENSG00000155657	ENST00000360870	T	0.61510	0.1	5.25	5.25	0.73442	.	.	.	.	.	T	0.53270	0.1786	N	0.14661	0.345	0.58432	D	0.999997	P	0.51537	0.946	P	0.55999	0.789	T	0.55471	-0.8136	9	0.48119	T	0.1	.	12.1667	0.54133	0.0:0.9165:0.0:0.0835	.	3821	Q8WZ42-6	.	Y	3821	ENSP00000354117:D3821Y	ENSP00000354117:D3821Y	D	-	1	0	TTN	179323911	0.119000	0.22226	0.012000	0.15200	0.849000	0.48306	2.393000	0.44442	2.610000	0.88304	0.655000	0.94253	GAC		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179615666	C	A	179615666	1	1	61	0	1	0	0	0	0	0	0	0	16775	913	32	2		2	TTN	2	179615666	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	399	179615666	63583707	1938	9923										
TTN	7273	broad.mit.edu	37	chr2	179615969	179615969	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagaagacgtatctaaaaGagataatttctttttctcca	5	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179615969G>T	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.L3720I|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L3720I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATCTAAAAGAGATAATTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	65	66					2																	179615969		2201	4297	6498	179324214	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1881C>A	2.37:g.179615969G>T			179324214	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	2.398	-0.338168	0.05278	.	.	ENSG00000155657	ENST00000360870	T	0.57436	0.4	5.55	0.466	0.16716	.	.	.	.	.	T	0.32526	0.0832	N	0.24115	0.695	0.09310	N	1	B	0.18610	0.029	B	0.14578	0.011	T	0.19353	-1.0308	9	0.22109	T	0.4	.	6.227	0.20714	0.3883:0.0:0.4928:0.1189	.	3720	Q8WZ42-6	.	I	3720	ENSP00000354117:L3720I	ENSP00000354117:L3720I	L	-	1	0	TTN	179324214	0.420000	0.25457	0.043000	0.18650	0.461000	0.32589	0.229000	0.17833	0.087000	0.17167	-0.208000	0.12717	CTT		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179615969	G	T	179615969	1	4	61	0	1	0	0	0	0	0	0	0	16775	942	33	2		2	TTN	2	179615969	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	303	179615969	63583404	1939	9924										
TTN	7273	broad.mit.edu	37	chr2	179621265	179621265	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagcacattccttagatagCtcagtgctttctgcaatttg	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179621265C>T	ENST00000591111.1	-	44	10528				TTN_ENST00000360870.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Silent_p.E3475E|TTN_ENST00000589042.1_Silent_p.E3646E|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E3475E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTAGATAGCTCAGTGCTTT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	2											102	101	101					2																	179621265		1953	4146	6099	179329510	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10303+2445G>A	2.37:g.179621265C>T			179329510	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179621265	C	T	179621265	1	4	61	0	1	0	0	0	0	0	0	0	16775	796	28	3		3	TTN	2	179621265	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5296	179621265	63578108	1940	9925										
TTN	7273	broad.mit.edu	37	chr2	179632645	179632645	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatatttctccttctgaatCtttattctatggatgaaatg	5	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179632645C>A	ENST00000591111.1	-	40	9536	c.9312G>T	c.(9310-9312)aaG>aaT	p.K3104N	TTN_ENST00000360870.5_Missense_Mutation_p.K3104N|TTN_ENST00000460472.2_Missense_Mutation_p.K3058N|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K3104N|TTN_ENST00000359218.5_Missense_Mutation_p.K3058N|TTN_ENST00000342175.6_Missense_Mutation_p.K3058N|TTN_ENST00000589042.1_Missense_Mutation_p.K3104N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13436	Ig-like 18.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K3104N(2)|p.K3058N(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTCTGAATCTTTATTCTAT	0.458																																																4	Substitution - Missense(4)	large_intestine(4)	2											80	81	81					2																	179632645		2203	4300	6503	179340890	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9312G>T	2.37:g.179632645C>A	ENSP00000465570:p.Lys3104Asn		179340890	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.45	1.355043	0.24512	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.8	3.02	0.34903	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.62466	0.2430	L	0.45352	1.415	0.22500	N	0.999047	B;B;B;B;P	0.42203	0.175;0.175;0.175;0.175;0.773	B;B;B;B;P	0.45829	0.081;0.081;0.081;0.129;0.494	T	0.53683	-0.8404	9	0.87932	D	0	.	7.798	0.29158	0.0:0.5582:0.0:0.4418	.	3058;3058;3058;3104;3104	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	N	3104;3058;3058;3058;3058;3104	ENSP00000343764:K3104N;ENSP00000434586:K3058N;ENSP00000340554:K3058N;ENSP00000352154:K3058N;ENSP00000354117:K3104N	ENSP00000340554:K3058N	K	-	3	2	TTN	179340890	1.000000	0.71417	0.903000	0.35520	0.730000	0.41778	0.983000	0.29552	0.353000	0.24079	0.561000	0.74099	AAG		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179632645	C	A	179632645	3	1	61	1	0	0	0	0	1	0	0	0	16775	912	32	2	101968	2	TTN	2	179632645	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11380	179632645	63566728	1941	9926										
TTN	7273	broad.mit.edu	37	chr2	179636057	179636057	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggccatcagactcacttCtgatgttgttagtcagtggt	11	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179636057C>T	ENST00000591111.1	-	34	8221	c.7997G>A	c.(7996-7998)aGa>aAa	p.R2666K	TTN_ENST00000360870.5_Missense_Mutation_p.R2666K|TTN_ENST00000460472.2_Missense_Mutation_p.R2620K|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R2666K|TTN_ENST00000359218.5_Missense_Mutation_p.R2620K|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R2620K|TTN_ENST00000589042.1_Missense_Mutation_p.R2666K|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12991	Ig-like 15.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R2620K(2)|p.R2666K(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGACTCACTTCTGATGTTGTT	0.453																																																4	Substitution - Missense(4)	large_intestine(4)	2											219	173	189					2																	179636057		2203	4300	6503	179344302	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7997G>A	2.37:g.179636057C>T	ENSP00000465570:p.Arg2666Lys		179344302	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.65	1.701109	0.30142	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	6.17	1.95	0.26073	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42040	0.1185	N	0.05534	-0.03	0.18873	N	0.999981	B;B;B;B;B	0.12013	0.0;0.0;0.0;0.0;0.005	B;B;B;B;B	0.11329	0.001;0.001;0.001;0.001;0.006	T	0.39881	-0.9592	9	0.87932	D	0	.	11.0772	0.48038	0.0:0.6686:0.0:0.3314	.	2620;2620;2620;2666;2666	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	K	2666;2620;2620;2620;2620;2666	ENSP00000343764:R2666K;ENSP00000434586:R2620K;ENSP00000340554:R2620K;ENSP00000352154:R2620K;ENSP00000354117:R2666K	ENSP00000340554:R2620K	R	-	2	0	TTN	179344302	0.910000	0.30920	1.000000	0.80357	0.576000	0.36127	0.331000	0.19733	0.501000	0.28013	-0.140000	0.14226	AGA		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179636057	C	T	179636057	3	4	61	1	0	0	0	0	1	0	0	0	16775	913	32	3	103307	3	TTN	2	179636057	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3412	179636057	63563316	1942	9927										
TTN	7273	broad.mit.edu	37	chr2	179641225	179641225	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaacaataagggtagcaGatgtgtgatctgttccatat	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179641225G>T	ENST00000591111.1	-	28	5590	c.5366C>A	c.(5365-5367)tCt>tAt	p.S1789Y	TTN_ENST00000360870.5_Missense_Mutation_p.S1789Y|TTN_ENST00000460472.2_Missense_Mutation_p.S1743Y|TTN-AS1_ENST00000610005.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S1789Y|TTN_ENST00000359218.5_Missense_Mutation_p.S1743Y|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S1743Y|TTN_ENST00000589042.1_Missense_Mutation_p.S1789Y|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12621	Ig-like 8.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.S1789Y(2)|p.S1743Y(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGGTAGCAGATGTGTGATC	0.408																																																4	Substitution - Missense(4)	large_intestine(4)	2											98	92	94					2																	179641225		2203	4300	6503	179349470	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.5366C>A	2.37:g.179641225G>T	ENSP00000465570:p.Ser1789Tyr		179349470	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	10.91	1.484693	0.26598	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.08	5.08	0.68730	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.86431	0.5931	M	0.92691	3.335	0.42916	D	0.994271	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.90171	0.4235	9	0.87932	D	0	.	18.4712	0.90776	0.0:0.0:1.0:0.0	.	1743;1743;1743;1789;1789	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	Y	1789;1743;1743;1743;1743;1789	ENSP00000343764:S1789Y;ENSP00000434586:S1743Y;ENSP00000340554:S1743Y;ENSP00000352154:S1743Y;ENSP00000354117:S1789Y	ENSP00000340554:S1743Y	S	-	2	0	TTN	179349470	1.000000	0.71417	0.999000	0.59377	0.808000	0.45660	9.789000	0.99068	2.376000	0.81061	0.655000	0.94253	TCT		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179641225	G	T	179641225	3	4	61	1	0	0	0	0	1	0	0	0	16775	942	33	2	105962	2	TTN	2	179641225	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5168	179641225	63558148	1943	9928										
TTN	7273	broad.mit.edu	37	chr2	179641740	179641740	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggctgacagtggaatcGattttaagggcagcttctcc	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179641740G>A	ENST00000591111.1	-	28	5075	c.4851C>T	c.(4849-4851)atC>atT	p.I1617I	TTN_ENST00000360870.5_Silent_p.I1617I|TTN_ENST00000460472.2_Silent_p.I1571I|TTN-AS1_ENST00000610005.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Silent_p.I1617I|TTN_ENST00000359218.5_Silent_p.I1571I|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000342175.6_Silent_p.I1571I|TTN_ENST00000589042.1_Silent_p.I1617I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12470	Ig-like 7.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.I1571I(3)|p.I1617I(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGTGGAATCGATTTTAAGGG	0.408																																																5	Substitution - coding silent(5)	large_intestine(5)	2											61	65	64					2																	179641740		2197	4296	6493	179349985	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4851C>T	2.37:g.179641740G>A			179349985	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179641740	G	A	179641740	2	1	61	1	0	0	0	0	0	0	0	1	16775	1048	37	1		1	TTN	2	179641740	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	515	179641740	63557633	1944	9929										
TTN	7273	broad.mit.edu	37	chr2	179642439	179642439	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcacgcttaccatcatgaAaccagaacgtctctggcata	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179642439A>C	ENST00000591111.1	-	25	4696	c.4472T>G	c.(4471-4473)tTt>tGt	p.F1491C	TTN_ENST00000360870.5_Missense_Mutation_p.F1491C|TTN_ENST00000460472.2_Missense_Mutation_p.F1445C|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.F1491C|TTN_ENST00000359218.5_Missense_Mutation_p.F1445C|TTN_ENST00000342175.6_Missense_Mutation_p.F1445C|TTN_ENST00000589042.1_Missense_Mutation_p.F1491C			Q8WZ42	TITIN_HUMAN	titin	12357	Ig-like 6.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.F1491C(2)|p.F1445C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCATCATGAAACCAGAACGT	0.328																																																3	Substitution - Missense(3)	large_intestine(3)	2											80	77	78					2																	179642439		2203	4300	6503	179350684	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4472T>G	2.37:g.179642439A>C	ENSP00000465570:p.Phe1491Cys		179350684	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	15.19	2.761285	0.49468	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89136	0.6629	M	0.92026	3.265	0.39912	D	0.974046	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.92074	0.5667	9	0.87932	D	0	.	16.1547	0.81649	1.0:0.0:0.0:0.0	.	1445;1445;1445;1491;1491	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	1491;1445;1445;1445;1445;1491	ENSP00000343764:F1491C;ENSP00000434586:F1445C;ENSP00000340554:F1445C;ENSP00000352154:F1445C;ENSP00000354117:F1491C	ENSP00000340554:F1445C	F	-	2	0	TTN	179350684	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.307000	0.96226	2.221000	0.72209	0.528000	0.53228	TTT		0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179642439	A	C	179642439	3	2	61	1	0	0	0	0	1	0	0	0	16775	14	1	4	106868	4	TTN	2	179642439	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	699	179642439	63556934	1945	9930										
TTN	7273	broad.mit.edu	37	chr2	179644012	179644012	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgacacccatcccctcaaGaattctataattcttgattc	4	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179644012G>T	ENST00000591111.1	-	23	4131	c.3907C>A	c.(3907-3909)Ctt>Att	p.L1303I	TTN_ENST00000360870.5_Missense_Mutation_p.L1303I|TTN_ENST00000460472.2_Missense_Mutation_p.L1257I|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L1303I|TTN_ENST00000359218.5_Missense_Mutation_p.L1257I|TTN_ENST00000342175.6_Missense_Mutation_p.L1257I|TTN_ENST00000589042.1_Missense_Mutation_p.L1303I			Q8WZ42	TITIN_HUMAN	titin	33500	Ig-like 5.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L1257I(3)|p.L1303I(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCCCCTCAAGAATTCTATAA	0.353																																																5	Substitution - Missense(5)	large_intestine(5)	2											50	53	52					2																	179644012		2203	4297	6500	179352257	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3907C>A	2.37:g.179644012G>T	ENSP00000465570:p.Leu1303Ile		179352257	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.48	1.651491	0.29336	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.72	2.8	0.32819	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43986	0.1272	N	0.17278	0.47	0.22226	N	0.999277	B;B;B;B;P	0.42296	0.033;0.033;0.033;0.033;0.775	B;B;B;B;B	0.32465	0.081;0.081;0.081;0.081;0.146	T	0.36065	-0.9763	9	0.87932	D	0	.	7.6308	0.28238	0.2148:0.1467:0.6385:0.0	.	1257;1257;1257;1303;1303	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	I	1303;1257;1257;1257;1257;1303	ENSP00000343764:L1303I;ENSP00000434586:L1257I;ENSP00000340554:L1257I;ENSP00000352154:L1257I;ENSP00000354117:L1303I	ENSP00000340554:L1257I	L	-	1	0	TTN	179352257	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.934000	0.40163	1.423000	0.47198	0.655000	0.94253	CTT		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179644012	G	T	179644012	3	4	61	1	0	0	0	0	1	0	0	0	16775	942	33	2	107441	2	TTN	2	179644012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1573	179644012	63555361	1946	9931										
TTN	7273	broad.mit.edu	37	chr2	179644857	179644857	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctgtttctccaactttaGgttcttgaacaaatgcagtc	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179644857G>T	ENST00000591111.1	-	22	3823	c.3599C>A	c.(3598-3600)cCt>cAt	p.P1200H	TTN_ENST00000360870.5_Missense_Mutation_p.P1200H|TTN_ENST00000460472.2_Missense_Mutation_p.P1154H|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P1200H|TTN_ENST00000359218.5_Missense_Mutation_p.P1154H|TTN_ENST00000342175.6_Missense_Mutation_p.P1154H|TTN_ENST00000589042.1_Missense_Mutation_p.P1200H			Q8WZ42	TITIN_HUMAN	titin	33413					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P1154H(2)|p.P1200H(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCAACTTTAGGTTCTTGAAC	0.353																																																4	Substitution - Missense(4)	large_intestine(4)	2											138	130	132					2																	179644857		2203	4300	6503	179353102	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3599C>A	2.37:g.179644857G>T	ENSP00000465570:p.Pro1200His		179353102	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	15.70	2.910977	0.52439	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.65364	-0.15;0.09;0.08;0.08;0.16	5.78	5.78	0.91487	Ribonuclease H-like (1);	.	.	.	.	T	0.73156	0.3551	L	0.34521	1.04	0.40519	D	0.98081	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.998;0.999	T	0.75545	-0.3280	9	0.87932	D	0	.	20.0175	0.97485	0.0:0.0:1.0:0.0	.	1154;1154;1154;1200;1200	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	H	1200;1154;1154;1154;1154;1200	ENSP00000343764:P1200H;ENSP00000434586:P1154H;ENSP00000340554:P1154H;ENSP00000352154:P1154H;ENSP00000354117:P1200H	ENSP00000340554:P1154H	P	-	2	0	TTN	179353102	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.468000	0.90393	2.730000	0.93505	0.650000	0.86243	CCT		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179644857	G	T	179644857	3	4	61	1	0	0	0	0	1	0	0	0	16775	1000	35	2	107753	2	TTN	2	179644857	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	845	179644857	63554516	1947	9932										
TTN	7273	broad.mit.edu	37	chr2	179650835	179650835	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctactgcagcaacaactgTtgctacagcttcagcctttt	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179650835T>G	ENST00000591111.1	-	14	2334	c.2110A>C	c.(2110-2112)Aca>Cca	p.T704P	TTN_ENST00000360870.5_Missense_Mutation_p.T704P|TTN_ENST00000460472.2_Missense_Mutation_p.T658P|TTN_ENST00000342992.6_Missense_Mutation_p.T704P|TTN_ENST00000359218.5_Missense_Mutation_p.T658P|TTN_ENST00000342175.6_Missense_Mutation_p.T658P|TTN_ENST00000589042.1_Missense_Mutation_p.T704P			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T658P(3)|p.T704P(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCAACAACTGTTGCTACAGCT	0.493																																																5	Substitution - Missense(5)	large_intestine(5)	2											53	55	54					2																	179650835		2203	4300	6503	179359080	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2110A>C	2.37:g.179650835T>G	ENSP00000465570:p.Thr704Pro		179359080	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	16.25	3.070634	0.55539	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000436599	T;T;T;T;T;T	0.70516	-0.49;-0.27;-0.27;-0.28;0.25;0.22	5.99	5.99	0.97316	Ribonuclease H-like (1);	.	.	.	.	T	0.78929	0.4361	L	0.36672	1.1	0.39488	D	0.968005	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.91635	0.996;0.996;0.996;0.996;0.999	T	0.81835	-0.0750	9	0.87932	D	0	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	658;658;658;704;704	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	P	704;658;658;658;658;704;208	ENSP00000343764:T704P;ENSP00000434586:T658P;ENSP00000340554:T658P;ENSP00000352154:T658P;ENSP00000354117:T704P;ENSP00000405517:T208P	ENSP00000340554:T658P	T	-	1	0	TTN	179359080	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.603000	0.82811	2.291000	0.77112	0.533000	0.62120	ACA		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179650835	T	G	179650835	3	3	61	1	0	0	0	0	1	0	0	0	16775	1725	60	4	109274	4	TTN	2	179650835	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5978	179650835	63548538	1948	9933										
TTN	7273	broad.mit.edu	37	chr2	179665387	179665387	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctctgcagtcgttgaacGaagttgggtggtgctgtctc	14	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179665387G>A	ENST00000591111.1	-	4	542	c.318C>T	c.(316-318)ttC>ttT	p.F106F	TTN_ENST00000360870.5_Silent_p.F106F|TTN_ENST00000460472.2_Silent_p.F106F|TTN_ENST00000342992.6_Silent_p.F106F|TTN_ENST00000359218.5_Silent_p.F106F|TTN_ENST00000342175.6_Silent_p.F106F|TTN_ENST00000589042.1_Silent_p.F106F			Q8WZ42	TITIN_HUMAN	titin	32724	Ig-like 2.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.F106F(4)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCGTTGAACGAAGTTGGGTG	0.512																																																4	Substitution - coding silent(4)	large_intestine(4)	2											122	100	107					2																	179665387		2203	4300	6503	179373632	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.318C>T	2.37:g.179665387G>A			179373632	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.512	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179665387	G	A	179665387	2	1	61	1	0	0	0	0	0	0	0	1	16775	1049	37	1		1	TTN	2	179665387	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14552	179665387	63533986	1949	9934										
CCDC141	285025	broad.mit.edu	37	chr2	179701907	179701907	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatcagcatgcattttctCccgtgtttctagcaaaccac	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179701907C>A	ENST00000420890.2	-	23	4156	c.4039G>T	c.(4039-4041)Gag>Tag	p.E1347*	CCDC141_ENST00000480419.1_5'UTR|CCDC141_ENST00000295723.5_Nonsense_Mutation_p.E772*	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1347								p.E1347K(1)|p.E772*(1)|p.E772K(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGCATTTTCTCCCGTGTTTCT	0.488																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	NS(2)|large_intestine(1)	2											69	59	62					2																	179701907		2203	4300	6503	179410152	SO:0001587	stop_gained	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.4039G>T	2.37:g.179701907C>A	ENSP00000395995:p.Glu1347*		179410152	H7C0P1|J3KNW6|Q8N8H3	Nonsense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	C	39	7.490513	0.98316	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	.	.	.	6.07	5.2	0.72013	.	0.407546	0.22727	N	0.056378	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-6.0835	11.0294	0.47763	0.0:0.858:0.0:0.142	.	.	.	.	X	1347;791;772	.	ENSP00000295723:E772X	E	-	1	0	CCDC141	179410152	0.808000	0.29022	0.038000	0.18304	0.031000	0.12232	2.164000	0.42387	1.589000	0.49982	-0.126000	0.14955	GAG		0.488	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179701907	C	A	179701907	4	1	61	1	0	0	0	0	0	1	0	0	2781	864	30	2	317	2	CCDC141	2	179701907	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36520	179701907	63497466	1950	9935										
CCDC141	285025	broad.mit.edu	37	chr2	179710434	179710434	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaatcataatggaagtcTtccaaattcggattcatctt	6	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179710434T>G	ENST00000420890.2	-	22	3510	c.3393A>C	c.(3391-3393)gaA>gaC	p.E1131D	CCDC141_ENST00000480419.1_5'UTR|CCDC141_ENST00000295723.5_Missense_Mutation_p.E556D	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1131								p.E556D(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			AATGGAAGTCTTCCAAATTCG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	111	114					2																	179710434		2203	4300	6503	179418679	SO:0001583	missense	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3393A>C	2.37:g.179710434T>G	ENSP00000395995:p.Glu1131Asp		179418679	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	T	8.632	0.893946	0.17613	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.51574	0.7;1.31;1.31	4.94	-2.11	0.07187	.	0.225655	0.31279	N	0.007923	T	0.31199	0.0789	L	0.29908	0.895	0.23809	N	0.996785	B;B	0.28552	0.193;0.215	B;B	0.37780	0.258;0.216	T	0.19321	-1.0309	10	0.32370	T	0.25	-8.7725	4.2701	0.10782	0.1542:0.3508:0.0:0.495	.	556;556	Q6ZP82;Q6ZP82-2	CC141_HUMAN;.	D	1131;575;556	ENSP00000395995:E1131D;ENSP00000344627:E575D;ENSP00000295723:E556D	ENSP00000295723:E556D	E	-	3	2	CCDC141	179418679	0.372000	0.25064	0.944000	0.38274	0.082000	0.17680	0.015000	0.13355	-0.109000	0.12044	-0.250000	0.11733	GAA		0.363	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		G	179710434	T	G	179710434	3	3	61	1	0	0	0	0	1	0	0	0	2781	1606	56	4	967	4	CCDC141	2	179710434	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8527	179710434	63488939	1951	9936										
CCDC141	285025	broad.mit.edu	37	chr2	179718242	179718242	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactgagggtgcaataaacTtattaaactgctggtggaga	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179718242T>G	ENST00000420890.2	-	20	3287	c.3170A>C	c.(3169-3171)aAg>aCg	p.K1057T	CCDC141_ENST00000295723.5_Missense_Mutation_p.K482T	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1057								p.K482T(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGCAATAAACTTATTAAACTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											143	142	142					2																	179718242		2203	4300	6503	179426487	SO:0001583	missense	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3170A>C	2.37:g.179718242T>G	ENSP00000395995:p.Lys1057Thr		179426487	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	T	18.17	3.563627	0.65651	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.36157	1.27;1.27;1.27	5.39	5.39	0.77823	.	0.000000	0.51477	D	0.000089	T	0.49558	0.1564	L	0.34521	1.04	0.37761	D	0.926334	D	0.89917	1.0	D	0.91635	0.999	T	0.54483	-0.8287	10	0.48119	T	0.1	-12.7564	15.4317	0.75105	0.0:0.0:0.0:1.0	.	482	Q6ZP82	CC141_HUMAN	T	1057;501;482	ENSP00000395995:K1057T;ENSP00000344627:K501T;ENSP00000295723:K482T	ENSP00000295723:K482T	K	-	2	0	CCDC141	179426487	1.000000	0.71417	0.998000	0.56505	0.478000	0.33099	5.012000	0.64017	2.030000	0.59900	0.533000	0.62120	AAG		0.433	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		G	179718242	T	G	179718242	3	3	61	1	0	0	0	0	1	0	0	0	2781	1609	56	4	1198	4	CCDC141	2	179718242	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7808	179718242	63481131	1952	9937										
CCDC141	285025	broad.mit.edu	37	chr2	179721108	179721108	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatttctttttgatatctTtgaatgagtctttgagctgt	8	4	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179721108T>G	ENST00000420890.2	-	18	2858	c.2741A>C	c.(2740-2742)aAa>aCa	p.K914T	CCDC141_ENST00000295723.5_Missense_Mutation_p.K339T	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	914								p.K339T(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TTTGATATCTTTGAATGAGTC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	50	50					2																	179721108		2198	4297	6495	179429353	SO:0001583	missense	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2741A>C	2.37:g.179721108T>G	ENSP00000395995:p.Lys914Thr		179429353	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	T	20.3	3.959841	0.74016	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	T;T;T;T	0.51574	0.7;1.35;1.35;1.28	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000017	T	0.58380	0.2118	L	0.34521	1.04	0.36135	D	0.846415	D	0.89917	1.0	D	0.91635	0.999	T	0.64554	-0.6380	10	0.39692	T	0.17	-22.4608	15.7394	0.77876	0.0:0.0:0.0:1.0	.	339	Q6ZP82	CC141_HUMAN	T	914;358;339;914	ENSP00000395995:K914T;ENSP00000344627:K358T;ENSP00000295723:K339T;ENSP00000390190:K914T	ENSP00000295723:K339T	K	-	2	0	CCDC141	179429353	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	3.257000	0.51500	2.122000	0.65172	0.455000	0.32223	AAA		0.289	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		G	179721108	T	G	179721108	3	3	61	1	0	0	0	0	1	0	0	0	2781	1841	64	4	1635	4	CCDC141	2	179721108	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2866	179721108	63478265	1953	9938										
CCDC141	285025	broad.mit.edu	37	chr2	179732885	179732885	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcatcacccagttccttCggctgctctacaaactccag	8	15	2	0	rs142582103		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179732885C>T	ENST00000420890.2	-	16	2559	c.2442G>A	c.(2440-2442)ccG>ccA	p.P814P	CCDC141_ENST00000295723.5_Silent_p.P239P	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	814								p.P239P(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CCAGTTCCTTCGGCTGCTCTA	0.468													C|||	1	0.000199681	0	0.0014	5008	,	,		16896	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C		1,4405	2.1+/-5.4	0,1,2202	114	102	106		2442	-5.5	0	2	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CCDC141	NM_173648.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		814/1531	179732885	2,13004	2203	4300	6503	179441130	SO:0001819	synonymous_variant	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2442G>A	2.37:g.179732885C>T			179441130	H7C0P1|J3KNW6|Q8N8H3	Silent	SNP	ENST00000420890.2	37																																																																																					0.468	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179732885	C	T	179732885	2	4	61	1	0	0	0	0	0	0	0	1	2781	871	31	1		1	CCDC141	2	179732885	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11777	179732885	63466488	1954	9939										
CCDC141	285025	broad.mit.edu	37	chr2	179733898	179733898	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaggatatcctcgtaatcCtggattctctctttctgttt	6	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179733898C>A	ENST00000420890.2	-	15	2457	c.2340G>T	c.(2338-2340)caG>caT	p.Q780H	CCDC141_ENST00000295723.5_Missense_Mutation_p.Q205H	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	780								p.Q205H(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CCTCGTAATCCTGGATTCTCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											184	163	170					2																	179733898		2203	4300	6503	179442143	SO:0001583	missense	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2340G>T	2.37:g.179733898C>A	ENSP00000395995:p.Gln780His		179442143	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	C	15.20	2.762809	0.49574	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	T;T;T;T	0.45276	0.9;1.49;1.49;1.52	5.49	-0.217	0.13149	.	0.505205	0.18328	N	0.144586	T	0.23249	0.0562	N	0.24115	0.695	0.24232	N	0.995394	B	0.14805	0.011	B	0.14578	0.011	T	0.11203	-1.0597	10	0.44086	T	0.13	-0.795	4.8734	0.13644	0.0:0.3217:0.3032:0.3751	.	205	Q6ZP82	CC141_HUMAN	H	780;224;205;780	ENSP00000395995:Q780H;ENSP00000344627:Q224H;ENSP00000295723:Q205H;ENSP00000390190:Q780H	ENSP00000295723:Q205H	Q	-	3	2	CCDC141	179442143	0.701000	0.27806	0.990000	0.47175	0.985000	0.73830	0.683000	0.25349	-0.191000	0.10448	-0.302000	0.09304	CAG		0.413	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179733898	C	A	179733898	3	1	61	1	0	0	0	0	1	0	0	0	2781	680	24	2	2048	2	CCDC141	2	179733898	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1013	179733898	63465475	1955	9940										
SESTD1	91404	broad.mit.edu	37	chr2	179974751	179974751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggactcccaaaatattgttCggttctaaaaatcaaaacac	5	9	2	0	rs139920232		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:179974751C>T	ENST00000428443.3	-	18	2282	c.1966G>A	c.(1966-1968)Gaa>Aaa	p.E656K		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	656							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.E656K(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AAATATTGTTCGGTTCTAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	LYS/GLU	0,4406		0,0,2203	103	95	97		1966	5.9	1	2	dbSNP_134	97	1,8599		0,1,4299	no	missense	SESTD1	NM_178123.4	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	656/697	179974751	1,13005	2203	4300	6503	179682996	SO:0001583	missense	91404			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1966G>A	2.37:g.179974751C>T	ENSP00000415332:p.Glu656Lys		179682996	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.932696	0.92458	0.0	1.16E-4	ENSG00000187231	ENST00000428443	T	0.06068	3.35	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.14917	0.0360	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	0.992;1.0	D;D	0.75484	0.935;0.986	T	0.18209	-1.0344	9	.	.	.	-22.9509	20.2187	0.98312	0.0:1.0:0.0:0.0	.	656;656	Q86VW0;B3KTX3	SESD1_HUMAN;.	K	656	ENSP00000415332:E656K	.	E	-	1	0	SESTD1	179682996	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.031000	0.76491	2.780000	0.95670	0.655000	0.94253	GAA		0.343	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		T	179974751	C	T	179974751	3	4	61	1	0	0	0	0	1	0	0	0	14164	893	31	1	128	1	SESTD1	2	179974751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240853	179974751	63224622	1956	9941										
SESTD1	91404	broad.mit.edu	37	chr2	180047865	180047865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatccatatttgtctgttCgaggcataatggaattgtca	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:180047865C>T	ENST00000428443.3	-	3	422	c.106G>A	c.(106-108)Gaa>Aaa	p.E36K	SESTD1_ENST00000486468.1_5'UTR	NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	36	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.E36K(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			TTTGTCTGTTCGAGGCATAAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	119	119					2																	180047865		2203	4300	6503	179756110	SO:0001583	missense	91404			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.106G>A	2.37:g.180047865C>T	ENSP00000415332:p.Glu36Lys		179756110	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	C	9.301	1.053161	0.19907	.	.	ENSG00000187231	ENST00000428443;ENST00000440010;ENST00000435047	T;T;T	0.62639	0.01;0.01;0.01	5.35	4.47	0.54385	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.141340	0.64402	D	0.000005	T	0.40719	0.1128	N	0.04297	-0.235	0.58432	D	0.999992	B	0.27416	0.178	B	0.28991	0.097	T	0.25293	-1.0136	9	.	.	.	-15.2268	16.3095	0.82864	0.0:0.8674:0.1326:0.0	.	36	Q86VW0	SESD1_HUMAN	K	36	ENSP00000415332:E36K;ENSP00000416164:E36K;ENSP00000410286:E36K	.	E	-	1	0	SESTD1	179756110	1.000000	0.71417	0.888000	0.34837	0.681000	0.39784	7.246000	0.78247	1.363000	0.46019	0.655000	0.94253	GAA		0.358	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		T	180047865	C	T	180047865	3	4	61	1	0	0	0	0	1	0	0	0	14164	893	31	1	2048	1	SESTD1	2	180047865	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73114	180047865	63151508	1957	9942										
ZNF385B	151126	broad.mit.edu	37	chr2	180409658	180409658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatcagggtaggtgtgcGcacaagagcaggaagggtag	16	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:180409658G>A	ENST00000410066.1	-	4	895	c.292C>T	c.(292-294)Cgc>Tgc	p.R98C	ZNF385B_ENST00000409343.1_Missense_Mutation_p.R22C|ZNF385B_ENST00000336917.5_5'UTR|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409692.1_5'UTR	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	98	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)	p.R98C(1)		breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GTAGGTGTGCGCACAAGAGCA	0.443																																					Colon(155;204 2491 32774 51842)											1	Substitution - Missense(1)	large_intestine(1)	2											183	159	167					2																	180409658		2203	4300	6503	180117903	SO:0001583	missense	151126			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.292C>T	2.37:g.180409658G>A	ENSP00000386845:p.Arg98Cys		180117903	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.858168	0.91433	.	.	ENSG00000144331	ENST00000410066;ENST00000409343;ENST00000439340	T;T;T	0.52983	1.35;1.29;0.64	5.87	5.87	0.94306	.	0.176515	0.52532	D	0.000063	T	0.68044	0.2958	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	T	0.67055	-0.5767	10	0.72032	D	0.01	-2.6355	20.5827	0.99408	0.0:0.0:1.0:0.0	.	98;22	Q569K4;Q569K4-2	Z385B_HUMAN;.	C	98;22;16	ENSP00000386845:R98C;ENSP00000386379:R22C;ENSP00000399198:R16C	ENSP00000386379:R22C	R	-	1	0	ZNF385B	180117903	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.923000	0.87546	2.941000	0.99782	0.655000	0.94253	CGC		0.443	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		A	180409658	G	A	180409658	3	1	61	1	0	0	0	0	1	0	0	0	17916	1087	38	1	1151	1	ZNF385B	2	180409658	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	361793	180409658	62789715	1958	9943										
ITGA4	3676	broad.mit.edu	37	chr2	182360630	182360630	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagatctaacactttgtttCtcatataagggcaaggaagt	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:182360630C>A	ENST00000397033.2	+	14	1936	c.1506C>A	c.(1504-1506)ttC>ttA	p.F502L		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	502					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.F502L(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	CACTTTGTTTCTCATATAAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											195	174	180					2																	182360630		1916	4142	6058	182068875	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1506C>A	2.37:g.182360630C>A	ENSP00000380227:p.Phe502Leu		182068875	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.335782	0.81801	.	.	ENSG00000115232	ENST00000425522;ENST00000397033;ENST00000233573	T;T	0.46063	0.88;0.88	5.8	4.84	0.62591	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.50240	0.1604	L	0.58428	1.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.56673	-0.7940	10	0.12766	T	0.61	.	3.3237	0.07059	0.0:0.445:0.0:0.555	.	502	P13612	ITA4_HUMAN	L	502	ENSP00000380227:F502L;ENSP00000233573:F502L	ENSP00000233573:F502L	F	+	3	2	ITGA4	182068875	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.157000	0.58144	1.327000	0.45338	0.650000	0.86243	TTC		0.418	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182360630	C	A	182360630	3	1	61	1	0	0	0	0	1	0	0	0	7899	912	32	2	1560	2	ITGA4	2	182360630	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1950972	182360630	60838743	1959	9944										
ITGA4	3676	broad.mit.edu	37	chr2	182396419	182396419	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccacattgtttaaatttCttgtgtaattttgggaaaat	7	4	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:182396419C>A	ENST00000397033.2	+	25	3130	c.2700C>A	c.(2698-2700)ttC>ttA	p.F900L		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	900					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.F900L(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GTTTAAATTTCTTGTGTAATT	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	2											72	71	72					2																	182396419		1806	4068	5874	182104664	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2700C>A	2.37:g.182396419C>A	ENSP00000380227:p.Phe900Leu		182104664	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	C	5.635	0.301923	0.10678	.	.	ENSG00000115232	ENST00000397033	T	0.41758	0.99	5.49	0.919	0.19392	.	0.612109	0.18211	N	0.148185	T	0.24353	0.0590	L	0.31207	0.915	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.12218	-1.0556	10	0.42905	T	0.14	.	2.8641	0.05595	0.1262:0.4933:0.1238:0.2568	.	900	P13612	ITA4_HUMAN	L	900	ENSP00000380227:F900L	ENSP00000380227:F900L	F	+	3	2	ITGA4	182104664	0.004000	0.15560	0.004000	0.12327	0.617000	0.37484	-0.023000	0.12456	0.240000	0.21263	0.557000	0.71058	TTC		0.308	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182396419	C	A	182396419	3	1	61	1	0	0	0	0	1	0	0	0	7899	912	32	2	2798	2	ITGA4	2	182396419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35789	182396419	60802954	1960	9945										
NEUROD1	4760	broad.mit.edu	37	chr2	182543404	182543404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttccaggtcctcatcttCgtcctcctcctctcccccgt	4	21	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:182543404C>T	ENST00000295108.3	-	2	641	c.184G>A	c.(184-186)Gaa>Aaa	p.E62K	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	62	Glu-rich (acidic).				amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.E62K(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			tcctcatcttcgtcctcctcc	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	107	117					2																	182543404		2203	4300	6503	182251649	SO:0001583	missense	4760			U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.184G>A	2.37:g.182543404C>T	ENSP00000295108:p.Glu62Lys		182251649	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.231201	0.79688	.	.	ENSG00000162992	ENST00000295108	D	0.95622	-3.76	5.9	5.9	0.94986	.	0.425765	0.24039	N	0.042114	D	0.91616	0.7351	L	0.52573	1.65	0.58432	D	0.999999	P	0.43094	0.799	B	0.17722	0.019	D	0.92066	0.5660	10	0.49607	T	0.09	-7.3566	17.7728	0.88497	0.0:1.0:0.0:0.0	.	62	Q13562	NDF1_HUMAN	K	62	ENSP00000295108:E62K	ENSP00000295108:E62K	E	-	1	0	NEUROD1	182251649	0.999000	0.42202	0.999000	0.59377	0.995000	0.86356	4.043000	0.57354	2.788000	0.95919	0.650000	0.86243	GAA		0.552	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		T	182543404	C	T	182543404	3	4	61	1	0	0	0	0	1	0	0	0	10379	893	31	1	890	1	NEUROD1	2	182543404	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146985	182543404	60655969	1961	9946										
SSFA2	6744	broad.mit.edu	37	chr2	182774685	182774685	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttaccagctaggtcttacGaagtcgaaaagaggtaagtg	11	7	1	1	rs143398479		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:182774685G>A	ENST00000431877.2	+	9	1652	c.1473G>A	c.(1471-1473)acG>acA	p.T491T	SSFA2_ENST00000428267.2_Silent_p.T338T|SSFA2_ENST00000320370.7_Silent_p.T491T|SSFA2_ENST00000409136.1_5'Flank|SSFA2_ENST00000409001.1_Silent_p.T491T	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	491						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T491T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TAGGTCTTACGAAGTCGAAAA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G	,	2,4404	4.2+/-10.8	0,2,2201	66	56	59		1473,1473	1.3	0.1	2	dbSNP_134	59	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SSFA2	NM_001130445.1,NM_006751.5	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	491/1260,491/1257	182774685	2,13004	2203	4300	6503	182482930	SO:0001819	synonymous_variant	6744			M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.1473G>A	2.37:g.182774685G>A			182482930	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Silent	SNP	ENST00000431877.2	37	CCDS46467.1																																																																																				0.378	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		A	182774685	G	A	182774685	2	1	61	1	0	0	0	0	0	0	0	1	15222	1045	37	1		1	SSFA2	2	182774685	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231281	182774685	60424688	1962	9947										
PPP1R1C	151242	broad.mit.edu	37	chr2	182852618	182852618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgattctcaatgagcataAccccccaggtaaagaagcat	8	10	1	3	rs181207388		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:182852618A>G	ENST00000409137.3	+	2	377	c.134A>G	c.(133-135)aAc>aGc	p.N45S	PPP1R1C_ENST00000280295.3_Missense_Mutation_p.N52S|PPP1R1C_ENST00000452904.1_Missense_Mutation_p.N45S|PPP1R1C_ENST00000475249.1_Intron|PPP1R1C_ENST00000409702.1_Missense_Mutation_p.N45S	NM_001261424.1|NM_001261425.1	NP_001248353.1|NP_001248354.1	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1C	45					cell cycle (GO:0007049)|cell division (GO:0051301)|negative regulation of catalytic activity (GO:0043086)|positive regulation of cell growth (GO:0030307)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)	p.N45S(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			AATGAGCATAACCCCCCAGGT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											207	195	199					2																	182852618		1914	4135	6049	182560863	SO:0001583	missense	151242			AF494535, BC017943	CCDS46468.1, CCDS58740.1	2q31.3	2012-04-17			ENSG00000150722	ENSG00000150722		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14940	protein-coding gene	gene with protein product		613240				11948623	Standard	NM_001261424		Approved	Inhibitor-1-like	uc010frm.2	Q8WVI7	OTTHUMG00000154326	ENST00000409137.3:c.134A>G	2.37:g.182852618A>G	ENSP00000386359:p.Asn45Ser		182560863	Q5HYJ5|Q8TD54	Missense_Mutation	SNP	ENST00000409137.3	37	CCDS46468.1	.	.	.	.	.	.	.	.	.	.	A	2.993	-0.207805	0.06180	.	.	ENSG00000150722	ENST00000452904;ENST00000409137;ENST00000280295;ENST00000409702	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	6.16	4.95	0.65309	.	0.369202	0.30940	N	0.008565	T	0.07279	0.0184	N	0.04508	-0.205	0.25643	N	0.986175	B;B	0.18461	0.003;0.028	B;B	0.15052	0.005;0.012	T	0.38351	-0.9665	10	0.02654	T	1	.	7.1933	0.25839	0.5573:0.3115:0.0:0.1312	.	52;45	Q8WVI7-2;Q8WVI7	.;PPR1C_HUMAN	S	45;45;52;45	ENSP00000399602:N45S;ENSP00000386359:N45S;ENSP00000280295:N52S;ENSP00000386778:N45S	ENSP00000280295:N52S	N	+	2	0	PPP1R1C	182560863	0.309000	0.24518	0.997000	0.53966	0.996000	0.88848	3.518000	0.53451	2.367000	0.80283	0.528000	0.53228	AAC		0.393	PPP1R1C-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334874.1	NM_001080545		G	182852618	A	G	182852618	3	3	61	1	0	0	0	0	1	0	0	0	12403	43	2	4	140	4	PPP1R1C	2	182852618	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	77933	182852618	60346755	1963	9948										
PDE1A	5136	broad.mit.edu	37	chr2	183104880	183104880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagcatgcacaatgctccGaaattttggtttttcctcag	7	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:183104880G>A	ENST00000410103.1	-	4	438	c.355C>T	c.(355-357)Cgg>Tgg	p.R119W	PDE1A_ENST00000358139.2_Missense_Mutation_p.R119W|PDE1A_ENST00000409365.1_Missense_Mutation_p.R103W|PDE1A_ENST00000346717.4_Missense_Mutation_p.R85W|PDE1A_ENST00000456212.1_Missense_Mutation_p.R119W|PDE1A_ENST00000351439.5_Missense_Mutation_p.R103W|PDE1A_ENST00000536095.1_Missense_Mutation_p.R15W|PDE1A_ENST00000482538.1_5'UTR|PDE1A_ENST00000435564.1_Missense_Mutation_p.R119W|PDE1A_ENST00000331935.6_Missense_Mutation_p.R119W	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	119					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.R119W(4)		endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	ACAATGCTCCGAAATTTTGGT	0.418																																																4	Substitution - Missense(4)	large_intestine(2)|skin(2)	2											168	162	164					2																	183104880		2203	4300	6503	182813125	SO:0001583	missense	5136				CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"Phosphodiesterases"	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.355C>T	2.37:g.183104880G>A	ENSP00000387037:p.Arg119Trp		182813125	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	37	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.048716	0.75846	.	.	ENSG00000115252	ENST00000435564;ENST00000346717;ENST00000536095;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T;T;T;T;T	0.75367	-0.93;-0.84;-0.83;-0.9;-0.93;-0.9;-0.92;-0.92;-0.92	5.26	5.26	0.73747	-cyclic nucleotide phosphodiesterase N-terminal (1);5&apos (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.85843	0.5791	M	0.78801	2.425	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.997;0.998;0.995	D	0.87288	0.2297	10	0.87932	D	0	.	14.7117	0.69238	0.0:0.0:0.8548:0.1452	.	15;85;119;103;119	B7Z3A7;P54750-3;P54750;P54750-2;P54750-4	.;.;PDE1A_HUMAN;.;.	W	119;85;15;103;119;103;119;119;119	ENSP00000410309:R119W;ENSP00000329112:R85W;ENSP00000439938:R15W;ENSP00000386767:R103W;ENSP00000331574:R119W;ENSP00000309269:R103W;ENSP00000387037:R119W;ENSP00000350858:R119W;ENSP00000408874:R119W	ENSP00000331574:R119W	R	-	1	2	PDE1A	182813125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.147000	0.50639	2.631000	0.89168	0.655000	0.94253	CGG		0.418	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			A	183104880	G	A	183104880	3	1	61	1	0	0	0	0	1	0	0	0	11664	1057	37	1	1378	1	PDE1A	2	183104880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252262	183104880	60094493	1964	9949										
NCKAP1	10787	broad.mit.edu	37	chr2	183866974	183866974	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataattaaatctaagtagttCtttgttaaatcaaagtttac	4	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:183866974C>A	ENST00000361354.4	-	5	765	c.393G>T	c.(391-393)aaG>aaT	p.K131N	NCKAP1_ENST00000360982.2_Missense_Mutation_p.K137N	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	131					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)	p.K137N(1)		breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			CTAAGTAGTTCTTTGTTAAAT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	59	58					2																	183866974		2202	4296	6498	183575219	SO:0001583	missense	10787			AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.393G>T	2.37:g.183866974C>A	ENSP00000355348:p.Lys131Asn		183575219	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.682035	0.68042	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.34859	1.34;1.34	5.41	5.41	0.78517	.	0.041576	0.85682	D	0.000000	T	0.47414	0.1444	M	0.82323	2.585	0.80722	D	1	B;B	0.27971	0.107;0.196	B;B	0.30316	0.114;0.069	T	0.45862	-0.9232	10	0.33940	T	0.23	-12.9614	19.5522	0.95324	0.0:1.0:0.0:0.0	.	131;137	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	N	131;137	ENSP00000355348:K131N;ENSP00000354251:K137N	ENSP00000354251:K137N	K	-	3	2	NCKAP1	183575219	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.196000	0.51020	2.689000	0.91719	0.655000	0.94253	AAG		0.299	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		A	183866974	C	A	183866974	3	1	61	1	0	0	0	0	1	0	0	0	10252	912	32	2	3101	2	NCKAP1	2	183866974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	762094	183866974	59332399	1965	9950										
DUSP19	142679	broad.mit.edu	37	chr2	183951833	183951833	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtgactttacatataaGagcatttctatattggatct	6	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:183951833G>T	ENST00000354221.4	+	3	514	c.339G>T	c.(337-339)aaG>aaT	p.K113N	DUSP19_ENST00000469344.1_Intron|DUSP19_ENST00000342619.6_Intron|AC064871.3_ENST00000444562.1_RNA	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	113					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)	p.K113N(1)		breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						TTACATATAAGAGCATTTCTA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											129	127	128					2																	183951833		2202	4298	6500	183660078	SO:0001583	missense	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.339G>T	2.37:g.183951833G>T	ENSP00000346160:p.Lys113Asn		183660078	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	g	17.22	3.334170	0.60853	.	.	ENSG00000162999	ENST00000354221	D	0.85629	-2.01	5.38	3.58	0.41010	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.042168	0.85682	D	0.000000	D	0.88887	0.6559	M	0.89414	3.03	0.49213	D	0.999767	P	0.43352	0.804	P	0.48089	0.566	D	0.87798	0.2623	10	0.54805	T	0.06	.	9.1732	0.37096	0.2213:0.0:0.7787:0.0	.	113	Q8WTR2	DUS19_HUMAN	N	113	ENSP00000346160:K113N	ENSP00000346160:K113N	K	+	3	2	DUSP19	183660078	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	1.733000	0.38156	0.756000	0.33013	0.651000	0.88453	AAG		0.299	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			T	183951833	G	T	183951833	3	4	61	1	0	0	0	0	1	0	0	0	4829	933	33	2	349	2	DUSP19	2	183951833	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84859	183951833	59247540	1966	9951										
DUSP19	142679	broad.mit.edu	37	chr2	183960263	183960263	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcatttaccagtgctttTtctttggtgaaaaatgcaag	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:183960263T>G	ENST00000354221.4	+	4	706	c.531T>G	c.(529-531)ttT>ttG	p.F177L	DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Missense_Mutation_p.F126L|AC064871.3_ENST00000413954.1_RNA|AC064871.3_ENST00000444562.1_RNA	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	177	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)	p.F177L(1)		breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						CCAGTGCTTTTTCTTTGGTGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	140	139					2																	183960263		2203	4300	6503	183668508	SO:0001583	missense	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.531T>G	2.37:g.183960263T>G	ENSP00000346160:p.Phe177Leu		183668508	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.250518	0.39797	.	.	ENSG00000162999	ENST00000342619;ENST00000354221	D;D	0.84442	-1.85;-1.85	5.74	1.8	0.24995	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.234802	0.50627	N	0.000104	T	0.66107	0.2756	N	0.11023	0.085	0.51482	D	0.999921	B;B	0.09022	0.002;0.0	B;B	0.15052	0.012;0.009	T	0.50676	-0.8800	10	0.12103	T	0.63	.	7.9137	0.29806	0.0:0.0687:0.2674:0.6639	.	126;177	Q8WTR2-2;Q8WTR2	.;DUS19_HUMAN	L	126;177	ENSP00000343905:F126L;ENSP00000346160:F177L	ENSP00000343905:F126L	F	+	3	2	DUSP19	183668508	1.000000	0.71417	0.990000	0.47175	0.794000	0.44872	0.855000	0.27805	0.427000	0.26145	0.482000	0.46254	TTT		0.413	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			G	183960263	T	G	183960263	3	3	61	1	0	0	0	0	1	0	0	0	4829	1838	64	4	545	4	DUSP19	2	183960263	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8430	183960263	59239110	1967	9952										
ZNF804A	91752	broad.mit.edu	37	chr2	185463741	185463741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcagcaacggacactttCgcaacatcaagggagttttc	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:185463741C>T	ENST00000302277.6	+	1	649	c.55C>T	c.(55-57)Cgc>Tgc	p.R19C		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	19							metal ion binding (GO:0046872)	p.R19C(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CGGACACTTTCGCAACATCAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	78	78					2																	185463741		2203	4300	6503	185171986	SO:0001583	missense	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.55C>T	2.37:g.185463741C>T	ENSP00000303252:p.Arg19Cys		185171986	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626554	0.87560	.	.	ENSG00000170396	ENST00000302277	T	0.11712	2.75	4.04	4.04	0.47022	.	0.000000	0.32753	U	0.005690	T	0.21062	0.0507	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03898	-1.0994	10	0.87932	D	0	.	14.8266	0.70117	0.0:1.0:0.0:0.0	.	19	Q7Z570	Z804A_HUMAN	C	19	ENSP00000303252:R19C	ENSP00000303252:R19C	R	+	1	0	ZNF804A	185171986	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.756000	0.74919	1.803000	0.52742	0.650000	0.86243	CGC		0.552	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185463741	C	T	185463741	3	4	61	1	0	0	0	0	1	0	0	0	18209	884	31	1	57	1	ZNF804A	2	185463741	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1503478	185463741	57735632	1968	9953										
ZNF804A	91752	broad.mit.edu	37	chr2	185801207	185801207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttaggaaataaatccacaGttcttgacatgtctaatgat	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:185801207G>T	ENST00000302277.6	+	4	1678	c.1084G>T	c.(1084-1086)Gtt>Ttt	p.V362F		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	362							metal ion binding (GO:0046872)	p.V362F(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TAAATCCACAGTTCTTGACAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	54	55					2																	185801207		2203	4300	6503	185509452	SO:0001583	missense	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1084G>T	2.37:g.185801207G>T	ENSP00000303252:p.Val362Phe		185509452	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	3.660	-0.069626	0.07228	.	.	ENSG00000170396	ENST00000302277	T	0.50813	0.73	5.6	-0.764	0.11027	.	2.163160	0.01787	N	0.032085	T	0.38453	0.1041	L	0.56769	1.78	0.09310	N	1	P	0.41265	0.744	B	0.34180	0.177	T	0.21381	-1.0247	10	0.35671	T	0.21	1.2065	2.4948	0.04619	0.2753:0.1134:0.4946:0.1167	.	362	Q7Z570	Z804A_HUMAN	F	362	ENSP00000303252:V362F	ENSP00000303252:V362F	V	+	1	0	ZNF804A	185509452	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.420000	0.21263	-0.183000	0.10585	-0.958000	0.02645	GTT		0.368	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185801207	G	T	185801207	3	4	61	1	0	0	0	0	1	0	0	0	18209	1029	36	2	1098	2	ZNF804A	2	185801207	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	337466	185801207	57398166	1969	9954										
ZNF804A	91752	broad.mit.edu	37	chr2	185802023	185802023	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaaatgctgggaaatatCtattggaaccaatttcagaa	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:185802023C>A	ENST00000302277.6	+	4	2494	c.1900C>A	c.(1900-1902)Cta>Ata	p.L634I		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	634							metal ion binding (GO:0046872)	p.L634I(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TGGGAAATATCTATTGGAACC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	106	103					2																	185802023		2203	4296	6499	185510268	SO:0001583	missense	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1900C>A	2.37:g.185802023C>A	ENSP00000303252:p.Leu634Ile		185510268	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	4.068	0.010449	0.07912	.	.	ENSG00000170396	ENST00000302277	T	0.05996	3.36	5.51	1.36	0.22044	.	1.284690	0.05745	N	0.602125	T	0.05960	0.0155	L	0.44542	1.39	0.09310	N	1	B	0.26195	0.144	B	0.18561	0.022	T	0.42849	-0.9427	10	0.33940	T	0.23	-0.2628	2.4147	0.04433	0.1156:0.4572:0.186:0.2412	.	634	Q7Z570	Z804A_HUMAN	I	634	ENSP00000303252:L634I	ENSP00000303252:L634I	L	+	1	2	ZNF804A	185510268	0.000000	0.05858	0.019000	0.16419	0.343000	0.28985	-1.965000	0.01511	0.290000	0.22444	0.655000	0.94253	CTA		0.358	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185802023	C	A	185802023	3	1	61	1	0	0	0	0	1	0	0	0	18209	912	32	2	1914	2	ZNF804A	2	185802023	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	816	185802023	57397350	1970	9955										
ZNF804A	91752	broad.mit.edu	37	chr2	185803350	185803350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccagctgccctcccacCccctagcacacctctgcagc	5	23	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:185803350C>T	ENST00000302277.6	+	4	3821	c.3227C>T	c.(3226-3228)cCc>cTc	p.P1076L		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1076							metal ion binding (GO:0046872)	p.P1076L(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						GCCCTCCCACCCCCTAGCACA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	87	89					2																	185803350		2203	4300	6503	185511595	SO:0001583	missense	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3227C>T	2.37:g.185803350C>T	ENSP00000303252:p.Pro1076Leu		185511595	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	5.053	0.195496	0.09599	.	.	ENSG00000170396	ENST00000302277	T	0.06687	3.27	4.54	3.66	0.41972	.	0.000000	0.38492	N	0.001673	T	0.11922	0.0290	L	0.55481	1.735	0.09310	N	0.999999	P	0.50066	0.931	P	0.45310	0.476	T	0.06625	-1.0816	10	0.66056	D	0.02	-10.5656	11.3835	0.49771	0.0:0.9125:0.0:0.0875	.	1076	Q7Z570	Z804A_HUMAN	L	1076	ENSP00000303252:P1076L	ENSP00000303252:P1076L	P	+	2	0	ZNF804A	185511595	0.054000	0.20591	0.043000	0.18650	0.273000	0.26683	3.157000	0.50716	1.124000	0.41980	0.313000	0.20887	CCC		0.493	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185803350	C	T	185803350	3	4	61	1	0	0	0	0	1	0	0	0	18209	623	22	3	3241	3	ZNF804A	2	185803350	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1327	185803350	57396023	1971	9956										
FSIP2	401024	broad.mit.edu	37	chr2	186670828	186670828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacagaatatgagaaggaaGtacttggatcagattctgaa	10	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:186670828G>A	ENST00000424728.1	+	17	16795	c.16795G>A	c.(16795-16797)Gta>Ata	p.V5599I	FSIP2_ENST00000343098.5_Missense_Mutation_p.V5688I			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5599								p.V297I(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TGAGAAGGAAGTACTTGGATC	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	2											65	67	66					2																	186670828		1813	4059	5872	186379073	SO:0001583	missense	401024			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.16795G>A	2.37:g.186670828G>A	ENSP00000401306:p.Val5599Ile		186379073	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	G	4.332	0.061022	0.08339	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.43688	0.94;0.95	5.32	-0.187	0.13268	.	.	.	.	.	T	0.18676	0.0448	N	0.11201	0.11	0.09310	N	1	.	.	.	.	.	.	T	0.28106	-1.0054	7	0.10377	T	0.69	.	7.5712	0.27909	0.6123:0.0:0.3877:0.0	.	.	.	.	I	5688;5599	ENSP00000344403:V5688I;ENSP00000401306:V5599I	ENSP00000344403:V5688I	V	+	1	0	FSIP2	186379073	0.001000	0.12720	0.000000	0.03702	0.283000	0.27025	0.678000	0.25277	0.051000	0.15978	-0.229000	0.12294	GTA		0.303	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186670828	G	A	186670828	3	1	61	1	0	0	0	0	1	0	0	0	6094	1029	36	3	17128	3	FSIP2	2	186670828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	867478	186670828	56528545	1972	9957										
FSIP2	401024	broad.mit.edu	37	chr2	186672797	186672797	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgaaaacatagttaattCtatttataccagtgttttaa	4	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:186672797C>A	ENST00000424728.1	+	17	18764	c.18764C>A	c.(18763-18765)tCt>tAt	p.S6255Y	FSIP2_ENST00000343098.5_Missense_Mutation_p.S6344Y			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6255								p.S953Y(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						ATAGTTAATTCTATTTATACC	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	2											36	34	34					2																	186672797		1807	4060	5867	186381042	SO:0001583	missense	401024			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18764C>A	2.37:g.186672797C>A	ENSP00000401306:p.Ser6255Tyr		186381042	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	C	0.733	-0.779053	0.02929	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.55588	0.51;0.51	5.2	2.16	0.27623	.	0.555584	0.16574	N	0.208467	T	0.43722	0.1260	N	0.19112	0.55	0.22081	N	0.999378	.	.	.	.	.	.	T	0.42447	-0.9451	8	0.87932	D	0	.	12.6787	0.56910	0.4149:0.5851:0.0:0.0	.	.	.	.	Y	6344;6255	ENSP00000344403:S6344Y;ENSP00000401306:S6255Y	ENSP00000344403:S6344Y	S	+	2	0	FSIP2	186381042	0.996000	0.38824	0.738000	0.30950	0.005000	0.04900	0.919000	0.28692	0.349000	0.23975	-2.941000	0.00086	TCT		0.333	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186672797	C	A	186672797	3	1	61	1	0	0	0	0	1	0	0	0	6094	913	32	2	19097	2	FSIP2	2	186672797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1969	186672797	56526576	1973	9958										
FSIP2	401024	broad.mit.edu	37	chr2	186673493	186673493	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagagctagacgttaataGaattgttcaaaaggcccaag	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:186673493G>T	ENST00000424728.1	+	17	19460	c.19460G>T	c.(19459-19461)aGa>aTa	p.R6487I	FSIP2_ENST00000343098.5_Missense_Mutation_p.R6576I			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6487								p.R1185I(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GACGTTAATAGAATTGTTCAA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	2											58	56	56					2																	186673493		1822	4062	5884	186381738	SO:0001583	missense	401024			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19460G>T	2.37:g.186673493G>T	ENSP00000401306:p.Arg6487Ile		186381738	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	G	16.23	3.064327	0.55432	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.58652	0.32;0.33	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000027	T	0.59528	0.2200	L	0.34521	1.04	0.48135	D	0.99959	.	.	.	.	.	.	T	0.61093	-0.7132	8	0.66056	D	0.02	.	14.6656	0.68904	0.0:0.0:1.0:0.0	.	.	.	.	I	6576;6487	ENSP00000344403:R6576I;ENSP00000401306:R6487I	ENSP00000344403:R6576I	R	+	2	0	FSIP2	186381738	0.972000	0.33761	0.900000	0.35374	0.106000	0.19336	1.694000	0.37752	2.838000	0.97847	0.591000	0.81541	AGA		0.323	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186673493	G	T	186673493	3	4	61	1	0	0	0	0	1	0	0	0	6094	942	33	2	19793	2	FSIP2	2	186673493	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	696	186673493	56525880	1974	9959										
ITGAV	3685	broad.mit.edu	37	chr2	187521024	187521024	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagcaaaagggagcaattCgacgagcactgtttctctac	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187521024C>T	ENST00000261023.3	+	17	1889	c.1615C>T	c.(1615-1617)Cga>Tga	p.R539*	ITGAV_ENST00000374907.3_Nonsense_Mutation_p.R503*|ITGAV_ENST00000433736.2_Nonsense_Mutation_p.R493*|AC017101.10_ENST00000453665.1_RNA	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	539					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.R539*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	GGGAGCAATTCGACGAGCACT	0.413																																					Melanoma(58;108 1995 6081)											1	Substitution - Nonsense(1)	large_intestine(1)	2											194	192	193					2																	187521024		2203	4300	6503	187229269	SO:0001587	stop_gained	3685				CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.1615C>T	2.37:g.187521024C>T	ENSP00000261023:p.Arg539*		187229269	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Nonsense_Mutation	SNP	ENST00000261023.3	37	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	C	40	8.372834	0.98781	.	.	ENSG00000138448	ENST00000261023;ENST00000374907;ENST00000433736	.	.	.	5.41	4.45	0.53987	.	0.048889	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8473	0.57837	0.2485:0.7515:0.0:0.0	.	.	.	.	X	539;503;493	.	ENSP00000261023:R539X	R	+	1	2	ITGAV	187229269	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.006000	0.63978	2.541000	0.85698	0.455000	0.32223	CGA		0.413	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		T	187521024	C	T	187521024	4	4	61	1	0	0	0	0	0	1	0	0	7909	876	31	1	1732	1	ITGAV	2	187521024	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	847531	187521024	55678349	1975	9960										
ITGAV	3685	broad.mit.edu	37	chr2	187532454	187532454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgggagcacaaggagaAccctgagactgaagaagatg	13	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187532454A>G	ENST00000261023.3	+	24	2658	c.2384A>G	c.(2383-2385)aAc>aGc	p.N795S	ITGAV_ENST00000374907.3_Missense_Mutation_p.N759S|ITGAV_ENST00000433736.2_Missense_Mutation_p.N749S|AC017101.10_ENST00000453665.1_RNA	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	795					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.N795S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CACAAGGAGAACCCTGAGACT	0.428																																					Melanoma(58;108 1995 6081)											1	Substitution - Missense(1)	large_intestine(1)	2											150	144	146					2																	187532454		2203	4300	6503	187240699	SO:0001583	missense	3685				CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2384A>G	2.37:g.187532454A>G	ENSP00000261023:p.Asn795Ser		187240699	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	37	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.705684	0.30232	.	.	ENSG00000138448	ENST00000261023;ENST00000374907;ENST00000433736	T;T;T	0.44482	0.92;0.92;0.92	5.51	4.34	0.51931	Integrin alpha-2 (1);	0.324637	0.36101	N	0.002781	T	0.32912	0.0845	L	0.38175	1.15	0.47065	D	0.9993	B;B;B	0.18166	0.01;0.011;0.026	B;B;B	0.18871	0.023;0.009;0.023	T	0.05716	-1.0868	10	0.25106	T	0.35	.	12.8457	0.57829	0.864:0.136:0.0:0.0	.	749;759;795	E7EWZ6;P06756-2;P06756	.;.;ITAV_HUMAN	S	795;759;749	ENSP00000261023:N795S;ENSP00000364042:N759S;ENSP00000404291:N749S	ENSP00000261023:N795S	N	+	2	0	ITGAV	187240699	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.661000	0.61518	0.895000	0.36342	0.528000	0.53228	AAC		0.428	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		G	187532454	A	G	187532454	3	3	61	1	0	0	0	0	1	0	0	0	7909	43	2	4	2529	4	ITGAV	2	187532454	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11430	187532454	55666919	1976	9961										
ITGAV	3685	broad.mit.edu	37	chr2	187540572	187540572	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcagaatcattcctattCtctgaagtcgtctgcttcat	5	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187540572C>A	ENST00000261023.3	+	28	3120	c.2846C>A	c.(2845-2847)tCt>tAt	p.S949Y	ITGAV_ENST00000374907.3_Missense_Mutation_p.S913Y|ITGAV_ENST00000433736.2_Missense_Mutation_p.S903Y|AC017101.10_ENST00000453665.1_RNA	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	949					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.S949Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CATTCCTATTCTCTGAAGTCG	0.333																																					Melanoma(58;108 1995 6081)											1	Substitution - Missense(1)	large_intestine(1)	2											67	68	68					2																	187540572		2203	4299	6502	187248817	SO:0001583	missense	3685				CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2846C>A	2.37:g.187540572C>A	ENSP00000261023:p.Ser949Tyr		187248817	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	37	CCDS2292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.96|18.96	3.733361|3.733361	0.69189|0.69189	.|.	.|.	ENSG00000138448|ENSG00000138448	ENST00000430709|ENST00000261023;ENST00000374907;ENST00000433736	.|T;T;T	.|0.50001	.|0.76;0.76;0.76	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.219770	.|0.40385	.|N	.|0.001110	T|T	0.61135|0.61135	0.2323|0.2323	L|L	0.59436|0.59436	1.845|1.845	0.42832|0.42832	D|D	0.994024|0.994024	.|P;D;P	.|0.54047	.|0.924;0.964;0.956	.|P;P;P	.|0.55824	.|0.459;0.785;0.459	T|T	0.64786|0.64786	-0.6325|-0.6325	5|10	.|0.62326	.|D	.|0.03	.|.	18.2525|18.2525	0.90009|0.90009	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|903;913;949	.|E7EWZ6;P06756-2;P06756	.|.;.;ITAV_HUMAN	I|Y	100|949;913;903	.|ENSP00000261023:S949Y;ENSP00000364042:S913Y;ENSP00000404291:S903Y	.|ENSP00000261023:S949Y	L|S	+|+	1|2	0|0	ITGAV|ITGAV	187248817|187248817	0.994000|0.994000	0.37717|0.37717	0.999000|0.999000	0.59377|0.59377	0.967000|0.967000	0.64934|0.64934	4.557000|4.557000	0.60782|0.60782	2.547000|2.547000	0.85894|0.85894	0.563000|0.563000	0.77884|0.77884	CTC|TCT		0.333	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		A	187540572	C	A	187540572	3	1	61	1	0	0	0	0	1	0	0	0	7909	913	32	2	3007	2	ITGAV	2	187540572	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8118	187540572	55658801	1977	9962										
FAM171B	165215	broad.mit.edu	37	chr2	187626444	187626444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatggtaaaaactcgggacGattttaaaatctacaatgaa	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187626444G>A	ENST00000304698.5	+	8	1578	c.1375G>A	c.(1375-1377)Gat>Aat	p.D459N		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	459						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.D459N(3)|p.D459H(1)		NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AACTCGGGACGATTTTAAAAT	0.368																																																4	Substitution - Missense(4)	large_intestine(2)|lung(1)|endometrium(1)	2											48	52	50					2																	187626444		2201	4297	6498	187334689	SO:0001583	missense	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1375G>A	2.37:g.187626444G>A	ENSP00000304108:p.Asp459Asn		187334689	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.855|1.855	-0.463988|-0.463988	0.04476|0.04476	.|.	.|.	ENSG00000144369|ENSG00000144369	ENST00000304698|ENST00000272804	T|.	0.30448|.	1.53|.	5.93|5.93	0.838|0.838	0.18902|0.18902	.|.	0.439260|.	0.28214|.	N|.	0.016164|.	T|T	0.08670|0.08670	0.0215|0.0215	N|N	0.02011|0.02011	-0.69|-0.69	0.23293|0.23293	N|N	0.997969|0.997969	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.36553|0.36553	-0.9743|-0.9743	10|6	0.02654|0.02654	T|T	1|1	-9.6007|-9.6007	5.3765|5.3765	0.16168|0.16168	0.5715:0.281:0.1475:0.0|0.5715:0.281:0.1475:0.0	.|.	459;460|.	Q6P995;A8K122|.	F171B_HUMAN;.|.	N|Q	459|426	ENSP00000304108:D459N|.	ENSP00000304108:D459N|ENSP00000272804:R426Q	D|R	+|+	1|2	0|0	FAM171B|FAM171B	187334689|187334689	0.998000|0.998000	0.40836|0.40836	0.990000|0.990000	0.47175|0.47175	0.974000|0.974000	0.67602|0.67602	1.698000|1.698000	0.37794|0.37794	0.114000|0.114000	0.18032|0.18032	-0.302000|-0.302000	0.09304|0.09304	GAT|CGA		0.368	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187626444	G	A	187626444	3	1	61	1	0	0	0	0	1	0	0	0	5507	1058	37	1	1405	1	FAM171B	2	187626444	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85872	187626444	55572929	1978	9963										
FAM171B	165215	broad.mit.edu	37	chr2	187627140	187627140	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgaggcactcctttataGacctgaaaaagggcaagaga	11	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187627140G>T	ENST00000304698.5	+	8	2274	c.2071G>T	c.(2071-2073)Gac>Tac	p.D691Y		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	691						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.D691Y(1)		NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CTCCTTTATAGACCTGAAAAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											62	65	64					2																	187627140		2203	4300	6503	187335385	SO:0001583	missense	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.2071G>T	2.37:g.187627140G>T	ENSP00000304108:p.Asp691Tyr		187335385	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122879	0.77436	.	.	ENSG00000144369	ENST00000304698	T	0.59083	0.29	6.02	6.02	0.97574	.	0.047134	0.85682	D	0.000000	T	0.74741	0.3756	L	0.60455	1.87	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.71184	0.972;0.972	T	0.74717	-0.3571	10	0.87932	D	0	-21.8107	20.547	0.99278	0.0:0.0:1.0:0.0	.	691;692	Q6P995;A8K122	F171B_HUMAN;.	Y	691	ENSP00000304108:D691Y	ENSP00000304108:D691Y	D	+	1	0	FAM171B	187335385	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.623000	0.83113	2.850000	0.98022	0.650000	0.86243	GAC		0.522	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		T	187627140	G	T	187627140	3	4	61	1	0	0	0	0	1	0	0	0	5507	942	33	2	2101	2	FAM171B	2	187627140	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	696	187627140	55572233	1979	9964										
ZSWIM2	151112	broad.mit.edu	37	chr2	187693219	187693219	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatagattatctattgttGtattttcataggcatctttt	6	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187693219G>T	ENST00000295131.2	-	9	1433	c.1394C>A	c.(1393-1395)aCa>aAa	p.T465K		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	465					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T465K(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATCTATTGTTGTATTTTCATA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	54	52					2																	187693219		2196	4293	6489	187401464	SO:0001583	missense	151112			AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1394C>A	2.37:g.187693219G>T	ENSP00000295131:p.Thr465Lys		187401464	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	g	3.985	-0.005556	0.07773	.	.	ENSG00000163012	ENST00000295131	T	0.21932	1.98	5.6	3.19	0.36642	.	0.626400	0.15219	N	0.274028	T	0.10380	0.0254	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24870	-1.0148	10	0.87932	D	0	-0.9495	6.0287	0.19669	0.7779:0.0:0.0786:0.1434	.	465	Q8NEG5	ZSWM2_HUMAN	K	465	ENSP00000295131:T465K	ENSP00000295131:T465K	T	-	2	0	ZSWIM2	187401464	0.939000	0.31865	0.001000	0.08648	0.000000	0.00434	2.288000	0.43514	0.389000	0.25086	-0.374000	0.07098	ACA		0.284	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		T	187693219	G	T	187693219	3	4	61	1	0	0	0	0	1	0	0	0	18280	1377	48	2	511	2	ZSWIM2	2	187693219	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66079	187693219	55506154	1980	9965										
ZSWIM2	151112	broad.mit.edu	37	chr2	187702088	187702088	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttattacagggaatcccaaGgtgtttgtccagtctctctt	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:187702088G>T	ENST00000295131.2	-	5	727	c.688C>A	c.(688-690)Ctt>Att	p.L230I		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	230					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L230I(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			GGAATCCCAAGGTGTTTGTCC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	120	121					2																	187702088		2203	4300	6503	187410333	SO:0001583	missense	151112			AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.688C>A	2.37:g.187702088G>T	ENSP00000295131:p.Leu230Ile		187410333	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578643	0.86645	.	.	ENSG00000163012	ENST00000295131	D	0.87966	-2.32	5.77	5.77	0.91146	Zinc finger, ZZ-type (2);	0.000000	0.45126	D	0.000386	D	0.91821	0.7412	L	0.58669	1.825	0.46631	D	0.999134	D	0.64830	0.994	D	0.67103	0.949	D	0.91804	0.5454	10	0.59425	D	0.04	-15.951	16.8897	0.86084	0.0:0.0:1.0:0.0	.	230	Q8NEG5	ZSWM2_HUMAN	I	230	ENSP00000295131:L230I	ENSP00000295131:L230I	L	-	1	0	ZSWIM2	187410333	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.134000	0.77268	2.729000	0.93468	0.591000	0.81541	CTT		0.363	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		T	187702088	G	T	187702088	3	4	61	1	0	0	0	0	1	0	0	0	18280	1000	35	2	1233	2	ZSWIM2	2	187702088	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8869	187702088	55497285	1981	9966										
TFPI	7035	broad.mit.edu	37	chr2	188343478	188343478	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaggcgttcagaaagacTtggtaaatatgagccgcatt	11	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:188343478T>G	ENST00000233156.3	-	6	923				AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000392365.1_Intron|TFPI_ENST00000409676.1_Missense_Mutation_p.Q227H|TFPI_ENST00000339091.4_Missense_Mutation_p.Q227H|AC007319.1_ENST00000453517.1_RNA	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)						blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q227H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	TCAGAAAGACTTGGTAAATAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											148	131	137					2																	188343478		2203	4300	6503	188051723	SO:0001627	intron_variant	7035				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.628+5372A>C	2.37:g.188343478T>G			188051723	O95103|Q53TS4	Missense_Mutation	SNP	ENST00000233156.3	37	CCDS2294.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.738869	0.69304	.	.	ENSG00000003436	ENST00000409676;ENST00000339091	T;T	0.66995	-0.24;-0.24	4.72	4.72	0.59763	.	.	.	.	.	T	0.78329	0.4266	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.78211	-0.2292	8	0.40728	T	0.16	.	11.9624	0.53015	0.0:0.0:0.0:1.0	.	227	P10646-2	.	H	227	ENSP00000386344:Q227H;ENSP00000342306:Q227H	ENSP00000342306:Q227H	Q	-	3	2	TFPI	188051723	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.777000	0.38604	1.738000	0.51689	0.455000	0.32223	CAA		0.343	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		G	188343478	T	G	188343478	1	3	61	0	1	0	0	0	0	0	0	0	15847	1606	56	4		4	TFPI	2	188343478	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	641390	188343478	54855895	1982	9967										
TFPI	7035	broad.mit.edu	37	chr2	188368484	188368484	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcatgtactttcttcatTgtgtaaatcatctctgaaat	6	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:188368484T>G	ENST00000233156.3	-	2	306	c.12A>C	c.(10-12)acA>acC	p.T4T	AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000392365.1_Silent_p.T4T|TFPI_ENST00000409676.1_Silent_p.T4T|TFPI_ENST00000339091.4_Silent_p.T4T|AC007319.1_ENST00000453517.1_RNA	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	4					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T4T(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	CTTTCTTCATTGTGTAAATCA	0.373																																																2	Substitution - coding silent(2)	large_intestine(2)	2											118	112	114					2																	188368484		2203	4300	6503	188076729	SO:0001819	synonymous_variant	7035				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.12A>C	2.37:g.188368484T>G			188076729	O95103|Q53TS4	Silent	SNP	ENST00000233156.3	37	CCDS2294.1																																																																																				0.373	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		G	188368484	T	G	188368484	2	3	61	1	0	0	0	0	0	0	0	1	15847	1799	63	4		4	TFPI	2	188368484	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	25006	188368484	54830889	1983	9968										
GULP1	51454	broad.mit.edu	37	chr2	189393889	189393889	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggagttgcaaatatcaatTtatggagtaaaaattctaga	9	3	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:189393889T>G	ENST00000409580.1	+	7	942	c.228T>G	c.(226-228)atT>atG	p.I76M	GULP1_ENST00000359135.3_Missense_Mutation_p.I76M|GULP1_ENST00000409843.1_Missense_Mutation_p.I76M|GULP1_ENST00000410051.1_Missense_Mutation_p.I76M|GULP1_ENST00000409609.1_Missense_Mutation_p.I76M|GULP1_ENST00000409805.1_Intron|GULP1_ENST00000409830.1_Missense_Mutation_p.I76M|GULP1_ENST00000409637.3_Missense_Mutation_p.I76M|GULP1_ENST00000479019.1_3'UTR			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	76	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)	p.I76M(1)		endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			AAATATCAATTTATGGAGTAA	0.294																																					Pancreas(178;563 2065 20199 42378 52815)											1	Substitution - Missense(1)	large_intestine(1)	2											42	48	46					2																	189393889		2195	4282	6477	189102134	SO:0001583	missense	51454			AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.228T>G	2.37:g.189393889T>G	ENSP00000386289:p.Ile76Met		189102134	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Missense_Mutation	SNP	ENST00000409580.1	37	CCDS2295.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246274	0.59103	.	.	ENSG00000144366	ENST00000409843;ENST00000409830;ENST00000410051;ENST00000359135;ENST00000409580;ENST00000409637;ENST00000409609	T;T;T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12;2.12;2.12	5.53	4.36	0.52297	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.053403	0.85682	D	0.000000	T	0.34890	0.0913	L	0.55213	1.73	0.58432	D	0.999994	D;P;D	0.76494	0.999;0.946;0.999	D;P;D	0.87578	0.998;0.823;0.996	T	0.11891	-1.0569	10	0.48119	T	0.1	-8.5929	4.5217	0.11962	0.3033:0.0809:0.0:0.6158	.	76;76;76	Q9UBP9;B8ZZ72;Q9UBP9-2	GULP1_HUMAN;.;.	M	76	ENSP00000387144:I76M;ENSP00000386732:I76M;ENSP00000387013:I76M;ENSP00000352047:I76M;ENSP00000386289:I76M;ENSP00000386402:I76M;ENSP00000386867:I76M	ENSP00000352047:I76M	I	+	3	3	GULP1	189102134	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.310000	0.33551	0.899000	0.36444	0.528000	0.53228	ATT		0.294	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		G	189393889	T	G	189393889	3	3	61	1	0	0	0	0	1	0	0	0	6922	1829	64	4	242	4	GULP1	2	189393889	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1025405	189393889	53805484	1984	9969										
COL3A1	1281	broad.mit.edu	37	chr2	189849587	189849587	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtgactcaggatccgttCtctgcgatgacataatatgt	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:189849587C>A	ENST00000304636.3	+	2	351	c.181C>A	c.(181-183)Ctc>Atc	p.L61I	COL3A1_ENST00000317840.5_Missense_Mutation_p.L61I	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	61	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.L61I(1)		NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	AGGATCCGTTCTCTGCGATGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											160	137	145					2																	189849587		2203	4299	6502	189557832	SO:0001583	missense	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.181C>A	2.37:g.189849587C>A	ENSP00000304408:p.Leu61Ile		189557832	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595235	0.86953	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	T;T	0.72051	-0.62;-0.62	5.19	5.19	0.71726	von Willebrand factor, type C (4);	0.000000	0.41396	D	0.000893	T	0.79203	0.4406	L	0.55990	1.75	0.54753	D	0.99998	D	0.63046	0.992	P	0.61070	0.883	T	0.75306	-0.3364	10	0.27082	T	0.32	.	19.0681	0.93122	0.0:1.0:0.0:0.0	.	61	P02461	CO3A1_HUMAN	I	61	ENSP00000304408:L61I;ENSP00000315243:L61I	ENSP00000304408:L61I	L	+	1	0	COL3A1	189557832	0.977000	0.34250	1.000000	0.80357	0.919000	0.55068	2.363000	0.44178	2.573000	0.86826	0.467000	0.42956	CTC		0.473	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189849587	C	A	189849587	3	1	61	1	0	0	0	0	1	0	0	0	3694	913	32	2	187	2	COL3A1	2	189849587	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455698	189849587	53349786	1985	9970										
COL5A2	1290	broad.mit.edu	37	chr2	189923576	189923576	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagattaaaatacttactCtaggtcctaacgggccaact	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:189923576C>A	ENST00000374866.3	-	32	2403	c.2129G>T	c.(2128-2130)aGa>aTa	p.R710I		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	710					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.R710I(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			AATACTTACTCTAGGTCCTAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											43	44	44					2																	189923576		2203	4300	6503	189631821	SO:0001630	splice_region_variant	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.2130+1G>T	2.37:g.189923576C>A			189631821	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.393887	0.83011	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.93547	-3.24	5.52	5.52	0.82312	.	0.000000	0.53938	D	0.000055	D	0.96090	0.8726	M	0.62266	1.93	0.80722	D	1	D;D	0.65815	0.995;0.985	D;D	0.77004	0.986;0.989	D	0.95347	0.8443	9	.	.	.	.	19.0449	0.93015	0.0:1.0:0.0:0.0	.	350;710	Q5PR22;P05997	.;CO5A2_HUMAN	I	710;350	ENSP00000364000:R710I	.	R	-	2	0	COL5A2	189631821	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.485000	0.81204	2.587000	0.87381	0.563000	0.77884	AGA		0.343	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	Missense_Mutation	A	189923576	C	A	189923576	5	1	61	1	0	0	0	0	0	0	1	0	3703	927	32	2	2462	2	COL5A2	2	189923576	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73989	189923576	53275797	1986	9971										
ANKAR	150709	broad.mit.edu	37	chr2	190584461	190584461	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctactggtttgtgatgaGcctgaagtacactctcgctg	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:190584461G>A	ENST00000520309.1	+	11	2476	c.2388G>A	c.(2386-2388)gaG>gaA	p.E796E	ANKAR_ENST00000438402.2_Silent_p.E796E|ANKAR_ENST00000431575.2_Silent_p.E725E|ANKAR_ENST00000313581.4_Silent_p.E796E|ANKAR_ENST00000281412.6_Silent_p.E560E	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	796						integral component of membrane (GO:0016021)		p.E725E(1)		breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			TTTGTGATGAGCCTGAAGTAC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											140	122	128					2																	190584461		2203	4300	6503	190292706	SO:0001819	synonymous_variant	150709			AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2388G>A	2.37:g.190584461G>A			190292706	Q3ZCS6|Q4G0M2|Q6ZU02	Silent	SNP	ENST00000520309.1	37	CCDS33351.2																																																																																				0.393	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		A	190584461	G	A	190584461	2	1	61	1	0	0	0	0	0	0	0	1	623	962	34	3		3	ANKAR	2	190584461	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	660885	190584461	52614912	1987	9972										
ANKAR	150709	broad.mit.edu	37	chr2	190592792	190592792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagcatttctggaaaaatCgttaactaaatatcttttaa	5	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:190592792C>T	ENST00000520309.1	+	13	2934	c.2846C>T	c.(2845-2847)tCg>tTg	p.S949L	ANKAR_ENST00000438402.2_Missense_Mutation_p.S949L|ANKAR_ENST00000431575.2_Missense_Mutation_p.S878L|ANKAR_ENST00000313581.4_Missense_Mutation_p.S949L|ANKAR_ENST00000281412.6_Missense_Mutation_p.S724L	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	949						integral component of membrane (GO:0016021)		p.S878L(1)		breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			CTGGAAAAATCGTTAACTAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	2											45	50	48					2																	190592792		2202	4300	6502	190301037	SO:0001583	missense	150709			AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2846C>T	2.37:g.190592792C>T	ENSP00000427882:p.Ser949Leu		190301037	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	37	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	C	12.30	1.895509	0.33442	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412;ENST00000374838	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.43	3.53	0.40419	.	0.748575	0.11776	N	0.530648	T	0.23532	0.0569	L	0.51422	1.61	0.09310	N	1	P	0.49358	0.923	B	0.34180	0.177	T	0.13442	-1.0509	10	0.59425	D	0.04	-0.5776	7.9392	0.29948	0.2094:0.7033:0.0:0.0873	.	25	E9PHS9	.	L	949;949;949;878;724;25	ENSP00000427882:S949L;ENSP00000313513:S949L;ENSP00000397243:S949L;ENSP00000393043:S878L;ENSP00000281412:S724L	ENSP00000281412:S724L	S	+	2	0	ANKAR	190301037	0.046000	0.20272	0.001000	0.08648	0.840000	0.47671	2.106000	0.41835	0.743000	0.32719	0.563000	0.77884	TCG		0.313	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		T	190592792	C	T	190592792	3	4	61	1	0	0	0	0	1	0	0	0	623	893	31	1	2892	1	ANKAR	2	190592792	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8331	190592792	52606581	1988	9973										
ANKAR	150709	broad.mit.edu	37	chr2	190603401	190603401	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagacttctactattgtCttgacaggtaagaaatgact	8	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:190603401C>A	ENST00000520309.1	+	19	3781	c.3693C>A	c.(3691-3693)gtC>gtA	p.V1231V	ANKAR_ENST00000438402.2_3'UTR|ANKAR_ENST00000431575.2_Silent_p.V1160V|ANKAR_ENST00000313581.4_Silent_p.V1231V|ANKAR_ENST00000281412.6_3'UTR	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	1231						integral component of membrane (GO:0016021)		p.V1160V(1)		breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			CTACTATTGTCTTGACAGGTA	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	2											113	109	110					2																	190603401		2202	4300	6502	190311646	SO:0001819	synonymous_variant	150709			AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.3693C>A	2.37:g.190603401C>A			190311646	Q3ZCS6|Q4G0M2|Q6ZU02	Silent	SNP	ENST00000520309.1	37	CCDS33351.2																																																																																				0.299	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		A	190603401	C	A	190603401	2	1	61	1	0	0	0	0	0	0	0	1	623	900	32	2		2	ANKAR	2	190603401	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10609	190603401	52595972	1989	9974										
PMS1	5378	broad.mit.edu	37	chr2	190660567	190660567	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctgttgatgcacctgtaAtggcaatgaagtactacacc	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:190660567A>C	ENST00000441310.2	+	3	438	c.205A>C	c.(205-207)Atg>Ctg	p.M69L	PMS1_ENST00000374826.4_Missense_Mutation_p.M69L|PMS1_ENST00000418224.3_5'UTR|PMS1_ENST00000447232.2_Missense_Mutation_p.M69L|PMS1_ENST00000432292.3_Intron|PMS1_ENST00000409985.1_Missense_Mutation_p.M69L|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000409823.3_Missense_Mutation_p.M69L	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	69					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)	p.M69L(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TGCACCTGTAATGGCAATGAA	0.368			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																														yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	1	Substitution - Missense(1)	large_intestine(1)	2											100	98	99					2																	190660567		2203	4300	6503	190368812	SO:0001583	missense	5378				CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.205A>C	2.37:g.190660567A>C	ENSP00000406490:p.Met69Leu		190368812	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	37	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254404	0.59212	.	.	ENSG00000064933	ENST00000441310;ENST00000409985;ENST00000409823;ENST00000374826;ENST00000424766;ENST00000447232;ENST00000420421	T;T;T;T;T;T;D	0.88354	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-2.37	5.78	5.78	0.91487	DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.101045	0.85682	D	0.000000	D	0.88562	0.6470	N	0.13140	0.3	0.80722	D	1	P;P;P;P;P;B;B	0.50156	0.756;0.642;0.898;0.932;0.549;0.379;0.379	P;P;P;D;P;P;P	0.63793	0.678;0.673;0.823;0.918;0.708;0.549;0.627	D	0.87833	0.2646	10	0.28530	T	0.3	-14.5419	16.1121	0.81271	1.0:0.0:0.0:0.0	.	69;69;69;69;69;69;69	B4DMF4;E9PC40;Q5FBZ4;Q5FBZ9;Q5FBZ3;Q5FBZ8;P54277	.;.;.;.;.;.;PMS1_HUMAN	L	69	ENSP00000406490:M69L;ENSP00000386623:M69L;ENSP00000387125:M69L;ENSP00000363959:M69L;ENSP00000410082:M69L;ENSP00000401064:M69L;ENSP00000391136:M69L	ENSP00000343888:M69L	M	+	1	0	PMS1	190368812	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	9.288000	0.96055	2.213000	0.71641	0.519000	0.50382	ATG		0.368	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			C	190660567	A	C	190660567	3	2	61	1	0	0	0	0	1	0	0	0	12173	101	4	4	211	4	PMS1	2	190660567	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	57166	190660567	52538806	1990	9975										
STAT4	6775	broad.mit.edu	37	chr2	191919243	191919243	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttacctccagcactggaCttcatttcctttggttgctt	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:191919243C>G	ENST00000392320.2	-	14	1538	c.1224G>C	c.(1222-1224)aaG>aaC	p.K408N	STAT4_ENST00000358470.4_Missense_Mutation_p.K408N	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	408					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.K408N(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CAGCACTGGACTTCATTTCCT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	115	112					2																	191919243		2203	4300	6503	191627488	SO:0001583	missense	6775				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1224G>C	2.37:g.191919243C>G	ENSP00000376134:p.Lys408Asn		191627488	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	37	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999030	0.54147	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	T;T	0.79845	-1.31;-1.31	5.0	3.17	0.36434	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.83133	0.5188	M	0.76838	2.35	0.80722	D	1	P;P;P	0.50528	0.936;0.936;0.936	P;P;P	0.52881	0.712;0.712;0.644	T	0.82833	-0.0262	10	0.87932	D	0	-25.8312	5.7349	0.18061	0.0:0.6709:0.0:0.3291	.	317;408;408	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	N	408	ENSP00000351255:K408N;ENSP00000376134:K408N	ENSP00000351255:K408N	K	-	3	2	STAT4	191627488	0.998000	0.40836	1.000000	0.80357	0.967000	0.64934	0.307000	0.19296	1.088000	0.41272	0.313000	0.20887	AAG		0.323	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		G	191919243	C	G	191919243	3	3	61	1	0	0	0	0	1	0	0	0	15306	564	20	5	1066	5	STAT4	2	191919243	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1258676	191919243	51280130	1991	9976										
STAT4	6775	broad.mit.edu	37	chr2	192012886	192012886	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaattgatccacctgctccAaaaacttgatttctaactgt	5	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192012886A>C	ENST00000392320.2	-	2	358	c.44T>G	c.(43-45)tTg>tGg	p.L15W	STAT4_ENST00000358470.4_Missense_Mutation_p.L15W|STAT4_ENST00000409995.1_Missense_Mutation_p.L15W	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	15					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.L15W(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CACCTGCTCCAAAAACTTGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											110	107	108					2																	192012886		2203	4300	6503	191721131	SO:0001583	missense	6775				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.44T>G	2.37:g.192012886A>C	ENSP00000376134:p.Leu15Trp		191721131	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	37	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596426	0.66332	.	.	ENSG00000138378	ENST00000358470;ENST00000392320;ENST00000409995;ENST00000450994;ENST00000432798	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.73	5.73	0.89815	STAT transcription factor, protein interaction (4);	0.000000	0.64402	D	0.000010	T	0.78375	0.4273	M	0.82517	2.595	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.995	T	0.81927	-0.0709	10	0.87932	D	0	-16.2208	16.0048	0.80354	1.0:0.0:0.0:0.0	.	15;15;15	B4DSY7;B4DV04;Q14765	.;.;STAT4_HUMAN	W	15	ENSP00000351255:L15W;ENSP00000376134:L15W;ENSP00000386288:L15W;ENSP00000412397:L15W;ENSP00000414322:L15W	ENSP00000351255:L15W	L	-	2	0	STAT4	191721131	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.288000	0.96055	2.190000	0.69967	0.533000	0.62120	TTG		0.368	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		C	192012886	A	C	192012886	3	2	61	1	0	0	0	0	1	0	0	0	15306	131	5	4	2294	4	STAT4	2	192012886	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	93643	192012886	51186487	1992	9977										
MYO1B	4430	broad.mit.edu	37	chr2	192228559	192228559	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagttcaagcccgaatctCgagtgaatggtctagatgaa	11	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192228559C>T	ENST00000392318.3	+	10	1118	c.871C>T	c.(871-873)Cga>Tga	p.R291*	MYO1B_ENST00000339514.4_Nonsense_Mutation_p.R291*|MYO1B_ENST00000304164.4_Nonsense_Mutation_p.R291*|MYO1B_ENST00000392316.1_Nonsense_Mutation_p.R291*	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	291	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R291R(2)|p.R291*(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GCCCGAATCTCGAGTGAATGG	0.438																																																3	Substitution - coding silent(2)|Substitution - Nonsense(1)	lung(2)|large_intestine(1)	2											132	121	125					2																	192228559		2203	4300	6503	191936804	SO:0001587	stop_gained	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.871C>T	2.37:g.192228559C>T	ENSP00000376132:p.Arg291*		191936804	O43794|Q7Z6L5	Nonsense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	33	5.243458	0.95272	.	.	ENSG00000128641	ENST00000339514;ENST00000439452;ENST00000392318;ENST00000304164;ENST00000451437;ENST00000392316	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	18.5018	0.90884	0.0:1.0:0.0:0.0	.	.	.	.	X	291	.	ENSP00000306382:R291X	R	+	1	2	MYO1B	191936804	1.000000	0.71417	0.945000	0.38365	0.853000	0.48598	7.423000	0.80229	2.810000	0.96702	0.650000	0.86243	CGA		0.438	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		T	192228559	C	T	192228559	4	4	61	1	0	0	0	0	0	1	0	0	10099	876	31	1	905	1	MYO1B	2	192228559	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	215673	192228559	50970814	1993	9978										
MYO1B	4430	broad.mit.edu	37	chr2	192257898	192257898	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccgcacacacttcctgCtaatgaaaaaaagccaaatt	5	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192257898C>A	ENST00000392318.3	+	20	2423	c.2176C>A	c.(2176-2178)Cta>Ata	p.L726I	MYO1B_ENST00000339514.4_Missense_Mutation_p.L726I|MYO1B_ENST00000304164.4_Missense_Mutation_p.L726I|MYO1B_ENST00000392316.1_Missense_Mutation_p.L726I|MYO1B_ENST00000439065.2_5'UTR	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	726	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.L726I(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			ACACTTCCTGCTAATGAAAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											98	95	96					2																	192257898		2203	4300	6503	191966143	SO:0001583	missense	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2176C>A	2.37:g.192257898C>A	ENSP00000376132:p.Leu726Ile		191966143	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675301	0.47781	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	6.05	5.0	0.66597	.	0.000000	0.64402	D	0.000001	T	0.65893	0.2735	L	0.45285	1.41	0.80722	D	1	B;B	0.27971	0.105;0.196	B;B	0.35240	0.097;0.198	T	0.61579	-0.7034	10	0.33141	T	0.24	.	13.9143	0.63887	0.0:0.8883:0.0:0.1117	.	726;726	O43795;O43795-2	MYO1B_HUMAN;.	I	726	ENSP00000341903:L726I;ENSP00000376132:L726I;ENSP00000306382:L726I;ENSP00000376130:L726I	ENSP00000306382:L726I	L	+	1	2	MYO1B	191966143	0.995000	0.38212	0.998000	0.56505	0.655000	0.38815	1.343000	0.33930	2.878000	0.98634	0.650000	0.86243	CTA		0.428	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		A	192257898	C	A	192257898	3	1	61	1	0	0	0	0	1	0	0	0	10099	796	28	2	2250	2	MYO1B	2	192257898	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29339	192257898	50941475	1994	9979										
MYO1B	4430	broad.mit.edu	37	chr2	192265111	192265111	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgattctgccctttaggctCgaaaaattctgcgggaactg	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192265111C>T	ENST00000392318.3	+	22	2546	c.2299C>T	c.(2299-2301)Cga>Tga	p.R767*	MYO1B_ENST00000339514.4_Nonsense_Mutation_p.R767*|MYO1B_ENST00000304164.4_Nonsense_Mutation_p.R767*|MYO1B_ENST00000392316.1_Nonsense_Mutation_p.R767*|MYO1B_ENST00000439065.2_Nonsense_Mutation_p.R41*	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	767	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R767*(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			CCTTTAGGCTCGAAAAATTCT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											80	85	83					2																	192265111		2203	4300	6503	191973356	SO:0001587	stop_gained	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2299C>T	2.37:g.192265111C>T	ENSP00000376132:p.Arg767*		191973356	O43794|Q7Z6L5	Nonsense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	40	8.016298	0.98610	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316;ENST00000439065	.	.	.	5.54	4.66	0.58398	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3204	0.66482	0.148:0.852:0.0:0.0	.	.	.	.	X	767;767;767;767;41	.	ENSP00000306382:R767X	R	+	1	2	MYO1B	191973356	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.432000	0.59922	1.303000	0.44873	0.650000	0.86243	CGA		0.453	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		T	192265111	C	T	192265111	4	4	61	1	0	0	0	0	0	1	0	0	10099	876	31	1	2381	1	MYO1B	2	192265111	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7213	192265111	50934262	1995	9980										
TMEFF2	23671	broad.mit.edu	37	chr2	192818493	192818493	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatactgaaatcgtacagGaccgggaacaacgtatagaa	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192818493G>A	ENST00000272771.5	-	9	2124	c.940C>T	c.(940-942)Cct>Tct	p.P314S	AC098617.1_ENST00000428980.2_RNA|TMEFF2_ENST00000392314.1_Missense_Mutation_p.P314S|AC098617.1_ENST00000424116.2_RNA	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	314	Required for shedding.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.P314S(1)		breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			AATCGTACAGGACCGGGAACA	0.443																																					Pancreas(50;1277 1381 28487 47072)											1	Substitution - Missense(1)	large_intestine(1)	2											137	117	124					2																	192818493		2203	4300	6503	192526738	SO:0001583	missense	23671			AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.940C>T	2.37:g.192818493G>A	ENSP00000272771:p.Pro314Ser		192526738	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	37	CCDS2314.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.897329	0.33535	.	.	ENSG00000144339	ENST00000392314;ENST00000272771	T;T	0.57752	0.38;2.62	5.86	5.86	0.93980	.	0.114616	0.64402	D	0.000007	T	0.36635	0.0974	N	0.12182	0.205	0.80722	D	1	B	0.17038	0.02	B	0.14023	0.01	T	0.25117	-1.0141	10	0.10377	T	0.69	-11.4153	20.1986	0.98248	0.0:0.0:1.0:0.0	.	314	Q9UIK5	TEFF2_HUMAN	S	314	ENSP00000376128:P314S;ENSP00000272771:P314S	ENSP00000272771:P314S	P	-	1	0	TMEFF2	192526738	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	6.033000	0.70925	2.781000	0.95711	0.650000	0.86243	CCT		0.443	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		A	192818493	G	A	192818493	3	1	61	1	0	0	0	0	1	0	0	0	16053	1174	41	3	192	3	TMEFF2	2	192818493	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	553382	192818493	50380880	1996	9981										
TMEFF2	23671	broad.mit.edu	37	chr2	192863870	192863870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcatgcattatcataagAtttcccatcagaagcgcaga	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:192863870A>G	ENST00000272771.5	-	6	1785	c.601T>C	c.(601-603)Tct>Cct	p.S201P	AC098617.1_ENST00000428980.2_RNA|TMEFF2_ENST00000487771.1_5'UTR|TMEFF2_ENST00000392314.1_Missense_Mutation_p.S201P|AC098617.1_ENST00000424116.2_RNA	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	201	Kazal-like 2. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.S201P(1)		breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TTATCATAAGATTTCCCATCA	0.368																																					Pancreas(50;1277 1381 28487 47072)											1	Substitution - Missense(1)	large_intestine(1)	2											133	125	127					2																	192863870		2203	4299	6502	192572115	SO:0001583	missense	23671			AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.601T>C	2.37:g.192863870A>G	ENSP00000272771:p.Ser201Pro		192572115	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	37	CCDS2314.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.788975	0.90367	.	.	ENSG00000144339	ENST00000392314;ENST00000272771	T;T	0.04360	3.64;3.64	5.74	5.74	0.90152	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.054825	0.85682	N	0.000000	T	0.25938	0.0632	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01413	-1.1361	10	0.66056	D	0.02	-12.7777	16.3426	0.83092	1.0:0.0:0.0:0.0	.	201	Q9UIK5	TEFF2_HUMAN	P	201	ENSP00000376128:S201P;ENSP00000272771:S201P	ENSP00000272771:S201P	S	-	1	0	TMEFF2	192572115	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	8.910000	0.92685	2.317000	0.78254	0.460000	0.39030	TCT		0.368	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		G	192863870	A	G	192863870	3	3	61	1	0	0	0	0	1	0	0	0	16053	333	12	4	543	4	TMEFF2	2	192863870	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	45377	192863870	50335503	1997	9982										
SLC39A10	57181	broad.mit.edu	37	chr2	196545682	196545682	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgataatgaaggtgaacttCgacatactagaaagagagaa	10	5	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196545682C>T	ENST00000409086.3	+	2	1191	c.916C>T	c.(916-918)Cga>Tga	p.R306*	SLC39A10_ENST00000359634.5_Nonsense_Mutation_p.R306*|SLC39A10_ENST00000541054.1_5'UTR	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	306					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.R306*(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			AGGTGAACTTCGACATACTAG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											93	82	86					2																	196545682		2203	4300	6503	196253927	SO:0001587	stop_gained	57181				CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.916C>T	2.37:g.196545682C>T	ENSP00000386766:p.Arg306*		196253927	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Nonsense_Mutation	SNP	ENST00000409086.3	37	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	C	37	6.417795	0.97550	.	.	ENSG00000196950	ENST00000409086;ENST00000359634	.	.	.	4.69	3.79	0.43588	.	0.736580	0.12915	N	0.428630	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3264	0.32160	0.1524:0.7673:0.0:0.0802	.	.	.	.	X	306	.	ENSP00000352655:R306X	R	+	1	2	SLC39A10	196253927	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	2.736000	0.47385	2.439000	0.82584	0.655000	0.94253	CGA		0.368	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		T	196545682	C	T	196545682	4	4	61	1	0	0	0	0	0	1	0	0	14650	876	31	1	918	1	SLC39A10	2	196545682	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3681812	196545682	46653691	1998	9983										
DNAH7	56171	broad.mit.edu	37	chr2	196636525	196636525	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatggcagcctcgatgtcGaagttgtttggaagtttgcc	12	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196636525G>A	ENST00000312428.6	-	61	11392	c.11292C>T	c.(11290-11292)ttC>ttT	p.F3764F	DNAH7_ENST00000409063.1_Silent_p.F247F	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3764					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.F3764F(2)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CCTCGATGTCGAAGTTGTTTG	0.448																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	2											261	242	248					2																	196636525		2013	4163	6176	196344770	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11292C>T	2.37:g.196636525G>A			196344770	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196636525	G	A	196636525	2	1	61	1	0	0	0	0	0	0	0	1	4617	1049	37	1		1	DNAH7	2	196636525	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90843	196636525	46562848	1999	9984										
DNAH7	56171	broad.mit.edu	37	chr2	196722144	196722144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacccatttgcacagaccttCggccgctgtagaagcatttc	9	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196722144C>T	ENST00000312428.6	-	44	8471	c.8371G>A	c.(8371-8373)Gaa>Aaa	p.E2791K		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2791	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.E2791K(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CACAGACCTTCGGCCGCTGTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	80	81					2																	196722144		1826	4079	5905	196430389	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.8371G>A	2.37:g.196722144C>T	ENSP00000311273:p.Glu2791Lys		196430389	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148022	0.94603	.	.	ENSG00000118997	ENST00000312428	T	0.56611	0.45	5.37	5.37	0.77165	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	T	0.69269	0.3092	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.61792	-0.6990	10	0.20046	T	0.44	.	18.9064	0.92464	0.0:1.0:0.0:0.0	.	2791	Q8WXX0	DYH7_HUMAN	K	2791	ENSP00000311273:E2791K	ENSP00000311273:E2791K	E	-	1	0	DNAH7	196430389	1.000000	0.71417	0.951000	0.38953	0.993000	0.82548	5.912000	0.69948	2.788000	0.95919	0.650000	0.86243	GAA		0.368	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196722144	C	T	196722144	3	4	61	1	0	0	0	0	1	0	0	0	4617	893	31	1	3791	1	DNAH7	2	196722144	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85619	196722144	46477229	2000	9985										
DNAH7	56171	broad.mit.edu	37	chr2	196737058	196737058	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccttgaatgacacgggaGaaatcacggaggttgaacaa	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196737058G>A	ENST00000312428.6	-	40	6649	c.6549C>T	c.(6547-6549)ttC>ttT	p.F2183F		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2183	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.F2183F(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TGACACGGGAGAAATCACGGA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											161	149	153					2																	196737058		1862	4102	5964	196445303	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.6549C>T	2.37:g.196737058G>A			196445303	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.393	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196737058	G	A	196737058	2	1	61	1	0	0	0	0	0	0	0	1	4617	933	33	3		3	DNAH7	2	196737058	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14914	196737058	46462315	2001	9986										
DNAH7	56171	broad.mit.edu	37	chr2	196774763	196774763	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaaaccttaaagaatttTcccaaagccaaataatccaa	2	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196774763T>C	ENST00000312428.6	-	25	4192	c.4092A>G	c.(4090-4092)ggA>ggG	p.G1364G		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1364	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.G1364G(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TAAAGAATTTTCCCAAAGCCA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											68	66	67					2																	196774763		1831	4093	5924	196483008	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4092A>G	2.37:g.196774763T>C			196483008	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.358	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196774763	T	C	196774763	2	2	61	1	0	0	0	0	0	0	0	1	4617	1770	62	4		4	DNAH7	2	196774763	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37705	196774763	46424610	2002	9987										
DNAH7	56171	broad.mit.edu	37	chr2	196791207	196791207	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccaaaagatttgggatacAcagagaacagtctgtccagg	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196791207A>G	ENST00000312428.6	-	22	3655	c.3555T>C	c.(3553-3555)tgT>tgC	p.C1185C		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1185	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.C1185C(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTTGGGATACACAGAGAACAG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	2											117	107	110					2																	196791207		1817	4074	5891	196499452	SO:0001819	synonymous_variant	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3555T>C	2.37:g.196791207A>G			196499452	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.358	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196791207	A	G	196791207	2	3	61	1	0	0	0	0	0	0	0	1	4617	157	6	4		4	DNAH7	2	196791207	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16444	196791207	46408166	2003	9988										
DNAH7	56171	broad.mit.edu	37	chr2	196865559	196865559	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaatggtgtcattatcaaGaatcagcctcatgatgaaac	7	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196865559G>T	ENST00000312428.6	-	12	1322	c.1222C>A	c.(1222-1224)Ctt>Att	p.L408I	DNAH7_ENST00000410072.1_Missense_Mutation_p.L408I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	408	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.L408I(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCATTATCAAGAATCAGCCTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											104	102	103					2																	196865559		1824	4075	5899	196573804	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.1222C>A	2.37:g.196865559G>T	ENSP00000311273:p.Leu408Ile		196573804	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.474840	0.63737	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23950	1.88;2.72	5.61	5.61	0.85477	.	.	.	.	.	T	0.33089	0.0851	M	0.66939	2.045	0.48040	D	0.999572	B	0.09022	0.002	B	0.08055	0.003	T	0.06463	-1.0825	9	0.49607	T	0.09	.	19.2477	0.93909	0.0:0.0:1.0:0.0	.	408	Q8WXX0	DYH7_HUMAN	I	408	ENSP00000311273:L408I;ENSP00000386260:L408I	ENSP00000311273:L408I	L	-	1	0	DNAH7	196573804	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.224000	0.51238	2.655000	0.90218	0.637000	0.83480	CTT		0.318	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196865559	G	T	196865559	3	4	61	1	0	0	0	0	1	0	0	0	4617	942	33	2	11068	2	DNAH7	2	196865559	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74352	196865559	46333814	2004	9989										
DNAH7	56171	broad.mit.edu	37	chr2	196889185	196889185	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggaagttcatctgtcttCttatcatctcctttctctcg	6	12	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196889185C>A	ENST00000312428.6	-	8	811	c.711G>T	c.(709-711)aaG>aaT	p.K237N	DNAH7_ENST00000410072.1_Missense_Mutation_p.K237N	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	237	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.K237N(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CATCTGTCTTCTTATCATCTC	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											94	89	91					2																	196889185		1816	4075	5891	196597430	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.711G>T	2.37:g.196889185C>A	ENSP00000311273:p.Lys237Asn		196597430	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662877	0.29515	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.22539	1.95;2.87	5.03	-0.936	0.10419	.	0.399649	0.25230	N	0.032167	T	0.15609	0.0376	M	0.64997	1.995	0.09310	N	1	B	0.25772	0.134	B	0.24155	0.051	T	0.31138	-0.9954	10	0.13853	T	0.58	.	6.0706	0.19887	0.0:0.2672:0.3886:0.3442	.	237	Q8WXX0	DYH7_HUMAN	N	237	ENSP00000311273:K237N;ENSP00000386260:K237N	ENSP00000311273:K237N	K	-	3	2	DNAH7	196597430	0.028000	0.19301	0.041000	0.18516	0.598000	0.36846	-0.103000	0.10940	-0.013000	0.14199	-0.345000	0.07892	AAG		0.303	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196889185	C	A	196889185	3	1	61	1	0	0	0	0	1	0	0	0	4617	912	32	2	11595	2	DNAH7	2	196889185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23626	196889185	46310188	2005	9990										
DNAH7	56171	broad.mit.edu	37	chr2	196912113	196912113	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacttctaaagttttctcGttctttatgtggagatttgc	8	6	3	1	rs199830438		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:196912113G>A	ENST00000312428.6	-	5	461	c.361C>T	c.(361-363)Cga>Tga	p.R121*	DNAH7_ENST00000410072.1_Nonsense_Mutation_p.R121*	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	121	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.R121*(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AAGTTTTCTCGTTCTTTATGT	0.388													G|||	1	0.000199681	0	0.0014	5008	,	,		16718	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	2											170	165	167					2																	196912113		1840	4080	5920	196620358	SO:0001587	stop_gained	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.361C>T	2.37:g.196912113G>A	ENSP00000311273:p.Arg121*		196620358	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Nonsense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722614	0.48728	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	.	.	.	5.2	2.31	0.28768	.	0.290168	0.27866	N	0.017532	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0742	0.48021	0.0:0.0:0.5194:0.4806	.	.	.	.	X	121;121;121;96	.	ENSP00000311273:R121X	R	-	1	2	DNAH7	196620358	0.982000	0.34865	0.983000	0.44433	0.097000	0.18754	0.631000	0.24568	0.293000	0.22520	-0.230000	0.12252	CGA		0.388	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196912113	G	A	196912113	4	1	61	1	0	0	0	0	0	1	0	0	4617	1153	40	1	11957	1	DNAH7	2	196912113	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22928	196912113	46287260	2006	9991										
HECW2	57520	broad.mit.edu	37	chr2	197135951	197135951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtaagatcaggttgacGctcctgtagaatttcaaaga	10	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197135951G>A	ENST00000260983.3	-	17	3483	c.3301C>T	c.(3301-3303)Cgt>Tgt	p.R1101C	HECW2_ENST00000409111.1_Missense_Mutation_p.R745C	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1101					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1101C(1)		biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCAGGTTGACGCTCCTGTAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	83	84					2																	197135951		2203	4300	6503	196844196	SO:0001583	missense	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.3301C>T	2.37:g.197135951G>A	ENSP00000260983:p.Arg1101Cys		196844196	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.443908	0.83993	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	D;D	0.85171	-1.95;-1.95	5.72	5.72	0.89469	.	0.054030	0.64402	D	0.000001	D	0.89241	0.6659	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	P	0.50791	0.65	D	0.90194	0.4252	10	0.87932	D	0	.	19.8791	0.96888	0.0:0.0:1.0:0.0	.	1101	Q9P2P5	HECW2_HUMAN	C	745;1101	ENSP00000386775:R745C;ENSP00000260983:R1101C	ENSP00000260983:R1101C	R	-	1	0	HECW2	196844196	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.302000	0.78861	2.706000	0.92434	0.467000	0.42956	CGT		0.328	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197135951	G	A	197135951	3	1	61	1	0	0	0	0	1	0	0	0	7064	1087	38	1	1469	1	HECW2	2	197135951	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223838	197135951	46063422	2007	9992										
CCDC150	284992	broad.mit.edu	37	chr2	197511125	197511125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacccacatcaacgctacaGcttctgaaacattcacagta	4	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197511125G>A	ENST00000389175.4	+	2	208	c.73G>A	c.(73-75)Gct>Act	p.A25T	CCDC150_ENST00000272831.7_5'UTR|CCDC150_ENST00000423093.2_5'UTR|CCDC150_ENST00000472405.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	25								p.A25T(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CAACGCTACAGCTTCTGAAAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											166	154	158					2																	197511125		1928	4118	6046	197219370	SO:0001583	missense	284992				CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.73G>A	2.37:g.197511125G>A	ENSP00000373827:p.Ala25Thr		197219370	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	37	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787994	0.70337	.	.	ENSG00000144395	ENST00000389175;ENST00000536389	T	0.30448	1.53	4.53	3.64	0.41730	.	0.000000	0.64402	D	0.000002	T	0.42108	0.1188	M	0.69823	2.125	0.80722	D	1	P;P	0.46142	0.832;0.873	P;B	0.51777	0.679;0.319	T	0.37663	-0.9696	10	0.72032	D	0.01	.	8.4106	0.32640	0.1071:0.0:0.8929:0.0	.	25;25	Q8NCX0;F5H6M2	CC150_HUMAN;.	T	25	ENSP00000373827:A25T	ENSP00000373827:A25T	A	+	1	0	CCDC150	197219370	0.974000	0.33945	1.000000	0.80357	0.898000	0.52572	0.590000	0.23954	1.263000	0.44181	0.655000	0.94253	GCT		0.418	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		A	197511125	G	A	197511125	3	1	61	1	0	0	0	0	1	0	0	0	2791	971	34	3	79	3	CCDC150	2	197511125	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	375174	197511125	45688248	2008	9993										
CCDC150	284992	broad.mit.edu	37	chr2	197521488	197521488	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgagtttctggtaaatcGaatgtgccgtcttgaaagcc	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197521488G>A	ENST00000389175.4	+	3	443	c.308G>A	c.(307-309)cGa>cAa	p.R103Q	CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000423093.2_Intron|CCDC150_ENST00000472405.2_5'UTR	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	103								p.R103Q(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGGTAAATCGAATGTGCCGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											121	116	118					2																	197521488		1844	4102	5946	197229733	SO:0001583	missense	284992				CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.308G>A	2.37:g.197521488G>A	ENSP00000373827:p.Arg103Gln		197229733	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	37	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876758	0.91664	.	.	ENSG00000144395	ENST00000389175;ENST00000536389	T	0.30714	1.52	5.03	5.03	0.67393	.	0.087795	0.45606	D	0.000345	T	0.54711	0.1875	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.53222	-0.8469	10	0.48119	T	0.1	-7.239	17.3013	0.87183	0.0:0.0:1.0:0.0	.	103;103	Q8NCX0;F5H6M2	CC150_HUMAN;.	Q	103	ENSP00000373827:R103Q	ENSP00000373827:R103Q	R	+	2	0	CCDC150	197229733	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.421000	0.59848	2.632000	0.89209	0.655000	0.94253	CGA		0.398	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		A	197521488	G	A	197521488	3	1	61	1	0	0	0	0	1	0	0	0	2791	1058	37	1	318	1	CCDC150	2	197521488	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10363	197521488	45677885	2009	9994										
GTF3C3	9330	broad.mit.edu	37	chr2	197631330	197631330	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagggccttctgataatAgtggattgcaagatgaatca	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197631330A>C	ENST00000263956.3	-	17	2586	c.2497T>G	c.(2497-2499)Tat>Gat	p.Y833D		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	833					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.Y833D(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TTCTGATAATAGTGGATTGCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											101	98	99					2																	197631330		2203	4300	6503	197339575	SO:0001583	missense	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.2497T>G	2.37:g.197631330A>C	ENSP00000263956:p.Tyr833Asp		197339575	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326426	0.81690	.	.	ENSG00000119041	ENST00000263956	T	0.63255	-0.03	4.78	4.78	0.61160	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.79458	0.4449	M	0.84156	2.68	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80957	-0.1150	10	0.42905	T	0.14	-18.6393	14.4609	0.67448	1.0:0.0:0.0:0.0	.	833	Q9Y5Q9	TF3C3_HUMAN	D	833	ENSP00000263956:Y833D	ENSP00000263956:Y833D	Y	-	1	0	GTF3C3	197339575	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.919000	0.92770	1.989000	0.58080	0.477000	0.44152	TAT		0.458	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			C	197631330	A	C	197631330	3	2	61	1	0	0	0	0	1	0	0	0	6895	420	15	4	171	4	GTF3C3	2	197631330	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	109842	197631330	45568043	2010	9995										
GTF3C3	9330	broad.mit.edu	37	chr2	197650293	197650293	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaatagcagaagtaacatCattggcttcatagtaactcc	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197650293C>A	ENST00000263956.3	-	7	1002	c.913G>T	c.(913-915)Gat>Tat	p.D305Y	GTF3C3_ENST00000470386.1_5'UTR|GTF3C3_ENST00000409364.3_Missense_Mutation_p.D305Y	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	305					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.D305Y(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAAGTAACATCATTGGCTTCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	95	97					2																	197650293		2202	4300	6502	197358538	SO:0001583	missense	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.913G>T	2.37:g.197650293C>A	ENSP00000263956:p.Asp305Tyr		197358538	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138412	0.77775	.	.	ENSG00000119041	ENST00000263956;ENST00000409364	T;T	0.42131	0.98;0.98	4.74	4.74	0.60224	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.58892	0.2154	L	0.50333	1.59	0.80722	D	1	D;D	0.67145	0.996;0.996	D;P	0.67725	0.953;0.862	T	0.62812	-0.6775	10	0.66056	D	0.02	-25.5628	17.7339	0.88387	0.0:1.0:0.0:0.0	.	305;305	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	Y	305	ENSP00000263956:D305Y;ENSP00000386465:D305Y	ENSP00000263956:D305Y	D	-	1	0	GTF3C3	197358538	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.094000	0.76944	2.176000	0.68965	0.462000	0.41574	GAT		0.328	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			A	197650293	C	A	197650293	3	1	61	1	0	0	0	0	1	0	0	0	6895	826	29	2	1795	2	GTF3C3	2	197650293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18963	197650293	45549080	2011	9996										
PGAP1	80055	broad.mit.edu	37	chr2	197750597	197750597	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaagcaaaaatccaactaTttgtatcctgttgatgaaca	6	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197750597T>G	ENST00000354764.4	-	11	1295	c.1181A>C	c.(1180-1182)aAt>aCt	p.N394T	PGAP1_ENST00000409475.1_Missense_Mutation_p.N394T|PGAP1_ENST00000409188.1_3'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	394					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.N394T(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						AATCCAACTATTTGTATCCTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	69	71					2																	197750597		2201	4297	6498	197458842	SO:0001583	missense	80055				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1181A>C	2.37:g.197750597T>G	ENSP00000346809:p.Asn394Thr		197458842	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	T	6.826	0.521557	0.13005	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000374738	.	.	.	4.81	3.63	0.41609	.	0.403282	0.25903	N	0.027551	T	0.19208	0.0461	N	0.03608	-0.345	0.80722	D	1	B;B	0.33073	0.023;0.396	B;B	0.26770	0.013;0.073	T	0.05550	-1.0878	9	0.20519	T	0.43	-11.5582	7.8848	0.29644	0.1833:0.0:0.0:0.8167	.	394;394	Q75T13-3;Q75T13	.;PGAP1_HUMAN	T	174;394;394;174	.	ENSP00000346809:N394T	N	-	2	0	PGAP1	197458842	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	0.838000	0.27572	0.951000	0.37770	0.533000	0.62120	AAT		0.303	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		G	197750597	T	G	197750597	3	3	61	1	0	0	0	0	1	0	0	0	11808	1493	52	4	1655	4	PGAP1	2	197750597	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	100304	197750597	45448776	2012	9997										
PGAP1	80055	broad.mit.edu	37	chr2	197781228	197781228	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatacaaagccaccagttCttcattgaagttcacactaa	4	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197781228C>A	ENST00000354764.4	-	3	505	c.391G>T	c.(391-393)Gaa>Taa	p.E131*	PGAP1_ENST00000409475.1_Nonsense_Mutation_p.E131*|PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Nonsense_Mutation_p.E89*	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	131					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.E131*(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						GCCACCAGTTCTTCATTGAAG	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											115	107	110					2																	197781228		2203	4300	6503	197489473	SO:0001587	stop_gained	80055				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.391G>T	2.37:g.197781228C>A	ENSP00000346809:p.Glu131*		197489473	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Nonsense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	37	6.447501	0.97572	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-24.0818	20.0008	0.97408	0.0:1.0:0.0:0.0	.	.	.	.	X	131;131;89	.	ENSP00000346809:E131X	E	-	1	0	PGAP1	197489473	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.434000	0.80377	2.796000	0.96246	0.644000	0.83932	GAA		0.383	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		A	197781228	C	A	197781228	4	1	61	1	0	0	0	0	0	1	0	0	11808	922	32	2	2477	2	PGAP1	2	197781228	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30631	197781228	45418145	2013	9998										
ANKRD44	91526	broad.mit.edu	37	chr2	197948209	197948209	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacagtggaaatgacaattCgcagctgcatagtgcaaagg	11	7	0	1	rs150062198	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:197948209C>T	ENST00000328737.2	-	14	1342	c.1266G>A	c.(1264-1266)gcG>gcA	p.A422A	ANKRD44_ENST00000477852.1_5'UTR|ANKRD44_ENST00000282272.8_Silent_p.A439A|ANKRD44_ENST00000539527.1_Silent_p.A375A|ANKRD44_ENST00000450567.1_Silent_p.A422A|ANKRD44_ENST00000409153.1_Silent_p.A447A|ANKRD44_ENST00000337207.5_Silent_p.A422A			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	447								p.A422A(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AATGACAATTCGCAGCTGCAT	0.468													C|||	2	0.000399361	0	0	5008	,	,		21622	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C		2,4404	4.2+/-10.8	0,2,2201	122	107	112		1341	-7.5	0.7	2	dbSNP_134	112	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ANKRD44	NM_001195144.1		0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538		447/994	197948209	7,12999	2203	4300	6503	197656454	SO:0001819	synonymous_variant	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1266G>A	2.37:g.197948209C>T			197656454	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																					0.468	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		T	197948209	C	T	197948209	2	4	61	1	0	0	0	0	0	0	0	1	672	871	31	1		1	ANKRD44	2	197948209	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166981	197948209	45251164	2014	9999										
COQ10B	80219	broad.mit.edu	37	chr2	198324793	198324793	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaaagaatattcagagaGaagaattttagggttcgtat	11	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198324793G>T	ENST00000263960.2	+	2	380	c.242G>T	c.(241-243)aGa>aTa	p.R81I	COQ10B_ENST00000545340.1_Missense_Mutation_p.R38I|COQ10B_ENST00000409010.1_Missense_Mutation_p.R53I|COQ10B_ENST00000409398.1_Intron	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	81						mitochondrial inner membrane (GO:0005743)		p.R81I(1)		endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			TATTCAGAGAGAAGAATTTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	47	47					2																	198324793		2202	4298	6500	198033038	SO:0001583	missense	80219			AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"coenzyme Q10 homolog B (yeast)"				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.242G>T	2.37:g.198324793G>T	ENSP00000263960:p.Arg81Ile		198033038	B7Z1Y4	Missense_Mutation	SNP	ENST00000263960.2	37	CCDS2319.1	.	.	.	.	.	.	.	.	.	.	G	35	5.590872	0.96590	.	.	ENSG00000115520	ENST00000263960;ENST00000545340;ENST00000409010	T;T;T	0.26660	1.72;1.77;1.75	5.62	5.62	0.85841	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.50171	0.1600	M	0.73217	2.22	0.80722	D	1	P;P	0.50443	0.84;0.935	P;P	0.59643	0.578;0.861	T	0.49234	-0.8961	10	0.72032	D	0.01	5.8095	19.6505	0.95798	0.0:0.0:1.0:0.0	.	53;81	B8ZZV9;Q9H8M1	.;CQ10B_HUMAN	I	81;38;53	ENSP00000263960:R81I;ENSP00000442520:R38I;ENSP00000387223:R53I	ENSP00000263960:R81I	R	+	2	0	COQ10B	198033038	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.816000	0.99350	2.636000	0.89361	0.561000	0.74099	AGA		0.363	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147		T	198324793	G	T	198324793	3	4	61	1	0	0	0	0	1	0	0	0	3750	942	33	2	248	2	COQ10B	2	198324793	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	376584	198324793	44874580	2015	10000										
HSPD1	3329	broad.mit.edu	37	chr2	198353095	198353095	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccaaggctggaatgcatcGaaggagggcacaaccccctc	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198353095G>A	ENST00000388968.3	-	10	1603	c.1336C>T	c.(1336-1338)Cga>Tga	p.R446*	HSPD1_ENST00000345042.2_Nonsense_Mutation_p.R446*	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	446					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)	p.R446*(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			GGAATGCATCGAAGGAGGGCA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											57	55	56					2																	198353095		2203	4300	6503	198061340	SO:0001587	stop_gained	3329			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"Heat Shock Proteins / Chaperonins"	5261	protein-coding gene	gene with protein product		118190	"heat shock 60kD protein 1 (chaperonin)", "spastic paraplegia 13 (autosomal dominant)"	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.1336C>T	2.37:g.198353095G>A	ENSP00000373620:p.Arg446*		198061340	B2R5M6|B7Z712|Q38L19|Q9UCR6	Nonsense_Mutation	SNP	ENST00000388968.3	37	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	G	38	6.656664	0.97739	.	.	ENSG00000144381	ENST00000388968;ENST00000345042	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0027	19.5044	0.95110	0.0:0.0:1.0:0.0	.	.	.	.	X	446	.	ENSP00000340019:R446X	R	-	1	2	HSPD1	198061340	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.399000	0.79935	2.685000	0.91497	0.555000	0.69702	CGA		0.403	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		A	198353095	G	A	198353095	4	1	61	1	0	0	0	0	0	1	0	0	7449	1066	37	1	397	1	HSPD1	2	198353095	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28302	198353095	44846278	2016	10001										
MOBKL3	25843	broad.mit.edu	37	chr2	198415045	198415045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaactaggatcagtatgcCgtaggatttacagaatattt	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198415045C>T	ENST00000323303.4	+	7	736	c.481C>T	c.(481-483)Cgt>Tgt	p.R161C	MOB4_ENST00000497443.1_3'UTR|MOB4_ENST00000233892.4_Missense_Mutation_p.R129C|HSPE1-MOB4_ENST00000604458.1_Missense_Mutation_p.R197C|MOB4_ENST00000448447.2_Missense_Mutation_p.R140C|MOB4_ENST00000409916.1_Missense_Mutation_p.R62C|MOB4_ENST00000409360.1_Missense_Mutation_p.R129C	NM_001202485.1|NM_015387.4	NP_001189414.1|NP_056202.2	Q9Y3A3	PHOCN_HUMAN	MOB family member 4, phocein	161					transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	metal ion binding (GO:0046872)	p.R161C(1)									ATCAGTATGCCGTAGGATTTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											153	153	153					2																	198415045		2203	4300	6503	198123290	SO:0001583	missense	25843			AF151853	CCDS2321.1, CCDS2322.1, CCDS46480.1	2q33.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000115540	ENSG00000115540		"MOB kinase activators"	17261	protein-coding gene	gene with protein product	"phocein", "phocein, Mob-like protein"	609361	"preimplantation protein 3", "MOB1, Mps One Binder kinase activator-like 3 (yeast)"	PREI3, MOBKL3		17853115, 10810093, 11230166, 11319234	Standard	NM_199482		Approved	MOB3, DKFZP564M112, CGI-95, 2C4D, PHOCN		Q9Y3A3	OTTHUMG00000132748	ENST00000323303.4:c.481C>T	2.37:g.198415045C>T	ENSP00000315702:p.Arg161Cys		198123290	B4DML0|Q53SE0|Q7Z4Y6|Q9H2P3|Q9H5J1|Q9Y4T8	Missense_Mutation	SNP	ENST00000323303.4	37	CCDS2321.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927856	0.73327	.	.	ENSG00000115540	ENST00000233892;ENST00000409916;ENST00000323303;ENST00000448447;ENST00000409360	.	.	.	5.24	4.36	0.52297	.	0.000000	0.85682	D	0.000000	D	0.86037	0.5837	H	0.94658	3.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89792	0.3969	9	0.62326	D	0.03	.	14.465	0.67477	0.0:0.9291:0.0:0.0709	.	140;161	Q9Y3A3-3;Q9Y3A3	.;PHOCN_HUMAN	C	129;62;161;140;129	.	ENSP00000233892:R129C	R	+	1	0	PHOCN	198123290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.697000	0.68295	1.574000	0.49760	0.650000	0.86243	CGT		0.333	MOB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256110.4	NM_015387		T	198415045	C	T	198415045	3	4	61	1	0	0	0	0	1	0	0	0	9717	652	23	1	507	1	MOBKL3	2	198415045	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61950	198415045	44784328	2017	10002										
RFTN2	130132	broad.mit.edu	37	chr2	198540173	198540173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttctagctttctaagtcCgcaccccatggcaaaatctg	7	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198540173C>T	ENST00000295049.4	-	1	546	c.10G>A	c.(10-12)Gga>Aga	p.G4R		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	4					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)		p.G4R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TTTCTAAGTCCGCACCCCATG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											111	121	118					2																	198540173		2203	4300	6503	198248418	SO:0001583	missense	130132			AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.10G>A	2.37:g.198540173C>T	ENSP00000295049:p.Gly4Arg		198248418	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	37	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.921053	0.92249	.	.	ENSG00000162944	ENST00000295049;ENST00000429081	T;T	0.42900	0.96;0.96	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.62062	-0.6933	10	0.87932	D	0	-27.5067	18.3002	0.90160	0.0:1.0:0.0:0.0	.	4	Q52LD8	RFTN2_HUMAN	R	4	ENSP00000295049:G4R;ENSP00000398128:G4R	ENSP00000295049:G4R	G	-	1	0	RFTN2	198248418	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.127000	0.77210	2.747000	0.94245	0.585000	0.79938	GGA		0.418	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		T	198540173	C	T	198540173	3	4	61	1	0	0	0	0	1	0	0	0	13296	661	23	1	1531	1	RFTN2	2	198540173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125128	198540173	44659200	2018	10003										
PLCL1	5334	broad.mit.edu	37	chr2	198948734	198948734	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatatttctgccataaaaGagatcagactggggaaaaac	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198948734G>T	ENST00000428675.1	+	2	891	c.493G>T	c.(493-495)Gag>Tag	p.E165*	PLCL1_ENST00000437704.2_Nonsense_Mutation_p.E67*	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	165	Interaction with PPP1C.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.E67*(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	TGCCATAAAAGAGATCAGACT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											91	98	96					2																	198948734		2203	4300	6503	198656979	SO:0001587	stop_gained	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.493G>T	2.37:g.198948734G>T	ENSP00000402861:p.Glu165*		198656979	Q3MJ90|Q53SD3|Q7Z3S3	Nonsense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	G	38	6.898841	0.97920	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	.	.	.	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1421	0.98061	0.0:0.0:1.0:0.0	.	.	.	.	X	165;67	.	.	E	+	1	0	PLCL1	198656979	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.800000	0.99124	2.836000	0.97738	0.655000	0.94253	GAG		0.453	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		T	198948734	G	T	198948734	4	4	61	1	0	0	0	0	0	1	0	0	12070	943	33	2	499	2	PLCL1	2	198948734	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	408561	198948734	44250639	2019	10004										
PLCL1	5334	broad.mit.edu	37	chr2	198949647	198949647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaacccatgtttcctttcGaagtgtcatagaggtaataa	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198949647G>A	ENST00000428675.1	+	2	1804	c.1406G>A	c.(1405-1407)cGa>cAa	p.R469Q	PLCL1_ENST00000437704.2_Missense_Mutation_p.R371Q	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	469	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.R371Q(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GTTTCCTTTCGAAGTGTCATA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	53	53					2																	198949647		2203	4300	6503	198657892	SO:0001583	missense	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1406G>A	2.37:g.198949647G>A	ENSP00000402861:p.Arg469Gln		198657892	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	G	10.67	1.414630	0.25465	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.65178	-0.14;-0.14	5.94	1.98	0.26296	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.650704	0.14405	N	0.321604	T	0.46073	0.1374	L	0.48642	1.525	0.42717	D	0.993666	B;B	0.32604	0.377;0.254	B;B	0.28232	0.087;0.055	T	0.23619	-1.0183	9	.	.	.	.	2.9874	0.05972	0.2537:0.1133:0.5166:0.1164	.	469;395	Q15111;B4DYZ4	PLCL1_HUMAN;.	Q	469;371	ENSP00000402861:R469Q;ENSP00000414138:R371Q	.	R	+	2	0	PLCL1	198657892	1.000000	0.71417	0.990000	0.47175	0.980000	0.70556	2.506000	0.45433	0.083000	0.17047	0.561000	0.74099	CGA		0.403	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198949647	G	A	198949647	3	1	61	1	0	0	0	0	1	0	0	0	12070	1058	37	1	1412	1	PLCL1	2	198949647	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	913	198949647	44249726	2020	10005										
PLCL1	5334	broad.mit.edu	37	chr2	198950188	198950188	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatccaagtgccatgaggatCgattccagtaacttgaatcc	8	10	0	2	rs151231252		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198950188C>T	ENST00000428675.1	+	2	2345	c.1947C>T	c.(1945-1947)atC>atT	p.I649I	PLCL1_ENST00000437704.2_Silent_p.I551I	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	649	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.I551I(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	CCATGAGGATCGATTCCAGTA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C		0,4406		0,0,2203	40	43	42		1947	-10.7	0.2	2	dbSNP_134	42	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PLCL1	NM_006226.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		649/1096	198950188	1,13003	2203	4299	6502	198658433	SO:0001819	synonymous_variant	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1947C>T	2.37:g.198950188C>T			198658433	Q3MJ90|Q53SD3|Q7Z3S3	Silent	SNP	ENST00000428675.1	37	CCDS2326.2																																																																																				0.423	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		T	198950188	C	T	198950188	2	4	61	1	0	0	0	0	0	0	0	1	12070	874	31	1		1	PLCL1	2	198950188	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541	198950188	44249185	2021	10006										
PLCL1	5334	broad.mit.edu	37	chr2	198950507	198950507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttgtatagagatacacGgaattccagcggattgttcg	11	6	0	1	rs141777553		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:198950507G>A	ENST00000428675.1	+	2	2664	c.2266G>A	c.(2266-2268)Gga>Aga	p.G756R	PLCL1_ENST00000437704.2_Missense_Mutation_p.G658R	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	756	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.G658R(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	AGAGATACACGGAATTCCAGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	ARG/GLY	0,4406		0,0,2203	74	72	72		2266	5.4	1	2	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLCL1	NM_006226.3	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	756/1096	198950507	1,13005	2203	4300	6503	198658752	SO:0001583	missense	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.2266G>A	2.37:g.198950507G>A	ENSP00000402861:p.Gly756Arg		198658752	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725236	0.68959	0.0	1.16E-4	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.17528	2.27;2.27	5.36	5.36	0.76844	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000004	T	0.53142	0.1778	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.61879	-0.6972	9	.	.	.	.	19.2914	0.94102	0.0:0.0:1.0:0.0	.	756;682	Q15111;B4DYZ4	PLCL1_HUMAN;.	R	756;658	ENSP00000402861:G756R;ENSP00000414138:G658R	.	G	+	1	0	PLCL1	198658752	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.643000	0.98464	2.793000	0.96121	0.561000	0.74099	GGA		0.398	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198950507	G	A	198950507	3	1	61	1	0	0	0	0	1	0	0	0	12070	1117	39	1	2272	1	PLCL1	2	198950507	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	319	198950507	44248866	2022	10007										
SATB2	23314	broad.mit.edu	37	chr2	200193515	200193515	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctctcatcctggtagatgCgatctcgctccacttctggc	8	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:200193515C>T	ENST00000417098.1	-	8	2108	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	SATB2_ENST00000443023.1_Missense_Mutation_p.R372H|SATB2_ENST00000428695.1_Missense_Mutation_p.R313H|RP11-486F17.1_ENST00000489557.2_RNA|SATB2_ENST00000260926.5_Missense_Mutation_p.R431H|SATB2_ENST00000457245.1_Missense_Mutation_p.R431H	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	431					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.R431H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CTGGTAGATGCGATCTCGCTC	0.562																																					Colon(30;262 767 11040 24421 36230)											1	Substitution - Missense(1)	large_intestine(1)	2											130	111	118					2																	200193515		2203	4300	6503	199901760	SO:0001583	missense	23314			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1292G>A	2.37:g.200193515C>T	ENSP00000401112:p.Arg431His		199901760	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	33	5.225896	0.95173	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.54071	0.61;0.62;0.61;0.59;0.61	4.98	4.98	0.66077	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.70518	0.3233	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.72447	-0.4291	10	0.72032	D	0.01	-13.8548	18.8143	0.92071	0.0:1.0:0.0:0.0	.	313;431	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	H	431;372;431;313;431	ENSP00000401112:R431H;ENSP00000388764:R372H;ENSP00000260926:R431H;ENSP00000388581:R313H;ENSP00000405420:R431H	ENSP00000260926:R431H	R	-	2	0	SATB2	199901760	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.609000	0.82925	2.747000	0.94245	0.650000	0.86243	CGC		0.562	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		T	200193515	C	T	200193515	3	4	61	1	0	0	0	0	1	0	0	0	13891	768	27	1	925	1	SATB2	2	200193515	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1243008	200193515	43005858	2023	10008										
C2orf60	129450	broad.mit.edu	37	chr2	200797839	200797839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaatgtgtaggaccattCgtcgtgcatagaagtcccta	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:200797839C>T	ENST00000354611.4	-	8	1164	c.899G>A	c.(898-900)cGa>cAa	p.R300Q	C2orf69_ENST00000491721.1_Intron|TYW5_ENST00000452512.2_5'UTR	NM_001039693.2	NP_001034782.1	A2RUC4	TYW5_HUMAN	tRNA-yW synthesizing protein 5	300					wybutosine biosynthetic process (GO:0031591)		iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.R300Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(1)	8						TAGGACCATTCGTCGTGCATA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	2											164	151	155					2																	200797839		1891	4117	6008	200506084	SO:0001583	missense	129450			AK095272	CCDS42795.1	2q33.1	2011-05-09	2011-05-09	2011-05-09	ENSG00000162971	ENSG00000162971			26754	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 60"	C2orf60		20739293	Standard	NM_001039693		Approved	FLJ37953	uc002uvi.4	A2RUC4	OTTHUMG00000132770	ENST00000354611.4:c.899G>A	2.37:g.200797839C>T	ENSP00000346627:p.Arg300Gln		200506084	B2RNE3|Q8N1R2	Missense_Mutation	SNP	ENST00000354611.4	37	CCDS42795.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.591830	0.46214	.	.	ENSG00000162971	ENST00000354611	T	0.71222	-0.55	5.77	2.31	0.28768	.	0.231901	0.36066	N	0.002802	T	0.56108	0.1963	L	0.37800	1.135	0.42037	D	0.991054	B	0.10296	0.003	B	0.04013	0.001	T	0.47086	-0.9144	10	0.28530	T	0.3	-4.0288	9.1789	0.37129	0.0:0.7153:0.0:0.2847	.	300	A2RUC4	TYW5_HUMAN	Q	300	ENSP00000346627:R300Q	ENSP00000346627:R300Q	R	-	2	0	TYW5	200506084	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.838000	0.55828	0.571000	0.29365	-0.345000	0.07892	CGA		0.413	TYW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256144.3	NM_001039693		T	200797839	C	T	200797839	3	4	61	1	0	0	0	0	1	0	0	0	2185	884	31	1	52	1	C2orf60	2	200797839	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	604324	200797839	42401534	2024	10009										
KCTD18	130535	broad.mit.edu	37	chr2	201357971	201357971	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtccaacactctatcagctCatgaggcacccgccagtagc	8	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201357971C>A	ENST00000359878.3	-	6	1198	c.688G>T	c.(688-690)Gag>Tag	p.E230*	KCTD18_ENST00000468413.1_5'UTR|KCTD18_ENST00000409157.1_Nonsense_Mutation_p.E230*	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	230					protein homooligomerization (GO:0051260)			p.E230*(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						TCTATCAGCTCATGAGGCACC	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											56	53	54					2																	201357971		2203	4300	6503	201066216	SO:0001587	stop_gained	130535			AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.688G>T	2.37:g.201357971C>A	ENSP00000352941:p.Glu230*		201066216	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Nonsense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	C	39	7.493916	0.98319	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	.	.	.	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.7895	18.9668	0.92700	0.0:1.0:0.0:0.0	.	.	.	.	X	230	.	ENSP00000352941:E230X	E	-	1	0	KCTD18	201066216	1.000000	0.71417	0.998000	0.56505	0.744000	0.42396	5.459000	0.66685	2.880000	0.98712	0.650000	0.86243	GAG		0.453	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		A	201357971	C	A	201357971	4	1	61	1	0	0	0	0	0	1	0	0	8126	835	29	2	600	2	KCTD18	2	201357971	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	560132	201357971	41841402	2025	10010										
SGOL2	151246	broad.mit.edu	37	chr2	201436604	201436604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatcccaaagttcaggtaAatttcaccaggagagtaaat	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201436604A>C	ENST00000357799.4	+	7	1633	c.1535A>C	c.(1534-1536)aAa>aCa	p.K512T		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	512					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.K512T(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AGTTCAGGTAAATTTCACCAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	88	88					2																	201436604		1801	4060	5861	201144849	SO:0001583	missense	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1535A>C	2.37:g.201436604A>C	ENSP00000350447:p.Lys512Thr		201144849	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.384173	0.42308	.	.	ENSG00000163535	ENST00000357799	T	0.44881	0.91	5.25	1.41	0.22369	.	0.411166	0.23487	N	0.047660	T	0.52108	0.1714	M	0.66939	2.045	0.18873	N	0.999981	D;D;D	0.63046	0.992;0.992;0.977	P;P;P	0.62298	0.9;0.9;0.787	T	0.40813	-0.9543	10	0.72032	D	0.01	-4.4621	5.4509	0.16565	0.6745:0.0:0.0735:0.252	.	512;512;512	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	T	512	ENSP00000350447:K512T	ENSP00000350447:K512T	K	+	2	0	SGOL2	201144849	0.000000	0.05858	0.011000	0.14972	0.837000	0.47467	0.125000	0.15749	0.145000	0.18977	0.477000	0.44152	AAA		0.318	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		C	201436604	A	C	201436604	3	2	61	1	0	0	0	0	1	0	0	0	14254	14	1	4	1557	4	SGOL2	2	201436604	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	78633	201436604	41762769	2026	10011										
SGOL2	151246	broad.mit.edu	37	chr2	201438270	201438270	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaataaaagaaggagagtgTcaggttaaaaaggtaaataa	11	1	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201438270T>G	ENST00000357799.4	+	7	3299	c.3201T>G	c.(3199-3201)tgT>tgG	p.C1067W		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	1067					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.C1067W(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AAGGAGAGTGTCAGGTTAAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											76	75	75					2																	201438270		1814	4081	5895	201146515	SO:0001583	missense	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.3201T>G	2.37:g.201438270T>G	ENSP00000350447:p.Cys1067Trp		201146515	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.966934	0.53507	.	.	ENSG00000163535	ENST00000357799	T	0.12569	2.67	5.38	2.36	0.29203	.	0.566213	0.16224	N	0.223913	T	0.26412	0.0645	L	0.57536	1.79	0.09310	N	1	D;D;D	0.89917	1.0;1.0;0.99	D;D;P	0.80764	0.994;0.994;0.723	T	0.05666	-1.0871	10	0.72032	D	0.01	5.4404	3.728	0.08482	0.2069:0.5863:0.0:0.2068	.	1067;1067;1067	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	W	1067	ENSP00000350447:C1067W	ENSP00000350447:C1067W	C	+	3	2	SGOL2	201146515	0.002000	0.14202	0.002000	0.10522	0.431000	0.31685	0.001000	0.13038	0.810000	0.34279	-0.248000	0.11899	TGT		0.368	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201438270	T	G	201438270	3	3	61	1	0	0	0	0	1	0	0	0	14254	1673	58	4	3223	4	SGOL2	2	201438270	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1666	201438270	41761103	2027	10012										
AOX1	316	broad.mit.edu	37	chr2	201477408	201477409	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaattcaggaatgagagtINScttttttggagaaggggatg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201477408_201477409insA	ENST00000374700.2	+	14	1581_1582	c.1340_1341insA	c.(1339-1344)gtctttfs	p.F448fs	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	448					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.F448fs*10(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GGAATGAGAGTCTTTTTTGGAG	0.475																																																1	Insertion - Frameshift(1)	large_intestine(1)	2																																								201185654	SO:0001589	frameshift_variant	316			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	Exception_encountered	2.37:g.201477408_201477409insA	ENSP00000363832:p.Phe448fs		201185653	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Frame_Shift_Ins	INS	ENST00000374700.2	37	CCDS33360.1																																																																																				0.475	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		A	201477409	-	A	201477408	7	5	61	1	0	1	1	0	0	0	0	0	729	1667	58	0	1394	0	AOX1	2	201477408	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	39138	201477408	41721965	2028	10013										
AOX1	316	broad.mit.edu	37	chr2	201523996	201523996	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggttctgtggtggcagatCtcaacggtttggcagtaaag	15	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201523996C>A	ENST00000374700.2	+	28	3521	c.3280C>A	c.(3280-3282)Ctc>Atc	p.L1094I	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1094					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.L1094I(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GGTGGCAGATCTCAACGGTTT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											166	150	155					2																	201523996		2203	4300	6503	201232241	SO:0001583	missense	316			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3280C>A	2.37:g.201523996C>A	ENSP00000363832:p.Leu1094Ile		201232241	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	C	9.234	1.036581	0.19669	.	.	ENSG00000138356	ENST00000374700	T	0.38077	1.16	5.15	1.23	0.21249	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.327716	0.32884	N	0.005527	T	0.20129	0.0484	N	0.25957	0.775	0.28838	N	0.896744	B	0.24576	0.106	B	0.29267	0.1	T	0.13335	-1.0513	10	0.23302	T	0.38	-14.6398	3.492	0.07641	0.1144:0.3273:0.4012:0.1571	.	1094	Q06278	ADO_HUMAN	I	1094	ENSP00000363832:L1094I	ENSP00000363832:L1094I	L	+	1	0	AOX1	201232241	1.000000	0.71417	0.873000	0.34254	0.899000	0.52679	1.257000	0.32932	0.046000	0.15833	-0.258000	0.10820	CTC		0.493	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		A	201523996	C	A	201523996	3	1	61	1	0	0	0	0	1	0	0	0	729	913	32	2	3390	2	AOX1	2	201523996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46588	201523996	41675377	2029	10014										
AOX1	316	broad.mit.edu	37	chr2	201533396	201533396	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatagaggaactgaattattCtccccagggcattctgcaca	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201533396C>A	ENST00000374700.2	+	33	3909	c.3668C>A	c.(3667-3669)tCt>tAt	p.S1223Y	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1223					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.S1223Y(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CTGAATTATTCTCCCCAGGGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	2											151	150	151					2																	201533396		2203	4300	6503	201241641	SO:0001583	missense	316			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3668C>A	2.37:g.201533396C>A	ENSP00000363832:p.Ser1223Tyr		201241641	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753275	0.69648	.	.	ENSG00000138356	ENST00000374700;ENST00000439380	T;T	0.46819	0.86;1.08	5.1	4.2	0.49525	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.054324	0.85682	D	0.000000	T	0.74688	0.3749	M	0.93678	3.445	0.80722	D	1	D	0.54964	0.969	D	0.64042	0.921	T	0.83117	-0.0120	10	0.87932	D	0	-27.9585	15.5026	0.75713	0.0:0.8611:0.1389:0.0	.	1223	Q06278	ADO_HUMAN	Y	1223;63	ENSP00000363832:S1223Y;ENSP00000413326:S63Y	ENSP00000363832:S1223Y	S	+	2	0	AOX1	201241641	1.000000	0.71417	0.987000	0.45799	0.774000	0.43823	5.514000	0.67043	1.350000	0.45770	0.563000	0.77884	TCT		0.433	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		A	201533396	C	A	201533396	3	1	61	1	0	0	0	0	1	0	0	0	729	913	32	2	3798	2	AOX1	2	201533396	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9400	201533396	41665977	2030	10015										
CLK1	1195	broad.mit.edu	37	chr2	201722697	201722697	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctaatctgatacttacaAagtactgttggggtctgttg	10	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201722697A>C	ENST00000321356.4	-	6	799	c.664T>G	c.(664-666)Ttc>Gtc	p.F222V	CLK1_ENST00000434813.2_Splice_Site_p.F264V|CLK1_ENST00000492793.1_5'Flank|CLK1_ENST00000409769.2_Splice_Site_p.F45V	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	222	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.F222V(1)		NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GATACTTACAAAGTACTGTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											140	141	141					2																	201722697		2203	4300	6503	201430942	SO:0001630	splice_region_variant	1195			L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.665+1T>G	2.37:g.201722697A>C			201430942	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.207693	0.58343	.	.	ENSG00000013441	ENST00000321356;ENST00000357369;ENST00000409769;ENST00000434813	T;T;T	0.19394	2.15;2.15;2.15	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.163089	0.56097	D	0.000030	T	0.23451	0.0567	L	0.31526	0.94	0.49299	D	0.999771	P;P;P;P	0.40515	0.719;0.719;0.719;0.555	P;P;P;B	0.48598	0.583;0.479;0.583;0.364	T	0.01909	-1.1249	10	0.49607	T	0.09	.	10.8883	0.46981	0.9241:0.0:0.0759:0.0	.	264;192;222;45	B4DFW7;E9PH13;P49759;B8ZZR0	.;.;CLK1_HUMAN;.	V	222;192;45;264	ENSP00000326830:F222V;ENSP00000386358:F45V;ENSP00000394734:F264V	ENSP00000326830:F222V	F	-	1	0	CLK1	201430942	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	5.303000	0.65738	2.178000	0.69098	0.460000	0.39030	TTC		0.368	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2		Missense_Mutation	C	201722697	A	C	201722697	5	2	61	1	0	0	0	0	0	0	1	0	3542	28	1	4	822	4	CLK1	2	201722697	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	189301	201722697	41476676	2031	10016										
FAM126B	285172	broad.mit.edu	37	chr2	201857057	201857057	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctataaatgatatcatcaaGaacttcctggccaaggtccc	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:201857057G>T	ENST00000418596.3	-	10	965	c.778C>A	c.(778-780)Ctt>Att	p.L260I	AC005037.3_ENST00000413848.1_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	260						intracellular (GO:0005622)		p.L260I(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						ATATCATCAAGAACTTCCTGG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											88	98	94					2																	201857057		2203	4300	6503	201565302	SO:0001583	missense	285172			BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.778C>A	2.37:g.201857057G>T	ENSP00000393667:p.Leu260Ile		201565302	B2RCG7|Q4ZG87|Q53TX6	Missense_Mutation	SNP	ENST00000418596.3	37	CCDS2335.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936880	0.73557	.	.	ENSG00000155744	ENST00000418596	T	0.78924	-1.22	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.84424	0.5469	M	0.75447	2.3	0.80722	D	1	P;D	0.71674	0.899;0.998	P;D	0.67725	0.639;0.953	T	0.81553	-0.0880	10	0.22706	T	0.39	-10.0643	9.8945	0.41309	0.1564:0.0:0.8436:0.0	.	66;260	B3KUG1;Q8IXS8	.;F126B_HUMAN	I	260	ENSP00000393667:L260I	ENSP00000393667:L260I	L	-	1	0	FAM126B	201565302	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.236000	0.51336	2.653000	0.90120	0.561000	0.74099	CTT		0.328	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822		T	201857057	G	T	201857057	3	4	61	1	0	0	0	0	1	0	0	0	5446	942	33	2	826	2	FAM126B	2	201857057	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134360	201857057	41342316	2032	10017										
CFLAR	8837	broad.mit.edu	37	chr2	202010147	202010147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacttaaggaacagcttgGcgctcaacgtaagaccacct	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202010147G>A	ENST00000309955.3	+	6	1168	c.653G>A	c.(652-654)gGc>gAc	p.G218D	CFLAR_ENST00000443227.1_Missense_Mutation_p.G122D|CFLAR_ENST00000340870.5_Missense_Mutation_p.G218D|CFLAR-AS1_ENST00000474886.2_RNA|CFLAR_ENST00000341582.6_Intron|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR-AS1_ENST00000594911.1_RNA|CFLAR_ENST00000479953.2_Missense_Mutation_p.G122D|CFLAR_ENST00000423241.2_Missense_Mutation_p.G218D|CFLAR-AS1_ENST00000598453.1_RNA|CFLAR_ENST00000457277.1_Missense_Mutation_p.G218D|CFLAR_ENST00000342795.5_Missense_Mutation_p.G218D|CFLAR_ENST00000355558.4_Missense_Mutation_p.G218D	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	218	Interaction with FADD.|Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 propeptide.|Interaction with caspase-8 subunits p18 and p10.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)	p.G218D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						GAACAGCTTGGCGCTCAACGT	0.318																																					Pancreas(16;548 657 22190 32864 42338)											1	Substitution - Missense(1)	large_intestine(1)	2											123	132	129					2																	202010147		2203	4299	6502	201718392	SO:0001583	missense	8837			AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"Endogenous ligands"	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.653G>A	2.37:g.202010147G>A	ENSP00000312455:p.Gly218Asp		201718392	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	37	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.253004	0.01457	.	.	ENSG00000003402	ENST00000309955;ENST00000443227;ENST00000355558;ENST00000340870;ENST00000342795;ENST00000423241;ENST00000457277	T;T;T;T;T;T;T	0.40756	3.8;3.79;1.02;3.67;1.04;3.8;3.67	5.27	2.19	0.27852	.	1.499790	0.03510	N	0.219430	T	0.14485	0.0350	N	0.00690	-1.25	0.09310	N	0.999993	B;B;B;B;B	0.11235	0.004;0.003;0.002;0.001;0.002	B;B;B;B;B	0.11329	0.006;0.002;0.003;0.001;0.004	T	0.20009	-1.0288	10	0.16896	T	0.51	-1.909	3.8249	0.08851	0.2514:0.2044:0.5442:0.0	.	122;218;218;218;218	O15519-3;C9JK38;O15519-11;O15519;O15519-12	.;.;.;CFLAR_HUMAN;.	D	218;122;218;218;218;218;218	ENSP00000312455:G218D;ENSP00000413270:G122D;ENSP00000347757:G218D;ENSP00000339326:G218D;ENSP00000342809:G218D;ENSP00000399420:G218D;ENSP00000411535:G218D	ENSP00000312455:G218D	G	+	2	0	CFLAR	201718392	0.002000	0.14202	0.446000	0.26920	0.086000	0.17979	-0.057000	0.11768	0.115000	0.18071	0.655000	0.94253	GGC		0.318	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879		A	202010147	G	A	202010147	3	1	61	1	0	0	0	0	1	0	0	0	3298	1203	42	3	735	3	CFLAR	2	202010147	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153090	202010147	41189226	2033	10018										
CASP10	843	broad.mit.edu	37	chr2	202073854	202073854	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatacacaataatgtgacGaaagtggaaatggagatggt	11	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202073854G>A	ENST00000272879.5	+	9	1168	c.984G>A	c.(982-984)acG>acA	p.T328T	CASP10_ENST00000286186.6_Silent_p.T328T|CASP10_ENST00000313728.7_Silent_p.T261T|CASP10_ENST00000346817.5_Silent_p.T285T|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000448480.1_Silent_p.T285T	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	328					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)	p.T328T(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						ATAATGTGACGAAAGTGGAAA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											127	124	125					2																	202073854		2203	4300	6503	201782099	SO:0001819	synonymous_variant	843			U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.984G>A	2.37:g.202073854G>A			201782099	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Silent	SNP	ENST00000272879.5	37	CCDS2338.1																																																																																				0.443	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		A	202073854	G	A	202073854	2	1	61	1	0	0	0	0	0	0	0	1	2675	1045	37	1		1	CASP10	2	202073854	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63707	202073854	41125519	2034	10019										
ALS2CR12	130540	broad.mit.edu	37	chr2	202172323	202172323	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctcctgactccatttcGaattttttggtcatcttttt	4	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202172323G>A	ENST00000286190.5	-	10	844	c.798C>T	c.(796-798)ttC>ttT	p.F266F	ALS2CR12_ENST00000439709.1_Silent_p.F266F|ALS2CR12_ENST00000448967.1_5'Flank|ALS2CR12_ENST00000392257.3_Silent_p.F266F|ALS2CR12_ENST00000405148.2_Silent_p.F266F			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	266					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)		p.F266F(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						ACTCCATTTCGAATTTTTTGG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											156	159	158					2																	202172323		2203	4298	6501	201880568	SO:0001819	synonymous_variant	130540			AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.798C>T	2.37:g.202172323G>A			201880568	G5E9S3|Q53TT6|Q8N1B6	Silent	SNP	ENST00000286190.5	37	CCDS2346.1	.	.	.	.	.	.	.	.	.	.	G	0.508	-0.867740	0.02590	.	.	ENSG00000155749	ENST00000415745	.	.	.	5.53	-0.054	0.13816	.	.	.	.	.	T	0.50888	0.1642	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35919	-0.9769	4	.	.	.	-8.4115	5.6157	0.17430	0.6368:0.1427:0.2205:0.0	.	.	.	.	L	41	.	.	S	-	2	0	ALS2CR12	201880568	0.992000	0.36948	0.993000	0.49108	0.026000	0.11368	0.295000	0.19065	-0.114000	0.11936	-0.300000	0.09419	TCG		0.383	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163		A	202172323	G	A	202172323	2	1	61	1	0	0	0	0	0	0	0	1	553	1049	37	1		1	ALS2CR12	2	202172323	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98469	202172323	41027050	2035	10020										
TRAK2	66008	broad.mit.edu	37	chr2	202252470	202252470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttctggcataaaacctCgaaggcaactggcactgctg	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202252470C>T	ENST00000332624.3	-	13	2080	c.1652G>A	c.(1651-1653)cGa>cAa	p.R551Q		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	551					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)	p.R551Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CATAAAACCTCGAAGGCAACT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	97	96					2																	202252470		2203	4300	6503	201960715	SO:0001583	missense	66008			AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1652G>A	2.37:g.202252470C>T	ENSP00000328875:p.Arg551Gln		201960715	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	C	31	5.059891	0.93846	.	.	ENSG00000115993	ENST00000332624;ENST00000542292	T	0.46819	0.86	5.63	5.63	0.86233	Trafficking kinesin-binding protein domain (1);	0.079231	0.51477	D	0.000086	T	0.63450	0.2512	L	0.48642	1.525	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.61441	-0.7062	10	0.49607	T	0.09	.	19.6777	0.95943	0.0:1.0:0.0:0.0	.	551	O60296	TRAK2_HUMAN	Q	551;457	ENSP00000328875:R551Q	ENSP00000328875:R551Q	R	-	2	0	TRAK2	201960715	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	5.408000	0.66368	2.669000	0.90835	0.650000	0.86243	CGA		0.483	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		T	202252470	C	T	202252470	3	4	61	1	0	0	0	0	1	0	0	0	16490	884	31	1	1108	1	TRAK2	2	202252470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80147	202252470	40946903	2036	10021										
STRADB	55437	broad.mit.edu	37	chr2	202343319	202343319	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgcaacaagatcctgaGaaaaggtaatattgatctct	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202343319G>T	ENST00000194530.3	+	10	1430	c.1065G>T	c.(1063-1065)gaG>gaT	p.E355D	STRADB_ENST00000392249.2_Missense_Mutation_p.E355D	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	355	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.E355D(1)		breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						AAGATCCTGAGAAAAGGTAAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	45	46					2																	202343319		2203	4300	6503	202051564	SO:0001583	missense	55437			AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.1065G>T	2.37:g.202343319G>T	ENSP00000194530:p.Glu355Asp		202051564	Q5BKY7|Q9P1L0	Missense_Mutation	SNP	ENST00000194530.3	37	CCDS2348.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.49|15.49	2.849048|2.849048	0.51270|0.51270	.|.	.|.	ENSG00000082146|ENSG00000082146	ENST00000194530;ENST00000539670;ENST00000392249;ENST00000392866|ENST00000415688	T;T|.	0.66638|.	-0.22;-0.22|.	5.83|5.83	3.72|3.72	0.42706|0.42706	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.54078|.	0.1836|.	L|L	0.28649|0.28649	0.875|0.875	0.54753|0.54753	D|D	0.999981|0.999981	D|.	0.56746|.	0.977|.	P|.	0.59546|.	0.859|.	T|.	0.57974|.	-0.7718|.	10|.	0.09338|0.56958	T|D	0.73|0.05	.|.	11.9626|11.9626	0.53017|0.53017	0.2082:0.0:0.7918:0.0|0.2082:0.0:0.7918:0.0	.|.	355|.	Q9C0K7|.	STRAB_HUMAN|.	D|X	355;355;355;217|26	ENSP00000194530:E355D;ENSP00000376080:E355D|.	ENSP00000194530:E355D|ENSP00000413574:E26X	E|E	+|+	3|1	2|0	STRADB|STRADB	202051564|202051564	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	2.847000|2.847000	0.48270|0.48270	1.473000|1.473000	0.48159|0.48159	0.655000|0.655000	0.94253|0.94253	GAG|GAA		0.358	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571		T	202343319	G	T	202343319	3	4	61	1	0	0	0	0	1	0	0	0	15364	933	33	2	1099	2	STRADB	2	202343319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90849	202343319	40856054	2037	10022										
ALS2CR11	151254	broad.mit.edu	37	chr2	202352460	202352460	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactttccactgtagctttCtcgttgcttgttaacctccg	6	12	1	0	rs567676487		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202352460C>A	ENST00000286195.3	-	15	1791	c.1747G>T	c.(1747-1749)Gaa>Taa	p.E583*	ALS2CR11_ENST00000439140.1_Nonsense_Mutation_p.E1780*|ALS2CR11_ENST00000482942.1_5'Flank|ALS2CR11_ENST00000439802.1_3'UTR	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	583								p.E583*(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CTGTAGCTTTCTCGTTGCTTG	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		18547	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	2											343	328	333					2																	202352460		2203	4300	6503	202060705	SO:0001587	stop_gained	151254			AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1747G>T	2.37:g.202352460C>A	ENSP00000286195:p.Glu583*		202060705	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Nonsense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	C	37	6.280240	0.97440	.	.	ENSG00000155754	ENST00000286195;ENST00000439140	.	.	.	4.85	1.81	0.25067	.	0.552015	0.15170	N	0.276713	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	3.9145	0.09217	0.0:0.5475:0.2238:0.2288	.	.	.	.	X	583;1780	.	ENSP00000286195:E583X	E	-	1	0	ALS2CR11	202060705	0.011000	0.17503	0.008000	0.14137	0.010000	0.07245	0.225000	0.17757	0.623000	0.30267	0.650000	0.86243	GAA		0.393	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		A	202352460	C	A	202352460	4	1	61	1	0	0	0	0	0	1	0	0	552	922	32	2	128	2	ALS2CR11	2	202352460	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9141	202352460	40846913	2038	10023										
ALS2CR11	151254	broad.mit.edu	37	chr2	202436740	202436740	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaattttctgaagaggttTtaactgaaaaaaatgtaagt	8	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202436740T>G	ENST00000286195.3	-	8	801	c.757A>C	c.(757-759)Aaa>Caa	p.K253Q	ALS2CR11_ENST00000439140.1_Missense_Mutation_p.K253Q|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.K253Q|ALS2CR11_ENST00000450242.1_Missense_Mutation_p.K253Q	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	253								p.K253Q(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TGAAGAGGTTTTAACTGAAAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	94	95					2																	202436740		2203	4300	6503	202144985	SO:0001583	missense	151254			AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.757A>C	2.37:g.202436740T>G	ENSP00000286195:p.Lys253Gln		202144985	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.193315	0.38707	.	.	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.49	4.29	0.51040	.	0.500285	0.19903	N	0.103465	T	0.58750	0.2144	M	0.63843	1.955	0.30305	N	0.789048	P;D;D	0.89917	0.94;0.991;1.0	P;D;D	0.80764	0.61;0.981;0.994	T	0.59757	-0.7394	10	0.56958	D	0.05	.	10.2845	0.43558	0.0:0.0:0.166:0.834	.	253;253;253	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	Q	253	ENSP00000286195:K253Q;ENSP00000400672:K253Q;ENSP00000409937:K253Q;ENSP00000399016:K253Q	ENSP00000286195:K253Q	K	-	1	0	ALS2CR11	202144985	1.000000	0.71417	1.000000	0.80357	0.206000	0.24218	2.457000	0.45005	0.866000	0.35629	0.482000	0.46254	AAA		0.323	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		G	202436740	T	G	202436740	3	3	61	1	0	0	0	0	1	0	0	0	552	1850	64	4	4888	4	ALS2CR11	2	202436740	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	84280	202436740	40762633	2039	10024										
ALS2CR11	151254	broad.mit.edu	37	chr2	202466489	202466489	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaatacttcacttcatcGaacttaattacagtgttctt	4	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202466489G>A	ENST00000286195.3	-	4	533	c.489C>T	c.(487-489)ttC>ttT	p.F163F	ALS2CR11_ENST00000439140.1_Silent_p.F163F|ALS2CR11_ENST00000439802.1_Silent_p.F163F|ALS2CR11_ENST00000450242.1_Silent_p.F163F	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	163								p.F163F(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TCACTTCATCGAACTTAATTA	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	2											109	102	104					2																	202466489		2201	4290	6491	202174734	SO:0001819	synonymous_variant	151254			AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.489C>T	2.37:g.202466489G>A			202174734	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	37	CCDS2349.1																																																																																				0.313	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		A	202466489	G	A	202466489	2	1	61	1	0	0	0	0	0	0	0	1	552	1049	37	1		1	ALS2CR11	2	202466489	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29749	202466489	40732884	2040	10025										
ALS2CR4	65062	broad.mit.edu	37	chr2	202494570	202494570	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacgatcagcagcctggaAtctccctaagaacacataac	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202494570A>C	ENST00000409883.2	-	8	675	c.559T>G	c.(559-561)Ttc>Gtc	p.F187V	TMEM237_ENST00000409444.2_Missense_Mutation_p.F179V|TMEM237_ENST00000466839.1_5'UTR	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	187					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.F187V(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						GCAGCCTGGAATCTCCCTAAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											98	96	97					2																	202494570		1899	4113	6012	202202815	SO:0001583	missense	65062			AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.559T>G	2.37:g.202494570A>C	ENSP00000386264:p.Phe187Val		202202815	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	ENST00000409883.2	37	CCDS46489.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.844155	0.91197	.	.	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684;ENST00000409099	.	.	.	5.77	5.77	0.91146	.	0.043101	0.85682	D	0.000000	T	0.79335	0.4428	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.81127	-0.1074	9	0.62326	D	0.03	-16.8574	16.3948	0.83586	1.0:0.0:0.0:0.0	.	187;211	E9PAR8;Q96Q45	.;TM237_HUMAN	V	179;187;187;209;92	.	ENSP00000386949:F92V	F	-	1	0	TMEM237	202202815	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.446000	0.90329	2.326000	0.78906	0.533000	0.62120	TTC		0.428	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		C	202494570	A	C	202494570	3	2	61	1	0	0	0	0	1	0	0	0	554	101	4	4	691	4	ALS2CR4	2	202494570	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	28081	202494570	40704803	2041	10026										
MPP4	58538	broad.mit.edu	37	chr2	202514799	202514799	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacctctactttacctgtGactatatatgaggttttcaa	6	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202514799G>T	ENST00000409474.3	-	19	1678	c.1471C>A	c.(1471-1473)Cac>Aac	p.H491N	MPP4_ENST00000409143.1_Missense_Mutation_p.H433N|MPP4_ENST00000396886.3_Missense_Mutation_p.H416N|MPP4_ENST00000428900.2_Missense_Mutation_p.H467N|MPP4_ENST00000447335.2_Missense_Mutation_p.H484N|MPP4_ENST00000359962.5_Missense_Mutation_p.H491N|MPP4_ENST00000315506.7_Missense_Mutation_p.H447N	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	491	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)		p.H491N(1)		kidney(1)|lung(11)	12						CTTTACCTGTGACTATATATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	88	92					2																	202514799		1829	4079	5908	202223044	SO:0001583	missense	58538			AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.1471C>A	2.37:g.202514799G>T	ENSP00000387278:p.His491Asn		202223044	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Missense_Mutation	SNP	ENST00000409474.3	37	CCDS46491.1	.	.	.	.	.	.	.	.	.	.	G	6.616	0.482063	0.12581	.	.	ENSG00000082126	ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000374605;ENST00000428900;ENST00000409143;ENST00000447335	T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49	5.36	5.36	0.76844	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.165624	0.52532	D	0.000066	T	0.11281	0.0275	N	0.25245	0.725	0.54753	D	0.999988	B;B;P;P;P;P;P;P	0.38863	0.423;0.015;0.65;0.65;0.598;0.504;0.65;0.46	B;B;B;B;B;B;B;B	0.40782	0.138;0.048;0.34;0.34;0.23;0.34;0.34;0.209	T	0.02294	-1.1181	10	0.02654	T	1	.	19.2914	0.94102	0.0:0.0:1.0:0.0	.	433;416;467;460;447;484;491;456	F6Q0Y6;B4DUF3;E7ET46;B7ZM19;Q96JB8-2;E7EUL8;Q96JB8;Q96JB8-4	.;.;.;.;.;.;MPP4_HUMAN;.	N	491;447;416;491;456;420;467;433;484	ENSP00000387278:H491N;ENSP00000319363:H447N;ENSP00000353047:H491N;ENSP00000416781:H467N;ENSP00000387293:H433N;ENSP00000406160:H484N	ENSP00000319363:H447N	H	-	1	0	MPP4	202223044	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	3.345000	0.52182	2.793000	0.96121	0.561000	0.74099	CAC		0.343	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			T	202514799	G	T	202514799	3	4	61	1	0	0	0	0	1	0	0	0	9766	1290	45	2	458	2	MPP4	2	202514799	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20229	202514799	40684574	2042	10027										
MPP4	58538	broad.mit.edu	37	chr2	202550672	202550672	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtttttcactaaacaaacAatcctcattgcttcctcact	3	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202550672A>G	ENST00000409474.3	-	6	669	c.462T>C	c.(460-462)atT>atC	p.I154I	MPP4_ENST00000409143.1_Silent_p.I127I|MPP4_ENST00000396886.3_Intron|MPP4_ENST00000428900.2_Silent_p.I154I|MPP4_ENST00000447335.2_Silent_p.I154I|MPP4_ENST00000359962.5_Silent_p.I154I|MPP4_ENST00000315506.7_Silent_p.I154I	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	154	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)		p.I154I(1)		kidney(1)|lung(11)	12						CTAAACAAACAATCCTCATTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	2											127	120	123					2																	202550672		1880	4104	5984	202258917	SO:0001819	synonymous_variant	58538			AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.462T>C	2.37:g.202550672A>G			202258917	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Silent	SNP	ENST00000409474.3	37	CCDS46491.1																																																																																				0.413	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			G	202550672	A	G	202550672	2	3	61	1	0	0	0	0	0	0	0	1	9766	126	5	4		4	MPP4	2	202550672	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	35873	202550672	40648701	2043	10028										
ALS2	57679	broad.mit.edu	37	chr2	202589025	202589025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatactgtacctagtgaTatcatcaaagacaccatatc	6	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:202589025T>C	ENST00000264276.6	-	21	3877	c.3505A>G	c.(3505-3507)Atc>Gtc	p.I1169V	ALS2_ENST00000457679.2_Missense_Mutation_p.I481V	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1169					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.I1169V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TACCTAGTGATATCATCAAAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	103	106					2																	202589025		1902	4118	6020	202297270	SO:0001583	missense	57679			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.3505A>G	2.37:g.202589025T>C	ENSP00000264276:p.Ile1169Val		202297270	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.794810	0.90453	.	.	ENSG00000003393	ENST00000264276;ENST00000457679	T;T	0.41065	1.01;1.01	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.51092	0.1654	N	0.25426	0.745	0.80722	D	1	D;B	0.76494	0.999;0.402	D;B	0.66084	0.941;0.258	T	0.51301	-0.8723	10	0.48119	T	0.1	.	16.3766	0.83401	0.0:0.0:0.0:1.0	.	1169;1169	Q6IQ41;Q96Q42	.;ALS2_HUMAN	V	1169;481	ENSP00000264276:I1169V;ENSP00000394823:I481V	ENSP00000264276:I1169V	I	-	1	0	ALS2	202297270	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.841000	0.86834	2.263000	0.75096	0.533000	0.62120	ATC		0.373	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		C	202589025	T	C	202589025	3	2	61	1	0	0	0	0	1	0	0	0	550	1406	49	4	1524	4	ALS2	2	202589025	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	38353	202589025	40610348	2044	10029										
BMPR2	659	broad.mit.edu	37	chr2	203379664	203379664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggaggcagcagcatccGaaccctctcttgatctagat	10	11	2	3	rs397514497		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:203379664G>A	ENST00000374580.4	+	5	1122	c.583G>A	c.(583-585)Gaa>Aaa	p.E195K	BMPR2_ENST00000374574.2_Missense_Mutation_p.E195K	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	195					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.E195K(2)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						AGCAGCATCCGAACCCTCTCT	0.398																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	2	GRCh37	CM085278	BMPR2	M							187	162	170					2																	203379664		2203	4300	6503	203087909	SO:0001583	missense	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.583G>A	2.37:g.203379664G>A	ENSP00000363708:p.Glu195Lys		203087909	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611801	0.87258	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	D;D	0.93659	-3.26;-3.26	5.92	5.92	0.95590	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	L	0.27053	0.805	0.80722	D	1	D;D	0.64830	0.985;0.994	P;P	0.47251	0.466;0.542	D	0.90167	0.4232	10	0.35671	T	0.21	.	20.327	0.98704	0.0:0.0:1.0:0.0	.	195;195	Q13161;Q13873	.;BMPR2_HUMAN	K	195	ENSP00000363708:E195K;ENSP00000363702:E195K	ENSP00000363702:E195K	E	+	1	0	BMPR2	203087909	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	9.123000	0.94387	2.794000	0.96219	0.650000	0.86243	GAA		0.398	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		A	203379664	G	A	203379664	3	1	61	1	0	0	0	0	1	0	0	0	1472	1059	37	1	601	1	BMPR2	2	203379664	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	790639	203379664	39819709	2045	10030										
BMPR2	659	broad.mit.edu	37	chr2	203420765	203420765	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagttgccaagatgaatAcaatcaatgcagcagaacct	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:203420765A>G	ENST00000374580.4	+	12	2916	c.2377A>G	c.(2377-2379)Aca>Gca	p.T793A	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	793					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.T793A(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						CAAGATGAATACAATCAATGC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	82	84					2																	203420765		2203	4300	6503	203129010	SO:0001583	missense	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2377A>G	2.37:g.203420765A>G	ENSP00000363708:p.Thr793Ala		203129010	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	12.77	2.038384	0.35989	.	.	ENSG00000204217	ENST00000374580	D	0.90324	-2.65	5.73	5.73	0.89815	.	0.096988	0.64402	D	0.000001	D	0.85274	0.5659	L	0.27053	0.805	0.80722	D	1	B	0.28512	0.214	B	0.24269	0.052	D	0.83726	0.0195	10	0.62326	D	0.03	.	16.0329	0.80593	1.0:0.0:0.0:0.0	.	793	Q13873	BMPR2_HUMAN	A	793	ENSP00000363708:T793A	ENSP00000363708:T793A	T	+	1	0	BMPR2	203129010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.905000	0.75714	2.197000	0.70478	0.533000	0.62120	ACA		0.438	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		G	203420765	A	G	203420765	3	3	61	1	0	0	0	0	1	0	0	0	1472	391	14	4	2423	4	BMPR2	2	203420765	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	41101	203420765	39778608	2046	10031										
BMPR2	659	broad.mit.edu	37	chr2	203421207	203421207	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagcacagaggcctaattCtctggatctttcagccacaa	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:203421207C>A	ENST00000374580.4	+	12	3358	c.2819C>A	c.(2818-2820)tCt>tAt	p.S940Y	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	940					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.S940Y(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						AGGCCTAATTCTCTGGATCTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											79	85	83					2																	203421207		2203	4300	6503	203129452	SO:0001583	missense	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2819C>A	2.37:g.203421207C>A	ENSP00000363708:p.Ser940Tyr		203129452	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114199	0.77210	.	.	ENSG00000204217	ENST00000374580	D	0.92699	-3.09	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94351	0.8184	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94332	0.7563	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	940	Q13873	BMPR2_HUMAN	Y	940	ENSP00000363708:S940Y	ENSP00000363708:S940Y	S	+	2	0	BMPR2	203129452	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.869000	0.75521	2.941000	0.99782	0.655000	0.94253	TCT		0.473	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		A	203421207	C	A	203421207	3	1	61	1	0	0	0	0	1	0	0	0	1472	913	32	2	2865	2	BMPR2	2	203421207	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	442	203421207	39778166	2047	10032										
ICA1L	130026	broad.mit.edu	37	chr2	203682156	203682156	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacctggtaggtagtgagCgaatgagatagcatattgca	14	5	0	2	rs144844508		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:203682156C>T	ENST00000392237.2	-	7	826	c.669G>A	c.(667-669)tcG>tcA	p.S223S	ICA1L_ENST00000358299.2_Silent_p.S223S	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	223	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.							p.S223S(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGTAGTGAGCGAATGAGATA	0.393													C|||	1	0.000199681	0	0.0014	5008	,	,		16360	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C		2,4404	4.2+/-10.8	0,2,2201	125	115	118		669	-11.9	0.1	2	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	ICA1L	NM_138468.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		223/483	203682156	2,13004	2203	4300	6503	203390401	SO:0001819	synonymous_variant	130026			AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.669G>A	2.37:g.203682156C>T			203390401	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Silent	SNP	ENST00000392237.2	37	CCDS2354.1																																																																																				0.393	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		T	203682156	C	T	203682156	2	4	61	1	0	0	0	0	0	0	0	1	7499	755	27	1		1	ICA1L	2	203682156	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	260949	203682156	39517217	2048	10033										
ICA1L	130026	broad.mit.edu	37	chr2	203682219	203682219	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttctgacaaacatccatCtttaacttgtcaaaagaagc	4	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:203682219C>A	ENST00000392237.2	-	7	763	c.606G>T	c.(604-606)aaG>aaT	p.K202N	ICA1L_ENST00000358299.2_Missense_Mutation_p.K202N	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	202	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.							p.K202N(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAACATCCATCTTTAACTTGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											113	100	105					2																	203682219		2203	4300	6503	203390464	SO:0001583	missense	130026			AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.606G>T	2.37:g.203682219C>A	ENSP00000376070:p.Lys202Asn		203390464	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	37	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242976	0.79912	.	.	ENSG00000163596	ENST00000392237;ENST00000358299	T;T	0.80653	-1.4;-1.4	5.96	5.09	0.68999	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.89649	0.6776	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90902	0.4769	10	0.87932	D	0	.	12.8176	0.57675	0.0:0.9213:0.0:0.0787	.	202	Q8NDH6	ICA1L_HUMAN	N	202	ENSP00000376070:K202N;ENSP00000351047:K202N	ENSP00000351047:K202N	K	-	3	2	ICA1L	203390464	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.162000	0.58177	1.527000	0.49086	0.655000	0.94253	AAG		0.368	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		A	203682219	C	A	203682219	3	1	61	1	0	0	0	0	1	0	0	0	7499	912	32	2	874	2	ICA1L	2	203682219	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63	203682219	39517154	2049	10034										
NBEAL1	65065	broad.mit.edu	37	chr2	204074005	204074005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatcttgggaaggacataTtgttgtctactccagcactg	9	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:204074005T>C	ENST00000449802.1	+	52	7991	c.7658T>C	c.(7657-7659)aTt>aCt	p.I2553T		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2553								p.I2553T(1)|p.I1263T(1)		NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GAAGGACATATTGTTGTCTAC	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	2											133	124	127					2																	204074005		1906	4126	6032	203782250	SO:0001583	missense	65065			AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7658T>C	2.37:g.204074005T>C	ENSP00000399903:p.Ile2553Thr		203782250	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.615954	0.46631	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.28895	5.0;1.59	5.26	4.11	0.48088	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.166570	0.52532	N	0.000065	T	0.37544	0.1007	M	0.81112	2.525	0.42602	D	0.993289	B;B;B	0.20368	0.044;0.005;0.002	B;B;B	0.29862	0.108;0.004;0.003	T	0.24584	-1.0156	10	0.52906	T	0.07	.	8.6282	0.33904	0.0:0.1579:0.0:0.8421	.	1263;2553;2542	D1MPS9;Q6ZS30;C9JGK5	.;NBEL1_HUMAN;.	T	2553;2463;568	ENSP00000399903:I2553T;ENSP00000388466:I568T	ENSP00000344985:I2463T	I	+	2	0	NBEAL1	203782250	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.495000	0.60353	0.854000	0.35336	0.377000	0.23210	ATT		0.438	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			C	204074005	T	C	204074005	3	2	61	1	0	0	0	0	1	0	0	0	10218	1493	52	4	7860	4	NBEAL1	2	204074005	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	391786	204074005	39125368	2050	10035										
ABI2	10152	broad.mit.edu	37	chr2	204245081	204245081	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctattgactatacaattCtagatgatattggacatgga	7	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:204245081C>A	ENST00000422511.2	+	3	467	c.436C>A	c.(436-438)Cta>Ata	p.L146I	ABI2_ENST00000261018.7_5'Flank|ABI2_ENST00000430418.1_Missense_Mutation_p.L146I|ABI2_ENST00000261016.6_Missense_Mutation_p.L101I|ABI2_ENST00000424558.1_Missense_Mutation_p.L146I|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000261017.5_Missense_Mutation_p.L146I|ABI2_ENST00000295851.5_Missense_Mutation_p.L146I			Q9NYB9	ABI2_HUMAN	abl-interactor 2	146					actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)	p.L146I(1)		breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						CTATACAATTCTAGATGATAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											84	89	87					2																	204245081		2203	4298	6501	203953326	SO:0001583	missense	10152			AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.436C>A	2.37:g.204245081C>A	ENSP00000396249:p.Leu146Ile		203953326	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.985819|3.985819	0.74589|0.74589	.|.	.|.	ENSG00000138443|ENSG00000138443	ENST00000451591|ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511	.|D;D;D;D;T;D;D	.|0.92199	.|-2.96;-2.99;-2.99;-2.99;-0.91;-2.96;-2.96	5.54|5.54	1.09|1.09	0.20402|0.20402	.|Abl-interactor, homeo-domain homologous domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95169|0.95169	0.8434|0.8434	M|M	0.82193|0.82193	2.58|2.58	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.76494	.|0.999;0.975;0.998;0.98;0.999	.|D;D;D;D;D	.|0.91635	.|0.999;0.981;0.99;0.989;0.999	D|D	0.93943|0.93943	0.7225|0.7225	5|10	.|0.87932	.|D	.|0	-10.9226|-10.9226	9.8515|9.8515	0.41059|0.41059	0.0:0.5678:0.0:0.4322|0.0:0.5678:0.0:0.4322	.|.	.|90;146;101;146;146	.|B7Z836;Q9NYB9-4;Q9NYB9-3;Q9NYB9;Q9NYB9-2	.|.;.;.;ABI2_HUMAN;.	L|I	17|146;146;146;146;101;146;146	.|ENSP00000295851:L146I;ENSP00000261017:L146I;ENSP00000408898:L146I;ENSP00000391433:L146I;ENSP00000261016:L101I;ENSP00000414703:L146I;ENSP00000396249:L146I	.|ENSP00000261016:L101I	F|L	+|+	3|1	2|2	ABI2|ABI2	203953326|203953326	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.005000|1.005000	0.29834|0.29834	0.289000|0.289000	0.22422|0.22422	0.591000|0.591000	0.81541|0.81541	TTC|CTA		0.323	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		A	204245081	C	A	204245081	3	1	61	1	0	0	0	0	1	0	0	0	89	912	32	2	446	2	ABI2	2	204245081	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171076	204245081	38954292	2051	10036										
RAPH1	65059	broad.mit.edu	37	chr2	204354694	204354694	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaatttctgagtagctttCgtttctgtgatttgacgctt	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:204354694C>T	ENST00000319170.5	-	4	644	c.345G>A	c.(343-345)acG>acA	p.T115T	RAPH1_ENST00000419464.1_Silent_p.T115T|RAPH1_ENST00000374489.2_Silent_p.T115T|RAPH1_ENST00000308091.4_Silent_p.T115T|RAPH1_ENST00000418114.1_Silent_p.T115T|RAPH1_ENST00000453034.1_Silent_p.T115T|RAPH1_ENST00000439222.1_Silent_p.T115T|RAPH1_ENST00000374493.3_Silent_p.T115T|RAPH1_ENST00000457812.1_Silent_p.T115T|RAPH1_ENST00000374488.2_Silent_p.T115T|RAPH1_ENST00000423104.1_Silent_p.T115T	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	115					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.T115T(1)		breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GAGTAGCTTTCGTTTCTGTGA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	2											235	227	230					2																	204354694		2203	4300	6503	204062939	SO:0001819	synonymous_variant	65059			AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.345G>A	2.37:g.204354694C>T			204062939	Q96Q37|Q9C0I2	Silent	SNP	ENST00000319170.5	37	CCDS2359.1																																																																																				0.433	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		T	204354694	C	T	204354694	2	4	61	1	0	0	0	0	0	0	0	1	13087	871	31	1		1	RAPH1	2	204354694	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109613	204354694	38844679	2052	10037										
CD28	940	broad.mit.edu	37	chr2	204599612	204599612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccctatgccccaccacgcGacttcgcagcctatcgctcc	7	20	0	0	rs201909740		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:204599612G>A	ENST00000324106.8	+	4	789	c.640G>A	c.(640-642)Gac>Aac	p.D214N	CD28_ENST00000374481.3_Missense_Mutation_p.D130N|CD28_ENST00000458610.2_Missense_Mutation_p.D228N|CD28_ENST00000374478.4_Missense_Mutation_p.D95N	NM_001243077.1|NM_006139.3	NP_001230006.1|NP_006130.1	P10747	CD28_HUMAN	CD28 molecule	214					apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cytokine biosynthetic process (GO:0042089)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|negative thymic T cell selection (GO:0045060)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of inflammatory response to antigenic stimulus (GO:0002863)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of mitosis (GO:0045840)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of viral genome replication (GO:0045070)|regulation of defense response to virus by virus (GO:0050690)|regulatory T cell differentiation (GO:0045066)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|SH3/SH2 adaptor activity (GO:0005070)	p.D214N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13						CCCACCACGCGACTTCGCAGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	63	61					2																	204599612		2203	4300	6503	204307857	SO:0001583	missense	940			J02988	CCDS2361.1, CCDS58749.1	2q33	2013-01-11	2006-03-28		ENSG00000178562	ENSG00000178562		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1653	protein-coding gene	gene with protein product	"T-cell-specific surface glycoprotein"	186760	"CD28 antigen (Tp44)"			1355979	Standard	NM_006139		Approved		uc002vah.4	P10747	OTTHUMG00000132878	ENST00000324106.8:c.640G>A	2.37:g.204599612G>A	ENSP00000324890:p.Asp214Asn		204307857	A8KAC1|Q13964|Q52M23|Q70WG0|Q8NI54|Q8NI55|Q8NI56|Q8WXJ2|Q9BYV0	Missense_Mutation	SNP	ENST00000324106.8	37	CCDS2361.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.144970	0.77888	.	.	ENSG00000178562	ENST00000374481;ENST00000458610;ENST00000324106;ENST00000374478	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000008	D	0.90103	0.6908	M	0.80982	2.52	0.44789	D	0.997792	D;D	0.89917	1.0;0.994	D;P	0.91635	0.999;0.586	D	0.89561	0.3806	10	0.44086	T	0.13	-52.5152	11.3728	0.49711	0.0854:0.0:0.9146:0.0	.	95;214	P10747-2;P10747	.;CD28_HUMAN	N	130;228;214;95	ENSP00000363605:D130N;ENSP00000393648:D228N;ENSP00000324890:D214N;ENSP00000363602:D95N	ENSP00000324890:D214N	D	+	1	0	CD28	204307857	0.999000	0.42202	0.952000	0.39060	0.563000	0.35712	3.319000	0.51983	2.555000	0.86185	0.655000	0.94253	GAC		0.612	CD28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256366.3	NM_006139		A	204599612	G	A	204599612	3	1	61	1	0	0	0	0	1	0	0	0	2999	1058	37	1	654	1	CD28	2	204599612	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244918	204599612	38599761	2053	10038										
CTLA4	1493	broad.mit.edu	37	chr2	204737436	204737436	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtgtttgacagctaaaGaaaagaagccctcttacaac	7	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:204737436G>T	ENST00000302823.3	+	4	730	c.573G>T	c.(571-573)aaG>aaT	p.K191N	CTLA4_ENST00000295854.6_Nonsense_Mutation_p.E155*|CTLA4_ENST00000427473.2_Nonsense_Mutation_p.E118*|CTLA4_ENST00000472206.1_Nonsense_Mutation_p.E60*|CTLA4_ENST00000487393.1_3'UTR	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	191					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.K191N(1)		large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	GACAGCTAAAGAAAAGAAGCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	85	85					2																	204737436		2203	4300	6503	204445681	SO:0001583	missense	1493				CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.573G>T	2.37:g.204737436G>T	ENSP00000303939:p.Lys191Asn		204445681	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	37	CCDS2362.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.28|15.28	2.787750|2.787750	0.49997|0.49997	.|.	.|.	ENSG00000163599|ENSG00000163599	ENST00000295854;ENST00000472206;ENST00000427473|ENST00000302823	.|T	.|0.36340	.|1.26	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.063176	.|0.64402	.|D	.|0.000006	.|T	.|0.40196	.|0.1107	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|P	.|0.55749	.|0.783	.|T	.|0.25187	.|-1.0139	.|10	0.66056|0.54805	D|T	0.02|0.06	-5.9658|-5.9658	17.0211|17.0211	0.86434|0.86434	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191	.|P16410	.|CTLA4_HUMAN	X|N	155;60;118|191	.|ENSP00000303939:K191N	ENSP00000295854:E155X|ENSP00000303939:K191N	E|K	+|+	1|3	0|2	CTLA4|CTLA4	204445681|204445681	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.105000|0.105000	0.19272|0.19272	3.197000|3.197000	0.51028|0.51028	2.700000|2.700000	0.92200|0.92200	0.561000|0.561000	0.74099|0.74099	GAA|AAG		0.398	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		T	204737436	G	T	204737436	3	4	61	1	0	0	0	0	1	0	0	0	4017	943	33	2	587	2	CTLA4	2	204737436	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137824	204737436	38461937	2054	10039										
NRP2	8828	broad.mit.edu	37	chr2	206548024	206548024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttctccaaaatggatatgTttcctctcacctgggttttc	6	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206548024T>C	ENST00000357785.5	+	1	41	c.10T>C	c.(10-12)Ttt>Ctt	p.F4L	NRP2_ENST00000357118.4_Missense_Mutation_p.F4L|NRP2_ENST00000272849.3_Missense_Mutation_p.F4L|NRP2_ENST00000355117.4_Missense_Mutation_p.F4L|NRP2_ENST00000540841.1_Missense_Mutation_p.F4L|NRP2_ENST00000412873.2_Missense_Mutation_p.F4L|NRP2_ENST00000360409.3_Missense_Mutation_p.F4L|NRP2_ENST00000417189.1_Missense_Mutation_p.F4L|NRP2_ENST00000540178.1_Missense_Mutation_p.F4L			Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.F4L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						AATGGATATGTTTCCTCTCAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											91	90	90					2																	206548024		2203	4300	6503	206256269	SO:0001583	missense	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.10T>C	2.37:g.206548024T>C	ENSP00000350432:p.Phe4Leu		206256269	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	t	6.695	0.496949	0.12762	.	.	ENSG00000118257	ENST00000340626;ENST00000360409;ENST00000540178;ENST00000540841;ENST00000355117;ENST00000450507;ENST00000417189;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849	D;D;D;D;T;D;D;D;D;D	0.88818	-2.1;-2.11;-2.13;-2.43;1.64;-2.43;-2.17;-2.16;-2.2;-2.19	5.71	-1.19	0.09585	.	0.764526	0.12565	N	0.457825	T	0.78323	0.4265	L	0.32530	0.975	0.23483	N	0.997585	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.64326	-0.6434	10	0.51188	T	0.08	-0.6657	2.0702	0.03612	0.1184:0.136:0.2459:0.4996	.	4;4;4;4;4;4	O60462-2;O60462-3;O60462;O60462-4;O60462-5;E9PF66	.;.;NRP2_HUMAN;.;.;.	L	4	ENSP00000353582:F4L;ENSP00000439658:F4L;ENSP00000439261:F4L;ENSP00000347238:F4L;ENSP00000404279:F4L;ENSP00000387519:F4L;ENSP00000349632:F4L;ENSP00000350432:F4L;ENSP00000407626:F4L;ENSP00000272849:F4L	ENSP00000272849:F4L	F	+	1	0	NRP2	206256269	1.000000	0.71417	0.995000	0.50966	0.013000	0.08279	0.458000	0.21892	-0.171000	0.10797	-1.168000	0.01747	TTT		0.403	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			C	206548024	T	C	206548024	3	2	61	1	0	0	0	0	1	0	0	0	10692	1725	60	4	12	4	NRP2	2	206548024	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1810588	206548024	36651349	2055	10040										
NRP2	8828	broad.mit.edu	37	chr2	206587264	206587264	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcgaatctcctgggtttCctgagaagtatccacacaac	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206587264C>A	ENST00000357785.5	+	4	527	c.496C>A	c.(496-498)Cct>Act	p.P166T	NRP2_ENST00000357118.4_Missense_Mutation_p.P166T|NRP2_ENST00000272849.3_Missense_Mutation_p.P166T|NRP2_ENST00000355117.4_Missense_Mutation_p.P166T|NRP2_ENST00000540841.1_Missense_Mutation_p.P166T|NRP2_ENST00000412873.2_Missense_Mutation_p.P166T|NRP2_ENST00000360409.3_Missense_Mutation_p.P166T|NRP2_ENST00000417189.1_Missense_Mutation_p.P166T|NRP2_ENST00000540178.1_Missense_Mutation_p.P166T			Q99435	NELL2_HUMAN	neuropilin 2	627	Laminin G-like.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P166T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						TCCTGGGTTTCCTGAGAAGTA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											137	126	130					2																	206587264		2203	4300	6503	206295509	SO:0001583	missense	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.496C>A	2.37:g.206587264C>A	ENSP00000350432:p.Pro166Thr		206295509	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.788049	0.90367	.	.	ENSG00000118257	ENST00000360409;ENST00000540178;ENST00000540841;ENST00000355117;ENST00000417189;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849	T;T;T;T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61	6.17	6.17	0.99709	CUB (5);	0.000000	0.85682	D	0.000000	T	0.80319	0.4601	H	0.95114	3.625	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999	D	0.84518	0.0626	10	0.87932	D	0	-17.0155	20.8794	0.99867	0.0:1.0:0.0:0.0	.	166;166;166;166;166;166	O60462-2;O60462-3;O60462;O60462-4;O60462-5;E9PF66	.;.;NRP2_HUMAN;.;.;.	T	166	ENSP00000353582:P166T;ENSP00000439658:P166T;ENSP00000439261:P166T;ENSP00000347238:P166T;ENSP00000387519:P166T;ENSP00000349632:P166T;ENSP00000350432:P166T;ENSP00000407626:P166T;ENSP00000272849:P166T	ENSP00000272849:P166T	P	+	1	0	NRP2	206295509	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CCT		0.463	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			A	206587264	C	A	206587264	3	1	61	1	0	0	0	0	1	0	0	0	10692	855	30	2	510	2	NRP2	2	206587264	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39240	206587264	36612109	2056	10041										
NRP2	8828	broad.mit.edu	37	chr2	206608213	206608213	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgcgcaagttcaaagtCtcctacagcctaaacggcaa	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206608213C>T	ENST00000357785.5	+	9	1609	c.1578C>T	c.(1576-1578)gtC>gtT	p.V526V	NRP2_ENST00000357118.4_Silent_p.V526V|NRP2_ENST00000272849.3_Silent_p.V526V|NRP2_ENST00000355117.4_Silent_p.V526V|NRP2_ENST00000540841.1_Silent_p.V526V|NRP2_ENST00000412873.2_Silent_p.V526V|NRP2_ENST00000360409.3_Silent_p.V526V|NRP2_ENST00000417189.1_Silent_p.V526V|NRP2_ENST00000540178.1_Silent_p.V526V			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.V526V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						AGTTCAAAGTCTCCTACAGCC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	2											78	84	82					2																	206608213		2203	4300	6503	206316458	SO:0001819	synonymous_variant	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1578C>T	2.37:g.206608213C>T			206316458	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																				0.542	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			T	206608213	C	T	206608213	2	4	61	1	0	0	0	0	0	0	0	1	10692	900	32	3		3	NRP2	2	206608213	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20949	206608213	36591160	2057	10042										
NRP2	8828	broad.mit.edu	37	chr2	206617600	206617600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggattcaattgcaacttcGatttcctcgaggagccctgt	10	11	1	0	rs150629453		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206617600G>A	ENST00000357785.5	+	12	1976	c.1945G>A	c.(1945-1947)Gat>Aat	p.D649N	NRP2_ENST00000357118.4_Missense_Mutation_p.D649N|NRP2_ENST00000272849.3_Missense_Mutation_p.D649N|NRP2_ENST00000540841.1_Missense_Mutation_p.D649N|NRP2_ENST00000412873.2_Missense_Mutation_p.D649N|NRP2_ENST00000360409.3_Missense_Mutation_p.D649N|NRP2_ENST00000540178.1_Missense_Mutation_p.D649N			Q99435	NELL2_HUMAN	neuropilin 2	639	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D649N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						TTGCAACTTCGATTTCCTCGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	64	63	63		1945,1945,1945,1945,1945	5.7	1	2	dbSNP_134	63	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	NRP2	NM_003872.2,NM_018534.3,NM_201266.1,NM_201267.1,NM_201279.1	23,23,23,23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	649/927,649/907,649/932,649/902,649/910	206617600	1,13005	2203	4300	6503	206325845	SO:0001583	missense	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1945G>A	2.37:g.206617600G>A	ENSP00000350432:p.Asp649Asn		206325845	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.794043	0.70452	0.0	1.16E-4	ENSG00000118257	ENST00000360409;ENST00000540178;ENST00000540841;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849	T;T;T;T;T;T;T	0.02552	4.25;4.25;4.25;4.25;4.25;4.25;4.25	5.71	5.71	0.89125	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.179144	0.64402	D	0.000014	T	0.13030	0.0316	L	0.52364	1.645	0.80722	D	1	P;P;D;P;P	0.89917	0.843;0.843;1.0;0.916;0.916	B;B;D;B;B	0.85130	0.133;0.133;0.997;0.348;0.348	T	0.00322	-1.1818	10	0.52906	T	0.07	-19.1175	19.8575	0.96767	0.0:0.0:1.0:0.0	.	649;649;649;649;649	O60462-2;O60462-3;O60462;O60462-4;O60462-5	.;.;NRP2_HUMAN;.;.	N	649	ENSP00000353582:D649N;ENSP00000439658:D649N;ENSP00000439261:D649N;ENSP00000349632:D649N;ENSP00000350432:D649N;ENSP00000407626:D649N;ENSP00000272849:D649N	ENSP00000272849:D649N	D	+	1	0	NRP2	206325845	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.473000	0.73572	2.698000	0.92095	0.561000	0.74099	GAT		0.522	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			A	206617600	G	A	206617600	3	1	61	1	0	0	0	0	1	0	0	0	10692	1058	37	1	2018	1	NRP2	2	206617600	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9387	206617600	36581773	2058	10043										
NRP2	8828	broad.mit.edu	37	chr2	206659554	206659554	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcgaccgacaaagaaaaGagctggctgtacaccctgga	10	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206659554G>T	ENST00000357785.5	+	17	2584	c.2553G>T	c.(2551-2553)aaG>aaT	p.K851N	NRP2_ENST00000540841.1_Missense_Mutation_p.K834N|NRP2_ENST00000412873.2_Missense_Mutation_p.K834N|NRP2_ENST00000360409.3_Missense_Mutation_p.K856N|NRP2_ENST00000540178.1_Missense_Mutation_p.K851N			Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.K856N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						ACAAAGAAAAGAGCTGGCTGT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	82	86					2																	206659554		2203	4300	6503	206367799	SO:0001583	missense	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.2553G>T	2.37:g.206659554G>T	ENSP00000350432:p.Lys851Asn		206367799	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	G	4.379	0.069932	0.08436	.	.	ENSG00000118257	ENST00000360409;ENST00000540178;ENST00000540841;ENST00000357785;ENST00000412873	D;D;D;D;D	0.87491	-2.22;-2.19;-2.2;-2.26;-2.26	5.93	4.13	0.48395	.	0.410884	0.30043	N	0.010553	T	0.70072	0.3182	N	0.03115	-0.41	0.80722	D	1	B;B;B	0.16396	0.017;0.007;0.009	B;B;B	0.15052	0.01;0.007;0.012	T	0.64837	-0.6313	10	0.31617	T	0.26	-26.2896	9.4105	0.38489	0.2795:0.0:0.7205:0.0	.	834;851;856	O60462-2;O60462-3;O60462	.;.;NRP2_HUMAN	N	856;851;834;851;834	ENSP00000353582:K856N;ENSP00000439658:K851N;ENSP00000439261:K834N;ENSP00000350432:K851N;ENSP00000407626:K834N	ENSP00000350432:K851N	K	+	3	2	NRP2	206367799	1.000000	0.71417	1.000000	0.80357	0.223000	0.24884	2.242000	0.43106	1.533000	0.49186	0.655000	0.94253	AAG		0.552	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			T	206659554	G	T	206659554	3	4	61	1	0	0	0	0	1	0	0	0	10692	933	33	2	2946	2	NRP2	2	206659554	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41954	206659554	36539819	2059	10044										
NDUFS1	4719	broad.mit.edu	37	chr2	206991506	206991506	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcgaacaagattaggagaGacttcttccaatctgttcct	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:206991506G>T	ENST00000233190.6	-	17	2213	c.1947C>A	c.(1945-1947)gtC>gtA	p.V649V	NDUFS1_ENST00000449699.1_Silent_p.V649V|NDUFS1_ENST00000455934.2_Silent_p.V663V|NDUFS1_ENST00000457011.1_Silent_p.V533V|NDUFS1_ENST00000432169.1_Silent_p.V538V|NDUFS1_ENST00000423725.1_Silent_p.V592V|NDUFS1_ENST00000440274.1_Silent_p.V613V	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	649			V -> F (in dbSNP:rs1044049). {ECO:0000269|PubMed:1935949}.		apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.V649V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GATTAGGAGAGACTTCTTCCA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	2											150	150	150					2																	206991506		2203	4300	6503	206699751	SO:0001819	synonymous_variant	4719				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1947C>A	2.37:g.206991506G>T			206699751	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	37	CCDS2366.1																																																																																				0.403	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		T	206991506	G	T	206991506	2	4	61	1	0	0	0	0	0	0	0	1	10322	929	33	2		2	NDUFS1	2	206991506	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	331952	206991506	36207867	2060	10045										
EEF1B2	1933	broad.mit.edu	37	chr2	207027212	207027212	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctgtttattgtttttaGaacctgcacttgttgccaag	8	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207027212G>T	ENST00000392222.2	+	5	772		c.e5-1		NDUFS1_ENST00000233190.6_5'Flank|SNORD51_ENST00000384320.2_RNA|SNORA41_ENST00000384675.1_RNA|EEF1B2_ENST00000236957.5_Splice_Site|NDUFS1_ENST00000423725.1_5'Flank|EEF1B2_ENST00000392221.1_Splice_Site	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)	p.?(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						ATTGTTTTTAGAACCTGCACT	0.363																																																1	Unknown(1)	large_intestine(1)	2											104	113	110					2																	207027212		2203	4300	6503	206735457	SO:0001630	splice_region_variant	1933			X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.398-1G>T	2.37:g.207027212G>T			206735457	A8K795|Q6IBH9	Splice_Site	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323571	0.60634	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2326	0.89938	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EEF1B2	206735457	1.000000	0.71417	0.995000	0.50966	0.824000	0.46624	8.710000	0.91388	2.308000	0.77769	0.655000	0.94253	.		0.363	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663	Intron	T	207027212	G	T	207027212	5	4	61	1	0	0	0	0	0	0	1	0	4936	956	33	2	415	2	EEF1B2	2	207027212	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35706	207027212	36172161	2061	10046										
GPR1	2825	broad.mit.edu	37	chr2	207040924	207040924	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattgagctgtttccaggaGacacagattcttggtttctg	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207040924G>T	ENST00000407325.2	-	3	1410	c.1048C>A	c.(1048-1050)Ctc>Atc	p.L350I	GPR1_ENST00000437420.1_Missense_Mutation_p.L350I	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	350					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.L350I(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		GTTTCCAGGAGACACAGATTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	59	60					2																	207040924		2203	4300	6503	206749169	SO:0001583	missense	2825				CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.1048C>A	2.37:g.207040924G>T	ENSP00000384345:p.Leu350Ile		206749169	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	37	CCDS2368.1	.	.	.	.	.	.	.	.	.	.	G	8.521	0.868669	0.17322	.	.	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.71817	-0.6;-0.6	5.56	5.56	0.83823	.	0.392413	0.22739	N	0.056236	T	0.50103	0.1596	N	0.08118	0	0.18873	N	0.999988	P	0.43094	0.799	B	0.40901	0.343	T	0.47923	-0.9079	10	0.41790	T	0.15	.	9.4686	0.38829	0.077:0.1443:0.7787:0.0	.	350	P46091	GPR1_HUMAN	I	350	ENSP00000384345:L350I;ENSP00000397535:L350I	ENSP00000384345:L350I	L	-	1	0	GPR1	206749169	0.006000	0.16342	0.988000	0.46212	0.062000	0.15995	0.748000	0.26305	2.636000	0.89361	0.655000	0.94253	CTC		0.418	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		T	207040924	G	T	207040924	3	4	61	1	0	0	0	0	1	0	0	0	6641	942	33	2	23	2	GPR1	2	207040924	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13712	207040924	36158449	2062	10047										
ZDBF2	57683	broad.mit.edu	37	chr2	207162004	207162004	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcacaggagtttgaccaGacagagtagacgtcaaatat	10	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207162004G>T	ENST00000374423.3	+	4	481	c.95G>T	c.(94-96)aGa>aTa	p.R32I		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	32							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R32I(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGTTTGACCAGACAGAGTAGA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	2											114	103	106					2																	207162004		1863	4113	5976	206870249	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.95G>T	2.37:g.207162004G>T	ENSP00000363545:p.Arg32Ile		206870249	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581597	0.46006	.	.	ENSG00000204186	ENST00000374423	T	0.52057	0.68	4.81	2.04	0.26737	Zinc finger, DBF-type (2);	.	.	.	.	T	0.28797	0.0714	N	0.19112	0.55	0.09310	N	0.999998	B	0.30634	0.288	B	0.28638	0.092	T	0.15896	-1.0421	9	0.44086	T	0.13	.	5.6109	0.17404	0.0:0.5259:0.2516:0.2225	.	32	Q9HCK1	ZDBF2_HUMAN	I	32	ENSP00000363545:R32I	ENSP00000363545:R32I	R	+	2	0	ZDBF2	206870249	0.006000	0.16342	0.009000	0.14445	0.575000	0.36095	0.384000	0.20668	0.203000	0.20529	0.484000	0.47621	AGA		0.383	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207162004	G	T	207162004	3	4	61	1	0	0	0	0	1	0	0	0	17638	942	33	2	101	2	ZDBF2	2	207162004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121080	207162004	36037369	2063	10048										
ZDBF2	57683	broad.mit.edu	37	chr2	207170018	207170018	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcgtatcagaaacataaaGaatcaaataggaaatcttta	5	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207170018G>T	ENST00000374423.3	+	5	1152	c.766G>T	c.(766-768)Gaa>Taa	p.E256*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	256							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E256*(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GAAACATAAAGAATCAAATAG	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											30	29	29					2																	207170018		1828	4084	5912	206878263	SO:0001587	stop_gained	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.766G>T	2.37:g.207170018G>T	ENSP00000363545:p.Glu256*		206878263	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588904	0.86851	.	.	ENSG00000204186	ENST00000374423	.	.	.	5.11	3.16	0.36331	.	0.000000	0.36972	N	0.002304	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	2.7319	0.05229	0.0953:0.1405:0.4383:0.3259	.	.	.	.	X	256	.	ENSP00000363545:E256X	E	+	1	0	ZDBF2	206878263	0.204000	0.23447	0.679000	0.29978	0.082000	0.17680	1.981000	0.40628	1.117000	0.41842	0.650000	0.86243	GAA		0.363	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207170018	G	T	207170018	4	4	61	1	0	0	0	0	0	1	0	0	17638	943	33	2	776	2	ZDBF2	2	207170018	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8014	207170018	36029355	2064	10049										
ZDBF2	57683	broad.mit.edu	37	chr2	207170663	207170663	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcccaaatgattgttaaaGaaataagtcttcagaatgca	6	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207170663G>T	ENST00000374423.3	+	5	1797	c.1411G>T	c.(1411-1413)Gaa>Taa	p.E471*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	471							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E471*(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GATTGTTAAAGAAATAAGTCT	0.333																																																2	Substitution - Nonsense(2)	large_intestine(2)	2											43	41	42					2																	207170663		1847	4090	5937	206878908	SO:0001587	stop_gained	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.1411G>T	2.37:g.207170663G>T	ENSP00000363545:p.Glu471*		206878908	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	38	6.993924	0.97987	.	.	ENSG00000204186	ENST00000374423	.	.	.	4.89	4.89	0.63831	.	0.851161	0.09773	N	0.757716	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	14.2831	0.66226	0.0:0.0:1.0:0.0	.	.	.	.	X	471	.	ENSP00000363545:E471X	E	+	1	0	ZDBF2	206878908	0.997000	0.39634	0.033000	0.17914	0.004000	0.04260	3.749000	0.55150	2.638000	0.89438	0.603000	0.83216	GAA		0.333	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207170663	G	T	207170663	4	4	61	1	0	0	0	0	0	1	0	0	17638	943	33	2	1421	2	ZDBF2	2	207170663	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	645	207170663	36028710	2065	10050										
ZDBF2	57683	broad.mit.edu	37	chr2	207171187	207171187	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagagggctgttgaaaaGataaatcttctgaaggagaa	11	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207171187G>T	ENST00000374423.3	+	5	2321	c.1935G>T	c.(1933-1935)aaG>aaT	p.K645N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	645							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.K645N(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CTGTTGAAAAGATAAATCTTC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	2											90	87	88					2																	207171187		1871	4112	5983	206879432	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.1935G>T	2.37:g.207171187G>T	ENSP00000363545:p.Lys645Asn		206879432	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	2.684	-0.274653	0.05679	.	.	ENSG00000204186	ENST00000374423	T	0.45276	0.9	4.06	-1.26	0.09376	.	1.078320	0.07314	N	0.876301	T	0.21427	0.0516	N	0.12182	0.205	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.20075	-1.0286	10	0.45353	T	0.12	.	3.4305	0.07426	0.4091:0.0:0.3992:0.1918	.	645	Q9HCK1	ZDBF2_HUMAN	N	645	ENSP00000363545:K645N	ENSP00000363545:K645N	K	+	3	2	ZDBF2	206879432	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	-0.207000	0.09384	-0.212000	0.10109	-0.302000	0.09304	AAG		0.423	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207171187	G	T	207171187	3	4	61	1	0	0	0	0	1	0	0	0	17638	933	33	2	1945	2	ZDBF2	2	207171187	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	524	207171187	36028186	2066	10051										
ZDBF2	57683	broad.mit.edu	37	chr2	207172439	207172439	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaactagcttttttgaagGaaaaacatgttaatctgaag	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207172439G>T	ENST00000374423.3	+	5	3573	c.3187G>T	c.(3187-3189)Gaa>Taa	p.E1063*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1063							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E1063*(2)|p.E1063K(1)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TTTTTTGAAGGAAAAACATGT	0.323																																																3	Substitution - Nonsense(2)|Substitution - Missense(1)	large_intestine(2)|NS(1)	2											55	54	54					2																	207172439		1816	4085	5901	206880684	SO:0001587	stop_gained	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3187G>T	2.37:g.207172439G>T	ENSP00000363545:p.Glu1063*		206880684	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	40	7.964113	0.98585	.	.	ENSG00000204186	ENST00000374423	.	.	.	3.39	1.48	0.22813	.	0.713313	0.11617	N	0.546171	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	4.6656	0.12664	0.1272:0.2254:0.6473:0.0	.	.	.	.	X	1063	.	ENSP00000363545:E1063X	E	+	1	0	ZDBF2	206880684	0.314000	0.24563	0.001000	0.08648	0.008000	0.06430	0.879000	0.28146	0.402000	0.25451	0.557000	0.71058	GAA		0.323	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207172439	G	T	207172439	4	4	61	1	0	0	0	0	0	1	0	0	17638	1175	41	2	3197	2	ZDBF2	2	207172439	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1252	207172439	36026934	2067	10052										
ZDBF2	57683	broad.mit.edu	37	chr2	207173188	207173188	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaataaatcttttgagggaGgaacatgtttgtctggatga	12	3	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207173188G>T	ENST00000374423.3	+	5	4322	c.3936G>T	c.(3934-3936)gaG>gaT	p.E1312D		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1312							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E1312D(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TTTTGAGGGAGGAACATGTTT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	2											38	37	37					2																	207173188		1833	4074	5907	206881433	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3936G>T	2.37:g.207173188G>T	ENSP00000363545:p.Glu1312Asp		206881433	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398419	0.42512	.	.	ENSG00000204186	ENST00000374423	T	0.50001	0.76	3.38	0.404	0.16355	.	.	.	.	.	T	0.51176	0.1659	M	0.64404	1.975	0.09310	N	1	D	0.61080	0.989	P	0.55391	0.775	T	0.41251	-0.9519	9	0.66056	D	0.02	.	2.683	0.05100	0.2679:0.0:0.5095:0.2226	.	1312	Q9HCK1	ZDBF2_HUMAN	D	1312	ENSP00000363545:E1312D	ENSP00000363545:E1312D	E	+	3	2	ZDBF2	206881433	0.952000	0.32445	0.185000	0.23176	0.010000	0.07245	0.433000	0.21477	0.061000	0.16311	-0.175000	0.13238	GAG		0.363	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207173188	G	T	207173188	3	4	61	1	0	0	0	0	1	0	0	0	17638	991	35	2	3946	2	ZDBF2	2	207173188	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	749	207173188	36026185	2068	10053										
ZDBF2	57683	broad.mit.edu	37	chr2	207173411	207173411	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcaaaaacctgtcaaaGaaataaatctttggaaggaa	7	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207173411G>A	ENST00000374423.3	+	5	4545	c.4159G>A	c.(4159-4161)Gaa>Aaa	p.E1387K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1387							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E1387K(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ACCTGTCAAAGAAATAAATCT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	2											45	43	44					2																	207173411		1823	4087	5910	206881656	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.4159G>A	2.37:g.207173411G>A	ENSP00000363545:p.Glu1387Lys		206881656	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.229661	0.39399	.	.	ENSG00000204186	ENST00000374423	T	0.48522	0.81	3.76	2.87	0.33458	.	.	.	.	.	T	0.56688	0.2002	M	0.67397	2.05	0.09310	N	1	D	0.61697	0.99	P	0.57620	0.824	T	0.42498	-0.9448	9	0.46703	T	0.11	.	7.1084	0.25376	0.1222:0.0:0.8778:0.0	.	1387	Q9HCK1	ZDBF2_HUMAN	K	1387	ENSP00000363545:E1387K	ENSP00000363545:E1387K	E	+	1	0	ZDBF2	206881656	0.663000	0.27448	0.013000	0.15412	0.222000	0.24845	1.236000	0.32683	1.156000	0.42514	0.650000	0.86243	GAA		0.353	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207173411	G	A	207173411	3	1	61	1	0	0	0	0	1	0	0	0	17638	943	33	3	4169	3	ZDBF2	2	207173411	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223	207173411	36025962	2069	10054										
ZDBF2	57683	broad.mit.edu	37	chr2	207173526	207173526	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtttgtgactgatcaatCttctgtacctgtcaaagaaa	7	8	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207173526C>A	ENST00000374423.3	+	5	4660	c.4274C>A	c.(4273-4275)tCt>tAt	p.S1425Y		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1425							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S1425Y(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ACTGATCAATCTTCTGTACCT	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	2											55	53	54					2																	207173526		1828	4088	5916	206881771	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.4274C>A	2.37:g.207173526C>A	ENSP00000363545:p.Ser1425Tyr		206881771	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	7.863	0.726446	0.15439	.	.	ENSG00000204186	ENST00000374423	T	0.55760	0.5	3.54	2.66	0.31614	.	.	.	.	.	T	0.62612	0.2442	L	0.58101	1.795	0.09310	N	1	D	0.69078	0.997	D	0.65573	0.936	T	0.48547	-0.9026	9	0.59425	D	0.04	.	6.6258	0.22828	0.0:0.8709:0.0:0.1291	.	1425	Q9HCK1	ZDBF2_HUMAN	Y	1425	ENSP00000363545:S1425Y	ENSP00000363545:S1425Y	S	+	2	0	ZDBF2	206881771	0.030000	0.19436	0.005000	0.12908	0.047000	0.14425	0.981000	0.29526	1.069000	0.40788	0.650000	0.86243	TCT		0.323	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207173526	C	A	207173526	3	1	61	1	0	0	0	0	1	0	0	0	17638	913	32	2	4284	2	ZDBF2	2	207173526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115	207173526	36025847	2070	10055										
ZDBF2	57683	broad.mit.edu	37	chr2	207174574	207174574	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaaagacacccttgtaaGaaggtatcttctgacttgaa	8	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207174574G>T	ENST00000374423.3	+	5	5708	c.5322G>T	c.(5320-5322)aaG>aaT	p.K1774N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1774							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.K1774N(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ACCCTTGTAAGAAGGTATCTT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2											56	57	57					2																	207174574		1863	4101	5964	206882819	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5322G>T	2.37:g.207174574G>T	ENSP00000363545:p.Lys1774Asn		206882819	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972597	0.34848	.	.	ENSG00000204186	ENST00000374423	T	0.57273	0.41	5.04	2.11	0.27256	.	.	.	.	.	T	0.43964	0.1271	L	0.46157	1.445	0.09310	N	1	P	0.41313	0.745	B	0.41236	0.351	T	0.39563	-0.9608	9	0.72032	D	0.01	.	4.9457	0.13987	0.2301:0.0:0.6037:0.1662	.	1774	Q9HCK1	ZDBF2_HUMAN	N	1774	ENSP00000363545:K1774N	ENSP00000363545:K1774N	K	+	3	2	ZDBF2	206882819	0.957000	0.32711	0.085000	0.20634	0.008000	0.06430	1.369000	0.34227	1.333000	0.45449	0.650000	0.86243	AAG		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207174574	G	T	207174574	3	4	61	1	0	0	0	0	1	0	0	0	17638	933	33	2	5332	2	ZDBF2	2	207174574	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1048	207174574	36024799	2071	10056										
ZDBF2	57683	broad.mit.edu	37	chr2	207175956	207175956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatactctgtctttttacGtcatagatatcagtccagga	7	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207175956G>A	ENST00000374423.3	+	5	7090	c.6704G>A	c.(6703-6705)cGt>cAt	p.R2235H		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2235							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R2235H(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GTCTTTTTACGTCATAGATAT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	2											37	37	37					2																	207175956		1817	4075	5892	206884201	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.6704G>A	2.37:g.207175956G>A	ENSP00000363545:p.Arg2235His		206884201	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137374	0.37728	.	.	ENSG00000204186	ENST00000374423	T	0.50548	0.74	5.46	0.00825	0.14074	.	.	.	.	.	T	0.27765	0.0683	L	0.36672	1.1	0.09310	N	1	B	0.23806	0.091	B	0.15870	0.014	T	0.18967	-1.0320	9	0.15066	T	0.55	.	1.7333	0.02936	0.2405:0.3202:0.3106:0.1287	.	2235	Q9HCK1	ZDBF2_HUMAN	H	2235	ENSP00000363545:R2235H	ENSP00000363545:R2235H	R	+	2	0	ZDBF2	206884201	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.158000	0.10070	0.051000	0.15978	-0.137000	0.14449	CGT		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207175956	G	A	207175956	3	1	61	1	0	0	0	0	1	0	0	0	17638	1145	40	1	6714	1	ZDBF2	2	207175956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1382	207175956	36023417	2072	10057										
DYTN	391475	broad.mit.edu	37	chr2	207516562	207516562	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacttcaaattgggcaaggCaatttgatcaacaagggcag	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207516562C>A	ENST00000452335.2	-	12	1833	c.1717G>T	c.(1717-1719)Gcc>Tcc	p.A573S	AC010731.4_ENST00000543490.1_lincRNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	573						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.A573S(2)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		TTGGGCAAGGCAATTTGATCA	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	2											66	68	68					2																	207516562		1970	4165	6135	207224807	SO:0001583	missense	391475			ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1717G>T	2.37:g.207516562C>A	ENSP00000396593:p.Ala573Ser		207224807		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	C	7.072	0.568445	0.13560	.	.	ENSG00000232125	ENST00000452335	T	0.14516	2.5	5.33	2.96	0.34315	.	.	.	.	.	T	0.08626	0.0214	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.30679	-0.9970	9	0.72032	D	0.01	-2.7316	7.7745	0.29029	0.0:0.1654:0.0:0.8346	.	573	A2CJ06	DYTN_HUMAN	S	573	ENSP00000396593:A573S	ENSP00000396593:A573S	A	-	1	0	DYTN	207224807	0.997000	0.39634	0.113000	0.21522	0.001000	0.01503	1.579000	0.36536	0.485000	0.27652	-1.004000	0.02495	GCC		0.453	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			A	207516562	C	A	207516562	3	1	61	1	0	0	0	0	1	0	0	0	4872	710	25	2	23	2	DYTN	2	207516562	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	340606	207516562	35682811	2073	10058										
DYTN	391475	broad.mit.edu	37	chr2	207572149	207572149	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagaaagttgctgcacaGaaagggagtgcttgcgagct	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207572149G>T	ENST00000452335.2	-	3	289	c.173C>A	c.(172-174)tCt>tAt	p.S58Y	DYTN_ENST00000477734.1_5'Flank	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	58						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.S58Y(2)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		TTGCTGCACAGAAAGGGAGTG	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	2											60	58	59					2																	207572149		1900	4133	6033	207280394	SO:0001583	missense	391475			ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.173C>A	2.37:g.207572149G>T	ENSP00000396593:p.Ser58Tyr		207280394		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.568557	0.28003	.	.	ENSG00000232125	ENST00000452335	T	0.66638	-0.22	4.87	4.87	0.63330	EF-hand domain, type 1 (1);	.	.	.	.	T	0.71796	0.3382	L	0.29908	0.895	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.63207	-0.6689	9	0.72032	D	0.01	-6.8196	12.7893	0.57523	0.0:0.0:0.8258:0.1742	.	58	A2CJ06	DYTN_HUMAN	Y	58	ENSP00000396593:S58Y	ENSP00000396593:S58Y	S	-	2	0	DYTN	207280394	1.000000	0.71417	0.047000	0.18901	0.003000	0.03518	4.457000	0.60088	2.673000	0.90976	0.655000	0.94253	TCT		0.522	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			T	207572149	G	T	207572149	3	4	61	1	0	0	0	0	1	0	0	0	4872	942	33	2	1603	2	DYTN	2	207572149	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55587	207572149	35627224	2074	10059										
MDH1B	130752	broad.mit.edu	37	chr2	207611134	207611134	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagaaaagacgatccctttCggaataccaaactggcctgc	8	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207611134C>T	ENST00000374412.3	-	8	1508	c.1233G>A	c.(1231-1233)ccG>ccA	p.P411P	MDH1B_ENST00000454776.2_Silent_p.P411P|MDH1B_ENST00000392214.2_Silent_p.P198P|MDH1B_ENST00000449792.1_Silent_p.P313P	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	411					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)	p.P411P(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		CGATCCCTTTCGGAATACCAA	0.393																																					Pancreas(76;29 1355 28675 37177 51207)											1	Substitution - coding silent(1)	large_intestine(1)	2											74	68	70					2																	207611134		2203	4300	6503	207319379	SO:0001819	synonymous_variant	130752				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.1233G>A	2.37:g.207611134C>T			207319379	A8K8M1|Q53TK9|Q8IV51	Silent	SNP	ENST00000374412.3	37	CCDS33365.1																																																																																				0.393	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		T	207611134	C	T	207611134	2	4	61	1	0	0	0	0	0	0	0	1	9439	871	31	1		1	MDH1B	2	207611134	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38985	207611134	35588239	2075	10060										
MDH1B	130752	broad.mit.edu	37	chr2	207620204	207620204	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcgtcaatatgggaattaGgttgtagcaggcaggagcag	14	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207620204G>T	ENST00000374412.3	-	5	714	c.439C>A	c.(439-441)Cta>Ata	p.L147I	MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000454776.2_Missense_Mutation_p.L147I|MDH1B_ENST00000449792.1_Missense_Mutation_p.L49I	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	147					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)	p.L147I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		ATGGGAATTAGGTTGTAGCAG	0.398																																					Pancreas(76;29 1355 28675 37177 51207)											1	Substitution - Missense(1)	large_intestine(1)	2											72	68	70					2																	207620204		2203	4300	6503	207328449	SO:0001583	missense	130752				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.439C>A	2.37:g.207620204G>T	ENSP00000363533:p.Leu147Ile		207328449	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510688	0.64522	.	.	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.56103	0.48;0.48;0.48	6.06	3.27	0.37495	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.68641	0.3023	M	0.82923	2.615	0.80722	D	1	D;P	0.55605	0.972;0.952	P;P	0.61592	0.891;0.78	T	0.70167	-0.4946	10	0.51188	T	0.08	-16.3172	10.2866	0.43570	0.213:0.0:0.787:0.0	.	147;147	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	I	147;49;147	ENSP00000363533:L147I;ENSP00000416577:L49I;ENSP00000389916:L147I	ENSP00000363533:L147I	L	-	1	2	MDH1B	207328449	0.961000	0.32948	0.104000	0.21259	0.068000	0.16541	1.534000	0.36051	0.867000	0.35654	0.650000	0.86243	CTA		0.398	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		T	207620204	G	T	207620204	3	4	61	1	0	0	0	0	1	0	0	0	9439	991	35	2	1149	2	MDH1B	2	207620204	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9070	207620204	35579169	2076	10061										
MDH1B	130752	broad.mit.edu	37	chr2	207625639	207625639	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttacctcccaaacctcagGacgttgtgtgattttatgta	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207625639G>T	ENST00000374412.3	-	2	396	c.121C>A	c.(121-123)Cct>Act	p.P41T	MDH1B_ENST00000454776.2_Missense_Mutation_p.P41T|MDH1B_ENST00000392214.2_Missense_Mutation_p.P41T|MDH1B_ENST00000449792.1_Intron	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	41					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)	p.P41T(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		CAAACCTCAGGACGTTGTGTG	0.348																																					Pancreas(76;29 1355 28675 37177 51207)											1	Substitution - Missense(1)	large_intestine(1)	2											134	135	135					2																	207625639		2203	4300	6503	207333884	SO:0001583	missense	130752				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.121C>A	2.37:g.207625639G>T	ENSP00000363533:p.Pro41Thr		207333884	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.106326	0.77096	.	.	ENSG00000138400	ENST00000374412;ENST00000454776;ENST00000392214	T;T;T	0.58797	0.31;0.31;0.31	5.62	5.62	0.85841	.	0.050671	0.85682	D	0.000000	T	0.78941	0.4363	M	0.81497	2.545	0.49130	D	0.999756	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.974	T	0.80571	-0.1323	10	0.87932	D	0	-21.2594	20.024	0.97514	0.0:0.0:1.0:0.0	.	41;41	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	T	41	ENSP00000363533:P41T;ENSP00000389916:P41T;ENSP00000376049:P41T	ENSP00000363533:P41T	P	-	1	0	MDH1B	207333884	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.887000	0.75616	2.809000	0.96659	0.655000	0.94253	CCT		0.348	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		T	207625639	G	T	207625639	3	4	61	1	0	0	0	0	1	0	0	0	9439	1174	41	2	1479	2	MDH1B	2	207625639	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5435	207625639	35573734	2077	10062										
FASTKD2	22868	broad.mit.edu	37	chr2	207631617	207631617	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaataactttcataacaGaatgcaatcaactgatatca	3	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207631617G>T	ENST00000236980.6	+	2	548	c.200G>T	c.(199-201)aGa>aTa	p.R67I	MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000392214.2_5'Flank|FASTKD2_ENST00000402774.3_Missense_Mutation_p.R67I|MDH1B_ENST00000374412.3_5'Flank|MDH1B_ENST00000449792.1_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.R67I	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	67					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.R67I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TTTCATAACAGAATGCAATCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											62	63	62					2																	207631617		2202	4300	6502	207339862	SO:0001583	missense	22868			BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.200G>T	2.37:g.207631617G>T	ENSP00000236980:p.Arg67Ile		207339862	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.357983	0.41801	.	.	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.47177	2.45;0.85;2.45;2.45	4.98	-0.283	0.12874	.	4.225000	0.00166	N	0.000011	T	0.45895	0.1365	L	0.40543	1.245	0.09310	N	1	D;P	0.53151	0.958;0.855	P;B	0.51135	0.66;0.36	T	0.26744	-1.0094	10	0.51188	T	0.08	-1.7575	0.9391	0.01351	0.3706:0.1528:0.3195:0.1571	.	67;67	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	I	67	ENSP00000236980:R67I;ENSP00000409927:R67I;ENSP00000385990:R67I;ENSP00000384929:R67I	ENSP00000236980:R67I	R	+	2	0	FASTKD2	207339862	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	0.409000	0.21082	0.040000	0.15660	-0.339000	0.08088	AGA		0.333	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207631617	G	T	207631617	3	4	61	1	0	0	0	0	1	0	0	0	5705	942	33	2	202	2	FASTKD2	2	207631617	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5978	207631617	35567756	2078	10063										
FASTKD2	22868	broad.mit.edu	37	chr2	207638988	207638988	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgaaaaccttggctttCgacctgttggtttaatggac	9	7	0	1	rs118203917		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207638988C>T	ENST00000236980.6	+	7	1642	c.1294C>T	c.(1294-1296)Cga>Tga	p.R432*	FASTKD2_ENST00000402774.3_Nonsense_Mutation_p.R432*|FASTKD2_ENST00000403094.3_Nonsense_Mutation_p.R432*	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	432					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.R432*(1)|p.R432G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		CCTTGGCTTTCGACCTGTTGG	0.303																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|prostate(1)	2	GRCh37	CM085400	FASTKD2	M	rs118203917						87	86	86					2																	207638988		2202	4296	6498	207347233	SO:0001587	stop_gained	22868			BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1294C>T	2.37:g.207638988C>T	ENSP00000236980:p.Arg432*		207347233	Q9NVX6|Q9Y2H7	Nonsense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	C	37	6.352057	0.97498	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	.	.	.	5.74	4.79	0.61399	.	0.349524	0.27402	N	0.019529	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-18.3065	16.4943	0.84223	0.1397:0.8603:0.0:0.0	.	.	.	.	X	432	.	ENSP00000236980:R432X	R	+	1	2	FASTKD2	207347233	1.000000	0.71417	0.998000	0.56505	0.075000	0.17131	3.036000	0.49767	2.703000	0.92315	0.655000	0.94253	CGA		0.303	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207638988	C	T	207638988	4	4	61	1	0	0	0	0	0	1	0	0	5705	876	31	1	1316	1	FASTKD2	2	207638988	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7371	207638988	35560385	2079	10064										
FASTKD2	22868	broad.mit.edu	37	chr2	207653617	207653617	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatacaacttctgctacaGatattcaaaggttgcttaca	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:207653617G>T	ENST00000236980.6	+	10	2236	c.1888G>T	c.(1888-1890)Gat>Tat	p.D630Y	FASTKD2_ENST00000402774.3_Missense_Mutation_p.D630Y|FASTKD2_ENST00000403094.3_Missense_Mutation_p.D630Y	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	630					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.D630Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TTCTGCTACAGATATTCAAAG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	2											60	59	59					2																	207653617		2203	4300	6503	207361862	SO:0001583	missense	22868			BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1888G>T	2.37:g.207653617G>T	ENSP00000236980:p.Asp630Tyr		207361862	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.841563	0.51057	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.16457	2.34;2.34;2.34	6.16	2.1	0.27182	.	1.402390	0.04345	N	0.354695	T	0.41282	0.1152	M	0.78801	2.425	0.26744	N	0.970335	D;P	0.76494	0.999;0.883	D;P	0.65874	0.939;0.541	T	0.03221	-1.1059	10	0.52906	T	0.07	-21.6252	6.8064	0.23780	0.4831:0.0:0.5169:0.0	.	630;630	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	Y	630	ENSP00000236980:D630Y;ENSP00000385990:D630Y;ENSP00000384929:D630Y	ENSP00000236980:D630Y	D	+	1	0	FASTKD2	207361862	0.726000	0.28059	0.954000	0.39281	0.785000	0.44390	0.024000	0.13555	0.081000	0.16988	-0.157000	0.13467	GAT		0.308	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207653617	G	T	207653617	3	4	61	1	0	0	0	0	1	0	0	0	5705	942	33	2	1922	2	FASTKD2	2	207653617	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14629	207653617	35545756	2080	10065										
FAM119A	151194	broad.mit.edu	37	chr2	208477792	208477792	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagtcctccttctggtttCtcttctgtgcttcgtaaata	6	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:208477792C>A	ENST00000411432.1	-	4	851	c.635G>T	c.(634-636)aGa>aTa	p.R212I	METTL21A_ENST00000426075.1_Missense_Mutation_p.R212I|METTL21A_ENST00000448007.2_Missense_Mutation_p.R212I|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000272839.3_Missense_Mutation_p.R230I|METTL21A_ENST00000406927.2_Missense_Mutation_p.R212I|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000442521.1_Missense_Mutation_p.R212I|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000448823.2_3'UTR	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	212					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)	p.R212I(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						CTTCTGGTTTCTCTTCTGTGC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	136	135					2																	208477792		2203	4300	6503	208186037	SO:0001583	missense	151194			AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"Hepatocellular carcinoma-associated antigen 557b", "heat shock protein 70kDa lysine (K) methyltransferase"	615257	"family with sequence similarity 119, member A"	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.635G>T	2.37:g.208477792C>A	ENSP00000415115:p.Arg212Ile		208186037	Q53RV0|Q8N1Z9|Q96GH6	Missense_Mutation	SNP	ENST00000411432.1	37	CCDS2376.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.408865	0.25378	.	.	ENSG00000144401	ENST00000411432;ENST00000448007;ENST00000272839;ENST00000406927;ENST00000426075;ENST00000442521	T;T;T;T;T;T	0.14766	2.49;2.49;2.48;2.49;2.49;2.49	4.76	2.96	0.34315	.	0.648932	0.16743	N	0.201379	T	0.13500	0.0327	L	0.50333	1.59	0.19300	N	0.999973	B	0.09022	0.002	B	0.04013	0.001	T	0.14008	-1.0488	10	0.54805	T	0.06	-19.5715	9.6896	0.40120	0.0:0.7404:0.0:0.2596	.	212	Q8WXB1	MT21A_HUMAN	I	212;212;230;212;212;212	ENSP00000415115:R212I;ENSP00000407622:R212I;ENSP00000272839:R230I;ENSP00000385481:R212I;ENSP00000403317:R212I;ENSP00000392062:R212I	ENSP00000272839:R230I	R	-	2	0	METTL21A	208186037	0.000000	0.05858	0.997000	0.53966	0.998000	0.95712	-0.241000	0.08940	1.379000	0.46325	0.561000	0.74099	AGA		0.363	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280		A	208477792	C	A	208477792	3	1	61	1	0	0	0	0	1	0	0	0	5429	913	32	2	25	2	FAM119A	2	208477792	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	824175	208477792	34721581	2081	10066										
PIKFYVE	200576	broad.mit.edu	37	chr2	209190769	209190769	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatgagatgctctacccgAgattattttgcagagcaggt	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209190769A>G	ENST00000264380.4	+	20	3392	c.3234A>G	c.(3232-3234)cgA>cgG	p.R1078R		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1078					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R1078R(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GCTCTACCCGAGATTATTTTG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	2											69	75	73					2																	209190769		2203	4300	6503	208899014	SO:0001819	synonymous_variant	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.3234A>G	2.37:g.209190769A>G			208899014	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																				0.423	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		G	209190769	A	G	209190769	2	3	61	1	0	0	0	0	0	0	0	1	11955	291	11	4		4	PIKFYVE	2	209190769	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	712977	209190769	34008604	2082	10067										
PIKFYVE	200576	broad.mit.edu	37	chr2	209191017	209191017	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatcgagccagaggaggaaGaattcagcccaaaaattcag	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209191017G>T	ENST00000264380.4	+	20	3640	c.3482G>T	c.(3481-3483)aGa>aTa	p.R1161I		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1161					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R1161I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						AGAGGAGGAAGAATTCAGCCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	68	69					2																	209191017		2203	4300	6503	208899262	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.3482G>T	2.37:g.209191017G>T	ENSP00000264380:p.Arg1161Ile		208899262	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699652	0.88830	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.47528	0.84;1.02	5.58	5.58	0.84498	.	0.097761	0.64402	D	0.000002	T	0.69305	0.3096	M	0.70842	2.15	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.78314	0.991;0.974	T	0.67914	-0.5547	9	.	.	.	-21.1173	19.5743	0.95436	0.0:0.0:1.0:0.0	.	1161;1105	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	I	1161;737;1105	ENSP00000264380:R1161I;ENSP00000405736:R1105I	.	R	+	2	0	PIKFYVE	208899262	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.511000	0.98006	2.611000	0.88343	0.655000	0.94253	AGA		0.468	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209191017	G	T	209191017	3	4	61	1	0	0	0	0	1	0	0	0	11955	942	33	2	3567	2	PIKFYVE	2	209191017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248	209191017	34008356	2083	10068										
PIKFYVE	200576	broad.mit.edu	37	chr2	209209896	209209896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgactcagtggaacagtgccGaagaagggcttccaacaaat	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209209896G>A	ENST00000264380.4	+	33	5247	c.5089G>A	c.(5089-5091)Gaa>Aaa	p.E1697K		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1697					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.E1697K(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GAACAGTGCCGAAGAAGGGCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	75	74					2																	209209896		2203	4300	6503	208918141	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5089G>A	2.37:g.209209896G>A	ENSP00000264380:p.Glu1697Lys		208918141	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.034902	0.54896	.	.	ENSG00000115020	ENST00000264380	T	0.29397	1.57	5.42	5.42	0.78866	.	0.125717	0.53938	D	0.000058	T	0.27489	0.0675	L	0.43152	1.355	0.80722	D	1	D	0.56521	0.976	B	0.41299	0.353	T	0.06643	-1.0815	10	0.10377	T	0.69	-20.9673	19.2334	0.93849	0.0:0.0:1.0:0.0	.	1697	Q9Y2I7	FYV1_HUMAN	K	1697	ENSP00000264380:E1697K	ENSP00000264380:E1697K	E	+	1	0	PIKFYVE	208918141	1.000000	0.71417	0.988000	0.46212	0.109000	0.19521	7.792000	0.85828	2.538000	0.85594	0.585000	0.79938	GAA		0.333	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		A	209209896	G	A	209209896	3	1	61	1	0	0	0	0	1	0	0	0	11955	1059	37	1	5226	1	PIKFYVE	2	209209896	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18879	209209896	33989477	2084	10069										
PIKFYVE	200576	broad.mit.edu	37	chr2	209214776	209214776	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggaggagatacacaaaaGaagcaactcataaatcctca	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209214776G>T	ENST00000264380.4	+	36	5561	c.5403G>T	c.(5401-5403)aaG>aaT	p.K1801N		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1801	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.K1801N(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ATACACAAAAGAAGCAACTCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											119	120	120					2																	209214776		2203	4299	6502	208923021	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5403G>T	2.37:g.209214776G>T	ENSP00000264380:p.Lys1801Asn		208923021	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.668498	0.67814	.	.	ENSG00000115020	ENST00000264380	T	0.30182	1.54	5.75	4.69	0.59074	Phosphatidylinositol-4-phosphate 5-kinase, core (1);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.31796	0.0808	L	0.31664	0.95	0.80722	D	1	D	0.54964	0.969	P	0.52159	0.691	T	0.01127	-1.1443	10	0.17832	T	0.49	-22.3263	15.3814	0.74658	0.0787:0.0:0.9213:0.0	.	1801	Q9Y2I7	FYV1_HUMAN	N	1801	ENSP00000264380:K1801N	ENSP00000264380:K1801N	K	+	3	2	PIKFYVE	208923021	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.610000	0.61155	2.725000	0.93324	0.655000	0.94253	AAG		0.343	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209214776	G	T	209214776	3	4	61	1	0	0	0	0	1	0	0	0	11955	933	33	2	5552	2	PIKFYVE	2	209214776	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4880	209214776	33984597	2085	10070										
PTH2R	5746	broad.mit.edu	37	chr2	209355366	209355366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttttgtctgcagggTttctttgtgtctatcatcta	7	8	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209355366T>C	ENST00000272847.2	+	12	1431	c.1218T>C	c.(1216-1218)ggT>ggC	p.G406G	PTH2R_ENST00000413482.1_3'UTR|AC019185.4_ENST00000424628.1_RNA	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	406					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)	p.G406G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	GTCTGCAGGGTTTCTTTGTGT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	2											215	201	206					2																	209355366		2203	4300	6503	209063611	SO:0001819	synonymous_variant	5746			BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1218T>C	2.37:g.209355366T>C			209063611	Q8N429	Silent	SNP	ENST00000272847.2	37	CCDS2383.1																																																																																				0.428	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		C	209355366	T	C	209355366	2	2	61	1	0	0	0	0	0	0	0	1	12795	1712	60	4		4	PTH2R	2	209355366	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	140590	209355366	33844007	2086	10071										
PTH2R	5746	broad.mit.edu	37	chr2	209358071	209358071	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgccatgtggcagccgcaGatgcggctcagtgctcacca	12	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:209358071G>T	ENST00000272847.2	+	13	1553	c.1340G>T	c.(1339-1341)aGa>aTa	p.R447I	PTH2R_ENST00000413482.1_3'UTR|AC019185.4_ENST00000424628.1_RNA	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	447					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)	p.R447I(2)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	GGCAGCCGCAGATGCGGCTCA	0.592																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											35	36	36					2																	209358071		2203	4300	6503	209066316	SO:0001583	missense	5746			BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1340G>T	2.37:g.209358071G>T	ENSP00000272847:p.Arg447Ile		209066316	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.418158	0.42918	.	.	ENSG00000144407	ENST00000272847	T	0.54479	0.57	5.76	5.76	0.90799	.	0.000000	0.39909	U	0.001231	T	0.61664	0.2365	M	0.70275	2.135	0.24385	N	0.994779	P;P	0.45011	0.848;0.848	P;P	0.47075	0.536;0.536	T	0.59768	-0.7392	9	.	.	.	.	17.4442	0.87574	0.0:0.0:1.0:0.0	.	336;447	B4DFN8;P49190	.;PTH2R_HUMAN	I	447	ENSP00000272847:R447I	.	R	+	2	0	PTH2R	209066316	1.000000	0.71417	0.163000	0.22734	0.005000	0.04900	4.749000	0.62155	2.720000	0.93068	0.591000	0.81541	AGA		0.592	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		T	209358071	G	T	209358071	3	4	61	1	0	0	0	0	1	0	0	0	12795	942	33	2	1390	2	PTH2R	2	209358071	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2705	209358071	33841302	2087	10072										
MAP2	4133	broad.mit.edu	37	chr2	210560710	210560710	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggaggaatttgtggagacCtgcccaagtgaacacaaagg	14	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:210560710C>A	ENST00000360351.4	+	7	4322	c.3816C>A	c.(3814-3816)acC>acA	p.T1272T	MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Silent_p.T1268T|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1272					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.T1272T(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TTGTGGAGACCTGCCCAAGTG	0.493																																					Pancreas(27;423 979 28787 29963)											1	Substitution - coding silent(1)	large_intestine(1)	2											140	140	140					2																	210560710		2203	4300	6503	210268955	SO:0001819	synonymous_variant	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3816C>A	2.37:g.210560710C>A			210268955	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																				0.493	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210560710	C	A	210560710	2	1	61	1	0	0	0	0	0	0	0	1	9265	668	24	2		2	MAP2	2	210560710	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1202639	210560710	32638663	2088	10073										
MAP2	4133	broad.mit.edu	37	chr2	210561750	210561750	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatactagaccaactcatctCtcctgtgttaagcggaaaac	6	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:210561750C>A	ENST00000360351.4	+	9	5003	c.4497C>A	c.(4495-4497)ctC>ctA	p.L1499L	MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Silent_p.L1495L|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000475600.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1499					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.L1499L(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CAACTCATCTCTCCTGTGTTA	0.383																																					Pancreas(27;423 979 28787 29963)											1	Substitution - coding silent(1)	large_intestine(1)	2											81	87	85					2																	210561750		2203	4300	6503	210269995	SO:0001819	synonymous_variant	4133				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4497C>A	2.37:g.210561750C>A			210269995	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																				0.383	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210561750	C	A	210561750	2	1	61	1	0	0	0	0	0	0	0	1	9265	900	32	2		2	MAP2	2	210561750	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1040	210561750	32637623	2089	10074										
C2orf67	151050	broad.mit.edu	37	chr2	210888874	210888874	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactgctactgaagttattAgggtattctttcaaaagcaa	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:210888874A>C	ENST00000281772.9	-	14	2879	c.2616T>G	c.(2614-2616)ccT>ccG	p.P872P	KANSL1L_ENST00000418791.1_Silent_p.P830P	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	872						histone acetyltransferase complex (GO:0000123)		p.P872P(1)									TGAAGTTATTAGGGTATTCTT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	2											75	75	75					2																	210888874		2203	4300	6503	210597119	SO:0001819	synonymous_variant	151050			AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.2616T>G	2.37:g.210888874A>C			210597119	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Silent	SNP	ENST00000281772.9	37	CCDS33370.1																																																																																				0.388	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		C	210888874	A	C	210888874	2	2	61	1	0	0	0	0	0	0	0	1	2192	407	15	4		4	C2orf67	2	210888874	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	327124	210888874	32310499	2090	10075										
C2orf67	151050	broad.mit.edu	37	chr2	211018574	211018574	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgccaggagcatctgcaAatgtttctgagttcttctag	9	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211018574A>C	ENST00000281772.9	-	2	996	c.733T>G	c.(733-735)Ttg>Gtg	p.L245V	KANSL1L_ENST00000457374.1_Missense_Mutation_p.L245V|KANSL1L_ENST00000418791.1_Missense_Mutation_p.L245V|KANSL1L_ENST00000429908.2_5'Flank|KANSL1L_ENST00000452086.1_Missense_Mutation_p.L245V	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	245						histone acetyltransferase complex (GO:0000123)		p.L245V(1)									AGCATCTGCAAATGTTTCTGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											84	82	82					2																	211018574		2203	4300	6503	210726819	SO:0001583	missense	151050			AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.733T>G	2.37:g.211018574A>C	ENSP00000281772:p.Leu245Val		210726819	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Missense_Mutation	SNP	ENST00000281772.9	37	CCDS33370.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124395	0.56613	.	.	ENSG00000144445	ENST00000281772;ENST00000418791;ENST00000457374;ENST00000452086	.	.	.	5.95	3.61	0.41365	.	0.000000	0.56097	D	0.000032	T	0.69628	0.3132	L	0.58428	1.81	0.35305	D	0.783377	D;D;D;D	0.76494	0.996;0.999;0.998;0.998	D;D;D;D	0.85130	0.929;0.997;0.99;0.99	T	0.76285	-0.3015	9	0.87932	D	0	.	10.1289	0.42667	0.866:0.0:0.134:0.0	.	245;245;245;245	A0AUZ9-4;A0AUZ9-3;A0AUZ9-2;A0AUZ9	.;.;.;CB067_HUMAN	V	245	.	ENSP00000281772:L245V	L	-	1	2	C2orf67	210726819	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.201000	0.42734	0.521000	0.28445	0.460000	0.39030	TTG		0.393	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		C	211018574	A	C	211018574	3	2	61	1	0	0	0	0	1	0	0	0	2192	11	1	4	2286	4	C2orf67	2	211018574	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	129700	211018574	32180799	2091	10076										
ACADL	33	broad.mit.edu	37	chr2	211085455	211085455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctggagaaaagattcttCgaattcctatatctgttaat	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211085455C>T	ENST00000233710.3	-	2	376	c.149G>A	c.(148-150)cGa>cAa	p.R50Q	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	50					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)	p.R50Q(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AAAGATTCTTCGAATTCCTAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	85	84					2																	211085455		2203	4300	6503	210793700	SO:0001583	missense	33			M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.149G>A	2.37:g.211085455C>T	ENSP00000233710:p.Arg50Gln		210793700	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	35	5.547013	0.96488	.	.	ENSG00000115361	ENST00000233710	D	0.98889	-5.21	5.69	5.69	0.88448	Acyl-CoA dehydrogenase/oxidase (1);	0.000000	0.85682	D	0.000000	D	0.97854	0.9295	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.99937	1.1373	10	0.87932	D	0	.	19.821	0.96592	0.0:1.0:0.0:0.0	.	50	P28330	ACADL_HUMAN	Q	50	ENSP00000233710:R50Q	ENSP00000233710:R50Q	R	-	2	0	ACADL	210793700	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.761000	0.74945	2.683000	0.91414	0.655000	0.94253	CGA		0.353	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		T	211085455	C	T	211085455	3	4	61	1	0	0	0	0	1	0	0	0	112	884	31	1	1183	1	ACADL	2	211085455	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66881	211085455	32113918	2092	10077										
CPS1	1373	broad.mit.edu	37	chr2	211421472	211421472	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaaaatgacgaggattttGacagctttcaaagtggtgag	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211421472G>T	ENST00000233072.5	+	1	211	c.15G>T	c.(13-15)ttG>ttT	p.L5F	CPS1_ENST00000430249.2_Missense_Mutation_p.L11F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	5					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.L5L(1)|p.L5F(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CGAGGATTTTGACAGCTTTCA	0.343																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	upper_aerodigestive_tract(1)|large_intestine(1)	2											81	83	83					2																	211421472		2203	4298	6501	211129717	SO:0001583	missense	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.15G>T	2.37:g.211421472G>T	ENSP00000233072:p.Leu5Phe		211129717	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032195	0.75504	.	.	ENSG00000021826	ENST00000417946;ENST00000518043;ENST00000523702;ENST00000430249;ENST00000539150;ENST00000233072;ENST00000544169;ENST00000536125	D;D;D;D;D	0.98075	-3.66;-3.66;-3.82;-4.7;-4.7	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.97430	0.9159	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.946;0.996	D	0.98552	1.0637	10	0.72032	D	0.01	-0.036	16.7312	0.85435	0.0:0.0:1.0:0.0	.	15;5	Q59HF8;P31327	.;CPSM_HUMAN	F	5;5;11;11;13;5;5;5	ENSP00000388496:L5F;ENSP00000430697:L5F;ENSP00000430644:L11F;ENSP00000402608:L11F;ENSP00000233072:L5F	ENSP00000233072:L5F	L	+	3	2	CPS1	211129717	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.446000	0.66600	2.706000	0.92434	0.655000	0.94253	TTG		0.343	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211421472	G	T	211421472	3	4	61	1	0	0	0	0	1	0	0	0	3829	1281	45	2	39	2	CPS1	2	211421472	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336017	211421472	31777901	2093	10078										
CPS1	1373	broad.mit.edu	37	chr2	211467030	211467030	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatctgtcccaacagagaGactttgatggacctcagcac	10	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211467030G>T	ENST00000233072.5	+	16	2008	c.1812G>T	c.(1810-1812)gaG>gaT	p.E604D	CPS1_ENST00000430249.2_Missense_Mutation_p.E610D|CPS1_ENST00000451903.2_Missense_Mutation_p.E153D	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	604	ATP-grasp 1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.E604D(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CCAACAGAGAGACTTTGATGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	2											146	134	138					2																	211467030		2203	4300	6503	211175275	SO:0001583	missense	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1812G>T	2.37:g.211467030G>T	ENSP00000233072:p.Glu604Asp		211175275	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	7.495	0.651548	0.14516	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97480	-4.4;-4.4;-4.4	5.63	3.6	0.41247	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.93983	0.8073	L	0.56124	1.755	0.42318	D	0.992244	B;B	0.19200	0.034;0.034	B;B	0.21360	0.034;0.034	D	0.90201	0.4257	10	0.33940	T	0.23	-12.8263	6.3556	0.21400	0.3264:0.0:0.6736:0.0	.	614;604	Q59HF8;P31327	.;CPSM_HUMAN	D	610;612;604;153	ENSP00000402608:E610D;ENSP00000233072:E604D;ENSP00000406136:E153D	ENSP00000233072:E604D	E	+	3	2	CPS1	211175275	1.000000	0.71417	0.998000	0.56505	0.021000	0.10359	0.723000	0.25939	1.403000	0.46800	-0.237000	0.12165	GAG		0.453	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211467030	G	T	211467030	3	4	61	1	0	0	0	0	1	0	0	0	3829	933	33	2	1896	2	CPS1	2	211467030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45558	211467030	31732343	2094	10079										
CPS1	1373	broad.mit.edu	37	chr2	211473252	211473252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcatggaacatctagccGaattggtagctctatgaaaa	8	7	3	1	rs571936934		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211473252G>A	ENST00000233072.5	+	19	2556	c.2360G>A	c.(2359-2361)cGa>cAa	p.R787Q	CPS1_ENST00000430249.2_Missense_Mutation_p.R793Q|CPS1_ENST00000451903.2_Missense_Mutation_p.R336Q	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	787					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.R787Q(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ACATCTAGCCGAATTGGTAGC	0.428													G|||	1	0.000199681	0	0	5008	,	,		18184	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											131	128	129					2																	211473252		2203	4300	6503	211181497	SO:0001583	missense	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2360G>A	2.37:g.211473252G>A	ENSP00000233072:p.Arg787Gln		211181497	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	9.450	1.090331	0.20471	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.94613	-3.47;-3.47;-3.47	5.86	4.03	0.46877	ATP-grasp fold, subdomain 2 (1);	0.294801	0.33712	N	0.004624	D	0.83533	0.5275	N	0.05441	-0.05	0.26941	N	0.966256	B;B	0.17667	0.023;0.023	B;B	0.04013	0.001;0.001	T	0.69551	-0.5115	10	0.13108	T	0.6	-11.2815	5.7178	0.17970	0.2699:0.0:0.6007:0.1294	.	797;787	Q59HF8;P31327	.;CPSM_HUMAN	Q	793;795;787;336	ENSP00000402608:R793Q;ENSP00000233072:R787Q;ENSP00000406136:R336Q	ENSP00000233072:R787Q	R	+	2	0	CPS1	211181497	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	1.894000	0.39768	0.891000	0.36235	-0.143000	0.13931	CGA		0.428	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			A	211473252	G	A	211473252	3	1	61	1	0	0	0	0	1	0	0	0	3829	1058	37	1	2456	1	CPS1	2	211473252	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6222	211473252	31726121	2095	10080										
CPS1	1373	broad.mit.edu	37	chr2	211518791	211518791	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgttgaaggggcccgaGaagtagaaatggacgctgtt	14	5	0	3	rs146968493		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211518791G>T	ENST00000233072.5	+	29	3719	c.3523G>T	c.(3523-3525)Gaa>Taa	p.E1175*	CPS1_ENST00000430249.2_Nonsense_Mutation_p.E1181*|CPS1_ENST00000451903.2_Nonsense_Mutation_p.E724*	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1175	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.E1175*(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	AGGGGCCCGAGAAGTAGAAAT	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											127	127	127					2																	211518791		2203	4300	6503	211227036	SO:0001587	stop_gained	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3523G>T	2.37:g.211518791G>T	ENSP00000233072:p.Glu1175*		211227036	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Nonsense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	43	10.071985	0.99330	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.1101	20.3472	0.98799	0.0:0.0:1.0:0.0	.	.	.	.	X	1181;1183;1175;724	.	ENSP00000233072:E1175X	E	+	1	0	CPS1	211227036	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.580000	0.90784	2.890000	0.99128	0.650000	0.86243	GAA		0.428	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211518791	G	T	211518791	4	4	61	1	0	0	0	0	0	1	0	0	3829	943	33	2	3659	2	CPS1	2	211518791	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45539	211518791	31680582	2096	10081										
CPS1	1373	broad.mit.edu	37	chr2	211525281	211525281	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttggggttgacttcattGatgtggccaccaaggtgatg	13	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:211525281G>T	ENST00000233072.5	+	32	4025	c.3829G>T	c.(3829-3831)Gat>Tat	p.D1277Y	CPS1_ENST00000430249.2_Missense_Mutation_p.D1283Y|CPS1_ENST00000451903.2_Missense_Mutation_p.D826Y	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1277	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.D1277Y(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TGACTTCATTGATGTGGCCAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											238	215	223					2																	211525281		2203	4300	6503	211233526	SO:0001583	missense	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3829G>T	2.37:g.211525281G>T	ENSP00000233072:p.Asp1277Tyr		211233526	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040359	0.75732	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	T;T;T	0.62788	-0.0;-0.0;-0.0	5.98	5.1	0.69264	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.137596	0.64402	D	0.000004	T	0.73281	0.3567	L	0.53249	1.67	0.50039	D	0.999847	D;D	0.58970	0.984;0.984	D;D	0.63381	0.914;0.914	T	0.75975	-0.3128	10	0.66056	D	0.02	-15.4524	14.9496	0.71060	0.0682:0.0:0.9318:0.0	.	1287;1277	Q59HF8;P31327	.;CPSM_HUMAN	Y	1283;1285;1277;826	ENSP00000402608:D1283Y;ENSP00000233072:D1277Y;ENSP00000406136:D826Y	ENSP00000233072:D1277Y	D	+	1	0	CPS1	211233526	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.067000	0.64357	1.531000	0.49152	0.655000	0.94253	GAT		0.408	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211525281	G	T	211525281	3	4	61	1	0	0	0	0	1	0	0	0	3829	1290	45	2	3977	2	CPS1	2	211525281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6490	211525281	31674092	2097	10082										
ERBB4	2066	broad.mit.edu	37	chr2	212251749	212251749	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgccattacagcaggagtCatcaaaaatctcagcagtag	10	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:212251749C>A	ENST00000342788.4	-	27	3620	c.3310G>T	c.(3310-3312)Gac>Tac	p.D1104Y	ERBB4_ENST00000402597.1_Missense_Mutation_p.D1094Y|ERBB4_ENST00000436443.1_Missense_Mutation_p.D1088Y	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1104					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D1104Y(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CAGCAGGAGTCATCAAAAATC	0.552										TSP Lung(8;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	2											131	120	124					2																	212251749		2203	4300	6503	211959994	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3310G>T	2.37:g.212251749C>A	ENSP00000342235:p.Asp1104Tyr		211959994	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777255	0.90195	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.78246	-1.15;-1.12;-1.16	5.73	5.73	0.89815	.	0.102685	0.64402	D	0.000004	D	0.84515	0.5489	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.76494	0.999;0.98;0.999;0.998	D;P;D;P	0.65874	0.939;0.804;0.939;0.87	D	0.85013	0.0907	10	0.66056	D	0.02	.	19.9017	0.96988	0.0:1.0:0.0:0.0	.	1078;1094;1088;1104	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	Y	1104;1088;1094	ENSP00000342235:D1104Y;ENSP00000403204:D1088Y;ENSP00000385565:D1094Y	ENSP00000342235:D1104Y	D	-	1	0	ERBB4	211959994	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.093000	0.76937	2.707000	0.92482	0.561000	0.74099	GAC		0.552	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212251749	C	A	212251749	3	1	61	1	0	0	0	0	1	0	0	0	5222	826	29	2	624	2	ERBB4	2	212251749	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726468	212251749	30947624	2098	10083										
ERBB4	2066	broad.mit.edu	37	chr2	212251837	212251837	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagggcacagacactccttgTtcagcagcaaaacctccatc	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:212251837T>C	ENST00000342788.4	-	27	3532	c.3222A>G	c.(3220-3222)gaA>gaG	p.E1074E	ERBB4_ENST00000402597.1_Silent_p.E1064E|ERBB4_ENST00000436443.1_Silent_p.E1058E	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1074					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E1074E(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACACTCCTTGTTCAGCAGCAA	0.438										TSP Lung(8;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	2											136	136	136					2																	212251837		2203	4300	6503	211960082	SO:0001819	synonymous_variant	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3222A>G	2.37:g.212251837T>C			211960082	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																				0.438	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212251837	T	C	212251837	2	2	61	1	0	0	0	0	0	0	0	1	5222	1722	60	4		4	ERBB4	2	212251837	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	88	212251837	30947536	2099	10084										
ERBB4	2066	broad.mit.edu	37	chr2	212288964	212288964	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctaataaatcagggatttCtcgcgttggaattccatcat	7	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:212288964C>A	ENST00000342788.4	-	23	3092	c.2782G>T	c.(2782-2784)Gaa>Taa	p.E928*	ERBB4_ENST00000402597.1_Nonsense_Mutation_p.E918*|ERBB4_ENST00000436443.1_Nonsense_Mutation_p.E928*	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	928	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E928*(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TCAGGGATTTCTCGCGTTGGA	0.383										TSP Lung(8;0.080)																																						1	Substitution - Nonsense(1)	large_intestine(1)	2											109	107	108					2																	212288964		2203	4300	6503	211997209	SO:0001587	stop_gained	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2782G>T	2.37:g.212288964C>A	ENSP00000342235:p.Glu928*		211997209	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Nonsense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	40	8.496525	0.98836	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	.	.	.	6.16	6.16	0.99307	.	0.093035	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	928;928;918	.	ENSP00000342235:E928X	E	-	1	0	ERBB4	211997209	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	GAA		0.383	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212288964	C	A	212288964	4	1	61	1	0	0	0	0	0	1	0	0	5222	922	32	2	1168	2	ERBB4	2	212288964	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37127	212288964	30910409	2100	10085										
SPAG16	79582	broad.mit.edu	37	chr2	214162055	214162055	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcaattcagatggcccaaGaacaggctacagatactgaa	9	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:214162055G>T	ENST00000331683.5	+	3	348	c.253G>T	c.(253-255)Gaa>Taa	p.E85*	SPAG16_ENST00000432529.2_Nonsense_Mutation_p.E85*|SPAG16_ENST00000447990.1_Nonsense_Mutation_p.E85*|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000272898.7_Nonsense_Mutation_p.E85*|SPAG16_ENST00000413312.1_Nonsense_Mutation_p.E54*|SPAG16_ENST00000374309.3_Missense_Mutation_p.K30N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	85					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.E85*(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		GATGGCCCAAGAACAGGCTAC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											82	85	84					2																	214162055		2203	4300	6503	213870300	SO:0001587	stop_gained	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.253G>T	2.37:g.214162055G>T	ENSP00000332592:p.Glu85*		213870300	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Nonsense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.939956|6.939956	0.97948|0.97948	.|.	.|.	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000413312;ENST00000272898;ENST00000447990|ENST00000374309	.|T	.|0.59224	.|0.28	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.276731|.	0.28865|.	N|.	0.013898|.	.|T	.|0.59998	.|0.2235	.|.	.|.	.|.	0.27668|0.27668	N|N	0.946844|0.946844	.|P;P	.|0.40731	.|0.608;0.728	.|B;P	.|0.44359	.|0.261;0.447	.|T	.|0.60120	.|-0.7325	.|8	0.45353|0.72032	T|D	0.12|0.01	.|.	14.9666|14.9666	0.71198|0.71198	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|30;21	.|B4DYB5;Q8N0X2-2	.|.;.	X|N	85;85;54;85;85|30	.|ENSP00000363428:K30N	ENSP00000272898:E85X|ENSP00000363428:K30N	E|K	+|+	1|3	0|2	SPAG16|SPAG16	213870300|213870300	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.798000|0.798000	0.45092|0.45092	3.935000|3.935000	0.56560|0.56560	2.624000|2.624000	0.88883|0.88883	0.557000|0.557000	0.71058|0.71058	GAA|AAG		0.373	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		T	214162055	G	T	214162055	4	4	61	1	0	0	0	0	0	1	0	0	15017	943	33	2	263	2	SPAG16	2	214162055	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1873091	214162055	29037318	2101	10086										
SPAG16	79582	broad.mit.edu	37	chr2	214204936	214204936	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagaacgtgattttcatCgaatgcatcataagcgaata	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:214204936C>T	ENST00000331683.5	+	6	681	c.586C>T	c.(586-588)Cga>Tga	p.R196*	SPAG16_ENST00000447990.1_Nonsense_Mutation_p.R196*|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000272898.7_Nonsense_Mutation_p.R196*|SPAG16_ENST00000413312.1_Nonsense_Mutation_p.R165*|SPAG16_ENST00000374309.3_Nonsense_Mutation_p.R102*	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	196					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.R196*(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		TGATTTTCATCGAATGCATCA	0.284																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											39	41	40					2																	214204936		2203	4296	6499	213913181	SO:0001587	stop_gained	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.586C>T	2.37:g.214204936C>T	ENSP00000332592:p.Arg196*		213913181	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Nonsense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	C	36	5.780015	0.96929	.	.	ENSG00000144451	ENST00000331683;ENST00000413312;ENST00000272898;ENST00000447990;ENST00000374309	.	.	.	5.96	5.96	0.96718	.	0.136610	0.46145	D	0.000306	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8098	0.57634	0.1632:0.8368:0.0:0.0	.	.	.	.	X	196;165;196;196;102	.	ENSP00000272898:R196X	R	+	1	2	SPAG16	213913181	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.106000	0.41835	2.832000	0.97577	0.655000	0.94253	CGA		0.284	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		T	214204936	C	T	214204936	4	4	61	1	0	0	0	0	0	1	0	0	15017	876	31	1	624	1	SPAG16	2	214204936	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42881	214204936	28994437	2102	10087										
VWC2L	402117	broad.mit.edu	37	chr2	215279262	215279262	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaagaagtaaaaaacttCtgtgaatatcacgggaaaaa	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215279262C>A	ENST00000312504.5	+	2	1147	c.345C>A	c.(343-345)ttC>ttA	p.F115L	AC107218.3_ENST00000412896.1_RNA|VWC2L_ENST00000427124.1_Missense_Mutation_p.F115L|AC107218.3_ENST00000437883.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	115	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)		p.F115L(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						TAAAAAACTTCTGTGAATATC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											43	41	42					2																	215279262		1847	4093	5940	214987507	SO:0001583	missense	402117			AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.345C>A	2.37:g.215279262C>A	ENSP00000308976:p.Phe115Leu		214987507	A6NC69|B2RUW7|B7X8X1	Missense_Mutation	SNP	ENST00000312504.5	37	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.570112	0.65765	.	.	ENSG00000174453	ENST00000312504;ENST00000427124	T;T	0.13196	2.61;2.61	5.51	3.17	0.36434	von Willebrand factor, type C (1);	0.000000	0.85682	D	0.000000	T	0.17152	0.0412	L	0.27053	0.805	0.46131	D	0.998888	P;P	0.52577	0.954;0.539	D;B	0.63597	0.916;0.372	T	0.09037	-1.0693	10	0.11794	T	0.64	-4.3458	9.0953	0.36636	0.0:0.1516:0.0:0.8484	.	115;115	B7ZW27;B2RUY7	.;VWC2L_HUMAN	L	115	ENSP00000308976:F115L;ENSP00000403779:F115L	ENSP00000308976:F115L	F	+	3	2	VWC2L	214987507	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.376000	0.52417	1.037000	0.40024	-0.302000	0.09304	TTC		0.378	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		A	215279262	C	A	215279262	3	1	61	1	0	0	0	0	1	0	0	0	17284	912	32	2	347	2	VWC2L	2	215279262	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1074326	215279262	27920111	2103	10088										
BARD1	580	broad.mit.edu	37	chr2	215645739	215645739	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcttagtgtctggagactCtatttgctcagccaatggta	10	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215645739C>A	ENST00000260947.4	-	4	993	c.859G>T	c.(859-861)Gag>Tag	p.E287*	BARD1_ENST00000471787.1_5'UTR|BARD1_ENST00000449967.2_Nonsense_Mutation_p.E143*	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	287					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E287*(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTGGAGACTCTATTTGCTCA	0.373									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	2											67	68	68					2																	215645739		2202	4298	6500	215353984	SO:0001587	stop_gained	580	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.859G>T	2.37:g.215645739C>A	ENSP00000260947:p.Glu287*		215353984	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Nonsense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	37	6.600408	0.97697	.	.	ENSG00000138376	ENST00000260947;ENST00000449967	.	.	.	5.62	5.62	0.85841	.	0.557738	0.17972	N	0.155827	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-2.2234	12.8695	0.57957	0.0:0.8838:0.0:0.1162	.	.	.	.	X	287;143	.	ENSP00000260947:E287X	E	-	1	0	BARD1	215353984	0.085000	0.21516	0.839000	0.33178	0.937000	0.57800	1.250000	0.32850	2.795000	0.96236	0.655000	0.94253	GAG		0.373	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		A	215645739	C	A	215645739	4	1	61	1	0	0	0	0	0	1	0	0	1313	922	32	2	1506	2	BARD1	2	215645739	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366477	215645739	27553634	2104	10089										
ABCA12	26154	broad.mit.edu	37	chr2	215802303	215802303	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatggtcactttgttattCttcaagtgaactttgacagt	7	8	3	2	rs543222287		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215802303C>A	ENST00000272895.7	-	51	7692	c.7473G>T	c.(7471-7473)aaG>aaT	p.K2491N	ABCA12_ENST00000389661.4_Missense_Mutation_p.K2173N|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2491					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.K2491N(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		CTTTGTTATTCTTCAAGTGAA	0.383																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											153	139	144					2																	215802303		2203	4300	6503	215510548	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7473G>T	2.37:g.215802303C>A	ENSP00000272895:p.Lys2491Asn		215510548	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	1.162	-0.643526	0.03531	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.89939	-2.58;-2.59	5.79	0.0452	0.14229	.	0.074337	0.56097	D	0.000024	T	0.76399	0.3982	L	0.28014	0.82	0.50467	D	0.999872	B;B	0.18166	0.026;0.02	B;B	0.18871	0.023;0.021	T	0.57195	-0.7853	10	0.15066	T	0.55	.	6.0416	0.19738	0.1307:0.3364:0.0:0.5329	.	2491;2173	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	2491;2173	ENSP00000272895:K2491N;ENSP00000374312:K2173N	ENSP00000272895:K2491N	K	-	3	2	ABCA12	215510548	0.185000	0.23213	0.530000	0.27963	0.160000	0.22226	-0.507000	0.06352	-0.293000	0.08986	-0.302000	0.09304	AAG		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215802303	C	A	215802303	3	1	61	1	0	0	0	0	1	0	0	0	30	912	32	2	326	2	ABCA12	2	215802303	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156564	215802303	27397070	2105	10090										
ABCA12	26154	broad.mit.edu	37	chr2	215809802	215809802	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaggtgccgtttcgacttCggatccatgccagagctcgg	13	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215809802C>T	ENST00000272895.7	-	49	7485	c.7266G>A	c.(7264-7266)ccG>ccA	p.P2422P	ABCA12_ENST00000389661.4_Silent_p.P2104P|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2422	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.P2422P(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		GTTTCGACTTCGGATCCATGC	0.363																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - coding silent(1)	large_intestine(1)	2											117	101	106					2																	215809802		2203	4300	6503	215518047	SO:0001819	synonymous_variant	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7266G>A	2.37:g.215809802C>T			215518047	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																				0.363	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215809802	C	T	215809802	2	4	61	1	0	0	0	0	0	0	0	1	30	871	31	1		1	ABCA12	2	215809802	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7499	215809802	27389571	2106	10091										
ABCA12	26154	broad.mit.edu	37	chr2	215821458	215821458	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcaggtaatttgaaaatCgcaatgataccaattgaaaa	7	5	0	3	rs143237945	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215821458C>T	ENST00000272895.7	-	42	6381	c.6162G>A	c.(6160-6162)gcG>gcA	p.A2054A	ABCA12_ENST00000389661.4_Silent_p.A1736A|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2054					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.A2054A(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		ATTTGAAAATCGCAATGATAC	0.358																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - coding silent(1)	large_intestine(1)	2	GRCh37	CD051282	ABCA12	D	rs143237945	C	,	0,4406		0,0,2203	110	109	109		5208,6162	-2.1	1	2	dbSNP_134	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	1736/2278,2054/2596	215821458	3,13003	2203	4300	6503	215529703	SO:0001819	synonymous_variant	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6162G>A	2.37:g.215821458C>T			215529703	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																				0.358	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215821458	C	T	215821458	2	4	61	1	0	0	0	0	0	0	0	1	30	871	31	1		1	ABCA12	2	215821458	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11656	215821458	27377915	2107	10092										
ABCA12	26154	broad.mit.edu	37	chr2	215823162	215823162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacagtgccactaaaatatCgattaaactgctgattctag	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215823162C>T	ENST00000272895.7	-	41	6175	c.5956G>A	c.(5956-5958)Gat>Aat	p.D1986N	ABCA12_ENST00000389661.4_Missense_Mutation_p.D1668N|AC072062.1_ENST00000420134.1_RNA|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1986					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.D1986N(3)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		ACTAAAATATCGATTAAACTG	0.393																																					Ovarian(66;664 1488 5121 34295)											3	Substitution - Missense(3)	large_intestine(1)|breast(1)|endometrium(1)	2											114	95	101					2																	215823162		2203	4300	6503	215531407	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5956G>A	2.37:g.215823162C>T	ENSP00000272895:p.Asp1986Asn		215531407	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631467	0.46944	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.86627	-2.15;-2.15	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000002	D	0.83723	0.5316	L	0.56280	1.765	0.80722	D	1	P;P	0.47034	0.889;0.5	B;B	0.39503	0.301;0.248	D	0.85797	0.1371	10	0.72032	D	0.01	.	13.0806	0.59112	0.0:0.9265:0.0:0.0735	.	1986;1668	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	1986;1668	ENSP00000272895:D1986N;ENSP00000374312:D1668N	ENSP00000272895:D1986N	D	-	1	0	ABCA12	215531407	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	3.732000	0.55021	2.765000	0.95021	0.650000	0.86243	GAT		0.393	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215823162	C	T	215823162	3	4	61	1	0	0	0	0	1	0	0	0	30	884	31	1	1883	1	ABCA12	2	215823162	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1704	215823162	27376211	2108	10093										
ABCA12	26154	broad.mit.edu	37	chr2	215823777	215823777	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggtcttgcactcctggAtaaggatggctatacatgat	10	8	2	1	rs192684455		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215823777A>C	ENST00000272895.7	-	40	6129	c.5910T>G	c.(5908-5910)taT>taG	p.Y1970*	ABCA12_ENST00000389661.4_Nonsense_Mutation_p.Y1652*|AC072062.1_ENST00000420134.1_RNA|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1970					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.Y1970*(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		GCACTCCTGGATAAGGATGGC	0.358																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Nonsense(1)	large_intestine(1)	2											242	211	221					2																	215823777		2203	4300	6503	215532022	SO:0001587	stop_gained	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5910T>G	2.37:g.215823777A>C	ENSP00000272895:p.Tyr1970*		215532022	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Nonsense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	45	11.322394	0.99546	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	.	.	.	5.45	-1.03	0.10102	.	0.000000	0.56097	D	0.000031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9712	0.47441	0.5336:0.0:0.4664:0.0	.	.	.	.	X	1970;1652	.	ENSP00000272895:Y1970X	Y	-	3	2	ABCA12	215532022	0.197000	0.23362	0.997000	0.53966	0.923000	0.55619	-0.594000	0.05733	-0.104000	0.12154	-0.417000	0.06048	TAT		0.358	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215823777	A	C	215823777	4	2	61	1	0	0	0	0	0	1	0	0	30	340	12	4	1933	4	ABCA12	2	215823777	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	615	215823777	27375596	2109	10094										
ABCA12	26154	broad.mit.edu	37	chr2	215839566	215839566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacattgctgagacaagtgCttccgtgctcgggtgataat	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215839566C>T	ENST00000272895.7	-	35	5623	c.5404G>A	c.(5404-5406)Gca>Aca	p.A1802T	ABCA12_ENST00000389661.4_Missense_Mutation_p.A1484T	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1802					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.A1802T(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		GAGACAAGTGCTTCCGTGCTC	0.383																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											157	156	157					2																	215839566		2203	4300	6503	215547811	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5404G>A	2.37:g.215839566C>T	ENSP00000272895:p.Ala1802Thr		215547811	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	1.002	-0.690751	0.03303	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.88354	-2.37;-2.36	5.7	-0.0916	0.13660	.	1.087510	0.07052	N	0.832121	D	0.82632	0.5079	N	0.25647	0.755	0.09310	N	1	B;B	0.24317	0.101;0.016	B;B	0.29440	0.102;0.04	T	0.63139	-0.6704	10	0.14252	T	0.57	.	13.8854	0.63706	0.1014:0.4381:0.4605:0.0	.	1802;1484	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	T	1802;1484	ENSP00000272895:A1802T;ENSP00000374312:A1484T	ENSP00000272895:A1802T	A	-	1	0	ABCA12	215547811	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.518000	0.22847	0.032000	0.15435	-0.188000	0.12872	GCA		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215839566	C	T	215839566	3	4	61	1	0	0	0	0	1	0	0	0	30	797	28	3	2459	3	ABCA12	2	215839566	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15789	215839566	27359807	2110	10095										
ABCA12	26154	broad.mit.edu	37	chr2	215846946	215846946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atataacatcccatatacttCggcgagaacatgggtcaact	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215846946C>T	ENST00000272895.7	-	30	4763	c.4544G>A	c.(4543-4545)cGa>cAa	p.R1515Q	ABCA12_ENST00000389661.4_Missense_Mutation_p.R1197Q	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1515	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.R1515Q(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		CCATATACTTCGGCGAGAACA	0.418																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											153	141	145					2																	215846946		2203	4300	6503	215555191	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4544G>A	2.37:g.215846946C>T	ENSP00000272895:p.Arg1515Gln		215555191	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	36	5.674091	0.96764	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.97232	-4.3;-4.3	5.65	5.65	0.86999	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.207947	0.32868	N	0.005560	D	0.97736	0.9257	L	0.52573	1.65	0.80722	D	1	D;D	0.69078	0.991;0.997	P;D	0.64776	0.564;0.929	D	0.98085	1.0406	10	0.72032	D	0.01	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	1515;1197	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	Q	1515;1197	ENSP00000272895:R1515Q;ENSP00000374312:R1197Q	ENSP00000272895:R1515Q	R	-	2	0	ABCA12	215555191	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	CGA		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215846946	C	T	215846946	3	4	61	1	0	0	0	0	1	0	0	0	30	884	31	1	3339	1	ABCA12	2	215846946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7380	215846946	27352427	2111	10096										
ABCA12	26154	broad.mit.edu	37	chr2	215847097	215847097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggctatatagtccagtatCttttaaagtccttcaaaaat	5	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215847097C>A	ENST00000272895.7	-	30	4612	c.4393G>T	c.(4393-4395)Gat>Tat	p.D1465Y	ABCA12_ENST00000389661.4_Missense_Mutation_p.D1147Y	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1465	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.D1465Y(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		AGTCCAGTATCTTTTAAAGTC	0.338																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											102	97	98					2																	215847097		2203	4300	6503	215555342	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4393G>T	2.37:g.215847097C>A	ENSP00000272895:p.Asp1465Tyr		215555342	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472806	0.63737	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.93859	-3.3;-3.3	5.45	5.45	0.79879	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.161162	0.43579	D	0.000556	D	0.94364	0.8188	L	0.28740	0.885	0.80722	D	1	P;D	0.62365	0.942;0.991	D;P	0.64506	0.926;0.905	D	0.94890	0.8047	10	0.87932	D	0	.	19.4736	0.94973	0.0:1.0:0.0:0.0	.	1465;1147	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	Y	1465;1147	ENSP00000272895:D1465Y;ENSP00000374312:D1147Y	ENSP00000272895:D1465Y	D	-	1	0	ABCA12	215555342	1.000000	0.71417	0.999000	0.59377	0.801000	0.45260	7.651000	0.83577	2.836000	0.97738	0.655000	0.94253	GAT		0.338	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215847097	C	A	215847097	3	1	61	1	0	0	0	0	1	0	0	0	30	913	32	2	3490	2	ABCA12	2	215847097	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151	215847097	27352276	2112	10097										
ABCA12	26154	broad.mit.edu	37	chr2	215866442	215866442	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgtcaatgttgttctcTaatttcagtcttagaatatc	6	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215866442T>G	ENST00000272895.7	-	21	2922	c.2703A>C	c.(2701-2703)ttA>ttC	p.L901F	ABCA12_ENST00000389661.4_Missense_Mutation_p.L583F	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	901					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.L901F(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TGTTGTTCTCTAATTTCAGTC	0.328																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	large_intestine(1)	2											99	95	96					2																	215866442		2202	4300	6502	215574687	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2703A>C	2.37:g.215866442T>G	ENSP00000272895:p.Leu901Phe		215574687	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.863308	0.51482	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.85556	-2.0;-2.0	5.77	0.687	0.18020	.	0.137832	0.33144	N	0.005223	D	0.90007	0.6880	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.75484	0.986;0.959	D	0.88169	0.2863	10	0.54805	T	0.06	.	10.8105	0.46545	0.0:0.3148:0.0:0.6852	.	901;583	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	F	901;583	ENSP00000272895:L901F;ENSP00000374312:L583F	ENSP00000272895:L901F	L	-	3	2	ABCA12	215574687	0.993000	0.37304	0.999000	0.59377	0.860000	0.49131	0.142000	0.16096	0.132000	0.18615	0.459000	0.35465	TTA		0.328	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215866442	T	G	215866442	3	3	61	1	0	0	0	0	1	0	0	0	30	1519	53	4	5216	4	ABCA12	2	215866442	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19345	215866442	27332931	2113	10098										
ABCA12	26154	broad.mit.edu	37	chr2	215875166	215875166	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcgggcatgttaatgatGtctttataaagggagaagca	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:215875166G>A	ENST00000272895.7	-	18	2580	c.2361C>T	c.(2359-2361)gaC>gaT	p.D787D	ABCA12_ENST00000389661.4_Silent_p.D469D	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	787					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.D787D(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TGTTAATGATGTCTTTATAAA	0.378																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - coding silent(1)	large_intestine(1)	2											81	79	79					2																	215875166		2203	4300	6503	215583411	SO:0001819	synonymous_variant	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2361C>T	2.37:g.215875166G>A			215583411	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																				0.378	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215875166	G	A	215875166	2	1	61	1	0	0	0	0	0	0	0	1	30	1368	48	3		3	ABCA12	2	215875166	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8724	215875166	27324207	2114	10099										
FN1	2335	broad.mit.edu	37	chr2	216238117	216238117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgacataaattgtatattCggttcccggttccaggcctg	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:216238117C>T	ENST00000359671.1	-	38	6167	c.5902G>A	c.(5902-5904)Gaa>Aaa	p.E1968K	FN1_ENST00000432072.2_Missense_Mutation_p.E1969K|FN1_ENST00000354785.4_Missense_Mutation_p.E2059K|FN1_ENST00000446046.1_Missense_Mutation_p.E1968K|FN1_ENST00000356005.4_Missense_Mutation_p.E1878K|FN1_ENST00000357867.4_Missense_Mutation_p.E1878K|FN1_ENST00000421182.1_Missense_Mutation_p.E1878K|FN1_ENST00000357009.2_Missense_Mutation_p.E1968K|FN1_ENST00000346544.3_Missense_Mutation_p.E1968K|FN1_ENST00000345488.5_Missense_Mutation_p.E1968K|FN1_ENST00000443816.1_Missense_Mutation_p.E1878K|FN1_ENST00000323926.6_Missense_Mutation_p.E2059K|FN1_ENST00000336916.4_Missense_Mutation_p.E1968K			P02751	FINC_HUMAN	fibronectin 1	1968	Binds to FBLN1.|Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.E1968K(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	ATTGTATATTCGGTTCCCGGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											149	149	149					2																	216238117		2203	4300	6503	215946362	SO:0001583	missense	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5902G>A	2.37:g.216238117C>T	ENSP00000352696:p.Glu1968Lys		215946362	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	C	20.2	3.947772	0.73787	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923;ENST00000438981	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.71953	0.3401	L	0.58302	1.8	0.24871	N	0.99228	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.996;0.999;1.0;1.0;0.999;0.999;0.999;1.0;1.0	D;D;D;D;P;D;D;D;D;D;D;D;D	0.87578	0.987;0.991;0.991;0.993;0.873;0.991;0.998;0.983;0.995;0.991;0.991;0.947;0.998	T	0.64162	-0.6472	10	0.56958	D	0.05	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1759;1968;1969;2059;1878;1878;1968;1968;1969;1878;1878;2059;1968	Q68CX6;F8W7G7;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	K	1878;2059;1968;1878;2059;1969;1968;1968;1968;1968;1968;1878;1969;1878;685;87	ENSP00000394423:E1878K;ENSP00000323534:E2059K;ENSP00000338200:E1968K;ENSP00000350534:E1878K;ENSP00000346839:E2059K;ENSP00000352696:E1968K;ENSP00000265312:E1968K;ENSP00000273049:E1968K;ENSP00000349509:E1968K;ENSP00000410422:E1968K;ENSP00000415018:E1878K;ENSP00000399538:E1969K;ENSP00000348285:E1878K;ENSP00000416139:E685K;ENSP00000392565:E87K	ENSP00000265313:E1969K	E	-	1	0	FN1	215946362	0.998000	0.40836	0.976000	0.42696	0.499000	0.33736	3.925000	0.56484	2.941000	0.99782	0.655000	0.94253	GAA		0.468	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216238117	C	T	216238117	3	4	61	1	0	0	0	0	1	0	0	0	5981	893	31	1	1290	1	FN1	2	216238117	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	362951	216238117	26961256	2115	10100										
FN1	2335	broad.mit.edu	37	chr2	216240046	216240046	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggtaatcctggcacgtggCggctgccatgataccagcaa	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:216240046C>T	ENST00000359671.1	-	37	6040	c.5775G>A	c.(5773-5775)ccG>ccA	p.P1925P	FN1_ENST00000432072.2_Silent_p.P1926P|FN1_ENST00000354785.4_Silent_p.P2016P|FN1_ENST00000446046.1_Silent_p.P1925P|FN1_ENST00000356005.4_Silent_p.P1835P|FN1_ENST00000357867.4_Silent_p.P1835P|FN1_ENST00000421182.1_Silent_p.P1835P|FN1_ENST00000357009.2_Silent_p.P1925P|FN1_ENST00000346544.3_Silent_p.P1925P|FN1_ENST00000345488.5_Silent_p.P1925P|FN1_ENST00000443816.1_Silent_p.P1835P|FN1_ENST00000323926.6_Silent_p.P2016P|FN1_ENST00000336916.4_Silent_p.P1925P			P02751	FINC_HUMAN	fibronectin 1	1925	Binds to FBLN1.|Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.P1925P(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	TGGCACGTGGCGGCTGCCATG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	2											55	58	57					2																	216240046		2203	4300	6503	215948291	SO:0001819	synonymous_variant	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5775G>A	2.37:g.216240046C>T			215948291	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																					0.537	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216240046	C	T	216240046	2	4	61	1	0	0	0	0	0	0	0	1	5981	755	27	1		1	FN1	2	216240046	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1929	216240046	26959327	2116	10101										
FN1	2335	broad.mit.edu	37	chr2	216271901	216271901	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgacaacaggtgtactttCttgattttcttccacagcat	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:216271901C>A	ENST00000359671.1	-	18	2927	c.2662G>T	c.(2662-2664)Gaa>Taa	p.E888*	FN1_ENST00000432072.2_Nonsense_Mutation_p.E888*|FN1_ENST00000354785.4_Nonsense_Mutation_p.E888*|FN1_ENST00000446046.1_Nonsense_Mutation_p.E888*|FN1_ENST00000356005.4_Nonsense_Mutation_p.E888*|FN1_ENST00000357867.4_Nonsense_Mutation_p.E888*|FN1_ENST00000421182.1_Nonsense_Mutation_p.E888*|FN1_ENST00000357009.2_Nonsense_Mutation_p.E888*|FN1_ENST00000346544.3_Nonsense_Mutation_p.E888*|FN1_ENST00000345488.5_Nonsense_Mutation_p.E888*|FN1_ENST00000443816.1_Nonsense_Mutation_p.E888*|FN1_ENST00000323926.6_Nonsense_Mutation_p.E888*|FN1_ENST00000336916.4_Nonsense_Mutation_p.E888*			P02751	FINC_HUMAN	fibronectin 1	888	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.E888*(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	GGTGTACTTTCTTGATTTTCT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											176	168	171					2																	216271901		2203	4300	6503	215980146	SO:0001587	stop_gained	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2662G>T	2.37:g.216271901C>A	ENSP00000352696:p.Glu888*		215980146	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Nonsense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	C	42	9.275169	0.99122	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	.	.	.	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.5204	0.95183	0.0:1.0:0.0:0.0	.	.	.	.	X	888	.	ENSP00000265313:E888X	E	-	1	0	FN1	215980146	1.000000	0.71417	0.999000	0.59377	0.293000	0.27360	7.487000	0.81328	2.598000	0.87819	0.655000	0.94253	GAA		0.418	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216271901	C	A	216271901	4	1	61	1	0	0	0	0	0	1	0	0	5981	922	32	2	4887	2	FN1	2	216271901	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31855	216271901	26927472	2117	10102										
SMARCAL1	50485	broad.mit.edu	37	chr2	217340037	217340037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccacctcatcagctgagCgggaggacctgtgccagcag	13	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:217340037C>T	ENST00000357276.4	+	15	2620	c.2290C>T	c.(2290-2292)Cgg>Tgg	p.R764W	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.R764W	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	764	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		R -> Q (in SIOD; abolishes annealing helicase activity; no effect on specific binding to fork DNA; no effect on recruitment to sites of DNA damage). {ECO:0000269|PubMed:11799392}.		cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.R764W(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		ATCAGCTGAGCGGGAGGACCT	0.627									Schimke Immuno-Osseous Dysplasia																																							1	Substitution - Missense(1)	large_intestine(1)	2											107	90	96					2																	217340037		2203	4300	6503	217048282	SO:0001583	missense	50485	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2290C>T	2.37:g.217340037C>T	ENSP00000349823:p.Arg764Trp		217048282	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.207495	0.58343	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000392128	D;D;D	0.97480	-4.4;-4.4;-2.63	5.06	4.17	0.49024	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99143	0.9704	H	0.99169	4.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98640	1.0675	10	0.87932	D	0	-16.7893	13.8807	0.63680	0.1535:0.8465:0.0:0.0	.	764	Q9NZC9	SMAL1_HUMAN	W	764;764;606	ENSP00000349823:R764W;ENSP00000350940:R764W;ENSP00000375974:R606W	ENSP00000349823:R764W	R	+	1	2	SMARCAL1	217048282	1.000000	0.71417	0.762000	0.31397	0.114000	0.19823	3.617000	0.54181	1.318000	0.45170	0.650000	0.86243	CGG		0.627	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			T	217340037	C	T	217340037	3	4	61	1	0	0	0	0	1	0	0	0	14810	759	27	1	2340	1	SMARCAL1	2	217340037	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1068136	217340037	25859336	2118	10103										
TNS1	7145	broad.mit.edu	37	chr2	218675026	218675026	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagggccggagctatctttCgattcatctgtggggtctaa	13	9	4	0	rs201334905		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218675026C>T	ENST00000171887.4	-	29	5189	c.4737G>A	c.(4735-4737)tcG>tcA	p.S1579S	TNS1_ENST00000430930.1_Silent_p.S1558S|TNS1_ENST00000419504.1_Silent_p.S1565S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1579					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.S1579S(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		AGCTATCTTTCGATTCATCTG	0.507													.|||	1	0.000199681	8e-04	0	5008	,	,		20424	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											108	103	105					2																	218675026		2203	4300	6503	218383271	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4737G>A	2.37:g.218675026C>T			218383271	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.507	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218675026	C	T	218675026	2	4	61	1	0	0	0	0	0	0	0	1	16382	871	31	1		1	TNS1	2	218675026	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1334989	218675026	24524347	2119	10104										
TNS1	7145	broad.mit.edu	37	chr2	218677939	218677939	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagggggacagctcaccGaagtttggctcattggggca	17	9	2	0	rs141774958		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218677939G>A	ENST00000171887.4	-	27	5093	c.4641C>T	c.(4639-4641)ttC>ttT	p.F1547F	TNS1_ENST00000430930.1_Splice_Site_p.F1526F|TNS1_ENST00000419504.1_Splice_Site_p.F1533F	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1547	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.F1547F(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		ACAGCTCACCGAAGTTTGGCT	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		16922	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G		1,4405	2.1+/-5.4	0,1,2202	50	52	51		4641	-6.6	0.9	2	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous-near-splice	TNS1	NM_022648.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1547/1736	218677939	1,13005	2203	4300	6503	218386184	SO:0001630	splice_region_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4642+1C>T	2.37:g.218677939G>A			218386184	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	Silent	A	218677939	G	A	218677939	5	1	61	1	0	0	0	0	0	0	1	0	16382	1072	37	1	594	1	TNS1	2	218677939	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2913	218677939	24521434	2120	10105										
TNS1	7145	broad.mit.edu	37	chr2	218679651	218679651	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccctgctccctggagatCtcaggcttgtaccaatactt	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218679651C>A	ENST00000171887.4	-	25	4853	c.4401G>T	c.(4399-4401)gaG>gaT	p.E1467D	TNS1_ENST00000430930.1_Missense_Mutation_p.E1446D|TNS1_ENST00000419504.1_Missense_Mutation_p.E1454D	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1467	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.E1467D(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		CCCTGGAGATCTCAGGCTTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	62	65					2																	218679651		2203	4300	6503	218387896	SO:0001583	missense	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4401G>T	2.37:g.218679651C>A	ENSP00000171887:p.Glu1467Asp		218387896	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	C	1.899	-0.453663	0.04540	.	.	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39	5.36	3.52	0.40303	SH2 motif (4);	0.212926	0.47093	N	0.000251	T	0.70745	0.3259	N	0.01482	-0.84	0.80722	D	1	B;B;B	0.18013	0.025;0.025;0.0	B;B;B	0.20184	0.028;0.025;0.006	T	0.67201	-0.5730	10	0.02654	T	1	.	16.7825	0.85566	0.0:0.5001:0.4999:0.0	.	1467;1446;1454	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	D	1467;605;1454;1446	ENSP00000171887:E1467D;ENSP00000394171:E605D;ENSP00000408724:E1454D;ENSP00000406016:E1446D	ENSP00000171887:E1467D	E	-	3	2	TNS1	218387896	0.997000	0.39634	1.000000	0.80357	0.813000	0.45954	0.384000	0.20668	0.794000	0.33899	0.563000	0.77884	GAG		0.537	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218679651	C	A	218679651	3	1	61	1	0	0	0	0	1	0	0	0	16382	912	32	2	842	2	TNS1	2	218679651	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1712	218679651	24519722	2121	10106										
TNS1	7145	broad.mit.edu	37	chr2	218682633	218682633	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggctgcggagtctggtgaCggggaggtggcagggctgct	21	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218682633C>T	ENST00000171887.4	-	24	4562	c.4110G>A	c.(4108-4110)ccG>ccA	p.P1370P	TNS1_ENST00000430930.1_Silent_p.P1349P|TNS1_ENST00000419504.1_Silent_p.P1357P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1370					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P1370P(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		AGTCTGGTGACGGGGAGGTGG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	2											43	41	42					2																	218682633		2203	4300	6503	218390878	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4110G>A	2.37:g.218682633C>T			218390878	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.667	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218682633	C	T	218682633	2	4	61	1	0	0	0	0	0	0	0	1	16382	523	19	1		1	TNS1	2	218682633	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2982	218682633	24516740	2122	10107										
TNS1	7145	broad.mit.edu	37	chr2	218745657	218745657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgatgcccactgaagttgtCgtaggagtcccagcggatga	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218745657C>T	ENST00000171887.4	-	16	1470	c.1018G>A	c.(1018-1020)Gac>Aac	p.D340N	TNS1_ENST00000430930.1_Missense_Mutation_p.D340N|TNS1_ENST00000419504.1_Missense_Mutation_p.D340N|TNS1_ENST00000310858.6_Missense_Mutation_p.D371N	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	340					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.D340N(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		CTGAAGTTGTCGTAGGAGTCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	124	131					2																	218745657		2203	4300	6503	218453902	SO:0001583	missense	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1018G>A	2.37:g.218745657C>T	ENSP00000171887:p.Asp340Asn		218453902	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.991759|3.991759	0.74703|0.74703	.|.	.|.	ENSG00000079308|ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858|ENST00000453356	D;D;D;D;D;D|.	0.95482|.	-2.79;-2.79;-2.79;-3.3;-3.69;-3.72|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.177663|.	0.48767|.	D|.	0.000166|.	T|T	0.69296|0.69296	0.3095|0.3095	L|L	0.54323|0.54323	1.7|1.7	0.47407|0.47407	D|D	0.999419|0.999419	D;B;B;B;B;B|.	0.67145|.	0.996;0.121;0.012;0.181;0.032;0.032|.	P;B;B;B;B;B|.	0.50617|.	0.646;0.016;0.006;0.027;0.008;0.005|.	T|T	0.66736|0.66736	-0.5848|-0.5848	10|5	0.66056|.	D|.	0.02|.	.|.	16.2227|16.2227	0.82267|0.82267	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	340;394;371;340;340;340|.	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55|.	.;.;.;TENS1_HUMAN;.;.|.	N|Q	340;340;340;465;408;371|115	ENSP00000171887:D340N;ENSP00000408724:D340N;ENSP00000406016:D340N;ENSP00000405460:D465N;ENSP00000400383:D408N;ENSP00000308321:D371N|.	ENSP00000171887:D340N|.	D|R	-|-	1|2	0|0	TNS1|TNS1	218453902|218453902	1.000000|1.000000	0.71417|0.71417	0.963000|0.963000	0.40424|0.40424	0.866000|0.866000	0.49608|0.49608	7.277000|7.277000	0.78572|0.78572	2.598000|2.598000	0.87819|0.87819	0.561000|0.561000	0.74099|0.74099	GAC|CGA		0.592	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218745657	C	T	218745657	3	4	61	1	0	0	0	0	1	0	0	0	16382	884	31	1	4261	1	TNS1	2	218745657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63024	218745657	24453716	2123	10108										
CXCR2	3579	broad.mit.edu	37	chr2	218999582	218999582	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctggaaaggtgaagatCttagtaattacagttacagc	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:218999582C>A	ENST00000318507.2	+	3	485	c.58C>A	c.(58-60)Ctt>Att	p.L20I		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	20					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)	p.L20I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						AGGTGAAGATCTTAGTAATTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											105	101	102					2																	218999582		2203	4300	6503	218707827	SO:0001583	missense	3579			U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6027	protein-coding gene	gene with protein product		146928	"interleukin 8 receptor, beta"	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.58C>A	2.37:g.218999582C>A	ENSP00000319635:p.Leu20Ile		218707827	Q8IUZ1|Q9P2T6|Q9P2T7	Missense_Mutation	SNP	ENST00000318507.2	37	CCDS2408.1	.	.	.	.	.	.	.	.	.	.	C	6.419	0.445420	0.12164	.	.	ENSG00000180871	ENST00000453237;ENST00000415392;ENST00000318507;ENST00000454148;ENST00000428565	T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13	3.89	-7.78	0.01223	.	.	.	.	.	T	0.20333	0.0489	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20306	-1.0279	9	0.22706	T	0.39	.	0.3198	0.00301	0.22:0.2242:0.2575:0.2982	.	20	P25025	CXCR2_HUMAN	I	20	ENSP00000413686:L20I;ENSP00000392348:L20I;ENSP00000319635:L20I;ENSP00000415148:L20I;ENSP00000392698:L20I	ENSP00000319635:L20I	L	+	1	0	CXCR2	218707827	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.921000	0.04008	-2.261000	0.00691	-1.528000	0.00924	CTT		0.398	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557		A	218999582	C	A	218999582	3	1	61	1	0	0	0	0	1	0	0	0	4097	913	32	2	60	2	CXCR2	2	218999582	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253925	218999582	24199791	2124	10109										
ARPC2	10109	broad.mit.edu	37	chr2	219103552	219103552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaacagggcagttatccAttatagggatgatgagacca	12	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219103552A>G	ENST00000295685.10	+	5	695	c.434A>G	c.(433-435)cAt>cGt	p.H145R	ARPC2_ENST00000477992.1_3'UTR|ARPC2_ENST00000315717.5_Missense_Mutation_p.H145R	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	145					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)	p.H145R(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		GCAGTTATCCATTATAGGGAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	72	73					2																	219103552		2203	4300	6503	218811797	SO:0001583	missense	10109			AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"Actin related protein 2/3 complex subunits"	705	protein-coding gene	gene with protein product		604224	"actin related protein 2/3 complex, subunit 2 (34 kD)"			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.434A>G	2.37:g.219103552A>G	ENSP00000295685:p.His145Arg		218811797	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	37	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754624	0.49362	.	.	ENSG00000163466	ENST00000315717;ENST00000295685	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.68329	0.2989	M	0.75447	2.3	0.80722	D	1	B	0.17268	0.021	B	0.17979	0.02	T	0.65853	-0.6067	9	0.46703	T	0.11	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	145	O15144	ARPC2_HUMAN	R	145	.	ENSP00000295685:H145R	H	+	2	0	ARPC2	218811797	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	9.139000	0.94554	2.371000	0.80710	0.533000	0.62120	CAT		0.438	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731		G	219103552	A	G	219103552	3	3	61	1	0	0	0	0	1	0	0	0	972	217	8	4	452	4	ARPC2	2	219103552	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	103970	219103552	24095821	2125	10110										
C2orf62	375307	broad.mit.edu	37	chr2	219227480	219227480	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaagactggagtgacttCtttcccctggagctcaatca	10	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219227480C>A	ENST00000289388.3	+	6	514	c.485C>A	c.(484-486)tCt>tAt	p.S162Y	C2orf62_ENST00000481940.1_Intron	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		162					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S162Y(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGAGTGACTTCTTTCCCCTGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	2											86	80	82					2																	219227480		2203	4300	6503	218935724	SO:0001583	missense	375307																														ENST00000289388.3:c.485C>A	2.37:g.219227480C>A	ENSP00000289388:p.Ser162Tyr		218935724		Missense_Mutation	SNP	ENST00000289388.3	37	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	0.725	-0.782205	0.02907	.	.	ENSG00000158428	ENST00000289388	.	.	.	4.55	-6.99	0.01605	.	1.282060	0.05319	N	0.526265	T	0.26521	0.0648	L	0.34521	1.04	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.21861	-1.0233	9	0.19590	T	0.45	-3.4522	8.8131	0.34978	0.221:0.542:0.0:0.2371	.	162	Q7Z7H3	CB062_HUMAN	Y	162	.	ENSP00000289388:S162Y	S	+	2	0	C2orf62	218935724	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.626000	0.02035	-0.969000	0.03573	-0.302000	0.09304	TCT		0.607	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			A	219227480	C	A	219227480	3	1	61	1	0	0	0	0	1	0	0	0	2187	913	32	2	507	2	C2orf62	2	219227480	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123928	219227480	23971893	2126	10111										
TTLL4	9654	broad.mit.edu	37	chr2	219611862	219611862	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcctgccccaggacgccaAgctcctgcgcaaagcgtggg	12	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219611862A>C	ENST00000392102.1	+	9	2451	c.2111A>C	c.(2110-2112)aAg>aCg	p.K704T	TTLL4_ENST00000258398.4_Missense_Mutation_p.K704T|TTLL4_ENST00000442769.1_Intron|TTLL4_ENST00000457313.1_Missense_Mutation_p.K539T	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	704	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)	p.K704T(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CAGGACGCCAAGCTCCTGCGC	0.567																																					GBM(172;1818 2053 15407 20943 49753)											1	Substitution - Missense(1)	large_intestine(1)	2											77	80	79					2																	219611862		2203	4300	6503	219320106	SO:0001583	missense	9654				CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.2111A>C	2.37:g.219611862A>C	ENSP00000375951:p.Lys704Thr		219320106	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.5|25.5	4.645693|4.645693	0.87958|0.87958	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000258398|ENST00000448224	T;T;T|.	0.08282|.	3.11;3.11;3.11|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64571|0.64571	0.2610|0.2610	L|L	0.49699|0.49699	1.58|1.58	0.58432|0.58432	D|D	0.999999|0.999999	D;P|.	0.67145|.	0.996;0.774|.	D;P|.	0.65684|.	0.937;0.684|.	T|T	0.61691|0.61691	-0.7011|-0.7011	10|5	0.40728|.	T|.	0.16|.	.|.	15.5295|15.5295	0.75942|0.75942	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	539;704|.	E9PH58;Q14679|.	.;TTLL4_HUMAN|.	T|R	539;704;704|36	ENSP00000393332:K539T;ENSP00000375951:K704T;ENSP00000258398:K704T|.	ENSP00000258398:K704T|.	K|S	+|+	2|1	0|0	TTLL4|TTLL4	219320106|219320106	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.950000|4.950000	0.63603|0.63603	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	AAG|AGC		0.567	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		C	219611862	A	C	219611862	3	2	61	1	0	0	0	0	1	0	0	0	16769	72	3	4	2137	4	TTLL4	2	219611862	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	384382	219611862	23587511	2127	10112										
TTLL4	9654	broad.mit.edu	37	chr2	219618860	219618860	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacctattccctccagaaaAcaaagctcctgtgaggttag	7	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219618860A>G	ENST00000392102.1	+	20	3688	c.3348A>G	c.(3346-3348)aaA>aaG	p.K1116K	TTLL4_ENST00000258398.4_Silent_p.K1116K|TTLL4_ENST00000442769.1_Silent_p.K1052K|TTLL4_ENST00000457313.1_Intron	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1116					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)	p.K1116K(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCTCCAGAAAACAAAGCTCCT	0.483																																					GBM(172;1818 2053 15407 20943 49753)											1	Substitution - coding silent(1)	large_intestine(1)	2											165	174	171					2																	219618860		2203	4300	6503	219327104	SO:0001819	synonymous_variant	9654				CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.3348A>G	2.37:g.219618860A>G			219327104	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	A	6.733	0.504065	0.12822	.	.	ENSG00000135912	ENST00000436668	.	.	.	4.62	-2.91	0.05631	.	.	.	.	.	T	0.20536	0.0494	.	.	.	0.27760	N	0.943864	.	.	.	.	.	.	T	0.31420	-0.9944	4	.	.	.	.	3.1681	0.06542	0.342:0.0:0.3387:0.3193	.	.	.	.	A	219	.	.	T	+	1	0	TTLL4	219327104	0.203000	0.23435	0.066000	0.19879	0.304000	0.27724	0.042000	0.13949	-0.253000	0.09514	-0.301000	0.09380	ACA		0.483	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		G	219618860	A	G	219618860	2	3	61	1	0	0	0	0	0	0	0	1	16769	40	2	4		4	TTLL4	2	219618860	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6998	219618860	23580513	2128	10113										
PRKAG3	53632	broad.mit.edu	37	chr2	219694751	219694751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagctagttgccatggcatCgtagcaggtgtgctcctgca	14	10	0	0	rs140696399	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219694751C>T	ENST00000529249.1	-	4	898	c.583G>A	c.(583-585)Gat>Aat	p.D195N	PRKAG3_ENST00000545803.1_Missense_Mutation_p.D11N|PRKAG3_ENST00000439262.2_Missense_Mutation_p.D170N|PRKAG3_ENST00000392098.3_Missense_Mutation_p.D195N			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	195					cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)	p.D195N(1)		large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	GCCATGGCATCGTAGCAGGTG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	ASN/ASP	3,4403	6.2+/-15.9	0,3,2200	83	73	76		583	4.3	0.9	2	dbSNP_134	76	0,8600		0,0,4300	yes	missense	PRKAG3	NM_017431.2	23	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	possibly-damaging	195/490	219694751	3,13003	2203	4300	6503	219402995	SO:0001583	missense	53632			AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.583G>A	2.37:g.219694751C>T	ENSP00000436068:p.Asp195Asn		219402995	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	.	.	.	.	.	.	.	.	.	.	C	30	5.051354	0.93740	6.81E-4	0.0	ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249;ENST00000392098	D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26	5.18	4.29	0.51040	.	0.046010	0.85682	D	0.000000	D	0.93067	0.7793	L	0.34521	1.04	0.80722	D	1	D;D;D	0.56746	0.965;0.977;0.961	P;P;B	0.57960	0.83;0.481;0.288	D	0.93720	0.7032	10	0.87932	D	0	-17.9651	13.7012	0.62611	0.1555:0.8445:0.0:0.0	.	195;170;195	B4DUK8;Q9UGI9-2;Q9UGI9	.;.;AAKG3_HUMAN	N	170;11;195;195	ENSP00000397133:D170N;ENSP00000444536:D11N;ENSP00000436068:D195N;ENSP00000375947:D195N	ENSP00000233944:D195N	D	-	1	0	PRKAG3	219402995	1.000000	0.71417	0.879000	0.34478	0.835000	0.47333	7.457000	0.80775	1.381000	0.46364	0.655000	0.94253	GAT		0.602	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1			T	219694751	C	T	219694751	3	4	61	1	0	0	0	0	1	0	0	0	12536	884	31	1	926	1	PRKAG3	2	219694751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75891	219694751	23504622	2129	10114										
CCDC108	255101	broad.mit.edu	37	chr2	219892515	219892515	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggggcagtcagaccttcGcgtccagaccaccatgatct	11	13	2	3	rs531146350		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219892515G>A	ENST00000341552.5	-	13	2151	c.2068C>T	c.(2068-2070)Cga>Tga	p.R690*	CCDC108_ENST00000441968.1_Nonsense_Mutation_p.R690*|CCDC108_ENST00000453220.1_Nonsense_Mutation_p.R690*|CCDC108_ENST00000409865.3_Nonsense_Mutation_p.R679*|CCDC108_ENST00000410037.1_Nonsense_Mutation_p.R625*	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	690						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.R690*(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		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)		TCAGACCTTCGCGTCCAGACC	0.637																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											74	68	70					2																	219892515		2203	4300	6503	219600759	SO:0001587	stop_gained	255101			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2068C>T	2.37:g.219892515G>A	ENSP00000340776:p.Arg690*		219600759	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Nonsense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	G	18.98	3.738593	0.69304	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000545086;ENST00000409865;ENST00000410037;ENST00000441164	.	.	.	5.18	1.28	0.21552	.	1.597030	0.03565	N	0.227746	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-2.202	2.0427	0.03553	0.2786:0.1229:0.4721:0.1263	.	.	.	.	X	690;690;690;166;679;625;624	.	ENSP00000340776:R690X	R	-	1	2	CCDC108	219600759	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.105000	0.15333	0.334000	0.23590	0.655000	0.94253	CGA		0.637	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		A	219892515	G	A	219892515	4	1	61	1	0	0	0	0	0	1	0	0	2749	1095	38	1	3801	1	CCDC108	2	219892515	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197764	219892515	23306858	2130	10115										
CCDC108	255101	broad.mit.edu	37	chr2	219894208	219894208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtgcagggtcatacgggCcttgcccaccagcgtcccaa	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:219894208C>T	ENST00000341552.5	-	11	1650	c.1567G>A	c.(1567-1569)Gcc>Acc	p.A523T	CCDC108_ENST00000441968.1_Missense_Mutation_p.A523T|CCDC108_ENST00000453220.1_Missense_Mutation_p.A523T|CCDC108_ENST00000409865.3_Missense_Mutation_p.A512T|CCDC108_ENST00000410037.1_Missense_Mutation_p.A458T	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	523						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.A523T(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		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)		GTCATACGGGCCTTGCCCACC	0.602											OREG0015211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											137	105	116					2																	219894208		2203	4300	6503	219602452	SO:0001583	missense	255101			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.1567G>A	2.37:g.219894208C>T	ENSP00000340776:p.Ala523Thr	2262	219602452	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	7.136	0.580830	0.13686	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.06687	3.58;3.58;3.58;3.27;3.28	5.18	1.36	0.22044	.	0.904934	0.09260	N	0.826660	T	0.04092	0.0114	N	0.16743	0.435	0.20873	N	0.999834	B;B	0.17465	0.022;0.022	B;B	0.12156	0.007;0.007	T	0.47535	-0.9110	10	0.08381	T	0.77	-10.0864	3.2718	0.06884	0.3033:0.2853:0.0:0.4114	.	512;523	E9PG25;Q6ZU64	.;CC108_HUMAN	T	523;523;523;512;458;457	ENSP00000340776:A523T;ENSP00000413377:A523T;ENSP00000409117:A523T;ENSP00000386945:A512T;ENSP00000386258:A458T	ENSP00000340776:A523T	A	-	1	0	CCDC108	219602452	0.219000	0.23619	0.991000	0.47740	0.749000	0.42624	-0.617000	0.05584	0.067000	0.16545	-0.169000	0.13324	GCC		0.602	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219894208	C	T	219894208	3	4	61	1	0	0	0	0	1	0	0	0	2749	739	26	3	4310	3	CCDC108	2	219894208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1693	219894208	23305165	2131	10116										
NHEJ1	79840	broad.mit.edu	37	chr2	220012382	220012382	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagaatgtcctcttacctcGaatcagcgtagccccactct	6	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220012382G>A	ENST00000356853.5	-	4	659	c.526C>T	c.(526-528)Cga>Tga	p.R176*	NHEJ1_ENST00000409720.1_Nonsense_Mutation_p.R176*	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	176					B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R176*(2)		kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		CTCTTACCTCGAATCAGCGTA	0.478								Non-homologous end-joining																																								2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	2											153	123	133					2																	220012382		2203	4300	6503	219720626	SO:0001587	stop_gained	79840			AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736			25737	protein-coding gene	gene with protein product		611290				16439204, 16439205	Standard	NM_024782		Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.526C>T	2.37:g.220012382G>A	ENSP00000349313:p.Arg176*		219720626	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	Nonsense_Mutation	SNP	ENST00000356853.5	37	CCDS2432.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600224	0.87055	.	.	ENSG00000187736	ENST00000409720;ENST00000356853;ENST00000426304;ENST00000457600	.	.	.	5.51	3.61	0.41365	.	0.000000	0.64402	U	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6048	0.62041	0.0:0.0:0.7187:0.2813	.	.	.	.	X	176;176;96;176	.	ENSP00000349313:R176X	R	-	1	2	NHEJ1	219720626	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	1.275000	0.33144	1.298000	0.44778	0.650000	0.86243	CGA		0.478	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256817.2	NM_024782		A	220012382	G	A	220012382	4	1	61	1	0	0	0	0	0	1	0	0	10433	1066	37	1	393	1	NHEJ1	2	220012382	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118174	220012382	23186991	2132	10117										
SLC23A3	151295	broad.mit.edu	37	chr2	220026721	220026721	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatctcttctggctcagaGgagcctccttcctcatcccc	7	18	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220026721G>T	ENST00000409878.3	-	12	1775	c.1743C>A	c.(1741-1743)tcC>tcA	p.S581S	NHEJ1_ENST00000356853.5_5'Flank|SLC23A3_ENST00000295738.7_Silent_p.S464S|SLC23A3_ENST00000396775.3_3'UTR|SLC23A3_ENST00000455516.2_Silent_p.S589S	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	581					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S464S(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGCTCAGAGGAGCCTCCTT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	2											43	45	44					2																	220026721		1902	4124	6026	219734965	SO:0001819	synonymous_variant	151295			BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"Solute carriers"	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.1743C>A	2.37:g.220026721G>T			219734965	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	CCDS46518.1																																																																																				0.587	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		T	220026721	G	T	220026721	2	4	61	1	0	0	0	0	0	0	0	1	14501	987	35	2		2	SLC23A3	2	220026721	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14339	220026721	23172652	2133	10118										
ABCB6	10058	broad.mit.edu	37	chr2	220079117	220079117	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggccctctgttaccgtctcGaagtttagcagagagtccac	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220079117G>A	ENST00000265316.3	-	7	1696	c.1380C>T	c.(1378-1380)ttC>ttT	p.F460F	ABCB6_ENST00000439002.2_Silent_p.F414F	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	460	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)	p.F460F(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		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)		TTACCGTCTCGAAGTTTAGCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	2											122	114	116					2																	220079117		2203	4300	6503	219787361	SO:0001819	synonymous_variant	10058			AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1380C>T	2.37:g.220079117G>A			219787361	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Silent	SNP	ENST00000265316.3	37	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.430016	0.25726	.	.	ENSG00000115657	ENST00000295750	.	.	.	5.93	-5.64	0.02466	.	.	.	.	.	T	0.65995	0.2745	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68217	-0.5467	4	.	.	.	-15.7085	17.6284	0.88099	0.433:0.0:0.567:0.0	.	.	.	.	L	308	.	.	S	-	2	0	ABCB6	219787361	0.918000	0.31147	0.927000	0.36925	0.985000	0.73830	0.045000	0.14013	-0.968000	0.03578	-1.021000	0.02439	TCG		0.572	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220079117	G	A	220079117	2	1	61	1	0	0	0	0	0	0	0	1	45	1049	37	1		1	ABCB6	2	220079117	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52396	220079117	23120256	2134	10119										
ABCB6	10058	broad.mit.edu	37	chr2	220082860	220082860	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcacctgctggcccaagTctgcccttgcccaccaccac	6	22	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220082860T>G	ENST00000265316.3	-	1	852	c.536A>C	c.(535-537)gAc>gCc	p.D179A	ABCB6_ENST00000439002.2_Missense_Mutation_p.D179A	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	179					brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)	p.D179A(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		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)		CTGGCCCAAGTCTGCCCTTGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											57	60	59					2																	220082860		2203	4300	6503	219791104	SO:0001583	missense	10058			AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.536A>C	2.37:g.220082860T>G	ENSP00000265316:p.Asp179Ala		219791104	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	37	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.06|14.06	2.423362|2.423362	0.43020|0.43020	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750;ENST00000427013	D;D|.	0.88124|.	-2.26;-2.34|.	5.03|5.03	3.9|3.9	0.45041|0.45041	.|.	0.521522|.	0.21080|.	N|.	0.080509|.	T|T	0.40196|0.40196	0.1107|0.1107	L|L	0.46157|0.46157	1.445|1.445	0.20821|0.20821	N|N	0.999843|0.999843	B;B|.	0.21147|.	0.052;0.038|.	B;B|.	0.26969|.	0.075;0.05|.	T|T	0.22487|0.22487	-1.0215|-1.0215	10|5	0.42905|.	T|.	0.14|.	-17.3355|-17.3355	7.3201|7.3201	0.26523|0.26523	0.0:0.0766:0.1469:0.7765|0.0:0.0766:0.1469:0.7765	.|.	179;179|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	A|P	179|73;157	ENSP00000265316:D179A;ENSP00000394333:D179A|.	ENSP00000265316:D179A|.	D|T	-|-	2|1	0|0	ABCB6|ABCB6	219791104|219791104	0.612000|0.612000	0.27000|0.27000	0.961000|0.961000	0.40146|0.40146	0.959000|0.959000	0.62525|0.62525	1.394000|1.394000	0.34509|0.34509	2.241000|2.241000	0.73720|0.73720	0.482000|0.482000	0.46254|0.46254	GAC|ACT		0.617	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		G	220082860	T	G	220082860	3	3	61	1	0	0	0	0	1	0	0	0	45	1667	58	4	2068	4	ABCB6	2	220082860	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3743	220082860	23116513	2135	10120										
ATG9A	79065	broad.mit.edu	37	chr2	220087385	220087385	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcagactcagattgtaaGgactggatagacgtaaagag	11	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220087385G>T	ENST00000409618.1	-	11	2269	c.1830C>A	c.(1828-1830)tcC>tcA	p.S610S	ATG9A_ENST00000361242.4_Silent_p.S610S|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000396761.2_Silent_p.S610S|ATG9A_ENST00000409422.1_Silent_p.S549S			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	610					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)		p.S610S(1)		endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGATTGTAAGGACTGGATAG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	2											181	191	188					2																	220087385		2052	4198	6250	219795629	SO:0001819	synonymous_variant	79065			AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1830C>A	2.37:g.220087385G>T			219795629	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	37	CCDS42820.1																																																																																				0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		T	220087385	G	T	220087385	2	4	61	1	0	0	0	0	0	0	0	1	1103	987	35	2		2	ATG9A	2	220087385	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4525	220087385	23111988	2136	10121										
STK16	8576	broad.mit.edu	37	chr2	220111441	220111441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacttctacgccctgaagcGaatcctgtgtcacgagcagc	9	14	2	1	rs548466076		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220111441G>A	ENST00000409638.3	+	3	321	c.149G>A	c.(148-150)cGa>cAa	p.R50Q	STK16_ENST00000409516.3_Intron|GLB1L_ENST00000295759.7_5'Flank|STK16_ENST00000396738.2_Missense_Mutation_p.R50Q|GLB1L_ENST00000392089.2_5'Flank|STK16_ENST00000409260.1_Missense_Mutation_p.R95Q|STK16_ENST00000486813.1_Intron|GLB1L_ENST00000356283.3_5'Flank|STK16_ENST00000409743.1_Missense_Mutation_p.R50Q	NM_001008910.2	NP_001008910.1	O75716	STK16_HUMAN	serine/threonine kinase 16	50	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|protein autophosphorylation (GO:0046777)	Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R50Q(2)		skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCTGAAGCGAATCCTGTGT	0.567													G|||	1	0.000199681	0	0	5008	,	,		21443	0.001		0	False		,,,				2504	0				Pancreas(34;887 922 17165 36961 39622)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											70	73	72					2																	220111441		2064	4205	6269	219819685	SO:0001583	missense	8576			AF060798	CCDS42822.1	2q35	2010-04-16			ENSG00000115661	ENSG00000115661			11394	protein-coding gene	gene with protein product		604719				9712705	Standard	NM_001008910		Approved	PKL12, MPSK	uc002vko.2	O75716	OTTHUMG00000154520	ENST00000409638.3:c.149G>A	2.37:g.220111441G>A	ENSP00000386928:p.Arg50Gln		219819685	A8K9H9|Q5U0F8|Q96KI2|Q9BUH4|Q9UEN3|Q9UP78	Missense_Mutation	SNP	ENST00000409638.3	37	CCDS42822.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477716	0.96291	.	.	ENSG00000115661	ENST00000409638;ENST00000396738;ENST00000409260;ENST00000409743	T;T;T;T	0.74106	2.05;2.05;-0.81;2.05	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85336	0.5673	L	0.58669	1.825	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.989;1.0	D	0.85246	0.1041	10	0.72032	D	0.01	-8.8762	20.3052	0.98627	0.0:0.0:1.0:0.0	.	50;50;95;50	B4DXY6;B8ZZI5;B8ZZN3;O75716	.;.;.;STK16_HUMAN	Q	50;50;95;50	ENSP00000386928:R50Q;ENSP00000379964:R50Q;ENSP00000387156:R95Q;ENSP00000386553:R50Q	ENSP00000379964:R50Q	R	+	2	0	STK16	219819685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.552000	0.82192	2.808000	0.96608	0.655000	0.94253	CGA		0.567	STK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335679.1			A	220111441	G	A	220111441	3	1	61	1	0	0	0	0	1	0	0	0	15328	1058	37	1	155	1	STK16	2	220111441	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24056	220111441	23087932	2137	10122										
TUBA4A	7277	broad.mit.edu	37	chr2	220116370	220116370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatagttgttggcagcatCctctttcccagtgatgagct	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220116370C>T	ENST00000248437.4	-	3	465	c.292G>A	c.(292-294)Gat>Aat	p.D98N	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000498660.1_5'UTR|TUBA4A_ENST00000392088.2_Missense_Mutation_p.D83N	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	98					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.D98N(1)|p.D83N(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	TTGGCAGCATCCTCTTTCCCA	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	2											118	103	108					2																	220116370		2203	4300	6503	219824614	SO:0001583	missense	7277			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.292G>A	2.37:g.220116370C>T	ENSP00000248437:p.Asp98Asn		219824614	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333518	0.81801	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000427737;ENST00000456818;ENST00000447205;ENST00000425551	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.06	5.06	0.68205	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.89770	0.6811	H	0.97131	3.945	0.80722	D	1	D	0.57899	0.981	D	0.74674	0.984	D	0.92991	0.6415	10	0.87932	D	0	.	18.6248	0.91333	0.0:1.0:0.0:0.0	.	98	P68366	TBA4A_HUMAN	N	98;83;83;121;83;100	ENSP00000248437:D98N;ENSP00000375938:D83N;ENSP00000408194:D83N;ENSP00000416992:D121N;ENSP00000396061:D83N;ENSP00000404740:D100N	ENSP00000248437:D98N	D	-	1	0	TUBA4A	219824614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.564000	0.82326	2.639000	0.89480	0.655000	0.94253	GAT		0.527	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		T	220116370	C	T	220116370	3	4	61	1	0	0	0	0	1	0	0	0	16789	855	30	3	1062	3	TUBA4A	2	220116370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4929	220116370	23083003	2138	10123										
OBSL1	23363	broad.mit.edu	37	chr2	220432655	220432655	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcattctctccttccaggAcgtcgagcttccggggcagg	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220432655A>C	ENST00000404537.1	-	3	1375	c.1319T>G	c.(1318-1320)gTc>gGc	p.V440G	OBSL1_ENST00000265318.4_Missense_Mutation_p.V440G|OBSL1_ENST00000373873.4_Missense_Mutation_p.V440G|OBSL1_ENST00000373876.1_Missense_Mutation_p.V440G|OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000603926.1_Missense_Mutation_p.V440G|OBSL1_ENST00000289656.3_Missense_Mutation_p.V27G	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	440					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)	p.V440G(1)					Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		TCCTTCCAGGACGTCGAGCTT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											30	34	32					2																	220432655		2053	4202	6255	220140899	SO:0001583	missense	23363			BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1319T>G	2.37:g.220432655A>C	ENSP00000385636:p.Val440Gly		220140899	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808138	0.50421	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873;ENST00000289656	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	4.46	4.46	0.54185	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.90882	0.7135	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.997;0.996;0.999	D	0.91561	0.5264	9	0.51188	T	0.08	.	13.8907	0.63738	1.0:0.0:0.0:0.0	.	440;27;440	O75147;A8MSZ8;O75147-2	OBSL1_HUMAN;.;.	G	440;440;440;440;27	ENSP00000265318:V440G;ENSP00000385636:V440G;ENSP00000362983:V440G;ENSP00000362980:V440G;ENSP00000289656:V27G	ENSP00000265318:V440G	V	-	2	0	OBSL1	220140899	1.000000	0.71417	0.901000	0.35422	0.037000	0.13140	9.024000	0.93689	1.879000	0.54435	0.454000	0.30748	GTC		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			C	220432655	A	C	220432655	3	2	61	1	0	0	0	0	1	0	0	0	10844	275	10	4	4599	4	OBSL1	2	220432655	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	316285	220432655	22766718	2139	10124										
SLC4A3	6508	broad.mit.edu	37	chr2	220498016	220498016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcccaacgatgacaaggAcagtggcttctttccccgaa	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220498016A>G	ENST00000358055.3	+	10	1810	c.1298A>G	c.(1297-1299)gAc>gGc	p.D433G	SLC4A3_ENST00000373760.2_Missense_Mutation_p.D433G|SLC4A3_ENST00000373762.3_Missense_Mutation_p.D460G|SLC4A3_ENST00000273063.6_Missense_Mutation_p.D460G|SLC4A3_ENST00000317151.3_Missense_Mutation_p.D433G			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	433					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.D460G(1)|p.D458fs*13(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GATGACAAGGACAGTGGCTTC	0.592																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|breast(1)	2											119	102	108					2																	220498016		2203	4300	6503	220206260	SO:0001583	missense	6508				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1298A>G	2.37:g.220498016A>G	ENSP00000350756:p.Asp433Gly		220206260	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.985786	0.74589	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91	4.99	4.99	0.66335	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.065016	0.64402	D	0.000016	T	0.59770	0.2218	N	0.19112	0.55	0.43160	D	0.994945	B;B	0.02656	0.0;0.0	B;B	0.10450	0.003;0.005	T	0.55872	-0.8072	10	0.25751	T	0.34	.	13.4364	0.61086	1.0:0.0:0.0:0.0	.	433;460	P48751;P48751-3	B3A3_HUMAN;.	G	433;433;460;460;433	ENSP00000350756:D433G;ENSP00000362865:D433G;ENSP00000273063:D460G;ENSP00000362867:D460G;ENSP00000314006:D433G	ENSP00000273063:D460G	D	+	2	0	SLC4A3	220206260	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.737000	0.74816	2.100000	0.63781	0.523000	0.50628	GAC		0.592	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		G	220498016	A	G	220498016	3	3	61	1	0	0	0	0	1	0	0	0	14692	275	10	4	1413	4	SLC4A3	2	220498016	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	65361	220498016	22701357	2140	10125										
SLC4A3	6508	broad.mit.edu	37	chr2	220506402	220506402	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatgctgaaccaaacttCgatgaggatggccaggatga	13	7	0	4	rs369285267		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:220506402C>T	ENST00000358055.3	+	23	4163	c.3651C>T	c.(3649-3651)ttC>ttT	p.F1217F	SLC4A3_ENST00000373760.2_Silent_p.F1217F|SLC4A3_ENST00000373762.3_Silent_p.F1244F|SLC4A3_ENST00000273063.6_Silent_p.F1244F|SLC4A3_ENST00000317151.3_Silent_p.F1217F			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	1217	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.F1244F(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AACCAAACTTCGATGAGGATG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	0,4406		0,0,2203	188	138	155		3651,3732	-6.8	0.9	2		155	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC4A3	NM_005070.3,NM_201574.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	1217/1233,1244/1260	220506402	1,13005	2203	4300	6503	220214646	SO:0001819	synonymous_variant	6508				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.3651C>T	2.37:g.220506402C>T			220214646	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	37	CCDS2445.1																																																																																				0.557	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220506402	C	T	220506402	2	4	61	1	0	0	0	0	0	0	0	1	14692	883	31	1		1	SLC4A3	2	220506402	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8386	220506402	22692971	2141	10126										
EPHA4	2043	broad.mit.edu	37	chr2	222321462	222321462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttcctggcagctgtccGaactatacgatagcttcgct	10	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:222321462G>A	ENST00000281821.2	-	7	1515	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W	EPHA4_ENST00000392071.4_Missense_Mutation_p.R441W|EPHA4_ENST00000409938.1_Missense_Mutation_p.R492W|EPHA4_ENST00000409854.1_Missense_Mutation_p.R492W	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	492	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)	p.R492W(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GCAGCTGTCCGAACTATACGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											126	111	116					2																	222321462		2203	4300	6503	222029706	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1474C>T	2.37:g.222321462G>A	ENSP00000281821:p.Arg492Trp		222029706	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766604	0.69878	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.91	0.324	0.15898	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.049258	0.85682	D	0.000000	T	0.76765	0.4033	M	0.89414	3.03	0.38114	D	0.937666	D	0.61697	0.99	D	0.64506	0.926	D	0.85008	0.0904	10	0.87932	D	0	.	16.2524	0.82492	0.0:0.0:0.3176:0.6823	.	492	P54764	EPHA4_HUMAN	W	492;492;492;441	ENSP00000281821:R492W;ENSP00000386276:R492W;ENSP00000386829:R492W;ENSP00000375923:R441W	ENSP00000281821:R492W	R	-	1	2	EPHA4	222029706	1.000000	0.71417	0.836000	0.33094	0.992000	0.81027	3.592000	0.53993	0.354000	0.24105	0.655000	0.94253	CGG		0.468	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			A	222321462	G	A	222321462	3	1	61	1	0	0	0	0	1	0	0	0	5182	1057	37	1	1530	1	EPHA4	2	222321462	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1815060	222321462	20877911	2142	10127										
SGPP2	130367	broad.mit.edu	37	chr2	223386543	223386543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtggccccgtccctccTcccctccagttgtaaaactg	8	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:223386543T>C	ENST00000321276.7	+	3	522	c.436T>C	c.(436-438)Tcc>Ccc	p.S146P		NM_152386.2	NP_689599.2	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphatase 2	146					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)	p.S146P(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	18		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		CCGTCCCTCCTCCCCTCCAGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	107	105					2																	223386543		2203	4300	6503	223094787	SO:0001583	missense	130367			AF542512	CCDS2453.1	2q36.3	2010-05-26	2010-05-26		ENSG00000163082	ENSG00000163082			19953	protein-coding gene	gene with protein product		612827				12411432	Standard	NM_152386		Approved	SPP2, FLJ39004	uc010zlo.2	Q8IWX5	OTTHUMG00000133156	ENST00000321276.7:c.436T>C	2.37:g.223386543T>C	ENSP00000315137:p.Ser146Pro		223094787	A3KPB4|Q8N8Q6	Missense_Mutation	SNP	ENST00000321276.7	37	CCDS2453.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.441336	0.83993	.	.	ENSG00000163082	ENST00000321276	T	0.75704	-0.96	4.83	4.83	0.62350	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.083567	0.50627	D	0.000114	D	0.83238	0.5211	M	0.69463	2.115	0.58432	D	0.999998	D	0.63046	0.992	D	0.64410	0.925	D	0.84666	0.0709	10	0.54805	T	0.06	-19.7105	14.4186	0.67168	0.0:0.0:0.0:1.0	.	146	Q8IWX5	SGPP2_HUMAN	P	146	ENSP00000315137:S146P	ENSP00000315137:S146P	S	+	1	0	SGPP2	223094787	1.000000	0.71417	0.990000	0.47175	0.876000	0.50452	5.026000	0.64103	1.809000	0.52856	0.533000	0.62120	TCC		0.498	SGPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256856.2			C	223386543	T	C	223386543	3	2	61	1	0	0	0	0	1	0	0	0	14257	1551	54	4	446	4	SGPP2	2	223386543	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1065081	223386543	19812830	2143	10128										
SGPP2	130367	broad.mit.edu	37	chr2	223423432	223423432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgttgatcctcttggttCgtcagcttgtacaaaatctc	8	9	3	1	rs371268936		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:223423432C>T	ENST00000321276.7	+	5	1101	c.1015C>T	c.(1015-1017)Cgt>Tgt	p.R339C		NM_152386.2	NP_689599.2	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphatase 2	339					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)	p.R339C(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	18		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		CCTCTTGGTTCGTCAGCTTGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG	0,4406		0,0,2203	125	115	119		1015	5.4	0.8	2		119	1,8599	1.2+/-3.3	0,1,4299	no	missense	SGPP2	NM_152386.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	339/400	223423432	1,13005	2203	4300	6503	223131676	SO:0001583	missense	130367			AF542512	CCDS2453.1	2q36.3	2010-05-26	2010-05-26		ENSG00000163082	ENSG00000163082			19953	protein-coding gene	gene with protein product		612827				12411432	Standard	NM_152386		Approved	SPP2, FLJ39004	uc010zlo.2	Q8IWX5	OTTHUMG00000133156	ENST00000321276.7:c.1015C>T	2.37:g.223423432C>T	ENSP00000315137:p.Arg339Cys		223131676	A3KPB4|Q8N8Q6	Missense_Mutation	SNP	ENST00000321276.7	37	CCDS2453.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.562992	0.86335	0.0	1.16E-4	ENSG00000163082	ENST00000321276	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.83036	0.5167	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84981	0.0888	9	0.87932	D	0	-14.0727	19.2014	0.93713	0.0:1.0:0.0:0.0	.	339	Q8IWX5	SGPP2_HUMAN	C	339	.	ENSP00000315137:R339C	R	+	1	0	SGPP2	223131676	1.000000	0.71417	0.846000	0.33378	0.954000	0.61252	6.485000	0.73625	2.533000	0.85409	0.655000	0.94253	CGT		0.468	SGPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256856.2			T	223423432	C	T	223423432	3	4	61	1	0	0	0	0	1	0	0	0	14257	884	31	1	1033	1	SGPP2	2	223423432	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36889	223423432	19775941	2144	10129										
FARSB	10056	broad.mit.edu	37	chr2	223507716	223507716	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttacttattatttccttCtcagatgtctaaaacaagcc	3	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:223507716C>A	ENST00000281828.6	-	3	386	c.123G>T	c.(121-123)gaG>gaT	p.E41D	FARSB_ENST00000536361.1_5'UTR	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	41					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)	p.E41D(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	TTATTTCCTTCTCAGATGTCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											44	43	43					2																	223507716		2203	4300	6503	223215960	SO:0001583	missense	10056			AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	17800	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, beta, cytoplasmic"	609690	"phenylalanyl-tRNA synthetase-like, beta subunit"	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.123G>T	2.37:g.223507716C>A	ENSP00000281828:p.Glu41Asp		223215960	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Missense_Mutation	SNP	ENST00000281828.6	37	CCDS2454.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235846	0.39498	.	.	ENSG00000116120	ENST00000281828	.	.	.	5.62	1.24	0.21308	DNA binding domain, putative (1);	0.000000	0.85682	D	0.000000	T	0.53642	0.1809	M	0.63428	1.95	0.80722	D	1	B;B	0.24258	0.1;0.056	B;B	0.23275	0.045;0.045	T	0.45175	-0.9279	9	0.27785	T	0.31	-9.9217	9.6189	0.39710	0.0:0.5876:0.0:0.4124	.	41;41	A8K666;Q9NSD9	.;SYFB_HUMAN	D	41	.	ENSP00000281828:E41D	E	-	3	2	FARSB	223215960	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	0.415000	0.21181	0.319000	0.23209	0.563000	0.77884	GAG		0.328	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687		A	223507716	C	A	223507716	3	1	61	1	0	0	0	0	1	0	0	0	5699	912	32	2	1706	2	FARSB	2	223507716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84284	223507716	19691657	2145	10130										
SCG2	7857	broad.mit.edu	37	chr2	224463191	224463191	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcatttttttctatattCtctttgctgtctctcacctc	3	11	5	0	rs144520828		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:224463191C>A	ENST00000305409.2	-	2	1042	c.810G>T	c.(808-810)gaG>gaT	p.E270D		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.E270D(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTTCTATATTCTCTTTGCTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	184	188	187		810	2.8	1	2	dbSNP_134	187	0,8600		0,0,4300	no	missense	SCG2	NM_003469.4	45	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging	270/618	224463191	1,13005	2203	4300	6503	224171435	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.810G>T	2.37:g.224463191C>A	ENSP00000304133:p.Glu270Asp		224171435	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.194047	0.58017	2.27E-4	0.0	ENSG00000171951	ENST00000305409;ENST00000450330	T	0.02140	4.43	5.56	2.81	0.32909	.	0.064020	0.64402	D	0.000013	T	0.09379	0.0231	M	0.68952	2.095	0.49798	D	0.999827	D	0.76494	0.999	D	0.72625	0.978	T	0.00583	-1.1659	10	0.66056	D	0.02	.	10.8438	0.46730	0.0:0.7976:0.0:0.2024	.	270	P13521	SCG2_HUMAN	D	270;130	ENSP00000304133:E270D	ENSP00000304133:E270D	E	-	3	2	SCG2	224171435	0.993000	0.37304	0.962000	0.40283	0.948000	0.59901	1.285000	0.33261	0.318000	0.23185	0.644000	0.83932	GAG		0.438	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224463191	C	A	224463191	3	1	61	1	0	0	0	0	1	0	0	0	13928	912	32	2	1047	2	SCG2	2	224463191	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	955475	224463191	18736182	2146	10131										
SCG2	7857	broad.mit.edu	37	chr2	224463499	224463499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaattctcttcatacatagGagggaattgcatgtgcttaa	10	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:224463499G>A	ENST00000305409.2	-	2	734	c.502C>T	c.(502-504)Cct>Tct	p.P168S		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.P168S(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCATACATAGGAGGGAATTGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	2											158	156	156					2																	224463499		2203	4300	6503	224171743	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.502C>T	2.37:g.224463499G>A	ENSP00000304133:p.Pro168Ser		224171743	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	G	2.554	-0.303468	0.05495	.	.	ENSG00000171951	ENST00000305409	T	0.01495	4.83	5.5	4.61	0.57282	.	0.409529	0.27460	N	0.019276	T	0.01870	0.0059	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.13407	0.009	T	0.43556	-0.9384	10	0.42905	T	0.14	.	9.9603	0.41693	0.0721:0.1397:0.7883:0.0	.	168	P13521	SCG2_HUMAN	S	168	ENSP00000304133:P168S	ENSP00000304133:P168S	P	-	1	0	SCG2	224171743	0.153000	0.22777	0.625000	0.29200	0.952000	0.60782	2.241000	0.43097	1.416000	0.47057	0.585000	0.79938	CCT		0.403	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224463499	G	A	224463499	3	1	61	1	0	0	0	0	1	0	0	0	13928	1174	41	3	1355	3	SCG2	2	224463499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	308	224463499	18735874	2147	10132										
SCG2	7857	broad.mit.edu	37	chr2	224463666	224463666	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaagcttcgagtattattCtcatccagtcttcttcactc	4	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:224463666C>A	ENST00000305409.2	-	2	567	c.335G>T	c.(334-336)aGa>aTa	p.R112I		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.R112I(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		GAGTATTATTCTCATCCAGTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											134	135	134					2																	224463666		2203	4300	6503	224171910	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.335G>T	2.37:g.224463666C>A	ENSP00000304133:p.Arg112Ile		224171910	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843061	0.71488	.	.	ENSG00000171951	ENST00000305409;ENST00000421386;ENST00000433889	T;T;T	0.02067	4.47;4.47;4.47	5.5	0.536	0.17138	.	0.491758	0.21916	N	0.067234	T	0.04497	0.0123	L	0.50333	1.59	0.50813	D	0.999894	P	0.42203	0.773	P	0.49226	0.603	T	0.42120	-0.9470	10	0.87932	D	0	.	9.1987	0.37244	0.0:0.4606:0.0:0.5394	.	112	P13521	SCG2_HUMAN	I	112	ENSP00000304133:R112I;ENSP00000394702:R112I;ENSP00000415468:R112I	ENSP00000304133:R112I	R	-	2	0	SCG2	224171910	0.008000	0.16893	0.983000	0.44433	0.989000	0.77384	0.675000	0.25232	0.086000	0.17137	0.585000	0.79938	AGA		0.443	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224463666	C	A	224463666	3	1	61	1	0	0	0	0	1	0	0	0	13928	913	32	2	1522	2	SCG2	2	224463666	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	167	224463666	18735707	2148	10133										
WDFY1	57590	broad.mit.edu	37	chr2	224760340	224760340	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtcccaccagaggcaggcGacactacctagggatttgtg	14	11	0	1	rs374832636		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:224760340G>A	ENST00000233055.4	-	7	708	c.606C>T	c.(604-606)gtC>gtT	p.V202V		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	202						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)	p.V202V(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		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)		AGAGGCAGGCGACACTACCTA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		1,4405	2.1+/-5.4	0,1,2202	53	49	50		606	-0.3	0.1	2		50	0,8600		0,0,4300	no	coding-synonymous	WDFY1	NM_020830.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		202/411	224760340	1,13005	2203	4300	6503	224468584	SO:0001819	synonymous_variant	57590			AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20451	protein-coding gene	gene with protein product			"WD40 and FYVE domain containing 1"			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.606C>T	2.37:g.224760340G>A			224468584	Q53S17|Q9H9D5|Q9P2B3	Silent	SNP	ENST00000233055.4	37	CCDS33387.1																																																																																				0.512	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830		A	224760340	G	A	224760340	2	1	61	1	0	0	0	0	0	0	0	1	17308	1045	37	1		1	WDFY1	2	224760340	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	296674	224760340	18439033	2149	10134										
MRPL44	65080	broad.mit.edu	37	chr2	224824613	224824613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggagcagttaacactgaGtgaagaattcccagtgcccc	11	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:224824613G>A	ENST00000258383.3	+	2	611	c.542G>A	c.(541-543)aGt>aAt	p.S181N		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	181	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.S181N(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTAACACTGAGTGAAGAATTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	115	116					2																	224824613		2203	4300	6503	224532857	SO:0001583	missense	65080			AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.542G>A	2.37:g.224824613G>A	ENSP00000258383:p.Ser181Asn		224532857	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	37	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880909	0.72294	.	.	ENSG00000135900	ENST00000258383	T	0.47177	0.85	5.7	5.7	0.88788	Ribonuclease III (3);	0.079417	0.85682	D	0.000000	T	0.57286	0.2043	M	0.80847	2.515	0.53688	D	0.999975	P	0.48694	0.914	P	0.45998	0.5	T	0.57745	-0.7758	10	0.27785	T	0.31	-14.7313	17.3321	0.87268	0.0:0.0:1.0:0.0	.	181	Q9H9J2	RM44_HUMAN	N	181	ENSP00000258383:S181N	ENSP00000258383:S181N	S	+	2	0	MRPL44	224532857	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	7.317000	0.79018	2.683000	0.91414	0.650000	0.86243	AGT		0.483	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		A	224824613	G	A	224824613	3	1	61	1	0	0	0	0	1	0	0	0	9838	1029	36	3	548	3	MRPL44	2	224824613	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64273	224824613	18374760	2150	10135										
DOCK10	55619	broad.mit.edu	37	chr2	225642996	225642996	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttcttcttcttcaaaAaagccctatggaacataatg	4	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:225642996A>C	ENST00000258390.7	-	51	5728	c.5661T>G	c.(5659-5661)ttT>ttG	p.F1887L	DOCK10_ENST00000409592.3_Missense_Mutation_p.F1881L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1887	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F1885L(1)|p.F394L(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		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)		CTTCTTCAAAAAAGCCCTATG	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	2											46	41	42					2																	225642996		1802	4067	5869	225351240	SO:0001583	missense	55619			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5661T>G	2.37:g.225642996A>C	ENSP00000258390:p.Phe1887Leu		225351240	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.79|10.79	1.448982|1.448982	0.26074|0.26074	.|.	.|.	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702|ENST00000535663	T;T|.	0.33216|.	1.42;1.43|.	6.16|6.16	3.82|3.82	0.43975|0.43975	.|.	0.048005|0.048005	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.52581|0.52581	0.1743|0.1743	L|L	0.46885|0.46885	1.475|1.475	0.45139|0.45139	D|D	0.998154|0.998154	B;D;P|.	0.58268|.	0.076;0.982;0.894|.	B;P;B|.	0.60541|.	0.113;0.876;0.358|.	T|T	0.37174|0.37174	-0.9717|-0.9717	10|7	0.87932|0.17832	D|T	0|0.49	.|.	8.3251|8.3251	0.32151|0.32151	0.786:0.0:0.214:0.0|0.786:0.0:0.214:0.0	.|.	1887;1881;549|.	Q96BY6;B3FL70;B4DEY4|.	DOC10_HUMAN;.;.|.	L|V	1881;1887;394|37	ENSP00000386694:F1881L;ENSP00000258390:F1887L|.	ENSP00000258390:F1887L|ENSP00000437947:F37V	F|F	-|-	3|1	2|0	DOCK10|DOCK10	225351240|225351240	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.980000|0.980000	0.70556|0.70556	1.995000|1.995000	0.40767|0.40767	0.574000|0.574000	0.29417|0.29417	0.528000|0.528000	0.53228|0.53228	TTT|TTT		0.318	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225642996	A	C	225642996	3	2	61	1	0	0	0	0	1	0	0	0	4696	11	1	4	923	4	DOCK10	2	225642996	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	818383	225642996	17556377	2151	10136										
DOCK10	55619	broad.mit.edu	37	chr2	225669928	225669928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaattctctttaccgtacGaaatcgttttcataatgtga	6	7	2	2	rs374472028		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:225669928G>A	ENST00000258390.7	-	36	4113	c.4046C>T	c.(4045-4047)tCg>tTg	p.S1349L	DOCK10_ENST00000409592.3_Missense_Mutation_p.S1343L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1349					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S1347L(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		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)		TTTACCGTACGAAATCGTTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	LEU/SER	1,3607		0,1,1803	92	88	89		4046	5.7	1	2		89	0,8122		0,0,4061	no	missense	DOCK10	NM_014689.2	145	0,1,5864	AA,AG,GG		0.0,0.0277,0.0085	probably-damaging	1349/2187	225669928	1,11729	1804	4061	5865	225378172	SO:0001583	missense	55619			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.4046C>T	2.37:g.225669928G>A	ENSP00000258390:p.Ser1349Leu		225378172	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.80|15.80	2.940208|2.940208	0.52972|0.52972	2.77E-4|2.77E-4	0.0|0.0	ENSG00000135905|ENSG00000135905	ENST00000422684|ENST00000409592;ENST00000258390	.|T;T	.|0.62498	.|4.65;0.02	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.064020	.|0.64402	.|D	.|0.000004	T|T	0.82084|0.82084	0.4960|0.4960	M|M	0.83384|0.83384	2.64|2.64	0.48288|0.48288	D|D	0.999628|0.999628	.|D;D;D;D	.|0.89917	.|1.0;0.999;1.0;0.999	.|D;D;D;D	.|0.77557	.|0.99;0.978;0.934;0.922	D|D	0.83400|0.83400	0.0022|0.0022	5|10	.|0.87932	.|D	.|0	.|.	20.2825|20.2825	0.98528|0.98528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1349;203;1343;11	.|Q96BY6;B4DF07;B3FL70;B4DEY4	.|DOC10_HUMAN;.;.;.	C|L	231|1343;1349	.|ENSP00000386694:S1343L;ENSP00000258390:S1349L	.|ENSP00000258390:S1349L	R|S	-|-	1|2	0|0	DOCK10|DOCK10	225378172|225378172	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.107000|0.107000	0.19398|0.19398	9.144000|9.144000	0.94629|0.94629	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	CGT|TCG		0.363	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225669928	G	A	225669928	3	1	61	1	0	0	0	0	1	0	0	0	4696	1059	37	1	2598	1	DOCK10	2	225669928	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26932	225669928	17529445	2152	10137										
DOCK10	55619	broad.mit.edu	37	chr2	225796382	225796382	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgagaagcctaggcttttCttgctgtagaaaaagaaaat	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:225796382C>A	ENST00000258390.7	-	2	194	c.127G>T	c.(127-129)Gaa>Taa	p.E43*	DOCK10_ENST00000409592.3_Nonsense_Mutation_p.E37*|DOCK10_ENST00000474102.1_5'UTR	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	43					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E43*(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		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)		CTAGGCTTTTCTTGCTGTAGA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											72	69	70					2																	225796382		1861	4101	5962	225504626	SO:0001587	stop_gained	55619			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.127G>T	2.37:g.225796382C>A	ENSP00000258390:p.Glu43*		225504626	B3FL70|O75178|Q9NW06|Q9NXI8	Nonsense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	36	5.852369	0.97030	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	.	.	.	5.59	4.71	0.59529	.	0.196730	0.52532	D	0.000070	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	14.2183	0.65807	0.0:0.9275:0.0:0.0725	.	.	.	.	X	37;43	.	ENSP00000258390:E43X	E	-	1	0	DOCK10	225504626	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.199000	0.58426	1.503000	0.48686	0.563000	0.77884	GAA		0.393	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225796382	C	A	225796382	4	1	61	1	0	0	0	0	0	1	0	0	4696	922	32	2	6653	2	DOCK10	2	225796382	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	126454	225796382	17402991	2153	10138										
KIAA1486	57624	broad.mit.edu	37	chr2	226378118	226378118	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtagggcgaggccacgaaGgaagttacgtgggcaaacat	15	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:226378118G>T	ENST00000272907.6	+	3	666	c.253G>T	c.(253-255)Gga>Tga	p.G85*	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	85					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.G85*(1)									AGGCCACGAAGGAAGTTACGT	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											74	76	75					2																	226378118		2010	4172	6182	226086362	SO:0001587	stop_gained	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.253G>T	2.37:g.226378118G>T	ENSP00000272907:p.Gly85*		226086362	A2RRN4|Q96NL2	Nonsense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	41	8.887037	0.98990	.	.	ENSG00000144460	ENST00000272907	.	.	.	5.41	5.41	0.78517	.	0.332930	0.27773	N	0.017914	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-6.6425	19.1985	0.93699	0.0:0.0:1.0:0.0	.	.	.	.	X	85	.	ENSP00000272907:G85X	G	+	1	0	KIAA1486	226086362	1.000000	0.71417	0.476000	0.27291	0.953000	0.61014	3.508000	0.53378	2.532000	0.85374	0.563000	0.77884	GGA		0.478	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226378118	G	T	226378118	4	4	61	1	0	0	0	0	0	1	0	0	8258	1001	35	2	259	2	KIAA1486	2	226378118	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	581736	226378118	16821255	2154	10139										
KIAA1486	57624	broad.mit.edu	37	chr2	226446994	226446994	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagacgccaaatgtgacttCgaccatcacagctgttcttc	7	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:226446994C>T	ENST00000272907.6	+	4	1274	c.861C>T	c.(859-861)ttC>ttT	p.F287F	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	287					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.F287F(1)									AATGTGACTTCGACCATCACA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	2											98	103	101					2																	226446994		2104	4215	6319	226155238	SO:0001819	synonymous_variant	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.861C>T	2.37:g.226446994C>T			226155238	A2RRN4|Q96NL2	Silent	SNP	ENST00000272907.6	37	CCDS46529.1																																																																																				0.572	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226446994	C	T	226446994	2	4	61	1	0	0	0	0	0	0	0	1	8258	883	31	1		1	KIAA1486	2	226446994	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68876	226446994	16752379	2155	10140										
IRS1	3667	broad.mit.edu	37	chr2	227659779	227659779	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctggcataggcgcttaAatcctcacttgagcggcggg	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:227659779A>C	ENST00000305123.5	-	1	4696	c.3676T>G	c.(3676-3678)Tta>Gta	p.L1226V	IRS1_ENST00000498335.1_5'UTR	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	1226					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.L1226V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TAGGCGCTTAAATCCTCACTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											142	157	152					2																	227659779		2203	4300	6503	227368023	SO:0001583	missense	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.3676T>G	2.37:g.227659779A>C	ENSP00000304895:p.Leu1226Val		227368023		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187959	0.38609	.	.	ENSG00000169047	ENST00000305123	T	0.61040	0.14	5.44	-5.16	0.02857	.	0.547119	0.14542	N	0.313240	T	0.39358	0.1075	L	0.39898	1.24	0.29030	N	0.88578	B	0.06786	0.001	B	0.04013	0.001	T	0.17745	-1.0359	10	0.30854	T	0.27	-0.5409	8.3921	0.32535	0.3339:0.2087:0.4574:0.0	.	1226	P35568	IRS1_HUMAN	V	1226	ENSP00000304895:L1226V	ENSP00000304895:L1226V	L	-	1	2	IRS1	227368023	0.137000	0.22531	0.961000	0.40146	0.996000	0.88848	0.094000	0.15107	-0.869000	0.04052	0.533000	0.62120	TTA		0.597	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		C	227659779	A	C	227659779	3	2	61	1	0	0	0	0	1	0	0	0	7861	11	1	4	56	4	IRS1	2	227659779	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1212785	227659779	15539594	2156	10141										
IRS1	3667	broad.mit.edu	37	chr2	227660928	227660928	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagctgtgtccacctttcGaggcagatggggctgcagaa	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:227660928G>A	ENST00000305123.5	-	1	3547	c.2527C>T	c.(2527-2529)Cga>Tga	p.R843*	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	843					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R843*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TCCACCTTTCGAGGCAGATGG	0.662																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											39	48	45					2																	227660928		2201	4299	6500	227369172	SO:0001587	stop_gained	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2527C>T	2.37:g.227660928G>A	ENSP00000304895:p.Arg843*		227369172		Nonsense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	G	49	15.112487	0.99822	.	.	ENSG00000169047	ENST00000305123	.	.	.	4.96	4.96	0.65561	.	0.207688	0.32028	N	0.006697	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-5.6879	7.9258	0.29874	0.0808:0.0:0.7583:0.1608	.	.	.	.	X	843	.	ENSP00000304895:R843X	R	-	1	2	IRS1	227369172	0.595000	0.26857	1.000000	0.80357	0.992000	0.81027	3.741000	0.55090	2.573000	0.86826	0.650000	0.86243	CGA		0.662	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		A	227660928	G	A	227660928	4	1	61	1	0	0	0	0	0	1	0	0	7861	1066	37	1	1205	1	IRS1	2	227660928	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1149	227660928	15538445	2157	10142										
RHBDD1	84236	broad.mit.edu	37	chr2	227729699	227729699	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaggaataaatctagaaaGaagactgggaagtagatggt	13	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:227729699G>T	ENST00000341329.3	+	2	532	c.290G>T	c.(289-291)aGa>aTa	p.R97I	RHBDD1_ENST00000392062.2_Missense_Mutation_p.R97I	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	97					apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.R97I(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		AATCTAGAAAGAAGACTGGGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											183	174	177					2																	227729699		2203	4300	6503	227437943	SO:0001583	missense	84236			AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.290G>T	2.37:g.227729699G>T	ENSP00000344779:p.Arg97Ile		227437943	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Missense_Mutation	SNP	ENST00000341329.3	37	CCDS2464.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231476	0.79688	.	.	ENSG00000144468	ENST00000424132;ENST00000341329;ENST00000392062;ENST00000423616;ENST00000448992	T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4	5.78	3.0	0.34707	Peptidase S54, rhomboid domain (1);	0.229922	0.48767	D	0.000175	T	0.37019	0.0988	M	0.84846	2.72	0.58432	D	0.999998	P;P	0.49090	0.718;0.919	P;P	0.55260	0.657;0.772	T	0.31971	-0.9924	10	0.66056	D	0.02	-15.3121	11.1118	0.48237	0.2012:0.0:0.7988:0.0	.	97;97	C9K011;Q8TEB9	.;RHBD1_HUMAN	I	97	ENSP00000400765:R97I;ENSP00000344779:R97I;ENSP00000375914:R97I;ENSP00000399694:R97I;ENSP00000388847:R97I	ENSP00000344779:R97I	R	+	2	0	RHBDD1	227437943	0.801000	0.28930	0.998000	0.56505	0.966000	0.64601	0.737000	0.26144	0.772000	0.33382	-0.244000	0.11960	AGA		0.428	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			T	227729699	G	T	227729699	3	4	61	1	0	0	0	0	1	0	0	0	13353	942	33	2	292	2	RHBDD1	2	227729699	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68771	227729699	15469674	2158	10143										
COL4A4	1286	broad.mit.edu	37	chr2	227907847	227907847	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctggccttccaggtgatcCtctgggcccttgaataccag	10	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:227907847C>A	ENST00000396625.3	-	36	3550	c.3343G>T	c.(3343-3345)Gga>Tga	p.G1115*	COL4A4_ENST00000329662.7_Nonsense_Mutation_p.G1115*	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1115	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.G1115*(1)		breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CCAGGTGATCCTCTGGGCCCT	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											47	43	44					2																	227907847		1880	4099	5979	227616091	SO:0001587	stop_gained	1286				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3343G>T	2.37:g.227907847C>A	ENSP00000379866:p.Gly1115*		227616091	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Nonsense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	41	8.722376	0.98929	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.3905	0.83533	0.0:1.0:0.0:0.0	.	.	.	.	X	1115	.	ENSP00000328553:G1115X	G	-	1	0	COL4A4	227616091	0.986000	0.35501	0.965000	0.40720	0.254000	0.26022	3.478000	0.53158	2.677000	0.91161	0.655000	0.94253	GGA		0.542	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227907847	C	A	227907847	4	1	61	1	0	0	0	0	0	1	0	0	3699	690	24	2	1781	2	COL4A4	2	227907847	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178148	227907847	15291526	2159	10144										
COL4A4	1286	broad.mit.edu	37	chr2	227942741	227942741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctgctttgcctggggggCccagaggtccaggaaatcct	14	12	0	1	rs374340855		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:227942741C>T	ENST00000396625.3	-	25	2063	c.1856G>A	c.(1855-1857)gGc>gAc	p.G619D	COL4A4_ENST00000329662.7_Missense_Mutation_p.G619D	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	619	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.G619D(1)		breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCCTGGGGGGCCCAGAGGTCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	ASP/GLY	1,3637		0,1,1818	31	34	33		1856	5.8	0.3	2		33	0,8164		0,0,4082	no	missense	COL4A4	NM_000092.4	94	0,1,5900	TT,TC,CC		0.0,0.0275,0.0085	probably-damaging	619/1691	227942741	1,11801	1819	4082	5901	227650985	SO:0001583	missense	1286				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1856G>A	2.37:g.227942741C>T	ENSP00000379866:p.Gly619Asp		227650985	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975393	0.53720	2.75E-4	0.0	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.99353	-5.77;-5.77	5.82	5.82	0.92795	.	.	.	.	.	D	0.99722	0.9892	H	0.98802	4.335	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97326	0.9947	9	0.72032	D	0.01	.	17.8873	0.88861	0.0:1.0:0.0:0.0	.	619	P53420	CO4A4_HUMAN	D	619	ENSP00000379866:G619D;ENSP00000328553:G619D	ENSP00000328553:G619D	G	-	2	0	COL4A4	227650985	0.987000	0.35691	0.344000	0.25628	0.011000	0.07611	5.087000	0.64480	2.765000	0.95021	0.650000	0.86243	GGC		0.587	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227942741	C	T	227942741	3	4	61	1	0	0	0	0	1	0	0	0	3699	739	26	3	3312	3	COL4A4	2	227942741	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34894	227942741	15256632	2160	10145										
COL4A3	1285	broad.mit.edu	37	chr2	228147096	228147096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggcagaagaggtaaaaCggggccaaagggagacccag	15	9	0	3	rs374379775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228147096C>T	ENST00000396578.3	+	32	2666	c.2504C>T	c.(2503-2505)aCg>aTg	p.T835M	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	835	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)	p.T835M(2)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGAGGTAAAACGGGGCCAAAG	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	2						C	MET/THR	1,3631		0,1,1815	84	85	85		2504	1.1	0	2		85	0,8152		0,0,4076	no	missense	COL4A3	NM_000091.4	81	0,1,5891	TT,TC,CC		0.0,0.0275,0.0085	benign	835/1671	228147096	1,11783	1816	4076	5892	227855340	SO:0001583	missense	1285				CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.2504C>T	2.37:g.228147096C>T	ENSP00000379823:p.Thr835Met		227855340	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	2.562	-0.301619	0.05495	2.75E-4	0.0	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93426	-3.22	5.57	1.09	0.20402	.	1.055380	0.07337	N	0.880161	D	0.88164	0.6363	L	0.38838	1.175	0.09310	N	1	B;B;B;B	0.21452	0.056;0.056;0.003;0.004	B;B;B;B	0.12837	0.008;0.008;0.005;0.008	T	0.76094	-0.3085	10	0.49607	T	0.09	.	5.5052	0.16850	0.1544:0.5346:0.0:0.3109	.	835;835;835;835	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	M	835	ENSP00000379823:T835M	ENSP00000323334:T835M	T	+	2	0	COL4A3	227855340	0.097000	0.21791	0.012000	0.15200	0.011000	0.07611	-0.307000	0.08167	0.123000	0.18342	-1.814000	0.00607	ACG		0.393	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228147096	C	T	228147096	3	4	61	1	0	0	0	0	1	0	0	0	3697	536	19	1	2630	1	COL4A3	2	228147096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	204355	228147096	15052277	2161	10146										
MFF	56947	broad.mit.edu	37	chr2	228205062	228205062	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgagtgaaaatgctgttCgccaaaatggacagctggtc	11	8	0	2	rs201498602		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228205062C>T	ENST00000353339.3	+	6	925	c.484C>T	c.(484-486)Cgc>Tgc	p.R162C	MFF_ENST00000304593.9_Missense_Mutation_p.R136C|MFF_ENST00000354503.6_Missense_Mutation_p.R136C|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000409565.1_Missense_Mutation_p.R136C|MFF_ENST00000524634.1_Missense_Mutation_p.R7C|MFF_ENST00000409616.1_Missense_Mutation_p.R136C|MFF_ENST00000392059.1_Missense_Mutation_p.R162C|MFF_ENST00000349901.7_Missense_Mutation_p.R136C|MFF_ENST00000337110.7_Missense_Mutation_p.R136C	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	162					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.R162C(2)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						AAATGCTGTTCGCCAAAATGG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	2						C	CYS/ARG	2,4404		0,2,2201	87	81	83		484	5.9	1	2		83	0,8600		0,0,4300	yes	missense	MFF	NM_020194.4	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	162/343	228205062	2,13004	2203	4300	6503	227913306	SO:0001583	missense	56947			AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"chromosome 2 open reading frame 33"	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.484C>T	2.37:g.228205062C>T	ENSP00000302037:p.Arg162Cys		227913306	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161242	0.94727	4.54E-4	0.0	ENSG00000168958	ENST00000304593;ENST00000353339;ENST00000354503;ENST00000530359;ENST00000531278;ENST00000409565;ENST00000452930;ENST00000409616;ENST00000337110;ENST00000534203;ENST00000524634;ENST00000349901;ENST00000392059;ENST00000456345	T;T	0.35973	1.28;1.28	5.95	5.95	0.96441	.	0.049048	0.85682	D	0.000000	T	0.61211	0.2329	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0	D;D;P;D;D;D	0.87578	0.978;0.97;0.731;0.966;0.939;0.998	T	0.59637	-0.7417	10	0.66056	D	0.02	-7.6269	20.3932	0.98965	0.0:1.0:0.0:0.0	.	136;136;136;136;136;162	Q9GZY8-4;Q9GZY8-3;Q9GZY8-5;C9JHF5;Q9GZY8-2;Q9GZY8	.;.;.;.;.;MFF_HUMAN	C	136;162;136;7;7;136;136;136;136;7;7;136;162;19	ENSP00000302037:R162C;ENSP00000375912:R162C	ENSP00000304898:R136C	R	+	1	0	MFF	227913306	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.430000	0.73391	2.824000	0.97209	0.655000	0.94253	CGC		0.398	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194		T	228205062	C	T	228205062	3	4	61	1	0	0	0	0	1	0	0	0	9549	884	31	1	498	1	MFF	2	228205062	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57966	228205062	14994311	2162	10147										
WDR69	164781	broad.mit.edu	37	chr2	228750096	228750096	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaatatgaaaaacatggaGaattaaagactaagtccata	8	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228750096G>T	ENST00000309931.2	+	2	153	c.70G>T	c.(70-72)Gaa>Taa	p.E24*	DAW1_ENST00000373666.2_Nonsense_Mutation_p.E24*|SNORA25_ENST00000607153.1_RNA|DAW1_ENST00000545118.1_Nonsense_Mutation_p.E9*	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	24						cilium (GO:0005929)		p.E24*(1)									AAAACATGGAGAATTAAAGAC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											108	115	113					2																	228750096		2203	4300	6503	228458340	SO:0001587	stop_gained	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.70G>T	2.37:g.228750096G>T	ENSP00000311899:p.Glu24*		228458340	Q6ZRY1|Q8N776	Nonsense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.045894	0.75846	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	.	.	.	5.52	3.72	0.42706	.	0.741162	0.12710	N	0.445635	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	9.2755	0.37696	0.0812:0.1535:0.7654:0.0	.	.	.	.	X	24;24;9;9	.	ENSP00000311899:E24X	E	+	1	0	WDR69	228458340	1.000000	0.71417	0.551000	0.28230	0.473000	0.32948	2.362000	0.44169	0.679000	0.31345	0.655000	0.94253	GAA		0.348	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		T	228750096	G	T	228750096	4	4	61	1	0	0	0	0	0	1	0	0	17359	943	33	2	76	2	WDR69	2	228750096	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	545034	228750096	14449277	2163	10148										
WDR69	164781	broad.mit.edu	37	chr2	228754634	228754634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctctactcacagcttcacGaacagagcaagtcaaacttt	5	13	4	1	rs549809115		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228754634G>A	ENST00000309931.2	+	3	259	c.176G>A	c.(175-177)cGa>cAa	p.R59Q	DAW1_ENST00000373666.2_Missense_Mutation_p.R59Q|SNORA25_ENST00000607153.1_RNA|DAW1_ENST00000472604.1_3'UTR|DAW1_ENST00000545118.1_Missense_Mutation_p.R44Q	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	59						cilium (GO:0005929)		p.R59Q(1)									ACAGCTTCACGAACAGAGCAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											90	87	88					2																	228754634		2203	4300	6503	228462878	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.176G>A	2.37:g.228754634G>A	ENSP00000311899:p.Arg59Gln		228462878	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.528176	0.44969	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	T;T;T;T	0.52057	0.76;0.7;0.81;0.68	5.45	3.55	0.40652	.	0.535392	0.18630	N	0.135603	T	0.41190	0.1148	M	0.79475	2.455	0.09310	N	1	P	0.34934	0.476	B	0.19946	0.027	T	0.28713	-1.0035	10	0.23891	T	0.37	.	9.5675	0.39407	0.1811:0.0:0.8189:0.0	.	59	Q8N136	WDR69_HUMAN	Q	59;59;44;44	ENSP00000362770:R59Q;ENSP00000311899:R59Q;ENSP00000394853:R44Q;ENSP00000437887:R44Q	ENSP00000311899:R59Q	R	+	2	0	WDR69	228462878	0.769000	0.28531	0.004000	0.12327	0.994000	0.84299	4.413000	0.59795	1.344000	0.45657	0.650000	0.86243	CGA		0.383	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		A	228754634	G	A	228754634	3	1	61	1	0	0	0	0	1	0	0	0	17359	1058	37	1	186	1	WDR69	2	228754634	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4538	228754634	14444739	2164	10149										
WDR69	164781	broad.mit.edu	37	chr2	228758522	228758522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgttagctttatcacagGaagctatgatcggacgtgca	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228758522G>T	ENST00000309931.2	+	5	412	c.329G>T	c.(328-330)gGa>gTa	p.G110V	DAW1_ENST00000373666.2_Missense_Mutation_p.G110V|DAW1_ENST00000472604.1_3'UTR|DAW1_ENST00000545118.1_Missense_Mutation_p.G95V	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	110						cilium (GO:0005929)		p.G110V(1)									TTTATCACAGGAAGCTATGAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	93	96					2																	228758522		2203	4300	6503	228466766	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.329G>T	2.37:g.228758522G>T	ENSP00000311899:p.Gly110Val		228466766	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504512	0.85176	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000545118	T;T;T	0.71341	-0.56;-0.56;-0.56	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83115	0.5184	M	0.65320	2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83890	0.0284	10	0.72032	D	0.01	.	18.4891	0.90841	0.0:0.0:1.0:0.0	.	110	Q8N136	WDR69_HUMAN	V	110;110;95	ENSP00000362770:G110V;ENSP00000311899:G110V;ENSP00000437887:G95V	ENSP00000311899:G110V	G	+	2	0	WDR69	228466766	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.659000	0.91116	2.692000	0.91855	0.650000	0.86243	GGA		0.448	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		T	228758522	G	T	228758522	3	4	61	1	0	0	0	0	1	0	0	0	17359	1174	41	2	347	2	WDR69	2	228758522	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3888	228758522	14440851	2165	10150										
SPHKAP	80309	broad.mit.edu	37	chr2	228846460	228846460	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccaagagccagtcaaaGagactcagtctcccatcctt	7	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228846460G>T	ENST00000392056.3	-	12	5122	c.5076C>A	c.(5074-5076)ctC>ctA	p.L1692L	SPHKAP_ENST00000344657.5_Silent_p.L1663L	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1692						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.L1711L(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		GCCAGTCAAAGAGACTCAGTC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	2											105	93	97					2																	228846460		2203	4300	6503	228554704	SO:0001819	synonymous_variant	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.5076C>A	2.37:g.228846460G>T			228554704	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																				0.448	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228846460	G	T	228846460	2	4	61	1	0	0	0	0	0	0	0	1	15087	929	33	2		2	SPHKAP	2	228846460	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87938	228846460	14352913	2166	10151										
SPHKAP	80309	broad.mit.edu	37	chr2	228881191	228881191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggatgtttttgtcattcGaatgcccttctgcttcctct	8	11	3	0	rs368612893		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228881191G>A	ENST00000392056.3	-	7	4425	c.4379C>T	c.(4378-4380)tCg>tTg	p.S1460L	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S1460L	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1460						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.S1460L(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		TTTGTCATTCGAATGCCCTTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	123	124					2																	228881191		2203	4300	6503	228589435	SO:0001583	missense	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4379C>T	2.37:g.228881191G>A	ENSP00000375909:p.Ser1460Leu		228589435	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	9.628	1.135662	0.21123	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11063	2.82;2.81	5.43	-3.31	0.04988	.	2.794460	0.00929	N	0.002686	T	0.02267	0.0070	N	0.00419	-1.52	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.32929	-0.9888	10	0.14252	T	0.57	.	0.6371	0.00804	0.3277:0.1193:0.2806:0.2724	.	491;1460;1460	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	L	1460	ENSP00000375909:S1460L;ENSP00000339886:S1460L	ENSP00000339886:S1460L	S	-	2	0	SPHKAP	228589435	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.443000	0.21644	-0.522000	0.06417	-0.290000	0.09829	TCG		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228881191	G	A	228881191	3	1	61	1	0	0	0	0	1	0	0	0	15087	1059	37	1	747	1	SPHKAP	2	228881191	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34731	228881191	14318182	2167	10152										
SPHKAP	80309	broad.mit.edu	37	chr2	228882000	228882000	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctgtagaactcctcagtGatgctctctgtgctggactg	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228882000G>T	ENST00000392056.3	-	7	3616	c.3570C>A	c.(3568-3570)atC>atA	p.I1190I	SPHKAP_ENST00000344657.5_Silent_p.I1190I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1190						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.I1190I(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		ACTCCTCAGTGATGCTCTCTG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	2											99	97	98					2																	228882000		2203	4300	6503	228590244	SO:0001819	synonymous_variant	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3570C>A	2.37:g.228882000G>T			228590244	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																				0.567	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228882000	G	T	228882000	2	4	61	1	0	0	0	0	0	0	0	1	15087	1280	45	2		2	SPHKAP	2	228882000	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	809	228882000	14317373	2168	10153										
SPHKAP	80309	broad.mit.edu	37	chr2	228883584	228883584	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgccagttcattcctgacGacattttctgagcacagggt	10	10	2	2	rs61752224		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228883584G>A	ENST00000392056.3	-	7	2032	c.1986C>T	c.(1984-1986)gtC>gtT	p.V662V	SPHKAP_ENST00000344657.5_Silent_p.V662V	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	662						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.V662V(3)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		CATTCCTGACGACATTTTCTG	0.443																																																3	Substitution - coding silent(3)	prostate(2)|large_intestine(1)	2											186	170	176					2																	228883584		2203	4300	6503	228591828	SO:0001819	synonymous_variant	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.1986C>T	2.37:g.228883584G>A			228591828	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																				0.443	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228883584	G	A	228883584	2	1	61	1	0	0	0	0	0	0	0	1	15087	1045	37	1		1	SPHKAP	2	228883584	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1584	228883584	14315789	2169	10154										
SPHKAP	80309	broad.mit.edu	37	chr2	228886494	228886494	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggtgagaaagtcttcctcGattgaagataaggaacagtt	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228886494G>A	ENST00000392056.3	-	6	676	c.630C>T	c.(628-630)atC>atT	p.I210I	SPHKAP_ENST00000344657.5_Silent_p.I210I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	210						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.I210I(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		AGTCTTCCTCGATTGAAGATA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	2											132	125	128					2																	228886494		2203	4300	6503	228594738	SO:0001819	synonymous_variant	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.630C>T	2.37:g.228886494G>A			228594738	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																				0.468	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228886494	G	A	228886494	2	1	61	1	0	0	0	0	0	0	0	1	15087	1048	37	1		1	SPHKAP	2	228886494	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2910	228886494	14312879	2170	10155										
SPHKAP	80309	broad.mit.edu	37	chr2	228890124	228890124	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttacctgtgaaacttcaaAatctgcctggagatttccag	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228890124A>C	ENST00000392056.3	-	5	473	c.427T>G	c.(427-429)Ttt>Gtt	p.F143V	SPHKAP_ENST00000344657.5_Missense_Mutation_p.F143V	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	143						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.F143V(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		GAAACTTCAAAATCTGCCTGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											102	100	100					2																	228890124		2203	4300	6503	228598368	SO:0001583	missense	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.427T>G	2.37:g.228890124A>C	ENSP00000375909:p.Phe143Val		228598368	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.536682	0.45176	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11495	2.77;2.77	5.93	3.59	0.41128	.	0.600564	0.19177	N	0.120782	T	0.07413	0.0187	N	0.19112	0.55	0.30488	N	0.771705	P;P	0.44090	0.483;0.826	B;P	0.45712	0.122;0.491	T	0.10683	-1.0619	10	0.18276	T	0.48	.	4.6096	0.12395	0.7086:0.0:0.1493:0.1421	.	143;143	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	V	143	ENSP00000375909:F143V;ENSP00000339886:F143V	ENSP00000339886:F143V	F	-	1	0	SPHKAP	228598368	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.752000	0.38349	1.074000	0.40909	0.533000	0.62120	TTT		0.378	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228890124	A	C	228890124	3	2	61	1	0	0	0	0	1	0	0	0	15087	14	1	4	4707	4	SPHKAP	2	228890124	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3630	228890124	14309249	2171	10156										
SPHKAP	80309	broad.mit.edu	37	chr2	228973649	228973649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagcaggctattgctgcGaagaacctggaggaacccag	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:228973649G>A	ENST00000392056.3	-	3	191	c.145C>T	c.(145-147)Cgc>Tgc	p.R49C	SPHKAP_ENST00000344657.5_Missense_Mutation_p.R49C	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	49						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.R49C(2)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		CTATTGCTGCGAAGAACCTGG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	2											58	61	60					2																	228973649		2203	4300	6503	228681893	SO:0001583	missense	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.145C>T	2.37:g.228973649G>A	ENSP00000375909:p.Arg49Cys		228681893	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.233443	0.22626	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.38077	1.16;1.16	5.55	0.466	0.16716	.	0.259855	0.38217	N	0.001764	T	0.14787	0.0357	N	0.04508	-0.205	0.42338	D	0.992323	B;B	0.15719	0.014;0.008	B;B	0.08055	0.003;0.003	T	0.05115	-1.0905	10	0.44086	T	0.13	-2.3443	7.349	0.26680	0.4683:0.0:0.5317:0.0	.	49;49	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	C	49	ENSP00000375909:R49C;ENSP00000339886:R49C	ENSP00000339886:R49C	R	-	1	0	SPHKAP	228681893	0.997000	0.39634	0.989000	0.46669	0.748000	0.42578	0.689000	0.25437	0.170000	0.19704	-0.150000	0.13652	CGC		0.413	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228973649	G	A	228973649	3	1	61	1	0	0	0	0	1	0	0	0	15087	1058	37	1	4997	1	SPHKAP	2	228973649	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83525	228973649	14225724	2172	10157										
DNER	92737	broad.mit.edu	37	chr2	230231704	230231704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattcaatgcggctgatgcGgcaaatccccacgatcagga	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:230231704G>A	ENST00000341772.4	-	12	2121	c.1987C>T	c.(1987-1989)Cgc>Tgc	p.R663C		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	663					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.R663C(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CGGCTGATGCGGCAAATCCCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	51	54					2																	230231704		2203	4300	6503	229939948	SO:0001583	missense	92737			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1987C>T	2.37:g.230231704G>A	ENSP00000345229:p.Arg663Cys		229939948	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603660	0.87157	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.86432	-2.12	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.88709	0.6510	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.88677	0.3199	10	0.48119	T	0.1	.	14.8894	0.70597	0.0:0.0:0.8566:0.1434	.	663	Q8NFT8	DNER_HUMAN	C	663;381	ENSP00000345229:R663C	ENSP00000345229:R663C	R	-	1	0	DNER	229939948	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.386000	0.79775	2.760000	0.94817	0.551000	0.68910	CGC		0.547	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		A	230231704	G	A	230231704	3	1	61	1	0	0	0	0	1	0	0	0	4678	1116	39	1	234	1	DNER	2	230231704	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1258055	230231704	12967669	2173	10158										
TRIP12	9320	broad.mit.edu	37	chr2	230672555	230672555	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaactgcaaaaatgccttCttttggtaaacatggcataa	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:230672555C>A	ENST00000283943.5	-	16	2399	c.2221G>T	c.(2221-2223)Gaa>Taa	p.E741*	TRIP12_ENST00000389045.3_Nonsense_Mutation_p.E444*|TRIP12_ENST00000389044.4_Nonsense_Mutation_p.E789*|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	741					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.E741*(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AAAATGCCTTCTTTTGGTAAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											114	94	101					2																	230672555		2203	4300	6503	230380799	SO:0001587	stop_gained	9320			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2221G>T	2.37:g.230672555C>A	ENSP00000283943:p.Glu741*		230380799	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Nonsense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	39	7.879227	0.98539	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1761	0.93603	0.0:1.0:0.0:0.0	.	.	.	.	X	741;444;789	.	ENSP00000283943:E741X	E	-	1	0	TRIP12	230380799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.643000	0.83403	2.602000	0.87976	0.467000	0.42956	GAA		0.373	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230672555	C	A	230672555	4	1	61	1	0	0	0	0	0	1	0	0	16596	922	32	2	3861	2	TRIP12	2	230672555	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	440851	230672555	12526818	2174	10159										
TRIP12	9320	broad.mit.edu	37	chr2	230679861	230679861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactacaacagcagaagatCgaggaagtgcttccatcatg	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:230679861C>T	ENST00000283943.5	-	10	1719	c.1541G>A	c.(1540-1542)cGa>cAa	p.R514Q	TRIP12_ENST00000389045.3_Missense_Mutation_p.R217Q|TRIP12_ENST00000389044.4_Missense_Mutation_p.R562Q|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	514					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.R514Q(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AGCAGAAGATCGAGGAAGTGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											154	159	157					2																	230679861		2203	4300	6503	230388105	SO:0001583	missense	9320			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1541G>A	2.37:g.230679861C>T	ENSP00000283943:p.Arg514Gln		230388105	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	31	5.097025	0.94197	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.33865	1.39;1.39;1.39	5.66	5.66	0.87406	Armadillo-like helical (1);Armadillo-type fold (1);	0.053611	0.64402	D	0.000001	T	0.58438	0.2122	M	0.61703	1.905	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;D;D	0.64042	0.921;0.921;0.921;0.921	T	0.58624	-0.7604	10	0.66056	D	0.02	.	19.8049	0.96527	0.0:1.0:0.0:0.0	.	520;217;562;514	D4HL82;Q14CF1;Q14CA3;Q14669	.;.;.;TRIPC_HUMAN	Q	514;217;562	ENSP00000283943:R514Q;ENSP00000373697:R217Q;ENSP00000373696:R562Q	ENSP00000283943:R514Q	R	-	2	0	TRIP12	230388105	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.364000	0.79526	2.672000	0.90937	0.558000	0.71614	CGA		0.373	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230679861	C	T	230679861	3	4	61	1	0	0	0	0	1	0	0	0	16596	884	31	1	4565	1	TRIP12	2	230679861	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7306	230679861	12519512	2175	10160										
SLC16A14	151473	broad.mit.edu	37	chr2	230910609	230910609	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaccctatcagcgcacaGatgaccgccaggccagcgta	10	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:230910609G>T	ENST00000295190.4	-	4	1691	c.1233C>A	c.(1231-1233)atC>atA	p.I411I		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	411						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.I411I(1)		NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		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)		TCAGCGCACAGATGACCGCCA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	2											92	81	85					2																	230910609		2203	4300	6503	230618853	SO:0001819	synonymous_variant	151473			BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.1233C>A	2.37:g.230910609G>T			230618853	A8KA08|Q53R92|Q96NI7	Silent	SNP	ENST00000295190.4	37	CCDS2473.1																																																																																				0.498	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		T	230910609	G	T	230910609	2	4	61	1	0	0	0	0	0	0	0	1	14444	932	33	2		2	SLC16A14	2	230910609	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	230748	230910609	12288764	2176	10161										
SLC16A14	151473	broad.mit.edu	37	chr2	230910902	230910902	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaaggctacaaacattcGatttgtaaatagagaggctg	9	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:230910902G>A	ENST00000295190.4	-	4	1398	c.940C>T	c.(940-942)Cga>Tga	p.R314*		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	314						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.R314*(1)		NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		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)		ACAAACATTCGATTTGTAAAT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											51	51	51					2																	230910902		2203	4300	6503	230619146	SO:0001587	stop_gained	151473			BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.940C>T	2.37:g.230910902G>A	ENSP00000295190:p.Arg314*		230619146	A8KA08|Q53R92|Q96NI7	Nonsense_Mutation	SNP	ENST00000295190.4	37	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.919851	0.73098	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034	.	.	.	4.77	2.85	0.33270	.	0.108145	0.40144	N	0.001161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4538	0.55691	0.0:0.0:0.4596:0.5404	.	.	.	.	X	314	.	ENSP00000295190:R314X	R	-	1	2	SLC16A14	230619146	0.658000	0.27402	0.012000	0.15200	0.399000	0.30720	1.944000	0.40263	1.198000	0.43158	0.511000	0.50034	CGA		0.453	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		A	230910902	G	A	230910902	4	1	61	1	0	0	0	0	0	1	0	0	14444	1066	37	1	600	1	SLC16A14	2	230910902	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293	230910902	12288471	2177	10162										
SP140	11262	broad.mit.edu	37	chr2	231101810	231101810	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttaggatggtcgcagaGatccagaacgtagagggtca	13	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231101810G>T	ENST00000392045.3	+	2	186	c.72G>T	c.(70-72)gaG>gaT	p.E24D	SP140_ENST00000544128.1_3'UTR|SP140_ENST00000373645.3_Missense_Mutation_p.E24D|SP140_ENST00000486687.2_Missense_Mutation_p.E24D|SP140_ENST00000417495.3_Missense_Mutation_p.E24D|SP140_ENST00000343805.6_Missense_Mutation_p.E24D|SP140_ENST00000420434.3_Missense_Mutation_p.E24D|SP140_ENST00000350136.5_Missense_Mutation_p.E4D	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	24	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E24D(2)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGGTCGCAGAGATCCAGAACG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	2											68	72	71					2																	231101810		2203	4300	6503	230810054	SO:0001583	missense	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.72G>T	2.37:g.231101810G>T	ENSP00000375899:p.Glu24Asp		230810054	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	G	2.861	-0.236136	0.05944	.	.	ENSG00000079263	ENST00000537563;ENST00000486687;ENST00000392044;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434;ENST00000373645	T;T;T;T;T;T	0.59364	0.49;0.75;0.56;0.27;0.49;0.78	3.67	-2.91	0.05631	Sp100 (1);	.	.	.	.	T	0.34687	0.0906	L	0.29908	0.895	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.08055	0.001;0.001;0.003;0.001;0.001;0.0	T	0.15925	-1.0420	9	0.22109	T	0.4	-2.1523	1.8249	0.03119	0.2575:0.2552:0.3672:0.1201	.	24;24;24;24;24;24	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75;Q6NSG4	.;.;.;LY10_HUMAN;.;.	D	24;24;24;4;24;24;24;24;24	ENSP00000440107:E24D;ENSP00000345846:E4D;ENSP00000375899:E24D;ENSP00000342096:E24D;ENSP00000398210:E24D;ENSP00000362749:E24D	ENSP00000342096:E24D	E	+	3	2	SP140	230810054	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.599000	0.02085	-1.136000	0.02892	-2.943000	0.00086	GAG		0.458	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231101810	G	T	231101810	3	4	61	1	0	0	0	0	1	0	0	0	14999	933	33	2	78	2	SP140	2	231101810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190908	231101810	12097563	2178	10163										
SP140	11262	broad.mit.edu	37	chr2	231101921	231101921	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcaataacaaggccattTcctttccttatgggcctccg	8	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231101921T>C	ENST00000392045.3	+	2	297	c.183T>C	c.(181-183)ttT>ttC	p.F61F	SP140_ENST00000544128.1_3'UTR|SP140_ENST00000373645.3_Silent_p.F61F|SP140_ENST00000486687.2_Silent_p.F61F|SP140_ENST00000417495.3_Silent_p.F61F|SP140_ENST00000343805.6_Silent_p.F61F|SP140_ENST00000420434.3_Silent_p.F61F|SP140_ENST00000350136.5_Silent_p.F41F	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	61	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.F61F(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CAAGGCCATTTCCTTTCCTTA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	2											90	89	89					2																	231101921		2203	4300	6503	230810165	SO:0001819	synonymous_variant	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.183T>C	2.37:g.231101921T>C			230810165	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	37	CCDS42831.1																																																																																				0.458	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		C	231101921	T	C	231101921	2	2	61	1	0	0	0	0	0	0	0	1	14999	1780	62	4		4	SP140	2	231101921	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	111	231101921	12097452	2179	10164										
SP140	11262	broad.mit.edu	37	chr2	231113604	231113604	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgtttatctgcagagacCtttgatctaaaaactcccca	5	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231113604C>A	ENST00000392045.3	+	9	1011	c.897C>A	c.(895-897)acC>acA	p.T299T	SP140_ENST00000486687.2_Silent_p.T223T|SP140_ENST00000417495.3_Silent_p.T246T|SP140_ENST00000343805.6_Silent_p.T273T|SP140_ENST00000420434.3_Silent_p.T299T|SP140_ENST00000350136.5_Silent_p.T229T	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	299					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T299T(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTGCAGAGACCTTTGATCTAA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	2											116	104	108					2																	231113604		1857	4091	5948	230821848	SO:0001819	synonymous_variant	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.897C>A	2.37:g.231113604C>A			230821848	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	37	CCDS42831.1																																																																																				0.448	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		A	231113604	C	A	231113604	2	1	61	1	0	0	0	0	0	0	0	1	14999	668	24	2		2	SP140	2	231113604	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11683	231113604	12085769	2180	10165										
SP140	11262	broad.mit.edu	37	chr2	231174695	231174695	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggggagctgttctgttgCgacacttgttcaagagtctt	14	7	3	1	rs186449912	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231174695C>T	ENST00000392045.3	+	23	2229	c.2115C>T	c.(2113-2115)tgC>tgT	p.C705C	SP140_ENST00000486687.2_Silent_p.C629C|SP140_ENST00000417495.3_Silent_p.C591C|SP140_ENST00000343805.6_Silent_p.C645C|SP140_ENST00000420434.3_Silent_p.C678C|SP140_ENST00000350136.5_Silent_p.C574C	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	705					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.C705C(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGTTCTGTTGCGACACTTGTT	0.512													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		21260	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C		3,4367	4.2+/-10.8	0,3,2182	179	192	188		2115	-4.4	0	2		188	4,8584	3.7+/-12.6	0,4,4290	no	coding-synonymous	SP140	NM_007237.4		0,7,6472	TT,TC,CC		0.0466,0.0686,0.054		705/868	231174695	7,12951	2185	4294	6479	230882939	SO:0001819	synonymous_variant	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.2115C>T	2.37:g.231174695C>T			230882939	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	37	CCDS42831.1																																																																																				0.512	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231174695	C	T	231174695	2	4	61	1	0	0	0	0	0	0	0	1	14999	776	27	1		1	SP140	2	231174695	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61091	231174695	12024678	2181	10166										
SP140L	93349	broad.mit.edu	37	chr2	231193491	231193491	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggctgaacggaggtgttTcacaagtagcaaatgagatg	16	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231193491T>G	ENST00000415673.2	+	2	138	c.52T>G	c.(52-54)Tca>Gca	p.S18A	SP140L_ENST00000396563.4_Missense_Mutation_p.S18A|SP140_ENST00000486687.2_Intron|SP140L_ENST00000444636.1_Missense_Mutation_p.S18A|SP140L_ENST00000243810.6_Missense_Mutation_p.S18A	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	18						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S18A(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						cggaggtgtttcacaagtagc	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2											101	108	105					2																	231193491		2201	4300	6501	230901735	SO:0001583	missense	93349			BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.52T>G	2.37:g.231193491T>G	ENSP00000397911:p.Ser18Ala		230901735	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	T	6.732	0.503812	0.12822	.	.	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	D;T;D;D	0.84730	-1.73;-1.35;-1.73;-1.89	2.06	-1.53	0.08611	.	.	.	.	.	T	0.74816	0.3766	N	0.08118	0	0.09310	N	1	P	0.41597	0.756	P	0.57283	0.817	T	0.64664	-0.6354	9	0.02654	T	1	.	5.4675	0.16652	0.0:0.4418:0.0:0.5582	.	18	Q9H930-4	.	A	18	ENSP00000395195:S18A;ENSP00000397911:S18A;ENSP00000243810:S18A;ENSP00000379811:S18A	ENSP00000243810:S18A	S	+	1	0	SP140L	230901735	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.220000	0.02971	-0.426000	0.07360	0.418000	0.28097	TCA		0.363	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		G	231193491	T	G	231193491	3	3	61	1	0	0	0	0	1	0	0	0	15000	1783	62	4	58	4	SP140L	2	231193491	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18796	231193491	12005882	2182	10167										
SP140L	93349	broad.mit.edu	37	chr2	231223814	231223814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacatgcaggaataccccGatttaattcacatttataaa	4	9	2	0	rs367871968		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231223814G>A	ENST00000415673.2	+	4	492	c.406G>A	c.(406-408)Gat>Aat	p.D136N	SP140L_ENST00000396563.4_Missense_Mutation_p.D136N|SP140L_ENST00000458341.1_Missense_Mutation_p.D49N|SP140L_ENST00000444636.1_Missense_Mutation_p.D136N|SP140L_ENST00000243810.6_Missense_Mutation_p.D136N	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	136	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D136N(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GGAATACCCCGATTTAATTCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	ASN/ASP	1,4403	2.1+/-5.4	0,1,2201	107	113	111		406	3.7	0	2		111	0,8600		0,0,4300	no	missense	SP140L	NM_138402.4	23	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	136/581	231223814	1,13003	2202	4300	6502	230932058	SO:0001583	missense	93349			BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.406G>A	2.37:g.231223814G>A	ENSP00000397911:p.Asp136Asn		230932058	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216394	0.58452	2.27E-4	0.0	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42	3.71	3.71	0.42584	.	.	.	.	.	D	0.95465	0.8527	L	0.56124	1.755	0.09310	N	1	P;D	0.89917	0.945;1.0	P;D	0.64144	0.637;0.922	D	0.88993	0.3416	8	.	.	.	.	11.6901	0.51510	0.0:0.0:1.0:0.0	.	49;136	Q9H930-3;Q9H930-4	.;.	N	136;136;136;136;49	ENSP00000395195:D136N;ENSP00000397911:D136N;ENSP00000243810:D136N;ENSP00000379811:D136N;ENSP00000395223:D49N	.	D	+	1	0	SP140L	230932058	0.007000	0.16637	0.007000	0.13788	0.087000	0.18053	0.337000	0.19841	1.998000	0.58463	0.561000	0.74099	GAT		0.363	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		A	231223814	G	A	231223814	3	1	61	1	0	0	0	0	1	0	0	0	15000	1058	37	1	420	1	SP140L	2	231223814	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30323	231223814	11975559	2183	10168										
CAB39	51719	broad.mit.edu	37	chr2	231655640	231655640	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaaagaaattctgtatggCacaaatgaaaaagagcctca	8	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231655640C>T	ENST00000258418.5	+	3	597	c.168C>T	c.(166-168)ggC>ggT	p.G56G	CAB39_ENST00000409788.3_Silent_p.G56G|CAB39_ENST00000484398.1_3'UTR|CAB39_ENST00000410084.3_Silent_p.G56G	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	56					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)	p.G56G(1)		central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		TTCTGTATGGCACAAATGAAA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	2											67	74	72					2																	231655640		2203	4300	6503	231363884	SO:0001819	synonymous_variant	51719			AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.168C>T	2.37:g.231655640C>T			231363884	A8K8L7	Silent	SNP	ENST00000258418.5	37	CCDS2478.1																																																																																				0.403	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289		T	231655640	C	T	231655640	2	4	61	1	0	0	0	0	0	0	0	1	2531	697	25	3		3	CAB39	2	231655640	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	431826	231655640	11543733	2184	10169										
PSMD1	5707	broad.mit.edu	37	chr2	231927233	231927233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagagaggttttatacGaagatgaaggtttccggagt	12	5	1	3	rs534841979		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231927233G>A	ENST00000308696.6	+	4	310	c.148G>A	c.(148-150)Gaa>Aaa	p.E50K	PSMD1_ENST00000373635.4_Missense_Mutation_p.E50K|PSMD1_ENST00000409643.1_Missense_Mutation_p.E50K	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	50					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.E50K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GGTTTTATACGAAGATGAAGG	0.403													G|||	1	0.000199681	0	0	5008	,	,		16102	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	2											81	86	85					2																	231927233		2203	4299	6502	231635477	SO:0001583	missense	5707			D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.148G>A	2.37:g.231927233G>A	ENSP00000309474:p.Glu50Lys		231635477	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	37	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	G	36	5.778912	0.96929	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000440838;ENST00000409643	T;T;T	0.31510	1.49;1.49;1.49	6.17	6.17	0.99709	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64724	0.2624	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.70487	0.852;0.969	T	0.66172	-0.5990	10	0.52906	T	0.07	-0.7263	20.8794	0.99867	0.0:0.0:1.0:0.0	.	50;50	Q99460;Q99460-2	PSMD1_HUMAN;.	K	50	ENSP00000309474:E50K;ENSP00000362738:E50K;ENSP00000386932:E50K	ENSP00000309474:E50K	E	+	1	0	PSMD1	231635477	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GAA		0.403	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			A	231927233	G	A	231927233	3	1	61	1	0	0	0	0	1	0	0	0	12726	1059	37	1	162	1	PSMD1	2	231927233	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	271593	231927233	11272140	2185	10170										
PSMD1	5707	broad.mit.edu	37	chr2	231934808	231934808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgcagaataaacagtttCggaataaagtactaagagtt	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231934808C>T	ENST00000308696.6	+	6	742	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	PSMD1_ENST00000373635.4_Missense_Mutation_p.R194W|PSMD1_ENST00000409643.1_Missense_Mutation_p.R194W	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	194					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.R194W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	TAAACAGTTTCGGAATAAAGT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	2											79	80	80					2																	231934808		2203	4297	6500	231643052	SO:0001583	missense	5707			D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.580C>T	2.37:g.231934808C>T	ENSP00000309474:p.Arg194Trp		231643052	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	37	CCDS2482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.8|23.8	4.462808|4.462808	0.84425|0.84425	.|.	.|.	ENSG00000173692|ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000440838;ENST00000409643|ENST00000444007	T;T;T|.	0.55588|.	0.51;0.51;0.51|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86527|0.86527	0.5954|0.5954	H|H	0.94964|0.94964	3.605|3.605	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	D|D	0.89522|0.89522	0.3779|0.3779	10|5	0.87932|.	D|.	0|.	-18.1046|-18.1046	14.9267|14.9267	0.70884|0.70884	0.143:0.857:0.0:0.0|0.143:0.857:0.0:0.0	.|.	194;194|.	Q99460;Q99460-2|.	PSMD1_HUMAN;.|.	W|L	194;194;200;194|93	ENSP00000309474:R194W;ENSP00000362738:R194W;ENSP00000386932:R194W|.	ENSP00000309474:R194W|.	R|S	+|+	1|2	2|0	PSMD1|PSMD1	231643052|231643052	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.676000|4.676000	0.61627|0.61627	2.779000|2.779000	0.95612|0.95612	0.591000|0.591000	0.81541|0.81541	CGG|TCG		0.313	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231934808	C	T	231934808	3	4	61	1	0	0	0	0	1	0	0	0	12726	875	31	1	602	1	PSMD1	2	231934808	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7575	231934808	11264565	2186	10171										
PSMD1	5707	broad.mit.edu	37	chr2	231944878	231944878	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaaaaagaagcattacaGttaatggcaacataccttcc	6	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:231944878G>T	ENST00000308696.6	+	12	1425	c.1263G>T	c.(1261-1263)caG>caT	p.Q421H	PSMD1_ENST00000373635.4_Missense_Mutation_p.Q421H|PSMD1_ENST00000409643.1_Missense_Mutation_p.Q421H	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	421					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.Q421H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	AAGCATTACAGTTAATGGCAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											121	108	112					2																	231944878		2203	4300	6503	231653122	SO:0001583	missense	5707			D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.1263G>T	2.37:g.231944878G>T	ENSP00000309474:p.Gln421His		231653122	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	37	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.445058	0.43429	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643	T;T;T	0.33865	1.39;1.39;1.39	6.07	2.3	0.28687	Armadillo-type fold (1);	0.048379	0.85682	D	0.000000	T	0.16811	0.0404	N	0.03608	-0.345	0.80722	D	1	B;B	0.19817	0.002;0.039	B;B	0.17979	0.02;0.016	T	0.06356	-1.0831	10	0.54805	T	0.06	-12.1575	10.9933	0.47561	0.2482:0.0:0.7518:0.0	.	421;421	Q99460;Q99460-2	PSMD1_HUMAN;.	H	421	ENSP00000309474:Q421H;ENSP00000362738:Q421H;ENSP00000386932:Q421H	ENSP00000309474:Q421H	Q	+	3	2	PSMD1	231653122	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.238000	0.43070	0.907000	0.36646	-0.140000	0.14226	CAG		0.383	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231944878	G	T	231944878	3	4	61	1	0	0	0	0	1	0	0	0	12726	1020	36	2	1309	2	PSMD1	2	231944878	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10070	231944878	11254495	2187	10172										
ARMC9	80210	broad.mit.edu	37	chr2	232070964	232070964	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcaatatgggggacattCtggctcatgaatctgaatta	10	6	4	2	rs376958829	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232070964C>A	ENST00000349938.4	+	2	207	c.13C>A	c.(13-15)Ctg>Atg	p.L5M	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	5						extracellular vesicular exosome (GO:0070062)		p.L5M(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		GGGGGACATTCTGGCTCATGA	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	2											119	117	118					2																	232070964		2203	4300	6503	231779208	SO:0001583	missense	80210			BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.13C>A	2.37:g.232070964C>A	ENSP00000258417:p.Leu5Met		231779208	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	37	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.994842	0.54041	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000440107	T;T	0.50813	2.15;0.73	5.2	2.44	0.29823	.	0.000000	0.64402	D	0.000003	T	0.55609	0.1931	L	0.51422	1.61	0.36440	D	0.865435	D	0.76494	0.999	D	0.71656	0.974	T	0.58769	-0.7578	10	0.41790	T	0.15	-11.967	7.5057	0.27542	0.0:0.6608:0.0:0.3392	.	5	Q7Z3E5	ARMC9_HUMAN	M	5	ENSP00000258417:L5M;ENSP00000387391:L5M	ENSP00000258417:L5M	L	+	1	2	ARMC9	231779208	0.875000	0.30112	0.806000	0.32338	0.882000	0.50991	0.615000	0.24329	0.606000	0.29965	0.655000	0.94253	CTG		0.353	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		A	232070964	C	A	232070964	3	1	61	1	0	0	0	0	1	0	0	0	959	912	32	2	15	2	ARMC9	2	232070964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	126086	232070964	11128409	2188	10173										
ARMC9	80210	broad.mit.edu	37	chr2	232091492	232091492	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttttcatcccagaaggaGaatggacaaagtaacaaagg	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232091492G>T	ENST00000349938.4	+	7	797	c.603G>T	c.(601-603)gaG>gaT	p.E201D	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	201						extracellular vesicular exosome (GO:0070062)		p.E201D(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		CCCAGAAGGAGAATGGACAAA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	2											101	101	101					2																	232091492		2203	4300	6503	231799736	SO:0001583	missense	80210			BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.603G>T	2.37:g.232091492G>T	ENSP00000258417:p.Glu201Asp		231799736	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	37	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688928	0.68271	.	.	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.18502	2.21	5.86	3.13	0.36017	.	0.226336	0.45361	D	0.000364	T	0.17704	0.0425	L	0.59436	1.845	0.37790	D	0.927331	B	0.19331	0.035	B	0.25759	0.063	T	0.06232	-1.0838	10	0.30078	T	0.28	-31.676	9.9154	0.41430	0.2146:0.0:0.7854:0.0	.	201	Q7Z3E5	ARMC9_HUMAN	D	201	ENSP00000258417:E201D	ENSP00000258417:E201D	E	+	3	2	ARMC9	231799736	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	1.813000	0.38962	0.401000	0.25424	-0.142000	0.14014	GAG		0.418	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		T	232091492	G	T	232091492	3	4	61	1	0	0	0	0	1	0	0	0	959	933	33	2	625	2	ARMC9	2	232091492	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20528	232091492	11107881	2189	10174										
B3GNT7	93010	broad.mit.edu	37	chr2	232262827	232262827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccggagaagtgcaggggcGatgtctacctgctggtggtt	16	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232262827G>A	ENST00000287590.5	+	2	658	c.397G>A	c.(397-399)Gat>Aat	p.D133N	B3GNT7_ENST00000479618.1_3'UTR	NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	133					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.D133N(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		GTGCAGGGGCGATGTCTACCT	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	2											23	25	24					2																	232262827		2038	4187	6225	231971071	SO:0001583	missense	93010			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"Beta 3-glycosyltransferases"	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.397G>A	2.37:g.232262827G>A	ENSP00000287590:p.Asp133Asn		231971071	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.673598	0.29693	.	.	ENSG00000156966	ENST00000287590	T	0.37058	1.22	5.27	4.39	0.52855	.	0.337134	0.34986	N	0.003526	T	0.37892	0.1020	M	0.68952	2.095	0.40439	D	0.98002	B	0.12013	0.005	B	0.08055	0.003	T	0.21690	-1.0238	10	0.30854	T	0.27	.	15.0425	0.71803	0.0:0.1427:0.8573:0.0	.	133	Q8NFL0	B3GN7_HUMAN	N	133	ENSP00000287590:D133N	ENSP00000287590:D133N	D	+	1	0	B3GNT7	231971071	0.932000	0.31603	0.046000	0.18839	0.051000	0.14879	2.372000	0.44257	1.196000	0.43129	0.655000	0.94253	GAT		0.662	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236		A	232262827	G	A	232262827	3	1	61	1	0	0	0	0	1	0	0	0	1263	1058	37	1	403	1	B3GNT7	2	232262827	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171335	232262827	10936546	2190	10175										
B3GNT7	93010	broad.mit.edu	37	chr2	232263248	232263248	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgtcctgcagcacgctcGgcccattcgcaggaaagaca	11	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232263248G>T	ENST00000287590.5	+	2	1079	c.818G>T	c.(817-819)cGg>cTg	p.R273L		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	273					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.R273L(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		CAGCACGCTCGGCCCATTCGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2											42	45	44					2																	232263248		2046	4183	6229	231971492	SO:0001583	missense	93010			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"Beta 3-glycosyltransferases"	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.818G>T	2.37:g.232263248G>T	ENSP00000287590:p.Arg273Leu		231971492	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.020810	0.35606	.	.	ENSG00000156966	ENST00000287590	T	0.42513	0.97	5.19	3.38	0.38709	.	0.226554	0.43260	D	0.000583	T	0.35595	0.0937	L	0.43646	1.37	0.32668	N	0.517203	P	0.40602	0.723	B	0.42386	0.386	T	0.44802	-0.9304	10	0.24483	T	0.36	.	10.2746	0.43501	0.1601:0.0:0.8399:0.0	.	273	Q8NFL0	B3GN7_HUMAN	L	273	ENSP00000287590:R273L	ENSP00000287590:R273L	R	+	2	0	B3GNT7	231971492	1.000000	0.71417	0.691000	0.30163	0.993000	0.82548	3.058000	0.49939	1.187000	0.43000	0.655000	0.94253	CGG		0.602	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236		T	232263248	G	T	232263248	3	4	61	1	0	0	0	0	1	0	0	0	1263	1116	39	2	824	2	B3GNT7	2	232263248	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	421	232263248	10936125	2191	10176										
NCL	4691	broad.mit.edu	37	chr2	232323764	232323764	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttaatttcattgccaaaGactttcaaaccagtgagttc	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232323764G>T	ENST00000322723.4	-	7	1353	c.1113C>A	c.(1111-1113)gtC>gtA	p.V371V	SNORD20_ENST00000384550.1_RNA|SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	371	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.V371V(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CATTGCCAAAGACTTTCAAAC	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	2											185	158	167					2																	232323764		2203	4300	6503	232032008	SO:0001819	synonymous_variant	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1113C>A	2.37:g.232323764G>T			232032008	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																				0.388	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232323764	G	T	232323764	2	4	61	1	0	0	0	0	0	0	0	1	10257	929	33	2		2	NCL	2	232323764	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60516	232323764	10875609	2192	10177										
DIS3L2	129563	broad.mit.edu	37	chr2	232894729	232894729	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgatggggttgttgctcGtaatagagccttaaatgggg	14	4	0	2	rs372013568		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232894729G>A	ENST00000409307.1	+	4	305	c.305G>A	c.(304-306)cGt>cAt	p.R102H	DIS3L2_ENST00000273009.6_Missense_Mutation_p.R102H|DIS3L2_ENST00000360410.4_Missense_Mutation_p.R102H|DIS3L2_ENST00000325385.7_Missense_Mutation_p.R102H|DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000409401.3_Missense_Mutation_p.R102H					DIS3 like 3'-5' exoribonuclease 2									p.R102H(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		GTTGTTGCTCGTAATAGAGCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											184	177	179					2																	232894729		1848	4099	5947	232602973	SO:0001583	missense	129563			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.305G>A	2.37:g.232894729G>A	ENSP00000386799:p.Arg102His		232602973		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	G	33	5.196379	0.94960	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000360410;ENST00000409401;ENST00000441279;ENST00000431466;ENST00000409307	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.80701	0.4673	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.972;0.998	D	0.83716	0.0190	10	0.87932	D	0	-10.2827	19.4689	0.94954	0.0:0.0:1.0:0.0	.	102;102	Q8IYB7;Q8IYB7-4	DI3L2_HUMAN;.	H	102	ENSP00000273009:R102H;ENSP00000315569:R102H;ENSP00000353584:R102H;ENSP00000386594:R102H;ENSP00000390467:R102H;ENSP00000386799:R102H	ENSP00000273009:R102H	R	+	2	0	DIS3L2	232602973	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.329000	0.90017	2.604000	0.88044	0.557000	0.71058	CGT		0.383	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		A	232894729	G	A	232894729	3	1	61	1	0	0	0	0	1	0	0	0	4548	1145	40	1	319	1	DIS3L2	2	232894729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	570965	232894729	10304644	2193	10178										
DIS3L2	129563	broad.mit.edu	37	chr2	232952211	232952211	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaggtagttaaaccagaGagcaatgacaaagaaacaga	9	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:232952211G>T	ENST00000409307.1	+	5	381	c.381G>T	c.(379-381)gaG>gaT	p.E127D	DIS3L2_ENST00000273009.6_Missense_Mutation_p.E127D|DIS3L2_ENST00000360410.4_Missense_Mutation_p.E127D|DIS3L2_ENST00000325385.7_Missense_Mutation_p.E127D|DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000409401.3_Missense_Mutation_p.E127D					DIS3 like 3'-5' exoribonuclease 2									p.E127D(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TTAAACCAGAGAGCAATGACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	2											46	47	47					2																	232952211		1862	4113	5975	232660455	SO:0001583	missense	129563			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.381G>T	2.37:g.232952211G>T	ENSP00000386799:p.Glu127Asp		232660455		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559781	0.27827	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000360410;ENST00000409401;ENST00000441279;ENST00000431466;ENST00000409307	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	5.65	0.588	0.17445	.	0.234947	0.33670	N	0.004670	T	0.22742	0.0549	N	0.16233	0.39	0.25466	N	0.98788	B;B	0.10296	0.0;0.003	B;B	0.13407	0.0;0.009	T	0.06445	-1.0826	10	0.20046	T	0.44	-15.7934	3.1878	0.06607	0.1587:0.1053:0.5343:0.2016	.	127;127	Q8IYB7;Q8IYB7-4	DI3L2_HUMAN;.	D	127	ENSP00000273009:E127D;ENSP00000315569:E127D;ENSP00000353584:E127D;ENSP00000386594:E127D;ENSP00000390467:E127D;ENSP00000386799:E127D	ENSP00000273009:E127D	E	+	3	2	DIS3L2	232660455	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	0.835000	0.27531	0.726000	0.32339	0.655000	0.94253	GAG		0.393	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		T	232952211	G	T	232952211	3	4	61	1	0	0	0	0	1	0	0	0	4548	933	33	2	399	2	DIS3L2	2	232952211	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57482	232952211	10247162	2194	10179										
DIS3L2	129563	broad.mit.edu	37	chr2	233001398	233001398	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcatctgccgcattgtgGactggaaggaggactgcaat	13	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233001398G>T	ENST00000409307.1	+	7	919	c.919G>T	c.(919-921)Gac>Tac	p.D307Y	DIS3L2_ENST00000273009.6_Missense_Mutation_p.D307Y|DIS3L2_ENST00000360410.4_Missense_Mutation_p.W326C|DIS3L2_ENST00000325385.7_Missense_Mutation_p.D307Y					DIS3 like 3'-5' exoribonuclease 2									p.D307Y(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CCGCATTGTGGACTGGAAGGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2											107	102	104					2																	233001398		1946	4143	6089	232709642	SO:0001583	missense	129563			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.919G>T	2.37:g.233001398G>T	ENSP00000386799:p.Asp307Tyr		232709642		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.025233|4.025233	0.75390|0.75390	.|.	.|.	ENSG00000144535|ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307|ENST00000360410	T;T;T|T	0.31769|0.41400	1.48;1.87;1.87|1.0	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.220497|.	0.47093|.	D|.	0.000247|.	T|T	0.58075|0.58075	0.2097|0.2097	L|L	0.50333|0.50333	1.59|1.59	0.39150|0.39150	D|D	0.962211|0.962211	P|.	0.34934|.	0.476|.	B|.	0.36719|.	0.231|.	T|T	0.57980|0.57980	-0.7717|-0.7717	10|7	0.66056|0.87932	D|D	0.02|0	-26.6988|-26.6988	20.6721|20.6721	0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	307|.	Q8IYB7|.	DI3L2_HUMAN|.	Y|C	307|326	ENSP00000273009:D307Y;ENSP00000315569:D307Y;ENSP00000386799:D307Y|ENSP00000353584:W326C	ENSP00000273009:D307Y|ENSP00000353584:W326C	D|W	+|+	1|3	0|0	DIS3L2|DIS3L2	232709642|232709642	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.444000|4.444000	0.60001|0.60001	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GAC|TGG		0.498	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		T	233001398	G	T	233001398	3	4	61	1	0	0	0	0	1	0	0	0	4548	1174	41	2	945	2	DIS3L2	2	233001398	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49187	233001398	10197975	2195	10180										
ALPPL2	251	broad.mit.edu	37	chr2	233271873	233271873	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaagaacctcatcatcttCctgggtgacggtgagtgagc	12	11	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233271873C>A	ENST00000295453.3	+	2	226	c.174C>A	c.(172-174)ttC>ttA	p.F58L		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	58					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)	p.F58L(1)		breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	TCATCATCTTCCTGGGTGACG	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	2											70	82	78					2																	233271873		2203	4300	6503	232980117	SO:0001583	missense	251			J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.174C>A	2.37:g.233271873C>A	ENSP00000295453:p.Phe58Leu		232980117	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985679	0.35036	.	.	ENSG00000163286	ENST00000295453	D	0.96967	-4.19	2.19	1.3	0.21679	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.94830	0.8330	L	0.48986	1.54	0.48632	D	0.999688	P	0.36944	0.574	P	0.48368	0.575	D	0.91678	0.5356	10	0.56958	D	0.05	.	6.0361	0.19708	0.0:0.732:0.0:0.268	.	58	P10696	PPBN_HUMAN	L	58	ENSP00000295453:F58L	ENSP00000295453:F58L	F	+	3	2	ALPPL2	232980117	1.000000	0.71417	0.969000	0.41365	0.072000	0.16883	1.393000	0.34497	0.476000	0.27440	0.205000	0.17691	TTC		0.677	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		A	233271873	C	A	233271873	3	1	61	1	0	0	0	0	1	0	0	0	549	854	30	2	180	2	ALPPL2	2	233271873	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	270475	233271873	9927500	2196	10181										
ECEL1	9427	broad.mit.edu	37	chr2	233349232	233349232	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgctgcatgtagtctgtCgccagcagcaccacctcctc	8	17	1	0	rs150091758	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233349232C>T	ENST00000304546.1	-	6	1344	c.1134G>A	c.(1132-1134)gcG>gcA	p.A378A	ECEL1_ENST00000409941.1_Silent_p.A378A	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	378					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)	p.A378A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGTAGTCTGTCGCCAGCAGCA	0.587													C|||	3	0.000599042	0.0023	0	5008	,	,		20197	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C		3,4403	6.2+/-15.9	0,3,2200	139	134	136		1134	-0.4	1	2	dbSNP_134	136	0,8600		0,0,4300	no	coding-synonymous	ECEL1	NM_004826.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		378/776	233349232	3,13003	2203	4300	6503	233057476	SO:0001819	synonymous_variant	9427			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1134G>A	2.37:g.233349232C>T			233057476	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.587	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		T	233349232	C	T	233349232	2	4	61	1	0	0	0	0	0	0	0	1	4902	871	31	1		1	ECEL1	2	233349232	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77359	233349232	9850141	2197	10182										
CHRNG	1146	broad.mit.edu	37	chr2	233409186	233409186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatggctcctcgggatggtCgatcacaactggggaggagg	17	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233409186C>T	ENST00000389494.3	+	10	1166	c.1145C>T	c.(1144-1146)tCg>tTg	p.S382L	CHRNG_ENST00000389492.3_Missense_Mutation_p.S330L	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	382					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)	p.S382L(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		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;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	TCGGGATGGTCGATCACAACT	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	72	72					2																	233409186		2203	4300	6503	233117430	SO:0001583	missense	1146			X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1967	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, gamma (muscle)"	100730	"cholinergic receptor, nicotinic, gamma"	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.1145C>T	2.37:g.233409186C>T	ENSP00000374145:p.Ser382Leu		233117430	B3KWM8|Q14DU4|Q53RG2	Missense_Mutation	SNP	ENST00000389494.3	37	CCDS33400.1	.	.	.	.	.	.	.	.	.	.	C	4.833	0.154877	0.09236	.	.	ENSG00000196811	ENST00000389494;ENST00000541596;ENST00000389492	D;D	0.86230	-2.09;-2.09	5.21	4.3	0.51218	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.612141	0.16371	N	0.217324	T	0.68329	0.2989	N	0.10707	0.03	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.53697	-0.8402	10	0.09843	T	0.71	.	4.0387	0.09741	0.1954:0.6062:0.0:0.1984	.	330;382	Q14DU4;P07510	.;ACHG_HUMAN	L	382;382;330	ENSP00000374145:S382L;ENSP00000374143:S330L	ENSP00000374143:S330L	S	+	2	0	CHRNG	233117430	0.000000	0.05858	0.004000	0.12327	0.758000	0.43043	0.840000	0.27600	1.123000	0.41961	0.462000	0.41574	TCG		0.667	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199		T	233409186	C	T	233409186	3	4	61	1	0	0	0	0	1	0	0	0	3402	893	31	1	1183	1	CHRNG	2	233409186	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59954	233409186	9790187	2198	10183										
EIF4E2	9470	broad.mit.edu	37	chr2	233429029	233429029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccacagtgacttccatCtcttcaaagaaggaattaaa	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233429029C>A	ENST00000258416.3	+	4	1016	c.343C>A	c.(343-345)Ctc>Atc	p.L115I	EIF4E2_ENST00000409514.1_Missense_Mutation_p.L115I|EIF4E2_ENST00000409167.3_Missense_Mutation_p.L70I|EIF4E2_ENST00000409098.1_Missense_Mutation_p.L115I|EIF4E2_ENST00000409394.1_Missense_Mutation_p.L70I|EIF4E2_ENST00000409495.1_Missense_Mutation_p.L115I|EIF4E2_ENST00000409322.1_Missense_Mutation_p.L70I	NM_004846.2	NP_004837.1	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E family member 2	115					cytokine-mediated signaling pathway (GO:0019221)|in utero embryonic development (GO:0001701)|negative regulation of translation (GO:0017148)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)|ubiquitin protein ligase binding (GO:0031625)	p.L115I(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8		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;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGACTTCCATCTCTTCAAAGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	2											40	36	37					2																	233429029		2203	4300	6503	233137273	SO:0001583	missense	9470			AF038957	CCDS2496.1, CCDS63158.1, CCDS63159.1, CCDS74671.1	2q37.1	2008-02-05	2006-11-13	2004-10-30	ENSG00000135930	ENSG00000135930			3293	protein-coding gene	gene with protein product		605895	"eukaryotic translation initiation factor 4E-like 3"	EIF4EL3		9653160, 9582349	Standard	XM_005246975		Approved	IF4e, 4EHP	uc002vta.3	O60573	OTTHUMG00000133256	ENST00000258416.3:c.343C>A	2.37:g.233429029C>A	ENSP00000258416:p.Leu115Ile		233137273	B8ZZJ9|O75349	Missense_Mutation	SNP	ENST00000258416.3	37	CCDS2496.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974732	0.53720	.	.	ENSG00000135930	ENST00000258416;ENST00000409514;ENST00000409098;ENST00000409495;ENST00000409167;ENST00000409322;ENST00000409394;ENST00000454501	T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.65	4.78	0.61160	Translation Initiation factor eIF- 4e-like  domain (2);Eukaryotic translation initiation factor 4E (eIF-4E), conserved site (1);	0.061322	0.64402	D	0.000003	T	0.66499	0.2795	M	0.81942	2.565	0.48087	D	0.999586	B;B;B	0.25272	0.122;0.04;0.028	B;B;B	0.43990	0.261;0.438;0.259	T	0.67260	-0.5715	10	0.49607	T	0.09	-18.4492	12.3963	0.55386	0.0:0.9185:0.0:0.0815	.	70;115;115	B4E1E4;B8ZZJ9;O60573	.;.;IF4E2_HUMAN	I	115;115;115;115;70;70;70;110	ENSP00000258416:L115I;ENSP00000387336:L115I;ENSP00000386996:L115I;ENSP00000386876:L115I;ENSP00000387328:L70I;ENSP00000386424:L70I;ENSP00000386983:L70I;ENSP00000390904:L110I	ENSP00000258416:L115I	L	+	1	0	EIF4E2	233137273	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.026000	0.70873	1.387000	0.46486	0.655000	0.94253	CTC		0.463	EIF4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257033.2	NM_004846		A	233429029	C	A	233429029	3	1	61	1	0	0	0	0	1	0	0	0	5043	913	32	2	357	2	EIF4E2	2	233429029	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19843	233429029	9770344	2199	10184										
GIGYF2	26058	broad.mit.edu	37	chr2	233625228	233625228	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtttctaccaaagaagtTttgatgaagtagagggtgtt	13	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233625228T>G	ENST00000409547.1	+	9	729	c.418T>G	c.(418-420)Ttt>Gtt	p.F140V	GIGYF2_ENST00000409480.1_Missense_Mutation_p.F140V|GIGYF2_ENST00000373563.4_Missense_Mutation_p.F140V|GIGYF2_ENST00000373566.3_Missense_Mutation_p.F140V|GIGYF2_ENST00000409196.3_Missense_Mutation_p.F140V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.F140V|AC064852.4_ENST00000427571.1_RNA	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	140	Arg-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.F140V(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CCAAAGAAGTTTTGATGAAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											175	164	168					2																	233625228		2203	4300	6503	233333472	SO:0001583	missense	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.418T>G	2.37:g.233625228T>G	ENSP00000386537:p.Phe140Val		233333472	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.734127	0.69189	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000456491;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000409196;ENST00000409451;ENST00000440945	T;T;T;T;T;T;T	0.74209	-0.66;-0.68;-0.66;-0.68;-0.69;-0.66;-0.82	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.80226	0.4584	L	0.35723	1.085	0.80722	D	1	P;D;B	0.76494	0.573;0.999;0.043	B;D;B	0.78314	0.168;0.991;0.056	T	0.80236	-0.1466	10	0.42905	T	0.14	-13.1413	15.2618	0.73628	0.0:0.0:0.0:1.0	.	140;140;140	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	V	140;140;55;140;140;140;140;140;140	ENSP00000362667:F140V;ENSP00000362664:F140V;ENSP00000386765:F140V;ENSP00000386537:F140V;ENSP00000387070:F140V;ENSP00000387170:F140V;ENSP00000410297:F140V	ENSP00000362664:F140V	F	+	1	0	GIGYF2	233333472	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.008000	0.58898	0.533000	0.62120	TTT		0.423	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233625228	T	G	233625228	3	3	61	1	0	0	0	0	1	0	0	0	6398	1841	64	4	436	4	GIGYF2	2	233625228	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	196199	233625228	9574145	2200	10185										
KCNJ13	3769	broad.mit.edu	37	chr2	233633487	233633487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagcgaattgaaaaagctCgattttttggccgggcaatc	10	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233633487C>T	ENST00000233826.3	-	3	636	c.497G>A	c.(496-498)cGa>cAa	p.R166Q	KCNJ13_ENST00000409779.1_Silent_p.S87S|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000373566.3_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.R166Q|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000452341.2_Intron|AC064852.4_ENST00000427571.1_RNA|GIGYF2_ENST00000409547.1_Intron	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	166					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)	p.R166Q(1)		endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TGAAAAAGCTCGATTTTTTGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	67	66					2																	233633487		2203	4300	6503	233341731	SO:0001583	missense	3769			AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.497G>A	2.37:g.233633487C>T	ENSP00000233826:p.Arg166Gln		233341731	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	37	CCDS2498.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223697	0.58668	.	.	ENSG00000115474	ENST00000233826;ENST00000410029;ENST00000438786	D;D;D	0.96913	-4.17;-4.17;-4.17	5.86	5.86	0.93980	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.98308	0.9439	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98755	1.0722	9	0.87932	D	0	.	20.2019	0.98263	0.0:1.0:0.0:0.0	.	166	O60928	IRK13_HUMAN	Q	166;166;86	ENSP00000233826:R166Q;ENSP00000386251:R166Q;ENSP00000407284:R86Q	ENSP00000233826:R166Q	R	-	2	0	KCNJ13	233341731	1.000000	0.71417	1.000000	0.80357	0.372000	0.29890	7.786000	0.85741	2.776000	0.95493	0.655000	0.94253	CGA		0.378	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		T	233633487	C	T	233633487	3	4	61	1	0	0	0	0	1	0	0	0	8068	884	31	1	589	1	KCNJ13	2	233633487	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8259	233633487	9565886	2201	10186										
GIGYF2	26058	broad.mit.edu	37	chr2	233697615	233697615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagaagaagcccagcgtCgattagaggagaaccggctg	14	8	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:233697615C>T	ENST00000409547.1	+	24	2889	c.2578C>T	c.(2578-2580)Cga>Tga	p.R860*	GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.R882*|GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.R860*|GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.R882*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.R854*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.R881*|GIGYF2_ENST00000452341.2_Nonsense_Mutation_p.R691*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	860	Gln-rich.|Glu-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.R860*(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGCCCAGCGTCGATTAGAGGA	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											17	19	18					2																	233697615		2178	4260	6438	233405859	SO:0001587	stop_gained	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2578C>T	2.37:g.233697615C>T	ENSP00000386537:p.Arg860*		233405859	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	44	10.910299	0.99487	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000452341	.	.	.	5.36	5.36	0.76844	.	0.075643	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9822	18.6765	0.91529	0.0:1.0:0.0:0.0	.	.	.	.	X	882;860;882;860;854;881;691	.	ENSP00000362664:R860X	R	+	1	2	GIGYF2	233405859	0.726000	0.28059	0.975000	0.42487	0.995000	0.86356	1.245000	0.32790	2.499000	0.84300	0.655000	0.94253	CGA		0.502	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233697615	C	T	233697615	4	4	61	1	0	0	0	0	0	1	0	0	6398	876	31	1	2726	1	GIGYF2	2	233697615	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64128	233697615	9501758	2202	10187										
DGKD	8527	broad.mit.edu	37	chr2	234368493	234368493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagccgccagggtacattCggattgtccacaagaaccgg	11	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234368493C>T	ENST00000264057.2	+	23	2797	c.2785C>T	c.(2785-2787)Cgg>Tgg	p.R929W	DGKD_ENST00000409813.3_Missense_Mutation_p.R885W	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	929					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R929W(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	AGGGTACATTCGGATTGTCCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	61	64					2																	234368493		2203	4300	6503	234033232	SO:0001583	missense	8527			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2785C>T	2.37:g.234368493C>T	ENSP00000264057:p.Arg929Trp		234033232	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	C	14.25	2.480864	0.44044	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.47869	0.83;0.83	4.35	4.35	0.52113	.	0.585599	0.16053	N	0.231871	T	0.38957	0.1060	L	0.42744	1.35	0.27273	N	0.958317	B;B	0.16603	0.011;0.018	B;B	0.15870	0.006;0.014	T	0.29792	-1.0000	10	0.66056	D	0.02	.	8.7284	0.34483	0.0:0.8578:0.0:0.1422	.	885;929	Q16760-2;Q16760	.;DGKD_HUMAN	W	929;885	ENSP00000264057:R929W;ENSP00000386455:R885W	ENSP00000264057:R929W	R	+	1	2	DGKD	234033232	0.974000	0.33945	0.842000	0.33263	0.972000	0.66771	2.240000	0.43088	2.442000	0.82660	0.462000	0.41574	CGG		0.632	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234368493	C	T	234368493	3	4	61	1	0	0	0	0	1	0	0	0	4478	875	31	1	2899	1	DGKD	2	234368493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	670878	234368493	8830880	2203	10188										
UGT1A9	54600	broad.mit.edu	37	chr2	234581245	234581245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacatttattatgccaccGttttttcaaaaatgccctag	6	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234581245G>A	ENST00000354728.4	+	1	747	c.665G>A	c.(664-666)cGt>cAt	p.R222H	UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Missense_Mutation_p.R222H			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	222					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)	p.R222H(2)		breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	TTATGCCACCGTTTTTTCAAA	0.428																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	2											215	224	221					2																	234581245		2203	4300	6503	234245984	SO:0001583	missense	54600			AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.665G>A	2.37:g.234581245G>A	ENSP00000346768:p.Arg222His		234245984	B8K285|P36509|Q9HAX0	Missense_Mutation	SNP	ENST00000354728.4	37	CCDS2505.1	.	.	.	.	.	.	.	.	.	.	G	4.521	0.096669	0.08681	.	.	ENSG00000241119	ENST00000354728	T	0.63913	-0.07	3.22	-5.2	0.02823	.	.	.	.	.	T	0.30823	0.0777	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.19451	-1.0305	9	0.16420	T	0.52	.	1.2724	0.02024	0.3067:0.2019:0.0882:0.4033	.	222;222	Q5DSZ5;O60656	.;UD19_HUMAN	H	222	ENSP00000346768:R222H	ENSP00000346768:R222H	R	+	2	0	UGT1A9	234245984	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.600000	0.05693	-0.368000	0.08040	-0.760000	0.03462	CGT		0.428	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		A	234581245	G	A	234581245	3	1	61	1	0	0	0	0	1	0	0	0	16992	1145	40	1	667	1	UGT1A9	2	234581245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	212752	234581245	8618128	2204	10189										
UGT1A6	54578	broad.mit.edu	37	chr2	234602507	234602507	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagaagaggaaagacttgtCtcaggttggtgggtttattt	13	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234602507C>T	ENST00000305139.6	+	1	996	c.857C>T	c.(856-858)tCt>tTt	p.S286F	UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000373424.1_Missense_Mutation_p.S19F|UGT1A6_ENST00000480628.1_3'UTR|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_Missense_Mutation_p.S19F|AC114812.8_ENST00000439336.1_RNA|UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	286					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S286F(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	AAAGACTTGTCTCAGGTTGGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											319	339	332					2																	234602507		2203	4300	6503	234267246	SO:0001583	missense	54578			M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"UDP glucuronosyltransferases"	12538	other	complex locus constituent		606431	"UDP glycosyltransferase 1 family, polypeptide A6"			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.857C>T	2.37:g.234602507C>T	ENSP00000303174:p.Ser286Phe		234267246	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777676	0.31502	.	.	ENSG00000167165	ENST00000373424;ENST00000305139;ENST00000406651	T;T;T	0.62232	3.19;3.19;0.04	5.11	2.23	0.28157	.	.	.	.	.	T	0.77552	0.4147	M	0.86097	2.795	0.09310	N	1	D;D	0.64830	0.992;0.994	D;D	0.71184	0.962;0.972	T	0.63346	-0.6658	9	0.87932	D	0	.	7.9151	0.29814	0.1207:0.6921:0.1174:0.0698	.	286;286	B8K289;P19224	.;UD16_HUMAN	F	19;286;19	ENSP00000362523:S19F;ENSP00000303174:S286F;ENSP00000386107:S19F	ENSP00000303174:S286F	S	+	2	0	UGT1A6	234267246	0.009000	0.17119	0.675000	0.29917	0.071000	0.16799	0.389000	0.20751	1.378000	0.46305	0.655000	0.94253	TCT		0.473	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		T	234602507	C	T	234602507	3	4	61	1	0	0	0	0	1	0	0	0	16989	913	32	3	859	3	UGT1A6	2	234602507	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21262	234602507	8596866	2205	10190										
UGT1A3	54659	broad.mit.edu	37	chr2	234638231	234638231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtggttttaacagacccCgttaacctctgcgcggcagt	11	11	1	1	rs138617806		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234638231C>T	ENST00000482026.1	+	1	478	c.459C>T	c.(457-459)ccC>ccT	p.P153P	UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609767.1_Silent_p.P153P|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	153					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)	p.P153P(1)		breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	TAACAGACCCCGTTAACCTCT	0.453													C|||	1	0.000199681	0	0.0014	5008	,	,		21587	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C	,,,,,,,,	0,4406		0,0,2203	191	198	195		,,,,,,459,,	-8.5	0	2	dbSNP_134	195	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,	,,,,,,153/535,,	234638231	1,13005	2203	4300	6503	234302970	SO:0001819	synonymous_variant	54659			M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"UDP glucuronosyltransferases"	12535	other	complex locus constituent		606428	"UDP glycosyltransferase 1 family, polypeptide A3"			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.459C>T	2.37:g.234638231C>T			234302970	B8K287	Silent	SNP	ENST00000482026.1	37	CCDS2509.1																																																																																				0.453	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		T	234638231	C	T	234638231	2	4	61	1	0	0	0	0	0	0	0	1	16986	639	23	1		1	UGT1A3	2	234638231	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35724	234638231	8561142	2206	10191										
HJURP	55355	broad.mit.edu	37	chr2	234749642	234749642	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactgtcatctgcccaggaGatttgaggcaatacttttga	10	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234749642G>T	ENST00000411486.2	-	8	1849	c.1784C>A	c.(1783-1785)tCt>tAt	p.S595Y	HJURP_ENST00000441687.1_Missense_Mutation_p.S510Y|HJURP_ENST00000432087.1_Missense_Mutation_p.S541Y|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	595					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.S595Y(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		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)		CTGCCCAGGAGATTTGAGGCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											103	107	105					2																	234749642		2203	4300	6503	234414381	SO:0001583	missense	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1784C>A	2.37:g.234749642G>T	ENSP00000414109:p.Ser595Tyr		234414381	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.324391	0.41197	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	4.24	3.36	0.38483	Holliday junction regulator protein family C-terminal repeat (1);	0.732493	0.11890	N	0.519736	T	0.79986	0.4541	M	0.62723	1.935	0.09310	N	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.75484	0.958;0.943;0.986	T	0.65833	-0.6072	10	0.87932	D	0	-6.8208	8.1327	0.31037	0.1081:0.0:0.8919:0.0	.	510;541;595	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	Y	595;541;510;510	ENSP00000414109:S595Y;ENSP00000407208:S541Y;ENSP00000401944:S510Y;ENSP00000393253:S510Y	ENSP00000414109:S595Y	S	-	2	0	HJURP	234414381	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.496000	0.22499	1.387000	0.46486	-0.251000	0.11542	TCT		0.388	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		T	234749642	G	T	234749642	3	4	61	1	0	0	0	0	1	0	0	0	7210	942	33	2	470	2	HJURP	2	234749642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111411	234749642	8449731	2207	10192										
HJURP	55355	broad.mit.edu	37	chr2	234750348	234750348	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggtctgttgacttcaaGaaaagctttttccaatttta	8	6	2	2	rs536819756		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234750348G>T	ENST00000411486.2	-	8	1143	c.1078C>A	c.(1078-1080)Ctt>Att	p.L360I	HJURP_ENST00000441687.1_Missense_Mutation_p.L275I|HJURP_ENST00000432087.1_Missense_Mutation_p.L306I|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	360					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.L360I(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		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)		TTGACTTCAAGAAAAGCTTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	76	75					2																	234750348		2203	4300	6503	234415087	SO:0001583	missense	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1078C>A	2.37:g.234750348G>T	ENSP00000414109:p.Leu360Ile		234415087	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.973124	0.34848	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.3	4.3	0.51218	Holliday junction recognition protein, HJURP (1);	0.712909	0.12734	N	0.443618	T	0.66167	0.2762	L	0.55481	1.735	0.09310	N	1	P;P;P	0.52061	0.938;0.938;0.95	P;P;P	0.56514	0.698;0.698;0.8	T	0.56153	-0.8026	10	0.48119	T	0.1	-7.2564	12.5854	0.56414	0.0:0.0:1.0:0.0	.	275;306;360	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	I	360;306;275;275	ENSP00000414109:L360I;ENSP00000407208:L306I;ENSP00000401944:L275I;ENSP00000393253:L275I	ENSP00000414109:L360I	L	-	1	0	HJURP	234415087	0.014000	0.17966	0.008000	0.14137	0.101000	0.19017	2.317000	0.43770	2.683000	0.91414	0.655000	0.94253	CTT		0.428	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		T	234750348	G	T	234750348	3	4	61	1	0	0	0	0	1	0	0	0	7210	942	33	2	1176	2	HJURP	2	234750348	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	706	234750348	8449025	2208	10193										
TRPM8	79054	broad.mit.edu	37	chr2	234846106	234846106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccaaggaatttcctaccGacgcctttggggatattcag	9	11	1	0	rs149029668		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234846106G>A	ENST00000324695.4	+	4	341	c.301G>A	c.(301-303)Gac>Aac	p.D101N	TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000409625.1_Missense_Mutation_p.D24N|TRPM8_ENST00000355722.4_Missense_Mutation_p.D51N	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	101					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.D101N(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ATTTCCTACCGACGCCTTTGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	151	150	150		301	5.7	0.1	2	dbSNP_134	150	0,8600		0,0,4300	no	missense	TRPM8	NM_024080.4	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	101/1105	234846106	1,13005	2203	4300	6503	234510845	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.301G>A	2.37:g.234846106G>A	ENSP00000323926:p.Asp101Asn		234510845	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276867	0.59758	2.27E-4	0.0	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.64438	-0.1;-0.1;-0.1	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	T	0.79341	0.4429	M	0.72118	2.19	0.80722	D	1	P;D	0.89917	0.803;1.0	B;D	0.83275	0.436;0.996	T	0.80074	-0.1534	10	0.62326	D	0.03	-32.7122	18.3402	0.90303	0.0:0.0:1.0:0.0	.	51;101	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	101;51;24	ENSP00000323926:D101N;ENSP00000347956:D51N;ENSP00000386771:D24N	ENSP00000323926:D101N	D	+	1	0	TRPM8	234510845	1.000000	0.71417	0.105000	0.21289	0.383000	0.30230	5.575000	0.67430	2.676000	0.91093	0.591000	0.81541	GAC		0.478	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234846106	G	A	234846106	3	1	61	1	0	0	0	0	1	0	0	0	16632	1058	37	1	311	1	TRPM8	2	234846106	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95758	234846106	8353267	2209	10194										
TRPM8	79054	broad.mit.edu	37	chr2	234847782	234847782	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaagccgcgcatgcgcaaGatcttcagccggctcatcta	10	14	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234847782G>T	ENST00000324695.4	+	5	529	c.489G>T	c.(487-489)aaG>aaT	p.K163N	TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000409625.1_Missense_Mutation_p.K86N|TRPM8_ENST00000355722.4_Missense_Mutation_p.K113N	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	163					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.K163N(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GCATGCGCAAGATCTTCAGCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	2											36	38	37					2																	234847782		2203	4300	6503	234512521	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.489G>T	2.37:g.234847782G>T	ENSP00000323926:p.Lys163Asn		234512521	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	g	13.74	2.328147	0.41197	.	.	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.57107	0.42;0.42;0.42	5.62	4.73	0.59995	.	0.000000	0.64402	D	0.000001	T	0.60741	0.2292	L	0.47016	1.485	0.80722	D	1	B;D	0.67145	0.02;0.996	B;D	0.67382	0.07;0.951	T	0.57539	-0.7794	10	0.30854	T	0.27	-38.1888	9.967	0.41730	0.1577:0.0:0.8423:0.0	.	113;163	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	163;113;86	ENSP00000323926:K163N;ENSP00000347956:K113N;ENSP00000386771:K86N	ENSP00000323926:K163N	K	+	3	2	TRPM8	234512521	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.901000	0.28445	1.359000	0.45940	0.586000	0.80456	AAG		0.607	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234847782	G	T	234847782	3	4	61	1	0	0	0	0	1	0	0	0	16632	933	33	2	503	2	TRPM8	2	234847782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1676	234847782	8351591	2210	10195										
TRPM8	79054	broad.mit.edu	37	chr2	234858655	234858655	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaaggctcgggccagatCgctgatgtgatcgctagcct	15	10	0	3	rs530123743		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234858655C>T	ENST00000324695.4	+	9	1045	c.1005C>T	c.(1003-1005)atC>atT	p.I335I	TRPM8_ENST00000433712.2_Silent_p.I23I|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	335					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.I335I(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CGGGCCAGATCGCTGATGTGA	0.552													C|||	1	0.000199681	0	0	5008	,	,		19233	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	2											86	80	82					2																	234858655		2203	4300	6503	234523394	SO:0001819	synonymous_variant	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1005C>T	2.37:g.234858655C>T			234523394	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Silent	SNP	ENST00000324695.4	37	CCDS33407.1																																																																																				0.552	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234858655	C	T	234858655	2	4	61	1	0	0	0	0	0	0	0	1	16632	874	31	1		1	TRPM8	2	234858655	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10873	234858655	8340718	2211	10196										
TRPM8	79054	broad.mit.edu	37	chr2	234891812	234891812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaggtggatattccgttCggtcatctacgagccctacc	11	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234891812C>T	ENST00000324695.4	+	20	2745	c.2705C>T	c.(2704-2706)tCg>tTg	p.S902L	TRPM8_ENST00000433712.2_Missense_Mutation_p.S480L	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	902					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S902L(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ATATTCCGTTCGGTCATCTAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	129	135					2																	234891812		2203	4300	6503	234556551	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.2705C>T	2.37:g.234891812C>T	ENSP00000323926:p.Ser902Leu		234556551	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891772	0.91889	.	.	ENSG00000144481	ENST00000324695;ENST00000433712;ENST00000456930	T;T;T	0.68765	-0.35;-0.35;-0.35	5.69	5.69	0.88448	Ion transport (1);	0.105027	0.42964	D	0.000624	T	0.79423	0.4443	L	0.54323	1.7	0.30689	N	0.751475	D;D	0.76494	0.997;0.999	D;D	0.80764	0.955;0.994	T	0.78388	-0.2223	10	0.62326	D	0.03	-5.8507	18.3913	0.90484	0.0:1.0:0.0:0.0	.	480;902	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	L	902;480;163	ENSP00000323926:S902L;ENSP00000404423:S480L;ENSP00000414198:S163L	ENSP00000323926:S902L	S	+	2	0	TRPM8	234556551	1.000000	0.71417	0.932000	0.37286	0.915000	0.54546	5.350000	0.66016	2.684000	0.91462	0.650000	0.86243	TCG		0.572	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234891812	C	T	234891812	3	4	61	1	0	0	0	0	1	0	0	0	16632	893	31	1	2779	1	TRPM8	2	234891812	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33157	234891812	8307561	2212	10197										
TRPM8	79054	broad.mit.edu	37	chr2	234916725	234916725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttgcagaatgaggcatcGatttagacaactggatacaa	9	7	1	3	rs139759512	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234916725G>A	ENST00000324695.4	+	24	3282	c.3242G>A	c.(3241-3243)cGa>cAa	p.R1081Q	TRPM8_ENST00000433712.2_Missense_Mutation_p.R659Q	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	1081					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R1081Q(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ATGAGGCATCGATTTAGACAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	GLN/ARG	0,4406		0,0,2203	235	225	228		3242	5.4	1	2	dbSNP_134	228	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRPM8	NM_024080.4	43	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging	1081/1105	234916725	3,13003	2203	4300	6503	234581464	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.3242G>A	2.37:g.234916725G>A	ENSP00000323926:p.Arg1081Gln		234581464	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.291084	0.59976	0.0	3.49E-4	ENSG00000144481	ENST00000324695;ENST00000433712;ENST00000456930	T;T;T	0.59638	0.25;0.3;0.45	5.45	5.45	0.79879	.	0.279849	0.25994	N	0.026981	T	0.45296	0.1335	L	0.40543	1.245	0.26162	N	0.979987	P;B	0.44946	0.846;0.029	B;B	0.33392	0.163;0.003	T	0.52616	-0.8552	10	0.49607	T	0.09	-23.7998	14.7965	0.69881	0.0:0.0:1.0:0.0	.	659;1081	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	Q	1081;659;342	ENSP00000323926:R1081Q;ENSP00000404423:R659Q;ENSP00000414198:R342Q	ENSP00000323926:R1081Q	R	+	2	0	TRPM8	234581464	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.966000	0.56795	2.580000	0.87095	0.655000	0.94253	CGA		0.343	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234916725	G	A	234916725	3	1	61	1	0	0	0	0	1	0	0	0	16632	1058	37	1	3332	1	TRPM8	2	234916725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24913	234916725	8282648	2213	10198										
SPP2	6694	broad.mit.edu	37	chr2	234959692	234959692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtaaaagtgaattcccagTcactgagtccgtatctgttt	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:234959692T>C	ENST00000168148.3	+	2	251	c.163T>C	c.(163-165)Tca>Cca	p.S55P	SPP2_ENST00000373368.1_Missense_Mutation_p.S55P|SPP2_ENST00000492481.1_3'UTR	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa	55					bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)	p.S55P(1)		breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		GAATTCCCAGTCACTGAGTCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	102	107					2																	234959692		2203	4300	6503	234624431	SO:0001583	missense	6694				CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"secreted phosphoprotein 2, 24kD"			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.163T>C	2.37:g.234959692T>C	ENSP00000168148:p.Ser55Pro		234624431	A4QMV3|Q3B892|Q546M5	Missense_Mutation	SNP	ENST00000168148.3	37	CCDS2511.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.864692	0.51482	.	.	ENSG00000072080	ENST00000373368;ENST00000168148	T;T	0.52057	0.68;0.68	5.39	-0.0335	0.13901	.	0.595286	0.17555	N	0.170025	T	0.57519	0.2059	M	0.67953	2.075	0.09310	N	1	D	0.71674	0.998	P	0.62649	0.905	T	0.49771	-0.8904	10	0.62326	D	0.03	-5.6794	7.4722	0.27355	0.1352:0.0:0.4487:0.4161	.	55	Q13103	SPP24_HUMAN	P	55	ENSP00000362466:S55P;ENSP00000168148:S55P	ENSP00000168148:S55P	S	+	1	0	SPP2	234624431	0.257000	0.24022	0.003000	0.11579	0.879000	0.50718	0.963000	0.29293	-0.227000	0.09884	0.533000	0.62120	TCA		0.478	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944		C	234959692	T	C	234959692	3	2	61	1	0	0	0	0	1	0	0	0	15126	1667	58	4	169	4	SPP2	2	234959692	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	42967	234959692	8239681	2214	10199										
AGAP1	116987	broad.mit.edu	37	chr2	236708095	236708095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagaaggaacttcggatcGatgttcctcccactgccaac	9	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:236708095G>A	ENST00000304032.8	+	8	1466	c.886G>A	c.(886-888)Gat>Aat	p.D296N	AGAP1_ENST00000428334.2_Missense_Mutation_p.D135N|AGAP1_ENST00000409457.1_Missense_Mutation_p.D296N|AGAP1_ENST00000336665.5_Missense_Mutation_p.D296N|AGAP1_ENST00000409538.1_Missense_Mutation_p.D561N	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	296					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)	p.D296N(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACTTCGGATCGATGTTCCTCC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	87	91					2																	236708095		2203	4300	6503	236372834	SO:0001583	missense	116987			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.886G>A	2.37:g.236708095G>A	ENSP00000307634:p.Asp296Asn		236372834	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.674993	0.67928	.	.	ENSG00000157985	ENST00000409457;ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.42494	0.1205	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.995	D;P	0.63488	0.915;0.736	T	0.09596	-1.0667	10	0.20046	T	0.44	.	18.7434	0.91782	0.0:0.0:1.0:0.0	.	296;296	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	N	296;296;296;561;135	ENSP00000387174:D296N;ENSP00000307634:D296N;ENSP00000338378:D296N;ENSP00000386897:D561N;ENSP00000411824:D135N	ENSP00000307634:D296N	D	+	1	0	AGAP1	236372834	1.000000	0.71417	0.240000	0.24138	0.344000	0.29017	9.712000	0.98738	2.430000	0.82344	0.655000	0.94253	GAT		0.532	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		A	236708095	G	A	236708095	3	1	61	1	0	0	0	0	1	0	0	0	366	1058	37	1	916	1	AGAP1	2	236708095	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1748403	236708095	6491278	2215	10200										
ASB18	401036	broad.mit.edu	37	chr2	237150030	237150030	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggtccatgaggggcttcAgatggtcgaggtcccctgcg	15	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:237150030A>G	ENST00000409749.3	-	2	220	c.221T>C	c.(220-222)cTg>cCg	p.L74P	ASB18_ENST00000330842.6_Missense_Mutation_p.L45P|AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	74					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.L45P(1)		large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		GAGGGGCTTCAGATGGTCGAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	85	85					2																	237150030		1969	4151	6120	236814769	SO:0001583	missense	401036			AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"Ankyrin repeat domain containing"	19770	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 18"			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.221T>C	2.37:g.237150030A>G	ENSP00000386532:p.Leu74Pro		236814769	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	37	CCDS46548.1	.	.	.	.	.	.	.	.	.	.	A	9.709	1.156512	0.21454	.	.	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.57752	0.38;0.38	5.12	2.76	0.32466	Ankyrin repeat-containing domain (1);	1.365880	0.05209	N	0.506468	T	0.68805	0.3041	L	0.58583	1.82	0.19775	N	0.999959	D;D	0.76494	0.999;0.999	D;D	0.70016	0.967;0.955	T	0.47182	-0.9137	10	0.87932	D	0	.	8.8387	0.35129	0.8456:0.0:0.1544:0.0	.	74;45	Q6ZVZ8;Q6ZVZ8-2	ASB18_HUMAN;.	P	45;74	ENSP00000329970:L45P;ENSP00000386532:L74P	ENSP00000329970:L45P	L	-	2	0	ASB18	236814769	0.759000	0.28416	0.001000	0.08648	0.017000	0.09413	4.582000	0.60957	0.305000	0.22832	0.533000	0.62120	CTG		0.522	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556		G	237150030	A	G	237150030	3	3	61	1	0	0	0	0	1	0	0	0	1023	188	7	4	1198	4	ASB18	2	237150030	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	441935	237150030	6049343	2216	10201										
IQCA1	79781	broad.mit.edu	37	chr2	237272452	237272452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatgcagcatcatttggaGgccatttttgccagggtatt	11	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:237272452G>A	ENST00000409907.3	-	15	2114	c.1840C>T	c.(1840-1842)Ctc>Ttc	p.L614F	IQCA1_ENST00000431676.2_Missense_Mutation_p.L573F|IQCA1_ENST00000309507.5_Missense_Mutation_p.L611F	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	614							ATP binding (GO:0005524)	p.L614F(1)|p.L622F(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						ATCATTTGGAGGCCATTTTTG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	2											166	163	164					2																	237272452		1968	4159	6127	236937191	SO:0001583	missense	79781			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1840C>T	2.37:g.237272452G>A	ENSP00000387347:p.Leu614Phe		236937191	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642828	0.67244	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.94576	-3.37;-3.38;-3.46	4.36	3.48	0.39840	ATPase, AAA-type, core (1);	0.122268	0.33938	N	0.004413	D	0.96632	0.8901	M	0.78916	2.43	0.51482	D	0.999921	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.77004	0.989;0.983;0.983	D	0.96427	0.9316	10	0.66056	D	0.02	.	12.3771	0.55285	0.0829:0.0:0.9171:0.0	.	573;622;614	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	F	614;622;611;573;611	ENSP00000387347:L614F;ENSP00000311951:L611F;ENSP00000407213:L573F	ENSP00000254653:L615F	L	-	1	0	IQCA1	236937191	1.000000	0.71417	0.978000	0.43139	0.876000	0.50452	3.951000	0.56684	0.951000	0.37770	0.561000	0.74099	CTC		0.448	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		A	237272452	G	A	237272452	3	1	61	1	0	0	0	0	1	0	0	0	7823	1000	35	3	648	3	IQCA1	2	237272452	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122422	237272452	5926921	2217	10202										
IQCA1	79781	broad.mit.edu	37	chr2	237402512	237402512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaaaaaatacttgggtaTgggaatatctaattgttgct	8	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:237402512T>C	ENST00000409907.3	-	3	629	c.355A>G	c.(355-357)Ata>Gta	p.I119V	IQCA1_ENST00000431676.2_Missense_Mutation_p.I119V|IQCA1_ENST00000309507.5_Missense_Mutation_p.I115V	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	119							ATP binding (GO:0005524)	p.I126V(1)|p.I119V(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TACTTGGGTATGGGAATATCT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	2											70	62	65					2																	237402512		1802	4072	5874	237067251	SO:0001583	missense	79781			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.355A>G	2.37:g.237402512T>C	ENSP00000387347:p.Ile119Val		237067251	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.24|15.24	2.775337|2.775337	0.49786|0.49786	.|.	.|.	ENSG00000132321|ENSG00000132321	ENST00000418802|ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	.|D;D;D	.|0.94138	.|-3.26;-3.27;-3.36	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	.|0.000000	.|0.64402	.|D	.|0.000009	D|D	0.93099|0.93099	0.7803|0.7803	L|L	0.46885|0.46885	1.475|1.475	0.41296|0.41296	D|D	0.987016|0.987016	.|P;P;P	.|0.50617	.|0.506;0.937;0.709	.|B;P;B	.|0.54401	.|0.338;0.751;0.412	D|D	0.91613|0.91613	0.5304|0.5304	5|10	.|0.26408	.|T	.|0.33	.|.	13.3781|13.3781	0.60752|0.60752	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|119;126;119	.|E7EWQ0;E9PH78;Q86XH1	.|.;.;IQCA1_HUMAN	R|V	137|119;126;115;119;115	.|ENSP00000387347:I119V;ENSP00000311951:I115V;ENSP00000407213:I119V	.|ENSP00000254653:I119V	H|I	-|-	2|1	0|0	IQCA1|IQCA1	237067251|237067251	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.646000|3.646000	0.54396|0.54396	1.849000|1.849000	0.53698|0.53698	0.460000|0.460000	0.39030|0.39030	CAT|ATA		0.338	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		C	237402512	T	C	237402512	3	2	61	1	0	0	0	0	1	0	0	0	7823	1464	51	4	2181	4	IQCA1	2	237402512	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	130060	237402512	5796861	2218	10203										
CXCR7	57007	broad.mit.edu	37	chr2	237489448	237489448	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaccagtggcccatgggcGagctcacgtgcaaagtcaca	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:237489448G>A	ENST00000272928.3	+	2	650	c.340G>A	c.(340-342)Gag>Aag	p.E114K		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	114					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.E114K(1)									GCCCATGGGCGAGCTCACGTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											236	201	213					2																	237489448		2203	4300	6503	237154187	SO:0001583	missense	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.340G>A	2.37:g.237489448G>A	ENSP00000272928:p.Glu114Lys		237154187	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231092	0.58777	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.71698	-0.59;-0.59	5.7	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.118034	0.56097	D	0.000026	T	0.70133	0.3189	L	0.37561	1.115	0.42859	D	0.994105	D	0.63880	0.993	P	0.55112	0.769	T	0.65932	-0.6048	10	0.09084	T	0.74	.	16.4302	0.83840	0.0:0.1316:0.8684:0.0	.	114	P25106	CXCR7_HUMAN	K	114	ENSP00000405945:E114K;ENSP00000272928:E114K	ENSP00000272928:E114K	E	+	1	0	CXCR7	237154187	1.000000	0.71417	0.849000	0.33467	0.832000	0.47134	5.445000	0.66594	1.358000	0.45922	0.655000	0.94253	GAG		0.567	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		A	237489448	G	A	237489448	3	1	61	1	0	0	0	0	1	0	0	0	4102	1059	37	1	342	1	CXCR7	2	237489448	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86936	237489448	5709925	2219	10204										
CXCR7	57007	broad.mit.edu	37	chr2	237489590	237489590	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaggaagaagatggtacGccgtgtcgtctgcatcctgg	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:237489590G>A	ENST00000272928.3	+	2	792	c.482G>A	c.(481-483)cGc>cAc	p.R161H		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	161					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.R161H(1)									AAGATGGTACGCCGTGTCGTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	2											185	159	168					2																	237489590		2203	4300	6503	237154329	SO:0001583	missense	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.482G>A	2.37:g.237489590G>A	ENSP00000272928:p.Arg161His		237154329	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349138	0.61183	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.37411	1.2;1.2	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.59500	0.2198	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	P	0.60345	0.873	T	0.59440	-0.7454	10	0.51188	T	0.08	.	19.8471	0.96713	0.0:0.0:1.0:0.0	.	161	P25106	CXCR7_HUMAN	H	161	ENSP00000405945:R161H;ENSP00000272928:R161H	ENSP00000272928:R161H	R	+	2	0	CXCR7	237154329	1.000000	0.71417	0.024000	0.17045	0.040000	0.13550	9.611000	0.98342	2.688000	0.91661	0.655000	0.94253	CGC		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		A	237489590	G	A	237489590	3	1	61	1	0	0	0	0	1	0	0	0	4102	1087	38	1	484	1	CXCR7	2	237489590	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142	237489590	5709783	2220	10205										
COL6A3	1293	broad.mit.edu	37	chr2	238243485	238243485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctcccagtggagtttggCgctgttctctgttatctcaa	9	12	3	0	rs551422404		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238243485C>T	ENST00000295550.4	-	41	9465	c.9013G>A	c.(9013-9015)Gcc>Acc	p.A3005T	COL6A3_ENST00000346358.4_Missense_Mutation_p.A2805T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2799T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A2804T|COL6A3_ENST00000472056.1_Missense_Mutation_p.A2398T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2799T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3005	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A3005T(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TGGAGTTTGGCGCTGTTCTCT	0.478													C|||	1	0.000199681	8e-04	0	5008	,	,		18098	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											85	90	88					2																	238243485		2203	4300	6503	237908224	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.9013G>A	2.37:g.238243485C>T	ENSP00000295550:p.Ala3005Thr		237908224	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.875367	0.33162	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47	5.29	5.29	0.74685	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000046	T	0.54951	0.1890	M	0.62723	1.935	0.41596	D	0.988825	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.949;0.977;0.949	T	0.57883	-0.7734	10	0.72032	D	0.01	.	18.9676	0.92702	0.0:1.0:0.0:0.0	.	2398;2799;3005	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	3005;2804;2799;2398;2799;2805	ENSP00000295550:A3005T;ENSP00000315609:A2804T;ENSP00000315873:A2799T;ENSP00000418285:A2398T;ENSP00000386844:A2799T;ENSP00000295546:A2805T	ENSP00000295550:A3005T	A	-	1	0	COL6A3	237908224	0.998000	0.40836	0.966000	0.40874	0.435000	0.31806	4.072000	0.57563	2.473000	0.83533	0.563000	0.77884	GCC		0.478	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238243485	C	T	238243485	3	4	61	1	0	0	0	0	1	0	0	0	3707	768	27	1	536	1	COL6A3	2	238243485	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	753895	238243485	4955888	2221	10206										
COL6A3	1293	broad.mit.edu	37	chr2	238244917	238244917	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctttgctgctacaggcttCgctgccgttgctggcttcac	12	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238244917C>T	ENST00000295550.4	-	40	9278	c.8826G>A	c.(8824-8826)gcG>gcA	p.A2942A	COL6A3_ENST00000346358.4_Silent_p.A2742A|COL6A3_ENST00000353578.4_Silent_p.A2736A|COL6A3_ENST00000347401.3_Silent_p.A2741A|COL6A3_ENST00000472056.1_Silent_p.A2335A|COL6A3_ENST00000409809.1_Silent_p.A2736A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2942	Ala-rich.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A2942A(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CTACAGGCTTCGCTGCCGTTG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	2											40	47	45					2																	238244917		2200	4299	6499	237909656	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8826G>A	2.37:g.238244917C>T			237909656	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.632	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238244917	C	T	238244917	2	4	61	1	0	0	0	0	0	0	0	1	3707	871	31	1		1	COL6A3	2	238244917	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1432	238244917	4954456	2222	10207										
COL6A3	1293	broad.mit.edu	37	chr2	238245103	238245103	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtggtggtcaccggcttCgtcgtagtcaccggcttcgt	14	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238245103C>T	ENST00000295550.4	-	40	9092	c.8640G>A	c.(8638-8640)acG>acA	p.T2880T	COL6A3_ENST00000346358.4_Silent_p.T2680T|COL6A3_ENST00000353578.4_Silent_p.T2674T|COL6A3_ENST00000347401.3_Silent_p.T2679T|COL6A3_ENST00000472056.1_Silent_p.T2273T|COL6A3_ENST00000409809.1_Silent_p.T2674T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2880	Nonhelical region.|Thr-rich.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.T2880T(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TCACCGGCTTCGTCGTAGTCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2											161	153	155					2																	238245103		2203	4300	6503	237909842	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8640G>A	2.37:g.238245103C>T			237909842	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238245103	C	T	238245103	2	4	61	1	0	0	0	0	0	0	0	1	3707	871	31	1		1	COL6A3	2	238245103	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	186	238245103	4954270	2223	10208										
COL6A3	1293	broad.mit.edu	37	chr2	238249185	238249185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactaatttgaagaagacgtCgtttggctcactggcgaagg	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238249185C>T	ENST00000295550.4	-	38	8826	c.8374G>A	c.(8374-8376)Gac>Aac	p.D2792N	COL6A3_ENST00000346358.4_Missense_Mutation_p.D2592N|COL6A3_ENST00000353578.4_Missense_Mutation_p.D2586N|COL6A3_ENST00000347401.3_Missense_Mutation_p.D2591N|COL6A3_ENST00000472056.1_Missense_Mutation_p.D2185N|COL6A3_ENST00000409809.1_Missense_Mutation_p.D2586N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2792	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D2792N(2)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		AAGAAGACGTCGTTTGGCTCA	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	2											112	98	103					2																	238249185		2203	4300	6503	237913924	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8374G>A	2.37:g.238249185C>T	ENSP00000295550:p.Asp2792Asn		237913924	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.487559	0.26686	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53;2.53	5.65	5.65	0.86999	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000029	T	0.41213	0.1149	M	0.73598	2.24	0.58432	D	0.999999	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.948;0.914;0.999	T	0.05937	-1.0855	10	0.49607	T	0.09	.	20.0965	0.97849	0.0:1.0:0.0:0.0	.	2185;2586;2792	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	N	2792;2591;2586;2185;2586;2592	ENSP00000295550:D2792N;ENSP00000315609:D2591N;ENSP00000315873:D2586N;ENSP00000418285:D2185N;ENSP00000386844:D2586N;ENSP00000295546:D2592N	ENSP00000295550:D2792N	D	-	1	0	COL6A3	237913924	1.000000	0.71417	0.246000	0.24233	0.095000	0.18619	4.496000	0.60360	2.824000	0.97209	0.655000	0.94253	GAC		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238249185	C	T	238249185	3	4	61	1	0	0	0	0	1	0	0	0	3707	884	31	1	1187	1	COL6A3	2	238249185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4082	238249185	4950188	2224	10209										
COL6A3	1293	broad.mit.edu	37	chr2	238249704	238249704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctaagatgaaagccatgtCgatgtccacatcgctccctg	9	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238249704C>T	ENST00000295550.4	-	38	8307	c.7855G>A	c.(7855-7857)Gac>Aac	p.D2619N	COL6A3_ENST00000346358.4_Missense_Mutation_p.D2419N|COL6A3_ENST00000353578.4_Missense_Mutation_p.D2413N|COL6A3_ENST00000347401.3_Missense_Mutation_p.D2418N|COL6A3_ENST00000472056.1_Missense_Mutation_p.D2012N|COL6A3_ENST00000409809.1_Missense_Mutation_p.D2413N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2619	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D2619N(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		AAAGCCATGTCGATGTCCACA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											178	174	175					2																	238249704		2203	4300	6503	237914443	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7855G>A	2.37:g.238249704C>T	ENSP00000295550:p.Asp2619Asn		237914443	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.268723	0.59540	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98;-2.98	5.05	5.05	0.67936	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000035	D	0.96516	0.8863	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.97087	0.9788	10	0.87932	D	0	.	18.7716	0.91894	0.0:1.0:0.0:0.0	.	2012;2413;2619	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	N	2619;2418;2413;2012;2413;2419	ENSP00000295550:D2619N;ENSP00000315609:D2418N;ENSP00000315873:D2413N;ENSP00000418285:D2012N;ENSP00000386844:D2413N;ENSP00000295546:D2419N	ENSP00000295550:D2619N	D	-	1	0	COL6A3	237914443	1.000000	0.71417	0.498000	0.27564	0.994000	0.84299	7.684000	0.84104	2.478000	0.83669	0.655000	0.94253	GAC		0.517	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238249704	C	T	238249704	3	4	61	1	0	0	0	0	1	0	0	0	3707	884	31	1	1706	1	COL6A3	2	238249704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	519	238249704	4949669	2225	10210										
COL6A3	1293	broad.mit.edu	37	chr2	238274642	238274642	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaacattctggtctctaGaaccatcaaaccccagaatc	4	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238274642G>T	ENST00000295550.4	-	12	5989	c.5537C>A	c.(5536-5538)tCt>tAt	p.S1846Y	COL6A3_ENST00000346358.4_Missense_Mutation_p.S1646Y|COL6A3_ENST00000353578.4_Missense_Mutation_p.S1640Y|COL6A3_ENST00000347401.3_Missense_Mutation_p.S1645Y|COL6A3_ENST00000472056.1_Missense_Mutation_p.S1239Y|COL6A3_ENST00000409809.1_Missense_Mutation_p.S1640Y	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1846	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S1846Y(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CTGGTCTCTAGAACCATCAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	64	63					2																	238274642		2203	4300	6503	237939381	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5537C>A	2.37:g.238274642G>T	ENSP00000295550:p.Ser1846Tyr		237939381	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365551	0.24684	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.44	5.44	0.79542	von Willebrand factor, type A (2);	0.149717	0.31177	N	0.008118	D	0.86826	0.6026	M	0.80746	2.51	0.51482	D	0.999928	D;D;D	0.89917	0.997;0.998;1.0	P;D;D	0.85130	0.898;0.953;0.997	D	0.88131	0.2838	10	0.87932	D	0	.	16.6397	0.85068	0.0:0.1296:0.8704:0.0	.	1239;1640;1846	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	Y	1846;1645;1640;1239;1640;1646	ENSP00000295550:S1846Y;ENSP00000315609:S1645Y;ENSP00000315873:S1640Y;ENSP00000418285:S1239Y;ENSP00000386844:S1640Y;ENSP00000295546:S1646Y	ENSP00000295550:S1846Y	S	-	2	0	COL6A3	237939381	1.000000	0.71417	0.462000	0.27118	0.471000	0.32888	6.011000	0.70760	2.723000	0.93209	0.655000	0.94253	TCT		0.502	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238274642	G	T	238274642	3	4	61	1	0	0	0	0	1	0	0	0	3707	942	33	2	4128	2	COL6A3	2	238274642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24938	238274642	4924731	2226	10211										
COL6A3	1293	broad.mit.edu	37	chr2	238285978	238285978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagaggaacagaatgtctCgcttgctctctgcaatgaag	10	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238285978C>T	ENST00000295550.4	-	7	2959	c.2507G>A	c.(2506-2508)cGa>cAa	p.R836Q	COL6A3_ENST00000346358.4_Missense_Mutation_p.R636Q|COL6A3_ENST00000392003.2_Missense_Mutation_p.R429Q|COL6A3_ENST00000353578.4_Missense_Mutation_p.R630Q|COL6A3_ENST00000347401.3_Missense_Mutation_p.R635Q|COL6A3_ENST00000392004.3_Missense_Mutation_p.R630Q|COL6A3_ENST00000472056.1_Missense_Mutation_p.R229Q|COL6A3_ENST00000409809.1_Missense_Mutation_p.R630Q	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	836	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R836Q(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CAGAATGTCTCGCTTGCTCTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	84	83					2																	238285978		2203	4300	6503	237950717	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.2507G>A	2.37:g.238285978C>T	ENSP00000295550:p.Arg836Gln		237950717	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650604	0.67472	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	T;T;T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21	5.75	4.88	0.63580	von Willebrand factor, type A (1);	0.175838	0.27181	N	0.020543	T	0.50820	0.1638	M	0.74647	2.275	0.33877	D	0.635681	P;D;D;D;D;P	0.71674	0.852;0.99;0.998;0.958;0.997;0.539	B;P;P;P;P;B	0.59703	0.079;0.787;0.862;0.511;0.847;0.04	T	0.63005	-0.6733	10	0.27785	T	0.31	.	8.8878	0.35414	0.0:0.7651:0.0:0.2349	.	636;229;429;630;630;836	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	Q	836;635;630;229;630;636;630;429;636	ENSP00000295550:R836Q;ENSP00000315609:R635Q;ENSP00000315873:R630Q;ENSP00000418285:R229Q;ENSP00000386844:R630Q;ENSP00000295546:R636Q;ENSP00000375861:R630Q;ENSP00000375860:R429Q;ENSP00000389539:R636Q	ENSP00000295550:R836Q	R	-	2	0	COL6A3	237950717	0.888000	0.30383	1.000000	0.80357	0.695000	0.40330	1.548000	0.36201	1.443000	0.47586	0.655000	0.94253	CGA		0.478	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238285978	C	T	238285978	3	4	61	1	0	0	0	0	1	0	0	0	3707	884	31	1	7225	1	COL6A3	2	238285978	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11336	238285978	4913395	2227	10212										
COL6A3	1293	broad.mit.edu	37	chr2	238289663	238289663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaacaccagggaggagtCgaaagcgatctcttccagct	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238289663C>T	ENST00000295550.4	-	5	2244	c.1792G>A	c.(1792-1794)Gac>Aac	p.D598N	COL6A3_ENST00000346358.4_Missense_Mutation_p.D598N|COL6A3_ENST00000392003.2_Missense_Mutation_p.D191N|COL6A3_ENST00000353578.4_Missense_Mutation_p.D392N|COL6A3_ENST00000347401.3_Missense_Mutation_p.D397N|COL6A3_ENST00000392004.3_Missense_Mutation_p.D392N|COL6A3_ENST00000472056.1_Missense_Mutation_p.D191N|COL6A3_ENST00000409809.1_Missense_Mutation_p.D392N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	598	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D598N(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		AGGGAGGAGTCGAAAGCGATC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	2											81	74	77					2																	238289663		2203	4300	6503	237954402	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1792G>A	2.37:g.238289663C>T	ENSP00000295550:p.Asp598Asn		237954402	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893663	0.52121	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.81	5.81	0.92471	von Willebrand factor, type A (3);	0.109102	0.40064	N	0.001193	D	0.89026	0.6598	L	0.55017	1.72	0.20563	N	0.999885	P;D;D;D;D;P	0.89917	0.854;0.999;0.992;1.0;1.0;0.854	B;D;D;D;D;B	0.76575	0.141;0.97;0.912;0.982;0.988;0.141	T	0.80547	-0.1334	10	0.20519	T	0.43	.	20.0804	0.97772	0.0:1.0:0.0:0.0	.	598;191;191;392;392;598	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	N	598;397;392;191;392;598;392;191;598	ENSP00000295550:D598N;ENSP00000315609:D397N;ENSP00000315873:D392N;ENSP00000418285:D191N;ENSP00000386844:D392N;ENSP00000295546:D598N;ENSP00000375861:D392N;ENSP00000375860:D191N;ENSP00000389539:D598N	ENSP00000295550:D598N	D	-	1	0	COL6A3	237954402	0.923000	0.31300	0.610000	0.28997	0.125000	0.20455	2.267000	0.43329	2.738000	0.93877	0.655000	0.94253	GAC		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238289663	C	T	238289663	3	4	61	1	0	0	0	0	1	0	0	0	3707	884	31	1	7948	1	COL6A3	2	238289663	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3685	238289663	4909710	2228	10213										
COL6A3	1293	broad.mit.edu	37	chr2	238296672	238296672	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaacatggttctgggctCatcgctaaactggaccaccc	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238296672C>A	ENST00000295550.4	-	4	1317	c.865G>T	c.(865-867)Gag>Tag	p.E289*	COL6A3_ENST00000346358.4_Nonsense_Mutation_p.E289*|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000353578.4_Nonsense_Mutation_p.E83*|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000392004.3_Nonsense_Mutation_p.E83*|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000409809.1_Nonsense_Mutation_p.E83*	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	289	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E289*(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		GTTCTGGGCTCATCGCTAAAC	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											86	81	82					2																	238296672		2203	4300	6503	237961411	SO:0001587	stop_gained	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.865G>T	2.37:g.238296672C>A	ENSP00000295550:p.Glu289*		237961411	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Nonsense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	34	5.411596	0.96072	.	.	ENSG00000163359	ENST00000295550;ENST00000353578;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000433762	.	.	.	5.11	5.11	0.69529	.	0.295679	0.23208	U	0.050707	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	14.5501	0.68059	0.0:0.8092:0.1908:0.0	.	.	.	.	X	289;83;83;289;83;289	.	ENSP00000295550:E289X	E	-	1	0	COL6A3	237961411	0.995000	0.38212	0.999000	0.59377	0.961000	0.63080	1.322000	0.33689	2.370000	0.80446	0.650000	0.86243	GAG		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238296672	C	A	238296672	4	1	61	1	0	0	0	0	0	1	0	0	3707	835	29	2	8879	2	COL6A3	2	238296672	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7009	238296672	4902701	2229	10214										
COL6A3	1293	broad.mit.edu	37	chr2	238296750	238296750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggagatttacaaggaagtCgagaatgactgcgaaattga	12	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238296750C>T	ENST00000295550.4	-	4	1239	c.787G>A	c.(787-789)Gac>Aac	p.D263N	COL6A3_ENST00000346358.4_Missense_Mutation_p.D263N|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000353578.4_Missense_Mutation_p.D57N|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000392004.3_Missense_Mutation_p.D57N|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000409809.1_Missense_Mutation_p.D57N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	263	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D263N(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		ACAAGGAAGTCGAGAATGACT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											66	67	67					2																	238296750		2203	4300	6503	237961489	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.787G>A	2.37:g.238296750C>T	ENSP00000295550:p.Asp263Asn		237961489	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.208567	0.58343	.	.	ENSG00000163359	ENST00000295550;ENST00000353578;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000433762	D;D;D;D;D;D	0.97642	-1.71;-1.71;-1.71;-1.71;-1.71;-4.47	5.43	4.56	0.56223	von Willebrand factor, type A (3);	0.000000	0.48286	U	0.000197	D	0.97081	0.9046	L	0.46614	1.455	0.48452	D	0.999653	P;D;D;P	0.89917	0.589;0.998;1.0;0.589	B;P;D;B	0.70487	0.156;0.904;0.969;0.156	D	0.95558	0.8627	10	0.18276	T	0.48	.	14.0324	0.64624	0.0:0.9271:0.0:0.0729	.	263;57;57;263	E9PCV6;E9PGQ9;P12111-2;P12111	.;.;.;CO6A3_HUMAN	N	263;57;57;263;57;263	ENSP00000295550:D263N;ENSP00000315873:D57N;ENSP00000386844:D57N;ENSP00000295546:D263N;ENSP00000375861:D57N;ENSP00000389539:D263N	ENSP00000295550:D263N	D	-	1	0	COL6A3	237961489	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.768000	0.55295	1.287000	0.44583	0.650000	0.86243	GAC		0.428	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238296750	C	T	238296750	3	4	61	1	0	0	0	0	1	0	0	0	3707	884	31	1	8957	1	COL6A3	2	238296750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78	238296750	4902623	2230	10215										
LRRFIP1	9208	broad.mit.edu	37	chr2	238671280	238671280	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggtgaaaaatgaaatCgtggcgaatgtggggaaaag	17	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238671280C>T	ENST00000392000.4	+	11	1041	c.924C>T	c.(922-924)atC>atT	p.I308I	LRRFIP1_ENST00000244815.5_Silent_p.I284I|LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Silent_p.I252I	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	308					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)	p.I308I(1)|p.I284I(1)		NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		AAAATGAAATCGTGGCGAATG	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	2											60	56	57					2																	238671280		2203	4300	6503	238336019	SO:0001819	synonymous_variant	9208			AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.924C>T	2.37:g.238671280C>T			238336019	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																				0.438	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		T	238671280	C	T	238671280	2	4	61	1	0	0	0	0	0	0	0	1	9056	874	31	1		1	LRRFIP1	2	238671280	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	374530	238671280	4528093	2231	10216										
RBM44	375316	broad.mit.edu	37	chr2	238726429	238726429	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacaagagactaattcaatGtaccacactgtatttgatgg	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238726429G>T	ENST00000409864.1	+	3	1124	c.870G>T	c.(868-870)atG>atT	p.M290I	RBM44_ENST00000316997.4_Missense_Mutation_p.M290I|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	289						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.M290I(2)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		CTAATTCAATGTACCACACTG	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	2											71	67	68					2																	238726429		1850	4092	5942	238391168	SO:0001583	missense	375316			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.870G>T	2.37:g.238726429G>T	ENSP00000386727:p.Met290Ile		238391168	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	G	1.432	-0.569887	0.03910	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.30981	1.51;1.51	5.65	0.472	0.16758	.	0.731043	0.13040	N	0.418604	T	0.29061	0.0722	M	0.65975	2.015	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.24621	-1.0155	10	0.34782	T	0.22	2.0711	8.8409	0.35142	0.4104:0.0:0.5896:0.0	.	289	Q6ZP01	RBM44_HUMAN	I	290	ENSP00000321179:M290I;ENSP00000386727:M290I	ENSP00000321179:M290I	M	+	3	0	RBM44	238391168	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.213000	0.09305	0.045000	0.15804	-0.122000	0.15005	ATG		0.358	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		T	238726429	G	T	238726429	3	4	61	1	0	0	0	0	1	0	0	0	13175	1377	48	2	876	2	RBM44	2	238726429	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55149	238726429	4472944	2232	10217										
RBM44	375316	broad.mit.edu	37	chr2	238727037	238727037	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaagaccttctgtagtatCtacatcaagcaacacagaga	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238727037C>A	ENST00000409864.1	+	3	1732	c.1478C>A	c.(1477-1479)tCt>tAt	p.S493Y	RBM44_ENST00000316997.4_Missense_Mutation_p.S493Y|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	492						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.S493Y(2)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TCTGTAGTATCTACATCAAGC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	2											86	80	82					2																	238727037		1915	4131	6046	238391776	SO:0001583	missense	375316			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1478C>A	2.37:g.238727037C>A	ENSP00000386727:p.Ser493Tyr		238391776	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973274	0.74246	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.39787	1.06;1.06	5.86	5.86	0.93980	.	0.092530	0.48286	D	0.000188	T	0.65249	0.2673	M	0.71581	2.175	0.37053	D	0.897707	D	0.89917	1.0	D	0.87578	0.998	T	0.71069	-0.4699	10	0.87932	D	0	-19.4409	16.9051	0.86124	0.0:1.0:0.0:0.0	.	492	Q6ZP01	RBM44_HUMAN	Y	493	ENSP00000321179:S493Y;ENSP00000386727:S493Y	ENSP00000321179:S493Y	S	+	2	0	RBM44	238391776	0.935000	0.31712	0.345000	0.25642	0.865000	0.49528	4.480000	0.60243	2.777000	0.95525	0.591000	0.81541	TCT		0.393	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		A	238727037	C	A	238727037	3	1	61	1	0	0	0	0	1	0	0	0	13175	913	32	2	1484	2	RBM44	2	238727037	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	608	238727037	4472336	2233	10218										
SCLY	51540	broad.mit.edu	37	chr2	238990838	238990838	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgtggacttccttacaatCgtggggcacaaggtaagtct	13	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:238990838C>T	ENST00000555827.1	+	6	829	c.765C>T	c.(763-765)atC>atT	p.I255I	SCLY_ENST00000422984.2_Silent_p.I161I|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Silent_p.I263I|SCLY_ENST00000373332.3_Silent_p.I173I|SCLY_ENST00000409736.2_Silent_p.I255I			Q96I15	SCLY_HUMAN	selenocysteine lyase	255					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.I255I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		TCCTTACAATCGTGGGGCACA	0.617																																					Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)											1	Substitution - coding silent(1)	large_intestine(1)	2											60	56	57					2																	238990838		2203	4299	6502	238655577	SO:0001819	synonymous_variant	51540			AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.765C>T	2.37:g.238990838C>T			238655577	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.962|6.962	0.547501|0.547501	0.13312|0.13312	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000437134;ENST00000440143|ENST00000431487	.|.	.|.	.|.	5.48|5.48	-1.83|-1.83	0.07833|0.07833	.|.	.|.	.|.	.|.	.|.	T|T	0.58552|0.58552	0.2130|0.2130	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55903|0.55903	-0.8067|-0.8067	4|4	.|.	.|.	.|.	-31.9455|-31.9455	12.4979|12.4979	0.55940|0.55940	0.0:0.3779:0.0:0.6221|0.0:0.3779:0.0:0.6221	.|.	.|.	.|.	.|.	C|L	99;33|101	.|.	.|.	R|S	+|+	1|2	0|0	SCLY|SCLY	238655577|238655577	0.002000|0.002000	0.14202|0.14202	0.855000|0.855000	0.33649|0.33649	0.090000|0.090000	0.18270|0.18270	-1.380000|-1.380000	0.02551|0.02551	-0.425000|-0.425000	0.07371|0.07371	-0.812000|-0.812000	0.03155|0.03155	CGT|TCG		0.617	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		T	238990838	C	T	238990838	2	4	61	1	0	0	0	0	0	0	0	1	13944	874	31	1		1	SCLY	2	238990838	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	263801	238990838	4208535	2234	10219										
ILKAP	80895	broad.mit.edu	37	chr2	239079309	239079309	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccttcccgggtctggatCttttcatcctaccagatgag	8	13	3	2	rs141848989	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:239079309C>A	ENST00000254654.3	-	12	1222	c.1047G>T	c.(1045-1047)aaG>aaT	p.K349N		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	349	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.K349N(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		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)		GGGTCTGGATCTTTTCATCCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	ASN/LYS	0,4406		0,0,2203	34	34	34		1047	4.8	1	2	dbSNP_134	34	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ILKAP	NM_030768.2	94	0,5,6498	AA,AC,CC		0.0581,0.0,0.0384	benign	349/393	239079309	5,13001	2203	4300	6503	238744048	SO:0001583	missense	80895			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.1047G>T	2.37:g.239079309C>A	ENSP00000254654:p.Lys349Asn		238744048	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.523841	0.44866	0.0	5.81E-4	ENSG00000132323	ENST00000254654	T	0.17528	2.27	5.69	4.82	0.62117	Protein phosphatase 2C-like (5);	0.520687	0.22651	N	0.057326	T	0.08403	0.0209	N	0.04805	-0.155	0.33587	D	0.600625	B	0.06786	0.001	B	0.11329	0.006	T	0.11616	-1.0580	10	0.34782	T	0.22	-14.0397	8.5911	0.33688	0.1515:0.7703:0.0:0.0782	.	349	Q9H0C8	ILKAP_HUMAN	N	349	ENSP00000254654:K349N	ENSP00000254654:K349N	K	-	3	2	ILKAP	238744048	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	0.505000	0.22642	1.404000	0.46819	0.563000	0.77884	AAG		0.602	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		A	239079309	C	A	239079309	3	1	61	1	0	0	0	0	1	0	0	0	7735	912	32	2	135	2	ILKAP	2	239079309	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88471	239079309	4120064	2235	10220										
ILKAP	80895	broad.mit.edu	37	chr2	239093923	239093923	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagcaaaatatgaaaccCgagtactgaaagaacgaatt	7	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:239093923C>T	ENST00000254654.3	-	6	606	c.431G>A	c.(430-432)cGg>cAg	p.R144Q		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	144	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.R144Q(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		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)		ATATGAAACCCGAGTACTGAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	61	61					2																	239093923		2203	4300	6503	238758662	SO:0001583	missense	80895			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.431G>A	2.37:g.239093923C>T	ENSP00000254654:p.Arg144Gln		238758662	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	35	5.477959	0.96291	.	.	ENSG00000132323	ENST00000254654;ENST00000457149	T;T	0.17054	2.3;2.3	5.98	5.98	0.97165	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.32645	0.0836	L	0.42245	1.32	0.80722	D	1	D	0.63046	0.992	P	0.58077	0.832	T	0.00448	-1.1733	10	0.72032	D	0.01	-1.2056	19.2296	0.93833	0.0:1.0:0.0:0.0	.	144	Q9H0C8	ILKAP_HUMAN	Q	144;142	ENSP00000254654:R144Q;ENSP00000395301:R142Q	ENSP00000254654:R144Q	R	-	2	0	ILKAP	238758662	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.032000	0.70918	2.835000	0.97688	0.650000	0.86243	CGG		0.333	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		T	239093923	C	T	239093923	3	4	61	1	0	0	0	0	1	0	0	0	7735	652	23	1	775	1	ILKAP	2	239093923	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14614	239093923	4105450	2236	10221										
ILKAP	80895	broad.mit.edu	37	chr2	239096800	239096800	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgggggcctacactcctCggtgatgtcgttcaggatga	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:239096800C>T	ENST00000254654.3	-	5	572	c.397G>A	c.(397-399)Gag>Aag	p.E133K		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	133	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.E133K(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		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)		CTACACTCCTCGGTGATGTCG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											127	89	102					2																	239096800		2203	4300	6503	238761539	SO:0001583	missense	80895			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.397G>A	2.37:g.239096800C>T	ENSP00000254654:p.Glu133Lys		238761539	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.478604	0.26511	.	.	ENSG00000132323	ENST00000254654;ENST00000457149	T;T	0.15603	2.41;2.41	5.84	4.95	0.65309	Protein phosphatase 2C-like (5);	0.583736	0.20281	N	0.095449	T	0.11623	0.0283	N	0.20807	0.61	0.34133	D	0.665479	B	0.20052	0.041	B	0.18561	0.022	T	0.15607	-1.0431	10	0.14252	T	0.57	-8.1018	14.1249	0.65213	0.0:0.7027:0.2973:0.0	.	133	Q9H0C8	ILKAP_HUMAN	K	133;131	ENSP00000254654:E133K;ENSP00000395301:E131K	ENSP00000254654:E133K	E	-	1	0	ILKAP	238761539	0.993000	0.37304	0.971000	0.41717	0.957000	0.61999	3.285000	0.51716	1.434000	0.47414	0.655000	0.94253	GAG		0.567	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		T	239096800	C	T	239096800	3	4	61	1	0	0	0	0	1	0	0	0	7735	893	31	1	813	1	ILKAP	2	239096800	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2877	239096800	4102573	2237	10222										
HDAC4	9759	broad.mit.edu	37	chr2	240061476	240061476	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggtccggagcctggggcGctgctgcacgcggagtctgc	18	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:240061476G>A	ENST00000345617.3	-	9	1673	c.882C>T	c.(880-882)agC>agT	p.S294S	HDAC4_ENST00000553145.1_5'UTR|HDAC4_ENST00000541256.1_Silent_p.S263S|HDAC4_ENST00000543185.1_5'UTR	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	294	Interaction with MEF2A.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.S294S(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		AGCCTGGGGCGCTGCTGCACG	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	2											54	57	56					2																	240061476		2203	4300	6503	239726413	SO:0001819	synonymous_variant	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.882C>T	2.37:g.240061476G>A			239726413	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	9.677	1.148243	0.21288	.	.	ENSG00000068024	ENST00000445704	.	.	.	4.47	-7.01	0.01594	.	.	.	.	.	T	0.63319	0.2501	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67074	-0.5762	4	.	.	.	.	16.4631	0.84070	0.7607:0.0:0.2393:0.0	.	.	.	.	V	38	.	.	A	-	2	0	HDAC4	239726413	0.001000	0.12720	0.719000	0.30619	0.866000	0.49608	-1.400000	0.02504	-1.629000	0.01546	-0.244000	0.11960	GCG		0.687	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240061476	G	A	240061476	2	1	61	1	0	0	0	0	0	0	0	1	7030	1078	38	1		1	HDAC4	2	240061476	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	964676	240061476	3137897	2238	10223										
OR6B3	150681	broad.mit.edu	37	chr2	240985431	240985431	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggtactgcagccctgggGccgtggggaagcccaccagg	17	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:240985431G>A	ENST00000319423.4	-	1	58	c.59C>T	c.(58-60)gCc>gTc	p.A20V		NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A20V(1)		endometrium(1)|large_intestine(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		CAGCCCTGGGGCCGTGGGGAA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	2											38	42	41					2																	240985431		2000	4184	6184	240634104	SO:0001583	missense	150681				CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"GPCR / Class A : Olfactory receptors"	15042	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 3 pseudogene"	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.59C>T	2.37:g.240985431G>A	ENSP00000322435:p.Ala20Val		240634104	Q6IFH3	Missense_Mutation	SNP	ENST00000319423.4	37	CCDS42837.1	.	.	.	.	.	.	.	.	.	.	G	1.987	-0.432664	0.04669	.	.	ENSG00000178586	ENST00000319423	T	0.01099	5.34	4.03	4.03	0.46877	.	1.456400	0.04760	N	0.426073	T	0.00967	0.0032	N	0.10685	0.025	0.30743	N	0.745979	B	0.17268	0.021	B	0.17979	0.02	T	0.25152	-1.0140	10	0.24483	T	0.36	.	7.8514	0.29457	0.1093:0.0:0.8907:0.0	.	20	Q8NGW1	OR6B3_HUMAN	V	20	ENSP00000322435:A20V	ENSP00000322435:A20V	A	-	2	0	OR6B3	240634104	0.000000	0.05858	0.163000	0.22734	0.028000	0.11728	-0.159000	0.10056	2.510000	0.84645	0.511000	0.50034	GCC		0.592	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1			A	240985431	G	A	240985431	3	1	61	1	0	0	0	0	1	0	0	0	11220	1203	42	3	939	3	OR6B3	2	240985431	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	923955	240985431	2213942	2239	10224										
OTOS	150677	broad.mit.edu	37	chr2	241078654	241078654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagtgggcaaagaaggttCgggccatgtcctcgatctgg	16	8	1	1	rs376456799		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:241078654C>T	ENST00000391989.2	-	5	433	c.203G>A	c.(202-204)cGa>cAa	p.R68Q	MYEOV2_ENST00000307266.3_5'Flank|MYEOV2_ENST00000607357.1_5'Flank|OTOS_ENST00000319460.1_Missense_Mutation_p.R68Q			Q8NHW6	OTOSP_HUMAN	otospiralin	68					sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)		p.R68Q(1)		endometrium(2)|large_intestine(1)|lung(3)	6		all_epithelial(40;2.79e-15)|Breast(86;3.04e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|Hepatocellular(293;0.148)|all_hematologic(139;0.158)|Melanoma(123;0.16)		Epithelial(32;2.56e-30)|all cancers(36;7.18e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.37e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.07e-06)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		AAAGAAGGTTCGGGCCATGTC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	GLN/ARG	0,4406	2.1+/-5.4	0,0,2203	73	74	74		203	3.5	1	2		74	1,8599	1.2+/-3.3	0,1,4299	no	missense	OTOS	NM_148961.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	68/90	241078654	1,13005	2203	4300	6503	240727327	SO:0001583	missense	150677				CCDS2533.1	2q37.3	2008-02-05			ENSG00000178602	ENSG00000178602			22644	protein-coding gene	gene with protein product		607877				12687421	Standard	NM_148961		Approved	OTOSP	uc002vyv.3	Q8NHW6	OTTHUMG00000133351	ENST00000391989.2:c.203G>A	2.37:g.241078654C>T	ENSP00000375849:p.Arg68Gln		240727327	Q53SW6	Missense_Mutation	SNP	ENST00000391989.2	37	CCDS2533.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477925	0.63849	0.0	1.16E-4	ENSG00000178602	ENST00000391989;ENST00000319460	T;T	0.62105	0.05;0.05	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.77471	0.4135	.	.	.	0.47511	D	0.999445	D	0.89917	1.0	D	0.79108	0.992	T	0.81156	-0.1061	9	0.87932	D	0	-15.6679	12.8596	0.57906	0.0:1.0:0.0:0.0	.	68	Q8NHW6	OTOSP_HUMAN	Q	68	ENSP00000375849:R68Q;ENSP00000322486:R68Q	ENSP00000322486:R68Q	R	-	2	0	OTOS	240727327	1.000000	0.71417	0.999000	0.59377	0.222000	0.24845	6.661000	0.74422	1.688000	0.51068	0.205000	0.17691	CGA		0.642	OTOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257181.3	NM_148961		T	241078654	C	T	241078654	3	4	61	1	0	0	0	0	1	0	0	0	11340	884	31	1	70	1	OTOS	2	241078654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93223	241078654	2120719	2240	10225										
CAPN10	11132	broad.mit.edu	37	chr2	241528855	241528855	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggttcctgtgtgcctgCgccgcgctgcagaagagcag	15	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:241528855C>T	ENST00000391984.2	+	2	433	c.237C>T	c.(235-237)tgC>tgT	p.C79C	CAPN10-AS1_ENST00000567819.1_RNA|CAPN10_ENST00000354082.4_Silent_p.C79C|CAPN10_ENST00000391982.2_Silent_p.C79C|CAPN10_ENST00000352879.4_Intron|CAPN10_ENST00000270364.7_Silent_p.C79C|CAPN10_ENST00000404753.3_Silent_p.C79C	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	79	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)	p.C79C(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		TGTGTGCCTGCGCCGCGCTGC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	2											62	71	68					2																	241528855		2203	4300	6503	241177528	SO:0001819	synonymous_variant	11132			AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.237C>T	2.37:g.241528855C>T			241177528	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Silent	SNP	ENST00000391984.2	37	CCDS42838.1																																																																																				0.627	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083		T	241528855	C	T	241528855	2	4	61	1	0	0	0	0	0	0	0	1	2629	776	27	1		1	CAPN10	2	241528855	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	450201	241528855	1670518	2241	10226										
SNED1	25992	broad.mit.edu	37	chr2	241988476	241988476	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaacatgaacacacagtgCccagatgggggctactgcat	11	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:241988476C>T	ENST00000310397.8	+	11	1542	c.1542C>T	c.(1540-1542)tgC>tgT	p.C514C	SNED1_ENST00000469006.1_3'UTR|SNED1_ENST00000405547.3_Silent_p.C514C|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.C514C|SNED1_ENST00000401884.1_Silent_p.C514C	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	514	Follistatin-like 2.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.C514C(1)		NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|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;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		ACACACAGTGCCCAGATGGGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	2											35	40	38					2																	241988476		2048	4203	6251	241637149	SO:0001819	synonymous_variant	25992			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1542C>T	2.37:g.241988476C>T			241637149	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.727|8.727	0.915824|0.915824	0.17907|0.17907	.|.	.|.	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	5.09|5.09	1.08|1.08	0.20341|0.20341	.|.	.|.	.|.	.|.	.|.	T|T	0.51890|0.51890	0.1701|0.1701	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39210|0.39210	-0.9625|-0.9625	4|4	.|.	.|.	.|.	.|.	5.825|5.825	0.18548|0.18548	0.0:0.4845:0.1418:0.3737|0.0:0.4845:0.1418:0.3737	.|.	.|.	.|.	.|.	V|S	172|211	.|.	.|.	A|P	+|+	2|1	0|0	SNED1|SNED1	241637149|241637149	0.999000|0.999000	0.42202|0.42202	0.953000|0.953000	0.39169|0.39169	0.814000|0.814000	0.46013|0.46013	0.372000|0.372000	0.20467|0.20467	0.309000|0.309000	0.22966|0.22966	0.563000|0.563000	0.77884|0.77884	GCC|CCC		0.582	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	241988476	C	T	241988476	2	4	61	1	0	0	0	0	0	0	0	1	14882	747	26	3		3	SNED1	2	241988476	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	459621	241988476	1210897	2242	10227										
SNED1	25992	broad.mit.edu	37	chr2	242026869	242026869	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagagctgtgaaagcacaaGcctcaagaagaccccaaaca	9	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242026869G>A	ENST00000310397.8	+	30	4184	c.4184G>A	c.(4183-4185)aGc>aAc	p.S1395N	MTERFD2_ENST00000464344.2_Intron|SNED1_ENST00000405547.3_Intron|SNED1_ENST00000342631.6_Missense_Mutation_p.S1362N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1395					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S1375N(1)		NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|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;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GAAAGCACAAGCCTCAAGAAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											40	40	40					2																	242026869		1908	4114	6022	241675542	SO:0001583	missense	25992			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.4184G>A	2.37:g.242026869G>A	ENSP00000308893:p.Ser1395Asn		241675542	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032690	0.35893	.	.	ENSG00000162804	ENST00000310397;ENST00000342631	D;D	0.83075	-1.66;-1.68	4.77	3.86	0.44501	.	0.346611	0.24211	N	0.040522	T	0.69052	0.3068	L	0.27053	0.805	0.09310	N	1	B;B	0.33413	0.281;0.411	B;B	0.33196	0.075;0.159	T	0.56013	-0.8049	10	0.16420	T	0.52	.	8.8641	0.35276	0.0:0.2002:0.6606:0.1391	.	1362;1395	B5MEF5;Q8TER0	.;SNED1_HUMAN	N	1395;1362	ENSP00000308893:S1395N;ENSP00000342992:S1362N	ENSP00000308893:S1395N	S	+	2	0	SNED1	241675542	0.001000	0.12720	0.007000	0.13788	0.199000	0.23934	0.955000	0.29188	2.202000	0.70862	0.561000	0.74099	AGC		0.527	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		A	242026869	G	A	242026869	3	1	61	1	0	0	0	0	1	0	0	0	14882	971	34	3	4302	3	SNED1	2	242026869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38393	242026869	1172504	2243	10228										
MTERFD2	130916	broad.mit.edu	37	chr2	242039151	242039151	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcctgcacatagttattGgatctaacacaagataactc	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242039151G>A	ENST00000391980.2	-	2	238	c.180C>T	c.(178-180)tcC>tcT	p.S60S	MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000407095.3_Silent_p.S60S|MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000495694.1_Silent_p.S60S	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		60					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)	p.S60S(1)		endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		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)		CATAGTTATTGGATCTAACAC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	2											86	84	84					2																	242039151		2203	4300	6503	241687824	SO:0001819	synonymous_variant	130916																														ENST00000391980.2:c.180C>T	2.37:g.242039151G>A			241687824	A8K6K0|Q9P0E0	Silent	SNP	ENST00000391980.2	37	CCDS2544.1																																																																																				0.493	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4			A	242039151	G	A	242039151	2	1	61	1	0	0	0	0	0	0	0	1	9950	1335	47	3		3	MTERFD2	2	242039151	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12282	242039151	1160222	2244	10229										
PASK	23178	broad.mit.edu	37	chr2	242054563	242054563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctccatcacaagctggaaGaacccttggttttcaaatat	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242054563G>T	ENST00000405260.1	-	14	3926	c.3228C>A	c.(3226-3228)ttC>ttA	p.F1076L	PASK_ENST00000403638.3_Missense_Mutation_p.F1076L|PASK_ENST00000539818.1_Missense_Mutation_p.F860L|PASK_ENST00000544142.1_Missense_Mutation_p.F890L|PASK_ENST00000234040.4_Missense_Mutation_p.F1076L|PASK_ENST00000475666.1_5'Flank|PASK_ENST00000358649.4_Missense_Mutation_p.F1076L	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1076	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.F1076L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		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)		CAAGCTGGAAGAACCCTTGGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											64	71	69					2																	242054563		2203	4300	6503	241703236	SO:0001583	missense	23178			U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3228C>A	2.37:g.242054563G>T	ENSP00000384016:p.Phe1076Leu		241703236	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401332	0.83120	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.5	2.17	0.27698	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000037	T	0.63546	0.2520	N	0.21508	0.67	0.45995	D	0.998807	D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;0.999	D;D;D;D;D	0.80764	0.992;0.994;0.986;0.993;0.992	T	0.64394	-0.6418	10	0.72032	D	0.01	.	9.8955	0.41316	0.3093:0.0:0.6907:0.0	.	1041;890;1076;1076;1076	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	L	1076;890;1076;1076;860;1076	ENSP00000234040:F1076L;ENSP00000441374:F890L;ENSP00000384016:F1076L;ENSP00000351475:F1076L;ENSP00000443083:F860L;ENSP00000384438:F1076L	ENSP00000234040:F1076L	F	-	3	2	PASK	241703236	1.000000	0.71417	0.995000	0.50966	0.923000	0.55619	1.541000	0.36126	0.629000	0.30376	0.563000	0.77884	TTC		0.488	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		T	242054563	G	T	242054563	3	4	61	1	0	0	0	0	1	0	0	0	11503	933	33	2	763	2	PASK	2	242054563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15412	242054563	1144810	2245	10230										
PPP1R7	5510	broad.mit.edu	37	chr2	242092955	242092955	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaacacagcagtggcatCgtggccgacctcagtgaaca	11	11	1	2	rs200351113		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242092955C>T	ENST00000234038.6	+	2	591	c.117C>T	c.(115-117)atC>atT	p.I39I	PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000404405.3_Silent_p.I39I|PPP1R7_ENST00000272983.8_Intron|PPP1R7_ENST00000407025.1_Silent_p.I39I|PPP1R7_ENST00000406106.3_Silent_p.I39I|PPP1R7_ENST00000401987.1_Intron	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	39					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)	p.I39I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		GCAGTGGCATCGTGGCCGACC	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		17610	0		0	False		,,,				2504	0				NSCLC(62;446 1299 5417 11238 27640)											1	Substitution - coding silent(1)	large_intestine(1)	2											113	104	107					2																	242092955		2203	4300	6503	241741628	SO:0001819	synonymous_variant	5510			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.117C>T	2.37:g.242092955C>T			241741628	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.585	-0.835256	0.02713	.	.	ENSG00000115685	ENST00000450367	.	.	.	4.61	-7.58	0.01313	.	.	.	.	.	T	0.34164	0.0888	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41520	-0.9504	4	.	.	.	-2.5855	1.1751	0.01833	0.3864:0.2177:0.2337:0.1622	.	.	.	.	L	20	.	.	S	+	2	0	PPP1R7	241741628	0.000000	0.05858	0.016000	0.15963	0.005000	0.04900	-1.618000	0.02049	-1.253000	0.02488	-0.367000	0.07326	TCG		0.577	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		T	242092955	C	T	242092955	2	4	61	1	0	0	0	0	0	0	0	1	12410	874	31	1		1	PPP1R7	2	242092955	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38392	242092955	1106418	2246	10231										
PPP1R7	5510	broad.mit.edu	37	chr2	242099783	242099783	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaatctgctgagaaacatCgaaggggttgacaagttgac	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242099783C>T	ENST00000234038.6	+	6	945	c.471C>T	c.(469-471)atC>atT	p.I157I	PPP1R7_ENST00000402734.1_Silent_p.I98I|PPP1R7_ENST00000404405.3_Silent_p.I151I|PPP1R7_ENST00000272983.8_Silent_p.I114I|PPP1R7_ENST00000407025.1_Silent_p.I157I|PPP1R7_ENST00000406106.3_Silent_p.I157I|PPP1R7_ENST00000485630.1_3'UTR|PPP1R7_ENST00000401987.1_Silent_p.I114I	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	157					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)	p.I157I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		TGAGAAACATCGAAGGGGTTG	0.338																																					NSCLC(62;446 1299 5417 11238 27640)											1	Substitution - coding silent(1)	large_intestine(1)	2											64	65	64					2																	242099783		2203	4300	6503	241748456	SO:0001819	synonymous_variant	5510			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.471C>T	2.37:g.242099783C>T			241748456	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.337787	0.24253	.	.	ENSG00000115685	ENST00000450367	.	.	.	5.52	-2.58	0.06228	.	.	.	.	.	T	0.58090	0.2098	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54957	-0.8215	4	.	.	.	-17.8448	12.4464	0.55653	0.0:0.4552:0.0:0.5448	.	.	.	.	L	132	.	.	S	+	2	0	PPP1R7	241748456	0.516000	0.26218	0.969000	0.41365	0.993000	0.82548	-0.352000	0.07701	-0.765000	0.04645	-0.302000	0.09304	TCG		0.338	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		T	242099783	C	T	242099783	2	4	61	1	0	0	0	0	0	0	0	1	12410	874	31	1		1	PPP1R7	2	242099783	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6828	242099783	1099590	2247	10232										
PPP1R7	5510	broad.mit.edu	37	chr2	242102743	242102743	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccaacctggagagtttgtTtttggggaaaaacaaaatta	9	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242102743T>G	ENST00000234038.6	+	7	1115	c.641T>G	c.(640-642)tTt>tGt	p.F214C	PPP1R7_ENST00000402734.1_Missense_Mutation_p.F155C|PPP1R7_ENST00000404405.3_Missense_Mutation_p.F208C|PPP1R7_ENST00000272983.8_Missense_Mutation_p.F171C|PPP1R7_ENST00000407025.1_Missense_Mutation_p.F214C|PPP1R7_ENST00000406106.3_Missense_Mutation_p.F214C|PPP1R7_ENST00000485630.1_3'UTR|PPP1R7_ENST00000401987.1_Missense_Mutation_p.F171C	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	214					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)	p.F214C(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		GAGAGTTTGTTTTTGGGGAAA	0.498																																					NSCLC(62;446 1299 5417 11238 27640)											1	Substitution - Missense(1)	large_intestine(1)	2											147	159	155					2																	242102743		2203	4300	6503	241751416	SO:0001583	missense	5510			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.641T>G	2.37:g.242102743T>G	ENSP00000234038:p.Phe214Cys		241751416	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Missense_Mutation	SNP	ENST00000234038.6	37	CCDS2546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.9|22.9	4.352514|4.352514	0.82132|0.82132	.|.	.|.	ENSG00000115685|ENSG00000115685	ENST00000438799;ENST00000402734;ENST00000423280;ENST00000407025;ENST00000272983;ENST00000234038;ENST00000404405;ENST00000406106;ENST00000401987|ENST00000450367	T;T;T;T;T;T;T;T;T|T	0.24908|0.23552	1.83;1.83;1.83;1.83;1.83;1.83;2.22;1.83;1.83|1.9	5.03|5.03	5.03|5.03	0.67393|0.67393	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.39784|0.39784	0.1091|0.1091	L|L	0.56340|0.56340	1.77|1.77	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0;0.999;1.0|.	D;D;D;D;D;D|.	0.85130|.	0.99;0.981;0.98;0.994;0.994;0.997|.	T|T	0.14035|0.14035	-1.0487|-1.0487	10|8	0.66056|0.48119	D|T	0.02|0.1	-13.9365|-13.9365	15.0693|15.0693	0.72024|0.72024	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	198;155;171;214;214;208|.	C9JD73;C9J177;Q15435-2;Q15435;Q15435-3;B5MBZ8|.	.;.;.;PP1R7_HUMAN;.;.|.	C|V	198;155;155;214;171;214;208;214;171|189	ENSP00000396376:F198C;ENSP00000385012:F155C;ENSP00000412092:F155C;ENSP00000385657:F214C;ENSP00000272983:F171C;ENSP00000234038:F214C;ENSP00000385498:F208C;ENSP00000385022:F214C;ENSP00000385466:F171C|ENSP00000392373:F189V	ENSP00000234038:F214C|ENSP00000392373:F189V	F|F	+|+	2|1	0|0	PPP1R7|PPP1R7	241751416|241751416	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	7.754000|7.754000	0.85163|0.85163	2.015000|2.015000	0.59207|0.59207	0.533000|0.533000	0.62120|0.62120	TTT|TTT		0.498	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		G	242102743	T	G	242102743	3	3	61	1	0	0	0	0	1	0	0	0	12410	1841	64	4	667	4	PPP1R7	2	242102743	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2960	242102743	1096630	2248	10233										
PPP1R7	5510	broad.mit.edu	37	chr2	242122214	242122214	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccctccgtgcggcagatCgatgccacgttcgtcaggtt	11	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242122214C>T	ENST00000234038.6	+	10	1533	c.1059C>T	c.(1057-1059)atC>atT	p.I353I	PPP1R7_ENST00000272983.8_Silent_p.I310I|PPP1R7_ENST00000407025.1_Silent_p.I353I	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	353	LRRCT.				positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)	p.I353I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		TGCGGCAGATCGATGCCACGT	0.612																																					NSCLC(62;446 1299 5417 11238 27640)											1	Substitution - coding silent(1)	large_intestine(1)	2											105	82	89					2																	242122214		2203	4300	6503	241770887	SO:0001819	synonymous_variant	5510			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.1059C>T	2.37:g.242122214C>T			241770887	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.172|9.172	1.021390|1.021390	0.19433|0.19433	.|.	.|.	ENSG00000115685|ENSG00000115685	ENST00000415769|ENST00000450367	.|.	.|.	.|.	5.19|5.19	2.01|2.01	0.26516|0.26516	.|.	.|.	.|.	.|.	.|.	.|T	.|0.53883	.|0.1824	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.40924	.|-0.9537	.|4	.|.	.|.	.|.	-19.3984|-19.3984	6.1351|6.1351	0.20227|0.20227	0.1214:0.539:0.0:0.3396|0.1214:0.539:0.0:0.3396	.|.	.|.	.|.	.|.	X|L	75|328	.|.	.|.	R|S	+|+	1|2	2|0	PPP1R7|PPP1R7	241770887|241770887	0.957000|0.957000	0.32711|0.32711	1.000000|1.000000	0.80357|0.80357	0.812000|0.812000	0.45895|0.45895	0.112000|0.112000	0.15479|0.15479	0.108000|0.108000	0.17862|0.17862	-1.595000|-1.595000	0.00837|0.00837	CGA|TCG		0.612	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		T	242122214	C	T	242122214	2	4	61	1	0	0	0	0	0	0	0	1	12410	874	31	1		1	PPP1R7	2	242122214	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19471	242122214	1077159	2249	10234										
ANO7	50636	broad.mit.edu	37	chr2	242140767	242140767	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagcaccaagaggcaccaAattgtgagtgggggttccct	12	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242140767A>C	ENST00000274979.8	+	7	874	c.771A>C	c.(769-771)caA>caC	p.Q257H	ANO7_ENST00000402430.3_Missense_Mutation_p.Q256H	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	257					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)	p.Q257H(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						AGAGGCACCAAATTGTGAGTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											95	79	84					2																	242140767		2203	4300	6503	241789440	SO:0001583	missense	50636			AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.771A>C	2.37:g.242140767A>C	ENSP00000274979:p.Gln257His		241789440	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.900269	0.52227	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	T;T	0.67171	-0.25;-0.25	3.76	1.88	0.25563	.	0.575399	0.15860	N	0.241042	T	0.69566	0.3125	M	0.67953	2.075	0.36917	D	0.8912	D	0.60575	0.988	P	0.54664	0.758	T	0.71391	-0.4607	10	0.66056	D	0.02	.	4.8033	0.13307	0.4088:0.0:0.5912:0.0	.	257	Q6IWH7	ANO7_HUMAN	H	257;256	ENSP00000274979:Q257H;ENSP00000385418:Q256H	ENSP00000274979:Q257H	Q	+	3	2	ANO7	241789440	0.310000	0.24527	0.977000	0.42913	0.900000	0.52787	-0.749000	0.04813	0.543000	0.28864	0.260000	0.18958	CAA		0.597	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		C	242140767	A	C	242140767	3	2	61	1	0	0	0	0	1	0	0	0	702	11	1	4	869	4	ANO7	2	242140767	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18553	242140767	1058606	2250	10235										
ANO7	50636	broad.mit.edu	37	chr2	242162653	242162653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcccagacctactggaatCttcttgccatccgcctggcc	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242162653C>A	ENST00000274979.8	+	22	2639	c.2536C>A	c.(2536-2538)Ctt>Att	p.L846I	ANO7_ENST00000402430.3_Missense_Mutation_p.L845I	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	846					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)	p.L846I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CTACTGGAATCTTCTTGCCAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2											249	212	225					2																	242162653		2203	4300	6503	241811326	SO:0001583	missense	50636			AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.2536C>A	2.37:g.242162653C>A	ENSP00000274979:p.Leu846Ile		241811326	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.96|11.96	1.793391|1.793391	0.31685|0.31685	.|.	.|.	ENSG00000146205|ENSG00000146205	ENST00000274979;ENST00000402430|ENST00000451047	T;T|.	0.63096|.	-0.02;-0.02|.	3.6|3.6	3.6|3.6	0.41247|0.41247	.|.	0.703959|.	0.12561|.	N|.	0.458172|.	T|T	0.41971|0.41971	0.1182|0.1182	L|L	0.33093|0.33093	0.98|0.98	0.33003|0.33003	D|D	0.526516|0.526516	D|.	0.69078|.	0.997|.	D|.	0.71656|.	0.974|.	T|T	0.52283|0.52283	-0.8596|-0.8596	10|5	0.17369|.	T|.	0.5|.	.|.	10.6055|10.6055	0.45392|0.45392	0.1927:0.8073:0.0:0.0|0.1927:0.8073:0.0:0.0	.|.	846|.	Q6IWH7|.	ANO7_HUMAN|.	I|Y	846;845|158	ENSP00000274979:L846I;ENSP00000385418:L845I|.	ENSP00000274979:L846I|.	L|S	+|+	1|2	0|0	ANO7|ANO7	241811326|241811326	0.519000|0.519000	0.26242|0.26242	0.669000|0.669000	0.29828|0.29828	0.497000|0.497000	0.33675|0.33675	1.154000|1.154000	0.31688|0.31688	1.719000|1.719000	0.51432|0.51432	0.467000|0.467000	0.42956|0.42956	CTT|TCT		0.587	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		A	242162653	C	A	242162653	3	1	61	1	0	0	0	0	1	0	0	0	702	913	32	2	2694	2	ANO7	2	242162653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21886	242162653	1036720	2251	10236										
HDLBP	3069	broad.mit.edu	37	chr2	242169675	242169675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccgctctgtgggaagcGaatgtccacctggaaggggt	16	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242169675G>A	ENST00000391975.1	-	26	3711	c.3484C>T	c.(3484-3486)Cgc>Tgc	p.R1162C	HDLBP_ENST00000427183.2_Missense_Mutation_p.R1129C|HDLBP_ENST00000391976.2_Missense_Mutation_p.R1162C|HDLBP_ENST00000310931.4_Missense_Mutation_p.R1162C	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1162	KH 14. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.R1162C(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		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)		TGTGGGAAGCGAATGTCCACC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											53	52	52					2																	242169675		2203	4300	6503	241818348	SO:0001583	missense	3069				CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3484C>T	2.37:g.242169675G>A	ENSP00000375836:p.Arg1162Cys		241818348	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.052241	0.55218	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183;ENST00000442730	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	5.91	3.18	0.36537	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.043242	0.85682	N	0.000000	T	0.51702	0.1690	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.982;0.992	T	0.51601	-0.8685	10	0.87932	D	0	-9.7325	11.3115	0.49366	0.195:0.0:0.805:0.0	.	1129;1162	E7EM71;Q00341	.;VIGLN_HUMAN	C	1162;1162;1162;1129;26	ENSP00000375836:R1162C;ENSP00000375837:R1162C;ENSP00000312042:R1162C;ENSP00000399139:R1129C;ENSP00000411211:R26C	ENSP00000312042:R1162C	R	-	1	0	HDLBP	241818348	1.000000	0.71417	0.930000	0.37139	0.125000	0.20455	4.597000	0.61062	0.420000	0.25954	-0.150000	0.13652	CGC		0.527	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		A	242169675	G	A	242169675	3	1	61	1	0	0	0	0	1	0	0	0	7046	1058	37	1	334	1	HDLBP	2	242169675	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7022	242169675	1029698	2252	10237										
FARP2	9855	broad.mit.edu	37	chr2	242407590	242407590	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaaagacatgacgaggtCctaacagaactggaaaaggc	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242407590C>T	ENST00000264042.3	+	18	2099	c.1929C>T	c.(1927-1929)gtC>gtT	p.V643V		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	643	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		V -> I (in dbSNP:rs41342147).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V643V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ATGACGAGGTCCTAACAGAAC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	2											166	168	167					2																	242407590		2203	4300	6503	242056263	SO:0001819	synonymous_variant	9855			AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1929C>T	2.37:g.242407590C>T			242056263	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1																																																																																				0.522	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			T	242407590	C	T	242407590	2	4	61	1	0	0	0	0	0	0	0	1	5696	842	30	3		3	FARP2	2	242407590	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	237915	242407590	791783	2253	10238										
C2orf85	285093	broad.mit.edu	37	chr2	242815145	242815145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatccccttcgcagtcttcGatgtcataaagcgcaagggc	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr2:242815145G>A	ENST00000343216.3	+	2	1466	c.1438G>A	c.(1438-1440)Gat>Aat	p.D480N		NM_173821.2	NP_776182.2												p.D480N(1)									CGCAGTCTTCGATGTCATAAA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											68	79	75					2																	242815145		2080	4195	6275	242463818	SO:0001583	missense	285093																														ENST00000343216.3:c.1438G>A	2.37:g.242815145G>A	ENSP00000345374:p.Asp480Asn		242463818		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	.	.	.	.	.	.	.	.	.	.	.	3.178	-0.168439	0.06461	.	.	ENSG00000188011	ENST00000343216	T	0.23147	1.92	2.14	-1.88	0.07713	.	.	.	.	.	T	0.12860	0.0312	N	0.14661	0.345	0.09310	N	1	B	0.21452	0.056	B	0.10450	0.005	T	0.24512	-1.0158	9	0.87932	D	0	-0.5758	5.867	0.18781	0.4754:0.0:0.5246:0.0	.	480	Q14D33	CB085_HUMAN	N	480	ENSP00000345374:D480N	ENSP00000345374:D480N	D	+	1	0	C2orf85	242463818	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-3.009000	0.00648	-0.440000	0.07211	0.196000	0.17591	GAT		0.632	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			A	242815145	G	A	242815145	3	1	61	1	0	0	0	0	1	0	0	0	2206	1058	37	1	1444	1	C2orf85	2	242815145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	407555	242815145	384228	2254	10239										
CHL1	10752	broad.mit.edu	37	chr3	383609	383609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagaattagaacacatcGaacaagatgaaagagtatac	7	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:383609G>A	ENST00000256509.2	+	7	1165	c.523G>A	c.(523-525)Gaa>Aaa	p.E175K	CHL1_ENST00000397491.2_Missense_Mutation_p.E175K	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	577	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.E175K(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AGAACACATCGAACAAGATGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											69	63	65					3																	383609		2203	4300	6503	358609	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.523G>A	3.37:g.383609G>A	ENSP00000256509:p.Glu175Lys		358609	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	4.846	0.157328	0.09236	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000435603	T;T;T	0.60040	1.12;1.12;0.22	5.43	-2.2	0.06994	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.552403	0.20138	N	0.098431	T	0.53769	0.1817	L	0.39020	1.185	0.09310	N	1	B;B;D	0.58620	0.317;0.317;0.983	B;B;P	0.55545	0.035;0.035;0.778	T	0.53872	-0.8377	10	0.37606	T	0.19	.	10.8119	0.46551	0.1586:0.6299:0.2115:0.0	.	175;175;175	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	K	175	ENSP00000256509:E175K;ENSP00000380628:E175K;ENSP00000397445:E175K	ENSP00000256509:E175K	E	+	1	0	CHL1	358609	0.026000	0.19158	0.000000	0.03702	0.600000	0.36913	0.744000	0.26245	-0.176000	0.10707	-0.282000	0.10007	GAA		0.368	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		A	383609	G	A	383609	3	1	61	1	0	0	0	0	1	0	0	0	3355	1059	37	1	541	1	CHL1	3	383609	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		383609	197638821	2255	10240										
CHL1	10752	broad.mit.edu	37	chr3	386290	386290	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaattccatcaagcaaaGaaaacccaaactgctgttgc	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:386290G>T	ENST00000256509.2	+	9	1388	c.746G>T	c.(745-747)aGa>aTa	p.R249I	CHL1_ENST00000397491.2_Missense_Mutation_p.R233I	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.R249I(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ATCAAGCAAAGAAAACCCAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	97	99					3																	386290		2203	4300	6503	361290	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.746G>T	3.37:g.386290G>T	ENSP00000256509:p.Arg249Ile		361290	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923280	0.92319	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.61742	0.08;0.16	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.79441	0.4446	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.993;0.988;0.997	T	0.82617	-0.0369	10	0.87932	D	0	.	17.5899	0.87993	0.0:0.0:1.0:0.0	.	233;233;249	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	I	249;233	ENSP00000256509:R249I;ENSP00000380628:R233I	ENSP00000256509:R249I	R	+	2	0	CHL1	361290	1.000000	0.71417	0.983000	0.44433	0.998000	0.95712	8.485000	0.90448	2.571000	0.86741	0.650000	0.86243	AGA		0.368	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	386290	G	T	386290	3	4	61	1	0	0	0	0	1	0	0	0	3355	942	33	2	772	2	CHL1	3	386290	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2681	386290	197636140	2256	10241										
CHL1	10752	broad.mit.edu	37	chr3	425551	425551	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcctctcaacccaaggaAatgattataaagtgggaggt	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:425551A>C	ENST00000256509.2	+	19	2871	c.2229A>C	c.(2227-2229)gaA>gaC	p.E743D	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.E727D	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.E743D(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AACCCAAGGAAATGATTATAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											148	148	148					3																	425551		2203	4299	6502	400551	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2229A>C	3.37:g.425551A>C	ENSP00000256509:p.Glu743Asp		400551	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.349314	0.24426	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.57752	0.38;0.38	4.67	2.24	0.28232	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.52468	0.1736	L	0.31371	0.925	0.42077	D	0.991231	P;P;D	0.63046	0.637;0.507;0.992	B;B;D	0.67900	0.303;0.205;0.954	T	0.50915	-0.8771	10	0.56958	D	0.05	.	4.8579	0.13568	0.6141:0.1482:0.2376:0.0	.	727;727;743	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	D	743;727	ENSP00000256509:E743D;ENSP00000380628:E727D	ENSP00000256509:E743D	E	+	3	2	CHL1	400551	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	1.390000	0.34464	0.252000	0.21531	-0.381000	0.06696	GAA		0.348	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		C	425551	A	C	425551	3	2	61	1	0	0	0	0	1	0	0	0	3355	11	1	4	2295	4	CHL1	3	425551	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	39261	425551	197596879	2257	10242										
CHL1	10752	broad.mit.edu	37	chr3	447193	447193	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctagtgacagtgatgaaaaGcctctcaaaggaagccttcg	10	9	2	3	rs572672771		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:447193G>T	ENST00000256509.2	+	28	4116	c.3474G>T	c.(3472-3474)aaG>aaT	p.K1158N	CHL1_ENST00000397491.2_Missense_Mutation_p.K1142N	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	524					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.K1158N(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTGATGAAAAGCCTCTCAAAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											62	60	61					3																	447193		2203	4300	6503	422193	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3474G>T	3.37:g.447193G>T	ENSP00000256509:p.Lys1158Asn		422193	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.31|19.31	3.803708|3.803708	0.70682|0.70682	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000256509;ENST00000397491|ENST00000445697	D;D|.	0.86562|.	-2.14;-2.14|.	5.72|5.72	-4.46|-4.46	0.03536|0.03536	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79563|0.79563	0.4467|0.4467	M|M	0.86420|0.86420	2.815|2.815	0.49582|0.49582	D|D	0.9998|0.9998	D;D|.	0.89917|.	0.978;1.0|.	P;D|.	0.91635|.	0.895;0.999|.	T|T	0.81450|0.81450	-0.0927|-0.0927	10|5	0.87932|.	D|.	0|.	.|.	17.6281|17.6281	0.88098|0.88098	0.3322:0.0:0.6678:0.0|0.3322:0.0:0.6678:0.0	.|.	1142;1158|.	O00533;O00533-2|.	CHL1_HUMAN;.|.	N|I	1158;1142|292	ENSP00000256509:K1158N;ENSP00000380628:K1142N|.	ENSP00000256509:K1158N|.	K|S	+|+	3|2	2|0	CHL1|CHL1	422193|422193	0.915000|0.915000	0.31059|0.31059	0.841000|0.841000	0.33234|0.33234	0.988000|0.988000	0.76386|0.76386	0.016000|0.016000	0.13377|0.13377	-1.172000|-1.172000	0.02762|0.02762	-0.294000|-0.294000	0.09567|0.09567	AAG|AGC		0.383	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	447193	G	T	447193	3	4	61	1	0	0	0	0	1	0	0	0	3355	962	34	2	3576	2	CHL1	3	447193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21642	447193	197575237	2258	10243										
CNTN6	27255	broad.mit.edu	37	chr3	1269508	1269508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttccttgaaggtggaaGcaaaatggcacagacattga	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:1269508G>T	ENST00000446702.2	+	4	816	c.189G>T	c.(187-189)aaG>aaT	p.K63N	CNTN6_ENST00000539053.1_5'UTR|CNTN6_ENST00000350110.2_Missense_Mutation_p.K63N			Q9UQ52	CNTN6_HUMAN	contactin 6	63	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.K63N(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GAAGGTGGAAGCAAAATGGCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	104	105					3																	1269508		2203	4300	6503	1244508	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.189G>T	3.37:g.1269508G>T	ENSP00000407822:p.Lys63Asn		1244508	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736013	0.69189	.	.	ENSG00000134115	ENST00000446702;ENST00000350110	T;T	0.40225	1.04;1.04	5.47	1.46	0.22682	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.303925	0.28214	N	0.016165	T	0.35307	0.0927	M	0.75447	2.3	0.80722	D	1	P	0.39748	0.686	B	0.37239	0.244	T	0.06826	-1.0805	10	0.27785	T	0.31	.	4.7339	0.12979	0.3059:0.0:0.5565:0.1376	.	63	Q9UQ52	CNTN6_HUMAN	N	63	ENSP00000407822:K63N;ENSP00000341882:K63N	ENSP00000341882:K63N	K	+	3	2	CNTN6	1244508	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	1.621000	0.36986	0.038000	0.15604	0.557000	0.71058	AAG		0.348	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		T	1269508	G	T	1269508	3	4	61	1	0	0	0	0	1	0	0	0	3651	962	34	2	199	2	CNTN6	3	1269508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	822315	1269508	196752922	2259	10244										
CNTN6	27255	broad.mit.edu	37	chr3	1424809	1424809	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgggtgtgtataataatGaaggagaaggatccctgagt	14	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:1424809G>T	ENST00000446702.2	+	18	2977	c.2350G>T	c.(2350-2352)Gaa>Taa	p.E784*	CNTN6_ENST00000539053.1_Nonsense_Mutation_p.E712*|CNTN6_ENST00000350110.2_Nonsense_Mutation_p.E784*			Q9UQ52	CNTN6_HUMAN	contactin 6	784	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.E784*(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GTATAATAATGAAGGAGAAGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											136	125	128					3																	1424809		2203	4300	6503	1399809	SO:0001587	stop_gained	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2350G>T	3.37:g.1424809G>T	ENSP00000407822:p.Glu784*		1399809	Q2KHM2	Nonsense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	44	11.081793	0.99513	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	.	.	.	6.08	4.28	0.50868	.	0.093647	0.46758	D	0.000276	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2714	0.31846	0.1359:0.1394:0.7247:0.0	.	.	.	.	X	784;712;784	.	ENSP00000341882:E784X	E	+	1	0	CNTN6	1399809	0.097000	0.21791	0.702000	0.30337	0.907000	0.53573	0.856000	0.27818	0.884000	0.36064	0.655000	0.94253	GAA		0.423	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		T	1424809	G	T	1424809	4	4	61	1	0	0	0	0	0	1	0	0	3651	1291	45	2	2416	2	CNTN6	3	1424809	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155301	1424809	196597621	2260	10245										
CNTN4	152330	broad.mit.edu	37	chr3	3080651	3080651	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcgaatgtcagtggtggCggaggcagcaaatctgaact	14	9	2	1	rs568318866	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3080651C>T	ENST00000397461.1	+	18	2511	c.2127C>T	c.(2125-2127)ggC>ggT	p.G709G	CNTN4_ENST00000448906.2_Silent_p.G381G|CNTN4_ENST00000418658.1_Silent_p.G709G|CNTN4_ENST00000397459.2_Silent_p.G381G|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000427331.1_Silent_p.G709G|CNTN4_ENST00000358480.3_Silent_p.G490G	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	709	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.G709G(1)|p.G381G(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TCAGTGGTGGCGGAGGCAGCA	0.468													C|||	3	0.000599042	0	0	5008	,	,		20282	0		0	False		,,,				2504	0.0031															2	Substitution - coding silent(2)	large_intestine(2)	3											100	95	97					3																	3080651		2203	4300	6503	3055651	SO:0001819	synonymous_variant	152330			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2127C>T	3.37:g.3080651C>T			3055651	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																				0.468	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			T	3080651	C	T	3080651	2	4	61	1	0	0	0	0	0	0	0	1	3649	755	27	1		1	CNTN4	3	3080651	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1655842	3080651	194941779	2261	10246										
CNTN4	152330	broad.mit.edu	37	chr3	3084058	3084058	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacagatattgaagttttCtgggcctccccactggagaa	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3084058C>A	ENST00000397461.1	+	20	2847	c.2463C>A	c.(2461-2463)ttC>ttA	p.F821L	CNTN4_ENST00000448906.2_Missense_Mutation_p.F493L|CNTN4_ENST00000418658.1_Missense_Mutation_p.F821L|CNTN4_ENST00000397459.2_Missense_Mutation_p.F493L|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000427331.1_Missense_Mutation_p.F821L|CNTN4_ENST00000358480.3_Missense_Mutation_p.F602L	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	821	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.F821L(1)|p.F493L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TTGAAGTTTTCTGGGCCTCCC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	3											104	99	101					3																	3084058		2203	4300	6503	3059058	SO:0001583	missense	152330			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2463C>A	3.37:g.3084058C>A	ENSP00000380602:p.Phe821Leu		3059058	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.939682	0.34189	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	T;T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49;0.49	5.61	4.73	0.59995	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.508110	0.21769	N	0.069384	T	0.33876	0.0878	N	0.22421	0.69	0.35285	D	0.781702	B;B	0.20368	0.004;0.044	B;B	0.19946	0.016;0.027	T	0.35450	-0.9788	10	0.18276	T	0.48	.	7.0687	0.25167	0.0:0.6745:0.1331:0.1924	.	820;821	Q8IWV2-3;Q8IWV2	.;CNTN4_HUMAN	L	821;821;821;602;493;493	ENSP00000396010:F821L;ENSP00000380602:F821L;ENSP00000413642:F821L;ENSP00000351267:F602L;ENSP00000380600:F493L;ENSP00000392077:F493L	ENSP00000351267:F602L	F	+	3	2	CNTN4	3059058	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	1.036000	0.30228	1.503000	0.48686	0.655000	0.94253	TTC		0.443	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			A	3084058	C	A	3084058	3	1	61	1	0	0	0	0	1	0	0	0	3649	912	32	2	2533	2	CNTN4	3	3084058	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3407	3084058	194938372	2262	10247										
CNTN4	152330	broad.mit.edu	37	chr3	3097904	3097904	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagctaggtccagtttatgAcaaaagttatctgaaggact	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3097904A>G	ENST00000397461.1	+	24	3465	c.3081A>G	c.(3079-3081)tgA>tgG	p.*1027W	CNTN4_ENST00000448906.2_Nonstop_Mutation_p.*699W|CNTN4_ENST00000418658.1_Nonstop_Mutation_p.*1027W|CNTN4_ENST00000397459.2_Nonstop_Mutation_p.*699W|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000427331.1_Nonstop_Mutation_p.*1027W|CNTN4_ENST00000358480.3_Nonstop_Mutation_p.*808W	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	0					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.*699W(1)|p.*1027W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		CCAGTTTATGACAAAAGTTAT	0.398																																																2	Nonstop extension(2)	large_intestine(2)	3											103	92	95					3																	3097904		2203	4300	6503	3072904	SO:0001578	stop_lost	152330			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.3081A>G	3.37:g.3097904A>G	ENSP00000380602:p.*1027Trpext*16		3072904	B2RAX3|Q8IX14|Q8TC35	Nonstop_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813180	0.50527	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6012	0.76626	1.0:0.0:0.0:0.0	.	.	.	.	W	1027;1027;1027;808;699;699	.	.	X	+	3	0	CNTN4	3072904	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	8.167000	0.89668	2.094000	0.63399	0.482000	0.46254	TGA		0.398	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			G	3097904	A	G	3097904	4	3	61	1	0	0	0	0	0	0	0	0	3649	288	10	4	3167	4	CNTN4	3	3097904	Nonstop_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13846	3097904	194924526	2263	10248										
IL5RA	3568	broad.mit.edu	37	chr3	3144448	3144448	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggtttccattgtaaaaGaacttgagccaaaccagtaa	7	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3144448G>T	ENST00000446632.2	-	4	713	c.139C>A	c.(139-141)Ctt>Att	p.L47I	SNORA43_ENST00000517240.1_RNA|IL5RA_ENST00000311981.8_Missense_Mutation_p.L47I|IL5RA_ENST00000256452.3_Missense_Mutation_p.L47I|IL5RA_ENST00000438560.1_Missense_Mutation_p.L47I|IL5RA_ENST00000456302.1_Missense_Mutation_p.L47I|IL5RA_ENST00000445864.2_Missense_Mutation_p.L47I|IL5RA_ENST00000383846.1_Missense_Mutation_p.L47I|IL5RA_ENST00000418488.2_Missense_Mutation_p.L47I|IL5RA_ENST00000430514.2_Missense_Mutation_p.L47I	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	47	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)	p.L47I(2)		cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		CATTGTAAAAGAACTTGAGCC	0.343																																					GBM(169;430 2801 24955 28528)											2	Substitution - Missense(2)	large_intestine(2)	3											92	90	91					3																	3144448		2203	4300	6503	3119448	SO:0001583	missense	3568			M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.139C>A	3.37:g.3144448G>T	ENSP00000412209:p.Leu47Ile		3119448	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267916	0.40095	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701;ENST00000427088	T;T;T;D;D;T;T;T;T;D;T	0.98362	0.92;0.92;0.92;-4.89;-4.89;0.92;0.92;0.92;0.92;-4.89;0.92	4.8	3.9	0.45041	Immunoglobulin-like fold (1);	0.113095	0.39909	N	0.001221	D	0.96479	0.8851	L	0.58669	1.825	0.34122	D	0.664254	P;P;P;B;P;P	0.40660	0.7;0.585;0.585;0.449;0.663;0.726	B;B;B;B;B;B	0.41202	0.106;0.215;0.215;0.106;0.35;0.26	D	0.96934	0.9683	10	0.21540	T	0.41	-14.2468	12.2029	0.54337	0.0:0.1723:0.8277:0.0	.	47;47;47;47;47;47	B4E2G0;Q01344-3;Q01344-2;Q01344;B3IU77;E7ERY4	.;.;.;IL5RA_HUMAN;.;.	I	47	ENSP00000412209:L47I;ENSP00000390753:L47I;ENSP00000256452:L47I;ENSP00000388858:L47I;ENSP00000402598:L47I;ENSP00000373358:L47I;ENSP00000309196:L47I;ENSP00000400400:L47I;ENSP00000392059:L47I;ENSP00000398117:L47I;ENSP00000391274:L47I	ENSP00000256452:L47I	L	-	1	0	IL5RA	3119448	1.000000	0.71417	0.245000	0.24217	0.913000	0.54294	3.231000	0.51294	1.086000	0.41228	0.557000	0.71058	CTT		0.343	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			T	3144448	G	T	3144448	3	4	61	1	0	0	0	0	1	0	0	0	7721	942	33	2	1185	2	IL5RA	3	3144448	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46544	3144448	194877982	2264	10249										
TRNT1	51095	broad.mit.edu	37	chr3	3189809	3189809	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaccaaatggaaaaagatGaacttctgagttacataaag	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3189809G>T	ENST00000251607.6	+	8	1378	c.1276G>T	c.(1276-1278)Gaa>Taa	p.E426*	TRNT1_ENST00000280591.6_Nonsense_Mutation_p.E406*	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	426					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)	p.E426*(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		GGAAAAAGATGAACTTCTGAG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											51	54	53					3																	3189809		2203	4299	6502	3164809	SO:0001587	stop_gained	51095			AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.1276G>T	3.37:g.3189809G>T	ENSP00000251607:p.Glu426*		3164809	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Nonsense_Mutation	SNP	ENST00000251607.6	37	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	G	37	6.349503	0.97494	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-5.1073	18.4335	0.90634	0.0:0.0:1.0:0.0	.	.	.	.	X	426;406	.	ENSP00000251607:E426X	E	+	1	0	TRNT1	3164809	1.000000	0.71417	0.984000	0.44739	0.998000	0.95712	9.073000	0.93992	2.430000	0.82344	0.655000	0.94253	GAA		0.378	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			T	3189809	G	T	3189809	4	4	61	1	0	0	0	0	0	1	0	0	16613	1291	45	2	1302	2	TRNT1	3	3189809	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45361	3189809	194832621	2265	10250										
CRBN	51185	broad.mit.edu	37	chr3	3215804	3215804	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccgcaccatactgacttCttgagggtgaaaaagctgaa	9	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3215804C>A	ENST00000231948.4	-	3	338	c.316G>T	c.(316-318)Gaa>Taa	p.E106*	CRBN_ENST00000432408.2_Nonsense_Mutation_p.E105*	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	106	Lon.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)	p.E106*(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	ATACTGACTTCTTGAGGGTGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											97	99	98					3																	3215804		2203	4300	6503	3190804	SO:0001587	stop_gained	51185			BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.316G>T	3.37:g.3215804C>A	ENSP00000231948:p.Glu106*		3190804	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Nonsense_Mutation	SNP	ENST00000231948.4	37	CCDS2562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.269964|7.269964	0.98175|0.98175	.|.	.|.	ENSG00000113851|ENSG00000113851	ENST00000231948;ENST00000432408;ENST00000546075|ENST00000424814;ENST00000450014	.|.	.|.	.|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79862	.|0.4519	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77720	.|-0.2482	.|3	0.27082|.	T|.	0.32|.	-30.7803|-30.7803	19.9479|19.9479	0.97190|0.97190	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	106;105;43|101	.|.	ENSP00000231948:E106X|.	E|K	-|-	1|3	0|2	CRBN|CRBN	3190804|3190804	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.972000|0.972000	0.66771|0.66771	5.913000|5.913000	0.69957|0.69957	2.704000|2.704000	0.92352|0.92352	0.650000|0.650000	0.86243|0.86243	GAA|AAG		0.418	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		A	3215804	C	A	3215804	4	1	61	1	0	0	0	0	0	1	0	0	3857	922	32	2	1048	2	CRBN	3	3215804	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25995	3215804	194806626	2266	10251										
LRRN1	57633	broad.mit.edu	37	chr3	3887235	3887235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcgagctcgtttctgtcGaccgctatgccctggataac	12	12	1	0	rs561448571		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:3887235G>A	ENST00000319331.3	+	2	1671	c.910G>A	c.(910-912)Gac>Aac	p.D304N	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	304						integral component of membrane (GO:0016021)		p.D304N(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		CGTTTCTGTCGACCGCTATGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											64	67	66					3																	3887235		2203	4300	6503	3862235	SO:0001583	missense	57633			AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.910G>A	3.37:g.3887235G>A	ENSP00000314901:p.Asp304Asn		3862235	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Missense_Mutation	SNP	ENST00000319331.3	37	CCDS33685.1	.	.	.	.	.	.	.	.	.	.	G	30	5.051610	0.93793	.	.	ENSG00000175928	ENST00000319331	T	0.24908	1.83	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.41465	0.1160	L	0.58669	1.825	0.80722	D	1	D	0.69078	0.997	P	0.53861	0.736	T	0.05451	-1.0884	10	0.32370	T	0.25	.	19.5917	0.95518	0.0:0.0:1.0:0.0	.	304	Q6UXK5	LRRN1_HUMAN	N	304	ENSP00000314901:D304N	ENSP00000314901:D304N	D	+	1	0	LRRN1	3862235	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.782000	0.99034	2.614000	0.88457	0.650000	0.86243	GAC		0.463	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		A	3887235	G	A	3887235	3	1	61	1	0	0	0	0	1	0	0	0	9063	1058	37	1	912	1	LRRN1	3	3887235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	671431	3887235	194135195	2267	10252										
SETMAR	6419	broad.mit.edu	37	chr3	4355431	4355431	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgttcccctcctgcaagCgattgacccttgaggtgagt	11	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4355431C>T	ENST00000358065.4	+	2	1073	c.1006C>T	c.(1006-1008)Cga>Tga	p.R336*	SETMAR_ENST00000425863.1_Nonsense_Mutation_p.R197*|SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000430981.1_Nonsense_Mutation_p.R336*	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	336	Histone-lysine N-methyltransferase.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)	p.R323*(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		CTCCTGCAAGCGATTGACCCT	0.502								Chromatin Structure																																								1	Substitution - Nonsense(1)	large_intestine(1)	3											104	96	99					3																	4355431		2203	4300	6503	4330431	SO:0001587	stop_gained	6419			U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1006C>T	3.37:g.4355431C>T	ENSP00000373354:p.Arg336*		4330431	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Nonsense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	C	17.02	3.282235	0.59867	.	.	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863;ENST00000358950	.	.	.	3.21	0.127	0.14727	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.5526	0.07853	0.4287:0.4357:0.0:0.1355	.	.	.	.	X	336;336;197;100	.	ENSP00000373354:R336X	R	+	1	2	SETMAR	4330431	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.450000	0.06803	0.001000	0.14605	-0.182000	0.12963	CGA		0.502	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		T	4355431	C	T	4355431	4	4	61	1	0	0	0	0	0	1	0	0	14177	760	27	1	1012	1	SETMAR	3	4355431	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	468196	4355431	193666999	2268	10253										
ITPR1	3708	broad.mit.edu	37	chr3	4699844	4699844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcctctcgaagtaggttgCggaatgcccaagaaaagatg	12	9	1	2	rs369055445		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4699844C>T	ENST00000443694.2	+	10	988	c.988C>T	c.(988-990)Cgg>Tgg	p.R330W	ITPR1_ENST00000302640.8_Missense_Mutation_p.R330W|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Missense_Mutation_p.R345W|ITPR1_ENST00000456211.2_Missense_Mutation_p.R330W|ITPR1_ENST00000354582.6_Missense_Mutation_p.R345W|ITPR1_ENST00000423119.2_Missense_Mutation_p.R345W			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	345	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.R330W(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AAGTAGGTTGCGGAATGCCCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											162	164	163					3																	4699844		1999	4157	6156	4674844	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.988C>T	3.37:g.4699844C>T	ENSP00000401671:p.Arg330Trp		4674844	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.675493	0.67928	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25	5.19	4.29	0.51040	MIR motif (2);MIR (2);	0.063262	0.64402	D	0.000004	D	0.86112	0.5855	M	0.68317	2.08	0.80722	D	1	B;B;B	0.22604	0.072;0.017;0.025	B;B;B	0.24269	0.052;0.027;0.02	D	0.83673	0.0167	10	0.62326	D	0.03	.	14.2884	0.66260	0.1546:0.8454:0.0:0.0	.	330;345;345	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	W	345;330;345;345;345;330;330	ENSP00000306253:R330W;ENSP00000346595:R345W;ENSP00000405934:R345W;ENSP00000349597:R345W;ENSP00000397885:R330W;ENSP00000401671:R330W	ENSP00000306253:R330W	R	+	1	2	ITPR1	4674844	1.000000	0.71417	0.894000	0.35097	0.573000	0.36030	2.851000	0.48302	1.121000	0.41925	0.655000	0.94253	CGG		0.498	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4699844	C	T	4699844	3	4	61	1	0	0	0	0	1	0	0	0	7941	759	27	1	1075	1	ITPR1	3	4699844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344413	4699844	193322586	2269	10254										
ITPR1	3708	broad.mit.edu	37	chr3	4735223	4735223	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctacaacgacagagcctCtttccagactctgatccaga	7	13	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4735223C>A	ENST00000443694.2	+	30	4034	c.4034C>A	c.(4033-4035)tCt>tAt	p.S1345Y	ITPR1_ENST00000423119.2_Missense_Mutation_p.S1351Y|ITPR1_ENST00000354582.6_Missense_Mutation_p.S1360Y|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Missense_Mutation_p.S1351Y|ITPR1_ENST00000302640.8_Missense_Mutation_p.S1345Y|ITPR1_ENST00000456211.2_Missense_Mutation_p.S1336Y			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1360					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.S1336Y(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GACAGAGCCTCTTTCCAGACT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											203	197	199					3																	4735223		2009	4196	6205	4710223	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.4034C>A	3.37:g.4735223C>A	ENSP00000401671:p.Ser1345Tyr		4710223	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728170	0.89390	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8;-3.8;-3.8	4.97	4.97	0.65823	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.97892	0.9307	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98628	1.0670	10	0.62326	D	0.03	.	18.238	0.89956	0.0:1.0:0.0:0.0	.	1360;1351	Q14643;G5E9P1	ITPR1_HUMAN;.	Y	1360;1345;1360;1351;1351;1336;1345	ENSP00000306253:S1345Y;ENSP00000346595:S1360Y;ENSP00000405934:S1351Y;ENSP00000349597:S1351Y;ENSP00000397885:S1336Y;ENSP00000401671:S1345Y	ENSP00000306253:S1345Y	S	+	2	0	ITPR1	4710223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.755000	0.85180	2.288000	0.76882	0.591000	0.81541	TCT		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4735223	C	A	4735223	3	1	61	1	0	0	0	0	1	0	0	0	7941	913	32	2	4201	2	ITPR1	3	4735223	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35379	4735223	193287207	2270	10255										
ITPR1	3708	broad.mit.edu	37	chr3	4808230	4808230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcactcctttttctgtcGcttgacagaagataagaagt	9	9	1	4	rs375517463		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4808230G>A	ENST00000443694.2	+	42	5516	c.5516G>A	c.(5515-5517)cGc>cAc	p.R1839H	ITPR1_ENST00000423119.2_Missense_Mutation_p.R1806H|ITPR1_ENST00000354582.6_Missense_Mutation_p.R1839H|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Missense_Mutation_p.R1806H|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1839H|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1791H			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1854					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.R1791H(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTTTTCTGTCGCTTGACAGAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG,HIS/ARG,HIS/ARG	0,3786		0,0,1893	72	72	72		5417,5516,5372	5.7	1	3		72	1,8237		0,1,4118	no	missense,missense,missense	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	29,29,29	0,1,6011	AA,AG,GG		0.0121,0.0,0.0083	benign,benign,benign	1806/2711,1839/2744,1791/2696	4808230	1,12023	1893	4119	6012	4783230	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.5516G>A	3.37:g.4808230G>A	ENSP00000401671:p.Arg1839His		4783230	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037182	0.93630	0.0	1.21E-4	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7;-2.7	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.93003	0.7773	L	0.58810	1.83	0.80722	D	1	B;D	0.65815	0.175;0.995	B;P	0.59288	0.015;0.855	D	0.89878	0.4028	10	0.15952	T	0.53	.	19.7686	0.96352	0.0:0.0:1.0:0.0	.	1854;1806	Q14643;G5E9P1	ITPR1_HUMAN;.	H	1854;1839;1839;1806;300;1806;1791;1839	ENSP00000306253:R1839H;ENSP00000346595:R1839H;ENSP00000405934:R1806H;ENSP00000349597:R1806H;ENSP00000397885:R1791H;ENSP00000401671:R1839H	ENSP00000306253:R1839H	R	+	2	0	ITPR1	4783230	1.000000	0.71417	0.987000	0.45799	0.779000	0.44077	9.740000	0.98839	2.665000	0.90641	0.591000	0.81541	CGC		0.423	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4808230	G	A	4808230	3	1	61	1	0	0	0	0	1	0	0	0	7941	1087	38	1	5731	1	ITPR1	3	4808230	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73007	4808230	193214200	2271	10256										
ITPR1	3708	broad.mit.edu	37	chr3	4817094	4817094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccctggaaagtctgaccGaatactgtcaaggaccttgc	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4817094G>A	ENST00000443694.2	+	44	6103	c.6103G>A	c.(6103-6105)Gaa>Aaa	p.E2035K	ITPR1_ENST00000423119.2_Missense_Mutation_p.E2002K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E2035K|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Missense_Mutation_p.E2002K|ITPR1_ENST00000302640.8_Missense_Mutation_p.E2035K|ITPR1_ENST00000456211.2_Missense_Mutation_p.E1987K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2050					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.E1987K(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AAGTCTGACCGAATACTGTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	100	101					3																	4817094		1857	4089	5946	4792094	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.6103G>A	3.37:g.4817094G>A	ENSP00000401671:p.Glu2035Lys		4792094	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836901	0.91117	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47;-4.47;-4.47	5.04	5.04	0.67666	RyR/IP3R Homology associated domain (1);	0.000000	0.85682	D	0.000000	D	0.98934	0.9638	M	0.94142	3.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99659	1.0993	10	0.87932	D	0	.	18.4209	0.90590	0.0:0.0:1.0:0.0	.	2050;2002	Q14643;G5E9P1	ITPR1_HUMAN;.	K	2050;2035;2035;2002;496;2002;1987;2035	ENSP00000306253:E2035K;ENSP00000346595:E2035K;ENSP00000405934:E2002K;ENSP00000349597:E2002K;ENSP00000397885:E1987K;ENSP00000401671:E2035K	ENSP00000306253:E2035K	E	+	1	0	ITPR1	4792094	1.000000	0.71417	0.700000	0.30305	0.489000	0.33432	9.772000	0.98984	2.349000	0.79799	0.655000	0.94253	GAA		0.413	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4817094	G	A	4817094	3	1	61	1	0	0	0	0	1	0	0	0	7941	1059	37	1	6326	1	ITPR1	3	4817094	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8864	4817094	193205336	2272	10257										
ITPR1	3708	broad.mit.edu	37	chr3	4854834	4854834	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctctcccagaaaccggcGagagtttggcaagcgagttc	11	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4854834G>A	ENST00000443694.2	+	54	7432	c.7432G>A	c.(7432-7434)Gag>Aag	p.E2478K	ITPR1_ENST00000423119.2_Missense_Mutation_p.E2445K|AC018816.3_ENST00000489771.1_5'Flank|ITPR1_ENST00000354582.6_Missense_Mutation_p.E2478K|ITPR1_ENST00000544951.1_Missense_Mutation_p.E456K|ITPR1_ENST00000357086.4_Missense_Mutation_p.E2445K|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000302640.8_Missense_Mutation_p.E2478K|ITPR1_ENST00000456211.2_Missense_Mutation_p.E2430K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2493	Interaction with ERP44. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.E2430K(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGAAACCGGCGAGAGTTTGGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	110	111					3																	4854834		1856	4099	5955	4829834	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7432G>A	3.37:g.4854834G>A	ENSP00000401671:p.Glu2478Lys		4829834	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.775227	0.31411	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.97328	-2.73;-2.72;-2.72;-2.72;-2.72;-4.34;-2.73	5.02	5.02	0.67125	Ion transport (1);	1.046670	0.07417	N	0.893435	D	0.91523	0.7323	N	0.14661	0.345	0.42268	D	0.992046	P;B;B	0.39601	0.68;0.0;0.0	B;B;B	0.30855	0.121;0.002;0.001	D	0.84319	0.0515	10	0.06365	T	0.9	.	15.5011	0.75700	0.0:0.0:1.0:0.0	.	456;2493;2445	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	2493;2478;2478;2445;939;2445;2430;456;2478	ENSP00000306253:E2478K;ENSP00000346595:E2478K;ENSP00000405934:E2445K;ENSP00000349597:E2445K;ENSP00000397885:E2430K;ENSP00000440564:E456K;ENSP00000401671:E2478K	ENSP00000306253:E2478K	E	+	1	0	ITPR1	4829834	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.603000	0.82811	2.324000	0.78689	0.557000	0.71058	GAG		0.478	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4854834	G	A	4854834	3	1	61	1	0	0	0	0	1	0	0	0	7941	1059	37	1	7695	1	ITPR1	3	4854834	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37740	4854834	193167596	2273	10258										
ITPR1	3708	broad.mit.edu	37	chr3	4856740	4856740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacctctcttttccaggaaCccctgtttgctgctagagtt	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:4856740C>T	ENST00000443694.2	+	56	7660	c.7660C>T	c.(7660-7662)Ccc>Tcc	p.P2554S	AC018816.3_ENST00000449914.1_Intron|ITPR1_ENST00000423119.2_Missense_Mutation_p.P2521S|AC018816.3_ENST00000489771.1_Intron|AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.P2554S|ITPR1_ENST00000544951.1_Missense_Mutation_p.P532S|ITPR1_ENST00000357086.4_Missense_Mutation_p.P2521S|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000302640.8_Missense_Mutation_p.P2554S|ITPR1_ENST00000456211.2_Missense_Mutation_p.P2506S			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2569					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.P2506S(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTTCCAGGAACCCCTGTTTGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											214	208	210					3																	4856740		1935	4161	6096	4831740	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7660C>T	3.37:g.4856740C>T	ENSP00000401671:p.Pro2554Ser		4831740	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.922129	0.33908	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86;-4.86;-4.86;-4.86	4.59	4.59	0.56863	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.96275	0.8785	N	0.17312	0.475	0.80722	D	1	B;B;B	0.24963	0.115;0.019;0.003	B;B;B	0.41174	0.349;0.047;0.037	D	0.94254	0.7496	10	0.22109	T	0.4	.	17.415	0.87497	0.0:1.0:0.0:0.0	.	532;2569;2521	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	S	2569;2554;2554;2521;1015;2521;2506;532;2554	ENSP00000306253:P2554S;ENSP00000346595:P2554S;ENSP00000405934:P2521S;ENSP00000349597:P2521S;ENSP00000397885:P2506S;ENSP00000440564:P532S;ENSP00000401671:P2554S	ENSP00000306253:P2554S	P	+	1	0	ITPR1	4831740	1.000000	0.71417	0.935000	0.37517	0.648000	0.38561	6.027000	0.70881	2.100000	0.63781	0.467000	0.42956	CCC		0.478	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4856740	C	T	4856740	3	4	61	1	0	0	0	0	1	0	0	0	7941	507	18	3	7931	3	ITPR1	3	4856740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1906	4856740	193165690	2274	10259										
EDEM1	9695	broad.mit.edu	37	chr3	5246800	5246800	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggttggaaagcagagtgGcctgggtgccgggctggact	19	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:5246800G>A	ENST00000256497.4	+	6	1224	c.1091G>A	c.(1090-1092)gGc>gAc	p.G364D	EDEM1_ENST00000445686.1_Missense_Mutation_p.G169D	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	364					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)	p.G364D(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		AAGCAGAGTGGCCTGGGTGCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											100	108	105					3																	5246800		2203	4300	6503	5221800	SO:0001583	missense	9695			D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1091G>A	3.37:g.5246800G>A	ENSP00000256497:p.Gly364Asp		5221800	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	37	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	G	32	5.105056	0.94245	.	.	ENSG00000134109	ENST00000419550;ENST00000256497;ENST00000445686	T;T	0.73258	-0.73;-0.73	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.89763	0.6809	H	0.96460	3.825	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.994;0.999;0.993	D	0.92871	0.6314	10	0.87932	D	0	-28.8111	19.1187	0.93353	0.0:0.0:1.0:0.0	.	169;364;142	B4DXP3;Q92611;B4DPV5	.;EDEM1_HUMAN;.	D	142;364;169	ENSP00000256497:G364D;ENSP00000394099:G169D	ENSP00000256497:G364D	G	+	2	0	EDEM1	5221800	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.507000	0.97996	2.501000	0.84356	0.650000	0.86243	GGC		0.478	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		A	5246800	G	A	5246800	3	1	61	1	0	0	0	0	1	0	0	0	4922	1203	42	3	1113	3	EDEM1	3	5246800	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	390060	5246800	192775630	2275	10260										
EDEM1	9695	broad.mit.edu	37	chr3	5251868	5251868	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttctctctaggcaaccaaGaatcccttctacctccatgt	5	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:5251868G>T	ENST00000256497.4	+	9	1651	c.1518G>T	c.(1516-1518)aaG>aaT	p.K506N	EDEM1_ENST00000445686.1_Missense_Mutation_p.K311N	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	506					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)	p.K506N(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		AGGCAACCAAGAATCCCTTCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	122	127					3																	5251868		2203	4300	6503	5226868	SO:0001583	missense	9695			D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1518G>T	3.37:g.5251868G>T	ENSP00000256497:p.Lys506Asn		5226868	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	37	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610508	0.87258	.	.	ENSG00000134109	ENST00000256497;ENST00000445686	T;T	0.73047	-0.71;-0.71	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.79317	0.4425	M	0.68317	2.08	0.80722	D	1	D	0.56287	0.975	P	0.53722	0.733	T	0.79855	-0.1627	10	0.48119	T	0.1	-33.7722	19.1123	0.93321	0.0:0.0:1.0:0.0	.	506	Q92611	EDEM1_HUMAN	N	506;311	ENSP00000256497:K506N;ENSP00000394099:K311N	ENSP00000256497:K506N	K	+	3	2	EDEM1	5226868	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.006000	0.70724	2.516000	0.84829	0.655000	0.94253	AAG		0.468	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		T	5251868	G	T	5251868	3	4	61	1	0	0	0	0	1	0	0	0	4922	933	33	2	1552	2	EDEM1	3	5251868	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5068	5251868	192770562	2276	10261										
GRM7	2917	broad.mit.edu	37	chr3	6903441	6903441	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgaacagtcgcttactttCgtccaggcgctcatccagaa	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:6903441C>T	ENST00000357716.4	+	1	640	c.366C>T	c.(364-366)ttC>ttT	p.F122F	GRM7_ENST00000402647.2_Silent_p.F122F|GRM7_ENST00000486284.1_Silent_p.F122F|GRM7_ENST00000403881.1_Silent_p.F122F|GRM7_ENST00000389336.4_Silent_p.F122F	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	122					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.F122L(1)|p.F122F(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CGCTTACTTTCGTCCAGGCGC	0.592																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|large_intestine(1)	3											70	67	68					3																	6903441		2203	4300	6503	6878441	SO:0001819	synonymous_variant	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.366C>T	3.37:g.6903441C>T			6878441	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																				0.592	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	6903441	C	T	6903441	2	4	61	1	0	0	0	0	0	0	0	1	6823	883	31	1		1	GRM7	3	6903441	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1651573	6903441	191118989	2277	10262										
GRM7	2917	broad.mit.edu	37	chr3	7494314	7494314	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaggagagaattggaaaaGattccaactatgagcaggag	13	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:7494314G>T	ENST00000357716.4	+	6	1469	c.1195G>T	c.(1195-1197)Gat>Tat	p.D399Y	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000402647.2_Missense_Mutation_p.D399Y|GRM7_ENST00000486284.1_Missense_Mutation_p.D399Y|GRM7_ENST00000403881.1_Missense_Mutation_p.D399Y|GRM7_ENST00000389336.4_Missense_Mutation_p.D399Y	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	399					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.D399Y(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AATTGGAAAAGATTCCAACTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	102	106					3																	7494314		2203	4300	6503	7469314	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1195G>T	3.37:g.7494314G>T	ENSP00000350348:p.Asp399Tyr		7469314	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153259	0.78114	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492;ENST00000445087	D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.88	5.88	0.94601	Extracellular ligand-binding receptor (1);	0.049461	0.85682	D	0.000000	D	0.91546	0.7330	M	0.87269	2.87	0.58432	D	0.999997	D;D;P	0.69078	0.997;0.997;0.794	D;D;P	0.70487	0.948;0.969;0.577	D	0.88668	0.3193	10	0.16896	T	0.51	.	18.8061	0.92038	0.0:0.0:1.0:0.0	.	399;399;399	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	Y	399;399;399;399;399;399;399;56	ENSP00000350348:D399Y;ENSP00000417536:D399Y;ENSP00000373987:D399Y;ENSP00000385664:D399Y;ENSP00000384585:D399Y;ENSP00000395035:D56Y	ENSP00000350348:D399Y	D	+	1	0	GRM7	7469314	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.961000	0.87903	2.782000	0.95742	0.655000	0.94253	GAT		0.433	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7494314	G	T	7494314	3	4	61	1	0	0	0	0	1	0	0	0	6823	942	33	2	1217	2	GRM7	3	7494314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	590873	7494314	190528116	2278	10263										
GRM7	2917	broad.mit.edu	37	chr3	7494394	7494394	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcacgcccttcaccacatGaacaaggatctctgtgctga	8	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:7494394G>T	ENST00000357716.4	+	6	1549	c.1275G>T	c.(1273-1275)atG>atT	p.M425I	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000402647.2_Missense_Mutation_p.M425I|GRM7_ENST00000486284.1_Missense_Mutation_p.M425I|GRM7_ENST00000403881.1_Missense_Mutation_p.M425I|GRM7_ENST00000389336.4_Missense_Mutation_p.M425I	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	425					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.M425I(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TTCACCACATGAACAAGGATC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	88	94					3																	7494394		2203	4300	6503	7469394	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1275G>T	3.37:g.7494394G>T	ENSP00000350348:p.Met425Ile		7469394	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237716	0.79800	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492;ENST00000445087	D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	5.88	5.88	0.94601	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89143	0.6631	M	0.73372	2.23	0.80722	D	1	P;D;P;P	0.54964	0.656;0.969;0.925;0.69	P;D;D;B	0.70227	0.679;0.968;0.954;0.379	D	0.87634	0.2518	10	0.42905	T	0.14	.	18.8061	0.92038	0.0:0.0:1.0:0.0	.	425;180;425;425	Q14831-5;Q59G95;Q14831;Q14831-2	.;.;GRM7_HUMAN;.	I	425;425;425;425;425;425;425;82	ENSP00000350348:M425I;ENSP00000417536:M425I;ENSP00000373987:M425I;ENSP00000385664:M425I;ENSP00000384585:M425I;ENSP00000395035:M82I	ENSP00000350348:M425I	M	+	3	0	GRM7	7469394	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.876000	0.87215	2.782000	0.95742	0.655000	0.94253	ATG		0.478	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7494394	G	T	7494394	3	4	61	1	0	0	0	0	1	0	0	0	6823	1290	45	2	1297	2	GRM7	3	7494394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80	7494394	190528036	2279	10264										
OXTR	5021	broad.mit.edu	37	chr3	8809060	8809060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagtcatcttgaccgtgcGgatcttggccttggagatga	13	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:8809060G>A	ENST00000316793.3	-	3	1438	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	272					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)	p.R272C(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	TTGACCGTGCGGATCTTGGCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	3											40	34	36					3																	8809060		2203	4300	6503	8784060	SO:0001583	missense	5021				CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.814C>T	3.37:g.8809060G>A	ENSP00000324270:p.Arg272Cys		8784060	Q15071	Missense_Mutation	SNP	ENST00000316793.3	37	CCDS2570.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965737	0.74131	.	.	ENSG00000180914	ENST00000316793	T	0.45276	0.9	4.97	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.185322	0.46758	D	0.000272	T	0.71056	0.3295	M	0.93507	3.425	0.53005	D	0.999968	D	0.89917	1.0	D	0.91635	0.999	T	0.78119	-0.2328	10	0.87932	D	0	-35.1524	11.7867	0.52047	0.0:0.0:0.6812:0.3188	.	272	P30559	OXYR_HUMAN	C	272	ENSP00000324270:R272C	ENSP00000324270:R272C	R	-	1	0	OXTR	8784060	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.825000	0.62708	1.212000	0.43366	-0.310000	0.09108	CGC		0.662	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			A	8809060	G	A	8809060	3	1	61	1	0	0	0	0	1	0	0	0	11369	1116	39	1	363	1	OXTR	3	8809060	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1314666	8809060	189213370	2280	10265										
RAD18	56852	broad.mit.edu	37	chr3	8983425	8983425	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatactttgacagcaagattCtttgaagaggaagaagcagg	11	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:8983425C>A	ENST00000264926.2	-	5	446	c.330G>T	c.(328-330)aaG>aaT	p.K110N	RAD18_ENST00000495087.1_5'UTR	NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	110					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)	p.K110N(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		CAGCAAGATTCTTTGAAGAGG	0.408								Rad6 pathway																																								1	Substitution - Missense(1)	large_intestine(1)	3											108	111	110					3																	8983425		2203	4300	6503	8958425	SO:0001583	missense	56852				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.330G>T	3.37:g.8983425C>A	ENSP00000264926:p.Lys110Asn		8958425	Q58F55|Q9NRT6	Missense_Mutation	SNP	ENST00000264926.2	37	CCDS2571.1	.	.	.	.	.	.	.	.	.	.	C	9.572	1.121191	0.20877	.	.	ENSG00000070950	ENST00000264926	T	0.25579	1.79	4.86	3.09	0.35607	.	0.072270	0.52532	D	0.000070	T	0.30103	0.0754	M	0.63428	1.95	0.28598	N	0.909302	D	0.54047	0.964	P	0.50136	0.632	T	0.10894	-1.0610	10	0.25751	T	0.34	-19.1887	7.3758	0.26827	0.0:0.805:0.0:0.195	.	110	Q9NS91	RAD18_HUMAN	N	110	ENSP00000264926:K110N	ENSP00000264926:K110N	K	-	3	2	RAD18	8958425	0.180000	0.23148	0.838000	0.33150	0.085000	0.17905	-0.005000	0.12855	0.654000	0.30846	-0.140000	0.14226	AAG		0.408	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165		A	8983425	C	A	8983425	3	1	61	1	0	0	0	0	1	0	0	0	13017	912	32	2	1193	2	RAD18	3	8983425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174365	8983425	189039005	2281	10266										
SRGAP3	9901	broad.mit.edu	37	chr3	9034706	9034706	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctggcctcgctgtcagcCttctggctcaggctgtcgga	13	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9034706C>A	ENST00000383836.3	-	20	2869	c.2442G>T	c.(2440-2442)aaG>aaT	p.K814N	SRGAP3_ENST00000360413.3_Missense_Mutation_p.K790N	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	814					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.K814N(1)	SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CGCTGTCAGCCTTCTGGCTCA	0.572			T	RAF1	pilocytic astrocytoma																																		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	1	Substitution - Missense(1)	large_intestine(1)	3											70	60	64					3																	9034706		2203	4300	6503	9009706	SO:0001583	missense	9901			AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2442G>T	3.37:g.9034706C>A	ENSP00000373347:p.Lys814Asn		9009706	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270334	0.59540	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.28454	1.61;2.03	5.41	4.53	0.55603	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	L	0.57536	1.79	0.58432	D	0.999995	D;D	0.61080	0.989;0.981	D;D	0.72625	0.978;0.95	T	0.39921	-0.9590	10	0.44086	T	0.13	.	10.0032	0.41942	0.0:0.8439:0.0:0.1561	.	790;814	O43295-2;O43295	.;SRGP2_HUMAN	N	814;790	ENSP00000373347:K814N;ENSP00000353587:K790N	ENSP00000353587:K790N	K	-	3	2	SRGAP3	9009706	0.998000	0.40836	0.999000	0.59377	0.998000	0.95712	0.606000	0.24194	1.268000	0.44264	0.591000	0.81541	AAG		0.572	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			A	9034706	C	A	9034706	3	1	61	1	0	0	0	0	1	0	0	0	15186	680	24	2	869	2	SRGAP3	3	9034706	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51281	9034706	188987724	2282	10267										
SRGAP3	9901	broad.mit.edu	37	chr3	9055525	9055525	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcggctgggttctccagTtctgtaacataaaggggcct	11	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9055525T>C	ENST00000383836.3	-	16	2242	c.1815A>G	c.(1813-1815)aaA>aaG	p.K605K	SRGAP3_ENST00000360413.3_Splice_Site_p.K581K|SRGAP3_ENST00000433332.3_5'Flank|SRGAP3-AS1_ENST00000414633.1_RNA	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	605	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.K605K(1)	SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GGTTCTCCAGTTCTGTAACAT	0.522			T	RAF1	pilocytic astrocytoma																																		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	1	Substitution - coding silent(1)	large_intestine(1)	3											103	99	100					3																	9055525		2203	4300	6503	9030525	SO:0001630	splice_region_variant	9901			AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.1814-1A>G	3.37:g.9055525T>C			9030525	Q8IX13|Q8IZV8	Silent	SNP	ENST00000383836.3	37	CCDS2572.1																																																																																				0.522	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		Silent	C	9055525	T	C	9055525	5	2	61	1	0	0	0	0	0	0	1	0	15186	1739	60	4	1512	4	SRGAP3	3	9055525	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20819	9055525	188966905	2283	10268										
THUMPD3	25917	broad.mit.edu	37	chr3	9412979	9412979	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatatcttagattattatgAaaatccagccatcaaagagg	6	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9412979A>C	ENST00000345094.3	+	4	900	c.566A>C	c.(565-567)gAa>gCa	p.E189A	THUMPD3_ENST00000452837.2_Missense_Mutation_p.E189A|THUMPD3_ENST00000515662.2_Missense_Mutation_p.E189A|SETD5-AS1_ENST00000468186.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	189	THUMP. {ECO:0000255|PROSITE- ProRule:PRU00529}.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.E189A(1)		NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		GATTATTATGAAAATCCAGCC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	73	71					3																	9412979		2203	4300	6503	9387979	SO:0001583	missense	25917			AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.566A>C	3.37:g.9412979A>C	ENSP00000339532:p.Glu189Ala		9387979	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	37	CCDS2573.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	16.18|16.18|16.18	3.051531|3.051531|3.051531	0.55218|0.55218|0.55218	.|.|.	.|.|.	ENSG00000134077|ENSG00000134077|ENSG00000134077	ENST00000452837;ENST00000345094;ENST00000515662|ENST00000441127|ENST00000416603	T;T;T|.|.	0.50001|.|.	0.76;0.76;0.76|.|.	5.94|5.94|5.94	5.94|5.94|5.94	0.96194|0.96194|0.96194	THUMP (2);|.|.	0.407546|.|.	0.30519|.|.	N|.|.	0.009454|.|.	T|T|.	0.71542|0.71542|.	0.3352|0.3352|.	M|M|M	0.62723|0.62723|0.62723	1.935|1.935|1.935	0.48511|0.48511|0.48511	D|D|D	0.99966|0.99966|0.99966	B|.|.	0.15473|.|.	0.013|.|.	B|.|.	0.12156|.|.	0.007|.|.	T|T|.	0.70281|0.70281|.	-0.4915|-0.4915|.	10|5|.	0.27785|.|.	T|.|.	0.31|.|.	-14.8037|-14.8037|-14.8037	15.3805|15.3805|15.3805	0.74651|0.74651|0.74651	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	189|.|.	Q9BV44|.|.	THUM3_HUMAN|.|.	A|Q|C	189|46|21	ENSP00000395893:E189A;ENSP00000339532:E189A;ENSP00000424064:E189A|.|.	ENSP00000339532:E189A|.|.	E|K|X	+|+|+	2|1|3	0|0|0	THUMPD3|THUMPD3|THUMPD3	9387979|9387979|9387979	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	4.241000|4.241000|4.241000	0.58707|0.58707|0.58707	2.279000|2.279000|2.279000	0.76181|0.76181|0.76181	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	GAA|AAA|TGA		0.338	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453		C	9412979	A	C	9412979	3	2	61	1	0	0	0	0	1	0	0	0	15923	246	9	4	576	4	THUMPD3	3	9412979	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	357454	9412979	188609451	2284	10269										
SETD5	55209	broad.mit.edu	37	chr3	9482366	9482366	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctgtaataacacagttaTtggttcccaaatgcaggtaa	9	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9482366T>G	ENST00000406341.1	+	7	984	c.794T>G	c.(793-795)aTt>aGt	p.I265S	SETD5_ENST00000402466.1_Missense_Mutation_p.I167S|SETD5_ENST00000302463.6_Missense_Mutation_p.I167S|SETD5_ENST00000402198.1_Missense_Mutation_p.I265S|SETD5_ENST00000407969.1_Missense_Mutation_p.I284S			Q9C0A6	SETD5_HUMAN	SET domain containing 5	265								p.I167S(1)|p.I265S(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		AACACAGTTATTGGTTCCCAA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	3											57	53	54					3																	9482366		1842	4102	5944	9457366	SO:0001583	missense	55209			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.794T>G	3.37:g.9482366T>G	ENSP00000383939:p.Ile265Ser		9457366	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	t	24.0	4.477728	0.84640	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000442373;ENST00000302463	T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;0.72;-1.39	5.36	5.36	0.76844	.	0.146153	0.48767	D	0.000169	T	0.70474	0.3228	N	0.08118	0	0.42575	D	0.99319	P;P;B	0.51791	0.948;0.791;0.049	P;B;B	0.47528	0.549;0.198;0.032	T	0.75510	-0.3292	10	0.42905	T	0.14	-14.8735	15.6572	0.77150	0.0:0.0:0.0:1.0	.	167;265;284	Q9C0A6-3;Q9C0A6;E7EWN3	.;SETD5_HUMAN;.	S	265;167;265;284;154;167	ENSP00000385852:I265S;ENSP00000384429:I167S;ENSP00000383939:I265S;ENSP00000384114:I284S;ENSP00000408837:I154S;ENSP00000302028:I167S	ENSP00000302028:I167S	I	+	2	0	SETD5	9457366	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.652000	0.83633	2.176000	0.68965	0.529000	0.55759	ATT		0.398	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9482366	T	G	9482366	3	3	61	1	0	0	0	0	1	0	0	0	14171	1493	52	4	816	4	SETD5	3	9482366	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	69387	9482366	188540064	2285	10270										
SETD5	55209	broad.mit.edu	37	chr3	9495466	9495466	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagggatgactcaaacatCatctgtaccccaagagacta	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9495466C>A	ENST00000406341.1	+	16	2580	c.2390C>A	c.(2389-2391)tCa>tAa	p.S797*	SETD5_ENST00000402466.1_Nonsense_Mutation_p.S699*|SETD5_ENST00000302463.6_Nonsense_Mutation_p.S699*|SETD5_ENST00000402198.1_Nonsense_Mutation_p.S797*|SETD5_ENST00000488236.1_3'UTR|SETD5_ENST00000407969.1_Nonsense_Mutation_p.S816*			Q9C0A6	SETD5_HUMAN	SET domain containing 5	797								p.S699*(1)|p.S797*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		ACTCAAACATCATCTGTACCC	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											126	121	123					3																	9495466		1869	4101	5970	9470466	SO:0001587	stop_gained	55209			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.2390C>A	3.37:g.9495466C>A	ENSP00000383939:p.Ser797*		9470466	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Nonsense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	C	46	12.789027	0.99696	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	.	.	.	5.52	5.52	0.82312	.	0.187589	0.37955	N	0.001866	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-1.3196	19.8024	0.96513	0.0:1.0:0.0:0.0	.	.	.	.	X	797;699;797;816;699	.	ENSP00000302028:S699X	S	+	2	0	SETD5	9470466	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.094000	0.57721	2.752000	0.94435	0.655000	0.94253	TCA		0.363	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		A	9495466	C	A	9495466	4	1	61	1	0	0	0	0	0	1	0	0	14171	838	29	2	2448	2	SETD5	3	9495466	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13100	9495466	188526964	2286	10271										
SETD5	55209	broad.mit.edu	37	chr3	9515110	9515110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcttcccctcacaaaaAattctccccatctcattcct	0	18	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9515110A>C	ENST00000406341.1	+	19	3576	c.3386A>C	c.(3385-3387)aAa>aCa	p.K1129T	SETD5_ENST00000402466.1_Missense_Mutation_p.K1031T|SETD5_ENST00000302463.6_Missense_Mutation_p.K1031T|SETD5_ENST00000402198.1_Missense_Mutation_p.K1129T|SETD5_ENST00000407969.1_Missense_Mutation_p.K1148T			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1129	Ser-rich.							p.K1129T(1)|p.K1031T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CCTCACAAAAAATTCTCCCCA	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	3											86	86	86					3																	9515110		1936	4152	6088	9490110	SO:0001583	missense	55209			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.3386A>C	3.37:g.9515110A>C	ENSP00000383939:p.Lys1129Thr		9490110	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.251|8.251	0.808975|0.808975	0.16537|0.16537	.|.	.|.	ENSG00000168137|ENSG00000168137	ENST00000399686|ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	T|D;D;D;D;D	0.44083|0.91631	0.93|-2.56;-2.88;-2.56;-2.55;-2.88	6.07|6.07	4.94|4.94	0.65067|0.65067	.|.	0.329145|0.329145	0.34879|0.34879	N|N	0.003619|0.003619	T|T	0.78432|0.78432	0.4282|0.4282	N|N	0.08118|0.08118	0|0	0.29938|0.29938	N|N	0.821301|0.821301	.|B;B;B	.|0.30236	.|0.274;0.137;0.035	.|B;B;B	.|0.30179	.|0.112;0.085;0.027	T|T	0.69243|0.69243	-0.5196|-0.5196	8|10	0.20046|0.14656	T|T	0.44|0.56	-17.7231|-17.7231	3.4814|3.4814	0.07603|0.07603	0.6953:0.0:0.3047:0.0|0.6953:0.0:0.3047:0.0	.|.	.|798;1031;1129	.|B3KXG4;Q9C0A6-3;Q9C0A6	.|.;.;SETD5_HUMAN	N|T	796|1129;1031;1129;1148;1031	ENSP00000382593:K796N|ENSP00000385852:K1129T;ENSP00000384429:K1031T;ENSP00000383939:K1129T;ENSP00000384114:K1148T;ENSP00000302028:K1031T	ENSP00000382593:K796N|ENSP00000302028:K1031T	K|K	+|+	3|2	2|0	SETD5|SETD5	9490110|9490110	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.995000|0.995000	0.86356|0.86356	4.357000|4.357000	0.59436|0.59436	2.330000|2.330000	0.79161|0.79161	0.477000|0.477000	0.44152|0.44152	AAA|AAA		0.527	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		C	9515110	A	C	9515110	3	2	61	1	0	0	0	0	1	0	0	0	14171	14	1	4	3456	4	SETD5	3	9515110	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	19644	9515110	188507320	2287	10272										
CPNE9	151835	broad.mit.edu	37	chr3	9754459	9754459	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctggacaagaaggacttCtttgggaaatcagacccctt	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9754459C>A	ENST00000383832.3	+	9	682	c.492C>A	c.(490-492)ttC>ttA	p.F164L	CPNE9_ENST00000383831.3_Missense_Mutation_p.F164L	NM_153635.2	NP_705899.2	Q8IYJ1	CPNE9_HUMAN	copine family member IX	164	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.F164L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16	Medulloblastoma(99;0.227)					AGAAGGACTTCTTTGGGAAAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											125	137	133					3																	9754459		2183	4300	6483	9729459	SO:0001583	missense	151835				CCDS2574.2	3p25.3	2008-10-30			ENSG00000144550	ENSG00000144550			24336	protein-coding gene	gene with protein product						9430674	Standard	XM_006712990		Approved	KIAA4217	uc003bsd.3	Q8IYJ1	OTTHUMG00000128418	ENST00000383832.3:c.492C>A	3.37:g.9754459C>A	ENSP00000373343:p.Phe164Leu		9729459	A1L430|A6NDX6|A8MSP8	Missense_Mutation	SNP	ENST00000383832.3	37	CCDS2574.2	.	.	.	.	.	.	.	.	.	.	C	14.32	2.499418	0.44455	.	.	ENSG00000144550	ENST00000383832;ENST00000383831	T;T	0.67865	-0.29;-0.29	5.15	5.15	0.70609	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	N	0.10809	0.05	0.58432	D	0.999999	B	0.11235	0.004	B	0.23150	0.044	T	0.44221	-0.9342	10	0.12103	T	0.63	.	18.2451	0.89982	0.0:1.0:0.0:0.0	.	164	Q8IYJ1	CPNE9_HUMAN	L	164	ENSP00000373343:F164L;ENSP00000373342:F164L	ENSP00000373342:F164L	F	+	3	2	CPNE9	9729459	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.203000	0.42752	2.417000	0.82017	0.655000	0.94253	TTC		0.537	CPNE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250205.4	NM_001033755		A	9754459	C	A	9754459	3	1	61	1	0	0	0	0	1	0	0	0	3825	912	32	2	522	2	CPNE9	3	9754459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	239349	9754459	188267971	2288	10273										
BRPF1	7862	broad.mit.edu	37	chr3	9784841	9784841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctgtgctccgccaggccCggcgccaggcagaaaaaatg	14	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9784841C>T	ENST00000457855.1	+	6	2208	c.2197C>T	c.(2197-2199)Cgg>Tgg	p.R733W	BRPF1_ENST00000302054.3_Missense_Mutation_p.R733W|BRPF1_ENST00000433861.2_Missense_Mutation_p.R733W|BRPF1_ENST00000383829.2_Missense_Mutation_p.R739W|BRPF1_ENST00000424362.1_Missense_Mutation_p.R733W			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	733	Interaction with MEAF6 and ING5.|Required for RUNX1 and RUNX2 transcriptional activation.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R739W(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					CCGCCAGGCCCGGCGCCAGGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	57	60					3																	9784841		2203	4300	6503	9759841	SO:0001583	missense	7862			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.2197C>T	3.37:g.9784841C>T	ENSP00000410210:p.Arg733Trp		9759841	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	37	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.530456	0.64860	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.19938	2.13;2.11;3.5;2.11;2.11	6.07	4.22	0.49857	Bromodomain (3);	0.053785	0.64402	D	0.000001	T	0.48095	0.1481	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.992;0.997;0.986;0.969	T	0.52465	-0.8572	10	0.87932	D	0	.	13.3594	0.60646	0.1263:0.7524:0.1213:0.0	.	733;733;739;733	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	W	733;733;739;733;733	ENSP00000402485:R733W;ENSP00000398863:R733W;ENSP00000373340:R739W;ENSP00000306297:R733W;ENSP00000410210:R733W	ENSP00000306297:R733W	R	+	1	2	BRPF1	9759841	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.889000	0.63171	0.842000	0.35045	0.655000	0.94253	CGG		0.592	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		T	9784841	C	T	9784841	3	4	61	1	0	0	0	0	1	0	0	0	1523	643	23	1	2237	1	BRPF1	3	9784841	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30382	9784841	188237589	2289	10274										
OGG1	4968	broad.mit.edu	37	chr3	9793482	9793482	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgcgacaagaccccatCgaatgccttttctcttttat	6	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9793482C>T	ENST00000344629.7	+	3	757	c.414C>T	c.(412-414)atC>atT	p.I138I	OGG1_ENST00000302008.8_Silent_p.I138I|OGG1_ENST00000302003.7_Silent_p.I138I|OGG1_ENST00000449570.2_Silent_p.I138I|OGG1_ENST00000383826.5_Silent_p.I138I|OGG1_ENST00000302036.7_Silent_p.I138I|OGG1_ENST00000339511.5_Silent_p.I138I|OGG1_ENST00000349503.5_Silent_p.I138I			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	138					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)	p.I138I(1)		kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					AAGACCCCATCGAATGCCTTT	0.572								Base excision repair (BER), DNA glycosylases																																								1	Substitution - coding silent(1)	large_intestine(1)	3											218	201	207					3																	9793482		2203	4300	6503	9768482	SO:0001819	synonymous_variant	4968			U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h"	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.414C>T	3.37:g.9793482C>T			9768482	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Silent	SNP	ENST00000344629.7	37	CCDS2581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.127|8.127	0.782121|0.782121	0.16189|0.16189	.|.	.|.	ENSG00000114026|ENSG00000114026	ENST00000352937|ENST00000441094;ENST00000426518	.|.	.|.	.|.	5.26|5.26	-4.76|-4.76	0.03229|0.03229	.|.	.|.	.|.	.|.	.|.	.|T	.|0.39600	.|0.1084	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.36939	.|-0.9727	.|4	.|.	.|.	.|.	-2.6952|-2.6952	3.6214|3.6214	0.08097|0.08097	0.0784:0.2606:0.2438:0.4172|0.0784:0.2606:0.2438:0.4172	.|.	.|.	.|.	.|.	X|L	44|36;48	.|.	.|.	R|S	+|+	1|2	2|0	OGG1|OGG1	9768482|9768482	0.000000|0.000000	0.05858|0.05858	0.044000|0.044000	0.18714|0.18714	0.871000|0.871000	0.50021|0.50021	-3.799000|-3.799000	0.00363|0.00363	-0.857000|-0.857000	0.04115|0.04115	-0.471000|-0.471000	0.05019|0.05019	CGA|TCG		0.572	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		T	9793482	C	T	9793482	2	4	61	1	0	0	0	0	0	0	0	1	10876	874	31	1		1	OGG1	3	9793482	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8641	9793482	188228948	2290	10275										
CAMK1	8536	broad.mit.edu	37	chr3	9801429	9801429	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaagtgccggatgaaatCtttggctaaacccccaagac	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9801429C>A	ENST00000256460.3	-	9	928	c.751G>T	c.(751-753)Gat>Tat	p.D251Y	OGG1_ENST00000302008.8_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.D251Y(1)		endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		CGGATGAAATCTTTGGCTAAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											122	121	122					3																	9801429		2203	4300	6503	9776429	SO:0001583	missense	8536			L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.751G>T	3.37:g.9801429C>A	ENSP00000256460:p.Asp251Tyr		9776429	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	37	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.7|25.7	4.660910|4.660910	0.88154|0.88154	.|.	.|.	ENSG00000134072|ENSG00000134072	ENST00000256460|ENST00000421120	T|.	0.50548|.	0.74|.	5.71|5.71	5.71|5.71	0.89125|0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87653|0.87653	0.6231|0.6231	H|H	0.94306|0.94306	3.52|3.52	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.74674|.	0.984;0.984|.	D|D	0.90470|0.90470	0.4452|0.4452	10|5	0.87932|.	D|.	0|.	-17.3687|-17.3687	19.4609|19.4609	0.94916|0.94916	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	251;251|.	Q14012;B0YIY3|.	KCC1A_HUMAN;.|.	Y|I	251|97	ENSP00000256460:D251Y|.	ENSP00000256460:D251Y|.	D|R	-|-	1|2	0|0	CAMK1|CAMK1	9776429|9776429	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.701000|7.701000	0.84566|0.84566	2.688000|2.688000	0.91661|0.91661	0.655000|0.655000	0.94253|0.94253	GAT|AGA		0.512	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		A	9801429	C	A	9801429	3	1	61	1	0	0	0	0	1	0	0	0	2602	913	32	2	377	2	CAMK1	3	9801429	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7947	9801429	188221001	2291	10276										
CAMK1	8536	broad.mit.edu	37	chr3	9803436	9803436	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctgtagtacagcagattCtctggcttgaagggcaggag	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9803436C>A	ENST00000256460.3	-	6	612	c.435G>T	c.(433-435)gaG>gaT	p.E145D	OGG1_ENST00000302008.8_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	145	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.E145D(1)		endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		ACAGCAGATTCTCTGGCTTGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											57	57	57					3																	9803436		2203	4300	6503	9778436	SO:0001583	missense	8536			L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.435G>T	3.37:g.9803436C>A	ENSP00000256460:p.Glu145Asp		9778436	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	37	CCDS2582.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244479	0.79912	.	.	ENSG00000134072	ENST00000256460;ENST00000411972	T;T	0.69040	0.92;-0.37	4.58	3.68	0.42216	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75309	0.3832	L	0.49778	1.585	0.80722	D	1	P	0.48589	0.912	D	0.65323	0.934	T	0.78137	-0.2321	10	0.87932	D	0	-27.6926	13.4815	0.61338	0.0:0.9194:0.0:0.0806	.	145	Q14012	KCC1A_HUMAN	D	145;101	ENSP00000256460:E145D;ENSP00000404587:E101D	ENSP00000256460:E145D	E	-	3	2	CAMK1	9778436	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.604000	0.46274	2.255000	0.74692	0.655000	0.94253	GAG		0.532	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		A	9803436	C	A	9803436	3	1	61	1	0	0	0	0	1	0	0	0	2602	912	32	2	705	2	CAMK1	3	9803436	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2007	9803436	188218994	2292	10277										
TADA3	10474	broad.mit.edu	37	chr3	9828898	9828898	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacctttagtgtccagttCggtcagtggccccatgaggc	11	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9828898C>A	ENST00000301964.2	-	5	1249	c.691G>T	c.(691-693)Gaa>Taa	p.E231*	TADA3_ENST00000492635.1_5'Flank|TADA3_ENST00000343450.2_Nonsense_Mutation_p.E231*|TADA3_ENST00000440161.1_Nonsense_Mutation_p.E231*	NM_006354.2	NP_006345.1	O75528	TADA3_HUMAN	transcriptional adaptor 3	231					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|intracellular estrogen receptor signaling pathway (GO:0030520)|mitotic nuclear division (GO:0007067)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of histone deacetylation (GO:0031063)|regulation of protein phosphorylation (GO:0001932)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of tubulin deacetylation (GO:0090043)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|intracellular (GO:0005622)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.E231*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16						GTGTCCAGTTCGGTCAGTGGC	0.632											OREG0015382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	3											106	113	111					3																	9828898		2203	4300	6503	9803898	SO:0001587	stop_gained	10474			AF069733	CCDS2583.1, CCDS2584.1	3p25.3	2010-08-13	2009-10-02	2009-10-02	ENSG00000171148	ENSG00000171148			19422	protein-coding gene	gene with protein product		602945	"transcriptional adaptor 3 (NGG1 homolog, yeast)-like"	TADA3L		9674425, 11707411	Standard	NM_006354		Approved	FLJ20221, FLJ21329, ADA3, hADA3, NGG1	uc010hcn.2	O75528	OTTHUMG00000128440	ENST00000301964.2:c.691G>T	3.37:g.9828898C>A	ENSP00000307684:p.Glu231*	659	9803898	Q6FI83|Q9UFS2	Nonsense_Mutation	SNP	ENST00000301964.2	37	CCDS2583.1	.	.	.	.	.	.	.	.	.	.	C	40	8.429532	0.98808	.	.	ENSG00000171148	ENST00000301964;ENST00000440161;ENST00000343450	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-32.1564	19.557	0.95354	0.0:1.0:0.0:0.0	.	.	.	.	X	231	.	ENSP00000307684:E231X	E	-	1	0	TADA3	9803898	1.000000	0.71417	0.998000	0.56505	0.369000	0.29798	7.267000	0.78462	2.630000	0.89119	0.655000	0.94253	GAA		0.632	TADA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250236.1			A	9828898	C	A	9828898	4	1	61	1	0	0	0	0	0	1	0	0	15551	893	31	2	631	2	TADA3	3	9828898	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25462	9828898	188193532	2293	10278										
PRRT3	285368	broad.mit.edu	37	chr3	9990983	9990983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaggcttctggccaatgCcaagtctggctgggcccctg	14	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:9990983C>T	ENST00000412055.1	-	2	946	c.817G>A	c.(817-819)Gca>Aca	p.A273T	PRRT3-AS1_ENST00000431558.1_RNA|PRRT3_ENST00000411976.2_Missense_Mutation_p.A273T	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	273	Pro-rich.					integral component of membrane (GO:0016021)		p.A273T(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CTGGCCAATGCCAAGTCTGGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	3											42	48	46					3																	9990983		2048	4198	6246	9965983	SO:0001583	missense	285368			AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.817G>A	3.37:g.9990983C>T	ENSP00000392511:p.Ala273Thr		9965983	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	C	7.261	0.605162	0.14002	.	.	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.25085	2.17;1.82	3.73	1.92	0.25849	.	0.307062	0.23700	N	0.045429	T	0.13970	0.0338	L	0.36672	1.1	0.25676	N	0.985849	P;B	0.35107	0.484;0.077	B;B	0.26770	0.073;0.021	T	0.13683	-1.0500	9	.	.	.	-5.2104	5.3032	0.15790	0.0:0.6786:0.2079:0.1135	.	273;273	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	T	273	ENSP00000392511:A273T;ENSP00000404512:A273T	.	A	-	1	0	PRRT3	9965983	0.009000	0.17119	0.698000	0.30274	0.046000	0.14306	0.525000	0.22956	0.553000	0.29044	-0.172000	0.13284	GCA		0.642	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		T	9990983	C	T	9990983	3	4	61	1	0	0	0	0	1	0	0	0	12645	739	26	3	2140	3	PRRT3	3	9990983	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162085	9990983	188031447	2294	10279										
FANCD2	2177	broad.mit.edu	37	chr3	10094090	10094090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcattttagattatctggAtaacatatcccctcagcaaa	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10094090A>G	ENST00000419585.1	+	18	1726	c.1565A>G	c.(1564-1566)gAt>gGt	p.D522G	FANCD2_ENST00000287647.3_Missense_Mutation_p.D522G|FANCD2_ENST00000383807.1_Missense_Mutation_p.D522G|FANCD2_ENST00000383806.1_Missense_Mutation_p.D522G			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	522					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.D522G(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GATTATCTGGATAACATATCC	0.388			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	1	Substitution - Missense(1)	large_intestine(1)	3											71	69	70					3																	10094090		2203	4300	6503	10069090	SO:0001583	missense	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1565A>G	3.37:g.10094090A>G	ENSP00000398754:p.Asp522Gly		10069090	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527288	0.85706	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.55	5.55	0.83447	.	0.284218	0.37483	N	0.002077	T	0.61048	0.2316	M	0.68952	2.095	0.42947	D	0.994367	D;D	0.57571	0.98;0.98	P;P	0.57324	0.818;0.818	T	0.62525	-0.6836	10	0.42905	T	0.14	.	13.791	0.63140	1.0:0.0:0.0:0.0	.	522;522	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	G	522	ENSP00000287647:D522G;ENSP00000373318:D522G;ENSP00000373317:D522G;ENSP00000398754:D522G	ENSP00000287647:D522G	D	+	2	0	FANCD2	10069090	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.043000	0.89432	2.148000	0.66965	0.524000	0.50904	GAT		0.388	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			G	10094090	A	G	10094090	3	3	61	1	0	0	0	0	1	0	0	0	5684	333	12	4	1631	4	FANCD2	3	10094090	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	103107	10094090	187928340	2295	10280										
FANCD2	2177	broad.mit.edu	37	chr3	10115024	10115024	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgtgaccctacgccatCtcatagaggccagctaaaca	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10115024C>A	ENST00000419585.1	+	28	2854	c.2693C>A	c.(2692-2694)tCt>tAt	p.S898Y	FANCD2_ENST00000287647.3_Missense_Mutation_p.S898Y|FANCD2_ENST00000383807.1_Missense_Mutation_p.S898Y|FANCD2_ENST00000383806.1_Missense_Mutation_p.S898Y			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	898					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.S898Y(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCTACGCCATCTCATAGAGGC	0.408			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	1	Substitution - Missense(1)	large_intestine(1)	3											126	133	130					3																	10115024		2203	4300	6503	10090024	SO:0001583	missense	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2693C>A	3.37:g.10115024C>A	ENSP00000398754:p.Ser898Tyr		10090024	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.173362	0.38413	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.83	4.06	0.47325	.	0.862673	0.10622	N	0.653206	T	0.56171	0.1967	L	0.51422	1.61	0.09310	N	1	D;D	0.61080	0.979;0.989	P;P	0.56823	0.807;0.807	T	0.42172	-0.9467	10	0.59425	D	0.04	.	9.1004	0.36664	0.0:0.8328:0.0:0.1672	.	898;898	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	Y	898	ENSP00000287647:S898Y;ENSP00000373318:S898Y;ENSP00000373317:S898Y;ENSP00000398754:S898Y	ENSP00000287647:S898Y	S	+	2	0	FANCD2	10090024	0.003000	0.15002	0.005000	0.12908	0.260000	0.26232	1.014000	0.29950	0.840000	0.34995	-0.143000	0.13931	TCT		0.408	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10115024	C	A	10115024	3	1	61	1	0	0	0	0	1	0	0	0	5684	913	32	2	2799	2	FANCD2	3	10115024	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20934	10115024	187907406	2296	10281										
FANCD2	2177	broad.mit.edu	37	chr3	10122847	10122847	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctgcccaagaaattgttCattgtgtttttcaactgctg	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10122847C>A	ENST00000419585.1	+	31	3201	c.3040C>A	c.(3040-3042)Cat>Aat	p.H1014N	FANCD2OS_ENST00000436517.1_5'Flank|FANCD2_ENST00000287647.3_Missense_Mutation_p.H1014N|FANCD2_ENST00000383807.1_Missense_Mutation_p.H1014N|FANCD2_ENST00000383806.1_Missense_Mutation_p.H1014N			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1014					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.H1014N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		AGAAATTGTTCATTGTGTTTT	0.398			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	1	Substitution - Missense(1)	large_intestine(1)	3											122	127	125					3																	10122847		2203	4300	6503	10097847	SO:0001583	missense	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.3040C>A	3.37:g.10122847C>A	ENSP00000398754:p.His1014Asn		10097847	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	C	1.958	-0.439486	0.04636	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.94	3.17	0.36434	.	0.940887	0.09190	N	0.836156	T	0.39809	0.1092	L	0.51422	1.61	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.004	T	0.33523	-0.9865	10	0.17369	T	0.5	.	8.0253	0.30434	0.1358:0.7513:0.0:0.1128	.	1014;1014	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	N	1014	ENSP00000287647:H1014N;ENSP00000373318:H1014N;ENSP00000373317:H1014N;ENSP00000398754:H1014N	ENSP00000287647:H1014N	H	+	1	0	FANCD2	10097847	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	-0.587000	0.05780	0.412000	0.25729	0.650000	0.86243	CAT		0.398	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10122847	C	A	10122847	3	1	61	1	0	0	0	0	1	0	0	0	5684	826	29	2	3158	2	FANCD2	3	10122847	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7823	10122847	187899583	2297	10282										
VHL	7428	broad.mit.edu	37	chr3	10191563	10191563	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcgtcaggtcgctctacGaagatctggaagaccaccca	9	13	3	2	rs367545984		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10191563G>A	ENST00000256474.2	+	3	1396	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	VHL_ENST00000345392.2_Missense_Mutation_p.E145K|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	186			E -> K (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911}.|Missing (in VHLD). {ECO:0000269|PubMed:8730290}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.E186*(3)|p.Y185_D187>*(1)|p.Y185fs*14(1)|p.E186fs*14(1)|p.Y185fs*11(1)|p.E186K(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTCGCTCTACGAAGATCTGGA	0.512		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	8	Substitution - Nonsense(3)|Deletion - Frameshift(3)|Complex - deletion inframe(1)|Substitution - Missense(1)	kidney(7)|large_intestine(1)	3	GRCh37	CM951297|CM951298	VHL	M		G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	78	71	73		556,433	5	1	3		73	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	VHL	NM_000551.3,NM_198156.2	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	186/214,145/173	10191563	1,13005	2203	4300	6503	10166563	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.556G>A	3.37:g.10191563G>A	ENSP00000256474:p.Glu186Lys		10166563	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.753977	0.89843	0.0	1.16E-4	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99820	-6.93;-6.93	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	L	0.51422	1.61	0.49582	D	0.999806	D;D	0.76494	0.999;0.992	D;P	0.64042	0.921;0.691	D	0.97461	1.0034	10	0.49607	T	0.09	-10.1279	16.1249	0.81386	0.0:0.0:1.0:0.0	.	145;186	P40337-2;P40337	.;VHL_HUMAN	K	186;145;104	ENSP00000256474:E186K;ENSP00000344757:E145K	ENSP00000256474:E186K	E	+	1	0	VHL	10166563	1.000000	0.71417	0.978000	0.43139	0.578000	0.36192	7.062000	0.76706	2.735000	0.93741	0.655000	0.94253	GAA		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10191563	G	A	10191563	3	1	61	1	0	0	0	0	1	0	0	0	17202	1059	37	1	566	1	VHL	3	10191563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68716	10191563	187830867	2298	10283										
TATDN2	9797	broad.mit.edu	37	chr3	10302249	10302249	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagttatagaccctcaagaGaaacccagtgaggagcccct	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10302249G>T	ENST00000287652.4	+	3	1894	c.843G>T	c.(841-843)gaG>gaT	p.E281D	TATDN2_ENST00000448281.2_Missense_Mutation_p.E281D|RP11-438J1.1_ENST00000450534.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	281					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.E281D(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						ACCCTCAAGAGAAACCCAGTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											75	79	77					3																	10302249		2203	4300	6503	10277249	SO:0001583	missense	9797			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.843G>T	3.37:g.10302249G>T	ENSP00000287652:p.Glu281Asp		10277249	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.036821	0.35893	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.24538	1.85;1.85	5.11	1.68	0.24146	.	0.000000	0.36519	N	0.002548	T	0.16471	0.0396	L	0.50333	1.59	0.09310	N	1	P	0.38922	0.651	B	0.35859	0.212	T	0.09058	-1.0692	10	0.31617	T	0.26	-2.5039	1.9117	0.03288	0.1345:0.1884:0.4831:0.194	.	281	Q93075	TATD2_HUMAN	D	281	ENSP00000287652:E281D;ENSP00000408736:E281D	ENSP00000287652:E281D	E	+	3	2	TATDN2	10277249	0.001000	0.12720	0.011000	0.14972	0.616000	0.37450	0.434000	0.21494	0.643000	0.30638	0.650000	0.86243	GAG		0.507	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10302249	G	T	10302249	3	4	61	1	0	0	0	0	1	0	0	0	15631	933	33	2	849	2	TATDN2	3	10302249	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110686	10302249	187720181	2299	10284										
ATP2B2	491	broad.mit.edu	37	chr3	10429962	10429962	+	Splice_Site	DEL	T	T	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaggggattaggcttaccTtttttgtctttcttctcttc							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10429962delT	ENST00000352432.4	-	5	975	c.906delA	c.(904-906)aaa>aa	p.K302fs	ATP2B2_ENST00000397077.1_Splice_Site_p.K302fs|ATP2B2_ENST00000383800.4_Splice_Site_p.K302fs|ATP2B2_ENST00000360273.2_Splice_Site_p.K302fs|ATP2B2_ENST00000343816.4_Splice_Site_p.K302fs			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	302					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.A303fs*56(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TAGGCTTACCTTTTTTGTCTT	0.453																																					Ovarian(125;1619 1709 15675 19819 38835)											1	Deletion - Frameshift(1)	large_intestine(1)	3											283	257	266					3																	10429962		2203	4300	6503	10404962	SO:0001630	splice_region_variant	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.907+1A>-	3.37:g.10429962delT			10404962	O00766|Q12994|Q16818	Frame_Shift_Del	DEL	ENST00000352432.4	37	CCDS33701.1																																																																																				0.453	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	Frame_Shift_Del	-	10429962	T	-	10429962	8	5	61	1	0	1	0	1	0	0	1	0	1141	1623	56	0	2897	0	ATP2B2	3	10429962	Splice_Site	DEL	T	TCGA-AG-A002-01A-01W-A00K-09	127713	10429962	187592468	2300	10285										
ATP2B2	491	broad.mit.edu	37	chr3	10443974	10443974	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagaatggcggccccctcGatccaacctgcctctgcctc	10	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:10443974G>A	ENST00000352432.4	-	3	525	c.456C>T	c.(454-456)atC>atT	p.I152I	ATP2B2_ENST00000397077.1_Silent_p.I152I|ATP2B2_ENST00000383800.4_Silent_p.I152I|ATP2B2_ENST00000360273.2_Silent_p.I152I|ATP2B2_ENST00000343816.4_Silent_p.I152I			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	152					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.I152I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CGGCCCCCTCGATCCAACCTG	0.587																																					Ovarian(125;1619 1709 15675 19819 38835)											1	Substitution - coding silent(1)	large_intestine(1)	3											75	85	82					3																	10443974		2203	4300	6503	10418974	SO:0001819	synonymous_variant	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.456C>T	3.37:g.10443974G>A			10418974	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																				0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10443974	G	A	10443974	2	1	61	1	0	0	0	0	0	0	0	1	1141	1048	37	1		1	ATP2B2	3	10443974	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14012	10443974	187578456	2301	10286										
SLC6A1	6529	broad.mit.edu	37	chr3	11059551	11059551	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttcctgatcccctatttCctgacactcatctttgcggg	7	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:11059551C>A	ENST00000287766.4	+	4	682	c.261C>A	c.(259-261)ttC>ttA	p.F87L	SLC6A1_ENST00000536032.1_Intron|SLC6A1-AS1_ENST00000414969.2_RNA|SLC6A1_ENST00000462473.1_3'UTR	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	87					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.F87L(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	TCCCCTATTTCCTGACACTCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	101	100					3																	11059551		2203	4300	6503	11034551	SO:0001583	missense	6529				CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"Solute carriers"	11042	protein-coding gene	gene with protein product	"GABA transporter 1"	137165	"solute carrier family 6 (neurotransmitter transporter, GABA), member 1"			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.261C>A	3.37:g.11059551C>A	ENSP00000287766:p.Phe87Leu		11034551	Q8N4K8	Missense_Mutation	SNP	ENST00000287766.4	37	CCDS2603.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901795	0.33535	.	.	ENSG00000157103	ENST00000287766	T	0.70631	-0.5	4.07	4.07	0.47477	.	0.065555	0.64402	D	0.000010	T	0.61048	0.2316	N	0.17764	0.52	0.80722	D	1	D	0.64830	0.994	P	0.54965	0.765	T	0.57653	-0.7774	10	0.06625	T	0.88	.	10.4974	0.44785	0.0:0.9102:0.0:0.0898	.	87	P30531	SC6A1_HUMAN	L	87	ENSP00000287766:F87L	ENSP00000287766:F87L	F	+	3	2	SLC6A1	11034551	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.935000	0.48963	2.273000	0.75805	0.563000	0.77884	TTC		0.597	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		A	11059551	C	A	11059551	3	1	61	1	0	0	0	0	1	0	0	0	14710	854	30	2	267	2	SLC6A1	3	11059551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	615577	11059551	186962879	2302	10287										
C3orf31	132001	broad.mit.edu	37	chr3	11885644	11885644	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttctttgaatgccatgcGacagggtcatctactgtgaa	11	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:11885644G>A	ENST00000444133.2	-	2	319	c.177C>T	c.(175-177)gtC>gtT	p.V59V	TAMM41_ENST00000273037.5_Silent_p.V59V|TAMM41_ENST00000455809.1_Silent_p.V59V			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	59					cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)	p.V59V(1)									AATGCCATGCGACAGGGTCAT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	3											72	71	72					3																	11885644		2203	4300	6503	11860644	SO:0001819	synonymous_variant	132001				CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"chromosome 3 open reading frame 31"	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.177C>T	3.37:g.11885644G>A			11860644	B4DIY7|C9J2U4	Silent	SNP	ENST00000444133.2	37																																																																																					0.403	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807		A	11885644	G	A	11885644	2	1	61	1	0	0	0	0	0	0	0	1	2227	1045	37	1		1	C3orf31	3	11885644	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	826093	11885644	186136786	2303	10288										
SYN2	7079	broad.mit.edu	37	chr3	12192757	12192757	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcccagctggtcgctatCtataagacactgggaggaga	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12192757C>A	ENST00000287814.4	-	0	1650				SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4						central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.I166I(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						TGGTCGCTATCTATAAGACAC	0.398																																					Melanoma(199;1446 2144 30617 38794 51714)											1	Substitution - coding silent(1)	large_intestine(1)	3											82	73	76					3																	12192757		1871	4104	5975	12167757	SO:0001628	intergenic_variant	6854			U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763		3.37:g.12192757C>A			12167757	B2R7K6	Silent	SNP	ENST00000287814.4	37	CCDS2608.1																																																																																				0.398	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		A	12192757	C	A	12192757	1	1	61	0	1	0	0	0	0	0	0	0	15480	903	32	2		2	SYN2	3	12192757	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	307113	12192757	185829673	2304	10289										
MKRN2	23609	broad.mit.edu	37	chr3	12613702	12613702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggagtggccttgatgacGtggaggccagcagctcctac	14	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12613702G>A	ENST00000170447.7	+	4	609	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	MKRN2_ENST00000448482.1_Missense_Mutation_p.V156M|MKRN2_ENST00000411987.1_Missense_Mutation_p.V115M	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	158					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.V158M(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						CCTTGATGACGTGGAGGCCAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	74	75					3																	12613702		2203	4300	6503	12588702	SO:0001583	missense	23609				CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"RING-type (C3HC4) zinc fingers"	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.472G>A	3.37:g.12613702G>A	ENSP00000170447:p.Val158Met		12588702	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	37	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	G	8.579	0.881769	0.17467	.	.	ENSG00000075975	ENST00000170447;ENST00000411987;ENST00000448482	T;T;T	0.23348	2.75;1.91;1.94	5.38	-10.8	0.00216	.	1.027450	0.07693	N	0.939060	T	0.08935	0.0221	N	0.08118	0	0.09310	N	1	P;P;P	0.40834	0.73;0.73;0.73	B;B;B	0.26969	0.075;0.046;0.046	T	0.44967	-0.9293	10	0.44086	T	0.13	.	15.3426	0.74309	0.0:0.5101:0.3769:0.1131	.	115;156;158	B4DPR4;C9J494;Q9H000	.;.;MKRN2_HUMAN	M	158;115;156	ENSP00000170447:V158M;ENSP00000396340:V115M;ENSP00000397983:V156M	ENSP00000170447:V158M	V	+	1	0	MKRN2	12588702	0.000000	0.05858	0.000000	0.03702	0.738000	0.42128	-3.879000	0.00344	-2.922000	0.00304	-1.289000	0.01358	GTG		0.632	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		A	12613702	G	A	12613702	3	1	61	1	0	0	0	0	1	0	0	0	9637	1145	40	1	486	1	MKRN2	3	12613702	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420945	12613702	185408728	2305	10290										
MKRN2	23609	broad.mit.edu	37	chr3	12623704	12623704	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtcgacatgacagagctCggggacctcttcatgcacct	11	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12623704C>T	ENST00000170447.7	+	8	1340	c.1203C>T	c.(1201-1203)ctC>ctT	p.L401L	MKRN2_ENST00000448482.1_Silent_p.L399L|MKRN2_ENST00000411987.1_Silent_p.L358L	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	401					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L401L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						TGACAGAGCTCGGGGACCTCT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	3											156	155	155					3																	12623704		2203	4300	6503	12598704	SO:0001819	synonymous_variant	23609				CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"RING-type (C3HC4) zinc fingers"	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.1203C>T	3.37:g.12623704C>T			12598704	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Silent	SNP	ENST00000170447.7	37	CCDS33702.1																																																																																				0.498	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		T	12623704	C	T	12623704	2	4	61	1	0	0	0	0	0	0	0	1	9637	871	31	1		1	MKRN2	3	12623704	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10002	12623704	185398726	2306	10291										
RAF1	5894	broad.mit.edu	37	chr3	12626680	12626680	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcatcagttcatacaataCgatgccataggagtagacat	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12626680C>T	ENST00000251849.4	-	15	2048	c.1609G>A	c.(1609-1611)Gta>Ata	p.V537I	RAF1_ENST00000442415.2_Missense_Mutation_p.V557I|RAF1_ENST00000542177.1_Missense_Mutation_p.V456I|RAF1_ENST00000534997.1_Missense_Mutation_p.V322I	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	537	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V537I(1)	ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCATACAATACGATGCCATAG	0.488			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																														Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	1	Substitution - Missense(1)	large_intestine(1)	3											97	80	85					3																	12626680		2203	4300	6503	12601680	SO:0001583	missense	5894	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.1609G>A	3.37:g.12626680C>T	ENSP00000251849:p.Val537Ile		12601680	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133002	0.77662	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3;-5.3	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055638	0.64402	N	0.000001	D	0.98302	0.9437	N	0.10972	0.075	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.87578	0.992;0.986;0.998	D	0.99924	1.1274	10	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	456;322;537	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	I	537;557;416;322;456	ENSP00000251849:V537I;ENSP00000401888:V557I;ENSP00000398591:V416I;ENSP00000441186:V322I;ENSP00000443567:V456I	ENSP00000251849:V537I	V	-	1	0	RAF1	12601680	1.000000	0.71417	0.985000	0.45067	0.203000	0.24098	7.646000	0.83445	2.941000	0.99782	0.655000	0.94253	GTA		0.488	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		T	12626680	C	T	12626680	3	4	61	1	0	0	0	0	1	0	0	0	13039	536	19	1	349	1	RAF1	3	12626680	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2976	12626680	185395750	2307	10292										
RAF1	5894	broad.mit.edu	37	chr3	12650355	12650355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagccacaagtctgacatCgaaatccattgagcaggaat	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12650355C>T	ENST00000251849.4	-	5	930	c.491G>A	c.(490-492)cGa>cAa	p.R164Q	RAF1_ENST00000442415.2_Missense_Mutation_p.R164Q|RAF1_ENST00000542177.1_Missense_Mutation_p.R83Q|RAF1_ENST00000534997.1_5'UTR	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	164					activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R164Q(1)	ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGTCTGACATCGAAATCCATT	0.433			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																														Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	1	Substitution - Missense(1)	large_intestine(1)	3											121	107	112					3																	12650355		2203	4300	6503	12625355	SO:0001583	missense	5894	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.491G>A	3.37:g.12650355C>T	ENSP00000251849:p.Arg164Gln		12625355	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.256163	0.80246	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000542177	D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09	5.52	4.65	0.58169	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.126719	0.53938	D	0.000050	D	0.91310	0.7260	L	0.33137	0.985	0.80722	D	1	D;D	0.62365	0.978;0.991	P;P	0.54210	0.745;0.73	D	0.91862	0.5500	10	0.62326	D	0.03	.	14.3149	0.66443	0.0:0.9288:0.0:0.0712	.	83;164	B4E0X2;P04049	.;RAF1_HUMAN	Q	164;164;76;83	ENSP00000251849:R164Q;ENSP00000401888:R164Q;ENSP00000398591:R76Q;ENSP00000443567:R83Q	ENSP00000251849:R164Q	R	-	2	0	RAF1	12625355	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.813000	0.86123	1.352000	0.45808	-0.251000	0.11542	CGA		0.433	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		T	12650355	C	T	12650355	3	4	61	1	0	0	0	0	1	0	0	0	13039	884	31	1	1507	1	RAF1	3	12650355	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23675	12650355	185372075	2308	10293										
RPL32	6161	broad.mit.edu	37	chr3	12877668	12877668	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgggcagctctttccacGatggctttgcggttcttgga	13	9	2	0	rs574066569		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:12877668G>A	ENST00000429711.2	-	4	432	c.333C>T	c.(331-333)atC>atT	p.I111I	RPL32_ENST00000396957.1_Silent_p.I111I|RPL32_ENST00000396953.2_Silent_p.I111I|RPL32_ENST00000435983.1_Silent_p.I111I|RPL32_ENST00000273223.6_Silent_p.I129I	NM_000994.3	NP_000985.1	P62910	RL32_HUMAN	ribosomal protein L32	111					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.I111I(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						CTCTTTCCACGATGGCTTTGC	0.507													G|||	1	0.000199681	0	0	5008	,	,		22599	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	3											74	66	69					3																	12877668		2203	4297	6500	12852668	SO:0001819	synonymous_variant	6161			CA436299, CF124158, CR608027	CCDS2614.1	3q13.3-q21	2011-04-06			ENSG00000144713	ENSG00000144713		"L ribosomal proteins"	10336	protein-coding gene	gene with protein product						9284913	Standard	NM_001007073		Approved	L32	uc003bxl.3	P62910	OTTHUMG00000129804	ENST00000429711.2:c.333C>T	3.37:g.12877668G>A			12852668	B2R4Q3|P02433	Silent	SNP	ENST00000429711.2	37	CCDS2614.1																																																																																				0.507	RPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252032.2	NM_000994		A	12877668	G	A	12877668	2	1	61	1	0	0	0	0	0	0	0	1	13619	1048	37	1		1	RPL32	3	12877668	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	227313	12877668	185144762	2309	10294										
XPC	7508	broad.mit.edu	37	chr3	14212029	14212029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcagatggtgtgccttCttgaggtcacttggaaagtc	11	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14212029C>A	ENST00000285021.7	-	3	535	c.321G>T	c.(319-321)aaG>aaT	p.K107N	XPC_ENST00000449060.2_Missense_Mutation_p.K107N	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	107	Glu-rich (acidic).				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)	p.K107N(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGTGTGCCTTCTTGAGGTCAC	0.418			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"xeroderma pigmentosum, complementation group C"		E	1	Substitution - Missense(1)	large_intestine(1)	3											273	252	259					3																	14212029		1897	4122	6019	14187033	SO:0001583	missense	7508	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"xeroderma pigmentosum group C protein"	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.321G>T	3.37:g.14212029C>A	ENSP00000285021:p.Lys107Asn		14187033	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.786198	0.49997	.	.	ENSG00000154767	ENST00000285021;ENST00000449060;ENST00000511155	T;T;T	0.53423	0.62;0.62;0.62	5.65	0.761	0.18448	.	0.605887	0.16260	N	0.222281	T	0.47078	0.1426	L	0.54323	1.7	0.09310	N	0.999995	B;D	0.53619	0.421;0.961	B;P	0.49637	0.203;0.617	T	0.35301	-0.9794	10	0.49607	T	0.09	-10.0556	8.4583	0.32912	0.0:0.4853:0.0:0.5147	.	107;107	E9PH69;Q01831	.;XPC_HUMAN	N	107;107;101	ENSP00000285021:K107N;ENSP00000404002:K107N;ENSP00000423867:K101N	ENSP00000285021:K107N	K	-	3	2	XPC	14187033	0.028000	0.19301	0.021000	0.16686	0.006000	0.05464	0.056000	0.14256	0.322000	0.23283	-0.143000	0.13931	AAG		0.418	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628		A	14212029	C	A	14212029	3	1	61	1	0	0	0	0	1	0	0	0	17481	912	32	2	1506	2	XPC	3	14212029	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1334361	14212029	183810401	2310	10295										
LSM3	27258	broad.mit.edu	37	chr3	14223156	14223156	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagaaatgaccgagagcttCgaggcagattacatgtaagt	12	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14223156C>T	ENST00000306024.3	+	2	621	c.118C>T	c.(118-120)Cga>Tga	p.R40*	XPC_ENST00000285021.7_5'Flank	NM_014463.2	NP_055278.1	P62310	LSM3_HUMAN	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)	40					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R40*(2)		central_nervous_system(1)|large_intestine(2)|ovary(1)	4						CCGAGAGCTTCGAGGCAGATT	0.428																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											92	97	96					3																	14223156		2203	4300	6503	14198160	SO:0001587	stop_gained	27258			AF182289	CCDS2619.1	3p25.1	2012-08-15			ENSG00000170860	ENSG00000170860			17874	protein-coding gene	gene with protein product		607283				10369684	Standard	NM_014463		Approved	YLR438C, SMX4, USS2	uc003byn.3	P62310	OTTHUMG00000129838	ENST00000306024.3:c.118C>T	3.37:g.14223156C>T	ENSP00000302160:p.Arg40*		14198160	Q6IAH0|Q9Y4Z1	Nonsense_Mutation	SNP	ENST00000306024.3	37	CCDS2619.1	.	.	.	.	.	.	.	.	.	.	C	42	9.444847	0.99172	.	.	ENSG00000170860	ENST00000306024	.	.	.	5.5	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.9528	14.0025	0.64442	0.2744:0.7256:0.0:0.0	.	.	.	.	X	40	.	ENSP00000302160:R40X	R	+	1	2	LSM3	14198160	0.980000	0.34600	0.997000	0.53966	0.981000	0.71138	2.571000	0.45990	1.285000	0.44548	0.655000	0.94253	CGA		0.428	LSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252078.3	NM_014463		T	14223156	C	T	14223156	4	4	61	1	0	0	0	0	0	1	0	0	9086	876	31	1	124	1	LSM3	3	14223156	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11127	14223156	183799274	2311	10296										
C3orf20	84077	broad.mit.edu	37	chr3	14724418	14724418	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcctaccccgtccgacatCttgggcctggaggtcagctt	12	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14724418C>A	ENST00000253697.3	+	3	650	c.198C>A	c.(196-198)atC>atA	p.I66I	C3orf20_ENST00000435614.1_Intron|C3orf20_ENST00000412910.1_Intron	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	66						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.I66I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CGTCCGACATCTTGGGCCTGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	3											108	107	107					3																	14724418		2203	4300	6503	14699422	SO:0001819	synonymous_variant	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.198C>A	3.37:g.14724418C>A			14699422	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	37	CCDS33706.1																																																																																				0.547	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		A	14724418	C	A	14724418	2	1	61	1	0	0	0	0	0	0	0	1	2219	903	32	2		2	C3orf20	3	14724418	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	501262	14724418	183298012	2312	10297										
C3orf20	84077	broad.mit.edu	37	chr3	14731588	14731588	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagcctgtctgagcttttCtctctctgctggaaaagaag	9	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14731588C>A	ENST00000253697.3	+	5	1162	c.710C>A	c.(709-711)tCt>tAt	p.S237Y	C3orf20_ENST00000435614.1_Missense_Mutation_p.S115Y|C3orf20_ENST00000412910.1_Missense_Mutation_p.S115Y	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	237						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.S237Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CTGAGCTTTTCTCTCTCTGCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	89	89					3																	14731588		2203	4300	6503	14706592	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.710C>A	3.37:g.14731588C>A	ENSP00000253697:p.Ser237Tyr		14706592	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.058712	0.55325	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.14022	2.82;2.54;2.54	4.56	4.56	0.56223	.	0.000000	0.40222	N	0.001142	T	0.25606	0.0623	L	0.36672	1.1	0.37229	D	0.905601	D	0.69078	0.997	D	0.66979	0.948	T	0.07829	-1.0752	10	0.87932	D	0	-18.0468	13.1961	0.59738	0.0:1.0:0.0:0.0	.	237	Q8ND61	CC020_HUMAN	Y	237;115;115	ENSP00000253697:S237Y;ENSP00000402933:S115Y;ENSP00000396081:S115Y	ENSP00000253697:S237Y	S	+	2	0	C3orf20	14706592	0.987000	0.35691	1.000000	0.80357	0.569000	0.35902	3.118000	0.50414	2.243000	0.73865	0.491000	0.48974	TCT		0.527	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		A	14731588	C	A	14731588	3	1	61	1	0	0	0	0	1	0	0	0	2219	913	32	2	720	2	C3orf20	3	14731588	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7170	14731588	183290842	2313	10298										
C3orf20	84077	broad.mit.edu	37	chr3	14745916	14745916	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacgaaactacaaggcaaaGatgccctctcatctaatgtt	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14745916G>T	ENST00000253697.3	+	7	1403	c.951G>T	c.(949-951)aaG>aaT	p.K317N	C3orf20_ENST00000495387.1_3'UTR|C3orf20_ENST00000435614.1_Missense_Mutation_p.K195N|C3orf20_ENST00000412910.1_Missense_Mutation_p.K195N	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	317						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.K317N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						ACAAGGCAAAGATGCCCTCTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											124	130	128					3																	14745916		2203	4300	6503	14720920	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.951G>T	3.37:g.14745916G>T	ENSP00000253697:p.Lys317Asn		14720920	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.726087	0.30593	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.13307	2.89;2.6;2.6	4.91	3.08	0.35506	.	0.286201	0.24957	N	0.034249	T	0.08537	0.0212	N	0.20986	0.625	0.09310	N	1	B	0.23735	0.09	B	0.22601	0.04	T	0.23332	-1.0191	10	0.46703	T	0.11	-12.8041	6.4231	0.21754	0.0961:0.0:0.7252:0.1786	.	317	Q8ND61	CC020_HUMAN	N	317;195;195	ENSP00000253697:K317N;ENSP00000402933:K195N;ENSP00000396081:K195N	ENSP00000253697:K317N	K	+	3	2	C3orf20	14720920	0.105000	0.21958	0.130000	0.21974	0.211000	0.24417	0.379000	0.20585	1.054000	0.40438	0.585000	0.79938	AAG		0.512	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14745916	G	T	14745916	3	4	61	1	0	0	0	0	1	0	0	0	2219	933	33	2	969	2	C3orf20	3	14745916	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14328	14745916	183276514	2314	10299										
FGD5	152273	broad.mit.edu	37	chr3	14862558	14862558	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcgcttcctggcactgacGtttaagaagaagacggagaa	12	8	0	5	rs368388794		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:14862558G>A	ENST00000285046.5	+	1	2090	c.1980G>A	c.(1978-1980)acG>acA	p.T660T	FGD5_ENST00000543601.1_Silent_p.T419T	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	660					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.T660T(1)|p.T419T(1)		NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						TGGCACTGACGTTTAAGAAGA	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	3						G		1,3951		0,1,1975	82	81	81		1980	-10.6	0	3		81	0,8340		0,0,4170	no	coding-synonymous	FGD5	NM_152536.3		0,1,6145	AA,AG,GG		0.0,0.0253,0.0081		660/1463	14862558	1,12291	1976	4170	6146	14837562	SO:0001819	synonymous_variant	152273			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1980G>A	3.37:g.14862558G>A			14837562	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1																																																																																				0.512	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14862558	G	A	14862558	2	1	61	1	0	0	0	0	0	0	0	1	5855	1132	40	1		1	FGD5	3	14862558	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116642	14862558	183159872	2315	10300										
ZFYVE20	64145	broad.mit.edu	37	chr3	15116043	15116043	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccacccgaaactgctccCtttctcgttccaactcccgt	5	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15116043C>A	ENST00000253699.3	-	14	2214	c.1601G>T	c.(1600-1602)aGg>aTg	p.R534M	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.R534M	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	534	Necessary for the interaction with EHD1.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.R534M(1)		NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						AAACTGCTCCCTTTCTCGTTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	97	99					3																	15116043		2203	4300	6503	15091047	SO:0001583	missense	64145			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.1601G>T	3.37:g.15116043C>A	ENSP00000253699:p.Arg534Met		15091047	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	8.954	0.968924	0.18659	.	.	ENSG00000131381	ENST00000253699;ENST00000476527	T;T	0.54279	0.58;0.58	5.73	-2.47	0.06442	.	1.097460	0.06776	N	0.784423	T	0.39886	0.1095	L	0.40543	1.245	0.09310	N	0.999994	B	0.29805	0.257	B	0.27380	0.079	T	0.32241	-0.9914	10	0.66056	D	0.02	-2.574	5.8873	0.18888	0.1219:0.4234:0.0:0.4547	.	534	Q9H1K0	RBNS5_HUMAN	M	534	ENSP00000253699:R534M;ENSP00000422551:R534M	ENSP00000253699:R534M	R	-	2	0	ZFYVE20	15091047	0.000000	0.05858	0.001000	0.08648	0.282000	0.26991	-0.581000	0.05820	-0.936000	0.03723	0.491000	0.48974	AGG		0.612	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15116043	C	A	15116043	3	1	61	1	0	0	0	0	1	0	0	0	17705	681	24	2	757	2	ZFYVE20	3	15116043	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253485	15116043	182906387	2316	10301										
ZFYVE20	64145	broad.mit.edu	37	chr3	15118603	15118603	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgagtatctgatcattCtctgcagccgcaaattgctt	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15118603C>A	ENST00000253699.3	-	12	1680	c.1067G>T	c.(1066-1068)aGa>aTa	p.R356I	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.R356I|ZFYVE20_ENST00000449964.2_5'Flank	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	356	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB4A.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.R356I(1)		NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						TCTGATCATTCTCTGCAGCCG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											189	177	181					3																	15118603		2203	4300	6503	15093607	SO:0001583	missense	64145			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.1067G>T	3.37:g.15118603C>A	ENSP00000253699:p.Arg356Ile		15093607	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.163507	0.78226	.	.	ENSG00000131381	ENST00000253699;ENST00000476527;ENST00000418832	T;T	0.55760	0.5;0.5	5.9	3.17	0.36434	.	0.181080	0.64402	D	0.000016	T	0.54743	0.1877	M	0.63843	1.955	0.80722	D	1	P	0.35383	0.498	B	0.43623	0.425	T	0.54463	-0.8290	10	0.72032	D	0.01	-19.3043	9.3162	0.37934	0.0:0.7286:0.0:0.2714	.	356	Q9H1K0	RBNS5_HUMAN	I	356;356;58	ENSP00000253699:R356I;ENSP00000422551:R356I	ENSP00000253699:R356I	R	-	2	0	ZFYVE20	15093607	1.000000	0.71417	0.996000	0.52242	0.953000	0.61014	1.533000	0.36040	0.407000	0.25591	0.591000	0.81541	AGA		0.458	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15118603	C	A	15118603	3	1	61	1	0	0	0	0	1	0	0	0	17705	913	32	2	1299	2	ZFYVE20	3	15118603	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2560	15118603	182903827	2317	10302										
CAPN7	23473	broad.mit.edu	37	chr3	15253696	15253696	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataactgagtatctggaaaGagttcaagctctacattcag	8	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15253696G>T	ENST00000253693.2	+	2	441	c.188G>T	c.(187-189)aGa>aTa	p.R63I		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	63					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)	p.R63I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						TATCTGGAAAGAGTTCAAGCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											76	77	77					3																	15253696		2203	4300	6503	15228700	SO:0001583	missense	23473			AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.188G>T	3.37:g.15253696G>T	ENSP00000253693:p.Arg63Ile		15228700		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	G	30	5.055981	0.93793	.	.	ENSG00000131375	ENST00000253693	T	0.57752	0.38	5.49	5.49	0.81192	MIT (2);	0.122489	0.53938	D	0.000056	T	0.77039	0.4072	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80609	-0.1306	10	0.87932	D	0	-18.5295	18.9685	0.92706	0.0:0.0:1.0:0.0	.	63	Q9Y6W3	CAN7_HUMAN	I	63	ENSP00000253693:R63I	ENSP00000253693:R63I	R	+	2	0	CAPN7	15228700	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.902000	0.92568	2.591000	0.87537	0.555000	0.69702	AGA		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		T	15253696	G	T	15253696	3	4	61	1	0	0	0	0	1	0	0	0	2637	942	33	2	194	2	CAPN7	3	15253696	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135093	15253696	182768734	2318	10303										
METTL6	131965	broad.mit.edu	37	chr3	15452882	15452882	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttattcaccgtctctcGaaacacatactcgtttacca	3	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15452882G>A	ENST00000443029.1	-	6	976	c.736C>T	c.(736-738)Cga>Tga	p.R246*	METTL6_ENST00000383790.3_Nonsense_Mutation_p.R246*|METTL6_ENST00000450816.2_Nonsense_Mutation_p.R201*			Q8TCB7	METL6_HUMAN	methyltransferase like 6	246							methyltransferase activity (GO:0008168)	p.R246*(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						ACCGTCTCTCGAAACACATAC	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											145	133	137					3																	15452882		1885	4110	5995	15427886	SO:0001587	stop_gained	131965			AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.736C>T	3.37:g.15452882G>A	ENSP00000407613:p.Arg246*		15427886	Q96LU4	Nonsense_Mutation	SNP	ENST00000443029.1	37	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	G	37	6.146775	0.97324	.	.	ENSG00000206562	ENST00000383790;ENST00000450816	.	.	.	5.45	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9032	13.7009	0.62608	0.0749:0.0:0.9251:0.0	.	.	.	.	X	246;201	.	ENSP00000373300:R246X	R	-	1	2	METTL6	15427886	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.041000	0.76558	1.312000	0.45043	0.555000	0.69702	CGA		0.443	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		A	15452882	G	A	15452882	4	1	61	1	0	0	0	0	0	1	0	0	9534	1066	37	1	122	1	METTL6	3	15452882	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199186	15452882	182569548	2319	10304										
METTL6	131965	broad.mit.edu	37	chr3	15467851	15467851	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccagtgtctgtctttgaaGaaattagtgctatttctttt	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15467851G>T	ENST00000443029.1	-	2	408	c.168C>A	c.(166-168)ttC>ttA	p.F56L	METTL6_ENST00000383790.3_Missense_Mutation_p.F56L|METTL6_ENST00000383789.5_Missense_Mutation_p.F56L|EAF1_ENST00000396842.2_5'Flank|EAF1_ENST00000432764.2_5'Flank|METTL6_ENST00000450816.2_Missense_Mutation_p.F56L			Q8TCB7	METL6_HUMAN	methyltransferase like 6	56							methyltransferase activity (GO:0008168)	p.F56L(2)		endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						TGTCTTTGAAGAAATTAGTGC	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	3											157	143	147					3																	15467851		1845	4092	5937	15442855	SO:0001583	missense	131965			AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.168C>A	3.37:g.15467851G>T	ENSP00000407613:p.Phe56Leu		15442855	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	37	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328892	0.81690	.	.	ENSG00000206562	ENST00000383790;ENST00000450816;ENST00000383789	T;T;T	0.66280	-0.2;-0.2;-0.2	5.54	3.36	0.38483	.	0.000000	0.85682	D	0.000000	T	0.82226	0.4991	H	0.95328	3.655	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.996	T	0.81364	-0.0966	10	0.87932	D	0	-13.8253	7.2447	0.26115	0.3772:0.0:0.6228:0.0	.	56;56;56	B4DDX3;Q8TCB7-2;Q8TCB7	.;.;METL6_HUMAN	L	56	ENSP00000373300:F56L;ENSP00000410726:F56L;ENSP00000373299:F56L	ENSP00000373299:F56L	F	-	3	2	METTL6	15442855	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.384000	0.52478	0.404000	0.25506	0.650000	0.86243	TTC		0.363	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		T	15467851	G	T	15467851	3	4	61	1	0	0	0	0	1	0	0	0	9534	933	33	2	706	2	METTL6	3	15467851	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14969	15467851	182554579	2320	10305										
HACL1	26061	broad.mit.edu	37	chr3	15602373	15602373	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaactggcgtctttattTacatattagagcgggtcagc	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:15602373T>C	ENST00000321169.5	-	17	2103	c.1736A>G	c.(1735-1737)tAa>tGa	p.*579*	HACL1_ENST00000451445.2_Silent_p.*497*|HACL1_ENST00000457447.2_Silent_p.*519*|HACL1_ENST00000435217.2_Silent_p.*338*|HACL1_ENST00000456194.2_Silent_p.*552*	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	0					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)	p.*579*(1)		NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CGTCTTTATTTACATATTAGA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	3											71	74	73					3																	15602373		2203	4300	6503	15577377	SO:0001819	synonymous_variant	26061			AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"2-hydroxyphytanoyl-CoA lyase"	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.1736A>G	3.37:g.15602373T>C			15577377	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Silent	SNP	ENST00000321169.5	37	CCDS2627.1																																																																																				0.323	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260		C	15602373	T	C	15602373	2	2	61	1	0	0	0	0	0	0	0	1	6962	1761	61	4		4	HACL1	3	15602373	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	134522	15602373	182420057	2321	10306										
GALNTL2	117248	broad.mit.edu	37	chr3	16260953	16260953	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcttgcagctgcaaaggaGactgggttgtcggacattcc	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:16260953G>T	ENST00000339732.5	+	7	1939	c.1436G>T	c.(1435-1437)aGa>aTa	p.R479I	GALNT15_ENST00000437509.1_Missense_Mutation_p.R479I	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	479					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R479I(1)									CTGCAAAGGAGACTGGGTTGT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											212	193	199					3																	16260953		2203	4300	6503	16235957	SO:0001583	missense	117248			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1436G>T	3.37:g.16260953G>T	ENSP00000344260:p.Arg479Ile		16235957	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.417881	0.83449	.	.	ENSG00000131386	ENST00000339732;ENST00000437509;ENST00000543679	T;T	0.71103	-0.54;-0.54	5.64	3.8	0.43715	.	0.243367	0.47455	D	0.000228	T	0.78984	0.4370	M	0.91818	3.245	0.80722	D	1	P	0.50710	0.938	P	0.45971	0.499	T	0.82719	-0.0318	10	0.87932	D	0	.	12.6843	0.56940	0.0:0.1264:0.742:0.1316	.	479	Q8N3T1	GLTL2_HUMAN	I	479;479;9	ENSP00000344260:R479I;ENSP00000395873:R479I	ENSP00000344260:R479I	R	+	2	0	GALNTL2	16235957	1.000000	0.71417	0.603000	0.28903	0.992000	0.81027	6.846000	0.75399	0.696000	0.31696	0.555000	0.69702	AGA		0.527	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		T	16260953	G	T	16260953	3	4	61	1	0	0	0	0	1	0	0	0	6242	942	33	2	1462	2	GALNTL2	3	16260953	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	658580	16260953	181761477	2322	10307										
RFTN1	23180	broad.mit.edu	37	chr3	16358557	16358557	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagggcccttcatctcctcGgagactccaccctcctgctg	8	18	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:16358557G>A	ENST00000334133.4	-	10	1787	c.1515C>T	c.(1513-1515)tcC>tcT	p.S505S	RFTN1_ENST00000432519.1_Silent_p.S469S|OXNAD1_ENST00000544043.1_Intron|OXNAD1_ENST00000435829.2_Intron|RP11-415F23.2_ENST00000607464.1_RNA|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000606098.1_Intron|OXNAD1_ENST00000605932.1_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	505					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)	p.S505S(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						TCATCTCCTCGGAGACTCCAC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	3											126	113	117					3																	16358557		2203	4300	6503	16333561	SO:0001819	synonymous_variant	23180			D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1515C>T	3.37:g.16358557G>A			16333561	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																				0.547	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		A	16358557	G	A	16358557	2	1	61	1	0	0	0	0	0	0	0	1	13295	1103	39	1		1	RFTN1	3	16358557	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97604	16358557	181663873	2323	10308										
RFTN1	23180	broad.mit.edu	37	chr3	16475390	16475390	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatcaggatggctctaaaGatgtgctccaggggcgtctt	13	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:16475390G>T	ENST00000334133.4	-	3	572	c.300C>A	c.(298-300)atC>atA	p.I100I	RFTN1_ENST00000432519.1_Silent_p.I64I	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	100					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)	p.I100I(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						TGGCTCTAAAGATGTGCTCCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	3											142	149	147					3																	16475390		2203	4300	6503	16450394	SO:0001819	synonymous_variant	23180			D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.300C>A	3.37:g.16475390G>T			16450394	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																				0.592	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		T	16475390	G	T	16475390	2	4	61	1	0	0	0	0	0	0	0	1	13295	932	33	2		2	RFTN1	3	16475390	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116833	16475390	181547040	2324	10309										
PLCL2	23228	broad.mit.edu	37	chr3	17052230	17052230	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatatattcgagctcttaaAatgggttgccggagtgttga	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:17052230A>C	ENST00000418129.2	+	2	1479	c.1014A>C	c.(1012-1014)aaA>aaC	p.K338N	PLCL2_ENST00000432376.1_Missense_Mutation_p.K338N|PLCL2_ENST00000460467.1_Intron|PLCL2_ENST00000396755.2_Missense_Mutation_p.K338N	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	464					B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.K338N(1)		breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						GAGCTCTTAAAATGGGTTGCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	113	112					3																	17052230		2203	4300	6503	17027234	SO:0001583	missense	23228			AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.1014A>C	3.37:g.17052230A>C	ENSP00000409637:p.Lys338Asn		17027234	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.87|15.87	2.959659|2.959659	0.53400|0.53400	.|.	.|.	ENSG00000154822|ENSG00000154822	ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376|ENST00000419842	T;T;T|T	0.64260|0.64260	-0.09;-0.09;-0.09|-0.09	5.96|5.96	0.883|0.883	0.19177|0.19177	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);|.	0.046630|0.046630	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.55768|0.55768	0.1941|0.1941	.|.	.|.	.|.	0.51012|0.51012	D|D	0.999908|0.999908	D|.	0.67145|.	0.996|.	D|.	0.66497|.	0.944|.	T|T	0.41928|0.41928	-0.9481|-0.9481	9|7	0.21540|0.21014	T|T	0.41|0.42	.|.	9.5535|9.5535	0.39324|0.39324	0.7197:0.0:0.2803:0.0|0.7197:0.0:0.2803:0.0	.|.	464|.	Q9UPR0|.	PLCL2_HUMAN|.	N|T	338;465;338;338|82	ENSP00000409637:K338N;ENSP00000379979:K338N;ENSP00000412836:K338N|ENSP00000404433:K82T	ENSP00000285094:K465N|ENSP00000404433:K82T	K|K	+|+	3|2	2|0	PLCL2|PLCL2	17027234|17027234	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	1.792000|1.792000	0.38754|0.38754	0.160000|0.160000	0.19432|0.19432	-0.250000|-0.250000	0.11733|0.11733	AAA|AAA		0.428	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			C	17052230	A	C	17052230	3	2	61	1	0	0	0	0	1	0	0	0	12071	11	1	4	1392	4	PLCL2	3	17052230	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	576840	17052230	180970200	2325	10310										
TBC1D5	9779	broad.mit.edu	37	chr3	17279689	17279689	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggcatgctttctgatttCatcagcctctgctgctgctg	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:17279689C>A	ENST00000253692.7	-	17	3218	c.1554G>T	c.(1552-1554)atG>atT	p.M518I	TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429924.2_Missense_Mutation_p.M470I|TBC1D5_ENST00000446818.2_Missense_Mutation_p.M518I|TBC1D5_ENST00000429383.4_Missense_Mutation_p.M518I	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	518						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)	p.M518I(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						TTTCTGATTTCATCAGCCTCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	59	59					3																	17279689		2203	4300	6503	17254693	SO:0001583	missense	9779			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1554G>T	3.37:g.17279689C>A	ENSP00000253692:p.Met518Ile		17254693	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	37	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.167034	0.38217	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.44083	1.51;1.51;1.51;0.93	5.89	5.89	0.94794	.	0.197406	0.56097	D	0.000029	T	0.39809	0.1092	L	0.47716	1.5	0.50171	D	0.999853	B;B;B;B	0.24882	0.011;0.113;0.025;0.025	B;B;B;B	0.17433	0.008;0.018;0.009;0.009	T	0.09422	-1.0675	10	0.33940	T	0.23	-16.7598	18.4274	0.90613	0.0:1.0:0.0:0.0	.	470;518;518;518	C9J3F6;C9JP52;B9A6K1;Q92609	.;.;.;TBCD5_HUMAN	I	518;518;518;470	ENSP00000253692:M518I;ENSP00000398127:M518I;ENSP00000402935:M518I;ENSP00000411925:M470I	ENSP00000253692:M518I	M	-	3	0	TBC1D5	17254693	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.553000	0.60753	2.781000	0.95711	0.555000	0.69702	ATG		0.463	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		A	17279689	C	A	17279689	3	1	61	1	0	0	0	0	1	0	0	0	15662	826	29	2	927	2	TBC1D5	3	17279689	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	227459	17279689	180742741	2326	10311										
SATB1	6304	broad.mit.edu	37	chr3	18438680	18438680	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgcttacccatcatatCttttgtcttcttgaaatgtt	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:18438680C>A	ENST00000338745.6	-	6	2476	c.742G>T	c.(742-744)Gat>Tat	p.D248Y	SATB1_ENST00000475083.1_5'Flank|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Missense_Mutation_p.D248Y|SATB1_ENST00000454909.2_Missense_Mutation_p.D248Y	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	248	Nuclear matrix targeting sequence (NMTS).				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D248Y(1)		NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CCCATCATATCTTTTGTCTTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											254	212	226					3																	18438680		2202	4300	6502	18413684	SO:0001583	missense	6304				CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.742G>T	3.37:g.18438680C>A	ENSP00000341024:p.Asp248Tyr		18413684	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	37	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657745	0.67586	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	D;D;D	0.86956	-2.19;-2.19;-2.19	5.9	5.9	0.94986	.	0.144833	0.64402	D	0.000010	T	0.81187	0.4770	N	0.16478	0.41	0.80722	D	1	B;B	0.16166	0.016;0.003	B;B	0.15052	0.012;0.002	T	0.74788	-0.3546	10	0.59425	D	0.04	-5.7408	20.2787	0.98501	0.0:1.0:0.0:0.0	.	248;248	Q01826-2;Q01826	.;SATB1_HUMAN	Y	248	ENSP00000341024:D248Y;ENSP00000399708:D248Y;ENSP00000399518:D248Y	ENSP00000341024:D248Y	D	-	1	0	SATB1	18413684	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.792000	0.85828	2.798000	0.96311	0.650000	0.86243	GAT		0.368	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		A	18438680	C	A	18438680	3	1	61	1	0	0	0	0	1	0	0	0	13890	913	32	2	1573	2	SATB1	3	18438680	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1158991	18438680	179583750	2327	10312										
KCNH8	131096	broad.mit.edu	37	chr3	19498417	19498417	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaatatgctcacaaattCgtggaagacattcagcatga	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:19498417C>T	ENST00000328405.2	+	11	2249	c.1983C>T	c.(1981-1983)ttC>ttT	p.F661F		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	661					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.F661F(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						CTCACAAATTCGTGGAAGACA	0.413																																					NSCLC(124;1625 1765 8018 24930 42026)											1	Substitution - coding silent(1)	large_intestine(1)	3											133	112	119					3																	19498417		2203	4298	6501	19473421	SO:0001819	synonymous_variant	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1983C>T	3.37:g.19498417C>T			19473421	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																				0.413	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19498417	C	T	19498417	2	4	61	1	0	0	0	0	0	0	0	1	8059	883	31	1		1	KCNH8	3	19498417	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1059737	19498417	178524013	2328	10313										
KCNH8	131096	broad.mit.edu	37	chr3	19575274	19575274	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccactaccaggttgtccaaGaaggtcatttgcaattttta	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:19575274G>T	ENST00000328405.2	+	16	3273	c.3007G>T	c.(3007-3009)Gaa>Taa	p.E1003*		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	1003	Ser-rich.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.E1003*(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						GGTTGTCCAAGAAGGTCATTT	0.458																																					NSCLC(124;1625 1765 8018 24930 42026)											1	Substitution - Nonsense(1)	large_intestine(1)	3											236	231	233					3																	19575274		2203	4300	6503	19550278	SO:0001587	stop_gained	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.3007G>T	3.37:g.19575274G>T	ENSP00000328813:p.Glu1003*		19550278	B7Z2I7|Q59GQ6	Nonsense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	40	8.335468	0.98764	.	.	ENSG00000183960	ENST00000328405	.	.	.	5.51	5.51	0.81932	.	0.000000	0.32314	U	0.006264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5405	0.45031	0.118:0.0:0.882:0.0	.	.	.	.	X	1003	.	.	E	+	1	0	KCNH8	19550278	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.133000	0.64764	2.593000	0.87608	0.655000	0.94253	GAA		0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19575274	G	T	19575274	4	4	61	1	0	0	0	0	0	1	0	0	8059	943	33	2	3069	2	KCNH8	3	19575274	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76857	19575274	178447156	2329	10314										
KAT2B	8850	broad.mit.edu	37	chr3	20187847	20187847	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaaaacaggcacaaattCgaaaagtttaccctggactt	7	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:20187847C>T	ENST00000263754.4	+	14	2499	c.2044C>T	c.(2044-2046)Cga>Tga	p.R682*		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	682					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.R682*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						GGCACAAATTCGAAAAGTTTA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											125	132	130					3																	20187847		2203	4300	6503	20162851	SO:0001587	stop_gained	8850			U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.2044C>T	3.37:g.20187847C>T	ENSP00000263754:p.Arg682*		20162851	Q6NSK1	Nonsense_Mutation	SNP	ENST00000263754.4	37	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	C	43	10.073624	0.99331	.	.	ENSG00000114166	ENST00000263754	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4628	20.1313	0.98000	0.0:1.0:0.0:0.0	.	.	.	.	X	682	.	ENSP00000263754:R682X	R	+	1	2	KAT2B	20162851	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.459000	0.45023	2.837000	0.97791	0.655000	0.94253	CGA		0.343	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		T	20187847	C	T	20187847	4	4	61	1	0	0	0	0	0	1	0	0	8003	876	31	1	2098	1	KAT2B	3	20187847	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	612573	20187847	177834583	2330	10315										
KAT2B	8850	broad.mit.edu	37	chr3	20189935	20189935	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatggaacctgtgaagaGaacagaagctccaggatatt	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:20189935G>T	ENST00000263754.4	+	17	2716	c.2261G>T	c.(2260-2262)aGa>aTa	p.R754I		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	754	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035, ECO:0000305}.				cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.R754I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CCTGTGAAGAGAACAGAAGCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											114	122	119					3																	20189935		2203	4300	6503	20164939	SO:0001583	missense	8850			U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.2261G>T	3.37:g.20189935G>T	ENSP00000263754:p.Arg754Ile		20164939	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	37	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.886054	0.72410	.	.	ENSG00000114166	ENST00000263754	T	0.31510	1.49	5.38	5.38	0.77491	Bromodomain (6);Bromodomain, conserved site (1);	0.041945	0.85682	D	0.000000	T	0.39384	0.1076	L	0.40543	1.245	0.80722	D	1	P	0.34864	0.473	P	0.44518	0.452	T	0.26573	-1.0099	10	0.72032	D	0.01	-23.6514	19.4914	0.95050	0.0:0.0:1.0:0.0	.	754	Q92831	KAT2B_HUMAN	I	754	ENSP00000263754:R754I	ENSP00000263754:R754I	R	+	2	0	KAT2B	20164939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.269000	0.78482	2.669000	0.90835	0.563000	0.77884	AGA		0.393	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		T	20189935	G	T	20189935	3	4	61	1	0	0	0	0	1	0	0	0	8003	942	33	2	2327	2	KAT2B	3	20189935	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2088	20189935	177832495	2331	10316										
SGOL1	151648	broad.mit.edu	37	chr3	20215781	20215781	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagaaccctccgtctctttTtcatctgtgtatttcagtgc	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:20215781T>G	ENST00000263753.4	-	6	1381	c.1242A>C	c.(1240-1242)gaA>gaC	p.E414D	SGOL1_ENST00000437051.1_Intron|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000417364.1_Intron|SGOL1_ENST00000443724.1_Intron|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000421451.1_Missense_Mutation_p.E414D|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000412868.1_Missense_Mutation_p.E414D|SGOL1_ENST00000419233.2_Intron|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000412997.1_Missense_Mutation_p.E414D|SGOL1_ENST00000383774.1_Intron|SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000425061.1_Intron	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	414					attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)	p.E414D(1)		kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						CCGTCTCTTTTTCATCTGTGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	116	114					3																	20215781		2203	4300	6503	20190785	SO:0001583	missense	151648			BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.1242A>C	3.37:g.20215781T>G	ENSP00000263753:p.Glu414Asp		20190785	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Missense_Mutation	SNP	ENST00000263753.4	37	CCDS33716.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480465	0.26598	.	.	ENSG00000129810	ENST00000263753;ENST00000421451;ENST00000412997;ENST00000412868	T;T;T;T	0.33654	1.4;1.4;1.42;1.42	5.47	1.88	0.25563	.	0.963326	0.08706	N	0.905666	T	0.28001	0.0690	L	0.54323	1.7	0.09310	N	1	B;B	0.32918	0.39;0.39	B;B	0.27380	0.079;0.079	T	0.22556	-1.0213	10	0.31617	T	0.26	.	3.8117	0.08799	0.1498:0.2496:0.0:0.6006	.	414;414	B5BUA4;Q5FBB7	.;SGOL1_HUMAN	D	414	ENSP00000263753:E414D;ENSP00000414129:E414D;ENSP00000410458:E414D;ENSP00000406880:E414D	ENSP00000263753:E414D	E	-	3	2	SGOL1	20190785	0.055000	0.20627	0.070000	0.20053	0.795000	0.44927	0.028000	0.13644	0.393000	0.25203	0.459000	0.35465	GAA		0.403	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484		G	20215781	T	G	20215781	3	3	61	1	0	0	0	0	1	0	0	0	14253	1838	64	4	479	4	SGOL1	3	20215781	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	25846	20215781	177806649	2332	10317										
ZNF385D	79750	broad.mit.edu	37	chr3	21478515	21478515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacagcaaccttgcatagcGaacagtaaagaagccgtttt	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:21478515G>A	ENST00000281523.2	-	5	1138	c.620C>T	c.(619-621)tCg>tTg	p.S207L	ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	207						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S207L(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						CTTGCATAGCGAACAGTAAAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											178	147	158					3																	21478515		2203	4300	6503	21453519	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.620C>T	3.37:g.21478515G>A	ENSP00000281523:p.Ser207Leu		21453519		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	G	36	5.702821	0.96812	.	.	ENSG00000151789	ENST00000281523	T	0.24151	1.87	6.09	6.09	0.99107	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.51941	0.1704	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.31724	-0.9933	10	0.45353	T	0.12	-7.6409	20.6789	0.99705	0.0:0.0:1.0:0.0	.	207	Q9H6B1	Z385D_HUMAN	L	207	ENSP00000281523:S207L	ENSP00000281523:S207L	S	-	2	0	ZNF385D	21453519	1.000000	0.71417	0.979000	0.43373	0.999000	0.98932	9.769000	0.98969	2.891000	0.99171	0.655000	0.94253	TCG		0.478	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21478515	G	A	21478515	3	1	61	1	0	0	0	0	1	0	0	0	17917	1059	37	1	583	1	ZNF385D	3	21478515	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1262734	21478515	176543915	2333	10318										
ZNF385D	79750	broad.mit.edu	37	chr3	21478639	21478639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagttgtcataacactgcTtttgcggatttccacagttg	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:21478639T>A	ENST00000281523.2	-	5	1014	c.496A>T	c.(496-498)Agc>Tgc	p.S166C	ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	166	Thr-rich.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S166C(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						ATAACACTGCTTTTGCGGATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											167	155	159					3																	21478639		2203	4300	6503	21453643	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.496A>T	3.37:g.21478639T>A	ENSP00000281523:p.Ser166Cys		21453643		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.511636	0.64522	.	.	ENSG00000151789	ENST00000281523	T	0.34072	1.38	6.09	6.09	0.99107	.	0.418241	0.29015	N	0.013401	T	0.30510	0.0767	N	0.14661	0.345	0.38998	D	0.959298	D	0.63046	0.992	P	0.46543	0.52	T	0.18524	-1.0334	10	0.51188	T	0.08	-5.5049	16.6542	0.85224	0.0:0.0:0.0:1.0	.	166	Q9H6B1	Z385D_HUMAN	C	166	ENSP00000281523:S166C	ENSP00000281523:S166C	S	-	1	0	ZNF385D	21453643	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.039000	0.57325	2.331000	0.79229	0.533000	0.62120	AGC		0.438	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21478639	T	A	21478639	3	1	61	1	0	0	0	0	1	0	0	0	17917	1609	56	5	707	5	ZNF385D	3	21478639	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	124	21478639	176543791	2334	10319										
NKIRAS1	28512	broad.mit.edu	37	chr3	23934592	23934592	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattactgatttttagttCtcagaattagagttcccttt	6	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:23934592C>A	ENST00000443659.2	-	4	1350	c.573G>T	c.(571-573)gaG>gaT	p.E191D	NKIRAS1_ENST00000425478.2_Missense_Mutation_p.E191D|NKIRAS1_ENST00000388759.3_Missense_Mutation_p.E191D|NKIRAS1_ENST00000437230.1_Missense_Mutation_p.E191D|NKIRAS1_ENST00000416026.2_Missense_Mutation_p.E191D|NKIRAS1_ENST00000412028.1_Missense_Mutation_p.E191D|NKIRAS1_ENST00000415901.2_Missense_Mutation_p.E191D|NKIRAS1_ENST00000421515.2_Missense_Mutation_p.E191D			Q9NYS0	KBRS1_HUMAN	NFKB inhibitor interacting Ras-like 1	191					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E191D(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	7						ATTTTTAGTTCTCAGAATTAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											97	96	96					3																	23934592		2203	4300	6503	23909596	SO:0001583	missense	28512			AF229839	CCDS33717.1	3p24.1	2014-05-09	2004-05-20		ENSG00000197885	ENSG00000197885			17899	protein-coding gene	gene with protein product		604496	"NFKB inhibitor interacting Ras-like protein 1"			10657303	Standard	NM_020345		Approved	KBRAS1, kappaB-Ras1	uc003ccj.3	Q9NYS0	OTTHUMG00000155605	ENST00000443659.2:c.573G>T	3.37:g.23934592C>A	ENSP00000393785:p.Glu191Asp		23909596	Q96K18	Missense_Mutation	SNP	ENST00000443659.2	37	CCDS33717.1	.	.	.	.	.	.	.	.	.	.	C	0.091	-1.167403	0.01660	.	.	ENSG00000197885	ENST00000388759;ENST00000443659;ENST00000421515;ENST00000425478;ENST00000437230;ENST00000412028;ENST00000415901;ENST00000416026	T;T;T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-0.76;-0.76;-0.76;-1.03	4.86	0.927	0.19437	.	0.128686	0.52532	D	0.000074	T	0.39200	0.1069	N	0.01729	-0.75	0.30951	N	0.7247	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.38200	-0.9672	10	0.02654	T	1	-8.0128	1.7395	0.02949	0.1322:0.3416:0.1293:0.397	.	191;191	G5E9P3;Q9NYS0	.;KBRS1_HUMAN	D	191	ENSP00000373411:E191D;ENSP00000393785:E191D;ENSP00000392307:E191D;ENSP00000400385:E191D;ENSP00000406543:E191D;ENSP00000396063:E191D;ENSP00000415225:E191D;ENSP00000394214:E191D	ENSP00000373411:E191D	E	-	3	2	NKIRAS1	23909596	0.996000	0.38824	0.999000	0.59377	0.377000	0.30045	0.289000	0.18957	0.245000	0.21373	0.591000	0.81541	GAG		0.348	NKIRAS1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340876.2	NM_020345		A	23934592	C	A	23934592	3	1	61	1	0	0	0	0	1	0	0	0	10475	912	32	2	9	2	NKIRAS1	3	23934592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2455953	23934592	174087838	2335	10320										
NR1D2	9975	broad.mit.edu	37	chr3	24001301	24001301	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtctgttggaatgtcaaGagatggtatgttcccagttt	11	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:24001301G>T	ENST00000312521.4	+	4	831	c.512G>T	c.(511-513)aGa>aTa	p.R171I	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	171	Hinge.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R171I(1)		NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						GGAATGTCAAGAGATGGTATG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											158	144	149					3																	24001301		2203	4300	6503	23976305	SO:0001583	missense	9975			BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.512G>T	3.37:g.24001301G>T	ENSP00000310006:p.Arg171Ile		23976305	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	37	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.485073	0.63962	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.97480	-4.4	5.85	5.85	0.93711	Nuclear hormone receptor, ligand-binding (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.98782	0.9590	M	0.89968	3.075	0.80722	D	1	D	0.67145	0.996	D	0.72982	0.979	D	0.99342	1.0912	10	0.87932	D	0	.	20.1589	0.98128	0.0:0.0:1.0:0.0	.	171	Q14995	NR1D2_HUMAN	I	171	ENSP00000310006:R171I	ENSP00000310006:R171I	R	+	2	0	NR1D2	23976305	1.000000	0.71417	0.977000	0.42913	0.083000	0.17756	8.042000	0.89430	2.769000	0.95229	0.650000	0.86243	AGA		0.398	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			T	24001301	G	T	24001301	3	4	61	1	0	0	0	0	1	0	0	0	10647	942	33	2	526	2	NR1D2	3	24001301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66709	24001301	174021129	2336	10321										
NR1D2	9975	broad.mit.edu	37	chr3	24003817	24003817	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggagaacggattcccaaGaacatggagcaatataattt	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:24003817G>T	ENST00000312521.4	+	5	1186	c.867G>T	c.(865-867)aaG>aaT	p.K289N	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	289	Ligand-binding.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.K289N(1)		NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						GGATTCCCAAGAACATGGAGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	59	60					3																	24003817		2203	4300	6503	23978821	SO:0001583	missense	9975			BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.867G>T	3.37:g.24003817G>T	ENSP00000310006:p.Lys289Asn		23978821	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	37	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299547	0.40694	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.92149	-2.98	5.84	2.09	0.27110	.	0.182555	0.46758	D	0.000277	D	0.82701	0.5094	N	0.22421	0.69	0.27932	N	0.937847	B	0.06786	0.001	B	0.06405	0.002	T	0.66889	-0.5809	10	0.16896	T	0.51	.	8.5247	0.33298	0.2968:0.0:0.7032:0.0	.	289	Q14995	NR1D2_HUMAN	N	289	ENSP00000310006:K289N	ENSP00000310006:K289N	K	+	3	2	NR1D2	23978821	0.928000	0.31464	0.993000	0.49108	0.880000	0.50808	0.479000	0.22228	0.381000	0.24851	0.655000	0.94253	AAG		0.458	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			T	24003817	G	T	24003817	3	4	61	1	0	0	0	0	1	0	0	0	10647	933	33	2	885	2	NR1D2	3	24003817	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2516	24003817	174018613	2337	10322										
TOP2B	7155	broad.mit.edu	37	chr3	25639883	25639883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcctagcccgaccggttCgtggcagagaaggtggctca	13	12	1	1	rs184041688		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:25639883C>T	ENST00000264331.4	-	36	4795	c.4796G>A	c.(4795-4797)cGa>cAa	p.R1599Q	TOP2B_ENST00000435706.2_Missense_Mutation_p.R1594Q|TOP2B_ENST00000540199.1_Missense_Mutation_p.R451Q|TOP2B_ENST00000542520.1_Missense_Mutation_p.R451Q	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1599					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.R1594Q(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	CCGACCGGTTCGTGGCAGAGA	0.413													C|||	1	0.000199681	0	0	5008	,	,		18073	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											89	91	91					3																	25639883		1866	4096	5962	25614887	SO:0001583	missense	7155			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.4796G>A	3.37:g.25639883C>T	ENSP00000264331:p.Arg1599Gln		25614887	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.05	3.751359	0.69533	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.64	5.64	0.86602	DTHCT (1);	0.064498	0.64402	D	0.000006	T	0.43411	0.1246	N	0.08118	0	0.58432	D	0.999994	D;D	0.59357	0.985;0.981	P;P	0.48873	0.593;0.458	T	0.50233	-0.8852	10	0.49607	T	0.09	-7.5049	17.8735	0.88818	0.0:1.0:0.0:0.0	.	1599;1594	Q02880;Q02880-2	TOP2B_HUMAN;.	Q	451;1594;1599;451	ENSP00000446023:R451Q;ENSP00000396704:R1594Q;ENSP00000264331:R1599Q;ENSP00000437352:R451Q	ENSP00000264331:R1599Q	R	-	2	0	TOP2B	25614887	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	6.298000	0.72763	2.662000	0.90505	0.591000	0.81541	CGA		0.413	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				T	25639883	C	T	25639883	3	4	61	1	0	0	0	0	1	0	0	0	16406	884	31	1	88	1	TOP2B	3	25639883	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1636066	25639883	172382547	2338	10323										
TOP2B	7155	broad.mit.edu	37	chr3	25646332	25646332	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaaaacagaagcagaatCttcttcattactgtcaaatt	5	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:25646332C>A	ENST00000264331.4	-	33	4407	c.4408G>T	c.(4408-4410)Gat>Tat	p.D1470Y	TOP2B_ENST00000435706.2_Missense_Mutation_p.D1465Y|TOP2B_ENST00000540199.1_Missense_Mutation_p.D322Y|TOP2B_ENST00000542520.1_Missense_Mutation_p.D322Y	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1470					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.D1465Y(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GAAGCAGAATCTTCTTCATTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	110	112					3																	25646332		1811	4068	5879	25621336	SO:0001583	missense	7155			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.4408G>T	3.37:g.25646332C>A	ENSP00000264331:p.Asp1470Tyr		25621336	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	C	19.71	3.878740	0.72294	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.49720	0.77;0.85;0.85;0.77	5.48	5.48	0.80851	.	0.262894	0.42964	D	0.000636	T	0.51261	0.1664	N	0.08118	0	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.995;0.996	T	0.61744	-0.7000	10	0.66056	D	0.02	-20.2424	17.9046	0.88914	0.0:1.0:0.0:0.0	.	1470;1465	Q02880;Q02880-2	TOP2B_HUMAN;.	Y	322;1465;1470;322	ENSP00000446023:D322Y;ENSP00000396704:D1465Y;ENSP00000264331:D1470Y;ENSP00000437352:D322Y	ENSP00000264331:D1470Y	D	-	1	0	TOP2B	25621336	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.225000	0.65294	2.722000	0.93159	0.563000	0.77884	GAT		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				A	25646332	C	A	25646332	3	1	61	1	0	0	0	0	1	0	0	0	16406	913	32	2	488	2	TOP2B	3	25646332	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6449	25646332	172376098	2339	10324										
TOP2B	7155	broad.mit.edu	37	chr3	25651069	25651069	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttctcaccaggctccttCttctccctcttaggtttggg	7	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:25651069C>A	ENST00000264331.4	-	29	3920	c.3921G>T	c.(3919-3921)aaG>aaT	p.K1307N	TOP2B_ENST00000435706.2_Missense_Mutation_p.K1302N|TOP2B_ENST00000540199.1_Missense_Mutation_p.K159N|TOP2B_ENST00000542520.1_Missense_Mutation_p.K159N|TOP2B_ENST00000475717.1_5'Flank	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1307					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.K1302N(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	CAGGCTCCTTCTTCTCCCTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	54	56					3																	25651069		1848	4089	5937	25626073	SO:0001583	missense	7155			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.3921G>T	3.37:g.25651069C>A	ENSP00000264331:p.Lys1307Asn		25626073	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	C	16.05	3.013150	0.54468	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.54479	0.57;0.82;0.83;0.57	5.72	1.66	0.24008	.	0.082849	0.85682	D	0.000000	T	0.62221	0.2410	M	0.64997	1.995	0.58432	D	0.999994	D;D	0.59357	0.975;0.985	P;P	0.61397	0.776;0.888	T	0.60110	-0.7327	10	0.59425	D	0.04	-11.6026	9.4004	0.38428	0.0:0.3389:0.0:0.6611	.	1307;1302	Q02880;Q02880-2	TOP2B_HUMAN;.	N	159;1302;1307;159	ENSP00000446023:K159N;ENSP00000396704:K1302N;ENSP00000264331:K1307N;ENSP00000437352:K159N	ENSP00000264331:K1307N	K	-	3	2	TOP2B	25626073	1.000000	0.71417	0.998000	0.56505	0.863000	0.49368	0.763000	0.26517	0.077000	0.16863	-0.438000	0.05819	AAG		0.383	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				A	25651069	C	A	25651069	3	1	61	1	0	0	0	0	1	0	0	0	16406	912	32	2	991	2	TOP2B	3	25651069	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4737	25651069	172371361	2340	10325										
TOP2B	7155	broad.mit.edu	37	chr3	25670600	25670600	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaattgtgatggatgaaatTaataagcaggccttttatgt	9	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:25670600T>G	ENST00000264331.4	-	14	1725	c.1726A>C	c.(1726-1728)Aat>Cat	p.N576H	TOP2B_ENST00000435706.2_Missense_Mutation_p.N571H	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	576	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.N571H(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TGGATGAAATTAATAAGCAGG	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	114	115					3																	25670600		1803	4071	5874	25645604	SO:0001583	missense	7155			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1726A>C	3.37:g.25670600T>G	ENSP00000264331:p.Asn576His		25645604	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	T	23.3	4.400460	0.83120	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.53206	0.63;0.63	5.19	5.19	0.71726	.	0.085999	0.85682	D	0.000000	T	0.80391	0.4614	H	0.98089	4.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88011	0.2762	10	0.87932	D	0	-6.73	15.3297	0.74196	0.0:0.0:0.0:1.0	.	571	Q02880-2	.	H	571;576;571	ENSP00000396704:N571H;ENSP00000264331:N576H	ENSP00000264331:N576H	N	-	1	0	TOP2B	25645604	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.078000	0.62432	0.528000	0.53228	AAT		0.269	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				G	25670600	T	G	25670600	3	3	61	1	0	0	0	0	1	0	0	0	16406	1754	61	4	3246	4	TOP2B	3	25670600	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19531	25670600	172351830	2341	10326										
NGLY1	55768	broad.mit.edu	37	chr3	25775392	25775392	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcccattaatagtgtctcGaagtaatgcttctttaacct	6	9	2	0	rs146140738	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:25775392G>A	ENST00000280700.5	-	8	1391	c.1231C>T	c.(1231-1233)Cga>Tga	p.R411*	NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000417874.2_Nonsense_Mutation_p.R369*|NGLY1_ENST00000428257.1_Nonsense_Mutation_p.R393*|NGLY1_ENST00000467224.1_5'UTR|NGLY1_ENST00000396649.3_Nonsense_Mutation_p.R411*	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	411					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)	p.R411*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						ATAGTGTCTCGAAGTAATGCT	0.358													G|||	2	0.000399361	8e-04	0	5008	,	,		16244	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	3											172	160	164					3																	25775392		2203	4300	6503	25750396	SO:0001587	stop_gained	55768			AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1231C>T	3.37:g.25775392G>A	ENSP00000280700:p.Arg411*		25750396	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Nonsense_Mutation	SNP	ENST00000280700.5	37	CCDS33719.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	40	8.271979	0.98737	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000396649;ENST00000308710;ENST00000417874	.	.	.	5.77	3.71	0.42584	.	0.120349	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-7.9369	14.9594	0.71144	0.0:0.0:0.6274:0.3726	.	.	.	.	X	393;411;411;390;369	.	ENSP00000280700:R411X	R	-	1	2	NGLY1	25750396	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.915000	0.48805	1.552000	0.49463	0.655000	0.94253	CGA		0.358	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			A	25775392	G	A	25775392	4	1	61	1	0	0	0	0	0	1	0	0	10429	1066	37	1	753	1	NGLY1	3	25775392	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104792	25775392	172247038	2342	10327										
NEK10	152110	broad.mit.edu	37	chr3	27326180	27326180	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctccttgtgtaagtatcGaagagctaagcacagcttga	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:27326180G>A	ENST00000429845.2	-	23	2289	c.1927C>T	c.(1927-1929)Cga>Tga	p.R643*	NEK10_ENST00000357467.2_Nonsense_Mutation_p.R40*|NEK10_ENST00000341435.5_Nonsense_Mutation_p.R643*			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R643*(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TGTAAGTATCGAAGAGCTAAG	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											128	121	123					3																	27326180		2203	4300	6503	27301184	SO:0001587	stop_gained	152110			AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1927C>T	3.37:g.27326180G>A	ENSP00000395849:p.Arg643*		27301184	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Nonsense_Mutation	SNP	ENST00000429845.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	44|44	11.069275|11.069275	0.99511|0.99511	.|.	.|.	ENSG00000163491|ENSG00000163491	ENST00000357467;ENST00000341435;ENST00000396636|ENST00000435584	.|.	.|.	.|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.057211|.	0.64402|.	D|.	0.000002|.	.|T	.|0.81113	.|0.4755	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.78534	.|-0.2167	.|3	0.02654|.	T|.	1|.	.|.	20.5373|20.5373	0.99239|0.99239	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	40;643;643|99	.|.	ENSP00000343847:R643X|.	R|S	-|-	1|2	2|0	NEK10|NEK10	27301184|27301184	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	3.945000|3.945000	0.56637|0.56637	2.857000|2.857000	0.98124|0.98124	0.650000|0.650000	0.86243|0.86243	CGA|TCG		0.373	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		A	27326180	G	A	27326180	4	1	61	1	0	0	0	0	0	1	0	0	10353	1066	37	1	223	1	NEK10	3	27326180	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1550788	27326180	170696250	2343	10328										
NEK10	152110	broad.mit.edu	37	chr3	27343247	27343247	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaagtcttctgataaatGaagctgctggattcggcctg	11	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:27343247G>T	ENST00000429845.2	-	14	1470	c.1108C>A	c.(1108-1110)Cat>Aat	p.H370N	NEK10_ENST00000341435.5_Missense_Mutation_p.H370N			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	370					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.H370N(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTGATAAATGAAGCTGCTGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											38	34	35					3																	27343247		1564	3577	5141	27318251	SO:0001583	missense	152110			AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1108C>A	3.37:g.27343247G>T	ENSP00000395849:p.His370Asn		27318251	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		.	.	.	.	.	.	.	.	.	.	G	13.20	2.166520	0.38217	.	.	ENSG00000163491	ENST00000341435;ENST00000396636	T	0.68624	-0.34	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.672210	0.14741	N	0.301170	T	0.43942	0.1270	N	0.08118	0	0.80722	D	1	B	0.30664	0.289	B	0.25614	0.062	T	0.40776	-0.9545	10	0.32370	T	0.25	.	10.5415	0.45035	0.1516:0.0:0.8484:0.0	.	370	Q6ZWH5	NEK10_HUMAN	N	370	ENSP00000343847:H370N	ENSP00000343847:H370N	H	-	1	0	NEK10	27318251	1.000000	0.71417	0.996000	0.52242	0.842000	0.47809	4.485000	0.60279	2.509000	0.84616	0.585000	0.79938	CAT		0.363	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		T	27343247	G	T	27343247	3	4	61	1	0	0	0	0	1	0	0	0	10353	1290	45	2	1078	2	NEK10	3	27343247	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17067	27343247	170679183	2344	10329										
NEK10	152110	broad.mit.edu	37	chr3	27385841	27385841	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggatgtttgctgaaatttCtctcattcttgtagtttata	8	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:27385841C>A	ENST00000429845.2	-	6	646	c.284G>T	c.(283-285)aGa>aTa	p.R95I	NEK10_ENST00000341435.5_Missense_Mutation_p.R95I			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	95					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R95I(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GCTGAAATTTCTCTCATTCTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	92	98					3																	27385841		1565	3580	5145	27360845	SO:0001583	missense	152110			AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.284G>T	3.37:g.27385841C>A	ENSP00000395849:p.Arg95Ile		27360845	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		.	.	.	.	.	.	.	.	.	.	C	26.9	4.779319	0.90195	.	.	ENSG00000163491	ENST00000341435;ENST00000396636;ENST00000435750;ENST00000429845	T;T;T	0.75821	-0.81;0.16;-0.97	5.76	5.76	0.90799	.	0.195974	0.51477	D	0.000093	D	0.83608	0.5291	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.68765	0.96	D	0.84200	0.0450	10	0.87932	D	0	.	18.1155	0.89553	0.0:1.0:0.0:0.0	.	95	Q6ZWH5	NEK10_HUMAN	I	95	ENSP00000343847:R95I;ENSP00000395338:R95I;ENSP00000395849:R95I	ENSP00000343847:R95I	R	-	2	0	NEK10	27360845	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.189000	0.65098	2.880000	0.98712	0.650000	0.86243	AGA		0.373	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		A	27385841	C	A	27385841	3	1	61	1	0	0	0	0	1	0	0	0	10353	913	32	2	1934	2	NEK10	3	27385841	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42594	27385841	170636589	2345	10330										
SLC4A7	9497	broad.mit.edu	37	chr3	27453232	27453232	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgaaacacaggaatctttCtcttttcctgaatttcacaa	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:27453232C>A	ENST00000295736.5	-	12	1710	c.1640G>T	c.(1639-1641)aGa>aTa	p.R547I	SLC4A7_ENST00000454389.1_Missense_Mutation_p.R556I|SLC4A7_ENST00000425128.2_Missense_Mutation_p.R539I|SLC4A7_ENST00000435667.2_Missense_Mutation_p.R432I|SLC4A7_ENST00000446700.1_Missense_Mutation_p.R539I|SLC4A7_ENST00000437179.1_Missense_Mutation_p.R428I|SLC4A7_ENST00000428386.1_Missense_Mutation_p.R423I|SLC4A7_ENST00000445684.1_Missense_Mutation_p.R543I|SLC4A7_ENST00000440156.1_Missense_Mutation_p.R543I|SLC4A7_ENST00000388777.4_Missense_Mutation_p.R97I|SLC4A7_ENST00000455077.1_Missense_Mutation_p.R428I	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	547					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.R547I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	AGGAATCTTTCTCTTTTCCTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											43	46	45					3																	27453232		2202	4300	6502	27428236	SO:0001583	missense	9497			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.1640G>T	3.37:g.27453232C>A	ENSP00000295736:p.Arg547Ile		27428236	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	C	32	5.109565	0.94292	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000425128;ENST00000428179	D;D;D;D;D;D;D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.63	5.63	0.86233	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.040549	0.85682	D	0.000000	D	0.92727	0.7688	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.998;1.0;0.996;0.996;0.998;0.999;1.0;0.996;0.993	D;D;D;D;D;D;D;D;D	0.97110	0.969;0.999;0.969;0.969;0.969;0.988;1.0;0.969;0.917	D	0.93170	0.6565	10	0.87932	D	0	.	20.054	0.97641	0.0:1.0:0.0:0.0	.	543;428;539;543;556;97;423;547;428	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	I	98;547;423;556;543;428;539;428;543;432;97;539;443	ENSP00000411031:R98I;ENSP00000295736:R547I;ENSP00000416368:R423I;ENSP00000390394:R556I;ENSP00000414797:R543I;ENSP00000394252:R428I;ENSP00000406605:R539I;ENSP00000407382:R428I;ENSP00000406804:R543I;ENSP00000395336:R432I;ENSP00000373429:R97I;ENSP00000401949:R539I;ENSP00000388703:R443I	ENSP00000295736:R547I	R	-	2	0	SLC4A7	27428236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.294000	0.78760	2.808000	0.96608	0.655000	0.94253	AGA		0.398	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		A	27453232	C	A	27453232	3	1	61	1	0	0	0	0	1	0	0	0	14695	913	32	2	2060	2	SLC4A7	3	27453232	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67391	27453232	170569198	2346	10331										
SLC4A7	9497	broad.mit.edu	37	chr3	27460089	27460089	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagataagaggtcatttCtgtcttttgctttataagct	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:27460089C>A	ENST00000295736.5	-	11	1590	c.1520G>T	c.(1519-1521)aGa>aTa	p.R507I	SLC4A7_ENST00000454389.1_Missense_Mutation_p.R516I|SLC4A7_ENST00000425128.2_Missense_Mutation_p.R499I|SLC4A7_ENST00000435667.2_Missense_Mutation_p.R392I|SLC4A7_ENST00000446700.1_Missense_Mutation_p.R499I|SLC4A7_ENST00000437179.1_Missense_Mutation_p.R388I|SLC4A7_ENST00000428386.1_Missense_Mutation_p.R383I|SLC4A7_ENST00000445684.1_Missense_Mutation_p.R503I|SLC4A7_ENST00000440156.1_Missense_Mutation_p.R503I|RN7SL859P_ENST00000578725.1_RNA|SLC4A7_ENST00000388777.4_Missense_Mutation_p.R57I|SLC4A7_ENST00000455077.1_Missense_Mutation_p.R388I	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	507					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.R507I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	GAGGTCATTTCTGTCTTTTGC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	76	77					3																	27460089		2202	4300	6502	27435093	SO:0001583	missense	9497			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.1520G>T	3.37:g.27460089C>A	ENSP00000295736:p.Arg507Ile		27435093	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	C	34	5.335156	0.95758	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000425128;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.73	5.73	0.89815	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.113243	0.64402	D	0.000004	D	0.87943	0.6305	M	0.89840	3.065	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.997;1.0;0.994;1.0;1.0;1.0	D	0.89616	0.3845	10	0.87932	D	0	.	19.8951	0.96955	0.0:1.0:0.0:0.0	.	503;388;499;503;516;57;383;507;388	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	I	58;507;383;516;503;388;499;388;503;392;57;499;403	ENSP00000411031:R58I;ENSP00000295736:R507I;ENSP00000416368:R383I;ENSP00000390394:R516I;ENSP00000414797:R503I;ENSP00000394252:R388I;ENSP00000406605:R499I;ENSP00000407382:R388I;ENSP00000406804:R503I;ENSP00000395336:R392I;ENSP00000373429:R57I;ENSP00000401949:R499I;ENSP00000388703:R403I	ENSP00000295736:R507I	R	-	2	0	SLC4A7	27435093	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.725000	0.84808	2.694000	0.91930	0.655000	0.94253	AGA		0.318	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		A	27460089	C	A	27460089	3	1	61	1	0	0	0	0	1	0	0	0	14695	913	32	2	2184	2	SLC4A7	3	27460089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6857	27460089	170562341	2347	10332										
ZCWPW2	152098	broad.mit.edu	37	chr3	28454571	28454571	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccttaatggataaagaAaaattggatgttaagattga	9	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:28454571A>C	ENST00000383768.2	+	3	200	c.12A>C	c.(10-12)gaA>gaC	p.E4D	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.E4D			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	4							zinc ion binding (GO:0008270)	p.E4D(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TGGATAAAGAAAAATTGGATG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	62	61					3																	28454571		2203	4300	6503	28429575	SO:0001583	missense	152098			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.12A>C	3.37:g.28454571A>C	ENSP00000373278:p.Glu4Asp		28429575		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406087	0.25378	.	.	ENSG00000206559	ENST00000420223;ENST00000383768;ENST00000421010	T;T	0.35048	1.33;1.33	5.16	1.46	0.22682	.	1.117560	0.07053	N	0.832244	T	0.23766	0.0575	L	0.27053	0.805	0.09310	N	1	B	0.26002	0.139	B	0.19391	0.025	T	0.26155	-1.0111	10	0.24483	T	0.36	0.7968	6.7144	0.23294	0.7032:0.0:0.2968:0.0	.	4	Q504Y3	ZCPW2_HUMAN	D	4	ENSP00000373278:E4D;ENSP00000412386:E4D	ENSP00000373278:E4D	E	+	3	2	ZCWPW2	28429575	0.969000	0.33509	0.010000	0.14722	0.061000	0.15899	2.582000	0.46085	0.073000	0.16731	-0.353000	0.07706	GAA		0.299	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		C	28454571	A	C	28454571	3	2	61	1	0	0	0	0	1	0	0	0	17637	11	1	4	14	4	ZCWPW2	3	28454571	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	994482	28454571	169567859	2348	10333										
ZCWPW2	152098	broad.mit.edu	37	chr3	28557063	28557063	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaagcaattttaaaatgCtcttttgaaaatgtttattc	6	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:28557063C>T	ENST00000383768.2	+	8	923	c.735C>T	c.(733-735)tgC>tgT	p.C245C	ZCWPW2_ENST00000421010.1_Silent_p.C245C			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	245							zinc ion binding (GO:0008270)	p.C245C(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TTTTAAAATGCTCTTTTGAAA	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	3											44	46	46					3																	28557063		2203	4295	6498	28532067	SO:0001819	synonymous_variant	152098			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.735C>T	3.37:g.28557063C>T			28532067		Silent	SNP	ENST00000383768.2	37	CCDS33723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.071|0.071	-1.201905|-1.201905	0.01581|0.01581	.|.	.|.	ENSG00000206559|ENSG00000206559	ENST00000457897|ENST00000419130	.|.	.|.	.|.	5.61|5.61	1.8|1.8	0.24995|0.24995	.|.	.|.	.|.	.|.	.|.	T|T	0.51449|0.51449	0.1675|0.1675	.|.	.|.	.|.	0.42466|0.42466	D|D	0.992807|0.992807	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39603|0.39603	-0.9606|-0.9606	4|4	.|.	.|.	.|.	2.2595|2.2595	4.7762|4.7762	0.13180|0.13180	0.1489:0.6053:0.0:0.2458|0.1489:0.6053:0.0:0.2458	.|.	.|.	.|.	.|.	V|F	68|130	.|.	.|.	A|L	+|+	2|1	0|0	ZCWPW2|ZCWPW2	28532067|28532067	0.010000|0.010000	0.17322|0.17322	0.872000|0.872000	0.34217|0.34217	0.055000|0.055000	0.15305|0.15305	-0.457000|-0.457000	0.06745|0.06745	0.337000|0.337000	0.23665|0.23665	-0.145000|-0.145000	0.13849|0.13849	GCT|CTC		0.303	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		T	28557063	C	T	28557063	2	4	61	1	0	0	0	0	0	0	0	1	17637	805	28	3		3	ZCWPW2	3	28557063	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102492	28557063	169465367	2349	10334										
RBMS3	27303	broad.mit.edu	37	chr3	29476320	29476320	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagcagcaacaacagcagCggggaacagttgagtaaaac	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:29476320C>T	ENST00000383767.2	+	2	498	c.162C>T	c.(160-162)agC>agT	p.S54S	RBMS3_ENST00000445033.1_Silent_p.S54S|RBMS3_ENST00000456853.1_Silent_p.S54S|RBMS3_ENST00000452462.1_Silent_p.S54S|RBMS3_ENST00000396583.3_Silent_p.S54S|RBMS3_ENST00000383766.2_Silent_p.S53S|RBMS3_ENST00000273139.9_Silent_p.S54S|RBMS3_ENST00000434693.2_Silent_p.S53S			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	54					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)	p.S54S(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				acaacagcagcGGGGAACAGT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	3											217	164	182					3																	29476320		2203	4300	6503	29451324	SO:0001819	synonymous_variant	27303			AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.162C>T	3.37:g.29476320C>T			29451324	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	37	CCDS33724.1																																																																																				0.552	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		T	29476320	C	T	29476320	2	4	61	1	0	0	0	0	0	0	0	1	13187	767	27	1		1	RBMS3	3	29476320	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	919257	29476320	168546110	2350	10335										
STT3B	201595	broad.mit.edu	37	chr3	31666425	31666425	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaccaggaatatcttagatGattttagagaagcttacttt	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:31666425G>T	ENST00000295770.2	+	12	1956	c.1747G>T	c.(1747-1749)Gat>Tat	p.D583Y		NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	583					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.D583Y(2)		autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TATCTTAGATGATTTTAGAGA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	3											127	128	128					3																	31666425		2203	4300	6503	31641429	SO:0001583	missense	201595			AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1747G>T	3.37:g.31666425G>T	ENSP00000295770:p.Asp583Tyr		31641429	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394070	0.83011	.	.	ENSG00000163527	ENST00000295770	D	0.90844	-2.74	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.97071	0.9043	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98283	1.0509	10	0.87932	D	0	-9.6778	18.8245	0.92111	0.0:0.0:1.0:0.0	.	583	Q8TCJ2	STT3B_HUMAN	Y	583	ENSP00000295770:D583Y	ENSP00000295770:D583Y	D	+	1	0	STT3B	31641429	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.524000	0.85096	0.313000	0.20887	GAT		0.358	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		T	31666425	G	T	31666425	3	4	61	1	0	0	0	0	1	0	0	0	15373	1290	45	2	1793	2	STT3B	3	31666425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2190105	31666425	166356005	2351	10336										
OSBPL10	114884	broad.mit.edu	37	chr3	31725525	31725525	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccccagcggtgatggccaGcagtaggtctgggtgcgcca	17	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:31725525G>A	ENST00000396556.2	-	8	1449	c.1327C>T	c.(1327-1329)Ctg>Ttg	p.L443L	OSBPL10_ENST00000438237.2_Silent_p.L379L	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	443					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.L443L(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		GTGATGGCCAGCAGTAGGTCT	0.537																																																2	Substitution - coding silent(2)	large_intestine(2)	3											58	61	60					3																	31725525		2203	4300	6503	31700529	SO:0001819	synonymous_variant	114884			AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1327C>T	3.37:g.31725525G>A			31700529	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1																																																																																				0.537	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	31725525	G	A	31725525	2	1	61	1	0	0	0	0	0	0	0	1	11306	962	34	3		3	OSBPL10	3	31725525	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59100	31725525	166296905	2352	10337										
GPD1L	23171	broad.mit.edu	37	chr3	32207371	32207371	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagttcaagagatgttgtCttgtcttcagagccatccag	9	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:32207371C>A	ENST00000282541.5	+	8	1226	c.1025C>A	c.(1024-1026)tCt>tAt	p.S342Y		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	342					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)	p.S342Y(1)		large_intestine(4)|lung(7)|ovary(1)	12						GAGATGTTGTCTTGTCTTCAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											198	165	176					3																	32207371		2203	4300	6503	32182375	SO:0001583	missense	23171			D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.1025C>A	3.37:g.32207371C>A	ENSP00000282541:p.Ser342Tyr		32182375	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.466213	0.26335	.	.	ENSG00000152642	ENST00000282541	T	0.64085	-0.08	5.81	3.1	0.35709	Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal (1);	0.479195	0.25663	N	0.029127	T	0.50274	0.1606	L	0.46157	1.445	0.39966	D	0.974731	P	0.35959	0.53	B	0.31191	0.125	T	0.50533	-0.8817	10	0.62326	D	0.03	-2.4825	9.5477	0.39291	0.0:0.7537:0.1182:0.1281	.	342	Q8N335	GPD1L_HUMAN	Y	342	ENSP00000282541:S342Y	ENSP00000282541:S342Y	S	+	2	0	GPD1L	32182375	0.000000	0.05858	0.417000	0.26559	0.015000	0.08874	1.237000	0.32695	0.396000	0.25283	-0.122000	0.15005	TCT		0.433	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141		A	32207371	C	A	32207371	3	1	61	1	0	0	0	0	1	0	0	0	6625	913	32	2	1055	2	GPD1L	3	32207371	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	481846	32207371	165815059	2353	10338										
TRIM71	131405	broad.mit.edu	37	chr3	32933287	32933287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggactttggcaacaatcGaatcctcgtcttctaattgc	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:32933287G>A	ENST00000383763.5	+	4	2654	c.2591G>A	c.(2590-2592)cGa>cAa	p.R864Q		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	864					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R864Q(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGCAACAATCGAATCCTCGTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	100	98					3																	32933287		2015	4163	6178	32908291	SO:0001583	missense	131405				CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.2591G>A	3.37:g.32933287G>A	ENSP00000373272:p.Arg864Gln		32908291		Missense_Mutation	SNP	ENST00000383763.5	37	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401530	0.83120	.	.	ENSG00000206557	ENST00000383763	T	0.77620	-1.11	5.87	5.87	0.94306	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89729	0.6799	M	0.89214	3.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87468	0.2412	10	0.25106	T	0.35	-9.5038	18.7681	0.91881	0.0:0.0:1.0:0.0	.	864	Q2Q1W2	LIN41_HUMAN	Q	864	ENSP00000373272:R864Q	ENSP00000373272:R864Q	R	+	2	0	TRIM71	32908291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.827000	0.99397	2.779000	0.95612	0.591000	0.81541	CGA		0.512	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		A	32933287	G	A	32933287	3	1	61	1	0	0	0	0	1	0	0	0	16584	1058	37	1	2605	1	TRIM71	3	32933287	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	725916	32933287	165089143	2354	10339										
UBP1	7342	broad.mit.edu	37	chr3	33438616	33438616	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctcctttgtcagttttaAtaagtcggcacctagagaag	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33438616A>C	ENST00000283629.3	-	12	1721	c.1192T>G	c.(1192-1194)Tta>Gta	p.L398V	UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Missense_Mutation_p.L362V|UBP1_ENST00000283628.5_Missense_Mutation_p.L398V	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	398					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.L398V(1)		breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GTCAGTTTTAATAAGTCGGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	76	76					3																	33438616		2203	4300	6503	33413620	SO:0001583	missense	7342			AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1192T>G	3.37:g.33438616A>C	ENSP00000283629:p.Leu398Val		33413620	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.289121	0.40494	.	.	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.39229	1.09;1.28;1.09	4.83	-7.46	0.01369	Sterile alpha motif/pointed domain (1);	0.083889	0.48286	D	0.000192	T	0.34366	0.0895	L	0.52573	1.65	0.45962	D	0.998786	B;B	0.28082	0.011;0.2	B;B	0.33620	0.011;0.167	T	0.11717	-1.0576	10	0.87932	D	0	-9.1521	14.3779	0.66892	0.7212:0.0:0.2788:0.0	.	362;398	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	V	398;362;398	ENSP00000283629:L398V;ENSP00000395558:L362V;ENSP00000283628:L398V	ENSP00000283628:L398V	L	-	1	2	UBP1	33413620	0.927000	0.31430	0.583000	0.28640	0.991000	0.79684	0.101000	0.15251	-1.723000	0.01375	-0.248000	0.11899	TTA		0.373	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		C	33438616	A	C	33438616	3	2	61	1	0	0	0	0	1	0	0	0	16935	98	4	4	450	4	UBP1	3	33438616	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	505329	33438616	164583814	2355	10340										
CLASP2	23122	broad.mit.edu	37	chr3	33540152	33540152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagaaacatcagtagtggGatcagctcctccagaacctg	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33540152G>A	ENST00000468888.2	-	39	4562	c.4516C>T	c.(4516-4518)Ccc>Tcc	p.P1506S	CLASP2_ENST00000307312.7_Missense_Mutation_p.P987S|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000399362.4_Missense_Mutation_p.P1505S|CLASP2_ENST00000359576.5_Missense_Mutation_p.P1497S|CLASP2_ENST00000461133.3_Missense_Mutation_p.P1265S|CLASP2_ENST00000480013.1_Missense_Mutation_p.P1285S			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1286					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.P1498S(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCAGTAGTGGGATCAGCTCCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											173	159	163					3																	33540152		1915	4125	6040	33515156	SO:0001583	missense	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4516C>T	3.37:g.33540152G>A	ENSP00000419974:p.Pro1506Ser		33515156	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.86|11.86	1.765355|1.765355	0.31228|0.31228	.|.	.|.	ENSG00000163539|ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133|ENST00000487553	T;T;T|.	0.15017|.	2.46;2.46;2.47|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.166717|.	0.53938|.	D|.	0.000045|.	T|T	0.14399|0.14399	0.0348|0.0348	N|N	0.02011|0.02011	-0.69|-0.69	0.18873|0.18873	N|N	0.999984|0.999984	B;B|.	0.11235|.	0.001;0.004|.	B;B|.	0.09377|.	0.004;0.004|.	T|T	0.14008|0.14008	-1.0488|-1.0488	10|5	0.02654|.	T|.	1|.	-5.2873|-5.2873	9.4662|9.4662	0.38813|0.38813	0.0:0.1431:0.6879:0.169|0.0:0.1431:0.6879:0.169	.|.	1497;1505|.	F5H604;E7ERI8|.	.;.|.	S|F	1506;1505;1497;987;1285;1265|211	ENSP00000419974:P1506S;ENSP00000382297:P1505S;ENSP00000352581:P1497S|.	ENSP00000304743:P987S|.	P|S	-|-	1|2	0|0	CLASP2|CLASP2	33515156|33515156	0.998000|0.998000	0.40836|0.40836	0.988000|0.988000	0.46212|0.46212	0.998000|0.998000	0.95712|0.95712	2.081000|2.081000	0.41596|0.41596	2.542000|2.542000	0.85734|0.85734	0.655000|0.655000	0.94253|0.94253	CCC|TCC		0.433	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		A	33540152	G	A	33540152	3	1	61	1	0	0	0	0	1	0	0	0	3461	1174	41	3	32	3	CLASP2	3	33540152	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101536	33540152	164482278	2356	10341										
CLASP2	23122	broad.mit.edu	37	chr3	33645687	33645687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttgctgtagaccatttgGaagaaaaagggcgactgcaa	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33645687G>A	ENST00000468888.2	-	17	1758	c.1712C>T	c.(1711-1713)tCc>tTc	p.S571F	CLASP2_ENST00000359576.5_Missense_Mutation_p.S570F|CLASP2_ENST00000307312.7_Missense_Mutation_p.S59F|CLASP2_ENST00000333778.6_Missense_Mutation_p.S347F|CLASP2_ENST00000539981.1_Missense_Mutation_p.S322F|CLASP2_ENST00000461133.3_Missense_Mutation_p.S337F|CLASP2_ENST00000399362.4_Missense_Mutation_p.S570F|CLASP2_ENST00000487200.1_Missense_Mutation_p.S343F|CLASP2_ENST00000313350.6_Missense_Mutation_p.S343F|CLASP2_ENST00000480013.1_Missense_Mutation_p.S337F			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	337	Interaction with microtubules, MAPRE1 and MAPRE3.|Ser-rich.				axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.S570F(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						AGACCATTTGGAAGAAAAAGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											29	28	28					3																	33645687		1781	4041	5822	33620691	SO:0001583	missense	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.1712C>T	3.37:g.33645687G>A	ENSP00000419974:p.Ser571Phe		33620691	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	G	19.27	3.794859	0.70452	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000539981;ENST00000480013;ENST00000461133;ENST00000313350;ENST00000487200;ENST00000333778	T;T;T	0.20881	2.04;2.05;2.04	5.35	5.35	0.76521	Armadillo-type fold (1);	0.123266	0.56097	D	0.000026	T	0.40272	0.1110	L	0.54323	1.7	0.44668	D	0.997659	D;D;D;D;D	0.64830	0.964;0.991;0.964;0.979;0.994	P;P;P;P;D	0.74348	0.65;0.762;0.65;0.81;0.983	T	0.03034	-1.1080	10	0.17832	T	0.49	-5.7924	17.2341	0.86994	0.0:0.0:1.0:0.0	.	347;337;343;343;570	E7ENG2;O75122;B3KR06;O75122-2;F5H604	.;CLAP2_HUMAN;.;.;.	F	571;570;570;59;322;337;337;343;343;347	ENSP00000419974:S571F;ENSP00000382297:S570F;ENSP00000352581:S570F	ENSP00000304743:S59F	S	-	2	0	CLASP2	33620691	1.000000	0.71417	0.994000	0.49952	0.708000	0.40852	5.994000	0.70623	2.668000	0.90789	0.563000	0.77884	TCC		0.323	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		A	33645687	G	A	33645687	3	1	61	1	0	0	0	0	1	0	0	0	3461	1174	41	3	2899	3	CLASP2	3	33645687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105535	33645687	164376743	2357	10342										
CLASP2	23122	broad.mit.edu	37	chr3	33648232	33648232	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcaccaggaaagtggttTctaagacccatgtatgtcct	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33648232T>G	ENST00000468888.2	-	16	1594	c.1548A>C	c.(1546-1548)agA>agC	p.R516S	CLASP2_ENST00000359576.5_Missense_Mutation_p.R515S|CLASP2_ENST00000307312.7_Missense_Mutation_p.R4S|CLASP2_ENST00000333778.6_Missense_Mutation_p.R292S|CLASP2_ENST00000539981.1_Missense_Mutation_p.R267S|CLASP2_ENST00000461133.3_Missense_Mutation_p.R282S|CLASP2_ENST00000399362.4_Missense_Mutation_p.R515S|CLASP2_ENST00000487200.1_Missense_Mutation_p.R288S|CLASP2_ENST00000313350.6_Missense_Mutation_p.R288S|CLASP2_ENST00000480013.1_Missense_Mutation_p.R282S			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	282	Interaction with microtubules, MAPRE1 and MAPRE3.|Ser-rich.				axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.R515S(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GAAAGTGGTTTCTAAGACCCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											134	132	133					3																	33648232		1833	4073	5906	33623236	SO:0001583	missense	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.1548A>C	3.37:g.33648232T>G	ENSP00000419974:p.Arg516Ser		33623236	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	T	18.15	3.560667	0.65538	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000539981;ENST00000480013;ENST00000461133;ENST00000313350;ENST00000487200;ENST00000333778	T;T;T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.02;0.02;0.02;1.59;1.59;1.59	5.05	2.57	0.30868	Armadillo-type fold (1);CLASP N-terminal domain (1);	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	L	0.37800	1.135	0.45427	D	0.998404	B;D;P;B;D	0.59767	0.07;0.986;0.898;0.067;0.969	B;P;P;B;P	0.58928	0.105;0.848;0.696;0.064;0.723	T	0.56798	-0.7919	10	0.45353	T	0.12	-19.5175	5.8385	0.18621	0.0:0.1479:0.1397:0.7123	.	292;282;288;288;515	E7ENG2;O75122;B3KR06;O75122-2;F5H604	.;CLAP2_HUMAN;.;.;.	S	516;515;515;4;267;282;282;288;288;292	ENSP00000419974:R516S;ENSP00000382297:R515S;ENSP00000352581:R515S;ENSP00000439039:R267S;ENSP00000417518:R282S;ENSP00000419305:R282S;ENSP00000324364:R288S;ENSP00000418939:R288S;ENSP00000327760:R292S	ENSP00000304743:R4S	R	-	3	2	CLASP2	33623236	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.182000	0.32029	0.319000	0.23209	0.533000	0.62120	AGA		0.348	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		G	33648232	T	G	33648232	3	3	61	1	0	0	0	0	1	0	0	0	3461	1780	62	4	3067	4	CLASP2	3	33648232	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2545	33648232	164374198	2358	10343										
PDCD6IP	10015	broad.mit.edu	37	chr3	33877666	33877666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacttcatttatcatgatcGagttccagaccttaaagatc	6	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33877666G>A	ENST00000307296.3	+	8	1342	c.965G>A	c.(964-966)cGa>cAa	p.R322Q	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.R327Q			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	322	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.R322Q(1)		central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TATCATGATCGAGTTCCAGAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											156	159	158					3																	33877666		2203	4300	6503	33852670	SO:0001583	missense	10015			BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.965G>A	3.37:g.33877666G>A	ENSP00000307387:p.Arg322Gln		33852670	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	G	36	5.760463	0.96906	.	.	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.17528	2.27;2.27	5.18	5.18	0.71444	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.40119	0.1104	M	0.76002	2.32	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.67103	0.949;0.949;0.949	T	0.19679	-1.0298	10	0.13853	T	0.58	-7.1397	18.691	0.91582	0.0:0.0:1.0:0.0	.	103;327;322	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	Q	322;327	ENSP00000307387:R322Q;ENSP00000411825:R327Q	ENSP00000307387:R322Q	R	+	2	0	PDCD6IP	33852670	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	9.852000	0.99516	2.407000	0.81776	0.650000	0.86243	CGA		0.393	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			A	33877666	G	A	33877666	3	1	61	1	0	0	0	0	1	0	0	0	11655	1058	37	1	1010	1	PDCD6IP	3	33877666	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229434	33877666	164144764	2359	10344										
PDCD6IP	10015	broad.mit.edu	37	chr3	33885643	33885643	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagaagcaaccgataatGatttaagagcaaaatttaag	8	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:33885643G>T	ENST00000307296.3	+	11	1776	c.1399G>T	c.(1399-1401)Gat>Tat	p.D467Y	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.D472Y			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	467	Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.D467Y(1)		central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						AACCGATAATGATTTAAGAGC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	82	83					3																	33885643		2203	4299	6502	33860647	SO:0001583	missense	10015			BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1399G>T	3.37:g.33885643G>T	ENSP00000307387:p.Asp467Tyr		33860647	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.696402	0.88830	.	.	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.30714	1.52;1.52	5.27	5.27	0.74061	.	0.199470	0.51477	D	0.000083	T	0.39572	0.1083	L	0.29908	0.895	0.80722	D	1	P;P;P	0.51653	0.947;0.947;0.905	P;P;P	0.54499	0.687;0.754;0.687	T	0.27400	-1.0075	10	0.72032	D	0.01	-11.0519	18.9033	0.92452	0.0:0.0:1.0:0.0	.	248;472;467	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	Y	467;472	ENSP00000307387:D467Y;ENSP00000411825:D472Y	ENSP00000307387:D467Y	D	+	1	0	PDCD6IP	33860647	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.221000	0.89774	2.474000	0.83562	0.557000	0.71058	GAT		0.328	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			T	33885643	G	T	33885643	3	4	61	1	0	0	0	0	1	0	0	0	11655	1290	45	2	1456	2	PDCD6IP	3	33885643	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7977	33885643	164136787	2360	10345										
STAC	6769	broad.mit.edu	37	chr3	36484894	36484894	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactttctttcaagaccaaGagtttacggagcaaaagtgc	8	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36484894G>T	ENST00000273183.3	+	2	450	c.150G>T	c.(148-150)aaG>aaT	p.K50N	STAC_ENST00000457375.2_Missense_Mutation_p.K50N|STAC_ENST00000476388.1_3'UTR	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	50					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)	p.K50N(1)		endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						TCAAGACCAAGAGTTTACGGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											75	61	66					3																	36484894		2203	4300	6503	36459898	SO:0001583	missense	6769			D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.150G>T	3.37:g.36484894G>T	ENSP00000273183:p.Lys50Asn		36459898	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	37	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569198	0.65765	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000434649	T;T;T	0.76839	-1.05;0.74;0.59	5.02	3.91	0.45181	.	0.000000	0.85682	D	0.000000	T	0.81631	0.4863	L	0.50333	1.59	0.52099	D	0.999942	D;D	0.71674	0.998;0.993	D;P	0.78314	0.991;0.738	T	0.81127	-0.1074	10	0.59425	D	0.04	.	6.9974	0.24791	0.2089:0.0:0.7911:0.0	.	50;50	E9PEA7;Q99469	.;STAC_HUMAN	N	50;50;39	ENSP00000273183:K50N;ENSP00000393713:K50N;ENSP00000398403:K39N	ENSP00000273183:K50N	K	+	3	2	STAC	36459898	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.443000	0.59994	2.486000	0.83907	0.650000	0.86243	AAG		0.473	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		T	36484894	G	T	36484894	3	4	61	1	0	0	0	0	1	0	0	0	15278	933	33	2	156	2	STAC	3	36484894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2599251	36484894	161537536	2361	10346										
STAC	6769	broad.mit.edu	37	chr3	36587685	36587685	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttccttggcattcagatCtgcgtgagttctgaagaaga	10	8	4	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36587685C>A	ENST00000273183.3	+	11	1413	c.1113C>A	c.(1111-1113)atC>atA	p.I371I	STAC_ENST00000457375.2_Silent_p.I310I	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	371					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)	p.I371I(1)		endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						GCATTCAGATCTGCGTGAGTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	3											112	102	106					3																	36587685		2203	4300	6503	36562689	SO:0001819	synonymous_variant	6769			D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.1113C>A	3.37:g.36587685C>A			36562689	B2R8S8	Silent	SNP	ENST00000273183.3	37	CCDS2662.1																																																																																				0.423	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		A	36587685	C	A	36587685	2	1	61	1	0	0	0	0	0	0	0	1	15278	903	32	2		2	STAC	3	36587685	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102791	36587685	161434745	2362	10347										
TRANK1	9881	broad.mit.edu	37	chr3	36872794	36872794	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctgtccacgtctgccttTttgaagttcccagccctggg	10	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36872794T>G	ENST00000429976.2	-	21	8395	c.8148A>C	c.(8146-8148)aaA>aaC	p.K2716N	TRANK1_ENST00000428977.2_Missense_Mutation_p.K2166N|TRANK1_ENST00000301807.6_Missense_Mutation_p.K2166N	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2716							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.K2166N(1)|p.K2716N(1)|p.K2159N(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						CGTCTGCCTTTTTGAAGTTCC	0.587																																																3	Substitution - Missense(3)	large_intestine(3)	3											54	57	56					3																	36872794		2047	4173	6220	36847798	SO:0001583	missense	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.8148A>C	3.37:g.36872794T>G	ENSP00000416168:p.Lys2716Asn		36847798	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	17.89	3.498928	0.64298	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.35789	1.29;1.71;1.29	5.49	3.09	0.35607	.	0.000000	0.64402	D	0.000004	T	0.44973	0.1319	L	0.34521	1.04	0.36014	D	0.83826	D	0.89917	1.0	D	0.85130	0.997	T	0.54761	-0.8245	10	0.87932	D	0	.	9.1105	0.36725	0.0:0.1546:0.0:0.8454	.	2716	O15050	TRNK1_HUMAN	N	2166;2716;2166	ENSP00000416826:K2166N;ENSP00000416168:K2716N;ENSP00000301807:K2166N	ENSP00000301807:K2166N	K	-	3	2	TRANK1	36847798	0.997000	0.39634	0.998000	0.56505	0.685000	0.39939	0.380000	0.20602	1.014000	0.39417	0.459000	0.35465	AAA		0.587	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		G	36872794	T	G	36872794	3	3	61	1	0	0	0	0	1	0	0	0	16494	1838	64	4	641	4	TRANK1	3	36872794	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	285109	36872794	161149636	2363	10348										
TRANK1	9881	broad.mit.edu	37	chr3	36874377	36874377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggcttccaaaagcaaccCgttgattgccaccaagttca	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36874377C>T	ENST00000429976.2	-	21	6812	c.6565G>A	c.(6565-6567)Ggg>Agg	p.G2189R	TRANK1_ENST00000428977.2_Missense_Mutation_p.G1639R|TRANK1_ENST00000301807.6_Missense_Mutation_p.G1639R	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2189							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.G2189R(1)|p.G1639R(1)|p.G1632R(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						AAAAGCAACCCGTTGATTGCC	0.378																																																3	Substitution - Missense(3)	large_intestine(3)	3											35	35	35					3																	36874377		1840	4086	5926	36849381	SO:0001583	missense	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.6565G>A	3.37:g.36874377C>T	ENSP00000416168:p.Gly2189Arg		36849381	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920590	0.33908	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34667	1.35;1.77;1.35	5.02	5.02	0.67125	.	0.000000	0.52532	D	0.000068	T	0.48768	0.1518	L	0.34521	1.04	0.38837	D	0.955986	D	0.89917	1.0	D	0.77004	0.989	T	0.53041	-0.8494	10	0.72032	D	0.01	.	14.4554	0.67413	0.1478:0.8522:0.0:0.0	.	2189	O15050	TRNK1_HUMAN	R	1639;2189;1639	ENSP00000416826:G1639R;ENSP00000416168:G2189R;ENSP00000301807:G1639R	ENSP00000301807:G1639R	G	-	1	0	TRANK1	36849381	0.993000	0.37304	0.113000	0.21522	0.330000	0.28571	3.934000	0.56553	2.500000	0.84329	0.455000	0.32223	GGG		0.378	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36874377	C	T	36874377	3	4	61	1	0	0	0	0	1	0	0	0	16494	652	23	1	2224	1	TRANK1	3	36874377	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1583	36874377	161148053	2364	10349										
TRANK1	9881	broad.mit.edu	37	chr3	36874778	36874778	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcattgttggtcactcttTtgagagccctgaccagactg	10	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36874778T>G	ENST00000429976.2	-	21	6411	c.6164A>C	c.(6163-6165)aAa>aCa	p.K2055T	TRANK1_ENST00000428977.2_Missense_Mutation_p.K1505T|TRANK1_ENST00000301807.6_Missense_Mutation_p.K1505T	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2055							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.K1498T(1)|p.K1505T(1)|p.K2055T(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GGTCACTCTTTTGAGAGCCCT	0.512																																																3	Substitution - Missense(3)	large_intestine(3)	3											46	46	46					3																	36874778		1878	4133	6011	36849782	SO:0001583	missense	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.6164A>C	3.37:g.36874778T>G	ENSP00000416168:p.Lys2055Thr		36849782	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	12.13	1.845949	0.32606	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.33865	1.39;1.81;1.39	4.5	0.779	0.18550	.	0.393432	0.20785	N	0.085739	T	0.23806	0.0576	L	0.27053	0.805	0.09310	N	1	P	0.46706	0.883	B	0.43508	0.422	T	0.09975	-1.0650	10	0.54805	T	0.06	.	6.3471	0.21355	0.0:0.1518:0.1356:0.7126	.	2055	O15050	TRNK1_HUMAN	T	1505;2055;1505	ENSP00000416826:K1505T;ENSP00000416168:K2055T;ENSP00000301807:K1505T	ENSP00000301807:K1505T	K	-	2	0	TRANK1	36849782	0.008000	0.16893	0.018000	0.16275	0.988000	0.76386	0.797000	0.26999	0.318000	0.23185	0.454000	0.30748	AAA		0.512	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		G	36874778	T	G	36874778	3	3	61	1	0	0	0	0	1	0	0	0	16494	1841	64	4	2625	4	TRANK1	3	36874778	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	401	36874778	161147652	2365	10350										
TRANK1	9881	broad.mit.edu	37	chr3	36875031	36875031	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagcagatatcaagtgcttCtctcagaatgtccttggtgt	9	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36875031C>A	ENST00000429976.2	-	21	6158	c.5911G>T	c.(5911-5913)Gaa>Taa	p.E1971*	TRANK1_ENST00000428977.2_Nonsense_Mutation_p.E1421*|TRANK1_ENST00000301807.6_Nonsense_Mutation_p.E1421*	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1971							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.E1971*(1)|p.E1421*(1)|p.E1414*(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCAAGTGCTTCTCTCAGAATG	0.552																																																3	Substitution - Nonsense(3)	large_intestine(3)	3											47	47	47					3																	36875031		1950	4136	6086	36850035	SO:0001587	stop_gained	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5911G>T	3.37:g.36875031C>A	ENSP00000416168:p.Glu1971*		36850035	Q8N8K0	Nonsense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	45	11.370453	0.99552	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	.	.	.	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	19.3274	0.94267	0.0:1.0:0.0:0.0	.	.	.	.	X	1421;1971;1421	.	ENSP00000301807:E1421X	E	-	1	0	TRANK1	36850035	0.998000	0.40836	0.995000	0.50966	0.983000	0.72400	3.046000	0.49846	2.648000	0.89879	0.561000	0.74099	GAA		0.552	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36875031	C	A	36875031	4	1	61	1	0	0	0	0	0	1	0	0	16494	922	32	2	2878	2	TRANK1	3	36875031	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253	36875031	161147399	2366	10351										
TRANK1	9881	broad.mit.edu	37	chr3	36875271	36875271	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccagctggtcttctatgtCtagctttgagaggacagcca	10	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36875271C>A	ENST00000429976.2	-	21	5918	c.5671G>T	c.(5671-5673)Gac>Tac	p.D1891Y	TRANK1_ENST00000428977.2_Missense_Mutation_p.D1341Y|TRANK1_ENST00000301807.6_Missense_Mutation_p.D1341Y	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1891							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.D1334Y(1)|p.D1891Y(1)|p.D1341Y(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCTTCTATGTCTAGCTTTGAG	0.483																																																3	Substitution - Missense(3)	large_intestine(3)	3											148	142	144					3																	36875271		1934	4146	6080	36850275	SO:0001583	missense	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5671G>T	3.37:g.36875271C>A	ENSP00000416168:p.Asp1891Tyr		36850275	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266442	0.40095	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.37235	1.21;1.63;1.21	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000015	T	0.52175	0.1718	L	0.32530	0.975	0.52501	D	0.999953	D	0.89917	1.0	D	0.87578	0.998	T	0.54043	-0.8352	10	0.72032	D	0.01	.	19.3274	0.94267	0.0:1.0:0.0:0.0	.	1891	O15050	TRNK1_HUMAN	Y	1341;1891;1341	ENSP00000416826:D1341Y;ENSP00000416168:D1891Y;ENSP00000301807:D1341Y	ENSP00000301807:D1341Y	D	-	1	0	TRANK1	36850275	0.961000	0.32948	0.107000	0.21349	0.355000	0.29361	2.902000	0.48703	2.648000	0.89879	0.561000	0.74099	GAC		0.483	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36875271	C	A	36875271	3	1	61	1	0	0	0	0	1	0	0	0	16494	913	32	2	3118	2	TRANK1	3	36875271	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240	36875271	161147159	2367	10352										
TRANK1	9881	broad.mit.edu	37	chr3	36876275	36876275	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccactgcaatagcagcttCttcaaaaagctcctcttggc	6	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36876275C>A	ENST00000429976.2	-	20	5756	c.5509G>T	c.(5509-5511)Gaa>Taa	p.E1837*	TRANK1_ENST00000428977.2_Nonsense_Mutation_p.E1287*|TRANK1_ENST00000301807.6_Nonsense_Mutation_p.E1287*	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1837							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.E1280*(1)|p.E1287*(1)|p.E1837*(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						ATAGCAGCTTCTTCAAAAAGC	0.478																																																3	Substitution - Nonsense(3)	large_intestine(3)	3											106	107	106					3																	36876275		1905	4116	6021	36851279	SO:0001587	stop_gained	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5509G>T	3.37:g.36876275C>A	ENSP00000416168:p.Glu1837*		36851279	Q8N8K0	Nonsense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	45	11.799525	0.99604	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	.	.	.	5.85	5.85	0.93711	.	0.104695	0.42548	D	0.000686	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	20.5471	0.99284	0.0:1.0:0.0:0.0	.	.	.	.	X	1287;1837;1287	.	ENSP00000301807:E1287X	E	-	1	0	TRANK1	36851279	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.359000	0.66074	2.941000	0.99782	0.655000	0.94253	GAA		0.478	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36876275	C	A	36876275	4	1	61	1	0	0	0	0	0	1	0	0	16494	922	32	2	3284	2	TRANK1	3	36876275	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1004	36876275	161146155	2368	10353										
TRANK1	9881	broad.mit.edu	37	chr3	36884146	36884146	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttggcgtagtaatctccCtgtgcaatccactccgcagg	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:36884146C>A	ENST00000429976.2	-	17	5362	c.5115G>T	c.(5113-5115)caG>caT	p.Q1705H	TRANK1_ENST00000463984.1_5'Flank|TRANK1_ENST00000428977.2_Missense_Mutation_p.Q1155H|TRANK1_ENST00000301807.6_Missense_Mutation_p.Q1155H	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1705							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.Q1155H(2)|p.Q1705H(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						AGTAATCTCCCTGTGCAATCC	0.493																																																3	Substitution - Missense(3)	large_intestine(3)	3											86	89	88					3																	36884146		1955	4135	6090	36859150	SO:0001583	missense	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5115G>T	3.37:g.36884146C>A	ENSP00000416168:p.Gln1705His		36859150	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	19.77	3.888728	0.72524	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.37411	1.2;1.62;1.2	5.46	-2.53	0.06326	Tetratricopeptide-like helical (1);	0.000000	0.53938	D	0.000055	T	0.37183	0.0994	L	0.27053	0.805	0.38779	D	0.954722	D	0.67145	0.996	P	0.59703	0.862	T	0.33214	-0.9877	10	0.66056	D	0.02	.	13.3266	0.60463	0.0:0.4817:0.0:0.5183	.	1705	O15050	TRNK1_HUMAN	H	1155;1705;1155	ENSP00000416826:Q1155H;ENSP00000416168:Q1705H;ENSP00000301807:Q1155H	ENSP00000301807:Q1155H	Q	-	3	2	TRANK1	36859150	0.997000	0.39634	0.832000	0.32986	0.864000	0.49448	0.204000	0.17335	-0.326000	0.08564	-0.312000	0.09012	CAG		0.493	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36884146	C	A	36884146	3	1	61	1	0	0	0	0	1	0	0	0	16494	680	24	2	3690	2	TRANK1	3	36884146	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7871	36884146	161138284	2369	10354										
EPM2AIP1	9852	broad.mit.edu	37	chr3	37032999	37032999	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcataaaactgccccaagtCtttgattctgtattcattcc	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37032999C>A	ENST00000322716.5	-	1	1796	c.1570G>T	c.(1570-1572)Gac>Tac	p.D524Y	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	524					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)		p.D524Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						TGCCCCAAGTCTTTGATTCTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											53	49	50					3																	37032999		1845	4081	5926	37008003	SO:0001583	missense	9852			AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1570G>T	3.37:g.37032999C>A	ENSP00000406027:p.Asp524Tyr		37008003	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	37	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.865124	0.51482	.	.	ENSG00000178567	ENST00000322716	T	0.14893	2.47	4.71	3.74	0.42951	.	.	.	.	.	T	0.17577	0.0422	L	0.53249	1.67	0.35983	D	0.836143	P	0.47191	0.891	B	0.44224	0.444	T	0.10613	-1.0622	9	0.59425	D	0.04	-6.2668	5.5465	0.17067	0.0:0.7822:0.0:0.2178	.	524	Q7L775	EPMIP_HUMAN	Y	524	ENSP00000406027:D524Y	ENSP00000406027:D524Y	D	-	1	0	EPM2AIP1	37008003	0.769000	0.28531	1.000000	0.80357	0.975000	0.68041	0.492000	0.22435	2.420000	0.82092	0.655000	0.94253	GAC		0.398	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		A	37032999	C	A	37032999	3	1	61	1	0	0	0	0	1	0	0	0	5197	913	32	2	257	2	EPM2AIP1	3	37032999	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	148853	37032999	160989431	2370	10355										
EPM2AIP1	9852	broad.mit.edu	37	chr3	37033211	37033211	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctatcaggatcaaatattTtttcatcttccttattttgc	3	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37033211T>G	ENST00000322716.5	-	1	1584	c.1358A>C	c.(1357-1359)aAa>aCa	p.K453T	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	453					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)		p.K453T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						ATCAAATATTTTTTCATCTTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											30	30	30					3																	37033211		1815	4063	5878	37008215	SO:0001583	missense	9852			AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1358A>C	3.37:g.37033211T>G	ENSP00000406027:p.Lys453Thr		37008215	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	37	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	T	10.67	1.414887	0.25465	.	.	ENSG00000178567	ENST00000322716	T	0.15017	2.46	4.71	2.16	0.27623	.	.	.	.	.	T	0.10465	0.0256	L	0.34521	1.04	0.21762	N	0.999553	B	0.09022	0.002	B	0.13407	0.009	T	0.38929	-0.9638	9	0.12766	T	0.61	-6.104	4.7331	0.12975	0.0:0.1018:0.1912:0.707	.	453	Q7L775	EPMIP_HUMAN	T	453	ENSP00000406027:K453T	ENSP00000406027:K453T	K	-	2	0	EPM2AIP1	37008215	0.001000	0.12720	0.936000	0.37596	0.957000	0.61999	0.264000	0.18497	0.818000	0.34468	0.533000	0.62120	AAA		0.328	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		G	37033211	T	G	37033211	3	3	61	1	0	0	0	0	1	0	0	0	5197	1841	64	4	469	4	EPM2AIP1	3	37033211	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	212	37033211	160989219	2371	10356										
MLH1	4292	broad.mit.edu	37	chr3	37056025	37056025	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagtgcatcttcttactCttcatcaaccgtaagttaaa	5	9	5	1	rs587779038		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37056025C>T	ENST00000231790.2	+	9	996	c.780C>T	c.(778-780)ctC>ctT	p.L260L	MLH1_ENST00000458205.2_Silent_p.L19L|MLH1_ENST00000455445.2_Silent_p.L19L|MLH1_ENST00000435176.1_Silent_p.L162L|MLH1_ENST00000536378.1_Silent_p.L19L|MLH1_ENST00000539477.1_Silent_p.L19L	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	260			L -> F (associated with HNPCC2; has no effect on ex vivo splicing assay). {ECO:0000269|PubMed:18561205}.|L -> R (in CRC). {ECO:0000269|PubMed:10882759}.|Missing (in HNPCC2).		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)|p.L260L(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TCTTCTTACTCTTCATCAACC	0.383		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	2	Whole gene deletion(1)|Substitution - coding silent(1)	ovary(1)|large_intestine(1)	3											62	57	59					3																	37056025		2203	4300	6503	37031029	SO:0001819	synonymous_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.780C>T	3.37:g.37056025C>T			37031029	B4DI13|B4DQ11|E9PCU2	Silent	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	C	9.840	1.190670	0.21954	.	.	ENSG00000076242	ENST00000456676	.	.	.	5.43	3.59	0.41128	.	.	.	.	.	T	0.60958	0.2309	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56251	-0.8010	4	.	.	.	-15.2486	10.3406	0.43875	0.0:0.6752:0.2555:0.0694	.	.	.	.	F	252	.	.	S	+	2	0	MLH1	37031029	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.820000	0.27323	0.626000	0.30322	0.591000	0.81541	TCT		0.383	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		T	37056025	C	T	37056025	2	4	61	1	0	0	0	0	0	0	0	1	9647	900	32	3		3	MLH1	3	37056025	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22814	37056025	160966405	2372	10357										
MLH1	4292	broad.mit.edu	37	chr3	37083786	37083786	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttctaccagatactcatTtatgattttgccaattttgg	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37083786T>G	ENST00000231790.2	+	15	1911	c.1695T>G	c.(1693-1695)atT>atG	p.I565M	MLH1_ENST00000458205.2_Missense_Mutation_p.I324M|MLH1_ENST00000455445.2_Missense_Mutation_p.I324M|MLH1_ENST00000435176.1_Missense_Mutation_p.I467M|MLH1_ENST00000536378.1_Missense_Mutation_p.I324M|MLH1_ENST00000539477.1_Missense_Mutation_p.I324M	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	565	Interaction with EXO1.		I -> F (in HNPCC2). {ECO:0000269|PubMed:9833759}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I565M(1)|p.0?(1)|p.?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						AGATACTCATTTATGATTTTG	0.343		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	3	Substitution - Missense(1)|Whole gene deletion(1)|Unknown(1)	ovary(1)|breast(1)|large_intestine(1)	3											239	231	234					3																	37083786		2201	4300	6501	37058790	SO:0001583	missense	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1695T>G	3.37:g.37083786T>G	ENSP00000231790:p.Ile565Met		37058790	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.40|13.40	2.226547|2.226547	0.39300|0.39300	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000456676|ENST00000231790;ENST00000383761;ENST00000421440;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	.|D;D;D;D;D;D	.|0.91740	.|-2.9;-2.9;-2.9;-2.9;-2.9;-2.9	5.44|5.44	0.404|0.404	0.16355|0.16355	.|.	.|0.264362	.|0.42821	.|D	.|0.000653	D|D	0.87775|0.87775	0.6262|0.6262	L|L	0.55103|0.55103	1.725|1.725	0.58432|0.58432	D|D	0.999991|0.999991	.|B;B;B;B	.|0.13594	.|0.008;0.005;0.008;0.002	.|B;B;B;B	.|0.28638	.|0.092;0.062;0.056;0.03	T|T	0.79045|0.79045	-0.1964|-0.1964	5|10	.|0.51188	.|T	.|0.08	-11.1017|-11.1017	5.7686|5.7686	0.18241|0.18241	0.12:0.2192:0.0:0.6607|0.12:0.2192:0.0:0.6607	.|.	.|467;324;565;565	.|E9PCU2;B4DI13;Q53GX1;P40692	.|.;.;.;MLH1_HUMAN	C|M	557|565;429;107;324;324;324;467;324	.|ENSP00000231790:I565M;ENSP00000402667:I324M;ENSP00000443665:I324M;ENSP00000398272:I324M;ENSP00000402564:I467M;ENSP00000444286:I324M	.|ENSP00000231790:I565M	F|I	+|+	2|3	0|3	MLH1|MLH1	37058790|37058790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.981000|0.981000	0.29526|0.29526	0.148000|0.148000	0.19059|0.19059	0.482000|0.482000	0.46254|0.46254	TTT|ATT		0.343	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37083786	T	G	37083786	3	3	61	1	0	0	0	0	1	0	0	0	9647	1829	64	4	1753	4	MLH1	3	37083786	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27761	37083786	160938644	2373	10358										
MLH1	4292	broad.mit.edu	37	chr3	37090083	37090083	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggactgcctatcttcattCttcgactagccactgaggtc	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37090083C>A	ENST00000231790.2	+	17	2188	c.1972C>A	c.(1972-1974)Ctt>Att	p.L658I	MLH1_ENST00000458205.2_Missense_Mutation_p.L417I|MLH1_ENST00000455445.2_Missense_Mutation_p.L417I|MLH1_ENST00000435176.1_Missense_Mutation_p.L560I|MLH1_ENST00000536378.1_Missense_Mutation_p.L417I|MLH1_ENST00000539477.1_Missense_Mutation_p.L417I	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	658					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)|p.L658I(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATCTTCATTCTTCGACTAGC	0.493		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	3											125	117	120					3																	37090083		2203	4300	6503	37065087	SO:0001583	missense	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1972C>A	3.37:g.37090083C>A	ENSP00000231790:p.Leu658Ile		37065087	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397563	0.83120	.	.	ENSG00000076242	ENST00000231790;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.96734	0.8934	M	0.86343	2.81	0.80722	D	1	D;D;P	0.76494	0.998;0.999;0.891	D;D;P	0.78314	0.991;0.978;0.854	D	0.96334	0.9246	10	0.49607	T	0.09	-15.7872	13.3539	0.60617	0.0:0.9283:0.0:0.0717	.	560;417;658	E9PCU2;B4DI13;P40692	.;.;MLH1_HUMAN	I	658;417;417;417;560;417	ENSP00000231790:L658I;ENSP00000402667:L417I;ENSP00000443665:L417I;ENSP00000398272:L417I;ENSP00000402564:L560I;ENSP00000444286:L417I	ENSP00000231790:L658I	L	+	1	0	MLH1	37065087	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	3.774000	0.55341	2.768000	0.95171	0.650000	0.86243	CTT		0.493	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		A	37090083	C	A	37090083	3	1	61	1	0	0	0	0	1	0	0	0	9647	913	32	2	2038	2	MLH1	3	37090083	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6297	37090083	160932347	2374	10359										
LRRFIP2	9209	broad.mit.edu	37	chr3	37125147	37125147	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgatttttcttcattttCtctataaaattctgccatct	2	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37125147C>A	ENST00000336686.4	-	19	1338	c.1258G>T	c.(1258-1260)Gaa>Taa	p.E420*	LRRFIP2_ENST00000354379.4_Nonsense_Mutation_p.E164*|LRRFIP2_ENST00000440230.1_Nonsense_Mutation_p.E188*|LRRFIP2_ENST00000396428.2_Nonsense_Mutation_p.E236*|LRRFIP2_ENST00000421276.2_Nonsense_Mutation_p.E188*|LRRFIP2_ENST00000421307.1_Nonsense_Mutation_p.E420*			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	420					Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.E420*(1)|p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TCTTCATTTTCTCTATAAAAT	0.368																																																2	Substitution - Nonsense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	3											149	150	149					3																	37125147		2203	4298	6501	37100151	SO:0001587	stop_gained	9209			AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1258G>T	3.37:g.37125147C>A	ENSP00000338727:p.Glu420*		37100151	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Nonsense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.170724|7.170724	0.98111|0.98111	.|.	.|.	ENSG00000093167|ENSG00000093167	ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230;ENST00000416425|ENST00000440742	.|T	.|0.59772	.|0.24	5.78|5.78	4.89|4.89	0.63831|0.63831	.|.	0.046027|.	0.85682|.	D|.	0.000000|.	.|T	.|0.73063	.|0.3539	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.79087	.|-0.1947	.|5	0.20519|0.87932	T|D	0.43|0	-8.1088|-8.1088	16.7311|16.7311	0.85435|0.85435	0.0:0.8705:0.1295:0.0|0.0:0.8705:0.1295:0.0	.|.	.|.	.|.	.|.	X|I	420;164;420;188;236;188;188|32	.|ENSP00000413026:R32I	ENSP00000338727:E420X|ENSP00000413026:R32I	E|R	-|-	1|2	0|0	LRRFIP2|LRRFIP2	37100151|37100151	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	4.612000|4.612000	0.61169|0.61169	1.415000|1.415000	0.47037|0.47037	0.561000|0.561000	0.74099|0.74099	GAA|AGA		0.368	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37125147	C	A	37125147	4	1	61	1	0	0	0	0	0	1	0	0	9057	922	32	2	947	2	LRRFIP2	3	37125147	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35064	37125147	160897283	2375	10360										
GOLGA4	2803	broad.mit.edu	37	chr3	37367050	37367050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttgctgtaagaaaaccGaagccttattagaagctaaa	7	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37367050G>A	ENST00000361924.2	+	14	4047	c.3673G>A	c.(3673-3675)Gaa>Aaa	p.E1225K	GOLGA4_ENST00000356847.4_Missense_Mutation_p.E1247K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1225	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.E1225K(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TAAGAAAACCGAAGCCTTATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											64	65	65					3																	37367050		2203	4299	6502	37342054	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.3673G>A	3.37:g.37367050G>A	ENSP00000354486:p.Glu1225Lys		37342054	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639269	0.29157	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.25749	1.78;1.78;1.78	5.53	4.64	0.57946	.	0.204773	0.24576	N	0.037342	T	0.14098	0.0341	N	0.24115	0.695	0.38754	D	0.954186	P;B;B;B	0.45474	0.859;0.333;0.333;0.137	B;B;B;B	0.33568	0.166;0.102;0.102;0.027	T	0.10291	-1.0636	10	0.16896	T	0.51	.	13.4548	0.61193	0.0765:0.0:0.9235:0.0	.	1225;1225;1247;1225	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	1225;1247;1096	ENSP00000354486:E1225K;ENSP00000349305:E1247K;ENSP00000405842:E1096K	ENSP00000349305:E1247K	E	+	1	0	GOLGA4	37342054	1.000000	0.71417	0.780000	0.31762	0.394000	0.30568	3.039000	0.49791	1.308000	0.44962	0.563000	0.77884	GAA		0.353	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37367050	G	A	37367050	3	1	61	1	0	0	0	0	1	0	0	0	6575	1059	37	1	3797	1	GOLGA4	3	37367050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241903	37367050	160655380	2376	10361										
GOLGA4	2803	broad.mit.edu	37	chr3	37367985	37367985	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagaggaccatattacccaGaaaactattgaaatagagtc	7	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37367985G>T	ENST00000361924.2	+	14	4982	c.4608G>T	c.(4606-4608)caG>caT	p.Q1536H	GOLGA4_ENST00000356847.4_Missense_Mutation_p.Q1558H|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1536	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.Q1536H(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATATTACCCAGAAAACTATTG	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	3											63	71	68					3																	37367985		2200	4290	6490	37342989	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4608G>T	3.37:g.37367985G>T	ENSP00000354486:p.Gln1536His		37342989	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	8.136	0.784235	0.16189	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.25414	1.81;1.8;1.81	5.44	5.44	0.79542	.	0.238696	0.21920	N	0.067161	T	0.45337	0.1337	M	0.72118	2.19	0.34153	D	0.66771	D;P;P;B	0.53151	0.958;0.911;0.911;0.013	P;P;P;B	0.53313	0.723;0.723;0.723;0.007	T	0.58115	-0.7693	10	0.52906	T	0.07	.	19.2623	0.93973	0.0:0.0:1.0:0.0	.	1536;1536;1558;1536	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	H	1536;1558;1407	ENSP00000354486:Q1536H;ENSP00000349305:Q1558H;ENSP00000405842:Q1407H	ENSP00000349305:Q1558H	Q	+	3	2	GOLGA4	37342989	1.000000	0.71417	0.993000	0.49108	0.206000	0.24218	2.813000	0.48002	2.550000	0.86006	0.462000	0.41574	CAG		0.313	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37367985	G	T	37367985	3	4	61	1	0	0	0	0	1	0	0	0	6575	933	33	2	4732	2	GOLGA4	3	37367985	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	935	37367985	160654445	2377	10362										
GOLGA4	2803	broad.mit.edu	37	chr3	37368058	37368058	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaggatattgaacacaaaGaattggttcagaaacttcaa	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37368058G>T	ENST00000361924.2	+	14	5055	c.4681G>T	c.(4681-4683)Gaa>Taa	p.E1561*	GOLGA4_ENST00000356847.4_Nonsense_Mutation_p.E1583*|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1561	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.E1561*(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGAACACAAAGAATTGGTTCA	0.308																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											69	80	76					3																	37368058		2198	4295	6493	37343062	SO:0001587	stop_gained	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4681G>T	3.37:g.37368058G>T	ENSP00000354486:p.Glu1561*		37343062	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Nonsense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	44	11.128092	0.99519	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	.	.	.	4.46	4.46	0.54185	.	0.214996	0.23594	N	0.046501	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	18.0125	0.89229	0.0:0.0:1.0:0.0	.	.	.	.	X	1561;1583;1432	.	ENSP00000349305:E1583X	E	+	1	0	GOLGA4	37343062	1.000000	0.71417	0.321000	0.25320	0.910000	0.53928	6.029000	0.70895	2.417000	0.82017	0.462000	0.41574	GAA		0.308	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37368058	G	T	37368058	4	4	61	1	0	0	0	0	0	1	0	0	6575	943	33	2	4805	2	GOLGA4	3	37368058	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73	37368058	160654372	2378	10363										
GOLGA4	2803	broad.mit.edu	37	chr3	37368234	37368234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagtgtgaaaagcaaagaGgaggagttaaaggcattgga	14	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37368234G>T	ENST00000361924.2	+	14	5231	c.4857G>T	c.(4855-4857)gaG>gaT	p.E1619D	GOLGA4_ENST00000356847.4_Missense_Mutation_p.E1641D|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1619	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.E1619D(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AAAGCAAAGAGGAGGAGTTAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											73	79	77					3																	37368234		2203	4300	6503	37343238	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4857G>T	3.37:g.37368234G>T	ENSP00000354486:p.Glu1619Asp		37343238	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	9.975	1.226548	0.22542	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.27104	1.7;1.69;1.7	5.23	-10.5	0.00291	.	0.210705	0.23859	N	0.043868	T	0.09158	0.0226	N	0.21373	0.66	0.09310	N	0.999997	B;B;B;B	0.17038	0.02;0.011;0.011;0.002	B;B;B;B	0.16722	0.016;0.016;0.016;0.004	T	0.06752	-1.0809	10	0.22109	T	0.4	.	4.316	0.10993	0.1453:0.1482:0.4355:0.271	.	1619;1619;1641;1619	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	D	1619;1641;1490	ENSP00000354486:E1619D;ENSP00000349305:E1641D;ENSP00000405842:E1490D	ENSP00000349305:E1641D	E	+	3	2	GOLGA4	37343238	0.000000	0.05858	0.183000	0.23137	0.861000	0.49209	-1.363000	0.02592	-2.973000	0.00285	-0.459000	0.05422	GAG		0.343	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37368234	G	T	37368234	3	4	61	1	0	0	0	0	1	0	0	0	6575	991	35	2	4981	2	GOLGA4	3	37368234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176	37368234	160654196	2379	10364										
GOLGA4	2803	broad.mit.edu	37	chr3	37368332	37368332	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaaaattgctgccattaAgaagcagttgttatctcaaa	6	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37368332A>C	ENST00000361924.2	+	14	5329	c.4955A>C	c.(4954-4956)aAg>aCg	p.K1652T	GOLGA4_ENST00000356847.4_Missense_Mutation_p.K1674T|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1652	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.K1652T(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GCTGCCATTAAGAAGCAGTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											73	79	77					3																	37368332		2201	4298	6499	37343336	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4955A>C	3.37:g.37368332A>C	ENSP00000354486:p.Lys1652Thr		37343336	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	18.65	3.669142	0.67814	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.31769	1.48;1.48;1.48	5.34	1.64	0.23874	.	0.224065	0.22677	N	0.056981	T	0.44435	0.1293	M	0.64997	1.995	0.24481	N	0.994344	D;D;D;D	0.67145	0.996;0.989;0.989;0.981	P;P;P;P	0.62298	0.9;0.787;0.787;0.617	T	0.23511	-1.0186	10	0.48119	T	0.1	.	9.5473	0.39288	0.7129:0.0:0.2871:0.0	.	1652;1652;1674;1652	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	T	1652;1674;1523	ENSP00000354486:K1652T;ENSP00000349305:K1674T;ENSP00000405842:K1523T	ENSP00000349305:K1674T	K	+	2	0	GOLGA4	37343336	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	0.800000	0.27042	0.356000	0.24157	0.459000	0.35465	AAG		0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		C	37368332	A	C	37368332	3	2	61	1	0	0	0	0	1	0	0	0	6575	72	3	4	5079	4	GOLGA4	3	37368332	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	98	37368332	160654098	2380	10365										
GOLGA4	2803	broad.mit.edu	37	chr3	37369291	37369291	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatactaaagaaagaatatGatcaagaaagggaagagaaa	9	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37369291G>T	ENST00000361924.2	+	14	6288	c.5914G>T	c.(5914-5916)Gat>Tat	p.D1972Y	GOLGA4_ENST00000356847.4_Missense_Mutation_p.D1994Y|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1972	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.D1972Y(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GAAAGAATATGATCAAGAAAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											58	63	61					3																	37369291		2201	4299	6500	37344295	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5914G>T	3.37:g.37369291G>T	ENSP00000354486:p.Asp1972Tyr		37344295	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.355716	0.24598	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.22743	1.94;1.94;1.94	4.63	4.63	0.57726	.	.	.	.	.	T	0.10423	0.0255	N	0.08118	0	0.09310	N	1	B;B;B;B	0.32717	0.381;0.106;0.145;0.001	B;B;B;B	0.30943	0.122;0.084;0.077;0.001	T	0.10590	-1.0623	9	0.51188	T	0.08	.	6.3252	0.21239	0.0942:0.0:0.6662:0.2396	.	1972;1972;1994;1972	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	Y	1972;1994;1843	ENSP00000354486:D1972Y;ENSP00000349305:D1994Y;ENSP00000405842:D1843Y	ENSP00000349305:D1994Y	D	+	1	0	GOLGA4	37344295	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.294000	0.51787	2.114000	0.64651	0.643000	0.83706	GAT		0.338	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37369291	G	T	37369291	3	4	61	1	0	0	0	0	1	0	0	0	6575	1290	45	2	6038	2	GOLGA4	3	37369291	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	959	37369291	160653139	2381	10366										
C3orf35	339883	broad.mit.edu	37	chr3	37476598	37476598	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggggccatcctgattctaGaattatcttggttcctggga	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37476598G>T	ENST00000328376.5	+	6	1469	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	164						integral component of membrane (GO:0016021)		p.E164*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CCTGATTCTAGAATTATCTTG	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											38	41	40					3																	37476598		1880	4095	5975	37451602	SO:0001587	stop_gained	339883			AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"AP20 region protein", "APRG1 tumor suppressor candidate"	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.490G>T	3.37:g.37476598G>T	ENSP00000331625:p.Glu164*		37451602	B7ZMA0|Q8IVJ5|Q8IVJ9	Nonsense_Mutation	SNP	ENST00000328376.5	37	CCDS43065.1	.	.	.	.	.	.	.	.	.	.	G	38	6.639797	0.97726	.	.	ENSG00000198590	ENST00000328376	.	.	.	0.565	0.565	0.17309	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	.	.	.	.	.	.	.	X	164	.	ENSP00000331625:E164X	E	+	1	0	C3orf35	37451602	0.021000	0.18746	0.006000	0.13384	0.006000	0.05464	0.364000	0.20325	0.556000	0.29098	0.563000	0.77884	GAA		0.502	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		T	37476598	G	T	37476598	4	4	61	1	0	0	0	0	0	1	0	0	2231	943	33	2	630	2	C3orf35	3	37476598	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107307	37476598	160545832	2382	10367										
ITGA9	3680	broad.mit.edu	37	chr3	37791972	37791972	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctacaacactggcccaaGcacccttccagggtcatctg	9	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37791972G>T	ENST00000264741.5	+	23	2709	c.2453G>T	c.(2452-2454)aGc>aTc	p.S818I	AC093415.2_ENST00000449586.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	818					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.S818I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		ACTGGCCCAAGCACCCTTCCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											160	136	144					3																	37791972		2203	4300	6503	37766976	SO:0001583	missense	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2453G>T	3.37:g.37791972G>T	ENSP00000264741:p.Ser818Ile		37766976	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402553	0.83230	.	.	ENSG00000144668	ENST00000264741	T	0.53640	0.61	5.42	5.42	0.78866	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.70245	0.3202	M	0.76328	2.33	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.73056	-0.4103	10	0.87932	D	0	.	18.3443	0.90315	0.0:0.0:1.0:0.0	.	818	Q13797	ITA9_HUMAN	I	818	ENSP00000264741:S818I	ENSP00000264741:S818I	S	+	2	0	ITGA9	37766976	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	5.942000	0.70203	2.692000	0.91855	0.561000	0.74099	AGC		0.478	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		T	37791972	G	T	37791972	3	4	61	1	0	0	0	0	1	0	0	0	7904	971	34	2	2543	2	ITGA9	3	37791972	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315374	37791972	160230458	2383	10368										
ITGA9	3680	broad.mit.edu	37	chr3	37826475	37826475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcttccacaggacagttCgtctgtcatccagttcatgt	8	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:37826475C>T	ENST00000264741.5	+	26	3051	c.2795C>T	c.(2794-2796)tCg>tTg	p.S932L	AC093415.2_ENST00000438136.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	932					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.S932L(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CAGGACAGTTCGTCTGTCATC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	89	92					3																	37826475		2203	4300	6503	37801479	SO:0001583	missense	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2795C>T	3.37:g.37826475C>T	ENSP00000264741:p.Ser932Leu		37801479	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880722	0.72294	.	.	ENSG00000144668	ENST00000264741	T	0.41758	0.99	5.91	5.91	0.95273	.	0.178832	0.51477	D	0.000097	T	0.35828	0.0945	L	0.41236	1.265	0.80722	D	1	B	0.28801	0.223	B	0.14578	0.011	T	0.06570	-1.0819	10	0.25751	T	0.34	.	19.061	0.93093	0.0:1.0:0.0:0.0	.	932	Q13797	ITA9_HUMAN	L	932	ENSP00000264741:S932L	ENSP00000264741:S932L	S	+	2	0	ITGA9	37801479	1.000000	0.71417	0.930000	0.37139	0.675000	0.39556	6.940000	0.75917	2.794000	0.96219	0.655000	0.94253	TCG		0.493	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		T	37826475	C	T	37826475	3	4	61	1	0	0	0	0	1	0	0	0	7904	893	31	1	2897	1	ITGA9	3	37826475	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34503	37826475	160195955	2384	10369										
PLCD1	5333	broad.mit.edu	37	chr3	38049574	38049574	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggaggaggcatcataatCttccaccaagaagcggatga	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38049574C>A	ENST00000334661.4	-	14	2338	c.2116G>T	c.(2116-2118)Gat>Tat	p.D706Y	PLCD1_ENST00000463876.1_Missense_Mutation_p.D727Y	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	706	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)	p.D706Y(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		GCATCATAATCTTCCACCAAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	106	110					3																	38049574		2203	4300	6503	38024578	SO:0001583	missense	5333				CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.2116G>T	3.37:g.38049574C>A	ENSP00000335600:p.Asp706Tyr		38024578	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.268263	0.59540	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.77098	-1.07;-1.07	5.11	5.11	0.69529	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.088941	0.85682	D	0.000000	D	0.92922	0.7748	H	0.97940	4.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95437	0.8522	10	0.87932	D	0	.	18.4971	0.90869	0.0:1.0:0.0:0.0	.	706;727	P51178;B3KR14	PLCD1_HUMAN;.	Y	727;706	ENSP00000430344:D727Y;ENSP00000335600:D706Y	ENSP00000335600:D706Y	D	-	1	0	PLCD1	38024578	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	7.773000	0.85462	2.555000	0.86185	0.655000	0.94253	GAT		0.527	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			A	38049574	C	A	38049574	3	1	61	1	0	0	0	0	1	0	0	0	12062	913	32	2	162	2	PLCD1	3	38049574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	223099	38049574	159972856	2385	10370										
DLEC1	9940	broad.mit.edu	37	chr3	38103775	38103775	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagaagcttgctgagttCgaagatgagttagaccacac	12	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38103775C>T	ENST00000308059.6	+	4	810	c.789C>T	c.(787-789)ttC>ttT	p.F263F	DLEC1_ENST00000346219.3_Silent_p.F263F|DLEC1_ENST00000452631.2_Silent_p.F263F					deleted in lung and esophageal cancer 1									p.F263F(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TTGCTGAGTTCGAAGATGAGT	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	3											88	82	84					3																	38103775		1977	4171	6148	38078779	SO:0001819	synonymous_variant	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.789C>T	3.37:g.38103775C>T			38078779		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																				0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38103775	C	T	38103775	2	4	61	1	0	0	0	0	0	0	0	1	4563	883	31	1		1	DLEC1	3	38103775	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54201	38103775	159918655	2386	10371										
DLEC1	9940	broad.mit.edu	37	chr3	38125714	38125714	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagtcctcccgccttccacGccatacttcgctctgggact	8	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38125714G>A	ENST00000308059.6	+	7	1260	c.1239G>A	c.(1237-1239)acG>acA	p.T413T	DLEC1_ENST00000346219.3_Silent_p.T413T|DLEC1_ENST00000452631.2_Silent_p.T413T|DLEC1_ENST00000469151.1_3'UTR					deleted in lung and esophageal cancer 1									p.T413T(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CGCCTTCCACGCCATACTTCG	0.463																																																2	Substitution - coding silent(2)	large_intestine(2)	3											113	123	120					3																	38125714		2075	4209	6284	38100718	SO:0001819	synonymous_variant	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1239G>A	3.37:g.38125714G>A			38100718		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																				0.463	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38125714	G	A	38125714	2	1	61	1	0	0	0	0	0	0	0	1	4563	1074	38	1		1	DLEC1	3	38125714	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21939	38125714	159896716	2387	10372										
ACAA1	30	broad.mit.edu	37	chr3	38167344	38167344	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaaggcctcattgatctcGaagatgtccacgtcactcac	8	13	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38167344G>A	ENST00000333167.8	-	10	1198	c.1026C>T	c.(1024-1026)ttC>ttT	p.F342F	Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000450296.1_Silent_p.F301F|ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000301810.7_Silent_p.F249F	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	342					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)	p.F342F(1)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CATTGATCTCGAAGATGTCCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											175	163	167					3																	38167344		2203	4300	6503	38142348	SO:0001819	synonymous_variant	30			X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.1026C>T	3.37:g.38167344G>A			38142348	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	37	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.253249	0.22965	.	.	ENSG00000060971	ENST00000452171;ENST00000421218	.	.	.	5.35	1.71	0.24356	.	.	.	.	.	T	0.57932	0.2087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51252	-0.8729	4	.	.	.	-13.3179	9.3415	0.38082	0.7173:0.0:0.2827:0.0	.	.	.	.	L	155;232	.	.	S	-	2	0	ACAA1	38142348	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.355000	0.44107	0.354000	0.24105	-0.238000	0.12139	TCG		0.602	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		A	38167344	G	A	38167344	2	1	61	1	0	0	0	0	0	0	0	1	104	1049	37	1		1	ACAA1	3	38167344	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41630	38167344	159855086	2388	10373										
MYD88	4615	broad.mit.edu	37	chr3	38182656	38182656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgactgatccccatcaagtAcaaggcaatgaagaaagagt	10	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38182656A>G	ENST00000396334.3	+	5	993	c.809A>G	c.(808-810)tAc>tGc	p.Y270C	MYD88_ENST00000424893.1_Missense_Mutation_p.Y225C|MYD88_ENST00000417037.2_Missense_Mutation_p.Y278C|MYD88_ENST00000443433.2_3'UTR|MYD88_ENST00000495303.1_3'UTR|MYD88_ENST00000481122.1_3'UTR	NM_002468.4	NP_002459.2	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	257	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.Y270C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCCATCAAGTACAAGGCAATG	0.562			Mis		ABC-DLBCL																																		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	1	Substitution - Missense(1)	large_intestine(1)	3											171	136	148					3																	38182656		2203	4300	6503	38157660	SO:0001583	missense	4615			U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000396334.3:c.809A>G	3.37:g.38182656A>G	ENSP00000379625:p.Tyr270Cys		38157660	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000396334.3	37	CCDS2674.2	.	.	.	.	.	.	.	.	.	.	A	16.08	3.020781	0.54576	.	.	ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.52	5.52	0.82312	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.058969	0.64402	D	0.000001	T	0.37156	0.0993	L	0.61218	1.895	0.80722	D	1	B;B;B	0.33022	0.163;0.394;0.196	B;P;B	0.45276	0.243;0.475;0.356	T	0.24083	-1.0170	10	0.56958	D	0.05	-24.4843	11.1341	0.48365	0.9255:0.0:0.0745:0.0	.	212;257;246	Q99836-2;Q99836;B4E3D6	.;MYD88_HUMAN;.	C	278;270;225;277;246	ENSP00000401399:Y278C;ENSP00000379625:Y270C;ENSP00000389979:Y225C;ENSP00000391753:Y277C	ENSP00000379625:Y270C	Y	+	2	0	MYD88	38157660	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.955000	0.56715	2.233000	0.73108	0.533000	0.62120	TAC		0.562	MYD88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253743.4	NM_002468		G	38182656	A	G	38182656	3	3	61	1	0	0	0	0	1	0	0	0	10053	391	14	4	851	4	MYD88	3	38182656	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	15312	38182656	159839774	2389	10374										
SLC22A13	9390	broad.mit.edu	37	chr3	38317845	38317845	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagctgctgcctttaccatCtcctatgtgtactctgccga	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38317845C>A	ENST00000311856.4	+	8	1354	c.1305C>A	c.(1303-1305)atC>atA	p.I435I		NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	435					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)	p.I435I(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		CCTTTACCATCTCCTATGTGT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	3											166	133	144					3																	38317845		2203	4300	6503	38292849	SO:0001819	synonymous_variant	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.1305C>A	3.37:g.38317845C>A			38292849	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																				0.587	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		A	38317845	C	A	38317845	2	1	61	1	0	0	0	0	0	0	0	1	14481	903	32	2		2	SLC22A13	3	38317845	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135189	38317845	159704585	2390	10375										
SLC22A14	9389	broad.mit.edu	37	chr3	38348012	38348012	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatctatcctgacgctaaGaagcgatcgctgatcaatga	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38348012G>T	ENST00000273173.4	+	1	586	c.495G>T	c.(493-495)aaG>aaT	p.K165N	SLC22A14_ENST00000448498.1_Missense_Mutation_p.K165N|RNU6-235P_ENST00000362644.1_RNA	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	165					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)	p.K165N(1)		central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		CTGACGCTAAGAAGCGATCGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											119	108	112					3																	38348012		2203	4300	6503	38323016	SO:0001583	missense	9389			AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.495G>T	3.37:g.38348012G>T	ENSP00000273173:p.Lys165Asn		38323016	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774719	0.49786	.	.	ENSG00000144671	ENST00000466887;ENST00000448498;ENST00000423219;ENST00000273173	T;T;T	0.66638	-0.22;0.02;0.02	5.06	0.79	0.18613	Major facilitator superfamily domain (1);	0.760161	0.13229	N	0.403775	T	0.63885	0.2549	L	0.55213	1.73	0.09310	N	1	P	0.43662	0.814	P	0.47915	0.561	T	0.53005	-0.8499	10	0.39692	T	0.17	.	6.8334	0.23923	0.1679:0.2739:0.5583:0.0	.	165	Q9Y267	S22AE_HUMAN	N	33;165;165;165	ENSP00000442528:K33N;ENSP00000396283:K165N;ENSP00000273173:K165N	ENSP00000273173:K165N	K	+	3	2	SLC22A14	38323016	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.488000	0.22371	0.017000	0.15025	-0.345000	0.07892	AAG		0.498	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		T	38348012	G	T	38348012	3	4	61	1	0	0	0	0	1	0	0	0	14482	933	33	2	497	2	SLC22A14	3	38348012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30167	38348012	159674418	2391	10376										
EXOG	9941	broad.mit.edu	37	chr3	38537907	38537907	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccggggttcccgtcgttttCtgagcggcttcgtggctggg	16	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38537907C>A	ENST00000287675.5	+	1	145	c.49C>A	c.(49-51)Ctg>Atg	p.L17M	EXOG_ENST00000422077.2_Missense_Mutation_p.L17M|EXOG_ENST00000358249.2_5'UTR	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	17					DNA catabolic process, endonucleolytic (GO:0000737)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.L17M(1)		central_nervous_system(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	17						CCGTCGTTTTCTGAGCGGCTT	0.672											OREG0015479	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	3											49	50	50					3																	38537907		2203	4300	6503	38512911	SO:0001583	missense	9941			AB020523	CCDS2680.1, CCDS46795.1	3p21.3	2010-05-07	2009-01-08	2009-01-08	ENSG00000157036	ENSG00000157036	3.1.30.-		3347	protein-coding gene	gene with protein product		604051	"endonuclease G-like 1", "endonuclease G-like 2"	ENDOGL1, ENDOGL2		10231028, 18187503	Standard	NM_005107		Approved	ENGL-a, ENGL, ENGL-b	uc003cih.2	Q9Y2C4	OTTHUMG00000131295	ENST00000287675.5:c.49C>A	3.37:g.38537907C>A	ENSP00000287675:p.Leu17Met	879	38512911	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Missense_Mutation	SNP	ENST00000287675.5	37	CCDS2680.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.091996	0.76756	.	.	ENSG00000157036	ENST00000287675;ENST00000422077	T;T	0.58060	0.77;0.36	5.04	-0.0844	0.13690	.	0.535975	0.16507	N	0.211419	T	0.42381	0.1200	L	0.32530	0.975	0.20307	N	0.999912	P;P	0.40794	0.729;0.61	P;B	0.45138	0.471;0.28	T	0.29640	-1.0005	10	0.45353	T	0.12	-3.7323	7.624	0.28202	0.0:0.642:0.1653:0.1927	.	17;17	Q9Y2C4-4;Q9Y2C4	.;EXOG_HUMAN	M	17	ENSP00000287675:L17M;ENSP00000404305:L17M	ENSP00000287675:L17M	L	+	1	2	EXOG	38512911	0.001000	0.12720	0.002000	0.10522	0.314000	0.28054	-0.621000	0.05559	0.126000	0.18424	0.655000	0.94253	CTG		0.672	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107		A	38537907	C	A	38537907	3	1	61	1	0	0	0	0	1	0	0	0	5325	912	32	2	51	2	EXOG	3	38537907	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	189895	38537907	159484523	2392	10377										
SCN5A	6331	broad.mit.edu	37	chr3	38674674	38674674	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgggcagcccctctcggCtctcctgcaaggtggttgag	13	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38674674C>A	ENST00000333535.4	-	2	274	c.125G>T	c.(124-126)aGc>aTc	p.S42I	SCN5A_ENST00000413689.1_Missense_Mutation_p.S42I|SCN5A_ENST00000451551.2_Missense_Mutation_p.S42I|SCN5A_ENST00000450102.2_Missense_Mutation_p.S42I|SCN5A_ENST00000423572.2_Missense_Mutation_p.S42I|SCN5A_ENST00000414099.2_Missense_Mutation_p.S42I|SCN5A_ENST00000425664.1_Missense_Mutation_p.S42I|SCN5A_ENST00000455624.2_Missense_Mutation_p.S42I|SCN5A_ENST00000443581.1_Missense_Mutation_p.S42I|SCN5A_ENST00000449557.2_Missense_Mutation_p.S42I			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	42					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.S42I(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CCCCTCTCGGCTCTCCTGCAA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	3											26	29	28					3																	38674674		1926	4125	6051	38649678	SO:0001583	missense	6331			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.125G>T	3.37:g.38674674C>A	ENSP00000328968:p.Ser42Ile		38649678	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452143	0.26074	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557;ENST00000327956	D;D;D;D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	4.55	4.55	0.56014	.	0.634187	0.18608	N	0.136255	T	0.76521	0.3999	L	0.38175	1.15	0.29836	N	0.829655	B;B;B;B;B;B	0.27732	0.139;0.03;0.139;0.097;0.187;0.156	B;B;B;B;B;B	0.35470	0.039;0.03;0.039;0.049;0.203;0.106	T	0.71823	-0.4476	10	0.40728	T	0.16	.	8.7289	0.34487	0.0:0.8596:0.0:0.1404	.	42;42;42;42;42;42	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	I	42	ENSP00000398962:S42I;ENSP00000398266:S42I;ENSP00000410257:S42I;ENSP00000388797:S42I;ENSP00000397915:S42I;ENSP00000416634:S42I;ENSP00000328968:S42I;ENSP00000399524:S42I;ENSP00000403355:S42I;ENSP00000413996:S42I;ENSP00000333674:S42I	ENSP00000333674:S42I	S	-	2	0	SCN5A	38649678	0.993000	0.37304	1.000000	0.80357	0.520000	0.34377	1.828000	0.39111	2.349000	0.79799	0.491000	0.48974	AGC		0.652	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38674674	C	A	38674674	3	1	61	1	0	0	0	0	1	0	0	0	13959	797	28	2	6129	2	SCN5A	3	38674674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136767	38674674	159347756	2393	10378										
SCN10A	6336	broad.mit.edu	37	chr3	38739769	38739769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcacagcatgctgttggCgaaggtctggaagttgaaca	15	7	1	1	rs529861077		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38739769C>T	ENST00000449082.2	-	27	4941	c.4942G>A	c.(4942-4944)Gcc>Acc	p.A1648T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1648					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A1648T(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	ATGCTGTTGGCGAAGGTCTGG	0.562													C|||	1	0.000199681	0	0	5008	,	,		20755	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											152	146	148					3																	38739769		2203	4300	6503	38714773	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4942G>A	3.37:g.38739769C>T	ENSP00000390600:p.Ala1648Thr		38714773	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811316	0.90707	.	.	ENSG00000185313	ENST00000449082	D	0.97455	-4.39	5.38	4.47	0.54385	Ion transport (1);	0.185590	0.46758	D	0.000261	D	0.96374	0.8817	N	0.26092	0.79	0.34447	D	0.700272	D	0.76494	0.999	P	0.59424	0.857	D	0.98755	1.0722	10	0.87932	D	0	.	16.297	0.82782	0.0:0.8683:0.1317:0.0	.	1648	Q9Y5Y9	SCNAA_HUMAN	T	1648	ENSP00000390600:A1648T	ENSP00000390600:A1648T	A	-	1	0	SCN10A	38714773	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.805000	0.62561	2.800000	0.96347	0.655000	0.94253	GCC		0.562	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38739769	C	T	38739769	3	4	61	1	0	0	0	0	1	0	0	0	13949	768	27	1	932	1	SCN10A	3	38739769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65095	38739769	159282661	2394	10379										
SCN10A	6336	broad.mit.edu	37	chr3	38753917	38753917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggatgggatggcgcccAccagggcatccaccaccacc	12	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38753917A>G	ENST00000449082.2	-	22	3823	c.3824T>C	c.(3823-3825)gTg>gCg	p.V1275A		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1275					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V1275A(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GATGGCGCCCACCAGGGCATC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	79	79					3																	38753917		2203	4300	6503	38728921	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3824T>C	3.37:g.38753917A>G	ENSP00000390600:p.Val1275Ala		38728921	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524221	0.85600	.	.	ENSG00000185313	ENST00000449082	D	0.98531	-4.98	4.88	4.88	0.63580	Ion transport (1);	0.194026	0.45361	D	0.000364	D	0.97971	0.9332	M	0.86864	2.845	0.43050	D	0.994657	P	0.49783	0.928	P	0.44597	0.454	D	0.98948	1.0793	10	0.87932	D	0	.	14.6606	0.68868	1.0:0.0:0.0:0.0	.	1275	Q9Y5Y9	SCNAA_HUMAN	A	1275	ENSP00000390600:V1275A	ENSP00000390600:V1275A	V	-	2	0	SCN10A	38728921	0.983000	0.35010	1.000000	0.80357	0.979000	0.70002	9.139000	0.94554	2.046000	0.60703	0.454000	0.30748	GTG		0.537	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		G	38753917	A	G	38753917	3	3	61	1	0	0	0	0	1	0	0	0	13949	159	6	4	2070	4	SCN10A	3	38753917	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	14148	38753917	159268513	2395	10380										
SCN10A	6336	broad.mit.edu	37	chr3	38768346	38768346	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgggagtttcaccaccagCtcaggctctgccttgggctg	13	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38768346C>T	ENST00000449082.2	-	16	2837	c.2838G>A	c.(2836-2838)gaG>gaA	p.E946E		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	946					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E946E(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TCACCACCAGCTCAGGCTCTG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	3											70	72	72					3																	38768346		2203	4300	6503	38743350	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2838G>A	3.37:g.38768346C>T			38743350	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.612	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38768346	C	T	38768346	2	4	61	1	0	0	0	0	0	0	0	1	13949	796	28	3		3	SCN10A	3	38768346	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14429	38768346	159254084	2396	10381										
SCN10A	6336	broad.mit.edu	37	chr3	38768447	38768447	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctggatccgtgccagggCcacctgcaggttgttcacct	12	14	1	0	rs201054824	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38768447C>T	ENST00000449082.2	-	16	2736	c.2737G>A	c.(2737-2739)Gcc>Acc	p.A913T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	913					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A913T(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CGTGCCAGGGCCACCTGCAGG	0.577													C|||	3	0.000599042	0	0	5008	,	,		20802	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	3											126	122	124					3																	38768447		2203	4300	6503	38743451	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2737G>A	3.37:g.38768447C>T	ENSP00000390600:p.Ala913Thr		38743451	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	35	5.517661	0.96416	.	.	ENSG00000185313	ENST00000449082	D	0.94650	-3.48	5.03	5.03	0.67393	Sodium ion transport-associated (1);	1.433960	0.04422	N	0.367694	D	0.98147	0.9388	M	0.86420	2.815	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.92885	0.6326	10	0.87932	D	0	.	18.5592	0.91094	0.0:1.0:0.0:0.0	.	913	Q9Y5Y9	SCNAA_HUMAN	T	913	ENSP00000390600:A913T	ENSP00000390600:A913T	A	-	1	0	SCN10A	38743451	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.923000	0.70045	2.637000	0.89404	0.561000	0.74099	GCC		0.577	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38768447	C	T	38768447	3	4	61	1	0	0	0	0	1	0	0	0	13949	739	26	3	3181	3	SCN10A	3	38768447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101	38768447	159253983	2397	10382										
SCN10A	6336	broad.mit.edu	37	chr3	38791655	38791655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctgacaagaaagtcttCttttgtcctgcatcgaatgc	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38791655C>A	ENST00000449082.2	-	12	1775	c.1776G>T	c.(1774-1776)aaG>aaT	p.K592N		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	592					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K592N(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGAAAGTCTTCTTTTGTCCTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	120	126					3																	38791655		2203	4300	6503	38766659	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1776G>T	3.37:g.38791655C>A	ENSP00000390600:p.Lys592Asn		38766659	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.441988	0.25900	.	.	ENSG00000185313	ENST00000449082	D	0.95821	-3.82	5.47	4.59	0.56863	.	2.339360	0.01581	N	0.021092	D	0.90841	0.7123	N	0.08118	0	0.27552	N	0.950466	B	0.06786	0.001	B	0.04013	0.001	T	0.79240	-0.1885	10	0.40728	T	0.16	.	11.6774	0.51438	0.0:0.917:0.0:0.083	.	592	Q9Y5Y9	SCNAA_HUMAN	N	592	ENSP00000390600:K592N	ENSP00000390600:K592N	K	-	3	2	SCN10A	38766659	1.000000	0.71417	0.226000	0.23910	0.543000	0.35085	2.575000	0.46025	1.521000	0.48983	0.655000	0.94253	AAG		0.453	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38791655	C	A	38791655	3	1	61	1	0	0	0	0	1	0	0	0	13949	912	32	2	4158	2	SCN10A	3	38791655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23208	38791655	159230775	2398	10383										
SCN10A	6336	broad.mit.edu	37	chr3	38793924	38793924	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactccctcagggagtgagAtatctcggccaggggaccgg	15	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38793924A>C	ENST00000449082.2	-	11	1540	c.1541T>G	c.(1540-1542)aTc>aGc	p.I514S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	514					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.I514S(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGGGAGTGAGATATCTCGGCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											42	46	45					3																	38793924		2203	4300	6503	38768928	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1541T>G	3.37:g.38793924A>C	ENSP00000390600:p.Ile514Ser		38768928	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	A	5.725	0.318304	0.10845	.	.	ENSG00000185313	ENST00000449082	D	0.95788	-3.81	4.8	-2.41	0.06562	.	4.297180	0.00357	N	0.000030	D	0.85695	0.5756	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.79505	-0.1776	10	0.42905	T	0.14	.	5.744	0.18110	0.5109:0.2625:0.2266:0.0	.	514	Q9Y5Y9	SCNAA_HUMAN	S	514	ENSP00000390600:I514S	ENSP00000390600:I514S	I	-	2	0	SCN10A	38768928	0.072000	0.21174	0.042000	0.18584	0.375000	0.29983	0.258000	0.18387	-0.149000	0.11215	-0.566000	0.04163	ATC		0.597	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		C	38793924	A	C	38793924	3	2	61	1	0	0	0	0	1	0	0	0	13949	333	12	4	4397	4	SCN10A	3	38793924	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2269	38793924	159228506	2399	10384										
SCN10A	6336	broad.mit.edu	37	chr3	38793988	38793988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcccggcgttttccagaggCgaggcctagaaaagactggg	15	10	0	3	rs146596599		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38793988C>T	ENST00000449082.2	-	11	1476	c.1477G>A	c.(1477-1479)Gcc>Acc	p.A493T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	493					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A493T(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TTTCCAGAGGCGAGGCCTAGA	0.552													C|||	1	0.000199681	8e-04	0	5008	,	,		18424	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	THR/ALA	1,4405		0,1,2202	24	26	25		1477	-4.2	0	3	dbSNP_134	25	0,8600		0,0,4300	no	missense	SCN10A	NM_006514.2	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	493/1957	38793988	1,13005	2203	4300	6503	38768992	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1477G>A	3.37:g.38793988C>T	ENSP00000390600:p.Ala493Thr		38768992	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	4.541	0.100380	0.08731	2.27E-4	0.0	ENSG00000185313	ENST00000449082	D	0.95447	-3.71	4.8	-4.15	0.03881	.	2.885830	0.00691	N	0.000734	D	0.83543	0.5277	N	0.01874	-0.695	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	D	0.83475	0.0061	10	0.02654	T	1	.	8.4211	0.32700	0.1112:0.4779:0.0:0.4109	.	493	Q9Y5Y9	SCNAA_HUMAN	T	493	ENSP00000390600:A493T	ENSP00000390600:A493T	A	-	1	0	SCN10A	38768992	0.000000	0.05858	0.036000	0.18154	0.762000	0.43233	-0.784000	0.04633	-0.814000	0.04352	-1.280000	0.01385	GCC		0.552	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38793988	C	T	38793988	3	4	61	1	0	0	0	0	1	0	0	0	13949	768	27	1	4461	1	SCN10A	3	38793988	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64	38793988	159228442	2400	10385										
SCN10A	6336	broad.mit.edu	37	chr3	38802855	38802855	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcactgagtgaatcagggcCcccacaatgaccttcaggcc	9	14	3	3	rs555884132		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38802855C>T	ENST00000449082.2	-	6	710	c.711G>A	c.(709-711)ggG>ggA	p.G237G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	237					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G237G(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GAATCAGGGCCCCCACAATGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	3											69	66	67					3																	38802855		2203	4300	6503	38777859	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.711G>A	3.37:g.38802855C>T			38777859	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.522	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38802855	C	T	38802855	2	4	61	1	0	0	0	0	0	0	0	1	13949	610	22	3		3	SCN10A	3	38802855	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8867	38802855	159219575	2401	10386										
SCN10A	6336	broad.mit.edu	37	chr3	38835242	38835242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctcttacccggtgtgtgCtgtagaacggatctagatcc	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38835242C>T	ENST00000449082.2	-	1	259	c.260G>A	c.(259-261)aGc>aAc	p.S87N		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	87					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.S87N(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CCGGTGTGTGCTGTAGAACGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											155	159	158					3																	38835242		2203	4300	6503	38810246	SO:0001583	missense	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.260G>A	3.37:g.38835242C>T	ENSP00000390600:p.Ser87Asn		38810246	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	7.601	0.672704	0.14776	.	.	ENSG00000185313	ENST00000449082	D	0.95756	-3.8	5.19	1.41	0.22369	.	0.534764	0.22637	N	0.057520	D	0.91791	0.7403	L	0.59436	1.845	0.09310	N	0.999994	B	0.14438	0.01	B	0.12156	0.007	T	0.79985	-0.1572	10	0.20046	T	0.44	.	8.9326	0.35680	0.0:0.5646:0.0:0.4354	.	87	Q9Y5Y9	SCNAA_HUMAN	N	87	ENSP00000390600:S87N	ENSP00000390600:S87N	S	-	2	0	SCN10A	38810246	0.000000	0.05858	0.991000	0.47740	0.740000	0.42216	-0.748000	0.04818	0.371000	0.24564	-0.251000	0.11542	AGC		0.572	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38835242	C	T	38835242	3	4	61	1	0	0	0	0	1	0	0	0	13949	797	28	3	5718	3	SCN10A	3	38835242	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32387	38835242	159187188	2402	10387										
SCN11A	11280	broad.mit.edu	37	chr3	38888584	38888584	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatatttatttggctttgcGacacgcaaaggctcaggcaa	10	8	1	1	rs150087925	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38888584G>A	ENST00000302328.3	-	26	5175	c.4977C>T	c.(4975-4977)gtC>gtT	p.V1659V	SCN11A_ENST00000450244.1_Silent_p.V1659V|SCN11A_ENST00000456224.3_Silent_p.V1621V	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1659					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V1659V(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTGGCTTTGCGACACGCAAAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		2,4404	4.2+/-10.8	0,2,2201	92	95	94		4977	0.1	0.8	3	dbSNP_134	94	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SCN11A	NM_014139.2		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		1659/1792	38888584	4,13002	2203	4300	6503	38863588	SO:0001819	synonymous_variant	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4977C>T	3.37:g.38888584G>A			38863588	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																				0.438	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38888584	G	A	38888584	2	1	61	1	0	0	0	0	0	0	0	1	13950	1045	37	1		1	SCN11A	3	38888584	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53342	38888584	159133846	2403	10388										
SCN11A	11280	broad.mit.edu	37	chr3	38889018	38889018	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggaaaaccagttcatacCcagaatggcatagataaaca	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38889018C>A	ENST00000302328.3	-	26	4741	c.4543G>T	c.(4543-4545)Ggt>Tgt	p.G1515C	SCN11A_ENST00000450244.1_Missense_Mutation_p.G1515C|SCN11A_ENST00000456224.3_Missense_Mutation_p.G1477C	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1515					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G1515C(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGTTCATACCCAGAATGGCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	81	81					3																	38889018		2203	4300	6503	38864022	SO:0001583	missense	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4543G>T	3.37:g.38889018C>A	ENSP00000307599:p.Gly1515Cys		38864022	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765414	0.69878	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224	D;D;D	0.97665	-4.48;-4.48;-4.48	5.67	5.67	0.87782	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99348	0.9771	H	0.99764	4.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98221	1.0478	10	0.87932	D	0	.	19.7659	0.96340	0.0:1.0:0.0:0.0	.	1515	Q9UI33	SCNBA_HUMAN	C	1515;1515;1477	ENSP00000307599:G1515C;ENSP00000400945:G1515C;ENSP00000416757:G1477C	ENSP00000307599:G1515C	G	-	1	0	SCN11A	38864022	1.000000	0.71417	0.689000	0.30133	0.363000	0.29612	7.811000	0.86092	2.663000	0.90544	0.637000	0.83480	GGT		0.418	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38889018	C	A	38889018	3	1	61	1	0	0	0	0	1	0	0	0	13950	623	22	2	836	2	SCN11A	3	38889018	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	434	38889018	159133412	2404	10389										
SCN11A	11280	broad.mit.edu	37	chr3	38892219	38892219	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctggcttgtgactatgtcGaacacgagaccttgacattt	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38892219G>A	ENST00000302328.3	-	25	4278	c.4080C>T	c.(4078-4080)ttC>ttT	p.F1360F	SCN11A_ENST00000450244.1_Silent_p.F1360F|SCN11A_ENST00000444237.2_Silent_p.F1360F|SCN11A_ENST00000456224.3_Silent_p.F1322F	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1360					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.F1360F(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGACTATGTCGAACACGAGAC	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	3											122	113	116					3																	38892219		2203	4300	6503	38867223	SO:0001819	synonymous_variant	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4080C>T	3.37:g.38892219G>A			38867223	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																				0.313	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38892219	G	A	38892219	2	1	61	1	0	0	0	0	0	0	0	1	13950	1049	37	1		1	SCN11A	3	38892219	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3201	38892219	159130211	2405	10390										
SCN11A	11280	broad.mit.edu	37	chr3	38926864	38926864	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagatcaatggtgctacaTtctgatagtatactggtaac	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38926864T>G	ENST00000302328.3	-	17	3177	c.2979A>C	c.(2977-2979)gaA>gaC	p.E993D	SCN11A_ENST00000450244.1_Missense_Mutation_p.E993D|SCN11A_ENST00000444237.2_Missense_Mutation_p.E993D|SCN11A_ENST00000456224.3_Missense_Mutation_p.E955D	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	993					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E993D(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGTGCTACATTCTGATAGTA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											145	132	137					3																	38926864		2203	4300	6503	38901868	SO:0001583	missense	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2979A>C	3.37:g.38926864T>G	ENSP00000307599:p.Glu993Asp		38901868	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.877339	0.72294	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.06	-2.58	0.06228	Sodium ion transport-associated (1);	65.989700	0.02430	U	0.083493	T	0.81640	0.4865	M	0.71581	2.175	0.32733	N	0.5088	B	0.20550	0.046	B	0.22601	0.04	T	0.65833	-0.6072	10	0.87932	D	0	.	0.3553	0.00355	0.2852:0.2552:0.1335:0.3261	.	993	Q9UI33	SCNBA_HUMAN	D	993;993;955;993	ENSP00000307599:E993D;ENSP00000400945:E993D;ENSP00000416757:E955D;ENSP00000408028:E993D	ENSP00000307599:E993D	E	-	3	2	SCN11A	38901868	0.993000	0.37304	0.929000	0.37066	0.996000	0.88848	-0.029000	0.12329	-0.182000	0.10602	0.533000	0.62120	GAA		0.428	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		G	38926864	T	G	38926864	3	3	61	1	0	0	0	0	1	0	0	0	13950	1490	52	4	2436	4	SCN11A	3	38926864	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34645	38926864	159095566	2406	10391										
SCN11A	11280	broad.mit.edu	37	chr3	38927672	38927672	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagagaacatgtcaatttCcacactttgaactctctggc	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38927672C>A	ENST00000302328.3	-	16	3091	c.2893G>T	c.(2893-2895)Gaa>Taa	p.E965*	SCN11A_ENST00000450244.1_Nonsense_Mutation_p.E965*|SCN11A_ENST00000444237.2_Nonsense_Mutation_p.E965*|SCN11A_ENST00000456224.3_Intron	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	965					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E965*(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGTCAATTTCCACACTTTGA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											138	124	129					3																	38927672		2203	4300	6503	38902676	SO:0001587	stop_gained	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2893G>T	3.37:g.38927672C>A	ENSP00000307599:p.Glu965*		38902676	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Nonsense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	40	7.967004	0.98585	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000444237	.	.	.	4.43	3.52	0.40303	.	787.273000	0.00166	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	9.9316	0.41525	0.0:0.7927:0.2073:0.0	.	.	.	.	X	965	.	ENSP00000307599:E965X	E	-	1	0	SCN11A	38902676	0.928000	0.31464	0.955000	0.39395	0.122000	0.20287	3.334000	0.52097	1.018000	0.39521	0.563000	0.77884	GAA		0.463	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38927672	C	A	38927672	4	1	61	1	0	0	0	0	0	1	0	0	13950	864	30	2	2526	2	SCN11A	3	38927672	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	808	38927672	159094758	2407	10392										
SCN11A	11280	broad.mit.edu	37	chr3	38950669	38950669	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagaagactgagtagagcCcagtagtacgcagggtctgc	14	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38950669C>A	ENST00000302328.3	-	9	1316	c.1118G>T	c.(1117-1119)gGg>gTg	p.G373V	AC116038.1_ENST00000401122.1_RNA|SCN11A_ENST00000450244.1_Missense_Mutation_p.G373V|SCN11A_ENST00000444237.2_Missense_Mutation_p.G373V|SCN11A_ENST00000456224.3_Missense_Mutation_p.G373V	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	373					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G373V(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAGTAGAGCCCAGTAGTACG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											129	126	127					3																	38950669		2203	4300	6503	38925673	SO:0001583	missense	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.1118G>T	3.37:g.38950669C>A	ENSP00000307599:p.Gly373Val		38925673	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857722	0.91433	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.98666	-5.06;-5.06;-5.06;-5.06	5.2	5.2	0.72013	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99333	0.9766	M	0.91561	3.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98965	1.0799	10	0.87932	D	0	.	18.7324	0.91739	0.0:1.0:0.0:0.0	.	373	Q9UI33	SCNBA_HUMAN	V	373	ENSP00000307599:G373V;ENSP00000400945:G373V;ENSP00000416757:G373V;ENSP00000408028:G373V	ENSP00000307599:G373V	G	-	2	0	SCN11A	38925673	1.000000	0.71417	0.076000	0.20297	0.384000	0.30261	7.704000	0.84595	2.431000	0.82371	0.460000	0.39030	GGG		0.458	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38950669	C	A	38950669	3	1	61	1	0	0	0	0	1	0	0	0	13950	623	22	2	4329	2	SCN11A	3	38950669	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22997	38950669	159071761	2408	10393										
SCN11A	11280	broad.mit.edu	37	chr3	38986936	38986936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgttactgttgctgttttTagcaggccctgtagccatga	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:38986936T>C	ENST00000302328.3	-	3	652	c.454A>G	c.(454-456)Aaa>Gaa	p.K152E	SCN11A_ENST00000450244.1_Missense_Mutation_p.K152E|SCN11A_ENST00000444237.2_Missense_Mutation_p.K152E|SCN11A_ENST00000456224.3_Missense_Mutation_p.K152E	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	152					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K152E(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ttgctgtttttagcaggccct	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											153	139	144					3																	38986936		2203	4300	6503	38961940	SO:0001583	missense	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.454A>G	3.37:g.38986936T>C	ENSP00000307599:p.Lys152Glu		38961940	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	1.688	-0.504708	0.04261	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.97279	-4.32;-4.32;-4.32;-4.32	5.07	2.56	0.30785	.	1.628810	0.03467	N	0.213091	D	0.91365	0.7276	N	0.04203	-0.255	0.09310	N	1	B	0.19331	0.035	B	0.17433	0.018	D	0.84325	0.0518	10	0.72032	D	0.01	.	4.7905	0.13247	0.0:0.1734:0.159:0.6676	.	152	Q9UI33	SCNBA_HUMAN	E	152	ENSP00000307599:K152E;ENSP00000400945:K152E;ENSP00000416757:K152E;ENSP00000408028:K152E	ENSP00000307599:K152E	K	-	1	0	SCN11A	38961940	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.111000	0.15458	0.324000	0.23333	0.459000	0.35465	AAA		0.398	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		C	38986936	T	C	38986936	3	2	61	1	0	0	0	0	1	0	0	0	13950	1763	61	4	5017	4	SCN11A	3	38986936	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	36267	38986936	159035494	2409	10394										
TTC21A	199223	broad.mit.edu	37	chr3	39177902	39177902	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaagaagaagtggaaaacTtgaagacattcctgccttct	9	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:39177902T>G	ENST00000431162.2	+	23	3154	c.3020T>G	c.(3019-3021)cTt>cGt	p.L1007R	TTC21A_ENST00000440121.1_Missense_Mutation_p.L959R|TTC21A_ENST00000301819.6_Missense_Mutation_p.L1008R|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1007								p.L1008R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AGTGGAAAACTTGAAGACATT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											151	153	152					3																	39177902		1874	4101	5975	39152906	SO:0001583	missense	199223			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.3020T>G	3.37:g.39177902T>G	ENSP00000398211:p.Leu1007Arg		39152906	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801372	0.70567	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.39787	1.06;1.06;1.06	4.79	4.79	0.61399	Tetratricopeptide repeat-containing (1);	0.104379	0.39615	N	0.001309	T	0.67970	0.2950	M	0.88640	2.97	0.47276	D	0.999375	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.74023	0.982;0.976;0.946	T	0.73678	-0.3907	10	0.51188	T	0.08	-7.0843	13.327	0.60465	0.0:0.0:0.0:1.0	.	959;1008;1007	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	R	1008;990;1007;959	ENSP00000301819:L1008R;ENSP00000398211:L1007R;ENSP00000410882:L959R	ENSP00000301819:L1008R	L	+	2	0	TTC21A	39152906	1.000000	0.71417	0.972000	0.41901	0.702000	0.40608	7.535000	0.82014	1.798000	0.52647	0.379000	0.24179	CTT		0.423	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		G	39177902	T	G	39177902	3	3	61	1	0	0	0	0	1	0	0	0	16727	1609	56	4	3113	4	TTC21A	3	39177902	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	190966	39177902	158844528	2410	10395										
XIRP1	165904	broad.mit.edu	37	chr3	39230653	39230653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagttctcaaagatccagCgcatgcactgaacgtcaccc	7	15	2	2	rs371716831		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:39230653C>T	ENST00000340369.3	-	2	512	c.284G>A	c.(283-285)cGc>cAc	p.R95H	XIRP1_ENST00000396251.1_Missense_Mutation_p.R95H|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	95					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.R95H(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AAAGATCCAGCGCATGCACTG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	71	70	70		284,284	4.9	1	3		70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	95/1122,95/1844	39230653	1,13005	2203	4300	6503	39205657	SO:0001583	missense	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.284G>A	3.37:g.39230653C>T	ENSP00000343140:p.Arg95His		39205657	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808871	0.70797	0.0	1.16E-4	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.39056	1.1;1.1	4.93	4.93	0.64822	.	0.122356	0.53938	U	0.000056	T	0.64260	0.2582	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	T	0.68183	-0.5476	10	0.87932	D	0	.	16.048	0.80734	0.0:1.0:0.0:0.0	.	95;95	Q702N8;Q702N8-2	XIRP1_HUMAN;.	H	95	ENSP00000379550:R95H;ENSP00000343140:R95H	ENSP00000343140:R95H	R	-	2	0	XIRP1	39205657	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.884000	0.63135	2.465000	0.83290	0.655000	0.94253	CGC		0.622	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39230653	C	T	39230653	3	4	61	1	0	0	0	0	1	0	0	0	17469	768	27	1	5251	1	XIRP1	3	39230653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52751	39230653	158791777	2411	10396										
CX3CR1	1524	broad.mit.edu	37	chr3	39307689	39307689	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagaagaaggcggtagtGaatttgcacatggcattgtg	14	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:39307689G>T	ENST00000541347.1	-	2	551	c.312C>A	c.(310-312)ttC>ttA	p.F104L	CX3CR1_ENST00000542107.1_Missense_Mutation_p.F104L|CX3CR1_ENST00000358309.3_Missense_Mutation_p.F136L|CX3CR1_ENST00000399220.2_Missense_Mutation_p.F104L	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	104					cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cerebral cortex cell migration (GO:0021795)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|macrophage chemotaxis (GO:0048246)|microglial cell activation involved in immune response (GO:0002282)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|response to wounding (GO:0009611)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|neuronal cell body membrane (GO:0032809)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-X3-C chemokine receptor activity (GO:0016495)|chemokine receptor activity (GO:0004950)	p.F104L(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AGGCGGTAGTGAATTTGCACA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											159	152	154					3																	39307689		1954	4146	6100	39282693	SO:0001583	missense	1524			BC028078	CCDS43069.1, CCDS54571.1	3p21.3	2012-08-08	2002-08-22		ENSG00000168329	ENSG00000168329		"GPCR / Class A : Chemokine receptors : C-X-3-C motif"	2558	protein-coding gene	gene with protein product		601470	"chemokine (C-X3-C) receptor 1"	GPR13, CMKBRL1		9726990, 7646814	Standard	NM_001171171		Approved	CMKDR1, V28, CCRL1	uc021wwc.1	P49238	OTTHUMG00000156249	ENST00000541347.1:c.312C>A	3.37:g.39307689G>T	ENSP00000439140:p.Phe104Leu		39282693	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.962827	0.00461	.	.	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107;ENST00000435290;ENST00000412814	T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35	5.54	0.458	0.16670	GPCR, rhodopsin-like superfamily (1);	0.750955	0.13033	N	0.419172	T	0.07638	0.0192	N	0.00778	-1.195	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32375	-0.9909	10	0.02654	T	1	.	1.5238	0.02521	0.2787:0.2339:0.3677:0.1197	.	104	P49238	CX3C1_HUMAN	L	104;112;136;104;104;104;104	ENSP00000382166:F104L;ENSP00000351059:F136L;ENSP00000439140:F104L;ENSP00000444928:F104L;ENSP00000394960:F104L;ENSP00000408835:F104L	ENSP00000351059:F136L	F	-	3	2	CX3CR1	39282693	0.000000	0.05858	0.091000	0.20842	0.164000	0.22412	0.031000	0.13710	0.026000	0.15269	-0.136000	0.14681	TTC		0.478	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337		T	39307689	G	T	39307689	3	4	61	1	0	0	0	0	1	0	0	0	4081	1281	45	2	759	2	CX3CR1	3	39307689	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77036	39307689	158714741	2412	10397										
ZNF621	285268	broad.mit.edu	37	chr3	40574077	40574077	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaatgttggaaagctttCggttgtaggtcactttttat	11	4	1	0	rs566518778		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:40574077C>T	ENST00000339296.5	+	5	1268	c.816C>T	c.(814-816)ttC>ttT	p.F272F	ZNF621_ENST00000403205.2_Silent_p.F272F|ZNF621_ENST00000431278.1_Silent_p.F161F|ZNF621_ENST00000310898.1_Intron|ZNF621_ENST00000490457.1_Intron	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	272					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F272F(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		GGAAAGCTTTCGGTTGTAGGT	0.438													C|||	1	0.000199681	0	0	5008	,	,		22534	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	3											68	77	74					3																	40574077		2203	4300	6503	40549081	SO:0001819	synonymous_variant	285268			AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"Zinc fingers, C2H2-type", "-"	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.816C>T	3.37:g.40574077C>T			40549081	Q14DC7|Q8TE91	Silent	SNP	ENST00000339296.5	37	CCDS2693.1																																																																																				0.438	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484		T	40574077	C	T	40574077	2	4	61	1	0	0	0	0	0	0	0	1	18084	883	31	1		1	ZNF621	3	40574077	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1266388	40574077	157448353	2413	10398										
ULK4	54986	broad.mit.edu	37	chr3	41759321	41759321	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccttgcctggagtggtcTttctgctgtctctctcgatg	11	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:41759321T>G	ENST00000301831.4	-	23	2816	c.2354A>C	c.(2353-2355)aAg>aCg	p.K785T		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	785					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K785T(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGGAGTGGTCTTTCTGCTGTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	134	133					3																	41759321		2019	4199	6218	41734325	SO:0001583	missense	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2354A>C	3.37:g.41759321T>G	ENSP00000301831:p.Lys785Thr		41734325	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.230258	0.79688	.	.	ENSG00000168038	ENST00000301831	T	0.65732	-0.17	5.3	4.14	0.48551	Armadillo-type fold (2);	0.116985	0.56097	U	0.000038	T	0.70954	0.3283	L	0.54323	1.7	0.80722	D	1	D	0.71674	0.998	D	0.63877	0.919	T	0.71781	-0.4489	10	0.66056	D	0.02	.	10.807	0.46524	0.0:0.0747:0.0:0.9253	.	785	Q96C45	ULK4_HUMAN	T	785	ENSP00000301831:K785T	ENSP00000301831:K785T	K	-	2	0	ULK4	41734325	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.254000	0.58798	0.870000	0.35726	0.459000	0.35465	AAG		0.453	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41759321	T	G	41759321	3	3	61	1	0	0	0	0	1	0	0	0	17018	1609	56	4	1533	4	ULK4	3	41759321	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1185244	41759321	156263109	2414	10399										
ULK4	54986	broad.mit.edu	37	chr3	41954312	41954312	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactacctgagactgagatCttcgacgcttgattcctgat	8	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:41954312C>A	ENST00000301831.4	-	9	1345	c.883G>T	c.(883-885)Gat>Tat	p.D295Y	ULK4_ENST00000420927.1_Missense_Mutation_p.D295Y	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	295					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D295Y(2)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AGACTGAGATCTTCGACGCTT	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	3											94	91	92					3																	41954312		1900	4111	6011	41929316	SO:0001583	missense	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.883G>T	3.37:g.41954312C>A	ENSP00000301831:p.Asp295Tyr		41929316	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.876521	0.51801	.	.	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.68624	0.48;-0.34	5.17	5.17	0.71159	Protein kinase-like domain (1);	0.739085	0.13690	N	0.369606	T	0.68256	0.2981	M	0.62723	1.935	0.80722	D	1	P;P	0.50710	0.938;0.938	B;B	0.43536	0.423;0.423	T	0.73424	-0.3987	10	0.87932	D	0	.	15.576	0.76387	0.0:1.0:0.0:0.0	.	295;295	B4E2M4;Q96C45	.;ULK4_HUMAN	Y	295	ENSP00000301831:D295Y;ENSP00000412187:D295Y	ENSP00000301831:D295Y	D	-	1	0	ULK4	41929316	0.074000	0.21230	0.009000	0.14445	0.001000	0.01503	1.747000	0.38298	2.420000	0.82092	0.655000	0.94253	GAT		0.383	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		A	41954312	C	A	41954312	3	1	61	1	0	0	0	0	1	0	0	0	17018	913	32	2	3060	2	ULK4	3	41954312	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	194991	41954312	156068118	2415	10400										
TRAK1	22906	broad.mit.edu	37	chr3	42242366	42242366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccaggttgtcaagcagaGatctctgaccccttctccca	7	15	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42242366G>T	ENST00000327628.5	+	12	1647	c.1247G>T	c.(1246-1248)aGa>aTa	p.R416I	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000449246.1_Missense_Mutation_p.R342I|TRAK1_ENST00000396175.1_Missense_Mutation_p.R358I|TRAK1_ENST00000341421.3_Missense_Mutation_p.R358I	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	416	Interaction with HGS.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R358I(2)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GTCAAGCAGAGATCTCTGACC	0.572																																					GBM(44;195 884 22595 31865 41850)											2	Substitution - Missense(2)	large_intestine(2)	3											145	126	132					3																	42242366		2203	4300	6503	42217370	SO:0001583	missense	22906				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1247G>T	3.37:g.42242366G>T	ENSP00000328998:p.Arg416Ile		42217370	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	33	5.213063	0.95069	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000449246;ENST00000396175;ENST00000341421;ENST00000427771	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.95	5.08	0.68730	Trafficking kinesin-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	L	0.48642	1.525	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.991;1.0	D;D;D;D;P;D	0.79784	0.99;0.993;0.993;0.982;0.882;0.991	T	0.64271	-0.6447	10	0.62326	D	0.03	.	14.3226	0.66496	0.0706:0.0:0.9294:0.0	.	342;358;416;358;342;416	B7Z218;C9JC32;B7Z347;Q9UPV9-2;E9PDS2;Q9UPV9	.;.;.;.;.;TRAK1_HUMAN	I	416;416;342;358;358;134	ENSP00000328998:R416I;ENSP00000410717:R342I;ENSP00000379478:R358I;ENSP00000340702:R358I;ENSP00000413729:R134I	ENSP00000328998:R416I	R	+	2	0	TRAK1	42217370	1.000000	0.71417	0.987000	0.45799	0.977000	0.68977	9.799000	0.99117	1.536000	0.49237	0.655000	0.94253	AGA		0.572	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		T	42242366	G	T	42242366	3	4	61	1	0	0	0	0	1	0	0	0	16489	942	33	2	1409	2	TRAK1	3	42242366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288054	42242366	155780064	2416	10401										
TRAK1	22906	broad.mit.edu	37	chr3	42251393	42251393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaagtgtactgccttaacGactttgaagaagatgacaca	9	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42251393G>A	ENST00000327628.5	+	14	2279	c.1879G>A	c.(1879-1881)Gac>Aac	p.D627N	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.D569N|TRAK1_ENST00000341421.3_Missense_Mutation_p.D569N	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	627					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.D569N(4)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CTGCCTTAACGACTTTGAAGA	0.587																																					GBM(44;195 884 22595 31865 41850)											4	Substitution - Missense(4)	large_intestine(4)	3											138	123	128					3																	42251393		2203	4300	6503	42226397	SO:0001583	missense	22906				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1879G>A	3.37:g.42251393G>A	ENSP00000328998:p.Asp627Asn		42226397	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595021	0.86953	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175;ENST00000341421	T;T;T	0.21031	2.17;2.13;2.03	5.31	5.31	0.75309	.	0.113159	0.56097	D	0.000026	T	0.30916	0.0780	M	0.70595	2.14	0.58432	D	0.999996	D;D;D;D;D	0.62365	0.968;0.984;0.968;0.991;0.975	B;B;B;B;B	0.43754	0.248;0.248;0.248;0.43;0.335	T	0.25152	-1.0140	10	0.87932	D	0	.	17.9657	0.89099	0.0:0.0:1.0:0.0	.	553;569;627;569;627	B7Z218;C9JC32;B7Z347;Q9UPV9-2;Q9UPV9	.;.;.;.;TRAK1_HUMAN	N	627;627;569;569	ENSP00000328998:D627N;ENSP00000379478:D569N;ENSP00000340702:D569N	ENSP00000328998:D627N	D	+	1	0	TRAK1	42226397	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.471000	0.80985	2.468000	0.83385	0.655000	0.94253	GAC		0.587	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		A	42251393	G	A	42251393	3	1	61	1	0	0	0	0	1	0	0	0	16489	1058	37	1	2049	1	TRAK1	3	42251393	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9027	42251393	155771037	2417	10402										
VIPR1	7433	broad.mit.edu	37	chr3	42573765	42573765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtttatttgcatcatccGaatcctgcttcagaaactgc	6	12	2	1	rs200704872		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42573765G>A	ENST00000325123.4	+	10	1063	c.950G>A	c.(949-951)cGa>cAa	p.R317Q	VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1_ENST00000433647.1_Missense_Mutation_p.R276Q|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1_ENST00000543411.1_Missense_Mutation_p.R269Q|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000438259.2_Missense_Mutation_p.R107Q|VIPR1-AS1_ENST00000452639.3_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	317					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.R317Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		TGCATCATCCGAATCCTGCTT	0.562													G|||	1	0.000199681	0	0.0014	5008	,	,		18265	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	GLN/ARG	0,4406		0,0,2203	156	143	147		950	4.6	1	3		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	VIPR1	NM_004624.3	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	317/458	42573765	1,13005	2203	4300	6503	42548769	SO:0001583	missense	7433			AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.950G>A	3.37:g.42573765G>A	ENSP00000327246:p.Arg317Gln		42548769	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Missense_Mutation	SNP	ENST00000325123.4	37	CCDS2698.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094534	0.94149	0.0	1.16E-4	ENSG00000114812	ENST00000433647;ENST00000543411;ENST00000438259;ENST00000325123	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	4.61	4.61	0.57282	GPCR, family 2-like (1);	0.071304	0.53938	D	0.000041	T	0.67144	0.2862	M	0.83692	2.655	0.58432	D	0.999994	D;D;D;D	0.76494	0.994;0.999;0.987;0.994	D;D;P;D	0.70227	0.964;0.968;0.757;0.964	T	0.72421	-0.4299	10	0.51188	T	0.08	.	17.4441	0.87574	0.0:0.0:1.0:0.0	.	290;107;269;317	B4DNY6;B4DEB5;F5H1F5;P32241	.;.;.;VIPR1_HUMAN	Q	276;269;107;317	ENSP00000394950:R276Q;ENSP00000445701:R269Q;ENSP00000415371:R107Q;ENSP00000327246:R317Q	ENSP00000327246:R317Q	R	+	2	0	VIPR1	42548769	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.807000	0.69157	2.110000	0.64415	0.655000	0.94253	CGA		0.562	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		A	42573765	G	A	42573765	3	1	61	1	0	0	0	0	1	0	0	0	17209	1058	37	1	988	1	VIPR1	3	42573765	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	322372	42573765	155448665	2418	10403										
NKTR	4820	broad.mit.edu	37	chr3	42681071	42681071	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcttaaaccgtagaccaaGaaatcaggagagttcaagtg	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42681071G>T	ENST00000232978.8	+	13	4063	c.3875G>T	c.(3874-3876)aGa>aTa	p.R1292I	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	1292					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R1292I(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		CGTAGACCAAGAAATCAGGAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	77	77					3																	42681071		2203	4300	6503	42656075	SO:0001583	missense	4820				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein"	161565	"natural killer-tumor recognition sequence"			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.3875G>T	3.37:g.42681071G>T	ENSP00000232978:p.Arg1292Ile		42656075		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.356694	0.82243	.	.	ENSG00000114857	ENST00000232978	T	0.34667	1.35	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.71909	-0.4450	10	0.87932	D	0	-24.9959	19.4228	0.94729	0.0:0.0:1.0:0.0	.	992;1292	Q6M1B8;P30414	.;NKTR_HUMAN	I	1292	ENSP00000232978:R1292I	ENSP00000232978:R1292I	R	+	2	0	NKTR	42656075	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	9.378000	0.97191	2.663000	0.90544	0.655000	0.94253	AGA		0.428	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		T	42681071	G	T	42681071	3	4	61	1	0	0	0	0	1	0	0	0	10479	942	33	2	3921	2	NKTR	3	42681071	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107306	42681071	155341359	2419	10404										
KBTBD5	131377	broad.mit.edu	37	chr3	42729760	42729760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagatcaaggacggcgagCgctgcctggactcggtcatg	16	10	2	1	rs577804609		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42729760C>T	ENST00000287777.4	+	2	1379	c.1279C>T	c.(1279-1281)Cgc>Tgc	p.R427C		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	427					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.R427C(1)									GGACGGCGAGCGCTGCCTGGA	0.667													C|||	1	0.000199681	0	0	5008	,	,		12163	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											51	47	48					3																	42729760		2203	4300	6503	42704764	SO:0001583	missense	131377			AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1279C>T	3.37:g.42729760C>T	ENSP00000287777:p.Arg427Cys		42704764	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	37	CCDS2703.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520481	0.44866	.	.	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.67698	-0.28	4.99	2.06	0.26882	Kelch-type beta propeller (1);	0.980252	0.08386	N	0.953749	T	0.59183	0.2175	L	0.43152	1.355	0.42006	D	0.990915	B	0.02656	0.0	B	0.01281	0.0	T	0.45948	-0.9226	10	0.51188	T	0.08	.	9.9993	0.41918	0.3926:0.4841:0.1232:0.0	.	427	Q2TBA0	KBTB5_HUMAN	C	427;172	ENSP00000287777:R427C	ENSP00000287777:R427C	R	+	1	0	KBTBD5	42704764	0.444000	0.25649	0.867000	0.34043	0.987000	0.75469	0.845000	0.27668	0.099000	0.17552	0.455000	0.32223	CGC		0.667	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		T	42729760	C	T	42729760	3	4	61	1	0	0	0	0	1	0	0	0	8017	768	27	1	1285	1	KBTBD5	3	42729760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48689	42729760	155292670	2420	10405										
CCDC13	152206	broad.mit.edu	37	chr3	42788757	42788757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctgaaagaccttctgtgCcatccgcagctcctgcttca	8	15	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42788757C>T	ENST00000310232.6	-	6	795	c.712G>A	c.(712-714)Gca>Aca	p.A238T	CCDC13_ENST00000435327.2_5'Flank|CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	238								p.A238T(1)		endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						ACCTTCTGTGCCATCCGCAGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											86	77	80					3																	42788757		2203	4300	6503	42763761	SO:0001583	missense	152206			AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.712G>A	3.37:g.42788757C>T	ENSP00000309836:p.Ala238Thr		42763761		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360122	0.82353	.	.	ENSG00000244607	ENST00000310232	T	0.28666	1.6	5.1	5.1	0.69264	.	0.101382	0.64402	D	0.000003	T	0.46833	0.1413	L	0.49126	1.545	0.51012	D	0.9999	D;D	0.89917	0.995;1.0	D;D	0.87578	0.909;0.998	T	0.28713	-1.0035	10	0.36615	T	0.2	.	11.5563	0.50750	0.0:0.9131:0.0:0.0869	.	238;238	Q96LI1;Q8IYE1	.;CCD13_HUMAN	T	238	ENSP00000309836:A238T	ENSP00000309836:A238T	A	-	1	0	CCDC13	42763761	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	3.939000	0.56591	2.363000	0.80096	0.655000	0.94253	GCA		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		T	42788757	C	T	42788757	3	4	61	1	0	0	0	0	1	0	0	0	2771	739	26	3	1479	3	CCDC13	3	42788757	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58997	42788757	155233673	2421	10406										
CCBP2	1238	broad.mit.edu	37	chr3	42906240	42906240	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgcaggcggatggttgaGatctatctgctgaatctggc	13	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42906240G>T	ENST00000422265.1	+	3	421	c.246G>T	c.(244-246)gaG>gaT	p.E82D	CYP8B1_ENST00000437102.1_Intron|ACKR2_ENST00000273145.2_Missense_Mutation_p.E82D|RP11-141M3.5_ENST00000471537.1_RNA|ACKR2_ENST00000442925.1_Missense_Mutation_p.E82D|KRBOX1_ENST00000426937.1_Intron	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	82					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.E82D(1)									GGATGGTTGAGATCTATCTGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	3											177	156	163					3																	42906240		2203	4300	6503	42881244	SO:0001583	missense	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.246G>T	3.37:g.42906240G>T	ENSP00000416996:p.Glu82Asp		42881244	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	G	2.795	-0.250420	0.05867	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.35605	1.3;1.3;1.3	5.28	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000144	T	0.12433	0.0302	N	0.04090	-0.28	0.80722	D	1	P;P	0.43169	0.8;0.58	B;B	0.37091	0.241;0.241	T	0.08513	-1.0718	9	.	.	.	.	2.6238	0.04924	0.1646:0.1442:0.5429:0.1484	.	82;82	O00590;Q7Z7I1	CCBP2_HUMAN;.	D	82	ENSP00000396150:E82D;ENSP00000416996:E82D;ENSP00000273145:E82D	.	E	+	3	2	CCBP2	42881244	0.269000	0.24143	0.106000	0.21319	0.217000	0.24651	0.340000	0.19892	0.620000	0.30215	0.563000	0.77884	GAG		0.542	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		T	42906240	G	T	42906240	3	4	61	1	0	0	0	0	1	0	0	0	2740	933	33	2	248	2	CCBP2	3	42906240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117483	42906240	155116190	2422	10407										
ZNF662	389114	broad.mit.edu	37	chr3	42956255	42956255	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgtgggaaggctttcagTtttcgatcacattgcattgc	11	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:42956255T>C	ENST00000541208.1	+	5	1059	c.690T>C	c.(688-690)agT>agC	p.S230S	ZNF662_ENST00000440367.2_Silent_p.S230S|ZNF662_ENST00000422021.1_Intron|ZNF662_ENST00000328199.6_Silent_p.S256S|KRBOX1_ENST00000426937.1_Intron			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S230S(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		AGGCTTTCAGTTTTCGATCAC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	3											109	110	110					3																	42956255		2203	4300	6503	42931259	SO:0001819	synonymous_variant	389114			AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"Zinc fingers, C2H2-type", "-"	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.690T>C	3.37:g.42956255T>C			42931259	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Silent	SNP	ENST00000541208.1	37	CCDS2708.1																																																																																				0.418	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404		C	42956255	T	C	42956255	2	2	61	1	0	0	0	0	0	0	0	1	18110	1722	60	4		4	ZNF662	3	42956255	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	50015	42956255	155066175	2423	10408										
SNRK	54861	broad.mit.edu	37	chr3	43381804	43381804	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacacggatgctacagagaGatcccaagagaagggcttct	11	10	2	3	rs368466705		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:43381804G>T	ENST00000296088.7	+	5	1061	c.757G>T	c.(757-759)Gat>Tat	p.D253Y	SNRK_ENST00000429705.2_Missense_Mutation_p.D253Y|SNRK_ENST00000437827.1_Missense_Mutation_p.D47Y|SNRK_ENST00000454177.1_Missense_Mutation_p.D253Y	NM_017719.4	NP_060189.3			SNF related kinase									p.D253Y(2)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		GCTACAGAGAGATCCCAAGAG	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	3											195	191	192					3																	43381804		1865	4110	5975	43356808	SO:0001583	missense	54861			D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.757G>T	3.37:g.43381804G>T	ENSP00000296088:p.Asp253Tyr		43356808		Missense_Mutation	SNP	ENST00000296088.7	37	CCDS43075.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.951986	0.92660	.	.	ENSG00000163788	ENST00000454177;ENST00000429705;ENST00000296088;ENST00000437827	D;D;D;T	0.86497	-2.13;-2.13;-2.13;-1.27	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95611	0.8573	H	0.94734	3.575	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.96481	0.9356	10	0.87932	D	0	.	19.3838	0.94548	0.0:0.0:1.0:0.0	.	253	Q9NRH2	SNRK_HUMAN	Y	253;253;253;47	ENSP00000401246:D253Y;ENSP00000411375:D253Y;ENSP00000296088:D253Y;ENSP00000409516:D47Y	ENSP00000296088:D253Y	D	+	1	0	SNRK	43356808	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.781000	0.99029	2.670000	0.90874	0.655000	0.94253	GAT		0.423	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		T	43381804	G	T	43381804	3	4	61	1	0	0	0	0	1	0	0	0	14888	942	33	2	767	2	SNRK	3	43381804	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	425549	43381804	154640626	2424	10409										
ANO10	55129	broad.mit.edu	37	chr3	43596803	43596803	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattggctgaaggttctgaGaatggacgtttgaagaccct	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:43596803G>A	ENST00000292246.3	-	10	1805	c.1635C>T	c.(1633-1635)ttC>ttT	p.F545F	ANO10_ENST00000396091.3_Silent_p.F479F|ANO10_ENST00000350459.4_Silent_p.F355F|ANO10_ENST00000414522.2_Silent_p.F545F|ANO10_ENST00000451430.2_Silent_p.F434F	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	545					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.F545F(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						AAGGTTCTGAGAATGGACGTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	3											94	92	93					3																	43596803		2203	4300	6503	43571807	SO:0001819	synonymous_variant	55129			AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.1635C>T	3.37:g.43596803G>A			43571807	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Silent	SNP	ENST00000292246.3	37	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	G	8.626	0.892624	0.17613	.	.	ENSG00000160746	ENST00000448045	.	.	.	5.52	2.29	0.28610	.	.	.	.	.	T	0.52403	0.1732	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42649	-0.9439	4	.	.	.	.	5.5255	0.16955	0.5468:0.0:0.4532:0.0	.	.	.	.	F	34	.	.	S	-	2	0	ANO10	43571807	0.998000	0.40836	0.635000	0.29338	0.939000	0.58152	2.289000	0.43523	0.678000	0.31325	0.655000	0.94253	TCT		0.363	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		A	43596803	G	A	43596803	2	1	61	1	0	0	0	0	0	0	0	1	696	933	33	3		3	ANO10	3	43596803	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214999	43596803	154425627	2425	10410										
ZNF445	353274	broad.mit.edu	37	chr3	44489119	44489119	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccacactgctgacacaGaaatgttttctccacagcgg	7	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44489119G>T	ENST00000396077.2	-	8	2391	c.2044C>A	c.(2044-2046)Ctg>Atg	p.L682M	ZNF445_ENST00000425708.2_Missense_Mutation_p.L682M	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	682					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L682M(2)		breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		TGCTGACACAGAAATGTTTTC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	3											77	75	75					3																	44489119		2203	4300	6503	44464123	SO:0001583	missense	353274			AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"Zinc fingers, C2H2-type", "-", "-", "-"	21018	protein-coding gene	gene with protein product			"zinc finger protein 168"	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.2044C>A	3.37:g.44489119G>T	ENSP00000379387:p.Leu682Met		44464123	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	37	CCDS2713.1	.	.	.	.	.	.	.	.	.	.	G	5.740	0.320970	0.10845	.	.	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.61274	0.12;0.12	3.88	-7.76	0.01232	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	2.326550	0.02051	N	0.050067	T	0.33352	0.0860	N	0.16656	0.425	0.09310	N	1	P;P	0.44309	0.728;0.832	B;B	0.39904	0.313;0.313	T	0.46247	-0.9205	10	0.59425	D	0.04	.	0.9001	0.01272	0.2844:0.2456:0.29:0.18	.	670;682	B7ZKX2;P59923	.;ZN445_HUMAN	M	682	ENSP00000413073:L682M;ENSP00000379387:L682M	ENSP00000379387:L682M	L	-	1	2	ZNF445	44464123	0.000000	0.05858	0.000000	0.03702	0.424000	0.31475	-1.878000	0.01630	-1.789000	0.01264	-0.383000	0.06682	CTG		0.468	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		T	44489119	G	T	44489119	3	4	61	1	0	0	0	0	1	0	0	0	17957	933	33	2	1055	2	ZNF445	3	44489119	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	892316	44489119	153533311	2426	10411										
ZNF445	353274	broad.mit.edu	37	chr3	44489817	44489817	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagtccactatgaattCtctgatgtaggctgaagccc	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44489817C>A	ENST00000396077.2	-	8	1693	c.1346G>T	c.(1345-1347)aGa>aTa	p.R449I	ZNF445_ENST00000425708.2_Missense_Mutation_p.R449I	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	449					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R449I(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		ACTATGAATTCTCTGATGTAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											149	151	151					3																	44489817		2203	4300	6503	44464821	SO:0001583	missense	353274			AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"Zinc fingers, C2H2-type", "-", "-", "-"	21018	protein-coding gene	gene with protein product			"zinc finger protein 168"	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.1346G>T	3.37:g.44489817C>A	ENSP00000379387:p.Arg449Ile		44464821	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	37	CCDS2713.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301209	0.81136	.	.	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.18338	2.22;2.22	4.14	2.29	0.28610	.	0.546597	0.16935	N	0.193512	T	0.16769	0.0403	M	0.63843	1.955	0.41187	D	0.986277	P;P	0.37330	0.59;0.59	B;B	0.30646	0.118;0.118	T	0.07195	-1.0785	10	0.62326	D	0.03	.	11.0815	0.48062	0.3205:0.6795:0.0:0.0	.	437;449	B7ZKX2;P59923	.;ZN445_HUMAN	I	449	ENSP00000413073:R449I;ENSP00000379387:R449I	ENSP00000379387:R449I	R	-	2	0	ZNF445	44464821	0.000000	0.05858	0.024000	0.17045	0.731000	0.41821	-0.281000	0.08456	0.665000	0.31066	-0.467000	0.05162	AGA		0.478	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		A	44489817	C	A	44489817	3	1	61	1	0	0	0	0	1	0	0	0	17957	913	32	2	1753	2	ZNF445	3	44489817	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	698	44489817	153532613	2427	10412										
ZNF167	55888	broad.mit.edu	37	chr3	44609843	44609843	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtagactacactcagaaGaaatggaaaagtctcacact	7	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44609843G>A	ENST00000273320.3	+	5	1158	c.729G>A	c.(727-729)aaG>aaA	p.K243K	ZKSCAN7_ENST00000426540.1_Silent_p.K243K|ZKSCAN7_ENST00000341840.3_Silent_p.K243K|ZKSCAN7_ENST00000431636.1_Silent_p.K243K|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Silent_p.K78K	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	243	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K243K(1)									ACACTCAGAAGAAATGGAAAA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	3											122	118	119					3																	44609843		2203	4300	6503	44584847	SO:0001819	synonymous_variant	55888			L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.729G>A	3.37:g.44609843G>A			44584847	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Silent	SNP	ENST00000273320.3	37	CCDS2715.1																																																																																				0.473	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		A	44609843	G	A	44609843	2	1	61	1	0	0	0	0	0	0	0	1	17780	933	33	3		3	ZNF167	3	44609843	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120026	44609843	153412587	2428	10413										
ZNF167	55888	broad.mit.edu	37	chr3	44611916	44611916	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccacacaggggaaaaaccCtatgaatgcagtgagtgtgg	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44611916C>A	ENST00000273320.3	+	6	1743	c.1314C>A	c.(1312-1314)ccC>ccA	p.P438P	ZKSCAN7_ENST00000426540.1_Silent_p.P438P|ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000431636.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	438					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P438P(1)									GGGAAAAACCCTATGAATGCA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	3											39	41	40					3																	44611916		2203	4299	6502	44586920	SO:0001819	synonymous_variant	55888			L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.1314C>A	3.37:g.44611916C>A			44586920	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Silent	SNP	ENST00000273320.3	37	CCDS2715.1																																																																																				0.463	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		A	44611916	C	A	44611916	2	1	61	1	0	0	0	0	0	0	0	1	17780	668	24	2		2	ZNF167	3	44611916	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2073	44611916	153410514	2429	10414										
ZNF167	55888	broad.mit.edu	37	chr3	44612650	44612650	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccttatggtacatcagaGaacccatactggggaaaaac	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44612650G>T	ENST00000273320.3	+	6	2477	c.2048G>T	c.(2047-2049)aGa>aTa	p.R683I	ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.R683I|ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000431636.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	683					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R683I(3)									GTACATCAGAGAACCCATACT	0.428																																																3	Substitution - Missense(3)	large_intestine(2)|breast(1)	3											113	118	116					3																	44612650		2203	4300	6503	44587654	SO:0001583	missense	55888			L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.2048G>T	3.37:g.44612650G>T	ENSP00000273320:p.Arg683Ile		44587654	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Missense_Mutation	SNP	ENST00000273320.3	37	CCDS2715.1	.	.	.	.	.	.	.	.	.	.	.	20.1	3.938188	0.73557	.	.	ENSG00000196345	ENST00000426540;ENST00000273320;ENST00000315777	T;T	0.02446	4.29;4.29	4.2	4.2	0.49525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36034	N	0.002826	T	0.09113	0.0225	L	0.33753	1.03	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.18147	-1.0346	10	0.72032	D	0.01	-11.2884	15.5027	0.75713	0.0:0.0:1.0:0.0	.	683	Q9P0L1	ZN167_HUMAN	I	683;683;121	ENSP00000395524:R683I;ENSP00000273320:R683I	ENSP00000273320:R683I	R	+	2	0	ZNF167	44587654	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	0.403000	0.20982	2.179000	0.69175	0.655000	0.94253	AGA		0.428	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		T	44612650	G	T	44612650	3	4	61	1	0	0	0	0	1	0	0	0	17780	942	33	2	2066	2	ZNF167	3	44612650	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	734	44612650	153409780	2430	10415										
ZNF167	55888	broad.mit.edu	37	chr3	44612832	44612832	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagcgaactcacactggaGagaagtcctcaggtctggct	11	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44612832G>T	ENST00000273320.3	+	6	2659	c.2230G>T	c.(2230-2232)Gag>Tag	p.E744*	ZKSCAN7_ENST00000426540.1_Nonsense_Mutation_p.E744*|ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000431636.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	744					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E744*(1)									TCACACTGGAGAGAAGTCCTC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											89	89	89					3																	44612832		2203	4300	6503	44587836	SO:0001587	stop_gained	55888			L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.2230G>T	3.37:g.44612832G>T	ENSP00000273320:p.Glu744*		44587836	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Nonsense_Mutation	SNP	ENST00000273320.3	37	CCDS2715.1	.	.	.	.	.	.	.	.	.	.	G	40	8.356794	0.98774	.	.	ENSG00000196345	ENST00000426540;ENST00000273320;ENST00000315777	.	.	.	4.09	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-1.5487	11.2428	0.48979	0.0952:0.0:0.9048:0.0	.	.	.	.	X	744;744;182	.	ENSP00000273320:E744X	E	+	1	0	ZNF167	44587836	1.000000	0.71417	0.459000	0.27081	0.918000	0.54935	7.032000	0.76498	2.118000	0.64928	0.655000	0.94253	GAG		0.463	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		T	44612832	G	T	44612832	4	4	61	1	0	0	0	0	0	1	0	0	17780	943	33	2	2248	2	ZNF167	3	44612832	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182	44612832	153409598	2431	10416										
ZNF660	285349	broad.mit.edu	37	chr3	44636561	44636561	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttctcaagttattctacaCttgagaacccacactaagga	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44636561C>T	ENST00000322734.2	+	3	1209	c.876C>T	c.(874-876)caC>caT	p.H292H	RP11-944L7.4_ENST00000457331.1_RNA	NM_173658.2	NP_775929.2	Q6AZW8	ZN660_HUMAN	zinc finger protein 660	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H292H(1)		large_intestine(2)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		TTATTCTACACTTGAGAACCC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	3											54	55	55					3																	44636561		2203	4300	6503	44611565	SO:0001819	synonymous_variant	285349			AK094189	CCDS2716.1	3p21.32	2013-01-08			ENSG00000144792	ENSG00000144792		"Zinc fingers, C2H2-type"	26720	protein-coding gene	gene with protein product							Standard	NM_173658		Approved	FLJ36870	uc003cnl.1	Q6AZW8	OTTHUMG00000133097	ENST00000322734.2:c.876C>T	3.37:g.44636561C>T			44611565	Q7Z331|Q8N9M8	Silent	SNP	ENST00000322734.2	37	CCDS2716.1																																																																																				0.403	ZNF660-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256756.4	NM_173658		T	44636561	C	T	44636561	2	4	61	1	0	0	0	0	0	0	0	1	18109	564	20	3		3	ZNF660	3	44636561	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23729	44636561	153385869	2432	10417										
ZNF197	10168	broad.mit.edu	37	chr3	44673979	44673979	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaggagttggtgatgttCgaggaggtgtcagtatgctt	15	4	2	1	rs377624140		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44673979C>T	ENST00000396058.1	+	4	824	c.657C>T	c.(655-657)ttC>ttT	p.F219F	ZNF197_ENST00000383744.4_Silent_p.F219F|RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383745.2_Silent_p.F219F|ZNF197_ENST00000344387.4_Silent_p.F219F			O14709	ZN197_HUMAN	zinc finger protein 197	219	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F219F(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		TGGTGATGTTCGAGGAGGTGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	3											296	250	266					3																	44673979		2203	4300	6503	44648983	SO:0001819	synonymous_variant	10168			AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.657C>T	3.37:g.44673979C>T			44648983	B2RAH8|Q86VG0	Silent	SNP	ENST00000396058.1	37	CCDS2717.1																																																																																				0.493	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		T	44673979	C	T	44673979	2	4	61	1	0	0	0	0	0	0	0	1	17798	883	31	1		1	ZNF197	3	44673979	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37418	44673979	153348451	2433	10418										
ZNF197	10168	broad.mit.edu	37	chr3	44683651	44683651	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagagaaacaaggccaaaaGtggaaggaattaggagacag	13	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44683651G>T	ENST00000396058.1	+	5	1196	c.1029G>T	c.(1027-1029)aaG>aaT	p.K343N	ZNF197_ENST00000383744.4_Intron|RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000344387.4_Missense_Mutation_p.K343N			O14709	ZN197_HUMAN	zinc finger protein 197	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K343N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		AAGGCCAAAAGTGGAAGGAAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											51	53	52					3																	44683651		2203	4300	6503	44658655	SO:0001583	missense	10168			AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.1029G>T	3.37:g.44683651G>T	ENSP00000379370:p.Lys343Asn		44658655	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	37	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	G	4.763	0.141900	0.09083	.	.	ENSG00000186448	ENST00000344387;ENST00000396058	T;T	0.06768	3.26;3.26	4.27	2.41	0.29592	.	.	.	.	.	T	0.05227	0.0139	N	0.24115	0.695	0.09310	N	1	P	0.36616	0.561	B	0.33042	0.157	T	0.36529	-0.9744	9	0.54805	T	0.06	.	4.5141	0.11926	0.2018:0.186:0.6122:0.0	.	343	O14709	ZN197_HUMAN	N	343	ENSP00000345809:K343N;ENSP00000379370:K343N	ENSP00000345809:K343N	K	+	3	2	ZNF197	44658655	0.000000	0.05858	0.027000	0.17364	0.008000	0.06430	-0.630000	0.05502	0.517000	0.28361	0.455000	0.32223	AAG		0.388	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		T	44683651	G	T	44683651	3	4	61	1	0	0	0	0	1	0	0	0	17798	1020	36	2	1047	2	ZNF197	3	44683651	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9672	44683651	153338779	2434	10419										
ZNF502	91392	broad.mit.edu	37	chr3	44762970	44762970	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtgtgggaaaacatttCgatgtcgatcatttcttact	9	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44762970C>T	ENST00000296091.4	+	4	917	c.661C>T	c.(661-663)Cga>Tga	p.R221*	ZNF502_ENST00000436624.2_Nonsense_Mutation_p.R221*|ZNF502_ENST00000449836.1_Nonsense_Mutation_p.R221*	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R221*(1)		NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		GAAAACATTTCGATGTCGATC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											160	166	164					3																	44762970		2203	4300	6503	44737974	SO:0001587	stop_gained	91392			AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.661C>T	3.37:g.44762970C>T	ENSP00000296091:p.Arg221*		44737974		Nonsense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.540358	0.65085	.	.	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624	.	.	.	4.7	-0.894	0.10563	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-2.004	6.2691	0.20945	0.6231:0.2127:0.0:0.1641	.	.	.	.	X	221	.	ENSP00000296091:R221X	R	+	1	2	ZNF502	44737974	0.000000	0.05858	0.042000	0.18584	0.995000	0.86356	-0.616000	0.05591	0.007000	0.14760	-0.182000	0.12963	CGA		0.398	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		T	44762970	C	T	44762970	4	4	61	1	0	0	0	0	0	1	0	0	17989	876	31	1	667	1	ZNF502	3	44762970	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79319	44762970	153259460	2435	10420										
ZNF501	115560	broad.mit.edu	37	chr3	44776697	44776697	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggcacagttcagcacttCttcgacatcagaggcttcat	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44776697C>A	ENST00000396048.2	+	3	1221	c.784C>A	c.(784-786)Ctt>Att	p.L262I	KIAA1143_ENST00000484437.1_5'Flank	NM_001258280.1|NM_145044.3	NP_001245209.1|NP_659481.2	Q96CX3	ZN501_HUMAN	zinc finger protein 501	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L262I(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00843)|KIRC - Kidney renal clear cell carcinoma(197;0.0463)|Kidney(197;0.0579)		TTCAGCACTTCTTCGACATCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											63	64	64					3																	44776697		1993	4192	6185	44751701	SO:0001583	missense	115560			BC013762	CCDS2720.2	3p21.32	2013-01-08			ENSG00000186446	ENSG00000186446		"Zinc fingers, C2H2-type"	23717	protein-coding gene	gene with protein product			"zinc finger protein 52"	ZNF52		1505991	Standard	NM_145044		Approved	MGC21738	uc003cnu.2	Q96CX3	OTTHUMG00000133048	ENST00000396048.2:c.784C>A	3.37:g.44776697C>A	ENSP00000379363:p.Leu262Ile		44751701	B4DLY7|Q96NU9	Missense_Mutation	SNP	ENST00000396048.2	37	CCDS2720.2	.	.	.	.	.	.	.	.	.	.	C	3.018	-0.202458	0.06219	.	.	ENSG00000186446	ENST00000396048;ENST00000332489	T	0.07567	3.18	3.06	-4.77	0.03219	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	N	0.17564	0.495	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45614	-0.9249	9	0.05351	T	0.99	.	0.2806	0.00244	0.2731:0.244:0.2525:0.2305	.	262	Q96CX3	ZN501_HUMAN	I	262;206	ENSP00000379363:L262I	ENSP00000330388:L206I	L	+	1	0	ZNF501	44751701	0.000000	0.05858	0.000000	0.03702	0.918000	0.54935	-0.432000	0.06956	-0.963000	0.03600	-1.097000	0.02148	CTT		0.393	ZNF501-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256654.4	NM_145044		A	44776697	C	A	44776697	3	1	61	1	0	0	0	0	1	0	0	0	17988	913	32	2	786	2	ZNF501	3	44776697	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13727	44776697	153245733	2436	10421										
KIAA1143	57456	broad.mit.edu	37	chr3	44795812	44795812	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttgaggctgttcatcttCtttgtcactgtgatccccat	7	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44795812C>A	ENST00000296121.4	-	2	216	c.157G>T	c.(157-159)Gaa>Taa	p.E53*	KIAA1143_ENST00000484437.1_5'UTR	NM_020696.3	NP_065747.1	Q96AT1	K1143_HUMAN	KIAA1143	53								p.E53*(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00847)|KIRC - Kidney renal clear cell carcinoma(197;0.0465)|Kidney(197;0.0582)		TGTTCATCTTCTTTGTCACTG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											110	108	108					3																	44795812		2203	4297	6500	44770816	SO:0001587	stop_gained	57456			AB032969	CCDS2721.1	3p21.31	2005-08-15			ENSG00000163807	ENSG00000163807			29198	protein-coding gene	gene with protein product						10574461	Standard	NM_020696		Approved		uc011bac.2	Q96AT1	OTTHUMG00000133088	ENST00000296121.4:c.157G>T	3.37:g.44795812C>A	ENSP00000296121:p.Glu53*		44770816	A8K0I4|Q96HJ8|Q9ULS7	Nonsense_Mutation	SNP	ENST00000296121.4	37	CCDS2721.1	.	.	.	.	.	.	.	.	.	.	C	34	5.363371	0.95877	.	.	ENSG00000163807	ENST00000296121	.	.	.	5.56	5.56	0.83823	.	0.138088	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.6152	19.5644	0.95388	0.0:1.0:0.0:0.0	.	.	.	.	X	53	.	ENSP00000296121:E53X	E	-	1	0	KIAA1143	44770816	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.623000	0.67757	2.617000	0.88574	0.655000	0.94253	GAA		0.418	KIAA1143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256746.1	NM_020696		A	44795812	C	A	44795812	4	1	61	1	0	0	0	0	0	1	0	0	8230	922	32	2	315	2	KIAA1143	3	44795812	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19115	44795812	153226618	2437	10422										
KIF15	56992	broad.mit.edu	37	chr3	44841853	44841853	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgagccagctccaagcTgaagtgaagaggctcaaaga	12	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44841853T>G	ENST00000326047.4	+	11	1295	c.1146T>G	c.(1144-1146)gcT>gcG	p.A382A	KIF15_ENST00000425755.1_Silent_p.A17A	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	382					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.A382A(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AGCTCCAAGCTGAAGTGAAGA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	3											93	87	89					3																	44841853		2203	4300	6503	44816857	SO:0001819	synonymous_variant	56992			AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.1146T>G	3.37:g.44841853T>G			44816857	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	37	CCDS33744.1																																																																																				0.433	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			G	44841853	T	G	44841853	2	3	61	1	0	0	0	0	0	0	0	1	8298	1567	55	4		4	KIF15	3	44841853	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	46041	44841853	153180577	2438	10423										
KIF15	56992	broad.mit.edu	37	chr3	44882662	44882662	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagcctctaagacttctTtggaacaccttgtaacaaag	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44882662T>G	ENST00000326047.4	+	29	3666	c.3517T>G	c.(3517-3519)Ttg>Gtg	p.L1173V	KIF15_ENST00000425755.1_Missense_Mutation_p.L808V	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1173					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.L1173V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TAAGACTTCTTTGGAACACCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											70	75	73					3																	44882662		2203	4300	6503	44857666	SO:0001583	missense	56992			AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3517T>G	3.37:g.44882662T>G	ENSP00000324020:p.Leu1173Val		44857666	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.299072	0.60195	.	.	ENSG00000163808	ENST00000326047;ENST00000396031;ENST00000425755	T;T	0.74526	-0.85;1.27	6.17	2.55	0.30701	.	0.000000	0.41294	D	0.000911	T	0.70211	0.3198	L	0.27053	0.805	0.29918	N	0.822958	D	0.69078	0.997	P	0.56700	0.804	T	0.67696	-0.5604	10	0.66056	D	0.02	.	8.203	0.31436	0.0:0.352:0.0:0.648	.	1173	Q9NS87	KIF15_HUMAN	V	1173;1170;808	ENSP00000324020:L1173V;ENSP00000389982:L808V	ENSP00000324020:L1173V	L	+	1	2	KIF15	44857666	0.547000	0.26465	0.572000	0.28498	0.953000	0.61014	0.246000	0.18160	0.211000	0.20683	0.533000	0.62120	TTG		0.358	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			G	44882662	T	G	44882662	3	3	61	1	0	0	0	0	1	0	0	0	8298	1838	64	4	3631	4	KIF15	3	44882662	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	40809	44882662	153139768	2439	10424										
TGM4	7047	broad.mit.edu	37	chr3	44945382	44945382	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatttgcggcaggaatttCcatgtgtggacggatgcctg	13	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44945382C>A	ENST00000296125.4	+	9	1046	c.978C>A	c.(976-978)ttC>ttA	p.F326L	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	326					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.F326L(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GCAGGAATTTCCATGTGTGGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											88	94	92					3																	44945382		2203	4300	6503	44920386	SO:0001583	missense	7047			BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.978C>A	3.37:g.44945382C>A	ENSP00000296125:p.Phe326Leu		44920386	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962231	0.53400	.	.	ENSG00000163810	ENST00000296125	T	0.52526	0.66	2.04	1.09	0.20402	Transglutaminase-like (2);	0.000000	0.46758	U	0.000269	T	0.66538	0.2799	M	0.88450	2.955	0.45777	D	0.998667	D	0.89917	1.0	D	0.91635	0.999	T	0.67313	-0.5702	10	0.72032	D	0.01	.	5.8513	0.18694	0.0:0.7226:0.0:0.2774	.	326	P49221	TGM4_HUMAN	L	326	ENSP00000296125:F326L	ENSP00000296125:F326L	F	+	3	2	TGM4	44920386	1.000000	0.71417	0.112000	0.21494	0.013000	0.08279	1.184000	0.32053	1.038000	0.40049	0.462000	0.41574	TTC		0.592	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44945382	C	A	44945382	3	1	61	1	0	0	0	0	1	0	0	0	15871	854	30	2	1012	2	TGM4	3	44945382	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62720	44945382	153077048	2440	10425										
TGM4	7047	broad.mit.edu	37	chr3	44948517	44948517	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtctatgacaccagattCgtcttctcagaagtgaatgg	9	8	3	4	rs138265891	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:44948517C>T	ENST00000296125.4	+	10	1220	c.1152C>T	c.(1150-1152)ttC>ttT	p.F384F		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	384					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.F384F(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	ACACCAGATTCGTCTTCTCAG	0.512													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		19946	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						C		4,4402	8.1+/-20.4	0,4,2199	123	110	115		1152	1	0	3	dbSNP_134	115	0,8600		0,0,4300	no	coding-synonymous	TGM4	NM_003241.3		0,4,6499	TT,TC,CC		0.0,0.0908,0.0308		384/685	44948517	4,13002	2203	4300	6503	44923521	SO:0001819	synonymous_variant	7047			BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.1152C>T	3.37:g.44948517C>T			44923521	Q16707|Q96QN4	Silent	SNP	ENST00000296125.4	37	CCDS2723.1																																																																																				0.512	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		T	44948517	C	T	44948517	2	4	61	1	0	0	0	0	0	0	0	1	15871	883	31	1		1	TGM4	3	44948517	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3135	44948517	153073913	2441	10426										
EXOSC7	23016	broad.mit.edu	37	chr3	45030718	45030718	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtccaacactagtgggtcCgccagggtcaagctggtgag	15	10	1	1	rs139012938		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:45030718C>A	ENST00000265564.7	+	2	192	c.144C>A	c.(142-144)tcC>tcA	p.S48S	EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	48					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)	p.S48S(1)		endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		CTAGTGGGTCCGCCAGGGTCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	3											156	128	138					3																	45030718		2203	4300	6503	45005722	SO:0001819	synonymous_variant	23016			BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.144C>A	3.37:g.45030718C>A			45005722	Q96E72	Silent	SNP	ENST00000265564.7	37	CCDS2725.1																																																																																				0.542	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		A	45030718	C	A	45030718	2	1	61	1	0	0	0	0	0	0	0	1	5332	639	23	2		2	EXOSC7	3	45030718	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82201	45030718	152991712	2442	10427										
LARS2	23395	broad.mit.edu	37	chr3	45441742	45441742	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgttctttcctagaaatcGaagccaaaattttacgtgct	7	9	1	1	rs368047098		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:45441742G>A	ENST00000415258.1	+	3	381	c.240G>A	c.(238-240)tcG>tcA	p.S80S	LARS2_ENST00000414984.1_Intron|LARS2_ENST00000265537.3_Silent_p.S80S			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	80					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.S80S(1)		endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	CCTAGAAATCGAAGCCAAAAT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		0,4406		0,0,2203	148	132	137		240	-2.9	1	3		137	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LARS2	NM_015340.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		80/904	45441742	1,13005	2203	4300	6503	45416746	SO:0001819	synonymous_variant	23395			AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	17095	protein-coding gene	gene with protein product	"leucine tRNA ligase 2, mitochondrial"	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.240G>A	3.37:g.45441742G>A			45416746		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																				0.388	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340		A	45441742	G	A	45441742	2	1	61	1	0	0	0	0	0	0	0	1	8657	1045	37	1		1	LARS2	3	45441742	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	411024	45441742	152580688	2443	10428										
SACM1L	22908	broad.mit.edu	37	chr3	45751128	45751128	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaattccaagaaatgagtCtcttggaaagggtaagcttg	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:45751128C>A	ENST00000389061.5	+	5	676	c.472C>A	c.(472-474)Ctc>Atc	p.L158I	SACM1L_ENST00000418611.1_Missense_Mutation_p.L55I|SACM1L_ENST00000541314.1_Missense_Mutation_p.L97I|SACM1L_ENST00000464524.1_3'UTR	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	158	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.L158I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		AGAAATGAGTCTCTTGGAAAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	76	77					3																	45751128		2203	4300	6503	45726132	SO:0001583	missense	22908			AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.472C>A	3.37:g.45751128C>A	ENSP00000373713:p.Leu158Ile		45726132	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.151471	0.78001	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000438671;ENST00000541314	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	6.08	5.2	0.72013	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.68274	0.2983	M	0.74258	2.255	0.47547	D	0.999458	P;P	0.49696	0.872;0.927	P;P	0.54706	0.759;0.759	T	0.70212	-0.4934	10	0.48119	T	0.1	-21.9755	11.0188	0.47705	0.1307:0.8032:0.0:0.0661	.	97;158	B4DK71;Q9NTJ5	.;SAC1_HUMAN	I	55;158;97;97	ENSP00000396387:L55I;ENSP00000373713:L158I;ENSP00000411966:L97I;ENSP00000443373:L97I	ENSP00000373713:L158I	L	+	1	0	SACM1L	45726132	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.763000	0.55257	1.569000	0.49696	0.591000	0.81541	CTC		0.323	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		A	45751128	C	A	45751128	3	1	61	1	0	0	0	0	1	0	0	0	13840	913	32	2	490	2	SACM1L	3	45751128	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	309386	45751128	152271302	2444	10429										
SACM1L	22908	broad.mit.edu	37	chr3	45785122	45785122	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaatggcaaagattttgtCgatgctcccagactggtcca	9	10	0	2	rs376313343		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:45785122C>T	ENST00000389061.5	+	20	1929	c.1725C>T	c.(1723-1725)gtC>gtT	p.V575V	SACM1L_ENST00000418611.1_Silent_p.V472V|SACM1L_ENST00000541314.1_Silent_p.V514V|RN7SL145P_ENST00000469955.2_RNA	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	575					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.V575V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		AAGATTTTGTCGATGCTCCCA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	3						T		0,4406		0,0,2203	134	134	134		1725	-10.9	0.4	3		134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SACM1L	NM_014016.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		575/588	45785122	1,13005	2203	4300	6503	45760126	SO:0001819	synonymous_variant	22908			AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1725C>T	3.37:g.45785122C>T			45760126	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Silent	SNP	ENST00000389061.5	37	CCDS33745.1																																																																																				0.428	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		T	45785122	C	T	45785122	2	4	61	1	0	0	0	0	0	0	0	1	13840	871	31	1		1	SACM1L	3	45785122	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33994	45785122	152237308	2445	10430										
CCR9	10803	broad.mit.edu	37	chr3	45943015	45943015	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaccctgatacaagccaaGaagtcttccaagcacaaagc	6	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:45943015G>T	ENST00000357632.2	+	3	915	c.735G>T	c.(733-735)aaG>aaT	p.K245N	CCR9_ENST00000355983.2_Missense_Mutation_p.K233N|LZTFL1_ENST00000539217.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Missense_Mutation_p.K233N|LZTFL1_ENST00000536047.1_Intron|CCR9_ENST00000422395.1_3'UTR	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	245					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.K245N(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TACAAGCCAAGAAGTCTTCCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	3											215	180	191					3																	45943015		2203	4300	6503	45918019	SO:0001583	missense	10803			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.735G>T	3.37:g.45943015G>T	ENSP00000350256:p.Lys245Asn		45918019	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	37	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.463270	0.63513	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.37584	1.19;1.19;1.19	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.332930	0.30920	N	0.008601	T	0.48874	0.1524	M	0.66439	2.03	0.46185	D	0.998911	P	0.42620	0.785	P	0.55455	0.776	T	0.52283	-0.8596	10	0.72032	D	0.01	.	6.4459	0.21875	0.2285:0.0:0.7715:0.0	.	245	P51686	CCR9_HUMAN	N	245;233;233	ENSP00000350256:K245N;ENSP00000379292:K233N;ENSP00000348260:K233N	ENSP00000348260:K233N	K	+	3	2	CCR9	45918019	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.117000	0.50407	2.289000	0.77006	0.563000	0.77884	AAG		0.483	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			T	45943015	G	T	45943015	3	4	61	1	0	0	0	0	1	0	0	0	2954	933	33	2	741	2	CCR9	3	45943015	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157893	45943015	152079415	2446	10431										
FYCO1	79443	broad.mit.edu	37	chr3	46014657	46014657	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacctcagtcagctcataGagttggcccacaatgtccga	9	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46014657G>T	ENST00000296137.2	-	6	667	c.462C>A	c.(460-462)ctC>ctA	p.L154L	FYCO1_ENST00000535325.1_Silent_p.L154L	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	154	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)	p.L154L(1)		NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TCAGCTCATAGAGTTGGCCCA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	3											110	105	106					3																	46014657		2203	4300	6503	45989661	SO:0001819	synonymous_variant	79443			AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.462C>A	3.37:g.46014657G>T			45989661	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																				0.478	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46014657	G	T	46014657	2	4	61	1	0	0	0	0	0	0	0	1	6144	929	33	2		2	FYCO1	3	46014657	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71642	46014657	152007773	2447	10432										
CCR3	1232	broad.mit.edu	37	chr3	46307077	46307077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgctgtgtttgcccttcGagcccggactgtcacttttg	10	13	1	0	rs56177184	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46307077G>A	ENST00000357422.2	+	4	971	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	CCR3_ENST00000541018.1_Missense_Mutation_p.R143Q|CCR3_ENST00000395940.2_Missense_Mutation_p.R143Q|CCR3_ENST00000395942.2_Missense_Mutation_p.R143Q|CCR3_ENST00000545097.1_Missense_Mutation_p.R164Q			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	143					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.R143Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		TTTGCCCTTCGAGCCCGGACT	0.498													G|||	3	0.000599042	0.0015	0	5008	,	,		19428	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											89	85	87					3																	46307077		2203	4300	6503	46282081	SO:0001583	missense	1232			AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.428G>A	3.37:g.46307077G>A	ENSP00000350003:p.Arg143Gln		46282081	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	37	CCDS2738.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	15.79	2.936696	0.52972	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09	5.86	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.266926	0.25288	N	0.031743	T	0.50343	0.1610	M	0.64080	1.96	0.09310	N	1	P;D	0.56746	0.938;0.977	P;P	0.53593	0.511;0.73	T	0.43861	-0.9365	10	0.66056	D	0.02	.	11.1683	0.48556	0.3112:0.0:0.6888:0.0	rs56177184	164;143	F5GWL6;P51677	.;CCR3_HUMAN	Q	143;164;143;143;143	ENSP00000350003:R143Q;ENSP00000441600:R164Q;ENSP00000440097:R143Q;ENSP00000379271:R143Q;ENSP00000379273:R143Q	ENSP00000350003:R143Q	R	+	2	0	CCR3	46282081	0.000000	0.05858	0.126000	0.21872	0.665000	0.39181	0.257000	0.18369	0.817000	0.34445	-0.140000	0.14226	CGA		0.498	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			A	46307077	G	A	46307077	3	1	61	1	0	0	0	0	1	0	0	0	2948	1058	37	1	497	1	CCR3	3	46307077	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	292420	46307077	151715353	2448	10433										
CCR3	1232	broad.mit.edu	37	chr3	46307366	46307366	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagtacaaggccatccgGctcatttttgtcatcatggc	8	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46307366G>A	ENST00000357422.2	+	4	1260	c.717G>A	c.(715-717)cgG>cgA	p.R239R	CCR3_ENST00000541018.1_Silent_p.R239R|CCR3_ENST00000395940.2_Silent_p.R239R|CCR3_ENST00000395942.2_Silent_p.R239R|CCR3_ENST00000545097.1_Silent_p.R260R			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	239					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.R239R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		AGGCCATCCGGCTCATTTTTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	3											75	74	74					3																	46307366		2203	4300	6503	46282370	SO:0001819	synonymous_variant	1232			AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.717G>A	3.37:g.46307366G>A			46282370	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Silent	SNP	ENST00000357422.2	37	CCDS2738.1																																																																																				0.448	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			A	46307366	G	A	46307366	2	1	61	1	0	0	0	0	0	0	0	1	2948	1190	42	3		3	CCR3	3	46307366	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	289	46307366	151715064	2449	10434										
LRRC2	79442	broad.mit.edu	37	chr3	46574379	46574379	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgaaacccacattgagttCtttcaggttcttcaaacaac	6	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46574379C>A	ENST00000395905.3	-	5	903	c.511G>T	c.(511-513)Gaa>Taa	p.E171*	LRRC2_ENST00000296144.3_Nonsense_Mutation_p.E171*	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	171								p.E171*(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		ACATTGAGTTCTTTCAGGTTC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											93	93	93					3																	46574379		2203	4300	6503	46549383	SO:0001587	stop_gained	79442			AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"leucine-rich repeat-containing 2"			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.511G>T	3.37:g.46574379C>A	ENSP00000379241:p.Glu171*		46549383	B2RDQ7|Q96LT5	Nonsense_Mutation	SNP	ENST00000395905.3	37	CCDS2741.1	.	.	.	.	.	.	.	.	.	.	C	37	6.301894	0.97458	.	.	ENSG00000163827	ENST00000395905;ENST00000296144	.	.	.	5.41	5.41	0.78517	.	0.151910	0.44688	D	0.000438	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	17.0743	0.86582	0.0:1.0:0.0:0.0	.	.	.	.	X	171	.	ENSP00000296144:E171X	E	-	1	0	LRRC2	46549383	1.000000	0.71417	0.997000	0.53966	0.930000	0.56654	6.912000	0.75753	2.707000	0.92482	0.563000	0.77884	GAA		0.348	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2			A	46574379	C	A	46574379	4	1	61	1	0	0	0	0	0	1	0	0	9005	922	32	2	624	2	LRRC2	3	46574379	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	267013	46574379	151448051	2450	10435										
LRRC2	79442	broad.mit.edu	37	chr3	46586715	46586715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcccttcctcctgcattCggccacaaagttccactcct	6	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46586715C>T	ENST00000395905.3	-	3	546	c.154G>A	c.(154-156)Gaa>Aaa	p.E52K	LRRC2_ENST00000496388.1_5'UTR|LRRC2_ENST00000296144.3_Missense_Mutation_p.E52K	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	52								p.E52K(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		CTCCTGCATTCGGCCACAAAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	79	80					3																	46586715		2203	4300	6503	46561719	SO:0001583	missense	79442			AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"leucine-rich repeat-containing 2"			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.154G>A	3.37:g.46586715C>T	ENSP00000379241:p.Glu52Lys		46561719	B2RDQ7|Q96LT5	Missense_Mutation	SNP	ENST00000395905.3	37	CCDS2741.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566515	0.65651	.	.	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.17691	2.26;2.26	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000001	T	0.25568	0.0622	L	0.29908	0.895	0.44302	D	0.997172	D	0.76494	0.999	D	0.73380	0.98	T	0.01136	-1.1440	10	0.02654	T	1	.	16.762	0.85514	0.0:1.0:0.0:0.0	.	52	Q9BYS8	LRRC2_HUMAN	K	52	ENSP00000379241:E52K;ENSP00000296144:E52K	ENSP00000296144:E52K	E	-	1	0	LRRC2	46561719	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.958000	0.63660	2.635000	0.89317	0.655000	0.94253	GAA		0.532	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2			T	46586715	C	T	46586715	3	4	61	1	0	0	0	0	1	0	0	0	9005	893	31	1	989	1	LRRC2	3	46586715	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12336	46586715	151435715	2451	10436										
CCDC12	151903	broad.mit.edu	37	chr3	46963756	46963756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaatggccctctgagtccGcttttttagtttctccagct	9	12	2	1	rs541633096		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:46963756G>A	ENST00000546280.1	-	6	435	c.388C>T	c.(388-390)Cgg>Tgg	p.R130W	CCDC12_ENST00000425441.1_Missense_Mutation_p.R143W|CCDC12_ENST00000605358.1_5'Flank|CCDC12_ENST00000292314.2_Missense_Mutation_p.R143W	NM_144716.3	NP_653317.2	Q8WUD4	CCD12_HUMAN	coiled-coil domain containing 12	130								p.R130W(1)		endometrium(1)|large_intestine(1)|urinary_tract(1)	3		Prostate(884;0.0143)|Ovarian(412;0.0448)|Acute lymphoblastic leukemia(5;0.143)		OV - Ovarian serous cystadenocarcinoma(275;2.2e-56)|BRCA - Breast invasive adenocarcinoma(193;0.00136)|KIRC - Kidney renal clear cell carcinoma(197;0.00703)|Kidney(197;0.00809)		CTCTGAGTCCGCTTTTTTAGT	0.617													G|||	1	0.000199681	0	0	5008	,	,		19756	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											176	164	168					3																	46963756		2203	4300	6503	46938760	SO:0001583	missense	151903			BC020830	CCDS2748.1, CCDS2748.2, CCDS2748.3, CCDS63612.1	3p21.31	2006-10-24			ENSG00000160799	ENSG00000160799			28332	protein-coding gene	gene with protein product						12477932	Standard	NM_001277074		Approved	MGC23918	uc003cqo.3	Q8WUD4	OTTHUMG00000133513	ENST00000546280.1:c.388C>T	3.37:g.46963756G>A	ENSP00000441327:p.Arg130Trp		46938760	Q8N8I4	Missense_Mutation	SNP	ENST00000546280.1	37		.	.	.	.	.	.	.	.	.	.	G	15.55	2.865355	0.51588	.	.	ENSG00000160799	ENST00000425441;ENST00000292314;ENST00000546280	.	.	.	4.91	0.0128	0.14093	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.86740	2.835	0.80722	D	1	D	0.54964	0.969	P	0.48063	0.565	T	0.77264	-0.2652	9	0.87932	D	0	.	13.104	0.59237	0.0:0.0:0.2706:0.7294	.	130	Q8WUD4	CCD12_HUMAN	W	143;143;130	.	ENSP00000292314:R143W	R	-	1	2	CCDC12	46938760	1.000000	0.71417	0.860000	0.33809	0.698000	0.40448	2.106000	0.41835	0.190000	0.20209	-1.431000	0.01090	CGG		0.617	CCDC12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144716		A	46963756	G	A	46963756	3	1	61	1	0	0	0	0	1	0	0	0	2761	1086	38	1	120	1	CCDC12	3	46963756	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	377041	46963756	151058674	2452	10437										
SETD2	29072	broad.mit.edu	37	chr3	47098948	47098948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttattgcggtctttaattCgtactttctttttagaagtt	7	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47098948C>T	ENST00000409792.3	-	15	6368	c.6326G>A	c.(6325-6327)cGa>cAa	p.R2109Q		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2109					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.R1606Q(1)|p.R2109Q(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GTCTTTAATTCGTACTTTCTT	0.398			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Missense(2)	large_intestine(2)	3											46	48	48					3																	47098948		2203	4300	6503	47073952	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6326G>A	3.37:g.47098948C>T	ENSP00000386759:p.Arg2109Gln		47073952	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463361	0.84425	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.22945	1.93	4.84	4.84	0.62591	.	0.000000	0.49916	D	0.000134	T	0.40570	0.1122	L	0.47716	1.5	0.48040	D	0.999572	D;D	0.76494	0.999;0.999	P;P	0.57204	0.815;0.815	T	0.18681	-1.0329	10	0.59425	D	0.04	.	18.4955	0.90864	0.0:1.0:0.0:0.0	.	2109;2109	F2Z317;Q9BYW2	.;SETD2_HUMAN	Q	2109	ENSP00000386759:R2109Q	ENSP00000386759:R2109Q	R	-	2	0	SETD2	47073952	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.179000	0.58290	2.686000	0.91538	0.561000	0.74099	CGA		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47098948	C	T	47098948	3	4	61	1	0	0	0	0	1	0	0	0	14168	884	31	1	1396	1	SETD2	3	47098948	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135192	47098948	150923482	2453	10438										
SETD2	29072	broad.mit.edu	37	chr3	47158131	47158131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accattcaatcatgagaagaCgattaagacaatcttcccca	5	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47158131C>T	ENST00000409792.3	-	4	4610	c.4568G>A	c.(4567-4569)cGt>cAt	p.R1523H		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1523	AWS. {ECO:0000255|PROSITE- ProRule:PRU00562}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.R1523H(1)|p.R1020H(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CATGAGAAGACGATTAAGACA	0.338			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Missense(2)	large_intestine(2)	3											130	130	130					3																	47158131		2203	4300	6503	47133135	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4568G>A	3.37:g.47158131C>T	ENSP00000386759:p.Arg1523His		47133135	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	34	5.324399	0.95708	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.81996	-1.56	5.93	5.93	0.95920	AWS (2);	0.000000	0.56097	D	0.000021	D	0.94791	0.8318	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.95708	0.8755	10	0.87932	D	0	.	20.3495	0.98807	0.0:1.0:0.0:0.0	.	1523;1523	F2Z317;Q9BYW2	.;SETD2_HUMAN	H	1523	ENSP00000386759:R1523H	ENSP00000386759:R1523H	R	-	2	0	SETD2	47133135	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	7.794000	0.85869	2.814000	0.96858	0.591000	0.81541	CGT		0.338	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47158131	C	T	47158131	3	4	61	1	0	0	0	0	1	0	0	0	14168	536	19	1	3198	1	SETD2	3	47158131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59183	47158131	150864299	2454	10439										
SETD2	29072	broad.mit.edu	37	chr3	47161964	47161964	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaagttttttgaaaaatCtttcttttcattcacagcta	3	7	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47161964C>A	ENST00000409792.3	-	3	4204	c.4162G>T	c.(4162-4164)Gat>Tat	p.D1388Y		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1388					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.D885Y(1)|p.D1388Y(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTTGAAAAATCTTTCTTTTCA	0.358			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Missense(2)	large_intestine(2)	3											63	65	64					3																	47161964		2203	4300	6503	47136968	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4162G>T	3.37:g.47161964C>A	ENSP00000386759:p.Asp1388Tyr		47136968	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902203	0.33628	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.89552	-2.53	5.18	5.18	0.71444	.	0.591211	0.15873	N	0.240423	T	0.81370	0.4808	N	0.19112	0.55	0.29097	N	0.881698	P;P	0.48162	0.906;0.906	B;B	0.38500	0.275;0.202	T	0.80037	-0.1550	10	0.87932	D	0	.	14.4781	0.67562	0.0:0.8533:0.1467:0.0	.	1388;1388	F2Z317;Q9BYW2	.;SETD2_HUMAN	Y	1388	ENSP00000386759:D1388Y	ENSP00000386759:D1388Y	D	-	1	0	SETD2	47136968	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.959000	0.49153	2.690000	0.91761	0.563000	0.77884	GAT		0.358	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47161964	C	A	47161964	3	1	61	1	0	0	0	0	1	0	0	0	14168	913	32	2	3608	2	SETD2	3	47161964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3833	47161964	150860466	2455	10440										
SETD2	29072	broad.mit.edu	37	chr3	47164577	47164577	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgaagtccttttagattCtctttctagttttgaagaat	6	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47164577C>A	ENST00000409792.3	-	3	1591	c.1549G>T	c.(1549-1551)Gaa>Taa	p.E517*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	517					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.E517*(1)|p.E14*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTTTAGATTCTCTTTCTAGT	0.383			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(2)	large_intestine(2)	3											70	66	67					3																	47164577		2153	4187	6340	47139581	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1549G>T	3.37:g.47164577C>A	ENSP00000386759:p.Glu517*		47139581	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	36	5.630334	0.96671	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	.	.	.	5.09	5.09	0.68999	.	0.201588	0.34725	N	0.003726	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.052	0.93050	0.0:1.0:0.0:0.0	.	.	.	.	X	517;517;517;473	.	ENSP00000386759:E517X	E	-	1	0	SETD2	47139581	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.242000	0.51384	2.801000	0.96364	0.650000	0.86243	GAA		0.383	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47164577	C	A	47164577	4	1	61	1	0	0	0	0	0	1	0	0	14168	922	32	2	6221	2	SETD2	3	47164577	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2613	47164577	150857853	2456	10441										
KIF9	64147	broad.mit.edu	37	chr3	47278101	47278101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcatcagccccttgttttCgtacttgcctgcaaggtgat	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47278101C>T	ENST00000265529.3	-	19	2613	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K	KIF9_ENST00000444589.2_Missense_Mutation_p.E580K|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000452770.2_Missense_Mutation_p.E645K|KIF9_ENST00000335044.2_Missense_Mutation_p.E645K|KIF9_ENST00000352910.4_Missense_Mutation_p.E487K|KIF9_ENST00000487440.1_5'Flank			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	645					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)	p.E645K(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CCCTTGTTTTCGTACTTGCCT	0.527																																					Colon(44;962 1147 15977 24541)											1	Substitution - Missense(1)	large_intestine(1)	3											107	90	95					3																	47278101		2203	4300	6503	47253105	SO:0001583	missense	64147			AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"Kinesins"	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1933G>A	3.37:g.47278101C>T	ENSP00000265529:p.Glu645Lys		47253105	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	.	.	.	.	.	.	.	.	.	.	C	4.433	0.080206	0.08533	.	.	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.67	4.79	0.61399	.	0.457832	0.25192	N	0.032455	T	0.32255	0.0823	L	0.36672	1.1	0.23848	N	0.996677	D;P	0.54964	0.969;0.469	B;B	0.42138	0.377;0.053	T	0.15464	-1.0436	10	0.07482	T	0.82	.	8.6646	0.34112	0.0:0.828:0.0:0.172	.	580;645	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	K	645;645;580;645;487	ENSP00000333942:E645K;ENSP00000265529:E645K;ENSP00000414987:E580K;ENSP00000391100:E645K;ENSP00000292334:E487K	ENSP00000265529:E645K	E	-	1	0	KIF9	47253105	0.627000	0.27129	0.803000	0.32268	0.154000	0.21943	0.986000	0.29590	1.398000	0.46701	0.561000	0.74099	GAA		0.527	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2			T	47278101	C	T	47278101	3	4	61	1	0	0	0	0	1	0	0	0	8331	893	31	1	455	1	KIF9	3	47278101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113524	47278101	150744329	2457	10442										
KLHL18	23276	broad.mit.edu	37	chr3	47364191	47364191	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcctgctgcacattccttCgagaacggtgaggtgatgtg	13	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47364191C>T	ENST00000232766.5	+	3	414	c.394C>T	c.(394-396)Cga>Tga	p.R132*	KLHL18_ENST00000455924.2_Nonsense_Mutation_p.R20*	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	132								p.R132*(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		CACATTCCTTCGAGAACGGTG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											71	63	66					3																	47364191		2203	4300	6503	47339195	SO:0001587	stop_gained	23276			AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"Kelch-like", "BTB/POZ domain containing"	29120	protein-coding gene	gene with protein product			"kelch-like 18 (Drosophila)"			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.394C>T	3.37:g.47364191C>T	ENSP00000232766:p.Arg132*		47339195	A8K612|Q7Z3E8|Q8N125	Nonsense_Mutation	SNP	ENST00000232766.5	37	CCDS33749.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910488	0.52439	.	.	ENSG00000114648	ENST00000232766;ENST00000437353;ENST00000455924	.	.	.	5.29	3.33	0.38152	.	0.212152	0.41712	D	0.000839	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	11.3802	0.49752	0.512:0.488:0.0:0.0	.	.	.	.	X	132;132;20	.	ENSP00000232766:R132X	R	+	1	2	KLHL18	47339195	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	3.262000	0.51538	1.447000	0.47661	0.655000	0.94253	CGA		0.512	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		T	47364191	C	T	47364191	4	4	61	1	0	0	0	0	0	1	0	0	8394	876	31	1	404	1	KLHL18	3	47364191	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86090	47364191	150658239	2458	10443										
SCAP	22937	broad.mit.edu	37	chr3	47462478	47462478	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaacagcatctgaaggaaGaagtcagacaccagccccac	8	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47462478G>T	ENST00000265565.5	-	11	1699	c.1287C>A	c.(1285-1287)ttC>ttA	p.F429L	SCAP_ENST00000441517.2_Missense_Mutation_p.F174L|SCAP_ENST00000545718.1_Missense_Mutation_p.F37L|SCAP_ENST00000465628.1_5'UTR	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	429	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)	p.F429L(1)		endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TCTGAAGGAAGAAGTCAGACA	0.592											OREG0015548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(149;978 1908 29304 37806 46700)											1	Substitution - Missense(1)	large_intestine(1)	3											138	128	132					3																	47462478		2203	4300	6503	47437482	SO:0001583	missense	22937			BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1287C>A	3.37:g.47462478G>T	ENSP00000265565:p.Phe429Leu	947	47437482	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	G	27.6	4.846987	0.91277	.	.	ENSG00000114650	ENST00000339815;ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718;ENST00000383739	D;D;D	0.98493	-4.96;-4.96;-4.96	5.25	4.38	0.52667	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	M	0.88906	2.99	0.58432	D	0.999994	D;D	0.76494	0.999;0.999	D;D	0.80764	0.991;0.994	D	0.99647	1.0990	10	0.87932	D	0	-37.6014	13.6505	0.62308	0.0749:0.0:0.9251:0.0	.	174;429	F8W921;Q12770	.;SCAP_HUMAN	L	429;56;429;174;37;122	ENSP00000265565:F429L;ENSP00000416847:F174L;ENSP00000438956:F37L	ENSP00000265565:F429L	F	-	3	2	SCAP	47437482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.053000	0.64269	1.465000	0.48006	0.561000	0.74099	TTC		0.592	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		T	47462478	G	T	47462478	3	4	61	1	0	0	0	0	1	0	0	0	13914	933	33	2	2604	2	SCAP	3	47462478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98287	47462478	150559952	2459	10444										
DHX30	22907	broad.mit.edu	37	chr3	47868873	47868873	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagagttcccacagcccaAaaatcttctcaacagtgtga	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47868873A>C	ENST00000445061.1	+	5	568	c.161A>C	c.(160-162)aAa>aCa	p.K54T	DHX30_ENST00000446256.2_Missense_Mutation_p.K15T|DHX30_ENST00000457607.1_Missense_Mutation_p.K82T|DHX30_ENST00000348968.4_Missense_Mutation_p.K26T	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	54	DRBM.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.K54T(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CCACAGCCCAAAAATCTTCTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											82	81	82					3																	47868873		2203	4300	6503	47843877	SO:0001583	missense	22907			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.161A>C	3.37:g.47868873A>C	ENSP00000405620:p.Lys54Thr		47843877	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	37	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314412	0.81358	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.07444	3.27;3.23;3.26;3.19	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	L	0.59436	1.845	0.53688	D	0.999979	P;D;D	0.55172	0.95;0.97;0.97	D;D;D	0.76575	0.972;0.988;0.988	T	0.00376	-1.1779	10	0.87932	D	0	.	13.2371	0.59974	1.0:0.0:0.0:0.0	.	54;15;82	Q7L2E3;Q7L2E3-3;Q7L2E3-2	DHX30_HUMAN;.;.	T	15;54;26;82	ENSP00000392601:K15T;ENSP00000405620:K54T;ENSP00000343442:K26T;ENSP00000394682:K82T	ENSP00000343442:K26T	K	+	2	0	DHX30	47843877	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.497000	0.66924	2.058000	0.61347	0.533000	0.62120	AAA		0.398	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		C	47868873	A	C	47868873	3	2	61	1	0	0	0	0	1	0	0	0	4515	14	1	4	182	4	DHX30	3	47868873	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	406395	47868873	150153557	2460	10445										
DHX30	22907	broad.mit.edu	37	chr3	47891174	47891174	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttcatggcagtcaagtcCaatggcagcgtcttcgtccg	10	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47891174C>A	ENST00000445061.1	+	21	3653	c.3246C>A	c.(3244-3246)tcC>tcA	p.S1082S	DHX30_ENST00000446256.2_Silent_p.S1043S|DHX30_ENST00000457607.1_Silent_p.S1110S|DHX30_ENST00000348968.4_Silent_p.S1054S|MIR1226_ENST00000408658.1_RNA	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	1082						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.S1082S(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CAGTCAAGTCCAATGGCAGCG	0.627											OREG0015550	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	3											91	82	85					3																	47891174		2203	4300	6503	47866178	SO:0001819	synonymous_variant	22907			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.3246C>A	3.37:g.47891174C>A		950	47866178	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Silent	SNP	ENST00000445061.1	37	CCDS2759.1																																																																																				0.627	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		A	47891174	C	A	47891174	2	1	61	1	0	0	0	0	0	0	0	1	4515	581	21	2		2	DHX30	3	47891174	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22301	47891174	150131256	2461	10446										
MAP4	4134	broad.mit.edu	37	chr3	47956314	47956314	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcctaacttacctgaggtCtctgaagaaagctcagaagg	9	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:47956314C>A	ENST00000360240.6	-	8	2510	c.1992G>T	c.(1990-1992)gaG>gaT	p.E664D	MAP4_ENST00000426837.2_Missense_Mutation_p.E681D|MAP4_ENST00000395734.3_Missense_Mutation_p.E664D|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	664					cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.E664D(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TACCTGAGGTCTCTGAAGAAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											158	163	162					3																	47956314		2203	4300	6503	47931318	SO:0001583	missense	4134				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1992G>T	3.37:g.47956314C>A	ENSP00000353375:p.Glu664Asp		47931318	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.126683	0.56721	.	.	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.08896	3.11;3.04;3.11	3.93	3.93	0.45458	.	.	.	.	.	T	0.15176	0.0366	M	0.68317	2.08	0.80722	D	1	D;D;D	0.59357	0.985;0.981;0.985	P;P;P	0.51170	0.661;0.581;0.526	T	0.08146	-1.0736	9	0.18710	T	0.47	-0.0532	12.1566	0.54081	0.0:1.0:0.0:0.0	.	641;664;664	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	D	664;681;664	ENSP00000379083:E664D;ENSP00000407602:E681D;ENSP00000353375:E664D	ENSP00000353375:E664D	E	-	3	2	MAP4	47931318	0.963000	0.33076	0.997000	0.53966	0.996000	0.88848	2.966000	0.49208	2.112000	0.64535	0.563000	0.77884	GAG		0.443	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		A	47956314	C	A	47956314	3	1	61	1	0	0	0	0	1	0	0	0	9288	912	32	2	2873	2	MAP4	3	47956314	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65140	47956314	150066116	2462	10447										
NME6	10201	broad.mit.edu	37	chr3	48338301	48338301	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcaggaacttgttgcttaGaatctgctgatgaacagcct	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48338301G>T	ENST00000452211.1	-	4	346	c.109C>A	c.(109-111)Cta>Ata	p.L37I	NME6_ENST00000444069.1_Intron|NME6_ENST00000447314.1_5'UTR|NME6_ENST00000415053.1_Missense_Mutation_p.L37I|NME6_ENST00000426723.1_Missense_Mutation_p.L37I|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000451657.1_Missense_Mutation_p.L37I|NME6_ENST00000442597.1_Missense_Mutation_p.L37I|NME6_ENST00000426689.2_Missense_Mutation_p.L37I|NME6_ENST00000435684.1_Missense_Mutation_p.L37I|NME6_ENST00000421967.1_Missense_Mutation_p.L45I|NME6_ENST00000450160.1_Missense_Mutation_p.L37I|NME6_ENST00000415644.1_Missense_Mutation_p.L37I			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	37					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.L45I(1)		breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TTGTTGCTTAGAATCTGCTGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	123	128					3																	48338301		2203	4300	6503	48313305	SO:0001583	missense	10201			AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.109C>A	3.37:g.48338301G>T	ENSP00000392352:p.Leu37Ile		48313305	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Missense_Mutation	SNP	ENST00000452211.1	37		.	.	.	.	.	.	.	.	.	.	G	18.91	3.724158	0.68959	.	.	ENSG00000172113	ENST00000421967;ENST00000426689;ENST00000452211;ENST00000426723;ENST00000450160;ENST00000415644;ENST00000415053;ENST00000442597;ENST00000451657;ENST00000435684;ENST00000425930;ENST00000456495;ENST00000447724	T;T;T;T;T;T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	4.47	3.6	0.41247	.	0.073957	0.56097	D	0.000033	T	0.51160	0.1658	L	0.41632	1.29	0.35868	D	0.828026	D;P;P;B	0.61697	0.99;0.942;0.465;0.051	P;P;B;B	0.56960	0.81;0.714;0.384;0.098	T	0.55579	-0.8119	10	0.22109	T	0.4	-3.1981	7.0653	0.25149	0.2005:0.0:0.7995:0.0	.	37;37;37;37	O75414-2;O75414-3;O75414;C9J9V6	.;.;NDK6_HUMAN;.	I	45;37;37;37;37;37;37;37;37;37;37;37;44	ENSP00000416658:L45I;ENSP00000440286:L37I;ENSP00000392352:L37I;ENSP00000391499:L37I;ENSP00000398070:L37I;ENSP00000394232:L37I;ENSP00000399582:L37I;ENSP00000406642:L37I;ENSP00000407933:L37I;ENSP00000393261:L37I;ENSP00000411116:L37I;ENSP00000392715:L37I;ENSP00000405755:L44I	ENSP00000399582:L37I	L	-	1	2	NME6	48313305	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	4.577000	0.60922	1.264000	0.44198	0.650000	0.86243	CTA		0.423	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793		T	48338301	G	T	48338301	3	4	61	1	0	0	0	0	1	0	0	0	10526	933	33	2	467	2	NME6	3	48338301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	381987	48338301	149684129	2463	10448										
FBXW12	285231	broad.mit.edu	37	chr3	48414804	48414804	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctctcccatagcattggAataggattgcagacagtgat	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48414804A>G	ENST00000296438.5	+	3	283	c.97A>G	c.(97-99)Aat>Gat	p.N33D	FBXW12_ENST00000436231.1_Intron|FBXW12_ENST00000415155.1_Missense_Mutation_p.N33D|FBXW12_ENST00000445170.1_Missense_Mutation_p.N14D	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	33	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.							p.N33D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATAGCATTGGAATAGGATTGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											209	204	206					3																	48414804		2203	4300	6503	48389808	SO:0001583	missense	285231			AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"F-boxes / WD-40 domains", "WD repeat domain containing"	20729	protein-coding gene	gene with protein product		609075	"F-box only protein 35", "F-box and WD-40 domain protein 12"	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.97A>G	3.37:g.48414804A>G	ENSP00000296438:p.Asn33Asp		48389808	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.840172	0.51057	.	.	ENSG00000164049	ENST00000296438;ENST00000445170;ENST00000415155	T;T;T	0.45276	0.9;1.78;0.9	2.82	-1.14	0.09741	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.692440	0.13613	N	0.374982	T	0.55417	0.1919	H	0.94542	3.55	0.09310	N	1	P;P;P	0.52170	0.939;0.951;0.951	P;P;P	0.49502	0.479;0.613;0.613	T	0.51387	-0.8712	10	0.59425	D	0.04	-1.7481	4.3506	0.11153	0.3733:0.4875:0.1393:0.0	.	14;33;33	E9PG36;Q494Z0;Q6X9E4	.;.;FBW12_HUMAN	D	33;14;33	ENSP00000296438:N33D;ENSP00000406139:N14D;ENSP00000414683:N33D	ENSP00000296438:N33D	N	+	1	0	FBXW12	48389808	0.373000	0.25073	0.062000	0.19696	0.274000	0.26718	0.274000	0.18680	-0.219000	0.10003	0.377000	0.23210	AAT		0.512	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102		G	48414804	A	G	48414804	3	3	61	1	0	0	0	0	1	0	0	0	5784	246	9	4	140	4	FBXW12	3	48414804	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	76503	48414804	149607626	2464	10449										
PLXNB1	5364	broad.mit.edu	37	chr3	48453928	48453928	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtgcggaggatgtcagtGaaatactcaagcttcccatg	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48453928G>A	ENST00000358536.4	-	26	5225	c.4956C>T	c.(4954-4956)ttC>ttT	p.F1652F	PLXNB1_ENST00000456774.1_Silent_p.F1469F|PLXNB1_ENST00000358459.4_Silent_p.F1469F|PLXNB1_ENST00000296440.6_Silent_p.F1652F|PLXNB1_ENST00000448774.2_Silent_p.F263F|PLXNB1_ENST00000465117.1_5'Flank	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1652					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.F1652F(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGATGTCAGTGAAATACTCAA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	3											73	69	70					3																	48453928		2203	4300	6503	48428932	SO:0001819	synonymous_variant	5364			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.4956C>T	3.37:g.48453928G>A			48428932	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	37	CCDS2765.1																																																																																				0.592	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48453928	G	A	48453928	2	1	61	1	0	0	0	0	0	0	0	1	12154	1281	45	3		3	PLXNB1	3	48453928	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39124	48453928	149568502	2465	10450										
COL7A1	1294	broad.mit.edu	37	chr3	48602258	48602258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggggtgggcagcggcgctCgcaggcctcacgggtcccaa	17	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48602258C>T	ENST00000328333.8	-	117	8883	c.8776G>A	c.(8776-8778)Gag>Aag	p.E2926K	UCN2_ENST00000273610.3_5'Flank|COL7A1_ENST00000470076.1_5'UTR|COL7A1_ENST00000454817.1_Missense_Mutation_p.E2894K	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2926	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.|Nonhelical region (NC2).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E2926K(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGCGGCGCTCGCAGGCCTCA	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	3											37	36	36					3																	48602258		2203	4300	6503	48577262	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.8776G>A	3.37:g.48602258C>T	ENSP00000332371:p.Glu2926Lys		48577262	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.221466	0.39300	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.60299	0.2;0.2	5.62	4.75	0.60458	Proteinase inhibitor I2, Kunitz metazoa (5);	0.160789	0.28230	N	0.016101	T	0.51958	0.1705	L	0.53561	1.675	0.40681	D	0.982302	B	0.31859	0.343	B	0.27076	0.076	T	0.56426	-0.7981	10	0.62326	D	0.03	.	13.203	0.59780	0.0:0.9223:0.0:0.0777	.	2926	Q02388	CO7A1_HUMAN	K	2926;2894	ENSP00000332371:E2926K;ENSP00000412569:E2894K	ENSP00000332371:E2926K	E	-	1	0	COL7A1	48577262	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	1.838000	0.39211	1.373000	0.46208	0.563000	0.77884	GAG		0.657	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48602258	C	T	48602258	3	4	61	1	0	0	0	0	1	0	0	0	3710	893	31	1	66	1	COL7A1	3	48602258	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	148330	48602258	149420172	2466	10451										
COL7A1	1294	broad.mit.edu	37	chr3	48619919	48619919	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgaggacccaccttctctcCttggcggccagtgggtcctg	12	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48619919C>A	ENST00000328333.8	-	45	4698	c.4591G>T	c.(4591-4593)Gga>Tga	p.G1531*	COL7A1_ENST00000454817.1_Nonsense_Mutation_p.G1531*	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1531	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G1531*(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCTTCTCTCCTTGGCGGCCA	0.602																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											97	102	101					3																	48619919		2203	4300	6503	48594923	SO:0001587	stop_gained	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.4591G>T	3.37:g.48619919C>A	ENSP00000332371:p.Gly1531*		48594923	Q14054|Q16507	Nonsense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	45	11.818278	0.99606	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	.	.	.	5.95	5.95	0.96441	.	0.000000	0.44285	D	0.000469	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.5348	0.87827	0.0:1.0:0.0:0.0	.	.	.	.	X	1531	.	ENSP00000332371:G1531X	G	-	1	0	COL7A1	48594923	0.999000	0.42202	1.000000	0.80357	0.774000	0.43823	5.376000	0.66178	2.826000	0.97356	0.563000	0.77884	GGA		0.602	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48619919	C	A	48619919	4	1	61	1	0	0	0	0	0	1	0	0	3710	690	24	2	4539	2	COL7A1	3	48619919	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17661	48619919	149402511	2467	10452										
COL7A1	1294	broad.mit.edu	37	chr3	48630046	48630046	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccccgatgctgttggcGtagagggcaatcacagtcac	12	13	2	1	rs121912830	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48630046G>A	ENST00000328333.8	-	7	1040	c.933C>T	c.(931-933)taC>taT	p.Y311Y	COL7A1_ENST00000454817.1_Silent_p.Y311Y	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	311	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y311Y(2)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGCTGTTGGCGTAGAGGGCAA	0.637													G|||	3	0.000599042	0.0015	0	5008	,	,		17644	0.001		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	3	GRCh37	CM950316	COL7A1	M	rs121912830	G		3,4403	8.1+/-20.4	0,3,2200	66	66	66	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	933	0.8	1	3	dbSNP_133	66	0,8600		0,0,4300	no	coding-synonymous	COL7A1	NM_000094.3		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		311/2945	48630046	3,13003	2203	4300	6503	48605050	SO:0001819	synonymous_variant	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.933C>T	3.37:g.48630046G>A			48605050	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																				0.637	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48630046	G	A	48630046	2	1	61	1	0	0	0	0	0	0	0	1	3710	1140	40	1		1	COL7A1	3	48630046	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10127	48630046	149392384	2468	10453										
COL7A1	1294	broad.mit.edu	37	chr3	48631006	48631006	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggccagctggggcaggaaGacatggtcagccacatggag	17	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48631006G>T	ENST00000328333.8	-	3	497	c.390C>A	c.(388-390)gtC>gtA	p.V130V	COL7A1_ENST00000454817.1_Silent_p.V130V	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	130	Nonhelical region (NC1).|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V130V(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGGGCAGGAAGACATGGTCAG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											102	92	95					3																	48631006		2203	4300	6503	48606010	SO:0001819	synonymous_variant	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.390C>A	3.37:g.48631006G>T			48606010	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																				0.602	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48631006	G	T	48631006	2	4	61	1	0	0	0	0	0	0	0	1	3710	929	33	2		2	COL7A1	3	48631006	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	960	48631006	149391424	2469	10454										
SLC25A20	788	broad.mit.edu	37	chr3	48929428	48929428	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacctctctaaaaagagtCttccggaaacagtcaaaggt	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:48929428C>A	ENST00000319017.4	-	2	381	c.183G>T	c.(181-183)aaG>aaT	p.K61N	SLC25A20_ENST00000544097.1_Missense_Mutation_p.K11N|SLC25A20_ENST00000430379.1_Missense_Mutation_p.K61N	NM_000387.5	NP_000378.1	O43772	MCAT_HUMAN	solute carrier family 25 (carnitine/acylcarnitine translocase), member 20	61					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.K61N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000168)|Kidney(197;0.00231)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	L-Carnitine(DB00583)	TAAAAAGAGTCTTCCGGAAAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											127	123	124					3																	48929428		2203	4300	6503	48904432	SO:0001583	missense	788			Y10319	CCDS2779.1	3p21.31	2013-05-22			ENSG00000178537	ENSG00000178537		"Solute carriers"	1421	protein-coding gene	gene with protein product	"carnitine-acylcarnitine carrier", "carnitine/acylcarnitine translocase"	613698		CACT		9399886, 9533014	Standard	NM_000387		Approved	CAC	uc003cva.4	O43772	OTTHUMG00000133538	ENST00000319017.4:c.183G>T	3.37:g.48929428C>A	ENSP00000326305:p.Lys61Asn		48904432	B2R7F4|Q9UIQ2	Missense_Mutation	SNP	ENST00000319017.4	37	CCDS2779.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.994748	0.74703	.	.	ENSG00000178537	ENST00000430379;ENST00000319017;ENST00000544097	T;T;T	0.80566	-1.39;-1.39;-1.39	5.16	5.16	0.70880	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.88757	0.6523	M	0.74546	2.27	0.80722	D	1	B;D	0.60575	0.376;0.988	B;D	0.65010	0.426;0.931	D	0.89266	0.3601	10	0.59425	D	0.04	-22.3046	17.5738	0.87942	0.0:1.0:0.0:0.0	.	61;61	C9JPE1;O43772	.;MCAT_HUMAN	N	61;61;11	ENSP00000388986:K61N;ENSP00000326305:K61N;ENSP00000438731:K11N	ENSP00000326305:K61N	K	-	3	2	SLC25A20	48904432	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.072000	0.50049	2.696000	0.92011	0.555000	0.69702	AAG		0.478	SLC25A20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257516.2	NM_000387		A	48929428	C	A	48929428	3	1	61	1	0	0	0	0	1	0	0	0	14520	912	32	2	754	2	SLC25A20	3	48929428	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298422	48929428	149093002	2470	10455										
ARIH2	10425	broad.mit.edu	37	chr3	49008127	49008127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagtgcaatcggtgcaacGaggtcttctggtaagagtga	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49008127G>A	ENST00000356401.4	+	8	1099	c.760G>A	c.(760-762)Gag>Aag	p.E254K	ARIH2_ENST00000490095.1_3'UTR|ARIH2_ENST00000449376.1_Missense_Mutation_p.E254K	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	254					developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E254K(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		TCGGTGCAACGAGGTCTTCTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	81	82					3																	49008127		2203	4300	6503	48983131	SO:0001583	missense	10425			AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"all-trans retinoic acid inducible RING finger"	605615	"ariadne (Drosophila) homolog 2", "ariadne homolog 2 (Drosophila)"			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.760G>A	3.37:g.49008127G>A	ENSP00000348769:p.Glu254Lys		48983131	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	37	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928520	0.92389	.	.	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	T;T	0.80393	-1.37;-1.37	5.42	5.42	0.78866	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	T	0.81470	0.4829	N	0.25890	0.77	0.80722	D	1	D;D;D	0.67145	0.991;0.996;0.978	P;P;P	0.57468	0.689;0.821;0.585	T	0.79754	-0.1670	10	0.30854	T	0.27	.	19.206	0.93730	0.0:0.0:1.0:0.0	.	261;254;254	B3KMG5;Q53ET9;O95376	.;.;ARI2_HUMAN	K	254;254;253;78	ENSP00000348769:E254K;ENSP00000403222:E254K	ENSP00000348769:E254K	E	+	1	0	ARIH2	48983131	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.425000	0.97467	2.534000	0.85438	0.561000	0.74099	GAG		0.587	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		A	49008127	G	A	49008127	3	1	61	1	0	0	0	0	1	0	0	0	924	1059	37	1	782	1	ARIH2	3	49008127	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78699	49008127	149014303	2471	10456										
IMPDH2	54870	broad.mit.edu	37	chr3	49064469	49064469	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaccaccaagtcttccctCtttgtcattatctacgtggg	7	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49064469C>A	ENST00000395443.2	-	0	3549				RP13-131K19.6_ENST00000607245.1_RNA|IMPDH2_ENST00000326739.4_Missense_Mutation_p.K181N	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1							nucleus (GO:0005634)		p.K181N(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		AGTCTTCCCTCTTTGTCATTA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											173	159	164					3																	49064469		2203	4300	6503	49039473	SO:0001628	intergenic_variant	3615				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772		3.37:g.49064469C>A			49039473	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	37	CCDS2787.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.05|14.05	2.420143|2.420143	0.42918|0.42918	.|.	.|.	ENSG00000178035|ENSG00000178035	ENST00000429182|ENST00000537036;ENST00000326739;ENST00000442157	.|D;D	.|0.94138	.|-3.36;-3.36	6.08|6.08	4.24|4.24	0.50183|0.50183	.|Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (2);IMP dehydrogenase/GMP reductase (1);	.|0.130377	.|0.64402	.|D	.|0.000001	.|D	.|0.93485	.|0.7921	M|M	0.79258|0.79258	2.445|2.445	0.53005|0.53005	D|D	0.999961|0.999961	.|B	.|0.23490	.|0.086	.|B	.|0.34779	.|0.189	.|D	.|0.92589	.|0.6081	.|10	.|0.62326	.|D	.|0.03	-22.1256|-22.1256	12.5042|12.5042	0.55972|0.55972	0.0:0.8189:0.1173:0.0638|0.0:0.8189:0.1173:0.0638	.|.	.|181	.|P12268	.|IMDH2_HUMAN	X|N	113|181;181;156	.|ENSP00000321584:K181N;ENSP00000403502:K156N	.|ENSP00000321584:K181N	E|K	-|-	1|3	0|2	IMPDH2|IMPDH2	49039473|49039473	0.959000|0.959000	0.32827|0.32827	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	1.523000|1.523000	0.35932|0.35932	1.586000|1.586000	0.49944|0.49944	0.655000|0.655000	0.94253|0.94253	GAG|AAG		0.498	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49064469	C	A	49064469	1	1	61	0	1	0	0	0	0	0	0	0	7748	912	32	2		2	IMPDH2	3	49064469	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56342	49064469	148957961	2472	10457										
IMPDH2	54870	broad.mit.edu	37	chr3	49065908	49065908	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtgactgtgtccatggGagaggaaaccagtggggtct	15	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49065908G>A	ENST00000395443.2	-	0	3549				RP13-131K19.6_ENST00000607245.1_RNA|IMPDH2_ENST00000326739.4_Missense_Mutation_p.P69S	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1							nucleus (GO:0005634)		p.P69S(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GTGTCCATGGGAGAGGAAACC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	3											70	70	70					3																	49065908		2203	4300	6503	49040912	SO:0001628	intergenic_variant	3615				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772		3.37:g.49065908G>A			49040912	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	37	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	G	36	5.751669	0.96890	.	.	ENSG00000178035	ENST00000537036;ENST00000326739;ENST00000442157	T;T	0.79454	-1.27;-1.2	5.82	5.82	0.92795	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.000000	0.85682	D	0.000000	D	0.89199	0.6647	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88444	0.3044	9	.	.	.	-22.4282	20.1054	0.97890	0.0:0.0:1.0:0.0	.	69	P12268	IMDH2_HUMAN	S	69	ENSP00000321584:P69S;ENSP00000403502:P69S	.	P	-	1	0	IMPDH2	49040912	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	9.712000	0.98738	2.757000	0.94681	0.655000	0.94253	CCC		0.552	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49065908	G	A	49065908	1	1	61	0	1	0	0	0	0	0	0	0	7748	1174	41	3		3	IMPDH2	3	49065908	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1439	49065908	148956522	2473	10458										
QRICH1	54870	broad.mit.edu	37	chr3	49081895	49081895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgaaccgaacataataaaGatcggagaaaatgtcatcta	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49081895G>T	ENST00000395443.2	-	6	2186	c.1714C>A	c.(1714-1716)Ctt>Att	p.L572I	QRICH1_ENST00000357496.2_Missense_Mutation_p.L572I|QRICH1_ENST00000479449.1_5'UTR|QRICH1_ENST00000424300.1_Missense_Mutation_p.L572I	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	572						nucleus (GO:0005634)		p.L572I(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		ACATAATAAAGATCGGAGAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											119	121	120					3																	49081895		2203	4300	6503	49056899	SO:0001583	missense	54870				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1714C>A	3.37:g.49081895G>T	ENSP00000378830:p.Leu572Ile		49056899	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	37	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287387	0.59976	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	5.8	5.8	0.92144	.	0.167279	0.53938	D	0.000048	T	0.39733	0.1089	L	0.27053	0.805	0.38670	D	0.952286	P	0.49783	0.928	B	0.39465	0.3	T	0.39663	-0.9603	9	0.37606	T	0.19	-2.5398	14.8412	0.70226	0.0:0.0:0.8562:0.1438	.	572	Q2TAL8	QRIC1_HUMAN	I	572	.	ENSP00000350094:L572I	L	-	1	0	QRICH1	49056899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.203000	0.77864	2.745000	0.94114	0.491000	0.48974	CTT		0.408	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		T	49081895	G	T	49081895	3	4	61	1	0	0	0	0	1	0	0	0	12916	942	33	2	636	2	QRICH1	3	49081895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15987	49081895	148940535	2474	10459										
QRICH1	54870	broad.mit.edu	37	chr3	49084551	49084551	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttctctagttcagcattCttggtctgggcccagttttt	8	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49084551C>A	ENST00000395443.2	-	4	1939	c.1467G>T	c.(1465-1467)aaG>aaT	p.K489N	QRICH1_ENST00000357496.2_Missense_Mutation_p.K489N|QRICH1_ENST00000479449.1_5'UTR|QRICH1_ENST00000424300.1_Missense_Mutation_p.K489N	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	489						nucleus (GO:0005634)		p.K489N(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GTTCAGCATTCTTGGTCTGGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											164	156	159					3																	49084551		2203	4300	6503	49059555	SO:0001583	missense	54870				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1467G>T	3.37:g.49084551C>A	ENSP00000378830:p.Lys489Asn		49059555	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	37	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093019	0.76756	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.76492	0.3995	M	0.63843	1.955	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.76889	-0.2792	9	0.66056	D	0.02	-5.3718	14.7773	0.69740	0.0:0.9316:0.0:0.0684	.	489	Q2TAL8	QRIC1_HUMAN	N	489	.	ENSP00000350094:K489N	K	-	3	2	QRICH1	49059555	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.684000	0.46951	2.894000	0.99253	0.591000	0.81541	AAG		0.473	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49084551	C	A	49084551	3	1	61	1	0	0	0	0	1	0	0	0	12916	912	32	2	891	2	QRICH1	3	49084551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2656	49084551	148937879	2475	10460										
LAMB2	3913	broad.mit.edu	37	chr3	49163560	49163560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcacccccactaaacatCtctagcaccaggacacgggg	8	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49163560C>A	ENST00000418109.1	-	18	2348	c.2184G>T	c.(2182-2184)gaG>gaT	p.E728D	LAMB2_ENST00000305544.4_Missense_Mutation_p.E728D|LAMB2_ENST00000464891.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	728	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E728D(1)		NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACTAAACATCTCTAGCACCA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	76	78					3																	49163560		2203	4300	6503	49138564	SO:0001583	missense	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2184G>T	3.37:g.49163560C>A	ENSP00000388325:p.Glu728Asp		49138564	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.805613	0.31961	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.35421	1.31;1.31	5.76	5.76	0.90799	Laminin IV (1);	0.053982	0.64402	D	0.000001	T	0.26955	0.0660	N	0.17082	0.46	0.58432	D	0.999997	D	0.56521	0.976	P	0.49387	0.609	T	0.02868	-1.1100	10	0.11182	T	0.66	.	10.6811	0.45815	0.0:0.7973:0.1321:0.0706	.	728	P55268	LAMB2_HUMAN	D	728	ENSP00000388325:E728D;ENSP00000307156:E728D	ENSP00000307156:E728D	E	-	3	2	LAMB2	49138564	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	1.674000	0.37544	2.732000	0.93576	0.655000	0.94253	GAG		0.592	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49163560	C	A	49163560	3	1	61	1	0	0	0	0	1	0	0	0	8633	912	32	2	3276	2	LAMB2	3	49163560	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79009	49163560	148858870	2476	10461										
LAMB2	3913	broad.mit.edu	37	chr3	49169830	49169830	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcacaaaggaagcacttCttttcgtcctgggttggatg	12	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49169830C>A	ENST00000418109.1	-	4	422	c.258G>T	c.(256-258)aaG>aaT	p.K86N	LAMB2_ENST00000305544.4_Missense_Mutation_p.K86N	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	86	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.K86N(1)		NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGAAGCACTTCTTTTCGTCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	121	118					3																	49169830		2203	4300	6503	49144834	SO:0001583	missense	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.258G>T	3.37:g.49169830C>A	ENSP00000388325:p.Lys86Asn		49144834	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.369034	0.61624	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.78924	-1.22;-1.22	4.41	3.45	0.39498	Laminin, N-terminal (3);	0.118890	0.56097	D	0.000039	D	0.85177	0.5637	M	0.87827	2.91	0.58432	D	0.999995	D	0.56287	0.975	P	0.59357	0.856	D	0.85438	0.1153	10	0.52906	T	0.07	.	7.7132	0.28690	0.0:0.8257:0.0:0.1743	.	86	P55268	LAMB2_HUMAN	N	86	ENSP00000388325:K86N;ENSP00000307156:K86N	ENSP00000307156:K86N	K	-	3	2	LAMB2	49144834	0.997000	0.39634	1.000000	0.80357	0.845000	0.48019	0.545000	0.23268	2.303000	0.77524	0.655000	0.94253	AAG		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49169830	C	A	49169830	3	1	61	1	0	0	0	0	1	0	0	0	8633	912	32	2	5258	2	LAMB2	3	49169830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6270	49169830	148852600	2477	10462										
CCDC36	339834	broad.mit.edu	37	chr3	49292916	49292916	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccttgagatgaagaaaaGatttgaagctgtaagtgtaa	10	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49292916G>T	ENST00000438782.1	+	7	862	c.626G>T	c.(625-627)aGa>aTa	p.R209I	CCDC36_ENST00000296449.5_Missense_Mutation_p.R209I|CCDC36_ENST00000452691.2_Missense_Mutation_p.R209I			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	209								p.R199I(1)		endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		ATGAAGAAAAGATTTGAAGCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											121	118	119					3																	49292916		2203	4300	6503	49267920	SO:0001583	missense	339834			AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"cancer/testis antigen 74"						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.626G>T	3.37:g.49292916G>T	ENSP00000391788:p.Arg209Ile		49267920	C9JJL0|Q05DG9|Q96LP7	Missense_Mutation	SNP	ENST00000438782.1	37	CCDS33755.2	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700628	0.48307	.	.	ENSG00000173421	ENST00000296449;ENST00000438782;ENST00000452691;ENST00000309062	T;T;T	0.15256	2.44;2.44;2.44	5.31	-10.6	0.00265	.	1.450240	0.04208	N	0.331241	T	0.08980	0.0222	L	0.29908	0.895	0.09310	N	1	B	0.28636	0.218	B	0.28139	0.086	T	0.14839	-1.0458	10	0.44086	T	0.13	0.0072	2.7502	0.05279	0.4136:0.3185:0.1126:0.1554	.	209	Q8IYA8	CCD36_HUMAN	I	209;209;209;189	ENSP00000296449:R209I;ENSP00000391788:R209I;ENSP00000407837:R209I	ENSP00000296449:R209I	R	+	2	0	CCDC36	49267920	0.000000	0.05858	0.000000	0.03702	0.642000	0.38348	-2.672000	0.00843	-2.542000	0.00485	0.591000	0.81541	AGA		0.398	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173		T	49292916	G	T	49292916	3	4	61	1	0	0	0	0	1	0	0	0	2814	942	33	2	648	2	CCDC36	3	49292916	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123086	49292916	148729514	2478	10463										
C3orf62	375341	broad.mit.edu	37	chr3	49314045	49314045	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaaggcagggttctcattCtcaggagcacatgggacagc	13	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49314045C>T	ENST00000343010.3	-	1	1297	c.261G>A	c.(259-261)gaG>gaA	p.E87E	MIR4271_ENST00000582451.1_RNA	NM_198562.2	NP_940964.1	Q6ZUJ4	CC062_HUMAN	chromosome 3 open reading frame 62	87								p.E87E(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGTTCTCATTCTCAGGAGCAC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	3											110	106	108					3																	49314045		2203	4300	6503	49289049	SO:0001819	synonymous_variant	375341			AK125642	CCDS2792.1	3p21.31	2006-02-11			ENSG00000188315	ENSG00000188315			24771	protein-coding gene	gene with protein product						12477932	Standard	NM_198562		Approved	FLJ43654	uc003cwn.2	Q6ZUJ4	OTTHUMG00000156819	ENST00000343010.3:c.261G>A	3.37:g.49314045C>T			49289049	Q6P7E9|Q7Z3X6	Silent	SNP	ENST00000343010.3	37	CCDS2792.1																																																																																				0.532	C3orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345990.1	NM_198562		T	49314045	C	T	49314045	2	4	61	1	0	0	0	0	0	0	0	1	2244	912	32	3		3	C3orf62	3	49314045	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21129	49314045	148708385	2479	10464										
TCTA	6988	broad.mit.edu	37	chr3	49452269	49452269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagggaaatggcagcaaacGaacctctcaaaacccacaga	8	12	2	1	rs142840341		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49452269G>A	ENST00000273590.3	+	3	507	c.286G>A	c.(286-288)Gaa>Aaa	p.E96K	RHOA_ENST00000422781.1_5'Flank|RHOA_ENST00000418115.1_5'Flank|RHOA_ENST00000454011.2_5'Flank|RHOA_ENST00000265538.3_5'Flank|AMT_ENST00000476226.1_5'Flank|TCTA_ENST00000493381.1_3'UTR	NM_022171.2	NP_071503.1	P57738	TCTA_HUMAN	T-cell leukemia translocation altered	96						integral component of membrane (GO:0016021)		p.E96K(1)		large_intestine(4)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCAGCAAACGAACCTCTCAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	LYS/GLU	0,4406		0,0,2203	107	93	98		286	4.1	1	3	dbSNP_134	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	TCTA	NM_022171.2	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	96/104	49452269	1,13005	2203	4300	6503	49427273	SO:0001583	missense	6988				CCDS2796.1	3p21	2012-02-27	2012-02-27		ENSG00000145022	ENSG00000145022			11692	protein-coding gene	gene with protein product		600690	"T-cell leukemia translocation altered gene"			7728759	Standard	NM_022171		Approved		uc003cwv.4	P57738	OTTHUMG00000156846	ENST00000273590.3:c.286G>A	3.37:g.49452269G>A	ENSP00000273590:p.Glu96Lys		49427273	B2R4I4|Q6I9U4|Q9BSB0	Missense_Mutation	SNP	ENST00000273590.3	37	CCDS2796.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.272521	0.59649	0.0	1.16E-4	ENSG00000145022	ENST00000273590	.	.	.	4.11	4.11	0.48088	.	0.064498	0.64402	D	0.000016	T	0.56202	0.1969	N	0.24115	0.695	0.40021	D	0.975405	D	0.59767	0.986	D	0.68192	0.956	T	0.61647	-0.7020	9	0.72032	D	0.01	-5.3533	12.0191	0.53333	0.0:0.0:1.0:0.0	.	96	P57738	TCTA_HUMAN	K	96	.	ENSP00000273590:E96K	E	+	1	0	TCTA	49427273	0.999000	0.42202	0.996000	0.52242	0.989000	0.77384	4.359000	0.59449	2.289000	0.77006	0.462000	0.41574	GAA		0.517	TCTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346210.1	NM_022171		A	49452269	G	A	49452269	3	1	61	1	0	0	0	0	1	0	0	0	15755	1059	37	1	296	1	TCTA	3	49452269	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138224	49452269	148570161	2480	10465										
DAG1	1605	broad.mit.edu	37	chr3	49569444	49569444	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccagcgcccagagctcaaGaaccatattgacagggtaga	10	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49569444G>T	ENST00000539901.1	+	3	2058	c.1500G>T	c.(1498-1500)aaG>aaT	p.K500N	DAG1_ENST00000541308.1_Missense_Mutation_p.K500N|DAG1_ENST00000538711.1_Missense_Mutation_p.K500N|DAG1_ENST00000308775.2_Missense_Mutation_p.K500N|DAG1_ENST00000515359.2_Missense_Mutation_p.K500N|DAG1_ENST00000545947.1_Missense_Mutation_p.K500N	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	500					basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)	p.K500N(1)		NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CAGAGCTCAAGAACCATATTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	64	66					3																	49569444		2203	4300	6503	49544448	SO:0001583	missense	1605			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.1500G>T	3.37:g.49569444G>T	ENSP00000439334:p.Lys500Asn		49544448	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	37	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648357	0.47258	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711	D;D;D;D;D;D	0.98419	-4.92;-4.92;-4.92;-4.92;-4.92;-4.92	5.76	3.64	0.41730	Dystroglycan-type cadherin-like (1);Cadherin-like (1);Immunoglobulin-like fold (1);	0.047323	0.85682	D	0.000000	D	0.95236	0.8455	L	0.36672	1.1	0.46654	D	0.999142	P	0.48998	0.918	B	0.43701	0.428	D	0.92853	0.6299	9	.	.	.	-30.1102	7.2147	0.25953	0.3229:0.0:0.6771:0.0	.	500	Q14118	DAG1_HUMAN	N	500	ENSP00000440705:K500N;ENSP00000312435:K500N;ENSP00000442600:K500N;ENSP00000440590:K500N;ENSP00000439334:K500N;ENSP00000438421:K500N	.	K	+	3	2	DAG1	49544448	0.426000	0.25506	1.000000	0.80357	0.998000	0.95712	-0.251000	0.08818	1.437000	0.47472	0.655000	0.94253	AAG		0.557	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			T	49569444	G	T	49569444	3	4	61	1	0	0	0	0	1	0	0	0	4231	933	33	2	1506	2	DAG1	3	49569444	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117175	49569444	148452986	2481	10466										
BSN	8927	broad.mit.edu	37	chr3	49690867	49690867	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaagcagtttctaaatgCtgagagtgcatacatggacc	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49690867C>A	ENST00000296452.4	+	5	3992	c.3878C>A	c.(3877-3879)gCt>gAt	p.A1293D		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1293					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.A1293D(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TTTCTAAATGCTGAGAGTGCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	3											58	60	59					3																	49690867		2203	4300	6503	49665871	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3878C>A	3.37:g.49690867C>A	ENSP00000296452:p.Ala1293Asp		49665871	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811612	0.50527	.	.	ENSG00000164061	ENST00000296452	T	0.19532	2.14	5.06	5.06	0.68205	.	0.128733	0.50627	D	0.000113	T	0.39145	0.1067	L	0.58428	1.81	0.53688	D	0.999977	D	0.63880	0.993	P	0.56343	0.796	T	0.20907	-1.0261	10	0.62326	D	0.03	.	18.4297	0.90620	0.0:1.0:0.0:0.0	.	1293	Q9UPA5	BSN_HUMAN	D	1293	ENSP00000296452:A1293D	ENSP00000296452:A1293D	A	+	2	0	BSN	49665871	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	7.804000	0.85993	2.363000	0.80096	0.462000	0.41574	GCT		0.547	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49690867	C	A	49690867	3	1	61	1	0	0	0	0	1	0	0	0	1533	797	28	2	3896	2	BSN	3	49690867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121423	49690867	148331563	2482	10467										
RNF123	63891	broad.mit.edu	37	chr3	49737750	49737750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggcacagtccgtggtgCaccaggtcctggacctcttg	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:49737750C>T	ENST00000327697.6	+	13	1219	c.1075C>T	c.(1075-1077)Cac>Tac	p.H359Y	RNF123_ENST00000432042.1_Missense_Mutation_p.H213Y	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	359					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.H359Y(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GTCCGTGGTGCACCAGGTCCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	3											108	82	91					3																	49737750		2203	4300	6503	49712754	SO:0001583	missense	63891			AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1075C>T	3.37:g.49737750C>T	ENSP00000328287:p.His359Tyr		49712754	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376144	0.24857	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75704	-0.66;-0.96	5.58	3.66	0.41972	.	0.672603	0.15707	N	0.248602	T	0.53077	0.1774	N	0.08118	0	0.80722	D	1	B;B	0.20368	0.031;0.044	B;B	0.19148	0.024;0.016	T	0.44937	-0.9295	10	0.22109	T	0.4	-6.71	11.3642	0.49662	0.1421:0.721:0.1369:0.0	.	213;359	C9J266;Q5XPI4	.;RN123_HUMAN	Y	359;359;213	ENSP00000328287:H359Y;ENSP00000392443:H213Y	ENSP00000328287:H359Y	H	+	1	0	RNF123	49712754	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.684000	0.54671	1.338000	0.45544	0.655000	0.94253	CAC		0.607	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49737750	C	T	49737750	3	4	61	1	0	0	0	0	1	0	0	0	13470	710	25	3	1121	3	RNF123	3	49737750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46883	49737750	148284680	2483	10468										
RBM6	10180	broad.mit.edu	37	chr3	50095855	50095855	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatcatgctaaagcgtatcTatcgttccacaccacctgag	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:50095855T>C	ENST00000266022.4	+	10	2249	c.1990T>C	c.(1990-1992)Tat>Cat	p.Y664H	RBM6_ENST00000442092.1_Missense_Mutation_p.Y142H|RBM6_ENST00000539992.1_Missense_Mutation_p.Y6H|RBM6_ENST00000422955.1_Missense_Mutation_p.Y142H|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000443081.1_Missense_Mutation_p.Y532H	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	664					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y664H(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		AAAGCGTATCTATCGTTCCAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											208	213	211					3																	50095855		2203	4300	6503	50070859	SO:0001583	missense	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1990T>C	3.37:g.50095855T>C	ENSP00000266022:p.Tyr664His		50070859	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.526360	0.64860	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000539992;ENST00000422955;ENST00000446471	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);	0.462380	0.21978	N	0.066348	T	0.08626	0.0214	N	0.08118	0	0.25291	N	0.989357	D;D	0.67145	0.991;0.996	P;D	0.64877	0.852;0.93	T	0.38908	-0.9639	9	.	.	.	-13.644	2.8825	0.05652	0.1516:0.0768:0.1398:0.6319	.	532;664	E9PGM9;P78332	.;RBM6_HUMAN	H	142;664;532;6;142;142	ENSP00000393530:Y142H;ENSP00000266022:Y664H;ENSP00000396466:Y532H;ENSP00000443165:Y6H;ENSP00000392939:Y142H	.	Y	+	1	0	RBM6	50070859	0.946000	0.32159	1.000000	0.80357	0.986000	0.74619	1.960000	0.40422	2.189000	0.69895	0.529000	0.55759	TAT		0.458	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		C	50095855	T	C	50095855	3	2	61	1	0	0	0	0	1	0	0	0	13181	1522	53	4	2024	4	RBM6	3	50095855	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	358105	50095855	147926575	2484	10469										
RBM6	10180	broad.mit.edu	37	chr3	50103853	50103853	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaactcactgactggaataAactggcttgtctgctttgca	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:50103853A>C	ENST00000266022.4	+	17	3120	c.2861A>C	c.(2860-2862)aAa>aCa	p.K954T	RBM6_ENST00000442092.1_Missense_Mutation_p.K432T|RBM6_ENST00000539992.1_Missense_Mutation_p.K296T|RBM6_ENST00000422955.1_Missense_Mutation_p.K432T|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000443081.1_Missense_Mutation_p.K822T|RBM6_ENST00000421682.1_5'UTR	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	954					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K954T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		GACTGGAATAAACTGGCTTGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											146	159	154					3																	50103853		2203	4300	6503	50078857	SO:0001583	missense	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2861A>C	3.37:g.50103853A>C	ENSP00000266022:p.Lys954Thr		50078857	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.895084	0.91962	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000539992;ENST00000422955	T;T;T;T;T	0.57595	0.39;0.9;0.91;0.45;0.39	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.75034	0.3795	M	0.82630	2.6	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.77278	-0.2647	9	.	.	.	-23.2864	16.5582	0.84512	1.0:0.0:0.0:0.0	.	954	P78332	RBM6_HUMAN	T	432;954;822;296;432	ENSP00000393530:K432T;ENSP00000266022:K954T;ENSP00000396466:K822T;ENSP00000443165:K296T;ENSP00000392939:K432T	.	K	+	2	0	RBM6	50078857	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.308000	0.77769	0.533000	0.62120	AAA		0.512	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		C	50103853	A	C	50103853	3	2	61	1	0	0	0	0	1	0	0	0	13181	14	1	4	2923	4	RBM6	3	50103853	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7998	50103853	147918577	2485	10470										
RBM6	10180	broad.mit.edu	37	chr3	50112659	50112659	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaacttgttgataaagaaGatatcgacactagcagcaaa	8	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:50112659G>T	ENST00000266022.4	+	20	3401	c.3142G>T	c.(3142-3144)Gat>Tat	p.D1048Y	RBM6_ENST00000442092.1_Missense_Mutation_p.D526Y|RBM6_ENST00000539992.1_Missense_Mutation_p.D390Y|RBM6_ENST00000422955.1_Missense_Mutation_p.D526Y|RBM6_ENST00000443081.1_Missense_Mutation_p.D916Y|RBM6_ENST00000421682.1_Missense_Mutation_p.D44Y	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	1048					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D1048Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TGATAAAGAAGATATCGACAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	81	81					3																	50112659		2203	4300	6503	50087663	SO:0001583	missense	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.3142G>T	3.37:g.50112659G>T	ENSP00000266022:p.Asp1048Tyr		50087663	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670421	0.47677	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000539992;ENST00000422955;ENST00000421682	T;T;T;T;T	0.44083	0.93;1.51;1.52;0.93;0.93	5.52	5.52	0.82312	.	0.703401	0.14360	N	0.324480	T	0.26666	0.0652	N	0.08118	0	0.34033	D	0.654086	P	0.36789	0.57	B	0.40101	0.319	T	0.30909	-0.9962	9	.	.	.	-3.1217	11.6806	0.51455	0.0818:0.0:0.9182:0.0	.	1048	P78332	RBM6_HUMAN	Y	526;1048;916;390;526;44	ENSP00000393530:D526Y;ENSP00000266022:D1048Y;ENSP00000396466:D916Y;ENSP00000443165:D390Y;ENSP00000392939:D526Y	.	D	+	1	0	RBM6	50087663	1.000000	0.71417	0.955000	0.39395	0.594000	0.36715	2.046000	0.41260	2.601000	0.87937	0.650000	0.86243	GAT		0.458	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		T	50112659	G	T	50112659	3	4	61	1	0	0	0	0	1	0	0	0	13181	942	33	2	3216	2	RBM6	3	50112659	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8806	50112659	147909771	2486	10471										
RBM5	10181	broad.mit.edu	37	chr3	50155773	50155773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctttcccaggctcaagttCggctaaagggagctggccta	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:50155773C>T	ENST00000347869.3	+	25	2507	c.2332C>T	c.(2332-2334)Cgg>Tgg	p.R778W	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	778	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.|Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R778W(1)		breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGCTCAAGTTCGGCTAAAGGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	66	70					3																	50155773		2203	4300	6503	50130777	SO:0001583	missense	10181			U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2332C>T	3.37:g.50155773C>T	ENSP00000343054:p.Arg778Trp		50130777	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	37	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887247	0.72410	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	T	0.34667	1.35	5.57	4.69	0.59074	D111/G-patch (3);	0.115139	0.56097	D	0.000027	T	0.69620	0.3131	H	0.96015	3.755	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	T	0.77958	-0.2392	10	0.46703	T	0.11	-13.8745	13.118	0.59311	0.4136:0.5864:0.0:0.0	.	778	P52756	RBM5_HUMAN	W	778;777;468	ENSP00000343054:R778W	ENSP00000343054:R778W	R	+	1	2	RBM5	50130777	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.221000	0.42917	1.319000	0.45190	0.655000	0.94253	CGG		0.582	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		T	50155773	C	T	50155773	3	4	61	1	0	0	0	0	1	0	0	0	13180	875	31	1	2426	1	RBM5	3	50155773	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43114	50155773	147866657	2487	10472										
SLC38A3	10991	broad.mit.edu	37	chr3	50252837	50252837	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcctgttgacagctgtcGccttgctctccagctactcc	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:50252837G>A	ENST00000420502.1	+	0	472									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		GACAGCTGTCGCCTTGCTCTC	0.612																																																0			3											92	94	93					3																	50252837		2007	4170	6177	50227841			10991			U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		3.37:g.50252837G>A			50227841		Missense_Mutation	SNP	ENST00000420502.1	37																																																																																					0.612	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		A	50252837	G	A	50252837	1	1	61	0	1	0	0	0	0	0	0	0	14642	1087	38	1		1	SLC38A3	3	50252837	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97064	50252837	147769593	2488	10473										
DOCK3	1795	broad.mit.edu	37	chr3	51112857	51112857	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaccagattagtgtctcaGatctctataagatggtaaga	10	7	2	4	rs369702617		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51112857G>T	ENST00000266037.9	+	7	558	c.535G>T	c.(535-537)Gat>Tat	p.D179Y		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	179					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D179Y(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TAGTGTCTCAGATCTCTATAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	76	76					3																	51112857		1881	4111	5992	51087897	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.535G>T	3.37:g.51112857G>T	ENSP00000266037:p.Asp179Tyr		51087897	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606334	0.87157	.	.	ENSG00000088538	ENST00000266037	T	0.49432	0.78	5.77	5.77	0.91146	.	0.186906	0.56097	D	0.000025	T	0.64011	0.2560	L	0.50333	1.59	0.80722	D	1	D	0.67145	0.996	D	0.67231	0.95	T	0.64024	-0.6504	10	0.87932	D	0	.	18.1283	0.89593	0.0:0.0:1.0:0.0	.	179	Q8IZD9	DOCK3_HUMAN	Y	179	ENSP00000266037:D179Y	ENSP00000266037:D179Y	D	+	1	0	DOCK3	51087897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.309000	0.89969	2.890000	0.99128	0.585000	0.79938	GAT		0.398	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51112857	G	T	51112857	3	4	61	1	0	0	0	0	1	0	0	0	4699	942	33	2	561	2	DOCK3	3	51112857	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	860020	51112857	146909573	2489	10474										
DOCK3	1795	broad.mit.edu	37	chr3	51196713	51196713	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagagagatttgtatatCgttgcccatgtgatccgaat	10	6	0	4	rs200460488		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51196713C>T	ENST00000266037.9	+	11	890	c.867C>T	c.(865-867)atC>atT	p.I289I		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	289					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.I289I(2)|p.I278I(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ATTTGTATATCGTTGCCCATG	0.358													C|||	1	0.000199681	0	0	5008	,	,		19607	0.001		0	False		,,,				2504	0															3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	3											132	124	126					3																	51196713		1865	4113	5978	51171753	SO:0001819	synonymous_variant	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.867C>T	3.37:g.51196713C>T			51171753	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																				0.358	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51196713	C	T	51196713	2	4	61	1	0	0	0	0	0	0	0	1	4699	874	31	1		1	DOCK3	3	51196713	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83856	51196713	146825717	2490	10475										
DOCK3	1795	broad.mit.edu	37	chr3	51198110	51198110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaagtaaaggaagaaaaGgattttgttcttaaggttta	10	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51198110G>T	ENST00000266037.9	+	12	1037	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	338					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.K338N(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AGGAAGAAAAGGATTTTGTTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	82	81					3																	51198110		1967	4138	6105	51173150	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1014G>T	3.37:g.51198110G>T	ENSP00000266037:p.Lys338Asn		51173150	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.832959	0.71258	.	.	ENSG00000088538	ENST00000266037	T	0.05786	3.39	5.8	2.04	0.26737	.	0.000000	0.85682	D	0.000000	T	0.12008	0.0292	M	0.64997	1.995	0.50171	D	0.999851	D	0.56035	0.974	P	0.53062	0.717	T	0.20538	-1.0272	10	0.19147	T	0.46	.	10.6215	0.45483	0.2562:0.0:0.7438:0.0	.	338	Q8IZD9	DOCK3_HUMAN	N	338	ENSP00000266037:K338N	ENSP00000266037:K338N	K	+	3	2	DOCK3	51173150	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.662000	0.25038	0.825000	0.34637	0.563000	0.77884	AAG		0.443	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51198110	G	T	51198110	3	4	61	1	0	0	0	0	1	0	0	0	4699	991	35	2	1060	2	DOCK3	3	51198110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1397	51198110	146824320	2491	10476										
DOCK3	1795	broad.mit.edu	37	chr3	51264863	51264863	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccacctgcgctttgagttCagacattgttccagtgagtt	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51264863C>A	ENST00000266037.9	+	16	1550	c.1527C>A	c.(1525-1527)ttC>ttA	p.F509L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	509	DHR-1.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.F509L(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GCTTTGAGTTCAGACATTGTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	80	81					3																	51264863		1840	4077	5917	51239903	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1527C>A	3.37:g.51264863C>A	ENSP00000266037:p.Phe509Leu		51239903	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654191	0.88056	.	.	ENSG00000088538	ENST00000266037	T	0.16073	2.37	6.05	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.30792	0.0776	M	0.63169	1.94	0.80722	D	1	P	0.44659	0.84	P	0.50754	0.649	T	0.01972	-1.1237	10	0.44086	T	0.13	.	15.5202	0.75859	0.0:0.9339:0.0:0.0661	.	509	Q8IZD9	DOCK3_HUMAN	L	509	ENSP00000266037:F509L	ENSP00000266037:F509L	F	+	3	2	DOCK3	51239903	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.089000	0.71384	1.574000	0.49760	-0.157000	0.13467	TTC		0.458	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51264863	C	A	51264863	3	1	61	1	0	0	0	0	1	0	0	0	4699	825	29	2	1589	2	DOCK3	3	51264863	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66753	51264863	146757567	2492	10477										
DOCK3	1795	broad.mit.edu	37	chr3	51312528	51312528	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatcccgccgcatcctgcTtcctgtggttctccatcaca	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51312528T>G	ENST00000266037.9	+	25	2590	c.2567T>G	c.(2566-2568)cTt>cGt	p.L856R		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	856					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.L856R(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CGCATCCTGCTTCCTGTGGTT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											197	197	197					3																	51312528		1922	4130	6052	51287568	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2567T>G	3.37:g.51312528T>G	ENSP00000266037:p.Leu856Arg		51287568	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.667248	0.88348	.	.	ENSG00000088538	ENST00000266037	T	0.70986	-0.53	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.84946	0.5585	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86867	0.2033	10	0.72032	D	0.01	.	16.2007	0.82071	0.0:0.0:0.0:1.0	.	856	Q8IZD9	DOCK3_HUMAN	R	856	ENSP00000266037:L856R	ENSP00000266037:L856R	L	+	2	0	DOCK3	51287568	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.219000	0.72066	0.528000	0.53228	CTT		0.493	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		G	51312528	T	G	51312528	3	3	61	1	0	0	0	0	1	0	0	0	4699	1609	56	4	2665	4	DOCK3	3	51312528	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	47665	51312528	146709902	2493	10478										
RBM15B	29890	broad.mit.edu	37	chr3	51431305	51431305	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcttctcaggaacctggtCtcctacttgaaacagaagca	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51431305C>A	ENST00000323686.4	+	1	2575	c.2475C>A	c.(2473-2475)gtC>gtA	p.V825V		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	825	Interaction with Epstein-Barr virus BMLF1.|SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.V825V(1)		endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGAACCTGGTCTCCTACTTGA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	3											27	31	30					3																	51431305		2203	4300	6503	51406345	SO:0001819	synonymous_variant	29890			AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2475C>A	3.37:g.51431305C>A			51406345	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	37	CCDS33764.1																																																																																				0.637	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		A	51431305	C	A	51431305	2	1	61	1	0	0	0	0	0	0	0	1	13154	900	32	2		2	RBM15B	3	51431305	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118777	51431305	146591125	2494	10479										
VPRBP	9730	broad.mit.edu	37	chr3	51477917	51477917	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagattctcgacaattccCtcctatagtaaaggaaatta	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51477917C>A	ENST00000335891.5	-	5	387	c.378G>T	c.(376-378)gaG>gaT	p.E126D				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	126					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)	p.E126D(1)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CGACAATTCCCTCCTATAGTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	57	57					3																	51477917		1819	4075	5894	51452957	SO:0001583	missense	9730			AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.378G>T	3.37:g.51477917C>A	ENSP00000338857:p.Glu126Asp		51452957	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	C	12.00	1.805785	0.31961	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.67698	-0.28;0.79	5.84	3.31	0.37934	Armadillo-type fold (1);	0.100664	0.64402	D	0.000002	T	0.62588	0.2440	N	0.16166	0.38	0.25933	N	0.982968	D	0.56035	0.974	D	0.70487	0.969	T	0.55140	-0.8187	10	0.14656	T	0.56	-18.7485	10.2545	0.43388	0.0:0.1354:0.0:0.8646	.	126	Q9Y4B6	VPRBP_HUMAN	D	126	ENSP00000338857:E126D;ENSP00000421724:E126D	ENSP00000338857:E126D	E	-	3	2	VPRBP	51452957	1.000000	0.71417	1.000000	0.80357	0.275000	0.26752	1.838000	0.39211	0.461000	0.27071	-0.455000	0.05494	GAG		0.358	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		A	51477917	C	A	51477917	3	1	61	1	0	0	0	0	1	0	0	0	17225	680	24	2	4058	2	VPRBP	3	51477917	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46612	51477917	146544513	2495	10480										
VPRBP	9730	broad.mit.edu	37	chr3	51505016	51505016	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctttttcaatcaattgaGacatcctagcacaaaggaaa	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51505016G>T	ENST00000335891.5	-	2	125	c.116C>A	c.(115-117)tCt>tAt	p.S39Y				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	39					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)	p.S39Y(1)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		AATCAATTGAGACATCCTAGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	86	89					3																	51505016		1861	4106	5967	51480056	SO:0001583	missense	9730			AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.116C>A	3.37:g.51505016G>T	ENSP00000338857:p.Ser39Tyr		51480056	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	G	21.1	4.099518	0.76983	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.61392	0.11;0.47	4.93	4.93	0.64822	.	0.078300	0.64402	D	0.000011	T	0.73713	0.3622	L	0.61218	1.895	0.33184	D	0.549983	D	0.58970	0.984	D	0.74348	0.983	T	0.81771	-0.0780	10	0.87932	D	0	-2.0949	16.9662	0.86286	0.0:0.0:1.0:0.0	.	39	Q9Y4B6	VPRBP_HUMAN	Y	39	ENSP00000338857:S39Y;ENSP00000421724:S39Y	ENSP00000338857:S39Y	S	-	2	0	VPRBP	51480056	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.688000	0.91260	2.281000	0.76405	0.449000	0.29647	TCT		0.403	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		T	51505016	G	T	51505016	3	4	61	1	0	0	0	0	1	0	0	0	17225	942	33	2	4332	2	VPRBP	3	51505016	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27099	51505016	146517414	2496	10481										
IQCF2	389123	broad.mit.edu	37	chr3	51895692	51895692	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggacaggccatgagggttCgattttgtgtaagagacatg	14	5	0	2	rs201262177		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51895692C>T	ENST00000333127.3	+	1	39	c.10C>T	c.(10-12)Cga>Tga	p.R4*	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	4								p.R4*(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CATGAGGGTTCGATTTTGTGT	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											123	108	113					3																	51895692		2203	4300	6503	51870732	SO:0001587	stop_gained	389123			AK128883	CCDS2835.1	3p21.31	2008-02-05			ENSG00000184345	ENSG00000184345			31815	protein-coding gene	gene with protein product							Standard	NM_203424		Approved		uc003dbt.1	Q8IXL9	OTTHUMG00000156914	ENST00000333127.3:c.10C>T	3.37:g.51895692C>T	ENSP00000329904:p.Arg4*		51870732		Nonsense_Mutation	SNP	ENST00000333127.3	37	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	c	19.10	3.762236	0.69763	.	.	ENSG00000184345	ENST00000333127	.	.	.	4.37	-2.8	0.05823	.	2.199260	0.02172	N	0.059762	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	3.1518	9.7073	0.40222	0.6516:0.2202:0.1282:0.0	.	.	.	.	X	4	.	ENSP00000329904:R4X	R	+	1	2	IQCF2	51870732	0.000000	0.05858	0.000000	0.03702	0.453000	0.32348	-0.391000	0.07323	-0.538000	0.06281	0.555000	0.69702	CGA		0.473	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		T	51895692	C	T	51895692	4	4	61	1	0	0	0	0	0	1	0	0	7829	876	31	1	12	1	IQCF2	3	51895692	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	390676	51895692	146126738	2497	10482										
IQCF1	132141	broad.mit.edu	37	chr3	51928912	51928912	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaaaagaccacttcattcCtttattgagaagggaataca	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51928912C>A	ENST00000310914.5	-	4	674	c.612G>T	c.(610-612)aaG>aaT	p.K204N		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	204								p.K204N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CACTTCATTCCTTTATTGAGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											60	61	61					3																	51928912		2203	4300	6503	51903952	SO:0001583	missense	132141			BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.612G>T	3.37:g.51928912C>A	ENSP00000307958:p.Lys204Asn		51903952	Q8N711	Missense_Mutation	SNP	ENST00000310914.5	37	CCDS2836.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.356144	0.24598	.	.	ENSG00000173389	ENST00000310914	T	0.50813	0.73	4.06	-1.08	0.09936	.	0.105105	0.42420	N	0.000712	T	0.36853	0.0982	M	0.73217	2.22	0.29175	N	0.876894	P	0.37781	0.608	B	0.33568	0.166	T	0.34004	-0.9846	10	0.87932	D	0	-11.1333	3.7593	0.08598	0.1639:0.4542:0.0:0.3818	.	204	Q8N6M8	IQCF1_HUMAN	N	204	ENSP00000307958:K204N	ENSP00000307958:K204N	K	-	3	2	IQCF1	51903952	0.721000	0.28007	0.548000	0.28192	0.047000	0.14425	-0.159000	0.10056	-0.227000	0.09884	-0.404000	0.06349	AAG		0.493	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397		A	51928912	C	A	51928912	3	1	61	1	0	0	0	0	1	0	0	0	7828	680	24	2	9	2	IQCF1	3	51928912	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33220	51928912	146093518	2498	10483										
IQCF1	132141	broad.mit.edu	37	chr3	51928987	51928987	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctccagctggagatgcagCtggttggctgtgactctgta	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51928987C>T	ENST00000310914.5	-	4	599	c.537G>A	c.(535-537)caG>caA	p.Q179Q		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	179								p.Q179Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGAGATGCAGCTGGTTGGCTG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											94	93	94					3																	51928987		2203	4300	6503	51904027	SO:0001819	synonymous_variant	132141			BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.537G>A	3.37:g.51928987C>T			51904027	Q8N711	Silent	SNP	ENST00000310914.5	37	CCDS2836.1																																																																																				0.527	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397		T	51928987	C	T	51928987	2	4	61	1	0	0	0	0	0	0	0	1	7828	796	28	3		3	IQCF1	3	51928987	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75	51928987	146093443	2499	10484										
RRP9	9136	broad.mit.edu	37	chr3	51972152	51972152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtagagcttggccaagcgcAgcttcttttcctgtgcagtt	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:51972152A>G	ENST00000232888.6	-	3	312	c.239T>C	c.(238-240)cTg>cCg	p.L80P		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	80	Glu-rich.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.L80P(1)|p.L80Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		GGCCAAGCGCAGCTTCTTTTC	0.637																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3											90	68	75					3																	51972152		2202	4300	6502	51947192	SO:0001583	missense	9136			AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"WD repeat domain containing"	16829	protein-coding gene	gene with protein product			"RNA, U3 small nucleolar interacting protein 2"	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.239T>C	3.37:g.51972152A>G	ENSP00000232888:p.Leu80Pro		51947192	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.455194	0.84209	.	.	ENSG00000114767	ENST00000232888	T	0.59364	0.27	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.75860	0.3907	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.79598	-0.1737	10	0.87932	D	0	-13.079	14.3203	0.66482	1.0:0.0:0.0:0.0	.	80	O43818	U3IP2_HUMAN	P	80	ENSP00000232888:L80P	ENSP00000232888:L80P	L	-	2	0	RRP9	51947192	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.752000	0.91632	2.025000	0.59659	0.460000	0.39030	CTG		0.637	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704		G	51972152	A	G	51972152	3	3	61	1	0	0	0	0	1	0	0	0	13728	188	7	4	1240	4	RRP9	3	51972152	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	43165	51972152	146050278	2500	10485										
DUSP7	1849	broad.mit.edu	37	chr3	52088014	52088014	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggctccagtggtcagaGatggggatctgcttgtaggt	15	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52088014G>T	ENST00000495880.1	-	2	1077	c.894C>A	c.(892-894)atC>atA	p.I298I	DUSP7_ENST00000296483.6_Silent_p.I247I			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	298					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.I247I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGTGGTCAGAGATGGGGATCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	3											206	190	195					3																	52088014		2203	4300	6503	52063054	SO:0001819	synonymous_variant	1849			X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.894C>A	3.37:g.52088014G>T			52063054	Q2M3J7|Q8NFJ0	Silent	SNP	ENST00000495880.1	37	CCDS33766.2																																																																																				0.567	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947		T	52088014	G	T	52088014	2	4	61	1	0	0	0	0	0	0	0	1	4841	932	33	2		2	DUSP7	3	52088014	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115862	52088014	145934416	2501	10486										
TLR9	54106	broad.mit.edu	37	chr3	52255658	52255658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactcctccagctgcccccGaagctcgttgtacacccagt	8	18	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52255658G>A	ENST00000360658.2	-	2	3307	c.2674C>T	c.(2674-2676)Cgg>Tgg	p.R892W	TLR9_ENST00000494383.1_Missense_Mutation_p.S1045L|TLR9_ENST00000597542.1_Missense_Mutation_p.R916W	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	892	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.R892W(1)		endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	AGCTGCCCCCGAAGCTCGTTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	80	79					3																	52255658		2203	4299	6502	52230698	SO:0001583	missense	54106			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2674C>T	3.37:g.52255658G>A	ENSP00000353874:p.Arg892Trp		52230698	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.13|13.13	2.144918|2.144918	0.37825|0.37825	.|.	.|.	ENSG00000239732|ENSG00000173366	ENST00000360658|ENST00000494383	T|.	0.08102|.	3.13|.	5.22|5.22	2.01|2.01	0.26516|0.26516	Toll/interleukin-1 receptor homology (TIR) domain (3);|.	0.000000|.	0.34652|.	N|.	0.003790|.	T|T	0.51873|0.51873	0.1700|0.1700	M|M	0.72118|0.72118	2.19|2.19	0.25111|0.25111	N|N	0.990713|0.990713	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.987;1.0|.	T|T	0.43081|0.43081	-0.9413|-0.9413	10|5	0.66056|.	D|.	0.02|.	.|.	7.3461|7.3461	0.26664|0.26664	0.0843:0.0:0.4787:0.4371|0.0843:0.0:0.4787:0.4371	.|.	989;892|.	B4E0A1;Q9NR96|.	.;TLR9_HUMAN|.	W|L	892|1045	ENSP00000353874:R892W|.	ENSP00000353874:R892W|.	R|S	-|-	1|2	2|0	TLR9|RP11-330H6.5	52230698|52230698	0.023000|0.023000	0.18921|0.18921	0.724000|0.724000	0.30704|0.30704	0.326000|0.326000	0.28443|0.28443	0.173000|0.173000	0.16724|0.16724	0.565000|0.565000	0.29255|0.29255	-0.122000|-0.122000	0.15005|0.15005	CGG|TCG		0.637	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			A	52255658	G	A	52255658	3	1	61	1	0	0	0	0	1	0	0	0	15997	1057	37	1	428	1	TLR9	3	52255658	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167644	52255658	145766772	2502	10487										
TLR9	54106	broad.mit.edu	37	chr3	52256386	52256386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggctcttggggaggttgCgcagggtttggggcaggagg	22	5	1	0	rs202082899		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52256386C>T	ENST00000360658.2	-	2	2579	c.1946G>A	c.(1945-1947)cGc>cAc	p.R649H	TLR9_ENST00000494383.1_Silent_p.A802A|TLR9_ENST00000597542.1_Missense_Mutation_p.R673H	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	649					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.R649H(1)		endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	GGGGAGGTTGCGCAGGGTTTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	66	67					3																	52256386		2203	4300	6503	52231426	SO:0001583	missense	54106			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.1946G>A	3.37:g.52256386C>T	ENSP00000353874:p.Arg649His		52231426	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	C	3.072	-0.190866	0.06299	.	.	ENSG00000239732	ENST00000360658	T	0.79940	-1.32	5.16	-8.81	0.00813	.	0.862721	0.09623	N	0.777332	T	0.59142	0.2172	N	0.17764	0.52	0.09310	N	1	B;B	0.21905	0.005;0.062	B;B	0.06405	0.0;0.002	T	0.43540	-0.9385	10	0.42905	T	0.14	.	7.9907	0.30239	0.0:0.4383:0.2279:0.3338	.	746;649	B4E0A1;Q9NR96	.;TLR9_HUMAN	H	649	ENSP00000353874:R649H	ENSP00000353874:R649H	R	-	2	0	TLR9	52231426	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-2.966000	0.00670	-1.475000	0.01876	-2.069000	0.00389	CGC		0.582	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			T	52256386	C	T	52256386	3	4	61	1	0	0	0	0	1	0	0	0	15997	768	27	1	1156	1	TLR9	3	52256386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	728	52256386	145766044	2503	10488										
DNAH1	25981	broad.mit.edu	37	chr3	52390733	52390733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcctgtggagagcaagcGctaccagaccatggagcgga	15	11	0	2	rs368357694		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52390733G>A	ENST00000420323.2	+	22	4058	c.3797G>A	c.(3796-3798)cGc>cAc	p.R1266H		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1266	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1266H(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		GAGAGCAAGCGCTACCAGACC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG	1,4067		0,1,2033	50	53	52		3797	5.4	1	3		52	0,8396		0,0,4198	no	missense	DNAH1	NM_015512.4	29	0,1,6231	AA,AG,GG		0.0,0.0246,0.0080	probably-damaging	1266/4266	52390733	1,12463	2034	4198	6232	52365773	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.3797G>A	3.37:g.52390733G>A	ENSP00000401514:p.Arg1266His		52365773	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671054	0.88348	2.46E-4	0.0	ENSG00000114841	ENST00000420323	T	0.63580	-0.05	5.41	5.41	0.78517	.	0.000000	0.52532	D	0.000070	D	0.83631	0.5296	M	0.89534	3.04	0.47374	D	0.999406	D	0.89917	1.0	D	0.83275	0.996	D	0.86152	0.1588	10	0.56958	D	0.05	.	19.185	0.93639	0.0:0.0:1.0:0.0	.	1266	C9JXH6	.	H	1266	ENSP00000401514:R1266H	ENSP00000401514:R1266H	R	+	2	0	DNAH1	52365773	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.612000	0.46343	2.541000	0.85698	0.555000	0.69702	CGC		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52390733	G	A	52390733	3	1	61	1	0	0	0	0	1	0	0	0	4608	1087	38	1	3879	1	DNAH1	3	52390733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134347	52390733	145631697	2504	10489										
DNAH1	25981	broad.mit.edu	37	chr3	52403946	52403946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcatcctggggctcatgCccttcatcgagtgctggctg	12	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52403946C>T	ENST00000420323.2	+	38	6310	c.6049C>T	c.(6049-6051)Ccc>Tcc	p.P2017S		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2017	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P2017S(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		GGGGCTCATGCCCTTCATCGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	95	93					3																	52403946		2054	4212	6266	52378986	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.6049C>T	3.37:g.52403946C>T	ENSP00000401514:p.Pro2017Ser		52378986	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430161	0.83776	.	.	ENSG00000114841	ENST00000420323	D	0.91237	-2.81	5.42	5.42	0.78866	.	0.000000	0.49916	D	0.000130	D	0.95912	0.8669	M	0.88512	2.96	0.80722	D	1	D	0.64830	0.994	D	0.65140	0.932	D	0.95998	0.8991	10	0.56958	D	0.05	.	19.2043	0.93723	0.0:1.0:0.0:0.0	.	2017	C9JXH6	.	S	2017	ENSP00000401514:P2017S	ENSP00000401514:P2017S	P	+	1	0	DNAH1	52378986	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	5.330000	0.65899	2.559000	0.86315	0.561000	0.74099	CCC		0.592	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52403946	C	T	52403946	3	4	61	1	0	0	0	0	1	0	0	0	4608	739	26	3	6195	3	DNAH1	3	52403946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13213	52403946	145618484	2505	10490										
DNAH1	25981	broad.mit.edu	37	chr3	52412647	52412647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacattgcccacttcacgGagccccttgtggaagccacc	8	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52412647G>A	ENST00000420323.2	+	47	7489	c.7228G>A	c.(7228-7230)Gag>Aag	p.E2410K		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2410	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E2410K(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		CCACTTCACGGAGCCCCTTGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	114	110					3																	52412647		2023	4188	6211	52387687	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.7228G>A	3.37:g.52412647G>A	ENSP00000401514:p.Glu2410Lys		52387687	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784666	0.49997	.	.	ENSG00000114841	ENST00000420323	T	0.35421	1.31	5.11	1.04	0.20106	.	0.633514	0.13702	N	0.368735	T	0.19087	0.0458	N	0.16233	0.39	0.35011	D	0.756872	B	0.06786	0.001	B	0.10450	0.005	T	0.29243	-1.0018	10	0.07482	T	0.82	.	10.823	0.46617	0.3019:0.0:0.6981:0.0	.	2410	C9JXH6	.	K	2410	ENSP00000401514:E2410K	ENSP00000401514:E2410K	E	+	1	0	DNAH1	52387687	0.902000	0.30710	0.004000	0.12327	0.888000	0.51559	1.197000	0.32211	0.326000	0.23384	0.563000	0.77884	GAG		0.617	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52412647	G	A	52412647	3	1	61	1	0	0	0	0	1	0	0	0	4608	1175	41	3	7410	3	DNAH1	3	52412647	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8701	52412647	145609783	2506	10491										
DNAH1	25981	broad.mit.edu	37	chr3	52417475	52417475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcccaatctgtatactgCggacgagcaggaccagatcg	10	12	1	1	rs373082854		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52417475C>T	ENST00000420323.2	+	51	8276	c.8015C>T	c.(8014-8016)gCg>gTg	p.A2672V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2672	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A2672V(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		CTGTATACTGCGGACGAGCAG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	VAL/ALA	1,4039		0,1,2019	81	81	81		8015	-4.9	0	3		81	0,8358		0,0,4179	no	missense	DNAH1	NM_015512.4	64	0,1,6198	TT,TC,CC		0.0,0.0248,0.0081	benign	2672/4266	52417475	1,12397	2020	4179	6199	52392515	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.8015C>T	3.37:g.52417475C>T	ENSP00000401514:p.Ala2672Val		52392515	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	3.972	-0.008122	0.07773	2.48E-4	0.0	ENSG00000114841	ENST00000420323	T	0.43294	0.95	4.87	-4.9	0.03094	.	3.650830	0.00976	N	0.003318	T	0.30885	0.0779	L	0.31476	0.935	0.09310	N	1	B	0.16603	0.018	B	0.14023	0.01	T	0.17077	-1.0381	10	0.27082	T	0.32	.	10.1514	0.42796	0.0:0.4331:0.087:0.4798	.	2672	C9JXH6	.	V	2672	ENSP00000401514:A2672V	ENSP00000401514:A2672V	A	+	2	0	DNAH1	52392515	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.148000	0.10219	-2.003000	0.00962	-2.053000	0.00404	GCG		0.557	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52417475	C	T	52417475	3	4	61	1	0	0	0	0	1	0	0	0	4608	768	27	1	8213	1	DNAH1	3	52417475	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4828	52417475	145604955	2507	10492										
NISCH	11188	broad.mit.edu	37	chr3	52526285	52526285	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccctcaccctcgtcttCgatgacgtgcaaggtcatga	10	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52526285C>T	ENST00000479054.1	+	22	4374	c.4302C>T	c.(4300-4302)ttC>ttT	p.F1434F	NISCH_ENST00000345716.4_Silent_p.F1434F			Q9Y2I1	NISCH_HUMAN	nischarin	1434					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.F1434F(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CCCTCGTCTTCGATGACGTGC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	3											138	136	136					3																	52526285		2203	4300	6503	52501325	SO:0001819	synonymous_variant	11188			AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.4302C>T	3.37:g.52526285C>T			52501325	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																				0.657	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52526285	C	T	52526285	2	4	61	1	0	0	0	0	0	0	0	1	10463	883	31	1		1	NISCH	3	52526285	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108810	52526285	145496145	2508	10493										
PBRM1	55193	broad.mit.edu	37	chr3	52702601	52702601	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactcttccatttttagtttCtgttggattttcatcaagtc	5	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52702601C>T	ENST00000296302.7	-	3	298	c.297G>A	c.(295-297)caG>caA	p.Q99Q	PBRM1_ENST00000409767.1_Silent_p.Q99Q|PBRM1_ENST00000409057.1_Silent_p.Q99Q|PBRM1_ENST00000356770.4_Silent_p.Q99Q|PBRM1_ENST00000394830.3_Silent_p.Q99Q|PBRM1_ENST00000409114.3_Silent_p.Q99Q|PBRM1_ENST00000410007.1_Silent_p.Q99Q|PBRM1_ENST00000337303.4_Silent_p.Q99Q			Q86U86	PB1_HUMAN	polybromo 1	99	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Q99Q(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTTTAGTTTCTGTTGGATTT	0.303			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																		Rec	yes		3	3p21	55193	polybromo 1		E	1	Substitution - coding silent(1)	large_intestine(1)	3											79	72	75					3																	52702601		2203	4298	6501	52677641	SO:0001819	synonymous_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.297G>A	3.37:g.52702601C>T			52677641	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																					0.303	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52702601	C	T	52702601	2	4	61	1	0	0	0	0	0	0	0	1	11522	912	32	3		3	PBRM1	3	52702601	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	176316	52702601	145319829	2509	10494										
NEK4	6787	broad.mit.edu	37	chr3	52799932	52799932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatccgataaactaaagAattcatatcttttgcattga	4	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52799932A>G	ENST00000233027.5	-	4	839	c.637T>C	c.(637-639)Tct>Cct	p.S213P	NEK4_ENST00000383721.4_Missense_Mutation_p.S213P|NEK4_ENST00000535191.1_Missense_Mutation_p.S124P	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.S213P(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TAAACTAAAGAATTCATATCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	82	81					3																	52799932		2203	4299	6502	52774972	SO:0001583	missense	6787			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.637T>C	3.37:g.52799932A>G	ENSP00000233027:p.Ser213Pro		52774972	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816683	0.90790	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79028	0.4377	L	0.53617	1.68	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.91635	0.999;0.994;0.996	T	0.80241	-0.1464	10	0.62326	D	0.03	.	16.2813	0.82687	1.0:0.0:0.0:0.0	.	124;213;213	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	P	213;124;213;124	ENSP00000233027:S213P;ENSP00000437703:S124P;ENSP00000373227:S213P;ENSP00000419666:S124P	ENSP00000233027:S213P	S	-	1	0	NEK4	52774972	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.244000	0.73946	0.533000	0.62120	TCT		0.328	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		G	52799932	A	G	52799932	3	3	61	1	0	0	0	0	1	0	0	0	10357	246	9	4	1940	4	NEK4	3	52799932	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	97331	52799932	145222498	2510	10495										
ITIH1	3697	broad.mit.edu	37	chr3	52816193	52816193	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaccactttgcccacttCtttgccccccaaaacctgac	3	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52816193C>A	ENST00000273283.2	+	8	864	c.840C>A	c.(838-840)ttC>ttA	p.F280L	ITIH1_ENST00000537050.1_5'UTR|ITIH1_ENST00000487686.1_3'UTR|ITIH1_ENST00000542827.1_Missense_Mutation_p.F280L|ITIH1_ENST00000540715.1_Missense_Mutation_p.F138L	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	280					hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F280L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		TTGCCCACTTCTTTGCCCCCC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	99	100					3																	52816193		2203	4300	6503	52791233	SO:0001583	missense	3697				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.840C>A	3.37:g.52816193C>A	ENSP00000273283:p.Phe280Leu		52791233	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396167	0.83011	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715	T;T;T	0.02737	4.18;4.68;4.55	5.69	4.81	0.61882	.	0.045751	0.85682	N	0.000000	T	0.16041	0.0386	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00179	-1.1950	10	0.87932	D	0	-28.4894	8.0936	0.30816	0.0:0.7611:0.0:0.2389	.	280	P19827	ITIH1_HUMAN	L	280;280;138	ENSP00000442584:F280L;ENSP00000273283:F280L;ENSP00000443973:F138L	ENSP00000273283:F280L	F	+	3	2	ITIH1	52791233	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.965000	0.29319	1.388000	0.46506	0.655000	0.94253	TTC		0.522	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		A	52816193	C	A	52816193	3	1	61	1	0	0	0	0	1	0	0	0	7924	912	32	2	870	2	ITIH1	3	52816193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16261	52816193	145206237	2511	10496										
ITIH1	3697	broad.mit.edu	37	chr3	52823792	52823792	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagttggaagtgactcCtcagaacattacgctgaacc	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52823792C>A	ENST00000273283.2	+	19	2267	c.2243C>A	c.(2242-2244)cCt>cAt	p.P748H	ITIH1_ENST00000537050.1_Missense_Mutation_p.P460H|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Missense_Mutation_p.P606H|ITIH1_ENST00000405128.3_Missense_Mutation_p.P114H	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	748	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.P748H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GAAGTGACTCCTCAGAACATT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											102	95	97					3																	52823792		2203	4300	6503	52798832	SO:0001583	missense	3697				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2243C>A	3.37:g.52823792C>A	ENSP00000273283:p.Pro748His		52798832	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711888	0.68730	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.13657	2.57;2.57;2.57;2.57;2.57	5.63	5.63	0.86233	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.058706	0.64402	D	0.000002	T	0.41328	0.1154	M	0.80746	2.51	0.43321	D	0.995347	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.79784	0.96;0.989;0.993;0.992	T	0.30179	-0.9987	10	0.87932	D	0	-12.4208	16.6082	0.84836	0.0:1.0:0.0:0.0	.	606;114;349;748	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	H	748;606;460;301;114	ENSP00000273283:P748H;ENSP00000443973:P606H;ENSP00000443847:P460H;ENSP00000395836:P301H;ENSP00000384589:P114H	ENSP00000273283:P748H	P	+	2	0	ITIH1	52798832	0.998000	0.40836	0.998000	0.56505	0.349000	0.29174	3.203000	0.51075	2.644000	0.89710	0.563000	0.77884	CCT		0.612	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		A	52823792	C	A	52823792	3	1	61	1	0	0	0	0	1	0	0	0	7924	681	24	2	2317	2	ITIH1	3	52823792	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7599	52823792	145198638	2512	10497										
SFMBT1	51460	broad.mit.edu	37	chr3	52945142	52945142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggcagaattcagtcacccGatctgctgttttcactatct	7	13	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52945142G>A	ENST00000394752.3	-	17	2165	c.1783C>T	c.(1783-1785)Cgg>Tgg	p.R595W	SFMBT1_ENST00000394750.1_Missense_Mutation_p.R595W|SFMBT1_ENST00000358080.2_Missense_Mutation_p.R595W|SFMBT1_ENST00000296295.6_Missense_Mutation_p.R595W	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	595					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)	p.R595W(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		TCAGTCACCCGATCTGCTGTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											156	145	149					3																	52945142		2203	4300	6503	52920182	SO:0001583	missense	51460			AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.1783C>T	3.37:g.52945142G>A	ENSP00000378235:p.Arg595Trp		52920182	Q402F7|Q96C73|Q9Y4Q9	Missense_Mutation	SNP	ENST00000394752.3	37	CCDS2867.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366111	0.82463	.	.	ENSG00000163935	ENST00000394752;ENST00000358080;ENST00000296295;ENST00000394750	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.87	5.87	0.94306	.	0.064498	0.64402	D	0.000005	T	0.34077	0.0885	L	0.36672	1.1	0.80722	D	1	B;P	0.41131	0.24;0.739	B;B	0.31686	0.068;0.134	T	0.10800	-1.0614	10	0.38643	T	0.18	.	20.206	0.98277	0.0:0.0:1.0:0.0	.	595;595	Q9UHJ3-2;Q9UHJ3	.;SMBT1_HUMAN	W	595	ENSP00000378235:R595W;ENSP00000350789:R595W;ENSP00000296295:R595W;ENSP00000378233:R595W	ENSP00000296295:R595W	R	-	1	2	SFMBT1	52920182	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.476000	0.81055	2.785000	0.95823	0.655000	0.94253	CGG		0.438	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		A	52945142	G	A	52945142	3	1	61	1	0	0	0	0	1	0	0	0	14194	1057	37	1	837	1	SFMBT1	3	52945142	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121350	52945142	145077288	2513	10498										
SFMBT1	51460	broad.mit.edu	37	chr3	52947542	52947542	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcctacacattgaggcagCtcagcaattcttcctttgtt	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52947542C>T	ENST00000394752.3	-	15	1954	c.1572G>A	c.(1570-1572)gaG>gaA	p.E524E	SFMBT1_ENST00000394750.1_Silent_p.E524E|SFMBT1_ENST00000358080.2_Silent_p.E524E|SFMBT1_ENST00000296295.6_Silent_p.E524E	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	524					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)	p.E524E(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		ATTGAGGCAGCTCAGCAATTC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	3											122	117	118					3																	52947542		2203	4300	6503	52922582	SO:0001819	synonymous_variant	51460			AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.1572G>A	3.37:g.52947542C>T			52922582	Q402F7|Q96C73|Q9Y4Q9	Silent	SNP	ENST00000394752.3	37	CCDS2867.1																																																																																				0.418	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		T	52947542	C	T	52947542	2	4	61	1	0	0	0	0	0	0	0	1	14194	796	28	3		3	SFMBT1	3	52947542	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2400	52947542	145074888	2514	10499										
SFMBT1	51460	broad.mit.edu	37	chr3	52977453	52977453	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatgtcacaccagaaatCtgctctccgatcctccccat	5	17	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:52977453C>T	ENST00000394752.3	-	4	662	c.280G>A	c.(280-282)Gat>Aat	p.D94N	SFMBT1_ENST00000394750.1_Missense_Mutation_p.D94N|SFMBT1_ENST00000358080.2_Missense_Mutation_p.D94N|SFMBT1_ENST00000296295.6_Missense_Mutation_p.D94N	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	94					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)	p.D94N(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		CACCAGAAATCTGCTCTCCGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	98	105					3																	52977453		2203	4300	6503	52952493	SO:0001583	missense	51460			AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.280G>A	3.37:g.52977453C>T	ENSP00000378235:p.Asp94Asn		52952493	Q402F7|Q96C73|Q9Y4Q9	Missense_Mutation	SNP	ENST00000394752.3	37	CCDS2867.1	.	.	.	.	.	.	.	.	.	.	C	36	5.890363	0.97074	.	.	ENSG00000163935	ENST00000394752;ENST00000358080;ENST00000296295;ENST00000394750;ENST00000482396;ENST00000483069	T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.98;0.47	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.79845	0.4516	M	0.91459	3.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.83977	0.0330	10	0.72032	D	0.01	.	19.5023	0.95100	0.0:1.0:0.0:0.0	.	94;94	Q9UHJ3-2;Q9UHJ3	.;SMBT1_HUMAN	N	94	ENSP00000378235:D94N;ENSP00000350789:D94N;ENSP00000296295:D94N;ENSP00000378233:D94N;ENSP00000418860:D94N;ENSP00000418950:D94N	ENSP00000296295:D94N	D	-	1	0	SFMBT1	52952493	1.000000	0.71417	0.979000	0.43373	0.998000	0.95712	7.452000	0.80683	2.602000	0.87976	0.650000	0.86243	GAT		0.507	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		T	52977453	C	T	52977453	3	4	61	1	0	0	0	0	1	0	0	0	14194	913	32	3	2392	3	SFMBT1	3	52977453	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29911	52977453	145044977	2515	10500										
CACNA1D	776	broad.mit.edu	37	chr3	53531458	53531458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcactcaataaccccatccGaagagcctgcattagtatag	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:53531458G>A	ENST00000350061.5	+	2	858	c.347G>A	c.(346-348)cGa>cAa	p.R116Q	CACNA1D_ENST00000422281.2_Missense_Mutation_p.R116Q|CACNA1D_ENST00000288139.4_Missense_Mutation_p.R116Q	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	116					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.R116Q(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AACCCCATCCGAAGAGCCTGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	102	98					3																	53531458		2203	4300	6503	53506498	SO:0001583	missense	776			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.347G>A	3.37:g.53531458G>A	ENSP00000288133:p.Arg116Gln		53506498	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	37	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	G	36	5.633503	0.96682	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281	T;T;T	0.76709	-1.04;-1.04;-1.04	5.83	5.83	0.93111	.	0.000000	0.50627	D	0.000117	D	0.90628	0.7061	M	0.88310	2.945	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.91481	0.5204	10	0.87932	D	0	.	20.1166	0.97939	0.0:0.0:1.0:0.0	.	116;116;116	B0FYA3;Q01668;Q01668-2	.;CAC1D_HUMAN;.	Q	116	ENSP00000288133:R116Q;ENSP00000288139:R116Q;ENSP00000409174:R116Q	ENSP00000288139:R116Q	R	+	2	0	CACNA1D	53506498	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.758000	0.94735	0.655000	0.94253	CGA		0.423	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53531458	G	A	53531458	3	1	61	1	0	0	0	0	1	0	0	0	2547	1058	37	1	353	1	CACNA1D	3	53531458	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	554005	53531458	144490972	2516	10501										
ACTR8	93973	broad.mit.edu	37	chr3	53907082	53907082	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtttttcatctcctaatcGaaactggtaaagcagggcag	9	9	2	0	rs201848227		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:53907082G>A	ENST00000335754.3	-	9	1238	c.1138C>T	c.(1138-1140)Cga>Tga	p.R380*	ACTR8_ENST00000482349.1_Nonsense_Mutation_p.R269*|ACTR8_ENST00000231909.7_Nonsense_Mutation_p.R85*|ACTR8_ENST00000488802.1_5'Flank	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	380					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.R85*(1)|p.R380*(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TCTCCTAATCGAAACTGGTAA	0.433													G|||	1	0.000199681	8e-04	0	5008	,	,		20437	0		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(2)	3											77	72	74					3																	53907082		2203	4300	6503	53882122	SO:0001587	stop_gained	93973				CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1138C>T	3.37:g.53907082G>A	ENSP00000336842:p.Arg380*		53882122	B3KSW7|Q8N566|Q9H663	Nonsense_Mutation	SNP	ENST00000335754.3	37	CCDS2875.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	39	7.503650	0.98325	.	.	ENSG00000113812	ENST00000335754;ENST00000482349;ENST00000231909	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0213	18.7629	0.91860	0.0:0.0:1.0:0.0	.	.	.	.	X	380;269;85	.	ENSP00000231909:R85X	R	-	1	2	ACTR8	53882122	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.917000	0.69989	2.941000	0.99782	0.655000	0.94253	CGA		0.433	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		A	53907082	G	A	53907082	4	1	61	1	0	0	0	0	0	1	0	0	217	1066	37	1	756	1	ACTR8	3	53907082	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	375624	53907082	144115348	2517	10502										
ACTR8	93973	broad.mit.edu	37	chr3	53909985	53909985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccttaccgagtattccGatgagacaccccatcctcca	6	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:53909985G>A	ENST00000335754.3	-	7	1001	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	ACTR8_ENST00000482349.1_Missense_Mutation_p.R190W|ACTR8_ENST00000231909.7_Missense_Mutation_p.R51W	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	301					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.R51W(1)|p.R301W(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		CGAGTATTCCGATGAGACACC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	3											172	160	164					3																	53909985		2203	4300	6503	53885025	SO:0001583	missense	93973				CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.901C>T	3.37:g.53909985G>A	ENSP00000336842:p.Arg301Trp		53885025	B3KSW7|Q8N566|Q9H663	Missense_Mutation	SNP	ENST00000335754.3	37	CCDS2875.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.433288	0.83776	.	.	ENSG00000113812	ENST00000335754;ENST00000482349;ENST00000231909	D;D;D	0.97553	-3.5;-3.5;-4.43	5.87	4.02	0.46733	.	0.000000	0.85682	D	0.000000	D	0.97723	0.9253	L	0.59436	1.845	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.97805	1.0247	10	0.66056	D	0.02	.	13.8846	0.63702	0.0:0.0:0.7222:0.2777	.	301;51	Q9H981;Q9H981-3	ARP8_HUMAN;.	W	301;190;51	ENSP00000336842:R301W;ENSP00000419429:R190W;ENSP00000231909:R51W	ENSP00000231909:R51W	R	-	1	2	ACTR8	53885025	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.679000	0.61649	0.870000	0.35726	0.655000	0.94253	CGG		0.448	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		A	53909985	G	A	53909985	3	1	61	1	0	0	0	0	1	0	0	0	217	1057	37	1	1001	1	ACTR8	3	53909985	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2903	53909985	144112445	2518	10503										
CACNA2D3	55799	broad.mit.edu	37	chr3	54786629	54786629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgtcttcccttcaggttCgcatcttcacatacctcatt	5	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:54786629C>T	ENST00000474759.1	+	12	1219	c.1171C>T	c.(1171-1173)Cgc>Tgc	p.R391C	CACNA2D3_ENST00000415676.2_Missense_Mutation_p.R391C|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.R391C|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.R297C	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	391	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R391C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CCTTCAGGTTCGCATCTTCAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											116	119	118					3																	54786629		2173	4263	6436	54761669	SO:0001583	missense	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1171C>T	3.37:g.54786629C>T	ENSP00000419101:p.Arg391Cys		54761669	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182541	0.94885	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	T;T;T;T	0.16196	2.36;2.36;2.36;2.36	6.02	6.02	0.97574	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.56659	0.2000	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66048	-0.6020	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	391	Q8IZS8	CA2D3_HUMAN	C	391;391;391;297;297;296	ENSP00000389506:R391C;ENSP00000419101:R391C;ENSP00000288197:R391C;ENSP00000417279:R297C	ENSP00000288197:R391C	R	+	1	0	CACNA2D3	54761669	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.216000	0.77974	2.865000	0.98341	0.655000	0.94253	CGC		0.512	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54786629	C	T	54786629	3	4	61	1	0	0	0	0	1	0	0	0	2556	884	31	1	1217	1	CACNA2D3	3	54786629	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	876644	54786629	143235801	2519	10504										
CACNA2D3	55799	broad.mit.edu	37	chr3	54872646	54872646	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacagatgtcccagtgaaaGaacttctgaagaccatcccc	8	13	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:54872646G>T	ENST00000474759.1	+	16	1570	c.1522G>T	c.(1522-1524)Gaa>Taa	p.E508*	CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.E508*|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.E508*|CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.E414*	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	508	Cache.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E508*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CCCAGTGAAAGAACTTCTGAA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											161	150	154					3																	54872646		1865	4123	5988	54847686	SO:0001587	stop_gained	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1522G>T	3.37:g.54872646G>T	ENSP00000419101:p.Glu508*		54847686	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	38	7.244420	0.98161	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-8.8092	18.077	0.89430	0.0:0.0:1.0:0.0	.	.	.	.	X	508;508;508;414;414;407	.	ENSP00000288197:E508X	E	+	1	0	CACNA2D3	54847686	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.680000	0.91225	2.717000	0.92951	0.655000	0.94253	GAA		0.408	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54872646	G	T	54872646	4	4	61	1	0	0	0	0	0	1	0	0	2556	943	33	2	1584	2	CACNA2D3	3	54872646	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86017	54872646	143149784	2520	10505										
CACNA2D3	55799	broad.mit.edu	37	chr3	54922006	54922006	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgataaagaattgatccaaGaagtcctttttgacgcggtg	11	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:54922006G>T	ENST00000474759.1	+	24	2125	c.2077G>T	c.(2077-2079)Gaa>Taa	p.E693*	CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.E693*|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.E693*|CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.E599*|CACNA2D3-AS1_ENST00000471265.1_RNA	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	693						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E693*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	ATTGATCCAAGAAGTCCTTTT	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											142	139	140					3																	54922006		1958	4159	6117	54897046	SO:0001587	stop_gained	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2077G>T	3.37:g.54922006G>T	ENSP00000419101:p.Glu693*		54897046	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	38	6.662052	0.97743	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-0.1782	17.8691	0.88806	0.0:0.0:1.0:0.0	.	.	.	.	X	693;693;693;599;599	.	ENSP00000288197:E693X	E	+	1	0	CACNA2D3	54897046	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.505000	0.81655	2.652000	0.90054	0.650000	0.86243	GAA		0.527	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54922006	G	T	54922006	4	4	61	1	0	0	0	0	0	1	0	0	2556	943	33	2	2171	2	CACNA2D3	3	54922006	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49360	54922006	143100424	2521	10506										
CACNA2D3	55799	broad.mit.edu	37	chr3	54933867	54933867	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacatccatccagctcctGgatgaacggaaatctcctgt	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:54933867G>A	ENST00000474759.1	+	27	2469	c.2421G>A	c.(2419-2421)ctG>ctA	p.L807L	CACNA2D3_ENST00000415676.2_Silent_p.L807L|CACNA2D3_ENST00000288197.5_Silent_p.L807L|CACNA2D3_ENST00000490478.1_Silent_p.L713L|CACNA2D3-AS1_ENST00000471265.1_RNA	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	807						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.L807L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	TCCAGCTCCTGGATGAACGGA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	3											76	75	76					3																	54933867		1942	4143	6085	54908907	SO:0001819	synonymous_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2421G>A	3.37:g.54933867G>A			54908907	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																				0.428	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	54933867	G	A	54933867	2	1	61	1	0	0	0	0	0	0	0	1	2556	1335	47	3		3	CACNA2D3	3	54933867	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11861	54933867	143088563	2522	10507										
LRTM1	57408	broad.mit.edu	37	chr3	54958646	54958646	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaatagacatgactgacCtttatagacaaatttctcca	4	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:54958646C>A	ENST00000273286.5	-	2	766	c.604G>T	c.(604-606)Ggg>Tgg	p.G202W	CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Splice_Site_p.G126W|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000490478.1_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	202	LRRCT.					integral component of membrane (GO:0016021)		p.G202W(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		CATGACTGACCTTTATAGACA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											74	78	76					3																	54958646		2203	4300	6503	54933686	SO:0001630	splice_region_variant	57408			AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.604+1G>T	3.37:g.54958646C>A			54933686	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	37	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460950	0.84317	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90133	4.19;-2.62	5.82	5.82	0.92795	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96172	0.8752	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95721	0.8766	9	.	.	.	.	20.0897	0.97814	0.0:1.0:0.0:0.0	.	202	Q9HBL6	LRTM1_HUMAN	W	202;126	ENSP00000273286:G202W;ENSP00000419772:G126W	.	G	-	1	0	LRTM1	54933686	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.295000	0.78780	2.744000	0.94065	0.655000	0.94253	GGG		0.448	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	Missense_Mutation	A	54958646	C	A	54958646	5	1	61	1	0	0	0	0	0	0	1	0	9073	695	24	2	441	2	LRTM1	3	54958646	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24779	54958646	143063784	2523	10508										
CACNA2D3	55799	broad.mit.edu	37	chr3	55052288	55052288	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaatatccagcattcgtCtctgagcgcaccatcaagga	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:55052288C>A	ENST00000474759.1	+	35	2979	c.2931C>A	c.(2929-2931)gtC>gtA	p.V977V	CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000415676.2_Silent_p.V977V|CACNA2D3_ENST00000288197.5_Silent_p.V977V|CACNA2D3_ENST00000490478.1_Silent_p.V883V	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	977						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.V977V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAGCATTCGTCTCTGAGCGCA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	3											88	85	86					3																	55052288		1935	4139	6074	55027328	SO:0001819	synonymous_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2931C>A	3.37:g.55052288C>A			55027328	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																				0.483	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	55052288	C	A	55052288	2	1	61	1	0	0	0	0	0	0	0	1	2556	900	32	2		2	CACNA2D3	3	55052288	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93642	55052288	142970142	2524	10509										
ERC2	26059	broad.mit.edu	37	chr3	55768862	55768862	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccatgacttcttcctgCgtctttttctttttggaggc	10	10	3	1	rs145037081	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:55768862C>T	ENST00000288221.6	-	15	2904	c.2649G>A	c.(2647-2649)acG>acA	p.T883T		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	883						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)		p.T883T(2)		breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CTTCTTCCTGCGTCTTTTTCT	0.458													C|||	8	0.00159744	0.0061	0	5008	,	,		17537	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	3						C		8,3710		0,8,1851	95	87	89		2649	-10.9	0.7	3	dbSNP_134	89	0,8244		0,0,4122	no	coding-synonymous	ERC2	NM_015576.1		0,8,5973	TT,TC,CC		0.0,0.2152,0.0669		883/958	55768862	8,11954	1859	4122	5981	55743902	SO:0001819	synonymous_variant	26059			AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2649G>A	3.37:g.55768862C>T			55743902	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1																																																																																				0.458	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		T	55768862	C	T	55768862	2	4	61	1	0	0	0	0	0	0	0	1	5224	755	27	1		1	ERC2	3	55768862	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	716574	55768862	142253568	2525	10510										
ERC2	26059	broad.mit.edu	37	chr3	55922539	55922539	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttggtggcatccagttcCtgtctggtcttctccagtgc	11	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:55922539C>A	ENST00000288221.6	-	14	2697	c.2442G>T	c.(2440-2442)caG>caT	p.Q814H		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	814						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)		p.Q814H(2)		breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CATCCAGTTCCTGTCTGGTCT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	3											232	238	236					3																	55922539		2096	4220	6316	55897579	SO:0001583	missense	26059			AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2442G>T	3.37:g.55922539C>A	ENSP00000288221:p.Gln814His		55897579	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.11|18.11	3.551290|3.551290	0.65311|0.65311	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.45668|.	0.89|.	5.79|5.79	-0.0473|-0.0473	0.13844|0.13844	.|.	0.119890|.	0.64402|.	D|.	0.000020|.	T|T	0.62612|0.62612	0.2442|0.2442	M|M	0.71581|0.71581	2.175|2.175	0.38584|0.38584	D|D	0.950254|0.950254	D|.	0.62365|.	0.991|.	D|.	0.75484|.	0.986|.	T|T	0.62015|0.62015	-0.6943|-0.6943	10|5	0.72032|.	D|.	0.01|.	-22.705|-22.705	9.2921|9.2921	0.37793|0.37793	0.0:0.3817:0.0:0.6183|0.0:0.3817:0.0:0.6183	.|.	814|.	O15083|.	ERC2_HUMAN|.	H|M	814|461	ENSP00000288221:Q814H|.	ENSP00000288221:Q814H|.	Q|R	-|-	3|2	2|0	ERC2|ERC2	55897579|55897579	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.988000|0.988000	0.76386|0.76386	1.665000|1.665000	0.37449|0.37449	0.048000|0.048000	0.15891|0.15891	0.561000|0.561000	0.74099|0.74099	CAG|AGG		0.517	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	55922539	C	A	55922539	3	1	61	1	0	0	0	0	1	0	0	0	5224	680	24	2	447	2	ERC2	3	55922539	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153677	55922539	142099891	2526	10511										
ERC2	26059	broad.mit.edu	37	chr3	56207482	56207482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagttcctaccttcatttCgatgacagtctggagagcct	8	12	2	2	rs571267313		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:56207482C>T	ENST00000288221.6	-	4	1396	c.1141G>A	c.(1141-1143)Gaa>Aaa	p.E381K		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	381						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)		p.E381K(2)		breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		ACCTTCATTTCGATGACAGTC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	3											86	90	89					3																	56207482		2109	4246	6355	56182522	SO:0001583	missense	26059			AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1141G>A	3.37:g.56207482C>T	ENSP00000288221:p.Glu381Lys		56182522	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	C	32	5.177087	0.94846	.	.	ENSG00000187672	ENST00000288221	T	0.49139	0.79	5.43	5.43	0.79202	.	0.141817	0.64402	D	0.000007	T	0.44664	0.1304	M	0.65975	2.015	0.54753	D	0.999985	P	0.45126	0.851	B	0.28465	0.09	T	0.58244	-0.7670	10	0.72032	D	0.01	-23.7569	19.6011	0.95561	0.0:1.0:0.0:0.0	.	381	O15083	ERC2_HUMAN	K	381	ENSP00000288221:E381K	ENSP00000288221:E381K	E	-	1	0	ERC2	56182522	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.345000	0.79337	2.703000	0.92315	0.557000	0.71058	GAA		0.468	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		T	56207482	C	T	56207482	3	4	61	1	0	0	0	0	1	0	0	0	5224	893	31	1	1778	1	ERC2	3	56207482	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	284943	56207482	141814948	2527	10512										
CCDC66	285331	broad.mit.edu	37	chr3	56651450	56651450	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatattccagcatcagaaaaGtaccctaaacagcttcaaaa	4	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:56651450G>T	ENST00000394672.3	+	14	2224	c.2154G>T	c.(2152-2154)aaG>aaT	p.K718N	CCDC66_ENST00000436465.2_Missense_Mutation_p.K718N|CCDC66_ENST00000326595.7_Missense_Mutation_p.K684N	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	718					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)			p.K601N(1)		breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CATCAGAAAAGTACCCTAAAC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											49	51	50					3																	56651450		2203	4299	6502	56626490	SO:0001583	missense	285331			AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2154G>T	3.37:g.56651450G>T	ENSP00000378167:p.Lys718Asn		56626490	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481597	0.63849	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.34072	1.39;1.38;1.38	5.68	2.8	0.32819	.	0.120472	0.49305	D	0.000153	T	0.48589	0.1508	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	T	0.49409	-0.8943	10	0.72032	D	0.01	-17.298	7.286	0.26340	0.2332:0.1292:0.6376:0.0	.	718	A2RUB6	CCD66_HUMAN	N	718;684;718	ENSP00000378167:K718N;ENSP00000326050:K684N;ENSP00000404320:K718N	ENSP00000326050:K684N	K	+	3	2	CCDC66	56626490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.555000	0.23422	1.409000	0.46915	0.563000	0.77884	AAG		0.358	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		T	56651450	G	T	56651450	3	4	61	1	0	0	0	0	1	0	0	0	2844	1020	36	2	2208	2	CCDC66	3	56651450	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	443968	56651450	141370980	2528	10513										
C3orf63	23272	broad.mit.edu	37	chr3	56681150	56681150	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatttttgaattcctttcGacactgaatcaaagaaaatt	4	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:56681150G>A	ENST00000493960.2	-	14	1625	c.1615C>T	c.(1615-1617)Cga>Tga	p.R539*	FAM208A_ENST00000355628.5_Nonsense_Mutation_p.R539*|FAM208A_ENST00000431842.2_Nonsense_Mutation_p.R143*	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	539							poly(A) RNA binding (GO:0044822)	p.R143*(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						AATTCCTTTCGACACTGAATC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											43	47	45					3																	56681150		2197	4296	6493	56656190	SO:0001587	stop_gained	23272			AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1615C>T	3.37:g.56681150G>A	ENSP00000417509:p.Arg539*		56656190	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Nonsense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	39	7.642696	0.98406	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	.	.	.	5.38	3.49	0.39957	.	0.000000	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4267	14.0096	0.64488	0.0:0.0:0.7156:0.2844	.	.	.	.	X	143;539;539	.	ENSP00000347845:R539X	R	-	1	2	C3orf63	56656190	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.955000	0.49121	0.741000	0.32674	0.655000	0.94253	CGA		0.348	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		A	56681150	G	A	56681150	4	1	61	1	0	0	0	0	0	1	0	0	2245	1066	37	1	3501	1	C3orf63	3	56681150	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29700	56681150	141341280	2529	10514										
IL17RD	54756	broad.mit.edu	37	chr3	57132039	57132039	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggaggatggaagggaacGaactgcttttcgaaccagtc	15	7	0	0	rs200249733		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57132039G>A	ENST00000296318.7	-	12	1780	c.1692C>T	c.(1690-1692)ttC>ttT	p.F564F	IL17RD_ENST00000320057.5_Silent_p.F420F|IL17RD_ENST00000463523.1_Silent_p.F420F|IL17RD_ENST00000427856.2_Silent_p.F540F	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	564					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.F420F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		GGAAGGGAACGAACTGCTTTT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											79	75	76					3																	57132039		2203	4300	6503	57107079	SO:0001819	synonymous_variant	54756			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.1692C>T	3.37:g.57132039G>A			57107079	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	37	CCDS2880.2																																																																																				0.527	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		A	57132039	G	A	57132039	2	1	61	1	0	0	0	0	0	0	0	1	7663	1049	37	1		1	IL17RD	3	57132039	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	450889	57132039	140890391	2530	10515										
IL17RD	54756	broad.mit.edu	37	chr3	57137148	57137148	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcataatgcatcacttttCttgttgtgttagtgtcatcc	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57137148C>A	ENST00000296318.7	-	9	927	c.839G>T	c.(838-840)aGa>aTa	p.R280I	IL17RD_ENST00000320057.5_Missense_Mutation_p.R136I|IL17RD_ENST00000463523.1_Missense_Mutation_p.R136I|IL17RD_ENST00000427856.2_Missense_Mutation_p.R256I	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	280					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R136I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		CATCACTTTTCTTGTTGTGTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											133	118	123					3																	57137148		2203	4299	6502	57112188	SO:0001583	missense	54756			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.839G>T	3.37:g.57137148C>A	ENSP00000296318:p.Arg280Ile		57112188	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	C	21.4	4.137342	0.77775	.	.	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.14391	2.51;2.54;2.53;2.54	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.29908	0.895	0.80722	D	1	D;P;P	0.53619	0.961;0.933;0.859	P;B;B	0.47744	0.556;0.312;0.428	T	0.00431	-1.1743	10	0.72032	D	0.01	-16.757	19.3887	0.94570	0.0:1.0:0.0:0.0	.	136;280;256	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	I	280;136;256;136	ENSP00000296318:R280I;ENSP00000322250:R136I;ENSP00000399209:R256I;ENSP00000417516:R136I	ENSP00000296318:R280I	R	-	2	0	IL17RD	57112188	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.342000	0.65970	2.826000	0.97356	0.655000	0.94253	AGA		0.353	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		A	57137148	C	A	57137148	3	1	61	1	0	0	0	0	1	0	0	0	7663	913	32	2	1400	2	IL17RD	3	57137148	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5109	57137148	140885282	2531	10516										
HESX1	8820	broad.mit.edu	37	chr3	57232312	57232312	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagttttgcacgccgattTtgaaaccaaatctaaagtta	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57232312T>G	ENST00000295934.3	-	4	507	c.471A>C	c.(469-471)caA>caC	p.Q157H	HESX1_ENST00000473921.1_Missense_Mutation_p.Q123H	NM_003865.2	NP_003856.1	Q9UBX0	HESX1_HUMAN	HESX homeobox 1	157					brain development (GO:0007420)|forebrain morphogenesis (GO:0048853)|negative regulation of transcription, DNA-templated (GO:0045892)|nose development (GO:0043584)|otic vesicle formation (GO:0030916)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.Q157H(1)		large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0109)|Kidney(284;0.0126)		CACGCCGATTTTGAAACCAAA	0.284																																					Esophageal Squamous(84;267 1272 9034 48993 52677)											1	Substitution - Missense(1)	large_intestine(1)	3											53	52	52					3																	57232312		2202	4299	6501	57207352	SO:0001583	missense	8820			AF059734	CCDS2881.1	3p14.3	2014-06-16	2007-02-16		ENSG00000163666	ENSG00000163666		"Homeoboxes / PRD class"	4877	protein-coding gene	gene with protein product		601802	"homeobox, ES cell expressed 1"			9373136, 9620767, 7876132	Standard	NM_003865		Approved	RPX, ANF	uc003din.4	Q9UBX0	OTTHUMG00000158597	ENST00000295934.3:c.471A>C	3.37:g.57232312T>G	ENSP00000295934:p.Gln157His		57207352	Q52LC5|Q99667	Missense_Mutation	SNP	ENST00000295934.3	37	CCDS2881.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.040891	0.55003	.	.	ENSG00000163666	ENST00000295934;ENST00000473921	D;D	0.97688	-4.49;-3.46	5.25	2.86	0.33363	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99202	0.9723	H	0.99659	4.685	0.49051	D	0.999744	D	0.89917	1.0	D	0.91635	0.999	D	0.97631	1.0142	10	0.87932	D	0	-17.868	7.5918	0.28025	0.0:0.2661:0.0:0.7339	.	157	Q9UBX0	HESX1_HUMAN	H	157;123	ENSP00000295934:Q157H;ENSP00000418918:Q123H	ENSP00000295934:Q157H	Q	-	3	2	HESX1	57207352	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.455000	0.35190	0.956000	0.37904	0.397000	0.26171	CAA		0.284	HESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351430.2			G	57232312	T	G	57232312	3	3	61	1	0	0	0	0	1	0	0	0	7093	1838	64	4	90	4	HESX1	3	57232312	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	95164	57232312	140790118	2532	10517										
HESX1	8820	broad.mit.edu	37	chr3	57232884	57232884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagtaattttcatatttcGaagctctttcttctggcatt	5	7	4	0	rs149663188		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57232884G>A	ENST00000295934.3	-	2	290	c.254C>T	c.(253-255)tCg>tTg	p.S85L	HESX1_ENST00000473921.1_Missense_Mutation_p.S85L	NM_003865.2	NP_003856.1	Q9UBX0	HESX1_HUMAN	HESX homeobox 1	85					brain development (GO:0007420)|forebrain morphogenesis (GO:0048853)|negative regulation of transcription, DNA-templated (GO:0045892)|nose development (GO:0043584)|otic vesicle formation (GO:0030916)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.S85L(1)		large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0109)|Kidney(284;0.0126)		TTCATATTTCGAAGCTCTTTC	0.418																																					Esophageal Squamous(84;267 1272 9034 48993 52677)											1	Substitution - Missense(1)	large_intestine(1)	3						A	LEU/SER	0,4406		0,0,2203	209	234	226		254	-3.7	0	3	dbSNP_134	226	1,8599	1.2+/-3.3	0,1,4299	no	missense	HESX1	NM_003865.2	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	85/186	57232884	1,13005	2203	4300	6503	57207924	SO:0001583	missense	8820			AF059734	CCDS2881.1	3p14.3	2014-06-16	2007-02-16		ENSG00000163666	ENSG00000163666		"Homeoboxes / PRD class"	4877	protein-coding gene	gene with protein product		601802	"homeobox, ES cell expressed 1"			9373136, 9620767, 7876132	Standard	NM_003865		Approved	RPX, ANF	uc003din.4	Q9UBX0	OTTHUMG00000158597	ENST00000295934.3:c.254C>T	3.37:g.57232884G>A	ENSP00000295934:p.Ser85Leu		57207924	Q52LC5|Q99667	Missense_Mutation	SNP	ENST00000295934.3	37	CCDS2881.1	.	.	.	.	.	.	.	.	.	.	g	5.828	0.336984	0.11013	0.0	1.16E-4	ENSG00000163666	ENST00000295934;ENST00000473921;ENST00000495160	D;D;T	0.93547	-3.24;-3.02;-1.44	5.74	-3.71	0.04424	.	1.034790	0.07635	N	0.929317	T	0.74680	0.3748	N	0.00483	-1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65965	-0.6040	10	0.22706	T	0.39	2.5002	7.8608	0.29509	0.5948:0.1043:0.3008:0.0	.	85	Q9UBX0	HESX1_HUMAN	L	85	ENSP00000295934:S85L;ENSP00000418918:S85L;ENSP00000419615:S85L	ENSP00000295934:S85L	S	-	2	0	HESX1	57207924	0.007000	0.16637	0.000000	0.03702	0.723000	0.41478	0.662000	0.25038	-0.964000	0.03595	-1.309000	0.01313	TCG		0.418	HESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351430.2			A	57232884	G	A	57232884	3	1	61	1	0	0	0	0	1	0	0	0	7093	1059	37	1	315	1	HESX1	3	57232884	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	572	57232884	140789546	2533	10518										
APPL1	26060	broad.mit.edu	37	chr3	57302510	57302510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaataaacaaaaacagattGaaaaggtatacagtcctaat	5	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57302510G>T	ENST00000288266.3	+	21	2125	c.1978G>T	c.(1978-1980)Gaa>Taa	p.E660*	ASB14_ENST00000487349.1_3'UTR|ASB14_ENST00000389601.3_3'UTR	NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	660					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.E660*(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		aaaacagattgaaaAGGTATA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											99	95	97					3																	57302510		2201	4300	6501	57277550	SO:0001587	stop_gained	26060			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1978G>T	3.37:g.57302510G>T	ENSP00000288266:p.Glu660*		57277550	Q9P2B9	Nonsense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	G	36	5.936004	0.97122	.	.	ENSG00000157500	ENST00000288266	.	.	.	3.86	3.86	0.44501	.	0.316340	0.31648	N	0.007282	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	13.5986	0.62004	0.0:0.0:1.0:0.0	.	.	.	.	X	660	.	ENSP00000288266:E660X	E	+	1	0	APPL1	57277550	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	4.233000	0.58651	2.428000	0.82296	0.557000	0.71058	GAA		0.338	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57302510	G	T	57302510	4	4	61	1	0	0	0	0	0	1	0	0	817	1291	45	2	2060	2	APPL1	3	57302510	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69626	57302510	140719920	2534	10519										
APPL1	26060	broad.mit.edu	37	chr3	57303587	57303587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacttggaagaacaaagtCggttgatagctgcttccagt	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57303587C>T	ENST00000288266.3	+	22	2149	c.2002C>T	c.(2002-2004)Cgg>Tgg	p.R668W	ASB14_ENST00000487349.1_3'UTR|ASB14_ENST00000389601.3_3'UTR	NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	668					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.R668W(2)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGAACAAAGTCGGTTGATAGC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	3											109	104	106					3																	57303587		2203	4300	6503	57278627	SO:0001583	missense	26060			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.2002C>T	3.37:g.57303587C>T	ENSP00000288266:p.Arg668Trp		57278627	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862194	0.71949	.	.	ENSG00000157500	ENST00000288266	T	0.11495	2.77	5.65	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.23806	0.0576	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.02009	-1.1230	10	0.87932	D	0	.	16.1283	0.81408	0.1347:0.8653:0.0:0.0	.	668	Q9UKG1	DP13A_HUMAN	W	668	ENSP00000288266:R668W	ENSP00000288266:R668W	R	+	1	2	APPL1	57278627	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.679000	0.68160	1.468000	0.48064	0.563000	0.77884	CGG		0.423	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57303587	C	T	57303587	3	4	61	1	0	0	0	0	1	0	0	0	817	875	31	1	2088	1	APPL1	3	57303587	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1077	57303587	140718843	2535	10520										
DNAH12	201625	broad.mit.edu	37	chr3	57494253	57494253	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctagaatgccaaggattaGaataatctaggcctctggaa	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57494253G>T	ENST00000351747.2	-	7	737	c.557C>A	c.(556-558)tCt>tAt	p.S186Y	DNAH12_ENST00000311202.6_Missense_Mutation_p.S186Y|DNAH12_ENST00000389536.4_Missense_Mutation_p.S186Y	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	186	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S186Y(2)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						CCAAGGATTAGAATAATCTAG	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	3											42	43	43					3																	57494253		2203	4299	6502	57469293	SO:0001583	missense	201625			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.557C>A	3.37:g.57494253G>T	ENSP00000295937:p.Ser186Tyr		57469293	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		.	.	.	.	.	.	.	.	.	.	G	15.75	2.925599	0.52759	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.24908	2.0;1.83;3.41;2.87	5.1	5.1	0.69264	.	0.082707	0.47093	D	0.000248	T	0.48077	0.1480	M	0.64997	1.995	0.80722	D	1	D;D	0.71674	0.998;0.994	D;P	0.63192	0.912;0.87	T	0.49916	-0.8888	10	0.72032	D	0.01	.	18.5128	0.90923	0.0:0.0:1.0:0.0	.	186;186	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	Y	186	ENSP00000295937:S186Y;ENSP00000418137:S186Y;ENSP00000374187:S186Y;ENSP00000312554:S186Y	ENSP00000312554:S186Y	S	-	2	0	DNAH12	57469293	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.963000	0.76055	2.370000	0.80446	0.585000	0.79938	TCT		0.318	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57494253	G	T	57494253	3	4	61	1	0	0	0	0	1	0	0	0	4611	942	33	2	8976	2	DNAH12	3	57494253	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190666	57494253	140528177	2536	10521										
ARF4	378	broad.mit.edu	37	chr3	57561286	57561286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacttactgttctgttacGaagagactgaagccctagtt	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57561286G>A	ENST00000303436.6	-	5	712	c.445C>T	c.(445-447)Cgt>Tgt	p.R149C	ARF4_ENST00000489843.1_Missense_Mutation_p.R40C|ARF4_ENST00000496292.1_Missense_Mutation_p.R122C	NM_001660.3	NP_001651.1	P18085	ARF4_HUMAN	ADP-ribosylation factor 4	149					activation of phospholipase D activity (GO:0031584)|brain development (GO:0007420)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein transport (GO:0015031)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to axon injury (GO:0048678)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	epidermal growth factor receptor binding (GO:0005154)|GTP binding (GO:0005525)	p.R149C(1)		large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)		GTTCTGTTACGAAGAGACTGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	98	102					3																	57561286		2203	4300	6503	57536326	SO:0001583	missense	378			M36341	CCDS2884.1	3p21.2-p21.1	2007-03-19			ENSG00000168374	ENSG00000168374		"ADP-ribosylation factors"	655	protein-coding gene	gene with protein product		601177	"ADP-ribosylation factor 2"	ARF2		2107548	Standard	NM_001660		Approved		uc003dix.4	P18085	OTTHUMG00000158601	ENST00000303436.6:c.445C>T	3.37:g.57561286G>A	ENSP00000306010:p.Arg149Cys		57536326	B2R7J7|P21371	Missense_Mutation	SNP	ENST00000303436.6	37	CCDS2884.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.142880	0.77888	.	.	ENSG00000168374	ENST00000303436;ENST00000496292	D;D	0.83250	-1.7;-1.7	5.75	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.91222	0.7234	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;0.998	P;P	0.62435	0.902;0.87	D	0.92479	0.5991	10	0.59425	D	0.04	-1.2058	14.6249	0.68614	0.0696:0.0:0.9304:0.0	.	122;149	C9JAK5;P18085	.;ARF4_HUMAN	C	149;122	ENSP00000306010:R149C;ENSP00000417501:R122C	ENSP00000306010:R149C	R	-	1	0	ARF4	57536326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.677000	0.54619	1.436000	0.47453	0.591000	0.81541	CGT		0.353	ARF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351443.1	NM_001660		A	57561286	G	A	57561286	3	1	61	1	0	0	0	0	1	0	0	0	846	1058	37	1	105	1	ARF4	3	57561286	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67033	57561286	140461144	2537	10522										
FAM116A	201627	broad.mit.edu	37	chr3	57627404	57627404	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtttaaggtctcctattcGaataatgtgtggccagtgct	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57627404G>A	ENST00000311128.5	-	12	1178	c.1108C>T	c.(1108-1110)Cga>Tga	p.R370*	RP11-755B10.2_ENST00000470427.1_RNA	NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	370					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R370*(1)									TCTCCTATTCGAATAATGTGT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											141	135	137					3																	57627404		2203	4300	6503	57602444	SO:0001587	stop_gained	201627			AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.1108C>T	3.37:g.57627404G>A	ENSP00000311401:p.Arg370*		57602444	Q7Z5T4|Q8N235|Q8TEG8	Nonsense_Mutation	SNP	ENST00000311128.5	37	CCDS33773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.0|23.0	4.368338|4.368338	0.82463|0.82463	.|.	.|.	ENSG00000174839|ENSG00000174839	ENST00000311128|ENST00000477344	.|.	.|.	.|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.67599	.|0.2910	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70088	.|-0.4968	.|3	0.02654|.	T|.	1|.	-14.2435|-14.2435	15.6037|15.6037	0.76646|0.76646	0.0:0.0:0.8619:0.1381|0.0:0.0:0.8619:0.1381	.|.	.|.	.|.	.|.	X|L	370|138	.|.	ENSP00000311401:R370X|.	R|S	-|-	1|2	2|0	FAM116A|FAM116A	57602444|57602444	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.386000|7.386000	0.79775|0.79775	2.618000|2.618000	0.88619|0.88619	0.585000|0.585000	0.79938|0.79938	CGA|TCG		0.358	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678		A	57627404	G	A	57627404	4	1	61	1	0	0	0	0	0	1	0	0	5423	1066	37	1	754	1	FAM116A	3	57627404	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66118	57627404	140395026	2538	10523										
SLMAP	7871	broad.mit.edu	37	chr3	57898130	57898130	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattgcagaggttacacatCgatactgagaatctccggga	10	9	1	2	rs79652350		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:57898130C>T	ENST00000428312.1	+	18	1765	c.1671C>T	c.(1669-1671)atC>atT	p.I557I	SLMAP_ENST00000295952.3_Silent_p.I540I|SLMAP_ENST00000495364.1_Silent_p.I91I|SLMAP_ENST00000442599.2_Silent_p.I25I|SLMAP_ENST00000494088.1_Silent_p.I50I|SLMAP_ENST00000295951.3_Silent_p.I540I|SLMAP_ENST00000472546.1_3'UTR|SLMAP_ENST00000449503.2_Silent_p.I519I|SLMAP_ENST00000416870.1_Silent_p.I50I			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	557					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)		p.I540I(1)		endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GGTTACACATCGATACTGAGA	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		20550	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											82	84	83					3																	57898130		2203	4300	6503	57873170	SO:0001819	synonymous_variant	7871			AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.1671C>T	3.37:g.57898130C>T			57873170	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37		1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	7.778|7.778	0.708994|0.708994	0.15239|0.15239	.|.	.|.	ENSG00000163681|ENSG00000163681	ENST00000416658;ENST00000438794|ENST00000417128	.|.	.|.	.|.	4.97|4.97	-4.05|-4.05	0.03998|0.03998	.|.	.|.	.|.	.|.	.|.	.|T	.|0.39384	.|0.1076	.|.	.|.	.|.	0.53005|0.53005	D|D	0.999963|0.999963	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.35226	.|-0.9797	.|4	.|.	.|.	.|.	1.0619|1.0619	3.0825|3.0825	0.06267|0.06267	0.1168:0.1417:0.4007:0.3408|0.1168:0.1417:0.4007:0.3408	.|.	.|.	.|.	.|.	X|L	165;95|141	.|.	.|.	R|S	+|+	1|2	2|0	SLMAP|SLMAP	57873170|57873170	0.091000|0.091000	0.21658|0.21658	0.808000|0.808000	0.32385|0.32385	0.872000|0.872000	0.50106|0.50106	-0.778000|-0.778000	0.04664|0.04664	-0.620000|-0.620000	0.05641|0.05641	-0.339000|-0.339000	0.08088|0.08088	CGA|TCG		0.398	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		T	57898130	C	T	57898130	2	4	61	1	0	0	0	0	0	0	0	1	14786	874	31	1		1	SLMAP	3	57898130	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	270726	57898130	140124300	2539	10524										
FLNB	2317	broad.mit.edu	37	chr3	58067371	58067371	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaggtcatcactcctgaaGaaatcattcacccggatgtg	8	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58067371G>T	ENST00000295956.4	+	4	820	c.655G>T	c.(655-657)Gaa>Taa	p.E219*	FLNB_ENST00000490882.1_Nonsense_Mutation_p.E219*|FLNB_ENST00000429972.2_Nonsense_Mutation_p.E219*|FLNB_ENST00000358537.3_Nonsense_Mutation_p.E219*|FLNB_ENST00000357272.4_Nonsense_Mutation_p.E219*|FLNB_ENST00000348383.5_Nonsense_Mutation_p.E219*|FLNB_ENST00000419752.2_Nonsense_Mutation_p.E50*|FLNB_ENST00000493452.1_Nonsense_Mutation_p.E50*	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	219	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.E219*(2)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CACTCCTGAAGAAATCATTCA	0.478																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											138	130	133					3																	58067371		2203	4300	6503	58042411	SO:0001587	stop_gained	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.655G>T	3.37:g.58067371G>T	ENSP00000295956:p.Glu219*		58042411	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Nonsense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	41	8.760785	0.98943	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	.	.	.	5.86	5.86	0.93980	.	0.086938	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5632	0.99335	0.0:0.0:1.0:0.0	.	.	.	.	X	219;219;219;219;219;219;50;50	.	ENSP00000295956:E219X	E	+	1	0	FLNB	58042411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.759000	0.98931	2.937000	0.99478	0.650000	0.86243	GAA		0.478	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58067371	G	T	58067371	4	4	61	1	0	0	0	0	0	1	0	0	5953	943	33	2	669	2	FLNB	3	58067371	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	169241	58067371	139955059	2540	10525										
FLNB	2317	broad.mit.edu	37	chr3	58094284	58094284	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctggaaaagctcccttaAagatatttgctcaggtaaat	8	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58094284A>C	ENST00000295956.4	+	13	2206	c.2041A>C	c.(2041-2043)Aag>Cag	p.K681Q	FLNB_ENST00000490882.1_Missense_Mutation_p.K681Q|FLNB_ENST00000429972.2_Missense_Mutation_p.K681Q|FLNB_ENST00000358537.3_Missense_Mutation_p.K681Q|FLNB_ENST00000357272.4_Missense_Mutation_p.K681Q|FLNB_ENST00000348383.5_Missense_Mutation_p.K681Q|FLNB_ENST00000419752.2_Missense_Mutation_p.K512Q|FLNB_ENST00000493452.1_Missense_Mutation_p.K512Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	681					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.K681Q(1)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		AGCTCCCTTAAAGATATTTGC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	67	67					3																	58094284		2203	4300	6503	58069324	SO:0001583	missense	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2041A>C	3.37:g.58094284A>C	ENSP00000295956:p.Lys681Gln		58069324	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.422169	0.83559	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.56	5.56	0.83823	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.087292	0.85682	D	0.000000	D	0.87597	0.6217	L	0.46947	1.48	0.58432	D	0.999999	D;B;D;B;D;D	0.64830	0.987;0.164;0.994;0.041;0.994;0.994	P;B;D;B;D;D	0.66979	0.772;0.196;0.948;0.138;0.948;0.948	D	0.86925	0.2069	10	0.40728	T	0.16	.	16.002	0.80301	1.0:0.0:0.0:0.0	.	681;681;512;512;681;681	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	681;681;681;681;681;681;512;512	ENSP00000295956:K681Q;ENSP00000420213:K681Q;ENSP00000351339:K681Q;ENSP00000415599:K681Q;ENSP00000232447:K681Q;ENSP00000349819:K681Q;ENSP00000418510:K512Q;ENSP00000414532:K512Q	ENSP00000295956:K681Q	K	+	1	0	FLNB	58069324	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.468000	0.80943	2.241000	0.73720	0.533000	0.62120	AAG		0.483	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		C	58094284	A	C	58094284	3	2	61	1	0	0	0	0	1	0	0	0	5953	15	1	4	2091	4	FLNB	3	58094284	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	26913	58094284	139928146	2541	10526										
DNASE1L3	1776	broad.mit.edu	37	chr3	58186823	58186823	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgcagggggataatcacGaagtctttgacagctgagaa	14	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58186823G>A	ENST00000394549.2	-	5	763	c.447C>T	c.(445-447)ttC>ttT	p.F149F	DNASE1L3_ENST00000318316.3_Silent_p.F149F|DNASE1L3_ENST00000483681.1_Silent_p.F149F|DNASE1L3_ENST00000486455.1_Silent_p.F119F	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	149					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)	p.F149F(1)		breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		GGATAATCACGAAGTCTTTGA	0.552																																					Esophageal Squamous(96;1069 1424 4841 43466 52325)											1	Substitution - coding silent(1)	large_intestine(1)	3											116	119	118					3																	58186823		2203	4300	6503	58161863	SO:0001819	synonymous_variant	1776			AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"DNase gamma"	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.447C>T	3.37:g.58186823G>A			58161863	B2R8B1|B7Z707|O75803	Silent	SNP	ENST00000394549.2	37	CCDS2886.1																																																																																				0.552	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944		A	58186823	G	A	58186823	2	1	61	1	0	0	0	0	0	0	0	1	4674	1049	37	1		1	DNASE1L3	3	58186823	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92539	58186823	139835607	2542	10527										
RPP14	11102	broad.mit.edu	37	chr3	58303179	58303179	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctaggtttctccatttCttcttgcattatctggtaat	5	9	6	0	rs570810632		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58303179C>A	ENST00000445193.3	+	6	742	c.331C>A	c.(331-333)Ctt>Att	p.L111I	RPP14_ENST00000477305.1_3'UTR|RPP14_ENST00000528153.1_5'Flank|RPP14_ENST00000466547.1_Missense_Mutation_p.L111I|RPP14_ENST00000295959.5_Missense_Mutation_p.L111I	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	111					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)	p.L111I(2)		large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		TTCTCCATTTCTTCTTGCATT	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	3											206	188	194					3																	58303179		2203	4300	6503	58278219	SO:0001583	missense	11102			AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"ribonuclease P 14kDa subunit"			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.331C>A	3.37:g.58303179C>A	ENSP00000412894:p.Leu111Ile		58278219	Q53X97	Missense_Mutation	SNP	ENST00000445193.3	37	CCDS2888.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.853569	0.91355	.	.	ENSG00000163684	ENST00000445193;ENST00000295959;ENST00000466547	.	.	.	5.91	5.91	0.95273	.	0.197721	0.43416	D	0.000566	T	0.79476	0.4452	M	0.72118	2.19	0.47819	D	0.999523	D	0.76494	0.999	D	0.87578	0.998	T	0.79640	-0.1719	9	0.62326	D	0.03	-0.8571	18.4816	0.90813	0.0:1.0:0.0:0.0	.	111	O95059	RPP14_HUMAN	I	111	.	ENSP00000295959:L111I	L	+	1	0	RPP14	58278219	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.498000	0.60373	2.804000	0.96469	0.650000	0.86243	CTT		0.383	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042		A	58303179	C	A	58303179	3	1	61	1	0	0	0	0	1	0	0	0	13646	913	32	2	349	2	RPP14	3	58303179	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116356	58303179	139719251	2543	10528										
PXK	54899	broad.mit.edu	37	chr3	58368363	58368363	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatcacaacaaatcatatCttgtctaattgtgagctggt	8	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58368363C>A	ENST00000356151.2	+	4	433	c.324C>A	c.(322-324)atC>atA	p.I108I	PXK_ENST00000479241.1_Silent_p.I91I|PXK_ENST00000302779.5_Silent_p.I91I|PXK_ENST00000484288.1_Silent_p.I108I|PXK_ENST00000383715.4_Silent_p.I91I|PXK_ENST00000536660.1_Intron|PXK_ENST00000383716.3_Silent_p.I75I|PXK_ENST00000463280.1_Silent_p.I75I	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase									p.I108I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		CAAATCATATCTTGTCTAATT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	3											127	115	119					3																	58368363		2203	4300	6503	58343403	SO:0001819	synonymous_variant	54899			AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.324C>A	3.37:g.58368363C>A			58343403		Silent	SNP	ENST00000356151.2	37	CCDS2889.1																																																																																				0.378	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		A	58368363	C	A	58368363	2	1	61	1	0	0	0	0	0	0	0	1	12886	903	32	2		2	PXK	3	58368363	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65184	58368363	139654067	2544	10529										
PXK	54899	broad.mit.edu	37	chr3	58381397	58381397	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaaaggcaaaaccaaaaGacccatttctaaagaagtac	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58381397G>T	ENST00000356151.2	+	9	842	c.733G>T	c.(733-735)Gac>Tac	p.D245Y	PXK_ENST00000479241.1_Missense_Mutation_p.D228Y|PXK_ENST00000302779.5_Missense_Mutation_p.D228Y|PXK_ENST00000484288.1_Missense_Mutation_p.D245Y|PXK_ENST00000383715.4_Missense_Mutation_p.D228Y|PXK_ENST00000536660.1_Missense_Mutation_p.D108Y|PXK_ENST00000383716.3_Missense_Mutation_p.D212Y|PXK_ENST00000463280.1_Missense_Mutation_p.D212Y	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase									p.D245Y(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		AAAACCAAAAGACCCATTTCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	80	79					3																	58381397		2203	4300	6503	58356437	SO:0001583	missense	54899			AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.733G>T	3.37:g.58381397G>T	ENSP00000348472:p.Asp245Tyr		58356437		Missense_Mutation	SNP	ENST00000356151.2	37	CCDS2889.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612730	0.46631	.	.	ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000536750	T;T;T;T;T;T;T;T	0.32988	2.2;2.19;2.2;1.46;1.45;1.46;1.43;2.2	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.248571	0.47455	D	0.000235	T	0.26195	0.0639	L	0.27053	0.805	0.58432	D	0.999999	B;B;B;B;B;B	0.16603	0.002;0.0;0.002;0.018;0.0;0.006	B;B;B;B;B;B	0.17722	0.002;0.001;0.003;0.019;0.001;0.003	T	0.03130	-1.1069	10	0.51188	T	0.08	-17.3108	17.6027	0.88029	0.0:0.0:1.0:0.0	.	212;212;212;245;228;245	E9PD56;Q7Z7A4-6;B4DID9;Q7Z7A4;Q7Z7A4-4;Q7Z7A4-2	.;.;.;PXK_HUMAN;.;.	Y	245;228;212;212;228;245;228;108;108	ENSP00000348472:D245Y;ENSP00000305045:D228Y;ENSP00000373222:D212Y;ENSP00000417903:D212Y;ENSP00000373221:D228Y;ENSP00000417915:D245Y;ENSP00000419049:D228Y;ENSP00000438356:D108Y	ENSP00000305045:D228Y	D	+	1	0	PXK	58356437	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.852000	0.92215	2.675000	0.91044	0.609000	0.83330	GAC		0.438	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		T	58381397	G	T	58381397	3	4	61	1	0	0	0	0	1	0	0	0	12886	942	33	2	767	2	PXK	3	58381397	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13034	58381397	139641033	2545	10530										
PDHB	5162	broad.mit.edu	37	chr3	58413899	58413899	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagcatccaggaaattgaaCgcaggacctaggagaaggaa	14	7	0	2	rs148770511		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58413899C>T	ENST00000302746.6	-	10	984	c.942G>A	c.(940-942)gcG>gcA	p.A314A	PDHB_ENST00000485460.1_Silent_p.A296A|PDHB_ENST00000474765.1_Missense_Mutation_p.V337I|RP11-802O23.3_ENST00000607214.1_RNA	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	314					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)	p.A314A(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	GGAAATTGAACGCAGGACCTA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											60	56	57					3																	58413899		2203	4300	6503	58388939	SO:0001819	synonymous_variant	5162				CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157	ENST00000302746.6:c.942G>A	3.37:g.58413899C>T			58388939	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Silent	SNP	ENST00000302746.6	37	CCDS2890.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.230081	0.39399	.	.	ENSG00000168291	ENST00000474765	D	0.96365	-3.99	6.16	-11.5	0.00074	.	.	.	.	.	D	0.88160	0.6362	.	.	.	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.74417	-0.3672	8	0.44086	T	0.13	-16.7915	0.8393	0.01146	0.2284:0.2793:0.2485:0.2438	.	337	C9J634	.	I	337	ENSP00000418448:V337I	ENSP00000418448:V337I	V	-	1	0	PDHB	58388939	0.109000	0.22037	0.704000	0.30370	0.975000	0.68041	-0.697000	0.05098	-1.742000	0.01342	-1.223000	0.01593	GTT		0.507	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1			T	58413899	C	T	58413899	2	4	61	1	0	0	0	0	0	0	0	1	11697	523	19	1		1	PDHB	3	58413899	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32502	58413899	139608531	2546	10531										
KCTD6	200845	broad.mit.edu	37	chr3	58487211	58487211	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattatcaccaggaagtttCtcttagggtccacctgatgg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58487211C>A	ENST00000355076.6	+	2	1549	c.566C>A	c.(565-567)tCt>tAt	p.S189Y	KCTD6_ENST00000404589.3_Missense_Mutation_p.S189Y|KCTD6_ENST00000490264.1_Missense_Mutation_p.S189Y	NM_153331.3	NP_699162.3	Q8NC69	KCTD6_HUMAN	potassium channel tetramerization domain containing 6	189					protein homooligomerization (GO:0051260)		ankyrin binding (GO:0030506)	p.S189Y(1)		endometrium(1)|large_intestine(2)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(55;0.000177)|Kidney(10;0.00229)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.148)		CAGGAAGTTTCTCTTAGGGTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	81	82					3																	58487211		2203	4300	6503	58462251	SO:0001583	missense	200845			AK074934	CCDS2891.1	3p21.2	2013-06-20	2013-06-20		ENSG00000168301	ENSG00000168301			22235	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 6"			21472142	Standard	NM_153331		Approved	MGC27385, KCASH3	uc003dkj.4	Q8NC69	OTTHUMG00000159161	ENST00000355076.6:c.566C>A	3.37:g.58487211C>A	ENSP00000347188:p.Ser189Tyr		58462251	B3KNI5|Q8NBS6|Q8TCA6	Missense_Mutation	SNP	ENST00000355076.6	37	CCDS2891.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.267046	0.40095	.	.	ENSG00000168301	ENST00000404589;ENST00000490264;ENST00000355076	T;T;T	0.24151	1.87;1.87;1.87	5.45	5.45	0.79879	.	0.053686	0.85682	D	0.000000	T	0.15435	0.0372	N	0.08118	0	0.51482	D	0.999923	B	0.33379	0.41	B	0.25884	0.064	T	0.08617	-1.0713	10	0.52906	T	0.07	.	19.2666	0.93988	0.0:1.0:0.0:0.0	.	189	Q8NC69	KCTD6_HUMAN	Y	189	ENSP00000384948:S189Y;ENSP00000417490:S189Y;ENSP00000347188:S189Y	ENSP00000347188:S189Y	S	+	2	0	KCTD6	58462251	0.980000	0.34600	0.995000	0.50966	0.997000	0.91878	3.227000	0.51262	2.555000	0.86185	0.591000	0.81541	TCT		0.448	KCTD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353591.1	NM_153331		A	58487211	C	A	58487211	3	1	61	1	0	0	0	0	1	0	0	0	8134	913	32	2	572	2	KCTD6	3	58487211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73312	58487211	139535219	2547	10532										
C3orf67	200844	broad.mit.edu	37	chr3	58817444	58817444	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagttccaggtggttgtgtCgtcactgctggtacttatgc	14	8	1	0	rs557149953		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:58817444C>T	ENST00000482387.1	-	10	1864	c.1768G>A	c.(1768-1770)Gac>Aac	p.D590N	RP11-147N17.1_ENST00000493123.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.D464N|RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	590								p.D464N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		GTGGTTGTGTCGTCACTGCTG	0.522													C|||	1	0.000199681	0	0	5008	,	,		19142	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											156	127	137					3																	58817444		2203	4300	6503	58792484	SO:0001583	missense	200844			AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.1768G>A	3.37:g.58817444C>T	ENSP00000417122:p.Asp590Asn		58792484	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.2|29.2	4.984950|4.984950	0.93044|0.93044	.|.	.|.	ENSG00000163689|ENSG00000163689	ENST00000295966;ENST00000482387|ENST00000486145	T;T|.	0.35236|.	1.45;1.32|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77039|0.77039	0.4072|0.4072	M|M	0.71036|0.71036	2.16|2.16	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.74054|0.74054	-0.3788|-0.3788	10|5	0.87932|.	D|.	0|.	-21.984|-21.984	20.3151|20.3151	0.98650|0.98650	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	464;590|.	Q6ZVT6-2;Q6ZVT6|.	.;CC067_HUMAN|.	N|Q	464;590|3	ENSP00000295966:D464N;ENSP00000417122:D590N|.	ENSP00000295966:D464N|.	D|R	-|-	1|2	0|0	C3orf67|C3orf67	58792484|58792484	0.995000|0.995000	0.38212|0.38212	0.976000|0.976000	0.42696|0.42696	0.984000|0.984000	0.73092|0.73092	5.763000|5.763000	0.68818|0.68818	2.809000|2.809000	0.96659|0.96659	0.467000|0.467000	0.42956|0.42956	GAC|CGA		0.522	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		T	58817444	C	T	58817444	3	4	61	1	0	0	0	0	1	0	0	0	2247	884	31	1	317	1	C3orf67	3	58817444	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	330233	58817444	139204986	2548	10533										
PTPRG	5793	broad.mit.edu	37	chr3	62254809	62254809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatgcctgctacactgttCgtcgtttttcaatcagaaat	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62254809C>T	ENST00000474889.1	+	20	3351	c.2974C>T	c.(2974-2976)Cgt>Tgt	p.R992C	PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.R963C	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	992	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R992C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CTACACTGTTCGTCGTTTTTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	95	98					3																	62254809		2203	4300	6503	62229849	SO:0001583	missense	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.2974C>T	3.37:g.62254809C>T	ENSP00000418112:p.Arg992Cys		62229849	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253295	0.80135	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.16073	2.37;2.37	5.82	5.82	0.92795	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.050957	0.85682	D	0.000000	T	0.62171	0.2406	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76727	-0.2853	10	0.87932	D	0	.	20.1143	0.97922	0.0:1.0:0.0:0.0	.	238;963;992	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	C	992;963	ENSP00000418112:R992C;ENSP00000295874:R963C	ENSP00000295874:R963C	R	+	1	0	PTPRG	62229849	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	4.742000	0.62103	2.765000	0.95021	0.650000	0.86243	CGT		0.393	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		T	62254809	C	T	62254809	3	4	61	1	0	0	0	0	1	0	0	0	12839	884	31	1	3052	1	PTPRG	3	62254809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3437365	62254809	135767621	2549	10534										
PTPRG	5793	broad.mit.edu	37	chr3	62262710	62262710	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaacagattacattaatgCttcttatatcatggtgagag	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62262710C>A	ENST00000474889.1	+	25	4000	c.3623C>A	c.(3622-3624)gCt>gAt	p.A1208D	PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000466893.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.A1179D	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1208	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A1208D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TACATTAATGCTTCTTATATC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											157	137	144					3																	62262710		2203	4300	6503	62237750	SO:0001583	missense	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.3623C>A	3.37:g.62262710C>A	ENSP00000418112:p.Ala1208Asp		62237750	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000854	0.93227	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.55413	0.52;0.52	5.72	5.72	0.89469	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.098400	0.64402	D	0.000001	D	0.85575	0.5728	H	0.99261	4.49	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.91030	0.4863	10	0.87932	D	0	.	20.2406	0.98372	0.0:1.0:0.0:0.0	.	454;1179;1208	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	D	1208;1179	ENSP00000418112:A1208D;ENSP00000295874:A1179D	ENSP00000295874:A1179D	A	+	2	0	PTPRG	62237750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.741000	0.84997	2.857000	0.98124	0.650000	0.86243	GCT		0.378	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		A	62262710	C	A	62262710	3	1	61	1	0	0	0	0	1	0	0	0	12839	797	28	2	3721	2	PTPRG	3	62262710	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7901	62262710	135759720	2550	10535										
FEZF2	55079	broad.mit.edu	37	chr3	62355881	62355881	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccctttgccgcaagtggcGcacgtgaaaggcttcttgtc	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62355881G>A	ENST00000283268.3	-	5	1551	c.1257C>T	c.(1255-1257)tgC>tgT	p.C419C	FEZF2_ENST00000475839.1_Silent_p.C419C|PTPRG-AS1_ENST00000490916.1_RNA|FEZF2_ENST00000486811.1_Silent_p.C419C|PTPRG-AS1_ENST00000495542.1_RNA	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	419					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.C419C(2)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		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)		CGCAAGTGGCGCACGTGAAAG	0.522																																					NSCLC(170;1772 2053 12525 15604 23984)											2	Substitution - coding silent(2)	large_intestine(2)	3											256	233	240					3																	62355881		2203	4300	6503	62330921	SO:0001819	synonymous_variant	55079			AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.1257C>T	3.37:g.62355881G>A			62330921	A8K349|Q9BZ91|Q9NWB9	Silent	SNP	ENST00000283268.3	37	CCDS2897.1																																																																																				0.522	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		A	62355881	G	A	62355881	2	1	61	1	0	0	0	0	0	0	0	1	5845	1079	38	1		1	FEZF2	3	62355881	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93171	62355881	135666549	2551	10536										
FEZF2	55079	broad.mit.edu	37	chr3	62357280	62357280	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccgcagactttgcacacGaacggtctggctccggtgtg	13	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62357280G>A	ENST00000283268.3	-	3	1209	c.915C>T	c.(913-915)ttC>ttT	p.F305F	FEZF2_ENST00000475839.1_Silent_p.F305F|PTPRG-AS1_ENST00000490916.1_RNA|FEZF2_ENST00000486811.1_Silent_p.F305F|PTPRG-AS1_ENST00000495542.1_RNA	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	305					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.F305F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		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)		CTTTGCACACGAACGGTCTGG	0.602																																					NSCLC(170;1772 2053 12525 15604 23984)											1	Substitution - coding silent(1)	large_intestine(1)	3											71	70	70					3																	62357280		2203	4300	6503	62332320	SO:0001819	synonymous_variant	55079			AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.915C>T	3.37:g.62357280G>A			62332320	A8K349|Q9BZ91|Q9NWB9	Silent	SNP	ENST00000283268.3	37	CCDS2897.1																																																																																				0.602	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		A	62357280	G	A	62357280	2	1	61	1	0	0	0	0	0	0	0	1	5845	1049	37	1		1	FEZF2	3	62357280	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1399	62357280	135665150	2552	10537										
CADPS	8618	broad.mit.edu	37	chr3	62451123	62451123	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actccttccaagatagtaacGaactagaaaaacagcaaaaa	5	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62451123G>A	ENST00000383710.4	-	26	3904	c.3555C>T	c.(3553-3555)ttC>ttT	p.F1185F	CADPS_ENST00000462768.1_5'UTR|CADPS_ENST00000357948.3_Silent_p.F1106F|CADPS_ENST00000283269.9_Silent_p.F1146F	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1185	Mediates targeting and association with DCVs. {ECO:0000250}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.F1146F(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		AGATAGTAACGAACTAGAAAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	3											93	100	98					3																	62451123		2203	4300	6503	62426163	SO:0001819	synonymous_variant	8618			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3555C>T	3.37:g.62451123G>A			62426163	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	37	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.281|7.281	0.609072|0.609072	0.14066|0.14066	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000466621|ENST00000473635	.|.	.|.	.|.	5.98|5.98	-2.5|-2.5	0.06384|0.06384	.|.	.|.	.|.	.|.	.|.	T|T	0.65863|0.65863	0.2732|0.2732	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.63808|0.63808	-0.6553|-0.6553	4|4	.|.	.|.	.|.	.|.	15.2763|15.2763	0.73745|0.73745	0.876:0.0:0.124:0.0|0.876:0.0:0.124:0.0	.|.	.|.	.|.	.|.	C|L	97|177	.|.	.|.	R|S	-|-	1|2	0|0	CADPS|CADPS	62426163|62426163	1.000000|1.000000	0.71417|0.71417	0.928000|0.928000	0.36995|0.36995	0.968000|0.968000	0.65278|0.65278	1.273000|1.273000	0.33121|0.33121	-0.712000|-0.712000	0.04988|0.04988	0.591000|0.591000	0.81541|0.81541	CGT|TCG		0.358	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62451123	G	A	62451123	2	1	61	1	0	0	0	0	0	0	0	1	2576	1049	37	1		1	CADPS	3	62451123	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93843	62451123	135571307	2553	10538										
CADPS	8618	broad.mit.edu	37	chr3	62739145	62739145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtaaaggagctgatgttCgaacttcttgatcccaagaa	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:62739145C>T	ENST00000383710.4	-	3	1208	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K	CADPS_ENST00000490353.2_Missense_Mutation_p.E287K|CADPS_ENST00000357948.3_Missense_Mutation_p.E287K|CADPS_ENST00000283269.9_Missense_Mutation_p.E287K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	287					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.E287K(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		AGCTGATGTTCGAACTTCTTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	75	76					3																	62739145		2203	4300	6503	62714185	SO:0001583	missense	8618			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.859G>A	3.37:g.62739145C>T	ENSP00000373215:p.Glu287Lys		62714185	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	37	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	35	5.480448	0.96307	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.92980	0.7766	M	0.81802	2.56	0.80722	D	1	D;D;P	0.71674	0.991;0.998;0.913	P;D;B	0.73380	0.871;0.98;0.11	D	0.92847	0.6294	10	0.66056	D	0.02	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	287;287;287	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	K	287	ENSP00000373215:E287K;ENSP00000350632:E287K;ENSP00000283269:E287K;ENSP00000418736:E287K	ENSP00000283269:E287K	E	-	1	0	CADPS	62714185	1.000000	0.71417	0.951000	0.38953	0.930000	0.56654	7.818000	0.86416	2.789000	0.95967	0.655000	0.94253	GAA		0.517	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62739145	C	T	62739145	3	4	61	1	0	0	0	0	1	0	0	0	2576	893	31	1	3387	1	CADPS	3	62739145	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	288022	62739145	135283285	2554	10539										
ATXN7	6314	broad.mit.edu	37	chr3	63981253	63981253	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccggacaaactctgtgccGacatcacaatgtggagtcag	10	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:63981253G>A	ENST00000295900.6	+	12	2305	c.1755G>A	c.(1753-1755)ccG>ccA	p.P585P	ATXN7_ENST00000487717.1_Silent_p.P585P|ATXN7_ENST00000538065.1_Silent_p.P585P|ATXN7_ENST00000398590.3_Silent_p.P585P|ATXN7_ENST00000484332.1_Silent_p.P440P	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	585					cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.P585P(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ACTCTGTGCCGACATCACAAT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											102	107	105					3																	63981253		2201	4299	6500	63956293	SO:0001819	synonymous_variant	6314			AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.1755G>A	3.37:g.63981253G>A			63956293	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Silent	SNP	ENST00000295900.6	37	CCDS43102.1																																																																																				0.507	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		A	63981253	G	A	63981253	2	1	61	1	0	0	0	0	0	0	0	1	1216	1045	37	1		1	ATXN7	3	63981253	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1242108	63981253	134041177	2555	10540										
PSMD6	9861	broad.mit.edu	37	chr3	64008044	64008044	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgccatcattgcatcgcGaatttcgctctctcctagat	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:64008044G>A	ENST00000295901.4	-	2	441	c.301C>T	c.(301-303)Cgc>Tgc	p.R101C	PSMD6_ENST00000394431.2_Missense_Mutation_p.R63C|PSMD6_ENST00000492933.1_Missense_Mutation_p.R154C|PSMD6_ENST00000482510.1_Missense_Mutation_p.R62C|RP11-245J9.6_ENST00000605919.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	101					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)	p.R101C(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		ATTGCATCGCGAATTTCGCTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											173	166	168					3																	64008044		2203	4300	6503	63983084	SO:0001583	missense	9861			AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.301C>T	3.37:g.64008044G>A	ENSP00000295901:p.Arg101Cys		63983084	A8K2E0|E9PHI9|Q6UV22	Missense_Mutation	SNP	ENST00000295901.4	37	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.735132	0.89482	.	.	ENSG00000163636	ENST00000295901;ENST00000492933;ENST00000394431;ENST00000482510;ENST00000497323;ENST00000478185	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	5.19	5.19	0.71726	.	0.053884	0.85682	D	0.000000	D	0.89805	0.6821	M	0.92412	3.305	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.973;0.977;0.997	D	0.91885	0.5519	10	0.87932	D	0	.	18.9179	0.92513	0.0:0.0:1.0:0.0	.	63;62;154;101	Q6UV22;E9PHI9;C9IZE4;Q15008	.;.;.;PSMD6_HUMAN	C	101;154;63;62;115;122	ENSP00000295901:R101C;ENSP00000418695:R154C;ENSP00000377952:R63C;ENSP00000419227:R62C;ENSP00000418887:R115C	ENSP00000295901:R101C	R	-	1	0	PSMD6	63983084	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	6.240000	0.72363	2.705000	0.92388	0.655000	0.94253	CGC		0.448	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814		A	64008044	G	A	64008044	3	1	61	1	0	0	0	0	1	0	0	0	12736	1058	37	1	896	1	PSMD6	3	64008044	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26791	64008044	134014386	2556	10541										
PRICKLE2	166336	broad.mit.edu	37	chr3	64085530	64085530	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacacattcattccagagtCtttgctgaggtcaggcatgg	11	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:64085530C>A	ENST00000295902.6	-	8	2317	c.1732G>T	c.(1732-1734)Gac>Tac	p.D578Y	RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2_ENST00000564377.1_Missense_Mutation_p.D634Y	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	578					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.D578Y(1)		breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		ATTCCAGAGTCTTTGCTGAGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	3											142	145	144					3																	64085530		2203	4300	6503	64060570	SO:0001583	missense	166336			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1732G>T	3.37:g.64085530C>A	ENSP00000295902:p.Asp578Tyr		64060570	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.237273	0.58886	.	.	ENSG00000163637	ENST00000295902	T	0.61274	0.12	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.67268	0.2875	L	0.50333	1.59	0.80722	D	1	D	0.58970	0.984	P	0.54372	0.75	T	0.68262	-0.5455	10	0.59425	D	0.04	-49.8215	19.6573	0.95847	0.0:1.0:0.0:0.0	.	578	Q7Z3G6	PRIC2_HUMAN	Y	578	ENSP00000295902:D578Y	ENSP00000295902:D578Y	D	-	1	0	PRICKLE2	64060570	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.037000	0.70956	2.655000	0.90218	0.591000	0.81541	GAC		0.567	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64085530	C	A	64085530	3	1	61	1	0	0	0	0	1	0	0	0	12521	913	32	2	806	2	PRICKLE2	3	64085530	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77486	64085530	133936900	2557	10542										
PRICKLE2	166336	broad.mit.edu	37	chr3	64138904	64138904	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattctgcatacaaggactcGaagcagtggcaacagtaggg	12	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:64138904G>A	ENST00000295902.6	-	6	1326	c.741C>T	c.(739-741)ttC>ttT	p.F247F	PRICKLE2_ENST00000564377.1_Silent_p.F303F	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	247	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.F247F(1)		breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		ACAAGGACTCGAAGCAGTGGC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											191	169	177					3																	64138904		2203	4300	6503	64113944	SO:0001819	synonymous_variant	166336			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.741C>T	3.37:g.64138904G>A			64113944	Q0VF44	Silent	SNP	ENST00000295902.6	37	CCDS2902.1																																																																																				0.507	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64138904	G	A	64138904	2	1	61	1	0	0	0	0	0	0	0	1	12521	1049	37	1		1	PRICKLE2	3	64138904	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53374	64138904	133883526	2558	10543										
ADAMTS9	56999	broad.mit.edu	37	chr3	64526846	64526846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggccgtgtaatccttccGacattggcagtcatcgcgcc	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:64526846G>A	ENST00000498707.1	-	36	5788	c.5446C>T	c.(5446-5448)Cgg>Tgg	p.R1816W	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.R1788W	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1816	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1816W(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		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)		TAATCCTTCCGACATTGGCAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	84	84					3																	64526846		2203	4300	6503	64501886	SO:0001583	missense	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.5446C>T	3.37:g.64526846G>A	ENSP00000418735:p.Arg1816Trp		64501886	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586098	0.66105	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.18657	2.2;2.2	5.73	4.85	0.62838	Peptidase M12B, GON-ADAMTSs (2);	0.000000	0.85682	D	0.000000	T	0.42562	0.1208	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.978	T	0.35226	-0.9797	10	0.72032	D	0.01	.	13.0483	0.58939	0.0:0.0:0.559:0.441	.	1788;1816	B7ZVX9;Q9P2N4	.;ATS9_HUMAN	W	1788;1816	ENSP00000295903:R1788W;ENSP00000418735:R1816W	ENSP00000295903:R1788W	R	-	1	2	ADAMTS9	64501886	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	1.893000	0.39758	1.400000	0.46741	0.655000	0.94253	CGG		0.463	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			A	64526846	G	A	64526846	3	1	61	1	0	0	0	0	1	0	0	0	273	1057	37	1	377	1	ADAMTS9	3	64526846	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	387942	64526846	133495584	2559	10544										
ADAMTS9	56999	broad.mit.edu	37	chr3	64587814	64587814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctggtcacactcactccGatcgatcacgtggtcactgt	8	14	4	0	rs371237082		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:64587814G>A	ENST00000498707.1	-	26	4165	c.3823C>T	c.(3823-3825)Cgg>Tgg	p.R1275W	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.R1247W	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1275	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1275W(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		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)		CACTCACTCCGATCGATCACG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3						T	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	179	154	162		3823	3.8	0.6	3		162	0,8600		0,0,4300	no	missense	ADAMTS9	NM_182920.1	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	1275/1936	64587814	1,13005	2203	4300	6503	64562854	SO:0001583	missense	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.3823C>T	3.37:g.64587814G>A	ENSP00000418735:p.Arg1275Trp		64562854	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	g	13.77	2.335256	0.41398	2.27E-4	0.0	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.61274	0.12;0.12	5.55	3.75	0.43078	.	0.782790	0.12266	N	0.484287	T	0.60025	0.2237	M	0.65677	2.01	0.34235	D	0.677001	D;D;P	0.55605	0.962;0.972;0.922	P;P;P	0.46320	0.512;0.471;0.512	T	0.69840	-0.5036	10	0.87932	D	0	.	9.8229	0.40894	0.0:0.234:0.499:0.267	.	1247;1275;1275	B7ZVX9;Q9P2N4-1;Q9P2N4	.;.;ATS9_HUMAN	W	1247;1275	ENSP00000295903:R1247W;ENSP00000418735:R1275W	ENSP00000295903:R1247W	R	-	1	2	ADAMTS9	64562854	0.002000	0.14202	0.625000	0.29200	0.408000	0.30992	0.733000	0.26087	0.889000	0.36185	-0.188000	0.12872	CGG		0.522	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			A	64587814	G	A	64587814	3	1	61	1	0	0	0	0	1	0	0	0	273	1057	37	1	2040	1	ADAMTS9	3	64587814	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60968	64587814	133434616	2560	10545										
MAGI1	9223	broad.mit.edu	37	chr3	65346916	65346916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccgcttcagaaacagacGaactctgcggccaccattct	7	16	3	2	rs201117026	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:65346916G>A	ENST00000497477.2	-	21	3390	c.3391C>T	c.(3391-3393)Cgt>Tgt	p.R1131C	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000402939.2_Missense_Mutation_p.R1198C|MAGI1_ENST00000330909.8_Missense_Mutation_p.R1226C|MAGI1_ENST00000483466.1_Missense_Mutation_p.R1227C			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1227	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.R1198C(2)|p.R1227C(2)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		AGAAACAGACGAACTCTGCGG	0.443													G|||	11	0.00219649	0	0	5008	,	,		18165	0		0	False		,,,				2504	0.0112															4	Substitution - Missense(4)	large_intestine(4)	3											142	131	134					3																	65346916		2203	4300	6503	65321956	SO:0001583	missense	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.3391C>T	3.37:g.65346916G>A	ENSP00000424369:p.Arg1131Cys		65321956	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	G	29.1	4.973719	0.92919	.	.	ENSG00000151276	ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	5.78	5.78	0.91487	.	0.110600	0.64402	D	0.000005	T	0.59622	0.2207	M	0.82132	2.575	0.80722	D	1	D;D;D;D	0.89917	0.994;1.0;1.0;0.998	D;D;D;D	0.67900	0.95;0.949;0.954;0.921	T	0.59925	-0.7362	10	0.51188	T	0.08	-20.0636	20.0278	0.97529	0.0:0.0:1.0:0.0	.	1131;1227;1198;1226	Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.;.;.;.	C	1198;1226;1122;1102;1227;1131;985	ENSP00000385450:R1198C;ENSP00000331157:R1226C;ENSP00000418177:R1102C;ENSP00000420323:R1227C;ENSP00000424369:R1131C;ENSP00000420796:R985C	ENSP00000331157:R1226C	R	-	1	0	MAGI1	65321956	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.868000	0.87116	2.717000	0.92951	0.650000	0.86243	CGT		0.443	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		A	65346916	G	A	65346916	3	1	61	1	0	0	0	0	1	0	0	0	9220	1058	37	1	947	1	MAGI1	3	65346916	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	759102	65346916	132675514	2561	10546										
MAGI1	9223	broad.mit.edu	37	chr3	66023951	66023951	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcgtgaaccctgctagtCcagtggttcttcttctggat	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:66023951C>T	ENST00000497477.2	-	1	32	c.33G>A	c.(31-33)tgG>tgA	p.W11*	MAGI1_ENST00000402939.2_Nonsense_Mutation_p.W11*|MAGI1_ENST00000330909.8_Nonsense_Mutation_p.W11*|MAGI1_ENST00000483466.1_Nonsense_Mutation_p.W11*			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	11					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.W11*(2)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CCCTGCTAGTCCAGTGGTTCT	0.597																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											57	62	60					3																	66023951		2148	4212	6360	65998991	SO:0001587	stop_gained	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.33G>A	3.37:g.66023951C>T	ENSP00000424369:p.Trp11*		65998991	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Nonsense_Mutation	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	40	7.927489	0.98565	.	.	ENSG00000151276	ENST00000402939;ENST00000330909;ENST00000483466;ENST00000497477	.	.	.	5.78	5.78	0.91487	.	0.135317	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5036	20.0009	0.97408	0.0:1.0:0.0:0.0	.	.	.	.	X	11	.	ENSP00000331157:W11X	W	-	3	0	MAGI1	65998991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.395000	0.79876	2.734000	0.93682	0.591000	0.81541	TGG		0.597	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	66023951	C	T	66023951	4	4	61	1	0	0	0	0	0	1	0	0	9220	856	30	3	4681	3	MAGI1	3	66023951	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	677035	66023951	131998479	2562	10547										
LRIG1	26018	broad.mit.edu	37	chr3	66512866	66512866	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagggggagactcacacttCctgtaggttcggcaagtcct	12	10	1	1	rs143616236	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:66512866C>A	ENST00000273261.3	-	2	810	c.286G>T	c.(286-288)Gaa>Taa	p.E96*	LRIG1_ENST00000383703.3_Nonsense_Mutation_p.E96*	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	96					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.E96*(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ACTCACACTTCCTGTAGGTTC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											87	82	83					3																	66512866		2203	4300	6503	66595556	SO:0001587	stop_gained	26018			AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.286G>T	3.37:g.66512866C>A	ENSP00000273261:p.Glu96*		66595556	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Nonsense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	C	41	9.058128	0.99051	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	18.1515	0.89676	0.0:1.0:0.0:0.0	.	.	.	.	X	96;96;23	.	ENSP00000273261:E96X	E	-	1	0	LRIG1	66595556	1.000000	0.71417	0.996000	0.52242	0.410000	0.31052	5.349000	0.66010	2.723000	0.93209	0.563000	0.77884	GAA		0.483	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66512866	C	A	66512866	4	1	61	1	0	0	0	0	0	1	0	0	8973	864	30	2	3067	2	LRIG1	3	66512866	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	488915	66512866	131509564	2563	10548										
KBTBD8	84541	broad.mit.edu	37	chr3	67058529	67058529	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatattgagctaaataaatGgactcgtaagaaagactttc	8	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:67058529G>T	ENST00000417314.2	+	4	1575	c.1526G>T	c.(1525-1527)tGg>tTg	p.W509L	KBTBD8_ENST00000295568.4_Missense_Mutation_p.W483L|KBTBD8_ENST00000460576.1_Missense_Mutation_p.W67L			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	509						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)		p.W483L(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		CTAAATAAATGGACTCGTAAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											133	128	130					3																	67058529		2203	4300	6503	67141219	SO:0001583	missense	84541			AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.1526G>T	3.37:g.67058529G>T	ENSP00000401878:p.Trp509Leu		67141219	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	37	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.095288	0.76870	.	.	ENSG00000163376	ENST00000295568;ENST00000460576;ENST00000417314	D;D;D	0.96940	-4.18;-4.18;-4.18	5.57	5.57	0.84162	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.98516	0.9505	M	0.89968	3.075	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.81914	0.992;0.995	D	0.99316	1.0905	10	0.87932	D	0	.	19.552	0.95324	0.0:0.0:1.0:0.0	.	67;509	B4DTW6;Q8NFY9	.;KBTB8_HUMAN	L	483;67;509	ENSP00000295568:W483L;ENSP00000419738:W67L;ENSP00000401878:W509L	ENSP00000295568:W483L	W	+	2	0	KBTBD8	67141219	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.435000	0.97529	2.629000	0.89072	0.650000	0.86243	TGG		0.373	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		T	67058529	G	T	67058529	3	4	61	1	0	0	0	0	1	0	0	0	8020	1357	47	2	1540	2	KBTBD8	3	67058529	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	545663	67058529	130963901	2564	10549										
KBTBD8	84541	broad.mit.edu	37	chr3	67058648	67058648	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgactgttgaagaacacGtcttcagaaccagcagaaaa	9	8	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:67058648G>A	ENST00000417314.2	+	4	1694	c.1645G>A	c.(1645-1647)Gtc>Atc	p.V549I	KBTBD8_ENST00000295568.4_Missense_Mutation_p.V523I|KBTBD8_ENST00000460576.1_Missense_Mutation_p.V107I			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	549						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)		p.V523I(2)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		TGAAGAACACGTCTTCAGAAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	3											109	107	107					3																	67058648		2203	4300	6503	67141338	SO:0001583	missense	84541			AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.1645G>A	3.37:g.67058648G>A	ENSP00000401878:p.Val549Ile		67141338	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	37	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	G	9.894	1.204911	0.22205	.	.	ENSG00000163376	ENST00000295568;ENST00000460576;ENST00000417314	T;T;T	0.71341	-0.55;-0.39;-0.56	5.57	3.75	0.43078	Kelch-type beta propeller (1);	5.341630	0.00885	N	0.002172	T	0.56543	0.1992	N	0.08118	0	0.47778	D	0.999512	B;B	0.15719	0.014;0.014	B;B	0.08055	0.002;0.003	T	0.23154	-1.0196	10	0.42905	T	0.14	.	10.8349	0.46681	0.1535:0.0:0.8465:0.0	.	107;549	B4DTW6;Q8NFY9	.;KBTB8_HUMAN	I	523;107;549	ENSP00000295568:V523I;ENSP00000419738:V107I;ENSP00000401878:V549I	ENSP00000295568:V523I	V	+	1	0	KBTBD8	67141338	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.716000	0.74702	1.331000	0.45412	0.650000	0.86243	GTC		0.423	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		A	67058648	G	A	67058648	3	1	61	1	0	0	0	0	1	0	0	0	8020	1145	40	1	1659	1	KBTBD8	3	67058648	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119	67058648	130963782	2565	10550										
C3orf64	285203	broad.mit.edu	37	chr3	69026864	69026864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacataaattcttctacatCgaaagagtagttggtgaact	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:69026864C>T	ENST00000383701.3	-	18	2231	c.1489G>A	c.(1489-1491)Gat>Aat	p.D497N	EOGT_ENST00000540955.1_Missense_Mutation_p.D221N|EOGT_ENST00000295571.5_Missense_Mutation_p.D413N|EOGT_ENST00000540764.1_Missense_Mutation_p.D396N	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	497					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)	p.D413N(1)									TCTTCTACATCGAAAGAGTAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	94	94					3																	69026864		2203	4300	6503	69109554	SO:0001583	missense	285203			AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	2.4.1.255		28526	protein-coding gene	gene with protein product	"AER61 glycosyltransferase"	614789	"chromosome 3 open reading frame 64"	C3orf64		22310717	Standard	NM_001278689		Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.1489G>A	3.37:g.69026864C>T	ENSP00000373206:p.Asp497Asn		69109554	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	Missense_Mutation	SNP	ENST00000383701.3	37		.	.	.	.	.	.	.	.	.	.	C	23.5	4.418000	0.83449	.	.	ENSG00000163378	ENST00000383701;ENST00000295571;ENST00000540955;ENST00000540764	.	.	.	5.52	5.52	0.82312	.	0.086932	0.85682	D	0.000000	T	0.76090	0.3939	M	0.66439	2.03	0.80722	D	1	P;D	0.67145	0.956;0.996	B;P	0.59424	0.303;0.857	T	0.77148	-0.2694	9	0.56958	D	0.05	.	19.4306	0.94762	0.0:1.0:0.0:0.0	.	497;413	Q5NDL2;Q5NDL2-3	AER61_HUMAN;.	N	497;413;221;396	.	ENSP00000295571:D413N	D	-	1	0	C3orf64	69109554	1.000000	0.71417	0.313000	0.25210	0.967000	0.64934	5.933000	0.70130	2.610000	0.88304	0.591000	0.81541	GAT		0.438	EOGT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343722.1	NM_173654		T	69026864	C	T	69026864	3	4	61	1	0	0	0	0	1	0	0	0	2246	884	31	1	98	1	C3orf64	3	69026864	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1968216	69026864	128995566	2566	10551										
UBA3	9039	broad.mit.edu	37	chr3	69113221	69113221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaagtaaaaaacttacgtCgatagaaagtgtcgttaaaa	7	5	1	1	rs373601125		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:69113221C>T	ENST00000361055.4	-	7	524	c.470G>A	c.(469-471)cGa>cAa	p.R157Q	UBA3_ENST00000540295.1_Intron|UBA3_ENST00000349511.4_Missense_Mutation_p.R143Q|UBA3_ENST00000415609.2_Missense_Mutation_p.R116Q	NM_003968.3	NP_003959.3	Q8TBC4	UBA3_HUMAN	ubiquitin-like modifier activating enzyme 3	157	Interaction with UBE2M N-terminus.				cellular protein modification process (GO:0006464)|endomitotic cell cycle (GO:0007113)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of cell cycle (GO:0051726)	cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|NEDD8 activating enzyme activity (GO:0019781)|protein heterodimerization activity (GO:0046982)	p.R157Q(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		AAACTTACGTCGATAGAAAGT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	GLN/ARG,GLN/ARG	1,4403	2.1+/-5.4	0,1,2201	54	55	55		470,428	5.9	1	3		55	0,8596		0,0,4298	no	missense,missense	UBA3	NM_003968.3,NM_198195.1	43,43	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	157/464,143/450	69113221	1,12999	2202	4298	6500	69195911	SO:0001583	missense	9039			AB012190	CCDS2909.1, CCDS2910.1	3p14.1	2013-09-26	2007-11-30	2007-11-30	ENSG00000144744	ENSG00000144744		"Ubiquitin-like modifier activating enzymes"	12470	protein-coding gene	gene with protein product	"NEDD8-activating enzyme E1 catalytic subunit", "NEDD8-activating enzyme E1 subunit 2"	603172	"ubiquitin-activating enzyme E1C (homologous to yeast UBA3)", "ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)"	UBE1C		9694792	Standard	NM_003968		Approved	hUba3, NAE2	uc003dno.3	Q8TBC4	OTTHUMG00000154325	ENST00000361055.4:c.470G>A	3.37:g.69113221C>T	ENSP00000354340:p.Arg157Gln		69195911	A6NLB5|A8K027|O76088|Q9NTU3	Missense_Mutation	SNP	ENST00000361055.4	37	CCDS2909.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191943	0.78902	2.27E-4	0.0	ENSG00000144744	ENST00000415609;ENST00000361055;ENST00000349511	T;T;T	0.29917	1.55;1.55;1.55	5.92	5.92	0.95590	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	N	0.20685	0.6	0.80722	D	1	P;P	0.50369	0.798;0.934	B;B	0.39840	0.207;0.311	T	0.01643	-1.1305	10	0.27082	T	0.32	-8.0353	19.9157	0.97061	0.0:1.0:0.0:0.0	.	143;157	Q8TBC4-2;Q8TBC4	.;UBA3_HUMAN	Q	116;157;143	ENSP00000400294:R116Q;ENSP00000354340:R157Q;ENSP00000340041:R143Q	ENSP00000340041:R143Q	R	-	2	0	UBA3	69195911	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.067000	0.64357	2.809000	0.96659	0.655000	0.94253	CGA		0.284	UBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334839.1	NM_198195		T	69113221	C	T	69113221	3	4	61	1	0	0	0	0	1	0	0	0	16869	884	31	1	969	1	UBA3	3	69113221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86357	69113221	128909209	2567	10552										
LMOD3	56203	broad.mit.edu	37	chr3	69171329	69171329	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacatataatcaacaagaGatttatgattgaagtttcct	5	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:69171329G>T	ENST00000420581.2	-	1	388	c.209C>A	c.(208-210)tCt>tAt	p.S70Y	LMOD3_ENST00000489031.1_Missense_Mutation_p.S70Y|LMOD3_ENST00000475434.1_Missense_Mutation_p.S70Y	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	70						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.S70Y(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		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)		ATCAACAAGAGATTTATGATT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	3											80	76	77					3																	69171329		1860	4104	5964	69254019	SO:0001583	missense	56203			AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.209C>A	3.37:g.69171329G>T	ENSP00000414670:p.Ser70Tyr		69254019	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	37	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333189	0.81801	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.31769	1.48;1.48;1.48	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62525	-0.6836	10	0.72032	D	0.01	-17.5402	19.8051	0.96529	0.0:0.0:1.0:0.0	.	70	Q0VAK6	LMOD3_HUMAN	Y	70	ENSP00000414670:S70Y;ENSP00000417210:S70Y;ENSP00000418645:S70Y	ENSP00000414670:S70Y	S	-	2	0	LMOD3	69254019	1.000000	0.71417	0.919000	0.36401	0.926000	0.56050	7.876000	0.87215	2.702000	0.92279	0.591000	0.81541	TCT		0.468	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		T	69171329	G	T	69171329	3	4	61	1	0	0	0	0	1	0	0	0	8882	942	33	2	1485	2	LMOD3	3	69171329	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58108	69171329	128851101	2568	10553										
FRMD4B	23150	broad.mit.edu	37	chr3	69225805	69225805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagaagcatttgtagaagAcactggaaataaaaatggaa	9	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:69225805A>G	ENST00000398540.3	-	22	2937	c.2854T>C	c.(2854-2856)Tct>Cct	p.S952P	FRMD4B_ENST00000478263.1_Missense_Mutation_p.S604P|FRMD4B_ENST00000542259.1_Missense_Mutation_p.S898P	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	952					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)		p.S898P(1)		NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TTTGTAGAAGACACTGGAAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	68	69					3																	69225805		1853	4103	5956	69308495	SO:0001583	missense	23150			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.2854T>C	3.37:g.69225805A>G	ENSP00000381549:p.Ser952Pro		69308495	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331824	0.81801	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.85955	-2.05;-2.02	5.69	5.69	0.88448	.	0.120249	0.64402	D	0.000020	D	0.91140	0.7210	M	0.68952	2.095	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.963	D	0.92019	0.5624	10	0.87932	D	0	-14.4619	14.5303	0.67920	1.0:0.0:0.0:0.0	.	796;952	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	P	952;898;604	ENSP00000381549:S952P;ENSP00000437658:S898P	ENSP00000381549:S952P	S	-	1	0	FRMD4B	69308495	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.534000	0.82004	2.180000	0.69256	0.482000	0.46254	TCT		0.383	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			G	69225805	A	G	69225805	3	3	61	1	0	0	0	0	1	0	0	0	6071	275	10	4	258	4	FRMD4B	3	69225805	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	54476	69225805	128796625	2569	10554										
MITF	4286	broad.mit.edu	37	chr3	70008425	70008425	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccattttcatcgcagaGacatgcgctggaacaaggga	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:70008425G>T	ENST00000448226.2	+	9	1160	c.1033G>T	c.(1033-1035)Gac>Tac	p.D345Y	MITF_ENST00000394351.3_Splice_Site_p.D238Y|MITF_ENST00000314557.6_Splice_Site_p.D232Y|MITF_ENST00000328528.6_Splice_Site_p.D338Y|MITF_ENST00000394355.2_Splice_Site_p.D314Y|MITF_ENST00000472437.1_Splice_Site_p.D287Y|MITF_ENST00000531774.1_Splice_Site_p.D176Y|MITF_ENST00000352241.4_Splice_Site_p.D339Y|MITF_ENST00000314589.5_Splice_Site_p.D323Y			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	345	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.D238Y(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		TCATCGCAGAGACATGCGCTG	0.378			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	1	Substitution - Missense(1)	large_intestine(1)	3											65	61	62					3																	70008425		2203	4300	6503	70091115	SO:0001630	splice_region_variant	4286				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.1032-1G>T	3.37:g.70008425G>T			70091115	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	G	29.0	4.968133	0.92855	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000472437;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	D;D;D;D;D;D;D;D;D;D	0.98120	-4.73;-4.73;-4.73;-4.73;-4.73;-4.73;-4.73;-4.73;-4.73;-4.73	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.99174	0.9714	H	0.94698	3.57	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.998;0.998;0.998;0.998;1.0;0.998	D;D;D;D;D;D;D	0.79784	0.992;0.987;0.987;0.987;0.987;0.993;0.987	D	0.99113	1.0847	9	.	.	.	.	20.2768	0.98488	0.0:0.0:1.0:0.0	.	287;238;232;314;323;338;339	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	Y	339;345;287;338;329;323;314;232;238;176	ENSP00000295600:D339Y;ENSP00000391803:D345Y;ENSP00000418845:D287Y;ENSP00000327867:D338Y;ENSP00000398639:D329Y;ENSP00000324443:D323Y;ENSP00000377884:D314Y;ENSP00000324246:D232Y;ENSP00000377880:D238Y;ENSP00000435909:D176Y	.	D	+	1	0	MITF	70091115	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.869000	0.99810	2.808000	0.96608	0.650000	0.86243	GAC		0.378	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159	Missense_Mutation	T	70008425	G	T	70008425	5	4	61	1	0	0	0	0	0	0	1	0	9626	956	33	2	1288	2	MITF	3	70008425	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	782620	70008425	128014005	2570	10555										
SHQ1	55164	broad.mit.edu	37	chr3	72799866	72799866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgggctgcttttaatgCagtttcttcctcctggacaa	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:72799866C>T	ENST00000325599.8	-	11	1442	c.1303G>A	c.(1303-1305)Gca>Aca	p.A435T	SHQ1_ENST00000463369.1_Missense_Mutation_p.A407T|SHQ1_ENST00000468371.1_5'UTR	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	435					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A435T(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		GCTTTTAATGCAGTTTCTTCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											23	19	20					3																	72799866		2194	4286	6480	72882556	SO:0001583	missense	55164			BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1303G>A	3.37:g.72799866C>T	ENSP00000315182:p.Ala435Thr		72882556	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	37	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.055587	0.36277	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.32272	1.48;1.46	5.74	1.88	0.25563	.	0.825722	0.11178	N	0.591225	T	0.15955	0.0384	N	0.16478	0.41	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.34453	-0.9828	10	0.15499	T	0.54	-10.9844	5.8337	0.18594	0.1223:0.606:0.0:0.2717	.	435	Q6PI26	SHQ1_HUMAN	T	435;407	ENSP00000315182:A435T;ENSP00000417452:A407T	ENSP00000315182:A435T	A	-	1	0	SHQ1	72882556	0.000000	0.05858	0.000000	0.03702	0.372000	0.29890	-0.000000	0.12993	0.336000	0.23639	0.655000	0.94253	GCA		0.507	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		T	72799866	C	T	72799866	3	4	61	1	0	0	0	0	1	0	0	0	14329	710	25	3	434	3	SHQ1	3	72799866	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2791441	72799866	125222564	2571	10556										
EBLN2	55096	broad.mit.edu	37	chr3	73111558	73111558	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattaaaaaagcagccaagtCtatgctagacccagcacata	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:73111558C>A	ENST00000533473.1	+	1	749	c.326C>A	c.(325-327)tCt>tAt	p.S109Y	PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	109								p.S109Y(1)		endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						GCAGCCAAGTCTATGCTAGAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	56	57					3																	73111558		1908	4110	6018	73194248	SO:0001583	missense	55096				CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.326C>A	3.37:g.73111558C>A	ENSP00000432104:p.Ser109Tyr		73194248	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	C	9.431	1.085634	0.20390	.	.	ENSG00000255423	ENST00000533473	.	.	.	0.458	0.458	0.16670	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.38639	0.1048	N	0.19112	0.55	0.09310	N	1	D	0.60160	0.987	D	0.67382	0.951	T	0.22173	-1.0224	7	0.87932	D	0	.	.	.	.	.	109	Q6P2I7	EBLN2_HUMAN	Y	109	.	ENSP00000432104:S109Y	S	+	2	0	EBLN2	73194248	0.039000	0.19947	0.002000	0.10522	0.002000	0.02628	0.305000	0.19254	0.482000	0.27582	0.484000	0.47621	TCT		0.423	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		A	73111558	C	A	73111558	3	1	61	1	0	0	0	0	1	0	0	0	4895	913	32	2	328	2	EBLN2	3	73111558	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	311692	73111558	124910872	2572	10557										
EBLN2	55096	broad.mit.edu	37	chr3	73111987	73111987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaccatgggttggagaatTaatgttcacacttctatttg	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:73111987T>C	ENST00000533473.1	+	1	1178	c.755T>C	c.(754-756)tTa>tCa	p.L252S	PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	252								p.L252S(1)		endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						GTTGGAGAATTAATGTTCACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											190	195	193					3																	73111987		1927	4119	6046	73194677	SO:0001583	missense	55096				CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.755T>C	3.37:g.73111987T>C	ENSP00000432104:p.Leu252Ser		73194677	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	T	9.950	1.219936	0.22373	.	.	ENSG00000255423	ENST00000533473	.	.	.	0.468	0.468	0.16732	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.38852	0.1056	N	0.19112	0.55	0.09310	N	1	D	0.63880	0.993	D	0.68943	0.961	T	0.22103	-1.0226	7	0.87932	D	0	.	.	.	.	.	252	Q6P2I7	EBLN2_HUMAN	S	252	.	ENSP00000432104:L252S	L	+	2	0	EBLN2	73194677	0.009000	0.17119	0.001000	0.08648	0.001000	0.01503	0.310000	0.19356	0.413000	0.25759	0.402000	0.26972	TTA		0.428	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		C	73111987	T	C	73111987	3	2	61	1	0	0	0	0	1	0	0	0	4895	1764	61	4	757	4	EBLN2	3	73111987	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	429	73111987	124910443	2573	10558										
PDZRN3	23024	broad.mit.edu	37	chr3	73433453	73433453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctgtgttgtaggcgctcGagctgtccttgtcggatttc	13	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:73433453G>A	ENST00000263666.4	-	10	2378	c.2264C>T	c.(2263-2265)tCg>tTg	p.S755L	PDZRN3_ENST00000466780.1_Missense_Mutation_p.S412L|PDZRN3_ENST00000462146.2_Missense_Mutation_p.S412L|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Missense_Mutation_p.S477L|PDZRN3_ENST00000479530.1_Missense_Mutation_p.S472L	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	755					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S755L(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GTAGGCGCTCGAGCTGTCCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	3											35	34	34					3																	73433453		2203	4300	6503	73516143	SO:0001583	missense	23024			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2264C>T	3.37:g.73433453G>A	ENSP00000263666:p.Ser755Leu		73516143	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.597000	0.87055	.	.	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000492909	T;T;T;T;T;T	0.16457	2.34;3.04;2.96;2.96;3.06;2.93	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.48804	0.1520	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.977;0.996;0.972;0.99	T	0.56763	-0.7925	10	0.87932	D	0	.	18.2651	0.90050	0.0:0.0:1.0:0.0	.	477;472;472;755	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	L	755;477;412;412;472;453	ENSP00000263666:S755L;ENSP00000442026:S477L;ENSP00000418168:S412L;ENSP00000418484:S412L;ENSP00000418624:S472L;ENSP00000419250:S453L	ENSP00000263666:S755L	S	-	2	0	PDZRN3	73516143	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.607000	0.82883	2.393000	0.81446	0.591000	0.81541	TCG		0.622	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		A	73433453	G	A	73433453	3	1	61	1	0	0	0	0	1	0	0	0	11740	1059	37	1	940	1	PDZRN3	3	73433453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	321466	73433453	124588977	2574	10559										
ROBO2	6092	broad.mit.edu	37	chr3	77623726	77623726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtctgcaggcgacatcttCgtggcagaatttagatgcca	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:77623726C>T	ENST00000461745.1	+	14	2948	c.2048C>T	c.(2047-2049)tCg>tTg	p.S683L	ROBO2_ENST00000332191.8_Missense_Mutation_p.S683L|ROBO2_ENST00000487694.3_Missense_Mutation_p.S699L	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	683	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.S683L(1)|p.S699L(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GCGACATCTTCGTGGCAGAAT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	3											101	91	94					3																	77623726		1917	4129	6046	77706416	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2048C>T	3.37:g.77623726C>T	ENSP00000417164:p.Ser683Leu		77706416	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	8.393	0.840121	0.16891	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57436	0.4;0.4;0.4	5.7	4.82	0.62117	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.147300	0.06721	N	0.774782	T	0.49389	0.1554	L	0.46157	1.445	0.25363	N	0.988766	B;B;B	0.27380	0.177;0.025;0.056	B;B;B	0.25884	0.064;0.05;0.041	T	0.49808	-0.8900	9	0.46703	T	0.11	.	10.706	0.45956	0.0:0.8315:0.0:0.1685	.	699;683;683	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	L	699;699;703;683;683;404	ENSP00000417335:S699L;ENSP00000417164:S683L;ENSP00000327536:S683L	ENSP00000327536:S683L	S	+	2	0	ROBO2	77706416	0.002000	0.14202	0.003000	0.11579	0.076000	0.17211	1.911000	0.39937	1.374000	0.46228	0.585000	0.79938	TCG		0.448	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77623726	C	T	77623726	3	4	61	1	0	0	0	0	1	0	0	0	13551	893	31	1	2104	1	ROBO2	3	77623726	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4190273	77623726	120398704	2575	10560										
ROBO2	6092	broad.mit.edu	37	chr3	77651534	77651534	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcattccaacagcatacatGaattggctgtcgatctgcct	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:77651534G>T	ENST00000461745.1	+	20	3928	c.3028G>T	c.(3028-3030)Gaa>Taa	p.E1010*	ROBO2_ENST00000332191.8_Nonsense_Mutation_p.E1010*|ROBO2_ENST00000487694.3_Nonsense_Mutation_p.E1026*	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1010					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.E1026*(1)|p.E1010*(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CAGCATACATGAATTGGCTGT	0.428																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											117	107	110					3																	77651534		1967	4164	6131	77734224	SO:0001587	stop_gained	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3028G>T	3.37:g.77651534G>T	ENSP00000417164:p.Glu1010*		77734224	O43608|Q19AB4|Q19AB5	Nonsense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	41|41|41	9.028693|9.028693|9.028693	0.99040|0.99040|0.99040	.|.|.	.|.|.	ENSG00000185008|ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000490991|ENST00000398467;ENST00000471893	.|.|.	.|.|.	.|.|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|.|.	0.46758|.|.	D|.|.	0.000277|.|.	.|T|.	.|0.80065|.	.|0.4555|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|.	.|0.77590|.	.|-0.2531|.	.|3|.	0.13853|.|.	T|.|.	0.58|.|.	.|.|.	20.1432|20.1432|20.1432	0.98067|0.98067|0.98067	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|I|L	1026;1026;1030;1010;1010|166|571;84	.|.|.	ENSP00000327536:E1010X|.|.	E|M|X	+|+|+	1|3|2	0|0|2	ROBO2|ROBO2|ROBO2	77734224|77734224|77734224	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.990000|0.990000|0.990000	0.47175|0.47175|0.47175	0.898000|0.898000|0.898000	0.52572|0.52572|0.52572	9.476000|9.476000|9.476000	0.97823|0.97823|0.97823	2.769000|2.769000|2.769000	0.95229|0.95229|0.95229	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAA|ATG|TGA		0.428	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77651534	G	T	77651534	4	4	61	1	0	0	0	0	0	1	0	0	13551	1291	45	2	3108	2	ROBO2	3	77651534	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27808	77651534	120370896	2576	10561										
ROBO1	6091	broad.mit.edu	37	chr3	78649271	78649271	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattatagatacctctaattCttcattattatcttctcctc	1	10	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78649271C>A	ENST00000464233.1	-	30	5046	c.4933G>T	c.(4933-4935)Gaa>Taa	p.E1645*	ROBO1_ENST00000495273.1_Nonsense_Mutation_p.E1600*|ROBO1_ENST00000436010.2_Nonsense_Mutation_p.E1606*|ROBO1_ENST00000467549.1_Nonsense_Mutation_p.E1545*|ROBO1_ENST00000466906.1_5'UTR	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1645					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.E1622*(1)|p.E1645*(1)|p.E1600*(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ACCTCTAATTCTTCATTATTA	0.353																																																3	Substitution - Nonsense(3)	large_intestine(3)	3											135	127	130					3																	78649271		1832	4081	5913	78731961	SO:0001587	stop_gained	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4933G>T	3.37:g.78649271C>A	ENSP00000420321:p.Glu1645*		78731961	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Nonsense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	44	10.997467	0.99500	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	.	.	.	5.61	5.61	0.85477	.	0.159083	0.56097	D	0.000035	.	.	.	.	.	.	0.51012	D	0.999909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6398	0.95753	0.0:1.0:0.0:0.0	.	.	.	.	X	1606;1600;1645;1600;1545;1649	.	.	E	-	1	0	ROBO1	78731961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.902000	0.69869	2.652000	0.90054	0.555000	0.69702	GAA		0.353	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78649271	C	A	78649271	4	1	61	1	0	0	0	0	0	1	0	0	13550	922	32	2	30	2	ROBO1	3	78649271	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	997737	78649271	119373159	2577	10562										
ROBO1	6091	broad.mit.edu	37	chr3	78663818	78663818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctgtgtaggtttctctgCgcagatgtcctggctggtgt	13	9	2	1	rs573160338		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78663818C>T	ENST00000464233.1	-	28	4528	c.4415G>A	c.(4414-4416)cGc>cAc	p.R1472H	ROBO1_ENST00000495273.1_Missense_Mutation_p.R1427H|ROBO1_ENST00000436010.2_Missense_Mutation_p.R1433H|ROBO1_ENST00000467549.1_Missense_Mutation_p.R1372H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1472					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.R1472H(1)|p.R1427H(1)|p.R1449H(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGTTTCTCTGCGCAGATGTCC	0.498																																																3	Substitution - Missense(3)	large_intestine(3)	3											131	135	134					3																	78663818		2002	4179	6181	78746508	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4415G>A	3.37:g.78663818C>T	ENSP00000420321:p.Arg1472His		78746508	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	35	5.555076	0.96514	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.68181	-0.25;-0.29;-0.26;-0.31	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.73837	0.3638	L	0.29908	0.895	0.80722	D	1	D;D;D;B;B	0.76494	0.999;0.997;0.999;0.099;0.236	D;B;P;B;B	0.80764	0.994;0.389;0.869;0.014;0.015	T	0.71230	-0.4654	9	.	.	.	.	19.327	0.94265	0.0:1.0:0.0:0.0	.	1436;1472;1427;1372;1433	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	H	1433;1427;1472;1427;1372;1476	ENSP00000406043:R1433H;ENSP00000420321:R1472H;ENSP00000420637:R1427H;ENSP00000417992:R1372H	.	R	-	2	0	ROBO1	78746508	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	4.408000	0.59761	2.636000	0.89361	0.585000	0.79938	CGC		0.498	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78663818	C	T	78663818	3	4	61	1	0	0	0	0	1	0	0	0	13550	768	27	1	556	1	ROBO1	3	78663818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14547	78663818	119358612	2578	10563										
ROBO1	6091	broad.mit.edu	37	chr3	78676538	78676538	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaacatgggctggagttCttcctgtggggagggagtca	16	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78676538C>T	ENST00000464233.1	-	26	3921	c.3808G>A	c.(3808-3810)Gaa>Aaa	p.E1270K	ROBO1_ENST00000495273.1_Missense_Mutation_p.E1225K|ROBO1_ENST00000436010.2_Missense_Mutation_p.E1231K|ROBO1_ENST00000467549.1_Missense_Mutation_p.E1170K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1270					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.E1225K(1)|p.E1247K(1)|p.E1270K(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGCTGGAGTTCTTCCTGTGGG	0.567																																																3	Substitution - Missense(3)	large_intestine(3)	3											52	61	58					3																	78676538		2164	4271	6435	78759228	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3808G>A	3.37:g.78676538C>T	ENSP00000420321:p.Glu1270Lys		78759228	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480389	0.84747	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.71103	-0.49;-0.53;-0.54;-0.31	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.77824	0.4188	L	0.32530	0.975	0.80722	D	1	D;P;D;P;P	0.67145	0.996;0.949;0.983;0.74;0.745	D;P;P;B;P	0.76071	0.987;0.694;0.701;0.214;0.545	T	0.75224	-0.3393	9	.	.	.	.	19.2858	0.94069	0.0:1.0:0.0:0.0	.	1234;1270;1225;1170;1231	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	K	1231;1225;1270;1225;1170;1274	ENSP00000406043:E1231K;ENSP00000420321:E1270K;ENSP00000420637:E1225K;ENSP00000417992:E1170K	.	E	-	1	0	ROBO1	78759228	1.000000	0.71417	0.978000	0.43139	0.203000	0.24098	7.772000	0.85439	2.630000	0.89119	0.561000	0.74099	GAA		0.567	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78676538	C	T	78676538	3	4	61	1	0	0	0	0	1	0	0	0	13550	922	32	3	1171	3	ROBO1	3	78676538	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12720	78676538	119345892	2579	10564										
ROBO1	6091	broad.mit.edu	37	chr3	78700930	78700930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtccgtttctcttcttgcGgtgtcgataaagccagatgc	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78700930G>A	ENST00000464233.1	-	19	2877	c.2764C>T	c.(2764-2766)Cgc>Tgc	p.R922C	ROBO1_ENST00000495273.1_Missense_Mutation_p.R886C|ROBO1_ENST00000436010.2_Missense_Mutation_p.R883C|ROBO1_ENST00000467549.1_Missense_Mutation_p.R886C	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	922					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.R899C(1)|p.R886C(1)|p.R922C(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CTCTTCTTGCGGTGTCGATAA	0.433																																																3	Substitution - Missense(3)	large_intestine(3)	3											90	86	87					3																	78700930		1975	4172	6147	78783620	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2764C>T	3.37:g.78700930G>A	ENSP00000420321:p.Arg922Cys		78783620	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553084	0.45487	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.67865	-0.26;-0.29;-0.11;-0.04	6.08	3.24	0.37175	.	0.000000	0.85682	D	0.000000	T	0.80768	0.4686	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;0.998;1.0;1.0	T	0.80663	-0.1282	9	.	.	.	.	15.9016	0.79380	0.0:0.0:0.4121:0.5879	.	886;922;886;886;883	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	C	883;886;922;886;886;926	ENSP00000406043:R883C;ENSP00000420321:R922C;ENSP00000420637:R886C;ENSP00000417992:R886C	.	R	-	1	0	ROBO1	78783620	1.000000	0.71417	0.914000	0.36105	0.034000	0.12701	2.061000	0.41403	0.411000	0.25702	0.655000	0.94253	CGC		0.433	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78700930	G	A	78700930	3	1	61	1	0	0	0	0	1	0	0	0	13550	1116	39	1	2243	1	ROBO1	3	78700930	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24392	78700930	119321500	2580	10565										
ROBO1	6091	broad.mit.edu	37	chr3	78708901	78708901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccaactaactagaattgCagttccgtttccatcattct	5	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78708901C>A	ENST00000464233.1	-	17	2490	c.2377G>T	c.(2377-2379)Gca>Tca	p.A793S	ROBO1_ENST00000495273.1_Missense_Mutation_p.A757S|ROBO1_ENST00000436010.2_Missense_Mutation_p.A754S|ROBO1_ENST00000467549.1_Missense_Mutation_p.A757S	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	793	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.A770S(1)|p.A793S(1)|p.A757S(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ACTAGAATTGCAGTTCCGTTT	0.383																																																3	Substitution - Missense(3)	large_intestine(3)	3											53	53	53					3																	78708901		1848	4092	5940	78791591	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2377G>T	3.37:g.78708901C>A	ENSP00000420321:p.Ala793Ser		78791591	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.697056	0.30142	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.95	5.07	0.68467	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.045914	0.85682	N	0.000000	T	0.40347	0.1113	N	0.01352	-0.895	0.47621	D	0.999474	B;B;D;B;B	0.89917	0.001;0.169;1.0;0.226;0.072	B;B;D;B;B	0.91635	0.004;0.267;0.999;0.267;0.122	T	0.57033	-0.7880	9	.	.	.	.	16.4882	0.84190	0.1322:0.8678:0.0:0.0	.	757;793;757;757;754	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	S	754;757;793;757;757;797	ENSP00000406043:A754S;ENSP00000420321:A793S;ENSP00000420637:A757S;ENSP00000417992:A757S	.	A	-	1	0	ROBO1	78791591	0.977000	0.34250	1.000000	0.80357	0.984000	0.73092	2.285000	0.43487	1.502000	0.48669	0.491000	0.48974	GCA		0.383	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78708901	C	A	78708901	3	1	61	1	0	0	0	0	1	0	0	0	13550	710	25	2	2638	2	ROBO1	3	78708901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7971	78708901	119313529	2581	10566										
ROBO1	6091	broad.mit.edu	37	chr3	78717122	78717122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaaggtaaattgcattaGgtttgagtcctttaatggca	11	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:78717122G>T	ENST00000464233.1	-	14	1990	c.1877C>A	c.(1876-1878)cCt>cAt	p.P626H	ROBO1_ENST00000495273.1_Missense_Mutation_p.P590H|ROBO1_ENST00000436010.2_Missense_Mutation_p.P587H|ROBO1_ENST00000467549.1_Missense_Mutation_p.P590H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	626	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.P590H(1)|p.P603H(1)|p.P626H(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AATTGCATTAGGTTTGAGTCC	0.413																																																3	Substitution - Missense(3)	large_intestine(3)	3											97	94	95					3																	78717122		1942	4148	6090	78799812	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1877C>A	3.37:g.78717122G>T	ENSP00000420321:p.Pro626His		78799812	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005982	0.93287	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414;ENST00000495961	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.84	5.84	0.93424	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87845	0.6280	H	0.94345	3.525	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0;1.0	D	0.90312	0.4338	9	.	.	.	.	20.139	0.98050	0.0:0.0:1.0:0.0	.	590;590;626;590;590;587	Q9Y6N7-3;Q1RMC7;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;.;ROBO1_HUMAN;.;.;.	H	587;590;626;590;590;630;163	ENSP00000406043:P587H;ENSP00000420321:P626H;ENSP00000420637:P590H;ENSP00000417992:P590H;ENSP00000418553:P163H	.	P	-	2	0	ROBO1	78799812	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.771000	0.98977	2.764000	0.94973	0.655000	0.94253	CCT		0.413	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78717122	G	T	78717122	3	4	61	1	0	0	0	0	1	0	0	0	13550	1000	35	2	3150	2	ROBO1	3	78717122	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8221	78717122	119305308	2582	10567										
GBE1	2632	broad.mit.edu	37	chr3	81720073	81720073	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttccataatccagtttTttgtatgggtacgaaaatgg	8	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:81720073T>G	ENST00000429644.2	-	3	988	c.345A>C	c.(343-345)aaA>aaC	p.K115N	GBE1_ENST00000489715.1_Missense_Mutation_p.K74N|GBE1_ENST00000477426.1_5'UTR	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	115					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.K115N(2)		breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AATCCAGTTTTTTGTATGGGT	0.358									Glycogen Storage Disease, type IV																																							2	Substitution - Missense(2)	large_intestine(2)	3											72	68	70					3																	81720073		1813	4090	5903	81802763	SO:0001583	missense	2632	Familial Cancer Database	Andersen Disease, Brancher deficiency		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"glycogen branching enzyme", "Andersen disease", "glycogen storage disease type IV"	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.345A>C	3.37:g.81720073T>G	ENSP00000410833:p.Lys115Asn		81802763	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.123697	0.37436	.	.	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715	T;T	0.18960	2.18;2.19	5.5	5.5	0.81552	Immunoglobulin E-set (1);Glycoside hydrolase, family 13, N-terminal (1);Immunoglobulin-like fold (1);	0.304797	0.35838	N	0.002955	T	0.26810	0.0656	L	0.41573	1.285	0.41283	D	0.986926	B;P	0.49447	0.08;0.924	B;P	0.52598	0.055;0.703	T	0.01945	-1.1242	10	0.49607	T	0.09	-11.6962	9.6647	0.39977	0.0:0.0818:0.0:0.9182	.	74;115	E9PGM4;Q04446	.;GLGB_HUMAN	N	115;166;74	ENSP00000410833:K115N;ENSP00000419638:K74N	ENSP00000264326:K166N	K	-	3	2	GBE1	81802763	0.995000	0.38212	1.000000	0.80357	0.719000	0.41307	0.096000	0.15147	2.084000	0.62774	0.528000	0.53228	AAA		0.358	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			G	81720073	T	G	81720073	3	3	61	1	0	0	0	0	1	0	0	0	6290	1838	64	4	1819	4	GBE1	3	81720073	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3002951	81720073	116302357	2583	10568										
CADM2	253559	broad.mit.edu	37	chr3	85961686	85961686	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagccatgcaggtgctagaAatacactgtaagtaaacact	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:85961686A>G	ENST00000407528.2	+	5	728	c.666A>G	c.(664-666)gaA>gaG	p.E222E	CADM2_ENST00000383699.3_Silent_p.E231E|CADM2_ENST00000405615.2_Silent_p.E224E	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	222					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.E224E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AGGTGCTAGAAATACACTGTA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											99	88	92					3																	85961686		2203	4300	6503	86044376	SO:0001819	synonymous_variant	253559			AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.666A>G	3.37:g.85961686A>G			86044376	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Silent	SNP	ENST00000407528.2	37	CCDS54614.1																																																																																				0.458	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		G	85961686	A	G	85961686	2	3	61	1	0	0	0	0	0	0	0	1	2573	11	1	4		4	CADM2	3	85961686	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4241613	85961686	112060744	2584	10569										
CADM2	253559	broad.mit.edu	37	chr3	86114860	86114860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctatctttctgcttggtcGatatctggcaaggcataaag	9	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:86114860G>A	ENST00000407528.2	+	9	1231	c.1169G>A	c.(1168-1170)cGa>cAa	p.R390Q	CADM2_ENST00000383699.3_Missense_Mutation_p.R359Q|CADM2_ENST00000405615.2_Missense_Mutation_p.R392Q	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	390					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.R392Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTGCTTGGTCGATATCTGGCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											201	171	181					3																	86114860		2203	4300	6503	86197550	SO:0001583	missense	253559			AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.1169G>A	3.37:g.86114860G>A	ENSP00000384575:p.Arg390Gln		86197550	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528575	0.85706	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.71698	-0.38;-0.59;-0.59	5.76	5.76	0.90799	Neurexin/syndecan/glycophorin C (1);	0.000000	0.85682	D	0.000000	D	0.84070	0.5391	M	0.77313	2.365	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79108	0.981;0.99;0.992	T	0.79495	-0.1780	10	0.19590	T	0.45	.	19.964	0.97260	0.0:0.0:1.0:0.0	.	392;359;390	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	Q	359;390;392	ENSP00000373200:R359Q;ENSP00000384575:R390Q;ENSP00000384193:R392Q	ENSP00000373200:R359Q	R	+	2	0	CADM2	86197550	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	8.062000	0.89475	2.721000	0.93114	0.650000	0.86243	CGA		0.408	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	86114860	G	A	86114860	3	1	61	1	0	0	0	0	1	0	0	0	2573	1058	37	1	1274	1	CADM2	3	86114860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153174	86114860	111907570	2585	10570										
CHMP2B	25978	broad.mit.edu	37	chr3	87294956	87294956	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctacggaaacagaagacGagaacttttgctgtaagttc	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:87294956G>A	ENST00000263780.4	+	3	457	c.219G>A	c.(217-219)acG>acA	p.T73T	CHMP2B_ENST00000472024.1_3'UTR|CHMP2B_ENST00000494980.1_Silent_p.T73T|CHMP2B_ENST00000471660.1_Silent_p.T32T	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	73					cell death (GO:0008219)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)	p.T73T(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	12	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		AACAGAAGACGAGAACTTTTG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	3											83	88	87					3																	87294956		2203	4300	6503	87377646	SO:0001819	synonymous_variant	25978			BC001553	CCDS2918.1, CCDS58840.1	3p12.1	2011-09-21	2011-09-21		ENSG00000083937	ENSG00000083937		"Charged multivesicular body proteins"	24537	protein-coding gene	gene with protein product	"VPS2 homolog B (S. cerevisiae)"	609512	"chromatin modifying protein 2B"			11559748	Standard	NM_014043		Approved	DKFZP564O123, CHMP2.5, VPS2B	uc003dqp.4	Q9UQN3	OTTHUMG00000158982	ENST00000263780.4:c.219G>A	3.37:g.87294956G>A			87377646	B4DJG8|Q53HC7|Q9Y4U6	Silent	SNP	ENST00000263780.4	37	CCDS2918.1																																																																																				0.363	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043		A	87294956	G	A	87294956	2	1	61	1	0	0	0	0	0	0	0	1	3361	1045	37	1		1	CHMP2B	3	87294956	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1180096	87294956	110727474	2586	10571										
CHMP2B	25978	broad.mit.edu	37	chr3	87302628	87302628	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatattgtgaatcaagttCttgatgaaattggaattgaa	10	2	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:87302628C>A	ENST00000263780.4	+	5	737	c.499C>A	c.(499-501)Ctt>Att	p.L167I	CHMP2B_ENST00000494980.1_Missense_Mutation_p.L137I|CHMP2B_ENST00000471660.1_Missense_Mutation_p.L126I	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	167					cell death (GO:0008219)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)	p.L167I(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	12	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GAATCAAGTTCTTGATGAAAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	101	102					3																	87302628		2203	4300	6503	87385318	SO:0001583	missense	25978			BC001553	CCDS2918.1, CCDS58840.1	3p12.1	2011-09-21	2011-09-21		ENSG00000083937	ENSG00000083937		"Charged multivesicular body proteins"	24537	protein-coding gene	gene with protein product	"VPS2 homolog B (S. cerevisiae)"	609512	"chromatin modifying protein 2B"			11559748	Standard	NM_014043		Approved	DKFZP564O123, CHMP2.5, VPS2B	uc003dqp.4	Q9UQN3	OTTHUMG00000158982	ENST00000263780.4:c.499C>A	3.37:g.87302628C>A	ENSP00000263780:p.Leu167Ile		87385318	B4DJG8|Q53HC7|Q9Y4U6	Missense_Mutation	SNP	ENST00000263780.4	37	CCDS2918.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759715	0.89932	.	.	ENSG00000083937	ENST00000471660;ENST00000263780;ENST00000494980	T;T;T	0.73363	-0.74;-0.74;-0.74	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.90772	0.7103	H	0.94423	3.535	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.997	D	0.92572	0.6067	10	0.87932	D	0	-32.3853	20.0499	0.97621	0.0:1.0:0.0:0.0	.	126;167	B4DJG8;Q9UQN3	.;CHM2B_HUMAN	I	126;167;137	ENSP00000419998:L126I;ENSP00000263780:L167I;ENSP00000418920:L137I	ENSP00000263780:L167I	L	+	1	0	CHMP2B	87385318	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.641000	0.61375	2.734000	0.93682	0.650000	0.86243	CTT		0.368	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043		A	87302628	C	A	87302628	3	1	61	1	0	0	0	0	1	0	0	0	3361	913	32	2	517	2	CHMP2B	3	87302628	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7672	87302628	110719802	2587	10572										
POU1F1	5449	broad.mit.edu	37	chr3	87309109	87309109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcagacttgttttcacccGtttttctctctgcctccggt	6	13	4	1	rs104893755		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:87309109G>A	ENST00000350375.2	-	6	935	c.811C>T	c.(811-813)Cgg>Tgg	p.R271W	POU1F1_ENST00000560656.1_3'UTR|POU1F1_ENST00000344265.3_Missense_Mutation_p.R297W	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	271			R -> W (in CPHD1). {ECO:0000269|PubMed:1472057, ECO:0000269|PubMed:1509262, ECO:0000269|PubMed:15928241, ECO:0000269|PubMed:7852536}.		B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R271W(1)		central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		GTTTTCACCCGTTTTTCTCTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3	GRCh37	CM920590	POU1F1	M	rs104893755						97	100	99					3																	87309109		2202	4300	6502	87391799	SO:0001583	missense	5449			D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"Homeoboxes / POU class"	9210	protein-coding gene	gene with protein product	"growth hormone factor 1"	173110	"POU domain class 1, transcription factor 1"	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.811C>T	3.37:g.87309109G>A	ENSP00000263781:p.Arg271Trp		87391799	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Missense_Mutation	SNP	ENST00000350375.2	37	CCDS2919.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835724	0.71373	.	.	ENSG00000064835	ENST00000350375;ENST00000344265	D;D	0.96774	-4.12;-4.12	6.06	2.98	0.34508	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	H	0.97158	3.95	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99899	1.1155	9	0.87932	D	0	.	13.8657	0.63588	0.0:0.0:0.3248:0.6752	.	297;271	P28069-2;P28069	.;PIT1_HUMAN	W	271;297	ENSP00000263781:R271W;ENSP00000342931:R297W	ENSP00000342931:R297W	R	-	1	2	POU1F1	87391799	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.730000	0.47335	0.848000	0.35191	0.650000	0.86243	CGG		0.373	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306		A	87309109	G	A	87309109	3	1	61	1	0	0	0	0	1	0	0	0	12300	1144	40	1	68	1	POU1F1	3	87309109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6481	87309109	110713321	2588	10573										
POU1F1	5449	broad.mit.edu	37	chr3	87313510	87313510	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttctggagaatccatgtCtattggctcttccaccaatt	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:87313510C>A	ENST00000350375.2	-	3	491	c.367G>T	c.(367-369)Gac>Tac	p.D123Y	POU1F1_ENST00000560656.1_Missense_Mutation_p.D123Y|POU1F1_ENST00000344265.3_Missense_Mutation_p.D149Y	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	123					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.D123Y(1)		central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		GAATCCATGTCTATTGGCTCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	120	119					3																	87313510		2203	4300	6503	87396200	SO:0001583	missense	5449			D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"Homeoboxes / POU class"	9210	protein-coding gene	gene with protein product	"growth hormone factor 1"	173110	"POU domain class 1, transcription factor 1"	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.367G>T	3.37:g.87313510C>A	ENSP00000263781:p.Asp123Tyr		87396200	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Missense_Mutation	SNP	ENST00000350375.2	37	CCDS2919.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215861	0.79352	.	.	ENSG00000064835	ENST00000350375;ENST00000344265	D;D	0.89617	-2.54;-2.53	5.64	5.64	0.86602	.	0.151781	0.64402	D	0.000017	D	0.94149	0.8123	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.94260	0.7501	10	0.87932	D	0	.	19.6984	0.96043	0.0:1.0:0.0:0.0	.	149;123	P28069-2;P28069	.;PIT1_HUMAN	Y	123;149	ENSP00000263781:D123Y;ENSP00000342931:D149Y	ENSP00000342931:D149Y	D	-	1	0	POU1F1	87396200	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	6.949000	0.75971	2.658000	0.90341	0.655000	0.94253	GAC		0.418	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306		A	87313510	C	A	87313510	3	1	61	1	0	0	0	0	1	0	0	0	12300	913	32	2	524	2	POU1F1	3	87313510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4401	87313510	110708920	2589	10574										
HTR1F	3355	broad.mit.edu	37	chr3	88040034	88040034	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actatcaactcccttgtgatCgctgcaattattgtgacccg	7	12	1	2	rs111422517	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:88040034C>T	ENST00000319595.4	+	1	189	c.135C>T	c.(133-135)atC>atT	p.I45I		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	45					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.I45I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	CCCTTGTGATCGCTGCAATTA	0.473													C|||	12	0.00239617	0.0076	0.0029	5008	,	,		17871	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						C		37,4369	41.6+/-74.8	0,37,2166	158	149	152		135	-8	0.8	3	dbSNP_132	152	0,8600		0,0,4300	no	coding-synonymous	HTR1F	NM_000866.3		0,37,6466	TT,TC,CC		0.0,0.8398,0.2845		45/367	88040034	37,12969	2203	4300	6503	88122724	SO:0001819	synonymous_variant	3355			L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5292	protein-coding gene	gene with protein product		182134	"5-hydroxytryptamine (serotonin) receptor 1F"			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.135C>T	3.37:g.88040034C>T			88122724		Silent	SNP	ENST00000319595.4	37	CCDS2920.1																																																																																				0.473	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866		T	88040034	C	T	88040034	2	4	61	1	0	0	0	0	0	0	0	1	7461	874	31	1		1	HTR1F	3	88040034	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726524	88040034	109982396	2590	10575										
CGGBP1	8545	broad.mit.edu	37	chr3	88104993	88104993	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcagaaccacattgcaaGaagtgcagaagagttttcct	9	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:88104993G>T	ENST00000398392.2	-	1	1466	c.134C>A	c.(133-135)tCt>tAt	p.S45Y	CGGBP1_ENST00000309534.6_Missense_Mutation_p.S45Y|CGGBP1_ENST00000474441.1_5'Flank|CGGBP1_ENST00000462901.1_Missense_Mutation_p.S45Y|CGGBP1_ENST00000482016.1_Missense_Mutation_p.S45Y			Q9UFW8	CGBP1_HUMAN	CGG triplet repeat binding protein 1	45					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.S45Y(2)		kidney(1)|large_intestine(2)|lung(2)	5		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)		CACATTGCAAGAAGTGCAGAA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	3											104	101	102					3																	88104993		1993	4177	6170	88187683	SO:0001583	missense	8545			AJ000258	CCDS43111.1	3p12-p11.1	2008-07-18			ENSG00000163320	ENSG00000163320			1888	protein-coding gene	gene with protein product	"p20-CGG binding protein"	603363				9201980, 14667814	Standard	NM_001195308		Approved	p20-CGGBP, CGGBP	uc003dqt.3	Q9UFW8	OTTHUMG00000159009	ENST00000398392.2:c.134C>A	3.37:g.88104993G>T	ENSP00000381429:p.Ser45Tyr		88187683	D3DU38|O15183	Missense_Mutation	SNP	ENST00000398392.2	37	CCDS43111.1	.	.	.	.	.	.	.	.	.	.	G	9.977	1.227033	0.22542	.	.	ENSG00000163320	ENST00000309534;ENST00000398392;ENST00000482016;ENST00000462901;ENST00000467332	.	.	.	5.94	5.94	0.96194	.	0.000000	0.38959	U	0.001514	T	0.38453	0.1041	N	0.19112	0.55	0.43494	D	0.995734	P	0.47910	0.902	B	0.38655	0.278	T	0.18023	-1.0350	9	0.27785	T	0.31	.	17.5861	0.87982	0.0:0.0:1.0:0.0	.	45	Q9UFW8	CGBP1_HUMAN	Y	45	.	ENSP00000381428:S45Y	S	-	2	0	CGGBP1	88187683	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.635000	0.61332	2.834000	0.97654	0.558000	0.71614	TCT		0.458	CGGBP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352955.1	NM_001008390		T	88104993	G	T	88104993	3	4	61	1	0	0	0	0	1	0	0	0	3308	942	33	2	373	2	CGGBP1	3	88104993	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64959	88104993	109917437	2591	10576										
ZNF654	55279	broad.mit.edu	37	chr3	88189527	88189527	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaaagactcatctagtaAtgagaaacaaactattagtc	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:88189527A>C	ENST00000309495.5	+	1	1274	c.1067A>C	c.(1066-1068)aAt>aCt	p.N356T	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	356					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N356T(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TCATCTAGTAATGAGAAACAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											39	36	37					3																	88189527		1835	4087	5922	88272217	SO:0001583	missense	55279			AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.1067A>C	3.37:g.88189527A>C	ENSP00000312141:p.Asn356Thr		88272217	Q9H791|Q9NV14	Missense_Mutation	SNP	ENST00000309495.5	37	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	A	5.889	0.348231	0.11126	.	.	ENSG00000175105	ENST00000309495	T	0.09723	2.95	5.53	3.16	0.36331	.	.	.	.	.	T	0.06325	0.0163	N	0.22421	0.69	0.26201	N	0.979446	B	0.28713	0.22	B	0.24541	0.054	T	0.38112	-0.9676	9	0.10377	T	0.69	.	8.5796	0.33621	0.7926:0.0:0.2074:0.0	.	356	Q8IZM8	ZN654_HUMAN	T	356	ENSP00000312141:N356T	ENSP00000312141:N356T	N	+	2	0	ZNF654	88272217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.398000	0.34554	0.919000	0.36945	0.533000	0.62120	AAT		0.358	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293		C	88189527	A	C	88189527	3	2	61	1	0	0	0	0	1	0	0	0	18106	101	4	4	1069	4	ZNF654	3	88189527	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	84534	88189527	109832903	2592	10577										
EPHA3	2042	broad.mit.edu	37	chr3	89448643	89448643	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagactgtatgtattattTcaatgcagtctagaggaggg	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:89448643T>G	ENST00000336596.2	+	7	1819				EPHA3_ENST00000494014.1_Intron|EPHA3_ENST00000452448.2_Missense_Mutation_p.F536C	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3						cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.F536C(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ATGTATTATTTCAATGCAGTC	0.408										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	large_intestine(1)	3											80	74	76					3																	89448643		2203	4300	6503	89531333	SO:0001627	intron_variant	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1594+13T>G	3.37:g.89448643T>G			89531333	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.390698	0.42410	.	.	ENSG00000044524	ENST00000452448	T	0.11169	2.8	5.53	4.35	0.52113	.	.	.	.	.	T	0.08044	0.0201	.	.	.	0.22779	N	0.998744	P	0.49447	0.924	B	0.39419	0.299	T	0.25847	-1.0120	7	.	.	.	.	6.7934	0.23711	0.1343:0.0723:0.0:0.7934	.	536	P29320-2	.	C	536	ENSP00000399926:F536C	.	F	+	2	0	EPHA3	89531333	0.814000	0.29104	0.011000	0.14972	0.272000	0.26649	3.050000	0.49877	0.901000	0.36495	0.460000	0.39030	TTC		0.408	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89448643	T	G	89448643	1	3	61	0	1	0	0	0	0	0	0	0	5181	1783	62	4		4	EPHA3	3	89448643	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1259116	89448643	108573787	2593	10578										
PROS1	5627	broad.mit.edu	37	chr3	93619648	93619648	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgataccaccatcatcctacCttcacaagactttgatttga	4	12	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:93619648C>A	ENST00000394236.3	-	7	1043	c.727G>T	c.(727-729)Gat>Tat	p.D243Y	PROS1_ENST00000407433.1_Splice_Site_p.D112Y	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	243	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		D -> N (in THPH5). {ECO:0000269|PubMed:11372770}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)	p.D243Y(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ATCATCCTACCTTCACAAGAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3	GRCh37	CM014079	PROS1	M							138	121	127					3																	93619648		2203	4300	6503	95102338	SO:0001630	splice_region_variant	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.727+1G>T	3.37:g.93619648C>A			95102338	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.261689	0.39995	.	.	ENSG00000184500	ENST00000394236;ENST00000407433	D;D	0.94828	-3.53;-3.53	4.08	4.08	0.47627	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98040	0.9354	H	0.97214	3.96	0.80722	D	1	D	0.71674	0.998	P	0.61397	0.888	D	0.99748	1.1017	9	.	.	.	.	16.8099	0.85716	0.0:1.0:0.0:0.0	.	243	P07225	PROS_HUMAN	Y	243;112	ENSP00000377783:D243Y;ENSP00000385794:D112Y	.	D	-	1	0	PROS1	95102338	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	6.014000	0.70784	2.269000	0.75478	0.591000	0.81541	GAT		0.423	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313	Missense_Mutation	A	93619648	C	A	93619648	5	1	61	1	0	0	0	0	0	0	1	0	12592	695	24	2	1339	2	PROS1	3	93619648	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4171005	93619648	104402782	2594	10579										
PROS1	5627	broad.mit.edu	37	chr3	93624637	93624637	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgctcttacctttacaatCtttcttatttgaaagcataa	3	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:93624637C>A	ENST00000394236.3	-	6	908	c.592G>T	c.(592-594)Gat>Tat	p.D198Y	PROS1_ENST00000407433.1_Missense_Mutation_p.D67Y	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	198	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)	p.D198Y(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCTTTACAATCTTTCTTATTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											62	63	62					3																	93624637		2203	4295	6498	95107327	SO:0001583	missense	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.592G>T	3.37:g.93624637C>A	ENSP00000377783:p.Asp198Tyr		95107327	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	C	8.385	0.838335	0.16891	.	.	ENSG00000184500	ENST00000394236;ENST00000407433;ENST00000348974	D;D;D	0.96365	-3.99;-3.99;-3.99	4.44	4.44	0.53790	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.526359	0.20817	N	0.085131	D	0.94618	0.8265	L	0.29908	0.895	0.41109	D	0.985725	D	0.55385	0.971	P	0.52710	0.707	D	0.94487	0.7698	10	0.72032	D	0.01	.	10.8451	0.46739	0.0:0.9133:0.0:0.0867	.	198	P07225	PROS_HUMAN	Y	198;67;230	ENSP00000377783:D198Y;ENSP00000385794:D67Y;ENSP00000330021:D230Y	ENSP00000330021:D230Y	D	-	1	0	PROS1	95107327	0.999000	0.42202	1.000000	0.80357	0.509000	0.34042	2.588000	0.46137	2.314000	0.78098	0.484000	0.47621	GAT		0.308	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		A	93624637	C	A	93624637	3	1	61	1	0	0	0	0	1	0	0	0	12592	913	32	2	1478	2	PROS1	3	93624637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4989	93624637	104397793	2595	10580										
PROS1	5627	broad.mit.edu	37	chr3	93624978	93624978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcagaggactacactggTctggaatggctgaaggaaat	14	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:93624978T>C	ENST00000394236.3	-	5	672	c.356A>G	c.(355-357)gAc>gGc	p.D119G	PROS1_ENST00000407433.1_5'UTR	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	119	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)	p.D119G(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ACTACACTGGTCTGGAATGGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											102	105	104					3																	93624978		2203	4300	6503	95107668	SO:0001583	missense	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.356A>G	3.37:g.93624978T>C	ENSP00000377783:p.Asp119Gly		95107668	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.747672	0.49257	.	.	ENSG00000184500	ENST00000394236;ENST00000348974	D;D	0.91996	-2.95;-2.21	4.44	4.44	0.53790	Epidermal growth factor-like, type 3 (1);	0.290270	0.36268	N	0.002689	D	0.91267	0.7247	M	0.80508	2.5	0.80722	D	1	P	0.46784	0.884	B	0.38842	0.283	D	0.92586	0.6079	10	0.87932	D	0	.	13.8635	0.63574	0.0:0.0:0.0:1.0	.	119	P07225	PROS_HUMAN	G	119;151	ENSP00000377783:D119G;ENSP00000330021:D151G	ENSP00000330021:D151G	D	-	2	0	PROS1	95107668	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.816000	0.69222	1.876000	0.54355	0.397000	0.26171	GAC		0.358	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		C	93624978	T	C	93624978	3	2	61	1	0	0	0	0	1	0	0	0	12592	1667	58	4	1718	4	PROS1	3	93624978	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	341	93624978	104397452	2596	10581										
DHFRL1	200895	broad.mit.edu	37	chr3	93779817	93779817	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccttctcacatacttcaAatttgtacttgatgtgtttc	4	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:93779817A>C	ENST00000394221.2	-	2	988	c.539T>G	c.(538-540)tTt>tGt	p.F180C	DHFRL1_ENST00000481631.1_Intron|DHFRL1_ENST00000314636.2_Missense_Mutation_p.F180C|NSUN3_ENST00000314622.4_5'Flank	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	180	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.				glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)	p.F180C(1)		kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						ACATACTTCAAATTTGTACTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	102	103					3																	93779817		2203	4300	6503	95262507	SO:0001583	missense	200895			AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"dihydrofolate reductase pseudogene 4"	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.539T>G	3.37:g.93779817A>C	ENSP00000377768:p.Phe180Cys		95262507	D3DN30|Q6P4I9	Missense_Mutation	SNP	ENST00000394221.2	37	CCDS2926.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.885398	0.33255	.	.	ENSG00000178700	ENST00000314636;ENST00000394221	T;T	0.76578	-1.03;-1.03	1.25	-0.145	0.13436	Dihydrofolate reductase domain (2);Dihydrofolate reductase-like domain (2);	0.068491	0.64402	U	0.000015	D	0.89298	0.6675	H	0.97635	4.045	0.54753	D	0.999984	D	0.89917	1.0	D	0.97110	1.0	D	0.84779	0.0772	10	0.87932	D	0	-10.2394	4.5235	0.11971	0.7128:0.0:0.0:0.2872	.	180	Q86XF0	DYRL1_HUMAN	C	180	ENSP00000319170:F180C;ENSP00000377768:F180C	ENSP00000319170:F180C	F	-	2	0	DHFRL1	95262507	1.000000	0.71417	0.998000	0.56505	0.612000	0.37316	1.500000	0.35682	-0.032000	0.13758	0.369000	0.22263	TTT		0.373	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815		C	93779817	A	C	93779817	3	2	61	1	0	0	0	0	1	0	0	0	4493	14	1	4	28	4	DHFRL1	3	93779817	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	154839	93779817	104242613	2597	10582										
NSUN3	63899	broad.mit.edu	37	chr3	93803060	93803060	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagggctatcacacactcTctcagggatctttacccaac	7	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:93803060T>A	ENST00000314622.4	+	3	443	c.232T>A	c.(232-234)Tct>Act	p.S78T		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	78							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.S78T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						TCACACACTCTCTCAGGGATC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	78	78					3																	93803060		2203	4300	6503	95285750	SO:0001583	missense	63899			BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"NOP2/Sun domain containing"	26208	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 3", "NOL1/NOP2/Sun domain family, member 3"			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.232T>A	3.37:g.93803060T>A	ENSP00000318986:p.Ser78Thr		95285750	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	37	CCDS2927.1	.	.	.	.	.	.	.	.	.	.	T	0.063	-1.219297	0.01542	.	.	ENSG00000178694	ENST00000314622	T	0.22743	1.94	5.81	1.69	0.24217	.	0.345124	0.34853	N	0.003639	T	0.08223	0.0205	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.38222	-0.9671	10	0.11794	T	0.64	-9.2137	7.2317	0.26046	0.0:0.1516:0.1255:0.7229	.	78	Q9H649	NSUN3_HUMAN	T	78	ENSP00000318986:S78T	ENSP00000318986:S78T	S	+	1	0	NSUN3	95285750	1.000000	0.71417	0.037000	0.18230	0.012000	0.07955	0.827000	0.27421	0.450000	0.26774	0.533000	0.62120	TCT		0.423	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072		A	93803060	T	A	93803060	3	1	61	1	0	0	0	0	1	0	0	0	10710	1551	54	5	242	5	NSUN3	3	93803060	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	23243	93803060	104219370	2598	10583										
EPHA6	285220	broad.mit.edu	37	chr3	97439161	97439161	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcgcctacagaaaattCtcctcagcaagcgatgcatg	8	13	2	1	rs376416003		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97439161C>T	ENST00000389672.5	+	15	2879	c.2841C>T	c.(2839-2841)ttC>ttT	p.F947F		NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	853						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)	p.F853F(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						ACAGAAAATTCTCCTCAGCAA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											87	92	90					3																	97439161		2066	4241	6307	98921851	SO:0001819	synonymous_variant	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.2841C>T	3.37:g.97439161C>T			98921851	D6RAL5	Silent	SNP	ENST00000389672.5	37	CCDS46876.1																																																																																				0.458	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		T	97439161	C	T	97439161	2	4	61	1	0	0	0	0	0	0	0	1	5184	912	32	3		3	EPHA6	3	97439161	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3636101	97439161	100583269	2599	10584										
CRYBG3	131544	broad.mit.edu	37	chr3	97596024	97596024	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcaagatgaacaagaaAattcttcctttactatatta	3	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97596024A>G	ENST00000182096.4	+	1	206	c.142A>G	c.(142-144)Aat>Gat	p.N48D		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	1996							carbohydrate binding (GO:0030246)	p.N48D(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TGAACAAGAAAATTCTTCCTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	60	60					3																	97596024		1831	4082	5913	99078714	SO:0001583	missense	131544					3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.142A>G	3.37:g.97596024A>G	ENSP00000182096:p.Asn48Asp		99078714	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	A	14.63	2.591446	0.46214	.	.	ENSG00000080200	ENST00000182096	T	0.77229	-1.08	5.6	3.18	0.36537	.	4.758750	0.00166	N	0.000019	T	0.71239	0.3316	L	0.34521	1.04	0.09310	N	0.999992	P	0.48694	0.914	B	0.41374	0.355	T	0.59532	-0.7437	10	0.72032	D	0.01	.	6.9681	0.24635	0.6125:0.3135:0.074:0.0	.	48	Q68DQ2	CRBG3_HUMAN	D	48	ENSP00000182096:N48D	ENSP00000182096:N48D	N	+	1	0	CRYBG3	99078714	0.775000	0.28604	0.659000	0.29680	0.854000	0.48673	2.341000	0.43983	0.399000	0.25367	-0.340000	0.08031	AAT		0.363	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		G	97596024	A	G	97596024	3	3	61	1	0	0	0	0	1	0	0	0	3919	14	1	4	144	4	CRYBG3	3	97596024	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	156863	97596024	100426406	2600	10585										
CRYBG3	131544	broad.mit.edu	37	chr3	97655645	97655645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagatggatagcttatgaaGgatccaatttcttgggaaga	11	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97655645G>A	ENST00000182096.4	+	16	2618	c.2554G>A	c.(2554-2556)Gga>Aga	p.G852R	CRYBG3_ENST00000485253.1_3'UTR|CRYBG3_ENST00000389622.2_Missense_Mutation_p.G59R	NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2800							carbohydrate binding (GO:0030246)	p.G852R(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						AGCTTATGAAGGATCCAATTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	88	91					3																	97655645		1837	4099	5936	99138335	SO:0001583	missense	131544					3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.2554G>A	3.37:g.97655645G>A	ENSP00000182096:p.Gly852Arg		99138335	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	G	18.38	3.612242	0.66672	.	.	ENSG00000080200	ENST00000182096;ENST00000495403;ENST00000389622	T;T;T	0.75154	-0.91;-0.91;-0.91	5.76	5.76	0.90799	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.193661	0.36482	N	0.002561	T	0.76955	0.4060	N	0.14661	0.345	0.51233	D	0.999913	D	0.89917	1.0	D	0.85130	0.997	T	0.75045	-0.3456	10	0.26408	T	0.33	.	19.5917	0.95518	0.0:0.0:1.0:0.0	.	852	Q68DQ2	CRBG3_HUMAN	R	852;58;59	ENSP00000182096:G852R;ENSP00000418420:G58R;ENSP00000374273:G59R	ENSP00000182096:G852R	G	+	1	0	CRYBG3	99138335	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.332000	0.72934	2.726000	0.93360	0.655000	0.94253	GGA		0.383	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		A	97655645	G	A	97655645	3	1	61	1	0	0	0	0	1	0	0	0	3919	1001	35	3	2616	3	CRYBG3	3	97655645	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59621	97655645	100366785	2601	10586										
OR5H14	403273	broad.mit.edu	37	chr3	97869038	97869038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccccacaggctgatgaccAagatatgatggagtctctat	9	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97869038A>G	ENST00000437310.1	+	1	869	c.809A>G	c.(808-810)cAa>cGa	p.Q270R	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q270R(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						GCTGATGACCAAGATATGATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											55	52	53					3																	97869038		2203	4299	6502	99351728	SO:0001583	missense	403273				CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.809A>G	3.37:g.97869038A>G	ENSP00000401706:p.Gln270Arg		99351728	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	A	5.086	0.201522	0.09652	.	.	ENSG00000236032	ENST00000437310	T	0.00152	8.66	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.314651	0.23043	N	0.052593	T	0.00144	0.0004	L	0.49640	1.575	0.09310	N	1	B	0.20459	0.045	B	0.26614	0.071	T	0.15607	-1.0431	10	0.39692	T	0.17	.	8.4219	0.32705	1.0:0.0:0.0:0.0	.	270	A6NHG9	O5H14_HUMAN	R	270	ENSP00000401706:Q270R	ENSP00000401706:Q270R	Q	+	2	0	OR5H14	99351728	0.000000	0.05858	0.465000	0.27155	0.561000	0.35649	-0.243000	0.08915	1.132000	0.42129	0.164000	0.16699	CAA		0.428	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			G	97869038	A	G	97869038	3	3	61	1	0	0	0	0	1	0	0	0	11191	130	5	4	811	4	OR5H14	3	97869038	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	213393	97869038	100153392	2602	10587										
OR5H15	403274	broad.mit.edu	37	chr3	97888137	97888137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctattaattttctaatGgtttttattttctcaggttc	4	6	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97888137G>T	ENST00000356526.2	+	1	594	c.594G>T	c.(592-594)atG>atT	p.M198I		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M198I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						ATTTTCTAATGGTTTTTATTT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											28	33	31					3																	97888137		2200	4286	6486	99370827	SO:0001583	missense	403274				CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.594G>T	3.37:g.97888137G>T	ENSP00000373195:p.Met198Ile		99370827		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	2.222	-0.378115	0.05000	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.36157	1.27	2.48	0.576	0.17380	GPCR, rhodopsin-like superfamily (1);	0.355632	0.24352	N	0.039264	T	0.19485	0.0468	N	0.25286	0.73	0.09310	N	1	B	0.13594	0.008	B	0.20384	0.029	T	0.11372	-1.0590	10	0.35671	T	0.21	.	4.4198	0.11474	0.4896:0.0:0.5104:0.0	.	198	A6NDH6	O5H15_HUMAN	I	198	ENSP00000373195:M198I	ENSP00000373195:M198I	M	+	3	0	OR5H15	99370827	0.000000	0.05858	0.004000	0.12327	0.021000	0.10359	-2.277000	0.01160	0.372000	0.24591	0.184000	0.17185	ATG		0.313	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			T	97888137	G	T	97888137	3	4	61	1	0	0	0	0	1	0	0	0	11192	1348	47	2	596	2	OR5H15	3	97888137	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19099	97888137	100134293	2603	10588										
OR5H6	79295	broad.mit.edu	37	chr3	97984096	97984096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcacaaaaatgttcaaaaGcaatgtttagatctcataca	4	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:97984096G>A	ENST00000383696.2	+	1	1009	c.968G>A	c.(967-969)aGc>aAc	p.S323N	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S323N(1)		cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ATGTTCAAAAGCAATGTTTAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											48	49	49					3																	97984096		2161	4268	6429	99466786	SO:0001583	missense	79295			BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"GPCR / Class A : Olfactory receptors"	14767	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily H, member 6"				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.968G>A	3.37:g.97984096G>A	ENSP00000373196:p.Ser323Asn		99466786	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	37	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	4.099	0.016431	0.07959	.	.	ENSG00000230301	ENST00000383696	T	0.37411	1.2	2.19	1.27	0.21489	.	0.652316	0.13345	N	0.394837	T	0.16557	0.0398	N	0.11364	0.135	0.09310	N	1	B	0.17465	0.022	B	0.22386	0.039	T	0.14282	-1.0478	10	0.36615	T	0.2	.	3.0382	0.06129	0.1839:0.295:0.5211:0.0	.	323	Q8NGV6	OR5H6_HUMAN	N	323	ENSP00000373196:S323N	ENSP00000373196:S323N	S	+	2	0	OR5H6	99466786	0.000000	0.05858	0.899000	0.35326	0.090000	0.18270	-0.122000	0.10627	1.220000	0.43490	0.194000	0.17425	AGC		0.348	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			A	97984096	G	A	97984096	3	1	61	1	0	0	0	0	1	0	0	0	11194	971	34	3	970	3	OR5H6	3	97984096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95959	97984096	100038334	2604	10589										
OR5H2	79310	broad.mit.edu	37	chr3	98001736	98001736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatttcatttcagggatgtCgaatgaggacatggaacagg	13	6	2	1	rs146308829		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98001736C>T	ENST00000355273.2	+	1	5	c.5C>T	c.(4-6)tCg>tTg	p.S2L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S2L(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						TCAGGGATGTCGAATGAGGAC	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		19929	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	LEU/SER	6,4400	11.4+/-27.6	0,6,2197	141	135	137		5	-2.5	0	3	dbSNP_134	137	2,8598	1.2+/-3.3	0,2,4298	yes	missense	OR5H2	NM_001005482.1	145	0,8,6495	TT,TC,CC		0.0233,0.1362,0.0615	possibly-damaging	2/315	98001736	8,12998	2203	4300	6503	99484426	SO:0001583	missense	79310				CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.5C>T	3.37:g.98001736C>T	ENSP00000347418:p.Ser2Leu		99484426	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	C	8.361	0.833092	0.16820	0.001362	2.33E-4	ENSG00000197938	ENST00000355273	T	0.00003	9.83	2.64	-2.55	0.06288	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	P	0.46912	0.886	B	0.35039	0.194	T	0.00934	-1.1509	9	0.35671	T	0.21	.	6.5361	0.22355	0.3434:0.2203:0.4363:0.0	.	2	Q8NGV7	OR5H2_HUMAN	L	2	ENSP00000347418:S2L	ENSP00000347418:S2L	S	+	2	0	OR5H2	99484426	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.847000	0.04331	-0.603000	0.05767	-0.413000	0.06143	TCG		0.398	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			T	98001736	C	T	98001736	3	4	61	1	0	0	0	0	1	0	0	0	11193	893	31	1	7	1	OR5H2	3	98001736	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17640	98001736	100020694	2605	10590										
OR5H2	79310	broad.mit.edu	37	chr3	98002086	98002086	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaactacagaatgttttCtcttggcaacaatggcatat	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98002086C>A	ENST00000355273.2	+	1	355	c.355C>A	c.(355-357)Ctc>Atc	p.L119I	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L119I(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						AGAATGTTTTCTCTTGGCAAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	104	106					3																	98002086		2203	4300	6503	99484776	SO:0001583	missense	79310				CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.355C>A	3.37:g.98002086C>A	ENSP00000347418:p.Leu119Ile		99484776	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	C	9.892	1.204372	0.22205	.	.	ENSG00000197938	ENST00000355273	T	0.12984	2.63	3.2	1.35	0.21983	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35646	U	0.003080	T	0.09686	0.0238	L	0.31845	0.965	0.09310	N	1	P	0.35959	0.53	B	0.36418	0.224	T	0.17471	-1.0368	10	0.52906	T	0.07	.	7.0341	0.24983	0.0:0.7654:0.0:0.2346	.	119	Q8NGV7	OR5H2_HUMAN	I	119	ENSP00000347418:L119I	ENSP00000347418:L119I	L	+	1	0	OR5H2	99484776	0.000000	0.05858	0.043000	0.18650	0.968000	0.65278	-0.177000	0.09796	0.198000	0.20407	0.543000	0.68304	CTC		0.363	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			A	98002086	C	A	98002086	3	1	61	1	0	0	0	0	1	0	0	0	11193	913	32	2	357	2	OR5H2	3	98002086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	350	98002086	100020344	2606	10591										
OR5K3	403277	broad.mit.edu	37	chr3	98109641	98109641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatggtggggaacattggTttggtggcattgatttatat	13	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98109641T>C	ENST00000383695.1	+	1	132	c.132T>C	c.(130-132)ggT>ggC	p.G44G	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	44			G -> D (in dbSNP:rs13068323).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G44G(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						GGAACATTGGTTTGGTGGCAT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	3											278	258	265					3																	98109641		2203	4300	6503	99592331	SO:0001819	synonymous_variant	403277				CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"GPCR / Class A : Olfactory receptors"	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.132T>C	3.37:g.98109641T>C			99592331		Silent	SNP	ENST00000383695.1	37	CCDS33803.1																																																																																				0.408	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			C	98109641	T	C	98109641	2	2	61	1	0	0	0	0	0	0	0	1	11199	1712	60	4		4	OR5K3	3	98109641	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	107555	98109641	99912789	2607	10592										
OR5K3	403277	broad.mit.edu	37	chr3	98109819	98109819	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatggcacaattttattttCtctgtcttgctgaaactaca	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98109819C>A	ENST00000383695.1	+	1	310	c.310C>A	c.(310-312)Ctc>Atc	p.L104I	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L104I(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						ATTTTATTTTCTCTGTCTTGC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											219	216	217					3																	98109819		2203	4300	6503	99592509	SO:0001583	missense	403277				CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"GPCR / Class A : Olfactory receptors"	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.310C>A	3.37:g.98109819C>A	ENSP00000373194:p.Leu104Ile		99592509		Missense_Mutation	SNP	ENST00000383695.1	37	CCDS33803.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894127	0.52121	.	.	ENSG00000206536	ENST00000383695	T	0.00381	7.63	5.15	1.61	0.23674	GPCR, rhodopsin-like superfamily (1);	0.179440	0.27035	N	0.021245	T	0.00300	0.0009	L	0.31526	0.94	0.22199	N	0.999292	P	0.41643	0.758	P	0.45660	0.489	T	0.51787	-0.8661	10	0.72032	D	0.01	-14.537	8.8562	0.35229	0.0:0.6729:0.0:0.3271	.	104	A6NET4	OR5K3_HUMAN	I	104	ENSP00000373194:L104I	ENSP00000373194:L104I	L	+	1	0	OR5K3	99592509	0.000000	0.05858	0.999000	0.59377	0.930000	0.56654	-1.118000	0.03280	0.171000	0.19730	0.603000	0.83216	CTC		0.438	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			A	98109819	C	A	98109819	3	1	61	1	0	0	0	0	1	0	0	0	11199	913	32	2	312	2	OR5K3	3	98109819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178	98109819	99912611	2608	10593										
OR5K1	26339	broad.mit.edu	37	chr3	98188632	98188632	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatctggctcttgtggattCttgctgtgcctgtgctatta	10	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98188632C>T	ENST00000332650.5	+	1	309	c.212C>T	c.(211-213)tCt>tTt	p.S71F		NM_001004736.2	NP_001004736.2	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K, member 1	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S71F(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(21)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTTGTGGATTCTTGCTGTGCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											157	169	165					3																	98188632		2203	4296	6499	99671322	SO:0001583	missense	26339			X64984	CCDS43115.1	3q11.2	2013-09-23			ENSG00000232382	ENSG00000232382		"GPCR / Class A : Olfactory receptors"	8349	protein-coding gene	gene with protein product						1370859	Standard	NM_001004736		Approved	HTPCRX10, HSHTPCRX10	uc003dsm.3	Q8NHB7	OTTHUMG00000160048	ENST00000332650.5:c.212C>T	3.37:g.98188632C>T	ENSP00000373193:p.Ser71Phe		99671322	B9EGY5|Q6IF46	Missense_Mutation	SNP	ENST00000332650.5	37	CCDS43115.1	.	.	.	.	.	.	.	.	.	.	C	1.527	-0.545244	0.04024	.	.	ENSG00000232382	ENST00000332650	T	0.01918	4.56	5.18	3.38	0.38709	GPCR, rhodopsin-like superfamily (1);	0.175802	0.27627	N	0.018528	T	0.00967	0.0032	N	0.01751	-0.74	0.09310	N	1	B	0.26775	0.159	B	0.30105	0.111	T	0.49934	-0.8886	10	0.12103	T	0.63	-19.0	6.3387	0.21310	0.0:0.7149:0.0:0.2851	.	71	Q8NHB7	OR5K1_HUMAN	F	71	ENSP00000373193:S71F	ENSP00000373193:S71F	S	+	2	0	OR5K1	99671322	0.301000	0.24444	0.102000	0.21198	0.080000	0.17528	3.616000	0.54174	1.186000	0.42985	-0.251000	0.11542	TCT		0.418	OR5K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359019.1			T	98188632	C	T	98188632	3	4	61	1	0	0	0	0	1	0	0	0	11197	913	32	3	214	3	OR5K1	3	98188632	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78813	98188632	99833798	2609	10594										
OR5K1	26339	broad.mit.edu	37	chr3	98188932	98188932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggttagttttctgtggatCgaatcacatcaaccactttt	7	8	3	0	rs199803370		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98188932C>T	ENST00000332650.5	+	1	609	c.512C>T	c.(511-513)tCg>tTg	p.S171L		NM_001004736.2	NP_001004736.2	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K, member 1	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S171L(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(21)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTCTGTGGATCGAATCACATC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	249	250	250		512	4.5	0	3		250	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR5K1	NM_001004736.2	145	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	171/309	98188932	2,13004	2203	4300	6503	99671622	SO:0001583	missense	26339			X64984	CCDS43115.1	3q11.2	2013-09-23			ENSG00000232382	ENSG00000232382		"GPCR / Class A : Olfactory receptors"	8349	protein-coding gene	gene with protein product						1370859	Standard	NM_001004736		Approved	HTPCRX10, HSHTPCRX10	uc003dsm.3	Q8NHB7	OTTHUMG00000160048	ENST00000332650.5:c.512C>T	3.37:g.98188932C>T	ENSP00000373193:p.Ser171Leu		99671622	B9EGY5|Q6IF46	Missense_Mutation	SNP	ENST00000332650.5	37	CCDS43115.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904258	0.33628	2.27E-4	1.16E-4	ENSG00000232382	ENST00000332650	T	0.38560	1.13	5.33	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.174299	0.27725	N	0.018113	T	0.58090	0.2098	M	0.78801	2.425	0.09310	N	1	D	0.56287	0.975	P	0.56612	0.802	T	0.55302	-0.8162	10	0.66056	D	0.02	-13.0723	11.7681	0.51943	0.0:0.9138:0.0:0.0862	.	171	Q8NHB7	OR5K1_HUMAN	L	171	ENSP00000373193:S171L	ENSP00000373193:S171L	S	+	2	0	OR5K1	99671622	0.000000	0.05858	0.043000	0.18650	0.066000	0.16364	0.199000	0.17237	1.247000	0.43917	-0.253000	0.11424	TCG		0.398	OR5K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359019.1			T	98188932	C	T	98188932	3	4	61	1	0	0	0	0	1	0	0	0	11197	893	31	1	514	1	OR5K1	3	98188932	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	300	98188932	99833498	2610	10595										
CLDND1	56650	broad.mit.edu	37	chr3	98240148	98240148	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaaatcactggaattttCttgaactggacttcgatatt	6	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98240148C>A	ENST00000503004.1	-	2	1000	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	CLDND1_ENST00000502288.1_Intron|CLDND1_ENST00000341181.6_Nonsense_Mutation_p.E41*|CLDND1_ENST00000513287.1_Nonsense_Mutation_p.E41*|CLDND1_ENST00000508503.1_5'UTR|CLDND1_ENST00000510545.1_Nonsense_Mutation_p.E41*|CLDND1_ENST00000437922.1_Nonsense_Mutation_p.E64*|CLDND1_ENST00000394181.2_Nonsense_Mutation_p.E41*|CLDND1_ENST00000511081.1_Intron|CLDND1_ENST00000394185.2_Nonsense_Mutation_p.E41*|RP11-227H4.5_ENST00000502999.1_RNA|CLDND1_ENST00000394180.2_Nonsense_Mutation_p.E41*|CLDND1_ENST00000507874.1_Nonsense_Mutation_p.E41*			Q9NY35	CLDN1_HUMAN	claudin domain containing 1	41						apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.E41*(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	9						CTGGAATTTTCTTGAACTGGA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											89	85	87					3																	98240148		2203	4300	6503	99722838	SO:0001587	stop_gained	56650			AF116664	CCDS2930.1, CCDS43116.1	3q12.1	2005-12-23	2005-12-23	2005-12-23		ENSG00000080822			1322	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 4"	C3orf4			Standard	NM_001040181		Approved		uc003dst.3	Q9NY35		ENST00000503004.1:c.121G>T	3.37:g.98240148C>A	ENSP00000421226:p.Glu41*		99722838	B3KQR1|D3DN36|F2Z2D9|Q502Y8|Q6UVX2|Q9BUZ9|Q9NZZ5|Q9Y4S9	Nonsense_Mutation	SNP	ENST00000503004.1	37	CCDS2930.1	.	.	.	.	.	.	.	.	.	.	C	37	6.341274	0.97489	.	.	ENSG00000080822	ENST00000507874;ENST00000341181;ENST00000437922;ENST00000394180;ENST00000503004;ENST00000394185;ENST00000394181;ENST00000510545;ENST00000513287;ENST00000511667;ENST00000513452;ENST00000502299;ENST00000508902;ENST00000514537;ENST00000515620;ENST00000507944;ENST00000508659;ENST00000503621;ENST00000508071;ENST00000513130;ENST00000506575	.	.	.	5.25	4.36	0.52297	.	0.368896	0.29424	N	0.012187	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-15.5785	12.9231	0.58243	0.1636:0.8364:0.0:0.0	.	.	.	.	X	41;41;64;41;41;41;41;41;41;19;41;41;41;41;41;41;41;19;41;41;41	.	ENSP00000340247:E41X	E	-	1	0	CLDND1	99722838	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.969000	0.63735	1.181000	0.42912	0.655000	0.94253	GAA		0.393	CLDND1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359071.1	NM_019895		A	98240148	C	A	98240148	4	1	61	1	0	0	0	0	0	1	0	0	3499	922	32	2	656	2	CLDND1	3	98240148	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51216	98240148	99782282	2611	10596										
ST3GAL6	10402	broad.mit.edu	37	chr3	98506953	98506953	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccgacttttttatccaGaatctgttttttcagatcct	4	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98506953G>T	ENST00000483910.1	+	7	794	c.505G>T	c.(505-507)Gaa>Taa	p.E169*	ST3GAL6_ENST00000394162.1_Nonsense_Mutation_p.E169*|ST3GAL6_ENST00000462152.1_3'UTR|ST3GAL6_ENST00000265261.6_Nonsense_Mutation_p.E51*	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	169					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)	p.E169*(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						TTTTTATCCAGAATCTGTTTT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											98	96	97					3																	98506953		2203	4300	6503	99989643	SO:0001587	stop_gained	10402			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.505G>T	3.37:g.98506953G>T	ENSP00000417376:p.Glu169*		99989643	B2RCH2|B3KMI1|D3DN39|F8W6U0	Nonsense_Mutation	SNP	ENST00000483910.1	37	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.291990	0.80914	.	.	ENSG00000064225	ENST00000483910;ENST00000265261;ENST00000497008;ENST00000486334;ENST00000394162;ENST00000485391;ENST00000492254;ENST00000485145	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.2332	17.2504	0.87041	0.0:0.0:1.0:0.0	.	.	.	.	X	169;51;137;169;169;137;192;83	.	ENSP00000265261:E51X	E	+	1	0	ST3GAL6	99989643	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.744000	0.74854	2.671000	0.90904	0.563000	0.77884	GAA		0.368	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		T	98506953	G	T	98506953	4	4	61	1	0	0	0	0	0	1	0	0	15258	943	33	2	527	2	ST3GAL6	3	98506953	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	266805	98506953	99515477	2612	10597										
ST3GAL6	10402	broad.mit.edu	37	chr3	98507177	98507177	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttactttcagaacactaAtggtttttggaagaaaccag	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98507177A>C	ENST00000483910.1	+	8	915	c.626A>C	c.(625-627)aAt>aCt	p.N209T	ST3GAL6_ENST00000394162.1_Missense_Mutation_p.N209T|ST3GAL6_ENST00000462152.1_3'UTR|ST3GAL6_ENST00000265261.6_Missense_Mutation_p.N91T	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	209					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)	p.N209T(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						CAGAACACTAATGGTTTTTGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	88	86					3																	98507177		2202	4300	6502	99989867	SO:0001583	missense	10402			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.626A>C	3.37:g.98507177A>C	ENSP00000417376:p.Asn209Thr		99989867	B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	37	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.584125	0.28268	.	.	ENSG00000064225	ENST00000483910;ENST00000265261;ENST00000486334;ENST00000394162;ENST00000485391;ENST00000492254;ENST00000485145	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	4.84	2.52	0.30459	.	0.989608	0.08238	N	0.976471	T	0.17365	0.0417	N	0.17312	0.475	0.21445	N	0.999684	B;B;B	0.24483	0.104;0.007;0.011	B;B;B	0.25614	0.062;0.039;0.014	T	0.30387	-0.9980	10	0.09590	T	0.72	-35.7446	7.4745	0.27368	0.8162:0.0:0.1838:0.0	.	232;91;209	C9J480;F8W6U0;Q9Y274	.;.;SIA10_HUMAN	T	209;91;209;209;177;232;123	ENSP00000417376:N209T;ENSP00000265261:N91T;ENSP00000418896:N209T;ENSP00000377717:N209T;ENSP00000418650:N177T;ENSP00000417201:N232T;ENSP00000419202:N123T	ENSP00000265261:N91T	N	+	2	0	ST3GAL6	99989867	0.007000	0.16637	0.915000	0.36163	0.994000	0.84299	1.226000	0.32563	0.987000	0.38709	0.460000	0.39030	AAT		0.323	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		C	98507177	A	C	98507177	3	2	61	1	0	0	0	0	1	0	0	0	15258	101	4	4	652	4	ST3GAL6	3	98507177	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	224	98507177	99515253	2613	10598										
ST3GAL6	10402	broad.mit.edu	37	chr3	98512582	98512582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattatagaaaaaaacctcGtaatcaacttgactcaagat	4	8	2	3	rs139832763		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:98512582G>T	ENST00000483910.1	+	10	1262	c.973G>T	c.(973-975)Gta>Tta	p.V325L	ST3GAL6_ENST00000394162.1_Missense_Mutation_p.V325L|ST3GAL6_ENST00000462152.1_3'UTR|ST3GAL6_ENST00000265261.6_Missense_Mutation_p.V207L	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	325					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)	p.V325L(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						AAAAAACCTCGTAATCAACTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											96	100	99					3																	98512582		2203	4300	6503	99995272	SO:0001583	missense	10402			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.973G>T	3.37:g.98512582G>T	ENSP00000417376:p.Val325Leu		99995272	B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	37	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.102413	0.56183	.	.	ENSG00000064225	ENST00000483910;ENST00000265261;ENST00000394162	T;T;T	0.27402	1.67;1.67;1.67	5.93	5.93	0.95920	.	0.101468	0.42682	D	0.000676	T	0.33294	0.0858	M	0.63428	1.95	0.41558	D	0.988616	B;B	0.32031	0.2;0.352	B;B	0.33521	0.108;0.165	T	0.17653	-1.0362	10	0.72032	D	0.01	-5.9043	11.1446	0.48424	0.083:0.0:0.917:0.0	.	207;325	F8W6U0;Q9Y274	.;SIA10_HUMAN	L	325;207;325	ENSP00000417376:V325L;ENSP00000265261:V207L;ENSP00000377717:V325L	ENSP00000265261:V207L	V	+	1	0	ST3GAL6	99995272	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	3.339000	0.52135	2.814000	0.96858	0.563000	0.77884	GTA		0.333	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		T	98512582	G	T	98512582	3	4	61	1	0	0	0	0	1	0	0	0	15258	1145	40	2	1007	2	ST3GAL6	3	98512582	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5405	98512582	99509848	2614	10599										
TBC1D23	55773	broad.mit.edu	37	chr3	100014147	100014147	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgattcccttttacagaGaagttattttaacacaagag	6	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100014147G>T	ENST00000394144.4	+	7	734	c.727G>T	c.(727-729)Gaa>Taa	p.E243*	TBC1D23_ENST00000344949.5_Splice_Site_p.E243*|TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000475134.1_Splice_Site_p.E106*	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	243					positive regulation of interleukin-6 production (GO:0032755)|regulation of inflammatory response (GO:0050727)|regulation of tumor necrosis factor production (GO:0032680)		Rab GTPase activator activity (GO:0005097)	p.E243*(1)		breast(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(10)|ovary(1)|prostate(2)|skin(2)	25						CTTTTACAGAGAAGTTATTTT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											64	67	66					3																	100014147		2203	4298	6501	101496837	SO:0001630	splice_region_variant	55773			AK001908	CCDS2936.1, CCDS56265.1	3q12.2	2013-07-10			ENSG00000036054	ENSG00000036054			25622	protein-coding gene	gene with protein product						22312129	Standard	NM_001199198		Approved	FLJ11046	uc003dtt.4	Q9NUY8	OTTHUMG00000159067	ENST00000394144.4:c.726-1G>T	3.37:g.100014147G>T			101496837	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Nonsense_Mutation	SNP	ENST00000394144.4	37	CCDS56265.1	.	.	.	.	.	.	.	.	.	.	G	37	6.074229	0.97262	.	.	ENSG00000036054	ENST00000344949;ENST00000394144;ENST00000475134	.	.	.	5.8	5.8	0.92144	.	0.248415	0.46442	D	0.000292	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0608	0.97674	0.0:0.0:1.0:0.0	.	.	.	.	X	243;243;106	.	.	E	+	1	0	TBC1D23	101496837	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.962000	0.93254	2.733000	0.93635	0.650000	0.86243	GAA		0.308	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309	Nonsense_Mutation	T	100014147	G	T	100014147	5	4	61	1	0	0	0	0	0	0	1	0	15652	956	33	2	753	2	TBC1D23	3	100014147	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1501565	100014147	98008283	2615	10600										
NIT2	56954	broad.mit.edu	37	chr3	100064474	100064474	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaaaaattacatttcaaGaatctaaaacattgagtccg	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100064474G>T	ENST00000394140.4	+	5	473	c.382G>T	c.(382-384)Gaa>Taa	p.E128*		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	128	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)	p.E128K(1)|p.E128*(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						TACATTTCAAGAATCTAAAAC	0.388																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(2)	3											115	108	110					3																	100064474		2203	4300	6503	101547164	SO:0001587	stop_gained	56954			AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.382G>T	3.37:g.100064474G>T	ENSP00000377696:p.Glu128*		101547164	B2R9A3|D3DN47|Q8WUF0	Nonsense_Mutation	SNP	ENST00000394140.4	37	CCDS33806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.9|25.9	4.683630|4.683630	0.88639|0.88639	.|.	.|.	ENSG00000114021|ENSG00000114021	ENST00000394140|ENST00000497785	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76471	.|0.3992	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74380	.|-0.3684	.|3	0.87932|.	D|.	0|.	-16.4056|-16.4056	19.4938|19.4938	0.95064|0.95064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	128|221	.|.	ENSP00000377696:E128X|.	E|R	+|+	1|2	0|0	NIT2|NIT2	101547164|101547164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	8.802000|8.802000	0.91910|0.91910	2.777000|2.777000	0.95525|0.95525	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.388	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202		T	100064474	G	T	100064474	4	4	61	1	0	0	0	0	0	1	0	0	10465	943	33	2	400	2	NIT2	3	100064474	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50327	100064474	97957956	2616	10601										
GPR128	84873	broad.mit.edu	37	chr3	100365565	100365565	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actactaattttgctgtattAatggtaaggatatacatagc	7	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100365565A>C	ENST00000273352.3	+	10	1531	c.1263A>C	c.(1261-1263)ttA>ttC	p.L421F	SNORA31_ENST00000517180.1_RNA|GPR128_ENST00000475887.1_Missense_Mutation_p.L126F	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	421	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L421F(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						TTGCTGTATTAATGGTAAGGA	0.408																																					Pancreas(87;185 1975 7223 18722)											1	Substitution - Missense(1)	large_intestine(1)	3											83	84	83					3																	100365565		2203	4300	6503	101848255	SO:0001583	missense	84873			AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.1263A>C	3.37:g.100365565A>C	ENSP00000273352:p.Leu421Phe		101848255	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.453039	0.63290	.	.	ENSG00000144820	ENST00000273352;ENST00000475887	T;T	0.75477	-0.94;-0.94	4.93	0.947	0.19555	GPS domain (3);	0.000000	0.45126	D	0.000385	D	0.83995	0.5375	M	0.85710	2.77	0.40377	D	0.979408	D;D	0.89917	0.999;1.0	D;D	0.91635	0.99;0.999	T	0.81295	-0.0997	10	0.51188	T	0.08	.	7.9533	0.30027	0.5425:0.0:0.4575:0.0	.	126;421	E9PHI0;Q96K78	.;GP128_HUMAN	F	421;126	ENSP00000273352:L421F;ENSP00000419788:L126F	ENSP00000273352:L421F	L	+	3	2	GPR128	101848255	0.779000	0.28652	0.992000	0.48379	0.975000	0.68041	-0.301000	0.08232	-0.019000	0.14055	0.533000	0.62120	TTA		0.408	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			C	100365565	A	C	100365565	3	2	61	1	0	0	0	0	1	0	0	0	6661	359	13	4	1301	4	GPR128	3	100365565	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	301091	100365565	97656865	2617	10602										
IMPG2	50939	broad.mit.edu	37	chr3	100948233	100948233	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtttcccacctctctggaAagctcactgctctcatacat	5	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100948233A>C	ENST00000193391.7	-	17	3811	c.3624T>G	c.(3622-3624)ctT>ctG	p.L1208L		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1208					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.L1208L(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	CCTCTCTGGAAAGCTCACTGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	3											153	132	139					3																	100948233		2203	4300	6503	102430923	SO:0001819	synonymous_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.3624T>G	3.37:g.100948233A>C			102430923	A8MWT5|Q9UKD4|Q9UKK5	Silent	SNP	ENST00000193391.7	37	CCDS2940.1																																																																																				0.542	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			C	100948233	A	C	100948233	2	2	61	1	0	0	0	0	0	0	0	1	7750	1	1	4		4	IMPG2	3	100948233	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	582668	100948233	97074197	2618	10603										
IMPG2	50939	broad.mit.edu	37	chr3	100963290	100963290	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcaagccacggcttggAcagtggttcagcgctcttct	10	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100963290A>C	ENST00000193391.7	-	13	2072	c.1885T>G	c.(1885-1887)Tcc>Gcc	p.S629A		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	629					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.S629A(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	CACGGCTTGGACAGTGGTTCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											122	115	118					3																	100963290		2203	4300	6503	102445980	SO:0001583	missense	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1885T>G	3.37:g.100963290A>C	ENSP00000193391:p.Ser629Ala		102445980	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	A	2.171	-0.389937	0.04932	.	.	ENSG00000081148	ENST00000193391	T	0.27256	1.68	5.87	0.379	0.16213	.	0.322330	0.28146	N	0.016432	T	0.13072	0.0317	L	0.32530	0.975	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.002	T	0.14227	-1.0480	10	0.29301	T	0.29	-5.2157	0.7281	0.00952	0.4529:0.1382:0.1393:0.2696	.	629;629	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	A	629	ENSP00000193391:S629A	ENSP00000193391:S629A	S	-	1	0	IMPG2	102445980	0.904000	0.30761	0.093000	0.20910	0.004000	0.04260	0.982000	0.29539	0.079000	0.16929	-0.321000	0.08615	TCC		0.433	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			C	100963290	A	C	100963290	3	2	61	1	0	0	0	0	1	0	0	0	7750	275	10	4	1868	4	IMPG2	3	100963290	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	15057	100963290	97059140	2619	10604										
IMPG2	50939	broad.mit.edu	37	chr3	100992506	100992506	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctgtactgcttccccaaAaggtggatactgaattctgc	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:100992506A>C	ENST00000193391.7	-	7	934	c.747T>G	c.(745-747)ctT>ctG	p.L249L		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	249	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.L249L(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GCTTCCCCAAAAGGTGGATAC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3											164	148	154					3																	100992506		2203	4300	6503	102475196	SO:0001819	synonymous_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.747T>G	3.37:g.100992506A>C			102475196	A8MWT5|Q9UKD4|Q9UKK5	Silent	SNP	ENST00000193391.7	37	CCDS2940.1																																																																																				0.388	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			C	100992506	A	C	100992506	2	2	61	1	0	0	0	0	0	0	0	1	7750	1	1	4		4	IMPG2	3	100992506	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29216	100992506	97029924	2620	10605										
IMPG2	50939	broad.mit.edu	37	chr3	101038554	101038554	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccactgtctttcagtttCtctgcggtccagaggctgtt	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101038554C>A	ENST00000193391.7	-	2	395	c.208G>T	c.(208-210)Gaa>Taa	p.E70*		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	70					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.E70*(2)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	CTTTCAGTTTCTCTGCGGTCC	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											144	146	145					3																	101038554		2203	4300	6503	102521244	SO:0001587	stop_gained	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.208G>T	3.37:g.101038554C>A	ENSP00000193391:p.Glu70*		102521244	A8MWT5|Q9UKD4|Q9UKK5	Nonsense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.691199	0.88735	.	.	ENSG00000081148	ENST00000193391	.	.	.	5.64	2.46	0.29980	.	0.363225	0.26891	N	0.021973	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-4.2426	10.598	0.45349	0.0:0.7639:0.0:0.2361	.	.	.	.	X	70	.	ENSP00000193391:E70X	E	-	1	0	IMPG2	102521244	0.971000	0.33674	0.120000	0.21714	0.450000	0.32258	1.591000	0.36665	0.755000	0.32990	0.563000	0.77884	GAA		0.453	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			A	101038554	C	A	101038554	4	1	61	1	0	0	0	0	0	1	0	0	7750	922	32	2	3589	2	IMPG2	3	101038554	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46048	101038554	96983876	2621	10606										
SENP7	57337	broad.mit.edu	37	chr3	101049208	101049208	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcactcaaagacagtgtCgaagtagtacgtagatcatt	9	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101049208C>T	ENST00000394095.2	-	20	2774	c.2721G>A	c.(2719-2721)tcG>tcA	p.S907S	SENP7_ENST00000394091.1_Silent_p.S743S|SENP7_ENST00000314261.7_Silent_p.S841S|SENP7_ENST00000348610.3_Silent_p.S874S|SENP7_ENST00000394085.3_Silent_p.S95S|SENP7_ENST00000394094.2_Silent_p.S842S|SENP7_ENST00000358203.3_Silent_p.S743S	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	907	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.S841S(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AAGACAGTGTCGAAGTAGTAC	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	3											102	99	100					3																	101049208		2203	4300	6503	102531898	SO:0001819	synonymous_variant	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2721G>A	3.37:g.101049208C>T			102531898	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																				0.308	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		T	101049208	C	T	101049208	2	4	61	1	0	0	0	0	0	0	0	1	14088	871	31	1		1	SENP7	3	101049208	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10654	101049208	96973222	2622	10607										
SENP7	57337	broad.mit.edu	37	chr3	101056353	101056353	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattagaggattaacttacGaaagatttggattatcttct	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101056353G>A	ENST00000394095.2	-	17	2533	c.2480C>T	c.(2479-2481)tCa>tTa	p.S827L	SENP7_ENST00000394091.1_Splice_Site_p.S663L|SENP7_ENST00000314261.7_Splice_Site_p.S761L|SENP7_ENST00000348610.3_Splice_Site_p.S794L|SENP7_ENST00000394094.2_Splice_Site_p.S762L|SENP7_ENST00000358203.3_Splice_Site_p.S663L	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	827	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.S761L(2)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ATTAACTTACGAAAGATTTGG	0.299																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	3											44	46	45					3																	101056353		2201	4294	6495	102539043	SO:0001630	splice_region_variant	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2480+1C>T	3.37:g.101056353G>A			102539043	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991348	0.93106	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47	5.68	5.68	0.88126	.	0.227351	0.38272	N	0.001745	T	0.57021	0.2025	M	0.70595	2.14	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;1.0;0.926	D;D;D;P	0.87578	0.998;0.983;0.991;0.732	T	0.58730	-0.7585	10	0.87932	D	0	-7.7948	17.5732	0.87941	0.0:0.0:1.0:0.0	.	663;761;794;827	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	L	827;762;761;663;663;794	ENSP00000377655:S827L;ENSP00000377654:S762L;ENSP00000313624:S761L;ENSP00000377651:S663L;ENSP00000350936:S663L;ENSP00000342159:S794L	ENSP00000313624:S761L	S	-	2	0	SENP7	102539043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.319000	0.89992	2.674000	0.91012	0.655000	0.94253	TCA		0.299	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	Missense_Mutation	A	101056353	G	A	101056353	5	1	61	1	0	0	0	0	0	0	1	0	14088	1072	37	1	704	1	SENP7	3	101056353	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7145	101056353	96966077	2623	10608										
SENP7	57337	broad.mit.edu	37	chr3	101062792	101062792	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggaaaatgaattcactaGattttgctacaaaaggaaaa	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101062792G>T	ENST00000394095.2	-	14	1897	c.1844C>A	c.(1843-1845)tCt>tAt	p.S615Y	SENP7_ENST00000394091.1_Missense_Mutation_p.S451Y|SENP7_ENST00000314261.7_Missense_Mutation_p.S549Y|SENP7_ENST00000348610.3_Missense_Mutation_p.S582Y|SENP7_ENST00000394094.2_Missense_Mutation_p.S550Y|SENP7_ENST00000358203.3_Missense_Mutation_p.S451Y	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	615						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.S549Y(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GAATTCACTAGATTTTGCTAC	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	3											28	26	27					3																	101062792		2201	4299	6500	102545482	SO:0001583	missense	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1844C>A	3.37:g.101062792G>T	ENSP00000377655:p.Ser615Tyr		102545482	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700219	0.48307	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.24723	1.84;1.86;1.86;1.86;1.86;1.84	4.72	3.84	0.44239	.	0.355317	0.24405	N	0.038807	T	0.32852	0.0843	L	0.27053	0.805	0.22489	N	0.999055	D;D;D;D	0.76494	0.996;0.998;0.999;0.999	D;D;D;P	0.68621	0.939;0.957;0.959;0.903	T	0.05533	-1.0879	10	0.72032	D	0.01	-0.0319	8.5211	0.33275	0.0876:0.1543:0.7581:0.0	.	451;549;582;615	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	Y	615;550;549;451;451;582	ENSP00000377655:S615Y;ENSP00000377654:S550Y;ENSP00000313624:S549Y;ENSP00000377651:S451Y;ENSP00000350936:S451Y;ENSP00000342159:S582Y	ENSP00000313624:S549Y	S	-	2	0	SENP7	102545482	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	4.515000	0.60489	0.965000	0.38133	-0.157000	0.13467	TCT		0.259	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		T	101062792	G	T	101062792	3	4	61	1	0	0	0	0	1	0	0	0	14088	942	33	2	1352	2	SENP7	3	101062792	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6439	101062792	96959638	2624	10609										
SENP7	57337	broad.mit.edu	37	chr3	101085353	101085353	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatggtattcaactcattCtcatccttctcaaccaggga	5	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101085353C>A	ENST00000394095.2	-	9	1292	c.1239G>T	c.(1237-1239)gaG>gaT	p.E413D	SENP7_ENST00000394091.1_Missense_Mutation_p.E249D|SENP7_ENST00000314261.7_Missense_Mutation_p.E347D|SENP7_ENST00000348610.3_Missense_Mutation_p.E380D|SENP7_ENST00000394094.2_Missense_Mutation_p.E348D|SENP7_ENST00000358203.3_Missense_Mutation_p.E249D	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	413						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.E347D(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCAACTCATTCTCATCCTTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											97	101	100					3																	101085353		2203	4300	6503	102568043	SO:0001583	missense	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1239G>T	3.37:g.101085353C>A	ENSP00000377655:p.Glu413Asp		102568043	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	C	7.164	0.586306	0.13749	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.20200	2.09;2.12;2.12;2.12;2.12;2.09	5.13	2.13	0.27403	.	0.855264	0.10425	N	0.676183	T	0.22551	0.0544	L	0.56769	1.78	0.09310	N	1	P;P;P;P	0.44241	0.792;0.792;0.829;0.737	B;B;B;B	0.43445	0.254;0.342;0.42;0.24	T	0.11991	-1.0565	10	0.33141	T	0.24	-0.1136	6.8101	0.23799	0.0:0.5649:0.3419:0.0933	.	249;347;380;413	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	D	413;348;347;249;249;380	ENSP00000377655:E413D;ENSP00000377654:E348D;ENSP00000313624:E347D;ENSP00000377651:E249D;ENSP00000350936:E249D;ENSP00000342159:E380D	ENSP00000313624:E347D	E	-	3	2	SENP7	102568043	0.002000	0.14202	0.246000	0.24233	0.059000	0.15707	-0.176000	0.09811	0.833000	0.34828	0.643000	0.83706	GAG		0.423	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101085353	C	A	101085353	3	1	61	1	0	0	0	0	1	0	0	0	14088	912	32	2	1977	2	SENP7	3	101085353	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22561	101085353	96937077	2625	10610										
SENP7	57337	broad.mit.edu	37	chr3	101086821	101086821	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtttctgctttcctgttcGagatgatcacaacctctact	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101086821G>A	ENST00000394095.2	-	8	884	c.831C>T	c.(829-831)ctC>ctT	p.L277L	SENP7_ENST00000394091.1_Silent_p.L113L|SENP7_ENST00000314261.7_Silent_p.L211L|SENP7_ENST00000348610.3_Silent_p.L244L|SENP7_ENST00000394094.2_Silent_p.L212L|SENP7_ENST00000358203.3_Silent_p.L113L	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	277						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.L211L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TTTCCTGTTCGAGATGATCAC	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	3											108	106	107					3																	101086821		2201	4299	6500	102569511	SO:0001819	synonymous_variant	57337				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.831C>T	3.37:g.101086821G>A			102569511	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																				0.333	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101086821	G	A	101086821	2	1	61	1	0	0	0	0	0	0	0	1	14088	1045	37	1		1	SENP7	3	101086821	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1468	101086821	96935609	2626	10611										
PCNP	57092	broad.mit.edu	37	chr3	101311594	101311594	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtccatgaccaagacaaTtaaatgatgttttgaaattg	7	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101311594T>G	ENST00000265260.3	+	5	655	c.534T>G	c.(532-534)aaT>aaG	p.N178K	PCNP_ENST00000469941.1_Missense_Mutation_p.N55K|PCNP_ENST00000296024.5_3'UTR|PCNP_ENST00000486406.1_3'UTR	NM_020357.1	NP_065090.1	Q8WW12	PCNP_HUMAN	PEST proteolytic signal containing nuclear protein	178					cell cycle (GO:0007049)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)		p.N178K(1)		large_intestine(1)|lung(1)	2						ACCAAGACAATTAAATGATGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											56	60	58					3																	101311594		2201	4300	6501	102794284	SO:0001583	missense	57092				CCDS2942.1	3q12.3	2006-03-09			ENSG00000081154	ENSG00000081154			30023	protein-coding gene	gene with protein product		615210				12176013	Standard	NM_020357		Approved		uc003dva.3	Q8WW12	OTTHUMG00000159108	ENST00000265260.3:c.534T>G	3.37:g.101311594T>G	ENSP00000265260:p.Asn178Lys		102794284	B2RBE7|D3DN52|Q53GF3|Q6AI44|Q96CU3|Q9NS81	Missense_Mutation	SNP	ENST00000265260.3	37	CCDS2942.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.714791	0.30413	.	.	ENSG00000081154	ENST00000265260	.	.	.	5.05	3.88	0.44766	.	0.145724	0.49305	D	0.000157	T	0.42517	0.1206	N	0.22421	0.69	0.80722	D	1	B	0.21905	0.062	B	0.17098	0.017	T	0.29549	-1.0008	9	0.59425	D	0.04	.	10.8915	0.46998	0.0:0.0751:0.0:0.9249	.	178	Q8WW12	PCNP_HUMAN	K	178	.	ENSP00000265260:N178K	N	+	3	2	PCNP	102794284	.	.	1.000000	0.80357	0.997000	0.91878	.	.	0.753000	0.32945	0.477000	0.44152	AAT		0.373	PCNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353338.2	NM_020357		G	101311594	T	G	101311594	3	3	61	1	0	0	0	0	1	0	0	0	11620	1490	52	4	552	4	PCNP	3	101311594	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	224773	101311594	96710836	2627	10612										
ZBTB11	27107	broad.mit.edu	37	chr3	101370201	101370201	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagagcttccatagtttCtcctgtcactaccacagtct	5	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101370201C>A	ENST00000312938.4	-	11	3551	c.2971G>T	c.(2971-2973)Gaa>Taa	p.E991*		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	991					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E991*(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCCATAGTTTCTCCTGTCACT	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											178	150	159					3																	101370201		2203	4300	6503	102852891	SO:0001587	stop_gained	27107			U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2971G>T	3.37:g.101370201C>A	ENSP00000326200:p.Glu991*		102852891	Q2NKP9	Nonsense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	45	11.922384	0.99617	.	.	ENSG00000066422	ENST00000312938	.	.	.	5.39	5.39	0.77823	.	0.054796	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-21.9091	19.5182	0.95174	0.0:1.0:0.0:0.0	.	.	.	.	X	991	.	ENSP00000326200:E991X	E	-	1	0	ZBTB11	102852891	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.445000	0.80570	2.692000	0.91855	0.555000	0.69702	GAA		0.433	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		A	101370201	C	A	101370201	4	1	61	1	0	0	0	0	0	1	0	0	17563	922	32	2	194	2	ZBTB11	3	101370201	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58607	101370201	96652229	2628	10613										
ZBTB11	27107	broad.mit.edu	37	chr3	101373592	101373592	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggctttggttggtgtttCttgaagtgcttgctgagtcc	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101373592C>A	ENST00000312938.4	-	8	2845	c.2265G>T	c.(2263-2265)aaG>aaT	p.K755N		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	755					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K755N(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GTTGGTGTTTCTTGAAGTGCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	116	115					3																	101373592		2203	4300	6503	102856282	SO:0001583	missense	27107			U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2265G>T	3.37:g.101373592C>A	ENSP00000326200:p.Lys755Asn		102856282	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.512834	0.85389	.	.	ENSG00000066422	ENST00000312938	T	0.12147	2.71	5.91	4.11	0.48088	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.046688	0.85682	D	0.000000	T	0.23289	0.0563	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02004	-1.1231	10	0.62326	D	0.03	-17.1721	11.8887	0.52616	0.0:0.8606:0.0:0.1394	.	755	O95625	ZBT11_HUMAN	N	755	ENSP00000326200:K755N	ENSP00000326200:K755N	K	-	3	2	ZBTB11	102856282	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.983000	0.49345	1.509000	0.48786	0.655000	0.94253	AAG		0.378	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		A	101373592	C	A	101373592	3	1	61	1	0	0	0	0	1	0	0	0	17563	912	32	2	912	2	ZBTB11	3	101373592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3391	101373592	96648838	2629	10614										
ZBTB11	27107	broad.mit.edu	37	chr3	101374975	101374975	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatactcatatgttcttgaaGactccgtttggtaacaaatg	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101374975G>T	ENST00000312938.4	-	7	2744	c.2164C>A	c.(2164-2166)Ctt>Att	p.L722I		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	722					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L722I(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TGTTCTTGAAGACTCCGTTTG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	63	65					3																	101374975		2203	4300	6503	102857665	SO:0001583	missense	27107			U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2164C>A	3.37:g.101374975G>T	ENSP00000326200:p.Leu722Ile		102857665	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203643	0.58234	.	.	ENSG00000066422	ENST00000312938	T	0.53857	0.6	6.05	6.05	0.98169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.064020	0.64402	D	0.000003	T	0.80706	0.4674	H	0.95402	3.665	0.80722	D	1	D	0.63046	0.992	P	0.61070	0.883	D	0.85369	0.1112	10	0.87932	D	0	-14.679	20.6013	0.99457	0.0:0.0:1.0:0.0	.	722	O95625	ZBT11_HUMAN	I	722	ENSP00000326200:L722I	ENSP00000326200:L722I	L	-	1	0	ZBTB11	102857665	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	5.368000	0.66133	2.878000	0.98634	0.650000	0.86243	CTT		0.308	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		T	101374975	G	T	101374975	3	4	61	1	0	0	0	0	1	0	0	0	17563	942	33	2	1017	2	ZBTB11	3	101374975	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1383	101374975	96647455	2630	10615										
FAM55C	91775	broad.mit.edu	37	chr3	101535699	101535699	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttctgggtattattataAagaccagtggaggcccagaa	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:101535699A>C	ENST00000491511.2	+	7	1939	c.983A>C	c.(982-984)aAa>aCa	p.K328T	NXPE3_ENST00000477909.1_Missense_Mutation_p.K328T|NXPE3_ENST00000422132.1_Missense_Mutation_p.K328T|NXPE3_ENST00000273347.5_Missense_Mutation_p.K328T	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	328						extracellular region (GO:0005576)		p.K328T(1)									TATTATTATAAAGACCAGTGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	84	83					3																	101535699		2203	4300	6503	103018389	SO:0001583	missense	91775			AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.983A>C	3.37:g.101535699A>C	ENSP00000417485:p.Lys328Thr		103018389	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	37	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858520	0.51376	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.12361	2.69;2.69;2.69;2.69	5.86	3.24	0.37175	.	0.509864	0.24525	N	0.037768	T	0.14184	0.0343	M	0.62723	1.935	0.32530	N	0.535114	B	0.12630	0.006	B	0.06405	0.002	T	0.12116	-1.0560	10	0.22706	T	0.39	-4.5844	10.2115	0.43143	0.8559:0.0:0.1441:0.0	.	328	Q969Y0	FA55C_HUMAN	T	328	ENSP00000273347:K328T;ENSP00000417485:K328T;ENSP00000418369:K328T;ENSP00000396421:K328T	ENSP00000273347:K328T	K	+	2	0	FAM55C	103018389	0.491000	0.26019	0.997000	0.53966	0.990000	0.78478	2.528000	0.45624	0.469000	0.27268	0.528000	0.53228	AAA		0.358	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		C	101535699	A	C	101535699	3	2	61	1	0	0	0	0	1	0	0	0	5605	14	1	4	997	4	FAM55C	3	101535699	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	160724	101535699	96486731	2631	10616										
ZPLD1	131368	broad.mit.edu	37	chr3	102157429	102157429	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgccaacctccacagtaGatttcctggtaagtgtaagc	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:102157429G>T	ENST00000491959.1	+	9	980	c.98G>T	c.(97-99)aGa>aTa	p.R33I	ZPLD1_ENST00000466937.1_Missense_Mutation_p.R33I|ZPLD1_ENST00000306176.1_Missense_Mutation_p.R49I			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	33						integral component of membrane (GO:0016021)		p.R49I(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						CTCCACAGTAGATTTCCTGGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	83	86					3																	102157429		2203	4300	6503	103640119	SO:0001583	missense	131368			AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.98G>T	3.37:g.102157429G>T	ENSP00000420265:p.Arg33Ile		103640119	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		.	.	.	.	.	.	.	.	.	.	G	24.5	4.537862	0.85917	.	.	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.82803	-1.62;-1.65;-1.62	5.26	5.26	0.73747	.	0.111702	0.64402	D	0.000004	T	0.81288	0.4791	L	0.36672	1.1	0.80722	D	1	P;P	0.48640	0.649;0.913	B;P	0.46510	0.198;0.519	T	0.81037	-0.1114	10	0.38643	T	0.18	-15.3424	18.8682	0.92301	0.0:0.0:1.0:0.0	.	49;33	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	I	33;49;33	ENSP00000420265:R33I;ENSP00000307801:R49I;ENSP00000418253:R33I	ENSP00000307801:R49I	R	+	2	0	ZPLD1	103640119	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.196000	0.89725	2.467000	0.83353	0.591000	0.81541	AGA		0.418	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		T	102157429	G	T	102157429	3	4	61	1	0	0	0	0	1	0	0	0	18260	942	33	2	152	2	ZPLD1	3	102157429	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	621730	102157429	95865001	2632	10617										
ZPLD1	131368	broad.mit.edu	37	chr3	102176650	102176650	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcggctatttctgtgagaGagaacaatggcacatttgtc	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:102176650G>T	ENST00000491959.1	+	12	1417	c.535G>T	c.(535-537)Gag>Tag	p.E179*	ZPLD1_ENST00000466937.1_Nonsense_Mutation_p.E179*|ZPLD1_ENST00000306176.1_Nonsense_Mutation_p.E195*			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	179	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)		p.E195*(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						TTCTGTGAGAGAGAACAATGG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											252	231	238					3																	102176650		2203	4300	6503	103659340	SO:0001587	stop_gained	131368			AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.535G>T	3.37:g.102176650G>T	ENSP00000420265:p.Glu179*		103659340	Q49AS1|Q8WU36	Nonsense_Mutation	SNP	ENST00000491959.1	37		.	.	.	.	.	.	.	.	.	.	G	38	6.954043	0.97960	.	.	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	.	.	.	4.99	4.99	0.66335	.	0.115142	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	4.4935	18.6514	0.91431	0.0:0.0:1.0:0.0	.	.	.	.	X	179;195;179	.	ENSP00000307801:E195X	E	+	1	0	ZPLD1	103659340	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.577000	0.82486	2.480000	0.83734	0.591000	0.81541	GAG		0.378	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		T	102176650	G	T	102176650	4	4	61	1	0	0	0	0	0	1	0	0	18260	943	33	2	601	2	ZPLD1	3	102176650	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19221	102176650	95845780	2633	10618										
BBX	56987	broad.mit.edu	37	chr3	107447682	107447682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaaacaagcctgtgaaatCcccaacacccactgtcaatc	4	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:107447682C>T	ENST00000325805.8	+	6	763	c.476C>T	c.(475-477)tCc>tTc	p.S159F	BBX_ENST00000416476.2_Missense_Mutation_p.S159F|BBX_ENST00000406780.1_Missense_Mutation_p.S159F|BBX_ENST00000415149.2_Missense_Mutation_p.S159F|BBX_ENST00000402543.1_Missense_Mutation_p.S159F			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	159					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S159F(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CCTGTGAAATCCCCAACACCC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											199	207	205					3																	107447682		2203	4300	6503	108930372	SO:0001583	missense	56987			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.476C>T	3.37:g.107447682C>T	ENSP00000319974:p.Ser159Phe		108930372	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915714	0.92178	.	.	ENSG00000114439	ENST00000415149;ENST00000402543;ENST00000325805;ENST00000427402;ENST00000416476;ENST00000456419;ENST00000402163;ENST00000406780;ENST00000449213;ENST00000429270	D;D;D;D;D;D;D;D;D;D	0.98762	-4.7;-4.71;-4.7;-5.12;-5.1;-5.1;-5.12;-4.7;-4.95;-4.66	6.02	6.02	0.97574	High mobility group, HMG1/HMG2 (1);	0.134990	0.64402	D	0.000002	D	0.98191	0.9402	N	0.24115	0.695	0.48975	D	0.999734	D;D;D;D	0.71674	0.987;0.996;0.994;0.998	P;P;P;D	0.63381	0.794;0.794;0.854;0.914	D	0.99818	1.1045	10	0.72032	D	0.01	-7.3028	20.5373	0.99239	0.0:1.0:0.0:0.0	.	159;159;159;159	C9JA69;Q8WY36;A2RRM7;Q8WY36-2	.;BBX_HUMAN;.;.	F	159	ENSP00000408358:S159F;ENSP00000385317:S159F;ENSP00000319974:S159F;ENSP00000413320:S159F;ENSP00000403860:S159F;ENSP00000413274:S159F;ENSP00000385518:S159F;ENSP00000385530:S159F;ENSP00000407662:S159F;ENSP00000414673:S159F	ENSP00000319974:S159F	S	+	2	0	BBX	108930372	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.678000	0.61641	2.857000	0.98124	0.650000	0.86243	TCC		0.423	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107447682	C	T	107447682	3	4	61	1	0	0	0	0	1	0	0	0	1344	855	30	3	486	3	BBX	3	107447682	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5271032	107447682	90574748	2634	10619										
BBX	56987	broad.mit.edu	37	chr3	107491949	107491949	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagaaaagcaaaatggatCgacatggaaatgataaatcc	9	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:107491949C>T	ENST00000325805.8	+	11	1668	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	BBX_ENST00000416476.2_Intron|BBX_ENST00000406780.1_Nonsense_Mutation_p.R461*|BBX_ENST00000415149.2_Nonsense_Mutation_p.R461*|BBX_ENST00000402543.1_Nonsense_Mutation_p.R461*			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	461	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R461*(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CAAAATGGATCGACATGGAAA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											57	60	59					3																	107491949		2203	4299	6502	108974639	SO:0001587	stop_gained	56987			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1381C>T	3.37:g.107491949C>T	ENSP00000319974:p.Arg461*		108974639	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Nonsense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	C	38	6.946164	0.97956	.	.	ENSG00000114439	ENST00000415149;ENST00000402543;ENST00000325805;ENST00000406780	.	.	.	6.07	5.2	0.72013	.	0.601594	0.17783	N	0.162153	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3842	16.9326	0.86195	0.1288:0.8712:0.0:0.0	.	.	.	.	X	461	.	ENSP00000319974:R461X	R	+	1	2	BBX	108974639	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.162000	0.42367	1.573000	0.49748	0.585000	0.79938	CGA		0.403	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107491949	C	T	107491949	4	4	61	1	0	0	0	0	0	1	0	0	1344	876	31	1	1411	1	BBX	3	107491949	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44267	107491949	90530481	2635	10620										
BBX	56987	broad.mit.edu	37	chr3	107492287	107492287	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacaccagagggtataaaAgcagaaccattgacccctat	9	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:107492287A>G	ENST00000325805.8	+	11	2006	c.1719A>G	c.(1717-1719)aaA>aaG	p.K573K	BBX_ENST00000416476.2_Intron|BBX_ENST00000406780.1_Silent_p.K573K|BBX_ENST00000415149.2_Silent_p.K573K|BBX_ENST00000402543.1_Silent_p.K573K			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	573					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K573K(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AGGGTATAAAAGCAGAACCAT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											95	91	92					3																	107492287		2203	4300	6503	108974977	SO:0001819	synonymous_variant	56987			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1719A>G	3.37:g.107492287A>G			108974977	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Silent	SNP	ENST00000325805.8	37	CCDS46881.1																																																																																				0.458	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		G	107492287	A	G	107492287	2	3	61	1	0	0	0	0	0	0	0	1	1344	69	3	4		4	BBX	3	107492287	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	338	107492287	90530143	2636	10621										
HHLA2	11148	broad.mit.edu	37	chr3	108076869	108076869	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatcaatgaatcccgattCtcatggaacaaagagctgat	7	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108076869C>A	ENST00000357759.5	+	6	1278	c.864C>A	c.(862-864)ttC>ttA	p.F288L	HHLA2_ENST00000467761.1_Missense_Mutation_p.F288L|HHLA2_ENST00000489514.2_Missense_Mutation_p.F288L|HHLA2_ENST00000491820.1_Missense_Mutation_p.F288L|HHLA2_ENST00000467562.1_Missense_Mutation_p.F224L	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	288	Ig-like V-type 2.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)		p.F288L(2)		endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						AATCCCGATTCTCATGGAACA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	3											154	149	151					3																	108076869		1845	4097	5942	109559559	SO:0001583	missense	11148			AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.864C>A	3.37:g.108076869C>A	ENSP00000350402:p.Phe288Leu		109559559	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.171|3.171	-0.169929|-0.169929	0.06461|0.06461	.|.	.|.	ENSG00000114455|ENSG00000114455	ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514|ENST00000482099	T;T;T;T;T|.	0.70045|.	-0.45;-0.45;-0.45;-0.45;-0.45|.	5.31|5.31	0.916|0.916	0.19373|0.19373	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.944627|.	0.08658|.	N|.	0.912941|.	T|T	0.19886|0.19886	0.0478|0.0478	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.17465|.	0.022;0.022;0.022|.	B;B;B|.	0.23716|.	0.048;0.048;0.048|.	T|T	0.23940|0.23940	-1.0174|-1.0174	10|5	0.27785|.	T|.	0.31|.	-14.9994|-14.9994	3.6021|3.6021	0.08028|0.08028	0.2043:0.5439:0.1466:0.1052|0.2043:0.5439:0.1466:0.1052	.|.	224;288;288|.	B4DKN2;C9J7D0;Q9UM44|.	.;.;HHLA2_HUMAN|.	L|I	288;224;288;288;288|191	ENSP00000418284:F288L;ENSP00000418345:F224L;ENSP00000350402:F288L;ENSP00000419207:F288L;ENSP00000417856:F288L|.	ENSP00000350402:F288L|.	F|L	+|+	3|1	2|0	HHLA2|HHLA2	109559559|109559559	0.924000|0.924000	0.31332|0.31332	0.003000|0.003000	0.11579|0.11579	0.043000|0.043000	0.13939|0.13939	0.259000|0.259000	0.18405|0.18405	-0.080000|-0.080000	0.12685|0.12685	-0.182000|-0.182000	0.12963|0.12963	TTC|CTC		0.378	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072		A	108076869	C	A	108076869	3	1	61	1	0	0	0	0	1	0	0	0	7116	912	32	2	878	2	HHLA2	3	108076869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	584582	108076869	89945561	2637	10622										
MYH15	22989	broad.mit.edu	37	chr3	108112896	108112896	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcaatggctgccttcttGgccttctcttctgcattttg	7	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108112896G>T	ENST00000273353.3	-	37	5357	c.5301C>A	c.(5299-5301)gcC>gcA	p.A1767A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1767						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A1767A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CTGCCTTCTTGGCCTTCTCTT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	3											116	122	120					3																	108112896		2045	4205	6250	109595586	SO:0001819	synonymous_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5301C>A	3.37:g.108112896G>T			109595586		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																				0.567	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108112896	G	T	108112896	2	4	61	1	0	0	0	0	0	0	0	1	10064	1335	47	2		2	MYH15	3	108112896	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36027	108112896	89909534	2638	10623										
MYH15	22989	broad.mit.edu	37	chr3	108112977	108112977	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaacatcagcctccagtttCttcttctggctgaggaggct	10	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108112977C>A	ENST00000273353.3	-	37	5276	c.5220G>T	c.(5218-5220)aaG>aaT	p.K1740N		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1740						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K1740N(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCTCCAGTTTCTTCTTCTGGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											93	95	94					3																	108112977		1978	4168	6146	109595667	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5220G>T	3.37:g.108112977C>A	ENSP00000273353:p.Lys1740Asn		109595667		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.764993	0.69878	.	.	ENSG00000144821	ENST00000273353	D	0.85629	-2.01	5.7	3.89	0.44902	Myosin tail (1);	.	.	.	.	D	0.91382	0.7281	M	0.77406	2.37	0.46279	D	0.998967	D	0.76494	0.999	D	0.83275	0.996	D	0.92145	0.5723	9	0.87932	D	0	.	12.3321	0.55046	0.0:0.8615:0.0:0.1385	.	1740	Q9Y2K3	MYH15_HUMAN	N	1740	ENSP00000273353:K1740N	ENSP00000273353:K1740N	K	-	3	2	MYH15	109595667	1.000000	0.71417	1.000000	0.80357	0.505000	0.33919	2.907000	0.48743	1.400000	0.46741	0.650000	0.86243	AAG		0.478	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		A	108112977	C	A	108112977	3	1	61	1	0	0	0	0	1	0	0	0	10064	912	32	2	644	2	MYH15	3	108112977	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81	108112977	89909453	2639	10624										
MYH15	22989	broad.mit.edu	37	chr3	108147716	108147716	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctagtttctctttcaaatCctttatttgagtctgtagca	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108147716C>A	ENST00000273353.3	-	28	3441	c.3385G>T	c.(3385-3387)Gat>Tat	p.D1129Y		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1129						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.D1129Y(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TCTTTCAAATCCTTTATTTGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											88	83	85					3																	108147716		1854	4089	5943	109630406	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3385G>T	3.37:g.108147716C>A	ENSP00000273353:p.Asp1129Tyr		109630406		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.745796	0.30955	.	.	ENSG00000144821	ENST00000273353	T	0.79653	-1.29	5.72	0.585	0.17428	Myosin tail (1);	.	.	.	.	T	0.73140	0.3549	L	0.29908	0.895	0.29966	N	0.819009	P	0.41232	0.743	P	0.47891	0.56	T	0.67681	-0.5608	9	0.87932	D	0	.	4.3178	0.11002	0.116:0.5029:0.2509:0.1303	.	1129	Q9Y2K3	MYH15_HUMAN	Y	1129	ENSP00000273353:D1129Y	ENSP00000273353:D1129Y	D	-	1	0	MYH15	109630406	0.801000	0.28930	0.089000	0.20774	0.118000	0.20060	1.463000	0.35277	-0.113000	0.11958	-0.142000	0.14014	GAT		0.388	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		A	108147716	C	A	108147716	3	1	61	1	0	0	0	0	1	0	0	0	10064	855	30	2	2515	2	MYH15	3	108147716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34739	108147716	89874714	2640	10625										
MYH15	22989	broad.mit.edu	37	chr3	108211371	108211371	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctctttttgtccagataGaatttgatagaatatgtggt	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108211371G>T	ENST00000273353.3	-	10	963	c.907C>A	c.(907-909)Cta>Ata	p.L303I		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	303	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.L303I(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TGTCCAGATAGAATTTGATAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											101	93	95					3																	108211371		1820	4084	5904	109694061	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.907C>A	3.37:g.108211371G>T	ENSP00000273353:p.Leu303Ile		109694061		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803114	0.50315	.	.	ENSG00000144821	ENST00000273353	D	0.91351	-2.83	4.89	0.723	0.18231	Myosin head, motor domain (2);	.	.	.	.	D	0.91549	0.7331	M	0.65320	2	0.09310	N	1	P	0.51791	0.948	P	0.59012	0.85	T	0.82055	-0.0647	9	0.59425	D	0.04	.	5.4756	0.16694	0.16:0.0:0.3518:0.4882	.	303	Q9Y2K3	MYH15_HUMAN	I	303	ENSP00000273353:L303I	ENSP00000273353:L303I	L	-	1	2	MYH15	109694061	1.000000	0.71417	0.879000	0.34478	0.840000	0.47671	0.869000	0.27996	0.413000	0.25759	0.650000	0.86243	CTA		0.368	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108211371	G	T	108211371	3	4	61	1	0	0	0	0	1	0	0	0	10064	933	33	2	5065	2	MYH15	3	108211371	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63655	108211371	89811059	2641	10626										
KIAA1524	57650	broad.mit.edu	37	chr3	108298222	108298222	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgccatcaccgtttatgaGaatattaaatattagttgaa	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108298222G>A	ENST00000295746.8	-	7	800	c.724C>T	c.(724-726)Ctc>Ttc	p.L242F	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.L83F	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	242					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L242F(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCGTTTATGAGAATATTAAAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											76	85	82					3																	108298222		2203	4299	6502	109780912	SO:0001583	missense	57650			AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.724C>T	3.37:g.108298222G>A	ENSP00000295746:p.Leu242Phe		109780912	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744561	0.69418	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.64438	-0.1;0.63	5.07	5.07	0.68467	Armadillo-type fold (1);	0.187520	0.48767	D	0.000163	T	0.73992	0.3658	L	0.54323	1.7	0.44523	D	0.997473	D	0.76494	0.999	D	0.67382	0.951	T	0.76307	-0.3007	10	0.72032	D	0.01	-4.3667	15.4498	0.75265	0.0:0.1487:0.8512:0.0	.	242	Q8TCG1	CIP2A_HUMAN	F	83;242	ENSP00000419487:L83F;ENSP00000295746:L242F	ENSP00000295746:L242F	L	-	1	0	KIAA1524	109780912	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.572000	0.67411	2.528000	0.85240	0.650000	0.86243	CTC		0.323	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		A	108298222	G	A	108298222	3	1	61	1	0	0	0	0	1	0	0	0	8260	942	33	3	2053	3	KIAA1524	3	108298222	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86851	108298222	89724208	2642	10627										
KIAA1524	57650	broad.mit.edu	37	chr3	108301905	108301905	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattatatgtattctgaagAcaatctctggtttcaatgtc	7	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108301905A>G	ENST00000295746.8	-	3	352	c.276T>C	c.(274-276)tgT>tgC	p.C92C	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_5'UTR	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	92					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.C92C(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TATTCTGAAGACAATCTCTGG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	3											57	58	57					3																	108301905		2203	4300	6503	109784595	SO:0001819	synonymous_variant	57650			AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.276T>C	3.37:g.108301905A>G			109784595	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Silent	SNP	ENST00000295746.8	37	CCDS33812.1																																																																																				0.363	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		G	108301905	A	G	108301905	2	3	61	1	0	0	0	0	0	0	0	1	8260	273	10	4		4	KIAA1524	3	108301905	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3683	108301905	89720525	2643	10628										
DZIP3	9666	broad.mit.edu	37	chr3	108381086	108381086	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcaacaagttgcttttgGaatcaataaggtttccaagt	7	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108381086G>A	ENST00000361582.3	+	21	2635	c.2405G>A	c.(2404-2406)gGa>gAa	p.G802E	DZIP3_ENST00000463306.1_Missense_Mutation_p.G802E	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	802					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G802E(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						GTTGCTTTTGGAATCAATAAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											50	51	50					3																	108381086		2202	4300	6502	109863776	SO:0001583	missense	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2405G>A	3.37:g.108381086G>A	ENSP00000355028:p.Gly802Glu		109863776	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	37	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.659901	0.67586	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	D;D	0.83419	-1.72;-1.72	5.09	5.09	0.68999	.	0.000000	0.51477	D	0.000085	D	0.86760	0.6010	L	0.47716	1.5	0.40099	D	0.976346	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	D	0.83365	0.0004	10	0.20519	T	0.43	-18.2322	13.8682	0.63600	0.0:0.0:1.0:0.0	.	420;802	D3DN61;Q86Y13	.;DZIP3_HUMAN	E	802	ENSP00000355028:G802E;ENSP00000419981:G802E	ENSP00000355028:G802E	G	+	2	0	DZIP3	109863776	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.235000	0.58666	2.644000	0.89710	0.563000	0.77884	GGA		0.333	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		A	108381086	G	A	108381086	3	1	61	1	0	0	0	0	1	0	0	0	4876	1174	41	3	2483	3	DZIP3	3	108381086	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79181	108381086	89641344	2644	10629										
TRAT1	50852	broad.mit.edu	37	chr3	108572699	108572699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagactgtttggattgatccGtgctaagagagaacctataa	10	7	0	4	rs79029897	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108572699G>A	ENST00000295756.6	+	6	766	c.536G>A	c.(535-537)cGt>cAt	p.R179H	TRAT1_ENST00000426646.1_Missense_Mutation_p.R142H	NM_016388.2	NP_057472.2	Q6PIZ9	TRAT1_HUMAN	T cell receptor associated transmembrane adaptor 1	179					cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of receptor recycling (GO:0001920)|negative regulation of transport (GO:0051051)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell receptor signaling pathway (GO:0050862)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R179H(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(3)	28						GGATTGATCCGTGCTAAGAGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	109	113	112		536	2.6	1	3	dbSNP_133	112	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRAT1	NM_016388.2	29	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	probably-damaging	179/187	108572699	4,13002	2203	4300	6503	110055389	SO:0001583	missense	50852			AJ240084	CCDS33813.1	3q13	2005-05-04	2005-05-04	2005-05-04	ENSG00000163519	ENSG00000163519			30698	protein-coding gene	gene with protein product		604962	"T cell receptor interacting molecule"	TCRIM		10663578, 9687533	Standard	NM_016388		Approved	HSPC062, TRIM	uc003dxi.1	Q6PIZ9	OTTHUMG00000159198	ENST00000295756.6:c.536G>A	3.37:g.108572699G>A	ENSP00000295756:p.Arg179His		110055389	Q9NZX5	Missense_Mutation	SNP	ENST00000295756.6	37	CCDS33813.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527449	0.44969	2.27E-4	3.49E-4	ENSG00000163519	ENST00000295756;ENST00000426646	T;T	0.31247	1.5;1.5	5.85	2.57	0.30868	.	0.303423	0.29080	N	0.013212	T	0.21590	0.0520	L	0.45137	1.4	0.32587	N	0.527755	B;B	0.27416	0.178;0.178	B;B	0.22880	0.042;0.025	T	0.16630	-1.0396	10	0.46703	T	0.11	-24.9599	5.7256	0.18010	0.3991:0.0:0.6009:0.0	.	142;179	C9JF66;Q6PIZ9	.;TRAT1_HUMAN	H	179;142	ENSP00000295756:R179H;ENSP00000410097:R142H	ENSP00000295756:R179H	R	+	2	0	TRAT1	110055389	1.000000	0.71417	0.999000	0.59377	0.534000	0.34807	1.510000	0.35790	0.748000	0.32831	-0.345000	0.07892	CGT		0.428	TRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353794.1	NM_016388		A	108572699	G	A	108572699	3	1	61	1	0	0	0	0	1	0	0	0	16506	1145	40	1	558	1	TRAT1	3	108572699	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191613	108572699	89449731	2645	10630										
MORC1	27136	broad.mit.edu	37	chr3	108682426	108682426	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcctctttatttttttTtcatattggaccatgtaagt	4	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108682426T>G	ENST00000483760.1	-	26	2614	c.2571A>C	c.(2569-2571)gaA>gaC	p.E857D	MORC1_ENST00000232603.5_Missense_Mutation_p.E878D					MORC family CW-type zinc finger 1									p.E878D(1)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						TTATTTTTTTTTCATATTGGA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	3											64	66	66					3																	108682426		2201	4296	6497	110165116	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2571A>C	3.37:g.108682426T>G	ENSP00000417282:p.Glu857Asp		110165116		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	T	16.41	3.116311	0.56505	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.18174	2.23;2.25	4.9	1.12	0.20585	.	0.149455	0.31156	N	0.008150	T	0.13798	0.0334	L	0.34521	1.04	0.29779	N	0.834181	P;P	0.50819	0.939;0.939	P;B	0.46362	0.514;0.396	T	0.09357	-1.0678	10	0.72032	D	0.01	-18.3506	6.1715	0.20421	0.0:0.3836:0.0:0.6164	.	857;878	E7ERX1;Q86VD1	.;MORC1_HUMAN	D	878;857	ENSP00000232603:E878D;ENSP00000417282:E857D	ENSP00000232603:E878D	E	-	3	2	MORC1	110165116	0.981000	0.34729	0.990000	0.47175	0.798000	0.45092	-0.143000	0.10296	0.039000	0.15632	0.402000	0.26972	GAA		0.279	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			G	108682426	T	G	108682426	3	3	61	1	0	0	0	0	1	0	0	0	9731	1838	64	4	328	4	MORC1	3	108682426	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	109727	108682426	89340004	2646	10631										
MORC1	27136	broad.mit.edu	37	chr3	108723729	108723729	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggtaatattagcaatctGacttctctttcaaaacagag	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108723729G>T	ENST00000483760.1	-	19	2000	c.1957C>A	c.(1957-1959)Cag>Aag	p.Q653K	MORC1_ENST00000232603.5_Missense_Mutation_p.Q674K					MORC family CW-type zinc finger 1									p.Q674K(1)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						TTAGCAATCTGACTTCTCTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	146	141					3																	108723729		2203	4300	6503	110206419	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1957C>A	3.37:g.108723729G>T	ENSP00000417282:p.Gln653Lys		110206419		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	G	0.185	-1.059006	0.01950	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05649	3.41;3.59	4.04	-0.627	0.11541	.	2.237700	0.02786	U	0.121471	T	0.03348	0.0097	N	0.12182	0.205	0.09310	N	1	B;B	0.29037	0.231;0.231	B;B	0.24006	0.037;0.05	T	0.33777	-0.9855	10	0.05833	T	0.94	23.2857	6.8844	0.24191	0.5857:0.0:0.4143:0.0	.	653;674	E7ERX1;Q86VD1	.;MORC1_HUMAN	K	674;653	ENSP00000232603:Q674K;ENSP00000417282:Q653K	ENSP00000232603:Q674K	Q	-	1	0	MORC1	110206419	0.002000	0.14202	0.006000	0.13384	0.171000	0.22731	0.212000	0.17497	-0.118000	0.11851	0.460000	0.39030	CAG		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108723729	G	T	108723729	3	4	61	1	0	0	0	0	1	0	0	0	9731	1299	45	2	970	2	MORC1	3	108723729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41303	108723729	89298701	2647	10632										
MORC1	27136	broad.mit.edu	37	chr3	108776277	108776277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacattccagcttggcttCggttttctacgttcactcca	7	12	2	1	rs201598350		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:108776277C>T	ENST00000483760.1	-	13	1131	c.1088G>A	c.(1087-1089)cGa>cAa	p.R363Q	MORC1_ENST00000232603.5_Missense_Mutation_p.R363Q					MORC family CW-type zinc finger 1									p.R363Q(1)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						AGCTTGGCTTCGGTTTTCTAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											127	120	122					3																	108776277		2203	4300	6503	110258967	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1088G>A	3.37:g.108776277C>T	ENSP00000417282:p.Arg363Gln		110258967		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	c	17.70	3.453494	0.63290	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.09073	3.02;3.05	4.6	-1.71	0.08133	.	1.156520	0.06730	N	0.776524	T	0.09949	0.0244	M	0.77820	2.39	0.21105	N	0.999781	P;B	0.36438	0.553;0.034	B;B	0.27887	0.084;0.032	T	0.23368	-1.0190	10	0.52906	T	0.07	-3.0E-4	5.9135	0.19041	0.0:0.4795:0.1279:0.3925	.	363;363	E7ERX1;Q86VD1	.;MORC1_HUMAN	Q	363	ENSP00000232603:R363Q;ENSP00000417282:R363Q	ENSP00000232603:R363Q	R	-	2	0	MORC1	110258967	0.732000	0.28121	0.953000	0.39169	0.954000	0.61252	-0.229000	0.09098	-0.651000	0.05415	-0.127000	0.14921	CGA		0.338	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108776277	C	T	108776277	3	4	61	1	0	0	0	0	1	0	0	0	9731	884	31	1	1930	1	MORC1	3	108776277	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52548	108776277	89246153	2648	10633										
PVRL3	25945	broad.mit.edu	37	chr3	110852564	110852565	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatctagcaacagaacctINSaaaaaattgcccttcccatt							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:110852564_110852565insA	ENST00000485303.1	+	6	1427_1428	c.1152_1153insA	c.(1153-1155)aaafs	p.K385fs	PVRL3_ENST00000319792.3_3'UTR|PVRL3_ENST00000493615.1_Intron	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	385					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)	p.L387fs*12(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						CAACAGAACCTAAAAAATTGCC	0.446																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								112335255	SO:0001589	frameshift_variant	25945			AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1158dupA	3.37:g.110852570_110852570dupA	ENSP00000418070:p.Lys385fs		112335254	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Frame_Shift_Ins	INS	ENST00000485303.1	37	CCDS2957.1																																																																																				0.446	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		A	110852565	-	A	110852564	7	5	61	1	0	1	1	0	0	0	0	0	12878	1509	53	0	1174	0	PVRL3	3	110852564	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	2076287	110852564	87169866	2649	10634										
PHLDB2	90102	broad.mit.edu	37	chr3	111693274	111693274	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttttgaattttagagtcCtaatccgttactcaccttta	4	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111693274C>A	ENST00000431670.2	+	18	4037	c.3626C>A	c.(3625-3627)cCt>cAt	p.P1209H	PHLDB2_ENST00000495180.1_Missense_Mutation_p.P700H|PHLDB2_ENST00000481953.1_Missense_Mutation_p.P1166H|PHLDB2_ENST00000412622.1_Missense_Mutation_p.P1166H|PHLDB2_ENST00000393925.3_Missense_Mutation_p.P1209H|PHLDB2_ENST00000393923.3_Missense_Mutation_p.P1193H	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1209	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)		p.P1166H(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TTTTAGAGTCCTAATCCGTTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											69	70	70					3																	111693274		2203	4300	6503	113175964	SO:0001583	missense	90102				CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3626C>A	3.37:g.111693274C>A	ENSP00000405405:p.Pro1209His		113175964	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	37	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.766242	0.49574	.	.	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	6.17	5.27	0.74061	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.86310	0.5902	M	0.76838	2.35	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.987;0.996;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.964;0.975;1.0;1.0	D	0.87186	0.2231	10	0.87932	D	0	.	16.638	0.85064	0.0:0.8706:0.1294:0.0	.	321;700;1209;1166;1193	Q658P8;E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;.;PHLB2_HUMAN;.;.	H	1193;1209;1166;1209;1166;700	ENSP00000377500:P1193H;ENSP00000405405:P1209H;ENSP00000405292:P1166H;ENSP00000377502:P1209H;ENSP00000418319:P1166H;ENSP00000420303:P700H	ENSP00000377500:P1193H	P	+	2	0	PHLDB2	113175964	1.000000	0.71417	0.986000	0.45419	0.113000	0.19764	6.079000	0.71291	2.941000	0.99782	0.655000	0.94253	CCT		0.338	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		A	111693274	C	A	111693274	3	1	61	1	0	0	0	0	1	0	0	0	11883	681	24	2	3777	2	PHLDB2	3	111693274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	840710	111693274	86329156	2650	10635										
TMPRSS7	344805	broad.mit.edu	37	chr3	111766737	111766737	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaatcaagtccatccaaatCgaagccgacaactgtgtcac	6	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111766737C>T	ENST00000452346.2	+	7	885	c.882C>T	c.(880-882)atC>atT	p.I294I	TMPRSS7_ENST00000419127.1_Silent_p.I168I			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	294	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.I23I(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CCATCCAAATCGAAGCCGACA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	3											104	107	106					3																	111766737		2099	4221	6320	113249427	SO:0001819	synonymous_variant	344805			BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.882C>T	3.37:g.111766737C>T			113249427	C9J8P7|E9PAS3|Q17RH4	Silent	SNP	ENST00000452346.2	37																																																																																					0.522	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111766737	C	T	111766737	2	4	61	1	0	0	0	0	0	0	0	1	16291	874	31	1		1	TMPRSS7	3	111766737	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73463	111766737	86255693	2651	10636										
TMPRSS7	344805	broad.mit.edu	37	chr3	111769544	111769544	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacacagtgttggtcaaaGacatcactggctttgaaggg	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111769544G>T	ENST00000452346.2	+	9	1120	c.1117G>T	c.(1117-1119)Gac>Tac	p.D373Y	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.D247Y			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	373	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D102Y(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GTTGGTCAAAGACATCACTGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											224	208	213					3																	111769544		1867	4098	5965	113252234	SO:0001583	missense	344805			BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1117G>T	3.37:g.111769544G>T	ENSP00000398236:p.Asp373Tyr		113252234	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	37		.	.	.	.	.	.	.	.	.	.	G	16.61	3.170789	0.57584	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	D;D	0.89681	-2.55;-2.53	4.86	4.86	0.63082	CUB (3);	0.233970	0.35349	N	0.003261	T	0.81950	0.4931	N	0.19112	0.55	0.33172	D	0.548408	P;P	0.43938	0.822;0.504	B;B	0.41174	0.349;0.237	D	0.85683	0.1302	10	0.33141	T	0.24	.	15.2533	0.73564	0.0:0.0:1.0:0.0	.	373;247	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	Y	373;361;347;247	ENSP00000398236:D373Y;ENSP00000411645:D247Y	ENSP00000411645:D247Y	D	+	1	0	TMPRSS7	113252234	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	6.311000	0.72835	2.404000	0.81709	0.460000	0.39030	GAC		0.398	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111769544	G	T	111769544	3	4	61	1	0	0	0	0	1	0	0	0	16291	942	33	2	761	2	TMPRSS7	3	111769544	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2807	111769544	86252886	2652	10637										
GCET2	257144	broad.mit.edu	37	chr3	111844102	111844102	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagatgacattctttcatCtggagaaagaaaatacactc	7	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111844102C>A	ENST00000308910.4	-	5	375		c.e5-1		C3orf52_ENST00000467942.2_Intron|GCSAM_ENST00000484193.1_Splice_Site	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility						negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)	p.?(1)									ATTCTTTCATCTGGAGAAAGA	0.373																																																1	Unknown(1)	large_intestine(1)	3											109	110	110					3																	111844102		2203	4300	6503	113326792	SO:0001630	splice_region_variant	257144			BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"human germinal center-associated lymphoma"	607792	"germinal center expressed transcript 2"	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.191-1G>T	3.37:g.111844102C>A			113326792	C9JD17|C9JUG6	Splice_Site	SNP	ENST00000308910.4	37	CCDS2964.1	.	.	.	.	.	.	.	.	.	.	C	9.267	1.044607	0.19748	.	.	ENSG00000174500	ENST00000308910;ENST00000484193;ENST00000460387;ENST00000488580;ENST00000487901	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4209	0.55520	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GCET2	113326792	0.978000	0.34361	0.920000	0.36463	0.172000	0.22775	3.018000	0.49625	2.656000	0.90262	0.561000	0.74099	.		0.373	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	Intron	A	111844102	C	A	111844102	5	1	61	1	0	0	0	0	0	0	1	0	6308	927	32	2	354	2	GCET2	3	111844102	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74558	111844102	86178328	2653	10638										
SLC9A10	285335	broad.mit.edu	37	chr3	111887880	111887880	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctactacataaatattagaGagctttagttgcatattgta	6	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111887880G>T	ENST00000305815.5	-	25	3333	c.3081C>A	c.(3079-3081)ctC>ctA	p.L1027L	SLC9C1_ENST00000487372.1_Silent_p.L979L	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1027					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.L1027L(1)									AAATATTAGAGAGCTTTAGTT	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	3											74	82	79					3																	111887880		2202	4294	6496	113370570	SO:0001819	synonymous_variant	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.3081C>A	3.37:g.111887880G>T			113370570	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																				0.279	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111887880	G	T	111887880	2	4	61	1	0	0	0	0	0	0	0	1	14747	929	33	2		2	SLC9A10	3	111887880	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43778	111887880	86134550	2654	10639										
SLC9A10	285335	broad.mit.edu	37	chr3	111918263	111918263	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgagcataacattaatttCttcctttgttttcacagtga	5	7	2	2	rs371139214		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111918263C>A	ENST00000305815.5	-	20	2680	c.2428G>T	c.(2428-2430)Gaa>Taa	p.E810*	SLC9C1_ENST00000487372.1_Nonsense_Mutation_p.E762*	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	810					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.E810*(1)									ACATTAATTTCTTCCTTTGTT	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	3						C	stop/GLU	1,4401	2.1+/-5.4	0,1,2200	75	78	77		2428	1.5	0.5	3		77	0,8596		0,0,4298	no	stop-gained	SLC9A10	NM_183061.1		0,1,6498	AA,AC,CC		0.0,0.0227,0.0077		810/1178	111918263	1,12997	2201	4298	6499	113400953	SO:0001587	stop_gained	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2428G>T	3.37:g.111918263C>A	ENSP00000306627:p.Glu810*		113400953	Q6ZRP4|Q7RTP2	Nonsense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	36	5.816894	0.96982	2.27E-4	0.0	ENSG00000172139	ENST00000305815;ENST00000487372	.	.	.	5.55	1.49	0.22878	.	0.353337	0.23883	N	0.043632	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	10.5832	0.45267	0.1295:0.3276:0.5429:0.0	.	.	.	.	X	810;762	.	ENSP00000306627:E810X	E	-	1	0	SLC9A10	113400953	0.554000	0.26522	0.517000	0.27799	0.085000	0.17905	0.518000	0.22847	-0.040000	0.13580	-0.152000	0.13540	GAA		0.289	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		A	111918263	C	A	111918263	4	1	61	1	0	0	0	0	0	1	0	0	14747	922	32	2	1145	2	SLC9A10	3	111918263	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30383	111918263	86104167	2655	10640										
SLC9A10	285335	broad.mit.edu	37	chr3	111923176	111923176	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaataagtattacatgtaaGatgccaattaatgtaattgc	6	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111923176G>T	ENST00000305815.5	-	17	2313	c.2061C>A	c.(2059-2061)atC>atA	p.I687I	SLC9C1_ENST00000487372.1_Silent_p.I639I	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	687					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.I687I(1)									TTACATGTAAGATGCCAATTA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	3											112	113	113					3																	111923176		2201	4295	6496	113405866	SO:0001819	synonymous_variant	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2061C>A	3.37:g.111923176G>T			113405866	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																				0.284	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111923176	G	T	111923176	2	4	61	1	0	0	0	0	0	0	0	1	14747	932	33	2		2	SLC9A10	3	111923176	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4913	111923176	86099254	2656	10641										
SLC9A10	285335	broad.mit.edu	37	chr3	111958848	111958848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttgatgtggcatcacGaagacctttgatacaaacac	8	8	1	3	rs186081653		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:111958848G>A	ENST00000305815.5	-	12	1537	c.1285C>T	c.(1285-1287)Cgt>Tgt	p.R429C	SLC9C1_ENST00000487372.1_Missense_Mutation_p.R381C	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	429					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.R429C(1)									GTGGCATCACGAAGACCTTTG	0.338													G|||	1	0.000199681	0	0.0014	5008	,	,		18721	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	CYS/ARG	0,4406		0,0,2203	92	82	86		1285	4.6	1	3		86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC9A10	NM_183061.1	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	429/1178	111958848	1,13005	2203	4300	6503	113441538	SO:0001583	missense	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1285C>T	3.37:g.111958848G>A	ENSP00000306627:p.Arg429Cys		113441538	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	15.78	2.933481	0.52866	0.0	1.16E-4	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77750	-1.12;-1.06	5.48	4.61	0.57282	.	0.206543	0.34853	N	0.003623	T	0.79155	0.4398	L	0.32530	0.975	0.42552	D	0.993117	B;D	0.89917	0.08;1.0	B;D	0.63957	0.014;0.92	T	0.79237	-0.1886	10	0.49607	T	0.09	-7.2332	10.1891	0.43015	0.0918:0.0:0.9082:0.0	.	381;429	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	C	429;381	ENSP00000306627:R429C;ENSP00000420688:R381C	ENSP00000306627:R429C	R	-	1	0	SLC9A10	113441538	0.970000	0.33590	0.973000	0.42090	0.764000	0.43329	2.416000	0.44644	1.313000	0.45069	0.511000	0.50034	CGT		0.338	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		A	111958848	G	A	111958848	3	1	61	1	0	0	0	0	1	0	0	0	14747	1058	37	1	2320	1	SLC9A10	3	111958848	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35672	111958848	86063582	2657	10642										
CD200	4345	broad.mit.edu	37	chr3	112068612	112068612	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtttccctggtaattcttCtcgtcctaatctcaatctta	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112068612C>T	ENST00000315711.8	+	5	805	c.748C>T	c.(748-750)Ctc>Ttc	p.L250F	CD200_ENST00000473539.1_Missense_Mutation_p.L275F|CD200_ENST00000383681.3_Missense_Mutation_p.L176F	NM_005944.5	NP_005935.4	P41217	OX2G_HUMAN	CD200 molecule	250					regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.L275F(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				GGTAATTCTTCTCGTCCTAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											122	110	114					3																	112068612		2203	4300	6503	113551302	SO:0001583	missense	4345				CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7203	protein-coding gene	gene with protein product		155970	"antigen identified by monoclonal antibody MRC OX-2", "CD200 antigen"	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000315711.8:c.748C>T	3.37:g.112068612C>T	ENSP00000312766:p.Leu250Phe		113551302	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000315711.8	37	CCDS2965.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043866	0.75732	.	.	ENSG00000091972	ENST00000315711;ENST00000473539;ENST00000383681	T;T;T	0.76968	0.54;-1.06;-0.93	5.22	5.22	0.72569	.	0.168545	0.28448	N	0.015314	T	0.81039	0.4740	L	0.27053	0.805	0.44570	D	0.997536	D;D;D;D;D	0.76494	0.999;0.999;0.998;0.999;0.999	D;D;D;D;D	0.83275	0.946;0.996;0.991;0.996;0.996	T	0.82259	-0.0546	10	0.62326	D	0.03	-11.5884	14.1585	0.65432	0.0:1.0:0.0:0.0	.	250;176;176;250;275	P41217;F8W7G1;B4DDZ6;P41217-2;P41217-3	OX2G_HUMAN;.;.;.;.	F	250;275;176	ENSP00000312766:L250F;ENSP00000420298:L275F;ENSP00000373179:L176F	ENSP00000312766:L250F	L	+	1	0	CD200	113551302	0.998000	0.40836	1.000000	0.80357	0.756000	0.42949	1.315000	0.33608	2.696000	0.92011	0.655000	0.94253	CTC		0.378	CD200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354078.1			T	112068612	C	T	112068612	3	4	61	1	0	0	0	0	1	0	0	0	2986	913	32	3	845	3	CD200	3	112068612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109764	112068612	85953818	2658	10643										
ATG3	64422	broad.mit.edu	37	chr3	112256665	112256665	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcataagttctggtttgcaAaatagcatcttcaccgccag	8	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112256665A>C	ENST00000283290.5	-	9	1017	c.583T>G	c.(583-585)Ttg>Gtg	p.L195V	ATG3_ENST00000495756.1_5'UTR|ATG3_ENST00000402314.2_Missense_Mutation_p.L195V	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	195					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)	p.L195V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						CTGGTTTGCAAAATAGCATCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											111	105	107					3																	112256665		2203	4300	6503	113739355	SO:0001583	missense	64422				CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"APG3 autophagy 3-like (S. cerevisiae)", "ATG3 autophagy related 3 homolog (S. cerevisiae)"	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.583T>G	3.37:g.112256665A>C	ENSP00000283290:p.Leu195Val		113739355	Q6PKC5|Q9H6L9	Missense_Mutation	SNP	ENST00000283290.5	37	CCDS2966.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.639033	0.47153	.	.	ENSG00000144848	ENST00000283290;ENST00000402314	.	.	.	5.72	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	L	0.49455	1.56	0.58432	D	0.999998	B;B	0.25312	0.044;0.123	B;B	0.29862	0.034;0.108	T	0.35226	-0.9797	9	0.21540	T	0.41	-1.9076	8.1486	0.31126	0.8004:0.0:0.1996:0.0	.	195;195	Q9NT62;Q9NT62-2	ATG3_HUMAN;.	V	195	.	ENSP00000283290:L195V	L	-	1	2	ATG3	113739355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.932000	0.56537	0.942000	0.37525	0.533000	0.62120	TTG		0.343	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488		C	112256665	A	C	112256665	3	2	61	1	0	0	0	0	1	0	0	0	1096	11	1	4	377	4	ATG3	3	112256665	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	188053	112256665	85765765	2659	10644										
SLC35A5	55032	broad.mit.edu	37	chr3	112299629	112299629	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatggaacaccacagccaGagttttcagtcacatccgtc	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112299629G>T	ENST00000492406.1	+	6	948	c.665G>T	c.(664-666)aGa>aTa	p.R222I	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	222					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)	p.R222I(1)		endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						ACCACAGCCAGAGTTTTCAGT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											138	130	133					3																	112299629		2203	4300	6503	113782319	SO:0001583	missense	55032			AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"Solute carriers"	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.665G>T	3.37:g.112299629G>T	ENSP00000417654:p.Arg222Ile		113782319	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Missense_Mutation	SNP	ENST00000492406.1	37	CCDS2967.1	.	.	.	.	.	.	.	.	.	.	G	9.728	1.161600	0.21538	.	.	ENSG00000138459	ENST00000492406	T	0.45276	0.9	5.76	3.01	0.34805	.	0.526178	0.23187	N	0.050942	T	0.29423	0.0733	L	0.38531	1.155	0.26699	N	0.971206	B	0.21688	0.059	B	0.18871	0.023	T	0.16867	-1.0388	9	.	.	.	-0.4977	8.63	0.33913	0.0687:0.0:0.6588:0.2725	.	222	Q9BS91	S35A5_HUMAN	I	222	ENSP00000417654:R222I	.	R	+	2	0	SLC35A5	113782319	0.201000	0.23410	0.557000	0.28306	0.466000	0.32739	0.840000	0.27600	0.366000	0.24427	-0.926000	0.02714	AGA		0.393	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		T	112299629	G	T	112299629	3	4	61	1	0	0	0	0	1	0	0	0	14611	942	33	2	683	2	SLC35A5	3	112299629	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42964	112299629	85722801	2660	10645										
CCDC80	151887	broad.mit.edu	37	chr3	112358377	112358377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacgcaacattcttgaccGagctgaggacccctcatctc	8	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112358377G>A	ENST00000206423.3	-	2	1329	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CCDC80_ENST00000439685.2_Missense_Mutation_p.R126W|CCDC80_ENST00000475181.1_5'UTR	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	126					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.R126W(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						ATTCTTGACCGAGCTGAGGAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	86	88					3																	112358377		2203	4300	6503	113841067	SO:0001583	missense	151887			AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.376C>T	3.37:g.112358377G>A	ENSP00000206423:p.Arg126Trp		113841067	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	37	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553486	0.65425	.	.	ENSG00000091986	ENST00000206423;ENST00000439685	T;T	0.55930	0.49;0.49	5.35	4.46	0.54185	.	0.114198	0.56097	D	0.000022	T	0.60157	0.2247	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;P	0.66196	0.942;0.94;0.877	T	0.64943	-0.6288	10	0.66056	D	0.02	-22.1387	15.4872	0.75575	0.0:0.0:0.8605:0.1395	.	137;126;126	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	W	126	ENSP00000206423:R126W;ENSP00000411814:R126W	ENSP00000206423:R126W	R	-	1	2	CCDC80	113841067	1.000000	0.71417	0.882000	0.34594	0.779000	0.44077	3.582000	0.53921	1.462000	0.47948	0.650000	0.86243	CGG		0.592	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112358377	G	A	112358377	3	1	61	1	0	0	0	0	1	0	0	0	2860	1057	37	1	2504	1	CCDC80	3	112358377	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58748	112358377	85664053	2661	10646										
CD200R1	131450	broad.mit.edu	37	chr3	112647875	112647875	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccttgcatactgcagttCtattcctgttttgaaacagg	8	10	1	1	rs200448544		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112647875C>A	ENST00000471858.1	-	4	720	c.488G>T	c.(487-489)aGa>aTa	p.R163I	CD200R1_ENST00000308611.3_Missense_Mutation_p.R186I|CD200R1_ENST00000295863.4_Missense_Mutation_p.R141I|CD200R1_ENST00000440122.2_3'UTR|CD200R1_ENST00000490004.1_3'UTR	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	163	Ig-like C2-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.R186I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TACTGCAGTTCTATTCCTGTT	0.468													C|||	1	0.000199681	0	0	5008	,	,		20343	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											76	69	71					3																	112647875		2203	4300	6503	114130565	SO:0001583	missense	131450			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.488G>T	3.37:g.112647875C>A	ENSP00000418928:p.Arg163Ile		114130565	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.01	2.110691	0.37242	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863	T;T;T	0.39229	1.09;1.09;2.81	5.43	1.63	0.23807	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.655787	0.15363	N	0.266299	T	0.31199	0.0789	N	0.11756	0.17	0.09310	N	1	B;P;P	0.51791	0.003;0.948;0.936	B;P;P	0.52267	0.01;0.694;0.568	T	0.11012	-1.0605	10	0.30854	T	0.27	.	8.2317	0.31601	0.0:0.6739:0.0:0.3261	.	141;163;186	B4E2U2;Q8TD46;Q8TD46-4	.;MO2R1_HUMAN;.	I	163;186;141	ENSP00000418928:R163I;ENSP00000311035:R186I;ENSP00000295863:R141I	ENSP00000295863:R141I	R	-	2	0	CD200R1	114130565	0.000000	0.05858	0.190000	0.23270	0.104000	0.19210	0.421000	0.21280	0.671000	0.31185	0.650000	0.86243	AGA		0.468	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		A	112647875	C	A	112647875	3	1	61	1	0	0	0	0	1	0	0	0	2987	913	32	2	505	2	CD200R1	3	112647875	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289498	112647875	85374555	2662	10647										
CD200R1	131450	broad.mit.edu	37	chr3	112693688	112693688	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagccctaggttagcagttCtccaagggcagagcatttct	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112693688C>A	ENST00000471858.1	-	1	249	c.17G>T	c.(16-18)aGa>aTa	p.R6I	CD200R1_ENST00000308611.3_Missense_Mutation_p.R6I|CD200R1_ENST00000295863.4_Missense_Mutation_p.R6I|CD200R1_ENST00000440122.2_Missense_Mutation_p.R6I|CD200R1_ENST00000490004.1_Missense_Mutation_p.R6I	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	6					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.R6I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						GTTAGCAGTTCTCCAAGGGCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											213	183	193					3																	112693688		2203	4300	6503	114176378	SO:0001583	missense	131450			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.17G>T	3.37:g.112693688C>A	ENSP00000418928:p.Arg6Ile		114176378	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.467398	0.63625	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.27557	2.17;2.26;1.92;1.66;1.72	5.66	3.46	0.39613	.	0.626729	0.13915	N	0.353946	T	0.23572	0.0570	L	0.41824	1.3	0.32706	N	0.512178	B;P;P;B;B	0.44380	0.121;0.713;0.834;0.261;0.379	B;B;B;B;B	0.41666	0.021;0.234;0.363;0.052;0.111	T	0.34104	-0.9842	10	0.51188	T	0.08	.	4.397	0.11367	0.2371:0.6287:0.0:0.1342	.	6;6;6;6;6	B4E2U2;Q8TD46-3;Q8TD46-2;Q8TD46;Q8TD46-4	.;.;.;MO2R1_HUMAN;.	I	6	ENSP00000418928:R6I;ENSP00000311035:R6I;ENSP00000295863:R6I;ENSP00000405733:R6I;ENSP00000418801:R6I	ENSP00000295863:R6I	R	-	2	0	CD200R1	114176378	0.939000	0.31865	0.930000	0.37139	0.998000	0.95712	1.543000	0.36147	1.501000	0.48654	0.655000	0.94253	AGA		0.468	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		A	112693688	C	A	112693688	3	1	61	1	0	0	0	0	1	0	0	0	2987	913	32	2	1108	2	CD200R1	3	112693688	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45813	112693688	85328742	2663	10648										
GTPBP8	29083	broad.mit.edu	37	chr3	112718376	112718376	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaatttgttaacatgaaAactcaaggatgttttcctca	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:112718376A>G	ENST00000383678.2	+	5	832	c.750A>G	c.(748-750)aaA>aaG	p.K250K	GTPBP8_ENST00000383677.3_Silent_p.K217K|GTPBP8_ENST00000473129.1_Silent_p.K100K|GTPBP8_ENST00000467752.1_Silent_p.K139K	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	250	EngB-type G.				barrier septum assembly (GO:0000917)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.K250K(1)		kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	6						TTAACATGAAAACTCAAGGAT	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	3											102	103	103					3																	112718376		2202	4299	6501	114201066	SO:0001819	synonymous_variant	29083			BC037163	CCDS33820.1, CCDS33821.1	3q13.2	2008-02-05			ENSG00000163607	ENSG00000163607			25007	protein-coding gene	gene with protein product							Standard	NM_014170		Approved	HSPC135	uc003dzn.3	Q8N3Z3	OTTHUMG00000159268	ENST00000383678.2:c.750A>G	3.37:g.112718376A>G			114201066	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Silent	SNP	ENST00000383678.2	37	CCDS33820.1																																																																																				0.289	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		G	112718376	A	G	112718376	2	3	61	1	0	0	0	0	0	0	0	1	6905	11	1	4		4	GTPBP8	3	112718376	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24688	112718376	85304054	2664	10649										
BOC	91653	broad.mit.edu	37	chr3	113005605	113005605	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtggaggagactggtgtCcccagcaccccgtaggggcc	16	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113005605C>A	ENST00000495514.1	+	20	3945	c.3241C>A	c.(3241-3243)Ccc>Acc	p.P1081T	BOC_ENST00000273395.4_Missense_Mutation_p.P1082T|BOC_ENST00000355385.3_Missense_Mutation_p.P1081T			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	1081					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.P1081T(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			AGACTGGTGTCCCCAGCACCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											134	145	142					3																	113005605		2203	4300	6503	114488295	SO:0001583	missense	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.3241C>A	3.37:g.113005605C>A	ENSP00000418663:p.Pro1081Thr		114488295	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.272913	0.40194	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.60424	0.19;0.19;0.19	5.51	2.63	0.31362	.	0.218916	0.37219	N	0.002181	T	0.40119	0.1104	L	0.27053	0.805	0.24527	N	0.994131	B;B	0.26845	0.161;0.1	B;B	0.27380	0.079;0.036	T	0.23691	-1.0181	10	0.38643	T	0.18	.	7.2639	0.26219	0.0:0.597:0.2547:0.1483	.	1082;1081	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	T	1081;1082;1081	ENSP00000418663:P1081T;ENSP00000273395:P1082T;ENSP00000347546:P1081T	ENSP00000273395:P1082T	P	+	1	0	BOC	114488295	0.942000	0.31987	0.993000	0.49108	0.951000	0.60555	0.155000	0.16362	0.377000	0.24735	-0.305000	0.09177	CCC		0.597	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		A	113005605	C	A	113005605	3	1	61	1	0	0	0	0	1	0	0	0	1482	855	30	2	3311	2	BOC	3	113005605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	287229	113005605	85016825	2665	10650										
WDR52	55779	broad.mit.edu	37	chr3	113115488	113115488	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttccgtcccgcaaaaatCgtgagcccttttggatcata	7	12	2	1	rs377529770		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113115488C>T	ENST00000295868.2	-	14	1818	c.1656G>A	c.(1654-1656)acG>acA	p.T552T	WDR52_ENST00000475568.1_5'UTR|WDR52_ENST00000393845.2_Silent_p.T552T	NM_018338.3	NP_060808.2												p.T552T(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						CCGCAAAAATCGTGAGCCCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	3						C	,	0,4406		0,0,2203	96	98	97		1656,1656	-3.4	0	3		97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	WDR52	NM_001164496.1,NM_018338.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	552/1855,552/983	113115488	1,13005	2203	4300	6503	114598178	SO:0001819	synonymous_variant	55779																														ENST00000295868.2:c.1656G>A	3.37:g.113115488C>T			114598178		Silent	SNP	ENST00000295868.2	37	CCDS2972.1																																																																																				0.383	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			T	113115488	C	T	113115488	2	4	61	1	0	0	0	0	0	0	0	1	17344	871	31	1		1	WDR52	3	113115488	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109883	113115488	84906942	2666	10651										
CCDC52	152185	broad.mit.edu	37	chr3	113169309	113169309	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catactttgtcgattcaattCtgcaatccgttcctccatac	4	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113169309C>A	ENST00000295872.4	-	15	2456	c.2197G>T	c.(2197-2199)Gaa>Taa	p.E733*		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	733					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)		p.E733*(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CGATTCAATTCTGCAATCCGT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											118	111	113					3																	113169309		2203	4300	6503	114651999	SO:0001587	stop_gained	152185			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.2197G>T	3.37:g.113169309C>A	ENSP00000295872:p.Glu733*		114651999	D3DN72|Q8WUX6	Nonsense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	C	40	8.453131	0.98817	.	.	ENSG00000163611	ENST00000295872	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.3703	16.3533	0.83225	0.0:1.0:0.0:0.0	.	.	.	.	X	733	.	ENSP00000295872:E733X	E	-	1	0	SPICE1	114651999	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	4.264000	0.58859	2.660000	0.90430	0.557000	0.71058	GAA		0.398	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113169309	C	A	113169309	4	1	61	1	0	0	0	0	0	1	0	0	2828	922	32	2	386	2	CCDC52	3	113169309	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53821	113169309	84853121	2667	10652										
CCDC52	152185	broad.mit.edu	37	chr3	113172461	113172461	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtgtcattatgtcctttCtttgtattaatgactcattt	5	7	3	1	rs562601249		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113172461C>A	ENST00000295872.4	-	14	2253	c.1994G>T	c.(1993-1995)aGa>aTa	p.R665I		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	665					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)		p.R665I(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TATGTCCTTTCTTTGTATTAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											154	153	153					3																	113172461		2203	4300	6503	114655151	SO:0001583	missense	152185			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1994G>T	3.37:g.113172461C>A	ENSP00000295872:p.Arg665Ile		114655151	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805333	0.70682	.	.	ENSG00000163611	ENST00000295872	T	0.32515	1.45	5.64	4.76	0.60689	.	0.210360	0.49916	D	0.000139	T	0.43500	0.1250	L	0.57536	1.79	0.48830	D	0.999713	D;P	0.58268	0.982;0.899	P;P	0.55455	0.776;0.667	T	0.32295	-0.9912	10	0.62326	D	0.03	-17.6482	12.2638	0.54665	0.0:0.9181:0.0:0.0819	.	561;665	B3KX77;Q8N0Z3	.;SPICE_HUMAN	I	665	ENSP00000295872:R665I	ENSP00000295872:R665I	R	-	2	0	SPICE1	114655151	0.996000	0.38824	1.000000	0.80357	0.932000	0.56968	1.006000	0.29847	2.654000	0.90174	0.563000	0.77884	AGA		0.428	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113172461	C	A	113172461	3	1	61	1	0	0	0	0	1	0	0	0	2828	913	32	2	593	2	CCDC52	3	113172461	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3152	113172461	84849969	2668	10653										
CCDC52	152185	broad.mit.edu	37	chr3	113212951	113212951	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctattagatgatcagatttCtccaacacatcttgcatctg	6	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113212951C>A	ENST00000295872.4	-	5	589	c.330G>T	c.(328-330)gaG>gaT	p.E110D		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	110					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)		p.E110D(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						GATCAGATTTCTCCAACACAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	90	92					3																	113212951		2203	4300	6503	114695641	SO:0001583	missense	152185			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.330G>T	3.37:g.113212951C>A	ENSP00000295872:p.Glu110Asp		114695641	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.596723	0.46318	.	.	ENSG00000163611	ENST00000295872;ENST00000495812;ENST00000480527	T	0.35973	1.28	5.18	3.04	0.35103	.	0.179163	0.49305	D	0.000155	T	0.51991	0.1707	M	0.71581	2.175	0.30915	N	0.728665	D;P	0.67145	0.996;0.899	D;B	0.75484	0.986;0.397	T	0.54503	-0.8284	10	0.52906	T	0.07	-8.4697	5.6061	0.17381	0.0:0.3708:0.0:0.6292	.	6;110	B3KX77;Q8N0Z3	.;SPICE_HUMAN	D	110	ENSP00000295872:E110D	ENSP00000295872:E110D	E	-	3	2	SPICE1	114695641	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	0.504000	0.22626	0.514000	0.28300	0.585000	0.79938	GAG		0.338	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113212951	C	A	113212951	3	1	61	1	0	0	0	0	1	0	0	0	2828	912	32	2	2293	2	CCDC52	3	113212951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40490	113212951	84809479	2669	10654										
KIAA2018	205717	broad.mit.edu	37	chr3	113379177	113379177	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactggagtcacagcagaaGatggtgtctggcttaagggc	14	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113379177G>T	ENST00000478658.1	-	5	1369	c.1352C>A	c.(1351-1353)tCt>tAt	p.S451Y	KIAA2018_ENST00000316407.4_Missense_Mutation_p.S451Y|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	451						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.S451Y(1)		NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CACAGCAGAAGATGGTGTCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	71	70					3																	113379177		2008	4182	6190	114861867	SO:0001583	missense	205717			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.1352C>A	3.37:g.113379177G>T	ENSP00000420721:p.Ser451Tyr		114861867	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885871	0.51908	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.17213	2.29;2.29	5.31	5.31	0.75309	.	0.589490	0.17491	N	0.172355	T	0.24890	0.0604	L	0.32530	0.975	0.44985	D	0.998008	D	0.53885	0.963	P	0.50490	0.642	T	0.01729	-1.1286	10	0.72032	D	0.01	-8.7574	18.9748	0.92731	0.0:0.0:1.0:0.0	.	451	Q68DE3	K2018_HUMAN	Y	451	ENSP00000320794:S451Y;ENSP00000420721:S451Y	ENSP00000320794:S451Y	S	-	2	0	KIAA2018	114861867	0.988000	0.35896	0.936000	0.37596	0.713000	0.41058	5.301000	0.65727	2.487000	0.83934	0.557000	0.71058	TCT		0.443	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113379177	G	T	113379177	3	4	61	1	0	0	0	0	1	0	0	0	8289	942	33	2	5389	2	KIAA2018	3	113379177	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166226	113379177	84643253	2670	10655										
ATP6V1A	523	broad.mit.edu	37	chr3	113517215	113517215	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaacacttcacagagttCgttcctctgaggacgaaagc	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113517215C>T	ENST00000273398.3	+	12	1524	c.1416C>T	c.(1414-1416)ttC>ttT	p.F472F	ATP6V1A_ENST00000538620.1_Silent_p.F439F	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	472					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.F472F(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	TCACAGAGTTCGTTCCTCTGA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	3											148	137	141					3																	113517215		2203	4300	6503	114999905	SO:0001819	synonymous_variant	523			L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1416C>T	3.37:g.113517215C>T			114999905	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Silent	SNP	ENST00000273398.3	37	CCDS2976.1																																																																																				0.438	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		T	113517215	C	T	113517215	2	4	61	1	0	0	0	0	0	0	0	1	1178	883	31	1		1	ATP6V1A	3	113517215	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138038	113517215	84505215	2671	10656										
GRAMD1C	54762	broad.mit.edu	37	chr3	113601612	113601612	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcagtttttcttcacatCttttggtgccagggatagaa	9	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113601612C>A	ENST00000358160.4	+	6	965	c.473C>A	c.(472-474)tCt>tAt	p.S158Y	GRAMD1C_ENST00000452134.2_5'UTR|GRAMD1C_ENST00000479212.1_3'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	158						integral component of membrane (GO:0016021)		p.S158Y(1)		NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						TTCTTCACATCTTTTGGTGCC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											173	176	175					3																	113601612		2203	4300	6503	115084302	SO:0001583	missense	54762				CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.473C>A	3.37:g.113601612C>A	ENSP00000350881:p.Ser158Tyr		115084302	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	37	CCDS33826.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977280	0.74360	.	.	ENSG00000178075	ENST00000358160	T	0.41758	0.99	5.52	4.64	0.57946	.	0.741502	0.13340	N	0.395245	T	0.50582	0.1624	M	0.87381	2.88	0.80722	D	1	B	0.30664	0.289	B	0.26517	0.07	T	0.55483	-0.8134	10	0.87932	D	0	.	13.4347	0.61077	0.1582:0.8418:0.0:0.0	.	158	Q8IYS0	GRM1C_HUMAN	Y	158	ENSP00000350881:S158Y	ENSP00000350881:S158Y	S	+	2	0	GRAMD1C	115084302	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.287000	0.78681	1.300000	0.44818	0.643000	0.83706	TCT		0.348	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		A	113601612	C	A	113601612	3	1	61	1	0	0	0	0	1	0	0	0	6770	913	32	2	495	2	GRAMD1C	3	113601612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84397	113601612	84420818	2672	10657										
ZDHHC23	254887	broad.mit.edu	37	chr3	113667698	113667698	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagaaaaagaaaaccgaaGaacctgaattggagcccctg	10	8	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113667698G>T	ENST00000330212.3	+	2	348	c.49G>T	c.(49-51)Gaa>Taa	p.E17*	RP11-255E6.6_ENST00000609657.1_RNA|ZDHHC23_ENST00000498275.1_Nonsense_Mutation_p.E11*	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	17					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.E17*(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						GAAAACCGAAGAACCTGAATT	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											164	161	162					3																	113667698		2203	4300	6503	115150388	SO:0001587	stop_gained	254887			AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"Zinc fingers, DHHC-type"	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.49G>T	3.37:g.113667698G>T	ENSP00000330485:p.Glu17*		115150388	D3DN76	Nonsense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	.	.	.	.	.	.	.	.	.	.	G	38	6.834381	0.97873	.	.	ENSG00000184307	ENST00000330212;ENST00000498275;ENST00000491556	.	.	.	5.38	3.6	0.41247	.	0.573004	0.18306	N	0.145255	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-10.9486	9.2199	0.37370	0.1707:0.0:0.8293:0.0	.	.	.	.	X	17;11;17	.	ENSP00000330485:E17X	E	+	1	0	ZDHHC23	115150388	0.614000	0.27017	0.899000	0.35326	0.951000	0.60555	2.734000	0.47368	0.658000	0.30925	0.591000	0.81541	GAA		0.478	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		T	113667698	G	T	113667698	4	4	61	1	0	0	0	0	0	1	0	0	17653	943	33	2	51	2	ZDHHC23	3	113667698	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66086	113667698	84354732	2673	10658										
ZDHHC23	254887	broad.mit.edu	37	chr3	113673114	113673114	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacaaaggatgaccccaaGggctcttccaagatgccagc	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113673114G>T	ENST00000330212.3	+	3	1028	c.729G>T	c.(727-729)aaG>aaT	p.K243N	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.K237N	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	243					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.K243N(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						ATGACCCCAAGGGCTCTTCCA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	67	67					3																	113673114		2203	4300	6503	115155804	SO:0001583	missense	254887			AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"Zinc fingers, DHHC-type"	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.729G>T	3.37:g.113673114G>T	ENSP00000330485:p.Lys243Asn		115155804	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	.	.	.	.	.	.	.	.	.	.	G	3.846	-0.032730	0.07543	.	.	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.25414	1.8;1.8	5.11	4.24	0.50183	.	0.676707	0.14914	N	0.291068	T	0.18215	0.0437	L	0.29908	0.895	0.09310	N	1	B	0.32010	0.351	B	0.31495	0.131	T	0.15037	-1.0451	10	0.22706	T	0.39	-12.9346	10.4658	0.44607	0.1696:0.0:0.8304:0.0	.	243	Q8IYP9	ZDH23_HUMAN	N	243;237	ENSP00000330485:K243N;ENSP00000417840:K237N	ENSP00000330485:K243N	K	+	3	2	ZDHHC23	115155804	1.000000	0.71417	0.059000	0.19551	0.055000	0.15305	3.622000	0.54217	1.375000	0.46248	0.561000	0.74099	AAG		0.602	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		T	113673114	G	T	113673114	3	4	61	1	0	0	0	0	1	0	0	0	17653	991	35	2	735	2	ZDHHC23	3	113673114	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5416	113673114	84349316	2674	10659										
KIAA1407	57577	broad.mit.edu	37	chr3	113737676	113737676	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttaatcctatgatcaaGaatcagcttgtgccaggcag	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113737676G>T	ENST00000295878.3	-	8	1158	c.1012C>A	c.(1012-1014)Ctt>Att	p.L338I	KIAA1407_ENST00000545063.1_Missense_Mutation_p.L169I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	338								p.L338I(1)		endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CTATGATCAAGAATCAGCTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											220	224	223					3																	113737676		2203	4300	6503	115220366	SO:0001583	missense	57577			AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1012C>A	3.37:g.113737676G>T	ENSP00000295878:p.Leu338Ile		115220366	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974628	0.53720	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.54675	1.21;0.56;0.59	5.76	3.6	0.41247	.	0.144448	0.47455	D	0.000221	T	0.47911	0.1471	M	0.66939	2.045	0.80722	D	1	B;P;B	0.40211	0.36;0.707;0.36	B;B;B	0.36244	0.22;0.22;0.22	T	0.51679	-0.8675	10	0.41790	T	0.15	.	11.6437	0.51249	0.0739:0.0:0.7995:0.1266	.	325;214;338	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	338;169;325	ENSP00000295878:L338I;ENSP00000446381:L169I;ENSP00000418099:L325I	ENSP00000295878:L338I	L	-	1	0	KIAA1407	115220366	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.882000	0.39648	1.399000	0.46721	0.655000	0.94253	CTT		0.473	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113737676	G	T	113737676	3	4	61	1	0	0	0	0	1	0	0	0	8250	942	33	2	1838	2	KIAA1407	3	113737676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64562	113737676	84284754	2675	10660										
DRD3	1814	broad.mit.edu	37	chr3	113858437	113858437	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtttcagcaccacataGattctggcatagacaaggac	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113858437G>A	ENST00000460779.1	-	6	922	c.633C>T	c.(631-633)atC>atT	p.I211I	DRD3_ENST00000295881.7_Silent_p.I211I|DRD3_ENST00000467632.1_Silent_p.I211I|DRD3_ENST00000383673.2_Silent_p.I211I	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3	211					acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)	p.I211I(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GCACCACATAGATTCTGGCAT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											193	184	187					3																	113858437		2203	4300	6503	115341127	SO:0001819	synonymous_variant	1814				CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"GPCR / Class A : Dopamine receptors"	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.633C>T	3.37:g.113858437G>A			115341127	A1A4V5|Q4VBM8	Silent	SNP	ENST00000460779.1	37	CCDS2978.1																																																																																				0.507	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3		A	113858437	G	A	113858437	2	1	61	1	0	0	0	0	0	0	0	1	4769	932	33	3		3	DRD3	3	113858437	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120761	113858437	84163993	2676	10661										
ZNF80	7634	broad.mit.edu	37	chr3	113955221	113955221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtgactccttgtatgtCgagtgagggaatagctgtag	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:113955221C>T	ENST00000482457.2	-	1	1204	c.701G>A	c.(700-702)cGa>cAa	p.R234Q	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R234Q(1)		NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CCTTGTATGTCGAGTGAGGGA	0.463																																					GBM(23;986 1114 21716)											1	Substitution - Missense(1)	large_intestine(1)	3											106	105	106					3																	113955221		2203	4300	6503	115437911	SO:0001583	missense	7634			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.701G>A	3.37:g.113955221C>T	ENSP00000417192:p.Arg234Gln		115437911	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.665248	0.00765	.	.	ENSG00000174255	ENST00000482457	T	0.26223	1.75	3.07	-3.01	0.05463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09024	0.0223	N	0.16708	0.43	0.09310	N	1	B	0.28880	0.226	B	0.25140	0.058	T	0.32107	-0.9919	9	0.05620	T	0.96	.	2.014	0.03494	0.1305:0.2732:0.1271:0.4693	.	234	P51504	ZNF80_HUMAN	Q	234	ENSP00000417192:R234Q	ENSP00000309812:R234Q	R	-	2	0	ZNF80	115437911	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-6.229000	0.00075	-1.222000	0.02587	-2.844000	0.00104	CGA		0.463	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		T	113955221	C	T	113955221	3	4	61	1	0	0	0	0	1	0	0	0	18207	884	31	1	124	1	ZNF80	3	113955221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96784	113955221	84067209	2677	10662										
ZBTB20	26137	broad.mit.edu	37	chr3	114070695	114070695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggttgatgctgtgaatgCgctcggtcatccccttgcaa	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:114070695C>T	ENST00000474710.1	-	4	408	c.230G>A	c.(229-231)cGc>cAc	p.R77H	ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000464560.1_Missense_Mutation_p.R4H|ZBTB20_ENST00000393785.2_Missense_Mutation_p.R4H|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20_ENST00000481632.1_Missense_Mutation_p.R4H|ZBTB20_ENST00000357258.3_Missense_Mutation_p.R4H|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000462705.1_Missense_Mutation_p.R4H|ZBTB20_ENST00000471418.1_Missense_Mutation_p.R4H	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	77						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R4H(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GCTGTGAATGCGCTCGGTCAT	0.537																																					NSCLC(69;748 1344 9802 11203 30933)											1	Substitution - Missense(1)	large_intestine(1)	3											75	76	76					3																	114070695		2202	4298	6500	115553385	SO:0001583	missense	26137			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.230G>A	3.37:g.114070695C>T	ENSP00000419153:p.Arg77His		115553385	Q63HP6|Q8N6R5|Q9Y410	Missense_Mutation	SNP	ENST00000474710.1	37	CCDS54626.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893482	0.91889	.	.	ENSG00000181722	ENST00000462705;ENST00000393785;ENST00000481632;ENST00000471418;ENST00000474710;ENST00000357258;ENST00000464560;ENST00000470311	T;T;T;T;T;T;T;T	0.46819	2.67;2.67;2.67;2.67;2.78;2.67;2.67;0.86	6.1	6.1	0.99115	BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.66426	0.2788	L	0.52011	1.625	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.65249	-0.6214	10	0.87932	D	0	.	20.7146	0.99709	0.0:1.0:0.0:0.0	.	77	Q9HC78	ZBT20_HUMAN	H	4;4;4;4;77;4;4;4	ENSP00000420324:R4H;ENSP00000377375:R4H;ENSP00000418092:R4H;ENSP00000419902:R4H;ENSP00000419153:R77H;ENSP00000349803:R4H;ENSP00000417307:R4H;ENSP00000420684:R4H	ENSP00000349803:R4H	R	-	2	0	ZBTB20	115553385	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.902000	0.99343	0.650000	0.86243	CGC		0.537	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		T	114070695	C	T	114070695	3	4	61	1	0	0	0	0	1	0	0	0	17568	768	27	1	2003	1	ZBTB20	3	114070695	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115474	114070695	83951735	2678	10663										
GAP43	2596	broad.mit.edu	37	chr3	115395334	115395334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggagcctaaacaagccGatgtgcctgctgctgtcact	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:115395334G>A	ENST00000305124.6	+	2	871	c.505G>A	c.(505-507)Gat>Aat	p.D169N	GAP43_ENST00000393780.3_Missense_Mutation_p.D205N	NM_002045.3	NP_002036.1	P17677	NEUM_HUMAN	growth associated protein 43	169					axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.D205Y(1)|p.D169Y(1)|p.D169N(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		TAAACAAGCCGATGTGCctgc	0.607																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	3											30	30	30					3																	115395334		2195	4290	6485	116878024	SO:0001583	missense	2596				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020			4140	protein-coding gene	gene with protein product	"neuron growth-associated protein 43", "neuromodulin", "nerve growth-related peptide GAP43", "axonal membrane protein GAP-43", "protein F1", "calmodulin-binding protein P-57", "neural phosphoprotein B-50"	162060				3272162, 8231732	Standard	NM_002045		Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000305124.6:c.505G>A	3.37:g.115395334G>A	ENSP00000305010:p.Asp169Asn		116878024	A8K0Y4	Missense_Mutation	SNP	ENST00000305124.6	37	CCDS33830.1	.	.	.	.	.	.	.	.	.	.	G	32	5.143388	0.94560	.	.	ENSG00000172020	ENST00000305124;ENST00000393780	T;T	0.52057	0.68;0.68	5.45	5.45	0.79879	Neuromodulin (GAP-43), C-terminal (1);	0.097702	0.64402	D	0.000002	T	0.69124	0.3076	M	0.66939	2.045	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.70132	-0.4956	10	0.72032	D	0.01	-16.7246	19.4735	0.94973	0.0:0.0:1.0:0.0	.	205;169	A8K0Y4;P17677	.;NEUM_HUMAN	N	169;205	ENSP00000305010:D169N;ENSP00000377372:D205N	ENSP00000305010:D169N	D	+	1	0	GAP43	116878024	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.176000	0.94839	2.836000	0.97738	0.655000	0.94253	GAT		0.607	GAP43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258216.2	NM_002045		A	115395334	G	A	115395334	3	1	61	1	0	0	0	0	1	0	0	0	6255	1058	37	1	653	1	GAP43	3	115395334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1324639	115395334	82627096	2679	10664										
ARHGAP31	57514	broad.mit.edu	37	chr3	119102036	119102036	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaatcatgtagatcaaatCtttaacaacggtgcacctgg	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119102036C>A	ENST00000264245.4	+	6	1177	c.645C>A	c.(643-645)atC>atA	p.I215I		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	215	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.I215I(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TAGATCAAATCTTTAACAACG	0.473																																					Pancreas(7;176 297 5394 51128 51241)											1	Substitution - coding silent(1)	large_intestine(1)	3											139	138	138					3																	119102036		2024	4182	6206	120584726	SO:0001819	synonymous_variant	57514				CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.645C>A	3.37:g.119102036C>A			120584726	Q9ULL6	Silent	SNP	ENST00000264245.4	37	CCDS43135.1																																																																																				0.473	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119102036	C	A	119102036	2	1	61	1	0	0	0	0	0	0	0	1	880	903	32	2		2	ARHGAP31	3	119102036	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3706702	119102036	78920394	2680	10665										
KTELC1	56983	broad.mit.edu	37	chr3	119205758	119205758	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcagaatacaccaaaaaCcaggcctggaaatctatgaa	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119205758C>T	ENST00000295588.4	+	7	801	c.717C>T	c.(715-717)aaC>aaT	p.N239N		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	239					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)	p.N239N(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						ACACCAAAAACCAGGCCTGGA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	3											134	136	135					3																	119205758		2203	4300	6503	120688448	SO:0001819	synonymous_variant	56983			BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"KDELC family like 1"	615618	"chromosome 3 open reading frame 9", "KTEL (Lys-Tyr-Glu-Leu) containing 1"	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.717C>T	3.37:g.119205758C>T			120688448	B2RD13|Q53GJ4|Q8N2T1	Silent	SNP	ENST00000295588.4	37	CCDS2988.1																																																																																				0.408	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305		T	119205758	C	T	119205758	2	4	61	1	0	0	0	0	0	0	0	1	8605	506	18	3		3	KTELC1	3	119205758	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103722	119205758	78816672	2681	10666										
CD80	941	broad.mit.edu	37	chr3	119263605	119263605	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatagtcagcaccattttCttctccttttgccagtagat	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119263605C>A	ENST00000264246.3	-	3	572	c.210G>T	c.(208-210)aaG>aaT	p.K70N	CD80_ENST00000383668.3_Missense_Mutation_p.K70N|CD80_ENST00000478182.1_Missense_Mutation_p.K70N|CD80_ENST00000383669.3_Missense_Mutation_p.K70N	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	70	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.K70N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	GCACCATTTTCTTCTCCTTTT	0.458																																					Melanoma(132;135 1764 1806 5833 14593)											1	Substitution - Missense(1)	large_intestine(1)	3											181	156	164					3																	119263605		2203	4300	6503	120746295	SO:0001583	missense	941				CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.210G>T	3.37:g.119263605C>A	ENSP00000264246:p.Lys70Asn		120746295	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	37	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	C	3.258	-0.151817	0.06585	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.13	-10.3	0.00346	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.319310	0.00824	N	0.001601	T	0.19208	0.0461	N	0.16656	0.425	0.09310	N	1	B;B;B;B	0.13145	0.006;0.004;0.007;0.007	B;B;B;B	0.14023	0.006;0.005;0.01;0.01	T	0.15065	-1.0450	10	0.19147	T	0.46	0.0323	2.4939	0.04617	0.1217:0.2711:0.3466:0.2605	.	70;70;70;70	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	N	70	ENSP00000264246:K70N;ENSP00000418364:K70N;ENSP00000373165:K70N;ENSP00000373164:K70N	ENSP00000264246:K70N	K	-	3	2	CD80	120746295	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.536000	0.00940	-3.115000	0.00240	-0.995000	0.02519	AAG		0.458	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		A	119263605	C	A	119263605	3	1	61	1	0	0	0	0	1	0	0	0	3044	912	32	2	672	2	CD80	3	119263605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57847	119263605	78758825	2682	10667										
POPDC2	64091	broad.mit.edu	37	chr3	119367498	119367498	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgtagctacatgaggtCtcagcagtcagagtgacctg	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119367498C>A	ENST00000264231.3	-	3	784	c.618G>T	c.(616-618)gaG>gaT	p.E206D	POPDC2_ENST00000538678.1_Missense_Mutation_p.E206D|POPDC2_ENST00000468801.1_Missense_Mutation_p.E206D|POPDC2_ENST00000493094.1_Missense_Mutation_p.E206D|POPDC2_ENST00000474523.1_5'UTR	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	206					regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)	p.E206D(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		TACATGAGGTCTCAGCAGTCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											37	40	39					3																	119367498		2202	4299	6501	120850188	SO:0001583	missense	64091			AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.618G>T	3.37:g.119367498C>A	ENSP00000264231:p.Glu206Asp		120850188	Q86UE7	Missense_Mutation	SNP	ENST00000264231.3	37	CCDS2992.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693811	0.48202	.	.	ENSG00000121577	ENST00000264231;ENST00000493094;ENST00000468801;ENST00000538678	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	4.94	4.94	0.65067	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.051780	0.85682	D	0.000000	T	0.34513	0.0900	N	0.21448	0.665	0.49389	D	0.999785	P;P	0.52692	0.88;0.955	P;P	0.58013	0.526;0.831	T	0.02365	-1.1170	10	0.27785	T	0.31	.	13.73	0.62781	0.0:0.9235:0.0:0.0765	.	206;206	Q9HBU9-2;Q9HBU9	.;POPD2_HUMAN	D	206	ENSP00000264231:E206D;ENSP00000417250:E206D;ENSP00000420715:E206D;ENSP00000438271:E206D	ENSP00000264231:E206D	E	-	3	2	POPDC2	120850188	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	2.487000	0.45268	2.557000	0.86248	0.462000	0.41574	GAG		0.473	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135		A	119367498	C	A	119367498	3	1	61	1	0	0	0	0	1	0	0	0	12286	912	32	2	484	2	POPDC2	3	119367498	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103893	119367498	78654932	2683	10668										
C3orf15	89876	broad.mit.edu	37	chr3	119456231	119456231	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcactgttggataagaagAataaagttcttgaagtaaag	11	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119456231A>C	ENST00000273390.5	+	11	1440	c.1363A>C	c.(1363-1365)Aat>Cat	p.N455H		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	0						mitochondrion (GO:0005739)		p.N455H(1)									GGATAAGAAGAATAAAGTTCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											62	65	64					3																	119456231		2203	4300	6503	120938921	SO:0001583	missense	89876			AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"AMY-1-associating protein expressed in testis 1", "MYCBP-binding protein", "spermatogenesis associated 26"	609910	"chromosome 3 open reading frame 15", "MYCBP/AMY-1-associated, testis expressed 1"	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.1363A>C	3.37:g.119456231A>C	ENSP00000273390:p.Asn455His		120938921	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	A	5.618	0.298761	0.10622	.	.	ENSG00000183833	ENST00000273390	T	0.23348	1.91	4.74	3.53	0.40419	.	0.680535	0.15571	N	0.255433	T	0.24547	0.0595	N	0.22421	0.69	0.80722	D	1	B;B;D;P	0.59767	0.043;0.043;0.986;0.899	B;B;P;P	0.51135	0.011;0.011;0.66;0.568	T	0.01319	-1.1386	10	0.37606	T	0.19	-3.2453	10.8379	0.46698	0.8584:0.0:0.0:0.1416	.	216;393;455;455	Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	.;.;.;.	H	455	ENSP00000273390:N455H	ENSP00000273390:N455H	N	+	1	0	C3orf15	120938921	1.000000	0.71417	0.921000	0.36526	0.068000	0.16541	3.259000	0.51515	0.887000	0.36136	0.402000	0.26972	AAT		0.348	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		C	119456231	A	C	119456231	3	2	61	1	0	0	0	0	1	0	0	0	2215	246	9	4	1405	4	C3orf15	3	119456231	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	88733	119456231	78566199	2684	10669										
GPR156	165829	broad.mit.edu	37	chr3	119886770	119886770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctctggggatctgagccGcctctttctggtaggagact	13	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119886770G>A	ENST00000464295.1	-	10	1999	c.1554C>T	c.(1552-1554)ggC>ggT	p.G518G	GPR156_ENST00000315843.3_Silent_p.G518G|GPR156_ENST00000461057.1_Silent_p.G514G			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	518						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)	p.G518G(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		GATCTGAGCCGCCTCTTTCTG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	3											113	126	121					3																	119886770		2203	4300	6503	121369460	SO:0001819	synonymous_variant	165829			AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.1554C>T	3.37:g.119886770G>A			121369460	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	37	CCDS2997.1																																																																																				0.572	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119886770	G	A	119886770	2	1	61	1	0	0	0	0	0	0	0	1	6681	1074	38	1		1	GPR156	3	119886770	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	430539	119886770	78135660	2685	10670										
GPR156	165829	broad.mit.edu	37	chr3	119892302	119892302	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggttttcctcttcaaatgCcttccattgcttcagctgtt	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:119892302C>A	ENST00000464295.1	-	9	1394	c.949G>T	c.(949-951)Gca>Tca	p.A317S	GPR156_ENST00000315843.3_Missense_Mutation_p.A317S|GPR156_ENST00000461057.1_Missense_Mutation_p.A313S			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	317						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)	p.A317S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		TCTTCAAATGCCTTCCATTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											203	183	189					3																	119892302		2203	4300	6503	121374992	SO:0001583	missense	165829			AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.949G>T	3.37:g.119892302C>A	ENSP00000417261:p.Ala317Ser		121374992	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	37	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866726	0.32977	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.23348	1.91;1.91;1.91	5.48	3.58	0.41010	.	0.317821	0.27792	N	0.017826	T	0.23806	0.0576	M	0.67953	2.075	0.27786	N	0.942993	P;P	0.35077	0.483;0.483	B;B	0.30943	0.122;0.122	T	0.13019	-1.0525	9	.	.	.	-5.8605	8.9517	0.35792	0.0:0.6408:0.2041:0.1551	.	313;317	E9PFZ4;Q8NFN8	.;GP156_HUMAN	S	317;317;313	ENSP00000417261:A317S;ENSP00000324553:A317S;ENSP00000418758:A313S	.	A	-	1	0	GPR156	121374992	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.641000	0.24720	1.324000	0.45282	0.462000	0.41574	GCA		0.398	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119892302	C	A	119892302	3	1	61	1	0	0	0	0	1	0	0	0	6681	739	26	2	1503	2	GPR156	3	119892302	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5532	119892302	78130128	2686	10671										
STXBP5L	9515	broad.mit.edu	37	chr3	120924773	120924773	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattttttttctttaggaaAaagtcaaagagaaggaagaa	8	2	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:120924773A>C	ENST00000273666.6	+	10	1152	c.881A>C	c.(880-882)aAa>aCa	p.K294T	STXBP5L_ENST00000497029.1_Missense_Mutation_p.K294T|STXBP5L_ENST00000471454.1_Missense_Mutation_p.K294T|STXBP5L_ENST00000472879.1_Missense_Mutation_p.K294T|STXBP5L_ENST00000492541.1_Missense_Mutation_p.K294T	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	294					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K294T(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		tCTTTAGGAAAAAGTCAAAGA	0.244																																																1	Substitution - Missense(1)	large_intestine(1)	3											35	34	34					3																	120924773		1778	4033	5811	122407463	SO:0001583	missense	9515			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.881A>C	3.37:g.120924773A>C	ENSP00000273666:p.Lys294Thr		122407463	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.921823	0.73213	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.38887	1.8;1.8;1.61;1.11;1.6;1.81	5.02	5.02	0.67125	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.048181	0.85682	D	0.000000	T	0.58878	0.2153	L	0.55743	1.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.58194	-0.7679	10	0.41790	T	0.15	-31.9659	14.3821	0.66919	1.0:0.0:0.0:0.0	.	294;294	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	T	294	ENSP00000273666:K294T;ENSP00000420019:K294T;ENSP00000419627:K294T;ENSP00000420287:K294T;ENSP00000420666:K294T;ENSP00000420167:K294T	ENSP00000273666:K294T	K	+	2	0	STXBP5L	122407463	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	6.999000	0.76283	1.871000	0.54225	0.240000	0.17902	AAA		0.244	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			C	120924773	A	C	120924773	3	2	61	1	0	0	0	0	1	0	0	0	15396	14	1	4	915	4	STXBP5L	3	120924773	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1032471	120924773	77097657	2687	10672										
STXBP5L	9515	broad.mit.edu	37	chr3	120973920	120973920	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctgcatatgtcataatTtataaattcagcagacatga	6	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:120973920T>G	ENST00000273666.6	+	16	1891	c.1620T>G	c.(1618-1620)atT>atG	p.I540M	STXBP5L_ENST00000497029.1_Missense_Mutation_p.I540M|STXBP5L_ENST00000471454.1_Missense_Mutation_p.I540M|STXBP5L_ENST00000472879.1_Missense_Mutation_p.I540M|STXBP5L_ENST00000492541.1_Missense_Mutation_p.I540M	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	540					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I540M(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		ATGTCATAATTTATAAATTCA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											43	42	42					3																	120973920		1802	4078	5880	122456610	SO:0001583	missense	9515			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1620T>G	3.37:g.120973920T>G	ENSP00000273666:p.Ile540Met		122456610	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077356	0.36662	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.68479	1.27;-0.33;-0.33;0.35;-0.33;-0.33	5.36	4.21	0.49690	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.205235	0.44483	D	0.000453	T	0.53077	0.1774	L	0.42245	1.32	0.42957	D	0.994393	P;P	0.40398	0.716;0.716	B;B	0.36186	0.146;0.219	T	0.56092	-0.8036	10	0.42905	T	0.14	-6.6623	8.0127	0.30363	0.0:0.1533:0.0:0.8467	.	540;540	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	M	540	ENSP00000273666:I540M;ENSP00000420019:I540M;ENSP00000419627:I540M;ENSP00000420287:I540M;ENSP00000420666:I540M;ENSP00000420167:I540M	ENSP00000273666:I540M	I	+	3	3	STXBP5L	122456610	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	1.001000	0.29783	2.027000	0.59764	0.482000	0.46254	ATT		0.313	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120973920	T	G	120973920	3	3	61	1	0	0	0	0	1	0	0	0	15396	1829	64	4	1678	4	STXBP5L	3	120973920	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	49147	120973920	77048510	2688	10673										
STXBP5L	9515	broad.mit.edu	37	chr3	121097652	121097652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgatgtttcaaaagtaaatCgctggggtcctggaagacca	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121097652C>T	ENST00000273666.6	+	22	2609	c.2338C>T	c.(2338-2340)Cgc>Tgc	p.R780C	STXBP5L_ENST00000497029.1_Intron|STXBP5L_ENST00000471454.1_Missense_Mutation_p.R756C|STXBP5L_ENST00000472879.1_Missense_Mutation_p.R756C|STXBP5L_ENST00000492541.1_Missense_Mutation_p.R780C	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	780					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R780C(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		AAAAGTAAATCGCTGGGGTCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											58	54	55					3																	121097652		1852	4103	5955	122580342	SO:0001583	missense	9515			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2338C>T	3.37:g.121097652C>T	ENSP00000273666:p.Arg780Cys		122580342	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890568	0.91889	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000492541	T;T;T;T	0.62788	1.59;-0.0;-0.0;-0.0	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.69142	0.3078	M	0.63843	1.955	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.50754	0.649;0.642	T	0.71626	-0.4536	10	0.48119	T	0.1	-6.6126	17.7945	0.88565	0.0:1.0:0.0:0.0	.	756;780	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	C	780;756;756;780	ENSP00000273666:R780C;ENSP00000420019:R756C;ENSP00000419627:R756C;ENSP00000420666:R780C	ENSP00000273666:R780C	R	+	1	0	STXBP5L	122580342	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.408000	0.66368	2.514000	0.84764	0.585000	0.79938	CGC		0.438	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			T	121097652	C	T	121097652	3	4	61	1	0	0	0	0	1	0	0	0	15396	884	31	1	2420	1	STXBP5L	3	121097652	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123732	121097652	76924778	2689	10674										
POLQ	10721	broad.mit.edu	37	chr3	121202286	121202286	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacaagaaagaagaagaaTtttatagctctggatgaagt	10	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121202286T>G	ENST00000264233.5	-	18	6045	c.5917A>C	c.(5917-5919)Att>Ctt	p.I1973L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1973					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.I2108L(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AGAAGAAGAATTTTATAGCTC	0.333								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - Missense(1)	large_intestine(1)	3											75	77	76					3																	121202286		2203	4300	6503	122684976	SO:0001583	missense	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.5917A>C	3.37:g.121202286T>G	ENSP00000264233:p.Ile1973Leu		122684976	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.003658	0.35320	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.21932	1.98	5.44	3.0	0.34707	Ribonuclease H-like (1);	0.498441	0.21298	N	0.076849	T	0.14227	0.0344	L	0.47716	1.5	0.21256	N	0.999744	B;P	0.35527	0.144;0.507	B;B	0.30029	0.014;0.11	T	0.17379	-1.0371	10	0.30854	T	0.27	.	5.1147	0.14829	0.0:0.1569:0.1542:0.6889	.	1973;1145	O75417;O75417-2	DPOLQ_HUMAN;.	L	1596;1973;2109	ENSP00000264233:I1973L	ENSP00000264233:I1973L	I	-	1	0	POLQ	122684976	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.504000	0.35726	0.348000	0.23949	0.374000	0.22700	ATT		0.333	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121202286	T	G	121202286	3	3	61	1	0	0	0	0	1	0	0	0	12239	1493	52	4	1907	4	POLQ	3	121202286	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	104634	121202286	76820144	2690	10675										
POLQ	10721	broad.mit.edu	37	chr3	121207776	121207776	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcattttcagttgccatCtgttgtattattttctctga	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121207776C>T	ENST00000264233.5	-	16	4130	c.4002G>A	c.(4000-4002)caG>caA	p.Q1334Q		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1334					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.Q1469Q(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAGTTGCCATCTGTTGTATTA	0.378								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - coding silent(1)	large_intestine(1)	3											198	174	182					3																	121207776		2203	4300	6503	122690466	SO:0001819	synonymous_variant	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4002G>A	3.37:g.121207776C>T			122690466	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																				0.378	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121207776	C	T	121207776	2	4	61	1	0	0	0	0	0	0	0	1	12239	912	32	3		3	POLQ	3	121207776	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5490	121207776	76814654	2691	10676										
POLQ	10721	broad.mit.edu	37	chr3	121208683	121208683	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttctgctcatcttttctGaattgaaattcaaaggtgcc	6	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121208683G>A	ENST00000264233.5	-	16	3223	c.3095C>T	c.(3094-3096)tCa>tTa	p.S1032L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1032					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.S1167L(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CATCTTTTCTGAATTGAAATT	0.423								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - Missense(1)	large_intestine(1)	3											67	75	72					3																	121208683		2202	4300	6502	122691373	SO:0001583	missense	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3095C>T	3.37:g.121208683G>A	ENSP00000264233:p.Ser1032Leu		122691373	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	8.749	0.920923	0.17982	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.50813	0.73	5.11	3.32	0.38043	.	0.946527	0.08872	N	0.881475	T	0.37461	0.1004	L	0.34521	1.04	0.26963	N	0.965773	B;B	0.27997	0.003;0.197	B;B	0.25614	0.006;0.062	T	0.30794	-0.9966	10	0.54805	T	0.06	.	8.7697	0.34724	0.1763:0.0:0.8237:0.0	.	1032;204	O75417;O75417-2	DPOLQ_HUMAN;.	L	655;1032;1168	ENSP00000264233:S1032L	ENSP00000264233:S1032L	S	-	2	0	POLQ	122691373	0.971000	0.33674	0.797000	0.32132	0.105000	0.19272	2.976000	0.49289	0.739000	0.32628	0.563000	0.77884	TCA		0.423	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121208683	G	A	121208683	3	1	61	1	0	0	0	0	1	0	0	0	12239	1294	45	3	4737	3	POLQ	3	121208683	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	907	121208683	76813747	2692	10677										
POLQ	10721	broad.mit.edu	37	chr3	121240949	121240949	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccatcacttccaggagttCtttttgttccagaattactg	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121240949C>A	ENST00000264233.5	-	8	1284	c.1156G>T	c.(1156-1158)Gaa>Taa	p.E386*	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	386	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.E521*(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCCAGGAGTTCTTTTTGTTCC	0.413								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											1	Substitution - Nonsense(1)	large_intestine(1)	3											138	137	137					3																	121240949		2203	4300	6503	122723639	SO:0001587	stop_gained	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1156G>T	3.37:g.121240949C>A	ENSP00000264233:p.Glu386*		122723639	O95160|Q6VMB5	Nonsense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	34	5.392847	0.96009	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	.	.	.	4.81	1.18	0.20946	.	0.444833	0.27513	N	0.019021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	8.4867	0.33076	0.0:0.6867:0.0:0.3133	.	.	.	.	X	9;386;523	.	ENSP00000264233:E386X	E	-	1	0	POLQ	122723639	0.918000	0.31147	0.900000	0.35374	0.901000	0.52897	2.539000	0.45718	-0.009000	0.14296	0.591000	0.81541	GAA		0.413	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121240949	C	A	121240949	4	1	61	1	0	0	0	0	0	1	0	0	12239	922	32	2	6708	2	POLQ	3	121240949	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32266	121240949	76781481	2693	10678										
ARGFX	503582	broad.mit.edu	37	chr3	121305442	121305442	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatggtagacttgggatttCtctgaccagagtactaataa	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121305442C>A	ENST00000334384.3	+	4	953	c.943C>A	c.(943-945)Ctc>Atc	p.L315I		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.L315I(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		CTTGGGATTTCTCTGACCAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											35	39	38					3																	121305442		2170	4292	6462	122788132	SO:0001583	missense	503582				CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"Homeoboxes / PRD class"	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.943C>A	3.37:g.121305442C>A	ENSP00000335578:p.Leu315Ile		122788132		Missense_Mutation	SNP	ENST00000334384.3	37	CCDS33834.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.752430	0.31046	.	.	ENSG00000186103	ENST00000334384	D	0.90069	-2.61	2.09	0.192	0.15134	.	1.139500	0.07022	N	0.826931	T	0.78149	0.4238	N	0.14661	0.345	0.09310	N	1	P	0.37233	0.588	B	0.36418	0.224	T	0.68922	-0.5281	10	0.87932	D	0	.	4.6639	0.12655	0.0:0.6622:0.0:0.3378	.	315	A6NJG6	ARGFX_HUMAN	I	315	ENSP00000335578:L315I	ENSP00000335578:L315I	L	+	1	0	ARGFX	122788132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.596000	0.05720	0.048000	0.15891	-0.278000	0.10074	CTC		0.388	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659		A	121305442	C	A	121305442	3	1	61	1	0	0	0	0	1	0	0	0	859	913	32	2	957	2	ARGFX	3	121305442	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64493	121305442	76716988	2694	10679										
FBXO40	51725	broad.mit.edu	37	chr3	121341005	121341005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgtgagagcaagaacaaGaatgactccgagaaagaaca	11	7	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121341005G>T	ENST00000338040.4	+	3	1143	c.729G>T	c.(727-729)aaG>aaT	p.K243N		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	243					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K243N(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		GCAAGAACAAGAATGACTCCG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											66	71	69					3																	121341005		2203	4300	6503	122823695	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.729G>T	3.37:g.121341005G>T	ENSP00000337510:p.Lys243Asn		122823695	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	G	0.058	-1.231153	0.01518	.	.	ENSG00000163833	ENST00000338040	T	0.44482	0.92	5.64	-0.282	0.12878	.	1.710450	0.02222	N	0.064086	T	0.20210	0.0486	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10660	-1.0620	10	0.22706	T	0.39	0.4045	3.6833	0.08319	0.0805:0.2375:0.4151:0.2669	.	243	Q9UH90	FBX40_HUMAN	N	243	ENSP00000337510:K243N	ENSP00000337510:K243N	K	+	3	2	FBXO40	122823695	0.000000	0.05858	0.000000	0.03702	0.163000	0.22366	-0.408000	0.07169	0.024000	0.15214	0.591000	0.81541	AAG		0.468	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121341005	G	T	121341005	3	4	61	1	0	0	0	0	1	0	0	0	5768	933	33	2	735	2	FBXO40	3	121341005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35563	121341005	76681425	2695	10680										
HCLS1	3059	broad.mit.edu	37	chr3	121350797	121350797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaatgtcagtgattacgtCgtccggatcaaaggaaagct	10	9	3	1	rs142545513		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121350797C>T	ENST00000314583.3	-	14	1448	c.1357G>A	c.(1357-1359)Gac>Aac	p.D453N	HCLS1_ENST00000428394.2_Missense_Mutation_p.D416N|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	453	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)	p.D453N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		GTGATTACGTCGTCCGGATCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	162	158	159		1357	5.5	1	3	dbSNP_134	159	0,8600		0,0,4300	no	missense	HCLS1	NM_005335.4	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	453/487	121350797	1,13005	2203	4300	6503	122833487	SO:0001583	missense	3059				CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"cortactin-like"	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1357G>A	3.37:g.121350797C>T	ENSP00000320176:p.Asp453Asn		122833487	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	37	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486176	0.84854	2.27E-4	0.0	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.64618	-0.11;-0.11	5.53	5.53	0.82687	Src homology-3 domain (5);	0.043614	0.85682	D	0.000000	T	0.81019	0.4736	M	0.83384	2.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	D	0.83597	0.0126	10	0.87932	D	0	-23.7167	16.9587	0.86266	0.0:1.0:0.0:0.0	.	416;453	E7EVW7;P14317	.;HCLS1_HUMAN	N	453;416	ENSP00000320176:D453N;ENSP00000387645:D416N	ENSP00000320176:D453N	D	-	1	0	HCLS1	122833487	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	7.453000	0.80700	2.607000	0.88179	0.563000	0.77884	GAC		0.502	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335		T	121350797	C	T	121350797	3	4	61	1	0	0	0	0	1	0	0	0	7016	884	31	1	107	1	HCLS1	3	121350797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9792	121350797	76671633	2696	10681										
GOLGB1	2804	broad.mit.edu	37	chr3	121412607	121412607	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggaaatgttaatctttaAttcttccatatggatggaca	7	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121412607A>G	ENST00000340645.5	-	13	6873	c.6748T>C	c.(6748-6750)Tta>Cta	p.L2250L	GOLGB1_ENST00000393667.3_Silent_p.L2255L	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2250					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.L2250L(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TTAATCTTTAATTCTTCCATA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	3											164	155	158					3																	121412607		2203	4300	6503	122895297	SO:0001819	synonymous_variant	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6748T>C	3.37:g.121412607A>G			122895297	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																				0.338	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		G	121412607	A	G	121412607	2	3	61	1	0	0	0	0	0	0	0	1	6585	98	4	4		4	GOLGB1	3	121412607	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	61810	121412607	76609823	2697	10682										
GOLGB1	2804	broad.mit.edu	37	chr3	121412682	121412682	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttctttgagtctaatttCttcttctttgctttgaatcg	5	8	6	2	rs186004105		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121412682C>A	ENST00000340645.5	-	13	6798	c.6673G>T	c.(6673-6675)Gaa>Taa	p.E2225*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.E2230*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2225					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.E2225*(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGTCTAATTTCTTCTTCTTTG	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											229	207	214					3																	121412682		2203	4300	6503	122895372	SO:0001587	stop_gained	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6673G>T	3.37:g.121412682C>A	ENSP00000341848:p.Glu2225*		122895372	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	47	13.519348	0.99747	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	.	.	.	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	17.4537	0.87600	0.0:1.0:0.0:0.0	.	.	.	.	X	2225;2230	.	ENSP00000341848:E2225X	E	-	1	0	GOLGB1	122895372	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.896000	0.69822	2.716000	0.92895	0.655000	0.94253	GAA		0.373	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121412682	C	A	121412682	4	1	61	1	0	0	0	0	0	1	0	0	6585	922	32	2	3146	2	GOLGB1	3	121412682	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75	121412682	76609748	2698	10683										
GOLGB1	2804	broad.mit.edu	37	chr3	121412904	121412904	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttccaagtggactttttCtctgcgcaaagcatccagtt	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121412904C>A	ENST00000340645.5	-	13	6576	c.6451G>T	c.(6451-6453)Gaa>Taa	p.E2151*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.E2156*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2151					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.E2151*(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGGACTTTTTCTCTGCGCAAA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											175	174	174					3																	121412904		2203	4300	6503	122895594	SO:0001587	stop_gained	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6451G>T	3.37:g.121412904C>A	ENSP00000341848:p.Glu2151*		122895594	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	46	12.699771	0.99689	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	.	.	.	5.75	5.75	0.90469	.	0.096990	0.44688	D	0.000422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	17.4537	0.87600	0.0:1.0:0.0:0.0	.	.	.	.	X	2151;2156	.	ENSP00000341848:E2151X	E	-	1	0	GOLGB1	122895594	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	7.731000	0.84895	2.716000	0.92895	0.655000	0.94253	GAA		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121412904	C	A	121412904	4	1	61	1	0	0	0	0	0	1	0	0	6585	922	32	2	3368	2	GOLGB1	3	121412904	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222	121412904	76609526	2699	10684										
GOLGB1	2804	broad.mit.edu	37	chr3	121413018	121413018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttgtttcatctggctttTaactgattctttatttgact	5	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121413018T>C	ENST00000340645.5	-	13	6462	c.6337A>G	c.(6337-6339)Aaa>Gaa	p.K2113E	GOLGB1_ENST00000393667.3_Missense_Mutation_p.K2118E	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2113					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K2113E(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		ATCTGGCTTTTAACTGATTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	3											180	184	183					3																	121413018		2203	4300	6503	122895708	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6337A>G	3.37:g.121413018T>C	ENSP00000341848:p.Lys2113Glu		122895708	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.758027	0.31137	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.16457	2.34;2.34	5.93	4.78	0.61160	.	0.187625	0.38005	N	0.001859	T	0.21387	0.0515	L	0.48642	1.525	0.32047	N	0.597421	D;P;P;P	0.54964	0.969;0.734;0.734;0.952	P;B;B;P	0.62491	0.903;0.391;0.391;0.767	T	0.22730	-1.0208	10	0.02654	T	1	.	4.865	0.13604	0.1644:0.0844:0.0:0.7512	.	2038;2118;2118;2113	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	E	2113;2118	ENSP00000341848:K2113E;ENSP00000377275:K2118E	ENSP00000341848:K2113E	K	-	1	0	GOLGB1	122895708	0.121000	0.22262	0.940000	0.37924	0.994000	0.84299	0.630000	0.24553	2.273000	0.75805	0.482000	0.46254	AAA		0.408	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121413018	T	C	121413018	3	2	61	1	0	0	0	0	1	0	0	0	6585	1763	61	4	3482	4	GOLGB1	3	121413018	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	114	121413018	76609412	2700	10685										
GOLGB1	2804	broad.mit.edu	37	chr3	121414880	121414880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttttagtgcttcttttCgggaaataagggcagcttgc	10	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121414880C>T	ENST00000340645.5	-	13	4600	c.4475G>A	c.(4474-4476)cGa>cAa	p.R1492Q	GOLGB1_ENST00000393667.3_Missense_Mutation_p.R1497Q	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1492					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.R1492Q(1)|p.R1492L(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGCTTCTTTTCGGGAAATAAG	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3											180	190	186					3																	121414880		2203	4299	6502	122897570	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.4475G>A	3.37:g.121414880C>T	ENSP00000341848:p.Arg1492Gln		122897570	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.693890	0.68386	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.61392	1.27;1.25;0.11	6.02	6.02	0.97574	.	0.000000	0.53938	D	0.000047	T	0.74535	0.3729	M	0.75264	2.295	0.58432	D	0.99999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;0.999;1.0	T	0.67593	-0.5631	10	0.13108	T	0.6	.	18.0346	0.89296	0.0:1.0:0.0:0.0	.	1417;1456;1497;1497;1492	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	Q	1492;1497;1456	ENSP00000341848:R1492Q;ENSP00000377275:R1497Q;ENSP00000418231:R1456Q	ENSP00000341848:R1492Q	R	-	2	0	GOLGB1	122897570	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.865000	0.98341	0.655000	0.94253	CGA		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		T	121414880	C	T	121414880	3	4	61	1	0	0	0	0	1	0	0	0	6585	884	31	1	5344	1	GOLGB1	3	121414880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1862	121414880	76607550	2701	10686										
GOLGB1	2804	broad.mit.edu	37	chr3	121415622	121415622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcttgggagttttccgtCtatggattcccttacttgaa	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121415622C>A	ENST00000340645.5	-	13	3858	c.3733G>T	c.(3733-3735)Gac>Tac	p.D1245Y	GOLGB1_ENST00000393667.3_Missense_Mutation_p.D1250Y	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1245					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.D1245Y(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGTTTTCCGTCTATGGATTCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											206	186	193					3																	121415622		2203	4300	6503	122898312	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3733G>T	3.37:g.121415622C>A	ENSP00000341848:p.Asp1245Tyr		122898312	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.689097	0.00738	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.26373	2.35;2.35;1.74	5.77	3.93	0.45458	.	0.508110	0.18210	N	0.148224	T	0.24699	0.0599	L	0.56769	1.78	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.002;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.006;0.006;0.004;0.004;0.003	T	0.19516	-1.0303	10	0.62326	D	0.03	.	7.5764	0.27939	0.1624:0.7525:0.0:0.0851	.	1170;1209;1250;1250;1245	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	Y	1245;1250;1209	ENSP00000341848:D1245Y;ENSP00000377275:D1250Y;ENSP00000418231:D1209Y	ENSP00000341848:D1245Y	D	-	1	0	GOLGB1	122898312	0.004000	0.15560	0.005000	0.12908	0.014000	0.08584	0.485000	0.22324	1.399000	0.46721	0.655000	0.94253	GAC		0.438	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121415622	C	A	121415622	3	1	61	1	0	0	0	0	1	0	0	0	6585	913	32	2	6086	2	GOLGB1	3	121415622	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	742	121415622	76606808	2702	10687										
GOLGB1	2804	broad.mit.edu	37	chr3	121435903	121435903	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcttttccagtagaatCttggactcctctctttctgt	5	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121435903C>A	ENST00000340645.5	-	9	1079	c.954G>T	c.(952-954)aaG>aaT	p.K318N	GOLGB1_ENST00000393667.3_Missense_Mutation_p.K323N	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	318					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K318N(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CCAGTAGAATCTTGGACTCCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											98	97	98					3																	121435903		2203	4300	6503	122918593	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.954G>T	3.37:g.121435903C>A	ENSP00000341848:p.Lys318Asn		122918593	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.15|11.15	1.553926|1.553926	0.27739|0.27739	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235|ENST00000489400	T;T;T|.	0.23950|.	2.45;2.45;1.88|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.365989|.	0.26824|.	N|.	0.022310|.	T|T	0.63010|0.63010	0.2475|0.2475	L|L	0.60455|0.60455	1.87|1.87	0.33169|0.33169	D|D	0.547953|0.547953	P;D;P;P;P|.	0.53312|.	0.879;0.959;0.879;0.928;0.879|.	B;P;B;P;B|.	0.50659|.	0.311;0.647;0.426;0.647;0.311|.	T|T	0.68834|0.68834	-0.5304|-0.5304	10|5	0.33940|.	T|.	0.23|.	.|.	16.144|16.144	0.81551|0.81551	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	243;282;323;323;318|.	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789|.	.;.;.;.;GOGB1_HUMAN|.	N|I	318;323;282;130|189	ENSP00000341848:K318N;ENSP00000377275:K323N;ENSP00000418231:K282N|.	ENSP00000341848:K318N|.	K|R	-|-	3|2	2|0	GOLGB1|GOLGB1	122918593|122918593	0.008000|0.008000	0.16893|0.16893	0.796000|0.796000	0.32109|0.32109	0.016000|0.016000	0.09150|0.09150	0.875000|0.875000	0.28079|0.28079	2.890000|2.890000	0.99128|0.99128	0.650000|0.650000	0.86243|0.86243	AAG|AGA		0.388	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121435903	C	A	121435903	3	1	61	1	0	0	0	0	1	0	0	0	6585	912	32	2	8881	2	GOLGB1	3	121435903	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20281	121435903	76586527	2703	10688										
IQCB1	9657	broad.mit.edu	37	chr3	121500623	121500623	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatagtcatccactcgtttCttcagttcaactcggcgtgc	7	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121500623C>A	ENST00000310864.6	-	13	1591	c.1377G>T	c.(1375-1377)aaG>aaT	p.K459N	IQCB1_ENST00000349820.6_Missense_Mutation_p.K326N	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	459					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)	p.K459N(1)		NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		CCACTCGTTTCTTCAGTTCAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											151	140	143					3																	121500623		2203	4300	6503	122983313	SO:0001583	missense	9657			D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1377G>T	3.37:g.121500623C>A	ENSP00000311505:p.Lys459Asn		122983313	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.224687	0.39300	.	.	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.79247	-1.25;-1.25	4.61	2.82	0.32997	.	0.158705	0.56097	D	0.000032	T	0.70124	0.3188	L	0.51422	1.61	0.33236	D	0.556563	B;B	0.34329	0.155;0.449	B;B	0.37091	0.051;0.241	T	0.73802	-0.3868	10	0.52906	T	0.07	-7.0424	7.1039	0.25353	0.0:0.7963:0.0:0.2037	.	459;326	Q15051;Q15051-2	IQCB1_HUMAN;.	N	459;326	ENSP00000311505:K459N;ENSP00000323756:K326N	ENSP00000311505:K459N	K	-	3	2	IQCB1	122983313	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	3.349000	0.52217	0.676000	0.31285	0.591000	0.81541	AAG		0.413	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		A	121500623	C	A	121500623	3	1	61	1	0	0	0	0	1	0	0	0	7824	912	32	2	431	2	IQCB1	3	121500623	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64720	121500623	76521807	2704	10689										
IQCB1	9657	broad.mit.edu	37	chr3	121500704	121500704	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttttcttacggcacttCgctaggaatttaagcgcctg	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121500704C>T	ENST00000310864.6	-	13	1510	c.1296G>A	c.(1294-1296)gcG>gcA	p.A432A	IQCB1_ENST00000349820.6_Silent_p.A299A	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	432	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)	p.A432A(1)		NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TACGGCACTTCGCTAGGAATT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	3											100	98	99					3																	121500704		2203	4300	6503	122983394	SO:0001819	synonymous_variant	9657			D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1296G>A	3.37:g.121500704C>T			122983394	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Silent	SNP	ENST00000310864.6	37	CCDS33837.1																																																																																				0.403	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		T	121500704	C	T	121500704	2	4	61	1	0	0	0	0	0	0	0	1	7824	871	31	1		1	IQCB1	3	121500704	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81	121500704	76521726	2705	10690										
SLC15A2	6565	broad.mit.edu	37	chr3	121613416	121613416	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaccacctagccctccaaaGaagccatctccggtgagtcc	8	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121613416G>T	ENST00000489711.1	+	1	481	c.93G>T	c.(91-93)aaG>aaT	p.K31N	SLC15A2_ENST00000295605.2_Missense_Mutation_p.K31N	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	31					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)	p.K31N(1)		NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GCCCTCCAAAGAAGCCATCTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											221	231	228					3																	121613416		2203	4300	6503	123096106	SO:0001583	missense	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.93G>T	3.37:g.121613416G>T	ENSP00000417085:p.Lys31Asn		123096106	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.136345	0.37728	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.59224	0.28;0.28	5.1	4.23	0.50019	Major facilitator superfamily domain, general substrate transporter (1);	0.402164	0.25596	N	0.029594	T	0.45236	0.1332	L	0.39147	1.195	0.32212	N	0.576427	B;B	0.32245	0.361;0.361	B;B	0.29440	0.102;0.102	T	0.57648	-0.7775	10	0.54805	T	0.06	-2.5899	8.955	0.35812	0.0985:0.0:0.9015:0.0	.	31;31	B4E2A7;Q16348	.;S15A2_HUMAN	N	31;24;31	ENSP00000417085:K31N;ENSP00000295605:K31N	ENSP00000295605:K31N	K	+	3	2	SLC15A2	123096106	1.000000	0.71417	0.992000	0.48379	0.731000	0.41821	2.283000	0.43470	1.378000	0.46305	0.557000	0.71058	AAG		0.512	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		T	121613416	G	T	121613416	3	4	61	1	0	0	0	0	1	0	0	0	14436	933	33	2	95	2	SLC15A2	3	121613416	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112712	121613416	76409014	2706	10691										
SLC15A2	6565	broad.mit.edu	37	chr3	121631956	121631956	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttggtggagaccagtttGaagaaaaacatgtaagaatc	10	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121631956G>T	ENST00000489711.1	+	5	905	c.517G>T	c.(517-519)Gaa>Taa	p.E173*	SLC15A2_ENST00000295605.2_Nonsense_Mutation_p.E142*	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	173					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)	p.E173*(1)		NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	AGACCAGTTTGAAGAAAAACA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											207	207	207					3																	121631956		2203	4300	6503	123114646	SO:0001587	stop_gained	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.517G>T	3.37:g.121631956G>T	ENSP00000417085:p.Glu173*		123114646	A8K1A5|B4E2A7	Nonsense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919668	0.92249	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605;ENST00000469013	.	.	.	6.05	5.13	0.70059	.	0.143150	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-20.8985	14.5457	0.68030	0.0:0.1472:0.8528:0.0	.	.	.	.	X	173;135;142;111	.	ENSP00000295605:E142X	E	+	1	0	SLC15A2	123114646	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.877000	0.69675	2.878000	0.98634	0.650000	0.86243	GAA		0.428	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		T	121631956	G	T	121631956	4	4	61	1	0	0	0	0	0	1	0	0	14436	1291	45	2	535	2	SLC15A2	3	121631956	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18540	121631956	76390474	2707	10692										
ILDR1	286676	broad.mit.edu	37	chr3	121707245	121707245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactccttccactatgagagCtgtctttctcctgggaaata	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121707245C>T	ENST00000344209.5	-	8	1736	c.1610G>A	c.(1609-1611)aGc>aAc	p.S537N	ILDR1_ENST00000273691.3_Missense_Mutation_p.S493N|ILDR1_ENST00000462014.1_Missense_Mutation_p.S505N|ILDR1_ENST00000393631.1_Missense_Mutation_p.S448N	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	537					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)	p.S493N(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		ACTATGAGAGCTGTCTTTCTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											172	137	149					3																	121707245		2203	4300	6503	123189935	SO:0001583	missense	286676			BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1610G>A	3.37:g.121707245C>T	ENSP00000345667:p.Ser537Asn		123189935	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210047	0.79240	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;D;T	0.83419	-1.12;-1.01;-1.72;-0.8	5.28	4.41	0.53225	.	0.072737	0.85682	D	0.000000	D	0.84110	0.5400	M	0.70275	2.135	0.53688	D	0.999977	B;B;B;P	0.44344	0.087;0.009;0.015;0.833	B;B;B;P	0.46825	0.043;0.012;0.027;0.528	D	0.83852	0.0263	10	0.42905	T	0.14	-20.3114	11.7991	0.52116	0.0:0.9156:0.0:0.0844	.	448;537;493;505	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	N	493;537;448;505	ENSP00000273691:S493N;ENSP00000345667:S537N;ENSP00000377251:S448N;ENSP00000419414:S505N	ENSP00000273691:S493N	S	-	2	0	ILDR1	123189935	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.370000	0.44240	1.472000	0.48140	0.650000	0.86243	AGC		0.428	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		T	121707245	C	T	121707245	3	4	61	1	0	0	0	0	1	0	0	0	7730	797	28	3	34	3	ILDR1	3	121707245	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75289	121707245	76315185	2708	10693										
CASR	846	broad.mit.edu	37	chr3	121981171	121981171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctactccattgcccacgCcttgcaagatatatatacct	5	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121981171C>T	ENST00000490131.1	+	4	1661	c.1289C>T	c.(1288-1290)gCc>gTc	p.A430V	CASR_ENST00000296154.5_Missense_Mutation_p.A430V|CASR_ENST00000498619.1_Missense_Mutation_p.A430V	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	430					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.A430V(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	ATTGCCCACGCCTTGCAAGAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	111	113					3																	121981171		2203	4300	6503	123463861	SO:0001583	missense	846			U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1289C>T	3.37:g.121981171C>T	ENSP00000418685:p.Ala430Val		123463861	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755944	0.89843	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.94828	-3.53;-3.53;-3.53	5.93	5.93	0.95920	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.98340	0.9449	H	0.96142	3.775	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	D	0.98847	1.0757	10	0.66056	D	0.02	.	19.3193	0.94231	0.0:1.0:0.0:0.0	.	430;430	E7ENE0;P41180	.;CASR_HUMAN	V	430	ENSP00000418685:A430V;ENSP00000420194:A430V;ENSP00000296154:A430V	ENSP00000296154:A430V	A	+	2	0	CASR	123463861	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.818000	0.86416	2.797000	0.96272	0.655000	0.94253	GCC		0.493	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	121981171	C	T	121981171	3	4	61	1	0	0	0	0	1	0	0	0	2688	739	26	3	1299	3	CASR	3	121981171	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	273926	121981171	76041259	2709	10694										
CASR	846	broad.mit.edu	37	chr3	121994750	121994750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacctggtggggaactattCcatcatcaactggcacctct	9	12	3	1	rs202112921		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:121994750C>T	ENST00000490131.1	+	5	1841	c.1469C>T	c.(1468-1470)tCc>tTc	p.S490F	CASR_ENST00000296154.5_Missense_Mutation_p.S490F|CASR_ENST00000498619.1_Missense_Mutation_p.S490F	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	490					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.S490F(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GGGAACTATTCCATCATCAAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											167	149	155					3																	121994750		2203	4300	6503	123477440	SO:0001583	missense	846			U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1469C>T	3.37:g.121994750C>T	ENSP00000418685:p.Ser490Phe		123477440	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.213785	0.79352	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.83075	-1.68;-1.68;-1.68	5.69	5.69	0.88448	Extracellular ligand-binding receptor (1);	0.048414	0.85682	D	0.000000	D	0.83741	0.5320	L	0.41492	1.28	0.53688	D	0.99997	P;P	0.52463	0.934;0.953	P;P	0.49637	0.617;0.559	D	0.85261	0.1050	10	0.87932	D	0	.	19.1688	0.93569	0.0:1.0:0.0:0.0	.	490;490	E7ENE0;P41180	.;CASR_HUMAN	F	490	ENSP00000418685:S490F;ENSP00000420194:S490F;ENSP00000296154:S490F	ENSP00000296154:S490F	S	+	2	0	CASR	123477440	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.911000	0.69939	2.840000	0.97914	0.655000	0.94253	TCC		0.488	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	121994750	C	T	121994750	3	4	61	1	0	0	0	0	1	0	0	0	2688	855	30	3	1483	3	CASR	3	121994750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13579	121994750	76027680	2710	10695										
KPNA1	3836	broad.mit.edu	37	chr3	122160928	122160928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaatgtttcccacagctCgcaaagcaggagaaaccact	8	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122160928C>T	ENST00000344337.6	-	10	1129	c.953G>A	c.(952-954)cGa>cAa	p.R318Q	KPNA1_ENST00000466923.1_5'UTR|RP11-299J3.8_ENST00000609469.1_RNA	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)	318	Binding to RAG1.|NLS binding site (minor). {ECO:0000250}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)	p.R318Q(1)		NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		TCCCACAGCTCGCAAAGCAGG	0.353																																					Melanoma(12;340 801 11196 19797)											1	Substitution - Missense(1)	large_intestine(1)	3											179	185	183					3																	122160928		2203	4300	6503	123643618	SO:0001583	missense	3836			S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"Importins", "Armadillo repeat containing"	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.953G>A	3.37:g.122160928C>T	ENSP00000343701:p.Arg318Gln		123643618	D3DN93|Q6IBQ9|Q9BQ56	Missense_Mutation	SNP	ENST00000344337.6	37	CCDS3013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708372	0.96821	.	.	ENSG00000114030	ENST00000344337;ENST00000465882	T;T	0.69806	-0.43;-0.43	5.17	5.17	0.71159	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88851	0.6549	H	0.97852	4.09	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.92756	0.6220	10	0.87932	D	0	-14.7106	17.8521	0.88750	0.0:1.0:0.0:0.0	.	318	P52294	IMA1_HUMAN	Q	318	ENSP00000343701:R318Q;ENSP00000419890:R318Q	ENSP00000343701:R318Q	R	-	2	0	KPNA1	123643618	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.625000	0.83145	2.692000	0.91855	0.655000	0.94253	CGA		0.353	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355740.1	NM_002264		T	122160928	C	T	122160928	3	4	61	1	0	0	0	0	1	0	0	0	8450	884	31	1	683	1	KPNA1	3	122160928	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166178	122160928	75861502	2711	10696										
KPNA1	3836	broad.mit.edu	37	chr3	122170460	122170460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattccgggtcatggtcaggCggttttgctttgaaaataac	11	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122170460C>T	ENST00000344337.6	-	8	850	c.674G>A	c.(673-675)cGc>cAc	p.R225H	KPNA1_ENST00000466923.1_5'UTR	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)	225	NLS binding site (major). {ECO:0000250}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)	p.R225H(1)		NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		CATGGTCAGGCGGTTTTGCTT	0.383																																					Melanoma(12;340 801 11196 19797)											1	Substitution - Missense(1)	large_intestine(1)	3											96	97	97					3																	122170460		2203	4300	6503	123653150	SO:0001583	missense	3836			S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"Importins", "Armadillo repeat containing"	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.674G>A	3.37:g.122170460C>T	ENSP00000343701:p.Arg225His		123653150	D3DN93|Q6IBQ9|Q9BQ56	Missense_Mutation	SNP	ENST00000344337.6	37	CCDS3013.1	.	.	.	.	.	.	.	.	.	.	C	34	5.383943	0.95967	.	.	ENSG00000114030	ENST00000344337;ENST00000465882	T;T	0.68765	-0.35;-0.35	4.81	4.81	0.61882	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83312	0.5227	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	D	0.86438	0.1765	10	0.66056	D	0.02	-5.1192	17.0429	0.86494	0.0:1.0:0.0:0.0	.	225	P52294	IMA1_HUMAN	H	225	ENSP00000343701:R225H;ENSP00000419890:R225H	ENSP00000343701:R225H	R	-	2	0	KPNA1	123653150	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.320000	0.79064	2.493000	0.84123	0.460000	0.39030	CGC		0.383	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355740.1	NM_002264		T	122170460	C	T	122170460	3	4	61	1	0	0	0	0	1	0	0	0	8450	768	27	1	970	1	KPNA1	3	122170460	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9532	122170460	75851970	2712	10697										
PARP9	83666	broad.mit.edu	37	chr3	122255885	122255885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgatattttctttcatttCgtcttgggttttttgttgct	7	5	3	1	rs369798989		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122255885C>T	ENST00000360356.2	-	9	2133	c.1906G>A	c.(1906-1908)Gaa>Aaa	p.E636K	PARP9_ENST00000471785.1_Missense_Mutation_p.E601K|PARP9_ENST00000492382.1_Missense_Mutation_p.E181K|PARP9_ENST00000462315.1_Missense_Mutation_p.E601K|PARP9_ENST00000477522.2_Missense_Mutation_p.E601K	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	636	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.E636K(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		TCTTTCATTTCGTCTTGGGTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	161	160	161		1906,1801,1801,1801,1801,1906	-0.6	0	3		161	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	636/855,601/820,601/820,601/820,601/711,636/855	122255885	1,13005	2203	4300	6503	123738575	SO:0001583	missense	83666			AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.1906G>A	3.37:g.122255885C>T	ENSP00000353512:p.Glu636Lys		123738575	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	C	2.770	-0.255801	0.05829	0.0	1.16E-4	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T;T	0.17691	3.27;2.96;3.13;3.13;2.26	4.42	-0.57	0.11753	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.903779	0.09396	N	0.807834	T	0.07098	0.0180	N	0.11560	0.145	0.09310	N	1	B;B;B;B	0.17268	0.004;0.021;0.003;0.003	B;B;B;B	0.08055	0.001;0.002;0.002;0.003	T	0.42241	-0.9463	10	0.07482	T	0.82	.	7.6497	0.28342	0.0:0.637:0.1315:0.2315	.	601;636;181;601	E9PFM7;Q8IXQ6;G5E9U8;Q8IXQ6-2	.;PARP9_HUMAN;.;.	K	636;181;601;601;559;601	ENSP00000353512:E636K;ENSP00000417664:E181K;ENSP00000419506:E601K;ENSP00000419001:E601K;ENSP00000418894:E601K	ENSP00000353512:E636K	E	-	1	0	PARP9	123738575	0.000000	0.05858	0.009000	0.14445	0.014000	0.08584	-0.360000	0.07622	-0.120000	0.11809	-1.305000	0.01319	GAA		0.343	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		T	122255885	C	T	122255885	3	4	61	1	0	0	0	0	1	0	0	0	11497	893	31	1	723	1	PARP9	3	122255885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85425	122255885	75766545	2713	10698										
PARP9	83666	broad.mit.edu	37	chr3	122274888	122274888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggacttcacacagctgacGctcattattttttaaaattt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122274888G>A	ENST00000360356.2	-	4	462	c.235C>T	c.(235-237)Cgt>Tgt	p.R79C	PARP9_ENST00000471785.1_Missense_Mutation_p.R44C|PARP9_ENST00000492382.1_Intron|PARP9_ENST00000462315.1_Missense_Mutation_p.R44C|PARP9_ENST00000477522.2_Missense_Mutation_p.R44C	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	79					cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R79C(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		CACAGCTGACGCTCATTATTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											47	47	47					3																	122274888		2203	4300	6503	123757578	SO:0001583	missense	83666			AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.235C>T	3.37:g.122274888G>A	ENSP00000353512:p.Arg79Cys		123757578	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.473267	0.26423	.	.	ENSG00000138496	ENST00000360356;ENST00000477522;ENST00000471785;ENST00000462315;ENST00000466126	T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91	5.31	1.26	0.21427	.	0.658159	0.14977	N	0.287477	T	0.15478	0.0373	N	0.08118	0	0.09310	N	1	P;P;P	0.52061	0.95;0.947;0.948	B;B;P	0.48030	0.361;0.27;0.564	T	0.09487	-1.0672	10	0.72032	D	0.01	.	6.7642	0.23558	0.1419:0.0:0.27:0.5881	.	44;79;44	E9PFM7;Q8IXQ6;Q8IXQ6-2	.;PARP9_HUMAN;.	C	79;44;44;44;57	ENSP00000353512:R79C;ENSP00000419506:R44C;ENSP00000419001:R44C;ENSP00000418894:R44C;ENSP00000419626:R57C	ENSP00000353512:R79C	R	-	1	0	PARP9	123757578	0.000000	0.05858	0.089000	0.20774	0.071000	0.16799	-0.156000	0.10100	0.451000	0.26802	-0.266000	0.10368	CGT		0.403	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		A	122274888	G	A	122274888	3	1	61	1	0	0	0	0	1	0	0	0	11497	1087	38	1	2414	1	PARP9	3	122274888	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19003	122274888	75747542	2714	10699										
PARP15	165631	broad.mit.edu	37	chr3	122345867	122345867	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaactttcagtccacattCtccatgactacatgtaagat	5	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122345867C>A	ENST00000464300.2	+	9	1491	c.1425C>A	c.(1423-1425)ttC>ttA	p.F475L	PARP15_ENST00000493645.1_Intron|PARP15_ENST00000310366.4_Missense_Mutation_p.F241L|PARP15_ENST00000483793.1_Intron|PARP15_ENST00000465304.1_3'UTR	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.F241L(1)|p.F475L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		AGTCCACATTCTCCATGACTA	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	3											70	68	69					3																	122345867		2203	4300	6503	123828557	SO:0001583	missense	165631			AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"Poly (ADP-ribose) polymerases"	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1425C>A	3.37:g.122345867C>A	ENSP00000417214:p.Phe475Leu		123828557	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	.	.	.	.	.	.	.	.	.	.	C	6.050	0.377549	0.11466	.	.	ENSG00000173200	ENST00000464300;ENST00000542823;ENST00000310366	T;T	0.11495	2.77;2.79	3.7	-2.64	0.06114	.	.	.	.	.	T	0.06462	0.0166	L	0.48642	1.525	0.09310	N	1	B;B;B	0.10296	0.002;0.0;0.003	B;B;B	0.09377	0.004;0.002;0.002	T	0.46359	-0.9197	9	0.10902	T	0.67	.	0.6387	0.00807	0.2811:0.228:0.2947:0.1961	.	241;222;453	Q460N3-2;F5H8I1;Q460N3	.;.;PAR15_HUMAN	L	475;222;241	ENSP00000417214:F475L;ENSP00000308436:F241L	ENSP00000308436:F241L	F	+	3	2	PARP15	123828557	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.619000	0.02048	-0.395000	0.07715	0.563000	0.77884	TTC		0.353	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615		A	122345867	C	A	122345867	3	1	61	1	0	0	0	0	1	0	0	0	11490	912	32	2	1528	2	PARP15	3	122345867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70979	122345867	75676563	2715	10700										
PARP14	54625	broad.mit.edu	37	chr3	122404133	122404133	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaaccccagatgaaatcGatcatgtctttgaagaggaa	9	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122404133G>T	ENST00000474629.2	+	2	555	c.289G>T	c.(289-291)Gat>Tat	p.D97Y		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	97					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.D97Y(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGATGAAATCGATCATGTCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											79	73	75					3																	122404133		1869	4109	5978	123886823	SO:0001583	missense	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.289G>T	3.37:g.122404133G>T	ENSP00000418194:p.Asp97Tyr		123886823	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.075|0.075	-1.194830|-1.194830	0.01594|0.01594	.|.	.|.	ENSG00000173193|ENSG00000173193	ENST00000474629;ENST00000398162|ENST00000494811	T|.	0.10382|.	2.88|.	3.97|3.97	2.96|2.96	0.34315|0.34315	.|.	0.900187|.	0.09734|.	N|.	0.762742|.	T|T	0.19846|0.19846	0.0477|0.0477	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B|.	0.24618|.	0.107|.	B|.	0.23150|.	0.044|.	T|T	0.22626|0.22626	-1.0211|-1.0211	10|5	0.66056|.	D|.	0.02|.	.|.	5.4232|5.4232	0.16411|0.16411	0.0:0.6808:0.1967:0.1225|0.0:0.6808:0.1967:0.1225	.|.	97|.	Q460N5|.	PAR14_HUMAN|.	Y|L	97|105	ENSP00000418194:D97Y|.	ENSP00000381228:D97Y|.	D|R	+|+	1|2	0|0	PARP14|PARP14	123886823|123886823	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.014000|0.014000	0.08584|0.08584	-1.036000|-1.036000	0.03560|0.03560	0.528000|0.528000	0.28580|0.28580	-0.295000|-0.295000	0.09555|0.09555	GAT|CGA		0.413	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122404133	G	T	122404133	3	4	61	1	0	0	0	0	1	0	0	0	11489	1058	37	2	295	2	PARP14	3	122404133	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58266	122404133	75618297	2716	10701										
PARP14	54625	broad.mit.edu	37	chr3	122411159	122411159	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaatcagatgtgtcagaaGaattggatacaaaactccct	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122411159G>T	ENST00000474629.2	+	4	633	c.367G>T	c.(367-369)Gaa>Taa	p.E123*		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.E123*(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TGTGTCAGAAGAATTGGATAC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											108	106	106					3																	122411159		1868	4098	5966	123893849	SO:0001587	stop_gained	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.367G>T	3.37:g.122411159G>T	ENSP00000418194:p.Glu123*		123893849	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Nonsense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	36	5.889568	0.97068	.	.	ENSG00000173193	ENST00000474629	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	13.9742	0.64262	0.0:0.0:1.0:0.0	.	.	.	.	X	123	.	ENSP00000418194:E123X	E	+	1	0	PARP14	123893849	0.797000	0.28877	0.406000	0.26421	0.680000	0.39746	1.597000	0.36729	2.661000	0.90470	0.655000	0.94253	GAA		0.378	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122411159	G	T	122411159	4	4	61	1	0	0	0	0	0	1	0	0	11489	943	33	2	381	2	PARP14	3	122411159	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7026	122411159	75611271	2717	10702										
PARP14	54625	broad.mit.edu	37	chr3	122418260	122418260	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacaccatcatggccacaAaactcgacttcaataaaatg	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122418260A>C	ENST00000474629.2	+	6	1125	c.859A>C	c.(859-861)Aaa>Caa	p.K287Q		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.K287Q(1)|p.K124Q(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CATGGCCACAAAACTCGACTT	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	3											74	68	70					3																	122418260		1909	4116	6025	123900950	SO:0001583	missense	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.859A>C	3.37:g.122418260A>C	ENSP00000418194:p.Lys287Gln		123900950	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	A	10.45	1.352498	0.24512	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.75477	-0.94	5.46	4.29	0.51040	.	0.172678	0.40064	N	0.001193	T	0.66446	0.2790	L	0.48642	1.525	0.22066	N	0.999382	B;B	0.30281	0.275;0.087	B;B	0.33454	0.164;0.054	T	0.53746	-0.8395	10	0.22109	T	0.4	.	11.0511	0.47889	0.5794:0.4206:0.0:0.0	.	287;287	Q460N5-4;Q460N5	.;PAR14_HUMAN	Q	287;206	ENSP00000418194:K287Q	ENSP00000381228:K206Q	K	+	1	0	PARP14	123900950	1.000000	0.71417	0.999000	0.59377	0.762000	0.43233	0.749000	0.26320	1.051000	0.40369	0.533000	0.62120	AAA		0.383	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122418260	A	C	122418260	3	2	61	1	0	0	0	0	1	0	0	0	11489	15	1	4	881	4	PARP14	3	122418260	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7101	122418260	75604170	2718	10703										
PARP14	54625	broad.mit.edu	37	chr3	122418645	122418645	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgggacaccataaaaaAtgatgtgaaagatgacagga	11	4	0	4	rs375891999		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122418645A>C	ENST00000474629.2	+	6	1510	c.1244A>C	c.(1243-1245)aAt>aCt	p.N415T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.N415T(1)|p.N252T(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		ACCATAAAAAATGATGTGAAA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	3											132	126	128					3																	122418645		1883	4112	5995	123901335	SO:0001583	missense	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1244A>C	3.37:g.122418645A>C	ENSP00000418194:p.Asn415Thr		123901335	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	A	4.639	0.118872	0.08881	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.09538	2.97	5.32	5.32	0.75619	.	1.025630	0.07740	N	0.946781	T	0.08758	0.0217	N	0.25647	0.755	0.09310	N	1	B;B	0.25772	0.038;0.134	B;B	0.20577	0.009;0.03	T	0.31530	-0.9940	10	0.11794	T	0.64	.	10.9314	0.47220	0.8433:0.1567:0.0:0.0	.	415;415	Q460N5-4;Q460N5	.;PAR14_HUMAN	T	415;334	ENSP00000418194:N415T	ENSP00000381228:N334T	N	+	2	0	PARP14	123901335	0.005000	0.15991	0.012000	0.15200	0.033000	0.12548	1.805000	0.38883	2.228000	0.72767	0.533000	0.62120	AAT		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122418645	A	C	122418645	3	2	61	1	0	0	0	0	1	0	0	0	11489	101	4	4	1266	4	PARP14	3	122418645	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	385	122418645	75603785	2719	10704										
PARP14	54625	broad.mit.edu	37	chr3	122419237	122419237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaagttcttcatggcaaGaaatggaaagggctcactca	10	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122419237G>T	ENST00000474629.2	+	6	2102	c.1836G>T	c.(1834-1836)aaG>aaT	p.K612N		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	612					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.K612N(1)|p.K449N(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTCATGGCAAGAAATGGAAAG	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	3											38	36	37					3																	122419237		1865	4093	5958	123901927	SO:0001583	missense	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1836G>T	3.37:g.122419237G>T	ENSP00000418194:p.Lys612Asn		123901927	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	7.802	0.713810	0.15306	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10288	2.89	5.35	-2.7	0.06004	.	0.920008	0.09291	N	0.822273	T	0.07908	0.0198	L	0.46157	1.445	0.09310	N	1	B;B	0.14438	0.01;0.006	B;B	0.11329	0.006;0.006	T	0.40924	-0.9537	10	0.32370	T	0.25	.	2.6082	0.04884	0.1511:0.1422:0.1826:0.5241	.	612;612	Q460N5-4;Q460N5	.;PAR14_HUMAN	N	612;531	ENSP00000418194:K612N	ENSP00000381228:K531N	K	+	3	2	PARP14	123901927	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.004000	0.03678	-0.280000	0.09154	0.655000	0.94253	AAG		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122419237	G	T	122419237	3	4	61	1	0	0	0	0	1	0	0	0	11489	933	33	2	1858	2	PARP14	3	122419237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	592	122419237	75603193	2720	10705										
DIRC2	84925	broad.mit.edu	37	chr3	122564617	122564617	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcattcacagcaattttCgatttttgatgattgcttta	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122564617C>T	ENST00000261038.5	+	5	1239	c.841C>T	c.(841-843)Cga>Tga	p.R281*		NM_032839.2	NP_116228.1	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2	281					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.R281*(1)		endometrium(2)|large_intestine(1)|lung(14)|prostate(1)	18				GBM - Glioblastoma multiforme(114;0.0614)		CAGCAATTTTCGATTTTTGAT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											104	91	96					3																	122564617		2203	4300	6503	124047307	SO:0001587	stop_gained	84925			AK027690	CCDS3018.1	3q21.1	2013-05-22			ENSG00000138463	ENSG00000138463		"Solute carriers"	16628	protein-coding gene	gene with protein product	"renal cell carcinoma 4", "disrupted in renal cancer protein 2"	602773				11912179	Standard	NM_032839		Approved	FLJ14784, RCC4	uc003efw.4	Q96SL1	OTTHUMG00000159553	ENST00000261038.5:c.841C>T	3.37:g.122564617C>T	ENSP00000261038:p.Arg281*		124047307	A8K561|Q8NBX9	Nonsense_Mutation	SNP	ENST00000261038.5	37	CCDS3018.1	.	.	.	.	.	.	.	.	.	.	C	39	7.590009	0.98378	.	.	ENSG00000138463	ENST00000261038	.	.	.	5.38	4.22	0.49857	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9351	0.41545	0.6661:0.3339:0.0:0.0	.	.	.	.	X	281	.	ENSP00000261038:R281X	R	+	1	2	DIRC2	124047307	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	1.874000	0.39568	0.879000	0.35944	-0.265000	0.10407	CGA		0.348	DIRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356180.2	NM_032839		T	122564617	C	T	122564617	4	4	61	1	0	0	0	0	0	1	0	0	4545	876	31	1	859	1	DIRC2	3	122564617	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145380	122564617	75457813	2721	10706										
SEMA5B	54437	broad.mit.edu	37	chr3	122634465	122634465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatcccgtgtcacattccGcacctgaagacacacatggg	8	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:122634465G>A	ENST00000357599.3	-	14	2196	c.1810C>T	c.(1810-1812)Cgg>Tgg	p.R604W	SEMA5B_ENST00000195173.4_Missense_Mutation_p.R604W|SEMA5B_ENST00000451055.2_Missense_Mutation_p.R658W	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	604					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R604W(1)|p.R658W(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GTCACATTCCGCACCTGAAGA	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	3											56	55	56					3																	122634465		2203	4300	6503	124117155	SO:0001583	missense	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1810C>T	3.37:g.122634465G>A	ENSP00000350215:p.Arg604Trp		124117155	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013262	0.54468	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	4.88	4.0	0.46444	.	0.050126	0.85682	D	0.000000	T	0.40886	0.1135	M	0.72894	2.215	0.45076	D	0.998097	D;D;D	0.89917	0.999;1.0;1.0	D;D;P	0.63488	0.91;0.915;0.88	T	0.31447	-0.9943	10	0.62326	D	0.03	.	11.2252	0.48880	0.0:0.0:0.5368:0.4632	.	546;604;604	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	W	604;604;546;658;604	ENSP00000350215:R604W;ENSP00000195173:R604W;ENSP00000389588:R658W;ENSP00000377208:R604W	ENSP00000195173:R604W	R	-	1	2	SEMA5B	124117155	1.000000	0.71417	0.996000	0.52242	0.657000	0.38888	1.502000	0.35704	1.259000	0.44117	0.561000	0.74099	CGG		0.567	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122634465	G	A	122634465	3	1	61	1	0	0	0	0	1	0	0	0	14075	1086	38	1	1685	1	SEMA5B	3	122634465	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69848	122634465	75387965	2722	10707										
ADCY5	111	broad.mit.edu	37	chr3	123039609	123039609	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactcacttgtccttggggtCttcaaagccctagaagagaa	9	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:123039609C>A	ENST00000462833.1	-	9	3310	c.2098G>T	c.(2098-2100)Gac>Tac	p.D700Y	ADCY5_ENST00000309879.5_Missense_Mutation_p.D350Y|ADCY5_ENST00000491190.1_Missense_Mutation_p.D333Y	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	700					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.D700Y(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		TCCTTGGGGTCTTCAAAGCCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	82	86					3																	123039609		2203	4300	6503	124522299	SO:0001583	missense	111			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.2098G>T	3.37:g.123039609C>A	ENSP00000419361:p.Asp700Tyr		124522299	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076304	0.76415	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	4.38	4.38	0.52667	.	0.000000	0.64402	D	0.000001	T	0.81508	0.4837	L	0.42245	1.32	0.80722	D	1	P;D	0.58970	0.827;0.984	P;P	0.62491	0.666;0.903	T	0.78588	-0.2146	10	0.25106	T	0.35	.	16.1074	0.81234	0.0:1.0:0.0:0.0	.	700;333	O95622;B3KWA8	ADCY5_HUMAN;.	Y	700;333;350;259	ENSP00000419361:D700Y;ENSP00000418537:D333Y;ENSP00000308685:D350Y;ENSP00000420082:D259Y	ENSP00000308685:D350Y	D	-	1	0	ADCY5	124522299	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.968000	0.76086	2.272000	0.75746	0.549000	0.68633	GAC		0.483	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		A	123039609	C	A	123039609	3	1	61	1	0	0	0	0	1	0	0	0	297	913	32	2	1739	2	ADCY5	3	123039609	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	405144	123039609	74982821	2723	10708										
ADCY5	111	broad.mit.edu	37	chr3	123044306	123044306	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgatcatggccttctcttCtttctggaagacgaacacag	10	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:123044306C>A	ENST00000462833.1	-	8	3163	c.1951G>T	c.(1951-1953)Gaa>Taa	p.E651*	ADCY5_ENST00000309879.5_Nonsense_Mutation_p.E301*|ADCY5_ENST00000491190.1_Nonsense_Mutation_p.E284*	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	651					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.E651*(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GCCTTCTCTTCTTTCTGGAAG	0.582																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											142	147	146					3																	123044306		2203	4300	6503	124526996	SO:0001587	stop_gained	111			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1951G>T	3.37:g.123044306C>A	ENSP00000419361:p.Glu651*		124526996	B7Z8A6|Q7RTV7|Q8NFM3	Nonsense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	50	16.511038	0.99865	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	.	.	.	4.99	4.99	0.66335	.	0.067708	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	18.4798	0.90807	0.0:1.0:0.0:0.0	.	.	.	.	X	651;284;301;210	.	ENSP00000308685:E301X	E	-	1	0	ADCY5	124526996	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.320000	0.79064	2.612000	0.88384	0.655000	0.94253	GAA		0.582	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		A	123044306	C	A	123044306	4	1	61	1	0	0	0	0	0	1	0	0	297	922	32	2	1890	2	ADCY5	3	123044306	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4697	123044306	74978124	2724	10709										
MYLK	4638	broad.mit.edu	37	chr3	123366251	123366251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttttcttttctacaagtCgaaagacctgtccaaatttc	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:123366251C>T	ENST00000475616.1	-	24	4438	c.4439G>A	c.(4438-4440)cGa>cAa	p.R1480Q	MYLK_ENST00000360772.3_Missense_Mutation_p.R1480Q|MYLK_ENST00000354792.5_Missense_Mutation_p.R280Q|MYLK_ENST00000346322.5_Missense_Mutation_p.R1411Q|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000359169.1_Missense_Mutation_p.R1480Q|MYLK_ENST00000360304.3_Missense_Mutation_p.R1480Q			Q15746	MYLK_HUMAN	myosin light chain kinase	1480	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.R1480Q(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTCTACAAGTCGAAAGACCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											66	64	65					3																	123366251		2203	4300	6503	124848941	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.4439G>A	3.37:g.123366251C>T	ENSP00000418335:p.Arg1480Gln		124848941	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.698334	0.88830	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.58	4.7	0.59300	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.53238	0.1784	L	0.39467	1.215	0.43835	D	0.996417	D;D;D;D;D	0.89917	0.966;1.0;0.997;0.998;0.973	P;P;P;P;P	0.61328	0.664;0.887;0.708;0.865;0.774	T	0.57757	-0.7756	9	0.87932	D	0	.	15.8758	0.79159	0.1366:0.8634:0.0:0.0	.	1480;1411;1480;1411;1480	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	Q	1480;1480;1480;1411;280;1480	ENSP00000354004:R1480Q;ENSP00000353452:R1480Q;ENSP00000352088:R1480Q;ENSP00000320622:R1411Q;ENSP00000346846:R280Q;ENSP00000418335:R1480Q	ENSP00000320622:R1411Q	R	-	2	0	MYLK	124848941	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.609000	0.54117	1.333000	0.45449	0.655000	0.94253	CGA		0.443	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		T	123366251	C	T	123366251	3	4	61	1	0	0	0	0	1	0	0	0	10086	884	31	1	1337	1	MYLK	3	123366251	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	321945	123366251	74656179	2725	10710										
MYLK	4638	broad.mit.edu	37	chr3	123512533	123512533	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacttcttacccgcccttcGaacttggcggtggctccttc	8	16	1	0	rs200095645		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:123512533G>A	ENST00000475616.1	-	1	155	c.156C>T	c.(154-156)ttC>ttT	p.F52F	MYLK_ENST00000346322.5_Silent_p.F52F|MYLK_ENST00000359169.1_Silent_p.F52F|MYLK_ENST00000360772.3_Silent_p.F52F|MYLK_ENST00000360304.3_Silent_p.F52F			Q15746	MYLK_HUMAN	myosin light chain kinase	52	Ig-like C2-type 1.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.F52F(2)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CCCGCCCTTCGAACTTGGCGG	0.602													G|||	1	0.000199681	8e-04	0	5008	,	,		16134	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|breast(1)	3											41	42	42					3																	123512533		2203	4300	6503	124995223	SO:0001819	synonymous_variant	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.156C>T	3.37:g.123512533G>A			124995223	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																				0.602	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123512533	G	A	123512533	2	1	61	1	0	0	0	0	0	0	0	1	10086	1049	37	1		1	MYLK	3	123512533	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146282	123512533	74509897	2726	10711										
KALRN	8997	broad.mit.edu	37	chr3	124165054	124165054	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatcgcgtgctgcatttCtggaccttgaagaagcggcg	14	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124165054C>A	ENST00000240874.3	+	20	3511	c.3354C>A	c.(3352-3354)ttC>ttA	p.F1118L	KALRN_ENST00000360013.3_Missense_Mutation_p.F1118L|KALRN_ENST00000460856.1_Missense_Mutation_p.F1109L	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1118					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F1118L(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TGCTGCATTTCTGGACCTTGA	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	3											114	105	108					3																	124165054		2203	4300	6503	125647744	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3354C>A	3.37:g.124165054C>A	ENSP00000240874:p.Phe1118Leu		125647744	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.87|15.87	2.962154|2.962154	0.53400|0.53400	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013|ENST00000354186	T;T;T|.	0.61510|.	0.1;0.1;0.1|.	5.22|5.22	4.34|4.34	0.51931|0.51931	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.38480|0.38480	0.1042|0.1042	N|N	0.17082|0.17082	0.46|0.46	0.80722|0.80722	D|D	1|1	B;B;P;P|.	0.52842|.	0.382;0.017;0.956;0.516|.	B;B;D;B|.	0.65010|.	0.206;0.016;0.931;0.373|.	T|T	0.16247|0.16247	-1.0409|-1.0409	10|5	0.10377|.	T|.	0.69|.	.|.	8.4085|8.4085	0.32629|0.32629	0.0:0.7678:0.0:0.2322|0.0:0.7678:0.0:0.2322	.|.	1109;464;1118;1118|.	C9IZQ6;F2Z3Q6;O60229;O60229-2|.	.;.;KALRN_HUMAN;.|.	L|Y	1109;1118;1118|1087	ENSP00000418611:F1109L;ENSP00000240874:F1118L;ENSP00000353109:F1118L|.	ENSP00000240874:F1118L|.	F|S	+|+	3|2	2|0	KALRN|KALRN	125647744|125647744	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	2.571000|2.571000	0.45990|0.45990	1.428000|1.428000	0.47296|0.47296	0.561000|0.561000	0.74099|0.74099	TTC|TCT		0.547	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124165054	C	A	124165054	3	1	61	1	0	0	0	0	1	0	0	0	7996	912	32	2	3432	2	KALRN	3	124165054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	652521	124165054	73857376	2727	10712										
KALRN	8997	broad.mit.edu	37	chr3	124415014	124415014	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaccctgaagatctgtaaTctgatgccccaagacagtgg	9	11	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124415014T>C	ENST00000291478.5	+	21	2683	c.2520T>C	c.(2518-2520)aaT>aaC	p.N840N	KALRN_ENST00000360013.3_Silent_p.N2537N|AC080008.1_ENST00000584173.1_RNA|KALRN_ENST00000428018.2_Silent_p.N808N	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2536					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N2537N(1)|p.N840N(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGATCTGTAATCTGATGCCCC	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	3											169	163	165					3																	124415014		2203	4300	6503	125897704	SO:0001819	synonymous_variant	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.2520T>C	3.37:g.124415014T>C			125897704	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.295731	0.23564	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.62	-2.88	0.05682	.	.	.	.	.	T	0.65873	0.2733	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65948	-0.6044	4	.	.	.	.	15.4624	0.75369	0.0:0.65:0.0:0.3499	.	.	.	.	T	2506	.	.	I	+	2	0	KALRN	125897704	0.840000	0.29493	0.987000	0.45799	0.987000	0.75469	0.142000	0.16096	-0.387000	0.07809	-0.290000	0.09829	ATC		0.468	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		C	124415014	T	C	124415014	2	2	61	1	0	0	0	0	0	0	0	1	7996	1432	50	4		4	KALRN	3	124415014	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	249960	124415014	73607416	2728	10713										
ITGB5	3693	broad.mit.edu	37	chr3	124527970	124527970	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaagatcctcaggctgatCccagactgacaactccactt	6	13	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124527970C>A	ENST00000296181.4	-	9	1458	c.1162G>T	c.(1162-1164)Gat>Tat	p.D388Y		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	388					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)	p.D388Y(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TCAGGCTGATCCCAGACTGAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	110	110					3																	124527970		2203	4300	6503	126010660	SO:0001583	missense	3693			J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1162G>T	3.37:g.124527970C>A	ENSP00000296181:p.Asp388Tyr		126010660	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	37	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.2|27.2	4.813421|4.813421	0.90790|0.90790	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000296181|ENST00000496703	D|.	0.93019|.	-3.15|.	5.63|5.63	5.63|5.63	0.86233|0.86233	Integrin beta subunit, N-terminal (2);|.	0.055265|.	0.64402|.	D|.	0.000001|.	T|T	0.72969|0.72969	0.3527|0.3527	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.76071|.	0.987|.	T|T	0.69587|0.69587	-0.5105|-0.5105	10|5	0.66056|.	D|.	0.02|.	.|.	19.2722|19.2722	0.94015|0.94015	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	388|.	P18084|.	ITB5_HUMAN|.	Y|V	388|154	ENSP00000296181:D388Y|.	ENSP00000296181:D388Y|.	D|G	-|-	1|2	0|0	ITGB5|ITGB5	126010660|126010660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.292000|5.292000	0.65673|0.65673	2.656000|2.656000	0.90262|0.90262	0.655000|0.655000	0.94253|0.94253	GAT|GGA		0.488	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		A	124527970	C	A	124527970	3	1	61	1	0	0	0	0	1	0	0	0	7919	855	30	2	1265	2	ITGB5	3	124527970	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	112956	124527970	73494460	2729	10714										
HEG1	57493	broad.mit.edu	37	chr3	124689532	124689532	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgctttcatcactgatGaaagacgggttatactgtcc	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124689532G>T	ENST00000311127.4	-	17	4177	c.4110C>A	c.(4108-4110)ttC>ttA	p.F1370L		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	1370					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.F1370L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						CATCACTGATGAAAGACGGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	89	91					3																	124689532		1901	4118	6019	126172222	SO:0001583	missense	57493			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.4110C>A	3.37:g.124689532G>T	ENSP00000311502:p.Phe1370Leu		126172222	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	35	5.481551	0.96307	.	.	ENSG00000173706	ENST00000311127;ENST00000487661	D;T	0.96522	-4.04;0.02	5.58	5.58	0.84498	.	0.000000	0.40818	U	0.001012	D	0.96694	0.8921	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	D	0.97746	1.0211	10	0.87932	D	0	.	19.5717	0.95423	0.0:0.0:1.0:0.0	.	1370	Q9ULI3	HEG1_HUMAN	L	1370;254	ENSP00000311502:F1370L;ENSP00000417648:F254L	ENSP00000311502:F1370L	F	-	3	2	HEG1	126172222	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	5.038000	0.64177	2.644000	0.89710	0.655000	0.94253	TTC		0.517	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124689532	G	T	124689532	3	4	61	1	0	0	0	0	1	0	0	0	7065	1281	45	2	39	2	HEG1	3	124689532	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161562	124689532	73332898	2730	10715										
HEG1	57493	broad.mit.edu	37	chr3	124732486	124732486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcagtgtccagaacaaccGaagtgttcggcatattaatg	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124732486G>A	ENST00000311127.4	-	6	2004	c.1937C>T	c.(1936-1938)tCg>tTg	p.S646L	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	646	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.S646L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						CAGAACAACCGAAGTGTTCGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	86	83					3																	124732486		2172	4270	6442	126215176	SO:0001583	missense	57493			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1937C>T	3.37:g.124732486G>A	ENSP00000311502:p.Ser646Leu		126215176	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696095	0.30052	.	.	ENSG00000173706	ENST00000311127	D	0.88431	-2.38	5.3	-0.773	0.10995	.	1.526370	0.05577	N	0.572204	T	0.72447	0.3461	N	0.01668	-0.77	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.04013	0.001;0.001	T	0.60692	-0.7213	10	0.46703	T	0.11	.	8.5588	0.33498	0.5612:0.0:0.4388:0.0	.	646;646	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	L	646	ENSP00000311502:S646L	ENSP00000311502:S646L	S	-	2	0	HEG1	126215176	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	0.115000	0.15540	-0.252000	0.09528	-0.253000	0.11424	TCG		0.517	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		A	124732486	G	A	124732486	3	1	61	1	0	0	0	0	1	0	0	0	7065	1059	37	1	2256	1	HEG1	3	124732486	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42954	124732486	73289944	2731	10716										
ZNF148	7707	broad.mit.edu	37	chr3	124951567	124951567	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacttatctggagttgttCttagtggagaattcattcct	11	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:124951567C>A	ENST00000360647.4	-	9	2488	c.2003G>T	c.(2002-2004)aGa>aTa	p.R668I	ZNF148_ENST00000485866.1_Missense_Mutation_p.R668I|ZNF148_ENST00000492394.1_Missense_Mutation_p.R668I|SLC12A8_ENST00000423114.2_Intron|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000484491.1_Missense_Mutation_p.R668I|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000468369.1_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	668					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R668I(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						TGGAGTTGTTCTTAGTGGAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											189	177	181					3																	124951567		2203	4300	6503	126434257	SO:0001583	missense	7707			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.2003G>T	3.37:g.124951567C>A	ENSP00000353863:p.Arg668Ile		126434257	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Missense_Mutation	SNP	ENST00000360647.4	37	CCDS3031.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.462561	0.63513	.	.	ENSG00000163848	ENST00000360647;ENST00000484491;ENST00000492394;ENST00000485866	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.66781	0.2824	L	0.44542	1.39	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.64841	-0.6312	10	0.45353	T	0.12	-17.0314	19.0462	0.93020	0.0:1.0:0.0:0.0	.	668	Q9UQR1	ZN148_HUMAN	I	668	ENSP00000353863:R668I;ENSP00000420335:R668I;ENSP00000419322:R668I;ENSP00000420448:R668I	ENSP00000353863:R668I	R	-	2	0	ZNF148	126434257	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.320000	0.79064	2.732000	0.93576	0.591000	0.81541	AGA		0.453	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		A	124951567	C	A	124951567	3	1	61	1	0	0	0	0	1	0	0	0	17773	913	32	2	385	2	ZNF148	3	124951567	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219081	124951567	73070863	2732	10717										
OSBPL11	114885	broad.mit.edu	37	chr3	125266271	125266271	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcagtttgccaccataaAatggcttggtatgaaaagtg	11	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:125266271A>C	ENST00000296220.5	-	10	2109	c.1820T>G	c.(1819-1821)tTt>tGt	p.F607C		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	607					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)	p.F607C(1)		NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						GCCACCATAAAATGGCTTGGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											129	121	124					3																	125266271		2203	4300	6503	126748961	SO:0001583	missense	114885			AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1820T>G	3.37:g.125266271A>C	ENSP00000296220:p.Phe607Cys		126748961	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	37	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.003653	0.74932	.	.	ENSG00000144909	ENST00000296220	T	0.31247	1.5	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.64349	0.2590	M	0.92738	3.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74725	-0.3568	10	0.87932	D	0	-16.3255	14.431	0.67251	1.0:0.0:0.0:0.0	.	607	Q9BXB4	OSB11_HUMAN	C	607	ENSP00000296220:F607C	ENSP00000296220:F607C	F	-	2	0	OSBPL11	126748961	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	8.821000	0.92009	1.997000	0.58415	0.383000	0.25322	TTT		0.368	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		C	125266271	A	C	125266271	3	2	61	1	0	0	0	0	1	0	0	0	11307	14	1	4	439	4	OSBPL11	3	125266271	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	314704	125266271	72756159	2733	10718										
OSBPL11	114885	broad.mit.edu	37	chr3	125295035	125295035	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttaattcatacttacttCtctgacttccacaagatggt	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:125295035C>A	ENST00000296220.5	-	5	953	c.664G>T	c.(664-666)Gaa>Taa	p.E222*		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	222					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)	p.E222*(1)		NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						ATACTTACTTCTCTGACTTCC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											121	127	125					3																	125295035		2203	4300	6503	126777725	SO:0001587	stop_gained	114885			AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.664G>T	3.37:g.125295035C>A	ENSP00000296220:p.Glu222*		126777725	A8K9I7	Nonsense_Mutation	SNP	ENST00000296220.5	37	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	C	40	8.034414	0.98621	.	.	ENSG00000144909	ENST00000296220	.	.	.	4.91	4.91	0.64330	.	0.391862	0.28135	N	0.016480	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-17.8889	18.2815	0.90099	0.0:1.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000296220:E222X	E	-	1	0	OSBPL11	126777725	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.250000	0.72435	2.544000	0.85801	0.557000	0.71058	GAA		0.333	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		A	125295035	C	A	125295035	4	1	61	1	0	0	0	0	0	1	0	0	11307	922	32	2	1615	2	OSBPL11	3	125295035	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28764	125295035	72727395	2734	10719										
ROPN1B	152015	broad.mit.edu	37	chr3	125694436	125694436	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgtcccgtggagagacGcctccggtgagagagcggtc	16	13	0	3	rs368373364		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:125694436G>A	ENST00000514116.1	+	4	462	c.147G>A	c.(145-147)acG>acA	p.T49T	ROPN1B_ENST00000511082.1_5'Flank|ROPN1B_ENST00000251776.4_Silent_p.T49T|ROPN1B_ENST00000505382.1_5'UTR			Q9BZX4	ROP1B_HUMAN	rhophilin associated tail protein 1B	49	RIIa.				acrosome reaction (GO:0007340)|cytokinesis (GO:0000910)|fusion of sperm to egg plasma membrane (GO:0007342)|Rho protein signal transduction (GO:0007266)|single organismal cell-cell adhesion (GO:0016337)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor signaling complex scaffold activity (GO:0030159)	p.T49T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(114;0.151)		GTGGAGAGACGCCTCCGGTGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		0,4406		0,0,2203	73	71	71		147	-0.3	1	3		71	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ROPN1B	NM_001012337.1		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		49/213	125694436	1,13001	2203	4298	6501	127177126	SO:0001819	synonymous_variant	152015			AF231410	CCDS33841.1	3q21.2	2011-01-20	2011-01-20		ENSG00000114547	ENSG00000114547			31927	protein-coding gene	gene with protein product			"ropporin, rhophilin associated protein 1B"				Standard	XM_005247137		Approved		uc003eih.3	Q9BZX4	OTTHUMG00000162651	ENST00000514116.1:c.147G>A	3.37:g.125694436G>A			127177126	D3DNA6|Q96BM7	Silent	SNP	ENST00000514116.1	37	CCDS33841.1																																																																																				0.522	ROPN1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369931.1	NM_001012337		A	125694436	G	A	125694436	2	1	61	1	0	0	0	0	0	0	0	1	13561	1074	38	1		1	ROPN1B	3	125694436	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	399401	125694436	72327994	2735	10720										
ALDH1L1	10840	broad.mit.edu	37	chr3	125822642	125822642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacctttcttcagtattCgaaggtcactgtcttgaccc	7	11	4	2	rs550440307	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:125822642C>T	ENST00000393434.2	-	23	3050	c.2701G>A	c.(2701-2703)Gaa>Aaa	p.E901K	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.E901K|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.E800K|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.E911K|ALDH1L1_ENST00000393431.2_3'UTR|SLC41A3_ENST00000508835.1_5'Flank	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	901	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.E901K(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CTTCAGTATTCGAAGGTCACT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											74	66	69					3																	125822642		2203	4300	6503	127305332	SO:0001583	missense	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2701G>A	3.37:g.125822642C>T	ENSP00000377083:p.Glu901Lys		127305332	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998654	0.74818	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.07216	3.21;3.21;3.21;3.21	4.7	4.7	0.59300	Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000001	T	0.08403	0.0209	N	0.01250	-0.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.59473	-0.7448	10	0.19147	T	0.46	.	15.1526	0.72713	0.0:1.0:0.0:0.0	.	800;901	E9PBX3;O75891	.;AL1L1_HUMAN	K	911;901;800;901	ENSP00000273450:E911K;ENSP00000420293:E901K;ENSP00000395881:E800K;ENSP00000377083:E901K	ENSP00000273450:E911K	E	-	1	0	ALDH1L1	127305332	1.000000	0.71417	0.930000	0.37139	0.551000	0.35334	5.964000	0.70379	2.433000	0.82419	0.573000	0.79308	GAA		0.597	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		T	125822642	C	T	125822642	3	4	61	1	0	0	0	0	1	0	0	0	494	893	31	1	11	1	ALDH1L1	3	125822642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128206	125822642	72199788	2736	10721										
ALDH1L1	10840	broad.mit.edu	37	chr3	125856771	125856771	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcattttctaactccaggCcatcacacagctccttcact	3	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:125856771C>G	ENST00000393434.2	-	10	1458	c.1109G>C	c.(1108-1110)gGc>gCc	p.G370A	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.G370A|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.G380A|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.G370A|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.G269A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	370	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.G370A(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	TAACTCCAGGCCATCACACAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	109	116					3																	125856771		2203	4300	6503	127339461	SO:0001583	missense	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1109G>C	3.37:g.125856771C>G	ENSP00000377083:p.Gly370Ala		127339461	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.413164	0.42817	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	4.4	4.4	0.53042	Acyl carrier protein-like (3);Phosphopantetheine-binding (1);	0.178693	0.48767	D	0.000167	T	0.55529	0.1926	M	0.70595	2.14	0.41941	D	0.990617	P;B;B	0.42456	0.78;0.368;0.368	B;B;B	0.41894	0.369;0.292;0.292	T	0.64664	-0.6354	10	0.62326	D	0.03	.	14.8647	0.70406	0.0:1.0:0.0:0.0	.	269;422;370	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	A	380;370;269;370;370	ENSP00000273450:G380A;ENSP00000420293:G370A;ENSP00000395881:G269A;ENSP00000377083:G370A;ENSP00000377081:G370A	ENSP00000273450:G380A	G	-	2	0	ALDH1L1	127339461	0.242000	0.23868	0.956000	0.39512	0.914000	0.54420	1.420000	0.34804	2.432000	0.82394	0.650000	0.86243	GGC		0.567	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		G	125856771	C	G	125856771	3	3	61	1	0	0	0	0	1	0	0	0	494	739	26	5	1655	5	ALDH1L1	3	125856771	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34129	125856771	72165659	2737	10722										
CCDC37	348807	broad.mit.edu	37	chr3	126152014	126152014	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagctcaaagcccgagtCttccacttcggcgagtacaa	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:126152014C>A	ENST00000352312.1	+	14	1488	c.1389C>A	c.(1387-1389)gtC>gtA	p.V463V	CCDC37_ENST00000393425.1_Silent_p.V464V|CCDC37_ENST00000505024.1_Silent_p.V464V	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	463								p.V463V(2)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		AAGCCCGAGTCTTCCACTTCG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	3											130	120	123					3																	126152014		2203	4300	6503	127634704	SO:0001819	synonymous_variant	348807			AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1389C>A	3.37:g.126152014C>A			127634704	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																				0.597	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126152014	C	A	126152014	2	1	61	1	0	0	0	0	0	0	0	1	2815	900	32	2		2	CCDC37	3	126152014	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	295243	126152014	71870416	2738	10723										
UROC1	131669	broad.mit.edu	37	chr3	126208173	126208173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctccctaaaggggctgtCggtgccgctcacgtcatggt	14	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:126208173C>T	ENST00000290868.2	-	17	1707	c.1654G>A	c.(1654-1656)Gac>Aac	p.D552N	UROC1_ENST00000383579.3_Missense_Mutation_p.D612N	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	552					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)	p.D552N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		AAGGGGCTGTCGGTGCCGCTC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											147	136	140					3																	126208173		2203	4300	6503	127690863	SO:0001583	missense	131669			AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1654G>A	3.37:g.126208173C>T	ENSP00000290868:p.Asp552Asn		127690863	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	37	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.854741	0.91355	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.45668	0.89;0.89	4.59	4.59	0.56863	Urocanase domain (2);Urocanase conserved site (1);	0.000000	0.85682	D	0.000000	T	0.74245	0.3691	H	0.95780	3.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.83202	-0.0078	10	0.87932	D	0	-10.501	15.247	0.73513	0.0:1.0:0.0:0.0	.	612;552	E9PE13;Q96N76	.;HUTU_HUMAN	N	552;612	ENSP00000290868:D552N;ENSP00000373073:D612N	ENSP00000290868:D552N	D	-	1	0	UROC1	127690863	1.000000	0.71417	0.989000	0.46669	0.773000	0.43773	6.781000	0.75068	2.247000	0.74100	0.491000	0.48974	GAC		0.537	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		T	126208173	C	T	126208173	3	4	61	1	0	0	0	0	1	0	0	0	17068	884	31	1	392	1	UROC1	3	126208173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56159	126208173	71814257	2739	10724										
MCM2	4171	broad.mit.edu	37	chr3	127325639	127325639	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgccagtcggccggcccCtttgaggtcaacatggagga	15	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127325639C>A	ENST00000265056.7	+	6	1324	c.1080C>A	c.(1078-1080)ccC>ccA	p.P360P		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	360					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)	p.P360P(1)		ovary(3)|skin(2)|stomach(1)	6						CGGCCGGCCCCTTTGAGGTCA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	3											59	65	63					3																	127325639		2203	4300	6503	128808329	SO:0001819	synonymous_variant	4171			X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.1080C>A	3.37:g.127325639C>A			128808329	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	C	8.324	0.825011	0.16678	.	.	ENSG00000073111	ENST00000491422	T	0.29397	1.57	5.0	2.84	0.33178	.	0.100706	0.64402	D	0.000001	T	0.41558	0.1164	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34825	-0.9813	7	0.87932	D	0	-35.8539	8.2589	0.31773	0.0:0.6554:0.1282:0.2164	.	.	.	.	H	223	ENSP00000420528:P223H	ENSP00000420528:P223H	P	+	2	0	MCM2	128808329	0.812000	0.29077	1.000000	0.80357	0.761000	0.43186	0.007000	0.13174	1.089000	0.41292	0.591000	0.81541	CCT		0.587	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			A	127325639	C	A	127325639	2	1	61	1	0	0	0	0	0	0	0	1	9416	668	24	2		2	MCM2	3	127325639	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1117466	127325639	70696791	2740	10725										
PODXL2	50512	broad.mit.edu	37	chr3	127379460	127379460	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctgtgaatggatcccaaGaagaagccaagcctcaggtc	10	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127379460G>T	ENST00000342480.6	+	3	628	c.589G>T	c.(589-591)Gaa>Taa	p.E197*		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	197	Glu-rich.				leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)	p.E197*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						TGGATCCCAAGAAGAAGCCAA	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											94	106	102					3																	127379460		2203	4300	6503	128862150	SO:0001587	stop_gained	50512			AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.589G>T	3.37:g.127379460G>T	ENSP00000345359:p.Glu197*		128862150	Q6UVY4|Q8WUV6	Nonsense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.104116	0.56291	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	.	.	.	4.28	4.28	0.50868	.	0.196900	0.34828	N	0.003659	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-14.2766	8.5298	0.33326	0.1086:0.0:0.8914:0.0	.	.	.	.	X	197	.	ENSP00000304498:E197X	E	+	1	0	PODXL2	128862150	1.000000	0.71417	0.083000	0.20561	0.485000	0.33311	3.636000	0.54317	2.095000	0.63458	0.491000	0.48974	GAA		0.572	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		T	127379460	G	T	127379460	4	4	61	1	0	0	0	0	0	1	0	0	12212	943	33	2	599	2	PODXL2	3	127379460	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53821	127379460	70642970	2741	10726										
PODXL2	50512	broad.mit.edu	37	chr3	127390334	127390334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcgcgggccagccaggtgCgcagcgactacggcacgctc	16	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127390334C>T	ENST00000342480.6	+	7	1522	c.1483C>T	c.(1483-1485)Cgc>Tgc	p.R495C	ABTB1_ENST00000393363.3_5'Flank|ABTB1_ENST00000453791.2_5'Flank|ABTB1_ENST00000468137.1_5'Flank|ABTB1_ENST00000232744.8_5'Flank	NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	495					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)	p.R495C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						CAGCCAGGTGCGCAGCGACTA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3											87	77	81					3																	127390334		2203	4300	6503	128873024	SO:0001583	missense	50512			AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.1483C>T	3.37:g.127390334C>T	ENSP00000345359:p.Arg495Cys		128873024	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301983	0.81136	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.27256	1.68	4.08	4.08	0.47627	.	0.067107	0.64402	D	0.000010	T	0.46964	0.1420	L	0.54323	1.7	0.49687	D	0.999815	D	0.89917	1.0	D	0.87578	0.998	T	0.52041	-0.8628	10	0.87932	D	0	-14.8574	16.3425	0.83092	0.0:1.0:0.0:0.0	.	495	Q9NZ53	PDXL2_HUMAN	C	495;420	ENSP00000345359:R495C	ENSP00000304498:R420C	R	+	1	0	PODXL2	128873024	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.149000	0.64863	1.838000	0.53458	0.289000	0.19496	CGC		0.627	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		T	127390334	C	T	127390334	3	4	61	1	0	0	0	0	1	0	0	0	12212	768	27	1	1509	1	PODXL2	3	127390334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10874	127390334	70632096	2742	10727										
MGLL	11343	broad.mit.edu	37	chr3	127500709	127500709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagcggccactgtgctctCcggctccatgggacacaaag	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127500709C>T	ENST00000434178.2	-	3	1051	c.155G>A	c.(154-156)gGa>gAa	p.G52E	MGLL_ENST00000398104.1_Missense_Mutation_p.G52E|MGLL_ENST00000453507.2_Missense_Mutation_p.G62E|MGLL_ENST00000265052.5_Missense_Mutation_p.G62E			Q99685	MGLL_HUMAN	monoglyceride lipase	52					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)	p.G52E(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						ACTGTGCTCTCCGGCTCCATG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3											47	49	49					3																	127500709		2047	4193	6240	128983399	SO:0001583	missense	11343			BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.155G>A	3.37:g.127500709C>T	ENSP00000402798:p.Gly52Glu		128983399	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	37	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.782096	0.49891	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000536024;ENST00000453507;ENST00000494830	T;T;T;T	0.73575	-0.76;-0.76;-0.76;0.62	5.19	3.35	0.38373	.	0.049719	0.85682	D	0.000000	D	0.89501	0.6733	H	0.96269	3.795	0.58432	D	0.999992	P;P;D;D	0.76494	0.95;0.95;0.999;0.991	D;D;D;D	0.91635	0.95;0.962;0.999;0.997	D	0.90635	0.4570	10	0.87932	D	0	-17.0391	11.9129	0.52749	0.0:0.6618:0.3382:0.0	.	62;52;52;62	B7Z9D1;B2ZGL7;Q99685;B3KRC2	.;.;MGLL_HUMAN;.	E	52;62;52;62;62;52	ENSP00000402798:G52E;ENSP00000265052:G62E;ENSP00000381176:G52E;ENSP00000417489:G52E	ENSP00000265052:G62E	G	-	2	0	MGLL	128983399	0.993000	0.37304	0.456000	0.27044	0.139000	0.21198	2.755000	0.47540	0.544000	0.28883	-0.463000	0.05309	GGA		0.627	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		T	127500709	C	T	127500709	3	4	61	1	0	0	0	0	1	0	0	0	9586	855	30	3	780	3	MGLL	3	127500709	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110375	127500709	70521721	2743	10728										
KBTBD12	166348	broad.mit.edu	37	chr3	127642473	127642473	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgatcttaacatatccaGagaagagagcattctggact	9	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127642473G>T	ENST00000405109.1	+	2	1036	c.569G>T	c.(568-570)aGa>aTa	p.R190I	KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000405256.1_Missense_Mutation_p.R190I|KBTBD12_ENST00000407609.3_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	190	BACK.							p.R190I(2)		endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						AACATATCCAGAGAAGAGAGC	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	3											54	50	51					3																	127642473		1867	4102	5969	129125163	SO:0001583	missense	166348				CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.569G>T	3.37:g.127642473G>T	ENSP00000385957:p.Arg190Ile		129125163	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	37	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	G	18.53	3.642971	0.67244	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.69306	-0.39;-0.39	5.75	5.75	0.90469	BTB/Kelch-associated (2);	.	.	.	.	D	0.82889	0.5135	M	0.79475	2.455	0.52501	D	0.999957	D	0.76494	0.999	D	0.71184	0.972	D	0.83939	0.0310	9	0.72032	D	0.01	.	19.9569	0.97222	0.0:0.0:1.0:0.0	.	190	Q3ZCT8	KBTBC_HUMAN	I	190	ENSP00000385957:R190I;ENSP00000385879:R190I	ENSP00000385957:R190I	R	+	2	0	KBTBD12	129125163	1.000000	0.71417	0.854000	0.33618	0.974000	0.67602	5.258000	0.65479	2.729000	0.93468	0.460000	0.39030	AGA		0.373	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		T	127642473	G	T	127642473	3	4	61	1	0	0	0	0	1	0	0	0	8012	942	33	2	571	2	KBTBD12	3	127642473	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141764	127642473	70379957	2744	10729										
KBTBD12	166348	broad.mit.edu	37	chr3	127646659	127646659	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttatgcacagctgaatttCgagaactctatgctctgggc	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127646659C>T	ENST00000405109.1	+	3	1590	c.1123C>T	c.(1123-1125)Cga>Tga	p.R375*	KBTBD12_ENST00000343941.4_Silent_p.F16F|KBTBD12_ENST00000405256.1_Nonsense_Mutation_p.R375*|KBTBD12_ENST00000407609.3_5'UTR|KBTBD12_ENST00000492025.1_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	375								p.R375*(1)		endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						AGCTGAATTTCGAGAACTCTA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											148	154	152					3																	127646659		2203	4300	6503	129129349	SO:0001587	stop_gained	166348				CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.1123C>T	3.37:g.127646659C>T	ENSP00000385957:p.Arg375*		129129349	B5MCC6|Q6ZRK1	Nonsense_Mutation	SNP	ENST00000405109.1	37	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	C	37	6.363783	0.97507	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0206	0.97499	0.0:1.0:0.0:0.0	.	.	.	.	X	375	.	ENSP00000385957:R375X	R	+	1	2	KBTBD12	129129349	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.403000	0.79983	2.731000	0.93534	0.591000	0.81541	CGA		0.363	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		T	127646659	C	T	127646659	4	4	61	1	0	0	0	0	0	1	0	0	8012	876	31	1	1129	1	KBTBD12	3	127646659	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4186	127646659	70375771	2745	10730										
RUVBL1	8607	broad.mit.edu	37	chr3	127800173	127800173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagttcactgatctcttCgacatgctctttctcaatgc	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127800173C>T	ENST00000322623.5	-	11	1390	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	RUVBL1_ENST00000464873.1_Intron|RUVBL1_ENST00000417360.1_3'UTR|RUVBL1_ENST00000480616.1_5'Flank|RUVBL1-AS1_ENST00000485218.1_RNA	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	431					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)	p.E431K(2)		endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		CTGATCTCTTCGACATGCTCT	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	3											169	151	157					3																	127800173		2203	4300	6503	129282863	SO:0001583	missense	8607			AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"INO80 complex subunits", "ATPases / AAA-type"	10474	protein-coding gene	gene with protein product	"pontin", "INO80 complex subunit H"	603449	"RuvB (E coli homolog)-like 1", "RuvB-like 1 (E. coli)", "RuvB-like AAA ATPase"			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.1291G>A	3.37:g.127800173C>T	ENSP00000318297:p.Glu431Lys		129282863	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Missense_Mutation	SNP	ENST00000322623.5	37	CCDS3047.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.483417	0.44147	.	.	ENSG00000175792	ENST00000322623;ENST00000478892	T	0.62941	-0.01	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.57770	0.2076	L	0.59967	1.855	0.80722	D	1	B	0.15141	0.012	B	0.06405	0.002	T	0.57075	-0.7873	10	0.08179	T	0.78	-33.4611	18.8651	0.92289	0.0:1.0:0.0:0.0	.	431	Q9Y265	RUVB1_HUMAN	K	431;242	ENSP00000318297:E431K	ENSP00000318297:E431K	E	-	1	0	RUVBL1	129282863	1.000000	0.71417	0.904000	0.35570	0.513000	0.34164	5.799000	0.69101	2.445000	0.82738	0.591000	0.81541	GAA		0.507	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			T	127800173	C	T	127800173	3	4	61	1	0	0	0	0	1	0	0	0	13789	893	31	1	83	1	RUVBL1	3	127800173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153514	127800173	70222257	2746	10731										
RUVBL1	8607	broad.mit.edu	37	chr3	127801415	127801415	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgggcacggattttaatGatcttttaaaggataaaaaa	9	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127801415G>A	ENST00000322623.5	-	10	1221	c.1122C>T	c.(1120-1122)atC>atT	p.I374I	RUVBL1_ENST00000464873.1_Intron|RUVBL1_ENST00000417360.1_Intron|RUVBL1_ENST00000480616.1_5'Flank	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	374					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)	p.I374I(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		GGATTTTAATGATCTTTTAAA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											107	81	90					3																	127801415		2203	4300	6503	129284105	SO:0001819	synonymous_variant	8607			AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"INO80 complex subunits", "ATPases / AAA-type"	10474	protein-coding gene	gene with protein product	"pontin", "INO80 complex subunit H"	603449	"RuvB (E coli homolog)-like 1", "RuvB-like 1 (E. coli)", "RuvB-like AAA ATPase"			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.1122C>T	3.37:g.127801415G>A			129284105	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Silent	SNP	ENST00000322623.5	37	CCDS3047.1																																																																																				0.458	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			A	127801415	G	A	127801415	2	1	61	1	0	0	0	0	0	0	0	1	13789	1280	45	3		3	RUVBL1	3	127801415	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1242	127801415	70221015	2747	10732										
EEFSEC	60678	broad.mit.edu	37	chr3	127981061	127981061	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagggcattccagagctCattgaggtactgtcatcttg	10	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:127981061C>A	ENST00000254730.6	+	3	669	c.615C>A	c.(613-615)ctC>ctA	p.L205L	EEFSEC_ENST00000483457.1_Silent_p.L205L	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	205	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)	p.L205L(1)		NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						TTCCAGAGCTCATTGAGGTAC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	3											78	87	84					3																	127981061		2203	4300	6503	129463751	SO:0001819	synonymous_variant	60678				CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"elongation factor for selenoprotein translation"	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.615C>A	3.37:g.127981061C>A			129463751	Q96HZ6	Silent	SNP	ENST00000254730.6	37	CCDS33849.1																																																																																				0.592	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937		A	127981061	C	A	127981061	2	1	61	1	0	0	0	0	0	0	0	1	4942	813	29	2		2	EEFSEC	3	127981061	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179646	127981061	70041369	2748	10733										
DNAJB8	165721	broad.mit.edu	37	chr3	128181439	128181439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgccgttcacagtcaccGacttgagctgcccgtcttcc	8	17	3	1	rs200292314		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:128181439G>A	ENST00000469083.1	-	2	3207	c.650C>T	c.(649-651)tCg>tTg	p.S217L	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Missense_Mutation_p.S217L			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	217					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)	p.S217L(1)		kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CACAGTCACCGACTTGAGCTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	173	137	149		650	4.6	0.9	3		149	0,8600		0,0,4300	no	missense	DNAJB8	NM_153330.2	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	217/233	128181439	1,13005	2203	4300	6503	129664129	SO:0001583	missense	165721				CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"Heat shock proteins / DNAJ (HSP40)"	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.650C>T	3.37:g.128181439G>A	ENSP00000417418:p.Ser217Leu		129664129	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	37	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332824	0.81801	2.27E-4	0.0	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.63096	-0.02;-0.02	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.82678	0.5089	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86461	0.1779	10	0.54805	T	0.06	.	17.3637	0.87358	0.0:0.0:1.0:0.0	.	217	Q8NHS0	DNJB8_HUMAN	L	217	ENSP00000417418:S217L;ENSP00000316053:S217L	ENSP00000316053:S217L	S	-	2	0	DNAJB8	129664129	1.000000	0.71417	0.938000	0.37757	0.448000	0.32197	7.047000	0.76599	2.093000	0.63338	0.555000	0.69702	TCG		0.627	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		A	128181439	G	A	128181439	3	1	61	1	0	0	0	0	1	0	0	0	4637	1059	37	1	52	1	DNAJB8	3	128181439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	200378	128181439	69840991	2749	10734										
KIAA1257	57501	broad.mit.edu	37	chr3	128706495	128706495	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccacgtcgtctgtgaagcCggcagtctttaatcggtaat	10	11	2	1	rs376957597	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:128706495C>A	ENST00000265068.5	-	4	798	c.631G>T	c.(631-633)Ggc>Tgc	p.G211C	KIAA1257_ENST00000511438.1_Missense_Mutation_p.G211C|KIAA1257_ENST00000515659.1_Missense_Mutation_p.G99C|KIAA1257_ENST00000510149.1_5'UTR	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN	KIAA1257	211								p.G211C(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						TCTGTGAAGCCGGCAGTCTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	134	135					3																	128706495		1848	4079	5927	130189185	SO:0001583	missense	57501			AB033083	CCDS46905.1	3q21.3	2011-11-07			ENSG00000114656	ENSG00000114656			29231	protein-coding gene	gene with protein product						10574462	Standard	NM_020741		Approved		uc003elj.4	Q9ULG3	OTTHUMG00000159946	ENST00000265068.5:c.631G>T	3.37:g.128706495C>A	ENSP00000265068:p.Gly211Cys		130189185	Q8IXY7|Q8N5T4	Missense_Mutation	SNP	ENST00000265068.5	37	CCDS46905.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421014	0.25639	.	.	ENSG00000114656	ENST00000511438;ENST00000265068;ENST00000515659	.	.	.	5.13	1.18	0.20946	.	1.276940	0.05705	N	0.594801	T	0.23572	0.0570	N	0.19112	0.55	0.09310	N	1	B;B	0.25667	0.131;0.131	B;B	0.27380	0.079;0.079	T	0.28586	-1.0039	9	0.37606	T	0.19	-1.7784	4.2781	0.10818	0.1632:0.5601:0.0:0.2768	.	211;211	Q9ULG3;D6RH05	K1257_HUMAN;.	C	211;211;99	.	ENSP00000265068:G211C	G	-	1	0	KIAA1257	130189185	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.417000	0.07088	0.258000	0.21686	-0.225000	0.12378	GGC		0.393	KIAA1257-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000358430.1	NM_020741		A	128706495	C	A	128706495	3	1	61	1	0	0	0	0	1	0	0	0	8239	652	23	2	618	2	KIAA1257	3	128706495	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	525056	128706495	69315935	2750	10735										
COPG	22820	broad.mit.edu	37	chr3	128982792	128982792	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgtgtcagaaatatcctCgcaaacacgccgtccttatg	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:128982792C>A	ENST00000314797.6	+	13	1278	c.1174C>A	c.(1174-1176)Cgc>Agc	p.R392S		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	392					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)	p.R392S(1)									GAAATATCCTCGCAAACACGC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	106	114					3																	128982792		2203	4300	6503	130465482	SO:0001583	missense	22820			AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1174C>A	3.37:g.128982792C>A	ENSP00000325002:p.Arg392Ser		130465482	A8K6M8|B3KMF6|Q54AC4	Missense_Mutation	SNP	ENST00000314797.6	37	CCDS33851.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.716661	0.30413	.	.	ENSG00000181789	ENST00000314797	T	0.11385	2.78	5.95	5.95	0.96441	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24005	0.0581	L	0.42744	1.35	0.58432	D	0.99999	D	0.64830	0.994	D	0.76575	0.988	T	0.01993	-1.1233	10	0.09338	T	0.73	-23.0508	17.887	0.88858	0.0:1.0:0.0:0.0	.	392	Q9Y678	COPG_HUMAN	S	392	ENSP00000325002:R392S	ENSP00000325002:R392S	R	+	1	0	COPG	130465482	1.000000	0.71417	0.998000	0.56505	0.113000	0.19764	4.810000	0.62598	2.824000	0.97209	0.655000	0.94253	CGC		0.557	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		A	128982792	C	A	128982792	3	1	61	1	0	0	0	0	1	0	0	0	3737	884	31	2	1224	2	COPG	3	128982792	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	276297	128982792	69039638	2751	10736										
COPG	22820	broad.mit.edu	37	chr3	128984448	128984448	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatcagcatcattgaagaGaactcagagagcaaggagac	10	8	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:128984448G>A	ENST00000314797.6	+	14	1385	c.1281G>A	c.(1279-1281)gaG>gaA	p.E427E		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	427					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)	p.E427E(1)									TCATTGAAGAGAACTCAGAGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	3											169	143	151					3																	128984448		2203	4300	6503	130467138	SO:0001819	synonymous_variant	22820			AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1281G>A	3.37:g.128984448G>A			130467138	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																				0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		A	128984448	G	A	128984448	2	1	61	1	0	0	0	0	0	0	0	1	3737	933	33	3		3	COPG	3	128984448	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1656	128984448	69037982	2752	10737										
COPG	22820	broad.mit.edu	37	chr3	128985910	128985910	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggagcccagaatgaagaGatgttacccagtatcttggt	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:128985910G>T	ENST00000314797.6	+	15	1616	c.1512G>T	c.(1510-1512)gaG>gaT	p.E504D		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	504					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)	p.E504D(1)									AGAATGAAGAGATGTTACCCA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											229	195	207					3																	128985910		2203	4300	6503	130468600	SO:0001583	missense	22820			AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1512G>T	3.37:g.128985910G>T	ENSP00000325002:p.Glu504Asp		130468600	A8K6M8|B3KMF6|Q54AC4	Missense_Mutation	SNP	ENST00000314797.6	37	CCDS33851.1	.	.	.	.	.	.	.	.	.	.	G	0.352	-0.944230	0.02322	.	.	ENSG00000181789	ENST00000314797	T	0.14266	2.52	6.17	0.238	0.15480	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.071627	0.56097	D	0.000022	T	0.04861	0.0131	N	0.05414	-0.055	0.31592	N	0.65382	B	0.02656	0.0	B	0.04013	0.001	T	0.36237	-0.9756	10	0.14252	T	0.57	-33.6489	5.1891	0.15199	0.1852:0.0:0.2255:0.5893	.	504	Q9Y678	COPG_HUMAN	D	504	ENSP00000325002:E504D	ENSP00000325002:E504D	E	+	3	2	COPG	130468600	1.000000	0.71417	0.004000	0.12327	0.007000	0.05969	1.227000	0.32576	0.095000	0.17434	-0.274000	0.10170	GAG		0.512	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		T	128985910	G	T	128985910	3	4	61	1	0	0	0	0	1	0	0	0	3737	933	33	2	1570	2	COPG	3	128985910	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1462	128985910	69036520	2753	10738										
IFT122	55764	broad.mit.edu	37	chr3	129218893	129218893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccatcgagatctgtggtgAccatggctgggttgacatgt	15	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129218893A>G	ENST00000348417.2	+	19	2434	c.2357A>G	c.(2356-2358)gAc>gGc	p.D786G	IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000504021.1_Missense_Mutation_p.D662G|IFT122_ENST00000507564.1_Missense_Mutation_p.D778G|IFT122_ENST00000349441.2_Missense_Mutation_p.D675G|IFT122_ENST00000347300.2_Missense_Mutation_p.D727G|IFT122_ENST00000296266.3_Missense_Mutation_p.D837G|IFT122_ENST00000440957.2_Missense_Mutation_p.D577G|IFT122_ENST00000431818.2_Missense_Mutation_p.D636G	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	786					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.D837G(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						ATCTGTGGTGACCATGGCTGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											186	156	166					3																	129218893		2203	4300	6503	130701583	SO:0001583	missense	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2357A>G	3.37:g.129218893A>G	ENSP00000324005:p.Asp786Gly		130701583	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.637528	0.47049	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522;ENST00000507221	T;T;T;T;T;T;T;T;T	0.61040	0.78;0.14;0.27;0.33;0.93;0.92;0.78;0.33;0.92	5.33	4.18	0.49190	.	0.322570	0.36101	N	0.002783	T	0.50684	0.1630	L	0.50333	1.59	0.41965	D	0.990723	B;B;B;B;B;B;B;B;B;B	0.25390	0.034;0.043;0.055;0.125;0.019;0.019;0.019;0.032;0.02;0.034	B;B;B;B;B;B;B;B;B;B	0.25614	0.022;0.047;0.033;0.062;0.017;0.017;0.017;0.038;0.01;0.036	T	0.50162	-0.8860	10	0.59425	D	0.04	-7.7428	10.2989	0.43639	0.921:0.0:0.079:0.0	.	577;112;778;173;662;626;675;727;786;837	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	G	727;837;778;727;636;662;675;786;626;577;283;148	ENSP00000323973:D727G;ENSP00000296266:D837G;ENSP00000425536:D778G;ENSP00000410946:D636G;ENSP00000422179:D662G;ENSP00000324165:D675G;ENSP00000324005:D786G;ENSP00000401569:D577G;ENSP00000424727:D283G	ENSP00000296266:D837G	D	+	2	0	IFT122	130701583	1.000000	0.71417	0.927000	0.36925	0.883000	0.51084	5.960000	0.70348	0.875000	0.35847	0.533000	0.62120	GAC		0.527	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		G	129218893	A	G	129218893	3	3	61	1	0	0	0	0	1	0	0	0	7576	275	10	4	2588	4	IFT122	3	129218893	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	232983	129218893	68803537	2754	10739										
IFT122	55764	broad.mit.edu	37	chr3	129223182	129223182	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctttgctttgggtgagaaGcatcctgagtttaaggatga	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129223182G>T	ENST00000348417.2	+	21	2645	c.2568G>T	c.(2566-2568)aaG>aaT	p.K856N	IFT122_ENST00000504021.1_Missense_Mutation_p.K732N|IFT122_ENST00000507564.1_Missense_Mutation_p.K848N|IFT122_ENST00000349441.2_Missense_Mutation_p.K745N|IFT122_ENST00000347300.2_Missense_Mutation_p.K797N|IFT122_ENST00000296266.3_Missense_Mutation_p.K907N|IFT122_ENST00000440957.2_Missense_Mutation_p.K647N|IFT122_ENST00000431818.2_Missense_Mutation_p.K706N	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	856					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.K907N(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TGGGTGAGAAGCATCCTGAGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											134	129	131					3																	129223182		2203	4300	6503	130705872	SO:0001583	missense	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2568G>T	3.37:g.129223182G>T	ENSP00000324005:p.Lys856Asn		130705872	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033699	0.54896	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522	T;T;T;T;T;T;T;T;T	0.62232	0.7;0.04;0.18;0.25;0.82;0.85;0.68;1.55;0.8	5.44	4.56	0.56223	.	0.098275	0.64402	D	0.000001	T	0.74298	0.3698	L	0.57536	1.79	0.80722	D	1	D;P;D;B;B;B;B;B;D;D	0.71674	0.996;0.481;0.994;0.318;0.04;0.086;0.086;0.037;0.997;0.998	P;B;D;B;B;B;B;B;P;D	0.74348	0.866;0.287;0.983;0.18;0.022;0.035;0.035;0.111;0.879;0.943	T	0.74487	-0.3649	10	0.44086	T	0.13	-28.592	14.0395	0.64665	0.073:0.0:0.927:0.0	.	647;182;848;243;732;696;745;797;856;907	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	N	797;907;848;797;706;732;745;856;696;647;353	ENSP00000323973:K797N;ENSP00000296266:K907N;ENSP00000425536:K848N;ENSP00000410946:K706N;ENSP00000422179:K732N;ENSP00000324165:K745N;ENSP00000324005:K856N;ENSP00000401569:K647N;ENSP00000424727:K353N	ENSP00000296266:K907N	K	+	3	2	IFT122	130705872	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.692000	0.54727	1.284000	0.44531	0.655000	0.94253	AAG		0.493	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		T	129223182	G	T	129223182	3	4	61	1	0	0	0	0	1	0	0	0	7576	962	34	2	2807	2	IFT122	3	129223182	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4289	129223182	68799248	2755	10740										
RHO	6010	broad.mit.edu	37	chr3	129247623	129247623	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacgtgcccttctccaatgCgacgggtgtggtacgcagcc	12	14	1	0	rs201340914		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129247623C>T	ENST00000296271.3	+	1	141	c.47C>T	c.(46-48)gCg>gTg	p.A16V		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	16					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.A16V(1)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	TTCTCCAATGCGACGGGTGTG	0.587													C|||	1	0.000199681	0	0.0014	5008	,	,		19925	0		0	False		,,,				2504	0				Esophageal Squamous(118;214 1623 30842 43234 46940)											1	Substitution - Missense(1)	large_intestine(1)	3											109	94	99					3																	129247623		2203	4300	6503	130730313	SO:0001583	missense	6010			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.47C>T	3.37:g.129247623C>T	ENSP00000296271:p.Ala16Val		130730313	Q16414|Q2M249	Missense_Mutation	SNP	ENST00000296271.3	37	CCDS3063.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	14.24	2.476688	0.44044	.	.	ENSG00000163914	ENST00000296271	D	0.93659	-3.26	5.51	0.299	0.15771	Rhodopsin, N-terminal (1);	0.910652	0.09514	N	0.791886	D	0.86715	0.5999	L	0.32530	0.975	0.23174	N	0.998174	B	0.15473	0.013	B	0.09377	0.004	T	0.74041	-0.3792	10	0.51188	T	0.08	.	3.4769	0.07587	0.6275:0.1583:0.1065:0.1077	.	16	P08100	OPSD_HUMAN	V	16	ENSP00000296271:A16V	ENSP00000296271:A16V	A	+	2	0	RHO	130730313	0.998000	0.40836	0.141000	0.22245	0.988000	0.76386	0.855000	0.27805	-0.182000	0.10602	0.585000	0.79938	GCG		0.587	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		T	129247623	C	T	129247623	3	4	61	1	0	0	0	0	1	0	0	0	13367	768	27	1	49	1	RHO	3	129247623	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24441	129247623	68774807	2756	10741										
RHO	6010	broad.mit.edu	37	chr3	129251528	129251528	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccaccagggctccaacttCggtcccatcttcatgaccat	6	17	2	1	rs377120794		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129251528C>T	ENST00000296271.3	+	4	943	c.849C>T	c.(847-849)ttC>ttT	p.F283F		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	283					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.F283F(1)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	GCTCCAACTTCGGTCCCATCT	0.547																																					Esophageal Squamous(118;214 1623 30842 43234 46940)											1	Substitution - coding silent(1)	large_intestine(1)	3						C		0,4406		0,0,2203	187	157	167		849	-2.1	1	3		167	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RHO	NM_000539.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		283/349	129251528	1,13005	2203	4300	6503	130734218	SO:0001819	synonymous_variant	6010			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.849C>T	3.37:g.129251528C>T			130734218	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																				0.547	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		T	129251528	C	T	129251528	2	4	61	1	0	0	0	0	0	0	0	1	13367	883	31	1		1	RHO	3	129251528	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3905	129251528	68770902	2757	10742										
PLXND1	23129	broad.mit.edu	37	chr3	129289977	129289977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttggggaggtagtccaggCggaacctgctgccccgctgt	17	11	0	0	rs200890421		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129289977C>T	ENST00000324093.4	-	18	3684	c.3506G>A	c.(3505-3507)cGc>cAc	p.R1169H	PLXND1_ENST00000393239.1_Missense_Mutation_p.R1169H	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1169					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.R1169H(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GTAGTCCAGGCGGAACCTGCT	0.632													C|||	1	0.000199681	0	0	5008	,	,		16502	0.001		0	False		,,,				2504	0				Ovarian(97;366 1484 3738 22084 39045)											1	Substitution - Missense(1)	large_intestine(1)	3						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	122	134	130		3506	1.8	1	3		130	0,8600		0,0,4300	no	missense	PLXND1	NM_015103.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	1169/1926	129289977	1,13005	2203	4300	6503	130772667	SO:0001583	missense	23129			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3506G>A	3.37:g.129289977C>T	ENSP00000317128:p.Arg1169His		130772667	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	7.868	0.727547	0.15439	2.27E-4	0.0	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.35789	1.34;1.29	4.91	1.82	0.25136	.	0.827446	0.10802	N	0.632620	T	0.19046	0.0457	N	0.08118	0	0.31426	N	0.67377	B	0.10296	0.003	B	0.04013	0.001	T	0.20538	-1.0272	10	0.37606	T	0.19	.	8.6862	0.34238	0.0:0.6509:0.0:0.3491	.	1169	Q9Y4D7	PLXD1_HUMAN	H	1169	ENSP00000317128:R1169H;ENSP00000376931:R1169H	ENSP00000317128:R1169H	R	-	2	0	PLXND1	130772667	0.987000	0.35691	0.998000	0.56505	0.644000	0.38419	0.254000	0.18314	0.065000	0.16485	-0.657000	0.03884	CGC		0.632	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129289977	C	T	129289977	3	4	61	1	0	0	0	0	1	0	0	0	12158	768	27	1	2347	1	PLXND1	3	129289977	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38449	129289977	68732453	2758	10743										
TMCC1	23023	broad.mit.edu	37	chr3	129390105	129390105	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttacttccaaccgttcGatctagtgtaaaaacaagag	7	10	1	1	rs564523106	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:129390105G>T	ENST00000393238.3	-	4	919	c.579C>A	c.(577-579)atC>atA	p.I193I	TMCC1_ENST00000426664.2_Silent_p.I79I|TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000329333.5_Silent_p.I14I	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	193						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.I193I(2)	PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						CCAACCGTTCGATCTAGTGTA	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	3											44	43	43					3																	129390105		2203	4300	6503	130872795	SO:0001819	synonymous_variant	23023			AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.579C>A	3.37:g.129390105G>T			130872795	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	37	CCDS33855.1																																																																																				0.468	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		T	129390105	G	T	129390105	2	4	61	1	0	0	0	0	0	0	0	1	16031	1048	37	2		2	TMCC1	3	129390105	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100128	129390105	68632325	2759	10744										
COL6A5	256076	broad.mit.edu	37	chr3	130187813	130187813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtgcttgattactttcAcattgcccccactccactga	5	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130187813A>G	ENST00000432398.2	+	38	7459	c.6965A>G	c.(6964-6966)cAc>cGc	p.H2322R	COL6A5_ENST00000265379.6_Missense_Mutation_p.H2322R	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2322	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.H361R(1)|p.H2322R(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GATTACTTTCACATTGCCCCC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	3											81	80	80					3																	130187813		2043	4180	6223	131670503	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6965A>G	3.37:g.130187813A>G	ENSP00000390895:p.His2322Arg		131670503	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	A	2.700	-0.271130	0.05716	.	.	ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.34	4.16	0.48862	von Willebrand factor, type A (3);	0.382752	0.22416	N	0.060359	T	0.74869	0.3773	L	0.34521	1.04	0.09310	N	1	P;P	0.39216	0.664;0.613	P;B	0.45538	0.484;0.352	T	0.61628	-0.7024	10	0.19147	T	0.46	.	4.7442	0.13029	0.7441:0.0:0.0883:0.1676	.	2322;2322	A8TX70;A8TX70-2	CO6A5_HUMAN;.	R	2322;2322;265;157	ENSP00000390895:H2322R;ENSP00000265379:H2322R;ENSP00000362250:H265R;ENSP00000424968:H157R	ENSP00000265379:H2322R	H	+	2	0	COL6A5	131670503	0.092000	0.21681	0.234000	0.24042	0.028000	0.11728	1.447000	0.35101	0.846000	0.35142	-0.341000	0.08007	CAC		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		G	130187813	A	G	130187813	3	3	61	1	0	0	0	0	1	0	0	0	3708	159	6	4	7111	4	COL6A5	3	130187813	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	797708	130187813	67834617	2760	10745										
COL6A5	256076	broad.mit.edu	37	chr3	130188078	130188078	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggaaaaacaaagttatCtttgtaatatctgctggcga	9	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130188078C>A	ENST00000432398.2	+	38	7724	c.7230C>A	c.(7228-7230)atC>atA	p.I2410I	COL6A5_ENST00000265379.6_Silent_p.I2410I	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2410	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.I449I(1)|p.I2410I(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACAAAGTTATCTTTGTAATAT	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	3											124	108	113					3																	130188078		1845	4097	5942	131670768	SO:0001819	synonymous_variant	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.7230C>A	3.37:g.130188078C>A			131670768	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	C	3.756	-0.050670	0.07407	.	.	ENSG00000172752	ENST00000512836	.	.	.	5.13	4.25	0.50352	.	.	.	.	.	T	0.54127	0.1839	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51616	-0.8683	4	.	.	.	.	4.6684	0.12676	0.1762:0.6442:0.0:0.1796	.	.	.	.	I	662	.	.	L	+	1	0	COL6A5	131670768	0.998000	0.40836	1.000000	0.80357	0.557000	0.35523	0.328000	0.19681	1.157000	0.42530	0.655000	0.94253	CTT		0.408	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130188078	C	A	130188078	2	1	61	1	0	0	0	0	0	0	0	1	3708	903	32	2		2	COL6A5	3	130188078	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	265	130188078	67834352	2761	10746										
COL6A5	256076	broad.mit.edu	37	chr3	130189718	130189718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccactctctctccaggtgCcatcaacaaatatcccaccg	5	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130189718C>T	ENST00000432398.2	+	39	7975	c.7481C>T	c.(7480-7482)gCc>gTc	p.A2494V	COL6A5_ENST00000265379.6_Missense_Mutation_p.A2494V	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2494	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A533V(1)|p.A2494V(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TCTCCAGGTGCCATCAACAAA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	3											75	73	74					3																	130189718		1888	4122	6010	131672408	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.7481C>T	3.37:g.130189718C>T	ENSP00000390895:p.Ala2494Val		131672408	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	C	16.08	3.020624	0.54576	.	.	ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	5.35	4.46	0.54185	.	0.123452	0.36444	N	0.002581	T	0.29423	0.0733	M	0.61703	1.905	0.23712	N	0.997043	D;D	0.69078	0.997;0.989	P;P	0.62089	0.898;0.796	T	0.06144	-1.0843	10	0.42905	T	0.14	.	12.0063	0.53261	0.0:0.8256:0.1744:0.0	.	2494;2494	A8TX70;A8TX70-2	CO6A5_HUMAN;.	V	2494;2494;437;329	ENSP00000390895:A2494V;ENSP00000265379:A2494V;ENSP00000362250:A437V;ENSP00000424968:A329V	ENSP00000265379:A2494V	A	+	2	0	COL6A5	131672408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.378000	0.34328	1.239000	0.43787	0.655000	0.94253	GCC		0.438	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130189718	C	T	130189718	3	4	61	1	0	0	0	0	1	0	0	0	3708	739	26	3	7631	3	COL6A5	3	130189718	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1640	130189718	67832712	2762	10747										
COL6A6	131873	broad.mit.edu	37	chr3	130282333	130282333	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacggagtgaaaatcatCtctgtaggggtgcagaaagc	13	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130282333C>A	ENST00000358511.6	+	2	517	c.486C>A	c.(484-486)atC>atA	p.I162I	COL6A6_ENST00000453409.2_Silent_p.I162I	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	162	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.I162I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGAAAATCATCTCTGTAGGGG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	3											60	61	60					3																	130282333		1918	4125	6043	131765023	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.486C>A	3.37:g.130282333C>A			131765023	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.488	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130282333	C	A	130282333	2	1	61	1	0	0	0	0	0	0	0	1	3709	903	32	2		2	COL6A6	3	130282333	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92615	130282333	67740097	2763	10748										
COL6A6	131873	broad.mit.edu	37	chr3	130284093	130284093	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctccccgaactgggaaggCctatactggagctgccatca	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130284093C>A	ENST00000358511.6	+	3	948	c.917C>A	c.(916-918)gCc>gAc	p.A306D	COL6A6_ENST00000453409.2_Missense_Mutation_p.A306D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	306	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A306D(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ACTGGGAAGGCCTATACTGGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	73	72					3																	130284093		1860	4101	5961	131766783	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.917C>A	3.37:g.130284093C>A	ENSP00000351310:p.Ala306Asp		131766783	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.738540	0.49045	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.77750	-1.12;-1.12	5.01	5.01	0.66863	von Willebrand factor, type A (3);	0.099840	0.44483	D	0.000448	D	0.87103	0.6094	M	0.75777	2.31	0.39769	D	0.972133	D	0.58268	0.982	P	0.62740	0.906	D	0.89186	0.3547	10	0.72032	D	0.01	.	18.2742	0.90078	0.0:1.0:0.0:0.0	.	306	A6NMZ7	CO6A6_HUMAN	D	306	ENSP00000351310:A306D;ENSP00000399236:A306D	ENSP00000351310:A306D	A	+	2	0	COL6A6	131766783	0.996000	0.38824	0.857000	0.33713	0.021000	0.10359	5.527000	0.67123	2.492000	0.84095	0.561000	0.74099	GCC		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130284093	C	A	130284093	3	1	61	1	0	0	0	0	1	0	0	0	3709	739	26	2	927	2	COL6A6	3	130284093	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1760	130284093	67738337	2764	10749										
COL6A6	131873	broad.mit.edu	37	chr3	130285863	130285863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagcaaagaagcagcgaGgaaacaaagttccatgccac	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130285863G>A	ENST00000358511.6	+	4	1631	c.1600G>A	c.(1600-1602)Gga>Aga	p.G534R	COL6A6_ENST00000453409.2_Missense_Mutation_p.G534R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	534	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G534R(2)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GAAGCAGCGAGGAAACAAAGT	0.473																																																2	Substitution - Missense(2)	large_intestine(1)|NS(1)	3											94	99	97					3																	130285863		1982	4163	6145	131768553	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1600G>A	3.37:g.130285863G>A	ENSP00000351310:p.Gly534Arg		131768553	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	3.078	-0.189581	0.06299	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.76578	-1.03;-1.03	5.24	2.44	0.29823	von Willebrand factor, type A (3);	0.461996	0.20205	N	0.097015	T	0.52141	0.1716	N	0.04705	-0.18	0.09310	N	1	B	0.20052	0.041	B	0.25291	0.059	T	0.36311	-0.9753	10	0.14656	T	0.56	.	5.942	0.19198	0.2905:0.1272:0.5823:0.0	.	534	A6NMZ7	CO6A6_HUMAN	R	534	ENSP00000351310:G534R;ENSP00000399236:G534R	ENSP00000351310:G534R	G	+	1	0	COL6A6	131768553	0.138000	0.22547	0.031000	0.17742	0.020000	0.10135	2.433000	0.44793	0.604000	0.29930	-0.291000	0.09656	GGA		0.473	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130285863	G	A	130285863	3	1	61	1	0	0	0	0	1	0	0	0	3709	1001	35	3	1614	3	COL6A6	3	130285863	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1770	130285863	67736567	2765	10750										
COL6A6	131873	broad.mit.edu	37	chr3	130287048	130287048	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggtgtagtccagttcagCgacatcaataaggaagagtt	11	6	2	1	rs142295956	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130287048C>T	ENST00000358511.6	+	5	2032	c.2001C>T	c.(1999-2001)agC>agT	p.S667S	COL6A6_ENST00000453409.2_Silent_p.S667S	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	667	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.S667S(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TCCAGTTCAGCGACATCAATA	0.423													C|||	3	0.000599042	0	0	5008	,	,		20537	0.003		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						C		0,3850		0,0,1925	179	174	176		2001	-5.8	0	3	dbSNP_134	176	2,8248		0,2,4123	no	coding-synonymous	COL6A6	NM_001102608.1		0,2,6048	TT,TC,CC		0.0242,0.0,0.0165		667/2264	130287048	2,12098	1925	4125	6050	131769738	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2001C>T	3.37:g.130287048C>T			131769738	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.423	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130287048	C	T	130287048	2	4	61	1	0	0	0	0	0	0	0	1	3709	767	27	1		1	COL6A6	3	130287048	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1185	130287048	67735382	2766	10751										
COL6A6	131873	broad.mit.edu	37	chr3	130293041	130293041	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaaaacatcaagcagatCtttggaaacacacacatcgg	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130293041C>A	ENST00000358511.6	+	7	3250	c.3219C>A	c.(3217-3219)atC>atA	p.I1073I	COL6A6_ENST00000453409.2_Silent_p.I1073I	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1073	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.I1073I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TCAAGCAGATCTTTGGAAACA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	3											93	90	91					3																	130293041		1960	4162	6122	131775731	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3219C>A	3.37:g.130293041C>A			131775731	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.483	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130293041	C	A	130293041	2	1	61	1	0	0	0	0	0	0	0	1	3709	903	32	2		2	COL6A6	3	130293041	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5993	130293041	67729389	2767	10752										
COL6A6	131873	broad.mit.edu	37	chr3	130293363	130293363	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctgtaccacagcgggtGaaagcagtaagtatttagca	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130293363G>T	ENST00000358511.6	+	7	3572	c.3541G>T	c.(3541-3543)Gaa>Taa	p.E1181*	COL6A6_ENST00000453409.2_Nonsense_Mutation_p.E1181*	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1181	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.E1181*(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CACAGCGGGTGAAAGCAGTAA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											40	39	39					3																	130293363		1944	4146	6090	131776053	SO:0001587	stop_gained	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3541G>T	3.37:g.130293363G>T	ENSP00000351310:p.Glu1181*		131776053	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Nonsense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	38	7.205013	0.98132	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	.	.	.	5.06	3.24	0.37175	.	0.841692	0.10359	N	0.684197	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5035	0.39033	0.2371:0.0:0.7629:0.0	.	.	.	.	X	1181	.	ENSP00000351310:E1181X	E	+	1	0	COL6A6	131776053	0.499000	0.26083	0.843000	0.33291	0.139000	0.21198	1.294000	0.33365	1.269000	0.44280	0.655000	0.94253	GAA		0.468	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130293363	G	T	130293363	4	4	61	1	0	0	0	0	0	1	0	0	3709	1291	45	2	3567	2	COL6A6	3	130293363	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	322	130293363	67729067	2768	10753										
COL6A6	131873	broad.mit.edu	37	chr3	130361685	130361685	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttttcctagggtgtgaaaGgagccaaaggcttggcttca	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130361685G>T	ENST00000358511.6	+	29	5195	c.5164G>T	c.(5164-5166)Gga>Tga	p.G1722*	COL6A6_ENST00000453409.2_Nonsense_Mutation_p.G1722*	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1722	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G1722*(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGGTGTGAAAGGAGCCAAAGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											146	131	136					3																	130361685		1868	4107	5975	131844375	SO:0001587	stop_gained	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.5164G>T	3.37:g.130361685G>T	ENSP00000351310:p.Gly1722*		131844375	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Nonsense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	45	11.838792	0.99609	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.7698	0.91887	0.0:0.0:1.0:0.0	.	.	.	.	X	1722	.	ENSP00000351310:G1722X	G	+	1	0	COL6A6	131844375	1.000000	0.71417	0.967000	0.41034	0.725000	0.41563	6.551000	0.73909	2.724000	0.93272	0.561000	0.74099	GGA		0.423	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130361685	G	T	130361685	4	4	61	1	0	0	0	0	0	1	0	0	3709	1001	35	2	5278	2	COL6A6	3	130361685	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68322	130361685	67660745	2769	10754										
COL6A6	131873	broad.mit.edu	37	chr3	130368040	130368040	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtgagagacattaaggtCcgggagaacagctgccccgt	14	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130368040C>T	ENST00000358511.6	+	32	5398	c.5367C>T	c.(5365-5367)gtC>gtT	p.V1789V	COL6A6_ENST00000453409.2_Silent_p.V1789V	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1789	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.V1789V(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ACATTAAGGTCCGGGAGAACA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	3											45	46	46					3																	130368040		1974	4155	6129	131850730	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.5367C>T	3.37:g.130368040C>T			131850730	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.572	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130368040	C	T	130368040	2	4	61	1	0	0	0	0	0	0	0	1	3709	842	30	3		3	COL6A6	3	130368040	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6355	130368040	67654390	2770	10755										
COL6A6	131873	broad.mit.edu	37	chr3	130368146	130368146	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacaagaagagtcaacttCtcagagaaattgaaactatt	6	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130368146C>A	ENST00000358511.6	+	32	5504	c.5473C>A	c.(5473-5475)Ctc>Atc	p.L1825I	COL6A6_ENST00000453409.2_Missense_Mutation_p.L1825I	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1825	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.L1825I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GAGTCAACTTCTCAGAGAAAT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3											27	28	28					3																	130368146		1900	4116	6016	131850836	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.5473C>A	3.37:g.130368146C>A	ENSP00000351310:p.Leu1825Ile		131850836	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.717578	0.30413	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.84442	-1.85;-1.85	5.45	5.45	0.79879	von Willebrand factor, type A (3);	.	.	.	.	D	0.85440	0.5697	M	0.64404	1.975	0.30026	N	0.813871	P	0.48089	0.905	P	0.45794	0.493	D	0.83414	0.0029	9	0.39692	T	0.17	.	14.1603	0.65443	0.1498:0.8502:0.0:0.0	.	1825	A6NMZ7	CO6A6_HUMAN	I	1825	ENSP00000351310:L1825I;ENSP00000399236:L1825I	ENSP00000351310:L1825I	L	+	1	0	COL6A6	131850836	0.332000	0.24722	0.110000	0.21437	0.004000	0.04260	0.810000	0.27183	2.560000	0.86352	0.462000	0.41574	CTC		0.522	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130368146	C	A	130368146	3	1	61	1	0	0	0	0	1	0	0	0	3709	913	32	2	5599	2	COL6A6	3	130368146	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106	130368146	67654284	2771	10756										
ATP2C1	27032	broad.mit.edu	37	chr3	130714897	130714897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatttcaggtctgcaatcGaagagggtaaagggatttat	11	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130714897G>A	ENST00000510168.1	+	23	2618	c.2068G>A	c.(2068-2070)Gaa>Aaa	p.E690K	ATP2C1_ENST00000505330.1_Missense_Mutation_p.E674K|ATP2C1_ENST00000504381.1_Missense_Mutation_p.E635K|ATP2C1_ENST00000422190.2_Missense_Mutation_p.E690K|ATP2C1_ENST00000393221.4_Missense_Mutation_p.E724K|ATP2C1_ENST00000513801.1_Missense_Mutation_p.E674K|ATP2C1_ENST00000504948.1_Missense_Mutation_p.E674K|ATP2C1_ENST00000328560.8_Missense_Mutation_p.E690K|ATP2C1_ENST00000533801.2_Missense_Mutation_p.E685K|ATP2C1_ENST00000428331.2_Missense_Mutation_p.E690K|ATP2C1_ENST00000507488.2_Missense_Mutation_p.E674K|ATP2C1_ENST00000359644.3_Missense_Mutation_p.E690K|ATP2C1_ENST00000508532.1_Missense_Mutation_p.E690K			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	690					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.E690K(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCTGCAATCGAAGAGGGTAA	0.299									Hailey-Hailey disease																												Esophageal Squamous(99;456 1443 27647 34099 42636)											1	Substitution - Missense(1)	large_intestine(1)	3											78	93	88					3																	130714897		2202	4297	6499	132197587	SO:0001583	missense	27032	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2068G>A	3.37:g.130714897G>A	ENSP00000427461:p.Glu690Lys		132197587	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Missense_Mutation	SNP	ENST00000510168.1	37	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	G	35	5.593587	0.96602	.	.	ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4	5.75	5.75	0.90469	ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97936	0.9321	L	0.55017	1.72	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.99;1.0;0.99;1.0;1.0	D;D;P;D;P;D;D	0.81914	0.995;0.988;0.754;0.995;0.754;0.995;0.988	D	0.97774	1.0228	10	0.44086	T	0.13	.	19.9312	0.97120	0.0:0.0:1.0:0.0	.	724;685;724;690;724;690;690	G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194	.;.;.;.;.;.;AT2C1_HUMAN	K	674;635;674;724;685;690;690;674;674;690;690;690;690;689	ENSP00000423774:E674K;ENSP00000425320:E635K;ENSP00000421326:E674K;ENSP00000376914:E724K;ENSP00000432956:E685K;ENSP00000427461:E690K;ENSP00000424783:E690K;ENSP00000423330:E674K;ENSP00000422872:E674K;ENSP00000329664:E690K;ENSP00000395809:E690K;ENSP00000352665:E690K;ENSP00000402677:E690K	ENSP00000329664:E690K	E	+	1	0	ATP2C1	132197587	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.689000	0.98673	2.720000	0.93068	0.491000	0.48974	GAA		0.299	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		A	130714897	G	A	130714897	3	1	61	1	0	0	0	0	1	0	0	0	1144	1059	37	1	2154	1	ATP2C1	3	130714897	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346751	130714897	67307533	2772	10757										
ASTE1	28990	broad.mit.edu	37	chr3	130733103	130733103	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttcagcgggggcatatGaccttgtggcattgaataga	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130733103G>A	ENST00000264992.3	-	6	2279	c.1838C>T	c.(1837-1839)tCa>tTa	p.S613L	ASTE1_ENST00000514044.1_Missense_Mutation_p.S638L|ATP2C1_ENST00000504381.1_Intron|ATP2C1_ENST00000422190.2_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000328560.8_Intron|ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000507488.2_Intron|ATP2C1_ENST00000359644.3_Intron	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	613					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.S613L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						GGGGGCATATGACCTTGTGGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	69	69					3																	130733103		2203	4300	6503	132215793	SO:0001583	missense	28990			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1838C>T	3.37:g.130733103G>A	ENSP00000264992:p.Ser613Leu		132215793	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	6.548	0.469317	0.12461	.	.	ENSG00000034533	ENST00000514044;ENST00000264992	.	.	.	5.51	4.61	0.57282	.	0.643351	0.16439	N	0.214380	T	0.43743	0.1261	L	0.59436	1.845	0.09310	N	1	B;B	0.21905	0.062;0.036	B;B	0.14578	0.011;0.011	T	0.31752	-0.9932	9	0.36615	T	0.2	-1.9989	11.4123	0.49933	0.0:0.0:0.6448:0.3552	.	638;613	D6RG30;Q2TB18	.;ASTE1_HUMAN	L	638;613	.	ENSP00000264992:S613L	S	-	2	0	ASTE1	132215793	0.069000	0.21087	0.002000	0.10522	0.199000	0.23934	2.616000	0.46376	1.393000	0.46605	0.557000	0.71058	TCA		0.413	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		A	130733103	G	A	130733103	3	1	61	1	0	0	0	0	1	0	0	0	1063	1294	45	3	205	3	ASTE1	3	130733103	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18206	130733103	67289327	2773	10758										
ASTE1	28990	broad.mit.edu	37	chr3	130743298	130743298	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttccttaacattttctcGatccttttttgggaggtatt	7	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130743298G>A	ENST00000264992.3	-	3	1294	c.853C>T	c.(853-855)Cga>Tga	p.R285*	ASTE1_ENST00000514044.1_Nonsense_Mutation_p.R285*|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000511262.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	285					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.R285*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						ACATTTTCTCGATCCTTTTTT	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											130	125	127					3																	130743298		2203	4300	6503	132225988	SO:0001587	stop_gained	28990			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.853C>T	3.37:g.130743298G>A	ENSP00000264992:p.Arg285*		132225988	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Nonsense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	40	8.269464	0.98735	.	.	ENSG00000034533	ENST00000514044;ENST00000264992;ENST00000446270	.	.	.	5.54	3.54	0.40534	.	0.277358	0.37577	N	0.002038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.6889	11.2993	0.49295	0.0:0.2062:0.634:0.1599	.	.	.	.	X	285	.	ENSP00000264992:R285X	R	-	1	2	ASTE1	132225988	0.016000	0.18221	0.582000	0.28627	0.972000	0.66771	1.224000	0.32539	1.329000	0.45376	-0.304000	0.09214	CGA		0.448	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		A	130743298	G	A	130743298	4	1	61	1	0	0	0	0	0	1	0	0	1063	1066	37	1	1202	1	ASTE1	3	130743298	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10195	130743298	67279132	2774	10759										
ASTE1	28990	broad.mit.edu	37	chr3	130743678	130743678	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaaagtcactatctgatGataacacagggcaattccaa	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130743678G>T	ENST00000264992.3	-	3	914	c.473C>A	c.(472-474)tCa>tAa	p.S158*	ASTE1_ENST00000514044.1_Nonsense_Mutation_p.S158*|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000511262.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	158					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.S158*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						ACTATCTGATGATAACACAGG	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											68	65	66					3																	130743678		2203	4300	6503	132226368	SO:0001587	stop_gained	28990			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.473C>A	3.37:g.130743678G>T	ENSP00000264992:p.Ser158*		132226368	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Nonsense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.022724	0.93462	.	.	ENSG00000034533	ENST00000514044;ENST00000264992;ENST00000446270	.	.	.	5.39	5.39	0.77823	.	0.102971	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4083	18.772	0.91896	0.0:0.0:1.0:0.0	.	.	.	.	X	158	.	ENSP00000264992:S158X	S	-	2	0	ASTE1	132226368	0.999000	0.42202	0.122000	0.21767	0.004000	0.04260	6.078000	0.71282	2.527000	0.85204	0.563000	0.77884	TCA		0.413	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		T	130743678	G	T	130743678	4	4	61	1	0	0	0	0	0	1	0	0	1063	1294	45	2	1582	2	ASTE1	3	130743678	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	380	130743678	67278752	2775	10760										
NEK11	28990	broad.mit.edu	37	chr3	130748560	130748560	+	5'Flank	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtttggagcaatgctgaAattccaagaggcagctaagt	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:130748560A>C	ENST00000264992.3	-	0	0				ASTE1_ENST00000514044.1_5'Flank|NEK11_ENST00000429253.2_Missense_Mutation_p.K3T|NEK11_ENST00000510769.1_Missense_Mutation_p.K3T|NEK11_ENST00000510688.1_Missense_Mutation_p.K3T|NEK11_ENST00000383366.4_Missense_Mutation_p.K3T|NEK11_ENST00000412440.2_5'UTR|NEK11_ENST00000507910.1_Missense_Mutation_p.K3T|NEK11_ENST00000508196.1_Missense_Mutation_p.K3T|NEK11_ENST00000356918.4_Missense_Mutation_p.K3T|NEK11_ENST00000511262.1_Missense_Mutation_p.K3T	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)						DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.K3T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						GCAATGCTGAAATTCCAAGAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	99	102					3																	130748560		2203	4300	6503	132231250	SO:0001631	upstream_gene_variant	79858			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644		3.37:g.130748560A>C	Exception_encountered		132231250	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.684536	0.68157	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T	0.71934	-0.56;-0.49;-0.61;-0.58;-0.58;-0.49;-0.61;-0.49	5.83	3.46	0.39613	.	0.108034	0.40728	N	0.001035	T	0.58793	0.2147	N	0.08118	0	0.80722	D	1	P;D;D;P;P	0.57571	0.873;0.98;0.98;0.919;0.873	P;P;P;P;P	0.52856	0.544;0.711;0.711;0.477;0.544	T	0.61362	-0.7078	10	0.59425	D	0.04	.	9.091	0.36610	0.7937:0.0:0.2063:0.0	.	3;3;3;3;3	Q8NG66-3;E9PHI8;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;NEK11_HUMAN;.	T	3	ENSP00000421549:K3T;ENSP00000397180:K3T;ENSP00000349389:K3T;ENSP00000423458:K3T;ENSP00000425114:K3T;ENSP00000372857:K3T;ENSP00000426662:K3T;ENSP00000421851:K3T	ENSP00000349389:K3T	K	+	2	0	NEK11	132231250	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	1.919000	0.40015	0.486000	0.27676	-0.256000	0.11100	AAA		0.403	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		C	130748560	A	C	130748560	1	2	61	0	1	0	0	0	0	0	0	0	10354	14	1	4		4	NEK11	3	130748560	5'Flank	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4882	130748560	67273870	2776	10761										
CPNE4	131034	broad.mit.edu	37	chr3	131624266	131624266	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttggcagcggactcatAaatgttgctcatcttcttca	9	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:131624266A>G	ENST00000512055.1	-	6	2148	c.22T>C	c.(22-24)Tat>Cat	p.Y8H	CPNE4_ENST00000511604.1_Missense_Mutation_p.Y8H|CPNE4_ENST00000429747.1_Missense_Mutation_p.Y8H|CPNE4_ENST00000512332.1_Missense_Mutation_p.Y26H|CPNE4_ENST00000502818.1_Missense_Mutation_p.Y26H			Q96A23	CPNE4_HUMAN	copine IV	8						extracellular vesicular exosome (GO:0070062)		p.Y8H(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						GCGGACTCATAAATGTTGCTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											54	53	53					3																	131624266		2203	4300	6503	133106956	SO:0001583	missense	131034			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.22T>C	3.37:g.131624266A>G	ENSP00000421705:p.Tyr8His		133106956	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.612395	0.46631	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881;ENST00000514999;ENST00000505957	T;T;T;T;T;T;T;T	0.55413	0.55;0.55;0.52;0.55;0.52;1.44;1.36;0.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.45637	0.1352	L	0.34521	1.04	0.58432	D	0.999994	P;P	0.49090	0.919;0.855	P;B	0.44990	0.466;0.36	T	0.30822	-0.9965	10	0.15952	T	0.53	-14.5677	15.7219	0.77718	1.0:0.0:0.0:0.0	.	26;8	Q96A23-2;Q96A23	.;CPNE4_HUMAN	H	8;8;26;8;26;8;8;8	ENSP00000421705:Y8H;ENSP00000411904:Y8H;ENSP00000424853:Y26H;ENSP00000423811:Y8H;ENSP00000421646:Y26H;ENSP00000425506:Y8H;ENSP00000427561:Y8H;ENSP00000421394:Y8H	ENSP00000411904:Y8H	Y	-	1	0	CPNE4	133106956	1.000000	0.71417	0.999000	0.59377	0.156000	0.22039	7.161000	0.77505	2.112000	0.64535	0.533000	0.62120	TAT		0.443	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		G	131624266	A	G	131624266	3	3	61	1	0	0	0	0	1	0	0	0	3820	362	13	4	1711	4	CPNE4	3	131624266	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	875706	131624266	66398164	2777	10762										
ACPP	55	broad.mit.edu	37	chr3	132051045	132051045	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctactctaggtttatattCgaagcacagacgttgaccgg	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132051045C>T	ENST00000336375.5	+	4	403	c.313C>T	c.(313-315)Cga>Tga	p.R105*	ACPP_ENST00000489084.1_3'UTR|ACPP_ENST00000475741.1_Nonsense_Mutation_p.R105*|ACPP_ENST00000351273.7_Nonsense_Mutation_p.R105*	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	105					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)	p.R105*(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						GGTTTATATTCGAAGCACAGA	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											144	144	144					3																	132051045		2203	4300	6503	133533735	SO:0001587	stop_gained	55				CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.313C>T	3.37:g.132051045C>T	ENSP00000337471:p.Arg105*		133533735	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Nonsense_Mutation	SNP	ENST00000336375.5	37	CCDS3073.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.129490	0.56721	.	.	ENSG00000014257	ENST00000336375;ENST00000495911;ENST00000475741;ENST00000351273	.	.	.	6.17	6.17	0.99709	.	0.351400	0.24818	N	0.035352	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4841	0.67603	0.147:0.853:0.0:0.0	.	.	.	.	X	105;76;105;105	.	ENSP00000337471:R105X	R	+	1	2	ACPP	133533735	0.979000	0.34478	0.474000	0.27266	0.073000	0.16967	2.813000	0.48002	2.941000	0.99782	0.655000	0.94253	CGA		0.458	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		T	132051045	C	T	132051045	4	4	61	1	0	0	0	0	0	1	0	0	167	876	31	1	327	1	ACPP	3	132051045	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426779	132051045	65971385	2778	10763										
ACPP	55	broad.mit.edu	37	chr3	132086646	132086646	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggactctgctggcagagaGaatcctatgggaacatctga	13	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132086646G>T	ENST00000351273.7	+	11	1287	c.1237G>T	c.(1237-1239)Gaa>Taa	p.E413*		NM_001134194.1	NP_001127666.1	P15309	PPAP_HUMAN	acid phosphatase, prostate	0					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)	p.E413*(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						CTGGCAGAGAGAATCCTATGG	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											332	279	295					3																	132086646		1568	3582	5150	133569336	SO:0001587	stop_gained	55				CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000351273.7:c.1237G>T	3.37:g.132086646G>T	ENSP00000323036:p.Glu413*		133569336	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Nonsense_Mutation	SNP	ENST00000351273.7	37	CCDS46916.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976914	0.92982	.	.	ENSG00000014257	ENST00000351273	.	.	.	4.8	3.92	0.45320	.	0.733817	0.12769	N	0.440701	.	.	.	.	.	.	0.44890	D	0.997906	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	9.7377	0.40397	0.0987:0.0:0.9013:0.0	.	.	.	.	X	413	.	ENSP00000323036:E413X	E	+	1	0	ACPP	133569336	1.000000	0.71417	0.960000	0.40013	0.931000	0.56810	2.683000	0.46943	1.348000	0.45733	0.655000	0.94253	GAA		0.488	ACPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356701.1	NM_001099		T	132086646	G	T	132086646	4	4	61	1	0	0	0	0	0	1	0	0	167	943	33	2	1302	2	ACPP	3	132086646	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35601	132086646	65935784	2779	10764										
DNAJC13	23317	broad.mit.edu	37	chr3	132192016	132192016	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagaagccagtggttcttCgaaagagaagacaaagaata	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132192016C>T	ENST00000260818.6	+	21	2484	c.2236C>T	c.(2236-2238)Cga>Tga	p.R746*		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	746					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.R746*(1)|p.R129*(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AGTGGTTCTTCGAAAGAGAAG	0.323																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											53	60	58					3																	132192016		2203	4299	6502	133674706	SO:0001587	stop_gained	23317			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2236C>T	3.37:g.132192016C>T	ENSP00000260818:p.Arg746*		133674706	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Nonsense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	C	41	8.992027	0.99029	.	.	ENSG00000138246	ENST00000260818	.	.	.	5.71	4.76	0.60689	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3834	0.60783	0.2365:0.7635:0.0:0.0	.	.	.	.	X	746	.	ENSP00000260818:R746X	R	+	1	2	DNAJC13	133674706	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.624000	0.46444	2.700000	0.92200	0.557000	0.71058	CGA		0.323	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132192016	C	T	132192016	4	4	61	1	0	0	0	0	0	1	0	0	4643	876	31	1	2314	1	DNAJC13	3	132192016	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105370	132192016	65830414	2780	10765										
CCRL1	51554	broad.mit.edu	37	chr3	132319735	132319735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgtgtctggatggctgCcatcttgctgagcatacccc	10	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132319735C>T	ENST00000249887.2	+	2	590	c.494C>T	c.(493-495)gCc>gTc	p.A165V	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000355458.3_Intron|ACAD11_ENST00000545291.1_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	165					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.A165V(1)									TGGATGGCTGCCATCTTGCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											29	28	28					3																	132319735		2202	4295	6497	133802425	SO:0001583	missense	51554			AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"GPCR / Class A : Chemokine receptors : Atypical"	1611	protein-coding gene	gene with protein product		606065	"chemokine (C-C motif) receptor-like 1"	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.494C>T	3.37:g.132319735C>T	ENSP00000249887:p.Ala165Val		133802425	B2R9U7	Missense_Mutation	SNP	ENST00000249887.2	37	CCDS3075.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623045	0.87460	.	.	ENSG00000129048	ENST00000249887;ENST00000424114	T	0.40756	1.02	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.105861	0.64402	D	0.000005	T	0.71264	0.3319	M	0.91920	3.255	0.58432	D	0.999996	D	0.76494	0.999	D	0.68943	0.961	T	0.77713	-0.2485	10	0.87932	D	0	.	16.2433	0.82426	0.0:0.8674:0.1326:0.0	.	165	Q9NPB9	CCRL1_HUMAN	V	165	ENSP00000249887:A165V	ENSP00000249887:A165V	A	+	2	0	CCRL1	133802425	1.000000	0.71417	0.795000	0.32087	0.985000	0.73830	5.978000	0.70501	2.732000	0.93576	0.655000	0.94253	GCC		0.458	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557		T	132319735	C	T	132319735	3	4	61	1	0	0	0	0	1	0	0	0	2955	739	26	3	496	3	CCRL1	3	132319735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127719	132319735	65702695	2781	10766										
CCRL1	51554	broad.mit.edu	37	chr3	132320254	132320254	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggagtttccttttgattCtgagggtcctacagagccaa	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132320254C>A	ENST00000249887.2	+	2	1109	c.1013C>A	c.(1012-1014)tCt>tAt	p.S338Y	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000355458.3_Intron|ACAD11_ENST00000545291.1_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	338					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.S338Y(1)									CCTTTTGATTCTGAGGGTCCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											13	12	12					3																	132320254		1858	4062	5920	133802944	SO:0001583	missense	51554			AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"GPCR / Class A : Chemokine receptors : Atypical"	1611	protein-coding gene	gene with protein product		606065	"chemokine (C-C motif) receptor-like 1"	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.1013C>A	3.37:g.132320254C>A	ENSP00000249887:p.Ser338Tyr		133802944	B2R9U7	Missense_Mutation	SNP	ENST00000249887.2	37	CCDS3075.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.242688	0.22796	.	.	ENSG00000129048	ENST00000249887	T	0.61627	0.09	5.67	5.67	0.87782	.	0.284373	0.32416	N	0.006139	T	0.39118	0.1066	N	0.08118	0	0.53688	D	0.999971	B	0.25719	0.132	B	0.18263	0.021	T	0.36962	-0.9726	10	0.87932	D	0	.	15.1294	0.72511	0.2084:0.7916:0.0:0.0	.	338	Q9NPB9	CCRL1_HUMAN	Y	338	ENSP00000249887:S338Y	ENSP00000249887:S338Y	S	+	2	0	CCRL1	133802944	0.074000	0.21230	0.949000	0.38748	0.993000	0.82548	1.686000	0.37669	2.697000	0.92050	0.655000	0.94253	TCT		0.403	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557		A	132320254	C	A	132320254	3	1	61	1	0	0	0	0	1	0	0	0	2955	913	32	2	1015	2	CCRL1	3	132320254	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	519	132320254	65702176	2782	10767										
ACAD11	84129	broad.mit.edu	37	chr3	132347192	132347192	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttttccttaccgtttggaGagttgtagtccagtttctgc	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132347192G>T	ENST00000264990.6	-	8	2033	c.1062C>A	c.(1060-1062)ctC>ctA	p.L354L	ACAD11_ENST00000355458.3_Silent_p.L354L|ACAD11_ENST00000489991.1_5'Flank|ACAD11_ENST00000545291.1_5'UTR|ACAD11_ENST00000481970.2_Silent_p.L354L	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	354					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.L354L(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						ACCGTTTGGAGAGTTGTAGTC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	3											97	95	96					3																	132347192		2203	4300	6503	133829882	SO:0001819	synonymous_variant	84129			BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1062C>A	3.37:g.132347192G>T			133829882	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Silent	SNP	ENST00000264990.6	37	CCDS3074.1																																																																																				0.378	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		T	132347192	G	T	132347192	2	4	61	1	0	0	0	0	0	0	0	1	109	929	33	2		2	ACAD11	3	132347192	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26938	132347192	65675238	2783	10768										
ACAD11	84129	broad.mit.edu	37	chr3	132363685	132363685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctggtggttttttcctgaGcacatatgtttgaaagccct	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:132363685G>A	ENST00000264990.6	-	2	1176	c.205C>T	c.(205-207)Ctc>Ttc	p.L69F	ACAD11_ENST00000355458.3_Missense_Mutation_p.L69F|ACAD11_ENST00000489991.1_Intron|ACAD11_ENST00000545291.1_5'UTR|ACAD11_ENST00000481970.2_Missense_Mutation_p.L69F	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	69					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.L69F(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						TTTTTCCTGAGCACATATGTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	108	106					3																	132363685		2203	4300	6503	133846375	SO:0001583	missense	84129			BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.205C>T	3.37:g.132363685G>A	ENSP00000264990:p.Leu69Phe		133846375	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	37	CCDS3074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.501152|4.501152	0.85176|0.85176	.|.	.|.	ENSG00000113971|ENSG00000240303;ENSG00000240303;ENSG00000240303;ENSG00000113971	ENST00000393144|ENST00000355458;ENST00000264990;ENST00000481970;ENST00000393156	.|T;T;T	.|0.46451	.|0.87;0.87;0.87	6.16|6.16	5.29|5.29	0.74685|0.74685	.|Aminoglycoside phosphotransferase (1);Protein kinase-like domain (1);	.|.	.|.	.|.	.|.	T|T	0.74997|0.74997	0.3790|0.3790	H|H	0.95504|0.95504	3.68|3.68	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;1.0;1.0	.|D;D;D	.|0.87578	.|0.994;0.998;0.99	D|D	0.83712|0.83712	0.0188|0.0188	6|9	0.25106|0.87932	T|D	0.35|0	.|.	15.6102|15.6102	0.76710|0.76710	0.0654:0.0:0.9346:0.0|0.0654:0.0:0.9346:0.0	.|.	.|231;69;69	.|Q7Z491;D6RDI8;Q709F0	.|.;.;ACD11_HUMAN	V|F	627|69;69;69;411	.|ENSP00000347636:L69F;ENSP00000264990:L69F;ENSP00000420907:L69F	ENSP00000376852:A627V|ENSP00000264990:L69F	A|L	-|-	2|1	0|0	NPHP3|NPHP3;ACAD11	133846375|133846375	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.933000|0.933000	0.57130|0.57130	6.905000|6.905000	0.75714|0.75714	1.628000|1.628000	0.50416|0.50416	-0.145000|-0.145000	0.13849|0.13849	GCT|CTC		0.318	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		A	132363685	G	A	132363685	3	1	61	1	0	0	0	0	1	0	0	0	109	971	34	3	2213	3	ACAD11	3	132363685	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16493	132363685	65658745	2784	10769										
TOPBP1	11073	broad.mit.edu	37	chr3	133362999	133362999	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcttttatgatgtttgcGatgttagattcattttcatt	6	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133362999G>A	ENST00000260810.5	-	11	1844	c.1713C>T	c.(1711-1713)atC>atT	p.I571I	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	571	BRCT 4. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)	p.I484I(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TGATGTTTGCGATGTTAGATT	0.398								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)											1	Substitution - coding silent(1)	large_intestine(1)	3											85	79	81					3																	133362999		1874	4102	5976	134845689	SO:0001819	synonymous_variant	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.1713C>T	3.37:g.133362999G>A			134845689	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																				0.398	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		A	133362999	G	A	133362999	2	1	61	1	0	0	0	0	0	0	0	1	16409	1048	37	1		1	TOPBP1	3	133362999	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	999314	133362999	64659431	2785	10770										
TOPBP1	11073	broad.mit.edu	37	chr3	133368715	133368715	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatttagctggttaaaacGaactccacctccactgttaa	5	11	1	0	rs369433427		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133368715G>A	ENST00000260810.5	-	9	1293	c.1162C>T	c.(1162-1164)Cgt>Tgt	p.R388C	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	388	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)	p.R301C(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TGGTTAAAACGAACTCCACCT	0.338								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)											1	Substitution - Missense(1)	large_intestine(1)	3						G	CYS/ARG	0,3694		0,0,1847	70	67	68		1162	4.8	1	3		68	1,8181		0,1,4090	no	missense	TOPBP1	NM_007027.3	180	0,1,5937	AA,AG,GG		0.0122,0.0,0.0084	probably-damaging	388/1523	133368715	1,11875	1847	4091	5938	134851405	SO:0001583	missense	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.1162C>T	3.37:g.133368715G>A	ENSP00000260810:p.Arg388Cys		134851405	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831791	0.71258	0.0	1.22E-4	ENSG00000163781	ENST00000260810	T	0.78364	-1.17	5.68	4.8	0.61643	BRCT (4);	0.000000	0.85682	D	0.000000	D	0.82829	0.5122	M	0.84773	2.715	0.80722	D	1	P	0.39480	0.675	P	0.44647	0.456	D	0.83418	0.0031	10	0.39692	T	0.17	.	15.0537	0.71894	0.0693:0.0:0.9307:0.0	.	388	Q92547	TOPB1_HUMAN	C	388	ENSP00000260810:R388C	ENSP00000260810:R388C	R	-	1	0	TOPBP1	134851405	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.121000	0.77160	2.678000	0.91216	0.650000	0.86243	CGT		0.338	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		A	133368715	G	A	133368715	3	1	61	1	0	0	0	0	1	0	0	0	16409	1058	37	1	3486	1	TOPBP1	3	133368715	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5716	133368715	64653715	2786	10771										
TF	7018	broad.mit.edu	37	chr3	133472449	133472449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctttcaggcaaacgaagCggatgctgtgacactggatg	12	9	2	1	rs41298977	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133472449C>T	ENST00000402696.3	+	3	712	c.227C>T	c.(226-228)gCg>gTg	p.A76V	TF_ENST00000475382.1_3'UTR|TF_ENST00000264998.3_5'UTR|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	76	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.		A -> V (in dbSNP:rs41298977).		blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.A76V(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	GCAAACGAAGCGGATGCTGTG	0.527													C|||	9	0.00179712	0	0	5008	,	,		16284	0.0089		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	VAL/ALA	0,4406		0,0,2203	141	123	129		227	5	0.4	3	dbSNP_127	129	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TF	NM_001063.3	64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	76/699	133472449	2,13004	2203	4300	6503	134955139	SO:0001583	missense	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.227C>T	3.37:g.133472449C>T	ENSP00000385834:p.Ala76Val		134955139	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	8	0.003663003663003663	0	0.0	0	0.0	8	0.013986013986013986	0	0.0	C	24.6	4.552024	0.86127	0.0	2.33E-4	ENSG00000091513	ENST00000402696;ENST00000466911	T;T	0.51574	0.7;0.7	4.99	4.99	0.66335	.	0.046660	0.85682	D	0.000000	T	0.64260	0.2582	M	0.90977	3.165	0.80722	D	1	D	0.76494	0.999	P	0.56278	0.795	T	0.76531	-0.2925	10	0.66056	D	0.02	-15.7114	17.5631	0.87912	0.0:1.0:0.0:0.0	rs41298977	76	P02787	TRFE_HUMAN	V	76;32	ENSP00000385834:A76V;ENSP00000417468:A32V	ENSP00000385834:A76V	A	+	2	0	TF	134955139	1.000000	0.71417	0.401000	0.26359	0.017000	0.09413	5.790000	0.69038	2.756000	0.94617	0.561000	0.74099	GCG		0.527	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133472449	C	T	133472449	3	4	61	1	0	0	0	0	1	0	0	0	15824	768	27	1	237	1	TF	3	133472449	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103734	133472449	64549981	2787	10772										
TF	7018	broad.mit.edu	37	chr3	133475676	133475676	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggctttccctccccagaGaacttggcaaacaaggctga	10	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133475676G>T	ENST00000402696.3	+	7	1178	c.693G>T	c.(691-693)gaG>gaT	p.E231D	TF_ENST00000264998.3_Splice_Site_p.E104D|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	231	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.E231D(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	CCTCCCCAGAGAACTTGGCAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											101	104	103					3																	133475676		2203	4300	6503	134958366	SO:0001630	splice_region_variant	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.692-1G>T	3.37:g.133475676G>T			134958366	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	.	.	.	.	.	.	.	.	.	.	G	9.470	1.095329	0.20471	.	.	ENSG00000091513	ENST00000402696;ENST00000482271;ENST00000264998	T;T;T	0.39229	1.09;1.09;1.09	5.18	2.09	0.27110	.	0.186910	0.56097	N	0.000029	T	0.38374	0.1038	M	0.66378	2.025	0.52099	D	0.99994	B	0.14438	0.01	B	0.28638	0.092	T	0.20874	-1.0262	10	0.52906	T	0.07	.	4.5758	0.12232	0.0891:0.1461:0.6138:0.1509	.	231	P02787	TRFE_HUMAN	D	231;104;104	ENSP00000385834:E231D;ENSP00000419338:E104D;ENSP00000264998:E104D	ENSP00000264998:E104D	E	+	3	2	TF	134958366	0.153000	0.22777	0.632000	0.29296	0.241000	0.25554	0.069000	0.14552	0.231000	0.21079	0.591000	0.81541	GAG		0.527	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	Missense_Mutation	T	133475676	G	T	133475676	5	4	61	1	0	0	0	0	0	0	1	0	15824	956	33	2	719	2	TF	3	133475676	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3227	133475676	64546754	2788	10773										
RYK	6259	broad.mit.edu	37	chr3	133878114	133878114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgattggctgggctattCggtaaccatctttcaggtat	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133878114C>T	ENST00000427044.2	-	15	1722	c.1112G>A	c.(1111-1113)cGa>cAa	p.R371Q	RYK_ENST00000296084.4_Missense_Mutation_p.R561Q			P34925	RYK_HUMAN	receptor-like tyrosine kinase	557	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|corpus callosum development (GO:0022038)|neuron differentiation (GO:0030182)|neuron projection development (GO:0031175)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of MAPK cascade (GO:0043410)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.R561Q(1)		lung(1)|ovary(3)	4						CTGGGCTATTCGGTAACCATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	67	67					3																	133878114		1932	4133	6065	135360804	SO:0001583	missense	6259			S59184	CCDS75016.1	3q22.1	2012-02-28	2012-02-28		ENSG00000163785	ENSG00000163785	2.7.10.1		10481	protein-coding gene	gene with protein product		600524	"JTK5A protein tyrosine kinase", "RYK receptor-like tyrosine kinase"	JTK5A		8386829	Standard	NM_001005861		Approved	D3S3195, RYK1, JTK5	uc003eqc.1	P34925	OTTHUMG00000159750	ENST00000427044.2:c.1112G>A	3.37:g.133878114C>T	ENSP00000399527:p.Arg371Gln		135360804	Q04696	Silent	SNP	ENST00000427044.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.190028|5.190028	0.94923|0.94923	.|.	.|.	ENSG00000163785|ENSG00000163785	ENST00000460933|ENST00000296084;ENST00000427044	.|D;D	.|0.84589	.|-1.87;-1.87	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94518|0.94518	0.8235|0.8235	M|M	0.92077|0.92077	3.27|3.27	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.75484	.|0.986;0.975	D|D	0.95242|0.95242	0.8352|0.8352	5|10	.|0.87932	.|D	.|0	-3.2019|-3.2019	19.7284|19.7284	0.96174|0.96174	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|557;560	.|P34925;P34925-2	.|RYK_HUMAN;.	K|Q	540|561;371	.|ENSP00000296084:R561Q;ENSP00000399527:R371Q	.|ENSP00000296084:R561Q	E|R	-|-	1|2	0|0	RYK|RYK	135360804|135360804	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.487000|7.487000	0.81328|0.81328	2.668000|2.668000	0.90789|0.90789	0.591000|0.591000	0.81541|0.81541	GAA|CGA		0.453	RYK-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001005861		T	133878114	C	T	133878114	3	4	61	1	0	0	0	0	1	0	0	0	13804	884	31	1	152	1	RYK	3	133878114	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402438	133878114	64144316	2789	10774										
RYK	6259	broad.mit.edu	37	chr3	133894834	133894834	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggccaggtagctcattCcacaggcaatctgaatagcc	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:133894834C>A	ENST00000427044.2	-	13	1398	c.788G>T	c.(787-789)gGa>gTa	p.G263V	RYK_ENST00000296084.4_Missense_Mutation_p.G453V			P34925	RYK_HUMAN	receptor-like tyrosine kinase	449					axon guidance (GO:0007411)|corpus callosum development (GO:0022038)|neuron differentiation (GO:0030182)|neuron projection development (GO:0031175)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of MAPK cascade (GO:0043410)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.G453V(1)		lung(1)|ovary(3)	4						GTAGCTCATTCCACAGGCAAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											50	50	50					3																	133894834		1983	4183	6166	135377524	SO:0001583	missense	6259			S59184	CCDS75016.1	3q22.1	2012-02-28	2012-02-28		ENSG00000163785	ENSG00000163785	2.7.10.1		10481	protein-coding gene	gene with protein product		600524	"JTK5A protein tyrosine kinase", "RYK receptor-like tyrosine kinase"	JTK5A		8386829	Standard	NM_001005861		Approved	D3S3195, RYK1, JTK5	uc003eqc.1	P34925	OTTHUMG00000159750	ENST00000427044.2:c.788G>T	3.37:g.133894834C>A	ENSP00000399527:p.Gly263Val		135377524	Q04696	Missense_Mutation	SNP	ENST00000427044.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.3|24.3	4.516231|4.516231	0.85495|0.85495	.|.	.|.	ENSG00000163785|ENSG00000163785	ENST00000460933|ENST00000296084;ENST00000427044	.|T;D	.|0.94046	.|-0.06;-3.34	5.66|5.66	5.66|5.66	0.87406|0.87406	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.98264	.|0.9425	H|H	0.98256|0.98256	4.185|4.185	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	.|D	.|0.98959	.|1.0797	.|10	.|0.87932	.|D	.|0	-6.1118|-6.1118	20.1253|20.1253	0.97977|0.97977	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|449;452	.|P34925;P34925-2	.|RYK_HUMAN;.	X|V	432|453;263	.|ENSP00000296084:G453V;ENSP00000399527:G263V	.|ENSP00000296084:G453V	E|G	-|-	1|2	0|0	RYK|RYK	135377524|135377524	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.997000|0.997000	0.91878|0.91878	7.445000|7.445000	0.80570|0.80570	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	GAA|GGA		0.463	RYK-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001005861		A	133894834	C	A	133894834	3	1	61	1	0	0	0	0	1	0	0	0	13804	855	30	2	484	2	RYK	3	133894834	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16720	133894834	64127596	2790	10775										
EPHB1	2047	broad.mit.edu	37	chr3	134670754	134670754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacatctctggtgattgctcGgggcacatgcatccccaacg	10	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:134670754G>A	ENST00000398015.3	+	3	1035	c.665G>A	c.(664-666)cGg>cAg	p.R222Q	EPHB1_ENST00000488154.1_Intron	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	222	Cys-rich.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.R222Q(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GTGATTGCTCGGGGCACATGC	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	3											175	170	172					3																	134670754		2042	4207	6249	136153444	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.665G>A	3.37:g.134670754G>A	ENSP00000381097:p.Arg222Gln		136153444	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597629	0.66332	.	.	ENSG00000154928	ENST00000398015	T	0.73469	-0.75	5.36	4.46	0.54185	.	0.062979	0.64402	D	0.000006	D	0.85566	0.5726	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.86389	0.1734	9	.	.	.	.	15.7549	0.78015	0.0:0.1369:0.863:0.0	.	222	P54762	EPHB1_HUMAN	Q	222	ENSP00000381097:R222Q	.	R	+	2	0	EPHB1	136153444	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.978000	0.88095	1.207000	0.43291	0.561000	0.74099	CGG		0.532	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134670754	G	A	134670754	3	1	61	1	0	0	0	0	1	0	0	0	5187	1116	39	1	675	1	EPHB1	3	134670754	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	775920	134670754	63351676	2791	10776										
EPHB1	2047	broad.mit.edu	37	chr3	134920412	134920412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagatgaattatgtgcatCgggacctggctgctaggaac	13	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:134920412C>T	ENST00000398015.3	+	12	2597	c.2227C>T	c.(2227-2229)Cgg>Tgg	p.R743W	EPHB1_ENST00000493838.1_Missense_Mutation_p.R304W	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	743	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.R743W(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						TTATGTGCATCGGGACCTGGC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	3											209	211	210					3																	134920412		2200	4300	6500	136403102	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2227C>T	3.37:g.134920412C>T	ENSP00000381097:p.Arg743Trp		136403102	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.769494	0.90020	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.75154	-0.91;-0.91	5.52	5.52	0.82312	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.082254	0.56097	D	0.000029	D	0.92557	0.7636	H	0.99740	4.74	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.95289	0.8393	10	0.87932	D	0	.	15.3348	0.74244	0.1403:0.8597:0.0:0.0	.	743	P54762	EPHB1_HUMAN	W	743;304	ENSP00000381097:R743W;ENSP00000419574:R304W	ENSP00000381097:R743W	R	+	1	2	EPHB1	136403102	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.213000	0.51153	2.755000	0.94549	0.563000	0.77884	CGG		0.547	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		T	134920412	C	T	134920412	3	4	61	1	0	0	0	0	1	0	0	0	5187	875	31	1	2273	1	EPHB1	3	134920412	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	249658	134920412	63102018	2792	10777										
PPP2R3A	5523	broad.mit.edu	37	chr3	135797264	135797264	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggagtggaaaaattacttCgacagagataagaaaaagca	10	4	0	2	rs147986508		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:135797264C>T	ENST00000264977.3	+	7	3217	c.2600C>T	c.(2599-2601)tCg>tTg	p.S867L	PPP2R3A_ENST00000334546.2_Missense_Mutation_p.S246L|PPP2R3A_ENST00000490467.1_Missense_Mutation_p.S131L|PPP2R3A_ENST00000492624.2_Missense_Mutation_p.S131L	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	867					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)	p.S867L(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAAATTACTTCGACAGAGATA	0.284													C|||	1	0.000199681	8e-04	0	5008	,	,		17857	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	LEU/SER,LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	66	66	66		392,2600,737	3.8	1	3	dbSNP_134	66	0,8596		0,0,4298	no	missense,missense,missense	PPP2R3A	NM_001190447.1,NM_002718.4,NM_181897.2	145,145,145	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign	131/415,867/1151,246/530	135797264	1,13001	2203	4298	6501	137279954	SO:0001583	missense	5523			L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.2600C>T	3.37:g.135797264C>T	ENSP00000264977:p.Ser867Leu		137279954	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	C	5.382	0.255734	0.10185	2.27E-4	0.0	ENSG00000073711	ENST00000264977;ENST00000490467;ENST00000334546;ENST00000492624	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	4.78	3.82	0.43975	.	0.294609	0.32055	N	0.006658	T	0.03220	0.0094	N	0.00067	-2.295	0.36282	D	0.855817	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.41305	-0.9516	10	0.02654	T	1	.	4.3672	0.11230	0.0:0.7253:0.0:0.2747	.	246;867	Q06190-2;Q06190	.;P2R3A_HUMAN	L	867;131;246;131	ENSP00000264977:S867L;ENSP00000419344:S131L;ENSP00000334748:S246L;ENSP00000417231:S131L	ENSP00000264977:S867L	S	+	2	0	PPP2R3A	137279954	0.823000	0.29233	0.959000	0.39883	0.949000	0.60115	2.437000	0.44828	2.480000	0.83734	0.655000	0.94253	TCG		0.284	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		T	135797264	C	T	135797264	3	4	61	1	0	0	0	0	1	0	0	0	12422	893	31	1	2758	1	PPP2R3A	3	135797264	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	876852	135797264	62225166	2793	10778										
MSL2	55167	broad.mit.edu	37	chr3	135870933	135870933	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacactcagtaacagagagtCtccaggttttatatcttcac	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:135870933C>A	ENST00000309993.2	-	2	1522	c.790G>T	c.(790-792)Gac>Tac	p.D264Y	MSL2_ENST00000434835.2_Missense_Mutation_p.D190Y	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	264					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D264Y(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						AACAGAGAGTCTCCAGGTTTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	65	63					3																	135870933		2203	4300	6503	137353623	SO:0001583	missense	55167			AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"RING-type (C3HC4) zinc fingers"	25544	protein-coding gene	gene with protein product	"male-specific lethal-2 homolog (Drosophila)"	614802	"ring finger protein 184", "male-specific lethal 2-like 1 (Drosophila)"	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.790G>T	3.37:g.135870933C>A	ENSP00000311827:p.Asp264Tyr		137353623	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	37	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710123	0.48517	.	.	ENSG00000174579	ENST00000309993;ENST00000434835	.	.	.	6.07	6.07	0.98685	.	0.063176	0.64402	D	0.000008	T	0.52948	0.1766	N	0.19112	0.55	0.39731	D	0.971614	P	0.42620	0.785	P	0.44990	0.466	T	0.57613	-0.7781	9	0.62326	D	0.03	-8.1314	19.6475	0.95784	0.0:1.0:0.0:0.0	.	264	Q9HCI7	MSL2_HUMAN	Y	264;190	.	ENSP00000311827:D264Y	D	-	1	0	MSL2	137353623	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.370000	0.52372	2.885000	0.99019	0.655000	0.94253	GAC		0.463	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		A	135870933	C	A	135870933	3	1	61	1	0	0	0	0	1	0	0	0	9908	913	32	2	947	2	MSL2	3	135870933	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73669	135870933	62151497	2794	10779										
STAG1	10274	broad.mit.edu	37	chr3	136078054	136078054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaatgtaagggcaaagcGacgtgccagttctttaatgc	10	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:136078054G>A	ENST00000383202.2	-	27	3128	c.2872C>T	c.(2872-2874)Cgc>Tgc	p.R958C	STAG1_ENST00000236698.5_Missense_Mutation_p.R958C|STAG1_ENST00000536929.1_Missense_Mutation_p.R542C|STAG1_ENST00000434713.2_Missense_Mutation_p.R698C	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	958					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R958C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AGGGCAAAGCGACGTGCCAGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	119	123					3																	136078054		2203	4300	6503	137560744	SO:0001583	missense	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2872C>T	3.37:g.136078054G>A	ENSP00000372689:p.Arg958Cys		137560744	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218062	0.79352	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.57107	1.0;1.06;0.42;0.56	5.81	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.75895	0.3912	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.80286	-0.1446	10	0.87932	D	0	.	14.1034	0.65072	0.0:0.0:0.7429:0.2571	.	958;958	Q6P275;Q8WVM7	.;STAG1_HUMAN	C	958;958;698;542	ENSP00000372689:R958C;ENSP00000236698:R958C;ENSP00000404396:R698C;ENSP00000445787:R542C	ENSP00000236698:R958C	R	-	1	0	STAG1	137560744	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.005000	0.57075	2.736000	0.93811	0.655000	0.94253	CGC		0.413	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		A	136078054	G	A	136078054	3	1	61	1	0	0	0	0	1	0	0	0	15281	1058	37	1	936	1	STAG1	3	136078054	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207121	136078054	61944376	2795	10780										
STAG1	10274	broad.mit.edu	37	chr3	136117666	136117666	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacactgcagtgcttgcacGactatctgtatcaaatgaaa	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:136117666G>A	ENST00000383202.2	-	22	2458	c.2202C>T	c.(2200-2202)gtC>gtT	p.V734V	STAG1_ENST00000236698.5_Silent_p.V734V|STAG1_ENST00000536929.1_Silent_p.V318V|STAG1_ENST00000434713.2_Silent_p.V508V	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	734					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.V734V(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GTGCTTGCACGACTATCTGTA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	3											58	57	57					3																	136117666		2203	4300	6503	137600356	SO:0001819	synonymous_variant	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2202C>T	3.37:g.136117666G>A			137600356	O00539|Q6P275	Silent	SNP	ENST00000383202.2	37	CCDS3090.1																																																																																				0.338	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		A	136117666	G	A	136117666	2	1	61	1	0	0	0	0	0	0	0	1	15281	1045	37	1		1	STAG1	3	136117666	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39612	136117666	61904764	2796	10781										
STAG1	10274	broad.mit.edu	37	chr3	136240172	136240172	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgctatactgacactgtcGaatcaggactccaataaatt	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:136240172G>A	ENST00000383202.2	-	7	815	c.559C>T	c.(559-561)Cga>Tga	p.R187*	STAG1_ENST00000480733.1_Nonsense_Mutation_p.R187*|STAG1_ENST00000236698.5_Nonsense_Mutation_p.R187*|STAG1_ENST00000434713.2_5'UTR	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	187					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R187*(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TGACACTGTCGAATCAGGACT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											103	99	100					3																	136240172		2203	4300	6503	137722862	SO:0001587	stop_gained	10274			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.559C>T	3.37:g.136240172G>A	ENSP00000372689:p.Arg187*		137722862	O00539|Q6P275	Nonsense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	G	38	6.682511	0.97759	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000480733	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0024	0.97423	0.0:0.0:1.0:0.0	.	.	.	.	X	187	.	ENSP00000236698:R187X	R	-	1	2	STAG1	137722862	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.722000	0.93159	0.467000	0.42956	CGA		0.398	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		A	136240172	G	A	136240172	4	1	61	1	0	0	0	0	0	1	0	0	15281	1066	37	1	3329	1	STAG1	3	136240172	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122506	136240172	61782258	2797	10782										
TMEM22	80723	broad.mit.edu	37	chr3	136574290	136574290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatatgtgtctgttctactGcagcattcttaggagtttat	8	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:136574290G>A	ENST00000446465.2	+	2	1616	c.988G>A	c.(988-990)Gca>Aca	p.A330T	SLC35G2_ENST00000393079.3_Missense_Mutation_p.A330T|RP11-85F14.5_ENST00000470236.1_RNA|RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000474250.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2									p.A330T(1)									CTGTTCTACTGCAGCATTCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											273	265	268					3																	136574290		2203	4300	6503	138056980	SO:0001583	missense	80723			BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"Solute carriers"	28480	protein-coding gene	gene with protein product			"transmembrane protein 22"	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.988G>A	3.37:g.136574290G>A	ENSP00000400839:p.Ala330Thr		138056980		Missense_Mutation	SNP	ENST00000446465.2	37	CCDS3091.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382664	0.61845	.	.	ENSG00000168917	ENST00000446465;ENST00000393079	T;T	0.52526	0.66;0.66	5.93	5.93	0.95920	Drug/metabolite transporter (1);	0.389157	0.28533	N	0.015015	T	0.41119	0.1145	N	0.22421	0.69	0.51767	D	0.999934	B	0.18013	0.025	B	0.27170	0.077	T	0.16070	-1.0415	10	0.45353	T	0.12	.	18.8972	0.92429	0.0:0.0:1.0:0.0	.	330	Q8TBE7	TMM22_HUMAN	T	330	ENSP00000400839:A330T;ENSP00000376794:A330T	ENSP00000376794:A330T	A	+	1	0	TMEM22	138056980	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.371000	0.73119	2.818000	0.97014	0.591000	0.81541	GCA		0.393	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		A	136574290	G	A	136574290	3	1	61	1	0	0	0	0	1	0	0	0	16182	1319	46	3	990	3	TMEM22	3	136574290	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334118	136574290	61448140	2798	10783										
NCK1	4690	broad.mit.edu	37	chr3	136664729	136664729	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtgggttctctgtcagaGaaattagcagcagtcgtcaa	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:136664729G>T	ENST00000481752.1	+	3	695	c.531G>T	c.(529-531)gaG>gaT	p.E177D	NCK1_ENST00000469404.1_Missense_Mutation_p.E113D|NCK1_ENST00000288986.2_Missense_Mutation_p.E177D			P16333	NCK1_HUMAN	NCK adaptor protein 1	177					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)	p.E177D(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						CTCTGTCAGAGAAATTAGCAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											207	202	204					3																	136664729		2203	4300	6503	138147419	SO:0001583	missense	4690			X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"SH2 domain containing"	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.531G>T	3.37:g.136664729G>T	ENSP00000417273:p.Glu177Asp		138147419	B7Z751|D3DNE3	Missense_Mutation	SNP	ENST00000481752.1	37	CCDS3092.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802648	0.31869	.	.	ENSG00000158092	ENST00000288986;ENST00000481752;ENST00000469404	T;T;T	0.68765	-0.32;-0.32;-0.35	6.16	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.49949	0.1587	L	0.31294	0.92	0.49389	D	0.99978	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.29882	-0.9997	10	0.19590	T	0.45	-8.8771	9.7147	0.40268	0.2226:0.0:0.7774:0.0	.	113;177	B7Z751;P16333	.;NCK1_HUMAN	D	177;177;113	ENSP00000288986:E177D;ENSP00000417273:E177D;ENSP00000419631:E113D	ENSP00000288986:E177D	E	+	3	2	NCK1	138147419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.700000	0.54786	0.496000	0.27904	0.650000	0.86243	GAG		0.438	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153		T	136664729	G	T	136664729	3	4	61	1	0	0	0	0	1	0	0	0	10250	933	33	2	537	2	NCK1	3	136664729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90439	136664729	61357701	2799	10784										
DZIP1L	199221	broad.mit.edu	37	chr3	137811281	137811281	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcatcccaaaataattTttttagtttatctatttccc	1	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:137811281T>G	ENST00000327532.2	-	5	1176	c.814A>C	c.(814-816)Aaa>Caa	p.K272Q	DZIP1L_ENST00000488595.1_5'UTR|DZIP1L_ENST00000469243.1_Missense_Mutation_p.K272Q	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	272					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)	p.K272Q(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CAAAATAATTTTTTTAGTTTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	123	121					3																	137811281		2203	4298	6501	139293971	SO:0001583	missense	199221			AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.814A>C	3.37:g.137811281T>G	ENSP00000332148:p.Lys272Gln		139293971	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.189503	0.00302	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.40756	1.02;1.02	5.56	0.603	0.17541	.	0.405930	0.23688	N	0.045542	T	0.20414	0.0491	N	0.04636	-0.2	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.13282	-1.0515	10	0.18276	T	0.48	-1.8536	15.7426	0.77914	0.0:0.0:0.7845:0.2155	.	272;272	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	Q	272	ENSP00000332148:K272Q;ENSP00000419486:K272Q	ENSP00000332148:K272Q	K	-	1	0	DZIP1L	139293971	0.997000	0.39634	0.032000	0.17829	0.014000	0.08584	0.878000	0.28126	0.086000	0.17137	0.528000	0.53228	AAA		0.333	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		G	137811281	T	G	137811281	3	3	61	1	0	0	0	0	1	0	0	0	4875	1850	64	4	1546	4	DZIP1L	3	137811281	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1146552	137811281	60211149	2800	10785										
ARMC8	25852	broad.mit.edu	37	chr3	137983011	137983011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatctgtgcagcagcttcGaaccagtttccaggatcatg	10	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:137983011G>A	ENST00000469044.1	+	14	1527	c.1256G>A	c.(1255-1257)cGa>cAa	p.R419Q	ARMC8_ENST00000538260.1_Missense_Mutation_p.R388Q|NME9_ENST00000536478.1_Intron|ARMC8_ENST00000461822.1_Missense_Mutation_p.R352Q|NME9_ENST00000383180.2_Intron|NME9_ENST00000341790.5_Intron|ARMC8_ENST00000481646.1_Missense_Mutation_p.R405Q|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000485396.1_Missense_Mutation_p.R346Q|ARMC8_ENST00000491704.1_Missense_Mutation_p.R377Q|ARMC8_ENST00000393058.3_Missense_Mutation_p.R409Q|NME9_ENST00000317876.4_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	419								p.R405Q(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						CAGCAGCTTCGAACCAGTTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	101	105					3																	137983011		1881	4115	5996	139465701	SO:0001583	missense	25852				CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1256G>A	3.37:g.137983011G>A	ENSP00000419413:p.Arg419Gln		139465701	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.326414	0.95708	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461822;ENST00000485396;ENST00000538260;ENST00000393058;ENST00000463485;ENST00000539459	T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;1.33;1.33;1.33;-0.15;1.54	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83285	0.5221	M	0.91249	3.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.962;1.0	D;P;D;B;D	0.72982	0.952;0.895;0.974;0.194;0.979	D	0.86229	0.1636	10	0.59425	D	0.04	-19.7815	17.1328	0.86730	0.0:0.0:1.0:0.0	.	346;352;388;419;405	B7Z637;B7Z441;F5GWK4;Q8IUR7;Q8IUR7-2	.;.;.;ARMC8_HUMAN;.	Q	405;419;377;352;346;388;409;313;276	ENSP00000420333:R405Q;ENSP00000419413:R419Q;ENSP00000417304:R377Q;ENSP00000420706:R352Q;ENSP00000417049:R346Q;ENSP00000441592:R388Q;ENSP00000376778:R409Q;ENSP00000417403:R313Q	ENSP00000376778:R409Q	R	+	2	0	ARMC8	139465701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.230000	0.95299	2.644000	0.89710	0.561000	0.74099	CGA		0.388	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		A	137983011	G	A	137983011	3	1	61	1	0	0	0	0	1	0	0	0	958	1058	37	1	1334	1	ARMC8	3	137983011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171730	137983011	60039419	2801	10786										
TXNDC6	347736	broad.mit.edu	37	chr3	138022444	138022444	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtcccggcttccatggAcggcattgaagggcatttct	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:138022444A>G	ENST00000333911.3	-	10	860	c.833T>C	c.(832-834)gTc>gCc	p.V278A	NME9_ENST00000536478.1_Missense_Mutation_p.V217A|NME9_ENST00000383180.2_Missense_Mutation_p.V217A|NME9_ENST00000341790.5_Missense_Mutation_p.V215A|NME9_ENST00000484930.1_Missense_Mutation_p.V215A|NME9_ENST00000317876.4_Missense_Mutation_p.V217A			Q86XW9	TXND6_HUMAN	NME/NM23 family member 9	278	NDK.				cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)	p.V217A(1)									GCTTCCATGGACGGCATTGAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	73	75					3																	138022444		2203	4300	6503	139505134	SO:0001583	missense	347736			AF196568	CCDS3099.1	3q22.3	2012-05-18	2012-05-18	2011-08-24	ENSG00000181322	ENSG00000181322			21343	protein-coding gene	gene with protein product			"thioredoxin domain containing 6", "NME gene family member 9", "NME family member 9"	TXNDC6		12569107, 19852809	Standard	NM_178130		Approved	TXL-2, NM23-H9	uc003ese.1	Q86XW9	OTTHUMG00000159823	ENST00000333911.3:c.833T>C	3.37:g.138022444A>G	ENSP00000335444:p.Val278Ala		139505134	Q7Z4A8|Q8N1V7	Missense_Mutation	SNP	ENST00000333911.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.73|16.73	3.202831|3.202831	0.58234|0.58234	.|.	.|.	ENSG00000181322|ENSG00000181322	ENST00000474690|ENST00000383180;ENST00000317876;ENST00000484930;ENST00000341790;ENST00000536478;ENST00000333911	.|T;T;T;T;T;T	.|0.60299	.|0.2;0.2;0.2;0.2;0.2;0.2	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.298215	.|0.31648	.|N	.|0.007290	T|T	0.61999|0.61999	0.2392|0.2392	.|.	.|.	.|.	0.40062|0.40062	D|D	0.975916|0.975916	.|B;P;P	.|0.44090	.|0.374;0.826;0.604	.|B;P;B	.|0.47603	.|0.204;0.551;0.234	T|T	0.65282|0.65282	-0.6206|-0.6206	4|9	.|0.49607	.|T	.|0.09	-16.4592|-16.4592	13.9736|13.9736	0.64257|0.64257	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|215;278;217	.|Q86XW9-3;Q86XW9;Q86XW9-2	.|.;TXND6_HUMAN;.	P|A	157|217;217;215;215;217;278	.|ENSP00000372667:V217A;ENSP00000321929:V217A;ENSP00000419882:V215A;ENSP00000341084:V215A;ENSP00000440143:V217A;ENSP00000335444:V278A	.|ENSP00000321929:V217A	S|V	-|-	1|2	0|0	TXNDC6|TXNDC6	139505134|139505134	1.000000|1.000000	0.71417|0.71417	0.697000|0.697000	0.30258|0.30258	0.450000|0.450000	0.32258|0.32258	6.761000|6.761000	0.74945|0.74945	2.188000|2.188000	0.69820|0.69820	0.459000|0.459000	0.35465|0.35465	TCC|GTC		0.443	NME9-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357583.1	NM_178130		G	138022444	A	G	138022444	3	3	61	1	0	0	0	0	1	0	0	0	16840	275	10	4	149	4	TXNDC6	3	138022444	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	39433	138022444	59999986	2802	10787										
CEP70	80321	broad.mit.edu	37	chr3	138251381	138251381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgaatttttctaatttTagattcatagtaatcaatta	4	3	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:138251381T>C	ENST00000264982.3	-	8	933	c.667A>G	c.(667-669)Aaa>Gaa	p.K223E	CEP70_ENST00000484888.1_Missense_Mutation_p.K223E|CEP70_ENST00000489254.1_Missense_Mutation_p.K71E|CEP70_ENST00000481834.1_Missense_Mutation_p.K223E|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000542237.1_Missense_Mutation_p.K203E	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	223					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.K223E(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						TTTCTAATTTTAGATTCATAG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	3											41	42	42					3																	138251381		2193	4266	6459	139734071	SO:0001583	missense	80321			AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.667A>G	3.37:g.138251381T>C	ENSP00000264982:p.Lys223Glu		139734071	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	37	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.475671	0.63737	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419	T;T;T;T;T;T;T;T	0.46451	1.47;1.48;0.9;1.47;1.47;1.46;0.87;0.87	4.51	4.51	0.55191	.	0.279639	0.33959	N	0.004384	T	0.52980	0.1768	L	0.54323	1.7	0.31050	N	0.715273	D;D;D;D	0.67145	0.996;0.996;0.973;0.996	D;D;P;D	0.77557	0.986;0.981;0.64;0.99	T	0.51919	-0.8644	10	0.15066	T	0.55	-23.4854	10.141	0.42736	0.0:0.0:0.0:1.0	.	71;203;223;223	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	E	223;203;71;223;205;223;202;203	ENSP00000264982:K223E;ENSP00000444128:K203E;ENSP00000417821:K71E;ENSP00000419231:K223E;ENSP00000419833:K205E;ENSP00000417465:K223E;ENSP00000418131:K202E;ENSP00000417819:K203E	ENSP00000264982:K223E	K	-	1	0	CEP70	139734071	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	2.502000	0.45398	1.873000	0.54277	0.460000	0.39030	AAA		0.303	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		C	138251381	T	C	138251381	3	2	61	1	0	0	0	0	1	0	0	0	3265	1763	61	4	1170	4	CEP70	3	138251381	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	228937	138251381	59771049	2803	10788										
PIK3CB	5291	broad.mit.edu	37	chr3	138403619	138403619	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttgattaaactatttaaAgtttttaacttattgagtgc	6	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:138403619A>C	ENST00000477593.1	-	16	2236	c.2163T>G	c.(2161-2163)acT>acG	p.T721T	PIK3CB_ENST00000544716.1_Silent_p.T167T|PIK3CB_ENST00000289153.2_Silent_p.T721T			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	721					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.T721T(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	AACTATTTAAAGTTTTTAACT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	3											73	73	73					3																	138403619		2203	4300	6503	139886309	SO:0001819	synonymous_variant	5291				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2163T>G	3.37:g.138403619A>C			139886309	D3DNF0|Q24JU2	Silent	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	A	9.577	1.122641	0.20877	.	.	ENSG00000051382	ENST00000493568	.	.	.	5.78	-0.0718	0.13742	.	.	.	.	.	T	0.40791	0.1131	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27157	-1.0082	4	.	.	.	-18.1991	1.6301	0.02731	0.4127:0.226:0.2493:0.112	.	.	.	.	R	353	.	.	L	-	2	0	PIK3CB	139886309	0.875000	0.30112	1.000000	0.80357	0.988000	0.76386	0.004000	0.13106	0.432000	0.26286	0.482000	0.46254	CTT		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			C	138403619	A	C	138403619	2	2	61	1	0	0	0	0	0	0	0	1	11945	59	3	4		4	PIK3CB	3	138403619	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	152238	138403619	59618811	2804	10789										
COPB2	9276	broad.mit.edu	37	chr3	139090601	139090601	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatgcaaactcctgagcaGatccaaagctcttgtttctc	6	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:139090601G>A	ENST00000333188.5	-	10	1350	c.1169C>T	c.(1168-1170)tCt>tTt	p.S390F	COPB2_ENST00000507777.1_Missense_Mutation_p.S361F	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	390					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.S390F(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						CTCCTGAGCAGATCCAAAGCT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											181	158	166					3																	139090601		2203	4300	6503	140573291	SO:0001583	missense	9276			BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.1169C>T	3.37:g.139090601G>A	ENSP00000329419:p.Ser390Phe		140573291	B4DZI8	Missense_Mutation	SNP	ENST00000333188.5	37	CCDS3108.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283338	0.80803	.	.	ENSG00000184432	ENST00000333188;ENST00000507777;ENST00000512309	T;D;D	0.90676	2.24;-2.71;-2.71	5.68	5.68	0.88126	WD40 repeat-like-containing domain (1);Coatomer, WD associated region (1);	0.000000	0.85682	D	0.000000	D	0.95893	0.8663	M	0.91818	3.245	0.80722	D	1	P	0.44816	0.844	P	0.55667	0.781	D	0.96039	0.9023	10	0.66056	D	0.02	-10.7881	19.7834	0.96426	0.0:0.0:1.0:0.0	.	390	P35606	COPB2_HUMAN	F	390;361;13	ENSP00000329419:S390F;ENSP00000422295:S361F;ENSP00000422917:S13F	ENSP00000329419:S390F	S	-	2	0	COPB2	140573291	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.790000	0.99075	2.682000	0.91365	0.561000	0.74099	TCT		0.473	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		A	139090601	G	A	139090601	3	1	61	1	0	0	0	0	1	0	0	0	3735	942	33	3	1603	3	COPB2	3	139090601	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	686982	139090601	58931829	2805	10790										
CLSTN2	64084	broad.mit.edu	37	chr3	140185522	140185522	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttgcggaaggacttCgaccaggctgacacctttcg	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:140185522C>T	ENST00000458420.3	+	8	1483	c.1293C>T	c.(1291-1293)ttC>ttT	p.F431F		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	431					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.F431F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GGAAGGACTTCGACCAGGCTG	0.552										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - coding silent(1)	large_intestine(1)	3											76	69	72					3																	140185522		2203	4300	6503	141668212	SO:0001819	synonymous_variant	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1293C>T	3.37:g.140185522C>T			141668212	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																				0.552	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140185522	C	T	140185522	2	4	61	1	0	0	0	0	0	0	0	1	3568	883	31	1		1	CLSTN2	3	140185522	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1094921	140185522	57836908	2806	10791										
CLSTN2	64084	broad.mit.edu	37	chr3	140275467	140275467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccaggcagttcccaacggCgggtgtgcggcgcctcaaag	14	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:140275467C>T	ENST00000458420.3	+	11	1977	c.1787C>T	c.(1786-1788)gCg>gTg	p.A596V		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	596					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.A596V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TTCCCAACGGCGGGTGTGCGG	0.577										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)	large_intestine(1)	3											103	92	96					3																	140275467		2203	4300	6503	141758157	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1787C>T	3.37:g.140275467C>T	ENSP00000402460:p.Ala596Val		141758157	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023842	0.54683	.	.	ENSG00000158258	ENST00000458420	T	0.30182	1.54	5.39	4.51	0.55191	.	0.047031	0.85682	D	0.000000	T	0.25121	0.0610	L	0.57536	1.79	0.42780	D	0.993867	P	0.44659	0.84	B	0.31390	0.129	T	0.08806	-1.0704	9	.	.	.	-31.2745	12.5874	0.56424	0.0:0.9177:0.0:0.0823	.	596	Q9H4D0	CSTN2_HUMAN	V	596	ENSP00000402460:A596V	.	A	+	2	0	CLSTN2	141758157	0.998000	0.40836	0.147000	0.22382	0.491000	0.33493	4.936000	0.63506	1.405000	0.46838	0.563000	0.77884	GCG		0.577	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140275467	C	T	140275467	3	4	61	1	0	0	0	0	1	0	0	0	3568	768	27	1	1829	1	CLSTN2	3	140275467	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89945	140275467	57746963	2807	10792										
TRIM42	287015	broad.mit.edu	37	chr3	140406786	140406786	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttacaaccatgaaagtgaAcgagatggatggtctgatcg	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:140406786A>T	ENST00000286349.3	+	3	1453	c.1262A>T	c.(1261-1263)aAc>aTc	p.N421I		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	421						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.N421S(1)|p.N421I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATGAAAGTGAACGAGATGGAT	0.478																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	3											95	89	91					3																	140406786		2203	4300	6503	141889476	SO:0001583	missense	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1262A>T	3.37:g.140406786A>T	ENSP00000286349:p.Asn421Ile		141889476	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	A	7.103	0.574417	0.13623	.	.	ENSG00000155890	ENST00000286349	T	0.38077	1.16	5.33	4.1	0.47936	.	0.412269	0.22548	N	0.058638	T	0.16896	0.0406	N	0.08118	0	0.09310	N	1	P	0.36438	0.553	B	0.32465	0.146	T	0.09314	-1.0680	10	0.38643	T	0.18	-9.4073	8.8646	0.35278	0.8111:0.1889:0.0:0.0	.	421	Q8IWZ5	TRI42_HUMAN	I	421	ENSP00000286349:N421I	ENSP00000286349:N421I	N	+	2	0	TRIM42	141889476	0.000000	0.05858	0.394000	0.26270	0.371000	0.29859	0.591000	0.23969	2.162000	0.67917	0.454000	0.30748	AAC		0.478	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140406786	A	T	140406786	3	4	61	1	0	0	0	0	1	0	0	0	16557	43	2	5	1272	5	TRIM42	3	140406786	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	131319	140406786	57615644	2808	10793										
ACPL2	92370	broad.mit.edu	37	chr3	141011760	141011760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcactctgtcaccagttCtcagtgccttgggcctttca	8	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:141011760C>A	ENST00000286353.4	+	6	1293	c.1156C>A	c.(1156-1158)Ctc>Atc	p.L386I	ACPL2_ENST00000502783.1_Missense_Mutation_p.L348I|ACPL2_ENST00000393010.2_Missense_Mutation_p.L386I|RP11-438D8.2_ENST00000507698.1_RNA|ACPL2_ENST00000504264.1_Missense_Mutation_p.L369I|ACPL2_ENST00000393007.1_Missense_Mutation_p.L370I|ACPL2_ENST00000508812.1_Missense_Mutation_p.L377I	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		386						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)	p.L386I(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						GTCACCAGTTCTCAGTGCCTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											176	145	156					3																	141011760		2203	4300	6503	142494450	SO:0001583	missense	92370																														ENST00000286353.4:c.1156C>A	3.37:g.141011760C>A	ENSP00000286353:p.Leu386Ile		142494450	D3DNF5|Q49AJ2|W0TR04	Missense_Mutation	SNP	ENST00000286353.4	37	CCDS3116.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343420	0.61073	.	.	ENSG00000155893	ENST00000286353;ENST00000502783;ENST00000393010;ENST00000504264;ENST00000508812;ENST00000393007;ENST00000332228	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.57373	0.2049	M	0.71296	2.17	0.58432	D	0.999999	D;D	0.67145	0.957;0.996	P;P	0.60886	0.86;0.88	T	0.59762	-0.7393	10	0.56958	D	0.05	.	10.3176	0.43747	0.0:0.911:0.0:0.089	.	369;386	B7Z3R9;Q8TE99	.;ACPL2_HUMAN	I	386;348;386;369;377;370;194	ENSP00000286353:L386I;ENSP00000422558:L348I;ENSP00000376733:L386I;ENSP00000426877:L369I;ENSP00000422901:L377I;ENSP00000376731:L370I	ENSP00000286353:L386I	L	+	1	0	ACPL2	142494450	1.000000	0.71417	0.952000	0.39060	0.997000	0.91878	5.757000	0.68766	2.570000	0.86706	0.655000	0.94253	CTC		0.537	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2			A	141011760	C	A	141011760	3	1	61	1	0	0	0	0	1	0	0	0	166	913	32	2	1174	2	ACPL2	3	141011760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	604974	141011760	57010670	2809	10794										
RASA2	5922	broad.mit.edu	37	chr3	141295886	141295886	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgagcagctttgtatttCttcgtttctttgctgtagcc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:141295886C>A	ENST00000452898.1	+	15	1563	c.1528C>A	c.(1528-1530)Ctt>Att	p.L510I	RASA2_ENST00000286364.3_Missense_Mutation_p.L510I	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	510	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.L510I(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						CTTTGTATTTCTTCGTTTCTT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	3											224	211	215					3																	141295886		2203	4300	6503	142778576	SO:0001583	missense	5922			AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"Pleckstrin homology (PH) domain containing"	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1528C>A	3.37:g.141295886C>A	ENSP00000391677:p.Leu510Ile		142778576	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	C	33	5.229802	0.95173	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	T;T	0.27890	1.64;1.64	5.85	5.85	0.93711	Ras GTPase-activating protein, conserved site (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.93898	3.47	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.76369	-0.2984	10	0.87932	D	0	.	20.1736	0.98170	0.0:1.0:0.0:0.0	.	102;510;510;510	E7EU60;A8K7K1;G3V0F9;Q15283	.;.;.;RASA2_HUMAN	I	510;510;102	ENSP00000286364:L510I;ENSP00000391677:L510I	ENSP00000286364:L510I	L	+	1	0	RASA2	142778576	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.372000	0.79612	2.767000	0.95098	0.557000	0.71058	CTT		0.363	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506		A	141295886	C	A	141295886	3	1	61	1	0	0	0	0	1	0	0	0	13098	913	32	2	1586	2	RASA2	3	141295886	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	284126	141295886	56726544	2810	10795										
GRK7	131890	broad.mit.edu	37	chr3	141497325	141497325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagcagcagcccatcggtCgccgcctcttccgtgacttc	11	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:141497325C>T	ENST00000264952.2	+	1	336	c.199C>T	c.(199-201)Cgc>Tgc	p.R67C		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	67	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)	p.R67C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GCCCATCGGTCGCCGCCTCTT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	3											22	21	21					3																	141497325		2196	4280	6476	142980015	SO:0001583	missense	131890				CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.199C>T	3.37:g.141497325C>T	ENSP00000264952:p.Arg67Cys		142980015		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.805066	0.50315	.	.	ENSG00000114124	ENST00000264952	T	0.02345	4.33	4.5	4.5	0.54988	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.227955	0.40302	N	0.001125	T	0.11110	0.0271	M	0.62723	1.935	0.42940	D	0.994342	D	0.89917	1.0	D	0.65773	0.938	T	0.00636	-1.1633	10	0.87932	D	0	-6.7824	12.3285	0.55024	0.2156:0.7844:0.0:0.0	.	67	Q8WTQ7	GRK7_HUMAN	C	67	ENSP00000264952:R67C	ENSP00000264952:R67C	R	+	1	0	GRK7	142980015	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	3.942000	0.56614	2.033000	0.60031	0.655000	0.94253	CGC		0.677	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		T	141497325	C	T	141497325	3	4	61	1	0	0	0	0	1	0	0	0	6815	884	31	1	201	1	GRK7	3	141497325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201439	141497325	56525105	2811	10796										
ATR	545	broad.mit.edu	37	chr3	142215936	142215936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctgggtcatttctagtCgagctacccagtttagagaa	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142215936C>T	ENST00000350721.4	-	33	5778	c.5657G>A	c.(5656-5658)cGa>cAa	p.R1886Q	ATR_ENST00000383101.3_Missense_Mutation_p.R1822Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1886	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R1886Q(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATTTCTAGTCGAGCTACCCA	0.448								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	3											84	91	89					3																	142215936		2203	4300	6503	143698626	SO:0001583	missense	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5657G>A	3.37:g.142215936C>T	ENSP00000343741:p.Arg1886Gln		143698626	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.944702	0.92593	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	D;D	0.83506	-1.73;-1.73	5.39	4.51	0.55191	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.000000	0.85682	D	0.000000	D	0.91616	0.7351	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	D	0.92705	0.6178	10	0.59425	D	0.04	-9.1816	15.4294	0.75081	0.14:0.86:0.0:0.0	.	1886	Q13535	ATR_HUMAN	Q	1886;1822	ENSP00000343741:R1886Q;ENSP00000372581:R1822Q	ENSP00000343741:R1886Q	R	-	2	0	ATR	143698626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.052000	0.71080	1.254000	0.44035	0.655000	0.94253	CGA		0.448	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142215936	C	T	142215936	3	4	61	1	0	0	0	0	1	0	0	0	1205	884	31	1	2337	1	ATR	3	142215936	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	718611	142215936	55806494	2812	10797										
ATR	545	broad.mit.edu	37	chr3	142218533	142218533	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagctgcttccactctgtaCgtgtttaattcatctgtcca	6	12	3	0	rs146463402		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142218533C>T	ENST00000350721.4	-	31	5437	c.5316G>A	c.(5314-5316)acG>acA	p.T1772T	ATR_ENST00000383101.3_Silent_p.T1708T	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1772	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T1772T(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CCACTCTGTACGTGTTTAATT	0.338								Other conserved DNA damage response genes					C|||	1	0.000199681	8e-04	0	5008	,	,		15431	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						C		1,4405	2.1+/-5.4	0,1,2202	132	129	130		5316	0.9	1	3	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous	ATR	NM_001184.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1772/2645	142218533	1,13005	2203	4300	6503	143701223	SO:0001819	synonymous_variant	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5316G>A	3.37:g.142218533C>T			143701223	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																				0.338	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142218533	C	T	142218533	2	4	61	1	0	0	0	0	0	0	0	1	1205	523	19	1		1	ATR	3	142218533	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2597	142218533	55803897	2813	10798										
ATR	545	broad.mit.edu	37	chr3	142242849	142242849	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttaccacaaatgtaaaatCttttccttgagtttcagttg	5	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142242849C>A	ENST00000350721.4	-	22	4259	c.4138G>T	c.(4138-4140)Gat>Tat	p.D1380Y	ATR_ENST00000383101.3_Missense_Mutation_p.D1316Y	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1380					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D1380Y(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AATGTAAAATCTTTTCCTTGA	0.373								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	3											99	95	96					3																	142242849		2203	4300	6503	143725539	SO:0001583	missense	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4138G>T	3.37:g.142242849C>A	ENSP00000343741:p.Asp1380Tyr		143725539	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	13.70	2.314855	0.40996	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.03663	3.85;3.86	5.39	5.39	0.77823	Armadillo-like helical (1);	0.751958	0.12891	N	0.430604	T	0.05410	0.0143	L	0.42245	1.32	0.38189	D	0.939857	B	0.32731	0.382	B	0.26310	0.068	T	0.45190	-0.9278	10	0.49607	T	0.09	-21.2478	16.5018	0.84259	0.0:0.8693:0.1307:0.0	.	1380	Q13535	ATR_HUMAN	Y	1380;1316	ENSP00000343741:D1380Y;ENSP00000372581:D1316Y	ENSP00000343741:D1380Y	D	-	1	0	ATR	143725539	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	1.504000	0.35726	2.661000	0.90470	0.655000	0.94253	GAT		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142242849	C	A	142242849	3	1	61	1	0	0	0	0	1	0	0	0	1205	913	32	2	3900	2	ATR	3	142242849	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24316	142242849	55779581	2814	10799										
ATR	545	broad.mit.edu	37	chr3	142268419	142268419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttattaaaatctctctacGattgacatttaattgttttc	4	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142268419G>A	ENST00000350721.4	-	15	3194	c.3073C>T	c.(3073-3075)Cgt>Tgt	p.R1025C	ATR_ENST00000383101.3_Missense_Mutation_p.R961C	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1025					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R1025C(2)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATCTCTCTACGATTGACATTT	0.363								Other conserved DNA damage response genes																																								2	Substitution - Missense(2)	large_intestine(1)|skin(1)	3											44	45	45					3																	142268419		2196	4299	6495	143751109	SO:0001583	missense	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.3073C>T	3.37:g.142268419G>A	ENSP00000343741:p.Arg1025Cys		143751109	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.540962	0.45280	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.65732	-0.17;-0.17	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.180025	0.49305	D	0.000153	T	0.50360	0.1611	L	0.27053	0.805	0.80722	D	1	B	0.27594	0.182	B	0.19148	0.024	T	0.44528	-0.9322	10	0.36615	T	0.2	-17.1135	17.7702	0.88489	0.0:0.0:1.0:0.0	.	1025	Q13535	ATR_HUMAN	C	1025;961	ENSP00000343741:R1025C;ENSP00000372581:R961C	ENSP00000343741:R1025C	R	-	1	0	ATR	143751109	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.124000	0.57924	2.635000	0.89317	0.655000	0.94253	CGT		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142268419	G	A	142268419	3	1	61	1	0	0	0	0	1	0	0	0	1205	1058	37	1	4993	1	ATR	3	142268419	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25570	142268419	55754011	2815	10800										
TRPC1	7220	broad.mit.edu	37	chr3	142521062	142521062	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaatttcttgggatgtttCttcttgttttgttttctttc	7	5	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142521062C>A	ENST00000476941.1	+	10	2119	c.1633C>A	c.(1633-1635)Ctt>Att	p.L545I	TRPC1_ENST00000273482.6_Missense_Mutation_p.L511I|RNU7-47P_ENST00000515978.1_RNA	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	545					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.L511I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						TGGGATGTTTCTTCTTGTTTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	104	104					3																	142521062		2203	4300	6503	144003752	SO:0001583	missense	7220			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1633C>A	3.37:g.142521062C>A	ENSP00000419313:p.Leu545Ile		144003752	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	37	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352392	0.82132	.	.	ENSG00000144935	ENST00000476941;ENST00000273482;ENST00000416210	D;D	0.98762	-5.12;-5.12	5.47	5.47	0.80525	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97105	0.9054	N	0.17474	0.49	0.80722	D	1	D;D;B	0.63046	0.98;0.992;0.067	P;P;B	0.57152	0.748;0.814;0.032	D	0.94452	0.7668	10	0.02654	T	1	-2.223	19.704	0.96066	0.0:1.0:0.0:0.0	.	511;545;511	A7VJS2;P48995;P48995-2	.;TRPC1_HUMAN;.	I	545;511;64	ENSP00000419313:L545I;ENSP00000273482:L511I	ENSP00000273482:L511I	L	+	1	0	TRPC1	144003752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.736000	0.84948	2.726000	0.93360	0.650000	0.86243	CTT		0.338	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		A	142521062	C	A	142521062	3	1	61	1	0	0	0	0	1	0	0	0	16618	913	32	2	1565	2	TRPC1	3	142521062	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252643	142521062	55501368	2816	10801										
PCOLCE2	26577	broad.mit.edu	37	chr3	142548549	142548549	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacccgtggttacagggaAtgtggtggtgacaggctgtt	15	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142548549A>C	ENST00000295992.3	-	6	1156	c.850T>G	c.(850-852)Ttc>Gtc	p.F284V	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	284					positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)	p.F284V(1)		NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						GTTACAGGGAATGTGGTGGTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											158	147	151					3																	142548549		2203	4300	6503	144031239	SO:0001583	missense	26577			AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.850T>G	3.37:g.142548549A>C	ENSP00000295992:p.Phe284Val		144031239	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	.	.	.	.	.	.	.	.	.	.	A	7.635	0.679654	0.14907	.	.	ENSG00000163710	ENST00000295992	T	0.18657	2.2	5.14	-10.3	0.00346	.	1.577250	0.03181	N	0.172083	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.10902	T	0.67	1.1122	14.4495	0.67374	0.2339:0.6191:0.147:0.0	.	284	Q9UKZ9	PCOC2_HUMAN	V	284	ENSP00000295992:F284V	ENSP00000295992:F284V	F	-	1	0	PCOLCE2	144031239	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-3.250000	0.00540	-1.342000	0.02222	-0.687000	0.03738	TTC		0.363	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		C	142548549	A	C	142548549	3	2	61	1	0	0	0	0	1	0	0	0	11626	101	4	4	413	4	PCOLCE2	3	142548549	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	27487	142548549	55473881	2817	10802										
PCOLCE2	26577	broad.mit.edu	37	chr3	142606597	142606597	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagactctccagtaagaaTgccaccacatgtgaaaacag	7	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142606597T>G	ENST00000295992.3	-	2	412	c.106A>C	c.(106-108)Att>Ctt	p.I36L	PCOLCE2_ENST00000461818.1_5'UTR|PCOLCE2_ENST00000485766.1_Missense_Mutation_p.I36L	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	36	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)	p.I36L(1)		NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						CCAGTAAGAATGCCACCACAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	71	71					3																	142606597		2203	4300	6503	144089287	SO:0001583	missense	26577			AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.106A>C	3.37:g.142606597T>G	ENSP00000295992:p.Ile36Leu		144089287	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.553241	0.45487	.	.	ENSG00000163710	ENST00000295992;ENST00000485766	T;T	0.17691	2.26;2.26	5.66	-0.589	0.11683	CUB (5);	0.254503	0.43579	D	0.000558	T	0.09642	0.0237	N	0.21373	0.66	0.26760	N	0.970018	B	0.22800	0.075	B	0.25759	0.063	T	0.33007	-0.9885	10	0.22109	T	0.4	-8.1091	9.2504	0.37551	0.0:0.3922:0.0:0.6078	.	36	Q9UKZ9	PCOC2_HUMAN	L	36	ENSP00000295992:I36L;ENSP00000419842:I36L	ENSP00000295992:I36L	I	-	1	0	PCOLCE2	144089287	1.000000	0.71417	0.938000	0.37757	0.948000	0.59901	1.645000	0.37238	-0.098000	0.12285	-0.250000	0.11733	ATT		0.368	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		G	142606597	T	G	142606597	3	3	61	1	0	0	0	0	1	0	0	0	11626	1464	51	4	1173	4	PCOLCE2	3	142606597	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	58048	142606597	55415833	2818	10803										
PAQR9	344838	broad.mit.edu	37	chr3	142681362	142681362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggtagaagtgcacgaagaGtgtggggttctccccacgca	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142681362G>A	ENST00000340634.3	-	1	816	c.817C>T	c.(817-819)Ctc>Ttc	p.L273F	RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	273						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L273F(1)		endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						TGCACGAAGAGTGTGGGGTTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	61	61					3																	142681362		2203	4300	6503	144164052	SO:0001583	missense	344838			AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.817C>T	3.37:g.142681362G>A	ENSP00000341564:p.Leu273Phe		144164052	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.235|8.235	0.805620|0.805620	0.16467|0.16467	.|.	.|.	ENSG00000188582|ENSG00000188582	ENST00000340634|ENST00000492509	T|T	0.27557|0.28666	1.66|1.6	5.63|5.63	4.75|4.75	0.60458|0.60458	.|.	0.178892|.	0.37304|.	N|.	0.002143|.	T|T	0.43433|0.43433	0.1247|0.1247	L|L	0.53249|0.53249	1.67|1.67	0.43564|0.43564	D|D	0.995886|0.995886	P|.	0.48230|.	0.907|.	P|.	0.55965|.	0.788|.	T|T	0.22977|0.22977	-1.0201|-1.0201	10|7	0.09843|0.37606	T|T	0.71|0.19	-47.4827|-47.4827	15.9798|15.9798	0.80097|0.80097	0.0:0.0:0.8642:0.1358|0.0:0.0:0.8642:0.1358	.|.	273|.	Q6ZVX9|.	PAQR9_HUMAN|.	F|I	273|13	ENSP00000341564:L273F|ENSP00000417945:T13I	ENSP00000341564:L273F|ENSP00000417945:T13I	L|T	-|-	1|2	0|0	PAQR9|PAQR9	144164052|144164052	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.869000|0.869000	0.49853|0.49853	5.665000|5.665000	0.68052|0.68052	1.368000|1.368000	0.46115|0.46115	0.655000|0.655000	0.94253|0.94253	CTC|ACT		0.612	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		A	142681362	G	A	142681362	3	1	61	1	0	0	0	0	1	0	0	0	11473	1029	36	3	320	3	PAQR9	3	142681362	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74765	142681362	55341068	2819	10804										
PAQR9	344838	broad.mit.edu	37	chr3	142681596	142681596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccacgtgccagcccaggcGctgctgcaagtatggagtca	13	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142681596G>A	ENST00000340634.3	-	1	582	c.583C>T	c.(583-585)Cgc>Tgc	p.R195C	RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	195						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R195C(1)		endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						CAGCCCAGGCGCTGCTGCAAG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	3											28	28	28					3																	142681596		2203	4300	6503	144164286	SO:0001583	missense	344838			AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.583C>T	3.37:g.142681596G>A	ENSP00000341564:p.Arg195Cys		144164286	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192373	0.58017	.	.	ENSG00000188582	ENST00000340634	T	0.24151	1.87	4.9	2.91	0.33838	.	0.127687	0.33834	N	0.004519	T	0.28566	0.0707	L	0.38175	1.15	0.41127	D	0.985852	D	0.55172	0.97	P	0.51266	0.664	T	0.06391	-1.0829	10	0.54805	T	0.06	-37.1054	12.3594	0.55194	0.0:0.0:0.565:0.435	.	195	Q6ZVX9	PAQR9_HUMAN	C	195	ENSP00000341564:R195C	ENSP00000341564:R195C	R	-	1	0	PAQR9	144164286	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	1.948000	0.40303	1.145000	0.42336	0.561000	0.74099	CGC		0.642	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		A	142681596	G	A	142681596	3	1	61	1	0	0	0	0	1	0	0	0	11473	1087	38	1	554	1	PAQR9	3	142681596	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	234	142681596	55340834	2820	10805										
SR140	23350	broad.mit.edu	37	chr3	142741903	142741903	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaacaaagaggattttgaGaaggtaatttaaaaaatgga	9	1	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:142741903G>A	ENST00000473835.2	+	12	1317	c.1227G>A	c.(1225-1227)gaG>gaA	p.E409E	U2SURP_ENST00000493598.2_Silent_p.E408E|U2SURP_ENST00000397933.2_Missense_Mutation_p.R15K	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	409					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E409E(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						AGGATTTTGAGAAGGTAATTT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	3											25	23	23					3																	142741903		1824	4085	5909	144224593	SO:0001819	synonymous_variant	23350			BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1227G>A	3.37:g.142741903G>A			144224593	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Silent	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.943705	0.53079	.	.	ENSG00000163714	ENST00000397933	.	.	.	5.93	5.04	0.67666	.	.	.	.	.	T	0.39809	0.1092	.	.	.	0.30131	N	0.804765	P	0.47841	0.901	B	0.39465	0.3	T	0.46735	-0.9170	7	0.72032	D	0.01	-10.3109	16.2738	0.82634	0.0:0.0:0.8663:0.1336	.	15	O15042-3	.	K	15	.	ENSP00000381027:R15K	R	+	2	0	U2SURP	144224593	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.012000	0.64017	1.465000	0.48006	0.655000	0.94253	AGA		0.373	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		A	142741903	G	A	142741903	2	1	61	1	0	0	0	0	0	0	0	1	15170	933	33	3		3	SR140	3	142741903	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60307	142741903	55280527	2821	10806										
SLC9A9	285195	broad.mit.edu	37	chr3	143214197	143214197	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggctccaagtataaaaaGagcattaaagatatgattct	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:143214197G>T	ENST00000316549.6	-	10	1391	c.1183C>A	c.(1183-1185)Ctt>Att	p.L395I		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	395					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)	p.L395I(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						AGTATAAAAAGAGCATTAAAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											92	95	94					3																	143214197		2203	4300	6503	144696887	SO:0001583	missense	285195			AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1183C>A	3.37:g.143214197G>T	ENSP00000320246:p.Leu395Ile		144696887	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.715137	0.30413	.	.	ENSG00000181804	ENST00000316549;ENST00000450105	T	0.15017	2.46	5.79	4.01	0.46588	Cation/H+ exchanger (1);	0.091087	0.42548	D	0.000692	T	0.10723	0.0262	N	0.10645	0.015	0.33510	D	0.59103	P	0.42296	0.775	B	0.43658	0.426	T	0.20538	-1.0272	10	0.21014	T	0.42	.	12.5724	0.56344	0.1937:0.0:0.8063:0.0	.	395	Q8IVB4	SL9A9_HUMAN	I	395;278	ENSP00000320246:L395I	ENSP00000320246:L395I	L	-	1	0	SLC9A9	144696887	1.000000	0.71417	0.886000	0.34754	0.643000	0.38383	2.041000	0.41213	0.395000	0.25257	-1.579000	0.00862	CTT		0.358	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		T	143214197	G	T	143214197	3	4	61	1	0	0	0	0	1	0	0	0	14758	942	33	2	782	2	SLC9A9	3	143214197	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	472294	143214197	54808233	2822	10807										
SLC9A9	285195	broad.mit.edu	37	chr3	143550976	143550976	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcagagttgatggactgAaagttagttttacacagtca	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:143550976A>G	ENST00000316549.6	-	2	471	c.263T>C	c.(262-264)tTc>tCc	p.F88S		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	88					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)	p.F88S(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						TGATGGACTGAAAGTTAGTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											168	162	164					3																	143550976		2203	4300	6503	145033666	SO:0001583	missense	285195			AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.263T>C	3.37:g.143550976A>G	ENSP00000320246:p.Phe88Ser		145033666	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	A	3.394	-0.123701	0.06795	.	.	ENSG00000181804	ENST00000316549;ENST00000474151	T;T	0.23147	1.92;1.92	5.14	5.14	0.70334	Cation/H+ exchanger (1);	0.233431	0.39083	N	0.001462	T	0.05823	0.0152	N	0.00707	-1.245	0.35638	D	0.810738	B	0.06786	0.001	B	0.06405	0.002	T	0.29397	-1.0013	10	0.08381	T	0.77	.	4.2563	0.10719	0.6751:0.2059:0.119:0.0	.	88	Q8IVB4	SL9A9_HUMAN	S	88	ENSP00000320246:F88S;ENSP00000418627:F88S	ENSP00000320246:F88S	F	-	2	0	SLC9A9	145033666	0.993000	0.37304	0.999000	0.59377	0.983000	0.72400	0.939000	0.28978	2.285000	0.76669	0.533000	0.62120	TTC		0.333	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		G	143550976	A	G	143550976	3	3	61	1	0	0	0	0	1	0	0	0	14758	246	9	4	1734	4	SLC9A9	3	143550976	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	336779	143550976	54471454	2823	10808										
C3orf58	205428	broad.mit.edu	37	chr3	143704466	143704466	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgtaaattatgttggaGaagaactgtggagttacttt	12	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:143704466G>T	ENST00000315691.3	+	2	1274	c.739G>T	c.(739-741)Gaa>Taa	p.E247*	C3orf58_ENST00000441925.2_Nonsense_Mutation_p.E9*|C3orf58_ENST00000495414.1_Nonsense_Mutation_p.E38*|C3orf58_ENST00000493396.1_Intron	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	247					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)		p.E247*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TTATGTTGGAGAAGAACTGTG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											160	156	157					3																	143704466		2203	4300	6503	145187156	SO:0001587	stop_gained	205428			AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.739G>T	3.37:g.143704466G>T	ENSP00000320081:p.Glu247*		145187156	B2RCF2|B7Z1W3	Nonsense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661188	0.88154	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000492452;ENST00000441925	.	.	.	5.24	5.24	0.73138	.	0.047774	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	18.8382	0.92171	0.0:0.0:1.0:0.0	.	.	.	.	X	247;38;53;9	.	ENSP00000320081:E247X	E	+	1	0	C3orf58	145187156	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.476000	0.97823	2.461000	0.83175	0.655000	0.94253	GAA		0.393	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		T	143704466	G	T	143704466	4	4	61	1	0	0	0	0	0	1	0	0	2242	943	33	2	779	2	C3orf58	3	143704466	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153490	143704466	54317964	2824	10809										
C3orf58	205428	broad.mit.edu	37	chr3	143704598	143704598	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcctggacgtcagctttGacaattttgcagttggtcct	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:143704598G>T	ENST00000315691.3	+	2	1406	c.871G>T	c.(871-873)Gac>Tac	p.D291Y	C3orf58_ENST00000441925.2_Missense_Mutation_p.D53Y|C3orf58_ENST00000495414.1_Missense_Mutation_p.D82Y|C3orf58_ENST00000493396.1_Intron	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	291					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)		p.D291Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CGTCAGCTTTGACAATTTTGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											159	144	149					3																	143704598		2203	4300	6503	145187288	SO:0001583	missense	205428			AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.871G>T	3.37:g.143704598G>T	ENSP00000320081:p.Asp291Tyr		145187288	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397918	0.83120	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000492452;ENST00000441925	T	0.35605	1.3	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.58722	0.2142	L	0.58428	1.81	0.80722	D	1	D;D	0.89917	0.982;1.0	P;D	0.83275	0.796;0.996	T	0.61637	-0.7022	10	0.72032	D	0.01	.	18.5536	0.91075	0.0:0.0:1.0:0.0	.	82;291	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	Y	291;82;97;53	ENSP00000320081:D291Y	ENSP00000320081:D291Y	D	+	1	0	C3orf58	145187288	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.392000	0.81423	0.563000	0.77884	GAC		0.383	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		T	143704598	G	T	143704598	3	4	61	1	0	0	0	0	1	0	0	0	2242	1290	45	2	911	2	C3orf58	3	143704598	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132	143704598	54317832	2825	10810										
C3orf58	205428	broad.mit.edu	37	chr3	143708552	143708552	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttcatgatccaccaagtGaaattgccaaagatggccgg	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:143708552G>T	ENST00000315691.3	+	3	1697	c.1162G>T	c.(1162-1164)Gaa>Taa	p.E388*	C3orf58_ENST00000441925.2_Nonsense_Mutation_p.E150*|C3orf58_ENST00000495414.1_Nonsense_Mutation_p.E179*|C3orf58_ENST00000493396.1_Intron	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	388					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)		p.E388*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCCACCAAGTGAAATTGCCAA	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											103	105	104					3																	143708552		2203	4300	6503	145191242	SO:0001587	stop_gained	205428			AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.1162G>T	3.37:g.143708552G>T	ENSP00000320081:p.Glu388*		145191242	B2RCF2|B7Z1W3	Nonsense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258030	0.80246	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000492452;ENST00000441925	.	.	.	5.91	5.91	0.95273	.	0.107783	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	388;179;194;150	.	ENSP00000320081:E388X	E	+	1	0	C3orf58	145191242	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.133000	0.77259	2.793000	0.96121	0.655000	0.94253	GAA		0.512	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		T	143708552	G	T	143708552	4	4	61	1	0	0	0	0	0	1	0	0	2242	1291	45	2	1206	2	C3orf58	3	143708552	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3954	143708552	54313878	2826	10811										
PLOD2	5352	broad.mit.edu	37	chr3	145790389	145790389	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgccgtaatgttccatttCttctaccaattcatcacagg	5	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:145790389C>A	ENST00000360060.3	-	16	1921	c.1744G>T	c.(1744-1746)Gaa>Taa	p.E582*	PLOD2_ENST00000461497.1_Nonsense_Mutation_p.E263*|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Nonsense_Mutation_p.E603*|PLOD2_ENST00000494950.1_Nonsense_Mutation_p.E548*	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	582					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)	p.E603*(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TGTTCCATTTCTTCTACCAAT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											118	106	110					3																	145790389		2203	4300	6503	147273079	SO:0001587	stop_gained	5352			U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1744G>T	3.37:g.145790389C>A	ENSP00000353170:p.Glu582*		147273079	B3KWS3|Q59ED2|Q8N170	Nonsense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	C	40	7.968004	0.98585	.	.	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000360060;ENST00000494950	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-16.0867	20.3248	0.98698	0.0:1.0:0.0:0.0	.	.	.	.	X	263;603;582;548	.	ENSP00000282903:E603X	E	-	1	0	PLOD2	147273079	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.818000	0.86416	2.818000	0.97014	0.655000	0.94253	GAA		0.368	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		A	145790389	C	A	145790389	4	1	61	1	0	0	0	0	0	1	0	0	12133	922	32	2	485	2	PLOD2	3	145790389	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2081837	145790389	52232041	2827	10812										
PLSCR4	57088	broad.mit.edu	37	chr3	145917660	145917660	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctgaagggtctctgcatTgtcatgatttctcggcccat	9	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:145917660T>G	ENST00000354952.2	-	6	804	c.564A>C	c.(562-564)acA>acC	p.T188T	PLSCR4_ENST00000383083.2_Intron|PLSCR4_ENST00000433593.2_Intron|PLSCR4_ENST00000493382.1_Silent_p.T188T|PLSCR4_ENST00000446574.2_Silent_p.T188T	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	188					cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)	p.T188T(1)		kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						GTCTCTGCATTGTCATGATTT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	3											101	96	97					3																	145917660		2203	4300	6503	147400350	SO:0001819	synonymous_variant	57088			AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.564A>C	3.37:g.145917660T>G			147400350	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Silent	SNP	ENST00000354952.2	37	CCDS3133.1																																																																																				0.507	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		G	145917660	T	G	145917660	2	3	61	1	0	0	0	0	0	0	0	1	12143	1799	63	4		4	PLSCR4	3	145917660	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	127271	145917660	52104770	2828	10813										
PLSCR4	57088	broad.mit.edu	37	chr3	145917752	145917752	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaagtcatctgtgtcttCggttacaatgtaaaccatct	8	8	4	0	rs539660710		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:145917752C>T	ENST00000354952.2	-	6	712	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	PLSCR4_ENST00000383083.2_Intron|PLSCR4_ENST00000433593.2_Intron|PLSCR4_ENST00000493382.1_Missense_Mutation_p.E158K|PLSCR4_ENST00000446574.2_Missense_Mutation_p.E158K	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	158					cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)	p.E158K(1)		kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						TCTGTGTCTTCGGTTACAATG	0.383													C|||	1	0.000199681	0	0	5008	,	,		18432	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											97	95	96					3																	145917752		2203	4300	6503	147400442	SO:0001583	missense	57088			AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.472G>A	3.37:g.145917752C>T	ENSP00000347038:p.Glu158Lys		147400442	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.391074	0.82902	.	.	ENSG00000114698	ENST00000354952;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000476202	T;T;T;T;T	0.31510	1.56;1.56;1.56;1.49;1.49	4.87	4.87	0.63330	.	0.000000	0.64402	D	0.000006	T	0.62122	0.2402	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69161	-0.5218	10	0.87932	D	0	.	17.3112	0.87211	0.0:1.0:0.0:0.0	.	158	Q9NRQ2	PLS4_HUMAN	K	158	ENSP00000347038:E158K;ENSP00000399315:E158K;ENSP00000419040:E158K;ENSP00000417896:E158K;ENSP00000418173:E158K	ENSP00000347038:E158K	E	-	1	0	PLSCR4	147400442	1.000000	0.71417	0.959000	0.39883	0.370000	0.29829	6.282000	0.72639	2.683000	0.91414	0.655000	0.94253	GAA		0.383	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		T	145917752	C	T	145917752	3	4	61	1	0	0	0	0	1	0	0	0	12143	893	31	1	533	1	PLSCR4	3	145917752	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92	145917752	52104678	2829	10814										
ZIC4	84107	broad.mit.edu	37	chr3	147108722	147108722	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgacacacgtaccattCgctcaagtcggcggtacgcg	11	15	1	1	rs372909087		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:147108722C>T	ENST00000383075.3	-	4	1512	c.1000G>A	c.(1000-1002)Gaa>Aaa	p.E334K	ZIC4_ENST00000491672.1_Missense_Mutation_p.E128K|ZIC4_ENST00000473123.1_Missense_Mutation_p.E334K|ZIC4_ENST00000525172.2_Missense_Mutation_p.E384K|ZIC4_ENST00000472749.2_5'UTR|ZIC4_ENST00000484399.1_Missense_Mutation_p.E334K|ZIC4_ENST00000425731.3_Missense_Mutation_p.E372K	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	334						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E334K(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						ACGTACCATTCGCTCAAGTCG	0.726																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	LYS/GLU,LYS/GLU,LYS/GLU	0,3930		0,0,1965	11	14	13		1150,1114,1000	5.2	1	3		13	1,8115		0,1,4057	no	missense,missense,missense	ZIC4	NM_001168378.1,NM_001168379.1,NM_032153.5	56,56,56	0,1,6022	TT,TC,CC		0.0123,0.0,0.0083	possibly-damaging,possibly-damaging,possibly-damaging	384/385,372/373,334/335	147108722	1,12045	1965	4058	6023	148591412	SO:0001583	missense	84107			AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.1000G>A	3.37:g.147108722C>T	ENSP00000372553:p.Glu334Lys		148591412	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	37	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567776	0.86439	0.0	1.23E-4	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672	T;T;T;T;T;T	0.13420	2.85;2.63;2.59;2.85;2.85;2.86	5.18	5.18	0.71444	.	0.000000	0.47455	D	0.000234	T	0.31295	0.0792	M	0.67397	2.05	0.39075	D	0.960788	D;D	0.76494	0.999;0.998	P;P	0.55222	0.771;0.709	T	0.19745	-1.0296	9	0.87932	D	0	.	18.2828	0.90103	0.0:1.0:0.0:0.0	.	384;334	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	K	334;372;384;334;334;128	ENSP00000372553:E334K;ENSP00000397695:E372K;ENSP00000435509:E384K;ENSP00000417855:E334K;ENSP00000420775:E334K;ENSP00000418277:E128K	ENSP00000372553:E334K	E	-	1	0	ZIC4	148591412	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	3.019000	0.49635	2.406000	0.81754	0.561000	0.74099	GAA		0.726	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			T	147108722	C	T	147108722	3	4	61	1	0	0	0	0	1	0	0	0	17720	893	31	1	12	1	ZIC4	3	147108722	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1190970	147108722	50913708	2830	10815										
ZIC1	7545	broad.mit.edu	37	chr3	147128456	147128456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggtgaccagcccgcgttCggagcactatgctgcgccgc	13	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:147128456C>T	ENST00000282928.4	+	1	1286	c.557C>T	c.(556-558)tCg>tTg	p.S186L		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	186					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S186L(1)		central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						AGCCCGCGTTCGGAGCACTAT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	3											38	42	40					3																	147128456		2203	4299	6502	148611146	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.557C>T	3.37:g.147128456C>T	ENSP00000282928:p.Ser186Leu		148611146	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849077	0.51270	.	.	ENSG00000152977	ENST00000282928	T	0.34859	1.34	3.31	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.25306	0.0615	N	0.22421	0.69	0.58432	D	0.999999	B	0.31655	0.334	B	0.26416	0.069	T	0.26360	-1.0105	10	0.72032	D	0.01	.	15.1323	0.72533	0.0:1.0:0.0:0.0	.	186	Q15915	ZIC1_HUMAN	L	186	ENSP00000282928:S186L	ENSP00000282928:S186L	S	+	2	0	ZIC1	148611146	0.995000	0.38212	0.993000	0.49108	0.965000	0.64279	7.329000	0.79170	1.847000	0.53656	0.549000	0.68633	TCG		0.672	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128456	C	T	147128456	3	4	61	1	0	0	0	0	1	0	0	0	17717	893	31	1	559	1	ZIC1	3	147128456	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19734	147128456	50893974	2831	10816										
ZIC1	7545	broad.mit.edu	37	chr3	147128499	147128499	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcacggctacgggcccatGaacgtgaacatggccgcgca	13	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:147128499G>T	ENST00000282928.4	+	1	1329	c.600G>T	c.(598-600)atG>atT	p.M200I		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	200					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M200I(1)		central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						ACGGGCCCATGAACGTGAACA	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	3											42	45	44					3																	147128499		2203	4299	6502	148611189	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.600G>T	3.37:g.147128499G>T	ENSP00000282928:p.Met200Ile		148611189	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.823632	0.50739	.	.	ENSG00000152977	ENST00000282928	T	0.41758	0.99	3.31	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.39572	0.1083	L	0.46157	1.445	0.80722	D	1	B	0.26876	0.162	B	0.30943	0.122	T	0.46303	-0.9201	10	0.54805	T	0.06	.	15.1323	0.72533	0.0:0.0:1.0:0.0	.	200	Q15915	ZIC1_HUMAN	I	200	ENSP00000282928:M200I	ENSP00000282928:M200I	M	+	3	0	ZIC1	148611189	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.286000	0.78671	1.847000	0.53656	0.549000	0.68633	ATG		0.657	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128499	G	T	147128499	3	4	61	1	0	0	0	0	1	0	0	0	17717	1290	45	2	602	2	ZIC1	3	147128499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43	147128499	50893931	2832	10817										
AGTR1	185	broad.mit.edu	37	chr3	148459237	148459237	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccaatgaagtcccgccttCgacgcacaatgcttgtagcc	8	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148459237C>T	ENST00000497524.1	+	2	806	c.415C>T	c.(415-417)Cga>Tga	p.R139*	AGTR1_ENST00000404754.2_Nonsense_Mutation_p.R139*|AGTR1_ENST00000402260.1_Nonsense_Mutation_p.R139*|AGTR1_ENST00000542281.1_Nonsense_Mutation_p.R139*|AGTR1_ENST00000474935.1_Nonsense_Mutation_p.R139*|AGTR1_ENST00000418473.2_Nonsense_Mutation_p.R139*|AGTR1_ENST00000475347.1_Nonsense_Mutation_p.R139*|AGTR1_ENST00000349243.3_Nonsense_Mutation_p.R139*|AGTR1_ENST00000461609.1_Nonsense_Mutation_p.R139*	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	139					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)	p.R139*(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	GTCCCGCCTTCGACGCACAAT	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											125	119	121					3																	148459237		2203	4300	6503	149941927	SO:0001587	stop_gained	185			M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"GPCR / Class A : Angiotensin receptors"	336	protein-coding gene	gene with protein product		106165	"angiotensin receptor 1B"	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.415C>T	3.37:g.148459237C>T	ENSP00000419422:p.Arg139*		149941927	Q13725|Q8TBK4	Nonsense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	C	38	6.949390	0.97956	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	.	.	.	5.8	5.8	0.92144	.	0.210147	0.40469	N	0.001081	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-9.1599	20.0706	0.97721	0.0:1.0:0.0:0.0	.	.	.	.	X	139	.	ENSP00000273430:R139X	R	+	1	2	AGTR1	149941927	0.920000	0.31207	0.997000	0.53966	0.992000	0.81027	1.869000	0.39519	2.744000	0.94065	0.655000	0.94253	CGA		0.478	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			T	148459237	C	T	148459237	4	4	61	1	0	0	0	0	0	1	0	0	401	876	31	1	417	1	AGTR1	3	148459237	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1330738	148459237	49563193	2833	10818										
AGTR1	185	broad.mit.edu	37	chr3	148459606	148459606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaccaaatattcacttttCtggatgtattgattcaacta	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148459606C>A	ENST00000497524.1	+	2	1175	c.784C>A	c.(784-786)Ctg>Atg	p.L262M	AGTR1_ENST00000404754.2_Missense_Mutation_p.L262M|AGTR1_ENST00000402260.1_Missense_Mutation_p.L262M|AGTR1_ENST00000542281.1_Missense_Mutation_p.L262M|AGTR1_ENST00000474935.1_Missense_Mutation_p.L262M|AGTR1_ENST00000418473.2_Missense_Mutation_p.L262M|AGTR1_ENST00000475347.1_Missense_Mutation_p.L262M|AGTR1_ENST00000349243.3_Missense_Mutation_p.L262M|AGTR1_ENST00000461609.1_Missense_Mutation_p.L262M	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	262					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)	p.L262M(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	ATTCACTTTTCTGGATGTATT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											76	77	77					3																	148459606		2203	4300	6503	149942296	SO:0001583	missense	185			M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"GPCR / Class A : Angiotensin receptors"	336	protein-coding gene	gene with protein product		106165	"angiotensin receptor 1B"	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.784C>A	3.37:g.148459606C>A	ENSP00000419422:p.Leu262Met		149942296	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	C	9.312	1.055737	0.19907	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.76	2.83	0.33086	GPCR, rhodopsin-like superfamily (1);	0.120855	0.56097	N	0.000033	T	0.31231	0.0790	L	0.33792	1.035	0.44595	D	0.997562	B	0.30793	0.295	B	0.35353	0.201	T	0.05037	-1.0910	10	0.35671	T	0.21	-3.0144	7.8396	0.29391	0.1286:0.7245:0.0:0.147	.	262	P30556	AGTR1_HUMAN	M	262	ENSP00000419422:L262M;ENSP00000273430:L262M;ENSP00000443186:L262M;ENSP00000398832:L262M;ENSP00000385612:L262M;ENSP00000419783:L262M;ENSP00000418084:L262M;ENSP00000418851:L262M;ENSP00000385641:L262M	ENSP00000273430:L262M	L	+	1	2	AGTR1	149942296	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	1.959000	0.40412	0.275000	0.22094	0.655000	0.94253	CTG		0.343	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			A	148459606	C	A	148459606	3	1	61	1	0	0	0	0	1	0	0	0	401	912	32	2	786	2	AGTR1	3	148459606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	369	148459606	49562824	2834	10819										
CPA3	1359	broad.mit.edu	37	chr3	148586763	148586763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatatgatggtggatttccGagttagtgagaaggaatccc	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148586763G>A	ENST00000296046.3	+	3	258	c.206G>A	c.(205-207)cGa>cAa	p.R69Q	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	69					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R69Q(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			GTGGATTTCCGAGTTAGTGAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	114	122					3																	148586763		2203	4300	6503	150069453	SO:0001583	missense	1359				CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"mast cell carboxypeptidase A", "tissue carboxypeptidase A"	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.206G>A	3.37:g.148586763G>A	ENSP00000296046:p.Arg69Gln		150069453	Q96E94	Missense_Mutation	SNP	ENST00000296046.3	37	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217068	0.39201	.	.	ENSG00000163751	ENST00000296046	T	0.15256	2.44	5.45	0.589	0.17452	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.573029	0.17237	N	0.181697	T	0.13927	0.0337	M	0.67569	2.06	0.31195	N	0.700526	B	0.31730	0.337	B	0.27076	0.076	T	0.11324	-1.0592	10	0.26408	T	0.33	.	4.7148	0.12889	0.4679:0.0:0.3843:0.1479	.	69	P15088	CBPA3_HUMAN	Q	69	ENSP00000296046:R69Q	ENSP00000296046:R69Q	R	+	2	0	CPA3	150069453	0.977000	0.34250	0.998000	0.56505	0.987000	0.75469	0.027000	0.13621	0.279000	0.22186	0.655000	0.94253	CGA		0.418	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870		A	148586763	G	A	148586763	3	1	61	1	0	0	0	0	1	0	0	0	3797	1058	37	1	216	1	CPA3	3	148586763	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127157	148586763	49435667	2835	10820										
HLTF	6596	broad.mit.edu	37	chr3	148757468	148757468	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtcagtcaatgcgtgcaTtagcgcattaatctgcaaaa	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148757468T>G	ENST00000310053.5	-	22	2708	c.2515A>C	c.(2515-2517)Atg>Ctg	p.M839L	HLTF_ENST00000392912.2_Missense_Mutation_p.M839L|HLTF_ENST00000494055.1_Missense_Mutation_p.M839L|HLTF_ENST00000465259.1_Missense_Mutation_p.M838L	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	839	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.M839L(2)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AATGCGTGCATTAGCGCATTA	0.294																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	3											50	50	50					3																	148757468		2201	4291	6492	150240158	SO:0001583	missense	6596			L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"RING-type (C3HC4) zinc fingers"	11099	protein-coding gene	gene with protein product		603257	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.2515A>C	3.37:g.148757468T>G	ENSP00000308944:p.Met839Leu		150240158	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.344971	0.41498	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000467858	T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72	5.89	5.89	0.94794	Helicase, C-terminal (1);	.	.	.	.	T	0.43144	0.1234	N	0.03016	-0.435	0.58432	D	0.999997	P;P;P	0.39480	0.493;0.675;0.493	B;B;B	0.35413	0.155;0.202;0.155	T	0.55528	-0.8127	9	0.06236	T	0.91	-20.4239	15.9856	0.80151	0.0:0.0:0.0:1.0	.	839;839;839	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	L	838;839;839;839;307	ENSP00000420745:M838L;ENSP00000308944:M839L;ENSP00000376644:M839L;ENSP00000420429:M839L;ENSP00000420106:M307L	ENSP00000308944:M839L	M	-	1	0	HLTF	150240158	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.234000	0.65343	2.254000	0.74563	0.528000	0.53228	ATG		0.294	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			G	148757468	T	G	148757468	3	3	61	1	0	0	0	0	1	0	0	0	7236	1493	52	4	530	4	HLTF	3	148757468	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	170705	148757468	49264962	2836	10821										
HLTF	6596	broad.mit.edu	37	chr3	148768141	148768141	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaagtgtacatctgattTtatatgttgtccaaactggt	7	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148768141T>G	ENST00000310053.5	-	15	1688	c.1495A>C	c.(1495-1497)Aaa>Caa	p.K499Q	HLTF_ENST00000392912.2_Missense_Mutation_p.K499Q|HLTF_ENST00000465259.1_Missense_Mutation_p.K498Q|HLTF_ENST00000494055.1_Missense_Mutation_p.K499Q	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	499	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K499Q(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			ACATCTGATTTTATATGTTGT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											57	61	60					3																	148768141		2201	4291	6492	150250831	SO:0001583	missense	6596			L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"RING-type (C3HC4) zinc fingers"	11099	protein-coding gene	gene with protein product		603257	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1495A>C	3.37:g.148768141T>G	ENSP00000308944:p.Lys499Gln		150250831	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.472392	0.63737	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.73	4.56	0.56223	DEAD-like helicase (2);SNF2-related (1);	.	.	.	.	D	0.92267	0.7547	L	0.52364	1.645	0.35084	D	0.763724	P;D;P	0.54601	0.93;0.967;0.93	P;P;P	0.52627	0.63;0.704;0.63	D	0.92194	0.5762	9	0.39692	T	0.17	-11.7036	7.2827	0.26320	0.0:0.0759:0.1478:0.7763	.	499;499;499	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	Q	498;499;499;499	ENSP00000420745:K498Q;ENSP00000308944:K499Q;ENSP00000376644:K499Q;ENSP00000420429:K499Q	ENSP00000308944:K499Q	K	-	1	0	HLTF	150250831	0.947000	0.32204	1.000000	0.80357	0.998000	0.95712	2.240000	0.43088	0.970000	0.38263	0.528000	0.53228	AAA		0.308	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			G	148768141	T	G	148768141	3	3	61	1	0	0	0	0	1	0	0	0	7236	1850	64	4	1578	4	HLTF	3	148768141	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10673	148768141	49254289	2837	10822										
HLTF	6596	broad.mit.edu	37	chr3	148789435	148789435	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaacaatttgtcaaattCtgttttaagctacaataaac	3	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148789435C>T	ENST00000310053.5	-	6	830	c.637G>A	c.(637-639)Gaa>Aaa	p.E213K	HLTF_ENST00000392912.2_Missense_Mutation_p.E213K|HLTF_ENST00000494055.1_Missense_Mutation_p.E213K|HLTF_ENST00000465259.1_Missense_Mutation_p.E213K	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	213				KTE -> PEF (in Ref. 6; AAB27691). {ECO:0000305}.	chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E213K(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TTGTCAAATTCTGTTTTAAGC	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	3											54	53	53					3																	148789435		2196	4294	6490	150272125	SO:0001583	missense	6596			L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"RING-type (C3HC4) zinc fingers"	11099	protein-coding gene	gene with protein product		603257	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.637G>A	3.37:g.148789435C>T	ENSP00000308944:p.Glu213Lys		150272125	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.928383	0.92389	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000416117;ENST00000392913	D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59	4.92	4.92	0.64577	.	.	.	.	.	D	0.89382	0.6699	L	0.34521	1.04	0.54753	D	0.999987	D;D;D	0.63046	0.972;0.992;0.992	P;P;P	0.57425	0.632;0.784;0.82	D	0.88009	0.2761	9	0.30854	T	0.27	-2.1684	17.2515	0.87043	0.0:1.0:0.0:0.0	.	213;213;213	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	K	213;213;213;213;210;210	ENSP00000420745:E213K;ENSP00000308944:E213K;ENSP00000376644:E213K;ENSP00000420429:E213K	ENSP00000308944:E213K	E	-	1	0	HLTF	150272125	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.504000	0.73704	2.431000	0.82371	0.655000	0.94253	GAA		0.259	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			T	148789435	C	T	148789435	3	4	61	1	0	0	0	0	1	0	0	0	7236	922	32	3	2472	3	HLTF	3	148789435	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21294	148789435	49232995	2838	10823										
HPS3	84343	broad.mit.edu	37	chr3	148872896	148872896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgttttgcttttagttCgagaaaagataccagtgtta	8	6	0	2	rs371551313		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148872896C>T	ENST00000296051.2	+	8	1543	c.1403C>T	c.(1402-1404)tCg>tTg	p.S468L	HPS3_ENST00000460120.1_Missense_Mutation_p.S303L	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	468					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.S468L(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			GCTTTTAGTTCGAGAAAAGAT	0.303									Hermansky-Pudlak syndrome				C|||	1	0.000199681	0	0	5008	,	,		18261	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	3						C	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	95	100	98		1403	4	1	3		98	0,8600		0,0,4300	no	missense	HPS3	NM_032383.3	145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	468/1005	148872896	1,13005	2203	4300	6503	150355586	SO:0001583	missense	84343	Familial Cancer Database	HPS, HPS1-8	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.1403C>T	3.37:g.148872896C>T	ENSP00000296051:p.Ser468Leu		150355586	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992880	0.54041	2.27E-4	0.0	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.71341	-0.56;-0.54	4.89	4.0	0.46444	.	0.188459	0.46442	D	0.000293	T	0.80654	0.4664	M	0.66939	2.045	0.58432	D	0.999998	D;P	0.89917	1.0;0.591	D;B	0.66497	0.944;0.049	T	0.82841	-0.0258	10	0.72032	D	0.01	-5.4211	13.2263	0.59916	0.1593:0.8406:0.0:0.0	.	303;468	G5E9V4;Q969F9	.;HPS3_HUMAN	L	468;303	ENSP00000296051:S468L;ENSP00000418230:S303L	ENSP00000296051:S468L	S	+	2	0	HPS3	150355586	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.057000	0.57455	1.388000	0.46506	0.655000	0.94253	TCG		0.303	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		T	148872896	C	T	148872896	3	4	61	1	0	0	0	0	1	0	0	0	7361	893	31	1	1433	1	HPS3	3	148872896	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83461	148872896	49149534	2839	10824										
CP	1356	broad.mit.edu	37	chr3	148896220	148896220	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatgcattttattgctttCtatgaattcctcatcatctt	3	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148896220C>T	ENST00000264613.6	-	16	3122	c.2860G>A	c.(2860-2862)Gaa>Aaa	p.E954K		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	954	F5/8 type A 3.|Plastocyanin-like 6.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.E954K(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TTATTGCTTTCTATGAATTCC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	3											117	108	111					3																	148896220		2201	4300	6501	150378910	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.2860G>A	3.37:g.148896220C>T	ENSP00000264613:p.Glu954Lys		150378910	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	33	5.276407	0.95459	.	.	ENSG00000047457	ENST00000479771;ENST00000264613;ENST00000494544	D;D;D	0.98701	-5.08;-5.08;-5.08	5.68	5.68	0.88126	Cupredoxin (2);	0.098183	0.64402	D	0.000001	D	0.98673	0.9555	L	0.55834	1.745	0.80722	D	1	D;D;P;P	0.57899	0.981;0.981;0.868;0.908	P;P;P;P	0.61533	0.852;0.89;0.494;0.783	D	0.99320	1.0906	10	0.48119	T	0.1	-27.1399	19.7948	0.96474	0.0:1.0:0.0:0.0	.	954;954;954;667	A8K5A4;P00450;Q1L857;B3KTA8	.;CERU_HUMAN;.;.	K	89;954;737	ENSP00000420367:E89K;ENSP00000264613:E954K;ENSP00000420545:E737K	ENSP00000264613:E954K	E	-	1	0	CP	150378910	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.757000	0.68766	2.687000	0.91594	0.650000	0.86243	GAA		0.289	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		T	148896220	C	T	148896220	3	4	61	1	0	0	0	0	1	0	0	0	3793	922	32	3	353	3	CP	3	148896220	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23324	148896220	49126210	2840	10825										
CP	1356	broad.mit.edu	37	chr3	148904388	148904388	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccgttctcctctccacaGatatgtgtttcctgaaaagt	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:148904388G>T	ENST00000264613.6	-	11	2258	c.1996C>A	c.(1996-1998)Ctg>Atg	p.L666M	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	666	F5/8 type A 2.|Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.L666M(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CCTCTCCACAGATATGTGTTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											180	160	167					3																	148904388		2203	4300	6503	150387078	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1996C>A	3.37:g.148904388G>T	ENSP00000264613:p.Leu666Met		150387078	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	G	4.126	0.021586	0.08006	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.99764	-6.68;-6.68	5.91	4.1	0.47936	Cupredoxin (2);	0.291161	0.34291	N	0.004083	D	0.98921	0.9634	L	0.52823	1.66	0.09310	N	1	B;B;B;B	0.23591	0.088;0.088;0.088;0.088	B;B;B;B	0.21546	0.035;0.035;0.035;0.035	D	0.98216	1.0475	10	0.37606	T	0.19	-1.1167	11.2353	0.48936	0.068:0.3555:0.5766:0.0	.	666;666;666;666	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	M	666;449	ENSP00000264613:L666M;ENSP00000420545:L449M	ENSP00000264613:L666M	L	-	1	2	CP	150387078	0.751000	0.28327	0.246000	0.24233	0.257000	0.26127	1.233000	0.32648	0.816000	0.34421	-0.126000	0.14955	CTG		0.468	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		T	148904388	G	T	148904388	3	4	61	1	0	0	0	0	1	0	0	0	3793	933	33	2	1237	2	CP	3	148904388	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8168	148904388	49118042	2841	10826										
TSC22D2	9819	broad.mit.edu	37	chr3	150176245	150176245	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaaagaattagttgaaaGaaactctttacttgaacgag	7	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150176245G>T	ENST00000361875.3	+	4	3181	c.2165G>T	c.(2164-2166)aGa>aTa	p.R722I	TSC22D2_ENST00000361136.2_Missense_Mutation_p.R698I	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	722					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R722I(1)		cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTAGTTGAAAGAAACTCTTTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											81	84	83					3																	150176245		2203	4300	6503	151658935	SO:0001583	missense	9819			AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.2165G>T	3.37:g.150176245G>T	ENSP00000354543:p.Arg722Ile		151658935	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	37	CCDS3149.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.608|9.608	1.130531|1.130531	0.21041|0.21041	.|.	.|.	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000543241;ENST00000361875;ENST00000361136	.|T;T	.|0.38887	.|1.11;1.27	5.38|5.38	3.6|3.6	0.41247|0.41247	.|.	.|0.205916	.|0.32624	.|N	.|0.005860	T|T	0.61337|0.61337	0.2339|0.2339	M|M	0.78801|0.78801	2.425|2.425	0.49213|0.49213	D|D	0.999762|0.999762	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.73708	.|0.933;0.981	T|T	0.63107|0.63107	-0.6711|-0.6711	5|10	.|0.87932	.|D	.|0	.|.	9.4194|9.4194	0.38541|0.38541	0.2172:0.0:0.7828:0.0|0.2172:0.0:0.7828:0.0	.|.	.|698;722	.|O75157-2;O75157	.|.;T22D2_HUMAN	N|I	145|171;722;698	.|ENSP00000354543:R722I;ENSP00000354893:R698I	.|ENSP00000354893:R698I	K|R	+|+	3|2	2|0	TSC22D2|TSC22D2	151658935|151658935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.111000|0.111000	0.19643|0.19643	7.637000|7.637000	0.83313|0.83313	0.774000|0.774000	0.33427|0.33427	-0.150000|-0.150000	0.13652|0.13652	AAG|AGA		0.353	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		T	150176245	G	T	150176245	3	4	61	1	0	0	0	0	1	0	0	0	16648	942	33	2	2179	2	TSC22D2	3	150176245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1271857	150176245	47846185	2842	10827										
EIF2A	83939	broad.mit.edu	37	chr3	150285701	150285701	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcttaggtggctgtctatGttccaggaagtaaaggtgca	12	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150285701G>T	ENST00000460851.1	+	8	671	c.562G>T	c.(562-564)Gtt>Ttt	p.V188F	SERP1_ENST00000490945.1_Intron|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000406576.3_Missense_Mutation_p.V127F|EIF2A_ENST00000487799.1_Missense_Mutation_p.V163F|EIF2A_ENST00000383043.3_Start_Codon_SNP_p.M1I|EIF2A_ENST00000273435.5_Missense_Mutation_p.V183F			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	188					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)	p.V163F(1)		cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GGCTGTCTATGTTCCAGGAAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	96	98					3																	150285701		1840	4078	5918	151768391	SO:0001583	missense	83939			AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.562G>T	3.37:g.150285701G>T	ENSP00000417229:p.Val188Phe		151768391	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Missense_Mutation	SNP	ENST00000460851.1	37	CCDS46935.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.0|26.0	4.699358|4.699358	0.88830|0.88830	.|.	.|.	ENSG00000144895|ENSG00000144895	ENST00000383043|ENST00000487799;ENST00000460851;ENST00000406576;ENST00000482093;ENST00000273435	T|T;T;T;T;T	0.39787|0.37915	1.06|1.19;1.18;1.18;1.17;3.25	6.03|6.03	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65238|0.65238	0.2672|0.2672	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.76494	.|0.999;0.992;0.945	.|D;D;P	.|0.73708	.|0.981;0.923;0.714	T|T	0.73062|0.73062	-0.4101|-0.4101	7|10	0.87932|0.87932	D|D	0|0	-22.7717|-22.7717	15.4819|15.4819	0.75534|0.75534	0.0662:0.0:0.9338:0.0|0.0662:0.0:0.9338:0.0	.|.	.|127;163;188	.|B4DF96;B4DQ14;Q9BY44	.|.;.;EIF2A_HUMAN	I|F	1|163;188;127;200;183	ENSP00000372513:M1I|ENSP00000420537:V163F;ENSP00000417229:V188F;ENSP00000385292:V127F;ENSP00000418698:V200F;ENSP00000273435:V183F	ENSP00000372513:M1I|ENSP00000273435:V183F	M|V	+|+	3|1	0|0	EIF2A|EIF2A	151768391|151768391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.375000|9.375000	0.97178|0.97178	1.551000|1.551000	0.49450|0.49450	0.655000|0.655000	0.94253|0.94253	ATG|GTT		0.338	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025		T	150285701	G	T	150285701	3	4	61	1	0	0	0	0	1	0	0	0	5006	1377	48	2	592	2	EIF2A	3	150285701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109456	150285701	47736729	2843	10828										
FAM194A	131831	broad.mit.edu	37	chr3	150384786	150384786	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgaatattgacctcccaAgatattgatgtataccctgg	7	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150384786A>C	ENST00000295910.6	-	13	1568	c.1516T>G	c.(1516-1518)Ttg>Gtg	p.L506V	FAM194A_ENST00000491361.1_Missense_Mutation_p.L360V	NM_152394.3	NP_689607.2												p.L506V(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TGACCTCCCAAGATATTGATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	115	115					3																	150384786		2203	4300	6503	151867476	SO:0001583	missense	131831																														ENST00000295910.6:c.1516T>G	3.37:g.150384786A>C	ENSP00000295910:p.Leu506Val		151867476		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076138	0.36662	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.11385	2.78;2.78	5.41	-0.154	0.13399	.	0.985177	0.08279	N	0.970221	T	0.08758	0.0217	M	0.61703	1.905	0.22552	N	0.99899	P	0.35793	0.521	B	0.28916	0.096	T	0.33007	-0.9885	10	0.28530	T	0.3	-2.315	1.1778	0.01839	0.3916:0.2617:0.22:0.1267	.	506	Q7L0X2	F194A_HUMAN	V	506;360;464	ENSP00000295910:L506V;ENSP00000419366:L360V	ENSP00000295910:L506V	L	-	1	2	FAM194A	151867476	0.006000	0.16342	0.983000	0.44433	0.891000	0.51852	0.003000	0.13083	-0.247000	0.09597	-0.316000	0.08728	TTG		0.383	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			C	150384786	A	C	150384786	3	2	61	1	0	0	0	0	1	0	0	0	5542	69	3	4	483	4	FAM194A	3	150384786	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	99085	150384786	47637644	2844	10829										
MED12L	116931	broad.mit.edu	37	chr3	150873963	150873963	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagagtggacacagatatCtaccagatatcttcgagagc	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150873963C>A	ENST00000474524.1	+	5	610	c.572C>A	c.(571-573)tCt>tAt	p.S191Y	MED12L_ENST00000422248.2_Missense_Mutation_p.S191Y|MED12L_ENST00000273432.4_Missense_Mutation_p.S191Y|MED12L_ENST00000309237.4_Missense_Mutation_p.S191Y	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	191						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.S191Y(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACACAGATATCTACCAGATAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	76	76					3																	150873963		2203	4300	6503	152356653	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.572C>A	3.37:g.150873963C>A	ENSP00000417235:p.Ser191Tyr		152356653	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.743516	0.49151	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.60171	0.53;0.53;0.44;0.21	4.78	4.78	0.61160	.	0.230975	0.34338	N	0.004041	T	0.55257	0.1909	L	0.36672	1.1	0.22127	N	0.999341	P;P;P;P	0.49559	0.545;0.61;0.681;0.925	B;B;B;P	0.51355	0.206;0.282;0.281;0.667	T	0.52917	-0.8511	10	0.87932	D	0	-11.5497	9.2238	0.37393	0.0:0.8335:0.0:0.1665	.	191;191;191;191	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	Y	191	ENSP00000403308:S191Y;ENSP00000310760:S191Y;ENSP00000417235:S191Y;ENSP00000273432:S191Y	ENSP00000273432:S191Y	S	+	2	0	MED12L	152356653	0.889000	0.30405	0.716000	0.30569	0.984000	0.73092	3.226000	0.51254	2.350000	0.79820	0.557000	0.71058	TCT		0.443	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	150873963	C	A	150873963	3	1	61	1	0	0	0	0	1	0	0	0	9459	913	32	2	590	2	MED12L	3	150873963	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	489177	150873963	47148467	2845	10830										
MED12L	116931	broad.mit.edu	37	chr3	150911392	150911392	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagccaagggaattaatttTtccatctaattatgacctcc	5	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150911392T>G	ENST00000474524.1	+	14	2122	c.2084T>G	c.(2083-2085)tTt>tGt	p.F695C	MED12L_ENST00000422248.2_Missense_Mutation_p.F695C|MED12L_ENST00000273432.4_Missense_Mutation_p.F555C|MED12L_ENST00000309237.4_Missense_Mutation_p.F730C	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	695						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.F695C(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GAATTAATTTTTCCATCTAAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											131	130	130					3																	150911392		2203	4300	6503	152394082	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2084T>G	3.37:g.150911392T>G	ENSP00000417235:p.Phe695Cys		152394082	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.80|17.80	3.479014|3.479014	0.63849|0.63849	.|.	.|.	ENSG00000144893|ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432|ENST00000480026	T;T;T;T|.	0.31510|.	1.49;1.49;1.49;1.49|.	5.3|5.3	5.3|5.3	0.74995|0.74995	Mediator complex, subunit Med12, LCEWAV-domain (1);|.	0.052405|0.052405	0.85682|0.85682	D|N	0.000000|0.000000	T|T	0.69842|0.69842	0.3156|0.3156	L|L	0.56769|0.56769	1.78|1.78	0.42635|0.42635	D|D	0.993398|0.993398	D;D;D;D|.	0.69078|.	0.967;0.997;0.997;0.973|.	P;D;P;P|.	0.65684|.	0.77;0.937;0.875;0.614|.	T|T	0.69228|0.69228	-0.5200|-0.5200	10|6	0.87932|.	D|.	0|.	-16.1304|-16.1304	15.2029|15.2029	0.73153|0.73153	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	555;695;695;730|.	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3|.	.;MD12L_HUMAN;.;.|.	C|L	695;730;695;555|44	ENSP00000403308:F695C;ENSP00000310760:F730C;ENSP00000417235:F695C;ENSP00000273432:F555C|.	ENSP00000273432:F555C|.	F|F	+|+	2|3	0|2	MED12L|MED12L	152394082|152394082	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.991000|0.991000	0.79684|0.79684	4.515000|4.515000	0.60489|0.60489	2.113000|2.113000	0.64589|0.64589	0.496000|0.496000	0.49642|0.49642	TTT|TTT		0.398	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	150911392	T	G	150911392	3	3	61	1	0	0	0	0	1	0	0	0	9459	1841	64	4	2138	4	MED12L	3	150911392	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37429	150911392	47111038	2846	10831										
GPR171	29909	broad.mit.edu	37	chr3	150916664	150916664	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccaatttcttccaaattcCtttttaaactccatacaacc	1	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150916664C>A	ENST00000309180.5	-	3	740	c.510G>T	c.(508-510)aaG>aaT	p.K170N	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_013308.3	NP_037440.3	O14626	GP171_HUMAN	G protein-coupled receptor 171	170					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.K170N(1)		endometrium(1)|kidney(4)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	15			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTCCAAATTCCTTTTTAAACT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											51	57	55					3																	150916664		2203	4300	6503	152399354	SO:0001583	missense	29909			AF002986	CCDS3155.1	3q25.1	2012-08-21			ENSG00000174946	ENSG00000174946		"GPCR / Class A : Orphans"	30057	protein-coding gene	gene with protein product	"platelet activating receptor homolog"					9370294	Standard	NM_013308		Approved	H963	uc003eyq.4	O14626	OTTHUMG00000159861	ENST00000309180.5:c.510G>T	3.37:g.150916664C>A	ENSP00000308479:p.Lys170Asn		152399354	D3DNJ4|Q8IV06	Missense_Mutation	SNP	ENST00000309180.5	37	CCDS3155.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.691985	0.00731	.	.	ENSG00000174946	ENST00000309180	T	0.39592	1.07	5.55	-4.01	0.04045	GPCR, rhodopsin-like superfamily (1);	0.809644	0.11310	N	0.577248	T	0.10680	0.0261	N	0.01576	-0.805	0.21386	N	0.999703	B	0.02656	0.0	B	0.01281	0.0	T	0.21484	-1.0244	10	0.16420	T	0.52	0.2538	0.8851	0.01243	0.1811:0.2044:0.2682:0.3463	.	170	O14626	GP171_HUMAN	N	170	ENSP00000308479:K170N	ENSP00000308479:K170N	K	-	3	2	GPR171	152399354	0.000000	0.05858	0.002000	0.10522	0.607000	0.37147	-1.055000	0.03493	-0.989000	0.03485	-0.150000	0.13652	AAG		0.328	GPR171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357793.1	NM_013308		A	150916664	C	A	150916664	3	1	61	1	0	0	0	0	1	0	0	0	6688	680	24	2	453	2	GPR171	3	150916664	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5272	150916664	47105766	2847	10832										
P2RY14	9934	broad.mit.edu	37	chr3	150931158	150931158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtctaggtcattctgaGcttttaatggaatgtgcaat	9	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:150931158G>A	ENST00000309170.3	-	3	1259	c.947C>T	c.(946-948)gCt>gTt	p.A316V	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|P2RY14_ENST00000424796.2_Missense_Mutation_p.A316V	NM_001081455.1|NM_014879.3	NP_001074924.1|NP_055694.3	Q15391	P2Y14_HUMAN	purinergic receptor P2Y, G-protein coupled, 14	316					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|UDP-activated nucleotide receptor activity (GO:0045029)	p.A316V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)	20			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTCATTCTGAGCTTTTAATGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											153	152	152					3																	150931158		2203	4300	6503	152413848	SO:0001583	missense	9934			D13626	CCDS3156.1	3q21-q25	2012-08-08	2004-07-12	2004-07-14	ENSG00000174944	ENSG00000174944		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	16442	protein-coding gene	gene with protein product		610116	"G protein-coupled receptor 105"	GPR105			Standard	NM_014879		Approved	KIAA0001	uc003eys.1	Q15391	OTTHUMG00000159859	ENST00000309170.3:c.947C>T	3.37:g.150931158G>A	ENSP00000308361:p.Ala316Val		152413848	Q8IYT7	Missense_Mutation	SNP	ENST00000309170.3	37	CCDS3156.1	.	.	.	.	.	.	.	.	.	.	G	7.870	0.727931	0.15507	.	.	ENSG00000174944	ENST00000309170;ENST00000424796	T;T	0.68765	-0.35;-0.35	5.36	-1.19	0.09585	.	0.892392	0.09465	N	0.798413	T	0.35451	0.0932	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16453	-1.0402	10	0.12766	T	0.61	-2.1311	1.4386	0.02349	0.3461:0.2298:0.3063:0.1178	.	316	Q15391	P2Y14_HUMAN	V	316	ENSP00000308361:A316V;ENSP00000408733:A316V	ENSP00000308361:A316V	A	-	2	0	P2RY14	152413848	0.000000	0.05858	0.000000	0.03702	0.505000	0.33919	-0.169000	0.09911	-0.237000	0.09739	0.650000	0.86243	GCT		0.378	P2RY14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357789.1	NM_014879		A	150931158	G	A	150931158	3	1	61	1	0	0	0	0	1	0	0	0	11382	971	34	3	73	3	P2RY14	3	150931158	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14494	150931158	47091272	2848	10833										
MED12L	116931	broad.mit.edu	37	chr3	151094873	151094873	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgcagacctaaataattCttctaattctggcatgagcc	7	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151094873C>A	ENST00000474524.1	+	28	4156	c.4118C>A	c.(4117-4119)tCt>tAt	p.S1373Y	MED12L_ENST00000273432.4_Missense_Mutation_p.S1233Y|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1373						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.S1373Y(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CTAAATAATTCTTCTAATTCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											89	90	90					3																	151094873		2203	4300	6503	152577563	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.4118C>A	3.37:g.151094873C>A	ENSP00000417235:p.Ser1373Tyr		152577563	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373130	0.82573	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.55588	0.51;0.51	5.93	5.93	0.95920	.	0.257927	0.32041	N	0.006664	T	0.60143	0.2246	L	0.36672	1.1	0.80722	D	1	D;P;P	0.57257	0.979;0.936;0.894	P;P;B	0.54312	0.748;0.466;0.365	T	0.61456	-0.7059	10	0.87932	D	0	-7.7695	19.9416	0.97165	0.0:1.0:0.0:0.0	.	1233;1372;1373	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	Y	1373;1233	ENSP00000417235:S1373Y;ENSP00000273432:S1233Y	ENSP00000273432:S1233Y	S	+	2	0	MED12L	152577563	1.000000	0.71417	0.052000	0.19188	0.915000	0.54546	5.091000	0.64505	2.798000	0.96311	0.655000	0.94253	TCT		0.413	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151094873	C	A	151094873	3	1	61	1	0	0	0	0	1	0	0	0	9459	913	32	2	4228	2	MED12L	3	151094873	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163715	151094873	46927557	2849	10834										
MED12L	116931	broad.mit.edu	37	chr3	151105609	151105609	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccacagggtctccaggtCtctacgaagcagaaggtgtc	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151105609C>A	ENST00000474524.1	+	35	5033	c.4995C>A	c.(4993-4995)gtC>gtA	p.V1665V	MED12L_ENST00000273432.4_Silent_p.V1525V	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1665						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.V1665V(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTCTCCAGGTCTCTACGAAGC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	3											86	91	89					3																	151105609		2203	4300	6503	152588299	SO:0001819	synonymous_variant	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.4995C>A	3.37:g.151105609C>A			152588299	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																				0.522	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151105609	C	A	151105609	2	1	61	1	0	0	0	0	0	0	0	1	9459	900	32	2		2	MED12L	3	151105609	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10736	151105609	46916821	2850	10835										
MED12L	116931	broad.mit.edu	37	chr3	151131061	151131061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccagacagccgcaagttcGacagcagcagagactcctcc	9	16	0	2	rs139235145	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151131061G>A	ENST00000474524.1	+	40	6208	c.6170G>A	c.(6169-6171)cGa>cAa	p.R2057Q	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2057	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.R2057Q(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CCGCAAGTTCGACAGCAGCAG	0.542													G|||	6	0.00119808	0	0	5008	,	,		19134	0		0	False		,,,				2504	0.0061															1	Substitution - Missense(1)	large_intestine(1)	3						G	GLN/ARG	0,4406		0,0,2203	68	65	66		6170	5.3	1	3	dbSNP_134	66	1,8599	1.2+/-3.3	0,1,4299	no	missense	MED12L	NM_053002.4	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	2057/2146	151131061	1,13005	2203	4300	6503	152613751	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6170G>A	3.37:g.151131061G>A	ENSP00000417235:p.Arg2057Gln		152613751	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833446	0.71258	0.0	1.16E-4	ENSG00000144893	ENST00000474524	T	0.55413	0.52	5.33	5.33	0.75918	.	0.420137	0.23510	N	0.047404	T	0.28300	0.0699	N	0.08118	0	0.80722	D	1	B	0.13145	0.007	B	0.04013	0.001	T	0.15694	-1.0428	10	0.07644	T	0.81	-10.9158	11.3155	0.49390	0.0843:0.0:0.9157:0.0	.	2057	Q86YW9	MD12L_HUMAN	Q	2057	ENSP00000417235:R2057Q	ENSP00000417235:R2057Q	R	+	2	0	MED12L	152613751	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.948000	0.56660	2.495000	0.84180	0.655000	0.94253	CGA		0.542	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151131061	G	A	151131061	3	1	61	1	0	0	0	0	1	0	0	0	9459	1058	37	1	6328	1	MED12L	3	151131061	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25452	151131061	46891369	2851	10836										
IGSF10	285313	broad.mit.edu	37	chr3	151155606	151155606	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtctcacagctgtggctTtaataacagttctgtttgta	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151155606T>G	ENST00000282466.3	-	6	6742	c.6743A>C	c.(6742-6744)aAa>aCa	p.K2248T	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2248	Ig-like C2-type 9.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.K2248T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCTGTGGCTTTAATAACAGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											111	99	103					3																	151155606		2203	4300	6503	152638296	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6743A>C	3.37:g.151155606T>G	ENSP00000282466:p.Lys2248Thr		152638296	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455411	0.43634	.	.	ENSG00000152580	ENST00000282466	T	0.70282	-0.47	5.22	0.97	0.19692	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.266780	0.26435	N	0.024382	T	0.76097	0.3940	L	0.53780	1.695	0.48341	D	0.999635	D;D	0.71674	0.998;0.974	D;P	0.68353	0.957;0.877	T	0.73036	-0.4109	10	0.49607	T	0.09	.	9.495	0.38982	0.0:0.2261:0.0:0.7739	.	2248;275	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	T	2248	ENSP00000282466:K2248T	ENSP00000282466:K2248T	K	-	2	0	IGSF10	152638296	1.000000	0.71417	0.385000	0.26158	0.548000	0.35241	1.664000	0.37439	0.211000	0.20683	0.482000	0.46254	AAA		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151155606	T	G	151155606	3	3	61	1	0	0	0	0	1	0	0	0	7618	1841	64	4	1132	4	IGSF10	3	151155606	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24545	151155606	46866824	2852	10837										
IGSF10	285313	broad.mit.edu	37	chr3	151161328	151161328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtggaggaccaatgttcCgtcaaccgtcaccacagcct	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151161328C>T	ENST00000282466.3	-	5	5406	c.5407G>A	c.(5407-5409)Gga>Aga	p.G1803R	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1803	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.G1803R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACCAATGTTCCGTCAACCGTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	82	85					3																	151161328		2203	4300	6503	152644018	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5407G>A	3.37:g.151161328C>T	ENSP00000282466:p.Gly1803Arg		152644018	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.970528	0.34754	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.68331	-0.32	5.26	5.26	0.73747	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47093	D	0.000243	T	0.80014	0.4546	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79652	-0.1714	9	.	.	.	.	15.9174	0.79531	0.0:0.8649:0.1351:0.0	.	1803	Q6WRI0	IGS10_HUMAN	R	1803;430	ENSP00000282466:G1803R	.	G	-	1	0	IGSF10	152644018	1.000000	0.71417	0.769000	0.31535	0.053000	0.15095	7.682000	0.84083	2.463000	0.83235	0.591000	0.81541	GGA		0.488	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151161328	C	T	151161328	3	4	61	1	0	0	0	0	1	0	0	0	7618	661	23	1	2520	1	IGSF10	3	151161328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5722	151161328	46861102	2853	10838										
IGSF10	285313	broad.mit.edu	37	chr3	151165153	151165153	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatggttgggtttatattCtttgacatggctgtagtttt	11	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151165153C>A	ENST00000282466.3	-	4	2615	c.2616G>T	c.(2614-2616)aaG>aaT	p.K872N		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	872					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.K872N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGTTTATATTCTTTGACATGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											296	301	299					3																	151165153		2203	4300	6503	152647843	SO:0001583	missense	285313			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.2616G>T	3.37:g.151165153C>A	ENSP00000282466:p.Lys872Asn		152647843	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	8.130	0.782778	0.16189	.	.	ENSG00000152580	ENST00000282466	T	0.69435	-0.4	5.31	1.83	0.25207	.	0.802103	0.10579	N	0.658169	T	0.40322	0.1112	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.19451	-1.0305	10	0.34782	T	0.22	.	3.1817	0.06587	0.1494:0.5388:0.1462:0.1656	.	872	Q6WRI0	IGS10_HUMAN	N	872	ENSP00000282466:K872N	ENSP00000282466:K872N	K	-	3	2	IGSF10	152647843	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	-0.239000	0.08965	1.218000	0.43458	0.591000	0.81541	AAG		0.403	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151165153	C	A	151165153	3	1	61	1	0	0	0	0	1	0	0	0	7618	912	32	2	5315	2	IGSF10	3	151165153	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3825	151165153	46857277	2854	10839										
AADACL2	344752	broad.mit.edu	37	chr3	151461900	151461900	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacagagggcttttgacttCctgaatagatggacggcaaa	12	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151461900C>A	ENST00000356517.3	+	3	490	c.381C>A	c.(379-381)ttC>ttA	p.F127L		NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	127						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.F105L(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CTTTTGACTTCCTGAATAGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											163	153	156					3																	151461900		2203	4300	6503	152944590	SO:0001583	missense	344752			BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.381C>A	3.37:g.151461900C>A	ENSP00000348911:p.Phe127Leu		152944590	Q5HYJ4	Missense_Mutation	SNP	ENST00000356517.3	37	CCDS3161.2	.	.	.	.	.	.	.	.	.	.	C	7.494	0.651240	0.14516	.	.	ENSG00000197953	ENST00000356517	T	0.58506	0.33	5.04	4.17	0.49024	Alpha/beta hydrolase fold-3 (1);	0.303220	0.33591	N	0.004744	T	0.31295	0.0792	N	0.05554	-0.025	0.25737	N	0.985206	B	0.02656	0.0	B	0.06405	0.002	T	0.14755	-1.0461	10	0.10636	T	0.68	-28.3554	9.0622	0.36442	0.0:0.8298:0.0:0.1702	.	127	Q6P093	ADCL2_HUMAN	L	127	ENSP00000348911:F127L	ENSP00000348911:F127L	F	+	3	2	AADACL2	152944590	0.152000	0.22762	0.002000	0.10522	0.046000	0.14306	0.001000	0.13038	1.491000	0.48482	0.655000	0.94253	TTC		0.353	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365		A	151461900	C	A	151461900	3	1	61	1	0	0	0	0	1	0	0	0	11	854	30	2	391	2	AADACL2	3	151461900	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296747	151461900	46560530	2855	10840										
AADAC	13	broad.mit.edu	37	chr3	151545584	151545584	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgtacctgtggaatcaaGtcatctcttcaaatttgtta	6	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:151545584G>T	ENST00000232892.7	+	5	950	c.824G>T	c.(823-825)aGt>aTt	p.S275I	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	275					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)	p.S275I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GTGGAATCAAGTCATCTCTTC	0.388																																					Ovarian(30;839 841 2699 32801 46334)											1	Substitution - Missense(1)	large_intestine(1)	3											62	65	64					3																	151545584		2203	4299	6502	153028274	SO:0001583	missense	13			L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.824G>T	3.37:g.151545584G>T	ENSP00000232892:p.Ser275Ile		153028274	A8K3L3|D3DNJ6|Q8N1A9	Missense_Mutation	SNP	ENST00000232892.7	37	CCDS33877.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.400216	0.42613	.	.	ENSG00000114771	ENST00000232892	T	0.58940	0.3	4.81	3.92	0.45320	.	0.342235	0.35151	N	0.003401	T	0.53433	0.1796	L	0.34521	1.04	0.09310	N	0.999999	P	0.42871	0.792	P	0.50537	0.643	T	0.42344	-0.9457	10	0.39692	T	0.17	-43.0589	8.6988	0.34312	0.0783:0.2897:0.632:0.0	.	275	P22760	AAAD_HUMAN	I	275	ENSP00000232892:S275I	ENSP00000232892:S275I	S	+	2	0	AADAC	153028274	0.027000	0.19231	0.013000	0.15412	0.981000	0.71138	2.319000	0.43788	0.977000	0.38444	0.591000	0.81541	AGT		0.388	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		T	151545584	G	T	151545584	3	4	61	1	0	0	0	0	1	0	0	0	10	1029	36	2	842	2	AADAC	3	151545584	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83684	151545584	46476846	2856	10841										
P2RY1	5028	broad.mit.edu	37	chr3	152554408	152554408	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatccctttccatgtgatGaaaacgatgaacttgagggc	9	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:152554408G>T	ENST00000305097.3	+	1	1673	c.837G>T	c.(835-837)atG>atT	p.M279I	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	279					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.M279I(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TCCATGTGATGAAAACGATGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	3											114	115	115					3																	152554408		2203	4300	6503	154037098	SO:0001583	missense	5028			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.837G>T	3.37:g.152554408G>T	ENSP00000304767:p.Met279Ile		154037098		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535538	0.85812	.	.	ENSG00000169860	ENST00000305097	T	0.71222	-0.55	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64594	0.2612	L	0.31294	0.92	0.80722	D	1	B	0.34349	0.45	B	0.40228	0.323	T	0.59172	-0.7504	10	0.16420	T	0.52	.	18.5615	0.91101	0.0:0.0:1.0:0.0	.	279	P47900	P2RY1_HUMAN	I	279	ENSP00000304767:M279I	ENSP00000304767:M279I	M	+	3	0	P2RY1	154037098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.731000	0.98807	2.618000	0.88619	0.563000	0.77884	ATG		0.443	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152554408	G	T	152554408	3	4	61	1	0	0	0	0	1	0	0	0	11377	1290	45	2	839	2	P2RY1	3	152554408	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1008824	152554408	45468022	2857	10842										
P2RY1	5028	broad.mit.edu	37	chr3	152554595	152554595	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcccgagccacaaggaaaGcttctagaagaagtgaggca	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:152554595G>T	ENST00000305097.3	+	1	1860	c.1024G>T	c.(1024-1026)Gct>Tct	p.A342S	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	342					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.A342S(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			CACAAGGAAAGCTTCTAGAAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											44	48	47					3																	152554595		2202	4299	6501	154037285	SO:0001583	missense	5028			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.1024G>T	3.37:g.152554595G>T	ENSP00000304767:p.Ala342Ser		154037285		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	G	7.809	0.715230	0.15306	.	.	ENSG00000169860	ENST00000305097	T	0.25749	1.78	5.2	5.2	0.72013	.	0.320424	0.28448	N	0.015309	T	0.12220	0.0297	N	0.08118	0	0.38253	D	0.941654	B	0.06786	0.001	B	0.04013	0.001	T	0.10776	-1.0615	10	0.07030	T	0.85	.	13.3738	0.60726	0.0:0.0:0.8322:0.1678	.	342	P47900	P2RY1_HUMAN	S	342	ENSP00000304767:A342S	ENSP00000304767:A342S	A	+	1	0	P2RY1	154037285	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	2.072000	0.41510	2.419000	0.82065	0.563000	0.77884	GCT		0.453	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152554595	G	T	152554595	3	4	61	1	0	0	0	0	1	0	0	0	11377	971	34	2	1026	2	P2RY1	3	152554595	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187	152554595	45467835	2858	10843										
RAP2B	5912	broad.mit.edu	37	chr3	152880572	152880572	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacgggctccttcatcgaGaagtacgacccgaccatcga	11	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:152880572G>T	ENST00000323534.2	+	1	544	c.90G>T	c.(88-90)gaG>gaT	p.E30D	RP11-529G21.2_ENST00000487827.1_RNA	NM_002886.2	NP_002877.2	P61225	RAP2B_HUMAN	RAP2B, member of RAS oncogene family	30					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)	p.E30D(1)		NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			CCTTCATCGAGAAGTACGACC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											79	77	78					3																	152880572		2203	4300	6503	154363262	SO:0001583	missense	5912				CCDS3170.1	3q25.2	2014-05-09			ENSG00000181467	ENSG00000181467			9862	protein-coding gene	gene with protein product	"Ras-related protein RAP-2B", "small GTP binding protein", "Ras family small GTP binding protein RAP2B"	179541				2118648	Standard	NM_002886		Approved		uc003ezr.3	P61225	OTTHUMG00000159655	ENST00000323534.2:c.90G>T	3.37:g.152880572G>T	ENSP00000319096:p.Glu30Asp		154363262	P17964|Q96EG5|Q9CXG0	Missense_Mutation	SNP	ENST00000323534.2	37	CCDS3170.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.246687	0.80024	.	.	ENSG00000181467	ENST00000323534	T	0.78364	-1.17	4.61	4.61	0.57282	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.79718	0.4494	L	0.33668	1.02	0.80722	D	1	P	0.50066	0.931	D	0.72982	0.979	T	0.72994	-0.4122	10	0.07813	T	0.8	.	14.9788	0.71296	0.0:0.0:1.0:0.0	.	30	P61225	RAP2B_HUMAN	D	30	ENSP00000319096:E30D	ENSP00000319096:E30D	E	+	3	2	RAP2B	154363262	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.784000	0.55416	2.367000	0.80283	0.563000	0.77884	GAG		0.617	RAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356707.1	NM_002886		T	152880572	G	T	152880572	3	4	61	1	0	0	0	0	1	0	0	0	13078	933	33	2	92	2	RAP2B	3	152880572	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325977	152880572	45141858	2859	10844										
SGEF	26084	broad.mit.edu	37	chr3	153973152	153973152	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaacgactacgagatggaGaaagaggctggtttcctatg	15	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:153973152G>T	ENST00000356448.4	+	15	2790	c.2506G>T	c.(2506-2508)Gaa>Taa	p.E836*	ARHGEF26_ENST00000483068.1_3'UTR|ARHGEF26_ENST00000465093.1_Nonsense_Mutation_p.E836*|ARHGEF26_ENST00000465817.1_Intron	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	836	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E836*(2)		endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						ACGAGATGGAGAAAGAGGCTG	0.468																																					GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)											2	Substitution - Nonsense(2)	large_intestine(2)	3											148	145	146					3																	153973152		1960	4155	6115	155455846	SO:0001587	stop_gained	26084			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.2506G>T	3.37:g.153973152G>T	ENSP00000348828:p.Glu836*		155455846	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Nonsense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	G	42	9.299682	0.99130	.	.	ENSG00000114790	ENST00000356448;ENST00000465093	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-29.8888	19.8936	0.96942	0.0:0.0:1.0:0.0	.	.	.	.	X	836	.	ENSP00000348828:E836X	E	+	1	0	ARHGEF26	155455846	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	6.109000	0.71528	2.793000	0.96121	0.655000	0.94253	GAA		0.468	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		T	153973152	G	T	153973152	4	4	61	1	0	0	0	0	0	1	0	0	14242	943	33	2	2346	2	SGEF	3	153973152	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1092580	153973152	44049278	2860	10845										
DHX36	170506	broad.mit.edu	37	chr3	154002755	154002755	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactccaagaggtgtcaattCttcttgtttatccaaagcgt	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154002755C>A	ENST00000496811.1	-	18	2133	c.2053G>T	c.(2053-2055)Gaa>Taa	p.E685*	DHX36_ENST00000308361.6_Nonsense_Mutation_p.E685*|DHX36_ENST00000329463.5_Nonsense_Mutation_p.E671*|DHX36_ENST00000544526.1_Nonsense_Mutation_p.E671*	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	685					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)	p.E685*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GGTGTCAATTCTTCTTGTTTA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											113	111	111					3																	154002755		2203	4300	6503	155485449	SO:0001587	stop_gained	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2053G>T	3.37:g.154002755C>A	ENSP00000417078:p.Glu685*		155485449	B2RB00|Q70JU3|Q8IYE5|Q9P240	Nonsense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	41|41	8.989230|8.989230	0.99027|0.99027	.|.	.|.	ENSG00000174953|ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941|ENST00000469977	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.089581|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79569	.|0.4468	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77807	.|-0.2450	.|3	0.21540|.	T|.	0.41|.	.|.	19.6173|19.6173	0.95639|0.95639	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	685;685;671;671;599|131	.|.	ENSP00000309296:E685X|.	E|K	-|-	1|3	0|2	DHX36|DHX36	155485449|155485449	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.701000|4.701000	0.61810|0.61810	2.647000|2.647000	0.89833|0.89833	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.378	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154002755	C	A	154002755	4	1	61	1	0	0	0	0	0	1	0	0	4520	922	32	2	1005	2	DHX36	3	154002755	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29603	154002755	44019675	2861	10846										
DHX36	170506	broad.mit.edu	37	chr3	154011591	154011591	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgaacaccaggaggggttCttttaaacacctgtaaaaat	8	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154011591C>A	ENST00000496811.1	-	14	1696	c.1616G>T	c.(1615-1617)aGa>aTa	p.R539I	DHX36_ENST00000308361.6_Missense_Mutation_p.R539I|DHX36_ENST00000329463.5_Missense_Mutation_p.R525I|DHX36_ENST00000544526.1_Missense_Mutation_p.R525I	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	539	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)	p.R539I(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AGGAGGGGTTCTTTTAAACAC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	3											66	70	68					3																	154011591		2203	4295	6498	155494285	SO:0001583	missense	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1616G>T	3.37:g.154011591C>A	ENSP00000417078:p.Arg539Ile		155494285	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.27|19.27	3.794661|3.794661	0.70452|0.70452	.|.	.|.	ENSG00000174953|ENSG00000174953	ENST00000469977|ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	.|T;T;T;T;T	.|0.77098	.|-1.07;-1.07;-1.07;-1.07;-1.07	5.92|5.92	-2.02|-2.02	0.07388|0.07388	.|Helicase, C-terminal (3);	.|0.392877	.|0.35615	.|N	.|0.003099	.|T	.|0.76786	.|0.4036	L|L	0.49571|0.49571	1.57|1.57	0.58432|0.58432	D|D	0.999992|0.999992	.|P;P;P	.|0.38767	.|0.594;0.594;0.646	.|P;P;P	.|0.48921	.|0.459;0.459;0.595	.|T	.|0.74393	.|-0.3680	.|10	.|0.56958	.|D	.|0.05	.|.	12.8673|12.8673	0.57946|0.57946	0.0:0.4017:0.0:0.5983|0.0:0.4017:0.0:0.5983	.|.	.|525;539;539	.|Q9H2U1-2;Q9H2U1-3;Q9H2U1	.|.;.;DHX36_HUMAN	X|I	19|539;539;525;525;453	.|ENSP00000417078:R539I;ENSP00000309296:R539I;ENSP00000444247:R525I;ENSP00000330113:R525I;ENSP00000419862:R453I	.|ENSP00000309296:R539I	E|R	-|-	1|2	0|0	DHX36|DHX36	155494285|155494285	0.993000|0.993000	0.37304|0.37304	0.979000|0.979000	0.43373|0.43373	0.944000|0.944000	0.59088|0.59088	0.328000|0.328000	0.19681|0.19681	-0.440000|-0.440000	0.07211|0.07211	-0.225000|-0.225000	0.12378|0.12378	GAA|AGA		0.299	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154011591	C	A	154011591	3	1	61	1	0	0	0	0	1	0	0	0	4520	913	32	2	1458	2	DHX36	3	154011591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8836	154011591	44010839	2862	10847										
GPR149	344758	broad.mit.edu	37	chr3	154055623	154055623	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctactgtgtctggaatggaGatattaatatcaccatcagg	9	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154055623G>T	ENST00000389740.2	-	4	2160	c.2061C>A	c.(2059-2061)atC>atA	p.I687I		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	687					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I687I(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CTGGAATGGAGATATTAATAT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	3											268	246	253					3																	154055623		1915	4142	6057	155538317	SO:0001819	synonymous_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2061C>A	3.37:g.154055623G>T			155538317		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																				0.433	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154055623	G	T	154055623	2	4	61	1	0	0	0	0	0	0	0	1	6674	932	33	2		2	GPR149	3	154055623	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44032	154055623	43966807	2863	10848										
GPR149	344758	broad.mit.edu	37	chr3	154146591	154146591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccggtccgaacacggtgtCggagctcggagagcatcccc	13	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154146591C>T	ENST00000389740.2	-	1	913	c.814G>A	c.(814-816)Gac>Aac	p.D272N		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	272					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D272N(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AACACGGTGTCGGAGCTCGGA	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	3											31	35	34					3																	154146591		1879	4115	5994	155629285	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.814G>A	3.37:g.154146591C>T	ENSP00000374390:p.Asp272Asn		155629285		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397902	0.42512	.	.	ENSG00000174948	ENST00000389740	T	0.28895	1.59	4.4	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.300662	0.36972	N	0.002310	T	0.26955	0.0660	M	0.66439	2.03	0.09310	N	1	P	0.44816	0.844	B	0.35655	0.207	T	0.30909	-0.9962	10	0.72032	D	0.01	-14.5785	7.8788	0.29610	0.0:0.7202:0.1492:0.1305	.	272	Q86SP6	GP149_HUMAN	N	272	ENSP00000374390:D272N	ENSP00000374390:D272N	D	-	1	0	GPR149	155629285	0.751000	0.28327	0.043000	0.18650	0.003000	0.03518	2.101000	0.41787	1.060000	0.40578	0.655000	0.94253	GAC		0.682	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154146591	C	T	154146591	3	4	61	1	0	0	0	0	1	0	0	0	6674	884	31	1	1397	1	GPR149	3	154146591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90968	154146591	43875839	2864	10849										
GPR149	344758	broad.mit.edu	37	chr3	154146749	154146749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtctcggcggctcctccGaacacagcaatcggtgagtg	14	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154146749G>A	ENST00000389740.2	-	1	755	c.656C>T	c.(655-657)tCg>tTg	p.S219L		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	219					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S219L(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CGGCTCCTCCGAACACAGCAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	3											51	57	55					3																	154146749		1920	4133	6053	155629443	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.656C>T	3.37:g.154146749G>A	ENSP00000374390:p.Ser219Leu		155629443		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154431	0.57259	.	.	ENSG00000174948	ENST00000389740	T	0.69806	-0.43	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.122271	0.56097	D	0.000024	T	0.81697	0.4877	M	0.76838	2.35	0.52099	D	0.999943	D	0.89917	1.0	D	0.91635	0.999	D	0.83861	0.0268	10	0.87932	D	0	-13.5881	14.7772	0.69738	0.0:0.1439:0.8561:0.0	.	219	Q86SP6	GP149_HUMAN	L	219	ENSP00000374390:S219L	ENSP00000374390:S219L	S	-	2	0	GPR149	155629443	1.000000	0.71417	0.905000	0.35620	0.147000	0.21601	6.861000	0.75478	2.541000	0.85698	0.655000	0.94253	TCG		0.577	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		A	154146749	G	A	154146749	3	1	61	1	0	0	0	0	1	0	0	0	6674	1059	37	1	1555	1	GPR149	3	154146749	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	158	154146749	43875681	2865	10850										
MME	4311	broad.mit.edu	37	chr3	154858002	154858002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacggctaaacctgaagatcGaaatgatccaatgcttctgt	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154858002G>A	ENST00000460393.1	+	10	998	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	MME_ENST00000492661.1_Missense_Mutation_p.R293Q|MME_ENST00000462745.1_Missense_Mutation_p.R293Q|MME_ENST00000360490.2_Missense_Mutation_p.R293Q|MME_ENST00000493237.1_Missense_Mutation_p.R293Q	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	293					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.R293Q(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CCTGAAGATCGAAATGATCCA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											76	70	72					3																	154858002		2203	4300	6503	156340696	SO:0001583	missense	4311				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.878G>A	3.37:g.154858002G>A	ENSP00000418525:p.Arg293Gln		156340696	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681353	0.88542	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.23	5.23	0.72850	Peptidase M13 (1);	0.140473	0.45867	D	0.000338	D	0.88081	0.6341	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.89682	0.3891	10	0.87932	D	0	-11.4936	19.1928	0.93674	0.0:0.0:1.0:0.0	.	293	P08473	NEP_HUMAN	Q	293	ENSP00000420389:R293Q;ENSP00000418525:R293Q;ENSP00000419653:R293Q;ENSP00000417079:R293Q;ENSP00000353679:R293Q	ENSP00000353679:R293Q	R	+	2	0	MME	156340696	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	8.363000	0.90103	2.596000	0.87737	0.655000	0.94253	CGA		0.308	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154858002	G	A	154858002	3	1	61	1	0	0	0	0	1	0	0	0	9675	1058	37	1	912	1	MME	3	154858002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	711253	154858002	43164428	2866	10851										
MME	4311	broad.mit.edu	37	chr3	154860030	154860030	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttttttttatacagagatCttcaaaatttaatgtcctgg	7	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154860030C>A	ENST00000460393.1	+	12	1219	c.1099C>A	c.(1099-1101)Ctt>Att	p.L367I	MME_ENST00000492661.1_Missense_Mutation_p.L367I|MME_ENST00000462745.1_Missense_Mutation_p.L367I|MME_ENST00000360490.2_Missense_Mutation_p.L367I|MME_ENST00000493237.1_Missense_Mutation_p.L367I	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	367					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.L367I(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	ATACAGAGATCTTCAAAATTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	3											92	98	96					3																	154860030		2202	4300	6502	156342724	SO:0001583	missense	4311				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1099C>A	3.37:g.154860030C>A	ENSP00000418525:p.Leu367Ile		156342724	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444407	0.25987	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.94	5.94	0.96194	Peptidase M13 (1);	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.39397	1.21	0.54753	D	0.999983	B	0.02656	0.0	B	0.16722	0.016	T	0.56105	-0.8034	10	0.19590	T	0.45	-21.2841	9.3309	0.38021	0.1452:0.7835:0.0:0.0713	.	367	P08473	NEP_HUMAN	I	367	ENSP00000420389:L367I;ENSP00000418525:L367I;ENSP00000419653:L367I;ENSP00000417079:L367I;ENSP00000353679:L367I	ENSP00000353679:L367I	L	+	1	0	MME	156342724	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.150000	0.42254	2.807000	0.96579	0.591000	0.81541	CTT		0.418	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154860030	C	A	154860030	3	1	61	1	0	0	0	0	1	0	0	0	9675	913	32	2	1141	2	MME	3	154860030	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2028	154860030	43162400	2867	10852										
MME	4311	broad.mit.edu	37	chr3	154862150	154862150	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgttctgatttgaggtCgaggatttgattgcacagat	11	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:154862150C>T	ENST00000460393.1	+	14	1440	c.1320C>T	c.(1318-1320)gtC>gtT	p.V440V	MME_ENST00000492661.1_Silent_p.V440V|MME_ENST00000462745.1_Silent_p.V440V|MME_ENST00000360490.2_Silent_p.V440V|MME_ENST00000493237.1_Silent_p.V440V	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	440					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.V440V(2)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	GATTTGAGGTCGAGGATTTGA	0.343																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	3											90	93	92					3																	154862150		2203	4300	6503	156344844	SO:0001819	synonymous_variant	4311				CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1320C>T	3.37:g.154862150C>T			156344844	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	37	CCDS3172.1																																																																																				0.343	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		T	154862150	C	T	154862150	2	4	61	1	0	0	0	0	0	0	0	1	9675	871	31	1		1	MME	3	154862150	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2120	154862150	43160280	2868	10853										
PLCH1	23007	broad.mit.edu	37	chr3	155271965	155271965	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtactactggctctccatCtgggccatcccaacagtcaa	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155271965C>T	ENST00000340059.7	-	8	1053	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	PLCH1_ENST00000414191.1_Missense_Mutation_p.D334N|PLCH1_ENST00000447496.2_Missense_Mutation_p.D352N|PLCH1_ENST00000334686.6_Missense_Mutation_p.D334N|PLCH1_ENST00000494598.1_Missense_Mutation_p.D352N|PLCH1_ENST00000460012.1_Missense_Mutation_p.D334N	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	352	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.D334N(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GGCTCTCCATCTGGGCCATCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	3											121	112	115					3																	155271965		2203	4300	6503	156754659	SO:0001583	missense	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.1054G>A	3.37:g.155271965C>T	ENSP00000345988:p.Asp352Asn		156754659	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165039	0.94727	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5	5.62	5.62	0.85841	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.050765	0.85682	D	0.000000	T	0.70527	0.3234	L	0.56280	1.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.996;0.998;0.984	T	0.71318	-0.4629	10	0.66056	D	0.02	.	19.6718	0.95914	0.0:1.0:0.0:0.0	.	334;352;352	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	N	352;334;352;352;334;334	ENSP00000419100:D352N;ENSP00000417502:D334N;ENSP00000402759:D352N;ENSP00000345988:D352N;ENSP00000335469:D334N;ENSP00000412977:D334N	ENSP00000335469:D334N	D	-	1	0	PLCH1	156754659	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	5.941000	0.70195	2.639000	0.89480	0.557000	0.71058	GAT		0.393	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155271965	C	T	155271965	3	4	61	1	0	0	0	0	1	0	0	0	12068	913	32	3	4106	3	PLCH1	3	155271965	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	409815	155271965	42750465	2869	10854										
PLCH1	23007	broad.mit.edu	37	chr3	155282848	155282848	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatccatgtcttggtacaCttcatggtgcaatgggttaa	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155282848C>A	ENST00000340059.7	-	7	888	c.889G>T	c.(889-891)Gtg>Ttg	p.V297L	PLCH1_ENST00000414191.1_Missense_Mutation_p.V279L|PLCH1_ENST00000447496.2_Missense_Mutation_p.V297L|PLCH1_ENST00000334686.6_Missense_Mutation_p.V279L|PLCH1_ENST00000494598.1_Missense_Mutation_p.V297L|PLCH1_ENST00000460012.1_Missense_Mutation_p.V279L	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	297					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.V279L(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TCTTGGTACACTTCATGGTGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											164	145	151					3																	155282848		2203	4300	6503	156765542	SO:0001583	missense	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.889G>T	3.37:g.155282848C>A	ENSP00000345988:p.Val297Leu		156765542	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671081	0.67814	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	5.11	5.11	0.69529	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.070148	0.56097	D	0.000026	T	0.49338	0.1551	M	0.84773	2.715	0.54753	D	0.999988	D;D;P	0.60575	0.985;0.988;0.918	P;D;P	0.65323	0.891;0.934;0.499	T	0.48811	-0.9002	10	0.22109	T	0.4	.	11.9577	0.52991	0.0:0.9205:0.0:0.0795	.	279;297;297	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	L	297;279;297;297;279;279	ENSP00000419100:V297L;ENSP00000417502:V279L;ENSP00000402759:V297L;ENSP00000345988:V297L;ENSP00000335469:V279L;ENSP00000412977:V279L	ENSP00000335469:V279L	V	-	1	0	PLCH1	156765542	1.000000	0.71417	0.919000	0.36401	0.995000	0.86356	4.852000	0.62904	2.371000	0.80710	0.655000	0.94253	GTG		0.458	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		A	155282848	C	A	155282848	3	1	61	1	0	0	0	0	1	0	0	0	12068	565	20	2	4275	2	PLCH1	3	155282848	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10883	155282848	42739582	2870	10855										
C3orf33	285315	broad.mit.edu	37	chr3	155481612	155481612	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgtgaactgtccagtaGattttagaatcatatttaag	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155481612G>T	ENST00000340171.2	-	5	677	c.579C>A	c.(577-579)atC>atA	p.I193I	C3orf33_ENST00000534941.1_Silent_p.I150I			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	193					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)	p.I144I(1)		breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTGTCCAGTAGATTTTAGAAT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	3											32	27	29					3																	155481612		1796	4054	5850	156964306	SO:0001819	synonymous_variant	285315			AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.579C>A	3.37:g.155481612G>T			156964306	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Silent	SNP	ENST00000340171.2	37																																																																																					0.348	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657		T	155481612	G	T	155481612	2	4	61	1	0	0	0	0	0	0	0	1	2229	932	33	2		2	C3orf33	3	155481612	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198764	155481612	42540818	2871	10856										
C3orf33	285315	broad.mit.edu	37	chr3	155493558	155493558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaaccattctcagttattCggcgtaatcgtccacgtagt	7	11	1	0	rs547864770		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155493558C>T	ENST00000340171.2	-	3	352	c.254G>A	c.(253-255)cGa>cAa	p.R85Q	C3orf33_ENST00000534941.1_Missense_Mutation_p.R42Q			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	85					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)	p.R36Q(1)		breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTCAGTTATTCGGCGTAATCG	0.308													C|||	1	0.000199681	8e-04	0	5008	,	,		14682	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											103	103	103					3																	155493558		1811	4066	5877	156976252	SO:0001583	missense	285315			AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.254G>A	3.37:g.155493558C>T	ENSP00000342512:p.Arg85Gln		156976252	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Missense_Mutation	SNP	ENST00000340171.2	37		.	.	.	.	.	.	.	.	.	.	C	10.34	1.322119	0.23994	.	.	ENSG00000174928	ENST00000534941;ENST00000340171;ENST00000537385	T;T	0.46819	0.86;0.86	5.45	1.63	0.23807	.	0.528800	0.19690	N	0.108289	T	0.29355	0.0731	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.16630	-1.0396	10	0.22706	T	0.39	-2.4076	9.1843	0.37160	0.0:0.6476:0.0:0.3524	.	85	Q6P1S2	CC033_HUMAN	Q	42;85;85	ENSP00000445446:R42Q;ENSP00000342512:R85Q	ENSP00000342512:R85Q	R	-	2	0	C3orf33	156976252	0.585000	0.26774	0.805000	0.32314	0.982000	0.71751	0.247000	0.18179	0.671000	0.31185	-0.137000	0.14449	CGA		0.308	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657		T	155493558	C	T	155493558	3	4	61	1	0	0	0	0	1	0	0	0	2229	884	31	1	642	1	C3orf33	3	155493558	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11946	155493558	42528872	2872	10857										
SLC33A1	9197	broad.mit.edu	37	chr3	155546024	155546024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttccttttgcatttccacGaagatgatccttcatcctgt	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155546024G>A	ENST00000392845.3	-	6	2005	c.1625C>T	c.(1624-1626)tCg>tTg	p.S542L	SLC33A1_ENST00000359479.3_Missense_Mutation_p.S542L			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	542					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)	p.S542L(2)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GCATTTCCACGAAGATGATCC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	3											110	111	111					3																	155546024		2203	4300	6503	157028718	SO:0001583	missense	9197			D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"Solute carriers"	95	protein-coding gene	gene with protein product		603690	"acetyl-Coenzyme A transporter", "spastic paraplegia 42 (autosomal dominant)"	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.1625C>T	3.37:g.155546024G>A	ENSP00000376587:p.Ser542Leu		157028718	B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	37	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036764	0.75617	.	.	ENSG00000169359	ENST00000392845;ENST00000359479;ENST00000496772	T;T;T	0.78126	-1.15;-1.15;-1.15	5.78	5.78	0.91487	.	0.118903	0.64402	D	0.000018	T	0.76271	0.3964	M	0.64170	1.965	0.80722	D	1	P	0.44044	0.825	B	0.36534	0.227	T	0.78904	-0.2020	10	0.52906	T	0.07	-10.4351	20.0585	0.97663	0.0:0.0:1.0:0.0	.	542	O00400	ACATN_HUMAN	L	542;542;178	ENSP00000376587:S542L;ENSP00000352456:S542L;ENSP00000419165:S178L	ENSP00000352456:S542L	S	-	2	0	SLC33A1	157028718	1.000000	0.71417	0.977000	0.42913	0.871000	0.50021	9.714000	0.98744	2.741000	0.93983	0.650000	0.86243	TCG		0.338	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733		A	155546024	G	A	155546024	3	1	61	1	0	0	0	0	1	0	0	0	14603	1059	37	1	28	1	SLC33A1	3	155546024	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52466	155546024	42476406	2873	10858										
KCNAB1	7881	broad.mit.edu	37	chr3	155861089	155861089	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaagactcagcctcaggCggcctgcaaacctgtgaggc	12	14	2	2	rs546028597	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:155861089C>T	ENST00000490337.1	+	1	339				KCNAB1_ENST00000471742.1_Missense_Mutation_p.A41V|KCNAB1_ENST00000389636.5_Intron	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)	p.A41V(2)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CAGCCTCAGGCGGCCTGCAAA	0.522													C|||	9	0.00179712	0	0	5008	,	,		16753	0		0	False		,,,				2504	0.0092															2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	3											58	56	57					3																	155861089		2203	4300	6503	157343783	SO:0001627	intron_variant	7881			U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22414C>T	3.37:g.155861089C>T			157343783	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	37	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	C	0.086	-1.175941	0.01646	.	.	ENSG00000169282	ENST00000471742	T	0.06449	3.3	5.17	0.952	0.19584	.	.	.	.	.	T	0.04363	0.0120	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	8	0.54805	T	0.06	.	1.1332	0.01749	0.2962:0.3231:0.2263:0.1544	.	41	Q14722-3	.	V	41	ENSP00000418956:A41V	ENSP00000418956:A41V	A	+	2	0	KCNAB1	157343783	0.003000	0.15002	0.006000	0.13384	0.046000	0.14306	0.118000	0.15605	0.166000	0.19597	-0.268000	0.10319	GCG		0.522	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		T	155861089	C	T	155861089	1	4	61	0	1	0	0	0	0	0	0	0	8030	768	27	1		1	KCNAB1	3	155861089	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	315065	155861089	42161341	2874	10859										
TIPARP	25976	broad.mit.edu	37	chr3	156396084	156396084	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttacaatccaatacattCtggacaccagtgataagctg	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:156396084C>A	ENST00000461166.1	+	2	1186	c.598C>A	c.(598-600)Ctg>Atg	p.L200M	TIPARP_ENST00000295924.7_Missense_Mutation_p.L200M|TIPARP_ENST00000486483.1_Missense_Mutation_p.L200M|TIPARP_ENST00000542783.1_Missense_Mutation_p.L200M	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	200					androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.L200M(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CCAATACATTCTGGACACCAG	0.423																																					Ovarian(171;276 1987 3319 6837 11197)											1	Substitution - Missense(1)	large_intestine(1)	3											89	90	90					3																	156396084		2203	4300	6503	157878778	SO:0001583	missense	25976			BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.598C>A	3.37:g.156396084C>A	ENSP00000420612:p.Leu200Met		157878778	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	Missense_Mutation	SNP	ENST00000461166.1	37	CCDS3177.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.706152	0.30232	.	.	ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783	T;T;T;T;T;T	0.31769	2.52;2.52;2.52;1.48;2.52;2.52	5.38	4.22	0.49857	.	0.117429	0.37857	N	0.001920	T	0.18383	0.0441	N	0.19112	0.55	0.38138	D	0.938357	P	0.44578	0.838	B	0.41691	0.364	T	0.07908	-1.0748	10	0.46703	T	0.11	.	5.1076	0.14793	0.1349:0.1507:0.0:0.7145	.	200	Q7Z3E1	PARPT_HUMAN	M	200	ENSP00000418757:L200M;ENSP00000295924:L200M;ENSP00000420612:L200M;ENSP00000419982:L200M;ENSP00000418829:L200M;ENSP00000438345:L200M	ENSP00000295924:L200M	L	+	1	2	TIPARP	157878778	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	1.332000	0.33805	0.877000	0.35895	-0.414000	0.06135	CTG		0.423	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		A	156396084	C	A	156396084	3	1	61	1	0	0	0	0	1	0	0	0	15963	912	32	2	600	2	TIPARP	3	156396084	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	534995	156396084	41626346	2875	10860										
TIPARP	25976	broad.mit.edu	37	chr3	156396212	156396212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagagaacggaattgaaatTtgcatggactttctgcaagg	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:156396212T>G	ENST00000461166.1	+	2	1314	c.726T>G	c.(724-726)atT>atG	p.I242M	TIPARP_ENST00000295924.7_Missense_Mutation_p.I242M|TIPARP_ENST00000486483.1_Missense_Mutation_p.I242M|TIPARP_ENST00000542783.1_Missense_Mutation_p.I242M	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	242					androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.I242M(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAATTGAAATTTGCATGGACT	0.453																																					Ovarian(171;276 1987 3319 6837 11197)											1	Substitution - Missense(1)	large_intestine(1)	3											142	149	147					3																	156396212		2203	4300	6503	157878906	SO:0001583	missense	25976			BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.726T>G	3.37:g.156396212T>G	ENSP00000420612:p.Ile242Met		157878906	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	Missense_Mutation	SNP	ENST00000461166.1	37	CCDS3177.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.733095	0.48939	.	.	ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783	T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88	5.54	1.94	0.25998	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	M	0.81497	2.545	0.43740	D	0.996238	D	0.89917	1.0	D	0.87578	0.998	T	0.56402	-0.7985	10	0.87932	D	0	.	3.5783	0.07942	0.1702:0.3574:0.0:0.4725	.	242	Q7Z3E1	PARPT_HUMAN	M	242	ENSP00000418757:I242M;ENSP00000295924:I242M;ENSP00000420612:I242M;ENSP00000419982:I242M;ENSP00000418829:I242M;ENSP00000438345:I242M	ENSP00000295924:I242M	I	+	3	3	TIPARP	157878906	0.975000	0.34042	1.000000	0.80357	0.988000	0.76386	0.098000	0.15189	0.406000	0.25560	-0.376000	0.06991	ATT		0.453	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		G	156396212	T	G	156396212	3	3	61	1	0	0	0	0	1	0	0	0	15963	1829	64	4	728	4	TIPARP	3	156396212	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	128	156396212	41626218	2876	10861										
TIPARP	25976	broad.mit.edu	37	chr3	156396354	156396354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgattctcaggagcacttgGaaagattttactgtaaccca	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:156396354G>A	ENST00000461166.1	+	2	1456	c.868G>A	c.(868-870)Gaa>Aaa	p.E290K	TIPARP_ENST00000295924.7_Missense_Mutation_p.E290K|TIPARP_ENST00000486483.1_Missense_Mutation_p.E290K|TIPARP_ENST00000542783.1_Missense_Mutation_p.E290K	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	290					androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.E290K(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GGAGCACTTGGAAAGATTTTA	0.363																																					Ovarian(171;276 1987 3319 6837 11197)											1	Substitution - Missense(1)	large_intestine(1)	3											70	72	71					3																	156396354		2203	4300	6503	157879048	SO:0001583	missense	25976			BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.868G>A	3.37:g.156396354G>A	ENSP00000420612:p.Glu290Lys		157879048	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	Missense_Mutation	SNP	ENST00000461166.1	37	CCDS3177.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791503	0.70452	.	.	ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783	T;T;T;T;T;T	0.59638	1.34;1.34;1.34;0.25;1.34;1.34	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.62073	0.2398	M	0.82193	2.58	0.80722	D	1	P	0.38535	0.635	B	0.32677	0.15	T	0.71206	-0.4661	10	0.87932	D	0	.	18.6261	0.91340	0.0:0.0:1.0:0.0	.	290	Q7Z3E1	PARPT_HUMAN	K	290	ENSP00000418757:E290K;ENSP00000295924:E290K;ENSP00000420612:E290K;ENSP00000419982:E290K;ENSP00000418829:E290K;ENSP00000438345:E290K	ENSP00000295924:E290K	E	+	1	0	TIPARP	157879048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.338000	0.96553	2.498000	0.84270	0.563000	0.77884	GAA		0.363	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		A	156396354	G	A	156396354	3	1	61	1	0	0	0	0	1	0	0	0	15963	1175	41	3	870	3	TIPARP	3	156396354	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142	156396354	41626076	2877	10862										
LEKR1	389170	broad.mit.edu	37	chr3	156710960	156710960	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactgtgaaagaaaagcaaGaagaagacataaagagaaga	11	3	0	8			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:156710960G>T	ENST00000470811.1	+	10	1426	c.91G>T	c.(91-93)Gaa>Taa	p.E31*	LEKR1_ENST00000356539.4_Nonsense_Mutation_p.E335*			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	31								p.E31*(1)		breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AGAAAAGCAAGAAGAAGACAT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											77	80	79					3																	156710960		2203	4297	6500	158193654	SO:0001587	stop_gained	389170			AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.91G>T	3.37:g.156710960G>T	ENSP00000418214:p.Glu31*		158193654		Nonsense_Mutation	SNP	ENST00000470811.1	37		.	.	.	.	.	.	.	.	.	.	G	22.6	4.316878	0.81469	.	.	ENSG00000178110	ENST00000470811;ENST00000356539	.	.	.	4.97	4.03	0.46877	.	0.105342	0.41823	D	0.000820	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-11.4194	13.5073	0.61491	0.0:0.1576:0.8424:0.0	.	.	.	.	X	31;335	.	ENSP00000348936:E335X	E	+	1	0	LEKR1	158193654	1.000000	0.71417	0.995000	0.50966	0.260000	0.26232	3.043000	0.49823	2.307000	0.77673	0.591000	0.81541	GAA		0.348	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		T	156710960	G	T	156710960	4	4	61	1	0	0	0	0	0	1	0	0	8739	943	33	2	1033	2	LEKR1	3	156710960	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	314606	156710960	41311470	2878	10863										
RSRC1	51319	broad.mit.edu	37	chr3	157921011	157921011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggataaagggaaggacaaGgaattacataacatcaaacg	10	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:157921011G>T	ENST00000295930.3	+	4	633	c.471G>T	c.(469-471)aaG>aaT	p.K157N	RSRC1_ENST00000496268.1_3'UTR|RSRC1_ENST00000475278.2_Missense_Mutation_p.K157N|RSRC1_ENST00000312179.6_Intron|RSRC1_ENST00000480820.1_Missense_Mutation_p.K157N|RSRC1_ENST00000464171.1_Intron	NM_001271838.1|NM_016625.2	NP_001258767.1|NP_057709.2	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	157					mRNA splicing, via spliceosome (GO:0000398)|nucleocytoplasmic transport (GO:0006913)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)		p.K157N(1)		cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	18			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			ggaaggacaaggaATTACATA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	103	100					3																	157921011		2203	4300	6503	159403705	SO:0001583	missense	51319			AF208853	CCDS3181.1, CCDS63822.1	3q25.32	2009-09-09			ENSG00000174891	ENSG00000174891			24152	protein-coding gene	gene with protein product	"splicing factor, arginine/serine-rich 21"	613352				15798186, 19065146	Standard	NM_001271838		Approved	MGC12197, BM-011, SRrp53, SFRS21	uc003fbu.2	Q96IZ7	OTTHUMG00000158758	ENST00000295930.3:c.471G>T	3.37:g.157921011G>T	ENSP00000295930:p.Lys157Asn		159403705	A8K2R9|Q96QK2|Q9NZE5	Missense_Mutation	SNP	ENST00000295930.3	37	CCDS3181.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.82|14.82	2.648411|2.648411	0.47258|0.47258	.|.	.|.	ENSG00000174891|ENSG00000174891	ENST00000482822|ENST00000480820;ENST00000494002;ENST00000295930;ENST00000471994;ENST00000475278;ENST00000476899	.|.	.|.	.|.	5.04|5.04	3.05|3.05	0.35203|0.35203	.|.	.|0.207512	.|0.48286	.|D	.|0.000190	.|T	.|0.45875	.|0.1364	L|L	0.48642|0.48642	1.525|1.525	0.41680|0.41680	D|D	0.989289|0.989289	.|B	.|0.15930	.|0.015	.|B	.|0.14578	.|0.011	.|T	.|0.40001	.|-0.9586	.|9	.|0.66056	.|D	.|0.02	.|.	5.2634|5.2634	0.15586|0.15586	0.2187:0.1679:0.6134:0.0|0.2187:0.1679:0.6134:0.0	.|.	.|157	.|Q96IZ7	.|RSRC1_HUMAN	X|N	51|157	.|.	.|ENSP00000295930:K157N	G|K	+|+	1|3	0|2	RSRC1|RSRC1	159403705|159403705	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.972000|0.972000	0.66771|0.66771	0.945000|0.945000	0.29056|0.29056	0.475000|0.475000	0.27415|0.27415	0.591000|0.591000	0.81541|0.81541	GGA|AAG		0.423	RSRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352063.2	NM_016625		T	157921011	G	T	157921011	3	4	61	1	0	0	0	0	1	0	0	0	13751	991	35	2	481	2	RSRC1	3	157921011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1210051	157921011	40101419	2879	10864										
GFM1	85476	broad.mit.edu	37	chr3	158378752	158378752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacagacaaagccaacagCggcctttctatggtaagcca	8	12	2	1	rs199976566		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:158378752C>T	ENST00000486715.1	+	10	1668	c.1311C>T	c.(1309-1311)agC>agT	p.S437S	GFM1_ENST00000478576.1_Silent_p.S437S|GFM1_ENST00000490261.1_3'UTR|GFM1_ENST00000264263.5_Silent_p.S456S	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1									p.S437S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AAGCCAACAGCGGCCTTTCTA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	3						T		0,4406		0,0,2203	119	118	118		1311	-0.6	0.1	3		118	1,8599	819.2+/-406.8	0,1,4299	yes	coding-synonymous	GFM1	NM_024996.5		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		437/752	158378752	1,13005	2203	4300	6503	159861446	SO:0001819	synonymous_variant	85476			AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"G translation elongation factor, mitochondrial"			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.1311C>T	3.37:g.158378752C>T			159861446		Silent	SNP	ENST00000486715.1	37	CCDS33885.1																																																																																				0.363	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		T	158378752	C	T	158378752	2	4	61	1	0	0	0	0	0	0	0	1	6361	767	27	1		1	GFM1	3	158378752	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	457741	158378752	39643678	2880	10865										
MFSD1	64747	broad.mit.edu	37	chr3	158522114	158522115	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttttctaggcagctaINStttttgctatgataatcctg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:158522114_158522115insT	ENST00000264266.8	+	2	232_233	c.170_171insT	c.(169-174)tattttfs	p.YF57fs	MFSD1_ENST00000392813.4_Frame_Shift_Ins_p.I105fs|RP11-379F4.9_ENST00000607044.1_RNA|MFSD1_ENST00000415822.2_Frame_Shift_Ins_p.YF106fs			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	57					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.C59fs*3(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CTAGGCAGCTATTTTTGCTATG	0.327																																					Pancreas(62;1186 1654 36636 37908)											1	Insertion - Frameshift(1)	large_intestine(1)	3																																								160004809	SO:0001589	frameshift_variant	64747			BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.175dupT	3.37:g.158522119_158522119dupT	ENSP00000264266:p.Tyr57fs		160004808	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Frame_Shift_Ins	INS	ENST00000264266.8	37																																																																																					0.327	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		T	158522115	-	T	158522114	7	5	61	1	0	1	1	0	0	0	0	0	9557	449	16	0	323	0	MFSD1	3	158522114	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	143362	158522114	39500316	2881	10866										
MFSD1	64747	broad.mit.edu	37	chr3	158531818	158531818	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgaagctttgttaggttCtgctggtcacacaaccctcg	10	10	2	1	rs9867246		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:158531818C>A	ENST00000264266.8	+	7	676	c.614C>A	c.(613-615)tCt>tAt	p.S205Y	MFSD1_ENST00000392813.4_Missense_Mutation_p.S215Y|MFSD1_ENST00000415822.2_Missense_Mutation_p.S254Y			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	205					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.S205Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTGTTAGGTTCTGCTGGTCAC	0.413																																					Pancreas(62;1186 1654 36636 37908)											1	Substitution - Missense(1)	large_intestine(1)	3											182	147	159					3																	158531818		2203	4300	6503	160014512	SO:0001583	missense	64747			BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.614C>A	3.37:g.158531818C>A	ENSP00000264266:p.Ser205Tyr		160014512	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		.	.	.	.	.	.	.	.	.	.	c	2.917	-0.224150	0.06061	.	.	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000361159;ENST00000477743	T;T;T;T	0.24350	2.1;2.11;2.13;1.86	4.9	4.9	0.64082	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.131953	0.52532	D	0.000067	T	0.22704	0.0548	L	0.54323	1.7	0.48696	D	0.999698	B;B	0.14012	0.009;0.003	B;B	0.20577	0.03;0.01	T	0.06935	-1.0799	10	0.02654	T	1	.	14.3318	0.66561	0.1576:0.8424:0.0:0.0	.	215;205	C9JS94;Q9H3U5	.;MFSD1_HUMAN	Y	254;215;205;129;39	ENSP00000403117:S254Y;ENSP00000376560:S215Y;ENSP00000264266:S205Y;ENSP00000417163:S39Y	ENSP00000264266:S205Y	S	+	2	0	MFSD1	160014512	0.006000	0.16342	1.000000	0.80357	0.584000	0.36387	1.250000	0.32850	2.424000	0.82194	0.650000	0.86243	TCT		0.413	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		A	158531818	C	A	158531818	3	1	61	1	0	0	0	0	1	0	0	0	9557	913	32	2	787	2	MFSD1	3	158531818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9704	158531818	39490612	2882	10867										
IL12A	3592	broad.mit.edu	37	chr3	159711541	159711541	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatgtaccaggtggagttCaagaccatgaatgcaaagct	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:159711541C>A	ENST00000305579.2	+	6	823	c.516C>A	c.(514-516)ttC>ttA	p.F172L	IL12A_ENST00000480787.1_Missense_Mutation_p.F134L|IL12A_ENST00000466512.1_Missense_Mutation_p.F158L|IL12A-AS1_ENST00000497452.1_RNA	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	138					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)	p.F172L(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGGTGGAGTTCAAGACCATGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											147	143	144					3																	159711541		2203	4300	6503	161194235	SO:0001583	missense	3592			M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.516C>A	3.37:g.159711541C>A	ENSP00000303231:p.Phe172Leu		161194235	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	37	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.021632	0.35701	.	.	ENSG00000168811	ENST00000305579;ENST00000480787;ENST00000466512	.	.	.	5.44	4.37	0.52481	.	0.263229	0.44285	N	0.000467	T	0.46502	0.1396	L	0.42245	1.32	0.36767	D	0.88357	B	0.19706	0.038	B	0.17979	0.02	T	0.49532	-0.8930	9	0.31617	T	0.26	-19.9236	9.9741	0.41772	0.0:0.8929:0.0:0.1071	.	172	O60595	.	L	172;134;158	.	ENSP00000303231:F172L	F	+	3	2	IL12A	161194235	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	1.689000	0.37700	2.551000	0.86045	0.655000	0.94253	TTC		0.438	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		A	159711541	C	A	159711541	3	1	61	1	0	0	0	0	1	0	0	0	7645	825	29	2	538	2	IL12A	3	159711541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1179723	159711541	38310889	2883	10868										
IFT80	57560	broad.mit.edu	37	chr3	159995155	159995155	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaacaaggccagcctgaaGaagtactatttcagcctcct	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:159995155G>A	ENST00000326448.7	-	18	2470	c.2038C>T	c.(2038-2040)Ctt>Ttt	p.L680F	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.L851F|IFT80_ENST00000483465.1_Missense_Mutation_p.L543F|IFT80_ENST00000496589.1_Missense_Mutation_p.L543F	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	680					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)		p.L680F(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CCAGCCTGAAGAAGTACTATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											120	120	120					3																	159995155		2203	4300	6503	161477849	SO:0001583	missense	57560			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.2038C>T	3.37:g.159995155G>A	ENSP00000312778:p.Leu680Phe		161477849	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.849884	0.71603	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	D;D;D	0.89617	-2.54;-2.54;-2.54	5.36	4.49	0.54785	.	0.000000	0.48767	U	0.000175	D	0.93621	0.7963	M	0.88105	2.93	0.58432	D	0.999999	D	0.76494	0.999	P	0.60345	0.873	D	0.93705	0.7019	10	0.72032	D	0.01	-19.9347	9.947	0.41616	0.1535:0.0:0.8465:0.0	.	680	Q9P2H3	IFT80_HUMAN	F	680;543;543	ENSP00000312778:L680F;ENSP00000418196:L543F;ENSP00000420646:L543F	ENSP00000312778:L680F	L	-	1	0	IFT80	161477849	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	5.157000	0.64911	1.243000	0.43853	0.655000	0.94253	CTT		0.358	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		A	159995155	G	A	159995155	3	1	61	1	0	0	0	0	1	0	0	0	7585	942	33	3	307	3	IFT80	3	159995155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283614	159995155	38027275	2884	10869										
IFT80	57560	broad.mit.edu	37	chr3	159997001	159997001	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaacaaagcgacaaagtcTcacagcatcttcccattttg	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:159997001T>G	ENST00000326448.7	-	16	2248	c.1816A>C	c.(1816-1818)Aga>Cga	p.R606R	RP11-432B6.3_ENST00000483754.1_Silent_p.R777R|IFT80_ENST00000483465.1_Silent_p.R469R|IFT80_ENST00000496589.1_Silent_p.R469R	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	606					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)		p.R606R(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CGACAAAGTCTCACAGCATCT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	3											87	83	84					3																	159997001		2203	4300	6503	161479695	SO:0001819	synonymous_variant	57560			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1816A>C	3.37:g.159997001T>G			161479695	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Silent	SNP	ENST00000326448.7	37	CCDS3188.1																																																																																				0.343	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		G	159997001	T	G	159997001	2	3	61	1	0	0	0	0	0	0	0	1	7585	1559	54	4		4	IFT80	3	159997001	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1846	159997001	38025429	2885	10870										
IFT80	57560	broad.mit.edu	37	chr3	160021752	160021752	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttctttgagatcaaataTaattggtgtgttccagttct	7	7	3	1	rs377753000		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160021752T>G	ENST00000326448.7	-	11	1534	c.1102A>C	c.(1102-1104)Ata>Cta	p.I368L	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.I539L|IFT80_ENST00000483465.1_Missense_Mutation_p.I231L|IFT80_ENST00000496589.1_Missense_Mutation_p.I231L	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	368					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)		p.I368L(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGATCAAATATAATTGGTGTG	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	72	70					3																	160021752		2202	4294	6496	161504446	SO:0001583	missense	57560			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1102A>C	3.37:g.160021752T>G	ENSP00000312778:p.Ile368Leu		161504446	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.432288	0.83776	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589;ENST00000483325	T;T;T	0.79033	2.34;-1.23;-1.23	5.26	5.26	0.73747	WD40 repeat-like-containing domain (1);	0.000000	0.64402	U	0.000013	T	0.80149	0.4570	M	0.87900	2.915	0.80722	D	1	P	0.47350	0.894	B	0.43950	0.437	T	0.80246	-0.1462	10	0.07990	T	0.79	.	14.8639	0.70401	0.0:0.0:0.0:1.0	.	368	Q9P2H3	IFT80_HUMAN	L	368;231;231;49	ENSP00000312778:I368L;ENSP00000418196:I231L;ENSP00000420646:I231L	ENSP00000312778:I368L	I	-	1	0	IFT80	161504446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.767000	0.68850	1.993000	0.58246	0.528000	0.53228	ATA		0.284	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		G	160021752	T	G	160021752	3	3	61	1	0	0	0	0	1	0	0	0	7585	1406	49	4	1271	4	IFT80	3	160021752	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24751	160021752	38000678	2886	10871										
SMC4	10051	broad.mit.edu	37	chr3	160120552	160120552	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttggctatcgagcacaaaAaataagatctaaaaaactct	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160120552A>T	ENST00000357388.3	+	4	858	c.407A>T	c.(406-408)aAa>aTa	p.K136I	SMC4_ENST00000462787.1_Missense_Mutation_p.K136I|SMC4_ENST00000360111.2_Missense_Mutation_p.K136I|SMC4_ENST00000469762.1_Missense_Mutation_p.K111I|MIR16-2_ENST00000362117.1_RNA|SMC4_ENST00000344722.5_Missense_Mutation_p.K136I|MIR15B_ENST00000385045.1_RNA|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	136					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.K136I(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CGAGCACAAAAAATAAGATCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											84	88	86					3																	160120552		2203	4300	6503	161603246	SO:0001583	missense	10051			AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.407A>T	3.37:g.160120552A>T	ENSP00000349961:p.Lys136Ile		161603246	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	A	31	5.063538	0.93898	.	.	ENSG00000113810	ENST00000497311;ENST00000357388;ENST00000465903;ENST00000485645;ENST00000360111;ENST00000392788;ENST00000472991;ENST00000467468;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000490207;ENST00000485867;ENST00000344722	T;T;T;T;T;T;T;T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.38	5.38	0.77491	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.86171	0.5869	M	0.93854	3.465	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.994	D	0.89840	0.4002	10	0.72032	D	0.01	-29.0305	15.3883	0.74723	1.0:0.0:0.0:0.0	.	136;111;136	Q9NTJ3-2;E9PD53;Q9NTJ3	.;.;SMC4_HUMAN	I	136;136;136;136;136;136;11;11;111;136;136;136;64;136	ENSP00000418820:K136I;ENSP00000349961:K136I;ENSP00000419247:K136I;ENSP00000420644:K136I;ENSP00000353225:K136I;ENSP00000417999:K11I;ENSP00000419360:K11I;ENSP00000417964:K111I;ENSP00000420121:K136I;ENSP00000420734:K136I;ENSP00000420817:K136I;ENSP00000417612:K64I;ENSP00000341382:K136I	ENSP00000341382:K136I	K	+	2	0	SMC4	161603246	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.284000	0.95882	2.034000	0.60081	0.402000	0.26972	AAA		0.328	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			T	160120552	A	T	160120552	3	4	61	1	0	0	0	0	1	0	0	0	14822	14	1	5	417	5	SMC4	3	160120552	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	98800	160120552	37901878	2887	10872										
SMC4	10051	broad.mit.edu	37	chr3	160122245	160122245	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgttggaaatcttcttCgaagccatggaattgacttg	11	6	2	1	rs368979205		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160122245C>T	ENST00000357388.3	+	5	1091	c.640C>T	c.(640-642)Cga>Tga	p.R214*	SMC4_ENST00000462787.1_Nonsense_Mutation_p.R214*|SMC4_ENST00000360111.2_Nonsense_Mutation_p.R214*|SMC4_ENST00000469762.1_Nonsense_Mutation_p.R189*|SMC4_ENST00000470240.1_3'UTR|MIR16-2_ENST00000362117.1_RNA|SMC4_ENST00000344722.5_Nonsense_Mutation_p.R214*|MIR15B_ENST00000385045.1_RNA|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	214					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.R214*(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AAATCTTCTTCGAAGCCATGG	0.313																																																2	Substitution - Nonsense(2)	large_intestine(2)	3						C	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	71	77	75		640,640	3.2	1	3		75	0,8596		0,0,4298	no	stop-gained,stop-gained	SMC4	NM_001002800.1,NM_005496.3	,	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	,	214/1289,214/1289	160122245	1,13001	2203	4298	6501	161604939	SO:0001587	stop_gained	10051			AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.640C>T	3.37:g.160122245C>T	ENSP00000349961:p.Arg214*		161604939	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Nonsense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	C	39	7.835362	0.98516	2.27E-4	0.0	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000392788;ENST00000472991;ENST00000467468;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000485867;ENST00000344722	.	.	.	6.16	3.18	0.36537	.	0.061018	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.0965	11.9534	0.52968	0.2523:0.6323:0.1154:0.0	.	.	.	.	X	214;214;214;89;89;189;214;214;142;214	.	ENSP00000341382:R214X	R	+	1	2	SMC4	161604939	0.996000	0.38824	1.000000	0.80357	0.998000	0.95712	3.290000	0.51755	0.834000	0.34852	0.650000	0.86243	CGA		0.313	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			T	160122245	C	T	160122245	4	4	61	1	0	0	0	0	0	1	0	0	14822	876	31	1	654	1	SMC4	3	160122245	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1693	160122245	37900185	2888	10873										
SMC4	10051	broad.mit.edu	37	chr3	160148846	160148846	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccagagatccagaaagaAcatcgcaatctgcttcaaga	7	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160148846A>G	ENST00000357388.3	+	20	3418	c.2967A>G	c.(2965-2967)gaA>gaG	p.E989E	SMC4_ENST00000462787.1_Intron|SMC4_ENST00000360111.2_Intron|SMC4_ENST00000469762.1_Silent_p.E964E|SMC4_ENST00000344722.5_Silent_p.E989E|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	989					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.E989E(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TCCAGAAAGAACATCGCAATC	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	3											53	55	54					3																	160148846		2203	4297	6500	161631540	SO:0001819	synonymous_variant	10051			AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2967A>G	3.37:g.160148846A>G			161631540	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Silent	SNP	ENST00000357388.3	37	CCDS3189.1																																																																																				0.333	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			G	160148846	A	G	160148846	2	3	61	1	0	0	0	0	0	0	0	1	14822	40	2	4		4	SMC4	3	160148846	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	26601	160148846	37873584	2889	10874										
TRIM59	286827	broad.mit.edu	37	chr3	160156323	160156323	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaatttgtggagtatattCttgattaattagattgccaa	7	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160156323C>T	ENST00000309784.4	-	3	834	c.649G>A	c.(649-651)Gaa>Aaa	p.E217K	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.E217K|TRIM59_ENST00000543469.1_Missense_Mutation_p.E217K	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	217					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E217K(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGAGTATATTCTTGATTAATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	81	80					3																	160156323		2201	4298	6499	161639017	SO:0001583	missense	286827			AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.649G>A	3.37:g.160156323C>T	ENSP00000311219:p.Glu217Lys		161639017	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	37	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.454382	0.63290	.	.	ENSG00000213186	ENST00000543469;ENST00000309784	T;T	0.23147	2.1;1.92	5.77	3.97	0.46021	.	0.306226	0.36972	N	0.002314	T	0.21103	0.0508	L	0.42245	1.32	0.29373	N	0.863845	B	0.10296	0.003	B	0.06405	0.002	T	0.10042	-1.0647	9	.	.	.	-20.6031	11.8766	0.52550	0.0:0.8061:0.0:0.1939	.	217	Q8IWR1	TRI59_HUMAN	K	217	ENSP00000444313:E217K;ENSP00000311219:E217K	.	E	-	1	0	TRIM59	161639017	0.861000	0.29849	1.000000	0.80357	0.976000	0.68499	1.020000	0.30027	1.449000	0.47699	0.561000	0.74099	GAA		0.338	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		T	160156323	C	T	160156323	3	4	61	1	0	0	0	0	1	0	0	0	16572	922	32	3	566	3	TRIM59	3	160156323	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7477	160156323	37866107	2890	10875										
KPNA4	3840	broad.mit.edu	37	chr3	160254612	160254612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaactacaacttcatttCgttgtcttctcatagtctac	3	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160254612C>T	ENST00000334256.4	-	2	391	c.86G>A	c.(85-87)cGa>cAa	p.R29Q		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	29	IBB. {ECO:0000255|PROSITE- ProRule:PRU00561}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)	p.R29Q(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			AACTTCATTTCGTTGTCTTCT	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	3											130	134	132					3																	160254612		2197	4277	6474	161737306	SO:0001583	missense	3840			AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.86G>A	3.37:g.160254612C>T	ENSP00000334373:p.Arg29Gln		161737306	A8K4S6|D3DNM2|O00190	Missense_Mutation	SNP	ENST00000334256.4	37	CCDS3191.1	.	.	.	.	.	.	.	.	.	.	C	33	5.286469	0.95517	.	.	ENSG00000186432	ENST00000334256	T	0.78003	-1.14	6.07	6.07	0.98685	Importin-alpha, importin-beta-binding domain (2);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.92004	0.7467	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.93008	0.6429	10	0.72032	D	0.01	-3.57	20.2543	0.98414	0.0:1.0:0.0:0.0	.	29	O00629	IMA4_HUMAN	Q	29	ENSP00000334373:R29Q	ENSP00000334373:R29Q	R	-	2	0	KPNA4	161737306	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	7.323000	0.79105	2.890000	0.99128	0.650000	0.86243	CGA		0.279	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		T	160254612	C	T	160254612	3	4	61	1	0	0	0	0	1	0	0	0	8453	884	31	1	1543	1	KPNA4	3	160254612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98289	160254612	37767818	2891	10876										
B3GALNT1	8706	broad.mit.edu	37	chr3	160804109	160804109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgtctaaaaaatcttgtCggattatgtcaccataaaga	7	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160804109C>T	ENST00000392781.2	-	8	1181	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.R145Q|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.R145Q|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.R145Q|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.R145Q|B3GALNT1_ENST00000392779.2_Missense_Mutation_p.R145Q	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	145					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.R145Q(2)		breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			AAAATCTTGTCGGATTATGTC	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	3											88	85	86					3																	160804109		2203	4300	6503	162286803	SO:0001583	missense	8706			Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"Blood group antigens", "Beta 3-glycosyltransferases"	918	protein-coding gene	gene with protein product	"globoside synthase", "P antigen synthase"	603094	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)", "UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.434G>A	3.37:g.160804109C>T	ENSP00000376532:p.Arg145Gln		162286803	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	37	CCDS3193.1	.	.	.	.	.	.	.	.	.	.	C	2.192	-0.385129	0.04966	.	.	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09	5.75	5.75	0.90469	.	0.102222	0.43579	D	0.000551	T	0.13628	0.0330	N	0.01019	-1.045	0.28629	N	0.907741	B	0.21753	0.06	B	0.12837	0.008	T	0.11916	-1.0568	10	0.02654	T	1	.	12.2651	0.54674	0.0:0.9228:0.0:0.0772	.	145	O75752	B3GL1_HUMAN	Q	145	ENSP00000323479:R145Q;ENSP00000376530:R145Q;ENSP00000376531:R145Q;ENSP00000376532:R145Q;ENSP00000418226:R145Q;ENSP00000420163:R145Q	ENSP00000323479:R145Q	R	-	2	0	B3GALNT1	162286803	0.000000	0.05858	0.992000	0.48379	0.795000	0.44927	0.888000	0.28268	2.713000	0.92767	0.462000	0.41574	CGA		0.383	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167		T	160804109	C	T	160804109	3	4	61	1	0	0	0	0	1	0	0	0	1246	884	31	1	565	1	B3GALNT1	3	160804109	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	549497	160804109	37218321	2892	10877										
NMD3	51068	broad.mit.edu	37	chr3	160942826	160942826	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtattccgaaacaagtctcGatttcgttctgcaaacaatg	8	9	2	0	rs534269025		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:160942826G>A	ENST00000460469.1	+	2	608	c.153G>A	c.(151-153)tcG>tcA	p.S51S	NMD3_ENST00000351193.2_Silent_p.S51S|NMD3_ENST00000478160.1_Intron|NMD3_ENST00000472947.1_Silent_p.S51S			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	51					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)	p.S51S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			AACAAGTCTCGATTTCGTTCT	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		16636	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											194	185	188					3																	160942826		2203	4300	6503	162425520	SO:0001819	synonymous_variant	51068			BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"NMD3 homolog (S. cerevisiae)"			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.153G>A	3.37:g.160942826G>A			162425520	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	37	CCDS3194.1																																																																																				0.413	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		A	160942826	G	A	160942826	2	1	61	1	0	0	0	0	0	0	0	1	10519	1045	37	1		1	NMD3	3	160942826	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138717	160942826	37079604	2893	10878										
OTOL1	131149	broad.mit.edu	37	chr3	161214959	161214959	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagagactggacagccaGgtattagaaaatataagaag	12	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:161214959G>T	ENST00000327928.4	+	1	364	c.364G>T	c.(364-366)Ggt>Tgt	p.G122C		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	122	Collagen-like 1.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.G122C(1)		central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TGGACAGCCAGGTATTAGAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	66	66					3																	161214959		1845	4093	5938	162697653	SO:0001630	splice_region_variant	131149				CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.364+1G>T	3.37:g.161214959G>T			162697653		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.918633	0.73098	.	.	ENSG00000182447	ENST00000327928	D	0.99369	-5.78	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	H	0.99312	4.51	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	D	0.97128	0.9816	10	0.87932	D	0	.	17.2473	0.87031	0.0:0.0:1.0:0.0	.	122	A6NHN0	OTOL1_HUMAN	C	122	ENSP00000330808:G122C	ENSP00000330808:G122C	G	+	1	0	OTOL1	162697653	1.000000	0.71417	0.999000	0.59377	0.775000	0.43874	7.187000	0.77730	2.673000	0.90976	0.650000	0.86243	GGT		0.428	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	Missense_Mutation	T	161214959	G	T	161214959	5	4	61	1	0	0	0	0	0	0	1	0	11335	1014	35	2	366	2	OTOL1	3	161214959	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272133	161214959	36807471	2894	10879										
SI	6476	broad.mit.edu	37	chr3	164733756	164733756	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaccaggataataatgtatCtcattccttctcctcttatt	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:164733756C>A	ENST00000264382.3	-	32	3934	c.3872G>T	c.(3871-3873)aGa>aTa	p.R1291I		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1291	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.R1291I(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AATAATGTATCTCATTCCTTC	0.398										HNSCC(35;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	3											164	171	169					3																	164733756		2203	4300	6503	166216450	SO:0001583	missense	6476			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.3872G>T	3.37:g.164733756C>A	ENSP00000264382:p.Arg1291Ile		166216450	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498856	0.64298	.	.	ENSG00000090402	ENST00000264382	D	0.93811	-3.29	5.06	2.22	0.28083	Glycoside hydrolase, superfamily (1);	0.210802	0.48767	D	0.000162	D	0.96658	0.8909	M	0.93016	3.37	0.47778	D	0.999513	D	0.76494	0.999	D	0.79784	0.993	D	0.95598	0.8660	10	0.87932	D	0	.	8.2414	0.31662	0.0:0.6833:0.0:0.3167	.	1291	P14410	SUIS_HUMAN	I	1291	ENSP00000264382:R1291I	ENSP00000264382:R1291I	R	-	2	0	SI	166216450	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	1.298000	0.33412	0.704000	0.31869	-0.218000	0.12543	AGA		0.398	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164733756	C	A	164733756	3	1	61	1	0	0	0	0	1	0	0	0	14334	913	32	2	1679	2	SI	3	164733756	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3518797	164733756	33288674	2895	10880										
SI	6476	broad.mit.edu	37	chr3	164750471	164750471	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgtgtgcacacaatatCtaatgtgttctgagaaaaat	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:164750471C>A	ENST00000264382.3	-	24	2637	c.2575G>T	c.(2575-2577)Gat>Tat	p.D859Y		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	859	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.D859Y(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	CACACAATATCTAATGTGTTC	0.323										HNSCC(35;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	3											88	82	84					3																	164750471		2202	4299	6501	166233165	SO:0001583	missense	6476			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2575G>T	3.37:g.164750471C>A	ENSP00000264382:p.Asp859Tyr		166233165	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	9.936	1.216284	0.22373	.	.	ENSG00000090402	ENST00000264382	D	0.89123	-2.47	4.78	-7.68	0.01268	.	1.904780	0.02047	N	0.049733	D	0.83087	0.5178	L	0.41573	1.285	0.09310	N	1	P	0.35050	0.482	B	0.32533	0.147	T	0.76030	-0.3108	10	0.59425	D	0.04	.	11.7054	0.51595	0.0:0.1664:0.1033:0.7303	.	859	P14410	SUIS_HUMAN	Y	859	ENSP00000264382:D859Y	ENSP00000264382:D859Y	D	-	1	0	SI	166233165	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.270000	0.02831	-1.923000	0.01065	-0.302000	0.09304	GAT		0.323	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164750471	C	A	164750471	3	1	61	1	0	0	0	0	1	0	0	0	14334	913	32	2	3008	2	SI	3	164750471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16715	164750471	33271959	2896	10881										
SI	6476	broad.mit.edu	37	chr3	164766991	164766991	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccagttctgcacagcatCcatgcaaattgttttggaat	7	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:164766991C>T	ENST00000264382.3	-	15	1701	c.1639G>A	c.(1639-1641)Gat>Aat	p.D547N		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	547	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.D547N(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TGCACAGCATCCATGCAAATT	0.328										HNSCC(35;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	3											94	86	89					3																	164766991		2203	4300	6503	166249685	SO:0001583	missense	6476			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1639G>A	3.37:g.164766991C>T	ENSP00000264382:p.Asp547Asn		166249685	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996079	0.93167	.	.	ENSG00000090402	ENST00000264382	D	0.94138	-3.36	5.24	5.24	0.73138	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96125	0.8737	M	0.68728	2.09	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	D	0.95896	0.8911	10	0.52906	T	0.07	.	18.1694	0.89740	0.0:1.0:0.0:0.0	.	547	P14410	SUIS_HUMAN	N	547	ENSP00000264382:D547N	ENSP00000264382:D547N	D	-	1	0	SI	166249685	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.578000	0.82498	2.613000	0.88420	0.460000	0.39030	GAT		0.328	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164766991	C	T	164766991	3	4	61	1	0	0	0	0	1	0	0	0	14334	855	30	3	3980	3	SI	3	164766991	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16520	164766991	33255439	2897	10882										
SLITRK3	22865	broad.mit.edu	37	chr3	164908359	164908359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatataatttcctcatagaaTtcctctgcagatacagttta	4	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:164908359T>C	ENST00000475390.1	-	2	703	c.260A>G	c.(259-261)aAt>aGt	p.N87S	SLITRK3_ENST00000241274.3_Missense_Mutation_p.N87S			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	87					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.N87S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						CCTCATAGAATTCCTCTGCAG	0.353										HNSCC(40;0.11)																																						1	Substitution - Missense(1)	large_intestine(1)	3											63	66	65					3																	164908359		2203	4299	6502	166391053	SO:0001583	missense	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.260A>G	3.37:g.164908359T>C	ENSP00000420091:p.Asn87Ser		166391053	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376937	0.61735	.	.	ENSG00000121871	ENST00000475390;ENST00000241274;ENST00000497724	T;T;D	0.87887	0.18;0.18;-2.31	6.11	6.11	0.99139	.	0.000000	0.40469	N	0.001097	D	0.94948	0.8366	M	0.92784	3.345	0.51233	D	0.999915	D	0.63880	0.993	D	0.68192	0.956	D	0.95770	0.8808	10	0.72032	D	0.01	-19.4118	16.7021	0.85357	0.0:0.0:0.0:1.0	.	87	O94933	SLIK3_HUMAN	S	87	ENSP00000420091:N87S;ENSP00000241274:N87S;ENSP00000419611:N87S	ENSP00000241274:N87S	N	-	2	0	SLITRK3	166391053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.343000	0.79666	0.533000	0.62120	AAT		0.353	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		C	164908359	T	C	164908359	3	2	61	1	0	0	0	0	1	0	0	0	14781	1493	52	4	2677	4	SLITRK3	3	164908359	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	141368	164908359	33114071	2898	10883										
SLITRK3	22865	broad.mit.edu	37	chr3	164908564	164908564	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagcaattgtgcttagaaGaattatccacaacatccttc	6	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:164908564G>T	ENST00000475390.1	-	2	498	c.55C>A	c.(55-57)Ctt>Att	p.L19I	SLITRK3_ENST00000241274.3_Missense_Mutation_p.L19I			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	19					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.L19I(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GTGCTTAGAAGAATTATCCAC	0.418										HNSCC(40;0.11)																																						1	Substitution - Missense(1)	large_intestine(1)	3											91	84	87					3																	164908564		2202	4300	6502	166391258	SO:0001583	missense	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.55C>A	3.37:g.164908564G>T	ENSP00000420091:p.Leu19Ile		166391258	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154407	0.57259	.	.	ENSG00000121871	ENST00000475390;ENST00000241274;ENST00000497724	T;T;T	0.70749	0.5;0.5;-0.51	6.01	6.01	0.97437	.	0.000000	0.34133	N	0.004231	T	0.79839	0.4515	L	0.41492	1.28	0.39453	D	0.967436	D	0.63880	0.993	D	0.67548	0.952	T	0.79303	-0.1859	10	0.52906	T	0.07	-16.3635	20.5182	0.99214	0.0:0.0:1.0:0.0	.	19	O94933	SLIK3_HUMAN	I	19	ENSP00000420091:L19I;ENSP00000241274:L19I;ENSP00000419611:L19I	ENSP00000241274:L19I	L	-	1	0	SLITRK3	166391258	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.161000	0.77505	2.860000	0.98153	0.655000	0.94253	CTT		0.418	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164908564	G	T	164908564	3	4	61	1	0	0	0	0	1	0	0	0	14781	942	33	2	2882	2	SLITRK3	3	164908564	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205	164908564	33113866	2899	10884										
BCHE	590	broad.mit.edu	37	chr3	165548409	165548409	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaccataaatccatatcAatacagtggcattttttggt	5	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:165548409A>C	ENST00000264381.3	-	2	579	c.413T>G	c.(412-414)tTg>tGg	p.L138W	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	138					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)	p.L138W(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	AATCCATATCAATACAGTGGC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											60	63	62					3																	165548409		2203	4300	6503	167031103	SO:0001583	missense	590			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.413T>G	3.37:g.165548409A>C	ENSP00000264381:p.Leu138Trp		167031103	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.693127	0.48202	.	.	ENSG00000114200	ENST00000264381	T	0.71934	-0.61	5.83	5.83	0.93111	Carboxylesterase, type B (1);	0.080786	0.85682	D	0.000000	D	0.87249	0.6130	M	0.92268	3.29	0.80722	D	1	D	0.69078	0.997	D	0.69307	0.963	D	0.90281	0.4315	10	0.87932	D	0	.	15.3793	0.74641	1.0:0.0:0.0:0.0	.	138	P06276	CHLE_HUMAN	W	138	ENSP00000264381:L138W	ENSP00000264381:L138W	L	-	2	0	BCHE	167031103	1.000000	0.71417	0.938000	0.37757	0.297000	0.27493	9.210000	0.95106	2.226000	0.72624	0.533000	0.62120	TTG		0.388	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			C	165548409	A	C	165548409	3	2	61	1	0	0	0	0	1	0	0	0	1359	131	5	4	1407	4	BCHE	3	165548409	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	639845	165548409	32474021	2900	10885										
SERPINI2	5276	broad.mit.edu	37	chr3	167184846	167184846	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatgggaaactttaccatCtgtttttctttctacccagg	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:167184846C>A	ENST00000476257.1	-	4	773	c.475G>T	c.(475-477)Gat>Tat	p.D159Y	SERPINI2_ENST00000461846.1_Missense_Mutation_p.D159Y|SERPINI2_ENST00000465031.1_5'Flank|SERPINI2_ENST00000471111.1_Missense_Mutation_p.D159Y|SERPINI2_ENST00000264677.4_Missense_Mutation_p.D159Y			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	159					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D159Y(1)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						ACTTTACCATCTGTTTTTCTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	69	68					3																	167184846		2202	4300	6502	168667540	SO:0001583	missense	5276			AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"Serine (or cysteine) peptidase inhibitors"	8945	protein-coding gene	gene with protein product		605587	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2", "serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.475G>T	3.37:g.167184846C>A	ENSP00000420621:p.Asp159Tyr		168667540		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.907855	0.33721	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	T;T;T;T;T;D	0.83250	-0.91;-0.91;-0.91;-0.91;-0.91;-1.7	5.7	4.83	0.62350	Serpin domain (3);	0.272597	0.41194	D	0.000936	D	0.87309	0.6145	L	0.60845	1.875	0.38726	D	0.953567	D;D	0.58268	0.982;0.982	D;D	0.64687	0.928;0.928	D	0.88409	0.3020	10	0.59425	D	0.04	.	10.0452	0.42182	0.0:0.7907:0.1376:0.0717	.	159;159	B4DDY9;O75830	.;SPI2_HUMAN	Y	159;159;159;159;159;144	ENSP00000420621:D159Y;ENSP00000417692:D159Y;ENSP00000264677:D159Y;ENSP00000419407:D159Y;ENSP00000417752:D159Y;ENSP00000419255:D144Y	ENSP00000264677:D159Y	D	-	1	0	SERPINI2	168667540	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.250000	0.32850	1.417000	0.47077	0.655000	0.94253	GAT		0.333	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		A	167184846	C	A	167184846	3	1	61	1	0	0	0	0	1	0	0	0	14156	913	32	2	770	2	SERPINI2	3	167184846	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1636437	167184846	30837584	2901	10886										
SERPINI1	5274	broad.mit.edu	37	chr3	167508239	167508239	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtgatgaaaattgccaaTtccttgtttgtgcaaaatgg	9	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:167508239T>G	ENST00000295777.5	+	3	761	c.330T>G	c.(328-330)aaT>aaG	p.N110K	SERPINI1_ENST00000446050.2_Missense_Mutation_p.N110K	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	110					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.N110K(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(7)|skin(2)	20						AAATTGCCAATTCCTTGTTTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	97	96					3																	167508239		2203	4300	6503	168990933	SO:0001583	missense	5274			Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"Serine (or cysteine) peptidase inhibitors"	8943	protein-coding gene	gene with protein product		602445	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.330T>G	3.37:g.167508239T>G	ENSP00000295777:p.Asn110Lys		168990933	A8K217|D3DNP1|Q6AHZ4	Missense_Mutation	SNP	ENST00000295777.5	37	CCDS3203.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469343	0.84533	.	.	ENSG00000163536	ENST00000472941;ENST00000446050;ENST00000295777;ENST00000472747	D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21	5.63	3.32	0.38043	Serpin domain (3);	0.042369	0.85682	D	0.000000	D	0.94857	0.8338	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.93648	0.6970	10	0.87932	D	0	.	5.0412	0.14460	0.0:0.3093:0.0:0.6907	.	110	Q99574	NEUS_HUMAN	K	110	ENSP00000420133:N110K;ENSP00000397373:N110K;ENSP00000295777:N110K;ENSP00000420561:N110K	ENSP00000295777:N110K	N	+	3	2	SERPINI1	168990933	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.028000	0.41088	2.145000	0.66743	0.528000	0.53228	AAT		0.328	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1			G	167508239	T	G	167508239	3	3	61	1	0	0	0	0	1	0	0	0	14155	1490	52	4	336	4	SERPINI1	3	167508239	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	323393	167508239	30514191	2902	10887										
GOLIM4	27333	broad.mit.edu	37	chr3	167764758	167764758	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcctttatttaatgtttCttgtgcttctaacttataaa	3	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:167764758C>T	ENST00000470487.1	-	3	981	c.292G>A	c.(292-294)Gaa>Aaa	p.E98K	GOLIM4_ENST00000309027.4_Missense_Mutation_p.E98K	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	98	Endosome targeting.|Golgi targeting.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E98K(1)		breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TTTAATGTTTCTTGTGCTTCT	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	3											24	27	26					3																	167764758		2167	4258	6425	169247452	SO:0001583	missense	27333			U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.292G>A	3.37:g.167764758C>T	ENSP00000417354:p.Glu98Lys		169247452		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521194	0.85600	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.98	5.98	0.97165	.	0.102226	0.64402	D	0.000001	T	0.75451	0.3851	L	0.53729	1.69	0.46927	D	0.99925	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.68413	-0.5415	9	0.23891	T	0.37	-23.069	18.7015	0.91621	0.0:1.0:0.0:0.0	.	98;98	F8W785;O00461	.;GOLI4_HUMAN	K	98	.	ENSP00000309893:E98K	E	-	1	0	GOLIM4	169247452	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.855000	0.62925	2.861000	0.98227	0.650000	0.86243	GAA		0.259	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			T	167764758	C	T	167764758	3	4	61	1	0	0	0	0	1	0	0	0	6586	922	32	3	1854	3	GOLIM4	3	167764758	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	256519	167764758	30257672	2903	10888										
MECOM	2122	broad.mit.edu	37	chr3	168812978	168812978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttattgtggatgttgcGaacatgcctttgcaagttag	10	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:168812978G>A	ENST00000464456.1	-	11	3514	c.2314C>T	c.(2314-2316)Cgc>Tgc	p.R772C	MECOM_ENST00000433243.2_Missense_Mutation_p.R782C|MECOM_ENST00000460814.1_Missense_Mutation_p.R772C|MECOM_ENST00000264674.3_Missense_Mutation_p.R846C|MECOM_ENST00000472280.1_Missense_Mutation_p.R782C|MECOM_ENST00000392736.3_Missense_Mutation_p.R781C|MECOM_ENST00000468789.1_Missense_Mutation_p.R781C|MECOM_ENST00000494292.1_Missense_Mutation_p.R960C	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R781C(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGGATGTTGCGAACATGCCTT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	3											136	118	125					3																	168812978		2203	4300	6503	170295672	SO:0001583	missense	2122			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2314C>T	3.37:g.168812978G>A	ENSP00000419770:p.Arg772Cys		170295672	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169400	0.38315	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78	5.64	4.75	0.60458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.55940	0.1952	M	0.85859	2.78	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;0.999	D;P;D;D;D	0.76575	0.979;0.797;0.988;0.96;0.971	T	0.65121	-0.6245	10	0.87932	D	0	-0.3271	15.7903	0.78350	0.0:0.0:0.8628:0.1372	.	969;773;960;846;781	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	C	846;781;772;782;960;781;772;782	ENSP00000264674:R846C;ENSP00000376493:R781C;ENSP00000419770:R772C;ENSP00000420048:R782C;ENSP00000417899:R960C;ENSP00000419995:R781C;ENSP00000420466:R772C;ENSP00000394302:R782C	ENSP00000264674:R846C	R	-	1	0	MECOM	170295672	1.000000	0.71417	0.983000	0.44433	0.393000	0.30537	7.814000	0.86154	1.361000	0.45981	0.561000	0.74099	CGC		0.338	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168812978	G	A	168812978	3	1	61	1	0	0	0	0	1	0	0	0	9452	1058	37	1	834	1	MECOM	3	168812978	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1048220	168812978	29209452	2904	10889										
ARPM1	84517	broad.mit.edu	37	chr3	169485981	169485981	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgctcaaaaaacatttCcgtgatctgttgccggttgg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169485981C>A	ENST00000330368.2	-	2	732	c.358G>T	c.(358-360)Gaa>Taa	p.E120*	RP11-816J6.3_ENST00000602879.1_RNA	NM_032487.4	NP_115876.3	Q9BYD9	ACTT3_HUMAN	actin-related protein T3	120						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)		p.E120*(1)									AAAAACATTTCCGTGATCTGT	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											89	91	90					3																	169485981		2203	4300	6503	170968675	SO:0001587	stop_gained	84517			AK055346	CCDS3206.1	3q26.2	2012-04-10			ENSG00000184378	ENSG00000184378			24022	protein-coding gene	gene with protein product	"actin related protein M1"	608534				11750065, 18692047	Standard	NM_032487		Approved	ARPM1	uc003ffs.2	Q9BYD9		ENST00000330368.2:c.358G>T	3.37:g.169485981C>A	ENSP00000333037:p.Glu120*		170968675	Q96IS0|Q96NJ0	Nonsense_Mutation	SNP	ENST00000330368.2	37	CCDS3206.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929265	0.73327	.	.	ENSG00000184378	ENST00000330368	.	.	.	4.84	3.96	0.45880	.	0.000000	0.56097	D	0.000037	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.98	0.58557	0.0:0.5575:0.4425:0.0	.	.	.	.	X	120	.	ENSP00000333037:E120X	E	-	1	0	AC078802.1	170968675	0.941000	0.31946	0.091000	0.20842	0.000000	0.00434	1.560000	0.36331	1.392000	0.46585	-0.175000	0.13238	GAA		0.507	ACTRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467797.1	NM_032487		A	169485981	C	A	169485981	4	1	61	1	0	0	0	0	0	1	0	0	977	864	30	2	764	2	ARPM1	3	169485981	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673003	169485981	28536449	2905	10890										
MYNN	55892	broad.mit.edu	37	chr3	169496770	169496770	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatcagaagtatctacaGatttgattcaggcaaatcct	7	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169496770G>T	ENST00000349841.5	+	3	1144	c.481G>T	c.(481-483)Gat>Tat	p.D161Y	RP11-362K14.5_ENST00000602342.1_RNA|MYNN_ENST00000356716.4_Missense_Mutation_p.D161Y|MYNN_ENST00000544106.1_Missense_Mutation_p.D161Y|MYNN_ENST00000392733.1_Missense_Mutation_p.D161Y	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.D161Y(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	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)			AGTATCTACAGATTTGATTCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											48	52	51					3																	169496770		2203	4300	6503	170979464	SO:0001583	missense	55892			AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.481G>T	3.37:g.169496770G>T	ENSP00000326240:p.Asp161Tyr		170979464	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Missense_Mutation	SNP	ENST00000349841.5	37	CCDS3207.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700899	0.48307	.	.	ENSG00000085274	ENST00000356716;ENST00000349841;ENST00000392733;ENST00000544106	T;T;T;T	0.10382	3.06;3.06;2.88;2.88	5.35	5.35	0.76521	.	0.330535	0.29799	N	0.011164	T	0.18257	0.0438	N	0.14661	0.345	0.36721	D	0.8812	D;D	0.76494	0.974;0.999	P;D	0.77557	0.66;0.99	T	0.17684	-1.0361	10	0.72032	D	0.01	.	14.6423	0.68734	0.0:0.1453:0.8547:0.0	.	161;161	Q9NPC7-2;Q9NPC7	.;MYNN_HUMAN	Y	161	ENSP00000349150:D161Y;ENSP00000326240:D161Y;ENSP00000376492:D161Y;ENSP00000440637:D161Y	ENSP00000326240:D161Y	D	+	1	0	MYNN	170979464	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	3.893000	0.56243	2.510000	0.84645	0.650000	0.86243	GAT		0.373	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657		T	169496770	G	T	169496770	3	4	61	1	0	0	0	0	1	0	0	0	10091	942	33	2	487	2	MYNN	3	169496770	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10789	169496770	28525660	2906	10891										
LRRC34	151827	broad.mit.edu	37	chr3	169514580	169514580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttcagatacagtgcatcAcataactgttgtataccact	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169514580A>G	ENST00000316515.7	-	7	1002	c.726T>C	c.(724-726)tgT>tgC	p.C242C	LRRC34_ENST00000446859.1_Silent_p.C287C|LRRC34_ENST00000522830.1_Silent_p.C226C|LRRC34_ENST00000524327.1_5'UTR|RP11-362K14.7_ENST00000602913.1_RNA|RP11-362K14.6_ENST00000602835.1_RNA|LRRC34_ENST00000522526.2_Silent_p.C255C	NM_153353.4	NP_699184.2	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34	242								p.C242C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)	10	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			ACAGTGCATCACATAACTGTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	3											140	117	125					3																	169514580		2203	4300	6503	170997274	SO:0001819	synonymous_variant	151827			AK095125	CCDS3208.1, CCDS3208.2, CCDS54672.1	3q26.2	2014-03-18			ENSG00000171757	ENSG00000171757			28408	protein-coding gene	gene with protein product						12477932	Standard	NM_153353		Approved	MGC27085	uc003ffy.3	Q8IZ02	OTTHUMG00000164419	ENST00000316515.7:c.726T>C	3.37:g.169514580A>G			170997274	B4DEJ7|E9PBH2|G5E9T7	Silent	SNP	ENST00000316515.7	37																																																																																					0.363	LRRC34-201	KNOWN	basic	protein_coding	protein_coding		NM_153353		G	169514580	A	G	169514580	2	3	61	1	0	0	0	0	0	0	0	1	9018	157	6	4		4	LRRC34	3	169514580	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	17810	169514580	28507850	2907	10892										
LRRIQ4	344657	broad.mit.edu	37	chr3	169550786	169550786	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttcagctttgaaagaaTtacggctggaggacaacttg	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169550786T>G	ENST00000340806.6	+	4	1345	c.1345T>G	c.(1345-1347)Tta>Gta	p.L449V		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	449								p.L449V(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						TTTGAAAGAATTACGGCTGGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											62	60	61					3																	169550786		1837	4089	5926	171033480	SO:0001583	missense	344657				CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.1345T>G	3.37:g.169550786T>G	ENSP00000342188:p.Leu449Val		171033480		Missense_Mutation	SNP	ENST00000340806.6	37	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.325889	0.41197	.	.	ENSG00000188306	ENST00000340806	T	0.80994	-1.44	5.56	0.403	0.16350	.	0.000000	0.49305	D	0.000153	D	0.84986	0.5594	L	0.60067	1.865	0.31963	N	0.608191	D	0.76494	0.999	D	0.74023	0.982	D	0.85000	0.0899	10	0.87932	D	0	.	10.8567	0.46802	0.0:0.5044:0.0:0.4956	.	449	A6NIV6	LRIQ4_HUMAN	V	449	ENSP00000342188:L449V	ENSP00000342188:L449V	L	+	1	2	LRRIQ4	171033480	0.982000	0.34865	0.899000	0.35326	0.374000	0.29953	0.099000	0.15210	0.075000	0.16796	-0.441000	0.05720	TTA		0.413	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		G	169550786	T	G	169550786	3	3	61	1	0	0	0	0	1	0	0	0	9060	1490	52	4	1359	4	LRRIQ4	3	169550786	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	36206	169550786	28471644	2908	10893										
LRRIQ4	344657	broad.mit.edu	37	chr3	169555341	169555341	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactactaaaaccacaaaaGaaaggaaagacctctccaaa	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169555341G>A	ENST00000340806.6	+	5	1605	c.1605G>A	c.(1603-1605)aaG>aaA	p.K535K		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	535								p.K535K(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						AACCACAAAAGAAAGGAAAGA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	3											60	55	57					3																	169555341		1844	4101	5945	171038035	SO:0001819	synonymous_variant	344657				CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.1605G>A	3.37:g.169555341G>A			171038035		Silent	SNP	ENST00000340806.6	37	CCDS46951.1																																																																																				0.368	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		A	169555341	G	A	169555341	2	1	61	1	0	0	0	0	0	0	0	1	9060	933	33	3		3	LRRIQ4	3	169555341	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4555	169555341	28467089	2909	10894										
LRRC31	79782	broad.mit.edu	37	chr3	169557856	169557856	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcctgtgaagctgggaGaatccatcttttcattccta	7	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169557856G>T	ENST00000316428.5	-	9	1630	c.1573C>A	c.(1573-1575)Ctc>Atc	p.L525I	LRRC31_ENST00000264676.5_Missense_Mutation_p.L469I|LRRC31_ENST00000523069.1_3'UTR	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	525								p.L525I(1)		cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			GAAGCTGGGAGAATCCATCTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											132	120	124					3																	169557856		1891	4115	6006	171040550	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1573C>A	3.37:g.169557856G>T	ENSP00000325978:p.Leu525Ile		171040550	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	G	2.628	-0.287059	0.05605	.	.	ENSG00000114248	ENST00000316428;ENST00000264676	T;T	0.12039	2.72;2.81	4.87	1.52	0.23074	.	0.514297	0.20145	N	0.098281	T	0.07098	0.0180	N	0.12182	0.205	0.27356	N	0.956111	P;B	0.36683	0.565;0.214	B;B	0.36092	0.217;0.031	T	0.30880	-0.9963	10	0.30078	T	0.28	-0.5607	9.3107	0.37903	0.0762:0.0:0.6459:0.2778	.	469;525	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	I	525;469	ENSP00000325978:L525I;ENSP00000264676:L469I	ENSP00000264676:L469I	L	-	1	0	LRRC31	171040550	0.785000	0.28726	0.007000	0.13788	0.071000	0.16799	0.870000	0.28010	0.424000	0.26061	0.650000	0.86243	CTC		0.398	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		T	169557856	G	T	169557856	3	4	61	1	0	0	0	0	1	0	0	0	9015	942	33	2	89	2	LRRC31	3	169557856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2515	169557856	28464574	2910	10895										
LRRC31	79782	broad.mit.edu	37	chr3	169569520	169569520	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaagaactgcccatctttTtgttggctgataaatccaat	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169569520T>C	ENST00000316428.5	-	7	1103	c.1046A>G	c.(1045-1047)aAa>aGa	p.K349R	LRRC31_ENST00000264676.5_Missense_Mutation_p.K293R|LRRC31_ENST00000397805.2_5'Flank|LRRC31_ENST00000523069.1_Missense_Mutation_p.K349R	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	349								p.K349R(1)		cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			GCCCATCTTTTTGTTGGCTGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											126	119	121					3																	169569520		1833	4087	5920	171052214	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1046A>G	3.37:g.169569520T>C	ENSP00000325978:p.Lys349Arg		171052214	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.575604	0.28092	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.53423	0.62;0.62;0.62	4.89	-1.6	0.08426	.	0.196490	0.52532	N	0.000075	T	0.22975	0.0555	N	0.10874	0.06	0.23371	N	0.997817	B;P	0.34639	0.096;0.461	B;B	0.35240	0.038;0.198	T	0.28681	-1.0036	10	0.21540	T	0.41	-2.9984	9.5527	0.39319	0.0:0.3873:0.0:0.6127	.	293;349	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	R	349;293;349	ENSP00000325978:K349R;ENSP00000264676:K293R;ENSP00000429145:K349R	ENSP00000264676:K293R	K	-	2	0	LRRC31	171052214	0.692000	0.27719	0.290000	0.24890	0.749000	0.42624	-0.110000	0.10824	-0.295000	0.08960	0.379000	0.24179	AAA		0.388	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		C	169569520	T	C	169569520	3	2	61	1	0	0	0	0	1	0	0	0	9015	1841	64	4	624	4	LRRC31	3	169569520	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11664	169569520	28452910	2911	10896										
LRRC31	79782	broad.mit.edu	37	chr3	169574609	169574609	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcctcccactttactgTtccaagacaaatttagctct	3	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169574609T>A	ENST00000316428.5	-	4	596	c.539A>T	c.(538-540)aAc>aTc	p.N180I	LRRC31_ENST00000264676.5_Missense_Mutation_p.N124I|LRRC31_ENST00000397805.2_5'UTR|LRRC31_ENST00000523069.1_Missense_Mutation_p.N180I	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	180								p.N180I(1)		cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CACTTTACTGTTCCAAGACAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											136	125	128					3																	169574609		1847	4098	5945	171057303	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.539A>T	3.37:g.169574609T>A	ENSP00000325978:p.Asn180Ile		171057303	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.809926	0.50421	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.62105	0.05;0.05;0.05	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.85084	0.5616	H	0.96208	3.785	0.47153	D	0.999335	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89811	0.3982	10	0.72032	D	0.01	-0.3502	14.3742	0.66862	0.0:0.0:0.0:1.0	.	124;180	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	I	180;124;180	ENSP00000325978:N180I;ENSP00000264676:N124I;ENSP00000429145:N180I	ENSP00000264676:N124I	N	-	2	0	LRRC31	171057303	1.000000	0.71417	0.982000	0.44146	0.112000	0.19704	5.564000	0.67359	1.800000	0.52685	0.528000	0.53228	AAC		0.413	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		A	169574609	T	A	169574609	3	1	61	1	0	0	0	0	1	0	0	0	9015	1725	60	5	1143	5	LRRC31	3	169574609	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5089	169574609	28447821	2912	10897										
LRRC31	79782	broad.mit.edu	37	chr3	169587528	169587528	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattggagcccctgagaaatTtgttgacagttgaagtctgg	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169587528T>G	ENST00000316428.5	-	1	125	c.68A>C	c.(67-69)aAa>aCa	p.K23T	LRRC31_ENST00000264676.5_Missense_Mutation_p.K23T|LRRC31_ENST00000397805.2_5'UTR|LRRC31_ENST00000523069.1_Missense_Mutation_p.K23T	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	23								p.K23T(2)		cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CCTGAGAAATTTGTTGACAGT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	3											136	127	129					3																	169587528		1825	4081	5906	171070222	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.68A>C	3.37:g.169587528T>G	ENSP00000325978:p.Lys23Thr		171070222	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	T	6.312	0.425736	0.11987	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.11930	2.94;2.73;3.19	4.93	-1.7	0.08159	.	0.611505	0.15321	N	0.268533	T	0.08223	0.0205	L	0.27053	0.805	0.09310	N	1	P;P	0.44429	0.835;0.745	B;B	0.38156	0.266;0.193	T	0.24728	-1.0152	10	0.62326	D	0.03	.	9.0511	0.36376	0.0:0.4504:0.0:0.5496	.	23;23	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	T	23	ENSP00000325978:K23T;ENSP00000264676:K23T;ENSP00000429145:K23T	ENSP00000264676:K23T	K	-	2	0	LRRC31	171070222	0.017000	0.18338	0.000000	0.03702	0.009000	0.06853	-0.052000	0.11865	-0.154000	0.11118	-0.371000	0.07208	AAA		0.453	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		G	169587528	T	G	169587528	3	3	61	1	0	0	0	0	1	0	0	0	9015	1841	64	4	1626	4	LRRC31	3	169587528	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12919	169587528	28434902	2913	10898										
GPR160	26996	broad.mit.edu	37	chr3	169802505	169802505	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagctcattgtctgttttCtcagtacctggttaccattt	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169802505C>A	ENST00000355897.5	+	4	1353	c.745C>A	c.(745-747)Ctc>Atc	p.L249I		NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	249						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.L249I(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TGTCTGTTTTCTCAGTACCTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											92	91	92					3																	169802505		2203	4300	6503	171285199	SO:0001583	missense	26996			AB083583	CCDS3211.1	3q26.2-q27	2012-08-21			ENSG00000173890	ENSG00000173890		"GPCR / Class A : Orphans"	23693	protein-coding gene	gene with protein product						12044878	Standard	NM_014373		Approved	GPCR150, GPCR1	uc003fgi.3	Q9UJ42	OTTHUMG00000158776	ENST00000355897.5:c.745C>A	3.37:g.169802505C>A	ENSP00000348161:p.Leu249Ile		171285199	D3DNQ2	Missense_Mutation	SNP	ENST00000355897.5	37	CCDS3211.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496009	0.44352	.	.	ENSG00000173890	ENST00000355897	.	.	.	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.082496	0.50627	D	0.000120	T	0.76702	0.4024	M	0.65498	2.005	0.39762	D	0.972035	D	0.89917	1.0	D	0.68621	0.959	T	0.79184	-0.1908	9	0.66056	D	0.02	.	15.4448	0.75220	0.1393:0.8607:0.0:0.0	.	249	Q9UJ42	GP160_HUMAN	I	249	.	ENSP00000348161:L249I	L	+	1	0	GPR160	171285199	1.000000	0.71417	0.987000	0.45799	0.004000	0.04260	2.973000	0.49264	2.683000	0.91414	0.655000	0.94253	CTC		0.313	GPR160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352167.1	NM_014373		A	169802505	C	A	169802505	3	1	61	1	0	0	0	0	1	0	0	0	6684	913	32	2	747	2	GPR160	3	169802505	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	214977	169802505	28219925	2914	10899										
PHC3	80012	broad.mit.edu	37	chr3	169824661	169824661	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatcgttttgaccgcaaAaattcattagcatatcccat	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:169824661A>C	ENST00000494943.1	-	12	2459	c.2391T>G	c.(2389-2391)ttT>ttG	p.F797L	PHC3_ENST00000467570.1_Missense_Mutation_p.F756L|PHC3_ENST00000495893.2_Missense_Mutation_p.F809L			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	797					multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.F778L(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TTGACCGCAAAAATTCATTAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	97	99					3																	169824661		1855	4091	5946	171307355	SO:0001583	missense	80012				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.2391T>G	3.37:g.169824661A>C	ENSP00000420271:p.Phe797Leu		171307355	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	37		.	.	.	.	.	.	.	.	.	.	A	25.3	4.622933	0.87460	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570	T;T;T	0.39997	1.05;1.05;1.05	5.95	4.82	0.62117	Zinc finger, FCS-type (1);	0.000000	0.64402	D	0.000001	T	0.55226	0.1907	L	0.61036	1.89	0.80722	D	1	D;B;B	0.67145	0.996;0.261;0.379	D;B;B	0.73380	0.98;0.082;0.169	T	0.56481	-0.7972	10	0.48119	T	0.1	-23.8061	6.3682	0.21468	0.7673:0.0:0.2327:0.0	.	756;797;809	E7EX82;Q8NDX5;Q8NDX5-7	.;PHC3_HUMAN;.	L	797;809;756	ENSP00000420271:F797L;ENSP00000420294:F809L;ENSP00000419089:F756L	ENSP00000419089:F756L	F	-	3	2	PHC3	171307355	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.951000	0.63610	2.276000	0.75962	0.528000	0.53228	TTT		0.368	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		C	169824661	A	C	169824661	3	2	61	1	0	0	0	0	1	0	0	0	11849	11	1	4	576	4	PHC3	3	169824661	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22156	169824661	28197769	2915	10900										
SKIL	6498	broad.mit.edu	37	chr3	170108139	170108139	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctccgcttcttgtgaaaGatgtcatttgtgaggatgat	10	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170108139G>T	ENST00000458537.3	+	4	2267	c.1558G>T	c.(1558-1560)Gat>Tat	p.D520Y	SKIL_ENST00000259119.4_Missense_Mutation_p.D520Y|SKIL_ENST00000413427.2_Missense_Mutation_p.D474Y|SKIL_ENST00000426052.2_Missense_Mutation_p.D500Y	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	520					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)	p.D520Y(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TCTTGTGAAAGATGTCATTTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											114	105	108					3																	170108139		2203	4300	6503	171590833	SO:0001583	missense	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.1558G>T	3.37:g.170108139G>T	ENSP00000415243:p.Asp520Tyr		171590833	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	37	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959409	0.74016	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.92149	-2.94;-2.94;-2.98;-2.94	5.66	5.66	0.87406	.	0.169589	0.51477	D	0.000087	D	0.94922	0.8358	L	0.56769	1.78	0.48632	D	0.999689	D;D	0.63880	0.993;0.991	P;P	0.61592	0.891;0.804	D	0.94759	0.7934	10	0.72032	D	0.01	-24.5806	20.1197	0.97955	0.0:0.0:1.0:0.0	.	474;520	P12757-3;P12757	.;SKIL_HUMAN	Y	520;500;474;520	ENSP00000259119:D520Y;ENSP00000406520:D500Y;ENSP00000400193:D474Y;ENSP00000415243:D520Y	ENSP00000259119:D520Y	D	+	1	0	SKIL	171590833	1.000000	0.71417	0.996000	0.52242	0.451000	0.32288	6.708000	0.74660	2.838000	0.97847	0.591000	0.81541	GAT		0.373	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		T	170108139	G	T	170108139	3	4	61	1	0	0	0	0	1	0	0	0	14395	942	33	2	1572	2	SKIL	3	170108139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283478	170108139	27914291	2916	10901										
SLC7A14	57709	broad.mit.edu	37	chr3	170198495	170198495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatgagataaatattttCggattcatcagcttctatgc	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170198495C>T	ENST00000231706.5	-	7	1891	c.1576G>A	c.(1576-1578)Gaa>Aaa	p.E526K	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	526					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.E526K(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			TAAATATTTTCGGATTCATCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											158	158	158					3																	170198495		2203	4300	6503	171681189	SO:0001583	missense	57709			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1576G>A	3.37:g.170198495C>T	ENSP00000231706:p.Glu526Lys		171681189	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	37	CCDS33892.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.061572	0.55432	.	.	ENSG00000013293	ENST00000231706	D	0.87412	-2.25	5.6	5.6	0.85130	.	0.249066	0.46758	D	0.000279	T	0.80711	0.4675	L	0.44542	1.39	0.80722	D	1	B	0.33857	0.429	B	0.22386	0.039	T	0.78529	-0.2169	10	0.07990	T	0.79	.	19.6072	0.95585	0.0:1.0:0.0:0.0	.	526	Q8TBB6	S7A14_HUMAN	K	526	ENSP00000231706:E526K	ENSP00000231706:E526K	E	-	1	0	SLC7A14	171681189	1.000000	0.71417	0.990000	0.47175	0.488000	0.33401	7.395000	0.79876	2.627000	0.88993	0.655000	0.94253	GAA		0.478	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		T	170198495	C	T	170198495	3	4	61	1	0	0	0	0	1	0	0	0	14733	893	31	1	747	1	SLC7A14	3	170198495	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90356	170198495	27823935	2917	10902										
SLC7A14	57709	broad.mit.edu	37	chr3	170204104	170204104	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcctctccagtggtggcGatgatgtcaaagccaatgaa	11	10	2	2	rs553438612	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170204104G>A	ENST00000231706.5	-	5	1128	c.813C>T	c.(811-813)atC>atT	p.I271I	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	271					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.I271I(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CAGTGGTGGCGATGATGTCAA	0.512													G|||	3	0.000599042	0	0	5008	,	,		20110	0		0	False		,,,				2504	0.0031															1	Substitution - coding silent(1)	large_intestine(1)	3											336	250	279					3																	170204104		2203	4300	6503	171686798	SO:0001819	synonymous_variant	57709			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.813C>T	3.37:g.170204104G>A			171686798	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																				0.512	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170204104	G	A	170204104	2	1	61	1	0	0	0	0	0	0	0	1	14733	1048	37	1		1	SLC7A14	3	170204104	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5609	170204104	27818326	2918	10903										
SLC7A14	57709	broad.mit.edu	37	chr3	170244714	170244714	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggggtccagcgaggtgaaGaagccactcatcttgagcga	15	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170244714G>T	ENST00000231706.5	-	2	327	c.12C>A	c.(10-12)ttC>ttA	p.F4L	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	4					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.F4L(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			GCGAGGTGAAGAAGCCACTCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	3											31	30	31					3																	170244714		2203	4300	6503	171727408	SO:0001583	missense	57709			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.12C>A	3.37:g.170244714G>T	ENSP00000231706:p.Phe4Leu		171727408	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	37	CCDS33892.1	.	.	.	.	.	.	.	.	.	.	G	0.702	-0.790598	0.02884	.	.	ENSG00000013293	ENST00000231706	D	0.84730	-1.89	5.08	3.25	0.37280	.	0.197860	0.45126	N	0.000395	T	0.58323	0.2114	N	0.01874	-0.695	0.28300	N	0.923169	B	0.02656	0.0	B	0.01281	0.0	T	0.51513	-0.8696	10	0.02654	T	1	.	8.3151	0.32095	0.244:0.0:0.756:0.0	.	4	Q8TBB6	S7A14_HUMAN	L	4	ENSP00000231706:F4L	ENSP00000231706:F4L	F	-	3	2	SLC7A14	171727408	1.000000	0.71417	0.979000	0.43373	0.402000	0.30811	0.933000	0.28897	0.621000	0.30232	0.561000	0.74099	TTC		0.562	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		T	170244714	G	T	170244714	3	4	61	1	0	0	0	0	1	0	0	0	14733	933	33	2	2331	2	SLC7A14	3	170244714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40610	170244714	27777716	2919	10904										
TNIK	23043	broad.mit.edu	37	chr3	170781740	170781740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttcctccagatcgcacgGatgcaaaaaatacctgtttg	7	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170781740G>A	ENST00000436636.2	-	33	4357	c.4013C>T	c.(4012-4014)tCc>tTc	p.S1338F	TNIK_ENST00000460047.1_Missense_Mutation_p.S1275F|TNIK_ENST00000538048.1_Missense_Mutation_p.S1290F|TNIK_ENST00000464785.1_5'UTR|TNIK_ENST00000369326.5_Missense_Mutation_p.S1316F|TNIK_ENST00000284483.8_Missense_Mutation_p.S1330F|TNIK_ENST00000357327.5_Missense_Mutation_p.S1309F|TNIK_ENST00000470834.1_Missense_Mutation_p.S1301F|TNIK_ENST00000475336.1_Missense_Mutation_p.S1246F|TNIK_ENST00000341852.6_Missense_Mutation_p.S1254F|TNIK_ENST00000488470.1_Missense_Mutation_p.S1283F	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1338					actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.S1338F(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGATCGCACGGATGCAAAAAA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	3											101	95	97					3																	170781740		1854	4101	5955	172264434	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.4013C>T	3.37:g.170781740G>A	ENSP00000399511:p.Ser1338Phe		172264434	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.719683	0.68844	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	D;D;D;D;D;D;D;D;D;D	0.82619	-1.59;-1.59;-1.62;-1.6;-1.59;-1.58;-1.6;-1.63;-1.62;-1.59	5.97	5.97	0.96955	Citron-like (1);	0.000000	0.85682	D	0.000000	D	0.92097	0.7495	M	0.80847	2.515	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.994;1.0;0.998;0.994;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D;D	0.91635	0.989;0.999;0.992;0.989;0.998;0.996;0.992;0.995	D	0.92064	0.5659	10	0.87932	D	0	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	1246;1301;1275;1254;1330;1309;1283;1338	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	F	1338;1316;1290;1254;1330;1246;1309;1275;1283;1301	ENSP00000399511:S1338F;ENSP00000358332:S1316F;ENSP00000443278:S1290F;ENSP00000345352:S1254F;ENSP00000284483:S1330F;ENSP00000418156:S1246F;ENSP00000349880:S1309F;ENSP00000418916:S1275F;ENSP00000418378:S1283F;ENSP00000419990:S1301F	ENSP00000284483:S1330F	S	-	2	0	TNIK	172264434	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.836000	0.97738	0.655000	0.94253	TCC		0.408	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170781740	G	A	170781740	3	1	61	1	0	0	0	0	1	0	0	0	16352	1174	41	3	73	3	TNIK	3	170781740	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	537026	170781740	27240690	2920	10905										
TNIK	23043	broad.mit.edu	37	chr3	170786785	170786785	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgctggagatctgcaaaaGactttaaaaatcaccccatt	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170786785G>T	ENST00000436636.2	-	30	3895	c.3551C>A	c.(3550-3552)tCt>tAt	p.S1184Y	TNIK_ENST00000460047.1_Splice_Site_p.S1121Y|TNIK_ENST00000538048.1_Splice_Site_p.S1136Y|TNIK_ENST00000369326.5_Splice_Site_p.S1162Y|TNIK_ENST00000284483.8_Splice_Site_p.S1176Y|TNIK_ENST00000357327.5_Splice_Site_p.S1155Y|TNIK_ENST00000470834.1_Splice_Site_p.S1147Y|TNIK_ENST00000475336.1_Splice_Site_p.S1092Y|TNIK_ENST00000341852.6_Splice_Site_p.S1100Y|TNIK_ENST00000488470.1_Splice_Site_p.S1129Y	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1184	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.S1184Y(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ATCTGCAAAAGACTTTAAAAA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	3											151	146	147					3																	170786785		1830	4081	5911	172269479	SO:0001630	splice_region_variant	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.3550-1C>A	3.37:g.170786785G>T			172269479	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593606	0.86953	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.04862	3.54;3.54;3.54;3.54;3.54;3.54;3.54;3.54;3.54;3.54	5.86	5.86	0.93980	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	M	0.80847	2.515	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;0.994;0.985;0.994;0.994;0.994;0.985;0.994;0.998	D;D;P;D;D;D;P;D;D	0.77557	0.99;0.989;0.835;0.989;0.989;0.917;0.835;0.989;0.96	T	0.00847	-1.1542	10	0.87932	D	0	.	20.1781	0.98191	0.0:0.0:1.0:0.0	.	1136;1092;1147;1121;1100;1176;1155;1129;1184	F5H5M9;Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;.;TNIK_HUMAN	Y	1184;1162;1136;1100;1176;1092;1155;1121;1129;1147	ENSP00000399511:S1184Y;ENSP00000358332:S1162Y;ENSP00000443278:S1136Y;ENSP00000345352:S1100Y;ENSP00000284483:S1176Y;ENSP00000418156:S1092Y;ENSP00000349880:S1155Y;ENSP00000418916:S1121Y;ENSP00000418378:S1129Y;ENSP00000419990:S1147Y	ENSP00000284483:S1176Y	S	-	2	0	TNIK	172269479	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.869000	0.99810	2.778000	0.95560	0.591000	0.81541	TCT		0.378	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	Missense_Mutation	T	170786785	G	T	170786785	5	4	61	1	0	0	0	0	0	0	1	0	16352	956	33	2	547	2	TNIK	3	170786785	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5045	170786785	27235645	2921	10906										
TNIK	23043	broad.mit.edu	37	chr3	170828506	170828506	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaagagaaagttttacctcGaactctggtgcgttcactgg	11	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170828506G>A	ENST00000436636.2	-	19	2625	c.2281C>T	c.(2281-2283)Cga>Tga	p.R761*	TNIK_ENST00000460047.1_Nonsense_Mutation_p.R706*|TNIK_ENST00000538048.1_Nonsense_Mutation_p.R706*|TNIK_ENST00000369326.5_Nonsense_Mutation_p.R732*|TNIK_ENST00000284483.8_Nonsense_Mutation_p.R761*|TNIK_ENST00000357327.5_Nonsense_Mutation_p.R732*|TNIK_ENST00000470834.1_Nonsense_Mutation_p.R732*|TNIK_ENST00000475336.1_Nonsense_Mutation_p.R677*|TNIK_ENST00000341852.6_Nonsense_Mutation_p.R677*|TNIK_ENST00000488470.1_Nonsense_Mutation_p.R706*	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	761	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R761*(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GTTTTACCTCGAACTCTGGTG	0.542																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											45	47	46					3																	170828506		1976	4172	6148	172311200	SO:0001587	stop_gained	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2281C>T	3.37:g.170828506G>A	ENSP00000399511:p.Arg761*		172311200	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Nonsense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	39	7.368756	0.98241	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	.	.	.	6.17	5.25	0.73442	.	0.136497	0.48767	D	0.000163	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2717	0.82624	0.0:0.0:0.7991:0.2009	.	.	.	.	X	761;732;706;677;761;677;732;706;706;732	.	ENSP00000284483:R761X	R	-	1	2	TNIK	172311200	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.405000	0.44548	2.941000	0.99782	0.655000	0.94253	CGA		0.542	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170828506	G	A	170828506	4	1	61	1	0	0	0	0	0	1	0	0	16352	1066	37	1	1861	1	TNIK	3	170828506	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41721	170828506	27193924	2922	10907										
TNIK	23043	broad.mit.edu	37	chr3	170884890	170884890	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgcgtctaacctttttCtcctcgcttcttctttgttc	5	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:170884890C>A	ENST00000436636.2	-	10	1287	c.943G>T	c.(943-945)Gaa>Taa	p.E315*	TNIK_ENST00000460047.1_Nonsense_Mutation_p.E315*|TNIK_ENST00000538048.1_Nonsense_Mutation_p.E315*|TNIK_ENST00000369326.5_Nonsense_Mutation_p.E315*|TNIK_ENST00000284483.8_Nonsense_Mutation_p.E315*|TNIK_ENST00000357327.5_Nonsense_Mutation_p.E315*|TNIK_ENST00000470834.1_Nonsense_Mutation_p.E315*|TNIK_ENST00000475336.1_Nonsense_Mutation_p.E315*|TNIK_ENST00000341852.6_Nonsense_Mutation_p.E315*|TNIK_ENST00000488470.1_Nonsense_Mutation_p.E315*	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	315	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.E315*(4)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TAACCTTTTTCTCCTCGCTTC	0.413																																																4	Substitution - Nonsense(4)	large_intestine(4)	3											171	151	157					3																	170884890		1905	4118	6023	172367584	SO:0001587	stop_gained	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.943G>T	3.37:g.170884890C>A	ENSP00000399511:p.Glu315*		172367584	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Nonsense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	C	38	6.651490	0.97734	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834;ENST00000468757	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.3798	0.94527	0.0:1.0:0.0:0.0	.	.	.	.	X	315;315;315;315;315;315;315;315;315;315;289	.	ENSP00000284483:E315X	E	-	1	0	TNIK	172367584	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.776000	0.85560	2.644000	0.89710	0.655000	0.94253	GAA		0.413	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170884890	C	A	170884890	4	1	61	1	0	0	0	0	0	1	0	0	16352	922	32	2	3235	2	TNIK	3	170884890	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56384	170884890	27137540	2923	10908										
PLD1	5337	broad.mit.edu	37	chr3	171320914	171320914	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcctctttggtcccaacaGaaggcagtaggctttcttca	10	11	3	1	rs376459861		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:171320914G>T	ENST00000351298.4	-	27	3305	c.3179C>A	c.(3178-3180)tCt>tAt	p.S1060Y	PLD1_ENST00000356327.5_Missense_Mutation_p.S1022Y|PLD1_ENST00000342215.6_3'UTR	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	1060					chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.S1060Y(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GGTCCCAACAGAAGGCAGTAG	0.473																																					NSCLC(149;2174 3517 34058)											1	Substitution - Missense(1)	large_intestine(1)	3											95	94	94					3																	171320914		2203	4300	6503	172803608	SO:0001583	missense	5337			U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.3179C>A	3.37:g.171320914G>T	ENSP00000342793:p.Ser1060Tyr		172803608		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180921	0.94846	.	.	ENSG00000075651	ENST00000356327;ENST00000351298	T;T	0.06142	3.34;3.34	6.07	6.07	0.98685	.	0.050414	0.85682	D	0.000000	T	0.18341	0.0440	L	0.46947	1.48	0.80722	D	1	B;D	0.65815	0.06;0.995	B;P	0.62649	0.094;0.905	T	0.01771	-1.1277	10	0.19147	T	0.46	-6.0633	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1045;1060	Q59EA4;Q13393	.;PLD1_HUMAN	Y	1022;1060	ENSP00000348681:S1022Y;ENSP00000342793:S1060Y	ENSP00000342793:S1060Y	S	-	2	0	PLD1	172803608	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.835000	0.99442	2.890000	0.99128	0.650000	0.86243	TCT		0.473	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		T	171320914	G	T	171320914	3	4	61	1	0	0	0	0	1	0	0	0	12076	942	33	2	49	2	PLD1	3	171320914	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436024	171320914	26701516	2924	10909										
PLD1	5337	broad.mit.edu	37	chr3	171410184	171410184	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcactattgatgccaagagCgagttccacctctttgtaga	8	10	2	3	rs369183504		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:171410184C>T	ENST00000351298.4	-	13	1402	c.1276G>A	c.(1276-1278)Gct>Act	p.A426T	snoU13_ENST00000458788.1_RNA|PLD1_ENST00000340989.4_Missense_Mutation_p.A426T|PLD1_ENST00000356327.5_Missense_Mutation_p.A426T|PLD1_ENST00000342215.6_Missense_Mutation_p.A426T	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	426					chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.A426T(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ATGCCAAGAGCGAGTTCCACC	0.418																																					NSCLC(149;2174 3517 34058)											1	Substitution - Missense(1)	large_intestine(1)	3						C	THR/ALA,THR/ALA	0,4406		0,0,2203	160	147	151		1276,1276	5.6	1	3		151	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	PLD1	NM_001130081.2,NM_002662.4	58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	426/1037,426/1075	171410184	2,13004	2203	4300	6503	172892878	SO:0001583	missense	5337			U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1276G>A	3.37:g.171410184C>T	ENSP00000342793:p.Ala426Thr		172892878		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	C	35	5.548521	0.96488	0.0	2.33E-4	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	L	0.60012	1.86	0.80722	D	1	D;P	0.89917	1.0;0.764	D;B	0.71184	0.972;0.371	T	0.29671	-1.0004	10	0.45353	T	0.12	-16.7302	19.9052	0.97004	0.0:1.0:0.0:0.0	.	449;426	Q59EA4;Q13393	.;PLD1_HUMAN	T	426	ENSP00000348681:A426T;ENSP00000342793:A426T;ENSP00000339936:A426T;ENSP00000340326:A426T	ENSP00000340326:A426T	A	-	1	0	PLD1	172892878	1.000000	0.71417	0.956000	0.39512	0.821000	0.46438	7.752000	0.85141	2.776000	0.95493	0.655000	0.94253	GCT		0.418	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		T	171410184	C	T	171410184	3	4	61	1	0	0	0	0	1	0	0	0	12076	768	27	1	2008	1	PLD1	3	171410184	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89270	171410184	26612246	2925	10910										
PLD1	5337	broad.mit.edu	37	chr3	171452705	171452705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgttttcagatgaacgggGcaaactgggcatctctcgag	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:171452705G>A	ENST00000351298.4	-	5	616	c.490C>T	c.(490-492)Ccc>Tcc	p.P164S	PLD1_ENST00000340989.4_Missense_Mutation_p.P164S|PLD1_ENST00000356327.5_Missense_Mutation_p.P164S|PLD1_ENST00000342215.6_Missense_Mutation_p.P164S	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	164	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.P164S(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GATGAACGGGGCAAACTGGGC	0.403																																					NSCLC(149;2174 3517 34058)											1	Substitution - Missense(1)	large_intestine(1)	3											145	151	149					3																	171452705		2203	4300	6503	172935399	SO:0001583	missense	5337			U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.490C>T	3.37:g.171452705G>A	ENSP00000342793:p.Pro164Ser		172935399		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686215	0.88639	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989	T;T;T;T	0.34667	3.27;3.26;1.35;3.12	5.82	5.82	0.92795	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.62245	0.2412	M	0.78916	2.43	0.80722	D	1	D;B	0.64830	0.994;0.118	D;B	0.69142	0.962;0.2	T	0.63056	-0.6722	10	0.56958	D	0.05	-16.465	17.8743	0.88821	0.0:0.0:1.0:0.0	.	187;164	Q59EA4;Q13393	.;PLD1_HUMAN	S	164	ENSP00000348681:P164S;ENSP00000342793:P164S;ENSP00000339936:P164S;ENSP00000340326:P164S	ENSP00000340326:P164S	P	-	1	0	PLD1	172935399	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	6.672000	0.74477	2.748000	0.94277	0.655000	0.94253	CCC		0.403	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171452705	G	A	171452705	3	1	61	1	0	0	0	0	1	0	0	0	12076	1203	42	3	2826	3	PLD1	3	171452705	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42521	171452705	26569725	2926	10911										
FNDC3B	64778	broad.mit.edu	37	chr3	171969311	171969311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaagaagcagcccaaagtCgaatgattcagacttgcaag	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:171969311C>T	ENST00000336824.4	+	6	869	c.770C>T	c.(769-771)tCg>tTg	p.S257L	FNDC3B_ENST00000415807.2_Missense_Mutation_p.S257L|FNDC3B_ENST00000416957.1_Missense_Mutation_p.S257L	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	257					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S257L(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGCCCAAAGTCGAATGATTCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											70	72	72					3																	171969311		2203	4300	6503	173452005	SO:0001583	missense	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.770C>T	3.37:g.171969311C>T	ENSP00000338523:p.Ser257Leu		173452005	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402789	0.62288	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.23950	1.88;1.88;1.88	5.64	5.64	0.86602	.	0.164902	0.53938	D	0.000041	T	0.31136	0.0787	L	0.57536	1.79	0.80722	D	1	P;P	0.50443	0.935;0.87	B;B	0.41571	0.36;0.069	T	0.04946	-1.0916	10	0.40728	T	0.16	-10.5655	19.6986	0.96043	0.0:1.0:0.0:0.0	.	257;257	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	L	257	ENSP00000411242:S257L;ENSP00000338523:S257L;ENSP00000389094:S257L	ENSP00000338523:S257L	S	+	2	0	FNDC3B	173452005	0.999000	0.42202	0.836000	0.33094	0.620000	0.37586	4.458000	0.60095	2.645000	0.89757	0.591000	0.81541	TCG		0.468	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	171969311	C	T	171969311	3	4	61	1	0	0	0	0	1	0	0	0	5989	893	31	1	788	1	FNDC3B	3	171969311	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	516606	171969311	26053119	2927	10912										
FNDC3B	64778	broad.mit.edu	37	chr3	172013157	172013157	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttttcttcctcaggtttCtaatattcaggcaagagcag	8	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:172013157C>A	ENST00000336824.4	+	8	953	c.854C>A	c.(853-855)tCt>tAt	p.S285Y	FNDC3B_ENST00000415807.2_Missense_Mutation_p.S285Y|FNDC3B_ENST00000416957.1_Missense_Mutation_p.S285Y	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	285	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S285Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CCTCAGGTTTCTAATATTCAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											173	171	171					3																	172013157		2203	4300	6503	173495851	SO:0001583	missense	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.854C>A	3.37:g.172013157C>A	ENSP00000338523:p.Ser285Tyr		173495851	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038973	0.75617	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.60299	0.2;0.2;0.2	5.98	5.98	0.97165	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.152355	0.64402	D	0.000012	T	0.78142	0.4237	M	0.79011	2.435	0.80722	D	1	P;D	0.69078	0.937;0.997	P;D	0.76071	0.797;0.987	T	0.79254	-0.1879	10	0.87932	D	0	-22.3578	19.2296	0.93833	0.0:1.0:0.0:0.0	.	285;285	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	Y	285	ENSP00000411242:S285Y;ENSP00000338523:S285Y;ENSP00000389094:S285Y	ENSP00000338523:S285Y	S	+	2	0	FNDC3B	173495851	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.715000	0.61909	2.835000	0.97688	0.650000	0.86243	TCT		0.433	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	172013157	C	A	172013157	3	1	61	1	0	0	0	0	1	0	0	0	5989	913	32	2	880	2	FNDC3B	3	172013157	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43846	172013157	26009273	2928	10913										
FNDC3B	64778	broad.mit.edu	37	chr3	172013251	172013251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttccttcccctacagttaCgaggtggccttatcagacaa	7	13	1	1	rs139237887		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:172013251C>T	ENST00000336824.4	+	8	1047	c.948C>T	c.(946-948)taC>taT	p.Y316Y	FNDC3B_ENST00000415807.2_Silent_p.Y316Y|FNDC3B_ENST00000416957.1_Silent_p.Y316Y	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	316	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.Y316Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CCTACAGTTACGAGGTGGCCT	0.428													C|||	1	0.000199681	0	0	5008	,	,		17639	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											159	153	155					3																	172013251		2203	4300	6503	173495945	SO:0001819	synonymous_variant	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.948C>T	3.37:g.172013251C>T			173495945	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																				0.428	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172013251	C	T	172013251	2	4	61	1	0	0	0	0	0	0	0	1	5989	547	19	1		1	FNDC3B	3	172013251	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94	172013251	26009179	2929	10914										
FNDC3B	64778	broad.mit.edu	37	chr3	172064193	172064193	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcaaagcaccttgtatttCttgtacacctgatggatgtg	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:172064193C>A	ENST00000336824.4	+	20	2426	c.2327C>A	c.(2326-2328)tCt>tAt	p.S776Y	FNDC3B_ENST00000415807.2_Missense_Mutation_p.S776Y|FNDC3B_ENST00000416957.1_Missense_Mutation_p.S776Y	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	776	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S776Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CCTTGTATTTCTTGTACACCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											231	204	213					3																	172064193		2203	4300	6503	173546887	SO:0001583	missense	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2327C>A	3.37:g.172064193C>A	ENSP00000338523:p.Ser776Tyr		173546887	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.691984	0.30052	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.55052	0.54;0.54;0.54	6.02	6.02	0.97574	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.170447	0.53938	D	0.000044	T	0.45034	0.1322	L	0.34521	1.04	0.80722	D	1	B	0.19706	0.038	B	0.25759	0.063	T	0.33727	-0.9857	10	0.56958	D	0.05	-24.0904	13.6966	0.62582	0.0:0.93:0.0:0.07	.	776	Q53EP0	FND3B_HUMAN	Y	776	ENSP00000411242:S776Y;ENSP00000338523:S776Y;ENSP00000389094:S776Y	ENSP00000338523:S776Y	S	+	2	0	FNDC3B	173546887	1.000000	0.71417	0.776000	0.31678	0.012000	0.07955	7.016000	0.76393	2.857000	0.98124	0.650000	0.86243	TCT		0.438	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	172064193	C	A	172064193	3	1	61	1	0	0	0	0	1	0	0	0	5989	913	32	2	2401	2	FNDC3B	3	172064193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50942	172064193	25958237	2930	10915										
GHSR	2693	broad.mit.edu	37	chr3	172166054	172166054	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaccacgaagagtgccacGcaggtggctgtgacgcccgc	13	16	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:172166054G>A	ENST00000241256.2	-	1	192	c.150C>T	c.(148-150)tgC>tgT	p.C50C	GHSR_ENST00000427970.1_Silent_p.C50C	NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	50					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)	p.C50C(2)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			AGAGTGCCACGCAGGTGGCTG	0.682																																					Esophageal Squamous(93;641 1401 20883 29581 34638)											2	Substitution - coding silent(2)	large_intestine(2)	3											32	33	33					3																	172166054		2203	4299	6502	173648748	SO:0001819	synonymous_variant	2693			AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"GPCR / Class A : Ghrelin receptors"	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.150C>T	3.37:g.172166054G>A			173648748	Q14D12|Q6ISR8|Q92848|Q96RJ7	Silent	SNP	ENST00000241256.2	37	CCDS3218.1																																																																																				0.682	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122		A	172166054	G	A	172166054	2	1	61	1	0	0	0	0	0	0	0	1	6395	1079	38	1		1	GHSR	3	172166054	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101861	172166054	25856376	2931	10916										
ECT2	1894	broad.mit.edu	37	chr3	172534527	172534527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactccaaaaagagctcttcGaagggctcttatgacatccc	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:172534527G>A	ENST00000392692.3	+	24	2731	c.2555G>A	c.(2554-2556)cGa>cAa	p.R852Q	ECT2_ENST00000441497.2_Missense_Mutation_p.R821Q|ECT2_ENST00000427830.1_Missense_Mutation_p.R821Q|ECT2_ENST00000417960.1_Missense_Mutation_p.R820Q|ECT2_ENST00000232458.5_Missense_Mutation_p.R821Q|ECT2_ENST00000540509.1_Missense_Mutation_p.R852Q	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	852					activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.R821Q(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			AGAGCTCTTCGAAGGGCTCTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	81	80					3																	172534527		2203	4299	6502	174017221	SO:0001583	missense	1894			AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"Rho guanine nucleotide exchange factors"	3155	protein-coding gene	gene with protein product		600586	"epithelial cell transforming sequence 2 oncogene"			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.2555G>A	3.37:g.172534527G>A	ENSP00000376457:p.Arg852Gln		174017221	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	37	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.946431	0.34377	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	T;T;T;T;T;T	0.64618	-0.08;-0.07;-0.11;-0.08;-0.08;-0.07	5.58	5.58	0.84498	.	0.058315	0.64402	D	0.000001	T	0.46927	0.1418	L	0.29908	0.895	0.41234	D	0.986592	B;B;B;B;B	0.22346	0.008;0.002;0.068;0.014;0.022	B;B;B;B;B	0.18263	0.003;0.002;0.021;0.006;0.006	T	0.39121	-0.9629	10	0.15066	T	0.55	-9.2605	11.7764	0.51987	0.0816:0.0:0.9184:0.0	.	852;297;852;821;820	Q9H8V3;Q96SJ9;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.;.	Q	821;852;821;820;821;852	ENSP00000232458:R821Q;ENSP00000376457:R852Q;ENSP00000401910:R821Q;ENSP00000415876:R820Q;ENSP00000412259:R821Q;ENSP00000443160:R852Q	ENSP00000232458:R821Q	R	+	2	0	ECT2	174017221	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	5.293000	0.65680	2.630000	0.89119	0.561000	0.74099	CGA		0.403	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		A	172534527	G	A	172534527	3	1	61	1	0	0	0	0	1	0	0	0	4912	1058	37	1	2548	1	ECT2	3	172534527	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	368473	172534527	25487903	2932	10917										
NLGN1	22871	broad.mit.edu	37	chr3	173322839	173322839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatgtgcaagaccagagcGaagactgcctatatttaaat	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:173322839G>A	ENST00000457714.1	+	3	880	c.451G>A	c.(451-453)Gaa>Aaa	p.E151K	NLGN1_ENST00000401917.3_Missense_Mutation_p.E151K|NLGN1_ENST00000545397.1_Missense_Mutation_p.E151K|NLGN1_ENST00000361589.4_Missense_Mutation_p.E151K	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	151					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.E151K(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			AGACCAGAGCGAAGACTGCCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	106	105					3																	173322839		2203	4300	6503	174805533	SO:0001583	missense	22871			AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.451G>A	3.37:g.173322839G>A	ENSP00000392500:p.Glu151Lys		174805533	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630505	0.87660	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19;-2.19	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	H	0.98276	4.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.97670	1.0166	10	0.87932	D	0	.	20.0185	0.97487	0.0:0.0:1.0:0.0	.	151;151	D2X2H5;Q8N2Q7-2	.;.	K	151	ENSP00000392500:E151K;ENSP00000354541:E151K;ENSP00000410374:E151K;ENSP00000441108:E151K;ENSP00000385750:E151K	ENSP00000354541:E151K	E	+	1	0	NLGN1	174805533	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.420000	0.97426	2.809000	0.96659	0.467000	0.42956	GAA		0.368	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173322839	G	A	173322839	3	1	61	1	0	0	0	0	1	0	0	0	10492	1059	37	1	453	1	NLGN1	3	173322839	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	788312	173322839	24699591	2933	10918										
NLGN1	22871	broad.mit.edu	37	chr3	173993199	173993199	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actagtgaaaacattggattCtttggtggtgaccccttaag	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:173993199C>A	ENST00000457714.1	+	5	1170	c.741C>A	c.(739-741)ttC>ttA	p.F247L	NLGN1_ENST00000401917.3_Missense_Mutation_p.F287L|NLGN1_ENST00000466350.1_3'UTR|NLGN1_ENST00000545397.1_Missense_Mutation_p.F247L|NLGN1_ENST00000361589.4_Missense_Mutation_p.F247L	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	264					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.F247L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ACATTGGATTCTTTGGTGGTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	102	103					3																	173993199		2203	4300	6503	175475893	SO:0001583	missense	22871			AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.741C>A	3.37:g.173993199C>A	ENSP00000392500:p.Phe247Leu		175475893	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.832368	0.32421	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	5.34	5.34	0.76211	.	0.170721	0.53938	D	0.000042	T	0.55529	0.1926	L	0.28649	0.875	0.58432	D	0.999999	B;B	0.29671	0.254;0.219	B;B	0.29524	0.103;0.054	T	0.50634	-0.8805	10	0.11182	T	0.66	.	19.5946	0.95530	0.0:1.0:0.0:0.0	.	287;247	D2X2H5;Q8N2Q7-2	.;.	L	247;247;287;247;287	ENSP00000392500:F247L;ENSP00000354541:F247L;ENSP00000410374:F287L;ENSP00000441108:F247L;ENSP00000385750:F287L	ENSP00000354541:F247L	F	+	3	2	NLGN1	175475893	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.838000	0.55828	2.937000	0.99478	0.650000	0.86243	TTC		0.438	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173993199	C	A	173993199	3	1	61	1	0	0	0	0	1	0	0	0	10492	912	32	2	751	2	NLGN1	3	173993199	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	670360	173993199	24029231	2934	10919										
NAALADL2	254827	broad.mit.edu	37	chr3	174814999	174814999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaattgcccttcagatgctCcatcttcaggaacagttgat	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:174814999C>T	ENST00000454872.1	+	2	591	c.463C>T	c.(463-465)Cca>Tca	p.P155S	NAALADL2_ENST00000473253.1_3'UTR|NAALADL2-AS3_ENST00000453180.1_RNA	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	155						integral component of membrane (GO:0016021)		p.P155S(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TTCAGATGCTCCATCTTCAGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	100	100					3																	174814999		1838	4090	5928	176297693	SO:0001583	missense	254827				CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"glutamate carboxypeptidase II-type non-peptidase homologue"	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.463C>T	3.37:g.174814999C>T	ENSP00000404705:p.Pro155Ser		176297693	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	C	2.989	-0.208511	0.06140	.	.	ENSG00000177694	ENST00000454872	T	0.32753	1.44	5.63	-4.36	0.03645	.	1.336820	0.04862	N	0.444289	T	0.11793	0.0287	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.10450	0.005;0.0	T	0.18555	-1.0333	9	.	.	.	0.0115	1.2279	0.01937	0.3044:0.1937:0.3136:0.1882	.	138;155	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	S	155	ENSP00000404705:P155S	.	P	+	1	0	NAALADL2	176297693	0.000000	0.05858	0.006000	0.13384	0.019000	0.09904	-0.829000	0.04415	-0.316000	0.08690	-0.485000	0.04761	CCA		0.358	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		T	174814999	C	T	174814999	3	4	61	1	0	0	0	0	1	0	0	0	10160	855	30	3	469	3	NAALADL2	3	174814999	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	821800	174814999	23207431	2935	10920										
NAALADL2	254827	broad.mit.edu	37	chr3	175520973	175520973	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatgtgttcaagagtgtCttggatgggaagaattgaga	14	3	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:175520973C>A	ENST00000454872.1	+	14	2498	c.2370C>A	c.(2368-2370)gtC>gtA	p.V790V		NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	790						integral component of membrane (GO:0016021)		p.V790V(2)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCAAGAGTGTCTTGGATGGGA	0.378																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	3											97	91	93					3																	175520973		1825	4072	5897	177003667	SO:0001819	synonymous_variant	254827				CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"glutamate carboxypeptidase II-type non-peptidase homologue"	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.2370C>A	3.37:g.175520973C>A			177003667	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Silent	SNP	ENST00000454872.1	37	CCDS46960.1																																																																																				0.378	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		A	175520973	C	A	175520973	2	1	61	1	0	0	0	0	0	0	0	1	10160	900	32	2		2	NAALADL2	3	175520973	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	705974	175520973	22501457	2936	10921										
ZMAT3	64393	broad.mit.edu	37	chr3	178742823	178742823	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactatacatatcccagattCtccatctcattcctgtaccg	3	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:178742823C>A	ENST00000311417.2	-	6	1593	c.852G>T	c.(850-852)gaG>gaT	p.E284D	ZMAT3_ENST00000432729.1_Missense_Mutation_p.E283D	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3									p.E284D(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			ATCCCAGATTCTCCATCTCAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											211	190	197					3																	178742823		2203	4300	6503	180225517	SO:0001583	missense	64393			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.852G>T	3.37:g.178742823C>A	ENSP00000311221:p.Glu284Asp		180225517		Missense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.592714	0.66219	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	T;T	0.52754	0.66;0.65	5.46	2.7	0.31948	.	0.000000	0.85682	D	0.000000	T	0.59335	0.2186	L	0.47716	1.5	0.54753	D	0.999984	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.967	T	0.56631	-0.7947	10	0.49607	T	0.09	-41.0285	12.9851	0.58588	0.0:0.8029:0.0:0.1971	.	283;284	Q9HA38-2;Q9HA38	.;ZMAT3_HUMAN	D	284;283	ENSP00000311221:E284D;ENSP00000396506:E283D	ENSP00000311221:E284D	E	-	3	2	ZMAT3	180225517	1.000000	0.71417	0.994000	0.49952	0.781000	0.44180	2.020000	0.41010	0.301000	0.22738	-0.813000	0.03139	GAG		0.433	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		A	178742823	C	A	178742823	3	1	61	1	0	0	0	0	1	0	0	0	17732	912	32	2	21	2	ZMAT3	3	178742823	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3221850	178742823	19279607	2937	10922										
MFN1	55669	broad.mit.edu	37	chr3	179069714	179069714	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagaatccggaacttgatCgaatagccactgaagatgat	9	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179069714C>T	ENST00000471841.1	+	3	265	c.139C>T	c.(139-141)Cga>Tga	p.R47*	MFN1_ENST00000280653.7_Nonsense_Mutation_p.R47*|MFN1_ENST00000263969.5_Nonsense_Mutation_p.R47*	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	47					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R47*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GGAACTTGATCGAATAGCCAC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											117	114	115					3																	179069714		2203	4300	6503	180552408	SO:0001587	stop_gained	55669			AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.139C>T	3.37:g.179069714C>T	ENSP00000420617:p.Arg47*		180552408	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Nonsense_Mutation	SNP	ENST00000471841.1	37	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572896	0.65765	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000467174;ENST00000263969	.	.	.	5.16	4.29	0.51040	.	0.210963	0.39909	N	0.001223	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-0.0592	11.1144	0.48252	0.1446:0.7162:0.1392:0.0	.	.	.	.	X	47	.	ENSP00000263969:R47X	R	+	1	2	MFN1	180552408	0.000000	0.05858	1.000000	0.80357	0.151000	0.21798	0.441000	0.21611	1.308000	0.44962	-0.463000	0.05309	CGA		0.353	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		T	179069714	C	T	179069714	4	4	61	1	0	0	0	0	0	1	0	0	9553	876	31	1	145	1	MFN1	3	179069714	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	326891	179069714	18952716	2938	10923										
MFN1	55669	broad.mit.edu	37	chr3	179096378	179096378	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttctttctagaaaatTtgaagccattacttccagct	5	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179096378T>G	ENST00000471841.1	+	14	1564	c.1438T>G	c.(1438-1440)Ttg>Gtg	p.L480V	MFN1_ENST00000280653.7_Intron|MFN1_ENST00000263969.5_Missense_Mutation_p.L480V	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	480					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L480V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TCTAGAAAATTTGAAGCCATT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											33	31	32					3																	179096378		2203	4300	6503	180579072	SO:0001583	missense	55669			AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1438T>G	3.37:g.179096378T>G	ENSP00000420617:p.Leu480Val		180579072	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	37	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.179099	0.38511	.	.	ENSG00000171109	ENST00000471841;ENST00000263969	D;D	0.88354	-2.37;-2.37	5.16	4.01	0.46588	.	0.059984	0.64402	D	0.000001	T	0.81955	0.4932	L	0.54323	1.7	0.80722	D	1	B;B	0.15930	0.015;0.008	B;B	0.14578	0.011;0.011	T	0.72181	-0.4368	10	0.15952	T	0.53	-9.9245	4.2825	0.10839	0.0:0.3023:0.0:0.6977	.	508;480	Q4AEJ4;Q8IWA4	.;MFN1_HUMAN	V	480	ENSP00000420617:L480V;ENSP00000263969:L480V	ENSP00000263969:L480V	L	+	1	2	MFN1	180579072	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	0.953000	0.29162	1.948000	0.56530	0.482000	0.46254	TTG		0.323	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		G	179096378	T	G	179096378	3	3	61	1	0	0	0	0	1	0	0	0	9553	1838	64	4	1488	4	MFN1	3	179096378	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26664	179096378	18926052	2939	10924										
MFN1	55669	broad.mit.edu	37	chr3	179103429	179103429	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagataatgcatcacaggaaGaactcatgattacattagta	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179103429G>T	ENST00000471841.1	+	15	1861	c.1735G>T	c.(1735-1737)Gaa>Taa	p.E579*	MFN1_ENST00000280653.7_Nonsense_Mutation_p.E468*|MFN1_ENST00000263969.5_Nonsense_Mutation_p.E579*	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	579					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E579*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			ATCACAGGAAGAACTCATGAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											126	116	120					3																	179103429		2203	4300	6503	180586123	SO:0001587	stop_gained	55669			AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1735G>T	3.37:g.179103429G>T	ENSP00000420617:p.Glu579*		180586123	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Nonsense_Mutation	SNP	ENST00000471841.1	37	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456449	0.63401	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000263969;ENST00000474903	.	.	.	5.62	5.62	0.85841	.	0.139418	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-20.9802	19.6718	0.95914	0.0:0.0:1.0:0.0	.	.	.	.	X	579;468;579;331	.	ENSP00000263969:E579X	E	+	1	0	MFN1	180586123	1.000000	0.71417	0.998000	0.56505	0.112000	0.19704	9.395000	0.97266	2.639000	0.89480	0.557000	0.71058	GAA		0.408	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		T	179103429	G	T	179103429	4	4	61	1	0	0	0	0	0	1	0	0	9553	943	33	2	1789	2	MFN1	3	179103429	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7051	179103429	18919001	2940	10925										
ACTL6A	86	broad.mit.edu	37	chr3	179304340	179304340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttctatttcagagtatgCggttgaaattgattgcaaat	8	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179304340C>T	ENST00000429709.2	+	13	1342	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	RP11-145M9.6_ENST00000610007.1_RNA|ACTL6A_ENST00000450518.2_Missense_Mutation_p.R335W|RP11-15L13.4_ENST00000608818.1_RNA|ACTL6A_ENST00000392662.1_Missense_Mutation_p.R335W	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	377					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)	p.R377W(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			TCAGAGTATGCGGTTGAAATT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											87	86	86					3																	179304340		2203	4300	6503	180787034	SO:0001583	missense	86			AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1129C>T	3.37:g.179304340C>T	ENSP00000397552:p.Arg377Trp		180787034	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	37	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923001	0.73213	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.95035	-3.59;-3.59;-3.59	5.91	4.96	0.65561	.	0.049963	0.85682	D	0.000000	D	0.97692	0.9243	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.98202	1.0468	10	0.87932	D	0	.	15.8813	0.79207	0.2222:0.7778:0.0:0.0	.	377	O96019	ACL6A_HUMAN	W	377;335;335	ENSP00000397552:R377W;ENSP00000394014:R335W;ENSP00000376430:R335W	ENSP00000376430:R335W	R	+	1	2	ACTL6A	180787034	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.909000	0.48758	2.793000	0.96121	0.655000	0.94253	CGG		0.343	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		T	179304340	C	T	179304340	3	4	61	1	0	0	0	0	1	0	0	0	198	759	27	1	1179	1	ACTL6A	3	179304340	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200911	179304340	18718090	2941	10926										
ACTL6A	86	broad.mit.edu	37	chr3	179305757	179305757	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatttccaagcaagaatatGaagaaggagggaagcagtgt	14	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179305757G>T	ENST00000429709.2	+	14	1462	c.1249G>T	c.(1249-1251)Gaa>Taa	p.E417*	ACTL6A_ENST00000450518.2_Nonsense_Mutation_p.E375*|ACTL6A_ENST00000392662.1_Nonsense_Mutation_p.E375*	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	417					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)	p.E417*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			GCAAGAATATGAAGAAGGAGG	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											83	97	92					3																	179305757		2203	4300	6503	180788451	SO:0001587	stop_gained	86			AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1249G>T	3.37:g.179305757G>T	ENSP00000397552:p.Glu417*		180788451	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Nonsense_Mutation	SNP	ENST00000429709.2	37	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	39	7.313032	0.98203	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	.	.	.	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.4434	0.99119	0.0:0.0:1.0:0.0	.	.	.	.	X	417;375;375	.	ENSP00000376430:E375X	E	+	1	0	ACTL6A	180788451	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.866000	0.99616	2.838000	0.97847	0.655000	0.94253	GAA		0.358	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		T	179305757	G	T	179305757	4	4	61	1	0	0	0	0	0	1	0	0	198	1291	45	2	1303	2	ACTL6A	3	179305757	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1417	179305757	18716673	2942	10927										
MRPL47	57129	broad.mit.edu	37	chr3	179306713	179306713	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggaaacttttttaaaaGaatttttgctttctttctct	5	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179306713G>T	ENST00000476781.1	-	7	729	c.700C>A	c.(700-702)Ctt>Att	p.L234I	MRPL47_ENST00000259038.2_Missense_Mutation_p.L214I|MRPL47_ENST00000392659.2_Missense_Mutation_p.L124I	NM_020409.2	NP_065142.2	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47	234					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)	p.L234I(2)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|stomach(1)	11	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TTTTTTAAAAGAATTTTTGCT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	3											67	73	71					3																	179306713		2203	4299	6502	180789407	SO:0001583	missense	57129			AF285120	CCDS3232.1, CCDS3233.1	3q26.33	2012-11-14			ENSG00000136522	ENSG00000136522		"Mitochondrial ribosomal proteins / large subunits"	16652	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma metastasis-related 1"	611852				11551941	Standard	NM_177988		Approved	CGI-204, NCM1	uc003fjz.3	Q9HD33	OTTHUMG00000157784	ENST00000476781.1:c.700C>A	3.37:g.179306713G>T	ENSP00000417602:p.Leu234Ile		180789407	Q6XRG1|Q8N5D1	Missense_Mutation	SNP	ENST00000476781.1	37	CCDS3232.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255462	0.22965	.	.	ENSG00000136522	ENST00000476781;ENST00000259038;ENST00000392659	T;T;T	0.61859	0.86;1.01;0.07	5.56	4.69	0.59074	.	0.000000	0.64402	D	0.000002	T	0.61590	0.2359	M	0.73217	2.22	0.21105	N	0.99979	P;P	0.50369	0.934;0.646	P;P	0.52217	0.693;0.497	T	0.56697	-0.7936	10	0.37606	T	0.19	-12.5997	5.4634	0.16630	0.2033:0.1597:0.637:0.0	.	214;234	Q9HD33-2;Q9HD33	.;RM47_HUMAN	I	234;214;124	ENSP00000417602:L234I;ENSP00000259038:L214I;ENSP00000376427:L124I	ENSP00000259038:L214I	L	-	1	0	MRPL47	180789407	1.000000	0.71417	0.331000	0.25455	0.094000	0.18550	2.131000	0.42074	1.490000	0.48466	0.591000	0.81541	CTT		0.338	MRPL47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349623.1	NM_020409		T	179306713	G	T	179306713	3	4	61	1	0	0	0	0	1	0	0	0	9841	942	33	2	56	2	MRPL47	3	179306713	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	956	179306713	18715717	2943	10928										
USP13	8975	broad.mit.edu	37	chr3	179399742	179399742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgttgaaagacattttcGaaaaactggacagagtgtat	9	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179399742G>A	ENST00000263966.3	+	2	716	c.245G>A	c.(244-246)cGa>cAa	p.R82Q	USP13_ENST00000496897.1_Missense_Mutation_p.R17Q|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	82					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R82P(1)|p.R82Q(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			AGACATTTTCGAAAAACTGGA	0.413																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3											160	159	159					3																	179399742		2203	4300	6503	180882436	SO:0001583	missense	8975			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.245G>A	3.37:g.179399742G>A	ENSP00000263966:p.Arg82Gln		180882436	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.120133	0.56613	.	.	ENSG00000058056	ENST00000263966;ENST00000496897	T;T	0.13657	2.57;2.59	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.08758	0.0217	N	0.20530	0.585	0.58432	D	0.999999	P;B	0.34462	0.454;0.044	B;B	0.20384	0.029;0.008	T	0.28618	-1.0038	10	0.11182	T	0.66	-9.5103	19.353	0.94398	0.0:0.0:1.0:0.0	.	82;82	Q92995;A8K2S3	UBP13_HUMAN;.	Q	82;17	ENSP00000263966:R82Q;ENSP00000417146:R17Q	ENSP00000263966:R82Q	R	+	2	0	USP13	180882436	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.479000	0.81095	2.677000	0.91161	0.557000	0.71058	CGA		0.413	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179399742	G	A	179399742	3	1	61	1	0	0	0	0	1	0	0	0	17084	1058	37	1	251	1	USP13	3	179399742	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93029	179399742	18622688	2944	10929										
USP13	8975	broad.mit.edu	37	chr3	179426583	179426583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggaagtgtgccagatgcGacctgcgagaaaacctctgg	14	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179426583G>A	ENST00000263966.3	+	6	1114	c.643G>A	c.(643-645)Gac>Aac	p.D215N	USP13_ENST00000496897.1_Missense_Mutation_p.D150N|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	215					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.D215N(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TGCCAGATGCGACCTGCGAGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	3											168	155	159					3																	179426583		2203	4300	6503	180909277	SO:0001583	missense	8975			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.643G>A	3.37:g.179426583G>A	ENSP00000263966:p.Asp215Asn		180909277	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	G	35	5.532044	0.96446	.	.	ENSG00000058056	ENST00000263966;ENST00000496897	T;T	0.33216	1.42;1.42	5.72	5.72	0.89469	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (3);	0.046026	0.85682	D	0.000000	T	0.57975	0.2090	M	0.74389	2.26	0.80722	D	1	D;D	0.69078	0.997;0.963	D;P	0.68353	0.957;0.748	T	0.58064	-0.7702	10	0.56958	D	0.05	-27.8724	19.8844	0.96908	0.0:0.0:1.0:0.0	.	215;215	Q92995;A8K2S3	UBP13_HUMAN;.	N	215;150	ENSP00000263966:D215N;ENSP00000417146:D150N	ENSP00000263966:D215N	D	+	1	0	USP13	180909277	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	9.382000	0.97209	2.684000	0.91462	0.650000	0.86243	GAC		0.502	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179426583	G	A	179426583	3	1	61	1	0	0	0	0	1	0	0	0	17084	1058	37	1	665	1	USP13	3	179426583	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26841	179426583	18595847	2945	10930										
USP13	8975	broad.mit.edu	37	chr3	179483558	179483558	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacagtgattttgtgattGagatggagaataatgccaat	11	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179483558G>T	ENST00000263966.3	+	19	2806	c.2335G>T	c.(2335-2337)Gag>Tag	p.E779*	USP13_ENST00000496897.1_Nonsense_Mutation_p.E714*	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	779	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.E779*(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TTTTGTGATTGAGATGGAGAA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											134	130	131					3																	179483558		2203	4300	6503	180966252	SO:0001587	stop_gained	8975			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.2335G>T	3.37:g.179483558G>T	ENSP00000263966:p.Glu779*		180966252	A8K2S3|B4DYF3|D3DNS2|Q96B25	Nonsense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	G	44	11.238184	0.99535	.	.	ENSG00000058056	ENST00000263966;ENST00000496897	.	.	.	5.61	5.61	0.85477	.	0.464342	0.24750	N	0.035911	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-12.6269	19.6288	0.95691	0.0:0.0:1.0:0.0	.	.	.	.	X	779;714	.	ENSP00000263966:E779X	E	+	1	0	USP13	180966252	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	6.181000	0.71988	2.632000	0.89209	0.655000	0.94253	GAG		0.408	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			T	179483558	G	T	179483558	4	4	61	1	0	0	0	0	0	1	0	0	17084	1291	45	2	2409	2	USP13	3	179483558	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56975	179483558	18538872	2946	10931										
PEX5L	51555	broad.mit.edu	37	chr3	179525577	179525577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttcctcgctgcggtctcCgttcgccaaggtcgccccga	12	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:179525577C>T	ENST00000467460.1	-	14	1891	c.1561G>A	c.(1561-1563)Gga>Aga	p.G521R	PEX5L_ENST00000485199.1_Missense_Mutation_p.G486R|PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000464614.1_Missense_Mutation_p.G413R|PEX5L_ENST00000465751.1_Missense_Mutation_p.G497R|PEX5L_ENST00000468741.1_Missense_Mutation_p.G329R|PEX5L_ENST00000392649.3_Missense_Mutation_p.G413R|PEX5L_ENST00000476138.1_Missense_Mutation_p.G478R|PEX5L_ENST00000263962.8_Missense_Mutation_p.G519R|PEX5L_ENST00000472994.1_Missense_Mutation_p.G462R	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	521					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)	p.G521R(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			CTGCGGTCTCCGTTCGCCAAG	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	3											119	125	123					3																	179525577		2203	4300	6503	181008271	SO:0001583	missense	51555			AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.1561G>A	3.37:g.179525577C>T	ENSP00000419975:p.Gly521Arg		181008271	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Missense_Mutation	SNP	ENST00000467460.1	37	CCDS3236.1	.	.	.	.	.	.	.	.	.	.	C	35	5.413575	0.96072	.	.	ENSG00000114757	ENST00000467460;ENST00000263962;ENST00000485199;ENST00000382596;ENST00000392649;ENST00000468741;ENST00000476138;ENST00000467440;ENST00000472994;ENST00000464614;ENST00000465751	T;T;T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	6.07	6.07	0.98685	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77205	0.4096	N	0.20807	0.61	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.997;0.995;0.998	T	0.79369	-0.1832	10	0.87932	D	0	-26.2478	20.6525	0.99598	0.0:1.0:0.0:0.0	.	462;497;413;519;486;521	E7EUZ0;E9PH97;E9PEC1;Q8IYB4-2;Q8IYB4-3;Q8IYB4	.;.;.;.;.;PEX5R_HUMAN	R	521;519;486;519;413;329;478;409;462;413;497	ENSP00000419975:G521R;ENSP00000263962:G519R;ENSP00000418440:G486R;ENSP00000376420:G413R;ENSP00000418665:G329R;ENSP00000420555:G478R;ENSP00000418054:G462R;ENSP00000417270:G413R;ENSP00000419348:G497R	ENSP00000263962:G519R	G	-	1	0	PEX5L	181008271	1.000000	0.71417	0.987000	0.45799	0.875000	0.50365	7.747000	0.85070	2.890000	0.99128	0.585000	0.79938	GGA		0.517	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		T	179525577	C	T	179525577	3	4	61	1	0	0	0	0	1	0	0	0	11780	661	23	1	327	1	PEX5L	3	179525577	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42019	179525577	18496853	2947	10932										
TTC14	151613	broad.mit.edu	37	chr3	180321035	180321035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaagaattagttctattcGggaattcggttttttcatgg	11	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:180321035G>A	ENST00000296015.4	+	3	542	c.410G>A	c.(409-411)cGg>cAg	p.R137Q	RP11-496B10.3_ENST00000472596.1_lincRNA|TTC14_ENST00000382584.4_Missense_Mutation_p.R137Q|TTC14_ENST00000412756.2_Missense_Mutation_p.R137Q	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	137	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.						RNA binding (GO:0003723)	p.R137Q(1)		endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			AGTTCTATTCGGGAATTCGGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	3											248	231	237					3																	180321035		2203	4300	6503	181803729	SO:0001583	missense	151613			AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.410G>A	3.37:g.180321035G>A	ENSP00000296015:p.Arg137Gln		181803729	G5E9X0|Q6UWJ7|Q8TF22	Missense_Mutation	SNP	ENST00000296015.4	37	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	G	35	5.429375	0.96131	.	.	ENSG00000163728	ENST00000296015;ENST00000491380;ENST00000412756;ENST00000382584;ENST00000492617;ENST00000495660	T;T	0.49432	0.78;0.81	5.71	5.71	0.89125	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.64918	0.2642	L	0.46157	1.445	0.80722	D	1	P;D;D	0.89917	0.923;0.963;1.0	P;P;D	0.80764	0.479;0.518;0.994	T	0.63989	-0.6512	10	0.56958	D	0.05	-9.132	19.8449	0.96704	0.0:0.0:1.0:0.0	.	137;137;137	Q96N46-2;G5E9X0;Q96N46	.;.;TTC14_HUMAN	Q	137;137;137;137;37;37	ENSP00000296015:R137Q;ENSP00000372027:R137Q	ENSP00000296015:R137Q	R	+	2	0	TTC14	181803729	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.213000	0.95133	2.680000	0.91292	0.655000	0.94253	CGG		0.373	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		A	180321035	G	A	180321035	3	1	61	1	0	0	0	0	1	0	0	0	16721	1116	39	1	420	1	TTC14	3	180321035	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	795458	180321035	17701395	2948	10933										
TTC14	151613	broad.mit.edu	37	chr3	180321103	180321103	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagagatatagcccacttaGaaatcacagtaagttatttt	7	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:180321103G>T	ENST00000296015.4	+	3	610	c.478G>T	c.(478-480)Gaa>Taa	p.E160*	RP11-496B10.3_ENST00000472596.1_lincRNA|TTC14_ENST00000382584.4_Nonsense_Mutation_p.E160*|TTC14_ENST00000412756.2_Nonsense_Mutation_p.E160*	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	160	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.						RNA binding (GO:0003723)	p.E160*(1)		endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			AGCCCACTTAGAAATCACAGT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											143	134	137					3																	180321103		2203	4300	6503	181803797	SO:0001587	stop_gained	151613			AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.478G>T	3.37:g.180321103G>T	ENSP00000296015:p.Glu160*		181803797	G5E9X0|Q6UWJ7|Q8TF22	Nonsense_Mutation	SNP	ENST00000296015.4	37	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	G	34	5.322880	0.95708	.	.	ENSG00000163728	ENST00000296015;ENST00000491380;ENST00000412756;ENST00000382584;ENST00000492617;ENST00000495660	.	.	.	5.71	5.71	0.89125	.	0.099265	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-25.0994	10.2697	0.43477	0.0715:0.1363:0.7922:0.0	.	.	.	.	X	160;160;160;160;60;60	.	ENSP00000296015:E160X	E	+	1	0	TTC14	181803797	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.200000	0.65158	2.680000	0.91292	0.655000	0.94253	GAA		0.348	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		T	180321103	G	T	180321103	4	4	61	1	0	0	0	0	0	1	0	0	16721	943	33	2	488	2	TTC14	3	180321103	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68	180321103	17701327	2949	10934										
CCDC39	339829	broad.mit.edu	37	chr3	180337121	180337121	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaacagctcttttttgttCttctagttgaatttttagct	5	7	4	1	rs587778820		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:180337121C>A	ENST00000442201.2	-	16	2310	c.2191G>T	c.(2191-2193)Gaa>Taa	p.E731*	CCDC39_ENST00000273654.4_3'UTR	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	731					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.E731*(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CTTTTTTGTTCTTCTAGTTGA	0.274																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											142	116	124					3																	180337121		1738	3990	5728	181819815	SO:0001587	stop_gained	339829			BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.2191G>T	3.37:g.180337121C>A	ENSP00000405708:p.Glu731*		181819815	B4E2H1	Nonsense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	C	39	7.355570	0.98231	.	.	ENSG00000145075	ENST00000442201	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	14.6714	0.68948	0.0:0.9285:0.0:0.0715	.	.	.	.	X	731	.	ENSP00000405708:E731X	E	-	1	0	CCDC39	181819815	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.879000	0.48522	2.577000	0.86979	0.655000	0.94253	GAA		0.274	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		A	180337121	C	A	180337121	4	1	61	1	0	0	0	0	0	1	0	0	2817	922	32	2	654	2	CCDC39	3	180337121	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16018	180337121	17685309	2950	10935										
ATP11B	23200	broad.mit.edu	37	chr3	182553890	182553890	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcctgtttatgttgttcGaagtggtggccttgtaaaaa	11	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182553890G>A	ENST00000323116.5	+	5	643	c.383G>A	c.(382-384)cGa>cAa	p.R128Q	ATP11B_ENST00000482794.1_3'UTR|ATP11B_ENST00000493826.1_Missense_Mutation_p.R128Q	NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	128					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R128Q(1)		breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TATGTTGTTCGAAGTGGTGGC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	3											112	111	112					3																	182553890		2203	4300	6503	184036584	SO:0001583	missense	23200			AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.383G>A	3.37:g.182553890G>A	ENSP00000321195:p.Arg128Gln		184036584	Q96FN1|Q9UKK7	Missense_Mutation	SNP	ENST00000323116.5	37	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.727780	0.69074	.	.	ENSG00000058063	ENST00000323116;ENST00000493826	D;D	0.93659	-3.26;-3.26	4.99	4.99	0.66335	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.90259	0.6954	L	0.27053	0.805	0.80722	D	1	P;B	0.42973	0.796;0.422	B;P	0.44732	0.252;0.459	D	0.88579	0.3135	10	0.22109	T	0.4	.	18.6389	0.91387	0.0:0.0:1.0:0.0	.	128;128	Q9Y2G3;B4DKX1	AT11B_HUMAN;.	Q	128	ENSP00000321195:R128Q;ENSP00000419032:R128Q	ENSP00000321195:R128Q	R	+	2	0	ATP11B	184036584	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.594000	0.82698	2.452000	0.82932	0.491000	0.48974	CGA		0.328	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		A	182553890	G	A	182553890	3	1	61	1	0	0	0	0	1	0	0	0	1121	1058	37	1	401	1	ATP11B	3	182553890	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2216769	182553890	15468540	2951	10936										
ATP11B	23200	broad.mit.edu	37	chr3	182585195	182585195	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttattggcaattctgaaGaaactatggaggttaaaact	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182585195G>T	ENST00000323116.5	+	15	1911	c.1651G>T	c.(1651-1653)Gaa>Taa	p.E551*		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	551					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.E551*(1)		breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			CAATTCTGAAGAAACTATGGA	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											149	150	150					3																	182585195		2203	4300	6503	184067889	SO:0001587	stop_gained	23200			AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.1651G>T	3.37:g.182585195G>T	ENSP00000321195:p.Glu551*		184067889	Q96FN1|Q9UKK7	Nonsense_Mutation	SNP	ENST00000323116.5	37	CCDS33896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	42|42	9.485713|9.485713	0.99184|0.99184	.|.	.|.	ENSG00000058063|ENSG00000058063	ENST00000323116|ENST00000498086	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.248012|.	0.40144|.	N|.	0.001177|.	.|T	.|0.74191	.|0.3684	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72966	.|-0.4131	.|4	0.10902|.	T|.	0.67|.	.|.	17.7602|17.7602	0.88462|0.88462	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	551|351	.|.	ENSP00000321195:E551X|.	E|K	+|+	1|3	0|2	ATP11B|ATP11B	184067889|184067889	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.343000|7.343000	0.79319|0.79319	2.527000|2.527000	0.85204|0.85204	0.471000|0.471000	0.43371|0.43371	GAA|AAG		0.294	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		T	182585195	G	T	182585195	4	4	61	1	0	0	0	0	0	1	0	0	1121	943	33	2	1709	2	ATP11B	3	182585195	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31305	182585195	15437235	2952	10937										
DCUN1D1	54165	broad.mit.edu	37	chr3	182683508	182683508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgaagatcataaactgacGaactttatccttctgcgatg	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182683508G>A	ENST00000292782.4	-	2	190	c.37C>T	c.(37-39)Cgt>Tgt	p.R13C	DCUN1D1_ENST00000469954.1_5'UTR	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1	13	UBA-like.					ubiquitin ligase complex (GO:0000151)		p.R13C(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ATAAACTGACGAACTTTATCC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	3											105	108	107					3																	182683508		2203	4299	6502	184166202	SO:0001583	missense	54165			AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"squamous cell carcinoma related oncogene"	605905	"DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.37C>T	3.37:g.182683508G>A	ENSP00000292782:p.Arg13Cys		184166202	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Missense_Mutation	SNP	ENST00000292782.4	37	CCDS3240.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135752	0.94517	.	.	ENSG00000043093	ENST00000292782;ENST00000458486	.	.	.	5.84	5.84	0.93424	UBA-like (1);	0.000000	0.85682	D	0.000000	D	0.83243	0.5212	M	0.85197	2.74	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	D	0.85000	0.0899	9	0.72032	D	0.01	-6.3724	20.1294	0.97995	0.0:0.0:1.0:0.0	.	13	Q96GG9	DCNL1_HUMAN	C	13	.	ENSP00000292782:R13C	R	-	1	0	DCUN1D1	184166202	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.758000	0.94735	0.591000	0.81541	CGT		0.308	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640		A	182683508	G	A	182683508	3	1	61	1	0	0	0	0	1	0	0	0	4319	1058	37	1	766	1	DCUN1D1	3	182683508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98313	182683508	15338922	2953	10938										
MCCC1	56922	broad.mit.edu	37	chr3	182759475	182759475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcatatattctagcttCgaaggcatggccctgcagag	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182759475C>T	ENST00000265594.4	-	11	1293	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	MCCC1_ENST00000492597.1_Missense_Mutation_p.E274K|MCCC1_ENST00000539926.1_Missense_Mutation_p.E248K	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	383	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)	p.E383K(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	ATTCTAGCTTCGAAGGCATGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	3											155	152	153					3																	182759475		2203	4300	6503	184242169	SO:0001583	missense	56922			AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1147G>A	3.37:g.182759475C>T	ENSP00000265594:p.Glu383Lys		184242169	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	C	34	5.306882	0.95629	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	5.45	5.45	0.79879	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.97005	0.9022	H	0.99800	4.79	0.80722	D	1	D;D;D	0.76494	0.999;0.99;0.999	D;P;D	0.69142	0.941;0.833;0.962	D	0.99081	1.0837	10	0.87932	D	0	.	19.2699	0.94004	0.0:1.0:0.0:0.0	.	336;274;383	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	K	383;274;233;248;336;336	ENSP00000265594:E383K;ENSP00000419898:E274K;ENSP00000441253:E248K;ENSP00000420433:E336K	ENSP00000265594:E383K	E	-	1	0	MCCC1	184242169	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	7.369000	0.79578	2.554000	0.86153	0.557000	0.71058	GAA		0.468	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		T	182759475	C	T	182759475	3	4	61	1	0	0	0	0	1	0	0	0	9404	893	31	1	1066	1	MCCC1	3	182759475	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75967	182759475	15262955	2954	10939										
LAMP3	27074	broad.mit.edu	37	chr3	182871711	182871711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttttgtgcagtgctatcGataaagttgctggaagggtg	14	5	0	0	rs115806403	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182871711G>A	ENST00000265598.3	-	2	773	c.518C>T	c.(517-519)tCg>tTg	p.S173L	LAMP3_ENST00000466939.1_Missense_Mutation_p.S149L	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	173	Thr-rich.				cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.S173L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CAGTGCTATCGATAAAGTTGC	0.547													g|||	3	0.000599042	0	0	5008	,	,		19053	0.002		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3											347	344	345					3																	182871711		2203	4300	6503	184354405	SO:0001583	missense	27074			AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"CD molecules"	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.518C>T	3.37:g.182871711G>A	ENSP00000265598:p.Ser173Leu		184354405	D3DNS4|O94781|Q8NEC8	Missense_Mutation	SNP	ENST00000265598.3	37	CCDS3242.1	3	0.0013736263736263737	0	0.0	0	0.0	2	0.0034965034965034965	1	0.0013192612137203166	g	11.25	1.581907	0.28180	.	.	ENSG00000078081	ENST00000265598;ENST00000466939;ENST00000476015	T;T;T	0.49139	1.45;1.45;0.79	5.62	2.22	0.28083	.	0.886440	0.09670	N	0.771297	T	0.31949	0.0813	L	0.51422	1.61	0.09310	N	1	P	0.45474	0.859	B	0.32465	0.146	T	0.16276	-1.0408	10	0.26408	T	0.33	-1.3541	4.1356	0.10169	0.2389:0.0:0.592:0.1691	.	173	Q9UQV4	LAMP3_HUMAN	L	173;149;173	ENSP00000265598:S173L;ENSP00000418912:S149L;ENSP00000419059:S173L	ENSP00000265598:S173L	S	-	2	0	LAMP3	184354405	0.110000	0.22057	0.000000	0.03702	0.001000	0.01503	0.882000	0.28186	0.447000	0.26695	0.655000	0.94253	TCG		0.547	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			A	182871711	G	A	182871711	3	1	61	1	0	0	0	0	1	0	0	0	8641	1059	37	1	752	1	LAMP3	3	182871711	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112236	182871711	15150719	2955	10940										
MCF2L2	23101	broad.mit.edu	37	chr3	182923938	182923938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatttctcaagtccatttCgactggcaatctcaaacttt	5	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182923938C>T	ENST00000328913.3	-	24	3074	c.2777G>A	c.(2776-2778)cGa>cAa	p.R926Q	MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.R926Q	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	926	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R926Q(2)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AAGTCCATTTCGACTGGCAAT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	3											202	172	182					3																	182923938		2203	4300	6503	184406632	SO:0001583	missense	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2777G>A	3.37:g.182923938C>T	ENSP00000328118:p.Arg926Gln		184406632	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	C	3.836	-0.034732	0.07543	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.43294	0.95;0.95	4.27	-7.16	0.01516	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	1.071290	0.07398	N	0.890319	T	0.18635	0.0447	N	0.05280	-0.08	0.09310	N	0.999999	B	0.14438	0.01	B	0.04013	0.001	T	0.34304	-0.9834	10	0.18276	T	0.48	.	12.7209	0.57142	0.0:0.1476:0.0:0.8524	.	926	Q86YR7	MF2L2_HUMAN	Q	926	ENSP00000328118:R926Q;ENSP00000420070:R926Q	ENSP00000328118:R926Q	R	-	2	0	MCF2L2	184406632	0.034000	0.19679	0.023000	0.16930	0.128000	0.20619	-1.509000	0.02264	-1.428000	0.01989	-1.375000	0.01183	CGA		0.438	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		T	182923938	C	T	182923938	3	4	61	1	0	0	0	0	1	0	0	0	9410	884	31	1	595	1	MCF2L2	3	182923938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52227	182923938	15098492	2956	10941										
MCF2L2	23101	broad.mit.edu	37	chr3	182933871	182933871	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctgaatctttggttctCtttggcccatcctgtggaaa	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:182933871C>A	ENST00000328913.3	-	22	2679	c.2382G>T	c.(2380-2382)aaG>aaT	p.K794N	MCF2L2_ENST00000473233.1_Missense_Mutation_p.K794N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	794	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K794N(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CTTTGGTTCTCTTTGGCCCAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											233	207	216					3																	182933871		2203	4300	6503	184416565	SO:0001583	missense	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2382G>T	3.37:g.182933871C>A	ENSP00000328118:p.Lys794Asn		184416565	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.362887	0.41902	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.01918	4.56;4.56	4.29	3.41	0.39046	Dbl homology (DH) domain (4);	0.059711	0.64402	D	0.000004	T	0.02119	0.0066	N	0.22421	0.69	0.80722	D	1	P	0.44877	0.845	B	0.41860	0.368	T	0.62393	-0.6864	10	0.72032	D	0.01	.	7.9968	0.30273	0.0:0.8878:0.0:0.1122	.	794	Q86YR7	MF2L2_HUMAN	N	794	ENSP00000328118:K794N;ENSP00000420070:K794N	ENSP00000328118:K794N	K	-	3	2	MCF2L2	184416565	1.000000	0.71417	0.912000	0.35992	0.666000	0.39218	1.175000	0.31944	1.171000	0.42768	0.655000	0.94253	AAG		0.448	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		A	182933871	C	A	182933871	3	1	61	1	0	0	0	0	1	0	0	0	9410	912	32	2	998	2	MCF2L2	3	182933871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9933	182933871	15088559	2957	10942										
MCF2L2	23101	broad.mit.edu	37	chr3	183056614	183056614	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcgttttaaactcatttcGatagtatttaatgccaatgt	5	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183056614G>T	ENST00000328913.3	-	5	757	c.460C>A	c.(460-462)Cga>Aga	p.R154R	MCF2L2_ENST00000447025.2_Silent_p.R154R|MCF2L2_ENST00000414362.2_Silent_p.R154R|MCF2L2_ENST00000473233.1_Silent_p.R154R	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	154	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R154*(2)|p.R154R(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AACTCATTTCGATAGTATTTA	0.438																																																3	Substitution - Nonsense(2)|Substitution - coding silent(1)	large_intestine(3)	3											120	109	112					3																	183056614		2203	4300	6503	184539308	SO:0001819	synonymous_variant	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.460C>A	3.37:g.183056614G>T			184539308	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	37	CCDS3243.1																																																																																				0.438	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		T	183056614	G	T	183056614	2	4	61	1	0	0	0	0	0	0	0	1	9410	1066	37	2		2	MCF2L2	3	183056614	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122743	183056614	14965816	2958	10943										
YEATS2	55689	broad.mit.edu	37	chr3	183439726	183439726	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaatcatcctgctatcaaGaaatttttggaatcaccatc	4	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183439726G>T	ENST00000305135.5	+	5	534	c.339G>T	c.(337-339)aaG>aaT	p.K113N		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	113					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)	p.K113N(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CTGCTATCAAGAAATTTTTGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	3											137	130	132					3																	183439726		1899	4126	6025	184922420	SO:0001583	missense	55689			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.339G>T	3.37:g.183439726G>T	ENSP00000306983:p.Lys113Asn		184922420	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.254957	0.80135	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.54675	0.56	5.58	5.58	0.84498	.	0.063178	0.64402	D	0.000008	T	0.67505	0.2900	M	0.72118	2.19	0.51767	D	0.999932	D	0.65815	0.995	P	0.55615	0.78	T	0.70952	-0.4732	10	0.72032	D	0.01	-18.7269	17.7345	0.88388	0.0:0.0:1.0:0.0	.	113	Q9ULM3	YETS2_HUMAN	N	113	ENSP00000306983:K113N	ENSP00000306983:K113N	K	+	3	2	YEATS2	184922420	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.029000	0.64121	2.631000	0.89168	0.591000	0.81541	AAG		0.348	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		T	183439726	G	T	183439726	3	4	61	1	0	0	0	0	1	0	0	0	17512	933	33	2	353	2	YEATS2	3	183439726	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	383112	183439726	14582704	2959	10944										
PARL	55486	broad.mit.edu	37	chr3	183584427	183584427	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacctcctttctgaagtCtccttctttttgtggtctta	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183584427C>A	ENST00000317096.4	-	3	508	c.448G>T	c.(448-450)Gac>Tac	p.D150Y	PARL_ENST00000311101.5_Missense_Mutation_p.D150Y|PARL_ENST00000435888.1_Missense_Mutation_p.D150Y	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	150					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.D150Y(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TTTCTGAAGTCTCCTTCTTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											136	131	132					3																	183584427		2203	4300	6503	185067121	SO:0001583	missense	55486			AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.448G>T	3.37:g.183584427C>A	ENSP00000325421:p.Asp150Tyr		185067121	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	37	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.383533	0.61845	.	.	ENSG00000175193	ENST00000317096;ENST00000311101;ENST00000435888	T;T;T	0.76968	-1.06;-1.06;-1.06	5.34	3.5	0.40072	.	0.153774	0.56097	D	0.000024	T	0.76955	0.4060	L	0.42245	1.32	0.42178	D	0.99167	P;P	0.48503	0.911;0.667	P;B	0.53102	0.718;0.285	T	0.77148	-0.2694	10	0.56958	D	0.05	-7.0016	9.1048	0.36692	0.0:0.7522:0.0:0.2478	.	150;150	Q9H300-2;Q9H300	.;PARL_HUMAN	Y	150	ENSP00000325421:D150Y;ENSP00000310676:D150Y;ENSP00000402137:D150Y	ENSP00000310676:D150Y	D	-	1	0	PARL	185067121	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.125000	0.42016	1.202000	0.43218	0.563000	0.77884	GAC		0.353	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		A	183584427	C	A	183584427	3	1	61	1	0	0	0	0	1	0	0	0	11482	913	32	2	723	2	PARL	3	183584427	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	144701	183584427	14438003	2960	10945										
ABCC5	10057	broad.mit.edu	37	chr3	183705647	183705647	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatccacacaacccttcGcagggaagcagcgtctggcc	11	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183705647G>A	ENST00000334444.6	-	5	742	c.502C>T	c.(502-504)Cga>Tga	p.R168*	ABCC5_ENST00000382494.2_Nonsense_Mutation_p.R168*|ABCC5_ENST00000427120.2_Nonsense_Mutation_p.R168*|ABCC5_ENST00000392579.2_Nonsense_Mutation_p.R168*|ABCC5_ENST00000265586.6_Nonsense_Mutation_p.R168*	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	168					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.R168G(2)|p.R168*(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	ACAACCCTTCGCAGGGAAGCA	0.552																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	lung(2)|large_intestine(1)	3											227	172	191					3																	183705647		2203	4300	6503	185188341	SO:0001587	stop_gained	10057			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.502C>T	3.37:g.183705647G>A	ENSP00000333926:p.Arg168*		185188341	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Nonsense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261369	0.80246	.	.	ENSG00000114770	ENST00000334444;ENST00000382495;ENST00000265586;ENST00000427120;ENST00000392579;ENST00000382494	.	.	.	5.99	5.1	0.69264	.	0.087739	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-8.4041	12.7224	0.57149	0.0:0.1259:0.7432:0.1309	.	.	.	.	X	168;104;168;168;168;168	.	ENSP00000265586:R168X	R	-	1	2	ABCC5	185188341	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.687000	0.54692	1.497000	0.48584	0.643000	0.83706	CGA		0.552	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183705647	G	A	183705647	4	1	61	1	0	0	0	0	0	1	0	0	56	1095	38	1	3955	1	ABCC5	3	183705647	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121220	183705647	14316783	2961	10946										
DVL3	1857	broad.mit.edu	37	chr3	183882687	183882687	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctggagaccaccagcttCtttgactcagatgaggatga	12	9	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183882687C>A	ENST00000313143.3	+	5	815	c.567C>A	c.(565-567)ttC>ttA	p.F189L	DVL3_ENST00000431765.1_Missense_Mutation_p.F189L|DVL3_ENST00000462665.1_3'UTR|EIF2B5_ENST00000444495.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	189					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)	p.F189L(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			CCACCAGCTTCTTTGACTCAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											71	72	72					3																	183882687		2203	4300	6503	185365381	SO:0001583	missense	1857			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.567C>A	3.37:g.183882687C>A	ENSP00000316054:p.Phe189Leu		185365381	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Missense_Mutation	SNP	ENST00000313143.3	37	CCDS3253.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784429	0.49997	.	.	ENSG00000161202	ENST00000313143;ENST00000415612;ENST00000431765;ENST00000423300	T;T;T	0.06294	3.76;3.78;3.32	5.18	5.18	0.71444	Dishevelled protein domain (1);	0.048194	0.85682	D	0.000000	T	0.10637	0.0260	L	0.50333	1.59	0.58432	D	0.999999	B;B	0.29481	0.245;0.245	B;B	0.35182	0.197;0.197	T	0.20974	-1.0259	10	0.23891	T	0.37	-19.2035	19.0742	0.93154	0.0:1.0:0.0:0.0	.	189;189	B4E3E5;Q92997	.;DVL3_HUMAN	L	189;189;189;87	ENSP00000316054:F189L;ENSP00000405885:F189L;ENSP00000393849:F87L	ENSP00000316054:F189L	F	+	3	2	DVL3	185365381	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.085000	0.50151	2.582000	0.87167	0.655000	0.94253	TTC		0.572	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		A	183882687	C	A	183882687	3	1	61	1	0	0	0	0	1	0	0	0	4848	912	32	2	585	2	DVL3	3	183882687	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177040	183882687	14139743	2962	10947										
ECE2	9718	broad.mit.edu	37	chr3	183975429	183975429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctggacttccccagtgCttcttttgatgtggtgctcg	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:183975429C>T	ENST00000402825.3	+	2	365	c.365C>T	c.(364-366)gCt>gTt	p.A122V	ECE2_ENST00000324557.4_Missense_Mutation_p.A122V|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	122	Methyltransferase-like region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.A122V(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTCCCCAGTGCTTCTTTTGAT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	63	64					3																	183975429		2203	4300	6503	185458123	SO:0001583	missense	9718			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.365C>T	3.37:g.183975429C>T	ENSP00000384223:p.Ala122Val		185458123	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600584	0.46423	.	.	ENSG00000145194	ENST00000324557;ENST00000402825	T;T	0.64260	-0.09;-0.09	5.88	1.95	0.26073	Methyltransferase type 11 (1);	.	.	.	.	T	0.65729	0.2719	M	0.76328	2.33	0.80722	D	1	B;B	0.25272	0.093;0.122	B;B	0.27076	0.057;0.076	T	0.65047	-0.6263	9	0.48119	T	0.1	-5.0349	19.7803	0.96413	0.0:0.6375:0.3625:0.0	.	122;122	O60344;O60344-4	ECE2_HUMAN;.	V	122	ENSP00000314295:A122V;ENSP00000384223:A122V	ENSP00000314295:A122V	A	+	2	0	ECE2	185458123	0.010000	0.17322	0.851000	0.33527	0.610000	0.37248	0.243000	0.18106	0.061000	0.16311	-0.165000	0.13383	GCT		0.612	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		T	183975429	C	T	183975429	3	4	61	1	0	0	0	0	1	0	0	0	4901	797	28	3	371	3	ECE2	3	183975429	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92742	183975429	14047001	2963	10948										
EIF4G1	1981	broad.mit.edu	37	chr3	184035243	184035243	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgatcccttcccagatCtcctacccagcctcccaggg	7	17	1	3	rs367604626		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184035243C>A	ENST00000346169.2	+	5	553	c.282C>A	c.(280-282)atC>atA	p.I94I	EIF4G1_ENST00000319274.6_Silent_p.I94I|EIF4G1_ENST00000424196.1_Silent_p.I101I|EIF4G1_ENST00000350481.5_Intron|EIF4G1_ENST00000342981.4_Silent_p.I94I|EIF4G1_ENST00000441154.1_5'Flank|EIF4G1_ENST00000352767.3_Silent_p.I101I|EIF4G1_ENST00000427845.1_Silent_p.I7I|EIF4G1_ENST00000434061.2_5'Flank|EIF4G1_ENST00000414031.1_Silent_p.I54I|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000382330.3_Silent_p.I101I|EIF4G1_ENST00000392537.2_Silent_p.I7I|EIF4G1_ENST00000411531.1_Silent_p.I54I	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	94					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.I94I(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTTCCCAGATCTCCTACCCAG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	3											59	64	63					3																	184035243		2203	4300	6503	185517937	SO:0001819	synonymous_variant	1981			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.282C>A	3.37:g.184035243C>A			185517937	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																				0.617	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184035243	C	A	184035243	2	1	61	1	0	0	0	0	0	0	0	1	5049	903	32	2		2	EIF4G1	3	184035243	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59814	184035243	13987187	2964	10949										
EIF4G1	1981	broad.mit.edu	37	chr3	184039575	184039575	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccaactgcccaacctgaGgaactgctcaacggagcccc	9	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184039575G>T	ENST00000346169.2	+	10	1474	c.1203G>T	c.(1201-1203)gaG>gaT	p.E401D	EIF4G1_ENST00000319274.6_Missense_Mutation_p.E401D|EIF4G1_ENST00000424196.1_Missense_Mutation_p.E408D|EIF4G1_ENST00000350481.5_Missense_Mutation_p.E237D|EIF4G1_ENST00000342981.4_Missense_Mutation_p.E401D|EIF4G1_ENST00000441154.1_Missense_Mutation_p.E237D|EIF4G1_ENST00000352767.3_Missense_Mutation_p.E408D|EIF4G1_ENST00000427845.1_Missense_Mutation_p.E314D|EIF4G1_ENST00000434061.2_Missense_Mutation_p.E205D|EIF4G1_ENST00000414031.1_Missense_Mutation_p.E361D|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000382330.3_Missense_Mutation_p.E408D|EIF4G1_ENST00000392537.2_Missense_Mutation_p.E314D|EIF4G1_ENST00000435046.2_Missense_Mutation_p.E205D|EIF4G1_ENST00000411531.1_Missense_Mutation_p.E361D	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	401					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.E401D(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCCAACCTGAGGAACTGCTCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											184	198	193					3																	184039575		2203	4300	6503	185522269	SO:0001583	missense	1981			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1203G>T	3.37:g.184039575G>T	ENSP00000316879:p.Glu401Asp		185522269	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087506	0.55968	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.38560	3.84;3.8;3.76;2.72;2.73;3.82;2.88;3.59;3.82;3.76;3.82;3.84;3.82;3.81;2.23;3.58;3.54;1.13;3.54	5.57	3.77	0.43336	.	0.463933	0.22976	N	0.053361	T	0.47377	0.1442	L	0.40543	1.245	0.37769	D	0.926596	P;B;P;B	0.52842	0.956;0.147;0.956;0.243	D;B;D;B	0.65010	0.931;0.055;0.931;0.079	T	0.46652	-0.9176	10	0.35671	T	0.21	-21.5665	6.0155	0.19601	0.161:0.0:0.6883:0.1508	.	408;401;401;408	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	D	401;361;314;401;408;408;342;237;408;314;401;401;408;361;237;237;205;205;205	ENSP00000316879:E401D;ENSP00000391935:E361D;ENSP00000376320:E314D;ENSP00000391412:E401D;ENSP00000413159:E408D;ENSP00000371767:E408D;ENSP00000403269:E342D;ENSP00000317600:E237D;ENSP00000338020:E408D;ENSP00000407682:E314D;ENSP00000343450:E401D;ENSP00000323737:E401D;ENSP00000416255:E408D;ENSP00000395974:E361D;ENSP00000398145:E237D;ENSP00000399858:E237D;ENSP00000411826:E205D;ENSP00000399969:E205D;ENSP00000404754:E205D	ENSP00000323737:E401D	E	+	3	2	EIF4G1	185522269	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.667000	0.46808	0.816000	0.34421	0.563000	0.77884	GAG		0.617	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		T	184039575	G	T	184039575	3	4	61	1	0	0	0	0	1	0	0	0	5049	991	35	2	1233	2	EIF4G1	3	184039575	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4332	184039575	13982855	2965	10950										
THPO	7066	broad.mit.edu	37	chr3	184090322	184090322	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacccttcctgagacagattCtgggagtgggtgtaggatgt	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184090322C>A	ENST00000204615.7	-	6	1255	c.1041G>T	c.(1039-1041)caG>caT	p.Q347H	THPO_ENST00000477594.1_5'Flank|THPO_ENST00000421442.2_3'UTR|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000445696.2_Missense_Mutation_p.Q343H	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	347					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)	p.Q347H(1)		NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGACAGATTCTGGGAGTGGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											109	108	109					3																	184090322		2203	4300	6503	185573016	SO:0001583	missense	7066				CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"Endogenous ligands"	11795	protein-coding gene	gene with protein product	"prepro-thrombopoietin", "megakaryocyte stimulating factor", "myeloproliferative leukemia virus oncogene ligand", "megakaryocyte growth and development factor", "MPL ligand", "megakaryocyte colony-stimulating factor", "c-mpl ligand", "thrombopoietin nirs variant 1"	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.1041G>T	3.37:g.184090322C>A	ENSP00000204615:p.Gln347His		185573016	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	CCDS3265.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400414	0.62177	.	.	ENSG00000090534	ENST00000204615;ENST00000445696;ENST00000353488	T;T	0.32272	1.46;1.46	4.7	2.88	0.33553	Four-helical cytokine, core (1);	0.584812	0.14713	N	0.302806	T	0.19366	0.0465	N	0.24115	0.695	0.80722	D	1	B;B	0.14012	0.009;0.005	B;B	0.10450	0.005;0.002	T	0.05818	-1.0862	10	0.87932	D	0	-23.1283	5.844	0.18652	0.1877:0.7137:0.0:0.0986	.	343;347	P40225-2;P40225	.;TPO_HUMAN	H	347;343;308	ENSP00000204615:Q347H;ENSP00000410763:Q343H	ENSP00000204615:Q347H	Q	-	3	2	THPO	185573016	0.407000	0.25352	0.929000	0.37066	0.773000	0.43773	0.502000	0.22594	0.558000	0.29135	0.467000	0.42956	CAG		0.597	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460		A	184090322	C	A	184090322	3	1	61	1	0	0	0	0	1	0	0	0	15911	912	32	2	24	2	THPO	3	184090322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50747	184090322	13932108	2966	10951										
VPS8	23355	broad.mit.edu	37	chr3	184557523	184557523	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtgggtacatctcatgGattggctttaatatttggta	11	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184557523G>T	ENST00000437079.3	+	7	689	c.518G>T	c.(517-519)gGa>gTa	p.G173V	VPS8_ENST00000436792.2_Missense_Mutation_p.G173V|VPS8_ENST00000446204.2_Missense_Mutation_p.G173V|VPS8_ENST00000424463.2_3'UTR|VPS8_ENST00000287546.4_Missense_Mutation_p.G173V	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	173							zinc ion binding (GO:0008270)	p.G173V(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			ACATCTCATGGATTGGCTTTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	3											143	129	134					3																	184557523		1835	4086	5921	186040217	SO:0001583	missense	23355			AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.518G>T	3.37:g.184557523G>T	ENSP00000397879:p.Gly173Val		186040217	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739509	0.89573	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204;ENST00000422105	T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;2.18	5.82	5.82	0.92795	.	0.049996	0.85682	D	0.000000	D	0.86264	0.5891	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86814	0.2000	10	0.87932	D	0	-26.6314	18.8801	0.92352	0.0:0.0:1.0:0.0	.	173;173	Q8N3P4-2;Q8N3P4-3	.;.	V	173	ENSP00000287546:G173V;ENSP00000397879:G173V;ENSP00000404704:G173V;ENSP00000405483:G173V;ENSP00000415161:G173V	ENSP00000287546:G173V	G	+	2	0	VPS8	186040217	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.815000	0.91973	2.756000	0.94617	0.563000	0.77884	GGA		0.313	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		T	184557523	G	T	184557523	3	4	61	1	0	0	0	0	1	0	0	0	17258	1174	41	2	540	2	VPS8	3	184557523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	467201	184557523	13464907	2967	10952										
C3orf70	285382	broad.mit.edu	37	chr3	184800809	184800809	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactctcacacagtcgtttCtatcgtttcaatcacttcca	5	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184800809C>A	ENST00000335012.2	-	2	929	c.739G>T	c.(739-741)Gaa>Taa	p.E247*		NM_001025266.1	NP_001020437.1	A6NLC5	CC070_HUMAN	chromosome 3 open reading frame 70	247								p.E247*(1)		breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|urinary_tract(1)	13						ACAGTCGTTTCTATCGTTTCA	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											121	125	124					3																	184800809		2203	4300	6503	186283503	SO:0001587	stop_gained	285382				CCDS33900.1	3q27	2008-08-08			ENSG00000187068	ENSG00000187068			33731	protein-coding gene	gene with protein product							Standard	NM_001025266		Approved		uc003fpd.3	A6NLC5	OTTHUMG00000156696	ENST00000335012.2:c.739G>T	3.37:g.184800809C>A	ENSP00000334974:p.Glu247*		186283503	B2RNY2|B9EH83	Nonsense_Mutation	SNP	ENST00000335012.2	37	CCDS33900.1	.	.	.	.	.	.	.	.	.	.	C	38	6.828121	0.97869	.	.	ENSG00000187068	ENST00000335012	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.51012	D	0.999901	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0492	0.97617	0.0:1.0:0.0:0.0	.	.	.	.	X	247	.	ENSP00000334974:E247X	E	-	1	0	C3orf70	186283503	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.836000	0.97738	0.655000	0.94253	GAA		0.522	C3orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345323.1	NM_001025266		A	184800809	C	A	184800809	4	1	61	1	0	0	0	0	0	1	0	0	2248	922	32	2	17	2	C3orf70	3	184800809	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	243286	184800809	13221621	2968	10953										
C3orf70	285382	broad.mit.edu	37	chr3	184800984	184800984	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgcattgatcccagagtcCtcagaacttgagggagaaga	11	9	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:184800984C>A	ENST00000335012.2	-	2	754	c.564G>T	c.(562-564)gaG>gaT	p.E188D		NM_001025266.1	NP_001020437.1	A6NLC5	CC070_HUMAN	chromosome 3 open reading frame 70	188								p.E188D(1)		breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|urinary_tract(1)	13						TCCCAGAGTCCTCAGAACTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	108	110					3																	184800984		2203	4300	6503	186283678	SO:0001583	missense	285382				CCDS33900.1	3q27	2008-08-08			ENSG00000187068	ENSG00000187068			33731	protein-coding gene	gene with protein product							Standard	NM_001025266		Approved		uc003fpd.3	A6NLC5	OTTHUMG00000156696	ENST00000335012.2:c.564G>T	3.37:g.184800984C>A	ENSP00000334974:p.Glu188Asp		186283678	B2RNY2|B9EH83	Missense_Mutation	SNP	ENST00000335012.2	37	CCDS33900.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737304	0.89482	.	.	ENSG00000187068	ENST00000335012	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.66906	0.2837	L	0.27053	0.805	0.58432	D	0.999999	D	0.67145	0.996	D	0.75484	0.986	T	0.71013	-0.4715	9	0.87932	D	0	.	18.7247	0.91710	0.0:1.0:0.0:0.0	.	188	A6NLC5	CC070_HUMAN	D	188	.	ENSP00000334974:E188D	E	-	3	2	C3orf70	186283678	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.416000	0.44644	2.534000	0.85438	0.655000	0.94253	GAG		0.473	C3orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345323.1	NM_001025266		A	184800984	C	A	184800984	3	1	61	1	0	0	0	0	1	0	0	0	2248	680	24	2	192	2	C3orf70	3	184800984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	175	184800984	13221446	2969	10954										
LIPH	200879	broad.mit.edu	37	chr3	185229345	185229345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagggaccttaacttcattCggagaatcctgagcttgtac	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:185229345C>T	ENST00000296252.4	-	9	1376	c.1235G>A	c.(1234-1236)cGa>cAa	p.R412Q	LIPH_ENST00000424591.2_Missense_Mutation_p.R378Q	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	412					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.R412Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			TAACTTCATTCGGAGAATCCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	108	110					3																	185229345		2203	4300	6503	186712039	SO:0001583	missense	200879			AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.1235G>A	3.37:g.185229345C>T	ENSP00000296252:p.Arg412Gln		186712039	A2IBA7|Q8TEC7	Missense_Mutation	SNP	ENST00000296252.4	37	CCDS3272.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.224776	0.39300	.	.	ENSG00000163898	ENST00000296252;ENST00000424591;ENST00000435679	D;D	0.88741	-2.42;-2.22	5.4	3.61	0.41365	.	0.478390	0.22028	N	0.065628	T	0.78110	0.4232	L	0.31120	0.905	0.32883	D	0.51079	B;B	0.31859	0.032;0.343	B;B	0.21546	0.008;0.035	T	0.74290	-0.3713	10	0.15066	T	0.55	-7.4006	9.051	0.36376	0.0:0.7573:0.0:0.2427	.	378;412	A2IBA6;Q8WWY8	.;LIPH_HUMAN	Q	412;378;56	ENSP00000296252:R412Q;ENSP00000396384:R378Q	ENSP00000296252:R412Q	R	-	2	0	LIPH	186712039	0.937000	0.31787	0.866000	0.34008	0.676000	0.39594	1.367000	0.34204	0.763000	0.33175	0.563000	0.77884	CGA		0.458	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			T	185229345	C	T	185229345	3	4	61	1	0	0	0	0	1	0	0	0	8848	884	31	1	128	1	LIPH	3	185229345	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	428361	185229345	12793085	2970	10955										
SENP2	59343	broad.mit.edu	37	chr3	185332452	185332452	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaggaggaaagtgtcaaTaattgagacaaaggaaaaga	11	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:185332452T>A	ENST00000296257.5	+	11	1274	c.1034T>A	c.(1033-1035)aTa>aAa	p.I345K	SENP2_ENST00000545472.1_Missense_Mutation_p.I335K|SENP2_ENST00000427465.2_Missense_Mutation_p.I169K	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	345					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)	p.I345K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			AAAGTGTCAATAATTGAGACA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											103	100	101					3																	185332452		2203	4300	6503	186815146	SO:0001583	missense	59343			AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"SUMO1/sentrin/SMT3 specific protease 2"			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.1034T>A	3.37:g.185332452T>A	ENSP00000296257:p.Ile345Lys		186815146	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	ENST00000296257.5	37	CCDS33902.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.376818	0.42105	.	.	ENSG00000163904	ENST00000545472;ENST00000296257;ENST00000437107;ENST00000427465;ENST00000444509	T;T;T;T	0.33438	1.86;1.87;1.9;1.41	5.37	1.42	0.22433	.	0.630104	0.15513	N	0.258430	T	0.12603	0.0306	N	0.14661	0.345	0.09310	N	1	B;B	0.23735	0.09;0.09	B;B	0.19148	0.024;0.024	T	0.32241	-0.9914	10	0.06365	T	0.9	-9.1113	5.868	0.18786	0.0:0.157:0.1397:0.7032	.	335;345	B4DQ42;Q9HC62	.;SENP2_HUMAN	K	335;345;216;169;52	ENSP00000439653:I335K;ENSP00000296257:I345K;ENSP00000394562:I169K;ENSP00000399201:I52K	ENSP00000296257:I345K	I	+	2	0	SENP2	186815146	0.001000	0.12720	0.888000	0.34837	0.928000	0.56348	0.345000	0.19979	0.460000	0.27045	-0.269000	0.10298	ATA		0.478	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627		A	185332452	T	A	185332452	3	1	61	1	0	0	0	0	1	0	0	0	14084	1406	49	5	1076	5	SENP2	3	185332452	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	103107	185332452	12689978	2971	10956										
TRA2B	6434	broad.mit.edu	37	chr3	185643391	185643391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaccgggtataatgccttCgggagcttcttctggatcta	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:185643391C>T	ENST00000453386.2	-	3	469	c.194G>A	c.(193-195)cGa>cAa	p.R65Q	TRA2B_ENST00000471134.1_5'Flank|TRA2B_ENST00000382191.4_5'UTR	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	65	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R65Q(1)		breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						ATAATGCCTTCGGGAGCTTCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	96	97					3																	185643391		2203	4300	6503	187126085	SO:0001583	missense	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"RNA binding motif (RRM) containing"	10781	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 156"	602719	"splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.194G>A	3.37:g.185643391C>T	ENSP00000416959:p.Arg65Gln		187126085	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Missense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.014712	0.93404	.	.	ENSG00000136527	ENST00000453386	T	0.24350	1.86	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.44787	0.1310	L	0.59436	1.845	0.80722	D	1	D;D	0.58620	0.983;0.983	P;P	0.61201	0.885;0.885	T	0.03576	-1.1023	10	0.14656	T	0.56	-3.3171	19.6509	0.95805	0.0:1.0:0.0:0.0	.	65;65	B2RDQ3;P62995	.;TRA2B_HUMAN	Q	65	ENSP00000416959:R65Q	ENSP00000416959:R65Q	R	-	2	0	TRA2B	187126085	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.048000	0.71046	2.941000	0.99782	0.655000	0.94253	CGA		0.463	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		T	185643391	C	T	185643391	3	4	61	1	0	0	0	0	1	0	0	0	16474	884	31	1	700	1	TRA2B	3	185643391	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	310939	185643391	12379039	2972	10957										
DGKG	1608	broad.mit.edu	37	chr3	186015890	186015890	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttgctggctccctccgtCgggtggtcagaggtctcgtg	15	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186015890C>T	ENST00000265022.3	-	4	812	c.273G>A	c.(271-273)ccG>ccA	p.P91P	DGKG_ENST00000344484.4_Silent_p.P91P|DGKG_ENST00000382164.4_Silent_p.P91P|DGKG_ENST00000544847.1_Silent_p.P91P	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	91					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.P91P(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CTCCCTCCGTCGGGTGGTCAG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	3											109	105	106					3																	186015890		2203	4300	6503	187498584	SO:0001819	synonymous_variant	1608			AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.273G>A	3.37:g.186015890C>T			187498584	B2RAH4|Q2M1H4|Q5FWG1	Silent	SNP	ENST00000265022.3	37	CCDS3274.1																																																																																				0.617	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			T	186015890	C	T	186015890	2	4	61	1	0	0	0	0	0	0	0	1	4480	871	31	1		1	DGKG	3	186015890	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	372499	186015890	12006540	2973	10958										
CRYGS	1427	broad.mit.edu	37	chr3	186257212	186257212	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgctggtattcagggtactCtccctgtggtaagatgtaca	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186257212C>A	ENST00000392499.2	-	3	535	c.196G>T	c.(196-198)Gag>Tag	p.E66*	CRYGS_ENST00000307944.5_Nonsense_Mutation_p.E66*	NM_017541.2	NP_060011.1	P22914	CRBS_HUMAN	crystallin, gamma S	66	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|morphogenesis of an epithelium (GO:0002009)		structural constituent of eye lens (GO:0005212)	p.E66*(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	11	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		TCAGGGTACTCTCCCTGTGGT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											117	92	100					3																	186257212		2203	4300	6503	187739906	SO:0001587	stop_gained	1427				CCDS3275.1	3q27.3	2013-02-14			ENSG00000213139	ENSG00000213139			2417	protein-coding gene	gene with protein product	"crystallin, gamma 8"	123730		CRYG8			Standard	NM_017541		Approved		uc003fqe.3	P22914	OTTHUMG00000156615	ENST00000392499.2:c.196G>T	3.37:g.186257212C>A	ENSP00000376287:p.Glu66*		187739906	B2RAF8	Nonsense_Mutation	SNP	ENST00000392499.2	37	CCDS3275.1	.	.	.	.	.	.	.	.	.	.	C	37	6.405208	0.97542	.	.	ENSG00000213139	ENST00000392499;ENST00000307944	.	.	.	6.17	6.17	0.99709	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	18.3732	0.90420	0.0:1.0:0.0:0.0	.	.	.	.	X	66	.	ENSP00000312099:E66X	E	-	1	0	CRYGS	187739906	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	6.059000	0.71133	2.941000	0.99782	0.655000	0.94253	GAG		0.522	CRYGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344784.1	NM_017541		A	186257212	C	A	186257212	4	1	61	1	0	0	0	0	0	1	0	0	3925	922	32	2	348	2	CRYGS	3	186257212	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241322	186257212	11765218	2974	10959										
TBCCD1	55171	broad.mit.edu	37	chr3	186281890	186281890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaagactatcaaatatttCgaagtaaagccacgccaggt	8	8	1	2	rs374199520		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186281890C>T	ENST00000424280.1	-	2	708	c.229G>A	c.(229-231)Gaa>Aaa	p.E77K	TBCCD1_ENST00000338733.5_Missense_Mutation_p.E77K|TBCCD1_ENST00000446782.1_Intron	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	77					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)		p.E77K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TCAAATATTTCGAAGTAAAGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	LYS/GLU,LYS/GLU	0,4406		0,0,2203	68	67	67		229,229	5.7	1	3		67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TBCCD1	NM_001134415.1,NM_018138.3	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	77/558,77/558	186281890	1,13005	2203	4300	6503	187764584	SO:0001583	missense	55171			BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.229G>A	3.37:g.186281890C>T	ENSP00000411253:p.Glu77Lys		187764584	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	37	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936340	0.92458	0.0	1.16E-4	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000413695;ENST00000430560	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.62392	0.2424	M	0.65975	2.015	0.80722	D	1	D	0.76494	0.999	D	0.64595	0.927	T	0.64279	-0.6445	10	0.72032	D	0.01	-14.0937	17.2023	0.86909	0.0:1.0:0.0:0.0	.	77	Q9NVR7	TBCC1_HUMAN	K	77	ENSP00000411253:E77K;ENSP00000341652:E77K;ENSP00000391109:E77K;ENSP00000407506:E77K	ENSP00000341652:E77K	E	-	1	0	TBCCD1	187764584	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.336000	0.79245	2.663000	0.90544	0.561000	0.74099	GAA		0.522	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		T	186281890	C	T	186281890	3	4	61	1	0	0	0	0	1	0	0	0	15671	893	31	1	1468	1	TBCCD1	3	186281890	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24678	186281890	11740540	2975	10960										
FETUB	26998	broad.mit.edu	37	chr3	186362658	186362658	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgcgaaatacaacaatgaGaacacatccaagcagtattc	6	10	0	1	rs148507156	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186362658G>T	ENST00000265029.3	+	4	644	c.543G>T	c.(541-543)gaG>gaT	p.E181D	FETUB_ENST00000539949.1_Missense_Mutation_p.E33D|RP11-134F2.2_ENST00000455926.1_RNA|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000488561.1_3'UTR|FETUB_ENST00000382134.3_Missense_Mutation_p.E116D|FETUB_ENST00000450521.1_Missense_Mutation_p.E181D|FETUB_ENST00000382136.3_Missense_Mutation_p.E144D	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	181	Cystatin fetuin-B-type 2. {ECO:0000255|PROSITE-ProRule:PRU00862}.				binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)	p.E181D(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		ACAACAATGAGAACACATCCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	3											108	104	106					3																	186362658		2203	4300	6503	187845352	SO:0001583	missense	26998			AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.543G>T	3.37:g.186362658G>T	ENSP00000265029:p.Glu181Asp		187845352	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	37	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.245826	0.22796	.	.	ENSG00000090512	ENST00000450521;ENST00000431018;ENST00000539949;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	5.29	1.43	0.22495	Proteinase inhibitor I25, cystatin (2);	0.178918	0.39615	N	0.001315	T	0.25865	0.0630	L	0.58583	1.82	0.09310	N	1	B;B;B	0.33807	0.071;0.426;0.148	B;B;B	0.34093	0.091;0.175;0.076	T	0.18116	-1.0347	10	0.72032	D	0.01	-4.4298	5.5611	0.17144	0.2381:0.1408:0.6211:0.0	.	144;116;181	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	D	181;33;33;181;116;144	ENSP00000404288:E181D;ENSP00000396581:E33D;ENSP00000443704:E33D;ENSP00000265029:E181D;ENSP00000371569:E116D;ENSP00000371571:E144D	ENSP00000265029:E181D	E	+	3	2	FETUB	187845352	0.004000	0.15560	0.002000	0.10522	0.224000	0.24922	0.081000	0.14823	0.044000	0.15775	-0.137000	0.14449	GAG		0.498	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375		T	186362658	G	T	186362658	3	4	61	1	0	0	0	0	1	0	0	0	5840	933	33	2	557	2	FETUB	3	186362658	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80768	186362658	11659772	2976	10961										
HRG	3273	broad.mit.edu	37	chr3	186395005	186395005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacctcctccagatgaaaGagatcactcacatggacccc	6	17	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186395005G>T	ENST00000232003.4	+	7	991	c.911G>T	c.(910-912)aGa>aTa	p.R304I		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	304	Pro-rich.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.R304I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		CCAGATGAAAGAGATCACTCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											212	174	187					3																	186395005		2203	4300	6503	187877699	SO:0001583	missense	3273				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.911G>T	3.37:g.186395005G>T	ENSP00000232003:p.Arg304Ile		187877699	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	G	9.901	1.206941	0.22205	.	.	ENSG00000113905	ENST00000232003	T	0.11821	2.74	3.43	-0.671	0.11381	.	0.255049	0.27986	N	0.017050	T	0.05135	0.0137	N	0.14661	0.345	0.09310	N	1	B	0.29432	0.244	B	0.23574	0.047	T	0.32428	-0.9907	10	0.25106	T	0.35	-3.4131	3.0508	0.06168	0.5125:0.2278:0.2597:0.0	.	304	P04196	HRG_HUMAN	I	304	ENSP00000232003:R304I	ENSP00000232003:R304I	R	+	2	0	HRG	187877699	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.824000	0.27379	0.082000	0.17018	-0.474000	0.04947	AGA		0.532	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		T	186395005	G	T	186395005	3	4	61	1	0	0	0	0	1	0	0	0	7375	942	33	2	937	2	HRG	3	186395005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32347	186395005	11627425	2977	10962										
KNG1	3827	broad.mit.edu	37	chr3	186460082	186460082	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccaaccacacaaatgaaaGaatcttattatttcgatctc	3	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186460082G>T	ENST00000265023.4	+	10	2109	c.1897G>T	c.(1897-1899)Gaa>Taa	p.E633*	RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000596632.1_RNA|KNG1_ENST00000287611.2_Intron|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596329.1_RNA	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	633					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.E633*(2)		endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		ACAAATGAAAGAATCTTATTA	0.368																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											100	96	97					3																	186460082		1824	4082	5906	187942776	SO:0001587	stop_gained	3827				CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1897G>T	3.37:g.186460082G>T	ENSP00000265023:p.Glu633*		187942776	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Nonsense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	G	37	6.155952	0.97334	.	.	ENSG00000113889	ENST00000265023	.	.	.	5.28	3.34	0.38264	.	0.310671	0.23926	N	0.043181	.	.	.	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.1728	6.5644	0.22503	0.0996:0.2298:0.6706:0.0	.	.	.	.	X	633	.	.	E	+	1	0	KNG1	187942776	0.011000	0.17503	0.292000	0.24919	0.017000	0.09413	0.620000	0.24403	1.378000	0.46305	0.563000	0.77884	GAA		0.368	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		T	186460082	G	T	186460082	4	4	61	1	0	0	0	0	0	1	0	0	8448	943	33	2	1935	2	KNG1	3	186460082	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65077	186460082	11562348	2978	10963										
RTP1	132112	broad.mit.edu	37	chr3	186915433	186915433	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtaaaagcgtgaccacaGatgagtggaagaaagtcttc	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186915433G>T	ENST00000312295.4	+	1	160	c.130G>T	c.(130-132)Gat>Tat	p.D44Y	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	44					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)	p.D44Y(1)		breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		CGTGACCACAGATGAGTGGAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	3											141	129	133					3																	186915433		2203	4300	6503	188398127	SO:0001583	missense	132112			BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.130G>T	3.37:g.186915433G>T	ENSP00000311712:p.Asp44Tyr		188398127		Missense_Mutation	SNP	ENST00000312295.4	37	CCDS3287.2	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085565	0.36758	.	.	ENSG00000175077	ENST00000312295	T	0.14766	2.48	5.69	5.69	0.88448	.	0.795910	0.12160	N	0.494091	T	0.08980	0.0222	N	0.08118	0	0.19775	N	0.999957	B	0.32425	0.371	B	0.27170	0.077	T	0.29882	-0.9997	10	0.59425	D	0.04	.	15.3155	0.74074	0.0:0.0:1.0:0.0	.	44	P59025	RTP1_HUMAN	Y	44	ENSP00000311712:D44Y	ENSP00000311712:D44Y	D	+	1	0	RTP1	188398127	0.938000	0.31826	0.927000	0.36925	0.550000	0.35303	3.481000	0.53179	2.699000	0.92147	0.655000	0.94253	GAT		0.527	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		T	186915433	G	T	186915433	3	4	61	1	0	0	0	0	1	0	0	0	13770	942	33	2	132	2	RTP1	3	186915433	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	455351	186915433	11106997	2979	10964										
MASP1	5648	broad.mit.edu	37	chr3	186943256	186943256	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggtgtgtttgacgccgaGatgctgttcattttcatctg	12	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:186943256G>T	ENST00000337774.5	-	13	1986	c.1597C>A	c.(1597-1599)Ctc>Atc	p.L533I		NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	533	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.L533I(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TTGACGCCGAGATGCTGTTCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											245	227	233					3																	186943256		2203	4300	6503	188425950	SO:0001583	missense	5648			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1597C>A	3.37:g.186943256G>T	ENSP00000336792:p.Leu533Ile		188425950	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	37	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.009483	0.35415	.	.	ENSG00000127241	ENST00000337774	D	0.92545	-3.06	5.9	5.9	0.94986	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85729	0.5764	N	0.16016	0.355	0.80722	D	1	B	0.23058	0.079	B	0.34590	0.186	T	0.79818	-0.1643	9	0.22706	T	0.39	.	11.0874	0.48095	0.0833:0.0:0.9167:0.0	.	533	P48740	MASP1_HUMAN	I	533	ENSP00000336792:L533I	ENSP00000336792:L533I	L	-	1	0	MASP1	188425950	0.663000	0.27448	0.756000	0.31282	0.632000	0.37999	1.332000	0.33805	2.793000	0.96121	0.563000	0.77884	CTC		0.532	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		T	186943256	G	T	186943256	3	4	61	1	0	0	0	0	1	0	0	0	9352	942	33	2	518	2	MASP1	3	186943256	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27823	186943256	11079174	2980	10965										
RTP4	64108	broad.mit.edu	37	chr3	187088738	187088738	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatatgagatgcctgagttCtcctcggatagcaccatgag	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:187088738C>A	ENST00000259030.2	+	2	428	c.318C>A	c.(316-318)ttC>ttA	p.F106L		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	106					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.F106L(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		TGCCTGAGTTCTCCTCGGATA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	3											67	64	65					3																	187088738		2203	4300	6503	188571432	SO:0001583	missense	64108			BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"Receptor transporter proteins"	23992	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 4"	609350	"receptor transporter protein 4"			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.318C>A	3.37:g.187088738C>A	ENSP00000259030:p.Phe106Leu		188571432	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811583	0.50527	.	.	ENSG00000136514	ENST00000259030	T	0.19938	2.11	4.09	4.09	0.47781	.	0.168001	0.52532	D	0.000065	T	0.39172	0.1068	M	0.62723	1.935	0.34053	D	0.656409	D	0.69078	0.997	D	0.68765	0.96	T	0.47407	-0.9120	10	0.38643	T	0.18	-30.4528	12.1226	0.53900	0.0:1.0:0.0:0.0	.	106	Q96DX8	RTP4_HUMAN	L	106	ENSP00000259030:F106L	ENSP00000259030:F106L	F	+	3	2	RTP4	188571432	1.000000	0.71417	0.985000	0.45067	0.274000	0.26718	2.945000	0.49043	2.589000	0.87451	0.655000	0.94253	TTC		0.512	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147		A	187088738	C	A	187088738	3	1	61	1	0	0	0	0	1	0	0	0	13773	912	32	2	324	2	RTP4	3	187088738	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145482	187088738	10933692	2981	10966										
BCL6	604	broad.mit.edu	37	chr3	187447188	187447188	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggctggcagtcagatttCtgggggctctgtggactaac	15	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:187447188C>A	ENST00000406870.2	-	5	1371	c.1005G>T	c.(1003-1005)caG>caT	p.Q335H	BCL6_ENST00000232014.4_Missense_Mutation_p.Q335H|RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000450123.2_Missense_Mutation_p.Q335H|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	335					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q335H(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		AGTCAGATTTCTGGGGGCTCT	0.592			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	1	Substitution - Missense(1)	large_intestine(1)	3											96	116	109					3																	187447188		2203	4300	6503	188929882	SO:0001583	missense	604				CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1005G>T	3.37:g.187447188C>A	ENSP00000384371:p.Gln335His		188929882	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991483	0.54041	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.08370	3.1;3.1;3.11	5.61	4.73	0.59995	.	0.054363	0.85682	D	0.000000	T	0.16769	0.0403	L	0.34521	1.04	0.43471	D	0.99568	D;D	0.67145	0.978;0.996	P;D	0.75484	0.753;0.986	T	0.10730	-1.0617	10	0.18276	T	0.48	.	13.6808	0.62484	0.0:0.9261:0.0:0.0739	.	335;335	B8PSA7;P41182	.;BCL6_HUMAN	H	335	ENSP00000384371:Q335H;ENSP00000232014:Q335H;ENSP00000413122:Q335H	ENSP00000232014:Q335H	Q	-	3	2	BCL6	188929882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.996000	0.29719	1.522000	0.49001	0.561000	0.74099	CAG		0.592	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187447188	C	A	187447188	3	1	61	1	0	0	0	0	1	0	0	0	1377	912	32	2	1139	2	BCL6	3	187447188	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	358450	187447188	10575242	2982	10967										
LPP	4026	broad.mit.edu	37	chr3	188584046	188584046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggagcggattctccgagCcaccgggaaggcctatcatc	12	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:188584046C>T	ENST00000312675.4	+	9	1715	c.1469C>T	c.(1468-1470)gCc>gTc	p.A490V	LPP_ENST00000543006.1_Missense_Mutation_p.A490V	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	490	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.A490V(1)	HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ATTCTCCGAGCCACCGGGAAG	0.562			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"																																		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	1	Substitution - Missense(1)	large_intestine(1)	3											171	145	154					3																	188584046		2203	4300	6503	190066740	SO:0001583	missense	4026			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1469C>T	3.37:g.188584046C>T	ENSP00000318089:p.Ala490Val		190066740	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	.	.	.	.	.	.	.	.	.	.	C	36	5.785582	0.96937	.	.	ENSG00000145012	ENST00000312675;ENST00000543006	D;D	0.89343	-2.5;-2.5	5.86	5.86	0.93980	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.94656	0.8277	M	0.77486	2.375	0.80722	D	1	D;D	0.69078	0.997;0.97	D;P	0.80764	0.994;0.85	D	0.94673	0.7858	10	0.87932	D	0	.	19.1605	0.93529	0.0:1.0:0.0:0.0	.	343;490	B7Z8W0;Q93052	.;LPP_HUMAN	V	490	ENSP00000318089:A490V;ENSP00000438891:A490V	ENSP00000318089:A490V	A	+	2	0	LPP	190066740	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.768000	0.95171	0.655000	0.94253	GCC		0.562	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		T	188584046	C	T	188584046	3	4	61	1	0	0	0	0	1	0	0	0	8952	739	26	3	1495	3	LPP	3	188584046	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1136858	188584046	9438384	2983	10968										
TP63	8626	broad.mit.edu	37	chr3	189455608	189455608	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagagcacacagacaaatGaattcctcagtccagaggtt	8	12	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:189455608G>T	ENST00000264731.3	+	2	231	c.142G>T	c.(142-144)Gaa>Taa	p.E48*	TP63_ENST00000440651.2_Nonsense_Mutation_p.E48*|TP63_ENST00000320472.5_Nonsense_Mutation_p.E48*|TP63_ENST00000418709.2_Nonsense_Mutation_p.E48*|TP63_ENST00000392460.3_Nonsense_Mutation_p.E48*|TP63_ENST00000382063.4_Nonsense_Mutation_p.E48*	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	48	Transcription activation.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)	p.E48*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ACAGACAAATGAATTCCTCAG	0.378										HNSCC(45;0.13)																																						1	Substitution - Nonsense(1)	large_intestine(1)	3											89	87	88					3																	189455608		2203	4300	6503	190938302	SO:0001587	stop_gained	8626			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.142G>T	3.37:g.189455608G>T	ENSP00000264731:p.Glu48*		190938302	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Nonsense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744512	0.89663	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063	.	.	.	5.56	5.56	0.83823	.	0.247085	0.37809	N	0.001937	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.0678	18.5098	0.90911	0.0:0.0:1.0:0.0	.	.	.	.	X	48	.	.	E	+	1	0	TP63	190938302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.274000	0.78538	2.605000	0.88082	0.655000	0.94253	GAA		0.378	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189455608	G	T	189455608	4	4	61	1	0	0	0	0	0	1	0	0	16432	1291	45	2	148	2	TP63	3	189455608	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	871562	189455608	8566822	2984	10969										
TP63	8626	broad.mit.edu	37	chr3	189584533	189584533	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccatgcccagtatgtaGaagatcccatcacaggaaga	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:189584533G>T	ENST00000264731.3	+	6	918	c.829G>T	c.(829-831)Gaa>Taa	p.E277*	TP63_ENST00000437221.1_Nonsense_Mutation_p.E183*|TP63_ENST00000449992.1_Nonsense_Mutation_p.E98*|TP63_ENST00000392461.3_Nonsense_Mutation_p.E183*|TP63_ENST00000392463.2_Nonsense_Mutation_p.E183*|TP63_ENST00000440651.2_Nonsense_Mutation_p.E277*|TP63_ENST00000456148.1_Nonsense_Mutation_p.E183*|TP63_ENST00000320472.5_Nonsense_Mutation_p.E277*|TP63_ENST00000418709.2_Nonsense_Mutation_p.E277*|TP63_ENST00000392460.3_Nonsense_Mutation_p.E277*|TP63_ENST00000354600.5_Nonsense_Mutation_p.E183*|TP63_ENST00000382063.4_Nonsense_Mutation_p.E192*	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	277					apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)	p.E277*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		CCAGTATGTAGAAGATCCCAT	0.443										HNSCC(45;0.13)																																						1	Substitution - Nonsense(1)	large_intestine(1)	3											98	86	90					3																	189584533		2203	4300	6503	191067227	SO:0001587	stop_gained	8626			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.829G>T	3.37:g.189584533G>T	ENSP00000264731:p.Glu277*		191067227	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Nonsense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	G	36	5.608062	0.96626	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000449992;ENST00000456148	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.1273	18.6853	0.91560	0.0:0.0:1.0:0.0	.	.	.	.	X	277;277;277;277;277;192;183;183;183;183;98;183	.	.	E	+	1	0	TP63	191067227	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.771000	0.98977	2.663000	0.90544	0.650000	0.86243	GAA		0.443	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189584533	G	T	189584533	4	4	61	1	0	0	0	0	0	1	0	0	16432	943	33	2	897	2	TP63	3	189584533	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128925	189584533	8437897	2985	10970										
LEPREL1	55214	broad.mit.edu	37	chr3	189713219	189713220	+	Missense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgcttccactgctttttCgagctggttaagctaaagag							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:189713219_189713220CG>TA	ENST00000319332.5	-	2	689_690	c.492_493CG>TA	c.(490-495)ctCGaa>ctTAaa	p.E165K	LEPREL1_ENST00000427335.2_5'UTR	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	165					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)	p.L164>?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ACTGCTTTTTCGAGCTGGTTAA	0.401																																																1	Complex(1)	large_intestine(1)	3																																								191195914	SO:0001583	missense	55214				CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.492_493delinsTA	3.37:g.189713219_189713220delinsTA	ENSP00000316881:p.Glu165Lys		191195913	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Missense_Mutation	DNP	ENST00000319332.5	37	CCDS3294.1																																																																																				0.401	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192		TA	189713220	CG	TA	189713219	3	4	61	1	0	0	0	0	1	0	0	0	8752	893	31	1	1689	1	LEPREL1	3	189713219	Missense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	128686	189713219	8309211	2986	10971										
IL1RAP	3556	broad.mit.edu	37	chr3	190363535	190363535	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatgcaaggaatgcggaaGaagaagaatttgtattactg	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:190363535G>T	ENST00000412504.2	+	10	1501	c.1249G>T	c.(1249-1251)Gaa>Taa	p.E417*	IL1RAP_ENST00000439062.1_Nonsense_Mutation_p.E417*|IL1RAP_ENST00000317757.3_Nonsense_Mutation_p.E417*|IL1RAP_ENST00000072516.3_Nonsense_Mutation_p.E417*|IL1RAP_ENST00000443369.2_Nonsense_Mutation_p.E417*|IL1RAP_ENST00000447382.1_Nonsense_Mutation_p.E417*			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	417	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)	p.E417*(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		GAATGCGGAAGAAGAAGAATT	0.393																																																2	Substitution - Nonsense(2)	large_intestine(2)	3											112	111	111					3																	190363535		2203	4300	6503	191846229	SO:0001587	stop_gained	3556			AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1249G>T	3.37:g.190363535G>T	ENSP00000412053:p.Glu417*		191846229	B1NLD0|D3DNW0|O14915|Q86WJ7	Nonsense_Mutation	SNP	ENST00000412504.2	37	CCDS3298.1	.	.	.	.	.	.	.	.	.	.	G	41	8.808261	0.98962	.	.	ENSG00000196083	ENST00000072516;ENST00000443369;ENST00000412504;ENST00000439062;ENST00000447382;ENST00000317757	.	.	.	5.63	5.63	0.86233	.	0.051048	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.678	0.91535	0.0:0.0:1.0:0.0	.	.	.	.	X	417	.	ENSP00000072516:E417X	E	+	1	0	IL1RAP	191846229	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.320000	0.96346	2.669000	0.90835	0.655000	0.94253	GAA		0.393	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1			T	190363535	G	T	190363535	4	4	61	1	0	0	0	0	0	1	0	0	7681	943	33	2	1303	2	IL1RAP	3	190363535	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	650316	190363535	7658895	2987	10972										
OSTN	344901	broad.mit.edu	37	chr3	190967852	190967852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagatcatccaaaaaggcGatttggtatccccatggatc	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:190967852G>A	ENST00000339051.1	+	3	344	c.344G>A	c.(343-345)cGa>cAa	p.R115Q	OSTN_ENST00000445281.1_Intron	NM_198184.1	NP_937827.1	P61366	OSTN_HUMAN	osteocrin	115		Cleavage. {ECO:0000255}.			cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|endochondral bone growth (GO:0003416)|negative regulation of glucose import (GO:0046325)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)	extracellular space (GO:0005615)		p.R115Q(2)		kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|skin(2)	13	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		CCAAAAAGGCGATTTGGTATC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	3											126	130	129					3																	190967852		2203	4300	6503	192450546	SO:0001583	missense	344901			AY398681	CCDS3299.1	3q29	2004-01-22			ENSG00000188729	ENSG00000188729			29961	protein-coding gene	gene with protein product		610280				14523025	Standard	NM_198184		Approved		uc011bsn.2	P61366	OTTHUMG00000156190	ENST00000339051.1:c.344G>A	3.37:g.190967852G>A	ENSP00000342356:p.Arg115Gln		192450546	A1A4U3	Missense_Mutation	SNP	ENST00000339051.1	37	CCDS3299.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773980	0.90108	.	.	ENSG00000188729	ENST00000339051	.	.	.	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000002	T	0.76637	0.4015	M	0.61703	1.905	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.78481	-0.2187	9	0.87932	D	0	-19.4972	14.9373	0.70967	0.0:0.0:1.0:0.0	.	115	P61366	OSTN_HUMAN	Q	115	.	ENSP00000342356:R115Q	R	+	2	0	OSTN	192450546	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	4.724000	0.61972	2.601000	0.87937	0.655000	0.94253	CGA		0.338	OSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343350.1	NM_198184		A	190967852	G	A	190967852	3	1	61	1	0	0	0	0	1	0	0	0	11330	1058	37	1	354	1	OSTN	3	190967852	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	604317	190967852	7054578	2988	10973										
CCDC50	152137	broad.mit.edu	37	chr3	191075806	191075806	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgagcatcatttggcatcGaacgttcagcggaaccgttt	11	9	2	1	rs370652793		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:191075806G>A	ENST00000392455.3	+	3	730	c.132G>A	c.(130-132)tcG>tcA	p.S44S	CCDC50_ENST00000392456.3_Silent_p.S44S	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	44						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)	p.S44S(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		ATTTGGCATCGAACGTTCAGC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	3											191	176	181					3																	191075806		2203	4300	6503	192558500	SO:0001819	synonymous_variant	152137			AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.132G>A	3.37:g.191075806G>A			192558500	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																				0.448	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		A	191075806	G	A	191075806	2	1	61	1	0	0	0	0	0	0	0	1	2826	1045	37	1		1	CCDC50	3	191075806	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107954	191075806	6946624	2989	10974										
CCDC50	152137	broad.mit.edu	37	chr3	191098627	191098627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtttaggaaatcgctcGacttctaatggctgaagaaa	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:191098627G>A	ENST00000392455.3	+	8	1218	c.620G>A	c.(619-621)cGa>cAa	p.R207Q	CCDC50_ENST00000392456.3_Missense_Mutation_p.R383Q	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	207						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)	p.R383Q(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAAATCGCTCGACTTCTAATG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											78	87	84					3																	191098627		2203	4300	6503	192581321	SO:0001583	missense	152137			AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.620G>A	3.37:g.191098627G>A	ENSP00000376249:p.Arg207Gln		192581321	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980152	0.92982	.	.	ENSG00000152492	ENST00000392455;ENST00000392456	T;T	0.44881	1.08;0.91	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.66005	0.2746	M	0.78049	2.395	0.35464	D	0.796733	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.75611	-0.3258	10	0.72032	D	0.01	.	15.3412	0.74300	0.0:0.0:1.0:0.0	.	207;383	Q8IVM0;Q8IVM0-2	CCD50_HUMAN;.	Q	207;383	ENSP00000376249:R207Q;ENSP00000376250:R383Q	ENSP00000376249:R207Q	R	+	2	0	CCDC50	192581321	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.894000	0.69806	2.683000	0.91414	0.655000	0.94253	CGA		0.378	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		A	191098627	G	A	191098627	3	1	61	1	0	0	0	0	1	0	0	0	2826	1058	37	1	1182	1	CCDC50	3	191098627	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22821	191098627	6923803	2990	10975										
FGF12	2257	broad.mit.edu	37	chr3	191861894	191861894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctccaatttcatgtagCgatggttctctgtacataca	6	9	3	0	rs369115025		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:191861894C>T	ENST00000454309.2	-	5	1461	c.636G>A	c.(634-636)tcG>tcA	p.S212S	FGF12_ENST00000264730.3_Silent_p.S150S|FGF12_ENST00000450716.1_Silent_p.S150S|FGF12_ENST00000445105.2_Silent_p.S150S|FGF12_ENST00000430714.1_Silent_p.S113S	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	212					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)	p.S212S(1)		endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		TTTCATGTAGCGATGGTTCTC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	3											289	253	265					3																	191861894		2203	4300	6503	193344588	SO:0001819	synonymous_variant	2257			U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"fibroblast growth factor 12B", "fibroblast growth factor homologous factor 1", "myocyte-activating factor", "fibroblast growth factor FGF-12b"	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.636G>A	3.37:g.191861894C>T			193344588	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Silent	SNP	ENST00000454309.2	37	CCDS3301.1																																																																																				0.348	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		T	191861894	C	T	191861894	2	4	61	1	0	0	0	0	0	0	0	1	5860	755	27	1		1	FGF12	3	191861894	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	763267	191861894	6160536	2991	10976										
ATP13A5	344905	broad.mit.edu	37	chr3	193062798	193062798	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacatcacttacctttgtCttttacaatgattgtaacct	3	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:193062798C>A	ENST00000342358.4	-	8	925	c.808G>T	c.(808-810)Gac>Tac	p.D270Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	270						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.D270Y(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTACCTTTGTCTTTTACAATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											209	180	190					3																	193062798		2203	4300	6503	194545492	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.808G>T	3.37:g.193062798C>A	ENSP00000341942:p.Asp270Tyr		194545492	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.968436	0.34754	.	.	ENSG00000187527	ENST00000342358	D	0.90385	-2.66	4.82	4.82	0.62117	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.476025	0.21020	N	0.081530	D	0.91297	0.7256	M	0.75615	2.305	0.38293	D	0.942761	P	0.41498	0.752	P	0.45474	0.482	D	0.92895	0.6334	10	0.72032	D	0.01	-1.6336	11.8737	0.52536	0.0:0.912:0.0:0.088	.	270	Q4VNC0	AT135_HUMAN	Y	270	ENSP00000341942:D270Y	ENSP00000341942:D270Y	D	-	1	0	ATP13A5	194545492	0.032000	0.19561	0.950000	0.38849	0.023000	0.10783	1.100000	0.31025	2.615000	0.88500	0.655000	0.94253	GAC		0.358	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193062798	C	A	193062798	3	1	61	1	0	0	0	0	1	0	0	0	1128	913	32	2	2938	2	ATP13A5	3	193062798	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1200904	193062798	4959632	2992	10977										
ATP13A3	79572	broad.mit.edu	37	chr3	194180573	194180573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcctattttcttcagtgGgattctcaattaaacaaact	6	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:194180573G>A	ENST00000439040.1	-	5	1144	c.353C>T	c.(352-354)cCc>cTc	p.P118L	ATP13A3_ENST00000256031.4_Missense_Mutation_p.P118L			Q9H7F0	AT133_HUMAN	ATPase type 13A3	118						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.P118L(1)		NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TTCTTCAGTGGGATTCTCAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											145	137	139					3																	194180573		1833	4096	5929	195661862	SO:0001583	missense	79572			AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"ATPases / P-type"	24113	protein-coding gene	gene with protein product	"ATPase family homolog up regulated in senescence cells"	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.353C>T	3.37:g.194180573G>A	ENSP00000416508:p.Pro118Leu		195661862	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	37	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.070653	0.00379	.	.	ENSG00000133657	ENST00000439040;ENST00000256031	D;D	0.85702	-2.02;-2.02	4.91	1.03	0.20045	.	0.952726	0.08693	N	0.907714	T	0.71187	0.3310	N	0.19112	0.55	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.52845	-0.8521	10	0.21540	T	0.41	1.4535	5.0574	0.14540	0.4072:0.0:0.4464:0.1464	.	118	Q9H7F0	AT133_HUMAN	L	118	ENSP00000416508:P118L;ENSP00000256031:P118L	ENSP00000256031:P118L	P	-	2	0	ATP13A3	195661862	0.022000	0.18835	0.036000	0.18154	0.054000	0.15201	0.238000	0.18004	-0.074000	0.12820	0.585000	0.79938	CCC		0.333	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		A	194180573	G	A	194180573	3	1	61	1	0	0	0	0	1	0	0	0	1126	1232	43	3	3443	3	ATP13A3	3	194180573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1117775	194180573	3841857	2993	10978										
ACAP2	23527	broad.mit.edu	37	chr3	195029559	195029559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgattattctgtattgaaaAccagcgcctacagaaacaca	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195029559A>G	ENST00000326793.6	-	11	1095	c.865T>C	c.(865-867)Ttt>Ctt	p.F289L		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	289	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.F289L(1)		cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TGTATTGAAAACCAGCGCCTA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	3											59	62	61					3																	195029559		2201	4286	6487	196510848	SO:0001583	missense	23527				CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.865T>C	3.37:g.195029559A>G	ENSP00000324287:p.Phe289Leu		196510848	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	37	CCDS33924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.9|28.9	4.957767|4.957767	0.92726|0.92726	.|.	.|.	ENSG00000114331|ENSG00000114331	ENST00000326793|ENST00000439758	T|.	0.10382|.	2.88|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88966|0.88966	0.6581|0.6581	H|H	0.98446|0.98446	4.235|4.235	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.93072|0.93072	0.6483|0.6483	10|5	0.87932|.	D|.	0|.	.|.	15.2535|15.2535	0.73568|0.73568	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	289|.	Q15057|.	ACAP2_HUMAN|.	L|A	289|163	ENSP00000324287:F289L|.	ENSP00000324287:F289L|.	F|V	-|-	1|2	0|0	ACAP2|ACAP2	196510848|196510848	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.875000|8.875000	0.92372|0.92372	2.189000|2.189000	0.69895|0.69895	0.528000|0.528000	0.53228|0.53228	TTT|GTT		0.299	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		G	195029559	A	G	195029559	3	3	61	1	0	0	0	0	1	0	0	0	119	43	2	4	1523	4	ACAP2	3	195029559	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	848986	195029559	2992871	2994	10979										
ACAP2	23527	broad.mit.edu	37	chr3	195057696	195057696	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatctcctttttgattgaaGaacattaatctgagggaaaa	8	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195057696G>T	ENST00000326793.6	-	7	768	c.538C>A	c.(538-540)Ctt>Att	p.L180I		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	180	BAR.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.L180I(1)		cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TTTGATTGAAGAACATTAATC	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	3											63	63	63					3																	195057696		2203	4292	6495	196538985	SO:0001583	missense	23527				CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.538C>A	3.37:g.195057696G>T	ENSP00000324287:p.Leu180Ile		196538985	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	37	CCDS33924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.03|16.03	3.006518|3.006518	0.54361|0.54361	.|.	.|.	ENSG00000114331|ENSG00000114331	ENST00000326793|ENST00000439758;ENST00000423531	T|.	0.05139|.	3.49|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67163|0.67163	0.2864|0.2864	L|L	0.41632|0.41632	1.29|1.29	0.80722|0.80722	D|D	1|1	P|.	0.45672|.	0.864|.	B|.	0.42214|.	0.38|.	T|T	0.61063|0.61063	-0.7138|-0.7138	10|5	0.10902|.	T|.	0.67|.	.|.	18.806|18.806	0.92037|0.92037	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	180|.	Q15057|.	ACAP2_HUMAN|.	I|Y	180|50;133	ENSP00000324287:L180I|.	ENSP00000324287:L180I|.	L|S	-|-	1|2	0|0	ACAP2|ACAP2	196538985|196538985	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.234000|7.234000	0.78134|0.78134	2.788000|2.788000	0.95919|0.95919	0.650000|0.650000	0.86243|0.86243	CTT|TCT		0.264	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		T	195057696	G	T	195057696	3	4	61	1	0	0	0	0	1	0	0	0	119	942	33	2	1866	2	ACAP2	3	195057696	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28137	195057696	2964734	2995	10980										
PPP1R2	5504	broad.mit.edu	37	chr3	195245893	195245893	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcatcatcatcatgtaGgtcttttgaaattaattgtc	5	7	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195245893G>T	ENST00000328432.3	-	5	853	c.493C>A	c.(493-495)Cta>Ata	p.L165I		NM_006241.4	NP_006232.1	P41236	IPP2_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 2	165					generation of precursor metabolites and energy (GO:0006091)|glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of signal transduction (GO:0009966)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)	p.L165I(1)		endometrium(2)|kidney(1)|large_intestine(1)|urinary_tract(2)	6	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)		TCATCATGTAGGTCTTTTGAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											146	145	146					3																	195245893		2202	4295	6497	196727182	SO:0001583	missense	5504			U68111	CCDS3309.1	3q29	2012-04-17			ENSG00000184203	ENSG00000184203	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9288	protein-coding gene	gene with protein product		601792				9126490, 8119416	Standard	XM_006713682		Approved	IPP2	uc003fup.3	P41236	OTTHUMG00000155887	ENST00000328432.3:c.493C>A	3.37:g.195245893G>T	ENSP00000328178:p.Leu165Ile		196727182		Missense_Mutation	SNP	ENST00000328432.3	37	CCDS3309.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.568853	0.65765	.	.	ENSG00000184203	ENST00000328432;ENST00000438848	.	.	.	5.36	4.49	0.54785	.	0.000000	0.64402	D	0.000004	T	0.75213	0.3819	M	0.72894	2.215	0.39762	D	0.972049	D	0.61697	0.99	D	0.67725	0.953	T	0.78081	-0.2343	9	0.54805	T	0.06	.	11.9486	0.52942	0.085:0.0:0.915:0.0	.	165	P41236	IPP2_HUMAN	I	165;139	.	ENSP00000328178:L165I	L	-	1	2	PPP1R2	196727182	1.000000	0.71417	0.978000	0.43139	0.964000	0.63967	3.871000	0.56077	1.393000	0.46605	0.467000	0.42956	CTA		0.343	PPP1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342133.1	NM_006241		T	195245893	G	T	195245893	3	4	61	1	0	0	0	0	1	0	0	0	12404	991	35	2	132	2	PPP1R2	3	195245893	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188197	195245893	2776537	2996	10981										
APOD	347	broad.mit.edu	37	chr3	195295973	195295973	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcatagttctcatagtcgGtggccaggatccagtacggt	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195295973G>A	ENST00000343267.3	-	5	729	c.368C>T	c.(367-369)aCc>aTc	p.T123I		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	123					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)	p.T123I(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCATAGTCGGTGGCCAGGAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											119	116	117					3																	195295973		2203	4300	6503	196777262	SO:0001583	missense	347				CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"Lipocalins", "Apolipoproteins"	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.368C>T	3.37:g.195295973G>A	ENSP00000345179:p.Thr123Ile		196777262	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.777779	0.90195	.	.	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.35789	1.29;1.29;1.29	5.92	5.92	0.95590	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.56601	0.1996	M	0.62209	1.925	0.80722	D	1	D	0.62365	0.991	D	0.76071	0.987	T	0.46176	-0.9210	10	0.29301	T	0.29	-35.9087	15.8208	0.78644	0.0:0.0:1.0:0.0	.	123	P05090	APOD_HUMAN	I	123;151;123	ENSP00000345179:T123I;ENSP00000415235:T151I;ENSP00000393076:T123I	ENSP00000345179:T123I	T	-	2	0	APOD	196777262	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.803000	0.91915	2.813000	0.96785	0.561000	0.74099	ACC		0.488	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		A	195295973	G	A	195295973	3	1	61	1	0	0	0	0	1	0	0	0	801	1261	44	3	205	3	APOD	3	195295973	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50080	195295973	2726457	2997	10982										
MUC4	4585	broad.mit.edu	37	chr3	195474167	195474167	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccgcccagggccccaaaGaagatgccgaagaacgcgtc	13	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195474167G>T	ENST00000346145.4	-	24	3450	c.3411C>A	c.(3409-3411)ttC>ttA	p.F1137L	MUC4_ENST00000475231.1_Missense_Mutation_p.F5321L|MUC4_ENST00000349607.4_Missense_Mutation_p.F1086L|MUC4_ENST00000463781.3_Missense_Mutation_p.F5373L	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2130					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.F1137L(1)|p.F5245L(1)|p.F5373L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	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)		GGGCCCCAAAGAAGATGCCGA	0.612																																																3	Substitution - Missense(3)	large_intestine(3)	3											75	72	73					3																	195474167		2203	4300	6503	196959838	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3411C>A	3.37:g.195474167G>T	ENSP00000304207:p.Phe1137Leu		196959838	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	g	13.16	2.152755	0.38021	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.26067	1.76;2.12;2.36;2.2	5.14	2.12	0.27331	.	0.310100	0.23105	N	0.051878	T	0.04137	0.0115	N	0.00193	-1.875	0.21147	N	0.999777	B;B;B;B;B;B	0.14438	0.01;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0;0.0	T	0.41787	-0.9489	10	0.02654	T	1	-13.1209	6.4845	0.22081	0.1899:0.1641:0.646:0.0	.	5245;1086;1137;5373;5321;2078	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	L	1086;1137;5373;5321;1873	ENSP00000338109:F1086L;ENSP00000304207:F1137L;ENSP00000417498:F5373L;ENSP00000420243:F5321L	ENSP00000304207:F1137L	F	-	3	2	MUC4	196959838	0.985000	0.35326	1.000000	0.80357	0.804000	0.45430	0.044000	0.13992	0.575000	0.29434	0.543000	0.68304	TTC		0.612	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195474167	G	T	195474167	3	4	61	1	0	0	0	0	1	0	0	0	10008	933	33	2	123	2	MUC4	3	195474167	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178194	195474167	2548263	2998	10983										
MUC4	4585	broad.mit.edu	37	chr3	195486080	195486080	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgaatcagcgtggtctgCcccttgtaggcttcaatcac	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195486080C>T	ENST00000346145.4	-	16	2232	c.2193G>A	c.(2191-2193)ggG>ggA	p.G731G	MUC4_ENST00000475231.1_Silent_p.G4915G|MUC4_ENST00000349607.4_Silent_p.G680G|MUC4_ENST00000463781.3_Silent_p.G4967G	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1724					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.G731G(1)|p.G4967G(1)|p.G4839G(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	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)		GCGTGGTCTGCCCCTTGTAGG	0.542																																																3	Substitution - coding silent(3)	large_intestine(3)	3											274	263	267					3																	195486080		2203	4300	6503	196971751	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.2193G>A	3.37:g.195486080C>T			196971751	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																				0.542	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195486080	C	T	195486080	2	4	61	1	0	0	0	0	0	0	0	1	10008	726	26	3		3	MUC4	3	195486080	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11913	195486080	2536350	2999	10984										
MUC4	4585	broad.mit.edu	37	chr3	195493607	195493607	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatcagtgggctgttttcGaaatagccatctccactgca	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195493607G>A	ENST00000346145.4	-	7	876	c.837C>T	c.(835-837)ttC>ttT	p.F279F	MUC4_ENST00000475231.1_Silent_p.F4463F|MUC4_ENST00000349607.4_Silent_p.F228F|MUC4_ENST00000463781.3_Silent_p.F4515F	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1272					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.F4387F(1)|p.F279F(1)|p.F4515F(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	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)		GGCTGTTTTCGAAATAGCCAT	0.547																																																3	Substitution - coding silent(3)	large_intestine(3)	3											124	105	112					3																	195493607		2203	4300	6503	196979278	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.837C>T	3.37:g.195493607G>A			196979278	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																				0.547	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195493607	G	A	195493607	2	1	61	1	0	0	0	0	0	0	0	1	10008	1049	37	1		1	MUC4	3	195493607	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7527	195493607	2528823	3000	10985										
OSTalpha	200931	broad.mit.edu	37	chr3	195960000	195960000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgacacgaatgtactaccGaaggaaagaccacaaggttg	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:195960000G>A	ENST00000296327.5	+	9	1162	c.953G>A	c.(952-954)cGa>cAa	p.R318Q	PCYT1A_ENST00000419333.1_Intron	NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	318					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)	p.R318Q(1)								Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ATGTACTACCGAAGGAAAGAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											188	163	171					3																	195960000		2203	4300	6503	197444397	SO:0001583	missense	200931				CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"Solute carriers"	29955	protein-coding gene	gene with protein product	"organic solute transporter, alpha subunit"	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.953G>A	3.37:g.195960000G>A	ENSP00000296327:p.Arg318Gln		197444397	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	37	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837000	0.91117	.	.	ENSG00000163959	ENST00000296327	T	0.41400	1.0	6.03	6.03	0.97812	.	0.000000	0.41294	D	0.000901	T	0.67552	0.2905	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.68483	0.958	T	0.66905	-0.5805	10	0.49607	T	0.09	-8.2829	19.1349	0.93424	0.0:0.0:1.0:0.0	.	318	Q86UW1	OSTA_HUMAN	Q	318	ENSP00000296327:R318Q	ENSP00000296327:R318Q	R	+	2	0	AC069257.9	197444397	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	6.209000	0.72171	2.861000	0.98227	0.655000	0.94253	CGA		0.458	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672		A	195960000	G	A	195960000	3	1	61	1	0	0	0	0	1	0	0	0	11331	1058	37	1	987	1	OSTalpha	3	195960000	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	466393	195960000	2062430	3001	10986										
TM4SF19	116211	broad.mit.edu	37	chr3	196051178	196051178	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgggtaaccatatttcCaagcttgtgtctgattgaag	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196051178C>T	ENST00000273695.3	-	4	538	c.413G>A	c.(412-414)tGg>tAg	p.W138*	TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19-AS1_ENST00000420226.1_RNA|TM4SF19_ENST00000442633.1_Nonsense_Mutation_p.W138*|TM4SF19_ENST00000446879.1_Nonsense_Mutation_p.W138*|TM4SF19-AS1_ENST00000444939.1_RNA|TM4SF19_ENST00000454715.1_Nonsense_Mutation_p.W112*	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	138						integral component of membrane (GO:0016021)		p.W138*(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ACCATATTTCCAAGCTTGTGT	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											100	92	95					3																	196051178		2203	4300	6503	197535575	SO:0001587	stop_gained	116211			BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.413G>A	3.37:g.196051178C>T	ENSP00000273695:p.Trp138*		197535575	B2RV20|E9PH22|Q336K7	Nonsense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.098726|5.098726	0.94197|0.94197	.|.	.|.	ENSG00000145107|ENSG00000145107	ENST00000440822|ENST00000446879;ENST00000454715;ENST00000273695	.|.	.|.	.|.	5.01|5.01	3.09|3.09	0.35607|0.35607	.|.	.|0.506550	.|0.17669	.|N	.|0.166027	T|.	0.39332|.	0.1074|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.10776|.	-1.0615|.	4|.	.|0.15952	.|T	.|0.53	-9.2936|-9.2936	5.6158|5.6158	0.17430|0.17430	0.0:0.669:0.2202:0.1108|0.0:0.669:0.2202:0.1108	.|.	.|.	.|.	.|.	R|X	6|138;112;138	.|.	.|ENSP00000273695:W138X	G|W	-|-	1|2	0|0	TM4SF19|TM4SF19	197535575|197535575	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	0.875000|0.875000	0.28079|0.28079	2.311000|2.311000	0.77944|0.77944	0.563000|0.563000	0.77884|0.77884	GGA|TGG		0.428	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461		T	196051178	C	T	196051178	4	4	61	1	0	0	0	0	0	1	0	0	16007	595	21	3	224	3	TM4SF19	3	196051178	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91178	196051178	1971252	3002	10987										
TM4SF19	116211	broad.mit.edu	37	chr3	196053869	196053869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcagccgtatctccagCccatcaaggagatgaggata	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196053869C>A	ENST00000273695.3	-	3	361	c.236G>T	c.(235-237)gGc>gTc	p.G79V	TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000442633.1_Missense_Mutation_p.G79V|TM4SF19_ENST00000446879.1_Missense_Mutation_p.G79V|TM4SF19-AS1_ENST00000444939.1_RNA|TM4SF19_ENST00000454715.1_Intron	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	79						integral component of membrane (GO:0016021)		p.G79V(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GTATCTCCAGCCCATCAAGGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											88	82	84					3																	196053869		2203	4300	6503	197538266	SO:0001583	missense	116211			BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.236G>T	3.37:g.196053869C>A	ENSP00000273695:p.Gly79Val		197538266	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.584304	0.65992	.	.	ENSG00000145107	ENST00000446879;ENST00000273695	T;T	0.30981	1.51;1.51	5.37	5.37	0.77165	.	0.262310	0.32918	N	0.005495	T	0.58466	0.2124	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.61267	-0.7097	10	0.49607	T	0.09	-12.5002	14.6173	0.68558	0.0:1.0:0.0:0.0	.	79;79	C9JCD5;Q96DZ7	.;T4S19_HUMAN	V	79	ENSP00000395280:G79V;ENSP00000273695:G79V	ENSP00000273695:G79V	G	-	2	0	TM4SF19	197538266	1.000000	0.71417	0.992000	0.48379	0.635000	0.38103	3.845000	0.55880	2.528000	0.85240	0.655000	0.94253	GGC		0.507	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461		A	196053869	C	A	196053869	3	1	61	1	0	0	0	0	1	0	0	0	16007	739	26	2	405	2	TM4SF19	3	196053869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2691	196053869	1968561	3003	10988										
UBXN7	26043	broad.mit.edu	37	chr3	196134247	196134247	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttcaagcatatgttttcCtacactttcacttgcacctg	5	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196134247C>A	ENST00000296328.4	-	2	165	c.91G>T	c.(91-93)Gga>Tga	p.G31*	UBXN7_ENST00000535858.1_Intron|UBXN7_ENST00000428095.1_Intron	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	31						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.G31*(2)		NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						ATATGTTTTCCTACACTTTCA	0.388																																																2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	3											153	136	142					3																	196134247		1878	4107	5985	197618644	SO:0001587	stop_gained	26043			AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.91G>T	3.37:g.196134247C>A	ENSP00000296328:p.Gly31*		197618644	D3DXB3|Q6ZP77|Q86X20|Q8N327	Nonsense_Mutation	SNP	ENST00000296328.4	37	CCDS43191.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.490279|5.490279	0.96339|0.96339	.|.	.|.	ENSG00000163960|ENSG00000163960	ENST00000296328|ENST00000381887	.|.	.|.	.|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75027	.|0.3794	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73424	.|-0.3987	.|4	0.72032|.	D|.	0.01|.	-14.5909|-14.5909	18.9054|18.9054	0.92458|0.92458	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|M	31|30	.|.	ENSP00000296328:G31X|.	G|R	-|-	1|2	0|0	UBXN7|UBXN7	197618644|197618644	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.123000|7.123000	0.77176|0.77176	2.558000|2.558000	0.86282|0.86282	0.650000|0.650000	0.86243|0.86243	GGA|AGG		0.388	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		A	196134247	C	A	196134247	4	1	61	1	0	0	0	0	0	1	0	0	16958	690	24	2	1418	2	UBXN7	3	196134247	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80378	196134247	1888183	3004	10989										
WDR53	348793	broad.mit.edu	37	chr3	196288061	196288061	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgaaagacaattgatttCttcttcattcacatgaaaat	4	7	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196288061C>A	ENST00000332629.5	-	3	853	c.286G>T	c.(286-288)Gaa>Taa	p.E96*	WDR53_ENST00000429115.1_Intron|WDR53_ENST00000433160.1_Intron	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	96								p.E96*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		CAATTGATTTCTTCTTCATTC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											131	127	129					3																	196288061		2203	4300	6503	197772458	SO:0001587	stop_gained	348793			BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"WD repeat domain containing"	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.286G>T	3.37:g.196288061C>A	ENSP00000328079:p.Glu96*		197772458	A0MNP1	Nonsense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	.	.	.	.	.	.	.	.	.	.	C	35	5.467717	0.96257	.	.	ENSG00000185798	ENST00000332629;ENST00000456677;ENST00000425888	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-4.3131	19.3331	0.94299	0.0:1.0:0.0:0.0	.	.	.	.	X	96	.	ENSP00000328079:E96X	E	-	1	0	WDR53	197772458	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.954000	0.76001	2.802000	0.96397	0.655000	0.94253	GAA		0.423	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627		A	196288061	C	A	196288061	4	1	61	1	0	0	0	0	0	1	0	0	17345	922	32	2	798	2	WDR53	3	196288061	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153814	196288061	1734369	3005	10990										
FBXO45	200933	broad.mit.edu	37	chr3	196311045	196311045	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttggacatggaagataaGactttagcttttgaacgtgg	11	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196311045G>T	ENST00000311630.6	+	3	1014	c.717G>T	c.(715-717)aaG>aaT	p.K239N	FBXO45_ENST00000440469.1_Missense_Mutation_p.K60N	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	239	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.K239N(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		TGGAAGATAAGACTTTAGCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											138	132	134					3																	196311045		1840	4088	5928	197795442	SO:0001583	missense	200933			AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.717G>T	3.37:g.196311045G>T	ENSP00000310332:p.Lys239Asn		197795442	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	G	9.675	1.147796	0.21288	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	T;T	0.60424	0.19;0.19	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.24275	0.0588	N	0.01140	-0.99	0.58432	D	0.999999	B	0.12630	0.006	B	0.15052	0.012	T	0.20174	-1.0283	10	0.23302	T	0.38	-6.6731	6.198	0.20559	0.2181:0.0:0.7819:0.0	.	239	P0C2W1	FBSP1_HUMAN	N	60;239	ENSP00000389868:K60N;ENSP00000310332:K239N	ENSP00000310332:K239N	K	+	3	2	FBXO45	197795442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.041000	0.64196	2.740000	0.93945	0.563000	0.77884	AAG		0.413	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			T	196311045	G	T	196311045	3	4	61	1	0	0	0	0	1	0	0	0	5773	933	33	2	727	2	FBXO45	3	196311045	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22984	196311045	1711385	3006	10991										
LRRC33	375387	broad.mit.edu	37	chr3	196388447	196388447	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgggactgcaagtgggagCggctggacctgggcctgctc	17	12	0	0	rs538217990		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196388447C>T	ENST00000328557.4	+	3	2136	c.1933C>T	c.(1933-1935)Cgg>Tgg	p.R645W		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	645					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R645W(1)									CAAGTGGGAGCGGCTGGACCT	0.637													C|||	1	0.000199681	0	0	5008	,	,		13101	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											78	86	83					3																	196388447		2203	4300	6503	197872844	SO:0001583	missense	375387			AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1933C>T	3.37:g.196388447C>T	ENSP00000328625:p.Arg645Trp		197872844		Missense_Mutation	SNP	ENST00000328557.4	37	CCDS3319.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.384754	0.42308	.	.	ENSG00000174004	ENST00000328557	T	0.48522	0.81	5.67	3.74	0.42951	.	1.021460	0.07786	N	0.954167	T	0.47377	0.1442	L	0.44542	1.39	0.20489	N	0.999893	D	0.65815	0.995	B	0.44315	0.446	T	0.44498	-0.9324	10	0.66056	D	0.02	.	13.8375	0.63419	0.4671:0.5329:0.0:0.0	.	645	Q86YC3	LRC33_HUMAN	W	645	ENSP00000328625:R645W	ENSP00000328625:R645W	R	+	1	2	LRRC33	197872844	0.001000	0.12720	0.924000	0.36721	0.756000	0.42949	1.049000	0.30392	1.457000	0.47850	0.655000	0.94253	CGG		0.637	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		T	196388447	C	T	196388447	3	4	61	1	0	0	0	0	1	0	0	0	9017	759	27	1	1939	1	LRRC33	3	196388447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77402	196388447	1633983	3007	10992										
C3orf34	84984	broad.mit.edu	37	chr3	196434508	196434508	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctcaatgtcataaacaaAatttggatcatccttcttct	3	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196434508A>T	ENST00000399942.4	-	2	595	c.301T>A	c.(301-303)Ttt>Att	p.F101I	CEP19_ENST00000409690.3_Missense_Mutation_p.F140I|RNU6-646P_ENST00000364571.1_RNA			Q96LK0	CEP19_HUMAN	centrosomal protein 19kDa	136						centriole (GO:0005814)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)		p.F136I(1)		NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	10						TCATAAACAAAATTTGGATCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	3											156	145	148					3																	196434508		1912	4126	6038	197918905	SO:0001583	missense	84984			BC007827	CCDS43193.2	3q29	2014-02-20	2011-05-06	2011-05-06	ENSG00000174007	ENSG00000174007			28209	protein-coding gene	gene with protein product		615586	"chromosome 3 open reading frame 34"	C3orf34		21399614	Standard	XM_005269370		Approved	MGC14126	uc011btw.2	Q96LK0	OTTHUMG00000153933	ENST00000399942.4:c.301T>A	3.37:g.196434508A>T	ENSP00000382823:p.Phe101Ile		197918905	B2RA74|Q96I48	Missense_Mutation	SNP	ENST00000399942.4	37		.	.	.	.	.	.	.	.	.	.	A	29.9	5.042648	0.93685	.	.	ENSG00000174007	ENST00000409690;ENST00000399942	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84012	0.0349	9	0.87932	D	0	-12.639	16.2026	0.82095	1.0:0.0:0.0:0.0	.	136	Q96LK0	CEP19_HUMAN	I	140;101	.	ENSP00000382823:F101I	F	-	1	0	CEP19	197918905	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.616000	0.90924	2.285000	0.76669	0.533000	0.62120	TTT		0.413	CEP19-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333081.1	NM_032898		T	196434508	A	T	196434508	3	4	61	1	0	0	0	0	1	0	0	0	2230	14	1	5	89	5	C3orf34	3	196434508	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	46061	196434508	1587922	3008	10993										
PIGX	54965	broad.mit.edu	37	chr3	196449344	196449344	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacttgcacacctgccgtCtcttaattaaacaggacatt	7	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196449344C>A	ENST00000421265.1	+	3	165	c.112C>A	c.(112-114)Ctc>Atc	p.L38I	PIGX_ENST00000495440.1_3'UTR|PIGX_ENST00000541663.1_5'UTR|PIGX_ENST00000314118.4_Missense_Mutation_p.L38I			Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class X	79					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.L38I(1)		endometrium(1)|large_intestine(5)|lung(4)|stomach(1)	11	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)		CACCTGCCGTCTCTTAATTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	3											171	173	172					3																	196449344		2203	4300	6503	197933741	SO:0001583	missense	54965			AK000529	CCDS3320.1, CCDS3320.2, CCDS54701.1	3q29	2013-02-26	2006-06-28		ENSG00000163964	ENSG00000163964		"Phosphatidylinositol glycan anchor biosynthesis"	26046	protein-coding gene	gene with protein product		610276	"phosphatidylinositol glycan, class X"			15635094	Standard	NM_017861		Approved	FLJ20522	uc010iaj.3	Q8TBF5	OTTHUMG00000155535	ENST00000421265.1:c.112C>A	3.37:g.196449344C>A	ENSP00000416446:p.Leu38Ile		197933741	Q9NWZ2	Missense_Mutation	SNP	ENST00000421265.1	37		.	.	.	.	.	.	.	.	.	.	C	15.63	2.890978	0.52014	.	.	ENSG00000163964	ENST00000426755;ENST00000392391;ENST00000314118;ENST00000296333;ENST00000421265;ENST00000451319	T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.27	6.05	5.16	0.70880	.	0.149777	0.44097	D	0.000491	T	0.33323	0.0859	L	0.58101	1.795	0.80722	D	1	P;P	0.38827	0.649;0.515	B;B	0.35770	0.21;0.163	T	0.06250	-1.0837	10	0.34782	T	0.22	-11.7553	12.2837	0.54779	0.0:0.7415:0.2585:0.0	.	79;79	Q8TBF5-2;Q8TBF5	.;PIGX_HUMAN	I	38;79;38;79;38;38	ENSP00000409073:L38I;ENSP00000376192:L79I;ENSP00000317301:L38I;ENSP00000296333:L79I;ENSP00000416446:L38I;ENSP00000390804:L38I	ENSP00000296333:L79I	L	+	1	0	PIGX	197933741	0.999000	0.42202	1.000000	0.80357	0.791000	0.44710	1.432000	0.34936	2.880000	0.98712	0.655000	0.94253	CTC		0.398	PIGX-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000340684.1	NM_017861		A	196449344	C	A	196449344	3	1	61	1	0	0	0	0	1	0	0	0	11934	913	32	2	245	2	PIGX	3	196449344	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14836	196449344	1573086	3009	10994										
PIGX	54965	broad.mit.edu	37	chr3	196454964	196454964	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaagatggagaagcctcGattgtggtcaataacccaga	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196454964G>A	ENST00000421265.1	+	4	419	c.366G>A	c.(364-366)tcG>tcA	p.S122S	PIGX_ENST00000541663.1_Silent_p.S55S|PIGX_ENST00000314118.4_Silent_p.S122S			Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class X	163					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.S122S(1)		endometrium(1)|large_intestine(5)|lung(4)|stomach(1)	11	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)		GAGAAGCCTCGATTGTGGTCA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	3											155	140	145					3																	196454964		2203	4300	6503	197939361	SO:0001819	synonymous_variant	54965			AK000529	CCDS3320.1, CCDS3320.2, CCDS54701.1	3q29	2013-02-26	2006-06-28		ENSG00000163964	ENSG00000163964		"Phosphatidylinositol glycan anchor biosynthesis"	26046	protein-coding gene	gene with protein product		610276	"phosphatidylinositol glycan, class X"			15635094	Standard	NM_017861		Approved	FLJ20522	uc010iaj.3	Q8TBF5	OTTHUMG00000155535	ENST00000421265.1:c.366G>A	3.37:g.196454964G>A			197939361	Q9NWZ2	Silent	SNP	ENST00000421265.1	37																																																																																					0.458	PIGX-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000340684.1	NM_017861		A	196454964	G	A	196454964	2	1	61	1	0	0	0	0	0	0	0	1	11934	1045	37	1		1	PIGX	3	196454964	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5620	196454964	1567466	3010	10995										
PIGX	54965	broad.mit.edu	37	chr3	196457908	196457908	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactcagaagtggcagcccCttgtgctttggagaatgagg	13	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196457908C>A	ENST00000314118.4	+	5	737	c.455C>A	c.(454-456)cCt>cAt	p.P152H	PIGX_ENST00000541663.1_Missense_Mutation_p.P103H	NM_017861.3	NP_060331.3	Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class X	193					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.P152H(1)		endometrium(1)|large_intestine(5)|lung(4)|stomach(1)	11	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)		GTGGCAGCCCCTTGTGCTTTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3											92	84	87					3																	196457908		2203	4300	6503	197942305	SO:0001583	missense	54965			AK000529	CCDS3320.1, CCDS3320.2, CCDS54701.1	3q29	2013-02-26	2006-06-28		ENSG00000163964	ENSG00000163964		"Phosphatidylinositol glycan anchor biosynthesis"	26046	protein-coding gene	gene with protein product		610276	"phosphatidylinositol glycan, class X"			15635094	Standard	NM_017861		Approved	FLJ20522	uc010iaj.3	Q8TBF5	OTTHUMG00000155535	ENST00000314118.4:c.455C>A	3.37:g.196457908C>A	ENSP00000317301:p.Pro152His		197942305	Q9NWZ2	Missense_Mutation	SNP	ENST00000314118.4	37		.	.	.	.	.	.	.	.	.	.	C	19.50	3.839274	0.71373	.	.	ENSG00000163964	ENST00000426755;ENST00000392391;ENST00000314118;ENST00000296333;ENST00000541663	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	4.94	4.94	0.65067	.	0.133715	0.49916	D	0.000122	T	0.51941	0.1704	M	0.64404	1.975	0.44595	D	0.997563	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.993	T	0.53753	-0.8394	10	0.72032	D	0.01	-5.8843	14.066	0.64828	0.0:1.0:0.0:0.0	.	211;193	Q8TBF5-2;Q8TBF5	.;PIGX_HUMAN	H	152;193;152;211;103	ENSP00000409073:P152H;ENSP00000376192:P193H;ENSP00000317301:P152H;ENSP00000296333:P211H;ENSP00000443269:P103H	ENSP00000296333:P211H	P	+	2	0	PIGX	197942305	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	4.102000	0.57776	2.451000	0.82905	0.644000	0.83932	CCT		0.388	PIGX-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017861		A	196457908	C	A	196457908	3	1	61	1	0	0	0	0	1	0	0	0	11934	681	24	2	654	2	PIGX	3	196457908	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2944	196457908	1564522	3011	10996										
PAK2	5062	broad.mit.edu	37	chr3	196509533	196509533	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatcatgtctgataacggaGaactggaagataagcctcca	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196509533G>T	ENST00000327134.3	+	2	338	c.16G>T	c.(16-18)Gaa>Taa	p.E6*	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	6					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)	p.E6*(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	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)		TGATAACGGAGAACTGGAAGA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											91	97	95					3																	196509533		2203	4300	6503	197993930	SO:0001587	stop_gained	5062			U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.16G>T	3.37:g.196509533G>T	ENSP00000314067:p.Glu6*		197993930	Q13154|Q6ISC3	Nonsense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	G	39	7.613493	0.98390	.	.	ENSG00000180370	ENST00000327134	.	.	.	5.21	5.21	0.72293	.	0.051698	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	18.756	0.91833	0.0:0.0:1.0:0.0	.	.	.	.	X	6	.	ENSP00000314067:E6X	E	+	1	0	PAK2	197993930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.260000	0.78391	2.456000	0.83038	0.655000	0.94253	GAA		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		T	196509533	G	T	196509533	4	4	61	1	0	0	0	0	0	1	0	0	11432	943	33	2	18	2	PAK2	3	196509533	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51625	196509533	1512897	3012	10997										
SENP5	205564	broad.mit.edu	37	chr3	196612407	196612407	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagactccaagcagagaagCtgttgtcatcagcaaagaat	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196612407C>A	ENST00000323460.5	+	2	604	c.355C>A	c.(355-357)Ctg>Atg	p.L119M	SENP5_ENST00000445299.2_Missense_Mutation_p.L119M|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	119					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.L119M(1)		NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AGCAGAGAAGCTGTTGTCATC	0.403																																					Ovarian(47;891 1095 11174 13858 51271)											1	Substitution - Missense(1)	large_intestine(1)	3											60	62	61					3																	196612407		2203	4300	6503	198096804	SO:0001583	missense	205564			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.355C>A	3.37:g.196612407C>A	ENSP00000327197:p.Leu119Met		198096804	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	37	CCDS3322.1	.	.	.	.	.	.	.	.	.	.	C	11.27	1.588336	0.28357	.	.	ENSG00000119231	ENST00000323460;ENST00000445299	T;T	0.31247	1.87;1.5	5.18	1.33	0.21861	.	0.433561	0.19574	N	0.111023	T	0.22322	0.0538	N	0.24115	0.695	0.80722	D	1	P;D	0.56521	0.535;0.976	B;P	0.48030	0.403;0.564	T	0.03875	-1.0996	10	0.87932	D	0	-8.0E-4	5.5835	0.17262	0.0:0.1686:0.1438:0.6876	.	119;119	B4DY82;Q96HI0	.;SENP5_HUMAN	M	119	ENSP00000327197:L119M;ENSP00000390231:L119M	ENSP00000327197:L119M	L	+	1	2	SENP5	198096804	0.955000	0.32602	0.460000	0.27093	0.400000	0.30750	0.202000	0.17295	0.119000	0.18210	-0.294000	0.09567	CTG		0.403	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		A	196612407	C	A	196612407	3	1	61	1	0	0	0	0	1	0	0	0	14086	796	28	2	357	2	SENP5	3	196612407	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102874	196612407	1410023	3013	10998										
SENP5	205564	broad.mit.edu	37	chr3	196626619	196626619	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggaagattaaaagatgtCtttaatgaagacttttctaa	7	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:196626619C>A	ENST00000323460.5	+	3	1845	c.1596C>A	c.(1594-1596)gtC>gtA	p.V532V	SENP5_ENST00000445299.2_Silent_p.V532V|SENP5_ENST00000419026.1_Silent_p.V22V	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	532					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.V532V(1)		NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TAAAAGATGTCTTTAATGAAG	0.303																																					Ovarian(47;891 1095 11174 13858 51271)											1	Substitution - coding silent(1)	large_intestine(1)	3											68	75	73					3																	196626619		2201	4296	6497	198111016	SO:0001819	synonymous_variant	205564			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1596C>A	3.37:g.196626619C>A			198111016	B4DY82|Q96SA5	Silent	SNP	ENST00000323460.5	37	CCDS3322.1																																																																																				0.303	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		A	196626619	C	A	196626619	2	1	61	1	0	0	0	0	0	0	0	1	14086	900	32	2		2	SENP5	3	196626619	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14212	196626619	1395811	3014	10999										
KIAA0226	9711	broad.mit.edu	37	chr3	197427516	197427516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggcaatgctggtatccGaatgggagcgaatgtggctt	16	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:197427516G>A	ENST00000296343.5	-	7	1228	c.1229C>T	c.(1228-1230)tCg>tTg	p.S410L	KIAA0226_ENST00000449205.1_Missense_Mutation_p.S410L|KIAA0226_ENST00000389665.5_Missense_Mutation_p.S410L|KIAA0226_ENST00000273582.5_Missense_Mutation_p.S350L|KIAA0226_ENST00000467303.1_5'Flank	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	410	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)		p.S243L(1)|p.S350L(1)|p.S410L(1)		NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GCTGGTATCCGAATGGGAGCG	0.547																																					Esophageal Squamous(3;167 355 3763 15924)											3	Substitution - Missense(3)	large_intestine(3)	3											84	85	85					3																	197427516		2024	4179	6203	198911913	SO:0001583	missense	9711			D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1229C>T	3.37:g.197427516G>A	ENSP00000296343:p.Ser410Leu		198911913	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.606947|4.606947	0.87157|0.87157	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000273582;ENST00000296343;ENST00000389665;ENST00000447048;ENST00000449205	.|.	.|.	.|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.74756|0.74756	0.3758|0.3758	L|L	0.48642|0.48642	1.525|1.525	0.52099|0.52099	D|D	0.99994|0.99994	.|D;D;D;D;D	.|0.89917	.|1.0;0.999;0.997;1.0;0.998	.|D;D;P;D;P	.|0.91635	.|0.996;0.993;0.803;0.999;0.814	T|T	0.76225|0.76225	-0.3037|-0.3037	5|9	.|0.66056	.|D	.|0.02	.|.	17.4945|17.4945	0.87713|0.87713	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|410;243;410;350;410	.|E9PEM3;Q5HYI6;Q92622-3;Q92622-2;Q92622	.|.;.;.;.;RUBIC_HUMAN	W|L	169|350;410;410;42;410	.|.	.|ENSP00000273582:S350L	R|S	-|-	1|2	2|0	KIAA0226|KIAA0226	198911913|198911913	1.000000|1.000000	0.71417|0.71417	0.932000|0.932000	0.37286|0.37286	0.734000|0.734000	0.41952|0.41952	7.496000|7.496000	0.81526|0.81526	2.556000|2.556000	0.86216|0.86216	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.547	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197427516	G	A	197427516	3	1	61	1	0	0	0	0	1	0	0	0	8183	1059	37	1	1794	1	KIAA0226	3	197427516	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	800897	197427516	594914	3015	11000										
LRCH3	84859	broad.mit.edu	37	chr3	197541800	197541800	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtcgcgaaatcgcctttCagaaattcctatagaagcat	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:197541800C>A	ENST00000425562.2	+	2	284	c.284C>A	c.(283-285)tCa>tAa	p.S95*	LRCH3_ENST00000414675.2_Nonsense_Mutation_p.S95*|LRCH3_ENST00000441090.2_Intron|LRCH3_ENST00000334859.4_Nonsense_Mutation_p.S95*|LRCH3_ENST00000438796.2_Nonsense_Mutation_p.S95*			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	95						cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.S95*(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AATCGCCTTTCAGAAATTCCT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											43	46	45					3																	197541800		2201	4297	6498	199026197	SO:0001587	stop_gained	84859			AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.284C>A	3.37:g.197541800C>A	ENSP00000393579:p.Ser95*		199026197	B4E0T7|Q96FP9|Q9NT52	Nonsense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	C	35	5.413081	0.96072	.	.	ENSG00000186001	ENST00000438796;ENST00000414675;ENST00000334859;ENST00000425562	.	.	.	5.6	5.6	0.85130	.	0.171234	0.40144	N	0.001161	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-13.8431	19.2738	0.94021	0.0:1.0:0.0:0.0	.	.	.	.	X	95	.	ENSP00000334375:S95X	S	+	2	0	LRCH3	199026197	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.394000	0.66285	2.654000	0.90174	0.650000	0.86243	TCA		0.308	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		A	197541800	C	A	197541800	4	1	61	1	0	0	0	0	0	1	0	0	8963	838	29	2	290	2	LRCH3	3	197541800	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114284	197541800	480630	3016	11001										
LMLN	89782	broad.mit.edu	37	chr3	197701931	197701931	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttgctccctgagaaaaaGaatcttgtaaaggtatgtaa	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:197701931G>T	ENST00000330198.4	+	3	358	c.336G>T	c.(334-336)aaG>aaT	p.K112N	LMLN_ENST00000332636.5_Missense_Mutation_p.K60N|LMLN_ENST00000420910.2_Missense_Mutation_p.K112N|LMLN_ENST00000482695.1_Missense_Mutation_p.K60N	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	112					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.K112N(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CTGAGAAAAAGAATCTTGTAA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	3											63	76	72					3																	197701931		2203	4300	6503	199186328	SO:0001583	missense	89782			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.336G>T	3.37:g.197701931G>T	ENSP00000328829:p.Lys112Asn		199186328	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	G	8.592	0.884810	0.17540	.	.	ENSG00000185621	ENST00000482695;ENST00000330198;ENST00000419117;ENST00000420910;ENST00000332636	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	4.44	0.686	0.18015	.	0.229573	0.41294	D	0.000911	T	0.31199	0.0789	L	0.42245	1.32	0.09310	N	0.999993	B;B;B;B	0.33266	0.01;0.404;0.355;0.008	B;B;B;B	0.36335	0.016;0.222;0.145;0.015	T	0.16512	-1.0400	10	0.49607	T	0.09	-6.5246	5.6931	0.17841	0.6196:0.0:0.3804:0.0	.	112;60;112;60	Q96KR4;F8WCE5;F8WB28;Q96KR4-2	LMLN_HUMAN;.;.;.	N	60;112;40;112;60	ENSP00000418324:K60N;ENSP00000328829:K112N;ENSP00000390872:K40N;ENSP00000410926:K112N;ENSP00000328611:K60N	ENSP00000328829:K112N	K	+	3	2	LMLN	199186328	0.659000	0.27411	0.701000	0.30321	0.793000	0.44817	0.593000	0.23999	0.260000	0.21731	-0.355000	0.07637	AAG		0.294	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		T	197701931	G	T	197701931	3	4	61	1	0	0	0	0	1	0	0	0	8871	933	33	2	346	2	LMLN	3	197701931	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160131	197701931	320499	3017	11002										
LMLN	89782	broad.mit.edu	37	chr3	197723056	197723056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttcttaggaggaagcacGaaaacattttgattgtccag	11	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr3:197723056G>A	ENST00000330198.4	+	10	1080	c.1058G>A	c.(1057-1059)cGa>cAa	p.R353Q	RNU6-621P_ENST00000364752.1_RNA|LMLN_ENST00000332636.5_Missense_Mutation_p.R301Q|LMLN_ENST00000420910.2_Missense_Mutation_p.R353Q|LMLN_ENST00000482695.1_Missense_Mutation_p.R301Q	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	353					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R353Q(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GAGGAAGCACGAAAACATTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											94	89	91					3																	197723056		2203	4300	6503	199207453	SO:0001583	missense	89782			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.1058G>A	3.37:g.197723056G>A	ENSP00000328829:p.Arg353Gln		199207453	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694473	0.88830	.	.	ENSG00000185621	ENST00000482695;ENST00000330198;ENST00000420910;ENST00000332636	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	4.87	4.87	0.63330	.	0.146929	0.42420	D	0.000711	T	0.64416	0.2596	L	0.42581	1.335	0.58432	D	0.999995	D;D;D;D;D	0.89917	0.986;0.99;1.0;0.998;0.987	P;P;D;D;P	0.74674	0.792;0.779;0.984;0.937;0.627	T	0.63305	-0.6667	10	0.44086	T	0.13	-6.58	15.5925	0.76543	0.0:0.0:1.0:0.0	.	353;301;353;345;301	Q96KR4;F8WCE5;F8WB28;B4DR62;Q96KR4-2	LMLN_HUMAN;.;.;.;.	Q	301;353;353;301	ENSP00000418324:R301Q;ENSP00000328829:R353Q;ENSP00000410926:R353Q;ENSP00000328611:R301Q	ENSP00000328829:R353Q	R	+	2	0	LMLN	199207453	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.043000	0.71004	2.533000	0.85409	0.543000	0.68304	CGA		0.363	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197723056	G	A	197723056	3	1	61	1	0	0	0	0	1	0	0	0	8871	1058	37	1	1096	1	LMLN	3	197723056	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21125	197723056	299374	3018	11003										
ZNF141	7700	broad.mit.edu	37	chr4	367454	367454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttagacggtccacagatCggagtcaacataagaaaatt	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:367454C>T	ENST00000240499.7	+	4	1377	c.1228C>T	c.(1228-1230)Cgg>Tgg	p.R410W	ZNF141_ENST00000512994.1_Intron|ZNF141_ENST00000505939.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	410					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R410W(1)		breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						GTCCACAGATCGGAGTCAACA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	80	78					4																	367454		2203	4300	6503	357454	SO:0001583	missense	7700			L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1228C>T	4.37:g.367454C>T	ENSP00000240499:p.Arg410Trp		357454	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305295	0.60305	.	.	ENSG00000131127	ENST00000240499	T	0.07567	3.18	1.24	0.227	0.15359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08133	0.0203	N	0.20845	0.615	0.09310	N	1	D	0.65815	0.995	P	0.54706	0.759	T	0.32428	-0.9907	8	.	.	.	.	3.3488	0.07145	0.0:0.4599:0.0:0.5401	.	410	Q15928	ZN141_HUMAN	W	410	ENSP00000240499:R410W	.	R	+	1	2	ZNF141	357454	0.000000	0.05858	0.030000	0.17652	0.920000	0.55202	-0.270000	0.08584	0.591000	0.29711	0.313000	0.20887	CGG		0.388	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		T	367454	C	T	367454	3	4	61	1	0	0	0	0	1	0	0	0	17769	875	31	1	1242	1	ZNF141	4	367454	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		367454	190786822	3019	11004										
ZNF721	170960	broad.mit.edu	37	chr4	435686	435686	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgaattCtcctatgtacataaaggatt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:435686C>A	ENST00000338977.5	-	2	2582	c.2534G>T	c.(2533-2535)aGa>aTa	p.R845I	ZNF721_ENST00000511833.2_Missense_Mutation_p.R857I|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	845					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R627I(1)|p.R857I(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGTATGAATTCTCCTATGTAC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	4											60	65	63					4																	435686		2115	4246	6361	425686	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2534G>T	4.37:g.435686C>A	ENSP00000340524:p.Arg845Ile		425686	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	10.65	1.411256	0.25465	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.24908	1.83;1.83	0.499	0.499	0.16914	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38241	0.1033	M	0.76574	2.34	0.29319	N	0.86748	D;D;D	0.64830	0.979;0.994;0.993	P;P;P	0.58928	0.52;0.848;0.764	T	0.26916	-1.0089	9	0.48119	T	0.1	.	3.513	0.07714	0.4439:0.5559:1.0E-4:1.0E-4	.	845;857;857	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	I	845;857	ENSP00000340524:R845I;ENSP00000428878:R857I	ENSP00000340524:R845I	R	-	2	0	ZNF721	425686	0.000000	0.05858	0.055000	0.19348	0.613000	0.37349	-0.121000	0.10643	0.519000	0.28406	0.194000	0.17425	AGA		0.393	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	435686	C	A	435686	3	1	61	1	0	0	0	0	1	0	0	0	18161	913	32	2	205	2	ZNF721	4	435686	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68232	435686	190718590	3020	11005										
ZNF721	170960	broad.mit.edu	37	chr4	436441	436441	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttctctccagtatgaatTttcttgtgttgattcaggtc	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:436441T>G	ENST00000338977.5	-	2	1827	c.1779A>C	c.(1777-1779)aaA>aaC	p.K593N	ZNF721_ENST00000511833.2_Missense_Mutation_p.K605N|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	593					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K375N(1)|p.K605N(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						CAGTATGAATTTTCTTGTGTT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	4											168	180	176					4																	436441		2061	4224	6285	426441	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1779A>C	4.37:g.436441T>G	ENSP00000340524:p.Lys593Asn		426441	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	T	11.40	1.627596	0.28978	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.24723	1.84;1.84	1.28	-0.408	0.12381	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15739	0.0379	N	0.25485	0.75	0.25759	N	0.984965	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.18366	-1.0339	9	0.54805	T	0.06	.	5.632	0.17516	0.0:0.0:0.2714:0.7285	.	593;605;605	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	N	593;605	ENSP00000340524:K593N;ENSP00000428878:K605N	ENSP00000340524:K593N	K	-	3	2	ZNF721	426441	0.000000	0.05858	0.019000	0.16419	0.038000	0.13279	-1.741000	0.01837	-1.220000	0.02594	-1.433000	0.01084	AAA		0.393	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	436441	T	G	436441	3	3	61	1	0	0	0	0	1	0	0	0	18161	1838	64	4	960	4	ZNF721	4	436441	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	755	436441	190717835	3021	11006										
ZNF721	170960	broad.mit.edu	37	chr4	436526	436526	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgaattCtcctatgtacataaaggttt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:436526C>A	ENST00000338977.5	-	2	1742	c.1694G>T	c.(1693-1695)aGa>aTa	p.R565I	ZNF721_ENST00000511833.2_Missense_Mutation_p.R577I|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	565					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R577I(1)|p.R347I(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGTATGAATTCTCCTATGTAC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											115	127	123					4																	436526		2128	4258	6386	426526	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1694G>T	4.37:g.436526C>A	ENSP00000340524:p.Arg565Ile		426526	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	13.94	2.387985	0.42308	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.24908	1.83;1.83	1.28	1.28	0.21552	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39358	0.1075	M	0.72479	2.2	0.42561	D	0.993149	D;D;D	0.69078	0.997;0.991;0.988	P;P;P	0.58928	0.848;0.848;0.764	T	0.24835	-1.0149	9	0.46703	T	0.11	.	8.0662	0.30661	0.0:1.0:0.0:0.0	.	565;577;577	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	I	565;577	ENSP00000340524:R565I;ENSP00000428878:R577I	ENSP00000340524:R565I	R	-	2	0	ZNF721	426526	0.000000	0.05858	0.014000	0.15608	0.285000	0.27093	-0.462000	0.06704	0.672000	0.31204	0.184000	0.17185	AGA		0.403	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	436526	C	A	436526	3	1	61	1	0	0	0	0	1	0	0	0	18161	913	32	2	1045	2	ZNF721	4	436526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85	436526	190717750	3022	11007										
ZNF721	170960	broad.mit.edu	37	chr4	437366	437366	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgaattCtcctatgtttagtaagggtt	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:437366C>A	ENST00000338977.5	-	2	902	c.854G>T	c.(853-855)aGa>aTa	p.R285I	ZNF721_ENST00000511833.2_Missense_Mutation_p.R297I|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R67I(1)|p.R297I(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGTATGAATTCTCCTATGTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	4											57	62	61					4																	437366		2055	4239	6294	427366	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.854G>T	4.37:g.437366C>A	ENSP00000340524:p.Arg285Ile		427366	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	7.303	0.613463	0.14066	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.24908	1.83;1.83	1.29	0.253	0.15551	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42154	0.1190	M	0.73753	2.245	0.09310	N	1	D;D;D	0.76494	0.999;0.996;0.995	D;D;D	0.76071	0.987;0.987;0.978	T	0.21381	-1.0247	9	0.45353	T	0.12	.	2.8764	0.05632	0.0:0.4858:0.2908:0.2233	.	285;297;297	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	I	285;297	ENSP00000340524:R285I;ENSP00000428878:R297I	ENSP00000340524:R285I	R	-	2	0	ZNF721	427366	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.002000	0.12924	-0.188000	0.10499	0.194000	0.17425	AGA		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	437366	C	A	437366	3	1	61	1	0	0	0	0	1	0	0	0	18161	913	32	2	1885	2	ZNF721	4	437366	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	840	437366	190716910	3023	11008										
ZNF721	170960	broad.mit.edu	37	chr4	437785	437785	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtttctctccagtatgaatTttcttgtgttgattcaggtc	9	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:437785T>G	ENST00000338977.5	-	2	483	c.435A>C	c.(433-435)aaA>aaC	p.K145N	ZNF721_ENST00000511833.2_Missense_Mutation_p.K157N|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K157N(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						CAGTATGAATTTTCTTGTGTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											150	161	158					4																	437785		2135	4270	6405	427785	SO:0001583	missense	170960			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.435A>C	4.37:g.437785T>G	ENSP00000340524:p.Lys145Asn		427785	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	T	11.02	1.514828	0.27123	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.24723	1.84;1.84	0.75	-0.75	0.11080	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32793	0.0841	L	0.41710	1.295	0.09310	N	1	D;P;P	0.62365	0.991;0.862;0.833	D;P;P	0.76071	0.987;0.684;0.556	T	0.17319	-1.0373	9	0.66056	D	0.02	.	2.1843	0.03882	0.0:0.2684:0.322:0.4096	.	145;157;157	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	N	145;157	ENSP00000340524:K145N;ENSP00000428878:K157N	ENSP00000340524:K145N	K	-	3	2	ZNF721	427785	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-1.687000	0.01927	-0.278000	0.09180	0.172000	0.16884	AAA		0.388	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	437785	T	G	437785	3	3	61	1	0	0	0	0	1	0	0	0	18161	1838	64	4	2304	4	ZNF721	4	437785	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	419	437785	190716491	3024	11009										
PIGG	54872	broad.mit.edu	37	chr4	524241	524241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggggtattattgaagctCgttttgtttatgtctttgtc	10	4	1	1	rs369841712		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:524241C>T	ENST00000453061.2	+	11	2384	c.2278C>T	c.(2278-2280)Cgt>Tgt	p.R760C	PIGG_ENST00000504346.1_Missense_Mutation_p.R671C|PIGG_ENST00000383028.4_Missense_Mutation_p.R627C|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000310340.5_Missense_Mutation_p.R752C	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	760					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.R752C(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						TATTGAAGCTCGTTTTGTTTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											110	111	111					4																	524241		2203	4300	6503	514241	SO:0001583	missense	54872				CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"Phosphatidylinositol glycan anchor biosynthesis"	25985	protein-coding gene	gene with protein product			"phosphatidylinositol glycan, class G"			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2278C>T	4.37:g.524241C>T	ENSP00000415203:p.Arg760Cys		514241	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746023	0.89663	.	.	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028	T;T;T;T	0.12039	3.05;3.05;2.73;2.72	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.39886	0.1095	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.987;0.994	T	0.03268	-1.1054	10	0.36615	T	0.2	-16.4773	17.5138	0.87767	0.0:1.0:0.0:0.0	.	627;760;752	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	C	752;760;671;627	ENSP00000311750:R752C;ENSP00000415203:R760C;ENSP00000424800:R671C;ENSP00000372494:R627C	ENSP00000311750:R752C	R	+	1	0	PIGG	514241	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.327000	0.65881	2.804000	0.96469	0.655000	0.94253	CGT		0.368	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733		T	524241	C	T	524241	3	4	61	1	0	0	0	0	1	0	0	0	11919	884	31	1	2320	1	PIGG	4	524241	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86456	524241	190630035	3025	11010										
PIGG	54872	broad.mit.edu	37	chr4	533025	533025	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacatcgttttggtgacatCtctgcgttatcatttattta	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:533025C>A	ENST00000453061.2	+	13	2925	c.2819C>A	c.(2818-2820)tCt>tAt	p.S940Y	PIGG_ENST00000504346.1_Missense_Mutation_p.S851Y|PIGG_ENST00000383028.4_Missense_Mutation_p.S807Y|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000310340.5_Missense_Mutation_p.S932Y	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	940					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.S932Y(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						TTGGTGACATCTCTGCGTTAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											192	169	177					4																	533025		2203	4300	6503	523025	SO:0001583	missense	54872				CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"Phosphatidylinositol glycan anchor biosynthesis"	25985	protein-coding gene	gene with protein product			"phosphatidylinositol glycan, class G"			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2819C>A	4.37:g.533025C>A	ENSP00000415203:p.Ser940Tyr		523025	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.275766	0.40294	.	.	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000453065	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.91	5.91	0.95273	.	0.487180	0.22098	N	0.064645	T	0.49695	0.1572	L	0.50333	1.59	0.42899	D	0.994222	D;D;D	0.56287	0.975;0.958;0.975	P;P;P	0.56514	0.8;0.456;0.658	T	0.35895	-0.9770	10	0.02654	T	1	-15.925	17.7902	0.88550	0.0:1.0:0.0:0.0	.	807;940;932	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	Y	932;940;851;807;96	ENSP00000311750:S932Y;ENSP00000415203:S940Y;ENSP00000424800:S851Y;ENSP00000372494:S807Y	ENSP00000311750:S932Y	S	+	2	0	PIGG	523025	0.710000	0.27896	0.662000	0.29724	0.781000	0.44180	3.109000	0.50345	2.813000	0.96785	0.655000	0.94253	TCT		0.403	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733		A	533025	C	A	533025	3	1	61	1	0	0	0	0	1	0	0	0	11919	913	32	2	2869	2	PIGG	4	533025	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8784	533025	190621251	3026	11011										
WHSC1	7468	broad.mit.edu	37	chr4	1952853	1952853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccatacgaaagtgcagacGaaacacaaactgaagtatct	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:1952853G>A	ENST00000382895.3	+	12	2367	c.1936G>A	c.(1936-1938)Gaa>Aaa	p.E646K	WHSC1_ENST00000382891.5_Missense_Mutation_p.E646K|WHSC1_ENST00000508803.1_Missense_Mutation_p.E646K|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382892.2_Missense_Mutation_p.E646K|WHSC1_ENST00000382888.3_5'Flank	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	646					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.E646K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		AAGTGCAGACGAAACACAAAC	0.532			T	IGH@	MM																																		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	1	Substitution - Missense(1)	large_intestine(1)	4											126	105	112					4																	1952853		2203	4300	6503	1922651	SO:0001583	missense	7468			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.1936G>A	4.37:g.1952853G>A	ENSP00000372351:p.Glu646Lys		1922651	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.537515|4.537515	0.85917|0.85917	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895|ENST00000514329	D;D;D;D|.	0.95756|.	-3.8;-3.8;-3.8;-3.8|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Zinc finger, FYVE/PHD-type (1);|.	0.000000|.	0.64402|.	D|.	0.000016|.	T|T	0.67859|0.67859	0.2938|0.2938	L|L	0.41824|0.41824	1.3|1.3	0.80722|0.80722	D|D	1|1	D|.	0.64830|.	0.994|.	P|.	0.50537|.	0.643|.	T|T	0.61865|0.61865	-0.6975|-0.6975	10|5	0.15952|.	T|.	0.53|.	.|.	19.9832|19.9832	0.97338|0.97338	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	646|.	O96028|.	NSD2_HUMAN|.	K|Q	646|58	ENSP00000423972:E646K;ENSP00000372347:E646K;ENSP00000372348:E646K;ENSP00000372351:E646K|.	ENSP00000372347:E646K|.	E|R	+|+	1|2	0|0	WHSC1|WHSC1	1922651|1922651	1.000000|1.000000	0.71417|0.71417	0.952000|0.952000	0.39060|0.39060	0.862000|0.862000	0.49288|0.49288	7.049000|7.049000	0.76613|0.76613	2.722000|2.722000	0.93159|0.93159	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.532	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		A	1952853	G	A	1952853	3	1	61	1	0	0	0	0	1	0	0	0	17402	1059	37	1	2046	1	WHSC1	4	1952853	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1419828	1952853	189201423	3027	11012										
POLN	353497	broad.mit.edu	37	chr4	2209995	2209995	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcctttattttcattatTtatattctccattaggaaat	3	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2209995T>G	ENST00000511885.2	-	5	786	c.433A>C	c.(433-435)Aat>Cat	p.N145H	POLN_ENST00000515357.1_5'UTR|POLN_ENST00000382865.1_Missense_Mutation_p.N145H			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	145					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)	p.N145H(1)		kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TTTTCATTATTTATATTCTCC	0.284								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	4											55	58	57					4																	2209995		2199	4297	6496	2179793	SO:0001583	missense	353497			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"DNA polymerases"	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.433A>C	4.37:g.2209995T>G	ENSP00000435506:p.Asn145His		2179793	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507706	0.64410	.	.	ENSG00000130997	ENST00000511885;ENST00000382865	T;T	0.04758	3.56;3.56	5.15	0.188	0.15114	.	1.704370	0.02675	N	0.109044	T	0.09949	0.0244	L	0.29908	0.895	0.09310	N	1	D;D	0.61080	0.989;0.989	P;P	0.57283	0.817;0.781	T	0.27502	-1.0072	10	0.54805	T	0.06	-1.5738	7.0534	0.25085	0.0:0.4248:0.0:0.5752	.	145;145	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	H	145	ENSP00000435506:N145H;ENSP00000372316:N145H	ENSP00000372316:N145H	N	-	1	0	POLN	2179793	0.000000	0.05858	0.000000	0.03702	0.473000	0.32948	0.103000	0.15292	0.025000	0.15241	0.459000	0.35465	AAT		0.284	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		G	2209995	T	G	2209995	3	3	61	1	0	0	0	0	1	0	0	0	12238	1841	64	4	2357	4	POLN	4	2209995	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	257142	2209995	188944281	3028	11013										
HAUS3	79441	broad.mit.edu	37	chr4	2240461	2240461	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaagttcttgaaccaaatTttcaagttgacgatatatgt	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2240461T>G	ENST00000243706.4	-	3	1448	c.1219A>C	c.(1219-1221)Aat>Cat	p.N407H	POLN_ENST00000515357.1_Intron|HAUS3_ENST00000506763.1_Missense_Mutation_p.N407H|HAUS3_ENST00000443786.2_Missense_Mutation_p.N407H|POLN_ENST00000511885.2_Intron	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	407					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.N407H(1)		breast(3)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						TGAACCAAATTTTCAAGTTGA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	106	106					4																	2240461		2202	4299	6501	2210259	SO:0001583	missense	79441			AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"HAUS augmin-like complex subunits"	28719	protein-coding gene	gene with protein product		613430	"chromosome 4 open reading frame 15"	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.1219A>C	4.37:g.2240461T>G	ENSP00000243706:p.Asn407His		2210259	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Missense_Mutation	SNP	ENST00000243706.4	37	CCDS33941.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384454	0.61845	.	.	ENSG00000214367	ENST00000506763;ENST00000243706;ENST00000443786	T;T	0.44083	0.93;0.93	5.87	5.87	0.94306	.	0.445839	0.24016	U	0.042339	T	0.49949	0.1587	L	0.47716	1.5	0.27965	N	0.936613	P;P	0.42993	0.797;0.797	P;P	0.50617	0.646;0.646	T	0.48714	-0.9011	10	0.45353	T	0.12	-21.6335	15.4439	0.75213	0.0:0.0:0.0:1.0	.	407;407	B4DF64;Q68CZ6	.;HAUS3_HUMAN	H	407	ENSP00000243706:N407H;ENSP00000392903:N407H	ENSP00000243706:N407H	N	-	1	0	HAUS3	2210259	0.998000	0.40836	0.932000	0.37286	0.457000	0.32468	4.104000	0.57790	2.233000	0.73108	0.482000	0.46254	AAT		0.299	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511		G	2240461	T	G	2240461	3	3	61	1	0	0	0	0	1	0	0	0	6988	1841	64	4	604	4	HAUS3	4	2240461	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	30466	2240461	188913815	3029	11014										
HAUS3	79441	broad.mit.edu	37	chr4	2242484	2242484	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttgcctgatttctgaaGaatgctaaaagcttccaatt	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2242484G>T	ENST00000243706.4	-	2	419	c.190C>A	c.(190-192)Ctt>Att	p.L64I	POLN_ENST00000515357.1_Intron|HAUS3_ENST00000506763.1_Missense_Mutation_p.L64I|HAUS3_ENST00000443786.2_Missense_Mutation_p.L64I|POLN_ENST00000511885.2_Intron	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	64					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.L64I(1)		breast(3)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GATTTCTGAAGAATGCTAAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											105	102	103					4																	2242484		2203	4300	6503	2212282	SO:0001583	missense	79441			AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"HAUS augmin-like complex subunits"	28719	protein-coding gene	gene with protein product		613430	"chromosome 4 open reading frame 15"	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.190C>A	4.37:g.2242484G>T	ENSP00000243706:p.Leu64Ile		2212282	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Missense_Mutation	SNP	ENST00000243706.4	37	CCDS33941.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598743	0.87055	.	.	ENSG00000214367	ENST00000506763;ENST00000243706;ENST00000443786	T;T	0.69435	-0.4;-0.4	4.94	4.94	0.65067	.	0.000000	0.64402	U	0.000005	D	0.82628	0.5078	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84117	0.0404	10	0.51188	T	0.08	-40.6406	17.5164	0.87775	0.0:0.0:1.0:0.0	.	64;64	B4DF64;Q68CZ6	.;HAUS3_HUMAN	I	64	ENSP00000243706:L64I;ENSP00000392903:L64I	ENSP00000243706:L64I	L	-	1	0	HAUS3	2212282	1.000000	0.71417	0.724000	0.30704	0.978000	0.69477	6.161000	0.71868	2.432000	0.82394	0.561000	0.74099	CTT		0.408	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511		T	2242484	G	T	2242484	3	4	61	1	0	0	0	0	1	0	0	0	6988	942	33	2	1637	2	HAUS3	4	2242484	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2023	2242484	188911792	3030	11015										
FAM193A	8603	broad.mit.edu	37	chr4	2648550	2648550	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggatcgacgcctatgtCgacgagcaggtgagtgccac	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2648550C>T	ENST00000324666.5	+	5	780	c.429C>T	c.(427-429)gtC>gtT	p.V143V	FAM193A_ENST00000505311.1_Silent_p.V143V|FAM193A_ENST00000545951.1_Silent_p.V143V|FAM193A_ENST00000382839.3_Silent_p.V143V|FAM193A_ENST00000502458.1_Silent_p.V143V	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	143								p.V143V(1)		NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						ACGCCTATGTCGACGAGCAGG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	4											65	57	60					4																	2648550		2203	4300	6503	2618348	SO:0001819	synonymous_variant	8603			AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.429C>T	4.37:g.2648550C>T			2618348	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Silent	SNP	ENST00000324666.5	37	CCDS58875.1																																																																																				0.622	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		T	2648550	C	T	2648550	2	4	61	1	0	0	0	0	0	0	0	1	5540	871	31	1		1	FAM193A	4	2648550	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	406066	2648550	188505726	3031	11016										
SH3BP2	6452	broad.mit.edu	37	chr4	2834735	2834735	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtcctggttgtgtgggacGaaacctctaacaaagtgagg	14	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2834735G>A	ENST00000356331.5	+	12	1768	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K	SH3BP2_ENST00000503393.2_Missense_Mutation_p.E560K|SH3BP2_ENST00000511747.1_Missense_Mutation_p.E503K|SH3BP2_ENST00000435136.2_Missense_Mutation_p.E503K|SH3BP2_ENST00000442312.2_Missense_Mutation_p.E531K|SH3BP2_ENST00000452765.2_Missense_Mutation_p.E503K	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	503	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.E503K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		TGTGTGGGACGAAACCTCTAA	0.622									Cherubism																																							1	Substitution - Missense(1)	large_intestine(1)	4											160	133	142					4																	2834735		2203	4300	6503	2804533	SO:0001583	missense	6452	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.1507G>A	4.37:g.2834735G>A	ENSP00000348685:p.Glu503Lys		2804533	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	37	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.236561	0.22711	.	.	ENSG00000087266	ENST00000452765;ENST00000442312;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.73	4.02	0.46733	SH2 motif (4);	0.694983	0.15105	N	0.280274	T	0.80874	0.4707	L	0.34521	1.04	0.19300	N	0.999978	B;B;B;B	0.24618	0.107;0.025;0.078;0.052	B;B;B;B	0.20184	0.028;0.009;0.005;0.011	T	0.67669	-0.5611	10	0.34782	T	0.22	-7.6615	6.0541	0.19802	0.2215:0.1373:0.6412:0.0	.	531;478;560;503	B4DT04;Q6ZVU3;D6R919;P78314	.;.;.;3BP2_HUMAN	K	503;531;503;503;560;503	ENSP00000409746:E503K;ENSP00000388152:E531K;ENSP00000403231:E503K;ENSP00000424846:E503K;ENSP00000422168:E560K;ENSP00000348685:E503K	ENSP00000348685:E503K	E	+	1	0	SH3BP2	2804533	0.036000	0.19791	0.025000	0.17156	0.069000	0.16628	1.565000	0.36386	0.797000	0.33971	0.655000	0.94253	GAA		0.622	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		A	2834735	G	A	2834735	3	1	61	1	0	0	0	0	1	0	0	0	14282	1059	37	1	1808	1	SH3BP2	4	2834735	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186185	2834735	188319541	3032	11017										
MFSD10	10227	broad.mit.edu	37	chr4	2934340	2934340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttaccatgccttgactgCgggccagaggcgagcccagg	13	14	0	2	rs201068903		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2934340C>T	ENST00000329687.4	-	4	1052	c.518G>A	c.(517-519)cGc>cAc	p.R173H	NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000507555.1_Missense_Mutation_p.R173H|MFSD10_ENST00000355443.4_Missense_Mutation_p.R173H|MFSD10_ENST00000508221.1_Missense_Mutation_p.R173H|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000514800.1_Missense_Mutation_p.R173H|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000507999.1_RNA	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	173					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)	p.R173H(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCCTTGACTGCGGGCCAGAGG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	4											81	92	89					4																	2934340		2203	4300	6503	2904138	SO:0001583	missense	10227			L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"tetracycline transporter like protein"	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.518G>A	4.37:g.2934340C>T	ENSP00000332646:p.Arg173His		2904138	Q07706	Missense_Mutation	SNP	ENST00000329687.4	37	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184696	0.57909	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	4.7	3.86	0.44501	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.113365	0.64402	N	0.000014	T	0.72112	0.3420	M	0.86573	2.825	0.58432	D	0.999999	B;B;B;B	0.33103	0.397;0.348;0.231;0.139	B;B;B;B	0.37989	0.262;0.243;0.146;0.179	T	0.73658	-0.3913	10	0.54805	T	0.06	-15.7931	11.7742	0.51977	0.0:0.9116:0.0:0.0884	.	173;173;173;173	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	H	173	ENSP00000426907:R173H;ENSP00000347619:R173H;ENSP00000332646:R173H;ENSP00000425757:R173H;ENSP00000423402:R173H	ENSP00000332646:R173H	R	-	2	0	MFSD10	2904138	0.995000	0.38212	0.996000	0.52242	0.806000	0.45545	2.954000	0.49113	0.985000	0.38656	0.655000	0.94253	CGC		0.632	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120		T	2934340	C	T	2934340	3	4	61	1	0	0	0	0	1	0	0	0	9558	768	27	1	885	1	MFSD10	4	2934340	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99605	2934340	188219936	3033	11018										
NOP14	8602	broad.mit.edu	37	chr4	2945868	2945868	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattaataagctcaggtataAacctctgggacaaagccaca	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2945868A>C	ENST00000314262.6	-	13	1871	c.1823T>G	c.(1822-1824)tTt>tGt	p.F608C	NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000398071.4_Missense_Mutation_p.F608C|NOP14_ENST00000507120.1_5'Flank|NOP14-AS1_ENST00000507702.1_RNA|NOP14-AS1_ENST00000512712.2_RNA|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000416614.2_Missense_Mutation_p.F608C|NOP14_ENST00000502735.1_Missense_Mutation_p.F608C|NOP14-AS1_ENST00000515194.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	608					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.F608C(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CTCAGGTATAAACCTCTGGGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	4											73	71	72					4																	2945868		2203	4300	6503	2915666	SO:0001583	missense	8602			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1823T>G	4.37:g.2945868A>C	ENSP00000315674:p.Phe608Cys		2915666	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	A	19.59	3.855331	0.71719	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.66157	0.2761	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.977;0.983	T	0.74019	-0.3799	10	0.87932	D	0	-16.0	15.5419	0.76057	1.0:0.0:0.0:0.0	.	401;608;608	Q96GC8;E9PFK5;P78316	.;.;NOP14_HUMAN	C	608;608;608;608;507	ENSP00000405068:F608C;ENSP00000315674:F608C;ENSP00000427415:F608C;ENSP00000381146:F608C	ENSP00000315674:F608C	F	-	2	0	NOP14	2915666	1.000000	0.71417	0.903000	0.35520	0.693000	0.40251	8.591000	0.90824	2.078000	0.62432	0.459000	0.35465	TTT		0.468	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		C	2945868	A	C	2945868	3	2	61	1	0	0	0	0	1	0	0	0	10567	14	1	4	774	4	NOP14	4	2945868	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11528	2945868	188208408	3034	11019										
NOP14	8602	broad.mit.edu	37	chr4	2952960	2952960	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctttccaagcattcttcGaagtctctcagcctgagcag	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:2952960G>A	ENST00000314262.6	-	7	931	c.883C>T	c.(883-885)Cga>Tga	p.R295*	NOP14_ENST00000398071.4_Nonsense_Mutation_p.R295*|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000416614.2_Nonsense_Mutation_p.R295*|NOP14_ENST00000502735.1_Nonsense_Mutation_p.R295*|NOP14-AS1_ENST00000515194.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	295					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.R295*(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						AGCATTCTTCGAAGTCTCTCA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											162	153	156					4																	2952960		2203	4300	6503	2922758	SO:0001587	stop_gained	8602			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.883C>T	4.37:g.2952960G>A	ENSP00000315674:p.Arg295*		2922758	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Nonsense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	G	33	5.263216	0.95399	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	.	.	.	5.4	5.4	0.78164	.	0.242526	0.39274	N	0.001405	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.5758	16.9489	0.86239	0.0:0.0:1.0:0.0	.	.	.	.	X	295;295;295;295;194	.	ENSP00000315674:R295X	R	-	1	2	NOP14	2922758	0.999000	0.42202	0.015000	0.15790	0.494000	0.33585	4.977000	0.63792	2.533000	0.85409	0.557000	0.71058	CGA		0.483	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		A	2952960	G	A	2952960	4	1	61	1	0	0	0	0	0	1	0	0	10567	1066	37	1	1738	1	NOP14	4	2952960	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7092	2952960	188201316	3035	11020										
HTT	3064	broad.mit.edu	37	chr4	3088673	3088673	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttatttttagaaagaaaGaactttcagctaccaagaaa	5	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:3088673G>T	ENST00000355072.5	+	2	416	c.271G>T	c.(271-273)Gaa>Taa	p.E91*		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	91					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.E91*(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TAGAAAGAAAGAACTTTCAGC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											59	57	57					4																	3088673		1815	4069	5884	3058471	SO:0001587	stop_gained	3064			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.271G>T	4.37:g.3088673G>T	ENSP00000347184:p.Glu91*		3058471	Q9UQB7	Nonsense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	38	7.143070	0.98092	.	.	ENSG00000197386	ENST00000355072	.	.	.	5.35	5.35	0.76521	.	0.094927	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.0226	0.92921	0.0:0.0:1.0:0.0	.	.	.	.	X	91	.	ENSP00000347184:E91X	E	+	1	0	HTT	3058471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.893000	0.87330	2.647000	0.89833	0.655000	0.94253	GAA		0.353	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3088673	G	T	3088673	4	4	61	1	0	0	0	0	0	1	0	0	7478	943	33	2	277	2	HTT	4	3088673	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135713	3088673	188065603	3036	11021										
HTT	3064	broad.mit.edu	37	chr4	3176738	3176738	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagctttaaaacagtacacGactacaacatgtgtgcagtt	7	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:3176738G>A	ENST00000355072.5	+	33	4456	c.4311G>A	c.(4309-4311)acG>acA	p.T1437T		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1437	Poly-Thr.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.T1437T(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AACAGTACACGACTACAACAT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	4											124	109	113					4																	3176738		1838	4090	5928	3146536	SO:0001819	synonymous_variant	3064			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.4311G>A	4.37:g.3176738G>A			3146536	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																				0.348	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3176738	G	A	3176738	2	1	61	1	0	0	0	0	0	0	0	1	7478	1045	37	1		1	HTT	4	3176738	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88065	3176738	187977538	3037	11022										
HTT	3064	broad.mit.edu	37	chr4	3182271	3182271	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgcagcccatagtccacGacctctttgtattaagagga	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:3182271G>A	ENST00000355072.5	+	36	4787	c.4642G>A	c.(4642-4644)Gac>Aac	p.D1548N		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1548					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.D1548N(2)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CATAGTCCACGACCTCTTTGT	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	4											99	99	99					4																	3182271		1880	4100	5980	3152069	SO:0001583	missense	3064			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.4642G>A	4.37:g.3182271G>A	ENSP00000347184:p.Asp1548Asn		3152069	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	36	5.732026	0.96856	.	.	ENSG00000197386	ENST00000355072	T	0.06294	3.32	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.21186	0.0510	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00028	-1.2298	10	0.45353	T	0.12	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1548	P42858	HD_HUMAN	N	1548	ENSP00000347184:D1548N	ENSP00000347184:D1548N	D	+	1	0	HTT	3152069	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	9.858000	0.99539	2.884000	0.98904	0.655000	0.94253	GAC		0.443	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3182271	G	A	3182271	3	1	61	1	0	0	0	0	1	0	0	0	7478	1058	37	1	4784	1	HTT	4	3182271	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5533	3182271	187972005	3038	11023										
OTOP1	133060	broad.mit.edu	37	chr4	4199541	4199541	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgccgactcgctcttggtCttggagcgcccaatatgaat	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:4199541C>A	ENST00000296358.4	-	5	1044	c.1020G>T	c.(1018-1020)aaG>aaT	p.K340N		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	340					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.K340N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CGCTCTTGGTCTTGGAGCGCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	4											50	49	49					4																	4199541		2203	4300	6503	4250442	SO:0001583	missense	133060			BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1020G>T	4.37:g.4199541C>A	ENSP00000296358:p.Lys340Asn		4250442	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	C	8.458	0.854726	0.17106	.	.	ENSG00000163982	ENST00000296358	T	0.23147	1.92	4.8	-0.22	0.13130	.	0.682474	0.14445	N	0.319180	T	0.40067	0.1102	L	0.57536	1.79	0.28810	N	0.898294	D	0.65815	0.995	D	0.65874	0.939	T	0.31110	-0.9955	10	0.35671	T	0.21	0.4019	10.5817	0.45259	0.0:0.4722:0.0:0.5278	.	340	Q7RTM1	OTOP1_HUMAN	N	340	ENSP00000296358:K340N	ENSP00000296358:K340N	K	-	3	2	OTOP1	4250442	0.000000	0.05858	0.252000	0.24328	0.190000	0.23558	-0.420000	0.07062	-0.372000	0.07992	0.404000	0.27445	AAG		0.582	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4199541	C	A	4199541	3	1	61	1	0	0	0	0	1	0	0	0	11336	912	32	2	826	2	OTOP1	4	4199541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1017270	4199541	186954735	3039	11024										
OTOP1	133060	broad.mit.edu	37	chr4	4199685	4199685	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgtcaactttgcgcccGatgttcttccacaggacgta	10	12	2	0	rs373873960		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:4199685G>A	ENST00000296358.4	-	5	900	c.876C>T	c.(874-876)atC>atT	p.I292I		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	292					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.I292I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTTTGCGCCCGATGTTCTTCC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	4											76	68	71					4																	4199685		2203	4300	6503	4250586	SO:0001819	synonymous_variant	133060			BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.876C>T	4.37:g.4199685G>A			4250586	A1L476	Silent	SNP	ENST00000296358.4	37	CCDS3372.1																																																																																				0.567	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4199685	G	A	4199685	2	1	61	1	0	0	0	0	0	0	0	1	11336	1048	37	1		1	OTOP1	4	4199685	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144	4199685	186954591	3040	11025										
LYAR	55646	broad.mit.edu	37	chr4	4281195	4281195	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttggaagcttcagaaaaGatattccacacctggtccag	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:4281195G>T	ENST00000343470.4	-	6	648	c.408C>A	c.(406-408)atC>atA	p.I136I	LYAR_ENST00000452476.1_Silent_p.I136I	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	136						nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.I136I(1)		endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTTCAGAAAAGATATTCCACA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											62	62	62					4																	4281195		2203	4300	6503	4332096	SO:0001819	synonymous_variant	55646			AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.408C>A	4.37:g.4281195G>T			4332096	D3DVS4|Q6FI78|Q9NYS1	Silent	SNP	ENST00000343470.4	37	CCDS3374.1																																																																																				0.318	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		T	4281195	G	T	4281195	2	4	61	1	0	0	0	0	0	0	0	1	9133	932	33	2		2	LYAR	4	4281195	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81510	4281195	186873081	3041	11026										
STX18	53407	broad.mit.edu	37	chr4	4426931	4426931	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcatttcaccaattagtcGctgattttcctgttcaaact	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:4426931G>A	ENST00000306200.2	-	8	784	c.721C>T	c.(721-723)Cga>Tga	p.R241*	STX18_ENST00000505286.1_Nonsense_Mutation_p.R241*	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	241					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R241*(1)		large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		CCAATTAGTCGCTGATTTTCC	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											150	124	133					4																	4426931		2203	4300	6503	4477832	SO:0001587	stop_gained	53407			AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.721C>T	4.37:g.4426931G>A	ENSP00000305810:p.Arg241*		4477832	Q596L3|Q5TZP5	Nonsense_Mutation	SNP	ENST00000306200.2	37	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658307	0.88154	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	.	.	.	5.3	4.37	0.52481	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-0.0885	14.9737	0.71254	0.0:0.0:0.7837:0.2163	.	.	.	.	X	241;241;160;160	.	ENSP00000305810:R241X	R	-	1	2	STX18	4477832	1.000000	0.71417	0.996000	0.52242	0.592000	0.36648	2.298000	0.43602	2.478000	0.83669	0.563000	0.77884	CGA		0.443	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			A	4426931	G	A	4426931	4	1	61	1	0	0	0	0	0	1	0	0	15380	1095	38	1	302	1	STX18	4	4426931	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	145736	4426931	186727345	3042	11027										
EVC2	132884	broad.mit.edu	37	chr4	5630288	5630288	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagtgttgagtggtacctCtcgtgcttctgaatgaggtg	14	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:5630288C>A	ENST00000344408.5	-	12	1937	c.1884G>T	c.(1882-1884)gaG>gaT	p.E628D	EVC2_ENST00000310917.2_Missense_Mutation_p.E548D|EVC2_ENST00000344938.1_Missense_Mutation_p.E628D	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	628					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E628D(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AGTGGTACCTCTCGTGCTTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	89	95					4																	5630288		2203	4300	6503	5681189	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1884G>T	4.37:g.5630288C>A	ENSP00000342144:p.Glu628Asp		5681189	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464796	0.43736	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.79352	-1.26;-1.26;-1.26	4.27	4.27	0.50696	.	0.062767	0.64402	D	0.000004	D	0.84392	0.5462	M	0.69823	2.125	0.39625	D	0.970096	D	0.71674	0.998	D	0.69654	0.965	D	0.84752	0.0757	10	0.46703	T	0.11	-20.5636	9.7417	0.40422	0.0:0.8924:0.0:0.1076	.	628	Q86UK5	LBN_HUMAN	D	628;548;628	ENSP00000339954:E628D;ENSP00000311683:E548D;ENSP00000342144:E628D	ENSP00000311683:E548D	E	-	3	2	EVC2	5681189	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	2.449000	0.44935	2.374000	0.81015	0.484000	0.47621	GAG		0.502	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5630288	C	A	5630288	3	1	61	1	0	0	0	0	1	0	0	0	5299	912	32	2	2086	2	EVC2	4	5630288	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1203357	5630288	185523988	3043	11028										
CRMP1	1400	broad.mit.edu	37	chr4	5851133	5851133	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacctgagctatcaaatCtccattttctgcatggacca	5	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:5851133C>A	ENST00000397890.2	-	6	821	c.607G>T	c.(607-609)Gat>Tat	p.D203Y	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Missense_Mutation_p.D201Y|CRMP1_ENST00000324989.7_Missense_Mutation_p.D317Y	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	203					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.D317Y(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		GCTATCAAATCTCCATTTTCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	93	95					4																	5851133		2203	4300	6503	5902034	SO:0001583	missense	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.607G>T	4.37:g.5851133C>A	ENSP00000380987:p.Asp203Tyr		5902034	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927565	0.73327	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.90197	-2.63;-2.63;-2.63	4.88	4.88	0.63580	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	M	0.86178	2.8	0.80722	D	1	D;D;D;D	0.89917	0.997;0.993;1.0;1.0	P;P;D;D	0.75484	0.878;0.707;0.97;0.986	D	0.96234	0.9170	10	0.87932	D	0	-16.7637	17.2084	0.86924	0.0:1.0:0.0:0.0	.	317;201;203;140	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	Y	317;203;203;201	ENSP00000321606:D317Y;ENSP00000380987:D203Y;ENSP00000425742:D201Y	ENSP00000321606:D317Y	D	-	1	0	CRMP1	5902034	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.165000	0.77544	2.540000	0.85666	0.603000	0.83216	GAT		0.443	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5851133	C	A	5851133	3	1	61	1	0	0	0	0	1	0	0	0	3896	913	32	2	1147	2	CRMP1	4	5851133	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220845	5851133	185303143	3044	11029										
JAKMIP1	152789	broad.mit.edu	37	chr4	6066618	6066618	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcttacatcgtccaagtCttcttcgggcgtggctgggg	13	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:6066618C>A	ENST00000282924.5	-	9	1905	c.1420G>T	c.(1420-1422)Gac>Tac	p.D474Y	JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.D474Y|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.D474Y|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.D289Y|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.D309Y	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	474	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)	p.D474Y(1)		NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCGTCCAAGTCTTCTTCGGGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	4											163	136	145					4																	6066618		2203	4300	6503	6117519	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1420G>T	4.37:g.6066618C>A	ENSP00000282924:p.Asp474Tyr		6117519	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524736	0.85600	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.39997	1.59;1.05;1.56;1.56;1.15	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000001	T	0.65770	0.2723	M	0.77313	2.365	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.998;0.998;0.999	T	0.71826	-0.4475	10	0.87932	D	0	.	16.0347	0.80617	0.0:1.0:0.0:0.0	.	309;474;289;474;474	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Y	474;289;474;366;474;474;309	ENSP00000386711:D474Y;ENSP00000387042:D289Y;ENSP00000282924:D474Y;ENSP00000386925:D474Y;ENSP00000386745:D309Y	ENSP00000282924:D474Y	D	-	1	0	JAKMIP1	6117519	1.000000	0.71417	0.975000	0.42487	0.982000	0.71751	7.140000	0.77322	2.202000	0.70862	0.561000	0.74099	GAC		0.537	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		A	6066618	C	A	6066618	3	1	61	1	0	0	0	0	1	0	0	0	7961	913	32	2	1202	2	JAKMIP1	4	6066618	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	215485	6066618	185087658	3045	11030										
KIAA0232	9778	broad.mit.edu	37	chr4	6864235	6864235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttctaatctttcaacaaGaacttgtagtccatggtccc	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:6864235G>T	ENST00000307659.5	+	7	2581	c.2126G>T	c.(2125-2127)aGa>aTa	p.R709I	KIAA0232_ENST00000425103.1_Missense_Mutation_p.R709I	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	709							ATP binding (GO:0005524)	p.R709I(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						CTTTCAACAAGAACTTGTAGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											66	61	62					4																	6864235		1840	4090	5930	6915136	SO:0001583	missense	9778			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.2126G>T	4.37:g.6864235G>T	ENSP00000303928:p.Arg709Ile		6915136	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	37	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.362386	0.82353	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.79452	0.4448	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80254	-0.1459	9	0.87932	D	0	-24.0831	19.8991	0.96978	0.0:0.0:1.0:0.0	.	709	Q92628	K0232_HUMAN	I	709	.	ENSP00000303928:R709I	R	+	2	0	KIAA0232	6915136	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.306000	0.96204	2.708000	0.92522	0.655000	0.94253	AGA		0.348	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		T	6864235	G	T	6864235	3	4	61	1	0	0	0	0	1	0	0	0	8184	942	33	2	2144	2	KIAA0232	4	6864235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	797617	6864235	184290041	3046	11031										
KIAA0232	9778	broad.mit.edu	37	chr4	6864327	6864327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccacacagtttaatgccGaagatattaattatgtagtt	6	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:6864327G>A	ENST00000307659.5	+	7	2673	c.2218G>A	c.(2218-2220)Gaa>Aaa	p.E740K	KIAA0232_ENST00000425103.1_Missense_Mutation_p.E740K	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	740							ATP binding (GO:0005524)	p.E740K(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						GTTTAATGCCGAAGATATTAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	58	59					4																	6864327		1828	4075	5903	6915228	SO:0001583	missense	9778			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.2218G>A	4.37:g.6864327G>A	ENSP00000303928:p.Glu740Lys		6915228	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	37	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.694496	0.68386	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.64	5.64	0.86602	.	0.254585	0.44902	N	0.000420	T	0.58736	0.2143	M	0.64997	1.995	0.80722	D	1	D	0.53151	0.958	B	0.40410	0.328	T	0.66555	-0.5894	9	0.72032	D	0.01	-14.9145	19.6918	0.96005	0.0:0.0:1.0:0.0	.	740	Q92628	K0232_HUMAN	K	740	.	ENSP00000303928:E740K	E	+	1	0	KIAA0232	6915228	1.000000	0.71417	0.979000	0.43373	0.968000	0.65278	9.386000	0.97228	2.660000	0.90430	0.591000	0.81541	GAA		0.343	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		A	6864327	G	A	6864327	3	1	61	1	0	0	0	0	1	0	0	0	8184	1059	37	1	2236	1	KIAA0232	4	6864327	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92	6864327	184289949	3047	11032										
KIAA0232	9778	broad.mit.edu	37	chr4	6864665	6864665	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgatgctgagttgttttcGgcagatgtaaataactactg	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:6864665G>A	ENST00000307659.5	+	7	3011	c.2556G>A	c.(2554-2556)tcG>tcA	p.S852S	KIAA0232_ENST00000425103.1_Silent_p.S852S	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	852							ATP binding (GO:0005524)	p.S852S(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						AGTTGTTTTCGGCAGATGTAA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	4											67	69	68					4																	6864665		1989	4191	6180	6915566	SO:0001819	synonymous_variant	9778			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.2556G>A	4.37:g.6864665G>A			6915566	A7E2D2	Silent	SNP	ENST00000307659.5	37	CCDS43209.1																																																																																				0.453	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		A	6864665	G	A	6864665	2	1	61	1	0	0	0	0	0	0	0	1	8184	1103	39	1		1	KIAA0232	4	6864665	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	338	6864665	184289611	3048	11033										
CCDC96	257236	broad.mit.edu	37	chr4	7043265	7043265	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctagggcggcctgggcctcGatttctgccagctgtgtctt	13	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:7043265G>A	ENST00000310085.4	-	1	1463	c.1401C>T	c.(1399-1401)atC>atT	p.I467I	RP11-367J11.2_ENST00000500031.1_RNA|TADA2B_ENST00000512388.1_5'Flank|TADA2B_ENST00000310074.7_5'Flank	NM_153376.2	NP_699207.1	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96	467								p.I467I(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11						CCTGGGCCTCGATTTCTGCCA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	4											214	212	213					4																	7043265		2203	4300	6503	7094166	SO:0001819	synonymous_variant	257236			AK075056	CCDS3395.1	4p16.1	2008-02-05			ENSG00000173013	ENSG00000173013			26900	protein-coding gene	gene with protein product							Standard	NM_153376		Approved	FLJ90575	uc003gjv.2	Q2M329	OTTHUMG00000125511	ENST00000310085.4:c.1401C>T	4.37:g.7043265G>A			7094166	Q8N2I7	Silent	SNP	ENST00000310085.4	37	CCDS3395.1																																																																																				0.552	CCDC96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246838.1	NM_153376		A	7043265	G	A	7043265	2	1	61	1	0	0	0	0	0	0	0	1	2880	1048	37	1		1	CCDC96	4	7043265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178600	7043265	184111011	3049	11034										
SORCS2	57537	broad.mit.edu	37	chr4	7398032	7398032	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtgatcttgatcctgacGaagtactaccacgcagacat	9	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:7398032G>A	ENST00000507866.2	+	2	607	c.498G>A	c.(496-498)acG>acA	p.T166T	SORCS2_ENST00000329016.9_5'UTR|SORCS2_ENST00000511199.1_3'UTR	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	166					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.T16T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGATCCTGACGAAGTACTACC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	4											125	121	122					4																	7398032		2002	4178	6180	7448933	SO:0001819	synonymous_variant	57537			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.498G>A	4.37:g.7398032G>A			7448933	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																				0.512	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		A	7398032	G	A	7398032	2	1	61	1	0	0	0	0	0	0	0	1	14968	1045	37	1		1	SORCS2	4	7398032	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	354767	7398032	183756244	3050	11035										
SORCS2	57537	broad.mit.edu	37	chr4	7717037	7717037	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacctacaccagcagccttGggtgagtgtgggtgcgggcc	16	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:7717037G>T	ENST00000507866.2	+	17	2360	c.2251G>T	c.(2251-2253)Ggg>Tgg	p.G751W	SORCS2_ENST00000329016.9_Splice_Site_p.G579W	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	751					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.G601W(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						CAGCAGCCTTGGGTGAGTGTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	75	73					4																	7717037		1995	4148	6143	7767937	SO:0001630	splice_region_variant	57537			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2252+1G>T	4.37:g.7717037G>T			7767937	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970346	0.74246	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.35421	1.31;1.43	3.71	3.71	0.42584	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.65790	0.2725	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75747	-0.3209	10	0.87932	D	0	.	16.0467	0.80725	0.0:0.0:1.0:0.0	.	579;751	B5MED8;Q96PQ0	.;SORC2_HUMAN	W	751;579	ENSP00000422185:G751W;ENSP00000329124:G579W	ENSP00000329124:G579W	G	+	1	0	SORCS2	7767937	1.000000	0.71417	0.991000	0.47740	0.845000	0.48019	7.655000	0.83696	2.064000	0.61679	0.655000	0.94253	GGG		0.627	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	Missense_Mutation	T	7717037	G	T	7717037	5	4	61	1	0	0	0	0	0	0	1	0	14968	1362	47	2	2317	2	SORCS2	4	7717037	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	319005	7717037	183437239	3051	11036										
HTRA3	94031	broad.mit.edu	37	chr4	8305989	8305989	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtgcaagaggttgcgccGaattcaccttctcagaggta	11	9	2	2	rs145508993		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:8305989G>A	ENST00000307358.2	+	8	1383	c.1179G>A	c.(1177-1179)ccG>ccA	p.P393P		NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	393	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.P393P(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						AGGTTGCGCCGAATTCACCTT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	4						A		1,4405	825.8+/-416.5	0,1,2202	68	68	68		1179	-9.1	0	4	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous	HTRA3	NM_053044.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		393/454	8305989	1,13005	2203	4300	6503	8356889	SO:0001819	synonymous_variant	94031			AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.1179G>A	4.37:g.8305989G>A			8356889	Q7Z7A2	Silent	SNP	ENST00000307358.2	37	CCDS3400.1																																																																																				0.597	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044		A	8305989	G	A	8305989	2	1	61	1	0	0	0	0	0	0	0	1	7476	1045	37	1		1	HTRA3	4	8305989	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	588952	8305989	182848287	3052	11037										
DRD5	1816	broad.mit.edu	37	chr4	9784494	9784494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcgcagcctgcgcgcccGacaccagcctgcgcgcttcc	12	20	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:9784494G>A	ENST00000304374.2	+	1	1237	c.841G>A	c.(841-843)Gac>Aac	p.D281N		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	281					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.D281N(2)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CTGCGCGCCCGACACCAGCCT	0.632																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											27	26	27					4																	9784494		2145	4237	6382	9393592	SO:0001583	missense	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.841G>A	4.37:g.9784494G>A	ENSP00000306129:p.Asp281Asn		9393592	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	9.675	1.147721	0.21288	.	.	ENSG00000169676	ENST00000304374	T	0.65916	-0.18	4.31	1.39	0.22231	GPCR, rhodopsin-like superfamily (1);	0.240475	0.41605	N	0.000850	T	0.41026	0.1141	N	0.21448	0.665	0.09310	N	1	B	0.26400	0.148	B	0.24541	0.054	T	0.18272	-1.0342	10	0.22109	T	0.4	.	8.0537	0.30593	0.1046:0.5317:0.3636:0.0	.	281	P21918	DRD5_HUMAN	N	281	ENSP00000306129:D281N	ENSP00000306129:D281N	D	+	1	0	DRD5	9393592	0.976000	0.34144	0.001000	0.08648	0.568000	0.35870	2.185000	0.42584	0.420000	0.25954	0.305000	0.20034	GAC		0.632	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			A	9784494	G	A	9784494	3	1	61	1	0	0	0	0	1	0	0	0	4771	1058	37	1	843	1	DRD5	4	9784494	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1478505	9784494	181369782	3053	11038										
DRD5	1816	broad.mit.edu	37	chr4	9784902	9784902	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatccacatgatgcccaacGccgttacccccggcaaccgg	8	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:9784902G>A	ENST00000304374.2	+	1	1645	c.1249G>A	c.(1249-1251)Gcc>Acc	p.A417T		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	417					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.A417T(2)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GATGCCCAACGCCGTTACCCC	0.557																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											92	77	82					4																	9784902		2203	4300	6503	9394000	SO:0001583	missense	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1249G>A	4.37:g.9784902G>A	ENSP00000306129:p.Ala417Thr		9394000	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	11.36	1.616362	0.28801	.	.	ENSG00000169676	ENST00000304374	T	0.66638	-0.22	4.84	4.84	0.62591	.	0.383933	0.25197	N	0.032419	T	0.59514	0.2199	L	0.52126	1.63	0.39639	D	0.970296	D	0.52996	0.957	B	0.38194	0.267	T	0.64728	-0.6339	10	0.33940	T	0.23	.	17.1374	0.86743	0.0:0.0:1.0:0.0	.	417	P21918	DRD5_HUMAN	T	417	ENSP00000306129:A417T	ENSP00000306129:A417T	A	+	1	0	DRD5	9394000	1.000000	0.71417	0.012000	0.15200	0.019000	0.09904	9.202000	0.95026	2.515000	0.84797	0.460000	0.39030	GCC		0.557	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			A	9784902	G	A	9784902	3	1	61	1	0	0	0	0	1	0	0	0	4771	1087	38	1	1251	1	DRD5	4	9784902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	408	9784902	181369374	3054	11039										
DRD5	1816	broad.mit.edu	37	chr4	9785072	9785072	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaataacacctttcaccccGaatggattccattaaactgc	4	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:9785072G>A	ENST00000304374.2	+	1	1815	c.1419G>A	c.(1417-1419)ccG>ccA	p.P473P		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	473					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.P473P(2)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CTTTCACCCCGAATGGATTCC	0.488																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	4											28	30	29					4																	9785072		2203	4300	6503	9394170	SO:0001819	synonymous_variant	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1419G>A	4.37:g.9785072G>A			9394170	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																				0.488	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			A	9785072	G	A	9785072	2	1	61	1	0	0	0	0	0	0	0	1	4771	1045	37	1		1	DRD5	4	9785072	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170	9785072	181369204	3055	11040										
SLC2A9	56606	broad.mit.edu	37	chr4	9828169	9828169	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacaaaatacaggtagataGcacctgtgatacaaattgta	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:9828169G>A	ENST00000264784.3	-	12	1528	c.1475C>T	c.(1474-1476)gCt>gTt	p.A492V	SLC2A9_ENST00000506583.1_Missense_Mutation_p.A463V|SLC2A9_ENST00000309065.3_Missense_Mutation_p.A463V	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	492					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)	p.A463V(1)|p.A492V(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	CAGGTAGATAGCACCTGTGAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	4											112	105	107					4																	9828169		2203	4300	6503	9437267	SO:0001583	missense	56606			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"Solute carriers"	13446	protein-coding gene	gene with protein product	"urate voltage-driven efflux transporter 1"	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.1475C>T	4.37:g.9828169G>A	ENSP00000264784:p.Ala492Val		9437267	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.465497	0.63513	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.42131	0.98;0.98;0.98	6.16	5.29	0.74685	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.250222	0.40385	N	0.001109	T	0.52533	0.1740	L	0.38838	1.175	0.36367	D	0.861073	D;D	0.63046	0.99;0.992	P;D	0.65773	0.897;0.938	T	0.54708	-0.8253	10	0.41790	T	0.15	.	15.447	0.75238	0.0:0.1385:0.8615:0.0	.	463;492	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	V	463;492;463	ENSP00000422209:A463V;ENSP00000264784:A492V;ENSP00000311383:A463V	ENSP00000264784:A492V	A	-	2	0	SLC2A9	9437267	1.000000	0.71417	0.789000	0.31954	0.238000	0.25445	5.750000	0.68712	2.937000	0.99478	0.650000	0.86243	GCT		0.413	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			A	9828169	G	A	9828169	3	1	61	1	0	0	0	0	1	0	0	0	14589	971	34	3	151	3	SLC2A9	4	9828169	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43097	9828169	181326107	3056	11041										
SLC2A9	56606	broad.mit.edu	37	chr4	10023029	10023029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactaggcccagttccttggAattcctattttgtttccttg	7	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:10023029A>G	ENST00000264784.3	-	1	78	c.25T>C	c.(25-27)Tcc>Ccc	p.S9P	SLC2A9_ENST00000506583.1_Intron|SLC2A9_ENST00000309065.3_Intron	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	9					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)	p.S9P(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	AGTTCCTTGGAATTCCTATTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	4											147	164	159					4																	10023029		2203	4300	6503	9632127	SO:0001583	missense	56606			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"Solute carriers"	13446	protein-coding gene	gene with protein product	"urate voltage-driven efflux transporter 1"	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.25T>C	4.37:g.10023029A>G	ENSP00000264784:p.Ser9Pro		9632127	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.005360	0.54254	.	.	ENSG00000109667	ENST00000264784	D	0.82255	-1.59	4.5	-2.83	0.05769	Major facilitator superfamily domain, general substrate transporter (1);	.	.	.	.	T	0.59838	0.2223	N	0.08118	0	0.19575	N	0.999963	B	0.06786	0.001	B	0.04013	0.001	T	0.43845	-0.9366	8	.	.	.	.	5.3465	0.16012	0.4131:0.1683:0.4186:0.0	.	9	Q9NRM0	GTR9_HUMAN	P	9	ENSP00000264784:S9P	.	S	-	1	0	SLC2A9	9632127	0.000000	0.05858	0.006000	0.13384	0.071000	0.16799	-0.272000	0.08560	-0.546000	0.06216	-0.408000	0.06270	TCC		0.602	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			G	10023029	A	G	10023029	3	3	61	1	0	0	0	0	1	0	0	0	14589	246	9	4	1645	4	SLC2A9	4	10023029	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	194860	10023029	181131247	3057	11042										
ZNF518B	85460	broad.mit.edu	37	chr4	10447310	10447310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccgtttcgcacctgcccTttcatgtactctcttcgtgt	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:10447310T>C	ENST00000326756.3	-	3	1081	c.643A>G	c.(643-645)Agg>Ggg	p.R215G		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	215					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R215G(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GCACCTGCCCTTTCATGTACT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											187	193	191					4																	10447310		2203	4300	6503	10056408	SO:0001583	missense	85460			AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.643A>G	4.37:g.10447310T>C	ENSP00000317614:p.Arg215Gly		10056408	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867454	0.51588	.	.	ENSG00000178163	ENST00000326756	T	0.01725	4.67	6.16	0.742	0.18341	.	0.610149	0.15116	N	0.279666	T	0.01287	0.0042	N	0.19112	0.55	0.26741	N	0.970387	P	0.43094	0.799	B	0.35550	0.205	T	0.52990	-0.8501	10	0.29301	T	0.29	-14.0701	10.8825	0.46946	0.0:0.0684:0.5823:0.3493	.	215	Q9C0D4	Z518B_HUMAN	G	215	ENSP00000317614:R215G	ENSP00000317614:R215G	R	-	1	2	ZNF518B	10056408	0.274000	0.24191	0.990000	0.47175	0.911000	0.54048	0.341000	0.19909	-0.101000	0.12219	0.528000	0.53228	AGG		0.428	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		C	10447310	T	C	10447310	3	2	61	1	0	0	0	0	1	0	0	0	18002	1608	56	4	2585	4	ZNF518B	4	10447310	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	424281	10447310	180706966	3058	11043										
CLNK	116449	broad.mit.edu	37	chr4	10492210	10492210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaaattcttgtagtgttCgatgatgtcttctactgaat	10	5	3	2	rs375814264		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:10492210C>T	ENST00000226951.6	-	19	1407	c.1168G>A	c.(1168-1170)Gaa>Aaa	p.E390K	CLNK_ENST00000515667.1_Missense_Mutation_p.E128K	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	390	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)	p.E390K(2)		NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TTGTAGTGTTCGATGATGTCT	0.378																																					GBM(87;402 1286 6949 13902 35851)											2	Substitution - Missense(2)	large_intestine(2)	4											89	91	90					4																	10492210		1893	4112	6005	10101308	SO:0001583	missense	116449			AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.1168G>A	4.37:g.10492210C>T	ENSP00000226951:p.Glu390Lys		10101308	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301462	0.81136	.	.	ENSG00000109684	ENST00000226951;ENST00000515667;ENST00000429087	D;D	0.89123	-2.47;-2.47	4.93	4.07	0.47477	SH2 motif (5);	0.530249	0.18837	N	0.129797	D	0.88020	0.6325	L	0.46567	1.45	0.80722	D	1	D	0.57899	0.981	P	0.50896	0.653	D	0.85876	0.1419	10	0.39692	T	0.17	-16.2797	11.2142	0.48817	0.0:0.7925:0.2075:0.0	.	390	Q7Z7G1	CLNK_HUMAN	K	390;128;354	ENSP00000226951:E390K;ENSP00000427256:E128K	ENSP00000226951:E390K	E	-	1	0	CLNK	10101308	0.989000	0.36119	0.992000	0.48379	0.988000	0.76386	2.881000	0.48538	1.166000	0.42689	0.655000	0.94253	GAA		0.378	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		T	10492210	C	T	10492210	3	4	61	1	0	0	0	0	1	0	0	0	3553	893	31	1	122	1	CLNK	4	10492210	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44900	10492210	180662066	3059	11044										
CLNK	116449	broad.mit.edu	37	chr4	10566357	10566357	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagatagaggtcctggtgtCtaacggaaggggagtgtcca	17	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:10566357C>A	ENST00000226951.6	-	7	576	c.337G>T	c.(337-339)Gac>Tac	p.D113Y	CLNK_ENST00000442825.2_Missense_Mutation_p.D71Y|CLNK_ENST00000507719.1_Missense_Mutation_p.D71Y	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	113					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)	p.D113Y(2)		NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						GTCCTGGTGTCTAACGGAAGG	0.438																																					GBM(87;402 1286 6949 13902 35851)											2	Substitution - Missense(2)	large_intestine(2)	4											213	199	203					4																	10566357		1978	4145	6123	10175455	SO:0001583	missense	116449			AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.337G>T	4.37:g.10566357C>A	ENSP00000226951:p.Asp113Tyr		10175455	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.324764	0.41197	.	.	ENSG00000109684	ENST00000226951;ENST00000429087;ENST00000442825;ENST00000507719	T;T;T	0.52983	1.72;0.64;0.64	5.39	0.0355	0.14188	.	1.774740	0.02936	N	0.139858	T	0.46328	0.1387	L	0.32530	0.975	0.09310	N	1	B;D	0.62365	0.1;0.991	B;P	0.55161	0.046;0.77	T	0.19289	-1.0310	10	0.41790	T	0.15	0.0773	1.0056	0.01486	0.2575:0.3366:0.2314:0.1746	.	71;113	Q7Z7G1-2;Q7Z7G1	.;CLNK_HUMAN	Y	113;113;71;71	ENSP00000226951:D113Y;ENSP00000390744:D71Y;ENSP00000427208:D71Y	ENSP00000226951:D113Y	D	-	1	0	CLNK	10175455	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.393000	0.07305	-0.285000	0.09089	-0.151000	0.13558	GAC		0.438	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		A	10566357	C	A	10566357	3	1	61	1	0	0	0	0	1	0	0	0	3553	913	32	2	1001	2	CLNK	4	10566357	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74147	10566357	180587919	3060	11045										
HS3ST1	9957	broad.mit.edu	37	chr4	11400771	11400771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggctcatgaaaatattCgtgcagtttattgagtagtt	9	4	1	2	rs370389171		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:11400771C>T	ENST00000002596.5	-	2	2033	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	287					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)	p.E287K(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TGAAAATATTCGTGCAGTTTA	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	4						C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	81	84	83		859	5.5	0.9	4		83	0,8600		0,0,4300	no	missense	HS3ST1	NM_005114.2	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	287/308	11400771	1,13005	2203	4300	6503	11009869	SO:0001583	missense	9957			AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.859G>A	4.37:g.11400771C>T	ENSP00000002596:p.Glu287Lys		11009869	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	37	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	C	5.030	0.191182	0.09547	2.27E-4	0.0	ENSG00000002587	ENST00000002596	T	0.55930	0.49	5.49	5.49	0.81192	Sulfotransferase domain (1);	0.350601	0.29653	N	0.011541	T	0.31606	0.0802	N	0.03177	-0.4	0.43708	D	0.99617	B	0.14438	0.01	B	0.10450	0.005	T	0.15607	-1.0431	10	0.16896	T	0.51	.	18.3674	0.90396	0.0:1.0:0.0:0.0	.	287	O14792	HS3S1_HUMAN	K	287	ENSP00000002596:E287K	ENSP00000002596:E287K	E	-	1	0	HS3ST1	11009869	0.996000	0.38824	0.918000	0.36340	0.411000	0.31082	2.461000	0.45040	2.571000	0.86741	0.655000	0.94253	GAA		0.488	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		T	11400771	C	T	11400771	3	4	61	1	0	0	0	0	1	0	0	0	7384	893	31	1	68	1	HS3ST1	4	11400771	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	834414	11400771	179753505	3061	11046										
RAB28	9364	broad.mit.edu	37	chr4	13462408	13462408	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtataccaatcttctaaattCtcaaagctttgataatttgt	4	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13462408C>A	ENST00000330852.5	-	4	520	c.306G>T	c.(304-306)gaG>gaT	p.E102D	RAB28_ENST00000288723.4_Missense_Mutation_p.E102D|RAB28_ENST00000338176.4_Missense_Mutation_p.E102D	NM_001017979.2	NP_001017979.1	P51157	RAB28_HUMAN	RAB28, member RAS oncogene family	102					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E102D(2)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	8						CTTCTAAATTCTCAAAGCTTT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	4											89	89	89					4																	13462408		2203	4300	6503	13071506	SO:0001583	missense	9364			X94703	CCDS3409.1, CCDS33961.1, CCDS54741.1	4p16.1	2014-04-24			ENSG00000157869	ENSG00000157869		"RAB, member RAS oncogene"	9768	protein-coding gene	gene with protein product		612994				8647132	Standard	NM_004249		Approved		uc003gmu.2	P51157	OTTHUMG00000090543	ENST00000330852.5:c.306G>T	4.37:g.13462408C>A	ENSP00000328551:p.Glu102Asp		13071506	G8JLC5|Q8IYR8|Q8NI05	Missense_Mutation	SNP	ENST00000330852.5	37	CCDS33961.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.22|15.22|15.22	2.768733|2.768733|2.768733	0.49680|0.49680|0.49680	.|.|.	.|.|.	ENSG00000157869|ENSG00000157869|ENSG00000157869	ENST00000330852;ENST00000288723;ENST00000338176|ENST00000511649|ENST00000510528	T;T;T|.|.	0.78003|.|.	-1.14;-1.14;-1.14|.|.	6.01|6.01|6.01	6.01|6.01|6.01	0.97437|0.97437|0.97437	Small GTP-binding protein domain (1);|.|.	0.000000|0.000000|.	0.85682|0.85682|.	D|D|.	0.000000|0.000000|.	T|.|T	0.47040|.|0.47040	0.1424|.|0.1424	L|L|L	0.35249|0.35249|0.35249	1.045|1.045|1.045	0.58432|0.58432|0.58432	D|D|D	0.999998|0.999998|0.999998	B;B|.|.	0.15141|.|.	0.001;0.012|.|.	B;B|.|.	0.15052|.|.	0.004;0.012|.|.	T|.|T	0.38243|.|0.38243	-0.9670|.|-0.9670	10|.|5	0.33141|0.62326|.	T|D|.	0.24|0.03|.	.|.|.	7.9031|7.9031|7.9031	0.29746|0.29746|0.29746	0.0:0.8142:0.0:0.1858|0.0:0.8142:0.0:0.1858|0.0:0.8142:0.0:0.1858	.|.|.	102;102|.|.	P51157;P51157-2|.|.	RAB28_HUMAN;.|.|.	D|X|I	102|25|17	ENSP00000328551:E102D;ENSP00000288723:E102D;ENSP00000340079:E102D|.|.	ENSP00000288723:E102D|ENSP00000424899:E25X|.	E|E|R	-|-|-	3|1|2	2|0|0	RAB28|RAB28|RAB28	13071506|13071506|13071506	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	1.085000|1.085000|1.085000	0.30840|0.30840|0.30840	2.861000|2.861000|2.861000	0.98227|0.98227|0.98227	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GAG|GAA|AGA		0.348	RAB28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207068.2	NM_001017979		A	13462408	C	A	13462408	3	1	61	1	0	0	0	0	1	0	0	0	12953	912	32	2	515	2	RAB28	4	13462408	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2061637	13462408	177691868	3062	11047										
BOD1L	259282	broad.mit.edu	37	chr4	13601206	13601206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgcaaatggtcctatttCggggcactccttgccatgct	9	13	0	0	rs370739251		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13601206C>T	ENST00000040738.5	-	10	7453	c.7318G>A	c.(7318-7320)Gaa>Aaa	p.E2440K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2440						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E2440K(1)									GGTCCTATTTCGGGGCACTCC	0.493											OREG0016115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	4						C	LYS/GLU	0,4406		0,0,2203	168	153	158		7318	-2.4	0	4		158	1,8599	1.2+/-3.3	0,1,4299	no	missense	BOD1L	NM_148894.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	2440/3052	13601206	1,13005	2203	4300	6503	13210304	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7318G>A	4.37:g.13601206C>T	ENSP00000040738:p.Glu2440Lys	688	13210304	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	9.226	1.034531	0.19590	0.0	1.16E-4	ENSG00000038219	ENST00000040738	T	0.08370	3.1	3.75	-2.41	0.06562	.	4.012110	0.00541	N	0.000235	T	0.03305	0.0096	N	0.08118	0	0.09310	N	1	B	0.23591	0.088	B	0.12156	0.007	T	0.28776	-1.0033	10	0.09338	T	0.73	.	1.3378	0.02148	0.273:0.3108:0.2703:0.146	.	2440	Q8NFC6	BOD1L_HUMAN	K	2440	ENSP00000040738:E2440K	ENSP00000040738:E2440K	E	-	1	0	BOD1L	13210304	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.155000	0.10115	-0.150000	0.11195	0.555000	0.69702	GAA		0.493	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13601206	C	T	13601206	3	4	61	1	0	0	0	0	1	0	0	0	1484	893	31	1	1905	1	BOD1L	4	13601206	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138798	13601206	177553070	3063	11048										
BOD1L	259282	broad.mit.edu	37	chr4	13602558	13602558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaactttttcgagctgaCtgtcactttgatcagatgca	7	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13602558C>T	ENST00000040738.5	-	10	6101	c.5966G>A	c.(5965-5967)aGt>aAt	p.S1989N		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1989						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S1989N(1)									TTCGAGCTGACTGTCACTTTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											129	121	124					4																	13602558		2203	4300	6503	13211656	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5966G>A	4.37:g.13602558C>T	ENSP00000040738:p.Ser1989Asn		13211656	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702856	0.30232	.	.	ENSG00000038219	ENST00000040738	T	0.10763	2.84	5.62	4.77	0.60923	.	0.437537	0.23868	N	0.043766	T	0.11452	0.0279	L	0.29908	0.895	0.26983	N	0.965324	P	0.44877	0.845	B	0.43478	0.421	T	0.04467	-1.0949	10	0.59425	D	0.04	-1.778	13.9052	0.63831	0.1526:0.8473:0.0:0.0	.	1989	Q8NFC6	BOD1L_HUMAN	N	1989	ENSP00000040738:S1989N	ENSP00000040738:S1989N	S	-	2	0	BOD1L	13211656	0.213000	0.23551	0.092000	0.20876	0.205000	0.24178	0.797000	0.26999	1.348000	0.45733	-0.314000	0.08810	AGT		0.483	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13602558	C	T	13602558	3	4	61	1	0	0	0	0	1	0	0	0	1484	565	20	3	3257	3	BOD1L	4	13602558	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1352	13602558	177551718	3064	11049										
BOD1L	259282	broad.mit.edu	37	chr4	13604502	13604502	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaccttctttgctgtcaCttgtcttaaggacttctgat	6	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13604502C>A	ENST00000040738.5	-	10	4157	c.4022G>T	c.(4021-4023)aGt>aTt	p.S1341I		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1341						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S1341I(1)									TTTGCTGTCACTTGTCTTAAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	4											159	154	156					4																	13604502		2203	4300	6503	13213600	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4022G>T	4.37:g.13604502C>A	ENSP00000040738:p.Ser1341Ile		13213600	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	15.97	2.988758	0.53934	.	.	ENSG00000038219	ENST00000040738	T	0.10099	2.91	5.55	2.89	0.33648	.	0.639490	0.15081	N	0.281654	T	0.10895	0.0266	L	0.27053	0.805	0.09310	N	1	P	0.48911	0.917	P	0.47470	0.548	T	0.13548	-1.0505	10	0.59425	D	0.04	-7.5534	8.9765	0.35939	0.0:0.7023:0.0:0.2977	.	1341	Q8NFC6	BOD1L_HUMAN	I	1341	ENSP00000040738:S1341I	ENSP00000040738:S1341I	S	-	2	0	BOD1L	13213600	0.000000	0.05858	0.006000	0.13384	0.901000	0.52897	0.034000	0.13776	0.299000	0.22661	0.655000	0.94253	AGT		0.473	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13604502	C	A	13604502	3	1	61	1	0	0	0	0	1	0	0	0	1484	565	20	2	5201	2	BOD1L	4	13604502	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1944	13604502	177549774	3065	11050										
BOD1L	259282	broad.mit.edu	37	chr4	13604737	13604737	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctccttgagcaacatgttCttcagcagctgtgtttttca	7	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13604737C>A	ENST00000040738.5	-	10	3922	c.3787G>T	c.(3787-3789)Gaa>Taa	p.E1263*		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1263						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E1263*(1)									GCAACATGTTCTTCAGCAGCT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											85	79	81					4																	13604737		2203	4300	6503	13213835	SO:0001587	stop_gained	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.3787G>T	4.37:g.13604737C>A	ENSP00000040738:p.Glu1263*		13213835	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Nonsense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	43	9.891644	0.99289	.	.	ENSG00000038219	ENST00000040738	.	.	.	5.7	5.7	0.88788	.	0.000000	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-3.7592	17.9922	0.89172	0.0:1.0:0.0:0.0	.	.	.	.	X	1263	.	ENSP00000040738:E1263X	E	-	1	0	BOD1L	13213835	0.990000	0.36364	0.448000	0.26945	0.019000	0.09904	3.243000	0.51392	2.684000	0.91462	0.655000	0.94253	GAA		0.403	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13604737	C	A	13604737	4	1	61	1	0	0	0	0	0	1	0	0	1484	922	32	2	5436	2	BOD1L	4	13604737	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235	13604737	177549539	3066	11051										
BOD1L	259282	broad.mit.edu	37	chr4	13605806	13605806	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagacttcaacacaagtttCtcttctaacaagctctttgt	4	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13605806C>A	ENST00000040738.5	-	10	2853	c.2718G>T	c.(2716-2718)gaG>gaT	p.E906D		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	906	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E906D(1)									ACACAAGTTTCTCTTCTAACA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											135	133	134					4																	13605806		2203	4300	6503	13214904	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.2718G>T	4.37:g.13605806C>A	ENSP00000040738:p.Glu906Asp		13214904	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	1.117	-0.656564	0.03480	.	.	ENSG00000038219	ENST00000040738	T	0.08458	3.09	5.4	-8.5	0.00927	.	0.674653	0.13673	N	0.370701	T	0.02047	0.0064	N	0.05230	-0.09	0.09310	N	1	B	0.14438	0.01	B	0.14578	0.011	T	0.36504	-0.9745	10	0.18710	T	0.47	-0.2034	0.0642	0.00017	0.2982:0.1812:0.2283:0.2923	.	906	Q8NFC6	BOD1L_HUMAN	D	906	ENSP00000040738:E906D	ENSP00000040738:E906D	E	-	3	2	BOD1L	13214904	0.549000	0.26481	0.008000	0.14137	0.484000	0.33280	-0.271000	0.08572	-1.468000	0.01892	0.555000	0.69702	GAG		0.378	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13605806	C	A	13605806	3	1	61	1	0	0	0	0	1	0	0	0	1484	912	32	2	6505	2	BOD1L	4	13605806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1069	13605806	177548470	3067	11052										
BOD1L	259282	broad.mit.edu	37	chr4	13606462	13606462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgtttctggggctcttCggtgcaaatttctgagcgtt	11	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13606462C>T	ENST00000040738.5	-	10	2197	c.2062G>A	c.(2062-2064)Gaa>Aaa	p.E688K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	688	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E688K(1)									TGGGGCTCTTCGGTGCAAATT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											260	278	272					4																	13606462		2203	4300	6503	13215560	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.2062G>A	4.37:g.13606462C>T	ENSP00000040738:p.Glu688Lys		13215560	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880638	0.51801	.	.	ENSG00000038219	ENST00000040738	T	0.12039	2.72	5.71	5.71	0.89125	.	0.305505	0.23664	N	0.045784	T	0.21307	0.0513	L	0.29908	0.895	0.39782	D	0.972319	D	0.69078	0.997	P	0.53809	0.735	T	0.00804	-1.1559	10	0.36615	T	0.2	-9.8996	19.8416	0.96692	0.0:1.0:0.0:0.0	.	688	Q8NFC6	BOD1L_HUMAN	K	688	ENSP00000040738:E688K	ENSP00000040738:E688K	E	-	1	0	BOD1L	13215560	0.999000	0.42202	0.951000	0.38953	0.054000	0.15201	5.360000	0.66086	2.694000	0.91930	0.563000	0.77884	GAA		0.408	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13606462	C	T	13606462	3	4	61	1	0	0	0	0	1	0	0	0	1484	893	31	1	7161	1	BOD1L	4	13606462	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	656	13606462	177547814	3068	11053										
BOD1L	259282	broad.mit.edu	37	chr4	13606585	13606585	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctttctaatttggattCatttttgttttcgtcaacta	4	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13606585C>A	ENST00000040738.5	-	10	2074	c.1939G>T	c.(1939-1941)Gaa>Taa	p.E647*		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	647	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E647*(1)									AATTTGGATTCATTTTTGTTT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											109	107	107					4																	13606585		2203	4300	6503	13215683	SO:0001587	stop_gained	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1939G>T	4.37:g.13606585C>A	ENSP00000040738:p.Glu647*		13215683	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Nonsense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	40	8.230253	0.98717	.	.	ENSG00000038219	ENST00000040738	.	.	.	5.71	5.71	0.89125	.	0.166757	0.28589	N	0.014811	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-1.7963	19.8416	0.96692	0.0:1.0:0.0:0.0	.	.	.	.	X	647	.	ENSP00000040738:E647X	E	-	1	0	BOD1L	13215683	1.000000	0.71417	0.888000	0.34837	0.952000	0.60782	5.677000	0.68142	2.694000	0.91930	0.563000	0.77884	GAA		0.408	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13606585	C	A	13606585	4	1	61	1	0	0	0	0	0	1	0	0	1484	835	29	2	7284	2	BOD1L	4	13606585	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123	13606585	177547691	3069	11054										
BOD1L	259282	broad.mit.edu	37	chr4	13612703	13612703	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtttgagtttttgttttaTtctgtttgttcttctcttca	6	5	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:13612703T>A	ENST00000040738.5	-	6	1481	c.1346A>T	c.(1345-1347)aAt>aTt	p.N449I		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	449	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N449I(1)									TTTTGTTTTATTCTGTTTGTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											141	126	131					4																	13612703		2202	4298	6500	13221801	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1346A>T	4.37:g.13612703T>A	ENSP00000040738:p.Asn449Ile		13221801	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	15.46	2.839067	0.51057	.	.	ENSG00000038219	ENST00000040738	T	0.08634	3.07	4.96	-3.08	0.05347	.	0.835046	0.10480	N	0.669671	T	0.08670	0.0215	L	0.59436	1.845	0.09310	N	1	P	0.40875	0.731	B	0.38428	0.273	T	0.15694	-1.0428	10	0.45353	T	0.12	-0.2899	8.763	0.34687	0.1063:0.464:0.0:0.4297	.	449	Q8NFC6	BOD1L_HUMAN	I	449	ENSP00000040738:N449I	ENSP00000040738:N449I	N	-	2	0	BOD1L	13221801	0.647000	0.27304	0.023000	0.16930	0.910000	0.53928	0.047000	0.14056	-0.614000	0.05687	-0.334000	0.08254	AAT		0.323	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13612703	T	A	13612703	3	1	61	1	0	0	0	0	1	0	0	0	1484	1493	52	5	7893	5	BOD1L	4	13612703	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6118	13612703	177541573	3070	11055										
CC2D2A	57545	broad.mit.edu	37	chr4	15518271	15518271	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagatggtttggagatgaCggcaggatcctagctctgcc	14	8	1	4	rs371086728	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:15518271C>T	ENST00000503292.1	+	12	1221	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	CC2D2A_ENST00000389652.5_Silent_p.D298D|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000424120.1_Silent_p.D347D|CC2D2A_ENST00000413206.1_Silent_p.D347D	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	347					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.D298D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						TTGGAGATGACGGCAGGATCC	0.453													C|||	4	0.000798722	0	0	5008	,	,		14350	0		0	False		,,,				2504	0.0041															1	Substitution - coding silent(1)	large_intestine(1)	4						C		2,3828		0,2,1913	62	65	64		1041	-6.7	0.7	4		64	9,8225		0,9,4108	no	coding-synonymous	CC2D2A	NM_001080522.2		0,11,6021	TT,TC,CC		0.1093,0.0522,0.0912		347/1621	15518271	11,12053	1915	4117	6032	15127369	SO:0001819	synonymous_variant	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.1041C>T	4.37:g.15518271C>T			15127369	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																				0.453	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		T	15518271	C	T	15518271	2	4	61	1	0	0	0	0	0	0	0	1	2734	535	19	1		1	CC2D2A	4	15518271	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1905568	15518271	175636005	3071	11056										
FBXL5	26234	broad.mit.edu	37	chr4	15638155	15638155	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaagatgtttccaaagcGatcccgtttttgtcagctga	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:15638155G>A	ENST00000341285.3	-	5	852	c.728C>T	c.(727-729)tCg>tTg	p.S243L	FBXL5_ENST00000382358.4_Missense_Mutation_p.S117L|FBXL5_ENST00000412094.2_Missense_Mutation_p.S226L	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	243	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)	p.S243L(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						tttccaaagCGATCCCGTTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	85	91					4																	15638155		2203	4300	6503	15247253	SO:0001583	missense	26234			AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"F-boxes / Leucine-rich repeats"	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.728C>T	4.37:g.15638155G>A	ENSP00000344866:p.Ser243Leu		15247253	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	37	CCDS3415.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.417908	0.83449	.	.	ENSG00000118564	ENST00000341285;ENST00000412094;ENST00000382358	T;T;T	0.40476	1.03;1.03;1.03	5.44	5.44	0.79542	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.40247	0.1109	L	0.43757	1.38	0.80722	D	1	P;D	0.53462	0.951;0.96	B;P	0.44394	0.32;0.448	T	0.35798	-0.9774	10	0.72032	D	0.01	-9.9537	13.8728	0.63629	0.0735:0.0:0.9265:0.0	.	226;243	Q9UKA1-2;Q9UKA1	.;FBXL5_HUMAN	L	243;226;117	ENSP00000344866:S243L;ENSP00000408679:S226L;ENSP00000371795:S117L	ENSP00000344866:S243L	S	-	2	0	FBXL5	15247253	1.000000	0.71417	0.978000	0.43139	0.939000	0.58152	4.935000	0.63498	2.701000	0.92244	0.591000	0.81541	TCG		0.363	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			A	15638155	G	A	15638155	3	1	61	1	0	0	0	0	1	0	0	0	5741	1059	37	1	1375	1	FBXL5	4	15638155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119884	15638155	175516121	3072	11057										
CD38	952	broad.mit.edu	37	chr4	15839779	15839779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccgcagtaaaatctttgAcaaaaacaggtacacattta	5	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:15839779A>G	ENST00000226279.3	+	5	787	c.650A>G	c.(649-651)gAc>gGc	p.D217G		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	217					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)	p.D217G(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						AAAATCTTTGACAAAAACAGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	127	131					4																	15839779		2203	4300	6503	15448877	SO:0001583	missense	952			D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.650A>G	4.37:g.15839779A>G	ENSP00000226279:p.Asp217Gly		15448877	O00121|O00122|Q96HY4	Missense_Mutation	SNP	ENST00000226279.3	37	CCDS3417.1	.	.	.	.	.	.	.	.	.	.	A	5.415	0.261738	0.10239	.	.	ENSG00000004468	ENST00000226279;ENST00000510674	T;T	0.44482	0.92;0.92	5.62	-0.967	0.10316	NAD(P)-binding domain (1);	1.130300	0.06280	N	0.697225	T	0.37073	0.0990	L	0.60455	1.87	0.09310	N	1	B	0.21905	0.062	B	0.23419	0.046	T	0.35425	-0.9789	10	0.13108	T	0.6	-3.0384	9.4587	0.38772	0.5347:0.0:0.4653:0.0	.	217	P28907	CD38_HUMAN	G	217;105	ENSP00000226279:D217G;ENSP00000423047:D105G	ENSP00000226279:D217G	D	+	2	0	CD38	15448877	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	-0.096000	0.11059	-0.063000	0.13065	0.459000	0.35465	GAC		0.363	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		G	15839779	A	G	15839779	3	3	61	1	0	0	0	0	1	0	0	0	3015	275	10	4	668	4	CD38	4	15839779	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	201624	15839779	175314497	3073	11058										
CD38	952	broad.mit.edu	37	chr4	15850222	15850222	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcttgcacatctgagatCtgagccagtcgctgtggttg	11	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:15850222C>A	ENST00000226279.3	+	8	1037	c.900C>A	c.(898-900)atC>atA	p.I300I		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	300					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)	p.I300I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						CATCTGAGATCTGAGCCAGTC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	4											152	122	132					4																	15850222		2203	4300	6503	15459320	SO:0001819	synonymous_variant	952			D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.900C>A	4.37:g.15850222C>A			15459320	O00121|O00122|Q96HY4	Silent	SNP	ENST00000226279.3	37	CCDS3417.1																																																																																				0.433	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		A	15850222	C	A	15850222	2	1	61	1	0	0	0	0	0	0	0	1	3015	903	32	2		2	CD38	4	15850222	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10443	15850222	175304054	3074	11059										
PROM1	8842	broad.mit.edu	37	chr4	16010622	16010622	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttctgtggatgtaactTtcagtgttattaacataaac	6	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:16010622T>G	ENST00000510224.1	-	12	1499	c.1251A>C	c.(1249-1251)gaA>gaC	p.E417D	RNU6-350P_ENST00000515949.1_RNA|PROM1_ENST00000540805.1_Missense_Mutation_p.E417D|PROM1_ENST00000447510.2_Missense_Mutation_p.E417D|PROM1_ENST00000539194.1_Missense_Mutation_p.E417D|PROM1_ENST00000508167.1_Missense_Mutation_p.E408D|PROM1_ENST00000505450.1_Missense_Mutation_p.E408D|PROM1_ENST00000543373.1_Missense_Mutation_p.E408D			O43490	PROM1_HUMAN	prominin 1	417					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)	p.E416D(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GGATGTAACTTTCAGTGTTAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	79	80					4																	16010622		1865	4103	5968	15619720	SO:0001583	missense	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1251A>C	4.37:g.16010622T>G	ENSP00000426809:p.Glu417Asp		15619720	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311352	0.60414	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.52	-1.75	0.08031	.	0.414820	0.28914	N	0.013732	T	0.41673	0.1169	M	0.70275	2.135	0.09310	N	1	P;P;P;P;P;P	0.51537	0.881;0.881;0.881;0.881;0.946;0.902	P;P;P;P;P;P	0.50537	0.614;0.614;0.511;0.614;0.592;0.643	T	0.45512	-0.9256	10	0.15952	T	0.53	-10.2098	7.6122	0.28137	0.0:0.6065:0.1691:0.2244	.	408;417;408;417;408;417	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	D	417;417;417;408;408;417;408	ENSP00000415481:E417D;ENSP00000438045:E417D;ENSP00000443620:E417D;ENSP00000426090:E408D;ENSP00000427346:E408D;ENSP00000426809:E417D;ENSP00000445526:E408D	ENSP00000415481:E417D	E	-	3	2	PROM1	15619720	0.094000	0.21725	0.001000	0.08648	0.028000	0.11728	0.186000	0.16978	-0.255000	0.09486	-0.256000	0.11100	GAA		0.393	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		G	16010622	T	G	16010622	3	3	61	1	0	0	0	0	1	0	0	0	12589	1838	64	4	1410	4	PROM1	4	16010622	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160400	16010622	175143654	3075	11060										
LDB2	9079	broad.mit.edu	37	chr4	16760787	16760787	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttctttcttactgtatcGctttggtccatcttccaaac	4	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:16760787G>A	ENST00000304523.5	-	2	552	c.229C>T	c.(229-231)Cga>Tga	p.R77*	LDB2_ENST00000515064.1_Nonsense_Mutation_p.R77*|LDB2_ENST00000441778.2_Nonsense_Mutation_p.R77*|LDB2_ENST00000502640.1_Nonsense_Mutation_p.R77*	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	77					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)	p.R77*(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						TTACTGTATCGCTTTGGTCCA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											87	85	86					4																	16760787		2203	4300	6503	16369885	SO:0001587	stop_gained	9079			AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.229C>T	4.37:g.16760787G>A	ENSP00000306772:p.Arg77*		16369885	O60619|O75480	Nonsense_Mutation	SNP	ENST00000304523.5	37	CCDS3420.1	.	.	.	.	.	.	.	.	.	.	G	37	6.600994	0.97697	.	.	ENSG00000169744	ENST00000515064;ENST00000441778;ENST00000304523;ENST00000502640;ENST00000506732	.	.	.	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.4041	13.7437	0.62862	0.0:0.0:0.8464:0.1536	.	.	.	.	X	77;77;77;77;53	.	ENSP00000306772:R77X	R	-	1	2	LDB2	16369885	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.390000	0.52523	2.763000	0.94921	0.561000	0.74099	CGA		0.428	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2			A	16760787	G	A	16760787	4	1	61	1	0	0	0	0	0	1	0	0	8718	1095	38	1	1029	1	LDB2	4	16760787	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	750165	16760787	174393489	3076	11061										
CLRN2	645104	broad.mit.edu	37	chr4	17528703	17528703	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgaggatatcttgtatTaatagccttcccctgttcac	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:17528703T>G	ENST00000511148.2	+	3	799	c.697T>G	c.(697-699)Taa>Gaa	p.*233E	snoU13_ENST00000459186.1_RNA	NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	0						integral component of membrane (GO:0016021)		p.*250E(1)		breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						TATCTTGTATTAATAGCCTTC	0.483																																																1	Nonstop extension(1)	large_intestine(1)	4											116	119	118					4																	17528703		2109	4220	6329	17137801	SO:0001578	stop_lost	645104				CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.697T>G	4.37:g.17528703T>G	ENSP00000424711:p.*233Gluext*1		17137801		Nonstop_Mutation	SNP	ENST00000511148.2	37	CCDS47032.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.924566	0.73213	.	.	ENSG00000249581	ENST00000511148	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8801	0.70525	0.0:0.0:0.0:1.0	.	.	.	.	E	233	.	.	X	+	1	0	CLRN2	17137801	1.000000	0.71417	0.137000	0.22149	0.937000	0.57800	7.233000	0.78125	2.007000	0.58848	0.460000	0.39030	TAA		0.483	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827		G	17528703	T	G	17528703	4	3	61	1	0	0	0	0	0	0	0	0	3564	1767	61	4	707	4	CLRN2	4	17528703	Nonstop_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	767916	17528703	173625573	3077	11062										
LAP3	51056	broad.mit.edu	37	chr4	17600150	17600150	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgcacacacgtttaacccGaaggtcatcctcaatgccgc	7	15	2	0	rs147122901		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:17600150G>A	ENST00000226299.4	+	10	1423	c.1149G>A	c.(1147-1149)ccG>ccA	p.P383P	LAP3_ENST00000606142.1_Silent_p.P352P|LAP3_ENST00000503467.1_3'UTR|AC006160.5_ENST00000511010.1_RNA	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	383					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.P383P(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						CGTTTAACCCGAAGGTCATCC	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		17800	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						G		2,4404	4.2+/-10.8	0,2,2201	200	151	168		1149	-10.1	0	4	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LAP3	NM_015907.2		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		383/520	17600150	3,13003	2203	4300	6503	17209248	SO:0001819	synonymous_variant	51056			AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.1149G>A	4.37:g.17600150G>A			17209248	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Silent	SNP	ENST00000226299.4	37	CCDS3422.1																																																																																				0.493	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			A	17600150	G	A	17600150	2	1	61	1	0	0	0	0	0	0	0	1	8645	1045	37	1		1	LAP3	4	17600150	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71447	17600150	173554126	3078	11063										
LAP3	51056	broad.mit.edu	37	chr4	17609189	17609189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcattgagttcttacttCgtttcagtcaagacaatgct	6	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:17609189C>T	ENST00000226299.4	+	13	1811	c.1537C>T	c.(1537-1539)Cgt>Tgt	p.R513C	LAP3_ENST00000606142.1_Missense_Mutation_p.R482C|LAP3_ENST00000503467.1_3'UTR|AC006160.5_ENST00000511010.1_RNA	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	513					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.R513C(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						GTTCTTACTTCGTTTCAGTCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											100	93	95					4																	17609189		2203	4300	6503	17218287	SO:0001583	missense	51056			AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.1537C>T	4.37:g.17609189C>T	ENSP00000226299:p.Arg513Cys		17218287	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.572517	0.45798	.	.	ENSG00000002549	ENST00000226299	T	0.47869	0.83	5.87	5.02	0.67125	.	0.335001	0.37761	N	0.001952	T	0.53867	0.1823	M	0.84082	2.675	0.48288	D	0.999622	D	0.67145	0.996	B	0.41271	0.352	T	0.66638	-0.5873	10	0.72032	D	0.01	-7.3905	16.5309	0.84359	0.1315:0.8684:0.0:0.0	.	513	P28838	AMPL_HUMAN	C	513	ENSP00000226299:R513C	ENSP00000226299:R513C	R	+	1	0	LAP3	17218287	0.980000	0.34600	0.013000	0.15412	0.046000	0.14306	3.964000	0.56780	1.484000	0.48361	0.655000	0.94253	CGT		0.393	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			T	17609189	C	T	17609189	3	4	61	1	0	0	0	0	1	0	0	0	8645	884	31	1	1587	1	LAP3	4	17609189	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9039	17609189	173545087	3079	11064										
SLIT2	9353	broad.mit.edu	37	chr4	20570499	20570499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattcaggtgtatttgtgCtgatggatttgaaggagaaa	14	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:20570499C>T	ENST00000504154.1	+	29	3212	c.2960C>T	c.(2959-2961)gCt>gTt	p.A987V	SLIT2_ENST00000503823.1_Missense_Mutation_p.A979V|SLIT2_ENST00000273739.5_Missense_Mutation_p.A991V|SLIT2_ENST00000503837.1_Missense_Mutation_p.A983V	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	987	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.A987V(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TGTATTTGTGCTGATGGATTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											169	169	169					4																	20570499		2203	4300	6503	20179597	SO:0001583	missense	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.2960C>T	4.37:g.20570499C>T	ENSP00000422591:p.Ala987Val		20179597	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.942109	0.73557	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837;ENST00000511508	T;T;T;T;D	0.92699	0.1;0.1;0.1;0.1;-3.09	5.45	5.45	0.79879	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.098159	0.64402	D	0.000001	D	0.89656	0.6778	L	0.41906	1.305	0.80722	D	1	B;B	0.16166	0.004;0.016	B;B	0.22386	0.007;0.039	D	0.84679	0.0716	10	0.39692	T	0.17	.	19.6632	0.95882	0.0:1.0:0.0:0.0	.	979;987	O94813-3;O94813	.;SLIT2_HUMAN	V	979;987;991;983;983;199	ENSP00000427548:A979V;ENSP00000422591:A987V;ENSP00000273739:A991V;ENSP00000422261:A983V;ENSP00000421975:A199V	ENSP00000273739:A991V	A	+	2	0	SLIT2	20179597	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.716000	0.92895	0.655000	0.94253	GCT		0.328	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20570499	C	T	20570499	3	4	61	1	0	0	0	0	1	0	0	0	14777	797	28	3	3074	3	SLIT2	4	20570499	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2961310	20570499	170583777	3080	11065										
SLIT2	9353	broad.mit.edu	37	chr4	20611778	20611778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgaattttgactctccaCtctatgtaggaggtaagctg	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:20611778C>A	ENST00000504154.1	+	34	4087	c.3835C>A	c.(3835-3837)Ctc>Atc	p.L1279I	SLIT2_ENST00000503823.1_Missense_Mutation_p.L1271I|SLIT2_ENST00000273739.5_Missense_Mutation_p.L1292I|SLIT2_ENST00000503837.1_Missense_Mutation_p.L1275I	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1279	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.L1279I(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TGACTCTCCACTCTATGTAGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											122	111	115					4																	20611778		2203	4300	6503	20220876	SO:0001583	missense	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.3835C>A	4.37:g.20611778C>A	ENSP00000422591:p.Leu1279Ile		20220876	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.99|15.99	2.995883|2.995883	0.54147|0.54147	.|.	.|.	ENSG00000145147|ENSG00000145147	ENST00000512993|ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	.|D;D;D;D	.|0.82255	.|-1.59;-1.59;-1.59;-1.59	5.83|5.83	4.99|4.99	0.66335|0.66335	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.124936	.|0.56097	.|D	.|0.000037	D|D	0.85410|0.85410	0.5690|0.5690	L|L	0.53617|0.53617	1.68|1.68	0.80722|0.80722	D|D	1|1	.|D;B	.|0.58268	.|0.982;0.438	.|P;P	.|0.55055	.|0.767;0.483	D|D	0.83960|0.83960	0.0321|0.0321	5|10	.|0.37606	.|T	.|0.19	.|.	14.3548|14.3548	0.66730|0.66730	0.0:0.9296:0.0:0.0704|0.0:0.9296:0.0:0.0704	.|.	.|1271;1279	.|O94813-3;O94813	.|.;SLIT2_HUMAN	Q|I	62|1271;1279;1292;1275;1275	.|ENSP00000427548:L1271I;ENSP00000422591:L1279I;ENSP00000273739:L1292I;ENSP00000422261:L1275I	.|ENSP00000273739:L1292I	H|L	+|+	3|1	2|0	SLIT2|SLIT2	20220876|20220876	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.788000|0.788000	0.44548|0.44548	4.831000|4.831000	0.62752|0.62752	2.770000|2.770000	0.95276|0.95276	0.655000|0.655000	0.94253|0.94253	CAC|CTC		0.428	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20611778	C	A	20611778	3	1	61	1	0	0	0	0	1	0	0	0	14777	565	20	2	3969	2	SLIT2	4	20611778	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41279	20611778	170542498	3081	11066										
GPR125	166647	broad.mit.edu	37	chr4	22414962	22414962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctgctccatgtgcaattCgacgcagtgtcacattaaca	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:22414962C>T	ENST00000334304.5	-	14	2344	c.2075G>A	c.(2074-2076)cGa>cAa	p.R692Q	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	692					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.R692Q(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				ATGTGCAATTCGACGCAGTGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											111	108	109					4																	22414962		2203	4300	6503	22024060	SO:0001583	missense	166647			AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2075G>A	4.37:g.22414962C>T	ENSP00000334952:p.Arg692Gln		22024060	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656881	0.67586	.	.	ENSG00000152990	ENST00000334304	T	0.53857	0.6	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.68513	0.3009	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.978;0.999	P;P	0.61275	0.549;0.886	T	0.62163	-0.6912	10	0.29301	T	0.29	-5.5867	20.1991	0.98252	0.0:1.0:0.0:0.0	.	549;692	Q8IWK6-3;Q8IWK6	.;GP125_HUMAN	Q	692	ENSP00000334952:R692Q	ENSP00000334952:R692Q	R	-	2	0	GPR125	22024060	0.991000	0.36638	0.933000	0.37362	0.753000	0.42808	2.939000	0.48995	2.775000	0.95449	0.650000	0.86243	CGA		0.443	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			T	22414962	C	T	22414962	3	4	61	1	0	0	0	0	1	0	0	0	6659	884	31	1	1914	1	GPR125	4	22414962	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1803184	22414962	168739314	3082	11067										
GPR125	166647	broad.mit.edu	37	chr4	22463423	22463423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactactaataagattgtttCggaggtccctgttaaaaata	7	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:22463423C>T	ENST00000334304.5	-	3	607	c.338G>A	c.(337-339)cGa>cAa	p.R113Q	GPR125_ENST00000502482.1_Missense_Mutation_p.R113Q	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	113					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.R113Q(2)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				AAGATTGTTTCGGAGGTCCCT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	4											61	64	63					4																	22463423		2203	4300	6503	22072521	SO:0001583	missense	166647			AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.338G>A	4.37:g.22463423C>T	ENSP00000334952:p.Arg113Gln		22072521	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480378	0.63849	.	.	ENSG00000152990	ENST00000334304;ENST00000502482	T;T	0.56776	0.44;0.44	5.71	5.71	0.89125	.	0.054599	0.64402	D	0.000001	T	0.42337	0.1198	L	0.31371	0.925	0.80722	D	1	P;P	0.46220	0.874;0.577	B;B	0.42087	0.375;0.166	T	0.42816	-0.9429	10	0.66056	D	0.02	-1.2018	10.8046	0.46509	0.0:0.9145:0.0:0.0855	.	113;113	Q8IWK6-2;Q8IWK6	.;GP125_HUMAN	Q	113	ENSP00000334952:R113Q;ENSP00000421006:R113Q	ENSP00000334952:R113Q	R	-	2	0	GPR125	22072521	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.687000	0.46976	2.709000	0.92574	0.655000	0.94253	CGA		0.338	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			T	22463423	C	T	22463423	3	4	61	1	0	0	0	0	1	0	0	0	6659	884	31	1	3695	1	GPR125	4	22463423	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48461	22463423	168690853	3083	11068										
DHX15	1665	broad.mit.edu	37	chr4	24534670	24534670	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcataacaccactgaaccgaTtcatgatctaaaaaggtaga	6	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:24534670T>G	ENST00000336812.4	-	12	2073	c.1917A>C	c.(1915-1917)gaA>gaC	p.E639D	DHX15_ENST00000508032.1_5'UTR	NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	639					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.E639D(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				ACTGAACCGATTCATGATCTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											126	137	133					4																	24534670		2203	4300	6503	24143768	SO:0001583	missense	1665			AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.1917A>C	4.37:g.24534670T>G	ENSP00000336741:p.Glu639Asp		24143768	Q9NQT7	Missense_Mutation	SNP	ENST00000336812.4	37	CCDS33966.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.512421	0.27123	.	.	ENSG00000109606	ENST00000336812;ENST00000535946	T	0.02656	4.21	5.89	-0.579	0.11720	.	0.000000	0.85682	D	0.000000	T	0.02267	0.0070	L	0.31207	0.915	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.002;0.002;0.003	T	0.52208	-0.8606	9	.	.	.	-19.6006	10.8776	0.46919	0.0:0.5752:0.0:0.4248	.	639;628;628	O43143;B4E0S6;F5H6K0	DHX15_HUMAN;.;.	D	639;628	ENSP00000336741:E639D	.	E	-	3	2	DHX15	24143768	0.999000	0.42202	0.998000	0.56505	0.990000	0.78478	0.611000	0.24268	-0.056000	0.13221	0.482000	0.46254	GAA		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		G	24534670	T	G	24534670	3	3	61	1	0	0	0	0	1	0	0	0	4512	1490	52	4	482	4	DHX15	4	24534670	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2071247	24534670	166619606	3084	11069										
DHX15	1665	broad.mit.edu	37	chr4	24556418	24556418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaatctggataactgttCgaattgctgcttcaagataa	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:24556418C>T	ENST00000336812.4	-	5	1166	c.1010G>A	c.(1009-1011)cGa>cAa	p.R337Q		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	337					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.R337Q(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				GATAACTGTTCGAATTGCTGC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											177	170	172					4																	24556418		2203	4300	6503	24165516	SO:0001583	missense	1665			AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.1010G>A	4.37:g.24556418C>T	ENSP00000336741:p.Arg337Gln		24165516	Q9NQT7	Missense_Mutation	SNP	ENST00000336812.4	37	CCDS33966.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653646	0.88056	.	.	ENSG00000109606	ENST00000336812;ENST00000535946	T	0.12569	2.67	6.05	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.28167	0.0695	L	0.58925	1.835	0.80722	D	1	D	0.89917	1.0	D	0.68192	0.956	T	0.06303	-1.0834	10	0.12766	T	0.61	.	13.2971	0.60303	0.0:0.87:0.0:0.13	.	337	O43143	DHX15_HUMAN	Q	337;326	ENSP00000336741:R337Q	ENSP00000336741:R337Q	R	-	2	0	DHX15	24165516	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.775000	0.68915	1.577000	0.49804	-0.145000	0.13849	CGA		0.378	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		T	24556418	C	T	24556418	3	4	61	1	0	0	0	0	1	0	0	0	4512	884	31	1	1417	1	DHX15	4	24556418	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21748	24556418	166597858	3085	11070										
LGI2	55203	broad.mit.edu	37	chr4	25014036	25014036	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttctccatgctgggctgCgcgatggccacgtacacatc	11	14	1	0	rs200496667		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25014036C>T	ENST00000382114.4	-	7	926	c.741G>A	c.(739-741)gcG>gcA	p.A247A		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	247						extracellular region (GO:0005576)		p.A247A(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				TGCTGGGCTGCGCGATGGCCA	0.488													C|||	1	0.000199681	0	0.0014	5008	,	,		21284	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4											151	125	134					4																	25014036		2203	4300	6503	24623134	SO:0001819	synonymous_variant	55203			AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.741G>A	4.37:g.25014036C>T			24623134	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																				0.488	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			T	25014036	C	T	25014036	2	4	61	1	0	0	0	0	0	0	0	1	8775	755	27	1		1	LGI2	4	25014036	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	457618	25014036	166140240	3086	11071										
LGI2	55203	broad.mit.edu	37	chr4	25019779	25019779	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttattacccctcaaatCtctaaaaatcaaaataaaac	0	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25019779C>A	ENST00000382114.4	-	6	672	c.487G>T	c.(487-489)Gat>Tat	p.D163Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	163						extracellular region (GO:0005576)		p.D163Y(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CCCCTCAAATCTCTAAAAATC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											70	71	71					4																	25019779		2203	4300	6503	24628877	SO:0001630	splice_region_variant	55203			AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.486-1G>T	4.37:g.25019779C>A			24628877	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	37	CCDS3431.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.501988|4.501988	0.85176|0.85176	.|.	.|.	ENSG00000153012|ENSG00000153012	ENST00000382114|ENST00000512108	T|.	0.59364|.	0.27|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.65354|.	0.2683|.	L|L	0.33668|0.33668	1.02|1.02	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|.	0.58561|.	-0.7615|.	10|.	0.42905|.	T|.	0.14|.	-27.5426|-27.5426	20.0781|20.0781	0.97751|0.97751	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	163|.	Q8N0V4|.	LGI2_HUMAN|.	Y|Y	163|153	ENSP00000371548:D163Y|.	ENSP00000371548:D163Y|.	D|X	-|-	1|3	0|2	LGI2|LGI2	24628877|24628877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	7.776000|7.776000	0.85560|0.85560	2.817000|2.817000	0.96982|0.96982	0.563000|0.563000	0.77884|0.77884	GAT|TAG		0.358	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		Missense_Mutation	A	25019779	C	A	25019779	5	1	61	1	0	0	0	0	0	0	1	0	8775	927	32	2	1162	2	LGI2	4	25019779	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5743	25019779	166134497	3087	11072										
SEPSECS	51091	broad.mit.edu	37	chr4	25128891	25128891	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaagaaattacctaaaGatatgggattgtgaggtgta	11	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25128891G>T	ENST00000382103.2	-	9	1187	c.1115C>A	c.(1114-1116)tCt>tAt	p.S372Y	SEPSECS_ENST00000302922.3_Missense_Mutation_p.S293Y|SEPSECS_ENST00000515272.1_5'UTR	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	372					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)	p.S293Y(1)		endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				ATTACCTAAAGATATGGGATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											131	133	132					4																	25128891		2203	4299	6502	24737989	SO:0001583	missense	51091			AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.1115C>A	4.37:g.25128891G>T	ENSP00000371535:p.Ser372Tyr		24737989	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	37	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	G	27.2	4.814139	0.90790	.	.	ENSG00000109618	ENST00000302922;ENST00000382103	D;D	0.83992	-1.79;-1.79	5.53	5.53	0.82687	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.93347	0.7879	M	0.91354	3.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94354	0.7582	10	0.87932	D	0	-28.1888	19.4447	0.94841	0.0:0.0:1.0:0.0	.	371;312;372	Q9HD40-3;A1A4F3;Q9HD40	.;.;SPCS_HUMAN	Y	293;372	ENSP00000305956:S293Y;ENSP00000371535:S372Y	ENSP00000305956:S293Y	S	-	2	0	SEPSECS	24737989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.566000	0.90734	2.613000	0.88420	0.650000	0.86243	TCT		0.338	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		T	25128891	G	T	25128891	3	4	61	1	0	0	0	0	1	0	0	0	14095	942	33	2	402	2	SEPSECS	4	25128891	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109112	25128891	166025385	3088	11073										
SEPSECS	51091	broad.mit.edu	37	chr4	25156669	25156669	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagtagaatgaatacacaGaatgcaatcaggcccaagtt	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25156669G>T	ENST00000382103.2	-	5	724	c.652C>A	c.(652-654)Ctg>Atg	p.L218M	SEPSECS_ENST00000302922.3_Missense_Mutation_p.L139M	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	218					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)	p.L139M(1)		endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				TGAATACACAGAATGCAATCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											140	121	128					4																	25156669		2203	4300	6503	24765767	SO:0001583	missense	51091			AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.652C>A	4.37:g.25156669G>T	ENSP00000371535:p.Leu218Met		24765767	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	37	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705320	0.68615	.	.	ENSG00000109618	ENST00000302922;ENST00000382103	D;D	0.82803	-1.65;-1.65	5.5	4.66	0.58398	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.070231	0.64402	D	0.000014	D	0.91338	0.7268	M	0.86097	2.795	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79784	0.978;0.966;0.993	D	0.92260	0.5816	10	0.56958	D	0.05	-13.2774	14.482	0.67590	0.0712:0.0:0.9288:0.0	.	217;158;218	Q9HD40-3;A1A4F3;Q9HD40	.;.;SPCS_HUMAN	M	139;218	ENSP00000305956:L139M;ENSP00000371535:L218M	ENSP00000305956:L139M	L	-	1	2	SEPSECS	24765767	1.000000	0.71417	0.940000	0.37924	0.820000	0.46376	7.532000	0.81985	1.460000	0.47911	0.650000	0.86243	CTG		0.418	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		T	25156669	G	T	25156669	3	4	61	1	0	0	0	0	1	0	0	0	14095	933	33	2	881	2	SEPSECS	4	25156669	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27778	25156669	165997607	3089	11074										
PI4K2B	55300	broad.mit.edu	37	chr4	25254052	25254052	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatttttccagaaagaatCtctcaaggttcaagtggaag	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25254052C>T	ENST00000264864.6	+	2	567	c.378C>T	c.(376-378)atC>atT	p.I126I	PI4K2B_ENST00000512921.1_Silent_p.I30I	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	126					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.I126I(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				CAGAAAGAATCTCTCAAGGTT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	4											111	118	116					4																	25254052		2203	4300	6503	24863150	SO:0001819	synonymous_variant	55300			AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.378C>T	4.37:g.25254052C>T			24863150	Q9NUW2	Silent	SNP	ENST00000264864.6	37	CCDS3433.1																																																																																				0.368	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		T	25254052	C	T	25254052	2	4	61	1	0	0	0	0	0	0	0	1	11903	903	32	3		3	PI4K2B	4	25254052	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97383	25254052	165900224	3090	11075										
ANAPC4	29945	broad.mit.edu	37	chr4	25404633	25404633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacttcaaagcattttttCggtggctttatgtgggtaag	10	5	1	0	rs201488708		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25404633C>T	ENST00000315368.3	+	17	1397	c.1255C>T	c.(1255-1257)Cgg>Tgg	p.R419W	ANAPC4_ENST00000510092.1_Missense_Mutation_p.R419W	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	419					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)	p.R419W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				AGCATTTTTTCGGTGGCTTTA	0.279													C|||	1	0.000199681	0	0	5008	,	,		13524	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											89	91	90					4																	25404633		2199	4297	6496	25013731	SO:0001583	missense	29945			AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.1255C>T	4.37:g.25404633C>T	ENSP00000318775:p.Arg419Trp		25013731	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	19.38	3.816149	0.70912	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.36520	1.25;1.25	5.26	5.26	0.73747	Anaphase-promoting complex subunit 4 long domain (1);	0.000000	0.85682	D	0.000000	T	0.57359	0.2048	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.59413	-0.7459	10	0.72032	D	0.01	-10.8341	14.1248	0.65213	0.1502:0.8498:0.0:0.0	.	419	Q9UJX5	APC4_HUMAN	W	419	ENSP00000318775:R419W;ENSP00000426654:R419W	ENSP00000318775:R419W	R	+	1	2	ANAPC4	25013731	0.995000	0.38212	1.000000	0.80357	0.990000	0.78478	2.956000	0.49129	2.629000	0.89072	0.655000	0.94253	CGG		0.279	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		T	25404633	C	T	25404633	3	4	61	1	0	0	0	0	1	0	0	0	604	875	31	1	1317	1	ANAPC4	4	25404633	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150581	25404633	165749643	3091	11076										
ANAPC4	29945	broad.mit.edu	37	chr4	25416116	25416116	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacacgtagattgttcaaaTttccttttctgtaagtatat	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25416116T>A	ENST00000315368.3	+	24	1856	c.1714T>A	c.(1714-1716)Ttt>Att	p.F572I	ANAPC4_ENST00000510092.1_Missense_Mutation_p.F573I	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	572					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)	p.F572I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				ATTGTTCAAATTTCCTTTTCT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	68	68					4																	25416116		2193	4291	6484	25025214	SO:0001583	missense	29945			AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.1714T>A	4.37:g.25416116T>A	ENSP00000318775:p.Phe572Ile		25025214	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.669332	0.29693	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.30981	1.51;1.51	5.76	5.76	0.90799	.	0.062472	0.64402	D	0.000001	T	0.18841	0.0452	N	0.24115	0.695	0.34432	D	0.698634	B	0.25667	0.131	B	0.22386	0.039	T	0.28839	-1.0031	10	0.19147	T	0.46	-30.1425	9.2515	0.37557	0.0:0.14:0.0:0.86	.	572	Q9UJX5	APC4_HUMAN	I	572;573	ENSP00000318775:F572I;ENSP00000426654:F573I	ENSP00000318775:F572I	F	+	1	0	ANAPC4	25025214	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	1.722000	0.38042	2.199000	0.70637	0.477000	0.44152	TTT		0.274	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		A	25416116	T	A	25416116	3	1	61	1	0	0	0	0	1	0	0	0	604	1493	52	5	1804	5	ANAPC4	4	25416116	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11483	25416116	165738160	3092	11077										
ANAPC4	29945	broad.mit.edu	37	chr4	25418160	25418160	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggtccagctgcctttgtCtttagtatataacagtgaag	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25418160C>A	ENST00000315368.3	+	27	2157	c.2015C>A	c.(2014-2016)tCt>tAt	p.S672Y	ANAPC4_ENST00000510092.1_Missense_Mutation_p.S673Y	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	672					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)	p.S672Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				CTGCCTTTGTCTTTAGTATAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	109	111					4																	25418160		2203	4300	6503	25027258	SO:0001583	missense	29945			AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.2015C>A	4.37:g.25418160C>A	ENSP00000318775:p.Ser672Tyr		25027258	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305898	0.81247	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.35236	1.32;1.32	5.68	5.68	0.88126	.	0.267830	0.44097	D	0.000484	T	0.38480	0.1042	L	0.29908	0.895	0.54753	D	0.999988	D	0.56521	0.976	P	0.47744	0.556	T	0.18023	-1.0350	10	0.59425	D	0.04	-26.1981	19.7941	0.96472	0.0:1.0:0.0:0.0	.	672	Q9UJX5	APC4_HUMAN	Y	672;673	ENSP00000318775:S672Y;ENSP00000426654:S673Y	ENSP00000318775:S672Y	S	+	2	0	ANAPC4	25027258	1.000000	0.71417	0.948000	0.38648	0.962000	0.63368	4.155000	0.58131	2.681000	0.91329	0.544000	0.68410	TCT		0.358	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		A	25418160	C	A	25418160	3	1	61	1	0	0	0	0	1	0	0	0	604	913	32	2	2117	2	ANAPC4	4	25418160	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2044	25418160	165736116	3093	11078										
SEL1L3	23231	broad.mit.edu	37	chr4	25789939	25789939	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaattgctgcttcgggattCttggccacaccttgctgccc	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:25789939C>A	ENST00000399878.3	-	13	2246	c.2124G>T	c.(2122-2124)aaG>aaT	p.K708N	SEL1L3_ENST00000502949.1_Missense_Mutation_p.K555N|SEL1L3_ENST00000264868.5_Missense_Mutation_p.K673N	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	708						integral component of membrane (GO:0016021)		p.K555N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CTTCGGGATTCTTGGCCACAC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											113	111	112					4																	25789939		1959	4142	6101	25399037	SO:0001583	missense	23231			BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.2124G>T	4.37:g.25789939C>A	ENSP00000382767:p.Lys708Asn		25399037	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789811	0.70337	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.54866	0.55;0.55;0.55	5.5	3.45	0.39498	Tetratricopeptide-like helical (1);	0.165194	0.52532	D	0.000077	T	0.50582	0.1624	N	0.14661	0.345	0.43803	D	0.996356	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.984	T	0.53795	-0.8388	10	0.66056	D	0.02	-26.0572	6.4537	0.21918	0.0:0.6291:0.0:0.3709	.	115;708	B4DTH5;Q68CR1	.;SE1L3_HUMAN	N	708;673;555	ENSP00000382767:K708N;ENSP00000264868:K673N;ENSP00000425438:K555N	ENSP00000264868:K673N	K	-	3	2	SEL1L3	25399037	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.580000	0.36547	1.318000	0.45170	0.563000	0.77884	AAG		0.463	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25789939	C	A	25789939	3	1	61	1	0	0	0	0	1	0	0	0	14049	912	32	2	1322	2	SEL1L3	4	25789939	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	371779	25789939	165364337	3094	11079										
RBPJ	3516	broad.mit.edu	37	chr4	26422267	26422267	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctatggcaacagtgatgAcattggtgtgttcctcagca	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:26422267A>G	ENST00000361572.6	+	5	649	c.455A>G	c.(454-456)gAc>gGc	p.D152G	RBPJ_ENST00000342295.1_Missense_Mutation_p.D152G|RBPJ_ENST00000348160.4_Missense_Mutation_p.D139G|RBPJ_ENST00000342320.4_Missense_Mutation_p.D138G|RBPJ_ENST00000507561.1_Missense_Mutation_p.D117G|RBPJ_ENST00000355476.3_Missense_Mutation_p.D138G|RBPJ_ENST00000504907.1_Missense_Mutation_p.D138G|RBPJ_ENST00000345843.3_Missense_Mutation_p.D137G			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	152					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D138G(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				AACAGTGATGACATTGGTGTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											94	82	86					4																	26422267		2203	4300	6503	26031365	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.455A>G	4.37:g.26422267A>G	ENSP00000354528:p.Asp152Gly		26031365	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.986172	0.93044	.	.	ENSG00000168214	ENST00000510778;ENST00000512671;ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000507574;ENST00000515573;ENST00000504907;ENST00000342320;ENST00000504938	D;D;D;D;D;D;D;D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.65	5.65	0.86999	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.042171	0.85682	D	0.000000	D	0.89322	0.6682	M	0.85373	2.75	0.80722	D	1	P;P;P;P;P;P	0.46912	0.886;0.886;0.71;0.662;0.662;0.814	P;P;P;P;P;P	0.51615	0.577;0.577;0.675;0.546;0.546;0.675	D	0.90845	0.4726	10	0.66056	D	0.02	-17.4941	15.8591	0.79009	1.0:0.0:0.0:0.0	.	152;138;139;138;137;152	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	G	175;152;137;152;152;139;138;117;117;117;138;138;117	ENSP00000427170:D175G;ENSP00000423644:D152G;ENSP00000305815:D137G;ENSP00000345206:D152G;ENSP00000354528:D152G;ENSP00000339699:D139G;ENSP00000347659:D138G;ENSP00000423907:D117G;ENSP00000422617:D117G;ENSP00000423406:D117G;ENSP00000423703:D138G;ENSP00000340124:D138G;ENSP00000424459:D117G	ENSP00000345206:D152G	D	+	2	0	RBPJ	26031365	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.095000	0.76952	2.150000	0.67090	0.528000	0.53228	GAC		0.383	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		G	26422267	A	G	26422267	3	3	61	1	0	0	0	0	1	0	0	0	13198	275	10	4	536	4	RBPJ	4	26422267	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	632328	26422267	164732009	3095	11080										
RBPJ	3516	broad.mit.edu	37	chr4	26426325	26426325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattatggacaaacagtcaAacttgtgtgctcagttactg	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:26426325A>C	ENST00000361572.6	+	7	940	c.746A>C	c.(745-747)aAa>aCa	p.K249T	RBPJ_ENST00000342295.1_Missense_Mutation_p.K249T|RBPJ_ENST00000348160.4_Missense_Mutation_p.K236T|RBPJ_ENST00000342320.4_Missense_Mutation_p.K235T|RBPJ_ENST00000507561.1_Missense_Mutation_p.K214T|RBPJ_ENST00000355476.3_Missense_Mutation_p.K235T|RBPJ_ENST00000504907.1_Missense_Mutation_p.K235T|RBPJ_ENST00000345843.3_Missense_Mutation_p.K234T			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	249					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K235T(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				CAAACAGTCAAACTTGTGTGC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											89	82	85					4																	26426325		2203	4300	6503	26035423	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.746A>C	4.37:g.26426325A>C	ENSP00000354528:p.Lys249Thr		26035423	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.393521	0.83011	.	.	ENSG00000168214	ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000504907;ENST00000342320	T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.51	5.51	0.81932	Beta-trefoil (2);	0.000000	0.85682	D	0.000000	T	0.53206	0.1782	M	0.65320	2	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.999;0.999	T	0.52668	-0.8545	10	0.48119	T	0.1	-20.0448	15.6	0.76616	1.0:0.0:0.0:0.0	.	249;235;236;235;234;249	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	T	234;249;249;236;235;214;235;235	ENSP00000305815:K234T;ENSP00000345206:K249T;ENSP00000354528:K249T;ENSP00000339699:K236T;ENSP00000347659:K235T;ENSP00000423907:K214T;ENSP00000423703:K235T;ENSP00000340124:K235T	ENSP00000345206:K249T	K	+	2	0	RBPJ	26035423	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	8.870000	0.92336	2.087000	0.62958	0.455000	0.32223	AAA		0.378	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		C	26426325	A	C	26426325	3	2	61	1	0	0	0	0	1	0	0	0	13198	14	1	4	835	4	RBPJ	4	26426325	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4058	26426325	164727951	3096	11081										
CCKAR	886	broad.mit.edu	37	chr4	26487312	26487312	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcggcacatattcgcggtCtggttgttatttttggtaaa	11	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:26487312C>A	ENST00000295589.3	-	3	767	c.573G>T	c.(571-573)caG>caT	p.Q191H		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	191					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)	p.Q191H(1)		NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	TATTCGCGGTCTGGTTGTTAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	112	113					4																	26487312		2203	4300	6503	26096410	SO:0001583	missense	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.573G>T	4.37:g.26487312C>A	ENSP00000295589:p.Gln191His		26096410	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.144578	0.37825	.	.	ENSG00000163394	ENST00000295589	T	0.37235	1.21	5.69	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	0.171410	0.50627	D	0.000114	T	0.38532	0.1044	L	0.31294	0.92	0.37278	D	0.907719	P	0.45011	0.848	P	0.53266	0.722	T	0.40850	-0.9541	10	0.46703	T	0.11	.	10.61	0.45417	0.0:0.7546:0.1697:0.0757	.	191	P32238	CCKAR_HUMAN	H	191	ENSP00000295589:Q191H	ENSP00000295589:Q191H	Q	-	3	2	CCKAR	26096410	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	2.480000	0.45206	1.397000	0.46682	0.650000	0.86243	CAG		0.403	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			A	26487312	C	A	26487312	3	1	61	1	0	0	0	0	1	0	0	0	2886	912	32	2	725	2	CCKAR	4	26487312	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60987	26487312	164666964	3097	11082										
STIM2	57620	broad.mit.edu	37	chr4	26959261	26959261	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagatatgaaatataaaGatgctactaataaacacagc	7	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:26959261G>T	ENST00000467011.1	+	3	735	c.310G>T	c.(310-312)Gat>Tat	p.D104Y	STIM2_ENST00000382009.3_Missense_Mutation_p.D191Y|STIM2_ENST00000465503.1_Missense_Mutation_p.D104Y|STIM2_ENST00000412829.2_Missense_Mutation_p.D191Y|STIM2_ENST00000237364.5_Missense_Mutation_p.D191Y|STIM2_ENST00000467087.1_Missense_Mutation_p.D104Y	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	104					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)	p.D191Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				GAAATATAAAGATGCTACTAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	4											109	117	114					4																	26959261		2203	4300	6503	26568359	SO:0001583	missense	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.310G>T	4.37:g.26959261G>T	ENSP00000419383:p.Asp104Tyr		26568359	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149850	0.78001	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503	T;T;T;T;T;T	0.80480	-1.33;-1.35;-1.35;-1.34;-1.38;-1.32	5.75	5.75	0.90469	.	0.104159	0.64402	D	0.000003	D	0.88168	0.6364	L	0.56199	1.76	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.88413	0.3023	10	0.72032	D	0.01	.	18.7177	0.91682	0.0:0.0:1.0:0.0	.	191;191;191	A6H8L7;E9PGD0;F5GXJ4	.;.;.	Y	104;191;191;104;191;104	ENSP00000419073:D104Y;ENSP00000371439:D191Y;ENSP00000237364:D191Y;ENSP00000419383:D104Y;ENSP00000404812:D191Y;ENSP00000417569:D104Y	ENSP00000237364:D191Y	D	+	1	0	STIM2	26568359	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.035000	0.64158	2.717000	0.92951	0.585000	0.79938	GAT		0.308	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		T	26959261	G	T	26959261	3	4	61	1	0	0	0	0	1	0	0	0	15323	942	33	2	320	2	STIM2	4	26959261	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	471949	26959261	164195015	3098	11083										
STIM2	57620	broad.mit.edu	37	chr4	27009179	27009179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatggctctgaaaaaggccGaaaaagaatttgaactgaga	11	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:27009179G>A	ENST00000467011.1	+	8	1431	c.1006G>A	c.(1006-1008)Gaa>Aaa	p.E336K	STIM2_ENST00000382009.3_Missense_Mutation_p.E423K|STIM2_ENST00000465503.1_Missense_Mutation_p.E336K|STIM2_ENST00000412829.2_Missense_Mutation_p.E423K|STIM2_ENST00000237364.5_Missense_Mutation_p.E423K|STIM2_ENST00000467087.1_Missense_Mutation_p.E336K	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	336					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)	p.E423K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				GAAAAAGGCCGAAAAAGAATT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	59	59					4																	27009179		2203	4300	6503	26618277	SO:0001583	missense	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.1006G>A	4.37:g.27009179G>A	ENSP00000419383:p.Glu336Lys		26618277	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856947	0.91433	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503;ENST00000473519	D;D;D;D;D;D;D	0.84800	-1.76;-1.74;-1.77;-1.78;-1.78;-1.73;-1.9	5.22	5.22	0.72569	.	0.105878	0.64402	D	0.000005	D	0.93051	0.7788	M	0.82630	2.6	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.986;0.981;0.981;0.992	D	0.93771	0.7075	10	0.87932	D	0	.	19.1387	0.93439	0.0:0.0:1.0:0.0	.	336;423;423;423	Q9P246;A6H8L7;E9PGD0;F5GXJ4	STIM2_HUMAN;.;.;.	K	336;423;423;336;423;336;44	ENSP00000419073:E336K;ENSP00000371439:E423K;ENSP00000237364:E423K;ENSP00000419383:E336K;ENSP00000404812:E423K;ENSP00000417569:E336K;ENSP00000420113:E44K	ENSP00000237364:E423K	E	+	1	0	STIM2	26618277	1.000000	0.71417	0.996000	0.52242	0.826000	0.46750	9.420000	0.97426	2.603000	0.88011	0.591000	0.81541	GAA		0.393	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		A	27009179	G	A	27009179	3	1	61	1	0	0	0	0	1	0	0	0	15323	1059	37	1	1036	1	STIM2	4	27009179	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49918	27009179	164145097	3099	11084										
STIM2	57620	broad.mit.edu	37	chr4	27019558	27019558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttgccctgcgctttatcGaaatgaagaggaggaagagg	14	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:27019558G>A	ENST00000467011.1	+	11	2140	c.1715G>A	c.(1714-1716)cGa>cAa	p.R572Q	STIM2_ENST00000382009.3_Missense_Mutation_p.R667Q|STIM2_ENST00000465503.1_Missense_Mutation_p.R580Q|STIM2_ENST00000412829.2_Missense_Mutation_p.R659Q|STIM2_ENST00000237364.5_Missense_Mutation_p.R659Q|STIM2_ENST00000467087.1_Missense_Mutation_p.R572Q	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	572					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)	p.R659Q(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				GCGCTTTATCGAAATGAAGAG	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	4											286	278	281					4																	27019558		2203	4300	6503	26628656	SO:0001583	missense	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.1715G>A	4.37:g.27019558G>A	ENSP00000419383:p.Arg572Gln		26628656	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	G	35	5.419534	0.96111	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503;ENST00000473519;ENST00000477474	T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.40543	1.245	0.58432	D	0.999997	D;D;D;D	0.76494	0.997;0.999;0.999;0.999	D;D;D;D	0.77557	0.968;0.978;0.978;0.99	T	0.60188	-0.7312	10	0.66056	D	0.02	.	18.9976	0.92819	0.0:0.0:1.0:0.0	.	572;659;667;659	Q9P246;A6H8L7;E9PGD0;F5GXJ4	STIM2_HUMAN;.;.;.	Q	572;667;659;572;659;580;280;174	ENSP00000419073:R572Q;ENSP00000371439:R667Q;ENSP00000237364:R659Q;ENSP00000419383:R572Q;ENSP00000404812:R659Q;ENSP00000417569:R580Q;ENSP00000420113:R280Q;ENSP00000419536:R174Q	ENSP00000237364:R659Q	R	+	2	0	STIM2	26628656	1.000000	0.71417	0.977000	0.42913	0.980000	0.70556	4.993000	0.63895	2.483000	0.83821	0.460000	0.39030	CGA		0.522	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		A	27019558	G	A	27019558	3	1	61	1	0	0	0	0	1	0	0	0	15323	1058	37	1	1785	1	STIM2	4	27019558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10379	27019558	164134718	3100	11085										
PCDH7	5099	broad.mit.edu	37	chr4	30724322	30724322	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgggcgcatccccctcaaGgacggggtggccaacgtggc	15	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:30724322G>T	ENST00000361762.2	+	1	2286	c.1278G>T	c.(1276-1278)aaG>aaT	p.K426N	PCDH7_ENST00000543491.1_Missense_Mutation_p.K426N	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	426	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K379N(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TCCCCCTCAAGGACGGGGTGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	4											44	42	43					4																	30724322		2203	4300	6503	30333420	SO:0001583	missense	5099			AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1278G>T	4.37:g.30724322G>T	ENSP00000355243:p.Lys426Asn		30333420	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.572|7.572	0.666990|0.666990	0.14710|0.14710	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.52295	.|0.69;0.67	5.48|5.48	2.68|2.68	0.31781|0.31781	.|Cadherin-like (1);	.|.	.|.	.|.	.|.	.|T	.|0.29783	.|0.0744	N|N	0.12182|0.12182	0.205|0.205	0.46586|0.46586	D|D	0.999112|0.999112	.|B;B;B	.|0.28933	.|0.222;0.222;0.228	.|B;B;B	.|0.35278	.|0.199;0.199;0.129	.|T	.|0.05852	.|-1.0860	.|9	.|0.31617	.|T	.|0.26	.|.	8.4303|8.4303	0.32753|0.32753	0.1366:0.1268:0.7366:0.0|0.1366:0.1268:0.7366:0.0	.|.	.|426;379;426	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	X|N	116|426;426;379	.|ENSP00000355243:K426N;ENSP00000441802:K426N	.|ENSP00000330302:K379N	G|K	+|+	1|3	0|2	PCDH7|PCDH7	30333420|30333420	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	2.695000|2.695000	0.47043|0.47043	0.690000|0.690000	0.31570|0.31570	0.655000|0.655000	0.94253|0.94253	GGA|AAG		0.617	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30724322	G	T	30724322	3	4	61	1	0	0	0	0	1	0	0	0	11547	991	35	2	1280	2	PCDH7	4	30724322	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3704764	30724322	160429954	3101	11086										
ARAP2	116984	broad.mit.edu	37	chr4	36121307	36121307	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggtaataaagctattttCtatgtccatttgtttgactt	6	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:36121307C>A	ENST00000303965.4	-	24	4417	c.3928G>T	c.(3928-3930)Gaa>Taa	p.E1310*		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1310					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.E1310*(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAGCTATTTTCTATGTCCATT	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											175	179	178					4																	36121307		2203	4297	6500	35797702	SO:0001587	stop_gained	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.3928G>T	4.37:g.36121307C>A	ENSP00000302895:p.Glu1310*		35797702	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Nonsense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	C	47	13.463816	0.99743	.	.	ENSG00000047365	ENST00000303965	.	.	.	5.06	5.06	0.68205	.	0.114475	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.6122	0.91290	0.0:1.0:0.0:0.0	.	.	.	.	X	1310	.	ENSP00000302895:E1310X	E	-	1	0	ARAP2	35797702	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.011000	0.70760	2.631000	0.89168	0.585000	0.79938	GAA		0.303	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36121307	C	A	36121307	4	1	61	1	0	0	0	0	0	1	0	0	839	922	32	2	1226	2	ARAP2	4	36121307	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5396985	36121307	155032969	3102	11087										
ARAP2	116984	broad.mit.edu	37	chr4	36214928	36214928	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaagatggaagatgaattCtcctcatttgaatcttttag	9	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:36214928C>A	ENST00000303965.4	-	4	1467	c.978G>T	c.(976-978)gaG>gaT	p.E326D		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	326					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.E326D(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAGATGAATTCTCCTCATTTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	67	66					4																	36214928		2203	4297	6500	35891323	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.978G>T	4.37:g.36214928C>A	ENSP00000302895:p.Glu326Asp		35891323	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846280	0.32606	.	.	ENSG00000047365	ENST00000303965	T	0.08896	3.04	5.57	1.4	0.22301	.	0.232737	0.36002	N	0.002857	T	0.03564	0.0102	N	0.17474	0.49	0.21897	N	0.999489	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.44159	-0.9346	10	0.10111	T	0.7	.	3.7018	0.08386	0.3483:0.4571:0.0:0.1945	.	256;326	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	D	326	ENSP00000302895:E326D	ENSP00000302895:E326D	E	-	3	2	ARAP2	35891323	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	0.058000	0.14301	0.316000	0.23135	0.591000	0.81541	GAG		0.313	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36214928	C	A	36214928	3	1	61	1	0	0	0	0	1	0	0	0	839	912	32	2	4256	2	ARAP2	4	36214928	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93621	36214928	154939348	3103	11088										
ARAP2	116984	broad.mit.edu	37	chr4	36231073	36231073	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatgctcattaggaaatcTtttatatccacatttacttc	3	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:36231073T>A	ENST00000303965.4	-	2	525	c.36A>T	c.(34-36)aaA>aaT	p.K12N		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	12	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.K12N(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTAGGAAATCTTTTATATCCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	77	75					4																	36231073		2191	4288	6479	35907468	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.36A>T	4.37:g.36231073T>A	ENSP00000302895:p.Lys12Asn		35907468	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.055494	0.36277	.	.	ENSG00000047365	ENST00000303965;ENST00000506189	T;T	0.64618	-0.11;-0.11	5.58	3.14	0.36123	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	1.240770	0.05286	N	0.520305	T	0.51517	0.1679	L	0.29908	0.895	0.22292	N	0.999221	B	0.32010	0.351	B	0.34038	0.174	T	0.42982	-0.9419	10	0.41790	T	0.15	.	6.0288	0.19669	0.0:0.141:0.137:0.7219	.	12	Q8WZ64	ARAP2_HUMAN	N	12	ENSP00000302895:K12N;ENSP00000422731:K12N	ENSP00000302895:K12N	K	-	3	2	ARAP2	35907468	0.996000	0.38824	0.981000	0.43875	0.612000	0.37316	1.617000	0.36943	0.412000	0.25729	0.524000	0.50904	AAA		0.393	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36231073	T	A	36231073	3	1	61	1	0	0	0	0	1	0	0	0	839	1606	56	5	5206	5	ARAP2	4	36231073	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	16145	36231073	154923203	3104	11089										
RELL1	768211	broad.mit.edu	37	chr4	37648998	37648998	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgttcacaccttcatttTtcatgatgtagtggacgatt	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:37648998T>G	ENST00000454158.2	-	3	465	c.377A>C	c.(376-378)aAa>aCa	p.K126T	RELL1_ENST00000314117.4_Missense_Mutation_p.K126T	NM_001085400.1	NP_001078869.1	Q8IUW5	RELL1_HUMAN	RELT-like 1	126						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)		p.K126T(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6						ACCTTCATTTTTCATGATGTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											99	88	92					4																	37648998		1876	4115	5991	37325393	SO:0001583	missense	768211			AK025431	CCDS43221.1	4p14	2011-10-11				ENSG00000181826			27379	protein-coding gene	gene with protein product		611212				16389068	Standard	NM_001085399		Approved		uc003gsz.2	Q8IUW5		ENST00000454158.2:c.377A>C	4.37:g.37648998T>G	ENSP00000398778:p.Lys126Thr		37325393	Q8NBK1	Missense_Mutation	SNP	ENST00000454158.2	37	CCDS43221.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.924891	0.73213	.	.	ENSG00000181826	ENST00000314117;ENST00000454158;ENST00000512114	T;T;T	0.34667	1.37;1.37;1.35	5.67	4.5	0.54988	.	0.137935	0.64402	D	0.000005	T	0.41766	0.1173	L	0.60455	1.87	0.47862	D	0.999538	D	0.57899	0.981	P	0.49637	0.617	T	0.39781	-0.9597	10	0.66056	D	0.02	-15.6449	10.0552	0.42241	0.0:0.0788:0.0:0.9212	.	126	Q8IUW5	RELL1_HUMAN	T	126;126;147	ENSP00000313385:K126T;ENSP00000398778:K126T;ENSP00000424031:K147T	ENSP00000313385:K126T	K	-	2	0	RELL1	37325393	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.510000	0.45468	2.164000	0.68074	0.533000	0.62120	AAA		0.358	RELL1-002	KNOWN	alternative_3_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360485.1	NM_001085400		G	37648998	T	G	37648998	3	3	61	1	0	0	0	0	1	0	0	0	13255	1841	64	4	454	4	RELL1	4	37648998	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1417925	37648998	153505278	3105	11090										
RELL1	768211	broad.mit.edu	37	chr4	37650923	37650923	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcaaccttttcctcttcGatatcttgctctgcttctgt	4	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:37650923G>A	ENST00000454158.2	-	2	376	c.288C>T	c.(286-288)atC>atT	p.I96I	RELL1_ENST00000314117.4_Silent_p.I96I	NM_001085400.1	NP_001078869.1	Q8IUW5	RELL1_HUMAN	RELT-like 1	96						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)		p.I96I(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6						TTTCCTCTTCGATATCTTGCT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	4											161	167	165					4																	37650923		1895	4114	6009	37327318	SO:0001819	synonymous_variant	768211			AK025431	CCDS43221.1	4p14	2011-10-11				ENSG00000181826			27379	protein-coding gene	gene with protein product		611212				16389068	Standard	NM_001085399		Approved		uc003gsz.2	Q8IUW5		ENST00000454158.2:c.288C>T	4.37:g.37650923G>A			37327318	Q8NBK1	Silent	SNP	ENST00000454158.2	37	CCDS43221.1																																																																																				0.408	RELL1-002	KNOWN	alternative_3_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360485.1	NM_001085400		A	37650923	G	A	37650923	2	1	61	1	0	0	0	0	0	0	0	1	13255	1048	37	1		1	RELL1	4	37650923	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1925	37650923	153503353	3106	11091										
TLR10	81793	broad.mit.edu	37	chr4	38775007	38775007	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctggtgggaatgcaataGaatggaatgggttccagtaa	13	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38775007G>T	ENST00000308973.4	-	4	2810	c.2205C>A	c.(2203-2205)ttC>ttA	p.F735L	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Missense_Mutation_p.F735L|TLR10_ENST00000508334.1_Missense_Mutation_p.F735L|TLR10_ENST00000506111.1_Missense_Mutation_p.F735L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	735	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.A16D(1)|p.F735L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GAATGCAATAGAATGGAATGG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	4											87	91	89					4																	38775007		2203	4300	6503	38451402	SO:0001583	missense	81793			AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.2205C>A	4.37:g.38775007G>T	ENSP00000308925:p.Phe735Leu		38451402	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	9.997	1.232491	0.22626	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.56	-4.7	0.03288	Toll/interleukin-1 receptor homology (TIR) domain (4);	1.197910	0.06351	N	0.709933	T	0.42653	0.1212	N	0.00112	-2.095	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	10	0.27785	T	0.31	.	10.8378	0.46698	0.0603:0.5529:0.2583:0.1285	.	735	Q9BXR5	TLR10_HUMAN	L	735	ENSP00000308925:F735L;ENSP00000421483:F735L;ENSP00000354459:F735L;ENSP00000424923:F735L	ENSP00000308925:F735L	F	-	3	2	TLR10	38451402	0.000000	0.05858	0.007000	0.13788	0.723000	0.41478	-2.525000	0.00948	-0.921000	0.03794	-0.181000	0.13052	TTC		0.403	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			T	38775007	G	T	38775007	3	4	61	1	0	0	0	0	1	0	0	0	15989	933	33	2	234	2	TLR10	4	38775007	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1124084	38775007	152379269	3107	11092										
TLR10	81793	broad.mit.edu	37	chr4	38775316	38775316	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaataaatgcgtggaatcgGacatttctcttgagttgttc	10	6	1	1	rs148341393		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38775316G>A	ENST00000308973.4	-	4	2501	c.1896C>T	c.(1894-1896)gtC>gtT	p.V632V	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Silent_p.V632V|TLR10_ENST00000508334.1_Silent_p.V632V|TLR10_ENST00000506111.1_Silent_p.V632V	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	632	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.V632V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CGTGGAATCGGACATTTCTCT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G	,,,,	0,4406		0,0,2203	138	130	133		1896,1896,1896,1854,1896	3.3	1	4	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	632/812,632/812,632/812,618/798,632/812	38775316	1,13005	2203	4300	6503	38451711	SO:0001819	synonymous_variant	81793			AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.1896C>T	4.37:g.38775316G>A			38451711	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																				0.418	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			A	38775316	G	A	38775316	2	1	61	1	0	0	0	0	0	0	0	1	15989	1161	41	3		3	TLR10	4	38775316	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	309	38775316	152378960	3108	11093										
TLR10	81793	broad.mit.edu	37	chr4	38776947	38776947	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgaattcaaaggttttgaGatccagctgttgaattctgt	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38776947G>A	ENST00000308973.4	-	4	870	c.265C>T	c.(265-267)Ctc>Ttc	p.L89F	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Missense_Mutation_p.L89F|TLR10_ENST00000508334.1_Missense_Mutation_p.L89F|TLR10_ENST00000506111.1_Missense_Mutation_p.L89F	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	89					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.L89F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						AAGGTTTTGAGATCCAGCTGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	61	61					4																	38776947		2203	4300	6503	38453342	SO:0001583	missense	81793			AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.265C>T	4.37:g.38776947G>A	ENSP00000308925:p.Leu89Phe		38453342	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.739439	0.00681	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334;ENST00000502321	T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;4.25	5.23	-3.23	0.05109	.	0.816262	0.10288	N	0.692715	T	0.32102	0.0818	L	0.45352	1.415	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.29088	-1.0023	10	0.13470	T	0.59	.	0.4875	0.00559	0.3701:0.1392:0.2068:0.2839	.	89	Q9BXR5	TLR10_HUMAN	F	89;89;89;89;75	ENSP00000308925:L89F;ENSP00000421483:L89F;ENSP00000354459:L89F;ENSP00000424923:L89F;ENSP00000427606:L75F	ENSP00000308925:L89F	L	-	1	0	TLR10	38453342	0.000000	0.05858	0.785000	0.31869	0.050000	0.14768	-0.400000	0.07241	-0.580000	0.05944	-1.104000	0.02111	CTC		0.353	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			A	38776947	G	A	38776947	3	1	61	1	0	0	0	0	1	0	0	0	15989	942	33	3	2174	3	TLR10	4	38776947	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1631	38776947	152377329	3109	11094										
TLR10	81793	broad.mit.edu	37	chr4	38777198	38777198	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaaaatatgtaaatgtttCtgatgagtctcattgtattt	6	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38777198C>A	ENST00000308973.4	-	4	619	c.14G>T	c.(13-15)aGa>aTa	p.R5I	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Missense_Mutation_p.R5I|TLR10_ENST00000508334.1_Missense_Mutation_p.R5I|TLR10_ENST00000506111.1_Missense_Mutation_p.R5I	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	5					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.R5I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GTAAATGTTTCTGATGAGTCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											58	61	60					4																	38777198		2203	4299	6502	38453593	SO:0001583	missense	81793			AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.14G>T	4.37:g.38777198C>A	ENSP00000308925:p.Arg5Ile		38453593	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	C	7.772	0.707582	0.15239	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.13901	2.55;2.55;2.55;2.55	5.36	4.5	0.54988	.	0.339514	0.21112	N	0.079978	T	0.09247	0.0228	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24012	-1.0172	10	0.36615	T	0.2	.	8.5205	0.33273	0.2577:0.5523:0.1901:0.0	.	5	Q9BXR5	TLR10_HUMAN	I	5	ENSP00000308925:R5I;ENSP00000421483:R5I;ENSP00000354459:R5I;ENSP00000424923:R5I	ENSP00000308925:R5I	R	-	2	0	TLR10	38453593	0.985000	0.35326	0.089000	0.20774	0.333000	0.28666	0.413000	0.21148	1.212000	0.43366	0.655000	0.94253	AGA		0.358	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			A	38777198	C	A	38777198	3	1	61	1	0	0	0	0	1	0	0	0	15989	913	32	2	2425	2	TLR10	4	38777198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	251	38777198	152377078	3110	11095										
TLR1	7096	broad.mit.edu	37	chr4	38798514	38798514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttcacccagaaagaatCgtgcccactatatgaaataa	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38798514C>T	ENST00000502213.2	-	3	2168	c.1939G>A	c.(1939-1941)Gat>Aat	p.D647N	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Missense_Mutation_p.D647N			Q15399	TLR1_HUMAN	toll-like receptor 1	647	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.D647N(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						CAGAAAGAATCGTGCCCACTA	0.448																																					GBM(5;216 373 40795 46382)											1	Substitution - Missense(1)	large_intestine(1)	4											94	95	94					4																	38798514		2203	4300	6503	38474909	SO:0001583	missense	7096			U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1939G>A	4.37:g.38798514C>T	ENSP00000421259:p.Asp647Asn		38474909	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673090	0.67928	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.08102	3.13;3.13	5.29	5.29	0.74685	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.080772	0.50627	D	0.000113	T	0.35307	0.0927	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.20638	-1.0269	10	0.87932	D	0	.	19.3152	0.94208	0.0:1.0:0.0:0.0	.	647	Q15399	TLR1_HUMAN	N	647	ENSP00000354932:D647N;ENSP00000421259:D647N	ENSP00000354932:D647N	D	-	1	0	TLR1	38474909	1.000000	0.71417	0.983000	0.44433	0.514000	0.34195	5.791000	0.69045	2.648000	0.89879	0.563000	0.77884	GAT		0.448	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38798514	C	T	38798514	3	4	61	1	0	0	0	0	1	0	0	0	15988	884	31	1	425	1	TLR1	4	38798514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21316	38798514	152355762	3111	11096										
TLR1	7096	broad.mit.edu	37	chr4	38799017	38799017	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccaggaaggtcagttaaaGaattgaaagcaacattgagt	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38799017G>T	ENST00000502213.2	-	3	1665	c.1436C>A	c.(1435-1437)tCt>tAt	p.S479Y	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Missense_Mutation_p.S479Y			Q15399	TLR1_HUMAN	toll-like receptor 1	479					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.S479Y(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						GTCAGTTAAAGAATTGAAAGC	0.403																																					GBM(5;216 373 40795 46382)											1	Substitution - Missense(1)	large_intestine(1)	4											69	73	72					4																	38799017		2203	4297	6500	38475412	SO:0001583	missense	7096			U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1436C>A	4.37:g.38799017G>T	ENSP00000421259:p.Ser479Tyr		38475412	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	G	8.371	0.835295	0.16820	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.60672	0.17;0.17	4.61	-1.64	0.08318	.	0.739162	0.12165	N	0.493602	T	0.37652	0.1011	L	0.38649	1.16	0.09310	N	0.999999	B	0.17038	0.02	B	0.18561	0.022	T	0.29427	-1.0012	10	0.48119	T	0.1	.	0.0517	0.00012	0.3079:0.1796:0.196:0.3166	.	479	Q15399	TLR1_HUMAN	Y	479	ENSP00000354932:S479Y;ENSP00000421259:S479Y	ENSP00000354932:S479Y	S	-	2	0	TLR1	38475412	0.000000	0.05858	0.201000	0.23476	0.981000	0.71138	-0.021000	0.12504	-0.257000	0.09459	0.650000	0.86243	TCT		0.403	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38799017	G	T	38799017	3	4	61	1	0	0	0	0	1	0	0	0	15988	942	33	2	928	2	TLR1	4	38799017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	503	38799017	152355259	3112	11097										
TLR1	7096	broad.mit.edu	37	chr4	38799708	38799708	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaatgttgtttaaggtaaGatttgataactttggatttg	9	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38799708G>T	ENST00000502213.2	-	3	974	c.745C>A	c.(745-747)Ctt>Att	p.L249I	TLR1_ENST00000308979.2_Missense_Mutation_p.L249I			Q15399	TLR1_HUMAN	toll-like receptor 1	249					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L249I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TTTAAGGTAAGATTTGATAAC	0.333																																					GBM(5;216 373 40795 46382)											1	Substitution - Missense(1)	large_intestine(1)	4											60	67	64					4																	38799708		2203	4300	6503	38476103	SO:0001583	missense	7096			U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.745C>A	4.37:g.38799708G>T	ENSP00000421259:p.Leu249Ile		38476103	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.464846	0.26335	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.69926	-0.44;-0.44	4.69	2.86	0.33363	.	0.000000	0.56097	D	0.000034	T	0.65616	0.2708	M	0.74389	2.26	0.27234	N	0.959338	D	0.53885	0.963	P	0.44447	0.45	T	0.62737	-0.6791	10	0.72032	D	0.01	.	8.7866	0.34825	0.2588:0.0:0.7412:0.0	.	249	Q15399	TLR1_HUMAN	I	249	ENSP00000354932:L249I;ENSP00000421259:L249I	ENSP00000354932:L249I	L	-	1	0	TLR1	38476103	0.996000	0.38824	0.285000	0.24819	0.005000	0.04900	2.217000	0.42880	0.618000	0.30179	-0.150000	0.13652	CTT		0.333	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38799708	G	T	38799708	3	4	61	1	0	0	0	0	1	0	0	0	15988	942	33	2	1619	2	TLR1	4	38799708	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	691	38799708	152354568	3113	11098										
FAM114A1	92689	broad.mit.edu	37	chr4	38879919	38879919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccccctgtgcagcctcagGatgccaacgccctggagccc	12	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38879919G>A	ENST00000358869.2	+	3	396	c.220G>A	c.(220-222)Gat>Aat	p.D74N	FAM114A1_ENST00000515037.1_Intron	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	74						cytoplasm (GO:0005737)		p.D74N(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GCAGCCTCAGGATGCCAACGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	4											40	41	41					4																	38879919		2203	4300	6503	38556314	SO:0001583	missense	92689				CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.220G>A	4.37:g.38879919G>A	ENSP00000351740:p.Asp74Asn		38556314	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.362939	0.24684	.	.	ENSG00000197712	ENST00000510213;ENST00000358869	T;T	0.23552	1.9;2.93	3.86	3.0	0.34707	.	0.485372	0.20233	N	0.096460	T	0.19725	0.0474	L	0.47716	1.5	0.09310	N	1	B	0.24186	0.099	B	0.19391	0.025	T	0.18999	-1.0319	10	0.17832	T	0.49	-8.1125	9.3801	0.38309	0.0:0.2192:0.7808:0.0	.	74	Q8IWE2	NXP20_HUMAN	N	74	ENSP00000422965:D74N;ENSP00000351740:D74N	ENSP00000351740:D74N	D	+	1	0	FAM114A1	38556314	0.047000	0.20315	0.003000	0.11579	0.002000	0.02628	1.420000	0.34804	0.943000	0.37553	0.484000	0.47621	GAT		0.597	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		A	38879919	G	A	38879919	3	1	61	1	0	0	0	0	1	0	0	0	5419	1174	41	3	222	3	FAM114A1	4	38879919	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80211	38879919	152274357	3114	11099										
FAM114A1	92689	broad.mit.edu	37	chr4	38933940	38933940	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaagtagcagaattaattCttcatggacaagaagaggaa	9	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:38933940C>A	ENST00000358869.2	+	12	1584	c.1408C>A	c.(1408-1410)Ctt>Att	p.L470I	FAM114A1_ENST00000515037.1_Missense_Mutation_p.L263I	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	470						cytoplasm (GO:0005737)		p.L470I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						AGAATTAATTCTTCATGGACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	68	68					4																	38933940		2203	4300	6503	38610335	SO:0001583	missense	92689				CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1408C>A	4.37:g.38933940C>A	ENSP00000351740:p.Leu470Ile		38610335	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360573	0.82353	.	.	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.47869	0.83;1.51	5.62	5.62	0.85841	.	0.114043	0.64402	D	0.000013	T	0.62221	0.2410	M	0.86502	2.82	0.58432	D	0.999992	P;P	0.43287	0.7;0.802	B;B	0.43331	0.215;0.416	T	0.70421	-0.4876	10	0.72032	D	0.01	-3.7732	19.6539	0.95828	0.0:1.0:0.0:0.0	.	263;470	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	I	263;470;263	ENSP00000424115:L263I;ENSP00000351740:L470I	ENSP00000347569:L263I	L	+	1	0	FAM114A1	38610335	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.697000	0.68295	2.653000	0.90120	0.467000	0.42956	CTT		0.358	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		A	38933940	C	A	38933940	3	1	61	1	0	0	0	0	1	0	0	0	5419	913	32	2	1446	2	FAM114A1	4	38933940	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54021	38933940	152220336	3115	11100										
KLHL5	51088	broad.mit.edu	37	chr4	39064478	39064478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggcttcaattggttaccGaaggtccagccaactggatt	10	9	1	0	rs201110544	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39064478G>A	ENST00000504108.1	+	1	627	c.344G>A	c.(343-345)cGa>cAa	p.R115Q	KLHL5_ENST00000261426.5_Missense_Mutation_p.R115Q|KLHL5_ENST00000359687.2_Missense_Mutation_p.R115Q|KLHL5_ENST00000508137.2_Intron|KLHL5_ENST00000381930.3_Missense_Mutation_p.R115Q|KLHL5_ENST00000261425.3_Missense_Mutation_p.R69Q	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	115						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R115Q(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						ATTGGTTACCGAAGGTCCAGC	0.473													G|||	3	0.000599042	8e-04	0	5008	,	,		17466	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	4						G	GLN/ARG,,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	83	81	82		206,,344,344	3.8	1	4		82	0,8600		0,0,4300	no	missense,intron,missense,missense	KLHL5	NM_001007075.2,NM_001171654.1,NM_015990.4,NM_199039.3	43,,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,,benign,benign	69/710,,115/756,115/695	39064478	1,13005	2203	4300	6503	38740873	SO:0001583	missense	51088			AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"Kelch-like", "BTB/POZ domain containing"	6356	protein-coding gene	gene with protein product		608064	"kelch (Drosophila)-like 5", "kelch-like 5 (Drosophila)"			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.344G>A	4.37:g.39064478G>A	ENSP00000423897:p.Arg115Gln		38740873	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Missense_Mutation	SNP	ENST00000504108.1	37	CCDS33974.1	.	.	.	.	.	.	.	.	.	.	G	8.428	0.847853	0.17034	2.27E-4	0.0	ENSG00000109790	ENST00000544221;ENST00000261425;ENST00000504108;ENST00000359687;ENST00000381930;ENST00000261426	T;T;T;T;T	0.73897	-0.52;-0.57;-0.49;-0.51;-0.79	5.53	3.81	0.43845	.	0.628267	0.15850	N	0.241565	T	0.49270	0.1547	N	0.08118	0	0.35924	D	0.83203	B;B;B	0.26258	0.005;0.003;0.145	B;B;B	0.12837	0.002;0.001;0.008	T	0.47129	-0.9141	10	0.08599	T	0.76	.	10.4548	0.44544	0.2096:0.0:0.7904:0.0	.	115;115;115	F8WAE7;Q96PQ7;Q96PQ7-2	.;KLHL5_HUMAN;.	Q	149;69;115;115;115;115	ENSP00000261425:R69Q;ENSP00000423897:R115Q;ENSP00000352716:R115Q;ENSP00000371355:R115Q;ENSP00000261426:R115Q	ENSP00000261425:R69Q	R	+	2	0	KLHL5	38740873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.685000	0.46959	0.823000	0.34589	-0.143000	0.13931	CGA		0.473	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1			A	39064478	G	A	39064478	3	1	61	1	0	0	0	0	1	0	0	0	8413	1058	37	1	346	1	KLHL5	4	39064478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130538	39064478	152089798	3116	11101										
KLHL5	51088	broad.mit.edu	37	chr4	39077652	39077652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtacatcagatgaatttTtccaagcccttaatcatgcc	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39077652T>C	ENST00000504108.1	+	2	872	c.589T>C	c.(589-591)Ttc>Ctc	p.F197L	KLHL5_ENST00000261426.5_Intron|KLHL5_ENST00000359687.2_Missense_Mutation_p.F197L|KLHL5_ENST00000508137.2_Missense_Mutation_p.F10L|KLHL5_ENST00000381930.3_Missense_Mutation_p.F197L|KLHL5_ENST00000261425.3_Missense_Mutation_p.F151L	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	197						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.F197L(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						AGATGAATTTTTCCAAGCCCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											126	126	126					4																	39077652		2203	4300	6503	38754047	SO:0001583	missense	51088			AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"Kelch-like", "BTB/POZ domain containing"	6356	protein-coding gene	gene with protein product		608064	"kelch (Drosophila)-like 5", "kelch-like 5 (Drosophila)"			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.589T>C	4.37:g.39077652T>C	ENSP00000423897:p.Phe197Leu		38754047	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Missense_Mutation	SNP	ENST00000504108.1	37	CCDS33974.1	.	.	.	.	.	.	.	.	.	.	T	31	5.075926	0.94000	.	.	ENSG00000109790	ENST00000544221;ENST00000261425;ENST00000508137;ENST00000504108;ENST00000359687;ENST00000381930	T;T;T;T;T	0.71461	-0.53;-0.54;-0.57;-0.49;-0.52	5.17	5.17	0.71159	BTB/POZ fold (1);	0.044153	0.85682	D	0.000000	T	0.75140	0.3809	L	0.29908	0.895	0.80722	D	1	D;D	0.64830	0.989;0.994	P;D	0.64595	0.847;0.927	T	0.78311	-0.2253	10	0.66056	D	0.02	.	15.2934	0.73885	0.0:0.0:0.0:1.0	.	197;197	Q96PQ7;Q96PQ7-2	KLHL5_HUMAN;.	L	231;151;10;197;197;197	ENSP00000261425:F151L;ENSP00000423080:F10L;ENSP00000423897:F197L;ENSP00000352716:F197L;ENSP00000371355:F197L	ENSP00000261425:F151L	F	+	1	0	KLHL5	38754047	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.951000	0.87819	2.085000	0.62840	0.482000	0.46254	TTC		0.343	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1			C	39077652	T	C	39077652	3	2	61	1	0	0	0	0	1	0	0	0	8413	1841	64	4	595	4	KLHL5	4	39077652	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	13174	39077652	152076624	3117	11102										
KLHL5	51088	broad.mit.edu	37	chr4	39088307	39088307	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacggaaagatctaagtaAacttttggcttatattaggc	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39088307A>C	ENST00000504108.1	+	5	1494	c.1211A>C	c.(1210-1212)aAa>aCa	p.K404T	KLHL5_ENST00000261426.5_Missense_Mutation_p.K343T|KLHL5_ENST00000359687.2_Missense_Mutation_p.K404T|KLHL5_ENST00000508137.2_Missense_Mutation_p.K217T|KLHL5_ENST00000381930.3_Missense_Mutation_p.K404T|KLHL5_ENST00000261425.3_Missense_Mutation_p.K358T	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	404						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.K404T(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						GATCTAAGTAAACTTTTGGCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											107	104	105					4																	39088307		2203	4300	6503	38764702	SO:0001583	missense	51088			AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"Kelch-like", "BTB/POZ domain containing"	6356	protein-coding gene	gene with protein product		608064	"kelch (Drosophila)-like 5", "kelch-like 5 (Drosophila)"			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.1211A>C	4.37:g.39088307A>C	ENSP00000423897:p.Lys404Thr		38764702	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Missense_Mutation	SNP	ENST00000504108.1	37	CCDS33974.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.376297	0.24857	.	.	ENSG00000109790	ENST00000544221;ENST00000261425;ENST00000508137;ENST00000504108;ENST00000359687;ENST00000381930;ENST00000261426	T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	5.36	2.8	0.32819	BTB/Kelch-associated (2);	0.357287	0.31102	N	0.008254	T	0.48554	0.1506	L	0.33710	1.025	0.30898	N	0.729563	B;B;B	0.29341	0.13;0.242;0.203	B;B;B	0.22386	0.039;0.038;0.039	T	0.44034	-0.9354	10	0.15066	T	0.55	.	9.9823	0.41821	0.859:0.0:0.141:0.0	.	343;404;404	F8WAE7;Q96PQ7;Q96PQ7-2	.;KLHL5_HUMAN;.	T	438;358;217;404;404;404;343	ENSP00000261425:K358T;ENSP00000423080:K217T;ENSP00000423897:K404T;ENSP00000352716:K404T;ENSP00000371355:K404T;ENSP00000261426:K343T	ENSP00000261425:K358T	K	+	2	0	KLHL5	38764702	0.938000	0.31826	0.998000	0.56505	0.989000	0.77384	0.837000	0.27558	0.308000	0.22923	0.397000	0.26171	AAA		0.358	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1			C	39088307	A	C	39088307	3	2	61	1	0	0	0	0	1	0	0	0	8413	14	1	4	1229	4	KLHL5	4	39088307	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10655	39088307	152065969	3118	11103										
WDR19	57728	broad.mit.edu	37	chr4	39255634	39255634	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacacaacaaaatggaaatCtatgcagatattattggtaa	6	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39255634C>A	ENST00000399820.3	+	26	3139	c.2985C>A	c.(2983-2985)atC>atA	p.I995I	WDR19_ENST00000288634.7_Silent_p.I835I	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	995					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)		p.I995I(1)		large_intestine(1)	1						AAATGGAAATCTATGCAGATA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	4											104	101	102					4																	39255634		1855	4107	5962	38932029	SO:0001819	synonymous_variant	57728			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.2985C>A	4.37:g.39255634C>A			38932029	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	37	CCDS47042.1																																																																																				0.358	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			A	39255634	C	A	39255634	2	1	61	1	0	0	0	0	0	0	0	1	17319	903	32	2		2	WDR19	4	39255634	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	167327	39255634	151898642	3119	11104										
RFC1	5981	broad.mit.edu	37	chr4	39291553	39291553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaattcttcattgtattccGaatccagggatgggcttgtg	10	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39291553G>A	ENST00000381897.1	-	24	3411	c.3278C>T	c.(3277-3279)tCg>tTg	p.S1093L	RFC1_ENST00000349703.2_Missense_Mutation_p.S1092L	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	1093					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.S1092L(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATTGTATTCCGAATCCAGGGA	0.413																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											1	Substitution - Missense(1)	large_intestine(1)	4											232	227	229					4																	39291553		2203	4300	6503	38967948	SO:0001583	missense	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.3278C>T	4.37:g.39291553G>A	ENSP00000371321:p.Ser1093Leu		38967948	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	G	8.266	0.812203	0.16537	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.12039	2.72;2.72	5.83	4.02	0.46733	.	0.367340	0.23935	N	0.043119	T	0.14743	0.0356	M	0.63843	1.955	0.23743	N	0.996967	B;B	0.14012	0.002;0.009	B;B	0.11329	0.0;0.006	T	0.12243	-1.0555	10	0.33940	T	0.23	-2.8882	9.3646	0.38217	0.1335:0.1198:0.7467:0.0	.	1093;1092	P35251;P35251-2	RFC1_HUMAN;.	L	1093;1092	ENSP00000371321:S1093L;ENSP00000261424:S1092L	ENSP00000261424:S1092L	S	-	2	0	RFC1	38967948	0.899000	0.30636	0.909000	0.35828	0.002000	0.02628	2.665000	0.46791	1.479000	0.48272	-0.254000	0.11334	TCG		0.413	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39291553	G	A	39291553	3	1	61	1	0	0	0	0	1	0	0	0	13281	1059	37	1	176	1	RFC1	4	39291553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35919	39291553	151862723	3120	11105										
RFC1	5981	broad.mit.edu	37	chr4	39304363	39304363	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaatcatcataccttaatCtgttcaacccgaggtctttg	5	11	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39304363C>A	ENST00000381897.1	-	17	2470	c.2337G>T	c.(2335-2337)caG>caT	p.Q779H	RFC1_ENST00000349703.2_Missense_Mutation_p.Q778H	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	779					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.Q778H(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATACCTTAATCTGTTCAACCC	0.308																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											1	Substitution - Missense(1)	large_intestine(1)	4											41	42	41					4																	39304363		2203	4298	6501	38980758	SO:0001583	missense	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2337G>T	4.37:g.39304363C>A	ENSP00000371321:p.Gln779His		38980758	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990659	0.74589	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.18174	2.23;2.23	6.02	2.44	0.29823	.	0.000000	0.85682	D	0.000000	T	0.47783	0.1464	M	0.92367	3.3	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.52268	-0.8598	10	0.87932	D	0	-16.4431	10.5434	0.45045	0.0:0.7429:0.0:0.2571	.	779;778	P35251;P35251-2	RFC1_HUMAN;.	H	779;778	ENSP00000371321:Q779H;ENSP00000261424:Q778H	ENSP00000261424:Q778H	Q	-	3	2	RFC1	38980758	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.205000	0.42770	0.154000	0.19237	0.655000	0.94253	CAG		0.308	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39304363	C	A	39304363	3	1	61	1	0	0	0	0	1	0	0	0	13281	912	32	2	1145	2	RFC1	4	39304363	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12810	39304363	151849913	3121	11106										
RFC1	5981	broad.mit.edu	37	chr4	39310647	39310647	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctccagtttggactctttCttcatcttaagaagtggaaa	7	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39310647C>A	ENST00000381897.1	-	13	1627	c.1494G>T	c.(1492-1494)aaG>aaT	p.K498N	RFC1_ENST00000349703.2_Missense_Mutation_p.K498N	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	498					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.K498N(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGGACTCTTTCTTCATCTTAA	0.358																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											1	Substitution - Missense(1)	large_intestine(1)	4											44	48	47					4																	39310647		2200	4295	6495	38987042	SO:0001583	missense	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1494G>T	4.37:g.39310647C>A	ENSP00000371321:p.Lys498Asn		38987042	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319572	0.41096	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.54479	0.57;0.57	5.91	4.16	0.48862	.	0.234776	0.50627	N	0.000117	T	0.50205	0.1602	M	0.65498	2.005	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.20184	0.008;0.028	T	0.47849	-0.9085	10	0.56958	D	0.05	-7.5716	9.5509	0.39310	0.1536:0.7756:0.0:0.0708	.	498;498	P35251;P35251-2	RFC1_HUMAN;.	N	498	ENSP00000371321:K498N;ENSP00000261424:K498N	ENSP00000261424:K498N	K	-	3	2	RFC1	38987042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.968000	0.29357	0.781000	0.33589	0.655000	0.94253	AAG		0.358	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39310647	C	A	39310647	3	1	61	1	0	0	0	0	1	0	0	0	13281	912	32	2	2001	2	RFC1	4	39310647	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6284	39310647	151843629	3122	11107										
RFC1	5981	broad.mit.edu	37	chr4	39322244	39322244	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcatatttactttgcttcCtaggactgtagctctttctt	5	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39322244C>A	ENST00000381897.1	-	9	987	c.854G>T	c.(853-855)aGg>aTg	p.R285M	RFC1_ENST00000349703.2_Missense_Mutation_p.R285M|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	285					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.R285M(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ACTTTGCTTCCTAGGACTGTA	0.353																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											1	Substitution - Missense(1)	large_intestine(1)	4											121	115	117					4																	39322244		2203	4300	6503	38998639	SO:0001583	missense	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.854G>T	4.37:g.39322244C>A	ENSP00000371321:p.Arg285Met		38998639	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.071997	0.36566	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.56103	0.48;0.48	6.06	0.768	0.18487	.	0.752620	0.13889	N	0.355740	T	0.30479	0.0766	N	0.14661	0.345	0.27435	N	0.953882	B;B	0.12630	0.003;0.006	B;B	0.12156	0.003;0.007	T	0.16837	-1.0389	10	0.48119	T	0.1	-1.5647	5.2862	0.15702	0.0:0.3019:0.1503:0.5478	.	285;285	P35251;P35251-2	RFC1_HUMAN;.	M	285	ENSP00000371321:R285M;ENSP00000261424:R285M	ENSP00000261424:R285M	R	-	2	0	RFC1	38998639	1.000000	0.71417	0.998000	0.56505	0.909000	0.53808	0.573000	0.23699	0.167000	0.19631	-0.290000	0.09829	AGG		0.353	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39322244	C	A	39322244	3	1	61	1	0	0	0	0	1	0	0	0	13281	681	24	2	2657	2	RFC1	4	39322244	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11597	39322244	151832032	3123	11108										
RPL9	6133	broad.mit.edu	37	chr4	39459852	39459852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaggctgagttctacatTgatgtgattgaagtccctcc	10	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39459852T>C	ENST00000449470.2	-	2	572	c.124A>G	c.(124-126)Aat>Gat	p.N42D	RPL9_ENST00000295955.9_Missense_Mutation_p.N42D|LIAS_ENST00000261434.3_5'Flank|LIAS_ENST00000513731.1_5'Flank|LIAS_ENST00000340169.2_5'Flank|LIAS_ENST00000381846.1_5'Flank	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9	42					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.N42D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						AGTTCTACATTGATGTGATTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											82	90	87					4																	39459852		2203	4299	6502	39136247	SO:0001583	missense	6133			D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"L ribosomal proteins"	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367	ENST00000449470.2:c.124A>G	4.37:g.39459852T>C	ENSP00000400467:p.Asn42Asp		39136247		Missense_Mutation	SNP	ENST00000449470.2	37	CCDS3452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.66|18.66	3.672439|3.672439	0.67928|0.67928	.|.	.|.	ENSG00000163682|ENSG00000163682	ENST00000295955;ENST00000449470;ENST00000394452;ENST00000503040;ENST00000504470|ENST00000508595	.|.	.|.	.|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Ribosomal protein L6, alpha-beta domain (3);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.59878|0.59878	0.2226|0.2226	L|L	0.39326|0.39326	1.205|1.205	0.58432|0.58432	D|D	0.999999|0.999999	B;B;B|.	0.09022|.	0.002;0.0;0.0|.	B;B;B|.	0.16722|.	0.016;0.011;0.016|.	T|T	0.56420|0.56420	-0.7982|-0.7982	9|5	0.22109|.	T|.	0.4|.	.|.	15.2836|15.2836	0.73810|0.73810	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	42;42;42|.	B4DLV8;B4E1M5;P32969|.	.;.;RL9_HUMAN|.	D|R	42|38	.|.	ENSP00000346022:N42D|.	N|Q	-|-	1|2	0|0	RPL9|RPL9	39136247|39136247	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.994000|0.994000	0.84299|0.84299	7.658000|7.658000	0.83755|0.83755	2.200000|2.200000	0.70718|0.70718	0.459000|0.459000	0.35465|0.35465	AAT|CAA		0.458	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1			C	39459852	T	C	39459852	3	2	61	1	0	0	0	0	1	0	0	0	13640	1812	63	4	474	4	RPL9	4	39459852	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	137608	39459852	151694424	3124	11109										
LIAS	6133	broad.mit.edu	37	chr4	39462506	39462506	+	5'Flank	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaccagaccttcaagatTttgtatctggtgatcttgca	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39462506T>G	ENST00000449470.2	-	0	0				RPL9_ENST00000295955.9_5'Flank|LIAS_ENST00000261434.3_Missense_Mutation_p.F48V|LIAS_ENST00000513731.1_Missense_Mutation_p.F48V|LIAS_ENST00000340169.2_Missense_Mutation_p.F48V|LIAS_ENST00000381846.1_Missense_Mutation_p.F48V|LIAS_ENST00000515061.1_3'UTR	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.F48V(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CCTTCAAGATTTTGTATCTGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	100	97					4																	39462506		2203	4300	6503	39138901	SO:0001631	upstream_gene_variant	11019			D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"L ribosomal proteins"	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367		4.37:g.39462506T>G	Exception_encountered		39138901		Missense_Mutation	SNP	ENST00000449470.2	37	CCDS3452.1	.	.	.	.	.	.	.	.	.	.	T	31	5.073446	0.94000	.	.	ENSG00000121897	ENST00000340169;ENST00000261434;ENST00000513731;ENST00000381846	D;D;T;D	0.85088	-1.72;-1.7;-1.19;-1.94	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.92061	0.7484	M	0.76170	2.325	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.996;0.995;0.992;0.999;1.0	D	0.92787	0.6245	10	0.87932	D	0	-24.1896	15.8056	0.78506	0.0:0.0:0.0:1.0	.	48;48;48;48;48	B4E0L7;C9JCF6;D6RCP8;O43766;Q6P5Q6	.;.;.;LIAS_HUMAN;.	V	48	ENSP00000340676:F48V;ENSP00000261434:F48V;ENSP00000425580:F48V;ENSP00000371270:F48V	ENSP00000261434:F48V	F	+	1	0	LIAS	39138901	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.430000	0.80321	2.323000	0.78572	0.528000	0.53228	TTT		0.393	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1			G	39462506	T	G	39462506	1	3	61	0	1	0	0	0	0	0	0	0	8801	1841	64	4		4	LIAS	4	39462506	5'Flank	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2654	39462506	151691770	3125	11110										
PDS5A	23244	broad.mit.edu	37	chr4	39868539	39868539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacatcgctgataataaccGaagggttgaattggcagatt	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39868539G>A	ENST00000303538.8	-	23	3123	c.2584C>T	c.(2584-2586)Cgg>Tgg	p.R862W		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)									p.R862W(1)		breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GATAATAACCGAAGGGTTGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											70	66	68					4																	39868539		1871	4117	5988	39544934	SO:0001583	missense	23244			AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.2584C>T	4.37:g.39868539G>A	ENSP00000303427:p.Arg862Trp		39544934		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.865982	0.91511	.	.	ENSG00000121892	ENST00000303538	T	0.66460	-0.21	5.54	5.54	0.83059	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83353	0.5236	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83567	0.0110	9	.	.	.	-9.2882	19.4681	0.94951	0.0:0.0:1.0:0.0	.	862	Q29RF7	PDS5A_HUMAN	W	862	ENSP00000303427:R862W	.	R	-	1	2	PDS5A	39544934	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.511000	0.67024	2.581000	0.87130	0.655000	0.94253	CGG		0.383	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		A	39868539	G	A	39868539	3	1	61	1	0	0	0	0	1	0	0	0	11722	1057	37	1	1473	1	PDS5A	4	39868539	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	406033	39868539	151285737	3126	11111										
PDS5A	23244	broad.mit.edu	37	chr4	39924318	39924318	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaccttccatgatgataGaactcatcaaatctagcatg	5	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:39924318G>T	ENST00000303538.8	-	6	1117	c.578C>A	c.(577-579)tCt>tAt	p.S193Y	PDS5A_ENST00000503396.1_Missense_Mutation_p.S193Y	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)									p.S193Y(1)		breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CATGATGATAGAACTCATCAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	105	108					4																	39924318		1874	4105	5979	39600713	SO:0001583	missense	23244			AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.578C>A	4.37:g.39924318G>T	ENSP00000303427:p.Ser193Tyr		39600713		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689780	0.88735	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.69685	-0.17;-0.42	5.75	5.75	0.90469	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80281	0.4594	L	0.60455	1.87	0.80722	D	1	D;D	0.76494	0.979;0.999	P;D	0.79784	0.896;0.993	T	0.76921	-0.2780	9	.	.	.	-14.2694	20.3046	0.98621	0.0:0.0:1.0:0.0	.	193;193	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	Y	193	ENSP00000303427:S193Y;ENSP00000426749:S193Y	.	S	-	2	0	PDS5A	39600713	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.878000	0.98634	0.650000	0.86243	TCT		0.333	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		T	39924318	G	T	39924318	3	4	61	1	0	0	0	0	1	0	0	0	11722	942	33	2	3580	2	PDS5A	4	39924318	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55779	39924318	151229958	3127	11112										
N4BP2	55728	broad.mit.edu	37	chr4	40122870	40122870	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtattaacaggaagattaGatggatttaagccgaaagtt	10	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:40122870G>T	ENST00000261435.6	+	9	3555	c.3139G>T	c.(3139-3141)Gat>Tat	p.D1047Y		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1047					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)	p.D1047Y(1)		breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AGGAAGATTAGATGGATTTAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											53	56	55					4																	40122870		2199	4297	6496	39799265	SO:0001583	missense	55728			AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3139G>T	4.37:g.40122870G>T	ENSP00000261435:p.Asp1047Tyr		39799265	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.50|16.50	3.140154|3.140154	0.56936|0.56936	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.21361|.	2.01|.	6.04|6.04	5.2|5.2	0.72013|0.72013	.|.	0.322733|.	0.32703|.	N|.	0.005745|.	T|T	0.66992|0.66992	0.2846|0.2846	M|M	0.61703|0.61703	1.905|1.905	0.34929|0.34929	D|D	0.749203|0.749203	D;D|.	0.76494|.	0.999;0.998|.	D;P|.	0.65874|.	0.939;0.87|.	T|T	0.75317|0.75317	-0.3360|-0.3360	10|5	0.66056|.	D|.	0.02|.	-17.4266|-17.4266	15.5397|15.5397	0.76031|0.76031	0.0661:0.0:0.9339:0.0|0.0661:0.0:0.9339:0.0	.|.	1047;1047|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	Y|I	1047;967|693	ENSP00000261435:D1047Y|.	ENSP00000261435:D1047Y|.	D|R	+|+	1|2	0|0	N4BP2|N4BP2	39799265|39799265	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.987000|0.987000	0.75469|0.75469	5.260000|5.260000	0.65490|0.65490	1.568000|1.568000	0.49683|0.49683	0.563000|0.563000	0.77884|0.77884	GAT|AGA		0.318	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		T	40122870	G	T	40122870	3	4	61	1	0	0	0	0	1	0	0	0	10140	942	33	2	3165	2	N4BP2	4	40122870	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198552	40122870	151031406	3128	11113										
N4BP2	55728	broad.mit.edu	37	chr4	40123067	40123067	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgaaagacttatatgaGaggtgcaataaagatattat	9	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:40123067G>T	ENST00000261435.6	+	9	3752	c.3336G>T	c.(3334-3336)gaG>gaT	p.E1112D		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1112					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)	p.E1112D(1)		breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ACTTATATGAGAGGTGCAATA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	75	73					4																	40123067		2201	4299	6500	39799462	SO:0001583	missense	55728			AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3336G>T	4.37:g.40123067G>T	ENSP00000261435:p.Glu1112Asp		39799462	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.59|15.59	2.878963|2.878963	0.51801|0.51801	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.23147|.	1.92|.	5.86|5.86	3.2|3.2	0.36748|0.36748	.|.	0.056024|0.056024	0.64402|0.64402	D|D	0.000002|0.000002	T|.	0.62134|.	0.2403|.	M|M	0.63843|0.63843	1.955|1.955	0.35897|0.35897	D|D	0.830133|0.830133	D;D|.	0.65815|.	0.995;0.991|.	D;P|.	0.67548|.	0.952;0.896|.	T|.	0.69939|.	-0.5009|.	10|.	0.49607|0.87932	T|D	0.09|0	-14.823|-14.823	7.9874|7.9874	0.30220|0.30220	0.4199:0.0:0.5801:0.0|0.4199:0.0:0.5801:0.0	.|.	1112;1112|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	D|X	1112;1032|759	ENSP00000261435:E1112D|.	ENSP00000261435:E1112D|ENSP00000426430:E759X	E|E	+|+	3|1	2|0	N4BP2|N4BP2	39799462|39799462	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	1.146000|1.146000	0.31589|0.31589	0.824000|0.824000	0.34613|0.34613	0.563000|0.563000	0.77884|0.77884	GAG|GAG		0.353	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		T	40123067	G	T	40123067	3	4	61	1	0	0	0	0	1	0	0	0	10140	933	33	2	3362	2	N4BP2	4	40123067	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197	40123067	151031209	3129	11114										
CHRNA9	55584	broad.mit.edu	37	chr4	40339234	40339234	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcattgtgtaggatgaaaGaaaccaaattctgactgctt	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:40339234G>T	ENST00000310169.2	+	3	357	c.218G>T	c.(217-219)aGa>aTa	p.R73I		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	73					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)	p.R73I(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	TAGGATGAAAGAAACCAAATT	0.443																																					Esophageal Squamous(115;1297 1602 22235 25158 43327)											1	Substitution - Missense(1)	large_intestine(1)	4											102	79	87					4																	40339234		2203	4300	6503	40033991	SO:0001583	missense	55584			AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	14079	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 9 (neuronal)"	605116	"cholinergic receptor, nicotinic, alpha polypeptide 9"				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.218G>T	4.37:g.40339234G>T	ENSP00000312663:p.Arg73Ile		40033991	Q14CY7|Q4W5A2|Q9NYV2	Missense_Mutation	SNP	ENST00000310169.2	37	CCDS3459.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759737	0.69763	.	.	ENSG00000174343	ENST00000310169	T	0.78924	-1.22	5.83	5.83	0.93111	Neurotransmitter-gated ion-channel ligand-binding (3);	0.128789	0.64402	D	0.000001	D	0.88948	0.6576	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.89255	0.3593	10	0.87932	D	0	.	20.1174	0.97942	0.0:0.0:1.0:0.0	.	73	Q9UGM1	ACHA9_HUMAN	I	73	ENSP00000312663:R73I	ENSP00000312663:R73I	R	+	2	0	CHRNA9	40033991	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	7.594000	0.82698	2.771000	0.95319	0.591000	0.81541	AGA		0.443	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			T	40339234	G	T	40339234	3	4	61	1	0	0	0	0	1	0	0	0	3395	942	33	2	228	2	CHRNA9	4	40339234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216167	40339234	150815042	3130	11115										
CHRNA9	55584	broad.mit.edu	37	chr4	40356519	40356519	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgatgactattttgatCatagcaagagcggattagtc	10	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:40356519C>A	ENST00000310169.2	+	5	1561	c.1422C>A	c.(1420-1422)atC>atA	p.I474I		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	474					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)	p.I474I(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	CTATTTTGATCATAGCAAGAG	0.378																																					Esophageal Squamous(115;1297 1602 22235 25158 43327)											1	Substitution - coding silent(1)	large_intestine(1)	4											152	146	148					4																	40356519		2203	4300	6503	40051276	SO:0001819	synonymous_variant	55584			AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	14079	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 9 (neuronal)"	605116	"cholinergic receptor, nicotinic, alpha polypeptide 9"				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.1422C>A	4.37:g.40356519C>A			40051276	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																				0.378	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			A	40356519	C	A	40356519	2	1	61	1	0	0	0	0	0	0	0	1	3395	816	29	2		2	CHRNA9	4	40356519	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17285	40356519	150797757	3131	11116										
RBM47	54502	broad.mit.edu	37	chr4	40440431	40440431	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcctcgcgcttcttcatCttggggatcccgccgatgaa	9	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:40440431C>T	ENST00000381793.2	-	3	876	c.480G>A	c.(478-480)aaG>aaA	p.K160K	RBM47_ENST00000515809.1_Intron|RBM47_ENST00000514014.1_Silent_p.K122K|RBM47_ENST00000319592.4_Silent_p.K160K|RBM47_ENST00000295971.7_Silent_p.K160K|RBM47_ENST00000381795.6_Silent_p.K160K			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	160	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K160K(2)		breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						GCTTCTTCATCTTGGGGATCC	0.627																																																2	Substitution - coding silent(2)	large_intestine(2)	4											47	42	44					4																	40440431		2200	4298	6498	40135188	SO:0001819	synonymous_variant	54502			AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.480G>A	4.37:g.40440431C>T			40135188	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Silent	SNP	ENST00000381793.2	37	CCDS43223.1																																																																																				0.627	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		T	40440431	C	T	40440431	2	4	61	1	0	0	0	0	0	0	0	1	13178	912	32	3		3	RBM47	4	40440431	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83912	40440431	150713845	3132	11117										
UCHL1	7345	broad.mit.edu	37	chr4	41270067	41270067	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagtccgcttctctgccGtggctctctgcaaggcagcc	12	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:41270067G>A	ENST00000284440.4	+	9	793	c.649G>A	c.(649-651)Gtg>Atg	p.V217M	UCHL1_ENST00000503431.1_Missense_Mutation_p.V217M|UCHL1_ENST00000508768.1_Missense_Mutation_p.V201M|UCHL1_ENST00000512788.1_Silent_p.P226P	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	217					adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.V217M(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CTTCTCTGCCGTGGCTCTCTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	4											68	59	62					4																	41270067		2203	4300	6503	40964824	SO:0001583	missense	7345			BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"Parkinson disease"	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.649G>A	4.37:g.41270067G>A	ENSP00000284440:p.Val217Met		40964824	Q4W5K6|Q71UM0	Missense_Mutation	SNP	ENST00000284440.4	37	CCDS3462.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684277	0.47991	.	.	ENSG00000154277	ENST00000284440;ENST00000508768	T;T	0.62788	-0.0;-0.0	5.12	5.12	0.69794	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (2);	0.206051	0.42053	D	0.000770	T	0.63343	0.2503	L	0.42632	1.34	0.80722	D	1	D	0.89917	1.0	P	0.54312	0.748	T	0.58289	-0.7662	10	0.02654	T	1	-22.1999	18.7483	0.91802	0.0:0.0:1.0:0.0	.	217	P09936	UCHL1_HUMAN	M	217;201	ENSP00000284440:V217M;ENSP00000426895:V201M	ENSP00000284440:V217M	V	+	1	0	UCHL1	40964824	1.000000	0.71417	0.961000	0.40146	0.932000	0.56968	6.955000	0.76007	2.660000	0.90430	0.563000	0.77884	GTG		0.498	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181		A	41270067	G	A	41270067	3	1	61	1	0	0	0	0	1	0	0	0	16960	1145	40	1	683	1	UCHL1	4	41270067	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	829636	41270067	149884209	3133	11118										
LIMCH1	22998	broad.mit.edu	37	chr4	41648621	41648621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgaggctgttctcgaacGcttggagatgccaaaaattc	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:41648621G>A	ENST00000313860.7	+	12	1430	c.1376G>A	c.(1375-1377)cGc>cAc	p.R459H	LIMCH1_ENST00000512946.1_Missense_Mutation_p.R459H|LIMCH1_ENST00000512820.1_Missense_Mutation_p.R447H|LIMCH1_ENST00000511496.1_Missense_Mutation_p.R300H|LIMCH1_ENST00000508501.1_Missense_Mutation_p.R459H|LIMCH1_ENST00000509277.1_Missense_Mutation_p.R293H|LIMCH1_ENST00000514096.1_Missense_Mutation_p.R300H|LIMCH1_ENST00000513024.1_Missense_Mutation_p.R288H|LIMCH1_ENST00000512632.1_Missense_Mutation_p.R459H|LIMCH1_ENST00000396595.3_Missense_Mutation_p.R305H|LIMCH1_ENST00000503057.1_Missense_Mutation_p.R844H|LIMCH1_ENST00000381753.4_Missense_Mutation_p.R293H	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	459					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.R459H(1)|p.R844H(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						GTTCTCGAACGCTTGGAGATG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	4											158	163	161					4																	41648621		2203	4300	6503	41343378	SO:0001583	missense	22998			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.1376G>A	4.37:g.41648621G>A	ENSP00000316891:p.Arg459His		41343378	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.4|24.4	4.522195|4.522195	0.85600|0.85600	.|.	.|.	ENSG00000064042|ENSG00000064042	ENST00000508466|ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.53640	.|0.84;1.23;1.21;1.23;0.84;1.24;0.62;0.62;0.61;0.84;0.84;0.62	5.61|5.61	4.76|4.76	0.60689|0.60689	.|.	.|0.062950	.|0.64402	.|D	.|0.000004	T|T	0.62270|0.62270	0.2414|0.2414	L|L	0.50333|0.50333	1.59|1.59	0.49915|0.49915	D|D	0.999835|0.999835	.|D;P;D;P;P;D;P;D;D;D;D	.|0.89917	.|0.999;0.796;0.999;0.87;0.87;1.0;0.87;1.0;1.0;1.0;1.0	.|D;B;D;B;B;D;B;D;D;D;D	.|0.87578	.|0.925;0.194;0.925;0.355;0.355;0.997;0.254;0.998;0.996;0.998;0.996	T|T	0.64015|0.64015	-0.6506|-0.6506	5|10	.|0.72032	.|D	.|0.01	-11.3778|-11.3778	13.9163|13.9163	0.63899|0.63899	0.0729:0.0:0.9271:0.0|0.0729:0.0:0.9271:0.0	.|.	.|210;293;459;293;305;844;288;447;459;459;459	.|B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.|.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	T|H	294|288;459;459;459;459;447;844;300;843;300;293;305;293	.|ENSP00000425222:R288H;ENSP00000424825:R459H;ENSP00000424645:R459H;ENSP00000316891:R459H;ENSP00000427045:R459H;ENSP00000424437:R447H;ENSP00000425631:R844H;ENSP00000421242:R300H;ENSP00000426334:R300H;ENSP00000422864:R293H;ENSP00000379840:R305H;ENSP00000371172:R293H	.|ENSP00000316891:R459H	A|R	+|+	1|2	0|0	LIMCH1|LIMCH1	41343378|41343378	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.953000|0.953000	0.61014|0.61014	4.586000|4.586000	0.60984|0.60984	2.627000|2.627000	0.88993|0.88993	0.591000|0.591000	0.81541|0.81541	GCT|CGC		0.488	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		A	41648621	G	A	41648621	3	1	61	1	0	0	0	0	1	0	0	0	8820	1087	38	1	1450	1	LIMCH1	4	41648621	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	378554	41648621	149505655	3134	11119										
LIMCH1	22998	broad.mit.edu	37	chr4	41648885	41648885	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactcccagcccaaaaattCtcaagatgttctgaagacct	5	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:41648885C>A	ENST00000313860.7	+	12	1694	c.1640C>A	c.(1639-1641)tCt>tAt	p.S547Y	LIMCH1_ENST00000512946.1_Missense_Mutation_p.S547Y|LIMCH1_ENST00000512820.1_Missense_Mutation_p.S535Y|LIMCH1_ENST00000511496.1_Missense_Mutation_p.S388Y|LIMCH1_ENST00000508501.1_Missense_Mutation_p.S547Y|LIMCH1_ENST00000509277.1_Missense_Mutation_p.S381Y|LIMCH1_ENST00000514096.1_Missense_Mutation_p.S388Y|LIMCH1_ENST00000513024.1_Missense_Mutation_p.S376Y|LIMCH1_ENST00000512632.1_Missense_Mutation_p.S547Y|LIMCH1_ENST00000396595.3_Missense_Mutation_p.S393Y|LIMCH1_ENST00000503057.1_Missense_Mutation_p.S932Y|LIMCH1_ENST00000381753.4_Missense_Mutation_p.S381Y	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	547					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.S547Y(1)|p.S932Y(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						CCCAAAAATTCTCAAGATGTT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	4											88	94	92					4																	41648885		2203	4300	6503	41343642	SO:0001583	missense	22998			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.1640C>A	4.37:g.41648885C>A	ENSP00000316891:p.Ser547Tyr		41343642	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.614722|4.614722	0.87359|0.87359	.|.	.|.	ENSG00000064042|ENSG00000064042	ENST00000508466|ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.49720	.|0.78;1.37;1.39;1.37;0.78;1.36;0.77;0.81;0.77;0.78;0.81;0.78	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.185181	.|0.47455	.|D	.|0.000239	T|T	0.65249|0.65249	0.2673|0.2673	L|L	0.48642|0.48642	1.525|1.525	0.43608|0.43608	D|D	0.995972|0.995972	.|D;D;D;D;D;D;D;D;D;D;D	.|0.69078	.|0.966;0.994;0.988;0.98;0.98;0.997;0.98;0.991;0.984;0.991;0.972	.|P;P;P;P;P;D;P;P;P;P;P	.|0.83275	.|0.702;0.885;0.862;0.844;0.844;0.996;0.844;0.904;0.736;0.865;0.794	T|T	0.64499|0.64499	-0.6393|-0.6393	5|10	.|0.62326	.|D	.|0.03	-14.2719|-14.2719	19.6863|19.6863	0.95981|0.95981	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|298;381;547;381;393;932;376;535;547;547;547	.|B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.|.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	I|Y	382|376;547;547;547;547;535;932;388;931;388;381;393;381	.|ENSP00000425222:S376Y;ENSP00000424825:S547Y;ENSP00000424645:S547Y;ENSP00000316891:S547Y;ENSP00000427045:S547Y;ENSP00000424437:S535Y;ENSP00000425631:S932Y;ENSP00000421242:S388Y;ENSP00000426334:S388Y;ENSP00000422864:S381Y;ENSP00000379840:S393Y;ENSP00000371172:S381Y	.|ENSP00000316891:S547Y	L|S	+|+	1|2	0|0	LIMCH1|LIMCH1	41343642|41343642	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.889000|0.889000	0.51656|0.51656	2.882000|2.882000	0.48546|0.48546	2.746000|2.746000	0.94184|0.94184	0.591000|0.591000	0.81541|0.81541	CTC|TCT		0.478	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		A	41648885	C	A	41648885	3	1	61	1	0	0	0	0	1	0	0	0	8820	913	32	2	1714	2	LIMCH1	4	41648885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	264	41648885	149505391	3135	11120										
LIMCH1	22998	broad.mit.edu	37	chr4	41664931	41664931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctgaagaatgatgtgtCggaagaaaaagaccagaaga	12	6	0	7	rs375067265		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:41664931C>T	ENST00000313860.7	+	15	2120	c.2066C>T	c.(2065-2067)tCg>tTg	p.S689L	LIMCH1_ENST00000512946.1_Missense_Mutation_p.S689L|LIMCH1_ENST00000512820.1_Missense_Mutation_p.S677L|LIMCH1_ENST00000511496.1_Missense_Mutation_p.S530L|LIMCH1_ENST00000508501.1_Missense_Mutation_p.S689L|LIMCH1_ENST00000509277.1_Missense_Mutation_p.S523L|LIMCH1_ENST00000514096.1_Missense_Mutation_p.S530L|LIMCH1_ENST00000513024.1_Missense_Mutation_p.S518L|LIMCH1_ENST00000512632.1_Missense_Mutation_p.S689L|LIMCH1_ENST00000396595.3_Missense_Mutation_p.S535L|LIMCH1_ENST00000503057.1_Missense_Mutation_p.S1074L|LIMCH1_ENST00000381753.4_Missense_Mutation_p.S523L	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	689					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.S1074L(1)|p.S689L(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						AATGATGTGTCGGAAGAAAAA	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	4						C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	69	68	68		2066,2066,1604,1568,2066	1	0	4		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	LIMCH1	NM_001112717.1,NM_001112718.1,NM_001112719.1,NM_001112720.1,NM_014988.2	145,145,145,145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	689/1058,689/1057,535/903,523/891,689/1084	41664931	1,13005	2203	4300	6503	41359688	SO:0001583	missense	22998			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.2066C>T	4.37:g.41664931C>T	ENSP00000316891:p.Ser689Leu		41359688	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.243|2.243	-0.373317|-0.373317	0.05034|0.05034	0.0|0.0	1.16E-4|1.16E-4	ENSG00000064042|ENSG00000064042	ENST00000508466|ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.46063	.|0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.08|5.08	1.01|1.01	0.19927|0.19927	.|.	.|0.992506	.|0.08195	.|N	.|0.983188	T|T	0.19967|0.19967	0.0480|0.0480	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B;B;B;B	.|0.15473	.|0.0;0.0;0.0;0.0;0.001;0.013;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B;B;B;B;B	.|0.13407	.|0.0;0.0;0.001;0.001;0.002;0.009;0.0;0.001;0.0;0.001;0.0	T|T	0.21999|0.21999	-1.0229|-1.0229	5|10	.|0.45353	.|T	.|0.12	-1.1145|-1.1145	1.7598|1.7598	0.02989|0.02989	0.1658:0.4859:0.1612:0.1872|0.1658:0.4859:0.1612:0.1872	.|.	.|440;523;689;523;535;1074;518;677;689;689;689	.|B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.|.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	W|L	524|518;689;689;689;689;677;1074;530;1073;530;523;535;523;42	.|ENSP00000425222:S518L;ENSP00000424825:S689L;ENSP00000424645:S689L;ENSP00000316891:S689L;ENSP00000427045:S689L;ENSP00000424437:S677L;ENSP00000425631:S1074L;ENSP00000421242:S530L;ENSP00000426334:S530L;ENSP00000422864:S523L;ENSP00000379840:S535L;ENSP00000371172:S523L	.|ENSP00000316891:S689L	R|S	+|+	1|2	2|0	LIMCH1|LIMCH1	41359688|41359688	0.083000|0.083000	0.21467|0.21467	0.036000|0.036000	0.18154|0.18154	0.001000|0.001000	0.01503|0.01503	0.450000|0.450000	0.21762|0.21762	0.525000|0.525000	0.28522|0.28522	-0.309000|-0.309000	0.09137|0.09137	CGG|TCG		0.478	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		T	41664931	C	T	41664931	3	4	61	1	0	0	0	0	1	0	0	0	8820	893	31	1	2152	1	LIMCH1	4	41664931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16046	41664931	149489345	3136	11121										
PHOX2B	8929	broad.mit.edu	37	chr4	41750422	41750422	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctctggtggtccctgaggGtgcccaggctgcaggatccc	15	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:41750422G>T	ENST00000226382.2	-	1	565	c.206C>A	c.(205-207)aCc>aAc	p.T69N	RP11-227F19.2_ENST00000510602.1_lincRNA|RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	69					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	p.T69N(1)		autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						GTCCCTGAGGGTGCCCAGGCT	0.617			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	1	Substitution - Missense(1)	large_intestine(1)	4											38	40	39					4																	41750422		2203	4300	6503	41445179	SO:0001583	missense	8929	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.206C>A	4.37:g.41750422G>T	ENSP00000226382:p.Thr69Asn		41445179	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	37	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.682612	0.29872	.	.	ENSG00000109132	ENST00000226382	D	0.90900	-2.75	5.56	4.66	0.58398	.	0.049916	0.85682	D	0.000000	T	0.79834	0.4514	N	0.08118	0	0.45930	D	0.998765	B	0.20368	0.044	B	0.13407	0.009	T	0.74624	-0.3603	10	0.14656	T	0.56	.	15.265	0.73654	0.0:0.2485:0.7515:0.0	.	69	Q99453	PHX2B_HUMAN	N	69	ENSP00000226382:T69N	ENSP00000226382:T69N	T	-	2	0	PHOX2B	41445179	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.353000	0.73032	2.615000	0.88500	0.561000	0.74099	ACC		0.617	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			T	41750422	G	T	41750422	3	4	61	1	0	0	0	0	1	0	0	0	11890	1261	44	2	750	2	PHOX2B	4	41750422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85491	41750422	149403854	3137	11122										
SLC30A9	10463	broad.mit.edu	37	chr4	42020145	42020145	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcagaaggtataggcacaGaactcaaagctccacttaag	9	10	1	2	rs552013390		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42020145G>T	ENST00000264451.7	+	3	472	c.292G>T	c.(292-294)Gaa>Taa	p.E98*		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	98					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E98*(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TATAGGCACAGAACTCAAAGC	0.259																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											39	40	40					4																	42020145		2202	4292	6494	41714902	SO:0001587	stop_gained	10463			AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.292G>T	4.37:g.42020145G>T	ENSP00000264451:p.Glu98*		41714902	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Nonsense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600425	0.66332	.	.	ENSG00000014824	ENST00000264451	.	.	.	5.35	3.61	0.41365	.	0.456397	0.25264	N	0.031927	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-12.9664	7.4064	0.26993	0.0904:0.1691:0.7405:0.0	.	.	.	.	X	98	.	ENSP00000264451:E98X	E	+	1	0	SLC30A9	41714902	0.970000	0.33590	0.954000	0.39281	0.537000	0.34900	1.694000	0.37752	0.640000	0.30582	-0.242000	0.12053	GAA		0.259	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			T	42020145	G	T	42020145	4	4	61	1	0	0	0	0	0	1	0	0	14599	943	33	2	302	2	SLC30A9	4	42020145	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	269723	42020145	149134131	3138	11123										
SLC30A9	10463	broad.mit.edu	37	chr4	42080286	42080286	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttatgcttaaacatggaGaaaatattattgatacttta	5	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42080286G>T	ENST00000264451.7	+	17	1786	c.1606G>T	c.(1606-1608)Gaa>Taa	p.E536*		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	536					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E536*(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TAAACATGGAGAAAATATTAT	0.284																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											53	59	57					4																	42080286		2201	4298	6499	41775043	SO:0001587	stop_gained	10463			AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.1606G>T	4.37:g.42080286G>T	ENSP00000264451:p.Glu536*		41775043	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Nonsense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	G	39	7.594098	0.98378	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-23.428	19.8737	0.96861	0.0:0.0:1.0:0.0	.	.	.	.	X	536;364	.	ENSP00000264451:E536X	E	+	1	0	SLC30A9	41775043	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.185000	0.94900	2.693000	0.91896	0.650000	0.86243	GAA		0.284	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			T	42080286	G	T	42080286	4	4	61	1	0	0	0	0	0	1	0	0	14599	943	33	2	1672	2	SLC30A9	4	42080286	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60141	42080286	149073990	3139	11124										
BEND4	389206	broad.mit.edu	37	chr4	42145764	42145764	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcagtgaaaaccctcaaAaaggcagaagtttgttgttt	10	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42145764A>C	ENST00000502486.1	-	3	1314	c.735T>G	c.(733-735)ttT>ttG	p.F245L	BEND4_ENST00000504360.1_Missense_Mutation_p.F241L	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	245								p.F241L(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						AAACCCTCAAAAAGGCAGAAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	119	118					4																	42145764		1905	4124	6029	41840521	SO:0001583	missense	389206			AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.735T>G	4.37:g.42145764A>C	ENSP00000421169:p.Phe245Leu		41840521	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	37	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.305084	0.40795	.	.	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	5.52	-6.15	0.02105	.	0.111270	0.64402	D	0.000008	T	0.40909	0.1136	N	0.24115	0.695	0.45621	D	0.99855	P;P;P	0.38335	0.627;0.493;0.627	B;B;B	0.39258	0.295;0.155;0.295	T	0.37033	-0.9723	9	0.66056	D	0.02	-15.0424	16.8761	0.86052	0.3816:0.0:0.6184:0.0	.	167;245;245	Q6ZU67-3;Q6ZU67;Q6ZU67-2	.;BEND4_HUMAN;.	L	116;245;241	.	ENSP00000412495:F116L	F	-	3	2	BEND4	41840521	0.936000	0.31750	0.371000	0.25978	0.063000	0.16089	0.118000	0.15605	-1.101000	0.03027	-0.912000	0.02778	TTT		0.478	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		C	42145764	A	C	42145764	3	2	61	1	0	0	0	0	1	0	0	0	1401	11	1	4	885	4	BEND4	4	42145764	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	65478	42145764	149008512	3140	11125										
BEND4	389206	broad.mit.edu	37	chr4	42145958	42145958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcctccacaatttaagaGgctaagaactcgactgcact	6	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42145958G>T	ENST00000502486.1	-	3	1120	c.541C>A	c.(541-543)Ctc>Atc	p.L181I	BEND4_ENST00000504360.1_Missense_Mutation_p.L177I	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	181								p.L177I(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						CAATTTAAGAGGCTAAGAACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											46	43	44					4																	42145958		1926	4134	6060	41840715	SO:0001583	missense	389206			AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.541C>A	4.37:g.42145958G>T	ENSP00000421169:p.Leu181Ile		41840715	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	37	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053965	0.55218	.	.	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	5.72	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;D;D	0.83275	0.996;0.991;0.996	T	0.70590	-0.4830	9	0.87932	D	0	-17.1521	14.6407	0.68723	0.0696:0.0:0.9304:0.0	.	103;181;181	Q6ZU67-3;Q6ZU67;Q6ZU67-2	.;BEND4_HUMAN;.	I	52;181;177	.	ENSP00000412495:L52I	L	-	1	0	BEND4	41840715	1.000000	0.71417	1.000000	0.80357	0.071000	0.16799	7.641000	0.83368	1.429000	0.47314	0.655000	0.94253	CTC		0.463	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		T	42145958	G	T	42145958	3	4	61	1	0	0	0	0	1	0	0	0	1401	1000	35	2	1079	2	BEND4	4	42145958	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194	42145958	149008318	3141	11126										
ATP8A1	10396	broad.mit.edu	37	chr4	42445676	42445676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcgatgctcccccatatcGctatgtggctgaactgtaga	11	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42445676G>A	ENST00000381668.5	-	33	3260	c.3029C>T	c.(3028-3030)gCg>gTg	p.A1010V	ATP8A1_ENST00000264449.10_Missense_Mutation_p.A995V|AC084010.1_ENST00000582816.1_RNA	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	1010					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.A1010V(2)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CCCCCATATCGCTATGTGGCT	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|NS(1)	4											98	87	91					4																	42445676		2203	4300	6503	42140433	SO:0001583	missense	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.3029C>T	4.37:g.42445676G>A	ENSP00000371084:p.Ala1010Val		42140433	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.464768	0.84425	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	D;D	0.89050	-2.46;-2.46	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	D	0.86460	0.5938	L	0.53561	1.675	0.80722	D	1	B;P;P	0.43633	0.268;0.813;0.813	B;B;B	0.36244	0.075;0.22;0.22	D	0.86479	0.1790	10	0.39692	T	0.17	.	19.4234	0.94730	0.0:0.0:1.0:0.0	.	995;1010;1002	Q32M35;Q9Y2Q0;E7EUK4	.;AT8A1_HUMAN;.	V	1010;995	ENSP00000371084:A1010V;ENSP00000264449:A995V	ENSP00000264449:A995V	A	-	2	0	ATP8A1	42140433	1.000000	0.71417	0.903000	0.35520	0.956000	0.61745	9.356000	0.97091	2.602000	0.87976	0.655000	0.94253	GCG		0.438	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		A	42445676	G	A	42445676	3	1	61	1	0	0	0	0	1	0	0	0	1193	1087	38	1	485	1	ATP8A1	4	42445676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	299718	42445676	148708600	3142	11127										
ATP8A1	10396	broad.mit.edu	37	chr4	42545974	42545974	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaactttccagatggagtgCgaacaatcactgacattctt	8	9	2	2	rs556457468		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42545974C>T	ENST00000381668.5	-	20	1913	c.1682G>A	c.(1681-1683)cGc>cAc	p.R561H	ATP8A1_ENST00000264449.10_Missense_Mutation_p.R546H	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	561					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R561H(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AGATGGAGTGCGAACAATCAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											109	94	99					4																	42545974		2203	4300	6503	42240731	SO:0001583	missense	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1682G>A	4.37:g.42545974C>T	ENSP00000371084:p.Arg561His		42240731	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732792	0.89482	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	D;D	0.83163	-1.69;-1.69	5.95	5.1	0.69264	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.93566	0.7946	H	0.94183	3.505	0.80722	D	1	D;D;D	0.89917	0.983;1.0;1.0	P;D;D	0.79784	0.494;0.993;0.993	D	0.95334	0.8432	10	0.87932	D	0	.	16.497	0.84247	0.1321:0.8679:0.0:0.0	.	546;546;561	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	H	561;546	ENSP00000371084:R561H;ENSP00000264449:R546H	ENSP00000264449:R546H	R	-	2	0	ATP8A1	42240731	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.864000	0.75494	1.503000	0.48686	0.650000	0.86243	CGC		0.333	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42545974	C	T	42545974	3	4	61	1	0	0	0	0	1	0	0	0	1193	768	27	1	1884	1	ATP8A1	4	42545974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100298	42545974	148608302	3143	11128										
ATP8A1	10396	broad.mit.edu	37	chr4	42551064	42551064	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacattgagcaattcatatcTttcttcctgccccagctaag	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42551064T>G	ENST00000381668.5	-	19	1849	c.1618A>C	c.(1618-1620)Aga>Cga	p.R540R	ATP8A1_ENST00000264449.10_Silent_p.R525R	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	540					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R540R(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AATTCATATCTTTCTTCCTGC	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	4											82	88	86					4																	42551064		2203	4297	6500	42245821	SO:0001819	synonymous_variant	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1618A>C	4.37:g.42551064T>G			42245821	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Silent	SNP	ENST00000381668.5	37	CCDS3466.1																																																																																				0.308	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		G	42551064	T	G	42551064	2	3	61	1	0	0	0	0	0	0	0	1	1193	1617	56	4		4	ATP8A1	4	42551064	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5090	42551064	148603212	3144	11129										
ATP8A1	10396	broad.mit.edu	37	chr4	42553235	42553235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatctataatcaccgagtCgggtgttcttccagtgaaaa	9	8	3	2	rs372291630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42553235C>T	ENST00000381668.5	-	18	1813	c.1582G>A	c.(1582-1584)Gac>Aac	p.D528N	ATP8A1_ENST00000264449.10_Missense_Mutation_p.D513N	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	528					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.D528N(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	ATCACCGAGTCGGGTGTTCTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	116	121	120		1537,1582	5.5	1	4		120	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	23,23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	513/1150,528/1165	42553235	1,13005	2203	4300	6503	42247992	SO:0001583	missense	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1582G>A	4.37:g.42553235C>T	ENSP00000371084:p.Asp528Asn		42247992	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	9.236	1.037010	0.19669	0.0	1.16E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.61158	0.13;0.13	5.49	5.49	0.81192	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.055179	0.64402	D	0.000001	T	0.33527	0.0866	N	0.11201	0.11	0.80722	D	1	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.13407	0.003;0.009;0.005	T	0.23440	-1.0188	10	0.09590	T	0.72	.	9.9511	0.41638	0.0:0.8496:0.0:0.1504	.	513;513;528	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	N	528;513	ENSP00000371084:D528N;ENSP00000264449:D513N	ENSP00000264449:D513N	D	-	1	0	ATP8A1	42247992	0.903000	0.30736	1.000000	0.80357	0.917000	0.54804	1.562000	0.36353	2.572000	0.86782	0.585000	0.79938	GAC		0.348	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42553235	C	T	42553235	3	4	61	1	0	0	0	0	1	0	0	0	1193	884	31	1	1992	1	ATP8A1	4	42553235	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2171	42553235	148601041	3145	11130										
ATP8A1	10396	broad.mit.edu	37	chr4	42581868	42581868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcttttccagaatgccttCgattccaaatggctgagccc	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42581868C>T	ENST00000381668.5	-	11	1193	c.962G>A	c.(961-963)cGa>cAa	p.R321Q	ATP8A1_ENST00000264449.10_Missense_Mutation_p.R321Q	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	321					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R321Q(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AGAATGCCTTCGATTCCAAAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											73	73	73					4																	42581868		2203	4300	6503	42276625	SO:0001583	missense	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.962G>A	4.37:g.42581868C>T	ENSP00000371084:p.Arg321Gln		42276625	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.383081	0.25031	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74421	-0.84;-0.84	5.86	5.01	0.66863	ATPase, P-type, ATPase-associated domain (1);	0.232071	0.39083	N	0.001465	T	0.56949	0.2020	L	0.31526	0.94	0.80722	D	1	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.08055	0.002;0.003;0.003	T	0.49881	-0.8892	10	0.15066	T	0.55	.	7.1084	0.25376	0.0:0.6937:0.1545:0.1518	.	321;321;321	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	Q	321	ENSP00000371084:R321Q;ENSP00000264449:R321Q	ENSP00000264449:R321Q	R	-	2	0	ATP8A1	42276625	0.993000	0.37304	1.000000	0.80357	0.924000	0.55760	0.307000	0.19296	2.937000	0.99478	0.650000	0.86243	CGA		0.338	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42581868	C	T	42581868	3	4	61	1	0	0	0	0	1	0	0	0	1193	884	31	1	2640	1	ATP8A1	4	42581868	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28633	42581868	148572408	3146	11131										
ATP8A1	10396	broad.mit.edu	37	chr4	42583721	42583721	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactgagctcctcgaagaaGaatctgatctgctcccagtg	9	12	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:42583721G>T	ENST00000381668.5	-	10	982	c.751C>A	c.(751-753)Ctt>Att	p.L251I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.L251I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	251					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.L251I(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CCTCGAAGAAGAATCTGATCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	124	128					4																	42583721		2203	4300	6503	42278478	SO:0001583	missense	10396			AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.751C>A	4.37:g.42583721G>T	ENSP00000371084:p.Leu251Ile		42278478	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253576	0.80135	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	D;D	0.90844	-2.74;-2.74	5.92	5.92	0.95590	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000001	D	0.95379	0.8500	M	0.76433	2.335	0.80722	D	1	D;D;D	0.89917	0.979;1.0;0.998	D;D;D	0.91635	0.982;0.999;0.951	D	0.94352	0.7580	10	0.48119	T	0.1	.	20.3151	0.98650	0.0:0.0:1.0:0.0	.	251;251;251	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	251	ENSP00000371084:L251I;ENSP00000264449:L251I	ENSP00000264449:L251I	L	-	1	0	ATP8A1	42278478	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.419000	0.73345	2.809000	0.96659	0.467000	0.42956	CTT		0.398	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42583721	G	T	42583721	3	4	61	1	0	0	0	0	1	0	0	0	1193	942	33	2	2855	2	ATP8A1	4	42583721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1853	42583721	148570555	3147	11132										
GRXCR1	389207	broad.mit.edu	37	chr4	43032519	43032519	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtgtacggcttgcaatGaaaatggtcttcagcgttgt	12	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:43032519G>T	ENST00000399770.2	+	4	835	c.835G>T	c.(835-837)Gaa>Taa	p.E279*		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	279					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)	p.E279*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GGCTTGCAATGAAAATGGTCT	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											158	148	151					4																	43032519		1901	4121	6022	42727276	SO:0001587	stop_gained	389207				CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.835G>T	4.37:g.43032519G>T	ENSP00000382670:p.Glu279*		42727276		Nonsense_Mutation	SNP	ENST00000399770.2	37	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.565966	0.86439	.	.	ENSG00000215203	ENST00000399770	.	.	.	5.64	5.64	0.86602	.	0.077879	0.49916	U	0.000123	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-11.6416	18.6692	0.91504	0.0:0.0:1.0:0.0	.	.	.	.	X	279	.	ENSP00000382670:E279X	E	+	1	0	GRXCR1	42727276	1.000000	0.71417	0.999000	0.59377	0.924000	0.55760	9.398000	0.97281	2.649000	0.89929	0.579000	0.79373	GAA		0.423	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		T	43032519	G	T	43032519	4	4	61	1	0	0	0	0	0	1	0	0	6833	1291	45	2	849	2	GRXCR1	4	43032519	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	448798	43032519	148121757	3148	11133										
GUF1	60558	broad.mit.edu	37	chr4	44688550	44688550	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagtgcatcgcaaaaatcCtctgagagctttggtatttg	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:44688550C>A	ENST00000281543.5	+	8	952	c.758C>A	c.(757-759)cCt>cAt	p.P253H	GUF1_ENST00000506793.1_3'UTR	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)									p.P253H(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CGCAAAAATCCTCTGAGAGCT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	4											91	87	88					4																	44688550		2203	4299	6502	44383307	SO:0001583	missense	60558				CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.758C>A	4.37:g.44688550C>A	ENSP00000281543:p.Pro253His		44383307		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.806905	0.90623	.	.	ENSG00000151806	ENST00000281543	T	0.37235	1.21	5.61	5.61	0.85477	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.052068	0.85682	D	0.000000	T	0.62804	0.2458	M	0.91300	3.195	0.80722	D	1	D	0.54397	0.966	P	0.53224	0.721	T	0.72603	-0.4243	10	0.87932	D	0	-1.5326	18.629	0.91352	0.0:1.0:0.0:0.0	.	253	Q8N442	GUF1_HUMAN	H	253	ENSP00000281543:P253H	ENSP00000281543:P253H	P	+	2	0	GUF1	44383307	0.995000	0.38212	0.985000	0.45067	0.988000	0.76386	2.344000	0.44010	2.658000	0.90341	0.585000	0.79938	CCT		0.303	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		A	44688550	C	A	44688550	3	1	61	1	0	0	0	0	1	0	0	0	6920	681	24	2	788	2	GUF1	4	44688550	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1656031	44688550	146465726	3149	11134										
GABRA2	2555	broad.mit.edu	37	chr4	46252531	46252531	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcttggagatggtggagaGaactggatcttttgaaagat	13	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:46252531G>T	ENST00000510861.1	-	10	1323	c.1150C>A	c.(1150-1152)Ctc>Atc	p.L384I	GABRA2_ENST00000381620.4_Missense_Mutation_p.L384I|GABRA2_ENST00000507069.1_Missense_Mutation_p.L444I|GABRA2_ENST00000356504.1_Missense_Mutation_p.L384I|GABRA2_ENST00000540012.1_Missense_Mutation_p.L389I|GABRA2_ENST00000514090.1_Missense_Mutation_p.L384I			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	384					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L384I(2)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	ATGGTGGAGAGAACTGGATCT	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											160	160	160					4																	46252531		2203	4299	6502	45947288	SO:0001583	missense	2555				CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.1150C>A	4.37:g.46252531G>T	ENSP00000421828:p.Leu384Ile		45947288	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	37	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732330	0.48939	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069	D;D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14;-2.14	5.96	5.96	0.96718	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.060792	0.64402	D	0.000002	D	0.84188	0.5417	N	0.21282	0.65	0.22457	N	0.999083	P;B	0.49961	0.93;0.153	P;B	0.48425	0.577;0.095	T	0.75473	-0.3305	10	0.23302	T	0.38	.	19.3998	0.94623	0.0:0.0:1.0:0.0	.	389;384	B7Z1H8;P47869	.;GBRA2_HUMAN	I	384;384;384;384;389;444	ENSP00000421828:L384I;ENSP00000421300:L384I;ENSP00000371033:L384I;ENSP00000348897:L384I;ENSP00000444409:L389I;ENSP00000427603:L444I	ENSP00000348897:L384I	L	-	1	0	GABRA2	45947288	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	4.011000	0.57124	2.827000	0.97445	0.655000	0.94253	CTC		0.418	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46252531	G	T	46252531	3	4	61	1	0	0	0	0	1	0	0	0	6180	942	33	2	209	2	GABRA2	4	46252531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1563981	46252531	144901745	3150	11135										
GABRA2	2555	broad.mit.edu	37	chr4	46264083	46264083	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcagttgcataagccaCtttggggagagaattccgag	13	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:46264083C>A	ENST00000510861.1	-	9	1092	c.919G>T	c.(919-921)Gtg>Ttg	p.V307L	GABRA2_ENST00000381620.4_Missense_Mutation_p.V307L|GABRA2_ENST00000515082.1_Missense_Mutation_p.V307L|GABRA2_ENST00000507069.1_Missense_Mutation_p.V307L|GABRA2_ENST00000356504.1_Missense_Mutation_p.V307L|GABRA2_ENST00000540012.1_Missense_Mutation_p.V252L|GABRA2_ENST00000514090.1_Missense_Mutation_p.V307L			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	307					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.V307L(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	GCATAAGCCACTTTGGGGAGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											129	118	122					4																	46264083		2203	4300	6503	45958840	SO:0001583	missense	2555				CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.919G>T	4.37:g.46264083C>A	ENSP00000421828:p.Val307Leu		45958840	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	37	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	C	33	5.246394	0.95305	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069;ENST00000515082	D;D;D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22;-2.22;-2.22	5.35	5.35	0.76521	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94660	0.8278	M	0.89095	3.005	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.996	D;D;D	0.87578	0.998;0.998;0.997	D	0.95256	0.8364	10	0.87932	D	0	.	18.4017	0.90519	0.0:1.0:0.0:0.0	.	252;307;307	B7Z1H8;G5E9Z6;P47869	.;.;GBRA2_HUMAN	L	307;307;307;307;252;307;307	ENSP00000421828:V307L;ENSP00000421300:V307L;ENSP00000371033:V307L;ENSP00000348897:V307L;ENSP00000444409:V252L;ENSP00000427603:V307L;ENSP00000423840:V307L	ENSP00000348897:V307L	V	-	1	0	GABRA2	45958840	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.765000	0.85310	2.676000	0.91093	0.591000	0.81541	GTG		0.393	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			A	46264083	C	A	46264083	3	1	61	1	0	0	0	0	1	0	0	0	6180	565	20	2	444	2	GABRA2	4	46264083	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11552	46264083	144890193	3151	11136										
GABRA2	2555	broad.mit.edu	37	chr4	46334637	46334637	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgaaaaactcaccatatCtgtatctgagacagggccaa	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:46334637C>A	ENST00000510861.1	-	4	423	c.250G>T	c.(250-252)Gat>Tat	p.D84Y	GABRA2_ENST00000381620.4_Missense_Mutation_p.D84Y|GABRA2_ENST00000515082.1_Missense_Mutation_p.D84Y|GABRA2_ENST00000507069.1_Missense_Mutation_p.D84Y|GABRA2_ENST00000356504.1_Missense_Mutation_p.D84Y|GABRA2_ENST00000540012.1_Intron|GABRA2_ENST00000514090.1_Missense_Mutation_p.D84Y			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	84					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.D84Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CTCACCATATCTGTATCTGAG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	4											80	84	82					4																	46334637		2203	4300	6503	46029394	SO:0001583	missense	2555				CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.250G>T	4.37:g.46334637C>A	ENSP00000421828:p.Asp84Tyr		46029394	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	37	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.655376	0.67586	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000507069;ENST00000515082;ENST00000503806;ENST00000506961	T;T;T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22	4.86	4.86	0.63082	Neurotransmitter-gated ion-channel ligand-binding (3);	0.051345	0.85682	D	0.000000	D	0.89420	0.6710	M	0.90595	3.13	0.80722	D	1	P;D	0.67145	0.9;0.996	P;D	0.67103	0.813;0.949	D	0.91391	0.5135	10	0.87932	D	0	.	15.8633	0.79043	0.0:1.0:0.0:0.0	.	84;84	G5E9Z6;P47869	.;GBRA2_HUMAN	Y	84	ENSP00000421828:D84Y;ENSP00000421300:D84Y;ENSP00000371033:D84Y;ENSP00000348897:D84Y;ENSP00000427603:D84Y;ENSP00000423840:D84Y;ENSP00000424362:D84Y;ENSP00000424093:D84Y	ENSP00000348897:D84Y	D	-	1	0	GABRA2	46029394	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.472000	0.66768	2.678000	0.91216	0.650000	0.86243	GAT		0.308	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			A	46334637	C	A	46334637	3	1	61	1	0	0	0	0	1	0	0	0	6180	913	32	2	1133	2	GABRA2	4	46334637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70554	46334637	144819639	3152	11137										
GABRA4	2557	broad.mit.edu	37	chr4	46930528	46930528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgaggcatatatccagttCggatagaagtaggagaagca	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:46930528C>T	ENST00000264318.3	-	9	2361	c.1379G>A	c.(1378-1380)cGa>cAa	p.R460Q		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	460					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R460Q(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	ATATCCAGTTCGGATAGAAGT	0.453																																					Ovarian(6;283 369 8234 12290 33402)											2	Substitution - Missense(2)	large_intestine(2)	4											107	98	101					4																	46930528		2203	4300	6503	46625285	SO:0001583	missense	2557				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1379G>A	4.37:g.46930528C>T	ENSP00000264318:p.Arg460Gln		46625285	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	C	4.639	0.118878	0.08881	.	.	ENSG00000109158	ENST00000264318	T	0.80824	-1.42	5.82	-0.503	0.12000	Neurotransmitter-gated ion-channel transmembrane domain (2);	3.167070	0.00834	N	0.001691	T	0.63780	0.2540	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49082	-0.8976	10	0.16896	T	0.51	.	4.4361	0.11550	0.3109:0.3851:0.0:0.3041	.	460	P48169	GBRA4_HUMAN	Q	460	ENSP00000264318:R460Q	ENSP00000264318:R460Q	R	-	2	0	GABRA4	46625285	0.008000	0.16893	0.003000	0.11579	0.004000	0.04260	0.805000	0.27112	-0.019000	0.14055	-0.355000	0.07637	CGA		0.453	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46930528	C	T	46930528	3	4	61	1	0	0	0	0	1	0	0	0	6182	884	31	1	289	1	GABRA4	4	46930528	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	595891	46930528	144223748	3153	11138										
GABRA4	2557	broad.mit.edu	37	chr4	46994881	46994881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctgttgtcataaccatCgagcaaactgtccaggatgc	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:46994881C>T	ENST00000264318.3	-	2	1151	c.169G>A	c.(169-171)Gat>Aat	p.D57N	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	57					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.D57N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TCATAACCATCGAGCAAACTG	0.473																																					Ovarian(6;283 369 8234 12290 33402)											1	Substitution - Missense(1)	large_intestine(1)	4											147	134	139					4																	46994881		2203	4300	6503	46689638	SO:0001583	missense	2557				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.169G>A	4.37:g.46994881C>T	ENSP00000264318:p.Asp57Asn		46689638	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.838910	0.51057	.	.	ENSG00000109158	ENST00000264318	T	0.79247	-1.25	5.46	5.46	0.80206	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.85548	0.5722	L	0.58354	1.805	0.53688	D	0.999974	D	0.89917	1.0	D	0.76071	0.987	D	0.86510	0.1809	10	0.72032	D	0.01	.	14.7935	0.69860	0.0:1.0:0.0:0.0	.	57	P48169	GBRA4_HUMAN	N	57	ENSP00000264318:D57N	ENSP00000264318:D57N	D	-	1	0	GABRA4	46689638	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	6.803000	0.75180	2.561000	0.86390	0.460000	0.39030	GAT		0.473	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46994881	C	T	46994881	3	4	61	1	0	0	0	0	1	0	0	0	6182	884	31	1	1527	1	GABRA4	4	46994881	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64353	46994881	144159395	3154	11139										
GABRB1	2560	broad.mit.edu	37	chr4	47163406	47163406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctactttctgaatgacaaGaaatcatttgtgcatggggt	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47163406G>T	ENST00000295454.3	+	4	673	c.381G>T	c.(379-381)aaG>aaT	p.K127N	GABRB1_ENST00000538619.1_Missense_Mutation_p.K57N	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	127					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)	p.K127N(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGAATGACAAGAAATCATTTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											164	157	159					4																	47163406		2203	4300	6503	46858163	SO:0001583	missense	2560				CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.381G>T	4.37:g.47163406G>T	ENSP00000295454:p.Lys127Asn		46858163	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	37	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453531	0.84209	.	.	ENSG00000163288	ENST00000513567;ENST00000295454;ENST00000538619	T;T;T	0.79653	-1.29;-1.29;-1.29	5.01	5.01	0.66863	Neurotransmitter-gated ion-channel ligand-binding (3);	0.073210	0.53938	D	0.000054	D	0.89770	0.6811	M	0.87269	2.87	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.85130	0.945;0.997	D	0.90706	0.4624	10	0.87932	D	0	-16.9901	10.9925	0.47557	0.0848:0.0:0.9152:0.0	.	57;127	F5GXV5;P18505	.;GBRB1_HUMAN	N	94;127;57	ENSP00000426753:K94N;ENSP00000295454:K127N;ENSP00000440330:K57N	ENSP00000295454:K127N	K	+	3	2	GABRB1	46858163	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.624000	0.67764	2.611000	0.88343	0.650000	0.86243	AAG		0.438	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			T	47163406	G	T	47163406	3	4	61	1	0	0	0	0	1	0	0	0	6185	933	33	2	395	2	GABRB1	4	47163406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168525	47163406	143990870	3155	11140										
COMMD8	54951	broad.mit.edu	37	chr4	47458742	47458742	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaactgattcaactgctgaAatatctataaaaataaaaac	3	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47458742A>C	ENST00000381571.4	-	3	294	c.227T>G	c.(226-228)tTt>tGt	p.F76C		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	76								p.F76C(1)		large_intestine(2)|lung(5)|prostate(1)	8						CAACTGCTGAAATATCTATAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	75	74					4																	47458742		2203	4300	6503	47153499	SO:0001583	missense	54951			AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.227T>G	4.37:g.47458742A>C	ENSP00000370984:p.Phe76Cys		47153499	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	37	CCDS3475.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.416854	0.42918	.	.	ENSG00000169019	ENST00000381571	T	0.09163	3.01	5.72	-1.92	0.07618	.	1.382530	0.03825	N	0.268236	T	0.07773	0.0195	N	0.08118	0	0.09310	N	1	B	0.29835	0.258	B	0.34452	0.183	T	0.44019	-0.9355	10	0.46703	T	0.11	-24.8776	11.2736	0.49153	0.6722:0.0:0.3278:0.0	.	76	Q9NX08	COMD8_HUMAN	C	76	ENSP00000370984:F76C	ENSP00000370984:F76C	F	-	2	0	COMMD8	47153499	0.687000	0.27671	0.409000	0.26459	0.593000	0.36681	0.299000	0.19138	-0.224000	0.09928	0.454000	0.30748	TTT		0.323	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845		C	47458742	A	C	47458742	3	2	61	1	0	0	0	0	1	0	0	0	3728	14	1	4	336	4	COMMD8	4	47458742	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	295336	47458742	143695534	3156	11141										
ATP10D	57205	broad.mit.edu	37	chr4	47560085	47560085	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagggcttaccaatgcacTttacggtctcggacaccaga	10	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47560085T>G	ENST00000273859.3	+	12	2498	c.2229T>G	c.(2227-2229)acT>acG	p.T743T	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	743					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.T743T(1)		NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						ACCAATGCACTTTACGGTCTC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	4											115	96	102					4																	47560085		2203	4300	6503	47254842	SO:0001819	synonymous_variant	57205			AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.2229T>G	4.37:g.47560085T>G			47254842	A2RRC8|D6REN2|Q8NC70|Q96SR3	Silent	SNP	ENST00000273859.3	37	CCDS3476.1																																																																																				0.537	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		G	47560085	T	G	47560085	2	3	61	1	0	0	0	0	0	0	0	1	1119	1596	56	4		4	ATP10D	4	47560085	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	101343	47560085	143594191	3157	11142										
CORIN	10699	broad.mit.edu	37	chr4	47682221	47682221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacacacccactccatggCgatgcagcgcccgtccccgc	8	20	1	0	rs149671375	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47682221C>T	ENST00000273857.4	-	8	1068	c.1069G>A	c.(1069-1071)Gcc>Acc	p.A357T	CORIN_ENST00000505909.1_Intron|CORIN_ENST00000504584.1_Intron|CORIN_ENST00000502252.1_Missense_Mutation_p.A290T|CORIN_ENST00000508498.1_Missense_Mutation_p.A218T	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	357	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.A357T(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						CACTCCATGGCGATGCAGCGC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	4											133	100	111					4																	47682221		2203	4300	6503	47376978	SO:0001583	missense	10699			AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.1069G>A	4.37:g.47682221C>T	ENSP00000273857:p.Ala357Thr		47376978	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	37	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	6.307	0.424828	0.11987	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252	D;D;D	0.95690	-3.78;-3.78;-3.78	5.93	-6.28	0.02020	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.407353	0.26489	N	0.024096	D	0.84329	0.5448	N	0.12422	0.21	0.09310	N	0.999999	B;B	0.18013	0.025;0.002	B;B	0.12156	0.007;0.001	T	0.74118	-0.3768	10	0.29301	T	0.29	.	6.1881	0.20508	0.3661:0.1615:0.0:0.4724	.	290;357	B4E1Y7;Q9Y5Q5	.;CORIN_HUMAN	T	357;218;290	ENSP00000273857:A357T;ENSP00000425597:A218T;ENSP00000424212:A290T	ENSP00000273857:A357T	A	-	1	0	CORIN	47376978	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-3.107000	0.00601	-1.073000	0.03137	-0.998000	0.02512	GCC		0.517	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			T	47682221	C	T	47682221	3	4	61	1	0	0	0	0	1	0	0	0	3758	768	27	1	2119	1	CORIN	4	47682221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122136	47682221	143472055	3158	11143										
CNGA1	1259	broad.mit.edu	37	chr4	47939215	47939215	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaaccatttaataaccctCttttccatatctttgcttac	1	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47939215C>A	ENST00000514170.1	-	11	1615	c.1296G>T	c.(1294-1296)aaG>aaT	p.K432N	CNGA1_ENST00000358519.4_Missense_Mutation_p.K432N|CNGA1_ENST00000544810.1_Missense_Mutation_p.K432N|CNGA1_ENST00000402813.3_Missense_Mutation_p.K501N|CNGA1_ENST00000420489.2_Missense_Mutation_p.K432N			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	432					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.K432N(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TAATAACCCTCTTTTCCATAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											125	121	123					4																	47939215		1865	4098	5963	47633972	SO:0001583	missense	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.1296G>T	4.37:g.47939215C>A	ENSP00000426862:p.Lys432Asn		47633972	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	C	2.678	-0.276063	0.05679	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	D;D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05;-4.05	5.22	4.36	0.52297	Cyclic nucleotide-binding-like (1);	0.047113	0.85682	D	0.000000	D	0.86531	0.5955	N	0.05280	-0.08	0.39855	D	0.973291	B;B	0.18013	0.025;0.025	B;B	0.09377	0.004;0.004	T	0.78558	-0.2158	10	0.09338	T	0.73	.	4.6045	0.12371	0.0:0.6076:0.1994:0.193	.	432;432	Q4W5E3;P29973	.;CNGA1_HUMAN	N	501;432;432;432;432	ENSP00000384264:K501N;ENSP00000426862:K432N;ENSP00000443401:K432N;ENSP00000351320:K432N;ENSP00000389881:K432N	ENSP00000351320:K432N	K	-	3	2	CNGA1	47633972	1.000000	0.71417	0.999000	0.59377	0.486000	0.33341	1.423000	0.34837	1.171000	0.42768	-0.479000	0.04858	AAG		0.343	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		A	47939215	C	A	47939215	3	1	61	1	0	0	0	0	1	0	0	0	3602	912	32	2	780	2	CNGA1	4	47939215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	256994	47939215	143215061	3159	11144										
CNGA1	1259	broad.mit.edu	37	chr4	47953446	47953446	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttttcattctctgattCttcagatgtagaggcactgt	10	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:47953446C>A	ENST00000514170.1	-	5	479	c.160G>T	c.(160-162)Gaa>Taa	p.E54*	CNGA1_ENST00000358519.4_Nonsense_Mutation_p.E54*|CNGA1_ENST00000544810.1_Nonsense_Mutation_p.E54*|CNGA1_ENST00000402813.3_Nonsense_Mutation_p.E123*|CNGA1_ENST00000420489.2_Nonsense_Mutation_p.E54*			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	54					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.E54*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TTCTCTGATTCTTCAGATGTA	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											113	104	106					4																	47953446		1917	4132	6049	47648203	SO:0001587	stop_gained	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.160G>T	4.37:g.47953446C>A	ENSP00000426862:p.Glu54*		47648203	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Nonsense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300117	0.40694	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489;ENST00000504722;ENST00000514520;ENST00000513178	.	.	.	4.98	4.98	0.66077	.	1.451810	0.04163	N	0.323361	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	13.9287	0.63981	0.0:1.0:0.0:0.0	.	.	.	.	X	123;54;54;54;54;54;54;54	.	ENSP00000351320:E54X	E	-	1	0	CNGA1	47648203	1.000000	0.71417	0.999000	0.59377	0.015000	0.08874	1.926000	0.40084	2.741000	0.93983	0.561000	0.74099	GAA		0.458	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		A	47953446	C	A	47953446	4	1	61	1	0	0	0	0	0	1	0	0	3602	922	32	2	1940	2	CNGA1	4	47953446	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14231	47953446	143200830	3160	11145										
TXK	7294	broad.mit.edu	37	chr4	48112578	48112578	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatttctaaattagttatTttgttttcagtcacatagtt	4	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48112578T>G	ENST00000264316.4	-	5	508	c.423A>C	c.(421-423)aaA>aaC	p.K141N	RNU6-868P_ENST00000517241.1_RNA|TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	141	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)	p.K141N(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						AATTAGTTATTTTGTTTTCAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	111	112					4																	48112578		2202	4298	6500	47807335	SO:0001583	missense	7294			L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"SH2 domain containing"	12434	protein-coding gene	gene with protein product		600058	"PTK4 protein tyrosine kinase 4"	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.423A>C	4.37:g.48112578T>G	ENSP00000264316:p.Lys141Asn		47807335	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223540	0.39300	.	.	ENSG00000074966	ENST00000264316	T	0.75050	-0.9	5.04	1.33	0.21861	Src homology-3 domain (2);	0.250151	0.27821	N	0.017701	T	0.58090	0.2098	N	0.16862	0.45	0.26922	N	0.966669	B	0.30584	0.286	B	0.37780	0.258	T	0.54536	-0.8279	10	0.72032	D	0.01	.	5.8747	0.18822	0.0:0.3372:0.0:0.6628	.	141	P42681	TXK_HUMAN	N	141	ENSP00000264316:K141N	ENSP00000264316:K141N	K	-	3	2	TXK	47807335	0.005000	0.15991	0.466000	0.27168	0.933000	0.57130	-0.304000	0.08199	0.417000	0.25871	-0.334000	0.08254	AAA		0.323	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		G	48112578	T	G	48112578	3	3	61	1	0	0	0	0	1	0	0	0	16826	1838	64	4	1204	4	TXK	4	48112578	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	159132	48112578	143041698	3161	11146										
ZAR1	326340	broad.mit.edu	37	chr4	48494993	48494993	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagaacttgtcagaagtcTtataacccttaccgagtgga	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48494993T>G	ENST00000327939.4	+	3	1135	c.1095T>G	c.(1093-1095)tcT>tcG	p.S365S		NM_175619.1	NP_783318.1	Q86SH2	ZAR1_HUMAN	zygote arrest 1	365					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.S365S(1)		endometrium(1)|large_intestine(4)	5						GTCAGAAGTCTTATAACCCTT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	4											126	118	121					4																	48494993		2203	4300	6503	48189750	SO:0001819	synonymous_variant	326340			AY193890	CCDS3483.1	4p11	2014-02-20			ENSG00000182223	ENSG00000182223			20436	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 6"	607520				12539046	Standard	NM_175619		Approved	Z3CXXC6	uc003gyd.3	Q86SH2	OTTHUMG00000102093	ENST00000327939.4:c.1095T>G	4.37:g.48494993T>G			48189750		Silent	SNP	ENST00000327939.4	37	CCDS3483.1																																																																																				0.403	ZAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219927.3			G	48494993	T	G	48494993	2	3	61	1	0	0	0	0	0	0	0	1	17555	1596	56	4		4	ZAR1	4	48494993	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	382415	48494993	142659283	3162	11147										
FRYL	285527	broad.mit.edu	37	chr4	48502084	48502084	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctacagctgatataaattCtttatttttcaaagtttcaa	4	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48502084C>A	ENST00000503238.1	-	60	8745	c.8746G>T	c.(8746-8748)Gaa>Taa	p.E2916*	FRYL_ENST00000264319.7_Nonsense_Mutation_p.E306*|FRYL_ENST00000537810.1_Nonsense_Mutation_p.E2916*|FRYL_ENST00000358350.4_Nonsense_Mutation_p.E2916*|FRYL_ENST00000507873.2_Nonsense_Mutation_p.E306*			O94915	FRYL_HUMAN	FRY-like	2916					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.E2916*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GATATAAATTCTTTATTTTTC	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											69	67	68					4																	48502084		1812	4065	5877	48196841	SO:0001587	stop_gained	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.8746G>T	4.37:g.48502084C>A	ENSP00000426064:p.Glu2916*		48196841	O95640|Q8WTZ5|Q9NT40	Nonsense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	53	20.765137	0.99934	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000264319;ENST00000507873	.	.	.	5.95	5.95	0.96441	.	0.159210	0.41001	U	0.000973	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	20.3719	0.98893	0.0:1.0:0.0:0.0	.	.	.	.	X	2916;2916;2916;306;306	.	ENSP00000264319:E306X	E	-	1	0	FRYL	48196841	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.818000	0.86416	2.826000	0.97356	0.491000	0.48974	GAA		0.343	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48502084	C	A	48502084	4	1	61	1	0	0	0	0	0	1	0	0	6083	922	32	2	303	2	FRYL	4	48502084	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7091	48502084	142652192	3163	11148										
FRYL	285527	broad.mit.edu	37	chr4	48512886	48512886	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagactgttgggcattctGaacacagcatcatcacttcc	7	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48512886G>A	ENST00000503238.1	-	55	8260	c.8261C>T	c.(8260-8262)tCa>tTa	p.S2754L	FRYL_ENST00000264319.7_Missense_Mutation_p.S150L|FRYL_ENST00000537810.1_Missense_Mutation_p.S2754L|FRYL_ENST00000358350.4_Missense_Mutation_p.S2754L|FRYL_ENST00000507873.2_Missense_Mutation_p.S150L			O94915	FRYL_HUMAN	FRY-like	2754					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.S2754L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TGGGCATTCTGAACACAGCAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											124	116	118					4																	48512886		1887	4108	5995	48207643	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.8261C>T	4.37:g.48512886G>A	ENSP00000426064:p.Ser2754Leu		48207643	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216577	0.58452	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000264319;ENST00000507873	T;T;T	0.23552	1.9;1.9;1.9	6.02	5.18	0.71444	.	0.095855	0.44097	U	0.000483	T	0.50939	0.1645	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	T	0.53788	-0.8389	10	0.56958	D	0.05	.	15.4711	0.75441	0.0663:0.0:0.9337:0.0	.	2754;2754;150	O94915;F5GX82;O94915-2	FRYL_HUMAN;.;.	L	2754;2754;2754;150;150	ENSP00000426064:S2754L;ENSP00000351113:S2754L;ENSP00000441114:S2754L	ENSP00000264319:S150L	S	-	2	0	FRYL	48207643	1.000000	0.71417	0.999000	0.59377	0.013000	0.08279	7.551000	0.82182	1.550000	0.49438	-0.157000	0.13467	TCA		0.373	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48512886	G	A	48512886	3	1	61	1	0	0	0	0	1	0	0	0	6083	1294	45	3	808	3	FRYL	4	48512886	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10802	48512886	142641390	3164	11149										
FRYL	285527	broad.mit.edu	37	chr4	48530028	48530028	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagattctggaccacagagaGaaagcacattcattagcttt	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48530028G>T	ENST00000503238.1	-	49	7099	c.7100C>A	c.(7099-7101)tCt>tAt	p.S2367Y	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.S2367Y|FRYL_ENST00000358350.4_Missense_Mutation_p.S2367Y|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	2367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.S2367Y(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						ACCACAGAGAGAAAGCACATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											120	106	111					4																	48530028		1838	4086	5924	48224785	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.7100C>A	4.37:g.48530028G>T	ENSP00000426064:p.Ser2367Tyr		48224785	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.5|28.5	4.922580|4.922580	0.92319|0.92319	.|.	.|.	ENSG00000075539|ENSG00000075539	ENST00000514617|ENST00000503238;ENST00000358350;ENST00000537810	.|T;T;T	.|0.26810	.|1.71;1.71;1.71	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.109281	.|0.64402	.|D	.|0.000005	T|T	0.47930|0.47930	0.1472|0.1472	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.76494	.|0.481;0.997;0.999	.|B;D;D	.|0.70935	.|0.305;0.971;0.968	T|T	0.10636|0.10636	-1.0621|-1.0621	5|10	.|0.22706	.|T	.|0.39	.|.	19.9983|19.9983	0.97395|0.97395	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1197;2367;2367	.|Q6ZR29;O94915;F5GX82	.|.;FRYL_HUMAN;.	L|Y	1236|2367	.|ENSP00000426064:S2367Y;ENSP00000351113:S2367Y;ENSP00000441114:S2367Y	.|ENSP00000351113:S2367Y	F|S	-|-	3|2	2|0	FRYL|FRYL	48224785|48224785	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.993000|0.993000	0.82548|0.82548	7.932000|7.932000	0.87634|0.87634	2.724000|2.724000	0.93272|0.93272	0.561000|0.561000	0.74099|0.74099	TTC|TCT		0.353	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48530028	G	T	48530028	3	4	61	1	0	0	0	0	1	0	0	0	6083	942	33	2	1993	2	FRYL	4	48530028	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17142	48530028	142624248	3165	11150										
FRYL	285527	broad.mit.edu	37	chr4	48559129	48559129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccgaccaggccagttcatCgccatactagatgcaatatg	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48559129C>T	ENST00000503238.1	-	32	4131	c.4132G>A	c.(4132-4134)Gat>Aat	p.D1378N	FRYL_ENST00000507711.1_Missense_Mutation_p.D1378N|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.D1378N|FRYL_ENST00000358350.4_Missense_Mutation_p.D1378N|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	1378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.D1378N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GCCAGTTCATCGCCATACTAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	65	67					4																	48559129		1951	4145	6096	48253886	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.4132G>A	4.37:g.48559129C>T	ENSP00000426064:p.Asp1378Asn		48253886	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.731600|4.731600	0.89390|0.89390	.|.	.|.	ENSG00000075539|ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711|ENST00000514617	T;T;T;T|.	0.52057|.	1.63;1.63;1.63;0.68|.	6.03|6.03	6.03|6.03	0.97812|0.97812	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73187|0.73187	0.3555|0.3555	L|L	0.55834|0.55834	1.745|1.745	0.80722|0.80722	D|D	1|1	D;P;D;D|.	0.89917|.	0.999;0.861;1.0;1.0|.	P;P;D;D|.	0.97110|.	0.9;0.649;1.0;0.985|.	T|T	0.67534|0.67534	-0.5646|-0.5646	10|5	0.42905|.	T|.	0.14|.	.|.	20.5666|20.5666	0.99351|0.99351	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1378;209;1378;1378|.	F2Z2S2;Q6ZR29;O94915;F5GX82|.	.;.;FRYL_HUMAN;.|.	N|Q	1378|248	ENSP00000426064:D1378N;ENSP00000351113:D1378N;ENSP00000441114:D1378N;ENSP00000421584:D1378N|.	ENSP00000351113:D1378N|.	D|R	-|-	1|2	0|0	FRYL|FRYL	48253886|48253886	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.326000|0.326000	0.28443|0.28443	7.818000|7.818000	0.86416|0.86416	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	GAT|CGA		0.383	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48559129	C	T	48559129	3	4	61	1	0	0	0	0	1	0	0	0	6083	884	31	1	5029	1	FRYL	4	48559129	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29101	48559129	142595147	3166	11151										
FRYL	285527	broad.mit.edu	37	chr4	48597671	48597671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcacgaggaaccacacttCgtgagccttttggaaaaagt	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48597671C>T	ENST00000503238.1	-	12	1183	c.1184G>A	c.(1183-1185)cGa>cAa	p.R395Q	FRYL_ENST00000506685.1_Missense_Mutation_p.R101Q|FRYL_ENST00000507711.1_Missense_Mutation_p.R395Q|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.R395Q|FRYL_ENST00000358350.4_Missense_Mutation_p.R395Q			O94915	FRYL_HUMAN	FRY-like	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.R395Q(2)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AACCACACTTCGTGAGCCTTT	0.378																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	4											90	80	83					4																	48597671		1866	4099	5965	48292428	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.1184G>A	4.37:g.48597671C>T	ENSP00000426064:p.Arg395Gln		48292428	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	37	6.164329	0.97338	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000506685	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.07	5.97	5.97	0.96955	Armadillo-type fold (1);	0.000000	0.64402	U	0.000002	D	0.83266	0.5217	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.77557	0.968;0.99	T	0.82973	-0.0191	10	0.56958	D	0.05	.	20.4238	0.99064	0.0:1.0:0.0:0.0	.	395;395	F2Z2S2;O94915	.;FRYL_HUMAN	Q	395;395;395;395;101	ENSP00000426064:R395Q;ENSP00000351113:R395Q;ENSP00000441114:R395Q;ENSP00000421584:R395Q	ENSP00000351113:R395Q	R	-	2	0	FRYL	48292428	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.818000	0.86416	2.834000	0.97654	0.650000	0.86243	CGA		0.378	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48597671	C	T	48597671	3	4	61	1	0	0	0	0	1	0	0	0	6083	884	31	1	8057	1	FRYL	4	48597671	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38542	48597671	142556605	3167	11152										
FRYL	285527	broad.mit.edu	37	chr4	48636338	48636338	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccattacaacttcaattttCttttcagcttgaacagcaaa	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48636338C>A	ENST00000503238.1	-	1	89	c.90G>T	c.(88-90)aaG>aaT	p.K30N	FRYL_ENST00000507711.1_Missense_Mutation_p.K30N|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.K30N|FRYL_ENST00000514783.1_5'Flank|FRYL_ENST00000358350.4_Missense_Mutation_p.K30N			O94915	FRYL_HUMAN	FRY-like	30					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.K30N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						CTTCAATTTTCTTTTCAGCTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	107	110					4																	48636338		1855	4094	5949	48331095	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.90G>T	4.37:g.48636338C>A	ENSP00000426064:p.Lys30Asn		48331095	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.189330	0.57909	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000505759	T;T;T;T	0.46451	1.87;1.87;1.87;0.87	5.0	4.14	0.48551	.	0.000000	0.64402	U	0.000001	T	0.43986	0.1272	N	0.22421	0.69	0.80722	D	1	P;P;B	0.51057	0.941;0.455;0.26	P;B;B	0.56960	0.81;0.137;0.054	T	0.33752	-0.9856	10	0.42905	T	0.14	.	14.268	0.66133	0.0:0.9239:0.0:0.0761	.	81;30;30	Q6ZNE6;F2Z2S2;O94915	.;.;FRYL_HUMAN	N	30;30;30;30;122	ENSP00000426064:K30N;ENSP00000351113:K30N;ENSP00000441114:K30N;ENSP00000421584:K30N	ENSP00000351113:K30N	K	-	3	2	FRYL	48331095	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.711000	0.54868	2.475000	0.83589	0.650000	0.86243	AAG		0.353	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48636338	C	A	48636338	3	1	61	1	0	0	0	0	1	0	0	0	6083	912	32	2	9195	2	FRYL	4	48636338	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38667	48636338	142517938	3168	11153										
OCIAD1	54940	broad.mit.edu	37	chr4	48853996	48853996	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcatattgtccaaggtaGaaacttctcttgaaatgaat	7	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:48853996G>T	ENST00000381473.3	+	7	965				OCIAD1_ENST00000509122.1_Intron|OCIAD1_ENST00000513391.2_Intron|OCIAD1_ENST00000264312.7_Intron|OCIAD1-AS1_ENST00000513576.1_RNA|OCIAD1_ENST00000512981.1_3'UTR|OCIAD1_ENST00000508293.1_Intron|OCIAD1_ENST00000444354.2_Intron|OCIAD1_ENST00000396448.2_Missense_Mutation_p.R184I|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000425583.2_Intron	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1							endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)		p.?(1)		breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						GTCCAAGGTAGAAACTTCTCT	0.358																																																1	Unknown(1)	large_intestine(1)	4											116	111	113					4																	48853996		2203	4300	6503	48548753	SO:0001627	intron_variant	54940			AF324350	CCDS3484.1, CCDS43228.1, CCDS47052.1	4p11	2010-03-19			ENSG00000109180	ENSG00000109180			16074	protein-coding gene	gene with protein product						11162530, 18328549	Standard	NM_017830		Approved	FLJ20455, TPA018, OCIA, Asrij	uc010igk.3	Q9NX40	OTTHUMG00000102095	ENST00000381473.3:c.547+4G>T	4.37:g.48853996G>T			48548753	C9K030|G8JLN7|Q9BZE8	Missense_Mutation	SNP	ENST00000381473.3	37	CCDS3484.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.507011	0.44558	.	.	ENSG00000109180	ENST00000396448	T	0.43688	0.94	5.0	3.14	0.36123	.	.	.	.	.	T	0.18800	0.0451	N	0.08118	0	0.80722	D	1	P	0.42518	0.782	B	0.37304	0.246	T	0.01448	-1.1352	8	.	.	.	.	7.4355	0.27154	0.0:0.2779:0.5565:0.1657	.	184	Q9NX40-2	.	I	184	ENSP00000379725:R184I	.	R	+	2	0	OCIAD1	48548753	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.024000	0.41049	2.474000	0.83562	0.467000	0.42956	AGA		0.358	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361812.3	NM_017830		T	48853996	G	T	48853996	1	4	61	0	1	0	0	0	0	0	0	0	10848	942	33	2		2	OCIAD1	4	48853996	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	217658	48853996	142300280	3169	11154										
CWH43	80157	broad.mit.edu	37	chr4	49052813	49052813	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaattatagagacaaccaGaaagtggtcatagaccacag	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:49052813G>T	ENST00000226432.4	+	15	2151	c.1968G>T	c.(1966-1968)caG>caT	p.Q656H	CWH43_ENST00000513409.1_Missense_Mutation_p.Q629H	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	656					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)		p.Q656H(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						GAGACAACCAGAAAGTGGTCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											63	64	64					4																	49052813		2203	4300	6503	48747570	SO:0001583	missense	80157				CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1968G>T	4.37:g.49052813G>T	ENSP00000226432:p.Gln656His		48747570	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	G	4.361	0.066598	0.08388	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.44482	1.51;0.92	5.13	3.38	0.38709	.	0.539313	0.17096	N	0.187170	T	0.25344	0.0616	N	0.24115	0.695	0.28477	N	0.91513	B	0.06786	0.001	B	0.04013	0.001	T	0.11641	-1.0579	9	.	.	.	.	7.7777	0.29048	0.0878:0.394:0.5182:0.0	.	656	Q9H720	PG2IP_HUMAN	H	656;629	ENSP00000226432:Q656H;ENSP00000422802:Q629H	.	Q	+	3	2	CWH43	48747570	1.000000	0.71417	1.000000	0.80357	0.084000	0.17831	0.558000	0.23469	1.498000	0.48600	0.655000	0.94253	CAG		0.408	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		T	49052813	G	T	49052813	3	4	61	1	0	0	0	0	1	0	0	0	4079	933	33	2	2026	2	CWH43	4	49052813	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198817	49052813	142101463	3170	11155										
LRRC66	339977	broad.mit.edu	37	chr4	52862107	52862107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgccggcagcctgcacatCgcgggtgcttctaacactcc	10	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:52862107C>T	ENST00000343457.3	-	4	1087	c.1081G>A	c.(1081-1083)Gat>Aat	p.D361N		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	361						integral component of membrane (GO:0016021)		p.D361N(1)		central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						GCCTGCACATCGCGGGTGCTT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	4											34	35	35					4																	52862107		1944	4148	6092	52556864	SO:0001583	missense	339977			BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.1081G>A	4.37:g.52862107C>T	ENSP00000341944:p.Asp361Asn		52556864		Missense_Mutation	SNP	ENST00000343457.3	37	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.113938	0.56398	.	.	ENSG00000188993	ENST00000343457	T	0.48522	0.81	4.45	3.61	0.41365	.	0.148988	0.31370	N	0.007767	T	0.39091	0.1065	L	0.59436	1.845	0.09310	N	1	D	0.57899	0.981	B	0.37943	0.261	T	0.41395	-0.9511	10	0.66056	D	0.02	-6.6743	9.6003	0.39601	0.0:0.8991:0.0:0.1009	.	361	Q68CR7	LRC66_HUMAN	N	361	ENSP00000341944:D361N	ENSP00000341944:D361N	D	-	1	0	LRRC66	52556864	0.031000	0.19500	0.003000	0.11579	0.004000	0.04260	2.092000	0.41700	0.988000	0.38734	0.467000	0.42956	GAT		0.592	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		T	52862107	C	T	52862107	3	4	61	1	0	0	0	0	1	0	0	0	9047	884	31	1	1565	1	LRRC66	4	52862107	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3809294	52862107	138292169	3171	11156										
LRRC66	339977	broad.mit.edu	37	chr4	52883690	52883690	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcattcagaattgaataaAatattgctttttcttgatgc	7	5	2	3	rs200866017		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:52883690A>C	ENST00000343457.3	-	1	96	c.90T>G	c.(88-90)atT>atG	p.I30M		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	30						integral component of membrane (GO:0016021)		p.I30M(1)		central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						AATTGAATAAAATATTGCTTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											30	31	31					4																	52883690		1803	4067	5870	52578447	SO:0001583	missense	339977			BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.90T>G	4.37:g.52883690A>C	ENSP00000341944:p.Ile30Met		52578447		Missense_Mutation	SNP	ENST00000343457.3	37	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	A	9.226	1.034682	0.19590	.	.	ENSG00000188993	ENST00000343457	T	0.30182	1.54	4.7	3.48	0.39840	.	0.905025	0.09245	N	0.828734	T	0.19805	0.0476	L	0.29908	0.895	0.09310	N	1	P	0.34662	0.462	B	0.29077	0.098	T	0.22626	-1.0211	10	0.59425	D	0.04	-0.6258	4.1929	0.10430	0.6808:0.2111:0.1081:0.0	.	30	Q68CR7	LRC66_HUMAN	M	30	ENSP00000341944:I30M	ENSP00000341944:I30M	I	-	3	3	LRRC66	52578447	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.284000	0.18864	0.789000	0.33779	0.455000	0.32223	ATT		0.328	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		C	52883690	A	C	52883690	3	2	61	1	0	0	0	0	1	0	0	0	9047	10	1	4	2568	4	LRRC66	4	52883690	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	21583	52883690	138270586	3172	11157										
SGCB	6443	broad.mit.edu	37	chr4	52890147	52890147	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtgtttccacaggggttGtctgagatttggcagcccat	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:52890147G>C	ENST00000381431.5	-	6	1155	c.933C>G	c.(931-933)gaC>gaG	p.D311E	SGCB_ENST00000535450.1_Missense_Mutation_p.D241E	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	311	Cys-rich.				cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.D311E(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			CACAGGGGTTGTCTGAGATTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											111	96	101					4																	52890147		2203	4300	6503	52584904	SO:0001583	missense	6443			U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.933C>G	4.37:g.52890147G>C	ENSP00000370839:p.Asp311Glu		52584904	B7Z635|O00661	Missense_Mutation	SNP	ENST00000381431.5	37	CCDS3488.1	.	.	.	.	.	.	.	.	.	.	G	7.741	0.701385	0.15172	.	.	ENSG00000163069	ENST00000381431;ENST00000535450	D;D	0.96168	-2.28;-3.93	5.54	5.54	0.83059	.	0.236507	0.49305	D	0.000160	D	0.90314	0.6970	L	0.37630	1.12	0.40538	D	0.980994	B;B	0.23316	0.083;0.083	B;B	0.22601	0.04;0.025	D	0.83903	0.0291	10	0.02654	T	1	-17.7472	12.2039	0.54340	0.078:0.0:0.922:0.0	.	241;311	B7Z635;Q16585	.;SGCB_HUMAN	E	311;241	ENSP00000370839:D311E;ENSP00000441199:D241E	ENSP00000370839:D311E	D	-	3	2	SGCB	52584904	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	3.994000	0.56994	2.751000	0.94390	0.591000	0.81541	GAC		0.448	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			C	52890147	G	C	52890147	3	2	61	1	0	0	0	0	1	0	0	0	14237	1368	48	5	27	5	SGCB	4	52890147	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6457	52890147	138264129	3173	11158										
SPATA18	132671	broad.mit.edu	37	chr4	52917876	52917876	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaatagtgagcgatggcGgaaaacctgaaaagactggt	15	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:52917876G>C	ENST00000295213.4	+	1	380	c.6G>C	c.(4-6)gcG>gcC	p.A2A	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Silent_p.A2A	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	2					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)		p.A2A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			GAGCGATGGCGGAAAACCTGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	4											122	119	120					4																	52917876		2203	4300	6503	52612633	SO:0001819	synonymous_variant	132671			BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.6G>C	4.37:g.52917876G>C			52612633	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Silent	SNP	ENST00000295213.4	37	CCDS3489.1																																																																																				0.562	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		C	52917876	G	C	52917876	2	2	61	1	0	0	0	0	0	0	0	1	15042	1103	39	5		5	SPATA18	4	52917876	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27729	52917876	138236400	3174	11159										
SPATA18	132671	broad.mit.edu	37	chr4	52938276	52938276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagctccgaaacctgaagGaggagatagctgttctgtct	11	9	2	2	rs144283037		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:52938276G>A	ENST00000295213.4	+	6	1086	c.712G>A	c.(712-714)Gag>Aag	p.E238K	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Missense_Mutation_p.E206K	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	238					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)		p.E238K(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			AAACCTGAAGGAGGAGATAGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	85	87					4																	52938276		2203	4300	6503	52633033	SO:0001583	missense	132671			BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.712G>A	4.37:g.52938276G>A	ENSP00000295213:p.Glu238Lys		52633033	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369842	0.61624	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	D;T	0.87334	-2.24;1.65	4.97	4.97	0.65823	.	0.387284	0.32578	N	0.005901	D	0.82609	0.5074	L	0.43152	1.355	0.41171	D	0.986166	B;B;P	0.41848	0.275;0.403;0.763	B;B;B	0.36608	0.088;0.088;0.229	D	0.85767	0.1353	10	0.72032	D	0.01	-14.9761	15.7736	0.78190	0.0:0.0:1.0:0.0	.	206;238;238	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	K	238;206	ENSP00000295213:E238K;ENSP00000415309:E206K	ENSP00000295213:E238K	E	+	1	0	SPATA18	52633033	1.000000	0.71417	0.985000	0.45067	0.021000	0.10359	7.045000	0.76585	2.567000	0.86603	0.650000	0.86243	GAG		0.478	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		A	52938276	G	A	52938276	3	1	61	1	0	0	0	0	1	0	0	0	15042	1175	41	3	734	3	SPATA18	4	52938276	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20400	52938276	138216000	3175	11160										
SCFD2	152579	broad.mit.edu	37	chr4	53751933	53751933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggttcctggcttcaacGatgccacaagatctttgacc	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:53751933G>A	ENST00000401642.3	-	8	2076	c.1943C>T	c.(1942-1944)tCg>tTg	p.S648L	SCFD2_ENST00000388940.4_Missense_Mutation_p.S603L	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	648					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.S648L(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TGGCTTCAACGATGCCACAAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	107	110					4																	53751933		2203	4300	6503	53446690	SO:0001583	missense	152579			AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1943C>T	4.37:g.53751933G>A	ENSP00000384182:p.Ser648Leu		53446690	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.200298	0.38905	.	.	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.80123	-1.34;-1.34	5.07	5.07	0.68467	.	0.317958	0.29034	N	0.013358	T	0.76666	0.4019	L	0.50333	1.59	0.09310	N	1	P;P	0.40144	0.655;0.704	B;B	0.35859	0.135;0.212	T	0.74203	-0.3741	10	0.72032	D	0.01	.	17.4297	0.87536	0.0:0.0:1.0:0.0	.	603;648	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	L	648;603	ENSP00000384182:S648L;ENSP00000373592:S603L	ENSP00000373592:S603L	S	-	2	0	SCFD2	53446690	0.859000	0.29813	0.018000	0.16275	0.022000	0.10575	6.537000	0.73847	2.373000	0.80994	0.561000	0.74099	TCG		0.547	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540		A	53751933	G	A	53751933	3	1	61	1	0	0	0	0	1	0	0	0	13927	1059	37	1	119	1	SCFD2	4	53751933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	813657	53751933	137402343	3176	11161										
SCFD2	152579	broad.mit.edu	37	chr4	53786966	53786966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagctccagcaatatcccGaagtgaagtaaagagttcat	9	10	1	2	rs149566585		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:53786966G>A	ENST00000401642.3	-	6	1766	c.1633C>T	c.(1633-1635)Cgg>Tgg	p.R545W	SCFD2_ENST00000388940.4_Missense_Mutation_p.R545W	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	545					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.R545W(2)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			GCAATATCCCGAAGTGAAGTA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	TRP/ARG	0,4406		0,0,2203	79	82	81		1633	2.2	0.5	4	dbSNP_134	81	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SCFD2	NM_152540.3	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	545/685	53786966	2,13004	2203	4300	6503	53481723	SO:0001583	missense	152579			AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1633C>T	4.37:g.53786966G>A	ENSP00000384182:p.Arg545Trp		53481723	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	G	9.605	1.129831	0.21041	0.0	2.33E-4	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.80214	-1.17;-1.35	4.96	2.23	0.28157	.	0.211954	0.39475	N	0.001355	T	0.72590	0.3479	L	0.56769	1.78	0.32982	D	0.523853	B;B	0.11235	0.003;0.004	B;B	0.10450	0.003;0.005	T	0.69347	-0.5169	10	0.54805	T	0.06	.	5.0223	0.14367	0.1877:0.1727:0.6396:0.0	.	545;545	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	W	545	ENSP00000384182:R545W;ENSP00000373592:R545W	ENSP00000373592:R545W	R	-	1	2	SCFD2	53481723	0.998000	0.40836	0.545000	0.28153	0.349000	0.29174	0.905000	0.28504	0.354000	0.24105	0.561000	0.74099	CGG		0.388	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540		A	53786966	G	A	53786966	3	1	61	1	0	0	0	0	1	0	0	0	13927	1057	37	1	437	1	SCFD2	4	53786966	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35033	53786966	137367310	3177	11162										
FIP1L1	81608	broad.mit.edu	37	chr4	54319224	54319224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagagagcgagaccgtgatCgggacagagaaagagaacgc	15	8	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:54319224C>T	ENST00000337488.6	+	16	1617	c.1423C>T	c.(1423-1425)Cgg>Tgg	p.R475W	FIP1L1_ENST00000358575.5_Missense_Mutation_p.R469W|FIP1L1_ENST00000306932.6_Missense_Mutation_p.R401W|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	475	Arg-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R475W(1)		large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			agaccgtgatcgggacagaga	0.507			T	PDGFRA	idiopathic hypereosinophilic syndrome																																		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	1	Substitution - Missense(1)	large_intestine(1)	4											79	70	73					4																	54319224		2203	4300	6503	54013981	SO:0001583	missense	81608			AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1423C>T	4.37:g.54319224C>T	ENSP00000336752:p.Arg475Trp		54013981	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.309777	0.81247	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	T;T;T	0.08282	3.11;3.11;3.11	5.18	4.33	0.51752	.	0.000000	0.64402	D	0.000012	T	0.26521	0.0648	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;P	0.71414	0.953;0.973;0.953;0.898	T	0.01920	-1.1247	10	0.87932	D	0	-9.5475	14.9741	0.71257	0.1442:0.8558:0.0:0.0	.	469;469;401;475	G3XAD6;B4DIR3;Q6UN15-3;Q6UN15	.;.;.;FIP1_HUMAN	W	475;469;401;132	ENSP00000336752:R475W;ENSP00000351383:R469W;ENSP00000302993:R401W	ENSP00000302993:R401W	R	+	1	2	FIP1L1	54013981	0.998000	0.40836	0.825000	0.32803	0.950000	0.60333	3.341000	0.52151	1.267000	0.44247	0.655000	0.94253	CGG		0.507	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		T	54319224	C	T	54319224	3	4	61	1	0	0	0	0	1	0	0	0	5915	875	31	1	1516	1	FIP1L1	4	54319224	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	532258	54319224	136835052	3178	11163										
LNX1	84708	broad.mit.edu	37	chr4	54344807	54344807	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagataggcaaatcccattCtctatgtgatgctccccctg	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:54344807C>A	ENST00000263925.7	-	8	1902	c.1588G>T	c.(1588-1590)Gaa>Taa	p.E530*	LNX1_ENST00000306888.2_Nonsense_Mutation_p.E434*|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	530	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E434*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AAATCCCATTCTCTATGTGAT	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											184	178	180					4																	54344807		2203	4300	6503	54039564	SO:0001587	stop_gained	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1588G>T	4.37:g.54344807C>A	ENSP00000263925:p.Glu530*		54039564	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Nonsense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	35	5.518369	0.96416	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	.	.	.	4.98	4.14	0.48551	.	0.047493	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	13.6393	0.62241	0.0:0.9254:0.0:0.0746	.	.	.	.	X	434;368;530	.	ENSP00000263925:E530X	E	-	1	0	LNX1	54039564	1.000000	0.71417	0.822000	0.32727	0.167000	0.22549	6.989000	0.76219	1.458000	0.47871	0.655000	0.94253	GAA		0.443	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			A	54344807	C	A	54344807	4	1	61	1	0	0	0	0	0	1	0	0	8889	922	32	2	614	2	LNX1	4	54344807	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25583	54344807	136809469	3179	11164										
LNX1	84708	broad.mit.edu	37	chr4	54364863	54364863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctggcgatcaccccatcaCgataaatgtgttggataatg	9	10	3	0	rs542109970		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:54364863C>T	ENST00000263925.7	-	5	1237	c.923G>A	c.(922-924)cGt>cAt	p.R308H	LNX1_ENST00000306888.2_Missense_Mutation_p.R212H|FIP1L1_ENST00000507166.1_Intron|LNX1-AS1_ENST00000502373.1_RNA|LNX1-AS1_ENST00000510785.1_RNA	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	308	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R212H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CACCCCATCACGATAAATGTG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	4											87	76	80					4																	54364863		2203	4300	6503	54059620	SO:0001583	missense	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.923G>A	4.37:g.54364863C>T	ENSP00000263925:p.Arg308His		54059620	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.448876	0.43531	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.28069	1.63;1.63	4.49	3.64	0.41730	PDZ/DHR/GLGF (4);	0.303860	0.34531	N	0.003888	T	0.25975	0.0633	L	0.52126	1.63	0.49051	D	0.999743	P;P	0.45396	0.633;0.857	B;B	0.39217	0.184;0.294	T	0.04991	-1.0913	10	0.56958	D	0.05	.	9.2944	0.37806	0.0:0.8345:0.0:0.1655	.	308;212	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	H	212;146;308	ENSP00000302879:R212H;ENSP00000263925:R308H	ENSP00000263925:R308H	R	-	2	0	LNX1	54059620	1.000000	0.71417	0.926000	0.36857	0.324000	0.28378	4.390000	0.59646	1.251000	0.43983	-0.258000	0.10820	CGT		0.502	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			T	54364863	C	T	54364863	3	4	61	1	0	0	0	0	1	0	0	0	8889	536	19	1	1291	1	LNX1	4	54364863	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20056	54364863	136789413	3180	11165										
LNX1	84708	broad.mit.edu	37	chr4	54364945	54364945	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaggctttcactgggatCtactcgattgatcttgatgc	11	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:54364945C>A	ENST00000263925.7	-	5	1155	c.841G>T	c.(841-843)Gat>Tat	p.D281Y	LNX1_ENST00000306888.2_Missense_Mutation_p.D185Y|FIP1L1_ENST00000507166.1_Intron|LNX1-AS1_ENST00000502373.1_RNA|LNX1-AS1_ENST00000510785.1_RNA	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	281	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D185Y(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCACTGGGATCTACTCGATTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	91	96					4																	54364945		2203	4300	6503	54059702	SO:0001583	missense	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.841G>T	4.37:g.54364945C>A	ENSP00000263925:p.Asp281Tyr		54059702	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.542819	0.45280	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.08896	3.04;4.47	4.49	3.61	0.41365	PDZ/DHR/GLGF (3);	0.105254	0.64402	D	0.000007	T	0.33731	0.0873	M	0.88640	2.97	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.981	T	0.41645	-0.9497	10	0.66056	D	0.02	.	14.4954	0.67683	0.0:0.852:0.148:0.0	.	281;185	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	Y	185;119;281	ENSP00000302879:D185Y;ENSP00000263925:D281Y	ENSP00000263925:D281Y	D	-	1	0	LNX1	54059702	0.687000	0.27671	0.910000	0.35882	0.241000	0.25554	1.342000	0.33919	1.189000	0.43028	0.561000	0.74099	GAT		0.453	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			A	54364945	C	A	54364945	3	1	61	1	0	0	0	0	1	0	0	0	8889	913	32	2	1373	2	LNX1	4	54364945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82	54364945	136789331	3181	11166										
LNX1	84708	broad.mit.edu	37	chr4	54374161	54374161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttgactcacccctagttCggttgctccggccagagtcc	9	15	1	2	rs201126543		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:54374161C>T	ENST00000263925.7	-	3	928	c.614G>A	c.(613-615)cGa>cAa	p.R205Q	LNX1-AS1_ENST00000511989.1_RNA|LNX1_ENST00000306888.2_Missense_Mutation_p.R109Q|FIP1L1_ENST00000507166.1_Intron|LNX1-AS1_ENST00000510785.1_RNA|LNX1-AS1_ENST00000514364.1_RNA	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	205	Interaction with MAGEB18.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R109Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			ACCCCTAGTTCGGTTGCTCCG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	4											30	27	28					4																	54374161		2201	4299	6500	54068918	SO:0001583	missense	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.614G>A	4.37:g.54374161C>T	ENSP00000263925:p.Arg205Gln		54068918	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100746	0.37048	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.08008	3.14;4.6	5.31	2.61	0.31194	.	0.373061	0.30329	N	0.009870	T	0.03827	0.0108	L	0.32530	0.975	0.34287	D	0.682783	P;B	0.34934	0.476;0.09	B;B	0.17433	0.018;0.01	T	0.42649	-0.9439	10	0.10377	T	0.69	.	4.0475	0.09779	0.1328:0.5959:0.1284:0.1429	.	205;109	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	Q	109;43;205	ENSP00000302879:R109Q;ENSP00000263925:R205Q	ENSP00000263925:R205Q	R	-	2	0	LNX1	54068918	0.054000	0.20591	0.718000	0.30602	0.437000	0.31866	0.114000	0.15520	0.231000	0.21079	0.555000	0.69702	CGA		0.552	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			T	54374161	C	T	54374161	3	4	61	1	0	0	0	0	1	0	0	0	8889	884	31	1	1608	1	LNX1	4	54374161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9216	54374161	136780115	3182	11167										
PDGFRA	5156	broad.mit.edu	37	chr4	55133561	55133561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaagacagtggagattacGaatgtgctgcccgccaggct	13	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55133561G>A	ENST00000257290.5	+	6	1196	c.865G>A	c.(865-867)Gaa>Aaa	p.E289K	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	289	Ig-like C2-type 3.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.E289K(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TGGAGATTACGAATGTGCTGC	0.468			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - Missense(1)	large_intestine(1)	4											88	90	89					4																	55133561		2203	4300	6503	54828318	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.865G>A	4.37:g.55133561G>A	ENSP00000257290:p.Glu289Lys		54828318	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.635536	0.67130	.	.	ENSG00000134853	ENST00000257290	T	0.67345	-0.26	5.67	3.88	0.44766	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.33005	U	0.005396	T	0.61388	0.2343	M	0.65975	2.015	0.80722	D	1	P;P	0.49862	0.884;0.929	B;B	0.41271	0.23;0.352	T	0.62426	-0.6857	10	0.07175	T	0.84	.	15.5903	0.76523	0.0:0.3916:0.6084:0.0	.	289;289	P16234-3;P16234	.;PGFRA_HUMAN	K	289	ENSP00000257290:E289K	ENSP00000257290:E289K	E	+	1	0	PDGFRA	54828318	0.952000	0.32445	0.888000	0.34837	0.988000	0.76386	1.551000	0.36233	0.712000	0.32039	0.313000	0.20887	GAA		0.468	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55133561	G	A	55133561	3	1	61	1	0	0	0	0	1	0	0	0	11692	1059	37	1	883	1	PDGFRA	4	55133561	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	759400	55133561	136020715	3183	11168										
PDGFRA	5156	broad.mit.edu	37	chr4	55143646	55143646	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtcatgaaagttgcagtGaagatgctaaaacgtaagtg	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55143646G>T	ENST00000257290.5	+	13	2209	c.1878G>T	c.(1876-1878)gtG>gtT	p.V626V	FIP1L1_ENST00000507166.1_Silent_p.V386V	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	626	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.V626V(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	AAGTTGCAGTGAAGATGCTAA	0.483			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - coding silent(1)	large_intestine(1)	4											121	122	121					4																	55143646		2203	4300	6503	54838403	SO:0001819	synonymous_variant	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1878G>T	4.37:g.55143646G>T			54838403	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																				0.483	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		T	55143646	G	T	55143646	2	4	61	1	0	0	0	0	0	0	0	1	11692	1277	45	2		2	PDGFRA	4	55143646	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10085	55143646	136010630	3184	11169										
PDGFRA	5156	broad.mit.edu	37	chr4	55146636	55146636	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtccagcctcatataagaaGaaatctatgttaggtaaaag	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55146636G>T	ENST00000257290.5	+	16	2641	c.2310G>T	c.(2308-2310)aaG>aaT	p.K770N	FIP1L1_ENST00000507166.1_Missense_Mutation_p.K530N	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	770	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.K770N(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CATATAAGAAGAAATCTATGT	0.388			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - Missense(1)	large_intestine(1)	4											55	52	53					4																	55146636		2203	4300	6503	54841393	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2310G>T	4.37:g.55146636G>T	ENSP00000257290:p.Lys770Asn		54841393	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789458	0.31685	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	T;T	0.80033	-1.33;-1.33	5.79	5.79	0.91817	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.33553	U	0.004800	T	0.68805	0.3041	N	0.21508	0.67	0.80722	D	1	P	0.37781	0.608	B	0.38378	0.272	T	0.65919	-0.6051	10	0.13470	T	0.59	.	14.2072	0.65741	0.0711:0.0:0.9289:0.0	.	770	P16234	PGFRA_HUMAN	N	530;770	ENSP00000423325:K530N;ENSP00000257290:K770N	ENSP00000423325:K530N	K	+	3	2	FIP1L1;PDGFRA	54841393	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.995000	0.63908	2.735000	0.93741	0.561000	0.74099	AAG		0.388	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		T	55146636	G	T	55146636	3	4	61	1	0	0	0	0	1	0	0	0	11692	933	33	2	2368	2	PDGFRA	4	55146636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2990	55146636	136007640	3185	11170										
PDGFRA	5156	broad.mit.edu	37	chr4	55155014	55155014	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattctactttctacaataAgatcaagagtgggtaccgga	10	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55155014A>C	ENST00000257290.5	+	20	3054	c.2723A>C	c.(2722-2724)aAg>aCg	p.K908T	FIP1L1_ENST00000507166.1_Missense_Mutation_p.K668T	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	908	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.K908T(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TTCTACAATAAGATCAAGAGT	0.522			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - Missense(1)	large_intestine(1)	4											93	87	89					4																	55155014		2203	4300	6503	54849771	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2723A>C	4.37:g.55155014A>C	ENSP00000257290:p.Lys908Thr		54849771	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872244	0.91587	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.88818	-2.43;-2.43	6.07	6.07	0.98685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.33346	U	0.005008	D	0.91626	0.7354	L	0.38531	1.155	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.91774	0.5430	10	0.49607	T	0.09	.	16.3021	0.82825	1.0:0.0:0.0:0.0	.	908	P16234	PGFRA_HUMAN	T	668;908	ENSP00000423325:K668T;ENSP00000257290:K908T	ENSP00000423325:K668T	K	+	2	0	FIP1L1;PDGFRA	54849771	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	4.211000	0.58507	2.326000	0.78906	0.533000	0.62120	AAG		0.522	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		C	55155014	A	C	55155014	3	2	61	1	0	0	0	0	1	0	0	0	11692	72	3	4	2797	4	PDGFRA	4	55155014	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8378	55155014	135999262	3186	11171										
KIT	3815	broad.mit.edu	37	chr4	55561832	55561832	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgagatcctggatgaaacGaatgagaataagcagaatga	11	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55561832G>A	ENST00000288135.5	+	2	319	c.222G>A	c.(220-222)acG>acA	p.T74T		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	74	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T74T(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGATGAAACGAATGAGAATA	0.458		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - coding silent(1)	large_intestine(1)	4											108	100	103					4																	55561832		2203	4300	6503	55256589	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.222G>A	4.37:g.55561832G>A			55256589	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.458	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			A	55561832	G	A	55561832	2	1	61	1	0	0	0	0	0	0	0	1	8350	1045	37	1		1	KIT	4	55561832	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	406818	55561832	135592444	3187	11172										
KIT	3815	broad.mit.edu	37	chr4	55569904	55569904	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcagactaaactacaggaGaaatataatagctggcatca	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55569904G>T	ENST00000288135.5	+	5	868	c.771G>T	c.(769-771)gaG>gaT	p.E257D		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	257	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E257D(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AACTACAGGAGAAATATAATA	0.338		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - Missense(1)	large_intestine(1)	4											68	69	69					4																	55569904		2203	4300	6503	55264661	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.771G>T	4.37:g.55569904G>T	ENSP00000288135:p.Glu257Asp		55264661	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	0.072	-1.201114	0.01581	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	D;D	0.83591	-1.74;-1.74	5.77	-1.84	0.07809	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.776670	0.02950	N	0.141616	T	0.64000	0.2559	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.15870	0.0;0.014	T	0.53774	-0.8391	10	0.12430	T	0.62	.	5.5516	0.17093	0.4517:0.0:0.3717:0.1766	.	257;257	P10721-2;P10721	.;KIT_HUMAN	D	257	ENSP00000288135:E257D;ENSP00000390987:E257D	ENSP00000288135:E257D	E	+	3	2	KIT	55264661	0.000000	0.05858	0.001000	0.08648	0.044000	0.14063	-0.230000	0.09083	-0.084000	0.12595	-0.312000	0.09012	GAG		0.338	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55569904	G	T	55569904	3	4	61	1	0	0	0	0	1	0	0	0	8350	933	33	2	789	2	KIT	4	55569904	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8072	55569904	135584372	3188	11173										
KIT	3815	broad.mit.edu	37	chr4	55602678	55602678	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaggctcgactacctgtGaagtggatggcacctgaaag	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55602678G>T	ENST00000288135.5	+	18	2596	c.2499G>T	c.(2497-2499)gtG>gtT	p.V833V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	833	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V833V(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GACTACCTGTGAAGTGGATGG	0.393		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - coding silent(1)	large_intestine(1)	4											122	119	120					4																	55602678		2203	4300	6503	55297435	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2499G>T	4.37:g.55602678G>T			55297435	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.393	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55602678	G	T	55602678	2	4	61	1	0	0	0	0	0	0	0	1	8350	1277	45	2		2	KIT	4	55602678	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32774	55602678	135551598	3189	11174										
KIT	3815	broad.mit.edu	37	chr4	55604629	55604629	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaactgcagccccaaccGacagaagcccgtggtagacc	10	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55604629G>A	ENST00000288135.5	+	21	2934	c.2837G>A	c.(2836-2838)cGa>cAa	p.R946Q		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	946					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R946Q(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGCCCCAACCGACAGAAGCCC	0.512		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - Missense(1)	large_intestine(1)	4											134	131	132					4																	55604629		2203	4300	6503	55299386	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2837G>A	4.37:g.55604629G>A	ENSP00000288135:p.Arg946Gln		55299386	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	1.881	-0.457865	0.04508	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.76839	-1.05;-1.05	5.17	-7.2	0.01495	.	1.764130	0.03452	N	0.210805	T	0.53012	0.1770	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.44922	-0.9296	10	0.24483	T	0.36	.	11.281	0.49195	0.6009:0.2401:0.1591:0.0	.	942;946	P10721-2;P10721	.;KIT_HUMAN	Q	946;942	ENSP00000288135:R946Q;ENSP00000390987:R942Q	ENSP00000288135:R946Q	R	+	2	0	KIT	55299386	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.129000	0.10515	-1.176000	0.02747	-1.157000	0.01802	CGA		0.512	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			A	55604629	G	A	55604629	3	1	61	1	0	0	0	0	1	0	0	0	8350	1058	37	1	2919	1	KIT	4	55604629	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1951	55604629	135549647	3190	11175										
KDR	3791	broad.mit.edu	37	chr4	55955601	55955601	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctttcaatcgcctacaaAattcttcatcaatctttacc	1	13	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:55955601A>C	ENST00000263923.4	-	25	3639	c.3344T>G	c.(3343-3345)tTt>tGt	p.F1115C	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.F1115C(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCGCCTACAAAATTCTTCATC	0.378			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - Missense(1)	large_intestine(1)	4											81	79	79					4																	55955601		2203	4300	6503	55650358	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3344T>G	4.37:g.55955601A>C	ENSP00000263923:p.Phe1115Cys		55650358	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.453779	0.63290	.	.	ENSG00000128052	ENST00000263923	D	0.83419	-1.72	5.57	5.57	0.84162	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.052843	0.85682	D	0.000000	D	0.88793	0.6533	L	0.49640	1.575	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89898	0.4042	10	0.87932	D	0	.	15.7104	0.77623	1.0:0.0:0.0:0.0	.	1115	P35968	VGFR2_HUMAN	C	1115	ENSP00000263923:F1115C	ENSP00000263923:F1115C	F	-	2	0	KDR	55650358	1.000000	0.71417	1.000000	0.80357	0.277000	0.26821	9.339000	0.96797	2.109000	0.64355	0.383000	0.25322	TTT		0.378	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			C	55955601	A	C	55955601	3	2	61	1	0	0	0	0	1	0	0	0	8160	14	1	4	750	4	KDR	4	55955601	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	350972	55955601	135198675	3191	11176										
CLOCK	9575	broad.mit.edu	37	chr4	56304676	56304676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaggagcagtcactaattTggtcacaagttgttgacctt	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:56304676T>C	ENST00000309964.4	-	21	2384	c.2134A>G	c.(2134-2136)Aaa>Gaa	p.K712E	CLOCK_ENST00000381322.1_Missense_Mutation_p.K712E|CLOCK_ENST00000513440.1_Missense_Mutation_p.K712E	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	712	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.K712E(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GTCACTAATTTGGTCACAAGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	69	74					4																	56304676		2203	4300	6503	55999433	SO:0001583	missense	9575			AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.2134A>G	4.37:g.56304676T>C	ENSP00000308741:p.Lys712Glu		55999433	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	T	32	5.108206	0.94292	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04234	3.67;3.67;3.67	5.73	5.73	0.89815	.	0.086182	0.85682	D	0.000000	T	0.18676	0.0448	M	0.74881	2.28	0.80722	D	1	D	0.67145	0.996	P	0.60173	0.87	T	0.00263	-1.1866	9	.	.	.	.	16.0255	0.80541	0.0:0.0:0.0:1.0	.	712	O15516	CLOCK_HUMAN	E	712	ENSP00000308741:K712E;ENSP00000370723:K712E;ENSP00000426983:K712E	.	K	-	1	0	CLOCK	55999433	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.195000	0.70347	0.477000	0.44152	AAA		0.413	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		C	56304676	T	C	56304676	3	2	61	1	0	0	0	0	1	0	0	0	3555	1821	63	4	414	4	CLOCK	4	56304676	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	349075	56304676	134849600	3192	11177										
CLOCK	9575	broad.mit.edu	37	chr4	56325326	56325326	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaactcaccactgtttaaaGatttgaaatttcctataaat	3	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:56325326G>T	ENST00000309964.4	-	9	912	c.662C>A	c.(661-663)tCt>tAt	p.S221Y	CLOCK_ENST00000381322.1_Missense_Mutation_p.S221Y|CLOCK_ENST00000513440.1_Missense_Mutation_p.S221Y	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	221					cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.S221Y(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			ACTGTTTAAAGATTTGAAATT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											43	44	44					4																	56325326		2203	4297	6500	56020083	SO:0001583	missense	9575			AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.662C>A	4.37:g.56325326G>T	ENSP00000308741:p.Ser221Tyr		56020083	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.260793	0.39995	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04551	3.6;3.6;3.6	5.78	5.78	0.91487	.	0.048550	0.85682	D	0.000000	T	0.10423	0.0255	M	0.81802	2.56	0.58432	D	0.999999	B	0.14438	0.01	B	0.14023	0.01	T	0.05869	-1.0859	10	0.26408	T	0.33	.	16.4798	0.84155	0.0:0.1396:0.8604:0.0	.	221	O15516	CLOCK_HUMAN	Y	221	ENSP00000308741:S221Y;ENSP00000370723:S221Y;ENSP00000426983:S221Y	ENSP00000308741:S221Y	S	-	2	0	CLOCK	56020083	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.939000	0.70179	2.738000	0.93877	0.591000	0.81541	TCT		0.318	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		T	56325326	G	T	56325326	3	4	61	1	0	0	0	0	1	0	0	0	3555	942	33	2	1934	2	CLOCK	4	56325326	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20650	56325326	134828950	3193	11178										
EXOC1	55763	broad.mit.edu	37	chr4	56730461	56730461	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagcagcactgctgaaaaGaatgcatttatttcatgcat	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:56730461G>T	ENST00000381295.2	+	4	672	c.324G>T	c.(322-324)aaG>aaT	p.K108N	EXOC1_ENST00000346134.7_Missense_Mutation_p.K108N|EXOC1_ENST00000349598.6_Missense_Mutation_p.K108N	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	108					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.K108N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					CTGCTGAAAAGAATGCATTTA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	4											46	45	46					4																	56730461		2202	4300	6502	56425218	SO:0001583	missense	55763			AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.324G>T	4.37:g.56730461G>T	ENSP00000370695:p.Lys108Asn		56425218	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.882957	0.72410	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.28	4.44	0.53790	.	0.044305	0.85682	D	0.000000	T	0.76543	0.4002	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.98	T	0.78663	-0.2116	9	0.59425	D	0.04	.	14.0695	0.64851	0.0737:0.0:0.9263:0.0	.	108;108	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	N	108	.	ENSP00000326514:K108N	K	+	3	2	EXOC1	56425218	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.603000	0.46266	1.341000	0.45600	0.557000	0.71058	AAG		0.294	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		T	56730461	G	T	56730461	3	4	61	1	0	0	0	0	1	0	0	0	5314	933	33	2	334	2	EXOC1	4	56730461	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	405135	56730461	134423815	3194	11179										
CEP135	9662	broad.mit.edu	37	chr4	56820499	56820499	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcaaagctaagaatgaaaGaattcaacaacttcaagaaa	7	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:56820499G>T	ENST00000257287.4	+	4	546	c.422G>T	c.(421-423)aGa>aTa	p.R141I	CEP135_ENST00000422247.2_Missense_Mutation_p.R141I	NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	141					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)	p.R141I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AAGAATGAAAGAATTCAACAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	71	71					4																	56820499		2203	4299	6502	56515256	SO:0001583	missense	9662			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.422G>T	4.37:g.56820499G>T	ENSP00000257287:p.Arg141Ile		56515256	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.978585	0.74360	.	.	ENSG00000174799	ENST00000422247;ENST00000257287	T	0.50548	0.74	5.54	1.82	0.25136	.	0.122766	0.53938	D	0.000044	T	0.51398	0.1672	L	0.58101	1.795	0.48762	D	0.999707	P;P	0.51147	0.942;0.883	P;P	0.53360	0.724;0.655	T	0.45833	-0.9234	10	0.52906	T	0.07	.	8.3362	0.32217	0.7006:0.0:0.2994:0.0	.	141;141	Q66GS9;Q66GS9-2	CP135_HUMAN;.	I	141	ENSP00000257287:R141I	ENSP00000257287:R141I	R	+	2	0	CEP135	56515256	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	3.884000	0.56175	0.089000	0.17243	-0.469000	0.05056	AGA		0.338	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56820499	G	T	56820499	3	4	61	1	0	0	0	0	1	0	0	0	3253	942	33	2	432	2	CEP135	4	56820499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90038	56820499	134333777	3195	11180										
CEP135	9662	broad.mit.edu	37	chr4	56878140	56878140	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtggagctattagaaaaaGaaattcaagaggtaatatat	10	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:56878140G>T	ENST00000257287.4	+	21	2915	c.2791G>T	c.(2791-2793)Gaa>Taa	p.E931*		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	931					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)	p.E931*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					ATTAGAAAAAGAAATTCAAGA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											36	39	38					4																	56878140		2203	4299	6502	56572897	SO:0001587	stop_gained	9662			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2791G>T	4.37:g.56878140G>T	ENSP00000257287:p.Glu931*		56572897	B2RMY0|O75130|Q58F25|Q9H8H7	Nonsense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	G	42	9.441957	0.99172	.	.	ENSG00000174799	ENST00000257287	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	20.181	0.98201	0.0:0.0:1.0:0.0	.	.	.	.	X	931	.	ENSP00000257287:E931X	E	+	1	0	CEP135	56572897	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.814000	0.91968	2.840000	0.97914	0.655000	0.94253	GAA		0.303	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56878140	G	T	56878140	4	4	61	1	0	0	0	0	0	1	0	0	3253	943	33	2	2869	2	CEP135	4	56878140	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57641	56878140	134276136	3196	11181										
KIAA1211	57482	broad.mit.edu	37	chr4	57173715	57173715	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagcaacagttgggcaaGaatatcaagtttgggcagcg	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57173715G>T	ENST00000504228.1	+	3	240	c.135G>T	c.(133-135)aaG>aaT	p.K45N	KIAA1211_ENST00000264229.6_Missense_Mutation_p.K45N|KIAA1211_ENST00000541073.1_Missense_Mutation_p.K38N			Q6ZU35	K1211_HUMAN	KIAA1211	45								p.K45N(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AGTTGGGCAAGAATATCAAGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4											77	76	76					4																	57173715		2017	4181	6198	56868472	SO:0001583	missense	57482			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.135G>T	4.37:g.57173715G>T	ENSP00000423366:p.Lys45Asn		56868472	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719942	0.48728	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073	T;T;T	0.14766	2.6;2.6;2.48	5.84	4.97	0.65823	.	.	.	.	.	T	0.20047	0.0482	M	0.65975	2.015	0.36345	D	0.859724	P;P	0.41188	0.741;0.741	B;B	0.43658	0.426;0.426	T	0.14200	-1.0481	9	0.62326	D	0.03	-43.7386	9.6356	0.39806	0.2231:0.0:0.7769:0.0	.	38;45	F5H1N7;Q6ZU35	.;K1211_HUMAN	N	45;45;38	ENSP00000264229:K45N;ENSP00000423366:K45N;ENSP00000444006:K38N	ENSP00000264229:K45N	K	+	3	2	KIAA1211	56868472	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	2.498000	0.45363	1.409000	0.46915	0.655000	0.94253	AAG		0.488	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57173715	G	T	57173715	3	4	61	1	0	0	0	0	1	0	0	0	8236	933	33	2	141	2	KIAA1211	4	57173715	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	295575	57173715	133980561	3197	11182										
AASDH	132949	broad.mit.edu	37	chr4	57204669	57204669	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggagaagagaagacttCtccaggaagttcataaacac	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57204669C>T	ENST00000205214.6	-	15	3376	c.3196G>A	c.(3196-3198)Gaa>Aaa	p.E1066K	AASDH_ENST00000513376.1_Missense_Mutation_p.E966K|AASDH_ENST00000434343.2_Missense_Mutation_p.E581K|AASDH_ENST00000451613.1_3'UTR	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1066					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.E1066K(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GAGAAGACTTCTCCAGGAAGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											77	73	74					4																	57204669		2203	4300	6503	56899426	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3196G>A	4.37:g.57204669C>T	ENSP00000205214:p.Glu1066Lys		56899426	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100570	0.76983	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.56611	0.45;0.45;0.45	6.04	5.15	0.70609	Quinonprotein alcohol dehydrogenase-like (2);	0.091610	0.85682	D	0.000000	T	0.67664	0.2917	M	0.78916	2.43	0.80722	D	1	D	0.58620	0.983	P	0.55785	0.784	T	0.71520	-0.4568	10	0.72032	D	0.01	-24.7125	15.3491	0.74368	0.0:0.746:0.254:0.0	.	1066	Q4L235	ACSF4_HUMAN	K	1066;966;581	ENSP00000205214:E1066K;ENSP00000423760:E966K;ENSP00000392158:E581K	ENSP00000205214:E1066K	E	-	1	0	AASDH	56899426	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.769000	0.47654	2.881000	0.98747	0.650000	0.86243	GAA		0.403	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57204669	C	T	57204669	3	4	61	1	0	0	0	0	1	0	0	0	22	922	32	3	104	3	AASDH	4	57204669	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30954	57204669	133949607	3198	11183										
PPAT	5471	broad.mit.edu	37	chr4	57272693	57272693	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgagcagcatttaccaattCgccattatgtgccacagcta	7	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57272693C>T	ENST00000264220.2	-	3	507	c.370G>A	c.(370-372)Gaa>Aaa	p.E124K	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	124	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.E124K(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TTTACCAATTCGCCATTATGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											157	133	142					4																	57272693		2203	4300	6503	56967450	SO:0001583	missense	5471				CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.370G>A	4.37:g.57272693C>T	ENSP00000264220:p.Glu124Lys		56967450		Missense_Mutation	SNP	ENST00000264220.2	37	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	C	35	5.487725	0.96323	.	.	ENSG00000128059	ENST00000264220	T	0.78707	-1.2	5.62	5.62	0.85841	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.000000	0.85682	D	0.000000	D	0.88720	0.6513	M	0.81682	2.555	0.80722	D	1	D	0.69078	0.997	D	0.67548	0.952	D	0.89484	0.3752	10	0.72032	D	0.01	-30.1128	19.6664	0.95894	0.0:1.0:0.0:0.0	.	124	Q06203	PUR1_HUMAN	K	124	ENSP00000264220:E124K	ENSP00000264220:E124K	E	-	1	0	PPAT	56967450	1.000000	0.71417	0.984000	0.44739	0.980000	0.70556	5.739000	0.68622	2.646000	0.89796	0.585000	0.79938	GAA		0.388	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		T	57272693	C	T	57272693	3	4	61	1	0	0	0	0	1	0	0	0	12333	893	31	1	1219	1	PPAT	4	57272693	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68024	57272693	133881583	3199	11184										
PPAT	5471	broad.mit.edu	37	chr4	57273841	57273841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatttgaatgttggcaccGaactcccatcactagtcaca	8	11	2	2	rs200714501		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57273841G>A	ENST00000264220.2	-	2	307	c.170C>T	c.(169-171)tCg>tTg	p.S57L	AC068620.1_ENST00000598320.1_5'Flank|PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	57	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.S57L(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TGTTGGCACCGAACTCCCATC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											156	132	140					4																	57273841		2203	4300	6503	56968598	SO:0001583	missense	5471				CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.170C>T	4.37:g.57273841G>A	ENSP00000264220:p.Ser57Leu		56968598		Missense_Mutation	SNP	ENST00000264220.2	37	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.493157	0.26774	.	.	ENSG00000128059	ENST00000264220	.	.	.	5.74	3.75	0.43078	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.541698	0.19132	N	0.121904	T	0.28764	0.0713	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.14035	-1.0487	9	0.30078	T	0.28	-1.913	10.3823	0.44119	0.0966:0.1383:0.765:0.0	.	57	Q06203	PUR1_HUMAN	L	57	.	ENSP00000264220:S57L	S	-	2	0	PPAT	56968598	0.999000	0.42202	0.430000	0.26722	0.916000	0.54674	2.817000	0.48034	1.417000	0.47077	0.591000	0.81541	TCG		0.408	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		A	57273841	G	A	57273841	3	1	61	1	0	0	0	0	1	0	0	0	12333	1059	37	1	1423	1	PPAT	4	57273841	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1148	57273841	133880435	3200	11185										
PAICS	10606	broad.mit.edu	37	chr4	57318158	57318158	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcattccatgtgaacttCgagtaacatctgcgcataaa	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57318158C>T	ENST00000512576.1	+	7	1053	c.892C>T	c.(892-894)Cga>Tga	p.R298*	PAICS_ENST00000514888.1_Nonsense_Mutation_p.R206*|PAICS_ENST00000264221.2_Nonsense_Mutation_p.R298*|PAICS_ENST00000399688.3_Nonsense_Mutation_p.R305*	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	298	AIR carboxylase.				'de novo' IMP biosynthetic process (GO:0006189)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|phosphoribosylaminoimidazole carboxylase activity (GO:0004638)|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity (GO:0004639)	p.R324*(1)		endometrium(1)|kidney(2)|large_intestine(1)|urinary_tract(1)	5	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	ATGTGAACTTCGAGTAACATC	0.408																																					GBM(53;429 1144 8755 40726)											1	Substitution - Nonsense(1)	large_intestine(1)	4											53	49	50					4																	57318158		1843	4097	5940	57012915	SO:0001587	stop_gained	10606			X53793	CCDS47060.1, CCDS47061.1	4q12	2012-07-13			ENSG00000128050	ENSG00000128050	4.1.1.21, 6.3.2.6		8587	protein-coding gene	gene with protein product		172439		PAIS		2253271, 8106516	Standard	NM_006452		Approved	ADE2H1, AIRC	uc003hbt.1	P22234	OTTHUMG00000160957	ENST00000512576.1:c.892C>T	4.37:g.57318158C>T	ENSP00000421096:p.Arg298*		57012915	E9PDH9|Q68CQ5	Nonsense_Mutation	SNP	ENST00000512576.1	37	CCDS47061.1	.	.	.	.	.	.	.	.	.	.	C	35	5.596517	0.96602	.	.	ENSG00000128050	ENST00000514888;ENST00000264221;ENST00000505164;ENST00000399688;ENST00000512576	.	.	.	4.89	3.06	0.35304	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.0721	13.574	0.61864	0.5798:0.4202:0.0:0.0	.	.	.	.	X	206;298;298;305;298	.	ENSP00000264221:R298X	R	+	1	2	PAICS	57012915	0.998000	0.40836	0.997000	0.53966	0.664000	0.39144	1.777000	0.38604	0.512000	0.28257	0.650000	0.86243	CGA		0.408	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452		T	57318158	C	T	57318158	4	4	61	1	0	0	0	0	0	1	0	0	11426	876	31	1	943	1	PAICS	4	57318158	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44317	57318158	133836118	3201	11186										
SRP72	6731	broad.mit.edu	37	chr4	57342839	57342839	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatttttctcctgtagatCtttgccgccgttcattatca	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57342839C>A	ENST00000342756.5	+	6	1334	c.613C>A	c.(613-615)Ctt>Att	p.L205I	SRP72_ENST00000510663.1_Missense_Mutation_p.L205I	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	205					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.L205I(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					TCCTGTAGATCTTTGCCGCCG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	107	107					4																	57342839		2201	4297	6498	57037596	SO:0001583	missense	6731			AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"Tetratricopeptide (TTC) repeat domain containing"	11303	protein-coding gene	gene with protein product		602122	"signal recognition particle 72kD"			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.613C>A	4.37:g.57342839C>A	ENSP00000342181:p.Leu205Ile		57037596	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566501	0.45694	.	.	ENSG00000174780	ENST00000342756;ENST00000537129;ENST00000510663;ENST00000505314	D;T	0.94184	-3.37;0.96	5.28	5.28	0.74379	Tetratricopeptide-like helical (1);	0.119442	0.64402	D	0.000018	D	0.95010	0.8385	M	0.66939	2.045	0.24190	N	0.995551	D;B;P	0.54047	0.964;0.399;0.848	P;P;B	0.58820	0.846;0.522;0.437	D	0.89636	0.3859	10	0.33940	T	0.23	.	14.4058	0.67081	0.0:1.0:0.0:0.0	.	205;205;205	G5E9Z8;Q86X80;O76094	.;.;SRP72_HUMAN	I	205;211;205;10	ENSP00000342181:L205I;ENSP00000424576:L205I	ENSP00000342181:L205I	L	+	1	0	SRP72	57037596	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	4.378000	0.59568	2.477000	0.83638	0.585000	0.79938	CTT		0.338	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			A	57342839	C	A	57342839	3	1	61	1	0	0	0	0	1	0	0	0	15196	913	32	2	635	2	SRP72	4	57342839	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24681	57342839	133811437	3202	11187										
HOPX	84525	broad.mit.edu	37	chr4	57514898	57514898	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctccttagtctgtgacGgatctgcactctgagggcag	11	12	4	2	rs76751592	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57514898G>A	ENST00000337881.7	-	3	866	c.210C>T	c.(208-210)tcC>tcT	p.S70S	HOPX_ENST00000553379.2_Silent_p.S70S|HOPX_ENST00000556614.2_Silent_p.S70S|HOPX_ENST00000508121.1_Silent_p.S88S|HOPX_ENST00000381260.3_3'UTR|HOPX_ENST00000554144.1_3'UTR|HOPX_ENST00000420433.1_Silent_p.S88S|HOPX_ENST00000556376.2_Silent_p.S70S|HOPX_ENST00000317745.7_Silent_p.S70S|HOPX_ENST00000555760.2_Silent_p.S70S|HOPX_ENST00000381255.3_Silent_p.S70S|HOPX_ENST00000503639.3_Silent_p.S70S	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox	70					heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S70S(2)		large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					AGTCTGTGACGGATCTGCACT	0.493													G|||	5	0.000998403	0.0038	0	5008	,	,		19630	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	4						G	,,,,	13,4393	20.2+/-43.8	0,13,2190	108	100	103		210,,264,210,210	-1	1	4	dbSNP_133	103	0,8600		0,0,4300	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous,coding-synonymous	HOPX	NM_001145459.1,NM_001145460.1,NM_032495.5,NM_139211.4,NM_139212.3	,,,,	0,13,6490	AA,AG,GG		0.0,0.2951,0.1	,,,,	70/74,,88/92,70/74,70/74	57514898	13,12993	2203	4300	6503	57209655	SO:0001819	synonymous_variant	84525				CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"Homeoboxes / PRD class"	24961	protein-coding gene	gene with protein product	"homeobox only domain"	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.210C>T	4.37:g.57514898G>A			57209655	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Silent	SNP	ENST00000337881.7	37	CCDS3507.1																																																																																				0.493	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4			A	57514898	G	A	57514898	2	1	61	1	0	0	0	0	0	0	0	1	7306	1103	39	1		1	HOPX	4	57514898	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172059	57514898	133639378	3203	11188										
SPINK2	6691	broad.mit.edu	37	chr4	57676321	57676321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcagcagggtccatttCgaatgattttaatattatga	7	7	1	2	rs143868606	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57676321C>T	ENST00000248701.4	-	4	318	c.239G>A	c.(238-240)cGa>cAa	p.R80Q	SPINK2_ENST00000506738.1_Missense_Mutation_p.R130Q|SPINK2_ENST00000504762.1_Missense_Mutation_p.R115Q	NM_021114.2	NP_066937.1	P20155	ISK2_HUMAN	serine peptidase inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)	80	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R80Q(1)		kidney(1)|large_intestine(1)|lung(2)	4	Glioma(25;0.08)|all_neural(26;0.181)					GGGTCCATTTCGAATGATTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	88	86	87		239	1	0	4	dbSNP_134	87	0,8600		0,0,4300	no	missense	SPINK2	NM_021114.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	80/85	57676321	1,13005	2203	4300	6503	57371078	SO:0001583	missense	6691			BC022514	CCDS3508.1, CCDS63971.1, CCDS63972.1, CCDS75128.1	4q12	2011-08-31	2005-08-17		ENSG00000128040	ENSG00000128040		"Serine peptidase inhibitors, Kazal type"	11245	protein-coding gene	gene with protein product		605753	"serine protease inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)"			8428671	Standard	NM_001271718		Approved	HUSI-II	uc031sep.1	P20155	OTTHUMG00000128769	ENST00000248701.4:c.239G>A	4.37:g.57676321C>T	ENSP00000248701:p.Arg80Gln		57371078	Q6FGH2	Missense_Mutation	SNP	ENST00000248701.4	37	CCDS3508.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711832	0.30322	2.27E-4	0.0	ENSG00000128040	ENST00000248701;ENST00000506738;ENST00000504762	T;T;T	0.74737	-0.87;-0.87;-0.87	5.16	0.988	0.19796	Proteinase inhibitor I1, Kazal (2);	0.365080	0.19723	N	0.107548	T	0.58004	0.2092	.	.	.	0.09310	N	1	B	0.24576	0.106	B	0.17979	0.02	T	0.45454	-0.9260	9	0.41790	T	0.15	-6.1753	7.0486	0.25061	0.0:0.5481:0.0:0.4519	.	80	P20155	ISK2_HUMAN	Q	80;130;115	ENSP00000248701:R80Q;ENSP00000425961:R130Q;ENSP00000423858:R115Q	ENSP00000248701:R80Q	R	-	2	0	SPINK2	57371078	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.296000	0.08287	-0.031000	0.13781	0.563000	0.77884	CGA		0.363	SPINK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250690.2	NM_021114		T	57676321	C	T	57676321	3	4	61	1	0	0	0	0	1	0	0	0	15099	884	31	1	19	1	SPINK2	4	57676321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161423	57676321	133477955	3204	11189										
REST	5978	broad.mit.edu	37	chr4	57796626	57796626	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattctttacatggtcctgtGaatgatgaggaatcttcaac	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57796626G>T	ENST00000309042.7	+	4	1916	c.1602G>T	c.(1600-1602)gtG>gtT	p.V534V		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	534	Lys-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.V534V(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					ATGGTCCTGTGAATGATGAGG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4											50	51	51					4																	57796626		2202	4300	6502	57491383	SO:0001819	synonymous_variant	5978			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1602G>T	4.37:g.57796626G>T			57491383	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																				0.378	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		T	57796626	G	T	57796626	2	4	61	1	0	0	0	0	0	0	0	1	13271	1277	45	2		2	REST	4	57796626	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120305	57796626	133357650	3205	11190										
REST	5978	broad.mit.edu	37	chr4	57797911	57797911	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagaatctcactggtataAattcaacagttgaagaacca	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57797911A>C	ENST00000309042.7	+	4	3201	c.2887A>C	c.(2887-2889)Aat>Cat	p.N963H		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	963					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N963H(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CACTGGTATAAATTCAACAGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	69	70					4																	57797911		2203	4300	6503	57492668	SO:0001583	missense	5978			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2887A>C	4.37:g.57797911A>C	ENSP00000311816:p.Asn963His		57492668	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848400	0.32699	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.07688	3.17	5.38	4.53	0.55603	.	0.796161	0.10976	N	0.613292	T	0.06371	0.0164	N	0.08118	0	0.09310	N	1	P;P	0.51791	0.948;0.776	B;B	0.43990	0.438;0.187	T	0.36841	-0.9731	10	0.51188	T	0.08	-13.1875	11.417	0.49958	0.0851:0.0:0.9149:0.0	.	940;963	F8WAN5;Q13127	.;REST_HUMAN	H	963;940	ENSP00000311816:N963H	ENSP00000311816:N963H	N	+	1	0	REST	57492668	0.004000	0.15560	0.003000	0.11579	0.000000	0.00434	0.632000	0.24583	1.474000	0.48178	-0.242000	0.12053	AAT		0.418	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		C	57797911	A	C	57797911	3	2	61	1	0	0	0	0	1	0	0	0	13271	14	1	4	2897	4	REST	4	57797911	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1285	57797911	133356365	3206	11191										
POLR2B	5431	broad.mit.edu	37	chr4	57881690	57881690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctatgatcagagatattcGagagagggagattcggatct	12	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57881690G>A	ENST00000381227.1	+	15	2236	c.1823G>A	c.(1822-1824)cGa>cAa	p.R608Q	POLR2B_ENST00000314595.5_Missense_Mutation_p.R608Q|POLR2B_ENST00000441246.2_Missense_Mutation_p.R601Q|POLR2B_ENST00000510355.1_3'UTR|POLR2B_ENST00000431623.2_Missense_Mutation_p.R533Q			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	608					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)	p.R608Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					AGAGATATTCGAGAGAGGGAG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											103	109	107					4																	57881690		2203	4300	6503	57576447	SO:0001583	missense	5431				CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1823G>A	4.37:g.57881690G>A	ENSP00000370625:p.Arg608Gln		57576447	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.951081	0.92660	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.74	5.74	0.90152	RNA polymerase Rpb2, domain 4 (1);	0.061153	0.64402	D	0.000010	T	0.79964	0.4537	M	0.79011	2.435	0.80722	D	1	P;P	0.42483	0.781;0.781	B;B	0.38296	0.27;0.27	T	0.82147	-0.0601	10	0.52906	T	0.07	.	19.9173	0.97066	0.0:0.0:1.0:0.0	.	533;608	C9J4M6;P30876	.;RPB2_HUMAN	Q	608;533;601;608	ENSP00000370625:R608Q;ENSP00000391096:R533Q;ENSP00000391452:R601Q;ENSP00000312735:R608Q	ENSP00000312735:R608Q	R	+	2	0	POLR2B	57576447	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.582000	0.98214	2.707000	0.92482	0.563000	0.77884	CGA		0.328	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		A	57881690	G	A	57881690	3	1	61	1	0	0	0	0	1	0	0	0	12246	1058	37	1	1877	1	POLR2B	4	57881690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83779	57881690	133272586	3207	11192										
POLR2B	5431	broad.mit.edu	37	chr4	57883874	57883874	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggtctatggaatatctacGatttagagagctgccagcag	11	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:57883874G>A	ENST00000381227.1	+	17	2716	c.2303G>A	c.(2302-2304)cGa>cAa	p.R768Q	POLR2B_ENST00000314595.5_Missense_Mutation_p.R768Q|POLR2B_ENST00000441246.2_Missense_Mutation_p.R761Q|POLR2B_ENST00000431623.2_Missense_Mutation_p.R693Q			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	768					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)	p.R768Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GAATATCTACGATTTAGAGAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											96	88	91					4																	57883874		2203	4300	6503	57578631	SO:0001583	missense	5431				CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2303G>A	4.37:g.57883874G>A	ENSP00000370625:p.Arg768Gln		57578631	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	G	35	5.511668	0.96402	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.23	5.23	0.72850	DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.000000	0.85682	D	0.000000	T	0.72581	0.3478	L	0.41961	1.31	0.80722	D	1	D;D	0.56287	0.975;0.975	P;P	0.49477	0.612;0.612	T	0.76165	-0.3059	10	0.66056	D	0.02	.	18.7829	0.91941	0.0:0.0:1.0:0.0	.	693;768	C9J4M6;P30876	.;RPB2_HUMAN	Q	768;693;761;768	ENSP00000370625:R768Q;ENSP00000391096:R693Q;ENSP00000391452:R761Q;ENSP00000312735:R768Q	ENSP00000312735:R768Q	R	+	2	0	POLR2B	57578631	1.000000	0.71417	0.619000	0.29118	0.978000	0.69477	9.683000	0.98657	2.437000	0.82529	0.462000	0.41574	CGA		0.428	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		A	57883874	G	A	57883874	3	1	61	1	0	0	0	0	1	0	0	0	12246	1058	37	1	2365	1	POLR2B	4	57883874	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2184	57883874	133270402	3208	11193										
LPHN3	23284	broad.mit.edu	37	chr4	62598867	62598867	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggaggcaaatctgacataGacctggcagtagatgagaat	14	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:62598867G>A	ENST00000514591.1	+	7	1119	c.790G>A	c.(790-792)Gac>Aac	p.D264N	LPHN3_ENST00000511324.1_Missense_Mutation_p.D332N|LPHN3_ENST00000506700.1_Missense_Mutation_p.D264N|LPHN3_ENST00000506746.1_Missense_Mutation_p.D332N|LPHN3_ENST00000512091.2_Missense_Mutation_p.D264N|LPHN3_ENST00000506720.1_Missense_Mutation_p.D332N|LPHN3_ENST00000514996.1_Missense_Mutation_p.D264N|LPHN3_ENST00000504896.1_Missense_Mutation_p.D264N|LPHN3_ENST00000508946.1_Missense_Mutation_p.D264N|LPHN3_ENST00000545650.1_Missense_Mutation_p.D264N|LPHN3_ENST00000514157.1_Missense_Mutation_p.D264N|LPHN3_ENST00000509896.1_Missense_Mutation_p.D332N|LPHN3_ENST00000507625.1_Missense_Mutation_p.D332N|LPHN3_ENST00000508693.1_Missense_Mutation_p.D332N|LPHN3_ENST00000507164.1_Missense_Mutation_p.D332N			Q9HAR2	LPHN3_HUMAN	latrophilin 3	264	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.D264N(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						ATCTGACATAGACCTGGCAGT	0.428																																																3	Substitution - Missense(3)	large_intestine(3)	4											77	70	72					4																	62598867		1928	4125	6053	62281462	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.790G>A	4.37:g.62598867G>A	ENSP00000422533:p.Asp264Asn		62281462	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407030	0.83230	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.97424	0.9157	M	0.91818	3.245	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.999;0.996	D;D;D	0.85130	0.997;0.997;0.987	D	0.98380	1.0558	10	0.87932	D	0	.	17.6225	0.88086	0.0:0.0:1.0:0.0	.	264;332;264	E9PE04;E7EN28;Q9HAR2-2	.;.;.	N	264;264;332;332;264;264;264;264;264;332;332;332;264;264;264;332;332;264	ENSP00000423388:D264N;ENSP00000422533:D264N;ENSP00000423787:D332N;ENSP00000425033:D332N;ENSP00000424120:D264N;ENSP00000439831:D264N;ENSP00000421476:D332N;ENSP00000424030:D332N;ENSP00000421372:D332N;ENSP00000425201:D264N;ENSP00000423434:D264N;ENSP00000421627:D264N;ENSP00000420931:D332N;ENSP00000425884:D332N;ENSP00000424258:D264N	ENSP00000280009:D264N	D	+	1	0	LPHN3	62281462	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.401000	0.81631	0.557000	0.71058	GAC		0.428	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62598867	G	A	62598867	3	1	61	1	0	0	0	0	1	0	0	0	8946	942	33	3	808	3	LPHN3	4	62598867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4714993	62598867	128555409	3209	11194										
LPHN3	23284	broad.mit.edu	37	chr4	62845421	62845421	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccgtaacaccatccacaaGaacctctgcatcagtctctt	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:62845421G>T	ENST00000514591.1	+	17	3071	c.2742G>T	c.(2740-2742)aaG>aaT	p.K914N	LPHN3_ENST00000511324.1_Missense_Mutation_p.K982N|LPHN3_ENST00000506700.1_Missense_Mutation_p.K914N|LPHN3_ENST00000506746.1_Missense_Mutation_p.K982N|LPHN3_ENST00000512091.2_Missense_Mutation_p.K914N|LPHN3_ENST00000506720.1_Missense_Mutation_p.K982N|LPHN3_ENST00000514996.1_Missense_Mutation_p.K914N|LPHN3_ENST00000504896.1_Missense_Mutation_p.K914N|LPHN3_ENST00000508946.1_Missense_Mutation_p.K914N|LPHN3_ENST00000545650.1_Missense_Mutation_p.K914N|LPHN3_ENST00000514157.1_Missense_Mutation_p.K914N|LPHN3_ENST00000509896.1_Missense_Mutation_p.K982N|LPHN3_ENST00000507625.1_Missense_Mutation_p.K982N|LPHN3_ENST00000508693.1_Missense_Mutation_p.K982N|LPHN3_ENST00000507164.1_Missense_Mutation_p.K982N			Q9HAR2	LPHN3_HUMAN	latrophilin 3	901					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.K914N(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CCATCCACAAGAACCTCTGCA	0.473																																																3	Substitution - Missense(3)	large_intestine(3)	4											177	179	178					4																	62845421		2066	4228	6294	62528016	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2742G>T	4.37:g.62845421G>T	ENSP00000422533:p.Lys914Asn		62528016	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.14|18.14	3.557270|3.557270	0.65425|0.65425	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.37411	.|1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2	5.5|5.5	4.47|4.47	0.54385|0.54385	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.63426	.|0.2510	M|M	0.90483|0.90483	3.12|3.12	0.51233|0.51233	D|D	0.999918|0.999918	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.998;0.996	.|T	.|0.69109	.|-0.5232	.|10	.|0.87932	.|D	.|0	.|.	9.5822|9.5822	0.39495|0.39495	0.2153:0.0:0.7847:0.0|0.2153:0.0:0.7847:0.0	.|.	.|914;901;914	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	X|N	372|914;914;982;982;914;914;901;914;982;982;982;914;914;914;982;982;914	.|ENSP00000423388:K914N;ENSP00000422533:K914N;ENSP00000423787:K982N;ENSP00000425033:K982N;ENSP00000424120:K914N;ENSP00000439831:K914N;ENSP00000421476:K982N;ENSP00000424030:K982N;ENSP00000421372:K982N;ENSP00000425201:K914N;ENSP00000423434:K914N;ENSP00000421627:K914N;ENSP00000420931:K982N;ENSP00000425884:K982N;ENSP00000424258:K914N	.|ENSP00000280009:K914N	E|K	+|+	1|3	0|2	LPHN3|LPHN3	62528016|62528016	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.693000|2.693000	0.47027|0.47027	2.580000|2.580000	0.87095|0.87095	0.467000|0.467000	0.42956|0.42956	GAA|AAG		0.473	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62845421	G	T	62845421	3	4	61	1	0	0	0	0	1	0	0	0	8946	933	33	2	2800	2	LPHN3	4	62845421	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246554	62845421	128308855	3210	11195										
TECRL	253017	broad.mit.edu	37	chr4	65274978	65274978	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaaaaagtgaaaatttCtcatatcatccttcagtatg	5	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:65274978C>A	ENST00000381210.3	-	1	202	c.92G>T	c.(91-93)aGa>aTa	p.R31I	TECRL_ENST00000507440.1_Missense_Mutation_p.R31I	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	31					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	p.R31I(1)		endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						GTGAAAATTTCTCATATCATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											120	121	121					4																	65274978		2203	4300	6503	64957573	SO:0001583	missense	253017			AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"glycoprotein, synaptic 2-like"					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.92G>T	4.37:g.65274978C>A	ENSP00000370607:p.Arg31Ile		64957573		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.200085	0.38905	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.50813	0.73;0.73;0.73	4.99	1.79	0.24919	.	0.587910	0.17004	N	0.190810	T	0.42743	0.1216	L	0.51422	1.61	0.42066	D	0.991189	P;P	0.45176	0.852;0.61	P;B	0.44518	0.452;0.147	T	0.40156	-0.9578	10	0.87932	D	0	-10.0544	7.3339	0.26599	0.0:0.6497:0.0:0.3503	.	31;31	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	I	31	ENSP00000426043:R31I;ENSP00000370607:R31I;ENSP00000422497:R31I	ENSP00000370607:R31I	R	-	2	0	TECRL	64957573	0.994000	0.37717	0.991000	0.47740	0.641000	0.38312	0.498000	0.22530	0.626000	0.30322	0.655000	0.94253	AGA		0.418	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		A	65274978	C	A	65274978	3	1	61	1	0	0	0	0	1	0	0	0	15785	913	32	2	1047	2	TECRL	4	65274978	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2429557	65274978	125879298	3211	11196										
EPHA5	2044	broad.mit.edu	37	chr4	66201722	66201722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccaacatgttgactattTcatcaaacttgggcctgcta	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:66201722T>C	ENST00000273854.3	-	16	3380	c.2780A>G	c.(2779-2781)gAa>gGa	p.E927G	EPHA5_ENST00000432638.2_Missense_Mutation_p.E764G|EPHA5_ENST00000511294.1_Missense_Mutation_p.E928G|EPHA5_ENST00000354839.4_Missense_Mutation_p.E905G	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	927	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.E927G(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GTTGACTATTTCATCAAACTT	0.483										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4											191	167	175					4																	66201722		2203	4299	6502	65884317	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2780A>G	4.37:g.66201722T>C	ENSP00000273854:p.Glu927Gly		65884317	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999265	0.74818	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.93	5.93	0.95920	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.193605	0.35970	N	0.002865	T	0.78616	0.4311	M	0.88775	2.98	0.58432	D	0.999999	P;P;P;P	0.41080	0.737;0.715;0.692;0.626	P;B;B;B	0.46299	0.511;0.431;0.377;0.198	T	0.82552	-0.0400	10	0.72032	D	0.01	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	906;928;905;927	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	G	927;764;905;928	ENSP00000273854:E927G;ENSP00000389208:E764G;ENSP00000346899:E905G;ENSP00000427638:E928G	ENSP00000273854:E927G	E	-	2	0	EPHA5	65884317	1.000000	0.71417	0.993000	0.49108	0.835000	0.47333	6.305000	0.72805	2.281000	0.76405	0.533000	0.62120	GAA		0.483	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		C	66201722	T	C	66201722	3	2	61	1	0	0	0	0	1	0	0	0	5183	1783	62	4	345	4	EPHA5	4	66201722	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	926744	66201722	124952554	3212	11197										
EPHA5	2044	broad.mit.edu	37	chr4	66467547	66467547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggtgtcagggaagacaGccaagtgtcgtaccacagaa	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:66467547G>A	ENST00000273854.3	-	3	1322	c.722C>T	c.(721-723)gCt>gTt	p.A241V	EPHA5_ENST00000432638.2_Missense_Mutation_p.A241V|EPHA5_ENST00000511294.1_Missense_Mutation_p.A241V|EPHA5_ENST00000354839.4_Missense_Mutation_p.A241V	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	241	Cys-rich.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.A241V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						AGGGAAGACAGCCAAGTGTCG	0.458										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4											69	65	67					4																	66467547		2203	4300	6503	66150142	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.722C>T	4.37:g.66467547G>A	ENSP00000273854:p.Ala241Val		66150142	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956075	0.92726	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.80214	-1.18;-1.35;-1.12;-1.17	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000009	D	0.90769	0.7102	M	0.79805	2.47	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.967;0.999;0.997	D	0.91080	0.4899	10	0.87932	D	0	.	20.1208	0.97960	0.0:0.0:1.0:0.0	.	241;241;241;241	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	V	241	ENSP00000273854:A241V;ENSP00000389208:A241V;ENSP00000346899:A241V;ENSP00000427638:A241V	ENSP00000273854:A241V	A	-	2	0	EPHA5	66150142	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	9.869000	0.99810	2.758000	0.94735	0.655000	0.94253	GCT		0.458	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66467547	G	A	66467547	3	1	61	1	0	0	0	0	1	0	0	0	5183	971	34	3	2455	3	EPHA5	4	66467547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	265825	66467547	124686729	3213	11198										
EPHA5	2044	broad.mit.edu	37	chr4	66467707	66467707	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcataacacggtcaccaaGatcaagttctgtaaagcttt	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:66467707G>T	ENST00000273854.3	-	3	1162	c.562C>A	c.(562-564)Ctt>Att	p.L188I	EPHA5_ENST00000432638.2_Missense_Mutation_p.L188I|EPHA5_ENST00000511294.1_Missense_Mutation_p.L188I|EPHA5_ENST00000354839.4_Missense_Mutation_p.L188I	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	188	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.L188I(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CGGTCACCAAGATCAAGTTCT	0.383										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4											107	100	102					4																	66467707		2203	4300	6503	66150302	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.562C>A	4.37:g.66467707G>T	ENSP00000273854:p.Leu188Ile		66150302	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.517203	0.44763	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.03801	3.8;3.8;3.8;3.8	5.83	5.83	0.93111	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.53938	D	0.000044	T	0.19087	0.0458	M	0.72894	2.215	0.54753	D	0.99998	D;P;D;P	0.76494	0.999;0.795;0.998;0.888	D;P;D;B	0.91635	0.999;0.596;0.999;0.406	T	0.00109	-1.2049	10	0.35671	T	0.21	.	13.3392	0.60535	0.072:0.0:0.928:0.0	.	188;188;188;188	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	I	188	ENSP00000273854:L188I;ENSP00000389208:L188I;ENSP00000346899:L188I;ENSP00000427638:L188I	ENSP00000273854:L188I	L	-	1	0	EPHA5	66150302	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	5.823000	0.69272	2.758000	0.94735	0.655000	0.94253	CTT		0.383	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66467707	G	T	66467707	3	4	61	1	0	0	0	0	1	0	0	0	5183	942	33	2	2615	2	EPHA5	4	66467707	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160	66467707	124686569	3214	11199										
TMPRSS11D	9407	broad.mit.edu	37	chr4	68693227	68693227	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtggcaatccagtcacgaGgattagagttgctaaaacat	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:68693227G>T	ENST00000283916.6	-	8	802	c.704C>A	c.(703-705)cCt>cAt	p.P235H	TMPRSS11D_ENST00000545541.1_Missense_Mutation_p.P118H|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	235	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.P235H(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CCAGTCACGAGGATTAGAGTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											35	34	34					4																	68693227		2203	4298	6501	68375822	SO:0001583	missense	9407			AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.704C>A	4.37:g.68693227G>T	ENSP00000283916:p.Pro235His		68375822	Q08AF6	Missense_Mutation	SNP	ENST00000283916.6	37	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717179	0.68844	.	.	ENSG00000153802	ENST00000283916;ENST00000545541	D;D	0.88586	-2.4;-2.4	5.58	5.58	0.84498	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.109704	0.41194	D	0.000930	D	0.94262	0.8157	M	0.80982	2.52	0.43885	D	0.996505	D	0.89917	1.0	D	0.73708	0.981	D	0.94386	0.7609	10	0.66056	D	0.02	.	15.4378	0.75160	0.0:0.0:1.0:0.0	.	235	O60235	TM11D_HUMAN	H	235;118	ENSP00000283916:P235H;ENSP00000442045:P118H	ENSP00000283916:P235H	P	-	2	0	TMPRSS11D	68375822	1.000000	0.71417	0.211000	0.23655	0.020000	0.10135	4.368000	0.59505	2.774000	0.95407	0.655000	0.94253	CCT		0.318	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		T	68693227	G	T	68693227	3	4	61	1	0	0	0	0	1	0	0	0	16280	1000	35	2	564	2	TMPRSS11D	4	68693227	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2225520	68693227	122461049	3215	11200										
TMPRSS11D	9407	broad.mit.edu	37	chr4	68725378	68725378	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattcagaaatcttgaagtCgaagttacacgtgctggcct	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:68725378C>T	ENST00000283916.6	-	2	125	c.27G>A	c.(25-27)tcG>tcA	p.S9S	TMPRSS11D_ENST00000545541.1_Intron|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11D_ENST00000509584.1_Intron	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	9					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.S9S(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						ATCTTGAAGTCGAAGTTACAC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	4											94	84	88					4																	68725378		2203	4300	6503	68407973	SO:0001819	synonymous_variant	9407			AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.27G>A	4.37:g.68725378C>T			68407973	Q08AF6	Silent	SNP	ENST00000283916.6	37	CCDS3518.1																																																																																				0.393	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		T	68725378	C	T	68725378	2	4	61	1	0	0	0	0	0	0	0	1	16280	871	31	1		1	TMPRSS11D	4	68725378	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32151	68725378	122428898	3216	11201										
TMPRSS11A	339967	broad.mit.edu	37	chr4	68784789	68784789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatctggcgtatgtcatccGaaaaggtgactctggaagag	12	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:68784789G>A	ENST00000334830.7	-	8	1609	c.863C>T	c.(862-864)tCg>tTg	p.S288L	TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.S285L|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.S284L			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	288	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			S -> P (in Ref. 1; AAD41463). {ECO:0000305}.	cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.S288L(2)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						TATGTCATCCGAAAAGGTGAC	0.443																																					NSCLC(26;2 894 10941 14480 22546)											2	Substitution - Missense(2)	large_intestine(2)	4											161	165	163					4																	68784789		2203	4300	6503	68467384	SO:0001583	missense	339967			AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.863C>T	4.37:g.68784789G>A	ENSP00000334611:p.Ser288Leu		68467384	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529581	0.44969	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42	5.36	5.36	0.76844	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.113273	0.39341	N	0.001393	D	0.94528	0.8238	M	0.83774	2.66	0.39621	D	0.970031	P;P	0.49862	0.929;0.929	B;B	0.41374	0.355;0.355	D	0.95933	0.8940	10	0.87932	D	0	.	16.5682	0.84604	0.0:0.0:1.0:0.0	.	285;288	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	L	284;288;285;252	ENSP00000426911:S284L;ENSP00000334611:S288L;ENSP00000379491:S285L;ENSP00000427621:S252L	ENSP00000334611:S288L	S	-	2	0	TMPRSS11A	68467384	0.976000	0.34144	0.312000	0.25196	0.086000	0.17979	2.020000	0.41010	2.512000	0.84698	0.591000	0.81541	TCG		0.443	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		A	68784789	G	A	68784789	3	1	61	1	0	0	0	0	1	0	0	0	16278	1059	37	1	414	1	TMPRSS11A	4	68784789	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59411	68784789	122369487	3217	11202										
TMPRSS11F	389208	broad.mit.edu	37	chr4	68956276	68956276	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgactcctttctataaactCtcttgaagatcttatgccat	4	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:68956276C>A	ENST00000356291.2	-	3	306	c.247G>T	c.(247-249)Gag>Tag	p.E83*		NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	83	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.E83*(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						TCTATAAACTCTCTTGAAGAT	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											69	71	71					4																	68956276		2203	4295	6498	68638871	SO:0001587	stop_gained	389208			AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.247G>T	4.37:g.68956276C>A	ENSP00000348639:p.Glu83*		68638871	A8MXX2	Nonsense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.771195	0.49680	.	.	ENSG00000198092	ENST00000356291	.	.	.	5.43	3.68	0.42216	.	0.119337	0.37577	N	0.002029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	12.7199	0.57136	0.0:0.6833:0.3167:0.0	.	.	.	.	X	83	.	ENSP00000348639:E83X	E	-	1	0	TMPRSS11F	68638871	0.998000	0.40836	0.999000	0.59377	0.164000	0.22412	1.505000	0.35736	0.765000	0.33221	-0.266000	0.10368	GAG		0.294	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68956276	C	A	68956276	4	1	61	1	0	0	0	0	0	1	0	0	16282	922	32	2	1101	2	TMPRSS11F	4	68956276	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171487	68956276	122198000	3218	11203										
TMPRSS11F	389208	broad.mit.edu	37	chr4	68956346	68956346	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaaagaggcaaggtaataGaaagacttatcatctgaaag	9	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:68956346G>A	ENST00000356291.2	-	3	236	c.177C>T	c.(175-177)ttC>ttT	p.F59F		NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	59	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.F59F(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						CAAGGTAATAGAAAGACTTAT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	4											60	64	63					4																	68956346		2201	4289	6490	68638941	SO:0001819	synonymous_variant	389208			AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.177C>T	4.37:g.68956346G>A			68638941	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																				0.333	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68956346	G	A	68956346	2	1	61	1	0	0	0	0	0	0	0	1	16282	933	33	3		3	TMPRSS11F	4	68956346	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70	68956346	122197930	3219	11204										
TMPRSS11B	132724	broad.mit.edu	37	chr4	69095086	69095086	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtactctgtaaaagaaacttCttcagcaagctgcacaaggg	9	9	3	1	rs149786976	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69095086C>A	ENST00000332644.5	-	8	996	c.835G>T	c.(835-837)Gaa>Taa	p.E279*		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	279	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.E279*(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						AAAGAAACTTCTTCAGCAAGC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	4						C	stop/GLU	10,4396	16.8+/-37.8	0,10,2193	91	89	90		835	2.3	0.1	4	dbSNP_134	90	0,8600		0,0,4300	yes	stop-gained	TMPRSS11B	NM_182502.3		0,10,6493	AA,AC,CC		0.0,0.227,0.0769		279/417	69095086	10,12996	2203	4300	6503	68777681	SO:0001587	stop_gained	132724			BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"Serine peptidases / Transmembrane"	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.835G>T	4.37:g.69095086C>A	ENSP00000330475:p.Glu279*		68777681	A8K4D9	Nonsense_Mutation	SNP	ENST00000332644.5	37	CCDS3521.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.329263	0.60743	0.00227	0.0	ENSG00000185873	ENST00000332644	.	.	.	4.99	2.28	0.28536	.	0.677300	0.12822	N	0.436324	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	4.2807	0.10831	0.0:0.5505:0.1703:0.2792	.	.	.	.	X	279	.	ENSP00000330475:E279X	E	-	1	0	TMPRSS11B	68777681	0.000000	0.05858	0.091000	0.20842	0.015000	0.08874	-0.278000	0.08490	0.370000	0.24538	0.650000	0.86243	GAA		0.373	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		A	69095086	C	A	69095086	4	1	61	1	0	0	0	0	0	1	0	0	16279	922	32	2	427	2	TMPRSS11B	4	69095086	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138740	69095086	122059190	3220	11205										
TMPRSS11B	132724	broad.mit.edu	37	chr4	69107480	69107480	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actccaagaaaaataaagatCgtagtccatagtggccaaga	8	8	0	3	rs371254373		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69107480C>T	ENST00000332644.5	-	2	212	c.51G>A	c.(49-51)acG>acA	p.T17T		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	17						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.T17T(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						AAATAAAGATCGTAGTCCATA	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	4						C		1,4405	2.1+/-5.4	0,1,2202	75	76	76		51	-8.4	0	4		76	0,8600		0,0,4300	no	coding-synonymous	TMPRSS11B	NM_182502.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		17/417	69107480	1,13005	2203	4300	6503	68790075	SO:0001819	synonymous_variant	132724			BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"Serine peptidases / Transmembrane"	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.51G>A	4.37:g.69107480C>T			68790075	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																				0.388	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		T	69107480	C	T	69107480	2	4	61	1	0	0	0	0	0	0	0	1	16279	871	31	1		1	TMPRSS11B	4	69107480	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12394	69107480	122046796	3221	11206										
YTHDC1	91746	broad.mit.edu	37	chr4	69202828	69202828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagtcactggcctcacttCgagtgtcataatcatttccc	7	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69202828C>T	ENST00000344157.4	-	4	1135	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	YTHDC1_ENST00000579690.1_Missense_Mutation_p.R267Q|YTHDC1_ENST00000355665.3_Missense_Mutation_p.R267Q	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	267					mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R267Q(2)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						GGCCTCACTTCGAGTGTCATA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	4											209	147	168					4																	69202828		2203	4300	6503	68885423	SO:0001583	missense	91746			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.800G>A	4.37:g.69202828C>T	ENSP00000339245:p.Arg267Gln		68885423	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.701637	0.68501	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.30182	1.54;1.6	5.73	4.89	0.63831	.	0.194283	0.45606	N	0.000349	T	0.25344	0.0616	L	0.29908	0.895	0.58432	D	0.999999	B;B	0.12630	0.006;0.003	B;B	0.09377	0.004;0.002	T	0.03175	-1.1064	10	0.62326	D	0.03	.	14.591	0.68365	0.0:0.9302:0.0:0.0698	.	267;267	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	Q	267	ENSP00000339245:R267Q;ENSP00000347888:R267Q	ENSP00000339245:R267Q	R	-	2	0	YTHDC1	68885423	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.021000	0.76425	1.442000	0.47568	0.585000	0.79938	CGA		0.468	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		T	69202828	C	T	69202828	3	4	61	1	0	0	0	0	1	0	0	0	17536	884	31	1	1439	1	YTHDC1	4	69202828	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95348	69202828	121951448	3222	11207										
UGT2B15	7367	broad.mit.edu	37	chr4	69403613	69403613	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgataatttcatgatattCtctttatagctgaaggataa	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69403613C>A	ENST00000317746.2	-	6	1365	c.1323G>T	c.(1321-1323)gaG>gaT	p.E441D		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	441					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.E441D(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TCATGATATTCTCTTTATAGC	0.368																																					Melanoma(18;649 833 28984 37818 38500)											1	Substitution - Missense(1)	large_intestine(1)	4											63	65	64					4																	69403613		2088	3911	5999	69086208	SO:0001583	missense	7367			U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"UDP glucuronosyltransferases"	12547	protein-coding gene	gene with protein product		601903	"UDP glycosyltransferase 2 family, polypeptide B17"			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1323G>T	4.37:g.69403613C>A	ENSP00000320401:p.Glu441Asp		69086208		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	C	3.806	-0.040681	0.07452	.	.	ENSG00000197888	ENST00000317746	T	0.64260	-0.09	2.85	1.04	0.20106	.	0.075834	0.50627	U	0.000109	T	0.66944	0.2841	M	0.82630	2.6	0.21861	N	0.999501	.	.	.	.	.	.	T	0.60505	-0.7250	8	0.72032	D	0.01	.	4.5506	0.12110	0.0:0.5544:0.0:0.4456	.	.	.	.	D	441	ENSP00000320401:E441D	ENSP00000320401:E441D	E	-	3	2	UGT2B17	69086208	0.992000	0.36948	0.048000	0.18961	0.062000	0.15995	0.199000	0.17237	0.518000	0.28383	0.195000	0.17529	GAG		0.368	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		A	69403613	C	A	69403613	3	1	61	1	0	0	0	0	1	0	0	0	16998	912	32	2	273	2	UGT2B15	4	69403613	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200785	69403613	121750663	3223	11208										
UGT2B15	7367	broad.mit.edu	37	chr4	69434109	69434109	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttatccaatggctgtattCtgtgggccacaccagcacct	8	12	1	0	rs373276207		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69434109C>A	ENST00000317746.2	-	1	136	c.94G>T	c.(94-96)Gaa>Taa	p.E32*		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	32					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.E32*(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TGGCTGTATTCTGTGGGCCAC	0.458																																					Melanoma(18;649 833 28984 37818 38500)											1	Substitution - Nonsense(1)	large_intestine(1)	4						C	stop/GLU	0,4204		0,0,2102	190	191	191		94	2.5	0.1	4		191	1,7973		0,1,3986	no	stop-gained	UGT2B17	NM_001077.3		0,1,6088	AA,AC,CC		0.0125,0.0,0.0082		32/531	69434109	1,12177	2102	3987	6089	69116704	SO:0001587	stop_gained	7367			U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"UDP glucuronosyltransferases"	12547	protein-coding gene	gene with protein product		601903	"UDP glycosyltransferase 2 family, polypeptide B17"			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.94G>T	4.37:g.69434109C>A	ENSP00000320401:p.Glu32*		69116704		Nonsense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	36	5.696949	0.96802	0.0	1.25E-4	ENSG00000197888	ENST00000317746	.	.	.	2.54	2.54	0.30619	.	0.167332	0.37393	U	0.002109	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.8359	0.46688	0.0:1.0:0.0:0.0	.	.	.	.	X	32	.	ENSP00000320401:E32X	E	-	1	0	UGT2B17	69116704	0.997000	0.39634	0.109000	0.21407	0.968000	0.65278	3.755000	0.55197	1.442000	0.47568	0.393000	0.25936	GAA		0.458	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		A	69434109	C	A	69434109	4	1	61	1	0	0	0	0	0	1	0	0	16998	922	32	2	1522	2	UGT2B15	4	69434109	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30496	69434109	121720167	3224	11209										
UGT2A3	79799	broad.mit.edu	37	chr4	69795633	69795633	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgccacacaggccagcagGaacccaatcacatctataga	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:69795633G>T	ENST00000251566.4	-	6	1512	c.1482C>A	c.(1480-1482)ttC>ttA	p.F494L	UGT2A3_ENST00000420231.2_Missense_Mutation_p.F205L	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	494					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.F494L(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AGGCCAGCAGGAACCCAATCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											64	64	64					4																	69795633		2203	4300	6503	69830222	SO:0001583	missense	79799				CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.1482C>A	4.37:g.69795633G>T	ENSP00000251566:p.Phe494Leu		69830222	Q9H6S4	Missense_Mutation	SNP	ENST00000251566.4	37	CCDS3525.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.327685	0.24080	.	.	ENSG00000135220	ENST00000251566;ENST00000420231	T;T	0.70986	-0.53;-0.53	2.22	1.34	0.21922	.	0.112278	0.64402	D	0.000009	T	0.74913	0.3779	M	0.70842	2.15	0.31876	N	0.619097	D	0.55385	0.971	P	0.56563	0.801	T	0.76066	-0.3095	10	0.87932	D	0	.	6.6328	0.22867	0.1625:0.0:0.8375:0.0	.	494	Q6UWM9	UD2A3_HUMAN	L	494;205	ENSP00000251566:F494L;ENSP00000440115:F205L	ENSP00000251566:F494L	F	-	3	2	UGT2A3	69830222	0.989000	0.36119	0.093000	0.20910	0.012000	0.07955	0.583000	0.23849	0.271000	0.22005	0.491000	0.48974	TTC		0.428	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		T	69795633	G	T	69795633	3	4	61	1	0	0	0	0	1	0	0	0	16995	1165	41	2	105	2	UGT2A3	4	69795633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	361524	69795633	121358643	3225	11210										
UGT2B11	10720	broad.mit.edu	37	chr4	70070338	70070338	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgccattggctccaccatGagttataaaagctctggttt	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70070338G>T	ENST00000446444.1	-	5	1128	c.1120C>A	c.(1120-1122)Cat>Aat	p.H374N	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	374					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.H374N(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						GCTCCACCATGAGTTATAAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											51	55	54					4																	70070338		2180	4251	6431	70104927	SO:0001583	missense	10720			AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"UDP glucuronosyltransferases"	12545	protein-coding gene	gene with protein product		603064	"UDP glycosyltransferase 2 family, polypeptide B11"			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1120C>A	4.37:g.70070338G>T	ENSP00000387683:p.His374Asn		70104927	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	11.83	1.754956	0.31046	.	.	ENSG00000213759	ENST00000446444	T	0.80738	-1.41	1.96	1.96	0.26148	.	0.000000	0.64402	U	0.000001	D	0.92662	0.7668	H	0.98818	4.34	0.28343	N	0.921241	D	0.89917	1.0	D	0.87578	0.998	D	0.85721	0.1325	10	0.87932	D	0	.	9.5515	0.39313	0.0:0.0:1.0:0.0	.	374	O75310	UDB11_HUMAN	N	374	ENSP00000387683:H374N	ENSP00000387683:H374N	H	-	1	0	UGT2B11	70104927	1.000000	0.71417	0.998000	0.56505	0.080000	0.17528	8.339000	0.90041	1.087000	0.41251	0.184000	0.17185	CAT		0.378	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073		T	70070338	G	T	70070338	3	4	61	1	0	0	0	0	1	0	0	0	16997	1290	45	2	477	2	UGT2B11	4	70070338	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	274705	70070338	121083938	3226	11211										
UGT2B11	10720	broad.mit.edu	37	chr4	70080039	70080039	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagttttttcataactttCttatttgaaactacatcttt	3	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70080039C>A	ENST00000446444.1	-	1	410	c.402G>T	c.(400-402)aaG>aaT	p.K134N	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	134					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.K134N(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TCATAACTTTCTTATTTGAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	66	64					4																	70080039		2203	4297	6500	70114628	SO:0001583	missense	10720			AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"UDP glucuronosyltransferases"	12545	protein-coding gene	gene with protein product		603064	"UDP glycosyltransferase 2 family, polypeptide B11"			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.402G>T	4.37:g.70080039C>A	ENSP00000387683:p.Lys134Asn		70114628	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	6.041	0.375990	0.11409	.	.	ENSG00000213759	ENST00000446444	T	0.63417	-0.04	1.96	1.05	0.20165	.	0.249736	0.31404	U	0.007709	T	0.69620	0.3131	M	0.83483	2.645	0.09310	N	1	P	0.43392	0.805	P	0.52672	0.706	T	0.60372	-0.7276	10	0.72032	D	0.01	.	6.0646	0.19856	0.0:0.8104:0.0:0.1896	.	134	O75310	UDB11_HUMAN	N	134	ENSP00000387683:K134N	ENSP00000387683:K134N	K	-	3	2	UGT2B11	70114628	0.000000	0.05858	0.020000	0.16555	0.057000	0.15508	-0.694000	0.05115	1.087000	0.41251	0.184000	0.17185	AAG		0.343	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073		A	70080039	C	A	70080039	3	1	61	1	0	0	0	0	1	0	0	0	16997	912	32	2	1211	2	UGT2B11	4	70080039	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9701	70080039	121074237	3227	11212										
UGT2B28	54490	broad.mit.edu	37	chr4	70146620	70146620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagatgtagtttcaaataaGaaagttatgaaaaaactaca	6	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70146620G>T	ENST00000335568.5	+	1	404	c.402G>T	c.(400-402)aaG>aaT	p.K134N	UGT2B28_ENST00000511240.1_Missense_Mutation_p.K134N	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	134					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.K134N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TTTCAAATAAGAAAGTTATGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											56	70	66					4																	70146620		2132	4277	6409	70181209	SO:0001583	missense	54490			AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"UDP glucuronosyltransferases"	13479	protein-coding gene	gene with protein product		606497	"UDP glycosyltransferase 2 family, polypeptide B28"			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.402G>T	4.37:g.70146620G>T	ENSP00000334276:p.Lys134Asn		70181209	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	.	.	.	.	.	.	.	.	.	.	-	10.39	1.338072	0.24253	.	.	ENSG00000135226	ENST00000335568;ENST00000511240	T;T	0.63417	-0.04;-0.04	2.18	1.26	0.21427	.	0.249736	0.31404	U	0.007709	T	0.72574	0.3477	M	0.71581	2.175	0.09310	N	1	D;P	0.89917	1.0;0.699	D;P	0.97110	1.0;0.616	T	0.61496	-0.7051	10	0.72032	D	0.01	.	7.0283	0.24952	0.1592:0.0:0.8408:0.0	.	134;134	Q9BY64-2;Q9BY64	.;UDB28_HUMAN	N	134	ENSP00000334276:K134N;ENSP00000427399:K134N	ENSP00000334276:K134N	K	+	3	2	UGT2B28	70181209	0.000000	0.05858	0.002000	0.10522	0.025000	0.11179	-1.152000	0.03172	0.220000	0.20860	0.184000	0.17185	AAG		0.328	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039		T	70146620	G	T	70146620	3	4	61	1	0	0	0	0	1	0	0	0	17000	933	33	2	404	2	UGT2B28	4	70146620	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66581	70146620	121007656	3228	11213										
SULT1B1	27284	broad.mit.edu	37	chr4	70596372	70596372	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcttctctagaaatctaaTgatcttcttgatttcctcct	4	10	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70596372T>G	ENST00000310613.3	-	7	922	c.625A>C	c.(625-627)Att>Ctt	p.I209L		NM_014465.3	NP_055280.2	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member 1	209					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|cellular biogenic amine metabolic process (GO:0006576)|epithelial cell differentiation (GO:0030855)|flavonoid metabolic process (GO:0009812)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|thyroid hormone metabolic process (GO:0042403)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|sulfotransferase activity (GO:0008146)	p.I209L(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(14)|prostate(1)|upper_aerodigestive_tract(1)	24						AGAAATCTAATGATCTTCTTG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											121	114	116					4																	70596372		2202	4300	6502	70630961	SO:0001583	missense	27284			D89479	CCDS3530.1	4q13.3	2008-02-05			ENSG00000173597	ENSG00000173597		"Sulfotransferases, cytosolic"	17845	protein-coding gene	gene with protein product		608436				11688987, 9443824	Standard	NM_014465		Approved	ST1B2	uc003hen.3	O43704	OTTHUMG00000129407	ENST00000310613.3:c.625A>C	4.37:g.70596372T>G	ENSP00000308770:p.Ile209Leu		70630961	O15497|Q96FI1|Q9UK34	Missense_Mutation	SNP	ENST00000310613.3	37	CCDS3530.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.511908	0.00984	.	.	ENSG00000173597	ENST00000310613	T	0.01474	4.85	4.09	-7.21	0.01490	Sulfotransferase domain (1);	1.915560	0.03114	N	0.162893	T	0.00784	0.0026	N	0.02225	-0.63	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48864	-0.8997	10	0.20046	T	0.44	.	4.6451	0.12568	0.1061:0.1275:0.1055:0.6609	.	209	O43704	ST1B1_HUMAN	L	209	ENSP00000308770:I209L	ENSP00000308770:I209L	I	-	1	0	SULT1B1	70630961	0.000000	0.05858	0.000000	0.03702	0.512000	0.34134	-2.112000	0.01332	-1.759000	0.01313	0.383000	0.25322	ATT		0.323	SULT1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251563.2	NM_014465		G	70596372	T	G	70596372	3	3	61	1	0	0	0	0	1	0	0	0	15415	1464	51	4	273	4	SULT1B1	4	70596372	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	449752	70596372	120557904	3229	11214										
SULT1E1	6783	broad.mit.edu	37	chr4	70720005	70720005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcttcacaattctaggaGaattcatctcatctaattgt	6	8	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70720005G>T	ENST00000226444.3	-	4	411	c.299C>A	c.(298-300)tCt>tAt	p.S100Y		NM_005420.2	NP_005411.1	P49888	ST1E1_HUMAN	sulfotransferase family 1E, estrogen-preferring, member 1	100					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	estrone sulfotransferase activity (GO:0004304)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid binding (GO:0005496)|steroid sulfotransferase activity (GO:0050294)	p.S100Y(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10					Acetaminophen(DB00316)|Cyclizine(DB01176)	AATTCTAGGAGAATTCATCTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											89	86	87					4																	70720005		2203	4300	6503	70754594	SO:0001583	missense	6783			BC027956	CCDS3531.1	4q13.1	2008-02-05	2004-02-06	2004-02-04	ENSG00000109193	ENSG00000109193	2.8.2.4	"Sulfotransferases, cytosolic"	11377	protein-coding gene	gene with protein product		600043	"sulfotransferase, estrogen-preferring"	STE		7961757	Standard	NM_005420		Approved	EST	uc003heo.3	P49888	OTTHUMG00000129403	ENST00000226444.3:c.299C>A	4.37:g.70720005G>T	ENSP00000226444:p.Ser100Tyr		70754594	Q8N6X5	Missense_Mutation	SNP	ENST00000226444.3	37	CCDS3531.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315147	0.40996	.	.	ENSG00000109193	ENST00000226444	T	0.02421	4.3	4.7	4.7	0.59300	Sulfotransferase domain (1);	0.702056	0.13742	N	0.365881	T	0.27765	0.0683	H	0.97983	4.12	0.51482	D	0.99992	D;D	0.89917	1.0;1.0	D;D	0.69142	0.962;0.962	T	0.39461	-0.9613	10	0.87932	D	0	.	15.5431	0.76070	0.0:0.0:1.0:0.0	.	100;100	Q53X91;P49888	.;ST1E1_HUMAN	Y	100	ENSP00000226444:S100Y	ENSP00000226444:S100Y	S	-	2	0	SULT1E1	70754594	0.997000	0.39634	0.775000	0.31657	0.104000	0.19210	4.160000	0.58164	2.621000	0.88768	0.655000	0.94253	TCT		0.318	SULT1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251559.1	NM_005420		T	70720005	G	T	70720005	3	4	61	1	0	0	0	0	1	0	0	0	15419	942	33	2	605	2	SULT1E1	4	70720005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123633	70720005	120434271	3230	11215										
CSN2	1447	broad.mit.edu	37	chr4	70823339	70823339	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcatcactctgcccttagTgtagacagtgtctttagctt	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:70823339T>C	ENST00000353151.3	-	5	339	c.328A>G	c.(328-330)Act>Gct	p.T110A		NM_001891.2	NP_001882.1	P61201	CSN2_HUMAN	casein beta	0					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.T110A(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|skin(2)	12						CTGCCCTTAGTGTAGACAGTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											130	124	126					4																	70823339		2203	4300	6503	70857928	SO:0001583	missense	1447			X17070	CCDS3532.1	4q21.1	2008-02-05			ENSG00000135222	ENSG00000135222			2447	protein-coding gene	gene with protein product		115460		CASB		1577486	Standard	NM_001891		Approved		uc003hes.4	P05814	OTTHUMG00000129409	ENST00000353151.3:c.328A>G	4.37:g.70823339T>C	ENSP00000341030:p.Thr110Ala		70857928	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	ENST00000353151.3	37	CCDS3532.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.332911	0.24167	.	.	ENSG00000135222	ENST00000353151	.	.	.	4.37	1.68	0.24146	.	0.424608	0.20470	N	0.091716	T	0.27559	0.0677	L	0.36672	1.1	0.09310	N	1	B	0.20671	0.047	B	0.12156	0.007	T	0.22695	-1.0209	9	0.87932	D	0	-23.1439	3.6745	0.08287	0.2065:0.0:0.588:0.2055	.	110	P05814	CASB_HUMAN	A	110	.	ENSP00000341030:T110A	T	-	1	0	CSN2	70857928	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-0.429000	0.06982	0.354000	0.24105	-0.219000	0.12488	ACT		0.458	CSN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251565.1			C	70823339	T	C	70823339	3	2	61	1	0	0	0	0	1	0	0	0	3954	1696	59	4	360	4	CSN2	4	70823339	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	103334	70823339	120330937	3231	11216										
CSN3	1448	broad.mit.edu	37	chr4	71115074	71115074	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccagctcctgccactgaAccaacggtggacagtgtagt	10	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71115074A>G	ENST00000304954.3	+	4	533	c.447A>G	c.(445-447)gaA>gaG	p.E149E		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	0					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.E149E(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						CTGCCACTGAACCAACGGTGG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	4											69	68	69					4																	71115074		2203	4300	6503	71149663	SO:0001819	synonymous_variant	1448			U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"casein, kappa"	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.447A>G	4.37:g.71115074A>G			71149663	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000304954.3	37	CCDS3538.1																																																																																				0.468	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212		G	71115074	A	G	71115074	2	3	61	1	0	0	0	0	0	0	0	1	3955	40	2	4		4	CSN3	4	71115074	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	291735	71115074	120039202	3232	11217										
AMTN	401138	broad.mit.edu	37	chr4	71396769	71396769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccagccacaaatcttcaCgagcctcatcatccattcct	3	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71396769C>T	ENST00000339336.4	+	8	501	c.371C>T	c.(370-372)aCg>aTg	p.T124M	AMTN_ENST00000504451.1_Missense_Mutation_p.T123M	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	124					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)		p.T124M(1)		NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			CAAATCTTCACGAGCCTCATC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4											41	43	42					4																	71396769		2203	4300	6503	71431358	SO:0001583	missense	401138			AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.371C>T	4.37:g.71396769C>T	ENSP00000341013:p.Thr124Met		71431358	Q0P503|Q0P506	Missense_Mutation	SNP	ENST00000339336.4	37	CCDS3542.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.577939	0.45902	.	.	ENSG00000187689	ENST00000339336;ENST00000504451	T;T	0.70045	-0.45;-0.45	5.79	5.79	0.91817	.	0.202573	0.35320	N	0.003282	T	0.72953	0.3525	L	0.29908	0.895	0.33706	D	0.615157	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	T	0.80207	-0.1478	10	0.87932	D	0	-3.7977	15.535	0.75996	0.0:1.0:0.0:0.0	.	123;124	Q6UX39-2;Q6UX39	.;AMTN_HUMAN	M	124;123	ENSP00000341013:T124M;ENSP00000422452:T123M	ENSP00000341013:T124M	T	+	2	0	AMTN	71431358	0.957000	0.32711	0.684000	0.30055	0.173000	0.22820	3.659000	0.54489	2.744000	0.94065	0.650000	0.86243	ACG		0.488	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557		T	71396769	C	T	71396769	3	4	61	1	0	0	0	0	1	0	0	0	590	536	19	1	397	1	AMTN	4	71396769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	281695	71396769	119757507	3233	11218										
ENAM	10117	broad.mit.edu	37	chr4	71509135	71509135	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccaactggagatgaagtCtttcctggacaaaatagatg	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71509135C>A	ENST00000396073.3	+	9	2273	c.1992C>A	c.(1990-1992)gtC>gtA	p.V664V	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	664					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.V664V(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			GAGATGAAGTCTTTCCTGGAC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											97	100	99					4																	71509135		2203	4300	6503	71727999	SO:0001819	synonymous_variant	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1992C>A	4.37:g.71509135C>A			71727999	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																				0.448	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		A	71509135	C	A	71509135	2	1	61	1	0	0	0	0	0	0	0	1	5125	900	32	2		2	ENAM	4	71509135	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	112366	71509135	119645141	3234	11219										
ENAM	10117	broad.mit.edu	37	chr4	71509251	71509251	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggaatatcttccctattCtttagataatccatcaaaac	3	9	3	1	rs375773209		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71509251C>T	ENST00000396073.3	+	9	2389	c.2108C>T	c.(2107-2109)tCt>tTt	p.S703F	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	703					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.S703F(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTTCCCTATTCTTTAGATAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											73	74	74					4																	71509251		2203	4300	6503	71728115	SO:0001583	missense	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.2108C>T	4.37:g.71509251C>T	ENSP00000379383:p.Ser703Phe		71728115	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	C	3.385	-0.125610	0.06795	.	.	ENSG00000132464	ENST00000396073	T	0.37058	1.22	6.01	4.28	0.50868	.	0.343710	0.25607	N	0.029501	T	0.38214	0.1032	M	0.63428	1.95	0.09310	N	1	B	0.27971	0.196	B	0.35813	0.211	T	0.39761	-0.9598	10	0.62326	D	0.03	-0.6969	8.0652	0.30657	0.1565:0.7634:0.0:0.0801	.	703	Q9NRM1	ENAM_HUMAN	F	703	ENSP00000379383:S703F	ENSP00000379383:S703F	S	+	2	0	ENAM	71728115	0.088000	0.21588	0.036000	0.18154	0.099000	0.18886	1.230000	0.32612	0.863000	0.35553	0.655000	0.94253	TCT		0.393	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		T	71509251	C	T	71509251	3	4	61	1	0	0	0	0	1	0	0	0	5125	913	32	3	2138	3	ENAM	4	71509251	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116	71509251	119645025	3235	11220										
IGJ	3512	broad.mit.edu	37	chr4	71527815	71527815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatgccacatacataattCggatgtttctctccacaatg	7	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71527815C>T	ENST00000254801.4	-	2	351	c.182G>A	c.(181-183)cGa>cAa	p.R61Q	ENAM_ENST00000472903.1_Intron|IGJ_ENST00000543780.1_Missense_Mutation_p.R77Q	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	61					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)	p.R61Q(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			ATACATAATTCGGATGTTTCT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	4											146	141	143					4																	71527815		2203	4300	6503	71746679	SO:0001583	missense	3512			M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"Immunoglobulins / IGJ linker"	5713	protein-coding gene	gene with protein product	"immunoglobulin J chain", "IgJ chain"	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.182G>A	4.37:g.71527815C>T	ENSP00000254801:p.Arg61Gln		71746679		Missense_Mutation	SNP	ENST00000254801.4	37	CCDS3545.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500367	0.64298	.	.	ENSG00000132465	ENST00000254801;ENST00000510437;ENST00000543780;ENST00000510614;ENST00000391614;ENST00000470866	.	.	.	5.43	5.43	0.79202	.	0.000000	0.56097	D	0.000039	T	0.67401	0.2889	L	0.36672	1.1	0.37448	D	0.914689	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.68930	-0.5279	9	0.37606	T	0.19	.	16.1719	0.81822	0.0:1.0:0.0:0.0	.	77;61	D6RHJ6;P01591	.;IGJ_HUMAN	Q	61;61;77;70;77;61	.	ENSP00000254801:R61Q	R	-	2	0	IGJ	71746679	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.296000	0.51802	2.554000	0.86153	0.650000	0.86243	CGA		0.398	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646		T	71527815	C	T	71527815	3	4	61	1	0	0	0	0	1	0	0	0	7613	884	31	1	309	1	IGJ	4	71527815	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18564	71527815	119626461	3236	11221										
GRSF1	2926	broad.mit.edu	37	chr4	71693716	71693716	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagaaccgacatgtgttcGaacttcattccttctgcttg	7	10	2	1	rs550281419		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71693716G>A	ENST00000254799.6	-	6	1105	c.988C>T	c.(988-990)Cga>Tga	p.R330*	GRSF1_ENST00000502323.1_Nonsense_Mutation_p.R168*|GRSF1_ENST00000508091.1_Intron|GRSF1_ENST00000439371.1_Nonsense_Mutation_p.R168*|GRSF1_ENST00000545193.1_Nonsense_Mutation_p.R212*	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	330					anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R330*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			ACATGTGTTCGAACTTCATTC	0.353													G|||	1	0.000199681	0	0	5008	,	,		19797	0		0	False		,,,				2504	0.001															1	Substitution - Nonsense(1)	large_intestine(1)	4											146	134	138					4																	71693716		1841	4088	5929	71912580	SO:0001587	stop_gained	2926			BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.988C>T	4.37:g.71693716G>A	ENSP00000254799:p.Arg330*		71912580	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Nonsense_Mutation	SNP	ENST00000254799.6	37	CCDS47069.1	.	.	.	.	.	.	.	.	.	.	G	41	8.840857	0.98974	.	.	ENSG00000132463	ENST00000254799;ENST00000439371;ENST00000540657;ENST00000499044;ENST00000502323;ENST00000545193	.	.	.	6.07	6.07	0.98685	.	0.268407	0.37857	N	0.001914	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.9839	19.424	0.94734	0.0:0.0:1.0:0.0	.	.	.	.	X	330;168;262;303;168;212	.	ENSP00000254799:R330X	R	-	1	2	GRSF1	71912580	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.415000	0.73328	2.890000	0.99128	0.585000	0.79938	CGA		0.353	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		A	71693716	G	A	71693716	4	1	61	1	0	0	0	0	0	1	0	0	6830	1066	37	1	470	1	GRSF1	4	71693716	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165901	71693716	119460560	3237	11222										
DCK	1633	broad.mit.edu	37	chr4	71895075	71895075	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctttcctcaggtcaaaGagtttttgagtactttgtga	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:71895075G>T	ENST00000286648.5	+	7	1160	c.763G>T	c.(763-765)Gag>Tag	p.E255*	DCK_ENST00000504952.1_Missense_Mutation_p.R287I|DCK_ENST00000504730.1_3'UTR	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	255					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)	p.E255*(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	TCAGGTCAAAGAGTTTTTGAG	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											76	75	75					4																	71895075		2203	4300	6503	72113939	SO:0001587	stop_gained	1633			M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.763G>T	4.37:g.71895075G>T	ENSP00000286648:p.Glu255*		72113939	B2R8V6|Q5TZY7|Q6FI11	Nonsense_Mutation	SNP	ENST00000286648.5	37	CCDS3548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.753236|7.753236	0.98471|0.98471	.|.	.|.	ENSG00000156136|ENSG00000156136	ENST00000286648|ENST00000504952	.|D	.|0.98822	.|-5.16	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.401672|.	0.29073|.	N|.	0.013222|.	.|D	.|0.99017	.|0.9664	.|.	.|.	.|.	0.50039|0.50039	D|D	0.999848|0.999848	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.99806	.|1.1038	.|6	0.16896|0.87932	T|D	0.51|0	.|.	18.1914|18.1914	0.89808|0.89808	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	255|287	.|ENSP00000421508:R287I	ENSP00000286648:E255X|ENSP00000421508:R287I	E|R	+|+	1|2	0|0	DCK|DCK	72113939|72113939	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	5.905000|5.905000	0.69893|0.69893	2.738000|2.738000	0.93877|0.93877	0.591000|0.591000	0.81541|0.81541	GAG|AGA		0.313	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2			T	71895075	G	T	71895075	4	4	61	1	0	0	0	0	0	1	0	0	4296	943	33	2	789	2	DCK	4	71895075	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	201359	71895075	119259201	3238	11223										
SLC4A4	8671	broad.mit.edu	37	chr4	72205111	72205111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgctgcagaacgcatccGattcatcttgggagaggagg	13	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:72205111G>A	ENST00000264485.5	+	4	395	c.278G>A	c.(277-279)cGa>cAa	p.R93Q	SLC4A4_ENST00000351898.6_Missense_Mutation_p.R93Q|SLC4A4_ENST00000512686.1_Missense_Mutation_p.R49Q|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.R93Q|SLC4A4_ENST00000340595.3_Missense_Mutation_p.R49Q	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	93					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.R49Q(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GAACGCATCCGATTCATCTTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	4											163	169	167					4																	72205111		2203	4300	6503	72423975	SO:0001583	missense	8671			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.278G>A	4.37:g.72205111G>A	ENSP00000264485:p.Arg93Gln		72423975	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959732	0.34565	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.76186	-0.97;-0.98;-0.6;0.18;-1.0	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.76730	0.4028	L	0.27053	0.805	0.80722	D	1	P;P;D;D;P	0.89917	0.887;0.595;0.964;1.0;0.852	B;B;P;D;B	0.87578	0.148;0.163;0.53;0.998;0.148	T	0.68573	-0.5373	10	0.02654	T	1	.	19.3765	0.94512	0.0:0.0:1.0:0.0	.	93;93;49;49;93	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R1	.;.;.;.;S4A4_HUMAN	Q	93;93;93;49;49	ENSP00000264485:R93Q;ENSP00000393557:R93Q;ENSP00000307349:R93Q;ENSP00000422400:R49Q;ENSP00000344272:R49Q	ENSP00000264485:R93Q	R	+	2	0	SLC4A4	72423975	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.566000	0.86566	0.591000	0.81541	CGA		0.557	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72205111	G	A	72205111	3	1	61	1	0	0	0	0	1	0	0	0	14693	1058	37	1	409	1	SLC4A4	4	72205111	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	310036	72205111	118949165	3239	11224										
SLC4A4	8671	broad.mit.edu	37	chr4	72316936	72316936	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaggtggagagaatgttCagatgaatggggatacgccc	14	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:72316936C>A	ENST00000264485.5	+	11	1357	c.1240C>A	c.(1240-1242)Cag>Aag	p.Q414K	SLC4A4_ENST00000351898.6_Missense_Mutation_p.Q414K|SLC4A4_ENST00000512686.1_Missense_Mutation_p.Q370K|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.Q414K|SLC4A4_ENST00000340595.3_Missense_Mutation_p.Q370K	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	414					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.Q370K(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	AGAGAATGTTCAGATGAATGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											180	154	163					4																	72316936		2203	4300	6503	72535800	SO:0001583	missense	8671			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.1240C>A	4.37:g.72316936C>A	ENSP00000264485:p.Gln414Lys		72535800	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.468431	0.43839	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.77358	-1.09;-1.09;-0.71;0.11;-1.08	6.08	6.08	0.98989	.	2.041620	0.01435	N	0.014897	D	0.87545	0.6204	M	0.70595	2.14	0.80722	D	1	B;D;B;B;B;B	0.58970	0.01;0.984;0.002;0.005;0.021;0.006	B;P;B;B;B;B	0.58454	0.013;0.839;0.012;0.009;0.022;0.009	T	0.75379	-0.3338	10	0.05833	T	0.94	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	414;414;370;370;394;414	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	K	414;414;414;370;370	ENSP00000264485:Q414K;ENSP00000393557:Q414K;ENSP00000307349:Q414K;ENSP00000422400:Q370K;ENSP00000344272:Q370K	ENSP00000264485:Q414K	Q	+	1	0	SLC4A4	72535800	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.463000	0.80869	2.894000	0.99253	0.655000	0.94253	CAG		0.438	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72316936	C	A	72316936	3	1	61	1	0	0	0	0	1	0	0	0	14693	827	29	2	1399	2	SLC4A4	4	72316936	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111825	72316936	118837340	3240	11225										
SLC4A4	8671	broad.mit.edu	37	chr4	72412159	72412159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtggtatgtagctgctacGgtcatctccattgctcacat	9	12	3	0	rs199806973		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:72412159G>A	ENST00000264485.5	+	19	2652	c.2535G>A	c.(2533-2535)acG>acA	p.T845T	SLC4A4_ENST00000351898.6_Intron|SLC4A4_ENST00000425175.1_Silent_p.T845T|SLC4A4_ENST00000340595.3_Silent_p.T801T	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	845					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.T801T(1)|p.T845T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TAGCTGCTACGGTCATCTCCA	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	4						G	,,	0,4406		0,0,2203	218	167	184		2535,2535,2403	-6.1	0.8	4		184	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,	845/1080,845/1095,801/1036	72412159	1,13003	2203	4299	6502	72631023	SO:0001819	synonymous_variant	8671			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2535G>A	4.37:g.72412159G>A			72631023	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	37	CCDS43236.1																																																																																				0.478	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72412159	G	A	72412159	2	1	61	1	0	0	0	0	0	0	0	1	14693	1103	39	1		1	SLC4A4	4	72412159	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95223	72412159	118742117	3241	11226										
GC	2638	broad.mit.edu	37	chr4	72631190	72631190	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcctgaacgcctcacaGatttcatcatttgtgggttc	7	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:72631190G>T	ENST00000273951.8	-	4	775	c.432C>A	c.(430-432)atC>atA	p.I144I	GC_ENST00000513476.1_Silent_p.I144I|GC_ENST00000504199.1_Silent_p.I163I|GC_ENST00000503472.1_5'UTR	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	144	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)	p.I144I(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	ACGCCTCACAGATTTCATCAT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											183	176	178					4																	72631190		2203	4300	6503	72850054	SO:0001819	synonymous_variant	2638			L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.432C>A	4.37:g.72631190G>T			72850054	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	37	CCDS3550.1																																																																																				0.448	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			T	72631190	G	T	72631190	2	4	61	1	0	0	0	0	0	0	0	1	6302	932	33	2		2	GC	4	72631190	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219031	72631190	118523086	3242	11227										
NPFFR2	10886	broad.mit.edu	37	chr4	72897794	72897794	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtccgcgggggacagacGtcggctgggattgagccggc	19	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:72897794G>A	ENST00000308744.6	+	1	274	c.176G>A	c.(175-177)cGt>cAt	p.R59H	NPFFR2_ENST00000344413.5_Missense_Mutation_p.R59H	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	59					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.R59H(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			GGGGACAGACGTCGGCTGGGA	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	4											32	36	35					4																	72897794		2203	4300	6503	73116658	SO:0001583	missense	10886			AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.176G>A	4.37:g.72897794G>A	ENSP00000307822:p.Arg59His		73116658	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.622314	0.28889	.	.	ENSG00000056291	ENST00000308744;ENST00000344413	T	0.76060	-0.99	2.8	1.03	0.20045	.	.	.	.	.	T	0.42245	0.1194	N	0.08118	0	0.09310	N	1	D	0.54772	0.968	B	0.29663	0.105	T	0.37454	-0.9705	9	0.44086	T	0.13	.	5.1384	0.14947	0.0:0.2333:0.5267:0.24	.	59	Q9Y5X5	NPFF2_HUMAN	H	59	ENSP00000307822:R59H	ENSP00000307822:R59H	R	+	2	0	NPFFR2	73116658	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.108000	0.15396	0.247000	0.21414	0.491000	0.48974	CGT		0.677	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		A	72897794	G	A	72897794	3	1	61	1	0	0	0	0	1	0	0	0	10609	1145	40	1	178	1	NPFFR2	4	72897794	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	266604	72897794	118256482	3243	11228										
ADAMTS3	9508	broad.mit.edu	37	chr4	73161478	73161478	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattatcacttttcctacgGcatccatatttagtgtactg	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73161478G>T	ENST00000286657.4	-	19	2652	c.2616C>A	c.(2614-2616)tgC>tgA	p.C872*		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	872	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.C872*(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTTCCTACGGCATCCATATT	0.368																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Nonsense(1)	large_intestine(1)	4											133	119	124					4																	73161478		2203	4300	6503	73380342	SO:0001587	stop_gained	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2616C>A	4.37:g.73161478G>T	ENSP00000286657:p.Cys872*		73380342	A1L3U9|Q9BXZ8	Nonsense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	G	39	7.462029	0.98299	.	.	ENSG00000156140	ENST00000286657	.	.	.	5.14	3.4	0.38934	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8367	0.46692	0.1524:0.0:0.8476:0.0	.	.	.	.	X	872	.	ENSP00000286657:C872X	C	-	3	2	ADAMTS3	73380342	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.341000	0.43983	1.159000	0.42565	-0.142000	0.14014	TGC		0.368	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73161478	G	T	73161478	4	4	61	1	0	0	0	0	0	1	0	0	267	1195	42	2	1017	2	ADAMTS3	4	73161478	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	263684	73161478	117992798	3244	11229										
ADAMTS3	9508	broad.mit.edu	37	chr4	73164028	73164028	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaacactgagaccagctCttcaaagcccactcaaaagt	7	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73164028C>A	ENST00000286657.4	-	18	2592	c.2556G>T	c.(2554-2556)aaG>aaT	p.K852N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	852	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K852N(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAGACCAGCTCTTCAAAGCCC	0.378																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Missense(1)	large_intestine(1)	4											142	129	134					4																	73164028		2203	4300	6503	73382892	SO:0001583	missense	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2556G>T	4.37:g.73164028C>A	ENSP00000286657:p.Lys852Asn		73382892	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116883	0.77323	.	.	ENSG00000156140	ENST00000286657	T	0.60424	0.19	5.73	3.98	0.46160	.	0.000000	0.85682	D	0.000000	T	0.71634	0.3363	M	0.76170	2.325	0.51767	D	0.999932	D	0.89917	1.0	D	0.97110	1.0	T	0.69468	-0.5137	10	0.21014	T	0.42	.	11.8311	0.52297	0.0:0.8037:0.0:0.1963	.	852	O15072	ATS3_HUMAN	N	852	ENSP00000286657:K852N	ENSP00000286657:K852N	K	-	3	2	ADAMTS3	73382892	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.603000	0.61105	1.412000	0.46977	0.650000	0.86243	AAG		0.378	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73164028	C	A	73164028	3	1	61	1	0	0	0	0	1	0	0	0	267	912	32	2	1081	2	ADAMTS3	4	73164028	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2550	73164028	117990248	3245	11230										
ADAMTS3	9508	broad.mit.edu	37	chr4	73171775	73171775	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggggtatatcaaacatcTtaaggtaccctttgcatgtg	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73171775T>G	ENST00000286657.4	-	16	2225	c.2189A>C	c.(2188-2190)aAg>aCg	p.K730T		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	730	Spacer.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K730T(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATCAAACATCTTAAGGTACCC	0.408																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Missense(1)	large_intestine(1)	4											106	108	107					4																	73171775		2203	4300	6503	73390639	SO:0001583	missense	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2189A>C	4.37:g.73171775T>G	ENSP00000286657:p.Lys730Thr		73390639	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.479220	0.84747	.	.	ENSG00000156140	ENST00000286657	T	0.52754	0.65	5.35	5.35	0.76521	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.65037	0.2653	M	0.68317	2.08	0.50813	D	0.999897	D	0.69078	0.997	D	0.72338	0.977	T	0.61816	-0.6985	10	0.24483	T	0.36	.	15.6325	0.76923	0.0:0.0:0.0:1.0	.	730	O15072	ATS3_HUMAN	T	730	ENSP00000286657:K730T	ENSP00000286657:K730T	K	-	2	0	ADAMTS3	73390639	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.608000	0.82898	2.150000	0.67090	0.528000	0.53228	AAG		0.408	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			G	73171775	T	G	73171775	3	3	61	1	0	0	0	0	1	0	0	0	267	1609	56	4	1456	4	ADAMTS3	4	73171775	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7747	73171775	117982501	3246	11231										
ADAMTS3	9508	broad.mit.edu	37	chr4	73176800	73176800	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacatatgctatatggatCtttgtaagaacagtgcgttc	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73176800C>A	ENST00000286657.4	-	14	2056	c.2020G>T	c.(2020-2022)Gat>Tat	p.D674Y		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	674	Cys-rich.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D674Y(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTATATGGATCTTTGTAAGAA	0.433																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Missense(1)	large_intestine(1)	4											226	177	194					4																	73176800		2203	4300	6503	73395664	SO:0001583	missense	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2020G>T	4.37:g.73176800C>A	ENSP00000286657:p.Asp674Tyr		73395664	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584824	0.86748	.	.	ENSG00000156140	ENST00000286657	T	0.69561	-0.41	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.82990	0.5157	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.83979	0.0331	10	0.66056	D	0.02	.	19.4627	0.94924	0.0:1.0:0.0:0.0	.	674	O15072	ATS3_HUMAN	Y	674	ENSP00000286657:D674Y	ENSP00000286657:D674Y	D	-	1	0	ADAMTS3	73395664	1.000000	0.71417	0.985000	0.45067	0.658000	0.38924	7.461000	0.80834	2.709000	0.92574	0.655000	0.94253	GAT		0.433	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73176800	C	A	73176800	3	1	61	1	0	0	0	0	1	0	0	0	267	913	32	2	1633	2	ADAMTS3	4	73176800	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5025	73176800	117977476	3247	11232										
ADAMTS3	9508	broad.mit.edu	37	chr4	73185068	73185068	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggatatatcttttcagttCttgaccactgcatcgggacc	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73185068C>A	ENST00000286657.4	-	9	1369	c.1333G>T	c.(1333-1335)Gaa>Taa	p.E445*		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	445	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E445*(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTTTTCAGTTCTTGACCACTG	0.448																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - Nonsense(1)	large_intestine(1)	4											142	118	126					4																	73185068		2203	4300	6503	73403932	SO:0001587	stop_gained	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1333G>T	4.37:g.73185068C>A	ENSP00000286657:p.Glu445*		73403932	A1L3U9|Q9BXZ8	Nonsense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	37	6.625934	0.97714	.	.	ENSG00000156140	ENST00000286657	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	20.0016	0.97412	0.0:1.0:0.0:0.0	.	.	.	.	X	445	.	ENSP00000286657:E445X	E	-	1	0	ADAMTS3	73403932	1.000000	0.71417	0.944000	0.38274	0.795000	0.44927	7.743000	0.85020	2.802000	0.96397	0.655000	0.94253	GAA		0.448	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73185068	C	A	73185068	4	1	61	1	0	0	0	0	0	1	0	0	267	922	32	2	2340	2	ADAMTS3	4	73185068	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8268	73185068	117969208	3248	11233										
COX18	285521	broad.mit.edu	37	chr4	73923972	73923972	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattctgtgaaaggcccacGaagctggagcataaccagta	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73923972G>A	ENST00000295890.4	-	6	952	c.861C>T	c.(859-861)ttC>ttT	p.F287F	COX18_ENST00000507544.2_Silent_p.F288F	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	287					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)	p.F287F(1)		large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAAGGCCCACGAAGCTGGAGC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	4											95	94	94					4																	73923972		2203	4300	6503	74142836	SO:0001819	synonymous_variant	285521			AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"Mitochondrial respiratory chain complex assembly factors"	26801	protein-coding gene	gene with protein product		610428	"COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)", "cytochrome c oxidase assembly homolog 18 (yeast)"			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.861C>T	4.37:g.73923972G>A			74142836	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Silent	SNP	ENST00000295890.4	37	CCDS3554.1																																																																																				0.408	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827		A	73923972	G	A	73923972	2	1	61	1	0	0	0	0	0	0	0	1	3773	1049	37	1		1	COX18	4	73923972	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	738904	73923972	117230304	3249	11234										
COX18	285521	broad.mit.edu	37	chr4	73931115	73931115	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattagcctcctcatattCtttagataagtgagcctaga	7	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73931115C>A	ENST00000295890.4	-	3	541	c.450G>T	c.(448-450)aaG>aaT	p.K150N	COX18_ENST00000507544.2_Missense_Mutation_p.K150N	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	150					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)	p.K150N(1)		large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCTCATATTCTTTAGATAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											87	86	87					4																	73931115		2203	4300	6503	74149979	SO:0001583	missense	285521			AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"Mitochondrial respiratory chain complex assembly factors"	26801	protein-coding gene	gene with protein product		610428	"COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)", "cytochrome c oxidase assembly homolog 18 (yeast)"			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.450G>T	4.37:g.73931115C>A	ENSP00000295890:p.Lys150Asn		74149979	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Missense_Mutation	SNP	ENST00000295890.4	37	CCDS3554.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043912	0.75732	.	.	ENSG00000163626	ENST00000295890;ENST00000507544	.	.	.	5.38	4.48	0.54585	.	0.231844	0.50627	D	0.000109	T	0.56426	0.1984	L	0.38175	1.15	0.48135	D	0.999593	B;B	0.18741	0.03;0.027	B;B	0.31337	0.128;0.128	T	0.52185	-0.8609	9	0.31617	T	0.26	-6.5363	16.4567	0.84019	0.0:0.8246:0.1754:0.0	.	150;150	B7ZL88;Q8N8Q8	.;COX18_HUMAN	N	150	.	ENSP00000295890:K150N	K	-	3	2	COX18	74149979	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	1.210000	0.32370	2.675000	0.91044	0.655000	0.94253	AAG		0.413	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827		A	73931115	C	A	73931115	3	1	61	1	0	0	0	0	1	0	0	0	3773	912	32	2	567	2	COX18	4	73931115	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7143	73931115	117223161	3250	11235										
ANKRD17	26057	broad.mit.edu	37	chr4	73984409	73984409	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaaagacttatacctttCtaaatgctgccataagagga	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:73984409C>A	ENST00000358602.4	-	22	4300	c.4184G>T	c.(4183-4185)aGa>aTa	p.R1395I	ANKRD17_ENST00000330838.6_Missense_Mutation_p.R1144I|ANKRD17_ENST00000509867.2_Missense_Mutation_p.R1282I|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1395					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1395I(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTATACCTTTCTAAATGCTGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											163	148	153					4																	73984409		2203	4300	6503	74203273	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.4184G>T	4.37:g.73984409C>A	ENSP00000351416:p.Arg1395Ile		74203273	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	32	5.133127	0.94517	.	.	ENSG00000132466	ENST00000358602;ENST00000330838;ENST00000509867	T;T;T	0.66099	-0.19;-0.19;-0.19	5.56	5.56	0.83823	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000020	T	0.71082	0.3298	N	0.25789	0.76	0.80722	D	1	D;D;D;D;P	0.76494	0.999;0.997;0.997;0.997;0.954	D;D;D;D;P	0.83275	0.991;0.994;0.994;0.996;0.691	T	0.73448	-0.3979	10	0.59425	D	0.04	.	19.535	0.95247	0.0:1.0:0.0:0.0	.	916;1394;1144;1395;1282	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	I	1395;1144;1282	ENSP00000351416:R1395I;ENSP00000332265:R1144I;ENSP00000427151:R1282I	ENSP00000332265:R1144I	R	-	2	0	ANKRD17	74203273	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.818000	0.86416	2.611000	0.88343	0.655000	0.94253	AGA		0.413	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	73984409	C	A	73984409	3	1	61	1	0	0	0	0	1	0	0	0	646	913	32	2	3679	2	ANKRD17	4	73984409	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53294	73984409	117169867	3251	11236										
ANKRD17	26057	broad.mit.edu	37	chr4	74005398	74005398	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactatcactccttgcagttCtgtaagatttgcgatggacc	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74005398C>A	ENST00000358602.4	-	15	3051	c.2935G>T	c.(2935-2937)Gaa>Taa	p.E979*	ANKRD17_ENST00000330838.6_Intron|ANKRD17_ENST00000509867.2_Nonsense_Mutation_p.E866*|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	979	Gln-rich.				blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E979*(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCTTGCAGTTCTGTAAGATTT	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											71	64	66					4																	74005398		2203	4300	6503	74224262	SO:0001587	stop_gained	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2935G>T	4.37:g.74005398C>A	ENSP00000351416:p.Glu979*		74224262	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Nonsense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	37	6.010228	0.97200	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000509867;ENST00000411811	.	.	.	5.87	5.87	0.94306	.	0.078469	0.53938	D	0.000060	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	979;979;866;979	.	ENSP00000351416:E979X	E	-	1	0	ANKRD17	74224262	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.265000	0.78442	2.941000	0.99782	0.655000	0.94253	GAA		0.547	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	74005398	C	A	74005398	4	1	61	1	0	0	0	0	0	1	0	0	646	922	32	2	4956	2	ANKRD17	4	74005398	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20989	74005398	117148878	3252	11237										
ANKRD17	26057	broad.mit.edu	37	chr4	74013036	74013036	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggtagaacaccctagttCtatatcggctcctgccttaa	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74013036C>T	ENST00000358602.4	-	9	1797	c.1681G>A	c.(1681-1683)Gaa>Aaa	p.E561K	ANKRD17_ENST00000330838.6_Missense_Mutation_p.E561K|ANKRD17_ENST00000509867.2_Missense_Mutation_p.E448K|ANKRD17_ENST00000514252.1_Intron	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	561					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E561K(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CACCCTAGTTCTATATCGGCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	85	84					4																	74013036		2202	4300	6502	74231900	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.1681G>A	4.37:g.74013036C>T	ENSP00000351416:p.Glu561Lys		74231900	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	36	5.637813	0.96693	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.15834	2.39;2.39;2.39	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000002	T	0.37732	0.1014	L	0.43598	1.365	0.48762	D	0.9997	D;D;D;D	0.76494	0.998;0.999;0.999;0.998	D;D;D;D	0.83275	0.995;0.996;0.994;0.987	T	0.04255	-1.0965	10	0.72032	D	0.01	.	19.7866	0.96442	0.0:1.0:0.0:0.0	.	561;561;561;448	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	K	561;561;561;448;561	ENSP00000351416:E561K;ENSP00000332265:E561K;ENSP00000427151:E448K	ENSP00000332265:E561K	E	-	1	0	ANKRD17	74231900	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.629000	0.83207	2.756000	0.94617	0.655000	0.94253	GAA		0.443	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		T	74013036	C	T	74013036	3	4	61	1	0	0	0	0	1	0	0	0	646	922	32	3	6234	3	ANKRD17	4	74013036	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7638	74013036	117141240	3253	11238										
ALB	213	broad.mit.edu	37	chr4	74275168	74275168	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcttttacagaatgttgCcaagctgctgataaagctgc	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74275168C>T	ENST00000503124.1	+	3	336	c.129C>T	c.(127-129)tgC>tgT	p.C43C	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Silent_p.C193C|ALB_ENST00000401494.3_Silent_p.C78C|ALB_ENST00000415165.2_Intron|ALB_ENST00000295897.4_Silent_p.C193C			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.C193C(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGAATGTTGCCAAGCTGCTG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	4											75	78	77					4																	74275168		2203	4299	6502	74494032	SO:0001819	synonymous_variant	213			V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.129C>T	4.37:g.74275168C>T			74494032	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	C	13.23	2.173902	0.38413	.	.	ENSG00000163631	ENST00000511370	.	.	.	5.55	-0.26	0.12967	.	.	.	.	.	T	0.59404	0.2191	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54702	-0.8254	4	.	.	.	-16.0207	12.3091	0.54918	0.0:0.5531:0.0:0.4469	.	.	.	.	S	38	.	.	P	+	1	0	ALB	74494032	0.020000	0.18652	0.020000	0.16555	0.062000	0.15995	0.033000	0.13754	-0.245000	0.09625	-1.094000	0.02160	CCA		0.373	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74275168	C	T	74275168	2	4	61	1	0	0	0	0	0	0	0	1	486	747	26	3		3	ALB	4	74275168	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	262132	74275168	116879108	3254	11239										
AFM	173	broad.mit.edu	37	chr4	74349679	74349679	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacttcaatagtactcaaaAatttatagaagataatattg	5	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74349679A>C	ENST00000226355.3	+	2	203	c.110A>C	c.(109-111)aAa>aCa	p.K37T		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	37	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)	p.K37T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTACTCAAAAATTTATAGAA	0.239																																																1	Substitution - Missense(1)	large_intestine(1)	4											23	27	26					4																	74349679		2101	4212	6313	74568543	SO:0001583	missense	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.110A>C	4.37:g.74349679A>C	ENSP00000226355:p.Lys37Thr		74568543	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	A	9.664	1.144812	0.21288	.	.	ENSG00000079557	ENST00000226355	T	0.73789	-0.78	4.8	2.25	0.28309	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.768392	0.12309	N	0.480386	T	0.67534	0.2903	L	0.60455	1.87	0.24564	N	0.993958	B	0.23937	0.094	B	0.29942	0.109	T	0.56183	-0.8021	10	0.32370	T	0.25	.	4.8902	0.13722	0.7128:0.1879:0.0994:0.0	.	37	P43652	AFAM_HUMAN	T	37	ENSP00000226355:K37T	ENSP00000226355:K37T	K	+	2	0	AFM	74568543	1.000000	0.71417	0.994000	0.49952	0.028000	0.11728	3.412000	0.52679	0.268000	0.21939	0.533000	0.62120	AAA		0.239	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			C	74349679	A	C	74349679	3	2	61	1	0	0	0	0	1	0	0	0	361	14	1	4	116	4	AFM	4	74349679	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	74511	74349679	116804597	3255	11240										
AFM	173	broad.mit.edu	37	chr4	74351683	74351683	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaaagaagactctgtttCttctataacaagaaatctga	6	8	5	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74351683C>A	ENST00000226355.3	+	4	468	c.375C>A	c.(373-375)ttC>ttA	p.F125L		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	125	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)	p.F125L(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GACTCTGTTTCTTCTATAACA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											103	104	104					4																	74351683		2203	4300	6503	74570547	SO:0001583	missense	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.375C>A	4.37:g.74351683C>A	ENSP00000226355:p.Phe125Leu		74570547	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049531	0.55218	.	.	ENSG00000079557	ENST00000226355	T	0.72615	-0.67	4.86	4.86	0.63082	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.060315	0.64402	D	0.000002	T	0.79064	0.4383	L	0.53249	1.67	0.46654	D	0.999143	D	0.89917	1.0	D	0.87578	0.998	T	0.75093	-0.3439	10	0.23891	T	0.37	.	13.8506	0.63494	0.0:1.0:0.0:0.0	.	125	P43652	AFAM_HUMAN	L	125	ENSP00000226355:F125L	ENSP00000226355:F125L	F	+	3	2	AFM	74570547	0.376000	0.25098	0.985000	0.45067	0.779000	0.44077	0.172000	0.16704	2.411000	0.81874	0.591000	0.81541	TTC		0.418	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			A	74351683	C	A	74351683	3	1	61	1	0	0	0	0	1	0	0	0	361	912	32	2	389	2	AFM	4	74351683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2004	74351683	116802593	3256	11241										
AFM	173	broad.mit.edu	37	chr4	74354425	74354425	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtagaagatgtttcttcCaactatgatggatgctgtga	10	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74354425C>A	ENST00000226355.3	+	7	885	c.792C>A	c.(790-792)tcC>tcA	p.S264S		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	264	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)	p.S264S(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATGTTTCTTCCAACTATGATG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	4											140	140	140					4																	74354425		2203	4300	6503	74573289	SO:0001819	synonymous_variant	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.792C>A	4.37:g.74354425C>A			74573289	A8K3E1|Q32MR3|Q4W5C5	Silent	SNP	ENST00000226355.3	37	CCDS3557.1																																																																																				0.363	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			A	74354425	C	A	74354425	2	1	61	1	0	0	0	0	0	0	0	1	361	581	21	2		2	AFM	4	74354425	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2742	74354425	116799851	3257	11242										
AFM	173	broad.mit.edu	37	chr4	74364929	74364929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttcactacttgctgtaCgctaagtgaagagtttgcct	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74364929C>T	ENST00000226355.3	+	11	1481	c.1388C>T	c.(1387-1389)aCg>aTg	p.T463M		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	463	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)	p.T463M(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACTTGCTGTACGCTAAGTGAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											159	139	146					4																	74364929		2203	4300	6503	74583793	SO:0001583	missense	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.1388C>T	4.37:g.74364929C>T	ENSP00000226355:p.Thr463Met		74583793	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	C	9.800	1.180275	0.21787	.	.	ENSG00000079557	ENST00000226355	T	0.73258	-0.73	5.55	3.8	0.43715	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.576081	0.17417	N	0.174987	T	0.67183	0.2866	L	0.55103	1.725	0.09310	N	1	D	0.54047	0.964	P	0.47786	0.557	T	0.59637	-0.7417	10	0.48119	T	0.1	.	6.3034	0.21125	0.1841:0.725:0.0:0.0909	.	463	P43652	AFAM_HUMAN	M	463	ENSP00000226355:T463M	ENSP00000226355:T463M	T	+	2	0	AFM	74583793	0.000000	0.05858	0.273000	0.24645	0.014000	0.08584	-0.369000	0.07533	1.329000	0.45376	0.655000	0.94253	ACG		0.413	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			T	74364929	C	T	74364929	3	4	61	1	0	0	0	0	1	0	0	0	361	536	19	1	1430	1	AFM	4	74364929	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10504	74364929	116789347	3258	11243										
IL8	3576	broad.mit.edu	37	chr4	74608172	74608172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taattttattttagggctgaGaattcataaaaaaattcatt	5	3	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74608172G>T	ENST00000307407.3	+	4	444	c.291G>T	c.(289-291)gaG>gaT	p.E97D		NM_000584.3	NP_000575.1	P10145	IL8_HUMAN		97					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|embryonic digestive tract development (GO:0048566)|endoplasmic reticulum unfolded protein response (GO:0030968)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of neutrophil chemotaxis (GO:0090023)|receptor internalization (GO:0031623)|regulation of cell adhesion (GO:0030155)|regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045091)|response to endoplasmic reticulum stress (GO:0034976)|response to molecule of bacterial origin (GO:0002237)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|interleukin-8 receptor binding (GO:0005153)	p.E97D(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(2)|urinary_tract(1)	6	Breast(15;0.00102)		all cancers(17;0.00169)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)	LUSC - Lung squamous cell carcinoma(721;0.008)		ttaGGGCTGAGAATTCATAAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											22	23	23					4																	74608172		2195	4293	6488	74827036	SO:0001583	missense	3576																														ENST00000307407.3:c.291G>T	4.37:g.74608172G>T	ENSP00000306512:p.Glu97Asp		74827036	B2R4L8|Q6FGF6|Q6LAE6|Q96RG6|Q9C077|Q9UCE1|Q9UCR8|Q9UCR9|Q9UCS0	Missense_Mutation	SNP	ENST00000307407.3	37	CCDS34005.1	.	.	.	.	.	.	.	.	.	.	G	9.499	1.102751	0.20632	.	.	ENSG00000169429	ENST00000307407	T	0.04083	3.71	4.29	1.55	0.23275	.	0.604084	0.18345	N	0.144041	T	0.03739	0.0106	.	.	.	0.47778	D	0.999518	B	0.17667	0.023	B	0.17098	0.017	T	0.43972	-0.9358	9	0.41790	T	0.15	-7.9781	4.3261	0.11041	0.2109:0.1892:0.5999:0.0	.	97	P10145	IL8_HUMAN	D	97	ENSP00000306512:E97D	ENSP00000306512:E97D	E	+	3	2	IL8	74827036	0.817000	0.29147	0.310000	0.25168	0.012000	0.07955	0.783000	0.26802	0.176000	0.19873	-0.965000	0.02619	GAG		0.318	IL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322211.1			T	74608172	G	T	74608172	3	4	61	1	0	0	0	0	1	0	0	0	7727	933	33	2	305	2	IL8	4	74608172	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	243243	74608172	116546104	3259	11244										
CXCL5	6374	broad.mit.edu	37	chr4	74864006	74864006	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgaactccttgcgtggtCtgtaaacaaacgcaacgcag	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:74864006C>A	ENST00000296027.4	-	2	356	c.159G>T	c.(157-159)caG>caT	p.Q53H		NM_002994.3	NP_002985.1	P42830	CXCL5_HUMAN	chemokine (C-X-C motif) ligand 5	53					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)	p.Q53H(1)		endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			CTTGCGTGGTCTGTAAACAAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	4											88	86	87					4																	74864006		2203	4300	6503	75082870	SO:0001583	missense	6374			X78686	CCDS34006.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163735		"Endogenous ligands"	10642	protein-coding gene	gene with protein product		600324	"small inducible cytokine subfamily B (Cys-X-Cys), member 5 (epithelial-derived neutrophil-activating peptide 78)"	SCYB5		7929219	Standard	NM_002994		Approved	ENA-78	uc003hhk.4	P42830		ENST00000296027.4:c.159G>T	4.37:g.74864006C>A	ENSP00000296027:p.Gln53His		75082870	Q96QE1	Missense_Mutation	SNP	ENST00000296027.4	37	CCDS34006.1	.	.	.	.	.	.	.	.	.	.	C	6.034	0.374577	0.11409	.	.	ENSG00000163735	ENST00000296027	T	0.05025	3.51	3.78	0.81	0.18732	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	1.733170	0.02825	N	0.125983	T	0.05135	0.0137	N	0.17594	0.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35500	-0.9786	10	0.37606	T	0.19	.	6.4159	0.21715	0.0:0.39:0.4191:0.1909	.	53	P42830	CXCL5_HUMAN	H	53	ENSP00000296027:Q53H	ENSP00000296027:Q53H	Q	-	3	2	CXCL5	75082870	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.186000	0.09670	0.800000	0.34041	-0.840000	0.03056	CAG		0.522	CXCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362749.1	NM_002994		A	74864006	C	A	74864006	3	1	61	1	0	0	0	0	1	0	0	0	4093	912	32	2	197	2	CXCL5	4	74864006	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	255834	74864006	116290270	3260	11245										
G3BP2	9908	broad.mit.edu	37	chr4	76570618	76570618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccaacagtggagcttcagCgacgctgtcctgtgaagcgg	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76570618C>T	ENST00000359707.4	-	12	2230	c.1445G>A	c.(1444-1446)cGc>cAc	p.R482H	G3BP2_ENST00000357854.3_Missense_Mutation_p.R449H|G3BP2_ENST00000395719.3_Missense_Mutation_p.R482H	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	482					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)	p.R482H(1)		breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GGAGCTTCAGCGACGCTGTCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	65	68					4																	76570618		2203	4300	6503	76789642	SO:0001583	missense	9908			AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.1445G>A	4.37:g.76570618C>T	ENSP00000352738:p.Arg482His		76789642	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	37	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516982	0.64634	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.79033	-1.2;-1.2;-1.23	6.17	4.44	0.53790	.	0.091257	0.85682	D	0.000000	D	0.82953	0.5149	L	0.44542	1.39	0.50632	D	0.999883	P;D	0.71674	0.93;0.998	B;D	0.72075	0.337;0.976	D	0.84743	0.0752	10	0.72032	D	0.01	-42.2467	13.5804	0.61898	0.0:0.8728:0.0:0.1272	.	449;482	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	H	482;482;449	ENSP00000379069:R482H;ENSP00000352738:R482H;ENSP00000350518:R449H	ENSP00000350518:R449H	R	-	2	0	G3BP2	76789642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.165000	0.77544	1.630000	0.50440	0.655000	0.94253	CGC		0.502	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		T	76570618	C	T	76570618	3	4	61	1	0	0	0	0	1	0	0	0	6161	768	27	1	7	1	G3BP2	4	76570618	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1706612	76570618	114583658	3261	11246										
G3BP2	9908	broad.mit.edu	37	chr4	76572294	76572294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgactatctggatagcGaattattctacggttgtcag	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76572294G>A	ENST00000359707.4	-	10	1761	c.976C>T	c.(976-978)Cgc>Tgc	p.R326C	G3BP2_ENST00000357854.3_Missense_Mutation_p.R293C|G3BP2_ENST00000395719.3_Missense_Mutation_p.R326C	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	326					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)	p.R326C(1)		breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCTGGATAGCGAATTATTCTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	107	108					4																	76572294		2203	4299	6502	76791318	SO:0001583	missense	9908			AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.976C>T	4.37:g.76572294G>A	ENSP00000352738:p.Arg326Cys		76791318	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	37	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879965	0.91740	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.79352	-1.26;-1.26;-1.24	6.04	5.2	0.72013	.	0.045801	0.85682	N	0.000000	D	0.87051	0.6081	M	0.71206	2.165	0.80722	D	1	B;D	0.89917	0.025;1.0	B;D	0.78314	0.007;0.991	D	0.88345	0.2977	10	0.66056	D	0.02	.	15.4346	0.75137	0.0663:0.0:0.9337:0.0	.	293;326	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	C	326;326;293	ENSP00000379069:R326C;ENSP00000352738:R326C;ENSP00000350518:R293C	ENSP00000350518:R293C	R	-	1	0	G3BP2	76791318	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.509000	0.81698	1.571000	0.49722	0.561000	0.74099	CGC		0.333	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		A	76572294	G	A	76572294	3	1	61	1	0	0	0	0	1	0	0	0	6161	1058	37	1	484	1	G3BP2	4	76572294	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1676	76572294	114581982	3262	11247										
USO1	8615	broad.mit.edu	37	chr4	76721933	76721933	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatcatgagtttacgaaGctggtaaaagaacttgaagg	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76721933G>A	ENST00000538159.1	+	17	1872	c.1872G>A	c.(1870-1872)aaG>aaA	p.K624K	USO1_ENST00000514213.2_Silent_p.K600K			O60763	USO1_HUMAN	USO1 vesicle transport factor	615	Globular head.				ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)	p.K624K(1)|p.K543K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGTTTACGAAGCTGGTAAAAG	0.333																																																2	Substitution - coding silent(2)	large_intestine(2)	4											61	56	57					4																	76721933		1807	4072	5879	76940957	SO:0001819	synonymous_variant	8615			AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"vesicle docking protein", "transcytosis associated protein"	603344	"USO1 homolog, vesicle docking protein (yeast)", "USO1 vesicle docking protein homolog (yeast)"			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.1872G>A	4.37:g.76721933G>A			76940957	B2RAQ0|Q6PK63|Q86TB8|Q8N592	Silent	SNP	ENST00000538159.1	37		.	.	.	.	.	.	.	.	.	.	G	6.907	0.536979	0.13188	.	.	ENSG00000138768	ENST00000441296	.	.	.	5.69	2.06	0.26882	.	.	.	.	.	T	0.58177	0.2104	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49579	-0.8925	4	.	.	.	.	9.369	0.38241	0.409:0.0:0.591:0.0	.	.	.	.	N	291	.	.	S	+	2	0	USO1	76940957	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.250000	0.32850	0.069000	0.16605	0.455000	0.32223	AGC		0.333	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003715		A	76721933	G	A	76721933	2	1	61	1	0	0	0	0	0	0	0	1	17079	962	34	3		3	USO1	4	76721933	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149639	76721933	114432343	3263	11248										
PPEF2	5470	broad.mit.edu	37	chr4	76788478	76788478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttaccgactttatctgCatcatgcttcttaaattcac	3	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76788478C>T	ENST00000286719.7	-	14	2100	c.1744G>A	c.(1744-1746)Gca>Aca	p.A582T		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	582	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)	p.A582T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ACTTTATCTGCATCATGCTTC	0.408																																					NSCLC(105;1359 1603 15961 44567 47947)											1	Substitution - Missense(1)	large_intestine(1)	4											56	58	58					4																	76788478		2203	4300	6503	77007502	SO:0001583	missense	5470			AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1744G>A	4.37:g.76788478C>T	ENSP00000286719:p.Ala582Thr		77007502	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	7.615	0.675520	0.14841	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.40225	1.04	6.04	-2.6	0.06190	EF-hand-like domain (1);	1.221100	0.05736	N	0.600467	T	0.20129	0.0484	N	0.11427	0.14	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.22277	-1.0221	10	0.11485	T	0.65	-5.2883	7.1762	0.25747	0.0:0.3409:0.2489:0.4102	.	582;582	O14830-2;O14830	.;PPE2_HUMAN	T	582	ENSP00000286719:A582T	ENSP00000286719:A582T	A	-	1	0	PPEF2	77007502	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.356000	0.07661	-0.455000	0.07054	0.561000	0.74099	GCA		0.408	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		T	76788478	C	T	76788478	3	4	61	1	0	0	0	0	1	0	0	0	12339	710	25	3	533	3	PPEF2	4	76788478	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66545	76788478	114365798	3264	11249										
CXCL9	4283	broad.mit.edu	37	chr4	76924789	76924789	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgagaacgttgagattttcGaactttcagaactttctttt	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76924789G>A	ENST00000264888.5	-	4	378	c.340C>T	c.(340-342)Cga>Tga	p.R114*	RP11-630D6.5_ENST00000501239.2_RNA	NM_002416.1	NP_002407.1	Q07325	CXCL9_HUMAN	chemokine (C-X-C motif) ligand 9	114					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)|defense response (GO:0006952)|defense response to virus (GO:0051607)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|regulation of cell proliferation (GO:0042127)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|cytokine activity (GO:0005125)	p.R114*(1)		large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(1)	11			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TGAGATTTTCGAACTTTCAGA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											184	173	177					4																	76924789		2202	4298	6500	77143813	SO:0001587	stop_gained	4283			X72755	CCDS34014.1	4q21	2013-02-25	2002-08-22	2002-08-23		ENSG00000138755		"Endogenous ligands"	7098	protein-coding gene	gene with protein product		601704	"monokine induced by gamma interferon"	CMK, MIG		8476424, 9730616	Standard	NM_002416		Approved	SCYB9, Humig, crg-10	uc003hjh.1	Q07325		ENST00000264888.5:c.340C>T	4.37:g.76924789G>A	ENSP00000354901:p.Arg114*		77143813	Q503B4	Nonsense_Mutation	SNP	ENST00000264888.5	37	CCDS34014.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222812	0.39300	.	.	ENSG00000138755	ENST00000264888	.	.	.	5.33	1.5	0.22942	.	14.147600	0.00166	N	0.000000	.	.	.	.	.	.	0.26429	N	0.975966	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	0.4425	6.0854	0.19964	0.0:0.0817:0.3148:0.6035	.	.	.	.	X	114	.	ENSP00000354901:R114X	R	-	1	2	CXCL9	77143813	0.013000	0.17824	0.004000	0.12327	0.003000	0.03518	0.426000	0.21363	0.184000	0.20083	-1.215000	0.01618	CGA		0.338	CXCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362819.1			A	76924789	G	A	76924789	4	1	61	1	0	0	0	0	0	1	0	0	4095	1066	37	1	41	1	CXCL9	4	76924789	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136311	76924789	114229487	3265	11250										
CXCL10	3627	broad.mit.edu	37	chr4	76943522	76943522	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaacagcaaacctaccttTccttgctaactgctttcagt	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76943522T>A	ENST00000306602.1	-	3	340	c.275A>T	c.(274-276)gAa>gTa	p.E92V	ART3_ENST00000341029.5_Intron	NM_001565.3	NP_001556.2	P02778	CXL10_HUMAN	chemokine (C-X-C motif) ligand 10	92					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to heat (GO:0034605)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|defense response to virus (GO:0051607)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell migration (GO:2000406)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein secretion (GO:0009306)|regulation of cell proliferation (GO:0042127)|regulation of protein kinase activity (GO:0045859)|response to auditory stimulus (GO:0010996)|response to cold (GO:0009409)|response to gamma radiation (GO:0010332)|response to vitamin D (GO:0033280)|signal transduction (GO:0007165)|T cell chemotaxis (GO:0010818)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cAMP-dependent protein kinase regulator activity (GO:0008603)|chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.E92V(1)		kidney(1)|large_intestine(1)|lung(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AACCTACCTTTCCTTGCTAAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											134	124	127					4																	76943522		1903	4122	6025	77162546	SO:0001583	missense	3627			X02530	CCDS43240.1	4q21	2013-02-25	2002-08-22	2002-08-23		ENSG00000169245		"Endogenous ligands"	10637	protein-coding gene	gene with protein product		147310	"small inducible cytokine subfamily B (Cys-X-Cys), member 10"	INP10, SCYB10		2437586, 3925348	Standard	NM_001565		Approved	IFI10, IP-10, crg-2, mob-1, C7, gIP-10	uc003hjl.4	P02778		ENST00000306602.1:c.275A>T	4.37:g.76943522T>A	ENSP00000305651:p.Glu92Val		77162546	Q96QJ5	Missense_Mutation	SNP	ENST00000306602.1	37	CCDS43240.1	.	.	.	.	.	.	.	.	.	.	T	5.844	0.339986	0.11069	.	.	ENSG00000169245	ENST00000306602	T	0.23552	1.9	4.88	0.984	0.19773	Chemokine interleukin-8-like domain (1);	1.066010	0.07242	N	0.864386	T	0.17408	0.0418	.	.	.	0.23243	N	0.998052	B	0.20671	0.047	B	0.14023	0.01	T	0.32981	-0.9886	9	0.72032	D	0.01	.	3.3809	0.07254	0.168:0.1857:0.0:0.6463	.	92	P02778	CXL10_HUMAN	V	92	ENSP00000305651:E92V	ENSP00000305651:E92V	E	-	2	0	CXCL10	77162546	0.552000	0.26505	0.223000	0.23860	0.001000	0.01503	0.534000	0.23098	0.094000	0.17404	-0.301000	0.09380	GAA		0.418	CXCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362817.1			A	76943522	T	A	76943522	3	1	61	1	0	0	0	0	1	0	0	0	4084	1783	62	5	29	5	CXCL10	4	76943522	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18733	76943522	114210754	3266	11251										
CXCL11	6373	broad.mit.edu	37	chr4	76956390	76956390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacttctattttgtcacagTtgttacttgggtacattatg	7	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:76956390T>C	ENST00000503860.1	-	3	545	c.167A>G	c.(166-168)aAc>aGc	p.N56S	CXCL11_ENST00000306621.3_Missense_Mutation_p.N56S|ART3_ENST00000341029.5_Intron			O14625	CXL11_HUMAN	chemokine (C-X-C motif) ligand 11	56					cell-cell signaling (GO:0007267)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|regulation of cell proliferation (GO:0042127)|signal transduction (GO:0007165)|T cell chemotaxis (GO:0010818)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)	p.N56S(1)		kidney(1)|large_intestine(3)|lung(1)|skin(1)	6			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TTTGTCACAGTTGTTACTTGG	0.393																																					Pancreas(31;57 931 1690 18027 37686)											1	Substitution - Missense(1)	large_intestine(1)	4											141	138	139					4																	76956390		2203	4300	6503	77175414	SO:0001583	missense	6373			U66096	CCDS3574.1	4q21	2013-02-25	2002-08-22	2002-08-23	ENSG00000169248	ENSG00000169248		"Endogenous ligands"	10638	protein-coding gene	gene with protein product		604852	"small inducible cytokine subfamily B (Cys-X-Cys), member 11"	SCYB9B, SCYB11		9730616	Standard	NM_005409		Approved	H174, b-R1, I-TAC, IP-9	uc003hjm.3	O14625	OTTHUMG00000130101	ENST00000503860.1:c.167A>G	4.37:g.76956390T>C	ENSP00000425819:p.Asn56Ser		77175414	Q53YA3|Q92840	Missense_Mutation	SNP	ENST00000503860.1	37	CCDS3574.1	.	.	.	.	.	.	.	.	.	.	T	1.567	-0.535040	0.04082	.	.	ENSG00000169248	ENST00000306621;ENST00000503860	T;T	0.04234	3.67;3.67	5.24	1.7	0.24286	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.429029	0.21687	N	0.070632	T	0.01835	0.0058	.	.	.	0.25548	N	0.987115	B	0.12013	0.005	B	0.15484	0.013	T	0.46816	-0.9164	9	0.07325	T	0.83	-10.1916	2.9472	0.05849	0.0:0.3764:0.2666:0.357	.	56	O14625	CXL11_HUMAN	S	56	ENSP00000306884:N56S;ENSP00000425819:N56S	ENSP00000306884:N56S	N	-	2	0	CXCL11	77175414	0.405000	0.25336	1.000000	0.80357	0.986000	0.74619	-0.014000	0.12656	1.028000	0.39785	0.377000	0.23210	AAC		0.393	CXCL11-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362816.1			C	76956390	T	C	76956390	3	2	61	1	0	0	0	0	1	0	0	0	4085	1725	60	4	129	4	CXCL11	4	76956390	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12868	76956390	114197886	3267	11252										
NUP54	53371	broad.mit.edu	37	chr4	77036569	77036569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtttcattcaatccatgttCgaccagctttatatcttcta	5	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77036569C>T	ENST00000264883.3	-	12	1614	c.1474G>A	c.(1474-1476)Gaa>Aaa	p.E492K	NUP54_ENST00000458189.2_Missense_Mutation_p.E312K|NUP54_ENST00000514987.1_Missense_Mutation_p.E444K|NUP54_ENST00000342467.6_Missense_Mutation_p.E276K	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	492					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.E492K(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						AATCCATGTTCGACCAGCTTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											165	148	153					4																	77036569		2203	4300	6503	77255593	SO:0001583	missense	53371			AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"nucleoporin 54kD"			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.1474G>A	4.37:g.77036569C>T	ENSP00000264883:p.Glu492Lys		77255593	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996194	0.74703	.	.	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.74351	0.3705	L	0.49126	1.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.982;0.99	T	0.64711	-0.6343	9	0.13108	T	0.6	-30.6642	20.5792	0.99380	0.0:1.0:0.0:0.0	.	444;276;492	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	K	492;276;444;312	.	ENSP00000264883:E492K	E	-	1	0	NUP54	77255593	1.000000	0.71417	0.998000	0.56505	0.765000	0.43378	7.431000	0.80335	2.873000	0.98535	0.561000	0.74099	GAA		0.368	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3			T	77036569	C	T	77036569	3	4	61	1	0	0	0	0	1	0	0	0	10798	893	31	1	53	1	NUP54	4	77036569	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80179	77036569	114117707	3268	11253										
NUP54	53371	broad.mit.edu	37	chr4	77045893	77045893	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcttttgtagctcactaAtatcttcagatatgatctgt	6	7	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77045893A>C	ENST00000264883.3	-	9	1213	c.1073T>G	c.(1072-1074)aTt>aGt	p.I358S	NUP54_ENST00000458189.2_Missense_Mutation_p.I178S|NUP54_ENST00000514987.1_Missense_Mutation_p.I310S|NUP54_ENST00000342467.6_Intron	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	358	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.I358S(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TAGCTCACTAATATCTTCAGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											102	98	100					4																	77045893		2202	4298	6500	77264917	SO:0001583	missense	53371			AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"nucleoporin 54kD"			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.1073T>G	4.37:g.77045893A>C	ENSP00000264883:p.Ile358Ser		77264917	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.500409	0.85176	.	.	ENSG00000138750	ENST00000264883;ENST00000514987;ENST00000458189	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.78547	0.4300	M	0.74258	2.255	0.80722	D	1	D;D	0.76494	0.999;0.983	D;P	0.70716	0.97;0.807	T	0.79014	-0.1976	9	0.46703	T	0.11	-22.6155	16.3979	0.83621	1.0:0.0:0.0:0.0	.	310;358	B4DT35;Q7Z3B4	.;NUP54_HUMAN	S	358;310;178	.	ENSP00000264883:I358S	I	-	2	0	NUP54	77264917	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.893000	0.92498	2.279000	0.76181	0.459000	0.35465	ATT		0.333	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3			C	77045893	A	C	77045893	3	2	61	1	0	0	0	0	1	0	0	0	10798	101	4	4	466	4	NUP54	4	77045893	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9324	77045893	114108383	3269	11254										
SCARB2	950	broad.mit.edu	37	chr4	77082873	77082873	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaaggcaatgtttaggttCgaatgaggggtgctctttca	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77082873C>T	ENST00000264896.2	-	12	1779	c.1430G>A	c.(1429-1431)cGa>cAa	p.R477Q	SCARB2_ENST00000452464.2_Missense_Mutation_p.R334Q	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	477					cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)	p.R477Q(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			TGTTTAGGTTCGAATGAGGGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											190	164	173					4																	77082873		2203	4300	6503	77301897	SO:0001583	missense	950			D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760			1665	protein-coding gene	gene with protein product		602257	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)"	CD36L2		1374238	Standard	NM_005506		Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000264896.2:c.1430G>A	4.37:g.77082873C>T	ENSP00000264896:p.Arg477Gln		77301897	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	37	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277240	0.95459	.	.	ENSG00000138760	ENST00000264896;ENST00000452464	T;D	0.91068	-0.38;-2.78	5.23	5.23	0.72850	.	0.318910	0.32134	N	0.006525	D	0.90913	0.7144	L	0.32530	0.975	0.38274	D	0.942237	D;D	0.76494	0.998;0.999	P;P	0.59115	0.623;0.852	D	0.91958	0.5576	10	0.51188	T	0.08	.	14.6832	0.69033	0.0:1.0:0.0:0.0	.	334;477	E7EM68;Q14108	.;SCRB2_HUMAN	Q	477;334	ENSP00000264896:R477Q;ENSP00000399154:R334Q	ENSP00000264896:R477Q	R	-	2	0	SCARB2	77301897	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.709000	0.54853	2.596000	0.87737	0.655000	0.94253	CGA		0.483	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506		T	77082873	C	T	77082873	3	4	61	1	0	0	0	0	1	0	0	0	13919	884	31	1	10	1	SCARB2	4	77082873	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36980	77082873	114071403	3270	11255										
CCDC158	339965	broad.mit.edu	37	chr4	77288740	77288740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctctgcattggtagcctCgatggctctctctttttcct	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77288740C>T	ENST00000388914.3	-	11	1689	c.1537G>A	c.(1537-1539)Gag>Aag	p.E513K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	513								p.E513K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TTGGTAGCCTCGATGGCTCTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	4											99	92	94					4																	77288740		1881	4115	5996	77507764	SO:0001583	missense	339965			BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.1537G>A	4.37:g.77288740C>T	ENSP00000373566:p.Glu513Lys		77507764	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510307	0.85282	.	.	ENSG00000163749	ENST00000388914	T	0.81163	-1.46	5.95	5.95	0.96441	.	0.000000	0.56097	D	0.000023	D	0.82751	0.5105	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.80549	-0.1333	10	0.28530	T	0.3	.	18.1671	0.89732	0.0:1.0:0.0:0.0	.	513	Q5M9N0	CD158_HUMAN	K	513	ENSP00000373566:E513K	ENSP00000373566:E513K	E	-	1	0	CCDC158	77507764	0.993000	0.37304	0.991000	0.47740	0.720000	0.41350	3.569000	0.53827	2.826000	0.97356	0.563000	0.77884	GAG		0.473	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		T	77288740	C	T	77288740	3	4	61	1	0	0	0	0	1	0	0	0	2796	893	31	1	1860	1	CCDC158	4	77288740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205867	77288740	113865536	3271	11256										
ANKRD56	345079	broad.mit.edu	37	chr4	77817856	77817856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgacaacgaatgctgcGaaagacagtcaatgaagggt	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77817856G>A	ENST00000334306.2	-	1	1146	c.1147C>T	c.(1147-1149)Cgc>Tgc	p.R383C		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	383								p.R383C(1)									CGAATGCTGCGAAAGACAGTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	77	75					4																	77817856		2203	4300	6503	78036880	SO:0001583	missense	345079				CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"Ankyrin repeat domain containing"	32958	protein-coding gene	gene with protein product			"ankyrin repeat domain 56"	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.1147C>T	4.37:g.77817856G>A	ENSP00000334879:p.Arg383Cys		78036880	B2RP29	Missense_Mutation	SNP	ENST00000334306.2	37	CCDS34017.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.236205	0.39498	.	.	ENSG00000186212	ENST00000334306	T	0.10192	2.9	4.41	4.41	0.53225	.	0.000000	0.35838	U	0.002952	T	0.19446	0.0467	L	0.29908	0.895	0.41153	D	0.986044	D	0.89917	1.0	D	0.71184	0.972	T	0.00986	-1.1490	10	0.87932	D	0	-4.5524	11.2228	0.48866	0.0:0.0:0.8166:0.1834	.	383	A6NEL2	ANR56_HUMAN	C	383	ENSP00000334879:R383C	ENSP00000334879:R383C	R	-	1	0	ANKRD56	78036880	0.995000	0.38212	0.954000	0.39281	0.053000	0.15095	1.597000	0.36729	2.281000	0.76405	0.655000	0.94253	CGC		0.567	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870		A	77817856	G	A	77817856	3	1	61	1	0	0	0	0	1	0	0	0	682	1058	37	1	1238	1	ANKRD56	4	77817856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	529116	77817856	113336420	3272	11257										
CCNI	10983	broad.mit.edu	37	chr4	77976425	77976425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcagaagttggttgcaggCcatacagtgaagtagttgct	13	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77976425C>T	ENST00000237654.4	-	6	1144	c.568G>A	c.(568-570)Gcc>Acc	p.A190T	CCNI_ENST00000504697.1_5'Flank|CCNI_ENST00000537948.1_Missense_Mutation_p.A176T	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	190					regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)			p.A190T(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						TGGTTGCAGGCCATACAGTGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											130	113	119					4																	77976425		2203	4300	6503	78195449	SO:0001583	missense	10983			D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.568G>A	4.37:g.77976425C>T	ENSP00000237654:p.Ala190Thr		78195449	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	37	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080318	0.76528	.	.	ENSG00000118816	ENST00000237654;ENST00000537948	T;T	0.15834	2.4;2.39	5.86	5.01	0.66863	Cyclin-like (1);	0.237030	0.49916	D	0.000128	T	0.17916	0.0430	L	0.45352	1.415	0.80722	D	1	B;B	0.18741	0.03;0.009	B;B	0.23574	0.037;0.047	T	0.01767	-1.1278	10	0.46703	T	0.11	-0.4085	14.774	0.69703	0.0:0.931:0.0:0.069	.	176;190	B7Z6X4;Q14094	.;CCNI_HUMAN	T	190;176	ENSP00000237654:A190T;ENSP00000441001:A176T	ENSP00000237654:A190T	A	-	1	0	CCNI	78195449	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.503000	0.60407	2.937000	0.99478	0.650000	0.86243	GCC		0.448	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835		T	77976425	C	T	77976425	3	4	61	1	0	0	0	0	1	0	0	0	2932	739	26	3	573	3	CCNI	4	77976425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158569	77976425	113177851	3273	11258										
CCNI	10983	broad.mit.edu	37	chr4	77977254	77977254	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctttagtactggaattCtctatccaaagcaaagggga	8	8	1	0	rs143512120		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:77977254C>A	ENST00000237654.4	-	5	896	c.320G>T	c.(319-321)aGa>aTa	p.R107I	CCNI_ENST00000504697.1_5'UTR|CCNI_ENST00000537948.1_Splice_Site_p.R93I	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	107					regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)			p.R107I(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						TACTGGAATTCTCTATCCAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	76	75					4																	77977254		2203	4300	6503	78196278	SO:0001630	splice_region_variant	10983			D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.319-1G>T	4.37:g.77977254C>A			78196278	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	37	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.254246	0.59212	.	.	ENSG00000118816	ENST00000237654;ENST00000537948;ENST00000505609	T;T;T	0.12569	2.67;2.67;2.67	6.16	5.28	0.74379	Cyclin, N-terminal (1);Cyclin-like (3);	0.091065	0.85682	D	0.000000	T	0.15305	0.0369	L	0.59436	1.845	0.80722	D	1	B;B	0.16603	0.018;0.0	B;B	0.19666	0.026;0.012	T	0.04579	-1.0941	10	0.22109	T	0.4	-0.6919	11.731	0.51737	0.0:0.9095:0.0:0.0905	.	93;107	B7Z6X4;Q14094	.;CCNI_HUMAN	I	107;93;107	ENSP00000237654:R107I;ENSP00000441001:R93I;ENSP00000426467:R107I	ENSP00000237654:R107I	R	-	2	0	CCNI	78196278	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.550000	0.53691	1.491000	0.48482	0.650000	0.86243	AGA		0.363	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835	Missense_Mutation	A	77977254	C	A	77977254	5	1	61	1	0	0	0	0	0	0	1	0	2932	927	32	2	825	2	CCNI	4	77977254	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	829	77977254	113177022	3274	11259										
MRPL1	65008	broad.mit.edu	37	chr4	78804460	78804460	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagaaaaaagatgaaataGaaaaaataaaagcatatccc	6	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:78804460G>T	ENST00000315567.8	+	3	537	c.208G>T	c.(208-210)Gaa>Taa	p.E70*	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	70					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.E70*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						AGATGAAATAGAAAAAATAAA	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											55	57	57					4																	78804460		2203	4300	6503	79023484	SO:0001587	stop_gained	65008			AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"Mitochondrial ribosomal proteins / large subunits"	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.208G>T	4.37:g.78804460G>T	ENSP00000315017:p.Glu70*		79023484	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Nonsense_Mutation	SNP	ENST00000315567.8	37	CCDS3583.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.99|15.99	2.996514|2.996514	0.54147|0.54147	.|.	.|.	ENSG00000169288|ENSG00000169288	ENST00000315567;ENST00000538314|ENST00000502384	.|.	.|.	.|.	6.14|6.14	5.25|5.25	0.73442|0.73442	.|.	0.374712|.	0.29948|.	N|.	0.010782|.	.|T	.|0.53514	.|0.1801	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.60989	.|-0.7153	.|3	0.17832|.	T|.	0.49|.	-27.5702|-27.5702	9.9516|9.9516	0.41642|0.41642	0.0746:0.1417:0.7837:0.0|0.0746:0.1417:0.7837:0.0	.|.	.|.	.|.	.|.	X|I	70;48|23	.|.	ENSP00000315017:E70X|.	E|R	+|+	1|2	0|0	MRPL1|MRPL1	79023484|79023484	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.307000|0.307000	0.27823|0.27823	2.305000|2.305000	0.43664|0.43664	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GAA|AGA		0.318	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		T	78804460	G	T	78804460	4	4	61	1	0	0	0	0	0	1	0	0	9804	943	33	2	218	2	MRPL1	4	78804460	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	827206	78804460	112349816	3275	11260										
MRPL1	65008	broad.mit.edu	37	chr4	78804575	78804575	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgttcacttacttaagaAatttcaaattcttgacttta	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:78804575A>C	ENST00000315567.8	+	3	652	c.323A>C	c.(322-324)aAa>aCa	p.K108T	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	108					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.K108T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						TTACTTAAGAAATTTCAAATT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											89	89	89					4																	78804575		2203	4299	6502	79023599	SO:0001583	missense	65008			AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"Mitochondrial ribosomal proteins / large subunits"	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.323A>C	4.37:g.78804575A>C	ENSP00000315017:p.Lys108Thr		79023599	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	SNP	ENST00000315567.8	37	CCDS3583.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.79|13.79	2.342436|2.342436	0.41498|0.41498	.|.	.|.	ENSG00000169288|ENSG00000169288	ENST00000502384|ENST00000315567;ENST00000538314	.|T	.|0.51574	.|0.7	6.04|6.04	4.85|4.85	0.62838|0.62838	.|Ribosomal protein L1, chordata (1);Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	.|0.329171	.|0.39020	.|N	.|0.001481	T|T	0.43188|0.43188	0.1236|0.1236	L|L	0.52266|0.52266	1.64|1.64	0.39358|0.39358	D|D	0.965875|0.965875	.|P;P	.|0.44776	.|0.727;0.843	.|B;P	.|0.44772	.|0.314;0.46	T|T	0.40289|0.40289	-0.9571|-0.9571	5|10	.|0.38643	.|T	.|0.18	-22.1707|-22.1707	7.5974|7.5974	0.28056|0.28056	0.7864:0.1403:0.0733:0.0|0.7864:0.1403:0.0733:0.0	.|.	.|86;108	.|A0PJ79;Q9BYD6	.|.;RM01_HUMAN	D|T	61|108;86	.|ENSP00000315017:K108T	.|ENSP00000315017:K108T	E|K	+|+	3|2	2|0	MRPL1|MRPL1	79023599|79023599	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.872000|0.872000	0.50106|0.50106	2.189000|2.189000	0.42621|0.42621	2.330000|2.330000	0.79161|0.79161	0.529000|0.529000	0.55759|0.55759	GAA|AAA		0.368	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		C	78804575	A	C	78804575	3	2	61	1	0	0	0	0	1	0	0	0	9804	14	1	4	333	4	MRPL1	4	78804575	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	115	78804575	112349701	3276	11261										
FRAS1	80144	broad.mit.edu	37	chr4	79285132	79285132	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcatgtgacaccaacctCgtgctgtcccacactggcac	7	17	1	1	rs535942655	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79285132C>T	ENST00000325942.6	+	22	3086	c.2646C>T	c.(2644-2646)ctC>ctT	p.L882L	FRAS1_ENST00000264895.6_Silent_p.L882L	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	882					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.L882L(2)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ACACCAACCTCGTGCTGTCCC	0.527													C|||	2	0.000399361	0	0	5008	,	,		20028	0		0	False		,,,				2504	0.002															2	Substitution - coding silent(2)	large_intestine(2)	4											72	76	75					4																	79285132		2096	4230	6326	79504156	SO:0001819	synonymous_variant	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2646C>T	4.37:g.79285132C>T			79504156	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1																																																																																				0.527	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79285132	C	T	79285132	2	4	61	1	0	0	0	0	0	0	0	1	6061	871	31	1		1	FRAS1	4	79285132	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	480557	79285132	111869144	3277	11262										
FRAS1	80144	broad.mit.edu	37	chr4	79367963	79367963	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggtgataagcaattcttCtttgagcctgcaagacctgg	11	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79367963C>A	ENST00000264895.6	+	43	6379	c.5939C>A	c.(5938-5940)tCt>tAt	p.S1980Y		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1980					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.S1980Y(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGCAATTCTTCTTTGAGCCTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	69	69					4																	79367963		1970	4172	6142	79586987	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.5939C>A	4.37:g.79367963C>A	ENSP00000264895:p.Ser1980Tyr		79586987	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.41|11.41	1.630952|1.630952	0.28978|0.28978	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.29397	.|1.57	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	.|0.058939	.|0.64402	.|D	.|0.000001	T|T	0.51500|0.51500	0.1678|0.1678	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.69142	.|0.962	T|T	0.39418|0.39418	-0.9615|-0.9615	5|10	.|0.30854	.|T	.|0.27	.|.	15.0802|15.0802	0.72108|0.72108	0.0:0.8587:0.1413:0.0|0.0:0.8587:0.1413:0.0	.|.	.|1980	.|E9PHH6	.|.	L|Y	208|1980	.|ENSP00000264895:S1980Y	.|ENSP00000264895:S1980Y	F|S	+|+	3|2	2|0	FRAS1|FRAS1	79586987|79586987	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.117000|0.117000	0.20001|0.20001	4.691000|4.691000	0.61738|0.61738	2.639000|2.639000	0.89480|0.89480	0.650000|0.650000	0.86243|0.86243	TTC|TCT		0.483	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79367963	C	A	79367963	3	1	61	1	0	0	0	0	1	0	0	0	6061	913	32	2	6184	2	FRAS1	4	79367963	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82831	79367963	111786313	3278	11263										
FRAS1	80144	broad.mit.edu	37	chr4	79387385	79387385	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtctgtcacattcaccatCgtgcagcctccacgccatgg	9	15	3	0	rs187011600	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79387385C>T	ENST00000264895.6	+	50	7493	c.7053C>T	c.(7051-7053)atC>atT	p.I2351I		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2351					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.I2351I(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CATTCACCATCGTGCAGCCTC	0.537													C|||	4	0.000798722	0.003	0	5008	,	,		20518	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						C		10,4288		0,10,2139	79	78	78		7053	-11.7	0.1	4		78	0,8538		0,0,4269	no	coding-synonymous	FRAS1	NM_025074.6		0,10,6408	TT,TC,CC		0.0,0.2327,0.0779		2351/4013	79387385	10,12826	2149	4269	6418	79606409	SO:0001819	synonymous_variant	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7053C>T	4.37:g.79387385C>T			79606409	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.017	0.983987	0.18889	0.002327	0.0	ENSG00000138759	ENST00000512123	.	.	.	5.83	-11.7	0.00046	.	.	.	.	.	T	0.45677	0.1354	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58736	-0.7584	4	.	.	.	.	8.9439	0.35747	0.1519:0.5431:0.1284:0.1766	.	.	.	.	C	580	.	.	R	+	1	0	FRAS1	79606409	0.000000	0.05858	0.067000	0.19924	0.935000	0.57460	-3.950000	0.00327	-2.603000	0.00450	-0.237000	0.12165	CGT		0.537	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79387385	C	T	79387385	2	4	61	1	0	0	0	0	0	0	0	1	6061	874	31	1		1	FRAS1	4	79387385	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19422	79387385	111766891	3279	11264										
FRAS1	80144	broad.mit.edu	37	chr4	79429941	79429941	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaccaaggaaggagtcaaGaaatccccctccccaggcta	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79429941G>T	ENST00000264895.6	+	63	10001	c.9561G>T	c.(9559-9561)aaG>aaT	p.K3187N		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3183					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.K3187N(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AAGGAGTCAAGAAATCCCCCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	4											47	51	50					4																	79429941		1982	4184	6166	79648965	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9561G>T	4.37:g.79429941G>T	ENSP00000264895:p.Lys3187Asn		79648965	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.70|16.70	3.195398|3.195398	0.58126|0.58126	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.78481	.|-1.18	5.62|5.62	2.94|2.94	0.34122|0.34122	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.78233	.|0.4251	L|L	0.35487|0.35487	1.065|1.065	0.80722|0.80722	D|D	1|1	.|D;D	.|0.63046	.|0.992;0.969	.|P;P	.|0.61397	.|0.888;0.711	.|T	.|0.76594	.|-0.2902	.|10	.|0.46703	.|T	.|0.11	.|.	11.0874|11.0874	0.48095|0.48095	0.2049:0.0:0.7951:0.0|0.2049:0.0:0.7951:0.0	.|.	.|3186;3187	.|Q86XX4-2;E9PHH6	.|.;.	X|N	1416|3187	.|ENSP00000264895:K3187N	.|ENSP00000264895:K3187N	E|K	+|+	1|3	0|2	FRAS1|FRAS1	79648965|79648965	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.772000|0.772000	0.43724|0.43724	3.394000|3.394000	0.52551|0.52551	0.729000|0.729000	0.32403|0.32403	0.585000|0.585000	0.79938|0.79938	GAA|AAG		0.547	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79429941	G	T	79429941	3	4	61	1	0	0	0	0	1	0	0	0	6061	933	33	2	9886	2	FRAS1	4	79429941	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42556	79429941	111724335	3280	11265										
FRAS1	80144	broad.mit.edu	37	chr4	79442733	79442733	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agataataagaatctacattCgagaggatggccgtcttgtc	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79442733C>T	ENST00000264895.6	+	68	11037	c.10597C>T	c.(10597-10599)Cga>Tga	p.R3533*		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3529					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.R3533*(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AATCTACATTCGAGAGGATGG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											96	92	93					4																	79442733		1875	4113	5988	79661757	SO:0001587	stop_gained	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10597C>T	4.37:g.79442733C>T	ENSP00000264895:p.Arg3533*		79661757	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Nonsense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	45|45	11.513810|11.513810	0.99570|0.99570	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	.|.	.|.	.|.	5.66|5.66	3.86|3.86	0.44501|0.44501	.|.	0.066329|.	0.64402|.	D|.	0.000020|.	.|T	.|0.69611	.|0.3130	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67364	.|-0.5689	.|4	0.02654|.	T|.	1|.	.|.	14.5428|14.5428	0.68008|0.68008	0.2754:0.7245:0.0:0.0|0.2754:0.7245:0.0:0.0	.|.	.|.	.|.	.|.	X|L	3533|1761	.|.	ENSP00000264895:R3533X|.	R|S	+|+	1|2	2|0	FRAS1|FRAS1	79661757|79661757	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	3.146000|3.146000	0.50631|0.50631	0.676000|0.676000	0.31285|0.31285	0.585000|0.585000	0.79938|0.79938	CGA|TCG		0.403	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79442733	C	T	79442733	4	4	61	1	0	0	0	0	0	1	0	0	6061	876	31	1	10942	1	FRAS1	4	79442733	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12792	79442733	111711543	3281	11266										
BMP2K	55589	broad.mit.edu	37	chr4	79772086	79772086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggtttacaggcactgggAtgtctactctataaactttg	9	7	2	0	rs368941274		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79772086A>G	ENST00000335016.5	+	7	925	c.759A>G	c.(757-759)ggA>ggG	p.G253G	BMP2K_ENST00000502871.1_Silent_p.G253G	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.G253G(2)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AGGCACTGGGATGTCTACTCT	0.368																																																2	Substitution - coding silent(2)	large_intestine(2)	4											135	121	126					4																	79772086		2203	4300	6503	79991110	SO:0001819	synonymous_variant	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.759A>G	4.37:g.79772086A>G			79991110	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1																																																																																				0.368	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		G	79772086	A	G	79772086	2	3	61	1	0	0	0	0	0	0	0	1	1461	320	12	4		4	BMP2K	4	79772086	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	329353	79772086	111382190	3282	11267										
BMP2K	55589	broad.mit.edu	37	chr4	79782575	79782575	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcagctcttcctgaaccGatgactgctagtgaagcagc	9	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79782575G>A	ENST00000335016.5	+	9	1186	c.1020G>A	c.(1018-1020)ccG>ccA	p.P340P	BMP2K_ENST00000502871.1_Silent_p.P340P	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	340					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.P340P(1)|p.R355Q(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TTCCTGAACCGATGACTGCTA	0.333																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	4											58	57	57					4																	79782575		2202	4300	6502	80001599	SO:0001819	synonymous_variant	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1020G>A	4.37:g.79782575G>A			80001599	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.33|13.33	2.205713|2.205713	0.39003|0.39003	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000264889|ENST00000502613	.|.	.|.	.|.	5.82|5.82	0.454|0.454	0.16644|0.16644	.|.	.|.	.|.	.|.	.|.	.|T	.|0.44307	.|0.1287	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.25152	.|-1.0140	.|4	.|.	.|.	.|.	.|-11.3717	3.8557|3.8557	0.08974|0.08974	0.1458:0.4706:0.2026:0.181|0.1458:0.4706:0.2026:0.181	.|.	.|.	.|.	.|.	.|N	-1|33	.|.	.|.	.|D	+|+	.|1	.|0	BMP2K|BMP2K	80001599|80001599	0.017000|0.017000	0.18338|0.18338	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	-1.088000|-1.088000	0.03379|0.03379	0.331000|0.331000	0.23511|0.23511	0.563000|0.563000	0.77884|0.77884	.|GAT		0.333	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		A	79782575	G	A	79782575	2	1	61	1	0	0	0	0	0	0	0	1	1461	1045	37	1		1	BMP2K	4	79782575	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10489	79782575	111371701	3283	11268										
BMP2K	55589	broad.mit.edu	37	chr4	79833143	79833143	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaacagtcccaaccagtcGaattagacccatttggtgct	7	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79833143G>A	ENST00000335016.5	+	16	3608	c.3442G>A	c.(3442-3444)Gaa>Aaa	p.E1148K	PAQR3_ENST00000295462.3_Intron|PAQR3_ENST00000512733.1_3'UTR|PAQR3_ENST00000515541.1_5'Flank	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1148					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.E1148K(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						CCAACCAGTCGAATTAGACCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											178	172	174					4																	79833143		1947	4126	6073	80052167	SO:0001583	missense	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.3442G>A	4.37:g.79833143G>A	ENSP00000334836:p.Glu1148Lys		80052167	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.71|12.71	2.018576|2.018576	0.35606|0.35606	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000335016|ENST00000502613	T|.	0.48201|.	0.82|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	1.478860|.	0.04250|.	N|.	0.338479|.	T|T	0.75102|0.75102	0.3804|0.3804	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.63192|.	0.912|.	T|T	0.72978|0.72978	-0.4127|-0.4127	10|5	0.56958|.	D|.	0.05|.	-20.4913|-20.4913	19.4202|19.4202	0.94719|0.94719	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1148|.	Q9NSY1|.	BMP2K_HUMAN|.	K|Q	1148|840	ENSP00000334836:E1148K|.	ENSP00000334836:E1148K|.	E|R	+|+	1|2	0|0	BMP2K|BMP2K	80052167|80052167	1.000000|1.000000	0.71417|0.71417	0.359000|0.359000	0.25824|0.25824	0.006000|0.006000	0.05464|0.05464	9.005000|9.005000	0.93587|0.93587	2.586000|2.586000	0.87340|0.87340	0.557000|0.557000	0.71058|0.71058	GAA|CGA		0.428	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		A	79833143	G	A	79833143	3	1	61	1	0	0	0	0	1	0	0	0	1461	1059	37	1	3542	1	BMP2K	4	79833143	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50568	79833143	111321133	3284	11269										
PAQR3	152559	broad.mit.edu	37	chr4	79841722	79841722	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaacatagtcaggacaagGcttgctatgtctgtactgca	10	8	2	1	rs370446003		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:79841722G>A	ENST00000512733.1	-	6	1120	c.907C>T	c.(907-909)Cct>Tct	p.P303S	PAQR3_ENST00000295462.3_3'UTR|PAQR3_ENST00000515541.1_Intron	NM_001040202.1	NP_001035292.1	Q6TCH7	PAQR3_HUMAN	progestin and adipoQ receptor family member III	303	Golgi targeting.				negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein phosphorylation (GO:0001933)|protein localization to Golgi apparatus (GO:0034067)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.P303S(1)		breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	8						TCAGGACAAGGCTTGCTATGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	SER/PRO	0,4406		0,0,2203	212	177	189		907	5.1	1	4		189	1,8599	1.2+/-3.3	0,1,4299	no	missense	PAQR3	NM_001040202.1	74	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	303/312	79841722	1,13005	2203	4300	6503	80060746	SO:0001583	missense	152559			AK055774	CCDS34020.1	4q21	2008-02-05				ENSG00000163291			30130	protein-coding gene	gene with protein product		614577				16044242	Standard	XM_006714104		Approved		uc003hlp.1	Q6TCH7		ENST00000512733.1:c.907C>T	4.37:g.79841722G>A	ENSP00000421981:p.Pro303Ser		80060746	A8K5B7|B3KP59|Q6PIQ1|Q86X05|Q8NCP9	Missense_Mutation	SNP	ENST00000512733.1	37	CCDS34020.1	.	.	.	.	.	.	.	.	.	.	G	7.833	0.720355	0.15372	0.0	1.16E-4	ENSG00000163291	ENST00000512733	T	0.20738	2.05	5.97	5.13	0.70059	.	0.097264	0.64402	D	0.000001	T	0.15652	0.0377	N	0.25094	0.71	0.80722	D	1	B	0.16396	0.017	B	0.14023	0.01	T	0.04737	-1.0930	10	0.24483	T	0.36	-6.1229	15.1078	0.72334	0.0676:0.0:0.9324:0.0	.	303	Q6TCH7	PAQR3_HUMAN	S	303	ENSP00000421981:P303S	ENSP00000425080:P303S	P	-	1	0	PAQR3	80060746	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	6.722000	0.74735	1.541000	0.49316	0.650000	0.86243	CCT		0.408	PAQR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363442.1	NM_177453		A	79841722	G	A	79841722	3	1	61	1	0	0	0	0	1	0	0	0	11467	1203	42	3	32	3	PAQR3	4	79841722	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8579	79841722	111312554	3285	11270										
NAA11	84779	broad.mit.edu	37	chr4	80246415	80246415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagactccttaggttctttgCtgtcactgccactttcttcg	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:80246415C>T	ENST00000286794.4	-	1	789	c.617G>A	c.(616-618)aGc>aAc	p.S206N	NAA11_ENST00000513733.1_5'UTR	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit	206					N-terminal protein amino acid acetylation (GO:0006474)	NatA complex (GO:0031415)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)	p.S206N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						AGGTTCTTTGCTGTCACTGCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	4											58	61	60					4																	80246415		2067	4214	6281	80465439	SO:0001583	missense	84779				CCDS47084.1	4q21.23	2010-05-07	2010-01-14	2010-01-14		ENSG00000156269	2.3.1.88	"N(alpha)-acetyltransferase subunits"	28125	protein-coding gene	gene with protein product			"ARD1 homolog B (S. cerevisiae)"	ARD1B		16638120, 19660095	Standard	NM_032693		Approved	ARD2, hARD2	uc003hlt.4	Q9BSU3		ENST00000286794.4:c.617G>A	4.37:g.80246415C>T	ENSP00000286794:p.Ser206Asn		80465439	Q66K19|Q6P479	Missense_Mutation	SNP	ENST00000286794.4	37	CCDS47084.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554829	0.27739	.	.	ENSG00000156269	ENST00000286794	T	0.56941	0.43	4.73	2.03	0.26663	.	0.183256	0.49916	U	0.000134	T	0.32645	0.0836	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.10706	-1.0618	10	0.22109	T	0.4	-4.2518	1.6151	0.02701	0.1485:0.4528:0.2034:0.1953	.	206	Q9BSU3	NAA11_HUMAN	N	206	ENSP00000286794:S206N	ENSP00000286794:S206N	S	-	2	0	NAA11	80465439	0.923000	0.31300	0.030000	0.17652	0.019000	0.09904	0.309000	0.19332	0.293000	0.22520	0.561000	0.74099	AGC		0.537	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362922.1			T	80246415	C	T	80246415	3	4	61	1	0	0	0	0	1	0	0	0	10147	797	28	3	76	3	NAA11	4	80246415	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	404693	80246415	110907861	3286	11271										
GK2	2712	broad.mit.edu	37	chr4	80328318	80328318	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttctttagcaagtcttTcaatgtctcctgaggtctct	6	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:80328318T>G	ENST00000358842.3	-	1	1054	c.1037A>C	c.(1036-1038)gAa>gCa	p.E346A		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	0					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.E346A(1)		autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						AGCAAGTCTTTCAATGTCTCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											121	115	117					4																	80328318		2203	4300	6503	80547342	SO:0001583	missense	2712			BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"Glycerol kinases"	4291	protein-coding gene	gene with protein product		600148	"glycerol kinase pseudogene 2"	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.1037A>C	4.37:g.80328318T>G	ENSP00000351706:p.Glu346Ala		80547342	Q7Z4Q4	Missense_Mutation	SNP	ENST00000358842.3	37	CCDS3585.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.247193	0.39697	.	.	ENSG00000196475	ENST00000358842	D	0.91068	-2.78	4.04	4.04	0.47022	Carbohydrate kinase, FGGY, C-terminal (1);	0.050169	0.85682	D	0.000000	D	0.94545	0.8243	M	0.81239	2.535	0.80722	D	1	D	0.64830	0.994	D	0.73380	0.98	D	0.94845	0.8008	10	0.87932	D	0	-2.1704	11.5957	0.50972	0.0:0.0:0.0:1.0	.	346	Q14410	GLPK2_HUMAN	A	346	ENSP00000351706:E346A	ENSP00000351706:E346A	E	-	2	0	GK2	80547342	1.000000	0.71417	0.713000	0.30519	0.210000	0.24377	3.837000	0.55820	2.068000	0.61886	0.477000	0.44152	GAA		0.433	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214		G	80328318	T	G	80328318	3	3	61	1	0	0	0	0	1	0	0	0	6441	1783	62	4	628	4	GK2	4	80328318	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	81903	80328318	110825958	3287	11272										
FGF5	2250	broad.mit.edu	37	chr4	81188189	81188189	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttctctgggcagccaaGgaagtggcttggagcagagc	15	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:81188189G>T	ENST00000312465.7	+	1	437	c.211G>T	c.(211-213)Gga>Tga	p.G71*	FGF5_ENST00000456523.3_Nonsense_Mutation_p.G71*	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	71					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)	p.G71*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						GGGCAGCCAAGGAAGTGGCTT	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											62	67	65					4																	81188189		2203	4300	6503	81407213	SO:0001587	stop_gained	2250			M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"Endogenous ligands"	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.211G>T	4.37:g.81188189G>T	ENSP00000311697:p.Gly71*		81407213	B2R554|O75846|Q3Y8M3|Q8NF90	Nonsense_Mutation	SNP	ENST00000312465.7	37	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	G	35	5.428207	0.96131	.	.	ENSG00000138675	ENST00000312465;ENST00000456523	.	.	.	5.41	5.41	0.78517	.	2.681430	0.02070	N	0.051474	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	17.1652	0.86814	0.0:0.0:1.0:0.0	.	.	.	.	X	71	.	ENSP00000311697:G71X	G	+	1	0	FGF5	81407213	1.000000	0.71417	0.048000	0.18961	0.741000	0.42261	5.549000	0.67261	2.816000	0.96949	0.561000	0.74099	GGA		0.607	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			T	81188189	G	T	81188189	4	4	61	1	0	0	0	0	0	1	0	0	5874	1001	35	2	213	2	FGF5	4	81188189	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	859871	81188189	109966087	3288	11273										
C4orf22	255119	broad.mit.edu	37	chr4	81791188	81791188	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaattctcatgggcaagaGatatcaggatacatcgacta	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:81791188G>T	ENST00000358105.3	+	4	424	c.375G>T	c.(373-375)gaG>gaT	p.E125D	C4orf22_ENST00000508675.1_Missense_Mutation_p.E142D	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	125								p.E125D(1)		NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						ATGGGCAAGAGATATCAGGAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											113	117	116					4																	81791188		2203	4300	6503	82010212	SO:0001583	missense	255119			BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.375G>T	4.37:g.81791188G>T	ENSP00000350818:p.Glu125Asp		82010212	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	37	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.162842	0.38217	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.38240	1.15;1.15	5.07	2.98	0.34508	.	0.000000	0.85682	D	0.000000	T	0.53400	0.1794	M	0.73217	2.22	0.31488	N	0.66631	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.58284	-0.7663	10	0.59425	D	0.04	-13.6276	7.0786	0.25219	0.3392:0.0:0.6608:0.0	.	142;125	E7EQ13;Q6V702	.;CD022_HUMAN	D	125;142	ENSP00000350818:E125D;ENSP00000425786:E142D	ENSP00000350818:E125D	E	+	3	2	C4orf22	82010212	0.992000	0.36948	0.992000	0.48379	0.073000	0.16967	1.759000	0.38420	0.324000	0.23333	0.585000	0.79938	GAG		0.363	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		T	81791188	G	T	81791188	3	4	61	1	0	0	0	0	1	0	0	0	2261	933	33	2	389	2	C4orf22	4	81791188	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	602999	81791188	109363088	3289	11274										
BMP3	651	broad.mit.edu	37	chr4	81967314	81967314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggtatatgccaatgatGccgccatttctgagccagaa	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:81967314G>T	ENST00000282701.2	+	2	1059	c.739G>T	c.(739-741)Gcc>Tcc	p.A247S		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	247					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)	p.A247S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						TGCCAATGATGCCGCCATTTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											100	101	101					4																	81967314		2203	4300	6503	82186338	SO:0001583	missense	651			M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.739G>T	4.37:g.81967314G>T	ENSP00000282701:p.Ala247Ser		82186338	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	G	5.282	0.237396	0.10023	.	.	ENSG00000152785	ENST00000282701	T	0.72051	-0.62	5.08	3.23	0.37069	.	0.099034	0.64402	D	0.000001	T	0.41282	0.1152	N	0.04746	-0.17	0.32784	N	0.502024	B	0.17268	0.021	B	0.14023	0.01	T	0.41574	-0.9501	10	0.08599	T	0.76	.	6.7077	0.23260	0.0895:0.0:0.6047:0.3058	.	247	P12645	BMP3_HUMAN	S	247	ENSP00000282701:A247S	ENSP00000282701:A247S	A	+	1	0	BMP3	82186338	1.000000	0.71417	1.000000	0.80357	0.272000	0.26649	4.591000	0.61019	1.515000	0.48885	0.655000	0.94253	GCC		0.478	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			T	81967314	G	T	81967314	3	4	61	1	0	0	0	0	1	0	0	0	1462	1319	46	2	745	2	BMP3	4	81967314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176126	81967314	109186962	3290	11275										
PRKG2	5593	broad.mit.edu	37	chr4	82088363	82088363	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttatcttcaggtaaattCttcagcaaggatacacttca	5	8	5	0	rs144720151	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:82088363C>A	ENST00000395578.1	-	6	980	c.864G>T	c.(862-864)aaG>aaT	p.K288N	PRKG2_ENST00000264399.1_Missense_Mutation_p.K288N|PRKG2_ENST00000418486.2_Missense_Mutation_p.K288N|RP11-100N20.1_ENST00000512502.1_RNA			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	288					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)	p.K288N(2)		NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CAGGTAAATTCTTCAGCAAGG	0.259													C|||	2	0.000399361	8e-04	0	5008	,	,		14246	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	4											26	28	27					4																	82088363		2186	4273	6459	82307387	SO:0001583	missense	5593			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.864G>T	4.37:g.82088363C>A	ENSP00000378945:p.Lys288Asn		82307387	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	37	CCDS3589.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	11.66	1.705631	0.30232	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	T;T;T	0.31247	1.5;1.5;1.5	5.87	5.03	0.67393	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.288863	0.38326	N	0.001728	T	0.43809	0.1264	M	0.74258	2.255	0.80722	D	1	P;B	0.48407	0.91;0.228	P;B	0.50352	0.638;0.133	T	0.39165	-0.9627	10	0.41790	T	0.15	-30.7822	11.9443	0.52920	0.0:0.8564:0.0:0.1436	.	288;288	E7EPE6;Q13237	.;KGP2_HUMAN	N	288	ENSP00000378945:K288N;ENSP00000264399:K288N;ENSP00000389038:K288N	ENSP00000264399:K288N	K	-	3	2	PRKG2	82307387	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.555000	0.36277	1.487000	0.48415	0.591000	0.81541	AAG		0.259	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82088363	C	A	82088363	3	1	61	1	0	0	0	0	1	0	0	0	12557	912	32	2	1480	2	PRKG2	4	82088363	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121049	82088363	109065913	3291	11276										
PRKG2	5593	broad.mit.edu	37	chr4	82092947	82092947	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctccccttggaacacctCtagtcgaccctctatcaagc	5	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:82092947C>A	ENST00000395578.1	-	4	756	c.640G>T	c.(640-642)Gag>Tag	p.E214*	RP11-100N20.1_ENST00000505175.1_RNA|PRKG2_ENST00000264399.1_Nonsense_Mutation_p.E214*|PRKG2_ENST00000418486.2_Nonsense_Mutation_p.E214*|RP11-100N20.1_ENST00000512502.1_RNA			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	214					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)	p.E214*(1)		NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TGGAACACCTCTAGTCGACCC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											81	84	83					4																	82092947		2203	4300	6503	82311971	SO:0001587	stop_gained	5593			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.640G>T	4.37:g.82092947C>A	ENSP00000378945:p.Glu214*		82311971	B4DMX3|E7EPE6|O00125|O60916	Nonsense_Mutation	SNP	ENST00000395578.1	37	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	C	39	7.518362	0.98332	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	.	.	.	5.42	5.42	0.78866	.	0.165696	0.52532	D	0.000073	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-31.9307	19.1736	0.93590	0.0:1.0:0.0:0.0	.	.	.	.	X	214	.	ENSP00000264399:E214X	E	-	1	0	PRKG2	82311971	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	7.109000	0.77062	2.711000	0.92665	0.655000	0.94253	GAG		0.383	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82092947	C	A	82092947	4	1	61	1	0	0	0	0	0	1	0	0	12557	922	32	2	1712	2	PRKG2	4	82092947	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4584	82092947	109061329	3292	11277										
RASGEF1B	153020	broad.mit.edu	37	chr4	82366972	82366972	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctaagtttcgtgttttCttccgttcactgtagcaact	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:82366972C>A	ENST00000264400.2	-	7	901	c.750G>T	c.(748-750)aaG>aaT	p.K250N	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.K208N|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.K249N	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	250	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.K250N(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						TTCGTGTTTTCTTCCGTTCAC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											95	90	91					4																	82366972		2203	4300	6503	82585996	SO:0001583	missense	153020			AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.750G>T	4.37:g.82366972C>A	ENSP00000264400:p.Lys250Asn		82585996	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.629123	0.46944	.	.	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927;ENST00000504863	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.5	4.59	0.56863	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.043609	0.85682	D	0.000000	T	0.38134	0.1029	M	0.70275	2.135	0.80722	D	1	B;B;B	0.22746	0.074;0.039;0.049	B;B;B	0.33254	0.085;0.099;0.16	T	0.16689	-1.0394	10	0.34782	T	0.22	.	14.5883	0.68344	0.0:0.9189:0.0:0.0811	.	208;249;250	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	N	249;250;208;95	ENSP00000425393:K249N;ENSP00000264400:K250N;ENSP00000338437:K208N;ENSP00000426929:K95N	ENSP00000264400:K250N	K	-	3	2	RASGEF1B	82585996	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	3.550000	0.53691	2.854000	0.98071	0.655000	0.94253	AAG		0.383	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545		A	82366972	C	A	82366972	3	1	61	1	0	0	0	0	1	0	0	0	13107	912	32	2	703	2	RASGEF1B	4	82366972	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274025	82366972	108787304	3293	11278										
ENOPH1	58478	broad.mit.edu	37	chr4	83369170	83369170	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtcagtcttttgaggaAacaggttgggacatttctgt	13	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83369170A>C	ENST00000273920.3	+	2	450	c.182A>C	c.(181-183)aAa>aCa	p.K61T	ENOPH1_ENST00000509635.1_5'UTR	NM_021204.3	NP_067027.1			enolase-phosphatase 1									p.K61T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|skin(1)	13						CTTTTGAGGAAACAGGTTGGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											76	72	74					4																	83369170		2203	4300	6503	83588194	SO:0001583	missense	58478				CCDS3594.1, CCDS75154.1	4q21.3	2013-05-29			ENSG00000145293	ENSG00000145293	3.1.3.77		24599	protein-coding gene	gene with protein product	"Enolase-phosphatase E1", "acireductone synthase"					15843022	Standard	XM_005263168		Approved	MASA, E1, mtnC	uc003hmv.3	Q9UHY7	OTTHUMG00000130295	ENST00000273920.3:c.182A>C	4.37:g.83369170A>C	ENSP00000273920:p.Lys61Thr		83588194		Missense_Mutation	SNP	ENST00000273920.3	37	CCDS3594.1	.	.	.	.	.	.	.	.	.	.	a	10.28	1.306908	0.23821	.	.	ENSG00000145293	ENST00000273920;ENST00000456931	T	0.05513	3.43	5.39	4.21	0.49690	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);2,3-diketo-5-methylthio-1-phosphopentane phosphatase (1);	0.088920	0.85682	D	0.000000	T	0.11324	0.0276	L	0.50333	1.59	0.80722	D	1	B	0.28419	0.211	B	0.42738	0.396	T	0.14783	-1.0460	10	0.22706	T	0.39	-14.8615	11.4494	0.50142	0.929:0.0:0.071:0.0	.	61	Q9UHY7	ENOPH_HUMAN	T	61	ENSP00000273920:K61T	ENSP00000273920:K61T	K	+	2	0	ENOPH1	83588194	1.000000	0.71417	0.998000	0.56505	0.085000	0.17905	6.962000	0.76048	1.001000	0.39076	0.524000	0.50904	AAA		0.408	ENOPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252638.2	NM_021204		C	83369170	A	C	83369170	3	2	61	1	0	0	0	0	1	0	0	0	5137	14	1	4	188	4	ENOPH1	4	83369170	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1002198	83369170	107785106	3294	11279										
SCD5	79966	broad.mit.edu	37	chr4	83602054	83602054	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtggtccctggaccactcGaagatgtcattctgcagaga	12	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83602054G>A	ENST00000319540.4	-	3	694	c.375C>T	c.(373-375)ttC>ttT	p.F125F	SCD5_ENST00000273908.4_Silent_p.F125F	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	125					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.F125F(4)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				TGGACCACTCGAAGATGTCAT	0.607																																																4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	4											62	68	66					4																	83602054		2203	4300	6503	83821078	SO:0001819	synonymous_variant	79966			AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.375C>T	4.37:g.83602054G>A			83821078	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Silent	SNP	ENST00000319540.4	37	CCDS34024.1																																																																																				0.607	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		A	83602054	G	A	83602054	2	1	61	1	0	0	0	0	0	0	0	1	13924	1049	37	1		1	SCD5	4	83602054	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232884	83602054	107552222	3295	11280										
SEC31A	22872	broad.mit.edu	37	chr4	83763306	83763306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcagacctgttctttgggaCgcaggcagctcactggcagc	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83763306C>T	ENST00000395310.2	-	22	3137	c.2955G>A	c.(2953-2955)gcG>gcA	p.A985A	SEC31A_ENST00000432794.1_Silent_p.A985A|SEC31A_ENST00000264405.5_Intron|SEC31A_ENST00000508502.1_Intron|SEC31A_ENST00000311785.7_Intron|SEC31A_ENST00000326950.5_Silent_p.A946A|SEC31A_ENST00000509142.1_Intron|SEC31A_ENST00000505984.1_Intron|SEC31A_ENST00000513858.1_Intron|SEC31A_ENST00000355196.2_Silent_p.A985A|SEC31A_ENST00000448323.1_Silent_p.A985A|SEC31A_ENST00000348405.4_Silent_p.A946A|SEC31A_ENST00000505472.1_Silent_p.A1016A|SEC31A_ENST00000443462.2_Intron|SEC31A_ENST00000500777.2_Intron	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	985	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)	p.A985A(1)	SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TTCTTTGGGACGCAGGCAGCT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	4											52	53	52					4																	83763306		2203	4300	6503	83982330	SO:0001819	synonymous_variant	22872			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2955G>A	4.37:g.83763306C>T			83982330	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	C	8.895	0.954859	0.18431	.	.	ENSG00000138674	ENST00000503937	.	.	.	5.83	0.0621	0.14343	.	.	.	.	.	T	0.57740	0.2074	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51545	-0.8692	4	.	.	.	-12.089	10.3419	0.43884	0.0:0.2941:0.0:0.7059	.	.	.	.	H	135	.	.	R	-	2	0	SEC31A	83982330	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	1.164000	0.31810	-0.096000	0.12329	-0.251000	0.11542	CGT		0.522	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		T	83763306	C	T	83763306	2	4	61	1	0	0	0	0	0	0	0	1	14035	523	19	1		1	SEC31A	4	83763306	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161252	83763306	107390970	3296	11281										
THAP9	79725	broad.mit.edu	37	chr4	83826068	83826068	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaaggagctgtgccttCtgtttctctatacaaggtat	9	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83826068C>A	ENST00000302236.5	+	2	311	c.260C>A	c.(259-261)tCt>tAt	p.S87Y		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	87					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.S87Y(1)|p.S87C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				GCTGTGCCTTCTGTTTCTCTA	0.353																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	4											65	67	66					4																	83826068		2203	4300	6503	84045092	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.260C>A	4.37:g.83826068C>A	ENSP00000305533:p.Ser87Tyr		84045092	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326897	0.60743	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.96685	-4.09	3.71	3.71	0.42584	Zinc finger, C2CH-type (4);	1.023770	0.07791	N	0.954918	D	0.97911	0.9313	M	0.74546	2.27	0.31428	N	0.673513	D	0.76494	0.999	D	0.87578	0.998	D	0.94319	0.7552	9	.	.	.	-21.5129	13.3075	0.60362	0.0:1.0:0.0:0.0	.	87	Q9H5L6	THAP9_HUMAN	Y	87	ENSP00000305533:S87Y	.	S	+	2	0	THAP9	84045092	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.352000	0.52239	2.386000	0.81285	0.650000	0.86243	TCT		0.353	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		A	83826068	C	A	83826068	3	1	61	1	0	0	0	0	1	0	0	0	15890	913	32	2	266	2	THAP9	4	83826068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62762	83826068	107328208	3297	11282										
THAP9	79725	broad.mit.edu	37	chr4	83827490	83827490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatagattcctcaaggtgTacatcttaaaggtaaagcaa	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83827490T>C	ENST00000302236.5	+	3	341	c.290T>C	c.(289-291)gTa>gCa	p.V97A		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	97					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.V97A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				CCTCAAGGTGTACATCTTAAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	85	84					4																	83827490		2202	4300	6502	84046514	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.290T>C	4.37:g.83827490T>C	ENSP00000305533:p.Val97Ala		84046514	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	T	4.488	0.090560	0.08632	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.36520	1.25	3.73	0.203	0.15195	.	1.945050	0.03045	N	0.153821	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16512	-1.0400	10	0.08179	T	0.78	-0.3777	5.8039	0.18430	0.0:0.3144:0.0:0.6856	.	97	Q9H5L6	THAP9_HUMAN	A	97	ENSP00000305533:V97A	ENSP00000305533:V97A	V	+	2	0	THAP9	84046514	0.007000	0.16637	0.007000	0.13788	0.672000	0.39443	-0.168000	0.09925	0.026000	0.15269	0.482000	0.46254	GTA		0.299	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		C	83827490	T	C	83827490	3	2	61	1	0	0	0	0	1	0	0	0	15890	1638	57	4	300	4	THAP9	4	83827490	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1422	83827490	107326786	3298	11283										
LIN54	132660	broad.mit.edu	37	chr4	83860850	83860850	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctgtggctggctagtagTtactatttgtgaagttggat	13	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83860850T>G	ENST00000340417.3	-	7	1659	c.1282A>C	c.(1282-1284)Act>Cct	p.T428P	LIN54_ENST00000395283.2_Missense_Mutation_p.T339P|LIN54_ENST00000446851.2_Missense_Mutation_p.T207P|LIN54_ENST00000395282.2_3'UTR|LIN54_ENST00000510557.1_Missense_Mutation_p.T207P|LIN54_ENST00000442461.2_Missense_Mutation_p.T207P|LIN54_ENST00000505397.1_Missense_Mutation_p.T428P|LIN54_ENST00000506560.1_Missense_Mutation_p.T339P	NM_194282.2	NP_919258.2	Q6MZP7	LIN54_HUMAN	lin-54 DREAM MuvB core complex component	428					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.T428P(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)	14		Hepatocellular(203;0.114)				TGGCTAGTAGTTACTATTTGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											166	148	154					4																	83860850		2203	4300	6503	84079874	SO:0001583	missense	132660			BX537919	CCDS3599.1, CCDS47089.1, CCDS75157.1	4q21.22	2014-07-17	2014-07-17		ENSG00000189308	ENSG00000189308			25397	protein-coding gene	gene with protein product	"CXC domain containing 1"	613367	"lin-54 homolog (C. elegans)"			21498570	Standard	XM_005262749		Approved	MIP120, DKFZp686L1814, JC8.6, CXCDC1	uc003hnx.3	Q6MZP7	OTTHUMG00000130287	ENST00000340417.3:c.1282A>C	4.37:g.83860850T>G	ENSP00000341947:p.Thr428Pro		84079874	Q32M68|Q32M69|Q6N071|Q76B60	Missense_Mutation	SNP	ENST00000340417.3	37	CCDS3599.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578033	0.45902	.	.	ENSG00000189308	ENST00000340417;ENST00000395283;ENST00000442461;ENST00000446851;ENST00000510557;ENST00000506560;ENST00000505397	.	.	.	6.17	6.17	0.99709	.	0.088141	0.85682	D	0.000000	T	0.53384	0.1793	N	0.19112	0.55	0.80722	D	1	D;D;D	0.65815	0.967;0.968;0.995	P;P;P	0.56278	0.693;0.655;0.795	T	0.51639	-0.8680	9	0.32370	T	0.25	-21.1707	16.8222	0.85835	0.0:0.0:0.0:1.0	.	339;300;428	Q6MZP7-2;Q7Z3G2;Q6MZP7	.;.;LIN54_HUMAN	P	428;339;207;207;207;339;428	.	ENSP00000341947:T428P	T	-	1	0	LIN54	84079874	1.000000	0.71417	0.443000	0.26883	0.065000	0.16274	4.237000	0.58681	2.371000	0.80710	0.533000	0.62120	ACT		0.453	LIN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252626.2	NM_194282		G	83860850	T	G	83860850	3	3	61	1	0	0	0	0	1	0	0	0	8833	1725	60	4	995	4	LIN54	4	83860850	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33360	83860850	107293426	3299	11284										
COPS4	51138	broad.mit.edu	37	chr4	83971076	83971076	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcatctatatatgagaaaGaagaagattggagaaatgca	10	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:83971076G>T	ENST00000264389.2	+	4	484	c.349G>T	c.(349-351)Gaa>Taa	p.E117*	COPS4_ENST00000509093.1_Nonsense_Mutation_p.E117*|COPS4_ENST00000503682.1_Nonsense_Mutation_p.E117*|COPS4_ENST00000511653.1_Nonsense_Mutation_p.E117*	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	117					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)		p.E117*(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				ATATGAGAAAGAAGAAGATTG	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											127	145	139					4																	83971076		2203	4299	6502	84190100	SO:0001587	stop_gained	51138			AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.349G>T	4.37:g.83971076G>T	ENSP00000264389:p.Glu117*		84190100	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Nonsense_Mutation	SNP	ENST00000264389.2	37	CCDS3600.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191547	0.78902	.	.	ENSG00000138663	ENST00000509093;ENST00000264389;ENST00000503682;ENST00000511653	.	.	.	5.64	5.64	0.86602	.	0.053050	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-10.3624	19.7164	0.96122	0.0:0.0:1.0:0.0	.	.	.	.	X	117	.	ENSP00000264389:E117X	E	+	1	0	COPS4	84190100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.670000	0.83925	2.662000	0.90505	0.650000	0.86243	GAA		0.333	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1			T	83971076	G	T	83971076	4	4	61	1	0	0	0	0	0	1	0	0	3741	943	33	2	363	2	COPS4	4	83971076	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110226	83971076	107183200	3300	11285										
PLAC8	51316	broad.mit.edu	37	chr4	84015875	84015875	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctctccttctgttgatatCtctcttgatttggcaaagag	9	9	4	3	rs183611787		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:84015875C>A	ENST00000509973.1	-	3	265	c.142G>T	c.(142-144)Gat>Tat	p.D48Y	PLAC8_ENST00000311507.4_Missense_Mutation_p.D105Y|PLAC8_ENST00000411416.2_Missense_Mutation_p.D105Y|PLAC8_ENST00000505406.1_Missense_Mutation_p.D105Y|PLAC8_ENST00000515389.1_5'UTR|PLAC8_ENST00000426923.2_Missense_Mutation_p.D105Y			Q9UHV8	PP13_HUMAN	placenta-specific 8	0	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)	p.D105Y(1)		large_intestine(2)|lung(3)|ovary(1)	6		Hepatocellular(203;0.114)				CTGTTGATATCTCTCTTGATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	105	108					4																	84015875		2203	4300	6503	84234899	SO:0001583	missense	51316			AF208846	CCDS3601.1	4q21.22	2006-05-20			ENSG00000145287	ENSG00000145287			19254	protein-coding gene	gene with protein product		607515				12758124, 12384430	Standard	NM_016619		Approved	onzin, C15	uc003hoe.3	Q9NZF1	OTTHUMG00000130294	ENST00000509973.1:c.142G>T	4.37:g.84015875C>A	ENSP00000423459:p.Asp48Tyr		84234899	C5HZ15	Missense_Mutation	SNP	ENST00000509973.1	37		.	.	.	.	.	.	.	.	.	.	C	19.61	3.860206	0.71834	.	.	ENSG00000145287	ENST00000311507;ENST00000411416;ENST00000509973;ENST00000505406;ENST00000426923	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.88310	2.945	0.54753	D	0.999988	D	0.89917	1.0	D	0.85130	0.997	D	0.87407	0.2373	9	0.87932	D	0	-28.5719	15.4799	0.75517	0.0:1.0:0.0:0.0	.	105	Q9NZF1	PLAC8_HUMAN	Y	105;105;48;105;105	.	ENSP00000309509:D105Y	D	-	1	0	PLAC8	84234899	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.015000	0.57152	2.418000	0.82041	0.655000	0.94253	GAT		0.358	PLAC8-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363078.1	NM_016619		A	84015875	C	A	84015875	3	1	61	1	0	0	0	0	1	0	0	0	12046	913	32	2	38	2	PLAC8	4	84015875	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44799	84015875	107138401	3301	11286										
COQ2	27235	broad.mit.edu	37	chr4	84185477	84185477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggttggagataaatttatTccaacaatcctcaggtctgt	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:84185477T>C	ENST00000311469.4	-	7	1140	c.1141A>G	c.(1141-1143)Aat>Gat	p.N381D	COQ2_ENST00000439031.2_Missense_Mutation_p.N344D	NM_015697.7	NP_056512.5	Q96H96	COQ2_HUMAN	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	331					cell death (GO:0008219)|glycerol metabolic process (GO:0006071)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	4-hydroxybenzoate decaprenyltransferase activity (GO:0002083)|4-hydroxybenzoate nonaprenyltransferase activity (GO:0047293)	p.N381D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)	8		Hepatocellular(203;0.114)				ATAAATTTATTCCAACAATCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											112	103	106					4																	84185477		1806	4070	5876	84404501	SO:0001583	missense	27235				CCDS47090.1, CCDS47090.2	4q21.23	2013-05-23	2013-05-23				2.5.1.39		25223	protein-coding gene	gene with protein product	"4-hydroxybenzoate polyprenyltransferase"	609825	"coenzyme Q2 homolog, prenyltransferase (yeast)"			15153069, 17332895	Standard	NM_015697		Approved	CL640, FLJ26072	uc003hog.3	Q96H96		ENST00000311469.4:c.1141A>G	4.37:g.84185477T>C	ENSP00000310873:p.Asn381Asp		84404501	O95331|Q1JQ78|Q684R2	Missense_Mutation	SNP	ENST00000311469.4	37	CCDS47090.2	.	.	.	.	.	.	.	.	.	.	T	8.452	0.853407	0.17106	.	.	ENSG00000173085	ENST00000311469;ENST00000439031	D;D	0.92249	-3.0;-3.0	6.17	1.45	0.22620	.	0.703054	0.14535	N	0.313652	T	0.80352	0.4607	N	0.12746	0.255	0.26806	N	0.969106	B	0.06786	0.001	B	0.08055	0.003	T	0.65602	-0.6128	10	0.23302	T	0.38	-10.3037	4.9179	0.13854	0.0:0.4066:0.148:0.4454	.	331	Q96H96	COQ2_HUMAN	D	381;344	ENSP00000310873:N381D;ENSP00000409275:N344D	ENSP00000310873:N381D	N	-	1	0	COQ2	84404501	1.000000	0.71417	0.572000	0.28498	0.742000	0.42306	1.387000	0.34430	0.152000	0.19188	-0.242000	0.12053	AAT		0.373	COQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363027.3	NM_015697		C	84185477	T	C	84185477	3	2	61	1	0	0	0	0	1	0	0	0	3751	1783	62	4	128	4	COQ2	4	84185477	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	169602	84185477	106968799	3302	11287										
HELQ	113510	broad.mit.edu	37	chr4	84342784	84342784	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagattttgtatatatcctcGaggcatattaaatttttcag	6	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:84342784G>A	ENST00000295488.3	-	15	3043	c.2881C>T	c.(2881-2883)Cga>Tga	p.R961*	HELQ_ENST00000510985.1_Nonsense_Mutation_p.R894*	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	961					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.R961*(1)		breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ATATATCCTCGAGGCATATTA	0.348								Other identified genes with known or suspected DNA repair function																																								1	Substitution - Nonsense(1)	large_intestine(1)	4											104	103	103					4																	84342784		2203	4300	6503	84561808	SO:0001587	stop_gained	113510			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2881C>T	4.37:g.84342784G>A	ENSP00000295488:p.Arg961*		84561808	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Nonsense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	G	42	9.179312	0.99091	.	.	ENSG00000163312	ENST00000295488;ENST00000510985	.	.	.	5.26	4.39	0.52855	.	0.071588	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0164	13.4043	0.60903	0.0:0.0:0.8427:0.1573	.	.	.	.	X	961;894	.	ENSP00000295488:R961X	R	-	1	2	HELQ	84561808	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.009000	0.57110	1.165000	0.42670	0.591000	0.81541	CGA		0.348	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		A	84342784	G	A	84342784	4	1	61	1	0	0	0	0	0	1	0	0	7068	1066	37	1	440	1	HELQ	4	84342784	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157307	84342784	106811492	3303	11288										
MRPS18C	51023	broad.mit.edu	37	chr4	84382149	84382149	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgggaagaaacagaaaGaaatcacaaaagcaattaag	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:84382149G>T	ENST00000295491.4	+	5	429	c.316G>T	c.(316-318)Gaa>Taa	p.E106*	MRPS18C_ENST00000507019.1_Nonsense_Mutation_p.E78*|MRPS18C_ENST00000507349.1_Missense_Mutation_p.K58N|FAM175A_ENST00000321945.7_3'UTR	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	106					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)	p.E106*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5		Hepatocellular(203;0.114)				GAAACAGAAAGAAATCACAAA	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											59	65	63					4																	84382149		2202	4297	6499	84601173	SO:0001587	stop_gained	51023				CCDS3604.1, CCDS75159.1	4q21.21-q21.23	2012-09-13			ENSG00000163319	ENSG00000163319		"Mitochondrial ribosomal proteins / small subunits"	16633	protein-coding gene	gene with protein product		611983				11279123, 10810093	Standard	XM_005263043		Approved	MRPS18-1, CGI-134, FLJ11146, FLJ22967	uc003hor.4	Q9Y3D5	OTTHUMG00000130430	ENST00000295491.4:c.316G>T	4.37:g.84382149G>T	ENSP00000295491:p.Glu106*		84601173		Nonsense_Mutation	SNP	ENST00000295491.4	37	CCDS3604.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	20.4|20.4|20.4	3.979087|3.979087|3.979087	0.74360|0.74360|0.74360	.|.|.	.|.|.	ENSG00000163319|ENSG00000163319|ENSG00000163319	ENST00000295491;ENST00000507019|ENST00000507349;ENST00000505719|ENST00000509970	.|.|.	.|.|.	.|.|.	5.03|5.03|5.03	5.03|5.03|5.03	0.67393|0.67393|0.67393	.|.|.	0.109676|.|.	0.64402|.|.	D|.|.	0.000012|.|.	.|T|T	.|0.74458|0.74458	.|0.3719|0.3719	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.73347|0.73347	.|-0.4011|-0.4011	.|5|4	0.28530|0.72032|.	T|D|.	0.3|0.01|.	-23.0463|-23.0463|-23.0463	18.5577|18.5577|18.5577	0.91090|0.91090|0.91090	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	106;78|58;82|76	.|.|.	ENSP00000295491:E106X|ENSP00000425268:K82N|.	E|K|R	+|+|+	1|3|2	0|2|0	MRPS18C|MRPS18C|MRPS18C	84601173|84601173|84601173	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	5.859000|5.859000|5.859000	0.69539|0.69539|0.69539	2.608000|2.608000|2.608000	0.88229|0.88229|0.88229	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAA|AAG|AGA		0.289	MRPS18C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252820.2			T	84382149	G	T	84382149	4	4	61	1	0	0	0	0	0	1	0	0	9860	943	33	2	334	2	MRPS18C	4	84382149	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39365	84382149	106772127	3304	11289										
AGPAT9	84803	broad.mit.edu	37	chr4	84516010	84516010	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttctaggttggccaggttCatggcggcttgatgggaatt	14	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:84516010C>A	ENST00000395226.2	+	8	969	c.751C>A	c.(751-753)Cat>Aat	p.H251N	AGPAT9_ENST00000264409.4_Missense_Mutation_p.H251N	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	251					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.H251N(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				TGGCCAGGTTCATGGCGGCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											161	164	163					4																	84516010		2203	4300	6503	84735034	SO:0001583	missense	84803			AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.751C>A	4.37:g.84516010C>A	ENSP00000378651:p.His251Asn		84735034	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	37	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199300	0.58126	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	D;D	0.93133	-3.17;-3.17	5.81	4.96	0.65561	Phospholipid/glycerol acyltransferase (2);	0.091303	0.85682	N	0.000000	D	0.93197	0.7833	M	0.77820	2.39	0.80722	D	1	B	0.10296	0.003	B	0.14578	0.011	D	0.90741	0.4650	10	0.72032	D	0.01	-5.3812	16.4153	0.83731	0.1323:0.8676:0.0:0.0	.	251	Q53EU6	GPAT3_HUMAN	N	251	ENSP00000378651:H251N;ENSP00000264409:H251N	ENSP00000264409:H251N	H	+	1	0	AGPAT9	84735034	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	6.075000	0.71261	1.443000	0.47586	0.655000	0.94253	CAT		0.413	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		A	84516010	C	A	84516010	3	1	61	1	0	0	0	0	1	0	0	0	392	826	29	2	777	2	AGPAT9	4	84516010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133861	84516010	106638266	3305	11290										
NKX6-1	4825	broad.mit.edu	37	chr4	85416961	85416961	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgggtctcgtgtgttttCtcttcccgtctttgtccaac	9	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85416961C>A	ENST00000295886.4	-	2	928	c.707G>T	c.(706-708)aGa>aTa	p.R236I	NKX6-1_ENST00000515820.2_5'UTR	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	236	Repressor domain. {ECO:0000250}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R236I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		CGTGTGTTTTCTCTTCCCGTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	95	93					4																	85416961		2203	4300	6503	85635985	SO:0001583	missense	4825			AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"Homeoboxes / ANTP class : NKL subclass"	7839	protein-coding gene	gene with protein product		602563	"NK homeobox (Drosophila), family 6, A", "NK6 transcription factor related, locus 1 (Drosophila)"	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.707G>T	4.37:g.85416961C>A	ENSP00000295886:p.Arg236Ile		85635985		Missense_Mutation	SNP	ENST00000295886.4	37	CCDS3607.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676272	0.88445	.	.	ENSG00000163623	ENST00000295886	D	0.95853	-3.83	5.55	5.55	0.83447	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.049871	0.85682	D	0.000000	D	0.96883	0.8982	L	0.50333	1.59	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	D	0.97207	0.9868	10	0.62326	D	0.03	-11.6583	18.0999	0.89503	0.0:1.0:0.0:0.0	.	236	P78426	NKX61_HUMAN	I	236	ENSP00000295886:R236I	ENSP00000295886:R236I	R	-	2	0	NKX6-1	85635985	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.644000	0.54381	2.606000	0.88127	0.655000	0.94253	AGA		0.493	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168		A	85416961	C	A	85416961	3	1	61	1	0	0	0	0	1	0	0	0	10488	913	32	2	404	2	NKX6-1	4	85416961	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	900951	85416961	105737315	3306	11291										
CDS1	1040	broad.mit.edu	37	chr4	85569737	85569737	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcccagcaaagtgctacaGcagttgttggtgcttcaacc	9	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85569737G>A	ENST00000295887.5	+	13	1707	c.1284G>A	c.(1282-1284)caG>caA	p.Q428Q		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> F (may increase breast cancer risk; dbSNP:rs137853011). {ECO:0000269|PubMed:15649950}.		cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.Q428Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		AAGTGCTACAGCAGTTGTTGG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	4											66	65	65					4																	85569737		2203	4300	6503	85788761	SO:0001819	synonymous_variant	1040			U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.1284G>A	4.37:g.85569737G>A			85788761	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	37	CCDS3608.1																																																																																				0.393	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			A	85569737	G	A	85569737	2	1	61	1	0	0	0	0	0	0	0	1	3183	962	34	3		3	CDS1	4	85569737	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152776	85569737	105584539	3307	11292										
WDFY3	23001	broad.mit.edu	37	chr4	85658388	85658388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcaatgagtggccttgCtgtagctatgtccacgtggc	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85658388C>T	ENST00000295888.4	-	41	7113	c.6706G>A	c.(6706-6708)Gca>Aca	p.A2236T	WDFY3_ENST00000322366.6_Missense_Mutation_p.A2236T	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2236					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.A2236T(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AGTGGCCTTGCTGTAGCTATG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											176	153	161					4																	85658388		2203	4300	6503	85877412	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6706G>A	4.37:g.85658388C>T	ENSP00000295888:p.Ala2236Thr		85877412	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.719095	0.48622	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.65364	-0.14;-0.15	5.13	5.13	0.70059	.	0.052312	0.85682	D	0.000000	T	0.50326	0.1609	L	0.28556	0.865	0.80722	D	1	B	0.18310	0.027	B	0.12837	0.008	T	0.46359	-0.9197	10	0.11485	T	0.65	.	18.5904	0.91210	0.0:1.0:0.0:0.0	.	2236	Q8IZQ1	WDFY3_HUMAN	T	2236	ENSP00000318466:A2236T;ENSP00000295888:A2236T	ENSP00000295888:A2236T	A	-	1	0	WDFY3	85877412	1.000000	0.71417	0.869000	0.34112	0.560000	0.35617	7.463000	0.80869	2.392000	0.81423	0.563000	0.77884	GCA		0.443	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85658388	C	T	85658388	3	4	61	1	0	0	0	0	1	0	0	0	17310	797	28	3	3986	3	WDFY3	4	85658388	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88651	85658388	105495888	3308	11293										
WDFY3	23001	broad.mit.edu	37	chr4	85661548	85661548	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacactgcatccagtgacaAtccctgtgatcttctctttg	6	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85661548A>C	ENST00000295888.4	-	39	6663	c.6256T>G	c.(6256-6258)Ttg>Gtg	p.L2086V	WDFY3_ENST00000322366.6_Missense_Mutation_p.L2086V	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2086					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.L2086V(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TCCAGTGACAATCCCTGTGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											170	147	155					4																	85661548		2203	4300	6503	85880572	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6256T>G	4.37:g.85661548A>C	ENSP00000295888:p.Leu2086Val		85880572	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	A	6.257	0.415585	0.11870	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.62498	0.02;0.02	5.46	-2.28	0.06826	.	0.000000	0.85682	D	0.000000	T	0.34513	0.0900	N	0.16368	0.405	0.44207	D	0.997034	B	0.31459	0.324	B	0.22386	0.039	T	0.27297	-1.0078	10	0.07990	T	0.79	.	12.5271	0.56093	0.4064:0.0:0.5936:0.0	.	2086	Q8IZQ1	WDFY3_HUMAN	V	2086	ENSP00000318466:L2086V;ENSP00000295888:L2086V	ENSP00000295888:L2086V	L	-	1	2	WDFY3	85880572	0.027000	0.19231	0.087000	0.20705	0.992000	0.81027	0.502000	0.22594	-0.396000	0.07703	0.383000	0.25322	TTG		0.383	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85661548	A	C	85661548	3	2	61	1	0	0	0	0	1	0	0	0	17310	98	4	4	4444	4	WDFY3	4	85661548	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3160	85661548	105492728	3309	11294										
WDFY3	23001	broad.mit.edu	37	chr4	85696122	85696122	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctcattaatttggcattCtttgaggcttcactataaga	6	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85696122C>A	ENST00000295888.4	-	29	5012	c.4605G>T	c.(4603-4605)aaG>aaT	p.K1535N	WDFY3_ENST00000322366.6_Missense_Mutation_p.K1535N	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1535					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.K1535N(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		ATTTGGCATTCTTTGAGGCTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											115	124	121					4																	85696122		2203	4300	6503	85915146	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.4605G>T	4.37:g.85696122C>A	ENSP00000295888:p.Lys1535Asn		85915146	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622178	0.28889	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.49432	0.78;0.78	5.33	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	N	0.19112	0.55	0.80722	D	1	B	0.17038	0.02	B	0.12837	0.008	T	0.07751	-1.0756	10	0.24483	T	0.36	.	11.2267	0.48888	0.0:0.8553:0.0:0.1447	.	1535	Q8IZQ1	WDFY3_HUMAN	N	1535	ENSP00000318466:K1535N;ENSP00000295888:K1535N	ENSP00000295888:K1535N	K	-	3	2	WDFY3	85915146	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.000000	0.40816	2.650000	0.89964	0.655000	0.94253	AAG		0.353	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85696122	C	A	85696122	3	1	61	1	0	0	0	0	1	0	0	0	17310	912	32	2	6135	2	WDFY3	4	85696122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34574	85696122	105458154	3310	11295										
WDFY3	23001	broad.mit.edu	37	chr4	85741252	85741252	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattacctgcatttgtgtttGatccttgaagaagcactgtc	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:85741252G>T	ENST00000295888.4	-	12	2086	c.1679C>A	c.(1678-1680)tCa>tAa	p.S560*	WDFY3_ENST00000322366.6_Nonsense_Mutation_p.S560*	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	560					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.S560*(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		ATTTGTGTTTGATCCTTGAAG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											200	215	210					4																	85741252		2203	4300	6503	85960276	SO:0001587	stop_gained	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.1679C>A	4.37:g.85741252G>T	ENSP00000295888:p.Ser560*		85960276	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Nonsense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	42	9.771155	0.99260	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	.	.	.	5.68	5.68	0.88126	.	0.129971	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	19.839	0.96675	0.0:0.0:1.0:0.0	.	.	.	.	X	560	.	ENSP00000295888:S560X	S	-	2	0	WDFY3	85960276	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.021000	0.93673	2.678000	0.91216	0.579000	0.79373	TCA		0.368	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85741252	G	T	85741252	4	4	61	1	0	0	0	0	0	1	0	0	17310	1294	45	2	9172	2	WDFY3	4	85741252	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45130	85741252	105413024	3311	11296										
ARHGAP24	83478	broad.mit.edu	37	chr4	86893267	86893267	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccagttattccttatgcGaagtatgaagattttttgtc	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:86893267G>A	ENST00000395184.1	+	6	1144	c.678G>A	c.(676-678)gcG>gcA	p.A226A	ARHGAP24_ENST00000264343.4_Silent_p.A133A|ARHGAP24_ENST00000395183.2_Silent_p.A131A|ARHGAP24_ENST00000503995.1_Silent_p.A226A	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	226	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)	p.A133A(2)|p.A226A(1)		breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		TTCCTTATGCGAAGTATGAAG	0.408																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	4											117	109	112					4																	86893267		2203	4300	6503	87112291	SO:0001819	synonymous_variant	83478			AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.678G>A	4.37:g.86893267G>A			87112291	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																				0.408	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		A	86893267	G	A	86893267	2	1	61	1	0	0	0	0	0	0	0	1	873	1045	37	1		1	ARHGAP24	4	86893267	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1152015	86893267	104261009	3312	11297										
MAPK10	5602	broad.mit.edu	37	chr4	86950395	86950395	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaccatttttagtcttttCttctgaattcattacttcct	2	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:86950395C>A	ENST00000359221.3	-	13	1733	c.1207G>T	c.(1207-1209)Gaa>Taa	p.E403*	MAPK10_ENST00000395157.3_Nonsense_Mutation_p.E258*|MAPK10_ENST00000395166.1_Nonsense_Mutation_p.E365*|MAPK10_ENST00000361569.2_Nonsense_Mutation_p.E403*|MAPK10_ENST00000395161.2_Nonsense_Mutation_p.E403*|MAPK10_ENST00000449047.2_Nonsense_Mutation_p.E258*|MAPK10_ENST00000395160.3_Nonsense_Mutation_p.E258*|MAPK10_ENST00000395169.3_Nonsense_Mutation_p.E365*			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	403					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)	p.E258*(1)		breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		TTAGTCTTTTCTTCTGAATTC	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											212	202	205					4																	86950395		2203	4300	6503	87169419	SO:0001587	stop_gained	5602			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1207G>T	4.37:g.86950395C>A	ENSP00000352157:p.Glu403*		87169419	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Nonsense_Mutation	SNP	ENST00000359221.3	37	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.458536|10.458536	0.99409|0.99409	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161|ENST00000515400	.|.	.|.	.|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76919	.|0.4055	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73959	.|-0.3818	.|4	0.66056|.	D|.	0.02|.	-23.2627|-23.2627	20.0074|20.0074	0.97437|0.97437	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	365;403;258;403;365;258;258;403|315	.|.	ENSP00000352157:E403X|.	E|R	-|-	1|2	0|0	MAPK10|MAPK10	87169419|87169419	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.918000|0.918000	0.54935|0.54935	6.746000|6.746000	0.74866|0.74866	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.343	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			A	86950395	C	A	86950395	4	1	61	1	0	0	0	0	0	1	0	0	9302	922	32	2	200	2	MAPK10	4	86950395	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57128	86950395	104203881	3313	11298										
PTPN13	5783	broad.mit.edu	37	chr4	87666275	87666275	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcaaccaagatgcccaaGatattggtaaggagaagcag	12	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87666275G>T	ENST00000411767.2	+	17	2707	c.2644G>T	c.(2644-2646)Gat>Tat	p.D882Y	PTPN13_ENST00000436978.1_Missense_Mutation_p.D882Y|PTPN13_ENST00000427191.2_Missense_Mutation_p.D882Y|PTPN13_ENST00000511467.1_Missense_Mutation_p.D882Y|PTPN13_ENST00000316707.6_Missense_Mutation_p.D882Y			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	882					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.D882Y(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AGATGCCCAAGATATTGGTAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	56	57					4																	87666275		1935	4152	6087	87885299	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.2644G>T	4.37:g.87666275G>T	ENSP00000407249:p.Asp882Tyr		87885299	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227559	0.79576	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.55234	0.57;0.58;1.15;0.53;0.58	5.35	5.35	0.76521	.	0.000000	0.47455	D	0.000232	T	0.65386	0.2686	L	0.60455	1.87	0.80722	D	1	P;P;P;P	0.47034	0.889;0.842;0.756;0.842	P;P;B;P	0.55222	0.771;0.477;0.377;0.581	T	0.68213	-0.5468	10	0.87932	D	0	.	17.2504	0.87041	0.0:0.0:1.0:0.0	.	882;882;882;882	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	Y	882;882;882;882;882;850	ENSP00000408368:D882Y;ENSP00000394794:D882Y;ENSP00000322675:D882Y;ENSP00000407249:D882Y;ENSP00000426626:D882Y	ENSP00000322675:D882Y	D	+	1	0	PTPN13	87885299	1.000000	0.71417	0.429000	0.26710	0.977000	0.68977	7.608000	0.82898	2.502000	0.84385	0.557000	0.71058	GAT		0.418	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87666275	G	T	87666275	3	4	61	1	0	0	0	0	1	0	0	0	12817	942	33	2	2706	2	PTPN13	4	87666275	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	715880	87666275	103488001	3314	11299										
PTPN13	5783	broad.mit.edu	37	chr4	87671632	87671632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccttgtagagagagcttCgtttaggagcctgaatctcc	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87671632C>T	ENST00000411767.2	+	18	2723	c.2660C>T	c.(2659-2661)tCg>tTg	p.S887L	PTPN13_ENST00000436978.1_Missense_Mutation_p.S887L|PTPN13_ENST00000427191.2_Missense_Mutation_p.S887L|PTPN13_ENST00000511467.1_Missense_Mutation_p.S887L|PTPN13_ENST00000316707.6_Intron			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	887					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.S887L(2)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GAGAGAGCTTCGTTTAGGAGC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	4											152	149	150					4																	87671632		1883	4121	6004	87890656	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.2660C>T	4.37:g.87671632C>T	ENSP00000407249:p.Ser887Leu		87890656	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319143	0.81469	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T	0.54675	0.56;0.62;0.61;0.62	5.9	5.9	0.94986	.	0.000000	0.43110	D	0.000609	T	0.70753	0.3260	M	0.62723	1.935	0.49798	D	0.999821	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.64410	0.925;0.918;0.925	T	0.70182	-0.4942	10	0.59425	D	0.04	.	20.274	0.98482	0.0:1.0:0.0:0.0	.	887;887;887	Q12923-3;Q12923;Q12923-4	.;PTN13_HUMAN;.	L	887;887;887;887;855	ENSP00000408368:S887L;ENSP00000394794:S887L;ENSP00000407249:S887L;ENSP00000426626:S887L	ENSP00000349909:S855L	S	+	2	0	PTPN13	87890656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.024000	0.70857	2.797000	0.96272	0.650000	0.86243	TCG		0.413	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87671632	C	T	87671632	3	4	61	1	0	0	0	0	1	0	0	0	12817	893	31	1	2726	1	PTPN13	4	87671632	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5357	87671632	103482644	3315	11300										
PTPN13	5783	broad.mit.edu	37	chr4	87674209	87674209	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatcccaagtacccttaAaagaaaatggtaggtttaca	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87674209A>C	ENST00000411767.2	+	20	3277	c.3214A>C	c.(3214-3216)Aaa>Caa	p.K1072Q	PTPN13_ENST00000436978.1_Missense_Mutation_p.K1072Q|PTPN13_ENST00000427191.2_Intron|PTPN13_ENST00000511467.1_Missense_Mutation_p.K1072Q|PTPN13_ENST00000316707.6_Intron			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1072					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.K1072Q(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AGTACCCTTAAAAGAAAATGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	80	81					4																	87674209		1829	4082	5911	87893233	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3214A>C	4.37:g.87674209A>C	ENSP00000407249:p.Lys1072Gln		87893233	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.418993	0.42918	.	.	ENSG00000163629	ENST00000436978;ENST00000411767;ENST00000511467	T;T;T	0.52057	0.68;0.68;0.68	5.08	5.08	0.68730	PDZ/DHR/GLGF (1);	0.000000	0.46145	D	0.000304	T	0.44052	0.1275	L	0.56769	1.78	0.38229	D	0.940998	B;P	0.36438	0.264;0.553	B;B	0.35353	0.044;0.201	T	0.49707	-0.8911	10	0.35671	T	0.21	.	12.8691	0.57955	1.0:0.0:0.0:0.0	.	1072;1072	Q12923;Q12923-4	PTN13_HUMAN;.	Q	1072	ENSP00000394794:K1072Q;ENSP00000407249:K1072Q;ENSP00000426626:K1072Q	ENSP00000407249:K1072Q	K	+	1	0	PTPN13	87893233	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	5.649000	0.67936	2.039000	0.60335	0.533000	0.62120	AAA		0.348	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87674209	A	C	87674209	3	2	61	1	0	0	0	0	1	0	0	0	12817	15	1	4	3288	4	PTPN13	4	87674209	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2577	87674209	103480067	3316	11301										
PTPN13	5783	broad.mit.edu	37	chr4	87683926	87683926	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgagatgaaaaactacatGaagaaatcttcctacatgca	6	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87683926G>T	ENST00000411767.2	+	24	3663	c.3600G>T	c.(3598-3600)atG>atT	p.M1200I	PTPN13_ENST00000436978.1_Missense_Mutation_p.M1200I|PTPN13_ENST00000427191.2_Missense_Mutation_p.M1181I|PTPN13_ENST00000511467.1_Missense_Mutation_p.M1200I|PTPN13_ENST00000316707.6_Missense_Mutation_p.M1009I			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1200					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.M1200I(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAAACTACATGAAGAAATCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											97	96	96					4																	87683926		1909	4119	6028	87902950	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3600G>T	4.37:g.87683926G>T	ENSP00000407249:p.Met1200Ile		87902950	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	6.332	0.429338	0.11987	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.50813	0.73;0.77;0.83;0.73;0.77	5.47	0.499	0.16914	.	0.547660	0.16582	N	0.208168	T	0.31482	0.0798	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.16166	0.001;0.013;0.016;0.013	B;B;B;B	0.17722	0.001;0.019;0.009;0.019	T	0.12837	-1.0532	10	0.27785	T	0.31	.	2.8659	0.05601	0.2888:0.1141:0.4681:0.129	.	1009;1181;1200;1200	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	I	1181;1200;1009;1200;1200;1149	ENSP00000408368:M1181I;ENSP00000394794:M1200I;ENSP00000322675:M1009I;ENSP00000407249:M1200I;ENSP00000426626:M1200I	ENSP00000322675:M1009I	M	+	3	0	PTPN13	87902950	0.459000	0.25768	0.996000	0.52242	0.526000	0.34562	0.424000	0.21330	0.372000	0.24591	0.650000	0.86243	ATG		0.428	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87683926	G	T	87683926	3	4	61	1	0	0	0	0	1	0	0	0	12817	1290	45	2	3690	2	PTPN13	4	87683926	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9717	87683926	103470350	3317	11302										
PTPN13	5783	broad.mit.edu	37	chr4	87684096	87684096	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgagagtgccagcttgtCtcaaagccaggtcaatggtt	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87684096C>A	ENST00000411767.2	+	24	3833	c.3770C>A	c.(3769-3771)tCt>tAt	p.S1257Y	PTPN13_ENST00000436978.1_Missense_Mutation_p.S1257Y|PTPN13_ENST00000427191.2_Missense_Mutation_p.S1238Y|PTPN13_ENST00000511467.1_Missense_Mutation_p.S1257Y|PTPN13_ENST00000316707.6_Missense_Mutation_p.S1066Y			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1257					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.S1257Y(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GCCAGCTTGTCTCAAAGCCAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	73	73					4																	87684096		1916	4135	6051	87903120	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3770C>A	4.37:g.87684096C>A	ENSP00000407249:p.Ser1257Tyr		87903120	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.782499	0.70222	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.54675	0.56;0.58;0.66;0.56;0.58	5.47	5.47	0.80525	.	0.000000	0.50627	D	0.000105	T	0.71400	0.3335	M	0.63843	1.955	0.36924	D	0.891553	D;D;D;D	0.76494	0.986;0.996;0.999;0.999	P;D;D;D	0.72338	0.858;0.93;0.949;0.977	T	0.76586	-0.2905	10	0.66056	D	0.02	.	19.3346	0.94309	0.0:1.0:0.0:0.0	.	1066;1238;1257;1257	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	Y	1238;1257;1066;1257;1257;1206	ENSP00000408368:S1238Y;ENSP00000394794:S1257Y;ENSP00000322675:S1066Y;ENSP00000407249:S1257Y;ENSP00000426626:S1257Y	ENSP00000322675:S1066Y	S	+	2	0	PTPN13	87903120	0.993000	0.37304	1.000000	0.80357	0.891000	0.51852	2.909000	0.48758	2.549000	0.85964	0.650000	0.86243	TCT		0.542	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87684096	C	A	87684096	3	1	61	1	0	0	0	0	1	0	0	0	12817	913	32	2	3860	2	PTPN13	4	87684096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	170	87684096	103470180	3318	11303										
PTPN13	5783	broad.mit.edu	37	chr4	87684202	87684202	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaatatccaaagccaccgaGaaagagactttcactgatag	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87684202G>T	ENST00000411767.2	+	24	3939	c.3876G>T	c.(3874-3876)gaG>gaT	p.E1292D	PTPN13_ENST00000436978.1_Missense_Mutation_p.E1292D|PTPN13_ENST00000427191.2_Missense_Mutation_p.E1273D|PTPN13_ENST00000511467.1_Missense_Mutation_p.E1292D|PTPN13_ENST00000316707.6_Missense_Mutation_p.E1101D			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1292					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.E1292D(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAGCCACCGAGAAAGAGACTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											80	78	79					4																	87684202		1865	4116	5981	87903226	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3876G>T	4.37:g.87684202G>T	ENSP00000407249:p.Glu1292Asp		87903226	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	g	10.90	1.481358	0.26598	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.53206	0.63;0.73;0.73;0.64;0.73	5.45	5.45	0.79879	.	0.000000	0.51477	D	0.000081	T	0.36799	0.0980	L	0.34521	1.04	0.33795	D	0.625925	B;B;B;B	0.13594	0.008;0.0;0.001;0.002	B;B;B;B	0.13407	0.009;0.004;0.003;0.006	T	0.41502	-0.9505	10	0.16896	T	0.51	.	14.8743	0.70483	0.0:0.1431:0.8569:0.0	.	1101;1273;1292;1292	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	D	1273;1292;1101;1292;1292;1241	ENSP00000408368:E1273D;ENSP00000394794:E1292D;ENSP00000322675:E1101D;ENSP00000407249:E1292D;ENSP00000426626:E1292D	ENSP00000322675:E1101D	E	+	3	2	PTPN13	87903226	1.000000	0.71417	0.735000	0.30896	0.095000	0.18619	2.227000	0.42972	2.546000	0.85860	0.645000	0.84053	GAG		0.458	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87684202	G	T	87684202	3	4	61	1	0	0	0	0	1	0	0	0	12817	933	33	2	3966	2	PTPN13	4	87684202	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	106	87684202	103470074	3319	11304										
PTPN13	5783	broad.mit.edu	37	chr4	87689108	87689108	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaacaactcaggtcaaaGactacagctttgtcactgaa	7	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87689108G>T	ENST00000411767.2	+	28	4531	c.4468G>T	c.(4468-4470)Gac>Tac	p.D1490Y	PTPN13_ENST00000436978.1_Missense_Mutation_p.D1495Y|PTPN13_ENST00000427191.2_Missense_Mutation_p.D1471Y|PTPN13_ENST00000511467.1_Missense_Mutation_p.D1495Y|PTPN13_ENST00000316707.6_Missense_Mutation_p.D1299Y			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1490					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.D1495Y(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TCAGGTCAAAGACTACAGCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	79	80					4																	87689108		1861	4101	5962	87908132	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4468G>T	4.37:g.87689108G>T	ENSP00000407249:p.Asp1490Tyr		87908132	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653638	0.88056	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.56444	0.47;0.5;0.58;0.46;0.5	5.77	5.77	0.91146	PDZ/DHR/GLGF (1);	0.000000	0.53938	D	0.000043	T	0.70928	0.3280	L	0.58101	1.795	0.58432	D	0.999999	D;B;D;D	0.89917	1.0;0.016;0.993;0.991	D;B;P;D	0.70935	0.971;0.053;0.906;0.944	T	0.71852	-0.4467	10	0.87932	D	0	.	19.9981	0.97395	0.0:0.0:1.0:0.0	.	1299;1471;1490;1495	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	Y	1471;1495;1299;1490;1495;1439	ENSP00000408368:D1471Y;ENSP00000394794:D1495Y;ENSP00000322675:D1299Y;ENSP00000407249:D1490Y;ENSP00000426626:D1495Y	ENSP00000322675:D1299Y	D	+	1	0	PTPN13	87908132	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	8.585000	0.90802	2.729000	0.93468	0.655000	0.94253	GAC		0.413	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87689108	G	T	87689108	3	4	61	1	0	0	0	0	1	0	0	0	12817	942	33	2	4589	2	PTPN13	4	87689108	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4906	87689108	103465168	3320	11305										
PTPN13	5783	broad.mit.edu	37	chr4	87707064	87707064	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatacagactgcgatggttCacctttacctgagtatttta	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87707064C>A	ENST00000411767.2	+	40	6383	c.6320C>A	c.(6319-6321)tCa>tAa	p.S2107*	PTPN13_ENST00000436978.1_Nonsense_Mutation_p.S2112*|PTPN13_ENST00000427191.2_Nonsense_Mutation_p.S2088*|PTPN13_ENST00000511467.1_Nonsense_Mutation_p.S2112*|PTPN13_ENST00000316707.6_Nonsense_Mutation_p.S1916*			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2107					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.S2112*(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TGCGATGGTTCACCTTTACCT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											64	58	60					4																	87707064		1867	4100	5967	87926088	SO:0001587	stop_gained	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6320C>A	4.37:g.87707064C>A	ENSP00000407249:p.Ser2107*		87926088	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Nonsense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	47	13.617373	0.99753	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	.	.	.	5.04	4.14	0.48551	.	0.185965	0.25900	N	0.027575	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5927	0.39557	0.143:0.7781:0.0:0.0789	.	.	.	.	X	2088;2112;1916;2107;2112;2056	.	ENSP00000322675:S1916X	S	+	2	0	PTPN13	87926088	0.998000	0.40836	0.106000	0.21319	0.324000	0.28378	2.285000	0.43487	2.478000	0.83669	0.460000	0.39030	TCA		0.358	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87707064	C	A	87707064	4	1	61	1	0	0	0	0	0	1	0	0	12817	838	29	2	6489	2	PTPN13	4	87707064	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17956	87707064	103447212	3321	11306										
PTPN13	5783	broad.mit.edu	37	chr4	87724993	87724993	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgctagatcaaggaattCcttctaaggagctggaggta	12	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87724993C>A	ENST00000411767.2	+	43	6700	c.6637C>A	c.(6637-6639)Cct>Act	p.P2213T	PTPN13_ENST00000436978.1_Missense_Mutation_p.P2218T|PTPN13_ENST00000427191.2_Missense_Mutation_p.P2194T|PTPN13_ENST00000511467.1_Missense_Mutation_p.P2218T|PTPN13_ENST00000316707.6_Missense_Mutation_p.P2022T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2213	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.P2218T(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TCAAGGAATTCCTTCTAAGGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	128	131					4																	87724993		1866	4100	5966	87944017	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6637C>A	4.37:g.87724993C>A	ENSP00000407249:p.Pro2213Thr		87944017	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177187	0.78564	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62	5.18	5.18	0.71444	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.49305	D	0.000148	T	0.35828	0.0945	M	0.62723	1.935	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.987;1.0;0.999;1.0	T	0.01591	-1.1317	10	0.28530	T	0.3	.	19.0623	0.93097	0.0:1.0:0.0:0.0	.	2022;2194;2213;2218	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	2194;2218;2022;2213;2218;2162	ENSP00000408368:P2194T;ENSP00000394794:P2218T;ENSP00000322675:P2022T;ENSP00000407249:P2213T;ENSP00000426626:P2218T	ENSP00000322675:P2022T	P	+	1	0	PTPN13	87944017	1.000000	0.71417	0.956000	0.39512	0.996000	0.88848	6.679000	0.74513	2.562000	0.86427	0.555000	0.69702	CCT		0.443	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87724993	C	A	87724993	3	1	61	1	0	0	0	0	1	0	0	0	12817	855	30	2	6818	2	PTPN13	4	87724993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17929	87724993	103429283	3322	11307										
PTPN13	5783	broad.mit.edu	37	chr4	87728798	87728798	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagttgggaaagaagagttCgtttacattgcctgccaagg	12	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87728798C>T	ENST00000411767.2	+	45	6894	c.6831C>T	c.(6829-6831)ttC>ttT	p.F2277F	PTPN13_ENST00000436978.1_Silent_p.F2282F|PTPN13_ENST00000427191.2_Silent_p.F2258F|PTPN13_ENST00000511467.1_Silent_p.F2282F|PTPN13_ENST00000316707.6_Silent_p.F2086F			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2277	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.F2282F(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAGAAGAGTTCGTTTACATTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											184	175	178					4																	87728798		1913	4122	6035	87947822	SO:0001819	synonymous_variant	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6831C>T	4.37:g.87728798C>T			87947822	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																				0.448	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87728798	C	T	87728798	2	4	61	1	0	0	0	0	0	0	0	1	12817	883	31	1		1	PTPN13	4	87728798	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3805	87728798	103425478	3323	11308										
SLC10A6	345274	broad.mit.edu	37	chr4	87770114	87770114	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcttccggatctccacgGaacatcccaaagagaacatg	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:87770114G>T	ENST00000273905.6	-	1	302	c.155C>A	c.(154-156)tCc>tAc	p.S52Y	SLC10A6_ENST00000505535.1_5'UTR	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	52					sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)	p.S52Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		GATCTCCACGGAACATCCCAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	4											76	56	63					4																	87770114		2203	4300	6503	87989138	SO:0001583	missense	345274			AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"Solute carriers"	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.155C>A	4.37:g.87770114G>T	ENSP00000273905:p.Ser52Tyr		87989138	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	37	CCDS3614.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.286564	0.59867	.	.	ENSG00000145283	ENST00000273905	T	0.11821	2.74	5.85	5.85	0.93711	.	0.077043	0.52532	D	0.000068	T	0.35799	0.0944	M	0.62723	1.935	0.49582	D	0.999804	D	0.64830	0.994	D	0.67103	0.949	T	0.01413	-1.1361	10	0.87932	D	0	-7.349	17.6669	0.88205	0.0:0.0:1.0:0.0	.	52	Q3KNW5	SOAT_HUMAN	Y	52	ENSP00000273905:S52Y	ENSP00000273905:S52Y	S	-	2	0	SLC10A6	87989138	1.000000	0.71417	0.981000	0.43875	0.031000	0.12232	6.294000	0.72738	2.768000	0.95171	0.655000	0.94253	TCC		0.557	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965		T	87770114	G	T	87770114	3	4	61	1	0	0	0	0	1	0	0	0	14415	1174	41	2	1002	2	SLC10A6	4	87770114	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41316	87770114	103384162	3324	11309										
AFF1	4299	broad.mit.edu	37	chr4	88047377	88047377	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggaagcagacacctgtggCcaggaccctcccaaaagtgc	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88047377C>T	ENST00000307808.6	+	13	3099	c.2679C>T	c.(2677-2679)ggC>ggT	p.G893G	AFF1_ENST00000395146.4_Silent_p.G900G|AFF1_ENST00000544085.1_Silent_p.G531G	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	893					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G893G(1)		breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		ACACCTGTGGCCAGGACCCTC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	4											77	75	76					4																	88047377		2203	4300	6503	88266401	SO:0001819	synonymous_variant	4299			L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.2679C>T	4.37:g.88047377C>T			88266401	B4DTU1|E9PBM3	Silent	SNP	ENST00000307808.6	37	CCDS3616.1																																																																																				0.577	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88047377	C	T	88047377	2	4	61	1	0	0	0	0	0	0	0	1	356	726	26	3		3	AFF1	4	88047377	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	277263	88047377	103106899	3325	11310										
SPARCL1	8404	broad.mit.edu	37	chr4	88415107	88415107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgtgcttattgacgttcGatgcattttcctcttccatt	7	9	1	1	rs200319615	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88415107G>A	ENST00000282470.6	-	4	1315	c.845C>T	c.(844-846)tCg>tTg	p.S282L	SPARCL1_ENST00000418378.1_Missense_Mutation_p.S282L|SPARCL1_ENST00000503414.1_Missense_Mutation_p.S157L	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	282					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S282L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ATTGACGTTCGATGCATTTTC	0.413													G|||	2	0.000399361	8e-04	0	5008	,	,		23764	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	4						G	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	362	353	356		845,845	4	0.1	4		356	0,8600		0,0,4300	no	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	145,145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	282/665,282/665	88415107	1,13005	2203	4300	6503	88634131	SO:0001583	missense	8404			X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"EF-hand domain containing"	11220	protein-coding gene	gene with protein product		606041	"SPARC-like 1 (mast9, hevin)"			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.845C>T	4.37:g.88415107G>A	ENSP00000282470:p.Ser282Leu		88634131	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.776762	0.49786	2.27E-4	0.0	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	T;T;T	0.26518	2.29;2.29;1.73	4.89	4.03	0.46877	.	0.537014	0.17396	N	0.175753	T	0.18383	0.0441	L	0.32530	0.975	0.09310	N	1	D;D	0.56521	0.957;0.976	B;B	0.41174	0.264;0.349	T	0.15578	-1.0432	10	0.87932	D	0	-3.3581	8.1785	0.31296	0.105:0.0:0.895:0.0	.	282;282	Q8N4S1;Q14515	.;SPRL1_HUMAN	L	282;282;157;157	ENSP00000282470:S282L;ENSP00000414856:S282L;ENSP00000422903:S157L	ENSP00000282470:S282L	S	-	2	0	SPARCL1	88634131	0.612000	0.27000	0.084000	0.20598	0.007000	0.05969	2.487000	0.45268	2.650000	0.89964	0.655000	0.94253	TCG		0.413	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2			A	88415107	G	A	88415107	3	1	61	1	0	0	0	0	1	0	0	0	15035	1059	37	1	1181	1	SPARCL1	4	88415107	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	367730	88415107	102739169	3326	11311										
DSPP	1834	broad.mit.edu	37	chr4	88533590	88533590	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaagggaatggctctaaGtgggcagaagtaggagggaa	19	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88533590G>T	ENST00000282478.7	+	3	285	c.252G>T	c.(250-252)aaG>aaT	p.K84N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.K84N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	84					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.K84N(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		ATGGCTCTAAGTGGGCAGAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	4											77	79	78					4																	88533590		1918	4141	6059	88752614	SO:0001583	missense	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.252G>T	4.37:g.88533590G>T	ENSP00000282478:p.Lys84Asn		88752614	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.843128	0.32606	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88431	-2.38;-2.38	5.24	3.5	0.40072	.	0.264107	0.19944	N	0.102585	T	0.76842	0.4044	N	0.08118	0	0.22081	N	0.999376	B	0.30281	0.275	B	0.30782	0.12	T	0.70368	-0.4891	10	0.72032	D	0.01	-10.4849	8.9832	0.35977	0.1802:0.0:0.8198:0.0	.	84	Q9NZW4	DSPP_HUMAN	N	84	ENSP00000382213:K84N;ENSP00000282478:K84N	ENSP00000282478:K84N	K	+	3	2	DSPP	88752614	0.994000	0.37717	0.986000	0.45419	0.322000	0.28314	1.317000	0.33631	1.211000	0.43351	0.460000	0.39030	AAG		0.468	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88533590	G	T	88533590	3	4	61	1	0	0	0	0	1	0	0	0	4793	1020	36	2	262	2	DSPP	4	88533590	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118483	88533590	102620686	3327	11312										
DMP1	1758	broad.mit.edu	37	chr4	88583911	88583911	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaggagaatctgtcccaGgaagagagccaaaacgtaga	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88583911G>A	ENST00000339673.6	+	6	1080	c.981G>A	c.(979-981)caG>caA	p.Q327Q	RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA|DMP1_ENST00000282479.7_Silent_p.Q311Q	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	327					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)	p.Q327Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		ATCTGTCCCAGGAAGAGAGCC	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	4											96	92	93					4																	88583911		2203	4300	6503	88802935	SO:0001819	synonymous_variant	1758			U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"dentin matrix acidic phosphoprotein"			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.981G>A	4.37:g.88583911G>A			88802935	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																				0.527	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			A	88583911	G	A	88583911	2	1	61	1	0	0	0	0	0	0	0	1	4594	991	35	3		3	DMP1	4	88583911	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50321	88583911	102570365	3328	11313										
MEPE	56955	broad.mit.edu	37	chr4	88766450	88766450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaccaagaagaatatggcGcagctctcatcagaaataac	8	9	2	4	rs148637496		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88766450G>A	ENST00000424957.3	+	4	503	c.430G>A	c.(430-432)Gca>Aca	p.A144T	MEPE_ENST00000540395.1_Missense_Mutation_p.A31T|MEPE_ENST00000361056.3_Missense_Mutation_p.A144T|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.A175T|MEPE_ENST00000497649.2_Missense_Mutation_p.A120T|MEPE_ENST00000560249.1_Missense_Mutation_p.A31T	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	144					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.A144T(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		AGAATATGGCGCAGCTCTCAT	0.428													G|||	1	0.000199681	0	0	5008	,	,		17066	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	67	66	66		430,91,91,91,430	-6	0	4	dbSNP_134	66	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	58,58,58,58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	144/526,31/413,31/413,31/413,144/526	88766450	1,13005	2203	4300	6503	88985474	SO:0001583	missense	56955			AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.430G>A	4.37:g.88766450G>A	ENSP00000416984:p.Ala144Thr		88985474	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	8.965	0.971637	0.18736	0.0	1.16E-4	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.53423	4.37;0.63;0.62;0.66;4.37	4.84	-6.02	0.02192	.	1.188580	0.06056	N	0.657516	T	0.23846	0.0577	L	0.33624	1.015	0.09310	N	1	P	0.38711	0.643	B	0.27715	0.082	T	0.14476	-1.0471	10	0.19147	T	0.46	-0.0246	4.3233	0.11027	0.5714:0.1098:0.2076:0.1112	.	144	Q9NQ76	MEPE_HUMAN	T	144;144;175;120;31;144	ENSP00000416984:A144T;ENSP00000378534:A175T;ENSP00000422747:A120T;ENSP00000443491:A31T;ENSP00000354341:A144T	ENSP00000354341:A144T	A	+	1	0	MEPE	88985474	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.239000	0.08965	-1.469000	0.01890	-0.829000	0.03081	GCA		0.428	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			A	88766450	G	A	88766450	3	1	61	1	0	0	0	0	1	0	0	0	9508	1087	38	1	440	1	MEPE	4	88766450	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182539	88766450	102387826	3329	11314										
PKD2	5311	broad.mit.edu	37	chr4	88989195	88989195	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcatttctagtggcgtttCttacgaagagtttcaagtgt	10	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:88989195C>A	ENST00000508588.1	+	8	1153	c.758C>A	c.(757-759)tCt>tAt	p.S253Y	PKD2_ENST00000237596.2_Missense_Mutation_p.S835Y|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.S253Y			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.S835Y(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		AGTGGCGTTTCTTACGAAGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	4											131	119	123					4																	88989195		2203	4300	6503	89208219	SO:0001583	missense	5311			U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"Voltage-gated ion channels / Transient receptor potential cation channels", "EF-hand domain containing"	9009	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 2"	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.758C>A	4.37:g.88989195C>A	ENSP00000427131:p.Ser253Tyr		89208219	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	C	17.01	3.279986	0.59758	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.92965	-0.38;-3.14;-3.14	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.96106	0.8731	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.96129	0.9091	10	0.87932	D	0	-15.9737	19.7939	0.96471	0.0:1.0:0.0:0.0	.	835	Q13563	PKD2_HUMAN	Y	835;253;253	ENSP00000237596:S835Y;ENSP00000427131:S253Y;ENSP00000425289:S253Y	ENSP00000237596:S835Y	S	+	2	0	PKD2	89208219	1.000000	0.71417	0.935000	0.37517	0.126000	0.20510	7.207000	0.77899	2.668000	0.90789	0.563000	0.77884	TCT		0.473	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		A	88989195	C	A	88989195	3	1	61	1	0	0	0	0	1	0	0	0	11997	913	32	2	2554	2	PKD2	4	88989195	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222745	88989195	102165081	3330	11315										
ABCG2	9429	broad.mit.edu	37	chr4	89042908	89042908	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatactagtcctttttctttCtcctccagacacaccacgga	4	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89042908C>A	ENST00000237612.3	-	6	1113	c.568G>T	c.(568-570)Gaa>Taa	p.E190*	ABCG2_ENST00000515655.1_Nonsense_Mutation_p.E190*	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	190	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.E190*(1)|p.E190K(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CTTTTTCTTTCTCCTCCAGAC	0.398																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|central_nervous_system(1)	4											153	147	149					4																	89042908		2203	4300	6503	89261932	SO:0001587	stop_gained	9429			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.568G>T	4.37:g.89042908C>A	ENSP00000237612:p.Glu190*		89261932	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Nonsense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	C	41	8.823638	0.98968	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-24.3157	19.1249	0.93378	0.0:1.0:0.0:0.0	.	.	.	.	X	190	.	ENSP00000237612:E190X	E	-	1	0	ABCG2	89261932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.782000	0.68973	2.618000	0.88619	0.655000	0.94253	GAA		0.398	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		A	89042908	C	A	89042908	4	1	61	1	0	0	0	0	0	1	0	0	69	922	32	2	1443	2	ABCG2	4	89042908	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53713	89042908	102111368	3331	11316										
ABCG2	9429	broad.mit.edu	37	chr4	89053728	89053728	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatactctcttatactcacGaagatttgcctccacctgtg	5	12	2	1	rs200415908		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89053728G>A	ENST00000237612.3	-	3	808	c.263C>T	c.(262-264)tCg>tTg	p.S88L	ABCG2_ENST00000515655.1_Splice_Site_p.S88L	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	88	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.S88L(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	TTATACTCACGAAGATTTGCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	LEU/SER	0,4406		0,0,2203	134	131	132		263	4.6	1	4		132	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice	ABCG2	NM_004827.2	145	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	88/656	89053728	3,13003	2203	4300	6503	89272752	SO:0001630	splice_region_variant	9429			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.263+1C>T	4.37:g.89053728G>A			89272752	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514890	0.64634	0.0	3.49E-4	ENSG00000118777	ENST00000515655;ENST00000237612;ENST00000505480;ENST00000503830	T;T;D;D	0.91945	0.94;0.94;-2.94;-2.94	5.41	4.57	0.56435	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.89022	0.6597	L	0.60455	1.87	0.80722	D	1	B;B	0.32101	0.356;0.102	B;B	0.29598	0.104;0.064	D	0.86136	0.1578	9	.	.	.	5.1723	13.0487	0.58942	0.0787:0.0:0.9213:0.0	.	88;88	Q9UNQ0-2;Q9UNQ0	.;ABCG2_HUMAN	L	88;88;126;106	ENSP00000426917:S88L;ENSP00000237612:S88L;ENSP00000426916:S126L;ENSP00000426934:S106L	.	S	-	2	0	ABCG2	89272752	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	7.178000	0.77657	1.279000	0.44446	0.655000	0.94253	TCG		0.388	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	Missense_Mutation	A	89053728	G	A	89053728	5	1	61	1	0	0	0	0	0	0	1	0	69	1072	37	1	1760	1	ABCG2	4	89053728	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10820	89053728	102100548	3332	11317										
HERC6	55008	broad.mit.edu	37	chr4	89334267	89334267	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatctgctcagagctctTccatgccattctccacacca	6	15	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89334267T>C	ENST00000264346.7	+	12	1466	c.1407T>C	c.(1405-1407)ctT>ctC	p.L469L	HERC6_ENST00000380265.5_Silent_p.L469L	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	469					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L469P(1)|p.L469L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		TCAGAGCTCTTCCATGCCATT	0.448																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	4											247	240	242					4																	89334267		1959	4176	6135	89553290	SO:0001819	synonymous_variant	55008			AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1407T>C	4.37:g.89334267T>C			89553290	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Silent	SNP	ENST00000264346.7	37	CCDS47098.1																																																																																				0.448	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			C	89334267	T	C	89334267	2	2	61	1	0	0	0	0	0	0	0	1	7083	1770	62	4		4	HERC6	4	89334267	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	280539	89334267	101820009	3333	11318										
HERC5	51191	broad.mit.edu	37	chr4	89400527	89400527	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtattgggcaactctgcaaGaatccactttcagcaaactg	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89400527G>T	ENST00000264350.3	+	13	1759	c.1606G>T	c.(1606-1608)Gaa>Taa	p.E536*	HERC5_ENST00000508159.1_Nonsense_Mutation_p.E174*	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	536					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.E536*(1)		NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		AACTCTGCAAGAATCCACTTT	0.368																																					Esophageal Squamous(39;887 1012 34045 50514)											1	Substitution - Nonsense(1)	large_intestine(1)	4											100	101	101					4																	89400527		2203	4300	6503	89619550	SO:0001587	stop_gained	51191			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1606G>T	4.37:g.89400527G>T	ENSP00000264350:p.Glu536*		89619550	B2RTQ1|Q69G20	Nonsense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	G	37	6.067172	0.97251	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	.	.	.	4.82	3.05	0.35203	.	0.621864	0.14545	N	0.313007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	7.4493	0.27229	0.2017:0.0:0.7983:0.0	.	.	.	.	X	536;174	.	ENSP00000264350:E536X	E	+	1	0	HERC5	89619550	0.653000	0.27358	0.103000	0.21229	0.548000	0.35241	1.217000	0.32455	1.264000	0.44198	0.585000	0.79938	GAA		0.368	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		T	89400527	G	T	89400527	4	4	61	1	0	0	0	0	0	1	0	0	7082	943	33	2	1656	2	HERC5	4	89400527	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66260	89400527	101753749	3334	11319										
HERC5	51191	broad.mit.edu	37	chr4	89407319	89407319	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttccaagtagacgaactCttgcaccgtctcaatttttt	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89407319C>A	ENST00000264350.3	+	14	1944	c.1791C>A	c.(1789-1791)ctC>ctA	p.L597L	HERC5_ENST00000508159.1_Silent_p.L235L	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	597					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.L597L(1)		NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		TAGACGAACTCTTGCACCGTC	0.328																																					Esophageal Squamous(39;887 1012 34045 50514)											1	Substitution - coding silent(1)	large_intestine(1)	4											135	137	136					4																	89407319		2203	4300	6503	89626342	SO:0001819	synonymous_variant	51191			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1791C>A	4.37:g.89407319C>A			89626342	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																				0.328	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		A	89407319	C	A	89407319	2	1	61	1	0	0	0	0	0	0	0	1	7082	900	32	2		2	HERC5	4	89407319	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6792	89407319	101746957	3335	11320										
HERC5	51191	broad.mit.edu	37	chr4	89408265	89408265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtcatattcagtcactttCcatttatctttaataatctg	4	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89408265C>T	ENST00000264350.3	+	15	2050	c.1897C>T	c.(1897-1899)Cca>Tca	p.P633S	HERC5_ENST00000508159.1_Missense_Mutation_p.P271S	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	633					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.P633S(1)		NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		CAGTCACTTTCCATTTATCTT	0.308																																					Esophageal Squamous(39;887 1012 34045 50514)											1	Substitution - Missense(1)	large_intestine(1)	4											96	96	96					4																	89408265		2202	4299	6501	89627288	SO:0001583	missense	51191			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1897C>T	4.37:g.89408265C>T	ENSP00000264350:p.Pro633Ser		89627288	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.426906	0.25726	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	T;T	0.77229	-1.08;-1.08	4.33	3.44	0.39384	.	0.100279	0.41294	N	0.000903	T	0.74612	0.3739	M	0.73962	2.25	0.26300	N	0.977999	B	0.21147	0.052	B	0.22601	0.04	T	0.67031	-0.5773	10	0.45353	T	0.12	.	9.2924	0.37795	0.0:0.8843:0.0:0.1157	.	633	Q9UII4	HERC5_HUMAN	S	633;271	ENSP00000264350:P633S;ENSP00000424129:P271S	ENSP00000264350:P633S	P	+	1	0	HERC5	89627288	1.000000	0.71417	1.000000	0.80357	0.232000	0.25224	2.088000	0.41663	1.335000	0.45486	0.591000	0.81541	CCA		0.308	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		T	89408265	C	T	89408265	3	4	61	1	0	0	0	0	1	0	0	0	7082	855	30	3	1955	3	HERC5	4	89408265	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	946	89408265	101746011	3336	11321										
HERC3	8916	broad.mit.edu	37	chr4	89575195	89575195	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttaatttattctagatCgagaatctccatgccatgta	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89575195C>T	ENST00000402738.1	+	7	927	c.688C>T	c.(688-690)Cga>Tga	p.R230*	HERC3_ENST00000407637.1_Nonsense_Mutation_p.R230*|HERC3_ENST00000264345.3_Nonsense_Mutation_p.R230*	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	230					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R230*(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TATTCTAGATCGAGAATCTCC	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											79	81	80					4																	89575195		2203	4300	6503	89794218	SO:0001587	stop_gained	8916			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.688C>T	4.37:g.89575195C>T	ENSP00000385684:p.Arg230*		89794218	A8K1S5|Q8IXX3	Nonsense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	C	38	6.802814	0.97849	.	.	ENSG00000138641	ENST00000402738;ENST00000407637;ENST00000264345	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7502	0.91810	0.0:1.0:0.0:0.0	.	.	.	.	X	230	.	ENSP00000264345:R230X	R	+	1	2	HERC3	89794218	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	3.436000	0.52856	2.664000	0.90586	0.655000	0.94253	CGA		0.368	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		T	89575195	C	T	89575195	4	4	61	1	0	0	0	0	0	1	0	0	7080	876	31	1	706	1	HERC3	4	89575195	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166930	89575195	101579081	3337	11322										
HERC3	8916	broad.mit.edu	37	chr4	89591036	89591036	+	Frame_Shift_Del	DEL	G	G	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtggtctcaggtatgcccGaaatatttcatgaagctggt					rs375113325		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89591036delG	ENST00000402738.1	+	15	1898	c.1659delG	c.(1657-1659)ccgfs	p.P553fs	HERC3_ENST00000543130.1_5'UTR|HERC3_ENST00000264345.3_Frame_Shift_Del_p.P553fs	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	553					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.K554fs*4(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		AGGTATGCCCGAAATATTTCA	0.363																																																1	Deletion - Frameshift(1)	large_intestine(1)	4											95	97	96					4																	89591036		2203	4300	6503	89810059	SO:0001589	frameshift_variant	8916			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1659delG	4.37:g.89591036delG	ENSP00000385684:p.Pro553fs		89810059	A8K1S5|Q8IXX3	Frame_Shift_Del	DEL	ENST00000402738.1	37	CCDS34028.1																																																																																				0.363	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		-	89591036	G	-	89591036	7	5	61	1	0	1	0	1	0	0	0	0	7080	1045	37	0	1709	0	HERC3	4	89591036	Frame_Shift_Del	DEL	G	TCGA-AG-A002-01A-01W-A00K-09	15841	89591036	101563240	3338	11323										
FAM13A	10144	broad.mit.edu	37	chr4	89689173	89689173	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatcatcaggtccagttCtctcatgagatcgtgtggaa	9	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89689173C>A	ENST00000264344.5	-	12	1703	c.1496G>T	c.(1495-1497)aGa>aTa	p.R499I	FAM13A_ENST00000508369.1_Missense_Mutation_p.R173I|FAM13A_ENST00000511976.1_Missense_Mutation_p.R85I|FAM13A_ENST00000513837.1_Missense_Mutation_p.R145I|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000503556.1_Missense_Mutation_p.R159I|FAM13A_ENST00000395002.2_Missense_Mutation_p.R173I	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	499					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R499I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						AGGTCCAGTTCTCTCATGAGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	94	96					4																	89689173		2203	4300	6503	89908196	SO:0001583	missense	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1496G>T	4.37:g.89689173C>A	ENSP00000264344:p.Arg499Ile		89908196	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956257	0.34565	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.60424	0.19;0.19;1.39;1.38;0.19;1.39	5.13	3.37	0.38596	.	0.492153	0.23789	N	0.044545	T	0.47875	0.1469	L	0.49350	1.555	0.21499	N	0.99967	B;B;B;B;B;B	0.18741	0.029;0.019;0.03;0.029;0.029;0.029	B;B;B;B;B;B	0.15052	0.012;0.011;0.005;0.012;0.012;0.012	T	0.36578	-0.9742	10	0.34782	T	0.22	.	8.9201	0.35605	0.0:0.7662:0.1542:0.0796	.	145;85;499;173;159;173	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	I	173;499;159;85;173;145	ENSP00000378450:R173I;ENSP00000264344:R499I;ENSP00000427189:R159I;ENSP00000421914:R85I;ENSP00000421562:R173I;ENSP00000423252:R145I	ENSP00000264344:R499I	R	-	2	0	FAM13A	89908196	0.550000	0.26489	0.002000	0.10522	0.006000	0.05464	1.125000	0.31332	0.718000	0.32166	-0.145000	0.13849	AGA		0.373	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			A	89689173	C	A	89689173	3	1	61	1	0	0	0	0	1	0	0	0	5468	913	32	2	1627	2	FAM13A	4	89689173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98137	89689173	101465103	3339	11324										
FAM13A	10144	broad.mit.edu	37	chr4	89772171	89772171	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaagaaaacatgccaacCtgggtaccaacttggcacta	8	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89772171C>A	ENST00000264344.5	-	7	1214	c.1007G>T	c.(1006-1008)aGt>aTt	p.S336I	FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000502459.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	336					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.S336I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						ACATGCCAACCTGGGTACCAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											161	159	160					4																	89772171		2203	4300	6503	89991194	SO:0001630	splice_region_variant	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1007+1G>T	4.37:g.89772171C>A			89991194	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.715251	0.30413	.	.	ENSG00000138640	ENST00000264344	T	0.65916	-0.18	4.33	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.50257	0.1605	L	0.50333	1.59	0.80722	D	1	B	0.27997	0.197	B	0.21708	0.036	T	0.45205	-0.9277	9	.	.	.	.	8.7696	0.34724	0.0:0.8961:0.0:0.1039	.	336	O94988	FA13A_HUMAN	I	336	ENSP00000264344:S336I	.	S	-	2	0	FAM13A	89991194	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	2.051000	0.41307	1.384000	0.46424	0.650000	0.86243	AGT		0.443	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		Missense_Mutation	A	89772171	C	A	89772171	5	1	61	1	0	0	0	0	0	0	1	0	5468	695	24	2	2169	2	FAM13A	4	89772171	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82998	89772171	101382105	3340	11325										
FAM13A	10144	broad.mit.edu	37	chr4	89827559	89827559	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggtggttttggcatgtCtctttctaagcctcttgtta	11	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:89827559C>A	ENST00000264344.5	-	6	1021	c.814G>T	c.(814-816)Gac>Tac	p.D272Y	FAM13A_ENST00000511976.1_Missense_Mutation_p.D63Y|FAM13A_ENST00000502459.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	272					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.D272Y(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TTTGGCATGTCTCTTTCTAAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											329	346	340					4																	89827559		2203	4300	6503	90046582	SO:0001583	missense	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.814G>T	4.37:g.89827559C>A	ENSP00000264344:p.Asp272Tyr		90046582	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797973	0.31777	.	.	ENSG00000138640	ENST00000264344;ENST00000511976	T;T	0.32753	2.19;1.44	4.42	3.58	0.41010	.	0.527164	0.17286	N	0.179825	T	0.19167	0.0460	N	0.08118	0	0.33780	D	0.624114	P;P	0.48407	0.693;0.91	P;P	0.45946	0.478;0.498	T	0.24225	-1.0166	10	0.59425	D	0.04	.	8.6759	0.34179	0.0:0.8978:0.0:0.1022	.	63;272	E9PGM7;O94988	.;FA13A_HUMAN	Y	272;63	ENSP00000264344:D272Y;ENSP00000421914:D63Y	ENSP00000264344:D272Y	D	-	1	0	FAM13A	90046582	0.990000	0.36364	0.209000	0.23619	0.852000	0.48524	1.766000	0.38491	1.451000	0.47736	0.655000	0.94253	GAC		0.358	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			A	89827559	C	A	89827559	3	1	61	1	0	0	0	0	1	0	0	0	5468	913	32	2	2366	2	FAM13A	4	89827559	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55388	89827559	101326717	3341	11326										
GPRIN3	285513	broad.mit.edu	37	chr4	90169765	90169765	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgttttgtggccgtttgtCgttttctctgcaaactcaga	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:90169765C>T	ENST00000609438.1	-	2	2015	c.1497G>A	c.(1495-1497)acG>acA	p.T499T	GPRIN3_ENST00000333209.4_Silent_p.T499T	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	499								p.T499T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		GGCCGTTTGTCGTTTTCTCTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	4											96	104	101					4																	90169765		2203	4300	6503	90388788	SO:0001819	synonymous_variant	285513			AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1497G>A	4.37:g.90169765C>T			90388788	Q8IVE4	Silent	SNP	ENST00000609438.1	37	CCDS34030.1																																																																																				0.448	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		T	90169765	C	T	90169765	2	4	61	1	0	0	0	0	0	0	0	1	6752	871	31	1		1	GPRIN3	4	90169765	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	342206	90169765	100984511	3342	11327										
MMRN1	22915	broad.mit.edu	37	chr4	90816604	90816604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctaaacacagttggagGcactggaggcattggaggcg	14	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:90816604G>A	ENST00000394980.1	+	2	801	c.482G>A	c.(481-483)gGc>gAc	p.G161D	MMRN1_ENST00000264790.2_Missense_Mutation_p.G161D|MMRN1_ENST00000394981.1_Missense_Mutation_p.G127D			Q13201	MMRN1_HUMAN	multimerin 1	161					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.G161D(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ACAGTtggaggcactggaggc	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	4											61	63	62					4																	90816604		2203	4300	6503	91035627	SO:0001583	missense	22915			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.482G>A	4.37:g.90816604G>A	ENSP00000378431:p.Gly161Asp		91035627	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.244700	0.39697	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981	T;T;T	0.73469	-0.04;-0.04;-0.75	2.8	1.93	0.25924	.	.	.	.	.	T	0.68449	0.3002	N	0.08118	0	0.09310	N	1	D;D	0.69078	0.997;0.994	D;D	0.70487	0.969;0.931	T	0.56792	-0.7920	9	0.45353	T	0.12	.	7.0407	0.25019	0.0:0.0:0.7303:0.2697	.	127;161	Q13201-2;Q13201	.;MMRN1_HUMAN	D	161;161;127	ENSP00000378431:G161D;ENSP00000264790:G161D;ENSP00000378432:G127D	ENSP00000264790:G161D	G	+	2	0	MMRN1	91035627	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.174000	0.16743	0.732000	0.32470	0.563000	0.77884	GGC		0.512	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90816604	G	A	90816604	3	1	61	1	0	0	0	0	1	0	0	0	9700	1203	42	3	484	3	MMRN1	4	90816604	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	646839	90816604	100337672	3343	11328										
MMRN1	22915	broad.mit.edu	37	chr4	90849027	90849027	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaagattgacaatatttCtttgactgtgaatgatgtaa	9	3	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:90849027C>T	ENST00000394980.1	+	6	1356	c.1037C>T	c.(1036-1038)tCt>tTt	p.S346F	MMRN1_ENST00000264790.2_Missense_Mutation_p.S346F|MMRN1_ENST00000508372.1_Missense_Mutation_p.S88F|MMRN1_ENST00000394981.1_Missense_Mutation_p.S312F			Q13201	MMRN1_HUMAN	multimerin 1	346					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.S346F(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GACAATATTTCTTTGACTGTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	117	113					4																	90849027		2203	4300	6503	91068050	SO:0001583	missense	22915			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1037C>T	4.37:g.90849027C>T	ENSP00000378431:p.Ser346Phe		91068050	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.226023	0.39300	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981;ENST00000508372	T;T;T;T	0.72835	0.0;0.0;-0.69;-0.36	5.11	5.11	0.69529	.	0.167236	0.41823	D	0.000819	D	0.82300	0.5007	L	0.58101	1.795	0.29819	N	0.830974	D;P	0.76494	0.999;0.926	D;B	0.73380	0.98;0.33	T	0.79063	-0.1957	10	0.66056	D	0.02	.	19.4148	0.94690	0.0:1.0:0.0:0.0	.	312;346	Q13201-2;Q13201	.;MMRN1_HUMAN	F	346;346;312;88	ENSP00000378431:S346F;ENSP00000264790:S346F;ENSP00000378432:S312F;ENSP00000426461:S88F	ENSP00000264790:S346F	S	+	2	0	MMRN1	91068050	1.000000	0.71417	1.000000	0.80357	0.181000	0.23173	3.462000	0.53042	2.747000	0.94245	0.585000	0.79938	TCT		0.358	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		T	90849027	C	T	90849027	3	4	61	1	0	0	0	0	1	0	0	0	9700	913	32	3	1055	3	MMRN1	4	90849027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32423	90849027	100305249	3344	11329										
MMRN1	22915	broad.mit.edu	37	chr4	90857043	90857043	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgactattataaataatGctattgatttcattcaagat	4	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:90857043G>T	ENST00000394980.1	+	7	2531	c.2212G>T	c.(2212-2214)Gct>Tct	p.A738S	MMRN1_ENST00000264790.2_Missense_Mutation_p.A738S|MMRN1_ENST00000508372.1_Missense_Mutation_p.A480S|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	738					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.A738S(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TATAAATAATGCTATTGATTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	61	60					4																	90857043		2203	4298	6501	91076066	SO:0001583	missense	22915			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2212G>T	4.37:g.90857043G>T	ENSP00000378431:p.Ala738Ser		91076066	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.472575	0.63737	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.76968	-0.82;-0.82;-1.06	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	D	0.87148	0.6105	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84729	0.0744	10	0.34782	T	0.22	.	19.6319	0.95708	0.0:0.0:1.0:0.0	.	738	Q13201	MMRN1_HUMAN	S	738;738;480	ENSP00000378431:A738S;ENSP00000264790:A738S;ENSP00000426461:A480S	ENSP00000264790:A738S	A	+	1	0	MMRN1	91076066	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	6.326000	0.72905	2.805000	0.96524	0.655000	0.94253	GCT		0.338	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		T	90857043	G	T	90857043	3	4	61	1	0	0	0	0	1	0	0	0	9700	1319	46	2	2234	2	MMRN1	4	90857043	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8016	90857043	100297233	3345	11330										
MMRN1	22915	broad.mit.edu	37	chr4	90857560	90857560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggcgttggaagcaaaatCtatccatctttcaattaact	6	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:90857560C>A	ENST00000394980.1	+	7	3048	c.2729C>A	c.(2728-2730)tCt>tAt	p.S910Y	MMRN1_ENST00000264790.2_Missense_Mutation_p.S910Y|MMRN1_ENST00000508372.1_Missense_Mutation_p.S652Y|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	910					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.S910Y(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GAAGCAAAATCTATCCATCTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	73	72					4																	90857560		2203	4300	6503	91076583	SO:0001583	missense	22915			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2729C>A	4.37:g.90857560C>A	ENSP00000378431:p.Ser910Tyr		91076583	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236412	0.58886	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.73789	-0.5;-0.5;-0.78	5.3	5.3	0.74995	.	0.078137	0.56097	D	0.000033	D	0.85745	0.5768	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.86160	0.1593	10	0.72032	D	0.01	.	19.852	0.96744	0.0:1.0:0.0:0.0	.	910	Q13201	MMRN1_HUMAN	Y	910;910;652	ENSP00000378431:S910Y;ENSP00000264790:S910Y;ENSP00000426461:S652Y	ENSP00000264790:S910Y	S	+	2	0	MMRN1	91076583	0.998000	0.40836	0.995000	0.50966	0.635000	0.38103	5.012000	0.64017	2.861000	0.98227	0.655000	0.94253	TCT		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90857560	C	A	90857560	3	1	61	1	0	0	0	0	1	0	0	0	9700	913	32	2	2751	2	MMRN1	4	90857560	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	517	90857560	100296716	3346	11331										
FAM190A	401145	broad.mit.edu	37	chr4	91229835	91229835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacaagatctttgacagagGattttgaaagggaaaaagag	11	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:91229835G>A	ENST00000509176.1	+	2	688	c.400G>A	c.(400-402)Gat>Aat	p.D134N	CCSER1_ENST00000432775.2_Missense_Mutation_p.D134N|CCSER1_ENST00000333691.8_Missense_Mutation_p.D134N	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	134								p.D134N(1)									TTTGACAGAGGATTTTGAAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											53	53	53					4																	91229835		1825	4079	5904	91448858	SO:0001583	missense	401145				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.400G>A	4.37:g.91229835G>A	ENSP00000425040:p.Asp134Asn		91448858	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207897	0.79240	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.58940	0.78;0.3;0.78	5.18	4.34	0.51931	.	0.107097	0.64402	N	0.000012	T	0.69251	0.3090	L	0.46157	1.445	0.41149	D	0.986019	D;B;B	0.89917	1.0;0.197;0.36	D;B;B	0.77004	0.989;0.09;0.181	T	0.73202	-0.4057	10	0.72032	D	0.01	-22.0979	14.4529	0.67397	0.0717:0.0:0.9283:0.0	.	134;134;134	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	N	134	ENSP00000425040:D134N;ENSP00000389283:D134N;ENSP00000329482:D134N	ENSP00000329482:D134N	D	+	1	0	FAM190A	91448858	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.190000	0.77755	1.508000	0.48769	0.655000	0.94253	GAT		0.363	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		A	91229835	G	A	91229835	3	1	61	1	0	0	0	0	1	0	0	0	5537	1174	41	3	402	3	FAM190A	4	91229835	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	372275	91229835	99924441	3347	11332										
TMSL3	401145	broad.mit.edu	37	chr4	91760123	91760123	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggatttttctcttgcgtCtctgtcttcttcagtttcgg	9	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:91760123C>T	ENST00000509176.1	+	8	2382				CCSER1_ENST00000333691.8_Intron	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1									p.E22E(1)									TCTCTTGCGTCTCTGTCTTCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	4											122	132	128					4																	91760123		1510	2708	4218	91979146	SO:0001627	intron_variant	7117				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2094+23127C>T	4.37:g.91760123C>T			91979146	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																				0.507	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	91760123	C	T	91760123	1	4	61	0	1	0	0	0	0	0	0	0	16298	912	32	3		3	TMSL3	4	91760123	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	530288	91760123	99394153	3348	11333										
GRID2	2895	broad.mit.edu	37	chr4	93511326	93511326	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaggatgatgaggtatttCgcactgcggttggtgacctt	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:93511326C>T	ENST00000282020.4	+	2	391	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C	GRID2_ENST00000510992.1_Missense_Mutation_p.R45C|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	45					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.R45C(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TGAGGTATTTCGCACTGCGGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											121	116	118					4																	93511326		2203	4300	6503	93730349	SO:0001583	missense	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.133C>T	4.37:g.93511326C>T	ENSP00000282020:p.Arg45Cys		93730349	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488961	0.84962	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	D;D	0.87029	-1.79;-2.2	5.83	5.83	0.93111	Extracellular ligand-binding receptor (1);	0.389572	0.22276	N	0.062185	D	0.89760	0.6808	N	0.22421	0.69	0.47621	D	0.999476	D;D	0.89917	0.999;1.0	P;D	0.71184	0.897;0.972	D	0.90821	0.4709	10	0.87932	D	0	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	45;45	E9PH24;O43424	.;GRID2_HUMAN	C	45	ENSP00000282020:R45C;ENSP00000421257:R45C	ENSP00000282020:R45C	R	+	1	0	GRID2	93730349	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.999000	0.70665	2.757000	0.94681	0.563000	0.77884	CGC		0.383	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	93511326	C	T	93511326	3	4	61	1	0	0	0	0	1	0	0	0	6793	884	31	1	139	1	GRID2	4	93511326	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1751203	93511326	97642950	3349	11334										
GRID2	2895	broad.mit.edu	37	chr4	94006399	94006399	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcacagagtatgcctggcaGaaattcattatattctatga	8	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:94006399G>A	ENST00000282020.4	+	3	756	c.498G>A	c.(496-498)caG>caA	p.Q166Q	GRID2_ENST00000510992.1_Intron|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	166					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.Q166Q(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		ATGCCTGGCAGAAATTCATTA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4											103	105	104					4																	94006399		2203	4300	6503	94225422	SO:0001819	synonymous_variant	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.498G>A	4.37:g.94006399G>A			94225422	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	37	CCDS3637.1																																																																																				0.378	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			A	94006399	G	A	94006399	2	1	61	1	0	0	0	0	0	0	0	1	6793	933	33	3		3	GRID2	4	94006399	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	495073	94006399	97147877	3350	11335										
GRID2	2895	broad.mit.edu	37	chr4	94547443	94547443	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatatggaaattatgctttCgtatgggatgcagctgtatt	10	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:94547443C>T	ENST00000282020.4	+	14	2475	c.2217C>T	c.(2215-2217)ttC>ttT	p.F739F	GRID2_ENST00000510992.1_Silent_p.F644F	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	739					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.F739F(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		ATTATGCTTTCGTATGGGATG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	4											134	124	128					4																	94547443		2203	4300	6503	94766466	SO:0001819	synonymous_variant	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2217C>T	4.37:g.94547443C>T			94766466	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	37	CCDS3637.1																																																																																				0.343	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94547443	C	T	94547443	2	4	61	1	0	0	0	0	0	0	0	1	6793	883	31	1		1	GRID2	4	94547443	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541044	94547443	96606833	3351	11336										
SMARCAD1	56916	broad.mit.edu	37	chr4	95204387	95204387	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatgttgttatacttcacGatattgactgtaatccttat	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:95204387G>T	ENST00000354268.4	+	22	2915	c.2842G>T	c.(2842-2844)Gat>Tat	p.D948Y	SMARCAD1_ENST00000509418.1_Missense_Mutation_p.D518Y|SMARCAD1_ENST00000457823.2_Missense_Mutation_p.D950Y			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	948	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.D948Y(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TATACTTCACGATATTGACTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											120	119	119					4																	95204387		2203	4300	6503	95423410	SO:0001583	missense	56916			AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2842G>T	4.37:g.95204387G>T	ENSP00000346217:p.Asp948Tyr		95423410	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953517	0.73902	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58	5.48	4.63	0.57726	Helicase, C-terminal (3);	0.000000	0.51477	D	0.000092	D	0.95683	0.8596	H	0.99842	4.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98021	1.0371	10	0.87932	D	0	-25.2621	16.3066	0.82849	0.0:0.1325:0.8675:0.0	.	948;950	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	Y	950;950;948;518	ENSP00000351947:D950Y;ENSP00000415576:D950Y;ENSP00000346217:D948Y;ENSP00000423286:D518Y	ENSP00000346217:D948Y	D	+	1	0	SMARCAD1	95423410	1.000000	0.71417	0.820000	0.32676	0.838000	0.47535	9.827000	0.99397	1.302000	0.44855	0.591000	0.81541	GAT		0.328	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		T	95204387	G	T	95204387	3	4	61	1	0	0	0	0	1	0	0	0	14809	1058	37	2	2930	2	SMARCAD1	4	95204387	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	656944	95204387	95949889	3352	11337										
PDLIM5	10611	broad.mit.edu	37	chr4	95496996	95496996	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccgtcactcctcccctgtTcgctgcatctggactgcatg	9	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:95496996T>C	ENST00000317968.4	+	5	657	c.521T>C	c.(520-522)tTc>tCc	p.F174S	PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.F52S	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	174					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)	p.F174S(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		CCTCCCCTGTTCGCTGCATCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	4											202	158	173					4																	95496996		2203	4300	6503	95716019	SO:0001583	missense	10611			AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.521T>C	4.37:g.95496996T>C	ENSP00000321746:p.Phe174Ser		95716019	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	T	9.779	1.174690	0.21704	.	.	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.57436	0.81;0.4	4.71	2.29	0.28610	.	0.491479	0.21433	N	0.074613	T	0.40040	0.1101	L	0.51422	1.61	0.21325	N	0.999728	B	0.06786	0.001	B	0.08055	0.003	T	0.23226	-1.0194	10	0.22109	T	0.4	.	5.9816	0.19411	0.0:0.1505:0.1383:0.7112	.	174	Q96HC4	PDLI5_HUMAN	S	174;52	ENSP00000321746:F174S;ENSP00000442187:F52S	ENSP00000321746:F174S	F	+	2	0	PDLIM5	95716019	0.608000	0.26966	0.124000	0.21820	0.872000	0.50106	0.978000	0.29488	0.287000	0.22375	0.533000	0.62120	TTC		0.572	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			C	95496996	T	C	95496996	3	2	61	1	0	0	0	0	1	0	0	0	11714	1783	62	4	535	4	PDLIM5	4	95496996	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	292609	95496996	95657280	3353	11338										
PDHA2	5161	broad.mit.edu	37	chr4	96761853	96761853	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgtaaatataaaggaaaCgatgagatctgtttgacttt	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:96761853C>T	ENST00000295266.4	+	1	615	c.552C>T	c.(550-552)aaC>aaT	p.N184N		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	184					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.N184N(3)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		ATAAAGGAAACGATGAGATCT	0.483																																																3	Substitution - coding silent(3)	prostate(1)|large_intestine(1)|lung(1)	4											61	66	64					4																	96761853		2203	4300	6503	96980876	SO:0001819	synonymous_variant	5161				CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.552C>T	4.37:g.96761853C>T			96980876	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Silent	SNP	ENST00000295266.4	37	CCDS3644.1																																																																																				0.483	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			T	96761853	C	T	96761853	2	4	61	1	0	0	0	0	0	0	0	1	11696	535	19	1		1	PDHA2	4	96761853	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1264857	96761853	94392423	3354	11339										
C4orf37	285555	broad.mit.edu	37	chr4	98761993	98761993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggcatgttttcttttagCcactaaactacgaggtggca	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:98761993C>T	ENST00000295268.3	-	9	1224	c.1135G>A	c.(1135-1137)Gct>Act	p.A379T	STPG2_ENST00000506482.1_Intron	NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	379								p.A379T(1)									TTTCTTTTAGCCACTAAACTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											102	107	105					4																	98761993		2203	4299	6502	98981016	SO:0001583	missense	285555			BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.1135G>A	4.37:g.98761993C>T	ENSP00000295268:p.Ala379Thr		98981016		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096110	0.76870	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.48836	0.8;2.65	5.47	5.47	0.80525	.	0.239038	0.34484	N	0.003926	T	0.67618	0.2912	M	0.66939	2.045	0.33994	D	0.649461	D	0.89917	1.0	D	0.78314	0.991	T	0.74121	-0.3767	10	0.42905	T	0.14	-9.5624	18.0973	0.89494	0.0:1.0:0.0:0.0	.	379	Q8N412	CD037_HUMAN	T	93;379	ENSP00000428346:A93T;ENSP00000295268:A379T	ENSP00000295268:A379T	A	-	1	0	C4orf37	98981016	0.987000	0.35691	0.582000	0.28627	0.936000	0.57629	4.222000	0.58580	2.578000	0.87016	0.585000	0.79938	GCT		0.408	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		T	98761993	C	T	98761993	3	4	61	1	0	0	0	0	1	0	0	0	2273	739	26	3	256	3	C4orf37	4	98761993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2000140	98761993	92392283	3355	11340										
RAP1GDS1	5910	broad.mit.edu	37	chr4	99341286	99341286	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacattaagaatgttaataGatgcacaaggtaaaagaaat	8	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:99341286G>T	ENST00000408927.3	+	11	1404	c.1291G>T	c.(1291-1293)Gat>Tat	p.D431Y	RAP1GDS1_ENST00000380158.4_Missense_Mutation_p.D383Y|RAP1GDS1_ENST00000408900.3_Missense_Mutation_p.D382Y|RAP1GDS1_ENST00000453712.2_Missense_Mutation_p.D432Y|RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.D432Y|RAP1GDS1_ENST00000264572.7_Missense_Mutation_p.D340Y	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	431					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)	p.D432Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		AATGTTAATAGATGCACAAGG	0.353			T	NUP98	T-ALL																																		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	1	Substitution - Missense(1)	large_intestine(1)	4											71	67	68					4																	99341286		1813	4075	5888	99560309	SO:0001583	missense	5910				CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.1291G>T	4.37:g.99341286G>T	ENSP00000386153:p.Asp431Tyr		99560309	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	ENST00000408927.3	37	CCDS43253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.253624|4.253624	0.80135|0.80135	.|.	.|.	ENSG00000138698|ENSG00000138698	ENST00000380158;ENST00000264572;ENST00000408927;ENST00000453712;ENST00000408900;ENST00000339360|ENST00000509501	T;T;T;T;T;T|.	0.53423|.	2.68;2.68;2.68;0.62;2.68;2.68|.	6.06|6.06	5.22|5.22	0.72569|0.72569	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73621|0.73621	0.3610|0.3610	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.996;0.998;1.0|.	D;D;D;D;D;D|.	0.91635|.	0.999;0.998;0.996;0.953;0.929;0.996|.	T|T	0.74054|0.74054	-0.3788|-0.3788	10|5	0.59425|.	D|.	0.04|.	-14.8147|-14.8147	15.57|15.57	0.76326|0.76326	0.066:0.0:0.934:0.0|0.066:0.0:0.934:0.0	.|.	340;382;383;431;432;432|.	E9PH06;P52306-2;Q499L7;P52306;Q4QQI8;G5E9P9|.	.;.;.;GDS1_HUMAN;.;.|.	Y|I	383;340;431;432;382;432|240	ENSP00000369503:D383Y;ENSP00000264572:D340Y;ENSP00000386153:D431Y;ENSP00000407157:D432Y;ENSP00000386223:D382Y;ENSP00000340454:D432Y|.	ENSP00000264572:D340Y|.	D|R	+|+	1|2	0|0	RAP1GDS1|RAP1GDS1	99560309|99560309	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.433000|9.433000	0.97501|0.97501	1.566000|1.566000	0.49654|0.49654	0.655000|0.655000	0.94253|0.94253	GAT|AGA		0.353	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		T	99341286	G	T	99341286	3	4	61	1	0	0	0	0	1	0	0	0	13076	942	33	2	1336	2	RAP1GDS1	4	99341286	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	579293	99341286	91812990	3356	11341										
ADH4	127	broad.mit.edu	37	chr4	100048367	100048367	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaaaactgaccaccaaaGaatgttccatttatagtacg	5	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100048367G>T	ENST00000265512.7	-	7	1046	c.972C>A	c.(970-972)ttC>ttA	p.F324L	ADH4_ENST00000508393.1_Missense_Mutation_p.F343L|ADH4_ENST00000423445.1_Missense_Mutation_p.F343L|ADH4_ENST00000505590.1_Missense_Mutation_p.F343L|RP11-696N14.1_ENST00000500358.2_RNA	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	324					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)	p.F324L(1)		NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		GACCACCAAAGAATGTTCCAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	69	68					4																	100048367		2203	4300	6503	100267390	SO:0001583	missense	127			M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.972C>A	4.37:g.100048367G>T	ENSP00000265512:p.Phe324Leu		100267390	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	.	.	.	.	.	.	.	.	.	.	G	9.654	1.142413	0.21205	.	.	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.03951	3.75;3.75;3.75;3.75	3.65	1.71	0.24356	Alcohol dehydrogenase, C-terminal (1);	1.827340	0.04039	U	0.302747	T	0.02418	0.0074	N	0.02129	-0.67	0.25967	N	0.982553	B;B	0.26602	0.154;0.0	B;B	0.26770	0.073;0.008	T	0.36962	-0.9726	10	0.87932	D	0	3.0E-4	3.2909	0.06948	0.1069:0.1553:0.5506:0.1871	.	343;324	P08319-2;P08319	.;ADH4_HUMAN	L	343;324;343;343	ENSP00000424630:F343L;ENSP00000265512:F324L;ENSP00000397939:F343L;ENSP00000425416:F343L	ENSP00000265512:F324L	F	-	3	2	ADH4	100267390	0.004000	0.15560	0.471000	0.27229	0.093000	0.18481	-0.185000	0.09684	0.415000	0.25817	0.655000	0.94253	TTC		0.338	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		T	100048367	G	T	100048367	3	4	61	1	0	0	0	0	1	0	0	0	310	933	33	2	182	2	ADH4	4	100048367	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	707081	100048367	91105909	3357	11342										
ADH1B	125	broad.mit.edu	37	chr4	100232766	100232766	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcaggaggtacccctacGatgacgcttgtgccacatgc	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100232766G>A	ENST00000305046.8	-	7	943	c.876C>T	c.(874-876)atC>atT	p.I292I	ADH1B_ENST00000394887.3_Silent_p.I252I			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	292					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)	p.I292I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GTACCCCTACGATGACGCTTG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	4											219	205	210					4																	100232766		2203	4300	6503	100451789	SO:0001819	synonymous_variant	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.876C>T	4.37:g.100232766G>A			100451789	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																				0.488	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		A	100232766	G	A	100232766	2	1	61	1	0	0	0	0	0	0	0	1	308	1048	37	1		1	ADH1B	4	100232766	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184399	100232766	90921510	3358	11343										
ADH1B	125	broad.mit.edu	37	chr4	100234999	100234999	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtgtcaagccgaccgatGacttcaaacgaaaaatccac	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100234999G>T	ENST00000305046.8	-	6	874	c.807C>A	c.(805-807)gtC>gtA	p.V269V	ADH1B_ENST00000394887.3_Silent_p.V229V			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	269					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)	p.V269V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCCGACCGATGACTTCAAACG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	4											213	213	213					4																	100234999		2203	4300	6503	100454022	SO:0001819	synonymous_variant	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.807C>A	4.37:g.100234999G>T			100454022	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																				0.443	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		T	100234999	G	T	100234999	2	4	61	1	0	0	0	0	0	0	0	1	308	1277	45	2		2	ADH1B	4	100234999	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2233	100234999	90919277	3359	11344										
ADH1C	126	broad.mit.edu	37	chr4	100264094	100264094	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctttagcctttgcaaatTtgtccttgttgatgtccaca	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100264094T>G	ENST00000510055.1	-	0	860				ADH1C_ENST00000515683.1_RNA			P00326	ADH1G_HUMAN	alcohol dehydrogenase 1C (class I), gamma polypeptide						ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|zinc ion binding (GO:0008270)								OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	CTTTGCAAATTTGTCCTTGTT	0.483																																																0			4											412	408	409					4																	100264094		2203	4300	6503	100483117			126			M12272		4q23	2010-03-16			ENSG00000248144	ENSG00000248144	1.1.1.1	"Alcohol dehydrogenases"	251	protein-coding gene	gene with protein product		103730		ADH3		3006456	Standard	NM_000669		Approved		uc031sgp.1	P00326	OTTHUMG00000161422		4.37:g.100264094T>G			100483117	Q4PJ18|Q5WRV0|Q6LBW4|Q6NWV0|Q6NZA7	Missense_Mutation	SNP	ENST00000510055.1	37																																																																																					0.483	ADH1C-004	KNOWN	mRNA_end_NF|basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000365189.2	NM_000669		G	100264094	T	G	100264094	1	3	61	0	1	0	0	0	0	0	0	0	309	1841	64	4		4	ADH1C	4	100264094	RNA	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	29095	100264094	90890182	3360	11345										
C4orf17	84103	broad.mit.edu	37	chr4	100434303	100434303	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagccatattatggctaGaaatgtaagctgctttctag	10	7	1	1	rs201368502	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100434303G>T	ENST00000326581.4	+	2	427	c.65G>T	c.(64-66)aGa>aTa	p.R22I	C4orf17_ENST00000514652.1_Missense_Mutation_p.R22I	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	22								p.R22I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		ATTATGGCTAGAAATGTAAGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	4											105	89	94					4																	100434303		2203	4300	6503	100653326	SO:0001583	missense	84103			AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.65G>T	4.37:g.100434303G>T	ENSP00000322582:p.Arg22Ile		100653326	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766335	0.69878	.	.	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.26067	1.78;1.76	4.88	4.88	0.63580	.	0.335152	0.26349	N	0.024897	T	0.44393	0.1291	M	0.64997	1.995	0.35991	D	0.836726	D	0.65815	0.995	D	0.68483	0.958	T	0.45396	-0.9264	10	0.25106	T	0.35	-12.819	13.3896	0.60816	0.0:0.0:1.0:0.0	.	22	Q53FE4	CD017_HUMAN	I	22	ENSP00000322582:R22I;ENSP00000427663:R22I	ENSP00000322582:R22I	R	+	2	0	C4orf17	100653326	0.917000	0.31117	0.114000	0.21550	0.076000	0.17211	3.948000	0.56660	2.518000	0.84900	0.650000	0.86243	AGA		0.468	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149		T	100434303	G	T	100434303	3	4	61	1	0	0	0	0	1	0	0	0	2258	942	33	2	67	2	C4orf17	4	100434303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170209	100434303	90719973	3361	11346										
MTTP	4547	broad.mit.edu	37	chr4	100503084	100503084	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacaactggtctctcattAaataatgaccggctgtacaa	6	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100503084A>G	ENST00000265517.5	+	2	287	c.84A>G	c.(82-84)ttA>ttG	p.L28L	MTTP_ENST00000511045.1_Silent_p.L55L|MTTP_ENST00000422897.2_Silent_p.L28L|MTTP_ENST00000457717.1_Silent_p.L28L			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	28	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.L28L(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GTCTCTCATTAAATAATGACC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	4											135	125	128					4																	100503084		2203	4300	6503	100722107	SO:0001819	synonymous_variant	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.84A>G	4.37:g.100503084A>G			100722107	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																				0.458	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			G	100503084	A	G	100503084	2	3	61	1	0	0	0	0	0	0	0	1	9994	359	13	4		4	MTTP	4	100503084	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	68781	100503084	90651192	3362	11347										
MTTP	4547	broad.mit.edu	37	chr4	100518334	100518334	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcacctcaggactgcgaaGaaagaagagatccttcaaat	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100518334G>T	ENST00000265517.5	+	8	1223	c.1020G>T	c.(1018-1020)aaG>aaT	p.K340N	MTTP_ENST00000511045.1_Missense_Mutation_p.K367N|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.K340N			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	340	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.K340N(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GGACTGCGAAGAAAGAAGAGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											95	96	96					4																	100518334		2203	4300	6503	100737357	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1020G>T	4.37:g.100518334G>T	ENSP00000265517:p.Lys340Asn		100737357	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390685	0.42410	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.68331	-0.32;-0.32;-0.32	5.27	4.44	0.53790	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.304109	0.37348	N	0.002128	T	0.62392	0.2424	M	0.67953	2.075	0.31409	N	0.675723	B;B	0.32010	0.336;0.351	B;B	0.36378	0.223;0.174	T	0.60924	-0.7166	10	0.11794	T	0.64	-25.9727	10.6892	0.45860	0.1659:0.0:0.8341:0.0	.	367;340	E9PBP6;P55157	.;MTP_HUMAN	N	367;340;340;340	ENSP00000427679:K367N;ENSP00000400821:K340N;ENSP00000265517:K340N	ENSP00000265517:K340N	K	+	3	2	MTTP	100737357	0.997000	0.39634	0.987000	0.45799	0.987000	0.75469	0.601000	0.24119	1.216000	0.43427	0.655000	0.94253	AAG		0.463	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			T	100518334	G	T	100518334	3	4	61	1	0	0	0	0	1	0	0	0	9994	933	33	2	1050	2	MTTP	4	100518334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15250	100518334	90635942	3363	11348										
MTTP	4547	broad.mit.edu	37	chr4	100534106	100534106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggactggaagccttaatcGcagccacccctgacgagggg	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100534106G>A	ENST00000265517.5	+	15	2229	c.2026G>A	c.(2026-2028)Gca>Aca	p.A676T	MTTP_ENST00000511045.1_Missense_Mutation_p.A703T|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.A676T			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	676					cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.A676T(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	AGCCTTAATCGCAGCCACCCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											136	134	135					4																	100534106		2203	4300	6503	100753129	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.2026G>A	4.37:g.100534106G>A	ENSP00000265517:p.Ala676Thr		100753129	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	G	36	5.669852	0.96754	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.64991	-0.13;-0.1;-0.1	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.76751	0.4031	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.914;0.996	T	0.70000	-0.4992	10	0.18276	T	0.48	-15.6636	19.7133	0.96105	0.0:0.0:1.0:0.0	.	703;676	E9PBP6;P55157	.;MTP_HUMAN	T	703;676;676	ENSP00000427679:A703T;ENSP00000400821:A676T;ENSP00000265517:A676T	ENSP00000265517:A676T	A	+	1	0	MTTP	100753129	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.307000	0.96226	2.659000	0.90383	0.650000	0.86243	GCA		0.483	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100534106	G	A	100534106	3	1	61	1	0	0	0	0	1	0	0	0	9994	1087	38	1	2084	1	MTTP	4	100534106	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15772	100534106	90620170	3364	11349										
DAPP1	27071	broad.mit.edu	37	chr4	100761457	100761457	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttttagggccaaagattCtgttaaacactttcatgttg	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100761457C>A	ENST00000512369.1	+	3	304	c.236C>A	c.(235-237)tCt>tAt	p.S79Y	DAPP1_ENST00000296414.7_Missense_Mutation_p.S79Y	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	79	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)	p.S79Y(1)		endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		GCCAAAGATTCTGTTAAACAC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											39	35	36					4																	100761457		1786	4064	5850	100980480	SO:0001583	missense	27071			AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.236C>A	4.37:g.100761457C>A	ENSP00000423602:p.Ser79Tyr		100980480	Q8TCK5|Q9UHF2	Missense_Mutation	SNP	ENST00000512369.1	37	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300156	0.81136	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	D;D	0.89415	-2.51;-2.51	5.35	5.35	0.76521	SH2 motif (5);	0.000000	0.85682	D	0.000000	D	0.94311	0.8172	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.991;0.997	D	0.94165	0.7418	10	0.52906	T	0.07	-7.8653	18.6905	0.91581	0.0:1.0:0.0:0.0	.	79;79;79	B4DW38;Q9UN19-2;Q9UN19	.;.;DAPP1_HUMAN	Y	79	ENSP00000296414:S79Y;ENSP00000423602:S79Y	ENSP00000296414:S79Y	S	+	2	0	DAPP1	100980480	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.069000	0.76755	2.510000	0.84645	0.655000	0.94253	TCT		0.279	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1			A	100761457	C	A	100761457	3	1	61	1	0	0	0	0	1	0	0	0	4245	913	32	2	246	2	DAPP1	4	100761457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	227351	100761457	90392819	3365	11350										
DNAJB14	79982	broad.mit.edu	37	chr4	100827712	100827712	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcatgtccactatgtcGatgctgatgttgttggctat	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:100827712G>A	ENST00000442697.2	-	5	848	c.694C>T	c.(694-696)Cga>Tga	p.R232*		NM_001031723.2|NM_001278310.1	NP_001026893.1|NP_001265239.1	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	232						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R147*(1)		kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)		CCACTATGTCGATGCTGATGT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											138	128	132					4																	100827712		2203	4300	6503	101046735	SO:0001587	stop_gained	79982			BC022248	CCDS34035.1, CCDS75171.1	4q23	2011-09-02			ENSG00000164031	ENSG00000164031		"Heat shock proteins / DNAJ (HSP40)"	25881	protein-coding gene	gene with protein product							Standard	NM_001031723		Approved	FLJ14281	uc003hvl.4	Q8TBM8	OTTHUMG00000131049	ENST00000442697.2:c.694C>T	4.37:g.100827712G>A	ENSP00000404381:p.Arg232*		101046735	Q6UXN1|Q7Z3P0|Q86TA7|Q86TM0|Q9GZU9	Nonsense_Mutation	SNP	ENST00000442697.2	37	CCDS34035.1	.	.	.	.	.	.	.	.	.	.	G	37	6.011784	0.97200	.	.	ENSG00000164031	ENST00000442697	.	.	.	5.55	5.55	0.83447	.	0.288681	0.33591	N	0.004745	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1032	0.93282	0.0:0.0:1.0:0.0	.	.	.	.	X	232	.	ENSP00000404381:R232X	R	-	1	2	DNAJB14	101046735	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.923000	0.87546	2.616000	0.88540	0.591000	0.81541	CGA		0.348	DNAJB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253696.2	NM_001031723.2		A	100827712	G	A	100827712	4	1	61	1	0	0	0	0	0	1	0	0	4630	1066	37	1	461	1	DNAJB14	4	100827712	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66255	100827712	90326564	3366	11351										
DDIT4L	115265	broad.mit.edu	37	chr4	101108893	101108893	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttttttcttaacaagtcGaaatcctgagctgaggatca	8	7	2	2	rs144358521		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:101108893G>A	ENST00000273990.2	-	3	737	c.523C>T	c.(523-525)Cga>Tga	p.R175*	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	175					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)		p.R175*(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		TTAACAAGTCGAAATCCTGAG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	4						G	stop/ARG	0,4406		0,0,2203	67	73	71		523	5	1	4	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	DDIT4L	NM_145244.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		175/194	101108893	1,13005	2203	4300	6503	101327916	SO:0001587	stop_gained	115265			BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"regulated in development and DNA damage response 2", " similar to Smhs1 protein"	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.523C>T	4.37:g.101108893G>A	ENSP00000354830:p.Arg175*		101327916	B2R7C3	Nonsense_Mutation	SNP	ENST00000273990.2	37	CCDS34036.1	.	.	.	.	.	.	.	.	.	.	G	37	6.082713	0.97267	0.0	1.16E-4	ENSG00000145358	ENST00000273990;ENST00000502763	.	.	.	5.95	5.04	0.67666	.	0.085570	0.49305	D	0.000157	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0474	10.269	0.43473	0.0769:0.0:0.7768:0.1462	.	.	.	.	X	175	.	ENSP00000354830:R175X	R	-	1	2	DDIT4L	101327916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.448000	0.44926	2.824000	0.97209	0.655000	0.94253	CGA		0.398	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244		A	101108893	G	A	101108893	4	1	61	1	0	0	0	0	0	1	0	0	4338	1066	37	1	62	1	DDIT4L	4	101108893	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281181	101108893	90045383	3367	11352										
PPP3CA	5530	broad.mit.edu	37	chr4	102117160	102117160	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattctcaatgcaacactctCttccagccttccctccttca	2	17	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:102117160C>A	ENST00000394854.3	-	2	855	c.172G>T	c.(172-174)Gag>Tag	p.E58*	PPP3CA_ENST00000507176.1_Intron|PPP3CA_ENST00000394853.4_Nonsense_Mutation_p.E58*|PPP3CA_ENST00000323055.6_Nonsense_Mutation_p.E58*|PPP3CA_ENST00000512215.1_Nonsense_Mutation_p.E58*|PPP3CA_ENST00000523694.2_Intron	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	58	Catalytic.				calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)	p.E58*(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		GCAACACTCTCTTCCAGCCTT	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											144	144	144					4																	102117160		2203	4300	6503	102336183	SO:0001587	stop_gained	5530				CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.172G>T	4.37:g.102117160C>A	ENSP00000378323:p.Glu58*		102336183	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Nonsense_Mutation	SNP	ENST00000394854.3	37	CCDS34037.1	.	.	.	.	.	.	.	.	.	.	C	46	12.331101	0.99658	.	.	ENSG00000138814	ENST00000512215;ENST00000394854;ENST00000323055;ENST00000394853;ENST00000529324;ENST00000525819	.	.	.	5.65	5.65	0.86999	.	0.118831	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-15.2381	19.0843	0.93196	0.0:1.0:0.0:0.0	.	.	.	.	X	58;58;58;58;8;8	.	ENSP00000320580:E58X	E	-	1	0	PPP3CA	102336183	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.496000	0.81526	2.824000	0.97209	0.655000	0.94253	GAG		0.433	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		A	102117160	C	A	102117160	4	1	61	1	0	0	0	0	0	1	0	0	12431	922	32	2	1445	2	PPP3CA	4	102117160	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1008267	102117160	89037116	3368	11353										
BANK1	55024	broad.mit.edu	37	chr4	102751344	102751344	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagactacatctctgtaatCcagagtatcatattcaaagg	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:102751344C>T	ENST00000322953.4	+	2	724	c.450C>T	c.(448-450)atC>atT	p.I150I	BANK1_ENST00000444316.2_Silent_p.I120I|BANK1_ENST00000428908.1_Intron|BANK1_ENST00000508653.1_Intron|BANK1_ENST00000504592.1_Silent_p.I135I	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	150	Interaction with ITPR2.				B cell activation (GO:0042113)			p.I150I(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TCTCTGTAATCCAGAGTATCA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											54	59	57					4																	102751344		2189	4297	6486	102970367	SO:0001819	synonymous_variant	55024			AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.450C>T	4.37:g.102751344C>T			102970367	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Silent	SNP	ENST00000322953.4	37	CCDS34038.1																																																																																				0.318	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		T	102751344	C	T	102751344	2	4	61	1	0	0	0	0	0	0	0	1	1310	845	30	3		3	BANK1	4	102751344	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	634184	102751344	88402932	3369	11354										
BANK1	55024	broad.mit.edu	37	chr4	102791758	102791758	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaacagcaaaggcaaaggAatgcctattcagaatggcag	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:102791758A>C	ENST00000322953.4	+	5	1134	c.860A>C	c.(859-861)gAa>gCa	p.E287A	BANK1_ENST00000444316.2_Missense_Mutation_p.E257A|BANK1_ENST00000428908.1_Missense_Mutation_p.E154A|BANK1_ENST00000508653.1_Missense_Mutation_p.E154A|BANK1_ENST00000504592.1_Missense_Mutation_p.E272A	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	287	DBB. {ECO:0000255|PROSITE- ProRule:PRU00707}.				B cell activation (GO:0042113)			p.E287A(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AAGGCAAAGGAATGCCTATTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	103	107					4																	102791758		2203	4300	6503	103010781	SO:0001583	missense	55024			AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.860A>C	4.37:g.102791758A>C	ENSP00000320509:p.Glu287Ala		103010781	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.487016	0.26686	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.19105	2.86;2.85;2.17;2.17;2.86	5.2	-5.15	0.02866	DBB domain (1);	0.848527	0.10200	N	0.703503	T	0.15176	0.0366	L	0.58101	1.795	0.09310	N	1	B;B;B	0.24823	0.01;0.112;0.112	B;B;B	0.24394	0.01;0.053;0.053	T	0.28586	-1.0039	10	0.38643	T	0.18	.	2.7692	0.05329	0.3733:0.1436:0.3673:0.1159	.	154;287;272	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	A	272;287;154;154;257	ENSP00000421443:E272A;ENSP00000320509:E287A;ENSP00000412748:E154A;ENSP00000422314:E154A;ENSP00000388817:E257A	ENSP00000320509:E287A	E	+	2	0	BANK1	103010781	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.581000	0.23819	-1.146000	0.02854	-0.290000	0.09829	GAA		0.398	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		C	102791758	A	C	102791758	3	2	61	1	0	0	0	0	1	0	0	0	1310	246	9	4	878	4	BANK1	4	102791758	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40414	102791758	88362518	3370	11355										
NFKB1	4790	broad.mit.edu	37	chr4	103459024	103459024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctttgcagagaggatttCgtttccgttatgtatgtgaa	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103459024C>T	ENST00000505458.1	+	5	443	c.166C>T	c.(166-168)Cgt>Tgt	p.R56C	NFKB1_ENST00000394820.4_Missense_Mutation_p.R56C|NFKB1_ENST00000226574.4_Missense_Mutation_p.R57C			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	56	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R57C(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	GAGAGGATTTCGTTTCCGTTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											159	144	149					4																	103459024		2203	4300	6503	103678052	SO:0001583	missense	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.166C>T	4.37:g.103459024C>T	ENSP00000424790:p.Arg56Cys		103678052	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923054	0.73213	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000511926;ENST00000507079;ENST00000505458;ENST00000509165	T;T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69;-0.69	5.24	5.24	0.73138	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.064276	0.64402	D	0.000015	D	0.87672	0.6236	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.90424	0.4419	10	0.87932	D	0	-13.6442	17.633	0.88114	0.0:1.0:0.0:0.0	.	56;57	P19838;P19838-2	NFKB1_HUMAN;.	C	57;56;64;65;56;57	ENSP00000226574:R57C;ENSP00000378297:R56C;ENSP00000420904:R64C;ENSP00000426147:R65C;ENSP00000424790:R56C;ENSP00000423877:R57C	ENSP00000226574:R57C	R	+	1	0	NFKB1	103678052	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	2.299000	0.43611	2.456000	0.83038	0.655000	0.94253	CGT		0.378	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			T	103459024	C	T	103459024	3	4	61	1	0	0	0	0	1	0	0	0	10406	884	31	1	183	1	NFKB1	4	103459024	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	667266	103459024	87695252	3371	11356										
NFKB1	4790	broad.mit.edu	37	chr4	103514630	103514630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctcatgcccaatttttCggatagtttcggcggtggta	12	8	1	0	rs371719137		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103514630C>T	ENST00000505458.1	+	12	1389	c.1112C>T	c.(1111-1113)tCg>tTg	p.S371L	NFKB1_ENST00000394820.4_Missense_Mutation_p.S371L|NFKB1_ENST00000226574.4_Missense_Mutation_p.S372L|NFKB1_ENST00000600343.1_Missense_Mutation_p.S191L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	371					apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S372L(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	CCCAATTTTTCGGATAGTTTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	LEU/SER,LEU/SER	0,4406		0,0,2203	145	155	152		1112,1115	4.7	0.9	4		152	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NFKB1	NM_001165412.1,NM_003998.3	145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	371/969,372/970	103514630	1,13005	2203	4300	6503	103733668	SO:0001583	missense	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1112C>T	4.37:g.103514630C>T	ENSP00000424790:p.Ser371Leu		103733668	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.455683	0.63401	0.0	1.16E-4	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458;ENST00000508584	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	4.74	4.74	0.60224	Immunoglobulin E-set (1);	0.169892	0.39274	N	0.001411	T	0.26304	0.0642	L	0.28344	0.845	0.43080	D	0.994734	P;P;P	0.45902	0.868;0.868;0.74	B;B;B	0.36134	0.155;0.155;0.218	T	0.09487	-1.0672	10	0.41790	T	0.15	.	17.7398	0.88404	0.0:1.0:0.0:0.0	.	191;371;372	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	L	372;371;371;165	ENSP00000226574:S372L;ENSP00000378297:S371L;ENSP00000424790:S371L;ENSP00000424815:S165L	ENSP00000226574:S372L	S	+	2	0	NFKB1	103733668	0.988000	0.35896	0.927000	0.36925	0.534000	0.34807	2.784000	0.47774	2.165000	0.68154	0.462000	0.41574	TCG		0.507	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			T	103514630	C	T	103514630	3	4	61	1	0	0	0	0	1	0	0	0	10406	893	31	1	1157	1	NFKB1	4	103514630	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55606	103514630	87639646	3372	11357										
NFKB1	4790	broad.mit.edu	37	chr4	103534700	103534700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccacctctcaggcccactCgctgcctctctcgcctgcct	7	21	2	0	rs142074302		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103534700C>T	ENST00000505458.1	+	23	2985	c.2708C>T	c.(2707-2709)tCg>tTg	p.S903L	NFKB1_ENST00000394820.4_Missense_Mutation_p.S903L|NFKB1_ENST00000226574.4_Missense_Mutation_p.S904L|NFKB1_ENST00000600343.1_Missense_Mutation_p.S723L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	903	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S904L(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	CAGGCCCACTCGCTGCCTCTC	0.542													C|||	1	0.000199681	0	0	5008	,	,		17217	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						C	LEU/SER,LEU/SER	0,4406		0,0,2203	52	41	45		2708,2711	-1	0	4	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NFKB1	NM_001165412.1,NM_003998.3	145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	903/969,904/970	103534700	1,13005	2203	4300	6503	103753746	SO:0001583	missense	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2708C>T	4.37:g.103534700C>T	ENSP00000424790:p.Ser903Leu		103753746	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.98	1.504697	0.26949	0.0	1.16E-4	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.36699	1.26;1.24;1.24	5.17	-1.0	0.10196	Ankyrin repeat-containing domain (1);	1.764740	0.03321	N	0.191927	T	0.19167	0.0460	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.002;0.002;0.008	B;B;B	0.08055	0.001;0.001;0.003	T	0.14282	-1.0478	10	0.35671	T	0.21	7.8393	5.2778	0.15659	0.0:0.4501:0.1363:0.4136	.	723;903;904	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	L	904;903;903	ENSP00000226574:S904L;ENSP00000378297:S903L;ENSP00000424790:S903L	ENSP00000226574:S904L	S	+	2	0	NFKB1	103753746	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-1.433000	0.02428	-0.645000	0.05458	-0.145000	0.13849	TCG		0.542	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			T	103534700	C	T	103534700	3	4	61	1	0	0	0	0	1	0	0	0	10406	893	31	1	2797	1	NFKB1	4	103534700	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20070	103534700	87619576	3373	11358										
MANBA	4126	broad.mit.edu	37	chr4	103595103	103595103	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttactcggtcctggaatGaatctgctgggatccagttt	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103595103G>T	ENST00000226578.4	-	8	1184	c.1085C>A	c.(1084-1086)tCa>tAa	p.S362*	MANBA_ENST00000505239.1_Nonsense_Mutation_p.S305*	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	362					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)	p.S362L(1)|p.S362*(1)		cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GTCCTGGAATGAATCTGCTGG	0.368																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	urinary_tract(1)|large_intestine(1)	4											78	85	83					4																	103595103		2203	4300	6503	103814151	SO:0001587	stop_gained	4126				CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.1085C>A	4.37:g.103595103G>T	ENSP00000226578:p.Ser362*		103814151	Q96BC3|Q9NYX9	Nonsense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	.	.	.	.	.	.	.	.	.	.	G	38	6.664987	0.97747	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	.	.	.	5.63	4.79	0.61399	.	0.387274	0.29616	N	0.011644	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.258	14.6467	0.68767	0.0699:0.0:0.9301:0.0	.	.	.	.	X	362;305	.	ENSP00000226578:S362X	S	-	2	0	MANBA	103814151	1.000000	0.71417	0.014000	0.15608	0.898000	0.52572	7.556000	0.82233	1.370000	0.46153	0.561000	0.74099	TCA		0.368	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			T	103595103	G	T	103595103	4	4	61	1	0	0	0	0	0	1	0	0	9249	1294	45	2	1594	2	MANBA	4	103595103	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60403	103595103	87559173	3374	11359										
UBE2D3	7323	broad.mit.edu	37	chr4	103747646	103747646	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccccgcgggttaccttaTtaatccgtttcagcgccata	8	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103747646T>C	ENST00000453744.2	-	2	533	c.20A>G	c.(19-21)aAt>aGt	p.N7S	UBE2D3_ENST00000394801.4_Missense_Mutation_p.N7S|UBE2D3_ENST00000357194.6_Intron|UBE2D3_ENST00000394804.2_Missense_Mutation_p.N7S|UBE2D3_ENST00000507845.1_5'Flank|UBE2D3_ENST00000394803.5_Missense_Mutation_p.N7S|UBE2D3_ENST00000513098.1_5'UTR|UBE2D3_ENST00000321805.7_Missense_Mutation_p.N7S|UBE2D3_ENST00000350435.7_5'Flank|UBE2D3_ENST00000343106.5_Missense_Mutation_p.N7S|UBE2D3_ENST00000349311.8_Missense_Mutation_p.N7S|UBE2D3_ENST00000338145.3_Missense_Mutation_p.N7S|RP11-10L12.4_ENST00000501133.2_RNA|UBE2D3_ENST00000504211.1_5'Flank|UBE2D3_ENST00000505207.1_5'Flank|UBE2D3_ENST00000502404.1_5'Flank	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3	7					apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)	p.N7S(1)		kidney(1)|lung(3)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		GGTTACCTTATTAATCCGTTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	4											214	202	206					4																	103747646		2203	4300	6503	103966781	SO:0001583	missense	7323			U39318	CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1	4q24	2011-05-19	2011-05-19		ENSG00000109332	ENSG00000109332		"Ubiquitin-conjugating enzymes E2"	12476	protein-coding gene	gene with protein product		602963	"ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)"			8530467	Standard	NM_181886		Approved	UbcH5C	uc003hwl.3	P61077	OTTHUMG00000131119	ENST00000453744.2:c.20A>G	4.37:g.103747646T>C	ENSP00000396901:p.Asn7Ser		103966781	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Missense_Mutation	SNP	ENST00000453744.2	37	CCDS3660.1	.	.	.	.	.	.	.	.	.	.	T	12.34	1.908033	0.33721	.	.	ENSG00000109332	ENST00000453744;ENST00000394801;ENST00000394803;ENST00000394804;ENST00000343106;ENST00000321805;ENST00000338145;ENST00000349311;ENST00000508238;ENST00000502690;ENST00000508249	T;T;T;T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	4.09	4.09	0.47781	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	.	.	.	.	T	0.21881	0.0527	N	0.10733	0.035	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.06006	-1.0851	9	0.29301	T	0.29	.	9.6582	0.39939	0.0:0.0:0.0:1.0	.	7;7	P61077;P61077-2	UB2D3_HUMAN;.	S	7	ENSP00000396901:N7S;ENSP00000378280:N7S;ENSP00000378282:N7S;ENSP00000378283:N7S;ENSP00000345285:N7S;ENSP00000318494:N7S;ENSP00000337208:N7S;ENSP00000344069:N7S;ENSP00000423487:N7S;ENSP00000425762:N7S;ENSP00000421310:N7S	ENSP00000318494:N7S	N	-	2	0	UBE2D3	103966781	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.033000	0.49743	1.836000	0.53414	0.455000	0.32223	AAT		0.547	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893		C	103747646	T	C	103747646	3	2	61	1	0	0	0	0	1	0	0	0	16890	1493	52	4	504	4	UBE2D3	4	103747646	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	152543	103747646	87406630	3375	11360										
NHEDC1	150159	broad.mit.edu	37	chr4	103832680	103832680	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttatagaggctatggcgtTattaagtataccacctgtag	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103832680T>G	ENST00000296422.7	-	8	985	c.844A>C	c.(844-846)Aac>Cac	p.N282H	SLC9B1_ENST00000512651.2_Intron|SLC9B1_ENST00000394789.3_Missense_Mutation_p.N282H	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	282					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.N282H(1)									GCTATGGCGTTATTAAGTATA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											37	37	37					4																	103832680		2031	3870	5901	104052129	SO:0001583	missense	150159			AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.844A>C	4.37:g.103832680T>G	ENSP00000296422:p.Asn282His		104052129	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Missense_Mutation	SNP	ENST00000296422.7	37	CCDS34041.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.406421	0.42715	.	.	ENSG00000164037	ENST00000394789;ENST00000296422;ENST00000511253;ENST00000514340	T;T;T;T	0.48201	2.43;2.43;0.82;2.43	4.36	3.13	0.36017	.	0.334817	0.33023	N	0.005373	T	0.66771	0.2823	M	0.83012	2.62	0.09310	N	1	D;D;D	0.71674	0.997;0.998;0.991	D;D;D	0.71184	0.929;0.972;0.929	T	0.59059	-0.7525	10	0.62326	D	0.03	-18.6878	10.1978	0.43065	0.0:0.0:0.1678:0.8322	.	50;282;282	Q4ZJI4-2;Q4ZJI4;Q4ZJI4-3	.;SL9B1_HUMAN;.	H	282;282;7;225	ENSP00000378269:N282H;ENSP00000296422:N282H;ENSP00000425544:N7H;ENSP00000426056:N225H	ENSP00000296422:N282H	N	-	1	0	SLC9B1	104052129	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.918000	0.28678	0.770000	0.33336	0.477000	0.44152	AAC		0.363	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		G	103832680	T	G	103832680	3	3	61	1	0	0	0	0	1	0	0	0	10431	1754	61	4	823	4	NHEDC1	4	103832680	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	85034	103832680	87321596	3376	11361										
NHEDC1	150159	broad.mit.edu	37	chr4	103866380	103866380	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcccattgccagggaaatTtcataatgaagtgtgaaaaa	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:103866380T>G	ENST00000296422.7	-	6	764	c.623A>C	c.(622-624)aAa>aCa	p.K208T	SLC9B1_ENST00000394789.3_Missense_Mutation_p.K208T	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	208					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.K208T(1)									CCAGGGAAATTTCATAATGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	88	87					4																	103866380		2203	4299	6502	104085829	SO:0001583	missense	150159			AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.623A>C	4.37:g.103866380T>G	ENSP00000296422:p.Lys208Thr		104085829	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Missense_Mutation	SNP	ENST00000296422.7	37	CCDS34041.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201521	0.38905	.	.	ENSG00000164037	ENST00000394789;ENST00000296422;ENST00000514340;ENST00000452285	T;T;T	0.15603	2.41;2.41;2.41	4.16	4.16	0.48862	.	0.679258	0.14406	N	0.321583	T	0.15003	0.0362	L	0.29908	0.895	0.09310	N	0.999996	B;B	0.33345	0.409;0.356	B;B	0.38755	0.281;0.185	T	0.15809	-1.0424	10	0.56958	D	0.05	-12.2706	8.1438	0.31100	0.0:0.0927:0.0:0.9073	.	208;208	Q4ZJI4;Q4ZJI4-3	SL9B1_HUMAN;.	T	208;208;151;208	ENSP00000378269:K208T;ENSP00000296422:K208T;ENSP00000426056:K151T	ENSP00000296422:K208T	K	-	2	0	SLC9B1	104085829	0.266000	0.24112	0.930000	0.37139	0.989000	0.77384	1.958000	0.40402	1.875000	0.54330	0.477000	0.44152	AAA		0.358	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		G	103866380	T	G	103866380	3	3	61	1	0	0	0	0	1	0	0	0	10431	1841	64	4	1052	4	NHEDC1	4	103866380	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33700	103866380	87287896	3377	11362										
BDH2	56898	broad.mit.edu	37	chr4	104003289	104003289	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctatttcttctgcagttgcGaatcttcccgtcttttgtct	7	11	5	0	rs181237399		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104003289G>A	ENST00000296424.4	-	9	753	c.633C>T	c.(631-633)ttC>ttT	p.F211F		NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	211					epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)	p.F211F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		CTGCAGTTGCGAATCTTCCCG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	4						G		1,4405	2.1+/-5.4	0,1,2202	142	124	130		633	1.1	1	4		130	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BDH2	NM_020139.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		211/246	104003289	2,13004	2203	4300	6503	104222738	SO:0001819	synonymous_variant	56898			AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	1.1.1.30	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	32389	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 15C, member 1"		"dehydrogenase/reductase (SDR family) member 6"	DHRS6		16380372, 19027726	Standard	XM_005263140		Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.633C>T	4.37:g.104003289G>A			104222738	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	Silent	SNP	ENST00000296424.4	37	CCDS3663.1																																																																																				0.463	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157159.2	NM_020139		A	104003289	G	A	104003289	2	1	61	1	0	0	0	0	0	0	0	1	1392	1049	37	1		1	BDH2	4	104003289	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136909	104003289	87150987	3378	11363										
CENPE	1062	broad.mit.edu	37	chr4	104029996	104029996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgagttatcaaaatagcGaactggatgaggtgatggta	12	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104029996G>A	ENST00000265148.3	-	48	8064	c.7975C>T	c.(7975-7977)Cgc>Tgc	p.R2659C	CENPE_ENST00000380026.3_Missense_Mutation_p.R2538C	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2659	Globular autoinhibitory domain. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.R2622C(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TCAAAATAGCGAACTGGATGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											128	125	126					4																	104029996		2203	4300	6503	104249445	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.7975C>T	4.37:g.104029996G>A	ENSP00000265148:p.Arg2659Cys		104249445	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959351	0.34565	.	.	ENSG00000138778	ENST00000265148;ENST00000380026	T;T	0.68181	-0.31;-0.3	5.19	3.23	0.37069	.	.	.	.	.	T	0.65606	0.2707	L	0.51422	1.61	0.22851	N	0.998654	D;D	0.71674	0.998;0.997	P;P	0.50896	0.653;0.451	T	0.56836	-0.7913	9	0.87932	D	0	.	6.7115	0.23280	0.0:0.1632:0.5787:0.2581	.	2538;2659	Q02224-3;Q02224	.;CENPE_HUMAN	C	2659;2538	ENSP00000265148:R2659C;ENSP00000369365:R2538C	ENSP00000265148:R2659C	R	-	1	0	CENPE	104249445	0.883000	0.30277	0.625000	0.29200	0.180000	0.23129	1.612000	0.36889	1.166000	0.42689	-0.175000	0.13238	CGC		0.368	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104029996	G	A	104029996	3	1	61	1	0	0	0	0	1	0	0	0	3236	1058	37	1	138	1	CENPE	4	104029996	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26707	104029996	87124280	3379	11364										
CENPE	1062	broad.mit.edu	37	chr4	104070361	104070361	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctttagaacttttctttCtttggttatagatttcactt	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104070361C>A	ENST00000265148.3	-	27	3690	c.3601G>T	c.(3601-3603)Gaa>Taa	p.E1201*	CENPE_ENST00000380026.3_Nonsense_Mutation_p.E1176*	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1201					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.E1201*(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ACTTTTCTTTCTTTGGTTATA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											86	91	89					4																	104070361		2202	4294	6496	104289810	SO:0001587	stop_gained	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3601G>T	4.37:g.104070361C>A	ENSP00000265148:p.Glu1201*		104289810	A6NKY9|A8K2U7|Q4LE75	Nonsense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	38	6.939402	0.97948	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	.	.	.	4.01	3.17	0.36434	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	10.15	0.42786	0.0:0.9043:0.0:0.0957	.	.	.	.	X	1201;1201;1176	.	ENSP00000265148:E1201X	E	-	1	0	CENPE	104289810	0.975000	0.34042	0.792000	0.32020	0.165000	0.22458	2.505000	0.45424	1.021000	0.39600	-0.150000	0.13652	GAA		0.333	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104070361	C	A	104070361	4	1	61	1	0	0	0	0	0	1	0	0	3236	922	32	2	4596	2	CENPE	4	104070361	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40365	104070361	87083915	3380	11365										
CENPE	1062	broad.mit.edu	37	chr4	104070427	104070427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccaactcaagcctctctgTttccatatgttccaatgtca	5	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104070427T>C	ENST00000265148.3	-	27	3624	c.3535A>G	c.(3535-3537)Aca>Gca	p.T1179A	CENPE_ENST00000380026.3_Missense_Mutation_p.T1154A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1179					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T1179A(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		AGCCTCTCTGTTTCCATATGT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	93	93					4																	104070427		2202	4297	6499	104289876	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3535A>G	4.37:g.104070427T>C	ENSP00000265148:p.Thr1179Ala		104289876	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	6.301	0.423618	0.11928	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.70282	-0.47;-0.47	4.0	4.0	0.46444	.	.	.	.	.	T	0.61148	0.2324	L	0.47716	1.5	0.09310	N	1	B;B	0.24721	0.11;0.006	B;B	0.25291	0.059;0.002	T	0.49041	-0.8980	9	0.26408	T	0.33	.	8.1317	0.31031	0.1794:0.0:0.0:0.8206	.	1154;1179	Q02224-3;Q02224	.;CENPE_HUMAN	A	1179;1179;1154	ENSP00000265148:T1179A;ENSP00000369365:T1154A	ENSP00000265148:T1179A	T	-	1	0	CENPE	104289876	0.000000	0.05858	0.415000	0.26534	0.065000	0.16274	0.154000	0.16343	1.790000	0.52503	0.482000	0.46254	ACA		0.303	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104070427	T	C	104070427	3	2	61	1	0	0	0	0	1	0	0	0	3236	1725	60	4	4662	4	CENPE	4	104070427	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	66	104070427	87083849	3381	11366										
CENPE	1062	broad.mit.edu	37	chr4	104072462	104072462	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttatggcatggttcttttCttgtgcaactatctcttgtt	7	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104072462C>A	ENST00000265148.3	-	26	3399	c.3310G>T	c.(3310-3312)Gaa>Taa	p.E1104*	CENPE_ENST00000380026.3_Nonsense_Mutation_p.E1079*	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1104					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.E1104*(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGGTTCTTTTCTTGTGCAACT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											136	120	125					4																	104072462		2203	4299	6502	104291911	SO:0001587	stop_gained	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3310G>T	4.37:g.104072462C>A	ENSP00000265148:p.Glu1104*		104291911	A6NKY9|A8K2U7|Q4LE75	Nonsense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	38	6.813675	0.97857	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	14.8472	0.70270	0.0:1.0:0.0:0.0	.	.	.	.	X	1104;1104;1079;1104	.	ENSP00000265148:E1104X	E	-	1	0	CENPE	104291911	1.000000	0.71417	0.991000	0.47740	0.575000	0.36095	3.316000	0.51960	2.257000	0.74773	0.655000	0.94253	GAA		0.348	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104072462	C	A	104072462	4	1	61	1	0	0	0	0	0	1	0	0	3236	922	32	2	4891	2	CENPE	4	104072462	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2035	104072462	87081814	3382	11367										
CENPE	1062	broad.mit.edu	37	chr4	104080032	104080032	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcctgaagttcttgggtCttgtaagaaagctttaaaaa	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104080032C>A	ENST00000265148.3	-	23	2702	c.2613G>T	c.(2611-2613)aaG>aaT	p.K871N	CENPE_ENST00000380026.3_Missense_Mutation_p.K846N	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	871					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.K871N(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GTTCTTGGGTCTTGTAAGAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											46	45	46					4																	104080032		2203	4296	6499	104299481	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2613G>T	4.37:g.104080032C>A	ENSP00000265148:p.Lys871Asn		104299481	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	5.485	0.274481	0.10403	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	D;D;D	0.82984	-1.67;-1.67;-1.67	4.81	-0.67	0.11384	.	.	.	.	.	D	0.83271	0.5218	M	0.70275	2.135	0.09310	N	1	P;B	0.52061	0.95;0.236	P;B	0.52424	0.698;0.064	T	0.72516	-0.4269	9	0.66056	D	0.02	.	3.8444	0.08928	0.2624:0.3297:0.0:0.4079	.	846;871	Q02224-3;Q02224	.;CENPE_HUMAN	N	871;871;846;871	ENSP00000265148:K871N;ENSP00000369365:K846N;ENSP00000423981:K871N	ENSP00000265148:K871N	K	-	3	2	CENPE	104299481	0.961000	0.32948	0.052000	0.19188	0.805000	0.45488	0.190000	0.17057	-0.053000	0.13289	0.650000	0.86243	AAG		0.368	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104080032	C	A	104080032	3	1	61	1	0	0	0	0	1	0	0	0	3236	912	32	2	5600	2	CENPE	4	104080032	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7570	104080032	87074244	3383	11368										
CENPE	1062	broad.mit.edu	37	chr4	104101560	104101560	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtactttctgaagcaaatCtttttcttccaaaagttggg	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104101560C>A	ENST00000265148.3	-	13	1239	c.1150G>T	c.(1150-1152)Gat>Tat	p.D384Y	CENPE_ENST00000380026.3_Missense_Mutation_p.D384Y|CENPE_ENST00000509120.1_5'UTR	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	384					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.D384Y(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGAAGCAAATCTTTTTCTTCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											91	92	92					4																	104101560		2203	4300	6503	104321009	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.1150G>T	4.37:g.104101560C>A	ENSP00000265148:p.Asp384Tyr		104321009	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835038	0.71373	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.69806	-0.43;-0.4;-0.1	5.23	5.23	0.72850	.	.	.	.	.	T	0.76564	0.4005	L	0.60455	1.87	0.44227	D	0.997068	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.979	T	0.77978	-0.2384	9	0.87932	D	0	.	9.5702	0.39422	0.0:0.8365:0.0:0.1635	.	384;384	Q02224-3;Q02224	.;CENPE_HUMAN	Y	384	ENSP00000265148:D384Y;ENSP00000369365:D384Y;ENSP00000423981:D384Y	ENSP00000265148:D384Y	D	-	1	0	CENPE	104321009	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	3.698000	0.54771	2.594000	0.87642	0.563000	0.77884	GAT		0.368	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104101560	C	A	104101560	3	1	61	1	0	0	0	0	1	0	0	0	3236	913	32	2	7103	2	CENPE	4	104101560	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21528	104101560	87052716	3384	11369										
TACR3	6870	broad.mit.edu	37	chr4	104511122	104511122	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgatgaaaggacaccagCgaaatgctctcttgaagcca	9	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:104511122C>T	ENST00000304883.2	-	5	1255	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	372					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.R372H(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		AGGACACCAGCGAAATGCTCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											82	81	81					4																	104511122		2203	4300	6503	104730571	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1115G>A	4.37:g.104511122C>T	ENSP00000303325:p.Arg372His		104730571	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188675	0.78789	.	.	ENSG00000169836	ENST00000304883	T	0.38887	1.11	5.81	5.81	0.92471	.	0.101452	0.64402	D	0.000005	T	0.46521	0.1397	M	0.67625	2.065	0.80722	D	1	B	0.23735	0.09	B	0.13407	0.009	T	0.42599	-0.9442	10	0.87932	D	0	.	19.0794	0.93175	0.0:1.0:0.0:0.0	.	372	P29371	NK3R_HUMAN	H	372	ENSP00000303325:R372H	ENSP00000303325:R372H	R	-	2	0	TACR3	104730571	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.650000	0.67944	2.746000	0.94184	0.591000	0.81541	CGC		0.448	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		T	104511122	C	T	104511122	3	4	61	1	0	0	0	0	1	0	0	0	15546	768	27	1	286	1	TACR3	4	104511122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	409562	104511122	86643154	3385	11370										
TET2	54790	broad.mit.edu	37	chr4	106156521	106156521	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtatgcagcccttctccGatgctttctgaaaggcctca	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:106156521G>A	ENST00000540549.1	+	3	2282	c.1422G>A	c.(1420-1422)ccG>ccA	p.P474P	TET2_ENST00000413648.2_Silent_p.P474P|TET2_ENST00000380013.4_Silent_p.P474P|TET2_ENST00000513237.1_Silent_p.P495P|TET2_ENST00000394764.1_Silent_p.P474P|TET2_ENST00000305737.2_Silent_p.P474P|TET2_ENST00000545826.1_Silent_p.P474P			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	474					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.P474P(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GCCCTTCTCCGATGCTTTCTG	0.438			"Mis N, F"		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - coding silent(1)	large_intestine(1)	4											108	103	104					4																	106156521		2203	4300	6503	106375970	SO:0001819	synonymous_variant	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.1422G>A	4.37:g.106156521G>A			106375970	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																				0.438	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106156521	G	A	106156521	2	1	61	1	0	0	0	0	0	0	0	1	15809	1045	37	1		1	TET2	4	106156521	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1645399	106156521	84997755	3386	11371										
TET2	54790	broad.mit.edu	37	chr4	106157443	106157443	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttggccagactaaagtgGaagaatgttttcatggtgaa	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:106157443G>T	ENST00000540549.1	+	3	3204	c.2344G>T	c.(2344-2346)Gaa>Taa	p.E782*	TET2_ENST00000413648.2_Nonsense_Mutation_p.E782*|TET2_ENST00000380013.4_Nonsense_Mutation_p.E782*|TET2_ENST00000513237.1_Nonsense_Mutation_p.E803*|TET2_ENST00000394764.1_Nonsense_Mutation_p.E782*|TET2_ENST00000305737.2_Nonsense_Mutation_p.E782*|TET2_ENST00000545826.1_Nonsense_Mutation_p.E782*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	782	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.E782*(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GACTAAAGTGGAAGAATGTTT	0.378			"Mis N, F"		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - Nonsense(1)	large_intestine(1)	4											59	61	60					4																	106157443		2202	4300	6502	106376892	SO:0001587	stop_gained	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.2344G>T	4.37:g.106157443G>T	ENSP00000442788:p.Glu782*		106376892	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	G	42	9.702343	0.99242	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648	.	.	.	5.91	5.91	0.95273	.	6.022120	0.00357	N	0.000024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	782;782;782;803;782;782;782	.	ENSP00000265149:E782X	E	+	1	0	TET2	106376892	1.000000	0.71417	0.945000	0.38365	0.977000	0.68977	3.452000	0.52971	2.793000	0.96121	0.655000	0.94253	GAA		0.378	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106157443	G	T	106157443	4	4	61	1	0	0	0	0	0	1	0	0	15809	1175	41	2	2346	2	TET2	4	106157443	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	922	106157443	84996833	3387	11372										
TET2	54790	broad.mit.edu	37	chr4	106158400	106158400	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaacagctgcttctgttCtcaataattttatagagtca	6	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:106158400C>A	ENST00000540549.1	+	3	4161	c.3301C>A	c.(3301-3303)Ctc>Atc	p.L1101I	TET2_ENST00000413648.2_Missense_Mutation_p.L1101I|TET2_ENST00000380013.4_Missense_Mutation_p.L1101I|TET2_ENST00000513237.1_Missense_Mutation_p.L1122I|TET2_ENST00000394764.1_Missense_Mutation_p.L1101I|TET2_ENST00000305737.2_Missense_Mutation_p.L1101I|TET2_ENST00000545826.1_Missense_Mutation_p.L1101I			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1101					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.L1101I(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TGCTTCTGTTCTCAATAATTT	0.383			"Mis N, F"		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Substitution - Missense(1)	large_intestine(1)	4											61	64	63					4																	106158400		2203	4300	6503	106377849	SO:0001583	missense	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.3301C>A	4.37:g.106158400C>A	ENSP00000442788:p.Leu1101Ile		106377849	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284543	0.59867	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648	T;T;T;T;T;T;T	0.24908	1.83;1.83;2.39;1.83;1.83;1.83;1.83	5.79	4.95	0.65309	.	0.499782	0.16173	N	0.226193	T	0.42108	0.1188	L	0.46741	1.465	0.32725	N	0.509795	D;D;D	0.76494	0.976;0.976;0.999	P;P;D	0.67382	0.834;0.873;0.951	T	0.54070	-0.8348	10	0.66056	D	0.02	.	11.7396	0.51786	0.0:0.8594:0.0:0.1406	.	1122;1101;1101	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	I	1101;1101;1101;1122;1101;1101;1101	ENSP00000306705:L1101I;ENSP00000442788:L1101I;ENSP00000442867:L1101I;ENSP00000425443:L1122I;ENSP00000369351:L1101I;ENSP00000378245:L1101I;ENSP00000391448:L1101I	ENSP00000265149:L1101I	L	+	1	0	TET2	106377849	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.009000	0.49552	1.449000	0.47699	0.655000	0.94253	CTC		0.383	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106158400	C	A	106158400	3	1	61	1	0	0	0	0	1	0	0	0	15809	913	32	2	3303	2	TET2	4	106158400	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	957	106158400	84995876	3388	11373										
PPA2	27068	broad.mit.edu	37	chr4	106292005	106292005	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactataccttcttcattaCtttctttatttggtgaagat	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:106292005C>T	ENST00000341695.5	-	11	995	c.965G>A	c.(964-966)aGt>aAt	p.S322N	PPA2_ENST00000432483.2_Missense_Mutation_p.S220N|PPA2_ENST00000354147.3_Missense_Mutation_p.S156N|PPA2_ENST00000357415.4_Missense_Mutation_p.S337N|PPA2_ENST00000348706.5_Missense_Mutation_p.S293N|PPA2_ENST00000380004.2_Missense_Mutation_p.S304N	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	322					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)	p.S322N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		TTCTTCATTACTTTCTTTATT	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	4											17	18	18					4																	106292005		2124	4195	6319	106511454	SO:0001583	missense	27068				CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.965G>A	4.37:g.106292005C>T	ENSP00000343885:p.Ser322Asn		106511454	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.	.	.	.	.	.	.	.	.	.	C	5.293	0.239423	0.10023	.	.	ENSG00000138777	ENST00000341695;ENST00000348706;ENST00000354147;ENST00000432483;ENST00000357415;ENST00000380004	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	4.23	-1.13	0.09775	.	0.468940	0.25264	N	0.031934	T	0.25419	0.0618	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.009;0.003;0.001;0.003	B;B;B;B;B	0.12837	0.008;0.008;0.003;0.001;0.001	T	0.11397	-1.0589	10	0.51188	T	0.08	-2.5914	3.6733	0.08283	0.1723:0.3795:0.0:0.4481	.	156;220;293;304;322	Q9H2U2-4;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.;.;.;.;IPYR2_HUMAN	N	322;293;156;220;337;304	ENSP00000343885:S322N;ENSP00000313061:S293N;ENSP00000340352:S156N;ENSP00000389957:S220N;ENSP00000349996:S337N;ENSP00000369340:S304N	ENSP00000343885:S322N	S	-	2	0	PPA2	106511454	0.000000	0.05858	0.006000	0.13384	0.352000	0.29268	-0.619000	0.05572	0.041000	0.15688	-0.355000	0.07637	AGT		0.259	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869		T	106292005	C	T	106292005	3	4	61	1	0	0	0	0	1	0	0	0	12318	565	20	3	47	3	PPA2	4	106292005	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133605	106292005	84862271	3389	11374										
PAPSS1	9061	broad.mit.edu	37	chr4	108615048	108615048	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggactaaagccaagatttTtattgagaccttgacgaata	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108615048T>G	ENST00000265174.4	-	3	562	c.290A>C	c.(289-291)aAa>aCa	p.K97T	PAPSS1_ENST00000511304.1_Intron	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	97					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)	p.K97T(1)		NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		GCCAAGATTTTTATTGAGACC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	123	128					4																	108615048		2203	4300	6503	108834497	SO:0001583	missense	9061			Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.290A>C	4.37:g.108615048T>G	ENSP00000265174:p.Lys97Thr		108834497	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	T	32	5.183960	0.94885	.	.	ENSG00000138801	ENST00000265174	T	0.79141	-1.24	5.67	5.67	0.87782	Adenylylsulphate kinase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.90662	0.7071	M	0.92604	3.325	0.80722	D	1	D	0.57899	0.981	D	0.74674	0.984	D	0.92835	0.6283	10	0.87932	D	0	-30.1002	15.9108	0.79473	0.0:0.0:0.0:1.0	.	97	O43252	PAPS1_HUMAN	T	97	ENSP00000265174:K97T	ENSP00000265174:K97T	K	-	2	0	PAPSS1	108834497	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	5.818000	0.69236	2.156000	0.67533	0.454000	0.30748	AAA		0.448	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2			G	108615048	T	G	108615048	3	3	61	1	0	0	0	0	1	0	0	0	11465	1841	64	4	1624	4	PAPSS1	4	108615048	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2323043	108615048	82539228	3390	11375										
SGMS2	166929	broad.mit.edu	37	chr4	108824539	108824539	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacttatttgttcatcaaaGaatgtaagtaatagcccatt	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108824539G>T	ENST00000394684.4	+	5	1281	c.724G>T	c.(724-726)Gaa>Taa	p.E242*	SGMS2_ENST00000394686.3_Nonsense_Mutation_p.E242*|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Nonsense_Mutation_p.E242*|RP11-286E11.1_ENST00000499098.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	242					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.E242*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		GTTCATCAAAGAATGTAAGTA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											97	90	92					4																	108824539		2203	4300	6503	109043988	SO:0001587	stop_gained	166929			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.724G>T	4.37:g.108824539G>T	ENSP00000378176:p.Glu242*		109043988	A8K2S9|B2RA61	Nonsense_Mutation	SNP	ENST00000394684.4	37	CCDS3677.1	.	.	.	.	.	.	.	.	.	.	G	38	6.950037	0.97956	.	.	ENSG00000164023	ENST00000394684;ENST00000503862;ENST00000359079;ENST00000394686	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-3.9353	19.5644	0.95388	0.0:0.0:1.0:0.0	.	.	.	.	X	242;69;242;242	.	ENSP00000351981:E242X	E	+	1	0	SGMS2	109043988	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	2.617000	0.88574	0.655000	0.94253	GAA		0.453	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		T	108824539	G	T	108824539	4	4	61	1	0	0	0	0	0	1	0	0	14252	943	33	2	734	2	SGMS2	4	108824539	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	209491	108824539	82329737	3391	11376										
SGMS2	166929	broad.mit.edu	37	chr4	108831517	108831517	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttacagaacttgaaggtCtcttcacagactaatttctt	5	9	3	3	rs370963195		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108831517C>A	ENST00000394684.4	+	7	1463	c.906C>A	c.(904-906)gtC>gtA	p.V302V	SGMS2_ENST00000394686.3_Silent_p.V302V|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Silent_p.V302V|RP11-286E11.1_ENST00000499098.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	302					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.V302V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		ACTTGAAGGTCTCTTCACAGA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	4											77	82	80					4																	108831517		2203	4300	6503	109050966	SO:0001819	synonymous_variant	166929			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.906C>A	4.37:g.108831517C>A			109050966	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	37	CCDS3677.1																																																																																				0.343	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		A	108831517	C	A	108831517	2	1	61	1	0	0	0	0	0	0	0	1	14252	900	32	2		2	SGMS2	4	108831517	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6978	108831517	82322759	3392	11377										
SGMS2	166929	broad.mit.edu	37	chr4	108831604	108831604	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacaaggctcaattccttgCtgcttctcctggccgctgtc	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108831604C>A	ENST00000394684.4	+	7	1550	c.993C>A	c.(991-993)tgC>tgA	p.C331*	SGMS2_ENST00000394686.3_Nonsense_Mutation_p.C331*|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Nonsense_Mutation_p.C331*|RP11-286E11.1_ENST00000499098.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	331					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.C331*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		CAATTCCTTGCTGCTTCTCCT	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											68	71	70					4																	108831604		2203	4300	6503	109051053	SO:0001587	stop_gained	166929			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.993C>A	4.37:g.108831604C>A	ENSP00000378176:p.Cys331*		109051053	A8K2S9|B2RA61	Nonsense_Mutation	SNP	ENST00000394684.4	37	CCDS3677.1	.	.	.	.	.	.	.	.	.	.	C	41	8.855715	0.98980	.	.	ENSG00000164023	ENST00000394684;ENST00000359079;ENST00000394686	.	.	.	6.07	5.24	0.73138	.	0.082501	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-16.6966	12.1502	0.54046	0.0:0.864:0.0:0.136	.	.	.	.	X	331	.	ENSP00000351981:C331X	C	+	3	2	SGMS2	109051053	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.935000	0.28924	1.583000	0.49898	0.655000	0.94253	TGC		0.423	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		A	108831604	C	A	108831604	4	1	61	1	0	0	0	0	0	1	0	0	14252	805	28	2	1011	2	SGMS2	4	108831604	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87	108831604	82322672	3393	11378										
SGMS2	166929	broad.mit.edu	37	chr4	108831700	108831700	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggtgaagacaatgagaaAtcgacctgaggagcaaaaca	11	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108831700A>C	ENST00000394684.4	+	7	1646	c.1089A>C	c.(1087-1089)aaA>aaC	p.K363N	SGMS2_ENST00000394686.3_Missense_Mutation_p.K363N|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Missense_Mutation_p.K363N|RP11-286E11.1_ENST00000499098.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	363					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.K363N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		ACAATGAGAAATCGACCTGAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											44	45	44					4																	108831700		2203	4300	6503	109051149	SO:0001583	missense	166929			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.1089A>C	4.37:g.108831700A>C	ENSP00000378176:p.Lys363Asn		109051149	A8K2S9|B2RA61	Missense_Mutation	SNP	ENST00000394684.4	37	CCDS3677.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990302	0.74589	.	.	ENSG00000164023	ENST00000394684;ENST00000359079;ENST00000394686	T;T;T	0.51817	0.69;0.69;0.69	6.07	1.13	0.20643	.	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	N	0.22421	0.69	0.44492	D	0.997432	D	0.57899	0.981	D	0.67231	0.95	T	0.45659	-0.9246	10	0.87932	D	0	-8.7719	10.0094	0.41977	0.4309:0.0:0.5691:0.0	.	363	Q8NHU3	SMS2_HUMAN	N	363	ENSP00000378176:K363N;ENSP00000351981:K363N;ENSP00000378178:K363N	ENSP00000351981:K363N	K	+	3	2	SGMS2	109051149	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	1.181000	0.32017	-0.043000	0.13513	0.533000	0.62120	AAA		0.428	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		C	108831700	A	C	108831700	3	2	61	1	0	0	0	0	1	0	0	0	14252	98	4	4	1107	4	SGMS2	4	108831700	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	96	108831700	82322576	3394	11379										
HADH	3033	broad.mit.edu	37	chr4	108930969	108930969	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaccagacagaggacatcCtggcaaaatccaaaaaggga	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:108930969C>T	ENST00000309522.3	+	2	336	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	HADH_ENST00000603302.1_Silent_p.L63L|HADH_ENST00000505878.1_Silent_p.L67L|HADH_ENST00000403312.1_Silent_p.L122L|HADH_ENST00000454409.2_Silent_p.L67L	NM_005327.4	NP_005318	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase	397					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)	p.L63L(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	15		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)		AGAGGACATCCTGGCAAAATC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4											99	98	98					4																	108930969		2203	4300	6503	109150418	SO:0001819	synonymous_variant	3033			X96752	CCDS3678.1, CCDS54790.1	4q22-q26	2012-10-02	2010-04-30		ENSG00000138796	ENSG00000138796	1.1.1.35		4799	protein-coding gene	gene with protein product		601609	"L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain", "hydroxyacyl-Coenzyme A dehydrogenase"	HADHSC		975867, 16176262	Standard	NM_001184705		Approved	HADH1, SCHAD	uc010ilx.3	Q16836	OTTHUMG00000131810	ENST00000309522.3:c.187C>T	4.37:g.108930969C>T			109150418	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000309522.3	37	CCDS3678.1																																																																																				0.378	HADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254750.2	NM_005327		T	108930969	C	T	108930969	2	4	61	1	0	0	0	0	0	0	0	1	6963	680	24	3		3	HADH	4	108930969	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99269	108930969	82223307	3395	11380										
AGXT2L1	64850	broad.mit.edu	37	chr4	109680999	109680999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtcgtggaggaatcgagAatttgtatttagcagttcca	12	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:109680999A>G	ENST00000296486.3	-	3	395	c.241T>C	c.(241-243)Tct>Cct	p.S81P	ETNPPL_ENST00000411864.2_Missense_Mutation_p.S75P|ETNPPL_ENST00000510706.1_Missense_Mutation_p.S41P|ETNPPL_ENST00000512646.1_Missense_Mutation_p.S23P	NM_001146590.1|NM_031279.3	NP_001140062.1|NP_112569.2	Q8TBG4	AT2L1_HUMAN	ethanolamine-phosphate phospho-lyase	81						mitochondrion (GO:0005739)	ethanolamine-phosphate phospho-lyase activity (GO:0050459)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.S81P(1)									AGGAATCGAGAATTTGTATTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											104	91	96					4																	109680999		2203	4300	6503	109900448	SO:0001583	missense	64850			AJ298293	CCDS3682.1, CCDS54792.1, CCDS54793.1	4q25	2013-06-12	2013-06-12	2013-06-12	ENSG00000164089	ENSG00000164089	4.2.3.2		14404	protein-coding gene	gene with protein product		614682	"alanine-glyoxylate aminotransferase 2-like 1"	AGXT2L1		7592550, 22241472	Standard	NM_031279		Approved		uc003hzc.3	Q8TBG4	OTTHUMG00000161036	ENST00000296486.3:c.241T>C	4.37:g.109680999A>G	ENSP00000296486:p.Ser81Pro		109900448	B7Z1Y0|E9PBY0|Q9H174	Missense_Mutation	SNP	ENST00000296486.3	37	CCDS3682.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.254225	0.22965	.	.	ENSG00000164089	ENST00000296486;ENST00000411864;ENST00000512646;ENST00000510706;ENST00000512320;ENST00000510723	T;T;T;T;D;D	0.85702	0.79;0.79;0.79;0.79;-2.02;-2.02	5.26	5.26	0.73747	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.181683	0.49916	N	0.000127	D	0.85177	0.5637	L	0.61036	1.89	0.51767	D	0.999935	P;B;B	0.37636	0.603;0.175;0.097	B;B;B	0.41764	0.366;0.132;0.16	D	0.84122	0.0407	9	.	.	.	-8.9024	15.1514	0.72703	1.0:0.0:0.0:0.0	.	23;75;81	E9PBY0;Q8TBG4-2;Q8TBG4	.;.;AT2L1_HUMAN	P	81;75;23;41;8;23	ENSP00000296486:S81P;ENSP00000392269:S75P;ENSP00000427065:S23P;ENSP00000423240:S41P;ENSP00000421217:S8P;ENSP00000426525:S23P	.	S	-	1	0	AGXT2L1	109900448	1.000000	0.71417	0.139000	0.22197	0.759000	0.43091	4.920000	0.63390	1.978000	0.57642	0.455000	0.32223	TCT		0.418	ETNPPL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363508.1	NM_031279		G	109680999	A	G	109680999	3	3	61	1	0	0	0	0	1	0	0	0	406	246	9	4	1302	4	AGXT2L1	4	109680999	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	750030	109680999	81473277	3396	11381										
AGXT2L1	64850	broad.mit.edu	37	chr4	109681437	109681437	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactattttgatgggatccgAtgcaaagaaaactttgcatg	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:109681437A>G	ENST00000296486.3	-	2	236	c.82T>C	c.(82-84)Tcg>Ccg	p.S28P	ETNPPL_ENST00000411864.2_Missense_Mutation_p.S28P|ETNPPL_ENST00000510706.1_5'UTR|ETNPPL_ENST00000512646.1_Intron	NM_001146590.1|NM_031279.3	NP_001140062.1|NP_112569.2	Q8TBG4	AT2L1_HUMAN	ethanolamine-phosphate phospho-lyase	28						mitochondrion (GO:0005739)	ethanolamine-phosphate phospho-lyase activity (GO:0050459)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.S28P(1)									ATGGGATCCGATGCAAAGAAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	92	92					4																	109681437		2203	4300	6503	109900886	SO:0001583	missense	64850			AJ298293	CCDS3682.1, CCDS54792.1, CCDS54793.1	4q25	2013-06-12	2013-06-12	2013-06-12	ENSG00000164089	ENSG00000164089	4.2.3.2		14404	protein-coding gene	gene with protein product		614682	"alanine-glyoxylate aminotransferase 2-like 1"	AGXT2L1		7592550, 22241472	Standard	NM_031279		Approved		uc003hzc.3	Q8TBG4	OTTHUMG00000161036	ENST00000296486.3:c.82T>C	4.37:g.109681437A>G	ENSP00000296486:p.Ser28Pro		109900886	B7Z1Y0|E9PBY0|Q9H174	Missense_Mutation	SNP	ENST00000296486.3	37	CCDS3682.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863783	0.51482	.	.	ENSG00000164089	ENST00000296486;ENST00000411864	T;T	0.42131	0.98;0.98	5.65	3.64	0.41730	.	0.543643	0.20194	N	0.097260	T	0.33265	0.0857	L	0.47190	1.495	0.80722	D	1	B;B	0.26744	0.134;0.158	B;B	0.35899	0.213;0.078	T	0.21793	-1.0235	9	.	.	.	-2.8329	1.9344	0.03333	0.3288:0.4049:0.0:0.2663	.	28;28	Q8TBG4-2;Q8TBG4	.;AT2L1_HUMAN	P	28	ENSP00000296486:S28P;ENSP00000392269:S28P	.	S	-	1	0	AGXT2L1	109900886	0.970000	0.33590	0.994000	0.49952	0.947000	0.59692	2.541000	0.45735	1.360000	0.45960	-0.445000	0.05633	TCG		0.433	ETNPPL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363508.1	NM_031279		G	109681437	A	G	109681437	3	3	61	1	0	0	0	0	1	0	0	0	406	333	12	4	1465	4	AGXT2L1	4	109681437	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	438	109681437	81472839	3397	11382										
COL25A1	84570	broad.mit.edu	37	chr4	110223040	110223040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtacaggcaagacaccaCggccaccactgacaggaggg	13	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110223040C>T	ENST00000399132.1	-	2	666	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	COL25A1_ENST00000399126.1_Missense_Mutation_p.V46M|AC004051.2_ENST00000500526.1_lincRNA|COL25A1_ENST00000399127.1_Missense_Mutation_p.V46M	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1									p.V46M(1)		NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CAAGACACCACGGCCACCACT	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	65	63					4																	110223040		2015	4162	6177	110442489	SO:0001583	missense	84570			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.136G>A	4.37:g.110223040C>T	ENSP00000382083:p.Val46Met		110442489		Missense_Mutation	SNP	ENST00000399132.1	37	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	C	10.35	1.325249	0.24080	.	.	ENSG00000188517	ENST00000399132;ENST00000333642;ENST00000401873;ENST00000399127;ENST00000399126;ENST00000443653;ENST00000505591	D;D;D	0.91945	-2.73;-2.85;-2.94	5.62	0.469	0.16741	.	0.775582	0.10957	N	0.615390	T	0.77157	0.4089	N	0.17082	0.46	0.19945	N	0.999946	P;B;B	0.41041	0.736;0.02;0.1	B;B;B	0.24394	0.053;0.01;0.012	T	0.68375	-0.5425	9	.	.	.	0.0096	3.1173	0.06379	0.1163:0.2821:0.4065:0.1951	.	46;46;46	A8MWQ5;Q9BXS0-2;Q9BXS0	.;.;COPA1_HUMAN	M	46	ENSP00000382083:V46M;ENSP00000382078:V46M;ENSP00000382077:V46M	.	V	-	1	0	COL25A1	110442489	0.000000	0.05858	0.029000	0.17559	0.580000	0.36256	-0.097000	0.11042	-0.187000	0.10516	-0.310000	0.09108	GTG		0.662	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		T	110223040	C	T	110223040	3	4	61	1	0	0	0	0	1	0	0	0	3690	536	19	1	2056	1	COL25A1	4	110223040	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541603	110223040	80931236	3398	11383										
SEC24B	10427	broad.mit.edu	37	chr4	110447413	110447413	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacttttcacggtaacttCtttgtccgttctactgattt	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110447413C>A	ENST00000265175.5	+	17	2878	c.2823C>A	c.(2821-2823)ttC>ttA	p.F941L	SEC24B_ENST00000399100.2_Missense_Mutation_p.F906L|SEC24B_ENST00000504968.2_Missense_Mutation_p.F971L	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	941					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.F906L(1)|p.F941L(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACGGTAACTTCTTTGTCCGTT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	4											204	186	191					4																	110447413		1855	4095	5950	110666862	SO:0001583	missense	10427			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2823C>A	4.37:g.110447413C>A	ENSP00000265175:p.Phe941Leu		110666862	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037459	0.75617	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.74421	-0.84;-0.84;-0.84	5.21	2.05	0.26809	Sec23/Sec24 beta-sandwich (1);	0.147998	0.64402	D	0.000009	T	0.79112	0.4391	M	0.78916	2.43	0.80722	D	1	P;P;D;P;P	0.63880	0.866;0.866;0.993;0.837;0.923	P;P;P;P;P	0.60068	0.618;0.6;0.868;0.69;0.632	T	0.76282	-0.3016	10	0.59425	D	0.04	-18.3042	2.5613	0.04772	0.2175:0.3511:0.0:0.4314	.	855;540;971;906;941	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	L	971;906;941	ENSP00000428564:F971L;ENSP00000382051:F906L;ENSP00000265175:F941L	ENSP00000265175:F941L	F	+	3	2	SEC24B	110666862	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.119000	0.31258	0.711000	0.32018	-0.218000	0.12543	TTC		0.353	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			A	110447413	C	A	110447413	3	1	61	1	0	0	0	0	1	0	0	0	14032	912	32	2	2889	2	SEC24B	4	110447413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	224373	110447413	80706863	3399	11384										
CASP6	839	broad.mit.edu	37	chr4	110610629	110610629	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaccagtgtgaggagttCtgtgaactctaaggaggagc	14	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110610629C>A	ENST00000265164.2	-	7	816	c.739G>T	c.(739-741)Gaa>Taa	p.E247*	CASP6_ENST00000352981.3_Nonsense_Mutation_p.E158*|CASP6_ENST00000510324.1_5'UTR|AC004067.5_ENST00000608733.1_RNA	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	247					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)	p.E247K(1)|p.E247*(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		GTGAGGAGTTCTGTGAACTCT	0.453																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	4											72	74	74					4																	110610629		2203	4300	6503	110830078	SO:0001587	stop_gained	839			U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"Caspases"	1507	protein-coding gene	gene with protein product		601532	"caspase 6, apoptosis-related cysteine protease"			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.739G>T	4.37:g.110610629C>A	ENSP00000265164:p.Glu247*		110830078	Q9BQE7	Nonsense_Mutation	SNP	ENST00000265164.2	37	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	C	37	6.411531	0.97546	.	.	ENSG00000138794	ENST00000352981;ENST00000265164	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	158;247	.	ENSP00000265164:E247X	E	-	1	0	CASP6	110830078	1.000000	0.71417	0.948000	0.38648	0.987000	0.75469	5.611000	0.67674	2.941000	0.99782	0.655000	0.94253	GAA		0.453	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226		A	110610629	C	A	110610629	4	1	61	1	0	0	0	0	0	1	0	0	2681	922	32	2	146	2	CASP6	4	110610629	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163216	110610629	80543647	3400	11385										
RRH	10692	broad.mit.edu	37	chr4	110749191	110749191	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttccctccaaaatgctaaGaaataatttaggcaacagtt	5	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110749191G>T	ENST00000317735.4	+	1	42	c.8G>T	c.(7-9)aGa>aTa	p.R3I		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	3					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.R3I(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		AAAATGCTAAGAAATAATTTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											131	133	133					4																	110749191		2203	4300	6503	110968640	SO:0001583	missense	10692			AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"GPCR / Class A : Opsin receptors"	10450	protein-coding gene	gene with protein product	"peropsin"	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.8G>T	4.37:g.110749191G>T	ENSP00000314992:p.Arg3Ile		110968640	A1A4V2|Q7RTS4	Missense_Mutation	SNP	ENST00000317735.4	37	CCDS3687.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.079779	0.36662	.	.	ENSG00000180245	ENST00000317735	T	0.56611	0.45	5.83	0.0298	0.14164	.	1.411240	0.03622	N	0.236608	T	0.42585	0.1209	L	0.40543	1.245	0.09310	N	0.999996	B	0.30763	0.294	B	0.19391	0.025	T	0.38394	-0.9663	10	0.87932	D	0	.	7.0653	0.25149	0.3858:0.0:0.5059:0.1084	.	3	O14718	OPSX_HUMAN	I	3	ENSP00000314992:R3I	ENSP00000314992:R3I	R	+	2	0	RRH	110968640	0.867000	0.29959	0.078000	0.20375	0.909000	0.53808	0.379000	0.20585	0.017000	0.15025	-0.237000	0.12165	AGA		0.368	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583		T	110749191	G	T	110749191	3	4	61	1	0	0	0	0	1	0	0	0	13717	942	33	2	10	2	RRH	4	110749191	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138562	110749191	80405085	3401	11386										
RRH	10692	broad.mit.edu	37	chr4	110754463	110754463	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatctgtatggaagttggaAatttggatacgcaggctgtc	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110754463A>C	ENST00000317735.4	+	2	309	c.275A>C	c.(274-276)aAa>aCa	p.K92T		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	92					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.K92T(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		GGAAGTTGGAAATTTGGATAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	66	68					4																	110754463		2203	4300	6503	110973912	SO:0001583	missense	10692			AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"GPCR / Class A : Opsin receptors"	10450	protein-coding gene	gene with protein product	"peropsin"	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.275A>C	4.37:g.110754463A>C	ENSP00000314992:p.Lys92Thr		110973912	A1A4V2|Q7RTS4	Missense_Mutation	SNP	ENST00000317735.4	37	CCDS3687.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.955032	0.73902	.	.	ENSG00000180245	ENST00000317735	T	0.19250	2.16	4.94	3.75	0.43078	GPCR, rhodopsin-like superfamily (1);	0.045911	0.85682	D	0.000000	T	0.31199	0.0789	L	0.33245	0.995	0.58432	D	0.999995	D	0.69078	0.997	D	0.67231	0.95	T	0.02683	-1.1124	10	0.66056	D	0.02	.	10.4659	0.44607	0.9223:0.0:0.0776:0.0	.	92	O14718	OPSX_HUMAN	T	92	ENSP00000314992:K92T	ENSP00000314992:K92T	K	+	2	0	RRH	110973912	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	4.973000	0.63763	0.829000	0.34733	0.482000	0.46254	AAA		0.373	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583		C	110754463	A	C	110754463	3	2	61	1	0	0	0	0	1	0	0	0	13717	14	1	4	281	4	RRH	4	110754463	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5272	110754463	80399813	3402	11387										
LRIT3	345193	broad.mit.edu	37	chr4	110788880	110788880	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgttgaccctgctatagtgCttctggatccactgatgact	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110788880C>A	ENST00000594814.1	+	3	673	c.673C>A	c.(673-675)Ctt>Att	p.L225I	LRIT3_ENST00000409621.2_Missense_Mutation_p.L42I|LRIT3_ENST00000327908.3_Missense_Mutation_p.L42I|LRIT3_ENST00000379920.3_Missense_Mutation_p.L180I	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	225	LRRCT.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.L180I(1)|p.L42I(1)		cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		TGCTATAGTGCTTCTGGATCC	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	4											146	123	131					4																	110788880		2203	4300	6503	111008329	SO:0001583	missense	345193			AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.673C>A	4.37:g.110788880C>A	ENSP00000469759:p.Leu225Ile		111008329	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791715	0.70452	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.59224	0.28;0.66;0.28	5.88	5.03	0.67393	.	0.062538	0.64402	D	0.000003	T	0.76004	0.3927	M	0.84683	2.71	0.42268	D	0.992044	D;D	0.89917	0.998;1.0	D;D	0.74023	0.942;0.982	T	0.78595	-0.2143	10	0.59425	D	0.04	.	11.5643	0.50796	0.0:0.8629:0.0:0.1371	.	180;42	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	I	42;180;42	ENSP00000328222:L42I;ENSP00000369252:L180I;ENSP00000386734:L42I	ENSP00000328222:L42I	L	+	1	0	LRIT3	111008329	1.000000	0.71417	0.997000	0.53966	0.654000	0.38779	1.932000	0.40143	2.789000	0.95967	0.655000	0.94253	CTT		0.458	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		A	110788880	C	A	110788880	3	1	61	1	0	0	0	0	1	0	0	0	8978	797	28	2	544	2	LRIT3	4	110788880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34417	110788880	80365396	3403	11388										
LRIT3	345193	broad.mit.edu	37	chr4	110791167	110791167	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcctcctccactgtttCttcaaccacaactctgagca	3	16	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:110791167C>A	ENST00000594814.1	+	4	1262	c.1262C>A	c.(1261-1263)tCt>tAt	p.S421Y	LRIT3_ENST00000409621.2_Missense_Mutation_p.S238Y|LRIT3_ENST00000327908.3_Missense_Mutation_p.S238Y|LRIT3_ENST00000379920.3_Missense_Mutation_p.S376Y	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	421	Ser-rich.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S238Y(1)|p.S376Y(1)		cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		tccactgtttcttcAACCACA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	4											130	122	125					4																	110791167		2203	4300	6503	111010616	SO:0001583	missense	345193			AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1262C>A	4.37:g.110791167C>A	ENSP00000469759:p.Ser421Tyr		111010616	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	C	12.80	2.048021	0.36085	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.59638	0.25;0.44;0.25	4.8	3.95	0.45737	.	0.659654	0.15802	N	0.243901	T	0.53077	0.1774	L	0.36672	1.1	0.09310	N	1	P;P	0.49635	0.764;0.926	B;P	0.47528	0.2;0.549	T	0.49062	-0.8978	10	0.66056	D	0.02	.	11.2857	0.49220	0.0:0.9065:0.0:0.0935	.	376;238	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	Y	238;376;238	ENSP00000328222:S238Y;ENSP00000369252:S376Y;ENSP00000386734:S238Y	ENSP00000328222:S238Y	S	+	2	0	LRIT3	111010616	0.973000	0.33851	0.250000	0.24296	0.509000	0.34042	3.724000	0.54962	2.198000	0.70561	0.655000	0.94253	TCT		0.468	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		A	110791167	C	A	110791167	3	1	61	1	0	0	0	0	1	0	0	0	8978	913	32	2	1137	2	LRIT3	4	110791167	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2287	110791167	80363109	3404	11389										
ENPEP	2028	broad.mit.edu	37	chr4	111441454	111441454	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaacgtgaacggtgtcaaGaacatcacacagaaacgctt	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:111441454G>T	ENST00000265162.5	+	10	2001	c.1659G>T	c.(1657-1659)aaG>aaT	p.K553N	RP11-380D23.1_ENST00000503998.1_RNA	NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	553					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.K553N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		ACGGTGTCAAGAACATCACAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4											140	125	130					4																	111441454		2203	4300	6503	111660903	SO:0001583	missense	2028			L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.1659G>T	4.37:g.111441454G>T	ENSP00000265162:p.Lys553Asn		111660903	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	4.198	0.035426	0.08148	.	.	ENSG00000138792	ENST00000265162	T	0.01388	4.95	5.52	-2.64	0.06114	.	1.013650	0.07876	N	0.968808	T	0.00845	0.0028	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49409	-0.8943	10	0.14656	T	0.56	.	1.0552	0.01589	0.3015:0.1029:0.1786:0.4171	.	553	Q07075	AMPE_HUMAN	N	553	ENSP00000265162:K553N	ENSP00000265162:K553N	K	+	3	2	ENPEP	111660903	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.091000	0.11146	-0.206000	0.10203	-0.142000	0.14014	AAG		0.438	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			T	111441454	G	T	111441454	3	4	61	1	0	0	0	0	1	0	0	0	5141	933	33	2	1697	2	ENPEP	4	111441454	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	650287	111441454	79712822	3405	11390										
NEUROG2	63973	broad.mit.edu	37	chr4	113436164	113436164	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccagatgtagttgtgggcGaagcgcagggtctcgatctt	15	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:113436164G>A	ENST00000313341.3	-	2	794	c.468C>T	c.(466-468)ttC>ttT	p.F156F	RP11-402J6.1_ENST00000504009.1_RNA|RP11-402J6.1_ENST00000506057.1_RNA	NM_024019.3	NP_076924.1	Q9H2A3	NGN2_HUMAN	neurogenin 2	156	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				axon guidance (GO:0007411)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)	p.F156F(1)		central_nervous_system(1)|large_intestine(3)|lung(6)|skin(2)	12		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)		AGTTGTGGGCGAAGCGCAGGG	0.701																																																1	Substitution - coding silent(1)	large_intestine(1)	4											48	48	48					4																	113436164		2203	4300	6503	113655613	SO:0001819	synonymous_variant	63973			AF303002	CCDS3698.1	4q25	2013-05-21			ENSG00000178403	ENSG00000178403		"Basic helix-loop-helix proteins"	13805	protein-coding gene	gene with protein product		606624					Standard	NM_024019		Approved	Atoh4, Math4A, ngn-2, bHLHa8, NGN2	uc003ias.3	Q9H2A3	OTTHUMG00000132907	ENST00000313341.3:c.468C>T	4.37:g.113436164G>A			113655613	Q8N416	Silent	SNP	ENST00000313341.3	37	CCDS3698.1																																																																																				0.701	NEUROG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256414.1	NM_024019		A	113436164	G	A	113436164	2	1	61	1	0	0	0	0	0	0	0	1	10384	1049	37	1		1	NEUROG2	4	113436164	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1994710	113436164	77718112	3406	11391										
C4orf21	55345	broad.mit.edu	37	chr4	113527240	113527240	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcttctttacttcccgagGaagagaactaggataaaata	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:113527240G>T	ENST00000505019.1	-	9	2851	c.2726C>A	c.(2725-2727)tCc>tAc	p.S909Y	C4orf21_ENST00000309071.5_Missense_Mutation_p.S909Y	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		909						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.S909Y(2)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ACTTCCCGAGGAAGAGAACTA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	4											66	75	72					4																	113527240		2203	4299	6502	113746689	SO:0001583	missense	55345																														ENST00000505019.1:c.2726C>A	4.37:g.113527240G>T	ENSP00000424737:p.Ser909Tyr		113746689	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		.	.	.	.	.	.	.	.	.	.	G	14.71	2.617942	0.46736	.	.	ENSG00000138658	ENST00000505019;ENST00000309071	D;T	0.84070	-1.8;1.69	5.03	5.03	0.67393	.	1.159930	0.06414	N	0.721095	D	0.88043	0.6331	L	0.47716	1.5	0.80722	D	1	D;D	0.58620	0.971;0.983	P;P	0.58873	0.751;0.847	T	0.80672	-0.1278	10	0.72032	D	0.01	5.5705	13.8469	0.63472	0.0:0.0:1.0:0.0	.	909;909	Q86YA3;G5EA02	CD021_HUMAN;.	Y	909	ENSP00000424737:S909Y;ENSP00000309095:S909Y	ENSP00000309095:S909Y	S	-	2	0	C4orf21	113746689	0.997000	0.39634	0.457000	0.27056	0.840000	0.47671	3.421000	0.52742	2.315000	0.78130	0.650000	0.86243	TCC		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			T	113527240	G	T	113527240	3	4	61	1	0	0	0	0	1	0	0	0	2260	1174	41	2	3668	2	C4orf21	4	113527240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91076	113527240	77627036	3407	11392										
ANK2	287	broad.mit.edu	37	chr4	114195738	114195738	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactgcacatctctgcccGggagggccaggtggatgtgg	15	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114195738G>A	ENST00000357077.4	+	15	1669	c.1616G>A	c.(1615-1617)cGg>cAg	p.R539Q	ANK2_ENST00000394537.3_Missense_Mutation_p.R539Q|ANK2_ENST00000264366.6_Missense_Mutation_p.R539Q|ANK2_ENST00000506722.1_Missense_Mutation_p.R518Q	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	539					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R539Q(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATCTCTGCCCGGGAGGGCCAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	90	91					4																	114195738		2203	4300	6503	114415187	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.1616G>A	4.37:g.114195738G>A	ENSP00000349588:p.Arg539Gln		114415187	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	36	5.839351	0.97009	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.62	5.62	0.85841	Ankyrin repeat-containing domain (3);	0.000000	0.53938	D	0.000059	T	0.64962	0.2646	N	0.10733	0.035	0.80722	D	1	D;P;D;P;D	0.89917	1.0;0.93;0.996;0.679;0.985	D;B;P;B;P	0.77557	0.99;0.156;0.827;0.069;0.685	T	0.71712	-0.4510	10	0.51188	T	0.08	.	19.6591	0.95857	0.0:0.0:1.0:0.0	.	539;539;539;518;518	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	Q	518;518;518;554;539;539;539;518	ENSP00000423799:R518Q;ENSP00000421011:R518Q;ENSP00000421067:R518Q;ENSP00000424722:R554Q;ENSP00000378044:R539Q;ENSP00000349588:R539Q;ENSP00000264366:R539Q	ENSP00000264366:R539Q	R	+	2	0	ANK2	114415187	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.792000	0.99085	2.631000	0.89168	0.650000	0.86243	CGG		0.527	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114195738	G	A	114195738	3	1	61	1	0	0	0	0	1	0	0	0	621	1116	39	1	1699	1	ANK2	4	114195738	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	668498	114195738	76958538	3408	11393										
ANK2	287	broad.mit.edu	37	chr4	114274518	114274518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcagtgtgcagagctctCggtctgagagaggattagtt	14	6	2	3	rs35249198	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114274518C>T	ENST00000357077.4	+	38	4797	c.4744C>T	c.(4744-4746)Cgg>Tgg	p.R1582W	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.R1549W|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1582					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R1582W(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GCAGAGCTCTCGGTCTGAGAG	0.408													C|||	16	0.00319489	0.0106	0	5008	,	,		21394	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						C	,TRP/ARG,	39,4367	40.0+/-72.8	1,37,2165	81	87	85		,4744,	4	0	4	dbSNP_126	85	10,8590	7.7+/-29.5	0,10,4290	yes	intron,missense,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,101,	1,47,6455	TT,TC,CC		0.1163,0.8852,0.3767	,possibly-damaging,	,1582/3958,	114274518	49,12957	2203	4300	6503	114493967	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4744C>T	4.37:g.114274518C>T	ENSP00000349588:p.Arg1582Trp		114493967	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	9	0.004120879120879121	7	0.014227642276422764	0	0.0	0	0.0	2	0.002638522427440633	C	7.739	0.700973	0.15172	0.008852	0.001163	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.68181	-0.06;-0.16;-0.27;-0.31	4.9	4.03	0.46877	.	1.073890	0.07232	N	0.862650	T	0.53706	0.1813	N	0.19112	0.55	0.37583	D	0.919903	P;D	0.56521	0.914;0.976	B;P	0.49047	0.316;0.599	T	0.54721	-0.8251	10	0.66056	D	0.02	.	11.0745	0.48023	0.1448:0.7156:0.1396:0.0	rs35249198	1549;1582	Q01484;Q01484-4	ANK2_HUMAN;.	W	1495;1597;1582;1549	ENSP00000421011:R1495W;ENSP00000424722:R1597W;ENSP00000349588:R1582W;ENSP00000264366:R1549W	ENSP00000264366:R1549W	R	+	1	2	ANK2	114493967	0.638000	0.27225	0.016000	0.15963	0.010000	0.07245	2.117000	0.41939	1.152000	0.42452	0.557000	0.71058	CGG		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114274518	C	T	114274518	3	4	61	1	0	0	0	0	1	0	0	0	621	875	31	1	4959	1	ANK2	4	114274518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78780	114274518	76879758	3409	11394										
ANK2	287	broad.mit.edu	37	chr4	114275276	114275276	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagacactctactctttcCtcttccgcaaaaactgaaag	5	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114275276C>A	ENST00000357077.4	+	38	5555	c.5502C>A	c.(5500-5502)tcC>tcA	p.S1834S	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Silent_p.S1801S|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1834	Repeat-rich region.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.S1834S(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTACTCTTTCCTCTTCCGCAA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	4											116	124	121					4																	114275276		2203	4300	6503	114494725	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.5502C>A	4.37:g.114275276C>A			114494725	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.507	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114275276	C	A	114275276	2	1	61	1	0	0	0	0	0	0	0	1	621	668	24	2		2	ANK2	4	114275276	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	758	114275276	76879000	3410	11395										
ANK2	287	broad.mit.edu	37	chr4	114290809	114290809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccccaacatccagcgagCggggaggctctcccatcata	10	15	2	1	rs199922285	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114290809C>T	ENST00000357077.4	+	43	11511	c.11458C>T	c.(11458-11460)Cgg>Tgg	p.R3820W	ANK2_ENST00000510275.2_Missense_Mutation_p.R387W|ANK2_ENST00000509550.1_Missense_Mutation_p.R911W|ANK2_ENST00000394537.3_Missense_Mutation_p.R1735W|ANK2_ENST00000264366.6_Missense_Mutation_p.R3787W|ANK2_ENST00000506722.1_Missense_Mutation_p.R1726W	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3820					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R3820W(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATCCAGCGAGCGGGGAGGCTC	0.577													C|||	2	0.000399361	0	0.0014	5008	,	,		17408	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	4											59	59	59					4																	114290809		2203	4300	6503	114510258	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.11458C>T	4.37:g.114290809C>T	ENSP00000349588:p.Arg3820Trp		114510258	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	11.87|11.87	1.767170|1.767170	0.31320|0.31320	.|.	.|.	ENSG00000145362|ENSG00000145362	ENST00000514960|ENST00000506722;ENST00000431447;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550;ENST00000510275;ENST00000505342	.|T;T;T;T;T;D;D	.|0.96300	.|-0.31;-0.29;-0.33;-0.34;-1.07;-2.06;-3.97	5.55|5.55	1.72|1.72	0.24424|0.24424	.|.	.|1.413780	.|0.04913	.|N	.|0.453559	D|D	0.93562|0.93562	0.7945|0.7945	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	.|P;B;P;D;B;B	.|0.57257	.|0.88;0.003;0.66;0.979;0.018;0.02	.|B;B;B;B;B;B	.|0.43123	.|0.153;0.002;0.083;0.409;0.01;0.021	D|D	0.85641|0.85641	0.1276|0.1276	5|10	.|0.87932	.|D	.|0	.|.	5.8414|5.8414	0.18635|0.18635	0.3686:0.4574:0.109:0.065|0.3686:0.4574:0.109:0.065	.|.	.|911;770;736;1735;3820;1726	.|E9PCH6;F8W694;Q7Z344;Q01484-2;Q01484-4;Q01484-5	.|.;.;.;.;.;.	V|W	736|1726;770;1735;3820;3787;1726;911;387;830	.|ENSP00000421067:R1726W;ENSP00000378044:R1735W;ENSP00000349588:R3820W;ENSP00000264366:R3787W;ENSP00000426944:R911W;ENSP00000421023:R387W;ENSP00000422498:R830W	.|ENSP00000264366:R3787W	A|R	+|+	2|1	0|2	ANK2|ANK2	114510258|114510258	0.008000|0.008000	0.16893|0.16893	0.001000|0.001000	0.08648|0.08648	0.042000|0.042000	0.13812|0.13812	0.219000|0.219000	0.17641|0.17641	0.058000|0.058000	0.16222|0.16222	0.650000|0.650000	0.86243|0.86243	GCG|CGG		0.577	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114290809	C	T	114290809	3	4	61	1	0	0	0	0	1	0	0	0	621	759	27	1	11693	1	ANK2	4	114290809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15533	114290809	76863467	3411	11396										
CAMK2D	817	broad.mit.edu	37	chr4	114469873	114469873	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaacactttctagaatctgCtgtatacaatgactgcaaag	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114469873C>A	ENST00000342666.5	-	6	353	c.354G>T	c.(352-354)caG>caT	p.Q118H	CAMK2D_ENST00000394524.3_Missense_Mutation_p.Q118H|CAMK2D_ENST00000379773.2_Missense_Mutation_p.Q118H|CAMK2D_ENST00000511664.1_Intron|CAMK2D_ENST00000418639.2_Missense_Mutation_p.Q118H|CAMK2D_ENST00000508738.1_Missense_Mutation_p.Q118H|CAMK2D_ENST00000394522.3_Missense_Mutation_p.Q118H|CAMK2D_ENST00000296402.5_Missense_Mutation_p.Q118H|CAMK2D_ENST00000394526.2_Missense_Mutation_p.Q118H|CAMK2D_ENST00000454265.2_Missense_Mutation_p.Q118H|CAMK2D_ENST00000429180.1_Missense_Mutation_p.Q118H|CAMK2D_ENST00000505990.1_Intron|CAMK2D_ENST00000515496.1_Missense_Mutation_p.Q118H|CAMK2D_ENST00000514328.1_Missense_Mutation_p.Q118H			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	118	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)	p.Q118H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		CTAGAATCTGCTGTATACAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											89	85	87					4																	114469873		2203	4300	6503	114689322	SO:0001583	missense	817			U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.354G>T	4.37:g.114469873C>A	ENSP00000339740:p.Gln118His		114689322	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Missense_Mutation	SNP	ENST00000342666.5	37	CCDS3703.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811753	0.50527	.	.	ENSG00000145349	ENST00000394524;ENST00000454265;ENST00000429180;ENST00000418639;ENST00000394526;ENST00000296402;ENST00000342666;ENST00000515496;ENST00000514328;ENST00000394522;ENST00000379773;ENST00000508738	T;T;T;T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.53	4.67	0.58626	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28699	0.0711	N	0.10685	0.025	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.15809	-1.0424	10	0.24483	T	0.36	.	13.4644	0.61245	0.0:0.9235:0.0:0.0765	.	118;118;118;118	Q13557-3;Q13557-6;Q13557-12;Q13557	.;.;.;KCC2D_HUMAN	H	118	ENSP00000378032:Q118H;ENSP00000415248:Q118H;ENSP00000415707:Q118H;ENSP00000406131:Q118H;ENSP00000378034:Q118H;ENSP00000296402:Q118H;ENSP00000339740:Q118H;ENSP00000423482:Q118H;ENSP00000423677:Q118H;ENSP00000378030:Q118H;ENSP00000369098:Q118H;ENSP00000422566:Q118H	ENSP00000296402:Q118H	Q	-	3	2	CAMK2D	114689322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.515000	0.60489	1.313000	0.45069	0.650000	0.86243	CAG		0.363	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2			A	114469873	C	A	114469873	3	1	61	1	0	0	0	0	1	0	0	0	2607	796	28	2	1292	2	CAMK2D	4	114469873	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179064	114469873	76684403	3412	11397										
ARSJ	79642	broad.mit.edu	37	chr4	114824392	114824392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataatggatcggtagtgttCgaaatacctgccaggagctt	12	7	0	0	rs200459738		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114824392C>T	ENST00000315366.7	-	2	1704	c.838G>A	c.(838-840)Gaa>Aaa	p.E280K	ARSJ_ENST00000541197.1_Missense_Mutation_p.E280K	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	280					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.E280K(1)		endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		CGGTAGTGTTCGAAATACCTG	0.418													C|||	1	0.000199681	0	0	5008	,	,		22078	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											119	110	112					4																	114824392		1962	4167	6129	115043841	SO:0001583	missense	79642				CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"Arylsulfatase family"	26286	protein-coding gene	gene with protein product		610010	"arylsulfatase J"			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.838G>A	4.37:g.114824392C>T	ENSP00000320219:p.Glu280Lys		115043841	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Missense_Mutation	SNP	ENST00000315366.7	37	CCDS43264.1	.	.	.	.	.	.	.	.	.	.	C	5.021	0.189605	0.09547	.	.	ENSG00000180801	ENST00000315366;ENST00000541197	D;D	0.96427	-4.01;-4.01	5.64	3.92	0.45320	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.134780	0.48286	N	0.000188	D	0.90577	0.7046	N	0.12961	0.28	0.37040	D	0.897114	P;P	0.38617	0.64;0.64	B;B	0.40199	0.265;0.322	D	0.87832	0.2645	10	0.10902	T	0.67	.	11.9815	0.53123	0.0:0.8604:0.0:0.1396	.	280;280	Q1HA39;Q5FYB0	.;ARSJ_HUMAN	K	280	ENSP00000320219:E280K;ENSP00000438836:E280K	ENSP00000320219:E280K	E	-	1	0	ARSJ	115043841	0.998000	0.40836	0.501000	0.27601	0.948000	0.59901	2.351000	0.44071	0.745000	0.32763	0.655000	0.94253	GAA		0.418	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590		T	114824392	C	T	114824392	3	4	61	1	0	0	0	0	1	0	0	0	996	893	31	1	965	1	ARSJ	4	114824392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	354519	114824392	76329884	3413	11398										
ARSJ	79642	broad.mit.edu	37	chr4	114824517	114824517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagtgtacatctgtgtgGagtatatgccattgtcatag	11	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:114824517G>A	ENST00000315366.7	-	2	1579	c.713C>T	c.(712-714)tCc>tTc	p.S238F	ARSJ_ENST00000541197.1_Missense_Mutation_p.S238F	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	238					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.S238F(1)		endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		CATCTGTGTGGAGTATATGCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											150	143	145					4																	114824517		2004	4178	6182	115043966	SO:0001583	missense	79642				CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"Arylsulfatase family"	26286	protein-coding gene	gene with protein product		610010	"arylsulfatase J"			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.713C>T	4.37:g.114824517G>A	ENSP00000320219:p.Ser238Phe		115043966	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Missense_Mutation	SNP	ENST00000315366.7	37	CCDS43264.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139073	0.77775	.	.	ENSG00000180801	ENST00000315366;ENST00000541197	D;D	0.98807	-5.15;-5.15	5.54	5.54	0.83059	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.64402	D	0.000002	D	0.99158	0.9709	M	0.83852	2.665	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99568	1.0970	10	0.39692	T	0.17	.	19.4812	0.95011	0.0:0.0:1.0:0.0	.	238;238	Q1HA39;Q5FYB0	.;ARSJ_HUMAN	F	238	ENSP00000320219:S238F;ENSP00000438836:S238F	ENSP00000320219:S238F	S	-	2	0	ARSJ	115043966	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.742000	0.98846	2.600000	0.87896	0.655000	0.94253	TCC		0.408	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590		A	114824517	G	A	114824517	3	1	61	1	0	0	0	0	1	0	0	0	996	1174	41	3	1090	3	ARSJ	4	114824517	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125	114824517	76329759	3414	11399										
UGT8	7368	broad.mit.edu	37	chr4	115544340	115544340	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggagattgacagcaatcGaactgtttgacatactggat	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:115544340G>A	ENST00000310836.6	+	2	826	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K	UGT8_ENST00000394511.3_Missense_Mutation_p.E102K	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	102					axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)	p.E102K(3)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		GACAGCAATCGAACTGTTTGA	0.463																																																3	Substitution - Missense(3)	large_intestine(3)	4											147	144	145					4																	115544340		2203	4300	6503	115763789	SO:0001583	missense	7368			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"UDP glucuronosyltransferases"	12555	protein-coding gene	gene with protein product	"2-hydroxyacylsphingosine 1-beta-galactosyltransferase"	601291	"UDP-galactose ceramide galactosyltransferase"	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.304G>A	4.37:g.115544340G>A	ENSP00000311648:p.Glu102Lys		115763789	B3KXU7|O00196	Missense_Mutation	SNP	ENST00000310836.6	37	CCDS3705.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.491704	0.84962	.	.	ENSG00000174607	ENST00000310836;ENST00000507710;ENST00000394511	T;T;T	0.07688	3.17;3.17;3.17	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.06917	0.0176	N	0.17594	0.5	0.80722	D	1	P	0.34837	0.472	B	0.34824	0.19	T	0.47381	-0.9122	10	0.15499	T	0.54	.	19.0796	0.93177	0.0:0.0:1.0:0.0	.	102	Q16880	CGT_HUMAN	K	102	ENSP00000311648:E102K;ENSP00000421446:E102K;ENSP00000378019:E102K	ENSP00000311648:E102K	E	+	1	0	UGT8	115763789	1.000000	0.71417	0.941000	0.38009	0.974000	0.67602	7.614000	0.82996	2.590000	0.87494	0.650000	0.86243	GAA		0.463	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	NM_003360		A	115544340	G	A	115544340	3	1	61	1	0	0	0	0	1	0	0	0	17005	1059	37	1	306	1	UGT8	4	115544340	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	719823	115544340	75609936	3415	11400										
UGT8	7368	broad.mit.edu	37	chr4	115597407	115597407	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaatggcaagtacaaaaGaaatggccatattaaacatg	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:115597407G>T	ENST00000310836.6	+	6	2111	c.1589G>T	c.(1588-1590)aGa>aTa	p.R530I	UGT8_ENST00000394511.3_Missense_Mutation_p.R530I	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	530					axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)	p.R530I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		AAGTACAAAAGAAATGGCCAT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											73	71	72					4																	115597407		2203	4300	6503	115816856	SO:0001583	missense	7368			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"UDP glucuronosyltransferases"	12555	protein-coding gene	gene with protein product	"2-hydroxyacylsphingosine 1-beta-galactosyltransferase"	601291	"UDP-galactose ceramide galactosyltransferase"	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.1589G>T	4.37:g.115597407G>T	ENSP00000311648:p.Arg530Ile		115816856	B3KXU7|O00196	Missense_Mutation	SNP	ENST00000310836.6	37	CCDS3705.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.259837	0.59321	.	.	ENSG00000174607	ENST00000310836;ENST00000394511	T;T	0.61158	0.13;0.13	6.06	5.22	0.72569	.	0.377447	0.34507	N	0.003918	T	0.39384	0.1076	N	0.08118	0	0.49798	D	0.999829	B	0.22480	0.07	B	0.28011	0.085	T	0.34551	-0.9824	10	0.62326	D	0.03	.	11.1657	0.48541	0.139:0.0:0.861:0.0	.	530	Q16880	CGT_HUMAN	I	530	ENSP00000311648:R530I;ENSP00000378019:R530I	ENSP00000311648:R530I	R	+	2	0	UGT8	115816856	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	4.660000	0.61511	1.569000	0.49696	0.655000	0.94253	AGA		0.318	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	NM_003360		T	115597407	G	T	115597407	3	4	61	1	0	0	0	0	1	0	0	0	17005	942	33	2	1607	2	UGT8	4	115597407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53067	115597407	75556869	3416	11401										
METTL14	57721	broad.mit.edu	37	chr4	119631236	119631236	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcagtgctcctaattccTacttgactggttgtacagaa	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:119631236T>C	ENST00000388822.5	+	11	1317	c.1150T>C	c.(1150-1152)Tac>Cac	p.Y384H	METTL14_ENST00000506780.1_Missense_Mutation_p.Y346H			Q9HCE5	MET14_HUMAN	methyltransferase like 14	384					mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)	p.Y384H(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						TCCTAATTCCTACTTGACTGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											104	105	105					4																	119631236		2203	4300	6503	119850684	SO:0001583	missense	57721			AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.1150T>C	4.37:g.119631236T>C	ENSP00000373474:p.Tyr384His		119850684	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	37	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454091	0.26161	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.62	4.49	0.54785	.	0.277182	0.39834	N	0.001243	T	0.37073	0.0990	L	0.48642	1.525	0.34414	D	0.696669	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.002	T	0.39078	-0.9631	9	0.15499	T	0.54	-12.3521	3.2249	0.06729	0.0:0.3408:0.0:0.6592	.	346;384	D6RBL4;Q9HCE5	.;MTL14_HUMAN	H	384;346	.	ENSP00000373474:Y384H	Y	+	1	0	METTL14	119850684	0.993000	0.37304	1.000000	0.80357	0.979000	0.70002	2.457000	0.45005	2.141000	0.66446	0.528000	0.53228	TAC		0.458	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		C	119631236	T	C	119631236	3	2	61	1	0	0	0	0	1	0	0	0	9528	1522	53	4	1192	4	METTL14	4	119631236	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4033829	119631236	71523040	3417	11402										
MYOZ2	51778	broad.mit.edu	37	chr4	120085416	120085416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaaaattcaacaccacaGctgtccctaagtactatcaa	4	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120085416G>A	ENST00000307128.5	+	5	640	c.427G>A	c.(427-429)Gct>Act	p.A143T		NM_016599.4	NP_057683.1			myozenin 2									p.A143T(1)		endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						CAACACCACAGCTGTCCCTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	76	75					4																	120085416		2203	4300	6503	120304864	SO:0001583	missense	51778			AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"chromosome 4 open reading frame 5"	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.427G>A	4.37:g.120085416G>A	ENSP00000306997:p.Ala143Thr		120304864		Missense_Mutation	SNP	ENST00000307128.5	37	CCDS3711.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470288	0.84533	.	.	ENSG00000172399	ENST00000307128	T	0.65732	-0.17	5.96	5.07	0.68467	.	0.258495	0.43260	D	0.000584	T	0.61223	0.2330	L	0.38531	1.155	0.46356	D	0.999002	P	0.48998	0.918	P	0.48425	0.577	T	0.64753	-0.6333	10	0.66056	D	0.02	-19.557	15.8698	0.79108	0.0:0.0:0.7924:0.2076	.	143	Q9NPC6	MYOZ2_HUMAN	T	143	ENSP00000306997:A143T	ENSP00000306997:A143T	A	+	1	0	MYOZ2	120304864	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	3.264000	0.51553	2.826000	0.97356	0.655000	0.94253	GCT		0.398	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2			A	120085416	G	A	120085416	3	1	61	1	0	0	0	0	1	0	0	0	10126	971	34	3	441	3	MYOZ2	4	120085416	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	454180	120085416	71068860	3418	11403										
USP53	54532	broad.mit.edu	37	chr4	120166520	120166520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaattggatatattccgacGaagcttgcgggttttgactg	12	7	0	1	rs201205533		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120166520G>A	ENST00000274030.6	+	6	1352	c.173G>A	c.(172-174)cGa>cAa	p.R58Q	USP53_ENST00000450251.1_Missense_Mutation_p.R58Q	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53									p.R58Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						ATATTCCGACGAAGCTTGCGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	GLN/ARG	0,3636		0,0,1818	214	193	200		173	5.2	1	4		200	5,8159		0,5,4077	yes	missense	USP53	NM_019050.2	43	0,5,5895	AA,AG,GG		0.0612,0.0,0.0424	probably-damaging	58/1074	120166520	5,11795	1818	4082	5900	120385968	SO:0001583	missense	54532			BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.173G>A	4.37:g.120166520G>A	ENSP00000274030:p.Arg58Gln		120385968		Missense_Mutation	SNP	ENST00000274030.6	37	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.216619	0.79352	0.0	6.12E-4	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.30714	1.52;1.52	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.186606	0.47093	D	0.000253	T	0.43233	0.1238	M	0.79475	2.455	0.41149	D	0.986014	P	0.47484	0.896	B	0.43809	0.432	T	0.51100	-0.8748	10	0.52906	T	0.07	-5.0866	19.1462	0.93469	0.0:0.0:1.0:0.0	.	58	Q70EK8	UBP53_HUMAN	Q	58	ENSP00000274030:R58Q;ENSP00000409906:R58Q	ENSP00000274030:R58Q	R	+	2	0	USP53	120385968	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.641000	0.98458	2.583000	0.87209	0.655000	0.94253	CGA		0.338	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		A	120166520	G	A	120166520	3	1	61	1	0	0	0	0	1	0	0	0	17124	1058	37	1	179	1	USP53	4	120166520	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81104	120166520	70987756	3419	11404										
FABP2	2169	broad.mit.edu	37	chr4	120240735	120240735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcggacagtattcagttCgtttccattgtctgtccgtt	8	10	3	0	rs375920710		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120240735C>T	ENST00000274024.3	-	3	591	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	102					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)	p.E102K(1)		breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	GTATTCAGTTCGTTTCCATTG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	LYS/GLU	0,4406		0,0,2203	130	122	124		304	4.6	0.2	4		124	2,8598	2.2+/-6.3	0,2,4298	no	missense	FABP2	NM_000134.3	56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	102/133	120240735	2,13004	2203	4300	6503	120460183	SO:0001583	missense	2169			J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"Fatty acid binding protein family"	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.304G>A	4.37:g.120240735C>T	ENSP00000274024:p.Glu102Lys		120460183	Q2NKJ1	Missense_Mutation	SNP	ENST00000274024.3	37	CCDS3712.1	.	.	.	.	.	.	.	.	.	.	C	7.451	0.642691	0.14451	0.0	2.33E-4	ENSG00000145384	ENST00000274024	T	0.44083	0.93	5.49	4.64	0.57946	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.650519	0.16263	N	0.222132	T	0.31888	0.0811	L	0.31207	0.915	0.09310	N	1	B	0.32893	0.389	B	0.33521	0.165	T	0.13124	-1.0521	10	0.23891	T	0.37	.	13.3814	0.60768	0.0:0.9236:0.0:0.0764	.	102	P12104	FABPI_HUMAN	K	102	ENSP00000274024:E102K	ENSP00000274024:E102K	E	-	1	0	FABP2	120460183	0.000000	0.05858	0.203000	0.23512	0.639000	0.38242	1.151000	0.31651	2.589000	0.87451	0.650000	0.86243	GAA		0.308	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134		T	120240735	C	T	120240735	3	4	61	1	0	0	0	0	1	0	0	0	5373	893	31	1	102	1	FABP2	4	120240735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74215	120240735	70913541	3420	11405										
PDE5A	8654	broad.mit.edu	37	chr4	120427077	120427077	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttataagttcaaaaaattCtcctcgcctcctacaatgtt	3	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120427077C>A	ENST00000354960.3	-	17	2519	c.2200G>T	c.(2200-2202)Gaa>Taa	p.E734*	PDE5A_ENST00000264805.5_Nonsense_Mutation_p.E692*|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000394439.1_Nonsense_Mutation_p.E682*	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	734	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.E734*(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TCAAAAAATTCTCCTCGCCTC	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											37	40	39					4																	120427077		2198	4283	6481	120646525	SO:0001587	stop_gained	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.2200G>T	4.37:g.120427077C>A	ENSP00000347046:p.Glu734*		120646525	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Nonsense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	44|44	11.244632|11.244632	0.99536|0.99536	.|.	.|.	ENSG00000138735|ENSG00000138735	ENST00000503412|ENST00000354960;ENST00000394439;ENST00000264805	.|.	.|.	.|.	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	0.178545|0.178545	0.64402|0.64402	D|D	0.000012|0.000012	T|.	0.60038|.	0.2238|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.50800|.	-0.8785|.	4|.	.|0.07990	.|T	.|0.79	.|.	19.9507|19.9507	0.97198|0.97198	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	85|734;682;692	.|.	.|ENSP00000264805:E692X	E|E	-|-	3|1	2|0	PDE5A|PDE5A	120646525|120646525	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.784000|6.784000	0.75084|0.75084	2.763000|2.763000	0.94921|0.94921	0.655000|0.655000	0.94253|0.94253	GAG|GAA		0.318	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		A	120427077	C	A	120427077	4	1	61	1	0	0	0	0	0	1	0	0	11675	922	32	2	447	2	PDE5A	4	120427077	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	186342	120427077	70727199	3421	11406										
PDE5A	8654	broad.mit.edu	37	chr4	120428818	120428818	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgattattttcaacgtggtCttatattcttcaatggagag	8	5	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120428818C>A	ENST00000354960.3	-	16	2449	c.2130G>T	c.(2128-2130)aaG>aaT	p.K710N	PDE5A_ENST00000264805.5_Missense_Mutation_p.K668N|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000394439.1_Missense_Mutation_p.K658N	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	710	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.K710N(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TCAACGTGGTCTTATATTCTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	87	86					4																	120428818		2203	4300	6503	120648266	SO:0001583	missense	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.2130G>T	4.37:g.120428818C>A	ENSP00000347046:p.Lys710Asn		120648266	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.5|21.5	4.152547|4.152547	0.78001|0.78001	.|.	.|.	ENSG00000138735|ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805|ENST00000503412	D;D;D|.	0.81579|.	-1.51;-1.51;-1.51|.	5.94|5.94	5.94|5.94	0.96194|0.96194	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72630|0.72630	0.3484|0.3484	L|L	0.53617|0.53617	1.68|1.68	0.80722|0.80722	D|D	1|1	B;P|.	0.40332|.	0.135;0.713|.	B;B|.	0.34991|.	0.069;0.193|.	T|T	0.67114|0.67114	-0.5752|-0.5752	10|5	0.45353|.	T|.	0.12|.	.|.	20.3658|20.3658	0.98878|0.98878	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	710;668|.	O76074;O76074-2|.	PDE5A_HUMAN;.|.	N|I	710;658;668|62	ENSP00000347046:K710N;ENSP00000377957:K658N;ENSP00000264805:K668N|.	ENSP00000264805:K668N|.	K|R	-|-	3|2	2|0	PDE5A|PDE5A	120648266|120648266	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.866000|0.866000	0.49608|0.49608	2.233000|2.233000	0.43027|0.43027	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	AAG|AGA		0.343	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		A	120428818	C	A	120428818	3	1	61	1	0	0	0	0	1	0	0	0	11675	912	32	2	521	2	PDE5A	4	120428818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1741	120428818	70725458	3422	11407										
PDE5A	8654	broad.mit.edu	37	chr4	120463729	120463729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaaactgttcgtcatttCggttgaaaggcttaaccttg	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:120463729C>T	ENST00000354960.3	-	10	1776	c.1457G>A	c.(1456-1458)cGa>cAa	p.R486Q	PDE5A_ENST00000264805.5_Missense_Mutation_p.R444Q|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000394439.1_Missense_Mutation_p.R434Q|PDE5A_ENST00000512739.1_5'UTR	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	486	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.R486Q(1)|p.L27L(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TTCGTCATTTCGGTTGAAAGG	0.428																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	4											138	131	133					4																	120463729		2203	4300	6503	120683177	SO:0001583	missense	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1457G>A	4.37:g.120463729C>T	ENSP00000347046:p.Arg486Gln		120683177	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604420	0.46423	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	T;T;T	0.68624	-0.34;-0.34;-0.34	5.37	3.57	0.40892	GAF (2);	0.344730	0.31847	N	0.006976	T	0.58609	0.2134	M	0.62723	1.935	0.40446	D	0.980095	B;B	0.10296	0.002;0.003	B;B	0.11329	0.006;0.004	T	0.53788	-0.8389	10	0.36615	T	0.2	.	6.167	0.20396	0.1513:0.6938:0.0:0.1549	.	486;444	O76074;O76074-2	PDE5A_HUMAN;.	Q	486;434;444	ENSP00000347046:R486Q;ENSP00000377957:R434Q;ENSP00000264805:R444Q	ENSP00000264805:R444Q	R	-	2	0	PDE5A	120683177	1.000000	0.71417	0.657000	0.29651	0.989000	0.77384	4.917000	0.63369	0.696000	0.31696	0.650000	0.86243	CGA		0.428	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		T	120463729	C	T	120463729	3	4	61	1	0	0	0	0	1	0	0	0	11675	884	31	1	1218	1	PDE5A	4	120463729	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34911	120463729	70690547	3423	11408										
PRDM5	11107	broad.mit.edu	37	chr4	121698424	121698424	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacagattttctccttttCtcctgtatgtgtctaaaagg	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:121698424C>A	ENST00000264808.3	-	13	1696	c.1456G>T	c.(1456-1458)Gaa>Taa	p.E486*	PRDM5_ENST00000515109.1_Nonsense_Mutation_p.E455*|PRDM5_ENST00000428209.2_Nonsense_Mutation_p.E455*	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	486					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E486*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTCTCCTTTTCTCCTGTATGT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											130	117	121					4																	121698424		2203	4300	6503	121917874	SO:0001587	stop_gained	11107			AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"Zinc fingers, C2H2-type"	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1456G>T	4.37:g.121698424C>A	ENSP00000264808:p.Glu486*		121917874	Q0VAI9|Q0VAJ0|Q6NXQ7	Nonsense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	C	40	8.326581	0.98762	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	.	.	.	5.42	4.58	0.56647	.	0.100029	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.8234	12.5191	0.56048	0.0:0.9231:0.0:0.0769	.	.	.	.	X	486;455;455	.	ENSP00000264808:E486X	E	-	1	0	PRDM5	121917874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.552000	0.82192	1.306000	0.44926	0.650000	0.86243	GAA		0.373	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			A	121698424	C	A	121698424	4	1	61	1	0	0	0	0	0	1	0	0	12494	922	32	2	452	2	PRDM5	4	121698424	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1234695	121698424	69455852	3424	11409										
C4orf31	79625	broad.mit.edu	37	chr4	121958608	121958608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcatagggtaactcagggTatggctgatcagattctgga	14	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:121958608T>C	ENST00000379692.4	-	4	1044	c.518A>G	c.(517-519)tAc>tGc	p.Y173C	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	173					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.Y173C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						TAACTCAGGGTATGGCTGATC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											192	195	194					4																	121958608		2062	4206	6268	122178058	SO:0001583	missense	79625			BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 31"	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.518A>G	4.37:g.121958608T>C	ENSP00000369014:p.Tyr173Cys		122178058	A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	ENST00000379692.4	37	CCDS3717.2	.	.	.	.	.	.	.	.	.	.	T	18.05	3.535992	0.64972	.	.	ENSG00000173376	ENST00000379692	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79560	-0.1753	9	0.87932	D	0	-27.6376	16.6093	0.84858	0.0:0.0:0.0:1.0	.	173	Q8TB73	NDNF_HUMAN	C	173	.	ENSP00000369014:Y173C	Y	-	2	0	NDNF	122178058	1.000000	0.71417	0.995000	0.50966	0.846000	0.48090	8.012000	0.88631	2.324000	0.78689	0.533000	0.62120	TAC		0.483	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574		C	121958608	T	C	121958608	3	2	61	1	0	0	0	0	1	0	0	0	2267	1638	57	4	1192	4	C4orf31	4	121958608	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	260184	121958608	69195668	3425	11410										
C4orf31	79625	broad.mit.edu	37	chr4	121966825	121966825	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttaggtgtatctctaaaGagataactgctaatttcagc	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:121966825G>T	ENST00000379692.4	-	2	694	c.168C>A	c.(166-168)ctC>ctA	p.L56L		NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	56					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.L56L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						TATCTCTAAAGAGATAACTGC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	4											66	63	64					4																	121966825		1823	4085	5908	122186275	SO:0001819	synonymous_variant	79625			BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 31"	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.168C>A	4.37:g.121966825G>T			122186275	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																				0.398	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574		T	121966825	G	T	121966825	2	4	61	1	0	0	0	0	0	0	0	1	2267	929	33	2		2	C4orf31	4	121966825	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8217	121966825	69187451	3426	11411										
TNIP3	79931	broad.mit.edu	37	chr4	122079859	122079859	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctttctttcatataactCtttcatacttctaaattgct	1	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122079859C>A	ENST00000509841.1	-	6	505	c.427G>T	c.(427-429)Gag>Tag	p.E143*	TNIP3_ENST00000507879.1_Nonsense_Mutation_p.E136*|TNIP3_ENST00000454328.1_Nonsense_Mutation_p.E66*|TNIP3_ENST00000057513.3_Nonsense_Mutation_p.E66*	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3									p.E66*(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						TCATATAACTCTTTCATACTT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											90	90	90					4																	122079859		2201	4300	6501	122299309	SO:0001587	stop_gained	79931			AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.427G>T	4.37:g.122079859C>A	ENSP00000426613:p.Glu143*		122299309		Nonsense_Mutation	SNP	ENST00000509841.1	37	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221231	0.79464	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	.	.	.	5.18	2.53	0.30540	.	0.622243	0.15656	N	0.251120	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-4.8963	6.0017	0.19525	0.0:0.6698:0.1569:0.1733	.	.	.	.	X	66;66;136;143	.	ENSP00000057513:E66X	E	-	1	0	TNIP3	122299309	0.274000	0.24191	0.483000	0.27378	0.658000	0.38924	0.389000	0.20751	0.423000	0.26033	-0.772000	0.03388	GAG		0.358	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		A	122079859	C	A	122079859	4	1	61	1	0	0	0	0	0	1	0	0	16355	922	32	2	817	2	TNIP3	4	122079859	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113034	122079859	69074417	3427	11412										
QRFPR	84109	broad.mit.edu	37	chr4	122254005	122254005	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacatttcttttccatgAatagttcgaagcactgaacc	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122254005A>C	ENST00000394427.2	-	4	1179	c.768T>G	c.(766-768)atT>atG	p.I256M	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	256				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.I256M(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						CTTTTCCATGAATAGTTCGAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											78	75	76					4																	122254005		2203	4300	6503	122473455	SO:0001583	missense	84109			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.768T>G	4.37:g.122254005A>C	ENSP00000377948:p.Ile256Met		122473455		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797480	0.31777	.	.	ENSG00000186867	ENST00000394427	T	0.72725	-0.68	6.17	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.218067	0.50627	D	0.000110	T	0.42245	0.1194	N	0.04820	-0.15	0.80722	D	1	B	0.32128	0.357	B	0.31245	0.126	T	0.08700	-1.0709	10	0.30854	T	0.27	.	5.4129	0.16358	0.5413:0.1421:0.3166:0.0	.	256	Q96P65	QRFPR_HUMAN	M	256	ENSP00000377948:I256M	ENSP00000377948:I256M	I	-	3	3	QRFPR	122473455	1.000000	0.71417	0.996000	0.52242	0.814000	0.46013	1.154000	0.31688	0.213000	0.20722	0.533000	0.62120	ATT		0.363	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		C	122254005	A	C	122254005	3	2	61	1	0	0	0	0	1	0	0	0	12915	242	9	4	539	4	QRFPR	4	122254005	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	174146	122254005	68900271	3428	11413										
QRFPR	84109	broad.mit.edu	37	chr4	122257982	122257982	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaagttgttgcacgtgccAcatgggtgatcctacgatga	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122257982A>G	ENST00000394427.2	-	3	952	c.541T>C	c.(541-543)Tgg>Cgg	p.W181R	QRFPR_ENST00000334383.5_Missense_Mutation_p.W181R	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	181					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.W181R(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						TGCACGTGCCACATGGGTGAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											245	232	236					4																	122257982		2203	4300	6503	122477432	SO:0001583	missense	84109			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.541T>C	4.37:g.122257982A>G	ENSP00000377948:p.Trp181Arg		122477432		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.255667	0.59321	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.37235	1.21;1.21	5.11	5.11	0.69529	GPCR, rhodopsin-like superfamily (1);	0.061993	0.64402	D	0.000002	T	0.51702	0.1690	L	0.57536	1.79	0.54753	D	0.999989	D;D	0.76494	0.999;0.998	D;D	0.70487	0.959;0.969	T	0.50808	-0.8784	10	0.45353	T	0.12	.	9.7021	0.40194	0.9218:0.0:0.0782:0.0	.	181;181	Q96P65;G4XH69	QRFPR_HUMAN;.	R	181	ENSP00000377948:W181R;ENSP00000335610:W181R	ENSP00000335610:W181R	W	-	1	0	QRFPR	122477432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.290000	0.59019	2.032000	0.59987	0.477000	0.44152	TGG		0.413	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		G	122257982	A	G	122257982	3	3	61	1	0	0	0	0	1	0	0	0	12915	159	6	4	770	4	QRFPR	4	122257982	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3977	122257982	68896294	3429	11414										
BBS7	55212	broad.mit.edu	37	chr4	122747030	122747030	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatgtcatgctgcatcgaaGaatgaaatcaatgcattttg	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122747030G>T	ENST00000264499.4	-	19	2316	c.2133C>A	c.(2131-2133)ttC>ttA	p.F711L	CCNA2_ENST00000274026.5_5'Flank	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	711					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.F711L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						CTGCATCGAAGAATGAAATCA	0.313									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	4											113	113	113					4																	122747030		2203	4297	6500	122966480	SO:0001583	missense	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.2133C>A	4.37:g.122747030G>T	ENSP00000264499:p.Phe711Leu		122966480	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011481	0.75046	.	.	ENSG00000138686	ENST00000264499;ENST00000507814	T;T	0.76060	-0.99;-0.99	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.84483	0.5482	M	0.82630	2.6	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.83371	0.0007	10	0.33940	T	0.23	-12.4128	9.7839	0.40664	0.1888:0.0:0.8112:0.0	.	711	Q8IWZ6	BBS7_HUMAN	L	711;134	ENSP00000264499:F711L;ENSP00000423250:F134L	ENSP00000264499:F711L	F	-	3	2	BBS7	122966480	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	1.954000	0.40362	2.746000	0.94184	0.591000	0.81541	TTC		0.313	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			T	122747030	G	T	122747030	3	4	61	1	0	0	0	0	1	0	0	0	1342	933	33	2	18	2	BBS7	4	122747030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	489048	122747030	68407246	3430	11415										
BBS7	55212	broad.mit.edu	37	chr4	122749340	122749340	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggttgctttttgtattCttcctgtaggtgatctgcct	10	8	2	1	rs113786007		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122749340C>A	ENST00000264499.4	-	18	2158	c.1975G>T	c.(1975-1977)Gaa>Taa	p.E659*	BBS7_ENST00000506636.1_Nonsense_Mutation_p.E659*	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	659					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.E659*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TTTTTGTATTCTTCCTGTAGG	0.363									Bardet-Biedl syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	4											193	191	192					4																	122749340		2203	4300	6503	122968790	SO:0001587	stop_gained	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.1975G>T	4.37:g.122749340C>A	ENSP00000264499:p.Glu659*		122968790	Q4W5P8|Q8N581|Q9NVI4	Nonsense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	C	41	8.547664	0.98859	.	.	ENSG00000138686	ENST00000264499;ENST00000507814;ENST00000506636	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-28.6241	19.5165	0.95167	0.0:1.0:0.0:0.0	.	.	.	.	X	659;82;659	.	ENSP00000264499:E659X	E	-	1	0	BBS7	122968790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.645000	0.83430	2.785000	0.95823	0.655000	0.94253	GAA		0.363	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			A	122749340	C	A	122749340	4	1	61	1	0	0	0	0	0	1	0	0	1342	922	32	2	185	2	BBS7	4	122749340	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2310	122749340	68404936	3431	11416										
BBS7	55212	broad.mit.edu	37	chr4	122756323	122756323	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgatcaataaagtgagttCtttgatggagtgaaagaggt	12	3	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122756323C>A	ENST00000264499.4	-	14	1670	c.1487G>T	c.(1486-1488)aGa>aTa	p.R496I	BBS7_ENST00000506636.1_Missense_Mutation_p.R496I	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	496					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.R496I(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AAAGTGAGTTCTTTGATGGAG	0.383									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	4											212	195	201					4																	122756323		2203	4300	6503	122975773	SO:0001583	missense	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.1487G>T	4.37:g.122756323C>A	ENSP00000264499:p.Arg496Ile		122975773	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283080	0.80803	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.97161	-4.27;-4.23	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.97589	0.9210	M	0.75264	2.295	0.80722	D	1	D	0.54964	0.969	P	0.53518	0.728	D	0.97114	0.9806	10	0.35671	T	0.21	-20.9082	18.9668	0.92700	0.0:1.0:0.0:0.0	.	496	Q8IWZ6	BBS7_HUMAN	I	496	ENSP00000264499:R496I;ENSP00000423626:R496I	ENSP00000264499:R496I	R	-	2	0	BBS7	122975773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.000000	0.70678	2.462000	0.83206	0.650000	0.86243	AGA		0.383	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			A	122756323	C	A	122756323	3	1	61	1	0	0	0	0	1	0	0	0	1342	913	32	2	689	2	BBS7	4	122756323	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6983	122756323	68397953	3432	11417										
BBS7	55212	broad.mit.edu	37	chr4	122770018	122770018	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaatatgtggacaccacGatttcatcatagctgtcttt	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122770018G>A	ENST00000264499.4	-	9	1098	c.915C>T	c.(913-915)atC>atT	p.I305I	BBS7_ENST00000506636.1_Silent_p.I305I	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	305					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.I305I(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TGGACACCACGATTTCATCAT	0.328									Bardet-Biedl syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	4											114	113	114					4																	122770018		2203	4300	6503	122989468	SO:0001819	synonymous_variant	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.915C>T	4.37:g.122770018G>A			122989468	Q4W5P8|Q8N581|Q9NVI4	Silent	SNP	ENST00000264499.4	37	CCDS3724.1																																																																																				0.328	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			A	122770018	G	A	122770018	2	1	61	1	0	0	0	0	0	0	0	1	1342	1048	37	1		1	BBS7	4	122770018	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13695	122770018	68384258	3433	11418										
TRPC3	7222	broad.mit.edu	37	chr4	122803560	122803560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgctttcaaaacataccGctttataagtcttttcatta	4	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:122803560G>A	ENST00000379645.3	-	11	2645	c.2572C>T	c.(2572-2574)Cgg>Tgg	p.R858W	TRPC3_ENST00000513531.1_Missense_Mutation_p.R730W|TRPC3_ENST00000264811.5_Missense_Mutation_p.R785W	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	773					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R785W(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AAAACATACCGCTTTATAAGT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											162	151	155					4																	122803560		2202	4299	6501	123023010	SO:0001583	missense	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2572C>T	4.37:g.122803560G>A	ENSP00000368966:p.Arg858Trp		123023010	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176266	0.78564	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.88741	-2.42;-2.42;-2.42	5.57	4.73	0.59995	.	0.000000	0.64402	D	0.000005	D	0.95661	0.8589	M	0.93197	3.39	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96542	0.9401	10	0.87932	D	0	-22.4656	13.8449	0.63461	0.0:0.0:0.7216:0.2784	.	773;730;858	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	W	785;858;730	ENSP00000264811:R785W;ENSP00000368966:R858W;ENSP00000426899:R730W	ENSP00000264811:R785W	R	-	1	2	TRPC3	123023010	1.000000	0.71417	0.984000	0.44739	0.995000	0.86356	4.067000	0.57527	1.478000	0.48253	0.585000	0.79938	CGG		0.318	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		A	122803560	G	A	122803560	3	1	61	1	0	0	0	0	1	0	0	0	16619	1086	38	1	201	1	TRPC3	4	122803560	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33542	122803560	68350716	3434	11419										
KIAA1109	84162	broad.mit.edu	37	chr4	123118402	123118402	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggctcatatttagaaattAatattccaatgacagttgaa	6	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123118402A>C	ENST00000264501.4	+	13	1634	c.1261A>C	c.(1261-1263)Aat>Cat	p.N421H	KIAA1109_ENST00000455637.1_Missense_Mutation_p.N421H|KIAA1109_ENST00000388738.3_Missense_Mutation_p.N421H|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	421					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.N421H(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTTAGAAATTAATATTCCAAT	0.229																																																1	Substitution - Missense(1)	large_intestine(1)	4											40	42	41					4																	123118402		1782	4006	5788	123337852	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1261A>C	4.37:g.123118402A>C	ENSP00000264501:p.Asn421His		123337852	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.6|26.6	4.751331|4.751331	0.89753|0.89753	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	D;D;D|.	0.94000|.	-3.33;-3.33;-3.33|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.998121|.	0.08113|.	N|.	0.995850|.	T|.	0.61788|.	0.2375|.	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999992|0.999992	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	T|.	0.58584|.	-0.7611|.	10|.	0.34782|.	T|.	0.22|.	.|.	15.9075|15.9075	0.79442|0.79442	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	421|.	Q2LD37|.	K1109_HUMAN|.	H|S	421|253	ENSP00000264501:N421H;ENSP00000373390:N421H;ENSP00000389925:N421H|.	ENSP00000264501:N421H|.	N|X	+|+	1|2	0|2	KIAA1109|KIAA1109	123337852|123337852	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.109000|7.109000	0.77062|0.77062	2.158000|2.158000	0.67659|0.67659	0.533000|0.533000	0.62120|0.62120	AAT|TAA		0.229	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123118402	A	C	123118402	3	2	61	1	0	0	0	0	1	0	0	0	8229	362	13	4	1303	4	KIAA1109	4	123118402	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	314842	123118402	68035874	3435	11420										
KIAA1109	84162	broad.mit.edu	37	chr4	123130483	123130483	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaaatggcgcaacgttaCtcaggaaaagtgagtacgta	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123130483C>A	ENST00000264501.4	+	18	2295	c.1922C>A	c.(1921-1923)aCt>aAt	p.T641N	KIAA1109_ENST00000455637.1_Missense_Mutation_p.T641N|KIAA1109_ENST00000388738.3_Missense_Mutation_p.T641N|KIAA1109_ENST00000495260.1_Intron			Q2LD37	K1109_HUMAN	KIAA1109	641					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T641N(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CGCAACGTTACTCAGGAAAAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											69	64	66					4																	123130483		1945	4141	6086	123349933	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1922C>A	4.37:g.123130483C>A	ENSP00000264501:p.Thr641Asn		123349933	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.107860|4.107860	0.77096|0.77096	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	T;T;T|.	0.26067|.	2.36;2.36;1.76|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.433652|.	0.16572|.	U|.	0.208573|.	T|.	0.71467|.	0.3343|.	L|L	0.60455|0.60455	1.87|1.87	0.50467|0.50467	D|D	0.999879|0.999879	D;P|.	0.76494|.	0.999;0.759|.	D;B|.	0.69479|.	0.964;0.328|.	T|.	0.70949|.	-0.4733|.	10|.	0.51188|.	T|.	0.08|.	.|.	17.6803|17.6803	0.88241|0.88241	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	641;641|.	Q2LD37-5;Q2LD37|.	.;K1109_HUMAN|.	N|X	641|473	ENSP00000264501:T641N;ENSP00000373390:T641N;ENSP00000389925:T641N|.	ENSP00000264501:T641N|.	T|Y	+|+	2|3	0|2	KIAA1109|KIAA1109	123349933|123349933	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.988000|0.988000	0.76386|0.76386	5.976000|5.976000	0.70484|0.70484	2.256000|2.256000	0.74724|0.74724	0.561000|0.561000	0.74099|0.74099	ACT|TAC		0.458	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123130483	C	A	123130483	3	1	61	1	0	0	0	0	1	0	0	0	8229	565	20	2	1984	2	KIAA1109	4	123130483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12081	123130483	68023793	3436	11421										
KIAA1109	84162	broad.mit.edu	37	chr4	123132184	123132184	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaacttcatgtagaaatGgaactttctccagattctca	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123132184G>T	ENST00000264501.4	+	20	2554	c.2181G>T	c.(2179-2181)atG>atT	p.M727I	KIAA1109_ENST00000455637.1_Missense_Mutation_p.M727I|KIAA1109_ENST00000388738.3_Missense_Mutation_p.M727I|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	727					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.M727I(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATGTAGAAATGGAACTTTCTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	90	92					4																	123132184		1829	4085	5914	123351634	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2181G>T	4.37:g.123132184G>T	ENSP00000264501:p.Met727Ile		123351634	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.76|14.76	2.630345|2.630345	0.46944|0.46944	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.20200	.|2.69;2.69;2.09	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	.|19.927700	.|0.00597	.|U	.|0.000369	.|T	.|0.17152	.|0.0412	N|N	0.13098|0.13098	0.295|0.295	0.46927|0.46927	D|D	0.999254|0.999254	.|B;B	.|0.22683	.|0.073;0.003	.|B;B	.|0.23716	.|0.048;0.003	.|T	.|0.07654	.|-1.0761	.|10	.|0.17832	.|T	.|0.49	.|.	12.0238|12.0238	0.53358|0.53358	0.0797:0.0:0.9203:0.0|0.0797:0.0:0.9203:0.0	.|.	.|727;727	.|Q2LD37-5;Q2LD37	.|.;K1109_HUMAN	X|I	560|727	.|ENSP00000264501:M727I;ENSP00000373390:M727I;ENSP00000389925:M727I	.|ENSP00000264501:M727I	G|M	+|+	1|3	0|0	KIAA1109|KIAA1109	123351634|123351634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.199000|4.199000	0.58426|0.58426	2.462000|2.462000	0.83206|0.83206	0.585000|0.585000	0.79938|0.79938	GGA|ATG		0.378	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123132184	G	T	123132184	3	4	61	1	0	0	0	0	1	0	0	0	8229	1348	47	2	2251	2	KIAA1109	4	123132184	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1701	123132184	68022092	3437	11422										
KIAA1109	84162	broad.mit.edu	37	chr4	123147936	123147936	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtatgaactggaaagaccGaaatcagttataatatgtca	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123147936G>A	ENST00000264501.4	+	24	3241	c.2868G>A	c.(2866-2868)ccG>ccA	p.P956P	KIAA1109_ENST00000455637.1_Silent_p.P956P|KIAA1109_ENST00000388738.3_Silent_p.P956P|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	956					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P956P(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGGAAAGACCGAAATCAGTTA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	4											168	160	163					4																	123147936		1902	4137	6039	123367386	SO:0001819	synonymous_variant	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2868G>A	4.37:g.123147936G>A			123367386	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	9.489	1.100136	0.20552	.	.	ENSG00000138688	ENST00000424425	.	.	.	5.72	-2.18	0.07037	.	.	.	.	.	T	0.41396	0.1157	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28933	-1.0028	4	.	.	.	.	2.5492	0.04744	0.275:0.4075:0.1214:0.1961	.	.	.	.	K	788	.	.	E	+	1	0	KIAA1109	123367386	0.031000	0.19500	0.970000	0.41538	0.970000	0.65996	-0.657000	0.05335	-0.509000	0.06532	-0.352000	0.07741	GAA		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123147936	G	A	123147936	2	1	61	1	0	0	0	0	0	0	0	1	8229	1045	37	1		1	KIAA1109	4	123147936	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15752	123147936	68006340	3438	11423										
KIAA1109	84162	broad.mit.edu	37	chr4	123168363	123168363	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaacctggtagaacatcaaAttttgataggtatgttcatg	9	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123168363A>C	ENST00000264501.4	+	35	5736	c.5363A>C	c.(5362-5364)aAt>aCt	p.N1788T	KIAA1109_ENST00000455637.1_Missense_Mutation_p.N1788T|KIAA1109_ENST00000388738.3_Missense_Mutation_p.N1788T			Q2LD37	K1109_HUMAN	KIAA1109	1788					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.N1788T(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGAACATCAAATTTTGATAGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	69	71					4																	123168363		1874	4107	5981	123387813	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5363A>C	4.37:g.123168363A>C	ENSP00000264501:p.Asn1788Thr		123387813	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.701|9.701	1.154467|1.154467	0.21371|0.21371	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000446180|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.22945	.|2.52;2.52;1.93	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.355912	.|0.17967	.|U	.|0.155972	T|T	0.13543|0.13543	0.0328|0.0328	N|N	0.14661|0.14661	0.345|0.345	0.24603|0.24603	N|N	0.993762|0.993762	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.20706|0.20706	-1.0267|-1.0267	5|10	.|0.02654	.|T	.|1	.|.	12.3513|12.3513	0.55151|0.55151	0.8202:0.1798:0.0:0.0|0.8202:0.1798:0.0:0.0	.|.	.|1787;1788	.|Q2LD37-2;Q2LD37	.|.;K1109_HUMAN	L|T	361|1788	.|ENSP00000264501:N1788T;ENSP00000373390:N1788T;ENSP00000389925:N1788T	.|ENSP00000264501:N1788T	I|N	+|+	1|2	0|0	KIAA1109|KIAA1109	123387813|123387813	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	3.174000|3.174000	0.50847|0.50847	2.207000|2.207000	0.71202|0.71202	0.477000|0.477000	0.44152|0.44152	ATT|AAT		0.358	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123168363	A	C	123168363	3	2	61	1	0	0	0	0	1	0	0	0	8229	101	4	4	5493	4	KIAA1109	4	123168363	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	20427	123168363	67985913	3439	11424										
KIAA1109	84162	broad.mit.edu	37	chr4	123170683	123170683	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctattccttttgagaagtcCaaagttttatttactcttga	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123170683C>A	ENST00000264501.4	+	36	5929	c.5556C>A	c.(5554-5556)tcC>tcA	p.S1852S	KIAA1109_ENST00000455637.1_Silent_p.S1852S|KIAA1109_ENST00000388738.3_Silent_p.S1852S			Q2LD37	K1109_HUMAN	KIAA1109	1852					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S1852S(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTGAGAAGTCCAAAGTTTTAT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	4											138	132	134					4																	123170683		1834	4079	5913	123390133	SO:0001819	synonymous_variant	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5556C>A	4.37:g.123170683C>A			123390133	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	8.834	0.940593	0.18281	.	.	ENSG00000138688	ENST00000446180	.	.	.	5.16	3.31	0.37934	.	.	.	.	.	T	0.55497	0.1924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50825	-0.8782	4	.	.	.	.	7.4321	0.27134	0.4043:0.3724:0.2232:0.0	.	.	.	.	Q	425	.	.	P	+	2	0	KIAA1109	123390133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.979000	0.29500	2.557000	0.86248	0.455000	0.32223	CCA		0.358	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123170683	C	A	123170683	2	1	61	1	0	0	0	0	0	0	0	1	8229	581	21	2		2	KIAA1109	4	123170683	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2320	123170683	67983593	3440	11425										
KIAA1109	84162	broad.mit.edu	37	chr4	123175973	123175973	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaaggcagctgaaccttTtaagcactgcaacaccagct	7	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123175973T>G	ENST00000264501.4	+	39	6461	c.6088T>G	c.(6088-6090)Tta>Gta	p.L2030V	KIAA1109_ENST00000455637.1_Missense_Mutation_p.L2030V|KIAA1109_ENST00000388738.3_Missense_Mutation_p.L2030V			Q2LD37	K1109_HUMAN	KIAA1109	2030					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L2030V(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GCTGAACCTTTTAAGCACTGC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											47	42	43					4																	123175973		1827	4077	5904	123395423	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.6088T>G	4.37:g.123175973T>G	ENSP00000264501:p.Leu2030Val		123395423	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.98|17.98	3.520879|3.520879	0.64747|0.64747	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000446180|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.63096	.|0.57;0.57;-0.02	5.86|5.86	2.09|2.09	0.27110|0.27110	.|.	.|0.000000	.|0.40385	.|U	.|0.001118	T|T	0.72550|0.72550	0.3474|0.3474	M|M	0.68317|0.68317	2.08|2.08	0.36470|0.36470	D|D	0.867196|0.867196	.|D;D	.|0.69078	.|0.996;0.997	.|D;D	.|0.75484	.|0.986;0.978	T|T	0.75113|0.75113	-0.3432|-0.3432	5|10	.|0.56958	.|D	.|0.05	.|.	8.4572|8.4572	0.32906|0.32906	0.0:0.4266:0.0:0.5734|0.0:0.4266:0.0:0.5734	.|.	.|2029;2030	.|Q2LD37-2;Q2LD37	.|.;K1109_HUMAN	L|V	602|2030	.|ENSP00000264501:L2030V;ENSP00000373390:L2030V;ENSP00000389925:L2030V	.|ENSP00000264501:L2030V	F|L	+|+	3|1	2|2	KIAA1109|KIAA1109	123395423|123395423	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.991000|0.991000	0.79684|0.79684	1.482000|1.482000	0.35486|0.35486	0.485000|0.485000	0.27652|0.27652	0.477000|0.477000	0.44152|0.44152	TTT|TTA		0.363	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123175973	T	G	123175973	3	3	61	1	0	0	0	0	1	0	0	0	8229	1838	64	4	6234	4	KIAA1109	4	123175973	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5290	123175973	67978303	3441	11426										
KIAA1109	84162	broad.mit.edu	37	chr4	123192807	123192807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagaatatgtataaattgCttaacttctattcacttatc	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123192807C>T	ENST00000264501.4	+	47	8501	c.8128C>T	c.(8128-8130)Ctt>Ttt	p.L2710F	KIAA1109_ENST00000455637.1_Missense_Mutation_p.L2710F|KIAA1109_ENST00000388738.3_Missense_Mutation_p.L2710F			Q2LD37	K1109_HUMAN	KIAA1109	2710					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L2710F(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTATAAATTGCTTAACTTCTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	56	57					4																	123192807		1864	4099	5963	123412257	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8128C>T	4.37:g.123192807C>T	ENSP00000264501:p.Leu2710Phe		123412257	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.184546|4.184546	0.78677|0.78677	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.44482	.|1.49;1.49;0.92	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.64402	.|D	.|0.000007	T|T	0.60856|0.60856	0.2301|0.2301	L|L	0.57536|0.57536	1.79|1.79	0.50171|0.50171	D|D	0.999858|0.999858	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.83275	.|0.996;0.996;0.994	T|T	0.61931|0.61931	-0.6961|-0.6961	5|10	.|0.87932	.|D	.|0	.|.	14.1901|14.1901	0.65633|0.65633	0.0:0.9287:0.0:0.0713|0.0:0.9287:0.0:0.0713	.|.	.|2710;2709;2710	.|Q2LD37-6;Q2LD37-2;Q2LD37	.|.;.;K1109_HUMAN	V|F	667|2710	.|ENSP00000264501:L2710F;ENSP00000373390:L2710F;ENSP00000389925:L2710F	.|ENSP00000264501:L2710F	A|L	+|+	2|1	0|0	KIAA1109|KIAA1109	123412257|123412257	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.993000|0.993000	0.82548|0.82548	3.070000|3.070000	0.50033|0.50033	2.738000|2.738000	0.93877|0.93877	0.591000|0.591000	0.81541|0.81541	GCT|CTT		0.363	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123192807	C	T	123192807	3	4	61	1	0	0	0	0	1	0	0	0	8229	797	28	3	8306	3	KIAA1109	4	123192807	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16834	123192807	67961469	3442	11427										
KIAA1109	84162	broad.mit.edu	37	chr4	123249512	123249512	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatatttacaggaaaccctCgtgagtaaccttattttaag	6	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123249512C>T	ENST00000264501.4	+	66	11622	c.11249C>T	c.(11248-11250)tCa>tTa	p.S3750L	KIAA1109_ENST00000388738.3_Splice_Site_p.S3750L			Q2LD37	K1109_HUMAN	KIAA1109	3750					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S3750L(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGGAAACCCTCGTGAGTAACC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											64	61	62					4																	123249512		1829	4078	5907	123468962	SO:0001630	splice_region_variant	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.11249+1C>T	4.37:g.123249512C>T			123468962	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.67|10.67	1.414870|1.414870	0.25465|0.25465	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707	.|T;T;T	.|0.30981	.|2.53;2.53;1.51	5.57|5.57	3.83|3.83	0.44106|0.44106	.|.	.|0.515132	.|0.18296	.|N	.|0.145562	T|T	0.18045|0.18045	0.0433|0.0433	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.05886|0.05886	-1.0858|-1.0858	5|10	.|0.12766	.|T	.|0.61	.|.	6.246|6.246	0.20818|0.20818	0.2471:0.6121:0.0:0.1407|0.2471:0.6121:0.0:0.1407	.|.	.|3749;3750	.|Q2LD37-4;Q2LD37	.|.;K1109_HUMAN	Y|L	161|3750;3750;454	.|ENSP00000264501:S3750L;ENSP00000373390:S3750L;ENSP00000410874:S454L	.|ENSP00000264501:S3750L	H|S	+|+	1|2	0|0	KIAA1109|KIAA1109	123468962|123468962	0.801000|0.801000	0.28930|0.28930	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	0.484000|0.484000	0.22308|0.22308	1.358000|1.358000	0.45922|0.45922	0.467000|0.467000	0.42956|0.42956	CAC|TCA		0.333	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	Missense_Mutation	T	123249512	C	T	123249512	5	4	61	1	0	0	0	0	0	0	1	0	8229	898	31	1	11503	1	KIAA1109	4	123249512	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56705	123249512	67904764	3443	11428										
IL2	3558	broad.mit.edu	37	chr4	123374938	123374938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaaagtttttgctttgaGctaaatttagcacttcctcc	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123374938G>A	ENST00000226730.4	-	3	562	c.278C>T	c.(277-279)gCt>gTt	p.A93V		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	93					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)	p.A93V(1)		endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	TTTGCTTTGAGCTAAATTTAG	0.368			T	TNFRSF17	intestinal T-cell lymphoma																																		Dom	yes		4	4q26-q27	3558	interleukin 2		L	1	Substitution - Missense(1)	large_intestine(1)	4											145	142	143					4																	123374938		2203	4300	6503	123594388	SO:0001583	missense	3558			U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"Interleukins and interleukin receptors"	6001	protein-coding gene	gene with protein product	"T cell growth factor"	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.278C>T	4.37:g.123374938G>A	ENSP00000226730:p.Ala93Val		123594388	P01585	Missense_Mutation	SNP	ENST00000226730.4	37	CCDS3726.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243892	0.79912	.	.	ENSG00000109471	ENST00000226730	.	.	.	3.99	2.18	0.27775	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.967882	0.08457	N	0.942974	T	0.50497	0.1619	L	0.53249	1.67	0.09310	N	1	D	0.67145	0.996	P	0.54815	0.761	T	0.35375	-0.9791	9	0.54805	T	0.06	1.475	8.8908	0.35432	0.0:0.0:0.5941:0.4059	.	93	P60568	IL2_HUMAN	V	93	.	ENSP00000226730:A93V	A	-	2	0	IL2	123594388	0.621000	0.27077	0.012000	0.15200	0.957000	0.61999	0.202000	0.17295	0.597000	0.29811	0.460000	0.39030	GCT		0.368	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2			A	123374938	G	A	123374938	3	1	61	1	0	0	0	0	1	0	0	0	7687	971	34	3	191	3	IL2	4	123374938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125426	123374938	67779338	3444	11429										
BBS12	166379	broad.mit.edu	37	chr4	123663572	123663572	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatagaggaattgcatggTctcaaagatgttgcctctca	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123663572T>C	ENST00000314218.3	+	2	718	c.525T>C	c.(523-525)ggT>ggC	p.G175G	BBS12_ENST00000542236.1_Silent_p.G175G	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	175					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)	p.G175G(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						AATTGCATGGTCTCAAAGATG	0.373									Bardet-Biedl syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	4											93	85	88					4																	123663572		2203	4300	6503	123883022	SO:0001819	synonymous_variant	166379	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.525T>C	4.37:g.123663572T>C			123883022	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																				0.373	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		C	123663572	T	C	123663572	2	2	61	1	0	0	0	0	0	0	0	1	1338	1654	58	4		4	BBS12	4	123663572	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	288634	123663572	67490704	3445	11430										
SPATA5	166378	broad.mit.edu	37	chr4	123978405	123978405	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcgccttccattattttCtttgatgaactggatgcctt	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:123978405C>A	ENST00000274008.4	+	13	2244	c.2175C>A	c.(2173-2175)ttC>ttA	p.F725L	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	725					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.F725L(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						CCATTATTTTCTTTGATGAAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											102	102	102					4																	123978405		2203	4300	6503	124197855	SO:0001583	missense	166378			AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.2175C>A	4.37:g.123978405C>A	ENSP00000274008:p.Phe725Leu		124197855	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Missense_Mutation	SNP	ENST00000274008.4	37	CCDS3730.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.294060	0.81025	.	.	ENSG00000145375	ENST00000274008	D	0.94092	-3.35	4.87	4.01	0.46588	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.95519	0.8544	M	0.63169	1.94	0.43160	D	0.994945	D	0.89917	1.0	D	0.97110	1.0	D	0.95812	0.8842	10	0.87932	D	0	-14.3803	12.651	0.56761	0.0:0.9189:0.0:0.0811	.	725	Q8NB90	SPAT5_HUMAN	L	725	ENSP00000274008:F725L	ENSP00000274008:F725L	F	+	3	2	SPATA5	124197855	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.174000	0.50847	1.386000	0.46466	0.655000	0.94253	TTC		0.373	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207		A	123978405	C	A	123978405	3	1	61	1	0	0	0	0	1	0	0	0	15050	912	32	2	2225	2	SPATA5	4	123978405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314833	123978405	67175871	3446	11431										
SPRY1	10252	broad.mit.edu	37	chr4	124322919	124322919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatacacagaagggccttCggtggtgaaaagacctgctc	12	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:124322919C>T	ENST00000394339.2	+	2	513	c.173C>T	c.(172-174)tCg>tTg	p.S58L	SPRY1_ENST00000339241.1_Missense_Mutation_p.S58L	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	58					epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.S58L(1)		NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						GAAGGGCCTTCGGTGGTGAAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											124	125	125					4																	124322919		2203	4300	6503	124542369	SO:0001583	missense	10252			AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.173C>T	4.37:g.124322919C>T	ENSP00000377871:p.Ser58Leu		124542369	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	37	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829839	0.91036	.	.	ENSG00000164056	ENST00000505319;ENST00000339241;ENST00000507703;ENST00000394339	T;T;T	0.55413	0.52;1.46;0.52	4.78	4.78	0.61160	.	0.166757	0.40908	D	0.000983	T	0.52693	0.1750	M	0.65975	2.015	0.58432	D	0.999998	D	0.57899	0.981	B	0.44315	0.446	T	0.53802	-0.8387	10	0.10636	T	0.68	-13.4393	17.6504	0.88162	0.0:1.0:0.0:0.0	.	58	O43609	SPY1_HUMAN	L	58	ENSP00000343785:S58L;ENSP00000421036:S58L;ENSP00000377871:S58L	ENSP00000343785:S58L	S	+	2	0	SPRY1	124542369	0.998000	0.40836	0.951000	0.38953	0.986000	0.74619	5.319000	0.65835	2.481000	0.83766	0.561000	0.74099	TCG		0.433	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			T	124322919	C	T	124322919	3	4	61	1	0	0	0	0	1	0	0	0	15144	893	31	1	175	1	SPRY1	4	124322919	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344514	124322919	66831357	3447	11432										
SPRY1	10252	broad.mit.edu	37	chr4	124323508	124323508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcacaatcacactgctgCtctagatacctgtgtatggg	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:124323508C>T	ENST00000394339.2	+	2	1102	c.762C>T	c.(760-762)tgC>tgT	p.C254C	SPRY1_ENST00000339241.1_Silent_p.C254C	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	254	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.C254C(1)		NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						CACACTGCTGCTCTAGATACC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	4											264	224	238					4																	124323508		2203	4300	6503	124542958	SO:0001819	synonymous_variant	10252			AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.762C>T	4.37:g.124323508C>T			124542958	D3DNX6|Q6PNE0	Silent	SNP	ENST00000394339.2	37	CCDS3731.1																																																																																				0.463	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			T	124323508	C	T	124323508	2	4	61	1	0	0	0	0	0	0	0	1	15144	805	28	3		3	SPRY1	4	124323508	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	589	124323508	66830768	3448	11433										
ANKRD50	57182	broad.mit.edu	37	chr4	125590153	125590153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattaccttttataatggtgTttcctttttatagttgaagc	6	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:125590153T>C	ENST00000504087.1	-	4	5316	c.4279A>G	c.(4279-4281)Aca>Gca	p.T1427A	ANKRD50_ENST00000515641.1_Missense_Mutation_p.T1248A	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1427								p.T1427A(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TATAATGGTGTTTCCTTTTTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	70	69					4																	125590153		2203	4300	6503	125809603	SO:0001583	missense	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.4279A>G	4.37:g.125590153T>C	ENSP00000425658:p.Thr1427Ala		125809603	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263730	0.80358	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.73152	-0.72;-0.61	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.74207	0.3686	N	0.24115	0.695	0.50313	D	0.999866	D	0.58970	0.984	D	0.65443	0.935	T	0.78262	-0.2272	10	0.87932	D	0	.	15.5138	0.75806	0.0:0.0:0.0:1.0	.	1427	Q9ULJ7	ANR50_HUMAN	A	1427;1248	ENSP00000425658:T1427A;ENSP00000425355:T1248A	ENSP00000425658:T1427A	T	-	1	0	ANKRD50	125809603	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.340000	0.79292	2.250000	0.74265	0.454000	0.30748	ACA		0.373	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		C	125590153	T	C	125590153	3	2	61	1	0	0	0	0	1	0	0	0	677	1725	60	4	14	4	ANKRD50	4	125590153	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1266645	125590153	65564123	3449	11434										
FAT4	79633	broad.mit.edu	37	chr4	126238811	126238811	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcaaagcagcaaagtgccGaacctgagcctaatcaaggt	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126238811G>A	ENST00000394329.3	+	1	1258	c.1245G>A	c.(1243-1245)ccG>ccA	p.P415P		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	415	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P415P(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCAAAGTGCCGAACCTGAGCC	0.592											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - coding silent(2)	large_intestine(2)	4											34	37	36					4																	126238811		2024	4195	6219	126458261	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1245G>A	4.37:g.126238811G>A		1548	126458261	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.592	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126238811	G	A	126238811	2	1	61	1	0	0	0	0	0	0	0	1	5711	1045	37	1		1	FAT4	4	126238811	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	648658	126238811	64915465	3450	11435										
FAT4	79633	broad.mit.edu	37	chr4	126239587	126239587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagtcatcaatggctcGcataaatgtgagtcttctgg	9	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126239587G>A	ENST00000394329.3	+	1	2034	c.2021G>A	c.(2020-2022)cGc>cAc	p.R674H		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	674	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R674H(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCAATGGCTCGCATAAATGTG	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	4											89	89	89					4																	126239587		1907	4122	6029	126459037	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.2021G>A	4.37:g.126239587G>A	ENSP00000377862:p.Arg674His		126459037	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	4.288	0.052591	0.08291	.	.	ENSG00000196159	ENST00000394329	T	0.01767	4.65	4.76	1.05	0.20165	Cadherin (4);Cadherin-like (1);	0.291323	0.18322	U	0.144774	T	0.01523	0.0049	L	0.33245	0.995	0.09310	N	1	B	0.22746	0.074	B	0.20184	0.028	T	0.46062	-0.9218	10	0.44086	T	0.13	.	4.319	0.11007	0.396:0.0:0.454:0.15	.	674	Q6V0I7	FAT4_HUMAN	H	674	ENSP00000377862:R674H	ENSP00000377862:R674H	R	+	2	0	FAT4	126459037	0.666000	0.27475	0.000000	0.03702	0.119000	0.20118	1.459000	0.35234	-0.018000	0.14079	0.655000	0.94253	CGC		0.483	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126239587	G	A	126239587	3	1	61	1	0	0	0	0	1	0	0	0	5711	1087	38	1	2023	1	FAT4	4	126239587	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	776	126239587	64914689	3451	11436										
FAT4	79633	broad.mit.edu	37	chr4	126240894	126240894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaattacacattttacttcGaagaagagcagagggctggg	11	8	0	3	rs377275274		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126240894G>A	ENST00000394329.3	+	1	3341	c.3328G>A	c.(3328-3330)Gaa>Aaa	p.E1110K		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1110	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1110K(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATTTTACTTCGAAGAAGAGCA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	LYS/GLU	0,3694		0,0,1847	162	155	157		3328	4.4	1	4		157	3,8155		0,3,4076	no	missense	FAT4	NM_024582.4	56	0,3,5923	AA,AG,GG		0.0368,0.0,0.0253	benign	1110/4982	126240894	3,11849	1847	4079	5926	126460344	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.3328G>A	4.37:g.126240894G>A	ENSP00000377862:p.Glu1110Lys		126460344	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058283	0.55325	0.0	3.68E-4	ENSG00000196159	ENST00000394329	T	0.52057	0.68	4.36	4.36	0.52297	Cadherin (3);Cadherin-like (1);	0.000000	0.35291	U	0.003311	T	0.44787	0.1310	N	0.12443	0.215	0.80722	D	1	D	0.69078	0.997	D	0.63793	0.918	T	0.24225	-1.0166	10	0.06891	T	0.86	.	17.0972	0.86638	0.0:0.0:1.0:0.0	.	1110	Q6V0I7	FAT4_HUMAN	K	1110	ENSP00000377862:E1110K	ENSP00000377862:E1110K	E	+	1	0	FAT4	126460344	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	5.227000	0.65305	2.247000	0.74100	0.462000	0.41574	GAA		0.388	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126240894	G	A	126240894	3	1	61	1	0	0	0	0	1	0	0	0	5711	1059	37	1	3330	1	FAT4	4	126240894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1307	126240894	64913382	3452	11437										
FAT4	79633	broad.mit.edu	37	chr4	126336758	126336758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaggtgccatcactgtcGctaaacctttggatagagaa	9	10	2	1	rs149686118		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126336758G>A	ENST00000394329.3	+	5	6653	c.6640G>A	c.(6640-6642)Gct>Act	p.A2214T	FAT4_ENST00000335110.5_Missense_Mutation_p.A512T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2214	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A2214T(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CATCACTGTCGCTAAACCTTT	0.468													G|||	1	0.000199681	0	0.0014	5008	,	,		17985	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	4						G	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	133	127	129		6640	4.6	1	4	dbSNP_134	129	0,8600		0,0,4300	no	missense	FAT4	NM_024582.4	58	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	2214/4982	126336758	2,13004	2203	4300	6503	126556208	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6640G>A	4.37:g.126336758G>A	ENSP00000377862:p.Ala2214Thr		126556208	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705870	0.68615	4.54E-4	0.0	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01767	4.65;4.65	5.46	4.61	0.57282	Cadherin (4);Cadherin-like (1);	0.000000	0.34133	U	0.004240	T	0.04003	0.0112	L	0.33293	1	0.44834	D	0.997846	B;D	0.60575	0.056;0.988	B;P	0.59221	0.016;0.854	T	0.64398	-0.6417	10	0.15952	T	0.53	.	13.772	0.63032	0.0734:0.0:0.9266:0.0	.	512;2214	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	T	2214;512	ENSP00000377862:A2214T;ENSP00000335169:A512T	ENSP00000335169:A512T	A	+	1	0	FAT4	126556208	1.000000	0.71417	0.997000	0.53966	0.655000	0.38815	7.868000	0.87116	1.303000	0.44873	0.557000	0.71058	GCT		0.468	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126336758	G	A	126336758	3	1	61	1	0	0	0	0	1	0	0	0	5711	1087	38	1	6658	1	FAT4	4	126336758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95864	126336758	64817518	3453	11438										
FAT4	79633	broad.mit.edu	37	chr4	126355580	126355580	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaagaatgcagttataaGgtcagtacattttcctttgt	7	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126355580G>T	ENST00000394329.3	+	7	7212	c.7199G>T	c.(7198-7200)aGg>aTg	p.R2400M	FAT4_ENST00000335110.5_Splice_Site_p.R698M	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2400	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R2400M(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCAGTTATAAGGTCAGTACAT	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	4											147	136	139					4																	126355580		2203	4300	6503	126575030	SO:0001630	splice_region_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7199+1G>T	4.37:g.126355580G>T			126575030	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569540	0.65765	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53857	0.6;0.6	5.0	5.0	0.66597	Cadherin (4);Cadherin-like (1);	0.188006	0.24504	U	0.037945	T	0.54854	0.1884	N	0.25957	0.775	0.80722	D	1	P;P	0.49783	0.824;0.928	B;P	0.53360	0.416;0.724	T	0.56631	-0.7947	10	0.49607	T	0.09	.	18.5243	0.90965	0.0:0.0:1.0:0.0	.	698;2400	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	M	2400;698	ENSP00000377862:R2400M;ENSP00000335169:R698M	ENSP00000335169:R698M	R	+	2	0	FAT4	126575030	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	8.434000	0.90294	2.596000	0.87737	0.655000	0.94253	AGG		0.313	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	Missense_Mutation	T	126355580	G	T	126355580	5	4	61	1	0	0	0	0	0	0	1	0	5711	1014	35	2	7225	2	FAT4	4	126355580	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18822	126355580	64798696	3454	11439										
FAT4	79633	broad.mit.edu	37	chr4	126367514	126367514	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggacaaatcatcaccagCgcattgttagatagggaaac	9	9	2	1	rs147010455	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126367514C>T	ENST00000394329.3	+	8	7273	c.7260C>T	c.(7258-7260)agC>agT	p.S2420S	FAT4_ENST00000335110.5_Silent_p.S718S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2420	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S2420S(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCATCACCAGCGCATTGTTAG	0.443													C|||	2	0.000399361	0	0	5008	,	,		16734	0.002		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	4											121	119	120					4																	126367514		2203	4300	6503	126586964	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7260C>T	4.37:g.126367514C>T			126586964	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.443	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126367514	C	T	126367514	2	4	61	1	0	0	0	0	0	0	0	1	5711	767	27	1		1	FAT4	4	126367514	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11934	126367514	64786762	3455	11440										
FAT4	79633	broad.mit.edu	37	chr4	126369795	126369795	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttctgtgcatgtaaaaGatggtggctcatttccaaag	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126369795G>T	ENST00000394329.3	+	9	7637	c.7624G>T	c.(7624-7626)Gat>Tat	p.D2542Y	FAT4_ENST00000335110.5_Missense_Mutation_p.D840Y	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2542	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D2542Y(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCATGTAAAAGATGGTGGCTC	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	4											82	81	81					4																	126369795		2203	4299	6502	126589245	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7624G>T	4.37:g.126369795G>T	ENSP00000377862:p.Asp2542Tyr		126589245	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519181	0.85495	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.80909	-1.43;-1.43	5.72	5.72	0.89469	Cadherin (4);Cadherin-like (1);	0.000000	0.35262	U	0.003325	D	0.94212	0.8142	H	0.98005	4.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.95822	0.8850	10	0.87932	D	0	.	19.8937	0.96942	0.0:0.0:1.0:0.0	.	840;2542;2542	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	Y	2542;840	ENSP00000377862:D2542Y;ENSP00000335169:D840Y	ENSP00000335169:D840Y	D	+	1	0	FAT4	126589245	1.000000	0.71417	0.991000	0.47740	0.830000	0.47004	9.666000	0.98612	2.716000	0.92895	0.650000	0.86243	GAT		0.428	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126369795	G	T	126369795	3	4	61	1	0	0	0	0	1	0	0	0	5711	942	33	2	7658	2	FAT4	4	126369795	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2281	126369795	64784481	3456	11441										
FAT4	79633	broad.mit.edu	37	chr4	126371531	126371531	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatagagatgcagcgatGaatggcttgattaagtacag	13	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126371531G>T	ENST00000394329.3	+	9	9373	c.9360G>T	c.(9358-9360)atG>atT	p.M3120I	FAT4_ENST00000335110.5_Missense_Mutation_p.M1418I	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3120	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.M3120I(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATGCAGCGATGAATGGCTTGA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	4											72	69	70					4																	126371531		2203	4300	6503	126590981	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9360G>T	4.37:g.126371531G>T	ENSP00000377862:p.Met3120Ile		126590981	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	12.03	1.815703	0.32145	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51325	0.71;0.71	5.63	5.63	0.86233	Cadherin (4);Cadherin-like (1);	0.000000	0.41396	U	0.000885	T	0.49150	0.1540	N	0.04508	-0.205	0.80722	D	1	P;D;D	0.61080	0.655;0.989;0.986	B;D;D	0.72338	0.194;0.977;0.974	T	0.58999	-0.7536	10	0.38643	T	0.18	.	19.7096	0.96089	0.0:0.0:1.0:0.0	.	1418;3120;3120	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	I	3120;1418	ENSP00000377862:M3120I;ENSP00000335169:M1418I	ENSP00000335169:M1418I	M	+	3	0	FAT4	126590981	1.000000	0.71417	1.000000	0.80357	0.131000	0.20780	7.766000	0.85320	2.652000	0.90054	0.655000	0.94253	ATG		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126371531	G	T	126371531	3	4	61	1	0	0	0	0	1	0	0	0	5711	1290	45	2	9394	2	FAT4	4	126371531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1736	126371531	64782745	3457	11442										
FAT4	79633	broad.mit.edu	37	chr4	126389785	126389785	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaaatttgccacgattaaAagtcatgccttattgcttta	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126389785A>C	ENST00000394329.3	+	11	12031	c.12018A>C	c.(12016-12018)aaA>aaC	p.K4006N	FAT4_ENST00000335110.5_Missense_Mutation_p.K2269N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4006	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K3971N(1)|p.K4006N(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCACGATTAAAAGTCATGCCT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	4											77	76	77					4																	126389785		2203	4300	6503	126609235	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12018A>C	4.37:g.126389785A>C	ENSP00000377862:p.Lys4006Asn		126609235	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	18.86	3.714373	0.68730	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.78595	-1.19;-1.19	5.13	3.96	0.45880	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.36482	U	0.002566	T	0.81866	0.4913	L	0.46819	1.47	0.48341	D	0.999636	D;D;P	0.76494	0.98;0.999;0.884	P;D;P	0.85130	0.814;0.997;0.586	T	0.80804	-0.1219	10	0.44086	T	0.13	.	9.3464	0.38111	0.8563:0.0:0.1437:0.0	.	2269;4006;4006	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	N	4006;2269	ENSP00000377862:K4006N;ENSP00000335169:K2269N	ENSP00000335169:K2269N	K	+	3	2	FAT4	126609235	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	4.182000	0.58310	1.943000	0.56356	0.473000	0.43528	AAA		0.393	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126389785	A	C	126389785	3	2	61	1	0	0	0	0	1	0	0	0	5711	11	1	4	12060	4	FAT4	4	126389785	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18254	126389785	64764491	3458	11443										
FAT4	79633	broad.mit.edu	37	chr4	126408530	126408530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaagtatattttacatccGatgcaggaattgctgggaaa	10	6	0	0	rs149301924	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:126408530G>A	ENST00000394329.3	+	16	12860	c.12847G>A	c.(12847-12849)Gat>Aat	p.D4283N	FAT4_ENST00000335110.5_Missense_Mutation_p.D2524N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4283	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D4226N(1)|p.D4283N(1)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTTTACATCCGATGCAGGAAT	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	56	59	58		12847	5.3	1	4	dbSNP_134	58	2,8596	2.2+/-6.3	0,2,4297	no	missense	FAT4	NM_024582.4	23	0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging	4283/4982	126408530	3,13001	2203	4299	6502	126627980	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12847G>A	4.37:g.126408530G>A	ENSP00000377862:p.Asp4283Asn		126627980	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882563	0.72294	2.27E-4	2.33E-4	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.79141	-1.24;-1.24	5.31	5.31	0.75309	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.35378	U	0.003259	T	0.79656	0.4483	N	0.24115	0.695	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.73739	-0.3888	10	0.10636	T	0.68	.	17.979	0.89134	0.0:0.0:1.0:0.0	.	2524;4283;4283	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	N	4283;2524	ENSP00000377862:D4283N;ENSP00000335169:D2524N	ENSP00000335169:D2524N	D	+	1	0	FAT4	126627980	1.000000	0.71417	0.994000	0.49952	0.647000	0.38526	8.746000	0.91604	2.482000	0.83794	0.650000	0.86243	GAT		0.323	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126408530	G	A	126408530	3	1	61	1	0	0	0	0	1	0	0	0	5711	1058	37	1	12909	1	FAT4	4	126408530	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18745	126408530	64745746	3459	11444										
INTU	27152	broad.mit.edu	37	chr4	128635096	128635096	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctattaatttacagaaaaaGaaaggactaaatagtggaga	8	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128635096G>T	ENST00000335251.6	+	15	2668	c.2565G>T	c.(2563-2565)aaG>aaT	p.K855N		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	855					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)		p.K855N(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TACAGAAAAAGAAAGGACTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	111	109					4																	128635096		2203	4300	6503	128854546	SO:0001583	missense	27152			BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2565G>T	4.37:g.128635096G>T	ENSP00000334003:p.Lys855Asn		128854546	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.296306	0.23650	.	.	ENSG00000164066	ENST00000335251	.	.	.	4.4	3.55	0.40652	.	0.420075	0.24204	N	0.040596	T	0.48429	0.1499	L	0.43152	1.355	0.80722	D	1	P	0.49783	0.928	P	0.50659	0.647	T	0.45308	-0.9270	9	0.46703	T	0.11	-12.7088	4.4508	0.11619	0.0847:0.1528:0.6051:0.1574	.	855	Q9ULD6	PDZD6_HUMAN	N	855	.	ENSP00000334003:K855N	K	+	3	2	INTU	128854546	1.000000	0.71417	0.994000	0.49952	0.144000	0.21451	1.570000	0.36439	1.050000	0.40346	0.650000	0.86243	AAG		0.338	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		T	128635096	G	T	128635096	3	4	61	1	0	0	0	0	1	0	0	0	7807	933	33	2	2623	2	INTU	4	128635096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2226566	128635096	62519180	3460	11445										
SLC25A31	83447	broad.mit.edu	37	chr4	128651816	128651816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtccaagacagcggtggCgcccatcgagcgggtgaagc	16	11	0	2	rs374027476		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128651816C>T	ENST00000281154.4	+	1	284	c.116C>T	c.(115-117)gCg>gTg	p.A39V		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	39					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.A39V(1)		NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						ACAGCGGTGGCGCCCATCGAG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	VAL/ALA	0,4406		0,0,2203	45	44	44		116	5	1	4		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC25A31	NM_031291.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	39/316	128651816	1,13005	2203	4300	6503	128871266	SO:0001583	missense	83447			AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.116C>T	4.37:g.128651816C>T	ENSP00000281154:p.Ala39Val		128871266		Missense_Mutation	SNP	ENST00000281154.4	37	CCDS3733.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.680273	0.88542	0.0	1.16E-4	ENSG00000151475	ENST00000281154	T	0.79141	-1.24	4.96	4.96	0.65561	Mitochondrial carrier domain (2);	0.000000	0.47852	D	0.000207	D	0.86772	0.6013	M	0.91510	3.215	0.51012	D	0.999905	D	0.69078	0.997	P	0.52267	0.694	D	0.90061	0.4156	10	0.87932	D	0	-12.3233	15.2429	0.73485	0.0:1.0:0.0:0.0	.	39	Q9H0C2	ADT4_HUMAN	V	39	ENSP00000281154:A39V	ENSP00000281154:A39V	A	+	2	0	SLC25A31	128871266	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	6.071000	0.71229	2.575000	0.86900	0.655000	0.94253	GCG		0.642	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		T	128651816	C	T	128651816	3	4	61	1	0	0	0	0	1	0	0	0	14532	768	27	1	118	1	SLC25A31	4	128651816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16720	128651816	62502460	3461	11446										
SLC25A31	83447	broad.mit.edu	37	chr4	128689940	128689940	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccaaagaaaactccatttCttgtctcctttttcattgct	4	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128689940C>A	ENST00000281154.4	+	5	835	c.667C>A	c.(667-669)Ctt>Att	p.L223I		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	223					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.L223I(1)		NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						AACTCCATTTCTTGTCTCCTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											111	102	105					4																	128689940		2203	4298	6501	128909390	SO:0001583	missense	83447			AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.667C>A	4.37:g.128689940C>A	ENSP00000281154:p.Leu223Ile		128909390		Missense_Mutation	SNP	ENST00000281154.4	37	CCDS3733.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.421703	0.01126	.	.	ENSG00000151475	ENST00000281154	T	0.80480	-1.38	4.59	2.82	0.32997	Mitochondrial carrier domain (2);	0.159738	0.29624	N	0.011634	T	0.71492	0.3346	L	0.52011	1.625	0.30183	N	0.800204	B	0.11235	0.004	B	0.12837	0.008	T	0.61978	-0.6951	10	0.27082	T	0.32	-16.0052	7.7938	0.29135	0.4472:0.4038:0.1489:0.0	.	223	Q9H0C2	ADT4_HUMAN	I	223	ENSP00000281154:L223I	ENSP00000281154:L223I	L	+	1	0	SLC25A31	128909390	0.214000	0.23563	1.000000	0.80357	0.001000	0.01503	-0.164000	0.09983	0.538000	0.28769	-0.518000	0.04402	CTT		0.323	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		A	128689940	C	A	128689940	3	1	61	1	0	0	0	0	1	0	0	0	14532	913	32	2	685	2	SLC25A31	4	128689940	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38124	128689940	62464336	3462	11447										
HSPA4L	22824	broad.mit.edu	37	chr4	128703746	128703746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcggctttctcaactgctAcattgctgtcgcgagaagtg	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128703746A>G	ENST00000296464.4	+	1	452	c.41A>G	c.(40-42)tAc>tGc	p.Y14C	HSPA4L_ENST00000505726.1_5'Flank|HSPA4L_ENST00000508776.1_Missense_Mutation_p.Y14C|HSPA4L_ENST00000439123.2_Missense_Mutation_p.Y45C	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	14					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.Y14C(1)		central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CTCAACTGCTACATTGCTGTC	0.587											OREG0016319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	4											170	130	144					4																	128703746		2203	4300	6503	128923196	SO:0001583	missense	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.41A>G	4.37:g.128703746A>G	ENSP00000296464:p.Tyr14Cys	1566	128923196	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.886872	0.33348	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000508549	T;T;T;T	0.01287	5.6;5.6;5.6;5.05	3.48	2.26	0.28386	.	0.078757	0.53938	D	0.000059	T	0.01254	0.0041	N	0.02865	-0.47	0.58432	D	0.999997	D;D	0.56287	0.975;0.975	P;P	0.53988	0.739;0.739	T	0.76157	-0.3062	10	0.27082	T	0.32	.	9.163	0.37035	0.8369:0.0:0.0:0.1631	.	14;14	A2ICT2;O95757	.;HS74L_HUMAN	C	14;45;14;14	ENSP00000422482:Y14C;ENSP00000393926:Y45C;ENSP00000296464:Y14C;ENSP00000427305:Y14C	ENSP00000296464:Y14C	Y	+	2	0	HSPA4L	128923196	1.000000	0.71417	0.999000	0.59377	0.114000	0.19823	7.957000	0.87870	0.507000	0.28148	0.460000	0.39030	TAC		0.587	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		G	128703746	A	G	128703746	3	3	61	1	0	0	0	0	1	0	0	0	7434	391	14	4	43	4	HSPA4L	4	128703746	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13806	128703746	62450530	3463	11448										
HSPA4L	22824	broad.mit.edu	37	chr4	128719825	128719825	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcttaaagagacttcagaAaatgctttgaagaaaccagt	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128719825A>G	ENST00000296464.4	+	4	801	c.390A>G	c.(388-390)gaA>gaG	p.E130E	HSPA4L_ENST00000505726.1_Silent_p.E104E|HSPA4L_ENST00000508776.1_Silent_p.E130E|HSPA4L_ENST00000439123.2_Silent_p.E161E	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	130					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.E130E(1)		central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AGACTTCAGAAAATGCTTTGA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	4											135	135	135					4																	128719825		2203	4300	6503	128939275	SO:0001819	synonymous_variant	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.390A>G	4.37:g.128719825A>G			128939275	A2ICT2|Q4W5M5|Q8IWA2	Silent	SNP	ENST00000296464.4	37	CCDS3734.1																																																																																				0.363	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		G	128719825	A	G	128719825	2	3	61	1	0	0	0	0	0	0	0	1	7434	11	1	4		4	HSPA4L	4	128719825	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16079	128719825	62434451	3464	11449										
PLK4	10733	broad.mit.edu	37	chr4	128803048	128803048	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgtctacagagctgagtcCattcacactggtttggaagt	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128803048C>A	ENST00000270861.5	+	2	367	c.93C>A	c.(91-93)tcC>tcA	p.S31S	PLK4_ENST00000507249.1_Silent_p.S31S|PLK4_ENST00000511942.1_3'UTR|PLK4_ENST00000513090.1_Silent_p.S31S|PLK4_ENST00000515069.1_Silent_p.S31S|PLK4_ENST00000514379.1_5'UTR	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	31	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S31S(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						GAGCTGAGTCCATTCACACTG	0.353																																					Colon(135;508 1718 19061 31832 42879)											1	Substitution - coding silent(1)	large_intestine(1)	4											111	110	110					4																	128803048		2203	4300	6503	129022498	SO:0001819	synonymous_variant	10733			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.93C>A	4.37:g.128803048C>A			129022498	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																				0.353	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			A	128803048	C	A	128803048	2	1	61	1	0	0	0	0	0	0	0	1	12129	581	21	2		2	PLK4	4	128803048	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83223	128803048	62351228	3465	11450										
PLK4	10733	broad.mit.edu	37	chr4	128813540	128813540	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatactggcgaaaatatCaatatgcttccaggtttgta	7	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128813540C>A	ENST00000270861.5	+	10	2333	c.2059C>A	c.(2059-2061)Caa>Aaa	p.Q687K	PLK4_ENST00000507249.1_Missense_Mutation_p.Q626K|PLK4_ENST00000513090.1_Missense_Mutation_p.Q655K|PLK4_ENST00000515069.1_Missense_Mutation_p.Q609K|PLK4_ENST00000514379.1_Missense_Mutation_p.Q646K|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	687					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.Q687K(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						GCGAAAATATCAATATGCTTC	0.308																																					Colon(135;508 1718 19061 31832 42879)											1	Substitution - Missense(1)	large_intestine(1)	4											78	76	77					4																	128813540		2202	4298	6500	129032990	SO:0001583	missense	10733			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2059C>A	4.37:g.128813540C>A	ENSP00000270861:p.Gln687Lys		129032990	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.61|18.61	3.660548|3.660548	0.67586|0.67586	.|.	.|.	ENSG00000142731|ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379|ENST00000508113	T;T;T;T;T|.	0.34667|.	1.35;1.35;1.35;1.35;1.35|.	5.41|5.41	4.51|4.51	0.55191|0.55191	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.69780|.	0.3149|.	L|L	0.58101|0.58101	1.795|1.795	0.53688|0.53688	D|D	0.999971|0.999971	D;D|.	0.71674|.	0.998;0.997|.	D;P|.	0.66979|.	0.948;0.888|.	T|.	0.68168|.	-0.5480|.	10|.	0.32370|.	T|.	0.25|.	-7.1537|-7.1537	15.5857|15.5857	0.76479|0.76479	0.0:0.862:0.138:0.0|0.0:0.862:0.138:0.0	.|.	655;687|.	O00444-2;O00444|.	.;PLK4_HUMAN|.	K|X	687;609;655;626;646|16	ENSP00000270861:Q687K;ENSP00000421774:Q609K;ENSP00000427554:Q655K;ENSP00000423412:Q626K;ENSP00000423582:Q646K|.	ENSP00000270861:Q687K|.	Q|S	+|+	1|2	0|0	PLK4|PLK4	129032990|129032990	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.667000|0.667000	0.39255|0.39255	4.526000|4.526000	0.60566|0.60566	2.532000|2.532000	0.85374|0.85374	0.305000|0.305000	0.20034|0.20034	CAA|TCA		0.308	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			A	128813540	C	A	128813540	3	1	61	1	0	0	0	0	1	0	0	0	12129	827	29	2	2097	2	PLK4	4	128813540	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10492	128813540	62340736	3466	11451										
PLK4	10733	broad.mit.edu	37	chr4	128816161	128816161	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcttctggaacagacatCtcttctaatagtctaaaaga	6	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128816161C>A	ENST00000270861.5	+	14	2890	c.2616C>A	c.(2614-2616)atC>atA	p.I872I	PLK4_ENST00000507249.1_Silent_p.I811I|PLK4_ENST00000513090.1_Silent_p.I840I|PLK4_ENST00000515069.1_Silent_p.I794I|PLK4_ENST00000514379.1_Silent_p.I831I|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	872					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I872I(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						GAACAGACATCTCTTCTAATA	0.348																																					Colon(135;508 1718 19061 31832 42879)											1	Substitution - coding silent(1)	large_intestine(1)	4											100	99	100					4																	128816161		2202	4300	6502	129035611	SO:0001819	synonymous_variant	10733			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2616C>A	4.37:g.128816161C>A			129035611	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																				0.348	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			A	128816161	C	A	128816161	2	1	61	1	0	0	0	0	0	0	0	1	12129	903	32	2		2	PLK4	4	128816161	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2621	128816161	62338115	3467	11452										
C4orf29	80167	broad.mit.edu	37	chr4	128951771	128951771	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggcctggttgtgaaatCcgatacttagaagggggtca	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128951771C>T	ENST00000444616.1	+	11	1432	c.1185C>T	c.(1183-1185)atC>atT	p.I395I	C4orf29_ENST00000388795.5_Silent_p.I347I|C4orf29_ENST00000398965.1_Silent_p.I395I			Q0P651	CD029_HUMAN	chromosome 4 open reading frame 29	395						extracellular region (GO:0005576)		p.I395I(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						GTTGTGAAATCCGATACTTAG	0.393																																																2	Substitution - coding silent(2)	large_intestine(2)	4											91	90	90					4																	128951771		1837	4088	5925	129171221	SO:0001819	synonymous_variant	80167			AK024759	CCDS47131.1	4q28.2	2008-02-05			ENSG00000164074	ENSG00000164074			26111	protein-coding gene	gene with protein product						12477932	Standard	XM_006714318		Approved	FLJ21106	uc021xrt.1	Q0P651	OTTHUMG00000133304	ENST00000444616.1:c.1185C>T	4.37:g.128951771C>T			129171221	A1A4W8|A1A4W9|Q9H7A7	Silent	SNP	ENST00000444616.1	37																																																																																					0.393	C4orf29-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257098.1	NM_001039717		T	128951771	C	T	128951771	2	4	61	1	0	0	0	0	0	0	0	1	2265	845	30	3		3	C4orf29	4	128951771	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135610	128951771	62202505	3468	11453										
LARP1B	55132	broad.mit.edu	37	chr4	128999036	128999036	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtaacagtgacagcaaaGaaaaccgggaaacaaaatta	9	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:128999036G>T	ENST00000326639.6	+	4	347	c.136G>T	c.(136-138)Gaa>Taa	p.E46*	LARP1B_ENST00000427266.1_Nonsense_Mutation_p.E46*|LARP1B_ENST00000264584.5_Nonsense_Mutation_p.E46*|LARP1B_ENST00000394288.3_Nonsense_Mutation_p.E46*|LARP1B_ENST00000512292.1_Nonsense_Mutation_p.E46*|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000432347.2_Nonsense_Mutation_p.E46*|LARP1B_ENST00000441387.1_Nonsense_Mutation_p.E46*	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	46						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E46*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TGACAGCAAAGAAAACCGGGA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											97	98	98					4																	128999036		2203	4300	6503	129218486	SO:0001587	stop_gained	55132				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.136G>T	4.37:g.128999036G>T	ENSP00000321997:p.Glu46*		129218486	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Nonsense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	31|31	5.097370|5.097370	0.94197|0.94197	.|.	.|.	ENSG00000138709|ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266|ENST00000507377	.|.	.|.	.|.	3.95|3.95	3.95|3.95	0.45737|0.45737	.|.	0.218756|.	0.40728|.	N|.	0.001023|.	.|T	.|0.71108	.|0.3301	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71629	.|-0.4535	.|4	0.66056|.	D|.	0.02|.	.|.	16.1373|16.1373	0.81494|0.81494	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	46|14	.|.	ENSP00000264584:E46X|.	E|R	+|+	1|2	0|0	LARP1B|LARP1B	129218486|129218486	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.436000|0.436000	0.31835|0.31835	4.985000|4.985000	0.63845|0.63845	2.206000|2.206000	0.71126|0.71126	0.471000|0.471000	0.43371|0.43371	GAA|AGA		0.393	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		T	128999036	G	T	128999036	4	4	61	1	0	0	0	0	0	1	0	0	8651	943	33	2	142	2	LARP1B	4	128999036	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47265	128999036	62155240	3469	11454										
LARP1B	55132	broad.mit.edu	37	chr4	129028332	129028332	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtagaaattgtggatgaGaaaatgagaaaaaagataga	12	0	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:129028332G>T	ENST00000326639.6	+	9	1063	c.852G>T	c.(850-852)gaG>gaT	p.E284D	LARP1B_ENST00000427266.1_Missense_Mutation_p.E284D|LARP1B_ENST00000264584.5_Missense_Mutation_p.E237D|LARP1B_ENST00000394288.3_Missense_Mutation_p.E284D|LARP1B_ENST00000512292.1_Missense_Mutation_p.E284D|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000432347.2_Missense_Mutation_p.E284D|LARP1B_ENST00000441387.1_Missense_Mutation_p.E284D	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	284	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E284D(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TTGTGGATGAGAAAATGAGAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											71	73	72					4																	129028332		2203	4300	6503	129247782	SO:0001583	missense	55132				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.852G>T	4.37:g.129028332G>T	ENSP00000321997:p.Glu284Asp		129247782	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.68|12.68	2.010025|2.010025	0.35415|0.35415	.|.	.|.	ENSG00000138709|ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266|ENST00000507377	T;T;T;T;T;T;T;T|.	0.36878|.	1.23;1.23;1.23;1.23;1.23;1.23;1.23;1.23|.	5.38|5.38	2.79|2.79	0.32731|0.32731	Winged helix-turn-helix transcription repressor DNA-binding (1);RNA-binding protein Lupus La (2);|.	0.346395|0.346395	0.30800|0.30800	N|N	0.008848|0.008848	T|.	0.40322|.	0.1112|.	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.18610|.	0.001;0.002;0.004;0.029|.	B;B;B;B|.	0.14023|.	0.003;0.01;0.01;0.01|.	T|.	0.20840|.	-1.0263|.	10|.	0.07644|0.49607	T|T	0.81|0.09	.|.	6.7185|6.7185	0.23316|0.23316	0.1892:0.0:0.685:0.1258|0.1892:0.0:0.685:0.1258	.|.	284;284;284;284|.	Q659C4;G3XAJ5;Q659C4-3;G3V0E9|.	LAR1B_HUMAN;.;.;.|.	D|X	284;284;237;284;284;237;284;284|253	ENSP00000321997:E284D;ENSP00000422850:E284D;ENSP00000427281:E237D;ENSP00000377829:E284D;ENSP00000390395:E284D;ENSP00000264584:E237D;ENSP00000396521:E284D;ENSP00000403586:E284D|.	ENSP00000264584:E237D|ENSP00000424383:E253X	E|E	+|+	3|1	2|0	LARP1B|LARP1B	129247782|129247782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	2.425000|2.425000	0.44723|0.44723	0.423000|0.423000	0.26033|0.26033	-0.794000|-0.794000	0.03295|0.03295	GAG|GAA		0.398	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		T	129028332	G	T	129028332	3	4	61	1	0	0	0	0	1	0	0	0	8651	933	33	2	878	2	LARP1B	4	129028332	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29296	129028332	62125944	3470	11455										
LARP1B	55132	broad.mit.edu	37	chr4	129121708	129121708	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaattggtcagtcccaaGaaatgaataccctctttcgt	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:129121708G>T	ENST00000326639.6	+	17	2408	c.2197G>T	c.(2197-2199)Gaa>Taa	p.E733*	LARP1B_ENST00000506199.1_3'UTR|LARP1B_ENST00000264584.5_Nonsense_Mutation_p.E674*|LARP1B_ENST00000354456.3_Nonsense_Mutation_p.E152*|LARP1B_ENST00000441387.1_Nonsense_Mutation_p.E733*	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	733						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E733*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TCAGTCCCAAGAAATGAATAC	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											39	37	38					4																	129121708		2202	4294	6496	129341158	SO:0001587	stop_gained	55132				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.2197G>T	4.37:g.129121708G>T	ENSP00000321997:p.Glu733*		129341158	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Nonsense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	G	40	8.012150	0.98610	.	.	ENSG00000138709	ENST00000326639;ENST00000264584;ENST00000441387;ENST00000354456	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.9187	0.88960	0.0:0.0:1.0:0.0	.	.	.	.	X	733;674;733;152	.	ENSP00000264584:E674X	E	+	1	0	LARP1B	129341158	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.384000	0.79751	2.467000	0.83353	0.561000	0.74099	GAA		0.318	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		T	129121708	G	T	129121708	4	4	61	1	0	0	0	0	0	1	0	0	8651	943	33	2	2389	2	LARP1B	4	129121708	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93376	129121708	62032568	3471	11456										
PHF17	79960	broad.mit.edu	37	chr4	129764138	129764138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttggtcccagaattcccGatcccagcataggagaagct	9	12	0	2	rs371320173		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:129764138G>A	ENST00000226319.6	+	3	363	c.83G>A	c.(82-84)cGa>cAa	p.R28Q	PHF17_ENST00000452328.2_Missense_Mutation_p.R28Q|PHF17_ENST00000511647.1_Missense_Mutation_p.R28Q|PHF17_ENST00000512960.1_Missense_Mutation_p.R28Q|PHF17_ENST00000413543.2_Missense_Mutation_p.R28Q	NM_199320.2	NP_955352.1												p.R28Q(1)		NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGAATTCCCGATCCCAGCAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	124	119	120		83,83	4.9	1	4		120	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PHF17	NM_024900.3,NM_199320.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	28/510,28/843	129764138	1,13005	2203	4300	6503	129983588	SO:0001583	missense	79960																														ENST00000226319.6:c.83G>A	4.37:g.129764138G>A	ENSP00000226319:p.Arg28Gln		129983588		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.065848	0.55539	0.0	1.16E-4	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000504089;ENST00000512960;ENST00000503785;ENST00000535321;ENST00000510308;ENST00000413543;ENST00000507833;ENST00000508997	T;T;T;T;T	0.43294	1.05;0.95;1.06;1.05;0.95	4.86	4.86	0.63082	.	0.354304	0.28677	N	0.014505	T	0.43634	0.1256	L	0.36672	1.1	0.41592	D	0.988809	D;D;D	0.63046	0.992;0.992;0.974	P;B;B	0.50490	0.642;0.381;0.243	T	0.24941	-1.0146	9	.	.	.	.	16.362	0.83271	0.0:0.0:1.0:0.0	.	28;28;28	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	Q	28	ENSP00000226319:R28Q;ENSP00000423737:R28Q;ENSP00000388015:R28Q;ENSP00000425730:R28Q;ENSP00000404211:R28Q	.	R	+	2	0	PHF17	129983588	1.000000	0.71417	0.982000	0.44146	0.992000	0.81027	4.665000	0.61547	2.512000	0.84698	0.561000	0.74099	CGA		0.448	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			A	129764138	G	A	129764138	3	1	61	1	0	0	0	0	1	0	0	0	11859	1058	37	1	89	1	PHF17	4	129764138	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	642430	129764138	61390138	3472	11457										
PCDH10	57575	broad.mit.edu	37	chr4	134073151	134073151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgcccggctcacttacaGcatcgtgcgtggcaacgaaa	11	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:134073151G>T	ENST00000264360.5	+	1	2682	c.1856G>T	c.(1855-1857)aGc>aTc	p.S619I	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	619	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S619I(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		CTCACTTACAGCATCGTGCGT	0.711																																																1	Substitution - Missense(1)	large_intestine(1)	4											33	37	35					4																	134073151		2165	4272	6437	134292601	SO:0001583	missense	57575			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1856G>T	4.37:g.134073151G>T	ENSP00000264360:p.Ser619Ile		134292601	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117606	0.56505	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.56103	0.48	4.5	4.5	0.54988	Cadherin (4);Cadherin-like (1);	0.000000	0.53938	D	0.000050	T	0.76263	0.3963	M	0.87328	2.875	0.80722	D	1	D;P	0.76494	0.999;0.699	D;P	0.87578	0.998;0.579	T	0.81300	-0.0995	10	0.62326	D	0.03	.	17.0032	0.86386	0.0:0.0:1.0:0.0	.	619;619	Q9P2E7;Q96SF0	PCD10_HUMAN;.	I	619	ENSP00000264360:S619I	ENSP00000264360:S619I	S	+	2	0	PCDH10	134292601	0.253000	0.23982	1.000000	0.80357	0.111000	0.19643	1.153000	0.31676	2.325000	0.78763	0.655000	0.94253	AGC		0.711	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		T	134073151	G	T	134073151	3	4	61	1	0	0	0	0	1	0	0	0	11538	971	34	2	1858	2	PCDH10	4	134073151	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4309013	134073151	57081125	3473	11458										
PCDH18	54510	broad.mit.edu	37	chr4	138442411	138442411	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgggattttgaaaatgCgtactggctgcccatgccgc	14	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:138442411C>T	ENST00000344876.4	-	4	3566	c.3180G>A	c.(3178-3180)acG>acA	p.T1060T	PCDH18_ENST00000412923.2_Silent_p.T1059T|PCDH18_ENST00000511115.1_Silent_p.T240T|PCDH18_ENST00000507846.1_Silent_p.T839T|PCDH18_ENST00000510305.1_Silent_p.T271T	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	1060	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T1060T(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TTTGAAAATGCGTACTGGCTG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	4											43	42	42					4																	138442411		2203	4300	6503	138661861	SO:0001819	synonymous_variant	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.3180G>A	4.37:g.138442411C>T			138661861	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.587	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138442411	C	T	138442411	2	4	61	1	0	0	0	0	0	0	0	1	11544	755	27	1		1	PCDH18	4	138442411	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4369260	138442411	52711865	3474	11459										
PCDH18	54510	broad.mit.edu	37	chr4	138450792	138450792	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtgggtgagttctaatgaGaaattctctggcacgtggtt	14	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:138450792G>T	ENST00000344876.4	-	1	2837	c.2451C>A	c.(2449-2451)ttC>ttA	p.F817L	PCDH18_ENST00000412923.2_Missense_Mutation_p.F817L|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.F597L|PCDH18_ENST00000510305.1_Missense_Mutation_p.F28L	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	817					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F817L(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GTTCTAATGAGAAATTCTCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	4											120	104	109					4																	138450792		2203	4300	6503	138670242	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2451C>A	4.37:g.138450792G>T	ENSP00000355082:p.Phe817Leu		138670242	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.367849	0.42003	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305	T;T;T;T	0.54279	0.73;0.67;0.58;1.51	5.29	3.54	0.40534	.	0.000000	0.45361	D	0.000362	T	0.54224	0.1845	L	0.57536	1.79	0.80722	D	1	P;D;P	0.56035	0.826;0.974;0.826	B;P;B	0.50659	0.292;0.647;0.292	T	0.49224	-0.8962	10	0.23891	T	0.37	.	10.8728	0.46894	0.153:0.0:0.847:0.0	.	597;817;817	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	L	817;817;597;28	ENSP00000355082:F817L;ENSP00000390688:F817L;ENSP00000425903:F597L;ENSP00000424269:F28L	ENSP00000355082:F817L	F	-	3	2	PCDH18	138670242	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.844000	0.48246	0.780000	0.33566	0.655000	0.94253	TTC		0.458	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138450792	G	T	138450792	3	4	61	1	0	0	0	0	1	0	0	0	11544	933	33	2	972	2	PCDH18	4	138450792	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8381	138450792	52703484	3475	11460										
PCDH18	54510	broad.mit.edu	37	chr4	138452718	138452718	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaatcattggcagagagCgagtatgtgtggagggaatt	14	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:138452718C>T	ENST00000344876.4	-	1	911	c.525G>A	c.(523-525)tcG>tcA	p.S175S	PCDH18_ENST00000412923.2_Silent_p.S175S|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_5'UTR|PCDH18_ENST00000510305.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	175	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S175S(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TGGCAGAGAGCGAGTATGTGT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	4											64	62	63					4																	138452718		2203	4300	6503	138672168	SO:0001819	synonymous_variant	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.525G>A	4.37:g.138452718C>T			138672168	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.473	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138452718	C	T	138452718	2	4	61	1	0	0	0	0	0	0	0	1	11544	755	27	1		1	PCDH18	4	138452718	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1926	138452718	52701558	3476	11461										
SLC7A11	23657	broad.mit.edu	37	chr4	139100419	139100419	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtcccatataataaagaGataatacgcagggactccag	8	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:139100419G>T	ENST00000280612.5	-	11	1675	c.1396C>A	c.(1396-1398)Ctc>Atc	p.L466I	SLC7A11-AS1_ENST00000510767.1_RNA	NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	466					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)	p.L466I(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	ATAATAAAGAGATAATACGCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	66	66					4																	139100419		2203	4299	6502	139319869	SO:0001583	missense	23657			AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"Solute carriers"	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.1396C>A	4.37:g.139100419G>T	ENSP00000280612:p.Leu466Ile		139319869	A8K2U4	Missense_Mutation	SNP	ENST00000280612.5	37	CCDS3742.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389363	0.42410	.	.	ENSG00000151012	ENST00000280612	D	0.91068	-2.78	5.45	4.42	0.53409	.	0.178950	0.48767	D	0.000161	D	0.85097	0.5619	L	0.35288	1.05	0.35864	D	0.827711	B	0.18013	0.025	B	0.18263	0.021	D	0.83443	0.0044	10	0.26408	T	0.33	.	15.0998	0.72266	0.0796:0.0:0.9204:0.0	.	466	Q9UPY5	XCT_HUMAN	I	466	ENSP00000280612:L466I	ENSP00000280612:L466I	L	-	1	0	SLC7A11	139319869	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.023000	0.57211	2.546000	0.85860	0.655000	0.94253	CTC		0.428	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2			T	139100419	G	T	139100419	3	4	61	1	0	0	0	0	1	0	0	0	14731	942	33	2	117	2	SLC7A11	4	139100419	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	647701	139100419	52053857	3477	11462										
ELF2	1998	broad.mit.edu	37	chr4	139981756	139981756	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatgaccactatgtttttCggcatatccttgaactgata	6	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:139981756C>T	ENST00000394235.2	-	9	1345	c.843G>A	c.(841-843)ccG>ccA	p.P281P	ELF2_ENST00000379549.2_Silent_p.P204P|ELF2_ENST00000265495.4_Silent_p.P281P|ELF2_ENST00000379550.1_Silent_p.P293P|ELF2_ENST00000510408.1_Silent_p.P221P|ELF2_ENST00000358635.3_Silent_p.P233P|ELF2_ENST00000515489.1_5'Flank	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)									p.P281P(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					CTATGTTTTTCGGCATATCCT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4											115	110	112					4																	139981756		2203	4300	6503	140201206	SO:0001819	synonymous_variant	1998			AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.843G>A	4.37:g.139981756C>T			140201206		Silent	SNP	ENST00000394235.2	37	CCDS3744.1																																																																																				0.378	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		T	139981756	C	T	139981756	2	4	61	1	0	0	0	0	0	0	0	1	5067	871	31	1		1	ELF2	4	139981756	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	881337	139981756	51172520	3478	11463										
ELF2	1998	broad.mit.edu	37	chr4	139993092	139993092	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtatccatgggttcagactCttcagttgacacctccacta	8	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:139993092C>A	ENST00000394235.2	-	6	920	c.418G>T	c.(418-420)Gag>Tag	p.E140*	ELF2_ENST00000379549.2_Nonsense_Mutation_p.E92*|ELF2_ENST00000265495.4_Nonsense_Mutation_p.E140*|ELF2_ENST00000379550.1_Nonsense_Mutation_p.E152*|ELF2_ENST00000510408.1_Nonsense_Mutation_p.E80*|ELF2_ENST00000358635.3_Nonsense_Mutation_p.E92*	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)									p.E140*(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					GGTTCAGACTCTTCAGTTGAC	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											151	146	148					4																	139993092		2203	4300	6503	140212542	SO:0001587	stop_gained	1998			AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.418G>T	4.37:g.139993092C>A	ENSP00000377782:p.Glu140*		140212542		Nonsense_Mutation	SNP	ENST00000394235.2	37	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	C	36	5.864478	0.97043	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000510408;ENST00000420916;ENST00000512627	.	.	.	5.87	5.87	0.94306	.	0.238872	0.49305	D	0.000160	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	92;140;152;140;92;80;92;80	.	.	E	-	1	0	ELF2	140212542	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.831000	0.75324	2.941000	0.99782	0.655000	0.94253	GAG		0.403	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		A	139993092	C	A	139993092	4	1	61	1	0	0	0	0	0	1	0	0	5067	922	32	2	1347	2	ELF2	4	139993092	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11336	139993092	51161184	3479	11464										
RAB33B	83452	broad.mit.edu	37	chr4	140393970	140393970	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttttcatagcctaccatCttggatagaagaatgcaaac	7	8	2	2	rs139890586		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:140393970C>A	ENST00000305626.5	+	2	769	c.380C>A	c.(379-381)tCt>tAt	p.S127Y		NM_031296.1	NP_112586.1	Q9H082	RB33B_HUMAN	RAB33B, member RAS oncogene family	127					autophagy (GO:0006914)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of retrograde vesicle-mediated transport, Golgi to ER (GO:2000156)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.S127Y(1)		large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4	all_hematologic(180;0.162)					AGCCTACCATCTTGGATAGAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											124	111	115					4																	140393970		2203	4300	6503	140613420	SO:0001583	missense	83452			AF350420	CCDS3747.1	4q28	2008-02-05			ENSG00000172007	ENSG00000172007		"RAB, member RAS oncogene"	16075	protein-coding gene	gene with protein product		605950					Standard	NM_031296		Approved	DKFZP434G099	uc003ihv.3	Q9H082	OTTHUMG00000133384	ENST00000305626.5:c.380C>A	4.37:g.140393970C>A	ENSP00000306496:p.Ser127Tyr		140613420	B2R987|Q4W5B0	Missense_Mutation	SNP	ENST00000305626.5	37	CCDS3747.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.317966	0.60524	.	.	ENSG00000172007	ENST00000305626	T	0.78003	-1.14	5.75	4.01	0.46588	Small GTP-binding protein domain (1);	0.102312	0.64402	D	0.000003	T	0.70552	0.3237	N	0.12569	0.235	0.09310	N	1	P	0.48640	0.913	P	0.53266	0.722	T	0.64554	-0.6380	10	0.66056	D	0.02	.	10.9451	0.47296	0.0:0.7977:0.0:0.2023	.	127	Q9H082	RB33B_HUMAN	Y	127	ENSP00000306496:S127Y	ENSP00000306496:S127Y	S	+	2	0	RAB33B	140613420	0.971000	0.33674	0.713000	0.30519	0.996000	0.88848	3.831000	0.55776	1.438000	0.47492	0.561000	0.74099	TCT		0.403	RAB33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257235.2	NM_031296		A	140393970	C	A	140393970	3	1	61	1	0	0	0	0	1	0	0	0	12960	913	32	2	386	2	RAB33B	4	140393970	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	400878	140393970	50760306	3480	11465										
SETD7	80854	broad.mit.edu	37	chr4	140454447	140454447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctacatacgtgccctggaGaactcccccatcttcgtaag	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:140454447G>T	ENST00000274031.3	-	3	880	c.244C>A	c.(244-246)Ctc>Atc	p.L82I	SETD7_ENST00000506866.2_Missense_Mutation_p.L82I|SETD7_ENST00000404104.3_Missense_Mutation_p.L82I|SETD7_ENST00000406354.1_Missense_Mutation_p.F64L	NM_030648.2	NP_085151.1	Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	82					chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)	p.L82I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					GTGCCCTGGAGAACTCCCCCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	4											109	95	99					4																	140454447		2203	4300	6503	140673897	SO:0001583	missense	80854			AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391		"Chromatin-modifying enzymes / K-methyltransferases"	30412	protein-coding gene	gene with protein product		606594				11850410, 11779497	Standard	NM_030648		Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000274031.3:c.244C>A	4.37:g.140454447G>T	ENSP00000274031:p.Leu82Ile		140673897	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	Missense_Mutation	SNP	ENST00000274031.3	37	CCDS3748.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.04|15.04	2.714661|2.714661	0.48622|0.48622	.|.	.|.	ENSG00000145391|ENSG00000145391	ENST00000406354|ENST00000506866;ENST00000274031;ENST00000404104	.|T;T;T	.|0.43294	.|0.98;0.98;0.95	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.31702|0.31702	0.0805|0.0805	N|N	0.11364|0.11364	0.135|0.135	0.33175|0.33175	D|D	0.548862|0.548862	.|D;P	.|0.54397	.|0.966;0.755	.|B;P	.|0.44647	.|0.284;0.456	T|T	0.29274|0.29274	-1.0017|-1.0017	6|10	0.87932|0.31617	D|T	0|0.26	-22.0062|-22.0062	19.8677|19.8677	0.96824|0.96824	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|82;82	.|B5MCZ8;Q8WTS6	.|.;SETD7_HUMAN	L|I	64|82	.|ENSP00000427300:L82I;ENSP00000274031:L82I;ENSP00000385913:L82I	ENSP00000384336:F64L|ENSP00000274031:L82I	F|L	-|-	3|1	2|0	SETD7|SETD7	140673897|140673897	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.977000|0.977000	0.68977|0.68977	4.970000|4.970000	0.63742|0.63742	2.709000|2.709000	0.92574|0.92574	0.655000|0.655000	0.94253|0.94253	TTC|CTC		0.498	SETD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257236.1	NM_030648		T	140454447	G	T	140454447	3	4	61	1	0	0	0	0	1	0	0	0	14173	942	33	2	880	2	SETD7	4	140454447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60477	140454447	50699829	3481	11466										
CLGN	1047	broad.mit.edu	37	chr4	141310404	141310404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcgtactcttcttttgcGtactgactttatcggcccat	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:141310404G>A	ENST00000325617.5	-	15	2247	c.1807C>T	c.(1807-1809)Cgc>Tgc	p.R603C	CLGN_ENST00000537281.1_Missense_Mutation_p.R603C|CLGN_ENST00000414773.1_Missense_Mutation_p.R603C	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	603					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)	p.R603C(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					CTTCTTTTGCGTACTGACTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											147	147	147					4																	141310404		2203	4300	6503	141529854	SO:0001583	missense	1047			D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1807C>T	4.37:g.141310404G>A	ENSP00000326699:p.Arg603Cys		141529854	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	37	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.340545	0.81911	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.56611	0.45;0.45;0.45	5.22	5.22	0.72569	.	0.132286	0.49305	D	0.000141	T	0.70928	0.3280	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.73329	-0.4017	10	0.87932	D	0	-4.9462	19.1343	0.93420	0.0:0.0:1.0:0.0	.	603	O14967	CLGN_HUMAN	C	603;603;603;520	ENSP00000326699:R603C;ENSP00000392782:R603C;ENSP00000439381:R603C	ENSP00000326699:R603C	R	-	1	0	CLGN	141529854	1.000000	0.71417	0.980000	0.43619	0.841000	0.47740	5.868000	0.69605	2.584000	0.87258	0.591000	0.81541	CGC		0.358	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362		A	141310404	G	A	141310404	3	1	61	1	0	0	0	0	1	0	0	0	3530	1145	40	1	29	1	CLGN	4	141310404	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	855957	141310404	49843872	3482	11467										
TBC1D9	23158	broad.mit.edu	37	chr4	141555221	141555221	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcccaaggaaagagaagaGcaaacattcccttgaactgc	9	10	0	3	rs375019047		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:141555221G>A	ENST00000442267.2	-	16	2701	c.2627C>T	c.(2626-2628)gCt>gTt	p.A876V		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	876							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.A876V(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				AAAGAGAAGAGCAAACATTCC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	4						G	VAL/ALA	1,4213		0,1,2106	73	75	74		2627	4.3	0	4		74	0,8446		0,0,4223	no	missense	TBC1D9	NM_015130.2	64	0,1,6329	AA,AG,GG		0.0,0.0237,0.0079	benign	876/1267	141555221	1,12659	2107	4223	6330	141774671	SO:0001583	missense	23158			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2627C>T	4.37:g.141555221G>A	ENSP00000411197:p.Ala876Val		141774671	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	1.850	-0.465351	0.04476	2.37E-4	0.0	ENSG00000109436	ENST00000442267	T	0.42900	0.96	6.02	4.29	0.51040	EF-hand-like domain (1);	0.600125	0.18532	N	0.138476	T	0.28566	0.0707	L	0.28694	0.88	0.24401	N	0.99471	B	0.02656	0.0	B	0.04013	0.001	T	0.16512	-1.0400	10	0.29301	T	0.29	-0.0084	7.8812	0.29623	0.1415:0.1322:0.7263:0.0	.	876	Q6ZT07	TBCD9_HUMAN	V	876	ENSP00000411197:A876V	ENSP00000411197:A876V	A	-	2	0	TBC1D9	141774671	0.076000	0.21285	0.029000	0.17559	0.005000	0.04900	1.610000	0.36869	0.867000	0.35654	-0.150000	0.13652	GCT		0.527	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141555221	G	A	141555221	3	1	61	1	0	0	0	0	1	0	0	0	15666	971	34	3	1197	3	TBC1D9	4	141555221	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244817	141555221	49599055	3483	11468										
RNF150	57484	broad.mit.edu	37	chr4	141888805	141888805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatccctggcatttgcatatCgaaacctctggatgtaataa	7	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:141888805C>T	ENST00000515673.2	-	2	740	c.707G>A	c.(706-708)cGa>cAa	p.R236Q	RNF150_ENST00000420921.2_Missense_Mutation_p.R95Q|RNF150_ENST00000515057.1_5'UTR|RNF150_ENST00000507500.1_Missense_Mutation_p.R236Q|RNF150_ENST00000379512.2_Missense_Mutation_p.R95Q|RNF150_ENST00000306799.3_Intron			Q9ULK6	RN150_HUMAN	ring finger protein 150	236						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R236Q(2)|p.R145Q(2)		breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					ATTTGCATATCGAAACCTCTG	0.378																																																4	Substitution - Missense(4)	large_intestine(4)	4											74	72	73					4																	141888805		2203	4300	6503	142108255	SO:0001583	missense	57484			AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.707G>A	4.37:g.141888805C>T	ENSP00000425840:p.Arg236Gln		142108255	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	37	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	C	36	5.627034	0.96671	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T	0.19938	2.11;2.11;3.1;3.12;2.24	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.50343	0.1610	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.988	T	0.34925	-0.9809	10	0.49607	T	0.09	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	236;236	Q9ULK6-3;Q9ULK6	.;RN150_HUMAN	Q	95;95;236;236;67	ENSP00000368827:R95Q;ENSP00000394581:R95Q;ENSP00000425840:R236Q;ENSP00000425568:R236Q;ENSP00000425947:R67Q	ENSP00000368827:R95Q	R	-	2	0	RNF150	142108255	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.890000	0.99128	0.650000	0.86243	CGA		0.378	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		T	141888805	C	T	141888805	3	4	61	1	0	0	0	0	1	0	0	0	13488	884	31	1	633	1	RNF150	4	141888805	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	333584	141888805	49265471	3484	11469										
ZNF330	27309	broad.mit.edu	37	chr4	142147987	142147987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggtgtatacagtactgGccttgcaatggtggtaagct	13	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:142147987G>A	ENST00000262990.4	+	5	506	c.278G>A	c.(277-279)gGc>gAc	p.G93D	ZNF330_ENST00000421169.2_Missense_Mutation_p.G33D	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	93						chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.G93D(1)		kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					TACAGTACTGGCCTTGCAATG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											261	231	241					4																	142147987		2203	4300	6503	142367437	SO:0001583	missense	27309			AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"Zinc fingers, C2H2-type"	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.278G>A	4.37:g.142147987G>A	ENSP00000262990:p.Gly93Asp		142367437	B2RDA3	Missense_Mutation	SNP	ENST00000262990.4	37	CCDS3754.1	.	.	.	.	.	.	.	.	.	.	G	38	6.749388	0.97809	.	.	ENSG00000109445	ENST00000262990;ENST00000512809;ENST00000503649;ENST00000512738;ENST00000421169	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	5.71	4.86	0.63082	.	0.046997	0.85682	D	0.000000	T	0.73426	0.3585	M	0.87547	2.89	0.80722	D	1	P;D	0.89917	0.468;1.0	B;D	0.97110	0.371;1.0	T	0.79883	-0.1615	10	0.87932	D	0	-9.7978	16.7055	0.85371	0.0:0.1296:0.8704:0.0	.	33;93	E9PDK6;Q9Y3S2	.;ZN330_HUMAN	D	93;93;93;93;33	ENSP00000262990:G93D;ENSP00000422599:G93D;ENSP00000422966:G93D;ENSP00000422251:G93D;ENSP00000397397:G33D	ENSP00000262990:G93D	G	+	2	0	ZNF330	142367437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.750000	0.98875	1.380000	0.46344	0.655000	0.94253	GGC		0.353	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487		A	142147987	G	A	142147987	3	1	61	1	0	0	0	0	1	0	0	0	17887	1203	42	3	292	3	ZNF330	4	142147987	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259182	142147987	49006289	3485	11470										
INPP4B	8821	broad.mit.edu	37	chr4	143159104	143159104	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacatctgctctcgaattCgcatccacttattgtcagat	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:143159104C>T	ENST00000513000.1	-	13	1182	c.749G>A	c.(748-750)cGa>cAa	p.R250Q	INPP4B_ENST00000262992.4_Missense_Mutation_p.R250Q|INPP4B_ENST00000508116.1_Missense_Mutation_p.R250Q|INPP4B_ENST00000308502.4_Missense_Mutation_p.R250Q|INPP4B_ENST00000509777.1_Missense_Mutation_p.R250Q	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	250					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.R250Q(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CTCTCGAATTCGCATCCACTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											47	46	46					4																	143159104		2201	4295	6496	143378554	SO:0001583	missense	8821			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.749G>A	4.37:g.143159104C>T	ENSP00000425487:p.Arg250Gln		143378554	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.635735	0.29068	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.49	0.805	0.18703	.	0.417260	0.24398	N	0.038872	T	0.20618	0.0496	L	0.38531	1.155	0.27235	N	0.959283	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.19943	-1.0290	10	0.23302	T	0.38	.	9.9828	0.41824	0.0:0.6665:0.0:0.3335	.	121;250	B7Z6T2;O15327	.;INP4B_HUMAN	Q	250;250;250;121;250;250;65;65;250;121	ENSP00000425487:R250Q;ENSP00000262992:R250Q;ENSP00000308441:R250Q;ENSP00000423954:R250Q;ENSP00000422793:R250Q;ENSP00000426207:R65Q;ENSP00000427250:R250Q;ENSP00000421065:R121Q	ENSP00000262992:R250Q	R	-	2	0	INPP4B	143378554	0.757000	0.28394	0.992000	0.48379	0.470000	0.32858	1.064000	0.30579	0.097000	0.17492	-0.150000	0.13652	CGA		0.318	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		T	143159104	C	T	143159104	3	4	61	1	0	0	0	0	1	0	0	0	7774	884	31	1	2085	1	INPP4B	4	143159104	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1011117	143159104	47995172	3486	11471										
INPP4B	8821	broad.mit.edu	37	chr4	143181683	143181683	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttatcttttccgctcacaCtttccggggctgtacattca	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:143181683C>A	ENST00000513000.1	-	12	1083	c.650G>T	c.(649-651)aGt>aTt	p.S217I	INPP4B_ENST00000262992.4_Missense_Mutation_p.S217I|INPP4B_ENST00000508116.1_Missense_Mutation_p.S217I|INPP4B_ENST00000308502.4_Missense_Mutation_p.S217I|INPP4B_ENST00000509777.1_Missense_Mutation_p.S217I	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	217					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.S217I(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TCCGCTCACACTTTCCGGGGC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	4											55	55	55					4																	143181683		2203	4300	6503	143401133	SO:0001583	missense	8821			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.650G>T	4.37:g.143181683C>A	ENSP00000425487:p.Ser217Ile		143401133	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.203326	0.38905	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.52	2.88	0.33553	.	0.616244	0.15738	N	0.247079	T	0.26448	0.0646	L	0.43923	1.385	0.09310	N	0.999997	B;P	0.37708	0.374;0.606	B;B	0.41135	0.203;0.348	T	0.11665	-1.0578	10	0.41790	T	0.15	.	5.757	0.18178	0.0:0.6288:0.1412:0.23	.	88;217	B7Z6T2;O15327	.;INP4B_HUMAN	I	217;217;217;88;217;217;32;32;217;88	ENSP00000425487:S217I;ENSP00000262992:S217I;ENSP00000308441:S217I;ENSP00000423954:S217I;ENSP00000422793:S217I;ENSP00000426207:S32I;ENSP00000427250:S217I;ENSP00000421065:S88I	ENSP00000262992:S217I	S	-	2	0	INPP4B	143401133	0.224000	0.23674	0.538000	0.28064	0.984000	0.73092	0.255000	0.18333	0.296000	0.22592	0.655000	0.94253	AGT		0.274	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		A	143181683	C	A	143181683	3	1	61	1	0	0	0	0	1	0	0	0	7774	565	20	2	2188	2	INPP4B	4	143181683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22579	143181683	47972593	3487	11472										
SMARCA5	8467	broad.mit.edu	37	chr4	144445600	144445600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaccaatgtttgcactcGatttgaagactctccatcgt	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:144445600G>A	ENST00000283131.3	+	4	962	c.500G>A	c.(499-501)cGa>cAa	p.R167Q		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	167					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R167Q(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GTTTGCACTCGATTTGAAGAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											107	105	105					4																	144445600		2203	4300	6503	144665050	SO:0001583	missense	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.500G>A	4.37:g.144445600G>A	ENSP00000283131:p.Arg167Gln		144665050		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066214	0.55539	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91124	-2.79	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	D	0.88232	0.6381	L	0.50333	1.59	0.58432	D	0.999995	B	0.24258	0.1	B	0.18871	0.023	D	0.83885	0.0281	10	0.23891	T	0.37	-23.4107	19.4826	0.95016	0.0:0.0:1.0:0.0	.	167	O60264	SMCA5_HUMAN	Q	167;110;110	ENSP00000283131:R167Q	ENSP00000283131:R167Q	R	+	2	0	SMARCA5	144665050	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.356000	0.73046	2.598000	0.87819	0.591000	0.81541	CGA		0.368	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			A	144445600	G	A	144445600	3	1	61	1	0	0	0	0	1	0	0	0	14808	1058	37	1	514	1	SMARCA5	4	144445600	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1263917	144445600	46708676	3488	11473										
SMARCA5	8467	broad.mit.edu	37	chr4	144456033	144456033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtccattcctccttcgtcGaattaaggctgatgttgaaa	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:144456033G>A	ENST00000283131.3	+	10	1646	c.1184G>A	c.(1183-1185)cGa>cAa	p.R395Q		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	395					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R395Q(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					CTCCTTCGTCGAATTAAGGCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											110	95	100					4																	144456033		2203	4300	6503	144675483	SO:0001583	missense	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.1184G>A	4.37:g.144456033G>A	ENSP00000283131:p.Arg395Gln		144675483		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	36	5.933636	0.97122	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.99961	-9.38	5.64	5.64	0.86602	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99977	0.9993	H	0.99689	4.705	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.98050	1.0387	10	0.87932	D	0	-11.8305	20.0804	0.97772	0.0:0.0:1.0:0.0	.	395	O60264	SMCA5_HUMAN	Q	395;338;338	ENSP00000283131:R395Q	ENSP00000283131:R395Q	R	+	2	0	SMARCA5	144675483	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.809000	0.99208	2.824000	0.97209	0.650000	0.86243	CGA		0.358	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			A	144456033	G	A	144456033	3	1	61	1	0	0	0	0	1	0	0	0	14808	1058	37	1	1222	1	SMARCA5	4	144456033	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10433	144456033	46698243	3489	11474										
SMARCA5	8467	broad.mit.edu	37	chr4	144467951	144467951	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaccaattggaataagaGagattttaaccagtttatca	6	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:144467951G>T	ENST00000283131.3	+	20	3005	c.2543G>T	c.(2542-2544)aGa>aTa	p.R848I		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	848	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R848I(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					TGGAATAAGAGAGATTTTAAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											83	86	85					4																	144467951		2203	4299	6502	144687401	SO:0001583	missense	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2543G>T	4.37:g.144467951G>T	ENSP00000283131:p.Arg848Ile		144687401		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996059	0.93167	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91843	-2.92	5.32	5.32	0.75619	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	D	0.94601	0.8260	M	0.93898	3.47	0.80722	D	1	P	0.35780	0.52	B	0.36030	0.216	D	0.95342	0.8439	10	0.87932	D	0	-6.5394	19.0086	0.92863	0.0:0.0:1.0:0.0	.	848	O60264	SMCA5_HUMAN	I	848;791;791	ENSP00000283131:R848I	ENSP00000283131:R848I	R	+	2	0	SMARCA5	144687401	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.559000	0.98135	2.487000	0.83934	0.655000	0.94253	AGA		0.333	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			T	144467951	G	T	144467951	3	4	61	1	0	0	0	0	1	0	0	0	14808	942	33	2	2621	2	SMARCA5	4	144467951	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11918	144467951	46686325	3490	11475										
SMARCA5	8467	broad.mit.edu	37	chr4	144468043	144468043	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaaggcaaaactccagaaGaagtcattgaatattcaggt	9	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:144468043G>T	ENST00000283131.3	+	20	3097	c.2635G>T	c.(2635-2637)Gaa>Taa	p.E879*		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	879	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.E879*(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					AACTCCAGAAGAAGTCATTGA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											85	92	89					4																	144468043		2202	4300	6502	144687493	SO:0001587	stop_gained	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2635G>T	4.37:g.144468043G>T	ENSP00000283131:p.Glu879*		144687493		Nonsense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	45	12.057546	0.99631	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-1.852	19.0701	0.93130	0.0:0.0:1.0:0.0	.	.	.	.	X	879;822;822	.	ENSP00000283131:E879X	E	+	1	0	SMARCA5	144687493	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.572000	0.98179	2.502000	0.84385	0.591000	0.81541	GAA		0.343	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			T	144468043	G	T	144468043	4	4	61	1	0	0	0	0	0	1	0	0	14808	943	33	2	2713	2	SMARCA5	4	144468043	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92	144468043	46686233	3491	11476										
GYPB	2994	broad.mit.edu	37	chr4	144922363	144922363	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtgatgagatgtaactCtttgtgactgaagaagaggt	13	4	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:144922363C>A	ENST00000502664.1	-	2	162	c.111G>T	c.(109-111)aaG>aaT	p.K37N	GYPB_ENST00000429670.2_Missense_Mutation_p.K37N|GYPB_ENST00000510196.2_5'UTR|GYPB_ENST00000283126.7_Missense_Mutation_p.K37N|RP11-673E1.4_ENST00000506982.1_RNA|GYPB_ENST00000513128.1_Intron	NM_002100.4	NP_002091	P06028	GLPB_HUMAN	glycophorin B (MNS blood group)	37						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.K37N(1)		breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGATGTAACTCTTTGTGACTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											132	166	154					4																	144922363		2196	4300	6496	145141813	SO:0001583	missense	2994				CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"CD molecules", "Blood group antigens"	4703	protein-coding gene	gene with protein product		111740	"glycophorin B (includes Ss blood group)", "glycophorin B (Ss blood group)"	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000502664.1:c.111G>T	4.37:g.144922363C>A	ENSP00000427690:p.Lys37Asn		145141813	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000502664.1	37	CCDS54809.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.291018	0.23564	.	.	ENSG00000250361	ENST00000283126;ENST00000502664;ENST00000429670	T;T;T	0.15139	2.45;2.45;2.85	1.46	-2.92	0.05615	.	.	.	.	.	T	0.30479	0.0766	.	.	.	0.09310	N	1	D	0.56287	0.975	D	0.65684	0.937	T	0.13980	-1.0489	8	0.62326	D	0.03	.	5.3838	0.16206	0.0:0.2514:0.5794:0.1692	.	37	E2QBW7	.	N	37	ENSP00000283126:K37N;ENSP00000427690:K37N;ENSP00000394200:K37N	ENSP00000283126:K37N	K	-	3	2	GYPB	145141813	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-1.290000	0.02777	-1.312000	0.02306	0.121000	0.15741	AAG		0.368	GYPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364791.1	NM_002100		A	144922363	C	A	144922363	3	1	61	1	0	0	0	0	1	0	0	0	6930	912	32	2	180	2	GYPB	4	144922363	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	454320	144922363	46231913	3492	11477										
HHIP	64399	broad.mit.edu	37	chr4	145573761	145573761	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttatggctttcagatatTttctgttaccaacaacacag	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:145573761T>G	ENST00000296575.3	+	2	939	c.284T>G	c.(283-285)tTt>tGt	p.F95C	HHIP_ENST00000511314.1_3'UTR|HHIP_ENST00000434550.2_Missense_Mutation_p.F95C|HHIP-AS1_ENST00000512359.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	95					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)	p.F95C(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		TTTCAGATATTTTCTGTTACC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	76	75					4																	145573761		2203	4299	6502	145793211	SO:0001583	missense	64399			AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.284T>G	4.37:g.145573761T>G	ENSP00000296575:p.Phe95Cys		145793211	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	37	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.729925	0.89390	.	.	ENSG00000164161	ENST00000296575;ENST00000434550	T;T	0.76839	-1.05;-1.05	5.83	5.83	0.93111	Folate receptor-like (1);	0.270588	0.40640	N	0.001059	D	0.83783	0.5329	L	0.53249	1.67	0.53005	D	0.999968	D;D	0.62365	0.975;0.991	P;P	0.59703	0.739;0.862	D	0.84769	0.0766	10	0.56958	D	0.05	-12.2154	16.2127	0.82178	0.0:0.0:0.0:1.0	.	95;95	Q96QV1;Q96QV1-2	HHIP_HUMAN;.	C	95	ENSP00000296575:F95C;ENSP00000408587:F95C	ENSP00000296575:F95C	F	+	2	0	HHIP	145793211	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.698000	0.84413	2.236000	0.73375	0.533000	0.62120	TTT		0.343	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			G	145573761	T	G	145573761	3	3	61	1	0	0	0	0	1	0	0	0	7113	1841	64	4	290	4	HHIP	4	145573761	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	651398	145573761	45580515	3493	11478										
MMAA	166785	broad.mit.edu	37	chr4	146563584	146563584	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaaaaatgcttactgagaGagggcacaaattatctgtgc	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:146563584G>T	ENST00000281317.5	+	3	1719	c.509G>T	c.(508-510)aGa>aTa	p.R170I	RP11-557J10.4_ENST00000504555.1_RNA|MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	170					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.R170I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTACTGAGAGAGGGCACAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											202	202	202					4																	146563584		2203	4300	6503	146783034	SO:0001583	missense	166785			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.509G>T	4.37:g.146563584G>T	ENSP00000281317:p.Arg170Ile		146783034	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.309085	0.60414	.	.	ENSG00000151611	ENST00000281317;ENST00000537246	D	0.91792	-2.91	5.56	3.54	0.40534	ATPase, AAA+ type, core (1);	0.352169	0.33895	N	0.004459	D	0.89480	0.6727	L	0.58101	1.795	0.80722	D	1	B;B	0.29646	0.199;0.253	B;B	0.34242	0.178;0.173	D	0.86934	0.2075	10	0.45353	T	0.12	-25.1325	9.2116	0.37322	0.2724:0.0:0.7276:0.0	.	170;170	Q8IVH4;D6RIS5	MMAA_HUMAN;.	I	170	ENSP00000281317:R170I	ENSP00000281317:R170I	R	+	2	0	MMAA	146783034	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.681000	0.46926	1.311000	0.45024	0.591000	0.81541	AGA		0.428	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			T	146563584	G	T	146563584	3	4	61	1	0	0	0	0	1	0	0	0	9669	942	33	2	515	2	MMAA	4	146563584	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	989823	146563584	44590692	3494	11479										
MMAA	166785	broad.mit.edu	37	chr4	146572263	146572263	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatggttgacatgtttgtTttactactgccaccagcagg	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:146572263T>G	ENST00000281317.5	+	5	1993	c.783T>G	c.(781-783)gtT>gtG	p.V261V	RP11-557J10.4_ENST00000504555.1_RNA|MMAA_ENST00000541599.1_Intron	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	261					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.V261V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACATGTTTGTTTTACTACTGC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	4											244	219	227					4																	146572263		2203	4300	6503	146791713	SO:0001819	synonymous_variant	166785			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.783T>G	4.37:g.146572263T>G			146791713	B3KX40|Q495G7	Silent	SNP	ENST00000281317.5	37	CCDS3766.1																																																																																				0.348	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			G	146572263	T	G	146572263	2	3	61	1	0	0	0	0	0	0	0	1	9669	1828	64	4		4	MMAA	4	146572263	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8679	146572263	44582013	3495	11480										
MMAA	166785	broad.mit.edu	37	chr4	146576305	146576305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccttttcgataggtaattCgtatttctgcccgaagtgga	9	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:146576305C>T	ENST00000281317.5	+	7	2186	c.976C>T	c.(976-978)Cgt>Tgt	p.R326C	MMAA_ENST00000541599.1_Missense_Mutation_p.R45C	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	326					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.R326C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATAGGTAATTCGTATTTCTGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	55	55					4																	146576305		2203	4300	6503	146795755	SO:0001583	missense	166785			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.976C>T	4.37:g.146576305C>T	ENSP00000281317:p.Arg326Cys		146795755	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.309160	0.81247	.	.	ENSG00000151611	ENST00000281317;ENST00000537246;ENST00000541599	D;D	0.90900	-2.75;-2.75	5.74	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.95027	0.8390	M	0.81179	2.53	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.94937	0.8088	10	0.49607	T	0.09	-13.2045	14.7177	0.69284	0.0:0.9307:0.0:0.0693	.	326	Q8IVH4	MMAA_HUMAN	C	326;326;45	ENSP00000281317:R326C;ENSP00000442284:R45C	ENSP00000281317:R326C	R	+	1	0	MMAA	146795755	1.000000	0.71417	0.894000	0.35097	0.850000	0.48378	7.456000	0.80751	1.448000	0.47680	-0.229000	0.12294	CGT		0.423	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			T	146576305	C	T	146576305	3	4	61	1	0	0	0	0	1	0	0	0	9669	884	31	1	998	1	MMAA	4	146576305	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4042	146576305	44577971	3496	11481										
ZNF827	152485	broad.mit.edu	37	chr4	146807011	146807011	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttccttgggttcctccttCaccagcaaaggcgagacgcc	9	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:146807011C>A	ENST00000508784.1	-	4	1793	c.1566G>T	c.(1564-1566)gtG>gtT	p.V522V	ZNF827_ENST00000379448.4_Silent_p.V522V|ZNF827_ENST00000513320.1_Silent_p.V172V			Q17R98	ZN827_HUMAN	zinc finger protein 827	522					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V522V(2)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					GTTCCTCCTTCACCAGCAAAG	0.577																																																2	Substitution - coding silent(2)	large_intestine(2)	4											108	101	103					4																	146807011		2203	4300	6503	147026461	SO:0001819	synonymous_variant	152485			AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.1566G>T	4.37:g.146807011C>A			147026461	B7ZL52|Q7Z4S7|Q8N279	Silent	SNP	ENST00000508784.1	37																																																																																					0.577	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		A	146807011	C	A	146807011	2	1	61	1	0	0	0	0	0	0	0	1	18219	813	29	2		2	ZNF827	4	146807011	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230706	146807011	44347265	3497	11482										
TTC29	83894	broad.mit.edu	37	chr4	147741344	147741344	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggctttgaaaattgtttCttgcaattttcacaaatttt	5	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:147741344C>A	ENST00000325106.4	-	10	1260	c.1034G>T	c.(1033-1035)aGa>aTa	p.R345I	TTC29_ENST00000513335.1_Missense_Mutation_p.R371I|TTC29_ENST00000398886.4_Missense_Mutation_p.R371I	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	345								p.R345I(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AAAATTGTTTCTTGCAATTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											113	108	109					4																	147741344		1814	4083	5897	147960794	SO:0001583	missense	83894			AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.1034G>T	4.37:g.147741344C>A	ENSP00000316740:p.Arg345Ile		147960794	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923669	0.73213	.	.	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000504425	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.91	0.594	0.17485	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.558686	0.20316	N	0.094733	T	0.78521	0.4296	L	0.46157	1.445	0.37903	D	0.931129	P;P;P	0.51147	0.942;0.911;0.942	P;P;P	0.58331	0.837;0.461;0.837	T	0.77056	-0.2729	10	0.56958	D	0.05	-4.337	8.2474	0.31698	0.0:0.3209:0.0:0.6791	.	345;371;345	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	I	371;371;345;345	ENSP00000423505:R371I;ENSP00000381861:R371I;ENSP00000316740:R345I;ENSP00000425778:R345I	ENSP00000316740:R345I	R	-	2	0	TTC29	147960794	1.000000	0.71417	0.519000	0.27824	0.960000	0.62799	1.018000	0.30002	0.129000	0.18514	0.650000	0.86243	AGA		0.333	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		A	147741344	C	A	147741344	3	1	61	1	0	0	0	0	1	0	0	0	16736	913	32	2	409	2	TTC29	4	147741344	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	934333	147741344	43412932	3498	11483										
TTC29	83894	broad.mit.edu	37	chr4	147830357	147830357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacttatgataaccatctCgcagcatgtccacacagata	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:147830357C>T	ENST00000325106.4	-	5	447	c.221G>A	c.(220-222)cGa>cAa	p.R74Q	TTC29_ENST00000513335.1_Missense_Mutation_p.R100Q|TTC29_ENST00000398886.4_Missense_Mutation_p.R100Q	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	74								p.R74Q(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					ATAACCATCTCGCAGCATGTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	4											58	58	58					4																	147830357		1925	4149	6074	148049807	SO:0001583	missense	83894			AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.221G>A	4.37:g.147830357C>T	ENSP00000316740:p.Arg74Gln		148049807	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.034977	0.54896	.	.	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.19532	2.14;2.14;2.14;2.14	5.05	2.91	0.33838	.	0.248820	0.35772	N	0.002983	T	0.12433	0.0302	L	0.28400	0.85	0.34758	D	0.732424	P;P;P	0.47545	0.578;0.897;0.735	B;B;B	0.36845	0.05;0.234;0.09	T	0.27806	-1.0063	10	0.29301	T	0.29	-5.4203	10.7407	0.46152	0.0:0.7992:0.0:0.2008	.	74;100;74	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	Q	100;100;74;74;74	ENSP00000423505:R100Q;ENSP00000381861:R100Q;ENSP00000316740:R74Q;ENSP00000425778:R74Q	ENSP00000316740:R74Q	R	-	2	0	TTC29	148049807	0.713000	0.27926	0.937000	0.37676	0.988000	0.76386	1.267000	0.33050	1.252000	0.44001	0.655000	0.94253	CGA		0.493	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		T	147830357	C	T	147830357	3	4	61	1	0	0	0	0	1	0	0	0	16736	884	31	1	1242	1	TTC29	4	147830357	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89013	147830357	43323919	3499	11484										
TMEM184C	55751	broad.mit.edu	37	chr4	148545976	148545976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatagctttgaaatatcccGgaattgcaatatatgtggat	10	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:148545976G>A	ENST00000296582.3	+	4	887	c.313G>A	c.(313-315)Gga>Aga	p.G105R	TMEM184C_ENST00000508208.1_Missense_Mutation_p.G105R	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	105						integral component of membrane (GO:0016021)		p.G105R(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						GAAATATCCCGGAATTGCAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											87	86	86					4																	148545976		2203	4300	6503	148765426	SO:0001583	missense	55751			AF305823	CCDS3770.1	4q31.22	2008-06-05	2008-06-05	2008-06-05		ENSG00000164168			25587	protein-coding gene	gene with protein product		613937	"transmembrane protein 34"	TMEM34			Standard	NM_018241		Approved	FLJ10846	uc003ila.4	Q9NVA4		ENST00000296582.3:c.313G>A	4.37:g.148545976G>A	ENSP00000296582:p.Gly105Arg		148765426	D3DP04|Q86X84|Q969I7|Q9NXM2	Missense_Mutation	SNP	ENST00000296582.3	37	CCDS3770.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252949	0.22965	.	.	ENSG00000164168	ENST00000296582;ENST00000508208	T;T	0.40476	1.03;1.03	5.12	3.93	0.45458	.	0.544310	0.22881	N	0.054516	T	0.18087	0.0434	N	0.03294	-0.36	0.23411	N	0.997732	B	0.02656	0.0	B	0.04013	0.001	T	0.18871	-1.0323	10	0.19590	T	0.45	-1.7914	8.3426	0.32252	0.846:0.0:0.154:0.0	.	105	Q9NVA4	T184C_HUMAN	R	105	ENSP00000296582:G105R;ENSP00000425940:G105R	ENSP00000296582:G105R	G	+	1	0	TMEM184C	148765426	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.707000	0.54838	0.902000	0.36520	-0.324000	0.08512	GGA		0.353	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1	NM_018241		A	148545976	G	A	148545976	3	1	61	1	0	0	0	0	1	0	0	0	16145	1117	39	1	327	1	TMEM184C	4	148545976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	715619	148545976	42608300	3500	11485										
ARHGAP10	79658	broad.mit.edu	37	chr4	148787883	148787883	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctgtcattttttcagggGatgtttaccttctatcatca	7	8	5	0	rs143552684		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:148787883G>A	ENST00000336498.3	+	7	857	c.618G>A	c.(616-618)ggG>ggA	p.G206G		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.G206G(1)		autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTTTTCAGGGGATGTTTACCT	0.363											OREG0016355	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	4						G		1,4405	2.1+/-5.4	0,1,2202	135	126	129		618	3.6	1	4	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ARHGAP10	NM_024605.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		206/787	148787883	2,13004	2203	4300	6503	149007333	SO:0001819	synonymous_variant	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.618G>A	4.37:g.148787883G>A		1720	149007333	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000336498.3	37	CCDS34075.1																																																																																				0.363	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		A	148787883	G	A	148787883	2	1	61	1	0	0	0	0	0	0	0	1	862	1161	41	3		3	ARHGAP10	4	148787883	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241907	148787883	42366393	3501	11486										
ARHGAP10	79658	broad.mit.edu	37	chr4	148796273	148796273	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagcaagtcagtttacagcCgaaggctacctgtatgtcca	10	11	1	0	rs374150548	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:148796273C>T	ENST00000336498.3	+	8	1043	c.804C>T	c.(802-804)gcC>gcT	p.A268A		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.A268A(1)		autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		AGTTTACAGCCGAAGGCTACC	0.453													C|||	8	0.00159744	0	0	5008	,	,		17207	0		0	False		,,,				2504	0.0082															1	Substitution - coding silent(1)	large_intestine(1)	4						C		1,4405	2.1+/-5.4	0,1,2202	85	81	83		804	-7.4	0.6	4		83	0,8600		0,0,4300	no	coding-synonymous	ARHGAP10	NM_024605.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		268/787	148796273	1,13005	2203	4300	6503	149015723	SO:0001819	synonymous_variant	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.804C>T	4.37:g.148796273C>T			149015723	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000336498.3	37	CCDS34075.1																																																																																				0.453	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		T	148796273	C	T	148796273	2	4	61	1	0	0	0	0	0	0	0	1	862	639	23	1		1	ARHGAP10	4	148796273	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8390	148796273	42358003	3502	11487										
NR3C2	4306	broad.mit.edu	37	chr4	149181258	149181258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatccagtagaaacacttCgtaaagtagagctggggaaa	11	6	0	3	rs552665133		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:149181258C>T	ENST00000358102.3	-	3	2131	c.1769G>A	c.(1768-1770)cGa>cAa	p.R590Q	NR3C2_ENST00000512865.1_Missense_Mutation_p.R590Q|NR3C2_ENST00000344721.4_Missense_Mutation_p.R590Q|NR3C2_ENST00000355292.3_Missense_Mutation_p.R590Q|NR3C2_ENST00000511528.1_Missense_Mutation_p.R590Q	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	590	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R590Q(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	AGAAACACTTCGTAAAGTAGA	0.413																																					Melanoma(27;428 957 40335 51025 51111)											1	Substitution - Missense(1)	large_intestine(1)	4											89	86	87					4																	149181258		2203	4300	6503	149400708	SO:0001583	missense	4306			M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.1769G>A	4.37:g.149181258C>T	ENSP00000350815:p.Arg590Gln		149400708	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719847	0.68844	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.89939	-2.58;-2.59;-2.58;-2.19;-2.19;-2.59	5.98	5.98	0.97165	.	0.065195	0.64402	D	0.000005	D	0.89955	0.6865	L	0.27053	0.805	0.43242	D	0.995153	D;D	0.89917	1.0;0.998	P;P	0.59546	0.859;0.831	D	0.87978	0.2741	9	.	.	.	.	20.452	0.99131	0.0:1.0:0.0:0.0	.	590;590	B0ZBF5;B0ZBF6	.;.	Q	590	ENSP00000341390:R590Q;ENSP00000347441:R590Q;ENSP00000350815:R590Q;ENSP00000423510:R590Q;ENSP00000343907:R590Q;ENSP00000421481:R590Q	.	R	-	2	0	NR3C2	149400708	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.046000	0.64226	2.838000	0.97847	0.591000	0.81541	CGA		0.413	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			T	149181258	C	T	149181258	3	4	61	1	0	0	0	0	1	0	0	0	10662	884	31	1	1213	1	NR3C2	4	149181258	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	384985	149181258	41973018	3503	11488										
DCLK2	166614	broad.mit.edu	37	chr4	151153843	151153843	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcgtttagggtggagatCtctttgatgcaattacttcg	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151153843C>A	ENST00000296550.7	+	10	2183	c.1429C>A	c.(1429-1431)Ctc>Atc	p.L477I	DCLK2_ENST00000506325.1_Missense_Mutation_p.L476I|DCLK2_ENST00000302176.8_Missense_Mutation_p.L494I	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	477	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L494I(1)|p.L477I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GGGTGGAGATCTCTTTGATGC	0.438																																					GBM(195;186 2215 13375 16801 37459)											2	Substitution - Missense(2)	large_intestine(2)	4											219	194	202					4																	151153843		2203	4300	6503	151373293	SO:0001583	missense	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"doublecortin and CaM kinase-like 2"	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1429C>A	4.37:g.151153843C>A	ENSP00000296550:p.Leu477Ile		151373293	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.544505	0.86022	.	.	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.72725	-0.68;-0.68;-0.68	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86867	0.6036	M	0.91354	3.2	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	0.996;0.99;1.0	D	0.88817	0.3296	10	0.87932	D	0	.	13.7	0.62602	0.0:0.93:0.0:0.07	.	494;476;477	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	I	477;476;494	ENSP00000296550:L477I;ENSP00000427235:L476I;ENSP00000303887:L494I	ENSP00000296550:L477I	L	+	1	0	DCLK2	151373293	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.601000	0.54059	2.865000	0.98341	0.655000	0.94253	CTC		0.438	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260		A	151153843	C	A	151153843	3	1	61	1	0	0	0	0	1	0	0	0	4298	913	32	2	1467	2	DCLK2	4	151153843	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1972585	151153843	40000433	3504	11489										
DCLK2	166614	broad.mit.edu	37	chr4	151160922	151160922	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatcctgatggaaccaagtCtttgaaactgggagactttg	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151160922C>A	ENST00000296550.7	+	11	2349	c.1595C>A	c.(1594-1596)tCt>tAt	p.S532Y	DCLK2_ENST00000506325.1_Missense_Mutation_p.S531Y|DCLK2_ENST00000302176.8_Missense_Mutation_p.S549Y	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	532	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S532Y(2)|p.S549Y(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GGAACCAAGTCTTTGAAACTG	0.433																																					GBM(195;186 2215 13375 16801 37459)											4	Substitution - Missense(4)	large_intestine(4)	4											143	144	144					4																	151160922		2203	4300	6503	151380372	SO:0001583	missense	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"doublecortin and CaM kinase-like 2"	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1595C>A	4.37:g.151160922C>A	ENSP00000296550:p.Ser532Tyr		151380372	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880366	0.91740	.	.	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.39406	1.08;1.08;1.08	5.84	5.84	0.93424	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	N	0.25094	0.71	0.80722	D	1	P;D;P	0.76494	0.86;0.999;0.621	P;D;P	0.83275	0.561;0.996;0.593	T	0.57533	-0.7795	10	0.72032	D	0.01	.	20.1381	0.98040	0.0:1.0:0.0:0.0	.	549;531;532	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	Y	532;531;549	ENSP00000296550:S532Y;ENSP00000427235:S531Y;ENSP00000303887:S549Y	ENSP00000296550:S532Y	S	+	2	0	DCLK2	151380372	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.456000	0.80751	2.763000	0.94921	0.650000	0.86243	TCT		0.433	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260		A	151160922	C	A	151160922	3	1	61	1	0	0	0	0	1	0	0	0	4298	913	32	2	1637	2	DCLK2	4	151160922	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7079	151160922	39993354	3505	11490										
LRBA	987	broad.mit.edu	37	chr4	151388829	151388829	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attactgagaaattaccttgGacaaatctctgaagttggtg	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151388829G>A	ENST00000357115.3	-	45	7052	c.6809C>T	c.(6808-6810)tCc>tTc	p.S2270F	LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000510413.1_Missense_Mutation_p.S2259F|LRBA_ENST00000535741.1_Missense_Mutation_p.S2259F|LRBA_ENST00000507224.1_Missense_Mutation_p.S2259F	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2270	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.S2270F(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AATTACCTTGGACAAATCTCT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	4											102	96	98					4																	151388829		2203	4299	6502	151608279	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6809C>T	4.37:g.151388829G>A	ENSP00000349629:p.Ser2270Phe		151608279	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.2|26.2	4.715359|4.715359	0.89112|0.89112	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.|D;D;D;D	.|0.82255	.|-1.59;-1.59;-1.59;-1.59	5.16|5.16	5.16|5.16	0.70880|0.70880	.|BEACH domain (4);	.|0.119820	.|0.64402	.|D	.|0.000017	D|D	0.95108|0.95108	0.8415|0.8415	H|H	0.98612|0.98612	4.28|4.28	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.91635	.|0.999;0.987;0.995	D|D	0.97037|0.97037	0.9754|0.9754	5|10	.|0.87932	.|D	.|0	.|.	19.0142|19.0142	0.92888|0.92888	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2270;2259;160	.|P50851;P50851-2;Q68D03	.|LRBA_HUMAN;.;.	S|F	912|2259;2259;2270;2259	.|ENSP00000446299:S2259F;ENSP00000421552:S2259F;ENSP00000349629:S2270F;ENSP00000422180:S2259F	.|ENSP00000349629:S2270F	P|S	-|-	1|2	0|0	LRBA|LRBA	151608279|151608279	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.900000|0.900000	0.52787|0.52787	9.789000|9.789000	0.99068|0.99068	2.549000|2.549000	0.85964|0.85964	0.585000|0.585000	0.79938|0.79938	CCA|TCC		0.299	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151388829	G	A	151388829	3	1	61	1	0	0	0	0	1	0	0	0	8960	1174	41	3	1838	3	LRBA	4	151388829	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	227907	151388829	39765447	3506	11491										
LRBA	987	broad.mit.edu	37	chr4	151408946	151408946	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtagatagttaaccactttCtttactgttgcagggtctgg	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151408946C>A	ENST00000357115.3	-	43	6765	c.6522G>T	c.(6520-6522)aaG>aaT	p.K2174N	LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000510413.1_Missense_Mutation_p.K2163N|LRBA_ENST00000535741.1_Missense_Mutation_p.K2163N|LRBA_ENST00000507224.1_Missense_Mutation_p.K2163N	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2174						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.K2174N(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TAACCACTTTCTTTACTGTTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											118	107	111					4																	151408946		2203	4299	6502	151628396	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6522G>T	4.37:g.151408946C>A	ENSP00000349629:p.Lys2174Asn		151628396	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.02|19.02	3.745156|3.745156	0.69418|0.69418	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224|ENST00000509835	T;T;T;T|.	0.57907|.	0.79;0.94;0.78;0.37|.	5.53|5.53	2.86|2.86	0.33363|0.33363	PH-BEACH domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58779|0.58779	0.2146|0.2146	L|L	0.56396|0.56396	1.775|1.775	0.80722|0.80722	D|D	1|1	D;B;D|.	0.76494|.	0.999;0.094;0.999|.	D;B;D|.	0.83275|.	0.985;0.173;0.996|.	T|T	0.53365|0.53365	-0.8449|-0.8449	10|5	0.21014|.	T|.	0.42|.	.|.	7.7985|7.7985	0.29160|0.29160	0.0:0.609:0.0:0.391|0.0:0.609:0.0:0.391	.|.	2174;2163;64|.	P50851;P50851-2;Q68D03|.	LRBA_HUMAN;.;.|.	N|I	2163;2163;2174;2163|816	ENSP00000446299:K2163N;ENSP00000421552:K2163N;ENSP00000349629:K2174N;ENSP00000422180:K2163N|.	ENSP00000349629:K2174N|.	K|R	-|-	3|2	2|0	LRBA|LRBA	151628396|151628396	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	0.825000|0.825000	0.27393|0.27393	0.697000|0.697000	0.31718|0.31718	0.585000|0.585000	0.79938|0.79938	AAG|AGA		0.378	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151408946	C	A	151408946	3	1	61	1	0	0	0	0	1	0	0	0	8960	912	32	2	2133	2	LRBA	4	151408946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20117	151408946	39745330	3507	11492										
LRBA	987	broad.mit.edu	37	chr4	151412118	151412118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtattttgcaaaagataacGacgagaaaagattgatcgta	9	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151412118G>A	ENST00000357115.3	-	42	6676	c.6433C>T	c.(6433-6435)Cgt>Tgt	p.R2145C	LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000510413.1_Missense_Mutation_p.R2134C|LRBA_ENST00000535741.1_Missense_Mutation_p.R2134C|LRBA_ENST00000507224.1_Missense_Mutation_p.R2134C	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2145						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R2145C(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAAAGATAACGACGAGAAAAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	107	109					4																	151412118		2203	4300	6503	151631568	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6433C>T	4.37:g.151412118G>A	ENSP00000349629:p.Arg2145Cys		151631568	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	34	5.341469	0.95783	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.64803	0.23;0.39;0.24;-0.12	5.26	5.26	0.73747	PH-BEACH domain (1);	0.138546	0.48767	D	0.000174	D	0.83234	0.5210	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.86281	0.1667	10	0.87932	D	0	.	19.2364	0.93862	0.0:0.0:1.0:0.0	.	2145;2134;35	P50851;P50851-2;Q68D03	LRBA_HUMAN;.;.	C	2134;2134;2145;2134	ENSP00000446299:R2134C;ENSP00000421552:R2134C;ENSP00000349629:R2145C;ENSP00000422180:R2134C	ENSP00000349629:R2145C	R	-	1	0	LRBA	151631568	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.616000	0.98359	2.626000	0.88956	0.650000	0.86243	CGT		0.383	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151412118	G	A	151412118	3	1	61	1	0	0	0	0	1	0	0	0	8960	1058	37	1	2226	1	LRBA	4	151412118	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3172	151412118	39742158	3508	11493										
LRBA	987	broad.mit.edu	37	chr4	151773402	151773402	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttccttcttgaaatattaAtttgtcatcattaccaaaca	2	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151773402A>C	ENST00000357115.3	-	23	3703	c.3460T>G	c.(3460-3462)Tta>Gta	p.L1154V	LRBA_ENST00000510413.1_Missense_Mutation_p.L1154V|LRBA_ENST00000535741.1_Missense_Mutation_p.L1154V|LRBA_ENST00000507224.1_Missense_Mutation_p.L1154V	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1154						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L1154V(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TGAAATATTAATTTGTCATCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											76	77	77					4																	151773402		2203	4300	6503	151992852	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3460T>G	4.37:g.151773402A>C	ENSP00000349629:p.Leu1154Val		151992852	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	A	0.579	-0.837944	0.02692	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.53640	1.02;1.18;1.02;0.61	5.67	-5.67	0.02444	.	1.374990	0.04653	N	0.407495	T	0.23094	0.0558	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.08911	-1.0699	10	0.29301	T	0.29	.	1.462	0.02398	0.2658:0.3499:0.1949:0.1894	.	1154;1154	P50851;P50851-2	LRBA_HUMAN;.	V	1154	ENSP00000446299:L1154V;ENSP00000421552:L1154V;ENSP00000349629:L1154V;ENSP00000422180:L1154V	ENSP00000349629:L1154V	L	-	1	2	LRBA	151992852	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.363000	0.07593	-0.664000	0.05324	-0.256000	0.11100	TTA		0.393	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151773402	A	C	151773402	3	2	61	1	0	0	0	0	1	0	0	0	8960	98	4	4	5275	4	LRBA	4	151773402	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	361284	151773402	39380874	3509	11494										
LRBA	987	broad.mit.edu	37	chr4	151774094	151774094	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtgtatttcaaaagtgAcctaggtgaaaaatgtacaa	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151774094A>G	ENST00000357115.3	-	23	3011	c.2768T>C	c.(2767-2769)gTc>gCc	p.V923A	LRBA_ENST00000510413.1_Splice_Site_p.V923A|LRBA_ENST00000535741.1_Splice_Site_p.V923A|LRBA_ENST00000507224.1_Splice_Site_p.V923A	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	923						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V923A(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TTCAAAAGTGACCTAGGTGAA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	4											78	77	77					4																	151774094		2203	4300	6503	151993544	SO:0001630	splice_region_variant	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.2767-1T>C	4.37:g.151774094A>G			151993544	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.441833	0.83993	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.65	5.65	0.86999	Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.82024	0.4947	M	0.78801	2.425	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.77557	0.989;0.99	D	0.83985	0.0334	10	0.62326	D	0.03	.	16.1611	0.81712	1.0:0.0:0.0:0.0	.	923;923	P50851;P50851-2	LRBA_HUMAN;.	A	923	ENSP00000446299:V923A;ENSP00000421552:V923A;ENSP00000349629:V923A;ENSP00000422180:V923A	ENSP00000349629:V923A	V	-	2	0	LRBA	151993544	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.417000	0.90247	2.272000	0.75746	0.460000	0.39030	GTC		0.284	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		Missense_Mutation	G	151774094	A	G	151774094	5	3	61	1	0	0	0	0	0	0	1	0	8960	289	10	4	5967	4	LRBA	4	151774094	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	692	151774094	39380182	3510	11495										
LRBA	987	broad.mit.edu	37	chr4	151829982	151829982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctcagcaaggaaaaggtCgctttctgctttgaatttaa	9	7	2	1	rs558200018		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:151829982C>T	ENST00000357115.3	-	10	1432	c.1189G>A	c.(1189-1191)Gac>Aac	p.D397N	LRBA_ENST00000510413.1_Missense_Mutation_p.D397N|LRBA_ENST00000535741.1_Missense_Mutation_p.D397N|LRBA_ENST00000507224.1_Missense_Mutation_p.D397N	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	397						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D397N(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AGGAAAAGGTCGCTTTCTGCT	0.378													C|||	1	0.000199681	8e-04	0	5008	,	,		19336	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											86	79	82					4																	151829982		2203	4300	6503	152049432	SO:0001583	missense	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1189G>A	4.37:g.151829982C>T	ENSP00000349629:p.Asp397Asn		152049432	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.691821	0.88735	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.82674	0.5088	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.99;0.996;0.998	T	0.82676	-0.0339	10	0.46703	T	0.11	.	19.2723	0.94015	0.0:1.0:0.0:0.0	.	397;397;397	E9PEM5;P50851;P50851-2	.;LRBA_HUMAN;.	N	397	ENSP00000446299:D397N;ENSP00000421552:D397N;ENSP00000349629:D397N;ENSP00000422180:D397N	ENSP00000349629:D397N	D	-	1	0	LRBA	152049432	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.772000	0.85439	2.622000	0.88805	0.563000	0.77884	GAC		0.378	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151829982	C	T	151829982	3	4	61	1	0	0	0	0	1	0	0	0	8960	884	31	1	7598	1	LRBA	4	151829982	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55888	151829982	39324294	3511	11496										
PRSS48	345062	broad.mit.edu	37	chr4	152200977	152200977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctgtatactccagccgcGttgtaggtggccaggatgct	12	11	0	0	rs370098536		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:152200977G>A	ENST00000455694.2	+	2	84	c.82G>A	c.(82-84)Gtt>Att	p.V28I	SH3D19_ENST00000604030.1_Intron|PRSS48_ENST00000441586.2_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48	28	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.V28I(2)		kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						CTCCAGCCGCGTTGTAGGTGG	0.532																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						G	ILE/VAL	0,4032		0,0,2016	105	104	104		82	-2.1	0	4		104	1,8369		0,1,4184	no	missense	PRSS48	NM_183375.2	29	0,1,6200	AA,AG,GG		0.0119,0.0,0.0081	benign	28/329	152200977	1,12401	2016	4185	6201	152420427	SO:0001583	missense	345062			BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"Serine peptidases / Serine peptidases"	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.82G>A	4.37:g.152200977G>A	ENSP00000401328:p.Val28Ile		152420427	Q08E82|Q0VAD4	Missense_Mutation	SNP	ENST00000455694.2	37	CCDS47145.1	.	.	.	.	.	.	.	.	.	.	g	0.748	-0.773731	0.02951	0.0	1.19E-4	ENSG00000189099	ENST00000455694	T	0.20881	2.04	4.86	-2.09	0.07232	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.943137	0.08605	N	0.920931	T	0.04452	0.0122	N	0.00436	-1.5	0.20307	N	0.999916	B	0.02656	0.0	B	0.06405	0.002	T	0.41538	-0.9503	10	0.02654	T	1	.	10.2864	0.43570	0.7199:0.0:0.2801:0.0	.	28	Q7RTY5	PRS48_HUMAN	I	28	ENSP00000401328:V28I	ENSP00000401328:V28I	V	+	1	0	PRSS48	152420427	0.182000	0.23173	0.000000	0.03702	0.006000	0.05464	0.822000	0.27352	-0.387000	0.07809	-0.247000	0.11927	GTT		0.532	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375		A	152200977	G	A	152200977	3	1	61	1	0	0	0	0	1	0	0	0	12664	1145	40	1	88	1	PRSS48	4	152200977	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	370995	152200977	38953299	3512	11497										
PRSS48	345062	broad.mit.edu	37	chr4	152203499	152203499	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatttgcttgcccagtgtcAcaaagcagttggcaattcca	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:152203499A>G	ENST00000455694.2	+	3	417	c.415A>G	c.(415-417)Aca>Gca	p.T139A	SH3D19_ENST00000604030.1_Intron|PRSS48_ENST00000441586.2_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48	139	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.T139A(1)		kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						GCCCAGTGTCACAAAGCAGTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	4											172	163	166					4																	152203499		2020	4181	6201	152422949	SO:0001583	missense	345062			BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"Serine peptidases / Serine peptidases"	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.415A>G	4.37:g.152203499A>G	ENSP00000401328:p.Thr139Ala		152422949	Q08E82|Q0VAD4	Missense_Mutation	SNP	ENST00000455694.2	37	CCDS47145.1	.	.	.	.	.	.	.	.	.	.	A	0.056	-1.235653	0.01505	.	.	ENSG00000189099	ENST00000455694	D	0.88124	-2.34	3.87	-0.719	0.11201	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.751015	0.10934	N	0.618084	T	0.65698	0.2716	N	0.05306	-0.075	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.53180	-0.8475	10	0.08381	T	0.77	.	3.6416	0.08169	0.4579:0.0:0.1134:0.4286	.	139	Q7RTY5	PRS48_HUMAN	A	139	ENSP00000401328:T139A	ENSP00000401328:T139A	T	+	1	0	PRSS48	152422949	0.000000	0.05858	0.046000	0.18839	0.005000	0.04900	-0.093000	0.11111	-0.096000	0.12329	-0.468000	0.05107	ACA		0.483	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375		G	152203499	A	G	152203499	3	3	61	1	0	0	0	0	1	0	0	0	12664	159	6	4	425	4	PRSS48	4	152203499	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2522	152203499	38950777	3513	11498										
PET112L	5188	broad.mit.edu	37	chr4	152681964	152681964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaaacagaataccctttCctcgtcttctgggccgtgtg	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:152681964C>A	ENST00000515812.1	-	1	187	c.171G>T	c.(169-171)agG>agT	p.R57S	PET112_ENST00000263985.6_Missense_Mutation_p.R57S|PET112_ENST00000508611.1_Missense_Mutation_p.R57S|PET112_ENST00000512306.1_Missense_Mutation_p.R57S														p.R57S(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						AATACCCTTTCCTCGTCTTCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	59	60					4																	152681964		2203	4300	6503	152901414	SO:0001583	missense	5188																														ENST00000515812.1:c.171G>T	4.37:g.152681964C>A	ENSP00000426859:p.Arg57Ser		152901414		Missense_Mutation	SNP	ENST00000515812.1	37		.	.	.	.	.	.	.	.	.	.	C	11.41	1.629988	0.28978	.	.	ENSG00000059691	ENST00000263985;ENST00000515812;ENST00000512306;ENST00000508611	T;T;T;T	0.46063	0.96;0.94;0.96;0.88	4.84	3.1	0.35709	.	0.442616	0.23852	N	0.043936	T	0.25382	0.0617	L	0.29908	0.895	0.27687	N	0.946234	B;B	0.22800	0.075;0.02	B;B	0.19946	0.027;0.027	T	0.19192	-1.0313	10	0.12103	T	0.63	-20.5352	7.479	0.27393	0.0:0.804:0.0:0.196	.	57;57	D6RDU9;O75879	.;GATB_HUMAN	S	57	ENSP00000263985:R57S;ENSP00000426859:R57S;ENSP00000420831:R57S;ENSP00000421105:R57S	ENSP00000263985:R57S	R	-	3	2	PET112	152901414	0.999000	0.42202	0.989000	0.46669	0.860000	0.49131	0.813000	0.27225	0.746000	0.32786	0.650000	0.86243	AGG		0.547	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			A	152681964	C	A	152681964	3	1	61	1	0	0	0	0	1	0	0	0	11765	854	30	2	1554	2	PET112L	4	152681964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	478465	152681964	38472312	3514	11499										
FBXW7	55294	broad.mit.edu	37	chr4	153244185	153244185	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccaatgtgactaggtttcGaataaattcacccgttttca	6	10	2	1	rs144247898		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153244185G>A	ENST00000281708.4	-	12	3201	c.1972C>T	c.(1972-1974)Cga>Tga	p.R658*	FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R658*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R658*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.R578*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.R482*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.R540*|RP11-461L13.3_ENST00000603766.1_lincRNA	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	658					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R658*(3)|p.R578*(1)|p.?(1)|p.R419*(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTAGGTTTCGAATAAATTCA	0.473			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	6	Substitution - Nonsense(5)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	4											167	164	165					4																	153244185		2203	4300	6503	153463635	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1972C>T	4.37:g.153244185G>A	ENSP00000281708:p.Arg658*		153463635	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.698056	0.88830	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	5.67	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7715	15.907	0.79439	0.0:0.0:0.8635:0.1365	.	.	.	.	X	658;540;578;482	.	ENSP00000263981:R578X	R	-	1	2	FBXW7	153463635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.632000	0.74281	1.377000	0.46286	0.655000	0.94253	CGA		0.473	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153244185	G	A	153244185	4	1	61	1	0	0	0	0	0	1	0	0	5788	1066	37	1	155	1	FBXW7	4	153244185	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	562221	153244185	37910091	3515	11500										
FBXW7	55294	broad.mit.edu	37	chr4	153268093	153268093	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatgtcacctgaaacatttTtagccattcctggaggcctg	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153268093T>G	ENST00000281708.4	-	4	1944	c.715A>C	c.(715-717)Aaa>Caa	p.K239Q	FBXW7_ENST00000603548.1_Missense_Mutation_p.K239Q|FBXW7_ENST00000603841.1_Missense_Mutation_p.K239Q|FBXW7_ENST00000263981.5_Missense_Mutation_p.K159Q|FBXW7_ENST00000393956.3_Missense_Mutation_p.K63Q|FBXW7_ENST00000296555.5_Missense_Mutation_p.K121Q	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	239					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.K239Q(2)|p.K159Q(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAAACATTTTTAGCCATTCC	0.433			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	4	Substitution - Missense(3)|Unknown(1)	large_intestine(3)|haematopoietic_and_lymphoid_tissue(1)	4											177	168	171					4																	153268093		2203	4300	6503	153487543	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.715A>C	4.37:g.153268093T>G	ENSP00000281708:p.Lys239Gln		153487543	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.550746	0.27739	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.55760	0.56;0.54;0.5;0.68	5.83	5.83	0.93111	.	0.057185	0.64402	D	0.000001	T	0.30572	0.0769	N	0.02802	-0.49	0.47123	D	0.999324	B;B;B;B	0.20988	0.01;0.05;0.004;0.009	B;B;B;B	0.15052	0.003;0.008;0.004;0.012	T	0.13469	-1.0508	10	0.30854	T	0.27	-24.7273	16.194	0.82011	0.0:0.0:0.0:1.0	.	63;239;121;159	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	Q	239;121;159;63	ENSP00000281708:K239Q;ENSP00000296555:K121Q;ENSP00000263981:K159Q;ENSP00000377528:K63Q	ENSP00000263981:K159Q	K	-	1	0	FBXW7	153487543	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.144000	0.71762	2.225000	0.72522	0.460000	0.39030	AAA		0.433	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153268093	T	G	153268093	3	3	61	1	0	0	0	0	1	0	0	0	5788	1850	64	4	1444	4	FBXW7	4	153268093	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	23908	153268093	37886183	3516	11501										
FBXW7	55294	broad.mit.edu	37	chr4	153271242	153271242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcccaaagaaaaagagCggacctcagaaccatggtcc	8	12	2	3	rs201753217		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153271242C>T	ENST00000281708.4	-	3	1765	c.536G>A	c.(535-537)cGc>cAc	p.R179H	FBXW7_ENST00000603548.1_Missense_Mutation_p.R179H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R179H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R99H|FBXW7_ENST00000393956.3_5'Flank|FBXW7_ENST00000296555.5_Missense_Mutation_p.R61H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	179					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R179H(2)|p.R99H(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGAAAAAGAGCGGACCTCAGA	0.308			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	3	Substitution - Missense(3)	large_intestine(3)	4						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4388		0,0,2194	28	29	29		182,296,536	5.3	1	4		29	1,8567		0,1,4283	yes	missense,missense,missense	FBXW7	NM_001013415.1,NM_018315.4,NM_033632.2	29,29,29	0,1,6477	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	61/590,99/628,179/708	153271242	1,12955	2194	4284	6478	153490692	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.536G>A	4.37:g.153271242C>T	ENSP00000281708:p.Arg179His		153490692	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891650	0.91889	0.0	1.17E-4	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981	T;T;T	0.58506	0.51;0.38;0.33	6.17	5.32	0.75619	.	0.114219	0.64402	D	0.000008	T	0.52901	0.1763	N	0.19112	0.55	0.80722	D	1	D;D;D	0.67145	0.996;0.986;0.994	P;B;P	0.49502	0.613;0.376;0.579	T	0.56842	-0.7912	10	0.46703	T	0.11	-12.0329	17.5427	0.87852	0.0:0.8763:0.1237:0.0	.	179;61;99	Q969H0;Q969H0-4;Q969H0-2	FBXW7_HUMAN;.;.	H	179;61;99	ENSP00000281708:R179H;ENSP00000296555:R61H;ENSP00000263981:R99H	ENSP00000263981:R99H	R	-	2	0	FBXW7	153490692	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.440000	0.80464	1.586000	0.49944	0.655000	0.94253	CGC		0.308	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153271242	C	T	153271242	3	4	61	1	0	0	0	0	1	0	0	0	5788	768	27	1	1627	1	FBXW7	4	153271242	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3149	153271242	37883034	3517	11502										
FBXW7	55294	broad.mit.edu	37	chr4	153273871	153273871	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtatcaaaccgcttctCgggacacacatacatacatg	6	13	3	0	rs34496200	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153273871C>T	ENST00000281708.4	-	3	1731				FBXW7_ENST00000603548.1_Intron|FBXW7_ENST00000603841.1_Intron|FBXW7_ENST00000263981.5_Silent_p.P4P|FBXW7_ENST00000296555.5_Intron	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase						cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.P4P(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AACCGCTTCTCGGGACACACA	0.473			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"								C|||	2	0.000399361	8e-04	0	5008	,	,		21950	0		0.001	False		,,,				2504	0						Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Substitution - coding silent(1)	large_intestine(1)	4						C	,,	3,4403	6.2+/-15.9	0,3,2200	66	64	65		,12,	5.2	1	4	dbSNP_126	65	2,8598	2.2+/-6.3	0,2,4298	no	intron,coding-synonymous,intron	FBXW7	NM_001013415.1,NM_018315.4,NM_033632.2	,,	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	,,	,4/628,	153273871	5,13001	2203	4300	6503	153493321	SO:0001627	intron_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.502-2595G>A	4.37:g.153273871C>T			153493321	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.473	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153273871	C	T	153273871	1	4	61	0	1	0	0	0	0	0	0	0	5788	871	31	1		1	FBXW7	4	153273871	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2629	153273871	37880405	3518	11503										
TIGD4	201798	broad.mit.edu	37	chr4	153691012	153691012	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcactttctcccttttgaGatttgaatcctgcctcttca	5	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153691012G>T	ENST00000304337.2	-	2	1965	c.1145C>A	c.(1144-1146)tCt>tAt	p.S382Y		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	382						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S382Y(1)		breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					TCCCTTTTGAGATTTGAATCC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	4											143	139	140					4																	153691012		2203	4300	6503	153910462	SO:0001583	missense	201798			AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.1145C>A	4.37:g.153691012G>T	ENSP00000355162:p.Ser382Tyr		153910462	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	0.464	-0.887692	0.02511	.	.	ENSG00000169989	ENST00000304337	T	0.15017	2.46	6.17	4.45	0.53987	.	0.631403	0.14281	N	0.329537	T	0.08268	0.0206	L	0.29908	0.895	0.09310	N	1	B	0.31730	0.337	B	0.24541	0.054	T	0.32561	-0.9902	10	0.02654	T	1	-4.8081	4.1994	0.10458	0.1384:0.1375:0.5982:0.1258	.	382	Q8IY51	TIGD4_HUMAN	Y	382	ENSP00000355162:S382Y	ENSP00000355162:S382Y	S	-	2	0	TIGD4	153910462	0.940000	0.31905	0.044000	0.18714	0.249000	0.25844	1.415000	0.34748	0.916000	0.36871	-0.150000	0.13652	TCT		0.423	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153691012	G	T	153691012	3	4	61	1	0	0	0	0	1	0	0	0	15937	942	33	2	397	2	TIGD4	4	153691012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	417141	153691012	37463264	3519	11504										
TIGD4	201798	broad.mit.edu	37	chr4	153691871	153691871	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttagacactgagcaattcGataccatctcattaatgcct	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153691871G>A	ENST00000304337.2	-	2	1106	c.286C>T	c.(286-288)Cga>Tga	p.R96*		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	96	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R96*(1)		breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					TGAGCAATTCGATACCATCTC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											118	111	114					4																	153691871		2203	4299	6502	153911321	SO:0001587	stop_gained	201798			AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.286C>T	4.37:g.153691871G>A	ENSP00000355162:p.Arg96*		153911321	Q96LP5	Nonsense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	42	9.611387	0.99219	.	.	ENSG00000169989	ENST00000304337	.	.	.	6.17	6.17	0.99709	.	0.000000	0.41097	D	0.000960	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-10.391	10.8184	0.46591	0.0:0.2341:0.6361:0.1297	.	.	.	.	X	96	.	ENSP00000355162:R96X	R	-	1	2	TIGD4	153911321	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.927000	0.40094	2.941000	0.99782	0.655000	0.94253	CGA		0.378	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		A	153691871	G	A	153691871	4	1	61	1	0	0	0	0	0	1	0	0	15937	1066	37	1	1256	1	TIGD4	4	153691871	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	859	153691871	37462405	3520	11505										
TIGD4	201798	broad.mit.edu	37	chr4	153692075	153692075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccactgcatttatgatgtCgatcttttcctcaatggata	6	9	2	1	rs200034910		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153692075C>T	ENST00000304337.2	-	2	902	c.82G>A	c.(82-84)Gac>Aac	p.D28N		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	28	HTH psq-type. {ECO:0000255|PROSITE- ProRule:PRU00320}.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D28N(2)		breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					TTTATGATGTCGATCTTTTCC	0.378													C|||	1	0.000199681	0	0	5008	,	,		19171	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|breast(1)	4						C	ASN/ASP	0,4406		0,0,2203	133	129	130		82	6.2	1	4		130	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TIGD4	NM_145720.3	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	28/513	153692075	1,13005	2203	4300	6503	153911525	SO:0001583	missense	201798			AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.82G>A	4.37:g.153692075C>T	ENSP00000355162:p.Asp28Asn		153911525	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.71	3.877671	0.72294	0.0	1.16E-4	ENSG00000169989	ENST00000304337	T	0.45276	0.9	6.17	6.17	0.99709	Homeodomain-related (1);Homeodomain-like (1);Helix-turn-helix, Psq-like (1);Centromere protein Cenp-B, DNA-binding domain 1 (1);	0.000000	0.53938	D	0.000044	T	0.50051	0.1593	N	0.17082	0.46	0.39152	D	0.962238	D	0.89917	1.0	D	0.68943	0.961	T	0.43988	-0.9357	10	0.29301	T	0.29	-19.6278	20.4898	0.99202	0.0:1.0:0.0:0.0	.	28	Q8IY51	TIGD4_HUMAN	N	28	ENSP00000355162:D28N	ENSP00000355162:D28N	D	-	1	0	TIGD4	153911525	0.999000	0.42202	0.995000	0.50966	0.986000	0.74619	5.145000	0.64839	2.941000	0.99782	0.655000	0.94253	GAC		0.378	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153692075	C	T	153692075	3	4	61	1	0	0	0	0	1	0	0	0	15937	884	31	1	1460	1	TIGD4	4	153692075	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	204	153692075	37462201	3521	11506										
FHDC1	85462	broad.mit.edu	37	chr4	153864540	153864540	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattccggaggagcaagttCgaggcaaaaccaacatctgg	11	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153864540C>T	ENST00000511601.1	+	2	519	c.331C>T	c.(331-333)Cga>Tga	p.R111*	FHDC1_ENST00000260008.3_Nonsense_Mutation_p.R111*			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	111	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.							p.R111*(1)	ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					GGAGCAAGTTCGAGGCAAAAC	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											124	139	134					4																	153864540		2203	4300	6503	154083990	SO:0001587	stop_gained	85462			AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.331C>T	4.37:g.153864540C>T	ENSP00000427567:p.Arg111*		154083990		Nonsense_Mutation	SNP	ENST00000511601.1	37	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	C	37	6.526670	0.97637	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	.	.	.	5.32	5.32	0.75619	.	0.056623	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	.	14.2393	0.65948	0.1491:0.8509:0.0:0.0	.	.	.	.	X	111	.	ENSP00000260008:R111X	R	+	1	2	FHDC1	154083990	0.999000	0.42202	0.808000	0.32385	0.987000	0.75469	3.906000	0.56340	2.656000	0.90262	0.563000	0.77884	CGA		0.488	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		T	153864540	C	T	153864540	4	4	61	1	0	0	0	0	0	1	0	0	5895	876	31	1	333	1	FHDC1	4	153864540	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	172465	153864540	37289736	3522	11507										
FHDC1	85462	broad.mit.edu	37	chr4	153893632	153893632	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagacaaaaaaaccatgaAactggatgaatgctttcaga	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:153893632A>C	ENST00000511601.1	+	11	1510	c.1322A>C	c.(1321-1323)aAa>aCa	p.K441T	FHDC1_ENST00000260008.3_Missense_Mutation_p.K441T			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	441	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.							p.K441T(1)	ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					AAAACCATGAAACTGGATGAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											103	106	105					4																	153893632		2203	4300	6503	154113082	SO:0001583	missense	85462			AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.1322A>C	4.37:g.153893632A>C	ENSP00000427567:p.Lys441Thr		154113082		Missense_Mutation	SNP	ENST00000511601.1	37	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220153	0.79464	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.62364	0.03;0.03	5.36	4.14	0.48551	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.201858	0.51477	N	0.000094	T	0.72930	0.3522	M	0.78344	2.41	0.53688	D	0.999979	D	0.53462	0.96	P	0.55260	0.772	T	0.74529	-0.3635	10	0.52906	T	0.07	.	12.2711	0.54706	0.8578:0.1422:0.0:0.0	.	441	Q9C0D6	FHDC1_HUMAN	T	441	ENSP00000427567:K441T;ENSP00000260008:K441T	ENSP00000260008:K441T	K	+	2	0	FHDC1	154113082	1.000000	0.71417	0.811000	0.32455	0.992000	0.81027	7.099000	0.76981	0.842000	0.35045	0.528000	0.53228	AAA		0.408	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		C	153893632	A	C	153893632	3	2	61	1	0	0	0	0	1	0	0	0	5895	14	1	4	1360	4	FHDC1	4	153893632	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29092	153893632	37260644	3523	11508										
TRIM2	23321	broad.mit.edu	37	chr4	154216766	154216766	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccacgggcgaggggctgcGgcagaccatcatcgggcagc	18	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154216766G>A	ENST00000437508.2	+	6	1208	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Missense_Mutation_p.R363Q	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	336					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R336Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		GAGGGGCTGCGGCAGACCATC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	4											47	44	45					4																	154216766		2203	4300	6503	154436216	SO:0001583	missense	23321			AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.1007G>A	4.37:g.154216766G>A	ENSP00000415812:p.Arg336Gln		154436216	D3DP09|O60272|Q9BSI9|Q9UFZ1	Missense_Mutation	SNP	ENST00000437508.2	37	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.642121	0.87859	.	.	ENSG00000109654	ENST00000437508;ENST00000338700	D;D	0.84516	-1.86;-1.86	5.38	5.38	0.77491	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.138014	0.64402	D	0.000010	D	0.89660	0.6779	L	0.54323	1.7	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.988	D	0.88400	0.3014	10	0.40728	T	0.16	-8.5711	13.7736	0.63039	0.074:0.0:0.926:0.0	.	363;336	D3DP09;Q9C040	.;TRIM2_HUMAN	Q	336;363	ENSP00000415812:R336Q;ENSP00000339659:R363Q	ENSP00000339659:R363Q	R	+	2	0	TRIM2	154436216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.343000	0.72986	2.676000	0.91093	0.561000	0.74099	CGG		0.612	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			A	154216766	G	A	154216766	3	1	61	1	0	0	0	0	1	0	0	0	16534	1116	39	1	1110	1	TRIM2	4	154216766	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	323134	154216766	36937510	3524	11509										
KIAA0922	23240	broad.mit.edu	37	chr4	154515006	154515006	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtgaattccagctcaccGaagcttgcccttacctggta	9	13	1	1	rs370464671		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154515006G>A	ENST00000409663.3	+	19	2027	c.1975G>A	c.(1975-1977)Gaa>Aaa	p.E659K	KIAA0922_ENST00000409959.3_Missense_Mutation_p.E660K|KIAA0922_ENST00000440693.1_Missense_Mutation_p.E576K	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	659						integral component of membrane (GO:0016021)		p.E512K(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CCAGCTCACCGAAGCTTGCCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	94	86	89		1978,1975	-4.9	0.5	4		89	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	660/1611,659/1610	154515006	1,13005	2203	4300	6503	154734456	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1975G>A	4.37:g.154515006G>A	ENSP00000386574:p.Glu659Lys		154734456	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.508704	0.00984	0.0	1.16E-4	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.16897	2.49;2.31;2.49;2.31	5.36	-4.88	0.03113	.	0.473316	0.25866	N	0.027786	T	0.04092	0.0114	N	0.02916	-0.46	0.09310	N	1	B;B;B	0.12013	0.002;0.005;0.003	B;B;B	0.06405	0.001;0.002;0.001	T	0.39623	-0.9605	10	0.10636	T	0.68	-1.8891	6.2675	0.20936	0.3439:0.2548:0.4013:0.0	.	576;660;659	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	K	659;576;660;437	ENSP00000386574:E659K;ENSP00000409663:E576K;ENSP00000386787:E660K;ENSP00000240487:E437K	ENSP00000240487:E437K	E	+	1	0	KIAA0922	154734456	0.268000	0.24133	0.472000	0.27241	0.589000	0.36550	-0.041000	0.12084	-0.494000	0.06669	-0.300000	0.09419	GAA		0.393	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154515006	G	A	154515006	3	1	61	1	0	0	0	0	1	0	0	0	8222	1059	37	1	2052	1	KIAA0922	4	154515006	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298240	154515006	36639270	3525	11510										
KIAA0922	23240	broad.mit.edu	37	chr4	154523429	154523429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgccaaggttatggattcGaggtgctggattgtcatcag	13	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154523429G>A	ENST00000409663.3	+	22	2441	c.2389G>A	c.(2389-2391)Gag>Aag	p.E797K	KIAA0922_ENST00000409959.3_Missense_Mutation_p.E798K|KIAA0922_ENST00000440693.1_Missense_Mutation_p.E714K	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	797						integral component of membrane (GO:0016021)		p.E650K(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TTATGGATTCGAGGTGCTGGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											180	176	178					4																	154523429		2203	4300	6503	154742879	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2389G>A	4.37:g.154523429G>A	ENSP00000386574:p.Glu797Lys		154742879	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129480	0.56721	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.16196	2.64;2.36;2.64;2.36	5.7	4.83	0.62350	.	0.048483	0.85682	D	0.000000	T	0.20981	0.0505	N	0.20807	0.61	0.80722	D	1	D;D;P	0.76494	0.999;0.996;0.76	P;D;B	0.62955	0.866;0.909;0.106	T	0.01762	-1.1279	10	0.02654	T	1	-18.5362	16.324	0.82965	0.0:0.1325:0.8675:0.0	.	714;798;797	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	K	797;714;798;575	ENSP00000386574:E797K;ENSP00000409663:E714K;ENSP00000386787:E798K;ENSP00000240487:E575K	ENSP00000240487:E575K	E	+	1	0	KIAA0922	154742879	1.000000	0.71417	0.966000	0.40874	0.507000	0.33981	4.460000	0.60108	1.333000	0.45449	0.655000	0.94253	GAG		0.393	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154523429	G	A	154523429	3	1	61	1	0	0	0	0	1	0	0	0	8222	1059	37	1	2478	1	KIAA0922	4	154523429	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8423	154523429	36630847	3526	11511										
KIAA0922	23240	broad.mit.edu	37	chr4	154533546	154533546	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaacaggacatacctttCgtagaggtctgtattttttt	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154533546C>T	ENST00000409663.3	+	26	3610	c.3558C>T	c.(3556-3558)ttC>ttT	p.F1186F	KIAA0922_ENST00000409959.3_Silent_p.F1187F|KIAA0922_ENST00000440693.1_Silent_p.F1103F	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1186						integral component of membrane (GO:0016021)		p.F1039F(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				ACATACCTTTCGTAGAGGTCT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	4											56	58	57					4																	154533546		2203	4299	6502	154752996	SO:0001819	synonymous_variant	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3558C>T	4.37:g.154533546C>T			154752996	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																				0.323	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		T	154533546	C	T	154533546	2	4	61	1	0	0	0	0	0	0	0	1	8222	883	31	1		1	KIAA0922	4	154533546	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10117	154533546	36620730	3527	11512										
KIAA0922	23240	broad.mit.edu	37	chr4	154555410	154555410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgtccattggaattgaaCgattacaatgcctttccaga	7	9	0	2	rs375228294		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154555410C>T	ENST00000409663.3	+	33	4444	c.4392C>T	c.(4390-4392)aaC>aaT	p.N1464N	KIAA0922_ENST00000409959.3_Silent_p.N1465N|KIAA0922_ENST00000440693.1_Silent_p.N1381N	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1464						integral component of membrane (GO:0016021)		p.N1317N(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TGGAATTGAACGATTACAATG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	4						C	,	1,4405	2.1+/-5.4	0,1,2202	163	160	161		4395,4392	1.6	1	4		161	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	1465/1611,1464/1610	154555410	1,13005	2203	4300	6503	154774860	SO:0001819	synonymous_variant	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.4392C>T	4.37:g.154555410C>T			154774860	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																				0.423	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		T	154555410	C	T	154555410	2	4	61	1	0	0	0	0	0	0	0	1	8222	535	19	1		1	KIAA0922	4	154555410	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21864	154555410	36598866	3528	11513										
KIAA0922	23240	broad.mit.edu	37	chr4	154557676	154557676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggactaccacagcgaataGgaatgcaaatttcccactgt	8	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154557676G>A	ENST00000409663.3	+	35	4830	c.4778G>A	c.(4777-4779)aGg>aAg	p.R1593K	KIAA0922_ENST00000409959.3_Missense_Mutation_p.R1594K|KIAA0922_ENST00000440693.1_Missense_Mutation_p.R1510K	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1593						integral component of membrane (GO:0016021)		p.R1446K(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				ACAGCGAATAGGAATGCAAAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	94	95					4																	154557676		2203	4300	6503	154777126	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.4778G>A	4.37:g.154557676G>A	ENSP00000386574:p.Arg1593Lys		154777126	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184097	0.78677	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.48522	1.11;0.81;1.1;0.85	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.59972	0.2233	L	0.27053	0.805	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.997	D;D;P	0.81914	0.99;0.995;0.907	T	0.62191	-0.6906	10	0.87932	D	0	-16.9387	20.3311	0.98718	0.0:0.0:1.0:0.0	.	1510;1594;1593	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	K	1593;1510;1594;1371	ENSP00000386574:R1593K;ENSP00000409663:R1510K;ENSP00000386787:R1594K;ENSP00000240487:R1371K	ENSP00000240487:R1371K	R	+	2	0	KIAA0922	154777126	1.000000	0.71417	0.147000	0.22382	0.295000	0.27426	9.113000	0.94321	2.797000	0.96272	0.655000	0.94253	AGG		0.433	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154557676	G	A	154557676	3	1	61	1	0	0	0	0	1	0	0	0	8222	1000	35	3	4919	3	KIAA0922	4	154557676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2266	154557676	36596600	3529	11514										
TLR2	7097	broad.mit.edu	37	chr4	154624906	154624906	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctggattgttagaattaGagtttgatgactgtaccctt	9	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154624906G>T	ENST00000260010.6	+	1	2255	c.847G>T	c.(847-849)Gag>Tag	p.E283*		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	283					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)	p.E283*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	GTTAGAATTAGAGTTTGATGA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											51	55	53					4																	154624906		2202	4299	6501	154844356	SO:0001587	stop_gained	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.847G>T	4.37:g.154624906G>T	ENSP00000260010:p.Glu283*		154844356	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Nonsense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	G	47	13.794305	0.99763	.	.	ENSG00000137462	ENST00000260010	.	.	.	5.91	5.06	0.68205	.	0.718192	0.13418	N	0.389377	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	10.6792	0.45804	0.1416:0.0:0.8584:0.0	.	.	.	.	X	283	.	ENSP00000260010:E283X	E	+	1	0	TLR2	154844356	0.497000	0.26067	0.966000	0.40874	0.334000	0.28698	2.004000	0.40854	2.802000	0.96397	0.655000	0.94253	GAG		0.323	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			T	154624906	G	T	154624906	4	4	61	1	0	0	0	0	0	1	0	0	15990	943	33	2	849	2	TLR2	4	154624906	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67230	154624906	36529370	3530	11515										
TLR2	7097	broad.mit.edu	37	chr4	154625309	154625309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactctgaaaaacttgactaAcattgatatcagtaagaata	5	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154625309A>G	ENST00000260010.6	+	1	2658	c.1250A>G	c.(1249-1251)aAc>aGc	p.N417S		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	417					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)	p.N417S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	AACTTGACTAACATTGATATC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											51	53	52					4																	154625309		2203	4300	6503	154844759	SO:0001583	missense	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.1250A>G	4.37:g.154625309A>G	ENSP00000260010:p.Asn417Ser		154844759	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	A	0.784	-0.761279	0.02996	.	.	ENSG00000137462	ENST00000260010	T	0.55052	0.54	5.42	-3.06	0.05379	.	0.797878	0.11531	N	0.554652	T	0.30008	0.0751	L	0.33624	1.015	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.18871	-1.0323	10	0.19147	T	0.46	.	1.5716	0.02616	0.4118:0.2207:0.2541:0.1134	.	417	O60603	TLR2_HUMAN	S	417	ENSP00000260010:N417S	ENSP00000260010:N417S	N	+	2	0	TLR2	154844759	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	0.125000	0.15749	-0.782000	0.04541	0.460000	0.39030	AAC		0.368	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			G	154625309	A	G	154625309	3	3	61	1	0	0	0	0	1	0	0	0	15990	43	2	4	1252	4	TLR2	4	154625309	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	403	154625309	36528967	3531	11516										
TLR2	7097	broad.mit.edu	37	chr4	154626141	154626141	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatcattgactccattgaAaagagccacaaaactgtctt	5	9	2	3	rs374310145		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154626141A>C	ENST00000260010.6	+	1	3490	c.2082A>C	c.(2080-2082)gaA>gaC	p.E694D		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	694	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)	p.E694D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	ACTCCATTGAAAAGAGCCACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4						A	ASP/GLU	0,4406		0,0,2203	114	113	113		2082	-8.7	0.8	4		113	1,8599	1.2+/-3.3	0,1,4299	no	missense	TLR2	NM_003264.3	45	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	probably-damaging	694/785	154626141	1,13005	2203	4300	6503	154845591	SO:0001583	missense	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.2082A>C	4.37:g.154626141A>C	ENSP00000260010:p.Glu694Asp		154845591	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.783285	0.49891	0.0	1.16E-4	ENSG00000137462	ENST00000260010	T	0.09350	2.99	5.83	-8.71	0.00848	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.055632	0.64402	D	0.000001	T	0.13457	0.0326	M	0.62266	1.93	0.43959	D	0.996639	B	0.32653	0.379	B	0.40038	0.317	T	0.15578	-1.0432	10	0.66056	D	0.02	.	17.1019	0.86652	0.2081:0.0969:0.695:0.0	.	694	O60603	TLR2_HUMAN	D	694	ENSP00000260010:E694D	ENSP00000260010:E694D	E	+	3	2	TLR2	154845591	0.665000	0.27466	0.840000	0.33206	0.984000	0.73092	-0.257000	0.08745	-1.194000	0.02684	-0.250000	0.11733	GAA		0.428	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			C	154626141	A	C	154626141	3	2	61	1	0	0	0	0	1	0	0	0	15990	11	1	4	2084	4	TLR2	4	154626141	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	832	154626141	36528135	3532	11517										
RNF175	285533	broad.mit.edu	37	chr4	154636703	154636703	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgattacaggaaagctggtAggtgttttcaatgagccctt	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154636703A>C	ENST00000347063.4	-	7	1114	c.742T>G	c.(742-744)Tac>Gac	p.Y248D	RNF175_ENST00000274068.4_Missense_Mutation_p.Y120D	NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	248						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.Y248D(2)		breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				GAAAGCTGGTAGGTGTTTTCA	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	4											82	80	81					4																	154636703		1970	4152	6122	154856153	SO:0001583	missense	285533			BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"RING-type (C3HC4) zinc fingers"	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.742T>G	4.37:g.154636703A>C	ENSP00000340979:p.Tyr248Asp		154856153	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.538540	0.45176	.	.	ENSG00000145428	ENST00000347063;ENST00000274068	T;T	0.43294	0.95;2.1	4.35	4.35	0.52113	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.075521	0.53938	D	0.000044	T	0.58438	0.2122	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.89917	1.0;0.997	D;P	0.76575	0.988;0.904	T	0.61912	-0.6965	10	0.87932	D	0	-16.9698	12.1458	0.54022	1.0:0.0:0.0:0.0	.	120;248	Q8NB61;Q8N4F7	.;RN175_HUMAN	D	248;120	ENSP00000340979:Y248D;ENSP00000274068:Y120D	ENSP00000274068:Y120D	Y	-	1	0	RNF175	154856153	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.202000	0.72131	2.179000	0.69175	0.482000	0.46254	TAC		0.478	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662		C	154636703	A	C	154636703	3	2	61	1	0	0	0	0	1	0	0	0	13500	420	15	4	256	4	RNF175	4	154636703	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10562	154636703	36517573	3533	11518										
SFRP2	6423	broad.mit.edu	37	chr4	154709889	154709889	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattgctgcgcttgtaggaGaagtcgggctggccaaagag	15	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:154709889G>T	ENST00000274063.4	-	1	383	c.99C>A	c.(97-99)ttC>ttA	p.F33L		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	33					bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.F33L(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				GCTTGTAGGAGAAGTCGGGCT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	4											33	38	36					4																	154709889		2202	4297	6499	154929339	SO:0001583	missense	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.99C>A	4.37:g.154709889G>T	ENSP00000274063:p.Phe33Leu		154929339	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	37	CCDS34082.1	.	.	.	.	.	.	.	.	.	.	G	5.916	0.352988	0.11182	.	.	ENSG00000145423	ENST00000274063	T	0.71934	-0.61	4.48	2.73	0.32206	.	0.059813	0.64402	D	0.000001	T	0.44705	0.1306	N	0.12746	0.255	0.35109	D	0.766004	B	0.11235	0.004	B	0.12837	0.008	T	0.32508	-0.9904	10	0.11182	T	0.66	.	5.9374	0.19173	0.1597:0.0:0.6867:0.1536	.	33	Q96HF1	SFRP2_HUMAN	L	33	ENSP00000274063:F33L	ENSP00000274063:F33L	F	-	3	2	SFRP2	154929339	1.000000	0.71417	0.988000	0.46212	0.842000	0.47809	0.534000	0.23098	0.442000	0.26555	-0.158000	0.13435	TTC		0.657	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			T	154709889	G	T	154709889	3	4	61	1	0	0	0	0	1	0	0	0	14199	933	33	2	800	2	SFRP2	4	154709889	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73186	154709889	36444387	3534	11519										
DCHS2	54798	broad.mit.edu	37	chr4	155156092	155156092	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatttgggctcccaactaaGaagataattccagtgatagt	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155156092G>T	ENST00000357232.4	-	25	8346	c.8347C>A	c.(8347-8349)Ctt>Att	p.L2783I		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2783					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L2783I(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TCCCAACTAAGAAGATAATTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	115	116					4																	155156092		2203	4300	6503	155375542	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8347C>A	4.37:g.155156092G>T	ENSP00000349768:p.Leu2783Ile		155375542	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040053	0.75732	.	.	ENSG00000197410	ENST00000357232	T	0.79749	-1.3	5.94	5.1	0.69264	.	0.000000	0.64402	D	0.000006	T	0.80670	0.4667	M	0.81942	2.565	0.80722	D	1	P	0.43287	0.802	B	0.36922	0.236	T	0.82625	-0.0365	10	0.51188	T	0.08	.	15.1152	0.72394	0.0677:0.0:0.9323:0.0	.	2783	Q6V1P9	PCD23_HUMAN	I	2783	ENSP00000349768:L2783I	ENSP00000349768:L2783I	L	-	1	0	DCHS2	155375542	1.000000	0.71417	0.634000	0.29324	0.945000	0.59286	4.777000	0.62361	1.521000	0.48983	0.557000	0.71058	CTT		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155156092	G	T	155156092	3	4	61	1	0	0	0	0	1	0	0	0	4294	942	33	2	407	2	DCHS2	4	155156092	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	446203	155156092	35998184	3535	11520										
DCHS2	54798	broad.mit.edu	37	chr4	155156457	155156457	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctgagtctgagcactttCtgtagggatgctcatttatc	11	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155156457C>A	ENST00000357232.4	-	25	7981	c.7982G>T	c.(7981-7983)aGa>aTa	p.R2661I		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2661					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R2661I(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGAGCACTTTCTGTAGGGATG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	4											96	90	92					4																	155156457		2203	4300	6503	155375907	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7982G>T	4.37:g.155156457C>A	ENSP00000349768:p.Arg2661Ile		155375907	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.048949	0.55110	.	.	ENSG00000197410	ENST00000357232	T	0.55760	0.5	5.54	4.69	0.59074	.	0.073895	0.53938	D	0.000048	T	0.67316	0.2880	M	0.67953	2.075	0.80722	D	1	D	0.69078	0.997	D	0.64595	0.927	T	0.64824	-0.6316	10	0.20046	T	0.44	.	16.2814	0.82692	0.0:0.8672:0.1328:0.0	.	2661	Q6V1P9	PCD23_HUMAN	I	2661	ENSP00000349768:R2661I	ENSP00000349768:R2661I	R	-	2	0	DCHS2	155375907	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	3.874000	0.56101	1.301000	0.44836	0.460000	0.39030	AGA		0.517	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156457	C	A	155156457	3	1	61	1	0	0	0	0	1	0	0	0	4294	913	32	2	772	2	DCHS2	4	155156457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	365	155156457	35997819	3536	11521										
DCHS2	54798	broad.mit.edu	37	chr4	155156682	155156682	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggcatcccgggtcactCtcaagtccgcatctaaagat	8	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155156682C>A	ENST00000357232.4	-	25	7756	c.7757G>T	c.(7756-7758)aGa>aTa	p.R2586I		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2586					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R2586I(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCGGGTCACTCTCAAGTCCGC	0.428																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											116	121	119					4																	155156682		2203	4299	6502	155376132	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7757G>T	4.37:g.155156682C>A	ENSP00000349768:p.Arg2586Ile		155376132	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	6.078	0.382646	0.11524	.	.	ENSG00000197410	ENST00000357232	T	0.54866	0.55	5.82	2.18	0.27775	.	0.455403	0.22763	N	0.055927	T	0.40909	0.1136	L	0.51422	1.61	0.39629	D	0.970159	B	0.14012	0.009	B	0.11329	0.006	T	0.31052	-0.9957	10	0.54805	T	0.06	.	3.9192	0.09236	0.1581:0.422:0.0:0.4199	.	2586	Q6V1P9	PCD23_HUMAN	I	2586	ENSP00000349768:R2586I	ENSP00000349768:R2586I	R	-	2	0	DCHS2	155376132	0.000000	0.05858	0.011000	0.14972	0.002000	0.02628	0.194000	0.17135	0.370000	0.24538	-0.444000	0.05651	AGA		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156682	C	A	155156682	3	1	61	1	0	0	0	0	1	0	0	0	4294	913	32	2	997	2	DCHS2	4	155156682	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	225	155156682	35997594	3537	11522										
DCHS2	54798	broad.mit.edu	37	chr4	155219387	155219387	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcattaacatcagtgacatAtacttttataattacagtgg	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155219387A>G	ENST00000357232.4	-	18	4713	c.4714T>C	c.(4714-4716)Tat>Cat	p.Y1572H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1572	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y1572H(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TCAGTGACATATACTTTTATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											100	100	100					4																	155219387		2203	4300	6503	155438837	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4714T>C	4.37:g.155219387A>G	ENSP00000349768:p.Tyr1572His		155438837	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.702804	0.00719	.	.	ENSG00000197410	ENST00000357232	T	0.50548	0.74	5.66	-4.99	0.03010	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	1.682020	0.02938	N	0.140159	T	0.19525	0.0469	N	0.04043	-0.29	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08932	-1.0698	10	0.14252	T	0.57	.	2.8186	0.05465	0.1644:0.1918:0.4443:0.1996	.	1572	Q6V1P9	PCD23_HUMAN	H	1572	ENSP00000349768:Y1572H	ENSP00000349768:Y1572H	Y	-	1	0	DCHS2	155438837	0.000000	0.05858	0.000000	0.03702	0.270000	0.26580	0.818000	0.27295	-0.659000	0.05359	-0.417000	0.06048	TAT		0.448	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155219387	A	G	155219387	3	3	61	1	0	0	0	0	1	0	0	0	4294	449	16	4	4068	4	DCHS2	4	155219387	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	62705	155219387	35934889	3538	11523										
DCHS2	54798	broad.mit.edu	37	chr4	155219828	155219828	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagagttctcctgacatctCatttatagtaaagcactcat	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155219828C>A	ENST00000357232.4	-	18	4272	c.4273G>T	c.(4273-4275)Gag>Tag	p.E1425*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1425	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1425*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCTGACATCTCATTTATAGTA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											69	72	71					4																	155219828		2203	4300	6503	155439278	SO:0001587	stop_gained	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4273G>T	4.37:g.155219828C>A	ENSP00000349768:p.Glu1425*		155439278	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	42	9.370901	0.99151	.	.	ENSG00000197410	ENST00000357232	.	.	.	5.86	4.01	0.46588	.	0.578909	0.17885	N	0.158706	.	.	.	.	.	.	0.29930	N	0.821981	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	5.6118	0.17410	0.0:0.6116:0.1522:0.2362	.	.	.	.	X	1425	.	ENSP00000349768:E1425X	E	-	1	0	DCHS2	155439278	0.030000	0.19436	0.113000	0.21522	0.800000	0.45204	0.531000	0.23052	1.594000	0.50039	0.650000	0.86243	GAG		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155219828	C	A	155219828	4	1	61	1	0	0	0	0	0	1	0	0	4294	835	29	2	4509	2	DCHS2	4	155219828	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	441	155219828	35934448	3539	11524										
DCHS2	54798	broad.mit.edu	37	chr4	155278421	155278421	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaaactgttcattacttcCttgtctgctgaaaagttgac	6	9	3	2	rs149265546	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155278421C>A	ENST00000357232.4	-	6	749	c.750G>T	c.(748-750)aaG>aaT	p.K250N	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	250	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K250K(1)|p.K250N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tcattacttccttgtctgctg	0.438																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	4											135	140	139					4																	155278421		2203	4300	6503	155497871	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.750G>T	4.37:g.155278421C>A	ENSP00000349768:p.Lys250Asn		155497871	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.438612	0.01098	.	.	ENSG00000197410	ENST00000357232	T	0.54479	0.57	0.772	-0.409	0.12378	Cadherin (1);	.	.	.	.	T	0.25344	0.0616	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.14531	-1.0469	9	0.26408	T	0.33	.	3.3522	0.07156	0.0:0.6434:0.0:0.3566	.	250	Q6V1P9	PCD23_HUMAN	N	250	ENSP00000349768:K250N	ENSP00000349768:K250N	K	-	3	2	DCHS2	155497871	0.006000	0.16342	0.002000	0.10522	0.002000	0.02628	-0.368000	0.07543	-0.217000	0.10033	-0.450000	0.05554	AAG		0.438	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155278421	C	A	155278421	3	1	61	1	0	0	0	0	1	0	0	0	4294	680	24	2	8176	2	DCHS2	4	155278421	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58593	155278421	35875855	3540	11525										
PLRG1	5356	broad.mit.edu	37	chr4	155457840	155457840	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaattccacattcattaAaatctctttctcttgataat	1	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155457840A>C	ENST00000499023.2	-	15	1668	c.1542T>G	c.(1540-1542)ttT>ttG	p.F514L	PLRG1_ENST00000393905.2_Missense_Mutation_p.F514L|PLRG1_ENST00000302078.5_Missense_Mutation_p.F505L	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	514					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.F514L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				ACATTCATTAAAATCTCTTTC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	4											43	46	45					4																	155457840		2197	4278	6475	155677290	SO:0001583	missense	5356			AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1542T>G	4.37:g.155457840A>C	ENSP00000424417:p.Phe514Leu		155677290	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	37	CCDS34083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.96|16.96	3.265243|3.265243	0.59431|0.59431	.|.	.|.	ENSG00000171566|ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078|ENST00000503251	T;T;T|T	0.65549|0.79352	-0.16;-0.16;-0.15|-1.26	5.4|5.4	4.2|4.2	0.49525|0.49525	.|.	0.045973|.	0.85682|.	D|.	0.000000|.	D|D	0.84433|0.84433	0.5471|0.5471	M|M	0.81239|0.81239	2.535|2.535	0.58432|0.58432	D|D	0.999991|0.999991	B;B|.	0.30686|.	0.29;0.275|.	B;B|.	0.32342|.	0.107;0.144|.	T|T	0.83180|0.83180	-0.0089|-0.0089	10|7	0.72032|0.38643	D|T	0.01|0.18	.|.	12.5742|12.5742	0.56355|0.56355	0.8611:0.1389:0.0:0.0|0.8611:0.1389:0.0:0.0	.|.	505;514|.	O43660-2;O43660|.	.;PLRG1_HUMAN|.	L|V	514;514;505|93	ENSP00000424417:F514L;ENSP00000377483:F514L;ENSP00000303191:F505L|ENSP00000426497:L93V	ENSP00000303191:F505L|ENSP00000426497:L93V	F|L	-|-	3|1	2|2	PLRG1|PLRG1	155677290|155677290	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.990000|0.990000	0.78478|0.78478	2.586000|2.586000	0.46119|0.46119	0.869000|0.869000	0.35703|0.35703	0.482000|0.482000	0.46254|0.46254	TTT|TTA		0.299	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155457840	A	C	155457840	3	2	61	1	0	0	0	0	1	0	0	0	12137	11	1	4	6	4	PLRG1	4	155457840	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	179419	155457840	35696436	3541	11526										
PLRG1	5356	broad.mit.edu	37	chr4	155459228	155459228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggaatttccactgctttAtgttatctggagaaccagat	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155459228A>G	ENST00000499023.2	-	13	1310	c.1184T>C	c.(1183-1185)aTa>aCa	p.I395T	PLRG1_ENST00000393905.2_Missense_Mutation_p.I395T|PLRG1_ENST00000302078.5_Missense_Mutation_p.I386T	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	395					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.I395T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CCACTGCTTTATGTTATCTGG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											37	39	38					4																	155459228		2203	4294	6497	155678678	SO:0001583	missense	5356			AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1184T>C	4.37:g.155459228A>G	ENSP00000424417:p.Ile395Thr		155678678	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	37	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.133851	0.56828	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000503251;ENST00000302078	T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42	5.71	5.71	0.89125	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81866	0.4913	M	0.91196	3.185	0.80722	D	1	D;P	0.57257	0.979;0.831	P;P	0.54140	0.743;0.724	D	0.86269	0.1660	10	0.66056	D	0.02	-24.4029	15.9707	0.80013	1.0:0.0:0.0:0.0	.	386;395	O43660-2;O43660	.;PLRG1_HUMAN	T	395;395;38;386	ENSP00000424417:I395T;ENSP00000377483:I395T;ENSP00000426497:I38T;ENSP00000303191:I386T	ENSP00000303191:I386T	I	-	2	0	PLRG1	155678678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.105000	0.94246	2.165000	0.68154	0.477000	0.44152	ATA		0.318	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		G	155459228	A	G	155459228	3	3	61	1	0	0	0	0	1	0	0	0	12137	449	16	4	372	4	PLRG1	4	155459228	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1388	155459228	35695048	3542	11527										
PLRG1	5356	broad.mit.edu	37	chr4	155461948	155461948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacttaccttattgtattCgagatcccagcatttcactt	4	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155461948C>T	ENST00000499023.2	-	9	952	c.826G>A	c.(826-828)Gaa>Aaa	p.E276K	PLRG1_ENST00000393905.2_Missense_Mutation_p.E276K|PLRG1_ENST00000302078.5_Missense_Mutation_p.E267K	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	276					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.E276K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTATTGTATTCGAGATCCCAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											108	111	110					4																	155461948		2203	4300	6503	155681398	SO:0001583	missense	5356			AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.826G>A	4.37:g.155461948C>T	ENSP00000424417:p.Glu276Lys		155681398	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	37	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	C	35	5.563191	0.96527	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078	D;D;D	0.81821	-1.54;-1.54;-1.54	5.83	5.83	0.93111	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.87569	0.6210	L	0.48877	1.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.985	D	0.86518	0.1814	10	0.49607	T	0.09	-31.8565	20.1141	0.97919	0.0:1.0:0.0:0.0	.	267;276	O43660-2;O43660	.;PLRG1_HUMAN	K	276;276;267	ENSP00000424417:E276K;ENSP00000377483:E276K;ENSP00000303191:E267K	ENSP00000303191:E267K	E	-	1	0	PLRG1	155681398	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	7.629000	0.83207	2.757000	0.94681	0.591000	0.81541	GAA		0.378	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		T	155461948	C	T	155461948	3	4	61	1	0	0	0	0	1	0	0	0	12137	893	31	1	746	1	PLRG1	4	155461948	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2720	155461948	35692328	3543	11528										
FGB	2244	broad.mit.edu	37	chr4	155488849	155488849	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactaaccttcgtgtgcttCgttcaatcctggaaaacctg	7	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155488849C>T	ENST00000302068.4	+	4	658	c.595C>T	c.(595-597)Cgt>Tgt	p.R199C	FGB_ENST00000509493.1_5'UTR|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	199					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)	p.R199C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TCGTGTGCTTCGTTCAATCCT	0.393																																					NSCLC(106;1133 1613 21870 46110 52656)											1	Substitution - Missense(1)	large_intestine(1)	4											118	113	115					4																	155488849		2203	4300	6503	155708299	SO:0001583	missense	2244				CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"Fibrinogen C domain containing", "Endogenous ligands"	3662	protein-coding gene	gene with protein product		134830	"fibrinogen, B beta polypeptide"				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.595C>T	4.37:g.155488849C>T	ENSP00000306099:p.Arg199Cys		155708299	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	37	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069115	0.93950	.	.	ENSG00000171564	ENST00000302068;ENST00000537843	D	0.83419	-1.72	5.77	5.77	0.91146	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.147452	0.64402	D	0.000004	D	0.91496	0.7315	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.984	D	0.91427	0.5163	10	0.87932	D	0	.	20.3473	0.98799	0.0:1.0:0.0:0.0	.	182;199	B4E1D3;P02675	.;FIBB_HUMAN	C	199;182	ENSP00000306099:R199C	ENSP00000306099:R199C	R	+	1	0	FGB	155708299	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.133000	0.57983	2.884000	0.98904	0.655000	0.94253	CGT		0.393	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141		T	155488849	C	T	155488849	3	4	61	1	0	0	0	0	1	0	0	0	5850	884	31	1	609	1	FGB	4	155488849	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26901	155488849	35665427	3544	11529										
FGA	2243	broad.mit.edu	37	chr4	155507125	155507125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacagtcagaaccatcttCggaggtcaccacttctttgg	11	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155507125C>T	ENST00000302053.3	-	5	1534	c.1456G>A	c.(1456-1458)Gaa>Aaa	p.E486K	FGA_ENST00000403106.3_Missense_Mutation_p.E486K	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	486					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.E486K(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GAACCATCTTCGGAGGTCACC	0.493																																					NSCLC(143;340 1922 20892 22370 48145)											1	Substitution - Missense(1)	large_intestine(1)	4	GRCh37	CM015840	FGA	M							148	144	145					4																	155507125		2203	4300	6503	155726575	SO:0001583	missense	2243				CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1456G>A	4.37:g.155507125C>T	ENSP00000306361:p.Glu486Lys		155726575	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.479430	0.26511	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.60548	0.18;0.18	5.99	4.09	0.47781	Fibrinogen alpha C domain (1);	13.202500	0.00166	N	0.000000	T	0.49525	0.1562	L	0.52759	1.655	0.09310	N	1	B;B	0.31817	0.341;0.066	B;B	0.22386	0.039;0.017	T	0.37865	-0.9687	10	0.33940	T	0.23	.	3.394	0.07299	0.1391:0.5806:0.1211:0.1592	.	486;486	P02671-2;P02671	.;FIBA_HUMAN	K	486	ENSP00000306361:E486K;ENSP00000385981:E486K	ENSP00000306361:E486K	E	-	1	0	FGA	155726575	0.254000	0.23992	0.110000	0.21437	0.297000	0.27493	0.576000	0.23744	1.377000	0.46286	0.655000	0.94253	GAA		0.493	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		T	155507125	C	T	155507125	3	4	61	1	0	0	0	0	1	0	0	0	5849	893	31	1	1196	1	FGA	4	155507125	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18276	155507125	35647151	3545	11530										
RBM46	166863	broad.mit.edu	37	chr4	155719083	155719083	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaagatatatgaatttcGacttatgatggaatttagtg	11	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155719083G>A	ENST00000281722.3	+	3	507	c.272G>A	c.(271-273)cGa>cAa	p.R91Q	RBM46_ENST00000514866.1_Missense_Mutation_p.R91Q|RBM46_ENST00000510397.1_Missense_Mutation_p.R91Q	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	91	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R91Q(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				TATGAATTTCGACTTATGATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											117	122	120					4																	155719083		2203	4300	6503	155938533	SO:0001583	missense	166863			BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.272G>A	4.37:g.155719083G>A	ENSP00000281722:p.Arg91Gln		155938533	B3KWU8|B4DZ27	Missense_Mutation	SNP	ENST00000281722.3	37	CCDS3790.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.800038	0.90538	.	.	ENSG00000151962	ENST00000514866;ENST00000281722;ENST00000510397;ENST00000512640	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	5.9	5.9	0.94986	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.43233	0.1238	M	0.64630	1.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.76575	0.971;0.988;0.968	T	0.14090	-1.0485	10	0.87932	D	0	-8.6364	20.2723	0.98479	0.0:0.0:1.0:0.0	.	91;91;91	B4DZ27;B3KWU8;Q8TBY0	.;.;RBM46_HUMAN	Q	91	ENSP00000424500:R91Q;ENSP00000281722:R91Q;ENSP00000422813:R91Q;ENSP00000426672:R91Q	ENSP00000281722:R91Q	R	+	2	0	RBM46	155938533	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.659000	0.98597	2.793000	0.96121	0.563000	0.77884	CGA		0.343	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		A	155719083	G	A	155719083	3	1	61	1	0	0	0	0	1	0	0	0	13177	1058	37	1	278	1	RBM46	4	155719083	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211958	155719083	35435193	3546	11531										
RBM46	166863	broad.mit.edu	37	chr4	155720128	155720128	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgggtaaagaaacttagaGattatgcttttgttcacttt	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:155720128G>T	ENST00000281722.3	+	4	1049	c.814G>T	c.(814-816)Gat>Tat	p.D272Y	RBM46_ENST00000514866.1_Missense_Mutation_p.D272Y|RBM46_ENST00000510397.1_Missense_Mutation_p.D272Y	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	272	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.D272Y(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				GAAACTTAGAGATTATGCTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											102	93	96					4																	155720128		2203	4300	6503	155939578	SO:0001583	missense	166863			BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.814G>T	4.37:g.155720128G>T	ENSP00000281722:p.Asp272Tyr		155939578	B3KWU8|B4DZ27	Missense_Mutation	SNP	ENST00000281722.3	37	CCDS3790.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814413	0.70912	.	.	ENSG00000151962	ENST00000514866;ENST00000281722;ENST00000510397	T;T;T	0.81330	-1.48;-1.48;-1.48	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.92948	0.7756	M	0.93241	3.395	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.997	D;D;D	0.80764	0.992;0.994;0.99	D	0.93621	0.6948	10	0.87932	D	0	-33.853	20.6439	0.99570	0.0:0.0:1.0:0.0	.	272;272;272	B4DZ27;B3KWU8;Q8TBY0	.;.;RBM46_HUMAN	Y	272	ENSP00000424500:D272Y;ENSP00000281722:D272Y;ENSP00000422813:D272Y	ENSP00000281722:D272Y	D	+	1	0	RBM46	155939578	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.271000	0.78506	2.884000	0.98904	0.655000	0.94253	GAT		0.353	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		T	155720128	G	T	155720128	3	4	61	1	0	0	0	0	1	0	0	0	13177	942	33	2	824	2	RBM46	4	155720128	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1045	155720128	35434148	3547	11532										
NPY2R	4887	broad.mit.edu	37	chr4	156136030	156136030	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacagtgttccacatcatCgccatgtgctccacttttgc	6	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156136030C>T	ENST00000329476.3	+	2	1428	c.939C>T	c.(937-939)atC>atT	p.I313I	NPY2R_ENST00000506608.1_Silent_p.I313I	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	313					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)	p.I313I(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TCCACATCATCGCCATGTGCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	4											124	98	107					4																	156136030		2203	4300	6503	156355480	SO:0001819	synonymous_variant	4887			U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.939C>T	4.37:g.156136030C>T			156355480	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																				0.542	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		T	156136030	C	T	156136030	2	4	61	1	0	0	0	0	0	0	0	1	10640	874	31	1		1	NPY2R	4	156136030	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	415902	156136030	35018246	3548	11533										
GUCY1A3	2982	broad.mit.edu	37	chr4	156618204	156618204	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagaaagtcttcctcaaaGaaaaaccagtcggagccgag	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156618204G>T	ENST00000296518.7	+	3	394	c.185G>T	c.(184-186)aGa>aTa	p.R62I	GUCY1A3_ENST00000515602.1_3'UTR|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.R62I|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.R62I|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.R62I|GUCY1A3_ENST00000393832.3_5'UTR|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.R62I|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.R62I			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	62					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.R62I(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		CTTCCTCAAAGAAAAACCAGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											97	100	99					4																	156618204		2203	4300	6503	156837654	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.185G>T	4.37:g.156618204G>T	ENSP00000296518:p.Arg62Ile		156837654	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663470	0.88251	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000296518;ENST00000513574	D;D;D;D;D;D	0.88509	-2.39;-2.39;-2.2;-2.39;-2.39;-2.39	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000001	D	0.93197	0.7833	M	0.63843	1.955	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.996	P;P;P	0.61800	0.894;0.894;0.894	D	0.92371	0.5905	10	0.51188	T	0.08	.	20.3334	0.98727	0.0:0.0:1.0:0.0	.	62;62;62	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	I	62	ENSP00000424361:R62I;ENSP00000421493:R62I;ENSP00000426968:R62I;ENSP00000412201:R62I;ENSP00000296518:R62I;ENSP00000426040:R62I	ENSP00000296518:R62I	R	+	2	0	GUCY1A3	156837654	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	6.525000	0.73795	2.818000	0.97014	0.591000	0.81541	AGA		0.453	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156618204	G	T	156618204	3	4	61	1	0	0	0	0	1	0	0	0	6915	942	33	2	187	2	GUCY1A3	4	156618204	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	482174	156618204	34536072	3549	11534										
GUCY1A3	2982	broad.mit.edu	37	chr4	156632169	156632169	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacatcgctattctgcaaGacatttccattccatttcat	3	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156632169G>T	ENST00000296518.7	+	6	1061	c.852G>T	c.(850-852)aaG>aaT	p.K284N	GUCY1A3_ENST00000513574.1_Missense_Mutation_p.K284N|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.K284N|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.K284N|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.K26N|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.K284N|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.K284N			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	284					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.K284N(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TATTCTGCAAGACATTTCCAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											95	89	91					4																	156632169		2203	4300	6503	156851619	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.852G>T	4.37:g.156632169G>T	ENSP00000296518:p.Lys284Asn		156851619	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882619	0.72410	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.76	4.91	0.64330	Haem NO binding associated (1);	0.000000	0.64402	D	0.000002	D	0.88055	0.6334	L	0.33792	1.035	0.46376	D	0.999011	P;P;P	0.43662	0.814;0.814;0.814	P;P;P	0.53146	0.698;0.698;0.719	D	0.86456	0.1776	10	0.35671	T	0.21	.	11.5476	0.50702	0.1391:0.0:0.8609:0.0	.	284;284;284	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	N	284;284;284;284;26;284;284	ENSP00000424361:K284N;ENSP00000421493:K284N;ENSP00000426968:K284N;ENSP00000412201:K284N;ENSP00000377418:K26N;ENSP00000296518:K284N;ENSP00000426040:K284N	ENSP00000296518:K284N	K	+	3	2	GUCY1A3	156851619	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.566000	0.45948	1.542000	0.49330	0.643000	0.83706	AAG		0.463	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156632169	G	T	156632169	3	4	61	1	0	0	0	0	1	0	0	0	6915	933	33	2	866	2	GUCY1A3	4	156632169	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13965	156632169	34522107	3550	11535										
GUCY1A3	2982	broad.mit.edu	37	chr4	156632281	156632281	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaaagcctaattttgaaGaatactttgaaattctgact	7	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156632281G>T	ENST00000296518.7	+	6	1173	c.964G>T	c.(964-966)Gaa>Taa	p.E322*	GUCY1A3_ENST00000513574.1_Nonsense_Mutation_p.E322*|GUCY1A3_ENST00000455639.2_Nonsense_Mutation_p.E322*|GUCY1A3_ENST00000511507.1_Nonsense_Mutation_p.E322*|GUCY1A3_ENST00000393832.3_Nonsense_Mutation_p.E64*|GUCY1A3_ENST00000511108.1_Nonsense_Mutation_p.E322*|GUCY1A3_ENST00000506455.1_Nonsense_Mutation_p.E322*			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	322				Missing (in Ref. 1; CAA47145). {ECO:0000305}.	blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.E322*(2)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TAATTTTGAAGAATACTTTGA	0.388																																																2	Substitution - Nonsense(2)	large_intestine(2)	4											67	70	69					4																	156632281		2203	4300	6503	156851731	SO:0001587	stop_gained	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.964G>T	4.37:g.156632281G>T	ENSP00000296518:p.Glu322*		156851731	D3DP19|D6RDW3|O43843|Q8TAH3	Nonsense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	41	8.546869	0.98857	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	.	.	.	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	20.3219	0.98684	0.0:0.0:1.0:0.0	.	.	.	.	X	322;322;322;322;64;322;322	.	ENSP00000296518:E322X	E	+	1	0	GUCY1A3	156851731	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	9.122000	0.94380	2.876000	0.98609	0.643000	0.83706	GAA		0.388	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156632281	G	T	156632281	4	4	61	1	0	0	0	0	0	1	0	0	6915	943	33	2	978	2	GUCY1A3	4	156632281	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112	156632281	34521995	3551	11536										
GUCY1A3	2982	broad.mit.edu	37	chr4	156634379	156634379	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctctcagacatcccaattCacaatgcactgagggatgtg	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156634379C>T	ENST00000296518.7	+	7	1425	c.1216C>T	c.(1216-1218)Cac>Tac	p.H406Y	GUCY1A3_ENST00000513574.1_Missense_Mutation_p.H406Y|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.H406Y|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.H406Y|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.H148Y|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.H406Y|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.H406Y			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	406					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.H406Y(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		CATCCCAATTCACAATGCACT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	4											93	90	91					4																	156634379		2203	4300	6503	156853829	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1216C>T	4.37:g.156634379C>T	ENSP00000296518:p.His406Tyr		156853829	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486357	0.84854	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.92249	-3.0;-3.0;-3.0;-3.0;-3.0;-3.0;-3.0	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000003	D	0.97084	0.9047	M	0.90595	3.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96949	0.9693	10	0.72032	D	0.01	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	406;406	B3KU69;Q02108	.;GCYA3_HUMAN	Y	406;406;406;406;148;406;406	ENSP00000424361:H406Y;ENSP00000421493:H406Y;ENSP00000426968:H406Y;ENSP00000412201:H406Y;ENSP00000377418:H148Y;ENSP00000296518:H406Y;ENSP00000426040:H406Y	ENSP00000296518:H406Y	H	+	1	0	GUCY1A3	156853829	1.000000	0.71417	0.997000	0.53966	0.742000	0.42306	7.461000	0.80834	2.861000	0.98227	0.655000	0.94253	CAC		0.498	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156634379	C	T	156634379	3	4	61	1	0	0	0	0	1	0	0	0	6915	826	29	3	1249	3	GUCY1A3	4	156634379	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2098	156634379	34519897	3552	11537										
GUCY1B3	2983	broad.mit.edu	37	chr4	156715085	156715085	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcaaaagaagaggatttTtatgaagatcttgacagatt	10	3	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156715085T>G	ENST00000264424.8	+	6	655	c.573T>G	c.(571-573)ttT>ttG	p.F191L	GUCY1B3_ENST00000505764.1_Missense_Mutation_p.F171L|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.F123L|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.F191L|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.F213L|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.F123L|GUCY1B3_ENST00000507146.1_Missense_Mutation_p.F123L	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	191					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.F191L(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		AAGAGGATTTTTATGAAGATC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	60	60					4																	156715085		1832	4078	5910	156934535	SO:0001583	missense	2983			AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.573T>G	4.37:g.156715085T>G	ENSP00000264424:p.Phe191Leu		156934535	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	37	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	T	9.603	1.129221	0.21041	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;T;D;T;D	0.81996	-1.56;-1.56;-1.56;-1.16;-1.56;-1.05;-1.56	6.03	0.607	0.17564	.	0.102254	0.64402	N	0.000002	T	0.56572	0.1994	N	0.04508	-0.205	0.36002	D	0.837454	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.0;0.0;0.004;0.0	T	0.47129	-0.9141	10	0.07990	T	0.79	.	7.1215	0.25448	0.0:0.2553:0.1114:0.6333	.	171;213;123;191;191	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	L	123;213;171;123;191;191;123	ENSP00000427226:F123L;ENSP00000426786:F213L;ENSP00000426319:F171L;ENSP00000422313:F123L;ENSP00000264424:F191L;ENSP00000420842:F191L;ENSP00000425065:F123L	ENSP00000264424:F191L	F	+	3	2	GUCY1B3	156934535	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.615000	0.24329	0.142000	0.18901	0.533000	0.62120	TTT		0.338	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			G	156715085	T	G	156715085	3	3	61	1	0	0	0	0	1	0	0	0	6916	1838	64	4	595	4	GUCY1B3	4	156715085	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	80706	156715085	34439191	3553	11538										
ACCN5	51802	broad.mit.edu	37	chr4	156757870	156757870	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccggctttgattcaacttCttggaaagatatttcaaagc	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156757870C>A	ENST00000537611.2	-	8	1252	c.1206G>T	c.(1204-1206)aaG>aaT	p.K402N		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	402					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)	p.K402N(1)									GATTCAACTTCTTGGAAAGAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											68	74	72					4																	156757870		2200	4300	6500	156977320	SO:0001583	missense	51802			AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.1206G>T	4.37:g.156757870C>A	ENSP00000442477:p.Lys402Asn		156977320		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	C	7.114	0.576526	0.13686	.	.	ENSG00000256394	ENST00000537611	T	0.66280	-0.2	4.8	3.07	0.35406	.	0.442496	0.21075	N	0.080584	T	0.48352	0.1495	L	0.56199	1.76	0.34935	D	0.7497	B	0.21821	0.061	B	0.25759	0.063	T	0.43097	-0.9412	10	0.17369	T	0.5	-16.0004	1.7614	0.02992	0.1637:0.4729:0.1592:0.2041	.	402	Q9NY37	ACCN5_HUMAN	N	402	ENSP00000442477:K402N	ENSP00000264432:K402N	K	-	3	2	ACCN5	156977320	0.004000	0.15560	1.000000	0.80357	0.631000	0.37964	-0.458000	0.06737	0.720000	0.32209	-0.122000	0.15005	AAG		0.323	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			A	156757870	C	A	156757870	3	1	61	1	0	0	0	0	1	0	0	0	132	912	32	2	323	2	ACCN5	4	156757870	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42785	156757870	34396406	3554	11539										
ACCN5	51802	broad.mit.edu	37	chr4	156784872	156784872	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggagatggcagtggtttCtttgaaaggcaaagctttat	14	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156784872C>A	ENST00000537611.2	-	2	121	c.75G>T	c.(73-75)aaG>aaT	p.K25N	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	25					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)	p.K25N(1)									GCAGTGGTTTCTTTGAAAGGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											95	96	96					4																	156784872		2203	4300	6503	157004322	SO:0001583	missense	51802			AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.75G>T	4.37:g.156784872C>A	ENSP00000442477:p.Lys25Asn		157004322		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	C	8.271	0.813325	0.16537	.	.	ENSG00000256394	ENST00000537611	T	0.69040	-0.37	4.34	3.49	0.39957	.	0.252624	0.26086	N	0.026425	T	0.62539	0.2436	M	0.72479	2.2	0.42564	D	0.993155	P	0.35656	0.514	B	0.38428	0.273	T	0.58148	-0.7687	10	0.25106	T	0.35	-1.0202	7.9459	0.29987	0.0:0.7418:0.0:0.2582	.	25	Q9NY37	ACCN5_HUMAN	N	25	ENSP00000442477:K25N	ENSP00000264432:K25N	K	-	3	2	ACCN5	157004322	0.997000	0.39634	0.081000	0.20488	0.109000	0.19521	1.663000	0.37429	1.139000	0.42245	0.650000	0.86243	AAG		0.383	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			A	156784872	C	A	156784872	3	1	61	1	0	0	0	0	1	0	0	0	132	912	32	2	1478	2	ACCN5	4	156784872	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27002	156784872	34369404	3555	11540										
TDO2	6999	broad.mit.edu	37	chr4	156825237	156825237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaaactggtgtgaatagaGccagcaaaggaggtcttatc	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156825237G>A	ENST00000536354.2	+	2	167	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase									p.A35T(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		TGTGAATAGAGCCAGCAAAGG	0.418																																					Colon(57;928 1036 2595 6946 26094)											1	Substitution - Missense(1)	large_intestine(1)	4											89	88	88					4																	156825237		2203	4300	6503	157044687	SO:0001583	missense	6999				CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.103G>A	4.37:g.156825237G>A	ENSP00000444788:p.Ala35Thr		157044687		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.002142	0.93227	.	.	ENSG00000151790	ENST00000536354	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.73830	0.3637	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.66384	-0.5937	9	0.16420	T	0.52	-14.2751	19.5862	0.95490	0.0:0.0:1.0:0.0	.	35	P48775	T23O_HUMAN	T	35	.	ENSP00000281525:A35T	A	+	1	0	TDO2	157044687	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	9.170000	0.94795	2.641000	0.89580	0.650000	0.86243	GCC		0.418	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		A	156825237	G	A	156825237	3	1	61	1	0	0	0	0	1	0	0	0	15766	971	34	3	109	3	TDO2	4	156825237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40365	156825237	34329039	3556	11541										
TDO2	6999	broad.mit.edu	37	chr4	156831237	156831237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccgactattagaaaacaaGataggtgttcttcagaacat	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156831237G>T	ENST00000536354.2	+	6	556	c.492G>T	c.(490-492)aaG>aaT	p.K164N		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase									p.K164N(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		TAGAAAACAAGATAGGTGTTC	0.398																																					Colon(57;928 1036 2595 6946 26094)											1	Substitution - Missense(1)	large_intestine(1)	4											95	99	98					4																	156831237		2203	4300	6503	157050687	SO:0001583	missense	6999				CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.492G>T	4.37:g.156831237G>T	ENSP00000444788:p.Lys164Asn		157050687		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634704	0.47049	.	.	ENSG00000151790	ENST00000506072;ENST00000536354	.	.	.	5.15	2.31	0.28768	.	0.087834	0.85682	D	0.000000	T	0.67429	0.2892	M	0.89287	3.02	0.58432	D	0.999997	B	0.29590	0.25	B	0.36567	0.228	T	0.67647	-0.5617	9	0.66056	D	0.02	-17.5733	8.0099	0.30347	0.3328:0.0:0.6672:0.0	.	164	P48775	T23O_HUMAN	N	57;164	.	ENSP00000281525:K164N	K	+	3	2	TDO2	157050687	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	1.352000	0.34033	0.609000	0.30018	-0.387000	0.06579	AAG		0.398	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		T	156831237	G	T	156831237	3	4	61	1	0	0	0	0	1	0	0	0	15766	933	33	2	514	2	TDO2	4	156831237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6000	156831237	34323039	3557	11542										
CTSO	1519	broad.mit.edu	37	chr4	156850694	156850694	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtcttatcagcacttacCtgttttatcaaacccagtta	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156850694C>T	ENST00000433477.3	-	6	907	c.838G>A	c.(838-840)Gga>Aga	p.G280R		NM_001334.2	NP_001325.1	P43235	CATK_HUMAN	cathepsin O	287					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)	p.G280R(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|prostate(1)	16	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)		CAGCACTTACCTGTTTTATCA	0.418																																					Pancreas(148;2303 2598 8989 35298)											1	Substitution - Missense(1)	large_intestine(1)	4											119	103	109					4																	156850694		2203	4300	6503	157070144	SO:0001630	splice_region_variant	1519			X77383	CCDS3794.1	4q32.1	2012-10-03			ENSG00000256043	ENSG00000256043		"Cathepsins"	2542	protein-coding gene	gene with protein product		600550		CTSO1		9790772	Standard	NM_001334		Approved		uc003ipg.3	P43234	OTTHUMG00000161942	ENST00000433477.3:c.838+1G>A	4.37:g.156850694C>T			157070144	Q6FHS6	Missense_Mutation	SNP	ENST00000433477.3	37	CCDS3794.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989908	0.93106	.	.	ENSG00000256043	ENST00000433477	T	0.32023	1.47	5.53	5.53	0.82687	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.49898	0.1584	L	0.45698	1.435	0.80722	D	1	D	0.57257	0.979	D	0.69654	0.965	T	0.29088	-1.0023	9	.	.	.	.	19.4522	0.94872	0.0:1.0:0.0:0.0	.	280	P43234	CATO_HUMAN	R	280	ENSP00000414904:G280R	.	G	-	1	0	CTSO	157070144	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.092000	0.76930	2.598000	0.87819	0.655000	0.94253	GGA		0.418	CTSO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366469.1	NM_001334	Missense_Mutation	T	156850694	C	T	156850694	5	4	61	1	0	0	0	0	0	0	1	0	4046	695	24	3	139	3	CTSO	4	156850694	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19457	156850694	34303582	3558	11543										
CTSO	1519	broad.mit.edu	37	chr4	156864397	156864397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaataaagaattcaagtatCgatgtctattaagactttcc	6	6	2	2	rs376990374		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:156864397C>T	ENST00000433477.3	-	2	224	c.155G>A	c.(154-156)cGa>cAa	p.R52Q		NM_001334.2	NP_001325.1	P43235	CATK_HUMAN	cathepsin O	0					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)	p.R52Q(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|prostate(1)	16	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)		ATTCAAGTATCGATGTCTATT	0.323																																					Pancreas(148;2303 2598 8989 35298)											1	Substitution - Missense(1)	large_intestine(1)	4						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	77	85	82		155	-1.7	0.9	4		82	0,8592		0,0,4296	no	missense	CTSO	NM_001334.2	43	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	benign	52/322	156864397	1,12997	2203	4296	6499	157083847	SO:0001583	missense	1519			X77383	CCDS3794.1	4q32.1	2012-10-03			ENSG00000256043	ENSG00000256043		"Cathepsins"	2542	protein-coding gene	gene with protein product		600550		CTSO1		9790772	Standard	NM_001334		Approved		uc003ipg.3	P43234	OTTHUMG00000161942	ENST00000433477.3:c.155G>A	4.37:g.156864397C>T	ENSP00000414904:p.Arg52Gln		157083847	Q6FHS6	Missense_Mutation	SNP	ENST00000433477.3	37	CCDS3794.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.438362	0.25900	2.27E-4	0.0	ENSG00000256043	ENST00000433477	T	0.28666	1.6	5.69	-1.68	0.08212	.	0.962280	0.08602	N	0.921346	T	0.17450	0.0419	N	0.25485	0.75	0.09310	N	1	B	0.28783	0.222	B	0.21708	0.036	T	0.25082	-1.0142	10	0.30854	T	0.27	.	6.6818	0.23125	0.1162:0.3968:0.0:0.487	.	52	P43234	CATO_HUMAN	Q	52	ENSP00000414904:R52Q	ENSP00000281527:R52Q	R	-	2	0	CTSO	157083847	0.000000	0.05858	0.948000	0.38648	0.381000	0.30169	-0.571000	0.05889	-0.037000	0.13646	-0.136000	0.14681	CGA		0.323	CTSO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366469.1	NM_001334		T	156864397	C	T	156864397	3	4	61	1	0	0	0	0	1	0	0	0	4046	884	31	1	838	1	CTSO	4	156864397	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13703	156864397	34289879	3559	11544										
PDGFC	56034	broad.mit.edu	37	chr4	157693890	157693890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagaagttgccaagttggCctatatagatcttctaagtc	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:157693890C>T	ENST00000502773.1	-	4	1141	c.651G>A	c.(649-651)agG>agA	p.R217R	PDGFC_ENST00000541126.1_Silent_p.R54R|PDGFC_ENST00000422544.2_Silent_p.R217R|PDGFC_ENST00000542208.1_Silent_p.R62R|PDGFC_ENST00000504672.1_5'UTR	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	217					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)	p.R217R(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		GCCAAGTTGGCCTATATAGAT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	4											67	65	66					4																	157693890		2203	4300	6503	157913340	SO:0001819	synonymous_variant	56034			AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.651G>A	4.37:g.157693890C>T			157913340	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																				0.388	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			T	157693890	C	T	157693890	2	4	61	1	0	0	0	0	0	0	0	1	11690	738	26	3		3	PDGFC	4	157693890	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	829493	157693890	33460386	3560	11545										
PDGFC	56034	broad.mit.edu	37	chr4	157771544	157771544	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtagacacagtaataattCtctcatgctgaggatcttgt	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:157771544C>T	ENST00000502773.1	-	2	633	c.143G>A	c.(142-144)aGa>aAa	p.R48K	PDGFC_ENST00000541126.1_Intron|PDGFC_ENST00000422544.2_Missense_Mutation_p.R48K|PDGFC_ENST00000542208.1_5'Flank	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	48	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)	p.R48K(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		AGTAATAATTCTCTCATGCTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											64	60	62					4																	157771544		2203	4300	6503	157990994	SO:0001583	missense	56034			AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.143G>A	4.37:g.157771544C>T	ENSP00000422464:p.Arg48Lys		157990994	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Missense_Mutation	SNP	ENST00000502773.1	37	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114667	0.37339	.	.	ENSG00000145431	ENST00000502773;ENST00000422544;ENST00000543489	T;T	0.14640	2.54;2.49	5.94	5.94	0.96194	CUB (2);	0.166021	0.51477	D	0.000098	T	0.04092	0.0114	N	0.00707	-1.245	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.45963	-0.9225	10	0.30078	T	0.28	-19.8101	9.2423	0.37504	0.0:0.8801:0.0:0.1199	.	48	Q9NRA1	PDGFC_HUMAN	K	48	ENSP00000422464:R48K;ENSP00000410048:R48K	ENSP00000410048:R48K	R	-	2	0	PDGFC	157990994	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.596000	0.67570	2.826000	0.97356	0.561000	0.74099	AGA		0.338	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			T	157771544	C	T	157771544	3	4	61	1	0	0	0	0	1	0	0	0	11690	913	32	3	914	3	PDGFC	4	157771544	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77654	157771544	33382732	3561	11546										
GRIA2	2891	broad.mit.edu	37	chr4	158142883	158142883	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagtagggatggttcagttTtccacttcggagttcagact	12	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:158142883T>G	ENST00000264426.9	+	2	432	c.153T>G	c.(151-153)ttT>ttG	p.F51L	GRIA2_ENST00000393815.2_Missense_Mutation_p.F4L|GRIA2_ENST00000449365.1_Missense_Mutation_p.F4L|GRIA2_ENST00000504801.1_Intron|GRIA2_ENST00000296526.7_Missense_Mutation_p.F51L|GRIA2_ENST00000507898.1_Missense_Mutation_p.F4L	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	51					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.F51L(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TGGTTCAGTTTTCCACTTCGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	4											123	123	123					4																	158142883		2203	4300	6503	158362333	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.153T>G	4.37:g.158142883T>G	ENSP00000264426:p.Phe51Leu		158362333	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.635978	0.67130	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000509417;ENST00000296526;ENST00000264426;ENST00000506284;ENST00000505888;ENST00000449365	T;T;T;T;T;T	0.14640	2.67;2.67;2.49;2.49;2.49;2.67	5.5	3.06	0.35304	.	0.050082	0.85682	D	0.000000	T	0.15998	0.0385	L	0.33485	1.01	0.41743	D	0.989627	B;B;B	0.23377	0.084;0.083;0.018	P;B;B	0.45099	0.469;0.342;0.005	T	0.12889	-1.0530	10	0.10902	T	0.67	.	9.0158	0.36168	0.0:0.2188:0.0:0.7812	.	51;51;4	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	L	4;4;51;51;51;4;4;4	ENSP00000426845:F4L;ENSP00000377403:F4L;ENSP00000425217:F51L;ENSP00000296526:F51L;ENSP00000264426:F51L;ENSP00000389837:F4L	ENSP00000264426:F51L	F	+	3	2	GRIA2	158362333	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.559000	0.23485	0.385000	0.24970	0.454000	0.30748	TTT		0.468	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			G	158142883	T	G	158142883	3	3	61	1	0	0	0	0	1	0	0	0	6789	1838	64	4	159	4	GRIA2	4	158142883	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	371339	158142883	33011393	3562	11547										
GRIA2	2891	broad.mit.edu	37	chr4	158257022	158257022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggatggttggagaacttgTatatggggtaagtatagctc	15	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:158257022T>C	ENST00000264426.9	+	10	1745	c.1466T>C	c.(1465-1467)gTa>gCa	p.V489A	GRIA2_ENST00000393815.2_Missense_Mutation_p.V442A|GRIA2_ENST00000449365.1_Missense_Mutation_p.V442A|GRIA2_ENST00000296526.7_Missense_Mutation_p.V489A|GRIA2_ENST00000507898.1_Missense_Mutation_p.V442A	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	489					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.V489A(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGAGAACTTGTATATGGGGTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	4											143	131	135					4																	158257022		2203	4300	6503	158476472	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1466T>C	4.37:g.158257022T>C	ENSP00000264426:p.Val489Ala		158476472	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.226678	0.79576	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27	5.64	5.64	0.86602	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.87977	0.6314	M	0.76938	2.355	0.80722	D	1	P;D;D	0.67145	0.842;0.996;0.985	P;D;D	0.73708	0.506;0.957;0.981	D	0.89439	0.3722	10	0.87932	D	0	.	16.1617	0.81721	0.0:0.0:0.0:1.0	.	489;489;442	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	A	442;442;489;489;442	ENSP00000426845:V442A;ENSP00000377403:V442A;ENSP00000296526:V489A;ENSP00000264426:V489A;ENSP00000389837:V442A	ENSP00000264426:V489A	V	+	2	0	GRIA2	158476472	1.000000	0.71417	0.981000	0.43875	0.995000	0.86356	7.997000	0.88414	2.275000	0.75901	0.528000	0.53228	GTA		0.413	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158257022	T	C	158257022	3	2	61	1	0	0	0	0	1	0	0	0	6789	1638	57	4	1504	4	GRIA2	4	158257022	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	114139	158257022	32897254	3563	11548										
TMEM144	55314	broad.mit.edu	37	chr4	159165493	159165493	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtatcttcatgtttaagGaaataaaggtatgtacaaga	11	3	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:159165493G>T	ENST00000296529.6	+	12	1466	c.946G>T	c.(946-948)Gaa>Taa	p.E316*	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	316						integral component of membrane (GO:0016021)		p.E316*(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CATGTTTAAGGAAATAAAGGT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											86	89	88					4																	159165493		2203	4300	6503	159384943	SO:0001587	stop_gained	55314			AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.946G>T	4.37:g.159165493G>T	ENSP00000296529:p.Glu316*		159384943	D3DP24|Q49A05|Q9NUT3	Nonsense_Mutation	SNP	ENST00000296529.6	37	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	G	40	8.286186	0.98742	.	.	ENSG00000164124	ENST00000296529	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.8108	17.7003	0.88292	0.0:0.0:1.0:0.0	.	.	.	.	X	316	.	ENSP00000296529:E316X	E	+	1	0	TMEM144	159384943	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.109000	0.77062	2.469000	0.83416	0.585000	0.79938	GAA		0.413	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		T	159165493	G	T	159165493	4	4	61	1	0	0	0	0	0	1	0	0	16097	1175	41	2	984	2	TMEM144	4	159165493	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	908471	159165493	31988783	3564	11549										
RXFP1	59350	broad.mit.edu	37	chr4	159533502	159533502	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacattttatggactaaattCtcttattctcttgtaagtac	4	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:159533502C>A	ENST00000307765.5	+	8	919	c.668C>A	c.(667-669)tCt>tAt	p.S223Y	RXFP1_ENST00000448688.2_Missense_Mutation_p.S142Y|RXFP1_ENST00000460056.2_Missense_Mutation_p.S142Y|RXFP1_ENST00000470033.1_Missense_Mutation_p.S190Y|RXFP1_ENST00000343542.5_Missense_Mutation_p.S223Y	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	223					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.S223Y(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		GGACTAAATTCTCTTATTCTC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	58	59					4																	159533502		1786	4060	5846	159752952	SO:0001583	missense	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.668C>A	4.37:g.159533502C>A	ENSP00000303248:p.Ser223Tyr		159752952	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	37	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.877169	0.72180	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;D;T	0.85258	3.43;3.43;4.09;-1.96;3.43	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.91106	0.7200	M	0.73753	2.245	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.986;1.0;0.986;0.97;0.983;0.999;1.0;1.0;1.0	D;D;D;P;P;D;D;D;D	0.97110	0.921;0.999;0.921;0.819;0.871;0.993;0.996;1.0;1.0	D	0.91426	0.5162	10	0.72032	D	0.01	.	11.5346	0.50631	0.0:0.9161:0.0:0.0839	.	234;250;142;223;190;142;93;160;223	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q4W5D9;Q9HBX9	.;.;.;.;.;.;.;.;RXFP1_HUMAN	Y	142;223;142;223;190;93	ENSP00000423306:S142Y;ENSP00000303248:S223Y;ENSP00000414885:S142Y;ENSP00000345889:S223Y;ENSP00000420712:S190Y	ENSP00000303248:S223Y	S	+	2	0	RXFP1	159752952	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.409000	0.59768	2.624000	0.88883	0.655000	0.94253	TCT		0.274	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		A	159533502	C	A	159533502	3	1	61	1	0	0	0	0	1	0	0	0	13796	913	32	2	698	2	RXFP1	4	159533502	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	368009	159533502	31620774	3565	11550										
RXFP1	59350	broad.mit.edu	37	chr4	159549832	159549832	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcacttaaatgaaaatacTtttgcacctctccagaaact	3	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:159549832T>A	ENST00000307765.5	+	11	1121	c.870T>A	c.(868-870)acT>acA	p.T290T	RXFP1_ENST00000448688.2_Silent_p.T185T|RXFP1_ENST00000460056.2_Silent_p.T209T|RXFP1_ENST00000470033.1_Silent_p.T257T|RXFP1_ENST00000343542.5_Silent_p.T290T	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	290					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.T290T(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		ATGAAAATACTTTTGCACCTC	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	4											44	43	43					4																	159549832		1796	4048	5844	159769282	SO:0001819	synonymous_variant	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.870T>A	4.37:g.159549832T>A			159769282	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Silent	SNP	ENST00000307765.5	37	CCDS43276.1																																																																																				0.294	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		A	159549832	T	A	159549832	2	1	61	1	0	0	0	0	0	0	0	1	13796	1596	56	5		5	RXFP1	4	159549832	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	16330	159549832	31604444	3566	11551										
RXFP1	59350	broad.mit.edu	37	chr4	159568025	159568025	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaatacaataagcatgcGcagctgtggatggagagtac	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:159568025G>A	ENST00000307765.5	+	16	1679	c.1428G>A	c.(1426-1428)gcG>gcA	p.A476A	RXFP1_ENST00000448688.2_Silent_p.A371A|RXFP1_ENST00000460056.2_Silent_p.A395A|RXFP1_ENST00000470033.1_Silent_p.A443A|RXFP1_ENST00000343542.5_Silent_p.A428A	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	476					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.A476A(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		ATAAGCATGCGCAGCTGTGGA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	4											135	126	129					4																	159568025		1911	4135	6046	159787475	SO:0001819	synonymous_variant	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1428G>A	4.37:g.159568025G>A			159787475	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Silent	SNP	ENST00000307765.5	37	CCDS43276.1																																																																																				0.413	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		A	159568025	G	A	159568025	2	1	61	1	0	0	0	0	0	0	0	1	13796	1074	38	1		1	RXFP1	4	159568025	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18193	159568025	31586251	3567	11552										
C4orf45	152940	broad.mit.edu	37	chr4	159836417	159836417	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatagcccatttggaatTtctctgatcagtgtcctcga	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:159836417T>G	ENST00000434826.2	-	4	535	c.451A>C	c.(451-453)Aat>Cat	p.N151H	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	151								p.N151H(1)		large_intestine(2)|lung(3)	5						CATTTGGAATTTCTCTGATCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	90	93					4																	159836417		1900	4131	6031	160055867	SO:0001583	missense	152940				CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.451A>C	4.37:g.159836417T>G	ENSP00000412215:p.Asn151His		160055867	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	37	CCDS47156.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237271	0.39498	.	.	ENSG00000164123	ENST00000434826	T	0.15952	2.38	5.83	1.72	0.24424	.	0.357331	0.26875	N	0.022044	T	0.14270	0.0345	L	0.59436	1.845	0.18873	N	0.999987	B	0.30281	0.275	B	0.28916	0.096	T	0.15464	-1.0436	9	.	.	.	-33.7465	5.6771	0.17755	0.0:0.1709:0.1562:0.6729	.	151	Q96LM5	CD045_HUMAN	H	151	ENSP00000412215:N151H	.	N	-	1	0	C4orf45	160055867	0.074000	0.21230	0.040000	0.18447	0.148000	0.21650	-0.394000	0.07296	0.452000	0.26830	0.533000	0.62120	AAT		0.453	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543		G	159836417	T	G	159836417	3	3	61	1	0	0	0	0	1	0	0	0	2279	1841	64	4	117	4	C4orf45	4	159836417	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	268392	159836417	31317859	3568	11553										
RAPGEF2	9693	broad.mit.edu	37	chr4	160225600	160225600	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcactagtgattctgggaGcagcagtctttctgatatct	9	8	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:160225600G>T	ENST00000264431.4	+	2	586	c.167G>T	c.(166-168)aGc>aTc	p.S56I	RAPGEF2_ENST00000504604.1_3'UTR	NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	56					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.S44I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GATTCTGGGAGCAGCAGTCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											167	156	160					4																	160225600		1909	4126	6035	160445050	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.167G>T	4.37:g.160225600G>T	ENSP00000264431:p.Ser56Ile		160445050	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918149	0.92249	.	.	ENSG00000109756	ENST00000505478;ENST00000510510;ENST00000264431;ENST00000514565	T	0.50813	0.73	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.70343	0.3213	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.72121	-0.4386	10	0.87932	D	0	.	19.8097	0.96542	0.0:0.0:1.0:0.0	.	56	Q9Y4G8	RPGF2_HUMAN	I	212;54;56;37	ENSP00000264431:S56I	ENSP00000264431:S56I	S	+	2	0	RAPGEF2	160445050	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.476000	0.97823	2.685000	0.91497	0.484000	0.47621	AGC		0.408	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		T	160225600	G	T	160225600	3	4	61	1	0	0	0	0	1	0	0	0	13081	971	34	2	173	2	RAPGEF2	4	160225600	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	389183	160225600	30928676	3569	11554										
RAPGEF2	9693	broad.mit.edu	37	chr4	160251609	160251609	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccaatggaagtgggcaaaAagttattggagtggtttaat	13	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:160251609A>C	ENST00000264431.4	+	7	1362	c.943A>C	c.(943-945)Aag>Cag	p.K315Q		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	315	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.K303Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		AGTGGGCAAAAAGTTATTGGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											134	125	128					4																	160251609		1824	4079	5903	160471059	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.943A>C	4.37:g.160251609A>C	ENSP00000264431:p.Lys315Gln		160471059	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.503700	0.64298	.	.	ENSG00000109756	ENST00000264431	T	0.54479	0.57	5.78	5.78	0.91487	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.59321	0.2185	M	0.63428	1.95	0.58432	D	0.999999	B	0.32467	0.372	B	0.41894	0.369	T	0.57347	-0.7827	10	0.36615	T	0.2	.	16.3979	0.83621	1.0:0.0:0.0:0.0	.	315	Q9Y4G8	RPGF2_HUMAN	Q	315	ENSP00000264431:K315Q	ENSP00000264431:K315Q	K	+	1	0	RAPGEF2	160471059	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.256000	0.78350	2.333000	0.79357	0.533000	0.62120	AAG		0.363	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		C	160251609	A	C	160251609	3	2	61	1	0	0	0	0	1	0	0	0	13081	15	1	4	969	4	RAPGEF2	4	160251609	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	26009	160251609	30902667	3570	11555										
RAPGEF2	9693	broad.mit.edu	37	chr4	160253809	160253809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagctgaaaaagatactcGacaagactcggatcagtatc	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:160253809G>A	ENST00000264431.4	+	11	2031	c.1612G>A	c.(1612-1614)Gac>Aac	p.D538N		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	538					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.D526N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		AAAGATACTCGACAAGACTCG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											92	83	86					4																	160253809		1902	4135	6037	160473259	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.1612G>A	4.37:g.160253809G>A	ENSP00000264431:p.Asp538Asn		160473259	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.5|29.5	5.008678|5.008678	0.93346|0.93346	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000264431|ENST00000512056	T|.	0.37915|.	1.17|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Ras guanine nucleotide exchange factor, domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73745|0.73745	0.3626|0.3626	M|M	0.61703|0.61703	1.905|1.905	0.58432|0.58432	D|D	0.999999|0.999999	P|.	0.48503|.	0.911|.	B|.	0.39876|.	0.312|.	T|T	0.71580|0.71580	-0.4550|-0.4550	10|5	0.30078|.	T|.	0.28|.	.|.	19.1708|19.1708	0.93576|0.93576	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	538|.	Q9Y4G8|.	RPGF2_HUMAN|.	N|Q	538|175	ENSP00000264431:D538N|.	ENSP00000264431:D538N|.	D|R	+|+	1|2	0|0	RAPGEF2|RAPGEF2	160473259|160473259	1.000000|1.000000	0.71417|0.71417	0.963000|0.963000	0.40424|0.40424	0.997000|0.997000	0.91878|0.91878	7.901000|7.901000	0.87382|0.87382	2.602000|2.602000	0.87976|0.87976	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.368	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		A	160253809	G	A	160253809	3	1	61	1	0	0	0	0	1	0	0	0	13081	1058	37	1	1654	1	RAPGEF2	4	160253809	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2200	160253809	30900467	3571	11556										
RAPGEF2	9693	broad.mit.edu	37	chr4	160273927	160273927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccagtattgttagcaattCgtcttttgactcagtgccag	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:160273927C>T	ENST00000264431.4	+	21	3892	c.3473C>T	c.(3472-3474)tCg>tTg	p.S1158L		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1158	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.S1146L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GTTAGCAATTCGTCTTTTGAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											123	117	119					4																	160273927		1935	4134	6069	160493377	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3473C>T	4.37:g.160273927C>T	ENSP00000264431:p.Ser1158Leu		160493377	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.191721|4.191721	0.78902|0.78902	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000510253|ENST00000264431	.|T	.|0.43294	.|0.95	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B	.|0.31290	.|0.318	.|B	.|0.26969	.|0.075	T|T	0.21245|0.21245	-1.0251|-1.0251	5|10	.|0.48119	.|T	.|0.1	.|.	19.9832|19.9832	0.97338|0.97338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1158	.|Q9Y4G8	.|RPGF2_HUMAN	C|L	215|1158	.|ENSP00000264431:S1158L	.|ENSP00000264431:S1158L	R|S	+|+	1|2	0|0	RAPGEF2|RAPGEF2	160493377|160493377	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.993000|0.993000	0.82548|0.82548	5.675000|5.675000	0.68123|0.68123	2.722000|2.722000	0.93159|0.93159	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.478	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		T	160273927	C	T	160273927	3	4	61	1	0	0	0	0	1	0	0	0	13081	893	31	1	3555	1	RAPGEF2	4	160273927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20118	160273927	30880349	3572	11557										
FSTL5	56884	broad.mit.edu	37	chr4	162307588	162307588	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcttcatctttatgaaGaataaatccaaacctgaaaa	5	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:162307588G>T	ENST00000306100.5	-	16	2291	c.1855C>A	c.(1855-1857)Ctt>Att	p.L619I	FSTL5_ENST00000427802.2_Missense_Mutation_p.L609I|FSTL5_ENST00000536695.1_Missense_Mutation_p.L618I|FSTL5_ENST00000379164.4_Missense_Mutation_p.L618I|RP11-234O6.2_ENST00000508189.1_RNA	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	619						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L619I(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TCTTTATGAAGAATAAATCCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	4											26	27	27					4																	162307588		2203	4299	6502	162527038	SO:0001583	missense	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1855C>A	4.37:g.162307588G>T	ENSP00000305334:p.Leu619Ile		162527038	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.396348	0.62177	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);	0.057395	0.64402	D	0.000001	T	0.36248	0.0960	L	0.60455	1.87	0.52501	D	0.999951	B;B;P	0.35612	0.451;0.452;0.512	B;B;B	0.36567	0.137;0.228;0.15	T	0.07829	-1.0752	10	0.41790	T	0.15	.	18.9897	0.92786	0.0:0.0:1.0:0.0	.	609;618;619	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	I	619;618;609;618	ENSP00000305334:L619I;ENSP00000368462:L618I;ENSP00000389270:L609I;ENSP00000440409:L618I	ENSP00000305334:L619I	L	-	1	0	FSTL5	162527038	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	5.140000	0.64807	2.732000	0.93576	0.563000	0.77884	CTT		0.343	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162307588	G	T	162307588	3	4	61	1	0	0	0	0	1	0	0	0	6099	942	33	2	692	2	FSTL5	4	162307588	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2033661	162307588	28846688	3573	11558										
FSTL5	56884	broad.mit.edu	37	chr4	162577528	162577528	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaataatattgttccttttCcagataatgggaggtctcag	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:162577528C>T	ENST00000306100.5	-	7	1282	c.846G>A	c.(844-846)tgG>tgA	p.W282*	FSTL5_ENST00000511170.1_5'UTR|FSTL5_ENST00000427802.2_Nonsense_Mutation_p.W281*|FSTL5_ENST00000536695.1_Nonsense_Mutation_p.W281*|FSTL5_ENST00000379164.4_Nonsense_Mutation_p.W281*	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	282	Ig-like 1.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.W282*(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TGTTCCTTTTCCAGATAATGG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											63	63	63					4																	162577528		2203	4300	6503	162796978	SO:0001587	stop_gained	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.846G>A	4.37:g.162577528C>T	ENSP00000305334:p.Trp282*		162796978	E9PCP6|Q9NSW7|Q9ULF7	Nonsense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	C	41	8.774941	0.98950	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	.	.	.	5.38	4.54	0.55810	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4143	0.60959	0.0:0.9241:0.0:0.0759	.	.	.	.	X	282;281;281;281	.	ENSP00000305334:W282X	W	-	3	0	FSTL5	162796978	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.421000	0.80204	1.396000	0.46663	0.650000	0.86243	TGG		0.353	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162577528	C	T	162577528	4	4	61	1	0	0	0	0	0	1	0	0	6099	856	30	3	1737	3	FSTL5	4	162577528	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	269940	162577528	28576748	3574	11559										
FSTL5	56884	broad.mit.edu	37	chr4	162577629	162577629	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtttctgatcttctggcaGactcaactggatcacttctg	8	10	6	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:162577629G>A	ENST00000306100.5	-	7	1181	c.745C>T	c.(745-747)Ctg>Ttg	p.L249L	FSTL5_ENST00000511170.1_5'UTR|FSTL5_ENST00000427802.2_Silent_p.L248L|FSTL5_ENST00000536695.1_Silent_p.L248L|FSTL5_ENST00000379164.4_Silent_p.L248L	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	249						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L249L(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TCTTCTGGCAGACTCAACTGG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	4											91	82	85					4																	162577629		2203	4300	6503	162797079	SO:0001819	synonymous_variant	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.745C>T	4.37:g.162577629G>A			162797079	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																				0.398	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		A	162577629	G	A	162577629	2	1	61	1	0	0	0	0	0	0	0	1	6099	933	33	3		3	FSTL5	4	162577629	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101	162577629	28576647	3575	11560										
NAF1	92345	broad.mit.edu	37	chr4	164069568	164069568	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagaataatagtgagttCttcaacagaaggcagttcct	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:164069568C>A	ENST00000274054.2	-	3	752	c.559G>T	c.(559-561)Gaa>Taa	p.E187*	NAF1_ENST00000422287.2_Nonsense_Mutation_p.E187*	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	187					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E187*(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				ATAGTGAGTTCTTCAACAGAA	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											82	96	91					4																	164069568		2203	4284	6487	164289018	SO:0001587	stop_gained	92345				CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.559G>T	4.37:g.164069568C>A	ENSP00000274054:p.Glu187*		164289018	D3DP28|E9PAZ2	Nonsense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	C	38	6.990347	0.97987	.	.	ENSG00000145414	ENST00000422287;ENST00000274054	.	.	.	5.17	5.17	0.71159	.	0.220676	0.38217	N	0.001776	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-18.7615	17.6713	0.88218	0.0:1.0:0.0:0.0	.	.	.	.	X	187	.	ENSP00000274054:E187X	E	-	1	0	NAF1	164289018	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.373000	0.59537	2.424000	0.82194	0.453000	0.30009	GAA		0.289	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		A	164069568	C	A	164069568	4	1	61	1	0	0	0	0	0	1	0	0	10170	922	32	2	1090	2	NAF1	4	164069568	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1491939	164069568	27084708	3576	11561										
NPY5R	4889	broad.mit.edu	37	chr4	164271825	164271825	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaactttaattttaataTcaattgccattgtcaggtat	4	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:164271825T>A	ENST00000515560.1	+	4	1922	c.400T>A	c.(400-402)Tca>Aca	p.S134T	NPY5R_ENST00000338566.3_Missense_Mutation_p.S134T|NPY5R_ENST00000506953.1_Missense_Mutation_p.S134T			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	134					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)	p.S134T(1)|p.L130fs*9(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				AATTTTAATATCAATTGCCAT	0.363																																					Melanoma(139;1287 1774 9781 19750 25599)											2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|breast(1)	4											194	195	194					4																	164271825		2203	4300	6503	164491275	SO:0001583	missense	4889			BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.400T>A	4.37:g.164271825T>A	ENSP00000423917:p.Ser134Thr		164491275	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	37	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650132	0.47362	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.37058	1.22;1.22;1.22	5.12	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000112	T	0.32526	0.0832	L	0.46614	1.455	0.45194	D	0.998203	P	0.40083	0.702	B	0.38655	0.278	T	0.08146	-1.0736	10	0.51188	T	0.08	.	12.2055	0.54350	0.0:0.0:0.143:0.857	.	134	Q15761	NPY5R_HUMAN	T	134	ENSP00000339377:S134T;ENSP00000423917:S134T;ENSP00000423474:S134T	ENSP00000339377:S134T	S	+	1	0	NPY5R	164491275	0.999000	0.42202	0.996000	0.52242	0.996000	0.88848	3.383000	0.52471	0.859000	0.35456	0.482000	0.46254	TCA		0.363	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		A	164271825	T	A	164271825	3	1	61	1	0	0	0	0	1	0	0	0	10641	1435	50	5	402	5	NPY5R	4	164271825	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	202257	164271825	26882451	3577	11562										
TKTL2	84076	broad.mit.edu	37	chr4	164394338	164394338	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcccaagcggttcacgtcGaagaccgccacgagattgtc	11	13	1	2	rs531922468		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:164394338G>A	ENST00000280605.3	-	1	709	c.549C>T	c.(547-549)ttC>ttT	p.F183F		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	183						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.F183F(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGTTCACGTCGAAGACCGCCA	0.522													G|||	1	0.000199681	8e-04	0	5008	,	,		17947	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4											67	69	68					4																	164394338		2203	4300	6503	164613788	SO:0001819	synonymous_variant	84076			BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.549C>T	4.37:g.164394338G>A			164613788	A4FVB4|Q8NCT0|Q96M82	Silent	SNP	ENST00000280605.3	37	CCDS3805.1																																																																																				0.522	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		A	164394338	G	A	164394338	2	1	61	1	0	0	0	0	0	0	0	1	15975	1049	37	1		1	TKTL2	4	164394338	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122513	164394338	26759938	3578	11563										
MARCH1	55016	broad.mit.edu	37	chr4	164450091	164450091	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtaggccttcagcctgcGccacaactgaacatagactt	9	12	1	2	rs138184332		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:164450091G>A	ENST00000503008.1	-	8	1655	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C	MARCH1_ENST00000514618.1_Missense_Mutation_p.R483C|MARCH1_ENST00000274056.7_Missense_Mutation_p.R227C|MARCH1_ENST00000339875.5_Missense_Mutation_p.R210C|RP11-218F10.3_ENST00000609356.1_lincRNA	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase	227	Responsible for down-regulation of CD86 and MHC class II cell surface expression. {ECO:0000250}.				antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R210C(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TTCAGCCTGCGCCACAACTGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	99	92	95		679,628	5.6	1	4	dbSNP_134	95	0,8600		0,0,4300	no	missense,missense	MARCH1	NM_001166373.1,NM_017923.3	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	227/290,210/273	164450091	1,13005	2203	4300	6503	164669541	SO:0001583	missense	55016			AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.679C>T	4.37:g.164450091G>A	ENSP00000427223:p.Arg227Cys		164669541	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.626599	0.87560	2.27E-4	0.0	ENSG00000145416	ENST00000274056;ENST00000503008;ENST00000514618;ENST00000339875	T;T;T;T	0.39056	1.55;1.55;1.1;1.17	5.58	5.58	0.84498	.	0.083825	0.46442	D	0.000298	T	0.62048	0.2396	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.70487	0.899;0.969	T	0.63752	-0.6566	10	0.87932	D	0	-13.3335	14.7338	0.69402	0.0:0.0:0.8552:0.1447	.	227;210	Q8TCQ1;Q8TCQ1-2	MARH1_HUMAN;.	C	227;227;483;210	ENSP00000274056:R227C;ENSP00000427223:R227C;ENSP00000421322:R483C;ENSP00000345676:R210C	ENSP00000274056:R227C	R	-	1	0	MARCH1	164669541	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.298000	0.59067	2.789000	0.95967	0.655000	0.94253	CGC		0.438	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		A	164450091	G	A	164450091	3	1	61	1	0	0	0	0	1	0	0	0	9328	1087	38	1	194	1	MARCH1	4	164450091	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55753	164450091	26704185	3579	11564										
TRIM60	166655	broad.mit.edu	37	chr4	165962195	165962195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgatatgaaagaaaaaaacGaaacatttgttatgacccaa	7	6	0	3	rs371675727		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:165962195G>A	ENST00000512596.1	+	3	1187	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	TRIM60_ENST00000508504.1_Missense_Mutation_p.R324Q|TRIM60_ENST00000341062.5_Missense_Mutation_p.R324Q	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	324	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R324Q(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		AGAAAAAAACGAAACATTTGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											104	106	105					4																	165962195		2203	4300	6503	166181645	SO:0001583	missense	166655			AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.971G>A	4.37:g.165962195G>A	ENSP00000421142:p.Arg324Gln		166181645	Q8NA35	Missense_Mutation	SNP	ENST00000512596.1	37	CCDS3808.1	.	.	.	.	.	.	.	.	.	.	g	2.421	-0.333126	0.05278	.	.	ENSG00000176979	ENST00000512596;ENST00000508504;ENST00000341062	T;T;T	0.06687	3.27;3.27;3.27	2.49	-4.98	0.03019	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.660443	0.11343	N	0.573786	T	0.01287	0.0042	N	0.00237	-1.79	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23940	-1.0174	10	0.02654	T	1	.	6.1076	0.20081	0.3102:0.3951:0.2948:0.0	.	324	Q495X7	TRI60_HUMAN	Q	324	ENSP00000421142:R324Q;ENSP00000426496:R324Q;ENSP00000343765:R324Q	ENSP00000343765:R324Q	R	+	2	0	TRIM60	166181645	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.965000	0.03829	-2.237000	0.00712	-2.294000	0.00264	CGA		0.418	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		A	165962195	G	A	165962195	3	1	61	1	0	0	0	0	1	0	0	0	16575	1058	37	1	973	1	TRIM60	4	165962195	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1512104	165962195	25192081	3580	11565										
TRIM60	166655	broad.mit.edu	37	chr4	165962580	165962580	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagccgtttggccttatttCtatactggaacagattccga	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:165962580C>A	ENST00000512596.1	+	3	1572	c.1356C>A	c.(1354-1356)ttC>ttA	p.F452L	TRIM60_ENST00000508504.1_Missense_Mutation_p.F452L|TRIM60_ENST00000341062.5_Missense_Mutation_p.F452L	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	452	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.F452L(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		GGCCTTATTTCTATACTGGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	58	57					4																	165962580		2201	4298	6499	166182030	SO:0001583	missense	166655			AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.1356C>A	4.37:g.165962580C>A	ENSP00000421142:p.Phe452Leu		166182030	Q8NA35	Missense_Mutation	SNP	ENST00000512596.1	37	CCDS3808.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697801	0.68386	.	.	ENSG00000176979	ENST00000512596;ENST00000508504;ENST00000341062	T;T;T	0.75938	-0.98;-0.98;-0.98	2.33	2.33	0.28932	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.43416	U	0.000576	D	0.82793	0.5114	M	0.72894	2.215	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72043	-0.4409	10	0.72032	D	0.01	.	10.7484	0.46194	0.0:1.0:0.0:0.0	.	452	Q495X7	TRI60_HUMAN	L	452	ENSP00000421142:F452L;ENSP00000426496:F452L;ENSP00000343765:F452L	ENSP00000343765:F452L	F	+	3	2	TRIM60	166182030	0.724000	0.28038	0.345000	0.25642	0.821000	0.46438	0.086000	0.14935	1.598000	0.50083	0.655000	0.94253	TTC		0.353	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		A	165962580	C	A	165962580	3	1	61	1	0	0	0	0	1	0	0	0	16575	912	32	2	1358	2	TRIM60	4	165962580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385	165962580	25191696	3581	11566										
KLHL2	11275	broad.mit.edu	37	chr4	166141201	166141201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctttcaaagtcatgaacGaattaagaaggtatcattat	7	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:166141201G>A	ENST00000226725.6	+	2	401	c.142G>A	c.(142-144)Gaa>Aaa	p.E48K	KLHL2_ENST00000538127.1_5'UTR|KLHL2_ENST00000421009.2_5'UTR|KLHL2_ENST00000514860.1_Missense_Mutation_p.E52K	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	48					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.E48K(1)		endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	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)		AGTCATGAACGAATTAAGAAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	4											33	32	33					4																	166141201		2201	4281	6482	166360651	SO:0001583	missense	11275			AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"Kelch-like", "BTB/POZ domain containing"	6353	protein-coding gene	gene with protein product	"mayven"	605774	"kelch (Drosophila)-like 2 (Mayven)", "kelch-like 2, Mayven (Drosophila)"			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.142G>A	4.37:g.166141201G>A	ENSP00000226725:p.Glu48Lys		166360651	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653820	0.47362	.	.	ENSG00000109466	ENST00000226725;ENST00000511305;ENST00000509704;ENST00000514860	T;D;T;T	0.90788	-0.34;-2.73;-0.34;-0.34	5.53	5.53	0.82687	BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.89715	0.6795	L	0.48935	1.535	0.80722	D	1	P;P	0.51147	0.942;0.942	P;P	0.46172	0.506;0.506	D	0.87318	0.2316	10	0.24483	T	0.36	.	19.8183	0.96579	0.0:0.0:1.0:0.0	.	52;48	B4DFH7;O95198	.;KLHL2_HUMAN	K	48;48;10;52	ENSP00000226725:E48K;ENSP00000422113:E48K;ENSP00000421324:E10K;ENSP00000424198:E52K	ENSP00000226725:E48K	E	+	1	0	KLHL2	166360651	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	9.246000	0.95438	2.761000	0.94854	0.650000	0.86243	GAA		0.353	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			A	166141201	G	A	166141201	3	1	61	1	0	0	0	0	1	0	0	0	8395	1059	37	1	190	1	KLHL2	4	166141201	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178621	166141201	25013075	3582	11567										
SC4MOL	6307	broad.mit.edu	37	chr4	166254711	166254711	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcatgaagccctttatttCttattctgtttacctggatt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:166254711C>A	ENST00000261507.6	+	2	362	c.189C>A	c.(187-189)ttC>ttA	p.F63L	MSMO1_ENST00000504317.1_Missense_Mutation_p.F63L|MSMO1_ENST00000393766.2_Intron	NM_006745.4	NP_006736.1	Q15800	MSMO1_HUMAN	methylsterol monooxygenase 1	63					cholesterol biosynthetic process (GO:0006695)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-4 methylsterol oxidase activity (GO:0000254)|iron ion binding (GO:0005506)	p.F63L(1)									CCCTTTATTTCTTATTCTGTT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	94	93					4																	166254711		2203	4298	6501	166474161	SO:0001583	missense	6307			U93162	CCDS3809.1, CCDS43280.1	4q32-q34	2013-03-04	2011-09-01	2011-09-01	ENSG00000052802	ENSG00000052802	1.14.13.72	"Fatty acid hydroxylase domain containing"	10545	protein-coding gene	gene with protein product		607545	"sterol-C4-methyl oxidase-like"	SC4MOL		8663358	Standard	NM_006745		Approved	DESP4, ERG25	uc003ire.3	Q15800	OTTHUMG00000161126	ENST00000261507.6:c.189C>A	4.37:g.166254711C>A	ENSP00000261507:p.Phe63Leu		166474161	A8K8Q3|A8MYF6|D3DP32|Q32Q24	Missense_Mutation	SNP	ENST00000261507.6	37	CCDS3809.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.186492	0.38609	.	.	ENSG00000052802	ENST00000261507;ENST00000507013;ENST00000504317;ENST00000505270	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	5.58	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.58278	0.2111	M	0.90145	3.09	0.80722	D	1	B;B	0.12013	0.005;0.003	B;B	0.15484	0.013;0.003	T	0.57435	-0.7812	10	0.46703	T	0.11	-18.31	10.0691	0.42322	0.0:0.7285:0.0:0.2715	.	63;63	D6R952;Q15800	.;MSMO1_HUMAN	L	63	ENSP00000261507:F63L;ENSP00000425241:F63L;ENSP00000423633:F63L;ENSP00000425112:F63L	ENSP00000261507:F63L	F	+	3	2	SC4MOL	166474161	1.000000	0.71417	0.968000	0.41197	0.790000	0.44656	1.956000	0.40382	0.718000	0.32166	0.561000	0.74099	TTC		0.279	MSMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363880.1	NM_006745		A	166254711	C	A	166254711	3	1	61	1	0	0	0	0	1	0	0	0	13902	912	32	2	191	2	SC4MOL	4	166254711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113510	166254711	24899565	3583	11568										
CPE	1363	broad.mit.edu	37	chr4	166405684	166405684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccaatcggccaccatgtCgcaagaatgatgatgacagc	9	13	0	4	rs138641684		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:166405684C>T	ENST00000402744.4	+	5	1181	c.901C>T	c.(901-903)Cgc>Tgc	p.R301C		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	301					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)	p.R301C(1)		endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GCCACCATGTCGCAAGAATGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	4						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	312	298	303		901	5.7	1	4	dbSNP_134	303	0,8600		0,0,4300	no	missense	CPE	NM_001873.2	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	301/477	166405684	1,13005	2203	4300	6503	166625134	SO:0001583	missense	1363			X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"carboxypeptidase H", "enkephalin convertase", "insulin granule-associated carboxypeptidase", "cobalt-stimulated chromaffin granule carboxypeptidase"	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.901C>T	4.37:g.166405684C>T	ENSP00000386104:p.Arg301Cys		166625134	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	37	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470956	0.63625	2.27E-4	0.0	ENSG00000109472	ENST00000402744;ENST00000261510	T	0.21932	1.98	5.67	5.67	0.87782	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.44623	0.1302	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.68039	0.955	T	0.08743	-1.0707	10	0.48119	T	0.1	-21.6932	20.1284	0.97992	0.0:1.0:0.0:0.0	.	301	P16870	CBPE_HUMAN	C	301;265	ENSP00000386104:R301C	ENSP00000261510:R265C	R	+	1	0	CPE	166625134	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	7.228000	0.78079	2.829000	0.97493	0.650000	0.86243	CGC		0.522	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873		T	166405684	C	T	166405684	3	4	61	1	0	0	0	0	1	0	0	0	3805	884	31	1	919	1	CPE	4	166405684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150973	166405684	24748592	3584	11569										
TLL1	7092	broad.mit.edu	37	chr4	166929162	166929162	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggagaaagatatgatttCgacagtatcatgcactatgc	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:166929162C>T	ENST00000061240.2	+	7	1526	c.879C>T	c.(877-879)ttC>ttT	p.F293F	TLL1_ENST00000513213.1_Silent_p.F293F|TLL1_ENST00000507499.1_Silent_p.F293F	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	293	Metalloprotease. {ECO:0000250}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.F293F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GATATGATTTCGACAGTATCA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	4											134	124	127					4																	166929162		2203	4300	6503	167148612	SO:0001819	synonymous_variant	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.879C>T	4.37:g.166929162C>T			167148612	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																				0.413	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	166929162	C	T	166929162	2	4	61	1	0	0	0	0	0	0	0	1	15984	883	31	1		1	TLL1	4	166929162	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	523478	166929162	24225114	3585	11570										
TLL1	7092	broad.mit.edu	37	chr4	166960510	166960510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgttttaaattttacaaCgatggatctatacaagagta	7	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:166960510C>T	ENST00000061240.2	+	10	1825	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	TLL1_ENST00000507499.1_Missense_Mutation_p.T393M	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	393	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T393M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AATTTTACAACGATGGATCTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	4											118	116	117					4																	166960510		2203	4300	6503	167179960	SO:0001583	missense	7092			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1178C>T	4.37:g.166960510C>T	ENSP00000061240:p.Thr393Met		167179960	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	37	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180692	0.57800	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.18657	2.2;2.2	5.62	5.62	0.85841	CUB (5);	0.000000	0.85682	U	0.000000	T	0.43299	0.1241	L	0.45470	1.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	T	0.17048	-1.0382	10	0.62326	D	0.03	.	19.6679	0.95900	0.0:1.0:0.0:0.0	.	393;393	E9PD25;O43897	.;TLL1_HUMAN	M	393	ENSP00000061240:T393M;ENSP00000426082:T393M	ENSP00000061240:T393M	T	+	2	0	TLL1	167179960	1.000000	0.71417	0.776000	0.31678	0.053000	0.15095	7.758000	0.85224	2.650000	0.89964	0.563000	0.77884	ACG		0.363	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	166960510	C	T	166960510	3	4	61	1	0	0	0	0	1	0	0	0	15984	536	19	1	1216	1	TLL1	4	166960510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31348	166960510	24193766	3586	11571										
SPOCK3	50859	broad.mit.edu	37	chr4	167656218	167656218	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatcgccactagcaaaatCtccggagatctcaaaatcta	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:167656218C>A	ENST00000357154.3	-	12	1302	c.1165G>T	c.(1165-1167)Gat>Tat	p.D389Y	SPOCK3_ENST00000504953.1_Missense_Mutation_p.D386Y|SPOCK3_ENST00000502330.1_Missense_Mutation_p.D389Y|SPOCK3_ENST00000421836.2_Missense_Mutation_p.D338Y|SPOCK3_ENST00000512681.1_Missense_Mutation_p.D291Y|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Missense_Mutation_p.D386Y|SPOCK3_ENST00000534949.1_Missense_Mutation_p.D293Y|SPOCK3_ENST00000510741.1_Missense_Mutation_p.D346Y|SPOCK3_ENST00000506886.1_Missense_Mutation_p.D389Y|SPOCK3_ENST00000535728.1_Missense_Mutation_p.D257Y|SPOCK3_ENST00000511269.1_Missense_Mutation_p.D386Y|SPOCK3_ENST00000541637.1_Missense_Mutation_p.D291Y|SPOCK3_ENST00000541354.1_Missense_Mutation_p.D269Y|SPOCK3_ENST00000511531.1_Missense_Mutation_p.D389Y	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	389					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)	p.D386Y(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		ctagcaaaatcTCCGGAGATC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											114	112	113					4																	167656218		2203	4300	6503	167892793	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1165G>T	4.37:g.167656218C>A	ENSP00000349677:p.Asp389Tyr		167892793	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500644	0.64298	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.49720	1.32;1.32;1.32;1.32;1.32;1.32;1.38;1.26;0.77;1.32;1.37;1.13;0.77;1.03	5.11	5.11	0.69529	.	0.052780	0.85682	D	0.000000	T	0.71013	0.3290	M	0.77486	2.375	0.58432	D	0.999995	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;1.0;1.0;0.998;0.997;0.999;0.997	T	0.75031	-0.3461	10	0.87932	D	0	-2.9254	18.5633	0.91108	0.0:1.0:0.0:0.0	.	291;293;338;398;346;386;389	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	Y	389;386;386;389;389;389;346;269;291;386;257;338;291;293	ENSP00000349677:D389Y;ENSP00000350153:D386Y;ENSP00000425570:D386Y;ENSP00000420920:D389Y;ENSP00000423421:D389Y;ENSP00000423606:D389Y;ENSP00000426716:D346Y;ENSP00000444789:D269Y;ENSP00000426318:D291Y;ENSP00000425502:D386Y;ENSP00000441396:D257Y;ENSP00000411344:D338Y;ENSP00000445430:D291Y;ENSP00000438142:D293Y	ENSP00000349677:D389Y	D	-	1	0	SPOCK3	167892793	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.206000	0.65192	2.557000	0.86248	0.632000	0.83419	GAT		0.318	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			A	167656218	C	A	167656218	3	1	61	1	0	0	0	0	1	0	0	0	15120	913	32	2	149	2	SPOCK3	4	167656218	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	695708	167656218	23498058	3587	11572										
SPOCK3	50859	broad.mit.edu	37	chr4	167833783	167833783	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctttacctgaaaagagtaGgtatgaccatctgaaccaca	8	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:167833783G>T	ENST00000357154.3	-	6	608	c.471C>A	c.(469-471)acC>acA	p.T157T	SPOCK3_ENST00000504953.1_Silent_p.T154T|SPOCK3_ENST00000502330.1_Silent_p.T157T|SPOCK3_ENST00000512648.1_Silent_p.T154T|SPOCK3_ENST00000421836.2_Silent_p.T106T|SPOCK3_ENST00000512681.1_Intron|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Silent_p.T154T|SPOCK3_ENST00000534949.1_Silent_p.T61T|SPOCK3_ENST00000510741.1_Silent_p.T154T|SPOCK3_ENST00000506886.1_Silent_p.T157T|SPOCK3_ENST00000535728.1_Silent_p.T65T|SPOCK3_ENST00000511269.1_Silent_p.T154T|SPOCK3_ENST00000541637.1_Intron|SPOCK3_ENST00000541354.1_Silent_p.T37T|SPOCK3_ENST00000511531.1_Silent_p.T157T	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	157	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)	p.T154T(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		GAAAAGAGTAGGTATGACCAT	0.423																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	4											114	110	112					4																	167833783		2203	4300	6503	168070358	SO:0001819	synonymous_variant	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.471C>A	4.37:g.167833783G>T			168070358	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																				0.423	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			T	167833783	G	T	167833783	2	4	61	1	0	0	0	0	0	0	0	1	15120	987	35	2		2	SPOCK3	4	167833783	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	177565	167833783	23320493	3588	11573										
DDX60	55601	broad.mit.edu	37	chr4	169158486	169158486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagtccatttacaagaaaActgacaaaaacaagattaga	6	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169158486A>G	ENST00000393743.3	-	32	4653	c.4362T>C	c.(4360-4362)agT>agC	p.S1454S		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1454					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.S1454S(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TTACAAGAAAACTGACAAAAA	0.358																																																2	Substitution - coding silent(2)	large_intestine(2)	4											52	50	50					4																	169158486		2203	4299	6502	169395061	SO:0001819	synonymous_variant	55601			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.4362T>C	4.37:g.169158486A>G			169395061	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																				0.358	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		G	169158486	A	G	169158486	2	3	61	1	0	0	0	0	0	0	0	1	4384	40	2	4		4	DDX60	4	169158486	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1324703	169158486	21995790	3589	11574										
DDX60	55601	broad.mit.edu	37	chr4	169172230	169172230	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaccttttctttcaaattTtactcgaccaaataccttct	1	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169172230T>G	ENST00000393743.3	-	28	4024	c.3733A>C	c.(3733-3735)Aaa>Caa	p.K1245Q	DDX60_ENST00000505393.1_5'Flank	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1245	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.K1245Q(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		CTTTCAAATTTTACTCGACCA	0.289																																																2	Substitution - Missense(2)	large_intestine(2)	4											105	109	108					4																	169172230		2201	4300	6501	169408805	SO:0001583	missense	55601			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.3733A>C	4.37:g.169172230T>G	ENSP00000377344:p.Lys1245Gln		169408805	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.532512	0.27387	.	.	ENSG00000137628	ENST00000393743	T	0.44482	0.92	5.12	3.91	0.45181	Helicase, C-terminal (1);	0.364791	0.26432	N	0.024413	T	0.33933	0.0880	L	0.45228	1.405	0.09310	N	1	B	0.26002	0.139	B	0.23275	0.045	T	0.19451	-1.0305	10	0.41790	T	0.15	.	10.9316	0.47222	0.1407:0.0:0.0:0.8593	.	1245	Q8IY21	DDX60_HUMAN	Q	1245	ENSP00000377344:K1245Q	ENSP00000377344:K1245Q	K	-	1	0	DDX60	169408805	0.038000	0.19896	0.001000	0.08648	0.027000	0.11550	2.625000	0.46452	0.771000	0.33359	0.383000	0.25322	AAA		0.289	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		G	169172230	T	G	169172230	3	3	61	1	0	0	0	0	1	0	0	0	4384	1850	64	4	1449	4	DDX60	4	169172230	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	13744	169172230	21982046	3590	11575										
DDX60	55601	broad.mit.edu	37	chr4	169176904	169176904	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttttaacttttcgaagtTtgttagccatgacatgggct	8	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169176904T>G	ENST00000393743.3	-	26	3806	c.3515A>C	c.(3514-3516)aAa>aCa	p.K1172T	DDX60_ENST00000505393.1_5'UTR	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1172					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.K1172T(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TTTTCGAAGTTTGTTAGCCAT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	4											118	116	117					4																	169176904		2202	4298	6500	169413479	SO:0001583	missense	55601			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.3515A>C	4.37:g.169176904T>G	ENSP00000377344:p.Lys1172Thr		169413479	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	t	12.84	2.059559	0.36373	.	.	ENSG00000137628	ENST00000393743;ENST00000537338	T	0.42900	0.96	4.94	3.77	0.43336	.	0.234286	0.30126	N	0.010355	T	0.41534	0.1163	M	0.72894	2.215	0.33329	D	0.568383	D	0.56287	0.975	P	0.44477	0.451	T	0.55471	-0.8136	10	0.26408	T	0.33	.	8.8439	0.35159	0.0:0.0861:0.0:0.9139	.	1172	Q8IY21	DDX60_HUMAN	T	1172;264	ENSP00000377344:K1172T	ENSP00000377344:K1172T	K	-	2	0	DDX60	169413479	0.994000	0.37717	0.903000	0.35520	0.356000	0.29392	0.677000	0.25262	0.918000	0.36919	0.378000	0.23410	AAA		0.368	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		G	169176904	T	G	169176904	3	3	61	1	0	0	0	0	1	0	0	0	4384	1841	64	4	1675	4	DDX60	4	169176904	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4674	169176904	21977372	3591	11576										
DDX60	55601	broad.mit.edu	37	chr4	169201497	169201497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacataccttcttcacttCggcaatgttctttccaggct	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169201497C>T	ENST00000393743.3	-	14	2258	c.1967G>A	c.(1966-1968)cGa>cAa	p.R656Q		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	656					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.R656Q(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TTCTTCACTTCGGCAATGTTC	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	4											84	78	80					4																	169201497		2202	4300	6502	169438072	SO:0001583	missense	55601			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.1967G>A	4.37:g.169201497C>T	ENSP00000377344:p.Arg656Gln		169438072	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	9.759	1.169466	0.21621	.	.	ENSG00000137628	ENST00000393743	T	0.18338	2.22	5.48	-8.31	0.01001	.	1.565850	0.03683	N	0.245871	T	0.08223	0.0205	N	0.04355	-0.22	0.09310	N	1	B	0.22346	0.068	B	0.12156	0.007	T	0.21484	-1.0244	10	0.36615	T	0.2	.	14.5318	0.67931	0.1068:0.751:0.0:0.1422	.	656	Q8IY21	DDX60_HUMAN	Q	656	ENSP00000377344:R656Q	ENSP00000377344:R656Q	R	-	2	0	DDX60	169438072	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.504000	0.00449	-1.654000	0.01499	0.563000	0.77884	CGA		0.363	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169201497	C	T	169201497	3	4	61	1	0	0	0	0	1	0	0	0	4384	884	31	1	3271	1	DDX60	4	169201497	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24593	169201497	21952779	3592	11577										
DDX60	55601	broad.mit.edu	37	chr4	169227682	169227682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagctgtgtttgtagatCgttcaggccttcgtctgcaa	11	8	2	1	rs545288798		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169227682C>T	ENST00000393743.3	-	5	745	c.454G>A	c.(454-456)Gat>Aat	p.D152N		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	152					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.D152N(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		GTTTGTAGATCGTTCAGGCCT	0.408													C|||	1	0.000199681	8e-04	0	5008	,	,		18139	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	4											102	106	105					4																	169227682		2203	4300	6503	169464257	SO:0001583	missense	55601			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.454G>A	4.37:g.169227682C>T	ENSP00000377344:p.Asp152Asn		169464257	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	3.788	-0.044330	0.07452	.	.	ENSG00000137628	ENST00000393743	T	0.19394	2.15	5.11	-6.05	0.02172	.	0.934725	0.08910	N	0.875946	T	0.11324	0.0276	L	0.31752	0.955	0.09310	N	1	B	0.15141	0.012	B	0.08055	0.003	T	0.33929	-0.9849	10	0.23302	T	0.38	.	7.1343	0.25519	0.0614:0.4703:0.1578:0.3105	.	152	Q8IY21	DDX60_HUMAN	N	152	ENSP00000377344:D152N	ENSP00000377344:D152N	D	-	1	0	DDX60	169464257	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-2.450000	0.01007	-1.152000	0.02832	0.563000	0.77884	GAT		0.408	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169227682	C	T	169227682	3	4	61	1	0	0	0	0	1	0	0	0	4384	884	31	1	4820	1	DDX60	4	169227682	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26185	169227682	21926594	3593	11578										
DDX60L	91351	broad.mit.edu	37	chr4	169294925	169294925	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctcatcaagtgagacacGagttgggagtcttcacattc	10	10	4	1	rs573671869	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169294925G>A	ENST00000511577.1	-	35	4915	c.4668C>T	c.(4666-4668)ctC>ctT	p.L1556L	DDX60L_ENST00000260184.7_Silent_p.L1556L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1556							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.L1557L(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AGTGAGACACGAGTTGGGAGT	0.408													G|||	2	0.000399361	0	0	5008	,	,		21368	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	4											159	160	160					4																	169294925		2190	4300	6490	169531500	SO:0001819	synonymous_variant	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4668C>T	4.37:g.169294925G>A			169531500	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																					0.408	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169294925	G	A	169294925	2	1	61	1	0	0	0	0	0	0	0	1	4385	1045	37	1		1	DDX60L	4	169294925	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67243	169294925	21859351	3594	11579										
DDX60L	91351	broad.mit.edu	37	chr4	169300925	169300925	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagtaaagtttcaaagtCtccatggctcttcgtctctt	6	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169300925C>T	ENST00000511577.1	-	31	4420	c.4173G>A	c.(4171-4173)gaG>gaA	p.E1391E	DDX60L_ENST00000260184.7_Silent_p.E1391E			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1391							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.E1392E(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GTTTCAAAGTCTCCATGGCTC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	4											81	79	80					4																	169300925		1861	4101	5962	169537500	SO:0001819	synonymous_variant	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4173G>A	4.37:g.169300925C>T			169537500	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																					0.348	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169300925	C	T	169300925	2	4	61	1	0	0	0	0	0	0	0	1	4385	912	32	3		3	DDX60L	4	169300925	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6000	169300925	21853351	3595	11580										
DDX60L	91351	broad.mit.edu	37	chr4	169317115	169317115	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctctgacgtactgagtCtttattcctggtaatttcag	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169317115C>A	ENST00000511577.1	-	27	3899	c.3652G>T	c.(3652-3654)Gac>Tac	p.D1218Y	DDX60L_ENST00000260184.7_Missense_Mutation_p.D1218Y|DDX60L_ENST00000505890.1_Missense_Mutation_p.D1219Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1218	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.D1219Y(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CGTACTGAGTCTTTATTCCTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											97	87	90					4																	169317115		1816	4068	5884	169553690	SO:0001583	missense	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3652G>T	4.37:g.169317115C>A	ENSP00000422423:p.Asp1218Tyr		169553690	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.065|5.065	0.197618|0.197618	0.09652|0.09652	.|.	.|.	ENSG00000181381|ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890|ENST00000514580	T;T;T|.	0.71698|.	-0.59;-0.59;0.93|.	1.7|1.7	1.7|1.7	0.24286|0.24286	Helicase, C-terminal (1);|.	.|.	.|.	.|.	.|.	T|T	0.24353|0.24353	0.0590|0.0590	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B;B;B|.	0.17465|.	0.004;0.022;0.004|.	B;B;B|.	0.25140|.	0.0;0.058;0.0|.	T|T	0.20405|0.20405	-1.0276|-1.0276	9|5	0.37606|.	T|.	0.19|.	.|.	6.827|6.827	0.23889|0.23889	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1218;1219;1218|.	E9PAP8;D6R906;Q5H9U9|.	.;.;DDX6L_HUMAN|.	Y|I	1218;1218;1219|105	ENSP00000260184:D1218Y;ENSP00000422423:D1218Y;ENSP00000422202:D1219Y|.	ENSP00000260184:D1218Y|.	D|R	-|-	1|2	0|0	DDX60L|DDX60L	169553690|169553690	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.002000|0.002000	0.02628|0.02628	0.408000|0.408000	0.21065|0.21065	1.230000|1.230000	0.43646|0.43646	0.313000|0.313000	0.20887|0.20887	GAC|AGA		0.333	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169317115	C	A	169317115	3	1	61	1	0	0	0	0	1	0	0	0	4385	913	32	2	1516	2	DDX60L	4	169317115	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16190	169317115	21837161	3596	11581										
DDX60L	91351	broad.mit.edu	37	chr4	169336825	169336825	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaagtctaacttcatatGattgatttttatatgaatgg	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169336825G>T	ENST00000511577.1	-	21	3099	c.2852C>A	c.(2851-2853)tCa>tAa	p.S951*	DDX60L_ENST00000260184.7_Nonsense_Mutation_p.S951*|DDX60L_ENST00000505890.1_Nonsense_Mutation_p.S951*			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	951							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.S951*(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AACTTCATATGATTGATTTTT	0.274																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											66	56	59					4																	169336825		1784	4061	5845	169573400	SO:0001587	stop_gained	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2852C>A	4.37:g.169336825G>T	ENSP00000422423:p.Ser951*		169573400	Q96ND6	Nonsense_Mutation	SNP	ENST00000511577.1	37		.	.	.	.	.	.	.	.	.	.	G	41	8.839528	0.98974	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	.	.	.	3.23	3.23	0.37069	.	0.000000	0.32386	U	0.006179	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3214	0.60434	0.0:0.0:1.0:0.0	.	.	.	.	X	951;951;951;647	.	ENSP00000260184:S951X	S	-	2	0	DDX60L	169573400	0.994000	0.37717	0.224000	0.23877	0.546000	0.35178	3.728000	0.54991	1.481000	0.48307	0.313000	0.20887	TCA		0.274	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169336825	G	T	169336825	4	4	61	1	0	0	0	0	0	1	0	0	4385	1294	45	2	2340	2	DDX60L	4	169336825	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19710	169336825	21817451	3597	11582										
DDX60L	91351	broad.mit.edu	37	chr4	169340492	169340492	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatcctttccacccatttTtggcgatgaggagcaagcaa	9	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169340492T>G	ENST00000511577.1	-	19	2818	c.2571A>C	c.(2569-2571)caA>caC	p.Q857H	DDX60L_ENST00000260184.7_Missense_Mutation_p.Q857H|DDX60L_ENST00000505890.1_Missense_Mutation_p.Q857H			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	857	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.Q857H(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CCACCCATTTTTGGCGATGAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											58	58	58					4																	169340492		2195	4300	6495	169577067	SO:0001583	missense	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2571A>C	4.37:g.169340492T>G	ENSP00000422423:p.Gln857His		169577067	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		.	.	.	.	.	.	.	.	.	.	T	16.87	3.241300	0.58995	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890	T;T;T	0.15139	2.45;2.45;2.45	3.49	-0.914	0.10497	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.36740	U	0.002425	T	0.31040	0.0784	L	0.58101	1.795	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.08106	-1.0738	10	0.49607	T	0.09	.	9.5369	0.39229	0.0:0.521:0.0:0.479	.	857;857	D6R906;Q5H9U9	.;DDX6L_HUMAN	H	857	ENSP00000260184:Q857H;ENSP00000422423:Q857H;ENSP00000422202:Q857H	ENSP00000260184:Q857H	Q	-	3	2	DDX60L	169577067	0.683000	0.27633	0.001000	0.08648	0.700000	0.40528	0.824000	0.27379	-0.397000	0.07691	-0.456000	0.05471	CAA		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		G	169340492	T	G	169340492	3	3	61	1	0	0	0	0	1	0	0	0	4385	1838	64	4	2629	4	DDX60L	4	169340492	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3667	169340492	21813784	3598	11583										
PALLD	23022	broad.mit.edu	37	chr4	169633002	169633002	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcaaagctaacagtaataAatctcttccaacaccagctg	6	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169633002A>C	ENST00000505667.1	+	10	2065	c.1892A>C	c.(1891-1893)aAa>aCa	p.K631T	PALLD_ENST00000335742.7_Missense_Mutation_p.K249T|PALLD_ENST00000512127.1_Missense_Mutation_p.K249T|PALLD_ENST00000261509.6_Missense_Mutation_p.K631T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	631					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)	p.K631T(1)|p.K249T(1)		breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AACAGTAATAAATCTCTTCCA	0.458									Pancreatic Cancer, Familial Clustering of																												Esophageal Squamous(109;1482 1532 18347 40239 51172)											2	Substitution - Missense(2)	large_intestine(2)	4											82	83	83					4																	169633002		2203	4300	6503	169869577	SO:0001583	missense	23022	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.1892A>C	4.37:g.169633002A>C	ENSP00000425556:p.Lys631Thr		169869577	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	A	2.481	-0.319693	0.05386	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127	T;T;T;T	0.64085	-0.08;-0.08;0.21;-0.02	5.81	1.83	0.25207	.	0.000000	0.33980	U	0.004364	T	0.43545	0.1252	L	0.45581	1.43	0.09310	N	1	B;B;B	0.10296	0.003;0.0;0.002	B;B;B	0.10450	0.005;0.0;0.005	T	0.17107	-1.0380	10	0.14252	T	0.57	.	0.894	0.01260	0.4764:0.1298:0.1444:0.2494	.	631;249;631	B7ZMM5;B3KTG2;B2RTX2	.;.;.	T	631;249;631;249	ENSP00000261509:K631T;ENSP00000336735:K249T;ENSP00000425556:K631T;ENSP00000426947:K249T	ENSP00000261509:K631T	K	+	2	0	PALLD	169869577	0.556000	0.26538	0.008000	0.14137	0.001000	0.01503	0.951000	0.29135	0.083000	0.17047	-0.408000	0.06270	AAA		0.458	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		C	169633002	A	C	169633002	3	2	61	1	0	0	0	0	1	0	0	0	11438	14	1	4	1926	4	PALLD	4	169633002	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	292510	169633002	21521274	3599	11584										
PALLD	23022	broad.mit.edu	37	chr4	169812173	169812173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacctggaacgaaaacttCgcttcaaggaggacctcctg	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:169812173C>T	ENST00000505667.1	+	11	2238	c.2065C>T	c.(2065-2067)Cgc>Tgc	p.R689C	PALLD_ENST00000335742.7_Missense_Mutation_p.R531C|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000507735.1_Missense_Mutation_p.R202C|PALLD_ENST00000512127.1_Missense_Mutation_p.R307C|PALLD_ENST00000261509.6_Missense_Mutation_p.R689C			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	913	Interaction with ARGBP2, SPIN90 and SRC.|Pro-rich.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)	p.R689C(1)|p.R531C(1)		breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		ACGAAAACTTCGCTTCAAGGA	0.463									Pancreatic Cancer, Familial Clustering of																												Esophageal Squamous(109;1482 1532 18347 40239 51172)											2	Substitution - Missense(2)	large_intestine(2)	4											85	82	83					4																	169812173		2203	4300	6503	170048748	SO:0001583	missense	23022	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2065C>T	4.37:g.169812173C>T	ENSP00000425556:p.Arg689Cys		170048748	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	C	31	5.091572	0.94149	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000507735	T;T;T;T;T	0.67345	-0.26;-0.25;-0.16;-0.22;0.14	5.2	5.2	0.72013	.	0.000000	0.32655	U	0.005813	T	0.81945	0.4930	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.996;0.994;0.997	T	0.81799	-0.0767	10	0.42905	T	0.14	.	18.728	0.91722	0.0:1.0:0.0:0.0	.	689;913;307;689	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	C	689;531;689;307;202	ENSP00000261509:R689C;ENSP00000336735:R531C;ENSP00000425556:R689C;ENSP00000426947:R307C;ENSP00000424016:R202C	ENSP00000261509:R689C	R	+	1	0	PALLD	170048748	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.703000	0.84585	2.423000	0.82170	0.591000	0.81541	CGC		0.463	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		T	169812173	C	T	169812173	3	4	61	1	0	0	0	0	1	0	0	0	11438	884	31	1	2610	1	PALLD	4	169812173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179171	169812173	21342103	3600	11585										
SH3RF1	57630	broad.mit.edu	37	chr4	170038875	170038875	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaccatggtcactccccGacttgtctggccagctgtag	10	14	2	1	rs368721358		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:170038875G>A	ENST00000284637.9	-	9	1917	c.1576C>T	c.(1576-1578)Cgg>Tgg	p.R526W	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	526	Interaction with AKT2. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R526W(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		GTCACTCCCCGACTTGTCTGG	0.582													G|||	1	0.000199681	0	0.0014	5008	,	,		16108	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						G	TRP/ARG	0,4406		0,0,2203	51	49	49		1576	3	0.1	4		49	2,8598	2.2+/-6.3	0,2,4298	no	missense	SH3RF1	NM_020870.3	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	526/889	170038875	2,13004	2203	4300	6503	170275450	SO:0001583	missense	57630			BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"RING-type (C3HC4) zinc fingers"	17650	protein-coding gene	gene with protein product	"plenty of SH3 domains"		"SH3 multiple domains 2"	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1576C>T	4.37:g.170038875G>A	ENSP00000284637:p.Arg526Trp		170275450	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	37	CCDS34099.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692727	0.48202	0.0	2.33E-4	ENSG00000154447	ENST00000284637	T	0.13657	2.57	5.72	3.01	0.34805	Src homology-3 domain (1);	0.169330	0.51477	D	0.000084	T	0.17492	0.0420	L	0.50333	1.59	0.40447	D	0.980106	D	0.61697	0.99	P	0.48952	0.596	T	0.01301	-1.1391	10	0.72032	D	0.01	-9.8535	8.6039	0.33762	0.067:0.0:0.5424:0.3905	.	526	Q7Z6J0	SH3R1_HUMAN	W	526	ENSP00000284637:R526W	ENSP00000284637:R526W	R	-	1	2	SH3RF1	170275450	1.000000	0.71417	0.055000	0.19348	0.432000	0.31715	2.546000	0.45778	0.325000	0.23359	0.561000	0.74099	CGG		0.582	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		A	170038875	G	A	170038875	3	1	61	1	0	0	0	0	1	0	0	0	14295	1057	37	1	1106	1	SH3RF1	4	170038875	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226702	170038875	21115401	3601	11586										
CLCN3	1182	broad.mit.edu	37	chr4	170638970	170638970	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggatcatcacaaagaaGaacatattagagcatctcga	9	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:170638970G>T	ENST00000513761.1	+	13	2925				CLCN3_ENST00000504131.2_Intron|CLCN3_ENST00000360642.3_Intron|CLCN3_ENST00000347613.4_Missense_Mutation_p.K798N	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3						chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.K798N(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		TCACAAAGAAGAACATATTAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											101	98	99					4																	170638970		2203	4300	6503	170875545	SO:0001627	intron_variant	1182			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2367-2088G>T	4.37:g.170638970G>T			170875545	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613716	0.87359	.	.	ENSG00000109572	ENST00000347613	D	0.93859	-3.3	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.97114	0.9057	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	D	0.96900	0.9659	9	0.87932	D	0	-8.2469	20.6439	0.99570	0.0:0.0:1.0:0.0	.	798	P51790-2	.	N	798	ENSP00000261514:K798N	ENSP00000261514:K798N	K	+	3	2	CLCN3	170875545	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.434000	0.97515	2.890000	0.99128	0.650000	0.86243	AAG		0.358	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			T	170638970	G	T	170638970	1	4	61	0	1	0	0	0	0	0	0	0	3470	933	33	2		2	CLCN3	4	170638970	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	600095	170638970	20515306	3602	11587										
MFAP3L	9848	broad.mit.edu	37	chr4	170912532	170912532	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttttcggggttggtattaGacatggctttcgtaaataat	11	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:170912532G>T	ENST00000361618.3	-	3	1534	c.1227C>A	c.(1225-1227)gtC>gtA	p.V409V	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Silent_p.V306V	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	409						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V409V(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		GTTGGTATTAGACATGGCTTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	4											148	135	140					4																	170912532		2203	4300	6503	171149107	SO:0001819	synonymous_variant	9848			AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"Immunoglobulin superfamily / I-set domain containing"	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.1227C>A	4.37:g.170912532G>T			171149107	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Silent	SNP	ENST00000361618.3	37	CCDS34103.1																																																																																				0.473	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		T	170912532	G	T	170912532	2	4	61	1	0	0	0	0	0	0	0	1	9546	929	33	2		2	MFAP3L	4	170912532	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273562	170912532	20241744	3603	11588										
GALNT7	51809	broad.mit.edu	37	chr4	174238797	174238797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttagatcagaggcttcGaaactgcttactgcattgat	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:174238797G>A	ENST00000265000.4	+	10	1704	c.1621G>A	c.(1621-1623)Gaa>Aaa	p.E541K		NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	541	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.E541K(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		CAGAGGCTTCGAAACTGCTTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	4											124	121	122					4																	174238797		2203	4300	6503	174475372	SO:0001583	missense	51809			AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.1621G>A	4.37:g.174238797G>A	ENSP00000265000:p.Glu541Lys		174475372	B3KQU3|Q7Z5W7|Q9UJ28	Missense_Mutation	SNP	ENST00000265000.4	37	CCDS3815.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.14|15.14	2.745155|2.745155	0.49151|0.49151	.|.	.|.	ENSG00000109586|ENSG00000109586	ENST00000265000|ENST00000503213	T|.	0.26223|.	1.75|.	4.75|4.75	4.75|4.75	0.60458|0.60458	Ricin B-related lectin (1);Ricin B lectin (2);|.	0.349077|.	0.35525|.	N|.	0.003151|.	T|T	0.77384|0.77384	0.4122|0.4122	M|M	0.77486|0.77486	2.375|2.375	0.80722|0.80722	D|D	1|1	B|.	0.31655|.	0.334|.	B|.	0.18561|.	0.022|.	T|T	0.78250|0.78250	-0.2277|-0.2277	10|5	0.44086|.	T|.	0.13|.	.|.	18.6221|18.6221	0.91324|0.91324	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	541|.	Q86SF2|.	GALT7_HUMAN|.	K|Q	541|111	ENSP00000265000:E541K|.	ENSP00000265000:E541K|.	E|R	+|+	1|2	0|0	GALNT7|GALNT7	174475372|174475372	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.756000|0.756000	0.42949|0.42949	9.781000|9.781000	0.99029|0.99029	2.566000|2.566000	0.86566|0.86566	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.393	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423		A	174238797	G	A	174238797	3	1	61	1	0	0	0	0	1	0	0	0	6238	1059	37	1	1659	1	GALNT7	4	174238797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3326265	174238797	16915479	3604	11589										
SAP30	8819	broad.mit.edu	37	chr4	174294593	174294593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacttaattcagagtgttcGaaacagaagaaagagaaaag	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:174294593G>A	ENST00000296504.3	+	2	608	c.368G>A	c.(367-369)cGa>cAa	p.R123Q	RP11-798M19.6_ENST00000609153.1_RNA	NM_003864.3	NP_003855.1			Sin3A-associated protein, 30kDa									p.R123Q(1)		large_intestine(1)|lung(2)|ovary(1)	4		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.15e-17)|Epithelial(43;4.33e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.62e-09)|STAD - Stomach adenocarcinoma(60;0.00278)|GBM - Glioblastoma multiforme(59;0.00659)|LUSC - Lung squamous cell carcinoma(193;0.0919)		CAGAGTGTTCGAAACAGAAGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											136	132	134					4																	174294593		2203	4300	6503	174531168	SO:0001583	missense	8819			AF055993	CCDS3817.1	4q34.1	2008-02-05	2006-02-02		ENSG00000164105	ENSG00000164105			10532	protein-coding gene	gene with protein product		603378	"sin3A-associated protein, 30kDa"			9651585	Standard	NM_003864		Approved		uc003itd.3	O75446	OTTHUMG00000160798	ENST00000296504.3:c.368G>A	4.37:g.174294593G>A	ENSP00000296504:p.Arg123Gln		174531168		Missense_Mutation	SNP	ENST00000296504.3	37	CCDS3817.1	.	.	.	.	.	.	.	.	.	.	G	36	5.792537	0.96945	.	.	ENSG00000164105	ENST00000296504	.	.	.	5.62	5.62	0.85841	.	0.138494	0.35936	N	0.002886	T	0.79924	0.4530	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81230	-0.1027	9	0.87932	D	0	-28.5905	19.6456	0.95775	0.0:0.0:1.0:0.0	.	123	O75446	SAP30_HUMAN	Q	123	.	ENSP00000296504:R123Q	R	+	2	0	SAP30	174531168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.727000	0.98787	2.630000	0.89119	0.655000	0.94253	CGA		0.348	SAP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362360.1	NM_003864		A	174294593	G	A	174294593	3	1	61	1	0	0	0	0	1	0	0	0	13870	1058	37	1	374	1	SAP30	4	174294593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55796	174294593	16859683	3605	11590										
KIAA1712	80817	broad.mit.edu	37	chr4	175231080	175231080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcttaagaaactgacttCgatagagaaaaggttagact	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:175231080C>T	ENST00000503780.1	+	8	1172	c.758C>T	c.(757-759)tCg>tTg	p.S253L	CEP44_ENST00000426172.1_Missense_Mutation_p.S253L|CEP44_ENST00000457424.2_Missense_Mutation_p.S253L|CEP44_ENST00000296519.4_Missense_Mutation_p.S253L	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	253						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)		p.S253L(1)		endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						AAACTGACTTCGATAGAGAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	4											67	73	71					4																	175231080		2203	4300	6503	175467655	SO:0001583	missense	80817			AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.758C>T	4.37:g.175231080C>T	ENSP00000423153:p.Ser253Leu		175467655	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	37	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.979512	0.00448	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000426172;ENST00000296519	T;T;T;T	0.39406	1.11;1.08;1.08;1.11	5.71	-5.99	0.02213	.	1.760470	0.02397	N	0.080302	T	0.09468	0.0233	N	0.00583	-1.355	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31166	-0.9953	10	0.02654	T	1	.	3.1926	0.06623	0.1208:0.1606:0.3153:0.4033	.	253;253	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	L	253	ENSP00000423153:S253L;ENSP00000389427:S253L;ENSP00000408221:S253L;ENSP00000296519:S253L	ENSP00000296519:S253L	S	+	2	0	CEP44	175467655	0.001000	0.12720	0.000000	0.03702	0.036000	0.12997	-0.168000	0.09925	-0.988000	0.03489	-1.900000	0.00529	TCG		0.348	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		T	175231080	C	T	175231080	3	4	61	1	0	0	0	0	1	0	0	0	8274	893	31	1	780	1	KIAA1712	4	175231080	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	936487	175231080	15923196	3606	11591										
GPM6A	2823	broad.mit.edu	37	chr4	176733370	176733370	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtccctcttccatattCtcttccatggctacctttct	4	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:176733370C>A	ENST00000280187.7	-	2	54	c.9G>T	c.(7-9)gaG>gaT	p.E3D	GPM6A_ENST00000393658.2_Missense_Mutation_p.E3D|RP11-806K15.1_ENST00000514864.1_RNA|GPM6A_ENST00000506894.1_Intron	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	3					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)	p.E3D(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CTTCCATATTCTCTTCCATGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											197	199	198					4																	176733370		2202	4300	6502	176970364	SO:0001583	missense	2823				CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.9G>T	4.37:g.176733370C>A	ENSP00000280187:p.Glu3Asp		176970364	B7Z642|E9PHI5|Q92602	Missense_Mutation	SNP	ENST00000280187.7	37	CCDS3824.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.204583	0.38905	.	.	ENSG00000150625	ENST00000280187;ENST00000393658;ENST00000513365;ENST00000503563	D;D;D	0.99264	-5.65;-5.65;-4.89	5.57	5.57	0.84162	.	0.326201	0.35708	N	0.003030	D	0.96914	0.8992	N	0.22421	0.69	0.80722	D	1	B	0.23316	0.083	B	0.23716	0.048	D	0.93911	0.7197	10	0.56958	D	0.05	.	10.3762	0.44083	0.0:0.8542:0.0:0.1458	.	3	P51674	GPM6A_HUMAN	D	3	ENSP00000280187:E3D;ENSP00000377268:E3D;ENSP00000423122:E3D	ENSP00000280187:E3D	E	-	3	2	GPM6A	176970364	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.339000	0.43965	2.779000	0.95612	0.655000	0.94253	GAG		0.338	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			A	176733370	C	A	176733370	3	1	61	1	0	0	0	0	1	0	0	0	6635	912	32	2	855	2	GPM6A	4	176733370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1502290	176733370	14420906	3607	11592										
WDR17	116966	broad.mit.edu	37	chr4	177049909	177049909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctcaagtgggtgttttaCgcatttggaatgtttcaaga	10	5	2	1	rs146789582	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177049909C>T	ENST00000280190.4	+	7	1039	c.883C>T	c.(883-885)Cgc>Tgc	p.R295C	WDR17_ENST00000393643.2_Missense_Mutation_p.R271C|WDR17_ENST00000507824.2_Missense_Mutation_p.R278C|WDR17_ENST00000508596.1_Missense_Mutation_p.R271C			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	295								p.R295C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GGGTGTTTTACGCATTTGGAA	0.303													C|||	2	0.000399361	8e-04	0	5008	,	,		14386	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						C	CYS/ARG,CYS/ARG	0,4404		0,0,2202	55	53	54		883,811	4.5	1	4	dbSNP_134	54	1,8579	1.2+/-3.3	0,1,4289	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	180,180	0,1,6491	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	295/1323,271/1284	177049909	1,12983	2202	4290	6492	177286903	SO:0001583	missense	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.883C>T	4.37:g.177049909C>T	ENSP00000280190:p.Arg295Cys		177286903	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	19.75	3.885671	0.72410	0.0	1.17E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.64260	-0.09;-0.09;-0.09	5.45	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.77857	0.4193	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80531	-0.1341	10	0.87932	D	0	-16.6086	14.1509	0.65384	0.2327:0.7673:0.0:0.0	.	271;295	E7EQX0;Q8IZU2	.;WDR17_HUMAN	C	271;271;295;278	ENSP00000422763:R271C;ENSP00000377258:R271C;ENSP00000280190:R295C	ENSP00000280190:R295C	R	+	1	0	WDR17	177286903	0.995000	0.38212	0.962000	0.40283	0.959000	0.62525	2.620000	0.46410	2.555000	0.86185	0.650000	0.86243	CGC		0.303	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177049909	C	T	177049909	3	4	61	1	0	0	0	0	1	0	0	0	17317	536	19	1	905	1	WDR17	4	177049909	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	316539	177049909	14104367	3608	11593										
WDR17	116966	broad.mit.edu	37	chr4	177093609	177093609	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttgaaactgtaaaataTtacttgttaagtcaagaacc	5	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177093609T>G	ENST00000280190.4	+	26	3459	c.3303T>G	c.(3301-3303)taT>taG	p.Y1101*	WDR17_ENST00000393643.2_Nonsense_Mutation_p.Y1077*|WDR17_ENST00000507824.2_Nonsense_Mutation_p.Y1076*|WDR17_ENST00000508596.1_Nonsense_Mutation_p.Y1062*			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1101								p.Y1101*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CTGTAAAATATTACTTGTTAA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											73	76	75					4																	177093609		2203	4299	6502	177330603	SO:0001587	stop_gained	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3303T>G	4.37:g.177093609T>G	ENSP00000280190:p.Tyr1101*		177330603	E7EQX0|Q0QD35	Nonsense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	42|42	9.740877|9.740877	0.99252|0.99252	.|.	.|.	ENSG00000150627|ENSG00000150627	ENST00000443118|ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	.|.	.|.	.|.	5.86|5.86	4.67|4.67	0.58626|0.58626	.|.	.|0.314478	.|0.30859	.|N	.|0.008727	T|.	0.25827|.	0.0629|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28138|.	-1.0053|.	3|.	.|0.02654	.|T	.|1	-15.1733|-15.1733	10.4218|10.4218	0.44354|0.44354	0.0:0.1298:0.0:0.8702|0.0:0.1298:0.0:0.8702	.|.	.|.	.|.	.|.	V|X	336|1062;1077;1101;1077	.|.	.|ENSP00000280190:Y1101X	L|Y	+|+	1|3	2|2	WDR17|WDR17	177330603|177330603	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.979000|0.979000	0.70002|0.70002	1.026000|1.026000	0.30103|0.30103	2.244000|2.244000	0.73946|0.73946	0.533000|0.533000	0.62120|0.62120	TTA|TAT		0.323	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			G	177093609	T	G	177093609	4	3	61	1	0	0	0	0	0	1	0	0	17317	1500	52	4	3401	4	WDR17	4	177093609	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	43700	177093609	14060667	3609	11594										
WDR17	116966	broad.mit.edu	37	chr4	177098225	177098225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtcagctattaaaacgtCgggaggtgtcagtaccttta	10	8	3	0	rs200502473		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177098225C>T	ENST00000280190.4	+	29	3739	c.3583C>T	c.(3583-3585)Cgg>Tgg	p.R1195W	WDR17_ENST00000393643.2_Missense_Mutation_p.R1171W|WDR17_ENST00000507824.2_Missense_Mutation_p.R1170W|WDR17_ENST00000508596.1_Missense_Mutation_p.R1156W			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1195								p.R1195W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		ATTAAAACGTCGGGAGGTGTC	0.353													C|||	1	0.000199681	8e-04	0	5008	,	,		16070	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											66	66	66					4																	177098225		2203	4300	6503	177335219	SO:0001583	missense	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3583C>T	4.37:g.177098225C>T	ENSP00000280190:p.Arg1195Trp		177335219	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	18.66|18.66	3.671996|3.671996	0.67928|0.67928	.|.	.|.	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.59638|.	0.25;0.25;0.25|.	5.85|5.85	2.75|2.75	0.32379|0.32379	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72301|0.72301	0.3443|0.3443	M|M	0.70595|0.70595	2.14|2.14	0.53688|0.53688	D|D	0.999979|0.999979	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.85130|.	0.969;0.997;0.997|.	T|T	0.73369|0.73369	-0.4004|-0.4004	10|5	0.87932|.	D|.	0|.	-20.0309|-20.0309	16.1509|16.1509	0.81622|0.81622	0.3578:0.6422:0.0:0.0|0.3578:0.6422:0.0:0.0	.|.	1171;1156;1195|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	W|L	1156;1171;1195;1171|429	ENSP00000422763:R1156W;ENSP00000377258:R1171W;ENSP00000280190:R1195W|.	ENSP00000280190:R1195W|.	R|S	+|+	1|2	2|0	WDR17|WDR17	177335219|177335219	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.934000|0.934000	0.57294|0.57294	1.006000|1.006000	0.29847|0.29847	0.753000|0.753000	0.32945|0.32945	0.644000|0.644000	0.83932|0.83932	CGG|TCG		0.353	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177098225	C	T	177098225	3	4	61	1	0	0	0	0	1	0	0	0	17317	875	31	1	3693	1	WDR17	4	177098225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4616	177098225	14056051	3610	11595										
WDR17	116966	broad.mit.edu	37	chr4	177098286	177098286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaattggatgcatggagagCttgcacacagtccaccaaca	11	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177098286C>T	ENST00000280190.4	+	29	3800	c.3644C>T	c.(3643-3645)gCt>gTt	p.A1215V	WDR17_ENST00000393643.2_Missense_Mutation_p.A1191V|WDR17_ENST00000507824.2_Missense_Mutation_p.A1190V|WDR17_ENST00000508596.1_Missense_Mutation_p.A1176V			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1215			A -> T (in dbSNP:rs17625943). {ECO:0000269|PubMed:15489334}.					p.A1215V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GCATGGAGAGCTTGCACACAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	61	61					4																	177098286		2203	4299	6502	177335280	SO:0001583	missense	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3644C>T	4.37:g.177098286C>T	ENSP00000280190:p.Ala1215Val		177335280	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692634	0.88735	.	.	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.55234	0.53;0.53;0.53	5.94	5.08	0.68730	.	0.192654	0.43579	D	0.000542	T	0.54565	0.1866	M	0.69823	2.125	0.54753	D	0.999987	P;P;P	0.45768	0.866;0.866;0.866	B;B;B	0.39503	0.301;0.301;0.301	T	0.62812	-0.6775	10	0.62326	D	0.03	-16.1407	17.0228	0.86438	0.0:0.8727:0.1273:0.0	.	1191;1176;1215	E7EP77;E7EQX0;Q8IZU2	.;.;WDR17_HUMAN	V	1176;1191;1215;1191	ENSP00000422763:A1176V;ENSP00000377258:A1191V;ENSP00000280190:A1215V	ENSP00000280190:A1215V	A	+	2	0	WDR17	177335280	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.223000	0.58587	1.491000	0.48482	0.644000	0.83932	GCT		0.378	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177098286	C	T	177098286	3	4	61	1	0	0	0	0	1	0	0	0	17317	797	28	3	3754	3	WDR17	4	177098286	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61	177098286	14055990	3611	11596										
SPATA4	132851	broad.mit.edu	37	chr4	177105940	177105940	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggtgcttttcaaggtttCttgtccatgtttctgatagg	10	7	3	1	rs73005175		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177105940C>A	ENST00000280191.2	-	6	1017	c.909G>T	c.(907-909)aaG>aaT	p.K303N	SPATA4_ENST00000515234.1_Missense_Mutation_p.K130N	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	303						cytoplasm (GO:0005737)		p.K303N(1)		NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TTCAAGGTTTCTTGTCCATGT	0.378													C|||	1	0.000199681	8e-04	0	5008	,	,		16832	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											142	124	130					4																	177105940		2203	4300	6503	177342934	SO:0001583	missense	132851			AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.909G>T	4.37:g.177105940C>A	ENSP00000280191:p.Lys303Asn		177342934	Q8NCS5|Q8WW15	Missense_Mutation	SNP	ENST00000280191.2	37	CCDS3826.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.239	1.037811	0.19669	.	.	ENSG00000150628	ENST00000280191;ENST00000515234	T	0.54279	0.58	3.62	-0.331	0.12679	.	0.842376	0.10000	N	0.728602	T	0.37892	0.1020	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.36040	-0.9764	10	0.72032	D	0.01	.	2.8165	0.05457	0.3873:0.3862:0.0:0.2264	.	303	Q8NEY3	SPAT4_HUMAN	N	303;130	ENSP00000280191:K303N	ENSP00000280191:K303N	K	-	3	2	SPATA4	177342934	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.320000	0.08028	-0.089000	0.12484	-0.302000	0.09304	AAG		0.378	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644		A	177105940	C	A	177105940	3	1	61	1	0	0	0	0	1	0	0	0	15049	912	32	2	12	2	SPATA4	4	177105940	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7654	177105940	14048336	3612	11597										
SPATA4	132851	broad.mit.edu	37	chr4	177114154	177114154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcttctatcaatatttcaGgcactccagctttacaatga	4	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177114154G>A	ENST00000280191.2	-	3	530	c.422C>T	c.(421-423)cCt>cTt	p.P141L	SPATA4_ENST00000515234.1_5'UTR	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	141						cytoplasm (GO:0005737)		p.P141L(1)		NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		CAATATTTCAGGCACTCCAGC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											61	64	63					4																	177114154		2203	4294	6497	177351148	SO:0001583	missense	132851			AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.422C>T	4.37:g.177114154G>A	ENSP00000280191:p.Pro141Leu		177351148	Q8NCS5|Q8WW15	Missense_Mutation	SNP	ENST00000280191.2	37	CCDS3826.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833484	0.71258	.	.	ENSG00000150628	ENST00000280191	T	0.21191	2.02	5.45	5.45	0.79879	.	0.276047	0.35349	N	0.003272	T	0.34716	0.0907	L	0.38175	1.15	0.80722	D	1	D	0.58970	0.984	D	0.63113	0.911	T	0.01010	-1.1482	10	0.41790	T	0.15	-15.4166	16.5682	0.84604	0.0:0.0:1.0:0.0	.	141	Q8NEY3	SPAT4_HUMAN	L	141	ENSP00000280191:P141L	ENSP00000280191:P141L	P	-	2	0	SPATA4	177351148	0.999000	0.42202	0.945000	0.38365	0.808000	0.45660	5.868000	0.69605	2.705000	0.92388	0.655000	0.94253	CCT		0.279	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644		A	177114154	G	A	177114154	3	1	61	1	0	0	0	0	1	0	0	0	15049	1000	35	3	511	3	SPATA4	4	177114154	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8214	177114154	14040122	3613	11598										
ASB5	140458	broad.mit.edu	37	chr4	177138092	177138092	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcagtaagtttacaatttCtgtgctggattgttgagcag	11	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177138092C>T	ENST00000296525.3	-	6	852	c.739G>A	c.(739-741)Gaa>Aaa	p.E247K	ASB5_ENST00000512254.1_Missense_Mutation_p.E194K	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	247					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.E247K(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		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)		TTTACAATTTCTGTGCTGGAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	4											193	185	187					4																	177138092		2203	4300	6503	177375086	SO:0001583	missense	140458			AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.739G>A	4.37:g.177138092C>T	ENSP00000296525:p.Glu247Lys		177375086	Q8N7B5	Missense_Mutation	SNP	ENST00000296525.3	37	CCDS3827.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.585779	0.66105	.	.	ENSG00000164122	ENST00000296525;ENST00000512254	T;T	0.70164	-0.46;-0.33	5.45	5.45	0.79879	Ankyrin repeat-containing domain (4);	0.224693	0.45867	D	0.000324	T	0.60676	0.2287	L	0.42581	1.335	0.80722	D	1	B;P	0.42483	0.279;0.781	B;B	0.35813	0.138;0.211	T	0.66268	-0.5966	10	0.59425	D	0.04	-31.8578	19.6512	0.95812	0.0:1.0:0.0:0.0	.	247;194	Q8WWX0;Q8N7B5	ASB5_HUMAN;.	K	247;194	ENSP00000296525:E247K;ENSP00000422877:E194K	ENSP00000296525:E247K	E	-	1	0	ASB5	177375086	0.996000	0.38824	0.095000	0.20976	0.620000	0.37586	4.243000	0.58721	2.712000	0.92718	0.591000	0.81541	GAA		0.398	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			T	177138092	C	T	177138092	3	4	61	1	0	0	0	0	1	0	0	0	1027	922	32	3	258	3	ASB5	4	177138092	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23938	177138092	14016184	3614	11599										
SPCS3	60559	broad.mit.edu	37	chr4	177248412	177248412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatattttttctttgacGatggaaatggtctcaagtga	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177248412G>A	ENST00000503362.1	+	4	507	c.394G>A	c.(394-396)Gat>Aat	p.D132N	SPCS3_ENST00000507001.1_3'UTR	NM_021928.3	NP_068747.1	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3 homolog (S. cerevisiae)	132					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)	p.D132N(1)		ovary(2)	2		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		TTTCTTTGACGATGGAAATGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											43	40	41					4																	177248412		1801	4067	5868	177485406	SO:0001583	missense	60559			AK092634	CCDS54823.1	4q34.2	2008-02-05				ENSG00000129128			26212	protein-coding gene	gene with protein product						12477932	Standard	NM_021928		Approved	FLJ22649, SPC22/23, SPC3, YLR066W, PRO3567	uc003iur.4	P61009		ENST00000503362.1:c.394G>A	4.37:g.177248412G>A	ENSP00000427463:p.Asp132Asn		177485406	P12280|Q9H0S7	Missense_Mutation	SNP	ENST00000503362.1	37	CCDS54823.1	.	.	.	.	.	.	.	.	.	.	G	32	5.191955	0.94923	.	.	ENSG00000129128	ENST00000503362	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.78629	0.4313	M	0.76574	2.34	0.80722	D	1	D	0.65815	0.995	D	0.70716	0.97	T	0.74153	-0.3757	9	0.24483	T	0.36	-7.8415	19.5183	0.95174	0.0:0.0:1.0:0.0	.	132	P61009	SPCS3_HUMAN	N	132	.	ENSP00000427463:D132N	D	+	1	0	SPCS3	177485406	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.444000	0.97578	2.633000	0.89246	0.655000	0.94253	GAT		0.323	SPCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362329.1	NM_021928		A	177248412	G	A	177248412	3	1	61	1	0	0	0	0	1	0	0	0	15064	1058	37	1	408	1	SPCS3	4	177248412	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110320	177248412	13905864	3615	11600										
VEGFC	7424	broad.mit.edu	37	chr4	177609002	177609002	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatccgaggaaaacataaAatcttcctgagccaggcatc	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:177609002A>C	ENST00000280193.2	-	5	1199	c.784T>G	c.(784-786)Ttt>Gtt	p.F262V	VEGFC_ENST00000507638.1_5'Flank|RP11-313E19.2_ENST00000504017.1_RNA|RP11-313E19.2_ENST00000509194.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	262					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.F262V(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		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)		GAAAACATAAAATCTTCCTGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											115	109	111					4																	177609002		1906	4128	6034	177845996	SO:0001583	missense	7424			BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.784T>G	4.37:g.177609002A>C	ENSP00000280193:p.Phe262Val		177845996	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	A	3.485	-0.105163	0.06967	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.33	4.15	0.48705	.	0.071591	0.56097	D	0.000037	T	0.36496	0.0969	L	0.36672	1.1	0.36364	D	0.860879	B	0.15473	0.013	B	0.06405	0.002	T	0.33317	-0.9873	9	0.19147	T	0.46	-6.7477	6.9833	0.24715	0.774:0.1505:0.0756:0.0	.	262	P49767	VEGFC_HUMAN	V	262	.	ENSP00000280193:F262V	F	-	1	0	VEGFC	177845996	0.997000	0.39634	0.905000	0.35620	0.032000	0.12392	2.348000	0.44045	2.152000	0.67230	0.528000	0.53228	TTT		0.428	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		C	177609002	A	C	177609002	3	2	61	1	0	0	0	0	1	0	0	0	17192	14	1	4	490	4	VEGFC	4	177609002	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	360590	177609002	13545274	3616	11601										
NEIL3	55247	broad.mit.edu	37	chr4	178256953	178256953	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaagatttgatttgtttCtttgactcatcagtagaact	6	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:178256953C>A	ENST00000264596.3	+	3	508	c.390C>A	c.(388-390)ttC>ttA	p.F130L		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	130					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)	p.F130L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TGATTTGTTTCTTTGACTCAT	0.353								Base excision repair (BER), DNA glycosylases																																								1	Substitution - Missense(1)	large_intestine(1)	4											58	62	61					4																	178256953		2201	4299	6500	178493947	SO:0001583	missense	55247			AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.390C>A	4.37:g.178256953C>A	ENSP00000264596:p.Phe130Leu		178493947	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.873222	0.72180	.	.	ENSG00000109674	ENST00000264596	T	0.28069	1.63	5.14	5.14	0.70334	DNA glycosylase/AP lyase, catalytic domain (2);	0.051110	0.85682	D	0.000000	T	0.47728	0.1461	M	0.75264	2.295	0.58432	D	0.999995	D	0.64830	0.994	P	0.58266	0.836	T	0.48969	-0.8987	10	0.66056	D	0.02	-9.943	9.4177	0.38532	0.0:0.8409:0.0:0.1591	.	130	Q8TAT5	NEIL3_HUMAN	L	130	ENSP00000264596:F130L	ENSP00000264596:F130L	F	+	3	2	NEIL3	178493947	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.210000	0.42816	2.666000	0.90696	0.561000	0.74099	TTC		0.353	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		A	178256953	C	A	178256953	3	1	61	1	0	0	0	0	1	0	0	0	10351	912	32	2	400	2	NEIL3	4	178256953	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	647951	178256953	12897323	3617	11602										
AGA	175	broad.mit.edu	37	chr4	178359952	178359952	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatctgaatgaagagcttGagaagcagtggtagataagt	12	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:178359952G>T	ENST00000264595.2	-	4	581	c.454C>A	c.(454-456)Caa>Aaa	p.Q152K	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	152					protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)	p.Q152K(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TGAAGAGCTTGAGAAGCAGTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	53	55					4																	178359952		2203	4300	6503	178596946	SO:0001583	missense	175			X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"glycosylasparaginase", "N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.454C>A	4.37:g.178359952G>T	ENSP00000264595:p.Gln152Lys		178596946	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Missense_Mutation	SNP	ENST00000264595.2	37	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.538122	0.00942	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	D;D	0.87179	-2.22;-2.03	5.65	1.9	0.25705	.	1.085000	0.06904	N	0.806466	T	0.71821	0.3385	N	0.12663	0.25	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56220	-0.8015	10	0.02654	T	1	-28.7697	6.7987	0.23738	0.0657:0.2279:0.582:0.1244	.	152	P20933	ASPG_HUMAN	K	152;37	ENSP00000264595:Q152K;ENSP00000423798:Q37K	ENSP00000264595:Q152K	Q	-	1	0	AGA	178596946	0.957000	0.32711	0.017000	0.16124	0.391000	0.30476	2.342000	0.43992	0.031000	0.15407	-0.127000	0.14921	CAA		0.338	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		T	178359952	G	T	178359952	3	4	61	1	0	0	0	0	1	0	0	0	365	1299	45	2	610	2	AGA	4	178359952	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102999	178359952	12794324	3618	11603										
ODZ3	55714	broad.mit.edu	37	chr4	183268050	183268050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccctcaccctgacagataCggagcacgaaaacaagtccg	9	14	1	2	rs180775304		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183268050C>T	ENST00000511685.1	+	3	602	c.479C>T	c.(478-480)aCg>aTg	p.T160M	TENM3_ENST00000406950.2_Missense_Mutation_p.T160M			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	160	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T160M(1)									CTGACAGATACGGAGCACGAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	76	75					4																	183268050		1995	4178	6173	183505044	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.479C>T	4.37:g.183268050C>T	ENSP00000424226:p.Thr160Met		183505044	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406859	0.62399	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.36340	1.26;1.26;1.26	4.58	4.58	0.56647	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.58864	0.2152	M	0.61703	1.905	0.47778	D	0.999519	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.62699	-0.6799	9	0.72032	D	0.01	.	17.9314	0.88998	0.0:1.0:0.0:0.0	.	160;160	D6RGC5;Q9P273	.;TEN3_HUMAN	M	160	ENSP00000421320:T160M;ENSP00000424226:T160M;ENSP00000385276:T160M	ENSP00000385276:T160M	T	+	2	0	ODZ3	183505044	1.000000	0.71417	0.930000	0.37139	0.991000	0.79684	7.609000	0.82925	2.532000	0.85374	0.563000	0.77884	ACG		0.527	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183268050	C	T	183268050	3	4	61	1	0	0	0	0	1	0	0	0	10867	536	19	1	485	1	ODZ3	4	183268050	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4908098	183268050	7886226	3619	11604										
ODZ3	55714	broad.mit.edu	37	chr4	183594202	183594202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaataacaccatagattccGgagaacttgatattggccga	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183594202G>A	ENST00000511685.1	+	7	1279	c.1156G>A	c.(1156-1158)Gga>Aga	p.G386R	TENM3_ENST00000406950.2_Missense_Mutation_p.G386R			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	386					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G386*(1)|p.G386R(1)									CATAGATTCCGGAGAACTTGA	0.363																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	4											35	33	33					4																	183594202		1811	4083	5894	183831196	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1156G>A	4.37:g.183594202G>A	ENSP00000424226:p.Gly386Arg		183831196	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862373	0.91511	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.40225	1.04;1.04	4.91	4.91	0.64330	.	.	.	.	.	T	0.67306	0.2879	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71361	-0.4616	9	0.87932	D	0	.	18.7292	0.91728	0.0:0.0:1.0:0.0	.	386	Q9P273	TEN3_HUMAN	R	386	ENSP00000424226:G386R;ENSP00000385276:G386R	ENSP00000385276:G386R	G	+	1	0	ODZ3	183831196	1.000000	0.71417	0.993000	0.49108	0.977000	0.68977	9.351000	0.97073	2.720000	0.93068	0.558000	0.71614	GGA		0.363	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183594202	G	A	183594202	3	1	61	1	0	0	0	0	1	0	0	0	10867	1117	39	1	1178	1	ODZ3	4	183594202	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	326152	183594202	7560074	3620	11605										
ODZ3	55714	broad.mit.edu	37	chr4	183664510	183664510	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggcagtctgtacgtaggCgatttcaactatgtgcggcg	14	8	2	0	rs189480567		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183664510C>T	ENST00000511685.1	+	19	3690	c.3567C>T	c.(3565-3567)ggC>ggT	p.G1189G	TENM3_ENST00000406950.2_Silent_p.G1189G|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1189					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1189G(1)									TGTACGTAGGCGATTTCAACT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	4											102	106	105					4																	183664510		1997	4173	6170	183901504	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3567C>T	4.37:g.183664510C>T			183901504	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.473	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183664510	C	T	183664510	2	4	61	1	0	0	0	0	0	0	0	1	10867	755	27	1		1	ODZ3	4	183664510	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70308	183664510	7489766	3621	11606										
ODZ3	55714	broad.mit.edu	37	chr4	183675643	183675643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactgaaaatcgtcaagttCgcattgctgctggacggccc	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183675643C>T	ENST00000511685.1	+	22	4246	c.4123C>T	c.(4123-4125)Cgc>Tgc	p.R1375C	TENM3_ENST00000406950.2_Missense_Mutation_p.R1375C|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1375					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R1375C(1)									TCGTCAAGTTCGCATTGCTGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	4											59	56	57					4																	183675643		1988	4176	6164	183912637	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4123C>T	4.37:g.183675643C>T	ENSP00000424226:p.Arg1375Cys		183912637	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723342	0.48728	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.90900	-2.75;-2.75	5.58	5.58	0.84498	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	D	0.92463	0.7607	M	0.83384	2.64	0.80722	D	1	D	0.69078	0.997	B	0.44315	0.446	D	0.93556	0.6891	9	0.87932	D	0	.	19.769	0.96353	0.0:1.0:0.0:0.0	.	1375	Q9P273	TEN3_HUMAN	C	1375	ENSP00000424226:R1375C;ENSP00000385276:R1375C	ENSP00000385276:R1375C	R	+	1	0	ODZ3	183912637	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	4.905000	0.63286	2.906000	0.99361	0.655000	0.94253	CGC		0.493	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183675643	C	T	183675643	3	4	61	1	0	0	0	0	1	0	0	0	10867	884	31	1	4205	1	ODZ3	4	183675643	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11133	183675643	7478633	3622	11607										
ODZ3	55714	broad.mit.edu	37	chr4	183710493	183710493	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggacaggggaggatcgtgtCtcgggtctttgctgatggta	17	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183710493C>T	ENST00000511685.1	+	25	5675	c.5552C>T	c.(5551-5553)tCt>tTt	p.S1851F	TENM3_ENST00000406950.2_Missense_Mutation_p.S1851F			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1851					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S1851F(1)									AGGATCGTGTCTCGGGTCTTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											87	87	87					4																	183710493		1977	4155	6132	183947487	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5552C>T	4.37:g.183710493C>T	ENSP00000424226:p.Ser1851Phe		183947487	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.260508	0.80246	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.87650	-2.28;-2.28	5.1	5.1	0.69264	.	.	.	.	.	D	0.92430	0.7597	M	0.81239	2.535	0.80722	D	1	D	0.61080	0.989	P	0.56278	0.795	D	0.93393	0.6753	9	0.87932	D	0	.	18.7243	0.91708	0.0:1.0:0.0:0.0	.	1851	Q9P273	TEN3_HUMAN	F	1851	ENSP00000424226:S1851F;ENSP00000385276:S1851F	ENSP00000385276:S1851F	S	+	2	0	ODZ3	183947487	1.000000	0.71417	0.724000	0.30704	0.766000	0.43426	7.583000	0.82559	2.644000	0.89710	0.591000	0.81541	TCT		0.443	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183710493	C	T	183710493	3	4	61	1	0	0	0	0	1	0	0	0	10867	913	32	3	5646	3	ODZ3	4	183710493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34850	183710493	7443783	3623	11608										
ODZ3	55714	broad.mit.edu	37	chr4	183713468	183713468	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagcggcagtacatcttCgaatacgatatgtgggaccg	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:183713468C>T	ENST00000511685.1	+	26	5766	c.5643C>T	c.(5641-5643)ttC>ttT	p.F1881F	TENM3_ENST00000406950.2_Silent_p.F1881F			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1881					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.F1881F(1)									AGTACATCTTCGAATACGATA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	4											95	97	97					4																	183713468		2044	4184	6228	183950462	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5643C>T	4.37:g.183713468C>T			183950462	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.498	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183713468	C	T	183713468	2	4	61	1	0	0	0	0	0	0	0	1	10867	883	31	1		1	ODZ3	4	183713468	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2975	183713468	7440808	3624	11609										
WWC2	80014	broad.mit.edu	37	chr4	184207126	184207126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttgttgccagttaaatCggagtgacagtgacagttca	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:184207126C>T	ENST00000403733.3	+	20	3254	c.3055C>T	c.(3055-3057)Cgg>Tgg	p.R1019W	WWC2_ENST00000508747.1_Missense_Mutation_p.R147W|WWC2_ENST00000448232.2_Missense_Mutation_p.R1043W|WWC2_ENST00000513834.1_Missense_Mutation_p.R970W|WWC2_ENST00000504005.1_Missense_Mutation_p.R701W	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1019					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.R1019W(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CCAGTTAAATCGGAGTGACAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											54	48	50					4																	184207126		2203	4300	6503	184444120	SO:0001583	missense	80014			BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3055C>T	4.37:g.184207126C>T	ENSP00000384222:p.Arg1019Trp		184444120	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288018	0.80803	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000012	D	0.83617	0.5293	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	D	0.86723	0.1943	10	0.87932	D	0	-16.1301	18.9946	0.92807	0.0:1.0:0.0:0.0	.	1043;1019;147;970	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	W	1019;970;1043;701;147	ENSP00000384222:R1019W;ENSP00000425054:R970W;ENSP00000398577:R1043W;ENSP00000427569:R701W;ENSP00000420835:R147W	ENSP00000384222:R1019W	R	+	1	2	WWC2	184444120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.710000	0.74670	2.716000	0.92895	0.655000	0.94253	CGG		0.408	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		T	184207126	C	T	184207126	3	4	61	1	0	0	0	0	1	0	0	0	17452	875	31	1	3133	1	WWC2	4	184207126	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	493658	184207126	6947150	3625	11610										
WWC2	80014	broad.mit.edu	37	chr4	184233556	184233556	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagttgatgaggcaagtCtccaaggacgtgtgtcggct	15	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:184233556C>A	ENST00000403733.3	+	22	3646	c.3447C>A	c.(3445-3447)gtC>gtA	p.V1149V	WWC2_ENST00000508747.1_Silent_p.V277V|WWC2_ENST00000448232.2_Silent_p.V1173V|WWC2_ENST00000513834.1_Silent_p.V1100V|WWC2_ENST00000504005.1_Silent_p.V831V	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1149					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.V1149V(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGAGGCAAGTCTCCAAGGACG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	4											117	119	118					4																	184233556		2203	4300	6503	184470550	SO:0001819	synonymous_variant	80014			BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3447C>A	4.37:g.184233556C>A			184470550	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	37	CCDS34109.2																																																																																				0.512	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		A	184233556	C	A	184233556	2	1	61	1	0	0	0	0	0	0	0	1	17452	900	32	2		2	WWC2	4	184233556	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26430	184233556	6920720	3626	11611										
ING2	3622	broad.mit.edu	37	chr4	184431464	184431464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaattgatgatgtctacGaaaaatataagaaagaagat	9	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:184431464G>A	ENST00000302327.3	+	2	404	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	ING2_ENST00000434682.2_Missense_Mutation_p.E28K	NM_001564.2	NP_001555.1	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	68					chromatin modification (GO:0016568)|male germ-line stem cell asymmetric division (GO:0048133)|male meiosis I (GO:0007141)|negative regulation of cell proliferation (GO:0008285)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cellular senescence (GO:2000772)|regulation of growth (GO:0040008)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|seminiferous tubule development (GO:0072520)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleus (GO:0005634)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.E68K(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	7		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)		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)		TGATGTCTACGAAAAATATAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	4											84	99	94					4																	184431464		2192	4293	6485	184668458	SO:0001583	missense	3622			AB012853	CCDS3833.1	4q35.1	2013-01-28	2005-02-10	2005-02-11	ENSG00000168556	ENSG00000168556		"Zinc fingers, PHD-type"	6063	protein-coding gene	gene with protein product		604215	"inhibitor of growth family, member 1-like"	ING1L		10072587	Standard	XM_005262982		Approved	p33ING2	uc003ivs.1	Q9H160	OTTHUMG00000150502	ENST00000302327.3:c.202G>A	4.37:g.184431464G>A	ENSP00000307183:p.Glu68Lys		184668458	B6ZDS1|O95698	Missense_Mutation	SNP	ENST00000302327.3	37	CCDS3833.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545290	0.65198	.	.	ENSG00000168556	ENST00000302327;ENST00000412117;ENST00000434682	.	.	.	5.54	5.54	0.83059	Double Clp-N motif (1);Inhibitor of growth protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83760	0.5324	M	0.86420	2.815	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.989	T	0.80301	-0.1440	9	0.21540	T	0.41	-17.2433	19.6745	0.95926	0.0:0.0:1.0:0.0	.	28;68	B6ZDS1;Q9H160	.;ING2_HUMAN	K	68;28;28	.	ENSP00000307183:E68K	E	+	1	0	ING2	184668458	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.222000	0.95196	2.880000	0.98712	0.650000	0.86243	GAA		0.318	ING2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318652.1	NM_001564		A	184431464	G	A	184431464	3	1	61	1	0	0	0	0	1	0	0	0	7757	1059	37	1	208	1	ING2	4	184431464	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197908	184431464	6722812	3627	11612										
ENPP6	133121	broad.mit.edu	37	chr4	185018484	185018484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccaaccttcccgcctgCcggtgctgttcatccaaaac	8	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:185018484C>T	ENST00000296741.2	-	7	1172	c.1031G>A	c.(1030-1032)gGc>gAc	p.G344D		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	344					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)	p.G344D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-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;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		TTCCCGCCTGCCGGTGCTGTT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	4											100	87	92					4																	185018484		2203	4300	6503	185255478	SO:0001583	missense	133121			AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.1031G>A	4.37:g.185018484C>T	ENSP00000296741:p.Gly344Asp		185255478	Q4W5Q1|Q96M57	Missense_Mutation	SNP	ENST00000296741.2	37	CCDS3834.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.187825	0.38609	.	.	ENSG00000164303	ENST00000296741	T	0.75938	-0.98	5.35	4.51	0.55191	Alkaline-phosphatase-like, core domain (1);	2.351530	0.01268	N	0.009395	T	0.78336	0.4267	M	0.73430	2.235	0.44652	D	0.997633	B	0.23990	0.095	B	0.24394	0.053	T	0.51810	-0.8658	10	0.22706	T	0.39	-23.3923	14.0991	0.65042	0.0:0.9269:0.0:0.0731	.	344	Q6UWR7	ENPP6_HUMAN	D	344	ENSP00000296741:G344D	ENSP00000296741:G344D	G	-	2	0	ENPP6	185255478	0.998000	0.40836	0.984000	0.44739	0.448000	0.32197	2.407000	0.44565	1.502000	0.48669	0.511000	0.50034	GGC		0.587	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343		T	185018484	C	T	185018484	3	4	61	1	0	0	0	0	1	0	0	0	5147	739	26	3	299	3	ENPP6	4	185018484	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	587020	185018484	6135792	3628	11613										
CASP3	836	broad.mit.edu	37	chr4	185552974	185552974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctacaacgatcccctctgAaaaagtttgttatttttttc	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:185552974A>G	ENST00000308394.4	-	6	690	c.428T>C	c.(427-429)tTc>tCc	p.F143S	CASP3_ENST00000523916.1_Missense_Mutation_p.F143S|CASP3_ENST00000393585.2_Missense_Mutation_p.F143S|CASP3_ENST00000517513.1_Missense_Mutation_p.F143S|CASP3_ENST00000393588.4_Missense_Mutation_p.F143S	NM_004346.3	NP_004337.2	P42574	CASP3_HUMAN	caspase 3, apoptosis-related cysteine peptidase	143					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell homeostasis (GO:0001782)|cell fate commitment (GO:0045165)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte differentiation (GO:0030218)|execution phase of apoptosis (GO:0097194)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|heart development (GO:0007507)|hippo signaling (GO:0035329)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|keratinocyte differentiation (GO:0030216)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|proteolysis (GO:0006508)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|release of cytochrome c from mitochondria (GO:0001836)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)|peptidase activity (GO:0008233)	p.F143S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592)		all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161)	Minocycline(DB01017)	ATCCCCTCTGAAAAAGTTTGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	4											86	88	87					4																	185552974		2203	4300	6503	185789968	SO:0001583	missense	836			BC016926	CCDS3836.1	4q34	2008-02-05	2005-08-17		ENSG00000164305	ENSG00000164305		"Caspases"	1504	protein-coding gene	gene with protein product		600636	"caspase 3, apoptosis-related cysteine protease"			8780721	Standard	NM_004346		Approved	CPP32, CPP32B, Yama, apopain	uc003iwi.3	P42574	OTTHUMG00000133681	ENST00000308394.4:c.428T>C	4.37:g.185552974A>G	ENSP00000311032:p.Phe143Ser		185789968	A8K5M2|D3DP53|Q96AN1|Q96KP2	Missense_Mutation	SNP	ENST00000308394.4	37	CCDS3836.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360555	0.82353	.	.	ENSG00000164305	ENST00000308394;ENST00000393585;ENST00000523916;ENST00000517513;ENST00000393588	T;T;T;T;T	0.29397	1.57;3.35;1.57;3.35;3.35	5.74	5.74	0.90152	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.044528	0.85682	D	0.000000	T	0.75339	0.3836	H	0.99634	4.67	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.95	D	0.87209	0.2246	10	0.87932	D	0	.	16.0347	0.80617	1.0:0.0:0.0:0.0	.	143;143	P42574;A8MVM1	CASP3_HUMAN;.	S	143	ENSP00000311032:F143S;ENSP00000377210:F143S;ENSP00000428929:F143S;ENSP00000428372:F143S;ENSP00000377213:F143S	ENSP00000311032:F143S	F	-	2	0	CASP3	185789968	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	6.078000	0.71282	2.194000	0.70268	0.459000	0.35465	TTC		0.373	CASP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257885.2	NM_004346		G	185552974	A	G	185552974	3	3	61	1	0	0	0	0	1	0	0	0	2678	246	9	4	417	4	CASP3	4	185552974	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	534490	185552974	5601302	3629	11614										
CCDC111	201973	broad.mit.edu	37	chr4	185582935	185582935	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattcaatttagaaaaaatCtcttacactgctatgaagtt	4	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:185582935C>A	ENST00000314970.6	+	5	719	c.286C>A	c.(286-288)Ctc>Atc	p.L96I	PRIMPOL_ENST00000512834.1_Missense_Mutation_p.L96I|PRIMPOL_ENST00000515774.1_5'UTR|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.L96I	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	96					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)	p.L96I(1)									TAGAAAAAATCTCTTACACTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	4											42	42	42					4																	185582935		2203	4299	6502	185819929	SO:0001583	missense	201973			AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.286C>A	4.37:g.185582935C>A	ENSP00000313816:p.Leu96Ile		185819929	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.701365	0.68501	.	.	ENSG00000164306	ENST00000314970;ENST00000503752;ENST00000512834	T;T;T	0.31769	1.48;1.48;1.48	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	L	0.49126	1.545	0.48341	D	0.999631	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.989	T	0.27773	-1.0064	10	0.39692	T	0.17	-0.0018	13.2776	0.60196	0.0:0.9277:0.0:0.0723	.	96;96	Q96LW4;D6RDM1	CC111_HUMAN;.	I	96	ENSP00000313816:L96I;ENSP00000420860:L96I;ENSP00000425316:L96I	ENSP00000313816:L96I	L	+	1	0	CCDC111	185819929	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.531000	0.60602	2.737000	0.93849	0.563000	0.77884	CTC		0.338	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		A	185582935	C	A	185582935	3	1	61	1	0	0	0	0	1	0	0	0	2754	913	32	2	296	2	CCDC111	4	185582935	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29961	185582935	5571341	3630	11615										
MLF1IP	201973	broad.mit.edu	37	chr4	185616499	185616499	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttcgcagatggctttcGgctcccagaagtgttcttgc	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:185616499G>A	ENST00000314970.6	+	0	2289				MLF1IP_ENST00000506535.1_5'Flank|MLF1IP_ENST00000281453.5_Silent_p.A400A	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)						mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)	p.A400A(1)									GATGGCTTTCGGCTCCCAGAA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	4											149	158	155					4																	185616499		2203	4300	6503	185853493	SO:0001628	intergenic_variant	79682			AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495		4.37:g.185616499G>A			185853493	D3DP55|D6RDM1|Q5HYJ9	Silent	SNP	ENST00000314970.6	37	CCDS3837.1																																																																																				0.388	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		A	185616499	G	A	185616499	1	1	61	0	1	0	0	0	0	0	0	0	9645	1103	39	1		1	MLF1IP	4	185616499	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33564	185616499	5537777	3631	11616										
SNX25	83891	broad.mit.edu	37	chr4	186241890	186241890	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaattctcttaatagattCttcagtttgaagatatcttg	5	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186241890C>A	ENST00000504273.1	+	8	1150	c.856C>A	c.(856-858)Ctt>Att	p.L286I	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Missense_Mutation_p.L286I			Q9H3E2	SNX25_HUMAN	sorting nexin 25	286					negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.L286I(1)		NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TTAATAGATTCTTCAGTTTGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	4											72	74	73					4																	186241890		2203	4300	6503	186478884	SO:0001583	missense	83891			AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.856C>A	4.37:g.186241890C>A	ENSP00000426255:p.Leu286Ile		186478884	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357453	0.61293	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.30714	1.52;1.52	5.26	5.26	0.73747	Regulator of G protein signalling superfamily (1);	0.071599	0.56097	D	0.000029	T	0.48390	0.1497	M	0.62723	1.935	0.42659	D	0.993479	D;D	0.63880	0.993;0.976	P;B	0.55999	0.789;0.433	T	0.37197	-0.9716	10	0.37606	T	0.19	-6.2615	19.2279	0.93824	0.0:1.0:0.0:0.0	.	57;286	Q8N6K3;Q9H3E2	.;SNX25_HUMAN	I	286	ENSP00000426255:L286I;ENSP00000264694:L286I	ENSP00000264694:L286I	L	+	1	0	SNX25	186478884	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	5.656000	0.67988	2.627000	0.88993	0.561000	0.74099	CTT		0.323	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		A	186241890	C	A	186241890	3	1	61	1	0	0	0	0	1	0	0	0	14933	913	32	2	882	2	SNX25	4	186241890	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	625391	186241890	4912386	3632	11617										
ANKRD37	353322	broad.mit.edu	37	chr4	186320760	186320760	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaaacagctgaagatctCgcttggtcatgtggatttcc	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186320760C>T	ENST00000335174.4	+	4	749	c.309C>T	c.(307-309)ctC>ctT	p.L103L		NM_181726.2	NP_859077.1	Q7Z713	ANR37_HUMAN	ankyrin repeat domain 37	103						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L103L(1)		NS(1)|large_intestine(1)|lung(1)	3		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.27e-25)|Epithelial(43;1.02e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.14e-11)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000118)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|COAD - Colon adenocarcinoma(29;0.00939)|READ - Rectum adenocarcinoma(43;0.155)		CTGAAGATCTCGCTTGGTCAT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	4											82	80	81					4																	186320760		2203	4300	6503	186557754	SO:0001819	synonymous_variant	353322			AY296056	CCDS3841.1	4q35.1	2013-01-11						"Ankyrin repeat domain containing"	29593	protein-coding gene	gene with protein product							Standard	NM_181726		Approved	Lrp2bp	uc003ixm.3	Q7Z713		ENST00000335174.4:c.309C>T	4.37:g.186320760C>T			186557754		Silent	SNP	ENST00000335174.4	37	CCDS3841.1																																																																																				0.353	ANKRD37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360673.1	NM_181726		T	186320760	C	T	186320760	2	4	61	1	0	0	0	0	0	0	0	1	667	871	31	1		1	ANKRD37	4	186320760	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78870	186320760	4833516	3633	11618										
UFSP2	55325	broad.mit.edu	37	chr4	186324648	186324649	+	Splice_Site	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttaaatggatacttaccINSttttccaaaataacttgcag							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186324648_186324649insT	ENST00000264689.6	-	11	1438_1439	c.1322_1323insA	c.(1321-1323)aag>aaAg	p.K441fs		NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	441						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	small conjugating protein-specific protease activity (GO:0019783)|thiolester hydrolase activity (GO:0016790)	p.W443fs*17(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		GGATACTTACCTTTTCCAAAAT	0.391																																																1	Insertion - Frameshift(1)	large_intestine(1)	4																																								186561643	SO:0001630	splice_region_variant	55325			AK002062	CCDS3842.1	4q35.1	2008-03-25	2008-03-25	2008-03-25	ENSG00000109775	ENSG00000109775			25640	protein-coding gene	gene with protein product		611482	"chromosome 4 open reading frame 20"	C4orf20		17182609	Standard	NM_018359		Approved	FLJ11200	uc003ixo.2	Q9NUQ7	OTTHUMG00000160441	ENST00000264689.6:c.1323+1->A	4.37:g.186324652_186324652dupT			186561642	Q6IA77|Q96FS3	Frame_Shift_Ins	INS	ENST00000264689.6	37	CCDS3842.1																																																																																				0.391	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359	Frame_Shift_Ins	T	186324649	-	T	186324648	8	5	61	1	0	1	1	0	0	0	1	0	16978	695	24	0	94	0	UFSP2	4	186324648	Splice_Site	INS	-	TCGA-AG-A002-01A-01W-A00K-09	3888	186324648	4829628	3634	11619										
CCDC110	256309	broad.mit.edu	37	chr4	186380209	186380210	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacattatatttactaattaINStttttttaaattctttaaga							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186380209_186380210insT	ENST00000307588.3	-	6	1606_1607	c.1531_1532insA	c.(1531-1533)atafs	p.I511fs	CCDC110_ENST00000510617.1_Frame_Shift_Ins_p.I511fs|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Frame_Shift_Ins_p.I474fs	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	511						nucleus (GO:0005634)		p.I511fs*3(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		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)		tttactaattatttttttaaat	0.277																																																1	Insertion - Frameshift(1)	large_intestine(1)	4							,	5,4089		0,5,2042					,	5.8	0			23	2,8102		0,2,4050	no	frameshift,frameshift	CCDC110	NM_152775.3,NM_001145411.1	,	0,7,6092	A1A1,A1R,RR		0.0247,0.1221,0.0574	,	,		7,12191				186617204	SO:0001589	frameshift_variant	256309			AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1532dupA	4.37:g.186380216_186380216dupT	ENSP00000306776:p.Ile511fs		186617203	Q86YI9|Q8N7W0	Frame_Shift_Ins	INS	ENST00000307588.3	37	CCDS3843.1																																																																																				0.277	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		T	186380210	-	T	186380209	7	5	61	1	0	1	1	0	0	0	0	0	2753	449	16	0	977	0	CCDC110	4	186380209	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	55561	186380209	4774067	3635	11620										
SORBS2	8470	broad.mit.edu	37	chr4	186548027	186548027	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggagaagagctagtgaaaGactttgtaagagtggtgctt	14	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186548027G>T	ENST00000284776.7	-	12	1390	c.881C>A	c.(880-882)tCt>tAt	p.S294Y	SORBS2_ENST00000437304.2_Missense_Mutation_p.S545Y|SORBS2_ENST00000448662.2_Missense_Mutation_p.S382Y|SORBS2_ENST00000355634.5_Missense_Mutation_p.S394Y|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000393528.3_Missense_Mutation_p.S387Y|SORBS2_ENST00000418609.1_Missense_Mutation_p.S198Y|SORBS2_ENST00000449407.2_Missense_Mutation_p.S365Y|SORBS2_ENST00000431808.1_Missense_Mutation_p.S294Y|SORBS2_ENST00000319471.9_Missense_Mutation_p.S452Y	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	294					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.S294Y(1)|p.S382Y(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCTAGTGAAAGACTTTGTAAG	0.493																																					Esophageal Squamous(153;41 2433 9491 36028)											2	Substitution - Missense(2)	large_intestine(2)	4											156	144	148					4																	186548027		2203	4300	6503	186785021	SO:0001583	missense	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.881C>A	4.37:g.186548027G>T	ENSP00000284776:p.Ser294Tyr		186785021	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.286626|4.286626	0.80803|0.80803	.|.	.|.	ENSG00000154556|ENSG00000154556	ENST00000445625|ENST00000284776;ENST00000448662;ENST00000431808;ENST00000418609;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454;ENST00000451974	.|T;T;T;T;T;T;T;T;T;T;T	.|0.38401	.|1.26;1.45;1.26;1.14;1.25;1.25;1.49;1.25;1.59;1.42;2.54	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|0.164731	.|0.56097	.|D	.|0.000035	T|T	0.51618|0.51618	0.1685|0.1685	L|L	0.43152|0.43152	1.355|1.355	0.40212|0.40212	D|D	0.977639|0.977639	.|P;D;D;B;D;D;D;B;P;D;P;P;D;D;D	.|0.71674	.|0.828;0.998;0.958;0.121;0.976;0.997;0.986;0.059;0.52;0.976;0.924;0.943;0.969;0.986;0.998	.|B;P;P;B;P;P;P;B;B;P;B;B;P;P;P	.|0.62649	.|0.34;0.904;0.635;0.101;0.564;0.905;0.814;0.074;0.221;0.556;0.34;0.423;0.742;0.742;0.904	T|T	0.48864|0.48864	-0.8997|-0.8997	5|10	.|0.45353	.|T	.|0.12	-7.8304|-7.8304	19.1442|19.1442	0.93458|0.93458	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|357;387;382;198;213;270;412;394;294;365;545;382;412;366;387	.|B7Z3D7;G3XAI0;C9JKV9;B7Z3X6;B7Z997;B3KPU4;O94875-4;B3KPQ7;O94875;E9PAS5;E9PAW4;B7Z1G5;O94875-5;O94875-3;O94875-2	.|.;.;.;.;.;.;.;.;SRBS2_HUMAN;.;.;.;.;.;.	I|Y	240|294;382;294;198;545;452;365;394;387;412;170	.|ENSP00000284776:S294Y;ENSP00000409158:S382Y;ENSP00000411764:S294Y;ENSP00000397482:S198Y;ENSP00000396008:S545Y;ENSP00000322182:S452Y;ENSP00000397262:S365Y;ENSP00000347852:S394Y;ENSP00000377162:S387Y;ENSP00000321983:S412Y;ENSP00000401818:S170Y	.|ENSP00000284776:S294Y	L|S	-|-	1|2	0|0	SORBS2|SORBS2	186785021|186785021	1.000000|1.000000	0.71417|0.71417	0.890000|0.890000	0.34922|0.34922	0.893000|0.893000	0.52053|0.52053	8.560000|8.560000	0.90712|0.90712	2.589000|2.589000	0.87451|0.87451	0.655000|0.655000	0.94253|0.94253	CTT|TCT		0.493	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186548027	G	T	186548027	3	4	61	1	0	0	0	0	1	0	0	0	14965	942	33	2	2461	2	SORBS2	4	186548027	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167818	186548027	4606249	3636	11621										
SORBS2	8470	broad.mit.edu	37	chr4	186567890	186567890	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatactccttggctcagaccGaaattttcttgtgtccactt	6	11	2	1	rs139199897		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:186567890G>A	ENST00000284776.7	-	10	1125	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	SORBS2_ENST00000437304.2_Missense_Mutation_p.R385W|SORBS2_ENST00000448662.2_Missense_Mutation_p.R275W|SORBS2_ENST00000355634.5_Missense_Mutation_p.R306W|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000393528.3_Missense_Mutation_p.R252W|SORBS2_ENST00000418609.1_Missense_Mutation_p.R110W|SORBS2_ENST00000449407.2_Missense_Mutation_p.R277W|SORBS2_ENST00000431808.1_Missense_Mutation_p.R206W|SORBS2_ENST00000319471.9_Missense_Mutation_p.R292W	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	206				R -> Q (in Ref. 5; AK225327). {ECO:0000305}.	actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.R275W(1)|p.R206W(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GGCTCAGACCGAAATTTTCTT	0.363													G|||	1	0.000199681	0	0	5008	,	,		17372	0		0.001	False		,,,				2504	0				Esophageal Squamous(153;41 2433 9491 36028)											2	Substitution - Missense(2)	large_intestine(2)	4						G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	113	113	113		829,874,823,1153,328,373,754,616	5.2	1	4	dbSNP_134	113	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense,missense	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	101,101,101,101,101,101,101,101	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	277/645,292/732,275/662,385/825,110/1005,125/493,252/667,206/1101	186567890	2,13004	2203	4300	6503	186804884	SO:0001583	missense	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.616C>T	4.37:g.186567890G>A	ENSP00000284776:p.Arg206Trp		186804884	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.9|25.9	4.689906|4.689906	0.88735|0.88735	4.54E-4|4.54E-4	0.0|0.0	ENSG00000154556|ENSG00000154556	ENST00000284776;ENST00000448662;ENST00000431808;ENST00000418609;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454;ENST00000451974|ENST00000438278	T;T;T;T;T;T;T;T;T;T;T|.	0.36520|.	1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25|.	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74733|0.74733	0.3755|0.3755	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.91635|.	0.993;0.995;0.998;0.998;0.994;0.994;0.998;0.993;0.998;0.998;0.997;0.992;0.993;0.999;0.995;0.999|.	T|T	0.72633|0.72633	-0.4234|-0.4234	10|5	0.87932|.	D|.	0|.	-20.4189|-20.4189	19.0427|19.0427	0.93008|0.93008	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	269;252;275;110;125;125;110;252;306;206;277;385;275;252;206;252|.	B7Z3D7;G3XAI0;C9JKV9;B7Z3X6;B7Z997;O94875-6;B3KPU4;O94875-4;B3KPQ7;O94875;E9PAS5;E9PAW4;B7Z1G5;O94875-5;O94875-3;O94875-2|.	.;.;.;.;.;.;.;.;.;SRBS2_HUMAN;.;.;.;.;.;.|.	W|L	206;275;206;110;385;292;277;306;252;252;63|149	ENSP00000284776:R206W;ENSP00000409158:R275W;ENSP00000411764:R206W;ENSP00000397482:R110W;ENSP00000396008:R385W;ENSP00000322182:R292W;ENSP00000397262:R277W;ENSP00000347852:R306W;ENSP00000377162:R252W;ENSP00000321983:R252W;ENSP00000401818:R63W|.	ENSP00000284776:R206W|.	R|S	-|-	1|2	2|0	SORBS2|SORBS2	186804884|186804884	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.935000|5.935000	0.70145|0.70145	2.722000|2.722000	0.93159|0.93159	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.363	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		A	186567890	G	A	186567890	3	1	61	1	0	0	0	0	1	0	0	0	14965	1057	37	1	3046	1	SORBS2	4	186567890	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19863	186567890	4586386	3637	11622										
TLR3	7098	broad.mit.edu	37	chr4	187004176	187004176	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttaatgaaattgggcaaGaactcacaggccaggaatgg	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187004176G>T	ENST00000296795.3	+	4	1440	c.1336G>T	c.(1336-1338)Gaa>Taa	p.E446*	TLR3_ENST00000504367.1_Nonsense_Mutation_p.E169*	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	446					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.E446*(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		AATTGGGCAAGAACTCACAGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											63	60	61					4																	187004176		2203	4300	6503	187241170	SO:0001587	stop_gained	7098			U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1336G>T	4.37:g.187004176G>T	ENSP00000296795:p.Glu446*		187241170	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Nonsense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	G	37	6.300725	0.97453	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	.	.	.	5.78	2.94	0.34122	.	0.508073	0.24012	N	0.042375	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	3.6193	0.08089	0.2006:0.1151:0.5659:0.1184	.	.	.	.	X	446;446;169	.	ENSP00000296795:E446X	E	+	1	0	TLR3	187241170	0.361000	0.24972	0.991000	0.47740	0.946000	0.59487	1.072000	0.30678	0.766000	0.33244	0.557000	0.71058	GAA		0.423	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			T	187004176	G	T	187004176	4	4	61	1	0	0	0	0	0	1	0	0	15991	943	33	2	1346	2	TLR3	4	187004176	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436286	187004176	4150100	3638	11623										
TLR3	7098	broad.mit.edu	37	chr4	187005911	187005911	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaccatgcactctgtttgCgaagaggaatgtttaaatct	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187005911C>T	ENST00000296795.3	+	5	2703	c.2599C>T	c.(2599-2601)Cga>Tga	p.R867*	TLR3_ENST00000504367.1_Nonsense_Mutation_p.R590*	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	867	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R867*(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		ACTCTGTTTGCGAAGAGGAAT	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											93	94	94					4																	187005911		2203	4300	6503	187242905	SO:0001587	stop_gained	7098			U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.2599C>T	4.37:g.187005911C>T	ENSP00000296795:p.Arg867*		187242905	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Nonsense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	C	41	8.539888	0.98854	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	.	.	.	6.02	1.79	0.24919	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8869	0.79258	0.6104:0.3895:0.0:0.0	.	.	.	.	X	867;867;590	.	ENSP00000296795:R867X	R	+	1	2	TLR3	187242905	0.618000	0.27051	0.998000	0.56505	0.914000	0.54420	0.842000	0.27627	0.384000	0.24942	-0.127000	0.14921	CGA		0.393	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			T	187005911	C	T	187005911	4	4	61	1	0	0	0	0	0	1	0	0	15991	760	27	1	2613	1	TLR3	4	187005911	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1735	187005911	4148365	3639	11624										
FAM149A	25854	broad.mit.edu	37	chr4	187086609	187086609	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcagttcctggatgccgCcttgtttctgtaagacagat	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187086609C>T	ENST00000356371.5	+	11	2028	c.2028C>T	c.(2026-2028)cgC>cgT	p.R676R	FAM149A_ENST00000502970.1_Silent_p.R385R|FAM149A_ENST00000227065.4_Silent_p.R385R|FAM149A_ENST00000514153.1_Silent_p.R385R|FAM149A_ENST00000503432.1_Silent_p.R385R|FAM149A_ENST00000389354.5_Silent_p.R385R			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	676								p.R385R(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CTGGATGCCGCCTTGTTTCTG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	4											97	93	95					4																	187086609		2203	4300	6503	187323603	SO:0001819	synonymous_variant	25854			AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2028C>T	4.37:g.187086609C>T			187323603	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.375|0.375	-0.931754|-0.931754	0.02359|0.02359	.|.	.|.	ENSG00000109794|ENSG00000109794	ENST00000510843|ENST00000512271	.|.	.|.	.|.	5.55|5.55	0.665|0.665	0.17896|0.17896	.|.	.|.	.|.	.|.	.|.	T|T	0.23054|0.23054	0.0557|0.0557	.|.	.|.	.|.	0.24686|0.24686	N|N	0.993331|0.993331	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24225|0.24225	-1.0166|-1.0166	4|4	.|.	.|.	.|.	-8.8792|-8.8792	3.025|3.025	0.06087|0.06087	0.1411:0.3304:0.3771:0.1515|0.1411:0.3304:0.3771:0.1515	.|.	.|.	.|.	.|.	V|S	63|63	.|.	.|.	A|P	+|+	2|1	0|0	FAM149A|FAM149A	187323603|187323603	0.002000|0.002000	0.14202|0.14202	0.233000|0.233000	0.24025|0.24025	0.015000|0.015000	0.08874|0.08874	-0.396000|-0.396000	0.07278|0.07278	-0.091000|-0.091000	0.12440|0.12440	0.655000|0.655000	0.94253|0.94253	GCC|CCT		0.478	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		T	187086609	C	T	187086609	2	4	61	1	0	0	0	0	0	0	0	1	5471	726	26	3		3	FAM149A	4	187086609	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80698	187086609	4067667	3640	11625										
CYP4V2	285440	broad.mit.edu	37	chr4	187118744	187118744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgattccgagtatgtccGtgcagtttataggtaaatgg	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187118744G>A	ENST00000378802.4	+	5	966	c.662G>A	c.(661-663)cGt>cAt	p.R221H		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	221					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.R221H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		GAGTATGTCCGTGCAGTTTAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	4											138	141	140					4																	187118744		2203	4300	6503	187355738	SO:0001583	missense	285440			AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"Cytochrome P450s"	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.662G>A	4.37:g.187118744G>A	ENSP00000368079:p.Arg221His		187355738	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652364	0.47362	.	.	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.69040	-0.37	5.2	3.47	0.39725	.	0.113275	0.56097	D	0.000022	T	0.58878	0.2153	L	0.54323	1.7	0.40846	D	0.983712	B	0.22003	0.063	B	0.20955	0.032	T	0.56823	-0.7915	10	0.49607	T	0.09	.	9.0645	0.36455	0.228:0.0:0.772:0.0	.	221	Q6ZWL3	CP4V2_HUMAN	H	221;199	ENSP00000368079:R221H	ENSP00000274118:R199H	R	+	2	0	CYP4V2	187355738	0.999000	0.42202	0.994000	0.49952	0.982000	0.71751	1.498000	0.35660	0.768000	0.33290	0.655000	0.94253	CGT		0.333	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612		A	187118744	G	A	187118744	3	1	61	1	0	0	0	0	1	0	0	0	4198	1145	40	1	680	1	CYP4V2	4	187118744	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32135	187118744	4035532	3641	11626										
CYP4V2	285440	broad.mit.edu	37	chr4	187120130	187120130	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgagtgagatgatatttCgaagaataaagatgccctgg	12	4	0	5	rs369063468		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187120130C>T	ENST00000378802.4	+	6	998	c.694C>T	c.(694-696)Cga>Tga	p.R232*		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	232					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.R232*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		GATGATATTTCGAAGAATAAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	4						C	stop/ARG	0,4406		0,0,2203	130	129	129		694	2.9	0	4		129	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	CYP4V2	NM_207352.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		232/526	187120130	1,13005	2203	4300	6503	187357124	SO:0001587	stop_gained	285440			AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"Cytochrome P450s"	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.694C>T	4.37:g.187120130C>T	ENSP00000368079:p.Arg232*		187357124	B7U6W2|Q6ZTM4	Nonsense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	.	.	.	.	.	.	.	.	.	.	C	36	5.624180	0.96660	0.0	1.16E-4	ENSG00000145476	ENST00000378802;ENST00000274118	.	.	.	4.77	2.93	0.34026	.	0.191557	0.43747	D	0.000534	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	13.1448	0.59454	0.3001:0.6999:0.0:0.0	.	.	.	.	X	232;210	.	ENSP00000274118:R210X	R	+	1	2	CYP4V2	187357124	0.002000	0.14202	0.011000	0.14972	0.307000	0.27823	1.701000	0.37825	0.546000	0.28920	0.644000	0.83932	CGA		0.368	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612		T	187120130	C	T	187120130	4	4	61	1	0	0	0	0	0	1	0	0	4198	876	31	1	716	1	CYP4V2	4	187120130	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1386	187120130	4034146	3642	11627										
KLKB1	3818	broad.mit.edu	37	chr4	187155158	187155158	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccctgccaaaagtacatCgaacaggtgcagtttctgga	10	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187155158C>T	ENST00000264690.6	+	4	461	c.274C>T	c.(274-276)Cga>Tga	p.R92*	KLKB1_ENST00000513864.1_Nonsense_Mutation_p.R92*	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	92	Apple 1. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.R92*(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		AAAAGTACATCGAACAGGTGC	0.348																																																2	Substitution - Nonsense(2)	large_intestine(2)	4											156	147	150					4																	187155158		2203	4300	6503	187392152	SO:0001587	stop_gained	3818			M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.274C>T	4.37:g.187155158C>T	ENSP00000264690:p.Arg92*		187392152	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Nonsense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.278849	0.23307	.	.	ENSG00000164344	ENST00000428196;ENST00000264690;ENST00000446598;ENST00000414291;ENST00000513864;ENST00000418715	.	.	.	4.73	0.326	0.15908	.	0.646568	0.13708	N	0.368356	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	6.7818	0.23650	0.6349:0.2641:0.0:0.101	.	.	.	.	X	92;92;54;54;92;54	.	ENSP00000264690:R92X	R	+	1	2	KLKB1	187392152	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-0.113000	0.10774	-0.047000	0.13423	0.650000	0.86243	CGA		0.348	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		T	187155158	C	T	187155158	4	4	61	1	0	0	0	0	0	1	0	0	8433	876	31	1	284	1	KLKB1	4	187155158	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35028	187155158	3999118	3643	11628										
KLKB1	3818	broad.mit.edu	37	chr4	187172752	187172752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttgcacaaagatgattcGctgtcagtttttcacttatt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187172752G>A	ENST00000264690.6	+	9	1167	c.980G>A	c.(979-981)cGc>cAc	p.R327H	KLKB1_ENST00000513864.1_Missense_Mutation_p.R327H	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	327	Apple 4. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.R327H(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		AAGATGATTCGCTGTCAGTTT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	4											94	101	98					4																	187172752		2202	4300	6502	187409746	SO:0001583	missense	3818			M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.980G>A	4.37:g.187172752G>A	ENSP00000264690:p.Arg327His		187409746	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.92|15.92	2.976451|2.976451	0.53720|0.53720	.|.	.|.	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690;ENST00000513864;ENST00000418715	.|D;D	.|0.89681	.|-2.55;-2.55	5.27|5.27	5.27|5.27	0.74061|0.74061	.|Apple domain (2);PAN-1 domain (1);Apple-like (1);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.92090|0.92090	0.7493|0.7493	L|L	0.37897|0.37897	1.145|1.145	0.41896|0.41896	D|D	0.990397|0.990397	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.83275	.|0.983;0.996;0.98	D|D	0.92657|0.92657	0.6138|0.6138	5|10	.|0.59425	.|D	.|0.04	.|.	19.2757|19.2757	0.94030|0.94030	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|289;327;327	.|E7EQA8;A8K9A9;P03952	.|.;.;KLKB1_HUMAN	T|H	375|327;327;289	.|ENSP00000264690:R327H;ENSP00000424469:R327H	.|ENSP00000264690:R327H	A|R	+|+	1|2	0|0	KLKB1|KLKB1	187409746|187409746	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.105000|0.105000	0.19272|0.19272	4.237000|4.237000	0.58681|0.58681	2.621000|2.621000	0.88768|0.88768	0.645000|0.645000	0.84053|0.84053	GCT|CGC		0.353	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		A	187172752	G	A	187172752	3	1	61	1	0	0	0	0	1	0	0	0	8433	1087	38	1	1010	1	KLKB1	4	187172752	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17594	187172752	3981524	3644	11629										
FAT1	2195	broad.mit.edu	37	chr4	187518086	187518086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttccgactaatcatcttaCggcagagaacaaacaccacc	5	13	2	1	rs200185840		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187518086C>T	ENST00000441802.2	-	25	12817	c.12608G>A	c.(12607-12609)cGt>cAt	p.R4203H	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4203					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R4203H(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AATCATCTTACGGCAGAGAAC	0.468										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											106	105	105					4																	187518086		1910	4117	6027	187755080	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12608G>A	4.37:g.187518086C>T	ENSP00000406229:p.Arg4203His		187755080		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.517678	0.85495	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.74421	-0.84	5.09	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.84401	0.5464	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.85199	0.1014	10	0.54805	T	0.06	.	14.1125	0.65132	0.0:0.926:0.0:0.074	.	4203	Q14517	FAT1_HUMAN	H	4203;4205	ENSP00000406229:R4203H	ENSP00000260147:R4205H	R	-	2	0	FAT1	187755080	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.927000	0.70080	2.652000	0.90054	0.555000	0.69702	CGT		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187518086	C	T	187518086	3	4	61	1	0	0	0	0	1	0	0	0	5708	536	19	1	1170	1	FAT1	4	187518086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	345334	187518086	3636190	3645	11630										
FAT1	2195	broad.mit.edu	37	chr4	187518150	187518150	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacacaacgattccaattcCttccgccaacccaatgttcc	3	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187518150C>A	ENST00000441802.2	-	25	12753	c.12544G>T	c.(12544-12546)Gga>Tga	p.G4182*	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4182					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G4182*(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATTCCAATTCCTTCCGCCAAC	0.507										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Nonsense(1)	large_intestine(1)	4											99	99	99					4																	187518150		1996	4180	6176	187755144	SO:0001587	stop_gained	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12544G>T	4.37:g.187518150C>A	ENSP00000406229:p.Gly4182*		187755144		Nonsense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	53	20.916198	0.99935	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	.	.	.	4.86	4.86	0.63082	.	0.057884	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	18.1658	0.89724	0.0:1.0:0.0:0.0	.	.	.	.	X	4182;4184	.	ENSP00000260147:G4184X	G	-	1	0	FAT1	187755144	1.000000	0.71417	0.958000	0.39756	0.044000	0.14063	5.841000	0.69409	2.541000	0.85698	0.561000	0.74099	GGA		0.507	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187518150	C	A	187518150	4	1	61	1	0	0	0	0	0	1	0	0	5708	690	24	2	1234	2	FAT1	4	187518150	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64	187518150	3636126	3646	11631										
FAT1	2195	broad.mit.edu	37	chr4	187539055	187539055	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtggaggatagctggatCttttcaccatgatctgatgc	12	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187539055C>A	ENST00000441802.2	-	10	8894	c.8685G>T	c.(8683-8685)aaG>aaT	p.K2895N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2895	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K2895N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATAGCTGGATCTTTTCACCAT	0.438										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											170	158	162					4																	187539055		1999	4171	6170	187776049	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8685G>T	4.37:g.187539055C>A	ENSP00000406229:p.Lys2895Asn		187776049		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	4.252	0.045807	0.08196	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.52526	0.66	4.86	4.01	0.46588	Cadherin (4);Cadherin-like (1);	0.157787	0.56097	D	0.000035	T	0.36358	0.0964	N	0.02973	-0.45	0.50632	D	0.999886	D	0.71674	0.998	D	0.68765	0.96	T	0.36841	-0.9731	10	0.56958	D	0.05	.	4.491	0.11813	0.0:0.7132:0.0:0.2868	.	2895	Q14517	FAT1_HUMAN	N	2895;2897	ENSP00000406229:K2895N	ENSP00000260147:K2897N	K	-	3	2	FAT1	187776049	1.000000	0.71417	0.942000	0.38095	0.063000	0.16089	1.767000	0.38501	2.682000	0.91365	0.650000	0.86243	AAG		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187539055	C	A	187539055	3	1	61	1	0	0	0	0	1	0	0	0	5708	912	32	2	5153	2	FAT1	4	187539055	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20905	187539055	3615221	3647	11632										
FAT1	2195	broad.mit.edu	37	chr4	187539780	187539780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctcctttgtagtgattaCgccggacagtttgttaattt	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187539780C>T	ENST00000441802.2	-	10	8169	c.7960G>A	c.(7960-7962)Gta>Ata	p.V2654I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2654	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2654I(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTAGTGATTACGCCGGACAGT	0.418										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											55	51	52					4																	187539780		1864	4112	5976	187776774	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7960G>A	4.37:g.187539780C>T	ENSP00000406229:p.Val2654Ile		187776774		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.427039	0.00186	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.52983	0.64	5.2	-5.61	0.02489	Cadherin (4);Cadherin-like (1);	0.618536	0.17318	N	0.178610	T	0.21427	0.0516	N	0.21240	0.645	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.07481	-1.0770	10	0.28530	T	0.3	.	1.8082	0.03085	0.1257:0.3303:0.208:0.3359	.	2654	Q14517	FAT1_HUMAN	I	2654;2656	ENSP00000406229:V2654I	ENSP00000260147:V2656I	V	-	1	0	FAT1	187776774	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.170000	0.00573	-1.095000	0.03050	0.655000	0.94253	GTA		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187539780	C	T	187539780	3	4	61	1	0	0	0	0	1	0	0	0	5708	536	19	1	5878	1	FAT1	4	187539780	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	725	187539780	3614496	3648	11633										
FAT1	2195	broad.mit.edu	37	chr4	187542027	187542027	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgcacttgaatcagcatCtgtagcatttactgtgatga	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187542027C>A	ENST00000441802.2	-	10	5922	c.5713G>T	c.(5713-5715)Gat>Tat	p.D1905Y		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1905	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1905Y(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GAATCAGCATCTGTAGCATTT	0.423										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											98	102	100					4																	187542027		1948	4136	6084	187779021	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5713G>T	4.37:g.187542027C>A	ENSP00000406229:p.Asp1905Tyr		187779021		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852268	0.51270	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.73789	-0.78	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92303	0.7558	H	0.98295	4.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94616	0.7809	10	0.87932	D	0	.	19.6941	0.96016	0.0:1.0:0.0:0.0	.	1905	Q14517	FAT1_HUMAN	Y	1905;1907	ENSP00000406229:D1905Y	ENSP00000260147:D1907Y	D	-	1	0	FAT1	187779021	1.000000	0.71417	0.995000	0.50966	0.161000	0.22273	7.458000	0.80787	2.885000	0.99019	0.655000	0.94253	GAT		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187542027	C	A	187542027	3	1	61	1	0	0	0	0	1	0	0	0	5708	913	32	2	8125	2	FAT1	4	187542027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2247	187542027	3612249	3649	11634										
FAT1	2195	broad.mit.edu	37	chr4	187542151	187542151	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacatgtactgttacattCgctgcatactcagcaaataa	5	9	1	0	rs375007936		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187542151C>T	ENST00000441802.2	-	10	5798	c.5589G>A	c.(5587-5589)gcG>gcA	p.A1863A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1863	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A1863A(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTGTTACATTCGCTGCATACT	0.393										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											2	Substitution - coding silent(2)	large_intestine(2)	4						C		0,3862		0,0,1931	67	67	67		5589	-7	0.9	4		67	1,8255		0,1,4127	no	coding-synonymous	FAT1	NM_005245.3		0,1,6058	TT,TC,CC		0.0121,0.0,0.0083		1863/4589	187542151	1,12117	1931	4128	6059	187779145	SO:0001819	synonymous_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5589G>A	4.37:g.187542151C>T			187779145		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.393	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187542151	C	T	187542151	2	4	61	1	0	0	0	0	0	0	0	1	5708	871	31	1		1	FAT1	4	187542151	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124	187542151	3612125	3650	11635										
FAT1	2195	broad.mit.edu	37	chr4	187628907	187628907	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctccctggttgtgtaatTtatttgcctgcaggagcttc	9	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187628907T>G	ENST00000441802.2	-	2	2284	c.2075A>C	c.(2074-2076)aAa>aCa	p.K692T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	692					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K692T(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTTGTGTAATTTATTTGCCTG	0.463										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											39	38	38					4																	187628907		1900	4123	6023	187865901	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2075A>C	4.37:g.187628907T>G	ENSP00000406229:p.Lys692Thr		187865901		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	7.917	0.737666	0.15574	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.57107	0.42	5.39	1.54	0.23209	.	0.045508	0.85682	D	0.000000	T	0.52306	0.1726	M	0.73217	2.22	0.54753	D	0.999984	P	0.43938	0.822	P	0.46299	0.511	T	0.47686	-0.9098	10	0.21540	T	0.41	.	9.7042	0.40205	0.0:0.2027:0.0:0.7973	.	692	Q14517	FAT1_HUMAN	T	692	ENSP00000406229:K692T	ENSP00000260147:K692T	K	-	2	0	FAT1	187865901	0.959000	0.32827	0.270000	0.24601	0.034000	0.12701	1.536000	0.36072	0.486000	0.27676	0.528000	0.53228	AAA		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187628907	T	G	187628907	3	3	61	1	0	0	0	0	1	0	0	0	5708	1841	64	4	11795	4	FAT1	4	187628907	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	86756	187628907	3525369	3651	11636										
FAT1	2195	broad.mit.edu	37	chr4	187630138	187630138	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaccattggcaccctgatCgcagtcatccactgtcacaa	7	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:187630138C>T	ENST00000441802.2	-	2	1053	c.844G>A	c.(844-846)Gat>Aat	p.D282N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	282					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D282N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GCACCCTGATCGCAGTCATCC	0.498										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)	large_intestine(1)	4											273	269	271					4																	187630138		2151	4252	6403	187867132	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.844G>A	4.37:g.187630138C>T	ENSP00000406229:p.Asp282Asn		187867132		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.134473	0.56828	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.79247	-1.25;-1.25	5.04	5.04	0.67666	Cadherin (1);	0.000000	0.85682	D	0.000000	D	0.90130	0.6916	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91596	0.5291	10	0.66056	D	0.02	.	18.5673	0.91121	0.0:1.0:0.0:0.0	.	282	Q14517	FAT1_HUMAN	N	282	ENSP00000406229:D282N;ENSP00000423736:D282N	ENSP00000260147:D282N	D	-	1	0	FAT1	187867132	1.000000	0.71417	0.982000	0.44146	0.087000	0.18053	7.651000	0.83577	2.613000	0.88420	0.591000	0.81541	GAT		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187630138	C	T	187630138	3	4	61	1	0	0	0	0	1	0	0	0	5708	884	31	1	13026	1	FAT1	4	187630138	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1231	187630138	3524138	3652	11637										
TRIML2	205860	broad.mit.edu	37	chr4	189012779	189012779	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccttttcagaggggggaaGacccagagagtccactcggt	14	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:189012779G>T	ENST00000512729.1	-	7	1286	c.912C>A	c.(910-912)gtC>gtA	p.V304V	TRIML2_ENST00000326754.3_Silent_p.V329V	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	304	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.V304V(1)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		GAGGGGGGAAGACCCAGAGAG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	4											132	148	143					4																	189012779		2203	4300	6503	189249773	SO:0001819	synonymous_variant	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.912C>A	4.37:g.189012779G>T			189249773	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																				0.567	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		T	189012779	G	T	189012779	2	4	61	1	0	0	0	0	0	0	0	1	16591	929	33	2		2	TRIML2	4	189012779	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1382641	189012779	2141497	3653	11638										
TRIML2	205860	broad.mit.edu	37	chr4	189022320	189022320	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattcctgctgtctctggaGattctgctcacactcttcat	7	13	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:189022320G>T	ENST00000512729.1	-	3	594	c.220C>A	c.(220-222)Ctc>Atc	p.L74I	TRIML2_ENST00000326754.3_Missense_Mutation_p.L74I|TRIML2_ENST00000536972.1_Missense_Mutation_p.L124I	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	74					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.L74I(1)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		TGTCTCTGGAGATTCTGCTCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											163	151	155					4																	189022320		2203	4300	6503	189259314	SO:0001583	missense	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.220C>A	4.37:g.189022320G>T	ENSP00000422581:p.Leu74Ile		189259314	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	37	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247902	0.22880	.	.	ENSG00000179046	ENST00000512729;ENST00000326754;ENST00000536972	T;T;T	0.59906	0.23;0.26;3.18	5.15	-3.36	0.04913	.	1.483990	0.04356	N	0.356598	T	0.32010	0.0815	N	0.14661	0.345	0.09310	N	1	B;B;P	0.39809	0.437;0.437;0.689	B;B;B	0.28305	0.088;0.072;0.072	T	0.17961	-1.0352	10	0.21014	T	0.42	.	9.1186	0.36773	0.2197:0.1509:0.6294:0.0	.	124;74;74	B7Z6J6;B7ZLC3;Q8N7C3	.;.;TRIMM_HUMAN	I	74;74;124	ENSP00000422581:L74I;ENSP00000317498:L74I;ENSP00000441236:L124I	ENSP00000317498:L74I	L	-	1	0	TRIML2	189259314	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.698000	0.05092	-0.669000	0.05289	-0.793000	0.03317	CTC		0.428	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		T	189022320	G	T	189022320	3	4	61	1	0	0	0	0	1	0	0	0	16591	942	33	2	963	2	TRIML2	4	189022320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9541	189022320	2131956	3654	11639										
TRIML1	339976	broad.mit.edu	37	chr4	189063625	189063625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtcaaagctcggctttcGaatctcttgaggtgagaata	10	8	2	2	rs112173910	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr4:189063625G>A	ENST00000332517.3	+	3	864	c.724G>A	c.(724-726)Gaa>Aaa	p.E242K	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	242					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E242K(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		CTCGGCTTTCGAATCTCTTGA	0.383													G|||	58	0.0115815	0.0378	0.0115	5008	,	,		17275	0		0	False		,,,				2504	0				Melanoma(31;213 1036 16579 23968 32372)											1	Substitution - Missense(1)	large_intestine(1)	4						G	LYS/GLU	167,4239	103.8+/-142.4	5,157,2041	67	74	72		724	3.6	0	4	dbSNP_132	72	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRIML1	NM_178556.3	56	5,160,6338	AA,AG,GG		0.0349,3.7903,1.3071	possibly-damaging	242/469	189063625	170,12836	2203	4300	6503	189300619	SO:0001583	missense	339976			AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.724G>A	4.37:g.189063625G>A	ENSP00000327738:p.Glu242Lys		189300619	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	31	0.014194139194139194	26	0.052845528455284556	5	0.013812154696132596	0	0.0	0	0.0	G	12.74	2.029493	0.35797	0.037903	3.49E-4	ENSG00000184108	ENST00000332517	T	0.05447	3.44	4.41	3.56	0.40772	.	0.247697	0.28914	N	0.013740	T	0.01092	0.0036	M	0.70275	2.135	0.09310	N	0.999999	P	0.36768	0.569	B	0.28139	0.086	T	0.23511	-1.0186	10	0.40728	T	0.16	-15.0726	10.5788	0.45244	0.0:0.1945:0.8055:0.0	.	242	Q8N9V2	TRIML_HUMAN	K	242	ENSP00000327738:E242K	ENSP00000327738:E242K	E	+	1	0	TRIML1	189300619	0.774000	0.28592	0.015000	0.15790	0.002000	0.02628	1.811000	0.38942	1.432000	0.47375	0.650000	0.86243	GAA		0.383	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		A	189063625	G	A	189063625	3	1	61	1	0	0	0	0	1	0	0	0	16590	1059	37	1	734	1	TRIML1	4	189063625	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41305	189063625	2090651	3655	11640										
PLEKHG4B	153478	broad.mit.edu	37	chr5	156195	156195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccgtgcaggaagtcgccGagttaattgaccagcatgag	12	10	0	2	rs138938524		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156195G>A	ENST00000283426.6	+	8	1200	c.1150G>A	c.(1150-1152)Gag>Aag	p.E384K		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	384							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E384K(2)|p.E384*(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGAAGTCGCCGAGTTAATTGA	0.582																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	large_intestine(2)|ovary(1)	5						G	LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	125	116	119		1150	0.6	0	5	dbSNP_134	119	0,8600		0,0,4300	no	missense	PLEKHG4B	NM_052909.3	56	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	possibly-damaging	384/1272	156195	3,13003	2203	4300	6503	209195	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1150G>A	5.37:g.156195G>A	ENSP00000283426:p.Glu384Lys		209195		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334320	0.41297	6.81E-4	0.0	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.30981	1.51;2.98	3.65	0.651	0.17817	.	.	.	.	.	T	0.30386	0.0763	M	0.63843	1.955	0.09310	N	1	D	0.67145	0.996	P	0.50570	0.644	T	0.17776	-1.0358	9	0.16420	T	0.52	.	2.1558	0.03811	0.1172:0.1948:0.4879:0.2001	.	384	Q96PX9	PKH4B_HUMAN	K	384;298	ENSP00000283426:E384K;ENSP00000422493:E298K	ENSP00000283426:E384K	E	+	1	0	PLEKHG4B	209195	0.997000	0.39634	0.000000	0.03702	0.006000	0.05464	5.044000	0.64214	-0.241000	0.09681	-0.373000	0.07131	GAG		0.582	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	156195	G	A	156195	3	1	61	1	0	0	0	0	1	0	0	0	12103	1059	37	1	1180	1	PLEKHG4B	5	156195	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		156195	180759065	3656	11641										
PLEKHG4B	153478	broad.mit.edu	37	chr5	169510	169510	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagagagggagtacattCggtgcttaggatacgtcatt	12	8	1	1	rs149174138	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169510C>A	ENST00000283426.6	+	12	2514	c.2464C>A	c.(2464-2466)Cgg>Agg	p.R822R		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	822	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R822R(1)|p.R13R(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGAGTACATTCGGTGCTTAGG	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	5											133	136	135					5																	169510		2203	4300	6503	222510	SO:0001819	synonymous_variant	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2464C>A	5.37:g.169510C>A			222510		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																				0.552	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	169510	C	A	169510	2	1	61	1	0	0	0	0	0	0	0	1	12103	875	31	2		2	PLEKHG4B	5	169510	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13315	169510	180745750	3657	11642										
CEP72	55722	broad.mit.edu	37	chr5	644452	644452	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagataaatctttggaagaGaacagtaggttaaaatcgct	9	4	1	2	rs556441577		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:644452G>T	ENST00000264935.5	+	10	1668	c.1578G>T	c.(1576-1578)gaG>gaT	p.E526D	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	526					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)		p.E526D(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTTTGGAAGAGAACAGTAGGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											146	149	148					5																	644452		2203	4300	6503	697452	SO:0001583	missense	55722			BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.1578G>T	5.37:g.644452G>T	ENSP00000264935:p.Glu526Asp		697452	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.072134	0.55646	.	.	ENSG00000112877	ENST00000264935	T	0.56275	0.47	4.64	1.79	0.24919	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	M	0.76328	2.33	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.62205	-0.6903	10	0.42905	T	0.14	-27.8963	7.3527	0.26700	0.2982:0.0:0.7018:0.0	.	526	Q9P209	CEP72_HUMAN	D	526	ENSP00000264935:E526D	ENSP00000264935:E526D	E	+	3	2	CEP72	697452	1.000000	0.71417	0.967000	0.41034	0.503000	0.33858	1.063000	0.30567	0.488000	0.27723	0.561000	0.74099	GAG		0.378	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140		T	644452	G	T	644452	3	4	61	1	0	0	0	0	1	0	0	0	3266	933	33	2	1616	2	CEP72	5	644452	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	474942	644452	180270808	3658	11643										
BRD9	65980	broad.mit.edu	37	chr5	889244	889244	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatccaggagcaattgcatcCgtgacaggaaaagcaaaaaa	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:889244C>T	ENST00000467963.1	-	5	664	c.498G>A	c.(496-498)acG>acA	p.T166T	BRD9_ENST00000483173.1_Silent_p.T113T|BRD9_ENST00000323510.4_Silent_p.T50T|BRD9_ENST00000494422.1_5'Flank|BRD9_ENST00000435709.2_Silent_p.T50T|BRD9_ENST00000388890.4_Silent_p.T50T	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	166	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)	p.T166T(1)|p.T50T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			CAATTGCATCCGTGACAGGAA	0.348																																																2	Substitution - coding silent(2)	large_intestine(2)	5											68	67	67					5																	889244		2203	4300	6503	942244	SO:0001819	synonymous_variant	65980			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.498G>A	5.37:g.889244C>T			942244	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Silent	SNP	ENST00000467963.1	37	CCDS34127.2																																																																																				0.348	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924		T	889244	C	T	889244	2	4	61	1	0	0	0	0	0	0	0	1	1510	639	23	1		1	BRD9	5	889244	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	244792	889244	180026016	3659	11644										
SLC12A7	10723	broad.mit.edu	37	chr5	1094320	1094320	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctctcttgttccacctcGacattgttgaggaatgggct	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:1094320G>A	ENST00000264930.5	-	2	211	c.168C>T	c.(166-168)gtC>gtT	p.V56V		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	56					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.V56V(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GTTCCACCTCGACATTGTTGA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	5											135	124	128					5																	1094320		2202	4300	6502	1147320	SO:0001819	synonymous_variant	10723			AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.168C>T	5.37:g.1094320G>A			1147320	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																				0.433	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		A	1094320	G	A	1094320	2	1	61	1	0	0	0	0	0	0	0	1	14425	1045	37	1		1	SLC12A7	5	1094320	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205076	1094320	179820940	3660	11645										
CLPTM1L	81037	broad.mit.edu	37	chr5	1334416	1334416	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactcacatggaacgctgcGacaaagaaggtcagcgccag	12	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:1334416G>A	ENST00000320895.5	-	7	1136	c.879C>T	c.(877-879)gtC>gtT	p.V293V	CLPTM1L_ENST00000507807.1_Silent_p.V160V|CLPTM1L_ENST00000320927.6_Silent_p.V293V	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	293					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.V293V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		GGAACGCTGCGACAAAGAAGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	5											86	91	89					5																	1334416		2203	4300	6503	1387416	SO:0001819	synonymous_variant	81037			AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"cisplatin resistance related protein"	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.879C>T	5.37:g.1334416G>A			1387416	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Silent	SNP	ENST00000320895.5	37	CCDS3862.1																																																																																				0.547	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		A	1334416	G	A	1334416	2	1	61	1	0	0	0	0	0	0	0	1	3561	1045	37	1		1	CLPTM1L	5	1334416	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	240096	1334416	179580844	3661	11646										
LPCAT1	79888	broad.mit.edu	37	chr5	1463877	1463877	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtctctgcacagctttcGaaatgtgtctgatccgggta	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:1463877G>A	ENST00000283415.3	-	14	1626	c.1494C>T	c.(1492-1494)ttC>ttT	p.F498F	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	498					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)	p.F498F(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CACAGCTTTCGAAATGTGTCT	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	5											117	115	115					5																	1463877		2203	4300	6503	1516877	SO:0001819	synonymous_variant	79888			BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1494C>T	5.37:g.1463877G>A			1516877	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																				0.537	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		A	1463877	G	A	1463877	2	1	61	1	0	0	0	0	0	0	0	1	8939	1049	37	1		1	LPCAT1	5	1463877	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129461	1463877	179451383	3662	11647										
ADAMTS16	170690	broad.mit.edu	37	chr5	5303846	5303846	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgctgccacaagcccaaGaagctgcagtggctggtgtc	13	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5303846G>A	ENST00000274181.7	+	20	3291	c.3153G>A	c.(3151-3153)aaG>aaA	p.K1051K		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	1051	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K1051K(2)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						ACAAGCCCAAGAAGCTGCAGT	0.652																																																2	Substitution - coding silent(2)	large_intestine(2)	5											27	31	30					5																	5303846		2095	4239	6334	5356846	SO:0001819	synonymous_variant	170690			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.3153G>A	5.37:g.5303846G>A			5356846	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																				0.652	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		A	5303846	G	A	5303846	2	1	61	1	0	0	0	0	0	0	0	1	261	933	33	3		3	ADAMTS16	5	5303846	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3839969	5303846	175611414	3663	11648										
KIAA0947	23379	broad.mit.edu	37	chr5	5462245	5462245	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtttctgcctctaggaGaaaattagattttaattctc	7	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5462245G>T	ENST00000296564.7	+	13	3020	c.2798G>T	c.(2797-2799)aGa>aTa	p.R933I		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		933					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.R933I(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GCCTCTAGGAGAAAATTAGAT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	5											38	38	38					5																	5462245		1812	4086	5898	5515245	SO:0001583	missense	23379																														ENST00000296564.7:c.2798G>T	5.37:g.5462245G>T	ENSP00000296564:p.Arg933Ile		5515245	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	g	16.04	3.010020	0.54361	.	.	ENSG00000164151	ENST00000296564	T	0.10382	2.88	5.29	-0.189	0.13260	.	0.337618	0.28940	N	0.013658	T	0.05960	0.0155	L	0.27053	0.805	0.09310	N	1	P	0.45634	0.863	B	0.41691	0.364	T	0.29088	-1.0023	10	0.66056	D	0.02	-9.6391	1.5346	0.02542	0.1863:0.3102:0.344:0.1594	.	933	Q9Y2F5	K0947_HUMAN	I	933	ENSP00000296564:R933I	ENSP00000296564:R933I	R	+	2	0	KIAA0947	5515245	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.232000	0.09055	0.580000	0.29522	0.461000	0.40582	AGA		0.388	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5462245	G	T	5462245	3	4	61	1	0	0	0	0	1	0	0	0	8223	942	33	2	2848	2	KIAA0947	5	5462245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	158399	5462245	175453015	3664	11649										
KIAA0947	23379	broad.mit.edu	37	chr5	5464037	5464037	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatctatgatcaaaacttCgagactcagattgttgcgtc	7	9	3	3	rs537938775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5464037C>T	ENST00000296564.7	+	13	4812	c.4590C>T	c.(4588-4590)ttC>ttT	p.F1530F		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1530					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.F1530F(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						ATCAAAACTTCGAGACTCAGA	0.373													C|||	1	0.000199681	8e-04	0	5008	,	,		21367	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											43	41	42					5																	5464037		1856	4096	5952	5517037	SO:0001819	synonymous_variant	23379																														ENST00000296564.7:c.4590C>T	5.37:g.5464037C>T			5517037	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																				0.373	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5464037	C	T	5464037	2	4	61	1	0	0	0	0	0	0	0	1	8223	883	31	1		1	KIAA0947	5	5464037	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1792	5464037	175451223	3665	11650										
KIAA0947	23379	broad.mit.edu	37	chr5	5466570	5466570	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttgtcggcaactcggaGacttggaaagagctcgtttg	13	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5466570G>T	ENST00000296564.7	+	14	6238	c.6016G>T	c.(6016-6018)Gac>Tac	p.D2006Y		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2006					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.D2006Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GCAACTCGGAGACTTGGAAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											163	149	154					5																	5466570		1862	4088	5950	5519570	SO:0001583	missense	23379																														ENST00000296564.7:c.6016G>T	5.37:g.5466570G>T	ENSP00000296564:p.Asp2006Tyr		5519570	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543376	0.86022	.	.	ENSG00000164151	ENST00000296564	T	0.21031	2.03	5.66	5.66	0.87406	.	.	.	.	.	T	0.44993	0.1320	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.29701	-1.0003	9	0.87932	D	0	-14.8584	17.2442	0.87022	0.0:0.0:1.0:0.0	.	2006	Q9Y2F5	K0947_HUMAN	Y	2006	ENSP00000296564:D2006Y	ENSP00000296564:D2006Y	D	+	1	0	KIAA0947	5519570	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.805000	0.75191	2.675000	0.91044	0.557000	0.71058	GAC		0.393	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5466570	G	T	5466570	3	4	61	1	0	0	0	0	1	0	0	0	8223	942	33	2	6070	2	KIAA0947	5	5466570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2533	5466570	175448690	3666	11651										
KIAA0947	23379	broad.mit.edu	37	chr5	5469000	5469000	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgtggcatgatatatttCtctctcaatcggtgattaat	7	7	2	2	rs375083449		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5469000C>A	ENST00000296564.7	+	15	6343	c.6121C>A	c.(6121-6123)Ctc>Atc	p.L2041I		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2041					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.L2041I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TGATATATTTCTCTCTCAATC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	ILE/LEU	0,3694		0,0,1847	102	98	99		6121	-6.5	0	5		99	1,8171		0,1,4085	no	missense	KIAA0947	NM_015325.1	5	0,1,5932	AA,AC,CC		0.0122,0.0,0.0084	benign	2041/2267	5469000	1,11865	1847	4086	5933	5522000	SO:0001583	missense	23379																														ENST00000296564.7:c.6121C>A	5.37:g.5469000C>A	ENSP00000296564:p.Leu2041Ile		5522000	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	C	6.617	0.482256	0.12581	0.0	1.22E-4	ENSG00000164151	ENST00000296564	T	0.10288	2.89	5.86	-6.53	0.01866	.	.	.	.	.	T	0.03305	0.0096	N	0.02539	-0.55	0.09310	N	1	B	0.09022	0.002	B	0.14578	0.011	T	0.48896	-0.8994	9	0.17369	T	0.5	4.1453	9.5342	0.39213	0.3008:0.489:0.2102:0.0	.	2041	Q9Y2F5	K0947_HUMAN	I	2041	ENSP00000296564:L2041I	ENSP00000296564:L2041I	L	+	1	0	KIAA0947	5522000	0.001000	0.12720	0.005000	0.12908	0.972000	0.66771	-0.258000	0.08733	-1.040000	0.03271	0.650000	0.86243	CTC		0.338	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			A	5469000	C	A	5469000	3	1	61	1	0	0	0	0	1	0	0	0	8223	913	32	2	6179	2	KIAA0947	5	5469000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2430	5469000	175446260	3667	11652										
KIAA0947	23379	broad.mit.edu	37	chr5	5486894	5486894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtgaaaaatattagttCggttattggtatgtttatac	9	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:5486894C>T	ENST00000296564.7	+	18	6803	c.6581C>T	c.(6580-6582)tCg>tTg	p.S2194L		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2194					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.S2194L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AATATTAGTTCGGTTATTGGT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											84	77	79					5																	5486894		1839	4098	5937	5539894	SO:0001583	missense	23379																														ENST00000296564.7:c.6581C>T	5.37:g.5486894C>T	ENSP00000296564:p.Ser2194Leu		5539894	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.873890	0.72180	.	.	ENSG00000164151	ENST00000296564	T	0.66995	-0.24	5.69	4.77	0.60923	.	.	.	.	.	T	0.69851	0.3157	L	0.47716	1.5	0.09310	N	1	D	0.69078	0.997	P	0.53954	0.738	T	0.62501	-0.6841	9	0.66056	D	0.02	-2.8543	11.8128	0.52192	0.0:0.8237:0.1763:0.0	.	2194	Q9Y2F5	K0947_HUMAN	L	2194	ENSP00000296564:S2194L	ENSP00000296564:S2194L	S	+	2	0	KIAA0947	5539894	0.013000	0.17824	0.009000	0.14445	0.961000	0.63080	2.215000	0.42862	2.685000	0.91497	0.655000	0.94253	TCG		0.328	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5486894	C	T	5486894	3	4	61	1	0	0	0	0	1	0	0	0	8223	893	31	1	6651	1	KIAA0947	5	5486894	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17894	5486894	175428366	3668	11653										
PAPD7	11044	broad.mit.edu	37	chr5	6737711	6737711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaggtggtgaaacggatcGaaactgtggtgaaagacctt	15	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:6737711G>A	ENST00000230859.6	+	2	184	c.55G>A	c.(55-57)Gaa>Aaa	p.E19K		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	249					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.E19K(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GAAACGGATCGAAACTGTGGT	0.433																																					NSCLC(7;212 333 5667 23379 46547)											1	Substitution - Missense(1)	large_intestine(1)	5											244	192	210					5																	6737711		2203	4300	6503	6790711	SO:0001583	missense	11044			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.55G>A	5.37:g.6737711G>A	ENSP00000230859:p.Glu19Lys		6790711	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	37	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631366	0.87660	.	.	ENSG00000112941	ENST00000230859;ENST00000515721	T	0.47177	0.85	5.05	5.05	0.67936	Nucleotidyl transferase domain (1);	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	L	0.28740	0.885	0.80722	D	1	P;P	0.51537	0.946;0.891	B;B	0.43331	0.416;0.416	T	0.34551	-0.9824	10	0.40728	T	0.16	-10.7623	18.4239	0.90602	0.0:0.0:1.0:0.0	.	19;19	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	K	19	ENSP00000230859:E19K	ENSP00000230859:E19K	E	+	1	0	PAPD7	6790711	1.000000	0.71417	0.998000	0.56505	0.872000	0.50106	8.832000	0.92079	2.346000	0.79739	0.484000	0.47621	GAA		0.433	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		A	6737711	G	A	6737711	3	1	61	1	0	0	0	0	1	0	0	0	11457	1059	37	1	57	1	PAPD7	5	6737711	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1250817	6737711	174177549	3669	11654										
PAPD7	11044	broad.mit.edu	37	chr5	6742698	6742698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggcagcggagttcatcaaGaattacatgaaggtactgtg	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:6742698G>T	ENST00000230859.6	+	5	483	c.354G>T	c.(352-354)aaG>aaT	p.K118N		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	348					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.K118N(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AGTTCATCAAGAATTACATGA	0.507																																					NSCLC(7;212 333 5667 23379 46547)											1	Substitution - Missense(1)	large_intestine(1)	5											76	72	73					5																	6742698		2203	4300	6503	6795698	SO:0001583	missense	11044			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.354G>T	5.37:g.6742698G>T	ENSP00000230859:p.Lys118Asn		6795698	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	37	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957205	0.73902	.	.	ENSG00000112941	ENST00000230859	T	0.43294	0.95	5.39	5.39	0.77823	Nucleotidyl transferase domain (1);	0.000000	0.85682	D	0.000000	T	0.50103	0.1596	L	0.53780	1.695	0.58432	D	0.999996	P;P	0.51240	0.885;0.943	P;P	0.53722	0.665;0.733	T	0.48139	-0.9061	10	0.49607	T	0.09	.	11.7653	0.51926	0.0805:0.0:0.9195:0.0	.	118;118	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	N	118	ENSP00000230859:K118N	ENSP00000230859:K118N	K	+	3	2	PAPD7	6795698	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.585000	0.46111	2.525000	0.85131	0.655000	0.94253	AAG		0.507	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		T	6742698	G	T	6742698	3	4	61	1	0	0	0	0	1	0	0	0	11457	933	33	2	368	2	PAPD7	5	6742698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4987	6742698	174172562	3670	11655										
PAPD7	11044	broad.mit.edu	37	chr5	6746444	6746444	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccggtattagaatcaaaGaaggaggtgcctatatcgcc	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:6746444G>T	ENST00000230859.6	+	7	742	c.613G>T	c.(613-615)Gaa>Taa	p.E205*		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	435					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.E205*(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TAGAATCAAAGAAGGAGGTGC	0.453																																					NSCLC(7;212 333 5667 23379 46547)											1	Substitution - Nonsense(1)	large_intestine(1)	5											96	105	102					5																	6746444		2203	4300	6503	6799444	SO:0001587	stop_gained	11044			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.613G>T	5.37:g.6746444G>T	ENSP00000230859:p.Glu205*		6799444	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Nonsense_Mutation	SNP	ENST00000230859.6	37	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	G	38	7.025086	0.98010	.	.	ENSG00000112941	ENST00000230859	.	.	.	5.77	4.79	0.61399	.	0.140259	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-0.7875	6.9471	0.24524	0.1925:0.0:0.8075:0.0	.	.	.	.	X	205	.	ENSP00000230859:E205X	E	+	1	0	PAPD7	6799444	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.305000	0.59110	2.724000	0.93272	0.561000	0.74099	GAA		0.453	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		T	6746444	G	T	6746444	4	4	61	1	0	0	0	0	0	1	0	0	11457	943	33	2	635	2	PAPD7	5	6746444	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3746	6746444	174168816	3671	11656										
PAPD7	11044	broad.mit.edu	37	chr5	6746517	6746517	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacagaccgtcgatgctgtGcattgaggaccccctgctgc	12	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:6746517G>T	ENST00000230859.6	+	7	815	c.686G>T	c.(685-687)tGc>tTc	p.C229F		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	459					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.C229F(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCGATGCTGTGCATTGAGGAC	0.572																																					NSCLC(7;212 333 5667 23379 46547)											1	Substitution - Missense(1)	large_intestine(1)	5											72	74	73					5																	6746517		2203	4300	6503	6799517	SO:0001583	missense	11044			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.686G>T	5.37:g.6746517G>T	ENSP00000230859:p.Cys229Phe		6799517	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	37	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775203	0.70107	.	.	ENSG00000112941	ENST00000230859	T	0.78707	-1.2	5.06	5.06	0.68205	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.87305	0.6144	M	0.84683	2.71	0.80722	D	1	D;D	0.59357	0.985;0.985	D;P	0.64144	0.922;0.886	D	0.88664	0.3191	10	0.66056	D	0.02	-7.2844	12.2007	0.54323	0.0785:0.0:0.9215:0.0	.	229;229	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	F	229	ENSP00000230859:C229F	ENSP00000230859:C229F	C	+	2	0	PAPD7	6799517	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.277000	0.58939	2.508000	0.84585	0.561000	0.74099	TGC		0.572	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		T	6746517	G	T	6746517	3	4	61	1	0	0	0	0	1	0	0	0	11457	1319	46	2	708	2	PAPD7	5	6746517	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73	6746517	174168743	3672	11657										
ADCY2	108	broad.mit.edu	37	chr5	7698376	7698376	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggagaatgaatgcatgaGaattaaaattttaggagact	10	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:7698376G>T	ENST00000338316.4	+	7	1087	c.998G>T	c.(997-999)aGa>aTa	p.R333I	ADCY2_ENST00000537121.1_Missense_Mutation_p.R153I	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	333					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.R333I(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GAATGCATGAGAATTAAAATT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											129	137	135					5																	7698376		2203	4300	6503	7751376	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.998G>T	5.37:g.7698376G>T	ENSP00000342952:p.Arg333Ile		7751376	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	32	5.162684	0.94727	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;T	0.81415	-1.49;-1.49	5.8	5.8	0.92144	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.92404	0.7589	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.93270	0.6651	10	0.87932	D	0	.	20.0545	0.97645	0.0:0.0:1.0:0.0	.	153;333	B7Z2C1;Q08462	.;ADCY2_HUMAN	I	333;184;153	ENSP00000342952:R333I;ENSP00000444803:R153I	ENSP00000342952:R333I	R	+	2	0	ADCY2	7751376	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.470000	0.97683	2.748000	0.94277	0.655000	0.94253	AGA		0.393	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7698376	G	T	7698376	3	4	61	1	0	0	0	0	1	0	0	0	294	942	33	2	1024	2	ADCY2	5	7698376	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	951859	7698376	173216884	3673	11658										
C5orf49	134121	broad.mit.edu	37	chr5	7835566	7835566	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcaacttctgatcataatCtaggcgcctcttaaaaatac	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:7835566C>A	ENST00000399810.2	-	2	661	c.193G>T	c.(193-195)Gat>Tat	p.D65Y	C5orf49_ENST00000509627.1_Missense_Mutation_p.D65Y	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	65								p.D65Y(1)		large_intestine(3)|lung(5)|skin(1)	9						TGATCATAATCTAGGCGCCTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											121	115	117					5																	7835566		1818	4076	5894	7888566	SO:0001583	missense	134121				CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.193G>T	5.37:g.7835566C>A	ENSP00000382708:p.Asp65Tyr		7888566		Missense_Mutation	SNP	ENST00000399810.2	37	CCDS43300.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757537	0.49468	.	.	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.33654	1.4;1.4	4.95	4.09	0.47781	.	.	.	.	.	T	0.41119	0.1145	L	0.38175	1.15	0.25521	N	0.98737	P	0.50528	0.936	P	0.53593	0.73	T	0.18429	-1.0337	9	0.62326	D	0.03	-8.882	10.7051	0.45950	0.0:0.9099:0.0:0.0901	.	65	A4QMS7	CE049_HUMAN	Y	65	ENSP00000382708:D65Y;ENSP00000426019:D65Y	ENSP00000382708:D65Y	D	-	1	0	C5orf49	7888566	0.910000	0.30920	0.053000	0.19242	0.601000	0.36947	2.461000	0.45040	1.232000	0.43678	0.561000	0.74099	GAT		0.368	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584		A	7835566	C	A	7835566	3	1	61	1	0	0	0	0	1	0	0	0	2313	913	32	2	258	2	C5orf49	5	7835566	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137190	7835566	173079694	3674	11659										
FASTKD3	79072	broad.mit.edu	37	chr5	7866971	7866971	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatggttccattaaggcaGaaatctgacgaggtgaaaat	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:7866971G>A	ENST00000264669.5	-	2	1362	c.1226C>T	c.(1225-1227)tCt>tTt	p.S409F	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	409					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.S409F(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CATTAAGGCAGAAATCTGACG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											54	55	55					5																	7866971		2203	4300	6503	7919971	SO:0001583	missense	79072			AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1226C>T	5.37:g.7866971G>A	ENSP00000264669:p.Ser409Phe		7919971	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	37	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741181	0.30865	.	.	ENSG00000124279	ENST00000264669	T	0.47177	0.85	4.95	4.05	0.47172	FAST kinase leucine-rich (1);	0.318470	0.32161	N	0.006481	T	0.57460	0.2055	L	0.47716	1.5	0.09310	N	0.999998	D	0.60160	0.987	D	0.63488	0.915	T	0.52366	-0.8585	10	0.22706	T	0.39	-12.9474	15.1736	0.72894	0.0:0.1416:0.8584:0.0	.	409	Q14CZ7	FAKD3_HUMAN	F	409	ENSP00000264669:S409F	ENSP00000264669:S409F	S	-	2	0	FASTKD3	7919971	0.998000	0.40836	0.001000	0.08648	0.106000	0.19336	4.848000	0.62874	1.231000	0.43661	0.655000	0.94253	TCT		0.378	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		A	7866971	G	A	7866971	3	1	61	1	0	0	0	0	1	0	0	0	5706	942	33	3	786	3	FASTKD3	5	7866971	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31405	7866971	173048289	3675	11660										
FASTKD3	79072	broad.mit.edu	37	chr5	7867316	7867316	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagcatttggctaatcaatTtaggactcaggttggaaact	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:7867316T>G	ENST00000264669.5	-	2	1017	c.881A>C	c.(880-882)aAa>aCa	p.K294T	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	294					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.K294T(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GCTAATCAATTTAGGACTCAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	100	96					5																	7867316		2203	4300	6503	7920316	SO:0001583	missense	79072			AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.881A>C	5.37:g.7867316T>G	ENSP00000264669:p.Lys294Thr		7920316	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	37	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	1.169	-0.641641	0.03531	.	.	ENSG00000124279	ENST00000264669	T	0.15256	2.44	4.85	-4.99	0.03010	.	0.822214	0.11526	N	0.555141	T	0.12433	0.0302	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.21724	-1.0237	10	0.23891	T	0.37	-1.1286	16.1468	0.81577	0.0:0.0641:0.7423:0.1937	.	294	Q14CZ7	FAKD3_HUMAN	T	294	ENSP00000264669:K294T	ENSP00000264669:K294T	K	-	2	0	FASTKD3	7920316	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.680000	0.05197	-1.092000	0.03062	-0.323000	0.08544	AAA		0.378	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867316	T	G	7867316	3	3	61	1	0	0	0	0	1	0	0	0	5706	1841	64	4	1131	4	FASTKD3	5	7867316	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	345	7867316	173047944	3676	11661										
SEMA5A	9037	broad.mit.edu	37	chr5	9154665	9154665	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtgctcccgcaggcccacGaacaggacactctggctgtg	12	15	1	0	rs377487102		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:9154665G>A	ENST00000382496.5	-	12	2081	c.1416C>T	c.(1414-1416)ttC>ttT	p.F472F		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	472	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.F472F(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCAGGCCCACGAACAGGACAC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	5											84	77	80					5																	9154665		2203	4300	6503	9207665	SO:0001819	synonymous_variant	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1416C>T	5.37:g.9154665G>A			9207665	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																				0.612	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			A	9154665	G	A	9154665	2	1	61	1	0	0	0	0	0	0	0	1	14074	1049	37	1		1	SEMA5A	5	9154665	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1287349	9154665	171760595	3677	11662										
SEMA5A	9037	broad.mit.edu	37	chr5	9237971	9237971	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgctgtaacaggcctttTtggtagcttcatcacactcc	7	12	2	0	rs371730082		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:9237971T>G	ENST00000382496.5	-	6	967	c.302A>C	c.(301-303)aAa>aCa	p.K101T		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	101	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.K101T(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						ACAGGCCTTTTTGGTAGCTTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											293	229	251					5																	9237971		2203	4300	6503	9290971	SO:0001583	missense	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.302A>C	5.37:g.9237971T>G	ENSP00000371936:p.Lys101Thr		9290971	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.35|13.35	2.210391|2.210391	0.39003|0.39003	.|.	.|.	ENSG00000112902|ENSG00000112902	ENST00000382496;ENST00000513968|ENST00000514923	T;T|.	0.10960|.	2.82;2.82|.	5.63|5.63	3.18|3.18	0.36537|0.36537	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);|.	0.143039|.	0.64402|.	D|.	0.000007|.	T|T	0.58595|0.58595	0.2133|0.2133	L|L	0.57536|0.57536	1.79|1.79	0.43334|0.43334	D|D	0.995371|0.995371	P|.	0.39131|.	0.661|.	P|.	0.44447|.	0.45|.	T|T	0.51725|0.51725	-0.8669|-0.8669	10|5	0.41790|.	T|.	0.15|.	.|.	7.4846|7.4846	0.27425|0.27425	0.0:0.1713:0.0:0.8287|0.0:0.1713:0.0:0.8287	.|.	101|.	Q13591|.	SEM5A_HUMAN|.	T|H	101|48	ENSP00000371936:K101T;ENSP00000421961:K101T|.	ENSP00000371936:K101T|.	K|Q	-|-	2|3	0|2	SEMA5A|SEMA5A	9290971|9290971	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.958000|0.958000	0.62258|0.62258	1.618000|1.618000	0.36954|0.36954	0.400000|0.400000	0.25396|0.25396	0.533000|0.533000	0.62120|0.62120	AAA|CAA		0.383	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			G	9237971	T	G	9237971	3	3	61	1	0	0	0	0	1	0	0	0	14074	1841	64	4	2994	4	SEMA5A	5	9237971	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	83306	9237971	171677289	3678	11663										
TAS2R1	50834	broad.mit.edu	37	chr5	9629254	9629254	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacttctctctcactgacaGcacttactgtggaggaggaa	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:9629254G>A	ENST00000382492.2	-	1	1209	c.891C>T	c.(889-891)tgC>tgT	p.C297C	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	297					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.C297C(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						CTCACTGACAGCACTTACTGT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	5											89	89	89					5																	9629254		2203	4300	6503	9682254	SO:0001819	synonymous_variant	50834			AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.891C>T	5.37:g.9629254G>A			9682254	Q646G8	Silent	SNP	ENST00000382492.2	37	CCDS3876.1																																																																																				0.413	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			A	9629254	G	A	9629254	2	1	61	1	0	0	0	0	0	0	0	1	15604	963	34	3		3	TAS2R1	5	9629254	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	391283	9629254	171286006	3679	11664										
FAM173B	134145	broad.mit.edu	37	chr5	10227742	10227742	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagttcacgttcaagtttCttctccaactgcagcatctg	6	12	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10227742C>A	ENST00000511437.1	-	5	525	c.513G>T	c.(511-513)aaG>aaT	p.K171N	FAM173B_ENST00000510047.1_Missense_Mutation_p.K154N|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_Missense_Mutation_p.K7N	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	171						integral component of membrane (GO:0016021)		p.K171N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						GTTCAAGTTTCTTCTCCAACT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	86	88					5																	10227742		1953	4156	6109	10280742	SO:0001583	missense	134145				CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.513G>T	5.37:g.10227742C>A	ENSP00000422338:p.Lys171Asn		10280742	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	37	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442257	0.43326	.	.	ENSG00000150756	ENST00000280330;ENST00000511437;ENST00000510047	T;T;T	0.21543	2.19;2.19;2.0	4.93	3.99	0.46301	.	0.420676	0.28042	N	0.016824	T	0.19446	0.0467	L	0.43152	1.355	0.42055	D	0.991138	B;B	0.20459	0.019;0.045	B;B	0.21546	0.012;0.035	T	0.03945	-1.0990	10	0.32370	T	0.25	-14.5423	13.7707	0.63023	0.0:0.8454:0.1546:0.0	.	154;171	E9PBZ4;Q6P4H8	.;F173B_HUMAN	N	7;171;154	ENSP00000280330:K7N;ENSP00000422338:K171N;ENSP00000420876:K154N	ENSP00000280330:K7N	K	-	3	2	FAM173B	10280742	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.285000	0.33261	2.455000	0.83008	0.650000	0.86243	AAG		0.468	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		A	10227742	C	A	10227742	3	1	61	1	0	0	0	0	1	0	0	0	5510	912	32	2	192	2	FAM173B	5	10227742	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	598488	10227742	170687518	3680	11665										
FAM173B	134145	broad.mit.edu	37	chr5	10239294	10239294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacggcaaacagacttttCgaagggctggcgttacaaac	10	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10239294C>T	ENST00000511437.1	-	2	203	c.191G>A	c.(190-192)cGa>cAa	p.R64Q	FAM173B_ENST00000510047.1_Missense_Mutation_p.R64Q|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_5'UTR	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	64						integral component of membrane (GO:0016021)		p.R64Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						ACAGACTTTTCGAAGGGCTGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	108	108					5																	10239294		2037	4175	6212	10292294	SO:0001583	missense	134145				CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.191G>A	5.37:g.10239294C>T	ENSP00000422338:p.Arg64Gln		10292294	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	37	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.641436	0.87859	.	.	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.25912	1.77;1.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	M	0.88181	2.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.992	T	0.68179	-0.5477	10	0.87932	D	0	-31.6697	17.7316	0.88379	0.0:1.0:0.0:0.0	.	64;64	E9PBZ4;Q6P4H8	.;F173B_HUMAN	Q	64	ENSP00000422338:R64Q;ENSP00000420876:R64Q	ENSP00000424210:R64Q	R	-	2	0	FAM173B	10292294	1.000000	0.71417	0.853000	0.33588	0.348000	0.29142	6.966000	0.76073	2.430000	0.82344	0.655000	0.94253	CGA		0.507	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		T	10239294	C	T	10239294	3	4	61	1	0	0	0	0	1	0	0	0	5510	884	31	1	526	1	FAM173B	5	10239294	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11552	10239294	170675966	3681	11666										
CCT5	22948	broad.mit.edu	37	chr5	10262652	10262652	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtcatccggaacctcatCcgcgataatcgtgtggtgta	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10262652C>T	ENST00000280326.4	+	9	1659	c.1239C>T	c.(1237-1239)atC>atT	p.I413I	CCT5_ENST00000515676.1_Silent_p.I375I|CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000515390.1_Silent_p.I358I|CCT5_ENST00000503026.1_Silent_p.I392I|CCT5_ENST00000506600.1_Silent_p.I320I	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	413					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)	p.I413I(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						GGAACCTCATCCGCGATAATC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	5											176	142	153					5																	10262652		2203	4300	6503	10315652	SO:0001819	synonymous_variant	22948			D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1239C>T	5.37:g.10262652C>T			10315652	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																				0.493	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			T	10262652	C	T	10262652	2	4	61	1	0	0	0	0	0	0	0	1	2962	845	30	3		3	CCT5	5	10262652	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23358	10262652	170652608	3682	11667										
MARCH6	10299	broad.mit.edu	37	chr5	10390608	10390608	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcggggcatcaccaaaAtgaggtaactcccctacccc	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10390608A>G	ENST00000274140.5	+	6	704	c.572A>G	c.(571-573)aAt>aGt	p.N191S	MARCH6_ENST00000503788.1_Missense_Mutation_p.N86S|MARCH6_ENST00000449913.2_Missense_Mutation_p.N143S	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	191					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N191S(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						CATCACCAAAATGAGGTAACT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	76	77					5																	10390608		2203	4300	6503	10443608	SO:0001583	missense	10299			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	30550	protein-coding gene	gene with protein product		613297	"membrane-associated ring finger (C3HC4) 6"			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.572A>G	5.37:g.10390608A>G	ENSP00000274140:p.Asn191Ser		10443608	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708459	0.48517	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140	T;T;T	0.43688	1.97;0.94;1.97	5.78	4.61	0.57282	.	0.091871	0.64402	D	0.000001	T	0.32466	0.0830	L	0.43152	1.355	0.80722	D	1	B;B;B	0.26547	0.152;0.02;0.126	B;B;B	0.25140	0.058;0.027;0.055	T	0.06180	-1.0841	10	0.09843	T	0.71	-4.2309	12.3921	0.55364	0.874:0.0:0.0:0.126	.	86;143;191	B4DKJ2;B4DT33;O60337	.;.;MARH6_HUMAN	S	143;86;191	ENSP00000414643:N143S;ENSP00000425930:N86S;ENSP00000274140:N191S	ENSP00000274140:N191S	N	+	2	0	MARCH6	10443608	1.000000	0.71417	0.930000	0.37139	0.965000	0.64279	6.160000	0.71862	0.998000	0.38996	0.528000	0.53228	AAT		0.478	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		G	10390608	A	G	10390608	3	3	61	1	0	0	0	0	1	0	0	0	9335	101	4	4	594	4	MARCH6	5	10390608	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	127956	10390608	170524652	3683	11668										
MARCH6	10299	broad.mit.edu	37	chr5	10433737	10433737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaacgactcgtgaactacGaacggaaatctggcaaacaa	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10433737G>A	ENST00000274140.5	+	26	2806	c.2674G>A	c.(2674-2676)Gaa>Aaa	p.E892K	MARCH6_ENST00000503788.1_Missense_Mutation_p.E787K|MARCH6_ENST00000449913.2_Missense_Mutation_p.E844K|MARCH6_ENST00000510792.1_Missense_Mutation_p.E590K	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	892					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E892K(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						CGTGAACTACGAACGGAAATC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											221	176	191					5																	10433737		2203	4300	6503	10486737	SO:0001583	missense	10299			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	30550	protein-coding gene	gene with protein product		613297	"membrane-associated ring finger (C3HC4) 6"			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.2674G>A	5.37:g.10433737G>A	ENSP00000274140:p.Glu892Lys		10486737	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	G	33	5.215864	0.95104	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.47528	1.84;0.84;1.84;0.84	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.68696	0.3029	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.998;1.0	D;P;P;P	0.72625	0.978;0.825;0.828;0.9	T	0.63211	-0.6688	10	0.23302	T	0.38	-20.9079	19.6511	0.95812	0.0:0.0:1.0:0.0	.	787;844;472;892	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	K	844;787;892;590	ENSP00000414643:E844K;ENSP00000425930:E787K;ENSP00000274140:E892K;ENSP00000424512:E590K	ENSP00000274140:E892K	E	+	1	0	MARCH6	10486737	1.000000	0.71417	0.882000	0.34594	0.919000	0.55068	9.241000	0.95402	2.646000	0.89796	0.563000	0.77884	GAA		0.428	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		A	10433737	G	A	10433737	3	1	61	1	0	0	0	0	1	0	0	0	9335	1059	37	1	2776	1	MARCH6	5	10433737	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43129	10433737	170481523	3684	11669										
DAP	1611	broad.mit.edu	37	chr5	10748365	10748365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggtgtttctgcacaattCgcattccaccagctttcact	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:10748365C>T	ENST00000230895.6	-	2	277	c.74G>A	c.(73-75)cGa>cAa	p.R25Q	DAP_ENST00000432074.2_Missense_Mutation_p.R25Q|DAP_ENST00000510546.1_5'UTR	NM_004394.2	NP_004385.1	P51397	DAP1_HUMAN	death-associated protein	25					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cellular response to amino acid starvation (GO:0034198)|negative regulation of autophagy (GO:0010507)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)		death domain binding (GO:0070513)	p.R25Q(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				CTGCACAATTCGCATTCCACC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											205	164	178					5																	10748365		2203	4300	6503	10801365	SO:0001583	missense	1611			X76105	CCDS3880.1	5p15.2	2008-07-18			ENSG00000112977	ENSG00000112977			2672	protein-coding gene	gene with protein product		600954				8530096, 7828849	Standard	NM_004394		Approved		uc003jez.4	P51397	OTTHUMG00000131041	ENST00000230895.6:c.74G>A	5.37:g.10748365C>T	ENSP00000230895:p.Arg25Gln		10801365	Q6FGC3|Q9BUC9	Missense_Mutation	SNP	ENST00000230895.6	37	CCDS3880.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816953	0.70912	.	.	ENSG00000112977	ENST00000230895;ENST00000432074	T;T	0.61859	0.07;0.07	5.04	3.24	0.37175	.	.	.	.	.	T	0.74558	0.3732	M	0.85099	2.735	0.35460	D	0.79644	D;D	0.89917	0.996;1.0	P;D	0.83275	0.643;0.996	T	0.78999	-0.1982	9	0.87932	D	0	.	7.5169	0.27606	0.1635:0.7504:0.0:0.0861	.	25;25	B4DQ75;P51397	.;DAP1_HUMAN	Q	25	ENSP00000230895:R25Q;ENSP00000394163:R25Q	ENSP00000230895:R25Q	R	-	2	0	DAP	10801365	1.000000	0.71417	0.391000	0.26233	0.951000	0.60555	4.581000	0.60949	0.519000	0.28406	0.655000	0.94253	CGA		0.502	DAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253687.1	NM_004394		T	10748365	C	T	10748365	3	4	61	1	0	0	0	0	1	0	0	0	4239	884	31	1	246	1	DAP	5	10748365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314628	10748365	170166895	3685	11670										
CTNND2	1501	broad.mit.edu	37	chr5	11411651	11411651	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgccacgtgacttactttCacctgtagaataatcctgtg	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:11411651C>A	ENST00000304623.8	-	5	625	c.436G>T	c.(436-438)Gaa>Taa	p.E146*	CTNND2_ENST00000503622.1_Nonsense_Mutation_p.E55*|CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000359640.2_Nonsense_Mutation_p.E146*|CTNND2_ENST00000511377.1_Nonsense_Mutation_p.E55*	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	146					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E146*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GACTTACTTTCACCTGTAGAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											152	142	145					5																	11411651		2203	4300	6503	11464651	SO:0001587	stop_gained	1501			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.436G>T	5.37:g.11411651C>A	ENSP00000307134:p.Glu146*		11464651	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Nonsense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	40	8.166475	0.98686	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000503622;ENST00000502551;ENST00000513598;ENST00000508761	.	.	.	5.96	5.96	0.96718	.	0.249863	0.34245	N	0.004132	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	.	.	.	X	146;146;55;55;132;55;132	.	ENSP00000307134:E146X	E	-	1	0	CTNND2	11464651	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	7.230000	0.78097	2.832000	0.97577	0.655000	0.94253	GAA		0.378	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11411651	C	A	11411651	4	1	61	1	0	0	0	0	0	1	0	0	4026	835	29	2	3313	2	CTNND2	5	11411651	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	663286	11411651	169503609	3686	11671										
CTNND2	1501	broad.mit.edu	37	chr5	11412150	11412150	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataagatagacattaccttGtgactgccactgaaactgct	7	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:11412150G>A	ENST00000304623.8	-	4	508	c.319C>T	c.(319-321)Caa>Taa	p.Q107*	CTNND2_ENST00000503622.1_Nonsense_Mutation_p.Q16*|CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000359640.2_Nonsense_Mutation_p.Q107*|CTNND2_ENST00000511377.1_Nonsense_Mutation_p.Q16*	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	107					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.Q107*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						ACATTACCTTGTGACTGCCAC	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											118	120	119					5																	11412150		2203	4298	6501	11465150	SO:0001587	stop_gained	1501			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.319C>T	5.37:g.11412150G>A	ENSP00000307134:p.Gln107*		11465150	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Nonsense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	39	7.387945	0.98252	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000503622;ENST00000502551;ENST00000513598;ENST00000508761	.	.	.	5.68	5.68	0.88126	.	0.664722	0.14774	N	0.299237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	13.7138	0.62685	0.0:0.0:0.8461:0.1538	.	.	.	.	X	107;107;16;16;93;16;93	.	ENSP00000307134:Q107X	Q	-	1	0	CTNND2	11465150	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	6.592000	0.74095	2.678000	0.91216	0.585000	0.79938	CAA		0.299	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11412150	G	A	11412150	4	1	61	1	0	0	0	0	0	1	0	0	4026	1386	48	3	3434	3	CTNND2	5	11412150	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	499	11412150	169503110	3687	11672										
DNAH5	1767	broad.mit.edu	37	chr5	13721199	13721199	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctatttttaatctcttCcccaaggcaatgatggaatc	6	9	2	1	rs144879072		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13721199C>A	ENST00000265104.4	-	71	12293	c.12189G>T	c.(12187-12189)ggG>ggT	p.G4063G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4063	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G4063G(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTAATCTCTTCCCCAAGGCAA	0.527									Kartagener syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	5											112	114	113					5																	13721199		2203	4300	6503	13774199	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12189G>T	5.37:g.13721199C>A			13774199	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.527	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13721199	C	A	13721199	2	1	61	1	0	0	0	0	0	0	0	1	4615	842	30	2		2	DNAH5	5	13721199	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2309049	13721199	167194061	3688	11673										
DNAH5	1767	broad.mit.edu	37	chr5	13769110	13769110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaaagctggttttgctgCttccagtttttcttcagcaa	7	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13769110C>T	ENST00000265104.4	-	58	9960	c.9856G>A	c.(9856-9858)Gca>Aca	p.A3286T	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3286	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A3286T(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GGTTTTGCTGCTTCCAGTTTT	0.463									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											224	210	215					5																	13769110		2203	4300	6503	13822110	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9856G>A	5.37:g.13769110C>T	ENSP00000265104:p.Ala3286Thr		13822110	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172107	0.94807	.	.	ENSG00000039139	ENST00000265104	T	0.74209	-0.82	5.76	4.89	0.63831	Dynein heavy chain, coiled coil stalk (1);	0.049230	0.85682	N	0.000000	D	0.89656	0.6778	H	0.95043	3.615	0.80722	D	1	D	0.56521	0.976	D	0.66979	0.948	D	0.92595	0.6086	10	0.66056	D	0.02	.	15.2786	0.73764	0.0:0.9325:0.0:0.0675	.	3286	Q8TE73	DYH5_HUMAN	T	3286	ENSP00000265104:A3286T	ENSP00000265104:A3286T	A	-	1	0	DNAH5	13822110	1.000000	0.71417	0.978000	0.43139	0.978000	0.69477	3.309000	0.51903	1.575000	0.49775	0.655000	0.94253	GCA		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13769110	C	T	13769110	3	4	61	1	0	0	0	0	1	0	0	0	4615	797	28	3	4106	3	DNAH5	5	13769110	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47911	13769110	167146150	3689	11674										
DNAH5	1767	broad.mit.edu	37	chr5	13777394	13777394	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgaaaataaaagtgattcCtttgccttgctgaccagctg	9	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13777394C>A	ENST00000265104.4	-	54	9126	c.9022G>T	c.(9022-9024)Gga>Tga	p.G3008*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3008	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G3008*(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAAGTGATTCCTTTGCCTTGC	0.333									Kartagener syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	5											114	108	110					5																	13777394		2203	4300	6503	13830394	SO:0001587	stop_gained	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9022G>T	5.37:g.13777394C>A	ENSP00000265104:p.Gly3008*		13830394	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	52	18.620224	0.99908	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1972	0.93695	0.0:1.0:0.0:0.0	.	.	.	.	X	3008	.	ENSP00000265104:G3008X	G	-	1	0	DNAH5	13830394	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.684000	0.84104	2.532000	0.85374	0.655000	0.94253	GGA		0.333	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13777394	C	A	13777394	4	1	61	1	0	0	0	0	0	1	0	0	4615	690	24	2	4956	2	DNAH5	5	13777394	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8284	13777394	167137866	3690	11675										
DNAH5	1767	broad.mit.edu	37	chr5	13792162	13792162	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctgccagacccgagaaaGatctcgtaggttaaacacat	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13792162G>A	ENST00000265104.4	-	50	8493	c.8389C>T	c.(8389-8391)Ctt>Ttt	p.L2797F		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2797	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L2797F(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ACCCGAGAAAGATCTCGTAGG	0.418									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											91	89	89					5																	13792162		2203	4300	6503	13845162	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8389C>T	5.37:g.13792162G>A	ENSP00000265104:p.Leu2797Phe		13845162	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.608284	0.87258	.	.	ENSG00000039139	ENST00000265104	T	0.42513	0.97	5.42	4.53	0.55603	.	0.060929	0.64402	D	0.000003	T	0.65698	0.2716	M	0.78285	2.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70648	-0.4814	10	0.59425	D	0.04	.	15.685	0.77402	0.0:0.0:0.8617:0.1383	.	2797	Q8TE73	DYH5_HUMAN	F	2797	ENSP00000265104:L2797F	ENSP00000265104:L2797F	L	-	1	0	DNAH5	13845162	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.607000	0.74163	1.385000	0.46445	0.591000	0.81541	CTT		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13792162	G	A	13792162	3	1	61	1	0	0	0	0	1	0	0	0	4615	942	33	3	5605	3	DNAH5	5	13792162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14768	13792162	167123098	3691	11676										
DNAH5	1767	broad.mit.edu	37	chr5	13793683	13793683	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattaaatatagagaactgcCtcttgagtctttggggtatg	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13793683C>A	ENST00000265104.4	-	49	8269	c.8165G>T	c.(8164-8166)aGg>aTg	p.R2722M		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2722	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2722M(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAGAACTGCCTCTTGAGTCT	0.498									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											160	161	160					5																	13793683		2203	4300	6503	13846683	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8165G>T	5.37:g.13793683C>A	ENSP00000265104:p.Arg2722Met		13846683	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191014	0.78789	.	.	ENSG00000039139	ENST00000265104	T	0.48201	0.82	5.7	4.83	0.62350	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.83640	0.5298	H	0.99800	4.79	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91756	0.5416	10	0.87932	D	0	.	16.1629	0.81732	0.1343:0.8657:0.0:0.0	.	2722	Q8TE73	DYH5_HUMAN	M	2722	ENSP00000265104:R2722M	ENSP00000265104:R2722M	R	-	2	0	DNAH5	13846683	1.000000	0.71417	0.999000	0.59377	0.883000	0.51084	7.687000	0.84139	1.400000	0.46741	0.557000	0.71058	AGG		0.498	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13793683	C	A	13793683	3	1	61	1	0	0	0	0	1	0	0	0	4615	681	24	2	5833	2	DNAH5	5	13793683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1521	13793683	167121577	3692	11677										
DNAH5	1767	broad.mit.edu	37	chr5	13807783	13807783	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatattttgacataaatcCtttaattattactgttttgg	4	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13807783C>A	ENST00000265104.4	-	47	7908	c.7804G>T	c.(7804-7806)Gga>Tga	p.G2602*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2602	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G2602*(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GACATAAATCCTTTAATTATT	0.348									Kartagener syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	5											124	118	120					5																	13807783		2203	4300	6503	13860783	SO:0001587	stop_gained	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.7804G>T	5.37:g.13807783C>A	ENSP00000265104:p.Gly2602*		13860783	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	49	15.058656	0.99820	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.87	5.87	0.94306	.	0.103153	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	16.5043	0.84266	0.1313:0.8687:0.0:0.0	.	.	.	.	X	2602	.	ENSP00000265104:G2602X	G	-	1	0	DNAH5	13860783	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	4.058000	0.57463	2.770000	0.95276	0.650000	0.86243	GGA		0.348	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13807783	C	A	13807783	4	1	61	1	0	0	0	0	0	1	0	0	4615	690	24	2	6202	2	DNAH5	5	13807783	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14100	13807783	167107477	3693	11678										
DNAH5	1767	broad.mit.edu	37	chr5	13830838	13830838	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgcaggtccagcaggggCtccccccatgctcattccca	10	18	1	0	rs143894811		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13830838C>A	ENST00000265104.4	-	36	6033	c.5929G>T	c.(5929-5931)Gcc>Tcc	p.A1977S		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1977	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A1977S(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCAGCAGGGGCTCCCCCCATG	0.512									Kartagener syndrome				C|||	1	0.000199681	0	0.0014	5008	,	,		16942	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											116	113	114					5																	13830838		2203	4300	6503	13883838	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5929G>T	5.37:g.13830838C>A	ENSP00000265104:p.Ala1977Ser		13883838	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	24.4	4.523966	0.85600	.	.	ENSG00000039139	ENST00000265104	T	0.13657	2.57	5.53	5.53	0.82687	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.28400	0.0702	L	0.52126	1.63	0.80722	D	1	P	0.50369	0.934	P	0.55824	0.785	T	0.00186	-1.1942	10	0.33141	T	0.24	.	19.4895	0.95044	0.0:1.0:0.0:0.0	.	1977	Q8TE73	DYH5_HUMAN	S	1977	ENSP00000265104:A1977S	ENSP00000265104:A1977S	A	-	1	0	DNAH5	13883838	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.818000	0.86416	2.596000	0.87737	0.655000	0.94253	GCC		0.512	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13830838	C	A	13830838	3	1	61	1	0	0	0	0	1	0	0	0	4615	797	28	2	8121	2	DNAH5	5	13830838	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23055	13830838	167084422	3694	11679										
DNAH5	1767	broad.mit.edu	37	chr5	13839610	13839610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtttcagccactcaaagtCcatgggactcttgatatgca	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13839610C>A	ENST00000265104.4	-	35	5841	c.5737G>T	c.(5737-5739)Gac>Tac	p.D1913Y		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1913	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D1913Y(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACTCAAAGTCCATGGGACTC	0.353									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											87	84	85					5																	13839610		2203	4300	6503	13892610	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5737G>T	5.37:g.13839610C>A	ENSP00000265104:p.Asp1913Tyr		13892610	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477987	0.63849	.	.	ENSG00000039139	ENST00000265104	T	0.30448	1.53	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	H	0.97707	4.06	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.83023	-0.0166	10	0.87932	D	0	.	17.1545	0.86787	0.0:1.0:0.0:0.0	.	1913	Q8TE73	DYH5_HUMAN	Y	1913	ENSP00000265104:D1913Y	ENSP00000265104:D1913Y	D	-	1	0	DNAH5	13892610	1.000000	0.71417	0.949000	0.38748	0.382000	0.30200	7.792000	0.85828	2.300000	0.77407	0.650000	0.86243	GAC		0.353	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13839610	C	A	13839610	3	1	61	1	0	0	0	0	1	0	0	0	4615	855	30	2	8317	2	DNAH5	5	13839610	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8772	13839610	167075650	3695	11680										
DNAH5	1767	broad.mit.edu	37	chr5	13868025	13868025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcagcttctcccaagcaTagtgcagtgtatcaactttg	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13868025T>C	ENST00000265104.4	-	25	4015	c.3911A>G	c.(3910-3912)tAt>tGt	p.Y1304C	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1304	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Y1304C(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTCCCAAGCATAGTGCAGTGT	0.418									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											120	103	109					5																	13868025		2203	4300	6503	13921025	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3911A>G	5.37:g.13868025T>C	ENSP00000265104:p.Tyr1304Cys		13921025	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.692056	0.48097	.	.	ENSG00000039139	ENST00000265104	T	0.23950	1.88	5.12	5.12	0.69794	.	0.131039	0.52532	D	0.000064	T	0.57695	0.2071	M	0.91818	3.245	0.58432	D	0.999997	D	0.76494	0.999	D	0.68765	0.96	T	0.65981	-0.6036	10	0.42905	T	0.14	.	14.9244	0.70866	0.0:0.0:0.0:1.0	.	1304	Q8TE73	DYH5_HUMAN	C	1304	ENSP00000265104:Y1304C	ENSP00000265104:Y1304C	Y	-	2	0	DNAH5	13921025	1.000000	0.71417	0.613000	0.29037	0.827000	0.46813	5.806000	0.69150	1.941000	0.56285	0.533000	0.62120	TAT		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13868025	T	C	13868025	3	2	61	1	0	0	0	0	1	0	0	0	4615	1406	49	4	10183	4	DNAH5	5	13868025	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	28415	13868025	167047235	3696	11681										
DNAH5	1767	broad.mit.edu	37	chr5	13871031	13871031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatgttttccatctcacTccggtattttttgttacagt	5	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13871031T>C	ENST00000265104.4	-	24	3783	c.3679A>G	c.(3679-3681)Agt>Ggt	p.S1227G	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1227	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S1227G(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCATCTCACTCCGGTATTTT	0.408									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											105	105	105					5																	13871031		2203	4300	6503	13924031	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3679A>G	5.37:g.13871031T>C	ENSP00000265104:p.Ser1227Gly		13924031	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.670168	0.29693	.	.	ENSG00000039139	ENST00000265104	T	0.24151	1.87	5.84	3.34	0.38264	.	0.496735	0.23620	N	0.046253	T	0.15609	0.0376	L	0.33485	1.01	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23084	-1.0198	10	0.27082	T	0.32	.	4.241	0.10648	0.1242:0.0668:0.1297:0.6793	.	1227	Q8TE73	DYH5_HUMAN	G	1227	ENSP00000265104:S1227G	ENSP00000265104:S1227G	S	-	1	0	DNAH5	13924031	0.038000	0.19896	0.996000	0.52242	0.993000	0.82548	1.046000	0.30354	0.420000	0.25954	0.533000	0.62120	AGT		0.408	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13871031	T	C	13871031	3	2	61	1	0	0	0	0	1	0	0	0	4615	1551	54	4	10419	4	DNAH5	5	13871031	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3006	13871031	167044229	3697	11682										
DNAH5	1767	broad.mit.edu	37	chr5	13871755	13871755	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttttggaaatagagaatCtgggactcaaattcagaaag	11	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13871755C>A	ENST00000265104.4	-	23	3620	c.3516G>T	c.(3514-3516)caG>caT	p.Q1172H	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1172	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Q1172H(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AATAGAGAATCTGGGACTCAA	0.398									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											122	136	131					5																	13871755		2203	4300	6503	13924755	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3516G>T	5.37:g.13871755C>A	ENSP00000265104:p.Gln1172His		13924755	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.473058	0.43942	.	.	ENSG00000039139	ENST00000265104	T	0.25085	1.82	5.99	5.99	0.97316	.	0.176544	0.51477	D	0.000091	T	0.26991	0.0661	L	0.56769	1.78	0.53688	D	0.999971	B	0.02656	0.0	B	0.08055	0.003	T	0.02950	-1.1090	10	0.54805	T	0.06	.	11.3742	0.49717	0.0:0.8925:0.0:0.1075	.	1172	Q8TE73	DYH5_HUMAN	H	1172	ENSP00000265104:Q1172H	ENSP00000265104:Q1172H	Q	-	3	2	DNAH5	13924755	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.691000	0.61738	2.840000	0.97914	0.655000	0.94253	CAG		0.398	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13871755	C	A	13871755	3	1	61	1	0	0	0	0	1	0	0	0	4615	912	32	2	10586	2	DNAH5	5	13871755	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	724	13871755	167043505	3698	11683										
DNAH5	1767	broad.mit.edu	37	chr5	13876877	13876877	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacattcttataatagttCttggtttgcacgggaatggg	11	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13876877C>A	ENST00000265104.4	-	22	3416	c.3312G>T	c.(3310-3312)aaG>aaT	p.K1104N	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1104	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K1104N(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TATAATAGTTCTTGGTTTGCA	0.333									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											92	100	97					5																	13876877		2203	4300	6503	13929877	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3312G>T	5.37:g.13876877C>A	ENSP00000265104:p.Lys1104Asn		13929877	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.221489	0.39300	.	.	ENSG00000039139	ENST00000265104	T	0.24350	1.86	5.5	3.68	0.42216	.	0.313497	0.38326	N	0.001722	T	0.14270	0.0345	N	0.16790	0.44	0.46028	D	0.998822	B	0.06786	0.001	B	0.09377	0.004	T	0.05767	-1.0865	10	0.51188	T	0.08	.	6.7977	0.23734	0.1472:0.7116:0.0:0.1412	.	1104	Q8TE73	DYH5_HUMAN	N	1104	ENSP00000265104:K1104N	ENSP00000265104:K1104N	K	-	3	2	DNAH5	13929877	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.088000	0.30877	1.442000	0.47568	-0.181000	0.13052	AAG		0.333	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13876877	C	A	13876877	3	1	61	1	0	0	0	0	1	0	0	0	4615	912	32	2	10794	2	DNAH5	5	13876877	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5122	13876877	167038383	3699	11684										
DNAH5	1767	broad.mit.edu	37	chr5	13885136	13885136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaggaatgaatacgtttgCgaatggcctctagtgtattc	12	6	1	2	rs200704983		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13885136C>T	ENST00000265104.4	-	19	3049	c.2945G>A	c.(2944-2946)cGc>cAc	p.R982H	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	982	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R982H(2)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AATACGTTTGCGAATGGCCTC	0.443									Kartagener syndrome				C|||	1	0.000199681	0	0	5008	,	,		16035	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	5											126	118	121					5																	13885136		2203	4300	6503	13938136	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2945G>A	5.37:g.13885136C>T	ENSP00000265104:p.Arg982His		13938136	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	22.0	4.237217	0.79800	.	.	ENSG00000039139	ENST00000265104	T	0.25579	1.79	5.73	5.73	0.89815	.	0.056303	0.64402	D	0.000001	T	0.35885	0.0947	M	0.78049	2.395	0.80722	D	1	B	0.30179	0.271	B	0.26310	0.068	T	0.21109	-1.0255	10	0.59425	D	0.04	.	19.9025	0.96993	0.0:1.0:0.0:0.0	.	982	Q8TE73	DYH5_HUMAN	H	982	ENSP00000265104:R982H	ENSP00000265104:R982H	R	-	2	0	DNAH5	13938136	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.251000	0.78297	2.722000	0.93159	0.655000	0.94253	CGC		0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13885136	C	T	13885136	3	4	61	1	0	0	0	0	1	0	0	0	4615	768	27	1	11173	1	DNAH5	5	13885136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8259	13885136	167030124	3700	11685										
DNAH5	1767	broad.mit.edu	37	chr5	13920716	13920716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaagtatgtcacactttCgaaggttcacctaattagaa	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13920716C>T	ENST00000265104.4	-	6	775	c.671G>A	c.(670-672)cGa>cAa	p.R224Q		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	224	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R224Q(2)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTCACACTTTCGAAGGTTCAC	0.393									Kartagener syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	5											106	103	104					5																	13920716		2202	4299	6501	13973716	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.671G>A	5.37:g.13920716C>T	ENSP00000265104:p.Arg224Gln		13973716	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	.	2.481	-0.319707	0.05386	.	.	ENSG00000039139	ENST00000265104	T	0.22743	1.94	6.07	3.46	0.39613	.	0.160905	0.52532	N	0.000074	T	0.09512	0.0234	N	0.08118	0	0.21933	N	0.999469	B	0.02656	0.0	B	0.04013	0.001	T	0.37572	-0.9700	10	0.12103	T	0.63	.	10.1659	0.42879	0.0:0.1769:0.0:0.8231	.	224	Q8TE73	DYH5_HUMAN	Q	224	ENSP00000265104:R224Q	ENSP00000265104:R224Q	R	-	2	0	DNAH5	13973716	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	4.758000	0.62220	0.190000	0.20209	-1.851000	0.00568	CGA		0.393	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13920716	C	T	13920716	3	4	61	1	0	0	0	0	1	0	0	0	4615	884	31	1	13499	1	DNAH5	5	13920716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35580	13920716	166994544	3701	11686										
DNAH5	1767	broad.mit.edu	37	chr5	13923496	13923496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcggtcacgaacaccttagGttttttaatctttccagaaa	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13923496G>T	ENST00000265104.4	-	4	435	c.331C>A	c.(331-333)Cct>Act	p.P111T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	111	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P111T(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AACACCTTAGGTTTTTTAATC	0.428									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											137	135	136					5																	13923496		2203	4300	6503	13976496	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.331C>A	5.37:g.13923496G>T	ENSP00000265104:p.Pro111Thr		13976496	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	9.792	1.178225	0.21787	.	.	ENSG00000039139	ENST00000265104	T	0.22336	1.96	5.68	5.68	0.88126	.	0.179769	0.49916	D	0.000137	T	0.25754	0.0627	L	0.57536	1.79	0.42313	D	0.992225	B	0.09022	0.002	B	0.09377	0.004	T	0.04900	-1.0919	10	0.23302	T	0.38	.	19.7966	0.96487	0.0:0.0:1.0:0.0	.	111	Q8TE73	DYH5_HUMAN	T	111	ENSP00000265104:P111T	ENSP00000265104:P111T	P	-	1	0	DNAH5	13976496	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	1.606000	0.36826	2.676000	0.91093	0.650000	0.86243	CCT		0.428	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13923496	G	T	13923496	3	4	61	1	0	0	0	0	1	0	0	0	4615	1261	44	2	13847	2	DNAH5	5	13923496	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2780	13923496	166991764	3702	11687										
DNAH5	1767	broad.mit.edu	37	chr5	13928280	13928280	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaaaaagttgatcaattCtttcaatctgggaaaaagaa	7	6	4	2	rs563017861		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:13928280C>A	ENST00000265104.4	-	3	304	c.200G>T	c.(199-201)aGa>aTa	p.R67I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	67	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R67I(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTGATCAATTCTTTCAATCTG	0.318									Kartagener syndrome				C|||	1	0.000199681	0	0.0014	5008	,	,		19786	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											87	89	88					5																	13928280		2203	4300	6503	13981280	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.200G>T	5.37:g.13928280C>A	ENSP00000265104:p.Arg67Ile		13981280	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010598	0.35511	.	.	ENSG00000039139	ENST00000265104	T	0.23754	1.89	5.21	4.33	0.51752	.	0.105878	0.64402	D	0.000004	T	0.21227	0.0511	L	0.38838	1.175	0.80722	D	1	B	0.23650	0.089	B	0.23275	0.045	T	0.03221	-1.1059	10	0.37606	T	0.19	.	13.518	0.61551	0.0:0.9245:0.0:0.0755	.	67	Q8TE73	DYH5_HUMAN	I	67	ENSP00000265104:R67I	ENSP00000265104:R67I	R	-	2	0	DNAH5	13981280	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	4.318000	0.59190	2.589000	0.87451	0.655000	0.94253	AGA		0.318	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13928280	C	A	13928280	3	1	61	1	0	0	0	0	1	0	0	0	4615	913	32	2	13982	2	DNAH5	5	13928280	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4784	13928280	166986980	3703	11688										
TRIO	7204	broad.mit.edu	37	chr5	14291124	14291124	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctggatttggagggacaGaagctgcttcagaggataca	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:14291124G>A	ENST00000344204.4	+	5	864	c.840G>A	c.(838-840)caG>caA	p.Q280Q	TRIO_ENST00000509967.2_Silent_p.Q231Q|TRIO_ENST00000537187.1_Silent_p.Q280Q	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	280					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Q280Q(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					TGGAGGGACAGAAGCTGCTTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	5											67	69	68					5																	14291124		2203	4300	6503	14344124	SO:0001819	synonymous_variant	7204			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.840G>A	5.37:g.14291124G>A			14344124	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																				0.517	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14291124	G	A	14291124	2	1	61	1	0	0	0	0	0	0	0	1	16592	933	33	3		3	TRIO	5	14291124	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	362844	14291124	166624136	3704	11689										
TRIO	7204	broad.mit.edu	37	chr5	14336771	14336771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accggattcaagatttcgttCggcgtgttgagcagcgaaag	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:14336771C>T	ENST00000344204.4	+	11	2005	c.1981C>T	c.(1981-1983)Cgg>Tgg	p.R661W	TRIO_ENST00000509967.2_Missense_Mutation_p.R612W|TRIO_ENST00000537187.1_Missense_Mutation_p.R661W	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	661					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R661W(2)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					AGATTTCGTTCGGCGTGTTGA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	5											106	92	97					5																	14336771		2203	4300	6503	14389771	SO:0001583	missense	7204			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.1981C>T	5.37:g.14336771C>T	ENSP00000339299:p.Arg661Trp		14389771	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548605	0.65311	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.52526	0.66;0.66;0.66	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.60586	0.2280	L	0.43152	1.355	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.999;0.998	T	0.62196	-0.6905	10	0.72032	D	0.01	.	13.3676	0.60694	0.2639:0.7361:0.0:0.0	.	612;661;661	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	W	661;661;612;348	ENSP00000339299:R661W;ENSP00000446348:R661W;ENSP00000445592:R612W	ENSP00000339299:R661W	R	+	1	2	TRIO	14389771	0.966000	0.33281	0.940000	0.37924	0.995000	0.86356	2.370000	0.44240	2.548000	0.85928	0.650000	0.86243	CGG		0.507	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		T	14336771	C	T	14336771	3	4	61	1	0	0	0	0	1	0	0	0	16592	875	31	1	2023	1	TRIO	5	14336771	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45647	14336771	166578489	3705	11690										
ANKH	56172	broad.mit.edu	37	chr5	14713763	14713763	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagccacccggtgagatgCgccctcactgtgactgttgg	12	13	2	2	rs146419748	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:14713763C>T	ENST00000284268.6	-	10	1485	c.1155G>A	c.(1153-1155)gcG>gcA	p.A385A	ANKH_ENST00000535119.1_Silent_p.A187A	NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	385					locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)	p.A385A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						CGGTGAGATGCGCCCTCACTG	0.617													C|||	2	0.000399361	0	0.0014	5008	,	,		18453	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											149	114	126					5																	14713763		2203	4300	6503	14766763	SO:0001819	synonymous_variant	56172			AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122			15492	protein-coding gene	gene with protein product		605145	"ankylosis, progressive (mouse) homolog", "craniometaphyseal dysplasia, Jackson type (dominant)", "ankylosis, progressive homolog (mouse)"	CCAL2, CMDJ		10894769, 12297989, 11326338	Standard	NM_054027		Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.1155G>A	5.37:g.14713763C>T			14766763	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	Silent	SNP	ENST00000284268.6	37	CCDS3885.1																																																																																				0.617	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207063.1	NM_054027		T	14713763	C	T	14713763	2	4	61	1	0	0	0	0	0	0	0	1	627	755	27	1		1	ANKH	5	14713763	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	376992	14713763	166201497	3706	11691										
FBXL7	23194	broad.mit.edu	37	chr5	15928004	15928004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtcctttgccagactccGacctgagcatgcgcacactg	9	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:15928004G>A	ENST00000504595.1	+	3	614	c.133G>A	c.(133-135)Gac>Aac	p.D45N	FBXL7_ENST00000510662.1_5'UTR|FBXL7_ENST00000329673.7_Missense_Mutation_p.D33N	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	45					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.D45N(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						GCCAGACTCCGACCTGAGCAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	5											87	93	91					5																	15928004		2045	4202	6247	15981004	SO:0001583	missense	23194			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.133G>A	5.37:g.15928004G>A	ENSP00000423630:p.Asp45Asn		15981004	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790606	0.90367	.	.	ENSG00000183580	ENST00000504595;ENST00000329673	T;T	0.09350	2.99;2.99	5.43	5.43	0.79202	.	0.102097	0.64402	D	0.000004	T	0.09992	0.0245	L	0.27053	0.805	0.80722	D	1	D	0.56746	0.977	B	0.43754	0.43	T	0.25363	-1.0134	10	0.09338	T	0.73	.	19.2506	0.93923	0.0:0.0:1.0:0.0	.	45	Q9UJT9	FBXL7_HUMAN	N	45;33	ENSP00000423630:D45N;ENSP00000329632:D33N	ENSP00000329632:D33N	D	+	1	0	FBXL7	15981004	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.206000	0.95056	2.571000	0.86741	0.563000	0.77884	GAC		0.537	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15928004	G	A	15928004	3	1	61	1	0	0	0	0	1	0	0	0	5743	1058	37	1	143	1	FBXL7	5	15928004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1214241	15928004	164987256	3707	11692										
FBXL7	23194	broad.mit.edu	37	chr5	15936632	15936632	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacccttgcatggcaaacaGatttccatccgctacctgga	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:15936632G>T	ENST00000504595.1	+	4	1294	c.813G>T	c.(811-813)caG>caT	p.Q271H	FBXL7_ENST00000510662.1_Missense_Mutation_p.Q224H|MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000329673.7_Missense_Mutation_p.Q259H	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	271					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.Q271H(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						ATGGCAAACAGATTTCCATCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	73	73					5																	15936632		2168	4265	6433	15989632	SO:0001583	missense	23194			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.813G>T	5.37:g.15936632G>T	ENSP00000423630:p.Gln271His		15989632	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680613	0.47886	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.52754	0.65;0.65;0.65	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.45013	0.1321	N	0.24115	0.695	0.58432	D	0.999997	D	0.63880	0.993	P	0.56751	0.805	T	0.18304	-1.0341	10	0.14252	T	0.57	.	12.5036	0.55970	0.0875:0.0:0.9125:0.0	.	271	Q9UJT9	FBXL7_HUMAN	H	271;224;259	ENSP00000423630:Q271H;ENSP00000425184:Q224H;ENSP00000329632:Q259H	ENSP00000329632:Q259H	Q	+	3	2	FBXL7	15989632	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.809000	0.62591	2.414000	0.81942	0.655000	0.94253	CAG		0.577	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		T	15936632	G	T	15936632	3	4	61	1	0	0	0	0	1	0	0	0	5743	933	33	2	827	2	FBXL7	5	15936632	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8628	15936632	164978628	3708	11693										
MARCH11	441061	broad.mit.edu	37	chr5	16067624	16067624	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctcccccgagctgttatCttctgataagtcttcatggg	8	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16067624C>A	ENST00000332432.8	-	4	1364	c.1165G>T	c.(1165-1167)Gat>Tat	p.D389Y		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	389					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D389Y(1)		NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						GAGCTGTTATCTTCTGATAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											189	183	185					5																	16067624		1935	4138	6073	16120624	SO:0001583	missense	441061			BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.1165G>T	5.37:g.16067624C>A	ENSP00000333181:p.Asp389Tyr		16120624	A7E2S6	Missense_Mutation	SNP	ENST00000332432.8	37	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.433337	0.43224	.	.	ENSG00000183654	ENST00000332432	T	0.19669	2.13	5.12	5.12	0.69794	.	0.125218	0.52532	D	0.000067	T	0.28433	0.0703	N	0.22421	0.69	0.46113	D	0.998874	D	0.61697	0.99	P	0.54759	0.76	T	0.04752	-1.0929	10	0.66056	D	0.02	-21.7086	18.9417	0.92608	0.0:1.0:0.0:0.0	.	389	A6NNE9	MARHB_HUMAN	Y	389	ENSP00000333181:D389Y	ENSP00000333181:D389Y	D	-	1	0	MARCH11	16120624	1.000000	0.71417	1.000000	0.80357	0.313000	0.28021	5.241000	0.65384	2.525000	0.85131	0.655000	0.94253	GAT		0.468	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		A	16067624	C	A	16067624	3	1	61	1	0	0	0	0	1	0	0	0	9330	913	32	2	47	2	MARCH11	5	16067624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130992	16067624	164847636	3709	11694										
ZNF622	90441	broad.mit.edu	37	chr5	16458672	16458672	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcatcatattccaagttCttttctgagggcaactcctc	5	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16458672C>A	ENST00000308683.2	-	4	1242	c.1116G>T	c.(1114-1116)aaG>aaT	p.K372N		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	372					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K372N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						ATTCCAAGTTCTTTTCTGAGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											138	136	136					5																	16458672		2203	4300	6503	16511672	SO:0001583	missense	90441			AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.1116G>T	5.37:g.16458672C>A	ENSP00000310042:p.Lys372Asn		16511672		Missense_Mutation	SNP	ENST00000308683.2	37	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403222	0.25291	.	.	ENSG00000173545	ENST00000308683	.	.	.	5.7	3.66	0.41972	.	0.129212	0.64402	D	0.000001	T	0.61949	0.2388	M	0.66939	2.045	0.51012	D	0.999904	D	0.59357	0.985	P	0.54590	0.756	T	0.58956	-0.7544	9	0.20046	T	0.44	-0.6284	8.5393	0.33382	0.0:0.6458:0.0:0.3542	.	372	Q969S3	ZN622_HUMAN	N	372	.	ENSP00000310042:K372N	K	-	3	2	ZNF622	16511672	0.498000	0.26075	0.814000	0.32528	0.126000	0.20510	0.871000	0.28023	1.161000	0.42604	0.650000	0.86243	AAG		0.403	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		A	16458672	C	A	16458672	3	1	61	1	0	0	0	0	1	0	0	0	18085	912	32	2	329	2	ZNF622	5	16458672	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	391048	16458672	164456588	3710	11695										
FAM134B	54463	broad.mit.edu	37	chr5	16475211	16475211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgaccactgtccaactgtTccttctttctcttgagctca	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16475211T>C	ENST00000306320.9	-	9	1219	c.1133A>G	c.(1132-1134)gAa>gGa	p.E378G	FAM134B_ENST00000399793.2_Missense_Mutation_p.E237G	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	378					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.E378G(1)		breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						GTCCAACTGTTCCTTCTTTCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											166	161	162					5																	16475211		1969	4160	6129	16528211	SO:0001583	missense	54463			BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.1133A>G	5.37:g.16475211T>C	ENSP00000304642:p.Glu378Gly		16528211	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	37	CCDS43304.1	.	.	.	.	.	.	.	.	.	.	T	7.522	0.656783	0.14580	.	.	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.47528	0.86;0.84	5.7	3.16	0.36331	.	0.924056	0.09236	N	0.829946	T	0.26702	0.0653	N	0.15975	0.35	0.24938	N	0.991878	P;B	0.39665	0.682;0.449	B;B	0.32980	0.156;0.098	T	0.07809	-1.0753	10	0.30078	T	0.28	-2.7684	7.047	0.25050	0.0:0.0709:0.2866:0.6425	.	378;237	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	G	237;378	ENSP00000382691:E237G;ENSP00000304642:E378G	ENSP00000304642:E378G	E	-	2	0	FAM134B	16528211	0.962000	0.33011	0.199000	0.23439	0.545000	0.35147	1.776000	0.38594	0.373000	0.24621	0.533000	0.62120	GAA		0.453	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		C	16475211	T	C	16475211	3	2	61	1	0	0	0	0	1	0	0	0	5462	1783	62	4	364	4	FAM134B	5	16475211	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	16539	16475211	164440049	3711	11696										
MYO10	4651	broad.mit.edu	37	chr5	16670653	16670653	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccacatcaaacagcgtCgagccatagccaggccactc	7	17	1	0	rs371241992	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16670653C>T	ENST00000513610.1	-	39	6319	c.5865G>A	c.(5863-5865)tcG>tcA	p.S1955S	MYO10_ENST00000427430.2_Silent_p.S1312S|MYO10_ENST00000274203.9_Silent_p.S1312S|MYO10_ENST00000505695.1_Silent_p.S1294S|MYO10_ENST00000515803.1_Silent_p.S1294S	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1955	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.S1955S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CAAACAGCGTCGAGCCATAGC	0.542													C|||	2	0.000399361	8e-04	0	5008	,	,		17410	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		2,4206		0,2,2102	52	54	53		5865	-11.8	0	5		53	0,8466		0,0,4233	no	coding-synonymous	MYO10	NM_012334.2		0,2,6335	TT,TC,CC		0.0,0.0475,0.0158		1955/2059	16670653	2,12672	2104	4233	6337	16723653	SO:0001819	synonymous_variant	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.5865G>A	5.37:g.16670653C>T			16723653	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																				0.542	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16670653	C	T	16670653	2	4	61	1	0	0	0	0	0	0	0	1	10092	871	31	1		1	MYO10	5	16670653	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	195442	16670653	164244607	3712	11697										
MYO10	4651	broad.mit.edu	37	chr5	16680091	16680091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgctgggtgggggtgtCgatcggggccttggtgtcag	20	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16680091C>T	ENST00000513610.1	-	33	4961	c.4507G>A	c.(4507-4509)Gac>Aac	p.D1503N	MYO10_ENST00000427430.2_Missense_Mutation_p.D860N|MYO10_ENST00000274203.9_Missense_Mutation_p.D860N|MYO10_ENST00000505695.1_Missense_Mutation_p.D842N|MYO10_ENST00000515803.1_Missense_Mutation_p.D842N	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1503					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.D1503N(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GTGGGGGTGTCGATCGGGGCC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	84	85					5																	16680091		1962	4163	6125	16733091	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4507G>A	5.37:g.16680091C>T	ENSP00000421280:p.Asp1503Asn		16733091	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.886690	0.91814	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23	5.46	5.46	0.80206	.	.	.	.	.	D	0.94182	0.8133	L	0.40543	1.245	0.80722	D	1	P;D;D	0.71674	0.931;0.998;0.997	B;P;P	0.57679	0.358;0.825;0.735	D	0.93788	0.7090	9	0.48119	T	0.1	.	19.6953	0.96022	0.0:1.0:0.0:0.0	.	382;1143;1503	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	N	1503;842;860;842;860	ENSP00000421280:D1503N;ENSP00000425051:D842N;ENSP00000274203:D860N;ENSP00000421170:D842N;ENSP00000391106:D860N	ENSP00000274203:D860N	D	-	1	0	MYO10	16733091	1.000000	0.71417	0.967000	0.41034	0.892000	0.51952	7.798000	0.85924	2.741000	0.93983	0.655000	0.94253	GAC		0.557	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16680091	C	T	16680091	3	4	61	1	0	0	0	0	1	0	0	0	10092	884	31	1	1705	1	MYO10	5	16680091	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9438	16680091	164235169	3713	11698										
MYO10	4651	broad.mit.edu	37	chr5	16701512	16701512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggcgtcgtcgtcggcttCgaagccctcatcgacctcct	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16701512C>T	ENST00000513610.1	-	25	3446	c.2992G>A	c.(2992-2994)Gaa>Aaa	p.E998K	MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000427430.2_Missense_Mutation_p.E355K|MYO10_ENST00000274203.9_Missense_Mutation_p.E355K|MYO10_ENST00000505695.1_Missense_Mutation_p.E337K|MYO10_ENST00000515803.1_Missense_Mutation_p.E337K	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	998					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.E998K(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TCGTCGGCTTCGAAGCCCTCA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											37	41	40					5																	16701512		2134	4239	6373	16754512	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2992G>A	5.37:g.16701512C>T	ENSP00000421280:p.Glu998Lys		16754512	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471396	0.43942	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.87650	-2.2;-2.28;-2.2;-2.28;-2.2	4.99	4.99	0.66335	.	.	.	.	.	T	0.78861	0.4350	L	0.27053	0.805	0.40995	D	0.984883	B;B	0.32382	0.185;0.368	B;B	0.20184	0.019;0.028	T	0.77011	-0.2746	9	0.23891	T	0.37	.	18.2828	0.90103	0.0:1.0:0.0:0.0	.	639;998	Q69YP8;Q9HD67	.;MYO10_HUMAN	K	998;337;355;337;355	ENSP00000421280:E998K;ENSP00000425051:E337K;ENSP00000274203:E355K;ENSP00000421170:E337K;ENSP00000391106:E355K	ENSP00000274203:E355K	E	-	1	0	MYO10	16754512	0.996000	0.38824	1.000000	0.80357	0.725000	0.41563	4.899000	0.63245	2.309000	0.77851	0.462000	0.41574	GAA		0.602	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16701512	C	T	16701512	3	4	61	1	0	0	0	0	1	0	0	0	10092	893	31	1	3252	1	MYO10	5	16701512	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21421	16701512	164213748	3714	11699										
MYO10	4651	broad.mit.edu	37	chr5	16703249	16703249	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatcaccacacaataaagGacctttctgtattgttttct	4	9	3	0	rs554883727		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16703249G>A	ENST00000513610.1	-	23	2749	c.2295C>T	c.(2293-2295)gtC>gtT	p.V765V	MYO10_ENST00000512061.1_5'UTR|MYO10_ENST00000427430.2_Silent_p.V122V|MYO10_ENST00000274203.9_Silent_p.V122V|MYO10_ENST00000505695.1_Silent_p.V104V|MYO10_ENST00000515803.1_Silent_p.V104V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	765	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.V765V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CACAATAAAGGACCTTTCTGT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	5											32	28	29					5																	16703249		1840	4086	5926	16756249	SO:0001819	synonymous_variant	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2295C>T	5.37:g.16703249G>A			16756249	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																				0.383	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16703249	G	A	16703249	2	1	61	1	0	0	0	0	0	0	0	1	10092	1161	41	3		3	MYO10	5	16703249	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1737	16703249	164212011	3715	11700										
MYO10	4651	broad.mit.edu	37	chr5	16794905	16794905	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcccggcgatgggctggTaggggttcacggaggccagg	19	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:16794905T>C	ENST00000513610.1	-	4	771	c.317A>G	c.(316-318)tAc>tGc	p.Y106C		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	106	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.Y106C(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GATGGGCTGGTAGGGGTTCAC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5											22	27	26					5																	16794905		2047	4196	6243	16847905	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.317A>G	5.37:g.16794905T>C	ENSP00000421280:p.Tyr106Cys		16847905	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.564043	0.86335	.	.	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000502436	D;D;D	0.91843	-2.92;-2.92;-2.92	5.19	5.19	0.71726	Myosin head, motor domain (3);	.	.	.	.	D	0.97232	0.9095	H	0.95294	3.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98450	1.0591	9	0.87932	D	0	.	15.0845	0.72142	0.0:0.0:0.0:1.0	.	73;106	E9PCN3;Q9HD67	.;MYO10_HUMAN	C	106;117;73	ENSP00000421280:Y106C;ENSP00000421309:Y117C;ENSP00000426783:Y73C	ENSP00000426783:Y73C	Y	-	2	0	MYO10	16847905	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.033000	0.88852	1.954000	0.56735	0.533000	0.62120	TAC		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16794905	T	C	16794905	3	2	61	1	0	0	0	0	1	0	0	0	10092	1638	57	4	6011	4	MYO10	5	16794905	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	91656	16794905	164120355	3716	11701										
CDH18	1016	broad.mit.edu	37	chr5	19483582	19483582	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggggattccaccatcagaGatcataatgggcagataata	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:19483582G>T	ENST00000507958.1	-	14	2700	c.1710C>A	c.(1708-1710)atC>atA	p.I570I	CDH18_ENST00000502796.1_Intron|CDH18_ENST00000382275.1_Silent_p.I570I|CDH18_ENST00000506372.1_Intron|CDH18_ENST00000274170.4_Silent_p.I570I			Q13634	CAD18_HUMAN	cadherin 18, type 2	570	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I570I(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CACCATCAGAGATCATAATGG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											96	81	86					5																	19483582		2203	4300	6503	19519339	SO:0001819	synonymous_variant	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1710C>A	5.37:g.19483582G>T			19519339	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																				0.498	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19483582	G	T	19483582	2	4	61	1	0	0	0	0	0	0	0	1	3109	932	33	2		2	CDH18	5	19483582	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2688677	19483582	161431678	3717	11702										
CDH18	1016	broad.mit.edu	37	chr5	19571872	19571872	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacccaagtgagaaaagcGaaaatcaagatgtgtatttg	11	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:19571872G>A	ENST00000507958.1	-	10	2059	c.1069C>T	c.(1069-1071)Cgc>Tgc	p.R357C	CDH18_ENST00000502796.1_Missense_Mutation_p.R357C|CDH18_ENST00000382275.1_Missense_Mutation_p.R357C|CDH18_ENST00000506372.1_Missense_Mutation_p.R357C|CDH18_ENST00000511273.1_Missense_Mutation_p.R357C|CDH18_ENST00000274170.4_Missense_Mutation_p.R357C			Q13634	CAD18_HUMAN	cadherin 18, type 2	357	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R357C(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TGAGAAAAGCGAAAATCAAGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	98	100					5																	19571872		2203	4300	6503	19607629	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1069C>T	5.37:g.19571872G>A	ENSP00000425093:p.Arg357Cys		19607629	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.558408	0.86231	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.61627	0.16;0.16;0.16;0.13;0.14;0.3;0.09	5.17	4.25	0.50352	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.81645	0.4866	H	0.94385	3.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.994	D	0.86571	0.1847	9	.	.	.	.	14.3707	0.66838	0.0:0.0:0.8523:0.1477	.	357;357	B4DHG6;Q13634	.;CAD18_HUMAN	C	357;357;357;357;357;357;303;357	ENSP00000371710:R357C;ENSP00000425093:R357C;ENSP00000274170:R357C;ENSP00000424931:R357C;ENSP00000422138:R357C;ENSP00000427383:R303C;ENSP00000425854:R357C	.	R	-	1	0	CDH18	19607629	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.162000	0.64942	2.591000	0.87537	0.655000	0.94253	CGC		0.378	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19571872	G	A	19571872	3	1	61	1	0	0	0	0	1	0	0	0	3109	1058	37	1	1327	1	CDH18	5	19571872	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88290	19571872	161343388	3718	11703										
CDH18	1016	broad.mit.edu	37	chr5	19591169	19591169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtatgttctttttaccttCtttaaagaaaggattccttc	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:19591169C>A	ENST00000507958.1	-	9	1986	c.996G>T	c.(994-996)aaG>aaT	p.K332N	CDH18_ENST00000502796.1_Missense_Mutation_p.K332N|CDH18_ENST00000382275.1_Missense_Mutation_p.K332N|CDH18_ENST00000506372.1_Missense_Mutation_p.K332N|CDH18_ENST00000511273.1_Missense_Mutation_p.K332N|CDH18_ENST00000274170.4_Missense_Mutation_p.K332N			Q13634	CAD18_HUMAN	cadherin 18, type 2	332	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K332N(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTTTTACCTTCTTTAAAGAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	73	76					5																	19591169		2203	4300	6503	19626926	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.996G>T	5.37:g.19591169C>A	ENSP00000425093:p.Lys332Asn		19626926	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552685	0.65425	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.24	-0.973	0.10297	Cadherin (5);Cadherin-like (1);	0.049189	0.85682	D	0.000000	T	0.51415	0.1673	L	0.45698	1.435	0.44261	D	0.997119	D;P	0.53619	0.961;0.866	P;P	0.60473	0.875;0.735	T	0.42498	-0.9448	9	.	.	.	.	10.2571	0.43403	0.0:0.4796:0.0:0.5204	.	332;332	B4DHG6;Q13634	.;CAD18_HUMAN	N	332;332;332;332;332;332;278;332	ENSP00000371710:K332N;ENSP00000425093:K332N;ENSP00000274170:K332N;ENSP00000424931:K332N;ENSP00000422138:K332N;ENSP00000427383:K278N;ENSP00000425854:K332N	.	K	-	3	2	CDH18	19626926	0.994000	0.37717	0.982000	0.44146	0.995000	0.86356	0.368000	0.20399	-0.268000	0.09312	0.650000	0.86243	AAG		0.403	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19591169	C	A	19591169	3	1	61	1	0	0	0	0	1	0	0	0	3109	912	32	2	1404	2	CDH18	5	19591169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19297	19591169	161324091	3719	11704										
CDH12	1010	broad.mit.edu	37	chr5	21817140	21817140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcctggaacaatattgtAttcaatttctgcattttgtc	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:21817140A>G	ENST00000382254.1	-	9	2002	c.916T>C	c.(916-918)Tac>Cac	p.Y306H	CDH12_ENST00000504376.2_Missense_Mutation_p.Y306H|CDH12_ENST00000521384.1_5'UTR|CDH12_ENST00000522262.1_Missense_Mutation_p.Y266H	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	306	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y306H(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						ACAATATTGTATTCAATTTCT	0.383										HNSCC(59;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	5											136	134	134					5																	21817140		2203	4300	6503	21852897	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.916T>C	5.37:g.21817140A>G	ENSP00000371689:p.Tyr306His		21852897	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.455704	0.84209	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.62941	-0.01;-0.01;-0.01	4.97	4.97	0.65823	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.88426	0.6433	H	0.99659	4.685	0.54753	D	0.999987	P;D	0.76494	0.868;0.999	P;D	0.76071	0.708;0.987	D	0.93450	0.6801	10	0.72032	D	0.01	.	14.936	0.70954	1.0:0.0:0.0:0.0	.	266;306	B7Z2U6;P55289	.;CAD12_HUMAN	H	306;306;266	ENSP00000423577:Y306H;ENSP00000371689:Y306H;ENSP00000428786:Y266H	ENSP00000371689:Y306H	Y	-	1	0	CDH12	21852897	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	8.748000	0.91615	1.971000	0.57363	0.477000	0.44152	TAC		0.383	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		G	21817140	A	G	21817140	3	3	61	1	0	0	0	0	1	0	0	0	3104	449	16	4	1496	4	CDH12	5	21817140	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2225971	21817140	159098120	3720	11705										
CDH12	1010	broad.mit.edu	37	chr5	21842381	21842381	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccttggcttggatgagtaCttgatattgttctttgactt	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:21842381C>A	ENST00000382254.1	-	8	1789	c.703G>T	c.(703-705)Gta>Tta	p.V235L	CDH12_ENST00000504376.2_Missense_Mutation_p.V235L|CDH12_ENST00000521384.1_5'UTR|CDH12_ENST00000522262.1_Missense_Mutation_p.V195L	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	235	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V235L(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TGGATGAGTACTTGATATTGT	0.398										HNSCC(59;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	5											268	211	230					5																	21842381		2203	4300	6503	21878138	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.703G>T	5.37:g.21842381C>A	ENSP00000371689:p.Val235Leu		21878138	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035549	0.93630	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.48201	1.02;1.02;0.82	5.34	5.34	0.76211	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.38188	0.1031	N	0.00446	-1.495	0.80722	D	1	D;D	0.69078	0.989;0.997	P;D	0.77004	0.831;0.989	T	0.70375	-0.4889	10	0.48119	T	0.1	.	19.0468	0.93022	0.0:1.0:0.0:0.0	.	195;235	B7Z2U6;P55289	.;CAD12_HUMAN	L	235;235;195	ENSP00000423577:V235L;ENSP00000371689:V235L;ENSP00000428786:V195L	ENSP00000371689:V235L	V	-	1	0	CDH12	21878138	1.000000	0.71417	0.994000	0.49952	0.937000	0.57800	5.923000	0.70045	2.480000	0.83734	0.655000	0.94253	GTA		0.398	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		A	21842381	C	A	21842381	3	1	61	1	0	0	0	0	1	0	0	0	3104	565	20	2	1713	2	CDH12	5	21842381	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25241	21842381	159072879	3721	11706										
PRDM9	56979	broad.mit.edu	37	chr5	23526562	23526562	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaaaccaaaggtcaagaGatcaaagaaaggtccaaact	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:23526562G>T	ENST00000296682.3	+	11	1547	c.1365G>T	c.(1363-1365)gaG>gaT	p.E455D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	455					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.E455D(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AAGGTCAAGAGATCAAAGAAA	0.478										HNSCC(3;0.000094)																																						2	Substitution - Missense(2)	large_intestine(1)|lung(1)	5											50	51	50					5																	23526562		2203	4300	6503	23562319	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1365G>T	5.37:g.23526562G>T	ENSP00000296682:p.Glu455Asp		23562319	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	8.221	0.802535	0.16397	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.09817	2.94	2.71	0.626	0.17670	.	0.646368	0.12813	N	0.437047	T	0.07999	0.0200	L	0.52126	1.63	0.09310	N	1	P	0.34662	0.462	B	0.33960	0.173	T	0.34030	-0.9845	10	0.15499	T	0.54	-5.7858	3.0916	0.06296	0.32:0.226:0.454:0.0	.	455	Q9NQV7	PRDM9_HUMAN	D	455;249	ENSP00000296682:E455D	ENSP00000253473:E249D	E	+	3	2	PRDM9	23562319	0.006000	0.16342	0.002000	0.10522	0.132000	0.20833	-2.403000	0.01046	0.112000	0.17975	-0.438000	0.05819	GAG		0.478	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23526562	G	T	23526562	3	4	61	1	0	0	0	0	1	0	0	0	12497	933	33	2	1403	2	PRDM9	5	23526562	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1684181	23526562	157388698	3722	11707										
CDH10	1008	broad.mit.edu	37	chr5	24487810	24487810	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccccaccaccatacatttCtgctagcttattaaaccgag	4	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:24487810C>A	ENST00000264463.4	-	12	2836	c.2329G>T	c.(2329-2331)Gaa>Taa	p.E777*	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	777					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E777*(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		CCATACATTTCTGCTAGCTTA	0.423										HNSCC(23;0.051)																																						1	Substitution - Nonsense(1)	large_intestine(1)	5											171	173	172					5																	24487810		2203	4300	6503	24523567	SO:0001587	stop_gained	1008			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.2329G>T	5.37:g.24487810C>A	ENSP00000264463:p.Glu777*		24523567	Q9ULB3	Nonsense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	C	44	10.660279	0.99445	.	.	ENSG00000040731	ENST00000264463	.	.	.	5.81	5.81	0.92471	.	0.090990	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.0503	0.93041	0.0:1.0:0.0:0.0	.	.	.	.	X	777	.	ENSP00000264463:E777X	E	-	1	0	CDH10	24523567	1.000000	0.71417	0.873000	0.34254	0.987000	0.75469	7.702000	0.84576	2.750000	0.94351	0.655000	0.94253	GAA		0.423	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		A	24487810	C	A	24487810	4	1	61	1	0	0	0	0	0	1	0	0	3102	922	32	2	41	2	CDH10	5	24487810	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	961248	24487810	156427450	3723	11708										
CDH10	1008	broad.mit.edu	37	chr5	24509922	24509922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcttcggctctcatagtCgagtggctgtataaaaaaat	9	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:24509922C>T	ENST00000264463.4	-	7	1516	c.1009G>A	c.(1009-1011)Gac>Aac	p.D337N		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	337	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D337N(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		CTCTCATAGTCGAGTGGCTGT	0.373										HNSCC(23;0.051)																																						1	Substitution - Missense(1)	large_intestine(1)	5											48	50	49					5																	24509922		2203	4300	6503	24545679	SO:0001583	missense	1008			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1009G>A	5.37:g.24509922C>T	ENSP00000264463:p.Asp337Asn		24545679	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816372	0.70912	.	.	ENSG00000040731	ENST00000264463	T	0.63417	-0.04	5.2	5.2	0.72013	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.71728	0.3374	M	0.84683	2.71	0.53688	D	0.999976	P	0.52692	0.955	P	0.45639	0.488	T	0.77925	-0.2405	10	0.54805	T	0.06	.	18.0841	0.89452	0.0:1.0:0.0:0.0	.	337	Q9Y6N8	CAD10_HUMAN	N	337	ENSP00000264463:D337N	ENSP00000264463:D337N	D	-	1	0	CDH10	24545679	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	7.432000	0.80349	2.595000	0.87683	0.561000	0.74099	GAC		0.373	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		T	24509922	C	T	24509922	3	4	61	1	0	0	0	0	1	0	0	0	3102	884	31	1	1381	1	CDH10	5	24509922	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22112	24509922	156405338	3724	11709										
CDH9	1007	broad.mit.edu	37	chr5	26886136	26886136	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggcactggttcaaaaaaGaatttgtgacctcggggagg	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:26886136G>T	ENST00000231021.4	-	10	1741	c.1569C>A	c.(1567-1569)ttC>ttA	p.F523L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	523	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F523L(2)|p.F523F(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GTTCAAAAAAGAATTTGTGAC	0.313																																					Melanoma(8;187 585 15745 40864 52829)											3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(2)|lung(1)	5											76	86	83					5																	26886136		2202	4300	6502	26921893	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1569C>A	5.37:g.26886136G>T	ENSP00000231021:p.Phe523Leu		26921893	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483928	0.63962	.	.	ENSG00000113100	ENST00000231021	T	0.48201	0.82	5.76	3.94	0.45596	Cadherin (4);Cadherin-like (1);	0.048575	0.85682	N	0.000000	T	0.70369	0.3216	M	0.90759	3.145	0.45087	D	0.998106	D;D	0.76494	0.997;0.999	D;D	0.74674	0.974;0.984	T	0.72849	-0.4168	9	.	.	.	.	9.0368	0.36293	0.2483:0.0:0.7517:0.0	.	116;523	B4DFP0;Q9ULB4	.;CADH9_HUMAN	L	523	ENSP00000231021:F523L	.	F	-	3	2	CDH9	26921893	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	1.682000	0.37628	0.743000	0.32719	0.467000	0.42956	TTC		0.313	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26886136	G	T	26886136	3	4	61	1	0	0	0	0	1	0	0	0	3123	933	33	2	812	2	CDH9	5	26886136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2376214	26886136	154029124	3725	11710										
CDH9	1007	broad.mit.edu	37	chr5	26889986	26889986	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaacaaatgtttcataatAcatggcaaattccggagcat	6	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:26889986A>G	ENST00000231021.4	-	9	1643	c.1471T>C	c.(1471-1473)Tat>Cat	p.Y491H		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	491	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y491H(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GTTTCATAATACATGGCAAAT	0.333																																					Melanoma(8;187 585 15745 40864 52829)											1	Substitution - Missense(1)	large_intestine(1)	5											122	124	123					5																	26889986		2203	4300	6503	26925743	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1471T>C	5.37:g.26889986A>G	ENSP00000231021:p.Tyr491His		26925743	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	A	9.818	1.184919	0.21870	.	.	ENSG00000113100	ENST00000231021	T	0.60672	0.17	5.31	5.31	0.75309	Cadherin (1);Cadherin-like (1);	0.400535	0.25848	N	0.027907	T	0.40670	0.1126	N	0.25647	0.755	0.37252	D	0.906623	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.39461	-0.9613	9	.	.	.	.	8.7488	0.34602	0.9141:0.0:0.0859:0.0	.	84;491	B4DFP0;Q9ULB4	.;CADH9_HUMAN	H	491	ENSP00000231021:Y491H	.	Y	-	1	0	CDH9	26925743	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.848000	0.69458	2.010000	0.58986	0.450000	0.29827	TAT		0.333	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26889986	A	G	26889986	3	3	61	1	0	0	0	0	1	0	0	0	3123	391	14	4	914	4	CDH9	5	26889986	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3850	26889986	154025274	3726	11711										
RNASEN	29102	broad.mit.edu	37	chr5	31515144	31515144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttttctgaatgagtgcatCgaatccacacaggcttaaga	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:31515144C>T	ENST00000511367.2	-	7	1485	c.1241G>A	c.(1240-1242)cGa>cAa	p.R414Q	DROSHA_ENST00000442743.1_Missense_Mutation_p.R377Q|DROSHA_ENST00000344624.3_Missense_Mutation_p.R414Q|DROSHA_ENST00000513349.1_Missense_Mutation_p.R377Q	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	414					defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.R414Q(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						ATGAGTGCATCGAATCCACAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	5											162	153	156					5																	31515144		1936	4134	6070	31550901	SO:0001583	missense	29102			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.1241G>A	5.37:g.31515144C>T	ENSP00000425979:p.Arg414Gln		31550901	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567150	0.96540	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000512302	T;T;T;T;T	0.65178	1.04;1.04;0.36;0.36;-0.14	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78457	0.4286	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	P;D;D	0.83275	0.787;0.996;0.996	T	0.77867	-0.2428	10	0.54805	T	0.06	-13.5039	19.8465	0.96710	0.0:1.0:0.0:0.0	.	346;377;414	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	Q	414;414;377;377;339;370;181	ENSP00000425979:R414Q;ENSP00000339845:R414Q;ENSP00000409335:R377Q;ENSP00000424161:R377Q;ENSP00000428782:R181Q	ENSP00000265075:R339Q	R	-	2	0	DROSHA	31550901	1.000000	0.71417	0.928000	0.36995	0.994000	0.84299	7.445000	0.80570	2.769000	0.95229	0.561000	0.74099	CGA		0.478	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		T	31515144	C	T	31515144	3	4	61	1	0	0	0	0	1	0	0	0	13454	884	31	1	2999	1	RNASEN	5	31515144	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4625158	31515144	149400116	3727	11712										
PDZD2	23037	broad.mit.edu	37	chr5	31983313	31983313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatctacctgatcatgctgCgtcgctttaagcacaaagcc	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:31983313C>T	ENST00000438447.1	+	3	917	c.529C>T	c.(529-531)Cgt>Tgt	p.R177C	PDZD2_ENST00000282493.3_Missense_Mutation_p.R177C			O15018	PDZD2_HUMAN	PDZ domain containing 2	177	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.R177C(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GATCATGCTGCGTCGCTTTAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	98	97					5																	31983313		2203	4300	6503	32019070	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.529C>T	5.37:g.31983313C>T	ENSP00000402033:p.Arg177Cys		32019070	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080081	0.76528	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.74315	-0.83;-0.83	5.23	4.37	0.52481	PDZ/DHR/GLGF (2);	0.000000	0.48286	D	0.000197	T	0.76535	0.4001	N	0.24115	0.695	0.80722	D	1	D;P	0.89917	1.0;0.84	D;B	0.85130	0.997;0.116	T	0.79174	-0.1912	10	0.87932	D	0	.	11.5757	0.50860	0.0:0.9143:0.0:0.0857	.	3;177	B4E3P2;O15018	.;PDZD2_HUMAN	C	177	ENSP00000402033:R177C;ENSP00000282493:R177C	ENSP00000282493:R177C	R	+	1	0	PDZD2	32019070	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.966000	0.76073	1.448000	0.47680	-0.142000	0.14014	CGT		0.522	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	31983313	C	T	31983313	3	4	61	1	0	0	0	0	1	0	0	0	11732	768	27	1	535	1	PDZD2	5	31983313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	468169	31983313	148931947	3728	11713										
PDZD2	23037	broad.mit.edu	37	chr5	31983413	31983413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagctgggtgaccgaactgCgaaaaaggggaaacgaacca	15	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:31983413C>T	ENST00000438447.1	+	3	1017	c.629C>T	c.(628-630)gCg>gTg	p.A210V	PDZD2_ENST00000282493.3_Missense_Mutation_p.A210V			O15018	PDZD2_HUMAN	PDZ domain containing 2	210					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.A210V(2)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GACCGAACTGCGAAAAAGGGG	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	5											90	88	89					5																	31983413		2203	4300	6503	32019170	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.629C>T	5.37:g.31983413C>T	ENSP00000402033:p.Ala210Val		32019170	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.579072	0.00879	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.66995	-0.24;-0.24	5.23	0.891	0.19224	.	0.842448	0.10159	N	0.708614	T	0.34308	0.0893	N	0.01874	-0.695	0.09310	N	1	B;B	0.12630	0.004;0.006	B;B	0.08055	0.003;0.002	T	0.20571	-1.0271	10	0.25751	T	0.34	.	5.2417	0.15475	0.0:0.5379:0.1728:0.2893	.	36;210	B4E3P2;O15018	.;PDZD2_HUMAN	V	210	ENSP00000402033:A210V;ENSP00000282493:A210V	ENSP00000282493:A210V	A	+	2	0	PDZD2	32019170	0.713000	0.27926	0.013000	0.15412	0.092000	0.18411	2.415000	0.44635	0.282000	0.22254	-0.172000	0.13284	GCG		0.542	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	31983413	C	T	31983413	3	4	61	1	0	0	0	0	1	0	0	0	11732	768	27	1	635	1	PDZD2	5	31983413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100	31983413	148931847	3729	11714										
PDZD2	23037	broad.mit.edu	37	chr5	32061208	32061208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccctccaggacccgttCgccttgtcatcggccggcac	10	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32061208C>T	ENST00000438447.1	+	14	2807	c.2419C>T	c.(2419-2421)Cgc>Tgc	p.R807C	PDZD2_ENST00000282493.3_Missense_Mutation_p.R807C			O15018	PDZD2_HUMAN	PDZ domain containing 2	807	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.R807C(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AGGACCCGTTCGCCTTGTCAT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	76	82					5																	32061208		2203	4300	6503	32096965	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2419C>T	5.37:g.32061208C>T	ENSP00000402033:p.Arg807Cys		32096965	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.476082	0.84640	.	.	ENSG00000133401	ENST00000438447;ENST00000282493	T;T	0.28255	1.62;1.62	5.76	4.82	0.62117	PDZ/DHR/GLGF (3);	0.000000	0.48286	D	0.000187	T	0.46521	0.1397	L	0.50847	1.595	0.50313	D	0.999865	D;D	0.89917	1.0;1.0	D;D	0.77004	0.959;0.989	T	0.33317	-0.9873	10	0.56958	D	0.05	.	10.6489	0.45636	0.3112:0.6888:0.0:0.0	.	633;807	B4E3P2;O15018	.;PDZD2_HUMAN	C	807	ENSP00000402033:R807C;ENSP00000282493:R807C	ENSP00000282493:R807C	R	+	1	0	PDZD2	32096965	0.999000	0.42202	0.995000	0.50966	0.987000	0.75469	4.074000	0.57577	2.726000	0.93360	0.655000	0.94253	CGC		0.532	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32061208	C	T	32061208	3	4	61	1	0	0	0	0	1	0	0	0	11732	884	31	1	2469	1	PDZD2	5	32061208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77795	32061208	148854052	3730	11715										
PDZD2	23037	broad.mit.edu	37	chr5	32074722	32074722	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaaagtgactgtcgctggCtttcagccaggtggagctgt	14	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32074722C>T	ENST00000438447.1	+	18	3898	c.3510C>T	c.(3508-3510)ggC>ggT	p.G1170G	PDZD2_ENST00000282493.3_Silent_p.G1170G			O15018	PDZD2_HUMAN	PDZ domain containing 2	1170					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.G1170G(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTGTCGCTGGCTTTCAGCCAG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											21	22	22					5																	32074722		2202	4299	6501	32110479	SO:0001819	synonymous_variant	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3510C>T	5.37:g.32074722C>T			32110479	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																				0.498	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074722	C	T	32074722	2	4	61	1	0	0	0	0	0	0	0	1	11732	784	28	3		3	PDZD2	5	32074722	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13514	32074722	148840538	3731	11716										
PDZD2	23037	broad.mit.edu	37	chr5	32088933	32088933	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagaaaccaaaaatgatCgctaggaggcccatcatggc	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32088933C>T	ENST00000438447.1	+	20	5767	c.5379C>T	c.(5377-5379)atC>atT	p.I1793I	PDZD2_ENST00000282493.3_Silent_p.I1793I			O15018	PDZD2_HUMAN	PDZ domain containing 2	1793					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.I1793I(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CAAAAATGATCGCTAGGAGGC	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	5											71	74	73					5																	32088933		2203	4300	6503	32124690	SO:0001819	synonymous_variant	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.5379C>T	5.37:g.32088933C>T			32124690	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																				0.428	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32088933	C	T	32088933	2	4	61	1	0	0	0	0	0	0	0	1	11732	874	31	1		1	PDZD2	5	32088933	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14211	32088933	148826327	3732	11717										
MTMR12	54545	broad.mit.edu	37	chr5	32239142	32239142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcggagatggttgcagcGatccaagaaacagtggccac	14	10	0	2	rs372093007		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32239142G>A	ENST00000382142.3	-	13	1479	c.1309C>T	c.(1309-1311)Cgc>Tgc	p.R437C	MTMR12_ENST00000264934.5_Missense_Mutation_p.R437C|MTMR12_ENST00000280285.5_Missense_Mutation_p.R437C	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	437	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)	p.R437C(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGGTTGCAGCGATCCAAGAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	82	86					5																	32239142		2203	4300	6503	32274899	SO:0001583	missense	54545			AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	18191	protein-coding gene	gene with protein product		606501	"phosphatidylinositol-3-phosphate associated protein"	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.1309C>T	5.37:g.32239142G>A	ENSP00000371577:p.Arg437Cys		32274899	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.284796	0.80803	.	.	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	D;D;D	0.98044	-4.68;-4.68;-4.68	5.54	5.54	0.83059	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.99196	0.9721	H	0.97214	3.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.98888	1.0772	10	0.87932	D	0	.	14.6599	0.68861	0.0:0.0:0.8546:0.1454	.	437;437;437	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	C	437	ENSP00000280285:R437C;ENSP00000371577:R437C;ENSP00000264934:R437C	ENSP00000264934:R437C	R	-	1	0	MTMR12	32274899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.850000	0.62889	2.759000	0.94783	0.563000	0.77884	CGC		0.502	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061		A	32239142	G	A	32239142	3	1	61	1	0	0	0	0	1	0	0	0	9971	1058	37	1	950	1	MTMR12	5	32239142	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	150209	32239142	148676118	3733	11718										
MTMR12	54545	broad.mit.edu	37	chr5	32274105	32274105	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcattatccaatgcagatTcatcatcacccaagaaggca	5	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32274105T>G	ENST00000382142.3	-	3	436	c.266A>C	c.(265-267)gAa>gCa	p.E89A	MTMR12_ENST00000264934.5_Missense_Mutation_p.E89A|MTMR12_ENST00000280285.5_Missense_Mutation_p.E89A	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	89						cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)	p.E89A(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CAATGCAGATTCATCATCACC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											201	176	185					5																	32274105		2203	4300	6503	32309862	SO:0001583	missense	54545			AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	18191	protein-coding gene	gene with protein product		606501	"phosphatidylinositol-3-phosphate associated protein"	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.266A>C	5.37:g.32274105T>G	ENSP00000371577:p.Glu89Ala		32309862	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	.	.	.	.	.	.	.	.	.	.	T	9.730	1.161892	0.21538	.	.	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	D;D;D	0.95554	-3.74;-3.39;-3.27	4.8	3.59	0.41128	.	0.901181	0.09614	N	0.778445	D	0.89128	0.6627	N	0.08118	0	0.27419	N	0.954351	P;B;B	0.39022	0.655;0.167;0.008	B;B;B	0.40677	0.337;0.107;0.004	T	0.80500	-0.1355	10	0.19590	T	0.45	.	9.5327	0.39205	0.0:0.0826:0.0:0.9174	.	89;89;89	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	A	89	ENSP00000280285:E89A;ENSP00000371577:E89A;ENSP00000264934:E89A	ENSP00000264934:E89A	E	-	2	0	MTMR12	32309862	0.653000	0.27358	0.089000	0.20774	0.968000	0.65278	3.341000	0.52151	0.733000	0.32492	0.448000	0.29417	GAA		0.468	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061		G	32274105	T	G	32274105	3	3	61	1	0	0	0	0	1	0	0	0	9971	1783	62	4	2033	4	MTMR12	5	32274105	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34963	32274105	148641155	3734	11719										
ZFR	51663	broad.mit.edu	37	chr5	32364344	32364344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggctctgagggctagaaGcactgctgattgctttctct	12	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32364344G>A	ENST00000265069.8	-	18	2975	c.2873C>T	c.(2872-2874)gCt>gTt	p.A958V	ZFR_ENST00000510369.1_5'UTR	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	958	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A958V(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AGGGCTAGAAGCACTGCTGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											79	82	81					5																	32364344		2203	4300	6503	32400101	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.2873C>T	5.37:g.32364344G>A	ENSP00000265069:p.Ala958Val		32400101	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465801	0.84425	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.49139	0.79	5.74	5.74	0.90152	DZF (2);	0.051668	0.85682	D	0.000000	T	0.68100	0.2964	M	0.74467	2.265	0.80722	D	1	D;P	0.61697	0.99;0.856	P;P	0.60949	0.881;0.652	T	0.68667	-0.5348	10	0.54805	T	0.06	.	19.9357	0.97140	0.0:0.0:1.0:0.0	.	937;958	B5MEH6;Q96KR1	.;ZFR_HUMAN	V	958;937	ENSP00000265069:A958V	ENSP00000265069:A958V	A	-	2	0	ZFR	32400101	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.338000	0.96553	2.715000	0.92844	0.655000	0.94253	GCT		0.353	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			A	32364344	G	A	32364344	3	1	61	1	0	0	0	0	1	0	0	0	17698	971	34	3	363	3	ZFR	5	32364344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90239	32364344	148550916	3735	11720										
ZFR	51663	broad.mit.edu	37	chr5	32379273	32379273	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgacagaggtctcgaagaAtgcgtatgataatcacacag	11	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32379273A>G	ENST00000265069.8	-	17	2885	c.2783T>C	c.(2782-2784)aTt>aCt	p.I928T	ZFR_ENST00000510369.1_5'UTR|AC008949.1_ENST00000411029.1_RNA	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	928	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.I928T(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GTCTCGAAGAATGCGTATGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											82	80	81					5																	32379273		2203	4300	6503	32415030	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.2783T>C	5.37:g.32379273A>G	ENSP00000265069:p.Ile928Thr		32415030	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729341	0.48833	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.54279	0.58	5.7	5.7	0.88788	DZF (2);	0.047570	0.85682	D	0.000000	T	0.72260	0.3438	M	0.84511	2.7	0.80722	D	1	P;P	0.51791	0.948;0.761	P;B	0.57371	0.819;0.419	T	0.77781	-0.2459	10	0.87932	D	0	.	15.9632	0.79948	1.0:0.0:0.0:0.0	.	907;928	B5MEH6;Q96KR1	.;ZFR_HUMAN	T	928;907	ENSP00000265069:I928T	ENSP00000265069:I928T	I	-	2	0	ZFR	32415030	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.310000	0.96267	2.171000	0.68590	0.482000	0.46254	ATT		0.383	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			G	32379273	A	G	32379273	3	3	61	1	0	0	0	0	1	0	0	0	17698	101	4	4	457	4	ZFR	5	32379273	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	14929	32379273	148535987	3736	11721										
ZFR	51663	broad.mit.edu	37	chr5	32390425	32390425	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcctggtcggactcccaGaaggcctaatgggcctggag	14	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32390425G>T	ENST00000265069.8	-	12	2200	c.2098C>A	c.(2098-2100)Ctg>Atg	p.L700M		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	700					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L700M(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		CGGACTCCCAGAAGGCCTAAT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	121	123					5																	32390425		2203	4300	6503	32426182	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.2098C>A	5.37:g.32390425G>T	ENSP00000265069:p.Leu700Met		32426182	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.868720	0.51588	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.05199	3.48	5.42	3.59	0.41128	.	0.000000	0.85682	D	0.000000	T	0.16727	0.0402	L	0.57536	1.79	0.54753	D	0.999988	D	0.65815	0.995	D	0.70487	0.969	T	0.01133	-1.1441	10	0.35671	T	0.21	.	8.9376	0.35708	0.233:0.0:0.767:0.0	.	700	Q96KR1	ZFR_HUMAN	M	700;678	ENSP00000265069:L700M	ENSP00000265069:L700M	L	-	1	2	ZFR	32426182	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.347000	0.59373	1.262000	0.44165	0.561000	0.74099	CTG		0.547	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			T	32390425	G	T	32390425	3	4	61	1	0	0	0	0	1	0	0	0	17698	933	33	2	1162	2	ZFR	5	32390425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11152	32390425	148524835	3737	11722										
C5orf23	4883	broad.mit.edu	37	chr5	32789654	32789654	+	3'UTR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagagagaaatgcatggGaaaagaacacctccttttct	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:32789654G>T	ENST00000265074.8	+	0	5172				AC026703.1_ENST00000326958.1_Silent_p.G49G	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)	p.G49G(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	AAATGCATGGGAAAAGAACAC	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	5											85	86	86					5																	32789654		2203	4300	6503	32825411	SO:0001624	3_prime_UTR_variant	79614				CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"guanylate cyclase C"	108962	"chromosome 5 open reading frame 23", "atrionatriuretic peptide receptor C", "natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)", "natriuretic peptide receptor C"	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.*3203G>T	5.37:g.32789654G>T			32825411	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	37	CCDS56357.1																																																																																				0.383	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		T	32789654	G	T	32789654	1	4	61	0	1	0	0	0	0	0	0	0	2292	1161	41	2		2	C5orf23	5	32789654	3'UTR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	399229	32789654	148125606	3738	11723										
TARS	6897	broad.mit.edu	37	chr5	33467050	33467050	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtacattgaataaaaaGattcgaaatgcacagttagc	9	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33467050G>T	ENST00000265112.3	+	18	2294	c.1983G>T	c.(1981-1983)aaG>aaT	p.K661N	TARS_ENST00000502553.1_Missense_Mutation_p.K661N|TARS_ENST00000455217.2_Missense_Mutation_p.K694N|TARS_ENST00000414361.2_Missense_Mutation_p.K540N|TARS_ENST00000541634.1_Missense_Mutation_p.K557N	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	661					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)	p.K661N(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	TGAATAAAAAGATTCGAAATG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	82	83					5																	33467050		2203	4300	6503	33502807	SO:0001583	missense	6897			AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.1983G>T	5.37:g.33467050G>T	ENSP00000265112:p.Lys661Asn		33502807	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Missense_Mutation	SNP	ENST00000265112.3	37	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	g	23.7	4.449714	0.84101	.	.	ENSG00000113407	ENST00000502553;ENST00000265112;ENST00000541634;ENST00000455217;ENST00000414361	D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96	5.62	4.76	0.60689	Anticodon-binding (3);	0.000000	0.85682	D	0.000000	D	0.95589	0.8566	H	0.98701	4.305	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.995;0.999	D;D;D;D	0.83275	0.996;0.991;0.972;0.991	D	0.97146	0.9828	10	0.87932	D	0	-28.0684	14.5126	0.67797	0.0702:0.0:0.9297:0.0	.	540;694;557;661	E7ERI3;B4DEG8;G3XAN9;P26639	.;.;.;SYTC_HUMAN	N	661;661;557;694;540	ENSP00000424387:K661N;ENSP00000265112:K661N;ENSP00000438469:K557N;ENSP00000387710:K694N;ENSP00000394291:K540N	ENSP00000265112:K661N	K	+	3	2	TARS	33502807	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.722000	0.74735	1.370000	0.46153	0.655000	0.94253	AAG		0.368	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		T	33467050	G	T	33467050	3	4	61	1	0	0	0	0	1	0	0	0	15598	933	33	2	2053	2	TARS	5	33467050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	677396	33467050	147448210	3739	11724										
TARS	6897	broad.mit.edu	37	chr5	33467802	33467802	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcagcaaacaggcagaaGaagaattttaatgaaaaaat	8	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33467802G>T	ENST00000265112.3	+	19	2472	c.2161G>T	c.(2161-2163)Gaa>Taa	p.E721*	TARS_ENST00000502553.1_Nonsense_Mutation_p.E721*|TARS_ENST00000455217.2_Nonsense_Mutation_p.E754*|TARS_ENST00000414361.2_Nonsense_Mutation_p.E600*|TARS_ENST00000541634.1_Nonsense_Mutation_p.E617*	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	721					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)	p.E721*(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	ACAGGCAGAAGAAGAATTTTA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											39	44	42					5																	33467802		2203	4300	6503	33503559	SO:0001587	stop_gained	6897			AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.2161G>T	5.37:g.33467802G>T	ENSP00000265112:p.Glu721*		33503559	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Nonsense_Mutation	SNP	ENST00000265112.3	37	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	g	40	8.271183	0.98735	.	.	ENSG00000113407	ENST00000502553;ENST00000265112;ENST00000541634;ENST00000455217;ENST00000414361	.	.	.	4.66	4.66	0.58398	.	0.050116	0.85682	D	0.000000	.	.	.	.	.	.	0.48040	D	0.999571	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.113	17.9177	0.88957	0.0:0.0:1.0:0.0	.	.	.	.	X	721;721;617;754;600	.	ENSP00000265112:E721X	E	+	1	0	TARS	33503559	1.000000	0.71417	0.991000	0.47740	0.978000	0.69477	9.676000	0.98643	2.301000	0.77427	0.557000	0.71058	GAA		0.423	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		T	33467802	G	T	33467802	4	4	61	1	0	0	0	0	0	1	0	0	15598	943	33	2	2235	2	TARS	5	33467802	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	752	33467802	147447458	3740	11725										
ADAMTS12	81792	broad.mit.edu	37	chr5	33577194	33577194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggtttccttgtcacatcGcaaggttcatcatggttctt	9	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33577194G>A	ENST00000504830.1	-	19	3272	c.2937C>T	c.(2935-2937)tgC>tgT	p.C979C	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Silent_p.C894C	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	979	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.C979C(2)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TTGTCACATCGCAAGGTTCAT	0.507										HNSCC(64;0.19)																																						2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	5											129	123	125					5																	33577194		2203	4300	6503	33612951	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2937C>T	5.37:g.33577194G>A			33612951	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33577194	G	A	33577194	2	1	61	1	0	0	0	0	0	0	0	1	257	1079	38	1		1	ADAMTS12	5	33577194	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109392	33577194	147338066	3741	11726										
ADAMTS12	81792	broad.mit.edu	37	chr5	33616160	33616160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgctccttttggaatgaGcccaatgtcaacataaccta	6	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33616160G>A	ENST00000504830.1	-	15	2496	c.2161C>T	c.(2161-2163)Ctc>Ttc	p.L721F	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.L636F	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	721	Spacer 1.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L721F(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TTTGGAATGAGCCCAATGTCA	0.438										HNSCC(64;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	5											76	72	73					5																	33616160		2203	4300	6503	33651917	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2161C>T	5.37:g.33616160G>A	ENSP00000422554:p.Leu721Phe		33651917	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912362	0.72983	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.52295	0.67;0.67	5.51	5.51	0.81932	ADAM-TS Spacer 1 (1);	0.205916	0.42294	D	0.000731	T	0.69468	0.3114	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.984;0.99	T	0.66240	-0.5973	10	0.10111	T	0.7	.	19.015	0.92890	0.0:0.0:1.0:0.0	.	636;721	P58397-3;P58397	.;ATS12_HUMAN	F	721;636	ENSP00000422554:L721F;ENSP00000344847:L636F	ENSP00000344847:L636F	L	-	1	0	ADAMTS12	33651917	0.988000	0.35896	0.985000	0.45067	0.936000	0.57629	1.975000	0.40569	2.558000	0.86282	0.561000	0.74099	CTC		0.438	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33616160	G	A	33616160	3	1	61	1	0	0	0	0	1	0	0	0	257	971	34	3	2663	3	ADAMTS12	5	33616160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38966	33616160	147299100	3742	11727										
ADAMTS12	81792	broad.mit.edu	37	chr5	33662086	33662086	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgggattgatactcttCtgccacttgcagaagctaga	9	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33662086C>T	ENST00000504830.1	-	6	1310	c.975G>A	c.(973-975)caG>caA	p.Q325Q	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Silent_p.Q325Q	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	325	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Q325Q(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TGATACTCTTCTGCCACTTGC	0.483										HNSCC(64;0.19)																																						1	Substitution - coding silent(1)	large_intestine(1)	5											204	168	180					5																	33662086		2203	4300	6503	33697843	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.975G>A	5.37:g.33662086C>T			33697843	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.483	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33662086	C	T	33662086	2	4	61	1	0	0	0	0	0	0	0	1	257	912	32	3		3	ADAMTS12	5	33662086	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45926	33662086	147253174	3743	11728										
RXFP3	51289	broad.mit.edu	37	chr5	33937295	33937295	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgacttcaaatggcccttCggcaaggccatgtgtaagat	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33937295C>T	ENST00000330120.3	+	1	805	c.450C>T	c.(448-450)ttC>ttT	p.F150F		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	150					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)	p.F150F(1)		endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						AATGGCCCTTCGGCAAGGCCA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	5											132	118	123					5																	33937295		2203	4300	6503	33973052	SO:0001819	synonymous_variant	51289			D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.450C>T	5.37:g.33937295C>T			33973052	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																				0.557	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		T	33937295	C	T	33937295	2	4	61	1	0	0	0	0	0	0	0	1	13798	883	31	1		1	RXFP3	5	33937295	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	275209	33937295	146977965	3744	11729										
SLC45A2	51151	broad.mit.edu	37	chr5	33963850	33963850	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgccagctctggatttacGtaaccatttttaactttctc	5	10	2	0	rs116887602	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33963850G>A	ENST00000296589.4	-	3	980	c.834C>T	c.(832-834)taC>taT	p.Y278Y	SLC45A2_ENST00000509381.1_Intron|SLC45A2_ENST00000382102.3_Silent_p.Y278Y|SLC45A2_ENST00000342059.3_Silent_p.Y219Y|SLC45A2_ENST00000345083.5_Intron	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	278					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.Y278Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						CTGGATTTACGTAACCATTTT	0.413													G|||	8	0.00159744	0	0	5008	,	,		20126	0.0079		0	False		,,,				2504	0				Ovarian(31;380 859 8490 22203 49048)											1	Substitution - coding silent(1)	large_intestine(1)	5	GRCh37	CM083852	SLC45A2	M	rs116887602						164	170	168					5																	33963850		2203	4300	6503	33999607	SO:0001819	synonymous_variant	51151			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.834C>T	5.37:g.33963850G>A			33999607	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000296589.4	37	CCDS3901.1																																																																																				0.413	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		A	33963850	G	A	33963850	2	1	61	1	0	0	0	0	0	0	0	1	14678	1140	40	1		1	SLC45A2	5	33963850	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26555	33963850	146951410	3745	11730										
SLC45A2	51151	broad.mit.edu	37	chr5	33982434	33982434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgggcccatcaatgaagtCggcagcaaaatcaaagagaa	11	8	2	2	rs121912621		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33982434C>T	ENST00000296589.4	-	2	615	c.469G>A	c.(469-471)Gac>Aac	p.D157N	SLC45A2_ENST00000509381.1_Missense_Mutation_p.D157N|SLC45A2_ENST00000382102.3_Missense_Mutation_p.D157N|SLC45A2_ENST00000342059.3_Intron|SLC45A2_ENST00000345083.5_Missense_Mutation_p.D157N	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	157			D -> N (in OCA4). {ECO:0000269|PubMed:14961451, ECO:0000269|PubMed:15656822, ECO:0000269|PubMed:17768386}.		developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.D157N(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						TCAATGAAGTCGGCAGCAAAA	0.468																																					Ovarian(31;380 859 8490 22203 49048)											1	Substitution - Missense(1)	large_intestine(1)	5	GRCh37	CM040825	SLC45A2	M	rs121912621						106	100	102					5																	33982434		2203	4300	6503	34018191	SO:0001583	missense	51151			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.469G>A	5.37:g.33982434C>T	ENSP00000296589:p.Asp157Asn		34018191	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	37	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441554	0.96187	.	.	ENSG00000164175	ENST00000296589;ENST00000382102;ENST00000509381;ENST00000345083	D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);	0.041280	0.85682	D	0.000000	D	0.96408	0.8828	M	0.76002	2.32	0.80722	A	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93696	0.7011	9	0.02654	T	1	-21.5253	19.1001	0.93270	0.0:1.0:0.0:0.0	.	157;157;157	D6RGY6;Q9UMX9-4;Q9UMX9	.;.;S45A2_HUMAN	N	157	ENSP00000296589:D157N;ENSP00000371534:D157N;ENSP00000421100:D157N;ENSP00000340444:D157N	ENSP00000296589:D157N	D	-	1	0	SLC45A2	34018191	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.720000	0.84759	2.601000	0.87937	0.551000	0.68910	GAC		0.468	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		T	33982434	C	T	33982434	3	4	61	1	0	0	0	0	1	0	0	0	14678	884	31	1	1162	1	SLC45A2	5	33982434	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18584	33982434	146932826	3746	11731										
SLC45A2	51151	broad.mit.edu	37	chr5	33984469	33984469	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggatggggctgaggaaccAcacaatgctgtacaggctgc	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33984469A>G	ENST00000296589.4	-	1	366	c.220T>C	c.(220-222)Tgg>Cgg	p.W74R	SLC45A2_ENST00000509381.1_Missense_Mutation_p.W74R|SLC45A2_ENST00000382102.3_Missense_Mutation_p.W74R|SLC45A2_ENST00000342059.3_Missense_Mutation_p.W74R|SLC45A2_ENST00000345083.5_Missense_Mutation_p.W74R	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	74					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.W74R(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						CTGAGGAACCACACAATGCTG	0.642																																					Ovarian(31;380 859 8490 22203 49048)											1	Substitution - Missense(1)	large_intestine(1)	5											56	48	50					5																	33984469		2203	4300	6503	34020226	SO:0001583	missense	51151			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.220T>C	5.37:g.33984469A>G	ENSP00000296589:p.Trp74Arg		34020226	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	37	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.692114	0.88735	.	.	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000509381;ENST00000345083	D;D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07;-3.07	5.62	5.62	0.85841	Major facilitator superfamily domain, general substrate transporter (1);	0.054998	0.85682	D	0.000000	D	0.96975	0.9012	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.97933	1.0321	10	0.87932	D	0	-8.2104	15.8205	0.78638	1.0:0.0:0.0:0.0	.	74;74;74	D6RGY6;Q9UMX9-4;Q9UMX9	.;.;S45A2_HUMAN	R	74	ENSP00000296589:W74R;ENSP00000341014:W74R;ENSP00000371534:W74R;ENSP00000421100:W74R;ENSP00000340444:W74R	ENSP00000296589:W74R	W	-	1	0	SLC45A2	34020226	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.271000	0.95698	2.137000	0.66172	0.450000	0.29827	TGG		0.642	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		G	33984469	A	G	33984469	3	3	61	1	0	0	0	0	1	0	0	0	14678	159	6	4	1415	4	SLC45A2	5	33984469	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2035	33984469	146930791	3747	11732										
AMACR	23600	broad.mit.edu	37	chr5	33989258	33989258	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagttaagctgataaatCtcttcgcggctgaatccaaa	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33989258C>A	ENST00000335606.6	-	5	1177	c.1089G>T	c.(1087-1089)gaG>gaT	p.E363D	AMACR_ENST00000502637.1_Missense_Mutation_p.E348D|RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000382085.3_Missense_Mutation_p.E363D|AMACR_ENST00000382072.2_3'UTR|AMACR_ENST00000514195.1_5'UTR	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	363					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)	p.E363D(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GCTGATAAATCTCTTCGCGGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											92	97	95					5																	33989258		2203	4300	6503	34025015	SO:0001583	missense	23600			AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.1089G>T	5.37:g.33989258C>A	ENSP00000334424:p.Glu363Asp		34025015	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	C	5.261	0.233521	0.09969	.	.	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.55760	0.5;0.5;0.5	5.51	1.79	0.24919	CoA-transferase family III domain (1);	0.149353	0.64402	D	0.000014	T	0.40398	0.1115	L	0.37507	1.11	0.80722	D	1	B;B;B	0.23490	0.086;0.051;0.051	B;B;B	0.29942	0.109;0.05;0.05	T	0.11421	-1.0588	10	0.32370	T	0.25	-34.3852	8.6655	0.34118	0.0:0.6451:0.0:0.3549	.	363;348;363	F8W9N1;D6RB81;Q9UHK6	.;.;AMACR_HUMAN	D	363;363;348	ENSP00000334424:E363D;ENSP00000371517:E363D;ENSP00000424351:E348D	ENSP00000334424:E363D	E	-	3	2	AMACR	34025015	0.940000	0.31905	0.973000	0.42090	0.231000	0.25187	0.055000	0.14229	0.110000	0.17919	0.573000	0.79308	GAG		0.403	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		A	33989258	C	A	33989258	3	1	61	1	0	0	0	0	1	0	0	0	562	912	32	2	121	2	AMACR	5	33989258	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4789	33989258	146926002	3748	11733										
AMACR	23600	broad.mit.edu	37	chr5	33989516	33989516	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccactctgccttcgtcttCtctgcaaatacatctgcaaa	4	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:33989516C>A	ENST00000335606.6	-	5	919	c.831G>T	c.(829-831)gaG>gaT	p.E277D	AMACR_ENST00000502637.1_Missense_Mutation_p.E262D|RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000382085.3_Missense_Mutation_p.E277D|AMACR_ENST00000382072.2_3'UTR|AMACR_ENST00000514195.1_5'UTR	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	277			E -> K (in dbSNP:rs2278008). {ECO:0000269|PubMed:10655068, ECO:0000269|PubMed:11060344, ECO:0000269|PubMed:15880524, ECO:0000269|Ref.4}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)	p.E277D(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CCTTCGTCTTCTCTGCAAATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											82	77	79					5																	33989516		2203	4300	6503	34025273	SO:0001583	missense	23600			AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.831G>T	5.37:g.33989516C>A	ENSP00000334424:p.Glu277Asp		34025273	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.823000	0.50739	.	.	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.51817	0.69;0.69;0.69	5.7	5.7	0.88788	CoA-transferase family III domain (2);	0.282172	0.40554	N	0.001063	T	0.45337	0.1337	L	0.49778	1.585	0.80722	D	1	B;B;B	0.21905	0.062;0.037;0.037	B;B;B	0.25614	0.062;0.017;0.017	T	0.33599	-0.9862	10	0.51188	T	0.08	-19.9153	14.3822	0.66919	0.0:0.9294:0.0:0.0706	.	277;262;277	F8W9N1;D6RB81;Q9UHK6	.;.;AMACR_HUMAN	D	277;277;262	ENSP00000334424:E277D;ENSP00000371517:E277D;ENSP00000424351:E262D	ENSP00000334424:E277D	E	-	3	2	AMACR	34025273	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.812000	0.38952	2.848000	0.98002	0.637000	0.83480	GAG		0.448	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		A	33989516	C	A	33989516	3	1	61	1	0	0	0	0	1	0	0	0	562	912	32	2	379	2	AMACR	5	33989516	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258	33989516	146925744	3749	11734										
RAI14	26064	broad.mit.edu	37	chr5	34808727	34808727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgtgcagattctctgcGaacacaagagccccataaac	8	12	1	2	rs201315302		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34808727G>A	ENST00000265109.3	+	7	705	c.418G>A	c.(418-420)Gaa>Aaa	p.E140K	RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000428746.2_Missense_Mutation_p.E140K|RAI14_ENST00000515799.1_Missense_Mutation_p.E143K|RAI14_ENST00000397449.1_Missense_Mutation_p.E133K|RAI14_ENST00000503673.1_Missense_Mutation_p.E140K|RAI14_ENST00000512629.1_Missense_Mutation_p.E140K|RAI14_ENST00000506376.1_Missense_Mutation_p.E132K	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	140						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E140K(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GATTCTCTGCGAACACAAGAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	128	114	118		418,418,418,394,427,418	5.5	0.8	5		118	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	56,56,56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	140/981,140/981,140/952,132/973,143/984,140/981	34808727	1,13005	2203	4300	6503	34844484	SO:0001583	missense	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.418G>A	5.37:g.34808727G>A	ENSP00000265109:p.Glu140Lys		34844484	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	35	5.480434	0.96307	0.0	1.16E-4	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000512625;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.17;-0.25;-0.25	5.5	5.5	0.81552	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.77089	0.4079	L	0.43554	1.36	0.51233	D	0.999916	D;D;P;D	0.89917	1.0;0.966;0.912;0.966	D;P;B;P	0.80764	0.994;0.503;0.335;0.503	T	0.78168	-0.2309	9	0.62326	D	0.03	-18.273	17.6004	0.88024	0.0:0.0:1.0:0.0	.	132;140;143;140	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	K	140;140;140;140;143;140;132;133	ENSP00000265109:E140K;ENSP00000422377:E140K;ENSP00000388725:E140K;ENSP00000422942:E140K;ENSP00000427123:E143K;ENSP00000425115:E140K;ENSP00000423854:E132K;ENSP00000380591:E133K	ENSP00000265109:E140K	E	+	1	0	RAI14	34844484	1.000000	0.71417	0.765000	0.31456	0.934000	0.57294	6.809000	0.75211	2.576000	0.86940	0.650000	0.86243	GAA		0.478	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		A	34808727	G	A	34808727	3	1	61	1	0	0	0	0	1	0	0	0	13045	1059	37	1	505	1	RAI14	5	34808727	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	819211	34808727	146106533	3750	11735										
RAI14	26064	broad.mit.edu	37	chr5	34823711	34823711	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatattgctctgttattgaGaatatgaataaggagaaagc	9	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34823711G>T	ENST00000265109.3	+	15	2051	c.1764G>T	c.(1762-1764)gaG>gaT	p.E588D	RAI14_ENST00000428746.2_Missense_Mutation_p.E588D|RAI14_ENST00000515799.1_Missense_Mutation_p.E591D|RAI14_ENST00000397449.1_Missense_Mutation_p.E581D|RAI14_ENST00000503673.1_Missense_Mutation_p.E588D|RAI14_ENST00000512629.1_Missense_Mutation_p.E559D|RAI14_ENST00000506376.1_Missense_Mutation_p.E580D	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	588						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E588D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					CTGTTATTGAGAATATGAATA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	61	60					5																	34823711		2203	4300	6503	34859468	SO:0001583	missense	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1764G>T	5.37:g.34823711G>T	ENSP00000265109:p.Glu588Asp		34859468	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	9.135	1.012477	0.19277	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.38722	1.18;1.12;1.18;1.18;1.18;1.22;1.21	5.42	3.65	0.41850	.	.	.	.	.	T	0.25568	0.0622	N	0.20986	0.625	0.36213	D	0.851471	B;B;B;B	0.21606	0.037;0.058;0.02;0.058	B;B;B;B	0.21151	0.024;0.017;0.033;0.017	T	0.14144	-1.0483	9	0.35671	T	0.21	-24.4833	5.1721	0.15116	0.2298:0.0:0.6159:0.1543	.	580;559;591;588	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	D	588;559;588;588;591;580;581	ENSP00000265109:E588D;ENSP00000422377:E559D;ENSP00000388725:E588D;ENSP00000422942:E588D;ENSP00000427123:E591D;ENSP00000423854:E580D;ENSP00000380591:E581D	ENSP00000265109:E588D	E	+	3	2	RAI14	34859468	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	2.821000	0.48065	0.681000	0.31386	0.555000	0.69702	GAG		0.363	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34823711	G	T	34823711	3	4	61	1	0	0	0	0	1	0	0	0	13045	933	33	2	1883	2	RAI14	5	34823711	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14984	34823711	146091549	3751	11736										
RAI14	26064	broad.mit.edu	37	chr5	34829863	34829863	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaacaacaccaggaggtCatatcagtttacagaatgca	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34829863C>T	ENST00000265109.3	+	17	3113	c.2826C>T	c.(2824-2826)gtC>gtT	p.V942V	RAI14_ENST00000428746.2_Silent_p.V942V|RAI14_ENST00000515799.1_Silent_p.V945V|RAI14_ENST00000397449.1_Silent_p.V935V|RAI14_ENST00000503673.1_Silent_p.V942V|RAI14_ENST00000512629.1_Silent_p.V913V|RAI14_ENST00000506376.1_Silent_p.V934V	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	942						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.V942V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					ACCAGGAGGTCATATCAGTTT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	5											127	114	119					5																	34829863		2203	4300	6503	34865620	SO:0001819	synonymous_variant	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2826C>T	5.37:g.34829863C>T			34865620	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																				0.368	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34829863	C	T	34829863	2	4	61	1	0	0	0	0	0	0	0	1	13045	813	29	3		3	RAI14	5	34829863	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6152	34829863	146085397	3752	11737										
RAI14	26064	broad.mit.edu	37	chr5	34830835	34830835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagtactgaagcaaatcCttaccatgtgtaaaaaccag	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34830835C>A	ENST00000265109.3	+	18	3195	c.2908C>A	c.(2908-2910)Ctt>Att	p.L970I	RAI14_ENST00000428746.2_Missense_Mutation_p.L970I|RAI14_ENST00000515799.1_Missense_Mutation_p.L973I|RAI14_ENST00000397449.1_Missense_Mutation_p.L963I|RAI14_ENST00000503673.1_Missense_Mutation_p.L970I|RAI14_ENST00000512629.1_Missense_Mutation_p.L941I|RAI14_ENST00000506376.1_Missense_Mutation_p.L962I	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	970						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.L970I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GAAGCAAATCCTTACCATGTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											143	132	136					5																	34830835		2203	4300	6503	34866592	SO:0001583	missense	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2908C>A	5.37:g.34830835C>A	ENSP00000265109:p.Leu970Ile		34866592	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.953458	0.53293	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.50001	0.82;0.76;0.82;0.82;0.84;0.89;0.87	5.5	5.5	0.81552	.	.	.	.	.	T	0.53916	0.1826	L	0.48642	1.525	0.53005	D	0.999963	P;P;P;P	0.51537	0.946;0.911;0.946;0.911	P;B;P;B	0.55667	0.781;0.432;0.636;0.432	T	0.55547	-0.8124	9	0.87932	D	0	-7.0201	10.8968	0.47027	0.0:0.8851:0.0:0.1149	.	962;941;973;970	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	I	970;941;970;970;973;962;963	ENSP00000265109:L970I;ENSP00000422377:L941I;ENSP00000388725:L970I;ENSP00000422942:L970I;ENSP00000427123:L973I;ENSP00000423854:L962I;ENSP00000380591:L963I	ENSP00000265109:L970I	L	+	1	0	RAI14	34866592	0.964000	0.33143	0.995000	0.50966	0.996000	0.88848	1.940000	0.40223	2.755000	0.94549	0.655000	0.94253	CTT		0.418	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		A	34830835	C	A	34830835	3	1	61	1	0	0	0	0	1	0	0	0	13045	681	24	2	3039	2	RAI14	5	34830835	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	972	34830835	146084425	3753	11738										
TTC23L	153657	broad.mit.edu	37	chr5	34863073	34863073	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacctggaaggcaaatacGacctcaaataaggagaaaga	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34863073G>A	ENST00000505624.1	+	5	553	c.450G>A	c.(448-450)acG>acA	p.T150T	TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	150			T -> M (in dbSNP:rs34566695).					p.T150T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						AGGCAAATACGACCTCAAATA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	5											114	112	113					5																	34863073		1986	4160	6146	34898830	SO:0001819	synonymous_variant	153657				CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.450G>A	5.37:g.34863073G>A			34898830	Q6RGS4|Q8N7R3|Q96LJ2	Silent	SNP	ENST00000505624.1	37	CCDS54840.1																																																																																				0.512	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725		A	34863073	G	A	34863073	2	1	61	1	0	0	0	0	0	0	0	1	16731	1045	37	1		1	TTC23L	5	34863073	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32238	34863073	146052187	3754	11739										
DNAJC21	134218	broad.mit.edu	37	chr5	34949663	34949663	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaggatgtacctggcaaaGattcatatctgcctgcagct	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:34949663G>T	ENST00000342382.4	+	10	1412				DNAJC21_ENST00000382021.2_Missense_Mutation_p.D401Y|DNAJC21_ENST00000512136.1_Intron|DNAJC21_ENST00000303525.7_Intron			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21						protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D401Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			acctggcaaagattcatatct	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											79	75	77					5																	34949663		2183	4265	6448	34985420	SO:0001627	intron_variant	134218				CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"Heat shock proteins / DNAJ (HSP40)"	27030	protein-coding gene	gene with protein product	"JJJ1 DnaJ domain protein homolog (S. cerevisiae)"					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.1186-612G>T	5.37:g.34949663G>T			34985420	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Missense_Mutation	SNP	ENST00000342382.4	37	CCDS34144.1	.	.	.	.	.	.	.	.	.	.	G	8.384	0.838159	0.16891	.	.	ENSG00000168724	ENST00000382021	T	0.49432	0.78	2.38	1.49	0.22878	.	1.188910	0.05798	N	0.611586	T	0.30417	0.0764	.	.	.	0.09310	N	1	P	0.34977	0.478	B	0.26094	0.066	T	0.23440	-1.0188	9	0.45353	T	0.12	.	4.9192	0.13862	0.1804:0.0:0.8196:0.0	.	401	Q5F1R6-2	.	Y	401	ENSP00000371451:D401Y	ENSP00000371451:D401Y	D	+	1	0	DNAJC21	34985420	0.000000	0.05858	0.005000	0.12908	0.278000	0.26855	0.055000	0.14229	0.553000	0.29044	0.484000	0.47621	GAT		0.408	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283		T	34949663	G	T	34949663	1	4	61	0	1	0	0	0	0	0	0	0	4651	942	33	2		2	DNAJC21	5	34949663	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86590	34949663	145965597	3755	11740										
PRLR	5618	broad.mit.edu	37	chr5	35068954	35068954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggacagccacagagatccAcacggttgtatcattcatgg	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35068954A>G	ENST00000382002.5	-	8	1138	c.712T>C	c.(712-714)Tgg>Cgg	p.W238R	PRLR_ENST00000310101.5_Missense_Mutation_p.W238R|PRLR_ENST00000513753.1_Missense_Mutation_p.W238R|PRLR_ENST00000231423.3_Missense_Mutation_p.W238R|PRLR_ENST00000542609.1_Missense_Mutation_p.W238R|PRLR_ENST00000509934.1_Intron|PRLR_ENST00000348262.3_Intron|PRLR_ENST00000397391.3_Intron|PRLR_ENST00000342362.5_Missense_Mutation_p.W137R|PRLR_ENST00000511486.1_Missense_Mutation_p.W137R	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	238					activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)	p.W238R(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	ACAGAGATCCACACGGTTGTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											118	107	110					5																	35068954		2203	4300	6503	35104711	SO:0001583	missense	5618				CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.712T>C	5.37:g.35068954A>G	ENSP00000371432:p.Trp238Arg		35104711	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593570	0.66219	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101	T;T;T;D;D;D;T	0.90004	-1.26;-1.2;-1.22;-2.6;-1.74;-2.6;-1.24	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.95978	0.8690	M	0.93594	3.435	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.998	D	0.96962	0.9702	10	0.87932	D	0	-8.4821	16.3634	0.83296	1.0:0.0:0.0:0.0	.	238;137;238;238	P16471;P16471-2;P16471-6;P16471-4	PRLR_HUMAN;.;.;.	R	238;238;238;137;238;137;238	ENSP00000231423:W238R;ENSP00000424841:W238R;ENSP00000441813:W238R;ENSP00000339213:W137R;ENSP00000371432:W238R;ENSP00000422556:W137R;ENSP00000309008:W238R	ENSP00000231423:W238R	W	-	1	0	PRLR	35104711	1.000000	0.71417	0.975000	0.42487	0.444000	0.32077	7.422000	0.80217	2.324000	0.78689	0.533000	0.62120	TGG		0.408	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2			G	35068954	A	G	35068954	3	3	61	1	0	0	0	0	1	0	0	0	12565	159	6	4	1168	4	PRLR	5	35068954	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	119291	35068954	145846306	3756	11741										
SPEF2	79925	broad.mit.edu	37	chr5	35654774	35654774	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcacgagagcaaagggaGaaaagacggcggaaattgtt	14	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35654774G>T	ENST00000356031.3	+	7	1078	c.924G>T	c.(922-924)gaG>gaT	p.E308D	SPEF2_ENST00000509059.1_Missense_Mutation_p.E308D|SPEF2_ENST00000440995.2_Missense_Mutation_p.E308D|SPEF2_ENST00000282469.6_Missense_Mutation_p.E308D	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	308					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)		p.E308D(2)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGCAAAGGGAGAAAAGACGGC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	5											83	82	83					5																	35654774		2203	4300	6503	35690531	SO:0001583	missense	79925			AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.924G>T	5.37:g.35654774G>T	ENSP00000348314:p.Glu308Asp		35690531	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.157747	0.78114	.	.	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000440995	T;T;T;T	0.19105	2.17;2.17;2.17;2.17	5.72	2.98	0.34508	.	0.108387	0.64402	D	0.000010	T	0.40815	0.1132	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.999	D;D;D	0.80764	0.978;0.994;0.96	T	0.10567	-1.0624	10	0.59425	D	0.04	.	8.4933	0.33112	0.3951:0.0:0.6049:0.0	.	308;308;308	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	D	308	ENSP00000282469:E308D;ENSP00000348314:E308D;ENSP00000421593:E308D;ENSP00000412125:E308D	ENSP00000282469:E308D	E	+	3	2	SPEF2	35690531	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.271000	0.33098	0.348000	0.23949	0.655000	0.94253	GAG		0.398	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		T	35654774	G	T	35654774	3	4	61	1	0	0	0	0	1	0	0	0	15074	933	33	2	950	2	SPEF2	5	35654774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	585820	35654774	145260486	3757	11742										
SPEF2	79925	broad.mit.edu	37	chr5	35807268	35807268	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaagacctaggtgccaaGaacctggagccaattgaagt	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35807268G>A	ENST00000356031.3	+	36	5446	c.5292G>A	c.(5290-5292)aaG>aaA	p.K1764K	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Silent_p.K1759K|SPEF2_ENST00000303129.4_Silent_p.K561K	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1764					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)		p.K1764K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAGGTGCCAAGAACCTGGAGC	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	5											137	133	134					5																	35807268		1814	4079	5893	35843025	SO:0001819	synonymous_variant	79925			AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.5292G>A	5.37:g.35807268G>A			35843025	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	37	CCDS43309.1																																																																																				0.353	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35807268	G	A	35807268	2	1	61	1	0	0	0	0	0	0	0	1	15074	933	33	3		3	SPEF2	5	35807268	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152494	35807268	145107992	3758	11743										
IL7R	3575	broad.mit.edu	37	chr5	35860956	35860956	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttgttcctccccaggaGacttggaagatgcagaactg	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35860956G>T	ENST00000303115.3	+	2	214	c.85G>T	c.(85-87)Gac>Tac	p.D29Y	IL7R_ENST00000506850.1_Missense_Mutation_p.D29Y|IL7R_ENST00000511982.1_Missense_Mutation_p.D29Y|IL7R_ENST00000511031.1_3'UTR|IL7R_ENST00000343305.4_Missense_Mutation_p.D29Y	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	29					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.D29Y(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			CTCCCCAGGAGACTTGGAAGA	0.438			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																																Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	1	Substitution - Missense(1)	large_intestine(1)	5											148	139	142					5																	35860956		2203	4299	6502	35896713	SO:0001583	missense	3575			M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.85G>T	5.37:g.35860956G>T	ENSP00000306157:p.Asp29Tyr		35896713	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180051	0.78564	.	.	ENSG00000168685	ENST00000508941;ENST00000515665;ENST00000303115;ENST00000343305;ENST00000506850;ENST00000511982	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	6.17	6.17	0.99709	.	0.767928	0.12510	N	0.462566	D	0.87018	0.6073	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.976	D;P	0.71184	0.972;0.556	D	0.84824	0.0798	10	0.62326	D	0.03	-6.3761	16.3795	0.83443	0.0:0.0:1.0:0.0	.	29;29	D6RGV2;P16871	.;IL7RA_HUMAN	Y	29	ENSP00000426426:D29Y;ENSP00000425538:D29Y;ENSP00000306157:D29Y;ENSP00000345819:D29Y;ENSP00000421207:D29Y;ENSP00000425309:D29Y	ENSP00000306157:D29Y	D	+	1	0	IL7R	35896713	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	4.489000	0.60309	2.941000	0.99782	0.655000	0.94253	GAC		0.438	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			T	35860956	G	T	35860956	3	4	61	1	0	0	0	0	1	0	0	0	7726	942	33	2	91	2	IL7R	5	35860956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53688	35860956	145054304	3759	11744										
CAPSL	133690	broad.mit.edu	37	chr5	35904706	35904706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacatcagtgtcaatggatgCgctcacacctgcatagtagt	9	11	3	0	rs568452046		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35904706C>T	ENST00000397367.2	-	5	694	c.568G>A	c.(568-570)Gca>Aca	p.A190T	CAPSL_ENST00000397366.1_Missense_Mutation_p.A190T	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	190	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.A190T(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			TCAATGGATGCGCTCACACCT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											119	112	115					5																	35904706		2203	4300	6503	35940463	SO:0001583	missense	133690			BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"EF-hand domain containing"	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.568G>A	5.37:g.35904706C>T	ENSP00000380524:p.Ala190Thr		35940463		Missense_Mutation	SNP	ENST00000397367.2	37	CCDS3912.2	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061954	0.76187	.	.	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623	T;T;D	0.92545	-0.31;-0.31;-3.06	6.04	6.04	0.98038	.	0.047892	0.85682	D	0.000000	D	0.93854	0.8034	M	0.89287	3.02	0.80722	D	1	D	0.54207	0.965	B	0.41666	0.363	D	0.94498	0.7707	10	0.66056	D	0.02	-17.928	20.5948	0.99439	0.0:1.0:0.0:0.0	.	190	Q8WWF8	CAPSL_HUMAN	T	190	ENSP00000380524:A190T;ENSP00000380523:A190T;ENSP00000424806:A190T	ENSP00000380523:A190T	A	-	1	0	CAPSL	35940463	1.000000	0.71417	0.580000	0.28601	0.414000	0.31173	7.463000	0.80869	2.873000	0.98535	0.563000	0.77884	GCA		0.498	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647		T	35904706	C	T	35904706	3	4	61	1	0	0	0	0	1	0	0	0	2645	768	27	1	62	1	CAPSL	5	35904706	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43750	35904706	145010554	3760	11745										
CAPSL	133690	broad.mit.edu	37	chr5	35910046	35910046	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcactccattccccattCtggtactttgggtggtgttt	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35910046C>A	ENST00000397367.2	-	4	573	c.447G>T	c.(445-447)caG>caT	p.Q149H	CAPSL_ENST00000514524.1_Missense_Mutation_p.Q149H|CAPSL_ENST00000397366.1_Missense_Mutation_p.Q149H	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	149						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.Q149H(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			ATTCCCCATTCTGGTACTTTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											199	198	199					5																	35910046		2203	4300	6503	35945803	SO:0001583	missense	133690			BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"EF-hand domain containing"	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.447G>T	5.37:g.35910046C>A	ENSP00000380524:p.Gln149His		35945803		Missense_Mutation	SNP	ENST00000397367.2	37	CCDS3912.2	.	.	.	.	.	.	.	.	.	.	C	15.08	2.727726	0.48833	.	.	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623;ENST00000514524	T;T;T;T	0.67865	-0.29;-0.29;-0.29;0.57	5.57	-0.983	0.10263	EF-hand-like domain (1);	0.107611	0.64402	D	0.000004	T	0.71617	0.3361	L	0.58583	1.82	0.49389	D	0.999789	P	0.40681	0.727	P	0.56343	0.796	T	0.67860	-0.5561	10	0.37606	T	0.19	-17.324	11.6176	0.51098	0.0:0.4887:0.0:0.5113	.	149	Q8WWF8	CAPSL_HUMAN	H	149	ENSP00000380524:Q149H;ENSP00000380523:Q149H;ENSP00000424806:Q149H;ENSP00000421018:Q149H	ENSP00000380523:Q149H	Q	-	3	2	CAPSL	35945803	0.958000	0.32768	0.997000	0.53966	0.622000	0.37654	0.105000	0.15333	-0.117000	0.11872	-0.391000	0.06502	CAG		0.373	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647		A	35910046	C	A	35910046	3	1	61	1	0	0	0	0	1	0	0	0	2645	912	32	2	187	2	CAPSL	5	35910046	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5340	35910046	145005214	3761	11746										
UGT3A1	133688	broad.mit.edu	37	chr5	35954310	35954310	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctacacctagcctcatgtCttcttcaccttcctggcccc	6	18	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35954310C>A	ENST00000274278.3	-	7	1923	c.1566G>T	c.(1564-1566)aaG>aaT	p.K522N	UGT3A1_ENST00000513233.1_5'Flank	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	522						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.K522N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGCCTCATGTCTTCTTCACCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											85	74	78					5																	35954310		2203	4300	6503	35990067	SO:0001583	missense	133688				CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"UDP glucuronosyltransferases"	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.1566G>T	5.37:g.35954310C>A	ENSP00000274278:p.Lys522Asn		35990067	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Missense_Mutation	SNP	ENST00000274278.3	37	CCDS3913.1	.	.	.	.	.	.	.	.	.	.	.	10.17	1.275998	0.23307	.	.	ENSG00000145626	ENST00000274278	T	0.62788	-0.0	3.35	1.46	0.22682	.	2.779510	0.02771	U	0.119702	T	0.40546	0.1121	N	0.08118	0	0.09310	N	1	P	0.41313	0.745	B	0.33196	0.159	T	0.42783	-0.9431	10	0.87932	D	0	.	6.7529	0.23497	0.0:0.5695:0.0:0.4305	.	522	Q6NUS8	UD3A1_HUMAN	N	522	ENSP00000274278:K522N	ENSP00000274278:K522N	K	-	3	2	UGT3A1	35990067	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.207000	0.17395	0.196000	0.20367	-1.026000	0.02426	AAG		0.602	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404		A	35954310	C	A	35954310	3	1	61	1	0	0	0	0	1	0	0	0	17003	912	32	2	9	2	UGT3A1	5	35954310	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44264	35954310	144960950	3762	11747										
UGT3A1	133688	broad.mit.edu	37	chr5	35965933	35965933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagttctcattctttaagGaatccattatatcctttctg	4	9	3	0	rs549468369		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:35965933G>A	ENST00000274278.3	-	4	755	c.398C>T	c.(397-399)tCc>tTc	p.S133F	UGT3A1_ENST00000503189.1_Missense_Mutation_p.S133F|UGT3A1_ENST00000513233.1_Intron|UGT3A1_ENST00000507113.1_Missense_Mutation_p.S99F|UGT3A1_ENST00000333811.4_Missense_Mutation_p.S79F	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	133						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.S133F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATTCTTTAAGGAATCCATTAT	0.338													G|||	1	0.000199681	0	0	5008	,	,		17866	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5											48	47	47					5																	35965933		2203	4300	6503	36001690	SO:0001583	missense	133688				CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"UDP glucuronosyltransferases"	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.398C>T	5.37:g.35965933G>A	ENSP00000274278:p.Ser133Phe		36001690	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Missense_Mutation	SNP	ENST00000274278.3	37	CCDS3913.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.244097	0.22796	.	.	ENSG00000145626	ENST00000274278;ENST00000503189;ENST00000507113;ENST00000333811	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	2.93	-0.304	0.12788	.	0.238761	0.34777	N	0.003681	T	0.36110	0.0955	N	0.26162	0.8	0.09310	N	1	B;B;B;B	0.19200	0.034;0.005;0.02;0.005	B;B;B;B	0.21360	0.034;0.012;0.021;0.02	T	0.13737	-1.0498	10	0.44086	T	0.13	.	4.0439	0.09764	0.3404:0.1851:0.4746:0.0	.	99;133;79;133	E9PD17;B7Z8Q8;G5E961;Q6NUS8	.;.;.;UD3A1_HUMAN	F	133;133;99;79	ENSP00000274278:S133F;ENSP00000427079:S133F;ENSP00000426100:S99F;ENSP00000328033:S79F	ENSP00000274278:S133F	S	-	2	0	UGT3A1	36001690	0.000000	0.05858	0.011000	0.14972	0.594000	0.36715	-0.240000	0.08952	0.023000	0.15187	0.313000	0.20887	TCC		0.338	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404		A	35965933	G	A	35965933	3	1	61	1	0	0	0	0	1	0	0	0	17003	1174	41	3	1271	3	UGT3A1	5	35965933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11623	35965933	144949327	3763	11748										
UGT3A2	167127	broad.mit.edu	37	chr5	36037990	36037990	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaccaaactttttggcttCtactcggaccatgttttcag	6	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36037990C>A	ENST00000282507.3	-	6	1305	c.1204G>T	c.(1204-1206)Gaa>Taa	p.E402*	UGT3A2_ENST00000504954.1_5'Flank|UGT3A2_ENST00000513300.1_Nonsense_Mutation_p.E368*|UGT3A2_ENST00000545528.1_Nonsense_Mutation_p.E100*	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	402					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.E402*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTTTTGGCTTCTACTCGGACC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											149	144	145					5																	36037990		2203	4300	6503	36073747	SO:0001587	stop_gained	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.1204G>T	5.37:g.36037990C>A	ENSP00000282507:p.Glu402*		36073747	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Nonsense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550027	0.86127	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	.	.	.	3.32	1.53	0.23141	.	0.167830	0.38326	U	0.001733	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.7063	0.23252	0.0:0.6768:0.0:0.3232	.	.	.	.	X	402;368;100	.	ENSP00000282507:E402X	E	-	1	0	UGT3A2	36073747	0.016000	0.18221	0.761000	0.31378	0.920000	0.55202	0.151000	0.16283	0.421000	0.25980	0.563000	0.77884	GAA		0.483	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		A	36037990	C	A	36037990	4	1	61	1	0	0	0	0	0	1	0	0	17004	922	32	2	375	2	UGT3A2	5	36037990	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72057	36037990	144877270	3764	11749										
UGT3A2	167127	broad.mit.edu	37	chr5	36039684	36039684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccatatcaccccttgggGtaggtgagcaaaggcattgt	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36039684G>A	ENST00000282507.3	-	5	1071	c.970C>T	c.(970-972)Ccc>Tcc	p.P324S	UGT3A2_ENST00000504954.1_5'Flank|UGT3A2_ENST00000513300.1_Missense_Mutation_p.P290S|UGT3A2_ENST00000545528.1_Missense_Mutation_p.P22S	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	324					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.P324S(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACCCCTTGGGGTAGGTGAGCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											143	131	135					5																	36039684		2203	4300	6503	36075441	SO:0001583	missense	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.970C>T	5.37:g.36039684G>A	ENSP00000282507:p.Pro324Ser		36075441	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.355297	0.24512	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.67865	-0.29;-0.29;-0.29	3.18	-2.47	0.06442	.	0.074676	0.53938	N	0.000051	T	0.57740	0.2074	L	0.60904	1.88	0.09310	N	1	B;B	0.15141	0.006;0.012	B;B	0.26416	0.069;0.035	T	0.53429	-0.8440	10	0.56958	D	0.05	.	9.0307	0.36258	0.5236:0.0:0.4764:0.0	.	290;324	E9PFK7;Q3SY77	.;UD3A2_HUMAN	S	324;290;22	ENSP00000282507:P324S;ENSP00000427404:P290S;ENSP00000445367:P22S	ENSP00000282507:P324S	P	-	1	0	UGT3A2	36075441	0.963000	0.33076	0.000000	0.03702	0.276000	0.26787	1.521000	0.35910	-0.639000	0.05502	-0.216000	0.12614	CCC		0.498	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		A	36039684	G	A	36039684	3	1	61	1	0	0	0	0	1	0	0	0	17004	1261	44	3	613	3	UGT3A2	5	36039684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1694	36039684	144875576	3765	11750										
LMBRD2	92255	broad.mit.edu	37	chr5	36105207	36105207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggatcatcagtgaatgTttctgcattaaaatccaaag	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36105207T>C	ENST00000296603.4	-	17	2452	c.1990A>G	c.(1990-1992)Aca>Gca	p.T664A		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	664						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.T664A(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCAGTGAATGTTTCTGCATTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											165	156	159					5																	36105207		2203	4300	6503	36140964	SO:0001583	missense	92255				CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.1990A>G	5.37:g.36105207T>C	ENSP00000296603:p.Thr664Ala		36140964	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	37	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068616	0.36470	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	.	.	.	5.49	3.1	0.35709	.	0.357359	0.31020	N	0.008413	T	0.44705	0.1306	L	0.47716	1.5	0.39544	D	0.968864	B	0.02656	0.0	B	0.04013	0.001	T	0.32025	-0.9922	9	0.38643	T	0.18	-2.76	5.1566	0.15038	0.1636:0.1521:0.0:0.6844	.	664	Q68DH5	LMBD2_HUMAN	A	664;558	.	ENSP00000296603:T664A	T	-	1	0	LMBRD2	36140964	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.750000	0.26334	0.468000	0.27243	0.454000	0.30748	ACA		0.398	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527		C	36105207	T	C	36105207	3	2	61	1	0	0	0	0	1	0	0	0	8867	1725	60	4	105	4	LMBRD2	5	36105207	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	65523	36105207	144810053	3766	11751										
LMBRD2	92255	broad.mit.edu	37	chr5	36124361	36124361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctttcattcactttacGaacctcctataaaaacagta	4	10	2	0	rs139182630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36124361G>A	ENST00000296603.4	-	7	1216	c.754C>T	c.(754-756)Cgt>Tgt	p.R252C		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	252						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R252C(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTCACTTTACGAACCTCCTAT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	CYS/ARG	0,4386		0,0,2193	47	45	46		754	4.8	1	5	dbSNP_134	46	2,8558	2.2+/-6.3	0,2,4278	no	missense	LMBRD2	NM_001007527.1	180	0,2,6471	AA,AG,GG		0.0234,0.0,0.0154	probably-damaging	252/696	36124361	2,12944	2193	4280	6473	36160118	SO:0001583	missense	92255				CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.754C>T	5.37:g.36124361G>A	ENSP00000296603:p.Arg252Cys		36160118	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	37	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914624	0.72983	0.0	2.34E-4	ENSG00000164187	ENST00000296603;ENST00000546130	T	0.32753	1.44	5.61	4.75	0.60458	LMBR1-like membrane protein (1);	0.048701	0.85682	N	0.000000	T	0.41259	0.1151	L	0.61218	1.895	0.80722	D	1	D	0.65815	0.995	P	0.50270	0.636	T	0.30090	-0.9990	10	0.40728	T	0.16	-5.6355	14.5522	0.68075	0.0707:0.0:0.9293:0.0	.	252	Q68DH5	LMBD2_HUMAN	C	252;146	ENSP00000296603:R252C	ENSP00000296603:R252C	R	-	1	0	LMBRD2	36160118	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.511000	0.60462	1.383000	0.46405	0.585000	0.79938	CGT		0.279	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527		A	36124361	G	A	36124361	3	1	61	1	0	0	0	0	1	0	0	0	8867	1058	37	1	1381	1	LMBRD2	5	36124361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19154	36124361	144790899	3767	11752										
SLC1A3	6507	broad.mit.edu	37	chr5	36629636	36629636	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcctggggaacttctgaTgaggatgttacagatgctgg	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36629636T>G	ENST00000265113.4	+	3	742	c.266T>G	c.(265-267)aTg>aGg	p.M89R	SLC1A3_ENST00000381918.3_Missense_Mutation_p.M89R	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	89					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.M89R(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAACTTCTGATGAGGATGTTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											275	253	260					5																	36629636		2203	4300	6503	36665393	SO:0001583	missense	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.266T>G	5.37:g.36629636T>G	ENSP00000265113:p.Met89Arg		36665393	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.235816	0.79800	.	.	ENSG00000079215	ENST00000265113;ENST00000513903;ENST00000505202;ENST00000513646;ENST00000381918	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	5.92	5.92	0.95590	Sodium:dicarboxylate symporter, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.81973	0.4936	M	0.92923	3.36	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.85130	0.968;0.997	D	0.86464	0.1781	10	0.87932	D	0	-34.1632	16.3526	0.83220	0.0:0.0:0.0:1.0	.	89;89	Q4JCQ8;P43003	.;EAA1_HUMAN	R	89	ENSP00000265113:M89R;ENSP00000427203:M89R;ENSP00000424986:M89R;ENSP00000420992:M89R;ENSP00000371343:M89R	ENSP00000265113:M89R	M	+	2	0	SLC1A3	36665393	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.673000	0.83973	2.255000	0.74692	0.533000	0.62120	ATG		0.413	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		G	36629636	T	G	36629636	3	3	61	1	0	0	0	0	1	0	0	0	14470	1464	51	4	289	4	SLC1A3	5	36629636	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	505275	36629636	144285624	3768	11753										
SLC1A3	6507	broad.mit.edu	37	chr5	36677244	36677244	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagagagttctttgattCtcttaacgaagccatcatga	8	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36677244C>A	ENST00000265113.4	+	6	1294	c.818C>A	c.(817-819)tCt>tAt	p.S273Y	SLC1A3_ENST00000381918.3_Missense_Mutation_p.S273Y|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	273					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.S273Y(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTCTTTGATTCTCTTAACGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											116	114	114					5																	36677244		2203	4300	6503	36713001	SO:0001583	missense	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.818C>A	5.37:g.36677244C>A	ENSP00000265113:p.Ser273Tyr		36713001	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.865057	0.51482	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.61742	0.08;0.08	5.92	1.71	0.24356	.	0.435856	0.30658	N	0.009160	T	0.72260	0.3438	M	0.81497	2.545	0.39452	D	0.967413	P;P	0.39282	0.666;0.645	P;B	0.52343	0.696;0.445	T	0.77400	-0.2602	10	0.36615	T	0.2	-5.6039	18.7288	0.91726	0.0:0.5144:0.4856:0.0	.	273;273	Q4JCQ8;P43003	.;EAA1_HUMAN	Y	273;221;273	ENSP00000265113:S273Y;ENSP00000371343:S273Y	ENSP00000265113:S273Y	S	+	2	0	SLC1A3	36713001	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.177000	0.50871	0.805000	0.34159	-0.165000	0.13383	TCT		0.418	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		A	36677244	C	A	36677244	3	1	61	1	0	0	0	0	1	0	0	0	14470	913	32	2	853	2	SLC1A3	5	36677244	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47608	36677244	144238016	3769	11754										
SLC1A3	6507	broad.mit.edu	37	chr5	36680569	36680569	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaagcgcgtcaccagattCgtgctccccgtaggagccac	11	15	1	1	rs372548093		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36680569C>T	ENST00000265113.4	+	8	1643	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC1A3_ENST00000381918.3_Silent_p.F389F|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	389					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.F389F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCACCAGATTCGTGCTCCCCG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C	,	1,4405	2.1+/-5.4	0,1,2202	106	92	97		1167,1167	-3.2	1	5		97	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC1A3	NM_001166695.1,NM_004172.4	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	389/498,389/543	36680569	1,13005	2203	4300	6503	36716326	SO:0001819	synonymous_variant	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1167C>T	5.37:g.36680569C>T			36716326	B2R5T3|Q4JCQ8	Silent	SNP	ENST00000265113.4	37	CCDS3919.1																																																																																				0.502	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		T	36680569	C	T	36680569	2	4	61	1	0	0	0	0	0	0	0	1	14470	883	31	1		1	SLC1A3	5	36680569	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3325	36680569	144234691	3770	11755										
NIPBL	25836	broad.mit.edu	37	chr5	36955643	36955643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagccttctctttaatgcacGaatagcagaagaggtgaact	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36955643G>A	ENST00000282516.8	+	3	633	c.134G>A	c.(133-135)cGa>cAa	p.R45Q	NIPBL_ENST00000448238.2_Missense_Mutation_p.R45Q	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	45					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.R45Q(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			TTTAATGCACGAATAGCAGAA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	5											140	129	132					5																	36955643		2203	4300	6503	36991400	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.134G>A	5.37:g.36955643G>A	ENSP00000282516:p.Arg45Gln		36991400	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652141	0.96724	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.96856	-4.13;-4.15	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.97986	0.9337	M	0.75264	2.295	0.47276	D	0.999373	D;D	0.71674	0.997;0.998	D;D	0.75484	0.968;0.986	D	0.98561	1.0641	10	0.66056	D	0.02	.	19.2931	0.94110	0.0:0.0:1.0:0.0	.	45;45	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	Q	45	ENSP00000282516:R45Q;ENSP00000406266:R45Q	ENSP00000282516:R45Q	R	+	2	0	NIPBL	36991400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.416000	0.97383	2.567000	0.86603	0.585000	0.79938	CGA		0.408	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36955643	G	A	36955643	3	1	61	1	0	0	0	0	1	0	0	0	10459	1058	37	1	140	1	NIPBL	5	36955643	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	275074	36955643	143959617	3771	11756										
NIPBL	25836	broad.mit.edu	37	chr5	36985275	36985275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactgaatgcaaacaaaacGagagcaccatagttgagcct	8	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36985275G>A	ENST00000282516.8	+	10	2492	c.1993G>A	c.(1993-1995)Gag>Aag	p.E665K	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.E665K	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	665					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.E665K(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			CAAACAAAACGAGAGCACCAT	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	5											97	96	96					5																	36985275		2203	4300	6503	37021032	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1993G>A	5.37:g.36985275G>A	ENSP00000282516:p.Glu665Lys		37021032	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	9.589	1.125528	0.20959	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.95035	-3.45;-3.59	5.98	5.98	0.97165	.	0.141721	0.49305	D	0.000152	D	0.89174	0.6640	N	0.19112	0.55	0.36041	D	0.8401	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	D	0.86366	0.1720	10	0.33141	T	0.24	.	14.2681	0.66135	0.0714:0.0:0.9286:0.0	.	665;665	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	K	665	ENSP00000282516:E665K;ENSP00000406266:E665K	ENSP00000282516:E665K	E	+	1	0	NIPBL	37021032	1.000000	0.71417	0.994000	0.49952	0.423000	0.31445	4.250000	0.58772	2.835000	0.97688	0.650000	0.86243	GAG		0.343	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36985275	G	A	36985275	3	1	61	1	0	0	0	0	1	0	0	0	10459	1059	37	1	2027	1	NIPBL	5	36985275	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29632	36985275	143929985	3772	11757										
NIPBL	25836	broad.mit.edu	37	chr5	36985581	36985581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggcatgacaataggaggGattctggaaagccatctaca	11	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:36985581G>A	ENST00000282516.8	+	10	2798	c.2299G>A	c.(2299-2301)Gat>Aat	p.D767N	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.D767N	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	767					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.D767N(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			CAATAGGAGGGATTCTGGAAA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	5											79	84	82					5																	36985581		2203	4298	6501	37021338	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2299G>A	5.37:g.36985581G>A	ENSP00000282516:p.Asp767Asn		37021338	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	9.548	1.115288	0.20795	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.93604	-3.25;-3.25	5.98	5.98	0.97165	.	0.053006	0.64402	D	0.000001	D	0.89787	0.6816	N	0.24115	0.695	0.40003	D	0.975196	P;P	0.42518	0.675;0.782	B;B	0.40256	0.107;0.324	D	0.89836	0.3999	10	0.46703	T	0.11	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	767;767	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	N	767	ENSP00000282516:D767N;ENSP00000406266:D767N	ENSP00000282516:D767N	D	+	1	0	NIPBL	37021338	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.246000	0.65411	2.835000	0.97688	0.650000	0.86243	GAT		0.423	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36985581	G	A	36985581	3	1	61	1	0	0	0	0	1	0	0	0	10459	1174	41	3	2333	3	NIPBL	5	36985581	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	306	36985581	143929679	3773	11758										
NIPBL	25836	broad.mit.edu	37	chr5	37061059	37061059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggacttcctgcggagtgAcatggctaattccaaaatca	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37061059A>G	ENST00000282516.8	+	45	8298	c.7799A>G	c.(7798-7800)gAc>gGc	p.D2600G	NIPBL_ENST00000448238.2_Missense_Mutation_p.D2600G	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2600					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.D2600G(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			CTGCGGAGTGACATGGCTAAT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	5											96	95	95					5																	37061059		2203	4300	6503	37096816	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.7799A>G	5.37:g.37061059A>G	ENSP00000282516:p.Asp2600Gly		37096816	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.86|13.86	2.364126|2.364126	0.41902|0.41902	.|.	.|.	ENSG00000164190|ENSG00000164190	ENST00000282516;ENST00000448238|ENST00000507919	D;D|.	0.93307|.	-3.2;-3.2|.	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.058454|.	0.64402|.	D|.	0.000002|.	T|T	0.50292|0.50292	0.1607|0.1607	N|N	0.20685|0.20685	0.6|0.6	0.39643|0.39643	D|D	0.970349|0.970349	B;B;B|.	0.09022|.	0.001;0.001;0.002|.	B;B;B|.	0.10450|.	0.004;0.004;0.005|.	T|T	0.50381|0.50381	-0.8835|-0.8835	10|5	0.16896|.	T|.	0.51|.	-12.5467|-12.5467	14.7964|14.7964	0.69881|0.69881	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2600;2600;2600|.	Q6IEH8;Q6KC79;Q6KC79-2|.	.;NIPBL_HUMAN;.|.	G|A	2600|106	ENSP00000282516:D2600G;ENSP00000406266:D2600G|.	ENSP00000282516:D2600G|.	D|T	+|+	2|1	0|0	NIPBL|NIPBL	37096816|37096816	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.807000|6.807000	0.75201|0.75201	1.944000|1.944000	0.56390|0.56390	0.482000|0.482000	0.46254|0.46254	GAC|ACA		0.363	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37061059	A	G	37061059	3	3	61	1	0	0	0	0	1	0	0	0	10459	275	10	4	7973	4	NIPBL	5	37061059	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	75478	37061059	143854201	3774	11759										
C5orf42	65250	broad.mit.edu	37	chr5	37108424	37108424	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaattgtgactctcatgaaGaatcttatggatttctgaag	10	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37108424G>T	ENST00000508244.1	-	50	9481	c.9388C>A	c.(9388-9390)Ctt>Att	p.L3130I	C5orf42_ENST00000425232.2_Missense_Mutation_p.L3130I|C5orf42_ENST00000274258.7_Missense_Mutation_p.L2028I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3130						integral component of membrane (GO:0016021)		p.L2028I(1)|p.L3130I(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTCTCATGAAGAATCTTATGG	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	5											120	115	117					5																	37108424		2203	4300	6503	37144181	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9388C>A	5.37:g.37108424G>T	ENSP00000421690:p.Leu3130Ile		37144181	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625406	0.66901	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	4.78	3.91	0.45181	.	0.100510	0.41001	D	0.000974	T	0.61887	0.2383	M	0.71036	2.16	0.09310	N	0.999996	P;P	0.52061	0.95;0.944	P;P	0.48270	0.562;0.572	T	0.59568	-0.7430	10	0.87932	D	0	.	11.2159	0.48825	0.0:0.185:0.815:0.0	.	3130;2028	E9PH94;Q9H799	.;CE042_HUMAN	I	3130;3130;2028;2196	ENSP00000421690:L3130I;ENSP00000389014:L3130I;ENSP00000274258:L2028I;ENSP00000424223:L2196I	ENSP00000274258:L2028I	L	-	1	0	C5orf42	37144181	0.996000	0.38824	0.056000	0.19401	0.031000	0.12232	3.428000	0.52792	1.359000	0.45940	0.655000	0.94253	CTT		0.408	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37108424	G	T	37108424	3	4	61	1	0	0	0	0	1	0	0	0	2307	942	33	2	213	2	C5orf42	5	37108424	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47365	37108424	143806836	3775	11760										
C5orf42	65250	broad.mit.edu	37	chr5	37165689	37165689	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattattaattatggaattCtctggtcgaaaagtcacatt	6	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37165689C>A	ENST00000508244.1	-	35	7578	c.7485G>T	c.(7483-7485)gaG>gaT	p.E2495D	C5orf42_ENST00000425232.2_Missense_Mutation_p.E2495D|C5orf42_ENST00000274258.7_Missense_Mutation_p.E1375D			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2495						integral component of membrane (GO:0016021)		p.E1375D(1)|p.E2495D(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTATGGAATTCTCTGGTCGAA	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	5											114	108	110					5																	37165689		2202	4300	6502	37201446	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7485G>T	5.37:g.37165689C>A	ENSP00000421690:p.Glu2495Asp		37201446	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	7.929	0.740183	0.15642	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.27402	1.73;1.73;1.67;1.69	5.3	3.38	0.38709	.	0.457271	0.18653	N	0.134937	T	0.19927	0.0479	L	0.34521	1.04	0.24544	N	0.994059	B;B	0.14438	0.004;0.01	B;B	0.16289	0.011;0.015	T	0.19386	-1.0307	10	0.15952	T	0.53	.	8.1883	0.31352	0.4159:0.4428:0.1413:0.0	.	2495;1375	E9PH94;Q9H799	.;CE042_HUMAN	D	2495;2495;1375;1543;1375	ENSP00000421690:E2495D;ENSP00000389014:E2495D;ENSP00000274258:E1375D;ENSP00000424223:E1543D	ENSP00000274258:E1375D	E	-	3	2	C5orf42	37201446	0.001000	0.12720	0.038000	0.18304	0.335000	0.28730	-0.591000	0.05753	1.205000	0.43262	0.462000	0.41574	GAG		0.348	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37165689	C	A	37165689	3	1	61	1	0	0	0	0	1	0	0	0	2307	912	32	2	2176	2	C5orf42	5	37165689	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57265	37165689	143749571	3776	11761										
C5orf42	65250	broad.mit.edu	37	chr5	37167173	37167173	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttactgtcctttccttgtCttacttcaggtggttctatt	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37167173C>T	ENST00000508244.1	-	34	7469	c.7376G>A	c.(7375-7377)aGa>aAa	p.R2459K	C5orf42_ENST00000425232.2_Missense_Mutation_p.R2459K|C5orf42_ENST00000274258.7_Missense_Mutation_p.R1339K			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2459						integral component of membrane (GO:0016021)		p.R1339K(1)|p.R2459K(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTTTCCTTGTCTTACTTCAGG	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	5											182	169	174					5																	37167173		2203	4300	6503	37202930	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7376G>A	5.37:g.37167173C>T	ENSP00000421690:p.Arg2459Lys		37202930	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052895	0.36181	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.25579	1.82;1.82;1.79;1.8	4.47	-1.18	0.09617	.	0.730125	0.12358	N	0.475913	T	0.16385	0.0394	L	0.48642	1.525	0.09310	N	1	B;B	0.20550	0.007;0.046	B;B	0.17722	0.007;0.019	T	0.25537	-1.0129	10	0.30854	T	0.27	.	1.732	0.02934	0.1246:0.3774:0.2578:0.2402	.	2459;1339	E9PH94;Q9H799	.;CE042_HUMAN	K	2459;2459;1339;1507;1339	ENSP00000421690:R2459K;ENSP00000389014:R2459K;ENSP00000274258:R1339K;ENSP00000424223:R1507K	ENSP00000274258:R1339K	R	-	2	0	C5orf42	37202930	0.989000	0.36119	0.050000	0.19076	0.965000	0.64279	0.233000	0.17911	-0.059000	0.13154	0.591000	0.81541	AGA		0.303	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37167173	C	T	37167173	3	4	61	1	0	0	0	0	1	0	0	0	2307	913	32	3	2289	3	C5orf42	5	37167173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1484	37167173	143748087	3777	11762										
C5orf42	65250	broad.mit.edu	37	chr5	37168933	37168933	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaatgaagtaatgacaatCttgggtattttctttcttct	8	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37168933C>A	ENST00000508244.1	-	33	7286	c.7193G>T	c.(7192-7194)aGa>aTa	p.R2398I	C5orf42_ENST00000425232.2_Missense_Mutation_p.R2398I|C5orf42_ENST00000274258.7_Missense_Mutation_p.R1278I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2398						integral component of membrane (GO:0016021)		p.R1278I(1)|p.R2398I(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TAATGACAATCTTGGGTATTT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	5											172	173	173					5																	37168933		2203	4300	6503	37204690	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7193G>T	5.37:g.37168933C>A	ENSP00000421690:p.Arg2398Ile		37204690	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959737	0.53400	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.24538	1.86;1.86;1.85;1.85	4.96	0.653	0.17828	.	0.903077	0.09324	N	0.817859	T	0.22126	0.0533	L	0.38175	1.15	0.09310	N	1	B;B	0.27791	0.189;0.189	B;B	0.32533	0.147;0.147	T	0.34601	-0.9822	10	0.52906	T	0.07	.	8.4991	0.33148	0.0:0.6753:0.0:0.3247	.	2398;1278	E9PH94;Q9H799	.;CE042_HUMAN	I	2398;2398;1278;1446;1278	ENSP00000421690:R2398I;ENSP00000389014:R2398I;ENSP00000274258:R1278I;ENSP00000424223:R1446I	ENSP00000274258:R1278I	R	-	2	0	C5orf42	37204690	0.023000	0.18921	0.000000	0.03702	0.334000	0.28698	1.363000	0.34159	-0.112000	0.11979	-0.152000	0.13540	AGA		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37168933	C	A	37168933	3	1	61	1	0	0	0	0	1	0	0	0	2307	913	32	2	2476	2	C5orf42	5	37168933	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1760	37168933	143746327	3778	11763										
C5orf42	65250	broad.mit.edu	37	chr5	37180183	37180183	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctacttctaaaagattCtcatcaatatctataaattc	2	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37180183C>T	ENST00000508244.1	-	27	5766	c.5673G>A	c.(5671-5673)gaG>gaA	p.E1891E	C5orf42_ENST00000425232.2_Silent_p.E1891E|C5orf42_ENST00000274258.7_Silent_p.E771E			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1891						integral component of membrane (GO:0016021)		p.E771E(1)|p.E1891E(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTAAAAGATTCTCATCAATAT	0.279																																																2	Substitution - coding silent(2)	large_intestine(2)	5											51	56	55					5																	37180183		2181	4255	6436	37215940	SO:0001819	synonymous_variant	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5673G>A	5.37:g.37180183C>T			37215940	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																				0.279	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37180183	C	T	37180183	2	4	61	1	0	0	0	0	0	0	0	1	2307	912	32	3		3	C5orf42	5	37180183	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11250	37180183	143735077	3779	11764										
C5orf42	65250	broad.mit.edu	37	chr5	37187933	37187933	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacacagagcacaaagttCtctgaagcaacctaaagcag	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37187933C>A	ENST00000508244.1	-	21	3916	c.3823G>T	c.(3823-3825)Gaa>Taa	p.E1275*	C5orf42_ENST00000425232.2_Nonsense_Mutation_p.E1275*|C5orf42_ENST00000274258.7_Nonsense_Mutation_p.E156*			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1275						integral component of membrane (GO:0016021)		p.E156*(1)|p.E1275*(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GCACAAAGTTCTCTGAAGCAA	0.353																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											77	73	74					5																	37187933		2203	4300	6503	37223690	SO:0001587	stop_gained	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3823G>T	5.37:g.37187933C>A	ENSP00000421690:p.Glu1275*		37223690	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Nonsense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	58	30.863966	0.99978	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	.	.	.	5.49	4.61	0.57282	.	0.153820	0.38959	N	0.001508	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.8438	0.78871	0.137:0.863:0.0:0.0	.	.	.	.	X	1275;1275;156;323;156	.	ENSP00000274258:E156X	E	-	1	0	C5orf42	37223690	1.000000	0.71417	0.998000	0.56505	0.790000	0.44656	6.568000	0.73987	1.425000	0.47237	0.491000	0.48974	GAA		0.353	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37187933	C	A	37187933	4	1	61	1	0	0	0	0	0	1	0	0	2307	922	32	2	5894	2	C5orf42	5	37187933	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7750	37187933	143727327	3780	11765										
WDR70	55100	broad.mit.edu	37	chr5	37703101	37703101	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcatagtcactggtacatCtattcaaagaggatgtggca	10	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37703101C>T	ENST00000265107.4	+	13	1484	c.1328C>T	c.(1327-1329)tCt>tTt	p.S443F	RNU6-484P_ENST00000384016.1_RNA|WDR70_ENST00000510699.1_3'UTR	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	443							enzyme binding (GO:0019899)	p.S443F(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACTGGTACATCTATTCAAAGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											119	110	113					5																	37703101		2203	4300	6503	37738858	SO:0001583	missense	55100			BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1328C>T	5.37:g.37703101C>T	ENSP00000265107:p.Ser443Phe		37738858	Q9H053	Missense_Mutation	SNP	ENST00000265107.4	37	CCDS34147.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150167	0.94645	.	.	ENSG00000082068	ENST00000265107	T	0.71698	-0.59	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84674	0.5524	M	0.84082	2.675	0.80722	D	1	D	0.71674	0.998	D	0.63488	0.915	D	0.83781	0.0225	10	0.40728	T	0.16	.	19.6155	0.95632	0.0:1.0:0.0:0.0	.	443	Q9NW82	WDR70_HUMAN	F	443	ENSP00000265107:S443F	ENSP00000265107:S443F	S	+	2	0	WDR70	37738858	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.036000	0.76524	2.801000	0.96364	0.650000	0.86243	TCT		0.413	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		T	37703101	C	T	37703101	3	4	61	1	0	0	0	0	1	0	0	0	17361	913	32	3	1378	3	WDR70	5	37703101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	515168	37703101	143212159	3781	11766										
WDR70	55100	broad.mit.edu	37	chr5	37727010	37727010	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggccgagttggaacccaCgggggcactctctcttccta	13	13	2	0	rs375996876		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37727010C>T	ENST00000265107.4	+	17	1896	c.1740C>T	c.(1738-1740)caC>caT	p.H580H		NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	580							enzyme binding (GO:0019899)	p.H580H(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTGGAACCCACGGGGGCACTC	0.448													C|||	1	0.000199681	0	0.0014	5008	,	,		17228	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	105	105	105		1740	-7	0.9	5		105	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR70	NM_018034.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		580/655	37727010	1,13005	2203	4300	6503	37762767	SO:0001819	synonymous_variant	55100			BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1740C>T	5.37:g.37727010C>T			37762767	Q9H053	Silent	SNP	ENST00000265107.4	37	CCDS34147.1																																																																																				0.448	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		T	37727010	C	T	37727010	2	4	61	1	0	0	0	0	0	0	0	1	17361	535	19	1		1	WDR70	5	37727010	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23909	37727010	143188250	3782	11767										
GDNF	2668	broad.mit.edu	37	chr5	37815942	37815942	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgttgtctcagctgcatcGcaagagccgctgcagtacct	10	13	1	1	rs368244196		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:37815942G>A	ENST00000326524.2	-	3	646	c.447C>T	c.(445-447)tgC>tgT	p.C149C	GDNF_ENST00000427982.1_Silent_p.C166C|GDNF_ENST00000515058.1_Silent_p.C123C|GDNF_ENST00000381826.4_Silent_p.C140C|GDNF_ENST00000344622.4_Silent_p.C123C	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	149					adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.C149C(1)		NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					CAGCTGCATCGCAAGAGCCGC	0.453													G|||	1	0.000199681	0	0	5008	,	,		17174	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						G	,,,	1,4405	2.1+/-5.4	0,1,2202	117	116	116		447,498,420,369	-4.9	0.6	5		116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GDNF	NM_000514.3,NM_001190468.1,NM_001190469.1,NM_199231.2	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	149/212,166/229,140/203,123/186	37815942	1,13005	2203	4300	6503	37851699	SO:0001819	synonymous_variant	2668				CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"Endogenous ligands"	4232	protein-coding gene	gene with protein product	"astrocyte-derived trophic factor", "glial cell line derived neurotrophic factor", "glial derived neurotrophic factor"	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.447C>T	5.37:g.37815942G>A			37851699	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Silent	SNP	ENST00000326524.2	37	CCDS3922.1																																																																																				0.453	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514		A	37815942	G	A	37815942	2	1	61	1	0	0	0	0	0	0	0	1	6342	1079	38	1		1	GDNF	5	37815942	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88932	37815942	143099318	3783	11768										
EGFLAM	133584	broad.mit.edu	37	chr5	38435318	38435318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgatgtgaagaagaactCgggtgtcctgaagcctttca	12	7	1	6	rs115665295		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:38435318C>T	ENST00000354891.3	+	16	2592	c.2246C>T	c.(2245-2247)tCg>tTg	p.S749L	EGFLAM_ENST00000397202.2_Missense_Mutation_p.S115L|EGFLAM_ENST00000322350.5_Missense_Mutation_p.S749L|EGFLAM_ENST00000336740.6_Missense_Mutation_p.S515L	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	749	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)	p.S749L(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AAGAAGAACTCGGGTGTCCTG	0.463													C|||	1	0.000199681	0	0	5008	,	,		17143	0		0.001	False		,,,				2504	0				Colon(62;485 1295 3347 17454)											1	Substitution - Missense(1)	large_intestine(1)	5						C	LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	105	104	104		2246,2246,1544	5.8	0.9	5	dbSNP_132	104	9,8591	7.7+/-29.5	0,9,4291	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	145,145,145	0,9,6494	TT,TC,CC		0.1047,0.0,0.0692	possibly-damaging,possibly-damaging,possibly-damaging	749/1018,749/1010,515/776	38435318	9,12997	2203	4300	6503	38471075	SO:0001583	missense	133584			AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2246C>T	5.37:g.38435318C>T	ENSP00000346964:p.Ser749Leu		38471075	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	8.586	0.883514	0.17467	0.0	0.001047	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	5.81	5.81	0.92471	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.058106	0.64402	D	0.000001	T	0.78104	0.4231	L	0.37897	1.145	0.80722	D	1	D;D;B	0.62365	0.989;0.991;0.376	P;P;B	0.51385	0.538;0.668;0.031	T	0.73610	-0.3928	10	0.23891	T	0.37	0.3086	20.0804	0.97772	0.0:1.0:0.0:0.0	.	515;749;749	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	L	749;749;515;115;515	ENSP00000346964:S749L;ENSP00000313084:S749L;ENSP00000337607:S515L;ENSP00000380385:S115L	ENSP00000313084:S749L	S	+	2	0	EGFLAM	38471075	1.000000	0.71417	0.908000	0.35775	0.057000	0.15508	7.173000	0.77612	2.738000	0.93877	0.655000	0.94253	TCG		0.463	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38435318	C	T	38435318	3	4	61	1	0	0	0	0	1	0	0	0	4977	893	31	1	2322	1	EGFLAM	5	38435318	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	619376	38435318	142479942	3784	11769										
LIFR	3977	broad.mit.edu	37	chr5	38481860	38481860	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtctatggatctaggaGagtctggagacactaaattc	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:38481860G>T	ENST00000263409.4	-	20	3293	c.3131C>A	c.(3130-3132)tCt>tAt	p.S1044Y	LIFR_ENST00000453190.2_Missense_Mutation_p.S1044Y	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	1044					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.S1044Y(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GGATCTAGGAGAGTCTGGAGA	0.413			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	1	Substitution - Missense(1)	large_intestine(1)	5											145	136	139					5																	38481860		2203	4300	6503	38517617	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.3131C>A	5.37:g.38481860G>T	ENSP00000263409:p.Ser1044Tyr		38517617	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331094	0.81690	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.59224	0.28;0.28	5.94	5.94	0.96194	.	0.201971	0.45606	D	0.000343	T	0.75295	0.3830	L	0.57536	1.79	0.52501	D	0.999952	D	0.89917	1.0	D	0.85130	0.997	T	0.75439	-0.3317	10	0.87932	D	0	-13.4226	20.3552	0.98837	0.0:0.0:1.0:0.0	.	1044	P42702	LIFR_HUMAN	Y	1044	ENSP00000263409:S1044Y;ENSP00000398368:S1044Y	ENSP00000263409:S1044Y	S	-	2	0	LIFR	38517617	1.000000	0.71417	0.961000	0.40146	0.989000	0.77384	6.473000	0.73572	2.812000	0.96745	0.557000	0.71058	TCT		0.413	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38481860	G	T	38481860	3	4	61	1	0	0	0	0	1	0	0	0	8803	942	33	2	166	2	LIFR	5	38481860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46542	38481860	142433400	3785	11770										
RICTOR	253260	broad.mit.edu	37	chr5	38949902	38949902	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgctggagatgccaaagCttcagagtgagataaggatg	13	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:38949902C>A	ENST00000357387.3	-	31	4078	c.4048G>T	c.(4048-4050)Gct>Tct	p.A1350S	RICTOR_ENST00000296782.5_Missense_Mutation_p.A1350S	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.A1350S(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GATGCCAAAGCTTCAGAGTGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											177	168	171					5																	38949902		2203	4299	6502	38985659	SO:0001583	missense	253260				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.4048G>T	5.37:g.38949902C>A	ENSP00000349959:p.Ala1350Ser		38985659		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955113	0.73902	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.51817	0.89;0.69	6.03	6.03	0.97812	.	0.091360	0.85682	D	0.000000	T	0.65729	0.2719	L	0.45581	1.43	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.64875	-0.6304	10	0.87932	D	0	-15.6829	20.5753	0.99366	0.0:1.0:0.0:0.0	.	1350;1350	Q6R327;Q6R327-3	RICTR_HUMAN;.	S	1350	ENSP00000349959:A1350S;ENSP00000296782:A1350S	ENSP00000296782:A1350S	A	-	1	0	RICTOR	38985659	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.456000	0.80751	2.868000	0.98415	0.557000	0.71058	GCT		0.393	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38949902	C	A	38949902	3	1	61	1	0	0	0	0	1	0	0	0	13395	797	28	2	1110	2	RICTOR	5	38949902	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	468042	38949902	141965358	3786	11771										
RICTOR	253260	broad.mit.edu	37	chr5	38950726	38950726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcctttatgggtccagatCggtcataaaatgttggctct	9	8	2	1	rs370517295		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:38950726C>T	ENST00000357387.3	-	31	3254	c.3224G>A	c.(3223-3225)cGa>cAa	p.R1075Q	RICTOR_ENST00000296782.5_Missense_Mutation_p.R1075Q	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.R1075Q(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GGGTCCAGATCGGTCATAAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG	0,4406		0,0,2203	120	126	124		3224	5.9	1	5		124	1,8599	1.2+/-3.3	0,1,4299	no	missense	RICTOR	NM_152756.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1075/1709	38950726	1,13005	2203	4300	6503	38986483	SO:0001583	missense	253260				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3224G>A	5.37:g.38950726C>T	ENSP00000349959:p.Arg1075Gln		38986483		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.137825	0.37728	0.0	1.16E-4	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.46819	0.88;0.86	5.86	5.86	0.93980	.	0.116079	0.56097	D	0.000030	T	0.34366	0.0895	N	0.19112	0.55	0.38474	D	0.947547	B;B	0.20780	0.028;0.048	B;B	0.10450	0.005;0.005	T	0.22068	-1.0227	10	0.87932	D	0	-9.8145	12.9949	0.58640	0.0:0.9261:0.0:0.0739	.	1075;1075	Q6R327;Q6R327-3	RICTR_HUMAN;.	Q	1075	ENSP00000349959:R1075Q;ENSP00000296782:R1075Q	ENSP00000296782:R1075Q	R	-	2	0	RICTOR	38986483	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.117000	0.50407	2.937000	0.99478	0.650000	0.86243	CGA		0.363	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38950726	C	T	38950726	3	4	61	1	0	0	0	0	1	0	0	0	13395	884	31	1	1934	1	RICTOR	5	38950726	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	824	38950726	141964534	3787	11772										
RICTOR	253260	broad.mit.edu	37	chr5	38982005	38982005	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcgcacatactgtcgagtCtttggatgattaagaaggtg	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:38982005C>A	ENST00000357387.3	-	8	747	c.717G>T	c.(715-717)aaG>aaT	p.K239N	RICTOR_ENST00000296782.5_Missense_Mutation_p.K239N	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.K239N(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					ACTGTCGAGTCTTTGGATGAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	5											120	125	124					5																	38982005		2203	4300	6503	39017762	SO:0001583	missense	253260				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.717G>T	5.37:g.38982005C>A	ENSP00000349959:p.Lys239Asn		39017762		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.552981	0.27739	.	.	ENSG00000164327	ENST00000357387;ENST00000296782;ENST00000514735	T;T;T	0.64438	-0.1;-0.1;-0.1	4.98	4.11	0.48088	Armadillo-like helical (1);Armadillo-type fold (1);	0.348627	0.34580	N	0.003856	T	0.45438	0.1342	N	0.22421	0.69	0.39725	D	0.971521	B;B;B;B	0.28636	0.131;0.085;0.011;0.218	B;B;B;B	0.25140	0.04;0.037;0.02;0.058	T	0.48514	-0.9029	10	0.87932	D	0	-8.5323	8.9629	0.35858	0.0:0.7722:0.1485:0.0793	.	239;239;239;239	Q8N6M7;E7ETT0;Q6R327;Q6R327-3	.;.;RICTR_HUMAN;.	N	239;239;223	ENSP00000349959:K239N;ENSP00000296782:K239N;ENSP00000423162:K223N	ENSP00000296782:K239N	K	-	3	2	RICTOR	39017762	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.733000	0.26087	1.083000	0.41159	0.467000	0.42956	AAG		0.313	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38982005	C	A	38982005	3	1	61	1	0	0	0	0	1	0	0	0	13395	912	32	2	4533	2	RICTOR	5	38982005	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31279	38982005	141933255	3788	11773										
DAB2	1601	broad.mit.edu	37	chr5	39376885	39376885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtctgctctcccttccgCgcgggcacagcaggtggctg	14	14	2	0	rs142209579	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:39376885C>T	ENST00000320816.6	-	12	2471	c.2004G>A	c.(2002-2004)gcG>gcA	p.A668A	DAB2_ENST00000545653.1_Silent_p.A647A|DAB2_ENST00000509337.1_Silent_p.A647A|DAB2_ENST00000339788.6_Silent_p.A450A	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	668	Required for interaction with GRB2 and CSK. {ECO:0000250}.|Required for interaction with MYO6. {ECO:0000250}.|Sufficient for interaction with GRB2. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)	p.A668A(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			CTCCCTTCCGCGCGGGCACAG	0.498											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0015	0	5008	,	,		19745	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		1,4405	2.1+/-5.4	0,1,2202	52	53	53		2004	-10.2	0	5	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	DAB2	NM_001343.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		668/771	39376885	1,13005	2203	4300	6503	39412642	SO:0001819	synonymous_variant	1601			U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.2004G>A	5.37:g.39376885C>T		885	39412642	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																				0.498	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		T	39376885	C	T	39376885	2	4	61	1	0	0	0	0	0	0	0	1	4224	755	27	1		1	DAB2	5	39376885	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	394880	39376885	141538375	3789	11774										
DAB2	1601	broad.mit.edu	37	chr5	39383131	39383131	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagatttgagagaatcaaaCgaagaaggtgtcgattggtc	14	4	1	4	rs200633845		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:39383131C>T	ENST00000320816.6	-	10	1397	c.930G>A	c.(928-930)tcG>tcA	p.S310S	DAB2_ENST00000545653.1_Silent_p.S289S|DAB2_ENST00000509337.1_Silent_p.S289S|DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000339788.6_Intron	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	310	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)	p.S310S(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			GAGAATCAAACGAAGAAGGTG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	5											123	128	126					5																	39383131		2203	4300	6503	39418888	SO:0001819	synonymous_variant	1601			U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.930G>A	5.37:g.39383131C>T			39418888	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																				0.458	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		T	39383131	C	T	39383131	2	4	61	1	0	0	0	0	0	0	0	1	4224	523	19	1		1	DAB2	5	39383131	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6246	39383131	141532129	3790	11775										
DAB2	1601	broad.mit.edu	37	chr5	39383331	39383331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagaattctgattggtgtCgatttcagagtttagatcca	9	5	2	4	rs374921039		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:39383331C>T	ENST00000320816.6	-	10	1197	c.730G>A	c.(730-732)Gac>Aac	p.D244N	DAB2_ENST00000545653.1_Missense_Mutation_p.D223N|DAB2_ENST00000509337.1_Missense_Mutation_p.D223N|DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000339788.6_Intron	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	244	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)	p.D244N(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGATTGGTGTCGATTTCAGAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	121	134	130		730	4.9	1	5		130	0,8600		0,0,4300	no	missense	DAB2	NM_001343.3	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	244/771	39383331	1,13005	2203	4300	6503	39419088	SO:0001583	missense	1601			U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.730G>A	5.37:g.39383331C>T	ENSP00000313391:p.Asp244Asn		39419088	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070449	0.55539	2.27E-4	0.0	ENSG00000153071	ENST00000320816;ENST00000545653;ENST00000509337	T;T;T	0.45668	1.12;0.89;0.89	5.87	4.95	0.65309	.	0.152506	0.56097	N	0.000026	T	0.42040	0.1185	M	0.61703	1.905	0.54753	D	0.999981	B;B	0.26845	0.028;0.161	B;B	0.25140	0.007;0.058	T	0.32719	-0.9896	10	0.45353	T	0.12	-4.4797	13.7862	0.63110	0.0:0.9197:0.0:0.0803	.	244;223	P98082;P98082-3	DAB2_HUMAN;.	N	244;223;223	ENSP00000313391:D244N;ENSP00000439919:D223N;ENSP00000426245:D223N	ENSP00000313391:D244N	D	-	1	0	DAB2	39419088	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.694000	0.68272	1.491000	0.48482	0.655000	0.94253	GAC		0.393	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		T	39383331	C	T	39383331	3	4	61	1	0	0	0	0	1	0	0	0	4224	884	31	1	1602	1	DAB2	5	39383331	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200	39383331	141531929	3791	11776										
PRKAA1	5562	broad.mit.edu	37	chr5	40765109	40765109	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgggcttgtcgccaaataGaaatctttggcttcattcat	10	8	3	1	rs116338283	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:40765109G>T	ENST00000397128.2	-	7	1061	c.1053C>A	c.(1051-1053)ttC>ttA	p.F351L	PRKAA1_ENST00000354209.3_Missense_Mutation_p.F366L	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	351	AIS.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)	p.F366L(1)		breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TCGCCAAATAGAAATCTTTGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	93	93					5																	40765109		1946	4135	6081	40800866	SO:0001583	missense	5562				CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"AMPK, alpha, 1"	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.1053C>A	5.37:g.40765109G>T	ENSP00000380317:p.Phe351Leu		40800866	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	37	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818970	0.71028	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.08370	3.1;3.1	6.16	2.99	0.34606	.	0.087173	0.85682	D	0.000000	T	0.20414	0.0491	M	0.75884	2.315	0.80722	D	1	D;D	0.76494	0.989;0.999	D;D	0.80764	0.977;0.994	T	0.15723	-1.0427	10	0.18710	T	0.47	-13.6275	5.1907	0.15209	0.2688:0.1489:0.5823:0.0	.	351;366	Q13131;Q13131-2	AAPK1_HUMAN;.	L	351;366	ENSP00000380317:F351L;ENSP00000346148:F366L	ENSP00000346148:F366L	F	-	3	2	AC008810.1	40800866	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.124000	0.42006	0.291000	0.22468	0.650000	0.86243	TTC		0.433	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		T	40765109	G	T	40765109	3	4	61	1	0	0	0	0	1	0	0	0	12527	933	33	2	638	2	PRKAA1	5	40765109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1381778	40765109	140150151	3792	11777										
CARD6	84674	broad.mit.edu	37	chr5	40852902	40852902	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaatctttcttcatcaaGatttgcctcttttggtgctt	5	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:40852902G>T	ENST00000254691.5	+	3	1667	c.1468G>T	c.(1468-1470)Gat>Tat	p.D490Y	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	490					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)			p.D490Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TCTTCATCAAGATTTGCCTCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											71	70	71					5																	40852902		2203	4300	6503	40888659	SO:0001583	missense	84674			AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1468G>T	5.37:g.40852902G>T	ENSP00000254691:p.Asp490Tyr		40888659	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068420	0.36470	.	.	ENSG00000132357	ENST00000254691	T	0.16196	2.36	5.2	5.2	0.72013	.	0.000000	0.56097	D	0.000026	T	0.40247	0.1109	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.19910	-1.0291	10	0.66056	D	0.02	-21.6541	9.6112	0.39663	0.0923:0.0:0.9077:0.0	.	490	Q9BX69	CARD6_HUMAN	Y	490	ENSP00000254691:D490Y	ENSP00000254691:D490Y	D	+	1	0	CARD6	40888659	0.981000	0.34729	0.045000	0.18777	0.065000	0.16274	3.222000	0.51223	2.709000	0.92574	0.650000	0.86243	GAT		0.428	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			T	40852902	G	T	40852902	3	4	61	1	0	0	0	0	1	0	0	0	2656	942	33	2	1478	2	CARD6	5	40852902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87793	40852902	140062358	3793	11778										
C7	730	broad.mit.edu	37	chr5	40962230	40962230	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtctttggttccaacaGaattctgtccatcacctcct	5	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:40962230G>T	ENST00000313164.9	+	13	2064	c.1705G>T	c.(1705-1707)Gaa>Taa	p.E569*		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	569	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.E569*(1)					Ovarian(839;0.0112)				GGTTCCAACAGAATTCTGTCC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											109	100	103					5																	40962230		1851	4090	5941	40997987	SO:0001587	stop_gained	730			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1705G>T	5.37:g.40962230G>T	ENSP00000322061:p.Glu569*		40997987	Q6P3T5|Q92489	Nonsense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	G	39	7.576668	0.98368	.	.	ENSG00000112936	ENST00000313164;ENST00000440677	.	.	.	5.96	1.09	0.20402	.	0.509194	0.22132	N	0.064177	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-6.3065	10.0788	0.42377	0.2275:0.0932:0.6793:0.0	.	.	.	.	X	569;409	.	ENSP00000322061:E569X	E	+	1	0	C7	40997987	1.000000	0.71417	0.223000	0.23860	0.696000	0.40369	1.809000	0.38922	-0.060000	0.13132	-2.151000	0.00333	GAA		0.333	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			T	40962230	G	T	40962230	4	4	61	1	0	0	0	0	0	1	0	0	2381	943	33	2	1755	2	C7	5	40962230	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109328	40962230	139953030	3794	11779										
C7	730	broad.mit.edu	37	chr5	40981528	40981528	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtctgccgagaagcatcGgagtgcgaggaagaagggtt	17	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:40981528G>A	ENST00000313164.9	+	18	2744	c.2385G>A	c.(2383-2385)tcG>tcA	p.S795S		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	795	Factor I module (FIM) 2.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.S795S(1)					Ovarian(839;0.0112)				GAGAAGCATCGGAGTGCGAGG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	5											62	63	63					5																	40981528		2104	4213	6317	41017285	SO:0001819	synonymous_variant	730			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.2385G>A	5.37:g.40981528G>A			41017285	Q6P3T5|Q92489	Silent	SNP	ENST00000313164.9	37	CCDS47201.1																																																																																				0.522	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			A	40981528	G	A	40981528	2	1	61	1	0	0	0	0	0	0	0	1	2381	1103	39	1		1	C7	5	40981528	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19298	40981528	139933732	3795	11780										
HEATR7B2	133558	broad.mit.edu	37	chr5	41012804	41012804	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttcctctaggaacatcaGaatttcttcatttgggatga	7	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:41012804G>T	ENST00000399564.4	-	30	3466	c.3016C>A	c.(3016-3018)Ctg>Atg	p.L1006M	MROH2B_ENST00000506092.2_Missense_Mutation_p.L561M	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1006								p.L1006M(1)									AGGAACATCAGAATTTCTTCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	5											122	118	119					5																	41012804		1893	4130	6023	41048561	SO:0001583	missense	133558				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.3016C>A	5.37:g.41012804G>T	ENSP00000382476:p.Leu1006Met		41048561	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	6.698	0.497436	0.12762	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.06294	3.32;3.32	6.04	3.15	0.36227	Armadillo-like helical (1);Armadillo-type fold (1);	1.067900	0.07296	N	0.873351	T	0.05456	0.0144	N	0.25647	0.755	0.09310	N	1	P	0.41569	0.755	B	0.35470	0.203	T	0.43605	-0.9381	10	0.45353	T	0.12	.	8.8902	0.35429	0.0:0.1462:0.5511:0.3028	.	1006	Q7Z745	HTRB2_HUMAN	M	561;711;1006	ENSP00000441504:L561M;ENSP00000382476:L1006M	ENSP00000296803:L711M	L	-	1	2	HEATR7B2	41048561	0.001000	0.12720	0.006000	0.13384	0.106000	0.19336	1.005000	0.29834	0.364000	0.24374	0.561000	0.74099	CTG		0.438	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41012804	G	T	41012804	3	4	61	1	0	0	0	0	1	0	0	0	7056	933	33	2	1793	2	HEATR7B2	5	41012804	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31276	41012804	139902456	3796	11781										
C6	729	broad.mit.edu	37	chr5	41142979	41142979	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcttcctgtttgcacatCttatagttcccacttcacag	4	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:41142979C>A	ENST00000263413.3	-	18	3017	c.2753G>T	c.(2752-2754)aGa>aTa	p.R918I	C6_ENST00000337836.5_Missense_Mutation_p.R918I	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	918	C5b-binding domain.|Factor I module (FIM) 2.|Kazal-like 2. {ECO:0000255|PROSITE- ProRule:PRU00798}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.R918I(1)		central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GTTTGCACATCTTATAGTTCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											242	200	214					5																	41142979		2203	4300	6503	41178736	SO:0001583	missense	729			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2753G>T	5.37:g.41142979C>A	ENSP00000263413:p.Arg918Ile		41178736		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	7.800	0.713448	0.15306	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.63744	-0.06;-0.06	5.71	-1.74	0.08056	Factor I / membrane attack complex (1);	0.445957	0.26556	N	0.023709	T	0.54013	0.1832	L	0.61387	1.9	0.19945	N	0.999945	B	0.20550	0.046	B	0.15870	0.014	T	0.49753	-0.8906	10	0.45353	T	0.12	-6.2965	12.1572	0.54083	0.0:0.2074:0.0:0.7926	.	918	P13671	CO6_HUMAN	I	918	ENSP00000338861:R918I;ENSP00000263413:R918I	ENSP00000263413:R918I	R	-	2	0	C6	41178736	0.053000	0.20554	0.005000	0.12908	0.178000	0.23041	-0.006000	0.12833	-0.434000	0.07275	-0.142000	0.14014	AGA		0.443	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41142979	C	A	41142979	3	1	61	1	0	0	0	0	1	0	0	0	2321	913	32	2	55	2	C6	5	41142979	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130175	41142979	139772281	3797	11782										
C6	729	broad.mit.edu	37	chr5	41159242	41159242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcttctccccctcacagcGtttccctcctcgttgggggg	10	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:41159242G>A	ENST00000263413.3	-	12	2062	c.1798C>T	c.(1798-1800)Cgc>Tgc	p.R600C	C6_ENST00000475349.1_5'Flank|C6_ENST00000337836.5_Missense_Mutation_p.R600C	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	600	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.R600C(1)		central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CCCTCACAGCGTTTCCCTCCT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	5											127	135	132					5																	41159242		2203	4300	6503	41194999	SO:0001583	missense	729			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1798C>T	5.37:g.41159242G>A	ENSP00000263413:p.Arg600Cys		41194999		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250039	0.39797	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.18016	2.24;2.24	5.64	-2.05	0.07321	.	0.382697	0.32578	N	0.005905	T	0.14313	0.0346	L	0.29908	0.895	0.09310	N	0.999995	P	0.47962	0.903	P	0.51833	0.681	T	0.11641	-1.0579	10	0.59425	D	0.04	0.1074	4.1569	0.10265	0.1118:0.2862:0.4055:0.1965	.	600	P13671	CO6_HUMAN	C	600	ENSP00000338861:R600C;ENSP00000263413:R600C	ENSP00000263413:R600C	R	-	1	0	C6	41194999	0.001000	0.12720	0.000000	0.03702	0.088000	0.18126	0.684000	0.25364	-0.301000	0.08882	0.650000	0.86243	CGC		0.488	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41159242	G	A	41159242	3	1	61	1	0	0	0	0	1	0	0	0	2321	1145	40	1	1034	1	C6	5	41159242	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16263	41159242	139756018	3798	11783										
OXCT1	5019	broad.mit.edu	37	chr5	41850252	41850252	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcaggaactccagccccGcctgcacggatcctctctgc	9	17	1	0	rs372032720	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:41850252G>A	ENST00000196371.5	-	5	604	c.444C>T	c.(442-444)ggC>ggT	p.G148G		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	148					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)	p.G148G(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	CTCCAGCCCCGCCTGCACGGA	0.507													g|||	2	0.000399361	0.0015	0	5008	,	,		18213	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						A		2,4404	4.2+/-10.8	0,2,2201	87	76	80		444	-10.2	0.5	5		80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OXCT1	NM_000436.3		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		148/521	41850252	3,13003	2203	4300	6503	41886009	SO:0001819	synonymous_variant	5019			U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"3-oxoacid CoA transferase"	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.444C>T	5.37:g.41850252G>A			41886009	B2R5V2|B7Z528	Silent	SNP	ENST00000196371.5	37	CCDS3937.1																																																																																				0.507	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		A	41850252	G	A	41850252	2	1	61	1	0	0	0	0	0	0	0	1	11360	1074	38	1		1	OXCT1	5	41850252	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	691010	41850252	139065008	3799	11784										
FBXO4	26272	broad.mit.edu	37	chr5	41927208	41927208	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggaatgaaactgtaagaGatccaattctgtggagatac	10	5	1	3	rs374881418		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:41927208G>T	ENST00000281623.3	+	2	339	c.283G>T	c.(283-285)Gat>Tat	p.D95Y	FBXO4_ENST00000296812.2_Missense_Mutation_p.D95Y|FBXO4_ENST00000509134.1_Missense_Mutation_p.D95Y	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	95	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.			D -> N (in Ref. 1; AAF04468). {ECO:0000305}.	positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)	p.D95Y(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				AACTGTAAGAGATCCAATTCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											181	179	180					5																	41927208		2203	4300	6503	41962965	SO:0001583	missense	26272			AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"F-boxes /  "other""	13583	protein-coding gene	gene with protein product		609090	"F-box only protein 4"			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.283G>T	5.37:g.41927208G>T	ENSP00000281623:p.Asp95Tyr		41962965	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	37	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792445	0.90453	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.61980	0.06;0.06;0.06	5.62	5.62	0.85841	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.83361	0.0002	10	0.87932	D	0	-23.3665	19.6604	0.95864	0.0:0.0:1.0:0.0	.	95;95;95	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	Y	95	ENSP00000296812:D95Y;ENSP00000281623:D95Y;ENSP00000421749:D95Y	ENSP00000281623:D95Y	D	+	1	0	FBXO4	41962965	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.114000	0.94329	2.648000	0.89879	0.655000	0.94253	GAT		0.363	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			T	41927208	G	T	41927208	3	4	61	1	0	0	0	0	1	0	0	0	5767	942	33	2	289	2	FBXO4	5	41927208	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76956	41927208	138988052	3800	11785										
SEPP1	6414	broad.mit.edu	37	chr5	42807160	42807160	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgattaacaacaatataaGaaatattagaatatccttct	4	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:42807160G>T	ENST00000514985.1	-	3	510	c.254C>A	c.(253-255)tCt>tAt	p.S85Y	CTD-2325A15.5_ENST00000606056.1_RNA|SEPP1_ENST00000509276.1_Intron|SEPP1_ENST00000511224.1_Missense_Mutation_p.S85Y|SEPP1_ENST00000507920.1_Intron|SEPP1_ENST00000506577.1_Missense_Mutation_p.S85Y	NM_005410.2	NP_005401.3	P49908	SEPP1_HUMAN	selenoprotein P, plasma, 1	85					brain development (GO:0007420)|growth (GO:0040007)|locomotory behavior (GO:0007626)|post-embryonic development (GO:0009791)|response to oxidative stress (GO:0006979)|selenium compound metabolic process (GO:0001887)|sexual reproduction (GO:0019953)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	selenium binding (GO:0008430)	p.S85Y(1)		kidney(10)|large_intestine(1)|lung(4)	15						AACAATATAAGAAATATTAGA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	73	73					5																	42807160		1788	4055	5843	42842917	SO:0001583	missense	6414			BC040075	CCDS43311.1	5q31	2012-03-01				ENSG00000250722			10751	protein-coding gene	gene with protein product		601484				8421687	Standard	NM_001085486		Approved	SeP	uc011cpu.2	P49908		ENST00000514985.1:c.254C>A	5.37:g.42807160G>T	ENSP00000420939:p.Ser85Tyr		42842917	Q6PD59|Q6PI43|Q6PI87|Q6PJF9	Missense_Mutation	SNP	ENST00000514985.1	37	CCDS43311.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.722612	0.68959	.	.	ENSG00000250722	ENST00000514985;ENST00000511224;ENST00000506577;ENST00000514218;ENST00000510965	T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31	5.49	5.49	0.81192	.	0.000000	0.43919	U	0.000511	T	0.56140	0.1965	M	0.63428	1.95	0.80722	D	1	.	.	.	.	.	.	T	0.56768	-0.7924	8	0.66056	D	0.02	.	19.3746	0.94503	0.0:0.0:1.0:0.0	.	.	.	.	Y	85	ENSP00000420939:S85Y;ENSP00000427671:S85Y;ENSP00000425915:S85Y;ENSP00000421626:S85Y;ENSP00000427414:S85Y	ENSP00000425915:S85Y	S	-	2	0	SEPP1	42842917	1.000000	0.71417	0.793000	0.32043	0.645000	0.38454	6.247000	0.72411	2.582000	0.87167	0.650000	0.86243	TCT		0.279	SEPP1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000367483.1	NM_005410		T	42807160	G	T	42807160	3	4	61	1	0	0	0	0	1	0	0	0	14094	942	33	2	903	2	SEPP1	5	42807160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	879952	42807160	138108100	3801	11786										
MGC42105	167359	broad.mit.edu	37	chr5	43277227	43277227	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagaggctactatcccgaGaaatctccagcatggaaaag	9	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43277227G>T	ENST00000512796.1	+	3	1860	c.361G>T	c.(361-363)Gaa>Taa	p.E121*	NIM1_ENST00000326035.2_Nonsense_Mutation_p.E121*			Q8IY84	NIM1_HUMAN		121	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.E121*(1)									ACTATCCCGAGAAATCTCCAG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											99	100	100					5																	43277227		2203	4300	6503	43312984	SO:0001587	stop_gained	167359																														ENST00000512796.1:c.361G>T	5.37:g.43277227G>T	ENSP00000420849:p.Glu121*		43312984	B3KVM1	Nonsense_Mutation	SNP	ENST00000512796.1	37	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	G	49	15.554882	0.99837	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.6629	0.95879	0.0:0.0:1.0:0.0	.	.	.	.	X	121	.	ENSP00000313572:E121X	E	+	1	0	AC114947.1	43312984	1.000000	0.71417	0.925000	0.36789	0.940000	0.58332	9.869000	0.99810	2.654000	0.90174	0.555000	0.69702	GAA		0.473	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			T	43277227	G	T	43277227	4	4	61	1	0	0	0	0	0	1	0	0	9582	943	33	2	367	2	MGC42105	5	43277227	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	470067	43277227	137638033	3802	11787										
C5orf28	64417	broad.mit.edu	37	chr5	43454051	43454051	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgcagtaaagcatgggtCttttcagtctcggatgccat	11	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43454051C>A	ENST00000500337.2	-	4	352	c.21G>T	c.(19-21)aaG>aaT	p.K7N	C5orf28_ENST00000537319.1_Intron|C5orf28_ENST00000397080.3_Missense_Mutation_p.K7N|C5orf28_ENST00000511525.1_Intron|C5orf28_ENST00000512085.1_Missense_Mutation_p.K7N|C5orf28_ENST00000510130.1_Intron			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	7						integral component of membrane (GO:0016021)		p.K7N(1)		breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					AAGCATGGGTCTTTTCAGTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											84	77	80					5																	43454051		2203	4300	6503	43489808	SO:0001583	missense	64417			AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.21G>T	5.37:g.43454051C>A	ENSP00000426067:p.Lys7Asn		43489808	B2RDA6|Q9H6Z2	Missense_Mutation	SNP	ENST00000500337.2	37	CCDS3945.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371499	0.61624	.	.	ENSG00000151881	ENST00000500337;ENST00000397080;ENST00000512085;ENST00000506860	.	.	.	5.4	3.61	0.41365	.	0.041772	0.85682	D	0.000000	T	0.74007	0.3660	M	0.73962	2.25	0.80722	D	1	D	0.63046	0.992	P	0.59357	0.856	T	0.76260	-0.3024	9	0.66056	D	0.02	-10.4898	12.4611	0.55733	0.0:0.8622:0.0:0.1378	.	7	Q0VDI3	CE028_HUMAN	N	7	.	ENSP00000380270:K7N	K	-	3	2	C5orf28	43489808	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	2.592000	0.46171	0.763000	0.33175	-0.291000	0.09656	AAG		0.423	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1	NM_022483		A	43454051	C	A	43454051	3	1	61	1	0	0	0	0	1	0	0	0	2295	912	32	2	634	2	C5orf28	5	43454051	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	176824	43454051	137461209	3803	11788										
C5orf34	375444	broad.mit.edu	37	chr5	43505892	43505892	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgagtgacagggccctgGgaagaacagaaaccactttt	12	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43505892G>T	ENST00000306862.2	-	4	1265	c.890C>A	c.(889-891)cCc>cAc	p.P297H	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	297								p.P297H(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					CAGGGCCCTGGGAAGAACAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											92	91	91					5																	43505892		2203	4300	6503	43541649	SO:0001583	missense	375444			AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.890C>A	5.37:g.43505892G>T	ENSP00000303490:p.Pro297His		43541649		Missense_Mutation	SNP	ENST00000306862.2	37	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231073	0.58777	.	.	ENSG00000172244	ENST00000306862;ENST00000509489	T	0.81247	-1.47	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.89636	0.6772	M	0.78637	2.42	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	D	0.91041	0.4871	10	0.87932	D	0	-5.9826	16.5572	0.84488	0.0:0.0:1.0:0.0	.	297	Q96MH7	CE034_HUMAN	H	297;183	ENSP00000303490:P297H	ENSP00000303490:P297H	P	-	2	0	C5orf34	43541649	1.000000	0.71417	1.000000	0.80357	0.447000	0.32167	5.152000	0.64882	2.351000	0.79841	0.591000	0.81541	CCC		0.403	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566		T	43505892	G	T	43505892	3	4	61	1	0	0	0	0	1	0	0	0	2299	1232	43	2	1066	2	C5orf34	5	43505892	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51841	43505892	137409368	3804	11789										
PAIP1	10605	broad.mit.edu	37	chr5	43529971	43529971	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagtaattcttggtatttCtcttggtaatctgtaagaca	7	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43529971C>A	ENST00000306846.3	-	10	1495	c.1263G>T	c.(1261-1263)gaG>gaT	p.E421D	PAIP1_ENST00000436644.2_Missense_Mutation_p.E342D|PAIP1_ENST00000338972.4_Missense_Mutation_p.E309D|PAIP1_ENST00000514514.1_Intron	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	421					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.E421D(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					CTTGGTATTTCTCTTGGTAAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	61	60					5																	43529971		2203	4300	6503	43565728	SO:0001583	missense	10605			AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.1263G>T	5.37:g.43529971C>A	ENSP00000302768:p.Glu421Asp		43565728	A6NKV8|O60455|Q96B61|Q9BS63	Missense_Mutation	SNP	ENST00000306846.3	37	CCDS3947.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.529057	0.27387	.	.	ENSG00000172239	ENST00000306846;ENST00000436644;ENST00000514816;ENST00000338972	T;T;T	0.35789	1.29;1.35;1.38	4.93	2.12	0.27331	.	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	L	0.50333	1.59	0.80722	D	1	B;B	0.32467	0.372;0.193	B;B	0.27796	0.064;0.083	T	0.07214	-1.0784	10	0.37606	T	0.19	-10.1287	9.6122	0.39670	0.0:0.6427:0.0:0.3573	.	421;342	Q9H074;Q9H074-2	PAIP1_HUMAN;.	D	421;342;22;309	ENSP00000302768:E421D;ENSP00000387729:E342D;ENSP00000339622:E309D	ENSP00000302768:E421D	E	-	3	2	PAIP1	43565728	0.997000	0.39634	1.000000	0.80357	0.923000	0.55619	0.379000	0.20585	0.756000	0.33013	0.484000	0.47621	GAG		0.323	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214024.1	NM_006451		A	43529971	C	A	43529971	3	1	61	1	0	0	0	0	1	0	0	0	11427	912	32	2	184	2	PAIP1	5	43529971	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24079	43529971	137385289	3805	11790										
PAIP1	10605	broad.mit.edu	37	chr5	43543182	43543182	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacaggtaattacacaggcGagctcccatataagagaaat	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43543182G>A	ENST00000306846.3	-	4	890	c.658C>T	c.(658-660)Cgc>Tgc	p.R220C	PAIP1_ENST00000436644.2_Missense_Mutation_p.R141C|PAIP1_ENST00000338972.4_Missense_Mutation_p.R108C|PAIP1_ENST00000514514.1_Missense_Mutation_p.R141C	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	220	MIF4G.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.R220S(1)|p.R220C(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					TTACACAGGCGAGCTCCCATA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	5											74	77	76					5																	43543182		2203	4300	6503	43578939	SO:0001583	missense	10605			AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.658C>T	5.37:g.43543182G>A	ENSP00000302768:p.Arg220Cys		43578939	A6NKV8|O60455|Q96B61|Q9BS63	Missense_Mutation	SNP	ENST00000306846.3	37	CCDS3947.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971728	0.74246	.	.	ENSG00000172239	ENST00000306846;ENST00000436644;ENST00000338972;ENST00000514514;ENST00000511321;ENST00000508537;ENST00000504075	T;T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73;1.73	5.34	5.34	0.76211	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.52451	0.1735	M	0.78637	2.42	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.56456	-0.7976	10	0.87932	D	0	-6.2871	14.5863	0.68328	0.0:0.0:0.7863:0.2137	.	141;220;141	D6REB4;Q9H074;Q9H074-2	.;PAIP1_HUMAN;.	C	220;141;108;141;108;108;4	ENSP00000302768:R220C;ENSP00000387729:R141C;ENSP00000339622:R108C;ENSP00000425084:R141C;ENSP00000425675:R108C;ENSP00000425736:R108C	ENSP00000302768:R220C	R	-	1	0	PAIP1	43578939	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.280000	0.51677	2.494000	0.84150	0.585000	0.79938	CGC		0.363	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214024.1	NM_006451		A	43543182	G	A	43543182	3	1	61	1	0	0	0	0	1	0	0	0	11427	1058	37	1	813	1	PAIP1	5	43543182	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13211	43543182	137372078	3806	11791										
PAIP1	10605	broad.mit.edu	37	chr5	43555938	43555938	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggtgtacttactgtgtaActggaagaataacctgaagg	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43555938A>C	ENST00000306846.3	-	2	661	c.429T>G	c.(427-429)agT>agG	p.S143R	PAIP1_ENST00000436644.2_Missense_Mutation_p.S64R|PAIP1_ENST00000338972.4_Missense_Mutation_p.S31R|PAIP1_ENST00000514514.1_Missense_Mutation_p.S64R	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	143	PABPC1-interacting motif-2 (PAM2).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.S143R(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					TTACTGTGTAACTGGAAGAAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											116	126	123					5																	43555938		2203	4300	6503	43591695	SO:0001583	missense	10605			AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.429T>G	5.37:g.43555938A>C	ENSP00000302768:p.Ser143Arg		43591695	A6NKV8|O60455|Q96B61|Q9BS63	Missense_Mutation	SNP	ENST00000306846.3	37	CCDS3947.1	.	.	.	.	.	.	.	.	.	.	A	5.494	0.276214	0.10403	.	.	ENSG00000172239	ENST00000306846;ENST00000436644;ENST00000338972;ENST00000514514;ENST00000511321;ENST00000508537;ENST00000515338	T;T;T;T;T;T	0.32753	1.46;1.44;1.53;1.44;1.52;1.56	4.9	3.73	0.42828	.	0.562024	0.18237	N	0.147378	T	0.12518	0.0304	N	0.08118	0	0.19775	N	0.999954	B;B;B	0.16166	0.009;0.016;0.016	B;B;B	0.13407	0.007;0.005;0.009	T	0.26710	-1.0095	10	0.16420	T	0.52	-4.9207	3.9735	0.09464	0.6644:0.0:0.18:0.1555	.	64;143;64	D6REB4;Q9H074;Q9H074-2	.;PAIP1_HUMAN;.	R	143;64;31;64;31;31;31	ENSP00000302768:S143R;ENSP00000387729:S64R;ENSP00000339622:S31R;ENSP00000425084:S64R;ENSP00000425675:S31R;ENSP00000425736:S31R	ENSP00000302768:S143R	S	-	3	2	PAIP1	43591695	0.997000	0.39634	1.000000	0.80357	0.572000	0.35998	0.463000	0.21972	0.728000	0.32382	0.459000	0.35465	AGT		0.403	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214024.1	NM_006451		C	43555938	A	C	43555938	3	2	61	1	0	0	0	0	1	0	0	0	11427	40	2	4	1050	4	PAIP1	5	43555938	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12756	43555938	137359322	3807	11792										
NNT	23530	broad.mit.edu	37	chr5	43613098	43613098	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtctcctgctggtgttcaGaacttggtcaagcagggttt	12	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43613098G>T	ENST00000264663.5	+	3	461	c.240G>T	c.(238-240)caG>caT	p.Q80H	NNT_ENST00000512996.2_5'UTR|NNT_ENST00000344920.4_Missense_Mutation_p.Q80H	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	80					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.Q80H(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CTGGTGTTCAGAACTTGGTCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											171	172	172					5																	43613098		2203	4300	6503	43648855	SO:0001583	missense	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.240G>T	5.37:g.43613098G>T	ENSP00000264663:p.Gln80His		43648855	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953477	0.73902	.	.	ENSG00000112992	ENST00000505678;ENST00000512422;ENST00000264663;ENST00000344920	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.7	2.96	0.34315	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-1 (1);Alanine dehydrogenase/PNT, N-terminal (1);	0.052113	0.85682	D	0.000000	T	0.76933	0.4057	L	0.39397	1.21	0.80722	D	1	P	0.45240	0.854	P	0.54924	0.764	T	0.75698	-0.3227	10	0.66056	D	0.02	-9.9121	7.7163	0.28706	0.3584:0.0:0.6416:0.0	.	80	Q13423	NNTM_HUMAN	H	80	ENSP00000427670:Q80H;ENSP00000421886:Q80H;ENSP00000264663:Q80H;ENSP00000343873:Q80H	ENSP00000264663:Q80H	Q	+	3	2	NNT	43648855	1.000000	0.71417	0.989000	0.46669	0.928000	0.56348	3.297000	0.51810	0.776000	0.33473	0.650000	0.86243	CAG		0.473	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		T	43613098	G	T	43613098	3	4	61	1	0	0	0	0	1	0	0	0	10541	933	33	2	246	2	NNT	5	43613098	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57160	43613098	137302162	3808	11793										
NNT	23530	broad.mit.edu	37	chr5	43644750	43644750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacacagacctgcccagccGaatggccactcaggccagca	9	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:43644750G>A	ENST00000264663.5	+	9	1357	c.1136G>A	c.(1135-1137)cGa>cAa	p.R379Q	NNT_ENST00000512996.2_Missense_Mutation_p.R248Q|NNT_ENST00000344920.4_Missense_Mutation_p.R379Q	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	379					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.R379Q(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CTGCCCAGCCGAATGGCCACT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	69	69					5																	43644750		2203	4300	6503	43680507	SO:0001583	missense	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.1136G>A	5.37:g.43644750G>A	ENSP00000264663:p.Arg379Gln		43680507	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.742617	0.89573	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.96011	-3.88;-3.88;-3.76	5.55	5.55	0.83447	.	0.204155	0.46145	D	0.000303	D	0.95033	0.8392	M	0.86953	2.85	0.58432	D	0.999998	P	0.47034	0.889	B	0.32724	0.151	D	0.95775	0.8812	10	0.62326	D	0.03	-1.3292	19.4893	0.95044	0.0:0.0:1.0:0.0	.	379	Q13423	NNTM_HUMAN	Q	379;379;248	ENSP00000264663:R379Q;ENSP00000343873:R379Q;ENSP00000426343:R248Q	ENSP00000264663:R379Q	R	+	2	0	NNT	43680507	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.399000	0.97285	2.619000	0.88677	0.655000	0.94253	CGA		0.413	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43644750	G	A	43644750	3	1	61	1	0	0	0	0	1	0	0	0	10541	1058	37	1	1166	1	NNT	5	43644750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31652	43644750	137270510	3809	11794										
MRPS30	10884	broad.mit.edu	37	chr5	44812047	44812047	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggattattctgttcctataGaaatccccactataaaatgt	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:44812047G>A	ENST00000507110.1	+	3	816	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K		NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	260					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.E260K(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					TGTTCCTATAGAAATCCCCAC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											79	81	81					5																	44812047		2203	4300	6503	44847804	SO:0001583	missense	10884			AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"Mitochondrial ribosomal proteins / small subunits"	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.778G>A	5.37:g.44812047G>A	ENSP00000424328:p.Glu260Lys		44847804	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	37	CCDS3951.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398352	0.83120	.	.	ENSG00000112996	ENST00000507110	T	0.17213	2.29	5.66	4.8	0.61643	.	0.189539	0.56097	D	0.000026	T	0.36744	0.0978	M	0.80183	2.485	0.53005	D	0.999962	D	0.56968	0.978	P	0.60236	0.871	T	0.14615	-1.0466	10	0.33940	T	0.23	-0.3208	10.3204	0.43762	0.072:0.1336:0.7944:0.0	.	260	Q9NP92	RT30_HUMAN	K	260	ENSP00000424328:E260K	ENSP00000424328:E260K	E	+	1	0	MRPS30	44847804	1.000000	0.71417	0.976000	0.42696	0.820000	0.46376	4.817000	0.62650	1.397000	0.46682	-0.126000	0.14955	GAA		0.308	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640		A	44812047	G	A	44812047	3	1	61	1	0	0	0	0	1	0	0	0	9870	943	33	3	788	3	MRPS30	5	44812047	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1167297	44812047	136103213	3810	11795										
HCN1	348980	broad.mit.edu	37	chr5	45267197	45267197	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaactagagtacctattcGatctagtcggtcaatggcaa	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:45267197G>A	ENST00000303230.4	-	7	1834	c.1777C>T	c.(1777-1779)Cga>Tga	p.R593*		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	593					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.R593*(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GTACCTATTCGATCTAGTCGG	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											136	128	130					5																	45267197		2203	4300	6503	45302954	SO:0001587	stop_gained	348980			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1777C>T	5.37:g.45267197G>A	ENSP00000307342:p.Arg593*		45302954		Nonsense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	38	7.066168	0.98040	.	.	ENSG00000164588	ENST00000303230	.	.	.	5.91	4.07	0.47477	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0462	0.64706	0.0:0.0:0.4388:0.5612	.	.	.	.	X	593	.	ENSP00000307342:R593X	R	-	1	2	HCN1	45302954	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.270000	0.51600	0.785000	0.33685	0.655000	0.94253	CGA		0.413	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45267197	G	A	45267197	4	1	61	1	0	0	0	0	0	1	0	0	7017	1066	37	1	903	1	HCN1	5	45267197	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	455150	45267197	135648063	3811	11796										
HCN1	348980	broad.mit.edu	37	chr5	45396619	45396619	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatactgccgcctcgaaGaatccagagactggattaaa	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:45396619G>T	ENST00000303230.4	-	4	1262	c.1205C>A	c.(1204-1206)tCt>tAt	p.S402Y		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	402					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.S402Y(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						CCGCCTCGAAGAATCCAGAGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											53	51	52					5																	45396619		2203	4300	6503	45432376	SO:0001583	missense	348980			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1205C>A	5.37:g.45396619G>T	ENSP00000307342:p.Ser402Tyr		45432376		Missense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923074	0.73213	.	.	ENSG00000164588	ENST00000303230	D	0.97114	-4.25	5.42	5.42	0.78866	Cyclic nucleotide-binding-like (1);	0.191792	0.36066	N	0.002804	D	0.96200	0.8761	M	0.78223	2.4	0.80722	D	1	P	0.41159	0.74	B	0.33690	0.168	D	0.96806	0.9593	10	0.87932	D	0	.	19.4084	0.94658	0.0:0.0:1.0:0.0	.	402	O60741	HCN1_HUMAN	Y	402	ENSP00000307342:S402Y	ENSP00000307342:S402Y	S	-	2	0	HCN1	45432376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.657000	0.98554	2.820000	0.97059	0.650000	0.86243	TCT		0.448	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		T	45396619	G	T	45396619	3	4	61	1	0	0	0	0	1	0	0	0	7017	942	33	2	1487	2	HCN1	5	45396619	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129422	45396619	135518641	3812	11797										
HCN1	348980	broad.mit.edu	37	chr5	45645649	45645649	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtaaagaatgtgattcCaactggtatgatgactagat	9	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:45645649C>A	ENST00000303230.4	-	2	544	c.487G>T	c.(487-489)Gga>Tga	p.G163*		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	163					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.G163*(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						AATGTGATTCCAACTGGTATG	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											70	71	71					5																	45645649		2203	4298	6501	45681406	SO:0001587	stop_gained	348980			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.487G>T	5.37:g.45645649C>A	ENSP00000307342:p.Gly163*		45681406		Nonsense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	C	37	6.077723	0.97262	.	.	ENSG00000164588	ENST00000303230	.	.	.	4.99	4.99	0.66335	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.2738	0.90077	0.0:1.0:0.0:0.0	.	.	.	.	X	163	.	ENSP00000307342:G163X	G	-	1	0	HCN1	45681406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.783000	0.85696	2.312000	0.78011	0.555000	0.69702	GGA		0.313	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45645649	C	A	45645649	4	1	61	1	0	0	0	0	0	1	0	0	7017	603	21	2	2213	2	HCN1	5	45645649	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	249030	45645649	135269611	3813	11798										
PELO	53918	broad.mit.edu	37	chr5	52096498	52096498	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggggaccaacatccaagaGaatgagtatgtcaagatggg	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52096498G>T	ENST00000274311.2	+	2	1255	c.270G>T	c.(268-270)gaG>gaT	p.E90D	ITGA1_ENST00000282588.6_Intron|ITGA1_ENST00000504086.1_Intron|PELO_ENST00000506949.1_Intron	NM_015946.4	NP_057030.3	Q9BRX2	PELO_HUMAN	pelota homolog (Drosophila)	90					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA catabolic process, non-stop decay (GO:0070481)|RNA surveillance (GO:0071025)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.E90D(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	11		Lung NSC(810;4.94e-05)|Breast(144;0.0848)				ACATCCAAGAGAATGAGTATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	69	70					5																	52096498		2203	4300	6503	52132255	SO:0001583	missense	53918				CCDS3956.1	5q11.2	2008-07-18	2001-11-28		ENSG00000152684	ENSG00000152684			8829	protein-coding gene	gene with protein product		605757	"pelota (Drosophila) homolog"			11060452	Standard	NM_015946		Approved		uc003jos.3	Q9BRX2	OTTHUMG00000096973	ENST00000274311.2:c.270G>T	5.37:g.52096498G>T	ENSP00000274311:p.Glu90Asp		52132255	Q9GZS6|Q9Y306	Missense_Mutation	SNP	ENST00000274311.2	37	CCDS3956.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483979	0.84854	.	.	ENSG00000152684	ENST00000274311	T	0.52057	0.68	5.66	3.89	0.44902	eRF1 domain 1/Pelota-like (1);	0.000000	0.85682	U	0.000000	T	0.66733	0.2819	M	0.89287	3.02	0.80722	D	1	D	0.54601	0.967	P	0.58391	0.838	T	0.68161	-0.5482	10	0.31617	T	0.26	-19.7339	12.2071	0.54358	0.1394:0.0:0.8606:0.0	.	90	Q9BRX2	PELO_HUMAN	D	90	ENSP00000274311:E90D	ENSP00000274311:E90D	E	+	3	2	PELO	52132255	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.022000	0.64078	0.747000	0.32809	0.563000	0.77884	GAG		0.587	PELO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214040.1	NM_015946		T	52096498	G	T	52096498	3	4	61	1	0	0	0	0	1	0	0	0	11755	933	33	2	272	2	PELO	5	52096498	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6450849	52096498	128818762	3814	11799										
ITGA1	3672	broad.mit.edu	37	chr5	52211305	52211305	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcacagcgtattccatcAggtggggatggtaagacact	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52211305A>C	ENST00000282588.6	+	15	2327	c.1869A>C	c.(1867-1869)tcA>tcC	p.S623S		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	623					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)	p.S623S(2)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				GTATTCCATCAGGTGGGGATG	0.378																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	5											139	141	141					5																	52211305		2203	4300	6503	52247062	SO:0001819	synonymous_variant	3672			X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1869A>C	5.37:g.52211305A>C			52247062	B2RNU0	Silent	SNP	ENST00000282588.6	37	CCDS3955.1																																																																																				0.378	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		C	52211305	A	C	52211305	2	2	61	1	0	0	0	0	0	0	0	1	7893	175	7	4		4	ITGA1	5	52211305	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	114807	52211305	128703955	3815	11800										
ITGA1	3672	broad.mit.edu	37	chr5	52235744	52235744	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagccaagtcaatgtttcGcttatcttgtggaaaccaac	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52235744G>A	ENST00000282588.6	+	26	3713	c.3255G>A	c.(3253-3255)tcG>tcA	p.S1085S	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	1085					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)	p.S1085S(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TCAATGTTTCGCTTATCTTGT	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	5											110	93	98					5																	52235744		2202	4299	6501	52271501	SO:0001819	synonymous_variant	3672			X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.3255G>A	5.37:g.52235744G>A			52271501	B2RNU0	Silent	SNP	ENST00000282588.6	37	CCDS3955.1																																																																																				0.299	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		A	52235744	G	A	52235744	2	1	61	1	0	0	0	0	0	0	0	1	7893	1074	38	1		1	ITGA1	5	52235744	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24439	52235744	128679516	3816	11801										
ITGA2	3673	broad.mit.edu	37	chr5	52366010	52366010	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccagggggttatttaaaGaaaacaatgaaaggtgcctg	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52366010G>T	ENST00000296585.5	+	17	2298	c.2155G>T	c.(2155-2157)Gaa>Taa	p.E719*		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	719					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.E719*(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GTTATTTAAAGAAAACAATGA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											59	61	60					5																	52366010		2202	4300	6502	52401767	SO:0001587	stop_gained	3673				CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2155G>T	5.37:g.52366010G>T	ENSP00000296585:p.Glu719*		52401767	Q14595	Nonsense_Mutation	SNP	ENST00000296585.5	37	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	G	34	5.296441	0.95574	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.86	5.86	0.93980	.	0.053180	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.1802	0.98196	0.0:0.0:1.0:0.0	.	.	.	.	X	719	.	ENSP00000296585:E719X	E	+	1	0	ITGA2	52401767	1.000000	0.71417	0.990000	0.47175	0.154000	0.21943	5.056000	0.64287	2.777000	0.95525	0.655000	0.94253	GAA		0.378	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		T	52366010	G	T	52366010	4	4	61	1	0	0	0	0	0	1	0	0	7896	943	33	2	2221	2	ITGA2	5	52366010	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130266	52366010	128549250	3817	11802										
FST	10468	broad.mit.edu	37	chr5	52779502	52779502	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgcactcctaaaggcaaGatgtaaagagcagccagaac	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52779502G>T	ENST00000256759.3	+	3	829	c.446G>T	c.(445-447)aGa>aTa	p.R149I	FST_ENST00000396947.3_Missense_Mutation_p.R149I	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	149	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)	p.R149I(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				CTAAAGGCAAGATGTAAAGAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											68	64	65					5																	52779502		2203	4300	6503	52815259	SO:0001583	missense	10468			M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.446G>T	5.37:g.52779502G>T	ENSP00000256759:p.Arg149Ile		52815259	B5BU94|Q9BTH0	Missense_Mutation	SNP	ENST00000256759.3	37	CCDS3959.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962751	0.74016	.	.	ENSG00000134363	ENST00000256759;ENST00000511025;ENST00000396947;ENST00000504226	T;T;T	0.04862	3.54;3.54;3.54	5.76	4.9	0.64082	Proteinase inhibitor I1, Kazal (2);	0.086103	0.85682	D	0.000000	T	0.08670	0.0215	L	0.43598	1.365	0.80722	D	1	P	0.45957	0.869	P	0.44597	0.454	T	0.10064	-1.0646	10	0.52906	T	0.07	-15.796	11.0007	0.47604	0.1423:0.0:0.8577:0.0	.	149	P19883	FST_HUMAN	I	149;149;149;21	ENSP00000256759:R149I;ENSP00000380151:R149I;ENSP00000426315:R21I	ENSP00000256759:R149I	R	+	2	0	FST	52815259	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	4.606000	0.61126	1.444000	0.47605	0.491000	0.48974	AGA		0.532	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		T	52779502	G	T	52779502	3	4	61	1	0	0	0	0	1	0	0	0	6095	942	33	2	456	2	FST	5	52779502	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	413492	52779502	128135758	3818	11803										
NDUFS4	4724	broad.mit.edu	37	chr5	52979017	52979017	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttatggtgcaaacttttCttggaacaaaagaacaagag	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:52979017C>A	ENST00000296684.5	+	5	522	c.494C>A	c.(493-495)tCt>tAt	p.S165Y		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	165					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.S165Y(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				GCAAACTTTTCTTGGAACAAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											115	119	118					5																	52979017		2203	4300	6503	53014774	SO:0001583	missense	4724			AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"Mitochondrial respiratory chain complex / Complex I"	7711	protein-coding gene	gene with protein product	"complex I 18kDa subunit"	602694	"NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.494C>A	5.37:g.52979017C>A	ENSP00000296684:p.Ser165Tyr		53014774	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	37	CCDS3960.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595344	0.86953	.	.	ENSG00000164258	ENST00000296684	T	0.78816	-1.21	5.96	5.96	0.96718	.	0.159550	0.64402	D	0.000018	D	0.85737	0.5766	M	0.76574	2.34	0.80722	D	1	D	0.54047	0.964	P	0.55055	0.767	D	0.83511	0.0080	10	0.36615	T	0.2	.	20.4008	0.98991	0.0:1.0:0.0:0.0	.	165	O43181	NDUS4_HUMAN	Y	165	ENSP00000296684:S165Y	ENSP00000296684:S165Y	S	+	2	0	NDUFS4	53014774	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.746000	0.74866	2.826000	0.97356	0.655000	0.94253	TCT		0.398	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495		A	52979017	C	A	52979017	3	1	61	1	0	0	0	0	1	0	0	0	10325	913	32	2	512	2	NDUFS4	5	52979017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	199515	52979017	127936243	3819	11804										
HSPB3	8988	broad.mit.edu	37	chr5	53751890	53751890	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcatcattcagaccttcGaaggctggctgctgataaaa	8	10	3	2	rs147724326	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:53751890G>T	ENST00000302005.1	+	1	446	c.271G>T	c.(271-273)Gaa>Taa	p.E91*		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	91					cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E91*(1)		breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				TCAGACCTTCGAAGGCTGGCT	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											111	103	106					5																	53751890		2203	4300	6503	53787647	SO:0001587	stop_gained	8988			Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"Heat shock proteins / HSPB"	5248	protein-coding gene	gene with protein product		604624	"heat shock 27kD protein 3"			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.271G>T	5.37:g.53751890G>T	ENSP00000303394:p.Glu91*		53787647		Nonsense_Mutation	SNP	ENST00000302005.1	37	CCDS3961.1	.	.	.	.	.	.	.	.	.	.	G	37	6.588102	0.97684	.	.	ENSG00000169271	ENST00000302005	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-16.2203	19.7612	0.96319	0.0:0.0:1.0:0.0	.	.	.	.	X	91	.	ENSP00000303394:E91X	E	+	1	0	HSPB3	53787647	1.000000	0.71417	0.996000	0.52242	0.874000	0.50279	7.692000	0.84203	2.646000	0.89796	0.655000	0.94253	GAA		0.517	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2			T	53751890	G	T	53751890	4	4	61	1	0	0	0	0	0	1	0	0	7442	1059	37	2	273	2	HSPB3	5	53751890	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	772873	53751890	127163370	3820	11805										
GZMA	3001	broad.mit.edu	37	chr5	54403644	54403644	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaaggtcccaggtcattCttggggctcactcaataacc	8	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54403644C>A	ENST00000274306.6	+	3	273	c.238C>A	c.(238-240)Ctt>Att	p.L80I		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	80	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.L80I(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CCAGGTCATTCTTGGGGCTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											116	111	112					5																	54403644		2203	4300	6503	54439401	SO:0001583	missense	3001				CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.238C>A	5.37:g.54403644C>A	ENSP00000274306:p.Leu80Ile		54439401	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	37	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.971327	0.53614	.	.	ENSG00000145649	ENST00000274306	D	0.90261	-2.64	6.03	6.03	0.97812	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.93661	0.7975	L	0.52823	1.66	0.43007	D	0.994531	D	0.67145	0.996	D	0.70227	0.968	D	0.93764	0.7069	10	0.72032	D	0.01	.	14.9453	0.71026	0.143:0.857:0.0:0.0	.	80	P12544	GRAA_HUMAN	I	80	ENSP00000274306:L80I	ENSP00000274306:L80I	L	+	1	0	GZMA	54439401	1.000000	0.71417	1.000000	0.80357	0.131000	0.20780	2.927000	0.48900	2.854000	0.98071	0.655000	0.94253	CTT		0.413	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144		A	54403644	C	A	54403644	3	1	61	1	0	0	0	0	1	0	0	0	6936	913	32	2	248	2	GZMA	5	54403644	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	651754	54403644	126511616	3821	11806										
GPX8	493869	broad.mit.edu	37	chr5	54456874	54456874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaactcacagacagaaattActtagggctgaaggaactgc	9	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54456874A>G	ENST00000503787.1	+	2	332	c.257A>G	c.(256-258)tAc>tGc	p.Y86C	CDC20B_ENST00000331730.3_Intron|CDC20B_ENST00000322374.6_Intron|GPX8_ENST00000506123.1_3'UTR|CDC20B_ENST00000334206.5_Intron|CDC20B_ENST00000296733.1_Intron|GPX8_ENST00000296734.6_Intron|CDC20B_ENST00000381375.2_Intron|GPX8_ENST00000515370.1_Missense_Mutation_p.Y35C	NM_001008397.2	NP_001008398.2	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8 (putative)	86					response to oxidative stress (GO:0006979)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)	p.Y86C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)	11					Glutathione(DB00143)	GACAGAAATTACTTAGGGCTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	67	68					5																	54456874		2203	4300	6503	54492631	SO:0001583	missense	493869			BC029424	CCDS34156.1	5q11.2	2008-09-29				ENSG00000164294			33100	protein-coding gene	gene with protein product							Standard	NM_001008397		Approved	UNQ847, EPLA847	uc003jpq.2	Q8TED1		ENST00000503787.1:c.257A>G	5.37:g.54456874A>G	ENSP00000423822:p.Tyr86Cys		54492631		Missense_Mutation	SNP	ENST00000503787.1	37	CCDS34156.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.080672	0.76528	.	.	ENSG00000164294	ENST00000503787;ENST00000515370	T;T	0.16897	2.31;2.31	5.53	5.53	0.82687	Thioredoxin-like fold (2);	0.055773	0.85682	D	0.000000	T	0.62429	0.2427	H	0.99357	4.53	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	T	0.80056	-0.1542	10	0.87932	D	0	.	15.6603	0.77182	1.0:0.0:0.0:0.0	.	35;86	E7ETY7;Q8TED1	.;GPX8_HUMAN	C	86;35	ENSP00000423822:Y86C;ENSP00000427466:Y35C	ENSP00000423822:Y86C	Y	+	2	0	GPX8	54492631	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.049000	0.76613	2.092000	0.63282	0.533000	0.62120	TAC		0.473	GPX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369717.1	NM_001008397		G	54456874	A	G	54456874	3	3	61	1	0	0	0	0	1	0	0	0	6767	391	14	4	263	4	GPX8	5	54456874	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	53230	54456874	126458386	3822	11807										
DHX29	54505	broad.mit.edu	37	chr5	54558599	54558599	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactttgtatagattatcttCcccacattgtcatacagtcc	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54558599C>T	ENST00000251636.5	-	24	3835	c.3687G>A	c.(3685-3687)ggG>ggA	p.G1229G	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	1229						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)	p.G1229G(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AGATTATCTTCCCCACATTGT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	5											194	184	187					5																	54558599		2203	4300	6503	54594356	SO:0001819	synonymous_variant	54505			AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.3687G>A	5.37:g.54558599C>T			54594356	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	37	CCDS34158.1																																																																																				0.463	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		T	54558599	C	T	54558599	2	4	61	1	0	0	0	0	0	0	0	1	4514	842	30	3		3	DHX29	5	54558599	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101725	54558599	126356661	3823	11808										
DHX29	54505	broad.mit.edu	37	chr5	54570457	54570457	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaccgttcagaataaaatCttctatcatttgatagaaga	6	6	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54570457C>A	ENST00000251636.5	-	16	2823	c.2675G>T	c.(2674-2676)aGa>aTa	p.R892I	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	892	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)	p.R892I(1)|p.R892K(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AGAATAAAATCTTCTATCATT	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	5											29	29	29					5																	54570457		2200	4284	6484	54606214	SO:0001583	missense	54505			AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.2675G>T	5.37:g.54570457C>A	ENSP00000251636:p.Arg892Ile		54606214	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Missense_Mutation	SNP	ENST00000251636.5	37	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543261	0.86022	.	.	ENSG00000067248	ENST00000251636	T	0.02656	4.21	4.99	4.99	0.66335	Helicase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.09247	0.0228	L	0.34521	1.04	0.80722	D	1	D	0.62365	0.991	D	0.65987	0.94	T	0.21690	-1.0238	10	0.51188	T	0.08	.	18.6257	0.91336	0.0:1.0:0.0:0.0	.	892	Q7Z478	DHX29_HUMAN	I	892	ENSP00000251636:R892I	ENSP00000251636:R892I	R	-	2	0	DHX29	54606214	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.221000	0.78016	2.478000	0.83669	0.563000	0.77884	AGA		0.313	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		A	54570457	C	A	54570457	3	1	61	1	0	0	0	0	1	0	0	0	4514	913	32	2	1482	2	DHX29	5	54570457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11858	54570457	126344803	3824	11809										
DHX29	54505	broad.mit.edu	37	chr5	54581678	54581678	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcttacatcatgaggttCtttctttttatctaaaatgg	5	6	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54581678C>A	ENST00000251636.5	-	9	1226	c.1078G>T	c.(1078-1080)Gaa>Taa	p.E360*	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	360						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)	p.E360*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TCATGAGGTTCTTTCTTTTTA	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											60	62	61					5																	54581678		2203	4297	6500	54617435	SO:0001587	stop_gained	54505			AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.1078G>T	5.37:g.54581678C>A	ENSP00000251636:p.Glu360*		54617435	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Nonsense_Mutation	SNP	ENST00000251636.5	37	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	C	38	6.969369	0.97971	.	.	ENSG00000067248	ENST00000251636	.	.	.	5.8	5.8	0.92144	.	0.240957	0.48286	D	0.000183	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	15.5169	0.75830	0.0:0.8623:0.1377:0.0	.	.	.	.	X	360	.	ENSP00000251636:E360X	E	-	1	0	DHX29	54617435	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.615000	0.67702	2.745000	0.94114	0.650000	0.86243	GAA		0.358	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		A	54581678	C	A	54581678	4	1	61	1	0	0	0	0	0	1	0	0	4514	922	32	2	3107	2	DHX29	5	54581678	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11221	54581678	126333582	3825	11810										
SKIV2L2	23517	broad.mit.edu	37	chr5	54683847	54683847	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgtagtagaagtacttCtgcgctgtagcaaagagagc	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54683847C>A	ENST00000230640.5	+	19	2352	c.2098C>A	c.(2098-2100)Ctg>Atg	p.L700M	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.L599M	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	700					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.L700M(1)		NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				AGAAGTACTTCTGCGCTGTAG	0.383																																					Melanoma(2;92 134 23744 29976 33782)											1	Substitution - Missense(1)	large_intestine(1)	5											104	104	104					5																	54683847		2203	4300	6503	54719604	SO:0001583	missense	23517			D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.2098C>A	5.37:g.54683847C>A	ENSP00000230640:p.Leu700Met		54719604	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763353	0.31228	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.36340	1.26;1.3	5.7	1.43	0.22495	.	0.145674	0.47093	D	0.000248	T	0.33789	0.0875	M	0.63428	1.95	0.42879	D	0.994163	P;B	0.36683	0.565;0.45	B;B	0.39562	0.215;0.303	T	0.11299	-1.0593	10	0.56958	D	0.05	-16.6034	6.8082	0.23788	0.1167:0.6002:0.0:0.2831	.	599;700	F5H7E2;P42285	.;SK2L2_HUMAN	M	700;599	ENSP00000230640:L700M;ENSP00000442583:L599M	ENSP00000230640:L700M	L	+	1	2	SKIV2L2	54719604	0.227000	0.23707	0.996000	0.52242	0.706000	0.40770	0.263000	0.18478	0.358000	0.24211	-0.384000	0.06662	CTG		0.383	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			A	54683847	C	A	54683847	3	1	61	1	0	0	0	0	1	0	0	0	14397	912	32	2	2172	2	SKIV2L2	5	54683847	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102169	54683847	126231413	3826	11811										
SLC38A9	153129	broad.mit.edu	37	chr5	54960688	54960688	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagctagtggtatccaacGaaactagataaaataagaga	8	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:54960688G>T	ENST00000396865.2	-	8	1121	c.530C>A	c.(529-531)tCg>tAg	p.S177*	SLC38A9_ENST00000539768.1_Nonsense_Mutation_p.S177*|SLC38A9_ENST00000512595.1_Nonsense_Mutation_p.S150*|SLC38A9_ENST00000515629.1_Nonsense_Mutation_p.S114*|SLC38A9_ENST00000318672.3_Nonsense_Mutation_p.S177*|SLC38A9_ENST00000416547.2_Nonsense_Mutation_p.S53*	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	177					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.S177*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				GGTATCCAACGAAACTAGATA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											29	27	28					5																	54960688		2203	4299	6502	54996445	SO:0001587	stop_gained	153129				CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"Solute carriers"	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.530C>A	5.37:g.54960688G>T	ENSP00000380074:p.Ser177*		54996445	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Nonsense_Mutation	SNP	ENST00000396865.2	37	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.832244	0.91036	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000511233;ENST00000512208	.	.	.	5.6	5.6	0.85130	.	0.324438	0.32459	N	0.006077	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1405	9.8329	0.40952	0.1576:0.0:0.8424:0.0	.	.	.	.	X	177;177;177;114;53;150;177;114	.	ENSP00000316596:S177X	S	-	2	0	SLC38A9	54996445	1.000000	0.71417	0.960000	0.40013	0.180000	0.23129	2.949000	0.49074	2.635000	0.89317	0.650000	0.86243	TCG		0.363	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514		T	54960688	G	T	54960688	4	4	61	1	0	0	0	0	0	1	0	0	14648	1059	37	2	1191	2	SLC38A9	5	54960688	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	276841	54960688	125954572	3827	11812										
DDX4	54514	broad.mit.edu	37	chr5	55056029	55056029	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatgttgtttgctttagaAatggatgatggaccttctcg	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:55056029A>C	ENST00000505374.1	+	4	221	c.129A>C	c.(127-129)gaA>gaC	p.E43D	SLC38A9_ENST00000504880.1_Intron|DDX4_ENST00000353507.5_Splice_Site_p.E43D|DDX4_ENST00000354991.5_Splice_Site_p.E43D|DDX4_ENST00000514278.2_Splice_Site_p.E43D|DDX4_ENST00000508580.1_3'UTR	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	43					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.E43D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TTGCTTTAGAAATGGATGATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											169	166	167					5																	55056029		2203	4300	6503	55091786	SO:0001630	splice_region_variant	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.128-1A>C	5.37:g.55056029A>C			55091786	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	37	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.307967	0.40895	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000506848;ENST00000514679;ENST00000354991;ENST00000511491	T;T;T;T;T;T;T	0.55930	1.97;1.92;1.99;3.44;0.57;1.97;0.49	5.04	3.86	0.44501	.	0.865722	0.10407	N	0.678438	T	0.35682	0.0940	N	0.24115	0.695	0.29330	N	0.866746	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.30001	-0.9993	10	0.18276	T	0.48	.	7.5938	0.28035	0.7911:0.0:0.0:0.2089	.	43;43;43	D6RDK4;Q9NQI0-2;Q9NQI0	.;.;DDX4_HUMAN	D	43	ENSP00000334167:E43D;ENSP00000425359:E43D;ENSP00000424838:E43D;ENSP00000427167:E43D;ENSP00000424112:E43D;ENSP00000347087:E43D;ENSP00000427522:E43D	ENSP00000334167:E43D	E	+	3	2	DDX4	55091786	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	0.922000	0.28734	0.897000	0.36392	0.460000	0.39030	GAA		0.373	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	Missense_Mutation	C	55056029	A	C	55056029	5	2	61	1	0	0	0	0	0	0	1	0	4366	28	1	4	139	4	DDX4	5	55056029	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	95341	55056029	125859231	3828	11813										
IL31RA	133396	broad.mit.edu	37	chr5	55178891	55178891	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaaaactgaaccacctaaGattttccgtgtgaaaccagt	8	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:55178891G>T	ENST00000447346.2	+	5	539	c.474G>T	c.(472-474)aaG>aaT	p.K158N	IL31RA_ENST00000490985.1_Missense_Mutation_p.K16N|IL31RA_ENST00000396836.2_Missense_Mutation_p.K158N|IL31RA_ENST00000297015.3_Missense_Mutation_p.K16N|IL31RA_ENST00000396834.1_Missense_Mutation_p.K139N|IL31RA_ENST00000354961.4_Missense_Mutation_p.K139N|IL31RA_ENST00000359040.5_Missense_Mutation_p.K158N	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	126	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)	p.K158N(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				AACCACCTAAGATTTTCCGTG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											98	97	97					5																	55178891		2203	4300	6503	55214648	SO:0001583	missense	133396			AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.474G>T	5.37:g.55178891G>T	ENSP00000415900:p.Lys158Asn		55214648	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	8.491	0.862063	0.17178	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.9	1.94	0.25998	Fibronectin, type III (4);Immunoglobulin-like fold (1);	5.822590	0.00447	N	0.000081	T	0.37972	0.1023	N	0.22421	0.69	0.09310	N	1	B;B;B;B;P	0.34546	0.175;0.302;0.302;0.202;0.456	B;B;B;B;B	0.30943	0.122;0.051;0.075;0.032;0.098	T	0.22977	-1.0201	10	0.27785	T	0.31	-0.0717	6.083	0.19952	0.1652:0.289:0.5458:0.0	.	126;158;139;158;158	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	N	158;139;158;158;16;16;139	ENSP00000380048:K158N;ENSP00000380046:K139N;ENSP00000415900:K158N;ENSP00000351935:K158N;ENSP00000297015:K16N;ENSP00000427533:K16N;ENSP00000347047:K139N	ENSP00000297015:K16N	K	+	3	2	IL31RA	55214648	0.751000	0.28327	0.265000	0.24526	0.606000	0.37113	0.937000	0.28951	0.373000	0.24621	-0.150000	0.13652	AAG		0.343	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		T	55178891	G	T	55178891	3	4	61	1	0	0	0	0	1	0	0	0	7712	933	33	2	492	2	IL31RA	5	55178891	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122862	55178891	125736369	3829	11814										
IL31RA	133396	broad.mit.edu	37	chr5	55195927	55195927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgggaagtctccagtgGccaccctgaggattccagct	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:55195927G>A	ENST00000447346.2	+	8	1101	c.1036G>A	c.(1036-1038)Gcc>Acc	p.A346T	IL31RA_ENST00000396836.2_Missense_Mutation_p.A346T|IL31RA_ENST00000297015.3_Missense_Mutation_p.A204T|IL31RA_ENST00000490985.1_Missense_Mutation_p.A204T|IL31RA_ENST00000359040.5_Missense_Mutation_p.A346T|IL31RA_ENST00000396834.1_Missense_Mutation_p.A327T|IL31RA_ENST00000354961.4_Missense_Mutation_p.A327T	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	314	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)	p.A346T(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTCTCCAGTGGCCACCCTGAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											112	123	120					5																	55195927		2203	4300	6503	55231684	SO:0001583	missense	133396			AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1036G>A	5.37:g.55195927G>A	ENSP00000415900:p.Ala346Thr		55231684	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	4.428	0.079229	0.08533	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35;2.35	4.41	0.531	0.17108	Fibronectin, type III (1);	0.527681	0.21180	N	0.078822	T	0.13927	0.0337	L	0.49350	1.555	0.09310	N	1	B;B;B;P;P	0.49358	0.037;0.145;0.145;0.457;0.923	B;B;B;B;B	0.42771	0.028;0.13;0.062;0.135;0.397	T	0.30060	-0.9991	10	0.11485	T	0.65	-11.3748	9.7356	0.40386	0.3367:0.0:0.6633:0.0	.	314;346;327;346;346	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	T	346;327;346;346;204;204;327	ENSP00000380048:A346T;ENSP00000380046:A327T;ENSP00000415900:A346T;ENSP00000351935:A346T;ENSP00000297015:A204T;ENSP00000427533:A204T;ENSP00000347047:A327T	ENSP00000297015:A204T	A	+	1	0	IL31RA	55231684	0.199000	0.23386	0.000000	0.03702	0.121000	0.20230	1.020000	0.30027	-0.234000	0.09782	-0.797000	0.03246	GCC		0.463	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		A	55195927	G	A	55195927	3	1	61	1	0	0	0	0	1	0	0	0	7712	1203	42	3	1066	3	IL31RA	5	55195927	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17036	55195927	125719333	3830	11815										
ANKRD55	79722	broad.mit.edu	37	chr5	55407469	55407469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgtcctcctctctgtatCggtccctgctgggatccttc	10	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:55407469C>T	ENST00000341048.4	-	10	1257	c.1106G>A	c.(1105-1107)cGa>cAa	p.R369Q	ANKRD55_ENST00000434982.2_Missense_Mutation_p.R81Q|ANKRD55_ENST00000504958.2_Missense_Mutation_p.R326Q|ANKRD55_ENST00000505970.2_5'UTR	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	369								p.R369Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CTCTCTGTATCGGTCCCTGCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											271	261	265					5																	55407469		2203	4300	6503	55443226	SO:0001583	missense	79722			AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"Ankyrin repeat domain containing"	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.1106G>A	5.37:g.55407469C>T	ENSP00000342295:p.Arg369Gln		55443226	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	37	CCDS34161.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	9.391|9.391	1.075527|1.075527	0.20227|0.20227	.|.	.|.	ENSG00000164512|ENSG00000164512	ENST00000505970|ENST00000507283;ENST00000341048;ENST00000504958;ENST00000434982	.|T;T;T	.|0.38560	.|1.38;1.13;1.46	5.32|5.32	-5.85|-5.85	0.02311|0.02311	.|.	.|0.952921	.|0.08637	.|N	.|0.916044	T|T	0.19565|0.19565	0.0470|0.0470	N|N	0.20986|0.20986	0.625|0.625	0.09310|0.09310	N|N	1|1	.|B;B	.|0.09022	.|0.0;0.002	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.18053|0.18053	-1.0349|-1.0349	6|10	0.18710|0.27785	T|T	0.47|0.31	.|.	1.1619|1.1619	0.01808|0.01808	0.1839:0.2306:0.1809:0.4046|0.1839:0.2306:0.1809:0.4046	.|.	.|369;368	.|B3KVT8;Q3KP44	.|.;ANR55_HUMAN	N|Q	114|369;369;326;81	.|ENSP00000342295:R369Q;ENSP00000424230:R326Q;ENSP00000429421:R81Q	ENSP00000422370:D114N|ENSP00000342295:R369Q	D|R	-|-	1|2	0|0	ANKRD55|ANKRD55	55443226|55443226	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.270000|0.270000	0.26580|0.26580	-1.687000|-1.687000	0.01927|0.01927	-1.301000|-1.301000	0.02338|0.02338	-0.252000|-0.252000	0.11476|0.11476	GAT|CGA		0.502	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669		T	55407469	C	T	55407469	3	4	61	1	0	0	0	0	1	0	0	0	681	884	31	1	750	1	ANKRD55	5	55407469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211542	55407469	125507791	3831	11816										
MAP3K1	4214	broad.mit.edu	37	chr5	56168531	56168531	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgtagatctaagtggaGatctcatgatttctacaggt	9	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:56168531G>T	ENST00000399503.3	+	8	1487	c.1487G>T	c.(1486-1488)aGa>aTa	p.R496I		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	496					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		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)		TCTAAGTGGAGATCTCATGAT	0.289																																																0			5											83	78	80					5																	56168531		1787	4065	5852	56204288	SO:0001583	missense	4214			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1487G>T	5.37:g.56168531G>T	ENSP00000382423:p.Arg496Ile		56204288		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175060	0.78564	.	.	ENSG00000095015	ENST00000399503	T	0.69175	-0.38	5.97	5.97	0.96955	Zinc finger, RING/FYVE/PHD-type (1);	0.055919	0.64402	D	0.000001	T	0.59335	0.2186	L	0.44542	1.39	0.58432	D	0.999998	P	0.44195	0.828	B	0.32624	0.149	T	0.66081	-0.6012	10	0.72032	D	0.01	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	496	Q13233	M3K1_HUMAN	I	496	ENSP00000382423:R496I	ENSP00000382423:R496I	R	+	2	0	MAP3K1	56204288	1.000000	0.71417	0.990000	0.47175	0.976000	0.68499	6.030000	0.70903	2.834000	0.97654	0.650000	0.86243	AGA		0.289	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		T	56168531	G	T	56168531	3	4	61	1	0	0	0	0	1	0	0	0	9273	942	33	2	1517	2	MAP3K1	5	56168531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	761062	56168531	124746729	3832	11817										
MAP3K1	4214	broad.mit.edu	37	chr5	56176993	56176993	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacaattggcaagaacttCttggccgcctttgtcttata	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:56176993C>A	ENST00000399503.3	+	13	2263	c.2263C>A	c.(2263-2265)Ctt>Att	p.L755I		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	755					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.L592I(1)		NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		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)		GCAAGAACTTCTTGGCCGCCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											151	135	140					5																	56176993		1826	4081	5907	56212750	SO:0001583	missense	4214			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2263C>A	5.37:g.56176993C>A	ENSP00000382423:p.Leu755Ile		56212750		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.503962	0.64410	.	.	ENSG00000095015	ENST00000399503	T	0.66280	-0.2	5.87	4.79	0.61399	.	0.000000	0.64402	D	0.000002	T	0.75110	0.3805	M	0.61703	1.905	0.52501	D	0.999953	D	0.69078	0.997	D	0.72625	0.978	T	0.76386	-0.2978	10	0.87932	D	0	.	13.67	0.62418	0.0:0.8966:0.0:0.1034	.	755	Q13233	M3K1_HUMAN	I	755	ENSP00000382423:L755I	ENSP00000382423:L755I	L	+	1	0	MAP3K1	56212750	0.975000	0.34042	1.000000	0.80357	0.991000	0.79684	2.259000	0.43259	2.941000	0.99782	0.655000	0.94253	CTT		0.368	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		A	56176993	C	A	56176993	3	1	61	1	0	0	0	0	1	0	0	0	9273	913	32	2	2313	2	MAP3K1	5	56176993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8462	56176993	124738267	3833	11818										
C5orf35	133383	broad.mit.edu	37	chr5	56207243	56207243	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttaaaccagaagaaattCtttacaagactttgggtttc	6	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:56207243C>A	ENST00000285947.2	+	2	732	c.346C>A	c.(346-348)Ctt>Att	p.L116I	AC008937.3_ENST00000453721.1_RNA|SETD9_ENST00000541720.1_Missense_Mutation_p.L116I|SETD9_ENST00000475908.1_3'UTR	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	116							methyltransferase activity (GO:0008168)	p.L116I(1)									AGAAGAAATTCTTTACAAGAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	79	79					5																	56207243		2203	4300	6503	56243000	SO:0001583	missense	133383			BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 35"	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.346C>A	5.37:g.56207243C>A	ENSP00000285947:p.Leu116Ile		56243000	F5H713	Missense_Mutation	SNP	ENST00000285947.2	37	CCDS3972.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836296	0.71373	.	.	ENSG00000155542	ENST00000285947;ENST00000541720	T;T	0.42513	1.05;0.97	5.57	4.69	0.59074	.	0.121446	0.56097	D	0.000025	T	0.45034	0.1322	L	0.60455	1.87	0.28747	N	0.90165	D	0.53885	0.963	P	0.50537	0.643	T	0.45131	-0.9282	10	0.42905	T	0.14	-15.0504	7.2682	0.26242	0.1398:0.7208:0.0:0.1394	.	116	Q8NE22	CE035_HUMAN	I	116	ENSP00000285947:L116I;ENSP00000442886:L116I	ENSP00000285947:L116I	L	+	1	0	C5orf35	56243000	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	1.473000	0.35387	1.326000	0.45319	0.655000	0.94253	CTT		0.398	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		A	56207243	C	A	56207243	3	1	61	1	0	0	0	0	1	0	0	0	2300	913	32	2	352	2	C5orf35	5	56207243	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30250	56207243	124708017	3834	11819										
MIER3	166968	broad.mit.edu	37	chr5	56229214	56229214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccaaagtaactggtcttCgttttcatatactgataaag	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:56229214C>T	ENST00000381199.3	-	8	617	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	MIER3_ENST00000381213.3_Missense_Mutation_p.E203K|MIER3_ENST00000409421.1_Missense_Mutation_p.E140K|MIER3_ENST00000381226.3_Missense_Mutation_p.E208K			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	203	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E203K(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		AACTGGTCTTCGTTTTCATAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	98	100					5																	56229214		2203	4300	6503	56264971	SO:0001583	missense	166968			BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.607G>A	5.37:g.56229214C>T	ENSP00000370596:p.Glu203Lys		56264971	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	Missense_Mutation	SNP	ENST00000381199.3	37		.	.	.	.	.	.	.	.	.	.	C	34	5.360806	0.95877	.	.	ENSG00000155545	ENST00000381226;ENST00000381213;ENST00000381199;ENST00000409421	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.4	5.4	0.78164	ELM2 domain (2);	0.140835	0.64402	D	0.000006	T	0.38081	0.1027	L	0.60957	1.885	0.80722	D	1	P;P;B	0.49253	0.91;0.921;0.311	B;B;B	0.43413	0.419;0.285;0.065	T	0.35450	-0.9788	10	0.72032	D	0.01	-7.2374	19.1664	0.93559	0.0:1.0:0.0:0.0	.	203;208;203	Q7Z3K6;Q7Z3K6-2;Q7Z3K6-3	MIER3_HUMAN;.;.	K	208;203;203;140	ENSP00000370624:E208K;ENSP00000370611:E203K;ENSP00000370596:E203K;ENSP00000386584:E140K	ENSP00000370596:E203K	E	-	1	0	MIER3	56264971	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.487000	0.81328	2.538000	0.85594	0.591000	0.81541	GAA		0.353	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622		T	56229214	C	T	56229214	3	4	61	1	0	0	0	0	1	0	0	0	9612	893	31	1	1066	1	MIER3	5	56229214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21971	56229214	124686046	3835	11820										
ACTBL2	345651	broad.mit.edu	37	chr5	56778460	56778460	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacagcccggggggcatcGtcaccaccaaagcctgcctt	10	16	1	0	rs374948712		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:56778460G>A	ENST00000423391.1	-	1	176	c.75C>T	c.(73-75)gaC>gaT	p.D25D	AC025470.1_ENST00000584598.1_RNA|CTD-2023N9.1_ENST00000506106.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	25						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.D25D(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		GGGGGGCATCGTCACCACCAA	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		20616	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						G		3,4403	6.2+/-15.9	0,3,2200	85	58	67		75	-6.9	0.6	5		67	0,8600		0,0,4300	no	coding-synonymous	ACTBL2	NM_001017992.2		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		25/377	56778460	3,13003	2203	4300	6503	56814217	SO:0001819	synonymous_variant	345651				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.75C>T	5.37:g.56778460G>A			56814217	B2RPJ1|Q562R2|Q562S9|Q562X8	Silent	SNP	ENST00000423391.1	37	CCDS34163.1																																																																																				0.582	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992		A	56778460	G	A	56778460	2	1	61	1	0	0	0	0	0	0	0	1	194	1136	40	1		1	ACTBL2	5	56778460	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	549246	56778460	124136800	3836	11821										
PLK2	10769	broad.mit.edu	37	chr5	57750454	57750454	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagggcatattccattcGattttttaattctgatgaac	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:57750454G>A	ENST00000274289.3	-	14	2314	c.2014C>T	c.(2014-2016)Cga>Tga	p.R672*	PLK2_ENST00000502671.1_Intron	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	672	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.R672*(1)		endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TATTCCATTCGATTTTTTAAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											152	143	146					5																	57750454		2203	4300	6503	57786211	SO:0001587	stop_gained	10769				CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.2014C>T	5.37:g.57750454G>A	ENSP00000274289:p.Arg672*		57786211	O60679|Q96CV7|Q9UE61	Nonsense_Mutation	SNP	ENST00000274289.3	37	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	G	40	8.216293	0.98709	.	.	ENSG00000145632	ENST00000274289	.	.	.	5.92	5.92	0.95590	.	0.054436	0.64402	D	0.000001	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.33	14.1764	0.65544	0.0:0.0:0.7515:0.2485	.	.	.	.	X	672	.	ENSP00000274289:R672X	R	-	1	2	PLK2	57786211	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.805000	0.62561	2.818000	0.97014	0.655000	0.94253	CGA		0.408	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		A	57750454	G	A	57750454	4	1	61	1	0	0	0	0	0	1	0	0	12127	1066	37	1	47	1	PLK2	5	57750454	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	971994	57750454	123164806	3837	11822										
PLK2	10769	broad.mit.edu	37	chr5	57751901	57751901	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtccctctgactatcatccGaatagcatccccaatctgct	5	15	3	1	rs148954251		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:57751901G>A	ENST00000274289.3	-	10	1636	c.1336C>T	c.(1336-1338)Cgg>Tgg	p.R446W	PLK2_ENST00000502671.1_Intron	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	446					G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.R446W(1)		endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		ACTATCATCCGAATAGCATCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110	104	106		1336	5	1	5	dbSNP_134	106	0,8600		0,0,4300	no	missense	PLK2	NM_006622.2	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	446/686	57751901	1,13005	2203	4300	6503	57787658	SO:0001583	missense	10769				CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.1336C>T	5.37:g.57751901G>A	ENSP00000274289:p.Arg446Trp		57787658	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	37	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.027044	0.93518	2.27E-4	0.0	ENSG00000145632	ENST00000274289	T	0.69926	-0.44	5.88	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	L	0.44542	1.39	0.80722	D	1	D	0.69078	0.997	P	0.53360	0.724	T	0.72527	-0.4266	10	0.66056	D	0.02	-15.7676	15.8492	0.78912	0.0:0.0:0.8637:0.1363	.	446	Q9NYY3	PLK2_HUMAN	W	446	ENSP00000274289:R446W	ENSP00000274289:R446W	R	-	1	2	PLK2	57787658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.279000	0.78599	2.788000	0.95919	0.650000	0.86243	CGG		0.468	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		A	57751901	G	A	57751901	3	1	61	1	0	0	0	0	1	0	0	0	12127	1057	37	1	741	1	PLK2	5	57751901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1447	57751901	123163359	3838	11823										
PLK2	10769	broad.mit.edu	37	chr5	57752839	57752839	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagctgctttcttaaaGaaattcttagctgggcttga	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:57752839G>T	ENST00000274289.3	-	8	1389	c.1089C>A	c.(1087-1089)ttC>ttA	p.F363L	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	363					G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.F363L(1)		endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		CTTTCTTAAAGAAATTCTTAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											61	66	64					5																	57752839		2203	4300	6503	57788596	SO:0001583	missense	10769				CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.1089C>A	5.37:g.57752839G>T	ENSP00000274289:p.Phe363Leu		57788596	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	37	CCDS3974.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.158|9.158	1.018017|1.018017	0.19355|0.19355	.|.	.|.	ENSG00000145632|ENSG00000145632	ENST00000274289;ENST00000537944|ENST00000442330	T|.	0.66280|.	-0.2|.	5.28|5.28	4.42|4.42	0.53409|0.53409	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53769|0.53769	0.1817|0.1817	N|N	0.21545|0.21545	0.675|0.675	0.80722|0.80722	D|D	1|1	B|.	0.24258|.	0.1|.	B|.	0.21917|.	0.037|.	T|T	0.58831|0.58831	-0.7567|-0.7567	10|6	0.02654|0.66056	T|D	1|0.02	-19.8084|-19.8084	13.6948|13.6948	0.62572|0.62572	0.0739:0.0:0.9261:0.0|0.0739:0.0:0.9261:0.0	.|.	363|.	Q9NYY3|.	PLK2_HUMAN|.	L|Y	363|349	ENSP00000274289:F363L|.	ENSP00000274289:F363L|ENSP00000401861:S349Y	F|S	-|-	3|2	2|0	PLK2|PLK2	57788596|57788596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.380000|5.380000	0.66202|0.66202	1.227000|1.227000	0.43598|0.43598	0.655000|0.655000	0.94253|0.94253	TTC|TCT		0.383	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		T	57752839	G	T	57752839	3	4	61	1	0	0	0	0	1	0	0	0	12127	933	33	2	996	2	PLK2	5	57752839	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	938	57752839	123162421	3839	11824										
GAPT	202309	broad.mit.edu	37	chr5	57790676	57790676	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtcctcccaaagctaaaGgaaaaaccgataaggaacta	8	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:57790676G>T	ENST00000396776.2	+	3	775	c.313G>T	c.(313-315)Gga>Tga	p.G105*	GAPT_ENST00000318469.2_Nonsense_Mutation_p.G105*	NM_152687.2	NP_689900.1	Q8N292	GAPT_HUMAN	GRB2-binding adaptor protein, transmembrane	105					B cell activation (GO:0042113)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G105*(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						CAAAGCTAAAGGAAAAACCGA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											76	77	76					5																	57790676		2203	4300	6503	57826433	SO:0001587	stop_gained	202309			AK090960	CCDS3975.1	5q11.2	2011-11-01	2008-10-07	2008-10-07	ENSG00000175857	ENSG00000175857			26588	protein-coding gene	gene with protein product	"GRB2-binding transmembrane adaptor"		"chromosome 5 open reading frame 29"	C5orf29			Standard	NM_152687		Approved	FLJ33641	uc003jro.1	Q8N292	OTTHUMG00000131219	ENST00000396776.2:c.313G>T	5.37:g.57790676G>T	ENSP00000379997:p.Gly105*		57826433		Nonsense_Mutation	SNP	ENST00000396776.2	37	CCDS3975.1	.	.	.	.	.	.	.	.	.	.	G	33	5.290918	0.95546	.	.	ENSG00000175857	ENST00000396776;ENST00000318469	.	.	.	5.05	1.3	0.21679	.	1.266820	0.05354	N	0.532383	.	.	.	.	.	.	0.53688	D	0.999974	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-2.6529	7.2771	0.26290	0.3578:0.0:0.6422:0.0	.	.	.	.	X	105	.	ENSP00000323075:G105X	G	+	1	0	GAPT	57826433	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.044000	0.13992	0.120000	0.18254	-0.150000	0.13652	GGA		0.398	GAPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253963.1	NM_152687		T	57790676	G	T	57790676	4	4	61	1	0	0	0	0	0	1	0	0	6258	1001	35	2	315	2	GAPT	5	57790676	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37837	57790676	123124584	3840	11825										
RAB3C	115827	broad.mit.edu	37	chr5	57913641	57913641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtcagcacagttgggatcGatttcaaagtaaaaactgta	9	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:57913641G>A	ENST00000282878.4	+	2	365	c.196G>A	c.(196-198)Gat>Aat	p.D66N		NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	66					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.D66N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		AGTTGGGATCGATTTCAAAGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	52	54					5																	57913641		2203	4299	6502	57949398	SO:0001583	missense	115827			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"RAB, member RAS oncogene"	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.196G>A	5.37:g.57913641G>A	ENSP00000282878:p.Asp66Asn		57949398		Missense_Mutation	SNP	ENST00000282878.4	37	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	G	35	5.486112	0.96323	.	.	ENSG00000152932	ENST00000282878	D	0.83335	-1.71	5.7	5.7	0.88788	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.91600	0.7346	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.91959	0.5577	10	0.87932	D	0	-21.409	19.8247	0.96612	0.0:0.0:1.0:0.0	.	66	Q96E17	RAB3C_HUMAN	N	66	ENSP00000282878:D66N	ENSP00000282878:D66N	D	+	1	0	RAB3C	57949398	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	9.869000	0.99810	2.696000	0.92011	0.655000	0.94253	GAT		0.408	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453		A	57913641	G	A	57913641	3	1	61	1	0	0	0	0	1	0	0	0	12970	1058	37	1	202	1	RAB3C	5	57913641	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122965	57913641	123001619	3841	11826										
RAB3C	115827	broad.mit.edu	37	chr5	58147050	58147050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcaagcagacatttgagCgccttgtggatatcatctgc	10	9	3	2	rs199852469		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:58147050C>T	ENST00000282878.4	+	5	725	c.556C>T	c.(556-558)Cgc>Tgc	p.R186C	CTD-2176I21.2_ENST00000510198.1_RNA	NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	186					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.R186C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		GACATTTGAGCGCCTTGTGGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	148	135	140		556	5.9	1	5		140	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RAB3C	NM_138453.2	180	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	186/228	58147050	2,13004	2203	4300	6503	58182807	SO:0001583	missense	115827			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"RAB, member RAS oncogene"	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.556C>T	5.37:g.58147050C>T	ENSP00000282878:p.Arg186Cys		58182807		Missense_Mutation	SNP	ENST00000282878.4	37	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.187296	0.78789	2.27E-4	1.16E-4	ENSG00000152932	ENST00000282878	T	0.80123	-1.34	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000013	T	0.75989	0.3925	L	0.38953	1.18	0.80722	D	1	B	0.34147	0.438	B	0.31751	0.135	T	0.75701	-0.3226	10	0.62326	D	0.03	-10.4721	20.3539	0.98825	0.0:1.0:0.0:0.0	.	186	Q96E17	RAB3C_HUMAN	C	186	ENSP00000282878:R186C	ENSP00000282878:R186C	R	+	1	0	RAB3C	58182807	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.946000	0.63576	2.826000	0.97356	0.655000	0.94253	CGC		0.433	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453		T	58147050	C	T	58147050	3	4	61	1	0	0	0	0	1	0	0	0	12970	768	27	1	574	1	RAB3C	5	58147050	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233409	58147050	122768210	3842	11827										
ERCC8	1161	broad.mit.edu	37	chr5	60200628	60200628	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttacaaacctgctaccaAacagtgcttggtggagactg	9	11	0	1	rs561001438		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:60200628A>G	ENST00000265038.5	-	5	514	c.472T>C	c.(472-474)Ttg>Ctg	p.L158L	ERCC8_ENST00000543101.1_Intron|ERCC8_ENST00000426742.2_Silent_p.L100L|ERCC8_ENST00000462279.1_5'UTR	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	158					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)	p.L158L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CCTGCTACCAAACAGTGCTTG	0.328													A|||	1	0.000199681	0	0	5008	,	,		8314	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	5											119	120	119					5																	60200628		2203	4298	6501	60236385	SO:0001819	synonymous_variant	1161			U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"WD repeat domain containing"	3439	protein-coding gene	gene with protein product		609412	"Cockayne syndrome 1 (classical)", "excision repair cross-complementing rodent repair deficiency, complementation group 8"	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.472T>C	5.37:g.60200628A>G			60236385	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	37	CCDS3978.1																																																																																				0.328	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082		G	60200628	A	G	60200628	2	3	61	1	0	0	0	0	0	0	0	1	5232	11	1	4		4	ERCC8	5	60200628	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2053578	60200628	120714632	3843	11828										
KIF2A	3796	broad.mit.edu	37	chr5	61653555	61653555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgtgtgtgtaagaaaacGaccactcaataaaaaaggta	9	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:61653555G>A	ENST00000401507.3	+	8	1003	c.692G>A	c.(691-693)cGa>cAa	p.R231Q	KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000407818.3_Missense_Mutation_p.R231Q|KIF2A_ENST00000506857.1_Missense_Mutation_p.R185Q|KIF2A_ENST00000381103.2_Missense_Mutation_p.R211Q	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	231	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R231Q(1)|p.R204Q(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		GTAAGAAAACGACCACTCAAT	0.254																																																2	Substitution - Missense(2)	large_intestine(2)	5											78	82	81					5																	61653555		2201	4297	6498	61689312	SO:0001583	missense	3796			BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.692G>A	5.37:g.61653555G>A	ENSP00000385622:p.Arg231Gln		61689312	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Missense_Mutation	SNP	ENST00000401507.3	37	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	G	34	5.377430	0.95945	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000514082;ENST00000407818;ENST00000506857	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	5.3	5.3	0.74995	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.96306	0.8795	H	0.99507	4.6	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98421	1.0577	10	0.87932	D	0	.	18.9318	0.92570	0.0:0.0:1.0:0.0	.	231;231;231;211	B4DM85;O00139-4;O00139;E9PB70	.;.;KIF2A_HUMAN;.	Q	231;211;212;231;185	ENSP00000385622:R231Q;ENSP00000370493:R211Q;ENSP00000423542:R212Q;ENSP00000385000:R231Q;ENSP00000423772:R185Q	ENSP00000370493:R211Q	R	+	2	0	KIF2A	61689312	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.484000	0.97940	2.459000	0.83118	0.585000	0.79938	CGA		0.254	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520		A	61653555	G	A	61653555	3	1	61	1	0	0	0	0	1	0	0	0	8318	1058	37	1	722	1	KIF2A	5	61653555	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1452927	61653555	119261705	3844	11829										
IPO11	51194	broad.mit.edu	37	chr5	61781275	61781275	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaggaggagattcttggAaatatagtttgagggtaagt	13	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:61781275A>G	ENST00000325324.6	+	12	1373	c.1204A>G	c.(1204-1206)Aaa>Gaa	p.K402E	KIF2A_ENST00000509663.2_Intron|IPO11_ENST00000409296.3_Missense_Mutation_p.K442E	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	402					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.K402E(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		AGATTCTTGGAAATATAGTTT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	111	105					5																	61781275		2203	4300	6503	61817032	SO:0001583	missense	51194			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.1204A>G	5.37:g.61781275A>G	ENSP00000316651:p.Lys402Glu		61817032	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552352	0.86127	.	.	ENSG00000086200	ENST00000325324;ENST00000409296	T;T	0.33654	1.4;1.4	5.21	5.21	0.72293	Armadillo-like helical (1);Armadillo-type fold (1);	0.047137	0.85682	D	0.000000	T	0.42607	0.1210	L	0.37850	1.14	0.80722	D	1	P;D	0.76494	0.916;0.999	P;D	0.64410	0.721;0.925	T	0.25779	-1.0122	10	0.02654	T	1	.	14.752	0.69533	1.0:0.0:0.0:0.0	.	442;402	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	E	402;442	ENSP00000316651:K402E;ENSP00000386992:K442E	ENSP00000316651:K402E	K	+	1	0	IPO11	61817032	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.183000	0.89700	1.962000	0.57031	0.528000	0.53228	AAA		0.294	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		G	61781275	A	G	61781275	3	3	61	1	0	0	0	0	1	0	0	0	7814	247	9	4	1370	4	IPO11	5	61781275	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	127720	61781275	119133985	3845	11830										
RNF180	285671	broad.mit.edu	37	chr5	63509432	63509432	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcctttctgtggggcccgTttagggggctttaattttgt	13	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:63509432T>C	ENST00000389100.4	+	4	351	c.279T>C	c.(277-279)cgT>cgC	p.R93R	RNF180_ENST00000381081.2_Intron|RNF180_ENST00000296615.6_Silent_p.R93R	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	93					adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R93R(1)		breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		GTGGGGCCCGTTTAGGGGGCT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											133	147	142					5																	63509432		2201	4300	6501	63545188	SO:0001819	synonymous_variant	285671			AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"RING-type (C3HC4) zinc fingers"	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.279T>C	5.37:g.63509432T>C			63545188	Q0JSU3|Q495A8|Q8NBD1	Silent	SNP	ENST00000389100.4	37	CCDS47219.1																																																																																				0.448	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		C	63509432	T	C	63509432	2	2	61	1	0	0	0	0	0	0	0	1	13501	1712	60	4		4	RNF180	5	63509432	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1728157	63509432	117405828	3846	11831										
SFRS12IP1	285672	broad.mit.edu	37	chr5	64020223	64020223	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctcagttactttctggaGaattcagaactattaggtgt	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64020223G>T	ENST00000513458.4	-	5	623	c.456C>A	c.(454-456)ttC>ttA	p.F152L		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	152					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.F152L(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						ACTTTCTGGAGAATTCAGAAC	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	5											35	36	35					5																	64020223		2203	4296	6499	64055979	SO:0001583	missense	285672			AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"p18 splicing regulatory protein"		"SFRS12-interacting protein 1"	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.456C>A	5.37:g.64020223G>T	ENSP00000427401:p.Phe152Leu		64055979	Q32NC8	Missense_Mutation	SNP	ENST00000513458.4	37	CCDS34171.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.257066	0.39896	.	.	ENSG00000153006	ENST00000513458	.	.	.	6.07	2.18	0.27775	.	0.855292	0.10954	N	0.615795	T	0.15089	0.0364	N	0.08118	0	0.23056	N	0.998366	B	0.02656	0.0	B	0.01281	0.0	T	0.32052	-0.9921	9	0.13108	T	0.6	3.5401	3.5782	0.07942	0.2817:0.0:0.5436:0.1747	.	152	Q8N9Q2	SR1IP_HUMAN	L	152	.	ENSP00000427401:F152L	F	-	3	2	SREK1IP1	64055979	0.997000	0.39634	0.997000	0.53966	0.935000	0.57460	0.578000	0.23773	0.392000	0.25172	0.655000	0.94253	TTC		0.294	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		T	64020223	G	T	64020223	3	4	61	1	0	0	0	0	1	0	0	0	14205	933	33	2	15	2	SFRS12IP1	5	64020223	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	510791	64020223	116895037	3847	11832										
ADAMTS6	11174	broad.mit.edu	37	chr5	64466507	64466507	+	5'UTR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgcattgatggaggccGaacagtttctagacagtcac	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64466507G>T	ENST00000314351.5	-	0	840							Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6							proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R232R(1)|p.R1061R(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		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)		GATGGAGGCCGAACAGTTTCT	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	5											96	84	88					5																	64466507		2203	4300	6503	64502263	SO:0001623	5_prime_UTR_variant	11174			AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000314351.5:c.-482C>A	5.37:g.64466507G>T			64502263	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000314351.5	37																																																																																					0.488	ADAMTS6-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000157334.2	NM_197941		T	64466507	G	T	64466507	1	4	61	0	1	0	0	0	0	0	0	0	270	1057	37	2		2	ADAMTS6	5	64466507	5'UTR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	446284	64466507	116448753	3848	11833										
ADAMTS6	11174	broad.mit.edu	37	chr5	64520778	64520778	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagtgaatcattgaagaAcccttcaatggcatcacatg	10	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64520778A>G								ADAMTS6 (26186 upstream) : ADAMTS6 (72256 downstream)														p.F722L(1)									TCATTGAAGAACCCTTCAATG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	87	93					5																	64520778		2203	4300	6503	64556534	SO:0001628	intergenic_variant	11174																															5.37:g.64520778A>G			64556534		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	A	12.99	2.104231	0.37145	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680	T;T	0.47528	0.84;0.84	5.55	5.55	0.83447	ADAM-TS Spacer 1 (1);	0.048832	0.85682	D	0.000000	T	0.16214	0.0390	N	0.00332	-1.63	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.26467	-1.0102	10	0.10902	T	0.67	.	15.7093	0.77612	1.0:0.0:0.0:0.0	.	722;722	D6R9L6;Q9UKP5	.;ATS6_HUMAN	L	722;672;722	ENSP00000370443:F722L;ENSP00000423551:F722L	ENSP00000261306:F672L	F	-	1	0	ADAMTS6	64556534	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.918000	0.69996	2.109000	0.64355	0.455000	0.32223	TTC	0	0.507									G	64520778	A	G	64520778	1	3	61	0	1	0	0	0	0	0	0	0	270	43	2	4		4	ADAMTS6	5	64520778	IGR	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	54271	64520778	116394482	3849	11834										
ADAMTS6	11174	broad.mit.edu	37	chr5	64625262	64625262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggccaatgtcttcattaAtgctgcagctcctttcaggc	8	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64625262A>G	ENST00000536360.1	-	9	1979	c.1166T>C	c.(1165-1167)aTt>aCt	p.I389T				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	389	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.I389T(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		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)		GTCTTCATTAATGCTGCAGCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											89	78	82					5																	64625262		2203	4300	6503	64661018	SO:0001583	missense	11174			AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.1166T>C	5.37:g.64625262A>G	ENSP00000440995:p.Ile389Thr		64661018	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Missense_Mutation	SNP	ENST00000536360.1	37		.	.	.	.	.	.	.	.	.	.	A	18.27	3.586958	0.66105	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	T;T;T	0.70399	-0.48;-0.48;-0.48	5.89	5.89	0.94794	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.84302	0.5442	M	0.76938	2.355	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.77557	0.99;0.981	D	0.86290	0.1673	10	0.87932	D	0	.	15.9526	0.79855	1.0:0.0:0.0:0.0	.	389;389	D6R9L6;Q9UKP5	.;ATS6_HUMAN	T	389	ENSP00000370443:I389T;ENSP00000423551:I389T;ENSP00000440995:I389T	ENSP00000261306:I389T	I	-	2	0	ADAMTS6	64661018	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.932000	0.92897	2.251000	0.74343	0.482000	0.46254	ATT		0.423	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		G	64625262	A	G	64625262	3	3	61	1	0	0	0	0	1	0	0	0	270	101	4	4	2255	4	ADAMTS6	5	64625262	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	104484	64625262	116289998	3850	11835										
PPWD1	23398	broad.mit.edu	37	chr5	64859300	64859300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgctgggttggacctttaCctgtggaggcaacactggcc	14	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64859300C>T	ENST00000261308.5	+	1	235	c.163C>T	c.(163-165)Cct>Tct	p.P55S	PPWD1_ENST00000535264.1_Silent_p.Y12Y|CENPK_ENST00000514814.1_5'Flank|CENPK_ENST00000396679.1_5'Flank|CENPK_ENST00000510693.1_5'Flank|CENPK_ENST00000508421.1_5'Flank|CENPK_ENST00000506282.2_5'Flank|CENPK_ENST00000510354.1_5'Flank|PPWD1_ENST00000538977.1_5'UTR	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	55					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.P55S(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TGGACCTTTACCTGTGGAGGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											76	65	69					5																	64859300		2203	4300	6503	64895056	SO:0001583	missense	23398			AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.163C>T	5.37:g.64859300C>T	ENSP00000261308:p.Pro55Ser		64895056	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	37	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220912	0.95139	.	.	ENSG00000113593	ENST00000261308	T	0.63744	-0.06	4.85	4.85	0.62838	.	0.053759	0.85682	D	0.000000	T	0.80182	0.4576	M	0.87682	2.9	0.80722	D	1	D	0.67145	0.996	P	0.60415	0.874	D	0.83369	0.0006	10	0.56958	D	0.05	.	18.5132	0.90925	0.0:1.0:0.0:0.0	.	55	Q96BP3	PPWD1_HUMAN	S	55	ENSP00000261308:P55S	ENSP00000261308:P55S	P	+	1	0	PPWD1	64895056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.018000	0.70811	2.658000	0.90341	0.591000	0.81541	CCT		0.552	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		T	64859300	C	T	64859300	3	4	61	1	0	0	0	0	1	0	0	0	12448	507	18	3	165	3	PPWD1	5	64859300	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	234038	64859300	116055960	3851	11836										
TRIM23	373	broad.mit.edu	37	chr5	64887748	64887748	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgagtagttcagtgatttCttctactgacagtgctccag	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64887748C>A	ENST00000231524.9	-	11	1944	c.1573G>T	c.(1573-1575)Gaa>Taa	p.E525*	TRIM23_ENST00000274327.7_Nonsense_Mutation_p.E525*|TRIM23_ENST00000381018.3_Nonsense_Mutation_p.E525*	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	525	ARF-like.				GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E525*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TCAGTGATTTCTTCTACTGAC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											83	81	82					5																	64887748		2203	4300	6503	64923504	SO:0001587	stop_gained	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.1573G>T	5.37:g.64887748C>A	ENSP00000231524:p.Glu525*		64923504	Q9BZY4|Q9BZY5	Nonsense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	C	40	8.081703	0.98643	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	.	.	.	5.71	5.71	0.89125	.	0.050018	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.8647	0.96799	0.0:1.0:0.0:0.0	.	.	.	.	X	525	.	ENSP00000231524:E525X	E	-	1	0	TRIM23	64923504	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.762000	0.85270	2.684000	0.91462	0.561000	0.74099	GAA		0.373	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		A	64887748	C	A	64887748	4	1	61	1	0	0	0	0	0	1	0	0	16537	922	32	2	222	2	TRIM23	5	64887748	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28448	64887748	116027512	3852	11837										
TRIM23	373	broad.mit.edu	37	chr5	64893000	64893000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttggtccaatgtgaactCgattatcctacaatttaaat	5	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64893000C>T	ENST00000231524.9	-	8	1558	c.1187G>A	c.(1186-1188)cGa>cAa	p.R396Q	TRIM23_ENST00000274327.7_Missense_Mutation_p.R396Q|TRIM23_ENST00000381018.3_Missense_Mutation_p.R396Q	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	396	ARF-like.				GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R396Q(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AATGTGAACTCGATTATCCTA	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	5											83	81	82					5																	64893000		2203	4300	6503	64928756	SO:0001583	missense	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.1187G>A	5.37:g.64893000C>T	ENSP00000231524:p.Arg396Gln		64928756	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	C	34	5.319483	0.95682	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.74106	-0.75;-0.74;-0.81	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.84902	0.5575	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.91635	0.979;0.999;0.996	D	0.84563	0.0651	10	0.66056	D	0.02	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	396;396;396	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	Q	396	ENSP00000231524:R396Q;ENSP00000370406:R396Q;ENSP00000274327:R396Q	ENSP00000231524:R396Q	R	-	2	0	TRIM23	64928756	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	7.487000	0.81328	2.833000	0.97629	0.585000	0.79938	CGA		0.318	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64893000	C	T	64893000	3	4	61	1	0	0	0	0	1	0	0	0	16537	884	31	1	620	1	TRIM23	5	64893000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5252	64893000	116022260	3853	11838										
TRIM23	373	broad.mit.edu	37	chr5	64905248	64905248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagatcataaaaataagctCgaatacatgaccgggcattc	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64905248C>T	ENST00000231524.9	-	6	1237	c.866G>A	c.(865-867)cGa>cAa	p.R289Q	TRIM23_ENST00000274327.7_Missense_Mutation_p.R289Q|TRIM23_ENST00000381018.3_Missense_Mutation_p.R289Q|TRIM23_ENST00000508808.1_5'UTR	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	289					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R289Q(3)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AAAATAAGCTCGAATACATGA	0.353																																																3	Substitution - Missense(3)	large_intestine(3)	5											85	78	80					5																	64905248		2203	4300	6503	64941004	SO:0001583	missense	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.866G>A	5.37:g.64905248C>T	ENSP00000231524:p.Arg289Gln		64941004	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	C	35	5.540007	0.96474	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.74632	-0.78;-0.78;-0.86	5.39	5.39	0.77823	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77805	0.4185	M	0.61703	1.905	0.80722	D	1	D;D;D	0.61697	0.957;0.99;0.975	B;P;B	0.46718	0.246;0.525;0.427	T	0.80216	-0.1474	10	0.56958	D	0.05	.	19.5154	0.95162	0.0:1.0:0.0:0.0	.	289;289;289	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	Q	289	ENSP00000231524:R289Q;ENSP00000370406:R289Q;ENSP00000274327:R289Q	ENSP00000231524:R289Q	R	-	2	0	TRIM23	64941004	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.445000	0.80570	2.685000	0.91497	0.655000	0.94253	CGA		0.353	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64905248	C	T	64905248	3	4	61	1	0	0	0	0	1	0	0	0	16537	884	31	1	949	1	TRIM23	5	64905248	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12248	64905248	116010012	3854	11839										
TRIM23	373	broad.mit.edu	37	chr5	64910015	64910015	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagctccaataaagcaaaAttttttttcaatccccagac	3	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64910015A>T	ENST00000231524.9	-	3	647	c.276T>A	c.(274-276)aaT>aaA	p.N92K	TRIM23_ENST00000274327.7_Missense_Mutation_p.N92K|TRIM23_ENST00000381018.3_Missense_Mutation_p.N92K	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	92					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N92K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		ATAAAGCAAAATTTTTTTTCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											100	106	104					5																	64910015		2203	4300	6503	64945771	SO:0001583	missense	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.276T>A	5.37:g.64910015A>T	ENSP00000231524:p.Asn92Lys		64945771	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831941	0.71258	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	D;D;D	0.94862	-3.54;-3.54;-3.54	5.04	3.82	0.43975	.	0.000000	0.85682	D	0.000000	D	0.97867	0.9299	H	0.97158	3.95	0.53688	D	0.999976	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.994;0.998;0.998	D	0.97112	0.9805	10	0.87932	D	0	.	9.0434	0.36331	0.7895:0.0:0.2105:0.0	.	92;92;92	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	K	92	ENSP00000231524:N92K;ENSP00000370406:N92K;ENSP00000274327:N92K	ENSP00000231524:N92K	N	-	3	2	TRIM23	64945771	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.762000	0.38451	0.717000	0.32145	0.477000	0.44152	AAT		0.358	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64910015	A	T	64910015	3	4	61	1	0	0	0	0	1	0	0	0	16537	98	4	5	1551	5	TRIM23	5	64910015	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4767	64910015	116005245	3855	11840										
C5orf44	80006	broad.mit.edu	37	chr5	64960393	64960393	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatatgaatatgatgacatCgcacaagtctgtgtggtatc	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64960393C>T	ENST00000399438.3	+	13	1554	c.1209C>T	c.(1207-1209)atC>atT	p.I403I	TRAPPC13_ENST00000438419.2_Silent_p.I404I|TRAPPC13_ENST00000231526.4_Silent_p.I397I|TRAPPC13_ENST00000505553.1_Silent_p.I398I|TRAPPC13_ENST00000545191.1_Silent_p.I405I	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	403				I -> V (in Ref. 5; AAI42995). {ECO:0000305}.				p.I403I(2)									ATGATGACATCGCACAAGTCT	0.373																																																2	Substitution - coding silent(2)	large_intestine(2)	5											83	77	79					5																	64960393		1884	4111	5995	64996149	SO:0001819	synonymous_variant	80006				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"Trs65-related"		"chromosome 5 open reading frame 44"	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.1209C>T	5.37:g.64960393C>T			64996149	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Silent	SNP	ENST00000399438.3	37	CCDS47222.1																																																																																				0.373	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941		T	64960393	C	T	64960393	2	4	61	1	0	0	0	0	0	0	0	1	2309	874	31	1		1	C5orf44	5	64960393	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50378	64960393	115954867	3856	11841										
SGTB	54557	broad.mit.edu	37	chr5	64981265	64981265	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacaatcctttatcgcatCtgtgtagtgacctaatttgc	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:64981265C>A	ENST00000381007.4	-	6	644	c.409G>T	c.(409-411)Gat>Tat	p.D137Y		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	137								p.D137Y(1)		large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		TTTATCGCATCTGTGTAGTGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											196	171	180					5																	64981265		2203	4300	6503	65017021	SO:0001583	missense	54557			AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.409G>T	5.37:g.64981265C>A	ENSP00000370395:p.Asp137Tyr		65017021		Missense_Mutation	SNP	ENST00000381007.4	37	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871593	0.72065	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	T;T	0.60797	0.16;0.16	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.046960	0.85682	D	0.000000	T	0.60130	0.2245	L	0.51853	1.615	0.58432	D	0.999997	P	0.42556	0.783	B	0.43916	0.436	T	0.61019	-0.7147	10	0.46703	T	0.11	-20.224	19.4332	0.94779	0.0:1.0:0.0:0.0	.	137	Q96EQ0	SGTB_HUMAN	Y	137	ENSP00000370395:D137Y;ENSP00000421447:D137Y	ENSP00000370395:D137Y	D	-	1	0	SGTB	65017021	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.433000	0.80362	2.659000	0.90383	0.655000	0.94253	GAT		0.388	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072		A	64981265	C	A	64981265	3	1	61	1	0	0	0	0	1	0	0	0	14263	913	32	2	529	2	SGTB	5	64981265	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20872	64981265	115933995	3857	11842										
NLN	57486	broad.mit.edu	37	chr5	65054652	65054652	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtagaagtaaagtatatAggtgggtcagatgcagaagc	14	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:65054652A>G	ENST00000380985.5	+	2	478	c.300A>G	c.(298-300)atA>atG	p.I100M	NLN_ENST00000502464.1_Intron	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	100						mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)	p.I100M(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		TAAAGTATATAGGTGGGTCAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											120	111	114					5																	65054652		2203	4300	6503	65090408	SO:0001630	splice_region_variant	57486			AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"angiotensin binding protein"	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.301+1A>G	5.37:g.65054652A>G			65090408	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	.	.	.	.	.	.	.	.	.	.	A	9.907	1.208427	0.22205	.	.	ENSG00000123213	ENST00000380985;ENST00000340159	T	0.50277	0.75	5.5	5.5	0.81552	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.222293	0.46145	D	0.000318	T	0.40171	0.1106	L	0.36672	1.1	0.80722	D	1	B;P	0.47962	0.002;0.903	B;B	0.39562	0.004;0.303	T	0.43114	-0.9411	10	0.66056	D	0.02	-30.227	15.622	0.76813	1.0:0.0:0.0:0.0	.	100;100	Q9BYT8;Q9BQD0	NEUL_HUMAN;.	M	100	ENSP00000370372:I100M	ENSP00000339283:I100M	I	+	3	3	NLN	65090408	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	1.785000	0.38684	2.102000	0.63906	0.533000	0.62120	ATA		0.408	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		Missense_Mutation	G	65054652	A	G	65054652	5	3	61	1	0	0	0	0	0	0	1	0	10498	434	15	4	306	4	NLN	5	65054652	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73387	65054652	115860608	3858	11843										
NLN	57486	broad.mit.edu	37	chr5	65105927	65105927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcttcataccaacacatCgctggatgctgcaagtgaat	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:65105927C>T	ENST00000380985.5	+	11	1956	c.1778C>T	c.(1777-1779)tCg>tTg	p.S593L	NLN_ENST00000502464.1_Missense_Mutation_p.S489L	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	593						mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)	p.S593L(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		ACCAACACATCGCTGGATGCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											118	113	115					5																	65105927		2203	4300	6503	65141683	SO:0001583	missense	57486			AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"angiotensin binding protein"	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1778C>T	5.37:g.65105927C>T	ENSP00000370372:p.Ser593Leu		65141683	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.422553	0.25639	.	.	ENSG00000123213	ENST00000380985;ENST00000502464;ENST00000340159;ENST00000511299	T;T;T	0.12147	2.71;2.71;2.71	5.9	5.03	0.67393	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.465778	0.26474	N	0.024167	T	0.13970	0.0338	L	0.33339	1.005	0.09310	N	0.999992	B;B	0.21753	0.06;0.06	B;B	0.26202	0.067;0.067	T	0.17198	-1.0377	10	0.62326	D	0.03	-1.1605	15.0887	0.72177	0.0:0.9322:0.0:0.0678	.	270;593	Q96K48;Q9BYT8	.;NEUL_HUMAN	L	593;489;593;303	ENSP00000370372:S593L;ENSP00000423214:S489L;ENSP00000427417:S303L	ENSP00000339283:S593L	S	+	2	0	NLN	65141683	0.005000	0.15991	0.003000	0.11579	0.205000	0.24178	1.895000	0.39778	1.509000	0.48786	-0.152000	0.13540	TCG		0.398	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1			T	65105927	C	T	65105927	3	4	61	1	0	0	0	0	1	0	0	0	10498	893	31	1	1820	1	NLN	5	65105927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51275	65105927	115809333	3859	11844										
ERBB2IP	55914	broad.mit.edu	37	chr5	65310528	65310528	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaatattagagcttagaGaaaaccagttaaaaatgttg	7	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:65310528G>A	ENST00000284037.5	+	7	897	c.508G>A	c.(508-510)Gaa>Aaa	p.E170K	ERBB2IP_ENST00000380943.2_Missense_Mutation_p.E170K|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.E170K|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.E170K|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.E170K|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.E170K|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.E170K|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.E170K|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.E170K|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.E170K	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	170					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)	p.E170K(1)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		AGAGCTTAGAGAAAACCAGTT	0.209																																																1	Substitution - Missense(1)	large_intestine(1)	5											26	27	27					5																	65310528		2155	4227	6382	65346284	SO:0001583	missense	55914				CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.508G>A	5.37:g.65310528G>A	ENSP00000284037:p.Glu170Lys		65346284	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285082	0.95517	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94;2.94;2.94;2.94;2.94;2.94	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	L	0.31371	0.925	0.80722	D	1	P;D;D;D;P;D;D;D	0.76494	0.95;0.986;0.997;0.999;0.852;0.999;0.992;0.998	D;P;D;D;P;D;D;D	0.83275	0.925;0.857;0.98;0.99;0.545;0.996;0.933;0.919	T	0.01165	-1.1431	10	0.87932	D	0	.	19.6673	0.95898	0.0:0.0:1.0:0.0	.	170;170;170;170;170;170;170;170	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	K	170	ENSP00000284037:E170K;ENSP00000370330:E170K;ENSP00000397833:E170K;ENSP00000370326:E170K;ENSP00000370323:E170K;ENSP00000370322:E170K;ENSP00000370325:E170K;ENSP00000422766:E170K;ENSP00000426632:E170K;ENSP00000422015:E170K	ENSP00000284037:E170K	E	+	1	0	ERBB2IP	65346284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.627000	0.90974	2.721000	0.93114	0.650000	0.86243	GAA		0.209	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65310528	G	A	65310528	3	1	61	1	0	0	0	0	1	0	0	0	5220	943	33	3	526	3	ERBB2IP	5	65310528	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	204601	65310528	115604732	3860	11845										
SFRS12	140890	broad.mit.edu	37	chr5	65466607	65466607	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagagagagaacgggaaaAagagcatgagaaggatcgag	16	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:65466607A>C	ENST00000380918.3	+	10	1628	c.968A>C	c.(967-969)aAa>aCa	p.K323T	SREK1_ENST00000334121.6_Missense_Mutation_p.K439T|SREK1_ENST00000284041.3_3'UTR	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1	323	Arg/Glu/Lys/Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K323T(1)		breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						gaacgggaaaaagagcatgag	0.418																																					GBM(10;31 347 27684 38976 41583)											1	Substitution - Missense(1)	large_intestine(1)	5											97	97	97					5																	65466607		2203	4298	6501	65502363	SO:0001583	missense	140890			AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"RNA binding motif (RRM) containing"	17882	protein-coding gene	gene with protein product	"serine-arginine-rich splicing regulatory protein 508"	609268	"splicing factor, arginine/serine-rich 12"	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.968A>C	5.37:g.65466607A>C	ENSP00000370305:p.Lys323Thr		65502363	A4FTW3|Q2M1J0|Q86X37	Missense_Mutation	SNP	ENST00000380918.3	37	CCDS3991.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.185907	0.57909	.	.	ENSG00000153914	ENST00000334121;ENST00000537482;ENST00000380918	T;T	0.45276	0.9;0.9	5.37	4.23	0.50019	.	0.394502	0.24191	N	0.040716	T	0.26738	0.0654	L	0.27053	0.805	0.29207	N	0.874847	P;P;P	0.52316	0.952;0.952;0.718	B;B;B	0.39617	0.305;0.305;0.217	T	0.17289	-1.0374	10	0.45353	T	0.12	.	9.064	0.36451	0.9163:0.0:0.0837:0.0	.	323;323;439	Q69YM5;Q8WXA9;Q8WXA9-2	.;SREK1_HUMAN;.	T	439;439;323	ENSP00000334538:K439T;ENSP00000370305:K323T	ENSP00000334538:K439T	K	+	2	0	SREK1	65502363	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	1.996000	0.40776	2.037000	0.60232	0.519000	0.50382	AAA		0.418	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1	NM_001077199		C	65466607	A	C	65466607	3	2	61	1	0	0	0	0	1	0	0	0	14204	14	1	4	1350	4	SFRS12	5	65466607	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	156079	65466607	115448653	3861	11846										
MAST4	375449	broad.mit.edu	37	chr5	66350237	66350237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctttttgatagttgccGaacaagcaaccggaaaagct	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66350237G>A	ENST00000403625.2	+	5	975	c.680G>A	c.(679-681)cGa>cAa	p.R227Q	MAST4_ENST00000261569.7_Missense_Mutation_p.R33Q|MAST4_ENST00000403666.1_Missense_Mutation_p.R38Q|MAST4_ENST00000404260.3_Missense_Mutation_p.R227Q|MAST4_ENST00000490016.2_Missense_Mutation_p.R38Q|MAST4_ENST00000405643.1_Missense_Mutation_p.R45Q	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	227						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R227Q(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GATAGTTGCCGAACAAGCAAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	68	69					5																	66350237		1883	4100	5983	66385993	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.680G>A	5.37:g.66350237G>A	ENSP00000385727:p.Arg227Gln		66385993	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	33	5.288148	0.95517	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000432426;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T	0.74106	-0.32;-0.32;1.26;-0.79;-0.81;-0.65	5.77	5.77	0.91146	.	0.225364	0.25089	U	0.033232	D	0.86012	0.5831	M	0.69358	2.11	0.32854	D	0.507104	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;P	0.78314	0.941;0.987;0.973;0.991;0.716	D	0.88093	0.2814	10	0.72032	D	0.01	-4.4909	19.9894	0.97361	0.0:0.0:1.0:0.0	.	45;227;33;38;38	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	Q	227;227;38;38;45;18;45;33;33;33	ENSP00000385048:R227Q;ENSP00000385727:R227Q;ENSP00000421739:R38Q;ENSP00000384313:R38Q;ENSP00000384099:R45Q;ENSP00000261569:R33Q	ENSP00000261569:R33Q	R	+	2	0	MAST4	66385993	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.398000	0.90195	2.726000	0.93360	0.561000	0.74099	CGA		0.423	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66350237	G	A	66350237	3	1	61	1	0	0	0	0	1	0	0	0	9357	1058	37	1	828	1	MAST4	5	66350237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	883630	66350237	114565023	3862	11847										
MAST4	375449	broad.mit.edu	37	chr5	66396356	66396356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaacatttctgtaccaccGaaagcatcgccactgagaac	6	13	1	1	rs578052517	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66396356G>A	ENST00000403625.2	+	8	1301	c.1006G>A	c.(1006-1008)Gaa>Aaa	p.E336K	MAST4_ENST00000261569.7_Missense_Mutation_p.E142K|MAST4_ENST00000403666.1_Missense_Mutation_p.E147K|MAST4_ENST00000404260.3_Missense_Mutation_p.E339K|MAST4_ENST00000490016.2_Missense_Mutation_p.E147K|MAST4_ENST00000405643.1_Missense_Mutation_p.E157K	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	339						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.E339K(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTGTACCACCGAAAGCATCGC	0.498													G|||	2	0.000399361	0	0	5008	,	,		18988	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											98	97	97					5																	66396356		2083	4221	6304	66432112	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.1006G>A	5.37:g.66396356G>A	ENSP00000385727:p.Glu336Lys		66432112	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	36	5.868118	0.97043	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26;1.26;1.26	6.07	6.07	0.98685	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.302177	0.26338	U	0.024947	T	0.67543	0.2904	M	0.86178	2.8	0.45607	D	0.998548	D;D;D;D;P	0.89917	1.0;1.0;1.0;0.998;0.922	D;D;D;D;B	0.81914	0.991;0.995;0.994;0.968;0.358	T	0.69650	-0.5088	10	0.72032	D	0.01	-12.3558	20.6593	0.99626	0.0:0.0:1.0:0.0	.	157;339;142;147;147	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	K	339;336;147;147;157;157;142;142;142	ENSP00000385048:E339K;ENSP00000385727:E336K;ENSP00000421739:E147K;ENSP00000384313:E147K;ENSP00000384099:E157K;ENSP00000261569:E142K;ENSP00000392478:E142K	ENSP00000261569:E142K	E	+	1	0	MAST4	66432112	1.000000	0.71417	0.973000	0.42090	0.985000	0.73830	9.476000	0.97823	2.885000	0.99019	0.655000	0.94253	GAA		0.498	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66396356	G	A	66396356	3	1	61	1	0	0	0	0	1	0	0	0	9357	1059	37	1	1166	1	MAST4	5	66396356	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46119	66396356	114518904	3863	11848										
MAST4	375449	broad.mit.edu	37	chr5	66445359	66445359	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacagaaaaaaagaaaatCtcggggaaagtcacaaagtc	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66445359C>T	ENST00000403625.2	+	24	3532	c.3237C>T	c.(3235-3237)atC>atT	p.I1079I	MAST4_ENST00000261569.7_Silent_p.I885I|MAST4_ENST00000403666.1_Silent_p.I890I|MAST4_ENST00000404260.3_Silent_p.I1082I|MAST4_ENST00000405643.1_Silent_p.I900I	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1082	Ser-rich.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.I1082I(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AAAAGAAAATCTCGGGGAAAG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	5											79	80	80					5																	66445359		1867	4118	5985	66481115	SO:0001819	synonymous_variant	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.3237C>T	5.37:g.66445359C>T			66481115	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1																																																																																				0.468	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66445359	C	T	66445359	2	4	61	1	0	0	0	0	0	0	0	1	9357	903	32	3		3	MAST4	5	66445359	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49003	66445359	114469901	3864	11849										
MAST4	375449	broad.mit.edu	37	chr5	66461057	66461057	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactccaaaaatctcctctCtgtgggaaggacccacccag	7	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66461057C>A	ENST00000403625.2	+	29	6345	c.6050C>A	c.(6049-6051)tCt>tAt	p.S2017Y	MAST4_ENST00000261569.7_Missense_Mutation_p.S1823Y|MAST4_ENST00000403666.1_Missense_Mutation_p.S1828Y|MAST4_ENST00000404260.3_Missense_Mutation_p.S2020Y|MAST4_ENST00000405643.1_Missense_Mutation_p.S1838Y	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2020						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S2020Y(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AATCTCCTCTCTGTGGGAAGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											19	23	22					5																	66461057		1879	4126	6005	66496813	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6050C>A	5.37:g.66461057C>A	ENSP00000385727:p.Ser2017Tyr		66496813	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781951	0.49891	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	T;T;T;T;T	0.69561	-0.39;-0.39;-0.41;-0.41;-0.38	4.89	4.03	0.46877	.	0.961889	0.08567	N	0.926656	T	0.53818	0.1820	L	0.29908	0.895	0.09310	N	1	P;P	0.46277	0.875;0.513	B;B	0.38327	0.271;0.181	T	0.45731	-0.9241	10	0.72032	D	0.01	-2.1659	9.0666	0.36467	0.0:0.9:0.0:0.1	.	2020;1828	O15021;O15021-3	MAST4_HUMAN;.	Y	2020;2017;1828;1838;1838;1823	ENSP00000385048:S2020Y;ENSP00000385727:S2017Y;ENSP00000384313:S1828Y;ENSP00000384099:S1838Y;ENSP00000261569:S1823Y	ENSP00000261569:S1823Y	S	+	2	0	MAST4	66496813	0.065000	0.20965	0.002000	0.10522	0.092000	0.18411	2.455000	0.44988	1.273000	0.44346	0.563000	0.77884	TCT		0.552	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66461057	C	A	66461057	3	1	61	1	0	0	0	0	1	0	0	0	9357	913	32	2	6294	2	MAST4	5	66461057	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15698	66461057	114454203	3865	11850										
CD180	4064	broad.mit.edu	37	chr5	66478756	66478756	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatagccaacaataataGaaatactatgagaaagaaaa	6	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66478756G>A	ENST00000256447.4	-	3	2072	c.1915C>T	c.(1915-1917)Cta>Tta	p.L639L	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	639					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L639L(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		AACAATAATAGAAATACTATG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	5											67	70	69					5																	66478756		2203	4300	6503	66514512	SO:0001819	synonymous_variant	4064			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1915C>T	5.37:g.66478756G>A			66514512	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	37	CCDS3992.1																																																																																				0.393	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		A	66478756	G	A	66478756	2	1	61	1	0	0	0	0	0	0	0	1	2978	933	33	3		3	CD180	5	66478756	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17699	66478756	114436504	3866	11851										
CD180	4064	broad.mit.edu	37	chr5	66479419	66479419	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttctagctgaggacattCtttgaatgcctgactctgga	11	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66479419C>A	ENST00000256447.4	-	3	1409	c.1252G>T	c.(1252-1254)Gaa>Taa	p.E418*		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	418					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E418*(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TGAGGACATTCTTTGAATGCC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											162	166	165					5																	66479419		2203	4300	6503	66515175	SO:0001587	stop_gained	4064			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1252G>T	5.37:g.66479419C>A	ENSP00000256447:p.Glu418*		66515175	B2R7Z7|Q32MM5	Nonsense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	C	34	5.352533	0.95830	.	.	ENSG00000134061	ENST00000256447	.	.	.	4.81	3.94	0.45596	.	0.170072	0.38897	N	0.001524	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	9.1378	0.36886	0.0:0.8301:0.0:0.1699	.	.	.	.	X	418	.	ENSP00000256447:E418X	E	-	1	0	CD180	66515175	0.130000	0.22417	0.473000	0.27253	0.917000	0.54804	2.478000	0.45189	1.224000	0.43551	0.563000	0.77884	GAA		0.463	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		A	66479419	C	A	66479419	4	1	61	1	0	0	0	0	0	1	0	0	2978	922	32	2	737	2	CD180	5	66479419	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	663	66479419	114435841	3867	11852										
CD180	4064	broad.mit.edu	37	chr5	66479672	66479672	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatttgacacaattgatcGaaatgatttacactgagaac	7	7	0	5	rs371541622		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:66479672G>A	ENST00000256447.4	-	3	1156	c.999C>T	c.(997-999)ttC>ttT	p.F333F		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	333					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F333F(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		ACAATTGATCGAAATGATTTA	0.448													A|||	1	0.000199681	0	0	5008	,	,		21860	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	5						A		0,4406		0,0,2203	111	107	108		999	3.7	0.1	5		108	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	CD180	NM_005582.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		333/662	66479672	1,13005	2203	4300	6503	66515428	SO:0001819	synonymous_variant	4064			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.999C>T	5.37:g.66479672G>A			66515428	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	37	CCDS3992.1																																																																																				0.448	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		A	66479672	G	A	66479672	2	1	61	1	0	0	0	0	0	0	0	1	2978	1049	37	1		1	CD180	5	66479672	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253	66479672	114435588	3868	11853										
PIK3R1	5295	broad.mit.edu	37	chr5	67589609	67589609	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatataacactcagtttcaaGaaaaaagtcgagaatatgat	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:67589609G>T	ENST00000521381.1	+	11	1988	c.1372G>T	c.(1372-1374)Gaa>Taa	p.E458*	PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.E95*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.E458*|PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.E188*|PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.E158*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.E458*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.E458*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	458					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.E458*(1)|p.0?(1)|p.?(1)|p.F456_R461>S(1)|p.F456_R461del(1)|p.Q457_R461del(1)|p.T454_D464del(1)|p.S460fs*5(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TCAGTTTCAAGAAAAAAGTCG	0.284			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	8	Deletion - In frame(3)|Insertion - Frameshift(1)|Substitution - Nonsense(1)|Unknown(1)|Whole gene deletion(1)|Complex - deletion inframe(1)	endometrium(5)|large_intestine(2)|lung(1)	5											44	48	47					5																	67589609		2187	4267	6454	67625365	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1372G>T	5.37:g.67589609G>T	ENSP00000428056:p.Glu458*		67625365	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	38	6.781465	0.97833	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-27.0866	19.0691	0.93125	0.0:0.0:1.0:0.0	.	.	.	.	X	458;458;458;458;158;95;188;131;95	.	ENSP00000274335:E458X	E	+	1	0	PIK3R1	67625365	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.285000	0.78660	2.822000	0.97130	0.650000	0.86243	GAA		0.284	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67589609	G	T	67589609	4	4	61	1	0	0	0	0	0	1	0	0	11949	943	33	2	1540	2	PIK3R1	5	67589609	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1109937	67589609	113325651	3869	11854										
PIK3R1	5295	broad.mit.edu	37	chr5	67590466	67590466	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacagcaaagaatacataGaaaagtttaaacgtgaaggc	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:67590466G>T	ENST00000521381.1	+	12	2144	c.1528G>T	c.(1528-1530)Gaa>Taa	p.E510*	PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.E147*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.E510*|PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.E240*|PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.E210*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.E510*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.E510*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	510					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.E510*(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AGAATACATAGAAAAGTTTAA	0.348			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	3	Substitution - Nonsense(1)|Whole gene deletion(1)|Unknown(1)	large_intestine(2)|lung(1)	5											71	72	72					5																	67590466		2203	4300	6503	67626222	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1528G>T	5.37:g.67590466G>T	ENSP00000428056:p.Glu510*		67626222	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	37	6.419378	0.97550	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-26.7526	19.2559	0.93945	0.0:0.0:1.0:0.0	.	.	.	.	X	510;510;510;510;210;240;183;147	.	ENSP00000274335:E510X	E	+	1	0	PIK3R1	67626222	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.601000	0.98297	2.861000	0.98227	0.650000	0.86243	GAA		0.348	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67590466	G	T	67590466	4	4	61	1	0	0	0	0	0	1	0	0	11949	943	33	2	1700	2	PIK3R1	5	67590466	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	857	67590466	113324794	3870	11855										
PIK3R1	5295	broad.mit.edu	37	chr5	67591270	67591270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgactcaaaaaggtgttCggcaaaagaagttgaacgag	13	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:67591270C>T	ENST00000521381.1	+	14	2384	c.1768C>T	c.(1768-1770)Cgg>Tgg	p.R590W	PIK3R1_ENST00000523872.1_Missense_Mutation_p.R227W|PIK3R1_ENST00000396611.1_Missense_Mutation_p.R590W|PIK3R1_ENST00000336483.5_Missense_Mutation_p.R320W|PIK3R1_ENST00000320694.8_Missense_Mutation_p.R290W|PIK3R1_ENST00000274335.5_Missense_Mutation_p.R590W|PIK3R1_ENST00000521657.1_Missense_Mutation_p.R590W	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	590					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.M582_D605>I(4)|p.R590W(1)|p.Y580fs*1(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAAAGGTGTTCGGCAAAAGAA	0.353			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	8	Complex - deletion inframe(4)|Substitution - Missense(1)|Whole gene deletion(1)|Deletion - Frameshift(1)|Unknown(1)	large_intestine(5)|lung(1)|ovary(1)|central_nervous_system(1)	5											151	153	152					5																	67591270		2203	4300	6503	67627026	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1768C>T	5.37:g.67591270C>T	ENSP00000428056:p.Arg590Trp		67627026	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332935	0.81801	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.59595	0.2205	M	0.83312	2.635	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;P;P;D	0.68483	0.957;0.883;0.883;0.958	T	0.66670	-0.5865	10	0.87932	D	0	-15.571	18.1606	0.89707	0.0:1.0:0.0:0.0	.	260;320;290;590	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	W	590;590;590;590;290;320;227	ENSP00000428056:R590W;ENSP00000429277:R590W;ENSP00000379855:R590W;ENSP00000274335:R590W;ENSP00000323512:R290W;ENSP00000338554:R320W;ENSP00000430098:R227W	ENSP00000274335:R590W	R	+	1	2	PIK3R1	67627026	0.989000	0.36119	0.998000	0.56505	0.979000	0.70002	2.855000	0.48333	2.515000	0.84797	0.460000	0.39030	CGG		0.353	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67591270	C	T	67591270	3	4	61	1	0	0	0	0	1	0	0	0	11949	875	31	1	1948	1	PIK3R1	5	67591270	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	804	67591270	113323990	3871	11856										
SLC30A5	64924	broad.mit.edu	37	chr5	68396694	68396694	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaggctgtgggacttttCgaatcatatgatctcctaaa	9	7	2	2	rs201023507		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:68396694C>T	ENST00000396591.3	+	2	754	c.144C>T	c.(142-144)ttC>ttT	p.F48F	SLC30A5_ENST00000380860.4_Silent_p.F48F|SLC30A5_ENST00000502979.1_Intron	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	48					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.F48F(2)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGGGACTTTTCGAATCATATG	0.299																																																2	Substitution - coding silent(2)	large_intestine(2)	5											72	72	72					5																	68396694		2203	4297	6500	68432450	SO:0001819	synonymous_variant	64924			AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.144C>T	5.37:g.68396694C>T			68432450	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																				0.299	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			T	68396694	C	T	68396694	2	4	61	1	0	0	0	0	0	0	0	1	14595	883	31	1		1	SLC30A5	5	68396694	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	805424	68396694	112518566	3872	11857										
SLC30A5	64924	broad.mit.edu	37	chr5	68412342	68412342	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagcatagctctcaatcGatccctaggtttattaagga	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:68412342G>A	ENST00000396591.3	+	10	1804	c.1194G>A	c.(1192-1194)tcG>tcA	p.S398S	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	398					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.S398S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GCTCTCAATCGATCCCTAGGT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	5											74	77	76					5																	68412342		2203	4300	6503	68448098	SO:0001819	synonymous_variant	64924			AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1194G>A	5.37:g.68412342G>A			68448098	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																				0.378	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			A	68412342	G	A	68412342	2	1	61	1	0	0	0	0	0	0	0	1	14595	1045	37	1		1	SLC30A5	5	68412342	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15648	68412342	112502918	3873	11858										
CENPH	64946	broad.mit.edu	37	chr5	68490517	68490517	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatgcaagaaaagcaaatCgaagcgtatgttatatttaa	7	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:68490517C>T	ENST00000283006.2	+	3	321	c.234C>T	c.(232-234)atC>atT	p.I78I	CENPH_ENST00000515001.1_Silent_p.I78I	NM_022909.3	NP_075060.1			centromere protein H									p.I78I(1)		kidney(15)|large_intestine(2)|lung(3)	20		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		AAAAGCAAATCGAAGCGTATG	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	5											41	45	44					5																	68490517		2201	4300	6501	68526273	SO:0001819	synonymous_variant	64946			AB035124	CCDS3998.1	5p15.2	2013-11-05			ENSG00000153044	ENSG00000153044			17268	protein-coding gene	gene with protein product		605607				11092768, 15502821	Standard	NM_022909		Approved		uc003jvp.3	Q9H3R5	OTTHUMG00000097816	ENST00000283006.2:c.234C>T	5.37:g.68490517C>T			68526273		Silent	SNP	ENST00000283006.2	37	CCDS3998.1	.	.	.	.	.	.	.	.	.	.	C	8.171	0.791732	0.16258	.	.	ENSG00000153044	ENST00000502689	.	.	.	5.01	-7.51	0.01346	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	-30.9689	3.6032	0.08032	0.1223:0.436:0.125:0.3168	.	.	.	.	X	43	.	.	R	+	1	2	CENPH	68526273	0.967000	0.33354	0.804000	0.32291	0.830000	0.47004	-0.402000	0.07223	-1.435000	0.01972	-0.768000	0.03414	CGA		0.279	CENPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215083.1			T	68490517	C	T	68490517	2	4	61	1	0	0	0	0	0	0	0	1	3238	874	31	1		1	CENPH	5	68490517	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78175	68490517	112424743	3874	11859										
CCDC125	202243	broad.mit.edu	37	chr5	68602685	68602685	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcctctatatttttaaaTctattatgatcaaattctat	2	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:68602685T>G	ENST00000396496.2	-	6	683	c.576A>C	c.(574-576)agA>agC	p.R192S	CCDC125_ENST00000511257.1_Missense_Mutation_p.R67S|CCDC125_ENST00000396499.1_Missense_Mutation_p.R192S|CCDC125_ENST00000460090.1_Intron|CCDC125_ENST00000383374.2_Missense_Mutation_p.R191S			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	192						cytoplasm (GO:0005737)		p.R192S(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		TATTTTTAAATCTATTATGAT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	5											48	57	54					5																	68602685		2181	4261	6442	68638441	SO:0001583	missense	202243			AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.576A>C	5.37:g.68602685T>G	ENSP00000379754:p.Arg192Ser		68638441	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.687970	0.68271	.	.	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000383374;ENST00000511257	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.82	5.82	0.92795	.	0.102256	0.64402	D	0.000002	T	0.68375	0.2994	M	0.76002	2.32	0.38166	D	0.939194	D;D	0.89917	0.999;1.0	D;D	0.85130	0.951;0.997	T	0.71961	-0.4434	10	0.42905	T	0.14	-2.0618	15.2084	0.73198	0.0:0.0:0.0:1.0	.	67;192	Q86Z20-2;Q86Z20	.;CC125_HUMAN	S	192;192;191;67	ENSP00000379754:R192S;ENSP00000379756:R192S;ENSP00000372865:R191S;ENSP00000426795:R67S	ENSP00000372865:R191S	R	-	3	2	CCDC125	68638441	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	3.482000	0.53186	2.231000	0.72958	0.529000	0.55759	AGA		0.274	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816		G	68602685	T	G	68602685	3	3	61	1	0	0	0	0	1	0	0	0	2767	1432	50	4	987	4	CCDC125	5	68602685	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	112168	68602685	112312575	3875	11860										
RAD17	5884	broad.mit.edu	37	chr5	68710012	68710012	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtctcttcctttgagtCagaatagtgccagtgaactg	10	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:68710012C>A	ENST00000509734.1	+	18	2617	c.1939C>A	c.(1939-1941)Cag>Aag	p.Q647K	RAD17_ENST00000361732.2_Missense_Mutation_p.Q636K|RAD17_ENST00000358030.2_Missense_Mutation_p.Q471K|MARVELD2_ENST00000325631.5_5'Flank|RAD17_ENST00000354312.3_Missense_Mutation_p.Q636K|RAD17_ENST00000282891.6_Missense_Mutation_p.Q550K|RAD17_ENST00000521422.1_Missense_Mutation_p.Q471K|RAD17_ENST00000504177.1_3'UTR|RAD17_ENST00000345306.6_Missense_Mutation_p.Q636K|RAD17_ENST00000354868.5_Missense_Mutation_p.Q636K|RAD17_ENST00000305138.4_Missense_Mutation_p.Q636K|RAD17_ENST00000380774.3_Missense_Mutation_p.Q647K			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	647	Interaction with MCM7.				cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.Q636K(1)					Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		TCCTTTGAGTCAGAATAGTGC	0.507								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	5											98	100	99					5																	68710012		2203	4300	6503	68745768	SO:0001583	missense	5884			AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"RAD1 (S. pombe) homolog"			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1939C>A	5.37:g.68710012C>A	ENSP00000426191:p.Gln647Lys		68745768	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.244300	0.22796	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T	0.24538	2.17;2.16;2.17;1.85;2.17;2.17;2.17;1.88;1.85;2.16	5.25	4.38	0.52667	.	0.222820	0.46442	D	0.000293	T	0.25827	0.0629	M	0.68952	2.095	0.37075	D	0.898691	P;P;P	0.47910	0.842;0.822;0.902	B;B;B	0.41510	0.196;0.359;0.359	T	0.20840	-1.0263	10	0.37606	T	0.19	-13.3761	7.5601	0.27847	0.0:0.7443:0.1664:0.0894	.	647;550;636	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	K	636;647;636;471;636;636;636;550;471;647	ENSP00000355226:Q636K;ENSP00000426191:Q647K;ENSP00000346938:Q636K;ENSP00000427743:Q471K;ENSP00000346271:Q636K;ENSP00000311227:Q636K;ENSP00000303134:Q636K;ENSP00000282891:Q550K;ENSP00000350725:Q471K;ENSP00000370151:Q647K	ENSP00000282891:Q550K	Q	+	1	0	RAD17	68745768	1.000000	0.71417	0.781000	0.31783	0.001000	0.01503	3.089000	0.50183	1.206000	0.43276	-0.140000	0.14226	CAG		0.507	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344		A	68710012	C	A	68710012	3	1	61	1	0	0	0	0	1	0	0	0	13016	827	29	2	2014	2	RAD17	5	68710012	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107327	68710012	112205248	3876	11861										
BDP1	55814	broad.mit.edu	37	chr5	70751776	70751776	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgccaggggctccacagcTtccaatccccagcgtggacg	13	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70751776T>G	ENST00000358731.4	+	1	335	c.72T>G	c.(70-72)gcT>gcG	p.A24A	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	24	Interaction with ZBTB43.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A24A(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		GCTCCACAGCTTCCAATCCCC	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	5											16	19	18					5																	70751776		1956	4139	6095	70787532	SO:0001819	synonymous_variant	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.72T>G	5.37:g.70751776T>G			70787532	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1																																																																																				0.682	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		G	70751776	T	G	70751776	2	3	61	1	0	0	0	0	0	0	0	1	1396	1596	56	4		4	BDP1	5	70751776	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2041764	70751776	110163484	3877	11862										
BDP1	55814	broad.mit.edu	37	chr5	70754525	70754525	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttaagtctagtgtcagtgTtccttcagaatctcatccct	8	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70754525T>C	ENST00000358731.4	+	2	595	c.332T>C	c.(331-333)gTt>gCt	p.V111A	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	111	Interaction with ZBTB43.|Ser-rich.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.V111A(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		AGTGTCAGTGTTCCTTCAGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											145	140	141					5																	70754525		1924	4138	6062	70790281	SO:0001583	missense	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.332T>C	5.37:g.70754525T>C	ENSP00000351575:p.Val111Ala		70790281	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.313553	0.23908	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000444711	T	0.18502	2.21	5.28	4.13	0.48395	.	0.331548	0.29431	N	0.012178	T	0.14227	0.0344	L	0.41824	1.3	0.80722	D	1	P;P;B	0.36144	0.539;0.537;0.347	B;B;B	0.42555	0.17;0.391;0.146	T	0.06445	-1.0826	10	0.06891	T	0.86	.	7.355	0.26714	0.0:0.102:0.0:0.898	.	111;111;111	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	A	111	ENSP00000351575:V111A	ENSP00000351575:V111A	V	+	2	0	BDP1	70790281	0.997000	0.39634	1.000000	0.80357	0.255000	0.26057	0.514000	0.22786	0.966000	0.38159	0.477000	0.44152	GTT		0.418	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		C	70754525	T	C	70754525	3	2	61	1	0	0	0	0	1	0	0	0	1396	1725	60	4	338	4	BDP1	5	70754525	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2749	70754525	110160735	3878	11863										
BDP1	55814	broad.mit.edu	37	chr5	70759924	70759924	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaaactgaaaagccatcGactccagtccagacaagaga	8	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70759924G>A	ENST00000358731.4	+	4	902	c.639G>A	c.(637-639)tcG>tcA	p.S213S	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	213	Interaction with ZBTB43.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.S213S(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		AAAAGCCATCGACTCCAGTCC	0.274																																																1	Substitution - coding silent(1)	large_intestine(1)	5											35	37	36					5																	70759924		1790	4067	5857	70795680	SO:0001819	synonymous_variant	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.639G>A	5.37:g.70759924G>A			70795680	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1																																																																																				0.274	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70759924	G	A	70759924	2	1	61	1	0	0	0	0	0	0	0	1	1396	1045	37	1		1	BDP1	5	70759924	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5399	70759924	110155336	3879	11864										
BDP1	55814	broad.mit.edu	37	chr5	70782334	70782334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagcgcccttttgacttcGatttttttgctcatttgctt	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70782334G>A	ENST00000358731.4	+	9	1356	c.1093G>A	c.(1093-1095)Gat>Aat	p.D365N	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	365	Required for phosphorylation by CSNK2A1.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D365N(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		TTTTGACTTCGATTTTTTTGC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	5											66	63	64					5																	70782334		1795	4064	5859	70818090	SO:0001583	missense	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.1093G>A	5.37:g.70782334G>A	ENSP00000351575:p.Asp365Asn		70818090	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.224542	0.39300	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000444711	T	0.03982	3.74	5.82	4.01	0.46588	.	0.234231	0.43919	D	0.000504	T	0.06142	0.0159	N	0.04746	-0.17	0.80722	D	1	P;D;P	0.89917	0.632;1.0;0.608	B;D;B	0.87578	0.147;0.998;0.163	T	0.52193	-0.8608	10	0.25106	T	0.35	.	7.6368	0.28272	0.1983:0.0:0.8017:0.0	.	365;365;365	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	N	365	ENSP00000351575:D365N	ENSP00000351575:D365N	D	+	1	0	BDP1	70818090	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.914000	0.39966	2.747000	0.94245	0.591000	0.81541	GAT		0.299	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70782334	G	A	70782334	3	1	61	1	0	0	0	0	1	0	0	0	1396	1058	37	1	1127	1	BDP1	5	70782334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22410	70782334	110132926	3880	11865										
BDP1	55814	broad.mit.edu	37	chr5	70786934	70786934	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgaaaaagttgagaaaaGaactgaccccatcctttcat	6	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70786934G>T	ENST00000358731.4	+	11	1879	c.1616G>T	c.(1615-1617)aGa>aTa	p.R539I	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	539					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R539I(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		GTTGAGAAAAGAACTGACCCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											147	137	141					5																	70786934		1890	4113	6003	70822690	SO:0001583	missense	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.1616G>T	5.37:g.70786934G>T	ENSP00000351575:p.Arg539Ile		70822690	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.240488	0.79912	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	T	0.62105	0.05	5.19	-1.77	0.07982	.	1.097650	0.06762	N	0.782056	T	0.66228	0.2768	L	0.54323	1.7	0.19775	N	0.999956	B;D;B	0.69078	0.123;0.997;0.27	B;D;B	0.65010	0.038;0.931;0.061	T	0.54944	-0.8217	10	0.66056	D	0.02	.	0.2731	0.00234	0.2839:0.1364:0.27:0.3096	.	539;539;539	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	I	539;539;119;539	ENSP00000351575:R539I	ENSP00000351575:R539I	R	+	2	0	BDP1	70822690	0.001000	0.12720	0.071000	0.20095	0.711000	0.40976	-0.009000	0.12765	-0.210000	0.10140	-0.284000	0.09977	AGA		0.408	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70786934	G	T	70786934	3	4	61	1	0	0	0	0	1	0	0	0	1396	942	33	2	1658	2	BDP1	5	70786934	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4600	70786934	110128326	3881	11866										
BDP1	55814	broad.mit.edu	37	chr5	70819908	70819908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccaaatgtcaccagaggtCgtggatcaaaacgagttcgg	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:70819908C>T	ENST00000358731.4	+	25	5793	c.5530C>T	c.(5530-5532)Cgt>Tgt	p.R1844C	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1844					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R1844C(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		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)		CACCAGAGGTCGTGGATCAAA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											81	82	82					5																	70819908		1909	4111	6020	70855664	SO:0001583	missense	55814			AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.5530C>T	5.37:g.70819908C>T	ENSP00000351575:p.Arg1844Cys		70855664	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989090	0.74589	.	.	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.35605	1.3	5.47	5.47	0.80525	.	0.000000	0.56097	D	0.000028	T	0.55970	0.1954	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.57219	-0.7849	10	0.87932	D	0	.	12.214	0.54396	0.17:0.83:0.0:0.0	.	1844;1844	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	C	1844;1424	ENSP00000351575:R1844C	ENSP00000351575:R1844C	R	+	1	0	BDP1	70855664	0.995000	0.38212	0.999000	0.59377	0.962000	0.63368	3.516000	0.53436	2.723000	0.93209	0.655000	0.94253	CGT		0.458	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70819908	C	T	70819908	3	4	61	1	0	0	0	0	1	0	0	0	1396	884	31	1	5628	1	BDP1	5	70819908	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32974	70819908	110095352	3882	11867										
MAP1B	4131	broad.mit.edu	37	chr5	71491772	71491772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctggagctaatcgaagacGaagagaaactgaaggaaact	12	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:71491772G>A	ENST00000296755.7	+	5	2888	c.2590G>A	c.(2590-2592)Gaa>Aaa	p.E864K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	864					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E864K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AATCGAAGACGAAGAGAAACT	0.493																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											126	124	125					5																	71491772		2203	4300	6503	71527528	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2590G>A	5.37:g.71491772G>A	ENSP00000296755:p.Glu864Lys		71527528	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.880021	0.51801	.	.	ENSG00000131711	ENST00000296755	T	0.03413	3.94	5.34	5.34	0.76211	.	0.192509	0.36167	N	0.002748	T	0.02970	0.0088	N	0.22421	0.69	0.50467	D	0.999875	P;B	0.36483	0.555;0.256	B;B	0.21546	0.035;0.035	T	0.61028	-0.7145	10	0.17369	T	0.5	-10.0824	19.0329	0.92965	0.0:0.0:1.0:0.0	.	738;864	A2BDK6;P46821	.;MAP1B_HUMAN	K	864	ENSP00000296755:E864K	ENSP00000296755:E864K	E	+	1	0	MAP1B	71527528	1.000000	0.71417	0.618000	0.29105	0.013000	0.08279	6.365000	0.73090	2.490000	0.84030	0.591000	0.81541	GAA		0.493	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71491772	G	A	71491772	3	1	61	1	0	0	0	0	1	0	0	0	9258	1059	37	1	2608	1	MAP1B	5	71491772	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	671864	71491772	109423488	3883	11868										
MAP1B	4131	broad.mit.edu	37	chr5	71492446	71492446	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcttcaattcatgatgaGactttacctggaggctcaga	9	9	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:71492446G>T	ENST00000296755.7	+	5	3562	c.3264G>T	c.(3262-3264)gaG>gaT	p.E1088D		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1088					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E1088D(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		TTCATGATGAGACTTTACCTG	0.547																																					Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5											54	57	56					5																	71492446		2203	4300	6503	71528202	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3264G>T	5.37:g.71492446G>T	ENSP00000296755:p.Glu1088Asp		71528202	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.218769	0.39201	.	.	ENSG00000131711	ENST00000296755	T	0.12672	2.66	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000003	T	0.09335	0.0230	L	0.27053	0.805	0.43793	D	0.996339	B;B	0.32071	0.355;0.355	B;B	0.28638	0.092;0.092	T	0.24835	-1.0149	10	0.28530	T	0.3	-25.8578	10.1889	0.43015	0.1477:0.0:0.8523:0.0	.	962;1088	A2BDK6;P46821	.;MAP1B_HUMAN	D	1088	ENSP00000296755:E1088D	ENSP00000296755:E1088D	E	+	3	2	MAP1B	71528202	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.550000	0.36223	2.666000	0.90696	0.655000	0.94253	GAG		0.547	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71492446	G	T	71492446	3	4	61	1	0	0	0	0	1	0	0	0	9258	933	33	2	3282	2	MAP1B	5	71492446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	674	71492446	109422814	3884	11869										
MAP1B	4131	broad.mit.edu	37	chr5	71495025	71495025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattattgagaagaccacacGgacccctgaagagggtgggt	13	8	0	4	rs139240427	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:71495025G>A	ENST00000296755.7	+	5	6141	c.5843G>A	c.(5842-5844)cGg>cAg	p.R1948Q		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1948					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.R1948Q(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AAGACCACACGGACCCCTGAA	0.473													G|||	3	0.000599042	0.0023	0	5008	,	,		18446	0		0	False		,,,				2504	0				Melanoma(17;367 822 11631 31730 47712)											1	Substitution - Missense(1)	large_intestine(1)	5						G	GLN/ARG	0,4406		0,0,2203	60	64	62		5843	4.2	1	5	dbSNP_134	62	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MAP1B	NM_005909.3	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1948/2469	71495025	1,13005	2203	4300	6503	71530781	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5843G>A	5.37:g.71495025G>A	ENSP00000296755:p.Arg1948Gln		71530781	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586879	0.28268	0.0	1.16E-4	ENSG00000131711	ENST00000296755	T	0.03124	4.04	5.11	4.25	0.50352	.	0.000000	0.56097	D	0.000035	T	0.03959	0.0111	N	0.08118	0	0.32613	N	0.524414	D;B	0.76494	0.999;0.052	P;B	0.56751	0.805;0.003	T	0.42732	-0.9434	10	0.35671	T	0.21	-9.0693	6.0492	0.19777	0.1609:0.0:0.6869:0.1522	.	1822;1948	A2BDK6;P46821	.;MAP1B_HUMAN	Q	1948	ENSP00000296755:R1948Q	ENSP00000296755:R1948Q	R	+	2	0	MAP1B	71530781	0.004000	0.15560	0.997000	0.53966	0.997000	0.91878	0.120000	0.15647	1.162000	0.42619	0.551000	0.68910	CGG		0.473	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71495025	G	A	71495025	3	1	61	1	0	0	0	0	1	0	0	0	9258	1116	39	1	5861	1	MAP1B	5	71495025	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2579	71495025	109420235	3885	11870										
MAP1B	4131	broad.mit.edu	37	chr5	71495320	71495320	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgttacgagactgcagaGaaaatcactagaacccctca	7	11	2	3	rs115914542	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:71495320G>T	ENST00000296755.7	+	5	6436	c.6138G>T	c.(6136-6138)gaG>gaT	p.E2046D		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2046					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E2046D(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		AGACTGCAGAGAAAATCACTA	0.458																																					Melanoma(17;367 822 11631 31730 47712)											2	Substitution - Missense(2)	large_intestine(2)	5											117	129	125					5																	71495320		2203	4300	6503	71531076	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6138G>T	5.37:g.71495320G>T	ENSP00000296755:p.Glu2046Asp		71531076	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.261966	0.23051	.	.	ENSG00000131711	ENST00000296755	T	0.03580	3.88	5.68	3.89	0.44902	.	0.000000	0.64402	D	0.000003	T	0.02380	0.0073	N	0.08118	0	0.38398	D	0.945586	B;B	0.15141	0.012;0.012	B;B	0.16722	0.016;0.016	T	0.52155	-0.8613	10	0.37606	T	0.19	-17.3826	10.4734	0.44650	0.0689:0.0:0.7961:0.1349	.	1920;2046	A2BDK6;P46821	.;MAP1B_HUMAN	D	2046	ENSP00000296755:E2046D	ENSP00000296755:E2046D	E	+	3	2	MAP1B	71531076	1.000000	0.71417	0.926000	0.36857	0.841000	0.47740	1.325000	0.33724	1.399000	0.46721	0.655000	0.94253	GAG		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71495320	G	T	71495320	3	4	61	1	0	0	0	0	1	0	0	0	9258	933	33	2	6156	2	MAP1B	5	71495320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	295	71495320	109419940	3886	11871										
FCHO2	115548	broad.mit.edu	37	chr5	72264391	72264391	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggacagatatcaacaaaaGaactagcagattttgtaagg	9	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:72264391G>T	ENST00000430046.2	+	2	216	c.100G>T	c.(100-102)Gaa>Taa	p.E34*	FCHO2_ENST00000512348.1_Nonsense_Mutation_p.E34*|FCHO2_ENST00000287761.6_Nonsense_Mutation_p.E34*|FCHO2_ENST00000341845.6_Nonsense_Mutation_p.E34*	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	34	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.|Mediates dimerization and binding to membranes enriched in Pi(4,5)-P2 and induces their tubulation.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.E34*(2)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		ATCAACAAAAGAACTAGCAGA	0.249																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											20	20	20					5																	72264391		1789	4034	5823	72300147	SO:0001587	stop_gained	115548			AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.100G>T	5.37:g.72264391G>T	ENSP00000393776:p.Glu34*		72300147	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Nonsense_Mutation	SNP	ENST00000430046.2	37	CCDS47230.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.334944|5.334944	0.95758|0.95758	.|.	.|.	ENSG00000157107|ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348;ENST00000287761|ENST00000507345	.|.	.|.	.|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75845	.|0.3905	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.76716	.|-0.2857	.|4	0.66056|0.48119	D|T	0.02|0.1	-19.875|-19.875	18.1947|18.1947	0.89817|0.89817	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	34|28	.|.	ENSP00000287761:E34X|ENSP00000426842:K28N	E|K	+|+	1|3	0|2	FCHO2|FCHO2	72300147|72300147	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	9.247000|9.247000	0.95444|0.95444	2.378000|2.378000	0.81104|0.81104	0.650000|0.650000	0.86243|0.86243	GAA|AAG		0.249	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		T	72264391	G	T	72264391	4	4	61	1	0	0	0	0	0	1	0	0	5807	943	33	2	106	2	FCHO2	5	72264391	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	769071	72264391	108650869	3887	11872										
ANKRA2	57763	broad.mit.edu	37	chr5	72858531	72858531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacacattcatatcaaatCggttaggcaatatgaatttc	5	8	2	1	rs200934847		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:72858531C>T	ENST00000296785.3	-	2	834	c.176G>A	c.(175-177)cGa>cAa	p.R59Q		NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	59						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)	p.R59Q(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		CATATCAAATCGGTTAGGCAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											221	212	215					5																	72858531		2203	4300	6503	72894287	SO:0001583	missense	57763			AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"Ankyrin repeat domain containing"	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.176G>A	5.37:g.72858531C>T	ENSP00000296785:p.Arg59Gln		72894287		Missense_Mutation	SNP	ENST00000296785.3	37	CCDS4020.1	.	.	.	.	.	.	.	.	.	.	C	34	5.369637	0.95900	.	.	ENSG00000164331	ENST00000296785;ENST00000504641	T;T	0.57752	0.5;0.38	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.66247	0.2770	L	0.44542	1.39	0.58432	D	0.999999	D;D	0.76494	0.999;0.994	D;P	0.80764	0.994;0.885	T	0.63355	-0.6656	10	0.35671	T	0.21	-9.7533	18.7735	0.91901	0.0:1.0:0.0:0.0	.	59;59	D6RBK8;Q9H9E1	.;ANRA2_HUMAN	Q	59	ENSP00000296785:R59Q;ENSP00000422643:R59Q	ENSP00000296785:R59Q	R	-	2	0	ANKRA2	72894287	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.711000	0.68400	2.426000	0.82243	0.655000	0.94253	CGA		0.403	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2	NM_023039		T	72858531	C	T	72858531	3	4	61	1	0	0	0	0	1	0	0	0	636	884	31	1	797	1	ANKRA2	5	72858531	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	594140	72858531	108056729	3888	11873										
RGNEF	64283	broad.mit.edu	37	chr5	73128269	73128269	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaagtctacgctaactgTatggtgattgatcaggtaag	12	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:73128269T>C	ENST00000426542.2	+	9	1151	c.1131T>C	c.(1129-1131)tgT>tgC	p.C377C	ARHGEF28_ENST00000437974.1_Silent_p.C377C|ARHGEF28_ENST00000296794.6_Silent_p.C377C|ARHGEF28_ENST00000513042.2_Silent_p.C377C|ARHGEF28_ENST00000545377.1_Silent_p.C377C|ARHGEF28_ENST00000296799.4_Silent_p.C64C|ARHGEF28_ENST00000287898.5_Silent_p.C377C			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	377					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)	p.C377C(1)									ACGCTAACTGTATGGTGATTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											73	67	69					5																	73128269		1985	4157	6142	73164025	SO:0001819	synonymous_variant	64283				CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1131T>C	5.37:g.73128269T>C			73164025	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																				0.448	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73128269	T	C	73128269	2	2	61	1	0	0	0	0	0	0	0	1	13320	1644	57	4		4	RGNEF	5	73128269	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	269738	73128269	107786991	3889	11874										
RGNEF	64283	broad.mit.edu	37	chr5	73189070	73189070	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaatctgatgaagacaaGaggaaagctgaagccagagt	13	5	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:73189070G>T	ENST00000426542.2	+	27	3635	c.3615G>T	c.(3613-3615)aaG>aaT	p.K1205N	ARHGEF28_ENST00000512883.1_Missense_Mutation_p.K169N|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.K1205N|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.K1205N|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.K1205N|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.K1205N|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.K892N|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.K1205N			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1205					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)	p.K169N(1)									ATGAAGACAAGAGGAAAGCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	75	76					5																	73189070		1948	4125	6073	73224826	SO:0001583	missense	64283				CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.3615G>T	5.37:g.73189070G>T	ENSP00000412175:p.Lys1205Asn		73224826	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666865	0.67814	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.33865	2.9;2.91;2.9;2.66;2.91;2.9;2.73;1.39	4.87	1.56	0.23342	.	.	.	.	.	T	0.38878	0.1057	M	0.62723	1.935	0.20703	N	0.999869	P;P;P;P;P	0.49307	0.922;0.871;0.73;0.835;0.723	P;P;P;P;B	0.47786	0.556;0.548;0.467;0.557;0.444	T	0.25012	-1.0144	9	0.87932	D	0	.	5.4355	0.16478	0.6043:0.0:0.3957:0.0	.	892;1205;1205;169;1205	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	N	1205;1205;1205;1205;1205;1205;892;169	ENSP00000296794:K1205N;ENSP00000441913:K1205N;ENSP00000441436:K1205N;ENSP00000287898:K1205N;ENSP00000411459:K1205N;ENSP00000412175:K1205N;ENSP00000296799:K892N;ENSP00000421081:K169N	ENSP00000287898:K1205N	K	+	3	2	RP11-428C6.1	73224826	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	1.020000	0.30027	0.587000	0.29643	0.655000	0.94253	AAG		0.458	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73189070	G	T	73189070	3	4	61	1	0	0	0	0	1	0	0	0	13320	933	33	2	3721	2	RGNEF	5	73189070	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60801	73189070	107726190	3890	11875										
HEXB	3074	broad.mit.edu	37	chr5	73981317	73981317	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcgccccggagaacttcTacatcagccacagccccaat	6	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:73981317T>G	ENST00000261416.7	+	1	349	c.232T>G	c.(232-234)Tac>Gac	p.Y78D	HEXB_ENST00000511181.1_Intron	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	78					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.Y78D(1)		endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		GGAGAACTTCTACATCAGCCA	0.697																																					Melanoma(66;841 1270 13391 18706 27225)											1	Substitution - Missense(1)	large_intestine(1)	5											22	27	26					5																	73981317		2202	4300	6502	74017073	SO:0001583	missense	3074			M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.232T>G	5.37:g.73981317T>G	ENSP00000261416:p.Tyr78Asp		74017073		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.809531	0.50421	.	.	ENSG00000049860	ENST00000261416	D	0.87571	-2.27	4.86	-2.71	0.05986	Acetylhexosaminidase, subunit a/b (1);	2.611440	0.00953	N	0.002994	T	0.68274	0.2983	N	0.03608	-0.345	0.40834	D	0.983617	B	0.02656	0.0	B	0.04013	0.001	T	0.58662	-0.7597	10	0.25106	T	0.35	1.5558	1.8636	0.03194	0.1268:0.2873:0.3492:0.2367	.	78	P07686	HEXB_HUMAN	D	78	ENSP00000261416:Y78D	ENSP00000261416:Y78D	Y	+	1	0	HEXB	74017073	0.001000	0.12720	0.006000	0.13384	0.817000	0.46193	-0.693000	0.05121	-0.391000	0.07763	0.459000	0.35465	TAC		0.697	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521		G	73981317	T	G	73981317	3	3	61	1	0	0	0	0	1	0	0	0	7095	1522	53	4	234	4	HEXB	5	73981317	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	792247	73981317	106933943	3891	11876										
GFM2	84340	broad.mit.edu	37	chr5	74021496	74021496	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttgagacacaggcagaaAtcatagttgtggaggtgcca	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74021496A>C	ENST00000296805.3	-	19	2454	c.1997T>G	c.(1996-1998)aTt>aGt	p.I666S	GFM2_ENST00000345239.2_Missense_Mutation_p.I619S|RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000515125.1_Intron|GFM2_ENST00000509430.1_Missense_Mutation_p.I666S	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.I666S(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		ACAGGCAGAAATCATAGTTGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											123	111	115					5																	74021496		2203	4300	6503	74057252	SO:0001583	missense	84340			AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1997T>G	5.37:g.74021496A>C	ENSP00000296805:p.Ile666Ser		74057252		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.845567	0.91197	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.48522	0.81;0.81;0.81	5.8	5.8	0.92144	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.169368	0.53938	D	0.000060	T	0.58424	0.2121	L	0.52573	1.65	0.80722	D	1	P;P;P	0.46064	0.845;0.73;0.872	P;B;P	0.54100	0.625;0.334;0.742	T	0.61013	-0.7148	10	0.87932	D	0	-14.8207	16.1606	0.81704	1.0:0.0:0.0:0.0	.	664;619;666	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	S	666;619;666	ENSP00000296805:I666S;ENSP00000296804:I619S;ENSP00000427004:I666S	ENSP00000296805:I666S	I	-	2	0	GFM2	74057252	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.199000	0.89731	2.227000	0.72691	0.460000	0.39030	ATT		0.423	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		C	74021496	A	C	74021496	3	2	61	1	0	0	0	0	1	0	0	0	6362	101	4	4	354	4	GFM2	5	74021496	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40179	74021496	106893764	3892	11877										
GFM2	84340	broad.mit.edu	37	chr5	74026188	74026188	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgattcgatcatgaataatCtctatatgtaactcccccat	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74026188C>A	ENST00000296805.3	-	17	2080	c.1623G>T	c.(1621-1623)gaG>gaT	p.E541D	GFM2_ENST00000345239.2_Missense_Mutation_p.E494D|GFM2_ENST00000515125.1_Intron|GFM2_ENST00000509430.1_Missense_Mutation_p.E541D	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.E541D(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CATGAATAATCTCTATATGTA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											111	104	106					5																	74026188		2203	4300	6503	74061944	SO:0001583	missense	84340			AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1623G>T	5.37:g.74026188C>A	ENSP00000296805:p.Glu541Asp		74061944		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402963	0.42613	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.73789	-0.78;-0.78;-0.78	5.64	1.72	0.24424	Elongation factor G/III/V (1);	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	L	0.31476	0.935	0.80722	D	1	B;B;B	0.23806	0.091;0.034;0.055	B;B;B	0.28991	0.097;0.034;0.045	T	0.32719	-0.9896	10	0.19590	T	0.45	-17.5606	6.2476	0.20827	0.1177:0.6064:0.0:0.276	.	541;494;541	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	D	541;494;541	ENSP00000296805:E541D;ENSP00000296804:E494D;ENSP00000427004:E541D	ENSP00000296805:E541D	E	-	3	2	GFM2	74061944	0.993000	0.37304	0.998000	0.56505	0.967000	0.64934	0.429000	0.21412	0.026000	0.15269	-0.378000	0.06908	GAG		0.403	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		A	74026188	C	A	74026188	3	1	61	1	0	0	0	0	1	0	0	0	6362	912	32	2	736	2	GFM2	5	74026188	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4692	74026188	106889072	3893	11878										
FAM169A	26049	broad.mit.edu	37	chr5	74137446	74137446	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacatgtaatcttcagcaGaattttccaattcctcatgg	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74137446G>A	ENST00000389156.4	-	2	146	c.56C>T	c.(55-57)tCt>tTt	p.S19F	FAM169A_ENST00000510496.1_Missense_Mutation_p.S19F|FAM169A_ENST00000380515.3_Missense_Mutation_p.S19F	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	19						membrane (GO:0016020)|nucleus (GO:0005634)		p.S19F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						ATCTTCAGCAGAATTTTCCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	96	99					5																	74137446		1843	4097	5940	74173202	SO:0001583	missense	26049				CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.56C>T	5.37:g.74137446G>A	ENSP00000373808:p.Ser19Phe		74173202	A8K1T9|Q6MZT0|Q9H989	Missense_Mutation	SNP	ENST00000389156.4	37	CCDS43330.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544593	0.86022	.	.	ENSG00000198780	ENST00000389156;ENST00000510496;ENST00000380515;ENST00000513277;ENST00000514200;ENST00000506954	T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28	5.61	4.7	0.59300	.	0.416994	0.22458	N	0.059796	T	0.51210	0.1661	L	0.50333	1.59	0.53688	D	0.999977	D;D	0.55385	0.971;0.971	P;P	0.59948	0.855;0.866	T	0.52177	-0.8610	10	0.72032	D	0.01	-11.3255	15.8823	0.79213	0.0:0.0:0.864:0.136	.	19;19	D6RB01;Q9Y6X4	.;F169A_HUMAN	F	19	ENSP00000373808:S19F;ENSP00000424578:S19F;ENSP00000369886:S19F;ENSP00000423631:S19F;ENSP00000423883:S19F;ENSP00000421451:S19F	ENSP00000369886:S19F	S	-	2	0	FAM169A	74173202	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	6.017000	0.70805	2.635000	0.89317	0.585000	0.79938	TCT		0.393	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2			A	74137446	G	A	74137446	3	1	61	1	0	0	0	0	1	0	0	0	5503	942	33	3	2004	3	FAM169A	5	74137446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111258	74137446	106777814	3894	11879										
GCNT4	51301	broad.mit.edu	37	chr5	74325367	74325367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggtatcaggtgccttacGatcataatggatgcagtaaa	11	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74325367G>A	ENST00000322348.4	-	1	1357	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	166					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.R166C(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		GGTGCCTTACGATCATAATGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											153	148	149					5																	74325367		2203	4300	6503	74361123	SO:0001583	missense	51301			AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	17973	protein-coding gene	gene with protein product	"core 2 beta-1,6-N-acetylglucosaminyltransferase 3", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"		"glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.496C>T	5.37:g.74325367G>A	ENSP00000317027:p.Arg166Cys		74361123		Missense_Mutation	SNP	ENST00000322348.4	37	CCDS4026.1	.	.	.	.	.	.	.	.	.	.	.	18.26	3.585464	0.66105	.	.	ENSG00000176928	ENST00000322348	T	0.12039	2.72	6.17	5.31	0.75309	.	0.565448	0.20533	N	0.090470	T	0.22166	0.0534	L	0.43923	1.385	0.39134	D	0.961906	D	0.56746	0.977	P	0.51055	0.657	T	0.01914	-1.1248	10	0.66056	D	0.02	-16.1396	15.7563	0.78030	0.065:0.0:0.935:0.0	.	166	Q9P109	GCNT4_HUMAN	C	166	ENSP00000317027:R166C	ENSP00000317027:R166C	R	-	1	0	GCNT4	74361123	1.000000	0.71417	0.895000	0.35142	0.931000	0.56810	4.719000	0.61937	1.626000	0.50381	0.655000	0.94253	CGT		0.378	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591		A	74325367	G	A	74325367	3	1	61	1	0	0	0	0	1	0	0	0	6323	1058	37	1	869	1	GCNT4	5	74325367	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187921	74325367	106589893	3895	11880										
GCNT4	51301	broad.mit.edu	37	chr5	74325802	74325802	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagagcagccatagggttaAaaacaggatgaaaactttct	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74325802A>C	ENST00000322348.4	-	1	922	c.61T>G	c.(61-63)Tta>Gta	p.L21V		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	21					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.L21V(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		CATAGGGTTAAAAACAGGATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											115	134	128					5																	74325802		2186	4243	6429	74361558	SO:0001583	missense	51301			AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	17973	protein-coding gene	gene with protein product	"core 2 beta-1,6-N-acetylglucosaminyltransferase 3", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"		"glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.61T>G	5.37:g.74325802A>C	ENSP00000317027:p.Leu21Val		74361558		Missense_Mutation	SNP	ENST00000322348.4	37	CCDS4026.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381576	0.24944	.	.	ENSG00000176928	ENST00000322348	T	0.10668	2.85	5.95	0.916	0.19373	.	0.374947	0.24145	N	0.041126	T	0.04952	0.0133	N	0.17082	0.46	0.27162	N	0.961137	B	0.16603	0.018	B	0.09377	0.004	T	0.42085	-0.9472	10	0.15952	T	0.53	-5.2213	5.3899	0.16237	0.4365:0.262:0.3016:0.0	.	21	Q9P109	GCNT4_HUMAN	V	21	ENSP00000317027:L21V	ENSP00000317027:L21V	L	-	1	2	GCNT4	74361558	0.998000	0.40836	0.989000	0.46669	0.998000	0.95712	0.777000	0.26718	-0.063000	0.13065	0.533000	0.62120	TTA		0.358	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591		C	74325802	A	C	74325802	3	2	61	1	0	0	0	0	1	0	0	0	6323	11	1	4	1304	4	GCNT4	5	74325802	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	435	74325802	106589458	3896	11881										
HMGCR	3156	broad.mit.edu	37	chr5	74655871	74655871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcccggcagcttgcccGaattgtgtgtgggaccgtaa	13	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74655871G>A	ENST00000287936.4	+	19	2675	c.2519G>A	c.(2518-2520)cGa>cAa	p.R840Q	HMGCR_ENST00000511206.1_Missense_Mutation_p.R840Q|HMGCR_ENST00000343975.5_Missense_Mutation_p.R787Q	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	840	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)	p.R840Q(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		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)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	CAGCTTGCCCGAATTGTGTGT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	128	130					5																	74655871		2203	4300	6503	74691627	SO:0001583	missense	3156				CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.2519G>A	5.37:g.74655871G>A	ENSP00000287936:p.Arg840Gln		74691627	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	37	CCDS4027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.77|14.77	2.635189|2.635189	0.47049|0.47049	.|.	.|.	ENSG00000113161|ENSG00000113161	ENST00000509085|ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975;ENST00000429286;ENST00000511986	.|T;T;T;T	.|0.46063	.|0.88;0.88;0.88;0.88	5.7|5.7	4.72|4.72	0.59763|0.59763	.|Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	.|0.215574	.|0.47455	.|D	.|0.000224	T|T	0.31231|0.31231	0.0790|0.0790	L|L	0.58101|0.58101	1.795|1.795	0.37332|0.37332	D|D	0.910009|0.910009	.|B;P;P;B;B	.|0.36010	.|0.152;0.514;0.532;0.074;0.152	.|B;B;B;B;B	.|0.30105	.|0.066;0.111;0.046;0.015;0.045	T|T	0.40117|0.40117	-0.9580|-0.9580	5|10	.|0.45353	.|T	.|0.12	-6.7176|-6.7176	3.7195|3.7195	0.08450|0.08450	0.3358:0.0:0.6642:0.0|0.3358:0.0:0.6642:0.0	.|.	.|840;771;217;787;840	.|B2R649;B7Z3Y9;B4DSB1;P04035-2;P04035	.|.;.;.;.;HMDH_HUMAN	K|Q	117|840;771;840;787;217;67	.|ENSP00000426745:R840Q;ENSP00000287936:R840Q;ENSP00000340816:R787Q;ENSP00000420871:R67Q	.|ENSP00000287936:R840Q	E|R	+|+	1|2	0|0	HMGCR|HMGCR	74691627|74691627	1.000000|1.000000	0.71417|0.71417	0.884000|0.884000	0.34674|0.34674	0.824000|0.824000	0.46624|0.46624	4.317000|4.317000	0.59184|0.59184	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	GAA|CGA		0.483	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			A	74655871	G	A	74655871	3	1	61	1	0	0	0	0	1	0	0	0	7252	1058	37	1	2589	1	HMGCR	5	74655871	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	330069	74655871	106259389	3897	11882										
POLK	51426	broad.mit.edu	37	chr5	74892363	74892363	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttggaaatatcagagaaTtcagatgactgtcagatact	8	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:74892363T>C	ENST00000241436.4	+	13	2017	c.1845T>C	c.(1843-1845)aaT>aaC	p.N615N	POLK_ENST00000352007.5_Silent_p.N417N|POLK_ENST00000380481.3_Silent_p.N525N|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000508526.1_Silent_p.N417N|POLK_ENST00000504026.1_Intron|CTC-366B18.2_ENST00000511329.1_RNA	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	615					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.N615N(2)		endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		TATCAGAGAATTCAGATGACT	0.373								DNA polymerases (catalytic subunits)																																								2	Substitution - coding silent(2)	large_intestine(2)	5											111	114	113					5																	74892363		2203	4300	6503	74928119	SO:0001819	synonymous_variant	51426			AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1845T>C	5.37:g.74892363T>C			74928119	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Silent	SNP	ENST00000241436.4	37	CCDS4030.1																																																																																				0.373	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74892363	T	C	74892363	2	2	61	1	0	0	0	0	0	0	0	1	12235	1490	52	4		4	POLK	5	74892363	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	236492	74892363	106022897	3898	11883										
SV2C	22987	broad.mit.edu	37	chr5	75428097	75428097	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtgtttgtcgttggcttCgtgttacccagtgctgagac	14	8	0	1	rs370011561	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:75428097C>T	ENST00000502798.2	+	2	964	c.522C>T	c.(520-522)ttC>ttT	p.F174F	SV2C_ENST00000322285.7_Silent_p.F174F	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	174					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.F174F(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		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)		TCGTTGGCTTCGTGTTACCCA	0.517													C|||	3	0.000599042	0.0015	0	5008	,	,		16619	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		3,4115		0,3,2056	182	170	174		522	-1.7	1	5		174	0,8422		0,0,4211	no	coding-synonymous	SV2C	NM_014979.1		0,3,6267	TT,TC,CC		0.0,0.0729,0.0239		174/728	75428097	3,12537	2059	4211	6270	75463853	SO:0001819	synonymous_variant	22987			AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.522C>T	5.37:g.75428097C>T			75463853	Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	37	CCDS43331.1																																																																																				0.517	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			T	75428097	C	T	75428097	2	4	61	1	0	0	0	0	0	0	0	1	15458	883	31	1		1	SV2C	5	75428097	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	535734	75428097	105487163	3899	11884										
IQGAP2	10788	broad.mit.edu	37	chr5	75757450	75757450	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggatgagaggaggcggcaGaacattgcttatgaatatct	13	5	1	3	rs373606679		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:75757450G>T	ENST00000274364.6	+	2	399	c.102G>T	c.(100-102)caG>caT	p.Q34H	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	34					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.Q34H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GGAGGCGGCAGAACATTGCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											147	121	130					5																	75757450		2203	4300	6503	75793206	SO:0001583	missense	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.102G>T	5.37:g.75757450G>T	ENSP00000274364:p.Gln34His		75793206	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342392	0.81911	.	.	ENSG00000145703	ENST00000274364;ENST00000514350	T;T	0.42900	0.96;0.96	4.05	4.05	0.47172	Calponin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.50372	-0.8836	10	0.44086	T	0.13	-13.8813	15.5184	0.75842	0.0:0.0:1.0:0.0	.	34	Q13576	IQGA2_HUMAN	H	34;7	ENSP00000274364:Q34H;ENSP00000423672:Q7H	ENSP00000274364:Q34H	Q	+	3	2	IQGAP2	75793206	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.821000	0.48065	2.267000	0.75376	0.491000	0.48974	CAG		0.428	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75757450	G	T	75757450	3	4	61	1	0	0	0	0	1	0	0	0	7836	933	33	2	108	2	IQGAP2	5	75757450	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	329353	75757450	105157810	3900	11885										
IQGAP2	10788	broad.mit.edu	37	chr5	75964614	75964614	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataattatgcctctaatcagCgagaagaatatctacttctc	5	9	4	2	rs377130667		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:75964614C>T	ENST00000274364.6	+	23	3085	c.2788C>T	c.(2788-2790)Cga>Tga	p.R930*	IQGAP2_ENST00000396234.3_Nonsense_Mutation_p.R426*|IQGAP2_ENST00000502745.1_Nonsense_Mutation_p.R426*|IQGAP2_ENST00000379730.3_Nonsense_Mutation_p.R432*	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	930	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.R930*(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CTCTAATCAGCGAGAAGAATA	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	5						C	stop/ARG	0,4406		0,0,2203	63	63	63		2788	4.6	1	5		63	1,8589		0,1,4294	no	stop-gained	IQGAP2	NM_006633.2		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		930/1576	75964614	1,12995	2203	4295	6498	76000370	SO:0001587	stop_gained	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.2788C>T	5.37:g.75964614C>T	ENSP00000274364:p.Arg930*		76000370	A8K4V1|B7Z8A4|J3KR91	Nonsense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	C	40	8.334068	0.98764	0.0	1.16E-4	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000502745	.	.	.	5.5	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.494	15.2221	0.73320	0.146:0.854:0.0:0.0	.	.	.	.	X	930;432;880;483;426;426	.	ENSP00000274364:R930X	R	+	1	2	IQGAP2	76000370	0.996000	0.38824	0.969000	0.41365	0.994000	0.84299	2.103000	0.41806	1.250000	0.43966	0.591000	0.81541	CGA		0.318	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75964614	C	T	75964614	4	4	61	1	0	0	0	0	0	1	0	0	7836	760	27	1	2878	1	IQGAP2	5	75964614	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	207164	75964614	104950646	3901	11886										
F2RL1	2150	broad.mit.edu	37	chr5	76129241	76129241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgatgatcagaatgctgcGatcttctgccatggatgaaa	11	8	3	4	rs2243062	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:76129241G>A	ENST00000296677.4	+	2	1015	c.809G>A	c.(808-810)cGa>cAa	p.R270Q		NM_005242.4	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	270			R -> Q (in dbSNP:rs2243062). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|chemokine (C-C motif) ligand 2 secretion (GO:0035926)|chemokine secretion (GO:0090195)|defense response to virus (GO:0051607)|establishment of endothelial barrier (GO:0061028)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|interleukin-1 beta secretion (GO:0050702)|interleukin-10 secretion (GO:0072608)|leukocyte migration (GO:0050900)|leukocyte proliferation (GO:0070661)|mature dendritic cell differentiation (GO:0097029)|negative regulation of chemokine secretion (GO:0090198)|negative regulation of JNK cascade (GO:0046329)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neutrophil activation (GO:0042119)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of cell migration (GO:0030335)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of eosinophil degranulation (GO:0043311)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of neutrophil mediated killing of gram-negative bacterium (GO:0070963)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of blood coagulation (GO:0030193)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of JNK cascade (GO:0046328)|T cell activation involved in immune response (GO:0002286)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)	p.R270Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	13		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)		AGAATGCTGCGATCTTCTGCC	0.488													G|||	60	0.0119808	0.0431	0.0043	5008	,	,		22489	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						G	GLN/ARG	181,4225	119.6+/-157.3	6,169,2028	147	141	143		809	-0.9	0	5	dbSNP_98	143	4,8596	3.7+/-12.6	1,2,4297	yes	missense	F2RL1	NM_005242.4	43	7,171,6325	AA,AG,GG		0.0465,4.108,1.4224	benign	270/398	76129241	185,12821	2203	4300	6503	76164997	SO:0001583	missense	2150			BC018130	CCDS4033.1	5q13	2012-08-08			ENSG00000164251	ENSG00000164251		"GPCR / Class A : Protease activated receptors"	3538	protein-coding gene	gene with protein product	"proteinase-activated receptor-2"	600933		GPR11		7937743, 7556175	Standard	NM_005242		Approved	PAR2	uc003keo.3	P55085	OTTHUMG00000102118	ENST00000296677.4:c.809G>A	5.37:g.76129241G>A	ENSP00000296677:p.Arg270Gln		76164997	Q13317|Q13346|Q53XJ8	Missense_Mutation	SNP	ENST00000296677.4	37	CCDS4033.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	G	1.108	-0.659185	0.03454	0.04108	4.65E-4	ENSG00000164251	ENST00000296677	T	0.42131	0.98	5.44	-0.913	0.10500	GPCR, rhodopsin-like superfamily (1);	0.912432	0.09444	N	0.801390	T	0.05914	0.0154	N	0.25144	0.715	0.09310	N	1	B	0.27117	0.168	B	0.20767	0.031	T	0.13176	-1.0519	9	.	.	.	-1.996	7.2765	0.26288	0.5656:0.1201:0.3142:0.0	rs2243062;rs16873832;rs52817305;rs2243062	270	P55085	PAR2_HUMAN	Q	270	ENSP00000296677:R270Q	.	R	+	2	0	F2RL1	76164997	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.344000	0.19962	-0.070000	0.12908	-0.126000	0.14955	CGA		0.488	F2RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219957.2			A	76129241	G	A	76129241	3	1	61	1	0	0	0	0	1	0	0	0	5357	1058	37	1	815	1	F2RL1	5	76129241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164627	76129241	104786019	3902	11887										
AGGF1	55109	broad.mit.edu	37	chr5	76331554	76331554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagacaagtggaccattttGcctcaaattcacaggtaata	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:76331554G>A	ENST00000312916.7	+	3	884	c.502G>A	c.(502-504)Gcc>Acc	p.A168T	AGGF1_ENST00000506806.1_Missense_Mutation_p.A168T|AGGF1_ENST00000503538.1_3'UTR	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	168					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)	p.A168T(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		GGACCATTTTGCCTCAAATTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	73	73					5																	76331554		2203	4299	6502	76367310	SO:0001583	missense	55109			AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.502G>A	5.37:g.76331554G>A	ENSP00000316109:p.Ala168Thr		76367310	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	G	8.828	0.939321	0.18281	.	.	ENSG00000164252	ENST00000312916;ENST00000506806	T;T	0.75938	1.2;-0.98	5.96	-0.0725	0.13739	.	1.066110	0.07162	N	0.850964	T	0.33760	0.0874	N	0.00436	-1.5	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.08055	0.001;0.003	T	0.25012	-1.0144	10	0.15952	T	0.53	-33.777	1.1854	0.01854	0.4854:0.179:0.1767:0.1589	.	168;168	Q8N302;Q8N302-3	AGGF1_HUMAN;.	T	168	ENSP00000316109:A168T;ENSP00000424733:A168T	ENSP00000316109:A168T	A	+	1	0	AGGF1	76367310	0.000000	0.05858	0.044000	0.18714	0.960000	0.62799	0.143000	0.16115	0.055000	0.16094	0.650000	0.86243	GCC		0.338	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76331554	G	A	76331554	3	1	61	1	0	0	0	0	1	0	0	0	382	1319	46	3	512	3	AGGF1	5	76331554	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202313	76331554	104583706	3903	11888										
PDE8B	8622	broad.mit.edu	37	chr5	76624826	76624826	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagccttctcattgcaggtcGatccgggccacaaatccctc	9	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:76624826G>A	ENST00000264917.5	+	4	639	c.594G>A	c.(592-594)tcG>tcA	p.S198S	PDE8B_ENST00000346042.3_Silent_p.S198S|PDE8B_ENST00000340978.3_Silent_p.S198S|PDE8B_ENST00000333194.4_Silent_p.S198S|PDE8B_ENST00000342343.4_Silent_p.S178S	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	198					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.S198S(1)	GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	ATTGCAGGTCGATCCGGGCCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	5											122	90	101					5																	76624826		2203	4300	6503	76660582	SO:0001819	synonymous_variant	8622			AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.594G>A	5.37:g.76624826G>A			76660582	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Silent	SNP	ENST00000264917.5	37	CCDS4037.1																																																																																				0.473	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		A	76624826	G	A	76624826	2	1	61	1	0	0	0	0	0	0	0	1	11685	1045	37	1		1	PDE8B	5	76624826	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293272	76624826	104290434	3904	11889										
WDR41	55255	broad.mit.edu	37	chr5	76734154	76734154	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatttgaaggctatacacGtataaaccccttccaactgc	5	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:76734154G>A	ENST00000296679.4	-	10	1290	c.915C>T	c.(913-915)taC>taT	p.Y305Y	WDR41_ENST00000507029.1_Silent_p.Y250Y|WDR41_ENST00000512033.1_5'Flank|WDR41_ENST00000414719.2_Silent_p.Y51Y	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	305						lysosomal membrane (GO:0005765)		p.Y305Y(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		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)		GGCTATACACGTATAAACCCC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	5											143	126	132					5																	76734154		2203	4300	6503	76769910	SO:0001819	synonymous_variant	55255			AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"WD repeat domain containing"	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.915C>T	5.37:g.76734154G>A			76769910	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1	.	.	.	.	.	.	.	.	.	.	G	9.936	1.216116	0.22373	.	.	ENSG00000164253	ENST00000511630	.	.	.	5.75	-7.8	0.01214	.	.	.	.	.	T	0.72382	0.3453	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75004	-0.3470	4	.	.	.	-13.2046	21.2754	0.99950	0.1842:0.0:0.8158:0.0	.	.	.	.	M	131	.	.	T	-	2	0	WDR41	76769910	0.318000	0.24598	0.794000	0.32065	0.993000	0.82548	-0.524000	0.06222	-1.345000	0.02214	-0.312000	0.09012	ACG		0.453	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		A	76734154	G	A	76734154	2	1	61	1	0	0	0	0	0	0	0	1	17334	1140	40	1		1	WDR41	5	76734154	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109328	76734154	104181106	3905	11890										
OTP	23440	broad.mit.edu	37	chr5	76932775	76932775	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtgaagcgcgtccggtgGcgcttctgcttctgttggcc	17	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:76932775G>A	ENST00000306422.3	-	2	1456	c.318C>T	c.(316-318)cgC>cgT	p.R106R	OTP_ENST00000515716.1_5'UTR	NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	106					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R106R(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		GCGTCCGGTGGCGCTTCTGCT	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	5											91	96	95					5																	76932775		2203	4300	6503	76968531	SO:0001819	synonymous_variant	23440				CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"Homeoboxes / PRD class"	8518	protein-coding gene	gene with protein product		604529	"orthopedia homolog (Drosophila)"			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.318C>T	5.37:g.76932775G>A			76968531		Silent	SNP	ENST00000306422.3	37	CCDS4039.1																																																																																				0.667	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2			A	76932775	G	A	76932775	2	1	61	1	0	0	0	0	0	0	0	1	11341	1190	42	3		3	OTP	5	76932775	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198621	76932775	103982485	3906	11891										
AP3B1	8546	broad.mit.edu	37	chr5	77511899	77511899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttccaagggctgacaaActgtgtccgagcatatcgag	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:77511899A>G	ENST00000255194.6	-	7	941	c.766T>C	c.(766-768)Ttt>Ctt	p.F256L	AP3B1_ENST00000519295.1_Missense_Mutation_p.F207L	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	256					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)	p.F256L(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GGGCTGACAAACTGTGTCCGA	0.398									Hermansky-Pudlak syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											122	117	119					5																	77511899		2203	4300	6503	77547655	SO:0001583	missense	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.766T>C	5.37:g.77511899A>G	ENSP00000255194:p.Phe256Leu		77547655	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.021940	0.93462	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.24538	1.85;1.85	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.47655	0.1457	L	0.60067	1.865	0.80722	D	1	D	0.71674	0.998	D	0.70016	0.967	T	0.47849	-0.9085	10	0.87932	D	0	-11.1959	15.6919	0.77461	1.0:0.0:0.0:0.0	.	256	O00203	AP3B1_HUMAN	L	256;207;256;160	ENSP00000255194:F256L;ENSP00000430597:F207L	ENSP00000255194:F256L	F	-	1	0	AP3B1	77547655	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.284000	0.95882	2.112000	0.64535	0.533000	0.62120	TTT		0.398	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			G	77511899	A	G	77511899	3	3	61	1	0	0	0	0	1	0	0	0	744	43	2	4	2602	4	AP3B1	5	77511899	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	579124	77511899	103403361	3907	11892										
AP3B1	8546	broad.mit.edu	37	chr5	77523208	77523208	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacctacctgtataattttTgtattgcatgggctgcattc	8	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:77523208T>G	ENST00000255194.6	-	5	699	c.524A>C	c.(523-525)cAa>cCa	p.Q175P	AP3B1_ENST00000519295.1_Missense_Mutation_p.Q126P	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	175					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)	p.Q175P(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GTATAATTTTTGTATTGCATG	0.358									Hermansky-Pudlak syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											127	119	122					5																	77523208		2203	4300	6503	77558964	SO:0001583	missense	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.524A>C	5.37:g.77523208T>G	ENSP00000255194:p.Gln175Pro		77558964	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	1.843	-0.466968	0.04476	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.23552	1.9;1.9	5.06	5.06	0.68205	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.04003	0.0112	N	0.00019	-2.8	0.58432	D	0.999999	B	0.09022	0.002	B	0.12156	0.007	T	0.46978	-0.9152	10	0.02654	T	1	-13.49	15.1337	0.72545	0.0:0.0:0.0:1.0	.	175	O00203	AP3B1_HUMAN	P	175;126;175;79	ENSP00000255194:Q175P;ENSP00000430597:Q126P	ENSP00000255194:Q175P	Q	-	2	0	AP3B1	77558964	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	3.947000	0.56652	2.021000	0.59480	0.460000	0.39030	CAA		0.358	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			G	77523208	T	G	77523208	3	3	61	1	0	0	0	0	1	0	0	0	744	1812	63	4	2852	4	AP3B1	5	77523208	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11309	77523208	103392052	3908	11893										
LHFPL2	10184	broad.mit.edu	37	chr5	77805755	77805755	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtggcctgccagaagccGctggcgatctcgccgaagct	14	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:77805755G>A	ENST00000515007.2	-	2	592	c.282C>T	c.(280-282)agC>agT	p.S94S	LHFPL2_ENST00000380345.2_Silent_p.S94S			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	94						integral component of membrane (GO:0016021)		p.S94S(1)		endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	6		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		GCCAGAAGCCGCTGGCGATCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	5											27	29	28					5																	77805755		2202	4298	6500	77841511	SO:0001819	synonymous_variant	10184			D86961	CCDS4042.1	5q13	2008-02-05			ENSG00000145685	ENSG00000145685			6588	protein-coding gene	gene with protein product		609718				10329012	Standard	NM_005779		Approved	KIAA0206	uc003kfo.3	Q6ZUX7	OTTHUMG00000107579	ENST00000515007.2:c.282C>T	5.37:g.77805755G>A			77841511	B2RMQ6|Q7Z5P0|Q92605	Silent	SNP	ENST00000515007.2	37	CCDS4042.1																																																																																				0.607	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779		A	77805755	G	A	77805755	2	1	61	1	0	0	0	0	0	0	0	1	8788	1078	38	1		1	LHFPL2	5	77805755	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282547	77805755	103109505	3909	11894										
DMGDH	29958	broad.mit.edu	37	chr5	78326677	78326677	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggaatgacatttgcaaaGagatggtccagtagtctaat	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78326677G>T	ENST00000255189.3	-	10	1690	c.1662C>A	c.(1660-1662)ctC>ctA	p.L554L	DMGDH_ENST00000540686.1_Silent_p.L174L|DMGDH_ENST00000380311.4_Silent_p.L353L	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	554					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)	p.L554L(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		CATTTGCAAAGAGATGGTCCA	0.383																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	5											127	120	122					5																	78326677		2203	4300	6503	78362433	SO:0001819	synonymous_variant	29958			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1662C>A	5.37:g.78326677G>T			78362433	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																				0.383	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		T	78326677	G	T	78326677	2	4	61	1	0	0	0	0	0	0	0	1	4592	929	33	2		2	DMGDH	5	78326677	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	520922	78326677	102588583	3910	11895										
BHMT2	23743	broad.mit.edu	37	chr5	78376542	78376542	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctgctgcctgtgacctCgccagggaagtggctggcaa	14	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78376542C>T	ENST00000255192.3	+	4	357	c.291C>T	c.(289-291)ctC>ctT	p.L97L	BHMT2_ENST00000521567.1_Intron|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	97	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.L97L(1)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		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)	CCTGTGACCTCGCCAGGGAAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	5											117	119	118					5																	78376542		2203	4300	6503	78412298	SO:0001819	synonymous_variant	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.291C>T	5.37:g.78376542C>T			78412298	B7Z516|Q9NXX7	Silent	SNP	ENST00000255192.3	37	CCDS4045.1																																																																																				0.438	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		T	78376542	C	T	78376542	2	4	61	1	0	0	0	0	0	0	0	1	1427	871	31	1		1	BHMT2	5	78376542	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49865	78376542	102538718	3911	11896										
BHMT2	23743	broad.mit.edu	37	chr5	78378752	78378752	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatgatataacccccggaGaatgtgctgtgaggctggtg	14	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78378752G>T	ENST00000255192.3	+	5	637	c.571G>T	c.(571-573)Gaa>Taa	p.E191*	DMGDH_ENST00000520388.1_Intron|BHMT2_ENST00000521567.1_Nonsense_Mutation_p.E127*	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	191	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.E191*(2)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		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)	AACCCCCGGAGAATGTGCTGT	0.473																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											235	221	226					5																	78378752		2203	4300	6503	78414508	SO:0001587	stop_gained	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.571G>T	5.37:g.78378752G>T	ENSP00000255192:p.Glu191*		78414508	B7Z516|Q9NXX7	Nonsense_Mutation	SNP	ENST00000255192.3	37	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946007	0.53079	.	.	ENSG00000132840	ENST00000255192;ENST00000521567	.	.	.	5.62	4.74	0.60224	.	0.191330	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-8.3173	15.9827	0.80125	0.0:0.2701:0.7299:0.0	.	.	.	.	X	191;127	.	ENSP00000255192:E191X	E	+	1	0	BHMT2	78414508	1.000000	0.71417	0.484000	0.27391	0.070000	0.16714	4.398000	0.59697	1.363000	0.46019	0.655000	0.94253	GAA		0.473	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		T	78378752	G	T	78378752	4	4	61	1	0	0	0	0	0	1	0	0	1427	943	33	2	589	2	BHMT2	5	78378752	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2210	78378752	102536508	3912	11897										
BHMT	635	broad.mit.edu	37	chr5	78416210	78416210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgcttgcgacatcgcccGacaagtggctgatgaaggag	14	10	0	2	rs111297335		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78416210G>A	ENST00000274353.5	+	4	430	c.323G>A	c.(322-324)cGa>cAa	p.R108Q	BHMT_ENST00000524080.1_Intron|DMGDH_ENST00000520388.1_5'UTR	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	108	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.R108Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GACATCGCCCGACAAGTGGCT	0.398													G|||	1	0.000199681	8e-04	0	5008	,	,		19314	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	55	54	55		323	4.3	1	5	dbSNP_132	55	0,8600		0,0,4300	no	missense	BHMT	NM_001713.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	108/407	78416210	1,13005	2203	4300	6503	78451966	SO:0001583	missense	635			BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.323G>A	5.37:g.78416210G>A	ENSP00000274353:p.Arg108Gln		78451966	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.72	3.458009	0.63401	2.27E-4	0.0	ENSG00000145692	ENST00000274353	T	0.40225	1.04	5.22	4.3	0.51218	Homocysteine S-methyltransferase (4);	0.050811	0.85682	D	0.000000	T	0.37517	0.1006	M	0.70903	2.155	0.80722	D	1	B	0.34226	0.443	B	0.24006	0.05	T	0.40572	-0.9556	10	0.54805	T	0.06	-31.8012	10.1664	0.42882	0.074:0.0:0.7889:0.1371	.	108	Q93088	BHMT1_HUMAN	Q	108	ENSP00000274353:R108Q	ENSP00000274353:R108Q	R	+	2	0	BHMT	78451966	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.538000	0.53597	2.602000	0.87976	0.557000	0.71058	CGA		0.398	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		A	78416210	G	A	78416210	3	1	61	1	0	0	0	0	1	0	0	0	1426	1058	37	1	337	1	BHMT	5	78416210	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37458	78416210	102499050	3913	11898										
BHMT	635	broad.mit.edu	37	chr5	78421875	78421875	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccactcacaggagcatCcatcattggtgtgaactgcc	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78421875C>A	ENST00000274353.5	+	6	739	c.632C>A	c.(631-633)tCc>tAc	p.S211Y	BHMT_ENST00000524080.1_Missense_Mutation_p.S58Y|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	211	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.S211Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ACAGGAGCATCCATCATTGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	85	86					5																	78421875		2203	4300	6503	78457631	SO:0001583	missense	635			BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.632C>A	5.37:g.78421875C>A	ENSP00000274353:p.Ser211Tyr		78457631	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.414148	0.42817	.	.	ENSG00000145692	ENST00000274353;ENST00000524080;ENST00000436224	T;T	0.30981	2.69;1.51	5.66	5.66	0.87406	Homocysteine S-methyltransferase (4);	0.300521	0.43416	D	0.000572	T	0.50446	0.1616	M	0.68952	2.095	0.53688	D	0.99997	D;P	0.56521	0.976;0.831	P;B	0.54706	0.759;0.198	T	0.50440	-0.8828	10	0.87932	D	0	-9.5325	20.1253	0.97977	0.0:1.0:0.0:0.0	.	58;211	E5RJH0;Q93088	.;BHMT1_HUMAN	Y	211;58;58	ENSP00000274353:S211Y;ENSP00000428240:S58Y	ENSP00000274353:S211Y	S	+	2	0	BHMT	78457631	0.991000	0.36638	0.985000	0.45067	0.290000	0.27261	4.645000	0.61404	2.832000	0.97577	0.655000	0.94253	TCC		0.493	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		A	78421875	C	A	78421875	3	1	61	1	0	0	0	0	1	0	0	0	1426	855	30	2	654	2	BHMT	5	78421875	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5665	78421875	102493385	3914	11899										
BHMT	635	broad.mit.edu	37	chr5	78423681	78423681	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgctgtggatttgagccCtaccacatcagggcaattgc	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78423681C>A	ENST00000274353.5	+	7	1019	c.912C>A	c.(910-912)ccC>ccA	p.P304P	BHMT_ENST00000524080.1_Silent_p.P151P|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	304	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.P304P(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GATTTGAGCCCTACCACATCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	5											46	47	47					5																	78423681		2203	4293	6496	78459437	SO:0001819	synonymous_variant	635			BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.912C>A	5.37:g.78423681C>A			78459437	Q9UNI9	Silent	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	C	9.261	1.043169	0.19748	.	.	ENSG00000145692	ENST00000436224	.	.	.	5.14	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.62829	0.2460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65763	-0.6089	6	0.87932	D	0	-12.6532	7.1087	0.25378	0.2249:0.6374:0.0:0.1377	.	.	.	.	H	151	.	ENSP00000405681:P151H	P	+	2	0	BHMT	78459437	0.906000	0.30813	1.000000	0.80357	0.987000	0.75469	0.091000	0.15046	2.547000	0.85894	0.650000	0.86243	CCT		0.542	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		A	78423681	C	A	78423681	2	1	61	1	0	0	0	0	0	0	0	1	1426	668	24	2		2	BHMT	5	78423681	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1806	78423681	102491579	3915	11900										
JMY	133746	broad.mit.edu	37	chr5	78611934	78611934	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgaagatgatagtaataAtatcttggcacaaataagga	9	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78611934A>C	ENST00000396137.4	+	10	3233	c.2771A>C	c.(2770-2772)aAt>aCt	p.N924T	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	924	WH2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.N570T(1)		endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		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)		GATAGTAATAATATCTTGGCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	102	104					5																	78611934		1876	4111	5987	78647690	SO:0001583	missense	133746			AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.2771A>C	5.37:g.78611934A>C	ENSP00000379441:p.Asn924Thr		78647690	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	A	19.92	3.917064	0.73098	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.56444	0.46	5.65	5.65	0.86999	Actin-binding WH2 (2);	0.049281	0.85682	D	0.000000	T	0.68906	0.3052	L	0.58810	1.83	0.52099	D	0.999946	D	0.76494	0.999	D	0.70487	0.969	T	0.71758	-0.4496	10	0.72032	D	0.01	.	15.8666	0.79069	1.0:0.0:0.0:0.0	.	924	Q8N9B5	JMY_HUMAN	T	913;924	ENSP00000379441:N924T	ENSP00000282259:N913T	N	+	2	0	JMY	78647690	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.751000	0.62169	2.157000	0.67596	0.523000	0.50628	AAT		0.413	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		C	78611934	A	C	78611934	3	2	61	1	0	0	0	0	1	0	0	0	7978	101	4	4	2809	4	JMY	5	78611934	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	188253	78611934	102303326	3916	11901										
HOMER1	9456	broad.mit.edu	37	chr5	78742947	78742947	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtcgagcagcttctttaaAttcctgaaacttttctgcaa	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78742947A>C	ENST00000334082.6	-	4	1758	c.316T>G	c.(316-318)Ttt>Gtt	p.F106V	HOMER1_ENST00000282260.6_Intron|HOMER1_ENST00000508576.1_Missense_Mutation_p.F106V|HOMER1_ENST00000535690.1_Intron	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)	106	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)	p.F106V(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		GCTTCTTTAAATTCCTGAAAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											129	125	126					5																	78742947		1819	4081	5900	78778703	SO:0001583	missense	9456			BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.316T>G	5.37:g.78742947A>C	ENSP00000334382:p.Phe106Val		78778703	B2R688|O96003|Q86YM5	Missense_Mutation	SNP	ENST00000334082.6	37	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	A	6.536	0.467079	0.12402	.	.	ENSG00000152413	ENST00000334082;ENST00000508576	D;D	0.98329	-4.87;-4.87	5.73	5.73	0.89815	EVH1 (3);Pleckstrin homology-type (1);	0.046591	0.85682	D	0.000000	D	0.88764	0.6525	N	0.00152	-1.975	0.80722	D	1	B;B	0.17465	0.003;0.022	B;B	0.26864	0.007;0.074	D	0.87488	0.2425	10	0.02654	T	1	-12.9511	15.9905	0.80202	1.0:0.0:0.0:0.0	.	106;106	Q86YM7-3;Q86YM7	.;HOME1_HUMAN	V	106	ENSP00000334382:F106V;ENSP00000426651:F106V	ENSP00000334382:F106V	F	-	1	0	HOMER1	78778703	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.148000	0.64857	2.166000	0.68216	0.533000	0.62120	TTT		0.338	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272		C	78742947	A	C	78742947	3	2	61	1	0	0	0	0	1	0	0	0	7299	101	4	4	772	4	HOMER1	5	78742947	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	131013	78742947	102172313	3917	11902										
PAPD4	167153	broad.mit.edu	37	chr5	78919085	78919085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttttcaggagattaagcGatgaaaaaaaccttcctctt	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78919085G>A	ENST00000296783.3	+	5	537	c.238G>A	c.(238-240)Gat>Aat	p.D80N	PAPD4_ENST00000428308.2_Missense_Mutation_p.D80N|PAPD4_ENST00000504233.1_Missense_Mutation_p.D80N|PAPD4_ENST00000423041.2_Missense_Mutation_p.D80N|PAPD4_ENST00000453514.1_Missense_Mutation_p.D80N			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	80					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)	p.D80N(1)		biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		GAGATTAAGCGATGAAAAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											80	74	76					5																	78919085		2203	4300	6503	78954841	SO:0001583	missense	167153			AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.238G>A	5.37:g.78919085G>A	ENSP00000296783:p.Asp80Asn		78954841	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	37	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.797026	0.50208	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.83	4.85	0.62838	.	0.489617	0.22606	N	0.057886	T	0.32285	0.0824	N	0.12182	0.205	0.32153	N	0.583938	B;B;B	0.10296	0.002;0.003;0.003	B;B;B	0.04013	0.001;0.001;0.001	T	0.27640	-1.0068	10	0.37606	T	0.19	-15.9872	9.4177	0.38532	0.1268:0.0:0.8732:0.0	.	80;80;80	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	N	80	ENSP00000397563:D80N;ENSP00000393412:D80N;ENSP00000396861:D80N;ENSP00000296783:D80N	ENSP00000296783:D80N	D	+	1	0	PAPD4	78954841	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.403000	0.44530	2.753000	0.94483	0.585000	0.79938	GAT		0.343	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		A	78919085	G	A	78919085	3	1	61	1	0	0	0	0	1	0	0	0	11455	1058	37	1	248	1	PAPD4	5	78919085	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176138	78919085	101996175	3918	11903										
PAPD4	167153	broad.mit.edu	37	chr5	78944899	78944899	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagttgaaaatcgagttCgtccgttagtgctggtgatt	11	6	1	2	rs376003386		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78944899C>T	ENST00000296783.3	+	11	1212	c.913C>T	c.(913-915)Cgt>Tgt	p.R305C	PAPD4_ENST00000428308.2_Missense_Mutation_p.R305C|PAPD4_ENST00000504233.1_Intron|PAPD4_ENST00000423041.2_Missense_Mutation_p.R301C|PAPD4_ENST00000453514.1_Missense_Mutation_p.R305C			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	305					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)	p.R305C(1)		biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		AAATCGAGTTCGTCCGTTAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	113	108	110		913,913,913	5.9	1	5		110	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PAPD4	NM_001114393.1,NM_001114394.1,NM_173797.3	180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	305/485,305/485,305/485	78944899	1,13005	2203	4300	6503	78980655	SO:0001583	missense	167153			AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.913C>T	5.37:g.78944899C>T	ENSP00000296783:p.Arg305Cys		78980655	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	37	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240340	0.79912	0.0	1.16E-4	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000428308;ENST00000296783	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.86	5.86	0.93980	.	0.095984	0.64402	D	0.000001	D	0.83413	0.5249	H	0.94183	3.505	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.70487	0.886;0.969	D	0.87299	0.2304	10	0.87932	D	0	-11.5768	19.7843	0.96430	0.0:1.0:0.0:0.0	.	305;301	Q6PIY7;Q6PIY7-2	GLD2_HUMAN;.	C	305;301;305;305	ENSP00000397563:R305C;ENSP00000393412:R301C;ENSP00000396861:R305C;ENSP00000296783:R305C	ENSP00000296783:R305C	R	+	1	0	PAPD4	78980655	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.727000	0.61993	2.774000	0.95407	0.585000	0.79938	CGT		0.368	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		T	78944899	C	T	78944899	3	4	61	1	0	0	0	0	1	0	0	0	11455	884	31	1	947	1	PAPD4	5	78944899	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25814	78944899	101970361	3919	11904										
PAPD4	167153	broad.mit.edu	37	chr5	78981047	78981047	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacagattgaaaaacaagaGagatttgaacagtatactac	8	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:78981047G>T	ENST00000296783.3	+	16	1705	c.1406G>T	c.(1405-1407)aGa>aTa	p.R469I	PAPD4_ENST00000428308.2_Missense_Mutation_p.R469I|PAPD4_ENST00000504233.1_Missense_Mutation_p.R426I|PAPD4_ENST00000423041.2_Missense_Mutation_p.R465I|PAPD4_ENST00000453514.1_Missense_Mutation_p.R469I			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	469					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)	p.R469I(1)		biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		AAAAACAAGAGAGATTTGAAC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											77	83	81					5																	78981047		2203	4300	6503	79016803	SO:0001583	missense	167153			AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.1406G>T	5.37:g.78981047G>T	ENSP00000296783:p.Arg469Ile		79016803	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	37	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.826622	0.50739	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.85	3.1	0.35709	.	0.196138	0.52532	D	0.000061	T	0.38348	0.1037	N	0.24115	0.695	0.49582	D	0.999809	B;P;P	0.49961	0.415;0.811;0.93	B;P;P	0.47941	0.254;0.562;0.459	T	0.11155	-1.0599	10	0.27785	T	0.31	-3.7406	4.7492	0.13052	0.2864:0.1557:0.558:0.0	.	469;465;426	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	I	469;465;426;469;469	ENSP00000397563:R469I;ENSP00000393412:R465I;ENSP00000421966:R426I;ENSP00000396861:R469I;ENSP00000296783:R469I	ENSP00000296783:R469I	R	+	2	0	PAPD4	79016803	1.000000	0.71417	0.900000	0.35374	0.965000	0.64279	1.777000	0.38604	0.384000	0.24942	0.563000	0.77884	AGA		0.318	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		T	78981047	G	T	78981047	3	4	61	1	0	0	0	0	1	0	0	0	11455	942	33	2	1460	2	PAPD4	5	78981047	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36148	78981047	101934213	3920	11905										
CMYA5	202333	broad.mit.edu	37	chr5	79026155	79026155	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattacccctgaacctgaaGattctaatttagtagaagaa	6	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79026155G>T	ENST00000446378.2	+	2	1598	c.1567G>T	c.(1567-1569)Gat>Tat	p.D523Y		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	523	Glu-rich.				negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.D523Y(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TGAACCTGAAGATTCTAATTT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	5											102	98	99					5																	79026155		1843	4094	5937	79061911	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.1567G>T	5.37:g.79026155G>T	ENSP00000394770:p.Asp523Tyr		79061911	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.316759	0.40996	.	.	ENSG00000164309	ENST00000446378	T	0.40756	1.02	5.8	4.92	0.64577	.	0.279515	0.25648	N	0.029239	T	0.44953	0.1318	L	0.34521	1.04	0.09310	N	1	D	0.67145	0.996	P	0.59703	0.862	T	0.36138	-0.9760	10	0.87932	D	0	.	7.5442	0.27757	0.0933:0.2606:0.6461:0.0	.	523	Q8N3K9	CMYA5_HUMAN	Y	523	ENSP00000394770:D523Y	ENSP00000394770:D523Y	D	+	1	0	CMYA5	79061911	0.000000	0.05858	0.734000	0.30879	0.452000	0.32318	0.169000	0.16641	2.758000	0.94735	0.563000	0.77884	GAT		0.423	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79026155	G	T	79026155	3	4	61	1	0	0	0	0	1	0	0	0	3596	942	33	2	1573	2	CMYA5	5	79026155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45108	79026155	101889105	3921	11906										
CMYA5	202333	broad.mit.edu	37	chr5	79029955	79029955	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggagatattttagataaGctaagtgaagaaacaggcca	11	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79029955G>A	ENST00000446378.2	+	2	5398	c.5367G>A	c.(5365-5367)aaG>aaA	p.K1789K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1789					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.K1789K(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TTTTAGATAAGCTAAGTGAAG	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	5											78	76	77					5																	79029955		1864	4096	5960	79065711	SO:0001819	synonymous_variant	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.5367G>A	5.37:g.79029955G>A			79065711	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																				0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79029955	G	A	79029955	2	1	61	1	0	0	0	0	0	0	0	1	3596	962	34	3		3	CMYA5	5	79029955	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3800	79029955	101885305	3922	11907										
CMYA5	202333	broad.mit.edu	37	chr5	79031104	79031104	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctgaggaaaagggaaaGaaaggaatttcatctttcaa	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79031104G>T	ENST00000446378.2	+	2	6547	c.6516G>T	c.(6514-6516)aaG>aaT	p.K2172N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2172					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.K2172N(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAAAGGGAAAGAAAGGAATTT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	5											63	63	63					5																	79031104		1883	4117	6000	79066860	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6516G>T	5.37:g.79031104G>T	ENSP00000394770:p.Lys2172Asn		79066860	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849821	0.51270	.	.	ENSG00000164309	ENST00000446378	T	0.21191	2.02	5.71	1.77	0.24775	.	0.344421	0.25032	N	0.033669	T	0.10852	0.0265	L	0.38175	1.15	0.20563	N	0.999889	P	0.49253	0.921	B	0.34489	0.184	T	0.28554	-1.0040	10	0.72032	D	0.01	.	3.5665	0.07901	0.2704:0.0:0.5531:0.1765	.	2172	Q8N3K9	CMYA5_HUMAN	N	2172	ENSP00000394770:K2172N	ENSP00000394770:K2172N	K	+	3	2	CMYA5	79066860	0.993000	0.37304	1.000000	0.80357	0.801000	0.45260	0.354000	0.20146	0.894000	0.36317	-0.145000	0.13849	AAG		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79031104	G	T	79031104	3	4	61	1	0	0	0	0	1	0	0	0	3596	933	33	2	6522	2	CMYA5	5	79031104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1149	79031104	101884156	3923	11908										
CMYA5	202333	broad.mit.edu	37	chr5	79032956	79032956	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaggatttccatctaaaGaatccgaaaggactttagct	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79032956G>A	ENST00000446378.2	+	2	8399	c.8368G>A	c.(8368-8370)Gaa>Aaa	p.E2790K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2790					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E2790K(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TCCATCTAAAGAATCCGAAAG	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	5											63	63	63					5																	79032956		1849	4085	5934	79068712	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.8368G>A	5.37:g.79032956G>A	ENSP00000394770:p.Glu2790Lys		79068712	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005864	0.35415	.	.	ENSG00000164309	ENST00000446378	T	0.44482	0.92	5.62	5.62	0.85841	.	0.440472	0.19328	N	0.116973	T	0.38585	0.1046	L	0.29908	0.895	0.21147	N	0.999776	P	0.47762	0.9	P	0.47299	0.543	T	0.33007	-0.9885	10	0.56958	D	0.05	.	11.8541	0.52427	0.081:0.0:0.919:0.0	.	2790	Q8N3K9	CMYA5_HUMAN	K	2790	ENSP00000394770:E2790K	ENSP00000394770:E2790K	E	+	1	0	CMYA5	79068712	0.380000	0.25131	0.102000	0.21198	0.102000	0.19082	1.977000	0.40589	2.662000	0.90505	0.655000	0.94253	GAA		0.393	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79032956	G	A	79032956	3	1	61	1	0	0	0	0	1	0	0	0	3596	943	33	3	8374	3	CMYA5	5	79032956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1852	79032956	101882304	3924	11909										
CMYA5	202333	broad.mit.edu	37	chr5	79033828	79033828	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaattaaatgttgaagaGaaactctcaaaggaagttac	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79033828G>T	ENST00000446378.2	+	2	9271	c.9240G>T	c.(9238-9240)gaG>gaT	p.E3080D		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3080				PQKLNVEEKLSKEVTEETISFPVSSVESALEHEYDLVKLDE -> SFKTIPLPDDSETVACHKTLKSRLEDEKVTPLKENKQK ETQ (in Ref. 3; AAH62664). {ECO:0000305}.	negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E3080D(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ATGTTGAAGAGAAACTCTCAA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	5											42	41	41					5																	79033828		1801	4067	5868	79069584	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9240G>T	5.37:g.79033828G>T	ENSP00000394770:p.Glu3080Asp		79069584	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	0.233	-1.019320	0.02078	.	.	ENSG00000164309	ENST00000446378	T	0.18657	2.2	5.84	1.24	0.21308	.	0.824437	0.10661	N	0.648728	T	0.11665	0.0284	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.31668	-0.9935	10	0.36615	T	0.2	.	7.4743	0.27368	0.2715:0.1442:0.5843:0.0	.	3080	Q8N3K9	CMYA5_HUMAN	D	3080	ENSP00000394770:E3080D	ENSP00000394770:E3080D	E	+	3	2	CMYA5	79069584	0.000000	0.05858	0.016000	0.15963	0.240000	0.25518	-0.031000	0.12287	0.041000	0.15688	-0.795000	0.03280	GAG		0.343	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79033828	G	T	79033828	3	4	61	1	0	0	0	0	1	0	0	0	3596	933	33	2	9246	2	CMYA5	5	79033828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	872	79033828	101881432	3925	11910										
CMYA5	202333	broad.mit.edu	37	chr5	79035047	79035047	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgggcagcgagaggaaaGaagaagaccaattatcatct	12	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79035047G>T	ENST00000446378.2	+	2	10490	c.10459G>T	c.(10459-10461)Gaa>Taa	p.E3487*		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3487					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E3487*(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CGAGAGGAAAGAAGAAGACCA	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											82	74	77					5																	79035047		1906	4123	6029	79070803	SO:0001587	stop_gained	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.10459G>T	5.37:g.79035047G>T	ENSP00000394770:p.Glu3487*		79070803	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Nonsense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	50	16.528481	0.99865	.	.	ENSG00000164309	ENST00000446378	.	.	.	5.44	5.44	0.79542	.	0.580079	0.15530	N	0.257567	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	15.0212	0.71632	0.0:0.0:0.8489:0.1511	.	.	.	.	X	3487	.	ENSP00000394770:E3487X	E	+	1	0	CMYA5	79070803	1.000000	0.71417	0.303000	0.25071	0.027000	0.11550	3.178000	0.50879	2.541000	0.85698	0.655000	0.94253	GAA		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79035047	G	T	79035047	4	4	61	1	0	0	0	0	0	1	0	0	3596	943	33	2	10465	2	CMYA5	5	79035047	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1219	79035047	101880213	3926	11911										
SPZ1	84654	broad.mit.edu	37	chr5	79617186	79617186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaacaagcaagcaatgaaGggtacattttggaaaaaaga	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79617186G>T	ENST00000296739.4	+	1	1397	c.1152G>T	c.(1150-1152)aaG>aaT	p.K384N		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	384					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K384N(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		AAGCAATGAAGGGTACATTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											81	79	80					5																	79617186		1857	4098	5955	79652942	SO:0001583	missense	84654				CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1152G>T	5.37:g.79617186G>T	ENSP00000369611:p.Lys384Asn		79652942	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031184	0.19590	.	.	ENSG00000164299	ENST00000296739	T	0.30981	1.51	3.34	-4.97	0.03029	.	0.856727	0.09896	N	0.741688	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.32160	0.358	B	0.29785	0.107	T	0.17684	-1.0361	10	0.48119	T	0.1	-8.7368	3.9738	0.09465	0.4314:0.0:0.3124:0.2562	.	384	Q9BXG8	SPZ1_HUMAN	N	384	ENSP00000369611:K384N	ENSP00000369611:K384N	K	+	3	2	SPZ1	79652942	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.071000	0.03437	-1.225000	0.02578	0.557000	0.71058	AAG		0.353	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		T	79617186	G	T	79617186	3	4	61	1	0	0	0	0	1	0	0	0	15166	991	35	2	1154	2	SPZ1	5	79617186	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	582139	79617186	101298074	3927	11912										
ZFYVE16	9765	broad.mit.edu	37	chr5	79733112	79733112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaatagagaaatcggagGaatcaaagaattgggtataa	10	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79733112G>A	ENST00000338008.5	+	3	788	c.608G>A	c.(607-609)gGa>gAa	p.G203E	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.G203E|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.G203E	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	203					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)	p.G203E(1)		breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GAAATCGGAGGAATCAAAGAA	0.313																																					Melanoma(150;1452 1854 16018 17851 37292)											1	Substitution - Missense(1)	large_intestine(1)	5											34	38	37					5																	79733112		2197	4294	6491	79768868	SO:0001583	missense	9765			AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.608G>A	5.37:g.79733112G>A	ENSP00000337159:p.Gly203Glu		79768868	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	37	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	G	1.939	-0.443955	0.04604	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.38240	1.15;1.15;1.15	5.15	0.974	0.19715	.	0.758897	0.11642	N	0.543713	T	0.18383	0.0441	L	0.27053	0.805	0.09310	N	1	P;B	0.36909	0.573;0.001	B;B	0.39217	0.294;0.002	T	0.16808	-1.0390	10	0.02654	T	1	-0.0233	2.4023	0.04404	0.1759:0.3827:0.3033:0.1381	.	203;203	Q7Z3T8-3;Q7Z3T8	.;ZFY16_HUMAN	E	203	ENSP00000337159:G203E;ENSP00000423663:G203E;ENSP00000426848:G203E	ENSP00000337159:G203E	G	+	2	0	ZFYVE16	79768868	0.000000	0.05858	0.006000	0.13384	0.424000	0.31475	0.025000	0.13577	0.628000	0.30357	0.467000	0.42956	GGA		0.313	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		A	79733112	G	A	79733112	3	1	61	1	0	0	0	0	1	0	0	0	17703	1174	41	3	614	3	ZFYVE16	5	79733112	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115926	79733112	101182148	3928	11913										
ZFYVE16	9765	broad.mit.edu	37	chr5	79768673	79768673	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaattacatgtgggaaagTtgatgcagtagacctgagag	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79768673T>G	ENST00000338008.5	+	15	4298	c.4118T>G	c.(4117-4119)gTt>gGt	p.V1373G	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.V1373G|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.V1373G	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1373					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)	p.V1373G(1)		breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TGTGGGAAAGTTGATGCAGTA	0.368																																					Melanoma(150;1452 1854 16018 17851 37292)											1	Substitution - Missense(1)	large_intestine(1)	5											100	102	101					5																	79768673		2203	4300	6503	79804429	SO:0001583	missense	9765			AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.4118T>G	5.37:g.79768673T>G	ENSP00000337159:p.Val1373Gly		79804429	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	37	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757723	0.49468	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.41400	1.0;1.0;1.0	5.74	3.36	0.38483	Domain of unknown function DUF3480 (1);	0.126329	0.35525	N	0.003154	T	0.37376	0.1001	L	0.47716	1.5	0.58432	D	0.999996	B;B	0.26318	0.146;0.024	B;B	0.32928	0.155;0.062	T	0.19451	-1.0305	10	0.66056	D	0.02	-8.3394	8.8083	0.34952	0.0:0.1615:0.0:0.8385	.	183;1373	B3KXA7;Q7Z3T8	.;ZFY16_HUMAN	G	1373	ENSP00000337159:V1373G;ENSP00000423663:V1373G;ENSP00000426848:V1373G	ENSP00000337159:V1373G	V	+	2	0	ZFYVE16	79804429	0.004000	0.15560	0.992000	0.48379	0.989000	0.77384	-0.067000	0.11579	0.445000	0.26639	0.533000	0.62120	GTT		0.368	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		G	79768673	T	G	79768673	3	3	61	1	0	0	0	0	1	0	0	0	17703	1725	60	4	4172	4	ZFYVE16	5	79768673	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	35561	79768673	101146587	3929	11914										
FAM151B	167555	broad.mit.edu	37	chr5	79815585	79815585	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcgtcctgtatggattAatgccgatattcttcctggt	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79815585A>G	ENST00000282226.4	+	4	546	c.391A>G	c.(391-393)Aat>Gat	p.N131D	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	131								p.N131D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		TGTATGGATTAATGCCGATAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											131	115	120					5																	79815585		2203	4300	6503	79851341	SO:0001583	missense	167555				CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.391A>G	5.37:g.79815585A>G	ENSP00000282226:p.Asn131Asp		79851341	A2RRE4	Missense_Mutation	SNP	ENST00000282226.4	37	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	a	27.0	4.788430	0.90367	.	.	ENSG00000152380	ENST00000282226	T	0.15372	2.43	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.49949	0.1587	M	0.91300	3.195	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.60959	-0.7159	10	0.66056	D	0.02	-20.9775	15.0519	0.71881	1.0:0.0:0.0:0.0	.	131	Q6UXP7	F151B_HUMAN	D	131	ENSP00000282226:N131D	ENSP00000282226:N131D	N	+	1	0	FAM151B	79851341	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.596000	0.82721	2.190000	0.69967	0.519000	0.50382	AAT		0.393	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548		G	79815585	A	G	79815585	3	3	61	1	0	0	0	0	1	0	0	0	5475	362	13	4	405	4	FAM151B	5	79815585	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	46912	79815585	101099675	3930	11915										
ANKRD34B	340120	broad.mit.edu	37	chr5	79855228	79855228	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccaaaaagcgtcagttccGtttcagaagaatgtgaaagt	10	7	2	3	rs147746790	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79855228G>A	ENST00000338682.3	-	5	1283	c.611C>T	c.(610-612)aCg>aTg	p.T204M		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	204						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T204M(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		CGTCAGTTCCGTTTCAGAAGA	0.488													G|||	3	0.000599042	0.0015	0	5008	,	,		20788	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	140	132	135		611	-0.5	0	5	dbSNP_134	135	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ANKRD34B	NM_001004441.2	81	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	204/515	79855228	2,13004	2203	4300	6503	79890984	SO:0001583	missense	340120				CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"Ankyrin repeat domain containing"	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.611C>T	5.37:g.79855228G>A	ENSP00000339802:p.Thr204Met		79890984	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	2.694	-0.272560	0.05716	2.27E-4	1.16E-4	ENSG00000189127	ENST00000338682	T	0.20332	2.08	5.74	-0.515	0.11954	.	0.351137	0.25636	N	0.029306	T	0.17534	0.0421	M	0.63428	1.95	0.09310	N	1	B	0.17268	0.021	B	0.09377	0.004	T	0.16364	-1.0405	10	0.48119	T	0.1	-2.2764	6.01	0.19569	0.3703:0.0:0.5082:0.1215	.	204	A5PLL1	AN34B_HUMAN	M	204	ENSP00000339802:T204M	ENSP00000339802:T204M	T	-	2	0	ANKRD34B	79890984	0.001000	0.12720	0.001000	0.08648	0.014000	0.08584	1.106000	0.31098	0.082000	0.17018	0.655000	0.94253	ACG		0.488	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		A	79855228	G	A	79855228	3	1	61	1	0	0	0	0	1	0	0	0	663	1145	40	1	937	1	ANKRD34B	5	79855228	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39643	79855228	101060032	3931	11916										
MSH3	4437	broad.mit.edu	37	chr5	79966110	79966110	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggatataagtatagattCtttggggaagatgcagaggt	14	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:79966110C>A	ENST00000265081.6	+	4	854	c.774C>A	c.(772-774)ttC>ttA	p.F258L		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	258	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)	p.F249L(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AGTATAGATTCTTTGGGGAAG	0.348								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)											1	Substitution - Missense(1)	large_intestine(1)	5											143	145	144					5																	79966110		2203	4300	6503	80001866	SO:0001583	missense	4437			U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.774C>A	5.37:g.79966110C>A	ENSP00000265081:p.Phe258Leu		80001866	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138791	0.77775	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86694	-2.16	5.67	4.81	0.61882	DNA mismatch repair protein MutS, N-terminal (2);DNA mismatch repair protein MutS-like, N-terminal (1);	0.051793	0.85682	D	0.000000	D	0.86138	0.5861	N	0.16037	0.36	0.43003	D	0.994522	D	0.76494	0.999	D	0.87578	0.998	D	0.84765	0.0764	9	.	.	.	-18.1755	11.3733	0.49713	0.0:0.853:0.0:0.147	.	258	P20585	MSH3_HUMAN	L	258;249	ENSP00000265081:F258L	.	F	+	3	2	MSH3	80001866	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.739000	0.55075	1.399000	0.46721	0.655000	0.94253	TTC		0.348	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		A	79966110	C	A	79966110	3	1	61	1	0	0	0	0	1	0	0	0	9901	912	32	2	788	2	MSH3	5	79966110	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110882	79966110	100949150	3932	11917										
MSH3	4437	broad.mit.edu	37	chr5	80021366	80021366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacagagttttatgcaaaaGatacagttgacatcaaaggt	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80021366G>T	ENST00000265081.6	+	9	1515	c.1435G>T	c.(1435-1437)Gat>Tat	p.D479Y	MSH3_ENST00000512258.1_3'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	479					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)	p.D470Y(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TTATGCAAAAGATACAGTTGA	0.338								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)											1	Substitution - Missense(1)	large_intestine(1)	5											129	127	128					5																	80021366		2203	4300	6503	80057122	SO:0001583	missense	4437			U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1435G>T	5.37:g.80021366G>T	ENSP00000265081:p.Asp479Tyr		80057122	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919138	0.52546	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.87809	-2.3	5.25	5.25	0.73442	DNA mismatch repair protein MutS, connector (2);	0.896444	0.09578	N	0.783292	D	0.90762	0.7100	L	0.50333	1.59	0.33022	D	0.528927	D	0.61080	0.989	P	0.61070	0.883	D	0.88502	0.3083	9	.	.	.	-13.6274	14.2877	0.66256	0.0:0.15:0.85:0.0	.	479	P20585	MSH3_HUMAN	Y	479;470	ENSP00000265081:D479Y	.	D	+	1	0	MSH3	80057122	1.000000	0.71417	0.914000	0.36105	0.587000	0.36485	3.135000	0.50546	2.613000	0.88420	0.579000	0.79373	GAT		0.338	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		T	80021366	G	T	80021366	3	4	61	1	0	0	0	0	1	0	0	0	9901	942	33	2	1469	2	MSH3	5	80021366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55256	80021366	100893894	3933	11918										
RASGRF2	5924	broad.mit.edu	37	chr5	80381719	80381719	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgccaaatcaaagctagaGgaactatccaggtatgccaa	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80381719G>T	ENST00000265080.4	+	8	1327	c.1260G>T	c.(1258-1260)gaG>gaT	p.E420D	RASGRF2_ENST00000502677.1_3'UTR	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	420	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E420D(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CAAAGCTAGAGGAACTATCCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	94	94					5																	80381719		2203	4300	6503	80417475	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.1260G>T	5.37:g.80381719G>T	ENSP00000265080:p.Glu420Asp		80417475	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447944	0.63178	.	.	ENSG00000113319	ENST00000265080	T	0.65549	-0.16	5.57	2.35	0.29111	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.67515	0.2901	L	0.52364	1.645	0.46874	D	0.999238	D;D	0.65815	0.995;0.986	D;D	0.70227	0.968;0.913	T	0.65721	-0.6099	10	0.56958	D	0.05	.	5.4801	0.16719	0.5129:0.0:0.4871:0.0	.	420;420	D6RAS9;O14827	.;RGRF2_HUMAN	D	420	ENSP00000265080:E420D	ENSP00000265080:E420D	E	+	3	2	RASGRF2	80417475	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	1.312000	0.33574	0.835000	0.34877	0.650000	0.86243	GAG		0.448	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		T	80381719	G	T	80381719	3	4	61	1	0	0	0	0	1	0	0	0	13110	991	35	2	1290	2	RASGRF2	5	80381719	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	360353	80381719	100533541	3934	11919										
CKMT2	1160	broad.mit.edu	37	chr5	80550830	80550830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcacccaagggcagttcGacgagcattacgtgctgtct	11	11	2	1	rs551718764		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80550830G>A	ENST00000424301.2	+	6	704	c.466G>A	c.(466-468)Gac>Aac	p.D156N	CKMT2-AS1_ENST00000505295.1_RNA|CKMT2_ENST00000254035.4_Missense_Mutation_p.D156N|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.D156N	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	156					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.D156N(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	AGGGCAGTTCGACGAGCATTA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5											55	56	56					5																	80550830		2203	4300	6503	80586586	SO:0001583	missense	1160				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.466G>A	5.37:g.80550830G>A	ENSP00000404203:p.Asp156Asn		80586586	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	ENST00000424301.2	37	CCDS4053.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035082	0.75617	.	.	ENSG00000131730	ENST00000254035;ENST00000511719;ENST00000437669;ENST00000424301	T;T;T;T	0.25414	2.64;1.8;2.64;2.64	5.8	5.8	0.92144	ATP:guanido phosphotransferase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65668	0.2713	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74765	-0.3554	10	0.72032	D	0.01	-28.0346	20.0693	0.97712	0.0:0.0:1.0:0.0	.	156	P17540	KCRS_HUMAN	N	156	ENSP00000254035:D156N;ENSP00000423264:D156N;ENSP00000410289:D156N;ENSP00000404203:D156N	ENSP00000254035:D156N	D	+	1	0	CKMT2	80586586	1.000000	0.71417	0.320000	0.25306	0.089000	0.18198	7.655000	0.83696	2.758000	0.94735	0.563000	0.77884	GAC		0.637	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		A	80550830	G	A	80550830	3	1	61	1	0	0	0	0	1	0	0	0	3457	1058	37	1	480	1	CKMT2	5	80550830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	169111	80550830	100364430	3935	11920										
CKMT2	1160	broad.mit.edu	37	chr5	80551031	80551031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaccagcagcggctcatcGatgtgagtagcagatggggc	16	9	1	2	rs371191747		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80551031G>A	ENST00000424301.2	+	6	905	c.667G>A	c.(667-669)Gat>Aat	p.D223N	CKMT2-AS1_ENST00000505295.1_RNA|CKMT2_ENST00000254035.4_Missense_Mutation_p.D223N|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.D223N	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	223	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.D223N(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	GCGGCTCATCGATGTGAGTAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	5											39	35	36					5																	80551031		2203	4300	6503	80586787	SO:0001583	missense	1160				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.667G>A	5.37:g.80551031G>A	ENSP00000404203:p.Asp223Asn		80586787	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	ENST00000424301.2	37	CCDS4053.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087936	0.55968	.	.	ENSG00000131730	ENST00000254035;ENST00000437669;ENST00000424301	T;T;T	0.11495	2.77;2.77;2.77	5.65	5.65	0.86999	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.099120	0.64402	D	0.000002	T	0.09291	0.0229	N	0.16130	0.375	0.80722	D	1	B	0.11235	0.004	B	0.15052	0.012	T	0.26258	-1.0108	10	0.40728	T	0.16	-37.2184	19.7278	0.96172	0.0:0.0:1.0:0.0	.	223	P17540	KCRS_HUMAN	N	223	ENSP00000254035:D223N;ENSP00000410289:D223N;ENSP00000404203:D223N	ENSP00000254035:D223N	D	+	1	0	CKMT2	80586787	1.000000	0.71417	0.997000	0.53966	0.356000	0.29392	9.470000	0.97683	2.681000	0.91329	0.563000	0.77884	GAT		0.632	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		A	80551031	G	A	80551031	3	1	61	1	0	0	0	0	1	0	0	0	3457	1058	37	1	681	1	CKMT2	5	80551031	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	201	80551031	100364229	3936	11921										
CKMT2	1160	broad.mit.edu	37	chr5	80554945	80554945	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttctacttgtaggtagaaCggttaatccaagaacgaggc	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80554945C>T	ENST00000424301.2	+	9	1124	c.886C>T	c.(886-888)Cgg>Tgg	p.R296W	CKMT2-AS1_ENST00000505295.1_RNA|CKMT2_ENST00000254035.4_Missense_Mutation_p.R296W|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.R296W	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	296	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.R296W(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	GTAGGTAGAACGGTTAATCCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											211	196	201					5																	80554945		2203	4300	6503	80590701	SO:0001583	missense	1160				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.886C>T	5.37:g.80554945C>T	ENSP00000404203:p.Arg296Trp		80590701	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	ENST00000424301.2	37	CCDS4053.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520452	0.64747	.	.	ENSG00000131730	ENST00000254035;ENST00000437669;ENST00000424301	T;T;T	0.23754	1.89;1.89;1.89	5.29	4.34	0.51931	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.195693	0.46442	D	0.000297	T	0.35248	0.0925	M	0.74258	2.255	0.51012	D	0.999908	D	0.61697	0.99	P	0.48114	0.567	T	0.28522	-1.0041	10	0.87932	D	0	-41.165	10.6946	0.45892	0.4316:0.5684:0.0:0.0	.	296	P17540	KCRS_HUMAN	W	296	ENSP00000254035:R296W;ENSP00000410289:R296W;ENSP00000404203:R296W	ENSP00000254035:R296W	R	+	1	2	CKMT2	80590701	0.997000	0.39634	0.968000	0.41197	0.685000	0.39939	1.263000	0.33004	2.483000	0.83821	0.591000	0.81541	CGG		0.468	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		T	80554945	C	T	80554945	3	4	61	1	0	0	0	0	1	0	0	0	3457	527	19	1	912	1	CKMT2	5	80554945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3914	80554945	100360315	3937	11922										
ACOT12	134526	broad.mit.edu	37	chr5	80626645	80626645	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacttacgatgcatgaattGctgtcaatagcatggatgag	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80626645G>T	ENST00000307624.3	-	14	1534	c.1506C>A	c.(1504-1506)agC>agA	p.S502R	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	502	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)	p.S502R(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		TGCATGAATTGCTGTCAATAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	80	82					5																	80626645		2203	4300	6503	80662401	SO:0001583	missense	134526			AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.1506C>A	5.37:g.80626645G>T	ENSP00000303246:p.Ser502Arg		80662401	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	G	8.992	0.978035	0.18812	.	.	ENSG00000172497	ENST00000307624	T	0.31510	1.49	5.74	3.96	0.45880	Lipid-binding START (2);START-like domain (1);	0.257712	0.46442	D	0.000298	T	0.41190	0.1148	M	0.73598	2.24	0.80722	D	1	B	0.33964	0.434	P	0.45610	0.487	T	0.27434	-1.0074	10	0.35671	T	0.21	-18.2073	8.069	0.30678	0.1785:0.0:0.8215:0.0	.	502	Q8WYK0	ACO12_HUMAN	R	502	ENSP00000303246:S502R	ENSP00000303246:S502R	S	-	3	2	ACOT12	80662401	0.191000	0.23288	0.613000	0.29037	0.012000	0.07955	1.856000	0.39389	1.439000	0.47511	-0.254000	0.11334	AGC		0.418	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		T	80626645	G	T	80626645	3	4	61	1	0	0	0	0	1	0	0	0	150	1310	46	2	169	2	ACOT12	5	80626645	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71700	80626645	100288615	3938	11923										
ACOT12	134526	broad.mit.edu	37	chr5	80655779	80655779	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtatcttcatgttgtaatcGaactttccttctctcagcag	7	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80655779G>A	ENST00000307624.3	-	5	467	c.439C>T	c.(439-441)Cga>Tga	p.R147*	ACOT12_ENST00000513751.1_Nonsense_Mutation_p.R147*	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	147					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)	p.R147*(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		TGTTGTAATCGAACTTTCCTT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											132	129	130					5																	80655779		2203	4300	6503	80691535	SO:0001587	stop_gained	134526			AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.439C>T	5.37:g.80655779G>A	ENSP00000303246:p.Arg147*		80691535	B3KVK9|Q5FWE9	Nonsense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.121210	0.56613	.	.	ENSG00000172497	ENST00000307624;ENST00000513751	.	.	.	5.04	3.07	0.35406	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9079	13.1836	0.59668	0.0:0.0:0.7144:0.2856	.	.	.	.	X	147	.	ENSP00000303246:R147X	R	-	1	2	ACOT12	80691535	1.000000	0.71417	0.958000	0.39756	0.533000	0.34776	2.560000	0.45896	1.203000	0.43233	0.655000	0.94253	CGA		0.313	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		A	80655779	G	A	80655779	4	1	61	1	0	0	0	0	0	1	0	0	150	1066	37	1	1272	1	ACOT12	5	80655779	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29134	80655779	100259481	3939	11924										
ACOT12	134526	broad.mit.edu	37	chr5	80659684	80659684	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaatgccagtgagcatatCctgtaccatgaccttgatac	7	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:80659684C>A	ENST00000307624.3	-	4	311	c.283G>T	c.(283-285)Gat>Tat	p.D95Y	ACOT12_ENST00000513751.1_Missense_Mutation_p.D95Y	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	95	Acyl coenzyme A hydrolase 1.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)	p.D95Y(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		GTGAGCATATCCTGTACCATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	104	105					5																	80659684		2203	4300	6503	80695440	SO:0001583	missense	134526			AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.283G>T	5.37:g.80659684C>A	ENSP00000303246:p.Asp95Tyr		80695440	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797466	0.70567	.	.	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.37915	1.17;1.17	6.06	6.06	0.98353	Thioesterase superfamily (1);	0.055536	0.64402	D	0.000001	T	0.72732	0.3497	H	0.94847	3.59	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.79487	-0.1783	10	0.87932	D	0	-5.212	19.3923	0.94587	0.0:1.0:0.0:0.0	.	95;95	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	Y	95	ENSP00000303246:D95Y;ENSP00000421628:D95Y	ENSP00000303246:D95Y	D	-	1	0	ACOT12	80695440	1.000000	0.71417	0.970000	0.41538	0.587000	0.36485	5.322000	0.65852	2.882000	0.98803	0.655000	0.94253	GAT		0.343	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		A	80659684	C	A	80659684	3	1	61	1	0	0	0	0	1	0	0	0	150	855	30	2	1432	2	ACOT12	5	80659684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3905	80659684	100255576	3940	11925										
VCAN	1462	broad.mit.edu	37	chr5	82779403	82779403	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtaacccatgcgctacaTaaaggtgagtgtgctaacaa	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82779403T>C	ENST00000265077.3	+	2	631	c.66T>C	c.(64-66)caT>caC	p.H22H	VCAN_ENST00000513984.1_Silent_p.H22H|VCAN_ENST00000512590.2_5'UTR|VCAN_ENST00000502527.2_Silent_p.H22H|VCAN_ENST00000342785.4_Silent_p.H22H|VCAN_ENST00000343200.5_Silent_p.H22H	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	22	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.H22H(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	ATGCGCTACATAAAGGTGAGT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	5											135	125	129					5																	82779403		2203	4299	6502	82815159	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.66T>C	5.37:g.82779403T>C			82815159	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.333	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82779403	T	C	82779403	2	2	61	1	0	0	0	0	0	0	0	1	17178	1403	49	4		4	VCAN	5	82779403	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2119719	82779403	98135857	3941	11926										
VCAN	1462	broad.mit.edu	37	chr5	82786075	82786075	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggacaaaaatggaaaaGatttgaaagagactactgtc	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82786075G>T	ENST00000265077.3	+	3	794	c.229G>T	c.(229-231)Gat>Tat	p.D77Y	VCAN_ENST00000513984.1_Missense_Mutation_p.D77Y|VCAN_ENST00000512590.2_Missense_Mutation_p.D29Y|VCAN_ENST00000502527.2_Missense_Mutation_p.D77Y|VCAN_ENST00000342785.4_Missense_Mutation_p.D77Y|VCAN_ENST00000343200.5_Missense_Mutation_p.D77Y	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	77	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.D77Y(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AAATGGAAAAGATTTGAAAGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	106	107					5																	82786075		2203	4300	6503	82821831	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.229G>T	5.37:g.82786075G>T	ENSP00000265077:p.Asp77Tyr		82821831	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003492	0.74932	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000513960;ENST00000513984;ENST00000502527	T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000005	T	0.78227	0.4250	L	0.59436	1.845	0.48087	D	0.999583	D;B;D;D;B	0.89917	1.0;0.051;1.0;1.0;0.34	D;B;D;D;B	0.97110	0.994;0.059;1.0;0.999;0.279	T	0.78763	-0.2077	10	0.87932	D	0	.	19.9898	0.97362	0.0:0.0:1.0:0.0	.	77;77;77;77;77	P13611-3;P13611-4;P13611-2;P13611;Q86W61	.;.;.;CSPG2_HUMAN;.	Y	77;77;77;29;77;77;77	ENSP00000265077:D77Y;ENSP00000340062:D77Y;ENSP00000342768:D77Y;ENSP00000425959:D29Y;ENSP00000426251:D77Y;ENSP00000426715:D77Y;ENSP00000421362:D77Y	ENSP00000265077:D77Y	D	+	1	0	VCAN	82821831	1.000000	0.71417	0.981000	0.43875	0.807000	0.45602	2.871000	0.48459	2.733000	0.93635	0.655000	0.94253	GAT		0.433	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82786075	G	T	82786075	3	4	61	1	0	0	0	0	1	0	0	0	17178	942	33	2	235	2	VCAN	5	82786075	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6672	82786075	98129185	3942	11927										
VCAN	1462	broad.mit.edu	37	chr5	82816285	82816285	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaaacagaagaagaagtCttctctgggatgaaactctc	10	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82816285C>T	ENST00000265077.3	+	7	2725	c.2160C>T	c.(2158-2160)gtC>gtT	p.V720V	VCAN_ENST00000512590.2_Silent_p.V672V|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Silent_p.V720V|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	720	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.V720V(2)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AAGAAGAAGTCTTCTCTGGGA	0.363																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	5											70	72	71					5																	82816285		2203	4300	6503	82852041	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2160C>T	5.37:g.82816285C>T			82852041	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.363	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82816285	C	T	82816285	2	4	61	1	0	0	0	0	0	0	0	1	17178	900	32	3		3	VCAN	5	82816285	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30210	82816285	98098975	3943	11928										
VCAN	1462	broad.mit.edu	37	chr5	82817633	82817633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttatggaagaaaccactActgagaaaacatccctagag	8	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82817633A>G	ENST00000265077.3	+	7	4073	c.3508A>G	c.(3508-3510)Act>Gct	p.T1170A	VCAN_ENST00000512590.2_Missense_Mutation_p.T1122A|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.T1170A|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1170	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.T1170A(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AGAAACCACTACTGAGAAAAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											102	104	103					5																	82817633		2203	4300	6503	82853389	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.3508A>G	5.37:g.82817633A>G	ENSP00000265077:p.Thr1170Ala		82853389	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.636184	0.00114	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.84873	-1.84;-1.89;-1.91	5.7	-1.26	0.09376	.	0.474634	0.19648	N	0.109293	T	0.64746	0.2626	N	0.25144	0.715	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.11329	0.006;0.002	T	0.46105	-0.9215	10	0.08179	T	0.78	.	1.9268	0.03319	0.5429:0.1248:0.2119:0.1204	.	1170;1170	P13611-3;P13611	.;CSPG2_HUMAN	A	1170;1170;1122	ENSP00000265077:T1170A;ENSP00000342768:T1170A;ENSP00000425959:T1122A	ENSP00000265077:T1170A	T	+	1	0	VCAN	82853389	0.000000	0.05858	0.263000	0.24496	0.014000	0.08584	0.199000	0.17237	0.093000	0.17368	-1.517000	0.00937	ACT		0.363	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82817633	A	G	82817633	3	3	61	1	0	0	0	0	1	0	0	0	17178	391	14	4	3530	4	VCAN	5	82817633	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1348	82817633	98097627	3944	11929										
VCAN	1462	broad.mit.edu	37	chr5	82832870	82832870	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtcatccaatagattcaGaatctaaagaagatgaacct	7	7	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82832870G>T	ENST00000265077.3	+	8	4613	c.4048G>T	c.(4048-4050)Gaa>Taa	p.E1350*	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Nonsense_Mutation_p.E363*	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1350	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.E1350*(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AATAGATTCAGAATCTAAAGA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											84	86	85					5																	82832870		2203	4300	6503	82868626	SO:0001587	stop_gained	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4048G>T	5.37:g.82832870G>T	ENSP00000265077:p.Glu1350*		82868626	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	47	13.371738	0.99738	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	.	.	.	5.71	4.66	0.58398	.	0.198109	0.35970	N	0.002875	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	15.5911	0.76530	0.0768:0.0:0.9232:0.0	.	.	.	.	X	1350;363;363	.	ENSP00000265077:E1350X	E	+	1	0	VCAN	82868626	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.623000	0.54224	2.703000	0.92315	0.555000	0.69702	GAA		0.338	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82832870	G	T	82832870	4	4	61	1	0	0	0	0	0	1	0	0	17178	943	33	2	4074	2	VCAN	5	82832870	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15237	82832870	98082390	3945	11930										
VCAN	1462	broad.mit.edu	37	chr5	82834539	82834539	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacccaaacatccagggaaaTagtgatttcagagcgattag	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82834539T>G	ENST00000265077.3	+	8	6282	c.5717T>G	c.(5716-5718)aTa>aGa	p.I1906R	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.I919R|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1906	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.I1906R(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	TCCAGGGAAATAGTGATTTCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	110	108					5																	82834539		2203	4300	6503	82870295	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5717T>G	5.37:g.82834539T>G	ENSP00000265077:p.Ile1906Arg		82870295	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	0.180	-1.062916	0.01950	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84944	-1.9;-1.92;3.29	5.71	-3.52	0.04682	.	0.959699	0.08689	N	0.908259	T	0.62466	0.2430	N	0.08118	0	0.09310	N	1	B;B	0.17038	0.02;0.0	B;B	0.18871	0.023;0.0	T	0.50197	-0.8856	10	0.16420	T	0.52	.	2.4967	0.04623	0.2023:0.3195:0.0726:0.4056	.	919;1906	P13611-2;P13611	.;CSPG2_HUMAN	R	1906;919;919	ENSP00000265077:I1906R;ENSP00000340062:I919R;ENSP00000426251:I919R	ENSP00000265077:I1906R	I	+	2	0	VCAN	82870295	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.597000	0.05713	-0.454000	0.07066	-1.216000	0.01612	ATA		0.418	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82834539	T	G	82834539	3	3	61	1	0	0	0	0	1	0	0	0	17178	1406	49	4	5743	4	VCAN	5	82834539	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1669	82834539	98080721	3946	11931										
VCAN	1462	broad.mit.edu	37	chr5	82836248	82836248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggtgccaagcgctaaaGctgttactgctgatggattc	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82836248G>A	ENST00000265077.3	+	8	7991	c.7426G>A	c.(7426-7428)Gct>Act	p.A2476T	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.A1489T|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2476	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.A2476T(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AAGCGCTAAAGCTGTTACTGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	89	91					5																	82836248		2203	4300	6503	82872004	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7426G>A	5.37:g.82836248G>A	ENSP00000265077:p.Ala2476Thr		82872004	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.632692	0.29068	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.39787	1.06;1.06	6.17	3.45	0.39498	.	0.396219	0.24347	N	0.039301	T	0.32734	0.0839	L	0.52364	1.645	0.09310	N	1	B;B	0.27351	0.176;0.11	B;B	0.21917	0.037;0.037	T	0.16778	-1.0391	10	0.21540	T	0.41	.	9.281	0.37729	0.2818:0.0:0.7182:0.0	.	1489;2476	P13611-2;P13611	.;CSPG2_HUMAN	T	2476;1489	ENSP00000265077:A2476T;ENSP00000340062:A1489T	ENSP00000265077:A2476T	A	+	1	0	VCAN	82872004	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	1.086000	0.30853	0.477000	0.27464	0.655000	0.94253	GCT		0.473	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82836248	G	A	82836248	3	1	61	1	0	0	0	0	1	0	0	0	17178	971	34	3	7452	3	VCAN	5	82836248	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1709	82836248	98079012	3947	11932										
VCAN	1462	broad.mit.edu	37	chr5	82837061	82837061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgggccaatttgaaaggActcaggaggagtatgaagac	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82837061A>G	ENST00000265077.3	+	8	8804	c.8239A>G	c.(8239-8241)Act>Gct	p.T2747A	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.T1760A|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2747	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.T2747A(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	ATTTGAAAGGACTCAGGAGGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	38	39					5																	82837061		2203	4300	6503	82872817	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8239A>G	5.37:g.82837061A>G	ENSP00000265077:p.Thr2747Ala		82872817	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.475686	0.44044	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.48836	0.8;0.8	6.17	5.0	0.66597	.	0.189468	0.38381	N	0.001716	T	0.43787	0.1263	M	0.61703	1.905	0.54753	D	0.999989	P;P	0.49559	0.925;0.877	P;B	0.44561	0.453;0.265	T	0.38607	-0.9653	10	0.33141	T	0.24	.	5.5346	0.17003	0.7251:0.167:0.1079:0.0	.	1760;2747	P13611-2;P13611	.;CSPG2_HUMAN	A	2747;1760	ENSP00000265077:T2747A;ENSP00000340062:T1760A	ENSP00000265077:T2747A	T	+	1	0	VCAN	82872817	0.999000	0.42202	0.997000	0.53966	0.905000	0.53344	2.420000	0.44679	1.132000	0.42129	0.533000	0.62120	ACT		0.423	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82837061	A	G	82837061	3	3	61	1	0	0	0	0	1	0	0	0	17178	275	10	4	8265	4	VCAN	5	82837061	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	813	82837061	98078199	3948	11933										
VCAN	1462	broad.mit.edu	37	chr5	82837810	82837810	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgccttggctaagtccAcagacttctgagaggcccac	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82837810A>G	ENST00000265077.3	+	8	9553	c.8988A>G	c.(8986-8988)ccA>ccG	p.P2996P	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Silent_p.P2009P|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2996	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.P2996P(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	GGCTAAGTCCACAGACTTCTG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5											53	55	54					5																	82837810		2203	4300	6503	82873566	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8988A>G	5.37:g.82837810A>G			82873566	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.502	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82837810	A	G	82837810	2	3	61	1	0	0	0	0	0	0	0	1	17178	146	6	4		4	VCAN	5	82837810	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	749	82837810	98077450	3949	11934										
VCAN	1462	broad.mit.edu	37	chr5	82849228	82849228	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacaaattccaagggcagtGctacaaatactttgcccatc	7	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82849228G>A	ENST00000265077.3	+	11	10104	c.9539G>A	c.(9538-9540)tGc>tAc	p.C3180Y	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Missense_Mutation_p.C1378Y|VCAN_ENST00000502527.2_Missense_Mutation_p.C439Y|VCAN_ENST00000342785.4_Missense_Mutation_p.C1426Y|VCAN_ENST00000343200.5_Missense_Mutation_p.C2193Y|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3180	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.C3180Y(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	CAAGGGCAGTGCTACAAATAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											138	119	126					5																	82849228		2203	4300	6503	82884984	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9539G>A	5.37:g.82849228G>A	ENSP00000265077:p.Cys3180Tyr		82884984	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	33	5.234071	0.95207	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	6.06	6.06	0.98353	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.64402	D	0.000001	T	0.75568	0.3867	H	0.96662	3.86	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;1.0;0.998;1.0	T	0.82876	-0.0240	10	0.87932	D	0	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	1426;439;2193;3180	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	Y	3180;2193;1426;1378;439	ENSP00000265077:C3180Y;ENSP00000340062:C2193Y;ENSP00000342768:C1426Y;ENSP00000425959:C1378Y;ENSP00000421362:C439Y	ENSP00000265077:C3180Y	C	+	2	0	VCAN	82884984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	TGC		0.498	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82849228	G	A	82849228	3	1	61	1	0	0	0	0	1	0	0	0	17178	1319	46	3	9577	3	VCAN	5	82849228	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11418	82849228	98066032	3950	11935										
VCAN	1462	broad.mit.edu	37	chr5	82849341	82849341	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaacaaatgtttgttaatCgtatgtaccaaatagatacg	7	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:82849341C>T	ENST00000265077.3	+	11	10217	c.9652C>T	c.(9652-9654)Cgt>Tgt	p.R3218C	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Splice_Site_p.R1416C|VCAN_ENST00000502527.2_Splice_Site_p.R477C|VCAN_ENST00000342785.4_Splice_Site_p.R1464C|VCAN_ENST00000343200.5_Splice_Site_p.R2231C|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3218	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.R3218C(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	GTTTGTTAATCGTATGTACCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	89	94					5																	82849341		2203	4300	6503	82885097	SO:0001630	splice_region_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9652+1C>T	5.37:g.82849341C>T			82885097	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198635	0.94997	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22	6.06	6.06	0.98353	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.64402	D	0.000006	T	0.44685	0.1305	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.994;1.0	T	0.11817	-1.0572	10	0.62326	D	0.03	.	20.6208	0.99490	0.0:1.0:0.0:0.0	.	1464;477;2231;3218	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	C	3218;2231;1464;1416;477	ENSP00000265077:R3218C;ENSP00000340062:R2231C;ENSP00000342768:R1464C;ENSP00000425959:R1416C;ENSP00000421362:R477C	ENSP00000265077:R3218C	R	+	1	0	VCAN	82885097	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	4.924000	0.63418	2.882000	0.98803	0.655000	0.94253	CGT		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	Missense_Mutation	T	82849341	C	T	82849341	5	4	61	1	0	0	0	0	0	0	1	0	17178	898	31	1	9690	1	VCAN	5	82849341	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113	82849341	98065919	3951	11936										
RASA1	5921	broad.mit.edu	37	chr5	86629109	86629109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagatagaaggcgtgtacGagctattctaccttacacaa	9	8	1	3	rs374823017		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:86629109G>A	ENST00000274376.6	+	4	1418	c.854G>A	c.(853-855)cGa>cAa	p.R285Q	RASA1_ENST00000456692.2_Missense_Mutation_p.R108Q|RASA1_ENST00000512763.1_Missense_Mutation_p.R118Q|RASA1_ENST00000506290.1_Missense_Mutation_p.R119Q	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	285	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.R285Q(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AGGCGTGTACGAGCTATTCTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	68	74	72		854,323	5.3	1	5		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RASA1	NM_002890.2,NM_022650.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	285/1048,108/871	86629109	1,13005	2203	4300	6503	86664865	SO:0001583	missense	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.854G>A	5.37:g.86629109G>A	ENSP00000274376:p.Arg285Gln		86664865	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374849	0.82573	0.0	1.16E-4	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.3	5.3	0.74995	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	T	0.41949	0.1181	L	0.41573	1.285	0.54753	D	0.999989	P;P;P;P;P	0.50528	0.87;0.936;0.87;0.843;0.743	B;B;B;B;B	0.39503	0.234;0.301;0.234;0.15;0.169	T	0.42310	-0.9459	10	0.46703	T	0.11	.	18.9403	0.92602	0.0:0.0:1.0:0.0	.	119;118;119;108;285	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	Q	285;318;108;118;119	ENSP00000274376:R285Q;ENSP00000411221:R108Q;ENSP00000422008:R118Q;ENSP00000420905:R119Q	ENSP00000274376:R285Q	R	+	2	0	RASA1	86664865	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.063000	0.71162	2.480000	0.83734	0.650000	0.86243	CGA		0.313	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		A	86629109	G	A	86629109	3	1	61	1	0	0	0	0	1	0	0	0	13097	1058	37	1	880	1	RASA1	5	86629109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3779768	86629109	94286151	3952	11937										
RASA1	5921	broad.mit.edu	37	chr5	86670028	86670028	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcccataaactcccagtaAaacattttactaatccatat	2	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:86670028A>C	ENST00000274376.6	+	14	2389	c.1825A>C	c.(1825-1827)Aaa>Caa	p.K609Q	RASA1_ENST00000456692.2_Missense_Mutation_p.K432Q|RASA1_ENST00000512763.1_Missense_Mutation_p.K442Q|RASA1_ENST00000506290.1_Missense_Mutation_p.K443Q|CTC-428H11.2_ENST00000607486.1_RNA	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	609	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.K609Q(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ACTCCCAGTAAAACATTTTAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	69	69					5																	86670028		2202	4300	6502	86705784	SO:0001583	missense	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1825A>C	5.37:g.86670028A>C	ENSP00000274376:p.Lys609Gln		86705784	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.591672	0.86953	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	5.4	5.4	0.78164	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.096519	0.85682	D	0.000000	D	0.82806	0.5117	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.997;0.998	D;D;D;D;D	0.70016	0.955;0.955;0.955;0.925;0.967	D	0.85062	0.0935	10	0.87932	D	0	.	15.7276	0.77774	1.0:0.0:0.0:0.0	.	443;442;443;432;609	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	Q	609;642;432;442;443	ENSP00000274376:K609Q;ENSP00000411221:K432Q;ENSP00000422008:K442Q;ENSP00000420905:K443Q	ENSP00000274376:K609Q	K	+	1	0	RASA1	86705784	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.283000	0.95860	2.180000	0.69256	0.454000	0.30748	AAA		0.338	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		C	86670028	A	C	86670028	3	2	61	1	0	0	0	0	1	0	0	0	13097	15	1	4	1891	4	RASA1	5	86670028	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40919	86670028	94245232	3953	11938										
RASA1	5921	broad.mit.edu	37	chr5	86681142	86681142	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatctcctattgctgcaaGaacactgatattagtggcta	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:86681142G>T	ENST00000274376.6	+	22	3347	c.2783G>T	c.(2782-2784)aGa>aTa	p.R928I	RASA1_ENST00000456692.2_Missense_Mutation_p.R751I|RASA1_ENST00000512763.1_Missense_Mutation_p.R761I|RASA1_ENST00000506290.1_Missense_Mutation_p.R762I	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	928	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.R928I(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ATTGCTGCAAGAACACTGATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											123	110	114					5																	86681142		2202	4300	6502	86716898	SO:0001583	missense	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2783G>T	5.37:g.86681142G>T	ENSP00000274376:p.Arg928Ile		86716898	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	G	33	5.218996	0.95104	.	.	ENSG00000145715	ENST00000274376;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.56	5.56	0.83823	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.044105	0.85682	D	0.000000	T	0.69762	0.3147	H	0.95151	3.63	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.997;0.995;0.997	T	0.78999	-0.1982	10	0.87932	D	0	.	19.4995	0.95089	0.0:0.0:1.0:0.0	.	762;761;762;751;928	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	I	928;751;761;762	ENSP00000274376:R928I;ENSP00000411221:R751I;ENSP00000422008:R761I;ENSP00000420905:R762I	ENSP00000274376:R928I	R	+	2	0	RASA1	86716898	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.536000	0.98067	2.777000	0.95525	0.591000	0.81541	AGA		0.358	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		T	86681142	G	T	86681142	3	4	61	1	0	0	0	0	1	0	0	0	13097	942	33	2	2881	2	RASA1	5	86681142	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11114	86681142	94234118	3954	11939										
TMEM161B	153396	broad.mit.edu	37	chr5	87502990	87502990	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgtagttaatgaaaataGaactttgctgcagaaggaaa	11	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:87502990G>T	ENST00000296595.6	-	6	578	c.454C>A	c.(454-456)Cta>Ata	p.L152I	TMEM161B_ENST00000512429.1_Missense_Mutation_p.L141I|TMEM161B_ENST00000509387.1_Missense_Mutation_p.L25I|TMEM161B_ENST00000514135.1_Missense_Mutation_p.L152I|TMEM161B_ENST00000511218.1_Intron|TMEM161B_ENST00000506536.1_Intron	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	152						integral component of membrane (GO:0016021)		p.L152I(1)		endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		AATGAAAATAGAACTTTGCTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											51	54	53					5																	87502990		2203	4296	6499	87538746	SO:0001583	missense	153396			BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.454C>A	5.37:g.87502990G>T	ENSP00000296595:p.Leu152Ile		87538746	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	37	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.703677	0.68501	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000512429;ENST00000443393;ENST00000509387	.	.	.	5.24	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.73598	2.24	0.80722	D	1	P	0.49447	0.924	P	0.53266	0.722	T	0.67043	-0.5770	9	0.62326	D	0.03	-25.572	6.4472	0.21883	0.1463:0.0:0.7026:0.1511	.	152	Q8NDZ6	T161B_HUMAN	I	152;152;141;152;25	.	ENSP00000296595:L152I	L	-	1	2	TMEM161B	87538746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.938000	0.63519	1.316000	0.45131	0.585000	0.79938	CTA		0.318	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354		T	87502990	G	T	87502990	3	4	61	1	0	0	0	0	1	0	0	0	16116	933	33	2	1037	2	TMEM161B	5	87502990	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	821848	87502990	93412270	3955	11940										
MEF2C	4208	broad.mit.edu	37	chr5	88056840	88056840	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatcatattatcaaattCttcattaatttttttgtatt	2	5	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:88056840C>T	ENST00000437473.2	-	4	820				MEF2C_ENST00000514028.1_Intron|MEF2C_ENST00000539796.1_Intron|MEF2C_ENST00000340208.5_Missense_Mutation_p.E141K|MEF2C_ENST00000506554.1_Intron|MEF2C_ENST00000424173.2_Missense_Mutation_p.E121K|MEF2C_ENST00000510942.1_Intron|MEF2C_ENST00000514015.1_Intron|MEF2C_ENST00000508569.1_Intron|MEF2C_ENST00000504921.2_Intron|MEF2C_ENST00000503554.1_Intron	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C						apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E121K(1)		breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		TTATCAAATTCTTCATTAATT	0.393										HNSCC(66;0.2)																																						1	Substitution - Missense(1)	large_intestine(1)	5											99	95	96					5																	88056840		1568	3582	5150	88092596	SO:0001627	intron_variant	4208			AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.402+161G>A	5.37:g.88056840C>T			88092596	C9JMZ0|D7F7N5|F8W7V7	Missense_Mutation	SNP	ENST00000437473.2	37	CCDS47245.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177290	0.78564	.	.	ENSG00000081189	ENST00000340208;ENST00000424173;ENST00000513252;ENST00000506716	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.9	5.9	0.94986	.	.	.	.	.	D	0.85509	0.5713	M	0.83953	2.67	0.80722	D	1	B;D	0.58620	0.126;0.983	B;D	0.63488	0.172;0.915	D	0.86466	0.1782	9	0.87932	D	0	.	20.2821	0.98520	0.0:1.0:0.0:0.0	.	121;141	C9JMZ0;F8W7V7	.;.	K	141;121;121;121	ENSP00000340874:E141K;ENSP00000389610:E121K;ENSP00000423826:E121K;ENSP00000423656:E121K	ENSP00000340874:E141K	E	-	1	0	MEF2C	88092596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.786000	0.95864	0.563000	0.77884	GAA		0.393	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		T	88056840	C	T	88056840	1	4	61	0	1	0	0	0	0	0	0	0	9487	922	32	3		3	MEF2C	5	88056840	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	553850	88056840	92858420	3956	11941										
LYSMD3	116068	broad.mit.edu	37	chr5	89815112	89815112	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcactgtaagcaagagaatCattagctggcaaaatttcct	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89815112C>A	ENST00000315948.6	-	3	589	c.445G>T	c.(445-447)Gat>Tat	p.D149Y	LYSMD3_ENST00000500869.2_Intron|LYSMD3_ENST00000509384.1_3'UTR	NM_198273.1	NP_938014.1	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain containing 3	149						integral component of membrane (GO:0016021)		p.D149Y(1)		breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		GCAAGAGAATCATTAGCTGGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	128	130					5																	89815112		1857	4092	5949	89850868	SO:0001583	missense	116068			BX537972	CCDS43338.1, CCDS68911.1	5q14.3	2010-12-09			ENSG00000176018	ENSG00000176018			26969	protein-coding gene	gene with protein product							Standard	NM_001286812		Approved	FLJ13542	uc003kjr.3	Q7Z3D4	OTTHUMG00000162667	ENST00000315948.6:c.445G>T	5.37:g.89815112C>A	ENSP00000314518:p.Asp149Tyr		89850868	Q5H9U0|Q6PEK0|Q9NTE9	Missense_Mutation	SNP	ENST00000315948.6	37	CCDS43338.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333029	0.60853	.	.	ENSG00000176018;ENSG00000259141	ENST00000315948;ENST00000554351	T	0.19532	2.14	5.73	5.73	0.89815	.	0.494876	0.23260	N	0.050152	T	0.28830	0.0715	L	0.60455	1.87	0.25033	N	0.991252	P	0.49447	0.924	P	0.46362	0.514	T	0.22765	-1.0207	10	0.66056	D	0.02	-8.5873	13.5583	0.61773	0.0:0.9195:0.0:0.0805	.	149	Q7Z3D4	LYSM3_HUMAN	Y	149	ENSP00000314518:D149Y	ENSP00000314518:D149Y	D	-	1	0	AC027323.1;LYSMD3	89850868	1.000000	0.71417	0.074000	0.20217	0.903000	0.53119	5.404000	0.66344	2.692000	0.91855	0.591000	0.81541	GAT		0.393	LYSMD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369987.2	XM_371760		A	89815112	C	A	89815112	3	1	61	1	0	0	0	0	1	0	0	0	9156	826	29	2	479	2	LYSMD3	5	89815112	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1758272	89815112	91100148	3957	11942										
GPR98	84059	broad.mit.edu	37	chr5	89914926	89914926	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcagcaaatgtgaagctTggatggccaaggactgttac	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89914926T>C	ENST00000405460.2	+	4	477	c.381T>C	c.(379-381)ctT>ctC	p.L127L		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	127			L -> R (in dbSNP:rs41311333). {ECO:0000269|PubMed:14740321}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.L127L(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATGTGAAGCTTGGATGGCCAA	0.249																																																1	Substitution - coding silent(1)	large_intestine(1)	5											39	36	37					5																	89914926		1803	4067	5870	89950682	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.381T>C	5.37:g.89914926T>C			89950682	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																				0.249	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89914926	T	C	89914926	2	2	61	1	0	0	0	0	0	0	0	1	6742	1799	63	4		4	GPR98	5	89914926	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	99814	89914926	91000334	3958	11943										
GPR98	84059	broad.mit.edu	37	chr5	89923401	89923401	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatttcaaatagttgatgAcaccataccggagattgctg	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89923401A>G	ENST00000405460.2	+	7	1142	c.1046A>G	c.(1045-1047)gAc>gGc	p.D349G		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	349	Calx-beta 3. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.D349G(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATAGTTGATGACACCATACCG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											175	169	171					5																	89923401		1887	4108	5995	89959157	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.1046A>G	5.37:g.89923401A>G	ENSP00000384582:p.Asp349Gly		89959157	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.769135	0.90020	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.56611	0.45	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.73125	0.3547	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76487	-0.2941	10	0.87932	D	0	.	16.2365	0.82377	1.0:0.0:0.0:0.0	.	349	Q8WXG9	GPR98_HUMAN	G	349	ENSP00000384582:D349G	ENSP00000296619:D349G	D	+	2	0	GPR98	89959157	1.000000	0.71417	0.931000	0.37212	0.998000	0.95712	9.065000	0.93941	2.238000	0.73509	0.477000	0.44152	GAC		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89923401	A	G	89923401	3	3	61	1	0	0	0	0	1	0	0	0	6742	275	10	4	1072	4	GPR98	5	89923401	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8475	89923401	90991859	3959	11944										
GPR98	84059	broad.mit.edu	37	chr5	89939793	89939793	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagcaaaggagatgctatCtatagtggtaatttattctg	10	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89939793C>A	ENST00000405460.2	+	14	2823	c.2727C>A	c.(2725-2727)atC>atA	p.I909I		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	909	Calx-beta 7. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.I909I(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAGATGCTATCTATAGTGGTA	0.264																																																1	Substitution - coding silent(1)	large_intestine(1)	5											104	100	101					5																	89939793		1831	4084	5915	89975549	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.2727C>A	5.37:g.89939793C>A			89975549	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	7.496	0.651663	0.14516	.	.	ENSG00000164199	ENST00000504142	.	.	.	5.35	1.18	0.20946	.	.	.	.	.	T	0.31918	0.0812	.	.	.	0.09310	N	0.999993	.	.	.	.	.	.	T	0.24297	-1.0164	4	.	.	.	.	6.9834	0.24715	0.2215:0.6054:0.1036:0.0695	.	.	.	.	I	498	.	.	L	+	1	2	GPR98	89975549	0.008000	0.16893	0.002000	0.10522	0.335000	0.28730	0.408000	0.21065	0.619000	0.30197	0.655000	0.94253	CTA		0.264	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	89939793	C	A	89939793	2	1	61	1	0	0	0	0	0	0	0	1	6742	903	32	2		2	GPR98	5	89939793	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16392	89939793	90975467	3960	11945										
GPR98	84059	broad.mit.edu	37	chr5	89949598	89949598	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccttcattataaaaccTtgggttccaatgctacatac	4	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89949598T>G	ENST00000405460.2	+	20	4303	c.4207T>G	c.(4207-4209)Ttg>Gtg	p.L1403V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1403					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.L1403V(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTATAAAACCTTGGGTTCCAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	94	97					5																	89949598		1867	4103	5970	89985354	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4207T>G	5.37:g.89949598T>G	ENSP00000384582:p.Leu1403Val		89985354	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.581|9.581	1.123560|1.123560	0.20959|0.20959	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.73152	.|-0.72	5.48|5.48	-2.78|-2.78	0.05859|0.05859	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.376030|0.376030	0.28042|0.28042	N|N	0.016829|0.016829	T|T	0.58250|0.58250	0.2109|0.2109	N|N	0.25647|0.25647	0.755|0.755	0.35547|0.35547	D|D	0.803572|0.803572	.|P	.|0.45531	.|0.86	.|P	.|0.49799	.|0.622	T|T	0.60850|0.60850	-0.7181|-0.7181	6|10	.|0.17832	.|T	.|0.49	.|.	10.383|10.383	0.44123|0.44123	0.0922:0.4905:0.0:0.4173|0.0922:0.4905:0.0:0.4173	.|.	.|1403	.|Q8WXG9	.|GPR98_HUMAN	R|V	991|1403	.|ENSP00000384582:L1403V	.|ENSP00000296619:L1403V	L|L	+|+	2|1	0|2	GPR98|GPR98	89985354|89985354	0.000000|0.000000	0.05858|0.05858	0.849000|0.849000	0.33467|0.33467	0.596000|0.596000	0.36781|0.36781	-0.392000|-0.392000	0.07314|0.07314	-0.781000|-0.781000	0.04548|0.04548	-2.229000|-2.229000	0.00292|0.00292	CTT|TTG		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89949598	T	G	89949598	3	3	61	1	0	0	0	0	1	0	0	0	6742	1606	56	4	4285	4	GPR98	5	89949598	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9805	89949598	90965662	3961	11946										
GPR98	84059	broad.mit.edu	37	chr5	89971992	89971992	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcctgaactggaaaaatcTtttaaagttgagttgttaaa	7	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89971992T>G	ENST00000405460.2	+	25	5505	c.5409T>G	c.(5407-5409)tcT>tcG	p.S1803S	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1803	Calx-beta 12. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.S1803S(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGGAAAAATCTTTTAAAGTTG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	5											44	43	44					5																	89971992		1812	4059	5871	90007748	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5409T>G	5.37:g.89971992T>G			90007748	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																				0.333	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89971992	T	G	89971992	2	3	61	1	0	0	0	0	0	0	0	1	6742	1596	56	4		4	GPR98	5	89971992	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22394	89971992	90943268	3962	11947										
GPR98	84059	broad.mit.edu	37	chr5	89990027	89990027	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctggacctacaggaaaaAcatgaccagggtagcatctc	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:89990027A>G	ENST00000405460.2	+	33	7550	c.7454A>G	c.(7453-7455)aAc>aGc	p.N2485S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2485	Calx-beta 17. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.N2485S(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TACAGGAAAAACATGACCAGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	5											75	74	74					5																	89990027		1949	4148	6097	90025783	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7454A>G	5.37:g.89990027A>G	ENSP00000384582:p.Asn2485Ser		90025783	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.8|23.8	4.455096|4.455096	0.84209|0.84209	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.34275|.	1.37|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73536|0.73536	0.3599|0.3599	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.85130|.	0.979;0.997|.	T|T	0.72750|0.72750	-0.4199|-0.4199	10|5	0.56958|.	D|.	0.05|.	.|.	16.3526|16.3526	0.83220|0.83220	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2485;2485|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	S|A	2485|51	ENSP00000384582:N2485S|.	ENSP00000296619:N2485S|.	N|T	+|+	2|1	0|0	GPR98|GPR98	90025783|90025783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.108000|9.108000	0.94275|0.94275	2.255000|2.255000	0.74692|0.74692	0.533000|0.533000	0.62120|0.62120	AAC|ACA		0.478	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89990027	A	G	89990027	3	3	61	1	0	0	0	0	1	0	0	0	6742	43	2	4	7584	4	GPR98	5	89990027	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18035	89990027	90925233	3963	11948										
GPR98	84059	broad.mit.edu	37	chr5	90052805	90052805	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacttaaagggcgctgggGaagttattactgcctatgag	12	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90052805G>T	ENST00000405460.2	+	57	11863	c.11767G>T	c.(11767-11769)Gaa>Taa	p.E3923*		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3923	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.E3923*(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGGCGCTGGGGAAGTTATTAC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											83	80	81					5																	90052805		1843	4082	5925	90088561	SO:0001587	stop_gained	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11767G>T	5.37:g.90052805G>T	ENSP00000384582:p.Glu3923*		90088561	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	52	18.968330	0.99913	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	.	.	.	5.3	5.3	0.74995	.	0.048550	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	19.3121	0.94192	0.0:0.0:1.0:0.0	.	.	.	.	X	3923	.	ENSP00000296619:E3923X	E	+	1	0	GPR98	90088561	1.000000	0.71417	0.387000	0.26183	0.032000	0.12392	5.379000	0.66196	2.636000	0.89361	0.467000	0.42956	GAA		0.393	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90052805	G	T	90052805	4	4	61	1	0	0	0	0	0	1	0	0	6742	1175	41	2	11993	2	GPR98	5	90052805	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62778	90052805	90862455	3964	11949										
GPR98	84059	broad.mit.edu	37	chr5	90072290	90072290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtgcatcaataattattCggggtgataagcgagcatca	11	6	2	1	rs534226753		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90072290C>T	ENST00000405460.2	+	61	12520	c.12424C>T	c.(12424-12426)Cgg>Tgg	p.R4142W		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4142	Calx-beta 28. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R4142W(2)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AATAATTATTCGGGGTGATAA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	5											104	103	104					5																	90072290		1922	4129	6051	90108046	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12424C>T	5.37:g.90072290C>T	ENSP00000384582:p.Arg4142Trp		90108046	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268763	0.40095	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.28069	1.63	5.27	4.37	0.52481	.	0.316290	0.31199	N	0.008073	T	0.33644	0.0870	L	0.50333	1.59	0.18873	N	0.999989	D	0.69078	0.997	P	0.50490	0.642	T	0.21449	-1.0245	10	0.62326	D	0.03	.	7.0323	0.24975	0.4295:0.491:0.0:0.0796	.	4142	Q8WXG9	GPR98_HUMAN	W	4142	ENSP00000384582:R4142W	ENSP00000296619:R4142W	R	+	1	2	GPR98	90108046	0.000000	0.05858	0.644000	0.29465	0.157000	0.22087	0.055000	0.14229	1.287000	0.44583	0.637000	0.83480	CGG		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90072290	C	T	90072290	3	4	61	1	0	0	0	0	1	0	0	0	6742	875	31	1	12666	1	GPR98	5	90072290	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19485	90072290	90842970	3965	11950										
GPR98	84059	broad.mit.edu	37	chr5	90078991	90078991	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggtgaggctacatggaActtatggctatgtgacagct	13	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90078991A>C	ENST00000405460.2	+	66	13378	c.13282A>C	c.(13282-13284)Act>Cct	p.T4428P	GPR98_ENST00000425867.2_Missense_Mutation_p.T89P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4428	Calx-beta 30. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.T4428P(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCTACATGGAACTTATGGCTA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											208	204	206					5																	90078991		2042	4201	6243	90114747	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13282A>C	5.37:g.90078991A>C	ENSP00000384582:p.Thr4428Pro		90114747	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	9.985	1.229172	0.22542	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.32023	1.47;1.47	6.17	2.47	0.30058	Na-Ca exchanger/integrin-beta4 (2);	0.442010	0.27000	N	0.021429	T	0.35913	0.0948	M	0.66506	2.035	0.09310	N	1	P;P;P	0.47484	0.896;0.896;0.874	P;B;B	0.46629	0.522;0.399;0.277	T	0.18366	-1.0339	10	0.54805	T	0.06	.	10.2435	0.43328	0.8118:0.0:0.1882:0.0	.	89;4428;89	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	P	4428;4428;89	ENSP00000384582:T4428P;ENSP00000392618:T89P	ENSP00000296619:T4428P	T	+	1	0	GPR98	90114747	0.066000	0.20996	0.017000	0.16124	0.017000	0.09413	1.820000	0.39032	0.562000	0.29204	0.533000	0.62120	ACT		0.468	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90078991	A	C	90078991	3	2	61	1	0	0	0	0	1	0	0	0	6742	43	2	4	13544	4	GPR98	5	90078991	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6701	90078991	90836269	3966	11951										
GPR98	84059	broad.mit.edu	37	chr5	90106345	90106345	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgagatagaagaatttTtttacattaaccttacttca	4	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90106345T>A	ENST00000405460.2	+	74	15364	c.15268T>A	c.(15268-15270)Ttt>Att	p.F5090I	GPR98_ENST00000425867.2_Missense_Mutation_p.F751I	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5090	Calx-beta 33. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.F5090I(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGAAGAATTTTTTTACATTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											63	64	64					5																	90106345		1805	4072	5877	90142101	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15268T>A	5.37:g.90106345T>A	ENSP00000384582:p.Phe5090Ile		90142101	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.327201	0.60743	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.57273	0.41;0.41	5.37	5.37	0.77165	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.77418	0.4127	M	0.89968	3.075	0.43385	D	0.995494	D;D;D	0.89917	0.993;1.0;0.992	D;D;P	0.75484	0.912;0.986;0.856	T	0.82386	-0.0483	9	.	.	.	.	15.6665	0.77234	0.0:0.0:0.0:1.0	.	751;5090;751	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	I	5090;5090;751	ENSP00000384582:F5090I;ENSP00000392618:F751I	.	F	+	1	0	GPR98	90142101	1.000000	0.71417	0.891000	0.34965	0.212000	0.24457	7.043000	0.76572	2.164000	0.68074	0.460000	0.39030	TTT		0.338	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90106345	T	A	90106345	3	1	61	1	0	0	0	0	1	0	0	0	6742	1841	64	5	15562	5	GPR98	5	90106345	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27354	90106345	90808915	3967	11952										
GPR98	84059	broad.mit.edu	37	chr5	90149337	90149337	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggaaacaatcttcctaCcctaaaaaataaggtaatct	5	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90149337C>T	ENST00000405460.2	+	80	17537	c.17441C>T	c.(17440-17442)aCc>aTc	p.T5814I	GPR98_ENST00000425867.2_Missense_Mutation_p.T1475I	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5814					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.T5814I(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AATCTTCCTACCCTAAAAAAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											50	47	48					5																	90149337		1840	4088	5928	90185093	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.17441C>T	5.37:g.90149337C>T	ENSP00000384582:p.Thr5814Ile		90185093	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	8.558	0.877189	0.17395	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.27402	1.73;1.67	5.26	5.26	0.73747	.	0.198994	0.53938	D	0.000059	T	0.13756	0.0333	N	0.03608	-0.345	0.26765	N	0.969912	B;B;B	0.11235	0.002;0.001;0.004	B;B;B	0.06405	0.001;0.001;0.002	T	0.14643	-1.0465	9	.	.	.	.	12.58	0.56386	0.0:0.9234:0.0:0.0766	.	1475;5814;1475	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	I	5814;5814;1475	ENSP00000384582:T5814I;ENSP00000392618:T1475I	.	T	+	2	0	GPR98	90185093	0.997000	0.39634	0.594000	0.28785	0.088000	0.18126	4.001000	0.57046	2.594000	0.87642	0.650000	0.86243	ACC		0.358	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90149337	C	T	90149337	3	4	61	1	0	0	0	0	1	0	0	0	6742	507	18	3	17759	3	GPR98	5	90149337	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42992	90149337	90765923	3968	11953										
ARRDC3	57561	broad.mit.edu	37	chr5	90669530	90669530	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggtggaggcaagaatcGaaactcctggatatatgcaa	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:90669530G>A	ENST00000265138.3	-	7	1425	c.1159C>T	c.(1159-1161)Cga>Tga	p.R387*	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	387					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)	p.R387*(1)		breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		GGCAAGAATCGAAACTCCTGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											148	134	139					5																	90669530		2203	4300	6503	90705286	SO:0001587	stop_gained	57561			AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.1159C>T	5.37:g.90669530G>A	ENSP00000265138:p.Arg387*		90705286	A8K6T8|Q9P2H1	Nonsense_Mutation	SNP	ENST00000265138.3	37	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	G	40	8.246455	0.98724	.	.	ENSG00000113369	ENST00000265138	.	.	.	5.86	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-30.7881	14.5387	0.67979	0.0:0.0:0.7334:0.2665	.	.	.	.	X	387	.	ENSP00000265138:R387X	R	-	1	2	ARRDC3	90705286	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	2.857000	0.48349	1.443000	0.47586	0.650000	0.86243	CGA		0.423	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		A	90669530	G	A	90669530	4	1	61	1	0	0	0	0	0	1	0	0	985	1066	37	1	93	1	ARRDC3	5	90669530	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	520193	90669530	90245730	3969	11954										
NR2F1	7025	broad.mit.edu	37	chr5	92924063	92924063	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatggaccacatccgcatcTtccaggagcaggtggagaag	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:92924063T>G	ENST00000327111.3	+	2	2591	c.904T>G	c.(904-906)Ttc>Gtc	p.F302V	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	302					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.F302V(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		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)		CATCCGCATCTTCCAGGAGCA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	5											39	40	40					5																	92924063		2202	4300	6502	92949819	SO:0001583	missense	7025			BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.904T>G	5.37:g.92924063T>G	ENSP00000325819:p.Phe302Val		92949819		Missense_Mutation	SNP	ENST00000327111.3	37	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.622557	0.87460	.	.	ENSG00000175745	ENST00000327111	D	0.96459	-4.02	4.12	2.96	0.34315	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.112601	0.64402	D	0.000009	D	0.96231	0.8771	M	0.68317	2.08	0.80722	D	1	P	0.48640	0.913	P	0.54100	0.742	D	0.95001	0.8143	10	0.87932	D	0	.	8.8128	0.34978	0.0:0.092:0.0:0.908	.	302	P10589	COT1_HUMAN	V	302	ENSP00000325819:F302V	ENSP00000325819:F302V	F	+	1	0	NR2F1	92949819	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.005000	0.70716	0.632000	0.30432	0.260000	0.18958	TTC		0.647	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		G	92924063	T	G	92924063	3	3	61	1	0	0	0	0	1	0	0	0	10658	1609	56	4	910	4	NR2F1	5	92924063	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2254533	92924063	87991197	3970	11955										
POU5F2	134187	broad.mit.edu	37	chr5	93077210	93077210	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggcatcggccctctgggGccgcccccaccactgcctgg	14	18	1	0	rs369781509		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:93077210G>A	ENST00000510627.4	-	1	133	c.60C>T	c.(58-60)ggC>ggT	p.G20G	RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_Intron|POU5F2_ENST00000606183.1_5'Flank|FAM172A_ENST00000509163.1_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	20					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-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;0.0415)|all cancers(79;2.03e-19)		GCCCTCTGGGGCCGCCCCCAC	0.682																																																0			5						T	,,,	0,3780		0,0,1890	13	16	15		,,,60	-4.1	0	5		15	1,8199		0,1,4099	no	intron,intron,intron,coding-synonymous	FAM172A,POU5F2	NM_001163417.1,NM_001163418.1,NM_032042.5,NM_153216.1	,,,	0,1,5989	AA,AG,GG		0.0122,0.0,0.0083	,,,	,,,20/329	93077210	1,11979	1890	4100	5990	93102966	SO:0001819	synonymous_variant	134187				CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.60C>T	5.37:g.93077210G>A			93102966	Q15169|Q6MZL7|Q8N748	Silent	SNP	ENST00000510627.4	37	CCDS59489.1																																																																																				0.682	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		A	93077210	G	A	93077210	2	1	61	1	0	0	0	0	0	0	0	1	12314	1190	42	3		3	POU5F2	5	93077210	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153147	93077210	87838050	3971	11956										
FAM172A	83989	broad.mit.edu	37	chr5	93410400	93410400	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggacctccctgctggatTtgtgccatgtttatccaaat	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:93410400T>G	ENST00000395965.3	-	2	199	c.57A>C	c.(55-57)caA>caC	p.Q19H	FAM172A_ENST00000504768.2_5'UTR|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_5'UTR|FAM172A_ENST00000509163.1_Intron	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	19						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.Q19H(1)		endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						CCTGCTGGATTTGTGCCATGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											129	118	122					5																	93410400		2203	4300	6503	93436156	SO:0001583	missense	83989				CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391			25365	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 21"	C5orf21		11230166	Standard	NM_032042		Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.57A>C	5.37:g.93410400T>G	ENSP00000379294:p.Gln19His		93436156	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Missense_Mutation	SNP	ENST00000395965.3	37	CCDS4069.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545361	0.65198	.	.	ENSG00000113391	ENST00000395965	T	0.48836	0.8	5.87	0.565	0.17309	.	0.283030	0.39985	N	0.001202	T	0.35038	0.0918	L	0.54323	1.7	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.002;0.003	T	0.15009	-1.0452	10	0.56958	D	0.05	-1.5904	2.8534	0.05564	0.1369:0.0754:0.2849:0.5028	.	19;19	Q8WUF8;Q8WUF8-2	F172A_HUMAN;.	H	19	ENSP00000379294:Q19H	ENSP00000379294:Q19H	Q	-	3	2	FAM172A	93436156	0.981000	0.34729	1.000000	0.80357	0.998000	0.95712	-0.147000	0.10234	0.083000	0.17047	0.528000	0.53228	CAA		0.348	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042		G	93410400	T	G	93410400	3	3	61	1	0	0	0	0	1	0	0	0	5508	1838	64	4	1233	4	FAM172A	5	93410400	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	333190	93410400	87504860	3972	11957										
MCTP1	79772	broad.mit.edu	37	chr5	94046581	94046581	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatggctgtgaacacacaGagggctacaatggccagcca	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94046581G>T	ENST00000515393.1	-	21	2771	c.2772C>A	c.(2770-2772)ctC>ctA	p.L924L	MCTP1_ENST00000514040.1_5'UTR|MCTP1_ENST00000312216.8_Silent_p.L703L|MCTP1_ENST00000505078.1_Silent_p.L440L|ANKRD32_ENST00000493934.1_Intron|MCTP1_ENST00000429576.2_Silent_p.L617L	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	924					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.L924L(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TGAACACACAGAGGGCTACAA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	5											97	82	88					5																	94046581		2203	4300	6503	94072337	SO:0001819	synonymous_variant	79772				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2772C>A	5.37:g.94046581G>T			94072337	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	37	CCDS34203.1																																																																																				0.463	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		T	94046581	G	T	94046581	2	4	61	1	0	0	0	0	0	0	0	1	9430	929	33	2		2	MCTP1	5	94046581	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	636181	94046581	86868679	3973	11958										
MCTP1	79772	broad.mit.edu	37	chr5	94244987	94244987	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatcccttttcccagcatCtttgtcccatgcagtgatat	5	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94244987C>A	ENST00000515393.1	-	10	1620	c.1621G>T	c.(1621-1623)Gat>Tat	p.D541Y	MCTP1_ENST00000312216.8_Missense_Mutation_p.D320Y|MCTP1_ENST00000505078.1_Missense_Mutation_p.D57Y|MCTP1_ENST00000505208.1_Missense_Mutation_p.D320Y|MCTP1_ENST00000429576.2_Missense_Mutation_p.D274Y	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	541	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.D541Y(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TTCCCAGCATCTTTGTCCCAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	83	85					5																	94244987		2203	4299	6502	94270743	SO:0001583	missense	79772				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1621G>T	5.37:g.94244987C>A	ENSP00000424126:p.Asp541Tyr		94270743	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	37	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660030	0.88154	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568	T;D;T;T;D;T;T;D	0.83335	0.53;-1.71;0.53;0.53;-1.71;0.53;0.53;-1.71	5.68	5.68	0.88126	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.95214	0.8448	H	0.98466	4.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.96383	0.9283	10	0.59425	D	0.04	-16.6365	19.7934	0.96469	0.0:1.0:0.0:0.0	.	541;274;320	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	Y	541;274;57;320;261;202;320;142	ENSP00000424126:D541Y;ENSP00000391639:D274Y;ENSP00000426417:D57Y;ENSP00000308957:D320Y;ENSP00000423410:D261Y;ENSP00000431075:D202Y;ENSP00000426438:D320Y;ENSP00000426294:D142Y	ENSP00000308957:D320Y	D	-	1	0	MCTP1	94270743	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.678000	0.91216	0.585000	0.79938	GAT		0.373	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94244987	C	A	94244987	3	1	61	1	0	0	0	0	1	0	0	0	9430	913	32	2	1434	2	MCTP1	5	94244987	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	198406	94244987	86670273	3974	11959										
MCTP1	79772	broad.mit.edu	37	chr5	94353134	94353134	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtccagctggtacattcCgggatcagccaaggggactt	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94353134C>A	ENST00000515393.1	-	2	774	c.775G>T	c.(775-777)Gga>Tga	p.G259*	MCTP1_ENST00000312216.8_Nonsense_Mutation_p.G38*|MCTP1_ENST00000505208.1_Nonsense_Mutation_p.G38*|MCTP1_ENST00000429576.2_Nonsense_Mutation_p.G38*	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	259	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.G259*(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TGGTACATTCCGGGATCAGCC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											133	125	127					5																	94353134		2203	4300	6503	94378890	SO:0001587	stop_gained	79772				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.775G>T	5.37:g.94353134C>A	ENSP00000424126:p.Gly259*		94378890	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Nonsense_Mutation	SNP	ENST00000515393.1	37	CCDS34203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.713891|6.713891	0.97784|0.97784	.|.	.|.	ENSG00000175471|ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000312216;ENST00000508509;ENST00000505208;ENST00000507214;ENST00000514780;ENST00000510732;ENST00000505465|ENST00000503301	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.177619|.	0.36703|.	N|.	0.002454|.	.|T	.|0.73552	.|0.3601	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72221	.|-0.4356	.|3	0.15499|.	T|.	0.54|.	-10.6333|-10.6333	16.9518|16.9518	0.86247|0.86247	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	259;38;38;38;38;20;19;53;38|67	.|.	ENSP00000308957:G38X|.	G|R	-|-	1|2	0|0	MCTP1|MCTP1	94378890|94378890	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	2.856000|2.856000	0.48341|0.48341	2.742000|2.742000	0.94016|0.94016	0.655000|0.655000	0.94253|0.94253	GGA|CGG		0.378	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94353134	C	A	94353134	4	1	61	1	0	0	0	0	0	1	0	0	9430	661	23	2	2312	2	MCTP1	5	94353134	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108147	94353134	86562126	3975	11960										
FAM81B	153643	broad.mit.edu	37	chr5	94727125	94727125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccttggtacattggcttCctcagaaaaaagaaaaaaat	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94727125C>T	ENST00000283357.5	+	1	78	c.32C>T	c.(31-33)tCc>tTc	p.S11F		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	11						nucleus (GO:0005634)		p.S11F(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		ACATTGGCTTCCTCAGAAAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											98	96	97					5																	94727125		1831	4084	5915	94752881	SO:0001583	missense	153643				CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.32C>T	5.37:g.94727125C>T	ENSP00000283357:p.Ser11Phe		94752881		Missense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	C	9.499	1.102661	0.20632	.	.	ENSG00000153347	ENST00000283357	T	0.22336	1.96	4.83	2.31	0.28768	.	.	.	.	.	T	0.08403	0.0209	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36866	-0.9730	9	0.16420	T	0.52	.	3.3556	0.07168	0.1999:0.1101:0.0:0.69	.	11	Q96LP2	FA81B_HUMAN	F	11	ENSP00000283357:S11F	ENSP00000283357:S11F	S	+	2	0	FAM81B	94752881	0.530000	0.26330	0.231000	0.23993	0.006000	0.05464	0.324000	0.19610	0.978000	0.38470	-0.471000	0.05019	TCC		0.373	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		T	94727125	C	T	94727125	3	4	61	1	0	0	0	0	1	0	0	0	5648	855	30	3	34	3	FAM81B	5	94727125	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	373991	94727125	86188135	3976	11961										
FAM81B	153643	broad.mit.edu	37	chr5	94749805	94749805	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggggacccatggctttCgaaaagaggaatcgctcgcc	13	11	0	1	rs10042271		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94749805C>T	ENST00000283357.5	+	4	494	c.448C>T	c.(448-450)Cga>Tga	p.R150*		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	150			R -> G (in dbSNP:rs10042271).			nucleus (GO:0005634)		p.R150*(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		CCATGGCTTTCGAAAAGAGGA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											96	96	96					5																	94749805		1981	4166	6147	94775561	SO:0001587	stop_gained	153643				CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.448C>T	5.37:g.94749805C>T	ENSP00000283357:p.Arg150*		94775561		Nonsense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117742	0.37339	.	.	ENSG00000153347	ENST00000283357	.	.	.	5.53	3.68	0.42216	.	0.995025	0.08161	N	0.988427	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	0.0016	12.0124	0.53295	0.3143:0.6857:0.0:0.0	.	.	.	.	X	150	.	ENSP00000283357:R150X	R	+	1	2	FAM81B	94775561	0.328000	0.24687	0.589000	0.28718	0.015000	0.08874	0.844000	0.27654	0.635000	0.30488	0.650000	0.86243	CGA		0.498	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		T	94749805	C	T	94749805	4	4	61	1	0	0	0	0	0	1	0	0	5648	876	31	1	462	1	FAM81B	5	94749805	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22680	94749805	86165455	3977	11962										
FAM81B	153643	broad.mit.edu	37	chr5	94782293	94782293	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactttcaagtaatctgtaCgaagaagttgagaataataa	7	5	3	2	rs200384844	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94782293C>T	ENST00000283357.5	+	8	967	c.921C>T	c.(919-921)taC>taT	p.Y307Y		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	307						nucleus (GO:0005634)		p.Y307Y(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		GTAATCTGTACGAAGAAGTTG	0.284													T|||	4	0.000798722	0.0015	0	5008	,	,		17341	0.001		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						T		7,3573		0,7,1783	32	30	31		921	1.7	0.2	5		31	3,8127		0,3,4062	no	coding-synonymous	FAM81B	NM_152548.2		0,10,5845	TT,TC,CC		0.0369,0.1955,0.0854		307/453	94782293	10,11700	1790	4065	5855	94808049	SO:0001819	synonymous_variant	153643				CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.921C>T	5.37:g.94782293C>T			94808049		Silent	SNP	ENST00000283357.5	37	CCDS43341.1																																																																																				0.284	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		T	94782293	C	T	94782293	2	4	61	1	0	0	0	0	0	0	0	1	5648	547	19	1		1	FAM81B	5	94782293	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32488	94782293	86132967	3978	11963										
ARSK	153642	broad.mit.edu	37	chr5	94918883	94918883	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcaacatttcacacatCtctttattggcttgaaaaag	4	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94918883C>A	ENST00000380009.4	+	4	885	c.680C>A	c.(679-681)tCt>tAt	p.S227Y		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	227					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.S227Y(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		TTTCACACATCTCTTTATTGG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											63	65	64					5																	94918883		2203	4299	6502	94944639	SO:0001583	missense	153642				CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.680C>A	5.37:g.94918883C>A	ENSP00000369346:p.Ser227Tyr		94944639	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	37	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447463	0.84101	.	.	ENSG00000164291	ENST00000380009	D	0.99900	-7.63	5.81	5.81	0.92471	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99887	0.9946	M	0.83603	2.65	0.80722	D	1	D	0.67145	0.996	D	0.68943	0.961	D	0.96747	0.9551	10	0.72032	D	0.01	-23.7996	20.0795	0.97766	0.0:1.0:0.0:0.0	.	227	Q6UWY0	ARSK_HUMAN	Y	227	ENSP00000369346:S227Y	ENSP00000369346:S227Y	S	+	2	0	ARSK	94944639	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.085000	0.76875	2.747000	0.94245	0.650000	0.86243	TCT		0.318	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		A	94918883	C	A	94918883	3	1	61	1	0	0	0	0	1	0	0	0	997	913	32	2	694	2	ARSK	5	94918883	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136590	94918883	85996377	3979	11964										
ARSK	153642	broad.mit.edu	37	chr5	94927300	94927300	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagtatcaaatgtggtttCtcttgtggatatttacccta	7	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94927300C>A	ENST00000380009.4	+	6	1272	c.1067C>A	c.(1066-1068)tCt>tAt	p.S356Y		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	356					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.S356Y(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		AATGTGGTTTCTCTTGTGGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											183	190	188					5																	94927300		2203	4300	6503	94953056	SO:0001583	missense	153642				CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1067C>A	5.37:g.94927300C>A	ENSP00000369346:p.Ser356Tyr		94953056	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	37	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.585543	0.86748	.	.	ENSG00000164291	ENST00000380009	D	0.99201	-5.55	5.84	5.84	0.93424	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99354	0.9773	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99466	1.0944	10	0.87932	D	0	-23.683	20.142	0.98061	0.0:1.0:0.0:0.0	.	356	Q6UWY0	ARSK_HUMAN	Y	356	ENSP00000369346:S356Y	ENSP00000369346:S356Y	S	+	2	0	ARSK	94953056	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.484000	0.81180	2.754000	0.94517	0.655000	0.94253	TCT		0.383	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		A	94927300	C	A	94927300	3	1	61	1	0	0	0	0	1	0	0	0	997	913	32	2	1089	2	ARSK	5	94927300	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8417	94927300	85987960	3980	11965										
RFESD	317671	broad.mit.edu	37	chr5	94992003	94992003	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacttcaaagtaattaagaGttcttcctgataaaaaatat	5	5	2	3	rs557639186		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:94992003G>T	ENST00000311364.4	+	5	1881	c.464G>T	c.(463-465)aGt>aTt	p.S155I	RFESD_ENST00000513950.2_3'UTR|SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000380005.4_Missense_Mutation_p.S208I|RFESD_ENST00000458310.1_Missense_Mutation_p.S208I	NM_173362.3	NP_775498.1	Q8TAC1	RFESD_HUMAN	Rieske (Fe-S) domain containing	155							2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)	p.S155I(1)|p.S208I(1)		autonomic_ganglia(2)|endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	6		all_cancers(142;0.000215)|all_epithelial(76;7.43e-07)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)|Colorectal(57;0.162)		all cancers(79;5.94e-17)		GTAATTAAGAGTTCTTCCTGA	0.294													G|||	1	0.000199681	0	0	5008	,	,		16626	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	5											42	51	48					5																	94992003		2202	4296	6498	95017759	SO:0001583	missense	317671			BC035110	CCDS4075.1, CCDS47248.1	5q15	2010-12-07			ENSG00000175449	ENSG00000175449			29587	protein-coding gene	gene with protein product						12477932	Standard	NM_173362		Approved		uc003klg.3	Q8TAC1	OTTHUMG00000121168	ENST00000311364.4:c.464G>T	5.37:g.94992003G>T	ENSP00000309229:p.Ser155Ile		95017759	J3KPH1	Missense_Mutation	SNP	ENST00000311364.4	37	CCDS4075.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725665	0.30593	.	.	ENSG00000175449	ENST00000380005;ENST00000311364;ENST00000458310	.	.	.	5.38	3.46	0.39613	.	0.427224	0.26658	N	0.023170	T	0.30759	0.0775	N	0.22421	0.69	0.37091	D	0.899431	B	0.06786	0.001	B	0.06405	0.002	T	0.15263	-1.0443	8	.	.	.	-16.0345	3.6484	0.08194	0.0894:0.1692:0.566:0.1754	.	155	Q8TAC1	RFESD_HUMAN	I	208;155;208	.	.	S	+	2	0	RFESD	95017759	0.013000	0.17824	0.972000	0.41901	0.710000	0.40934	0.084000	0.14891	1.249000	0.43950	0.467000	0.42956	AGT		0.294	RFESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241654.1	NM_173362		T	94992003	G	T	94992003	3	4	61	1	0	0	0	0	1	0	0	0	13286	1029	36	2	641	2	RFESD	5	94992003	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64703	94992003	85923257	3981	11966										
RHOBTB3	22836	broad.mit.edu	37	chr5	95091379	95091379	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggtgctagccatgaatCttcaggcaacccaccattac	7	14	2	1	rs528922224		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95091379C>A	ENST00000379982.3	+	6	1470	c.962C>A	c.(961-963)tCt>tAt	p.S321Y	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	321	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)	p.S321Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AGCCATGAATCTTCAGGCAAC	0.423													C|||	1	0.000199681	0	0	5008	,	,		18927	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5											132	128	129					5																	95091379		2203	4300	6503	95117135	SO:0001583	missense	22836			AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.962C>A	5.37:g.95091379C>A	ENSP00000369318:p.Ser321Tyr		95117135	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.940033	0.34283	.	.	ENSG00000164292	ENST00000379982	T	0.70749	-0.51	6.08	5.21	0.72293	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (1);	0.428168	0.27971	N	0.017116	T	0.57227	0.2039	N	0.14661	0.345	0.58432	D	0.999997	B	0.24721	0.11	B	0.29267	0.1	T	0.57906	-0.7730	10	0.62326	D	0.03	-3.1792	14.4997	0.67711	0.0:0.9296:0.0:0.0704	.	321	O94955	RHBT3_HUMAN	Y	321	ENSP00000369318:S321Y	ENSP00000369318:S321Y	S	+	2	0	RHOBTB3	95117135	0.013000	0.17824	0.009000	0.14445	0.462000	0.32619	2.576000	0.46033	2.894000	0.99253	0.591000	0.81541	TCT		0.423	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		A	95091379	C	A	95091379	3	1	61	1	0	0	0	0	1	0	0	0	13372	913	32	2	984	2	RHOBTB3	5	95091379	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99376	95091379	85823881	3982	11967										
RHOBTB3	22836	broad.mit.edu	37	chr5	95099241	95099241	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgggaagaattggaagaaGatatcaggaagaagttgaaa	14	1	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95099241G>T	ENST00000379982.3	+	7	1586	c.1078G>T	c.(1078-1080)Gat>Tat	p.D360Y	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	360					ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)	p.D360Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		ATTGGAAGAAGATATCAGGAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	5											93	98	96					5																	95099241		2203	4297	6500	95124997	SO:0001583	missense	22836			AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1078G>T	5.37:g.95099241G>T	ENSP00000369318:p.Asp360Tyr		95124997	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.912343	0.52439	.	.	ENSG00000164292	ENST00000379982	T	0.65916	-0.18	5.48	5.48	0.80851	BTB/POZ-like (1);	0.162902	0.53938	D	0.000043	T	0.47600	0.1454	N	0.24115	0.695	0.80722	D	1	P	0.35612	0.512	B	0.31390	0.129	T	0.53592	-0.8417	10	0.59425	D	0.04	-19.2992	14.0718	0.64865	0.0:0.2723:0.7277:0.0	.	360	O94955	RHBT3_HUMAN	Y	360	ENSP00000369318:D360Y	ENSP00000369318:D360Y	D	+	1	0	RHOBTB3	95124997	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	2.132000	0.42083	2.572000	0.86782	0.655000	0.94253	GAT		0.318	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		T	95099241	G	T	95099241	3	4	61	1	0	0	0	0	1	0	0	0	13372	942	33	2	1104	2	RHOBTB3	5	95099241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7862	95099241	85816019	3983	11968										
RHOBTB3	22836	broad.mit.edu	37	chr5	95128802	95128802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaagcacagatggccgtCgaatatgtacttgaagcagc	11	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95128802C>T	ENST00000379982.3	+	12	2268	c.1760C>T	c.(1759-1761)tCg>tTg	p.S587L	GLRX_ENST00000508780.1_Intron|GLRX_ENST00000507605.1_Intron|RHOBTB3_ENST00000504179.1_Missense_Mutation_p.S218L	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	587	Interaction with Rab9.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)	p.S587L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AGATGGCCGTCGAATATGTAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											127	123	124					5																	95128802		2203	4300	6503	95154558	SO:0001583	missense	22836			AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1760C>T	5.37:g.95128802C>T	ENSP00000369318:p.Ser587Leu		95154558	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.771549	0.90108	.	.	ENSG00000164292	ENST00000379982;ENST00000504179;ENST00000514198	T;T	0.75260	-0.23;-0.92	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.81616	0.4860	L	0.51422	1.61	0.80722	D	1	D	0.69078	0.997	P	0.56474	0.799	T	0.81752	-0.0789	10	0.87932	D	0	-11.855	20.4745	0.99168	0.0:1.0:0.0:0.0	.	587	O94955	RHBT3_HUMAN	L	587;218;33	ENSP00000369318:S587L;ENSP00000422360:S218L	ENSP00000369318:S587L	S	+	2	0	RHOBTB3	95154558	1.000000	0.71417	0.977000	0.42913	0.942000	0.58702	6.322000	0.72886	2.941000	0.99782	0.655000	0.94253	TCG		0.363	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		T	95128802	C	T	95128802	3	4	61	1	0	0	0	0	1	0	0	0	13372	893	31	1	1806	1	RHOBTB3	5	95128802	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29561	95128802	85786458	3984	11969										
GLRX	2745	broad.mit.edu	37	chr5	95158187	95158187	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcccgtgagctgttgcaaAtaatcttgaatctcgttagt	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95158187A>C	ENST00000379979.4	-	1	231	c.180T>G	c.(178-180)taT>taG	p.Y60*	GLRX_ENST00000508780.1_Nonsense_Mutation_p.Y60*|GLRX_ENST00000505427.1_Nonsense_Mutation_p.Y60*|GLRX_ENST00000512469.2_Nonsense_Mutation_p.Y60*|GLRX_ENST00000237858.6_Nonsense_Mutation_p.Y60*|GLRX_ENST00000507605.1_5'Flank	NM_002064.2	NP_002055.1	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)	60	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of membrane potential (GO:0045838)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein deglutathionylation (GO:0080058)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|glutathione oxidoreductase activity (GO:0097573)|protein N-terminus binding (GO:0047485)	p.Y60*(1)		endometrium(3)|large_intestine(1)|lung(1)	5		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	GCTGTTGCAAATAATCTTGAA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											173	156	162					5																	95158187		2203	4300	6503	95183943	SO:0001587	stop_gained	2745				CCDS4078.1	5q14	2008-02-05			ENSG00000173221	ENSG00000173221			4330	protein-coding gene	gene with protein product		600443				8838810	Standard	NM_002064		Approved	GRX, GRX1	uc021ybo.1	P35754	OTTHUMG00000121167	ENST00000379979.4:c.180T>G	5.37:g.95158187A>C	ENSP00000369314:p.Tyr60*		95183943	B2R4L2|Q3KQS1|Q6ICT1	Nonsense_Mutation	SNP	ENST00000379979.4	37	CCDS4078.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495761	0.85069	.	.	ENSG00000173221	ENST00000508780;ENST00000237858;ENST00000379979;ENST00000505427;ENST00000512469	.	.	.	5.15	1.37	0.22104	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.5312	6.9061	0.24309	0.7265:0.0:0.2735:0.0	.	.	.	.	X	60	.	ENSP00000237858:Y60X	Y	-	3	2	GLRX	95183943	0.876000	0.30132	0.495000	0.27527	0.611000	0.37282	0.475000	0.22164	0.087000	0.17167	0.482000	0.46254	TAT		0.473	GLRX-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370267.1	NM_002064		C	95158187	A	C	95158187	4	2	61	1	0	0	0	0	0	1	0	0	6479	108	4	4	148	4	GLRX	5	95158187	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29385	95158187	85757073	3985	11970										
ELL2	22936	broad.mit.edu	37	chr5	95226885	95226885	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctagctacagtctccatCctggcatgcaaagctctgta	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95226885C>A	ENST00000237853.4	-	10	2032	c.1683G>T	c.(1681-1683)agG>agT	p.R561S	ELL2_ENST00000431061.2_Missense_Mutation_p.R311S	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	561					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.R561S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CAGTCTCCATCCTGGCATGCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											184	176	179					5																	95226885		2203	4300	6503	95252641	SO:0001583	missense	22936			U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1683G>T	5.37:g.95226885C>A	ENSP00000237853:p.Arg561Ser		95252641	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.24|19.24	3.790361|3.790361	0.70337|0.70337	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000508757|ENST00000237853;ENST00000431061	.|T;T	.|0.23552	.|1.9;1.9	5.96|5.96	-0.101|-0.101	0.13618|0.13618	.|Occludin/RNA polymerase II elongation factor, ELL domain (1);	.|0.132802	.|0.64402	.|D	.|0.000002	T|T	0.34919|0.34919	0.0914|0.0914	M|M	0.74881|0.74881	2.28|2.28	0.49915|0.49915	D|D	0.999835|0.999835	.|P	.|0.50156	.|0.932	.|P	.|0.51945	.|0.685	T|T	0.13388|0.13388	-1.0511|-1.0511	5|10	.|0.87932	.|D	.|0	-5.9241|-5.9241	7.1241|7.1241	0.25461|0.25461	0.0:0.3842:0.1182:0.4976|0.0:0.3842:0.1182:0.4976	.|.	.|561	.|O00472	.|ELL2_HUMAN	V|S	79|561;311	.|ENSP00000237853:R561S;ENSP00000399704:R311S	.|ENSP00000237853:R561S	G|R	-|-	2|3	0|2	ELL2|ELL2	95252641|95252641	0.229000|0.229000	0.23729|0.23729	0.992000|0.992000	0.48379|0.48379	0.989000|0.989000	0.77384|0.77384	-0.412000|-0.412000	0.07132|0.07132	-0.099000|-0.099000	0.12263|0.12263	-0.142000|-0.142000	0.14014|0.14014	GGA|AGG		0.388	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		A	95226885	C	A	95226885	3	1	61	1	0	0	0	0	1	0	0	0	5076	854	30	2	251	2	ELL2	5	95226885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68698	95226885	85688375	3986	11971										
PCSK1	5122	broad.mit.edu	37	chr5	95735803	95735803	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatcaagcctgctccattCtttttccatccagggttatt	5	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:95735803C>A	ENST00000311106.3	-	10	1521	c.1284G>T	c.(1282-1284)aaG>aaT	p.K428N	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.K381N	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	428	Peptidase S8.				cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.K428N(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CTGCTCCATTCTTTTTCCATC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											120	117	118					5																	95735803		2203	4300	6503	95761559	SO:0001583	missense	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1284G>T	5.37:g.95735803C>A	ENSP00000308024:p.Lys428Asn		95761559	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.453288	0.63290	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	D;D	0.88124	-2.34;-2.34	5.35	4.49	0.54785	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.043838	0.85682	D	0.000000	D	0.88691	0.6505	L	0.52573	1.65	0.47476	D	0.999431	P;D	0.56287	0.627;0.975	P;P	0.60886	0.449;0.88	D	0.86025	0.1509	10	0.27785	T	0.31	-18.9402	10.076	0.42360	0.0:0.8451:0.0:0.1549	.	381;428	E9PHA1;P29120	.;NEC1_HUMAN	N	428;381	ENSP00000308024:K428N;ENSP00000421600:K381N	ENSP00000308024:K428N	K	-	3	2	PCSK1	95761559	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.125000	0.31332	1.392000	0.46585	0.557000	0.71058	AAG		0.527	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		A	95735803	C	A	95735803	3	1	61	1	0	0	0	0	1	0	0	0	11631	912	32	2	997	2	PCSK1	5	95735803	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	508918	95735803	85179457	3987	11972										
ERAP1	51752	broad.mit.edu	37	chr5	96118783	96118783	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccattggattccttccactTtctgaaatagccttctgccc	5	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96118783T>G	ENST00000443439.2	-	15	2323	c.2257A>C	c.(2257-2259)Aag>Cag	p.K753Q	CTD-2260A17.1_ENST00000602972.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.K753Q|ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	753					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.K753Q(1)		endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TCCTTCCACTTTCTGAAATAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											129	119	122					5																	96118783		2203	4300	6503	96144539	SO:0001583	missense	51752			AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2257A>C	5.37:g.96118783T>G	ENSP00000406304:p.Lys753Gln		96144539	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	T	5.663	0.306931	0.10733	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.05996	3.36;3.36	5.82	-3.03	0.05429	.	1.429220	0.04110	N	0.314441	T	0.02455	0.0075	N	0.10809	0.05	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.35871	-0.9771	10	0.02654	T	1	.	1.4138	0.02297	0.1194:0.2504:0.2627:0.3675	.	753;753;753	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	Q	753	ENSP00000296754:K753Q;ENSP00000406304:K753Q	ENSP00000296754:K753Q	K	-	1	0	ERAP1	96144539	0.000000	0.05858	0.007000	0.13788	0.749000	0.42624	-0.909000	0.04058	-0.238000	0.09724	0.482000	0.46254	AAG		0.458	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		G	96118783	T	G	96118783	3	3	61	1	0	0	0	0	1	0	0	0	5216	1850	64	4	621	4	ERAP1	5	96118783	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	382980	96118783	84796477	3988	11973										
ERAP1	51752	broad.mit.edu	37	chr5	96119660	96119661	+	Frame_Shift_Del	DEL	TT	TT	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacttcattcatatctcTtttctccattaacttataca					rs150327661	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	TT	TT	TT	-	TT	TT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96119660_96119661delTT	ENST00000443439.2	-	14	2133_2134	c.2067_2068delAA	c.(2065-2070)aaaagafs	p.R690fs	CTD-2260A17.1_ENST00000602972.1_RNA|ERAP1_ENST00000296754.3_Frame_Shift_Del_p.R690fs|ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	690					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.D691fs*3(1)		endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTCATATCTCTTTTCTCCATTA	0.317																																																1	Deletion - Frameshift(1)	large_intestine(1)	5																																								96145417	SO:0001589	frameshift_variant	51752			AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2067_2068delAA	5.37:g.96119662_96119663delTT	ENSP00000406304:p.Arg690fs		96145416	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Frame_Shift_Del	DEL	ENST00000443439.2	37	CCDS47250.1																																																																																				0.317	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		-	96119661	TT	-	96119660	7	5	61	1	0	1	0	1	0	0	0	0	5216	1617	56	0	814	0	ERAP1	5	96119660	Frame_Shift_Del	DEL	TT	TCGA-AG-A002-01A-01W-A00K-09	877	96119660	84795600	3989	11974										
ERAP1	51752	broad.mit.edu	37	chr5	96136649	96136649	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaggcaggttcatcaaaGcagggaaaggccattctagc	12	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96136649G>T	ENST00000443439.2	-	3	645	c.579C>A	c.(577-579)tgC>tgA	p.C193*	ERAP1_ENST00000296754.3_Nonsense_Mutation_p.C193*	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	193					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.C193*(1)		endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		GTTCATCAAAGCAGGGAAAGG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											117	113	115					5																	96136649		2203	4300	6503	96162405	SO:0001587	stop_gained	51752			AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.579C>A	5.37:g.96136649G>T	ENSP00000406304:p.Cys193*		96162405	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Nonsense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.436730	0.83885	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384;ENST00000508227	.	.	.	5.72	1.38	0.22167	.	0.091135	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8896	0.35425	0.5481:0.0:0.4519:0.0	.	.	.	.	X	193;193;193;5	.	ENSP00000296754:C193X	C	-	3	2	ERAP1	96162405	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.694000	0.25512	0.167000	0.19631	0.655000	0.94253	TGC		0.428	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		T	96136649	G	T	96136649	4	4	61	1	0	0	0	0	0	1	0	0	5216	963	34	2	2347	2	ERAP1	5	96136649	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16989	96136649	84778611	3990	11975										
ERAP2	64167	broad.mit.edu	37	chr5	96228110	96228110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagacctcttctgcttccGataaactgtgggtcaccaga	8	13	3	2	rs200808443		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96228110G>A	ENST00000437043.3	+	6	1789	c.1078G>A	c.(1078-1080)Gat>Aat	p.D360N	ERAP2_ENST00000379904.4_Missense_Mutation_p.D315N|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	360					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D360N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TTCTGCTTCCGATAAACTGTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	112	117					5																	96228110		2203	4300	6503	96253866	SO:0001583	missense	64167			AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1078G>A	5.37:g.96228110G>A	ENSP00000400376:p.Asp360Asn		96253866	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.98|14.98	2.696305|2.696305	0.48202|0.48202	.|.	.|.	ENSG00000164308|ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904|ENST00000508077	T;T;T;T|.	0.02709|.	4.19;4.19;4.19;4.19|.	4.29|4.29	2.44|2.44	0.29823|0.29823	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);|.	0.222920|.	0.34959|.	N|.	0.003559|.	T|T	0.25382|0.25382	0.0617|0.0617	L|L	0.28694|0.28694	0.88|0.88	0.20638|0.20638	N|N	0.99988|0.99988	B;B|.	0.32396|.	0.369;0.112|.	B;B|.	0.34452|.	0.163;0.183|.	T|T	0.18808|0.18808	-1.0325|-1.0325	10|5	0.02654|.	T|.	1|.	.|.	4.5257|4.5257	0.11980|0.11980	0.2776:0.1776:0.5448:0.0|0.2776:0.1776:0.5448:0.0	.|.	315;360|.	Q6P179-3;Q6P179|.	.;ERAP2_HUMAN|.	N|Q	360;360;360;315|66	ENSP00000400376:D360N;ENSP00000421175:D360N;ENSP00000421849:D360N;ENSP00000369235:D315N|.	ENSP00000369235:D315N|.	D|R	+|+	1|2	0|0	ERAP2|ERAP2	96253866|96253866	0.952000|0.952000	0.32445|0.32445	0.014000|0.014000	0.15608|0.15608	0.677000|0.677000	0.39632|0.39632	2.163000|2.163000	0.42377|0.42377	0.931000|0.931000	0.37242|0.37242	0.563000|0.563000	0.77884|0.77884	GAT|CGA		0.453	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		A	96228110	G	A	96228110	3	1	61	1	0	0	0	0	1	0	0	0	5217	1058	37	1	1096	1	ERAP2	5	96228110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91461	96228110	84687150	3991	11976										
ERAP2	64167	broad.mit.edu	37	chr5	96232513	96232513	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaataattcagtacttaaaGaagttcagctatagaaatgc	8	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96232513G>T	ENST00000437043.3	+	9	2160	c.1449G>T	c.(1447-1449)aaG>aaT	p.K483N	ERAP2_ENST00000379904.4_Missense_Mutation_p.K438N|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	483					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.K483N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		AGTACTTAAAGAAGTTCAGCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											100	110	107					5																	96232513		2203	4298	6501	96258269	SO:0001583	missense	64167			AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1449G>T	5.37:g.96232513G>T	ENSP00000400376:p.Lys483Asn		96258269	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.335|9.335	1.061481|1.061481	0.19987|0.19987	.|.	.|.	ENSG00000164308|ENSG00000164308	ENST00000508077|ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	.|T;T;T;T	.|0.05258	.|3.47;3.47;3.47;3.47	5.19|5.19	2.15|2.15	0.27550|0.27550	.|.	.|0.482284	.|0.21414	.|N	.|0.074939	.|T	.|0.04182	.|0.0116	L|L	0.28458|0.28458	0.855|0.855	0.27947|0.27947	N|N	0.937297|0.937297	.|B;B	.|0.10296	.|0.003;0.002	.|B;B	.|0.17979	.|0.02;0.009	.|T	.|0.37731	.|-0.9693	.|10	.|0.22706	.|T	.|0.39	.|.	4.0292|4.0292	0.09701|0.09701	0.0805:0.1382:0.4977:0.2836|0.0805:0.1382:0.4977:0.2836	.|.	.|438;483	.|Q6P179-3;Q6P179	.|.;ERAP2_HUMAN	X|N	146|483;483;483;438	.|ENSP00000400376:K483N;ENSP00000421175:K483N;ENSP00000421849:K483N;ENSP00000369235:K438N	.|ENSP00000369235:K438N	E|K	+|+	1|3	0|2	ERAP2|ERAP2	96258269|96258269	0.377000|0.377000	0.25106|0.25106	0.989000|0.989000	0.46669|0.46669	0.956000|0.956000	0.61745|0.61745	0.820000|0.820000	0.27323|0.27323	0.659000|0.659000	0.30945|0.30945	0.563000|0.563000	0.77884|0.77884	GAA|AAG		0.328	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		T	96232513	G	T	96232513	3	4	61	1	0	0	0	0	1	0	0	0	5217	933	33	2	1479	2	ERAP2	5	96232513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4403	96232513	84682747	3992	11977										
ERAP2	64167	broad.mit.edu	37	chr5	96249161	96249161	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacccatcttctgaaaaAgttggtattcattttcatcc	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96249161A>C	ENST00000437043.3	+	17	3368	c.2657A>C	c.(2656-2658)aAa>aCa	p.K886T	ERAP2_ENST00000379904.4_Splice_Site_p.K841T|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	886					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.K886T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		CTTCTGAAAAAGTTGGTATTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											51	48	49					5																	96249161		2203	4300	6503	96274917	SO:0001630	splice_region_variant	64167			AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.2657+1A>C	5.37:g.96249161A>C			96274917	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.45|16.45	3.126064|3.126064	0.56721|0.56721	.|.	.|.	ENSG00000164308|ENSG00000164308	ENST00000512869|ENST00000437043;ENST00000379904	T|T;T	0.06371|0.07114	3.31|3.22;3.22	4.94|4.94	2.36|2.36	0.29203|0.29203	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.12987|0.12987	0.0315|0.0315	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|B;B	.|0.32396	.|0.369;0.13	.|B;B	.|0.41466	.|0.358;0.299	T|T	0.03344|0.03344	-1.1046|-1.1046	8|10	0.52906|0.37606	T|T	0.07|0.19	.|.	6.2485|6.2485	0.20832|0.20832	0.6732:0.167:0.0:0.1598|0.6732:0.167:0.0:0.1598	.|.	.|841;886	.|Q6P179-3;Q6P179	.|.;ERAP2_HUMAN	N|T	40|886;841	ENSP00000425415:K40N|ENSP00000400376:K886T;ENSP00000369235:K841T	ENSP00000425415:K40N|ENSP00000369235:K841T	K|K	+|+	3|2	2|0	ERAP2|ERAP2	96274917|96274917	1.000000|1.000000	0.71417|0.71417	0.934000|0.934000	0.37439|0.37439	0.417000|0.417000	0.31264|0.31264	4.139000|4.139000	0.58024|0.58024	0.251000|0.251000	0.21505|0.21505	0.460000|0.460000	0.39030|0.39030	AAA|AAA		0.398	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	Missense_Mutation	C	96249161	A	C	96249161	5	2	61	1	0	0	0	0	0	0	1	0	5217	86	3	4	2719	4	ERAP2	5	96249161	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16648	96249161	84666099	3993	11978										
LNPEP	4012	broad.mit.edu	37	chr5	96314892	96314892	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacagcatgtttgaggaaGaaccagatgtggtggattta	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96314892G>T	ENST00000231368.5	+	2	762	c.70G>T	c.(70-72)Gaa>Taa	p.E24*	LNPEP_ENST00000395770.3_Nonsense_Mutation_p.E10*	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	24					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E24*(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		GTTTGAGGAAGAACCAGATGT	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											83	89	87					5																	96314892		2203	4300	6503	96340648	SO:0001587	stop_gained	4012			D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.70G>T	5.37:g.96314892G>T	ENSP00000231368:p.Glu24*		96340648	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Nonsense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	G	39	7.798082	0.98495	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	.	.	.	5.96	5.96	0.96718	.	0.048409	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.989	0.97359	0.0:0.0:1.0:0.0	.	.	.	.	X	24;10	.	ENSP00000231368:E24X	E	+	1	0	LNPEP	96340648	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.830000	0.97506	0.585000	0.79938	GAA		0.463	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		T	96314892	G	T	96314892	4	4	61	1	0	0	0	0	0	1	0	0	8888	943	33	2	76	2	LNPEP	5	96314892	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65731	96314892	84600368	3994	11979										
LNPEP	4012	broad.mit.edu	37	chr5	96360289	96360289	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgacaaaggctggtcaTtccttttgggcaaatacatt	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96360289T>A	ENST00000231368.5	+	15	3318	c.2626T>A	c.(2626-2628)Ttc>Atc	p.F876I	LNPEP_ENST00000395770.3_Missense_Mutation_p.F862I	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	876					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F876I(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		AGGCTGGTCATTCCTTTTGGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											90	83	85					5																	96360289		2203	4300	6503	96386045	SO:0001583	missense	4012			D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.2626T>A	5.37:g.96360289T>A	ENSP00000231368:p.Phe876Ile		96386045	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345458	0.61073	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.05319	3.46;3.46	5.96	5.96	0.96718	.	0.233064	0.52532	D	0.000068	T	0.16128	0.0388	M	0.68317	2.08	0.45837	D	0.998705	B	0.34290	0.447	B	0.44044	0.439	T	0.00348	-1.1799	10	0.62326	D	0.03	.	16.1099	0.81255	0.0:0.0:0.0:1.0	.	876	Q9UIQ6	LCAP_HUMAN	I	876;862	ENSP00000231368:F876I;ENSP00000379117:F862I	ENSP00000231368:F876I	F	+	1	0	LNPEP	96386045	0.998000	0.40836	0.939000	0.37840	0.099000	0.18886	3.142000	0.50601	2.285000	0.76669	0.533000	0.62120	TTC		0.423	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		A	96360289	T	A	96360289	3	1	61	1	0	0	0	0	1	0	0	0	8888	1493	52	5	2684	5	LNPEP	5	96360289	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	45397	96360289	84554971	3995	11980										
LIX1	167410	broad.mit.edu	37	chr5	96430694	96430694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccagggccatgtggctgcGcatcttttcatctagagaat	11	10	3	1	rs139339824		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96430694G>A	ENST00000274382.4	-	6	902	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	203								p.R203C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		ATGTGGCTGCGCATCTTTTCA	0.512													G|||	1	0.000199681	0	0	5008	,	,		18822	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	65	68	67		607	4.9	1	5	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	missense	LIX1	NM_153234.4	180	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	203/283	96430694	2,13004	2203	4300	6503	96456450	SO:0001583	missense	167410				CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.607C>T	5.37:g.96430694G>A	ENSP00000274382:p.Arg203Cys		96456450	A8K4R9|Q8N7I2	Missense_Mutation	SNP	ENST00000274382.4	37	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114088	0.77210	2.27E-4	1.16E-4	ENSG00000145721	ENST00000274382	T	0.59364	0.27	5.85	4.9	0.64082	.	0.048188	0.85682	D	0.000000	T	0.72598	0.3480	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	P	0.62435	0.902	T	0.75736	-0.3213	10	0.87932	D	0	-17.0073	15.9275	0.79632	0.0:0.0:0.8231:0.1769	.	203	Q8N485	LIX1_HUMAN	C	203	ENSP00000274382:R203C	ENSP00000274382:R203C	R	-	1	0	LIX1	96456450	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.525000	0.45598	2.773000	0.95371	0.655000	0.94253	CGC		0.512	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96430694	G	A	96430694	3	1	61	1	0	0	0	0	1	0	0	0	8855	1087	38	1	245	1	LIX1	5	96430694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70405	96430694	84484566	3996	11981										
LIX1	167410	broad.mit.edu	37	chr5	96432537	96432537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgggaacactttgtttcacGaagggcttttaggcttccat	10	9	1	0	rs139105148		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:96432537G>A	ENST00000274382.4	-	5	833	c.538C>T	c.(538-540)Cgt>Tgt	p.R180C	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	180								p.R180C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		TTTGTTTCACGAAGGGCTTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	106	102	103		538	5.3	1	5	dbSNP_134	103	0,8600		0,0,4300	no	missense	LIX1	NM_153234.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	180/283	96432537	1,13005	2203	4300	6503	96458293	SO:0001583	missense	167410				CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.538C>T	5.37:g.96432537G>A	ENSP00000274382:p.Arg180Cys		96458293	A8K4R9|Q8N7I2	Missense_Mutation	SNP	ENST00000274382.4	37	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137829	0.77775	2.27E-4	0.0	ENSG00000145721	ENST00000274382	T	0.59224	0.28	6.17	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.73171	0.3553	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.68765	0.96	T	0.74968	-0.3483	10	0.87932	D	0	-8.4011	13.8944	0.63761	0.0:0.0:0.7356:0.2643	.	180	Q8N485	LIX1_HUMAN	C	180	ENSP00000274382:R180C	ENSP00000274382:R180C	R	-	1	0	LIX1	96458293	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	2.765000	0.47621	2.941000	0.99782	0.655000	0.94253	CGT		0.428	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96432537	G	A	96432537	3	1	61	1	0	0	0	0	1	0	0	0	8855	1058	37	1	318	1	LIX1	5	96432537	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1843	96432537	84482723	3997	11982										
CHD1	1105	broad.mit.edu	37	chr5	98236685	98236685	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcttggcgacgagaacttCttttatcattatcataatct	6	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:98236685C>A	ENST00000284049.3	-	6	838	c.689G>T	c.(688-690)aGa>aTa	p.R230I		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	230					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.R230I(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ACGAGAACTTCTTTTATCATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											155	150	152					5																	98236685		2203	4300	6503	98264585	SO:0001583	missense	1105			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.689G>T	5.37:g.98236685C>A	ENSP00000284049:p.Arg230Ile		98264585	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	32	5.111234	0.94339	.	.	ENSG00000153922	ENST00000284049	D	0.90955	-2.76	5.51	5.51	0.81932	.	0.000000	0.35378	U	0.003253	D	0.92120	0.7502	M	0.69358	2.11	0.80722	D	1	P	0.48640	0.913	P	0.47075	0.536	D	0.92631	0.6116	10	0.66056	D	0.02	.	19.7788	0.96409	0.0:1.0:0.0:0.0	.	230	O14646	CHD1_HUMAN	I	230	ENSP00000284049:R230I	ENSP00000284049:R230I	R	-	2	0	CHD1	98264585	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.340000	0.59328	2.749000	0.94314	0.460000	0.39030	AGA		0.358	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98236685	C	A	98236685	3	1	61	1	0	0	0	0	1	0	0	0	3329	913	32	2	4563	2	CHD1	5	98236685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1804148	98236685	82678575	3998	11983										
SLCO4C1	353189	broad.mit.edu	37	chr5	101631936	101631936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggctggaggggacaaaagCcaagttctcaatacctttgg	13	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:101631936C>T	ENST00000310954.6	-	1	317	c.31G>A	c.(31-33)Gct>Act	p.A11T		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1									p.A11T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GGGACAAAAGCCAAGTTCTCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	82	79					5																	101631936		2203	4300	6503	101659835	SO:0001583	missense	353189			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.31G>A	5.37:g.101631936C>T	ENSP00000309741:p.Ala11Thr		101659835		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265248	0.59431	.	.	ENSG00000173930	ENST00000310954	T	0.44482	0.92	4.11	4.11	0.48088	.	1.154150	0.06696	N	0.770459	T	0.43853	0.1266	L	0.55481	1.735	0.29023	N	0.886171	P	0.46784	0.884	B	0.40825	0.341	T	0.43507	-0.9387	10	0.51188	T	0.08	.	13.1695	0.59589	0.0:1.0:0.0:0.0	.	11	Q6ZQN7	SO4C1_HUMAN	T	11	ENSP00000309741:A11T	ENSP00000309741:A11T	A	-	1	0	SLCO4C1	101659835	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	3.247000	0.51422	2.095000	0.63458	0.591000	0.81541	GCT		0.582	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		T	101631936	C	T	101631936	3	4	61	1	0	0	0	0	1	0	0	0	14767	739	26	3	2195	3	SLCO4C1	5	101631936	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3395251	101631936	79283324	3999	11984										
PAM	5066	broad.mit.edu	37	chr5	102343348	102343348	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaaatgtatttgcaatTtcatatataccaggtatttc	7	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:102343348T>G	ENST00000438793.3	+	19	2672	c.2202T>G	c.(2200-2202)atT>atG	p.I734M	PAM_ENST00000346918.2_Missense_Mutation_p.I734M|PAM_ENST00000304400.7_Missense_Mutation_p.I734M|PAM_ENST00000455264.2_Missense_Mutation_p.I734M|PAM_ENST00000348126.2_Missense_Mutation_p.I627M|PAM_ENST00000274392.9_Missense_Mutation_p.I637M|PAM_ENST00000379787.4_Missense_Mutation_p.I114M	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	734	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)	p.I734M(2)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TATTTGCAATTTCATATATAC	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	5											80	84	83					5																	102343348		2203	4300	6503	102371247	SO:0001583	missense	5066			AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.2202T>G	5.37:g.102343348T>G	ENSP00000396493:p.Ile734Met		102371247	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	14.69|14.69|14.69	2.610059|2.610059|2.610059	0.46527|0.46527|0.46527	.|.|.	.|.|.	ENSG00000145730|ENSG00000145730|ENSG00000145730	ENST00000504691|ENST00000379799|ENST00000438793;ENST00000346918;ENST00000348126;ENST00000379787;ENST00000304400;ENST00000274392;ENST00000455264	.|.|D;D;D;T;D;D;D	.|.|0.91295	.|.|-2.82;-2.82;-2.82;0.33;-2.82;-2.82;-2.82	5.28|5.28|5.28	4.08|4.08|4.08	0.47627|0.47627|0.47627	.|.|Six-bladed beta-propeller, TolB-like (1);	.|.|0.097209	.|.|0.64402	.|.|D	.|.|0.000001	D|D|D	0.92087|0.92087|0.92087	0.7492|0.7492|0.7492	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.46279|0.46279|0.46279	D|D|D	0.998963|0.998963|0.998963	.|.|P;P;P;P;P;P	.|.|0.46064	.|.|0.872;0.798;0.872;0.458;0.872;0.872	.|.|D;P;D;P;D;D	.|.|0.68192	.|.|0.956;0.904;0.956;0.613;0.956;0.956	D|D|D	0.90638|0.90638|0.90638	0.4572|0.4572|0.4572	5|5|10	.|.|0.54805	.|.|T	.|.|0.06	.|.|.	7.4636|7.4636|7.4636	0.27310|0.27310|0.27310	0.0:0.0731:0.1421:0.7848|0.0:0.0731:0.1421:0.7848|0.0:0.0731:0.1421:0.7848	.|.|.	.|.|637;734;734;734;734;627	.|.|F8WE90;P19021;P19021-4;P19021-3;P19021-5;P19021-2	.|.|.;AMD_HUMAN;.;.;.;.	C|V|M	29|507|734;734;627;114;734;637;734	.|.|ENSP00000396493:I734M;ENSP00000282992:I734M;ENSP00000314638:I627M;ENSP00000369113:I114M;ENSP00000306100:I734M;ENSP00000274392:I637M;ENSP00000403461:I734M	.|.|ENSP00000274392:I637M	F|F|I	+|+|+	2|1|3	0|0|3	PAM|PAM|PAM	102371247|102371247|102371247	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	2.168000|2.168000|2.168000	0.42424|0.42424|0.42424	0.974000|0.974000|0.974000	0.38366|0.38366|0.38366	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TTT|TTC|ATT		0.323	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		G	102343348	T	G	102343348	3	3	61	1	0	0	0	0	1	0	0	0	11443	1829	64	4	2276	4	PAM	5	102343348	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	711412	102343348	78571912	4000	11985										
GIN1	54826	broad.mit.edu	37	chr5	102432431	102432431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttcctttgtcttaaaaCttcatgacccacttttaaat	2	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:102432431C>T	ENST00000399004.2	-	7	1202	c.1108G>A	c.(1108-1110)Gtt>Att	p.V370I	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	370					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.V370I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TGTCTTAAAACTTCATGACCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											179	168	171					5																	102432431		1824	4080	5904	102460330	SO:0001583	missense	54826			BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1108G>A	5.37:g.102432431C>T	ENSP00000381970:p.Val370Ile		102460330	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227453	0.79576	.	.	ENSG00000145723	ENST00000399004	T	0.31247	1.5	5.77	4.91	0.64330	.	0.000000	0.51477	D	0.000096	T	0.24736	0.0600	L	0.29908	0.895	0.80722	D	1	B	0.22541	0.071	B	0.19666	0.026	T	0.04635	-1.0937	10	0.87932	D	0	-1.8514	12.9022	0.58130	0.0:0.9252:0.0:0.0748	.	370	Q9NXP7	GIN1_HUMAN	I	370	ENSP00000381970:V370I	ENSP00000381970:V370I	V	-	1	0	GIN1	102460330	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.264000	0.51553	1.445000	0.47624	0.655000	0.94253	GTT		0.343	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		T	102432431	C	T	102432431	3	4	61	1	0	0	0	0	1	0	0	0	6406	565	20	3	468	3	GIN1	5	102432431	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89083	102432431	78482829	4001	11986										
GIN1	54826	broad.mit.edu	37	chr5	102442551	102442551	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagactttctttttttcctCttctgaaacaattaccaaac	2	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:102442551C>A	ENST00000399004.2	-	3	296	c.202G>T	c.(202-204)Gag>Tag	p.E68*	GIN1_ENST00000511400.1_5'Flank|GIN1_ENST00000508629.1_Nonsense_Mutation_p.E68*	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	68					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.E68*(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TTTTTTTCCTCTTCTGAAACA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											79	72	74					5																	102442551		1828	4080	5908	102470450	SO:0001587	stop_gained	54826			BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.202G>T	5.37:g.102442551C>A	ENSP00000381970:p.Glu68*		102470450	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Nonsense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733320	0.69189	.	.	ENSG00000145723	ENST00000399004;ENST00000508629	.	.	.	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-17.2306	18.8203	0.92094	0.0:1.0:0.0:0.0	.	.	.	.	X	68	.	ENSP00000381970:E68X	E	-	1	0	GIN1	102470450	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	4.770000	0.62309	2.880000	0.98712	0.650000	0.86243	GAG		0.328	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		A	102442551	C	A	102442551	4	1	61	1	0	0	0	0	0	1	0	0	6406	922	32	2	1390	2	GIN1	5	102442551	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10120	102442551	78472709	4002	11987										
PPIP5K2	23262	broad.mit.edu	37	chr5	102503000	102503000	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacttctcaaatcagacatCgaatggaagatcctaaatca	6	9	3	3	rs147568161		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:102503000C>T	ENST00000358359.3	+	18	2547	c.2038C>T	c.(2038-2040)Cga>Tga	p.R680*	PPIP5K2_ENST00000414217.1_Nonsense_Mutation_p.R680*|PPIP5K2_ENST00000321521.9_Nonsense_Mutation_p.R680*|PPIP5K2_ENST00000513500.1_3'UTR	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	680					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)	p.R680*(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AATCAGACATCGAATGGAAGA	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	5						C	stop/ARG	0,4404		0,0,2202	73	79	77		2038	4.5	1	5	dbSNP_134	77	1,8583	1.2+/-3.3	0,1,4291	no	stop-gained	PPIP5K2	NM_015216.2		0,1,6493	TT,TC,CC		0.0116,0.0,0.0077		680/1223	102503000	1,12987	2202	4292	6494	102530899	SO:0001587	stop_gained	23262			AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.2038C>T	5.37:g.102503000C>T	ENSP00000351126:p.Arg680*		102530899	A1NI53|A6NGS8|Q8TB50	Nonsense_Mutation	SNP	ENST00000358359.3	37		.	.	.	.	.	.	.	.	.	.	C	39	7.648399	0.98409	0.0	1.16E-4	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217	.	.	.	5.43	4.48	0.54585	.	0.171954	0.38663	N	0.001612	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8768	0.57994	0.2479:0.7521:0.0:0.0	.	.	.	.	X	680	.	ENSP00000313070:R680X	R	+	1	2	PPIP5K2	102530899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.263000	0.33004	2.536000	0.85505	0.460000	0.39030	CGA		0.289	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		T	102503000	C	T	102503000	4	4	61	1	0	0	0	0	0	1	0	0	12367	876	31	1	2104	1	PPIP5K2	5	102503000	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60449	102503000	78412260	4003	11988										
EFNA5	1946	broad.mit.edu	37	chr5	106722984	106722984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgttaacatcgaaaacacGatcatgaacacctatagttt	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:106722984G>A	ENST00000333274.6	-	4	798	c.517C>T	c.(517-519)Cgt>Tgt	p.R173C	EFNA5_ENST00000510359.1_5'UTR|EFNA5_ENST00000509503.1_Intron	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	173					axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)	p.R173C(1)		large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		TCGAAAACACGATCATGAACA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											87	83	85					5																	106722984		2200	4300	6500	106750883	SO:0001583	missense	1946			U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.517C>T	5.37:g.106722984G>A	ENSP00000328777:p.Arg173Cys		106750883		Missense_Mutation	SNP	ENST00000333274.6	37	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488775	0.84962	.	.	ENSG00000184349	ENST00000333274	D	0.96365	-3.99	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.95570	0.8560	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	P	0.54706	0.759	D	0.95792	0.8825	10	0.56958	D	0.05	-6.4087	20.0628	0.97684	0.0:0.0:1.0:0.0	.	173	P52803	EFNA5_HUMAN	C	173	ENSP00000328777:R173C	ENSP00000328777:R173C	R	-	1	0	EFNA5	106750883	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.745000	0.94114	0.655000	0.94253	CGT		0.338	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		A	106722984	G	A	106722984	3	1	61	1	0	0	0	0	1	0	0	0	4965	1058	37	1	177	1	EFNA5	5	106722984	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4219984	106722984	74192276	4004	11989										
EFNA5	1946	broad.mit.edu	37	chr5	106762962	106762962	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgaattcaaatcctagaGaaaagggagtgaagagctgg	13	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:106762962G>A	ENST00000333274.6	-	2	655	c.374C>T	c.(373-375)tCt>tTt	p.S125F	EFNA5_ENST00000509503.1_Missense_Mutation_p.S125F	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	125	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)	p.S125F(1)		large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		AAATCCTAGAGAAAAGGGAGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											54	56	55					5																	106762962		2202	4300	6502	106790861	SO:0001583	missense	1946			U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.374C>T	5.37:g.106762962G>A	ENSP00000328777:p.Ser125Phe		106790861		Missense_Mutation	SNP	ENST00000333274.6	37	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469729	0.84533	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	T;T	0.45276	0.9;0.9	6.17	6.17	0.99709	Ephrin, conserved site (1);Cupredoxin (2);	0.000000	0.85682	D	0.000000	T	0.73032	0.3535	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.75590	-0.3265	10	0.72032	D	0.01	-14.226	20.8794	0.99867	0.0:0.0:1.0:0.0	.	125;125	D6RDV5;P52803	.;EFNA5_HUMAN	F	125	ENSP00000328777:S125F;ENSP00000426989:S125F	ENSP00000328777:S125F	S	-	2	0	EFNA5	106790861	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	TCT		0.443	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		A	106762962	G	A	106762962	3	1	61	1	0	0	0	0	1	0	0	0	4965	942	33	3	328	3	EFNA5	5	106762962	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39978	106762962	74152298	4005	11990										
EFNA5	1946	broad.mit.edu	37	chr5	106763065	106763065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccctttggaagtgtggtCgcaggcactgtagccatcaa	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:106763065C>T	ENST00000333274.6	-	2	552	c.271G>A	c.(271-273)Gac>Aac	p.D91N	EFNA5_ENST00000509503.1_Missense_Mutation_p.D91N	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	91	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)	p.D91N(1)		large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		GAAGTGTGGTCGCAGGCACTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											131	128	129					5																	106763065		2202	4300	6502	106790964	SO:0001583	missense	1946			U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.271G>A	5.37:g.106763065C>T	ENSP00000328777:p.Asp91Asn		106790964		Missense_Mutation	SNP	ENST00000333274.6	37	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399097	0.62177	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	D;D	0.92965	-3.14;-3.14	6.06	6.06	0.98353	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.87414	0.6171	L	0.33624	1.015	0.80722	D	1	B;B	0.28026	0.198;0.04	B;B	0.22152	0.038;0.031	T	0.83322	-0.0017	10	0.09843	T	0.71	-18.6451	20.6208	0.99490	0.0:1.0:0.0:0.0	.	91;91	D6RDV5;P52803	.;EFNA5_HUMAN	N	91	ENSP00000328777:D91N;ENSP00000426989:D91N	ENSP00000328777:D91N	D	-	1	0	EFNA5	106790964	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	GAC		0.498	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		T	106763065	C	T	106763065	3	4	61	1	0	0	0	0	1	0	0	0	4965	884	31	1	431	1	EFNA5	5	106763065	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103	106763065	74152195	4006	11991										
FBXL17	64839	broad.mit.edu	37	chr5	107521861	107521861	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagagattgagagagctaaGatttttgcacctcttgacaa	9	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:107521861G>T	ENST00000542267.1	-	6	2108	c.1702C>A	c.(1702-1704)Ctt>Att	p.L568I	FBXL17_ENST00000359660.5_Missense_Mutation_p.L170I|FBXL17_ENST00000496714.1_Missense_Mutation_p.L170I	NM_001163315.2	NP_001156787.2	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	568								p.L170I(1)		endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		AGAGAGCTAAGATTTTTGCAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	91	92					5																	107521861		2202	4300	6502	107549760	SO:0001583	missense	64839			AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743		"F-boxes / Leucine-rich repeats"	13615	protein-coding gene	gene with protein product		609083	"F-box only protein 13"	FBXO13			Standard	NM_001163315		Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000542267.1:c.1702C>A	5.37:g.107521861G>T	ENSP00000437464:p.Leu568Ile		107549760	A1A4E3	Missense_Mutation	SNP	ENST00000542267.1	37	CCDS54886.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.131383	0.77549	.	.	ENSG00000145743	ENST00000359660;ENST00000542267;ENST00000496714	T;T;T	0.53423	0.62;0.62;0.62	5.46	4.58	0.56647	.	0.143577	0.47455	D	0.000224	T	0.59183	0.2175	L	0.48642	1.525	0.44579	D	0.997549	D;D	0.76494	0.999;0.997	P;D	0.64042	0.883;0.921	T	0.60737	-0.7204	10	0.51188	T	0.08	.	14.4059	0.67081	0.0716:0.0:0.9284:0.0	.	568;170	Q9UF56;Q9UF56-2	FXL17_HUMAN;.	I	170;568;170	ENSP00000352683:L170I;ENSP00000437464:L568I;ENSP00000418111:L170I	ENSP00000352683:L170I	L	-	1	0	FBXL17	107549760	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.476000	0.81055	1.416000	0.47057	0.591000	0.81541	CTT		0.348	FBXL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	107521861	G	T	107521861	3	4	61	1	0	0	0	0	1	0	0	0	5732	942	33	2	419	2	FBXL17	5	107521861	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	758796	107521861	73393399	4007	11992										
FER	2241	broad.mit.edu	37	chr5	108168596	108168596	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggacaagcagcaggtgaaGaaaagttacataggtgttca	12	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:108168596G>T	ENST00000281092.4	+	4	717	c.333G>T	c.(331-333)aaG>aaT	p.K111N	FER_ENST00000502752.1_3'UTR|CTD-2197I11.1_ENST00000510935.1_RNA|FER_ENST00000438717.2_Intron|FER_ENST00000536402.1_Missense_Mutation_p.K111N	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	111	Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.K111N(1)		NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AGCAGGTGAAGAAAAGTTACA	0.393																																					Colon(146;1051 1799 9836 27344 47401)											1	Substitution - Missense(1)	large_intestine(1)	5											170	152	158					5																	108168596		2202	4300	6502	108196495	SO:0001583	missense	2241			J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.333G>T	5.37:g.108168596G>T	ENSP00000281092:p.Lys111Asn		108196495	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618346	0.87359	.	.	ENSG00000151422	ENST00000281092;ENST00000536402	T;T	0.44083	0.93;0.93	6.11	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.56156	0.1966	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	T	0.59048	-0.7527	10	0.87932	D	0	-18.1337	11.8346	0.52316	0.1351:0.0:0.8649:0.0	.	111;111	Q6PEJ9;P16591	.;FER_HUMAN	N	111	ENSP00000281092:K111N;ENSP00000442627:K111N	ENSP00000281092:K111N	K	+	3	2	FER	108196495	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.534000	0.53568	1.569000	0.49696	0.655000	0.94253	AAG		0.393	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		T	108168596	G	T	108168596	3	4	61	1	0	0	0	0	1	0	0	0	5832	933	33	2	339	2	FER	5	108168596	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	646735	108168596	72746664	4008	11993										
FER	2241	broad.mit.edu	37	chr5	108219175	108219175	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggctgttttggagttagaGaagagaattgaagaatcttc	13	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:108219175G>T	ENST00000281092.4	+	9	1386	c.1002G>T	c.(1000-1002)gaG>gaT	p.E334D	FER_ENST00000438717.2_Missense_Mutation_p.E159D|FER_ENST00000536402.1_Intron	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	334					actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.E334D(1)		NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TGGAGTTAGAGAAGAGAATTG	0.338																																					Colon(146;1051 1799 9836 27344 47401)											1	Substitution - Missense(1)	large_intestine(1)	5											99	108	105					5																	108219175		2202	4299	6501	108247074	SO:0001583	missense	2241			J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1002G>T	5.37:g.108219175G>T	ENSP00000281092:p.Glu334Asp		108247074	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.956975	0.34565	.	.	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.75704	-0.94;-0.96	5.4	-0.236	0.13067	.	0.142496	0.64402	D	0.000008	T	0.62319	0.2418	L	0.40543	1.245	0.38644	D	0.951679	B	0.12013	0.005	B	0.11329	0.006	T	0.56408	-0.7984	10	0.48119	T	0.1	-18.5795	11.1609	0.48516	0.5034:0.0:0.4966:0.0	.	334	P16591	FER_HUMAN	D	334;159	ENSP00000281092:E334D;ENSP00000394297:E159D	ENSP00000281092:E334D	E	+	3	2	FER	108247074	0.999000	0.42202	0.998000	0.56505	0.990000	0.78478	0.298000	0.19120	0.008000	0.14787	0.585000	0.79938	GAG		0.338	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		T	108219175	G	T	108219175	3	4	61	1	0	0	0	0	1	0	0	0	5832	933	33	2	1028	2	FER	5	108219175	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50579	108219175	72696085	4009	11994										
FER	2241	broad.mit.edu	37	chr5	108382853	108382853	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtcaaacttataggagtTtgcacacaaagacagcctgt	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:108382853T>C	ENST00000281092.4	+	16	2262	c.1878T>C	c.(1876-1878)gtT>gtC	p.V626V	FER_ENST00000438717.2_Silent_p.V451V	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	626	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.V626V(1)		NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTATAGGAGTTTGCACACAAA	0.308																																					Colon(146;1051 1799 9836 27344 47401)											1	Substitution - coding silent(1)	large_intestine(1)	5											114	108	110					5																	108382853		2202	4298	6500	108410752	SO:0001819	synonymous_variant	2241			J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1878T>C	5.37:g.108382853T>C			108410752	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																				0.308	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		C	108382853	T	C	108382853	2	2	61	1	0	0	0	0	0	0	0	1	5832	1828	64	4		4	FER	5	108382853	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	163678	108382853	72532407	4010	11995										
MAN2A1	4124	broad.mit.edu	37	chr5	109155562	109155562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaactcctttgttttacttCggtttgatcaaactggactt	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:109155562C>T	ENST00000261483.4	+	14	3354	c.2302C>T	c.(2302-2304)Cgg>Tgg	p.R768W		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	768					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.R768W(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		TGTTTTACTTCGGTTTGATCA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	5											107	127	120					5																	109155562		2201	4294	6495	109183461	SO:0001583	missense	4124				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2302C>T	5.37:g.109155562C>T	ENSP00000261483:p.Arg768Trp		109183461	Q16767	Missense_Mutation	SNP	ENST00000261483.4	37	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	6.152	0.396239	0.11638	.	.	ENSG00000112893	ENST00000261483	T	0.79141	-1.24	6.06	-5.26	0.02772	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	1.156610	0.05829	N	0.617215	T	0.51449	0.1675	N	0.03000	-0.44	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42155	-0.9468	10	0.48119	T	0.1	5.2866	8.3076	0.32051	0.0:0.1685:0.2:0.6315	.	768	Q16706	MA2A1_HUMAN	W	768	ENSP00000261483:R768W	ENSP00000261483:R768W	R	+	1	2	MAN2A1	109183461	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.033000	0.13754	-0.518000	0.06452	-0.302000	0.09304	CGG		0.303	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			T	109155562	C	T	109155562	3	4	61	1	0	0	0	0	1	0	0	0	9244	875	31	1	2356	1	MAN2A1	5	109155562	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	772709	109155562	71759698	4011	11996										
MAN2A1	4124	broad.mit.edu	37	chr5	109156017	109156017	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacaaaagtggtgcctacCtcttcttacctgatggtaat	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:109156017C>A	ENST00000261483.4	+	15	3477	c.2425C>A	c.(2425-2427)Ctc>Atc	p.L809I		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	809					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.L809I(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		TGGTGCCTACCTCTTCTTACC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	92	93					5																	109156017		2202	4300	6502	109183916	SO:0001583	missense	4124				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2425C>A	5.37:g.109156017C>A	ENSP00000261483:p.Leu809Ile		109183916	Q16767	Missense_Mutation	SNP	ENST00000261483.4	37	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468374	0.84533	.	.	ENSG00000112893	ENST00000261483	D	0.83837	-1.77	5.97	5.11	0.69529	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	D	0.90497	0.7023	M	0.79123	2.44	0.58432	D	0.999999	D	0.71674	0.998	D	0.79108	0.992	D	0.90746	0.4653	10	0.48119	T	0.1	-15.2381	14.7124	0.69244	0.0:0.9304:0.0:0.0696	.	809	Q16706	MA2A1_HUMAN	I	809	ENSP00000261483:L809I	ENSP00000261483:L809I	L	+	1	0	MAN2A1	109183916	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	3.257000	0.51500	1.542000	0.49330	0.655000	0.94253	CTC		0.353	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			A	109156017	C	A	109156017	3	1	61	1	0	0	0	0	1	0	0	0	9244	681	24	2	2483	2	MAN2A1	5	109156017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455	109156017	71759243	4012	11997										
SLC25A46	91137	broad.mit.edu	37	chr5	110091182	110091182	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagggaggttttacataaatGgagtcctaaacaaataggag	11	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:110091182G>T	ENST00000355943.3	+	6	707	c.581G>T	c.(580-582)tGg>tTg	p.W194L	SLC25A46_ENST00000509442.2_Missense_Mutation_p.W103L|SLC25A46_ENST00000504098.1_Missense_Mutation_p.W48L|SLC25A46_ENST00000509432.1_5'UTR|SLC25A46_ENST00000513807.1_Missense_Mutation_p.W32L|SLC25A46_ENST00000447245.2_Missense_Mutation_p.W194L|SLC25A46_ENST00000513706.1_3'UTR	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	194					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.W194L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		TTACATAAATGGAGTCCTAAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	5											53	61	58					5																	110091182		2202	4290	6492	110119081	SO:0001583	missense	91137			BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"Solute carriers"	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.581G>T	5.37:g.110091182G>T	ENSP00000348211:p.Trp194Leu		110119081	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Missense_Mutation	SNP	ENST00000355943.3	37	CCDS4100.1	.	.	.	.	.	.	.	.	.	.	G	9.308	1.054934	0.19907	.	.	ENSG00000164209	ENST00000513807;ENST00000509442;ENST00000355943;ENST00000514046;ENST00000447245;ENST00000504098	D;T;T;T;T	0.82167	-1.58;-1.05;-1.05;-1.05;-1.05	5.62	4.74	0.60224	Mitochondrial carrier domain (2);	0.105251	0.64402	N	0.000001	T	0.80232	0.4585	M	0.67953	2.075	0.53005	D	0.999967	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.0	T	0.74954	-0.3488	10	0.10636	T	0.68	-2.2584	16.1307	0.81436	0.0:0.0:0.8657:0.1342	.	103;194	B4DY98;Q96AG3	.;S2546_HUMAN	L	32;103;194;48;194;48	ENSP00000421134:W32L;ENSP00000424136:W103L;ENSP00000348211:W194L;ENSP00000399717:W194L;ENSP00000425708:W48L	ENSP00000348211:W194L	W	+	2	0	SLC25A46	110119081	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.823000	0.69272	1.341000	0.45600	0.655000	0.94253	TGG		0.274	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773		T	110091182	G	T	110091182	3	4	61	1	0	0	0	0	1	0	0	0	14548	1357	47	2	603	2	SLC25A46	5	110091182	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	935165	110091182	70824078	4013	11998										
SLC25A46	91137	broad.mit.edu	37	chr5	110097445	110097445	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgttttacagattaccaAaattatttactctacacttc	3	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:110097445A>C	ENST00000355943.3	+	8	1346	c.1220A>C	c.(1219-1221)aAa>aCa	p.K407T	SLC25A46_ENST00000509442.2_Missense_Mutation_p.K316T|SLC25A46_ENST00000504098.1_Missense_Mutation_p.K261T|SLC25A46_ENST00000509432.1_Missense_Mutation_p.K194T|SLC25A46_ENST00000513807.1_Missense_Mutation_p.K245T|SLC25A46_ENST00000447245.2_Missense_Mutation_p.K326T|SLC25A46_ENST00000513706.1_3'UTR	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	407					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.K407T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		CAGATTACCAAAATTATTTAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											64	66	65					5																	110097445		2196	4297	6493	110125344	SO:0001583	missense	91137			BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"Solute carriers"	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.1220A>C	5.37:g.110097445A>C	ENSP00000348211:p.Lys407Thr		110125344	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Missense_Mutation	SNP	ENST00000355943.3	37	CCDS4100.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.838576	0.71373	.	.	ENSG00000164209	ENST00000513807;ENST00000509442;ENST00000355943;ENST00000514046;ENST00000447245;ENST00000504098;ENST00000509432	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.92	5.92	0.95590	Mitochondrial carrier domain (1);	0.043127	0.85682	D	0.000000	D	0.86871	0.6037	M	0.66378	2.025	0.80722	D	1	D;D	0.76494	0.98;0.999	P;D	0.72075	0.833;0.976	D	0.87826	0.2641	10	0.66056	D	0.02	-13.112	16.3604	0.83263	1.0:0.0:0.0:0.0	.	316;407	B4DY98;Q96AG3	.;S2546_HUMAN	T	245;316;407;261;326;261;194	ENSP00000421134:K245T;ENSP00000424136:K316T;ENSP00000348211:K407T;ENSP00000399717:K326T;ENSP00000425708:K261T;ENSP00000426604:K194T	ENSP00000348211:K407T	K	+	2	0	SLC25A46	110125344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.623000	0.67757	2.260000	0.74910	0.528000	0.53228	AAA		0.338	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773		C	110097445	A	C	110097445	3	2	61	1	0	0	0	0	1	0	0	0	14548	14	1	4	1250	4	SLC25A46	5	110097445	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6263	110097445	70817815	4014	11999										
CAMK4	814	broad.mit.edu	37	chr5	110710590	110710590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagataggagttcttcttCgcctctcacatccaaacatt	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:110710590C>T	ENST00000282356.4	+	3	681	c.283C>T	c.(283-285)Cgc>Tgc	p.R95C	CAMK4_ENST00000512453.1_Missense_Mutation_p.R95C	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	95	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.R95C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGTTCTTCTTCGCCTCTCACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											97	91	93					5																	110710590		2202	4300	6502	110738489	SO:0001583	missense	814			D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.283C>T	5.37:g.110710590C>T	ENSP00000282356:p.Arg95Cys		110738489	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.369036	0.82463	.	.	ENSG00000152495	ENST00000508074;ENST00000512453;ENST00000282356	T;T;T	0.67698	-0.28;-0.28;-0.28	5.77	4.9	0.64082	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79131	0.4394	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.81464	-0.0921	10	0.72032	D	0.01	.	15.3044	0.73982	0.1408:0.8592:0.0:0.0	.	95	Q16566	KCC4_HUMAN	C	95	ENSP00000426940:R95C;ENSP00000422634:R95C;ENSP00000282356:R95C	ENSP00000282356:R95C	R	+	1	0	CAMK4	110738489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.657000	0.61490	1.433000	0.47394	0.650000	0.86243	CGC		0.393	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		T	110710590	C	T	110710590	3	4	61	1	0	0	0	0	1	0	0	0	2611	884	31	1	293	1	CAMK4	5	110710590	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	613145	110710590	70204670	4015	12000										
STARD4	134429	broad.mit.edu	37	chr5	110837779	110837779	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatctataacaccttgggCtttgtagctggagaaaaaaa	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:110837779C>A	ENST00000296632.3	-	4	297	c.163G>T	c.(163-165)Gcc>Tcc	p.A55S	STARD4_ENST00000512160.1_Intron|STARD4_ENST00000502322.1_Missense_Mutation_p.A55S|STARD4_ENST00000511569.1_5'UTR|STARD4_ENST00000509887.1_Intron	NM_139164.1	NP_631903.1	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain containing 4	55	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)	p.A55S(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	12		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		ACACCTTGGGCTTTGTAGCTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	112	110					5																	110837779		2202	4300	6502	110865678	SO:0001583	missense	134429			AF480299	CCDS4104.1	5q22	2011-09-12	2007-08-16		ENSG00000164211	ENSG00000164211		"StAR-related lipid transfer (START) domain containing"	18058	protein-coding gene	gene with protein product		607049	"START domain containing 4, sterol regulated"			12011452	Standard	NM_139164		Approved		uc003kph.1	Q96DR4	OTTHUMG00000128793	ENST00000296632.3:c.163G>T	5.37:g.110837779C>A	ENSP00000296632:p.Ala55Ser		110865678	Q86TN9	Missense_Mutation	SNP	ENST00000296632.3	37	CCDS4104.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447257	0.63178	.	.	ENSG00000164211	ENST00000296632;ENST00000505803;ENST00000502322	T;T;T	0.50001	0.76;0.76;0.76	5.94	5.94	0.96194	Lipid-binding START (2);START-like domain (1);	0.238543	0.36932	N	0.002339	T	0.50701	0.1631	M	0.62723	1.935	0.80722	D	1	B;P	0.35401	0.319;0.499	B;P	0.44359	0.201;0.447	T	0.40459	-0.9562	10	0.20519	T	0.43	-3.2249	10.6683	0.45743	0.0:0.8587:0.0:0.1413	.	55;55	Q86TN9;Q96DR4	.;STAR4_HUMAN	S	55	ENSP00000296632:A55S;ENSP00000427478:A55S;ENSP00000427639:A55S	ENSP00000296632:A55S	A	-	1	0	STARD4	110865678	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	2.649000	0.46656	2.821000	0.97095	0.655000	0.94253	GCC		0.373	STARD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250720.1	NM_139164		A	110837779	C	A	110837779	3	1	61	1	0	0	0	0	1	0	0	0	15298	797	28	2	466	2	STARD4	5	110837779	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127189	110837779	70077481	4016	12001										
EPB41L4A	64097	broad.mit.edu	37	chr5	111519713	111519713	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataaaaagagtccacatacGaacgagatctgtgtctggat	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:111519713G>A	ENST00000261486.5	-	18	1898	c.1622C>T	c.(1621-1623)tCg>tTg	p.S541L	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	541						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.S541L(1)|p.S168L(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GTCCACATACGAACGAGATCT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	5											170	157	161					5																	111519713		1877	4093	5970	111547612	SO:0001630	splice_region_variant	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1622+1C>T	5.37:g.111519713G>A			111547612	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.542091	0.65198	.	.	ENSG00000129595	ENST00000261486	D	0.83837	-1.77	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000001	D	0.91164	0.7217	M	0.69823	2.125	0.52099	D	0.999948	D;D	0.89917	0.991;1.0	B;D	0.83275	0.426;0.996	D	0.89126	0.3506	9	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	541;168	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	L	541	ENSP00000261486:S541L	.	S	-	2	0	EPB41L4A	111547612	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.642000	0.83385	2.941000	0.99782	0.655000	0.94253	TCG		0.403	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Missense_Mutation	A	111519713	G	A	111519713	5	1	61	1	0	0	0	0	0	0	1	0	5168	1072	37	1	462	1	EPB41L4A	5	111519713	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681934	111519713	69395547	4017	12002										
EPB41L4A	64097	broad.mit.edu	37	chr5	111530269	111530269	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatattgagatattacctgtTtctctttttccggtattctc	5	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:111530269T>G	ENST00000261486.5	-	17	1774	c.1498A>C	c.(1498-1500)Aac>Cac	p.N500H	CTC-459M5.2_ENST00000515563.1_RNA|EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000506875.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	500						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.N500H(1)|p.N127H(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TATTACCTGTTTCTCTTTTTC	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	5											78	75	76					5																	111530269		1809	4069	5878	111558168	SO:0001583	missense	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1498A>C	5.37:g.111530269T>G	ENSP00000261486:p.Asn500His		111558168	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.170939	0.38315	.	.	ENSG00000129595	ENST00000261486	D	0.82526	-1.62	5.09	3.91	0.45181	.	0.213426	0.46442	N	0.000292	T	0.73426	0.3585	L	0.36672	1.1	0.28889	N	0.893948	B;B	0.16802	0.009;0.019	B;B	0.16289	0.012;0.015	T	0.65010	-0.6272	10	0.40728	T	0.16	.	8.9304	0.35666	0.0:0.0:0.1878:0.8122	.	500;127	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	H	500	ENSP00000261486:N500H	ENSP00000261486:N500H	N	-	1	0	EPB41L4A	111558168	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.937000	0.48979	0.935000	0.37341	0.528000	0.53228	AAC		0.383	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			G	111530269	T	G	111530269	3	3	61	1	0	0	0	0	1	0	0	0	5168	1841	64	4	590	4	EPB41L4A	5	111530269	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10556	111530269	69384991	4018	12003										
EPB41L4A	64097	broad.mit.edu	37	chr5	111600633	111600633	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctatggcttcttcaagttCttccttctgatcaggaacaa	6	10	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:111600633C>A	ENST00000261486.5	-	6	790	c.514G>T	c.(514-516)Gaa>Taa	p.E172*		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	172	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.E172*(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TCTTCAAGTTCTTCCTTCTGA	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											173	161	164					5																	111600633		1834	4097	5931	111628532	SO:0001587	stop_gained	64097			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.514G>T	5.37:g.111600633C>A	ENSP00000261486:p.Glu172*		111628532	A4FUI6	Nonsense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	40	8.481469	0.98829	.	.	ENSG00000129595	ENST00000261486	.	.	.	5.46	5.46	0.80206	.	0.067034	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.0769	0.89430	0.0:1.0:0.0:0.0	.	.	.	.	X	172	.	ENSP00000261486:E172X	E	-	1	0	EPB41L4A	111628532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.052000	0.71080	2.568000	0.86640	0.650000	0.86243	GAA		0.358	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111600633	C	A	111600633	4	1	61	1	0	0	0	0	0	1	0	0	5168	922	32	2	1618	2	EPB41L4A	5	111600633	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70364	111600633	69314627	4019	12004										
APC	324	broad.mit.edu	37	chr5	112103071	112103071	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtactggatatttagaaGaacttgagaaagagaggtaa	11	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112103071G>A	ENST00000457016.1	+	4	786	c.406G>A	c.(406-408)Gaa>Aaa	p.E136K	APC_ENST00000508376.2_Missense_Mutation_p.E136K|APC_ENST00000257430.4_Missense_Mutation_p.E136K			P25054	APC_HUMAN	adenomatous polyposis coli	136	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E136K(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATATTTAGAAGAACTTGAGAA	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	5											78	78	78					5																	112103071		2202	4300	6502	112130970	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.406G>A	5.37:g.112103071G>A	ENSP00000413133:p.Glu136Lys		112130970	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142195	0.94560	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05;-3.05	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.94355	0.8185	L	0.42245	1.32	0.53688	D	0.999977	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.978	D	0.93357	0.6723	9	.	.	.	-21.5101	19.2099	0.93749	0.0:0.0:1.0:0.0	.	138;136	Q4LE70;P25054	.;APC_HUMAN	K	136;146;136;136;136	ENSP00000413133:E136K;ENSP00000423224:E146K;ENSP00000257430:E136K;ENSP00000427089:E136K;ENSP00000423828:E136K	.	E	+	1	0	APC	112130970	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.780000	0.85658	2.547000	0.85894	0.585000	0.79938	GAA		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112103071	G	A	112103071	3	1	61	1	0	0	0	0	1	0	0	0	763	943	33	3	416	3	APC	5	112103071	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	502438	112103071	68812189	4020	12005										
APC	324	broad.mit.edu	37	chr5	112173612	112173612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacttatcagaaacttttgAcaatatagacaatttaagtc	5	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112173612A>G	ENST00000457016.1	+	16	2701	c.2321A>G	c.(2320-2322)gAc>gGc	p.D774G	APC_ENST00000508376.2_Missense_Mutation_p.D774G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.D774G			P25054	APC_HUMAN	adenomatous polyposis coli	774	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.D774G(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAACTTTTGACAATATAGAC	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											61	62	62					5																	112173612		2202	4300	6502	112201511	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2321A>G	5.37:g.112173612A>G	ENSP00000413133:p.Asp774Gly		112201511	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.312998	0.60414	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;T;D;D;T	0.92199	-2.99;0.9;-2.99;-2.99;0.9	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.92938	0.7753	L	0.57536	1.79	0.80722	D	1	B;B	0.33964	0.434;0.434	B;P	0.44696	0.298;0.458	D	0.91382	0.5128	10	0.36615	T	0.2	-15.5051	16.8061	0.85666	1.0:0.0:0.0:0.0	.	776;774	Q4LE70;P25054	.;APC_HUMAN	G	774;756;774;774;774	ENSP00000413133:D774G;ENSP00000423224:D756G;ENSP00000257430:D774G;ENSP00000427089:D774G;ENSP00000423828:D774G	ENSP00000257430:D774G	D	+	2	0	APC	112201511	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	GAC		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173612	A	G	112173612	3	3	61	1	0	0	0	0	1	0	0	0	763	275	10	4	2379	4	APC	5	112173612	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	70541	112173612	68741648	4021	12006										
APC	324	broad.mit.edu	37	chr5	112175490	112175490	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatagttttgagagtcgttCgattgccagctccgttcaga	11	8	1	3	rs267600319		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112175490C>T	ENST00000457016.1	+	16	4579	c.4199C>T	c.(4198-4200)tCg>tTg	p.S1400L	APC_ENST00000508376.2_Missense_Mutation_p.S1400L|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1400L			P25054	APC_HUMAN	adenomatous polyposis coli	1400	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1400*(6)|p.S1400fs*1(6)|p.Y1376fs*41(1)|p.?(1)|p.S1400L(1)|p.K1192fs*3(1)|p.S1400fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAGAGTCGTTCGATTGCCAGC	0.478		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	17	Deletion - Frameshift(9)|Substitution - Nonsense(6)|Unknown(1)|Substitution - Missense(1)	large_intestine(15)|soft_tissue(1)|skin(1)	5	GRCh37	CM995167	APC	M							109	102	104					5																	112175490		2202	4300	6502	112203389	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4199C>T	5.37:g.112175490C>T	ENSP00000413133:p.Ser1400Leu		112203389	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245123	0.79912	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91894	-2.93;-2.93;-2.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.95389	0.8503	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.93788	0.7090	9	.	.	.	-9.695	20.4898	0.99202	0.0:1.0:0.0:0.0	.	1402;1400	Q4LE70;P25054	.;APC_HUMAN	L	1400	ENSP00000413133:S1400L;ENSP00000257430:S1400L;ENSP00000427089:S1400L	.	S	+	2	0	APC	112203389	1.000000	0.71417	0.721000	0.30653	0.765000	0.43378	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCG		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175490	C	T	112175490	3	4	61	1	0	0	0	0	1	0	0	0	763	893	31	1	4257	1	APC	5	112175490	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1878	112175490	68739770	4022	12007										
APC	324	broad.mit.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	61	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149	112175639	68739621	4023	12008										
APC	324	broad.mit.edu	37	chr5	112175897	112175897	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaaatgacaatgggaatGaaacagaatcagagcagcct	11	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112175897G>T	ENST00000457016.1	+	16	4986	c.4606G>T	c.(4606-4608)Gaa>Taa	p.E1536*	APC_ENST00000508376.2_Nonsense_Mutation_p.E1536*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1536*			P25054	APC_HUMAN	adenomatous polyposis coli	1536	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1536*(4)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAATGGGAATGAAACAGAATC	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Substitution - Nonsense(4)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(3)|thyroid(1)|soft_tissue(1)|skin(1)	5											76	81	79					5																	112175897		2202	4300	6502	112203796	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4606G>T	5.37:g.112175897G>T	ENSP00000413133:p.Glu1536*		112203796	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	42	9.668045	0.99234	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.9312	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	X	1536	.	.	E	+	1	0	APC	112203796	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.842000	0.86851	2.937000	0.99478	0.650000	0.86243	GAA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175897	G	T	112175897	4	4	61	1	0	0	0	0	0	1	0	0	763	1291	45	2	4664	2	APC	5	112175897	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	258	112175897	68739363	4024	12009										
APC	324	broad.mit.edu	37	chr5	112179573	112179573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctatagtggaacgtacccCattcagttctagcagctcaa	7	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112179573C>T	ENST00000457016.1	+	16	8662	c.8282C>T	c.(8281-8283)cCa>cTa	p.P2761L	APC_ENST00000508376.2_Missense_Mutation_p.P2761L|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.P2761L			P25054	APC_HUMAN	adenomatous polyposis coli	2761	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.P2761L(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAACGTACCCCATTCAGTTCT	0.453		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											73	74	73					5																	112179573		2202	4299	6501	112207472	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.8282C>T	5.37:g.112179573C>T	ENSP00000413133:p.Pro2761Leu		112207472	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.381724	0.61845	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	T;T;T	0.78003	-1.14;-1.14;-1.14	5.92	5.92	0.95590	EB-1 binding (1);	0.000000	0.85682	D	0.000000	T	0.74688	0.3749	L	0.29908	0.895	0.80722	D	1	P;P	0.47484	0.896;0.896	P;P	0.46419	0.516;0.516	T	0.71596	-0.4545	9	.	.	.	-16.8033	20.3248	0.98698	0.0:1.0:0.0:0.0	.	2763;2761	Q4LE70;P25054	.;APC_HUMAN	L	2761	ENSP00000413133:P2761L;ENSP00000257430:P2761L;ENSP00000427089:P2761L	.	P	+	2	0	APC	112207472	1.000000	0.71417	0.973000	0.42090	0.946000	0.59487	6.453000	0.73488	2.818000	0.97014	0.655000	0.94253	CCA		0.453	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112179573	C	T	112179573	3	4	61	1	0	0	0	0	1	0	0	0	763	594	21	3	8340	3	APC	5	112179573	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3676	112179573	68735687	4025	12010										
MCC	4163	broad.mit.edu	37	chr5	112364657	112364657	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgctttagatcattcacGaactctgcagattgctgatg	9	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112364657G>A	ENST00000302475.4	-	16	2846	c.2283C>T	c.(2281-2283)ttC>ttT	p.F761F	MCC_ENST00000408903.3_Silent_p.F951F|MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Silent_p.F698F	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	761					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.F951F(1)|p.F761F(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		GATCATTCACGAACTCTGCAG	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	5											175	177	176					5																	112364657		2202	4300	6502	112392556	SO:0001819	synonymous_variant	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.2283C>T	5.37:g.112364657G>A			112392556	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																				0.507	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		A	112364657	G	A	112364657	2	1	61	1	0	0	0	0	0	0	0	1	9403	1049	37	1		1	MCC	5	112364657	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185084	112364657	68550603	4026	12011										
TSSK1B	83942	broad.mit.edu	37	chr5	112770512	112770512	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaggaggtagcctcgtcGcttgaggacagcagcgtcat	13	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112770512G>A	ENST00000390666.3	-	1	216	c.25C>T	c.(25-27)Cga>Tga	p.R9*	CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	9					multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R9*(2)		large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		TAGCCTCGTCGCTTGAGGACA	0.547																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											42	44	43					5																	112770512		2135	4268	6403	112798411	SO:0001587	stop_gained	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"serine/threonine kinase 22D (spermiogenesis associated)", "testis-specific serine kinase 1"	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.25C>T	5.37:g.112770512G>A	ENSP00000375081:p.Arg9*		112798411	B2R8D9	Nonsense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.558400	0.65538	.	.	ENSG00000212122	ENST00000390666	.	.	.	2.67	0.564	0.17302	.	0.640100	0.11147	U	0.594584	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	6.6988	0.23213	0.0:0.0:0.4911:0.5089	.	.	.	.	X	9	.	ENSP00000375081:R9X	R	-	1	2	TSSK1B	112798411	0.581000	0.26741	1.000000	0.80357	0.615000	0.37417	0.856000	0.27818	0.490000	0.27771	-0.224000	0.12420	CGA		0.547	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		A	112770512	G	A	112770512	4	1	61	1	0	0	0	0	0	1	0	0	16708	1095	38	1	1082	1	TSSK1B	5	112770512	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	405855	112770512	68144748	4027	12012										
YTHDC2	64848	broad.mit.edu	37	chr5	112862360	112862360	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgaaaagaggagaatccGaatttgattcttttaggcag	11	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112862360G>A	ENST00000161863.4	+	4	766	c.553G>A	c.(553-555)Gaa>Aaa	p.E185K	YTHDC2_ENST00000515883.1_Missense_Mutation_p.E185K	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	185					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.E185K(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AGGAGAATCCGAATTTGATTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	88	87					5																	112862360		2202	4300	6502	112890259	SO:0001583	missense	64848			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.553G>A	5.37:g.112862360G>A	ENSP00000161863:p.Glu185Lys		112890259	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.195298	0.58017	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000514720;ENST00000511372	T;T	0.07327	4.19;3.2	5.52	5.52	0.82312	.	0.200495	0.51477	D	0.000085	T	0.06280	0.0162	N	0.21448	0.665	0.54753	D	0.999981	B	0.17465	0.022	B	0.08055	0.003	T	0.40515	-0.9559	10	0.16420	T	0.52	.	13.0706	0.59059	0.0738:0.0:0.9262:0.0	.	185	Q9H6S0	YTDC2_HUMAN	K	185;185;125;95	ENSP00000161863:E185K;ENSP00000423101:E185K	ENSP00000161863:E185K	E	+	1	0	YTHDC2	112890259	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.599000	0.82757	2.753000	0.94483	0.467000	0.42956	GAA		0.348	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		A	112862360	G	A	112862360	3	1	61	1	0	0	0	0	1	0	0	0	17537	1059	37	1	567	1	YTHDC2	5	112862360	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91848	112862360	68052900	4028	12013										
YTHDC2	64848	broad.mit.edu	37	chr5	112929045	112929045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgctccagttatgggaaCgtcttcccttgggagaaaaa	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:112929045C>T	ENST00000161863.4	+	29	4471	c.4258C>T	c.(4258-4260)Cgt>Tgt	p.R1420C		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1420					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.R1420C(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GTTATGGGAACGTCTTCCCTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	98	100					5																	112929045		2202	4300	6502	112956944	SO:0001583	missense	64848			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4258C>T	5.37:g.112929045C>T	ENSP00000161863:p.Arg1420Cys		112956944	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129828	0.77549	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.32023	1.47	5.98	5.98	0.97165	YTH domain (1);	0.056624	0.64402	D	0.000003	T	0.47414	0.1444	M	0.62723	1.935	0.80722	D	1	D	0.67145	0.996	P	0.55999	0.789	T	0.42632	-0.9440	10	0.87932	D	0	.	15.1811	0.72960	0.141:0.859:0.0:0.0	.	1420	Q9H6S0	YTDC2_HUMAN	C	1420;1330	ENSP00000161863:R1420C	ENSP00000161863:R1420C	R	+	1	0	YTHDC2	112956944	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.957000	0.49137	2.839000	0.97877	0.650000	0.86243	CGT		0.368	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		T	112929045	C	T	112929045	3	4	61	1	0	0	0	0	1	0	0	0	17537	536	19	1	4372	1	YTHDC2	5	112929045	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66685	112929045	67986215	4029	12014										
KCNN2	3781	broad.mit.edu	37	chr5	113831648	113831648	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgaaaggagtgaagacttCgagaagaggattgttaccct	12	6	0	4	rs150495473		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:113831648C>T	ENST00000512097.3	+	9	2527	c.1509C>T	c.(1507-1509)ttC>ttT	p.F503F	KCNN2_ENST00000503706.1_Silent_p.F155F|RP11-492A10.1_ENST00000514115.1_RNA|KCNN2_ENST00000264773.3_Silent_p.F503F			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	503					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.F155F(1)|p.F503F(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	GTGAAGACTTCGAGAAGAGGA	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	5											115	120	119					5																	113831648		2202	4300	6502	113859547	SO:0001819	synonymous_variant	3781			AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.1509C>T	5.37:g.113831648C>T			113859547	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	37	CCDS4114.1																																																																																				0.438	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113831648	C	T	113831648	2	4	61	1	0	0	0	0	0	0	0	1	8100	883	31	1		1	KCNN2	5	113831648	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	902603	113831648	67083612	4030	12015										
PGGT1B	5229	broad.mit.edu	37	chr5	114557652	114557652	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttttctgaaaaaacttCttctagtttacccatcagac	3	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:114557652C>A	ENST00000419445.1	-	7	732	c.712G>T	c.(712-714)Gaa>Taa	p.E238*	PGGT1B_ENST00000514178.1_5'UTR|PGGT1B_ENST00000379615.3_Intron	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	238					negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)	p.E238*(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		GAAAAAACTTCTTCTAGTTTA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											96	93	94					5																	114557652		2202	4300	6502	114585551	SO:0001587	stop_gained	5229				CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219			8895	protein-coding gene	gene with protein product		602031				8106351	Standard	NM_005023		Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.712G>T	5.37:g.114557652C>A	ENSP00000404676:p.Glu238*		114585551	Q5MJP9	Nonsense_Mutation	SNP	ENST00000419445.1	37	CCDS4116.1	.	.	.	.	.	.	.	.	.	.	C	35	5.422755	0.96111	.	.	ENSG00000164219	ENST00000419445	.	.	.	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-22.653	18.3496	0.90333	0.0:1.0:0.0:0.0	.	.	.	.	X	238	.	ENSP00000404676:E238X	E	-	1	0	PGGT1B	114585551	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.827000	0.69300	2.403000	0.81681	0.585000	0.79938	GAA		0.363	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023		A	114557652	C	A	114557652	4	1	61	1	0	0	0	0	0	1	0	0	11820	922	32	2	433	2	PGGT1B	5	114557652	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726004	114557652	66357608	4031	12016										
AP3S1	1176	broad.mit.edu	37	chr5	115202422	115202422	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccatttggtatctaagaGagatgaaaatgtttgtaatt	8	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:115202422G>T	ENST00000316788.7	+	2	682	c.125G>T	c.(124-126)aGa>aTa	p.R42I		NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	42					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.R42I(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		GTATCTAAGAGAGATGAAAAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											66	70	69					5																	115202422		2202	4293	6495	115230321	SO:0001583	missense	1176			D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.125G>T	5.37:g.115202422G>T	ENSP00000325369:p.Arg42Ile		115230321	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Missense_Mutation	SNP	ENST00000316788.7	37	CCDS4123.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034178	0.93575	.	.	ENSG00000177879	ENST00000316788	T	0.60920	0.15	4.96	4.96	0.65561	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.85427	0.5694	H	0.98155	4.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.995;0.994	D	0.90847	0.4728	10	0.87932	D	0	-18.8792	18.6851	0.91560	0.0:0.0:1.0:0.0	.	42;42;42	B2R4I8;Q92572;F5H459	.;AP3S1_HUMAN;.	I	42	ENSP00000325369:R42I	ENSP00000325369:R42I	R	+	2	0	AP3S1	115230321	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.585000	0.98223	2.702000	0.92279	0.655000	0.94253	AGA		0.308	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2			T	115202422	G	T	115202422	3	4	61	1	0	0	0	0	1	0	0	0	749	942	33	2	131	2	AP3S1	5	115202422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	644770	115202422	65712838	4032	12017										
AQPEP	206338	broad.mit.edu	37	chr5	115335464	115335464	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttcctttatagaatgaGatctttttttctaacatttt	3	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:115335464G>T	ENST00000357872.4	+	7	1504	c.1380G>T	c.(1378-1380)gaG>gaT	p.E460D	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		460						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E460D(1)									TATAGAATGAGATCTTTTTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											53	56	55					5																	115335464		2201	4300	6501	115363363	SO:0001583	missense	206338																														ENST00000357872.4:c.1380G>T	5.37:g.115335464G>T	ENSP00000350541:p.Glu460Asp		115363363	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.887525	0.00527	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02974	4.09	5.77	-0.0472	0.13844	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.681845	0.14147	N	0.338275	T	0.03608	0.0103	L	0.37750	1.13	0.19300	N	0.999973	P	0.48589	0.912	P	0.51516	0.672	T	0.10405	-1.0631	10	0.02654	T	1	.	9.7276	0.40342	0.4391:0.0:0.5609:0.0	.	460	Q6Q4G3	AMPQ_HUMAN	D	460;449	ENSP00000350541:E460D	ENSP00000350541:E460D	E	+	3	2	AC010282.1	115363363	0.012000	0.17670	0.086000	0.20670	0.103000	0.19146	-0.010000	0.12743	0.081000	0.16988	0.655000	0.94253	GAG		0.363	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115335464	G	T	115335464	3	4	61	1	0	0	0	0	1	0	0	0	834	933	33	2	1406	2	AQPEP	5	115335464	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133042	115335464	65579796	4033	12018										
COMMD10	51397	broad.mit.edu	37	chr5	115428320	115428320	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagacaagacaaagctgaaGcatttgtcaatacgtggtct	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:115428320G>T	ENST00000274458.4	+	4	384	c.322G>T	c.(322-324)Gca>Tca	p.A108S	COMMD10_ENST00000515539.1_Missense_Mutation_p.A94S	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	108								p.A108S(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(2)	9		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		CAAAGCTGAAGCATTTGTCAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											98	88	91					5																	115428320		2202	4300	6502	115456219	SO:0001583	missense	51397			AY542165	CCDS34215.1	5q23.1	2008-02-05				ENSG00000145781			30201	protein-coding gene	gene with protein product						15799966	Standard	NM_016144		Approved	PTD002	uc003krt.1	Q9Y6G5		ENST00000274458.4:c.322G>T	5.37:g.115428320G>T	ENSP00000274458:p.Ala108Ser		115456219	D3DT07|Q9P077	Missense_Mutation	SNP	ENST00000274458.4	37	CCDS34215.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180732	0.57800	.	.	ENSG00000145781	ENST00000274458;ENST00000515539;ENST00000506589	T;T;T	0.11821	2.74;2.74;2.74	6.17	4.4	0.53042	.	0.160113	0.56097	D	0.000040	T	0.16685	0.0401	L	0.60455	1.87	0.40275	D	0.978334	P	0.41232	0.743	B	0.40506	0.331	T	0.01729	-1.1286	10	0.51188	T	0.08	-8.1293	11.4751	0.50293	0.0683:0.1261:0.8056:0.0	.	108	Q9Y6G5	COMDA_HUMAN	S	108;94;64	ENSP00000274458:A108S;ENSP00000427319:A94S;ENSP00000424611:A64S	ENSP00000274458:A108S	A	+	1	0	COMMD10	115456219	1.000000	0.71417	0.971000	0.41717	0.984000	0.73092	5.321000	0.65846	0.938000	0.37419	0.655000	0.94253	GCA		0.383	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371033.1	NM_016144		T	115428320	G	T	115428320	3	4	61	1	0	0	0	0	1	0	0	0	3721	971	34	2	336	2	COMMD10	5	115428320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92856	115428320	65486940	4034	12019										
DMXL1	1657	broad.mit.edu	37	chr5	118469205	118469205	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggtgtcctttgtttccaGaattccagtagctttcccca	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:118469205G>T	ENST00000311085.8	+	12	1666	c.1586G>T	c.(1585-1587)aGa>aTa	p.R529I	DMXL1_ENST00000539542.1_Missense_Mutation_p.R529I	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	529								p.R529I(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TTTGTTTCCAGAATTCCAGTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	109	108					5																	118469205		2202	4300	6502	118497104	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1586G>T	5.37:g.118469205G>T	ENSP00000309690:p.Arg529Ile		118497104		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.427955	0.83667	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.65732	-0.17;-0.17;-0.17	5.36	5.36	0.76844	WD40 repeat-like-containing domain (1);	0.041421	0.85682	D	0.000000	T	0.78528	0.4297	M	0.73430	2.235	0.80722	D	1	D;D	0.71674	0.998;0.982	D;P	0.62955	0.909;0.813	T	0.81109	-0.1082	10	0.87932	D	0	-19.7877	19.0891	0.93219	0.0:0.0:1.0:0.0	.	529;529	F5H269;Q9Y485	.;DMXL1_HUMAN	I	529	ENSP00000427692:R529I;ENSP00000309690:R529I;ENSP00000439479:R529I	ENSP00000309690:R529I	R	+	2	0	DMXL1	118497104	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.533000	0.85409	0.591000	0.81541	AGA		0.373	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118469205	G	T	118469205	3	4	61	1	0	0	0	0	1	0	0	0	4605	942	33	2	1632	2	DMXL1	5	118469205	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3040885	118469205	62446055	4035	12020										
DMXL1	1657	broad.mit.edu	37	chr5	118469657	118469657	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgctctaaatattgaaGaatgctctttgacacaacaa	6	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:118469657G>T	ENST00000311085.8	+	12	2118	c.2038G>T	c.(2038-2040)Gaa>Taa	p.E680*	DMXL1_ENST00000539542.1_Nonsense_Mutation_p.E680*	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	680								p.E680*(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AAATATTGAAGAATGCTCTTT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											112	109	110					5																	118469657		2202	4300	6502	118497556	SO:0001587	stop_gained	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2038G>T	5.37:g.118469657G>T	ENSP00000309690:p.Glu680*		118497556		Nonsense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265078	0.80358	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	.	.	.	5.25	5.25	0.73442	.	0.766089	0.13133	N	0.411246	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.2078	18.8237	0.92108	0.0:0.0:1.0:0.0	.	.	.	.	X	680	.	.	E	+	1	0	DMXL1	118497556	1.000000	0.71417	0.982000	0.44146	0.117000	0.20001	4.785000	0.62418	2.448000	0.82819	0.305000	0.20034	GAA		0.408	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118469657	G	T	118469657	4	4	61	1	0	0	0	0	0	1	0	0	4605	943	33	2	2084	2	DMXL1	5	118469657	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	452	118469657	62445603	4036	12021										
DMXL1	1657	broad.mit.edu	37	chr5	118485175	118485175	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccccaccttttcctgtttCtttatcgtgggtccgggatg	9	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:118485175C>A	ENST00000311085.8	+	18	3733	c.3653C>A	c.(3652-3654)tCt>tAt	p.S1218Y	DMXL1_ENST00000539542.1_Missense_Mutation_p.S1218Y	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1218								p.S1218Y(1)|p.S1218C(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TTTCCTGTTTCTTTATCGTGG	0.443																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	5											137	138	138					5																	118485175		2202	4300	6502	118513074	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3653C>A	5.37:g.118485175C>A	ENSP00000309690:p.Ser1218Tyr		118513074		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252414	0.59212	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.01584	4.75;4.75	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.10165	0.0249	M	0.76574	2.34	0.58432	D	0.999998	D;D	0.71674	0.998;0.985	D;P	0.69824	0.966;0.901	T	0.21314	-1.0249	10	0.26408	T	0.33	-17.336	19.5134	0.95153	0.0:1.0:0.0:0.0	.	1218;1218	F5H269;Q9Y485	.;DMXL1_HUMAN	Y	1218	ENSP00000309690:S1218Y;ENSP00000439479:S1218Y	ENSP00000309690:S1218Y	S	+	2	0	DMXL1	118513074	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.696000	0.92011	0.655000	0.94253	TCT		0.443	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118485175	C	A	118485175	3	1	61	1	0	0	0	0	1	0	0	0	4605	913	32	2	3723	2	DMXL1	5	118485175	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15518	118485175	62430085	4037	12022										
DMXL1	1657	broad.mit.edu	37	chr5	118485283	118485283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaacctgttataacagattCgtacagtgggagcactccat	9	9	0	2	rs533249807		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:118485283C>T	ENST00000311085.8	+	18	3841	c.3761C>T	c.(3760-3762)tCg>tTg	p.S1254L	DMXL1_ENST00000539542.1_Missense_Mutation_p.S1254L	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1254								p.S1254L(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		ATAACAGATTCGTACAGTGGG	0.433													C|||	1	0.000199681	0	0	5008	,	,		21070	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5											73	68	70					5																	118485283		2202	4300	6502	118513182	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3761C>T	5.37:g.118485283C>T	ENSP00000309690:p.Ser1254Leu		118513182		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674297	0.67928	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.10288	2.9;2.89	5.39	5.39	0.77823	.	0.206543	0.42821	D	0.000647	T	0.12220	0.0297	L	0.57536	1.79	0.80722	D	1	P;P	0.39094	0.659;0.573	B;B	0.22753	0.041;0.038	T	0.05099	-1.0906	10	0.46703	T	0.11	-11.5299	19.5134	0.95153	0.0:1.0:0.0:0.0	.	1254;1254	F5H269;Q9Y485	.;DMXL1_HUMAN	L	1254	ENSP00000309690:S1254L;ENSP00000439479:S1254L	ENSP00000309690:S1254L	S	+	2	0	DMXL1	118513182	0.998000	0.40836	0.985000	0.45067	0.978000	0.69477	3.865000	0.56033	2.696000	0.92011	0.655000	0.94253	TCG		0.433	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118485283	C	T	118485283	3	4	61	1	0	0	0	0	1	0	0	0	4605	893	31	1	3831	1	DMXL1	5	118485283	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108	118485283	62429977	4038	12023										
PRR16	51334	broad.mit.edu	37	chr5	120021842	120021842	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctatcctcacggtcctgaGaaagccaaaccctccaccac	6	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:120021842G>A	ENST00000407149.2	+	2	562	c.353G>A	c.(352-354)aGa>aAa	p.R118K	PRR16_ENST00000446965.1_Missense_Mutation_p.R48K|PRR16_ENST00000379551.2_Missense_Mutation_p.R95K|PRR16_ENST00000505123.1_Missense_Mutation_p.R48K			Q569H4	LARGN_HUMAN	proline rich 16	118	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)			p.R95K(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		ACGGTCCTGAGAAAGCCAAAC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											139	121	127					5																	120021842		2203	4300	6503	120049741	SO:0001583	missense	51334			AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.353G>A	5.37:g.120021842G>A	ENSP00000385118:p.Arg118Lys		120049741	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	37		.	.	.	.	.	.	.	.	.	.	G	10.22	1.289416	0.23478	.	.	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	5.71	5.71	0.89125	.	0.051119	0.85682	D	0.000000	T	0.39009	0.1062	L	0.38175	1.15	0.34945	D	0.750661	B;B	0.27625	0.183;0.183	B;B	0.32465	0.017;0.146	T	0.41466	-0.9507	9	.	.	.	-0.1802	18.6986	0.91611	0.0:0.0:1.0:0.0	.	118;95	Q569H4;Q569H4-3	PRR16_HUMAN;.	K	118;95;48;48;48	ENSP00000385118:R118K;ENSP00000368869:R95K;ENSP00000421256:R48K;ENSP00000423446:R48K;ENSP00000405491:R48K	.	R	+	2	0	PRR16	120049741	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.307000	0.78920	2.709000	0.92574	0.644000	0.83932	AGA		0.527	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		A	120021842	G	A	120021842	3	1	61	1	0	0	0	0	1	0	0	0	12623	942	33	3	290	3	PRR16	5	120021842	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1536559	120021842	60893418	4039	12024										
SRFBP1	153443	broad.mit.edu	37	chr5	121355985	121355985	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccaatacataattcaaaGgaaaaaatagcaaagatgga	6	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121355985G>T	ENST00000339397.4	+	6	627	c.555G>T	c.(553-555)aaG>aaT	p.K185N		NM_152546.2	NP_689759.2			serum response factor binding protein 1									p.K185N(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		ATAATTCAAAGGAAAAAATAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											114	104	107					5																	121355985		1859	4088	5947	121383884	SO:0001583	missense	153443			AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.555G>T	5.37:g.121355985G>T	ENSP00000341324:p.Lys185Asn		121383884		Missense_Mutation	SNP	ENST00000339397.4	37	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.250268	0.22880	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.45	1.84	0.25277	.	0.421060	0.26492	N	0.024070	T	0.42268	0.1195	M	0.63428	1.95	0.22873	N	0.998623	D	0.53619	0.961	P	0.47206	0.541	T	0.29731	-1.0002	9	0.51188	T	0.08	-13.5293	8.6863	0.34240	0.6903:0.0:0.3097:0.0	.	185	Q8NEF9	SRFB1_HUMAN	N	185	.	ENSP00000341324:K185N	K	+	3	2	SRFBP1	121383884	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	-0.032000	0.12266	0.874000	0.35823	0.467000	0.42956	AAG		0.368	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		T	121355985	G	T	121355985	3	4	61	1	0	0	0	0	1	0	0	0	15183	991	35	2	577	2	SRFBP1	5	121355985	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1334143	121355985	59559275	4040	12025										
SRFBP1	153443	broad.mit.edu	37	chr5	121356488	121356488	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttatctggatctaaaaGctctagaaggtaagattctt	7	7	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121356488G>T	ENST00000339397.4	+	6	1130	c.1058G>T	c.(1057-1059)aGc>aTc	p.S353I	SRFBP1_ENST00000504881.1_3'UTR	NM_152546.2	NP_689759.2			serum response factor binding protein 1									p.S353I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		GGATCTAAAAGCTCTAGAAGG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	38	39					5																	121356488		1801	4080	5881	121384387	SO:0001583	missense	153443			AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.1058G>T	5.37:g.121356488G>T	ENSP00000341324:p.Ser353Ile		121384387		Missense_Mutation	SNP	ENST00000339397.4	37	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217511	0.39201	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.35	2.58	0.30949	.	0.930944	0.09364	N	0.812366	T	0.34629	0.0904	L	0.51422	1.61	0.09310	N	1	B	0.17268	0.021	B	0.15870	0.014	T	0.34354	-0.9832	9	0.51188	T	0.08	-0.012	3.8577	0.08982	0.3036:0.0:0.5308:0.1655	.	353	Q8NEF9	SRFB1_HUMAN	I	353	.	ENSP00000341324:S353I	S	+	2	0	SRFBP1	121384387	0.844000	0.29557	0.886000	0.34754	0.722000	0.41435	1.585000	0.36600	0.331000	0.23511	-0.253000	0.11424	AGC		0.313	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		T	121356488	G	T	121356488	3	4	61	1	0	0	0	0	1	0	0	0	15183	971	34	2	1080	2	SRFBP1	5	121356488	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	503	121356488	59558772	4041	12026										
SRFBP1	153443	broad.mit.edu	37	chr5	121362759	121362759	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgggaagcaagcagaaggCgaaaagaacagcaatctaat	11	7	1	2	rs562977263		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121362759C>T	ENST00000339397.4	+	8	1300	c.1228C>T	c.(1228-1230)Cga>Tga	p.R410*	SRFBP1_ENST00000504881.1_Intron	NM_152546.2	NP_689759.2			serum response factor binding protein 1									p.R410*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AAGCAGAAGGCGAAAAGAACA	0.363													C|||	1	0.000199681	0	0	5008	,	,		15628	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	5											47	45	46					5																	121362759		1835	4090	5925	121390658	SO:0001587	stop_gained	153443			AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.1228C>T	5.37:g.121362759C>T	ENSP00000341324:p.Arg410*		121390658		Nonsense_Mutation	SNP	ENST00000339397.4	37	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	C	37	6.268854	0.97426	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.76	3.98	0.46160	.	0.060687	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.7732	10.9237	0.47180	0.1307:0.8022:0.0:0.0671	.	.	.	.	X	410	.	ENSP00000341324:R410X	R	+	1	2	SRFBP1	121390658	1.000000	0.71417	0.979000	0.43373	0.945000	0.59286	3.375000	0.52410	0.785000	0.33685	0.655000	0.94253	CGA		0.363	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		T	121362759	C	T	121362759	4	4	61	1	0	0	0	0	0	1	0	0	15183	760	27	1	1258	1	SRFBP1	5	121362759	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6271	121362759	59552501	4042	12027										
ZNF474	133923	broad.mit.edu	37	chr5	121487810	121487810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactcctattctagcctttCcccagaaacagagagtgtta	7	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121487810C>T	ENST00000296600.4	+	2	508	c.125C>T	c.(124-126)tCc>tTc	p.S42F	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	42							metal ion binding (GO:0046872)	p.S42F(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		TCTAGCCTTTCCCCAGAAACA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	102	99					5																	121487810		2203	4300	6503	121515709	SO:0001583	missense	133923			AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.125C>T	5.37:g.121487810C>T	ENSP00000296600:p.Ser42Phe		121515709	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	3.023	-0.201249	0.06219	.	.	ENSG00000164185	ENST00000296600;ENST00000504912	T	0.48836	0.8	5.58	-4.06	0.03986	.	3.371230	0.01961	U	0.043330	T	0.30541	0.0768	N	0.19112	0.55	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.14172	-1.0482	10	0.29301	T	0.29	4.1434	7.1515	0.25614	0.0:0.4522:0.3502:0.1976	.	42	Q6S9Z5	ZN474_HUMAN	F	42	ENSP00000296600:S42F	ENSP00000296600:S42F	S	+	2	0	ZNF474	121515709	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.680000	0.05197	-0.586000	0.05898	-1.004000	0.02495	TCC		0.388	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121487810	C	T	121487810	3	4	61	1	0	0	0	0	1	0	0	0	17971	855	30	3	127	3	ZNF474	5	121487810	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125051	121487810	59427450	4043	12028										
SNCAIP	9627	broad.mit.edu	37	chr5	121767749	121767749	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaaggattttccaagccTtattcattacgcaggttgct	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121767749T>G	ENST00000261368.8	+	6	1530	c.1268T>G	c.(1267-1269)cTt>cGt	p.L423R	SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000261367.7_Missense_Mutation_p.L470R|SNCAIP_ENST00000379533.2_Missense_Mutation_p.L470R|SNCAIP_ENST00000503116.2_Missense_Mutation_p.L470R|SNCAIP_ENST00000379536.2_Missense_Mutation_p.L363R|SNCAIP_ENST00000542191.1_5'UTR|SNCAIP_ENST00000379538.3_Missense_Mutation_p.L57R|SNCAIP_ENST00000414317.2_Intron	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	423					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.L470R(2)|p.L423R(1)		NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TTTCCAAGCCTTATTCATTAC	0.388																																																3	Substitution - Missense(3)	large_intestine(3)	5											113	101	105					5																	121767749		2203	4300	6503	121795648	SO:0001583	missense	9627			AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1268T>G	5.37:g.121767749T>G	ENSP00000261368:p.Leu423Arg		121795648	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.261668	0.80358	.	.	ENSG00000064692	ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000447854;ENST00000503116	T;T;T;T;T;T;T	0.65364	-0.15;0.57;0.57;-0.15;-0.15;0.57;0.57	4.84	4.84	0.62591	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.73102	0.3544	L	0.46157	1.445	0.80722	D	1	D;D;D;D;P;D;D;D	0.89917	0.997;0.999;0.998;1.0;0.867;1.0;0.999;0.999	D;D;D;D;B;D;D;D	0.91635	0.993;0.996;0.994;0.999;0.317;0.999;0.996;0.998	T	0.74976	-0.3480	10	0.54805	T	0.06	-13.0093	14.7375	0.69427	0.0:0.0:0.0:1.0	.	363;51;470;363;57;57;470;423	D6R9G8;Q9NVG1;Q9Y6H5-6;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	R	363;423;470;363;57;470;63;470	ENSP00000422106:L363R;ENSP00000261368:L423R;ENSP00000368848:L470R;ENSP00000368851:L363R;ENSP00000368854:L57R;ENSP00000261367:L470R;ENSP00000423199:L470R	ENSP00000261367:L470R	L	+	2	0	SNCAIP	121795648	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	7.434000	0.80377	1.948000	0.56530	0.528000	0.53228	CTT		0.388	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			G	121767749	T	G	121767749	3	3	61	1	0	0	0	0	1	0	0	0	14878	1609	56	4	1286	4	SNCAIP	5	121767749	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	279939	121767749	59147511	4044	12029										
SNCAIP	9627	broad.mit.edu	37	chr5	121776414	121776414	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcaacagtgccgttcacGtagcctcacagcatggctac	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:121776414G>A	ENST00000261368.8	+	7	1649	c.1387G>A	c.(1387-1389)Gta>Ata	p.V463I	SNCAIP_ENST00000504884.2_3'UTR|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000261367.7_Missense_Mutation_p.V510I|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379533.2_Missense_Mutation_p.V510I|SNCAIP_ENST00000503116.2_Missense_Mutation_p.V510I|SNCAIP_ENST00000379536.2_Missense_Mutation_p.V403I|SNCAIP_ENST00000542191.1_Missense_Mutation_p.V21I|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000379538.3_Missense_Mutation_p.V97I|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000414317.2_Missense_Mutation_p.V65I	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	463					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.V510I(2)|p.V463I(1)		NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TGCCGTTCACGTAGCCTCACA	0.418																																																3	Substitution - Missense(3)	large_intestine(3)	5											145	136	139					5																	121776414		2203	4300	6503	121804313	SO:0001583	missense	9627			AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1387G>A	5.37:g.121776414G>A	ENSP00000261368:p.Val463Ile		121804313	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	G	6.738	0.504981	0.12822	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854;ENST00000503116	T;T;T;T;T;T;T;T;T	0.64803	-0.02;-0.12;-0.03;-0.03;-0.12;-0.12;-0.03;-0.03;0.12	5.23	4.33	0.51752	Ankyrin repeat-containing domain (4);	0.199013	0.44285	N	0.000475	T	0.41050	0.1142	N	0.16708	0.43	0.36731	D	0.881722	B;B;B;B;B;B;B;B;B	0.21071	0.002;0.004;0.051;0.009;0.007;0.004;0.025;0.001;0.031	B;B;B;B;B;B;B;B;B	0.17433	0.002;0.002;0.015;0.008;0.006;0.002;0.006;0.001;0.018	T	0.38156	-0.9674	10	0.25106	T	0.35	-14.5961	7.2356	0.26067	0.3006:0.0:0.6994:0.0	.	403;91;65;510;403;97;97;510;463	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-6;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;.;SNCAP_HUMAN	I	21;403;463;510;403;97;510;65;103;510	ENSP00000441681:V21I;ENSP00000422106:V403I;ENSP00000261368:V463I;ENSP00000368848:V510I;ENSP00000368851:V403I;ENSP00000368854:V97I;ENSP00000261367:V510I;ENSP00000394392:V65I;ENSP00000423199:V510I	ENSP00000261367:V510I	V	+	1	0	SNCAIP	121804313	0.914000	0.31030	0.113000	0.21522	0.163000	0.22366	1.397000	0.34543	1.339000	0.45563	0.655000	0.94253	GTA		0.418	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121776414	G	A	121776414	3	1	61	1	0	0	0	0	1	0	0	0	14878	1145	40	1	1409	1	SNCAIP	5	121776414	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8665	121776414	59138846	4045	12030										
SNX2	6643	broad.mit.edu	37	chr5	122163289	122163289	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagaacgagtgaaggattTtaaaaccgttatcatcaagt	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:122163289T>G	ENST00000379516.2	+	14	1565	c.1457T>G	c.(1456-1458)tTt>tGt	p.F486C	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Missense_Mutation_p.F369C	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	486					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.F486C(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		GTGAAGGATTTTAAAACCGTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	87	86					5																	122163289		2203	4300	6503	122191188	SO:0001583	missense	6643			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1457T>G	5.37:g.122163289T>G	ENSP00000368831:p.Phe486Cys		122191188	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Missense_Mutation	SNP	ENST00000379516.2	37	CCDS34217.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.460563	0.84317	.	.	ENSG00000205302	ENST00000379516;ENST00000514949	T;T	0.43294	0.95;0.95	5.59	5.59	0.84812	Vps5 C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	M	0.90369	3.11	0.80722	D	1	P	0.40660	0.726	P	0.49665	0.618	T	0.72027	-0.4414	10	0.87932	D	0	-0.0691	16.0576	0.80816	0.0:0.0:0.0:1.0	.	486	O60749	SNX2_HUMAN	C	486;369	ENSP00000368831:F486C;ENSP00000421663:F369C	ENSP00000368831:F486C	F	+	2	0	SNX2	122191188	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.972000	0.88022	2.245000	0.73994	0.454000	0.30748	TTT		0.308	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		G	122163289	T	G	122163289	3	3	61	1	0	0	0	0	1	0	0	0	14928	1841	64	4	1511	4	SNX2	5	122163289	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	386875	122163289	58751971	4046	12031										
CEP120	153241	broad.mit.edu	37	chr5	122714086	122714086	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccaagtcaattagagtttTttgaagttttccttctagaa	6	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:122714086T>A	ENST00000306467.5	-	15	2444	c.2140A>T	c.(2140-2142)Aaa>Taa	p.K714*	CEP120_ENST00000306481.6_Nonsense_Mutation_p.K688*|CEP120_ENST00000328236.5_Nonsense_Mutation_p.K714*			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	714					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.K714*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						ATTAGAGTTTTTTGAAGTTTT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											99	105	103					5																	122714086		2203	4300	6503	122741985	SO:0001587	stop_gained	153241			AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"coiled-coil domain containing 100"	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.2140A>T	5.37:g.122714086T>A	ENSP00000303058:p.Lys714*		122741985	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Nonsense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	T	40	8.101309	0.98654	.	.	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	.	.	.	5.8	4.62	0.57501	.	0.094329	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.4962	13.2867	0.60247	0.0:0.0:0.1319:0.8681	.	.	.	.	X	714;714;688;688	.	ENSP00000303058:K714X	K	-	1	0	CEP120	122741985	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	3.703000	0.54808	0.990000	0.38787	0.460000	0.39030	AAA		0.348	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		A	122714086	T	A	122714086	4	1	61	1	0	0	0	0	0	1	0	0	3252	1850	64	5	844	5	CEP120	5	122714086	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	550797	122714086	58201174	4047	12032										
CSNK1G3	1456	broad.mit.edu	37	chr5	122911482	122911482	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagagatgtaaaacctgaGaacttcttaataggacgacc	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:122911482G>T	ENST00000361991.2	+	5	528	c.498G>T	c.(496-498)gaG>gaT	p.E166D	CSNK1G3_ENST00000521364.1_Missense_Mutation_p.E166D|CSNK1G3_ENST00000510842.2_Missense_Mutation_p.E166D|CSNK1G3_ENST00000395411.1_Missense_Mutation_p.E166D|CSNK1G3_ENST00000345990.4_Missense_Mutation_p.E166D|CSNK1G3_ENST00000395412.1_Missense_Mutation_p.E166D|CSNK1G3_ENST00000511130.2_Missense_Mutation_p.E53D|CSNK1G3_ENST00000512718.3_Missense_Mutation_p.E91D|CSNK1G3_ENST00000360683.2_Missense_Mutation_p.E166D			Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3	166	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E166D(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1)	15		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		TAAAACCTGAGAACTTCTTAA	0.343																																					Pancreas(187;2868 2964 4353 6297)											1	Substitution - Missense(1)	large_intestine(1)	5											70	71	70					5																	122911482		2203	4300	6503	122939381	SO:0001583	missense	1456			AF049090	CCDS4135.1, CCDS34218.1, CCDS43355.1, CCDS59491.1, CCDS59492.1, CCDS59493.1	5q23	2013-01-17			ENSG00000151292	ENSG00000151292			2456	protein-coding gene	gene with protein product		604253				9925945	Standard	NM_004384		Approved		uc031skv.1	Q9Y6M4	OTTHUMG00000128923	ENST00000361991.2:c.498G>T	5.37:g.122911482G>T	ENSP00000354942:p.Glu166Asp		122939381	A8K040|B4DSH2|B7Z9Q4|E7EVD0|Q86WZ7|Q9Y6M3	Missense_Mutation	SNP	ENST00000361991.2	37	CCDS4135.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.587757	0.28268	.	.	ENSG00000151292	ENST00000395412;ENST00000395411;ENST00000345990;ENST00000511130;ENST00000512718;ENST00000521364;ENST00000510842;ENST00000361991;ENST00000360683	T;T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	4.85	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.15696	0.0378	N	0.04636	-0.2	0.53005	D	0.999961	D;P;D;B;D;P	0.61697	0.99;0.868;0.99;0.351;0.97;0.6	P;P;P;B;P;B	0.62649	0.905;0.732;0.905;0.237;0.865;0.407	T	0.17107	-1.0380	10	0.02654	T	1	.	9.4185	0.38536	0.1636:0.0:0.8364:0.0	.	91;166;53;166;166;166	B4DSH2;A8K040;E7EVD0;Q9Y6M4-3;Q9Y6M4;Q9Y6M4-2	.;.;.;.;KC1G3_HUMAN;.	D	166;166;166;53;91;166;166;166;166	ENSP00000378807:E166D;ENSP00000378806:E166D;ENSP00000334735:E166D;ENSP00000421385:E53D;ENSP00000421998:E91D;ENSP00000429412:E166D;ENSP00000423838:E166D;ENSP00000354942:E166D;ENSP00000353904:E166D	ENSP00000334735:E166D	E	+	3	2	CSNK1G3	122939381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.885000	0.28227	2.620000	0.88729	0.650000	0.86243	GAG		0.343	CSNK1G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250900.1	NM_004384		T	122911482	G	T	122911482	3	4	61	1	0	0	0	0	1	0	0	0	3962	933	33	2	516	2	CSNK1G3	5	122911482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197396	122911482	58003778	4048	12033										
ZNF608	57507	broad.mit.edu	37	chr5	124036833	124036833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacccacagaacgagtccGaaccaaaagctgttcaaccg	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:124036833G>A	ENST00000306315.5	-	2	1471	c.1036C>T	c.(1036-1038)Cgg>Tgg	p.R346W	ZNF608_ENST00000504926.1_5'UTR	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	346							metal ion binding (GO:0046872)	p.R346W(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		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)		GAACGAGTCCGAACCAAAAGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											145	132	136					5																	124036833		2203	4300	6503	124064732	SO:0001583	missense	57507			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1036C>T	5.37:g.124036833G>A	ENSP00000307746:p.Arg346Trp		124064732	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526544	0.85600	.	.	ENSG00000168916	ENST00000306315;ENST00000509799;ENST00000513986	T	0.53423	0.62	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000001	T	0.61223	0.2330	L	0.29908	0.895	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.62599	-0.6820	10	0.87932	D	0	-20.0531	20.3539	0.98825	0.0:0.0:1.0:0.0	.	346	Q9ULD9	ZN608_HUMAN	W	346	ENSP00000307746:R346W	ENSP00000307746:R346W	R	-	1	2	ZNF608	124064732	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.397000	0.59690	2.826000	0.97356	0.655000	0.94253	CGG		0.512	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	124036833	G	A	124036833	3	1	61	1	0	0	0	0	1	0	0	0	18073	1057	37	1	3534	1	ZNF608	5	124036833	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1125351	124036833	56878427	4049	12034										
ALDH7A1	501	broad.mit.edu	37	chr5	125882022	125882022	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccttttcttaccaagtaGaccttctcatgtactgtttc	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:125882022G>A	ENST00000409134.3	-	17	1778	c.1559C>T	c.(1558-1560)tCt>tTt	p.S520F	ALDH7A1_ENST00000447989.2_Missense_Mutation_p.S483F|ALDH7A1_ENST00000553117.1_Missense_Mutation_p.S456F	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	520					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)	p.S492F(1)		endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		TTACCAAGTAGACCTTCTCAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	5											141	133	136					5																	125882022		2203	4300	6503	125909921	SO:0001583	missense	501			S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"Aldehyde dehydrogenases"	877	protein-coding gene	gene with protein product	"antiquitin 1", "26g turgor protein homolog", "alpha-aminoadipic semialdehyde dehydrogenase", "alpha-AASA dehydrogenase", "delta1-piperideine-6-carboxylate dehydrogenease", "P6c dehydrogenase"	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.1559C>T	5.37:g.125882022G>A	ENSP00000387123:p.Ser520Phe		125909921	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Missense_Mutation	SNP	ENST00000409134.3	37	CCDS4137.2	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137669	0.77775	.	.	ENSG00000164904	ENST00000409134;ENST00000553117;ENST00000447989;ENST00000437170	D;D;D	0.90788	-2.73;-2.73;-2.73	4.12	4.12	0.48240	Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.95850	0.8649	M	0.88775	2.98	0.58432	D	0.999992	D;D	0.89917	0.999;1.0	D;D	0.91635	0.982;0.999	D	0.96599	0.9443	10	0.66056	D	0.02	.	16.4811	0.84158	0.0:0.0:1.0:0.0	.	483;520	E7EPT3;P49419	.;AL7A1_HUMAN	F	520;456;483;328	ENSP00000387123:S520F;ENSP00000448593:S456F;ENSP00000414132:S483F	ENSP00000387123:S520F	S	-	2	0	ALDH7A1	125909921	1.000000	0.71417	0.926000	0.36857	0.893000	0.52053	9.123000	0.94387	2.285000	0.76669	0.313000	0.20887	TCT		0.438	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		A	125882022	G	A	125882022	3	1	61	1	0	0	0	0	1	0	0	0	504	942	33	3	68	3	ALDH7A1	5	125882022	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1845189	125882022	55033238	4050	12035										
LMNB1	4001	broad.mit.edu	37	chr5	126140573	126140574	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctactgcacttggtgacINSaaaaaaagtttagagggaga							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:126140573_126140574insA	ENST00000261366.5	+	2	826_827	c.465_466insA	c.(466-468)aaafs	p.K156fs	LMNB1_ENST00000460265.1_3'UTR|LMNB1_ENST00000395354.1_Frame_Shift_Ins_p.K156fs	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	156	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)	p.S158fs*30(1)|p.D155E(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		CACTTGGTGACAAAAAAAGTTT	0.446																																																2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(2)	5																																								126168473	SO:0001589	frameshift_variant	4001			L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"Intermediate filaments type V, lamins"	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.472dupA	5.37:g.126140580_126140580dupA	ENSP00000261366:p.Lys156fs		126168472	B2R6J6|Q3SYN7|Q96EI6	Frame_Shift_Ins	INS	ENST00000261366.5	37	CCDS4140.1																																																																																				0.446	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573		A	126140574	-	A	126140573	7	5	61	1	0	1	1	0	0	0	0	0	8873	477	17	0	471	0	LMNB1	5	126140573	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	258551	126140573	54774687	4051	12036										
LMNB1	4001	broad.mit.edu	37	chr5	126154684	126154684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaaagacaactctcgtcGcatgctgacagacaaagaga	9	9	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:126154684G>A	ENST00000261366.5	+	6	1371	c.1010G>A	c.(1009-1011)cGc>cAc	p.R337H	LMNB1_ENST00000460265.1_3'UTR|LMNB1_ENST00000395354.1_Missense_Mutation_p.R337H	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	337	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)	p.R337H(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		AACTCTCGTCGCATGCTGACA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											114	113	113					5																	126154684		2203	4300	6503	126182583	SO:0001583	missense	4001			L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"Intermediate filaments type V, lamins"	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.1010G>A	5.37:g.126154684G>A	ENSP00000261366:p.Arg337His		126182583	B2R6J6|Q3SYN7|Q96EI6	Missense_Mutation	SNP	ENST00000261366.5	37	CCDS4140.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181669	0.57800	.	.	ENSG00000113368	ENST00000261366;ENST00000395354	D;D	0.89123	-2.47;-2.47	5.74	2.85	0.33270	Filament (1);	0.296362	0.35555	N	0.003139	D	0.84401	0.5464	M	0.67397	2.05	0.49130	D	0.999759	B	0.30482	0.281	B	0.29942	0.109	T	0.82110	-0.0619	10	0.52906	T	0.07	.	4.4832	0.11776	0.2698:0.0:0.5645:0.1657	.	337	P20700	LMNB1_HUMAN	H	337	ENSP00000261366:R337H;ENSP00000378761:R337H	ENSP00000261366:R337H	R	+	2	0	LMNB1	126182583	0.860000	0.29831	1.000000	0.80357	0.986000	0.74619	1.506000	0.35747	1.576000	0.49790	0.563000	0.77884	CGC		0.403	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573		A	126154684	G	A	126154684	3	1	61	1	0	0	0	0	1	0	0	0	8873	1087	38	1	1032	1	LMNB1	5	126154684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14111	126154684	54760576	4052	12037										
SLC12A2	6558	broad.mit.edu	37	chr5	127448600	127448600	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagtaaaggagtcgtgaAgtttggctggatcaagggtg	16	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127448600A>C	ENST00000262461.2	+	2	1040	c.851A>C	c.(850-852)aAg>aCg	p.K284T	SLC12A2_ENST00000343225.4_Missense_Mutation_p.K284T	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	284					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)	p.K284T(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	GGAGTCGTGAAGTTTGGCTGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	122	123					5																	127448600		2203	4300	6503	127476499	SO:0001583	missense	6558				CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.851A>C	5.37:g.127448600A>C	ENSP00000262461:p.Lys284Thr		127476499	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	37	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.933186	0.73442	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.89617	-2.52;-2.54	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.95893	0.8663	H	0.95224	3.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.987	D	0.96969	0.9707	10	0.87932	D	0	.	13.7851	0.63105	1.0:0.0:0.0:0.0	.	284;284	P55011-3;P55011	.;S12A2_HUMAN	T	284	ENSP00000262461:K284T;ENSP00000340878:K284T	ENSP00000262461:K284T	K	+	2	0	SLC12A2	127476499	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.543000	0.73874	2.137000	0.66172	0.455000	0.32223	AAG		0.388	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		C	127448600	A	C	127448600	3	2	61	1	0	0	0	0	1	0	0	0	14420	72	3	4	857	4	SLC12A2	5	127448600	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1293916	127448600	53466660	4053	12038										
SLC12A2	6558	broad.mit.edu	37	chr5	127469897	127469897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgaaatcaatgatatccGaattattggagccattacag	8	6	1	3	rs537215758		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127469897G>A	ENST00000262461.2	+	6	1418	c.1229G>A	c.(1228-1230)cGa>cAa	p.R410Q	SLC12A2_ENST00000343225.4_Missense_Mutation_p.R410Q	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	410					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)	p.R410Q(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	AATGATATCCGAATTATTGGA	0.318													G|||	1	0.000199681	0	0.0014	5008	,	,		17901	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											146	158	154					5																	127469897		2203	4300	6503	127497796	SO:0001583	missense	6558				CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1229G>A	5.37:g.127469897G>A	ENSP00000262461:p.Arg410Gln		127497796	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	37	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	G	35	5.516799	0.96402	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.86769	-2.17;-2.17	4.94	4.94	0.65067	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.94185	0.8134	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94908	0.8062	10	0.87932	D	0	.	18.3647	0.90386	0.0:0.0:1.0:0.0	.	410;410	P55011-3;P55011	.;S12A2_HUMAN	Q	410	ENSP00000262461:R410Q;ENSP00000340878:R410Q	ENSP00000262461:R410Q	R	+	2	0	SLC12A2	127497796	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.232000	0.95325	2.591000	0.87537	0.655000	0.94253	CGA		0.318	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		A	127469897	G	A	127469897	3	1	61	1	0	0	0	0	1	0	0	0	14420	1058	37	1	1251	1	SLC12A2	5	127469897	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21297	127469897	53445363	4054	12039										
FBN2	2201	broad.mit.edu	37	chr5	127636561	127636561	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggacagatgcatctgaaGgatccctccaaattctgaca	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127636561G>T	ENST00000508053.1	-	54	7088	c.6114C>A	c.(6112-6114)tcC>tcA	p.S2038S	FBN2_ENST00000262464.4_Silent_p.S2038S			P35556	FBN2_HUMAN	fibrillin 2	2038	EGF-like 34; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.S2038S(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGCATCTGAAGGATCCCTCCA	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	5											93	91	92					5																	127636561		2203	4300	6503	127664460	SO:0001819	synonymous_variant	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.6114C>A	5.37:g.127636561G>T			127664460	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																				0.418	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127636561	G	T	127636561	2	4	61	1	0	0	0	0	0	0	0	1	5722	987	35	2		2	FBN2	5	127636561	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166664	127636561	53278699	4055	12040										
FBN2	2201	broad.mit.edu	37	chr5	127640772	127640772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttctaaacattcattgcGatctaaaacagaaaaaaata	3	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127640772G>A	ENST00000508053.1	-	51	6651	c.5677C>T	c.(5677-5679)Cgc>Tgc	p.R1893C	FBN2_ENST00000262464.4_Missense_Mutation_p.R1893C			P35556	FBN2_HUMAN	fibrillin 2	1893	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R1893C(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CATTCATTGCGATCTAAAACA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	5											64	54	58					5																	127640772		2203	4300	6503	127668671	SO:0001583	missense	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.5677C>T	5.37:g.127640772G>A	ENSP00000424571:p.Arg1893Cys		127668671	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129563	0.77549	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.91945	-2.94;-2.94	5.03	4.14	0.48551	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.56097	D	0.000032	D	0.94460	0.8217	M	0.64997	1.995	0.58432	D	0.999999	D	0.89917	1.0	D	0.68765	0.96	D	0.93877	0.7167	10	0.49607	T	0.09	.	14.0176	0.64533	0.0744:0.0:0.9256:0.0	.	1893	P35556	FBN2_HUMAN	C	1893	ENSP00000262464:R1893C;ENSP00000424571:R1893C	ENSP00000262464:R1893C	R	-	1	0	FBN2	127668671	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.601000	0.98297	2.619000	0.88677	0.467000	0.42956	CGC		0.323	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127640772	G	A	127640772	3	1	61	1	0	0	0	0	1	0	0	0	5722	1058	37	1	3145	1	FBN2	5	127640772	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4211	127640772	53274488	4056	12041										
FBN2	2201	broad.mit.edu	37	chr5	127668692	127668692	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacatgaggcatgcatgtcGcagttatgagcaccaatttc	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127668692G>A	ENST00000508053.1	-	38	5108	c.4134C>T	c.(4132-4134)tgC>tgT	p.C1378C	FBN2_ENST00000262464.4_Silent_p.C1378C|FBN2_ENST00000508989.1_Silent_p.C1345C|FBN2_ENST00000507835.1_Silent_p.C228C			P35556	FBN2_HUMAN	fibrillin 2	1378	EGF-like 22; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.C1378C(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CATGCATGTCGCAGTTATGAG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	5											156	140	146					5																	127668692		2203	4300	6503	127696591	SO:0001819	synonymous_variant	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4134C>T	5.37:g.127668692G>A			127696591	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																				0.383	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127668692	G	A	127668692	2	1	61	1	0	0	0	0	0	0	0	1	5722	1079	38	1		1	FBN2	5	127668692	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27920	127668692	53246568	4057	12042										
FBN2	2201	broad.mit.edu	37	chr5	127674667	127674667	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagccactttcatagccttCgaagcactcgcactcaaagc	7	14	2	0	rs200060005		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127674667C>T	ENST00000508053.1	-	32	4404	c.3430G>A	c.(3430-3432)Gaa>Aaa	p.E1144K	FBN2_ENST00000262464.4_Missense_Mutation_p.E1144K|FBN2_ENST00000508989.1_Missense_Mutation_p.E1111K|FBN2_ENST00000507835.1_5'UTR			P35556	FBN2_HUMAN	fibrillin 2	1144	EGF-like 16; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.E1144K(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCATAGCCTTCGAAGCACTCG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	85	92					5																	127674667		2203	4300	6503	127702566	SO:0001583	missense	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3430G>A	5.37:g.127674667C>T	ENSP00000424571:p.Glu1144Lys		127702566	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818681	0.71028	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.92348	-3.02;-3.02;-3.02	5.13	4.25	0.50352	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.496860	0.21340	N	0.076149	D	0.87354	0.6156	L	0.28649	0.875	0.54753	D	0.999984	P;P	0.44478	0.836;0.799	B;B	0.40782	0.34;0.298	D	0.85726	0.1328	10	0.27785	T	0.31	.	16.2378	0.82389	0.0:0.8672:0.1328:0.0	.	1111;1144	D6RJI3;P35556	.;FBN2_HUMAN	K	1144;1144;1111	ENSP00000262464:E1144K;ENSP00000424571:E1144K;ENSP00000425596:E1111K	ENSP00000262464:E1144K	E	-	1	0	FBN2	127702566	0.989000	0.36119	1.000000	0.80357	0.972000	0.66771	2.420000	0.44679	1.491000	0.48482	0.585000	0.79938	GAA		0.507	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127674667	C	T	127674667	3	4	61	1	0	0	0	0	1	0	0	0	5722	893	31	1	5468	1	FBN2	5	127674667	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5975	127674667	53240593	4058	12043										
FBN2	2201	broad.mit.edu	37	chr5	127855016	127855016	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacacaagcacagcggttgGgtccgatgcaacgtccacca	10	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:127855016G>T	ENST00000508053.1	-	11	1552	c.578C>A	c.(577-579)cCc>cAc	p.P193H	FBN2_ENST00000262464.4_Missense_Mutation_p.P193H|FBN2_ENST00000508989.1_Missense_Mutation_p.P160H			P35556	FBN2_HUMAN	fibrillin 2	193	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.			GPNR -> AQP (in Ref. 1; AAA18950). {ECO:0000305}.	anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.P193H(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACAGCGGTTGGGTCCGATGCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	77	79					5																	127855016		2203	4300	6503	127882915	SO:0001583	missense	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.578C>A	5.37:g.127855016G>T	ENSP00000424571:p.Pro193His		127882915	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739395	0.89573	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989;ENST00000502468	D;D;D;T	0.91631	-2.88;-2.88;-2.88;1.82	5.17	5.17	0.71159	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000001	D	0.96160	0.8748	M	0.79926	2.475	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.997;0.997	D	0.95469	0.8550	10	0.48119	T	0.1	.	18.8636	0.92282	0.0:0.0:1.0:0.0	.	160;193;160;193	P35556-2;E9PHW4;D6RJI3;P35556	.;.;.;FBN2_HUMAN	H	193;193;160;193	ENSP00000262464:P193H;ENSP00000424571:P193H;ENSP00000425596:P160H;ENSP00000424753:P193H	ENSP00000262464:P193H	P	-	2	0	FBN2	127882915	1.000000	0.71417	0.998000	0.56505	0.917000	0.54804	9.529000	0.98049	2.861000	0.98227	0.655000	0.94253	CCC		0.408	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127855016	G	T	127855016	3	4	61	1	0	0	0	0	1	0	0	0	5722	1232	43	2	8404	2	FBN2	5	127855016	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180349	127855016	53060244	4059	12044										
SLC27A6	28965	broad.mit.edu	37	chr5	128302114	128302114	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcagcagagtggcccatgTcttcctgaaccattcctctc	9	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:128302114T>C	ENST00000262462.4	+	1	1294	c.284T>C	c.(283-285)gTc>gCc	p.V95A	SLC27A6_ENST00000506176.1_Missense_Mutation_p.V95A|SLC27A6_ENST00000395266.1_Missense_Mutation_p.V95A			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	95					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.V95A(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		GTGGCCCATGTCTTCCTGAAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	84	87					5																	128302114		2203	4300	6503	128330013	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.284T>C	5.37:g.128302114T>C	ENSP00000262462:p.Val95Ala		128330013	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	T	0.300	-0.974681	0.02215	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.37915	1.17;1.17;1.17	4.31	0.703	0.18116	AMP-dependent synthetase/ligase (1);	0.247257	0.40144	N	0.001175	T	0.16085	0.0387	N	0.11698	0.16	0.20196	N	0.999929	B	0.02656	0.0	B	0.11329	0.006	T	0.28170	-1.0052	10	0.12103	T	0.63	-7.4172	8.1536	0.31156	0.0:0.2466:0.0:0.7534	.	95	Q9Y2P4	S27A6_HUMAN	A	95	ENSP00000262462:V95A;ENSP00000378684:V95A;ENSP00000421024:V95A	ENSP00000262462:V95A	V	+	2	0	SLC27A6	128330013	0.945000	0.32115	0.014000	0.15608	0.877000	0.50540	1.091000	0.30915	0.124000	0.18369	0.528000	0.53228	GTC		0.517	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		C	128302114	T	C	128302114	3	2	61	1	0	0	0	0	1	0	0	0	14567	1667	58	4	286	4	SLC27A6	5	128302114	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	447098	128302114	52613146	4060	12045										
SLC27A6	28965	broad.mit.edu	37	chr5	128368967	128368967	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataatgttaggggaaataAaactttaagatttttatatc	6	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:128368967A>C	ENST00000262462.4	+	10	2862	c.1852A>C	c.(1852-1854)Aaa>Caa	p.K618Q	SLC27A6_ENST00000506176.1_Missense_Mutation_p.K618Q|SLC27A6_ENST00000395266.1_Missense_Mutation_p.K618Q			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	618				K -> N (in Ref. 3; CAG33410). {ECO:0000305}.	long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.K618Q(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		AGGGGAAATAAAACTTTAAGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	5											32	34	33					5																	128368967		2202	4289	6491	128396866	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.1852A>C	5.37:g.128368967A>C	ENSP00000262462:p.Lys618Gln		128396866	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970562	0.53614	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.58060	0.36;0.36;0.36	4.03	4.03	0.46877	.	0.177671	0.48767	D	0.000171	T	0.74427	0.3715	M	0.88241	2.94	0.48341	D	0.999637	D	0.62365	0.991	D	0.68353	0.957	T	0.79883	-0.1615	9	.	.	.	-0.1447	13.6642	0.62384	1.0:0.0:0.0:0.0	.	618	Q9Y2P4	S27A6_HUMAN	Q	618	ENSP00000262462:K618Q;ENSP00000378684:K618Q;ENSP00000421024:K618Q	.	K	+	1	0	SLC27A6	128396866	1.000000	0.71417	0.747000	0.31113	0.275000	0.26752	5.846000	0.69444	2.053000	0.61076	0.477000	0.44152	AAA		0.328	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		C	128368967	A	C	128368967	3	2	61	1	0	0	0	0	1	0	0	0	14567	15	1	4	1890	4	SLC27A6	5	128368967	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	66853	128368967	52546293	4061	12046										
ADAMTS19	171019	broad.mit.edu	37	chr5	128956447	128956447	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagatttggaaagatttCtcaggtatggaggtcactta	12	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:128956447C>T	ENST00000274487.4	+	9	1742	c.1597C>T	c.(1597-1599)Ctc>Ttc	p.L533F	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	533	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L533F(1)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		GGAAAGATTTCTCAGGTATGG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											214	205	208					5																	128956447		2203	4300	6503	128984346	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1597C>T	5.37:g.128956447C>T	ENSP00000274487:p.Leu533Phe		128984346		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563184	0.86335	.	.	ENSG00000145808	ENST00000274487	D	0.89196	-2.48	4.51	4.51	0.55191	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000010	D	0.92880	0.7735	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91831	0.5475	9	.	.	.	.	18.5315	0.90993	0.0:1.0:0.0:0.0	.	533	Q8TE59	ATS19_HUMAN	F	533	ENSP00000274487:L533F	.	L	+	1	0	ADAMTS19	128984346	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.625000	0.74248	2.783000	0.95769	0.655000	0.94253	CTC		0.403	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	128956447	C	T	128956447	3	4	61	1	0	0	0	0	1	0	0	0	264	913	32	3	1631	3	ADAMTS19	5	128956447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	587480	128956447	51958813	4062	12047										
ADAMTS19	171019	broad.mit.edu	37	chr5	128957941	128957941	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatccgcagagtgtcaattCtgtgatggttccctccaagc	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:128957941C>A	ENST00000274487.4	+	10	1797	c.1652C>A	c.(1651-1653)tCt>tAt	p.S551Y	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	551	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S551Y(1)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		AGTGTCAATTCTGTGATGGTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											151	132	138					5																	128957941		2203	4300	6503	128985840	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1652C>A	5.37:g.128957941C>A	ENSP00000274487:p.Ser551Tyr		128985840		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634409	0.87660	.	.	ENSG00000145808	ENST00000274487	T	0.66280	-0.2	4.42	4.42	0.53409	Metallopeptidase, catalytic domain (1);	0.283303	0.30791	N	0.008869	T	0.66336	0.2779	L	0.35723	1.085	0.58432	D	0.999999	D	0.64830	0.994	P	0.56278	0.795	T	0.63712	-0.6575	9	.	.	.	.	18.3455	0.90321	0.0:1.0:0.0:0.0	.	551	Q8TE59	ATS19_HUMAN	Y	551	ENSP00000274487:S551Y	.	S	+	2	0	ADAMTS19	128985840	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.059000	0.49947	2.741000	0.93983	0.585000	0.79938	TCT		0.443	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		A	128957941	C	A	128957941	3	1	61	1	0	0	0	0	1	0	0	0	264	913	32	2	1690	2	ADAMTS19	5	128957941	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1494	128957941	51957319	4063	12048										
ADAMTS19	171019	broad.mit.edu	37	chr5	129030517	129030517	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagccagagccacagattCgaaagtgcaatgagcaacca	9	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:129030517C>T	ENST00000274487.4	+	19	3050	c.2905C>T	c.(2905-2907)Cga>Tga	p.R969*	CTC-575N7.1_ENST00000503616.1_RNA|ADAMTS19_ENST00000509467.1_3'UTR	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	969	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R969*(2)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		GCCACAGATTCGAAAGTGCAA	0.393																																																2	Substitution - Nonsense(2)	large_intestine(1)|skin(1)	5											161	149	153					5																	129030517		2203	4300	6503	129058416	SO:0001587	stop_gained	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2905C>T	5.37:g.129030517C>T	ENSP00000274487:p.Arg969*		129058416		Nonsense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	42	9.563879	0.99205	.	.	ENSG00000145808	ENST00000274487	.	.	.	4.08	4.08	0.47627	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.596	0.88012	0.0:1.0:0.0:0.0	.	.	.	.	X	969	.	.	R	+	1	2	ADAMTS19	129058416	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.216000	0.42871	2.566000	0.86566	0.555000	0.69702	CGA		0.393	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	129030517	C	T	129030517	4	4	61	1	0	0	0	0	0	1	0	0	264	876	31	1	2979	1	ADAMTS19	5	129030517	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72576	129030517	51884743	4064	12049										
CDC42SE2	56990	broad.mit.edu	37	chr5	130726736	130726736	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggaggttatggaggtggAatgcctgccaatgtccagat	15	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:130726736A>C	ENST00000505065.1	+	5	728	c.207A>C	c.(205-207)ggA>ggC	p.G69G	CDC42SE2_ENST00000503291.1_Silent_p.G42G|CDC42SE2_ENST00000395246.1_Silent_p.G69G|CDC42SE2_ENST00000360515.3_Silent_p.G69G			Q9NRR3	C42S2_HUMAN	CDC42 small effector 2	69					phagocytosis (GO:0006909)|regulation of cell shape (GO:0008360)|regulation of signal transduction (GO:0009966)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.G69G(1)		breast(1)|large_intestine(1)|skin(1)	3		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGGAGGTGGAATGCCTGCCA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											128	117	121					5																	130726736		2203	4300	6503	130754635	SO:0001819	synonymous_variant	56990			AF189692	CCDS34224.1	5q31.1	2008-02-05				ENSG00000158985			18547	protein-coding gene	gene with protein product						10816584	Standard	NM_020240		Approved	FLJ21967, SPEC2	uc003kvj.3	Q9NRR3		ENST00000505065.1:c.207A>C	5.37:g.130726736A>C			130754635	B2R622|Q4KMT9	Silent	SNP	ENST00000505065.1	37	CCDS34224.1																																																																																				0.498	CDC42SE2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370104.1	NM_020240		C	130726736	A	C	130726736	2	2	61	1	0	0	0	0	0	0	0	1	3086	233	9	4		4	CDC42SE2	5	130726736	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1696219	130726736	50188524	4065	12050										
RAPGEF6	51735	broad.mit.edu	37	chr5	130766761	130766761	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacactgcccacaagttCtagagcagcttttagaacag	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:130766761C>A	ENST00000509018.1	-	26	4461	c.4256G>T	c.(4255-4257)aGa>aTa	p.R1419I	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.R1432I|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.R1469I|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.R1427I|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.R1427I	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1419	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.R1432I(1)|p.R1419I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CCCACAAGTTCTAGAGCAGCT	0.448																																					Melanoma(168;435 1955 13113 13877 23213)											2	Substitution - Missense(2)	large_intestine(2)	5											116	118	118					5																	130766761		2203	4300	6503	130794660	SO:0001583	missense	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.4256G>T	5.37:g.130766761C>A	ENSP00000421684:p.Arg1419Ile		130794660	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.475612	0.43942	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.26660	1.83;1.72;1.72;1.83;1.92	5.11	4.19	0.49359	.	0.240155	0.40469	N	0.001093	T	0.20251	0.0487	L	0.44542	1.39	0.80722	D	1	B;B;B;B;B	0.27264	0.097;0.105;0.173;0.156;0.059	B;B;B;B;B	0.28385	0.049;0.041;0.027;0.089;0.041	T	0.06826	-1.0805	10	0.52906	T	0.07	.	6.4294	0.21788	0.161:0.6834:0.0:0.1556	.	1427;1427;1469;1432;1419	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	I	1419;1432;1427;1427;1432;1469	ENSP00000421684:R1419I;ENSP00000309298:R1432I;ENSP00000426081:R1427I;ENSP00000296859:R1427I;ENSP00000426948:R1469I	ENSP00000426948:R1469I	R	-	2	0	RAPGEF6;FNIP1	130794660	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	1.716000	0.37981	2.552000	0.86080	0.655000	0.94253	AGA		0.448	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		A	130766761	C	A	130766761	3	1	61	1	0	0	0	0	1	0	0	0	13085	913	32	2	561	2	RAPGEF6	5	130766761	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40025	130766761	50148499	4066	12051										
RAPGEF6	51735	broad.mit.edu	37	chr5	130788805	130788805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcattcgaacaacttggcGgatttccttggaaatcattc	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:130788805G>A	ENST00000509018.1	-	21	3347	c.3142C>T	c.(3142-3144)Cgc>Tgc	p.R1048C	RAPGEF6_ENST00000512052.1_Missense_Mutation_p.R763C|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.R1053C|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.R1048C|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.R1098C|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.R1048C|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.R1048C	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1048	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.R1098C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ACAACTTGGCGGATTTCCTTG	0.343																																					Melanoma(168;435 1955 13113 13877 23213)											1	Substitution - Missense(1)	large_intestine(1)	5											103	103	103					5																	130788805		2203	4300	6503	130816704	SO:0001583	missense	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3142C>T	5.37:g.130788805G>A	ENSP00000421684:p.Arg1048Cys		130816704	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110806	0.77210	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000514667	T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4	4.94	4.94	0.65067	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;0.973;0.999;0.999;0.999;1.0;0.999	T	0.77943	-0.2398	10	0.87932	D	0	.	18.5281	0.90980	0.0:0.0:1.0:0.0	.	1048;1048;1048;763;1098;1053;1048	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	C	1048;1053;1048;1048;1053;763;1048;1098	ENSP00000421684:R1048C;ENSP00000309298:R1053C;ENSP00000426081:R1048C;ENSP00000296859:R1048C;ENSP00000426910:R763C;ENSP00000311419:R1048C;ENSP00000426948:R1098C	ENSP00000426948:R1098C	R	-	1	0	RAPGEF6;FNIP1	130816704	1.000000	0.71417	0.987000	0.45799	0.991000	0.79684	6.393000	0.73217	2.460000	0.83146	0.467000	0.42956	CGC		0.343	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		A	130788805	G	A	130788805	3	1	61	1	0	0	0	0	1	0	0	0	13085	1116	39	1	2158	1	RAPGEF6	5	130788805	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22044	130788805	50126455	4067	12052										
FNIP1	96459	broad.mit.edu	37	chr5	131008399	131008399	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaggacatactctgattCttctatttcacctttctcta	4	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131008399C>T	ENST00000510461.1	-	14	1833	c.1738G>A	c.(1738-1740)Gaa>Aaa	p.E580K	FNIP1_ENST00000307954.8_Missense_Mutation_p.E535K|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.E552K	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	580					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.E580K(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TACTCTGATTCTTCTATTTCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											164	154	157					5																	131008399		2203	4300	6503	131036298	SO:0001583	missense	96459			DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.1738G>A	5.37:g.131008399C>T	ENSP00000421985:p.Glu580Lys		131036298	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614732	0.87359	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.14022	2.54;2.54;2.54	5.83	5.83	0.93111	.	.	.	.	.	T	0.40398	0.1115	M	0.69823	2.125	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.992	D;D;D	0.80764	0.994;0.994;0.936	T	0.05869	-1.0859	9	0.59425	D	0.04	-11.0845	20.126	0.97982	0.0:1.0:0.0:0.0	.	580;552;580	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	K	552;535;340;580	ENSP00000309266:E552K;ENSP00000310453:E535K;ENSP00000421985:E580K	ENSP00000310453:E535K	E	-	1	0	FNIP1	131036298	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.487000	0.81328	2.749000	0.94314	0.655000	0.94253	GAA		0.353	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		T	131008399	C	T	131008399	3	4	61	1	0	0	0	0	1	0	0	0	5994	922	32	3	1782	3	FNIP1	5	131008399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219594	131008399	49906861	4068	12053										
ACSL6	23305	broad.mit.edu	37	chr5	131305833	131305833	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcctacctgaggtccagtCgccaggagtggtgaaggtac	13	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131305833C>A	ENST00000379240.1	-	15	1573	c.1420G>T	c.(1420-1422)Gac>Tac	p.D474Y	ACSL6_ENST00000543479.1_Missense_Mutation_p.D474Y|ACSL6_ENST00000431707.1_Missense_Mutation_p.D454Y|ACSL6_ENST00000544770.1_Missense_Mutation_p.D383Y|AC034228.4_ENST00000446275.1_RNA|ACSL6_ENST00000379255.1_Missense_Mutation_p.D399Y|ACSL6_ENST00000379249.3_Missense_Mutation_p.D474Y|ACSL6_ENST00000379244.1_Missense_Mutation_p.D474Y|ACSL6_ENST00000379272.2_Missense_Mutation_p.D489Y|ACSL6_ENST00000379246.1_Missense_Mutation_p.D485Y|ACSL6_ENST00000296869.4_Missense_Mutation_p.D499Y|ACSL6_ENST00000379264.2_Missense_Mutation_p.D499Y|ACSL6_ENST00000357096.1_Missense_Mutation_p.D399Y			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	474					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)	p.D499Y(2)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAGGTCCAGTCGCCAGGAGTG	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	5											171	150	157					5																	131305833		2203	4300	6503	131333732	SO:0001583	missense	23305			AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.1420G>T	5.37:g.131305833C>A	ENSP00000368542:p.Asp474Tyr		131333732	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	37		.	.	.	.	.	.	.	.	.	.	C	25.8	4.674750	0.88445	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479	T;T;T;T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9	5.42	5.42	0.78866	AMP-dependent synthetase/ligase (1);	0.089346	0.85682	D	0.000000	T	0.73410	0.3583	M	0.90922	3.16	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.994;0.997;0.999;0.997;0.997;0.997;0.997	T	0.79458	-0.1795	10	0.66056	D	0.02	.	19.2739	0.94023	0.0:1.0:0.0:0.0	.	474;489;464;474;399;499;499	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	Y	474;499;489;399;399;499;485;474;383;474;454;474	ENSP00000368551:D474Y;ENSP00000368566:D499Y;ENSP00000368574:D489Y;ENSP00000349608:D399Y;ENSP00000368557:D399Y;ENSP00000296869:D499Y;ENSP00000368548:D485Y;ENSP00000368546:D474Y;ENSP00000445154:D383Y;ENSP00000368542:D474Y;ENSP00000413329:D454Y;ENSP00000442124:D474Y	ENSP00000296869:D499Y	D	-	1	0	ACSL6	131333732	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.792000	0.85828	2.575000	0.86900	0.644000	0.83932	GAC		0.498	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		A	131305833	C	A	131305833	3	1	61	1	0	0	0	0	1	0	0	0	181	884	31	2	701	2	ACSL6	5	131305833	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	297434	131305833	49609427	4069	12054										
SLC22A5	6584	broad.mit.edu	37	chr5	131728297	131728297	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatcctgtctccctacttCgtttaccttggtaagtccca	6	14	1	0	rs150457229		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131728297C>T	ENST00000245407.3	+	8	1661	c.1440C>T	c.(1438-1440)ttC>ttT	p.F480F	SLC22A5_ENST00000435065.2_Silent_p.F504F|SLC22A5_ENST00000479605.1_3'UTR	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	480					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)	p.F480F(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	CTCCCTACTTCGTTTACCTTG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	133	97	109		1440	-7.5	0	5	dbSNP_134	109	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC22A5	NM_003060.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		480/558	131728297	2,13004	2203	4300	6503	131756196	SO:0001819	synonymous_variant	6584			AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"Solute carriers"	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.1440C>T	5.37:g.131728297C>T			131756196	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Silent	SNP	ENST00000245407.3	37	CCDS4154.1																																																																																				0.542	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060		T	131728297	C	T	131728297	2	4	61	1	0	0	0	0	0	0	0	1	14494	883	31	1		1	SLC22A5	5	131728297	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	422464	131728297	49186963	4070	12055										
RAD50	10111	broad.mit.edu	37	chr5	131893077	131893077	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttggaatagaggacaaaGataagcaaattatcactttc	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131893077G>T	ENST00000265335.6	+	1	448	c.61G>T	c.(61-63)Gat>Tat	p.D21Y	RAD50_ENST00000378823.3_5'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	21					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.D21Y(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGGACAAAGATAAGCAAAT	0.483								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	5											123	130	128					5																	131893077		2203	4300	6503	131920976	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.61G>T	5.37:g.131893077G>T	ENSP00000265335:p.Asp21Tyr		131920976	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693958	0.88735	.	.	ENSG00000113522	ENST00000265335;ENST00000453394	T;T	0.08984	3.03;3.03	5.72	5.72	0.89469	.	0.043031	0.85682	D	0.000000	T	0.23014	0.0556	M	0.65975	2.015	0.80722	D	1	D	0.63880	0.993	D	0.63381	0.914	T	0.00090	-1.2087	10	0.72032	D	0.01	-22.7513	10.7592	0.46256	0.0861:0.0:0.9139:0.0	.	21	Q92878	RAD50_HUMAN	Y	21	ENSP00000265335:D21Y;ENSP00000400049:D21Y	ENSP00000265335:D21Y	D	+	1	0	RAD50	131920976	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.418000	0.80167	2.700000	0.92200	0.655000	0.94253	GAT		0.483	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131893077	G	T	131893077	3	4	61	1	0	0	0	0	1	0	0	0	13021	942	33	2	63	2	RAD50	5	131893077	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164780	131893077	49022183	4071	12056										
RAD50	10111	broad.mit.edu	37	chr5	131915128	131915128	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgtcatcaagaagattCtaattggcctttaagtgaag	8	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131915128C>A	ENST00000265335.6	+	4	872	c.485C>A	c.(484-486)tCt>tAt	p.S162Y	RAD50_ENST00000378823.3_Missense_Mutation_p.S23Y			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	162					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.S23Y(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAAGAAGATTCTAATTGGCCT	0.373								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	5											101	107	105					5																	131915128		2203	4300	6503	131943027	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.485C>A	5.37:g.131915128C>A	ENSP00000265335:p.Ser162Tyr		131943027	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.662414	0.88251	.	.	ENSG00000113522	ENST00000416135;ENST00000378823;ENST00000265335;ENST00000453394	T;T;T;T	0.27256	1.68;2.77;3.01;3.01	5.69	5.69	0.88448	.	0.098303	0.64402	D	0.000001	T	0.61261	0.2333	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68708	-0.5337	10	0.87932	D	0	-7.7968	18.8012	0.92018	0.0:1.0:0.0:0.0	.	162	Q92878	RAD50_HUMAN	Y	63;23;162;162	ENSP00000389515:S63Y;ENSP00000368100:S23Y;ENSP00000265335:S162Y;ENSP00000400049:S162Y	ENSP00000265335:S162Y	S	+	2	0	RAD50	131943027	1.000000	0.71417	0.962000	0.40283	0.990000	0.78478	7.818000	0.86416	2.683000	0.91414	0.591000	0.81541	TCT		0.373	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		A	131915128	C	A	131915128	3	1	61	1	0	0	0	0	1	0	0	0	13021	913	32	2	499	2	RAD50	5	131915128	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22051	131915128	49000132	4072	12057										
RAD50	10111	broad.mit.edu	37	chr5	131915579	131915579	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaagccttagaaacacttCggcaggtacgtcagacacaa	8	10	1	2	rs28903087	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131915579C>T	ENST00000265335.6	+	5	964	c.577C>T	c.(577-579)Cgg>Tgg	p.R193W	RAD50_ENST00000487596.1_3'UTR|RAD50_ENST00000378823.3_Missense_Mutation_p.R54W			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	193			R -> W (in dbSNP:rs28903087).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.R54W(1)|p.R193W(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAAACACTTCGGCAGGTACG	0.313								Homologous recombination																																								2	Substitution - Missense(2)	large_intestine(2)	5						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	65	65	65		577	4.7	1	5	dbSNP_125	65	0,8598		0,0,4299	no	missense	RAD50	NM_005732.3	101	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	193/1313	131915579	1,13003	2203	4299	6502	131943478	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.577C>T	5.37:g.131915579C>T	ENSP00000265335:p.Arg193Trp		131943478	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128635	0.77549	2.27E-4	0.0	ENSG00000113522	ENST00000416135;ENST00000378823;ENST00000265335;ENST00000453394	T;T;T;T	0.24723	1.84;3.34;3.06;3.06	5.54	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.54029	-0.8354	10	0.72032	D	0.01	-11.4505	12.943	0.58357	0.2946:0.7054:0.0:0.0	rs28903087;rs28903087	193	Q92878	RAD50_HUMAN	W	94;54;193;193	ENSP00000389515:R94W;ENSP00000368100:R54W;ENSP00000265335:R193W;ENSP00000400049:R193W	ENSP00000265335:R193W	R	+	1	2	RAD50	131943478	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.498000	0.60373	1.443000	0.47586	0.655000	0.94253	CGG		0.313	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131915579	C	T	131915579	3	4	61	1	0	0	0	0	1	0	0	0	13021	875	31	1	595	1	RAD50	5	131915579	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	451	131915579	48999681	4073	12058										
RAD50	10111	broad.mit.edu	37	chr5	131925514	131925514	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggattcttgaactggaccaGgagctcataaaagctgtaag	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:131925514G>T	ENST00000265335.6	+	9	1824	c.1437G>T	c.(1435-1437)caG>caT	p.Q479H	RAD50_ENST00000378823.3_Missense_Mutation_p.Q340H			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	479					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.Q479H(1)|p.Q340H(1)		breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AACTGGACCAGGAGCTCATAA	0.303								Homologous recombination																																								2	Substitution - Missense(2)	large_intestine(2)	5											76	76	76					5																	131925514		2203	4299	6502	131953413	SO:0001583	missense	10111			Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.1437G>T	5.37:g.131925514G>T	ENSP00000265335:p.Gln479His		131953413	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226173	0.39300	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.08008	3.49;3.71;3.14	5.43	4.5	0.54988	.	0.442840	0.27600	N	0.018642	T	0.07234	0.0183	L	0.36672	1.1	0.34884	D	0.744901	B	0.29085	0.232	B	0.28139	0.086	T	0.10064	-1.0646	10	0.48119	T	0.1	-1.6933	8.0483	0.30562	0.0795:0.0:0.761:0.1595	.	479	Q92878	RAD50_HUMAN	H	340;479;479	ENSP00000368100:Q340H;ENSP00000265335:Q479H;ENSP00000400049:Q479H	ENSP00000265335:Q479H	Q	+	3	2	RAD50	131953413	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.152000	0.31663	2.710000	0.92621	0.650000	0.86243	CAG		0.303	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131925514	G	T	131925514	3	4	61	1	0	0	0	0	1	0	0	0	13021	991	35	2	1471	2	RAD50	5	131925514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9935	131925514	48989746	4074	12059										
KIF3A	11127	broad.mit.edu	37	chr5	132038661	132038661	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagattcttcaagaagtttCtcttgttcctcagctttggc	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132038661C>A	ENST00000378746.4	-	11	1700	c.1482G>T	c.(1480-1482)gaG>gaT	p.E494D	AC004237.1_ENST00000431165.1_RNA|KIF3A_ENST00000487055.1_5'UTR|KIF3A_ENST00000378735.1_Missense_Mutation_p.E497D|KIF3A_ENST00000403231.1_Missense_Mutation_p.E521D	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	494					anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)	p.E494D(1)		endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAAGAAGTTTCTCTTGTTCCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											196	194	195					5																	132038661		2203	4300	6503	132066560	SO:0001583	missense	11127			AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"Kinesins"	6319	protein-coding gene	gene with protein product	"kinesin family protein 3A"	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.1482G>T	5.37:g.132038661C>A	ENSP00000368020:p.Glu494Asp		132066560	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Missense_Mutation	SNP	ENST00000378746.4	37	CCDS34235.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.691818	0.68271	.	.	ENSG00000131437	ENST00000378746;ENST00000378735;ENST00000541316;ENST00000450441;ENST00000403231	T;T;T;T	0.73897	-0.7;3.63;2.95;-0.79	6.17	1.32	0.21799	.	0.000000	0.85682	D	0.000000	D	0.85075	0.5614	M	0.88640	2.97	0.54753	D	0.999989	P;P;P;P	0.52842	0.956;0.956;0.956;0.956	D;D;D;D	0.65010	0.931;0.931;0.931;0.931	T	0.83332	-0.0012	10	0.45353	T	0.12	.	10.9879	0.47532	0.0:0.5441:0.0:0.4559	.	521;521;494;520	E9PES4;B4DHG8;Q9Y496;Q2UVF2	.;.;KIF3A_HUMAN;.	D	494;497;521;22;521	ENSP00000368020:E494D;ENSP00000368009:E497D;ENSP00000405619:E22D;ENSP00000385808:E521D	ENSP00000368009:E497D	E	-	3	2	KIF3A	132066560	0.990000	0.36364	0.997000	0.53966	0.992000	0.81027	0.369000	0.20416	-0.041000	0.13558	-0.136000	0.14681	GAG		0.423	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054		A	132038661	C	A	132038661	3	1	61	1	0	0	0	0	1	0	0	0	8321	912	32	2	645	2	KIF3A	5	132038661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113147	132038661	48876599	4075	12060										
SHROOM1	134549	broad.mit.edu	37	chr5	132161019	132161019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgggcagccatccgacctCgtgatcttcaaacttagcca	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132161019C>T	ENST00000378679.3	-	4	1618	c.814G>A	c.(814-816)Gag>Aag	p.E272K	SHROOM1_ENST00000319854.3_Missense_Mutation_p.E272K|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000378676.1_Missense_Mutation_p.E272K	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	272					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)	p.E272K(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CATCCGACCTCGTGATCTTCA	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	5											33	34	33					5																	132161019		2200	4300	6500	132188918	SO:0001583	missense	134549			AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.814G>A	5.37:g.132161019C>T	ENSP00000367950:p.Glu272Lys		132188918	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184619	0.38609	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676;ENST00000440118	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	3.27	-0.341	0.12639	.	0.522752	0.17233	N	0.181872	T	0.08846	0.0219	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.04013	0.001;0.0	T	0.38286	-0.9668	10	0.02654	T	1	.	7.3771	0.26835	0.0:0.5331:0.2866:0.1803	.	272;272	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	K	272	ENSP00000367950:E272K;ENSP00000324245:E272K;ENSP00000367947:E272K;ENSP00000388049:E272K	ENSP00000324245:E272K	E	-	1	0	SHROOM1	132188918	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.025000	0.13577	-0.132000	0.11557	-0.216000	0.12614	GAG		0.657	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132161019	C	T	132161019	3	4	61	1	0	0	0	0	1	0	0	0	14330	893	31	1	1772	1	SHROOM1	5	132161019	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122358	132161019	48754241	4076	12061										
AFF4	27125	broad.mit.edu	37	chr5	132232018	132232018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaacccttcacaaaccttAtgcttcctcttgcctttgtt	3	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132232018A>T	ENST00000265343.5	-	11	2683	c.2304T>A	c.(2302-2304)caT>caA	p.H768Q	AFF4_ENST00000378595.3_Missense_Mutation_p.H768Q	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	768					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H768Q(1)	SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CACAAACCTTATGCTTCCTCT	0.433																																					Ovarian(126;889 1733 2942 10745 11605)											1	Substitution - Missense(1)	large_intestine(1)	5											99	99	99					5																	132232018		2203	4300	6503	132259917	SO:0001583	missense	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2304T>A	5.37:g.132232018A>T	ENSP00000265343:p.His768Gln		132259917	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.230151	0.58777	.	.	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.65916	-0.18;-0.18	5.03	3.88	0.44766	.	0.103005	0.64402	D	0.000003	T	0.72708	0.3494	M	0.75777	2.31	0.51233	D	0.99991	D;D	0.76494	0.999;0.997	D;D	0.80764	0.994;0.992	T	0.69510	-0.5126	10	0.17832	T	0.49	-11.112	7.8157	0.29258	0.7572:0.0:0.2428:0.0	.	768;768	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	Q	768	ENSP00000265343:H768Q;ENSP00000367858:H768Q	ENSP00000265343:H768Q	H	-	3	2	AFF4	132259917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.898000	0.48672	0.874000	0.35823	0.533000	0.62120	CAT		0.433	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		T	132232018	A	T	132232018	3	4	61	1	0	0	0	0	1	0	0	0	359	446	16	5	1231	5	AFF4	5	132232018	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	70999	132232018	48683242	4077	12062										
AFF4	27125	broad.mit.edu	37	chr5	132232837	132232837	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagccttgagatgatgggatGttactgtccactgaagaggc	13	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132232837G>A	ENST00000265343.5	-	11	1864	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N	AFF4_ENST00000378595.3_Silent_p.N495N	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	495					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N495N(1)	SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGATGGGATGTTACTGTCCA	0.478																																					Ovarian(126;889 1733 2942 10745 11605)											1	Substitution - coding silent(1)	large_intestine(1)	5											167	164	165					5																	132232837		2203	4300	6503	132260736	SO:0001819	synonymous_variant	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.1485C>T	5.37:g.132232837G>A			132260736	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Silent	SNP	ENST00000265343.5	37	CCDS4164.1																																																																																				0.478	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		A	132232837	G	A	132232837	2	1	61	1	0	0	0	0	0	0	0	1	359	1368	48	3		3	AFF4	5	132232837	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	819	132232837	48682423	4078	12063										
AFF4	27125	broad.mit.edu	37	chr5	132238167	132238167	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccatttgaagttttagaaGgattatatctttctggaaca	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132238167G>T	ENST00000265343.5	-	7	1479	c.1100C>A	c.(1099-1101)cCt>cAt	p.P367H	AFF4_ENST00000378595.3_Missense_Mutation_p.P367H|AFF4_ENST00000491831.1_5'Flank	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	367	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P367H(1)	SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTTTTAGAAGGATTATATCT	0.289																																					Ovarian(126;889 1733 2942 10745 11605)											1	Substitution - Missense(1)	large_intestine(1)	5											62	68	66					5																	132238167		2203	4300	6503	132266066	SO:0001583	missense	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.1100C>A	5.37:g.132238167G>T	ENSP00000265343:p.Pro367His		132266066	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.99|19.99	3.927898|3.927898	0.73327|0.73327	.|.	.|.	ENSG00000072364|ENSG00000072364	ENST00000425658|ENST00000265343;ENST00000378595	.|T;T	.|0.65916	.|-0.18;-0.18	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	.|0.880807	.|0.10020	.|N	.|0.726076	T|T	0.72843|0.72843	0.3511|0.3511	M|M	0.66939|0.66939	2.045|2.045	0.42234|0.42234	D|D	0.991908|0.991908	.|D;P	.|0.60575	.|0.988;0.808	.|P;P	.|0.49528	.|0.614;0.529	T|T	0.74188|0.74188	-0.3746|-0.3746	5|10	.|0.66056	.|D	.|0.02	-5.6182|-5.6182	19.6101|19.6101	0.95602|0.95602	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|367;367	.|Q9UHB7-2;Q9UHB7	.|.;AFF4_HUMAN	I|H	63|367	.|ENSP00000265343:P367H;ENSP00000367858:P367H	.|ENSP00000265343:P367H	L|P	-|-	1|2	0|0	AFF4|AFF4	132266066|132266066	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.703000|0.703000	0.40648|0.40648	6.906000|6.906000	0.75719|0.75719	2.640000|2.640000	0.89533|0.89533	0.650000|0.650000	0.86243|0.86243	CTT|CCT		0.289	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		T	132238167	G	T	132238167	3	4	61	1	0	0	0	0	1	0	0	0	359	1000	35	2	2451	2	AFF4	5	132238167	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5330	132238167	48677093	4079	12064										
HSPA4	3308	broad.mit.edu	37	chr5	132412504	132412504	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggagtgtgagaaactcaaGaaattgatgagtgcaaatgc	12	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132412504G>T	ENST00000304858.2	+	7	1111	c.822G>T	c.(820-822)aaG>aaT	p.K274N	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	274					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.K274N(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAAACTCAAGAAATTGATGA	0.348																																					Colon(114;1299 1588 6063 12302 48757)											1	Substitution - Missense(1)	large_intestine(1)	5											115	115	115					5																	132412504		2203	4300	6503	132440403	SO:0001583	missense	3308			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.822G>T	5.37:g.132412504G>T	ENSP00000302961:p.Lys274Asn		132440403	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.077690	0.76528	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.61040	0.14	5.52	4.64	0.57946	.	0.000000	0.85682	D	0.000000	D	0.83151	0.5192	H	0.97682	4.055	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.87712	0.2567	10	0.87932	D	0	-13.987	12.5174	0.56040	0.1322:0.0:0.8678:0.0	.	274	P34932	HSP74_HUMAN	N	274	ENSP00000302961:K274N	ENSP00000302961:K274N	K	+	3	2	HSPA4	132440403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.905000	0.48727	2.748000	0.94277	0.591000	0.81541	AAG		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		T	132412504	G	T	132412504	3	4	61	1	0	0	0	0	1	0	0	0	7433	933	33	2	848	2	HSPA4	5	132412504	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	174337	132412504	48502756	4080	12065										
HSPA4	3308	broad.mit.edu	37	chr5	132424177	132424177	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaaagagaagatcagcaAatttttcggtaaagaactta	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132424177A>C	ENST00000304858.2	+	9	1356	c.1067A>C	c.(1066-1068)aAa>aCa	p.K356T	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	356					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.K356T(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAGATCAGCAAATTTTTCGGT	0.358																																					Colon(114;1299 1588 6063 12302 48757)											1	Substitution - Missense(1)	large_intestine(1)	5											120	110	113					5																	132424177		2203	4300	6503	132452076	SO:0001583	missense	3308			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1067A>C	5.37:g.132424177A>C	ENSP00000302961:p.Lys356Thr		132452076	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.366878	0.82463	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.31510	1.49	6.02	4.87	0.63330	.	0.126547	0.64402	D	0.000001	T	0.39937	0.1097	M	0.73430	2.235	0.58432	D	0.999994	B	0.24186	0.099	B	0.37015	0.239	T	0.32851	-0.9891	10	0.62326	D	0.03	-17.1424	9.109	0.36716	0.8611:0.0:0.1389:0.0	.	356	P34932	HSP74_HUMAN	T	356	ENSP00000302961:K356T	ENSP00000302961:K356T	K	+	2	0	HSPA4	132452076	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.625000	0.54238	1.111000	0.41721	0.528000	0.53228	AAA		0.358	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		C	132424177	A	C	132424177	3	2	61	1	0	0	0	0	1	0	0	0	7433	14	1	4	1101	4	HSPA4	5	132424177	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11673	132424177	48491083	4081	12066										
HSPA4	3308	broad.mit.edu	37	chr5	132439659	132439659	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagctaaatctgcagaacAagcagagtttgaccatggat	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:132439659A>G	ENST00000304858.2	+	18	2549	c.2260A>G	c.(2260-2262)Aag>Gag	p.K754E		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	754					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.K754E(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGCAGAACAAGCAGAGTTT	0.363																																					Colon(114;1299 1588 6063 12302 48757)											1	Substitution - Missense(1)	large_intestine(1)	5											132	128	130					5																	132439659		2203	4300	6503	132467558	SO:0001583	missense	3308			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.2260A>G	5.37:g.132439659A>G	ENSP00000302961:p.Lys754Glu		132467558	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880296	0.72294	.	.	ENSG00000170606	ENST00000304858	T	0.01323	5.01	5.87	5.87	0.94306	.	0.176798	0.64402	D	0.000010	T	0.02571	0.0078	M	0.71871	2.18	0.80722	D	1	P	0.37781	0.608	B	0.29862	0.108	T	0.58555	-0.7616	10	0.32370	T	0.25	-21.2343	16.2678	0.82600	1.0:0.0:0.0:0.0	.	754	P34932	HSP74_HUMAN	E	754	ENSP00000302961:K754E	ENSP00000302961:K754E	K	+	1	0	HSPA4	132467558	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.716000	0.91420	2.232000	0.73038	0.523000	0.50628	AAG		0.363	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		G	132439659	A	G	132439659	3	3	61	1	0	0	0	0	1	0	0	0	7433	131	5	4	2330	4	HSPA4	5	132439659	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	15482	132439659	48475601	4082	12067										
TCF7	6932	broad.mit.edu	37	chr5	133473798	133473798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccccaactctctctctacGaacatttcaacagcccacat	2	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:133473798G>A	ENST00000321584.4	+	4	686	c.490G>A	c.(490-492)Gaa>Aaa	p.E164K	TCF7_ENST00000395023.1_Missense_Mutation_p.E49K|TCF7_ENST00000517478.1_3'UTR|TCF7_ENST00000321603.6_Missense_Mutation_p.E164K|TCF7_ENST00000395029.1_Missense_Mutation_p.E164K|TCF7_ENST00000342854.5_Missense_Mutation_p.E164K|TCF7_ENST00000378560.4_Missense_Mutation_p.E49K|TCF7_ENST00000378564.1_Missense_Mutation_p.E164K|TCF7_ENST00000518915.1_Missense_Mutation_p.E49K|TCF7_ENST00000432532.2_Missense_Mutation_p.E49K|TCF7_ENST00000520958.1_Missense_Mutation_p.E49K			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	164					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E164K(2)		kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCTCTCTACGAACATTTCAA	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	5											128	119	122					5																	133473798		2203	4300	6503	133501697	SO:0001583	missense	6932			Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.490G>A	5.37:g.133473798G>A	ENSP00000326540:p.Glu164Lys		133501697	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		.	.	.	.	.	.	.	.	.	.	G	18.57	3.653312	0.67472	.	.	ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000518887;ENST00000517851;ENST00000521639;ENST00000522375;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023;ENST00000519037	D;D;D;D;D;D;D;D;D;D;T	0.99282	-5.68;-5.65;-5.66;-5.67;-5.67;-5.59;-5.61;-5.64;-5.6;-5.64;0.7	4.52	4.52	0.55395	CTNNB1 binding, N-teminal (1);	0.313405	0.29280	N	0.012602	D	0.99214	0.9727	M	0.77616	2.38	0.42677	D	0.993534	P;D;D;B	0.76494	0.607;0.991;0.999;0.33	B;P;P;B	0.62740	0.086;0.689;0.906;0.049	D	0.99136	1.0854	10	0.87932	D	0	.	14.5747	0.68238	0.0:0.0:1.0:0.0	.	164;164;164;164	P36402-9;B7WNT5;P36402;P36402-5	.;.;TCF7_HUMAN;.	K	164;164;164;164;164;164;49;49;49;49;49;49;49;49;49;24	ENSP00000340347:E164K;ENSP00000326654:E164K;ENSP00000326540:E164K;ENSP00000367827:E164K;ENSP00000378472:E164K;ENSP00000367822:E49K;ENSP00000397946:E49K;ENSP00000429547:E49K;ENSP00000430179:E49K;ENSP00000378469:E49K;ENSP00000429696:E24K	ENSP00000326540:E164K	E	+	1	0	TCF7	133501697	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	5.586000	0.67503	2.346000	0.79739	0.557000	0.71058	GAA		0.592	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		A	133473798	G	A	133473798	3	1	61	1	0	0	0	0	1	0	0	0	15735	1059	37	1	504	1	TCF7	5	133473798	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1034139	133473798	47441462	4083	12068										
TCF7	6932	broad.mit.edu	37	chr5	133478466	133478466	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaagaagccaaccatcaaGaagcccctcaatgccttcat	6	15	3	2	rs199840705		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:133478466G>T	ENST00000321584.4	+	7	1006	c.810G>T	c.(808-810)aaG>aaT	p.K270N	TCF7_ENST00000395023.1_Missense_Mutation_p.K155N|TCF7_ENST00000321603.6_Missense_Mutation_p.K270N|TCF7_ENST00000395029.1_Missense_Mutation_p.K270N|TCF7_ENST00000342854.5_Missense_Mutation_p.K270N|TCF7_ENST00000378560.4_Missense_Mutation_p.K155N|TCF7_ENST00000378564.1_Missense_Mutation_p.K270N|TCF7_ENST00000518915.1_Missense_Mutation_p.K155N|TCF7_ENST00000432532.2_Missense_Mutation_p.K155N|TCF7_ENST00000520958.1_Missense_Mutation_p.K155N			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	270					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.K270N(2)		kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAACCATCAAGAAGCCCCTCA	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	5											128	116	120					5																	133478466		2203	4300	6503	133506365	SO:0001583	missense	6932			Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.810G>T	5.37:g.133478466G>T	ENSP00000326540:p.Lys270Asn		133506365	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.115208|4.115208	0.77210|0.77210	.|.	.|.	ENSG00000081059|ENSG00000081059	ENST00000517855|ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023;ENST00000519037;ENST00000517799	.|D;D;D;D;D;D;D;D;D;D;T;D	.|0.99070	.|-5.39;-5.39;-5.39;-5.39;-5.39;-5.39;-5.39;-5.39;-5.39;-5.39;-0.4;-5.39	5.82|5.82	3.78|3.78	0.43462|0.43462	.|High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.99501	.|0.9822	H|H	0.97240|0.97240	3.965|3.965	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;0.999;1.0;0.997;1.0;1.0	.|D;D;D;D;D;D	.|0.97110	.|1.0;0.994;0.994;0.994;0.998;0.996	.|D	.|0.98218	.|1.0476	.|10	.|0.87932	.|D	.|0	.|.	12.0637|12.0637	0.53576|0.53576	0.1844:0.0:0.8156:0.0|0.1844:0.0:0.8156:0.0	.|.	.|84;270;270;68;270;270	.|B3KSI6;P36402-9;B7WNT5;B3KQ75;P36402;P36402-5	.|.;.;.;.;TCF7_HUMAN;.	X|N	59|270;270;270;270;270;270;155;155;155;155;155;130;48	.|ENSP00000340347:K270N;ENSP00000326654:K270N;ENSP00000326540:K270N;ENSP00000367827:K270N;ENSP00000378472:K270N;ENSP00000367822:K155N;ENSP00000397946:K155N;ENSP00000429547:K155N;ENSP00000430179:K155N;ENSP00000378469:K155N;ENSP00000429696:K130N;ENSP00000427968:K48N	.|ENSP00000326540:K270N	E|K	+|+	1|3	0|2	TCF7|TCF7	133506365|133506365	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.390000|3.390000	0.52523|0.52523	1.444000|1.444000	0.47605|0.47605	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.542	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		T	133478466	G	T	133478466	3	4	61	1	0	0	0	0	1	0	0	0	15735	933	33	2	836	2	TCF7	5	133478466	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4668	133478466	47436794	4084	12069										
CDKL3	51265	broad.mit.edu	37	chr5	133640179	133640179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgtcagatctggaaaaaTtcagcttccttttgttctca	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:133640179T>C	ENST00000265334.4	-	11	1656	c.1538A>G	c.(1537-1539)aAt>aGt	p.N513S	CDKL3_ENST00000521118.1_Missense_Mutation_p.N513S|CDKL3_ENST00000523054.1_Missense_Mutation_p.N324S|CDKL3_ENST00000609383.1_3'UTR|CDKL3_ENST00000536186.1_Missense_Mutation_p.N218S|CDKL3_ENST00000435240.2_Missense_Mutation_p.N218S|CDKL3_ENST00000609654.1_Missense_Mutation_p.N324S|CTD-2410N18.4_ENST00000518409.1_RNA	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	513					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)	p.N513S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGGAAAAATTCAGCTTCCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											165	143	149					5																	133640179		1567	3581	5148	133668078	SO:0001583	missense	51265			AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"Cyclin-dependent kinases"	15483	protein-coding gene	gene with protein product	"serine-threonine protein kinase NKIAMRE"	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.1538A>G	5.37:g.133640179T>C	ENSP00000265334:p.Asn513Ser		133668078	D3DQA0|D3DQA1|Q9P114	Missense_Mutation	SNP	ENST00000265334.4	37	CCDS47264.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.082456	0.36758	.	.	ENSG00000006837	ENST00000536186;ENST00000435240;ENST00000265334;ENST00000523054;ENST00000521118	T;T;T;T;T	0.73258	0.77;0.74;-0.68;-0.55;-0.73	5.75	4.58	0.56647	.	0.095145	0.46758	N	0.000271	T	0.61236	0.2331	L	0.32530	0.975	0.80722	D	1	B;P;P;B;B	0.47545	0.312;0.513;0.897;0.247;0.028	B;B;B;B;B	0.43809	0.067;0.191;0.432;0.033;0.008	T	0.62515	-0.6838	10	0.59425	D	0.04	-31.7314	9.7533	0.40490	0.0:0.08:0.0:0.92	.	324;218;218;324;513	B4DX41;B4DRK6;B4DGS2;B7Z2C5;Q8IVW4	.;.;.;.;CDKL3_HUMAN	S	218;218;513;324;513	ENSP00000441545:N218S;ENSP00000399807:N218S;ENSP00000265334:N513S;ENSP00000428500:N324S;ENSP00000428689:N513S	ENSP00000265334:N513S	N	-	2	0	CDKL3	133668078	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.442000	0.35046	0.995000	0.38917	0.533000	0.62120	AAT		0.373	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575		C	133640179	T	C	133640179	3	2	61	1	0	0	0	0	1	0	0	0	3161	1493	52	4	252	4	CDKL3	5	133640179	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	161713	133640179	47275081	4085	12070										
PHF15	23338	broad.mit.edu	37	chr5	133873686	133873686	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctctctgcaggtcatgcGacatctacatccgcatcaag	7	14	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:133873686G>A	ENST00000402835.1	+	3	321	c.66G>A	c.(64-66)gcG>gcA	p.A22A	PHF15_ENST00000361895.2_Silent_p.A22A|PHF15_ENST00000282605.4_Silent_p.A22A|PHF15_ENST00000395003.1_Silent_p.A22A														p.A22A(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGGTCATGCGACATCTACAT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											88	82	84					5																	133873686		2203	4300	6503	133901585	SO:0001819	synonymous_variant	23338																														ENST00000402835.1:c.66G>A	5.37:g.133873686G>A			133901585		Silent	SNP	ENST00000402835.1	37																																																																																					0.572	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			A	133873686	G	A	133873686	2	1	61	1	0	0	0	0	0	0	0	1	11857	1045	37	1		1	PHF15	5	133873686	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	233507	133873686	47041574	4086	12071										
SEC24A	10802	broad.mit.edu	37	chr5	134053762	134053762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacttaattcctcagggaGcactcaacatcagtgataga	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134053762G>A	ENST00000398844.2	+	20	3157	c.2869G>A	c.(2869-2871)Gca>Aca	p.A957T	RNU6-757P_ENST00000410334.1_RNA	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	957					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.A957T(1)		NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCTCAGGGAGCACTCAACAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											115	111	112					5																	134053762		1852	4106	5958	134081661	SO:0001583	missense	10802			AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.2869G>A	5.37:g.134053762G>A	ENSP00000381823:p.Ala957Thr		134081661	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	37	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415532	0.62511	.	.	ENSG00000113615	ENST00000398844	T	0.27720	1.65	5.53	5.53	0.82687	.	0.049477	0.85682	D	0.000000	T	0.31979	0.0814	L	0.59436	1.845	0.80722	D	1	B;B	0.13145	0.001;0.007	B;B	0.08055	0.001;0.003	T	0.21280	-1.0250	10	0.10377	T	0.69	-5.7698	19.4671	0.94946	0.0:0.0:1.0:0.0	.	721;957	B4E205;O95486	.;SC24A_HUMAN	T	957	ENSP00000381823:A957T	ENSP00000381823:A957T	A	+	1	0	SEC24A	134081661	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.719000	0.74718	2.614000	0.88457	0.467000	0.42956	GCA		0.398	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			A	134053762	G	A	134053762	3	1	61	1	0	0	0	0	1	0	0	0	14031	971	34	3	2947	3	SEC24A	5	134053762	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180076	134053762	46861498	4087	12072										
DDX46	9879	broad.mit.edu	37	chr5	134117631	134117631	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattcttcagaggaggaagaAgttgatcttcagacagccct	10	8	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134117631A>C	ENST00000354283.4	+	8	1035	c.900A>C	c.(898-900)gaA>gaC	p.E300D	DDX46_ENST00000452510.2_Missense_Mutation_p.E300D			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	300					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.E300D(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGAGGAAGAAGTTGATCTTC	0.363																																					Colon(13;391 453 4901 21675 24897)											1	Substitution - Missense(1)	large_intestine(1)	5											48	48	48					5																	134117631		2203	4300	6503	134145530	SO:0001583	missense	9879				CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.900A>C	5.37:g.134117631A>C	ENSP00000346236:p.Glu300Asp		134145530	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	37	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	A	11.10	1.539390	0.27475	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.09630	2.96;2.96	5.65	3.2	0.36748	.	0.098954	0.64402	D	0.000001	T	0.06096	0.0158	N	0.16602	0.42	0.54753	D	0.999986	B	0.13594	0.008	B	0.12837	0.008	T	0.33523	-0.9865	10	0.11794	T	0.64	-26.7535	10.0177	0.42024	0.8613:0.0:0.1387:0.0	.	300	Q7L014	DDX46_HUMAN	D	300	ENSP00000416534:E300D;ENSP00000346236:E300D	ENSP00000346236:E300D	E	+	3	2	DDX46	134145530	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.232000	0.43018	0.392000	0.25172	0.368000	0.22195	GAA		0.363	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		C	134117631	A	C	134117631	3	2	61	1	0	0	0	0	1	0	0	0	4370	69	3	4	930	4	DDX46	5	134117631	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	63869	134117631	46797629	4088	12073										
DDX46	9879	broad.mit.edu	37	chr5	134147406	134147406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggggaaaataattaaaaaGagtagtgggttctctggtaa	13	2	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134147406G>T	ENST00000354283.4	+	18	2442	c.2307G>T	c.(2305-2307)aaG>aaT	p.K769N	DDX46_ENST00000452510.2_Missense_Mutation_p.K769N			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	769					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.K769N(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TAATTAAAAAGAGTAGTGGGT	0.313																																					Colon(13;391 453 4901 21675 24897)											1	Substitution - Missense(1)	large_intestine(1)	5											76	84	81					5																	134147406		2203	4300	6503	134175305	SO:0001583	missense	9879				CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2307G>T	5.37:g.134147406G>T	ENSP00000346236:p.Lys769Asn		134175305	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	37	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.258608	0.23051	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.26810	1.71;1.71	4.93	2.12	0.27331	.	0.084378	0.85682	D	0.000000	T	0.18718	0.0449	L	0.45137	1.4	0.43803	D	0.996356	B	0.16166	0.016	B	0.20184	0.028	T	0.06303	-1.0834	10	0.18276	T	0.48	-19.3165	8.5783	0.33612	0.4058:0.0:0.5942:0.0	.	769	Q7L014	DDX46_HUMAN	N	769	ENSP00000416534:K769N;ENSP00000346236:K769N	ENSP00000346236:K769N	K	+	3	2	DDX46	134175305	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.943000	0.49026	0.596000	0.29794	0.491000	0.48974	AAG		0.313	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		T	134147406	G	T	134147406	3	4	61	1	0	0	0	0	1	0	0	0	4370	933	33	2	2377	2	DDX46	5	134147406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29775	134147406	46767854	4089	12074										
DDX46	9879	broad.mit.edu	37	chr5	134154652	134154652	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacttccctcctggcaaaGaacccaaggaaggcgagcgg	11	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134154652G>T	ENST00000354283.4	+	21	3067	c.2932G>T	c.(2932-2934)Gaa>Taa	p.E978*	DDX46_ENST00000452510.2_Nonsense_Mutation_p.E979*			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	978					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.E978*(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCCTGGCAAAGAACCCAAGGA	0.418																																					Colon(13;391 453 4901 21675 24897)											1	Substitution - Nonsense(1)	large_intestine(1)	5											94	92	92					5																	134154652		2203	4300	6503	134182551	SO:0001587	stop_gained	9879				CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2932G>T	5.37:g.134154652G>T	ENSP00000346236:p.Glu978*		134182551	O94894|Q96EI0|Q9Y658	Nonsense_Mutation	SNP	ENST00000354283.4	37	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	G	44	10.651649	0.99444	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	.	.	.	5.71	5.71	0.89125	.	0.044719	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-26.9445	19.8505	0.96738	0.0:0.0:1.0:0.0	.	.	.	.	X	979;978	.	ENSP00000346236:E978X	E	+	1	0	DDX46	134182551	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.799000	0.99117	2.688000	0.91661	0.655000	0.94253	GAA		0.418	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		T	134154652	G	T	134154652	4	4	61	1	0	0	0	0	0	1	0	0	4370	943	33	2	3014	2	DDX46	5	134154652	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7246	134154652	46760608	4090	12075										
TXNDC15	79770	broad.mit.edu	37	chr5	134235320	134235320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattatgtatgctaccattcGaactgagagtattcggtggc	10	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134235320G>A	ENST00000358387.4	+	5	1653	c.1028G>A	c.(1027-1029)cGa>cAa	p.R343Q	TXNDC15_ENST00000546290.1_Missense_Mutation_p.R320Q	NM_024715.3	NP_078991.3	Q96J42	TXD15_HUMAN	thioredoxin domain containing 15	343					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.R343Q(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCTACCATTCGAACTGAGAGT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	5											128	124	126					5																	134235320		2203	4300	6503	134263219	SO:0001583	missense	79770			AK026278	CCDS4180.1	5q31.1	2008-02-05	2007-08-16	2007-08-16	ENSG00000113621	ENSG00000113621			20652	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 14"	C5orf14			Standard	NM_024715		Approved	2310047H23Rik, FLJ22625	uc003lac.1	Q96J42	OTTHUMG00000129115	ENST00000358387.4:c.1028G>A	5.37:g.134235320G>A	ENSP00000351157:p.Arg343Gln		134263219	D3DQA9|Q96MT2|Q9H639	Missense_Mutation	SNP	ENST00000358387.4	37	CCDS4180.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.97|18.97	3.735373|3.735373	0.69189|0.69189	.|.	.|.	ENSG00000113621|ENSG00000113621	ENST00000508779|ENST00000441965;ENST00000358387;ENST00000546290	.|T;T	.|0.53206	.|0.63;0.64	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.062950	.|0.64402	.|D	.|0.000004	T|T	0.31009|0.31009	0.0783|0.0783	N|N	0.17082|0.17082	0.46|0.46	0.54753|0.54753	D|D	0.999986|0.999986	.|D	.|0.57257	.|0.979	.|B	.|0.40410	.|0.328	T|T	0.06661|0.06661	-1.0814|-1.0814	5|10	.|0.31617	.|T	.|0.26	-20.0855|-20.0855	13.1886|13.1886	0.59697|0.59697	0.0724:0.0:0.9276:0.0|0.0724:0.0:0.9276:0.0	.|.	.|343	.|Q96J42	.|TXD15_HUMAN	K|Q	327|327;343;320	.|ENSP00000351157:R343Q;ENSP00000443942:R320Q	.|ENSP00000351157:R343Q	E|R	+|+	1|2	0|0	TXNDC15|TXNDC15	134263219|134263219	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.089000|5.089000	0.64492|0.64492	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.393	TXNDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251160.1	NM_024715		A	134235320	G	A	134235320	3	1	61	1	0	0	0	0	1	0	0	0	16834	1058	37	1	1046	1	TXNDC15	5	134235320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80668	134235320	46679940	4091	12076										
H2AFY	9555	broad.mit.edu	37	chr5	134686525	134686525	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattacctacttcaccacCgatgtagaagtcagtgtttg	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134686525C>T	ENST00000511689.1	-	6	1282				H2AFY_ENST00000312469.4_Missense_Mutation_p.G223S|H2AFY_ENST00000423969.2_Intron|CTC-349C3.1_ENST00000554670.1_3'UTR|H2AFY_ENST00000304332.4_Intron|H2AFY_ENST00000510038.1_Intron|H2AFY_ENST00000512507.1_Intron	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y						chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)	p.G223S(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTTCACCACCGATGTAGAAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	104	114					5																	134686525		2203	4300	6503	134714424	SO:0001627	intron_variant	9555			AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.688+2110G>A	5.37:g.134686525C>T			134714424	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Missense_Mutation	SNP	ENST00000511689.1	37	CCDS4185.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801327	0.70567	.	.	ENSG00000113648	ENST00000312469	T	0.32988	1.43	6.05	6.05	0.98169	.	.	.	.	.	T	0.27419	0.0673	.	.	.	0.80722	D	1	P	0.42908	0.793	B	0.39531	0.302	T	0.01688	-1.1295	8	0.16420	T	0.52	.	20.6013	0.99457	0.0:1.0:0.0:0.0	.	223	O75367-2	.	S	223	ENSP00000310169:G223S	ENSP00000310169:G223S	G	-	1	0	H2AFY	134714424	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.709000	0.84645	2.878000	0.98634	0.650000	0.86243	GGT		0.512	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		T	134686525	C	T	134686525	1	4	61	0	1	0	0	0	0	0	0	0	6950	652	23	1		1	H2AFY	5	134686525	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	451205	134686525	46228735	4092	12077										
H2AFY	9555	broad.mit.edu	37	chr5	134724685	134724685	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtacttggggtggcctttCttgatgtaccgcagcatccg	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134724685C>A	ENST00000511689.1	-	2	692	c.99G>T	c.(97-99)aaG>aaT	p.K33N	H2AFY_ENST00000312469.4_Missense_Mutation_p.K33N|H2AFY_ENST00000423969.2_Missense_Mutation_p.K33N|H2AFY_ENST00000304332.4_Missense_Mutation_p.K33N|H2AFY_ENST00000510038.1_Missense_Mutation_p.K33N	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	33	Histone H2A.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)	p.K33N(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGTGGCCTTTCTTGATGTACC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											114	96	102					5																	134724685		2203	4300	6503	134752584	SO:0001583	missense	9555			AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.99G>T	5.37:g.134724685C>A	ENSP00000423563:p.Lys33Asn		134752584	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Missense_Mutation	SNP	ENST00000511689.1	37	CCDS4185.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.014681	0.93404	.	.	ENSG00000113648	ENST00000511689;ENST00000304332;ENST00000312469;ENST00000423969;ENST00000510038	T;T;T;D;T	0.89746	-0.4;-0.4;-0.4;-2.56;-0.4	5.11	5.11	0.69529	Histone-fold (2);Histone core (1);Histone H2A (2);	0.049495	0.85682	D	0.000000	D	0.96793	0.8953	H	0.99130	4.44	0.80722	D	1	B;P;P;D	0.60160	0.379;0.933;0.873;0.987	B;P;P;P	0.60012	0.247;0.544;0.544;0.867	D	0.98476	1.0603	10	0.87932	D	0	.	18.7267	0.91716	0.0:1.0:0.0:0.0	.	33;33;33;33	B4DJC3;O75367-3;O75367-2;O75367	.;.;.;H2AY_HUMAN	N	33	ENSP00000423563:K33N;ENSP00000302572:K33N;ENSP00000310169:K33N;ENSP00000415121:K33N;ENSP00000424971:K33N	ENSP00000302572:K33N	K	-	3	2	H2AFY	134752584	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.877000	0.56123	2.665000	0.90641	0.573000	0.79308	AAG		0.587	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		A	134724685	C	A	134724685	3	1	61	1	0	0	0	0	1	0	0	0	6950	912	32	2	1146	2	H2AFY	5	134724685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38160	134724685	46190575	4093	12078										
CXCL14	9547	broad.mit.edu	37	chr5	134907551	134907551	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtttttcaccctattcttCgtagaccctggggagaaaaa	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:134907551C>T	ENST00000337225.5	-	4	792	c.328G>A	c.(328-330)Gaa>Aaa	p.E110K	CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.E98K	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	110					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inner ear development (GO:0048839)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	chemokine activity (GO:0008009)	p.E110K(1)		large_intestine(2)|lung(2)|prostate(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCCTATTCTTCGTAGACCCTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											61	61	61					5																	134907551		2203	4300	6503	134935450	SO:0001583	missense	9547			AF073957	CCDS4188.1	5q31	2010-04-30	2002-08-22	2002-08-23	ENSG00000145824	ENSG00000145824			10640	protein-coding gene	gene with protein product	"breast and kidney"	604186	"small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK)"	SCYB14		10049774	Standard	NM_004887		Approved	BRAK, NJAC, bolekine, Kec, MIP-2g, BMAC, KS1	uc003lay.3	O95715	OTTHUMG00000129139	ENST00000337225.5:c.328G>A	5.37:g.134907551C>T	ENSP00000337065:p.Glu110Lys		134935450	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	ENST00000337225.5	37	CCDS4188.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.712158	0.68730	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	.	.	.	4.64	4.64	0.57946	.	0.065374	0.64402	D	0.000012	T	0.64283	0.2584	L	0.29908	0.895	0.58432	D	0.999994	D	0.76494	0.999	D	0.68621	0.959	T	0.67643	-0.5618	9	0.72032	D	0.01	-2.2703	14.7191	0.69291	0.0:1.0:0.0:0.0	.	110	O95715	CXL14_HUMAN	K	110;98	.	ENSP00000337065:E110K	E	-	1	0	CXCL14	134935450	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.622000	0.61240	2.563000	0.86464	0.655000	0.94253	GAA		0.428	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004887		T	134907551	C	T	134907551	3	4	61	1	0	0	0	0	1	0	0	0	4088	893	31	1	11	1	CXCL14	5	134907551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	182866	134907551	46007709	4094	12079										
LOC153328	153328	broad.mit.edu	37	chr5	135188504	135188504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgcagacacaaccgtttCgggacggtaagaggccaggg	15	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135188504C>T	ENST00000420621.1	+	4	587	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W	SLC25A48_ENST00000274513.5_Missense_Mutation_p.R139W|SLC25A48_ENST00000425402.1_Intron|SLC25A48_ENST00000412661.2_Missense_Mutation_p.R139W|SLC25A48_ENST00000433282.2_Missense_Mutation_p.R85W			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	139					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.R139W(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						ACAACCGTTTCGGGACGGTAA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	5											24	27	26					5																	135188504		1973	4149	6122	135216403	SO:0001583	missense	153328				CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.415C>T	5.37:g.135188504C>T	ENSP00000407973:p.Arg139Trp		135216403	Q8TAV9	Missense_Mutation	SNP	ENST00000420621.1	37		.	.	.	.	.	.	.	.	.	.	C	16.98	3.271608	0.59649	.	.	ENSG00000145832	ENST00000274513;ENST00000420621;ENST00000433282;ENST00000412661	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	5.08	5.08	0.68730	.	1.383300	0.04904	N	0.451766	T	0.82217	0.4989	L	0.38838	1.175	0.25951	N	0.982743	D;D	0.69078	0.997;0.997	P;P	0.55785	0.711;0.784	T	0.71879	-0.4459	10	0.72032	D	0.01	-16.6873	14.3307	0.66553	0.1578:0.8422:0.0:0.0	.	139;139	Q6ZT89-3;Q6ZT89-2	.;.	W	139;139;85;139	ENSP00000274513:R139W;ENSP00000407973:R139W;ENSP00000399834:R85W;ENSP00000413049:R139W	ENSP00000274513:R139W	R	+	1	2	SLC25A48	135216403	0.497000	0.26067	0.961000	0.40146	0.466000	0.32739	1.155000	0.31700	2.359000	0.80004	0.462000	0.41574	CGG		0.592	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		T	135188504	C	T	135188504	3	4	61	1	0	0	0	0	1	0	0	0	8897	875	31	1	429	1	LOC153328	5	135188504	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280953	135188504	45726756	4095	12080										
IL9	3578	broad.mit.edu	37	chr5	135228163	135228163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtcagcgcgttgcctgCcgtggtttggttgcatggct	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135228163C>T	ENST00000274520.1	-	5	362	c.352G>A	c.(352-354)Gca>Aca	p.A118T		NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	118					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)		p.A118T(1)		large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCGTTGCCTGCCGTGGTTTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											74	81	79					5																	135228163		2203	4300	6503	135256062	SO:0001583	missense	3578			S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"Interleukins and interleukin receptors"	6029	protein-coding gene	gene with protein product	"p40 T-cell and mast cell growth factor", "T-cell growth factor p40", "p40 cytokine", "homolog of mouse T cell and mast cell growth factor 40"	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.352G>A	5.37:g.135228163C>T	ENSP00000274520:p.Ala118Thr		135256062		Missense_Mutation	SNP	ENST00000274520.1	37	CCDS4189.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.303382	0.40795	.	.	ENSG00000145839	ENST00000274520	T	0.49432	0.78	5.48	-0.814	0.10846	.	0.978844	0.08359	N	0.958021	T	0.27663	0.0680	N	0.19112	0.55	0.09310	N	1	B	0.17465	0.022	B	0.15052	0.012	T	0.20706	-1.0267	10	0.27082	T	0.32	0.0468	4.786	0.13225	0.0:0.4336:0.1647:0.4017	.	118	P15248	IL9_HUMAN	T	118	ENSP00000274520:A118T	ENSP00000274520:A118T	A	-	1	0	IL9	135256062	0.000000	0.05858	0.002000	0.10522	0.092000	0.18411	-0.986000	0.03747	-0.062000	0.13088	0.655000	0.94253	GCA		0.428	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590		T	135228163	C	T	135228163	3	4	61	1	0	0	0	0	1	0	0	0	7728	739	26	3	86	3	IL9	5	135228163	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39659	135228163	45687097	4096	12081										
FBXL21	3950	broad.mit.edu	37	chr5	135272512	135272512	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggtggaatgaagtttttCatatttctgacctttggaga	12	4	2	3	rs141254114	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135272512C>A	ENST00000522943.1	-	4	418				LECT2_ENST00000471827.1_5'Flank|FBXL21_ENST00000297158.9_RNA|FBXL21_ENST00000467490.1_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.H77N(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGAAGTTTTTCATATTTCTGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	122	124					5																	135272512		1864	4098	5962	135300411	SO:0001627	intron_variant	26223			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000522943.1:c.290-14389G>T	5.37:g.135272512C>A			135300411	B2RA90|O14565|Q52M49	Missense_Mutation	SNP	ENST00000522943.1	37																																																																																					0.378	LECT2-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000381629.1	NM_002302		A	135272512	C	A	135272512	1	1	61	0	1	0	0	0	0	0	0	0	5737	826	29	2		2	FBXL21	5	135272512	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44349	135272512	45642748	4097	12082										
FBXL21	3950	broad.mit.edu	37	chr5	135276280	135276280	+	5'UTR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatccttcattgaagattCttgtggccaataatagtgac	8	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135276280C>A	ENST00000471827.1	-	0	481				FBXL21_ENST00000297158.9_RNA|LECT2_ENST00000522943.1_Intron|FBXL21_ENST00000467490.1_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.L40I(1)|p.L198I(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATTGAAGATTCTTGTGGCCAA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	5											100	99	99					5																	135276280		1869	4105	5974	135304179	SO:0001623	5_prime_UTR_variant	26223			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000471827.1:c.-331G>T	5.37:g.135276280C>A			135304179	B2RA90|O14565|Q52M49	Missense_Mutation	SNP	ENST00000471827.1	37																																																																																					0.343	LECT2-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000342497.1	NM_002302		A	135276280	C	A	135276280	1	1	61	0	1	0	0	0	0	0	0	0	5737	913	32	2		2	FBXL21	5	135276280	5'UTR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3768	135276280	45638980	4098	12083										
FBXL21	3950	broad.mit.edu	37	chr5	135276992	135276992	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgagacgttcttcaaagaaGaaacccctgttactcacctt	6	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135276992G>A	ENST00000522943.1	-	3	418				LECT2_ENST00000471827.1_Intron|FBXL21_ENST00000297158.9_RNA|FBXL21_ENST00000467490.1_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.E313K(1)|p.E155K(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTTCAAAGAAGAAACCCCTGT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	5											121	117	118					5																	135276992		1865	4097	5962	135304891	SO:0001627	intron_variant	26223			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000522943.1:c.289+9919C>T	5.37:g.135276992G>A			135304891	B2RA90|O14565|Q52M49	Missense_Mutation	SNP	ENST00000522943.1	37																																																																																					0.408	LECT2-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000381629.1	NM_002302		A	135276992	G	A	135276992	1	1	61	0	1	0	0	0	0	0	0	0	5737	943	33	3		3	FBXL21	5	135276992	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	712	135276992	45638268	4099	12084										
LECT2	3950	broad.mit.edu	37	chr5	135286985	135286985	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcctggcccacaatcatTccagtgaatggtgcgtacac	8	13	2	1	rs201408239		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135286985T>C	ENST00000274507.1	-	3	416	c.216A>G	c.(214-216)ggA>ggG	p.G72G	LECT2_ENST00000514447.2_Silent_p.G72G|LECT2_ENST00000512872.1_5'UTR|LECT2_ENST00000471827.1_5'UTR|LECT2_ENST00000522943.1_Silent_p.G72G|FBXL21_ENST00000467490.1_RNA	NM_002302.2	NP_002293.2	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2	72					chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.G72G(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCACAATCATTCCAGTGAATG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	5											138	126	130					5																	135286985		2203	4300	6503	135314884	SO:0001819	synonymous_variant	3950			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000274507.1:c.216A>G	5.37:g.135286985T>C			135314884	B2RA90|O14565|Q52M49	Silent	SNP	ENST00000274507.1	37	CCDS4190.1																																																																																				0.458	LECT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251209.1	NM_002302		C	135286985	T	C	135286985	2	2	61	1	0	0	0	0	0	0	0	1	8735	1770	62	4		4	LECT2	5	135286985	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9993	135286985	45628275	4100	12085										
SMAD5	4090	broad.mit.edu	37	chr5	135489526	135489526	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctggaaacaaggtgatgAggaggagaaatgggcagaaa	18	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135489526A>G	ENST00000545279.1	+	3	437	c.77A>G	c.(76-78)gAg>gGg	p.E26G	SMAD5_ENST00000545620.1_Missense_Mutation_p.E26G|SMAD5_ENST00000514641.2_3'UTR	NM_001001419.1|NM_005903.5	NP_001001419.1|NP_005894.3	Q99717	SMAD5_HUMAN	SMAD family member 5	26	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle contraction (GO:0060048)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|embryonic pattern specification (GO:0009880)|erythrocyte differentiation (GO:0030218)|germ cell development (GO:0007281)|intracellular signal transduction (GO:0035556)|Mullerian duct regression (GO:0001880)|osteoblast fate commitment (GO:0002051)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin protein ligase binding (GO:0031625)	p.E26G(1)		central_nervous_system(1)|large_intestine(4)|lung(3)	8			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAAGGTGATGAGGAGGAGAAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	90	89					5																	135489526		2099	4269	6368	135517425	SO:0001583	missense	4090			U59913	CCDS75308.1	5q31	2008-02-05	2006-11-06	2004-05-26		ENSG00000113658		"SMADs"	6771	protein-coding gene	gene with protein product		603110	"MAD, mothers against decapentaplegic homolog 5 (Drosophila)", "SMAD, mothers against DPP homolog 5 (Drosophila)"	MADH5		8673135	Standard	NM_005903		Approved	Dwfc, JV5-1	uc003lbl.1	Q99717		ENST00000545279.1:c.77A>G	5.37:g.135489526A>G	ENSP00000441954:p.Glu26Gly		135517425	O14688|Q15798|Q9UQA1	Missense_Mutation	SNP	ENST00000545279.1	37		.	.	.	.	.	.	.	.	.	.	A	24.2	4.501851	0.85176	.	.	ENSG00000113658	ENST00000507118;ENST00000511116;ENST00000545279;ENST00000545620;ENST00000506223	T;T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64;-0.64	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.83899	0.5354	M	0.76727	2.345	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.84754	0.0758	10	0.52906	T	0.07	.	16.3594	0.83251	1.0:0.0:0.0:0.0	.	26	F5GWU7	.	G	26	ENSP00000425749:E26G;ENSP00000424279:E26G;ENSP00000441954:E26G;ENSP00000446474:E26G;ENSP00000422954:E26G	ENSP00000422954:E26G	E	+	2	0	SMAD5	135517425	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.233000	0.95337	2.266000	0.75297	0.455000	0.32223	GAG		0.448	SMAD5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005903		G	135489526	A	G	135489526	3	3	61	1	0	0	0	0	1	0	0	0	14798	304	11	4	79	4	SMAD5	5	135489526	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	202541	135489526	45425734	4101	12086										
TRPC7	57113	broad.mit.edu	37	chr5	135602072	135602072	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccaagaagattgtaaaaGaaactgcatgagctacaaac	7	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135602072G>T	ENST00000513104.1	-	5	1463	c.1181C>A	c.(1180-1182)tCt>tAt	p.S394Y	TRPC7_ENST00000355180.3_Missense_Mutation_p.S333Y|TRPC7_ENST00000426057.2_Missense_Mutation_p.S278Y	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	394					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S394Y(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GATTGTAAAAGAAACTGCATG	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	5											108	100	102					5																	135602072		1835	4102	5937	135629971	SO:0001583	missense	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.1181C>A	5.37:g.135602072G>T	ENSP00000426070:p.Ser394Tyr		135629971	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	37	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.0|26.0	4.692030|4.692030	0.88735|0.88735	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753|ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	.|T;T;T	.|0.69175	.|0.29;-0.38;0.29	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.86855|0.86855	0.6033|0.6033	M|M	0.94021|0.94021	3.485|3.485	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D;D;D	.|0.89917	.|1.0;0.994;0.998;0.998	.|D;D;D;D	.|0.77557	.|0.99;0.987;0.97;0.952	D|D	0.89943|0.89943	0.4074|0.4074	5|10	.|0.87932	.|D	.|0	-10.072|-10.072	18.9943|18.9943	0.92806|0.92806	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|278;333;339;394	.|Q8IWP7;F5H5U9;Q70T25;Q9HCX4	.|.;.;.;TRPC7_HUMAN	L|Y	277;332;338|333;278;394;394	.|ENSP00000347312:S333Y;ENSP00000441628:S278Y;ENSP00000426070:S394Y	.|ENSP00000265193:S394Y	F|S	-|-	3|2	2|0	TRPC7|TRPC7	135629971|135629971	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.595000|9.595000	0.98260|0.98260	2.706000|2.706000	0.92434|0.92434	0.563000|0.563000	0.77884|0.77884	TTC|TCT		0.408	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		T	135602072	G	T	135602072	3	4	61	1	0	0	0	0	1	0	0	0	16624	942	33	2	1439	2	TRPC7	5	135602072	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112546	135602072	45313188	4102	12087										
TRPC7	57113	broad.mit.edu	37	chr5	135651448	135651448	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatccttgcattgcataGataacttcctgtaatcgttc	5	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:135651448G>T	ENST00000513104.1	-	3	1082	c.800C>A	c.(799-801)tCt>tAt	p.S267Y	TRPC7_ENST00000355180.3_Intron|TRPC7-AS2_ENST00000513958.1_RNA|TRPC7_ENST00000426057.2_Intron	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	267					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S267Y(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCATTGCATAGATAACTTCCT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	5											66	68	67					5																	135651448		2069	4228	6297	135679347	SO:0001583	missense	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.800C>A	5.37:g.135651448G>T	ENSP00000426070:p.Ser267Tyr		135679347	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	37	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.854030	0.91355	.	.	ENSG00000069018	ENST00000513104;ENST00000265193	T	0.63913	-0.07	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.83220	0.5207	M	0.88310	2.945	0.80722	D	1	D;P	0.69078	0.997;0.834	D;P	0.72075	0.976;0.784	D	0.85275	0.1058	10	0.87932	D	0	-13.7371	19.8946	0.96949	0.0:0.0:1.0:0.0	.	267;267	Q70T25;Q9HCX4	.;TRPC7_HUMAN	Y	267	ENSP00000426070:S267Y	ENSP00000265193:S267Y	S	-	2	0	TRPC7	135679347	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.937000	0.99478	0.650000	0.86243	TCT		0.483	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		T	135651448	G	T	135651448	3	4	61	1	0	0	0	0	1	0	0	0	16624	942	33	2	1828	2	TRPC7	5	135651448	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49376	135651448	45263812	4103	12088										
SPOCK1	6695	broad.mit.edu	37	chr5	136448205	136448205	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttgcacttgaccaaattCgaaggtccaacccagtgttt	9	11	0	1	rs144155642	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:136448205C>T	ENST00000394945.1	-	5	562	c.393G>A	c.(391-393)tcG>tcA	p.S131S	SPOCK1_ENST00000282223.7_Silent_p.S131S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	131	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S131S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGACCAAATTCGAAGGTCCAA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	102	98	99		393	-0.2	0.7	5	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SPOCK1	NM_004598.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		131/440	136448205	2,13004	2203	4300	6503	136476104	SO:0001819	synonymous_variant	6695			AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.393G>A	5.37:g.136448205C>T			136476104	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	37	CCDS4191.1																																																																																				0.493	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		T	136448205	C	T	136448205	2	4	61	1	0	0	0	0	0	0	0	1	15118	871	31	1		1	SPOCK1	5	136448205	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	796757	136448205	44467055	4104	12089										
KLHL3	26249	broad.mit.edu	37	chr5	136997685	136997685	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctctaaacgggtttctttCtcataattgatccatgagat	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:136997685C>A	ENST00000309755.4	-	7	1115	c.672G>T	c.(670-672)gaG>gaT	p.E224D	KLHL3_ENST00000541417.1_Missense_Mutation_p.E104D|KLHL3_ENST00000394937.3_Missense_Mutation_p.E224D|KLHL3_ENST00000508657.1_Missense_Mutation_p.E192D|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000506491.1_Missense_Mutation_p.E142D	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	224	BACK.				distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.E224D(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		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)		GGGTTTCTTTCTCATAATTGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											134	115	121					5																	136997685		2203	4300	6503	137025584	SO:0001583	missense	26249			AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.672G>T	5.37:g.136997685C>A	ENSP00000312397:p.Glu224Asp		137025584	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Missense_Mutation	SNP	ENST00000309755.4	37	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	5.273	0.235831	0.10023	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755;ENST00000541417;ENST00000505853;ENST00000394937	T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	4.99	4.12	0.48240	BTB/Kelch-associated (2);	0.107097	0.64402	D	0.000006	T	0.13457	0.0326	N	0.00021	-2.745	0.49051	D	0.999742	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.17979	0.004;0.004;0.02	T	0.41645	-0.9497	10	0.02654	T	1	.	6.7885	0.23687	0.0:0.6983:0.1466:0.1551	.	184;224;224	D6RH21;Q9UH77;Q8N4I8	.;KLHL3_HUMAN;.	D	142;192;224;104;184;224	ENSP00000424828:E142D;ENSP00000422099:E192D;ENSP00000312397:E224D;ENSP00000440319:E104D;ENSP00000426173:E184D;ENSP00000378395:E224D	ENSP00000312397:E224D	E	-	3	2	KLHL3	137025584	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.342000	0.33919	1.472000	0.48140	0.655000	0.94253	GAG		0.418	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			A	136997685	C	A	136997685	3	1	61	1	0	0	0	0	1	0	0	0	8404	912	32	2	1127	2	KLHL3	5	136997685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	549480	136997685	43917575	4105	12090										
MYOT	9499	broad.mit.edu	37	chr5	137206353	137206353	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactaagcatgtttaactacGaacgtccaaaacacttcatc	4	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137206353G>A	ENST00000239926.4	+	2	387	c.13G>A	c.(13-15)Gaa>Aaa	p.E5K	RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000509812.1_Intron|MYOT_ENST00000421631.2_Intron|MYOT_ENST00000515645.1_Intron	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	5					muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.E5K(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GTTTAACTACGAACGTCCAAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											125	135	132					5																	137206353		2203	4300	6503	137234252	SO:0001583	missense	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.13G>A	5.37:g.137206353G>A	ENSP00000239926:p.Glu5Lys		137234252	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776207	0.90195	.	.	ENSG00000120729	ENST00000239926	T	0.70749	-0.51	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000012	T	0.79822	0.4512	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.79962	-0.1582	10	0.52906	T	0.07	.	17.5608	0.87906	0.0:0.0:1.0:0.0	.	5	Q9UBF9	MYOTI_HUMAN	K	5	ENSP00000239926:E5K	ENSP00000239926:E5K	E	+	1	0	MYOT	137234252	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.066000	0.64351	2.582000	0.87167	0.650000	0.86243	GAA		0.468	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		A	137206353	G	A	137206353	3	1	61	1	0	0	0	0	1	0	0	0	10124	1059	37	1	15	1	MYOT	5	137206353	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208668	137206353	43708907	4106	12091										
MYOT	9499	broad.mit.edu	37	chr5	137206519	137206519	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctcctcaacactgagctCtcacatcaccatgtcctcct	4	18	3	1	rs121908458		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137206519C>T	ENST00000239926.4	+	2	553	c.179C>T	c.(178-180)tCt>tTt	p.S60F	RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000509812.1_Intron|MYOT_ENST00000421631.2_Intron|MYOT_ENST00000515645.1_Intron	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	60			S -> C (in MFM3). {ECO:0000269|PubMed:15111675}.|S -> F (in MFM3). {ECO:0000269|PubMed:15111675}.		muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.S60F(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ACACTGAGCTCTCACATCACC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5	GRCh37	CM041092|CM041093	MYOT	M	rs121908458	C	,PHE/SER	0,4406		0,0,2203	143	128	133	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,179	6	1	5	dbSNP_133	133	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	MYOT	NM_001135940.1,NM_006790.2	,155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging	,60/499	137206519	1,13005	2203	4300	6503	137234418	SO:0001583	missense	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.179C>T	5.37:g.137206519C>T	ENSP00000239926:p.Ser60Phe		137234418	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629351	0.67015	0.0	1.16E-4	ENSG00000120729	ENST00000239926	T	0.70749	-0.51	6.02	6.02	0.97574	.	0.093220	0.46758	D	0.000266	T	0.65048	0.2654	N	0.24115	0.695	0.80722	D	1	P	0.52061	0.95	P	0.46320	0.512	T	0.65166	-0.6234	10	0.40728	T	0.16	.	18.7178	0.91682	0.0:1.0:0.0:0.0	.	60	Q9UBF9	MYOTI_HUMAN	F	60	ENSP00000239926:S60F	ENSP00000239926:S60F	S	+	2	0	MYOT	137234418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.360000	0.66086	2.857000	0.98124	0.650000	0.86243	TCT		0.527	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		T	137206519	C	T	137206519	3	4	61	1	0	0	0	0	1	0	0	0	10124	913	32	3	181	3	MYOT	5	137206519	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166	137206519	43708741	4107	12092										
MYOT	9499	broad.mit.edu	37	chr5	137217717	137217717	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgcaatccaggagaaaTtttacccaccacgtttcatt	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137217717T>G	ENST00000239926.4	+	6	1113	c.739T>G	c.(739-741)Ttt>Gtt	p.F247V	RP11-381K20.2_ENST00000508281.2_RNA|RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000509812.1_Intron|MYOT_ENST00000421631.2_Missense_Mutation_p.F63V|MYOT_ENST00000515645.1_Missense_Mutation_p.F132V	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	247	Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.F247V(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CCAGGAGAAATTTTACCCACC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											114	113	113					5																	137217717		2203	4300	6503	137245616	SO:0001583	missense	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.739T>G	5.37:g.137217717T>G	ENSP00000239926:p.Phe247Val		137245616	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.997170	0.74818	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.68479	-0.29;-0.21;-0.33	5.65	4.46	0.54185	.	0.160787	0.44483	D	0.000460	T	0.53367	0.1792	N	0.24115	0.695	0.40751	D	0.98291	P	0.52842	0.956	P	0.45071	0.468	T	0.48468	-0.9033	10	0.17832	T	0.49	.	12.764	0.57380	0.0:0.0:0.1372:0.8628	.	247	Q9UBF9	MYOTI_HUMAN	V	247;63;132	ENSP00000239926:F247V;ENSP00000391185:F63V;ENSP00000426281:F132V	ENSP00000239926:F247V	F	+	1	0	MYOT	137245616	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.952000	0.70282	0.940000	0.37473	0.383000	0.25322	TTT		0.383	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		G	137217717	T	G	137217717	3	3	61	1	0	0	0	0	1	0	0	0	10124	1493	52	4	757	4	MYOT	5	137217717	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11198	137217717	43697543	4108	12093										
MYOT	9499	broad.mit.edu	37	chr5	137222999	137222999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaaggtttgaatgtaaaAcaagcttttaacccagaagg	11	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137222999A>G	ENST00000239926.4	+	10	1796	c.1422A>G	c.(1420-1422)aaA>aaG	p.K474K	RP11-381K20.2_ENST00000508281.2_RNA|RP11-381K20.2_ENST00000514616.1_RNA|PKD2L2_ENST00000290431.5_5'Flank|PKD2L2_ENST00000350250.4_5'Flank|PKD2L2_ENST00000502810.1_5'Flank|PKD2L2_ENST00000508883.1_5'Flank|MYOT_ENST00000421631.2_Silent_p.K290K|MYOT_ENST00000515645.1_Silent_p.K359K|PKD2L2_ENST00000508638.1_5'Flank	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	474	Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.K474K(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGAATGTAAAACAAGCTTTTA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	5											82	84	84					5																	137222999		2203	4300	6503	137250898	SO:0001819	synonymous_variant	9499			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.1422A>G	5.37:g.137222999A>G			137250898	A0A4R6|B4DT79	Silent	SNP	ENST00000239926.4	37	CCDS4194.1																																																																																				0.398	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		G	137222999	A	G	137222999	2	3	61	1	0	0	0	0	0	0	0	1	10124	40	2	4		4	MYOT	5	137222999	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5282	137222999	43692261	4109	12094										
FAM13B	51306	broad.mit.edu	37	chr5	137275930	137275930	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcttatatggattttgaaGaatcttgtttgcttataaga	7	3	2	3	rs201567292		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137275930G>T	ENST00000033079.3	-	23	3183	c.2732C>A	c.(2731-2733)tCt>tAt	p.S911Y	PKD2L2_ENST00000290431.5_3'UTR|FAM13B_ENST00000425075.2_Missense_Mutation_p.S787Y|FAM13B_ENST00000420893.2_Missense_Mutation_p.S883Y|PKD2L2_ENST00000502810.1_3'UTR|PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000508638.1_3'UTR	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	911					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.S911Y(1)		endometrium(4)|kidney(2)|lung(5)	11						GGATTTTGAAGAATCTTGTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											123	121	121					5																	137275930		2203	4300	6503	137303829	SO:0001583	missense	51306			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2732C>A	5.37:g.137275930G>T	ENSP00000033079:p.Ser911Tyr		137303829	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.842947	0.71488	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.25749	2.88;1.78;2.89	5.37	5.37	0.77165	.	0.058912	0.64402	D	0.000001	T	0.14830	0.0358	N	0.14661	0.345	0.53688	D	0.999973	P;B;B	0.38473	0.633;0.11;0.319	B;B;B	0.31495	0.131;0.016;0.09	T	0.05550	-1.0878	10	0.45353	T	0.12	-8.8573	14.3165	0.66454	0.0:0.0:0.8515:0.1485	.	787;883;911	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	Y	911;787;883	ENSP00000033079:S911Y;ENSP00000394669:S787Y;ENSP00000388521:S883Y	ENSP00000033079:S911Y	S	-	2	0	FAM13B	137303829	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.156000	0.71840	2.679000	0.91253	0.591000	0.81541	TCT		0.358	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			T	137275930	G	T	137275930	3	4	61	1	0	0	0	0	1	0	0	0	5469	942	33	2	19	2	FAM13B	5	137275930	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52931	137275930	43639330	4110	12095										
FAM13B	51306	broad.mit.edu	37	chr5	137342688	137342688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagctattaccttgttgccGtaacactatttgattccagg	8	9	0	2	rs576080082		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137342688G>A	ENST00000033079.3	-	7	1290	c.839C>T	c.(838-840)aCg>aTg	p.T280M	FAM13B_ENST00000425075.2_Missense_Mutation_p.T162M|FAM13B_ENST00000420893.2_Missense_Mutation_p.T280M	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	280					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.T280M(1)		endometrium(4)|kidney(2)|lung(5)	11						CCTTGTTGCCGTAACACTATT	0.368													G|||	1	0.000199681	0	0	5008	,	,		18437	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5											217	193	202					5																	137342688		2203	4300	6503	137370587	SO:0001583	missense	51306			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.839C>T	5.37:g.137342688G>A	ENSP00000033079:p.Thr280Met		137370587	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580044	0.28180	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.23552	3.02;1.9;3.02	5.82	-1.21	0.09524	.	0.856614	0.10735	N	0.640139	T	0.14657	0.0354	N	0.22421	0.69	0.24566	N	0.993945	B;B;B	0.15473	0.013;0.005;0.007	B;B;B	0.11329	0.006;0.004;0.002	T	0.25293	-1.0136	10	0.46703	T	0.11	0.4382	5.8972	0.18945	0.2553:0.0:0.5237:0.221	.	162;280;280	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	M	280;162;280	ENSP00000033079:T280M;ENSP00000394669:T162M;ENSP00000388521:T280M	ENSP00000033079:T280M	T	-	2	0	FAM13B	137370587	1.000000	0.71417	0.979000	0.43373	0.931000	0.56810	1.045000	0.30341	-0.113000	0.11958	-0.198000	0.12761	ACG		0.368	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			A	137342688	G	A	137342688	3	1	61	1	0	0	0	0	1	0	0	0	5469	1145	40	1	2046	1	FAM13B	5	137342688	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66758	137342688	43572572	4111	12096										
FAM13B	51306	broad.mit.edu	37	chr5	137354051	137354051	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataacaggttcaggaagttCttgaagaaaaaatctaagaa	9	4	3	3	rs148088678	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137354051C>A	ENST00000033079.3	-	4	761	c.310G>T	c.(310-312)Gaa>Taa	p.E104*	FAM13B_ENST00000425075.2_5'UTR|FAM13B_ENST00000420893.2_Nonsense_Mutation_p.E104*	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	104	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.E104*(1)		endometrium(4)|kidney(2)|lung(5)	11						TCAGGAAGTTCTTGAAGAAAA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											111	107	108					5																	137354051		2203	4300	6503	137381950	SO:0001587	stop_gained	51306			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.310G>T	5.37:g.137354051C>A	ENSP00000033079:p.Glu104*		137381950	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Nonsense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	38	6.979382	0.97979	.	.	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.3175	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	104	.	ENSP00000033079:E104X	E	-	1	0	FAM13B	137381950	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.440000	0.80464	2.890000	0.99128	0.650000	0.86243	GAA		0.408	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			A	137354051	C	A	137354051	4	1	61	1	0	0	0	0	0	1	0	0	5469	922	32	2	2587	2	FAM13B	5	137354051	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11363	137354051	43561209	4112	12097										
WNT8A	7478	broad.mit.edu	37	chr5	137426419	137426419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagggccactgggtgcccgCtgaggccttccttcctagcg	14	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137426419C>T	ENST00000398754.1	+	6	718	c.713C>T	c.(712-714)gCt>gTt	p.A238V	WNT8A_ENST00000506684.1_Missense_Mutation_p.A256V	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	238					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.A238V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGGGTGCCCGCTGAGGCCTTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											45	50	48					5																	137426419		1948	4147	6095	137454318	SO:0001583	missense	7478			AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"Wingless-type MMTV integration sites"	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.713C>T	5.37:g.137426419C>T	ENSP00000381739:p.Ala238Val		137454318	Q96S51	Missense_Mutation	SNP	ENST00000398754.1	37	CCDS43368.1	.	.	.	.	.	.	.	.	.	.	C	7.169	0.587328	0.13812	.	.	ENSG00000061492	ENST00000506684;ENST00000504809;ENST00000398754	T;T;T	0.76060	-0.99;-0.99;-0.99	4.85	3.02	0.34903	.	0.391843	0.28262	N	0.015999	T	0.57489	0.2057	L	0.35542	1.07	0.09310	N	0.999999	B;B;B	0.18013	0.025;0.011;0.001	B;B;B	0.21360	0.034;0.034;0.01	T	0.36696	-0.9737	10	0.15952	T	0.53	.	6.334	0.21287	0.136:0.6592:0.1315:0.0733	.	256;256;238	D6RF47;D6RF94;Q9H1J5	.;.;WNT8A_HUMAN	V	256;256;238	ENSP00000426653:A256V;ENSP00000424809:A256V;ENSP00000381739:A238V	ENSP00000354726:A238V	A	+	2	0	WNT8A	137454318	0.002000	0.14202	0.002000	0.10522	0.108000	0.19459	1.520000	0.35899	0.609000	0.30018	0.557000	0.71058	GCT		0.547	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244		T	137426419	C	T	137426419	3	4	61	1	0	0	0	0	1	0	0	0	17436	797	28	3	735	3	WNT8A	5	137426419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72368	137426419	43488841	4113	12098										
BRD8	10902	broad.mit.edu	37	chr5	137488401	137488401	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcattgctcaactcagagtCattgggatgatcttgttcag	10	8	6	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137488401C>A	ENST00000254900.5	-	21	2997	c.2626G>T	c.(2626-2628)Gac>Tac	p.D876Y		NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	876					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.D876Y(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AACTCAGAGTCATTGGGATGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											125	124	124					5																	137488401		2203	4300	6503	137516300	SO:0001583	missense	10902			AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.2626G>T	5.37:g.137488401C>A	ENSP00000254900:p.Asp876Tyr		137516300	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801746	0.70682	.	.	ENSG00000112983	ENST00000254900	T	0.35421	1.31	5.39	5.39	0.77823	.	0.217349	0.29572	N	0.011766	T	0.40767	0.1130	L	0.27053	0.805	0.80722	D	1	D	0.59767	0.986	P	0.54499	0.754	T	0.23084	-1.0198	10	0.62326	D	0.03	-0.3705	16.0138	0.80422	0.0:1.0:0.0:0.0	.	876	Q9H0E9	BRD8_HUMAN	Y	876	ENSP00000254900:D876Y	ENSP00000254900:D876Y	D	-	1	0	BRD8	137516300	0.943000	0.32029	1.000000	0.80357	0.935000	0.57460	0.943000	0.29030	2.795000	0.96236	0.655000	0.94253	GAC		0.458	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		A	137488401	C	A	137488401	3	1	61	1	0	0	0	0	1	0	0	0	1509	826	29	2	1109	2	BRD8	5	137488401	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61982	137488401	43426859	4114	12099										
CDC25C	995	broad.mit.edu	37	chr5	137627764	137627764	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcttggcctgttcaagttCtctggcatcgacggggagcg	14	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137627764C>A	ENST00000323760.6	-	8	935	c.657G>T	c.(655-657)gaG>gaT	p.E219D	CDC25C_ENST00000357274.3_Missense_Mutation_p.E176D|CDC25C_ENST00000415130.2_Missense_Mutation_p.E146D|CDC25C_ENST00000514555.1_Missense_Mutation_p.E189D|CDC25C_ENST00000513970.1_Missense_Mutation_p.E219D|CDC25C_ENST00000348983.3_Missense_Mutation_p.E146D|CDC25C_ENST00000356505.3_Missense_Mutation_p.E189D	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	219					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)	p.E219D(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TGTTCAAGTTCTCTGGCATCG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											146	152	150					5																	137627764		2203	4300	6503	137655663	SO:0001583	missense	995			M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"Protein tyrosine phosphatases / Class III Cys-based PTPs", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1727	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 60"	157680	"cell division cycle 25C", "cell division cycle 25 homolog C (S. cerevisiae)", "cell division cycle 25 homolog C (S. pombe)"	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.657G>T	5.37:g.137627764C>A	ENSP00000321656:p.Glu219Asp		137655663	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.065|5.065	0.197634|0.197634	0.09652|0.09652	.|.	.|.	ENSG00000158402|ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022|ENST00000514017	T;T;T;T;T;T;T;T|.	0.23950|.	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88|.	3.09|3.09	2.22|2.22	0.28083|0.28083	.|.	1.118840|1.118840	0.06726|0.06726	N|N	0.775842|0.775842	T|.	0.23330|.	0.0564|.	N|N	0.12746|0.12746	0.255|0.255	0.26961|0.26961	N|N	0.965807|0.965807	B;B;B;B|.	0.17465|.	0.0;0.0;0.022;0.0|.	B;B;B;B|.	0.15052|.	0.001;0.001;0.012;0.001|.	T|.	0.06144|.	-1.0843|.	10|.	0.13108|0.06236	T|T	0.6|0.91	-7.948|-7.948	11.4698|11.4698	0.50261|0.50261	0.0:0.7983:0.2017:0.0|0.0:0.7983:0.2017:0.0	.|.	236;189;146;219|.	G3V1P6;P30307-2;P30307-4;P30307|.	.;.;.;MPIP3_HUMAN|.	D|X	219;189;176;146;146;219;236;189;219|14	ENSP00000321656:E219D;ENSP00000348898:E189D;ENSP00000349821:E176D;ENSP00000345205:E146D;ENSP00000392631:E146D;ENSP00000424795:E219D;ENSP00000425470:E189D;ENSP00000427251:E219D|.	ENSP00000321656:E219D|ENSP00000423525:E14X	E|E	-|-	3|1	2|0	CDC25C|CDC25C	137655663|137655663	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.461000|0.461000	0.32589|0.32589	1.322000|1.322000	0.33689|0.33689	0.851000|0.851000	0.35264|0.35264	0.557000|0.557000	0.71058|0.71058	GAG|GAA		0.448	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			A	137627764	C	A	137627764	3	1	61	1	0	0	0	0	1	0	0	0	3070	912	32	2	792	2	CDC25C	5	137627764	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139363	137627764	43287496	4115	12100										
FAM53C	51307	broad.mit.edu	37	chr5	137680523	137680523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccttccagaaggtgcttCctggaggggcctgccccact	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137680523C>T	ENST00000239906.5	+	4	574	c.146C>T	c.(145-147)tCc>tTc	p.S49F	RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000507506.1_3'UTR|FAM53C_ENST00000513056.1_Intron|FAM53C_ENST00000434981.2_Missense_Mutation_p.S49F	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	49								p.S49F(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GAAGGTGCTTCCTGGAGGGGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											47	50	49					5																	137680523		2203	4300	6503	137708422	SO:0001583	missense	51307			AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"chromosome 5 open reading frame 6"	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.146C>T	5.37:g.137680523C>T	ENSP00000239906:p.Ser49Phe		137708422	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	37	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.263895	0.59431	.	.	ENSG00000120709	ENST00000434981;ENST00000239906;ENST00000511276	T;T;T	0.48201	0.82;0.82;0.82	5.13	5.13	0.70059	.	0.206938	0.40385	N	0.001103	T	0.44329	0.1288	L	0.47716	1.5	0.80722	D	1	P	0.47484	0.896	B	0.39738	0.308	T	0.52616	-0.8552	10	0.87932	D	0	-12.2577	17.5187	0.87781	0.0:1.0:0.0:0.0	.	49	Q9NYF3	FA53C_HUMAN	F	49;49;39	ENSP00000403705:S49F;ENSP00000239906:S49F;ENSP00000427610:S39F	ENSP00000239906:S49F	S	+	2	0	FAM53C	137708422	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.825000	0.55730	2.659000	0.90383	0.563000	0.77884	TCC		0.453	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605		T	137680523	C	T	137680523	3	4	61	1	0	0	0	0	1	0	0	0	5600	855	30	3	156	3	FAM53C	5	137680523	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52759	137680523	43234737	4116	12101										
FAM53C	51307	broad.mit.edu	37	chr5	137681298	137681298	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactttgacaagatgaatcaGgtgggaccagcaagactagg	13	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137681298G>T	ENST00000239906.5	+	4	1349	c.921G>T	c.(919-921)caG>caT	p.Q307H	RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000513056.1_3'UTR|FAM53C_ENST00000434981.2_Splice_Site_p.Q307H	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	307								p.Q307H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AGATGAATCAGGTGGGACCAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											34	40	38					5																	137681298		2197	4283	6480	137709197	SO:0001630	splice_region_variant	51307			AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"chromosome 5 open reading frame 6"	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.921+1G>T	5.37:g.137681298G>T			137709197	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	37	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306271	0.81247	.	.	ENSG00000120709	ENST00000434981;ENST00000239906	T;T	0.55930	0.49;0.49	5.55	5.55	0.83447	.	0.055558	0.64402	N	0.000001	T	0.73705	0.3621	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74839	-0.3528	10	0.66056	D	0.02	-9.2544	18.4386	0.90656	0.0:0.0:1.0:0.0	.	307	Q9NYF3	FA53C_HUMAN	H	307	ENSP00000403705:Q307H;ENSP00000239906:Q307H	ENSP00000239906:Q307H	Q	+	3	2	FAM53C	137709197	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.117000	0.94347	2.894000	0.99253	0.655000	0.94253	CAG		0.582	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605	Missense_Mutation	T	137681298	G	T	137681298	5	4	61	1	0	0	0	0	0	0	1	0	5600	1014	35	2	931	2	FAM53C	5	137681298	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	775	137681298	43233962	4117	12102										
KDM3B	51780	broad.mit.edu	37	chr5	137726930	137726930	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcccaaactttacctaccAgtaactacttcactactgtt	3	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137726930A>C	ENST00000314358.5	+	8	1809	c.1609A>C	c.(1609-1611)Agt>Cgt	p.S537R	KDM3B_ENST00000394866.1_Missense_Mutation_p.S193R|KDM3B_ENST00000542866.1_Intron	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	537					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.S537R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						TTTACCTACCAGTAACTACTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											96	99	98					5																	137726930		2203	4300	6503	137754829	SO:0001583	missense	51780			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.1609A>C	5.37:g.137726930A>C	ENSP00000326563:p.Ser537Arg		137754829	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960016	0.53400	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866	T;T	0.42131	0.98;0.98	5.57	5.57	0.84162	.	0.197079	0.56097	D	0.000039	T	0.36771	0.0979	L	0.27053	0.805	0.80722	D	1	B;B	0.26512	0.126;0.151	B;B	0.32533	0.147;0.095	T	0.27365	-1.0076	10	0.72032	D	0.01	-3.302	15.713	0.77646	1.0:0.0:0.0:0.0	.	193;537	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	R	537;327;193	ENSP00000326563:S537R;ENSP00000378335:S193R	ENSP00000326563:S537R	S	+	1	0	KDM3B	137754829	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.307000	0.72815	2.115000	0.64714	0.533000	0.62120	AGT		0.443	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137726930	A	C	137726930	3	2	61	1	0	0	0	0	1	0	0	0	8148	188	7	4	1639	4	KDM3B	5	137726930	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	45632	137726930	43188330	4118	12103										
KDM3B	51780	broad.mit.edu	37	chr5	137766019	137766019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacctggaccagaccctcCgtaagcgactctatgaggag	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137766019C>T	ENST00000314358.5	+	22	5175	c.4975C>T	c.(4975-4977)Cgt>Tgt	p.R1659C	KDM3B_ENST00000394866.1_Missense_Mutation_p.R1315C|KDM3B_ENST00000542866.1_Missense_Mutation_p.R691C	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1659	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.R1659C(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						CCAGACCCTCCGTAAGCGACT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	5											136	127	130					5																	137766019		2203	4300	6503	137793918	SO:0001583	missense	51780			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.4975C>T	5.37:g.137766019C>T	ENSP00000326563:p.Arg1659Cys		137793918	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	C	34	5.361144	0.95877	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.74209	-0.82;-0.82;-0.82	5.71	5.71	0.89125	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.88097	0.6345	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.88967	0.3398	10	0.87932	D	0	-4.8933	19.8446	0.96704	0.0:1.0:0.0:0.0	.	1315;1659	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	C	1659;1449;1315;691	ENSP00000326563:R1659C;ENSP00000378335:R1315C;ENSP00000439462:R691C	ENSP00000326563:R1659C	R	+	1	0	KDM3B	137793918	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.773000	0.62331	2.698000	0.92095	0.655000	0.94253	CGT		0.522	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		T	137766019	C	T	137766019	3	4	61	1	0	0	0	0	1	0	0	0	8148	652	23	1	5061	1	KDM3B	5	137766019	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39089	137766019	43149241	4119	12104										
REEP2	51308	broad.mit.edu	37	chr5	137776743	137776743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacccagcctattcttcctAcaaggccgtgaagacaaaaa	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137776743A>G	ENST00000254901.5	+	2	193	c.71A>G	c.(70-72)tAc>tGc	p.Y24C	REEP2_ENST00000506158.1_5'UTR|REEP2_ENST00000464751.2_3'UTR|REEP2_ENST00000378339.2_Missense_Mutation_p.Y24C	NM_016606.2	NP_057690.2	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	24					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein transport into membrane raft (GO:0032596)|regulation of intracellular transport (GO:0032386)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.Y24C(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TATTCTTCCTACAAGGCCGTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	88	93					5																	137776743		2203	4300	6503	137804642	SO:0001583	missense	51308			AK056193	CCDS4205.1, CCDS64259.1	5q31	2014-03-12	2006-02-07	2006-02-07	ENSG00000132563	ENSG00000132563		"Receptor accessory proteins"	17975	protein-coding gene	gene with protein product		609347	"chromosome 5 open reading frame 19"	C5orf19		16271481, 15550249, 24388663	Standard	NM_016606		Approved	SGC32445, SPG72	uc003lda.4	Q9BRK0	OTTHUMG00000129205	ENST00000254901.5:c.71A>G	5.37:g.137776743A>G	ENSP00000254901:p.Tyr24Cys		137804642	Q53EM8|Q9NYF2	Missense_Mutation	SNP	ENST00000254901.5	37	CCDS4205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.2|27.2	4.814086|4.814086	0.90790|0.90790	.|.	.|.	ENSG00000132563|ENSG00000132563	ENST00000512126|ENST00000378339;ENST00000254901	.|D;D	.|0.93133	.|-3.17;-3.17	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97321|0.97321	0.9124|0.9124	M|M	0.92507|0.92507	3.315|3.315	0.80722|0.80722	D|D	1|1	.|D;D	.|0.69078	.|0.971;0.997	.|D;D	.|0.70016	.|0.916;0.967	D|D	0.98342|0.98342	1.0539|1.0539	5|10	.|0.87932	.|D	.|0	-2.5634|-2.5634	15.5299|15.5299	0.75952|0.75952	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|24;24	.|A8K3D2;Q9BRK0	.|.;REEP2_HUMAN	A|C	62|24	.|ENSP00000367590:Y24C;ENSP00000254901:Y24C	.|ENSP00000254901:Y24C	T|Y	+|+	1|2	0|0	REEP2|REEP2	137804642|137804642	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	8.679000|8.679000	0.91220|0.91220	2.139000|2.139000	0.66308|0.66308	0.459000|0.459000	0.35465|0.35465	ACA|TAC		0.582	REEP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251284.1	NM_016606		G	137776743	A	G	137776743	3	3	61	1	0	0	0	0	1	0	0	0	13242	391	14	4	77	4	REEP2	5	137776743	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10724	137776743	43138517	4120	12105										
ETF1	2107	broad.mit.edu	37	chr5	137847174	137847174	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccgatacctattaatttCttctcttgaatgaatttcac	3	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:137847174C>A	ENST00000360541.5	-	7	1073	c.852G>T	c.(850-852)aaG>aaT	p.K284N	ETF1_ENST00000503014.1_Missense_Mutation_p.K270N|ETF1_ENST00000499810.2_Missense_Mutation_p.K251N	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	284					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)	p.K284N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTATTAATTTCTTCTCTTGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											81	77	78					5																	137847174		2203	4299	6502	137875073	SO:0001583	missense	2107			AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.852G>T	5.37:g.137847174C>A	ENSP00000353741:p.Lys284Asn		137875073	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Missense_Mutation	SNP	ENST00000360541.5	37	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470685	0.84533	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014	.	.	.	5.74	5.74	0.90152	eRF1 domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.88651	0.6494	H	0.98594	4.275	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.998	D	0.92213	0.5778	9	0.87932	D	0	-7.1697	14.1394	0.65311	0.0:0.9261:0.0:0.0739	.	270;251;284	B7Z7P8;Q96CG1;P62495	.;.;ERF1_HUMAN	N	251;284;270	.	ENSP00000353741:K284N	K	-	3	2	ETF1	137875073	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.056000	0.41355	2.715000	0.92844	0.655000	0.94253	AAG		0.358	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		A	137847174	C	A	137847174	3	1	61	1	0	0	0	0	1	0	0	0	5281	912	32	2	481	2	ETF1	5	137847174	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70431	137847174	43068086	4121	12106										
CTNNA1	1495	broad.mit.edu	37	chr5	138117662	138117662	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcaagtgggatcctaaaAgtctagagatcaggactctg	10	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138117662A>C	ENST00000302763.7	+	2	139	c.49A>C	c.(49-51)Agt>Cgt	p.S17R	CTNNA1_ENST00000355078.5_5'UTR|CTNNA1_ENST00000518825.1_Missense_Mutation_p.S17R	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	17	Involved in homodimerization.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)	p.S17R(1)		NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GGATCCTAAAAGTCTAGAGAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	5											85	78	81					5																	138117662		2203	4300	6503	138145561	SO:0001583	missense	1495			D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.49A>C	5.37:g.138117662A>C	ENSP00000304669:p.Ser17Arg		138145561	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.985685	0.53934	.	.	ENSG00000044115	ENST00000517980;ENST00000522227;ENST00000524127;ENST00000523912;ENST00000520339;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518245;ENST00000519113;ENST00000520158;ENST00000518825	T;T;T;T;T;T;T;T;T;T	0.73152	-0.16;-0.17;0.83;-0.72;-0.16;1.6;0.4;-0.14;0.26;1.59	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.69691	0.3139	L	0.45581	1.43	0.80722	D	1	B;P	0.36683	0.02;0.565	B;B	0.41088	0.012;0.347	T	0.70568	-0.4836	10	0.49607	T	0.09	-12.2844	16.0937	0.81106	1.0:0.0:0.0:0.0	.	17;17	G3XAM7;P35221	.;CTNA1_HUMAN	R	17	ENSP00000428439:S17R;ENSP00000429636:S17R;ENSP00000428049:S17R;ENSP00000430304:S17R;ENSP00000428202:S17R;ENSP00000304669:S17R;ENSP00000428457:S17R;ENSP00000430078:S17R;ENSP00000429457:S17R;ENSP00000427821:S17R	ENSP00000304669:S17R	S	+	1	0	CTNNA1	138145561	1.000000	0.71417	1.000000	0.80357	0.191000	0.23601	9.248000	0.95456	2.281000	0.76405	0.528000	0.53228	AGT		0.388	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		C	138117662	A	C	138117662	3	2	61	1	0	0	0	0	1	0	0	0	4018	72	3	4	51	4	CTNNA1	5	138117662	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	270488	138117662	42797598	4122	12107										
LRRTM2	26045	broad.mit.edu	37	chr5	138209445	138209445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtttcaaacactgtcaagtCgatggctttgatttcatttc	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138209445C>A	ENST00000274711.6	-	2	1183	c.805G>T	c.(805-807)Gac>Tac	p.D269Y	LRRTM2_ENST00000523537.1_5'Flank|LRRTM2_ENST00000518785.1_3'UTR|LRRTM2_ENST00000521094.2_Intron|CTNNA1_ENST00000520400.1_Intron|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000540387.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000518825.1_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	269					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.D269Y(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACTGTCAAGTCGATGGCTTTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											286	279	282					5																	138209445		1923	4139	6062	138237344	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.805G>T	5.37:g.138209445C>A	ENSP00000274711:p.Asp269Tyr		138237344	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.624717	0.46840	.	.	ENSG00000146006	ENST00000274711	T	0.04862	3.54	5.48	5.48	0.80851	.	0.195195	0.44688	D	0.000430	T	0.20088	0.0483	M	0.62209	1.925	0.49389	D	0.99978	D;D	0.61697	0.967;0.99	P;P	0.56788	0.806;0.802	T	0.00017	-1.2378	10	0.72032	D	0.01	.	19.1486	0.93479	0.0:1.0:0.0:0.0	.	135;269	B7Z4G4;O43300	.;LRRT2_HUMAN	Y	269	ENSP00000274711:D269Y	ENSP00000274711:D269Y	D	-	1	0	LRRTM2	138237344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.865000	0.69583	2.861000	0.98227	0.650000	0.86243	GAC		0.413	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			A	138209445	C	A	138209445	3	1	61	1	0	0	0	0	1	0	0	0	9069	884	31	2	749	2	LRRTM2	5	138209445	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91783	138209445	42705815	4123	12108										
LRRTM2	26045	broad.mit.edu	37	chr5	138209781	138209781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcaaggtctgcagcttccGaaggccatagaagagctctg	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138209781G>A	ENST00000274711.6	-	2	847	c.469C>T	c.(469-471)Cgg>Tgg	p.R157W	LRRTM2_ENST00000523537.1_5'UTR|LRRTM2_ENST00000518785.1_Missense_Mutation_p.S14L|LRRTM2_ENST00000521094.2_Intron|CTNNA1_ENST00000520400.1_Intron|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000540387.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000518825.1_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	157					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.R157W(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGCAGCTTCCGAAGGCCATAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											46	47	47					5																	138209781		1890	4130	6020	138237680	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.469C>T	5.37:g.138209781G>A	ENSP00000274711:p.Arg157Trp		138237680	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.63|10.63	1.403305|1.403305	0.25291|0.25291	.|.	.|.	ENSG00000146006|ENSG00000146006	ENST00000274711|ENST00000518785	T|.	0.60171|.	0.21|.	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74268|0.74268	0.3694|0.3694	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.996;1.0|.	T|T	0.75402|0.75402	-0.3330|-0.3330	10|6	0.66056|0.87932	D|D	0.02|0	.|.	19.1682|19.1682	0.93565|0.93565	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	23;157|.	B7Z4G4;O43300|.	.;LRRT2_HUMAN|.	W|L	157|14	ENSP00000274711:R157W|.	ENSP00000274711:R157W|ENSP00000428398:S14L	R|S	-|-	1|2	2|0	LRRTM2|LRRTM2	138237680|138237680	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.140000|6.140000	0.71738|0.71738	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.483	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			A	138209781	G	A	138209781	3	1	61	1	0	0	0	0	1	0	0	0	9069	1057	37	1	1085	1	LRRTM2	5	138209781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336	138209781	42705479	4124	12109										
LRRTM2	26045	broad.mit.edu	37	chr5	138210022	138210022	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcaaattgatctctttcGagctctgtgatgtgattgtg	11	7	2	3	rs183535931		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138210022G>A	ENST00000274711.6	-	2	606	c.228C>T	c.(226-228)ctC>ctT	p.L76L	LRRTM2_ENST00000523537.1_Intron|LRRTM2_ENST00000518785.1_Intron|LRRTM2_ENST00000521094.2_Intron|CTNNA1_ENST00000520400.1_Intron|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000540387.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000518825.1_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	76					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.L76L(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GATCTCTTTCGAGCTCTGTGA	0.463													G|||	1	0.000199681	0	0	5008	,	,		18091	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						G	,	0,3870		0,0,1935	79	76	77		,228	-7.2	0.9	5		77	1,8309		0,1,4154	no	intron,coding-synonymous	CTNNA1,LRRTM2	NM_001903.2,NM_015564.2	,	0,1,6089	AA,AG,GG		0.012,0.0,0.0082	,	,76/517	138210022	1,12179	1935	4155	6090	138237921	SO:0001819	synonymous_variant	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.228C>T	5.37:g.138210022G>A			138237921	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Silent	SNP	ENST00000274711.6	37	CCDS47272.1																																																																																				0.463	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			A	138210022	G	A	138210022	2	1	61	1	0	0	0	0	0	0	0	1	9069	1045	37	1		1	LRRTM2	5	138210022	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241	138210022	42705238	4125	12110										
SIL1	64374	broad.mit.edu	37	chr5	138287545	138287545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgcagggctcccccttCgatggcctccacctggacct	9	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138287545C>T	ENST00000394817.2	-	8	935	c.796G>A	c.(796-798)Gaa>Aaa	p.E266K	SIL1_ENST00000265195.5_Missense_Mutation_p.E266K|SIL1_ENST00000509534.1_Missense_Mutation_p.E273K|SIL1_ENST00000515008.1_5'UTR	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	266					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)	p.E266K(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GCTCCCCCTTCGATGGCCTCC	0.627									Marinesco-Sjgren syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											113	105	108					5																	138287545		2203	4300	6503	138315444	SO:0001583	missense	64374	Familial Cancer Database	Marinesco-Sjogren syndrome	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"Marinesco-Sjogren syndrome", "SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.796G>A	5.37:g.138287545C>T	ENSP00000378294:p.Glu266Lys		138315444	D3DQC2|Q8N2L3	Missense_Mutation	SNP	ENST00000394817.2	37	CCDS4209.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759218	0.89843	.	.	ENSG00000120725	ENST00000394817;ENST00000265195;ENST00000537511;ENST00000509534;ENST00000505945	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	4.75	4.75	0.60458	Armadillo-like helical (1);Armadillo-type fold (1);	0.052151	0.85682	D	0.000000	T	0.70263	0.3204	M	0.84948	2.725	0.54753	D	0.999987	P;D;D	0.76494	0.468;0.999;0.997	B;P;P	0.59171	0.089;0.853;0.775	T	0.72507	-0.4272	10	0.37606	T	0.19	-11.3637	14.6129	0.68529	0.0:1.0:0.0:0.0	.	72;273;266	A0RZB6;D6REA1;Q9H173	.;.;SIL1_HUMAN	K	266;266;181;273;72	ENSP00000378294:E266K;ENSP00000265195:E266K;ENSP00000426858:E273K;ENSP00000425136:E72K	ENSP00000265195:E266K	E	-	1	0	SIL1	138315444	1.000000	0.71417	0.907000	0.35723	0.716000	0.41182	6.234000	0.72326	2.471000	0.83476	0.655000	0.94253	GAA		0.627	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464		T	138287545	C	T	138287545	3	4	61	1	0	0	0	0	1	0	0	0	14358	893	31	1	601	1	SIL1	5	138287545	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77523	138287545	42627715	4126	12111										
MATR3	9782	broad.mit.edu	37	chr5	138661220	138661220	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagaaccaggtgctgaatCttctgagaacgctgatgatc	10	10	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138661220C>A	ENST00000394805.3	+	13	2575	c.2240C>A	c.(2239-2241)tCt>tAt	p.S747Y	MATR3_ENST00000394800.2_Missense_Mutation_p.S795Y|MATR3_ENST00000510056.1_Missense_Mutation_p.S747Y|MATR3_ENST00000509990.1_Missense_Mutation_p.S747Y|MATR3_ENST00000504203.1_Missense_Mutation_p.S409Y|MATR3_ENST00000503811.1_Missense_Mutation_p.S459Y|MATR3_ENST00000361059.2_Missense_Mutation_p.S747Y|MATR3_ENST00000502929.1_Missense_Mutation_p.S795Y|MATR3_ENST00000502499.1_Missense_Mutation_p.S409Y	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	747					cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)	p.S747Y(1)|p.S183Y(1)		breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GGTGCTGAATCTTCTGAGAAC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	5											95	94	95					5																	138661220		2203	4300	6503	138689119	SO:0001583	missense	9782			M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"myopathy, distal 2"	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.2240C>A	5.37:g.138661220C>A	ENSP00000378284:p.Ser747Tyr		138689119	B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Missense_Mutation	SNP	ENST00000394805.3	37	CCDS4210.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937252	0.73557	.	.	ENSG00000015479	ENST00000509990;ENST00000361059;ENST00000504203;ENST00000502929;ENST00000394800;ENST00000394805;ENST00000502499;ENST00000510056;ENST00000503811;ENST00000337359	T;T;T;T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12	4.64	4.64	0.57946	.	0.563097	0.20196	N	0.097205	T	0.78033	0.4220	N	0.14661	0.345	0.38400	D	0.945644	P;P;P;D;P	0.63880	0.875;0.826;0.875;0.993;0.826	B;B;B;D;B	0.66196	0.198;0.446;0.198;0.942;0.446	T	0.81006	-0.1128	10	0.46703	T	0.11	-7.8094	16.2359	0.82375	0.0:1.0:0.0:0.0	.	459;747;459;795;747	B7ZAV5;D6REM6;B4DRS1;A8MXP9;P43243	.;.;.;.;MATR3_HUMAN	Y	747;747;409;795;795;747;409;747;459;183	ENSP00000423533:S747Y;ENSP00000354346:S747Y;ENSP00000421218:S409Y;ENSP00000422319:S795Y;ENSP00000378279:S795Y;ENSP00000378284:S747Y;ENSP00000426030:S409Y;ENSP00000426743:S747Y;ENSP00000423587:S459Y	ENSP00000338208:S183Y	S	+	2	0	MATR3	138689119	0.999000	0.42202	1.000000	0.80357	0.967000	0.64934	1.610000	0.36869	2.575000	0.86900	0.650000	0.86243	TCT		0.403	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834		A	138661220	C	A	138661220	3	1	61	1	0	0	0	0	1	0	0	0	9367	913	32	2	2286	2	MATR3	5	138661220	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	373675	138661220	42254040	4127	12112										
SLC23A1	9963	broad.mit.edu	37	chr5	138718271	138718271	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctctgtgggtagcggggtCgaggggtccctggtggtttc	20	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138718271C>T	ENST00000348729.3	-	2	106	c.60G>A	c.(58-60)tcG>tcA	p.S20S	SLC23A1_ENST00000353963.3_Silent_p.S20S|SLC23A1_ENST00000503919.1_5'UTR	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	20					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)	p.S20S(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	GTAGCGGGGTCGAGGGGTCCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	5											110	93	99					5																	138718271		2203	4300	6503	138746170	SO:0001819	synonymous_variant	9963			AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.60G>A	5.37:g.138718271C>T			138746170	O95191|Q8WWB6|Q9UGH4|Q9UI39	Silent	SNP	ENST00000348729.3	37	CCDS4212.1																																																																																				0.552	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		T	138718271	C	T	138718271	2	4	61	1	0	0	0	0	0	0	0	1	14499	871	31	1		1	SLC23A1	5	138718271	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57051	138718271	42196989	4128	12113										
DNAJC18	202052	broad.mit.edu	37	chr5	138755806	138755806	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatccttctctattgttttCtccaagtcatgcagagaagc	6	10	3	1	rs575204241		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:138755806C>T	ENST00000302060.5	-	7	968	c.888G>A	c.(886-888)gaG>gaA	p.E296E		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	296						integral component of membrane (GO:0016021)		p.E296E(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTATTGTTTTCTCCAAGTCAT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	5											146	139	142					5																	138755806		2203	4300	6503	138783705	SO:0001819	synonymous_variant	202052			AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.888G>A	5.37:g.138755806C>T			138783705		Silent	SNP	ENST00000302060.5	37	CCDS4214.1	.	.	.	.	.	.	.	.	.	.	C	0.153	-1.089332	0.01873	.	.	ENSG00000170464	ENST00000514052	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	T	0.74558	0.3732	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72814	-0.4179	4	.	.	.	-1.5866	18.1041	0.89515	0.0:1.0:0.0:0.0	.	.	.	.	K	88	.	.	R	-	2	0	DNAJC18	138783705	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	3.018000	0.49625	2.623000	0.88846	0.561000	0.74099	AGA		0.413	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		T	138755806	C	T	138755806	2	4	61	1	0	0	0	0	0	0	0	1	4648	912	32	3		3	DNAJC18	5	138755806	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37535	138755806	42159454	4129	12114										
PSD2	84249	broad.mit.edu	37	chr5	139217238	139217238	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcctgacaaagctctatCggagggtgacctgaagaacg	13	10	1	4	rs370966922		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:139217238C>T	ENST00000274710.3	+	12	1899	c.1694C>T	c.(1693-1695)tCg>tTg	p.S565L		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	565	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.S565L(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAGCTCTATCGGAGGGTGAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	LEU/SER	0,4406		0,0,2203	105	86	93		1694	5.3	1	5		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	PSD2	NM_032289.2	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	565/772	139217238	1,13005	2203	4300	6503	139197422	SO:0001583	missense	84249			AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1694C>T	5.37:g.139217238C>T	ENSP00000274710:p.Ser565Leu		139197422	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	37	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	31	5.071408	0.93950	0.0	1.16E-4	ENSG00000146005	ENST00000274710	T	0.78924	-1.22	5.31	5.31	0.75309	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.87458	0.6182	M	0.79693	2.465	0.80722	D	1	D	0.71674	0.998	D	0.63113	0.911	D	0.85938	0.1456	10	0.30854	T	0.27	.	18.9763	0.92738	0.0:1.0:0.0:0.0	.	565	Q9BQI7	PSD2_HUMAN	L	565	ENSP00000274710:S565L	ENSP00000274710:S565L	S	+	2	0	PSD2	139197422	1.000000	0.71417	0.982000	0.44146	0.934000	0.57294	7.778000	0.85637	2.482000	0.83794	0.478000	0.44815	TCG		0.592	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139217238	C	T	139217238	3	4	61	1	0	0	0	0	1	0	0	0	12681	893	31	1	1736	1	PSD2	5	139217238	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	461432	139217238	41698022	4130	12115										
PFDN1	5201	broad.mit.edu	37	chr5	139661036	139661036	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccaataaaaacttacttCtagttctttaattttttctt	2	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:139661036C>A	ENST00000261813.4	-	3	330	c.283G>T	c.(283-285)Gaa>Taa	p.E95*	PFDN1_ENST00000514611.1_Intron|PFDN1_ENST00000524074.1_Nonsense_Mutation_p.E95*|PFDN1_ENST00000510217.1_3'UTR|CYSTM1_ENST00000509789.2_Intron	NM_002622.4	NP_002613.2	O60925	PFD1_HUMAN	prefoldin subunit 1	95					'de novo' posttranslational protein folding (GO:0051084)|actin cytoskeleton organization (GO:0030036)|B cell activation (GO:0042113)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|cerebellum development (GO:0021549)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|telencephalon development (GO:0021537)	prefoldin complex (GO:0016272)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E95*(1)		endometrium(2)|large_intestine(3)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACTTACTTCTAGTTCTTTA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											85	77	80					5																	139661036		2201	4295	6496	139641220	SO:0001587	stop_gained	5201			Y17392	CCDS4222.1	5q31	2008-02-05	2006-02-24		ENSG00000113068	ENSG00000113068			8866	protein-coding gene	gene with protein product		604897	"prefoldin 1"			9630229	Standard	XM_005268465		Approved	PFD1	uc003lff.1	O60925	OTTHUMG00000129249	ENST00000261813.4:c.283G>T	5.37:g.139661036C>A	ENSP00000261813:p.Glu95*		139641220	B2RD02|Q53F95|Q96EX6	Nonsense_Mutation	SNP	ENST00000261813.4	37	CCDS4222.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983716	0.93044	.	.	ENSG00000113068	ENST00000261813;ENST00000524074	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-13.3262	17.8368	0.88700	0.0:1.0:0.0:0.0	.	.	.	.	X	95	.	ENSP00000261813:E95X	E	-	1	0	PFDN1	139641220	1.000000	0.71417	0.994000	0.49952	0.881000	0.50899	5.144000	0.64832	2.751000	0.94390	0.650000	0.86243	GAA		0.328	PFDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251354.3	NM_002622		A	139661036	C	A	139661036	4	1	61	1	0	0	0	0	0	1	0	0	11786	922	32	2	93	2	PFDN1	5	139661036	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	443798	139661036	41254224	4131	12116										
SLC4A9	83697	broad.mit.edu	37	chr5	139751880	139751880	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagggtcttctcaccacaGgaactcctctggctggatga	12	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:139751880G>T	ENST00000230993.6	+	20	2831	c.2796G>T	c.(2794-2796)caG>caT	p.Q932H	SLC4A9_ENST00000506757.2_Missense_Mutation_p.Q908H|SLC4A9_ENST00000506545.1_Missense_Mutation_p.Q845H|SLC4A9_ENST00000432095.2_Missense_Mutation_p.Q894H|CTC-329D1.2_ENST00000507521.1_RNA|SLC4A9_ENST00000507527.1_Missense_Mutation_p.Q932H	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	932	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.Q906H(1)|p.Q932H(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCACCACAGGAACTCCTCT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	5											32	33	33					5																	139751880		1887	4107	5994	139732064	SO:0001583	missense	83697			AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2796G>T	5.37:g.139751880G>T	ENSP00000230993:p.Gln932His		139732064	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	37	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655255	0.14580	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	4.89	2.09	0.27110	.	0.096923	0.44097	D	0.000491	T	0.36413	0.0966	N	0.02736	-0.51	0.32296	N	0.565595	D;B;B;B	0.63046	0.992;0.282;0.055;0.069	D;B;B;B	0.72075	0.976;0.043;0.051;0.069	T	0.43925	-0.9361	10	0.21014	T	0.42	.	0.7754	0.01031	0.2401:0.1312:0.3785:0.2501	.	845;932;894;908	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	H	932;908;894;845;932	ENSP00000230993:Q932H;ENSP00000424424:Q908H;ENSP00000410056:Q894H;ENSP00000422855:Q845H;ENSP00000427661:Q932H	ENSP00000230993:Q932H	Q	+	3	2	SLC4A9	139732064	0.005000	0.15991	1.000000	0.80357	0.991000	0.79684	-1.112000	0.03299	0.252000	0.21531	-0.312000	0.09012	CAG		0.567	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		T	139751880	G	T	139751880	3	4	61	1	0	0	0	0	1	0	0	0	14697	991	35	2	2802	2	SLC4A9	5	139751880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90844	139751880	41163380	4132	12117										
ANKHD1	54882	broad.mit.edu	37	chr5	139906001	139906001	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccaagaagaaaagacaaGtactgctacttccaaaactc	5	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:139906001G>T	ENST00000360839.2	+	26	5067	c.4913G>T	c.(4912-4914)aGt>aTt	p.S1638I	ANKHD1_ENST00000544120.1_Missense_Mutation_p.S21I|SNORD45_ENST00000363181.1_RNA|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.S1638I|ANKHD1_ENST00000297183.6_Missense_Mutation_p.S1638I	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1638						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.S1638I(2)		breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAAAGACAAGTACTGCTACT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	5											93	98	96					5																	139906001		2203	4299	6502	139886185	SO:0001583	missense	404734			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4913G>T	5.37:g.139906001G>T	ENSP00000354085:p.Ser1638Ile		139886185	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.461|2.461	-0.324195|-0.324195	0.05350|0.05350	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000435794;ENST00000432301|ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219	.|T;T;T;T;T;T	.|0.23552	.|1.9;1.9;1.9;1.9;2.0;1.9	5.34|5.34	1.23|1.23	0.21249|0.21249	.|.	.|0.350607	.|0.33419	.|N	.|0.004928	T|T	0.15349|0.15349	0.0370|0.0370	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B	.|0.04013	.|0.001;0.001;0.0;0.001;0.0;0.0	T|T	0.15521|0.15521	-1.0434|-1.0434	5|10	.|0.38643	.|T	.|0.18	.|.	4.8833|4.8833	0.13690|0.13690	0.2925:0.0:0.5393:0.1682|0.2925:0.0:0.5393:0.1682	.|.	.|21;68;1638;1638;1638;1638	.|Q8IWG5;Q9H059;E9PF56;Q8IWZ3-4;Q8IWZ2;Q8IWZ3	.|.;.;.;.;.;ANKH1_HUMAN	N|I	128;88|1638;1638;1638;294;73;160;21;1638	.|ENSP00000354085:S1638I;ENSP00000297183:S1638I;ENSP00000393204:S294I;ENSP00000390034:S160I;ENSP00000437687:S21I;ENSP00000432016:S1638I	.|ENSP00000432016:S1638I	K|S	+|+	3|2	2|0	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139886185|139886185	0.759000|0.759000	0.28416|0.28416	0.017000|0.017000	0.16124|0.16124	0.075000|0.075000	0.17131|0.17131	1.861000|1.861000	0.39438|0.39438	0.145000|0.145000	0.18977|0.18977	-0.142000|-0.142000	0.14014|0.14014	AAG|AGT		0.388	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139906001	G	T	139906001	3	4	61	1	0	0	0	0	1	0	0	0	628	1029	36	2	5121	2	ANKHD1	5	139906001	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154121	139906001	41009259	4133	12118										
ANKHD1	54882	broad.mit.edu	37	chr5	139909017	139909017	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccagtctatttttgttacGaatccagttactttaacacc	4	12	1	0	rs200760213		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:139909017G>A	ENST00000360839.2	+	29	6640	c.6486G>A	c.(6484-6486)acG>acA	p.T2162T	ANKHD1_ENST00000544120.1_Silent_p.T545T|SNORD45_ENST00000363181.1_RNA|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.T2162T|ANKHD1_ENST00000297183.6_Silent_p.T2162T	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2162						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.T2162T(2)		breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTTGTTACGAATCCAGTTA	0.458													A|||	1	0.000199681	0	0	5008	,	,		22338	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	5											158	159	159					5																	139909017		2203	4300	6503	139889201	SO:0001819	synonymous_variant	404734			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.6486G>A	5.37:g.139909017G>A			139889201	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	CCDS4225.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	2.781	-0.253409	0.05829	.	.	ENSG00000131503	ENST00000435794;ENST00000432301	.	.	.	5.35	2.8	0.32819	.	.	.	.	.	T	0.54951	0.1890	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46091	-0.9216	4	.	.	.	.	6.6046	0.22718	0.6181:0.248:0.1339:0.0	.	.	.	.	K	653;613	.	.	E	+	1	0	ANKHD1	139889201	0.290000	0.24343	1.000000	0.80357	0.984000	0.73092	-0.061000	0.11693	0.472000	0.27344	-0.332000	0.08345	GAA		0.458	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		A	139909017	G	A	139909017	2	1	61	1	0	0	0	0	0	0	0	1	628	1045	37	1		1	ANKHD1	5	139909017	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3016	139909017	41006243	4134	12119										
HARS2	23438	broad.mit.edu	37	chr5	140077256	140077256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttattgcagagctttggGattctggaatcaaggtatgg	13	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140077256G>A	ENST00000230771.3	+	11	1523	c.1300G>A	c.(1300-1302)Gat>Aat	p.D434N	HARS2_ENST00000448069.2_Missense_Mutation_p.D262N|HARS2_ENST00000432671.2_Missense_Mutation_p.D320N|HARS2_ENST00000508522.1_Missense_Mutation_p.D409N|HARS2_ENST00000435019.2_Missense_Mutation_p.D394N|ZMAT2_ENST00000274712.3_5'Flank|HARS2_ENST00000437649.2_Missense_Mutation_p.D360N	NM_012208.2	NP_036340.1	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2, mitochondrial	434					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)|poly(A) RNA binding (GO:0044822)	p.D434N(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(10)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGCTTTGGGATTCTGGAAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											121	127	125					5																	140077256		2203	4300	6503	140057440	SO:0001583	missense	23438			U18937	CCDS4238.1, CCDS64267.1	5q31.3	2012-07-20	2012-07-20	2007-02-23	ENSG00000112855	ENSG00000112855	6.1.1.21	"Aminoacyl tRNA synthetases / Class II"	4817	protein-coding gene	gene with protein product	"histidine tRNA ligase 2, mitochondrial (putative)"	600783	"histidyl-tRNA synthetase-like"	HARSL		7755634, 21464306	Standard	NM_012208		Approved	HO3, HARSR	uc003lgx.3	P49590	OTTHUMG00000129500	ENST00000230771.3:c.1300G>A	5.37:g.140077256G>A	ENSP00000230771:p.Asp434Asn		140057440	B4DDY8	Missense_Mutation	SNP	ENST00000230771.3	37	CCDS4238.1	.	.	.	.	.	.	.	.	.	.	g	13.39	2.222770	0.39300	.	.	ENSG00000112855	ENST00000230771;ENST00000435019;ENST00000437649;ENST00000432671;ENST00000508522;ENST00000448069;ENST00000427675	D;D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6	5.67	2.98	0.34508	Anticodon-binding (3);	0.194094	0.56097	N	0.000029	T	0.71888	0.3393	L	0.29908	0.895	0.51233	D	0.999914	B;B;B;B;B	0.23806	0.023;0.02;0.055;0.02;0.091	B;B;B;B;B	0.28991	0.042;0.06;0.085;0.06;0.097	T	0.58956	-0.7544	10	0.20046	T	0.44	-1.1668	9.1982	0.37242	0.268:0.0:0.732:0.0	.	287;262;360;409;434	E9PD60;B4DQ67;E9PG66;B4DDY8;P49590	.;.;.;.;SYHM_HUMAN	N	434;394;360;320;409;262;273	ENSP00000230771:D434N;ENSP00000412887:D394N;ENSP00000411708:D360N;ENSP00000415007:D320N;ENSP00000423616:D409N;ENSP00000407105:D262N	ENSP00000230771:D434N	D	+	1	0	HARS2	140057440	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	3.992000	0.56980	0.357000	0.24183	-0.126000	0.14955	GAT		0.473	HARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251670.2	NM_012208		A	140077256	G	A	140077256	3	1	61	1	0	0	0	0	1	0	0	0	6981	1174	41	3	1342	3	HARS2	5	140077256	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168239	140077256	40838004	4135	12120										
PCDHA1	56147	broad.mit.edu	37	chr5	140167282	140167282	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtgaaggagaacaacccGccgggctgccacatcttcac	10	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140167282G>A	ENST00000504120.2	+	1	1407	c.1407G>A	c.(1405-1407)ccG>ccA	p.P469P	PCDHA1_ENST00000378133.3_Silent_p.P469P|PCDHA1_ENST00000394633.3_Silent_p.P469P	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	469	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P469P(2)		breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAACAACCCGCCGGGCTGCC	0.677																																																2	Substitution - coding silent(2)	large_intestine(2)	5											55	62	60					5																	140167282		2203	4295	6498	140147466	SO:0001819	synonymous_variant	56147			AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1407G>A	5.37:g.140167282G>A			140147466	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																				0.677	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		A	140167282	G	A	140167282	2	1	61	1	0	0	0	0	0	0	0	1	11550	1074	38	1		1	PCDHA1	5	140167282	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90026	140167282	40747978	4136	12121										
PCDHA3	56145	broad.mit.edu	37	chr5	140181115	140181115	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctggaggtgatcgtggaCaggccgctgcaggttttcca	14	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140181115C>G	ENST00000522353.2	+	1	333	c.333C>G	c.(331-333)gaC>gaG	p.D111E	PCDHA3_ENST00000532566.2_Missense_Mutation_p.D111E|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	111	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D111E(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGATCGTGGACAGGCCGCTGC	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	5											123	137	132					5																	140181115		2203	4300	6503	140161299	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.333C>G	5.37:g.140181115C>G	ENSP00000429808:p.Asp111Glu		140161299	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	c	5.138	0.211047	0.09757	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.21031	2.03;2.03	4.35	2.49	0.30216	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.152498	0.29551	N	0.011832	T	0.08537	0.0212	N	0.05330	-0.07	0.09310	N	0.99999	B;B	0.18863	0.031;0.008	B;B	0.15484	0.013;0.007	T	0.38520	-0.9657	10	0.11794	T	0.64	.	7.728	0.28771	0.0:0.3715:0.4749:0.1536	.	111;111	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	E	111	ENSP00000429808:D111E;ENSP00000434086:D111E	ENSP00000429808:D111E	D	+	3	2	PCDHA3	140161299	0.000000	0.05858	0.660000	0.29694	0.948000	0.59901	-1.274000	0.02820	0.347000	0.23924	0.467000	0.42956	GAC		0.507	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		G	140181115	C	G	140181115	3	3	61	1	0	0	0	0	1	0	0	0	11556	477	17	5	335	5	PCDHA3	5	140181115	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13833	140181115	40734145	4137	12122										
PCDHA3	56145	broad.mit.edu	37	chr5	140181584	140181584	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgaccgttaacgccaccGatttggatgaaggagtaaat	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140181584G>A	ENST00000522353.2	+	1	802	c.802G>A	c.(802-804)Gat>Aat	p.D268N	PCDHA3_ENST00000532566.2_Missense_Mutation_p.D268N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	268	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D268N(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAACGCCACCGATTTGGATGA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	5											72	69	70					5																	140181584		2203	4300	6503	140161768	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.802G>A	5.37:g.140181584G>A	ENSP00000429808:p.Asp268Asn		140161768	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	18.06	3.540044	0.65085	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.74526	-0.85;-0.85	4.79	4.79	0.61399	Cadherin (5);Cadherin-like (1);	0.000000	0.42964	U	0.000623	D	0.92041	0.7478	H	0.99404	4.55	0.38396	D	0.945538	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95576	0.8642	10	0.87932	D	0	.	13.8824	0.63689	0.0:0.1529:0.8471:0.0	.	268;268	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	N	268	ENSP00000429808:D268N;ENSP00000434086:D268N	ENSP00000429808:D268N	D	+	1	0	PCDHA3	140161768	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	9.866000	0.99616	2.378000	0.81104	0.467000	0.42956	GAT		0.423	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140181584	G	A	140181584	3	1	61	1	0	0	0	0	1	0	0	0	11556	1058	37	1	804	1	PCDHA3	5	140181584	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	469	140181584	40733676	4138	12123										
PCDHA4	56144	broad.mit.edu	37	chr5	140187154	140187154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggtgagggacattaacGataacccgccggtgttccca	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140187154G>A	ENST00000530339.1	+	1	382	c.382G>A	c.(382-384)Gat>Aat	p.D128N	PCDHA4_ENST00000356878.4_Missense_Mutation_p.D128N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.D128N|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	128	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D128N(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACATTAACGATAACCCGCC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	5											75	78	77					5																	140187154		2203	4300	6503	140167338	SO:0001583	missense	56144			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.382G>A	5.37:g.140187154G>A	ENSP00000435300:p.Asp128Asn		140167338	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	20.3	3.970463	0.74246	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.64085	-0.08;-0.08;-0.08	4.62	4.62	0.57501	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.42420	U	0.000718	D	0.88336	0.6409	H	0.99211	4.47	0.43863	D	0.996461	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.93713	0.7026	10	0.87932	D	0	.	17.8071	0.88605	0.0:0.0:1.0:0.0	.	128;128;128	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	N	128	ENSP00000423470:D128N;ENSP00000349344:D128N;ENSP00000435300:D128N	ENSP00000349344:D128N	D	+	1	0	PCDHA4	140167338	1.000000	0.71417	0.997000	0.53966	0.385000	0.30292	6.591000	0.74090	2.284000	0.76573	0.563000	0.77884	GAT		0.602	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140187154	G	A	140187154	3	1	61	1	0	0	0	0	1	0	0	0	11557	1058	37	1	384	1	PCDHA4	5	140187154	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5570	140187154	40728106	4139	12124										
PCDHA4	56144	broad.mit.edu	37	chr5	140187722	140187722	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagaaagcaaatcctatgAaattattgtagagggcattg	10	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140187722A>C	ENST00000530339.1	+	1	950	c.950A>C	c.(949-951)gAa>gCa	p.E317A	PCDHA4_ENST00000356878.4_Missense_Mutation_p.E317A|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.E317A|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	317	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E317A(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATCCTATGAAATTATTGTA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	5											107	114	112					5																	140187722		2203	4300	6503	140167906	SO:0001583	missense	56144			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.950A>C	5.37:g.140187722A>C	ENSP00000435300:p.Glu317Ala		140167906	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	a	15.68	2.905074	0.52333	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.54479	0.57;0.57;0.57	4.34	4.34	0.51931	Cadherin (4);Cadherin-like (1);	0.178185	0.26159	U	0.025995	T	0.71022	0.3291	M	0.84433	2.695	0.26225	N	0.979109	P;P;D	0.58970	0.744;0.952;0.984	P;P;D	0.64595	0.598;0.894;0.927	T	0.65492	-0.6155	10	0.87932	D	0	.	10.0983	0.42488	0.9161:0.0:0.0839:0.0	.	317;317;317	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	A	317	ENSP00000423470:E317A;ENSP00000349344:E317A;ENSP00000435300:E317A	ENSP00000349344:E317A	E	+	2	0	PCDHA4	140167906	0.928000	0.31464	0.971000	0.41717	0.985000	0.73830	3.463000	0.53050	1.735000	0.51646	0.383000	0.25322	GAA		0.363	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		C	140187722	A	C	140187722	3	2	61	1	0	0	0	0	1	0	0	0	11557	246	9	4	952	4	PCDHA4	5	140187722	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	568	140187722	40727538	4140	12125										
PCDHA4	56144	broad.mit.edu	37	chr5	140188590	140188590	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactcgggctacaacgcgtgGctttcgtacgagctgcagcc	13	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140188590G>A	ENST00000530339.1	+	1	1818	c.1818G>A	c.(1816-1818)tgG>tgA	p.W606*	PCDHA4_ENST00000356878.4_Nonsense_Mutation_p.W606*|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Nonsense_Mutation_p.W606*|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	606	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.W606*(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACGCGTGGCTTTCGTACG	0.672																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											117	108	111					5																	140188590		2203	4299	6502	140168774	SO:0001587	stop_gained	56144			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1818G>A	5.37:g.140188590G>A	ENSP00000435300:p.Trp606*		140168774	O75285|Q2M253	Nonsense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	37	5.983979	0.97173	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	.	.	.	4.08	4.08	0.47627	.	0.000000	0.37437	U	0.002095	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6588	0.85236	0.0:0.0:1.0:0.0	.	.	.	.	X	606	.	ENSP00000349344:W606X	W	+	3	0	PCDHA4	140168774	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.953000	0.63624	2.006000	0.58801	0.484000	0.47621	TGG		0.672	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140188590	G	A	140188590	4	1	61	1	0	0	0	0	0	1	0	0	11557	1212	42	3	1820	3	PCDHA4	5	140188590	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	868	140188590	40726670	4141	12126										
PCDHA5	56143	broad.mit.edu	37	chr5	140203464	140203464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacgtgtacctgatcatcGccatctgtgcggtgtccagc	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140203464G>A	ENST00000529859.1	+	1	2104	c.2104G>A	c.(2104-2106)Gcc>Acc	p.A702T	PCDHA5_ENST00000529619.1_Missense_Mutation_p.A702T|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A702T|PCDHA4_ENST00000530339.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	702					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A702T(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGATCATCGCCATCTGTGC	0.692																																																2	Substitution - Missense(2)	large_intestine(2)	5											63	62	63					5																	140203464		2203	4298	6501	140183648	SO:0001583	missense	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2104G>A	5.37:g.140203464G>A	ENSP00000436557:p.Ala702Thr		140183648	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.057332	0.55325	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.20463	2.07;2.07;2.07	4.06	4.06	0.47325	.	.	.	.	.	T	0.54431	0.1858	M	0.93062	3.375	0.24607	N	0.993747	D;D;D	0.89917	0.999;0.998;1.0	D;D;D	0.70716	0.962;0.95;0.97	T	0.53244	-0.8466	9	0.87932	D	0	.	13.255	0.60073	0.0:0.0:0.8408:0.1592	.	702;702;702	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	T	702	ENSP00000433416:A702T;ENSP00000436557:A702T;ENSP00000367366:A702T	ENSP00000367366:A702T	A	+	1	0	PCDHA5	140183648	0.952000	0.32445	0.996000	0.52242	0.246000	0.25737	2.041000	0.41213	1.987000	0.57996	0.491000	0.48974	GCC		0.692	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140203464	G	A	140203464	3	1	61	1	0	0	0	0	1	0	0	0	11558	1087	38	1	2106	1	PCDHA5	5	140203464	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14874	140203464	40711796	4142	12127										
PCDHA6	56142	broad.mit.edu	37	chr5	140208267	140208267	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaattgggctcttattaaaGaaatccttggacagagagga	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140208267G>T	ENST00000529310.1	+	1	705	c.591G>T	c.(589-591)aaG>aaT	p.K197N	PCDHA6_ENST00000527624.1_Missense_Mutation_p.K197N|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	197	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.K197N(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTATTAAAGAAATCCTTGG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	5											67	72	70					5																	140208267		2203	4300	6503	140188451	SO:0001583	missense	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.591G>T	5.37:g.140208267G>T	ENSP00000433378:p.Lys197Asn		140188451	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	G	5.714	0.316181	0.10789	.	.	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.53206	0.63;0.63	3.7	-1.37	0.09056	Cadherin (4);Cadherin-like (1);	0.426470	0.16778	U	0.199907	T	0.39091	0.1065	L	0.33093	0.98	0.23872	N	0.996605	B;B;B	0.21905	0.014;0.062;0.008	B;B;B	0.37304	0.058;0.246;0.025	T	0.49799	-0.8901	10	0.72032	D	0.01	.	8.4655	0.32953	0.4739:0.0:0.5261:0.0	.	197;197;197	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	N	197	ENSP00000433378:K197N;ENSP00000434113:K197N	ENSP00000434113:K197N	K	+	3	2	PCDHA6	140188451	0.000000	0.05858	0.619000	0.29118	0.272000	0.26649	-0.268000	0.08607	-0.129000	0.11620	0.313000	0.20887	AAG		0.433	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		T	140208267	G	T	140208267	3	4	61	1	0	0	0	0	1	0	0	0	11559	933	33	2	593	2	PCDHA6	5	140208267	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4803	140208267	40706993	4143	12128										
PCDHA6	56142	broad.mit.edu	37	chr5	140208626	140208626	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacaagaaaacttatacaAaatcctcattgacgccacgg	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140208626A>G	ENST00000529310.1	+	1	1064	c.950A>G	c.(949-951)aAa>aGa	p.K317R	PCDHA6_ENST00000527624.1_Missense_Mutation_p.K317R|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	317	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.K317R(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACTTATACAAAATCCTCATT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	5											35	39	38					5																	140208626		2195	4278	6473	140188810	SO:0001583	missense	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.950A>G	5.37:g.140208626A>G	ENSP00000433378:p.Lys317Arg		140188810	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	A	3.065	-0.192315	0.06259	.	.	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.01745	4.66;4.66	3.7	2.53	0.30540	Cadherin (4);Cadherin-like (1);	0.406531	0.17688	U	0.165396	T	0.01421	0.0046	N	0.13198	0.31	0.09310	N	1	B;B;B	0.19445	0.006;0.013;0.036	B;B;B	0.19666	0.026;0.026;0.026	T	0.46735	-0.9170	10	0.72032	D	0.01	.	8.0989	0.30846	0.8202:0.0:0.1798:0.0	.	317;317;317	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	R	317	ENSP00000433378:K317R;ENSP00000434113:K317R	ENSP00000434113:K317R	K	+	2	0	PCDHA6	140188810	0.014000	0.17966	0.777000	0.31699	0.022000	0.10575	2.833000	0.48159	0.599000	0.29845	0.260000	0.18958	AAA		0.413	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		G	140208626	A	G	140208626	3	3	61	1	0	0	0	0	1	0	0	0	11559	14	1	4	952	4	PCDHA6	5	140208626	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	359	140208626	40706634	4144	12129										
PCDHA6	56142	broad.mit.edu	37	chr5	140208972	140208972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgcgcgggacgggggctcGccttcgctgtgggccaccgc	17	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140208972G>A	ENST00000529310.1	+	1	1410	c.1296G>A	c.(1294-1296)tcG>tcA	p.S432S	PCDHA6_ENST00000527624.1_Silent_p.S432S|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	432	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S432S(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGGGGCTCGCCTTCGCTGT	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	5											66	77	73					5																	140208972		2203	4298	6501	140189156	SO:0001819	synonymous_variant	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1296G>A	5.37:g.140208972G>A			140189156	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																				0.622	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140208972	G	A	140208972	2	1	61	1	0	0	0	0	0	0	0	1	11559	1074	38	1		1	PCDHA6	5	140208972	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346	140208972	40706288	4145	12130										
PCDHA8	56140	broad.mit.edu	37	chr5	140221233	140221233	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatccacctggaggtgatCgtggacaggccgctgcaggt	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140221233C>T	ENST00000531613.1	+	1	327	c.327C>T	c.(325-327)atC>atT	p.I109I	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.I109I|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	109	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.I109I(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGGTGATCGTGGACAGGC	0.542																																																2	Substitution - coding silent(2)	large_intestine(2)	5											75	92	87					5																	140221233		2203	4297	6500	140201417	SO:0001819	synonymous_variant	56140			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.327C>T	5.37:g.140221233C>T			140201417	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																				0.542	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140221233	C	T	140221233	2	4	61	1	0	0	0	0	0	0	0	1	11561	874	31	1		1	PCDHA8	5	140221233	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12261	140221233	40694027	4146	12131										
PCDHA9	9752	broad.mit.edu	37	chr5	140229709	140229709	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcgcgacgcgggcgtgccGcctctgggcagcaacgtgac	17	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140229709G>A	ENST00000532602.1	+	1	2662	c.1629G>A	c.(1627-1629)ccG>ccA	p.P543P	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Silent_p.P543P|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P543P(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGCGTGCCGCCTCTGGGCA	0.682																																					Melanoma(55;1800 1972 14909)											2	Substitution - coding silent(2)	large_intestine(2)	5											59	66	64					5																	140229709		2195	4267	6462	140209893	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1629G>A	5.37:g.140229709G>A			140209893	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.682	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229709	G	A	140229709	2	1	61	1	0	0	0	0	0	0	0	1	11562	1074	38	1		1	PCDHA9	5	140229709	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8476	140229709	40685551	4147	12132										
PCDHA9	9752	broad.mit.edu	37	chr5	140229839	140229839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgctgcggtcggtgggcGccggcgtagtggtggggaag	23	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140229839G>A	ENST00000532602.1	+	1	2792	c.1759G>A	c.(1759-1761)Gcc>Acc	p.A587T	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.A587T|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	587					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A587T(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCGGTGGGCGCCGGCGTAGT	0.667																																					Melanoma(55;1800 1972 14909)											2	Substitution - Missense(2)	large_intestine(2)	5											51	58	56					5																	140229839		2196	4268	6464	140210023	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1759G>A	5.37:g.140229839G>A	ENSP00000436042:p.Ala587Thr		140210023	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.733054	0.30684	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.20598	2.06;2.06	3.36	2.44	0.29823	Cadherin (1);Cadherin-like (1);	0.289408	0.17547	U	0.170301	T	0.15176	0.0366	L	0.46885	1.475	0.09310	N	1	B;P	0.44260	0.25;0.83	B;B	0.34652	0.087;0.187	T	0.14392	-1.0474	10	0.87932	D	0	.	7.2873	0.26346	0.097:0.336:0.5671:0.0	.	587;587	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	T	587	ENSP00000436042:A587T;ENSP00000367362:A587T	ENSP00000367362:A587T	A	+	1	0	PCDHA9	140210023	0.000000	0.05858	0.406000	0.26421	0.550000	0.35303	0.196000	0.17176	0.665000	0.31066	0.313000	0.20887	GCC		0.667	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229839	G	A	140229839	3	1	61	1	0	0	0	0	1	0	0	0	11562	1087	38	1	1761	1	PCDHA9	5	140229839	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130	140229839	40685421	4148	12133										
PCDHA9	9752	broad.mit.edu	37	chr5	140230009	140230009	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggacgaaacggacgcaccGcgccagcgcctactggtgct	13	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140230009G>A	ENST00000532602.1	+	1	2962	c.1929G>A	c.(1927-1929)ccG>ccA	p.P643P	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Silent_p.P643P|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	643	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P643P(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGACGCACCGCGCCAGCGCC	0.687																																					Melanoma(55;1800 1972 14909)											2	Substitution - coding silent(2)	large_intestine(2)	5											53	56	55					5																	140230009		2197	4272	6469	140210193	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1929G>A	5.37:g.140230009G>A			140210193	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.687	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140230009	G	A	140230009	2	1	61	1	0	0	0	0	0	0	0	1	11562	1074	38	1		1	PCDHA9	5	140230009	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170	140230009	40685251	4149	12134										
PCDHA9	9752	broad.mit.edu	37	chr5	140230497	140230497	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttttctagcattttatTtatttatataattttttttc	4	3	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140230497T>A	ENST00000532602.1	+	1	3427				PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.F806Y|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F806Y(1)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCattttatttatttatata	0.383																																					Melanoma(55;1800 1972 14909)											1	Substitution - Missense(1)	large_intestine(1)	5											25	29	28					5																	140230497		2076	4212	6288	140210681	SO:0001627	intron_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2394+23T>A	5.37:g.140230497T>A			140210681	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	t	1.288	-0.608380	0.03717	.	.	ENSG00000204961	ENST00000378122	T	0.51071	0.72	2.92	0.107	0.14544	.	.	.	.	.	T	0.31918	0.0812	.	.	.	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.20638	-1.0269	8	0.35671	T	0.21	.	7.1857	0.25799	0.4883:0.0:0.0:0.5117	.	806	Q9Y5H5-2	.	Y	806	ENSP00000367362:F806Y	ENSP00000367362:F806Y	F	+	2	0	PCDHA9	140210681	0.008000	0.16893	0.000000	0.03702	0.061000	0.15899	0.534000	0.23098	-0.099000	0.12263	-1.258000	0.01471	TTT		0.383	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140230497	T	A	140230497	1	1	61	0	1	0	0	0	0	0	0	0	11562	1841	64	5		5	PCDHA9	5	140230497	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	488	140230497	40684763	4150	12135										
PCDHA10	56139	broad.mit.edu	37	chr5	140235705	140235705	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctcctcgcagcctgggaGgtggggagcggccagctcca	15	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140235705G>T	ENST00000307360.5	+	1	72	c.72G>T	c.(70-72)gaG>gaT	p.E24D	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.E24D|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	24					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E24D(2)		NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCCTGGGAGGTGGGGAGCG	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	5											56	65	62					5																	140235705		2196	4272	6468	140215889	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.72G>T	5.37:g.140235705G>T	ENSP00000304234:p.Glu24Asp		140215889	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.776785	0.00640	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.55234	0.53;0.63	4.31	-0.945	0.10388	.	.	.	.	.	T	0.39172	0.1068	L	0.49513	1.565	0.09310	N	1	B;B;B	0.18013	0.008;0.025;0.003	B;B;B	0.20577	0.03;0.021;0.017	T	0.28138	-1.0053	9	0.25106	T	0.35	.	3.6019	0.08028	0.2726:0.1051:0.5101:0.1122	.	24;24;24	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	D	24	ENSP00000421030:E24D;ENSP00000304234:E24D	ENSP00000304234:E24D	E	+	3	2	PCDHA10	140215889	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.018000	0.12568	-0.323000	0.08602	-1.134000	0.01955	GAG		0.612	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140235705	G	T	140235705	3	4	61	1	0	0	0	0	1	0	0	0	11551	991	35	2	74	2	PCDHA10	5	140235705	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5208	140235705	40679555	4151	12136										
PCDHA10	56139	broad.mit.edu	37	chr5	140236002	140236002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtggacgtggaagtgaaGgacattaacgacaacccgcc	12	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140236002G>T	ENST00000307360.5	+	1	369	c.369G>T	c.(367-369)aaG>aaT	p.K123N	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.K123N|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	123	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.K123N(2)		NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAAGTGAAGGACATTAACG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	5											130	131	130					5																	140236002		2198	4275	6473	140216186	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.369G>T	5.37:g.140236002G>T	ENSP00000304234:p.Lys123Asn		140216186	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	9.057	0.993554	0.19043	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.55234	0.53;0.64	4.45	2.67	0.31697	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.57169	0.2035	L	0.52573	1.65	0.22975	N	0.99849	D;P;P	0.57571	0.98;0.711;0.868	P;B;P	0.58577	0.841;0.365;0.452	T	0.42616	-0.9441	9	0.27082	T	0.32	.	8.0579	0.30617	0.1474:0.13:0.7225:0.0	.	123;123;123	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	N	123	ENSP00000421030:K123N;ENSP00000304234:K123N	ENSP00000304234:K123N	K	+	3	2	PCDHA10	140216186	0.000000	0.05858	0.961000	0.40146	0.798000	0.45092	-0.293000	0.08320	0.640000	0.30582	0.556000	0.70494	AAG		0.557	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140236002	G	T	140236002	3	4	61	1	0	0	0	0	1	0	0	0	11551	991	35	2	371	2	PCDHA10	5	140236002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297	140236002	40679258	4152	12137										
PCDHA10	56139	broad.mit.edu	37	chr5	140236519	140236519	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggaaattttggataaacGaaaggacgggagaaataaaa	12	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140236519G>A	ENST00000307360.5	+	1	886	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.E296K|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	296	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E296K(2)		NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGGATAAACGAAAGGACGGG	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	5											76	74	75					5																	140236519		2196	4267	6463	140216703	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.886G>A	5.37:g.140236519G>A	ENSP00000304234:p.Glu296Lys		140216703	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	2.780	-0.253696	0.05829	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.51574	0.7;0.7	4.29	2.44	0.29823	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.29126	0.0724	L	0.31120	0.905	0.09310	N	1	B;B;B	0.26708	0.026;0.157;0.031	B;B;B	0.19666	0.026;0.015;0.016	T	0.21965	-1.0230	9	0.49607	T	0.09	.	1.226	0.01933	0.1761:0.1952:0.4276:0.2012	.	296;296;296	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	K	296	ENSP00000421030:E296K;ENSP00000304234:E296K	ENSP00000304234:E296K	E	+	1	0	PCDHA10	140216703	0.000000	0.05858	0.138000	0.22173	0.192000	0.23643	-2.774000	0.00777	1.114000	0.41781	0.561000	0.74099	GAA		0.373	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140236519	G	A	140236519	3	1	61	1	0	0	0	0	1	0	0	0	11551	1059	37	1	888	1	PCDHA10	5	140236519	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	517	140236519	40678741	4153	12138										
PCDHA11	56138	broad.mit.edu	37	chr5	140249490	140249490	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcaaactaaacgccacaGaccgagacgaaggagtcaat	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140249490G>T	ENST00000398640.2	+	1	802	c.802G>T	c.(802-804)Gac>Tac	p.D268Y	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	268	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D268Y(1)		breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACGCCACAGACCGAGACGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											34	34	34					5																	140249490		1929	4147	6076	140229674	SO:0001583	missense	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.802G>T	5.37:g.140249490G>T	ENSP00000381636:p.Asp268Tyr		140229674	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335538	0.41398	.	.	ENSG00000249158	ENST00000398640	T	0.75260	-0.92	5.71	5.71	0.89125	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.94006	0.8080	H	0.99954	5.04	0.54753	D	0.99998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96838	0.9616	9	0.87932	D	0	.	19.8557	0.96758	0.0:0.0:1.0:0.0	.	268;268	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	Y	268	ENSP00000381636:D268Y	ENSP00000381636:D268Y	D	+	1	0	PCDHA11	140229674	1.000000	0.71417	0.957000	0.39632	0.036000	0.12997	9.593000	0.98250	2.707000	0.92482	0.655000	0.94253	GAC		0.383	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140249490	G	T	140249490	3	4	61	1	0	0	0	0	1	0	0	0	11552	942	33	2	804	2	PCDHA11	5	140249490	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12971	140249490	40665770	4154	12139										
PCDHA12	56137	broad.mit.edu	37	chr5	140255297	140255297	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctggaggtaaatctgcaGaatggcattttgtttgtgaa	11	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140255297G>T	ENST00000398631.2	+	1	240	c.240G>T	c.(238-240)caG>caT	p.Q80H	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q80H(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAATCTGCAGAATGGCATTT	0.622																																					Pancreas(113;759 1672 13322 24104 50104)											1	Substitution - Missense(1)	large_intestine(1)	5											84	99	94					5																	140255297		2203	4295	6498	140235481	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.240G>T	5.37:g.140255297G>T	ENSP00000381628:p.Gln80His		140235481	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.554640	0.65425	.	.	ENSG00000251664	ENST00000398631	T	0.28454	1.61	5.18	5.18	0.71444	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.52597	0.1744	M	0.82433	2.59	0.24444	N	0.994513	P;D	0.69078	0.704;0.997	B;P	0.57679	0.121;0.825	T	0.52223	-0.8604	9	0.87932	D	0	.	11.7681	0.51943	0.0818:0.0:0.9182:0.0	.	80;80	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	H	80	ENSP00000381628:Q80H	ENSP00000381628:Q80H	Q	+	3	2	PCDHA12	140235481	0.357000	0.24938	1.000000	0.80357	0.996000	0.88848	0.344000	0.19962	2.421000	0.82119	0.591000	0.81541	CAG		0.622	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140255297	G	T	140255297	3	4	61	1	0	0	0	0	1	0	0	0	11553	933	33	2	242	2	PCDHA12	5	140255297	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5807	140255297	40659963	4155	12140										
PCDHA12	56137	broad.mit.edu	37	chr5	140255897	140255897	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggagaaatttcctatggGatcaaaatgattttgccagt	9	5	1	2	rs557901977		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140255897G>A	ENST00000398631.2	+	1	840	c.840G>A	c.(838-840)ggG>ggA	p.G280G	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	280	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G280G(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCCTATGGGATCAAAATGA	0.353																																					Pancreas(113;759 1672 13322 24104 50104)											1	Substitution - coding silent(1)	large_intestine(1)	5											107	112	110					5																	140255897		1849	4103	5952	140236081	SO:0001819	synonymous_variant	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.840G>A	5.37:g.140255897G>A			140236081	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																				0.353	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140255897	G	A	140255897	2	1	61	1	0	0	0	0	0	0	0	1	11553	1161	41	3		3	PCDHA12	5	140255897	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	600	140255897	40659363	4156	12141										
PCDHA13	56136	broad.mit.edu	37	chr5	140262644	140262644	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaacattagtgatcaagcTaaatgccacagatcctgatg	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140262644T>G	ENST00000289272.2	+	1	791	c.791T>G	c.(790-792)cTa>cGa	p.L264R	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.L264R|PCDHA10_ENST00000307360.5_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	264	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L264R(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGATCAAGCTAAATGCCACA	0.418																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											101	97	98					5																	140262644		2203	4300	6503	140242828	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.791T>G	5.37:g.140262644T>G	ENSP00000289272:p.Leu264Arg		140242828	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.761956	0.69763	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.57107	0.42;0.42	5.58	5.58	0.84498	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.80243	0.4587	H	0.94183	3.505	0.31573	N	0.656089	D;D;D	0.76494	0.993;0.999;0.999	D;D;D	0.79108	0.992;0.979;0.983	D	0.86084	0.1546	9	0.87932	D	0	.	15.4067	0.74884	0.0:0.0:0.0:1.0	.	264;264;264	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	R	264	ENSP00000386821:L264R;ENSP00000289272:L264R	ENSP00000289272:L264R	L	+	2	0	PCDHA13	140242828	0.981000	0.34729	0.877000	0.34402	0.916000	0.54674	7.930000	0.87610	2.118000	0.64928	0.459000	0.35465	CTA		0.418	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		G	140262644	T	G	140262644	3	3	61	1	0	0	0	0	1	0	0	0	11554	1522	53	4	793	4	PCDHA13	5	140262644	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6747	140262644	40652616	4157	12142										
PCDHA13	56136	broad.mit.edu	37	chr5	140262739	140262739	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtatatgcatttaccataAatccgaacaatggagaaatt	7	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140262739A>C	ENST00000289272.2	+	1	886	c.886A>C	c.(886-888)Aat>Cat	p.N296H	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.N296H|PCDHA10_ENST00000307360.5_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	296	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N296H(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTTACCATAAATCCGAACAA	0.373																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											63	68	66					5																	140262739		2203	4300	6503	140242923	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.886A>C	5.37:g.140262739A>C	ENSP00000289272:p.Asn296His		140242923	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	A	9.397	1.077112	0.20227	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.62788	-0.0;-0.0	5.58	-5.68	0.02436	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.52008	0.1708	L	0.46947	1.48	0.09310	N	1	B;B;B	0.16396	0.003;0.017;0.013	B;B;B	0.28709	0.042;0.093;0.035	T	0.54241	-0.8323	9	0.56958	D	0.05	.	9.6622	0.39962	0.2826:0.2098:0.5075:0.0	.	296;296;296	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	H	296	ENSP00000386821:N296H;ENSP00000289272:N296H	ENSP00000289272:N296H	N	+	1	0	PCDHA13	140242923	0.000000	0.05858	0.005000	0.12908	0.712000	0.41017	-0.127000	0.10547	-0.808000	0.04387	0.459000	0.35465	AAT		0.373	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		C	140262739	A	C	140262739	3	2	61	1	0	0	0	0	1	0	0	0	11554	14	1	4	888	4	PCDHA13	5	140262739	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	95	140262739	40652521	4158	12143										
PCDHA13	56136	broad.mit.edu	37	chr5	140264248	140264248	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcagaatgcttgaaagagGtaagcttatattttaaaaaa	7	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140264248G>A	ENST00000289272.2	+	1	2394		c.e1+1		PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Splice_Site|PCDHA10_ENST00000307360.5_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGAAAGAGGTAAGCTTATA	0.423																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Unknown(1)	large_intestine(1)	5											28	34	32					5																	140264248		2203	4300	6503	140244432	SO:0001630	splice_region_variant	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2394+1G>A	5.37:g.140264248G>A			140244432	O75277	Splice_Site	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.843974	0.32606	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6253	0.84968	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCDHA13	140244432	1.000000	0.71417	0.202000	0.23494	0.016000	0.09150	4.266000	0.58871	2.219000	0.72066	0.655000	0.94253	.		0.423	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	Intron	A	140264248	G	A	140264248	5	1	61	1	0	0	0	0	0	0	1	0	11554	1275	44	3	2397	3	PCDHA13	5	140264248	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1509	140264248	40651012	4159	12144										
PCDHAC1	56135	broad.mit.edu	37	chr5	140307515	140307515	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggacttcctgactctttcGaacccagtacctgaggacgc	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140307515G>A	ENST00000253807.2	+	1	1038	c.1038G>A	c.(1036-1038)tcG>tcA	p.S346S	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.S346S|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	346					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S346S(1)		NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTCTTTCGAACCCAGTAC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	5											140	131	134					5																	140307515		2203	4300	6503	140287699	SO:0001819	synonymous_variant	56135			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1038G>A	5.37:g.140307515G>A			140287699	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																				0.517	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		A	140307515	G	A	140307515	2	1	61	1	0	0	0	0	0	0	0	1	11563	1045	37	1		1	PCDHAC1	5	140307515	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43267	140307515	40607745	4160	12145										
PCDHAC1	56135	broad.mit.edu	37	chr5	140308359	140308359	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcttagttcttcccactGatgcagttaagcagagggtg	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140308359G>A	ENST00000253807.2	+	1	1882	c.1882G>A	c.(1882-1884)Gat>Aat	p.D628N	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.D628N|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	628	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D628N(1)		NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTCCCACTGATGCAGTTAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											91	87	88					5																	140308359		2203	4300	6503	140288543	SO:0001583	missense	56135			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1882G>A	5.37:g.140308359G>A	ENSP00000253807:p.Asp628Asn		140288543	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425269	0.62733	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.51071	0.72;0.72	5.95	5.95	0.96441	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.73040	0.3536	M	0.79926	2.475	0.36727	D	0.881505	D;D	0.89917	0.998;1.0	D;D	0.85130	0.958;0.997	T	0.77832	-0.2441	9	0.72032	D	0.01	.	20.3747	0.98911	0.0:0.0:1.0:0.0	.	628;628	Q9H158;Q9H158-2	PCDC1_HUMAN;.	N	628	ENSP00000386356:D628N;ENSP00000253807:D628N	ENSP00000253807:D628N	D	+	1	0	PCDHAC1	140288543	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	9.240000	0.95396	2.817000	0.96982	0.563000	0.77884	GAT		0.532	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		A	140308359	G	A	140308359	3	1	61	1	0	0	0	0	1	0	0	0	11563	1290	45	3	1884	3	PCDHAC1	5	140308359	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	844	140308359	40606901	4161	12146										
PCDHAC2	56134	broad.mit.edu	37	chr5	140347077	140347077	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgctcgggtacggcacaGatctctgtgcgtgtcctgga	14	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140347077G>T	ENST00000289269.5	+	1	1258	c.726G>T	c.(724-726)caG>caT	p.Q242H	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	242	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.Q242H(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTACGGCACAGATCTCTGTGC	0.622																																					Melanoma(190;638 2083 3390 11909 52360)											1	Substitution - Missense(1)	large_intestine(1)	5											62	62	62					5																	140347077		2203	4300	6503	140327261	SO:0001583	missense	56134			AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.726G>T	5.37:g.140347077G>T	ENSP00000289269:p.Gln242His		140327261	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	37	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.044993	0.36085	.	.	ENSG00000243232	ENST00000289269	T	0.54279	0.58	5.72	3.93	0.45458	Cadherin (4);Cadherin-like (1);	0.000000	0.39834	N	0.001252	T	0.62575	0.2439	L	0.60957	1.885	0.45284	D	0.998288	P;D	0.71674	0.48;0.998	B;D	0.68943	0.333;0.961	T	0.57717	-0.7763	10	0.23891	T	0.37	.	9.3449	0.38102	0.2166:0.0:0.7834:0.0	.	242;242	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	H	242	ENSP00000289269:Q242H	ENSP00000289269:Q242H	Q	+	3	2	PCDHAC2	140327261	0.947000	0.32204	0.993000	0.49108	0.985000	0.73830	0.956000	0.29202	0.772000	0.33382	0.561000	0.74099	CAG		0.622	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		T	140347077	G	T	140347077	3	4	61	1	0	0	0	0	1	0	0	0	11564	933	33	2	728	2	PCDHAC2	5	140347077	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38718	140347077	40568183	4162	12147										
PCDHB1	29930	broad.mit.edu	37	chr5	140431319	140431319	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagatttgtttgtgaaggaGaaactggatcgggagtcact	15	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140431319G>T	ENST00000306549.3	+	1	341	c.264G>T	c.(262-264)gaG>gaT	p.E88D		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E88D(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTGTGAAGGAGAAACTGGATC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											71	76	74					5																	140431319		2203	4300	6503	140411503	SO:0001583	missense	29930			AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.264G>T	5.37:g.140431319G>T	ENSP00000307234:p.Glu88Asp		140411503	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	G	9.720	1.159500	0.21454	.	.	ENSG00000171815	ENST00000306549	T	0.32988	1.43	5.81	4.95	0.65309	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.48286	D	0.000197	T	0.26882	0.0658	L	0.56199	1.76	0.31584	N	0.654755	B	0.22909	0.077	B	0.23150	0.044	T	0.27806	-1.0063	10	0.44086	T	0.13	.	6.4025	0.21646	0.1398:0.0:0.6113:0.2489	.	88	Q9Y5F3	PCDB1_HUMAN	D	88	ENSP00000307234:E88D	ENSP00000307234:E88D	E	+	3	2	PCDHB1	140411503	0.175000	0.23083	1.000000	0.80357	0.995000	0.86356	-0.259000	0.08721	1.476000	0.48215	0.655000	0.94253	GAG		0.587	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		T	140431319	G	T	140431319	3	4	61	1	0	0	0	0	1	0	0	0	11565	933	33	2	266	2	PCDHB1	5	140431319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84242	140431319	40483941	4163	12148										
PCDHB1	29930	broad.mit.edu	37	chr5	140432112	140432112	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgatggtctcctctgtgTccagcccactccctgaagac	9	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140432112T>C	ENST00000306549.3	+	1	1134	c.1057T>C	c.(1057-1059)Tcc>Ccc	p.S353P		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	353	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S353P(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCCTCTGTGTCCAGCCCACT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											127	116	120					5																	140432112		2203	4300	6503	140412296	SO:0001583	missense	29930			AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1057T>C	5.37:g.140432112T>C	ENSP00000307234:p.Ser353Pro		140412296	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614979	0.46631	.	.	ENSG00000171815	ENST00000306549	T	0.02682	4.2	6.17	3.67	0.42095	Cadherin (2);Cadherin-like (1);	0.153560	0.30676	N	0.009107	T	0.04452	0.0122	L	0.53561	1.675	0.09310	N	1	P	0.38617	0.64	B	0.38296	0.27	T	0.22312	-1.0220	10	0.72032	D	0.01	.	11.291	0.49250	0.3676:0.0:0.0:0.6324	.	353	Q9Y5F3	PCDB1_HUMAN	P	353	ENSP00000307234:S353P	ENSP00000307234:S353P	S	+	1	0	PCDHB1	140412296	0.001000	0.12720	0.998000	0.56505	0.995000	0.86356	1.195000	0.32186	1.120000	0.41904	0.533000	0.62120	TCC		0.532	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		C	140432112	T	C	140432112	3	2	61	1	0	0	0	0	1	0	0	0	11565	1667	58	4	1059	4	PCDHB1	5	140432112	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	793	140432112	40483148	4164	12149										
PCDHB2	56133	broad.mit.edu	37	chr5	140474532	140474532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggccaatttgttaaaagAcctggggctggagataggag	15	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140474532A>G	ENST00000194155.4	+	1	306	c.158A>G	c.(157-159)gAc>gGc	p.D53G		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	53	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D53G(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTGTTAAAAGACCTGGGGCTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	64	62					5																	140474532		2203	4300	6503	140454716	SO:0001583	missense	56133			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.158A>G	5.37:g.140474532A>G	ENSP00000194155:p.Asp53Gly		140454716	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	A	17.77	3.470511	0.63625	.	.	ENSG00000112852	ENST00000194155	T	0.61627	0.09	5.37	4.13	0.48395	Cadherin, N-terminal (1);Cadherin (1);	.	.	.	.	T	0.79822	0.4512	M	0.92219	3.285	0.44677	D	0.997668	D	0.67145	0.996	D	0.81914	0.995	D	0.84525	0.0630	9	0.72032	D	0.01	.	12.6261	0.56630	0.8627:0.1373:0.0:0.0	.	53	Q9Y5E7	PCDB2_HUMAN	G	53	ENSP00000194155:D53G	ENSP00000194155:D53G	D	+	2	0	PCDHB2	140454716	1.000000	0.71417	0.999000	0.59377	0.700000	0.40528	7.350000	0.79385	2.164000	0.68074	0.533000	0.62120	GAC		0.512	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		G	140474532	A	G	140474532	3	3	61	1	0	0	0	0	1	0	0	0	11573	275	10	4	160	4	PCDHB2	5	140474532	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	42420	140474532	40440728	4165	12150										
PCDHB2	56133	broad.mit.edu	37	chr5	140476071	140476071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcccttcgtgctgtaccCgctgcagaacggctccgcgc	11	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140476071C>T	ENST00000194155.4	+	1	1845	c.1697C>T	c.(1696-1698)cCg>cTg	p.P566L		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	566					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.P566L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGCTGTACCCGCTGCAGAAC	0.741																																																1	Substitution - Missense(1)	large_intestine(1)	5											10	12	11					5																	140476071		2141	4136	6277	140456255	SO:0001583	missense	56133			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1697C>T	5.37:g.140476071C>T	ENSP00000194155:p.Pro566Leu		140456255	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.958622	0.74016	.	.	ENSG00000112852	ENST00000194155	T	0.60920	0.15	4.5	4.5	0.54988	Cadherin-like (1);	.	.	.	.	D	0.83069	0.5174	H	0.95950	3.745	0.58432	D	0.999998	D	0.89917	1.0	D	0.69479	0.964	D	0.89429	0.3715	9	0.87932	D	0	.	17.2624	0.87073	0.0:1.0:0.0:0.0	.	566	Q9Y5E7	PCDB2_HUMAN	L	566	ENSP00000194155:P566L	ENSP00000194155:P566L	P	+	2	0	PCDHB2	140456255	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.590000	0.61013	2.223000	0.72356	0.556000	0.70494	CCG		0.741	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		T	140476071	C	T	140476071	3	4	61	1	0	0	0	0	1	0	0	0	11573	652	23	1	1699	1	PCDHB2	5	140476071	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1539	140476071	40439189	4166	12151										
PCDHB3	56132	broad.mit.edu	37	chr5	140480531	140480531	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagctatgcggccccacaGaaccatgcatactacatttt	8	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140480531G>T	ENST00000231130.2	+	1	298	c.298G>T	c.(298-300)Gaa>Taa	p.E100*	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	100	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E100*(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCCCCACAGAACCATGCAT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											86	91	89					5																	140480531		2203	4300	6503	140460715	SO:0001587	stop_gained	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.298G>T	5.37:g.140480531G>T	ENSP00000231130:p.Glu100*		140460715	B2R8P2	Nonsense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.140771	0.56936	.	.	ENSG00000113205	ENST00000231130	.	.	.	4.7	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	14.3757	0.66874	0.0:0.0:0.8522:0.1478	.	.	.	.	X	100	.	ENSP00000231130:E100X	E	+	1	0	PCDHB3	140460715	0.000000	0.05858	0.251000	0.24312	0.994000	0.84299	0.107000	0.15375	2.305000	0.77605	0.655000	0.94253	GAA		0.438	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140480531	G	T	140480531	4	4	61	1	0	0	0	0	0	1	0	0	11574	943	33	2	300	2	PCDHB3	5	140480531	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4460	140480531	40434729	4167	12152										
PCDHB3	56132	broad.mit.edu	37	chr5	140481092	140481092	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttttcatgcttctgaaGaaattcgcaaaacttttcag	5	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140481092G>T	ENST00000231130.2	+	1	859	c.859G>T	c.(859-861)Gaa>Taa	p.E287*	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	287	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E287*(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTTCTGAAGAAATTCGCAA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											47	52	51					5																	140481092		2203	4300	6503	140461276	SO:0001587	stop_gained	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.859G>T	5.37:g.140481092G>T	ENSP00000231130:p.Glu287*		140461276	B2R8P2	Nonsense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.877958	0.72294	.	.	ENSG00000113205	ENST00000231130	.	.	.	4.93	3.0	0.34707	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	5.9812	0.19409	0.1683:0.1712:0.6605:0.0	.	.	.	.	X	287	.	ENSP00000231130:E287X	E	+	1	0	PCDHB3	140461276	0.000000	0.05858	1.000000	0.80357	0.993000	0.82548	0.366000	0.20365	2.438000	0.82558	0.655000	0.94253	GAA		0.363	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140481092	G	T	140481092	4	4	61	1	0	0	0	0	0	1	0	0	11574	943	33	2	861	2	PCDHB3	5	140481092	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	561	140481092	40434168	4168	12153										
PCDHB3	56132	broad.mit.edu	37	chr5	140482357	140482357	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttttcggtgctcctgttCgtggcggtgcggctgtgcag	15	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140482357C>T	ENST00000231130.2	+	1	2124	c.2124C>T	c.(2122-2124)ttC>ttT	p.F708F	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	708					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.F708F(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTCCTGTTCGTGGCGGTGC	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	5											63	66	65					5																	140482357		2137	4186	6323	140462541	SO:0001819	synonymous_variant	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.2124C>T	5.37:g.140482357C>T			140462541	B2R8P2	Silent	SNP	ENST00000231130.2	37	CCDS4245.1																																																																																				0.687	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140482357	C	T	140482357	2	4	61	1	0	0	0	0	0	0	0	1	11574	883	31	1		1	PCDHB3	5	140482357	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1265	140482357	40432903	4169	12154										
PCDHB5	26167	broad.mit.edu	37	chr5	140516950	140516950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggtggtgctggtcaaggAcaatggcgagcctccgcgct	16	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140516950A>G	ENST00000231134.5	+	1	2151	c.1934A>G	c.(1933-1935)gAc>gGc	p.D645G		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	645	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D645G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGGTCAAGGACAATGGCGAG	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	5											22	26	25					5																	140516950		2102	4097	6199	140497134	SO:0001583	missense	26167			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1934A>G	5.37:g.140516950A>G	ENSP00000231134:p.Asp645Gly		140497134	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198666	0.58126	.	.	ENSG00000113209	ENST00000231134	T	0.68765	-0.35	4.71	4.71	0.59529	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.89698	0.6790	H	0.99675	4.695	0.43740	D	0.996239	D	0.89917	1.0	D	0.74674	0.984	D	0.94094	0.7356	9	0.87932	D	0	.	14.5112	0.67789	1.0:0.0:0.0:0.0	.	645	Q9Y5E4	PCDB5_HUMAN	G	645	ENSP00000231134:D645G	ENSP00000231134:D645G	D	+	2	0	PCDHB5	140497134	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	7.288000	0.78691	1.892000	0.54788	0.352000	0.21897	GAC		0.721	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		G	140516950	A	G	140516950	3	3	61	1	0	0	0	0	1	0	0	0	11576	275	10	4	1936	4	PCDHB5	5	140516950	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	34593	140516950	40398310	4170	12155										
PCDHB5	26167	broad.mit.edu	37	chr5	140517137	140517137	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttttcggtgctcctgttCgtggcagtgcggctgtgcag	14	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140517137C>T	ENST00000231134.5	+	1	2338	c.2121C>T	c.(2119-2121)ttC>ttT	p.F707F		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	707					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F707F(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTCCTGTTCGTGGCAGTGC	0.692																																																1	Substitution - coding silent(1)	large_intestine(1)	5											87	94	92					5																	140517137		2201	4296	6497	140497321	SO:0001819	synonymous_variant	26167			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2121C>T	5.37:g.140517137C>T			140497321	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	37	CCDS4247.1																																																																																				0.692	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		T	140517137	C	T	140517137	2	4	61	1	0	0	0	0	0	0	0	1	11576	883	31	1		1	PCDHB5	5	140517137	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187	140517137	40398123	4171	12156										
PCDHB6	56130	broad.mit.edu	37	chr5	140531462	140531462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccccggcgttgagcagcGaggcgctggtgcgcttgctg	17	13	0	1	rs374444657		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140531462G>A	ENST00000231136.1	+	1	1624	c.1624G>A	c.(1624-1626)Gag>Aag	p.E542K	PCDHB6_ENST00000543635.1_Missense_Mutation_p.E406K	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	542	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E542K(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTTGAGCAGCGAGGCGCTGGT	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	5											49	56	54					5																	140531462		2201	4299	6500	140511646	SO:0001583	missense	56130			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1624G>A	5.37:g.140531462G>A	ENSP00000231136:p.Glu542Lys		140511646	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.509298	0.44660	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01705	4.68;4.68	4.19	0.953	0.19590	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01489	0.0048	N	0.05124	-0.11	0.24382	N	0.994788	P	0.43909	0.821	B	0.44044	0.439	T	0.54146	-0.8337	9	0.87932	D	0	.	9.8575	0.41094	0.1653:0.518:0.3167:0.0	.	542	Q9Y5E3	PCDB6_HUMAN	K	406;542;327	ENSP00000438466:E406K;ENSP00000231136:E542K	ENSP00000231136:E542K	E	+	1	0	PCDHB6	140511646	0.000000	0.05858	0.998000	0.56505	0.947000	0.59692	0.140000	0.16056	0.342000	0.23796	0.556000	0.70494	GAG		0.687	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		A	140531462	G	A	140531462	3	1	61	1	0	0	0	0	1	0	0	0	11577	1059	37	1	1626	1	PCDHB6	5	140531462	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14325	140531462	40383798	4172	12157										
PCDHB6	56130	broad.mit.edu	37	chr5	140531942	140531942	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcgtcgctcttcctctttTcggtgctcctgttcgtggcg	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140531942T>G	ENST00000231136.1	+	1	2104	c.2104T>G	c.(2104-2106)Tcg>Gcg	p.S702A	PCDHB6_ENST00000543635.1_Missense_Mutation_p.S566A	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	702					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S702A(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCCTCTTTTCGGTGCTCCT	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	93	89					5																	140531942		2201	4287	6488	140512126	SO:0001583	missense	56130			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2104T>G	5.37:g.140531942T>G	ENSP00000231136:p.Ser702Ala		140512126	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.486295	0.26686	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.16457	2.34;2.34	4.55	3.34	0.38264	.	.	.	.	.	T	0.28962	0.0719	L	0.38175	1.15	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.06110	-1.0845	9	0.72032	D	0.01	.	8.5918	0.33693	0.3079:0.0:0.0:0.6921	.	702	Q9Y5E3	PCDB6_HUMAN	A	566;702	ENSP00000438466:S566A;ENSP00000231136:S702A	ENSP00000231136:S702A	S	+	1	0	PCDHB6	140512126	0.003000	0.15002	0.002000	0.10522	0.731000	0.41821	1.034000	0.30204	0.671000	0.31185	0.454000	0.30748	TCG		0.687	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		G	140531942	T	G	140531942	3	3	61	1	0	0	0	0	1	0	0	0	11577	1783	62	4	2106	4	PCDHB6	5	140531942	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	480	140531942	40383318	4173	12158										
PCDHB7	56129	broad.mit.edu	37	chr5	140552816	140552816	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatcacgctccagtatttCtagacagagagatttccttg	8	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140552816C>A	ENST00000231137.3	+	1	574	c.400C>A	c.(400-402)Cta>Ata	p.L134I		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	134					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L134I(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCAGTATTTCTAGACAGAGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											59	64	62					5																	140552816		2203	4300	6503	140533000	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.400C>A	5.37:g.140552816C>A	ENSP00000231137:p.Leu134Ile		140533000	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	C	0.205	-1.041352	0.02013	.	.	ENSG00000113212	ENST00000231137	T	0.20598	2.06	4.61	3.72	0.42706	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.28300	0.0699	M	0.75777	2.31	0.09310	N	1	P	0.45672	0.864	P	0.46543	0.52	T	0.08973	-1.0696	9	0.22109	T	0.4	.	8.5221	0.33282	0.0:0.7582:0.0:0.2418	.	134	Q9Y5E2	PCDB7_HUMAN	I	134	ENSP00000231137:L134I	ENSP00000231137:L134I	L	+	1	2	PCDHB7	140533000	0.000000	0.05858	0.962000	0.40283	0.100000	0.18952	-1.183000	0.03079	2.248000	0.74166	0.655000	0.94253	CTA		0.448	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140552816	C	A	140552816	3	1	61	1	0	0	0	0	1	0	0	0	11578	912	32	2	402	2	PCDHB7	5	140552816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20874	140552816	40362444	4174	12159										
PCDHB7	56129	broad.mit.edu	37	chr5	140552891	140552891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcctagagagtgcacagGattcagatgttggaaccaac	10	9	2	2	rs201008826		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140552891G>A	ENST00000231137.3	+	1	649	c.475G>A	c.(475-477)Gat>Aat	p.D159N		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D159N(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGTGCACAGGATTCAGATGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	5											56	58	57					5																	140552891		2203	4300	6503	140533075	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.475G>A	5.37:g.140552891G>A	ENSP00000231137:p.Asp159Asn		140533075	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578865	0.86645	.	.	ENSG00000113212	ENST00000231137	T	0.41400	1.0	4.61	4.61	0.57282	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.82093	0.4962	H	0.99900	4.915	0.52501	D	0.999955	D	0.89917	1.0	D	0.97110	1.0	D	0.91527	0.5239	9	0.87932	D	0	.	17.4139	0.87494	0.0:0.0:1.0:0.0	.	159	Q9Y5E2	PCDB7_HUMAN	N	159	ENSP00000231137:D159N	ENSP00000231137:D159N	D	+	1	0	PCDHB7	140533075	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.809000	0.99208	2.248000	0.74166	0.655000	0.94253	GAT		0.448	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140552891	G	A	140552891	3	1	61	1	0	0	0	0	1	0	0	0	11578	1174	41	3	477	3	PCDHB7	5	140552891	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75	140552891	40362369	4175	12160										
PCDHB7	56129	broad.mit.edu	37	chr5	140553173	140553173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacaaggtgcaggtgcccGaaaatagccccgttggttcc	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140553173G>A	ENST00000231137.3	+	1	931	c.757G>A	c.(757-759)Gaa>Aaa	p.E253K		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	253	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E253K(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCAGGTGCCCGAAAATAGCCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	5											65	70	69					5																	140553173		2203	4300	6503	140533357	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.757G>A	5.37:g.140553173G>A	ENSP00000231137:p.Glu253Lys		140533357	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294126	0.60086	.	.	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.76316	-1.01	4.61	4.61	0.57282	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.92691	0.7677	H	0.98111	4.15	0.49798	D	0.999827	D	0.89917	1.0	D	0.97110	1.0	D	0.95632	0.8690	9	0.87932	D	0	.	17.4139	0.87494	0.0:0.0:1.0:0.0	.	253	Q9Y5E2	PCDB7_HUMAN	K	253;36	ENSP00000231137:E253K	ENSP00000231137:E253K	E	+	1	0	PCDHB7	140533357	1.000000	0.71417	0.034000	0.17996	0.077000	0.17291	9.783000	0.99037	2.248000	0.74166	0.655000	0.94253	GAA		0.517	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140553173	G	A	140553173	3	1	61	1	0	0	0	0	1	0	0	0	11578	1059	37	1	759	1	PCDHB7	5	140553173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282	140553173	40362087	4176	12161										
PCDHB16	57717	broad.mit.edu	37	chr5	140564258	140564258	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttttcggtgctcctgttCgtggcggtgcggctgtgcag	15	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140564258C>T	ENST00000361016.2	+	1	3279	c.2124C>T	c.(2122-2124)ttC>ttT	p.F708F		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	708					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F708F(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTCCTGTTCGTGGCGGTGC	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	5											73	82	79					5																	140564258		2199	4290	6489	140544442	SO:0001819	synonymous_variant	57717			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2124C>T	5.37:g.140564258C>T			140544442	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																				0.687	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140564258	C	T	140564258	2	4	61	1	0	0	0	0	0	0	0	1	11572	883	31	1		1	PCDHB16	5	140564258	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11085	140564258	40351002	4177	12162										
PCDHB10	56126	broad.mit.edu	37	chr5	140573400	140573400	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcactatcaccgtcactgaCttggggacacccaggctgaa	9	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140573400C>A	ENST00000239446.4	+	1	1459	c.1275C>A	c.(1273-1275)gaC>gaA	p.D425E		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	425	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D425E(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGTCACTGACTTGGGGACAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											104	101	102					5																	140573400		2203	4300	6503	140553584	SO:0001583	missense	56126			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1275C>A	5.37:g.140573400C>A	ENSP00000239446:p.Asp425Glu		140553584	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726488	0.30593	.	.	ENSG00000120324	ENST00000239446	T	0.67865	-0.29	3.22	1.38	0.22167	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.87977	0.6314	H	0.99379	4.54	0.23095	N	0.998309	D	0.89917	1.0	D	0.97110	1.0	T	0.75830	-0.3179	9	0.87932	D	0	.	8.2953	0.31982	0.0:0.71:0.0:0.29	.	425	Q9UN67	PCDBA_HUMAN	E	425	ENSP00000239446:D425E	ENSP00000239446:D425E	D	+	3	2	PCDHB10	140553584	0.000000	0.05858	0.033000	0.17914	0.472000	0.32918	-1.723000	0.01866	0.698000	0.31739	0.549000	0.68633	GAC		0.512	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573400	C	A	140573400	3	1	61	1	0	0	0	0	1	0	0	0	11566	564	20	2	1277	2	PCDHB10	5	140573400	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9142	140573400	40341860	4178	12163										
PCDHB10	56126	broad.mit.edu	37	chr5	140573743	140573743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagaccgcggctcccccGcgctgagcagagaggcgctg	14	17	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140573743G>A	ENST00000239446.4	+	1	1802	c.1618G>A	c.(1618-1620)Gcg>Acg	p.A540T		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	540	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A540T(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCTCCCCCGCGCTGAGCAG	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	5											43	60	54					5																	140573743		2198	4297	6495	140553927	SO:0001583	missense	56126			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1618G>A	5.37:g.140573743G>A	ENSP00000239446:p.Ala540Thr		140553927	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	g	16.42	3.117862	0.56505	.	.	ENSG00000120324	ENST00000239446	T	0.03181	4.02	3.53	-1.23	0.09465	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.10809	0.0264	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.72338	0.977	T	0.16541	-1.0399	9	0.62326	D	0.03	.	4.8786	0.13668	0.0854:0.389:0.3897:0.1359	.	540	Q9UN67	PCDBA_HUMAN	T	540	ENSP00000239446:A540T	ENSP00000239446:A540T	A	+	1	0	PCDHB10	140553927	0.000000	0.05858	0.352000	0.25734	0.941000	0.58515	-0.605000	0.05661	-0.033000	0.13736	0.549000	0.68633	GCG		0.697	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573743	G	A	140573743	3	1	61	1	0	0	0	0	1	0	0	0	11566	1087	38	1	1620	1	PCDHB10	5	140573743	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	343	140573743	40341517	4179	12164										
PCDHB11	56125	broad.mit.edu	37	chr5	140579801	140579801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtcccgttggtgctgtgTtcttactagaaagtgcgaag	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140579801T>C	ENST00000354757.3	+	1	454	c.454T>C	c.(454-456)Ttc>Ctc	p.F152L	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	152	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.F152L(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGTGCTGTGTTCTTACTAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	114	111					5																	140579801		2203	4300	6503	140559985	SO:0001583	missense	56125			AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.454T>C	5.37:g.140579801T>C	ENSP00000346802:p.Phe152Leu		140559985	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.540165	0.65085	.	.	ENSG00000197479	ENST00000354757	T	0.47177	0.85	2.8	1.57	0.23409	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.60792	0.2296	M	0.71871	2.18	0.20403	N	0.999905	P	0.36874	0.572	P	0.55577	0.779	T	0.54302	-0.8314	9	0.52906	T	0.07	.	6.7601	0.23536	0.3774:0.0:0.0:0.6226	.	152	Q9Y5F2	PCDBB_HUMAN	L	152	ENSP00000346802:F152L	ENSP00000346802:F152L	F	+	1	0	PCDHB11	140559985	0.993000	0.37304	0.002000	0.10522	0.909000	0.53808	4.574000	0.60900	0.275000	0.22094	0.383000	0.25322	TTC		0.398	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		C	140579801	T	C	140579801	3	2	61	1	0	0	0	0	1	0	0	0	11567	1725	60	4	456	4	PCDHB11	5	140579801	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6058	140579801	40335459	4180	12165										
PCDHB12	56124	broad.mit.edu	37	chr5	140589503	140589503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggtgatggatgtaaacGacaacgctcctgaaatcact	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140589503G>A	ENST00000239450.2	+	1	1213	c.1024G>A	c.(1024-1026)Gac>Aac	p.D342N	PCDHB12_ENST00000541609.1_Missense_Mutation_p.D5N	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	342	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D342N(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGATGTAAACGACAACGCTCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											85	84	84					5																	140589503		2202	4300	6502	140569687	SO:0001583	missense	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1024G>A	5.37:g.140589503G>A	ENSP00000239450:p.Asp342Asn		140569687	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205659	0.79127	.	.	ENSG00000120328	ENST00000541609;ENST00000239450	T;T	0.64085	-0.08;-0.08	4.06	4.06	0.47325	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.84311	0.5444	H	0.96833	3.89	0.35846	D	0.826402	D	0.89917	1.0	D	0.81914	0.995	D	0.90831	0.4716	9	0.87932	D	0	.	11.3121	0.49370	0.0945:0.0:0.9055:0.0	.	342	Q9Y5F1	PCDBC_HUMAN	N	5;342	ENSP00000440199:D5N;ENSP00000239450:D342N	ENSP00000239450:D342N	D	+	1	0	PCDHB12	140569687	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	4.182000	0.58310	1.969000	0.57287	0.491000	0.48974	GAC		0.418	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		A	140589503	G	A	140589503	3	1	61	1	0	0	0	0	1	0	0	0	11568	1058	37	1	1026	1	PCDHB12	5	140589503	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9702	140589503	40325757	4181	12166										
PCDHB12	56124	broad.mit.edu	37	chr5	140589653	140589653	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccggaggacatcccattcGtgctaaaatcttcggtaaat	8	11	1	0	rs201620775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140589653G>A	ENST00000239450.2	+	1	1363	c.1174G>A	c.(1174-1176)Gtg>Atg	p.V392M	PCDHB12_ENST00000541609.1_Missense_Mutation_p.V55M	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	392	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.V392M(3)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CATCCCATTCGTGCTAAAATC	0.473																																																3	Substitution - Missense(3)	large_intestine(1)|stomach(1)|pancreas(1)	5											65	65	65					5																	140589653		2203	4300	6503	140569837	SO:0001583	missense	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1174G>A	5.37:g.140589653G>A	ENSP00000239450:p.Val392Met		140569837	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	1.461	-0.562455	0.03939	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.51817	0.69;0.69	3.87	-3.13	0.05266	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.40473	0.1118	M	0.62088	1.915	0.09310	N	1	B	0.29805	0.257	B	0.33254	0.16	T	0.42275	-0.9461	9	0.51188	T	0.08	.	5.076	0.14632	0.4002:0.2645:0.3354:0.0	.	392	Q9Y5F1	PCDBC_HUMAN	M	55;392;12	ENSP00000440199:V55M;ENSP00000239450:V392M	ENSP00000239450:V392M	V	+	1	0	PCDHB12	140569837	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-1.666000	0.01963	-0.715000	0.04968	-0.479000	0.04858	GTG		0.473	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		A	140589653	G	A	140589653	3	1	61	1	0	0	0	0	1	0	0	0	11568	1145	40	1	1176	1	PCDHB12	5	140589653	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	150	140589653	40325607	4182	12167										
PCDHB13	56123	broad.mit.edu	37	chr5	140594625	140594625	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaaaaaacaactcgatttCgaaaaacttcagtcctatga	4	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140594625C>T	ENST00000341948.4	+	1	1117	c.930C>T	c.(928-930)ttC>ttT	p.F310F		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	310	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F310F(2)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACTCGATTTCGAAAAACTTC	0.378																																																2	Substitution - coding silent(2)	large_intestine(2)	5																																								140574809	SO:0001819	synonymous_variant	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.930C>T	5.37:g.140594625C>T			140574809	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																				0.378	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		T	140594625	C	T	140594625	2	4	61	1	0	0	0	0	0	0	0	1	11569	883	31	1		1	PCDHB13	5	140594625	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4972	140594625	40320635	4183	12168										
PCDHB13	56123	broad.mit.edu	37	chr5	140595806	140595806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttcgctcttcctcttttCggtgctcctgttcgtggcgg	11	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140595806C>T	ENST00000341948.4	+	1	2298	c.2111C>T	c.(2110-2112)tCg>tTg	p.S704L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	704					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S704L(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCCTCTTTTCGGTGCTCCTG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	5											91	98	96					5																	140595806		2201	4289	6490	140575990	SO:0001583	missense	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.2111C>T	5.37:g.140595806C>T	ENSP00000345491:p.Ser704Leu		140575990	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	-	14.94	2.684665	0.47991	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.20463	2.07	3.5	-1.21	0.09524	.	.	.	.	.	T	0.47358	0.1441	H	0.96970	3.915	0.09310	N	1	D	0.62365	0.991	P	0.53035	0.716	T	0.45381	-0.9265	9	0.56958	D	0.05	.	9.6602	0.39950	0.0:0.3473:0.5625:0.0902	.	704	Q9Y5F0	PCDBD_HUMAN	L	704;704;650	ENSP00000345491:S704L	ENSP00000345491:S704L	S	+	2	0	PCDHB13	140575990	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.009000	0.03660	-0.623000	0.05618	-0.736000	0.03550	TCG		0.687	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		T	140595806	C	T	140595806	3	4	61	1	0	0	0	0	1	0	0	0	11569	893	31	1	2113	1	PCDHB13	5	140595806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1181	140595806	40319454	4184	12169										
PCDHB15	56121	broad.mit.edu	37	chr5	140626044	140626044	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctaagcagcctttcaggaGaaattcgactaattaaaaaa	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140626044G>T	ENST00000231173.3	+	1	898	c.898G>T	c.(898-900)Gaa>Taa	p.E300*		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	300	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E300*(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTTTCAGGAGAAATTCGACT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											68	72	70					5																	140626044		2203	4300	6503	140606228	SO:0001587	stop_gained	56121			AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.898G>T	5.37:g.140626044G>T	ENSP00000231173:p.Glu300*		140606228	Q8IUX5	Nonsense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.699120	0.68501	.	.	ENSG00000113248	ENST00000231173	.	.	.	4.8	3.93	0.45458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	8.2825	0.31908	0.251:0.0:0.749:0.0	.	.	.	.	X	300	.	ENSP00000231173:E300X	E	+	1	0	PCDHB15	140606228	0.989000	0.36119	1.000000	0.80357	0.805000	0.45488	2.269000	0.43346	1.139000	0.42245	0.491000	0.48974	GAA		0.398	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		T	140626044	G	T	140626044	4	4	61	1	0	0	0	0	0	1	0	0	11571	943	33	2	900	2	PCDHB15	5	140626044	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30238	140626044	40289216	4185	12170										
TAF7	6879	broad.mit.edu	37	chr5	140698862	140698862	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgtctctccagatcttcCtccgtgtcaatgatgtttat	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140698862C>A	ENST00000313368.5	-	1	1468	c.750G>T	c.(748-750)gaG>gaT	p.E250D		NM_005642.2	NP_005633.2	Q15545	TAF7_HUMAN	TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55kDa	250					DNA-templated transcription, initiation (GO:0006352)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of histone acetylation (GO:0035067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermine transport (GO:0000296)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	histone acetyltransferase binding (GO:0035035)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|vitamin D receptor binding (GO:0042809)	p.E250D(1)		central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGATCTTCCTCCGTGTCAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											259	244	249					5																	140698862		2203	4300	6503	140679046	SO:0001583	missense	6879			AF349038	CCDS4259.1	5q31	2008-02-05	2002-08-29	2001-12-07	ENSG00000178913	ENSG00000178913			11541	protein-coding gene	gene with protein product		600573	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, F, 55kD"	TAF2F		7824954	Standard	NM_005642		Approved	TAFII55	uc003ljg.3	Q15545	OTTHUMG00000129628	ENST00000313368.5:c.750G>T	5.37:g.140698862C>A	ENSP00000312709:p.Glu250Asp		140679046	B2RBV9|Q13036	Missense_Mutation	SNP	ENST00000313368.5	37	CCDS4259.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974383	0.53720	.	.	ENSG00000178913	ENST00000313368	T	0.26518	1.73	4.54	-0.326	0.12698	.	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	L	0.59436	1.845	0.49299	D	0.999778	D	0.69078	0.997	D	0.72625	0.978	T	0.05886	-1.0858	10	0.44086	T	0.13	-23.5272	8.7454	0.34583	0.0:0.5838:0.0:0.4162	.	250	Q15545	TAF7_HUMAN	D	250	ENSP00000312709:E250D	ENSP00000312709:E250D	E	-	3	2	TAF7	140679046	0.998000	0.40836	0.993000	0.49108	0.986000	0.74619	0.588000	0.23924	-0.188000	0.10499	-0.136000	0.14681	GAG		0.443	TAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251823.2	NM_005642		A	140698862	C	A	140698862	3	1	61	1	0	0	0	0	1	0	0	0	15571	680	24	2	303	2	TAF7	5	140698862	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72818	140698862	40216398	4186	12171										
PCDHGA1	56114	broad.mit.edu	37	chr5	140710707	140710707	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgactccaggtaccagagtCtcattgccttttgggcaaga	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140710707C>A	ENST00000517417.1	+	1	456	c.456C>A	c.(454-456)gtC>gtA	p.V152V	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Silent_p.V152V	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	152	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs2472647). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V152V(1)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTACCAGAGTCTCATTGCCTT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	5											108	115	113					5																	140710707		2203	4300	6503	140690891	SO:0001819	synonymous_variant	56114			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.456C>A	5.37:g.140710707C>A			140690891	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																				0.428	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140710707	C	A	140710707	2	1	61	1	0	0	0	0	0	0	0	1	11581	900	32	2		2	PCDHGA1	5	140710707	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11845	140710707	40204553	4187	12172										
PCDHGA1	56114	broad.mit.edu	37	chr5	140711330	140711330	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgcagttccagaaaactTtcctcctgggaccataattg	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140711330T>G	ENST00000517417.1	+	1	1079	c.1079T>G	c.(1078-1080)tTt>tGt	p.F360C	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.F360C	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	360	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F360C(1)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGAAAACTTTCCTCCTGGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											52	50	51					5																	140711330		2203	4300	6503	140691514	SO:0001583	missense	56114			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1079T>G	5.37:g.140711330T>G	ENSP00000431083:p.Phe360Cys		140691514	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.259203	0.23051	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.01745	4.66;4.66	3.99	0.421	0.16451	Cadherin (3);Cadherin-like (1);	0.549198	0.14905	U	0.291581	T	0.01287	0.0042	N	0.19112	0.55	0.22342	N	0.999181	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.46062	-0.9218	10	0.45353	T	0.12	.	4.7734	0.13167	0.0:0.4592:0.2:0.3407	.	360;360	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	C	360	ENSP00000431083:F360C;ENSP00000367345:F360C	ENSP00000367345:F360C	F	+	2	0	PCDHGA1	140691514	0.000000	0.05858	0.999000	0.59377	0.986000	0.74619	0.439000	0.21575	0.241000	0.21283	0.528000	0.53228	TTT		0.428	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140711330	T	G	140711330	3	3	61	1	0	0	0	0	1	0	0	0	11581	1841	64	4	1081	4	PCDHGA1	5	140711330	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	623	140711330	40203930	4188	12173										
PCDHGA1	56114	broad.mit.edu	37	chr5	140712638	140712638	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctatcagcaccccagtCtttacttgaagacaaaaagg	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140712638C>A	ENST00000517417.1	+	1	2387	c.2387C>A	c.(2386-2388)tCt>tAt	p.S796Y	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.S796Y	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	796					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S796Y(1)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACCCCAGTCTTTACTTGAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											71	78	76					5																	140712638		2203	4300	6503	140692822	SO:0001583	missense	56114			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2387C>A	5.37:g.140712638C>A	ENSP00000431083:p.Ser796Tyr		140692822	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	.	12.42	1.933493	0.34096	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	D;T	0.95622	-3.76;0.68	4.14	-1.34	0.09143	.	1.079070	0.07300	N	0.873951	D	0.91216	0.7232	L	0.39020	1.185	0.09310	N	1	B;B	0.33044	0.378;0.395	B;B	0.38500	0.275;0.197	T	0.82971	-0.0192	10	0.87932	D	0	.	1.3972	0.02263	0.2642:0.331:0.2479:0.1568	.	796;796	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	Y	796	ENSP00000431083:S796Y;ENSP00000367345:S796Y	ENSP00000367345:S796Y	S	+	2	0	PCDHGA1	140692822	0.013000	0.17824	0.005000	0.12908	0.971000	0.66376	1.369000	0.34227	-0.434000	0.07275	0.585000	0.79938	TCT		0.423	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140712638	C	A	140712638	3	1	61	1	0	0	0	0	1	0	0	0	11581	913	32	2	2389	2	PCDHGA1	5	140712638	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1308	140712638	40202622	4189	12174										
PCDHGA2	56113	broad.mit.edu	37	chr5	140720178	140720178	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccactcagtagcaatgtatCattaagcctgttcgtgctgg	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140720178C>A	ENST00000394576.2	+	1	1640	c.1640C>A	c.(1639-1641)tCa>tAa	p.S547*	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	547	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S547*(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAATGTATCATTAAGCCTG	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											168	166	167					5																	140720178		2203	4300	6503	140700362	SO:0001587	stop_gained	56113			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1640C>A	5.37:g.140720178C>A	ENSP00000378077:p.Ser547*		140700362	Q52LL6|Q9Y5D5	Nonsense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	13.83	2.354826	0.41700	.	.	ENSG00000081853	ENST00000394576	.	.	.	4.88	4.0	0.46444	.	0.000000	0.36519	U	0.002555	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2257	0.73348	0.0:0.8584:0.1416:0.0	.	.	.	.	X	547	.	ENSP00000378077:S547X	S	+	2	0	PCDHGA2	140700362	0.009000	0.17119	0.020000	0.16555	0.026000	0.11368	1.726000	0.38085	1.185000	0.42971	0.485000	0.47835	TCA		0.587	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		A	140720178	C	A	140720178	4	1	61	1	0	0	0	0	0	1	0	0	11585	838	29	2	1642	2	PCDHGA2	5	140720178	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7540	140720178	40195082	4190	12175										
PCDHGA3	56112	broad.mit.edu	37	chr5	140723973	140723973	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtagaaatagaaattaaaGatattaatgataatgctcct	6	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140723973G>T	ENST00000253812.6	+	1	373	c.373G>T	c.(373-375)Gat>Tat	p.D125Y	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	125	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D125Y(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAATTAAAGATATTAATGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											22	22	22					5																	140723973		1837	4109	5946	140704157	SO:0001583	missense	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.373G>T	5.37:g.140723973G>T	ENSP00000253812:p.Asp125Tyr		140704157	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.950210	0.73787	.	.	ENSG00000254245	ENST00000253812	T	0.80033	-1.33	5.65	5.65	0.86999	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.34110	U	0.004243	D	0.95661	0.8589	H	0.99940	5	0.48830	D	0.99971	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97717	1.0194	10	0.87932	D	0	.	19.7068	0.96076	0.0:0.0:1.0:0.0	.	125;125	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	Y	125	ENSP00000253812:D125Y	ENSP00000253812:D125Y	D	+	1	0	PCDHGA3	140704157	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	9.663000	0.98605	2.824000	0.97209	0.655000	0.94253	GAT		0.363	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140723973	G	T	140723973	3	4	61	1	0	0	0	0	1	0	0	0	11586	942	33	2	375	2	PCDHGA3	5	140723973	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3795	140723973	40191287	4191	12176										
PCDHGA3	56112	broad.mit.edu	37	chr5	140725322	140725322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacagacggttccactggCgtggagctggcgcctcgctc	13	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140725322C>T	ENST00000253812.6	+	1	1722	c.1722C>T	c.(1720-1722)ggC>ggT	p.G574G	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	574	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G574G(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTCCACTGGCGTGGAGCTGG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	5											102	111	108					5																	140725322		2203	4300	6503	140705506	SO:0001819	synonymous_variant	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1722C>T	5.37:g.140725322C>T			140705506	Q9Y5D4	Silent	SNP	ENST00000253812.6	37	CCDS47290.1																																																																																				0.667	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140725322	C	T	140725322	2	4	61	1	0	0	0	0	0	0	0	1	11586	755	27	1		1	PCDHGA3	5	140725322	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1349	140725322	40189938	4192	12177										
PCDHGB1	56104	broad.mit.edu	37	chr5	140730929	140730929	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatagccctcataaaagtgCgagacaaggattctgggcaa	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140730929C>T	ENST00000523390.1	+	1	1102	c.1102C>T	c.(1102-1104)Cga>Tga	p.R368*	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	368	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R368*(4)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATAAAAGTGCGAGACAAGGA	0.433																																																4	Substitution - Nonsense(4)	large_intestine(4)	5											43	42	42					5																	140730929		1908	4124	6032	140711113	SO:0001587	stop_gained	56104			AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1102C>T	5.37:g.140730929C>T	ENSP00000429273:p.Arg368*		140711113	Q3SY75|Q9Y5C8	Nonsense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	23.2	4.385450	0.82792	.	.	ENSG00000254221	ENST00000523390	.	.	.	5.49	-1.73	0.08081	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	11.1443	0.48422	0.6713:0.2645:0.0:0.0642	.	.	.	.	X	368	.	ENSP00000429273:R368X	R	+	1	2	PCDHGB1	140711113	0.000000	0.05858	0.001000	0.08648	0.996000	0.88848	-3.032000	0.00637	-0.205000	0.10219	0.563000	0.77884	CGA		0.433	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		T	140730929	C	T	140730929	4	4	61	1	0	0	0	0	0	1	0	0	11593	760	27	1	1104	1	PCDHGB1	5	140730929	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5607	140730929	40184331	4193	12178										
PCDHGB2	56103	broad.mit.edu	37	chr5	140739862	140739862	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggaaacctcgccaaggatCtggggctcagcgtccgggac	14	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140739862C>A	ENST00000522605.1	+	1	160	c.160C>A	c.(160-162)Ctg>Atg	p.L54M	PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	54	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L54M(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCAAGGATCTGGGGCTCAG	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	5											49	51	51					5																	140739862		1844	4089	5933	140720046	SO:0001583	missense	56103			AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.160C>A	5.37:g.140739862C>A	ENSP00000429018:p.Leu54Met		140720046	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	13.76	2.333815	0.41297	.	.	ENSG00000253910	ENST00000522605	T	0.59364	0.27	5.11	4.24	0.50183	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	D	0.82926	0.5143	H	0.96111	3.77	0.26501	N	0.974775	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77840	-0.2438	9	0.87932	D	0	.	13.3384	0.60530	0.0:0.9224:0.0:0.0776	.	54;54	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	M	54	ENSP00000429018:L54M	ENSP00000429018:L54M	L	+	1	2	PCDHGB2	140720046	0.621000	0.27077	0.993000	0.49108	0.423000	0.31445	0.026000	0.13599	1.275000	0.44379	0.563000	0.77884	CTG		0.562	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140739862	C	A	140739862	3	1	61	1	0	0	0	0	1	0	0	0	11594	912	32	2	162	2	PCDHGB2	5	140739862	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8933	140739862	40175398	4194	12179										
PCDHGA5	56110	broad.mit.edu	37	chr5	140744800	140744800	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattccaacctgggggaaatCtcaactctacaatcactgga	8	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140744800C>A	ENST00000518069.1	+	1	903	c.903C>A	c.(901-903)atC>atA	p.I301I	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	301	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I301I(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGGGAAATCTCAACTCTAC	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	5											39	40	40					5																	140744800		1888	4117	6005	140724984	SO:0001819	synonymous_variant	56110			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.903C>A	5.37:g.140744800C>A			140724984	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	37	CCDS54925.1																																																																																				0.453	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140744800	C	A	140744800	2	1	61	1	0	0	0	0	0	0	0	1	11588	903	32	2		2	PCDHGA5	5	140744800	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4938	140744800	40170460	4195	12180										
PCDHGB3	56102	broad.mit.edu	37	chr5	140750029	140750029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctatttctcttcctgctctCtttgttagaccaggttctct	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140750029C>A	ENST00000576222.1	+	1	199	c.68C>A	c.(67-69)tCt>tAt	p.S23Y	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	23					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCTGCTCTCTTTGTTAGAC	0.582																																																0			5											51	58	56					5																	140750029		1886	4105	5991	140730213	SO:0001583	missense	56102			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.68C>A	5.37:g.140750029C>A	ENSP00000461862:p.Ser23Tyr		140730213	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.582	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140750029	C	A	140750029	3	1	61	1	0	0	0	0	1	0	0	0	11595	913	32	2	70	2	PCDHGB3	5	140750029	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5229	140750029	40165231	4196	12181										
PCDHGB3	56102	broad.mit.edu	37	chr5	140751376	140751376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcctggagcctccattgCgcatgtcagagcctcggatc	11	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140751376C>T	ENST00000576222.1	+	1	1546	c.1415C>T	c.(1414-1416)gCg>gTg	p.A472V	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	472	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCCATTGCGCATGTCAGA	0.577																																																0			5											112	115	114					5																	140751376		2101	4234	6335	140731560	SO:0001583	missense	56102			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1415C>T	5.37:g.140751376C>T	ENSP00000461862:p.Ala472Val		140731560	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.577	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140751376	C	T	140751376	3	4	61	1	0	0	0	0	1	0	0	0	11595	768	27	1	1417	1	PCDHGB3	5	140751376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1347	140751376	40163884	4197	12182										
PCDHGB3	56102	broad.mit.edu	37	chr5	140751630	140751630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttggtggacgaccgcaacGacaatgcaccgctggtgctg	14	11	0	0	rs571325193		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140751630G>A	ENST00000576222.1	+	1	1800	c.1669G>A	c.(1669-1671)Gac>Aac	p.D557N	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	557	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGACCGCAACGACAATGCACC	0.662																																																0			5											37	47	44					5																	140751630		2191	4296	6487	140731814	SO:0001583	missense	56102			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1669G>A	5.37:g.140751630G>A	ENSP00000461862:p.Asp557Asn		140731814	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.662	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751630	G	A	140751630	3	1	61	1	0	0	0	0	1	0	0	0	11595	1058	37	1	1671	1	PCDHGB3	5	140751630	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	254	140751630	40163630	4198	12183										
PCDHGA6	56109	broad.mit.edu	37	chr5	140753848	140753848	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggagcacggagtccgcatCgtctccagaggtaggatgca	15	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140753848C>T	ENST00000517434.1	+	1	198	c.198C>T	c.(196-198)atC>atT	p.I66I	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	66	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I66I(1)		breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGTCCGCATCGTCTCCAGAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5											52	59	57					5																	140753848		2200	4300	6500	140734032	SO:0001819	synonymous_variant	56109			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.198C>T	5.37:g.140753848C>T			140734032	A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	37	CCDS54926.1																																																																																				0.592	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140753848	C	T	140753848	2	4	61	1	0	0	0	0	0	0	0	1	11589	874	31	1		1	PCDHGA6	5	140753848	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2218	140753848	40161412	4199	12184										
PCDHGA6	56109	broad.mit.edu	37	chr5	140755889	140755889	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgggcgtggaaggggttCgggctttcctgcagacctat	16	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140755889C>T	ENST00000517434.1	+	1	2239	c.2239C>T	c.(2239-2241)Cgg>Tgg	p.R747W	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	747					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R747W(1)		breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAGGGGTTCGGGCTTTCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											78	82	81					5																	140755889		2203	4300	6503	140736073	SO:0001583	missense	56109			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2239C>T	5.37:g.140755889C>T	ENSP00000429601:p.Arg747Trp		140736073	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	13.16	2.154203	0.38021	.	.	ENSG00000253731	ENST00000517434	T	0.45276	0.9	5.15	2.18	0.27775	.	0.404413	0.13708	U	0.368302	T	0.45776	0.1359	M	0.81179	2.53	0.22835	N	0.998676	P;P	0.48640	0.913;0.747	B;B	0.42087	0.375;0.256	T	0.42515	-0.9447	10	0.66056	D	0.02	.	10.0326	0.42109	0.2723:0.5958:0.1319:0.0	.	747;747	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	W	747	ENSP00000429601:R747W	ENSP00000429601:R747W	R	+	1	2	PCDHGA6	140736073	0.003000	0.15002	0.995000	0.50966	0.410000	0.31052	-0.001000	0.12947	0.843000	0.35070	0.655000	0.94253	CGG		0.597	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140755889	C	T	140755889	3	4	61	1	0	0	0	0	1	0	0	0	11589	875	31	1	2241	1	PCDHGA6	5	140755889	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2041	140755889	40159371	4200	12185										
PCDHGA7	56108	broad.mit.edu	37	chr5	140762865	140762865	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgacaacgttccaagattCttgacggaagaaataaatgt	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140762865C>A	ENST00000518325.1	+	1	399	c.399C>A	c.(397-399)ttC>ttA	p.F133L	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	133	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F133F(1)|p.F133L(1)		NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAAGATTCTTGACGGAAG	0.418																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	5											62	68	66					5																	140762865		1919	4140	6059	140743049	SO:0001583	missense	56108			AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.399C>A	5.37:g.140762865C>A	ENSP00000430024:p.Phe133Leu		140743049	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	16.56	3.158710	0.57368	.	.	ENSG00000253537	ENST00000518325	T	0.28895	1.59	5.01	4.13	0.48395	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.73337	0.3574	H	0.99924	4.96	0.26487	N	0.975011	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.71178	-0.4669	9	0.87932	D	0	.	9.002	0.36088	0.0:0.7764:0.0:0.2236	.	133;133	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	L	133	ENSP00000430024:F133L	ENSP00000430024:F133L	F	+	3	2	PCDHGA7	140743049	0.109000	0.22037	0.980000	0.43619	0.846000	0.48090	0.405000	0.21015	2.475000	0.83589	0.655000	0.94253	TTC		0.418	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		A	140762865	C	A	140762865	3	1	61	1	0	0	0	0	1	0	0	0	11590	912	32	2	401	2	PCDHGA7	5	140762865	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6976	140762865	40152395	4201	12186										
PCDHGA7	56108	broad.mit.edu	37	chr5	140764512	140764512	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagccttgagccctccgaCggtccttacaactatgacct	9	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140764512C>T	ENST00000518325.1	+	1	2046	c.2046C>T	c.(2044-2046)gaC>gaT	p.D682D	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	682	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D682D(1)		NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCCTCCGACGGTCCTTACA	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	5											58	66	63					5																	140764512		2203	4300	6503	140744696	SO:0001819	synonymous_variant	56108			AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.2046C>T	5.37:g.140764512C>T			140744696	B2RN87|Q9Y5D0	Silent	SNP	ENST00000518325.1	37	CCDS54927.1																																																																																				0.627	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		T	140764512	C	T	140764512	2	4	61	1	0	0	0	0	0	0	0	1	11590	535	19	1		1	PCDHGA7	5	140764512	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1647	140764512	40150748	4202	12187										
PCDHGA7	56108	broad.mit.edu	37	chr5	140764604	140764604	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgtcctcgtactgctggCgctcaggctgcggcgctggc	14	15	1	0	rs189127761	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140764604C>T	ENST00000518325.1	+	1	2138	c.2138C>T	c.(2137-2139)gCg>gTg	p.A713V	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	713					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A713V(1)		NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTACTGCTGGCGCTCAGGCTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	62	60					5																	140764604		2203	4300	6503	140744788	SO:0001583	missense	56108			AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.2138C>T	5.37:g.140764604C>T	ENSP00000430024:p.Ala713Val		140744788	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	13.14	2.149452	0.37923	.	.	ENSG00000253537	ENST00000518325	T	0.52295	0.67	4.93	3.13	0.36017	.	.	.	.	.	T	0.37865	0.1019	L	0.49640	1.575	0.19775	N	0.99996	B;P	0.35107	0.087;0.484	B;B	0.31337	0.037;0.128	T	0.19976	-1.0289	9	0.42905	T	0.14	.	7.0638	0.25141	0.0:0.7074:0.142:0.1506	.	713;713	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	V	713	ENSP00000430024:A713V	ENSP00000430024:A713V	A	+	2	0	PCDHGA7	140744788	0.001000	0.12720	0.415000	0.26534	0.496000	0.33645	0.529000	0.23019	0.589000	0.29677	0.563000	0.77884	GCG		0.632	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		T	140764604	C	T	140764604	3	4	61	1	0	0	0	0	1	0	0	0	11590	768	27	1	2140	1	PCDHGA7	5	140764604	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92	140764604	40150656	4203	12188										
PCDHGB4	8641	broad.mit.edu	37	chr5	140769029	140769029	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgagcagctgcgcgccttCgaactcacactgcaggcccg	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140769029C>T	ENST00000519479.1	+	1	1578	c.1578C>T	c.(1576-1578)ttC>ttT	p.F526F	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	526	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F526F(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGCGCCTTCGAACTCACAC	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	5											39	44	43					5																	140769029		2042	4189	6231	140749213	SO:0001819	synonymous_variant	8641			AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1578C>T	5.37:g.140769029C>T			140749213	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	37	CCDS54928.1																																																																																				0.677	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140769029	C	T	140769029	2	4	61	1	0	0	0	0	0	0	0	1	11596	883	31	1		1	PCDHGB4	5	140769029	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4425	140769029	40146231	4204	12189										
PCDHGB4	8641	broad.mit.edu	37	chr5	140769121	140769121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacgaccgcaacgacaatgCgccacgggtgctgtaccccg	13	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140769121C>T	ENST00000519479.1	+	1	1670	c.1670C>T	c.(1669-1671)gCg>gTg	p.A557V	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	557	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A557V(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGACAATGCGCCACGGGTG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	5											37	47	43					5																	140769121		2145	4251	6396	140749305	SO:0001583	missense	8641			AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1670C>T	5.37:g.140769121C>T	ENSP00000428288:p.Ala557Val		140749305	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	15.15	2.746614	0.49257	.	.	ENSG00000253953	ENST00000519479	T	0.42513	0.97	5.05	5.05	0.67936	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.47469	0.1447	M	0.66560	2.04	0.27628	N	0.948121	P;P	0.49635	0.921;0.926	B;B	0.41764	0.366;0.271	T	0.52064	-0.8625	9	0.54805	T	0.06	.	18.4161	0.90571	0.0:1.0:0.0:0.0	.	557;557	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	V	557	ENSP00000428288:A557V	ENSP00000428288:A557V	A	+	2	0	PCDHGB4	140749305	0.092000	0.21681	1.000000	0.80357	0.053000	0.15095	2.943000	0.49026	2.503000	0.84419	0.563000	0.77884	GCG		0.667	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140769121	C	T	140769121	3	4	61	1	0	0	0	0	1	0	0	0	11596	768	27	1	1672	1	PCDHGB4	5	140769121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92	140769121	40146139	4205	12190										
PCDHGA8	9708	broad.mit.edu	37	chr5	140774388	140774388	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtggctgacagcatccccGaagtcctgaccgagttgggc	13	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140774388G>A	ENST00000398604.2	+	1	2008	c.2008G>A	c.(2008-2010)Gaa>Aaa	p.E670K	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	670	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E670K(1)		endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCATCCCCGAAGTCCTGAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											44	50	48					5																	140774388		2203	4297	6500	140754572	SO:0001583	missense	9708			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.2008G>A	5.37:g.140774388G>A	ENSP00000381605:p.Glu670Lys		140754572	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	31	5.069461	0.93950	.	.	ENSG00000253767	ENST00000398604	T	0.50001	0.76	5.03	5.03	0.67393	Cadherin (1);	0.000000	0.31233	U	0.008006	T	0.39835	0.1093	L	0.52126	1.63	0.32309	N	0.563997	B;P	0.40032	0.239;0.699	B;B	0.33254	0.077;0.16	T	0.60556	-0.7240	10	0.87932	D	0	.	12.462	0.55736	0.0813:0.0:0.9187:0.0	.	670;670	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	K	670	ENSP00000381605:E670K	ENSP00000381605:E670K	E	+	1	0	PCDHGA8	140754572	0.987000	0.35691	0.183000	0.23137	0.871000	0.50021	2.859000	0.48364	2.348000	0.79779	0.655000	0.94253	GAA		0.627	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		A	140774388	G	A	140774388	3	1	61	1	0	0	0	0	1	0	0	0	11591	1059	37	1	2010	1	PCDHGA8	5	140774388	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5267	140774388	40140872	4206	12191										
PCDHGB5	56102	broad.mit.edu	37	chr5	140778319	140778319	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaacaacagagttaccatCgtttagtcctgactgccttg	10	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140778319C>T	ENST00000576222.1	+	1	2546				PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGTTACCATCGTTTAGTCCT	0.498																																																0			5																																								140758503	SO:0001627	intron_variant	56101			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+25943C>T	5.37:g.140778319C>T			140758503	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.498	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140778319	C	T	140778319	1	4	61	0	1	0	0	0	0	0	0	0	11597	884	31	1		1	PCDHGB5	5	140778319	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3931	140778319	40136941	4207	12192										
PCDHGB5	56102	broad.mit.edu	37	chr5	140778759	140778759	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaaatgattctggaaaaCgcggtgcctggaacactaat	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140778759C>T	ENST00000576222.1	+	1	2546				PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTGGAAAACGCGGTGCCTG	0.378																																																0			5											79	79	79					5																	140778759		1876	4106	5982	140758943	SO:0001627	intron_variant	56101			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26383C>T	5.37:g.140778759C>T			140758943	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.378	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140778759	C	T	140778759	1	4	61	0	1	0	0	0	0	0	0	0	11597	535	19	1		1	PCDHGB5	5	140778759	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	440	140778759	40136501	4208	12193										
PCDHGB5	56102	broad.mit.edu	37	chr5	140779346	140779346	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcgtgttggtgggcgaccGaaacgacaacgcaccgcggg	17	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140779346G>A	ENST00000576222.1	+	1	2546				PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGGCGACCGAAACGACAAC	0.682																																																0			5											28	36	33					5																	140779346		2060	4216	6276	140759530	SO:0001627	intron_variant	56101			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26970G>A	5.37:g.140779346G>A			140759530	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.682	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140779346	G	A	140779346	1	1	61	0	1	0	0	0	0	0	0	0	11597	1058	37	1		1	PCDHGB5	5	140779346	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	587	140779346	40135914	4209	12194										
PCDHGA9	56107	broad.mit.edu	37	chr5	140783114	140783114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagctggtgctggagcgcGccctggacagggaggaggca	19	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140783114G>A	ENST00000573521.1	+	1	595	c.595G>A	c.(595-597)Gcc>Acc	p.A199T	PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	199	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGAGCGCGCCCTGGACAG	0.637																																																0			5											38	43	41					5																	140783114		2045	4185	6230	140763298	SO:0001583	missense	56107			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.595G>A	5.37:g.140783114G>A	ENSP00000460274:p.Ala199Thr		140763298	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.637	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		A	140783114	G	A	140783114	3	1	61	1	0	0	0	0	1	0	0	0	11592	1087	38	1	597	1	PCDHGA9	5	140783114	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3768	140783114	40132146	4210	12195										
PCDHGA9	56107	broad.mit.edu	37	chr5	140783683	140783683	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtctgttctatccaggaGaatctatcttttacattaga	7	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140783683G>T	ENST00000573521.1	+	1	1164	c.1164G>T	c.(1162-1164)gaG>gaT	p.E388D	PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	388	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTATCCAGGAGAATCTATCTT	0.403																																																0			5											33	33	33					5																	140783683		1866	4102	5968	140763867	SO:0001583	missense	56107			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1164G>T	5.37:g.140783683G>T	ENSP00000460274:p.Glu388Asp		140763867	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.403	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		T	140783683	G	T	140783683	3	4	61	1	0	0	0	0	1	0	0	0	11592	933	33	2	1166	2	PCDHGA9	5	140783683	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	569	140783683	40131577	4211	12196										
PCDHGB6	56100	broad.mit.edu	37	chr5	140788951	140788951	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagacattccattcaagatTtattcttcttccaataacta	2	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140788951T>G	ENST00000520790.1	+	1	1182	c.1182T>G	c.(1180-1182)atT>atG	p.I394M	PCDHGA9_ENST00000573521.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	394	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I394M(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATTCAAGATTTATTCTTCTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											50	53	52					5																	140788951		1920	4138	6058	140769135	SO:0001583	missense	56100			AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.1182T>G	5.37:g.140788951T>G	ENSP00000428603:p.Ile394Met		140769135	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	t	11.71	1.720291	0.30503	.	.	ENSG00000253305	ENST00000520790	T	0.64803	-0.12	5.47	-0.593	0.11667	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.75443	0.3850	M	0.88570	2.965	0.09310	N	1	D;D	0.67145	0.996;0.995	D;D	0.72338	0.977;0.962	T	0.61806	-0.6987	9	0.66056	D	0.02	.	1.8193	0.03107	0.2275:0.1412:0.105:0.5262	.	394;394	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	M	394	ENSP00000428603:I394M	ENSP00000428603:I394M	I	+	3	3	PCDHGB6	140769135	0.000000	0.05858	0.196000	0.23383	0.821000	0.46438	-1.705000	0.01896	0.046000	0.15833	0.460000	0.39030	ATT		0.453	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		G	140788951	T	G	140788951	3	3	61	1	0	0	0	0	1	0	0	0	11598	1829	64	4	1184	4	PCDHGB6	5	140788951	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5268	140788951	40126309	4212	12197										
PCDHGB6	56100	broad.mit.edu	37	chr5	140789274	140789274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctagagcccctggcggtgtCgtcatacgtgtcagtgagcg	14	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140789274C>T	ENST00000520790.1	+	1	1505	c.1505C>T	c.(1504-1506)tCg>tTg	p.S502L	PCDHGA9_ENST00000573521.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	502	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S502L(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCGGTGTCGTCATACGTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	5											20	23	22					5																	140789274		2030	4185	6215	140769458	SO:0001583	missense	56100			AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.1505C>T	5.37:g.140789274C>T	ENSP00000428603:p.Ser502Leu		140769458	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	c	9.564	1.119244	0.20877	.	.	ENSG00000253305	ENST00000520790	T	0.03094	4.05	5.36	3.22	0.36961	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06188	0.0160	M	0.63428	1.95	0.23780	N	0.996868	B;B	0.22346	0.068;0.055	B;B	0.26693	0.072;0.043	T	0.26643	-1.0097	9	0.54805	T	0.06	.	8.6264	0.33892	0.0:0.7488:0.147:0.1043	.	502;502	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	L	502	ENSP00000428603:S502L	ENSP00000428603:S502L	S	+	2	0	PCDHGB6	140769458	0.098000	0.21812	0.642000	0.29436	0.033000	0.12548	2.767000	0.47637	0.408000	0.25621	0.462000	0.41574	TCG		0.647	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140789274	C	T	140789274	3	4	61	1	0	0	0	0	1	0	0	0	11598	893	31	1	1507	1	PCDHGB6	5	140789274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323	140789274	40125986	4213	12198										
PCDHGA10	56106	broad.mit.edu	37	chr5	140793453	140793453	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtcagtgtgactgtcttCgatgcaaatgacaacgcgcc	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140793453C>T	ENST00000398610.2	+	1	711	c.711C>T	c.(709-711)ttC>ttT	p.F237F	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	237	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F237F(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTGTCTTCGATGCAAATG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											45	48	47					5																	140793453		2063	4207	6270	140773637	SO:0001819	synonymous_variant	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.711C>T	5.37:g.140793453C>T			140773637	Q9Y5E0	Silent	SNP	ENST00000398610.2	37	CCDS47292.1																																																																																				0.572	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140793453	C	T	140793453	2	4	61	1	0	0	0	0	0	0	0	1	11582	883	31	1		1	PCDHGA10	5	140793453	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4179	140793453	40121807	4214	12199										
PCDHGA10	56106	broad.mit.edu	37	chr5	140793565	140793565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagccaccgacagggacGaaggtgccaatggagaagtg	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140793565G>A	ENST00000398610.2	+	1	823	c.823G>A	c.(823-825)Gaa>Aaa	p.E275K	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E275K(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGACAGGGACGAAGGTGCCAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											32	35	34					5																	140793565		1974	4176	6150	140773749	SO:0001583	missense	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.823G>A	5.37:g.140793565G>A	ENSP00000381611:p.Glu275Lys		140773749	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	17.40	3.379284	0.61735	.	.	ENSG00000253846	ENST00000398610	T	0.01725	4.67	5.26	5.26	0.73747	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.10766	0.0263	M	0.83312	2.635	0.23984	N	0.99626	D;D	0.69078	0.996;0.997	P;P	0.58520	0.752;0.84	T	0.01819	-1.1267	9	0.66056	D	0.02	.	18.8598	0.92267	0.0:0.0:1.0:0.0	.	275;275	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	K	275	ENSP00000381611:E275K	ENSP00000381611:E275K	E	+	1	0	PCDHGA10	140773749	0.927000	0.31430	0.991000	0.47740	0.852000	0.48524	2.128000	0.42045	2.462000	0.83206	0.455000	0.32223	GAA		0.463	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140793565	G	A	140793565	3	1	61	1	0	0	0	0	1	0	0	0	11582	1059	37	1	825	1	PCDHGA10	5	140793565	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112	140793565	40121695	4215	12200										
PCDHGA10	56106	broad.mit.edu	37	chr5	140794470	140794470	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctccccacagacggttcCacaggcgtggagctggcgcc	13	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140794470C>A	ENST00000398610.2	+	1	1728	c.1728C>A	c.(1726-1728)tcC>tcA	p.S576S	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	576	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S576S(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGACGGTTCCACAGGCGTGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	5											123	140	134					5																	140794470		2203	4300	6503	140774654	SO:0001819	synonymous_variant	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1728C>A	5.37:g.140794470C>A			140774654	Q9Y5E0	Silent	SNP	ENST00000398610.2	37	CCDS47292.1																																																																																				0.652	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140794470	C	A	140794470	2	1	61	1	0	0	0	0	0	0	0	1	11582	581	21	2		2	PCDHGA10	5	140794470	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	905	140794470	40120790	4216	12201										
PCDHGB7	56099	broad.mit.edu	37	chr5	140797501	140797501	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgctgctgcctttgttCtaccccacgctgtgtgagcc	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140797501C>A	ENST00000398594.2	+	1	75	c.75C>A	c.(73-75)ttC>ttA	p.F25L	PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	25					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F25L(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCCTTTGTTCTACCCCACGC	0.647											OREG0016863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	5											40	41	41					5																	140797501		1926	4125	6051	140777685	SO:0001583	missense	56099			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.75C>A	5.37:g.140797501C>A	ENSP00000381594:p.Phe25Leu	1659	140777685	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	c	12.27	1.888659	0.33348	.	.	ENSG00000254122	ENST00000398594	T	0.51325	0.71	5.92	5.01	0.66863	Cadherin-like (1);	0.000000	0.34245	U	0.004121	T	0.22859	0.0552	N	0.08118	0	0.22446	N	0.999096	B;B	0.13594	0.008;0.007	B;B	0.23275	0.029;0.045	T	0.22941	-1.0202	10	0.09590	T	0.72	.	7.052	0.25079	0.0:0.7063:0.1496:0.1441	.	25;25	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	L	25	ENSP00000381594:F25L	ENSP00000381594:F25L	F	+	3	2	PCDHGB7	140777685	0.002000	0.14202	1.000000	0.80357	0.970000	0.65996	-0.067000	0.11579	2.822000	0.97130	0.650000	0.86243	TTC		0.647	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		A	140797501	C	A	140797501	3	1	61	1	0	0	0	0	1	0	0	0	11599	912	32	2	77	2	PCDHGB7	5	140797501	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3031	140797501	40117759	4217	12202										
PCDHGB7	56099	broad.mit.edu	37	chr5	140798394	140798394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaacatagaagcaaaagAccgaggatctctctcaacac	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140798394A>G	ENST00000398594.2	+	1	968	c.968A>G	c.(967-969)gAc>gGc	p.D323G	PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	323	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D323G(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGCAAAAGACCGAGGATCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											75	70	71					5																	140798394		1881	4100	5981	140778578	SO:0001583	missense	56099			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.968A>G	5.37:g.140798394A>G	ENSP00000381594:p.Asp323Gly		140778578	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	a	18.43	3.622786	0.66787	.	.	ENSG00000254122	ENST00000398594	T	0.80566	-1.39	5.7	5.7	0.88788	Cadherin (5);Cadherin-like (1);	0.000000	0.33854	U	0.004499	D	0.93897	0.8047	H	0.98525	4.255	0.43110	D	0.994818	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96349	0.9257	10	0.87932	D	0	.	15.6434	0.77025	1.0:0.0:0.0:0.0	.	323;323	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	G	323	ENSP00000381594:D323G	ENSP00000381594:D323G	D	+	2	0	PCDHGB7	140778578	1.000000	0.71417	0.998000	0.56505	0.809000	0.45718	7.470000	0.80973	2.189000	0.69895	0.459000	0.35465	GAC		0.393	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		G	140798394	A	G	140798394	3	3	61	1	0	0	0	0	1	0	0	0	11599	275	10	4	970	4	PCDHGB7	5	140798394	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	893	140798394	40116866	4218	12203										
PCDHGB7	56099	broad.mit.edu	37	chr5	140798470	140798470	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaacagcccagaaataatCatcacgtcactctctgatca	5	13	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140798470C>A	ENST00000398594.2	+	1	1044	c.1044C>A	c.(1042-1044)atC>atA	p.I348I	PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	348	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I348I(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAAATAATCATCACGTCAC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											75	70	72					5																	140798470		1883	4109	5992	140778654	SO:0001819	synonymous_variant	56099			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1044C>A	5.37:g.140798470C>A			140778654	Q9UN63	Silent	SNP	ENST00000398594.2	37	CCDS47293.1																																																																																				0.448	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		A	140798470	C	A	140798470	2	1	61	1	0	0	0	0	0	0	0	1	11599	816	29	2		2	PCDHGB7	5	140798470	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76	140798470	40116790	4219	12204										
PCDHGA11	56105	broad.mit.edu	37	chr5	140801943	140801943	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggagaaaatggtcaagtCtcctgttttattcctaacca	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140801943C>A	ENST00000398587.2	+	1	1182	c.1149C>A	c.(1147-1149)gtC>gtA	p.V383V	PCDHGA11_ENST00000518882.1_Silent_p.V383V|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	383	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V383V(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGGTCAAGTCTCCTGTTTTA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	5											35	34	34					5																	140801943		1820	4078	5898	140782127	SO:0001819	synonymous_variant	56105			AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1149C>A	5.37:g.140801943C>A			140782127	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																				0.378	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		A	140801943	C	A	140801943	2	1	61	1	0	0	0	0	0	0	0	1	11583	900	32	2		2	PCDHGA11	5	140801943	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3473	140801943	40113317	4220	12205										
PCDHGA11	56105	broad.mit.edu	37	chr5	140802450	140802450	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtgtcgctgagcctgttCgtgctggaccagaacgacaa	12	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140802450C>T	ENST00000398587.2	+	1	1689	c.1656C>T	c.(1654-1656)ttC>ttT	p.F552F	PCDHGA11_ENST00000518882.1_Silent_p.F552F|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F552F(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGCCTGTTCGTGCTGGACC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	5											157	177	170					5																	140802450		2203	4300	6503	140782634	SO:0001819	synonymous_variant	56105			AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1656C>T	5.37:g.140802450C>T			140782634	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																				0.617	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		T	140802450	C	T	140802450	2	4	61	1	0	0	0	0	0	0	0	1	11583	883	31	1		1	PCDHGA11	5	140802450	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	507	140802450	40112810	4221	12206										
PCDHGA12	26025	broad.mit.edu	37	chr5	140811390	140811390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcacctctctcgccagctCggttcccgaaaactctccca	5	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140811390C>T	ENST00000252085.3	+	1	1206	c.1064C>T	c.(1063-1065)tCg>tTg	p.S355L	PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	355	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S355L(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCGCCAGCTCGGTTCCCGAA	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	5											78	78	78					5																	140811390		2203	4300	6503	140791574	SO:0001583	missense	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1064C>T	5.37:g.140811390C>T	ENSP00000252085:p.Ser355Leu		140791574	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	c	13.71	2.317218	0.40996	.	.	ENSG00000253159	ENST00000252085	T	0.02631	4.22	4.54	4.54	0.55810	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.09024	0.0223	M	0.84846	2.72	0.18873	N	0.999983	B;B	0.28208	0.203;0.151	B;B	0.30782	0.073;0.12	T	0.03807	-1.1002	9	0.59425	D	0.04	.	17.077	0.86589	0.0:1.0:0.0:0.0	.	355;355	O60330-2;O60330	.;PCDGC_HUMAN	L	355	ENSP00000252085:S355L	ENSP00000252085:S355L	S	+	2	0	PCDHGA12	140791574	0.011000	0.17503	0.881000	0.34555	0.564000	0.35744	2.585000	0.46111	2.348000	0.79779	0.655000	0.94253	TCG		0.483	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140811390	C	T	140811390	3	4	61	1	0	0	0	0	1	0	0	0	11584	893	31	1	1066	1	PCDHGA12	5	140811390	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8940	140811390	40103870	4222	12207										
PCDHGA12	26025	broad.mit.edu	37	chr5	140811453	140811453	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtaaatgaccaagattCtgaggaaaacggacaggtga	11	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140811453C>A	ENST00000252085.3	+	1	1269	c.1127C>A	c.(1126-1128)tCt>tAt	p.S376Y	PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	376	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S376Y(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACCAAGATTCTGAGGAAAAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	5											51	58	56					5																	140811453		2203	4300	6503	140791637	SO:0001583	missense	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1127C>A	5.37:g.140811453C>A	ENSP00000252085:p.Ser376Tyr		140791637	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	c	17.29	3.352164	0.61183	.	.	ENSG00000253159	ENST00000252085	T	0.02709	4.19	4.69	4.69	0.59074	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17280	0.0415	H	0.94886	3.595	0.37328	D	0.909842	P;P	0.49185	0.882;0.92	P;P	0.52031	0.688;0.678	T	0.32025	-0.9922	9	0.72032	D	0.01	.	17.4157	0.87499	0.0:1.0:0.0:0.0	.	376;376	O60330-2;O60330	.;PCDGC_HUMAN	Y	376	ENSP00000252085:S376Y	ENSP00000252085:S376Y	S	+	2	0	PCDHGA12	140791637	0.996000	0.38824	1.000000	0.80357	0.710000	0.40934	3.818000	0.55678	2.425000	0.82216	0.655000	0.94253	TCT		0.423	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811453	C	A	140811453	3	1	61	1	0	0	0	0	1	0	0	0	11584	913	32	2	1129	2	PCDHGA12	5	140811453	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63	140811453	40103807	4223	12208										
PCDHGA12	26025	broad.mit.edu	37	chr5	140811553	140811553	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttagtcacagacatagtCttggatagggaacaggttcc	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140811553C>A	ENST00000252085.3	+	1	1369	c.1227C>A	c.(1225-1227)gtC>gtA	p.V409V	PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	409	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V409V(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGACATAGTCTTGGATAGGG	0.463																																																2	Substitution - coding silent(2)	large_intestine(2)	5											41	46	45					5																	140811553		2203	4300	6503	140791737	SO:0001819	synonymous_variant	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1227C>A	5.37:g.140811553C>A			140791737	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																				0.463	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811553	C	A	140811553	2	1	61	1	0	0	0	0	0	0	0	1	11584	900	32	2		2	PCDHGA12	5	140811553	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100	140811553	40103707	4224	12209										
PCDHGA12	26025	broad.mit.edu	37	chr5	140812012	140812012	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgacaatgcgcccgagatCctgtaccccgccctccccac	7	20	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140812012C>A	ENST00000252085.3	+	1	1828	c.1686C>A	c.(1684-1686)atC>atA	p.I562I	PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	562	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I562I(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCCGAGATCCTGTACCCCG	0.662																																																2	Substitution - coding silent(2)	large_intestine(2)	5											131	145	140					5																	140812012		2203	4300	6503	140792196	SO:0001819	synonymous_variant	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1686C>A	5.37:g.140812012C>A			140792196	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																				0.662	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140812012	C	A	140812012	2	1	61	1	0	0	0	0	0	0	0	1	11584	845	30	2		2	PCDHGA12	5	140812012	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	459	140812012	40103248	4225	12210										
PCDHGC3	5098	broad.mit.edu	37	chr5	140857056	140857056	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaaccctccacaatcttCtcaatcttcctacgacgttt	3	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140857056C>A	ENST00000308177.3	+	1	1477	c.1373C>A	c.(1372-1374)tCt>tAt	p.S458Y	RN7SL68P_ENST00000488078.2_RNA|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	458	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S458Y(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACAATCTTCTCAATCTTCC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	5											149	152	151					5																	140857056		2203	4300	6503	140837240	SO:0001583	missense	5098			AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1373C>A	5.37:g.140857056C>A	ENSP00000312070:p.Ser458Tyr		140837240	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	37	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.984480	0.35036	.	.	ENSG00000240184	ENST00000308177	T	0.61510	0.1	5.19	4.32	0.51571	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.60534	0.2276	M	0.79258	2.445	0.09310	N	1	P;P	0.52842	0.956;0.755	P;B	0.44732	0.459;0.367	T	0.58335	-0.7654	9	0.62326	D	0.03	.	9.0771	0.36529	0.1461:0.78:0.0:0.0739	.	458;458	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	Y	458	ENSP00000312070:S458Y	ENSP00000312070:S458Y	S	+	2	0	PCDHGC3	140837240	0.002000	0.14202	0.996000	0.52242	0.930000	0.56654	1.249000	0.32839	1.555000	0.49500	0.655000	0.94253	TCT		0.542	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		A	140857056	C	A	140857056	3	1	61	1	0	0	0	0	1	0	0	0	11600	913	32	2	1375	2	PCDHGC3	5	140857056	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45044	140857056	40058204	4226	12211										
PCDHGC4	56098	broad.mit.edu	37	chr5	140865374	140865374	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcggactaccgcctggtgCtgactgctgtcgatggaggg	15	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140865374C>A	ENST00000306593.1	+	1	634	c.634C>A	c.(634-636)Ctg>Atg	p.L212M	PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	212	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L212M(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCCTGGTGCTGACTGCTGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	5											31	34	33					5																	140865374		2203	4300	6503	140845558	SO:0001583	missense	56098			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.634C>A	5.37:g.140865374C>A	ENSP00000306918:p.Leu212Met		140845558	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700141	0.48307	.	.	ENSG00000242419	ENST00000306593	T	0.23147	1.92	5.0	5.0	0.66597	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.59252	0.2180	M	0.92784	3.345	0.27124	N	0.962052	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.58901	-0.7554	9	0.87932	D	0	.	11.5769	0.50866	0.0:0.9179:0.0:0.0821	.	212;212	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	M	212	ENSP00000306918:L212M	ENSP00000306918:L212M	L	+	1	2	PCDHGC4	140845558	0.279000	0.24239	1.000000	0.80357	0.996000	0.88848	0.887000	0.28254	2.596000	0.87737	0.561000	0.74099	CTG		0.612	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		A	140865374	C	A	140865374	3	1	61	1	0	0	0	0	1	0	0	0	11601	796	28	2	636	2	PCDHGC4	5	140865374	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8318	140865374	40049886	4227	12212										
PCDHGC4	56098	broad.mit.edu	37	chr5	140865597	140865597	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatttcagtggtcatacccCtgatcgtgtaagaaacctct	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:140865597C>A	ENST00000306593.1	+	1	857	c.857C>A	c.(856-858)cCt>cAt	p.P286H	PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	286	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P286H(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCATACCCCTGATCGTGTA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											79	89	85					5																	140865597		2203	4300	6503	140845781	SO:0001583	missense	56098			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.857C>A	5.37:g.140865597C>A	ENSP00000306918:p.Pro286His		140845781	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.587991	0.46110	.	.	ENSG00000242419	ENST00000306593	T	0.61392	0.11	4.87	3.99	0.46301	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74351	0.3705	M	0.70787	2.145	0.31113	N	0.709781	D;D	0.89917	1.0;1.0	D;D	0.79108	0.976;0.992	T	0.76410	-0.2969	9	0.52906	T	0.07	.	15.1228	0.72457	0.0:0.8581:0.1419:0.0	.	286;286	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	H	286	ENSP00000306918:P286H	ENSP00000306918:P286H	P	+	2	0	PCDHGC4	140845781	0.986000	0.35501	1.000000	0.80357	0.975000	0.68041	3.020000	0.49643	1.249000	0.43950	0.462000	0.41574	CCT		0.507	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		A	140865597	C	A	140865597	3	1	61	1	0	0	0	0	1	0	0	0	11601	681	24	2	859	2	PCDHGC4	5	140865597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	223	140865597	40049663	4228	12213										
RELL2	285613	broad.mit.edu	37	chr5	141017850	141017850	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggctatatatgctcttcCtgcttgtgctggtcttcttc	9	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141017850C>A	ENST00000297164.3	+	1	1258	c.58C>A	c.(58-60)Ctg>Atg	p.L20M	RELL2_ENST00000444782.1_Missense_Mutation_p.L20M|RELL2_ENST00000518856.1_Intron|RELL2_ENST00000518025.1_3'UTR|RELL2_ENST00000521367.1_Intron|FCHSD1_ENST00000523856.1_5'Flank|HDAC3_ENST00000305264.3_5'Flank	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	20					positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L20M(1)		large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATGCTCTTCCTGCTTGTGCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											202	189	194					5																	141017850		2203	4300	6503	140998034	SO:0001583	missense	285613			AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"chromosome 5 open reading frame 16"	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.58C>A	5.37:g.141017850C>A	ENSP00000297164:p.Leu20Met		140998034	D3DQE2|Q6P4E7|Q6UXY2	Missense_Mutation	SNP	ENST00000297164.3	37	CCDS4265.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.781234	0.70222	.	.	ENSG00000164620	ENST00000444782;ENST00000297164	T;T	0.16196	2.36;2.36	5.87	5.87	0.94306	.	0.000000	0.56097	D	0.000034	T	0.30854	0.0778	N	0.19112	0.55	0.51482	D	0.999925	D	0.89917	1.0	D	0.97110	1.0	T	0.05533	-1.0879	10	0.59425	D	0.04	-6.6829	19.8177	0.96578	0.0:1.0:0.0:0.0	.	20	Q8NC24	RELL2_HUMAN	M	20	ENSP00000409443:L20M;ENSP00000297164:L20M	ENSP00000297164:L20M	L	+	1	2	RELL2	140998034	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.911000	0.39937	2.778000	0.95560	0.650000	0.86243	CTG		0.627	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2	NM_173828		A	141017850	C	A	141017850	3	1	61	1	0	0	0	0	1	0	0	0	13256	680	24	2	60	2	RELL2	5	141017850	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152253	141017850	39897410	4229	12214										
FCHSD1	89848	broad.mit.edu	37	chr5	141028814	141028814	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccatacagcttccgacttCggctcagctcccggacagac	9	17	1	1	rs200855332		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141028814C>T	ENST00000435817.2	-	6	487	c.437G>A	c.(436-438)cGa>cAa	p.R146Q	FCHSD1_ENST00000522126.1_Missense_Mutation_p.R70Q|FCHSD1_ENST00000522783.1_Missense_Mutation_p.R144Q|FCHSD1_ENST00000519800.1_Missense_Mutation_p.R144Q|FCHSD1_ENST00000523856.1_5'Flank	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	146								p.R146Q(1)	FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCCGACTTCGGCTCAGCTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG	0,4280		0,0,2140	107	123	118		437	5.1	1	5		118	4,8492		0,4,4244	no	missense	FCHSD1	NM_033449.2	43	0,4,6384	TT,TC,CC		0.0471,0.0,0.0313	possibly-damaging	146/691	141028814	4,12772	2140	4248	6388	141008998	SO:0001583	missense	89848			AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.437G>A	5.37:g.141028814C>T	ENSP00000399259:p.Arg146Gln		141008998	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265929	0.80358	0.0	4.71E-4	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783;ENST00000519800	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.11	5.11	0.69529	.	0.264830	0.28589	N	0.014804	T	0.11239	0.0274	L	0.36672	1.1	0.30553	N	0.765236	P	0.50710	0.938	B	0.41174	0.349	T	0.08411	-1.0723	10	0.66056	D	0.02	-11.6664	8.2676	0.31824	0.0:0.8578:0.0:0.1422	.	146	Q86WN1	FCSD1_HUMAN	Q	146;70;144;144	ENSP00000399259:R146Q;ENSP00000427796:R70Q;ENSP00000428677:R144Q;ENSP00000428776:R144Q	ENSP00000399259:R146Q	R	-	2	0	FCHSD1	141008998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.625000	0.54238	2.368000	0.80403	0.561000	0.74099	CGA		0.602	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		T	141028814	C	T	141028814	3	4	61	1	0	0	0	0	1	0	0	0	5808	884	31	1	1695	1	FCHSD1	5	141028814	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10964	141028814	39886446	4230	12215										
FCHSD1	89848	broad.mit.edu	37	chr5	141029952	141029952	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactcccgttcaatggctgCcctctgcttgctgtaggatc	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141029952C>A	ENST00000435817.2	-	3	189	c.139G>T	c.(139-141)Gca>Tca	p.A47S	FCHSD1_ENST00000522126.1_5'UTR|FCHSD1_ENST00000522783.1_Missense_Mutation_p.A47S|FCHSD1_ENST00000519800.1_Missense_Mutation_p.A47S|FCHSD1_ENST00000523856.1_5'Flank	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	47	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.							p.A47S(1)	FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAATGGCTGCCCTCTGCTTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	109	108					5																	141029952		1974	4158	6132	141010136	SO:0001583	missense	89848			AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.139G>T	5.37:g.141029952C>A	ENSP00000399259:p.Ala47Ser		141010136	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	c	18.60	3.658350	0.67586	.	.	ENSG00000197948	ENST00000435817;ENST00000522783;ENST00000519800	T;T;T	0.19669	2.13;2.13;2.13	5.04	5.04	0.67666	Fps/Fes/Fer/CIP4 homology (2);	0.152719	0.40222	N	0.001143	T	0.26048	0.0635	L	0.33189	0.99	0.40048	D	0.975732	D	0.55605	0.972	P	0.55303	0.773	T	0.01648	-1.1304	10	0.25751	T	0.34	-16.1355	12.1819	0.54216	0.1705:0.8295:0.0:0.0	.	47	Q86WN1	FCSD1_HUMAN	S	47	ENSP00000399259:A47S;ENSP00000428677:A47S;ENSP00000428776:A47S	ENSP00000399259:A47S	A	-	1	0	FCHSD1	141010136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.064000	0.41432	2.329000	0.79093	0.556000	0.70494	GCA		0.517	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		A	141029952	C	A	141029952	3	1	61	1	0	0	0	0	1	0	0	0	5808	739	26	2	2005	2	FCHSD1	5	141029952	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1138	141029952	39885308	4231	12216										
ARAP3	64411	broad.mit.edu	37	chr5	141039454	141039454	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaacagcagagccaagttCcgcgtgcacatctggtttag	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141039454C>G	ENST00000239440.4	-	22	3224	c.3159G>C	c.(3157-3159)cgG>cgC	p.R1053R	ARAP3_ENST00000513878.1_Silent_p.R715R|ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000508305.1_Silent_p.R884R	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1053	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.R1053R(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GAGCCAAGTTCCGCGTGCACA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	5											59	50	53					5																	141039454		2203	4298	6501	141019638	SO:0001819	synonymous_variant	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3159G>C	5.37:g.141039454C>G			141019638	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																				0.557	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		G	141039454	C	G	141039454	2	3	61	1	0	0	0	0	0	0	0	1	840	842	30	5		5	ARAP3	5	141039454	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9502	141039454	39875806	4232	12217										
ARAP3	64411	broad.mit.edu	37	chr5	141050901	141050901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctcctcgccttcaaaggCctcaacacagaggagctggg	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141050901C>A	ENST00000239440.4	-	13	1986	c.1921G>T	c.(1921-1923)Gcc>Tcc	p.A641S	ARAP3_ENST00000513878.1_Missense_Mutation_p.A303S|ARAP3_ENST00000508305.1_Missense_Mutation_p.A563S	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	641					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.A641S(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CCTTCAAAGGCCTCAACACAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	67	69					5																	141050901		2203	4300	6503	141031085	SO:0001583	missense	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1921G>T	5.37:g.141050901C>A	ENSP00000239440:p.Ala641Ser		141031085	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	9.065	0.995349	0.19043	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.15718	2.4;3.17;3.0	2.69	0.82	0.18793	.	1.654710	0.03701	N	0.248613	T	0.11965	0.0291	L	0.34521	1.04	0.09310	N	1	B;P;B	0.42941	0.015;0.794;0.049	B;B;B	0.39805	0.007;0.31;0.024	T	0.17715	-1.0360	10	0.07325	T	0.83	.	5.1428	0.14969	0.0:0.7041:0.0:0.2959	.	303;563;641	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	S	563;641;303	ENSP00000421826:A563S;ENSP00000239440:A641S;ENSP00000421468:A303S	ENSP00000239440:A641S	A	-	1	0	ARAP3	141031085	0.495000	0.26051	0.003000	0.11579	0.554000	0.35429	0.336000	0.19823	0.191000	0.20236	0.563000	0.77884	GCC		0.627	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141050901	C	A	141050901	3	1	61	1	0	0	0	0	1	0	0	0	840	739	26	2	2797	2	ARAP3	5	141050901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11447	141050901	39864359	4233	12218										
KIAA0141	9812	broad.mit.edu	37	chr5	141318237	141318237	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgcagaagtgggcatctCggagccagcctggaagcctc	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141318237C>T	ENST00000432126.2	+	12	1595	c.1461C>T	c.(1459-1461)ctC>ctT	p.L487L	KIAA0141_ENST00000194118.4_Silent_p.L487L	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	487					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)		p.L487L(1)		endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGGCATCTCGGAGCCAGCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											93	92	93					5																	141318237		2203	4300	6503	141298421	SO:0001819	synonymous_variant	9812			BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1461C>T	5.37:g.141318237C>T			141298421	Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	C	4.995	0.184788	0.09495	.	.	ENSG00000081791	ENST00000507481	.	.	.	5.11	-7.93	0.01156	.	.	.	.	.	T	0.26991	0.0661	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31806	-0.9930	4	.	.	.	-5.39	8.7739	0.34749	0.0:0.1856:0.2196:0.5948	.	.	.	.	L	189	.	.	S	+	2	0	KIAA0141	141298421	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-3.682000	0.00394	-1.623000	0.01558	-0.136000	0.14681	TCG		0.572	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141318237	C	T	141318237	2	4	61	1	0	0	0	0	0	0	0	1	8177	871	31	1		1	KIAA0141	5	141318237	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	267336	141318237	39597023	4234	12219										
PCDH12	51294	broad.mit.edu	37	chr5	141336893	141336893	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcaaagtgctcactgggaGacagagtgtaggtgtgcagg	17	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141336893G>T	ENST00000231484.3	-	1	1734	c.524C>A	c.(523-525)tCt>tAt	p.S175Y	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	175	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S175Y(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCACTGGGAGACAGAGTGTA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											109	123	118					5																	141336893		2203	4300	6503	141317077	SO:0001583	missense	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.524C>A	5.37:g.141336893G>T	ENSP00000231484:p.Ser175Tyr		141317077	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033441	0.54896	.	.	ENSG00000113555	ENST00000231484	T	0.54479	0.57	4.98	4.98	0.66077	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.81336	0.4801	H	0.96805	3.885	0.49299	D	0.999773	D	0.89917	1.0	D	0.72338	0.977	D	0.87540	0.2458	10	0.87932	D	0	.	15.7994	0.78439	0.0:0.0:1.0:0.0	.	175	Q9NPG4	PCD12_HUMAN	Y	175	ENSP00000231484:S175Y	ENSP00000231484:S175Y	S	-	2	0	PCDH12	141317077	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	6.458000	0.73509	2.605000	0.88082	0.655000	0.94253	TCT		0.547	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141336893	G	T	141336893	3	4	61	1	0	0	0	0	1	0	0	0	11541	942	33	2	3046	2	PCDH12	5	141336893	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18656	141336893	39578367	4235	12220										
PCDH12	51294	broad.mit.edu	37	chr5	141337279	141337279	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcctgggacagcttcccGatcactgtaccagatggcac	10	13	1	1	rs144137657		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:141337279G>A	ENST00000231484.3	-	1	1348	c.138C>T	c.(136-138)atC>atT	p.I46I	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	46	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I46I(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAGCTTCCCGATCACTGTAC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G		1,4405	2.1+/-5.4	0,1,2202	90	92	91		138	-1.1	1	5	dbSNP_134	91	0,8600		0,0,4300	no	coding-synonymous	PCDH12	NM_016580.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		46/1185	141337279	1,13005	2203	4300	6503	141317463	SO:0001819	synonymous_variant	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.138C>T	5.37:g.141337279G>A			141317463	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																				0.587	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141337279	G	A	141337279	2	1	61	1	0	0	0	0	0	0	0	1	11541	1048	37	1		1	PCDH12	5	141337279	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	386	141337279	39577981	4236	12221										
ARHGAP26	23092	broad.mit.edu	37	chr5	142593624	142593624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacatgactcagaactttCgttcacagcaggcacggtct	9	11	3	3	rs182566788		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:142593624C>T	ENST00000274498.4	+	22	2705	c.2327C>T	c.(2326-2328)tCg>tTg	p.S776L	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.S721L|ARHGAP26_ENST00000486650.1_3'UTR	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	776	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.S776L(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCAGAACTTTCGTTCACAGCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	5											56	44	48					5																	142593624		2203	4300	6503	142573817	SO:0001583	missense	23092			AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.2327C>T	5.37:g.142593624C>T	ENSP00000274498:p.Ser776Leu		142573817	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.308235|5.308235	0.95629|0.95629	.|.	.|.	ENSG00000145819|ENSG00000145819	ENST00000443674;ENST00000418236;ENST00000425417|ENST00000274498;ENST00000378004	.|T;T	.|0.23754	.|1.89;1.89	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Src homology-3 domain (4);	.|0.139951	.|0.49916	.|D	.|0.000132	T|T	0.68824|0.68824	0.3043|0.3043	H|H	0.97940|0.97940	4.11|4.11	0.51482|0.51482	D|D	0.999928|0.999928	.|D;D	.|0.71674	.|0.998;0.997	.|D;D	.|0.76575	.|0.988;0.947	T|T	0.81745|0.81745	-0.0792|-0.0792	5|10	.|0.66056	.|D	.|0.02	.|.	19.113|19.113	0.93326|0.93326	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|776;721	.|Q9UNA1;Q9UNA1-2	.|RHG26_HUMAN;.	C|L	350;256;58|776;721	.|ENSP00000274498:S776L;ENSP00000367243:S721L	.|ENSP00000274498:S776L	R|S	+|+	1|2	0|0	ARHGAP26|ARHGAP26	142573817|142573817	1.000000|1.000000	0.71417|0.71417	0.877000|0.877000	0.34402|0.34402	0.910000|0.910000	0.53928|0.53928	7.248000|7.248000	0.78268|0.78268	2.494000|2.494000	0.84150|0.84150	0.650000|0.650000	0.86243|0.86243	CGT|TCG		0.483	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		T	142593624	C	T	142593624	3	4	61	1	0	0	0	0	1	0	0	0	875	893	31	1	2413	1	ARHGAP26	5	142593624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1256345	142593624	38321636	4237	12222										
NR3C1	2908	broad.mit.edu	37	chr5	142680269	142680269	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaggattttcagaggtttCttgtgagactcctgtagtgg	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:142680269C>A	ENST00000343796.2	-	5	2521	c.1528G>T	c.(1528-1530)Gaa>Taa	p.E510*	NR3C1_ENST00000394464.2_Nonsense_Mutation_p.E510*|NR3C1_ENST00000424646.2_Nonsense_Mutation_p.E484*|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000231509.3_Nonsense_Mutation_p.E511*|NR3C1_ENST00000503201.1_Nonsense_Mutation_p.E510*|NR3C1_ENST00000416954.2_Nonsense_Mutation_p.E113*|NR3C1_ENST00000504572.1_Nonsense_Mutation_p.E511*|NR3C1_ENST00000415690.2_Nonsense_Mutation_p.E510*|NR3C1_ENST00000394466.2_Nonsense_Mutation_p.E511*	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	510	Hinge.|Interaction with CLOCK.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)	p.E511*(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TCAGAGGTTTCTTGTGAGACT	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											137	128	131					5																	142680269		2203	4300	6503	142660462	SO:0001587	stop_gained	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1528G>T	5.37:g.142680269C>A	ENSP00000343205:p.Glu510*		142660462	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Nonsense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	C	39	7.518150	0.98332	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	.	.	.	5.83	4.97	0.65823	.	0.466719	0.25146	N	0.032786	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	14.7154	0.69265	0.0:0.9309:0.0:0.0691	.	.	.	.	X	510;510;510;484;511;511;511;113;510	.	ENSP00000231509:E511X	E	-	1	0	NR3C1	142660462	1.000000	0.71417	0.992000	0.48379	0.323000	0.28346	4.917000	0.63369	1.466000	0.48025	0.655000	0.94253	GAA		0.393	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			A	142680269	C	A	142680269	4	1	61	1	0	0	0	0	0	1	0	0	10661	922	32	2	877	2	NR3C1	5	142680269	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86645	142680269	38234991	4238	12223										
NR3C1	2908	broad.mit.edu	37	chr5	142779553	142779553	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccaggggtgcagagttcGatgaaatcttctttttctgt	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:142779553G>A	ENST00000343796.2	-	2	1845	c.852C>T	c.(850-852)atC>atT	p.I284I	NR3C1_ENST00000394464.2_Silent_p.I284I|NR3C1_ENST00000424646.2_Silent_p.I284I|NR3C1_ENST00000231509.3_Silent_p.I284I|NR3C1_ENST00000503201.1_Silent_p.I284I|NR3C1_ENST00000416954.2_Intron|NR3C1_ENST00000504572.1_Silent_p.I284I|NR3C1_ENST00000415690.2_Silent_p.I284I|NR3C1_ENST00000394466.2_Silent_p.I284I	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	284	Modulating.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)	p.I284I(2)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TGCAGAGTTCGATGAAATCTT	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	5											99	104	102					5																	142779553		2203	4300	6503	142759746	SO:0001819	synonymous_variant	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.852C>T	5.37:g.142779553G>A			142759746	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Silent	SNP	ENST00000343796.2	37	CCDS4278.1																																																																																				0.413	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			A	142779553	G	A	142779553	2	1	61	1	0	0	0	0	0	0	0	1	10661	1048	37	1		1	NR3C1	5	142779553	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99284	142779553	38135707	4239	12224										
KCTD16	57528	broad.mit.edu	37	chr5	143586849	143586849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtttcggagagttccccGgattttggtttgtggaagga	14	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:143586849G>A	ENST00000507359.3	+	2	1663	c.572G>A	c.(571-573)cGg>cAg	p.R191Q	KCTD16_ENST00000512467.1_Missense_Mutation_p.R191Q	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	191					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)		p.R191Q(2)		large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGAGTTCCCCGGATTTTGGTT	0.512																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	5											58	62	60					5																	143586849		2203	4300	6503	143567042	SO:0001583	missense	57528			AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.572G>A	5.37:g.143586849G>A	ENSP00000426548:p.Arg191Gln		143567042	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	37	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.621679	0.87460	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.67865	-0.29;-0.29	5.69	5.69	0.88448	.	0.113744	0.64402	D	0.000017	T	0.74612	0.3739	M	0.85630	2.765	0.80722	D	1	D	0.59357	0.985	B	0.43331	0.416	T	0.81050	-0.1108	10	0.87932	D	0	.	19.8182	0.96579	0.0:0.0:1.0:0.0	.	191	Q68DU8	KCD16_HUMAN	Q	191	ENSP00000424151:R191Q;ENSP00000426548:R191Q	ENSP00000426548:R191Q	R	+	2	0	KCTD16	143567042	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.807000	0.99171	2.700000	0.92200	0.561000	0.74099	CGG		0.512	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		A	143586849	G	A	143586849	3	1	61	1	0	0	0	0	1	0	0	0	8124	1116	39	1	574	1	KCTD16	5	143586849	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	807296	143586849	37328411	4240	12225										
GRXCR2	643226	broad.mit.edu	37	chr5	145246210	145246210	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaattttcctcacaaaatCtctcttgtccattggggttc	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145246210C>A	ENST00000377976.1	-	2	417	c.418G>T	c.(418-420)Gat>Tat	p.D140Y		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	140						cell projection (GO:0042995)		p.D140Y(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CTCACAAAATCTCTCTTGTCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	124	125					5																	145246210		2203	4300	6503	145226403	SO:0001583	missense	643226				CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.418G>T	5.37:g.145246210C>A	ENSP00000367214:p.Asp140Tyr		145226403		Missense_Mutation	SNP	ENST00000377976.1	37	CCDS34263.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.247666	0.59103	.	.	ENSG00000204928	ENST00000377976	T	0.25085	1.82	5.42	5.42	0.78866	.	0.103621	0.64402	D	0.000003	T	0.40815	0.1132	L	0.51422	1.61	0.38631	D	0.951363	D	0.59357	0.985	P	0.55303	0.773	T	0.16928	-1.0386	10	0.40728	T	0.16	-11.5763	19.2175	0.93783	0.0:1.0:0.0:0.0	.	140	A6NFK2	GRCR2_HUMAN	Y	140	ENSP00000367214:D140Y	ENSP00000367214:D140Y	D	-	1	0	GRXCR2	145226403	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	2.582000	0.46085	2.536000	0.85505	0.455000	0.32223	GAT		0.418	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2			A	145246210	C	A	145246210	3	1	61	1	0	0	0	0	1	0	0	0	6834	913	32	2	336	2	GRXCR2	5	145246210	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1659361	145246210	35669050	4241	12226										
LARS	51520	broad.mit.edu	37	chr5	145502107	145502107	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagcagtcttccctgattTtatcttctgcttcggaggca	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145502107T>G	ENST00000394434.2	-	30	3306	c.3140A>C	c.(3139-3141)aAa>aCa	p.K1047T	RP11-118M9.3_ENST00000514002.1_RNA|LARS_ENST00000274562.9_Missense_Mutation_p.K1020T|LARS_ENST00000510191.1_Missense_Mutation_p.K993T|LARS_ENST00000545646.1_Missense_Mutation_p.K1001T	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	1047					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.K1047T(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TTCCCTGATTTTATCTTCTGC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	5											147	138	141					5																	145502107		2203	4300	6503	145482300	SO:0001583	missense	51520			AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.3140A>C	5.37:g.145502107T>G	ENSP00000377954:p.Lys1047Thr		145482300	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	37	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111606	0.56398	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.67345	-0.25;-0.25;-0.24;-0.26	5.63	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.65984	0.2744	M	0.75447	2.3	0.80722	D	1	B;B;B	0.26081	0.017;0.141;0.07	B;B;B	0.26094	0.066;0.041;0.066	T	0.62567	-0.6827	10	0.33940	T	0.23	.	13.0696	0.59053	0.0:0.0:0.1343:0.8657	.	1020;1001;1047	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	T	1047;1001;356;993;1020	ENSP00000377954:K1047T;ENSP00000437791:K1001T;ENSP00000426005:K993T;ENSP00000274562:K1020T	ENSP00000274562:K1020T	K	-	2	0	LARS	145482300	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.613000	0.67688	1.041000	0.40125	0.533000	0.62120	AAA		0.348	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		G	145502107	T	G	145502107	3	3	61	1	0	0	0	0	1	0	0	0	8656	1841	64	4	402	4	LARS	5	145502107	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	255897	145502107	35413153	4242	12227										
RBM27	54439	broad.mit.edu	37	chr5	145613128	145613128	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccaccccctcctcctggGcttcctcctccaccacctcc	3	25	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145613128G>A	ENST00000265271.5	+	7	1132	c.966G>A	c.(964-966)ggG>ggA	p.G322G	RBM27_ENST00000506502.1_Silent_p.G322G	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	322	Pro-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G322G(2)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCCTCCTGGGCTTCCTCCTC	0.582																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	5											171	157	161					5																	145613128		1568	3582	5150	145593321	SO:0001819	synonymous_variant	54439			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.966G>A	5.37:g.145613128G>A			145593321	Q8IYW9	Silent	SNP	ENST00000265271.5	37	CCDS43378.1																																																																																				0.582	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		A	145613128	G	A	145613128	2	1	61	1	0	0	0	0	0	0	0	1	13164	1190	42	3		3	RBM27	5	145613128	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111021	145613128	35302132	4243	12228										
POU4F3	5459	broad.mit.edu	37	chr5	145719977	145719977	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaccagagacagaaacaGaaacgaatgaagtattcggc	10	8	0	4	rs543894486		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145719977G>T	ENST00000230732.4	+	2	1076	c.987G>T	c.(985-987)caG>caT	p.Q329H	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	329					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q329H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GACAGAAACAGAAACGAATGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	5											48	47	47					5																	145719977		2203	4300	6503	145700170	SO:0001583	missense	5459			U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.987G>T	5.37:g.145719977G>T	ENSP00000230732:p.Gln329His		145700170	O60557|Q2M3F8	Missense_Mutation	SNP	ENST00000230732.4	37	CCDS4281.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064980	0.55432	.	.	ENSG00000091010	ENST00000230732	D	0.96232	-3.95	4.62	4.62	0.57501	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.95965	0.8686	N	0.16833	0.445	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97234	0.9886	10	0.87932	D	0	.	16.3979	0.83621	0.0:0.0:1.0:0.0	.	329	Q15319	PO4F3_HUMAN	H	329	ENSP00000230732:Q329H	ENSP00000230732:Q329H	Q	+	3	2	POU4F3	145700170	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.511000	0.67024	2.372000	0.80975	0.462000	0.41574	CAG		0.562	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		T	145719977	G	T	145719977	3	4	61	1	0	0	0	0	1	0	0	0	12311	933	33	2	993	2	POU4F3	5	145719977	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	106849	145719977	35195283	4244	12229										
TCERG1	10915	broad.mit.edu	37	chr5	145836747	145836747	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttttgtgaattaacagaGaccacctttcatgcctcctc	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145836747G>T	ENST00000296702.5	+	3	325	c.287G>T	c.(286-288)aGa>aTa	p.R96I	TCERG1_ENST00000394421.2_Splice_Site_p.R96I	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	96	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.R96I(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATTAACAGAGACCACCTTTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5											158	149	152					5																	145836747		2203	4300	6503	145816940	SO:0001630	splice_region_variant	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.286-1G>T	5.37:g.145836747G>T			145816940	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.048518	0.75846	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.25414	1.82;1.8	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.41259	0.1151	L	0.32530	0.975	0.80722	D	1	D;D;D	0.65815	0.995;0.994;0.99	D;D;D	0.72982	0.979;0.975;0.944	T	0.08932	-1.0698	10	0.32370	T	0.25	-18.845	18.9097	0.92477	0.0:0.0:1.0:0.0	.	96;96;96	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	I	96	ENSP00000296702:R96I;ENSP00000377943:R96I	ENSP00000296702:R96I	R	+	2	0	TCERG1	145816940	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.448000	0.97600	2.463000	0.83235	0.491000	0.48974	AGA		0.418	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	Missense_Mutation	T	145836747	G	T	145836747	5	4	61	1	0	0	0	0	0	0	1	0	15724	956	33	2	297	2	TCERG1	5	145836747	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116770	145836747	35078513	4245	12230										
TCERG1	10915	broad.mit.edu	37	chr5	145838886	145838886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaactgctacttcagttgCgcagacagtatcaagtgagt	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145838886C>T	ENST00000296702.5	+	4	916	c.878C>T	c.(877-879)gCg>gTg	p.A293V	TCERG1_ENST00000394421.2_Missense_Mutation_p.A293V	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	293	Thr-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.A293V(2)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTTCAGTTGCGCAGACAGTA	0.463																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	5											157	145	149					5																	145838886		2203	4300	6503	145819079	SO:0001583	missense	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.878C>T	5.37:g.145838886C>T	ENSP00000296702:p.Ala293Val		145819079	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	C	5.247	0.230989	0.09969	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.77098	-1.07;-1.07	5.33	3.55	0.40652	.	0.206931	0.43747	D	0.000526	T	0.62356	0.2421	N	0.24115	0.695	0.31980	N	0.606	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.57888	-0.7733	10	0.17369	T	0.5	-0.2268	12.0659	0.53588	0.0:0.8775:0.0:0.1225	.	293;293;293	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	V	293	ENSP00000296702:A293V;ENSP00000377943:A293V	ENSP00000296702:A293V	A	+	2	0	TCERG1	145819079	0.951000	0.32395	0.878000	0.34440	0.941000	0.58515	1.940000	0.40223	0.735000	0.32537	0.563000	0.77884	GCG		0.463	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145838886	C	T	145838886	3	4	61	1	0	0	0	0	1	0	0	0	15724	768	27	1	892	1	TCERG1	5	145838886	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2139	145838886	35076374	4246	12231										
TCERG1	10915	broad.mit.edu	37	chr5	145882992	145882992	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacttggacagtcagtctCgatggagcaaagtaaaagac	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145882992C>T	ENST00000296702.5	+	17	2475	c.2437C>T	c.(2437-2439)Cga>Tga	p.R813*	TCERG1_ENST00000509787.1_3'UTR|TCERG1_ENST00000394421.2_Nonsense_Mutation_p.R792*	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	813	FF 3.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.R813*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTCAGTCTCGATGGAGCAA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											89	82	84					5																	145882992		2203	4299	6502	145863185	SO:0001587	stop_gained	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.2437C>T	5.37:g.145882992C>T	ENSP00000296702:p.Arg813*		145863185	Q2NKN2|Q59EA1	Nonsense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	C	41	8.545074	0.98857	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	.	.	.	5.05	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2342	15.0326	0.71720	0.1437:0.8563:0.0:0.0	.	.	.	.	X	813;792	.	ENSP00000296702:R813X	R	+	1	2	TCERG1	145863185	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.597000	0.67577	1.226000	0.43582	0.591000	0.81541	CGA		0.353	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145882992	C	T	145882992	4	4	61	1	0	0	0	0	0	1	0	0	15724	876	31	1	2503	1	TCERG1	5	145882992	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44106	145882992	35032268	4247	12232										
TCERG1	10915	broad.mit.edu	37	chr5	145883531	145883531	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagcagcacaaacgagaaGaagctatccagaatttcaaa	9	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145883531G>T	ENST00000296702.5	+	18	2730	c.2692G>T	c.(2692-2694)Gaa>Taa	p.E898*	TCERG1_ENST00000509787.1_3'UTR|TCERG1_ENST00000394421.2_Nonsense_Mutation_p.E877*	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	898	FF 4.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.E898*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAACGAGAAGAAGCTATCCA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											102	104	103					5																	145883531		2203	4300	6503	145863724	SO:0001587	stop_gained	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.2692G>T	5.37:g.145883531G>T	ENSP00000296702:p.Glu898*		145863724	Q2NKN2|Q59EA1	Nonsense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	41	8.871294	0.98984	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-20.6489	19.9855	0.97347	0.0:0.0:1.0:0.0	.	.	.	.	X	898;877	.	ENSP00000296702:E898X	E	+	1	0	TCERG1	145863724	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.603000	0.98315	2.806000	0.96561	0.655000	0.94253	GAA		0.378	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145883531	G	T	145883531	4	4	61	1	0	0	0	0	0	1	0	0	15724	943	33	2	2762	2	TCERG1	5	145883531	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	539	145883531	35031729	4248	12233										
TCERG1	10915	broad.mit.edu	37	chr5	145890075	145890075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattttacagaatgacaaacGgtatctagtactggactgtg	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:145890075G>A	ENST00000296702.5	+	22	3205	c.3167G>A	c.(3166-3168)cGg>cAg	p.R1056Q	TCERG1_ENST00000394421.2_Missense_Mutation_p.R1035Q	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	1056	FF 6.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.R1056Q(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATGACAAACGGTATCTAGTA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											96	94	95					5																	145890075		2203	4300	6503	145870268	SO:0001583	missense	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.3167G>A	5.37:g.145890075G>A	ENSP00000296702:p.Arg1056Gln		145870268	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449778	0.84101	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.56611	0.45;0.45	6.16	6.16	0.99307	FF domain (2);	0.000000	0.85682	D	0.000000	T	0.76378	0.3979	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.992	T	0.74867	-0.3518	10	0.51188	T	0.08	-7.2318	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1035;1056	O14776-2;O14776	.;TCRG1_HUMAN	Q	1056;1035	ENSP00000296702:R1056Q;ENSP00000377943:R1035Q	ENSP00000296702:R1056Q	R	+	2	0	TCERG1	145870268	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.804000	0.99143	2.937000	0.99478	0.650000	0.86243	CGG		0.428	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		A	145890075	G	A	145890075	3	1	61	1	0	0	0	0	1	0	0	0	15724	1116	39	1	3253	1	TCERG1	5	145890075	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6544	145890075	35025185	4249	12234										
STK32A	202374	broad.mit.edu	37	chr5	146658905	146658905	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaatgaagtgagaaatgtCttcaaggaactccagatcat	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:146658905C>A	ENST00000397936.3	+	4	537	c.204C>A	c.(202-204)gtC>gtA	p.V68V	STK32A_ENST00000398523.3_Silent_p.V68V|STK32A_ENST00000398521.3_Silent_p.V68V|STK32A_ENST00000541094.1_Silent_p.V68V	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	68	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.V68V(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGAAATGTCTTCAAGGAAC	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	5											87	92	91					5																	146658905		1938	4163	6101	146639098	SO:0001819	synonymous_variant	202374				CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.204C>A	5.37:g.146658905C>A			146639098	B3KSY0	Silent	SNP	ENST00000397936.3	37	CCDS47299.1																																																																																				0.413	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001		A	146658905	C	A	146658905	2	1	61	1	0	0	0	0	0	0	0	1	15336	900	32	2		2	STK32A	5	146658905	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	768830	146658905	34256355	4250	12235										
DPYSL3	1809	broad.mit.edu	37	chr5	146795309	146795309	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcacttcctgcttgacGctgtcattccagtgggtgat	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:146795309G>A	ENST00000398514.3	-	4	812	c.441C>T	c.(439-441)agC>agT	p.S147S	DPYSL3_ENST00000343218.5_Silent_p.S261S|DPYSL3_ENST00000534907.1_Intron	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	147					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)	p.S147S(1)		breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGCTTGACGCTGTCATTCC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	5											252	261	258					5																	146795309		2129	4241	6370	146775502	SO:0001819	synonymous_variant	1809			D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.441C>T	5.37:g.146795309G>A			146775502	B3SXQ8|Q93012	Silent	SNP	ENST00000398514.3	37	CCDS43381.1																																																																																				0.547	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		A	146795309	G	A	146795309	2	1	61	1	0	0	0	0	0	0	0	1	4759	1078	38	1		1	DPYSL3	5	146795309	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136404	146795309	34119951	4251	12236										
JAKMIP2	9832	broad.mit.edu	37	chr5	147015807	147015807	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctaaaagctcctggtttCtcttaatgaaaagttgttta	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:147015807C>A	ENST00000265272.5	-	12	2122	c.1655G>T	c.(1654-1656)aGa>aTa	p.R552I	JAKMIP2_ENST00000507386.1_Intron|JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R510I	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	552						Golgi apparatus (GO:0005794)		p.R552I(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCTGGTTTCTCTTAATGAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	94	99					5																	147015807		2203	4300	6503	146996000	SO:0001583	missense	9832			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1655G>T	5.37:g.147015807C>A	ENSP00000265272:p.Arg552Ile		146996000	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065853	0.76187	.	.	ENSG00000176049	ENST00000265272;ENST00000333010	T;T	0.25414	1.81;1.8	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.29223	0.0727	L	0.52759	1.655	0.80722	D	1	P;P;P	0.43701	0.815;0.815;0.815	B;B;B	0.39258	0.295;0.295;0.295	T	0.01235	-1.1410	10	0.37606	T	0.19	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	510;552;552	B4DSG0;Q96AA8-3;Q96AA8	.;.;JKIP2_HUMAN	I	552;510	ENSP00000265272:R552I;ENSP00000328989:R510I	ENSP00000265272:R552I	R	-	2	0	JAKMIP2	146996000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.308000	0.65768	2.873000	0.98535	0.563000	0.77884	AGA		0.473	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		A	147015807	C	A	147015807	3	1	61	1	0	0	0	0	1	0	0	0	7962	913	32	2	817	2	JAKMIP2	5	147015807	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220498	147015807	33899453	4252	12237										
JAKMIP2	9832	broad.mit.edu	37	chr5	147040808	147040808	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagacttgagcctctggatCtctccatcacgtaccttcac	7	15	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:147040808C>A	ENST00000265272.5	-	3	797	c.330G>T	c.(328-330)gaG>gaT	p.E110D	JAKMIP2_ENST00000507386.1_Missense_Mutation_p.E110D|JAKMIP2_ENST00000333010.6_Missense_Mutation_p.E68D	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	110						Golgi apparatus (GO:0005794)		p.E110D(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCTGGATCTCTCCATCAC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											175	166	169					5																	147040808		2203	4300	6503	147021001	SO:0001583	missense	9832			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.330G>T	5.37:g.147040808C>A	ENSP00000265272:p.Glu110Asp		147021001	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344186	0.61073	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.09255	3.0;3.0;3.0	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.25269	0.0614	M	0.63843	1.955	0.58432	D	0.999996	D;D;D;D	0.56035	0.974;0.974;0.974;0.974	D;D;D;D	0.67725	0.953;0.953;0.953;0.953	T	0.00215	-1.1911	10	0.37606	T	0.19	.	9.8813	0.41236	0.0:0.8683:0.0:0.1317	.	68;110;110;110	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	D	110;110;68;110	ENSP00000421398:E110D;ENSP00000265272:E110D;ENSP00000328989:E68D	ENSP00000265272:E110D	E	-	3	2	JAKMIP2	147021001	1.000000	0.71417	1.000000	0.80357	0.392000	0.30506	3.160000	0.50739	2.529000	0.85273	0.563000	0.77884	GAG		0.567	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		A	147040808	C	A	147040808	3	1	61	1	0	0	0	0	1	0	0	0	7962	912	32	2	2178	2	JAKMIP2	5	147040808	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25001	147040808	33874452	4253	12238										
SPINK5	11005	broad.mit.edu	37	chr5	147480973	147480973	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaatcaagaaacaaaagaCaatctaagagtacagcttcc	6	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:147480973C>T	ENST00000256084.7	+	14	1318	c.1276C>T	c.(1276-1278)Caa>Taa	p.Q426*	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Nonsense_Mutation_p.Q426*|SPINK5_ENST00000398454.1_Nonsense_Mutation_p.Q426*	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	426					anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q426*(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACAAAAGACAATCTAAGAG	0.388																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											137	120	125					5																	147480973		1857	4106	5963	147461166	SO:0001587	stop_gained	11005			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1276C>T	5.37:g.147480973C>T	ENSP00000256084:p.Gln426*		147461166	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Nonsense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.834290	0.32421	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	.	.	.	3.72	2.86	0.33363	.	0.834828	0.10258	N	0.696336	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-14.1334	12.0995	0.53774	0.0:0.8239:0.1761:0.0	.	.	.	.	X	426;426;407;426	.	ENSP00000256084:Q426X	Q	+	1	0	SPINK5	147461166	0.480000	0.25933	0.975000	0.42487	0.160000	0.22226	-0.099000	0.11007	0.553000	0.29044	-0.810000	0.03169	CAA		0.388	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147480973	C	T	147480973	4	4	61	1	0	0	0	0	0	1	0	0	15101	479	17	3	1330	3	SPINK5	5	147480973	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	440165	147480973	33434287	4254	12239										
SPINK5	11005	broad.mit.edu	37	chr5	147505098	147505098	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttcaggaccagtgcagAcaggttcagaatgaagcgga	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:147505098A>T	ENST00000256084.7	+	29	2781				SPINK5_ENST00000359874.3_Missense_Mutation_p.R917S	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5						anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R917S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAGTGCAGACAGGTTCAGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											69	58	62					5																	147505098		1568	3582	5150	147485291	SO:0001627	intron_variant	11005			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2740-188A>T	5.37:g.147505098A>T			147485291	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	A	3.952	-0.012151	0.07727	.	.	ENSG00000133710	ENST00000359874	T	0.39997	1.05	4.44	1.86	0.25419	.	2.473690	0.01264	N	0.009276	T	0.24198	0.0586	.	.	.	0.58432	D	0.999994	B	0.17465	0.022	B	0.16289	0.015	T	0.38585	-0.9654	9	0.08599	T	0.76	-0.4245	5.3021	0.15783	0.7133:0.0:0.2867:0.0	.	917	Q9NQ38-3	.	S	917	ENSP00000352936:R917S	ENSP00000352936:R917S	R	+	3	2	SPINK5	147485291	0.105000	0.21958	0.843000	0.33291	0.415000	0.31203	0.230000	0.17852	0.384000	0.24942	0.533000	0.62120	AGA		0.463	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147505098	A	T	147505098	1	4	61	0	1	0	0	0	0	0	0	0	15101	272	10	5		5	SPINK5	5	147505098	Intron	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24125	147505098	33410162	4255	12240										
HTR4	3360	broad.mit.edu	37	chr5	147889584	147889584	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggttgaacttcctcttttCtatctgagagttggagggag	12	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:147889584C>A	ENST00000377888.3	-	6	649	c.511G>T	c.(511-513)Gaa>Taa	p.E171*	HTR4_ENST00000360693.3_Nonsense_Mutation_p.E171*|HTR4_ENST00000520514.1_Nonsense_Mutation_p.E171*|HTR4_ENST00000521530.1_Nonsense_Mutation_p.E171*|HTR4_ENST00000517929.1_Nonsense_Mutation_p.E171*|HTR4_ENST00000314512.6_Nonsense_Mutation_p.E171*|HTR4_ENST00000362016.2_Nonsense_Mutation_p.E185*|HTR4_ENST00000521735.1_Nonsense_Mutation_p.E171*|HTR4_ENST00000354217.2_Nonsense_Mutation_p.E171*	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	171					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.E171*(1)		endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	TTCCTCTTTTCTATCTGAGAG	0.448																																					GBM(120;370 1604 14007 17804 41573)											1	Substitution - Nonsense(1)	large_intestine(1)	5											59	58	58					5																	147889584		2203	4299	6502	147869777	SO:0001587	stop_gained	3360			Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5299	protein-coding gene	gene with protein product		602164	"5-hydroxytryptamine (serotonin) receptor 4"			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000377888.3:c.511G>T	5.37:g.147889584C>A	ENSP00000367120:p.Glu171*		147869777	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Nonsense_Mutation	SNP	ENST00000377888.3	37	CCDS4291.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191306	0.78902	.	.	ENSG00000164270	ENST00000521530;ENST00000354217;ENST00000314512;ENST00000521735;ENST00000517929;ENST00000520514;ENST00000377888;ENST00000360693;ENST00000362016	.	.	.	5.65	5.65	0.86999	.	0.090660	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	14.7812	0.69769	0.0:0.855:0.145:0.0	.	.	.	.	X	171;171;171;171;171;171;171;171;185	.	ENSP00000314906:E171X	E	-	1	0	HTR4	147869777	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.966000	0.56795	2.681000	0.91329	0.563000	0.77884	GAA		0.448	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870		A	147889584	C	A	147889584	4	1	61	1	0	0	0	0	0	1	0	0	7470	922	32	2	959	2	HTR4	5	147889584	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	384486	147889584	33025676	4256	12241										
SH3TC2	79628	broad.mit.edu	37	chr5	148407348	148407348	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaagggcaggacctcctcGtgccggcctaggctcaggag	15	13	1	0	rs576049662		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:148407348G>A	ENST00000515425.1	-	11	2048	c.1947C>T	c.(1945-1947)caC>caT	p.H649H	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Silent_p.H196H|SH3TC2_ENST00000512049.1_Silent_p.H642H|SH3TC2_ENST00000394358.2_Silent_p.H534H	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	649					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)		p.H649H(1)|p.H534H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCTCCTCGTGCCGGCCTA	0.637													g|||	1	0.000199681	0	0	5008	,	,		17842	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	5											35	41	39					5																	148407348		2203	4300	6503	148387541	SO:0001819	synonymous_variant	79628			AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1947C>T	5.37:g.148407348G>A			148387541	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																				0.637	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148407348	G	A	148407348	2	1	61	1	0	0	0	0	0	0	0	1	14299	1136	40	1		1	SH3TC2	5	148407348	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	517764	148407348	32507912	4257	12242										
AFAP1L1	134265	broad.mit.edu	37	chr5	148719587	148719587	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggaatgggaaatgaagaaGacctaggaagaggatgagga	16	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:148719587G>T	ENST00000296721.4	+	19	2399	c.2301G>T	c.(2299-2301)aaG>aaT	p.K767N	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.K724N	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	767						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K767N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATGAAGAAGACCTAGGAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											112	102	105					5																	148719587		2203	4300	6503	148699780	SO:0001583	missense	134265			AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.2301G>T	5.37:g.148719587G>T	ENSP00000296721:p.Lys767Asn		148699780	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.411067	0.42817	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.15372	2.43;2.51	5.93	3.17	0.36434	.	0.182235	0.47852	D	0.000209	T	0.14485	0.0350	N	0.20881	0.62	0.23838	N	0.996701	D;B	0.56746	0.977;0.068	P;B	0.53593	0.73;0.022	T	0.07520	-1.0768	10	0.07644	T	0.81	-33.3217	9.0311	0.36260	0.2693:0.0:0.7307:0.0	.	724;767	Q8TED9-2;Q8TED9	.;AF1L1_HUMAN	N	767;724	ENSP00000296721:K767N;ENSP00000424427:K724N	ENSP00000296721:K767N	K	+	3	2	AFAP1L1	148699780	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.912000	0.39946	1.524000	0.49035	0.561000	0.74099	AAG		0.413	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		T	148719587	G	T	148719587	3	4	61	1	0	0	0	0	1	0	0	0	354	933	33	2	2375	2	AFAP1L1	5	148719587	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	312239	148719587	32195673	4258	12243										
SLC26A2	1836	broad.mit.edu	37	chr5	149357695	149357695	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggtacctcccgtcacatCtctgtgggcatttttggagt	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149357695C>A	ENST00000286298.4	+	2	748	c.480C>A	c.(478-480)atC>atA	p.I160I		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	160					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.I160I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCCGTCACATCTCTGTGGGCA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	5											156	145	149					5																	149357695		2203	4300	6503	149337888	SO:0001819	synonymous_variant	1836			U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.480C>A	5.37:g.149357695C>A			149337888	A8K2U3|B2R6J1|Q6N051	Silent	SNP	ENST00000286298.4	37	CCDS4300.1																																																																																				0.463	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		A	149357695	C	A	149357695	2	1	61	1	0	0	0	0	0	0	0	1	14554	903	32	2		2	SLC26A2	5	149357695	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	638108	149357695	31557565	4259	12244										
TIGD6	81789	broad.mit.edu	37	chr5	149375858	149375858	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacagctcccacaactttCattttctcctccagagagaa	4	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149375858C>A	ENST00000296736.3	-	2	828	c.54G>T	c.(52-54)atG>atT	p.M18I	TIGD6_ENST00000515406.2_Missense_Mutation_p.M18I	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	18	HTH psq-type. {ECO:0000255|PROSITE- ProRule:PRU00320}.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.M18I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCACAACTTTCATTTTCTCCT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	81	78					5																	149375858		2203	4300	6503	149356051	SO:0001583	missense	81789			AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.54G>T	5.37:g.149375858C>A	ENSP00000296736:p.Met18Ile		149356051	B3KTZ8|Q96MQ4|Q9H0X7	Missense_Mutation	SNP	ENST00000296736.3	37	CCDS4301.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.822926	0.00589	.	.	ENSG00000164296	ENST00000296736;ENST00000515406	T;T	0.39592	1.07;1.07	4.66	2.85	0.33270	Homeodomain-related (1);Homeodomain-like (1);Helix-turn-helix, Psq-like (1);Centromere protein Cenp-B, DNA-binding domain 1 (1);	0.170937	0.27710	N	0.018176	T	0.12008	0.0292	N	0.01267	-0.92	0.21147	N	0.999771	B	0.15930	0.015	B	0.15870	0.014	T	0.21586	-1.0241	10	0.13108	T	0.6	.	3.3188	0.07043	0.1794:0.5524:0.1738:0.0944	.	18	Q17RP2	TIGD6_HUMAN	I	18	ENSP00000296736:M18I;ENSP00000425318:M18I	ENSP00000296736:M18I	M	-	3	0	TIGD6	149356051	0.600000	0.26899	0.999000	0.59377	0.414000	0.31173	0.071000	0.14594	0.688000	0.31529	-0.315000	0.08773	ATG		0.473	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		A	149375858	C	A	149375858	3	1	61	1	0	0	0	0	1	0	0	0	15939	826	29	2	1515	2	TIGD6	5	149375858	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18163	149375858	31539402	4260	12245										
PDGFRB	5159	broad.mit.edu	37	chr5	149515193	149515193	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtgggtgcaaaagtattCtcccgtgtctagcccagtga	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149515193C>A	ENST00000261799.4	-	3	758	c.289G>T	c.(289-291)Gaa>Taa	p.E97*		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	97	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.E97*(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAAAAGTATTCTCCCGTGTCT	0.592			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	1	Substitution - Nonsense(1)	large_intestine(1)	5											130	125	127					5																	149515193		2203	4300	6503	149495386	SO:0001587	stop_gained	5159			M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.289G>T	5.37:g.149515193C>A	ENSP00000261799:p.Glu97*		149495386	B5A957|Q8N5L4	Nonsense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	.	.	.	.	.	.	.	.	.	.	C	39	7.460644	0.98299	.	.	ENSG00000113721	ENST00000261799;ENST00000517488;ENST00000517957	.	.	.	5.42	5.42	0.78866	.	0.102890	0.42548	D	0.000686	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	13.8972	0.63781	0.0:0.8477:0.1523:0.0	.	.	.	.	X	97;33;97	.	ENSP00000261799:E97X	E	-	1	0	PDGFRB	149495386	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.668000	0.54554	2.539000	0.85634	0.561000	0.74099	GAA		0.592	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		A	149515193	C	A	149515193	4	1	61	1	0	0	0	0	0	1	0	0	11693	922	32	2	3115	2	PDGFRB	5	149515193	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139335	149515193	31400067	4261	12246										
ARSI	340075	broad.mit.edu	37	chr5	149677480	149677480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccggcttgtccgttgctttCgcttgagcaggggactgtgg	15	11	0	1	rs143451969	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149677480C>T	ENST00000328668.7	-	2	1586	c.1007G>A	c.(1006-1008)cGa>cAa	p.R336Q		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	336					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.R336Q(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCGTTGCTTTCGCTTGAGCAG	0.627													C|||	9	0.00179712	0.0068	0	5008	,	,		20486	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG	29,4377	31.7+/-61.6	0,29,2174	40	40	40		1007	3.6	1	5	dbSNP_134	40	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ARSI	NM_001012301.2	43	0,30,6473	TT,TC,CC		0.0116,0.6582,0.2307	possibly-damaging	336/570	149677480	30,12976	2203	4300	6503	149657673	SO:0001583	missense	340075			AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.1007G>A	5.37:g.149677480C>T	ENSP00000333395:p.Arg336Gln		149657673	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	CCDS34275.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	5.022	0.189718	0.09547	0.006582	1.16E-4	ENSG00000183876	ENST00000328668;ENST00000515301	D;D	0.96365	-3.99;-3.99	4.46	3.58	0.41010	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.315498	0.31589	N	0.007382	D	0.87196	0.6117	L	0.31207	0.915	0.30918	N	0.728352	P	0.40875	0.731	B	0.36808	0.233	D	0.84888	0.0835	10	0.13470	T	0.59	.	7.2893	0.26356	0.0:0.7275:0.0:0.2725	.	336	Q5FYB1	ARSI_HUMAN	Q	336;193	ENSP00000333395:R336Q;ENSP00000426879:R193Q	ENSP00000333395:R336Q	R	-	2	0	ARSI	149657673	0.720000	0.27996	0.986000	0.45419	0.991000	0.79684	1.391000	0.34475	1.190000	0.43042	0.561000	0.74099	CGA		0.627	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		T	149677480	C	T	149677480	3	4	61	1	0	0	0	0	1	0	0	0	995	884	31	1	706	1	ARSI	5	149677480	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162287	149677480	31237780	4262	12247										
TCOF1	6949	broad.mit.edu	37	chr5	149767492	149767492	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccccctctgatttttgtcGaccctaatcgtagtccagct	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149767492G>A	ENST00000504761.2	+	18	2887	c.2887G>A	c.(2887-2889)Gac>Aac	p.D963N	TCOF1_ENST00000323668.7_Missense_Mutation_p.D886N|TCOF1_ENST00000513346.1_Missense_Mutation_p.D1000N|TCOF1_ENST00000451292.1_Missense_Mutation_p.D1000N|TCOF1_ENST00000377797.3_Missense_Mutation_p.D963N|TCOF1_ENST00000445265.2_Missense_Mutation_p.D886N|TCOF1_ENST00000439160.2_Missense_Mutation_p.D963N			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	963					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.D886N(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATTTTTGTCGACCCTAATCG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	5											44	52	49					5																	149767492		2203	4300	6503	149747685	SO:0001583	missense	6949				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2887G>A	5.37:g.149767492G>A	ENSP00000421655:p.Asp963Asn		149747685	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965074	0.34659	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.77098	-1.07;-0.97;-0.96;-0.91;0.06;-0.92;-0.96;-0.92	5.8	4.0	0.46444	.	0.141481	0.33040	N	0.005349	T	0.55353	0.1915	N	0.25647	0.755	0.23984	N	0.99627	P;P;P;P;P;P	0.51351	0.792;0.944;0.944;0.944;0.907;0.944	B;B;B;B;B;B	0.34180	0.115;0.177;0.177;0.177;0.086;0.177	T	0.49744	-0.8907	10	0.12430	T	0.62	-13.3975	8.3713	0.32417	0.1821:0.0:0.8179:0.0	.	472;963;886;963;963;886	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;.;TCOF_HUMAN;.	N	1000;963;886;886;963;963;963;1000	ENSP00000400939:D1000N;ENSP00000367028:D963N;ENSP00000409944:D886N;ENSP00000325223:D886N;ENSP00000406888:D963N;ENSP00000390717:D963N;ENSP00000421655:D963N;ENSP00000427484:D1000N	ENSP00000325223:D886N	D	+	1	0	TCOF1	149747685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.886000	0.48578	0.775000	0.33450	0.655000	0.94253	GAC		0.562	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		A	149767492	G	A	149767492	3	1	61	1	0	0	0	0	1	0	0	0	15747	1058	37	1	2979	1	TCOF1	5	149767492	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90012	149767492	31147768	4263	12248										
TCOF1	6949	broad.mit.edu	37	chr5	149772950	149772950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtctctcctctcaggtTatatgacccctggactaacc	6	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149772950T>G	ENST00000504761.2	+	23	3616	c.3616T>G	c.(3616-3618)Tat>Gat	p.Y1206D	TCOF1_ENST00000323668.7_Missense_Mutation_p.Y1129D|TCOF1_ENST00000513346.1_Missense_Mutation_p.Y1206D|TCOF1_ENST00000451292.1_Missense_Mutation_p.Y1243D|TCOF1_ENST00000377797.3_Missense_Mutation_p.Y1207D|TCOF1_ENST00000445265.2_Missense_Mutation_p.Y1130D|TCOF1_ENST00000439160.2_Missense_Mutation_p.Y1169D			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1206					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.Y1129D(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCTCAGGTTATATGACCCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											74	70	72					5																	149772950		2203	4300	6503	149753143	SO:0001583	missense	6949				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.3616T>G	5.37:g.149772950T>G	ENSP00000421655:p.Tyr1206Asp		149753143	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.091583	0.55968	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	4.64	3.48	0.39840	.	0.418931	0.17841	N	0.160219	T	0.64768	0.2628	L	0.32530	0.975	0.25613	N	0.986482	P;P;P;D;P	0.65815	0.95;0.95;0.95;0.995;0.95	P;P;P;P;P	0.56278	0.776;0.776;0.776;0.795;0.776	T	0.55328	-0.8158	10	0.66056	D	0.02	0.5076	6.9228	0.24397	0.0:0.1035:0.0:0.8965	.	1169;1129;1168;1206;1130	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	D	1243;1207;1130;1129;1169;1168;1206;1206	ENSP00000400939:Y1243D;ENSP00000367028:Y1207D;ENSP00000409944:Y1130D;ENSP00000325223:Y1129D;ENSP00000406888:Y1169D;ENSP00000390717:Y1168D;ENSP00000421655:Y1206D;ENSP00000427484:Y1206D	ENSP00000325223:Y1129D	Y	+	1	0	TCOF1	149753143	0.967000	0.33354	0.995000	0.50966	0.989000	0.77384	1.063000	0.30567	0.925000	0.37094	0.459000	0.35465	TAT		0.567	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		G	149772950	T	G	149772950	3	3	61	1	0	0	0	0	1	0	0	0	15747	1754	61	4	3731	4	TCOF1	5	149772950	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5458	149772950	31142310	4264	12249										
TCOF1	6949	broad.mit.edu	37	chr5	149776283	149776283	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaagaaagggaaggggtCtcttggctcccaaggggcca	17	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:149776283C>T	ENST00000504761.2	+	24	4220	c.4220C>T	c.(4219-4221)tCt>tTt	p.S1407F	TCOF1_ENST00000323668.7_Missense_Mutation_p.S1330F|TCOF1_ENST00000513346.1_Missense_Mutation_p.S1407F|TCOF1_ENST00000451292.1_Missense_Mutation_p.S1444F|TCOF1_ENST00000377797.3_Missense_Mutation_p.S1408F|TCOF1_ENST00000445265.2_Missense_Mutation_p.S1331F|TCOF1_ENST00000439160.2_Missense_Mutation_p.S1370F			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1407					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.S1330F(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGAAGGGGTCTCTTGGCTCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	5											24	21	22					5																	149776283		2203	4300	6503	149756476	SO:0001583	missense	6949				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.4220C>T	5.37:g.149776283C>T	ENSP00000421655:p.Ser1407Phe		149756476	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.821156	0.32237	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.76709	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03;-1.03;-1.04	4.42	3.52	0.40303	.	0.404294	0.18486	N	0.139793	T	0.78898	0.4356	L	0.56769	1.78	0.09310	N	1	P;P;P;P;P	0.47350	0.891;0.891;0.891;0.894;0.891	P;P;P;B;P	0.51355	0.667;0.667;0.667;0.365;0.667	T	0.70454	-0.4867	10	0.72032	D	0.01	-0.0629	8.8296	0.35076	0.0:0.8877:0.0:0.1123	.	1370;1330;1369;1407;1331	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	F	1444;1408;1331;1330;1370;1369;1407;1407	ENSP00000400939:S1444F;ENSP00000367028:S1408F;ENSP00000409944:S1331F;ENSP00000325223:S1330F;ENSP00000406888:S1370F;ENSP00000390717:S1369F;ENSP00000421655:S1407F;ENSP00000427484:S1407F	ENSP00000325223:S1330F	S	+	2	0	TCOF1	149756476	0.000000	0.05858	0.245000	0.24217	0.221000	0.24807	0.364000	0.20325	2.160000	0.67779	0.561000	0.74099	TCT		0.537	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		T	149776283	C	T	149776283	3	4	61	1	0	0	0	0	1	0	0	0	15747	913	32	3	4339	3	TCOF1	5	149776283	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3333	149776283	31138977	4265	12250										
RBM22	55696	broad.mit.edu	37	chr5	150071375	150071375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtcctgagaaggatagtGgattggtcctggagcccgca	16	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150071375G>T	ENST00000199814.4	-	11	1322	c.1201C>A	c.(1201-1203)Cac>Aac	p.H401N	RBM22_ENST00000447771.2_Missense_Mutation_p.H352N|RBM22_ENST00000540000.1_Missense_Mutation_p.H352N	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	401	Pro-rich.				cellular response to drug (GO:0035690)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of RNA splicing (GO:0033120)|protein import into nucleus, translocation (GO:0000060)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|snRNA binding (GO:0017069)	p.H401N(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAGGATAGTGGATTGGTCCT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											113	109	110					5																	150071375		2203	4300	6503	150051568	SO:0001583	missense	55696			AL136933	CCDS34278.1	5q33.1	2013-02-12			ENSG00000086589	ENSG00000086589		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	25503	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 47"	612430				20013661, 19133299	Standard	NM_018047		Approved	FLJ10290, ZC3H16, fSAP47, Cwc2	uc031slu.1	Q9NW64	OTTHUMG00000163589	ENST00000199814.4:c.1201C>A	5.37:g.150071375G>T	ENSP00000199814:p.His401Asn		150051568	A6NDM5|B4DLI9|O95607	Missense_Mutation	SNP	ENST00000199814.4	37	CCDS34278.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.019446	0.75275	.	.	ENSG00000086589	ENST00000199814;ENST00000540000;ENST00000447771	.	.	.	5.68	4.82	0.62117	.	0.044666	0.85682	D	0.000000	T	0.72914	0.3520	L	0.57536	1.79	0.58432	D	0.999998	P	0.39094	0.659	P	0.55391	0.775	T	0.71961	-0.4434	9	0.40728	T	0.16	-32.1025	14.6137	0.68534	0.0698:0.0:0.9302:0.0	.	401	Q9NW64	RBM22_HUMAN	N	401;352;352	.	ENSP00000199814:H401N	H	-	1	0	RBM22	150051568	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.476000	0.97823	1.431000	0.47355	-0.136000	0.14681	CAC		0.552	RBM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374431.2	NM_018047		T	150071375	G	T	150071375	3	4	61	1	0	0	0	0	1	0	0	0	13159	1348	47	2	65	2	RBM22	5	150071375	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	295092	150071375	30843885	4266	12251										
ANXA6	309	broad.mit.edu	37	chr5	150484829	150484829	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggatttgtaaagtttgtCggcaaagaagagaggcttgt	13	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150484829C>T	ENST00000354546.5	-	24	2043	c.1816G>A	c.(1816-1818)Gac>Aac	p.D606N	ANXA6_ENST00000356496.5_Missense_Mutation_p.D600N|ANXA6_ENST00000521512.1_Missense_Mutation_p.D393N|ANXA6_ENST00000377751.5_Missense_Mutation_p.D263N|ANXA6_ENST00000523714.1_Missense_Mutation_p.D574N	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	606					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)	p.D606N(1)		endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TAAAGTTTGTCGGCAAAGAAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	5											166	157	160					5																	150484829		1958	4158	6116	150465022	SO:0001583	missense	309			J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"Annexins"	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.1816G>A	5.37:g.150484829C>T	ENSP00000346550:p.Asp606Asn		150465022	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Missense_Mutation	SNP	ENST00000354546.5	37	CCDS47315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.9|28.9	4.962457|4.962457	0.92791|0.92791	.|.	.|.	ENSG00000197043|ENSG00000197043	ENST00000354546;ENST00000523714;ENST00000377751;ENST00000356496;ENST00000521512;ENST00000540153|ENST00000522664	T;T;T;T;T|.	0.03330|.	3.97;3.97;3.97;3.97;3.97|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.056107|.	0.64402|.	D|.	0.000002|.	T|T	0.51176|0.51176	0.1659|0.1659	N|N	0.20445|0.20445	0.575|0.575	0.80722|0.80722	D|D	1|1	D;D;D|.	0.71674|.	0.997;0.998;0.997|.	D;P;D|.	0.64877|.	0.921;0.899;0.93|.	T|T	0.47209|0.47209	-0.9135|-0.9135	10|5	0.87932|.	D|.	0|.	.|.	15.9723|15.9723	0.80031|0.80031	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	393;600;606|.	E5RK69;A6NN80;P08133|.	.;.;ANXA6_HUMAN|.	N|Q	606;574;263;600;393;480|2	ENSP00000346550:D606N;ENSP00000430517:D574N;ENSP00000366980:D263N;ENSP00000348889:D600N;ENSP00000430420:D393N|.	ENSP00000346550:D606N|.	D|R	-|-	1|2	0|0	ANXA6|ANXA6	150465022|150465022	0.994000|0.994000	0.37717|0.37717	0.964000|0.964000	0.40570|0.40570	0.954000|0.954000	0.61252|0.61252	3.235000|3.235000	0.51328|0.51328	2.371000|2.371000	0.80710|0.80710	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.478	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155		T	150484829	C	T	150484829	3	4	61	1	0	0	0	0	1	0	0	0	722	884	31	1	217	1	ANXA6	5	150484829	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	413454	150484829	30430431	4267	12252										
CCDC69	26112	broad.mit.edu	37	chr5	150578618	150578618	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctcatccagtctgtctcGaagctctagctccctttcct	6	16	4	0	rs114476897		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150578618G>A	ENST00000355417.2	-	4	433	c.259C>T	c.(259-261)Cga>Tga	p.R87*	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	87								p.R87*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGTCTGTCTCGAAGCTCTAGC	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	5						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	232	203	213		259	3.1	0.1	5	dbSNP_132	213	0,8600		0,0,4300	no	stop-gained	CCDC69	NM_015621.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		87/297	150578618	1,13005	2203	4300	6503	150558811	SO:0001587	stop_gained	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.259C>T	5.37:g.150578618G>A	ENSP00000347586:p.Arg87*		150558811	A8K9X6	Nonsense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.419406	0.62622	2.27E-4	0.0	ENSG00000198624	ENST00000355417	.	.	.	4.94	3.1	0.35709	.	1.691730	0.03180	N	0.171883	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	0.7704	6.9132	0.24346	0.0976:0.188:0.7143:0.0	.	.	.	.	X	87	.	ENSP00000347586:R87X	R	-	1	2	CCDC69	150558811	0.110000	0.22057	0.072000	0.20136	0.360000	0.29518	0.644000	0.24766	1.282000	0.44496	0.491000	0.48974	CGA		0.572	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		A	150578618	G	A	150578618	4	1	61	1	0	0	0	0	0	1	0	0	2847	1066	37	1	655	1	CCDC69	5	150578618	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93789	150578618	30336642	4268	12253										
FAT2	2196	broad.mit.edu	37	chr5	150885420	150885420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactagggggccgagagggCatcagatcttccaggttctg	16	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150885420C>T	ENST00000261800.5	-	23	12768	c.12756G>A	c.(12754-12756)atG>atA	p.M4252I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4252					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.M4252I(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCGAGAGGGCATCAGATCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	103	98					5																	150885420		2203	4300	6503	150865613	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12756G>A	5.37:g.150885420C>T	ENSP00000261800:p.Met4252Ile		150865613	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.02|12.02	1.811959|1.811959	0.32053|0.32053	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.69435	.|-0.4	5.02|5.02	3.2|3.2	0.36748|0.36748	.|.	.|0.643258	.|0.15207	.|N	.|0.274695	T|T	0.32941|0.32941	0.0846|0.0846	N|N	0.00926|0.00926	-1.1|-1.1	0.28450|0.28450	N|N	0.916365|0.916365	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.22941|0.22941	-1.0202|-1.0202	5|10	.|0.25751	.|T	.|0.34	.|.	7.4501|7.4501	0.27234|0.27234	0.0:0.587:0.266:0.147|0.0:0.587:0.266:0.147	.|.	.|4252;1357	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	T|I	1025|4252	.|ENSP00000261800:M4252I	.|ENSP00000261800:M4252I	A|M	-|-	1|3	0|0	FAT2|FAT2	150865613|150865613	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.956000|0.956000	0.61745|0.61745	1.351000|1.351000	0.34022|0.34022	0.488000|0.488000	0.27723|0.27723	0.561000|0.561000	0.74099|0.74099	GCC|ATG		0.622	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150885420	C	T	150885420	3	4	61	1	0	0	0	0	1	0	0	0	5709	710	25	3	297	3	FAT2	5	150885420	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	306802	150885420	30029840	4269	12254										
FAT2	2196	broad.mit.edu	37	chr5	150911476	150911476	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccccgtggtggcgtcgatGgaaaagtggccttcggctga	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150911476G>T	ENST00000261800.5	-	13	9495	c.9483C>A	c.(9481-9483)tcC>tcA	p.S3161S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3161	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S3161S(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGCGTCGATGGAAAAGTGGC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	5											57	62	60					5																	150911476		2202	4298	6500	150891669	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9483C>A	5.37:g.150911476G>T			150891669	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	9.498	1.102503	0.20632	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.25	4.38	0.52667	.	.	.	.	.	T	0.58524	0.2128	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55903	-0.8067	4	.	.	.	.	8.1055	0.30883	0.0778:0.0:0.6616:0.2606	.	.	.	.	N	20	.	.	H	-	1	0	FAT2	150891669	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	0.865000	0.27940	1.222000	0.43521	0.557000	0.71058	CAT		0.652	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150911476	G	T	150911476	2	4	61	1	0	0	0	0	0	0	0	1	5709	1335	47	2		2	FAT2	5	150911476	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26056	150911476	30003784	4270	12255										
FAT2	2196	broad.mit.edu	37	chr5	150921996	150921996	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagcattgtcattctcatCtgtaatggagacctgaacca	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150921996C>A	ENST00000261800.5	-	9	8704	c.8692G>T	c.(8692-8694)Gat>Tat	p.D2898Y		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2898	Cadherin 25. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D2898Y(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCATTCTCATCTGTAATGGAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											193	185	188					5																	150921996		2203	4300	6503	150902189	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.8692G>T	5.37:g.150921996C>A	ENSP00000261800:p.Asp2898Tyr		150902189	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909246	0.72868	.	.	ENSG00000086570	ENST00000261800	T	0.69175	-0.38	6.05	6.05	0.98169	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.64402	D	0.000004	D	0.90638	0.7064	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93686	0.7003	10	0.87932	D	0	.	20.6013	0.99457	0.0:1.0:0.0:0.0	.	2898	Q9NYQ8	FAT2_HUMAN	Y	2898	ENSP00000261800:D2898Y	ENSP00000261800:D2898Y	D	-	1	0	FAT2	150902189	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.755000	0.85180	2.878000	0.98634	0.650000	0.86243	GAT		0.512	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150921996	C	A	150921996	3	1	61	1	0	0	0	0	1	0	0	0	5709	913	32	2	4417	2	FAT2	5	150921996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10520	150921996	29993264	4271	12256										
FAT2	2196	broad.mit.edu	37	chr5	150923293	150923293	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtgttgatgtacacaggCacagttgctcggaagactcc	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150923293C>A	ENST00000261800.5	-	9	7407	c.7395G>T	c.(7393-7395)gtG>gtT	p.V2465V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2465	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2465V(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTACACAGGCACAGTTGCTC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	5											88	85	86					5																	150923293		2203	4300	6503	150903486	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7395G>T	5.37:g.150923293C>A			150903486	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.448	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150923293	C	A	150923293	2	1	61	1	0	0	0	0	0	0	0	1	5709	697	25	2		2	FAT2	5	150923293	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1297	150923293	29991967	4272	12257										
FAT2	2196	broad.mit.edu	37	chr5	150923407	150923407	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgatgagctgttaatgaaGaagtgcctgtcctgattgcc	11	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150923407G>T	ENST00000261800.5	-	9	7293	c.7281C>A	c.(7279-7281)ttC>ttA	p.F2427L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2427	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F2427L(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTTAATGAAGAAGTGCCTGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	5											54	51	52					5																	150923407		2203	4300	6503	150903600	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7281C>A	5.37:g.150923407G>T	ENSP00000261800:p.Phe2427Leu		150903600	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059736	0.55325	.	.	ENSG00000086570	ENST00000261800	T	0.70749	-0.51	5.58	3.43	0.39272	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000001	D	0.85952	0.5817	M	0.93016	3.37	0.49798	D	0.999827	D	0.76494	0.999	D	0.85130	0.997	D	0.87891	0.2684	10	0.62326	D	0.03	.	11.1948	0.48707	0.274:0.0:0.726:0.0	.	2427	Q9NYQ8	FAT2_HUMAN	L	2427	ENSP00000261800:F2427L	ENSP00000261800:F2427L	F	-	3	2	FAT2	150903600	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.341000	0.52151	1.322000	0.45245	0.561000	0.74099	TTC		0.468	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150923407	G	T	150923407	3	4	61	1	0	0	0	0	1	0	0	0	5709	933	33	2	5828	2	FAT2	5	150923407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114	150923407	29991853	4273	12258										
FAT2	2196	broad.mit.edu	37	chr5	150923556	150923556	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattgaggttgtctgaactCtggggggttgtcattgatat	13	4	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150923556C>A	ENST00000261800.5	-	9	7144	c.7132G>T	c.(7132-7134)Gag>Tag	p.E2378*		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2378	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E2378*(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTCTGAACTCTGGGGGGTTG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											79	76	77					5																	150923556		2203	4300	6503	150903749	SO:0001587	stop_gained	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7132G>T	5.37:g.150923556C>A	ENSP00000261800:p.Glu2378*		150903749	O75091|Q9NSR7	Nonsense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	47	13.395765	0.99739	.	.	ENSG00000086570	ENST00000261800	.	.	.	5.58	4.71	0.59529	.	0.198177	0.35495	N	0.003164	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	11.9164	0.52767	0.0:0.8578:0.0:0.1422	.	.	.	.	X	2378	.	ENSP00000261800:E2378X	E	-	1	0	FAT2	150903749	0.978000	0.34361	0.997000	0.53966	0.802000	0.45316	2.615000	0.46368	1.325000	0.45301	0.561000	0.74099	GAG		0.483	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150923556	C	A	150923556	4	1	61	1	0	0	0	0	0	1	0	0	5709	922	32	2	5977	2	FAT2	5	150923556	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149	150923556	29991704	4274	12259										
FAT2	2196	broad.mit.edu	37	chr5	150924390	150924390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaacagccccatttgtccCcaagtcctcatcagtggcag	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150924390C>T	ENST00000261800.5	-	9	6310	c.6298G>A	c.(6298-6300)Ggg>Agg	p.G2100R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2100	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G2100R(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCATTTGTCCCCAAGTCCTCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											122	127	125					5																	150924390		2203	4300	6503	150904583	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.6298G>A	5.37:g.150924390C>T	ENSP00000261800:p.Gly2100Arg		150904583	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351135	0.82132	.	.	ENSG00000086570	ENST00000261800	T	0.66280	-0.2	5.63	5.63	0.86233	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000004	D	0.84763	0.5544	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87793	0.2620	10	0.72032	D	0.01	.	19.6811	0.95964	0.0:1.0:0.0:0.0	.	2100	Q9NYQ8	FAT2_HUMAN	R	2100	ENSP00000261800:G2100R	ENSP00000261800:G2100R	G	-	1	0	FAT2	150904583	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.747000	0.85070	2.658000	0.90341	0.561000	0.74099	GGG		0.443	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150924390	C	T	150924390	3	4	61	1	0	0	0	0	1	0	0	0	5709	623	22	3	6811	3	FAT2	5	150924390	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	834	150924390	29990870	4275	12260										
FAT2	2196	broad.mit.edu	37	chr5	150934142	150934142	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattgaagagcttgtgggaGaatataggtggattgtcatt	13	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150934142G>T	ENST00000261800.5	-	4	3738	c.3726C>A	c.(3724-3726)ttC>ttA	p.F1242L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1242	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F1242L(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTTGTGGGAGAATATAGGTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											166	143	151					5																	150934142		2203	4300	6503	150914335	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3726C>A	5.37:g.150934142G>T	ENSP00000261800:p.Phe1242Leu		150914335	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.308248	0.40895	.	.	ENSG00000086570	ENST00000261800	T	0.78707	-1.2	5.46	2.72	0.32119	Cadherin (2);Cadherin-like (1);	0.000000	0.64402	D	0.000005	T	0.77837	0.4190	M	0.87269	2.87	0.51767	D	0.999939	P	0.38617	0.64	B	0.37015	0.239	T	0.75858	-0.3169	10	0.59425	D	0.04	.	8.995	0.36048	0.3577:0.0:0.6423:0.0	.	1242	Q9NYQ8	FAT2_HUMAN	L	1242	ENSP00000261800:F1242L	ENSP00000261800:F1242L	F	-	3	2	FAT2	150914335	1.000000	0.71417	0.991000	0.47740	0.423000	0.31445	2.570000	0.45981	0.365000	0.24400	0.655000	0.94253	TTC		0.567	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150934142	G	T	150934142	3	4	61	1	0	0	0	0	1	0	0	0	5709	933	33	2	9403	2	FAT2	5	150934142	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9752	150934142	29981118	4276	12261										
FAT2	2196	broad.mit.edu	37	chr5	150945681	150945681	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagacagtcccggggggcaGgtcctctggaaccttcagcc	13	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150945681G>T	ENST00000261800.5	-	1	2824	c.2812C>A	c.(2812-2814)Ctg>Atg	p.L938M		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	938	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L938M(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCGGGGGGCAGGTCCTCTGGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											55	50	52					5																	150945681		2203	4300	6503	150925874	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2812C>A	5.37:g.150945681G>T	ENSP00000261800:p.Leu938Met		150925874	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	10.91	1.483895	0.26598	.	.	ENSG00000086570	ENST00000261800	T	0.52754	0.65	5.51	-1.13	0.09775	Cadherin (3);Cadherin-like (1);	0.398345	0.21508	N	0.073407	T	0.36608	0.0973	L	0.47078	1.49	0.28931	N	0.891562	B	0.21606	0.058	B	0.35688	0.208	T	0.28681	-1.0036	10	0.34782	T	0.22	.	2.7304	0.05225	0.2636:0.1083:0.5111:0.117	.	938	Q9NYQ8	FAT2_HUMAN	M	938	ENSP00000261800:L938M	ENSP00000261800:L938M	L	-	1	2	FAT2	150925874	0.915000	0.31059	0.984000	0.44739	0.945000	0.59286	0.067000	0.14510	0.020000	0.15106	0.561000	0.74099	CTG		0.552	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150945681	G	T	150945681	3	4	61	1	0	0	0	0	1	0	0	0	5709	991	35	2	10329	2	FAT2	5	150945681	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11539	150945681	29969579	4277	12262										
FAT2	2196	broad.mit.edu	37	chr5	150947935	150947935	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctctgaccttgtgttaaaGgcataatagaactcagcatt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150947935G>T	ENST00000261800.5	-	1	570	c.558C>A	c.(556-558)gcC>gcA	p.A186A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	186	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A186A(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTGTGTTAAAGGCATAATAGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	5											126	115	119					5																	150947935		2203	4300	6503	150928128	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.558C>A	5.37:g.150947935G>T			150928128	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.532	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150947935	G	T	150947935	2	4	61	1	0	0	0	0	0	0	0	1	5709	987	35	2		2	FAT2	5	150947935	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2254	150947935	29967325	4278	12263										
FAT2	2196	broad.mit.edu	37	chr5	150948381	150948381	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatagatggtggcattgtAatgggagtgtgtgaagtgcc	15	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:150948381A>G	ENST00000261800.5	-	1	124	c.112T>C	c.(112-114)Tac>Cac	p.Y38H		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	38	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y38H(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGGCATTGTAATGGGAGTGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											108	110	109					5																	150948381		2203	4300	6503	150928574	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.112T>C	5.37:g.150948381A>G	ENSP00000261800:p.Tyr38His		150928574	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102904	0.76983	.	.	ENSG00000086570	ENST00000261800	T	0.66638	-0.22	5.36	5.36	0.76844	Cadherin (2);Cadherin-like (1);	0.000000	0.64402	D	0.000014	D	0.86948	0.6056	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90631	0.4567	10	0.62326	D	0.03	.	15.3536	0.74409	1.0:0.0:0.0:0.0	.	38	Q9NYQ8	FAT2_HUMAN	H	38	ENSP00000261800:Y38H	ENSP00000261800:Y38H	Y	-	1	0	FAT2	150928574	1.000000	0.71417	0.871000	0.34182	0.982000	0.71751	9.262000	0.95591	2.023000	0.59567	0.459000	0.35465	TAC		0.507	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150948381	A	G	150948381	3	3	61	1	0	0	0	0	1	0	0	0	5709	362	13	4	13029	4	FAT2	5	150948381	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	446	150948381	29966879	4279	12264										
SPARC	6678	broad.mit.edu	37	chr5	151051214	151051214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgttgttctcatccagctCgcacaccttgccgtgtttgc	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:151051214C>T	ENST00000231061.4	-	5	563	c.250G>A	c.(250-252)Gag>Aag	p.E84K		NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	84	Follistatin-like.				blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)	p.E84K(1)		central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		TCATCCAGCTCGCACACCTTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	5											177	136	150					5																	151051214		2203	4300	6503	151031407	SO:0001583	missense	6678				CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"cysteine-rich protein", "osteonectin"	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.250G>A	5.37:g.151051214C>T	ENSP00000231061:p.Glu84Lys		151031407	D3DQH9|Q6IBK4	Missense_Mutation	SNP	ENST00000231061.4	37	CCDS4318.1	.	.	.	.	.	.	.	.	.	.	C	33	5.287798	0.95517	.	.	ENSG00000113140	ENST00000231061;ENST00000539687	T;T	0.48201	0.82;0.82	5.39	5.39	0.77823	Follistatin-like, N-terminal (1);Osteonectin-like, conserved site (1);Follistatin/Osteonectin EGF domain (1);	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	L	0.48174	1.505	0.80722	D	1	D	0.57257	0.979	P	0.57425	0.82	T	0.45833	-0.9234	10	0.06891	T	0.86	-29.0986	19.1452	0.93463	0.0:1.0:0.0:0.0	.	84	P09486	SPRC_HUMAN	K	84	ENSP00000231061:E84K;ENSP00000444998:E84K	ENSP00000231061:E84K	E	-	1	0	SPARC	151031407	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.276000	0.78559	2.517000	0.84864	0.561000	0.74099	GAG		0.592	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118		T	151051214	C	T	151051214	3	4	61	1	0	0	0	0	1	0	0	0	15034	893	31	1	685	1	SPARC	5	151051214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102833	151051214	29864046	4280	12265										
G3BP1	10146	broad.mit.edu	37	chr5	151179526	151179526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaagagtgcgagaacaacGaataaatattcctccccaaa	6	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:151179526G>A	ENST00000394123.3	+	9	1065	c.920G>A	c.(919-921)cGa>cAa	p.R307Q	G3BP1_ENST00000543466.1_Missense_Mutation_p.R125Q|G3BP1_ENST00000356245.3_Missense_Mutation_p.R307Q			Q13283	G3BP1_HUMAN	GTPase activating protein (SH3 domain) binding protein 1	307					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Ras protein signal transduction (GO:0007265)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.R307Q(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|skin(3)|urinary_tract(2)	29		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			CGAGAACAACGAATAAATATT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5											38	40	39					5																	151179526		2203	4300	6503	151159719	SO:0001583	missense	10146			BC006997	CCDS4319.1	5q33.1	2013-02-12	2006-11-01		ENSG00000145907	ENSG00000145907		"RNA binding motif (RRM) containing"	30292	protein-coding gene	gene with protein product	"Ras-GTPase-activating protein SH3-domain-binding protein"	608431				8649363, 9889278	Standard	NM_005754		Approved	HDH-VIII, G3BP	uc003lum.3	Q13283	OTTHUMG00000130123	ENST00000394123.3:c.920G>A	5.37:g.151179526G>A	ENSP00000377681:p.Arg307Gln		151159719	Q5HYE9	Missense_Mutation	SNP	ENST00000394123.3	37	CCDS4319.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390704	0.62066	.	.	ENSG00000145907	ENST00000394123;ENST00000543466;ENST00000356245;ENST00000274596	T;T;T	0.73681	-0.66;-0.77;-0.66	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.70727	0.3257	M	0.80183	2.485	0.58432	D	0.999999	P	0.37997	0.614	B	0.24394	0.053	T	0.72424	-0.4298	10	0.13108	T	0.6	-18.7807	18.4052	0.90533	0.0:0.0:1.0:0.0	.	307	Q13283	G3BP1_HUMAN	Q	307;125;307;149	ENSP00000377681:R307Q;ENSP00000445035:R125Q;ENSP00000348578:R307Q	ENSP00000274596:R149Q	R	+	2	0	G3BP1	151159719	1.000000	0.71417	0.978000	0.43139	0.965000	0.64279	6.851000	0.75425	2.415000	0.81967	0.650000	0.86243	CGA		0.463	G3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252431.1	NM_005754		A	151179526	G	A	151179526	3	1	61	1	0	0	0	0	1	0	0	0	6160	1058	37	1	950	1	G3BP1	5	151179526	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128312	151179526	29735734	4281	12266										
NMUR2	56923	broad.mit.edu	37	chr5	151784024	151784024	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataggaaggaggtgacctgGatgatgaaattgtagatcca	13	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:151784024G>T	ENST00000255262.3	-	1	816	c.651C>A	c.(649-651)atC>atA	p.I217I	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	217					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.I217I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AGGTGACCTGGATGATGAAAT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	5											170	159	162					5																	151784024		2203	4300	6503	151764217	SO:0001819	synonymous_variant	56923			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.651C>A	5.37:g.151784024G>T			151764217	Q7LC54|Q96AM5|Q9NRA6	Silent	SNP	ENST00000255262.3	37	CCDS4321.1																																																																																				0.532	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151784024	G	T	151784024	2	4	61	1	0	0	0	0	0	0	0	1	10538	1164	41	2		2	NMUR2	5	151784024	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	604498	151784024	29131236	4282	12267										
FAM114A2	10827	broad.mit.edu	37	chr5	153414408	153414408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttactctctggtttggcacCttggtcaacagactcagaat	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:153414408C>A	ENST00000351797.4	-	2	182	c.106G>T	c.(106-108)Ggt>Tgt	p.G36C	FAM114A2_ENST00000520313.1_Splice_Site_p.G36C|FAM114A2_ENST00000522858.1_Missense_Mutation_p.G36C|FAM114A2_ENST00000520667.1_Missense_Mutation_p.G36C	NM_018691.2	NP_061161.2	Q9NRY5	F1142_HUMAN	family with sequence similarity 114, member A2	36							purine nucleotide binding (GO:0017076)	p.G36C(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)|urinary_tract(1)	18						GGTTTGGCACCTTGGTCAACA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											175	178	177					5																	153414408		2203	4300	6503	153394601	SO:0001583	missense	10827			AF159700	CCDS4323.1	5q31-q33	2008-06-13	2008-06-13	2008-06-13	ENSG00000055147	ENSG00000055147			1333	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 3"	C5orf3		10843801	Standard	XM_005268359		Approved	133K02	uc003lvc.3	Q9NRY5	OTTHUMG00000130147	ENST00000351797.4:c.106G>T	5.37:g.153414408C>A	ENSP00000341597:p.Gly36Cys		153394601	B2R8D8|Q9H7E0	Missense_Mutation	SNP	ENST00000351797.4	37	CCDS4323.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.006441	0.35415	.	.	ENSG00000055147	ENST00000351797;ENST00000522858;ENST00000520667;ENST00000433795;ENST00000520313;ENST00000522395;ENST00000523705;ENST00000519808;ENST00000518102;ENST00000522634;ENST00000517605	T;T;T;T;T;T;T	0.44083	2.53;2.53;2.53;1.0;1.53;1.52;0.93	5.79	-0.643	0.11482	.	0.440036	0.22011	N	0.065871	T	0.35998	0.0951	N	0.08118	0	0.21064	N	0.999799	D;B	0.89917	1.0;0.412	D;B	0.97110	1.0;0.161	T	0.21724	-1.0237	10	0.56958	D	0.05	-0.0029	6.5511	0.22433	0.0:0.35:0.1268:0.5232	.	36;36	E7ESJ7;Q9NRY5	.;F1142_HUMAN	C	36	ENSP00000341597:G36C;ENSP00000430489:G36C;ENSP00000430384:G36C;ENSP00000429088:G36C;ENSP00000430186:G36C;ENSP00000428827:G36C;ENSP00000429753:G36C	ENSP00000341597:G36C	G	-	1	0	FAM114A2	153394601	0.001000	0.12720	0.013000	0.15412	0.974000	0.67602	0.743000	0.26231	-0.099000	0.12263	-0.312000	0.09012	GGT;GGT;GGT;GGT;GGC;GGT;GGT;GGT;GGT;GGT;GGT		0.453	FAM114A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252455.1	NM_018691		A	153414408	C	A	153414408	3	1	61	1	0	0	0	0	1	0	0	0	5420	681	24	2	1463	2	FAM114A2	5	153414408	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1630384	153414408	27500852	4283	12268										
LARP1	23367	broad.mit.edu	37	chr5	154172313	154172313	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaatcaggggaggaaaaGaatggagatgaggattgcca	16	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154172313G>A	ENST00000336314.4	+	4	489	c.465G>A	c.(463-465)aaG>aaA	p.K155K		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	232					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.K232K(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGGAGGAAAAGAATGGAGATG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	5											138	136	136					5																	154172313		2203	4300	6503	154152506	SO:0001819	synonymous_variant	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.465G>A	5.37:g.154172313G>A			154152506	O94836|Q8N4M2|Q8NB73|Q9UFD7	Silent	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	G	9.718	1.158952	0.21454	.	.	ENSG00000155506	ENST00000517616	.	.	.	5.93	5.06	0.68205	.	.	.	.	.	T	0.63803	0.2542	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62525	-0.6836	4	.	.	.	-22.7624	11.8789	0.52562	0.1393:0.0:0.8607:0.0	.	.	.	.	K	135	.	.	E	+	1	0	LARP1	154152506	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.133000	0.42093	1.497000	0.48584	0.655000	0.94253	GAA		0.498	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		A	154172313	G	A	154172313	2	1	61	1	0	0	0	0	0	0	0	1	8650	933	33	3		3	LARP1	5	154172313	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	757905	154172313	26742947	4284	12269										
LARP1	23367	broad.mit.edu	37	chr5	154173443	154173443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccggagcctgcctggcacGaccaggatgagacatcgagt	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154173443G>A	ENST00000336314.4	+	6	745	c.721G>A	c.(721-723)Gac>Aac	p.D241N		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	318					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.D318N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGCCTGGCACGACCAGGATGA	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	5											65	78	73					5																	154173443		2203	4300	6503	154153636	SO:0001583	missense	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.721G>A	5.37:g.154173443G>A	ENSP00000336721:p.Asp241Asn		154153636	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.321193|5.321193	0.95682|0.95682	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000336314;ENST00000518297;ENST00000524248|ENST00000518194	T;T;T|.	0.35973|.	1.73;1.28;1.29|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67562|0.67562	0.2906|0.2906	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.996;1.0|.	P;D|.	0.77004|.	0.715;0.989|.	T|T	0.61676|0.61676	-0.7014|-0.7014	10|5	0.23302|.	T|.	0.38|.	-24.3644|-24.3644	19.843|19.843	0.96697|0.96697	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	318;241|.	Q6PKG0;Q6PKG0-3|.	LARP1_HUMAN;.|.	N|Q	241;318;113|79	ENSP00000336721:D241N;ENSP00000428589:D318N;ENSP00000429904:D113N|.	ENSP00000336721:D241N|.	D|R	+|+	1|2	0|0	LARP1|LARP1	154153636|154153636	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.670000|9.670000	0.98625|0.98625	2.679000|2.679000	0.91253|0.91253	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.692	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		A	154173443	G	A	154173443	3	1	61	1	0	0	0	0	1	0	0	0	8650	1058	37	1	743	1	LARP1	5	154173443	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1130	154173443	26741817	4285	12270										
LARP1	23367	broad.mit.edu	37	chr5	154179551	154179551	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctgacctggattctgaGaactggattgaagtgaagaa	12	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154179551G>T	ENST00000336314.4	+	10	1458	c.1434G>T	c.(1432-1434)gaG>gaT	p.E478D		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	555	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.E555D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGGATTCTGAGAACTGGATTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											64	60	61					5																	154179551		2203	4300	6503	154159744	SO:0001583	missense	23367			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1434G>T	5.37:g.154179551G>T	ENSP00000336721:p.Glu478Asp		154159744	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107363	0.37145	.	.	ENSG00000155506	ENST00000336314;ENST00000518297;ENST00000524248;ENST00000523163;ENST00000518742	T;T;T;T;T	0.47177	1.83;1.37;1.41;0.87;0.85	5.96	0.822	0.18806	.	0.089357	0.85682	N	0.000000	T	0.31167	0.0788	L	0.44542	1.39	0.44611	D	0.997584	B;B	0.16603	0.014;0.018	B;B	0.19946	0.012;0.027	T	0.06899	-1.0801	10	0.30854	T	0.27	-25.6312	2.0054	0.03476	0.3466:0.1173:0.4156:0.1205	.	555;478	Q6PKG0;Q6PKG0-3	LARP1_HUMAN;.	D	478;555;350;263;153	ENSP00000336721:E478D;ENSP00000428589:E555D;ENSP00000429904:E350D;ENSP00000430438:E263D;ENSP00000431072:E153D	ENSP00000336721:E478D	E	+	3	2	LARP1	154159744	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	0.606000	0.24194	0.102000	0.17638	0.655000	0.94253	GAG		0.582	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		T	154179551	G	T	154179551	3	4	61	1	0	0	0	0	1	0	0	0	8650	933	33	2	1472	2	LARP1	5	154179551	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6108	154179551	26735709	4286	12271										
C5orf4	10826	broad.mit.edu	37	chr5	154210386	154210386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcttgccgacctgaattCggtagcgagagatgaagtta	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154210386C>T	ENST00000326080.5	-	5	764	c.341G>A	c.(340-342)cGa>cAa	p.R114Q	FAXDC2_ENST00000518651.1_Missense_Mutation_p.R91Q|FAXDC2_ENST00000523997.1_5'UTR|FAXDC2_ENST00000517938.1_Missense_Mutation_p.R91Q|MIR378H_ENST00000579966.1_RNA|FAXDC2_ENST00000520968.1_Intron	NM_032385.3	NP_115761.2	Q96IV6	FXDC2_HUMAN	fatty acid hydroxylase domain containing 2	114					fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)	p.R114Q(2)									GACCTGAATTCGGTAGCGAGA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	5											117	114	115					5																	154210386		1963	4152	6115	154190579	SO:0001583	missense	10826			AF159165	CCDS43390.1	5q31-q32	2013-03-04	2013-03-04	2013-03-04	ENSG00000170271	ENSG00000170271		"Fatty acid hydroxylase domain containing"	1334	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 4"	C5orf4		10843801	Standard	NM_032385		Approved	FLJ13758	uc003lvs.4	Q96IV6	OTTHUMG00000164141	ENST00000326080.5:c.341G>A	5.37:g.154210386C>T	ENSP00000320604:p.Arg114Gln		154190579	B4DIE1|Q9BSX6|Q9H8C7	Missense_Mutation	SNP	ENST00000326080.5	37	CCDS43390.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770349	0.90108	.	.	ENSG00000170271	ENST00000326080;ENST00000517938;ENST00000519501;ENST00000518651	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.54240	0.1846	M	0.80028	2.48	0.80722	D	1	P	0.38922	0.651	B	0.28232	0.087	T	0.65455	-0.6164	10	0.66056	D	0.02	.	18.2391	0.89960	0.0:1.0:0.0:0.0	.	114	Q96IV6	CE004_HUMAN	Q	114;91;91;91	ENSP00000320604:R114Q;ENSP00000430286:R91Q;ENSP00000429837:R91Q;ENSP00000429876:R91Q	ENSP00000320604:R114Q	R	-	2	0	C5orf4	154190579	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.048000	0.76606	2.405000	0.81733	0.655000	0.94253	CGA		0.468	FAXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377429.1	NM_032385		T	154210386	C	T	154210386	3	4	61	1	0	0	0	0	1	0	0	0	2304	884	31	1	680	1	C5orf4	5	154210386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30835	154210386	26704874	4287	12272										
GEMIN5	25929	broad.mit.edu	37	chr5	154287187	154287187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagggtaattccggctcccGtgcttgctcctccccttctt	8	16	1	0	rs200476714		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154287187G>A	ENST00000285873.7	-	16	2434	c.2359C>T	c.(2359-2361)Cgg>Tgg	p.R787W		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	787					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)	p.R787W(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCGGCTCCCGTGCTTGCTCC	0.498													G|||	1	0.000199681	0	0	5008	,	,		17400	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											152	132	138					5																	154287187		2203	4300	6503	154267380	SO:0001583	missense	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2359C>T	5.37:g.154287187G>A	ENSP00000285873:p.Arg787Trp		154267380	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.94	1.491680	0.26774	.	.	ENSG00000082516	ENST00000285873	T	0.70631	-0.5	5.33	3.37	0.38596	.	1.655010	0.02727	N	0.114597	T	0.66761	0.2822	L	0.36672	1.1	0.09310	N	1	D;D	0.56968	0.978;0.978	B;B	0.40410	0.328;0.328	T	0.63341	-0.6659	10	0.72032	D	0.01	-1.6832	14.1953	0.65667	0.0:0.2846:0.7154:0.0	.	786;787	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	W	787	ENSP00000285873:R787W	ENSP00000285873:R787W	R	-	1	2	GEMIN5	154267380	0.111000	0.22076	0.213000	0.23690	0.099000	0.18886	3.127000	0.50484	1.332000	0.45431	0.563000	0.77884	CGG		0.498	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			A	154287187	G	A	154287187	3	1	61	1	0	0	0	0	1	0	0	0	6351	1144	40	1	2219	1	GEMIN5	5	154287187	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76801	154287187	26628073	4288	12273										
GEMIN5	25929	broad.mit.edu	37	chr5	154307007	154307007	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtttgtaaaggacataAattaaacacaattcttgaat	5	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154307007A>C	ENST00000285873.7	-	7	1093	c.1018T>G	c.(1018-1020)Tta>Gta	p.L340V		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	340					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)	p.L340V(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAAGGACATAAATTAAACACA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	117	120					5																	154307007		2203	4300	6503	154287200	SO:0001583	missense	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.1018T>G	5.37:g.154307007A>C	ENSP00000285873:p.Leu340Val		154287200	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.945364	0.53079	.	.	ENSG00000082516	ENST00000285873	T	0.04862	3.54	5.67	3.23	0.37069	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.070774	0.56097	D	0.000031	T	0.09024	0.0223	N	0.14661	0.345	0.37160	D	0.902557	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.44298	-0.9337	10	0.18710	T	0.47	-8.7338	8.3391	0.32232	0.6902:0.0:0.3098:0.0	.	339;340	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	V	340	ENSP00000285873:L340V	ENSP00000285873:L340V	L	-	1	2	GEMIN5	154287200	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.676000	0.37565	0.405000	0.25532	0.482000	0.46254	TTA		0.383	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			C	154307007	A	C	154307007	3	2	61	1	0	0	0	0	1	0	0	0	6351	11	1	4	3596	4	GEMIN5	5	154307007	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	19820	154307007	26608253	4289	12274										
KIF4B	285643	broad.mit.edu	37	chr5	154394811	154394811	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaattgaaagaaaatgtagaGataatttgtaacctgcagca	9	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154394811G>T	ENST00000435029.4	+	1	1552	c.1392G>T	c.(1390-1392)gaG>gaT	p.E464D		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	464					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.E464D(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAAATGTAGAGATAATTTGTA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	5											84	90	88					5																	154394811		2203	4300	6503	154375004	SO:0001583	missense	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.1392G>T	5.37:g.154394811G>T	ENSP00000387875:p.Glu464Asp		154375004		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	g	12.77	2.037274	0.35893	.	.	ENSG00000226650	ENST00000435029	T	0.70986	-0.53	1.46	1.46	0.22682	.	.	.	.	.	T	0.64527	0.2606	M	0.65498	2.005	0.40646	D	0.981997	B	0.25441	0.126	B	0.25140	0.058	T	0.63229	-0.6684	9	0.36615	T	0.2	.	8.8518	0.35203	0.0:0.0:1.0:0.0	.	464	Q2VIQ3	KIF4B_HUMAN	D	464	ENSP00000387875:E464D	ENSP00000387875:E464D	E	+	3	2	KIF4B	154375004	1.000000	0.71417	0.824000	0.32777	0.922000	0.55478	0.458000	0.21892	1.131000	0.42111	0.455000	0.32223	GAG		0.458	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			T	154394811	G	T	154394811	3	4	61	1	0	0	0	0	1	0	0	0	8325	933	33	2	1394	2	KIF4B	5	154394811	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87804	154394811	26520449	4290	12275										
KIF4B	285643	broad.mit.edu	37	chr5	154395452	154395452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaatacagttgaaagaacGagaccgtaagaggcaatatg	11	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:154395452G>A	ENST00000435029.4	+	1	2193	c.2033G>A	c.(2032-2034)cGa>cAa	p.R678Q		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	678	Interaction with PRC1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.R678Q(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTGAAAGAACGAGACCGTAAG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	5											131	133	133					5																	154395452		2203	4300	6503	154375645	SO:0001583	missense	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2033G>A	5.37:g.154395452G>A	ENSP00000387875:p.Arg678Gln		154375645		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	g	0.331	-0.956107	0.02267	.	.	ENSG00000226650	ENST00000435029	T	0.16457	2.34	2.54	0.612	0.17591	.	.	.	.	.	T	0.07098	0.0180	N	0.10809	0.05	0.29129	N	0.879782	B	0.11235	0.004	B	0.06405	0.002	T	0.42849	-0.9427	9	0.14252	T	0.57	.	4.9797	0.14158	0.3319:0.0:0.6681:0.0	.	678	Q2VIQ3	KIF4B_HUMAN	Q	678	ENSP00000387875:R678Q	ENSP00000387875:R678Q	R	+	2	0	KIF4B	154375645	1.000000	0.71417	0.482000	0.27366	0.585000	0.36419	0.500000	0.22562	-0.169000	0.10834	-0.253000	0.11424	CGA		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			A	154395452	G	A	154395452	3	1	61	1	0	0	0	0	1	0	0	0	8325	1058	37	1	2035	1	KIF4B	5	154395452	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	641	154395452	26519808	4291	12276										
HAVCR1	26762	broad.mit.edu	37	chr5	156479611	156479611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaacagtggtgctcgttCgaacagtcgtgacggttgga	15	7	0	1	rs369837589		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156479611C>T	ENST00000339252.3	-	3	966	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	HAVCR1_ENST00000522693.1_Missense_Mutation_p.R145Q|HAVCR1_ENST00000523175.1_Missense_Mutation_p.R145Q|HAVCR1_ENST00000425854.1_Missense_Mutation_p.R145Q|HAVCR1_ENST00000544197.1_Missense_Mutation_p.R145Q	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.R145Q(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGTGCTCGTTCGAACAGTCGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG,GLN/ARG,GLN/ARG	0,4300		0,0,2150	467	465	466		434,434,434	-0.3	0	5		466	2,8496		0,2,4247	no	missense,missense,missense	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	43,43,43	0,2,6397	TT,TC,CC		0.0235,0.0,0.0156	benign,benign,benign	145/365,145/365,145/365	156479611	2,12796	2150	4249	6399	156412189	SO:0001583	missense	26762			AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.434G>A	5.37:g.156479611C>T	ENSP00000344844:p.Arg145Gln		156412189	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	CCDS43392.1	.	.	.	.	.	.	.	.	.	.	C	0.111	-1.138494	0.01742	0.0	2.35E-4	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.15139	2.45;2.51;2.51;2.45;2.51;2.45	0.158	-0.317	0.12736	.	.	.	.	.	T	0.06462	0.0166	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37641	-0.9697	9	0.13470	T	0.59	.	3.5988	0.08016	0.0:0.2671:0.4858:0.2471	.	145;145	F1CME6;Q96D42	.;HAVR1_HUMAN	Q	145	ENSP00000428524:R145Q;ENSP00000427898:R145Q;ENSP00000344844:R145Q;ENSP00000403333:R145Q;ENSP00000440258:R145Q;ENSP00000428422:R145Q	ENSP00000344844:R145Q	R	-	2	0	HAVCR1	156412189	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.159000	0.10056	-2.720000	0.00389	-2.710000	0.00134	CGA		0.463	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			T	156479611	C	T	156479611	3	4	61	1	0	0	0	0	1	0	0	0	6994	884	31	1	684	1	HAVCR1	5	156479611	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2084159	156479611	24435649	4292	12277										
MED7	9443	broad.mit.edu	37	chr5	156566122	156566122	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttaagatcttctagtttCtcttctcgttttatactccc	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156566122C>A	ENST00000286317.5	-	2	702	c.321G>T	c.(319-321)gaG>gaT	p.E107D	MED7_ENST00000420343.1_Missense_Mutation_p.E107D	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	107					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)	p.E107D(1)		kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTCTAGTTTCTCTTCTCGTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	5											73	78	76					5																	156566122		2203	4300	6503	156498700	SO:0001583	missense	9443			AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868			2378	protein-coding gene	gene with protein product		605045	"cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa"	CRSP9		9989412	Standard	NM_004270		Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.321G>T	5.37:g.156566122C>A	ENSP00000286317:p.Glu107Asp		156498700		Missense_Mutation	SNP	ENST00000286317.5	37	CCDS4334.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.423500	0.43020	.	.	ENSG00000155868	ENST00000286317;ENST00000420343;ENST00000524289	.	.	.	5.91	1.07	0.20283	.	0.000000	0.85682	D	0.000000	T	0.64103	0.2568	M	0.66939	2.045	0.80722	D	1	B	0.23540	0.087	B	0.40940	0.344	T	0.58109	-0.7694	9	0.30078	T	0.28	-16.2262	10.2431	0.43324	0.0:0.6711:0.0:0.3289	.	107	O43513	MED7_HUMAN	D	107	.	ENSP00000286317:E107D	E	-	3	2	MED7	156498700	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.198000	0.32223	0.395000	0.25257	-0.136000	0.14681	GAG		0.368	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270		A	156566122	C	A	156566122	3	1	61	1	0	0	0	0	1	0	0	0	9482	912	32	2	384	2	MED7	5	156566122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86511	156566122	24349138	4293	12278										
FAM71B	153745	broad.mit.edu	37	chr5	156590199	156590199	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactggcggcccccgccatCgaggtggaagtaccttccaa	12	14	0	1	rs369213663		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156590199C>T	ENST00000302938.4	-	2	1172	c.1077G>A	c.(1075-1077)tcG>tcA	p.S359S		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	359						nucleus (GO:0005634)		p.S359S(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCCCCGCCATCGAGGTGGAAG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	35	38	37		1077	-4	0	5		37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAM71B	NM_130899.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		359/606	156590199	1,13005	2203	4300	6503	156522777	SO:0001819	synonymous_variant	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1077G>A	5.37:g.156590199C>T			156522777	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																				0.572	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156590199	C	T	156590199	2	4	61	1	0	0	0	0	0	0	0	1	5627	871	31	1		1	FAM71B	5	156590199	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24077	156590199	24325061	4294	12279										
FAM71B	153745	broad.mit.edu	37	chr5	156592899	156592899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacatgctgttcacagattTtagttggttgggccagaacc	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156592899T>G	ENST00000302938.4	-	1	376	c.281A>C	c.(280-282)aAa>aCa	p.K94T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	94						nucleus (GO:0005634)		p.K94T(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCACAGATTTTAGTTGGTTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											87	84	85					5																	156592899		2203	4300	6503	156525477	SO:0001583	missense	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.281A>C	5.37:g.156592899T>G	ENSP00000305596:p.Lys94Thr		156525477	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	T	0.115	-1.132950	0.01756	.	.	ENSG00000170613	ENST00000302938	T	0.03689	3.84	4.67	0.5	0.16919	.	0.660669	0.14023	N	0.346689	T	0.01661	0.0053	N	0.05510	-0.035	0.09310	N	1	B	0.17038	0.02	B	0.08055	0.003	T	0.49194	-0.8965	10	0.12103	T	0.63	-18.1015	5.0076	0.14295	0.0:0.0985:0.3624:0.5391	.	94	Q8TC56	FA71B_HUMAN	T	94	ENSP00000305596:K94T	ENSP00000305596:K94T	K	-	2	0	FAM71B	156525477	0.002000	0.14202	0.002000	0.10522	0.016000	0.09150	0.565000	0.23578	0.330000	0.23485	0.460000	0.39030	AAA		0.547	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		G	156592899	T	G	156592899	3	3	61	1	0	0	0	0	1	0	0	0	5627	1841	64	4	1544	4	FAM71B	5	156592899	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2700	156592899	24322361	4295	12280										
ITK	3702	broad.mit.edu	37	chr5	156607997	156607997	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaactggatcatgaacaaCtttatcctcctggaagaaca	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156607997C>T	ENST00000422843.3	+	1	161	c.9C>T	c.(7-9)aaC>aaT	p.N3N		NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	3					activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.N3N(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	TCATGAACAACTTTATCCTCC	0.443			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	1	Substitution - coding silent(1)	large_intestine(1)	5											85	79	81					5																	156607997		2203	4300	6503	156540575	SO:0001819	synonymous_variant	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.9C>T	5.37:g.156607997C>T			156540575	B2R752|Q32ML7	Silent	SNP	ENST00000422843.3	37	CCDS4336.1																																																																																				0.443	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156607997	C	T	156607997	2	4	61	1	0	0	0	0	0	0	0	1	7930	564	20	3		3	ITK	5	156607997	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15098	156607997	24307263	4296	12281										
ITK	3702	broad.mit.edu	37	chr5	156635937	156635937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtccattgagctctcccGaatcaaatgtgttgagattg	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156635937G>A	ENST00000422843.3	+	2	328	c.176G>A	c.(175-177)cGa>cAa	p.R59Q	CTB-4E7.1_ENST00000519375.1_RNA	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	59	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R59Q(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	GAGCTCTCCCGAATCAAATGT	0.458			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	1	Substitution - Missense(1)	large_intestine(1)	5											122	109	114					5																	156635937		2203	4300	6503	156568515	SO:0001583	missense	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.176G>A	5.37:g.156635937G>A	ENSP00000398655:p.Arg59Gln		156568515	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.434269	0.83776	.	.	ENSG00000113263	ENST00000422843	T	0.74947	-0.89	5.31	5.31	0.75309	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.187688	0.44483	D	0.000452	T	0.70710	0.3255	L	0.43152	1.355	0.28451	N	0.916353	D	0.57571	0.98	P	0.46940	0.532	T	0.70454	-0.4867	10	0.66056	D	0.02	.	11.9447	0.52922	0.0844:0.0:0.9156:0.0	.	59	Q08881	ITK_HUMAN	Q	59	ENSP00000398655:R59Q	ENSP00000398655:R59Q	R	+	2	0	ITK	156568515	1.000000	0.71417	0.993000	0.49108	0.870000	0.49936	4.997000	0.63921	2.458000	0.83093	0.561000	0.74099	CGA		0.458	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			A	156635937	G	A	156635937	3	1	61	1	0	0	0	0	1	0	0	0	7930	1058	37	1	182	1	ITK	5	156635937	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27940	156635937	24279323	4297	12282										
ITK	3702	broad.mit.edu	37	chr5	156638364	156638364	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagccggcagcgctgggtgCtggcccttaaagaaggtaat	15	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156638364C>T	ENST00000422843.3	+	3	462	c.310C>T	c.(310-312)Ctg>Ttg	p.L104L	CTB-4E7.1_ENST00000519375.1_RNA	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	104	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.L104L(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	GCGCTGGGTGCTGGCCCTTAA	0.483			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	1	Substitution - coding silent(1)	large_intestine(1)	5											103	98	100					5																	156638364		2203	4300	6503	156570942	SO:0001819	synonymous_variant	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.310C>T	5.37:g.156638364C>T			156570942	B2R752|Q32ML7	Silent	SNP	ENST00000422843.3	37	CCDS4336.1																																																																																				0.483	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156638364	C	T	156638364	2	4	61	1	0	0	0	0	0	0	0	1	7930	796	28	3		3	ITK	5	156638364	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2427	156638364	24276896	4298	12283										
ITK	3702	broad.mit.edu	37	chr5	156668697	156668697	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccagtttgttttgggaggCagaaagccccagttacagca	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156668697C>T	ENST00000422843.3	+	11	1179	c.1027C>T	c.(1027-1029)Cag>Tag	p.Q343*	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	343					activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.Q343*(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	TTTTGGGAGGCAGAAAGCCCC	0.483			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	1	Substitution - Nonsense(1)	large_intestine(1)	5											85	72	76					5																	156668697		2203	4300	6503	156601275	SO:0001587	stop_gained	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1027C>T	5.37:g.156668697C>T	ENSP00000398655:p.Gln343*		156601275	B2R752|Q32ML7	Nonsense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	C	37	6.353640	0.97498	.	.	ENSG00000113263	ENST00000422843	.	.	.	6.08	5.14	0.70334	.	0.488922	0.24786	N	0.035619	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8509	0.63496	0.2345:0.7655:0.0:0.0	.	.	.	.	X	343	.	ENSP00000398655:Q343X	Q	+	1	0	ITK	156601275	0.561000	0.26578	1.000000	0.80357	0.505000	0.33919	0.745000	0.26259	2.894000	0.99253	0.655000	0.94253	CAG		0.483	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156668697	C	T	156668697	4	4	61	1	0	0	0	0	0	1	0	0	7930	711	25	3	1069	3	ITK	5	156668697	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30333	156668697	24246563	4299	12284										
CYFIP2	408263	broad.mit.edu	37	chr5	156766139	156766139	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatgacgctggacagcttCgatgccatgttccgagaggc	12	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156766139C>T	ENST00000312349.4	-	0	2125				CYFIP2_ENST00000541131.1_Silent_p.F745F|CYFIP2_ENST00000377576.3_Silent_p.F820F|CYFIP2_ENST00000521420.1_Silent_p.F794F|CYFIP2_ENST00000435847.2_Silent_p.F519F|CYFIP2_ENST00000318218.6_Silent_p.F845F|CYFIP2_ENST00000442283.2_Silent_p.F105F|CYFIP2_ENST00000522463.1_Silent_p.F624F|CYFIP2_ENST00000347377.6_Silent_p.F820F	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9							integral component of membrane (GO:0016021)		p.F845F(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						TGGACAGCTTCGATGCCATGT	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	5											84	92	89					5																	156766139		2184	4296	6480	156698717	SO:0001628	intergenic_variant	26999			BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248		5.37:g.156766139C>T			156698717	A8K0Y6	Silent	SNP	ENST00000312349.4	37	CCDS4337.1																																																																																				0.547	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		T	156766139	C	T	156766139	1	4	61	0	1	0	0	0	0	0	0	0	4144	883	31	1		1	CYFIP2	5	156766139	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97442	156766139	24149121	4300	12285										
CYFIP2	26999	broad.mit.edu	37	chr5	156786060	156786060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagctcctacaggaatttCgtggggccacctcatttcaa	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156786060C>T	ENST00000442283.2	+	25	2856	c.574C>T	c.(574-576)Cgt>Tgt	p.R192C	CYFIP2_ENST00000541131.1_Silent_p.F832F|CYFIP2_ENST00000377576.3_Silent_p.F907F|CYFIP2_ENST00000521420.1_Silent_p.F881F|CYFIP2_ENST00000435847.2_Silent_p.F606F|CYFIP2_ENST00000318218.6_Silent_p.F932F|CYFIP2_ENST00000522463.1_Silent_p.F711F|CYFIP2_ENST00000347377.6_Silent_p.F907F	NM_001037333.1	NP_001032410.1			cytoplasmic FMR1 interacting protein 2									p.F932F(2)		breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACAGGAATTTCGTGGGGCCAC	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	5											188	191	190					5																	156786060		1990	4166	6156	156718638	SO:0001583	missense	26999			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000442283.2:c.574C>T	5.37:g.156786060C>T	ENSP00000390948:p.Arg192Cys		156718638		Silent	SNP	ENST00000442283.2	37		.	.	.	.	.	.	.	.	.	.	C	14.08	2.430157	0.43122	.	.	ENSG00000055163	ENST00000442283	T	0.21543	2.0	5.28	-4.01	0.04045	.	.	.	.	.	T	0.29783	0.0744	.	.	.	0.27376	N	0.955557	.	.	.	.	.	.	T	0.43507	-0.9387	6	0.87932	D	0	-27.2951	15.4154	0.74962	0.0:0.4586:0.0:0.5414	.	.	.	.	C	192	ENSP00000390948:R192C	ENSP00000390948:R192C	R	+	1	0	CYFIP2	156718638	0.000000	0.05858	0.915000	0.36163	0.895000	0.52256	-1.768000	0.01794	-1.006000	0.03412	-0.907000	0.02831	CGT		0.488	CYFIP2-205	KNOWN	basic	protein_coding	protein_coding		NM_001037332		T	156786060	C	T	156786060	3	4	61	1	0	0	0	0	1	0	0	0	4144	883	31	1	2811	1	CYFIP2	5	156786060	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19921	156786060	24129200	4301	12286										
CYFIP2	26999	broad.mit.edu	37	chr5	156816394	156816394	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggagcgccatgcagttCgtgtactgcatccctgtggg	14	11	0	0	rs267600516		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:156816394C>T	ENST00000521420.1	+	28	3418	c.3327C>T	c.(3325-3327)ttC>ttT	p.F1109F	CYFIP2_ENST00000541131.1_Silent_p.F1060F|CYFIP2_ENST00000377576.3_Silent_p.F1135F|CYFIP2_ENST00000435847.2_Silent_p.F834F|CYFIP2_ENST00000318218.6_Silent_p.F1160F|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000522463.1_Silent_p.F939F|CYFIP2_ENST00000347377.6_Silent_p.F1135F					cytoplasmic FMR1 interacting protein 2									p.F1160F(2)		breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCATGCAGTTCGTGTACTGCA	0.617																																																2	Substitution - coding silent(2)	large_intestine(2)	5						C	,,	0,4312		0,0,2156	53	61	59		3405,3405,3405	-3.9	0.9	5		59	1,8559		0,1,4279	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,1,6435	TT,TC,CC		0.0117,0.0,0.0078	,,	1135/1254,1135/1254,1135/1254	156816394	1,12871	2156	4280	6436	156748972	SO:0001819	synonymous_variant	26999			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3327C>T	5.37:g.156816394C>T			156748972		Silent	SNP	ENST00000521420.1	37																																																																																					0.617	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156816394	C	T	156816394	2	4	61	1	0	0	0	0	0	0	0	1	4144	883	31	1		1	CYFIP2	5	156816394	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30334	156816394	24098866	4302	12287										
SOX30	11063	broad.mit.edu	37	chr5	157075817	157075817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctttggctagtgctggtCggtggatccttgcccaaacc	12	11	0	0	rs574355786		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:157075817C>T	ENST00000265007.6	-	2	1396	c.1055G>A	c.(1054-1056)cGa>cAa	p.R352Q	SOX30_ENST00000519442.1_Missense_Mutation_p.R47Q|SOX30_ENST00000311371.5_Missense_Mutation_p.R352Q	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	352					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R352Q(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TAGTGCTGGTCGGTGGATCCT	0.463													C|||	1	0.000199681	8e-04	0	5008	,	,		17487	0		0	False		,,,				2504	0				Esophageal Squamous(31;525 799 19355 21125 41744)											1	Substitution - Missense(1)	large_intestine(1)	5											187	175	179					5																	157075817		2203	4300	6503	157008395	SO:0001583	missense	11063			AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1055G>A	5.37:g.157075817C>T	ENSP00000265007:p.Arg352Gln		157008395	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	C	33	5.241420	0.95272	.	.	ENSG00000039600	ENST00000311371;ENST00000265007;ENST00000519442	D;D;D	0.98633	-5.04;-5.04;-5.04	5.67	5.67	0.87782	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.64402	D	0.000008	D	0.99168	0.9712	M	0.81614	2.55	0.46061	D	0.998846	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	D	0.99826	1.1050	10	0.87932	D	0	.	19.7658	0.96340	0.0:1.0:0.0:0.0	.	47;352;352	B4DXW7;O94993-2;O94993	.;.;SOX30_HUMAN	Q	352;352;47	ENSP00000309343:R352Q;ENSP00000265007:R352Q;ENSP00000427984:R47Q	ENSP00000265007:R352Q	R	-	2	0	SOX30	157008395	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.448000	0.73469	2.661000	0.90470	0.555000	0.69702	CGA		0.463	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157075817	C	T	157075817	3	4	61	1	0	0	0	0	1	0	0	0	14989	884	31	1	1222	1	SOX30	5	157075817	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	259423	157075817	23839443	4303	12288										
LSM11	134353	broad.mit.edu	37	chr5	157178487	157178487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcactttcaagggacttCggggcgtctgtacaggcttc	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:157178487C>T	ENST00000286307.5	+	2	594	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W		NM_173491.2	NP_775762.1	P83369	LSM11_HUMAN	LSM11, U7 small nuclear RNA associated	180	SM 1.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U7 snRNP (GO:0005683)	U7 snRNA binding (GO:0071209)	p.R180W(1)		breast(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	7	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CAAGGGACTTCGGGGCGTCTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	5											137	132	134					5																	157178487		2203	4300	6503	157111065	SO:0001583	missense	134353			AK095592	CCDS4342.1	5q33.3	2008-02-05	2004-04-28		ENSG00000155858	ENSG00000155858			30860	protein-coding gene	gene with protein product			"LSM11 homolog, U7 small nuclear RNA associated (S. cerevisiae)"			12975319	Standard	NM_173491		Approved	FLJ38273	uc003lxe.1	P83369	OTTHUMG00000130255	ENST00000286307.5:c.538C>T	5.37:g.157178487C>T	ENSP00000286307:p.Arg180Trp		157111065	A0AVQ1|Q7Z7P0|Q8N975	Missense_Mutation	SNP	ENST00000286307.5	37	CCDS4342.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756550	0.89843	.	.	ENSG00000155858	ENST00000286307	.	.	.	5.87	5.87	0.94306	Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (2);	0.000000	0.85682	D	0.000000	D	0.84511	0.5488	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85183	0.1005	9	0.87932	D	0	-12.0939	20.5827	0.99408	0.0:1.0:0.0:0.0	.	180	P83369	LSM11_HUMAN	W	180	.	ENSP00000286307:R180W	R	+	1	2	LSM11	157111065	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	4.794000	0.62482	2.941000	0.99782	0.655000	0.94253	CGG		0.498	LSM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252580.2	NM_173491		T	157178487	C	T	157178487	3	4	61	1	0	0	0	0	1	0	0	0	9081	875	31	1	544	1	LSM11	5	157178487	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102670	157178487	23736773	4304	12289										
CLINT1	9685	broad.mit.edu	37	chr5	157241238	157241238	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtaaatcataaatgtgttCtctggcacttgtaacaacac	6	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:157241238C>A	ENST00000411809.2	-	4	511	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	CLINT1_ENST00000296951.5_Nonsense_Mutation_p.E85*|CLINT1_ENST00000523908.1_Nonsense_Mutation_p.E103*|CLINT1_ENST00000523094.1_Nonsense_Mutation_p.E85*|CLINT1_ENST00000530742.1_Nonsense_Mutation_p.E85*	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	103	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)	p.E85*(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TAAATGTGTTCTCTGGCACTT	0.353																																					Colon(22;427 587 2170 6147 14291)											2	Substitution - Nonsense(2)	large_intestine(2)	5											80	78	78					5																	157241238		1856	4106	5962	157173816	SO:0001587	stop_gained	9685			AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.307G>T	5.37:g.157241238C>A	ENSP00000388340:p.Glu103*		157173816	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Nonsense_Mutation	SNP	ENST00000411809.2	37	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	C	37	6.375668	0.97515	.	.	ENSG00000113282	ENST00000523094;ENST00000530742;ENST00000411809;ENST00000296951;ENST00000523908	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	17.1358	20.0966	0.97849	0.0:1.0:0.0:0.0	.	.	.	.	X	85;85;103;85;103	.	ENSP00000296951:E85X	E	-	1	0	CLINT1	157173816	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.751000	0.94390	0.650000	0.86243	GAA		0.353	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		A	157241238	C	A	157241238	4	1	61	1	0	0	0	0	0	1	0	0	3537	922	32	2	1606	2	CLINT1	5	157241238	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62751	157241238	23674022	4305	12290										
RNF145	153830	broad.mit.edu	37	chr5	158585758	158585758	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagccccttcctggttatCtggtcgtctggcaatgtact	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:158585758C>T	ENST00000424310.2	-	11	2271	c.1912G>A	c.(1912-1914)Gat>Aat	p.D638N	RNF145_ENST00000519865.1_Missense_Mutation_p.D638N|RNF145_ENST00000518802.1_Missense_Mutation_p.D668N|RNF145_ENST00000521606.2_Missense_Mutation_p.D655N|RNF145_ENST00000520638.1_Missense_Mutation_p.D652N|RNF145_ENST00000274542.2_Missense_Mutation_p.D666N|RNF145_ENST00000518284.1_5'UTR	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	638						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.D666N(1)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCTGGTTATCTGGTCGTCTG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											149	151	150					5																	158585758		2203	4300	6503	158518336	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1912G>A	5.37:g.158585758C>T	ENSP00000409064:p.Asp638Asn		158518336	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	C	3.430	-0.116304	0.06881	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.76968	-1.06;-1.05;-1.05;-1.06;-1.06;-1.06;-1.05	5.11	2.32	0.28847	.	1.284980	0.05159	N	0.497344	T	0.59918	0.2229	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.44772	-0.9306	10	0.17369	T	0.5	0.4761	4.9321	0.13923	0.1534:0.6189:0.1479:0.0798	.	655;652;668;638;666	B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;RN145_HUMAN;.	N	666;638;638;654;655;668;638;652	ENSP00000274542:D666N;ENSP00000430397:D638N;ENSP00000409064:D638N;ENSP00000430753:D654N;ENSP00000445115:D655N;ENSP00000430955:D668N;ENSP00000429071:D652N	ENSP00000274542:D666N	D	-	1	0	RNF145	158518336	0.000000	0.05858	0.029000	0.17559	0.721000	0.41392	0.331000	0.19733	0.540000	0.28808	0.655000	0.94253	GAT		0.502	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		T	158585758	C	T	158585758	3	4	61	1	0	0	0	0	1	0	0	0	13484	913	32	3	83	3	RNF145	5	158585758	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1344520	158585758	22329502	4306	12291										
RNF145	153830	broad.mit.edu	37	chr5	158585904	158585904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggctgtagaactggctcaGttcctaatcctggaagctgg	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:158585904G>A	ENST00000424310.2	-	11	2125	c.1766C>T	c.(1765-1767)aCt>aTt	p.T589I	RNF145_ENST00000519865.1_Missense_Mutation_p.T589I|RNF145_ENST00000518802.1_Missense_Mutation_p.T619I|RNF145_ENST00000521606.2_Missense_Mutation_p.T606I|RNF145_ENST00000520638.1_Missense_Mutation_p.T603I|RNF145_ENST00000274542.2_Missense_Mutation_p.T617I|RNF145_ENST00000518284.1_5'UTR	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	589						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.T617I(1)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AACTGGCTCAGTTCCTAATCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											62	61	61					5																	158585904		2203	4300	6503	158518482	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1766C>T	5.37:g.158585904G>A	ENSP00000409064:p.Thr589Ile		158518482	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996602	0.35226	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.78707	-1.19;-1.19;-1.19;-1.19;-1.19;-1.2;-1.18	5.18	5.18	0.71444	.	0.544310	0.21148	N	0.079368	T	0.74733	0.3755	L	0.46157	1.445	0.29115	N	0.880602	B;B;B;B;B	0.19583	0.037;0.002;0.01;0.011;0.018	B;B;B;B;B	0.23419	0.029;0.007;0.021;0.006;0.046	T	0.67377	-0.5686	10	0.38643	T	0.18	-1.2993	18.6996	0.91615	0.0:0.0:1.0:0.0	.	606;603;619;589;617	B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;RN145_HUMAN;.	I	617;589;589;605;606;619;589;603	ENSP00000274542:T617I;ENSP00000430397:T589I;ENSP00000409064:T589I;ENSP00000430753:T605I;ENSP00000445115:T606I;ENSP00000430955:T619I;ENSP00000429071:T603I	ENSP00000274542:T617I	T	-	2	0	RNF145	158518482	0.583000	0.26757	0.015000	0.15790	0.986000	0.74619	3.163000	0.50763	2.415000	0.81967	0.655000	0.94253	ACT		0.527	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		A	158585904	G	A	158585904	3	1	61	1	0	0	0	0	1	0	0	0	13484	1029	36	3	229	3	RNF145	5	158585904	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146	158585904	22329356	4307	12292										
IL12B	3593	broad.mit.edu	37	chr5	158750222	158750222	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttttgccagagcctaaGacctcactgctctggtccaa	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:158750222G>T	ENST00000231228.2	-	3	659	c.204C>A	c.(202-204)gtC>gtA	p.V68V		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	68	Ig-like C2-type.				cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)	p.V68V(1)		cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGAGCCTAAGACCTCACTGC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	5											98	88	91					5																	158750222		2203	4300	6503	158682800	SO:0001819	synonymous_variant	3593			M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5970	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor-2", "cytotoxic lymphocyte maturation factor 2, p40", "interleukin 12, p40", "natural killer cell stimulatory factor, 40 kD subunit", "interleukin-12 beta chain", "IL12, subunit p40"	161561	"interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.204C>A	5.37:g.158750222G>T			158682800		Silent	SNP	ENST00000231228.2	37	CCDS4346.1																																																																																				0.537	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187		T	158750222	G	T	158750222	2	4	61	1	0	0	0	0	0	0	0	1	7646	929	33	2		2	IL12B	5	158750222	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164318	158750222	22165038	4308	12293										
ADRA1B	147	broad.mit.edu	37	chr5	159344141	159344141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcctgcaaccggcacctgCggacgcccaccaactacttc	9	18	0	0	rs571519472		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159344141C>T	ENST00000306675.3	+	1	352	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	77					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)	p.R77W(2)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	CCGGCACCTGCGGACGCCCAC	0.612																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	5											108	103	105					5																	159344141		2203	4300	6503	159276719	SO:0001583	missense	147			L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"GPCR / Class A : Adrenoceptors : alpha"	278	protein-coding gene	gene with protein product		104220	"adrenergic, alpha-1B-, receptor"				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.229C>T	5.37:g.159344141C>T	ENSP00000306662:p.Arg77Trp		159276719	B0LPE1	Missense_Mutation	SNP	ENST00000306675.3	37	CCDS4347.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.467446	0.63625	.	.	ENSG00000170214	ENST00000306675	T	0.45276	0.9	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.73536	0.3599	H	0.95328	3.655	0.46396	D	0.999024	D	0.89917	1.0	D	0.85130	0.997	T	0.81337	-0.0978	10	0.87932	D	0	.	13.3092	0.60370	0.1588:0.8412:0.0:0.0	.	77	P35368	ADA1B_HUMAN	W	77	ENSP00000306662:R77W	ENSP00000306662:R77W	R	+	1	2	ADRA1B	159276719	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.239000	0.51360	2.536000	0.85505	0.462000	0.41574	CGG		0.612	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1			T	159344141	C	T	159344141	3	4	61	1	0	0	0	0	1	0	0	0	335	759	27	1	231	1	ADRA1B	5	159344141	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	593919	159344141	21571119	4309	12294										
ADRA1B	147	broad.mit.edu	37	chr5	159344473	159344473	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttgggtggaaggagccGgcacccaacgatgacaagga	14	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159344473G>A	ENST00000306675.3	+	1	684	c.561G>A	c.(559-561)ccG>ccA	p.P187P		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	187					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)	p.P187P(1)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	GGAAGGAGCCGGCACCCAACG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	5											99	95	96					5																	159344473		2203	4300	6503	159277051	SO:0001819	synonymous_variant	147			L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"GPCR / Class A : Adrenoceptors : alpha"	278	protein-coding gene	gene with protein product		104220	"adrenergic, alpha-1B-, receptor"				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.561G>A	5.37:g.159344473G>A			159277051	B0LPE1	Silent	SNP	ENST00000306675.3	37	CCDS4347.1																																																																																				0.607	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1			A	159344473	G	A	159344473	2	1	61	1	0	0	0	0	0	0	0	1	335	1103	39	1		1	ADRA1B	5	159344473	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	332	159344473	21570787	4310	12295										
TTC1	7265	broad.mit.edu	37	chr5	159492045	159492045	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcgtactccatcaatttCgttcaaaatccaaataataa	4	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159492045C>A	ENST00000231238.5	+	8	962	c.852C>A	c.(850-852)ttC>ttA	p.F284L	TTC1_ENST00000522793.1_Missense_Mutation_p.F284L|TTC1_ENST00000520274.1_3'UTR	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	284					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)	p.F284L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		CCATCAATTTCGTTCAAAATC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											56	57	56					5																	159492045		2203	4300	6503	159424623	SO:0001583	missense	7265			U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"Tetratricopeptide (TTC) repeat domain containing"	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.852C>A	5.37:g.159492045C>A	ENSP00000231238:p.Phe284Leu		159424623	B2RCT2|D3DQJ8|Q9BVT3	Missense_Mutation	SNP	ENST00000231238.5	37	CCDS4348.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580131	0.86645	.	.	ENSG00000113312	ENST00000231238;ENST00000522793	T;T	0.38722	1.12;1.12	5.44	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67439	0.2893	M	0.89658	3.05	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.71951	-0.4437	10	0.56958	D	0.05	-21.1854	11.0951	0.48139	0.0:0.0746:0.0:0.9254	.	284	Q99614	TTC1_HUMAN	L	284	ENSP00000231238:F284L;ENSP00000429225:F284L	ENSP00000231238:F284L	F	+	3	2	TTC1	159424623	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.027000	0.49697	0.993000	0.38866	-0.290000	0.09829	TTC		0.423	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314		A	159492045	C	A	159492045	3	1	61	1	0	0	0	0	1	0	0	0	16718	883	31	2	878	2	TTC1	5	159492045	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147572	159492045	21423215	4311	12296										
PWWP2A	114825	broad.mit.edu	37	chr5	159505169	159505169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccagcagcctgctaatgtCtttgtgctgaaatatagtaa	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159505169C>A	ENST00000523662.1	-	3	1589	c.1556G>T	c.(1555-1557)aGa>aTa	p.R519I	PWWP2A_ENST00000456329.3_Missense_Mutation_p.R559I	NM_001267035.1	NP_001253964.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	0								p.R559I(1)		kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGCTAATGTCTTTGTGCTGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	5											61	59	60					5																	159505169		1878	4101	5979	159437747	SO:0001583	missense	114825				CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000523662.1:c.1556G>T	5.37:g.159505169C>A	ENSP00000428143:p.Arg519Ile		159437747	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Missense_Mutation	SNP	ENST00000523662.1	37	CCDS58990.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421900	0.62622	.	.	ENSG00000170234	ENST00000456329;ENST00000523662	T;T	0.35236	1.32;1.44	6.08	6.08	0.98989	.	.	.	.	.	T	0.64023	0.2561	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.65117	-0.6246	8	0.87932	D	0	.	18.4365	0.90648	0.0:1.0:0.0:0.0	.	519;559	G5EA07;Q96N64-2	.;.	I	559;519	ENSP00000390462:R559I;ENSP00000428143:R519I	ENSP00000390462:R559I	R	-	2	0	PWWP2A	159437747	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.719000	0.61937	2.894000	0.99253	0.655000	0.94253	AGA		0.378	PWWP2A-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000374091.1			A	159505169	C	A	159505169	3	1	61	1	0	0	0	0	1	0	0	0	12882	913	32	2	10	2	PWWP2A	5	159505169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13124	159505169	21410091	4312	12297										
PWWP2A	114825	broad.mit.edu	37	chr5	159520275	159520275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagctaggattctgatatCgacgtgtgaaatggactttt	11	6	1	3	rs374605320		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159520275C>T	ENST00000307063.7	-	2	1416	c.1382G>A	c.(1381-1383)cGa>cAa	p.R461Q	PWWP2A_ENST00000456329.3_Missense_Mutation_p.R461Q|PWWP2A_ENST00000523662.1_Missense_Mutation_p.R461Q	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	461								p.R461Q(1)		kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATTCTGATATCGACGTGTGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	GLN/ARG,GLN/ARG	0,3734		0,0,1867	86	79	81		1382,1382	5.5	0.5	5		81	2,8208		0,2,4103	no	missense,missense	PWWP2A	NM_001130864.1,NM_052927.2	43,43	0,2,5970	TT,TC,CC		0.0244,0.0,0.0167	probably-damaging,probably-damaging	461/756,461/561	159520275	2,11942	1867	4105	5972	159452853	SO:0001583	missense	114825				CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.1382G>A	5.37:g.159520275C>T	ENSP00000305151:p.Arg461Gln		159452853	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Missense_Mutation	SNP	ENST00000307063.7	37	CCDS47332.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.101176	0.56183	0.0	2.44E-4	ENSG00000170234	ENST00000456329;ENST00000523662;ENST00000307063	T;T;T	0.24908	1.83;1.83;1.83	5.54	5.54	0.83059	.	0.055197	0.64402	D	0.000001	T	0.18593	0.0446	N	0.19112	0.55	0.80722	D	1	P;D;D	0.55800	0.954;0.973;0.973	B;B;B	0.39935	0.166;0.314;0.314	T	0.02533	-1.1145	10	0.26408	T	0.33	-1.8136	19.1388	0.93439	0.0:1.0:0.0:0.0	.	461;461;461	Q96N64;G5EA07;Q96N64-2	PWP2A_HUMAN;.;.	Q	461	ENSP00000390462:R461Q;ENSP00000428143:R461Q;ENSP00000305151:R461Q	ENSP00000305151:R461Q	R	-	2	0	PWWP2A	159452853	0.999000	0.42202	0.536000	0.28039	0.991000	0.79684	4.173000	0.58249	2.625000	0.88918	0.558000	0.71614	CGA		0.418	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			T	159520275	C	T	159520275	3	4	61	1	0	0	0	0	1	0	0	0	12882	884	31	1	1031	1	PWWP2A	5	159520275	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15106	159520275	21394985	4313	12298										
C5orf54	63920	broad.mit.edu	37	chr5	159821438	159821438	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attactgctcttgtggtgaaGaaactgatttatttcttcat	7	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159821438G>T	ENST00000408953.3	-	2	1567	c.1060C>A	c.(1060-1062)Ctt>Att	p.L354I	C5orf54_ENST00000523213.1_Missense_Mutation_p.L354I	NM_022090.3	NP_071373.2												p.L354I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						ttgtggtgaagaaactgattt	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	5											33	34	34					5																	159821438		2202	4298	6500	159754016	SO:0001583	missense	63920																														ENST00000408953.3:c.1060C>A	5.37:g.159821438G>T	ENSP00000386184:p.Leu354Ile		159754016		Missense_Mutation	SNP	ENST00000408953.3	37	CCDS34283.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535371	0.45176	.	.	ENSG00000221886	ENST00000408953;ENST00000523213	T;T	0.31247	1.5;1.5	2.78	2.78	0.32641	.	.	.	.	.	T	0.45796	0.1360	L	0.58583	1.82	0.23366	N	0.997826	D	0.64830	0.994	D	0.63381	0.914	T	0.14980	-1.0453	9	0.66056	D	0.02	.	9.2447	0.37518	0.0:0.0:1.0:0.0	.	354	Q8IZ13	CE054_HUMAN	I	354	ENSP00000386184:L354I;ENSP00000428831:L354I	ENSP00000386184:L354I	L	-	1	0	C5orf54	159754016	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.857000	0.48349	1.880000	0.54463	0.655000	0.94253	CTT		0.333	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1			T	159821438	G	T	159821438	3	4	61	1	0	0	0	0	1	0	0	0	2316	942	33	2	728	2	C5orf54	5	159821438	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	301163	159821438	21093822	4314	12299										
C5orf54	63920	broad.mit.edu	37	chr5	159821712	159821712	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaactacgatatgaggtatCtcttttttcacgtaggcaac	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159821712C>A	ENST00000408953.3	-	2	1293	c.786G>T	c.(784-786)gaG>gaT	p.E262D	C5orf54_ENST00000523213.1_Missense_Mutation_p.E262D	NM_022090.3	NP_071373.2												p.E262D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						tatgaggtatctcttttttca	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											140	134	136					5																	159821712		2203	4300	6503	159754290	SO:0001583	missense	63920																														ENST00000408953.3:c.786G>T	5.37:g.159821712C>A	ENSP00000386184:p.Glu262Asp		159754290		Missense_Mutation	SNP	ENST00000408953.3	37	CCDS34283.1	.	.	.	.	.	.	.	.	.	.	C	4.454	0.084161	0.08583	.	.	ENSG00000221886	ENST00000408953;ENST00000523213	T;T	0.14766	2.48;2.48	2.84	-1.6	0.08426	.	.	.	.	.	T	0.04724	0.0128	N	0.04724	-0.175	0.24740	N	0.99305	B	0.02656	0.0	B	0.01281	0.0	T	0.44143	-0.9347	9	0.14656	T	0.56	.	3.6151	0.08074	0.1724:0.614:0.0:0.2136	.	262	Q8IZ13	CE054_HUMAN	D	262	ENSP00000386184:E262D;ENSP00000428831:E262D	ENSP00000386184:E262D	E	-	3	2	C5orf54	159754290	0.165000	0.22948	0.734000	0.30879	0.814000	0.46013	-0.012000	0.12699	-0.400000	0.07656	0.655000	0.94253	GAG		0.403	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1			A	159821712	C	A	159821712	3	1	61	1	0	0	0	0	1	0	0	0	2316	912	32	2	1002	2	C5orf54	5	159821712	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274	159821712	21093548	4315	12300										
C5orf54	63920	broad.mit.edu	37	chr5	159821898	159821898	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaagagaaattcttctacGatctctctttcttttatata	4	8	5	2	rs373610961		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:159821898G>A	ENST00000408953.3	-	2	1107	c.600C>T	c.(598-600)atC>atT	p.I200I	C5orf54_ENST00000523213.1_Silent_p.I200I	NM_022090.3	NP_071373.2												p.I200I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						attcttctacgatctctcttt	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G		0,4406		0,0,2203	57	56	56		600	-1.8	0.1	5		56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C5orf54	NM_022090.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		200/595	159821898	1,13005	2203	4300	6503	159754476	SO:0001819	synonymous_variant	63920																														ENST00000408953.3:c.600C>T	5.37:g.159821898G>A			159754476		Silent	SNP	ENST00000408953.3	37	CCDS34283.1																																																																																				0.408	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1			A	159821898	G	A	159821898	2	1	61	1	0	0	0	0	0	0	0	1	2316	1048	37	1		1	C5orf54	5	159821898	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186	159821898	21093362	4316	12301										
GABRB2	2561	broad.mit.edu	37	chr5	160886849	160886849	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacattgtcaaggtataaTcctgtaaatgtgagaaaaaa	8	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:160886849T>C	ENST00000393959.1	-	4	238	c.239A>G	c.(238-240)gAt>gGt	p.D80G	GABRB2_ENST00000353437.6_Splice_Site_p.D80G|GABRB2_ENST00000517547.1_Intron|GABRB2_ENST00000274547.2_Splice_Site_p.D80G|GABRB2_ENST00000517901.1_Splice_Site_p.D17G|GABRB2_ENST00000520240.1_Splice_Site_p.D80G			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	80					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.D80G(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	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)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAAGGTATAATCCTGTAAATG	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	5											45	44	45					5																	160886849		2203	4300	6503	160819427	SO:0001630	splice_region_variant	2561				CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.238-1A>G	5.37:g.160886849T>C			160819427	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	37	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.493480	0.84962	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901	T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21	4.97	4.97	0.65823	Neurotransmitter-gated ion-channel ligand-binding (3);	0.052351	0.85682	D	0.000000	D	0.91620	0.7352	H	0.96301	3.8	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.997;0.999	D	0.94222	0.7468	10	0.87932	D	0	.	14.9655	0.71188	0.0:0.0:0.0:1.0	.	80;17;80;80	B7Z4P0;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	G	80;80;80;80;17	ENSP00000377531:D80G;ENSP00000274547:D80G;ENSP00000274546:D80G;ENSP00000429320:D80G;ENSP00000430532:D17G	ENSP00000274547:D80G	D	-	2	0	GABRB2	160819427	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.903000	0.87398	1.988000	0.58038	0.533000	0.62120	GAT		0.353	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1		Missense_Mutation	C	160886849	T	C	160886849	5	2	61	1	0	0	0	0	0	0	1	0	6186	1449	50	4	1327	4	GABRB2	5	160886849	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1064951	160886849	20028411	4317	12302										
GABRA1	2554	broad.mit.edu	37	chr5	161318045	161318045	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagagtctgtaccagcaaGaactgtctttggtaagtccc	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:161318045G>A	ENST00000428797.2	+	9	1200	c.845G>A	c.(844-846)aGa>aAa	p.R282K	GABRA1_ENST00000393943.4_Missense_Mutation_p.R282K|GABRA1_ENST00000420560.1_Missense_Mutation_p.R282K|GABRA1_ENST00000437025.2_Missense_Mutation_p.R282K|GABRA1_ENST00000444819.1_Missense_Mutation_p.R282K|GABRA1_ENST00000023897.6_Missense_Mutation_p.R282K	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	282					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R282K(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	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;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GTACCAGCAAGAACTGTCTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											107	106	106					5																	161318045		2203	4300	6503	161250623	SO:0001583	missense	2554				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.845G>A	5.37:g.161318045G>A	ENSP00000393097:p.Arg282Lys		161250623	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	37	5.981347	0.97168	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	D;D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69;-1.69	5.52	5.52	0.82312	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94437	0.8210	H	0.96239	3.79	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	D	0.95800	0.8832	10	0.87932	D	0	.	19.4464	0.94849	0.0:0.0:1.0:0.0	.	282	P14867	GBRA1_HUMAN	K	282	ENSP00000023897:R282K;ENSP00000393097:R282K;ENSP00000377517:R282K;ENSP00000415441:R282K;ENSP00000408041:R282K;ENSP00000414232:R282K	ENSP00000023897:R282K	R	+	2	0	GABRA1	161250623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.695000	0.98691	2.603000	0.88011	0.650000	0.86243	AGA		0.393	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161318045	G	A	161318045	3	1	61	1	0	0	0	0	1	0	0	0	6179	942	33	3	871	3	GABRA1	5	161318045	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	431196	161318045	19597215	4318	12303										
GABRA1	2554	broad.mit.edu	37	chr5	161324131	161324131	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagccaaagaaagtaaaGgatcctcttattaagaaaaa	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:161324131G>T	ENST00000428797.2	+	11	1429	c.1074G>T	c.(1072-1074)aaG>aaT	p.K358N	GABRA1_ENST00000393943.4_Missense_Mutation_p.K358N|GABRA1_ENST00000420560.1_Missense_Mutation_p.K358N|GABRA1_ENST00000437025.2_Missense_Mutation_p.K358N|GABRA1_ENST00000444819.1_Missense_Mutation_p.K358N|GABRA1_ENST00000023897.6_Missense_Mutation_p.K358N	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	358					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.K358N(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	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;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	AGAAAGTAAAGGATCCTCTTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											85	97	93					5																	161324131		2203	4300	6503	161256709	SO:0001583	missense	2554				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.1074G>T	5.37:g.161324131G>T	ENSP00000393097:p.Lys358Asn		161256709	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	13.51	2.259046	0.39896	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.32	-0.646	0.11472	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.000000	0.85682	D	0.000000	T	0.78323	0.4265	L	0.47190	1.495	0.58432	D	0.999996	P	0.48998	0.918	P	0.54856	0.762	T	0.71859	-0.4465	10	0.13470	T	0.59	.	11.1746	0.48593	0.4355:0.0:0.5645:0.0	.	358	P14867	GBRA1_HUMAN	N	358	ENSP00000023897:K358N;ENSP00000393097:K358N;ENSP00000377517:K358N;ENSP00000415441:K358N;ENSP00000408041:K358N;ENSP00000414232:K358N	ENSP00000023897:K358N	K	+	3	2	GABRA1	161256709	0.999000	0.42202	0.983000	0.44433	0.995000	0.86356	0.494000	0.22467	-0.377000	0.07930	0.563000	0.77884	AAG		0.423	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		T	161324131	G	T	161324131	3	4	61	1	0	0	0	0	1	0	0	0	6179	991	35	2	1108	2	GABRA1	5	161324131	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6086	161324131	19591129	4319	12304										
GABRG2	2566	broad.mit.edu	37	chr5	161530912	161530912	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatggctatccacgtgaaGaaattgtttatcaatggaag	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:161530912G>T	ENST00000361925.4	+	6	869	c.649G>T	c.(649-651)Gaa>Taa	p.E217*	GABRG2_ENST00000414552.2_Nonsense_Mutation_p.E257*|GABRG2_ENST00000356592.3_Nonsense_Mutation_p.E217*|GABRG2_ENST00000393933.4_Nonsense_Mutation_p.E122*			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	217					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.E217*(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	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)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCCACGTGAAGAAATTGTTTA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											103	98	100					5																	161530912		2203	4300	6503	161463490	SO:0001587	stop_gained	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.649G>T	5.37:g.161530912G>T	ENSP00000354651:p.Glu217*		161463490	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Nonsense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	G	42	9.223287	0.99105	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.5165	0.95167	0.0:0.0:1.0:0.0	.	.	.	.	X	217;257;217;122;122	.	ENSP00000349000:E217X	E	+	1	0	GABRG2	161463490	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.751000	0.98889	2.615000	0.88500	0.655000	0.94253	GAA		0.388	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			T	161530912	G	T	161530912	4	4	61	1	0	0	0	0	0	1	0	0	6191	943	33	2	795	2	GABRG2	5	161530912	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206781	161530912	19384348	4320	12305										
GABRG2	2566	broad.mit.edu	37	chr5	161531011	161531011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtctaagaaataccaccGaagtagtgaagacaacttcc	8	9	1	3	rs549251133		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:161531011G>A	ENST00000361925.4	+	6	968	c.748G>A	c.(748-750)Gaa>Aaa	p.E250K	GABRG2_ENST00000414552.2_Missense_Mutation_p.E290K|GABRG2_ENST00000356592.3_Missense_Mutation_p.E250K|GABRG2_ENST00000393933.4_Missense_Mutation_p.E155K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	250					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.E250K(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	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)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAATACCACCGAAGTAGTGAA	0.378													G|||	1	0.000199681	0	0	5008	,	,		14895	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	5											80	78	79					5																	161531011		2203	4300	6503	161463589	SO:0001583	missense	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.748G>A	5.37:g.161531011G>A	ENSP00000354651:p.Glu250Lys		161463589	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.599145	0.66332	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	T;T;T;T;T	0.79352	-1.26;-1.14;-1.26;-1.26;-1.26	5.39	3.59	0.41128	Neurotransmitter-gated ion-channel ligand-binding (3);	0.260839	0.45126	D	0.000395	T	0.67449	0.2894	N	0.21240	0.645	0.58432	D	0.999993	P;P;P	0.46784	0.622;0.884;0.859	B;P;B	0.45195	0.284;0.473;0.342	T	0.67971	-0.5532	10	0.72032	D	0.01	.	9.7937	0.40722	0.0735:0.0:0.786:0.1406	.	290;250;250	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	K	250;290;250;155;155	ENSP00000349000:E250K;ENSP00000410732:E290K;ENSP00000354651:E250K;ENSP00000377510:E155K;ENSP00000430182:E155K	ENSP00000349000:E250K	E	+	1	0	GABRG2	161463589	1.000000	0.71417	0.515000	0.27774	0.583000	0.36354	6.454000	0.73493	0.639000	0.30564	0.655000	0.94253	GAA		0.378	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161531011	G	A	161531011	3	1	61	1	0	0	0	0	1	0	0	0	6191	1059	37	1	894	1	GABRG2	5	161531011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99	161531011	19384249	4321	12306										
CCNG1	900	broad.mit.edu	37	chr5	162866403	162866403	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgataatggcctcagaatGactgcaagactaagggactt	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:162866403G>T	ENST00000340828.2	+	2	365	c.141G>T	c.(139-141)atG>atT	p.M47I	RP11-541P9.3_ENST00000458002.2_RNA|CCNG1_ENST00000511683.2_Intron|CCNG1_ENST00000504553.1_5'Flank|CCNG1_ENST00000510664.1_Intron|CCNG1_ENST00000512163.1_Intron|CCNG1_ENST00000393929.1_Missense_Mutation_p.M47I|RP11-541P9.3_ENST00000503504.1_RNA	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	47					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.M47I(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		GCCTCAGAATGACTGCAAGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											132	124	127					5																	162866403		2203	4300	6503	162798981	SO:0001583	missense	900			D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.141G>T	5.37:g.162866403G>T	ENSP00000344635:p.Met47Ile		162798981	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Missense_Mutation	SNP	ENST00000340828.2	37	CCDS4360.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556541	0.45487	.	.	ENSG00000113328	ENST00000393929;ENST00000340828;ENST00000510097;ENST00000511490	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.01	5.01	0.66863	Cyclin, N-terminal (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.07458	0.0188	N	0.05351	-0.065	0.80722	D	1	B	0.19073	0.033	B	0.18263	0.021	T	0.11591	-1.0581	10	0.02654	T	1	-0.4491	18.3492	0.90331	0.0:0.0:1.0:0.0	.	47	P51959	CCNG1_HUMAN	I	47	ENSP00000377506:M47I;ENSP00000344635:M47I;ENSP00000423791:M47I;ENSP00000421132:M47I	ENSP00000344635:M47I	M	+	3	0	CCNG1	162798981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.283000	0.95860	2.332000	0.79248	0.467000	0.42956	ATG		0.428	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		T	162866403	G	T	162866403	3	4	61	1	0	0	0	0	1	0	0	0	2929	1290	45	2	143	2	CCNG1	5	162866403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1335392	162866403	18048857	4322	12307										
MAT2B	27430	broad.mit.edu	37	chr5	162945236	162945236	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaggagcacaacgtccgaGaaatgctcagcttgactgct	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:162945236G>T	ENST00000321757.6	+	7	1011	c.872G>T	c.(871-873)aGa>aTa	p.R291I	MAT2B_ENST00000521838.2_3'UTR|MAT2B_ENST00000280969.5_Missense_Mutation_p.R280I|MAT2B_ENST00000518095.1_3'UTR	NM_013283.3	NP_037415.1	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta	291					cellular nitrogen compound metabolic process (GO:0034641)|extracellular polysaccharide biosynthetic process (GO:0045226)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|regulation of catalytic activity (GO:0050790)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|methionine adenosyltransferase complex (GO:0048269)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dTDP-4-dehydrorhamnose reductase activity (GO:0008831)|enzyme binding (GO:0019899)|methionine adenosyltransferase regulator activity (GO:0048270)	p.R280I(1)		endometrium(3)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	14	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)	CAACGTCCGAGAAATGCTCAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											82	76	78					5																	162945236		2203	4300	6503	162877814	SO:0001583	missense	27430			AF182814	CCDS4364.1, CCDS4365.1	5q34-q35	2011-09-14			ENSG00000038274	ENSG00000038274		"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	6905	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 23E, member 1"	605527				9055605, 10644686, 19027726	Standard	NM_182796		Approved	MATIIbeta, SDR23E1	uc003lzk.4	Q9NZL9	OTTHUMG00000130379	ENST00000321757.6:c.872G>T	5.37:g.162945236G>T	ENSP00000325425:p.Arg291Ile		162877814	B2R5Y6|Q1WAI7|Q27J92|Q3LIE8|Q567T7|Q6NYC7|Q9BS89|Q9H3E1|Q9UJ54	Missense_Mutation	SNP	ENST00000321757.6	37	CCDS4365.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.885727	0.33255	.	.	ENSG00000038274	ENST00000280969;ENST00000321757;ENST00000415433	T;T	0.44881	0.91;0.91	6.07	3.34	0.38264	.	0.310535	0.35708	N	0.003036	T	0.37517	0.1006	M	0.62088	1.915	0.23043	N	0.998384	B;B	0.11235	0.004;0.002	B;B	0.14578	0.011;0.004	T	0.26121	-1.0112	10	0.23302	T	0.38	.	10.2629	0.43438	0.3231:0.0:0.6769:0.0	.	291;280	Q9NZL9;Q9NZL9-2	MAT2B_HUMAN;.	I	280;291;185	ENSP00000280969:R280I;ENSP00000325425:R291I	ENSP00000280969:R280I	R	+	2	0	MAT2B	162877814	0.624000	0.27102	0.986000	0.45419	0.984000	0.73092	0.428000	0.21395	0.442000	0.26555	0.655000	0.94253	AGA		0.408	MAT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252749.2	NM_013283		T	162945236	G	T	162945236	3	4	61	1	0	0	0	0	1	0	0	0	9361	942	33	2	932	2	MAT2B	5	162945236	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78833	162945236	17970024	4323	12308										
ODZ2	57451	broad.mit.edu	37	chr5	167622189	167622189	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctttctcagcttggtttCtctcatccgaggccaagtag	9	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167622189C>A	ENST00000518659.1	+	15	2828	c.2789C>A	c.(2788-2790)tCt>tAt	p.S930Y	TENM2_ENST00000519204.1_Missense_Mutation_p.S809Y|TENM2_ENST00000520394.1_Missense_Mutation_p.S698Y|TENM2_ENST00000403607.2_Missense_Mutation_p.S754Y|TENM2_ENST00000545108.1_Missense_Mutation_p.S930Y	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	930					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.S763Y(1)|p.S930Y(1)									AGCTTGGTTTCTCTCATCCGA	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	5											93	96	95					5																	167622189		1988	4173	6161	167554767	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.2789C>A	5.37:g.167622189C>A	ENSP00000429430:p.Ser930Tyr		167554767	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	23.3	4.401024	0.83120	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.92699	-2.6;-2.6;-2.72;-3.07;-3.09	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.96097	0.8728	M	0.74467	2.265	0.52099	D	0.999944	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.992	D	0.96158	0.9113	10	0.87932	D	0	.	19.7096	0.96089	0.0:1.0:0.0:0.0	.	930;930;698	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Y	930;930;809;698;754	ENSP00000429430:S930Y;ENSP00000438635:S930Y;ENSP00000428964:S809Y;ENSP00000427874:S698Y;ENSP00000384905:S754Y	ENSP00000384905:S754Y	S	+	2	0	ODZ2	167554767	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.007000	0.70731	2.652000	0.90054	0.655000	0.94253	TCT		0.512	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167622189	C	A	167622189	3	1	61	1	0	0	0	0	1	0	0	0	10866	913	32	2	2820	2	ODZ2	5	167622189	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4676953	167622189	13293071	4324	12309										
ODZ2	57451	broad.mit.edu	37	chr5	167630770	167630770	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccctccttcagggattCgagctggacccctccaacct	8	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167630770C>T	ENST00000518659.1	+	18	3546	c.3507C>T	c.(3505-3507)ttC>ttT	p.F1169F	TENM2_ENST00000519204.1_Silent_p.F1048F|TENM2_ENST00000520394.1_Silent_p.F937F|TENM2_ENST00000403607.2_Silent_p.F993F|TENM2_ENST00000545108.1_Silent_p.F1169F	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1169					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.F1002F(1)|p.F1169F(1)									TTCAGGGATTCGAGCTGGACC	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	5											144	137	139					5																	167630770		1880	4103	5983	167563348	SO:0001819	synonymous_variant	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3507C>T	5.37:g.167630770C>T			167563348	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																					0.498	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167630770	C	T	167630770	2	4	61	1	0	0	0	0	0	0	0	1	10866	883	31	1		1	ODZ2	5	167630770	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8581	167630770	13284490	4325	12310										
ODZ2	57451	broad.mit.edu	37	chr5	167645807	167645807	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatgggaattccctgaaGatccgtcgggacagcagtgg	13	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167645807G>T	ENST00000518659.1	+	23	4950	c.4911G>T	c.(4909-4911)aaG>aaT	p.K1637N	TENM2_ENST00000519204.1_Missense_Mutation_p.K1516N|TENM2_ENST00000520394.1_Missense_Mutation_p.K1398N|TENM2_ENST00000403607.2_Missense_Mutation_p.K1461N|TENM2_ENST00000545108.1_Missense_Mutation_p.K1636N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1637					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.K1637N(1)|p.K1470N(1)									ATTCCCTGAAGATCCGTCGGG	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	5											129	130	129					5																	167645807		2053	4204	6257	167578385	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4911G>T	5.37:g.167645807G>T	ENSP00000429430:p.Lys1637Asn		167578385	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	13.03	2.116808	0.37339	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.56776	1.53;0.44;1.53;1.53;1.53	5.85	5.85	0.93711	.	0.084363	0.85682	D	0.000000	T	0.47021	0.1423	L	0.29908	0.895	0.49915	D	0.999834	P;P;P	0.48640	0.913;0.858;0.873	P;B;P	0.50314	0.637;0.434;0.544	T	0.25047	-1.0143	10	0.19147	T	0.46	.	10.5201	0.44914	0.143:0.0:0.857:0.0	.	1636;1637;1398	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	N	1637;1636;1516;1398;1461	ENSP00000429430:K1637N;ENSP00000438635:K1636N;ENSP00000428964:K1516N;ENSP00000427874:K1398N;ENSP00000384905:K1461N	ENSP00000384905:K1461N	K	+	3	2	ODZ2	167578385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.145000	0.58065	2.767000	0.95098	0.655000	0.94253	AAG		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167645807	G	T	167645807	3	4	61	1	0	0	0	0	1	0	0	0	10866	933	33	2	4974	2	ODZ2	5	167645807	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15037	167645807	13269453	4326	12311										
ODZ2	57451	broad.mit.edu	37	chr5	167689735	167689735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgagggatattacgtgcttCccgtggagcaatacccagag	12	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167689735C>T	ENST00000518659.1	+	29	8284	c.8245C>T	c.(8245-8247)Ccc>Tcc	p.P2749S	TENM2_ENST00000519204.1_Missense_Mutation_p.P2628S|TENM2_ENST00000520394.1_Missense_Mutation_p.P2510S|TENM2_ENST00000403607.2_Missense_Mutation_p.P2573S|TENM2_ENST00000545108.1_Missense_Mutation_p.P2748S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2749					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.P2749S(1)|p.P2582S(1)									TTACGTGCTTCCCGTGGAGCA	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	5											35	37	37					5																	167689735		2020	4177	6197	167622313	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.8245C>T	5.37:g.167689735C>T	ENSP00000429430:p.Pro2749Ser		167622313	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	0.833	-0.744665	0.03065	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.87491	-1.78;-1.77;-1.88;-2.26;-2.25	5.25	5.25	0.73442	.	0.194658	0.56097	N	0.000031	D	0.82444	0.5038	N	0.02213	-0.635	0.54753	D	0.999987	B;B;D	0.67145	0.15;0.016;0.996	B;B;D	0.78314	0.085;0.028;0.991	T	0.77632	-0.2515	10	0.02654	T	1	.	19.1991	0.93704	0.0:1.0:0.0:0.0	.	2748;2749;2510	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2749;2748;2628;2510;2573	ENSP00000429430:P2749S;ENSP00000438635:P2748S;ENSP00000428964:P2628S;ENSP00000427874:P2510S;ENSP00000384905:P2573S	ENSP00000384905:P2573S	P	+	1	0	ODZ2	167622313	1.000000	0.71417	0.883000	0.34634	0.730000	0.41778	5.968000	0.70413	2.620000	0.88729	0.561000	0.74099	CCC		0.542	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167689735	C	T	167689735	3	4	61	1	0	0	0	0	1	0	0	0	10866	855	30	3	8332	3	ODZ2	5	167689735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43928	167689735	13225525	4327	12312										
WWC1	23286	broad.mit.edu	37	chr5	167855774	167855774	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagcagtgggtgcgacccGaattcagattgccctgaagt	14	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167855774G>T	ENST00000265293.4	+	13	2484	c.1982G>T	c.(1981-1983)cGa>cTa	p.R661L	WWC1_ENST00000521089.1_Missense_Mutation_p.R661L	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	661	C2.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)	p.R661L(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GGTGCGACCCGAATTCAGATT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											128	119	122					5																	167855774		2203	4300	6503	167788352	SO:0001583	missense	23286			AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.1982G>T	5.37:g.167855774G>T	ENSP00000265293:p.Arg661Leu		167788352	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.188694	0.38609	.	.	ENSG00000113645	ENST00000265293;ENST00000521089	T;T	0.19669	2.13;2.13	5.56	3.76	0.43208	C2 calcium/lipid-binding domain, CaLB (1);	0.208186	0.40469	N	0.001083	T	0.14356	0.0347	L	0.40543	1.245	0.38685	D	0.952623	B;B;B;B	0.32573	0.376;0.123;0.094;0.075	B;B;B;B	0.19666	0.016;0.026;0.018;0.006	T	0.08513	-1.0718	10	0.87932	D	0	.	7.236	0.26070	0.3728:0.0:0.6272:0.0	.	661;567;567;661	Q8IX03-2;F5H498;B3KX05;Q8IX03	.;.;.;KIBRA_HUMAN	L	661	ENSP00000265293:R661L;ENSP00000427772:R661L	ENSP00000265293:R661L	R	+	2	0	WWC1	167788352	1.000000	0.71417	0.886000	0.34754	0.648000	0.38561	2.040000	0.41203	0.687000	0.31509	0.561000	0.74099	CGA		0.547	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		T	167855774	G	T	167855774	3	4	61	1	0	0	0	0	1	0	0	0	17451	1058	37	2	2032	2	WWC1	5	167855774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166039	167855774	13059486	4328	12313										
WWC1	23286	broad.mit.edu	37	chr5	167858408	167858408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagaagaccttaagagtcGatgtctgtaccaccgacagg	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167858408G>A	ENST00000265293.4	+	15	2741	c.2239G>A	c.(2239-2241)Gat>Aat	p.D747N	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Missense_Mutation_p.D747N	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	747	C2.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)	p.D747N(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CTTAAGAGTCGATGTCTGTAC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											61	55	57					5																	167858408		2203	4300	6503	167790986	SO:0001583	missense	23286			AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2239G>A	5.37:g.167858408G>A	ENSP00000265293:p.Asp747Asn		167790986	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.50|19.50	3.838425|3.838425	0.71373|0.71373	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038|ENST00000393895;ENST00000524228	T;T;T|.	0.33438|.	1.41;1.41;1.41|.	5.24|5.24	5.24|5.24	0.73138|0.73138	C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71375|0.71375	0.3332|0.3332	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	D;D;P;D|.	0.89917|.	1.0;1.0;0.862;1.0|.	D;D;P;D|.	0.91635|.	0.979;0.999;0.514;0.997|.	T|T	0.68674|0.68674	-0.5346|-0.5346	10|5	0.30078|.	T|.	0.28|.	.|.	18.8505|18.8505	0.92227|0.92227	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	747;653;653;747|.	Q8IX03-2;F5H498;B3KX05;Q8IX03|.	.;.;.;KIBRA_HUMAN|.	N|Q	747;747;73|708;523	ENSP00000265293:D747N;ENSP00000427772:D747N;ENSP00000428084:D73N|.	ENSP00000265293:D747N|.	D|R	+|+	1|2	0|0	WWC1|WWC1	167790986|167790986	1.000000|1.000000	0.71417|0.71417	0.866000|0.866000	0.34008|0.34008	0.990000|0.990000	0.78478|0.78478	8.950000|8.950000	0.93019|0.93019	2.440000|2.440000	0.82611|0.82611	0.655000|0.655000	0.94253|0.94253	GAT|CGA		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		A	167858408	G	A	167858408	3	1	61	1	0	0	0	0	1	0	0	0	17451	1058	37	1	2297	1	WWC1	5	167858408	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2634	167858408	13056852	4329	12314										
RARS	5917	broad.mit.edu	37	chr5	167915736	167915736	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtatcgactgaatattcttCgaaaggtgagtactttgggt	11	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167915736C>T	ENST00000231572.3	+	2	229	c.175C>T	c.(175-177)Cga>Tga	p.R59*	RARS_ENST00000538719.1_5'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	59	Could be involved in the assembly of the multisynthetase complex.				arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R59*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GAATATTCTTCGAAAGGTGAG	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											51	55	54					5																	167915736		2199	4298	6497	167848314	SO:0001587	stop_gained	5917			BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.175C>T	5.37:g.167915736C>T	ENSP00000231572:p.Arg59*		167848314	B2RBS9|Q53GY4|Q9BWA1	Nonsense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033018	0.75504	.	.	ENSG00000113643	ENST00000231572	.	.	.	5.64	5.64	0.86602	.	0.547455	0.19868	N	0.104265	.	.	.	.	.	.	0.31047	N	0.715684	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-25.4974	15.0818	0.72119	0.2091:0.7909:0.0:0.0	.	.	.	.	X	59	.	ENSP00000231572:R59X	R	+	1	2	RARS	167848314	0.214000	0.23563	0.686000	0.30086	0.318000	0.28184	1.955000	0.40372	2.655000	0.90218	0.462000	0.41574	CGA		0.338	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		T	167915736	C	T	167915736	4	4	61	1	0	0	0	0	0	1	0	0	13095	876	31	1	181	1	RARS	5	167915736	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57328	167915736	12999524	4330	12315										
PANK3	79646	broad.mit.edu	37	chr5	167990927	167990927	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaacctggcaaaccaaatCtttcataatctcctccataa	2	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:167990927C>A	ENST00000239231.6	-	4	1095	c.779G>T	c.(778-780)aGa>aTa	p.R260I	PANK3_ENST00000520504.1_Intron|MIR103A1_ENST00000362165.1_RNA	NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	260					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.R260I(2)		NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CAAACCAAATCTTTCATAATC	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	5											116	121	119					5																	167990927		2203	4300	6503	167923505	SO:0001583	missense	79646			AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137			19365	protein-coding gene	gene with protein product		606161				11479594	Standard	NM_024594		Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.779G>T	5.37:g.167990927C>A	ENSP00000239231:p.Arg260Ile		167923505	D3DQL1|Q53FJ9|Q7RTX4	Missense_Mutation	SNP	ENST00000239231.6	37	CCDS4368.1	.	.	.	.	.	.	.	.	.	.	C	34	5.310934	0.95629	.	.	ENSG00000120137	ENST00000239231	D	0.99567	-6.18	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.99542	0.9836	M	0.85197	2.74	0.80722	D	1	P	0.45240	0.854	P	0.57009	0.811	D	0.98036	1.0379	10	0.62326	D	0.03	-16.5051	17.4478	0.87583	0.0:1.0:0.0:0.0	.	260	Q9H999	PANK3_HUMAN	I	260	ENSP00000239231:R260I	ENSP00000239231:R260I	R	-	2	0	PANK3	167923505	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.669000	0.83911	2.432000	0.82394	0.591000	0.81541	AGA		0.383	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252793.2	NM_024594		A	167990927	C	A	167990927	3	1	61	1	0	0	0	0	1	0	0	0	11449	913	32	2	349	2	PANK3	5	167990927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75191	167990927	12924333	4331	12316										
SLIT3	6586	broad.mit.edu	37	chr5	168180044	168180044	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagggacagcagtctcaccGaactcaggccggcaaaggtg	14	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:168180044G>A	ENST00000519560.1	-	18	2308	c.1889C>T	c.(1888-1890)tCg>tTg	p.S630L	SLIT3_ENST00000332966.8_Missense_Mutation_p.S630L|SLIT3_ENST00000404867.3_Missense_Mutation_p.S630L	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	630					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.S630L(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGTCTCACCGAACTCAGGCC	0.557																																					Ovarian(29;311 847 10864 17279 24903)											1	Substitution - Missense(1)	large_intestine(1)	5											143	101	115					5																	168180044		2203	4300	6503	168112622	SO:0001583	missense	6586			AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1889C>T	5.37:g.168180044G>A	ENSP00000430333:p.Ser630Leu		168112622	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.673086	0.88445	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.59906	0.23;0.23;0.23	5.34	4.46	0.54185	.	0.307696	0.36628	N	0.002487	T	0.65344	0.2682	L	0.37800	1.135	0.80722	D	1	D	0.76494	0.999	D	0.66084	0.941	T	0.68743	-0.5328	10	0.87932	D	0	.	13.7188	0.62714	0.0741:0.0:0.9259:0.0	.	630	O75094	SLIT3_HUMAN	L	630	ENSP00000430333:S630L;ENSP00000332164:S630L;ENSP00000384890:S630L	ENSP00000332164:S630L	S	-	2	0	SLIT3	168112622	1.000000	0.71417	0.160000	0.22671	0.904000	0.53231	8.008000	0.88588	1.253000	0.44018	0.655000	0.94253	TCG		0.557	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168180044	G	A	168180044	3	1	61	1	0	0	0	0	1	0	0	0	14778	1059	37	1	2758	1	SLIT3	5	168180044	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189117	168180044	12735216	4332	12317										
CCDC99	54908	broad.mit.edu	37	chr5	169018215	169018215	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatggacaggaagtgaatgAactaaaaactaaggttggga	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169018215A>G	ENST00000265295.4	+	3	602	c.323A>G	c.(322-324)gAa>gGa	p.E108G	SPDL1_ENST00000510751.1_3'UTR	NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1									p.E108G(1)									GAAGTGAATGAACTAAAAACT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											101	104	103					5																	169018215		2203	4300	6503	168950793	SO:0001583	missense	54908			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.323A>G	5.37:g.169018215A>G	ENSP00000265295:p.Glu108Gly		168950793		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.25|11.25	1.582203|1.582203	0.28180|0.28180	.|.	.|.	ENSG00000040275|ENSG00000040275	ENST00000265295;ENST00000274631;ENST00000508247;ENST00000513941;ENST00000513795|ENST00000505977	T|.	0.35421|.	1.31|.	5.37|5.37	2.81|2.81	0.32909|0.32909	.|.	0.253208|.	0.45126|.	N|.	0.000387|.	T|.	0.44912|.	0.1316|.	L|L	0.35854|0.35854	1.095|1.095	0.36859|0.36859	D|D	0.88831|0.88831	B;B|.	0.30455|.	0.28;0.082|.	B;B|.	0.31337|.	0.128;0.058|.	T|.	0.39187|.	-0.9626|.	10|.	0.38643|.	T|.	0.18|.	-5.0538|-5.0538	7.538|7.538	0.27721|0.27721	0.8037:0.0:0.0698:0.1266|0.8037:0.0:0.0698:0.1266	.|.	108;108|.	Q96EA4-2;Q96EA4|.	.;SPDLY_HUMAN|.	G|W	108|36	ENSP00000265295:E108G|.	ENSP00000265295:E108G|.	E|X	+|+	2|3	0|0	CCDC99|CCDC99	168950793|168950793	1.000000|1.000000	0.71417|0.71417	0.132000|0.132000	0.22025|0.22025	0.439000|0.439000	0.31926|0.31926	4.866000|4.866000	0.63005|0.63005	0.352000|0.352000	0.24053|0.24053	0.533000|0.533000	0.62120|0.62120	GAA|TGA		0.353	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		G	169018215	A	G	169018215	3	3	61	1	0	0	0	0	1	0	0	0	2882	246	9	4	329	4	CCDC99	5	169018215	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	838171	169018215	11897045	4333	12318										
CCDC99	54908	broad.mit.edu	37	chr5	169025500	169025500	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttatatgacagtatggaAtctaagccttcagtcgactc	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169025500A>C	ENST00000265295.4	+	9	1332	c.1053A>C	c.(1051-1053)gaA>gaC	p.E351D		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1									p.E351D(1)									ACAGTATGGAATCTAAGCCTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											117	123	121					5																	169025500		2203	4300	6503	168958078	SO:0001583	missense	54908			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1053A>C	5.37:g.169025500A>C	ENSP00000265295:p.Glu351Asp		168958078		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.01|17.01	3.280191|3.280191	0.59758|0.59758	.|.	.|.	ENSG00000040275|ENSG00000040275	ENST00000265295;ENST00000274631|ENST00000505977	T|.	0.35605|.	1.3|.	5.85|5.85	3.45|3.45	0.39498|0.39498	.|.	0.342683|.	0.32852|.	N|.	0.005567|.	T|T	0.43897|0.43897	0.1268|0.1268	M|M	0.64997|0.64997	1.995|1.995	0.23210|0.23210	N|N	0.998114|0.998114	D;B;B|.	0.76494|.	0.999;0.021;0.021|.	D;B;B|.	0.66602|.	0.945;0.021;0.021|.	T|T	0.34950|0.34950	-0.9808|-0.9808	10|5	0.12430|.	T|.	0.62|.	-7.8548|-7.8548	5.3317|5.3317	0.15936|0.15936	0.7277:0.0:0.1419:0.1304|0.7277:0.0:0.1419:0.1304	.|.	273;252;351|.	B4E393;Q96EA4-2;Q96EA4|.	.;.;SPDLY_HUMAN|.	D|L	351;252|272	ENSP00000265295:E351D|.	ENSP00000265295:E351D|.	E|I	+|+	3|1	2|0	CCDC99|CCDC99	168958078|168958078	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.975000|0.975000	0.68041|0.68041	2.036000|2.036000	0.41165|0.41165	0.464000|0.464000	0.27142|0.27142	0.523000|0.523000	0.50628|0.50628	GAA|ATC		0.308	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		C	169025500	A	C	169025500	3	2	61	1	0	0	0	0	1	0	0	0	2882	98	4	4	1083	4	CCDC99	5	169025500	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7285	169025500	11889760	4334	12319										
CCDC99	54908	broad.mit.edu	37	chr5	169028293	169028293	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttattctcagagacagttgAagtgcctgtactgaaaaaga	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169028293A>G	ENST00000265295.4	+	11	1613	c.1334A>G	c.(1333-1335)gAa>gGa	p.E445G		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1									p.E445G(1)									GAGACAGTTGAAGTGCCTGTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	5											62	65	64					5																	169028293		2203	4300	6503	168960871	SO:0001583	missense	54908			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1334A>G	5.37:g.169028293A>G	ENSP00000265295:p.Glu445Gly		168960871		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.517019	0.27123	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.34859	1.34	5.77	3.32	0.38043	.	0.485116	0.23142	N	0.051442	T	0.29914	0.0748	L	0.51422	1.61	0.09310	N	1	B;B;B	0.28933	0.228;0.003;0.005	B;B;B	0.30855	0.121;0.004;0.004	T	0.22941	-1.0202	10	0.46703	T	0.11	-0.5429	5.8003	0.18410	0.7384:0.0:0.1365:0.1251	.	367;346;445	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	G	445;346	ENSP00000265295:E445G	ENSP00000265295:E445G	E	+	2	0	CCDC99	168960871	1.000000	0.71417	0.721000	0.30653	0.563000	0.35712	3.484000	0.53201	0.422000	0.26005	-0.262000	0.10625	GAA		0.413	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		G	169028293	A	G	169028293	3	3	61	1	0	0	0	0	1	0	0	0	2882	246	9	4	1372	4	CCDC99	5	169028293	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2793	169028293	11886967	4335	12320										
DOCK2	1794	broad.mit.edu	37	chr5	169122929	169122929	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcagggactgaggaggccCtttggggtggcaggtaaggg	20	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169122929C>A	ENST00000256935.8	+	10	1046	c.966C>A	c.(964-966)ccC>ccA	p.P322P		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	322					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.P322P(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAGGAGGCCCTTTGGGGTGG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	5											66	68	68					5																	169122929		2203	4300	6503	169055507	SO:0001819	synonymous_variant	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.966C>A	5.37:g.169122929C>A			169055507	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.463	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169122929	C	A	169122929	2	1	61	1	0	0	0	0	0	0	0	1	4698	668	24	2		2	DOCK2	5	169122929	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94636	169122929	11792331	4336	12321										
DOCK2	1794	broad.mit.edu	37	chr5	169141039	169141039	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttgtttccagggggacaGcaagaagatggaggatgcca	16	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169141039G>A	ENST00000256935.8	+	18	1747	c.1667G>A	c.(1666-1668)aGc>aAc	p.S556N	DOCK2_ENST00000520908.1_Missense_Mutation_p.S48N|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	556	DHR-1.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.S556N(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGGGGGACAGCAAGAAGATG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	66	67					5																	169141039		2203	4300	6503	169073617	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.1667G>A	5.37:g.169141039G>A	ENSP00000256935:p.Ser556Asn		169073617	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	7.134	0.580399	0.13686	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908	T;T	0.13778	2.56;3.3	5.9	5.9	0.94986	.	0.074541	0.85682	D	0.000000	T	0.24774	0.0601	L	0.28776	0.89	0.80722	D	1	D;B;D	0.71674	0.998;0.198;0.98	D;B;P	0.77557	0.99;0.085;0.833	T	0.01630	-1.1308	10	0.06494	T	0.89	.	20.2768	0.98488	0.0:0.0:1.0:0.0	.	48;556;556	E7ERW7;E5RFJ0;Q92608	.;.;DOCK2_HUMAN	N	556;74;48	ENSP00000256935:S556N;ENSP00000429283:S48N	ENSP00000256935:S556N	S	+	2	0	DOCK2	169073617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.537000	0.60643	2.797000	0.96272	0.655000	0.94253	AGC		0.547	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169141039	G	A	169141039	3	1	61	1	0	0	0	0	1	0	0	0	4698	971	34	3	1737	3	DOCK2	5	169141039	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18110	169141039	11774221	4337	12322										
DOCK2	1794	broad.mit.edu	37	chr5	169477280	169477280	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaagtgttcatctaccgCgggaaggaatatgagcgaag	12	7	2	1	rs142465529		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169477280C>T	ENST00000256935.8	+	41	4172	c.4092C>T	c.(4090-4092)cgC>cgT	p.R1364R	DOCK2_ENST00000520908.1_Silent_p.R856R|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.R425R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1364	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R1364R(2)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCATCTACCGCGGGAAGGAAT	0.507																																																2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	5						C		3,4403	6.2+/-15.9	0,3,2200	142	145	144		4092	-10.1	0.9	5	dbSNP_134	144	0,8600		0,0,4300	no	coding-synonymous	DOCK2	NM_004946.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		1364/1831	169477280	3,13003	2203	4300	6503	169409858	SO:0001819	synonymous_variant	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4092C>T	5.37:g.169477280C>T			169409858	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.507	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169477280	C	T	169477280	2	4	61	1	0	0	0	0	0	0	0	1	4698	755	27	1		1	DOCK2	5	169477280	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336241	169477280	11437980	4338	12323										
LCP2	3937	broad.mit.edu	37	chr5	169693867	169693867	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgatctaggggaggtttCgtgcttctgtctattgaagg	14	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:169693867C>T	ENST00000046794.5	-	10	1332	c.717G>A	c.(715-717)acG>acA	p.T239T	LCP2_ENST00000521416.1_Silent_p.T34T	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	239					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)		p.T239T(2)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	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)		GGGGAGGTTTCGTGCTTCTGT	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	5											232	228	229					5																	169693867		1872	4095	5967	169626445	SO:0001819	synonymous_variant	3937				CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.717G>A	5.37:g.169693867C>T			169626445	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																				0.468	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		T	169693867	C	T	169693867	2	4	61	1	0	0	0	0	0	0	0	1	8714	871	31	1		1	LCP2	5	169693867	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	216587	169693867	11221393	4339	12324										
KCNIP1	30820	broad.mit.edu	37	chr5	170139862	170139862	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcactctttcctagacatCgcctggtggtattaccagta	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170139862C>T	ENST00000411494.1	+	2	66	c.66C>T	c.(64-66)atC>atT	p.I22I	KCNIP1_ENST00000434108.1_Intron|KCNIP1_ENST00000520740.1_Intron|KCNIP1_ENST00000328939.4_Intron|KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000390656.4_Intron			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	22					detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)	p.I22I(1)		autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCTAGACATCGCCTGGTGGT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	5											175	165	168					5																	170139862		2203	4300	6503	170072440	SO:0001819	synonymous_variant	30820			AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.66C>T	5.37:g.170139862C>T			170072440	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Silent	SNP	ENST00000411494.1	37	CCDS34286.1																																																																																				0.413	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			T	170139862	C	T	170139862	2	4	61	1	0	0	0	0	0	0	0	1	8060	874	31	1		1	KCNIP1	5	170139862	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	445995	170139862	10775398	4340	12325										
KCNIP1	30820	broad.mit.edu	37	chr5	170148874	170148874	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattacctcttcaatgccttCgacaccactcagacaggctc	5	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170148874C>T	ENST00000411494.1	+	5	327	c.327C>T	c.(325-327)ttC>ttT	p.F109F	KCNIP1_ENST00000434108.1_Silent_p.F123F|KCNIP1_ENST00000520740.1_Silent_p.F70F|KCNIP1_ENST00000328939.4_Silent_p.F98F|KCNIP1_ENST00000377360.4_Silent_p.F107F|KCNIP1_ENST00000390656.4_Silent_p.F98F			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	109	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)	p.F109F(1)		autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCAATGCCTTCGACACCACTC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	5											243	214	224					5																	170148874		2203	4300	6503	170081452	SO:0001819	synonymous_variant	30820			AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.327C>T	5.37:g.170148874C>T			170081452	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Silent	SNP	ENST00000411494.1	37	CCDS34286.1																																																																																				0.547	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			T	170148874	C	T	170148874	2	4	61	1	0	0	0	0	0	0	0	1	8060	883	31	1		1	KCNIP1	5	170148874	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9012	170148874	10766386	4341	12326										
RANBP17	64901	broad.mit.edu	37	chr5	170395343	170395343	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcttggatcagtttcgtAaaacatatgttggtgatcaa	10	5	3	1	rs372324017		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170395343A>C	ENST00000523189.1	+	14	1836	c.1672A>C	c.(1672-1674)Aaa>Caa	p.K558Q		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	558					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.K558Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCAGTTTCGTAAAACATATGT	0.343			T	TRD@	ALL																																		Dom	yes		5	5q34	64901	RAN binding protein 17		L	1	Substitution - Missense(1)	large_intestine(1)	5											85	87	87					5																	170395343		2203	4300	6503	170327948	SO:0001583	missense	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1672A>C	5.37:g.170395343A>C	ENSP00000427975:p.Lys558Gln		170327948	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425510	0.62733	.	.	ENSG00000204764	ENST00000523189;ENST00000545246	T	0.68181	-0.31	5.67	5.67	0.87782	Armadillo-type fold (1);	0.000000	0.64402	D	0.000009	D	0.83922	0.5359	M	0.89287	3.02	0.42039	D	0.991067	D	0.76494	0.999	D	0.75484	0.986	D	0.87212	0.2248	10	0.72032	D	0.01	-19.8415	14.1338	0.65273	1.0:0.0:0.0:0.0	.	558	Q9H2T7	RBP17_HUMAN	Q	558;454	ENSP00000427975:K558Q	ENSP00000373770:K558Q	K	+	1	0	RANBP17	170327948	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.560000	0.73950	2.158000	0.67659	0.482000	0.46254	AAA		0.343	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		C	170395343	A	C	170395343	3	2	61	1	0	0	0	0	1	0	0	0	13064	363	13	4	1726	4	RANBP17	5	170395343	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	246469	170395343	10519917	4342	12327										
RANBP17	64901	broad.mit.edu	37	chr5	170610373	170610373	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgacaatcatagtctcagCgacttcaggtgtcgaacaac	9	10	3	1	rs140812950	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170610373C>T	ENST00000523189.1	+	18	2141	c.1977C>T	c.(1975-1977)agC>agT	p.S659S	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	659					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.S659S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATAGTCTCAGCGACTTCAGGT	0.403			T	TRD@	ALL								C|||	15	0.00299521	0.0106	0.0014	5008	,	,		16524	0		0	False		,,,				2504	0						Dom	yes		5	5q34	64901	RAN binding protein 17		L	1	Substitution - coding silent(1)	large_intestine(1)	5						C		69,4337	61.7+/-98.7	1,67,2135	115	101	106		1977	-0.3	1	5	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RANBP17	NM_022897.3		1,68,6434	TT,TC,CC		0.0116,1.566,0.5382		659/1089	170610373	70,12936	2203	4300	6503	170542978	SO:0001819	synonymous_variant	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1977C>T	5.37:g.170610373C>T			170542978	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																				0.403	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		T	170610373	C	T	170610373	2	4	61	1	0	0	0	0	0	0	0	1	13064	767	27	1		1	RANBP17	5	170610373	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	215030	170610373	10304887	4343	12328										
RANBP17	64901	broad.mit.edu	37	chr5	170626766	170626766	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacaacaactttaaacaaGaagatgtaaaggtgggtttg	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170626766G>T	ENST00000523189.1	+	19	2295	c.2131G>T	c.(2131-2133)Gaa>Taa	p.E711*	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	711					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.E711*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTTTAAACAAGAAGATGTAAA	0.343			T	TRD@	ALL																																		Dom	yes		5	5q34	64901	RAN binding protein 17		L	1	Substitution - Nonsense(1)	large_intestine(1)	5											96	95	96					5																	170626766		2203	4300	6503	170559371	SO:0001587	stop_gained	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.2131G>T	5.37:g.170626766G>T	ENSP00000427975:p.Glu711*		170559371	Q8IU74	Nonsense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	G	38	7.130979	0.98085	.	.	ENSG00000204764	ENST00000523189;ENST00000534916	.	.	.	6.17	6.17	0.99709	.	0.092825	0.46442	D	0.000289	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-10.2823	16.2608	0.82541	0.0:0.1316:0.8683:0.0	.	.	.	.	X	711;141	.	ENSP00000427975:E711X	E	+	1	0	RANBP17	170559371	1.000000	0.71417	0.990000	0.47175	0.835000	0.47333	4.122000	0.57910	2.941000	0.99782	0.655000	0.94253	GAA		0.343	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		T	170626766	G	T	170626766	4	4	61	1	0	0	0	0	0	1	0	0	13064	943	33	2	2205	2	RANBP17	5	170626766	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16393	170626766	10288494	4344	12329										
RANBP17	64901	broad.mit.edu	37	chr5	170632558	170632558	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgggctggcaagagatcttCgagggattgcctttgcactg	14	9	1	1	rs200104921		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170632558C>T	ENST00000523189.1	+	20	2337	c.2173C>T	c.(2173-2175)Cga>Tga	p.R725*	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	725					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.R725*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AAGAGATCTTCGAGGGATTGC	0.463			T	TRD@	ALL								C|||	1	0.000199681	0	0.0014	5008	,	,		20704	0		0	False		,,,				2504	0						Dom	yes		5	5q34	64901	RAN binding protein 17		L	1	Substitution - Nonsense(1)	large_intestine(1)	5											199	168	179					5																	170632558		2203	4300	6503	170565163	SO:0001587	stop_gained	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.2173C>T	5.37:g.170632558C>T	ENSP00000427975:p.Arg725*		170565163	Q8IU74	Nonsense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	38	6.731075	0.97796	.	.	ENSG00000204764	ENST00000523189;ENST00000534916	.	.	.	5.96	5.96	0.96718	.	0.000000	0.49916	D	0.000130	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7285	20.017	0.97481	0.0:1.0:0.0:0.0	.	.	.	.	X	725;155	.	ENSP00000427975:R725X	R	+	1	2	RANBP17	170565163	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.878000	0.48515	2.832000	0.97577	0.655000	0.94253	CGA		0.463	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		T	170632558	C	T	170632558	4	4	61	1	0	0	0	0	0	1	0	0	13064	876	31	1	2251	1	RANBP17	5	170632558	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5792	170632558	10282702	4345	12330										
NPM1	4869	broad.mit.edu	37	chr5	170827867	170827867	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgagatactccagccaaaAatgcacaaaagtcaaatcag	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:170827867A>C	ENST00000296930.5	+	8	908	c.607A>C	c.(607-609)Aat>Cat	p.N203H	NPM1_ENST00000393820.2_Missense_Mutation_p.N203H|NPM1_ENST00000351986.6_Intron|NPM1_ENST00000517671.1_Missense_Mutation_p.N203H	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	203					cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.N203H(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCAGCCAAAAATGCACAAAA	0.388			"T, F "	"ALK, RARA, MLF1"	"NHL, APL, AML"																																		Dom	yes		5	5q35	4869	"nucleophosmin (nucleolar phosphoprotein B23, numatrin)"		L	1	Substitution - Missense(1)	large_intestine(1)	5											77	74	75					5																	170827867		2203	4300	6503	170760472	SO:0001583	missense	4869			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1"	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.607A>C	5.37:g.170827867A>C	ENSP00000296930:p.Asn203His		170760472	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Missense_Mutation	SNP	ENST00000296930.5	37	CCDS4376.1	.	.	.	.	.	.	.	.	.	.	A	18.76	3.692052	0.68271	.	.	ENSG00000181163	ENST00000517671;ENST00000296930;ENST00000393820	T;T;T	0.17528	2.27;2.27;2.27	4.39	4.39	0.52855	.	0.251786	0.38605	U	0.001623	T	0.25644	0.0624	M	0.85197	2.74	0.22601	N	0.998946	B;B	0.28233	0.204;0.094	B;B	0.27500	0.064;0.08	T	0.24548	-1.0157	10	0.72032	D	0.01	.	11.2959	0.49277	1.0:0.0:0.0:0.0	.	203;203	P06748;Q9BYG9	NPM_HUMAN;.	H	203	ENSP00000428755:N203H;ENSP00000296930:N203H;ENSP00000377408:N203H	ENSP00000296930:N203H	N	+	1	0	NPM1	170760472	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.985000	0.63845	1.747000	0.51819	0.459000	0.35465	AAT		0.388	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520		C	170827867	A	C	170827867	3	2	61	1	0	0	0	0	1	0	0	0	10618	14	1	4	637	4	NPM1	5	170827867	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	195309	170827867	10087393	4346	12331										
STK10	6793	broad.mit.edu	37	chr5	171517361	171517361	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtttttttgtacagtttCgggtcctggccagggaaaac	13	7	0	0	rs148086376		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:171517361C>T	ENST00000176763.5	-	10	1903	c.1560G>A	c.(1558-1560)ccG>ccA	p.P520P	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	520			P -> L (in dbSNP:rs17074311).		cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.P520P(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGTACAGTTTCGGGTCCTGGC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		1,4405	2.1+/-5.4	0,1,2202	191	178	183		1560	-9.2	0.1	5	dbSNP_134	183	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	STK10	NM_005990.3		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		520/969	171517361	3,13003	2203	4300	6503	171449966	SO:0001819	synonymous_variant	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1560G>A	5.37:g.171517361C>T			171449966	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																				0.532	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		T	171517361	C	T	171517361	2	4	61	1	0	0	0	0	0	0	0	1	15325	871	31	1		1	STK10	5	171517361	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	689494	171517361	9397899	4347	12332										
SH3PXD2B	285590	broad.mit.edu	37	chr5	171765783	171765783	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggacctctgacctctgGgagcggcctggatgacgaag	15	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:171765783G>T	ENST00000311601.5	-	13	2496	c.2326C>A	c.(2326-2328)Cca>Aca	p.P776T	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	776	Pro-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)	p.P776T(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGACCTCTGGGAGCGGCCTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	44	43					5																	171765783		2203	4300	6503	171698388	SO:0001583	missense	285590			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.2326C>A	5.37:g.171765783G>T	ENSP00000309714:p.Pro776Thr		171698388	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.257491	0.22965	.	.	ENSG00000174705	ENST00000311601	T	0.61510	0.1	5.29	4.41	0.53225	.	0.370433	0.28847	N	0.013942	T	0.43809	0.1264	L	0.32530	0.975	0.25513	N	0.987446	B	0.02656	0.0	B	0.04013	0.001	T	0.24190	-1.0167	9	.	.	.	-3.9149	10.9228	0.47174	0.0:0.0:0.6588:0.3412	.	776	A1X283	SPD2B_HUMAN	T	776	ENSP00000309714:P776T	.	P	-	1	0	SH3PXD2B	171698388	1.000000	0.71417	0.996000	0.52242	0.039000	0.13416	1.956000	0.40382	1.190000	0.43042	0.462000	0.41574	CCA		0.617	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		T	171765783	G	T	171765783	3	4	61	1	0	0	0	0	1	0	0	0	14294	1232	43	2	413	2	SH3PXD2B	5	171765783	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248422	171765783	9149477	4348	12333										
SH3PXD2B	285590	broad.mit.edu	37	chr5	171774307	171774307	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggtcatgtcccggcgagGagggggtctctgcctcatct	14	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:171774307G>T	ENST00000311601.5	-	11	1212	c.1042C>A	c.(1042-1044)Cct>Act	p.P348T	SH3PXD2B_ENST00000519643.1_Missense_Mutation_p.P348T	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	348					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)	p.P348T(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCCGGCGAGGAGGGGGTCTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	92	96					5																	171774307		2203	4300	6503	171706912	SO:0001583	missense	285590			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1042C>A	5.37:g.171774307G>T	ENSP00000309714:p.Pro348Thr		171706912	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280881	0.80692	.	.	ENSG00000174705	ENST00000519643;ENST00000311601	T;T	0.68181	0.25;-0.31	5.12	5.12	0.69794	.	0.056011	0.64402	D	0.000001	T	0.81024	0.4737	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82731	-0.0312	10	0.66056	D	0.02	-7.1639	16.4003	0.83639	0.0:0.0:1.0:0.0	.	348	A1X283	SPD2B_HUMAN	T	348	ENSP00000430890:P348T;ENSP00000309714:P348T	ENSP00000309714:P348T	P	-	1	0	SH3PXD2B	171706912	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.942000	0.92970	2.532000	0.85374	0.462000	0.41574	CCT		0.557	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		T	171774307	G	T	171774307	3	4	61	1	0	0	0	0	1	0	0	0	14294	1174	41	2	1705	2	SH3PXD2B	5	171774307	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8524	171774307	9140953	4349	12334										
C5orf41	153222	broad.mit.edu	37	chr5	172517654	172517654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgattccctttattaccccGattcacttttcagtgtcaaa	4	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:172517654G>A	ENST00000296953.2	+	4	791	c.472G>A	c.(472-474)Gat>Aat	p.D158N	CREBRF_ENST00000540014.1_Missense_Mutation_p.D158N|CREBRF_ENST00000520420.1_Missense_Mutation_p.D158N|CREBRF_ENST00000522692.1_Missense_Mutation_p.D158N	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	158					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D158N(1)									TTATTACCCCGATTCACTTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											84	79	81					5																	172517654		2203	4300	6503	172450260	SO:0001583	missense	153222			AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.472G>A	5.37:g.172517654G>A	ENSP00000296953:p.Asp158Asn		172450260	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	37	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321696	0.81580	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	6.08	6.08	0.98989	.	0.137944	0.64402	D	0.000005	T	0.63010	0.2475	L	0.27053	0.805	0.54753	D	0.999989	P;P	0.39624	0.456;0.681	B;B	0.36885	0.158;0.235	T	0.66575	-0.5889	10	0.72032	D	0.01	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	158;158	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	N	158	ENSP00000431107:D158N;ENSP00000296953:D158N;ENSP00000440075:D158N;ENSP00000428290:D158N	ENSP00000296953:D158N	D	+	1	0	C5orf41	172450260	1.000000	0.71417	0.919000	0.36401	0.961000	0.63080	7.639000	0.83342	2.894000	0.99253	0.655000	0.94253	GAT		0.403	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		A	172517654	G	A	172517654	3	1	61	1	0	0	0	0	1	0	0	0	2306	1058	37	1	482	1	C5orf41	5	172517654	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	743347	172517654	8397606	4350	12335										
C5orf41	153222	broad.mit.edu	37	chr5	172537650	172537650	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattagtgacctgactccaGtcagtgagcttcccttaaca	8	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:172537650G>T	ENST00000296953.2	+	6	1862	c.1543G>T	c.(1543-1545)Gtc>Ttc	p.V515F	CREBRF_ENST00000540014.1_Missense_Mutation_p.V517F	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	515					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V515F(1)									CCTGACTCCAGTCAGTGAGCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	72	72					5																	172537650		2203	4300	6503	172470256	SO:0001583	missense	153222			AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1543G>T	5.37:g.172537650G>T	ENSP00000296953:p.Val515Phe		172470256	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	37	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	G	33	5.202625	0.94997	.	.	ENSG00000164463	ENST00000296953;ENST00000540014;ENST00000538538;ENST00000393776	T;T	0.22945	1.93;1.93	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	M	0.67397	2.05	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.51857	-0.8652	10	0.87932	D	0	.	20.0545	0.97645	0.0:0.0:1.0:0.0	.	515	Q8IUR6	CE041_HUMAN	F	515;517;515;515	ENSP00000296953:V515F;ENSP00000440075:V517F	ENSP00000296953:V515F	V	+	1	0	C5orf41	172470256	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.858000	0.99539	2.748000	0.94277	0.655000	0.94253	GTC		0.423	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		T	172537650	G	T	172537650	3	4	61	1	0	0	0	0	1	0	0	0	2306	1029	36	2	1593	2	C5orf41	5	172537650	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19996	172537650	8377610	4351	12336										
STC2	8614	broad.mit.edu	37	chr5	172752877	172752877	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatggatttttacctgggcAtcaaattttccagcgttgtg	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:172752877A>G	ENST00000265087.4	-	2	1597	c.288T>C	c.(286-288)gaT>gaC	p.D96D	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	96					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.D96D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTACCTGGGCATCAAATTTTC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	5											295	327	316					5																	172752877		2203	4300	6503	172685483	SO:0001819	synonymous_variant	8614			AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.288T>C	5.37:g.172752877A>G			172685483		Silent	SNP	ENST00000265087.4	37	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.651330	0.29336	.	.	ENSG00000113739	ENST00000520648	.	.	.	5.6	3.24	0.37175	.	.	.	.	.	T	0.58850	0.2151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52177	-0.8610	4	.	.	.	-19.9261	9.3583	0.38179	0.7923:0.0:0.2077:0.0	.	.	.	.	R	50	.	.	C	-	1	0	STC2	172685483	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.418000	0.52721	0.427000	0.26145	0.533000	0.62120	TGC		0.438	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		G	172752877	A	G	172752877	2	3	61	1	0	0	0	0	0	0	0	1	15315	214	8	4		4	STC2	5	172752877	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	215227	172752877	8162383	4352	12337										
CPEB4	80315	broad.mit.edu	37	chr5	173376531	173376531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagatcacagctagttttCgtcgctttggccctctgatt	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:173376531C>T	ENST00000265085.5	+	6	2931	c.1477C>T	c.(1477-1479)Cgt>Tgt	p.R493C	CPEB4_ENST00000517880.1_Missense_Mutation_p.R86C|CPEB4_ENST00000520867.1_Missense_Mutation_p.R468C|CPEB4_ENST00000522336.1_Missense_Mutation_p.R103C|CPEB4_ENST00000334035.5_Missense_Mutation_p.R476C|CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000519835.1_Missense_Mutation_p.R468C	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	493	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R493C(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			AGCTAGTTTTCGTCGCTTTGG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	101	101					5																	173376531		2203	4300	6503	173309137	SO:0001583	missense	80315			BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.1477C>T	5.37:g.173376531C>T	ENSP00000265085:p.Arg493Cys		173309137	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004837	0.74932	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835;ENST00000522336;ENST00000517880	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.9	5.9	0.94986	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.050062	0.85682	D	0.000000	T	0.22003	0.0530	L	0.39692	1.235	0.80722	D	1	B;B;B;B;B	0.22211	0.052;0.019;0.066;0.006;0.024	B;B;B;B;B	0.30716	0.1;0.037;0.119;0.041;0.1	T	0.02484	-1.1152	10	0.56958	D	0.05	-12.8948	20.2683	0.98464	0.0:1.0:0.0:0.0	.	468;476;468;103;493	B7ZLQ8;Q17RY0-2;E5RJM0;E5RFP2;Q17RY0	.;.;.;.;CPEB4_HUMAN	C	493;468;476;468;103;86	ENSP00000265085:R493C;ENSP00000429092:R468C;ENSP00000334533:R476C;ENSP00000429048:R468C;ENSP00000430345:R103C;ENSP00000427990:R86C	ENSP00000265085:R493C	R	+	1	0	CPEB4	173309137	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.132000	0.50523	2.800000	0.96347	0.591000	0.81541	CGT		0.308	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		T	173376531	C	T	173376531	3	4	61	1	0	0	0	0	1	0	0	0	3809	884	31	1	1499	1	CPEB4	5	173376531	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	623654	173376531	7538729	4353	12338										
THOC3	84321	broad.mit.edu	37	chr5	175387024	175387024	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttccggcttcccggctgCtgtcatatttgccgtctttg	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:175387024C>A	ENST00000265097.4	-	6	1094	c.1004G>T	c.(1003-1005)aGc>aTc	p.S335I	RP11-91H12.4_ENST00000502813.1_RNA|THOC3_ENST00000514861.1_Missense_Mutation_p.S150I|THOC3_ENST00000510300.1_5'Flank	NM_032361.2	NP_115737.1	Q96J01	THOC3_HUMAN	THO complex 3	335					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)	p.S335I(1)		endometrium(1)|kidney(1)|large_intestine(2)	4	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		TTCCCGGCTGCTGTCATATTT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											15	19	17					5																	175387024		1932	3727	5659	175319630	SO:0001583	missense	84321			BC006849	CCDS4397.1	5q35.3	2013-02-11			ENSG00000051596	ENSG00000051596		"WD repeat domain containing", "THO complex subunits"	19072	protein-coding gene	gene with protein product		606929				11979277	Standard	NM_032361		Approved	TEX1, MGC5469	uc003mdg.5	Q96J01	OTTHUMG00000130658	ENST00000265097.4:c.1004G>T	5.37:g.175387024C>A	ENSP00000265097:p.Ser335Ile		175319630	Q6NZ53	Missense_Mutation	SNP	ENST00000265097.4	37	CCDS4397.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.865446	0.32977	.	.	ENSG00000051596	ENST00000265097;ENST00000514861	T;T	0.75821	0.19;-0.97	5.13	5.13	0.70059	.	0.108133	0.64402	D	0.000004	T	0.62551	0.2437	L	0.34521	1.04	0.80722	D	1	B	0.33413	0.411	B	0.31337	0.128	T	0.64457	-0.6403	10	0.48119	T	0.1	-20.1912	11.1085	0.48218	0.0:0.9152:0.0:0.0848	.	335	Q96J01	THOC3_HUMAN	I	335;150	ENSP00000265097:S335I;ENSP00000425039:S150I	ENSP00000265097:S335I	S	-	2	0	THOC3	175319630	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	2.623000	0.46435	2.380000	0.81148	0.609000	0.83330	AGC		0.552	THOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253148.1			A	175387024	C	A	175387024	3	1	61	1	0	0	0	0	1	0	0	0	15905	797	28	2	55	2	THOC3	5	175387024	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2010493	175387024	5528236	4354	12339										
FAM153B	202134	broad.mit.edu	37	chr5	175528581	175528581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacccagacacactggccGaacgtacgtattctgggatc	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:175528581G>A	ENST00000253490.4	+	12	718	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	FAM153B_ENST00000510151.1_Missense_Mutation_p.E144K|FAM153B_ENST00000515817.1_Missense_Mutation_p.E144K|FAM153B_ENST00000512862.1_Intron			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	221								p.E221K(1)|p.E221*(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CACACTGGCCGAACGTACGTA	0.463																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	5											137	147	143					5																	175528581		2203	4300	6503	175461187	SO:0001583	missense	202134			AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.661G>A	5.37:g.175528581G>A	ENSP00000253490:p.Glu221Lys		175461187	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	G	9.067	0.995865	0.19043	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.752	-1.5	0.08691	.	.	.	.	.	T	0.07638	0.0192	N	0.08118	0	0.09310	N	1	P	0.50943	0.94	B	0.32149	0.141	T	0.23976	-1.0173	8	0.41790	T	0.15	.	2.9269	0.05787	0.664:0.0:0.336:0.0	.	221	P0C7A2	F153B_HUMAN	K	144;221	.	ENSP00000253490:E221K	E	+	1	0	FAM153B	175461187	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.024000	0.12435	-0.193000	0.10415	-1.169000	0.01745	GAA		0.463	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529		A	175528581	G	A	175528581	3	1	61	1	0	0	0	0	1	0	0	0	5477	1059	37	1	707	1	FAM153B	5	175528581	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141557	175528581	5386679	4355	12340										
HK3	3101	broad.mit.edu	37	chr5	176318090	176318090	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcacaaactcctggcttCtgggctccaccctatgcccc	8	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176318090C>T	ENST00000292432.5	-	4	453	c.362G>A	c.(361-363)aGa>aAa	p.R121K		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	121	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)	p.R121K(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			CTCCTGGCTTCTGGGCTCCAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	5											59	59	59					5																	176318090		2203	4300	6503	176250696	SO:0001583	missense	3101				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.362G>A	5.37:g.176318090C>T	ENSP00000292432:p.Arg121Lys		176250696	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.764699	0.31228	.	.	ENSG00000160883	ENST00000292432	D	0.98105	-4.72	4.96	2.04	0.26737	Hexokinase, N-terminal (1);	0.246767	0.30068	N	0.010490	D	0.87220	0.6123	N	0.01352	-0.895	0.25726	N	0.985329	B	0.02656	0.0	B	0.15052	0.012	T	0.79776	-0.1661	10	0.24483	T	0.36	.	2.4991	0.04629	0.2131:0.4444:0.0:0.3425	.	121	P52790	HXK3_HUMAN	K	121	ENSP00000292432:R121K	ENSP00000292432:R121K	R	-	2	0	HK3	176250696	0.976000	0.34144	1.000000	0.80357	0.991000	0.79684	0.430000	0.21428	1.222000	0.43521	0.561000	0.74099	AGA		0.627	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			T	176318090	C	T	176318090	3	4	61	1	0	0	0	0	1	0	0	0	7213	913	32	3	2473	3	HK3	5	176318090	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	789509	176318090	4597170	4356	12341										
UIMC1	51720	broad.mit.edu	37	chr5	176395702	176395702	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtcttcatctcccatatCttctgagatgcattcatttt	4	10	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176395702C>A	ENST00000377227.4	-	6	1186	c.1054G>T	c.(1054-1056)Gat>Tat	p.D352Y	UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000377219.2_Missense_Mutation_p.D352Y|UIMC1_ENST00000506128.1_Intron|UIMC1_ENST00000511320.1_Missense_Mutation_p.D352Y			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	352	AIR.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)	p.D352Y(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTCCCATATCTTCTGAGATG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											164	156	159					5																	176395702		2203	4300	6503	176328308	SO:0001583	missense	51720			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1054G>T	5.37:g.176395702C>A	ENSP00000366434:p.Asp352Tyr		176328308	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.178604	0.57692	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000377220	T;T;T	0.29917	1.55;1.55;1.55	5.88	5.0	0.66597	.	0.127873	0.48767	D	0.000179	T	0.51092	0.1654	M	0.61703	1.905	0.46927	D	0.999251	D;D	0.76494	0.999;0.998	D;D	0.65443	0.935;0.935	T	0.50866	-0.8777	10	0.72032	D	0.01	.	15.3007	0.73949	0.0:0.9319:0.0:0.0681	.	352;274	Q96RL1;Q96RL1-3	UIMC1_HUMAN;.	Y	352;352;352;274	ENSP00000366434:D352Y;ENSP00000366425:D352Y;ENSP00000421926:D352Y	ENSP00000366425:D352Y	D	-	1	0	UIMC1	176328308	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	3.708000	0.54845	2.785000	0.95823	0.650000	0.86243	GAT		0.453	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		A	176395702	C	A	176395702	3	1	61	1	0	0	0	0	1	0	0	0	17011	913	32	2	1145	2	UIMC1	5	176395702	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77612	176395702	4519558	4357	12342										
ZNF346	23567	broad.mit.edu	37	chr5	176477784	176477784	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagagatgatagacccaGacaagttctgcagcctctgc	10	10	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176477784G>T	ENST00000358149.3	+	5	593	c.550G>T	c.(550-552)Gac>Tac	p.D184Y	ZNF346_ENST00000506693.1_Missense_Mutation_p.D86Y|ZNF346_ENST00000512315.1_Intron|ZNF346-IT1_ENST00000515264.1_RNA|ZNF346_ENST00000503039.1_Missense_Mutation_p.D209Y|ZNF346_ENST00000261948.4_Missense_Mutation_p.D209Y|ZNF346_ENST00000503425.1_Missense_Mutation_p.D152Y|ZNF346_ENST00000511834.1_Missense_Mutation_p.D200Y	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346	184					positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D184Y(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	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)			GATAGACCCAGACAAGTTCTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	5											110	104	106					5																	176477784		2203	4300	6503	176410390	SO:0001583	missense	23567			AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.550G>T	5.37:g.176477784G>T	ENSP00000350869:p.Asp184Tyr		176410390	B7Z367|Q68CV9|Q6ZMW1	Missense_Mutation	SNP	ENST00000358149.3	37	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021937	0.75275	.	.	ENSG00000113761	ENST00000358149;ENST00000506693;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.47	5.47	0.80525	Zinc finger, U1-type (1);	0.232106	0.49305	D	0.000156	T	0.61986	0.2391	M	0.77103	2.36	0.35412	D	0.792535	D;D;D;D	0.62365	0.98;0.971;0.991;0.971	P;P;D;P	0.64144	0.73;0.789;0.922;0.691	T	0.72846	-0.4169	10	0.54805	T	0.06	.	12.6395	0.56702	0.0755:0.0:0.9245:0.0	.	86;152;209;184	B7Z4J8;B7Z367;Q9UL40-2;Q9UL40	.;.;.;ZN346_HUMAN	Y	184;86;152;209;200;209	ENSP00000350869:D184Y;ENSP00000423515:D86Y;ENSP00000421212:D152Y;ENSP00000261948:D209Y;ENSP00000425725:D200Y;ENSP00000424495:D209Y	ENSP00000261948:D209Y	D	+	1	0	ZNF346	176410390	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.783000	0.62403	2.544000	0.85801	0.655000	0.94253	GAC		0.473	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279		T	176477784	G	T	176477784	3	4	61	1	0	0	0	0	1	0	0	0	17899	942	33	2	568	2	ZNF346	5	176477784	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82082	176477784	4437476	4358	12343										
NSD1	64324	broad.mit.edu	37	chr5	176665503	176665503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaattgctagttaaaaCgccaggtaaggtggggttgg	16	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176665503C>T	ENST00000439151.2	+	7	4232	c.4187C>T	c.(4186-4188)aCg>aTg	p.T1396M	NSD1_ENST00000361032.4_Missense_Mutation_p.T1293M|NSD1_ENST00000354179.4_Missense_Mutation_p.T1127M|NSD1_ENST00000347982.4_Missense_Mutation_p.T1127M	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1396					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.T1396M(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	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)		CTAGTTAAAACGCCAGGTAAG	0.488			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Substitution - Missense(2)	large_intestine(2)	5											82	84	84					5																	176665503		2203	4300	6503	176598109	SO:0001583	missense	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.4187C>T	5.37:g.176665503C>T	ENSP00000395929:p.Thr1396Met		176598109	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.546017	0.65198	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93133	-3.06;-3.06;-3.06;-3.17	4.58	4.58	0.56647	.	0.296239	0.28952	N	0.013609	D	0.88209	0.6375	N	0.14661	0.345	0.29239	N	0.872729	P;D;D	0.60575	0.726;0.986;0.988	B;B;P	0.46339	0.276;0.385;0.513	D	0.85465	0.1169	10	0.72032	D	0.01	.	13.1909	0.59711	0.0:1.0:0.0:0.0	.	1127;1293;1396	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	M	1127;1396;1127;1293	ENSP00000346111:T1127M;ENSP00000395929:T1396M;ENSP00000343209:T1127M;ENSP00000354310:T1293M	ENSP00000343209:T1127M	T	+	2	0	NSD1	176598109	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.688000	0.37690	2.832000	0.97577	0.655000	0.94253	ACG		0.488	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176665503	C	T	176665503	3	4	61	1	0	0	0	0	1	0	0	0	10700	536	19	1	4209	1	NSD1	5	176665503	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187719	176665503	4249757	4359	12344										
NSD1	64324	broad.mit.edu	37	chr5	176671259	176671259	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccacatcttattcaaaaGattttggtggaggtgagtat	11	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176671259G>T	ENST00000439151.2	+	9	4411	c.4366G>T	c.(4366-4368)Gat>Tat	p.D1456Y	NSD1_ENST00000361032.4_Missense_Mutation_p.D1353Y|NSD1_ENST00000354179.4_Missense_Mutation_p.D1187Y|NSD1_ENST00000347982.4_Missense_Mutation_p.D1187Y	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1456					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.D1456Y(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	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)		TTATTCAAAAGATTTTGGTGG	0.343			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Substitution - Missense(2)	large_intestine(2)	5											106	98	100					5																	176671259		2203	4300	6503	176603865	SO:0001583	missense	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.4366G>T	5.37:g.176671259G>T	ENSP00000395929:p.Asp1456Tyr		176603865	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523663	0.44866	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93547	-3.13;-3.14;-3.13;-3.24	5.32	3.52	0.40303	.	0.393706	0.24294	N	0.039792	D	0.87301	0.6143	N	0.08118	0	0.26704	N	0.971108	P;P;P	0.42649	0.547;0.786;0.681	B;P;B	0.47251	0.347;0.542;0.119	T	0.81344	-0.0975	10	0.87932	D	0	.	8.8712	0.35316	0.0819:0.1495:0.7686:0.0	.	1187;1353;1456	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	Y	1187;1456;1187;1353	ENSP00000346111:D1187Y;ENSP00000395929:D1456Y;ENSP00000343209:D1187Y;ENSP00000354310:D1353Y	ENSP00000343209:D1187Y	D	+	1	0	NSD1	176603865	1.000000	0.71417	0.938000	0.37757	0.579000	0.36224	2.496000	0.45346	0.723000	0.32274	0.655000	0.94253	GAT		0.343	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176671259	G	T	176671259	3	4	61	1	0	0	0	0	1	0	0	0	10700	942	33	2	4396	2	NSD1	5	176671259	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5756	176671259	4244001	4360	12345										
LMAN2	10960	broad.mit.edu	37	chr5	176764467	176764467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtccagcgcccatccttgCtgtggtcgtaggacagggag	15	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176764467C>T	ENST00000303127.7	-	5	776	c.572G>A	c.(571-573)aGc>aAc	p.S191N	LMAN2_ENST00000515209.1_Missense_Mutation_p.S191N|LMAN2_ENST00000506310.1_Splice_Site	NM_006816.2	NP_006807.1	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2	191	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				positive regulation of phagocytosis (GO:0050766)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|heat shock protein binding (GO:0031072)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)	p.S191N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCATCCTTGCTGTGGTCGTA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5											86	72	76					5																	176764467		2203	4300	6503	176697073	SO:0001583	missense	10960			U10362	CCDS4417.1	5q35	2008-02-05		2003-07-04	ENSG00000169223	ENSG00000169223			16986	protein-coding gene	gene with protein product		609551	"chromosome 5 open reading frame 8"	C5orf8		12609988	Standard	NM_006816		Approved	GP36B, VIP36	uc003mge.3	Q12907	OTTHUMG00000130860	ENST00000303127.7:c.572G>A	5.37:g.176764467C>T	ENSP00000303366:p.Ser191Asn		176697073	Q53HH1	Missense_Mutation	SNP	ENST00000303127.7	37	CCDS4417.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631361	0.87660	.	.	ENSG00000169223	ENST00000303127;ENST00000539488;ENST00000515209;ENST00000502560;ENST00000513877	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.98	5.98	0.97165	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.040953	0.85682	D	0.000000	T	0.54240	0.1846	L	0.31420	0.93	0.47819	D	0.99952	B;B	0.34349	0.146;0.45	B;B	0.33196	0.036;0.159	T	0.51236	-0.8731	10	0.38643	T	0.18	-13.6504	20.0665	0.97706	0.0:1.0:0.0:0.0	.	191;191	Q12907;D6RBV2	LMAN2_HUMAN;.	N	191;120;191;184;120	ENSP00000303366:S191N;ENSP00000423998:S191N;ENSP00000425229:S184N;ENSP00000427377:S120N	ENSP00000303366:S191N	S	-	2	0	LMAN2	176697073	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.022000	0.70839	2.847000	0.97988	0.591000	0.81541	AGC		0.637	LMAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253434.1	NM_006816		T	176764467	C	T	176764467	3	4	61	1	0	0	0	0	1	0	0	0	8862	797	28	3	514	3	LMAN2	5	176764467	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93208	176764467	4150793	4361	12346										
DBN1	1627	broad.mit.edu	37	chr5	176887509	176887509	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctttcctgctgcttgaaGaactcccttgggttgtcagg	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:176887509G>T	ENST00000309007.5	-	10	1098	c.879C>A	c.(877-879)ttC>ttA	p.F293L	DBN1_ENST00000292385.5_Missense_Mutation_p.F295L|DBN1_ENST00000393565.1_Missense_Mutation_p.F293L|DBN1_ENST00000393563.4_Missense_Mutation_p.F25L|DBN1_ENST00000512501.1_Missense_Mutation_p.F25L	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	293					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.F293L(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			GCTGCTTGAAGAACTCCCTTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	5											166	160	162					5																	176887509		2203	4300	6503	176820115	SO:0001583	missense	1627				CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.879C>A	5.37:g.176887509G>T	ENSP00000308532:p.Phe293Leu		176820115	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.674418	0.67928	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563;ENST00000477391	T;T;T;T;T	0.63580	1.55;1.54;1.49;-0.05;0.41	4.54	2.77	0.32553	.	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	L	0.52364	1.645	0.42043	D	0.991082	D;D;D;D	0.76494	0.99;0.999;0.997;0.998	D;D;D;D	0.76071	0.979;0.986;0.97;0.987	T	0.67401	-0.5680	10	0.44086	T	0.13	-4.762	9.7068	0.40220	0.1734:0.0:0.8266:0.0	.	243;293;293;295	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	L	293;295;293;25;25;292	ENSP00000308532:F293L;ENSP00000292385:F295L;ENSP00000377195:F293L;ENSP00000423208:F25L;ENSP00000377193:F25L	ENSP00000292385:F295L	F	-	3	2	DBN1	176820115	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.941000	0.56607	0.555000	0.29079	-0.258000	0.10820	TTC		0.612	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		T	176887509	G	T	176887509	3	4	61	1	0	0	0	0	1	0	0	0	4258	933	33	2	1090	2	DBN1	5	176887509	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123042	176887509	4027751	4362	12347										
N4BP3	23138	broad.mit.edu	37	chr5	177548554	177548554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaactggcccagaagctggCggagatcttcagtctgaaga	14	9	3	4	rs187860405		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:177548554C>T	ENST00000274605.5	+	5	1546	c.1187C>T	c.(1186-1188)gCg>gTg	p.A396V		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	396						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)		p.A396V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	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)			CAGAAGCTGGCGGAGATCTTC	0.642													C|||	1	0.000199681	0	0.0014	5008	,	,		17137	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											78	88	84					5																	177548554		2203	4300	6503	177481160	SO:0001583	missense	23138			AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.1187C>T	5.37:g.177548554C>T	ENSP00000274605:p.Ala396Val		177481160	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Missense_Mutation	SNP	ENST00000274605.5	37	CCDS34307.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	25.8	4.673118	0.88445	.	.	ENSG00000145911	ENST00000274605	T	0.46819	0.86	5.05	5.05	0.67936	.	0.095669	0.64402	D	0.000001	T	0.54727	0.1876	L	0.36672	1.1	0.39949	D	0.97451	D	0.76494	0.999	D	0.65573	0.936	T	0.55270	-0.8167	10	0.42905	T	0.14	-10.2065	11.7713	0.51960	0.0:0.8224:0.1776:0.0	.	396	O15049	N4BP3_HUMAN	V	396	ENSP00000274605:A396V	ENSP00000274605:A396V	A	+	2	0	N4BP3	177481160	1.000000	0.71417	0.952000	0.39060	0.984000	0.73092	5.873000	0.69644	2.362000	0.80069	0.561000	0.74099	GCG		0.642	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111		T	177548554	C	T	177548554	3	4	61	1	0	0	0	0	1	0	0	0	10143	768	27	1	1201	1	N4BP3	5	177548554	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	661045	177548554	3366706	4363	12348										
HNRNPAB	85007	broad.mit.edu	37	chr5	177637267	177637267	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggctacggccccggctacGactacagtaagtaggagaga	13	11	0	1	rs528992480		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:177637267G>A	ENST00000308158.5	-	13	1619				HNRNPAB_ENST00000506339.1_Missense_Mutation_p.D303N|HNRNPAB_ENST00000358344.3_Missense_Mutation_p.D308N|HNRNPAB_ENST00000506259.1_Intron|HNRNPAB_ENST00000504898.1_Missense_Mutation_p.D308N|HNRNPAB_ENST00000515193.1_Intron|PHYKPL_ENST00000481811.1_Intron|HNRNPAB_ENST00000355836.5_Intron|HNRNPAB_ENST00000514633.1_Intron	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.D308N(1)								L-Alanine(DB00160)	CCCCGGCTACGACTACAGTAA	0.637													G|||	1	0.000199681	0	0	5008	,	,		15948	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											34	36	35					5																	177637267		2203	4300	6503	177569873	SO:0001627	intron_variant	3182			BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1351-1351C>T	5.37:g.177637267G>A			177569873	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Missense_Mutation	SNP	ENST00000308158.5	37	CCDS4434.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.956114	0.53293	.	.	ENSG00000197451	ENST00000358344;ENST00000506339;ENST00000504898	D;D;D	0.89343	-2.5;-2.5;-2.5	5.97	4.2	0.49525	.	0.000000	0.85682	D	0.000000	D	0.88206	0.6374	M	0.89095	3.005	0.80722	D	1	B	0.32526	0.374	B	0.19391	0.025	D	0.84840	0.0807	10	0.35671	T	0.21	.	10.8245	0.46625	0.1516:0.0:0.8484:0.0	.	308	Q99729-2	.	N	308;303;308	ENSP00000351108:D308N;ENSP00000422501:D303N;ENSP00000425031:D308N	ENSP00000351108:D308N	D	+	1	0	HNRNPAB	177569873	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.269000	0.78482	0.864000	0.35578	0.655000	0.94253	GAC		0.637	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		A	177637267	G	A	177637267	1	1	61	0	1	0	0	0	0	0	0	0	7282	1058	37	1		1	HNRNPAB	5	177637267	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88713	177637267	3277993	4364	12349										
COL23A1	91522	broad.mit.edu	37	chr5	177669362	177669362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctctccacgctcgctccGatcacctttctctcctcggg	6	19	3	0	rs201802684		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:177669362G>A	ENST00000390654.3	-	26	1831	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	492	Collagen-like 5.|Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R492W(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CGCTCGCTCCGATCACCTTTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											56	61	60					5																	177669362		2065	4203	6268	177601968	SO:0001583	missense	91522			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"Collagens"	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1474C>T	5.37:g.177669362G>A	ENSP00000375069:p.Arg492Trp		177601968	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.423671	0.43020	.	.	ENSG00000050767	ENST00000390654	D	0.96200	-3.94	4.6	2.53	0.30540	.	0.104701	0.37577	N	0.002036	D	0.96103	0.8730	L	0.56396	1.775	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.94974	0.8119	10	0.62326	D	0.03	-0.3945	8.7521	0.34622	0.0:0.0:0.4903:0.5097	.	492	Q86Y22	CONA1_HUMAN	W	492	ENSP00000375069:R492W	ENSP00000375069:R492W	R	-	1	2	COL23A1	177601968	0.996000	0.38824	0.991000	0.47740	0.946000	0.59487	2.143000	0.42187	0.896000	0.36366	0.455000	0.32223	CGG		0.602	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		A	177669362	G	A	177669362	3	1	61	1	0	0	0	0	1	0	0	0	3688	1057	37	1	164	1	COL23A1	5	177669362	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32095	177669362	3245898	4365	12350										
ZNF354A	6940	broad.mit.edu	37	chr5	178139180	178139180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtatgaattctctgatgtgCaatacgtgatgagctttgtc	10	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178139180C>T	ENST00000335815.2	-	5	1896	c.1699G>A	c.(1699-1701)Gca>Aca	p.A567T		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	567					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A567T(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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)	all cancers(165;0.185)		CTCTGATGTGCAATACGTGAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											92	90	91					5																	178139180		2203	4300	6503	178071786	SO:0001583	missense	6940			AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"Zinc fingers, C2H2-type", "-"	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1699G>A	5.37:g.178139180C>T	ENSP00000337122:p.Ala567Thr		178071786	Q9UNJ8	Missense_Mutation	SNP	ENST00000335815.2	37	CCDS4438.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.885798	0.33348	.	.	ENSG00000169131	ENST00000335815	T	0.01015	5.44	4.7	3.82	0.43975	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32819	N	0.005601	T	0.01287	0.0042	N	0.10874	0.06	0.09310	N	1	D	0.76494	0.999	D	0.85130	0.997	T	0.60895	-0.7172	10	0.12766	T	0.61	-2.4028	6.4063	0.21666	0.0:0.8069:0.0:0.1931	.	567	O60765	Z354A_HUMAN	T	567	ENSP00000337122:A567T	ENSP00000337122:A567T	A	-	1	0	ZNF354A	178071786	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-0.112000	0.10791	2.589000	0.87451	0.650000	0.86243	GCA		0.343	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649		T	178139180	C	T	178139180	3	4	61	1	0	0	0	0	1	0	0	0	17903	710	25	3	122	3	ZNF354A	5	178139180	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	469818	178139180	2776080	4366	12351										
ZNF354B	117608	broad.mit.edu	37	chr5	178309990	178309990	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattaagcaacagagattTgctaaagaaaaaactccatc	5	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178309990T>C	ENST00000322434.3	+	5	763	c.537T>C	c.(535-537)ttT>ttC	p.F179F	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F179F(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AACAGAGATTTGCTAAAGAAA	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	5											32	34	33					5																	178309990		2192	4285	6477	178242596	SO:0001819	synonymous_variant	117608			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.537T>C	5.37:g.178309990T>C			178242596	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																				0.308	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		C	178309990	T	C	178309990	2	2	61	1	0	0	0	0	0	0	0	1	17904	1809	63	4		4	ZNF354B	5	178309990	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	170810	178309990	2605270	4367	12352										
ZNF354B	117608	broad.mit.edu	37	chr5	178310238	178310238	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttattcaacatcaaaGaactcatacaggagagaaac	6	9	4	2	rs564522787		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178310238G>T	ENST00000322434.3	+	5	1011	c.785G>T	c.(784-786)aGa>aTa	p.R262I	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R262I(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAACATCAAAGAACTCATACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											60	68	66					5																	178310238		2202	4299	6501	178242844	SO:0001583	missense	117608			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.785G>T	5.37:g.178310238G>T	ENSP00000327143:p.Arg262Ile		178242844	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342395	0.24339	.	.	ENSG00000178338	ENST00000322434	T	0.24908	1.83	3.28	1.18	0.20946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18341	0.0440	M	0.66506	2.035	0.44067	D	0.996813	P	0.43788	0.817	B	0.34536	0.185	T	0.10086	-1.0645	9	0.45353	T	0.12	.	1.9258	0.03316	0.1225:0.2016:0.4694:0.2066	.	262	Q96LW1	Z354B_HUMAN	I	262	ENSP00000327143:R262I	ENSP00000327143:R262I	R	+	2	0	ZNF354B	178242844	0.000000	0.05858	1.000000	0.80357	0.946000	0.59487	0.841000	0.27613	0.549000	0.28973	0.561000	0.74099	AGA		0.363	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		T	178310238	G	T	178310238	3	4	61	1	0	0	0	0	1	0	0	0	17904	942	33	2	799	2	ZNF354B	5	178310238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248	178310238	2605022	4368	12353										
ZFP2	80108	broad.mit.edu	37	chr5	178358763	178358763	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccttactgtacatcaaaGaattcatactggagagaaac	6	10	2	2	rs376749929		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178358763G>T	ENST00000361362.2	+	5	979	c.449G>T	c.(448-450)aGa>aTa	p.R150I	ZFP2_ENST00000503510.2_Missense_Mutation_p.R150I|ZFP2_ENST00000520301.1_Missense_Mutation_p.R150I|ZFP2_ENST00000523286.1_Missense_Mutation_p.R150I	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R150I(2)		NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		GTACATCAAAGAATTCATACT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	5						G	ILE/ARG	0,4406		0,0,2203	52	55	54		449	3.8	1	5		54	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZFP2	NM_030613.2	97	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	150/462	178358763	1,13005	2203	4300	6503	178291369	SO:0001583	missense	80108			AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.449G>T	5.37:g.178358763G>T	ENSP00000354453:p.Arg150Ile		178291369	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	g	15.72	2.915461	0.52546	0.0	1.16E-4	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.71	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35151	N	0.003406	T	0.50922	0.1644	M	0.80332	2.49	0.47183	D	0.99934	D	0.89917	1.0	D	0.85130	0.997	T	0.54964	-0.8214	10	0.56958	D	0.05	-15.0571	12.0605	0.53561	0.0:0.0:0.8266:0.1734	.	150	Q6ZN57	ZFP2_HUMAN	I	150	ENSP00000354453:R150I;ENSP00000430980:R150I;ENSP00000430531:R150I;ENSP00000438114:R150I	ENSP00000354453:R150I	R	+	2	0	ZFP2	178291369	0.080000	0.21391	1.000000	0.80357	0.837000	0.47467	2.428000	0.44749	1.176000	0.42840	0.591000	0.81541	AGA		0.413	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		T	178358763	G	T	178358763	3	4	61	1	0	0	0	0	1	0	0	0	17680	942	33	2	451	2	ZFP2	5	178358763	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48525	178358763	2556497	4369	12354										
ZNF454	285676	broad.mit.edu	37	chr5	178391963	178391963	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagtgagtgtggaaaagtCttctctaagagttcaactct	10	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178391963C>A	ENST00000320129.3	+	5	861	c.558C>A	c.(556-558)gtC>gtA	p.V186V	ZNF454_ENST00000519564.1_Silent_p.V186V	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V186V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		GTGGAAAAGTCTTCTCTAAGA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	5											52	54	53					5																	178391963		2203	4300	6503	178324569	SO:0001819	synonymous_variant	285676			AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.558C>A	5.37:g.178391963C>A			178324569	Q2M1P2|Q2M323	Silent	SNP	ENST00000320129.3	37	CCDS4441.1																																																																																				0.343	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		A	178391963	C	A	178391963	2	1	61	1	0	0	0	0	0	0	0	1	17962	900	32	2		2	ZNF454	5	178391963	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33200	178391963	2523297	4370	12355										
ZNF454	285676	broad.mit.edu	37	chr5	178392328	178392328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaacatttgtgaaaaagCctttgtgtgcagggcacacc	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178392328C>T	ENST00000320129.3	+	5	1226	c.923C>T	c.(922-924)gCc>gTc	p.A308V	ZNF454_ENST00000519564.1_Missense_Mutation_p.A308V	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	308					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A308V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		TGTGAAAAAGCCTTTGTGTGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											50	54	53					5																	178392328		2203	4300	6503	178324934	SO:0001583	missense	285676			AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.923C>T	5.37:g.178392328C>T	ENSP00000326249:p.Ala308Val		178324934	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.756395	0.31137	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.13778	2.56;2.56	4.45	3.5	0.40072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41001	D	0.000974	T	0.21881	0.0527	L	0.40543	1.245	0.29475	N	0.856755	D	0.57257	0.979	P	0.60236	0.871	T	0.00837	-1.1546	10	0.56958	D	0.05	-10.2114	10.4618	0.44583	0.0:0.6918:0.3082:0.0	.	308	Q8N9F8	ZN454_HUMAN	V	308	ENSP00000326249:A308V;ENSP00000430354:A308V	ENSP00000326249:A308V	A	+	2	0	ZNF454	178324934	0.000000	0.05858	1.000000	0.80357	0.050000	0.14768	0.072000	0.14617	2.462000	0.83206	0.650000	0.86243	GCC		0.373	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		T	178392328	C	T	178392328	3	4	61	1	0	0	0	0	1	0	0	0	17962	739	26	3	937	3	ZNF454	5	178392328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	365	178392328	2522932	4371	12356										
ZNF354C	30832	broad.mit.edu	37	chr5	178505686	178505686	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctgattcattttaggtTtcaagacttggcttgaaaca	7	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178505686T>G	ENST00000315475.6	+	5	559	c.253T>G	c.(253-255)Ttc>Gtc	p.F85V		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	85					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F85V(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CATTTTAGGTTTCAAGACTTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	5											39	41	40					5																	178505686		2200	4300	6500	178438292	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.253T>G	5.37:g.178505686T>G	ENSP00000324064:p.Phe85Val		178438292	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	T	1.175	-0.639753	0.03557	.	.	ENSG00000177932	ENST00000315475	T	0.04809	3.55	4.09	2.82	0.32997	.	.	.	.	.	T	0.02767	0.0083	N	0.14661	0.345	0.09310	N	1	B	0.20671	0.047	B	0.19946	0.027	T	0.45585	-0.9251	9	0.19590	T	0.45	-6.0203	4.4743	0.11727	0.1931:0.0:0.2005:0.6064	.	85	Q86Y25	Z354C_HUMAN	V	85	ENSP00000324064:F85V	ENSP00000324064:F85V	F	+	1	0	ZNF354C	178438292	0.000000	0.05858	0.975000	0.42487	0.214000	0.24535	-0.098000	0.11024	1.826000	0.53198	0.482000	0.46254	TTC		0.363	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178505686	T	G	178505686	3	3	61	1	0	0	0	0	1	0	0	0	17905	1841	64	4	267	4	ZNF354C	5	178505686	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	113358	178505686	2409574	4372	12357										
ZNF354C	30832	broad.mit.edu	37	chr5	178506660	178506660	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgaattcacactggacaAaaaccttatcagtgcaacga	7	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:178506660A>C	ENST00000315475.6	+	5	1533	c.1227A>C	c.(1225-1227)caA>caC	p.Q409H		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q409H(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		ACACTGGACAAAAACCTTATC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	5											125	123	124					5																	178506660		2203	4300	6503	178439266	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1227A>C	5.37:g.178506660A>C	ENSP00000324064:p.Gln409His		178439266	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	12.42	1.931259	0.34096	.	.	ENSG00000177932	ENST00000315475	T	0.19250	2.16	4.22	1.93	0.25924	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31638	0.0803	L	0.45352	1.415	0.35669	D	0.813153	D	0.71674	0.998	D	0.68943	0.961	T	0.33085	-0.9882	9	0.87932	D	0	-16.8824	6.66	0.23009	0.3173:0.0:0.6827:0.0	.	409	Q86Y25	Z354C_HUMAN	H	409	ENSP00000324064:Q409H	ENSP00000324064:Q409H	Q	+	3	2	ZNF354C	178439266	0.998000	0.40836	0.978000	0.43139	0.256000	0.26092	0.339000	0.19875	0.281000	0.22233	0.482000	0.46254	CAA		0.393	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			C	178506660	A	C	178506660	3	2	61	1	0	0	0	0	1	0	0	0	17905	11	1	4	1241	4	ZNF354C	5	178506660	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	974	178506660	2408600	4373	12358										
MAML1	9794	broad.mit.edu	37	chr5	179193383	179193383	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccttccagctacaagcaaGacttcactaactccaaactg	5	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:179193383G>T	ENST00000292599.3	+	2	1635	c.1372G>T	c.(1372-1374)Gac>Tac	p.D458Y	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)									p.D458Y(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTACAAGCAAGACTTCACTAA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	94	92					5																	179193383		2203	4300	6503	179125989	SO:0001583	missense	9794			D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1372G>T	5.37:g.179193383G>T	ENSP00000292599:p.Asp458Tyr		179125989		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.943448	0.53079	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	T	0.26223	1.75	5.18	5.18	0.71444	.	0.132935	0.51477	D	0.000090	T	0.49490	0.1560	M	0.64997	1.995	0.80722	D	1	D;D	0.76494	0.999;0.996	D;P	0.68353	0.957;0.838	T	0.49293	-0.8955	10	0.59425	D	0.04	-18.7028	18.6847	0.91559	0.0:0.0:1.0:0.0	.	495;458	Q59GH4;Q92585	.;MAML1_HUMAN	Y	458;495	ENSP00000292599:D458Y	ENSP00000292599:D458Y	D	+	1	0	MAML1	179125989	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	9.143000	0.94623	2.415000	0.81967	0.563000	0.77884	GAC		0.582	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		T	179193383	G	T	179193383	3	4	61	1	0	0	0	0	1	0	0	0	9235	942	33	2	1378	2	MAML1	5	179193383	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	686723	179193383	1721877	4374	12359										
RASGEF1C	255426	broad.mit.edu	37	chr5	179541508	179541508	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattcaggaagtagatgtCtttgatgagcaggctgaaga	12	6	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:179541508C>A	ENST00000393371.2	-	10	1413	c.1117G>T	c.(1117-1119)Gac>Tac	p.D373Y	RASGEF1C_ENST00000522500.1_Missense_Mutation_p.D222Y|RASGEF1C_ENST00000361132.4_Missense_Mutation_p.D373Y			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	373	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D373Y(1)		breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGTAGATGTCTTTGATGAGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											75	61	65					5																	179541508		2203	4300	6503	179474114	SO:0001583	missense	255426			AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090			27400	protein-coding gene	gene with protein product						12477932	Standard	XM_006714839		Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.1117G>T	5.37:g.179541508C>A	ENSP00000377037:p.Asp373Tyr		179474114	D3DWQ7|Q7Z4T0|Q8NA49	Missense_Mutation	SNP	ENST00000393371.2	37	CCDS4452.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970313	0.74246	.	.	ENSG00000146090	ENST00000361132;ENST00000393371;ENST00000522500	T;T;T	0.54479	0.57;0.57;0.57	4.58	3.71	0.42584	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.053240	0.64402	D	0.000001	T	0.80358	0.4608	H	0.97315	3.98	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84833	0.0803	10	0.87932	D	0	.	10.8943	0.47012	0.0:0.9056:0.0:0.0944	.	373	Q8N431	RGF1C_HUMAN	Y	373;373;222	ENSP00000354963:D373Y;ENSP00000377037:D373Y;ENSP00000429114:D222Y	ENSP00000354963:D373Y	D	-	1	0	RASGEF1C	179474114	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.300000	0.65721	1.058000	0.40530	0.313000	0.20887	GAC		0.602	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062		A	179541508	C	A	179541508	3	1	61	1	0	0	0	0	1	0	0	0	13108	913	32	2	299	2	RASGEF1C	5	179541508	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	348125	179541508	1373752	4375	12360										
MAPK9	5601	broad.mit.edu	37	chr5	179669588	179669588	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactttttattttgtctcGctcagattctgatgggaata	7	7	3	2	rs373601817		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:179669588G>A	ENST00000452135.2	-	8	1154	c.856C>T	c.(856-858)Cga>Tga	p.R286*	MAPK9_ENST00000455781.1_Nonsense_Mutation_p.R286*|MAPK9_ENST00000524170.1_5'Flank|MAPK9_ENST00000343111.6_Nonsense_Mutation_p.R286*|MAPK9_ENST00000347470.4_Intron|MAPK9_ENST00000393360.3_Nonsense_Mutation_p.R286*|MAPK9_ENST00000397072.3_3'UTR			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	286	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)	p.R286*(2)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATTTTGTCTCGCTCAGATTCT	0.343																																																2	Substitution - Nonsense(2)	large_intestine(2)	5						G	stop/ARG,stop/ARG,stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	99	95	96		856,856,856,856	2.6	1	5		96	0,8600		0,0,4300	no	stop-gained,stop-gained,stop-gained,stop-gained	MAPK9	NM_002752.4,NM_139068.2,NM_139069.2,NM_139070.2	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	286/425,286/383,286/383,286/425	179669588	1,13005	2203	4300	6503	179602194	SO:0001587	stop_gained	5601			U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.856C>T	5.37:g.179669588G>A	ENSP00000394560:p.Arg286*		179602194	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Nonsense_Mutation	SNP	ENST00000452135.2	37	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	G	36	5.967603	0.97156	2.27E-4	0.0	ENSG00000050748	ENST00000452135;ENST00000393360;ENST00000455781;ENST00000343111	.	.	.	5.5	2.56	0.30785	.	0.070953	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-5.6091	9.3065	0.37878	0.0682:0.0:0.675:0.2567	.	.	.	.	X	286	.	ENSP00000345524:R286X	R	-	1	2	MAPK9	179602194	1.000000	0.71417	0.989000	0.46669	0.664000	0.39144	5.382000	0.66213	0.667000	0.31107	0.650000	0.86243	CGA		0.343	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			A	179669588	G	A	179669588	4	1	61	1	0	0	0	0	0	1	0	0	9317	1095	38	1	443	1	MAPK9	5	179669588	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128080	179669588	1245672	4376	12361										
GFPT2	9945	broad.mit.edu	37	chr5	179729564	179729564	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagtatcgtccttggaGcacagtataatggggcgacc	11	10	1	0	rs368071602		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:179729564G>A	ENST00000253778.8	-	18	2032	c.1863C>T	c.(1861-1863)tgC>tgT	p.C621C		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	621	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.C621C(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CGTCCTTGGAGCACAGTATAA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G		0,4112		0,0,2056	120	120	120		1863	2.4	1	5		120	4,8414		0,4,4205	no	coding-synonymous	GFPT2	NM_005110.2		0,4,6261	AA,AG,GG		0.0475,0.0,0.0319		621/683	179729564	4,12526	2056	4209	6265	179662170	SO:0001819	synonymous_variant	9945			AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1863C>T	5.37:g.179729564G>A			179662170	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	37	CCDS43411.1																																																																																				0.488	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		A	179729564	G	A	179729564	2	1	61	1	0	0	0	0	0	0	0	1	6366	963	34	3		3	GFPT2	5	179729564	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59976	179729564	1185696	4377	12362										
CNOT6	57472	broad.mit.edu	37	chr5	179996148	179996148	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacagaaaaacaacttattCttgtggctaacgcccacatg	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:179996148C>A	ENST00000393356.1	+	12	1490	c.1066C>A	c.(1066-1068)Ctt>Att	p.L356I	CNOT6_ENST00000261951.4_Missense_Mutation_p.L356I			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	356	Nuclease domain. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)	p.L356I(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		ACAACTTATTCTTGTGGCTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	5											74	73	73					5																	179996148		2203	4300	6503	179928754	SO:0001583	missense	57472			AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.1066C>A	5.37:g.179996148C>A	ENSP00000377024:p.Leu356Ile		179928754	A7MD46|D3DWR0	Missense_Mutation	SNP	ENST00000393356.1	37	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	C	4.794	0.147671	0.09134	.	.	ENSG00000113300	ENST00000261951;ENST00000393356	D;D	0.82433	-1.61;-1.61	6.04	6.04	0.98038	Endonuclease/exonuclease/phosphatase (2);	0.060511	0.64402	D	0.000002	T	0.72827	0.3509	N	0.20328	0.56	0.80722	D	1	B	0.20052	0.041	B	0.24269	0.052	T	0.66156	-0.5994	9	.	.	.	-10.7688	15.3271	0.74172	0.1397:0.8603:0.0:0.0	.	356	Q9ULM6	CNOT6_HUMAN	I	356	ENSP00000261951:L356I;ENSP00000377024:L356I	.	L	+	1	0	CNOT6	179928754	1.000000	0.71417	0.972000	0.41901	0.022000	0.10575	3.108000	0.50337	2.873000	0.98535	0.563000	0.77884	CTT		0.398	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455		A	179996148	C	A	179996148	3	1	61	1	0	0	0	0	1	0	0	0	3628	913	32	2	1100	2	CNOT6	5	179996148	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	266584	179996148	919112	4378	12363										
MGAT1	4245	broad.mit.edu	37	chr5	180219025	180219025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgtggctcacacccttgCggccaaaggtcatcgttctt	10	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:180219025C>T	ENST00000446023.2	-	3	1697	c.947G>A	c.(946-948)cGc>cAc	p.R316H	MGAT1_ENST00000307826.4_Missense_Mutation_p.R316H|MGAT1_ENST00000427865.2_Missense_Mutation_p.R316H|MGAT1_ENST00000393340.3_Missense_Mutation_p.R316H|MGAT1_ENST00000333055.3_Missense_Mutation_p.R316H	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	316					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)	p.R316H(1)		endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACACCCTTGCGGCCAAAGGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											65	71	69					5																	180219025		2203	4300	6503	180151631	SO:0001583	missense	4245			M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.947G>A	5.37:g.180219025C>T	ENSP00000404718:p.Arg316His		180151631	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733411	0.89482	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.90003	0.6879	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.90748	0.4655	10	0.72032	D	0.01	-18.5842	16.6011	0.84816	0.0:1.0:0.0:0.0	.	316	P26572	MGAT1_HUMAN	H	316;316;316;316;173;316	ENSP00000332073:R316H;ENSP00000311888:R316H;ENSP00000404718:R316H;ENSP00000377010:R316H;ENSP00000402838:R316H	ENSP00000311888:R316H	R	-	2	0	MGAT1	180151631	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.055000	0.76656	2.586000	0.87340	0.655000	0.94253	CGC		0.597	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		T	180219025	C	T	180219025	3	4	61	1	0	0	0	0	1	0	0	0	9572	768	27	1	394	1	MGAT1	5	180219025	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222877	180219025	696235	4379	12364										
BTNL3	10917	broad.mit.edu	37	chr5	180432406	180432406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgaaaactgtaacccataGaaaagctccccaggaggtgc	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:180432406G>T	ENST00000342868.6	+	8	1119	c.935G>T	c.(934-936)aGa>aTa	p.R312I	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	312	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)		p.R312I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-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;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GTAACCCATAGAAAAGCTCCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	5											50	56	54					5																	180432406		2193	4294	6487	180365012	SO:0001583	missense	10917			AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1143	protein-coding gene	gene with protein product	"butyrophilin-like receptor"	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.935G>T	5.37:g.180432406G>T	ENSP00000341787:p.Arg312Ile		180365012	Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	37	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.360655	0.24598	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.10860	2.83	2.55	-0.734	0.11140	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.18551	0.0445	L	0.45698	1.435	0.09310	N	1	D;D	0.67145	0.996;0.99	D;P	0.63488	0.915;0.728	T	0.16070	-1.0415	9	0.37606	T	0.19	.	7.1614	0.25667	0.4042:0.0:0.5958:0.0	.	278;312	C9JDC2;Q6UXE8	.;BTNL3_HUMAN	I	312;278	ENSP00000341787:R312I	ENSP00000341787:R312I	R	+	2	0	BTNL3	180365012	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.134000	0.10436	-0.148000	0.11234	0.184000	0.17185	AGA		0.542	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975		T	180432406	G	T	180432406	3	4	61	1	0	0	0	0	1	0	0	0	1569	942	33	2	965	2	BTNL3	5	180432406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213381	180432406	482854	4380	12365										
TRIM41	90933	broad.mit.edu	37	chr5	180651714	180651714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccctgaagctcttctgcGaggtagacgaagaggccatc	12	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:180651714G>A	ENST00000315073.5	+	1	1425	c.715G>A	c.(715-717)Gag>Aag	p.E239K	TRIM41_ENST00000351937.5_Missense_Mutation_p.E239K|MIR4638_ENST00000581158.1_RNA|CTC-338M12.7_ENST00000499096.2_RNA	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	239					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E239K(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTCTTCTGCGAGGTAGACGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	61	64					5																	180651714		2203	4300	6503	180584320	SO:0001583	missense	90933			AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.715G>A	5.37:g.180651714G>A	ENSP00000320869:p.Glu239Lys		180584320	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544899	0.45280	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	T;T	0.42131	0.98;0.98	5.01	4.14	0.48551	Zinc finger, B-box (3);	0.000000	0.53938	D	0.000041	T	0.40815	0.1132	N	0.16743	0.435	0.37560	D	0.919045	D;B;B	0.71674	0.998;0.038;0.038	P;B;B	0.60415	0.874;0.008;0.008	T	0.37361	-0.9709	10	0.30078	T	0.28	.	11.1244	0.48308	0.0909:0.0:0.9091:0.0	.	239;239;239	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	K	239;239;118	ENSP00000336749:E239K;ENSP00000320869:E239K	ENSP00000320869:E239K	E	+	1	0	TRIM41	180584320	0.973000	0.33851	1.000000	0.80357	0.983000	0.72400	1.741000	0.38238	1.088000	0.41272	0.491000	0.48974	GAG		0.592	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		A	180651714	G	A	180651714	3	1	61	1	0	0	0	0	1	0	0	0	16556	1059	37	1	717	1	TRIM41	5	180651714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219308	180651714	263546	4381	12366										
TRIM41	90933	broad.mit.edu	37	chr5	180661307	180661307	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcggccgactgctgcgtActgggggcccagggcttccg	15	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr5:180661307A>G	ENST00000315073.5	+	6	2135	c.1425A>G	c.(1423-1425)gtA>gtG	p.V475V	TRIM41_ENST00000351937.5_Silent_p.V475V|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	475	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.V475V(2)		NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACTGCTGCGTACTGGGGGCCC	0.726																																																2	Substitution - coding silent(2)	large_intestine(2)	5											15	18	17					5																	180661307		2035	4022	6057	180593913	SO:0001819	synonymous_variant	90933			AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1425A>G	5.37:g.180661307A>G			180593913	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Silent	SNP	ENST00000315073.5	37	CCDS4466.1																																																																																				0.726	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		G	180661307	A	G	180661307	2	3	61	1	0	0	0	0	0	0	0	1	16556	378	14	4		4	TRIM41	5	180661307	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9593	180661307	253953	4382	12367										
IRF4	3662	broad.mit.edu	37	chr6	407593	407593	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgccattcctctattcaaGaatgaaaaatgtcaagatga	6	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:407593G>T	ENST00000380956.4	+	9	1477	c.1351G>T	c.(1351-1353)Gaa>Taa	p.E451*		NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	451					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.E451*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CTCTATTCAAGAATGAAAAAT	0.413			T	IGH@	MM																																		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	1	Substitution - Nonsense(1)	large_intestine(1)	6											64	65	65					6																	407593		2203	4300	6503	352593	SO:0001587	stop_gained	3662			U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.1351G>T	6.37:g.407593G>T	ENSP00000370343:p.Glu451*		352593	Q5VUI7|Q99660	Nonsense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	G	37	6.301761	0.97458	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	.	.	.	5.51	5.51	0.81932	.	0.799759	0.11784	N	0.529910	.	.	.	.	.	.	0.35176	D	0.772002	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.4315	0.94772	0.0:0.0:1.0:0.0	.	.	.	.	X	451;480	.	ENSP00000370343:E451X	E	+	1	0	IRF4	352593	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.789000	0.85783	2.600000	0.87896	0.655000	0.94253	GAA		0.413	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	407593	G	T	407593	4	4	61	1	0	0	0	0	0	1	0	0	7853	943	33	2	1381	2	IRF4	6	407593	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		407593	170707474	4383	12368										
SERPINB6	5269	broad.mit.edu	37	chr6	2954880	2954880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctggacttctctacggCgctgataaagtcaagctcct	8	11	3	1	rs368785463		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:2954880C>T	ENST00000380520.1	-	3	2370	c.376G>A	c.(376-378)Gcc>Acc	p.A126T	SERPINB6_ENST00000380539.1_Missense_Mutation_p.A126T|SERPINB6_ENST00000335686.5_Missense_Mutation_p.A126T|SERPINB6_ENST00000380546.3_Missense_Mutation_p.A126T|SERPINB6_ENST00000380524.1_Missense_Mutation_p.A126T|SERPINB6_ENST00000380529.1_Missense_Mutation_p.A126T			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	126					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A126T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	TTCTCTACGGCGCTGATAAAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	THR/ALA,THR/ALA	0,4406		0,0,2203	165	155	159		376,376	4.3	0	6		159	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SERPINB6	NM_001195291.1,NM_004568.5	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	126/377,126/377	2954880	1,13005	2203	4300	6503	2899879	SO:0001583	missense	5269			Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.376G>A	6.37:g.2954880C>T	ENSP00000369891:p.Ala126Thr		2899879	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Missense_Mutation	SNP	ENST00000380520.1	37	CCDS4479.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402525	0.25291	0.0	1.16E-4	ENSG00000124570	ENST00000380524;ENST00000380520;ENST00000335686;ENST00000380529;ENST00000380539;ENST00000380546	D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.22	4.34	0.51931	Serpin domain (3);	0.670320	0.16382	N	0.216849	T	0.73946	0.3652	M	0.77820	2.39	0.09310	N	1	P	0.39003	0.654	B	0.40901	0.343	T	0.68153	-0.5484	10	0.45353	T	0.12	.	8.4231	0.32712	0.1557:0.7643:0.0:0.0799	.	126	P35237	SPB6_HUMAN	T	126	ENSP00000369896:A126T;ENSP00000369891:A126T;ENSP00000338358:A126T;ENSP00000369901:A126T;ENSP00000369912:A126T;ENSP00000369919:A126T	ENSP00000338358:A126T	A	-	1	0	SERPINB6	2899879	0.006000	0.16342	0.007000	0.13788	0.005000	0.04900	2.113000	0.41902	1.491000	0.48482	0.650000	0.86243	GCC		0.398	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1			T	2954880	C	T	2954880	3	4	61	1	0	0	0	0	1	0	0	0	14142	768	27	1	770	1	SERPINB6	6	2954880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2547287	2954880	168160187	4384	12369										
TUBB2B	347733	broad.mit.edu	37	chr6	3225000	3225000	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatctacgcctcgtcctcGccctcctcctcctcgaactc	6	21	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:3225000G>A	ENST00000259818.7	-	4	1514	c.1323C>T	c.(1321-1323)ggC>ggT	p.G441G	TUBB2B_ENST00000473006.1_5'UTR	NM_178012.4	NP_821080.1	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B class IIb	441					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|neuron migration (GO:0001764)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.G441G(1)		kidney(2)|large_intestine(5)|lung(1)|prostate(1)|skin(1)	10	Ovarian(93;0.0386)	all_hematologic(90;0.108)				CCTCGTCCTCGCCCTCCTCCT	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	6											84	61	69					6																	3225000		2203	4300	6503	3169999	SO:0001819	synonymous_variant	347733			BC001352	CCDS4485.1	6p25.2	2011-10-10	2011-10-10		ENSG00000137285	ENSG00000137285		"Tubulins"	30829	protein-coding gene	gene with protein product	"class IIb beta-tubulin"	612850	"tubulin, beta 2B"			8619474, 9110174	Standard	NM_178012		Approved	MGC8685, DKFZp566F223, bA506K6.1	uc003mvg.3	Q9BVA1	OTTHUMG00000014143	ENST00000259818.7:c.1323C>T	6.37:g.3225000G>A			3169999	A8K068	Silent	SNP	ENST00000259818.7	37	CCDS4485.1																																																																																				0.647	TUBB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039680.2	NM_178012		A	3225000	G	A	3225000	2	1	61	1	0	0	0	0	0	0	0	1	16795	1074	38	1		1	TUBB2B	6	3225000	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	270120	3225000	167890067	4385	12370										
PRPF4B	8899	broad.mit.edu	37	chr6	4032029	4032029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgataaagagggtatgtCtccagcaaaaagaactaaac	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4032029C>A	ENST00000337659.6	+	2	378	c.278C>A	c.(277-279)tCt>tAt	p.S93Y	PRPF4B_ENST00000538861.1_Missense_Mutation_p.S79Y	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	93	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S93Y(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GAGGGTATGTCTCCAGCAAAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	82	83					6																	4032029		2203	4300	6503	3977028	SO:0001583	missense	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.278C>A	6.37:g.4032029C>A	ENSP00000337194:p.Ser93Tyr		3977028	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406793	0.62399	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.70399	-0.48;-0.48	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000005	T	0.71273	0.3320	L	0.29908	0.895	0.52099	D	0.999941	D	0.61697	0.99	D	0.69142	0.962	T	0.76105	-0.3081	10	0.87932	D	0	.	16.6747	0.85275	0.0:1.0:0.0:0.0	.	93	Q13523	PRP4B_HUMAN	Y	93;79	ENSP00000337194:S93Y;ENSP00000439331:S79Y	ENSP00000337194:S93Y	S	+	2	0	PRPF4B	3977028	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.276000	0.72601	2.511000	0.84671	0.462000	0.41574	TCT		0.333	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			A	4032029	C	A	4032029	3	1	61	1	0	0	0	0	1	0	0	0	12607	913	32	2	284	2	PRPF4B	6	4032029	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	807029	4032029	167083038	4386	12371										
PRPF4B	8899	broad.mit.edu	37	chr6	4032160	4032160	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctggtatggggctcattTtgcaaggttatgagtctggc	14	6	3	1	rs149525756		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4032160T>G	ENST00000337659.6	+	2	509	c.409T>G	c.(409-411)Ttg>Gtg	p.L137V	PRPF4B_ENST00000538861.1_Missense_Mutation_p.L123V	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	137	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L137V(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GGGGCTCATTTTGCAAGGTTA	0.418													T|||	1	0.000199681	0	0	5008	,	,		19720	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											81	88	86					6																	4032160		2203	4300	6503	3977159	SO:0001583	missense	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.409T>G	6.37:g.4032160T>G	ENSP00000337194:p.Leu137Val		3977159	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	16.02	3.003471	0.54254	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.71341	-0.56;-0.51	5.54	3.07	0.35406	.	0.000000	0.53938	D	0.000053	T	0.68924	0.3054	L	0.50333	1.59	0.49130	D	0.999751	D	0.63880	0.993	D	0.70016	0.967	T	0.70502	-0.4854	10	0.59425	D	0.04	.	9.2309	0.37437	0.0:0.1562:0.0:0.8438	.	137	Q13523	PRP4B_HUMAN	V	137;123	ENSP00000337194:L137V;ENSP00000439331:L123V	ENSP00000337194:L137V	L	+	1	2	PRPF4B	3977159	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	0.861000	0.27885	0.353000	0.24079	0.379000	0.24179	TTG		0.418	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			G	4032160	T	G	4032160	3	3	61	1	0	0	0	0	1	0	0	0	12607	1838	64	4	415	4	PRPF4B	6	4032160	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	131	4032160	167082907	4387	12372										
PRPF4B	8899	broad.mit.edu	37	chr6	4037801	4037801	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagcagatctcctcggaGaaggtaaagacatttcatcc	9	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4037801G>T	ENST00000337659.6	+	3	1509	c.1409G>T	c.(1408-1410)aGa>aTa	p.R470I	PRPF4B_ENST00000538861.1_Missense_Mutation_p.R456I	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	470	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R470I(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				TCTCCTCGGAGAAGGTAAAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	66	71					6																	4037801		2203	4300	6503	3982800	SO:0001583	missense	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1409G>T	6.37:g.4037801G>T	ENSP00000337194:p.Arg470Ile		3982800	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736471	0.69189	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.70749	-0.5;-0.51	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.63651	0.2529	M	0.61703	1.905	0.80722	D	1	D	0.56968	0.978	B	0.42738	0.396	T	0.71603	-0.4543	10	0.62326	D	0.03	.	18.4896	0.90842	0.0:0.0:1.0:0.0	.	470	Q13523	PRP4B_HUMAN	I	470;456	ENSP00000337194:R470I;ENSP00000439331:R456I	ENSP00000337194:R470I	R	+	2	0	PRPF4B	3982800	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	4.857000	0.62939	2.342000	0.79632	0.561000	0.74099	AGA		0.438	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			T	4037801	G	T	4037801	3	4	61	1	0	0	0	0	1	0	0	0	12607	942	33	2	1419	2	PRPF4B	6	4037801	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5641	4037801	167077266	4388	12373										
PRPF4B	8899	broad.mit.edu	37	chr6	4041050	4041050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcttgcgaaggcggtctcGatcacgcggtggtcgtagac	15	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4041050G>A	ENST00000337659.6	+	4	1557	c.1457G>A	c.(1456-1458)cGa>cAa	p.R486Q	PRPF4B_ENST00000538861.1_Missense_Mutation_p.R472Q	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	486	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R486Q(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AGGCGGTCTCGATCACGCGGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											65	70	68					6																	4041050		2203	4300	6503	3986049	SO:0001583	missense	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1457G>A	6.37:g.4041050G>A	ENSP00000337194:p.Arg486Gln		3986049	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.452050	0.63290	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.70869	-0.5;-0.52	5.49	5.49	0.81192	.	0.111160	0.39083	N	0.001475	T	0.37972	0.1023	L	0.34521	1.04	0.50632	D	0.99988	P	0.35328	0.495	B	0.19946	0.027	T	0.37686	-0.9695	10	0.15952	T	0.53	.	13.0158	0.58757	0.074:0.0:0.926:0.0	.	486	Q13523	PRP4B_HUMAN	Q	486;472	ENSP00000337194:R486Q;ENSP00000439331:R472Q	ENSP00000337194:R486Q	R	+	2	0	PRPF4B	3986049	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.743000	0.55104	2.735000	0.93741	0.591000	0.81541	CGA		0.433	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			A	4041050	G	A	4041050	3	1	61	1	0	0	0	0	1	0	0	0	12607	1058	37	1	1471	1	PRPF4B	6	4041050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3249	4041050	167074017	4389	12374										
PRPF4B	8899	broad.mit.edu	37	chr6	4057346	4057346	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgaactctatactggaaaAattttattccctggcaaaac	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4057346A>C	ENST00000337659.6	+	13	2758	c.2658A>C	c.(2656-2658)aaA>aaC	p.K886N	PRPF4B_ENST00000538861.1_Missense_Mutation_p.K872N	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	886	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K375N(1)|p.K886N(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				ATACTGGAAAAATTTTATTCC	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	6											96	96	96					6																	4057346		2203	4300	6503	4002345	SO:0001583	missense	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.2658A>C	6.37:g.4057346A>C	ENSP00000337194:p.Lys886Asn		4002345	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560938	0.45590	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.67171	-0.25;-0.25	6.04	2.33	0.28932	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66839	0.2830	L	0.53561	1.675	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.68648	-0.5353	10	0.66056	D	0.02	.	9.7957	0.40733	0.7793:0.0:0.2207:0.0	.	886	Q13523	PRP4B_HUMAN	N	886;872	ENSP00000337194:K886N;ENSP00000439331:K872N	ENSP00000337194:K886N	K	+	3	2	PRPF4B	4002345	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.560000	0.36331	0.167000	0.19631	0.460000	0.39030	AAA		0.343	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			C	4057346	A	C	4057346	3	2	61	1	0	0	0	0	1	0	0	0	12607	11	1	4	2708	4	PRPF4B	6	4057346	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16296	4057346	167057721	4390	12375										
PRPF4B	8899	broad.mit.edu	37	chr6	4058968	4058968	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttgttttgtagatgattCgaaaaggtgtgttcaaagat	11	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4058968C>T	ENST00000337659.6	+	14	2840	c.2740C>T	c.(2740-2742)Cga>Tga	p.R914*	PRPF4B_ENST00000538861.1_Nonsense_Mutation_p.R900*|PRPF4B_ENST00000494674.1_3'UTR	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	914	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R403*(1)|p.R914*(1)		breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GTAGATGATTCGAAAAGGTGT	0.294																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											50	49	50					6																	4058968		2203	4298	6501	4003967	SO:0001587	stop_gained	8899			U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.2740C>T	6.37:g.4058968C>T	ENSP00000337194:p.Arg914*		4003967	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Nonsense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	C	35	5.570608	0.96540	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	.	.	.	5.93	3.95	0.45737	.	0.000000	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6523	0.85219	0.2478:0.7521:0.0:0.0	.	.	.	.	X	914;900	.	ENSP00000337194:R914X	R	+	1	2	PRPF4B	4003967	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.723000	0.47277	1.472000	0.48140	0.655000	0.94253	CGA		0.294	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			T	4058968	C	T	4058968	4	4	61	1	0	0	0	0	0	1	0	0	12607	876	31	1	2794	1	PRPF4B	6	4058968	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1622	4058968	167056099	4391	12376										
C6orf146	222826	broad.mit.edu	37	chr6	4069220	4069220	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaggtttgaatgagagttCttggcatggacttaaaatag	12	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4069220C>A	ENST00000274673.3	-	7	1640	c.1237G>T	c.(1237-1239)Gaa>Taa	p.E413*	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	413								p.E413*(1)									AATGAGAGTTCTTGGCATGGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											114	115	115					6																	4069220		2203	4300	6503	4014219	SO:0001587	stop_gained	222826			BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1237G>T	6.37:g.4069220C>A	ENSP00000274673:p.Glu413*		4014219	Q5JYK1	Nonsense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751902	0.89753	.	.	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	.	.	.	4.76	4.76	0.60689	.	0.398250	0.25055	N	0.033498	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-9.6916	13.1418	0.59438	0.0:1.0:0.0:0.0	.	.	.	.	X	413;260;541	.	ENSP00000274673:E413X	E	-	1	0	C6orf146	4014219	0.996000	0.38824	0.335000	0.25508	0.107000	0.19398	1.552000	0.36244	2.471000	0.83476	0.460000	0.39030	GAA		0.383	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		A	4069220	C	A	4069220	4	1	61	1	0	0	0	0	0	1	0	0	2341	922	32	2	293	2	C6orf146	6	4069220	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10252	4069220	167045847	4392	12377										
C6orf146	222826	broad.mit.edu	37	chr6	4069599	4069599	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccagtaaacgagttatCaagtgttcaacagaggtttc	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4069599C>A	ENST00000274673.3	-	7	1261	c.858G>T	c.(856-858)ttG>ttT	p.L286F	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	286								p.L286F(1)									AACGAGTTATCAAGTGTTCAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											113	111	112					6																	4069599		2203	4300	6503	4014598	SO:0001583	missense	222826			BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.858G>T	6.37:g.4069599C>A	ENSP00000274673:p.Leu286Phe		4014598	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824796	0.50739	.	.	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	T	0.26067	1.76	5.43	4.54	0.55810	.	0.191235	0.34067	N	0.004284	T	0.33585	0.0868	M	0.67953	2.075	0.09310	N	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.14035	-1.0487	10	0.48119	T	0.1	-9.8763	11.8424	0.52361	0.0:0.8245:0.1755:0.0	.	286	Q8IXS0	CF146_HUMAN	F	286;133;414	ENSP00000274673:L286F	ENSP00000274673:L286F	L	-	3	2	C6orf146	4014598	0.938000	0.31826	0.047000	0.18901	0.819000	0.46315	0.150000	0.16263	1.468000	0.48064	0.650000	0.86243	TTG		0.423	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		A	4069599	C	A	4069599	3	1	61	1	0	0	0	0	1	0	0	0	2341	825	29	2	672	2	C6orf146	6	4069599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	379	4069599	167045468	4393	12378										
CDYL	9425	broad.mit.edu	37	chr6	4935846	4935846	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaaaggaaatttattgaCgacagaagagaccagccttt	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4935846C>T	ENST00000328908.5	+	5	1082	c.951C>T	c.(949-951)gaC>gaT	p.D317D	CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Silent_p.D263D|CDYL_ENST00000343762.5_Silent_p.D131D|CDYL_ENST00000449732.2_Silent_p.D131D			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	317					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.D317D(2)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AATTTATTGACGACAGAAGAG	0.458																																																2	Substitution - coding silent(2)	large_intestine(2)	6											115	112	113					6																	4935846		2203	4300	6503	4880845	SO:0001819	synonymous_variant	9425			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.951C>T	6.37:g.4935846C>T			4880845	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																					0.458	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		T	4935846	C	T	4935846	2	4	61	1	0	0	0	0	0	0	0	1	3191	535	19	1		1	CDYL	6	4935846	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	866247	4935846	166179221	4394	12379										
CDYL	9425	broad.mit.edu	37	chr6	4943786	4943786	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttcattttagaaacttCgtgaatactttcattcaatt	3	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4943786C>T	ENST00000328908.5	+	7	1421	c.1290C>T	c.(1288-1290)ttC>ttT	p.F430F	CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Silent_p.F376F|CDYL_ENST00000343762.5_Silent_p.F244F|CDYL_ENST00000449732.2_Silent_p.F244F			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	430					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.F430F(3)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		TTAGAAACTTCGTGAATACTT	0.338																																																3	Substitution - coding silent(3)	large_intestine(3)	6											64	67	66					6																	4943786		2203	4300	6503	4888785	SO:0001819	synonymous_variant	9425			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.1290C>T	6.37:g.4943786C>T			4888785	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																					0.338	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		T	4943786	C	T	4943786	2	4	61	1	0	0	0	0	0	0	0	1	3191	883	31	1		1	CDYL	6	4943786	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7940	4943786	166171281	4395	12380										
CDYL	9425	broad.mit.edu	37	chr6	4943889	4943889	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttgcgatgtggtttggGctaatgaaaaggcttggttt	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4943889G>T	ENST00000328908.5	+	7	1524	c.1393G>T	c.(1393-1395)Gct>Tct	p.A465S	CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Missense_Mutation_p.A411S|CDYL_ENST00000343762.5_Missense_Mutation_p.A279S|CDYL_ENST00000449732.2_Missense_Mutation_p.A279S			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	465					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.A465S(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		TGTGGTTTGGGCTAATGAAAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											151	147	148					6																	4943889		2203	4300	6503	4888888	SO:0001583	missense	9425			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.1393G>T	6.37:g.4943889G>T	ENSP00000330512:p.Ala465Ser		4888888	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		.	.	.	.	.	.	.	.	.	.	G	35	5.525392	0.96431	.	.	ENSG00000153046	ENST00000328908;ENST00000397588;ENST00000449732;ENST00000343762	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.63	5.63	0.86233	Crotonase, core (1);	0.000000	0.85682	D	0.000000	T	0.71048	0.3294	M	0.80746	2.51	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.75484	0.986;0.986	T	0.74699	-0.3577	10	0.87932	D	0	.	18.669	0.91504	0.0:0.0:1.0:0.0	.	411;465	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	S	465;411;279;279	ENSP00000330512:A465S;ENSP00000380718:A411S;ENSP00000394076:A279S;ENSP00000340908:A279S	ENSP00000330512:A465S	A	+	1	0	CDYL	4888888	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.640000	0.98453	2.644000	0.89710	0.655000	0.94253	GCT		0.443	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		T	4943889	G	T	4943889	3	4	61	1	0	0	0	0	1	0	0	0	3191	1203	42	2	1249	2	CDYL	6	4943889	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103	4943889	166171178	4396	12381										
RPP40	10799	broad.mit.edu	37	chr6	4995410	4995410	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgttctcctccttttcGaaaaccatgttcattttttt	3	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:4995410G>A	ENST00000380051.2	-	8	1038	c.994C>T	c.(994-996)Cga>Tga	p.R332*	RPP40_ENST00000464646.1_Nonsense_Mutation_p.R272*|RPP40_ENST00000319533.5_Nonsense_Mutation_p.R309*	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	332					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)	p.R332*(1)		NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				CCTCCTTTTCGAAAACCATGT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											75	76	76					6																	4995410		2203	4300	6503	4940409	SO:0001587	stop_gained	10799			U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"ribonuclease P1", "ribonuclease P 40kDa subunit"	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.994C>T	6.37:g.4995410G>A	ENSP00000369391:p.Arg332*		4940409	Q5VX97|Q8WVK8	Nonsense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487181	0.26686	.	.	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	.	.	.	5.07	1.29	0.21616	.	1.273270	0.05010	N	0.470744	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-8.923	10.4971	0.44783	0.351:0.0:0.649:0.0	.	.	.	.	X	332;309;272	.	ENSP00000317998:R309X	R	-	1	2	RPP40	4940409	1.000000	0.71417	0.001000	0.08648	0.064000	0.16182	3.228000	0.51270	-0.277000	0.09193	-0.797000	0.03246	CGA		0.398	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638		A	4995410	G	A	4995410	4	1	61	1	0	0	0	0	0	1	0	0	13651	1066	37	1	101	1	RPP40	6	4995410	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51521	4995410	166119657	4397	12382										
NRN1	51299	broad.mit.edu	37	chr6	5999314	5999314	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccgctgccgcagagttcGaataagctgccttggatgtt	12	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:5999314G>A	ENST00000244766.2	-	3	541	c.324C>T	c.(322-324)ttC>ttT	p.F108F	NRN1_ENST00000495850.1_5'UTR	NM_001278710.1|NM_016588.2	NP_001265639.1|NP_057672.1	Q9NPD7	NRN1_HUMAN	neuritin 1	108					nervous system development (GO:0007399)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|anchored component of membrane (GO:0031225)|cell junction (GO:0030054)|synapse (GO:0045202)		p.F108F(1)		endometrium(2)|large_intestine(2)|lung(4)	8	Ovarian(93;0.0816)	all_hematologic(90;0.151)		OV - Ovarian serous cystadenocarcinoma(45;0.00415)		CGCAGAGTTCGAATAAGCTGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											86	80	82					6																	5999314		2203	4300	6503	5944313	SO:0001819	synonymous_variant	51299			AF136631	CCDS4495.1, CCDS75393.1	6p25.1	2008-02-05			ENSG00000124785	ENSG00000124785			17972	protein-coding gene	gene with protein product		607409				9122250	Standard	NM_016588		Approved	NRN	uc003mwu.3	Q9NPD7	OTTHUMG00000014184	ENST00000244766.2:c.324C>T	6.37:g.5999314G>A			5944313	B2RA93|Q7Z4Y1	Silent	SNP	ENST00000244766.2	37	CCDS4495.1																																																																																				0.582	NRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039753.1			A	5999314	G	A	5999314	2	1	61	1	0	0	0	0	0	0	0	1	10689	1049	37	1		1	NRN1	6	5999314	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1003904	5999314	165115753	4398	12383										
RREB1	6239	broad.mit.edu	37	chr6	7231542	7231542	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgctggcctccattgcccaGatcatctcatctgtatcctc	6	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:7231542G>T	ENST00000349384.6	+	10	3524	c.3210G>T	c.(3208-3210)caG>caT	p.Q1070H	RREB1_ENST00000334984.6_Missense_Mutation_p.Q1070H|RREB1_ENST00000379938.2_Missense_Mutation_p.Q1070H|RREB1_ENST00000379933.3_Missense_Mutation_p.Q1070H	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1070					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q1070H(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCATTGCCCAGATCATCTCAT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6											37	45	42					6																	7231542		2203	4300	6503	7176541	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3210G>T	6.37:g.7231542G>T	ENSP00000305560:p.Gln1070His		7176541	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244987	0.79912	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.27557	1.83;1.83;1.83;1.66	5.84	4.98	0.66077	.	0.000000	0.56097	D	0.000021	T	0.41994	0.1183	M	0.66939	2.045	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.46076	-0.9217	10	0.72032	D	0.01	-54.9402	11.19	0.48679	0.1401:0.0:0.8599:0.0	.	1070;1070;1070	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	H	1070	ENSP00000369265:Q1070H;ENSP00000369270:Q1070H;ENSP00000305560:Q1070H;ENSP00000335574:Q1070H	ENSP00000335574:Q1070H	Q	+	3	2	RREB1	7176541	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.556000	0.67307	1.473000	0.48159	-0.150000	0.13652	CAG		0.642	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7231542	G	T	7231542	3	4	61	1	0	0	0	0	1	0	0	0	13716	933	33	2	3236	2	RREB1	6	7231542	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1232228	7231542	163883525	4399	12384										
CAGE1	285782	broad.mit.edu	37	chr6	7374037	7374037	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaatcttcatctgtagttCtttaaccctcttctctaaat	4	10	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:7374037C>A	ENST00000512086.1	-	5	1217	c.1015G>T	c.(1015-1017)Gaa>Taa	p.E339*	CAGE1_ENST00000509324.1_5'Flank|CAGE1_ENST00000338150.4_Nonsense_Mutation_p.E339*|CAGE1_ENST00000296742.7_Nonsense_Mutation_p.E203*|CAGE1_ENST00000379918.4_Nonsense_Mutation_p.E339*|CAGE1_ENST00000502583.1_Nonsense_Mutation_p.E339*			Q8TC20	CAGE1_HUMAN	cancer antigen 1	339								p.E339*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					ATCTGTAGTTCTTTAACCCTC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											121	107	111					6																	7374037		1846	4104	5950	7319036	SO:0001587	stop_gained	285782			BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"cancer/testis antigen 95"	608304	"cancer/testis antigen 3"	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.1015G>T	6.37:g.7374037C>A	ENSP00000427583:p.Glu339*		7319036	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Nonsense_Mutation	SNP	ENST00000512086.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.448282	0.96205	.	.	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	.	.	.	5.42	5.42	0.78866	.	0.094643	0.46442	D	0.000297	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-20.9155	14.7243	0.69332	0.0:1.0:0.0:0.0	.	.	.	.	X	339;339;339;203;339;339;339;351	.	ENSP00000296742:E203X	E	-	1	0	CAGE1	7319036	0.998000	0.40836	0.327000	0.25402	0.803000	0.45373	1.884000	0.39668	2.553000	0.86117	0.591000	0.81541	GAA		0.328	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		A	7374037	C	A	7374037	4	1	61	1	0	0	0	0	0	1	0	0	2578	922	32	2	1650	2	CAGE1	6	7374037	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142495	7374037	163741030	4400	12385										
RIOK1	83732	broad.mit.edu	37	chr6	7403054	7403054	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttcttattcaagatttCgtcatggctattgtaaagga	7	5	3	1	rs138314843		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:7403054C>T	ENST00000379834.2	+	8	1198	c.691C>T	c.(691-693)Cgt>Tgt	p.R231C		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	231	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R224C(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					TTCAAGATTTCGTCATGGCTA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	CYS/ARG,	1,4405	2.1+/-5.4	0,1,2202	67	70	69		691,	6.2	1	6	dbSNP_134	69	0,8600		0,0,4300	yes	missense,utr-5	RIOK1	NM_031480.2,NM_153005.1	180,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,	231/569,	7403054	1,13005	2203	4300	6503	7348053	SO:0001583	missense	83732			BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"RIO kinase 1 (yeast)"				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.691C>T	6.37:g.7403054C>T	ENSP00000369162:p.Arg231Cys		7348053	B2RB28|Q8NDC8|Q96NV9	Missense_Mutation	SNP	ENST00000379834.2	37	CCDS4500.1	.	.	.	.	.	.	.	.	.	.	C	33	5.261834	0.95368	2.27E-4	0.0	ENSG00000124784	ENST00000379834	T	0.07800	3.16	6.17	6.17	0.99709	RIO kinase (1);Protein kinase-like domain (1);RIO-like kinase (1);	0.000000	0.85682	D	0.000000	T	0.41026	0.1141	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58284	-0.7663	10	0.87932	D	0	-14.4981	19.8676	0.96824	0.0:1.0:0.0:0.0	.	231	Q9BRS2	RIOK1_HUMAN	C	231	ENSP00000369162:R231C	ENSP00000369162:R231C	R	+	1	0	RIOK1	7348053	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.401000	0.79962	2.941000	0.99782	0.655000	0.94253	CGT		0.318	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480		T	7403054	C	T	7403054	3	4	61	1	0	0	0	0	1	0	0	0	13414	884	31	1	721	1	RIOK1	6	7403054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29017	7403054	163712013	4401	12386										
DSP	1832	broad.mit.edu	37	chr6	7581641	7581641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgaggagaggacgaagcGaagcggacagtgataaaaat	14	6	0	3	rs142885240	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:7581641G>A	ENST00000379802.3	+	23	5559	c.5218G>A	c.(5218-5220)Gaa>Aaa	p.E1740K	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1740	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E1740K(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGGACGAAGCGAAGCGGACAG	0.507													G|||	2	0.000399361	0	0	5008	,	,		17292	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	121	126	124		,5218	5.1	0	6	dbSNP_134	124	11,8589	8.4+/-32.0	0,11,4289	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,56	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,possibly-damaging	,1740/2872	7581641	12,12994	2203	4300	6503	7526640	SO:0001583	missense	1832			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.5218G>A	6.37:g.7581641G>A	ENSP00000369129:p.Glu1740Lys		7526640	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686523	0.29962	2.27E-4	0.001279	ENSG00000096696	ENST00000379802	T	0.74526	-0.85	5.98	5.09	0.68999	.	0.087662	0.48767	D	0.000161	T	0.46658	0.1404	L	0.36672	1.1	0.80722	D	1	D	0.53745	0.962	B	0.33960	0.173	T	0.51068	-0.8752	10	0.22706	T	0.39	.	17.0821	0.86601	0.0:0.1268:0.8732:0.0	.	1740	P15924	DESP_HUMAN	K	1740	ENSP00000369129:E1740K	ENSP00000369129:E1740K	E	+	1	0	DSP	7526640	1.000000	0.71417	0.049000	0.19019	0.282000	0.26991	3.140000	0.50585	1.496000	0.48567	0.650000	0.86243	GAA		0.507	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7581641	G	A	7581641	3	1	61	1	0	0	0	0	1	0	0	0	4792	1059	37	1	5308	1	DSP	6	7581641	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178587	7581641	163533426	4402	12387										
TXNDC5	81567	broad.mit.edu	37	chr6	7883385	7883385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaactgtgttcctaaagttCgtctttcgcttggctcagga	9	11	2	0	rs530530741		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:7883385C>T	ENST00000379757.4	-	10	1328	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	TXNDC5_ENST00000539054.1_Missense_Mutation_p.E359K|TXNDC5_ENST00000473453.1_Missense_Mutation_p.E323K|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	431					apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)	p.E431K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					TCCTAAAGTTCGTCTTTCGCT	0.557													C|||	1	0.000199681	0	0	5008	,	,		17811	0		0.001	False		,,,				2504	0				Ovarian(119;1430 1625 3928 26125 34589)											1	Substitution - Missense(1)	large_intestine(1)	6											158	115	130					6																	7883385		2203	4300	6503	7828384	SO:0001583	missense	81567			AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"Protein disulfide isomerases"	21073	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 15"		"thioredoxin domain containing 5"				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.1291G>A	6.37:g.7883385C>T	ENSP00000369081:p.Glu431Lys		7828384	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	37	CCDS4505.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518717	0.85495	.	.	ENSG00000239264	ENST00000539054;ENST00000379757;ENST00000473453	T;T;T	0.03860	3.8;3.78;3.83	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	0.977;1.0	P;D	0.79784	0.672;0.993	T	0.01982	-1.1235	10	0.87932	D	0	.	20.063	0.97692	0.0:1.0:0.0:0.0	.	359;431	Q86UY0;Q8NBS9	.;TXND5_HUMAN	K	359;431;323	ENSP00000442453:E359K;ENSP00000369081:E431K;ENSP00000420784:E323K	ENSP00000442453:E359K	E	-	1	0	TXNDC5	7828384	1.000000	0.71417	0.110000	0.21437	0.083000	0.17756	6.631000	0.74277	2.735000	0.93741	0.655000	0.94253	GAA		0.557	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		T	7883385	C	T	7883385	3	4	61	1	0	0	0	0	1	0	0	0	16839	893	31	1	11	1	TXNDC5	6	7883385	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	301744	7883385	163231682	4403	12388										
GCNT2	2651	broad.mit.edu	37	chr6	10529382	10529382	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgctatgagtacatggttCgaagccactatgtaacagaa	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10529382C>T	ENST00000379597.3	+	1	794	c.238C>T	c.(238-240)Cga>Tga	p.R80*	GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Nonsense_Mutation_p.R80*|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	80					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.R80*(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		GTACATGGTTCGAAGCCACTA	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											124	130	128					6																	10529382		2203	4300	6503	10637368	SO:0001587	stop_gained	2651			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.238C>T	6.37:g.10529382C>T	ENSP00000368917:p.Arg80*		10637368		Nonsense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	C	37	6.013081	0.97200	.	.	ENSG00000111846	ENST00000495262;ENST00000379597	.	.	.	5.43	5.43	0.79202	.	0.350897	0.27659	N	0.018390	.	.	.	.	.	.	0.23082	N	0.998323	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-19.4036	13.8371	0.63415	0.153:0.847:0.0:0.0	.	.	.	.	X	80	.	ENSP00000368917:R80X	R	+	1	2	GCNT2	10637368	0.000000	0.05858	0.009000	0.14445	0.324000	0.28378	0.505000	0.22642	2.563000	0.86464	0.555000	0.69702	CGA		0.433	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		T	10529382	C	T	10529382	4	4	61	1	0	0	0	0	0	1	0	0	6321	876	31	1	240	1	GCNT2	6	10529382	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2645997	10529382	160585685	4404	12389										
GCNT2	2651	broad.mit.edu	37	chr6	10529972	10529972	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagggactttgctaacttCgtcctccaagaccagctcgc	8	14	0	1	rs532935757		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10529972C>T	ENST00000379597.3	+	1	1384	c.828C>T	c.(826-828)ttC>ttT	p.F276F	GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Silent_p.F276F|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	276					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.F276F(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTGCTAACTTCGTCCTCCAAG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	6											134	126	129					6																	10529972		2203	4300	6503	10637958	SO:0001819	synonymous_variant	2651			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.828C>T	6.37:g.10529972C>T			10637958		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																				0.488	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		T	10529972	C	T	10529972	2	4	61	1	0	0	0	0	0	0	0	1	6321	883	31	1		1	GCNT2	6	10529972	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	590	10529972	160585095	4405	12390										
GCNT2	2651	broad.mit.edu	37	chr6	10556722	10556722	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaattatttttatcgtcttCtctgtgttcaattttggggg	9	5	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10556722C>T	ENST00000379597.3	+	1	1481				GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Silent_p.F22F|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.F22F(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTATCGTCTTCTCTGTGTTCA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	6											101	99	100					6																	10556722		2203	4300	6503	10664708	SO:0001627	intron_variant	2651			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.925+26653C>T	6.37:g.10556722C>T			10664708		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																				0.388	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		T	10556722	C	T	10556722	1	4	61	0	1	0	0	0	0	0	0	0	6321	912	32	3		3	GCNT2	6	10556722	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26750	10556722	160558345	4406	12391										
GCNT2	2651	broad.mit.edu	37	chr6	10586695	10586695	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgcttcaaagacagagtCtgtggtttatgcaggcattt	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10586695C>A	ENST00000379597.3	+	2	1481				GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.S158Y|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.S158Y(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AAGACAGAGTCTGTGGTTTAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6											127	122	124					6																	10586695		2203	4300	6503	10694681	SO:0001627	intron_variant	2651			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34889C>A	6.37:g.10586695C>A			10694681		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	C	7.480	0.648510	0.14516	.	.	ENSG00000111846	ENST00000265012	T	0.12672	2.66	5.58	2.81	0.32909	.	.	.	.	.	T	0.04861	0.0131	L	0.46157	1.445	0.19300	N	0.99997	B	0.16396	0.017	B	0.24974	0.057	T	0.39522	-0.9610	9	0.72032	D	0.01	.	6.6955	0.23197	0.1174:0.5631:0.2516:0.068	.	158	Q8NFS9	GNT2C_HUMAN	Y	158	ENSP00000265012:S158Y	ENSP00000265012:S158Y	S	+	2	0	GCNT2	10694681	0.000000	0.05858	0.040000	0.18447	0.568000	0.35870	0.381000	0.20619	0.297000	0.22615	-0.140000	0.14226	TCT		0.478	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		A	10586695	C	A	10586695	1	1	61	0	1	0	0	0	0	0	0	0	6321	913	32	2		2	GCNT2	6	10586695	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29973	10586695	160528372	4407	12392										
MAK	4117	broad.mit.edu	37	chr6	10791917	10791917	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaatcttaccgaaatggaGaatcttttttccttttttct	5	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10791917G>T	ENST00000313243.2	-	10	1689	c.1307C>A	c.(1306-1308)tCt>tAt	p.S436Y	MAK_ENST00000474039.1_Missense_Mutation_p.S436Y|MAK_ENST00000538030.1_Missense_Mutation_p.S436Y|RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000354489.2_Missense_Mutation_p.S436Y			P20794	MAK_HUMAN	male germ cell-associated kinase	436					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)	p.S436Y(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CCGAAATGGAGAATCTTTTTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											46	49	48					6																	10791917		2203	4300	6503	10899903	SO:0001583	missense	4117				CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1307C>A	6.37:g.10791917G>T	ENSP00000313021:p.Ser436Tyr		10899903	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	G	8.818	0.936939	0.18206	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.72725	-0.68;-0.68;-0.67	5.25	1.32	0.21799	.	0.920541	0.09167	N	0.839425	T	0.48750	0.1517	M	0.62723	1.935	0.44890	D	0.997909	B	0.33477	0.413	B	0.35813	0.211	T	0.56226	-0.8014	10	0.54805	T	0.06	.	2.7053	0.05160	0.2723:0.1186:0.4878:0.1213	.	436	P20794	MAK_HUMAN	Y	436	ENSP00000313021:S436Y;ENSP00000346484:S436Y;ENSP00000442250:S436Y	ENSP00000313021:S436Y	S	-	2	0	MAK	10899903	0.854000	0.29725	0.729000	0.30791	0.153000	0.21895	0.993000	0.29680	0.282000	0.22254	-0.150000	0.13652	TCT		0.348	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		T	10791917	G	T	10791917	3	4	61	1	0	0	0	0	1	0	0	0	9227	942	33	2	584	2	MAK	6	10791917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205222	10791917	160323150	4408	12393										
GCM2	9247	broad.mit.edu	37	chr6	10874321	10874321	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagacacacatcccaagtCtctgcttcatctgtcctaga	6	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10874321C>A	ENST00000379491.4	-	5	1575	c.1428G>T	c.(1426-1428)gaG>gaT	p.E476D	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	476					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.E476D(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CATCCCAAGTCTCTGCTTCAT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	67	68					6																	10874321		2203	4300	6503	10982307	SO:0001583	missense	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.1428G>T	6.37:g.10874321C>A	ENSP00000368805:p.Glu476Asp		10982307	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.323965	0.24080	.	.	ENSG00000124827	ENST00000379491	T	0.68624	-0.34	5.27	-3.09	0.05331	.	0.180277	0.48286	N	0.000190	T	0.21761	0.0524	L	0.31845	0.965	0.53688	D	0.999976	B	0.21606	0.058	B	0.17098	0.017	T	0.08229	-1.0732	10	0.20519	T	0.43	-18.2543	0.5356	0.00636	0.2454:0.3074:0.2053:0.2419	.	476	O75603	GCM2_HUMAN	D	476	ENSP00000368805:E476D	ENSP00000368805:E476D	E	-	3	2	GCM2	10982307	0.010000	0.17322	0.011000	0.14972	0.838000	0.47535	-0.082000	0.11304	-0.572000	0.06006	0.591000	0.81541	GAG		0.517	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			A	10874321	C	A	10874321	3	1	61	1	0	0	0	0	1	0	0	0	6318	912	32	2	96	2	GCM2	6	10874321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82404	10874321	160240746	4409	12394										
GCM2	9247	broad.mit.edu	37	chr6	10876732	10876732	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttggttacggggtatccGctgtgccctcgacaaggaat	13	9	0	0	rs145276001	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10876732G>A	ENST00000379491.4	-	3	549	c.402C>T	c.(400-402)agC>agT	p.S134S	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	134					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.S134S(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CGGGGTATCCGCTGTGCCCTC	0.478													G|||	2	0.000399361	0.0015	0	5008	,	,		20088	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						G		3,4403	6.2+/-15.9	0,3,2200	105	90	95		402	-7.8	0.4	6	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GCM2	NM_004752.3		0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308		134/507	10876732	4,13002	2203	4300	6503	10984718	SO:0001819	synonymous_variant	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.402C>T	6.37:g.10876732G>A			10984718	D3GDV6|Q5THN5	Silent	SNP	ENST00000379491.4	37	CCDS4517.1																																																																																				0.478	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			A	10876732	G	A	10876732	2	1	61	1	0	0	0	0	0	0	0	1	6318	1078	38	1		1	GCM2	6	10876732	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2411	10876732	160238335	4410	12395										
SYCP2L	221711	broad.mit.edu	37	chr6	10912948	10912948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattagagaaattttggatcGacttcaacctaggaagtcag	9	6	2	1	rs375562683		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10912948G>A	ENST00000283141.6	+	13	1257	c.961G>A	c.(961-963)Gac>Aac	p.D321N	RP11-637O19.3_ENST00000480294.1_3'UTR|SYCP2L_ENST00000543878.1_Missense_Mutation_p.D162N	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	321						nucleus (GO:0005634)		p.D321N(1)		breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ATTTTGGATCGACTTCAACCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	105	108					6																	10912948		1846	4080	5926	11020934	SO:0001583	missense	221711			AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.961G>A	6.37:g.10912948G>A	ENSP00000283141:p.Asp321Asn		11020934	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	37	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227519	0.79576	.	.	ENSG00000153157	ENST00000543878;ENST00000283141	T;T	0.71579	-0.58;0.42	5.42	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.81322	0.4798	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.97110	0.839;1.0	D	0.85247	0.1042	10	0.87932	D	0	-5.5838	15.9513	0.79840	0.0:0.1353:0.8647:0.0	.	162;321	B4DFB8;Q5T4T6	.;SYC2L_HUMAN	N	162;321	ENSP00000440676:D162N;ENSP00000283141:D321N	ENSP00000283141:D321N	D	+	1	0	SYCP2L	11020934	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	7.569000	0.82380	1.284000	0.44531	-0.150000	0.13652	GAC		0.348	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		A	10912948	G	A	10912948	3	1	61	1	0	0	0	0	1	0	0	0	15472	1058	37	1	1011	1	SYCP2L	6	10912948	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36216	10912948	160202119	4411	12396										
SYCP2L	221711	broad.mit.edu	37	chr6	10956428	10956428	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgaacggttctgccattCtcccaacctttgaaaacttc	5	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:10956428C>A	ENST00000283141.6	+	25	2412	c.2116C>A	c.(2116-2118)Ctc>Atc	p.L706I		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	706						nucleus (GO:0005634)		p.L706I(1)		breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TTCTGCCATTCTCCCAACCTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	67	69					6																	10956428		1823	4089	5912	11064414	SO:0001583	missense	221711			AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.2116C>A	6.37:g.10956428C>A	ENSP00000283141:p.Leu706Ile		11064414	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	37	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	C	0.553	-0.848558	0.02651	.	.	ENSG00000153157	ENST00000283141	T	0.15372	2.43	5.76	-0.581	0.11713	.	0.400583	0.22752	N	0.056062	T	0.01189	0.0039	N	0.02011	-0.69	0.09310	N	0.999999	B	0.12630	0.006	B	0.10450	0.005	T	0.44452	-0.9327	10	0.14656	T	0.56	-0.1132	5.289	0.15717	0.4361:0.3244:0.2394:0.0	.	706	Q5T4T6	SYC2L_HUMAN	I	706	ENSP00000283141:L706I	ENSP00000283141:L706I	L	+	1	0	SYCP2L	11064414	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.353000	0.07691	-0.320000	0.08640	0.655000	0.94253	CTC		0.358	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		A	10956428	C	A	10956428	3	1	61	1	0	0	0	0	1	0	0	0	15472	913	32	2	2214	2	SYCP2L	6	10956428	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43480	10956428	160158639	4412	12397										
ERVFRDE1	405754	broad.mit.edu	37	chr6	11105315	11105315	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagattagggtcccatcGataggaaatatgtaattccg	9	7	1	1	rs200815152		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:11105315G>A	ENST00000472091.1	-	2	604	c.229C>T	c.(229-231)Cga>Tga	p.R77*	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Nonsense_Mutation_p.R77*	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	77					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)		p.R77*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						GGGTCCCATCGATAGGAAATA	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											133	120	125					6																	11105315		2203	4300	6503	11213301	SO:0001587	stop_gained	405754			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.229C>T	6.37:g.11105315G>A	ENSP00000420174:p.Arg77*		11213301		Nonsense_Mutation	SNP	ENST00000472091.1	37	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	G	36	5.666458	0.96745	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	.	.	.	0.235	0.235	0.15431	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	.	.	.	.	.	.	.	X	77	.	ENSP00000420174:R77X	R	-	1	2	ERVFRD-1	11213301	0.834000	0.29399	0.470000	0.27216	0.472000	0.32918	0.364000	0.20325	0.308000	0.22923	0.313000	0.20887	CGA		0.458	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		A	11105315	G	A	11105315	4	1	61	1	0	0	0	0	0	1	0	0	5259	1066	37	1	1391	1	ERVFRDE1	6	11105315	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148887	11105315	160009752	4413	12398										
NEDD9	4739	broad.mit.edu	37	chr6	11213906	11213906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtctcccttgcgaaaggCcagttcctcggcacactctg	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:11213906C>T	ENST00000379446.5	-	2	233	c.67G>A	c.(67-69)Gcc>Acc	p.A23T	NEDD9_ENST00000379433.5_Missense_Mutation_p.A23T|NEDD9_ENST00000504387.1_Missense_Mutation_p.A23T|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	23	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.A23T(2)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			TTGCGAAAGGCCAGTTCCTCG	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	6											117	102	107					6																	11213906		2203	4300	6503	11321892	SO:0001583	missense	4739			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"Cas scaffolding proteins"	7733	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 2", "Cas-like"	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.67G>A	6.37:g.11213906C>T	ENSP00000368759:p.Ala23Thr		11321892	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.039356	0.75617	.	.	ENSG00000111859	ENST00000379446;ENST00000504387;ENST00000379433;ENST00000513989;ENST00000397378	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	6.17	6.17	0.99709	Src homology-3 domain (4);	0.047700	0.85682	D	0.000000	T	0.15565	0.0375	N	0.03903	-0.33	0.80722	D	1	P;D;D	0.76494	0.725;0.999;0.999	P;D;D	0.85130	0.544;0.997;0.981	T	0.37033	-0.9723	10	0.37606	T	0.19	-34.0678	15.581	0.76439	0.1377:0.8623:0.0:0.0	.	23;23;23	G5E9Y9;Q5XKI0;Q14511	.;.;CASL_HUMAN	T	23;23;23;17;23	ENSP00000368759:A23T;ENSP00000422871:A23T;ENSP00000368745:A23T;ENSP00000421282:A17T;ENSP00000380534:A23T	ENSP00000368745:A23T	A	-	1	0	NEDD9	11321892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.596000	0.67570	2.941000	0.99782	0.655000	0.94253	GCC		0.527	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		T	11213906	C	T	11213906	3	4	61	1	0	0	0	0	1	0	0	0	10344	739	26	3	2531	3	NEDD9	6	11213906	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108591	11213906	159901161	4414	12399										
TMEM170B	100113407	broad.mit.edu	37	chr6	11565900	11565900	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgcttttcctttcagaGatgtggtactggatcttcct	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:11565900G>T	ENST00000379426.1	+	2	99	c.99G>T	c.(97-99)gaG>gaT	p.E33D	TMEM170B_ENST00000543875.1_Splice_Site_p.E33D	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	33						integral component of membrane (GO:0016021)		p.E33D(1)		large_intestine(3)|lung(5)	8						TCCTTTCAGAGATGTGGTACT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											299	278	285					6																	11565900		1947	4141	6088	11673886	SO:0001630	splice_region_variant	100113407				CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	ENST00000379426.1:c.98-1G>T	6.37:g.11565900G>T			11673886		Missense_Mutation	SNP	ENST00000379426.1	37	CCDS43425.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.418924	0.62622	.	.	ENSG00000205269	ENST00000543875;ENST00000379426	.	.	.	5.54	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.43144	0.1234	L	0.49350	1.555	0.54753	D	0.999981	P	0.42409	0.779	B	0.43623	0.425	T	0.49670	-0.8915	9	0.54805	T	0.06	.	10.7759	0.46350	0.1717:0.0:0.8283:0.0	.	33	Q5T4T1	T170B_HUMAN	D	33	.	ENSP00000368737:E33D	E	+	3	2	TMEM170B	11673886	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.776000	0.68924	2.608000	0.88229	0.558000	0.71614	GAG		0.423	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829	Missense_Mutation	T	11565900	G	T	11565900	5	4	61	1	0	0	0	0	0	0	1	0	16126	956	33	2	105	2	TMEM170B	6	11565900	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	351994	11565900	159549167	4415	12400										
TMEM170B	100113407	broad.mit.edu	37	chr6	11575717	11575717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaacatggcccctttgGaagcgctggtatggggcgtt	16	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:11575717G>A	ENST00000379426.1	+	3	322	c.322G>A	c.(322-324)Gaa>Aaa	p.E108K	TMEM170B_ENST00000543875.1_Missense_Mutation_p.E108K	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	108						integral component of membrane (GO:0016021)		p.E108K(1)		large_intestine(3)|lung(5)	8						GGCCCCTTTGGAAGCGCTGGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											186	181	183					6																	11575717		1955	4145	6100	11683703	SO:0001583	missense	100113407				CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	ENST00000379426.1:c.322G>A	6.37:g.11575717G>A	ENSP00000368737:p.Glu108Lys		11683703		Missense_Mutation	SNP	ENST00000379426.1	37	CCDS43425.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504658	0.85176	.	.	ENSG00000205269	ENST00000543875;ENST00000379426	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.66416	0.2787	L	0.50333	1.59	0.80722	D	1	D	0.59767	0.986	P	0.61800	0.894	T	0.62459	-0.6850	9	0.33141	T	0.24	-37.3358	19.0673	0.93116	0.0:0.0:1.0:0.0	.	108	Q5T4T1	T170B_HUMAN	K	108	.	ENSP00000368737:E108K	E	+	1	0	TMEM170B	11683703	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.466000	0.97665	2.502000	0.84385	0.579000	0.79373	GAA		0.473	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829		A	11575717	G	A	11575717	3	1	61	1	0	0	0	0	1	0	0	0	16126	1175	41	3	332	3	TMEM170B	6	11575717	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9817	11575717	159539350	4416	12401										
C6orf105	84830	broad.mit.edu	37	chr6	11735842	11735842	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagccagcaaggtgagTcctgtcttctttgatggata	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:11735842T>C	ENST00000414691.3	-	4	875	c.465A>G	c.(463-465)ggA>ggG	p.G155G	ADTRP_ENST00000229583.5_Silent_p.G173G|ADTRP_ENST00000379413.2_Silent_p.G155G|ADTRP_ENST00000514824.1_5'UTR	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G155G(1)									GCAAGGTGAGTCCTGTCTTCT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	6											85	76	79					6																	11735842		2203	4300	6503	11843828	SO:0001819	synonymous_variant	84830			AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"androgen-induced 1-like"	614348	"chromosome 6 open reading frame 105"	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.465A>G	6.37:g.11735842T>C			11843828	B2R7T9|B4DV39|Q5THW1	Silent	SNP	ENST00000414691.3	37	CCDS4521.1																																																																																				0.483	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744		C	11735842	T	C	11735842	2	2	61	1	0	0	0	0	0	0	0	1	2324	1654	58	4		4	C6orf105	6	11735842	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160125	11735842	159379225	4417	12402										
HIVEP1	3096	broad.mit.edu	37	chr6	12121650	12121650	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagcagtccagaaaatgTgataggtgactttttgctac	9	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:12121650T>C	ENST00000379388.2	+	4	1954	c.1622T>C	c.(1621-1623)gTg>gCg	p.V541A		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	541					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V541A(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CCAGAAAATGTGATAGGTGAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											55	53	53					6																	12121650		2005	4183	6188	12229636	SO:0001583	missense	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.1622T>C	6.37:g.12121650T>C	ENSP00000368698:p.Val541Ala		12229636	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	T	2.157	-0.393101	0.04899	.	.	ENSG00000095951	ENST00000379388	T	0.10099	2.91	5.61	1.89	0.25635	.	0.531081	0.14195	N	0.335043	T	0.02418	0.0074	L	0.41027	1.25	0.20975	N	0.999812	B	0.06786	0.001	B	0.08055	0.003	T	0.45293	-0.9271	9	.	.	.	-3.7613	5.9058	0.19001	0.0:0.1552:0.1393:0.7055	.	541	P15822	ZEP1_HUMAN	A	541	ENSP00000368698:V541A	.	V	+	2	0	HIVEP1	12229636	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.365000	0.20348	0.382000	0.24878	0.533000	0.62120	GTG		0.458	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		C	12121650	T	C	12121650	3	2	61	1	0	0	0	0	1	0	0	0	7207	1696	59	4	1632	4	HIVEP1	6	12121650	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	385808	12121650	158993417	4418	12403										
HIVEP1	3096	broad.mit.edu	37	chr6	12122765	12122765	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaaatgaaagtcatgttCttggtactggacagtccctg	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:12122765C>A	ENST00000379388.2	+	4	3069	c.2737C>A	c.(2737-2739)Ctt>Att	p.L913I		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	913					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L913I(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AAGTCATGTTCTTGGTACTGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											57	58	58					6																	12122765		2033	4188	6221	12230751	SO:0001583	missense	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.2737C>A	6.37:g.12122765C>A	ENSP00000368698:p.Leu913Ile		12230751	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.395252	0.25205	.	.	ENSG00000095951	ENST00000379388	T	0.11277	2.79	6.02	5.14	0.70334	.	0.277746	0.19518	N	0.112357	T	0.08268	0.0206	M	0.73319	2.225	0.80722	D	1	P	0.49635	0.926	B	0.42882	0.401	T	0.07731	-1.0757	9	.	.	.	-7.2476	11.3941	0.49832	0.0:0.805:0.1277:0.0674	.	913	P15822	ZEP1_HUMAN	I	913	ENSP00000368698:L913I	.	L	+	1	0	HIVEP1	12230751	0.902000	0.30710	0.005000	0.12908	0.126000	0.20510	2.056000	0.41355	1.521000	0.48983	0.655000	0.94253	CTT		0.537	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		A	12122765	C	A	12122765	3	1	61	1	0	0	0	0	1	0	0	0	7207	913	32	2	2747	2	HIVEP1	6	12122765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1115	12122765	158992302	4419	12404										
HIVEP1	3096	broad.mit.edu	37	chr6	12124863	12124863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattgacagcatgtctaattCgcatcctctgctaccaccag	6	13	2	1	rs373301856		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:12124863C>T	ENST00000379388.2	+	4	5167	c.4835C>T	c.(4834-4836)tCg>tTg	p.S1612L	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1612					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S1612L(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ATGTCTAATTCGCATCCTCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	LEU/SER	0,4122		0,0,2061	122	122	122		4835	4.4	0	6		122	1,8391		0,1,4195	no	missense	HIVEP1	NM_002114.2	145	0,1,6256	TT,TC,CC		0.0119,0.0,0.0080	possibly-damaging	1612/2719	12124863	1,12513	2061	4196	6257	12232849	SO:0001583	missense	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4835C>T	6.37:g.12124863C>T	ENSP00000368698:p.Ser1612Leu		12232849	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.850533	0.51270	0.0	1.19E-4	ENSG00000095951	ENST00000379388	T	0.09630	2.96	5.24	4.36	0.52297	.	0.330324	0.17166	N	0.184441	T	0.06188	0.0160	M	0.73598	2.24	0.22280	N	0.999239	P	0.45986	0.87	B	0.33846	0.171	T	0.11227	-1.0596	9	.	.	.	-1.2047	15.8325	0.78764	0.0:0.8639:0.1361:0.0	.	1612	P15822	ZEP1_HUMAN	L	1612	ENSP00000368698:S1612L	.	S	+	2	0	HIVEP1	12232849	0.033000	0.19621	0.002000	0.10522	0.003000	0.03518	2.663000	0.46774	1.395000	0.46643	0.650000	0.86243	TCG		0.458	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12124863	C	T	12124863	3	4	61	1	0	0	0	0	1	0	0	0	7207	893	31	1	4845	1	HIVEP1	6	12124863	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2098	12124863	158990204	4420	12405										
HIVEP1	3096	broad.mit.edu	37	chr6	12161713	12161713	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagcgatctggatatgatCttgaagaatctgatggccca	11	7	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:12161713C>T	ENST00000379388.2	+	8	6861	c.6529C>T	c.(6529-6531)Ctt>Ttt	p.L2177F	HIVEP1_ENST00000541134.1_Missense_Mutation_p.L42F	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2177					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L2177F(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGGATATGATCTTGAAGAATC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	91	88					6																	12161713		1997	4175	6172	12269699	SO:0001583	missense	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6529C>T	6.37:g.12161713C>T	ENSP00000368698:p.Leu2177Phe		12269699	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.433521	0.62955	.	.	ENSG00000095951	ENST00000379388;ENST00000442081;ENST00000541134;ENST00000542327	T;T	0.33654	2.9;1.4	5.77	3.85	0.44370	.	0.277119	0.19473	N	0.113405	T	0.10465	0.0256	L	0.49126	1.545	0.33567	D	0.598129	P	0.42735	0.788	B	0.33750	0.169	T	0.06180	-1.0841	10	0.11794	T	0.64	-9.3251	7.2537	0.26164	0.1714:0.5186:0.31:0.0	.	2177	P15822	ZEP1_HUMAN	F	2177;104;42;159	ENSP00000368698:L2177F;ENSP00000445617:L42F	ENSP00000368698:L2177F	L	+	1	0	HIVEP1	12269699	0.994000	0.37717	0.263000	0.24496	0.870000	0.49936	4.838000	0.62803	1.381000	0.46364	0.655000	0.94253	CTT		0.428	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12161713	C	T	12161713	3	4	61	1	0	0	0	0	1	0	0	0	7207	913	32	3	6555	3	HIVEP1	6	12161713	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36850	12161713	158953354	4421	12406										
TBC1D7	51256	broad.mit.edu	37	chr6	13306704	13306704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaaggttaataaaatttCgacagctacaaaaactagga	6	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:13306704C>T	ENST00000379300.3	-	7	964	c.721G>A	c.(721-723)Gaa>Aaa	p.E241K	TBC1D7_ENST00000343141.4_Missense_Mutation_p.E195K|TBC1D7_ENST00000356436.4_Missense_Mutation_p.E241K|TBC1D7_ENST00000607658.1_3'UTR|TBC1D7_ENST00000607532.1_5'Flank|TBC1D7_ENST00000379307.2_Missense_Mutation_p.E214K	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	241					activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.E241K(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			AATAAAATTTCGACAGCTACA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	74	71					6																	13306704		2203	4295	6498	13414683	SO:0001583	missense	51256			AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.721G>A	6.37:g.13306704C>T	ENSP00000368602:p.Glu241Lys		13414683	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Missense_Mutation	SNP	ENST00000379300.3	37	CCDS4523.1	.	.	.	.	.	.	.	.	.	.	C	31	5.073744	0.94000	.	.	ENSG00000145979	ENST00000334971;ENST00000356436;ENST00000379300;ENST00000379307;ENST00000343141;ENST00000452989;ENST00000450347;ENST00000422136	T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0	5.87	5.87	0.94306	Rab-GAP/TBC domain (2);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.78916	2.43	0.80722	D	1	D;D;D	0.76494	0.986;0.994;0.999	P;P;D	0.63703	0.507;0.768;0.917	T	0.04454	-1.0950	10	0.41790	T	0.15	-24.4491	19.5705	0.95413	0.0:1.0:0.0:0.0	.	195;214;241	Q2TU37;Q9P0N9-2;Q9P0N9	.;.;TBCD7_HUMAN	K	182;241;241;214;195;214;214;241	ENSP00000348813:E241K;ENSP00000368602:E241K;ENSP00000368609:E214K;ENSP00000343100:E195K;ENSP00000414292:E214K;ENSP00000404680:E214K;ENSP00000394425:E241K	ENSP00000334212:E182K	E	-	1	0	TBC1D7	13414683	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.908000	0.75730	2.941000	0.99782	0.655000	0.94253	GAA		0.308	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		T	13306704	C	T	13306704	3	4	61	1	0	0	0	0	1	0	0	0	15663	893	31	1	168	1	TBC1D7	6	13306704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1144991	13306704	157808363	4422	12407										
SIRT5	23408	broad.mit.edu	37	chr6	13604714	13604714	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtttcttttcagtcatttGatctccatctcatctctaat	4	10	6	1	rs199651501		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:13604714G>T	ENST00000379262.4	+	10	1082	c.864G>T	c.(862-864)ttG>ttT	p.L288F	SIRT5_ENST00000606117.1_Intron|SIRT5_ENST00000397350.2_Intron|SIRT5_ENST00000359782.3_Intron	NM_031244.3	NP_112534.1			sirtuin 5									p.L288F(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			TCAGTCATTTGATCTCCATCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	119	118					6																	13604714		2203	4300	6503	13712693	SO:0001583	missense	23408			AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5", "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000379262.4:c.864G>T	6.37:g.13604714G>T	ENSP00000368564:p.Leu288Phe		13712693		Missense_Mutation	SNP	ENST00000379262.4	37	CCDS4527.1	.	.	.	.	.	.	.	.	.	.	G	5.004	0.186360	0.09495	.	.	ENSG00000124523	ENST00000379262	T	0.44083	0.93	2.17	1.23	0.21249	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.42275	-0.9461	8	0.09590	T	0.72	.	6.447	0.21882	0.0:0.3091:0.6909:0.0	.	288	Q9NXA8-2	.	F	288	ENSP00000368564:L288F	ENSP00000368564:L288F	L	+	3	2	SIRT5	13712693	0.007000	0.16637	0.003000	0.11579	0.009000	0.06853	2.061000	0.41403	0.451000	0.26802	0.467000	0.42956	TTG		0.348	SIRT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039907.1			T	13604714	G	T	13604714	3	4	61	1	0	0	0	0	1	0	0	0	14378	1281	45	2	894	2	SIRT5	6	13604714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298010	13604714	157510353	4423	12408										
CCDC90A	63933	broad.mit.edu	37	chr6	13792179	13792179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggccagcaacctcagtttCgatcttcctgtctgtctggg	11	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:13792179C>T	ENST00000379170.4	-	8	1093	c.955G>A	c.(955-957)Gaa>Aaa	p.E319K		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	319					calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)		p.E319K(1)									ACCTCAGTTTCGATCTTCCTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	108	118					6																	13792179		2203	4300	6503	13900158	SO:0001583	missense	63933			BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 79", "coiled-coil domain containing 90A"	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.955G>A	6.37:g.13792179C>T	ENSP00000368468:p.Glu319Lys		13900158	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	37	CCDS35495.1	.	.	.	.	.	.	.	.	.	.	C	35	5.481023	0.96307	.	.	ENSG00000050393	ENST00000379170	T	0.50813	0.73	5.42	5.42	0.78866	.	0.087388	0.85682	D	0.000000	T	0.54398	0.1856	L	0.57536	1.79	0.80722	D	1	D	0.64830	0.994	P	0.59357	0.856	T	0.52124	-0.8617	10	0.44086	T	0.13	-6.2727	18.006	0.89209	0.0:1.0:0.0:0.0	.	319	Q96AQ8	CC90A_HUMAN	K	319	ENSP00000368468:E319K	ENSP00000368468:E319K	E	-	1	0	CCDC90A	13900158	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	6.649000	0.74364	2.550000	0.86006	0.655000	0.94253	GAA		0.438	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102		T	13792179	C	T	13792179	3	4	61	1	0	0	0	0	1	0	0	0	2874	893	31	1	132	1	CCDC90A	6	13792179	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187465	13792179	157322888	4424	12409										
RNF182	221687	broad.mit.edu	37	chr6	13977507	13977507	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcctctacaagatcataGactttggggactccccacaa	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:13977507G>T	ENST00000488300.1	+	3	680	c.157G>T	c.(157-159)Gac>Tac	p.D53Y	RNF182_ENST00000537388.1_Missense_Mutation_p.D53Y|RNF182_ENST00000537663.1_Missense_Mutation_p.D53Y|RNF182_ENST00000544682.1_Missense_Mutation_p.D53Y	NM_152737.3	NP_689950.1	Q8N6D2	RN182_HUMAN	ring finger protein 182	53					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D53Y(1)		cervix(1)|large_intestine(7)|liver(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			CAAGATCATAGACTTTGGGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											165	156	159					6																	13977507		2203	4300	6503	14085486	SO:0001583	missense	221687			AK090576	CCDS4531.1	6p23	2013-01-09			ENSG00000180537	ENSG00000180537		"RING-type (C3HC4) zinc fingers"	28522	protein-coding gene	gene with protein product						12477932	Standard	NM_152737		Approved	MGC33993	uc003nbg.3	Q8N6D2	OTTHUMG00000014280	ENST00000488300.1:c.157G>T	6.37:g.13977507G>T	ENSP00000420465:p.Asp53Tyr		14085486	B2RDG2|Q8NBG3	Missense_Mutation	SNP	ENST00000488300.1	37	CCDS4531.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024815	0.75390	.	.	ENSG00000180537	ENST00000537663;ENST00000488300;ENST00000544682;ENST00000420478;ENST00000423553;ENST00000537388	D;D;D;T;T;D	0.86432	-2.12;-2.12;-2.12;-0.29;-0.29;-2.12	5.52	3.68	0.42216	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.405101	0.27253	N	0.020210	D	0.88463	0.6443	M	0.83483	2.645	0.52501	D	0.999956	P	0.51057	0.941	P	0.54174	0.744	D	0.88745	0.3246	9	.	.	.	-22.9684	11.3221	0.49428	0.0693:0.1265:0.8042:0.0	.	53	Q8N6D2	RN182_HUMAN	Y	53	ENSP00000443228:D53Y;ENSP00000420465:D53Y;ENSP00000442021:D53Y;ENSP00000419329:D53Y;ENSP00000418717:D53Y;ENSP00000441271:D53Y	.	D	+	1	0	RNF182	14085486	1.000000	0.71417	0.991000	0.47740	0.926000	0.56050	6.354000	0.73036	1.342000	0.45619	0.563000	0.77884	GAC		0.463	RNF182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039911.2	NM_152737		T	13977507	G	T	13977507	3	4	61	1	0	0	0	0	1	0	0	0	13503	942	33	2	159	2	RNF182	6	13977507	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185328	13977507	157137560	4425	12410										
JARID2	3720	broad.mit.edu	37	chr6	15452403	15452403	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttacctttctctgccttCgaggtaagactttgcaacca	6	12	2	1	rs371399734		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:15452403C>T	ENST00000341776.2	+	4	734	c.490C>T	c.(490-492)Cga>Tga	p.R164*	JARID2_ENST00000541660.1_Nonsense_Mutation_p.R126*|JARID2_ENST00000397311.3_5'UTR	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	164					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R164*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TCTCTGCCTTCGAGGTAAGAC	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	6						C	stop/ARG	0,4406		0,0,2203	73	68	70		490	5.4	1	6		70	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	JARID2	NM_004973.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		164/1247	15452403	1,13005	2203	4300	6503	15560382	SO:0001587	stop_gained	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.490C>T	6.37:g.15452403C>T	ENSP00000341280:p.Arg164*		15560382	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Nonsense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	C	38	6.644455	0.97730	0.0	1.16E-4	ENSG00000008083	ENST00000341776;ENST00000541660	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5322	14.0707	0.64858	0.1506:0.8494:0.0:0.0	.	.	.	.	X	164;126	.	ENSP00000341280:R164X	R	+	1	2	JARID2	15560382	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.496000	0.53288	2.513000	0.84729	0.655000	0.94253	CGA		0.468	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15452403	C	T	15452403	4	4	61	1	0	0	0	0	0	1	0	0	7966	876	31	1	504	1	JARID2	6	15452403	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1474896	15452403	155662664	4426	12411										
JARID2	3720	broad.mit.edu	37	chr6	15497178	15497178	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgatccgctcatctacatCgagtcggtccgcgctcaggt	10	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:15497178C>T	ENST00000341776.2	+	7	1966	c.1722C>T	c.(1720-1722)atC>atT	p.I574I	JARID2_ENST00000541660.1_Silent_p.I536I|JARID2_ENST00000397311.3_Silent_p.I402I	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	574	JmjN. {ECO:0000255|PROSITE- ProRule:PRU00537}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.I574I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TCATCTACATCGAGTCGGTCC	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	6											55	49	51					6																	15497178		2203	4300	6503	15605157	SO:0001819	synonymous_variant	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1722C>T	6.37:g.15497178C>T			15605157	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																				0.662	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15497178	C	T	15497178	2	4	61	1	0	0	0	0	0	0	0	1	7966	874	31	1		1	JARID2	6	15497178	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44775	15497178	155617889	4427	12412										
JARID2	3720	broad.mit.edu	37	chr6	15501261	15501261	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcgcatccccagaactgCccaggaccggctggccaagc	12	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:15501261C>A	ENST00000341776.2	+	8	2313	c.2069C>A	c.(2068-2070)gCc>gAc	p.A690D	JARID2_ENST00000541660.1_Missense_Mutation_p.A652D|JARID2_ENST00000397311.3_Missense_Mutation_p.A518D	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	690	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A690D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				CCCAGAACTGCCCAGGACCGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	77	73					6																	15501261		2203	4300	6503	15609240	SO:0001583	missense	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2069C>A	6.37:g.15501261C>A	ENSP00000341280:p.Ala690Asp		15609240	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.882693	0.91740	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.45668	0.89;0.89;0.89	5.15	5.15	0.70609	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	T	0.60728	0.2291	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.66073	-0.6014	10	0.87932	D	0	-13.4379	18.621	0.91321	0.0:1.0:0.0:0.0	.	652;690	F5H590;Q92833	.;JARD2_HUMAN	D	690;518;652	ENSP00000341280:A690D;ENSP00000380478:A518D;ENSP00000444623:A652D	ENSP00000341280:A690D	A	+	2	0	JARID2	15609240	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.625000	0.83145	2.396000	0.81511	0.561000	0.74099	GCC		0.577	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15501261	C	A	15501261	3	1	61	1	0	0	0	0	1	0	0	0	7966	739	26	2	2099	2	JARID2	6	15501261	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4083	15501261	155613806	4428	12413										
ATXN1	6310	broad.mit.edu	37	chr6	16328137	16328137	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctggcataggttccactGtattgggaggacccaatgaa	12	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:16328137G>T	ENST00000244769.4	-	8	1341	c.405C>A	c.(403-405)taC>taA	p.Y135*	ATXN1_ENST00000436367.1_Nonsense_Mutation_p.Y135*	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	135					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.Y135*(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				AGGTTCCACTGTATTGGGAGG	0.657																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											72	76	75					6																	16328137		2203	4300	6503	16436116	SO:0001587	stop_gained	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.405C>A	6.37:g.16328137G>T	ENSP00000244769:p.Tyr135*		16436116	Q17S02|Q9UJG2|Q9Y4J1	Nonsense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	41	9.020921	0.99038	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	.	.	.	5.11	2.28	0.28536	.	0.057614	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.033	8.8418	0.35146	0.3683:0.0:0.6317:0.0	.	.	.	.	X	135	.	ENSP00000244769:Y135X	Y	-	3	2	ATXN1	16436116	1.000000	0.71417	0.992000	0.48379	0.199000	0.23934	1.729000	0.38115	0.534000	0.28695	0.467000	0.42956	TAC		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		T	16328137	G	T	16328137	4	4	61	1	0	0	0	0	0	1	0	0	1210	1372	48	2	2050	2	ATXN1	6	16328137	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	826876	16328137	154786930	4429	12414										
RBM24	221662	broad.mit.edu	37	chr6	17292141	17292141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcagctgctgctgctgccGccgccgctgctgcctatgac	12	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17292141G>A	ENST00000379052.5	+	4	738	c.502G>A	c.(502-504)Gcc>Acc	p.A168T	RBM24_ENST00000318204.5_Missense_Mutation_p.A123T|RBM24_ENST00000508508.1_3'UTR|RBM24_ENST00000425446.2_Missense_Mutation_p.A110T	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	168	Ala-rich.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)	p.A123T(1)		endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			tgctgctgccgccgccgctgc	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											19	26	24					6																	17292141		2145	4161	6306	17400120	SO:0001583	missense	221662			BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"RNA binding motif (RRM) containing"	21539	protein-coding gene	gene with protein product			"RNA-binding region (RNP1, RRM) containing 6"	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.502G>A	6.37:g.17292141G>A	ENSP00000368341:p.Ala168Thr		17400120	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Missense_Mutation	SNP	ENST00000379052.5	37	CCDS47378.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474843	0.43942	.	.	ENSG00000112183	ENST00000379052;ENST00000425446;ENST00000318204	T;T;T	0.30714	1.52;1.52;1.52	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.37376	0.1001	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.985	T	0.01819	-1.1267	10	0.19590	T	0.45	-23.1528	19.8414	0.96690	0.0:0.0:1.0:0.0	.	123;168	Q9BX46-2;Q9BX46	.;RBM24_HUMAN	T	168;110;123	ENSP00000368341:A168T;ENSP00000396898:A110T;ENSP00000319551:A123T	ENSP00000319551:A123T	A	+	1	0	RBM24	17400120	1.000000	0.71417	0.994000	0.49952	0.956000	0.61745	7.529000	0.81952	2.695000	0.91970	0.591000	0.81541	GCC		0.597	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020		A	17292141	G	A	17292141	3	1	61	1	0	0	0	0	1	0	0	0	13161	1087	38	1	549	1	RBM24	6	17292141	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	964004	17292141	153822926	4430	12415										
CAP2	10486	broad.mit.edu	37	chr6	17539541	17539541	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcgttttctgtcctctcCtctgggcctggccttcctcc	8	17	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17539541C>A	ENST00000229922.2	+	8	1210	c.678C>A	c.(676-678)tcC>tcA	p.S226S	CAP2_ENST00000465994.1_Silent_p.S162S|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000489374.1_Silent_p.S114S|CAP2_ENST00000378990.2_Silent_p.S200S	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	226					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)		p.S226S(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			CTGTCCTCTCCTCTGGGCCTG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	6											249	210	223					6																	17539541		2203	4300	6503	17647520	SO:0001819	synonymous_variant	10486			BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.678C>A	6.37:g.17539541C>A			17647520	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																				0.542	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			A	17539541	C	A	17539541	2	1	61	1	0	0	0	0	0	0	0	1	2626	668	24	2		2	CAP2	6	17539541	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	247400	17539541	153575526	4431	12416										
CAP2	10486	broad.mit.edu	37	chr6	17541337	17541337	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcttatccttctcaaaaAcatgccccagtgttggagtt	6	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17541337A>G	ENST00000229922.2	+	9	1492	c.960A>G	c.(958-960)aaA>aaG	p.K320K	CAP2_ENST00000465994.1_Silent_p.K256K|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000489374.1_Silent_p.K208K|CAP2_ENST00000378990.2_Silent_p.K294K	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	320	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)		p.K320K(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			CTTCTCAAAAACATGCCCCAG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	6											135	118	124					6																	17541337		2203	4300	6503	17649316	SO:0001819	synonymous_variant	10486			BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.960A>G	6.37:g.17541337A>G			17649316	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																				0.453	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			G	17541337	A	G	17541337	2	3	61	1	0	0	0	0	0	0	0	1	2626	40	2	4		4	CAP2	6	17541337	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1796	17541337	153573730	4432	12417										
NUP153	9972	broad.mit.edu	37	chr6	17637604	17637604	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacacaagttccaggtttCggtgtttcacaggctacaca	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17637604C>T	ENST00000262077.2	-	16	2243	c.2244G>A	c.(2242-2244)ccG>ccA	p.P748P	NUP153_ENST00000537253.1_Silent_p.P779P	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	748					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.P748P(2)		NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TTCCAGGTTTCGGTGTTTCAC	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	6											183	180	181					6																	17637604		2203	4300	6503	17745583	SO:0001819	synonymous_variant	9972			Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.2244G>A	6.37:g.17637604C>T			17745583	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	37	CCDS4541.1																																																																																				0.433	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			T	17637604	C	T	17637604	2	4	61	1	0	0	0	0	0	0	0	1	10786	871	31	1		1	NUP153	6	17637604	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96267	17637604	153477463	4433	12418										
KIF13A	63971	broad.mit.edu	37	chr6	17765136	17765136	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtgaacttattagcttCctgttaatagcttccagctc	8	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17765136C>A	ENST00000259711.6	-	39	4728	c.4623G>T	c.(4621-4623)agG>agT	p.R1541S	KIF13A_ENST00000378826.2_Missense_Mutation_p.R1506S|KIF13A_ENST00000378843.2_Missense_Mutation_p.R1493S|KIF13A_ENST00000378816.5_Missense_Mutation_p.R1506S|KIF13A_ENST00000378814.5_Missense_Mutation_p.R1493S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1541					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1541S(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TTATTAGCTTCCTGTTAATAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											49	47	48					6																	17765136		1879	4113	5992	17873115	SO:0001583	missense	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.4623G>T	6.37:g.17765136C>A	ENSP00000259711:p.Arg1541Ser		17873115	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.471739	0.26423	.	.	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.74106	-0.79;1.69;-0.74;-0.81;-0.79;-0.81	5.92	2.78	0.32641	.	0.552272	0.18280	N	0.146053	T	0.30572	0.0769	N	0.14661	0.345	0.25913	N	0.983203	B;B;B;B	0.13145	0.0;0.0;0.007;0.0	B;B;B;B	0.13407	0.002;0.001;0.009;0.001	T	0.21449	-1.0245	10	0.09084	T	0.74	.	10.6119	0.45427	0.0:0.7145:0.0:0.2855	.	1493;1506;1541;1493	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	S	1493;545;1541;1506;1493;1506	ENSP00000368091:R1493S;ENSP00000425616:R545S;ENSP00000259711:R1541S;ENSP00000368103:R1506S;ENSP00000368120:R1493S;ENSP00000368093:R1506S	ENSP00000259711:R1541S	R	-	3	2	KIF13A	17873115	1.000000	0.71417	0.976000	0.42696	0.572000	0.35998	2.205000	0.42770	0.856000	0.35383	0.585000	0.79938	AGG		0.423	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17765136	C	A	17765136	3	1	61	1	0	0	0	0	1	0	0	0	8295	854	30	2	823	2	KIF13A	6	17765136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127532	17765136	153349931	4434	12419										
KIF13A	63971	broad.mit.edu	37	chr6	17779201	17779201	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggagccgttcaagactcaGaatgttttccacctgcagca	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17779201G>T	ENST00000259711.6	-	33	4174	c.4069C>A	c.(4069-4071)Ctg>Atg	p.L1357M	KIF13A_ENST00000378826.2_Missense_Mutation_p.L1357M|KIF13A_ENST00000378843.2_Missense_Mutation_p.L1344M|KIF13A_ENST00000378816.5_Missense_Mutation_p.L1357M|KIF13A_ENST00000378814.5_Missense_Mutation_p.L1344M	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1357					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L1357M(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCAAGACTCAGAATGTTTTCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	95	96					6																	17779201		2122	4244	6366	17887180	SO:0001583	missense	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.4069C>A	6.37:g.17779201G>T	ENSP00000259711:p.Leu1357Met		17887180	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.77|18.77	3.694217|3.694217	0.68386|0.68386	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000358380|ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	.|D;T;D;D;D;D	.|0.82081	.|-1.53;0.75;-1.57;-1.52;-1.53;-1.52	5.36|5.36	3.54|3.54	0.40534|0.40534	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88459|0.88459	0.6442|0.6442	M|M	0.82823|0.82823	2.61|2.61	0.52501|0.52501	D|D	0.999953|0.999953	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;0.999;1.0;0.999	D|D	0.89880|0.89880	0.4029|0.4029	5|10	.|0.87932	.|D	.|0	.|.	11.2789|11.2789	0.49181|0.49181	0.2421:0.0:0.7579:0.0|0.2421:0.0:0.7579:0.0	.|.	.|1344;1357;1357;1344	.|Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.|.;.;KI13A_HUMAN;.	L|M	750|1344;361;1357;1357;1344;1357	.|ENSP00000368091:L1344M;ENSP00000425616:L361M;ENSP00000259711:L1357M;ENSP00000368103:L1357M;ENSP00000368120:L1344M;ENSP00000368093:L1357M	.|ENSP00000259711:L1357M	F|L	-|-	3|1	2|2	KIF13A|KIF13A	17887180|17887180	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.998000|0.998000	0.95712|0.95712	2.116000|2.116000	0.41930|0.41930	1.391000|1.391000	0.46566|0.46566	0.561000|0.561000	0.74099|0.74099	TTC|CTG		0.512	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			T	17779201	G	T	17779201	3	4	61	1	0	0	0	0	1	0	0	0	8295	933	33	2	1401	2	KIF13A	6	17779201	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14065	17779201	153335866	4435	12420										
KIF13A	63971	broad.mit.edu	37	chr6	17856348	17856348	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcacttgaaaaccacttCttgacctaaaaaacaagaca	5	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:17856348C>A	ENST00000259711.6	-	5	331	c.226G>T	c.(226-228)Gaa>Taa	p.E76*	KIF13A_ENST00000378826.2_Nonsense_Mutation_p.E76*|KIF13A_ENST00000378843.2_Nonsense_Mutation_p.E76*|KIF13A_ENST00000378816.5_Nonsense_Mutation_p.E76*|KIF13A_ENST00000378814.5_Nonsense_Mutation_p.E76*	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	76	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E76*(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AAAACCACTTCTTGACCTAAA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											53	49	50					6																	17856348		1792	4061	5853	17964327	SO:0001587	stop_gained	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.226G>T	6.37:g.17856348C>A	ENSP00000259711:p.Glu76*		17964327	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Nonsense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.372496	0.82573	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	.	.	.	5.87	5.87	0.94306	.	0.051954	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	16.7906	0.85589	0.0:0.8715:0.1285:0.0	.	.	.	.	X	76	.	ENSP00000259711:E76X	E	-	1	0	KIF13A	17964327	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.620000	0.67736	2.941000	0.99782	0.655000	0.94253	GAA		0.303	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17856348	C	A	17856348	4	1	61	1	0	0	0	0	0	1	0	0	8295	922	32	2	5356	2	KIF13A	6	17856348	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77147	17856348	153258719	4436	12421										
NHLRC1	378884	broad.mit.edu	37	chr6	18122594	18122594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcagcaccggcaggcagtCgctggtgtcgcagccccggc	16	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:18122594C>T	ENST00000340650.3	-	1	257	c.244G>A	c.(244-246)Gac>Aac	p.D82N		NM_198586.2	NP_940988.2	Q6VVB1	NHLC1_HUMAN	NHL repeat containing E3 ubiquitin protein ligase 1	82					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|positive regulation of protein ubiquitination (GO:0031398)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D82N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(2)	11	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.165)	all cancers(50;0.0451)|Epithelial(50;0.0493)			GGCAGGCAGTCGCTGGTGTCG	0.746																																																1	Substitution - Missense(1)	large_intestine(1)	6											5	7	6					6																	18122594		2044	3988	6032	18230573	SO:0001583	missense	378884			AY324849	CCDS4542.1	6p22.3	2014-01-28	2013-12-12		ENSG00000187566	ENSG00000187566			21576	protein-coding gene	gene with protein product	"epilepsy, progressive myoclonus type 2B"	608072	"NHL repeat containing 1"			12958597	Standard	NM_198586		Approved	bA204B7.2, EPM2B, malin	uc003ncl.1	Q6VVB1	OTTHUMG00000014315	ENST00000340650.3:c.244G>A	6.37:g.18122594C>T	ENSP00000345464:p.Asp82Asn		18230573	Q3SYB1|Q5VUK7|Q6IMH1	Missense_Mutation	SNP	ENST00000340650.3	37	CCDS4542.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067166	0.36470	.	.	ENSG00000187566	ENST00000340650	D	0.93712	-3.27	5.23	4.35	0.52113	.	0.251598	0.39687	N	0.001281	D	0.82967	0.5152	L	0.51422	1.61	0.30047	N	0.812138	D	0.53151	0.958	B	0.40864	0.342	T	0.76413	-0.2968	10	0.29301	T	0.29	-23.1509	8.3937	0.32544	0.1558:0.7661:0.0:0.0781	.	82	Q6VVB1	NHLC1_HUMAN	N	82	ENSP00000345464:D82N	ENSP00000345464:D82N	D	-	1	0	NHLRC1	18230573	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	3.904000	0.56325	1.163000	0.42636	-0.181000	0.13052	GAC		0.746	NHLRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039958.1			T	18122594	C	T	18122594	3	4	61	1	0	0	0	0	1	0	0	0	10436	884	31	1	947	1	NHLRC1	6	18122594	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	266246	18122594	152992473	4437	12422										
TPMT	7172	broad.mit.edu	37	chr6	18139903	18139903	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattcaacctacctgggaaGatcaaaaatactgcaacagt	7	9	2	1	rs372997906		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:18139903G>T	ENST00000309983.4	-	5	497	c.412C>A	c.(412-414)Ctt>Att	p.L138I		NM_000367.2	NP_000358.1	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	138					methylation (GO:0032259)|nucleobase-containing compound metabolic process (GO:0006139)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	thiopurine S-methyltransferase activity (GO:0008119)	p.L138I(1)		large_intestine(2)|lung(1)	3	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Azathioprine(DB00993)|Bendroflumethiazide(DB00436)|Cefazolin(DB01327)|Mercaptopurine(DB01033)|Olsalazine(DB01250)|Trichlormethiazide(DB01021)	TACCTGGGAAGATCAAAAATA	0.363																																					Colon(190;1381 2791 16728 32493)											1	Substitution - Missense(1)	large_intestine(1)	6											69	72	71					6																	18139903		2203	4300	6503	18247882	SO:0001583	missense	7172				CCDS4543.1	6p22.3	2014-09-17			ENSG00000137364	ENSG00000137364	2.1.1.67		12014	protein-coding gene	gene with protein product		187680				8316220	Standard	NM_000367		Approved		uc003ncm.3	P51580	OTTHUMG00000014317	ENST00000309983.4:c.412C>A	6.37:g.18139903G>T	ENSP00000312304:p.Leu138Ile		18247882	O14806|O15423|O15424|O15425|O15426|O15515|O15548|O43213|Q5VUK6|Q9UBE6|Q9UBT8|Q9UE62	Missense_Mutation	SNP	ENST00000309983.4	37	CCDS4543.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196938	0.58126	.	.	ENSG00000137364	ENST00000309983	T	0.75704	-0.96	5.21	2.43	0.29744	.	0.211536	0.47455	D	0.000230	T	0.72526	0.3471	M	0.83852	2.665	0.35742	D	0.818766	B;B	0.24483	0.104;0.018	P;B	0.47864	0.559;0.196	T	0.71361	-0.4616	10	0.48119	T	0.1	-10.3876	3.3494	0.07147	0.3103:0.0:0.5146:0.1751	.	138;138	Q9BS45;P51580	.;TPMT_HUMAN	I	138	ENSP00000312304:L138I	ENSP00000312304:L138I	L	-	1	0	TPMT	18247882	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	1.342000	0.33919	0.577000	0.29470	-0.347000	0.07816	CTT		0.363	TPMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039960.1			T	18139903	G	T	18139903	3	4	61	1	0	0	0	0	1	0	0	0	16449	942	33	2	345	2	TPMT	6	18139903	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17309	18139903	152975164	4438	12423										
CDKAL1	54901	broad.mit.edu	37	chr6	20955687	20955687	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttgaccagtgaagacacGggggcttatggcagagatat	15	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:20955687G>A	ENST00000378610.1	+	8	790	c.780G>A	c.(778-780)acG>acA	p.T260T	CDKAL1_ENST00000378624.4_Silent_p.T190T|CDKAL1_ENST00000274695.4_Silent_p.T260T			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	260					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.T260T(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	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)			GTGAAGACACGGGGGCTTATG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	6											139	134	135					6																	20955687		2203	4300	6503	21063666	SO:0001819	synonymous_variant	54901			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.780G>A	6.37:g.20955687G>A			21063666	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																				0.468	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		A	20955687	G	A	20955687	2	1	61	1	0	0	0	0	0	0	0	1	3158	1103	39	1		1	CDKAL1	6	20955687	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2815784	20955687	150159380	4439	12424										
PRL	5617	broad.mit.edu	37	chr6	22294709	22294709	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacggcgcggtcaaacaggtCtcgaagggtcacctggcatc	14	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:22294709C>A	ENST00000306482.1	-	2	651	c.133G>T	c.(133-135)Gac>Tac	p.D45Y	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	45					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)	p.D45Y(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					TCAAACAGGTCTCGAAGGGTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	6											77	70	72					6																	22294709		2203	4300	6503	22402688	SO:0001583	missense	5617			D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.133G>T	6.37:g.22294709C>A	ENSP00000302150:p.Asp45Tyr		22402688	Q15199|Q92996	Missense_Mutation	SNP	ENST00000306482.1	37	CCDS4548.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603159	0.66445	.	.	ENSG00000172179	ENST00000306482	D	0.90563	-2.69	5.85	5.85	0.93711	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.278761	0.44483	D	0.000443	D	0.94716	0.8295	M	0.72479	2.2	0.53688	D	0.999977	B;D	0.71674	0.382;0.998	B;D	0.75020	0.345;0.985	D	0.94486	0.7697	10	0.87932	D	0	-3.7208	20.1542	0.98100	0.0:1.0:0.0:0.0	.	45;46	P01236;Q5I0G2	PRL_HUMAN;.	Y	45	ENSP00000302150:D45Y	ENSP00000302150:D45Y	D	-	1	0	PRL	22402688	0.981000	0.34729	0.918000	0.36340	0.766000	0.43426	3.787000	0.55439	2.767000	0.95098	0.563000	0.77884	GAC		0.602	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948		A	22294709	C	A	22294709	3	1	61	1	0	0	0	0	1	0	0	0	12562	913	32	2	566	2	PRL	6	22294709	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1339022	22294709	148820358	4440	12425										
NRSN1	140767	broad.mit.edu	37	chr6	24134677	24134677	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggactgtacagcctcaaTttgggagtatgaggatgatt	13	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24134677T>G	ENST00000378491.4	+	3	423	c.122T>G	c.(121-123)aTt>aGt	p.I41S	NRSN1_ENST00000378478.1_Missense_Mutation_p.I41S|NRSN1_ENST00000378475.1_Missense_Mutation_p.I41S	NM_080723.4	NP_542454.3			neurensin 1									p.I41S(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	22						ACAGCCTCAATTTGGGAGTAT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											132	116	121					6																	24134677		2203	4300	6503	24242656	SO:0001583	missense	140767			AF418980	CCDS4549.1	6p22.1	2008-02-05	2006-07-04	2006-07-04	ENSG00000152954	ENSG00000152954			17881	protein-coding gene	gene with protein product			"vesicular membrane protein p24"	VMP		12463420	Standard	NM_080723		Approved	p24	uc010jpq.1	Q8IZ57	OTTHUMG00000016406	ENST00000378491.4:c.122T>G	6.37:g.24134677T>G	ENSP00000367752:p.Ile41Ser		24242656		Missense_Mutation	SNP	ENST00000378491.4	37	CCDS4549.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.424551	0.83667	.	.	ENSG00000152954	ENST00000378491;ENST00000378478;ENST00000378477;ENST00000378475	T;T;T	0.20738	2.05;2.05;2.05	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.37544	0.1007	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.26395	-1.0104	10	0.87932	D	0	-11.3363	16.0421	0.80691	0.0:0.0:0.0:1.0	.	41	Q8IZ57	NRSN1_HUMAN	S	41	ENSP00000367752:I41S;ENSP00000367739:I41S;ENSP00000367736:I41S	ENSP00000367736:I41S	I	+	2	0	NRSN1	24242656	1.000000	0.71417	0.995000	0.50966	0.851000	0.48451	7.671000	0.83941	2.192000	0.70111	0.533000	0.62120	ATT		0.502	NRSN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043866.1	NM_080723		G	24134677	T	G	24134677	3	3	61	1	0	0	0	0	1	0	0	0	10693	1493	52	4	124	4	NRSN1	6	24134677	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1839968	24134677	146980390	4441	12426										
DCDC2	51473	broad.mit.edu	37	chr6	24353827	24353827	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacttccattggtcttttCttgatttctcctatgtccaa	4	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24353827C>A	ENST00000378454.3	-	2	619	c.318G>T	c.(316-318)aaG>aaT	p.K106N		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	106					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)			p.K106N(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TTGGTCTTTTCTTGATTTCTC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	88	89					6																	24353827		2201	4298	6499	24461806	SO:0001583	missense	51473			AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.318G>T	6.37:g.24353827C>A	ENSP00000367715:p.Lys106Asn		24461806	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.62|19.62	3.862273|3.862273	0.71949|0.71949	.|.	.|.	ENSG00000146038|ENSG00000146038	ENST00000378454;ENST00000451359|ENST00000436313	D|.	0.86769|.	-2.17|.	4.7|4.7	4.7|4.7	0.59300|0.59300	Doublecortin domain (2);|.	0.157620|.	0.56097|.	D|.	0.000039|.	T|T	0.60077|0.60077	0.2241|0.2241	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	P|.	0.50272|.	0.933|.	P|.	0.46479|.	0.518|.	T|T	0.57207|0.57207	-0.7851|-0.7851	10|5	0.20519|.	T|.	0.43|.	-0.0567|-0.0567	17.797|17.797	0.88575|0.88575	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	106|.	Q9UHG0|.	DCDC2_HUMAN|.	N|I	106|74	ENSP00000367715:K106N|.	ENSP00000367715:K106N|.	K|R	-|-	3|2	2|0	DCDC2|DCDC2	24461806|24461806	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	2.930000|2.930000	0.48924|0.48924	2.591000|2.591000	0.87537|0.87537	0.650000|0.650000	0.86243|0.86243	AAG|AGA		0.274	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		A	24353827	C	A	24353827	3	1	61	1	0	0	0	0	1	0	0	0	4291	912	32	2	1148	2	DCDC2	6	24353827	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219150	24353827	146761240	4442	12427										
MRS2	57380	broad.mit.edu	37	chr6	24423172	24423172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttctcttttaggaccataGaattttttggctgattacag	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24423172G>T	ENST00000378386.3	+	10	1208	c.1115G>T	c.(1114-1116)aGa>aTa	p.R372I	MRS2_ENST00000443868.2_Missense_Mutation_p.R375I|MRS2_ENST00000543597.1_Missense_Mutation_p.R81I|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000378353.1_Missense_Mutation_p.R372I|MRS2_ENST00000535061.1_Missense_Mutation_p.R322I	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	372						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)	p.R372K(1)|p.R372I(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						TAGGACCATAGAATTTTTTGG	0.443																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											147	138	141					6																	24423172		2203	4300	6503	24531151	SO:0001583	missense	57380			AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"MRS2-like, magnesium homeostasis factor (S. cerevisiae)", "MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.1115G>T	6.37:g.24423172G>T	ENSP00000367637:p.Arg372Ile		24531151	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Missense_Mutation	SNP	ENST00000378386.3	37	CCDS4552.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.705547	0.30232	.	.	ENSG00000124532	ENST00000543597;ENST00000535061;ENST00000378386;ENST00000378353;ENST00000443868	T;T;T;T;T	0.46063	0.88;1.53;1.5;0.93;1.5	6.15	6.15	0.99193	.	0.105135	0.64402	D	0.000007	T	0.18882	0.0453	L	0.32530	0.975	0.40091	D	0.976257	B;P;B;B	0.35527	0.32;0.507;0.366;0.083	B;B;B;B	0.34093	0.121;0.175;0.08;0.047	T	0.03534	-1.1027	10	0.22706	T	0.39	-24.363	13.9607	0.64177	0.0687:0.0:0.9313:0.0	.	322;375;372;372	F5GWH3;B4DQL2;Q9HD23;Q9HD23-2	.;.;MRS2_HUMAN;.	I	81;322;372;372;375	ENSP00000438118:R81I;ENSP00000441839:R322I;ENSP00000367637:R372I;ENSP00000367604:R372I;ENSP00000399585:R375I	ENSP00000367604:R372I	R	+	2	0	MRS2	24531151	0.998000	0.40836	0.085000	0.20634	0.373000	0.29922	7.853000	0.86934	2.932000	0.99384	0.643000	0.83706	AGA		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			T	24423172	G	T	24423172	3	4	61	1	0	0	0	0	1	0	0	0	9881	942	33	2	1153	2	MRS2	6	24423172	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69345	24423172	146691895	4443	12428										
GPLD1	2822	broad.mit.edu	37	chr6	24446036	24446036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggctctttttctcatctCggatgtgtaacaaatggccc	8	11	3	0	rs566324510		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24446036C>T	ENST00000230036.1	-	19	1954	c.1844G>A	c.(1843-1845)cGa>cAa	p.R615Q		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	615					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)	p.R615Q(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						TTTCTCATCTCGGATGTGTAA	0.532													C|||	1	0.000199681	0	0	5008	,	,		20460	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											105	103	103					6																	24446036		2203	4300	6503	24554015	SO:0001583	missense	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1844G>A	6.37:g.24446036C>T	ENSP00000230036:p.Arg615Gln		24554015	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.221119	0.39201	.	.	ENSG00000112293	ENST00000230036	T	0.64803	-0.12	5.49	-2.38	0.06622	.	1.427420	0.04182	N	0.326777	T	0.21103	0.0508	N	0.20685	0.6	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.14476	-1.0471	10	0.10902	T	0.67	5.0E-4	12.3407	0.55093	0.0:0.2967:0.0:0.7033	.	615	P80108	PHLD_HUMAN	Q	615	ENSP00000230036:R615Q	ENSP00000230036:R615Q	R	-	2	0	GPLD1	24554015	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.364000	0.02590	-0.573000	0.05998	0.655000	0.94253	CGA		0.532	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24446036	C	T	24446036	3	4	61	1	0	0	0	0	1	0	0	0	6634	884	31	1	706	1	GPLD1	6	24446036	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22864	24446036	146669031	4444	12429										
GPLD1	2822	broad.mit.edu	37	chr6	24456737	24456737	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatacgtaccagccaagcctCgcataaggaaatgacaagaa	8	10	0	2	rs1139464		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24456737C>T	ENST00000230036.1	-	13	1247	c.1137G>A	c.(1135-1137)gcG>gcA	p.A379A		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	379					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)	p.A379A(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						AGCCAAGCCTCGCATAAGGAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	6											142	132	135					6																	24456737		2203	4300	6503	24564716	SO:0001819	synonymous_variant	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1137G>A	6.37:g.24456737C>T			24564716	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Silent	SNP	ENST00000230036.1	37	CCDS4553.1																																																																																				0.358	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24456737	C	T	24456737	2	4	61	1	0	0	0	0	0	0	0	1	6634	871	31	1		1	GPLD1	6	24456737	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10701	24456737	146658330	4445	12430										
KIAA0319	9856	broad.mit.edu	37	chr6	24547397	24547397	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgaactgcgccattatCtgtcctttgagcaataactg	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24547397C>A	ENST00000378214.3	-	21	3739	c.3215G>T	c.(3214-3216)aGa>aTa	p.R1072I	KIAA0319_ENST00000543707.1_Missense_Mutation_p.R1072I|KIAA0319_ENST00000430948.2_Missense_Mutation_p.R1027I|KIAA0319_ENST00000537886.1_Missense_Mutation_p.R1011I|KIAA0319_ENST00000535378.1_Missense_Mutation_p.R1063I	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	1072					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1072I(1)		breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						GCGCCATTATCTGTCCTTTGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											195	182	186					6																	24547397		2203	4300	6503	24655376	SO:0001583	missense	9856			AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.3215G>T	6.37:g.24547397C>A	ENSP00000367459:p.Arg1072Ile		24655376	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977635	0.74360	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.19532	2.14;2.77;2.79;2.76;2.76	4.76	3.88	0.44766	.	0.084025	0.47852	D	0.000218	T	0.29588	0.0738	L	0.53249	1.67	0.50813	D	0.999899	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.997;0.994	T	0.08229	-1.0732	10	0.87932	D	0	.	12.7607	0.57363	0.0:0.9209:0.0:0.0791	.	1011;1063;1072	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	I	1011;1063;1027;1072;1072	ENSP00000439700:R1011I;ENSP00000442403:R1063I;ENSP00000401086:R1027I;ENSP00000367459:R1072I;ENSP00000437656:R1072I	ENSP00000367459:R1072I	R	-	2	0	KIAA0319	24655376	1.000000	0.71417	0.952000	0.39060	0.920000	0.55202	5.105000	0.64591	1.204000	0.43247	0.655000	0.94253	AGA		0.433	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		A	24547397	C	A	24547397	3	1	61	1	0	0	0	0	1	0	0	0	8189	913	32	2	7	2	KIAA0319	6	24547397	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90660	24547397	146567670	4446	12431										
C6orf62	81688	broad.mit.edu	37	chr6	24716477	24716477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggaatctcgcacaccttTcaggatattttcttcataat	6	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24716477T>C	ENST00000378119.4	-	2	2372	c.205A>G	c.(205-207)Aaa>Gaa	p.K69E	C6orf62_ENST00000540769.1_Missense_Mutation_p.K11E|C6orf62_ENST00000378102.3_Missense_Mutation_p.K40E	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	69						intracellular (GO:0005622)		p.K69E(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						CGCACACCTTTCAGGATATTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	84	83					6																	24716477		2203	4300	6503	24824456	SO:0001583	missense	81688			AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.205A>G	6.37:g.24716477T>C	ENSP00000367359:p.Lys69Glu		24824456	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	37	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739868	0.49045	.	.	ENSG00000112308	ENST00000378119;ENST00000540769;ENST00000378102	T;T;T	0.35236	1.32;1.32;1.32	5.83	5.83	0.93111	.	0.100488	0.64402	D	0.000002	T	0.11793	0.0287	N	0.12182	0.205	0.42996	D	0.994502	B	0.33612	0.419	B	0.31614	0.133	T	0.09185	-1.0686	10	0.28530	T	0.3	-2.3629	16.192	0.81996	0.0:0.0:0.0:1.0	.	69	Q9GZU0	CF062_HUMAN	E	69;11;40	ENSP00000367359:K69E;ENSP00000446225:K11E;ENSP00000367342:K40E	ENSP00000367342:K40E	K	-	1	0	C6orf62	24824456	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.848000	0.55903	2.229000	0.72834	0.482000	0.46254	AAA		0.383	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		C	24716477	T	C	24716477	3	2	61	1	0	0	0	0	1	0	0	0	2374	1792	62	4	500	4	C6orf62	6	24716477	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	169080	24716477	146398590	4447	12432										
FAM65B	9750	broad.mit.edu	37	chr6	24873987	24873987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttcagtttggcctgagGcttcttgagagcggaggaat	13	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:24873987G>A	ENST00000259698.4	-	3	317	c.142C>T	c.(142-144)Cct>Tct	p.P48S	FAM65B_ENST00000540914.1_Missense_Mutation_p.P48S|FAM65B_ENST00000538035.1_Missense_Mutation_p.P77S|FAM65B_ENST00000378023.4_Missense_Mutation_p.P48S|FAM65B_ENST00000510784.2_Missense_Mutation_p.P82S	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	48					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)		p.P48S(2)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						TTGGCCTGAGGCTTCTTGAGA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	6											108	95	99					6																	24873987		1831	4092	5923	24981966	SO:0001583	missense	9750			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.142C>T	6.37:g.24873987G>A	ENSP00000259698:p.Pro48Ser		24981966	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155372	0.78114	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.01871	4.59;4.59;4.59;4.59;4.59	5.53	4.61	0.57282	.	0.050046	0.85682	D	0.000000	T	0.04048	0.0113	L	0.42245	1.32	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.71656	0.929;0.974;0.929;0.962	T	0.61187	-0.7113	10	0.30854	T	0.27	-18.32	15.1785	0.72934	0.0:0.0:0.8585:0.1415	.	82;77;48;48	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	S	48;77;48;48;82	ENSP00000259698:P48S;ENSP00000441138:P77S;ENSP00000367262:P48S;ENSP00000438425:P48S;ENSP00000441305:P82S	ENSP00000259698:P48S	P	-	1	0	FAM65B	24981966	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.316000	0.72857	2.605000	0.88082	0.655000	0.94253	CCT		0.438	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			A	24873987	G	A	24873987	3	1	61	1	0	0	0	0	1	0	0	0	5619	1203	42	3	3158	3	FAM65B	6	24873987	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157510	24873987	146241080	4448	12433										
HIST1H2AA	221613	broad.mit.edu	37	chr6	25726541	25726541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgagtttttttgttatcgCgagacgcattgcctgccagc	11	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25726541C>T	ENST00000297012.3	-	1	249	c.215G>A	c.(214-216)cGc>cAc	p.R72H	HIST1H2BA_ENST00000274764.2_5'Flank	NM_170745.3	NP_734466.1	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	72						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R72H(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(8)	13						TTTGTTATCGCGAGACGCATT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											286	230	249					6																	25726541		2203	4300	6503	25834520	SO:0001583	missense	221613			AY131982	CCDS4562.1	6p22.2	2011-01-27	2006-10-11		ENSG00000164508	ENSG00000164508		"Histones / Replication-dependent"	18729	protein-coding gene	gene with protein product		613499	"H2A histone family, member R", "histone 1, H2aa"			12408966	Standard	NM_170745		Approved	bA317E16.2, H2AFR	uc003nfc.3	Q96QV6	OTTHUMG00000014407	ENST00000297012.3:c.215G>A	6.37:g.25726541C>T	ENSP00000297012:p.Arg72His		25834520		Missense_Mutation	SNP	ENST00000297012.3	37	CCDS4562.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.288585	0.23478	.	.	ENSG00000164508	ENST00000297012	T	0.69306	-0.39	3.55	0.791	0.18619	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.49305	D	0.000152	T	0.46795	0.1411	M	0.84082	2.675	0.25952	N	0.982731	B	0.02656	0.0	B	0.04013	0.001	T	0.53479	-0.8433	10	0.72032	D	0.01	.	7.3667	0.26776	0.0:0.6861:0.0:0.3139	.	72	Q96QV6	H2A1A_HUMAN	H	72	ENSP00000297012:R72H	ENSP00000297012:R72H	R	-	2	0	HIST1H2AA	25834520	0.424000	0.25490	0.001000	0.08648	0.001000	0.01503	1.862000	0.39448	0.155000	0.19261	0.650000	0.86243	CGC		0.527	HIST1H2AA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040065.1	NM_170745		T	25726541	C	T	25726541	3	4	61	1	0	0	0	0	1	0	0	0	7149	768	27	1	184	1	HIST1H2AA	6	25726541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	852554	25726541	145388526	4449	12434										
HIST1H2BA	255626	broad.mit.edu	37	chr6	25727399	25727399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggctcactacagcaagcGctccaccatttcttccagag	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25727399G>A	ENST00000274764.2	+	1	263	c.263G>A	c.(262-264)cGc>cAc	p.R88H	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	88					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R88H(1)		breast(1)|kidney(1)	2						TACAGCAAGCGCTCCACCATT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											348	258	289					6																	25727399		2203	4300	6503	25835378	SO:0001583	missense	255626			AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"Histones / Replication-dependent"	18730	protein-coding gene	gene with protein product		609904	"H2B histone family, member U, (testis-specific)", "histone 1, H2ba"			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.263G>A	6.37:g.25727399G>A	ENSP00000274764:p.Arg88His		25835378	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Missense_Mutation	SNP	ENST00000274764.2	37	CCDS4563.1	.	.	.	.	.	.	.	.	.	.	G	9.584	1.124308	0.20959	.	.	ENSG00000146047	ENST00000274764	T	0.77358	-1.09	3.32	0.44	0.16572	Histone-fold (2);Histone core (1);	0.162877	0.38605	N	0.001624	T	0.78848	0.4348	M	0.88181	2.935	0.45528	D	0.998487	D	0.76494	0.999	P	0.59221	0.854	T	0.76277	-0.3018	10	0.49607	T	0.09	.	5.2561	0.15548	0.1916:0.0:0.6456:0.1628	.	88	Q96A08	H2B1A_HUMAN	H	88	ENSP00000274764:R88H	ENSP00000274764:R88H	R	+	2	0	HIST1H2BA	25835378	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	4.368000	0.59505	0.068000	0.16574	0.644000	0.83932	CGC		0.512	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610		A	25727399	G	A	25727399	3	1	61	1	0	0	0	0	1	0	0	0	7161	1087	38	1	265	1	HIST1H2BA	6	25727399	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	858	25727399	145387668	4450	12435										
SLC17A1	6568	broad.mit.edu	37	chr6	25801200	25801200	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaacatgctttaataaatCcaaaatatctatgcataaaa	3	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25801200C>A	ENST00000244527.4	-	11	1302	c.1187G>T	c.(1186-1188)gGa>gTa	p.G396V	SLC17A1_ENST00000476801.1_Missense_Mutation_p.G396V|SLC17A1_ENST00000468082.1_Missense_Mutation_p.G342V|SLC17A1_ENST00000427328.1_Missense_Mutation_p.G342V	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	396					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)	p.G396V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						TTTAATAAATCCAAAATATCT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											78	78	78					6																	25801200		2203	4295	6498	25909179	SO:0001583	missense	6568				CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.1187G>T	6.37:g.25801200C>A	ENSP00000244527:p.Gly396Val		25909179	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.164752	0.38217	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.70749	-0.51;-0.26;-0.51;-0.26	3.67	0.845	0.18950	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.576183	0.14720	N	0.302389	T	0.60663	0.2286	M	0.79693	2.465	0.54753	D	0.999986	B;P	0.43477	0.441;0.808	B;P	0.44811	0.331;0.461	T	0.62562	-0.6828	10	0.72032	D	0.01	.	6.7926	0.23707	0.1906:0.4388:0.3706:0.0	.	342;396	Q14916-2;Q14916	.;NPT1_HUMAN	V	396;342;396;342	ENSP00000244527:G396V;ENSP00000410549:G342V;ENSP00000420614:G396V;ENSP00000420546:G342V	ENSP00000244527:G396V	G	-	2	0	SLC17A1	25909179	0.465000	0.25815	0.716000	0.30569	0.167000	0.22549	0.819000	0.27308	0.161000	0.19458	0.655000	0.94253	GGA		0.313	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			A	25801200	C	A	25801200	3	1	61	1	0	0	0	0	1	0	0	0	14453	855	30	2	224	2	SLC17A1	6	25801200	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73801	25801200	145313867	4451	12436										
SLC17A1	6568	broad.mit.edu	37	chr6	25826804	25826804	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgctgtgctgttattataAcattacaacagtgcacaagg	8	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25826804A>G	ENST00000244527.4	-	3	207	c.92T>C	c.(91-93)gTt>gCt	p.V31A	SLC17A1_ENST00000476801.1_Missense_Mutation_p.V31A|SLC17A1_ENST00000468082.1_Missense_Mutation_p.V31A|SLC17A1_ENST00000427328.1_Missense_Mutation_p.V31A	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	31					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)	p.V31A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						TGTTATTATAACATTACAACA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											137	114	122					6																	25826804		2203	4300	6503	25934783	SO:0001583	missense	6568				CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.92T>C	6.37:g.25826804A>G	ENSP00000244527:p.Val31Ala		25934783	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.641837	0.29157	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	3.29	2.1	0.27182	Major facilitator superfamily domain, general substrate transporter (1);	1.493010	0.04814	N	0.435798	T	0.19604	0.0471	N	0.21583	0.68	0.09310	N	1	P;P	0.36183	0.486;0.542	B;B	0.42462	0.185;0.388	T	0.25950	-1.0117	10	0.09590	T	0.72	.	6.6532	0.22973	0.7554:0.2446:0.0:0.0	.	31;31	Q14916-2;Q14916	.;NPT1_HUMAN	A	31	ENSP00000244527:V31A;ENSP00000410549:V31A;ENSP00000420614:V31A;ENSP00000420546:V31A	ENSP00000244527:V31A	V	-	2	0	SLC17A1	25934783	0.000000	0.05858	0.001000	0.08648	0.065000	0.16274	0.714000	0.25808	0.626000	0.30322	0.533000	0.62120	GTT		0.448	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			G	25826804	A	G	25826804	3	3	61	1	0	0	0	0	1	0	0	0	14453	43	2	4	1351	4	SLC17A1	6	25826804	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	25604	25826804	145288263	4452	12437										
SLC17A2	10246	broad.mit.edu	37	chr6	25916003	25916003	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcacagtgatcaatctgaGaagattcctggacaaaagga	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25916003G>T	ENST00000265425.3	-	8	1044	c.1024C>A	c.(1024-1026)Ctc>Atc	p.L342I	SLC17A2_ENST00000377850.3_Missense_Mutation_p.L342I|SLC17A2_ENST00000360488.3_Missense_Mutation_p.L342I			O00624	NPT3_HUMAN	solute carrier family 17, member 2	342					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)	p.L342I(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						ATCAATCTGAGAAGATTCCTG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											78	77	77					6																	25916003		2203	4300	6503	26023982	SO:0001583	missense	10246			U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"Solute carriers"	10930	protein-coding gene	gene with protein product		611049	"solute carrier family 17 (sodium phosphate), member 2"			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.1024C>A	6.37:g.25916003G>T	ENSP00000265425:p.Leu342Ile		26023982	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	37		.	.	.	.	.	.	.	.	.	.	G	23.8	4.457516	0.84317	.	.	ENSG00000112337	ENST00000360488;ENST00000377850;ENST00000265425	T;T;T	0.60797	0.16;0.16;0.16	4.93	4.93	0.64822	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.47852	D	0.000208	T	0.56187	0.1968	L	0.48986	1.54	0.37970	D	0.933267	D;D;P	0.60575	0.967;0.988;0.86	P;P;P	0.58391	0.838;0.838;0.614	T	0.52503	-0.8567	10	0.32370	T	0.25	.	13.9025	0.63815	0.0:0.0:1.0:0.0	.	342;342;342	O00624;A6NK81;O00624-2	NPT3_HUMAN;.;.	I	342	ENSP00000353677:L342I;ENSP00000367081:L342I;ENSP00000265425:L342I	ENSP00000265425:L342I	L	-	1	0	SLC17A2	26023982	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.884000	0.48562	2.730000	0.93505	0.650000	0.86243	CTC		0.468	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1			T	25916003	G	T	25916003	3	4	61	1	0	0	0	0	1	0	0	0	14454	942	33	2	298	2	SLC17A2	6	25916003	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89199	25916003	145199064	4453	12438										
SLC17A2	10246	broad.mit.edu	37	chr6	25916985	25916985	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgatggtgcacaaccaGaaatggctgaaaaaacccag	11	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:25916985G>T	ENST00000265425.3	-	7	878	c.858C>A	c.(856-858)ttC>ttA	p.F286L	SLC17A2_ENST00000377850.3_Missense_Mutation_p.F286L|SLC17A2_ENST00000360488.3_Missense_Mutation_p.F286L			O00624	NPT3_HUMAN	solute carrier family 17, member 2	286					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)	p.F286L(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						TGCACAACCAGAAATGGCTGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											124	111	115					6																	25916985		2203	4300	6503	26024964	SO:0001583	missense	10246			U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"Solute carriers"	10930	protein-coding gene	gene with protein product		611049	"solute carrier family 17 (sodium phosphate), member 2"			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.858C>A	6.37:g.25916985G>T	ENSP00000265425:p.Phe286Leu		26024964	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	37		.	.	.	.	.	.	.	.	.	.	G	13.44	2.237841	0.39598	.	.	ENSG00000112337	ENST00000360488;ENST00000377850;ENST00000265425	T;T;T	0.59638	0.25;0.25;0.25	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000019	T	0.27832	0.0685	N	0.25201	0.72	0.43708	D	0.99617	B;B;B	0.22414	0.011;0.011;0.069	B;B;B	0.25614	0.034;0.034;0.062	T	0.08371	-1.0725	10	0.23891	T	0.37	.	13.2415	0.59999	0.0:0.0:1.0:0.0	.	286;286;286	O00624;A6NK81;O00624-2	NPT3_HUMAN;.;.	L	286	ENSP00000353677:F286L;ENSP00000367081:F286L;ENSP00000265425:F286L	ENSP00000265425:F286L	F	-	3	2	SLC17A2	26024964	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.897000	0.63231	2.557000	0.86248	0.563000	0.77884	TTC		0.448	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1			T	25916985	G	T	25916985	3	4	61	1	0	0	0	0	1	0	0	0	14454	933	33	2	468	2	SLC17A2	6	25916985	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	982	25916985	145198082	4454	12439										
HIST1H4A	8359	broad.mit.edu	37	chr6	26022088	26022088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactcgcggggtgctcaaggTgtttttggagaacgtgatcc	15	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26022088T>C	ENST00000359907.3	+	1	182	c.182T>C	c.(181-183)gTg>gCg	p.V61A		NM_003538.3	NP_003529.1	P62805	H4_HUMAN	histone cluster 1, H4a	61					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)	p.V61A(1)		large_intestine(1)|skin(1)	2						GTGCTCAAGGTGTTTTTGGAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	111	114					6																	26022088		2203	4300	6503	26130067	SO:0001583	missense	8359			X60481	CCDS4571.1	6p22.1	2011-01-27	2006-10-11	2003-03-07	ENSG00000196176	ENSG00000278637		"Histones / Replication-dependent"	4781	protein-coding gene	gene with protein product		602822	"H4 histone family, member A", "histone 1, H4a"	H4FA		9119399, 12408966	Standard	NM_003538		Approved		uc003nfq.3	P62805	OTTHUMG00000014419	ENST00000359907.3:c.182T>C	6.37:g.26022088T>C	ENSP00000352980:p.Val61Ala		26130067	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000359907.3	37	CCDS4571.1	.	.	.	.	.	.	.	.	.	.	t	16.28	3.078011	0.55753	.	.	ENSG00000196176	ENST00000359907	T	0.64260	-0.09	4.09	4.09	0.47781	.	.	.	.	.	T	0.58308	0.2113	.	.	.	0.43564	D	0.995884	.	.	.	.	.	.	T	0.59637	-0.7417	5	.	.	.	.	12.9803	0.58559	0.0:0.0:0.0:1.0	.	.	.	.	A	61	ENSP00000352980:V61A	.	V	+	2	0	HIST1H4A	26130067	1.000000	0.71417	0.997000	0.53966	0.352000	0.29268	6.016000	0.70798	1.783000	0.52377	0.533000	0.62120	GTG		0.617	HIST1H4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040081.1	NM_003538		C	26022088	T	C	26022088	3	2	61	1	0	0	0	0	1	0	0	0	7186	1696	59	4	184	4	HIST1H4A	6	26022088	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	105103	26022088	145092979	4455	12440										
HIST1H2BB	3018	broad.mit.edu	37	chr6	26043521	26043521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacttatttagagctagtgTacttggtaactgccttagtg	10	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26043521T>C	ENST00000357905.2	-	1	364	c.365A>G	c.(364-366)tAc>tGc	p.Y122C	HIST1H3C_ENST00000540144.1_5'Flank	NM_021062.2	NP_066406.1	P33778	H2B1B_HUMAN	histone cluster 1, H2bb	122					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Y122C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						AGAGCTAGTGTACTTGGTAAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											30	30	30					6																	26043521		2203	4300	6503	26151500	SO:0001583	missense	3018			AF531285	CCDS4575.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196226			"Histones / Replication-dependent"	4751	protein-coding gene	gene with protein product		602803	"H2B histone family, member F", "histone 1, H2bb"	H2BFF		8227173, 12408966	Standard	NM_021062		Approved	H2B/f	uc003nfu.3	P33778	OTTHUMG00000014421	ENST00000357905.2:c.365A>G	6.37:g.26043521T>C	ENSP00000350580:p.Tyr122Cys		26151500	Q4KN36	Missense_Mutation	SNP	ENST00000357905.2	37	CCDS4575.1	.	.	.	.	.	.	.	.	.	.	t	9.719	1.159263	0.21454	.	.	ENSG00000196226	ENST00000357905	T	0.43294	0.95	5.08	5.08	0.68730	Histone-fold (2);	0.000000	0.53938	U	0.000052	T	0.46171	0.1379	H	0.95114	3.625	0.47994	D	0.999569	B	0.11235	0.004	B	0.11329	0.006	T	0.59941	-0.7359	10	0.66056	D	0.02	.	14.3169	0.66457	0.0:0.0:0.0:1.0	.	122	P33778	H2B1B_HUMAN	C	122	ENSP00000350580:Y122C	ENSP00000350580:Y122C	Y	-	2	0	HIST1H2BB	26151500	1.000000	0.71417	1.000000	0.80357	0.348000	0.29142	8.036000	0.88901	2.020000	0.59435	0.383000	0.25322	TAC		0.502	HIST1H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040083.1	NM_021062		C	26043521	T	C	26043521	3	2	61	1	0	0	0	0	1	0	0	0	7162	1638	57	4	19	4	HIST1H2BB	6	26043521	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	21433	26043521	145071546	4456	12441										
BTN3A2	11118	broad.mit.edu	37	chr6	26370573	26370573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttctaatcttcacgtcGaagtgaagggttatgaggat	13	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26370573G>A	ENST00000356386.2	+	5	645	c.457G>A	c.(457-459)Gaa>Aaa	p.E153K	BTN3A2_ENST00000527422.1_Missense_Mutation_p.E153K|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000508906.2_Missense_Mutation_p.E111K|BTN3A2_ENST00000396948.1_Missense_Mutation_p.E153K|BTN3A2_ENST00000377708.2_Missense_Mutation_p.E153K|BTN3A2_ENST00000396934.3_Missense_Mutation_p.E130K	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	153					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E153K(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TCTTCACGTCGAAGTGAAGGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	87	91					6																	26370573		2203	4300	6503	26478552	SO:0001583	missense	11118			U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.457G>A	6.37:g.26370573G>A	ENSP00000348751:p.Glu153Lys		26478552	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	.	.	.	.	.	.	.	.	.	.	g	13.81	2.349604	0.41599	.	.	ENSG00000186470	ENST00000532865;ENST00000530653;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T;T	0.13657	2.57;3.37;4.02;4.02;3.88;4.02;4.02;4.43	2.84	-5.69	0.02428	Immunoglobulin-like fold (1);	.	.	.	.	T	0.04952	0.0133	M	0.67700	2.07	0.09310	N	1	D;P	0.56035	0.974;0.923	P;B	0.44696	0.458;0.207	T	0.03249	-1.1056	9	0.37606	T	0.19	.	4.5092	0.11903	0.1229:0.5794:0.1682:0.1295	.	130;153	F8W6E0;P78410	.;BT3A2_HUMAN	K	111;111;153;153;153;130;153;153;111	ENSP00000435952:E111K;ENSP00000434102:E111K;ENSP00000432138:E153K;ENSP00000348751:E153K;ENSP00000380140:E130K;ENSP00000366937:E153K;ENSP00000380152:E153K;ENSP00000442687:E111K	ENSP00000348751:E153K	E	+	1	0	BTN3A2	26478552	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.941000	0.01542	-1.394000	0.02077	0.405000	0.27470	GAA		0.512	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			A	26370573	G	A	26370573	3	1	61	1	0	0	0	0	1	0	0	0	1566	1059	37	1	467	1	BTN3A2	6	26370573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	327052	26370573	144744494	4457	12442										
BTN3A3	10384	broad.mit.edu	37	chr6	26444502	26444502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagatggtgacttctacGaaaaagccctggtggagctg	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26444502G>A	ENST00000244519.2	+	4	646	c.403G>A	c.(403-405)Gaa>Aaa	p.E135K	BTN3A3_ENST00000361232.3_Missense_Mutation_p.E93K|BTN3A3_ENST00000339789.4_Missense_Mutation_p.E93K	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	135	Ig-like V-type 1.				T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.E135K(1)		cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						TGACTTCTACGAAAAAGCCCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											133	131	131					6																	26444502		2203	4300	6503	26552481	SO:0001583	missense	10384			U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.403G>A	6.37:g.26444502G>A	ENSP00000244519:p.Glu135Lys		26552481	B4DWI7|E9PCP5	Missense_Mutation	SNP	ENST00000244519.2	37	CCDS4611.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135639	0.77662	.	.	ENSG00000111801	ENST00000494393;ENST00000482451;ENST00000244519;ENST00000339789;ENST00000471353;ENST00000361232;ENST00000487627;ENST00000496719;ENST00000490254;ENST00000476281;ENST00000487272	T;T;T;T;T;T;T;T;T;T	0.06933	3.24;4.22;4.22;4.22;4.22;4.22;4.22;4.22;4.22;4.22	2.5	1.58	0.23477	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04497	0.0123	L	0.59967	1.855	0.09310	N	1	P;D	0.55172	0.931;0.97	B;P	0.45506	0.307;0.483	T	0.31833	-0.9929	9	0.44086	T	0.13	.	9.0583	0.36419	0.0:0.2292:0.7708:0.0	.	93;135	E9PCP5;O00478	.;BT3A3_HUMAN	K	135;117;135;93;93;93;93;135;93;93;93	ENSP00000417234:E135K;ENSP00000419312:E117K;ENSP00000244519:E135K;ENSP00000344968:E93K;ENSP00000417717:E93K;ENSP00000355238:E93K;ENSP00000420339:E93K;ENSP00000420147:E135K;ENSP00000419736:E93K;ENSP00000419445:E93K	ENSP00000244519:E135K	E	+	1	0	BTN3A3	26552481	0.000000	0.05858	0.001000	0.08648	0.930000	0.56654	0.132000	0.15891	0.570000	0.29347	0.555000	0.69702	GAA		0.502	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994		A	26444502	G	A	26444502	3	1	61	1	0	0	0	0	1	0	0	0	1567	1059	37	1	409	1	BTN3A3	6	26444502	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73929	26444502	144670565	4458	12443										
BTN1A1	696	broad.mit.edu	37	chr6	26502086	26502086	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatccgtggcgtcagagtCtctgacgacggggagtacac	15	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26502086C>A	ENST00000244513.6	+	2	414	c.348C>A	c.(346-348)gtC>gtA	p.V116V		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	116	Ig-like V-type 1.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)	p.V116V(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						GCGTCAGAGTCTCTGACGACG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	6											39	41	40					6																	26502086		2201	4295	6496	26610065	SO:0001819	synonymous_variant	696			U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.348C>A	6.37:g.26502086C>A			26610065	Q4VAN3|Q4VAN4|Q9H458	Silent	SNP	ENST00000244513.6	37	CCDS4614.1																																																																																				0.622	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732		A	26502086	C	A	26502086	2	1	61	1	0	0	0	0	0	0	0	1	1562	900	32	2		2	BTN1A1	6	26502086	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57584	26502086	144612981	4459	12444										
ABT1	29777	broad.mit.edu	37	chr6	26598209	26598209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagcggtcctacaccaaGgactacaccgagggatgggt	12	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:26598209G>T	ENST00000274849.1	+	2	340	c.309G>T	c.(307-309)aaG>aaT	p.K103N		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	103	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.K103N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CCTACACCAAGGACTACACCG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											57	53	54					6																	26598209		2203	4300	6503	26706188	SO:0001583	missense	29777			AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.309G>T	6.37:g.26598209G>T	ENSP00000274849:p.Lys103Asn		26706188		Missense_Mutation	SNP	ENST00000274849.1	37	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363229	0.82353	.	.	ENSG00000146109	ENST00000274849	.	.	.	5.23	2.35	0.29111	Nucleotide-binding, alpha-beta plait (1);	0.327319	0.35555	N	0.003140	T	0.36496	0.0969	L	0.35854	1.095	0.39955	D	0.97458	D	0.64830	0.994	P	0.57548	0.823	T	0.12682	-1.0538	9	0.25751	T	0.34	-0.7713	8.1855	0.31337	0.2826:0.0:0.7174:0.0	.	103	Q9ULW3	ABT1_HUMAN	N	103	.	ENSP00000274849:K103N	K	+	3	2	ABT1	26706188	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.807000	0.47955	0.260000	0.21731	0.563000	0.77884	AAG		0.622	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1			T	26598209	G	T	26598209	3	4	61	1	0	0	0	0	1	0	0	0	101	991	35	2	315	2	ABT1	6	26598209	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96123	26598209	144516858	4460	12445										
ZNF391	346157	broad.mit.edu	37	chr6	27368192	27368192	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctcagggtcctacaaatGaagaagactataaaaacgaa	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27368192G>T	ENST00000244576.4	+	3	588	c.43G>T	c.(43-45)Gaa>Taa	p.E15*		NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	15					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E15*(2)		endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						TCCTACAAATGAAGAAGACTA	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											97	89	92					6																	27368192		1845	4095	5940	27476171	SO:0001587	stop_gained	346157			BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.43G>T	6.37:g.27368192G>T	ENSP00000244576:p.Glu15*		27476171	B4DH77	Nonsense_Mutation	SNP	ENST00000244576.4	37	CCDS43429.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711936	0.68730	.	.	ENSG00000124613	ENST00000244576;ENST00000461521	.	.	.	3.74	0.76	0.18442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	4.5162	0.11935	0.2069:0.0:0.6181:0.1749	.	.	.	.	X	15	.	ENSP00000244576:E15X	E	+	1	0	ZNF391	27476171	0.000000	0.05858	0.045000	0.18777	0.512000	0.34134	0.411000	0.21115	0.275000	0.22094	0.655000	0.94253	GAA		0.423	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		T	27368192	G	T	27368192	4	4	61	1	0	0	0	0	0	1	0	0	17918	1291	45	2	45	2	ZNF391	6	27368192	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	769983	27368192	143746875	4461	12446										
ZNF391	346157	broad.mit.edu	37	chr6	27368259	27368259	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgcacagaagaaatcctCttttgagaacacagtggtca	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27368259C>A	ENST00000244576.4	+	3	655	c.110C>A	c.(109-111)tCt>tAt	p.S37Y		NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	37					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S37Y(2)		endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						AAGAAATCCTCTTTTGAGAAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	6											114	105	108					6																	27368259		1868	4095	5963	27476238	SO:0001583	missense	346157			BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.110C>A	6.37:g.27368259C>A	ENSP00000244576:p.Ser37Tyr		27476238	B4DH77	Missense_Mutation	SNP	ENST00000244576.4	37	CCDS43429.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.323921	0.41096	.	.	ENSG00000124613	ENST00000244576;ENST00000461521	T;T	0.08370	3.1;6.01	3.42	-0.61	0.11604	.	.	.	.	.	T	0.02267	0.0070	L	0.61387	1.9	0.09310	N	1	B	0.23128	0.08	B	0.21917	0.037	T	0.45425	-0.9262	9	0.35671	T	0.21	.	0.3005	0.00272	0.1974:0.2912:0.1942:0.3173	.	37	Q9UJN7	ZN391_HUMAN	Y	37	ENSP00000244576:S37Y;ENSP00000419498:S37Y	ENSP00000244576:S37Y	S	+	2	0	ZNF391	27476238	0.000000	0.05858	0.018000	0.16275	0.670000	0.39368	-0.044000	0.12023	-0.040000	0.13580	0.655000	0.94253	TCT		0.423	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		A	27368259	C	A	27368259	3	1	61	1	0	0	0	0	1	0	0	0	17918	913	32	2	112	2	ZNF391	6	27368259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67	27368259	143746808	4462	12447										
ZNF391	346157	broad.mit.edu	37	chr6	27368953	27368953	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcgcttactgaacatcaGagaacacacactggggagaa	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27368953G>A	ENST00000244576.4	+	3	1349	c.804G>A	c.(802-804)caG>caA	p.Q268Q	RP1-153G14.4_ENST00000607727.1_lincRNA	NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q268Q(1)		endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						CTGAACATCAGAGAACACACA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	6											63	70	67					6																	27368953		2196	4296	6492	27476932	SO:0001819	synonymous_variant	346157			BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.804G>A	6.37:g.27368953G>A			27476932	B4DH77	Silent	SNP	ENST00000244576.4	37	CCDS43429.1																																																																																				0.448	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		A	27368953	G	A	27368953	2	1	61	1	0	0	0	0	0	0	0	1	17918	933	33	3		3	ZNF391	6	27368953	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	694	27368953	143746114	4463	12448										
ZNF391	346157	broad.mit.edu	37	chr6	27369096	27369096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtggaaagggcttcagtcGaagctcatcccttattattc	10	9	2	0	rs372035777		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27369096G>A	ENST00000244576.4	+	3	1492	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	RP1-153G14.4_ENST00000607727.1_lincRNA	NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R316Q(2)		endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						GGCTTCAGTCGAAGCTCATCC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	6						G	GLN/ARG	2,4130		0,2,2064	76	79	78		947	-1.1	0	6		78	0,8482		0,0,4241	no	missense	ZNF391	NM_001076781.1	43	0,2,6305	AA,AG,GG		0.0,0.0484,0.0159	probably-damaging	316/359	27369096	2,12612	2066	4241	6307	27477075	SO:0001583	missense	346157			BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.947G>A	6.37:g.27369096G>A	ENSP00000244576:p.Arg316Gln		27477075	B4DH77	Missense_Mutation	SNP	ENST00000244576.4	37	CCDS43429.1	.	.	.	.	.	.	.	.	.	.	G	0.931	-0.712537	0.03206	4.84E-4	0.0	ENSG00000124613	ENST00000244576	T	0.07444	3.19	3.91	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00552	0.0018	N	0.11364	0.135	0.09310	N	1	P	0.44139	0.827	B	0.19391	0.025	T	0.39482	-0.9612	9	0.02654	T	1	.	4.4301	0.11524	0.4016:0.172:0.4264:0.0	.	316	Q9UJN7	ZN391_HUMAN	Q	316	ENSP00000244576:R316Q	ENSP00000244576:R316Q	R	+	2	0	ZNF391	27477075	0.000000	0.05858	0.044000	0.18714	0.793000	0.44817	0.134000	0.15932	0.155000	0.19261	0.557000	0.71058	CGA		0.463	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		A	27369096	G	A	27369096	3	1	61	1	0	0	0	0	1	0	0	0	17918	1058	37	1	949	1	ZNF391	6	27369096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143	27369096	143745971	4464	12449										
ZNF184	7738	broad.mit.edu	37	chr6	27419185	27419185	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctctcctgaatgaattCtctggtgctgaatgagatat	9	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27419185C>A	ENST00000211936.6	-	6	2437	c.2153G>T	c.(2152-2154)aGa>aTa	p.R718I	ZNF184_ENST00000377419.1_Missense_Mutation_p.R718I	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	718					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R718I(1)		breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TGAATGAATTCTCTGGTGCTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											142	146	145					6																	27419185		2203	4300	6503	27527164	SO:0001583	missense	7738			U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.2153G>T	6.37:g.27419185C>A	ENSP00000211936:p.Arg718Ile		27527164	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.097292	0.37048	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087	T;T	0.10005	2.92;2.92	4.95	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.118619	0.38778	N	0.001568	T	0.05410	0.0143	M	0.61703	1.905	0.46954	D	0.999263	P	0.44776	0.843	B	0.36922	0.236	T	0.18999	-1.0319	10	0.46703	T	0.11	.	10.2604	0.43423	0.0:0.9012:0.0:0.0988	.	718	Q99676	ZN184_HUMAN	I	718;718;634	ENSP00000211936:R718I;ENSP00000366636:R718I	ENSP00000211936:R718I	R	-	2	0	ZNF184	27527164	0.000000	0.05858	0.973000	0.42090	0.988000	0.76386	0.508000	0.22692	1.289000	0.44618	0.591000	0.81541	AGA		0.403	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		A	27419185	C	A	27419185	3	1	61	1	0	0	0	0	1	0	0	0	17790	913	32	2	106	2	ZNF184	6	27419185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50089	27419185	143695882	4465	12450										
ZNF184	7738	broad.mit.edu	37	chr6	27419906	27419906	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaaggcctttccacattCattgcatttgtaaggttttt	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27419906C>A	ENST00000211936.6	-	6	1716	c.1432G>T	c.(1432-1434)Gaa>Taa	p.E478*	ZNF184_ENST00000377419.1_Nonsense_Mutation_p.E478*	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E478*(1)		breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TTTCCACATTCATTGCATTTG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											81	76	78					6																	27419906		2203	4300	6503	27527885	SO:0001587	stop_gained	7738			U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1432G>T	6.37:g.27419906C>A	ENSP00000211936:p.Glu478*		27527885	B2R715|O60792|Q8TBA9	Nonsense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	C	37	6.269881	0.97431	.	.	ENSG00000096654	ENST00000211936;ENST00000377419	.	.	.	5.27	5.27	0.74061	.	0.130764	0.35262	N	0.003338	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	16.4094	0.83703	0.0:1.0:0.0:0.0	.	.	.	.	X	478	.	ENSP00000211936:E478X	E	-	1	0	ZNF184	27527885	0.000000	0.05858	0.553000	0.28255	0.999000	0.98932	0.659000	0.24994	2.744000	0.94065	0.655000	0.94253	GAA		0.408	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		A	27419906	C	A	27419906	4	1	61	1	0	0	0	0	0	1	0	0	17790	835	29	2	827	2	ZNF184	6	27419906	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	721	27419906	143695161	4466	12451										
ZNF184	7738	broad.mit.edu	37	chr6	27420219	27420219	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttgagtaaggtgtgtgctCctggtgaaggttttatcaca	13	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27420219C>A	ENST00000211936.6	-	6	1403	c.1119G>T	c.(1117-1119)agG>agT	p.R373S	ZNF184_ENST00000377419.1_Missense_Mutation_p.R373S	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	373					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R373S(1)		breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						GGTGTGTGCTCCTGGTGAAGG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											53	54	54					6																	27420219		2203	4300	6503	27528198	SO:0001583	missense	7738			U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1119G>T	6.37:g.27420219C>A	ENSP00000211936:p.Arg373Ser		27528198	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857732	0.32791	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087;ENST00000538681	T;T	0.16743	2.32;2.32	5.25	3.44	0.39384	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000036	T	0.01489	0.0048	N	0.03324	-0.35	0.09310	N	1	B	0.30455	0.28	B	0.20955	0.032	T	0.41858	-0.9485	10	0.15066	T	0.55	.	5.2067	0.15295	0.1639:0.6627:0.0:0.1734	.	373	Q99676	ZN184_HUMAN	S	373;373;373;61	ENSP00000211936:R373S;ENSP00000366636:R373S	ENSP00000211936:R373S	R	-	3	2	ZNF184	27528198	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.368000	0.07543	1.453000	0.47775	0.650000	0.86243	AGG		0.383	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		A	27420219	C	A	27420219	3	1	61	1	0	0	0	0	1	0	0	0	17790	854	30	2	1140	2	ZNF184	6	27420219	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	313	27420219	143694848	4467	12452										
HIST1H2BM	8342	broad.mit.edu	37	chr6	27783011	27783011	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaggctatgggaatcatgAactccttcgtcaacgacatc	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27783011A>C	ENST00000359465.4	+	1	190	c.190A>C	c.(190-192)Aac>Cac	p.N64H	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	64					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N64H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						GGGAATCATGAACTCCTTCGT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											169	157	161					6																	27783011		2203	4300	6503	27890990	SO:0001583	missense	8342			Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"Histones / Replication-dependent"	4750	protein-coding gene	gene with protein product		602802	"H2B histone family, member E", "histone 1, H2bm"	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.190A>C	6.37:g.27783011A>C	ENSP00000352442:p.Asn64His		27890990	Q6NWQ3	Missense_Mutation	SNP	ENST00000359465.4	37	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	15.34	2.805458	0.50315	.	.	ENSG00000196374	ENST00000359465	T	0.22134	1.97	4.17	4.17	0.49024	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000007	T	0.51227	0.1662	H	0.96889	3.9	0.58432	D	0.999999	D	0.71674	0.998	D	0.74674	0.984	T	0.68625	-0.5359	10	0.87932	D	0	.	12.8248	0.57714	1.0:0.0:0.0:0.0	.	64	Q99879	H2B1M_HUMAN	H	64	ENSP00000352442:N64H	ENSP00000352442:N64H	N	+	1	0	HIST1H2BM	27890990	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	8.604000	0.90877	1.869000	0.54173	0.460000	0.39030	AAC		0.552	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		C	27783011	A	C	27783011	3	2	61	1	0	0	0	0	1	0	0	0	7173	246	9	4	192	4	HIST1H2BM	6	27783011	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	362792	27783011	143332056	4468	12453										
OR2B2	81697	broad.mit.edu	37	chr6	27879649	27879649	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaattgctaaagccactaAtccaggatgcagctgccaac	8	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27879649A>T	ENST00000303324.2	-	1	525	c.449T>A	c.(448-450)aTt>aAt	p.I150N		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I150N(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						AAAGCCACTAATCCAGGATGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											78	75	76					6																	27879649		2203	4300	6503	27987628	SO:0001583	missense	81697			Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"GPCR / Class A : Olfactory receptors"	13966	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 9"	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.449T>A	6.37:g.27879649A>T	ENSP00000304419:p.Ile150Asn		27987628	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.556663	0.45487	.	.	ENSG00000168131	ENST00000303324	T	0.42131	0.98	4.42	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.673320	0.11958	U	0.513001	T	0.34077	0.0885	M	0.75884	2.315	0.09310	N	1	P	0.48294	0.908	P	0.50136	0.632	T	0.22941	-1.0202	10	0.62326	D	0.03	.	6.3086	0.21153	0.7932:0.0:0.2068:0.0	.	150	Q9GZK3	OR2B2_HUMAN	N	150	ENSP00000304419:I150N	ENSP00000304419:I150N	I	-	2	0	OR2B2	27987628	0.000000	0.05858	0.176000	0.23000	0.818000	0.46254	1.249000	0.32839	0.782000	0.33613	0.460000	0.39030	ATT		0.463	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			T	27879649	A	T	27879649	3	4	61	1	0	0	0	0	1	0	0	0	11020	101	4	5	628	5	OR2B2	6	27879649	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	96638	27879649	143235418	4469	12454										
OR2B2	81697	broad.mit.edu	37	chr6	27879758	27879758	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcacatgacggccaggaGaagacattctgtggaaccca	11	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27879758G>T	ENST00000303324.2	-	1	416	c.340C>A	c.(340-342)Ctc>Atc	p.L114I		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L114I(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						ACGGCCAGGAGAAGACATTCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6											108	98	101					6																	27879758		2203	4300	6503	27987737	SO:0001583	missense	81697			Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"GPCR / Class A : Olfactory receptors"	13966	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 9"	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.340C>A	6.37:g.27879758G>T	ENSP00000304419:p.Leu114Ile		27987737	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.983860	0.35036	.	.	ENSG00000168131	ENST00000303324	T	0.12984	2.63	4.52	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35291	U	0.003309	T	0.26048	0.0635	M	0.84948	2.725	0.09310	N	1	D	0.71674	0.998	D	0.83275	0.996	T	0.07366	-1.0776	10	0.66056	D	0.02	.	10.9497	0.47321	0.0961:0.0:0.9039:0.0	.	114	Q9GZK3	OR2B2_HUMAN	I	114	ENSP00000304419:L114I	ENSP00000304419:L114I	L	-	1	0	OR2B2	27987737	0.598000	0.26882	0.994000	0.49952	0.450000	0.32258	1.292000	0.33342	1.185000	0.42971	0.563000	0.77884	CTC		0.478	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			T	27879758	G	T	27879758	3	4	61	1	0	0	0	0	1	0	0	0	11020	942	33	2	737	2	OR2B2	6	27879758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109	27879758	143235309	4470	12455										
OR2B2	81697	broad.mit.edu	37	chr6	27879871	27879871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcatttgtggaactgtaCttgtggtatagcaaaggtcc	11	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:27879871C>A	ENST00000303324.2	-	1	303	c.227G>T	c.(226-228)aGt>aTt	p.S76I		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S76I(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						TGGAACTGTACTTGTGGTATA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											160	140	147					6																	27879871		2203	4300	6503	27987850	SO:0001583	missense	81697			Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"GPCR / Class A : Olfactory receptors"	13966	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 9"	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.227G>T	6.37:g.27879871C>A	ENSP00000304419:p.Ser76Ile		27987850	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512850	0.27123	.	.	ENSG00000168131	ENST00000303324	T	0.00348	8.0	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45867	U	0.000324	T	0.00210	0.0006	M	0.73430	2.235	0.09310	N	1	P	0.52842	0.956	P	0.48368	0.575	T	0.34229	-0.9837	10	0.87932	D	0	.	11.4182	0.49965	0.0:0.8161:0.1839:0.0	.	76	Q9GZK3	OR2B2_HUMAN	I	76	ENSP00000304419:S76I	ENSP00000304419:S76I	S	-	2	0	OR2B2	27987850	0.000000	0.05858	0.768000	0.31515	0.167000	0.22549	-1.985000	0.01485	2.428000	0.82296	0.563000	0.77884	AGT		0.433	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			A	27879871	C	A	27879871	3	1	61	1	0	0	0	0	1	0	0	0	11020	565	20	2	850	2	OR2B2	6	27879871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113	27879871	143235196	4471	12456										
ZSCAN16	80345	broad.mit.edu	37	chr6	28093321	28093321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctcacaaaagtgcagtCctcacaggagggaactctat	9	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28093321C>T	ENST00000340487.4	+	2	249	c.100C>T	c.(100-102)Cct>Tct	p.P34S	ZSCAN16-AS1_ENST00000600652.1_RNA|ZSCAN16-AS1_ENST00000602810.1_RNA	NM_025231.1	NP_079507.1	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16	34					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P34S(1)		large_intestine(5)|liver(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						AAAGTGCAGTCCTCACAGGAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	6											194	199	197					6																	28093321		2203	4300	6503	28201300	SO:0001583	missense	80345			AK025844	CCDS4644.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000196812	ENSG00000196812		"-", "Zinc fingers, C2H2-type"	20813	protein-coding gene	gene with protein product			"zinc finger protein 392", "zinc finger protein 435"	ZNF392, ZNF435			Standard	NM_025231		Approved	FLJ22191, dJ265C24.3	uc003nkm.3	Q9H4T2	OTTHUMG00000014509	ENST00000340487.4:c.100C>T	6.37:g.28093321C>T	ENSP00000366527:p.Pro34Ser		28201300	Q9H6K2	Missense_Mutation	SNP	ENST00000340487.4	37	CCDS4644.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.490762	0.26774	.	.	ENSG00000196812	ENST00000340487	T	0.05447	3.44	3.65	2.72	0.32119	Retrovirus capsid, C-terminal (1);	.	.	.	.	T	0.01835	0.0058	L	0.50333	1.59	0.09310	N	1	B;B	0.30793	0.057;0.295	B;B	0.24701	0.01;0.055	T	0.44787	-0.9305	9	0.16420	T	0.52	.	8.7414	0.34560	0.0:0.7663:0.2337:0.0	.	34;34	B4DFB7;Q9H4T2	.;ZSC16_HUMAN	S	34	ENSP00000366527:P34S	ENSP00000366527:P34S	P	+	1	0	ZSCAN16	28201300	0.000000	0.05858	0.023000	0.16930	0.681000	0.39784	0.432000	0.21461	0.799000	0.34018	0.557000	0.71058	CCT		0.522	ZSCAN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040177.1	NM_025231		T	28093321	C	T	28093321	3	4	61	1	0	0	0	0	1	0	0	0	18268	855	30	3	102	3	ZSCAN16	6	28093321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213450	28093321	143021746	4472	12457										
ZNF192	7745	broad.mit.edu	37	chr6	28121776	28121776	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccacagtggtgaaaaatCtgaatccataagcgtttagg	9	7	1	2	rs374105856		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28121776C>A	ENST00000330236.6	+	6	1902	c.1718C>A	c.(1717-1719)tCt>tAt	p.S573Y	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.S573Y	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	573					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S573Y(1)									GGTGAAAAATCTGAATCCATA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	96	97					6																	28121776		2203	4300	6503	28229755	SO:0001583	missense	7745				CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.1718C>A	6.37:g.28121776C>A	ENSP00000332750:p.Ser573Tyr		28229755	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	37	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126603	0.37533	.	.	ENSG00000198315	ENST00000330236;ENST00000457389	T;T	0.06768	3.26;3.26	5.44	3.59	0.41128	Zinc finger, C2H2 (1);	0.392212	0.22197	N	0.063286	T	0.04092	0.0114	L	0.54323	1.7	0.80722	D	1	B	0.32425	0.371	B	0.30716	0.119	T	0.14868	-1.0457	10	0.87932	D	0	.	9.6044	0.39624	0.1402:0.7833:0.0:0.0765	.	573	Q15776	ZN192_HUMAN	Y	573	ENSP00000332750:S573Y;ENSP00000402948:S573Y	ENSP00000332750:S573Y	S	+	2	0	ZNF192	28229755	0.998000	0.40836	0.972000	0.41901	0.946000	0.59487	3.070000	0.50033	1.234000	0.43709	0.655000	0.94253	TCT		0.423	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			A	28121776	C	A	28121776	3	1	61	1	0	0	0	0	1	0	0	0	17795	913	32	2	1736	2	ZNF192	6	28121776	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28455	28121776	142993291	4473	12458										
NKAPL	222698	broad.mit.edu	37	chr6	28227462	28227462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcactgctatgcagaagaaCggcagtcagcggaagactac	12	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28227462C>T	ENST00000343684.3	+	1	365	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	105								p.R105W(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						TGCAGAAGAACGGCAGTCAGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											69	69	69					6																	28227462		2203	4300	6503	28335441	SO:0001583	missense	222698			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 194"	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.313C>T	6.37:g.28227462C>T	ENSP00000345716:p.Arg105Trp		28335441	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.104958	0.37145	.	.	ENSG00000189134	ENST00000343684	T	0.15487	2.42	4.77	-2.11	0.07187	.	0.634420	0.16795	N	0.199208	T	0.04452	0.0122	M	0.65975	2.015	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.35226	-0.9797	10	0.36615	T	0.2	-0.0126	1.511	0.02496	0.1413:0.4193:0.1455:0.2939	.	105	Q5M9Q1	NKAPL_HUMAN	W	105	ENSP00000345716:R105W	ENSP00000345716:R105W	R	+	1	2	NKAPL	28335441	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.869000	0.04232	-0.533000	0.06323	0.655000	0.94253	CGG		0.582	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			T	28227462	C	T	28227462	3	4	61	1	0	0	0	0	1	0	0	0	10471	527	19	1	315	1	NKAPL	6	28227462	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105686	28227462	142887605	4474	12459										
NKAPL	222698	broad.mit.edu	37	chr6	28227693	28227693	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataggaaaaagaagaccagtCgttcaagaaacaagaaaaaa	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28227693C>T	ENST00000343684.3	+	1	596	c.544C>T	c.(544-546)Cgt>Tgt	p.R182C	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	182	Lys-rich.							p.R182C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GAAGACCAGTCGTTCAAGAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											36	44	41					6																	28227693		2203	4298	6501	28335672	SO:0001583	missense	222698			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 194"	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.544C>T	6.37:g.28227693C>T	ENSP00000345716:p.Arg182Cys		28335672	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272190	0.23221	.	.	ENSG00000189134	ENST00000343684	T	0.14266	2.52	4.74	2.95	0.34219	.	.	.	.	.	T	0.08935	0.0221	L	0.44542	1.39	0.09310	N	0.999999	D	0.76494	0.999	P	0.54856	0.762	T	0.13495	-1.0507	9	0.62326	D	0.03	5.0E-4	5.9821	0.19413	0.1877:0.7159:0.0:0.0965	.	182	Q5M9Q1	NKAPL_HUMAN	C	182	ENSP00000345716:R182C	ENSP00000345716:R182C	R	+	1	0	NKAPL	28335672	0.605000	0.26941	0.301000	0.25044	0.525000	0.34531	0.937000	0.28951	0.722000	0.32252	0.655000	0.94253	CGT		0.383	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			T	28227693	C	T	28227693	3	4	61	1	0	0	0	0	1	0	0	0	10471	884	31	1	546	1	NKAPL	6	28227693	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	231	28227693	142887374	4475	12460										
ZNF187	0	broad.mit.edu	37	chr6	28244371	28244371	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgagaagccttatcagtGcaatgagtgtggcaaagtct	13	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28244371G>C								NKAPL (15635 upstream) : PGBD1 (4942 downstream)																							CCTTATCAGTGCAATGAGTGT	0.433																																																0			6											66	68	68					6																	28244371		2069	4230	6299	28352350	SO:0001628	intergenic_variant	7741																															6.37:g.28244371G>C			28352350		Missense_Mutation	SNP		37																																																																																				0	0.433									C	28244371	G	C	28244371	1	2	61	0	1	0	0	0	0	0	0	0	17792	1319	46	5		5	ZNF187	6	28244371	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16678	28244371	142870696	4476	12461										
PGBD1	84547	broad.mit.edu	37	chr6	28269597	28269597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattcgtgagaacaggaccGaaaaatgtccccttatgaat	8	9	0	2	rs200203742		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28269597G>A	ENST00000405948.2	+	7	2386	c.1966G>A	c.(1966-1968)Gaa>Aaa	p.E656K	PGBD1_ENST00000259883.3_Missense_Mutation_p.E656K	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	656						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E656K(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						GAACAGGACCGAAAAATGTCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	87	87					6																	28269597		2203	4300	6503	28377576	SO:0001583	missense	84547			D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1966G>A	6.37:g.28269597G>A	ENSP00000385213:p.Glu656Lys		28377576	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036827	0.54896	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01388	4.95;4.95	4.76	3.88	0.44766	.	0.643417	0.14046	N	0.345079	T	0.00524	0.0017	L	0.41710	1.295	0.25659	N	0.986029	P	0.39903	0.694	B	0.37780	0.258	T	0.41556	-0.9502	10	0.11182	T	0.66	-5.526	8.7917	0.34854	0.1027:0.0:0.8973:0.0	.	656	Q96JS3	PGBD1_HUMAN	K	656	ENSP00000385213:E656K;ENSP00000259883:E656K	ENSP00000259883:E656K	E	+	1	0	PGBD1	28377576	0.997000	0.39634	0.900000	0.35374	0.946000	0.59487	2.279000	0.43435	1.356000	0.45884	0.655000	0.94253	GAA		0.373	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			A	28269597	G	A	28269597	3	1	61	1	0	0	0	0	1	0	0	0	11811	1059	37	1	1988	1	PGBD1	6	28269597	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25226	28269597	142845470	4477	12462										
SCAND3	114821	broad.mit.edu	37	chr6	28541333	28541333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgttttgaatataaatgtCgcttaagttttgatggtttc	8	3	0	2	rs150277871	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28541333C>T	ENST00000452236.2	-	4	2950	c.2333G>A	c.(2332-2334)cGa>cAa	p.R778Q	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1												p.R778Q(1)		NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						atataaatgtcgcttaagttt	0.333													C|||	3	0.000599042	0	0	5008	,	,		18583	0		0.003	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						C	GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	60	56	57		2333	2.3	1	6	dbSNP_134	57	37,8559	24.0+/-70.4	0,37,4261	yes	missense	SCAND3	NM_052923.1	43	0,41,6460	TT,TC,CC		0.4304,0.0908,0.3153	possibly-damaging	778/1326	28541333	41,12961	2203	4298	6501	28649312	SO:0001583	missense	114821																														ENST00000452236.2:c.2333G>A	6.37:g.28541333C>T	ENSP00000395259:p.Arg778Gln		28649312		Missense_Mutation	SNP	ENST00000452236.2	37	CCDS34355.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.13	3.037053	0.54896	9.08E-4	0.004304	ENSG00000232040	ENST00000452236	T	0.02158	4.42	2.27	2.27	0.28462	.	0.124609	0.29246	U	0.012714	T	0.03520	0.0101	M	0.63843	1.955	0.26074	N	0.981186	D	0.61697	0.99	D	0.67725	0.953	T	0.25257	-1.0137	10	0.66056	D	0.02	.	8.144	0.31100	0.0:1.0:0.0:0.0	.	778	Q6R2W3	SCND3_HUMAN	Q	778	ENSP00000395259:R778Q	ENSP00000395259:R778Q	R	-	2	0	SCAND3	28649312	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	1.852000	0.39348	1.581000	0.49865	0.655000	0.94253	CGA		0.333	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			T	28541333	C	T	28541333	3	4	61	1	0	0	0	0	1	0	0	0	13913	884	31	1	1648	1	SCAND3	6	28541333	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271736	28541333	142573734	4478	12463										
SCAND3	114821	broad.mit.edu	37	chr6	28542810	28542810	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggctcttaaagtattttCtaactctttgtcagcctgat	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28542810C>A	ENST00000452236.2	-	3	2289	c.1672G>T	c.(1672-1674)Gaa>Taa	p.E558*	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1												p.E558*(1)		NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						AAAGTATTTTCTAACTCTTTG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											87	86	86					6																	28542810		2203	4300	6503	28650789	SO:0001587	stop_gained	114821																														ENST00000452236.2:c.1672G>T	6.37:g.28542810C>A	ENSP00000395259:p.Glu558*		28650789		Nonsense_Mutation	SNP	ENST00000452236.2	37	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	C	41	9.123980	0.99073	.	.	ENSG00000232040	ENST00000452236	.	.	.	3.41	3.41	0.39046	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	10.5109	0.44862	0.0:1.0:0.0:0.0	.	.	.	.	X	558	.	ENSP00000395259:E558X	E	-	1	0	SCAND3	28650789	0.116000	0.22171	0.097000	0.21041	0.977000	0.68977	0.501000	0.22578	1.913000	0.55393	0.563000	0.77884	GAA		0.398	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			A	28542810	C	A	28542810	4	1	61	1	0	0	0	0	0	1	0	0	13913	922	32	2	2313	2	SCAND3	6	28542810	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1477	28542810	142572257	4479	12464										
SCAND3	114821	broad.mit.edu	37	chr6	28542901	28542901	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgggacaagcccagtttAgcttcagagctaaatgcact	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28542901A>C	ENST00000452236.2	-	3	2198	c.1581T>G	c.(1579-1581)gcT>gcG	p.A527A	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1												p.A527A(1)		NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						AGCCCAGTTTAGCTTCAGAGC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	6											118	116	116					6																	28542901		2203	4300	6503	28650880	SO:0001819	synonymous_variant	114821																														ENST00000452236.2:c.1581T>G	6.37:g.28542901A>C			28650880		Silent	SNP	ENST00000452236.2	37	CCDS34355.1																																																																																				0.408	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			C	28542901	A	C	28542901	2	2	61	1	0	0	0	0	0	0	0	1	13913	407	15	4		4	SCAND3	6	28542901	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	91	28542901	142572166	4480	12465										
SCAND3	114821	broad.mit.edu	37	chr6	28543116	28543116	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatggacaattttcaattCtggccaaatattactgagtt	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:28543116C>A	ENST00000452236.2	-	3	1983	c.1366G>T	c.(1366-1368)Gaa>Taa	p.E456*	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1												p.E456*(1)		NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						ATTTTCAATTCTGGCCAAATA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											65	67	66					6																	28543116		2203	4300	6503	28651095	SO:0001587	stop_gained	114821																														ENST00000452236.2:c.1366G>T	6.37:g.28543116C>A	ENSP00000395259:p.Glu456*		28651095		Nonsense_Mutation	SNP	ENST00000452236.2	37	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	C	41	8.712347	0.98925	.	.	ENSG00000232040	ENST00000452236	.	.	.	2.95	2.06	0.26882	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	7.6318	0.28243	0.0:0.8625:0.0:0.1375	.	.	.	.	X	456	.	ENSP00000395259:E456X	E	-	1	0	SCAND3	28651095	0.973000	0.33851	1.000000	0.80357	0.996000	0.88848	0.530000	0.23036	1.668000	0.50843	0.563000	0.77884	GAA		0.423	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			A	28543116	C	A	28543116	4	1	61	1	0	0	0	0	0	1	0	0	13913	922	32	2	2619	2	SCAND3	6	28543116	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	215	28543116	142571951	4481	12466										
OR2W1	26692	broad.mit.edu	37	chr6	29012509	29012509	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggccaaactaatactccaGatcatgataatcatctttag	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29012509G>T	ENST00000377175.1	-	1	508	c.444C>A	c.(442-444)atC>atA	p.I148I		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I148I(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						TAATACTCCAGATCATGATAA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	6											96	94	94					6																	29012509		1511	2709	4220	29120488	SO:0001819	synonymous_variant	26692			AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"GPCR / Class A : Olfactory receptors"	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.444C>A	6.37:g.29012509G>T			29120488	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Silent	SNP	ENST00000377175.1	37	CCDS4656.1																																																																																				0.373	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2			T	29012509	G	T	29012509	2	4	61	1	0	0	0	0	0	0	0	1	11063	932	33	2		2	OR2W1	6	29012509	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	469393	29012509	142102558	4482	12467										
OR14J1	442191	broad.mit.edu	37	chr6	29275118	29275118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattgtgctctcctacattCgcatcttctctacagtgctg	6	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29275118C>T	ENST00000377160.2	+	1	716	c.652C>T	c.(652-654)Cgc>Tgc	p.R218C		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R218C(1)		endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						CTCCTACATTCGCATCTTCTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											164	169	167					6																	29275118		1511	2709	4220	29383097	SO:0001583	missense	442191				CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"GPCR / Class A : Olfactory receptors"	13971	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily U, member 1"	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.652C>T	6.37:g.29275118C>T	ENSP00000366365:p.Arg218Cys		29383097	A2BEC2|B0V078|Q5ST27	Missense_Mutation	SNP	ENST00000377160.2	37	CCDS34362.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.086134	0.36855	.	.	ENSG00000204695	ENST00000377160	T	0.00099	8.73	4.86	2.94	0.34122	GPCR, rhodopsin-like superfamily (1);	0.846689	0.09943	N	0.735688	T	0.00073	0.0002	L	0.28274	0.84	0.09310	N	1	D	0.69078	0.997	P	0.53185	0.72	T	0.01492	-1.1341	10	0.34782	T	0.22	.	7.3129	0.26485	0.0:0.6427:0.0:0.3573	.	218	Q9UGF5	O14J1_HUMAN	C	218	ENSP00000366365:R218C	ENSP00000366365:R218C	R	+	1	0	OR14J1	29383097	0.000000	0.05858	0.005000	0.12908	0.442000	0.32017	-0.720000	0.04969	1.268000	0.44264	0.650000	0.86243	CGC		0.463	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2			T	29275118	C	T	29275118	3	4	61	1	0	0	0	0	1	0	0	0	10979	884	31	1	654	1	OR14J1	6	29275118	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	262609	29275118	141839949	4483	12468										
OR5V1	81696	broad.mit.edu	37	chr6	29323965	29323965	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatagctgtttgattctttCtttccatgatgtcgcctggt	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29323965C>A	ENST00000377154.1	-	4	307	c.8G>T	c.(7-9)aGa>aTa	p.R3I	OR5V1_ENST00000543825.1_Missense_Mutation_p.R3I			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R3I(1)		breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTGATTCTTTCTTTCCATGAT	0.348																																					Ovarian(32;43 883 21137 32120 42650)											1	Substitution - Missense(1)	large_intestine(1)	6											54	54	54					6																	29323965		2151	4196	6347	29431944	SO:0001583	missense	81696				CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.8G>T	6.37:g.29323965C>A	ENSP00000366359:p.Arg3Ile		29431944	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	C	2.343	-0.350657	0.05173	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.09817	2.94;2.94	3.96	-1.35	0.09114	.	0.261544	0.20203	N	0.097059	T	0.01905	0.0060	L	0.33189	0.99	0.09310	N	1	B	0.24823	0.112	B	0.19666	0.026	T	0.44697	-0.9311	10	0.27785	T	0.31	-4.4132	5.981	0.19407	0.1289:0.352:0.0:0.5191	.	3	Q9UGF6	OR5V1_HUMAN	I	3	ENSP00000366359:R3I;ENSP00000443309:R3I	ENSP00000366356:R3I	R	-	2	0	OR5V1	29431944	0.000000	0.05858	0.003000	0.11579	0.050000	0.14768	-0.988000	0.03739	-0.297000	0.08934	-0.310000	0.09108	AGA		0.348	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			A	29323965	C	A	29323965	3	1	61	1	0	0	0	0	1	0	0	0	11215	913	32	2	960	2	OR5V1	6	29323965	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48847	29323965	141791102	4484	12469										
OR12D3	81797	broad.mit.edu	37	chr6	29342605	29342605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgacagaatgcatcagagCgtaaaagaagctgatgagcc	11	8	1	6	rs151096169		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29342605C>T	ENST00000396806.3	-	1	463	c.460G>A	c.(460-462)Gct>Act	p.A154T	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A154T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						TGCATCAGAGCGTAAAAGAAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	THR/ALA	1,3017		0,1,1508	61	62	62		460	4.2	0.2	6	dbSNP_134	62	0,5418		0,0,2709	no	missense	OR12D3	NM_030959.2	58	0,1,4217	TT,TC,CC		0.0,0.0331,0.0119	probably-damaging	154/317	29342605	1,8435	1509	2709	4218	29450584	SO:0001583	missense	81797				CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.460G>A	6.37:g.29342605C>T	ENSP00000380023:p.Ala154Thr		29450584	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509489	0.44660	3.31E-4	0.0	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.39056	1.1	4.18	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.43919	0.1269	M	0.61703	1.905	0.24595	N	0.993802	D	0.89917	1.0	D	0.75484	0.986	T	0.37454	-0.9705	9	0.66056	D	0.02	-8.6486	5.3109	0.15829	0.2618:0.6352:0.0:0.103	.	154	Q9UGF7	O12D3_HUMAN	T	154	ENSP00000380023:A154T	ENSP00000366348:A154T	A	-	1	0	OR12D3	29450584	0.000000	0.05858	0.197000	0.23402	0.291000	0.27294	-0.382000	0.07408	2.142000	0.66516	0.195000	0.17529	GCT		0.483	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			T	29342605	C	T	29342605	3	4	61	1	0	0	0	0	1	0	0	0	10963	768	27	1	494	1	OR12D3	6	29342605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18640	29342605	141772462	4485	12470										
OR12D3	81797	broad.mit.edu	37	chr6	29343059	29343059	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattcattgtagtgacattCtccattgctctgggaagcaa	8	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29343059C>A	ENST00000396806.3	-	1	9	c.6G>T	c.(4-6)gaG>gaT	p.E2D	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E2D(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						TAGTGACATTCTCCATTGCTC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											31	34	33					6																	29343059		1489	2689	4178	29451038	SO:0001583	missense	81797				CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.6G>T	6.37:g.29343059C>A	ENSP00000380023:p.Glu2Asp		29451038	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	c	3.233	-0.157039	0.06544	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.01406	4.93	4.34	-0.148	0.13424	.	.	.	.	.	T	0.00440	0.0014	L	0.41415	1.275	0.09310	N	0.999997	B	0.10296	0.003	B	0.09377	0.004	T	0.42949	-0.9421	9	0.28530	T	0.3	-0.1701	3.4493	0.07493	0.4232:0.2824:0.0:0.2945	.	2	Q9UGF7	O12D3_HUMAN	D	2	ENSP00000380023:E2D	ENSP00000366348:E2D	E	-	3	2	OR12D3	29451038	0.000000	0.05858	0.016000	0.15963	0.799000	0.45148	-0.928000	0.03980	0.094000	0.17404	0.431000	0.28591	GAG		0.333	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			A	29343059	C	A	29343059	3	1	61	1	0	0	0	0	1	0	0	0	10963	912	32	2	948	2	OR12D3	6	29343059	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	454	29343059	141772008	4486	12471										
OR11A1	26531	broad.mit.edu	37	chr6	29394864	29394864	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgagcaagccaggcccacGaaaagcataaagtcacagta	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29394864G>A	ENST00000377149.1	-	5	1027	c.555C>T	c.(553-555)ttC>ttT	p.F185F	OR11A1_ENST00000377148.1_Silent_p.F185F|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Silent_p.F185F			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F185F(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CCAGGCCCACGAAAAGCATAA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	6											49	49	49					6																	29394864		1509	2707	4216	29502843	SO:0001819	synonymous_variant	26531				CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.555C>T	6.37:g.29394864G>A			29502843	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Silent	SNP	ENST00000377149.1	37	CCDS34363.1																																																																																				0.512	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			A	29394864	G	A	29394864	2	1	61	1	0	0	0	0	0	0	0	1	10955	1049	37	1		1	OR11A1	6	29394864	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51805	29394864	141720203	4487	12472										
OR2H1	26716	broad.mit.edu	37	chr6	29430435	29430435	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaacaaggagataaagCgagcactcaggaggttacta	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29430435C>T	ENST00000377136.1	+	4	1354	c.889C>T	c.(889-891)Cga>Tga	p.R297*	OR2H1_ENST00000396792.2_Nonsense_Mutation_p.R297*|OR2H1_ENST00000377132.1_Nonsense_Mutation_p.R297*|OR2H1_ENST00000442615.1_Nonsense_Mutation_p.R297*|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377133.1_Nonsense_Mutation_p.R297*			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R297*(1)		large_intestine(5)|lung(12)	17						GGAGATAAAGCGAGCACTCAG	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											64	66	65					6																	29430435		1510	2707	4217	29538414	SO:0001587	stop_gained	26716			AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.889C>T	6.37:g.29430435C>T	ENSP00000366340:p.Arg297*		29538414	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Nonsense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568741	0.65765	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	.	.	.	3.18	-0.73	0.11154	.	0.658896	0.13367	N	0.393254	.	.	.	.	.	.	0.25250	N	0.98969	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	4.705	0.12846	0.4837:0.169:0.3473:0.0	.	.	.	.	X	297	.	ENSP00000366336:R297X	R	+	1	2	OR2H1	29538414	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.021000	0.12504	-0.113000	0.11958	-0.324000	0.08512	CGA		0.463	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			T	29430435	C	T	29430435	4	4	61	1	0	0	0	0	0	1	0	0	11032	760	27	1	891	1	OR2H1	6	29430435	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35571	29430435	141684632	4488	12473										
MAS1L	116511	broad.mit.edu	37	chr6	29454673	29454673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctggcttatctgctaacGcccgttggagaatcactctg	9	13	4	1	rs566796111	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29454673G>A	ENST00000377127.3	-	1	1065	c.1007C>T	c.(1006-1008)gCg>gTg	p.A336V		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	336					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A336V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						ATCTGCTAACGCCCGTTGGAG	0.493													G|||	2	0.000399361	0.0015	0	5008	,	,		17088	0		0	False		,,,				2504	0				NSCLC(153;755 1987 3859 11251 32945)											1	Substitution - Missense(1)	large_intestine(1)	6											137	138	138					6																	29454673		2203	4300	6503	29562652	SO:0001583	missense	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.1007C>T	6.37:g.29454673G>A	ENSP00000366331:p.Ala336Val		29562652	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	G	8.581	0.882339	0.17467	.	.	ENSG00000204687	ENST00000377127	T	0.36878	1.23	2.23	0.27	0.15635	.	.	.	.	.	T	0.10680	0.0261	L	0.45285	1.41	0.09310	N	1	B	0.27700	0.186	B	0.29942	0.109	T	0.33033	-0.9884	9	0.44086	T	0.13	.	2.6171	0.04907	0.2894:0.0:0.4883:0.2223	.	336	P35410	MAS1L_HUMAN	V	336	ENSP00000366331:A336V	ENSP00000366331:A336V	A	-	2	0	MAS1L	29562652	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.361000	0.07612	-0.075000	0.12798	-0.364000	0.07487	GCG		0.493	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		A	29454673	G	A	29454673	3	1	61	1	0	0	0	0	1	0	0	0	9351	1087	38	1	131	1	MAS1L	6	29454673	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24238	29454673	141660394	4489	12474										
MAS1L	116511	broad.mit.edu	37	chr6	29455365	29455365	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtataccatgtagggattCgtggccccacagcaaagcag	11	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29455365C>T	ENST00000377127.3	-	1	373	c.315G>A	c.(313-315)acG>acA	p.T105T		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	105					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T105T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						TGTAGGGATTCGTGGCCCCAC	0.537																																					NSCLC(153;755 1987 3859 11251 32945)											1	Substitution - coding silent(1)	large_intestine(1)	6											69	64	66					6																	29455365		2203	4300	6503	29563344	SO:0001819	synonymous_variant	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.315G>A	6.37:g.29455365C>T			29563344	Q5SUN5	Silent	SNP	ENST00000377127.3	37	CCDS4661.1																																																																																				0.537	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		T	29455365	C	T	29455365	2	4	61	1	0	0	0	0	0	0	0	1	9351	871	31	1		1	MAS1L	6	29455365	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	692	29455365	141659702	4490	12475										
MAS1L	116511	broad.mit.edu	37	chr6	29455563	29455563	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagataccaggtttgggttCtgtgcctcctggtcaccact	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29455563C>A	ENST00000377127.3	-	1	175	c.117G>T	c.(115-117)caG>caT	p.Q39H		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	39					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Q39H(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						GGTTTGGGTTCTGTGCCTCCT	0.507																																					NSCLC(153;755 1987 3859 11251 32945)											1	Substitution - Missense(1)	large_intestine(1)	6											83	85	84					6																	29455563		2203	4300	6503	29563542	SO:0001583	missense	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.117G>T	6.37:g.29455563C>A	ENSP00000366331:p.Gln39His		29563542	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	C	6.148	0.395427	0.11638	.	.	ENSG00000204687	ENST00000377127	T	0.03982	3.74	0.493	0.493	0.16878	.	.	.	.	.	T	0.00666	0.0022	N	0.08118	0	0.09310	N	1	P	0.47034	0.889	B	0.31290	0.127	T	0.50294	-0.8845	8	0.42905	T	0.14	.	.	.	.	.	39	P35410	MAS1L_HUMAN	H	39	ENSP00000366331:Q39H	ENSP00000366331:Q39H	Q	-	3	2	MAS1L	29563542	0.017000	0.18338	0.016000	0.15963	0.022000	0.10575	1.242000	0.32755	0.545000	0.28902	0.395000	0.25975	CAG		0.507	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		A	29455563	C	A	29455563	3	1	61	1	0	0	0	0	1	0	0	0	9351	912	32	2	1021	2	MAS1L	6	29455563	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	198	29455563	141659504	4491	12476										
GABBR1	2550	broad.mit.edu	37	chr6	29574676	29574676	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctctccagtggtacctCaatggtccggtgcagagggt	12	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29574676C>A	ENST00000377034.4	-	18	2550	c.2215G>T	c.(2215-2217)Gag>Tag	p.E739*	GABBR1_ENST00000377016.4_Nonsense_Mutation_p.E677*|GABBR1_ENST00000377012.4_Nonsense_Mutation_p.E622*|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000355973.3_Nonsense_Mutation_p.E622*	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	739					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.E739*(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	AGTGGTACCTCAATGGTCCGG	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											64	54	57					6																	29574676		1511	2709	4220	29682655	SO:0001587	stop_gained	2550			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2215G>T	6.37:g.29574676C>A	ENSP00000366233:p.Glu739*		29682655	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Nonsense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.055650|8.055650	0.98632|0.98632	.|.	.|.	ENSG00000204681|ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034|ENST00000485026	.|.	.|.	.|.	4.35|4.35	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.35671|.	T|.	0.21|.	-13.3019|-13.3019	14.7425|14.7425	0.69467|0.69467	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	622;677;622;739|119	.|.	ENSP00000348248:E622X|.	E|X	-|-	1|2	0|2	GABBR1|GABBR1	29682655|29682655	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.364000|0.364000	0.29643|0.29643	7.286000|7.286000	0.78671|0.78671	2.121000|2.121000	0.65114|0.65114	0.563000|0.563000	0.77884|0.77884	GAG|TGA		0.597	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			A	29574676	C	A	29574676	4	1	61	1	0	0	0	0	0	1	0	0	6174	835	29	2	694	2	GABBR1	6	29574676	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119113	29574676	141540391	4492	12477										
GABBR1	2550	broad.mit.edu	37	chr6	29577098	29577098	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacggagataaagagtttCtgtgacaggaagcggaatgt	15	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29577098C>T	ENST00000377034.4	-	15	2102	c.1767G>A	c.(1765-1767)caG>caA	p.Q589Q	GABBR1_ENST00000377016.4_Silent_p.Q527Q|GABBR1_ENST00000377012.4_Silent_p.Q472Q|GABBR1_ENST00000376977.3_Intron|GABBR1_ENST00000355973.3_Silent_p.Q472Q	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	589					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.Q589Q(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	TAAAGAGTTTCTGTGACAGGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	6											118	94	103					6																	29577098		1511	2709	4220	29685077	SO:0001819	synonymous_variant	2550			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1767G>A	6.37:g.29577098C>T			29685077	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																				0.522	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29577098	C	T	29577098	2	4	61	1	0	0	0	0	0	0	0	1	6174	912	32	3		3	GABBR1	6	29577098	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2422	29577098	141537969	4493	12478										
GABBR1	2550	broad.mit.edu	37	chr6	29581160	29581160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagggccagtgccaaggCccagatggcatcataggcca	13	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29581160C>T	ENST00000377034.4	-	12	1761	c.1426G>A	c.(1426-1428)Gcc>Acc	p.A476T	GABBR1_ENST00000377016.4_Missense_Mutation_p.A414T|GABBR1_ENST00000377012.4_Missense_Mutation_p.A359T|GABBR1_ENST00000376977.3_Missense_Mutation_p.A476T|GABBR1_ENST00000355973.3_Missense_Mutation_p.A359T	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	476					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.A476T(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	AGTGCCAAGGCCCAGATGGCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	121	118					6																	29581160		1510	2709	4219	29689139	SO:0001583	missense	2550			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1426G>A	6.37:g.29581160C>T	ENSP00000366233:p.Ala476Thr		29689139	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	35	5.428446	0.96131	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95	5.84	5.84	0.93424	Extracellular ligand-binding receptor (1);	0.108366	0.64402	D	0.000007	D	0.85496	0.5710	L	0.58354	1.805	0.80722	D	1	B;P;P;P	0.43938	0.3;0.802;0.698;0.822	B;P;P;P	0.51055	0.223;0.592;0.618;0.657	D	0.84323	0.0517	10	0.40728	T	0.16	-18.8442	17.64	0.88133	0.0:1.0:0.0:0.0	.	476;414;476;359	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	T	359;476;414;359;476	ENSP00000348248:A359T;ENSP00000366176:A476T;ENSP00000366215:A414T;ENSP00000366211:A359T;ENSP00000366233:A476T	ENSP00000348248:A359T	A	-	1	0	GABBR1	29689139	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.421000	0.80204	2.769000	0.95229	0.655000	0.94253	GCC		0.552	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29581160	C	T	29581160	3	4	61	1	0	0	0	0	1	0	0	0	6174	739	26	3	1507	3	GABBR1	6	29581160	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4062	29581160	141533907	4494	12479										
ZFP57	346171	broad.mit.edu	37	chr6	29644661	29644661	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcttagtctcctcaccttCttcacccgtgcctccctcca	4	19	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29644661C>A	ENST00000488757.1	-	1	270	c.120G>T	c.(118-120)aaG>aaT	p.K40N	ZFP57_ENST00000376881.3_Missense_Mutation_p.K20N|ZFP57_ENST00000376883.1_Missense_Mutation_p.K20N	NM_001109809.2	NP_001103279.2	Q9NU63	ZFP57_HUMAN	ZFP57 zinc finger protein	0	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				DNA methylation involved in embryo development (GO:0043045)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system development (GO:0007422)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	nuclear heterochromatin (GO:0005720)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K20N(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5)	44						TCCTCACCTTCTTCACCCGTG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											131	123	125					6																	29644661		1967	4143	6110	29752640	SO:0001583	missense	346171			AL050328	CCDS43436.1, CCDS43436.2	6p22.1	2013-01-08	2012-11-27	2005-07-20	ENSG00000204644	ENSG00000204644		"Zinc fingers, C2H2-type", "-"	18791	protein-coding gene	gene with protein product		612192	"chromosome 6 open reading frame 40", "zinc finger protein 57 homolog (mouse)"	C6orf40			Standard	NM_001109809		Approved	ZNF698, bA145L22, bA145L22.2	uc011dlw.2	Q9NU63	OTTHUMG00000031158	ENST00000488757.1:c.120G>T	6.37:g.29644661C>A	ENSP00000418259:p.Lys40Asn		29752640	B0S894|B0V254|B2RXJ7|Q5SSB1	Missense_Mutation	SNP	ENST00000488757.1	37	CCDS43436.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.344838	0.41498	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	T;T;T	0.05382	3.45;3.68;3.68	4.11	1.36	0.22044	.	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	0.09310	N	0.999994	P;P	0.51351	0.944;0.944	P;P	0.49853	0.624;0.624	T	0.42749	-0.9433	9	0.17832	T	0.49	.	5.9825	0.19415	0.0:0.6784:0.0:0.3216	.	40;20	Q9NU63-3;Q9NU63-2	.;.	N	40;20;20	ENSP00000418259:K40N;ENSP00000366078:K20N;ENSP00000366080:K20N	ENSP00000366078:K20N	K	-	3	2	ZFP57	29752640	0.000000	0.05858	0.409000	0.26459	0.837000	0.47467	-0.640000	0.05440	0.295000	0.22570	0.655000	0.94253	AAG		0.552	ZFP57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355773.1	XM_294093		A	29644661	C	A	29644661	3	1	61	1	0	0	0	0	1	0	0	0	17690	912	32	2	1506	2	ZFP57	6	29644661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63501	29644661	141470406	4495	12480										
HLA-F	3134	broad.mit.edu	37	chr6	29694860	29694860	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggccttgcaaagccttCgctttggcttcggctttagg	11	11	1	0	rs57486551	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29694860C>T	ENST00000376861.1	+	0	1544				HLA-F_ENST00000475996.1_Intron|HLA-F_ENST00000259951.7_Missense_Mutation_p.R413C|HLA-F_ENST00000440587.2_Intron			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.R413C(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GCAAAGCCTTCGCTTTGGCTT	0.488													C|||	10	0.00199681	0.0061	0.0029	5008	,	,		17637	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						C	CYS/ARG	7,2757		0,7,1375	221	250	240		1237	-1.1	0.4	6	dbSNP_129	240	0,5258		0,0,2629	no	missense	HLA-F	NM_001098479.1	180	0,7,4004	TT,TC,CC		0.0,0.2533,0.0873	possibly-damaging	413/443	29694860	7,8015	1382	2629	4011	29802839	SO:0001628	intergenic_variant	3134			AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156		6.37:g.29694860C>T			29802839	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Missense_Mutation	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	8.328	0.825901	0.16749	0.002533	0.0	ENSG00000204642	ENST00000449921;ENST00000259951	T	0.00922	5.54	0.62	-1.07	0.09968	.	.	.	.	.	T	0.00271	0.0008	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49390	-0.8945	9	0.87932	D	0	.	1.4855	0.02446	0.3167:0.289:0.0:0.3943	rs57486551;rs61743557	413	P30511-3	.	C	390;413	ENSP00000259951:R413C	ENSP00000259951:R413C	R	+	1	0	HLA-F	29802839	0.905000	0.30787	0.412000	0.26496	0.047000	0.14425	-0.664000	0.05292	-0.438000	0.07232	-0.436000	0.05848	CGC		0.488	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		T	29694860	C	T	29694860	1	4	61	0	1	0	0	0	0	0	0	0	7232	884	31	1		1	HLA-F	6	29694860	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50199	29694860	141420207	4496	12481										
HLA-G	3135	broad.mit.edu	37	chr6	29797599	29797599	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcctttcccagagcagtCttccctgcccaccatcccca	4	21	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29797599C>A	ENST00000360323.6	+	5	926	c.902C>A	c.(901-903)tCt>tAt	p.S301Y	HLA-G_ENST00000376818.3_Missense_Mutation_p.S209Y|HLA-G_ENST00000376815.3_Missense_Mutation_p.S117Y|HLA-G_ENST00000428701.1_Missense_Mutation_p.S301Y|HLA-G_ENST00000376828.2_Missense_Mutation_p.S306Y			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	301	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.S301Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CCAGAGCAGTCTTCCCTGCCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	84	89					6																	29797599		2203	4300	6503	29905578	SO:0001583	missense	3135				CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.902C>A	6.37:g.29797599C>A	ENSP00000353472:p.Ser301Tyr		29905578		Missense_Mutation	SNP	ENST00000360323.6	37	CCDS4668.1	.	.	.	.	.	.	.	.	.	.	.	11.09	1.535552	0.27475	.	.	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323;ENST00000376818;ENST00000376815	T;T;T;T;T	0.00882	5.86;5.84;5.84;5.58;5.76	2.23	1.15	0.20763	Immunoglobulin-like fold (1);	2.614290	0.02505	U	0.090914	T	0.03915	0.0110	H	0.95712	3.71	0.09310	N	1	B;D;P;D	0.76494	0.224;0.984;0.842;0.999	B;D;B;D	0.85130	0.096;0.928;0.099;0.997	T	0.29397	-1.0013	10	0.87932	D	0	.	6.2866	0.21037	0.2893:0.7106:0.0:0.0	.	117;306;209;301	Q29897;Q5RJ85;Q31611;P17693	.;.;.;HLAG_HUMAN	Y	306;301;301;209;117	ENSP00000366024:S306Y;ENSP00000412927:S301Y;ENSP00000353472:S301Y;ENSP00000366014:S209Y;ENSP00000366011:S117Y	ENSP00000353472:S301Y	S	+	2	0	HLA-G	29905578	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-0.231000	0.09069	0.948000	0.37687	0.291000	0.19559	TCT		0.582	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		A	29797599	C	A	29797599	3	1	61	1	0	0	0	0	1	0	0	0	7233	913	32	2	920	2	HLA-G	6	29797599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102739	29797599	141317468	4497	12482										
HLA-A	3105	broad.mit.edu	37	chr6	29911983	29911983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccctgggcttctaccctgCggagatcacactgacctggc	12	15	2	2	rs150135282		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:29911983C>T	ENST00000396634.1	+	6	1045	c.704C>T	c.(703-705)gCg>gTg	p.A235V	HLA-A_ENST00000376806.5_Missense_Mutation_p.A235V|HLA-A_ENST00000376802.2_Missense_Mutation_p.A235V|HLA-A_ENST00000376809.5_Missense_Mutation_p.A235V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	235	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.A235V(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TTCTACCCTGCGGAGATCACA	0.632									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																																						1	Substitution - Missense(1)	large_intestine(1)	6						C	VAL/ALA	0,3012		0,0,1506	52	68	62		704	-4.4	0.4	6	dbSNP_134	62	1,5397		0,1,2698	no	missense	HLA-A	NM_002116.7	64	0,1,4204	TT,TC,CC		0.0185,0.0,0.0119	probably-damaging	235/366	29911983	1,8409	1506	2699	4205	30019962	SO:0001583	missense	3105	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.704C>T	6.37:g.29911983C>T	ENSP00000379873:p.Ala235Val		30019962	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	13.07	2.127152	0.37533	0.0	1.85E-4	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	3.69	-4.39	0.03611	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.407067	0.17516	U	0.171440	T	0.15003	0.0362	M	0.68317	2.08	0.09310	N	1	D;D;D;D;D;D;D	0.89917	0.999;0.997;1.0;0.997;1.0;0.995;0.997	D;P;D;P;D;P;P	0.83275	0.955;0.824;0.996;0.885;0.996;0.885;0.885	T	0.03898	-1.0994	10	0.87932	D	0	.	3.5053	0.07688	0.5454:0.2272:0.1347:0.0927	.	114;235;235;235;235;235;235	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	V	235;235;23;235;235	ENSP00000379873:A235V;ENSP00000366002:A235V;ENSP00000366005:A235V;ENSP00000365998:A235V	ENSP00000365998:A235V	A	+	2	0	HLA-A	30019962	0.000000	0.05858	0.397000	0.26308	0.997000	0.91878	-0.498000	0.06420	-1.153000	0.02829	0.485000	0.47835	GCG		0.632	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		T	29911983	C	T	29911983	3	4	61	1	0	0	0	0	1	0	0	0	7216	768	27	1	718	1	HLA-A	6	29911983	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114384	29911983	141203084	4498	12483										
RNF39	80352	broad.mit.edu	37	chr6	30043369	30043369	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgggcgcatccatggaaagCcaggatctggacgccgcccc	13	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30043369C>T	ENST00000244360.6	-	1	295	c.198G>A	c.(196-198)tgG>tgA	p.W66*	RNF39_ENST00000376751.3_Nonsense_Mutation_p.W66*	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	66						cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.W66*(1)									CCATGGAAAGCCAGGATCTGG	0.701																																					NSCLC(8;188 360 1520 20207 31481)											1	Substitution - Nonsense(1)	large_intestine(1)	6											17	20	19					6																	30043369		2200	4297	6497	30151348	SO:0001587	stop_gained	80352			AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"RING-type (C3HC4) zinc fingers"	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.198G>A	6.37:g.30043369C>T	ENSP00000244360:p.Trp66*		30151348	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Nonsense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	c	19.16	3.772800	0.69992	.	.	ENSG00000204618	ENST00000376751;ENST00000244360;ENST00000376746	.	.	.	4.04	2.02	0.26589	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	6.403	0.21648	0.1487:0.6596:0.0:0.1917	.	.	.	.	X	66	.	ENSP00000244360:W66X	W	-	3	0	RNF39	30151348	0.450000	0.25697	0.004000	0.12327	0.006000	0.05464	1.728000	0.38105	0.308000	0.22923	-1.800000	0.00619	TGG		0.701	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		T	30043369	C	T	30043369	4	4	61	1	0	0	0	0	0	1	0	0	13528	740	26	3	1080	3	RNF39	6	30043369	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131386	30043369	141071698	4499	12484										
TRIM10	10107	broad.mit.edu	37	chr6	30122009	30122009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctcctctggccgcagccGaagctcccccttccgctgca	8	22	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30122009G>A	ENST00000449742.2	-	7	1258	c.1183C>T	c.(1183-1185)Cgg>Tgg	p.R395W	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	395	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R395W(1)		ovary(1)	1						GGCCGCAGCCGAAGCTCCCCC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	6											43	31	35					6																	30122009		1510	2706	4216	30229988	SO:0001583	missense	10107			Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1183C>T	6.37:g.30122009G>A	ENSP00000397073:p.Arg395Trp		30229988	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	37	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.767471	0.31320	.	.	ENSG00000204613	ENST00000449742;ENST00000376706	T	0.70631	-0.5	5.49	1.23	0.21249	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.118609	0.37715	N	0.001961	T	0.72740	0.3498	M	0.73430	2.235	0.09310	N	0.999999	D	0.76494	0.999	D	0.63381	0.914	T	0.69705	-0.5073	10	0.66056	D	0.02	.	14.0514	0.64739	0.0:0.0:0.3124:0.6876	.	395	Q9UDY6	TRI10_HUMAN	W	395	ENSP00000397073:R395W	ENSP00000365896:R395W	R	-	1	2	TRIM10	30229988	0.000000	0.05858	0.008000	0.14137	0.135000	0.20990	-1.067000	0.03451	0.325000	0.23359	0.643000	0.83706	CGG		0.682	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			A	30122009	G	A	30122009	3	1	61	1	0	0	0	0	1	0	0	0	16526	1057	37	1	354	1	TRIM10	6	30122009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78640	30122009	140993058	4500	12485										
TRIM10	10107	broad.mit.edu	37	chr6	30122254	30122254	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagtctgagggtctagaGaaatgtgagctgtggggata	18	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30122254G>T	ENST00000449742.2	-	7	1013	c.938C>A	c.(937-939)tCt>tAt	p.S313Y	TRIM10_ENST00000376704.3_Missense_Mutation_p.S313Y	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	313	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.S313F(1)|p.S313Y(1)		ovary(1)	1						AGGGTCTAGAGAAATGTGAGC	0.537																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	6											53	65	61					6																	30122254		1508	2707	4215	30230233	SO:0001583	missense	10107			Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.938C>A	6.37:g.30122254G>T	ENSP00000397073:p.Ser313Tyr		30230233	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	37	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759475	0.49468	.	.	ENSG00000204613	ENST00000449742;ENST00000376704;ENST00000376706	T;T	0.10960	2.82;2.82	6.01	5.14	0.70334	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.222920	0.32314	N	0.006273	T	0.14787	0.0357	M	0.83118	2.625	0.34943	D	0.750491	P;P	0.43542	0.81;0.773	B;P	0.48840	0.255;0.592	T	0.00915	-1.1516	10	0.72032	D	0.01	.	9.8027	0.40775	0.1552:0.0:0.8448:0.0	.	313;313	Q9UDY6;Q9UDY6-2	TRI10_HUMAN;.	Y	313	ENSP00000397073:S313Y;ENSP00000365894:S313Y	ENSP00000365894:S313Y	S	-	2	0	TRIM10	30230233	0.016000	0.18221	0.863000	0.33907	0.866000	0.49608	1.546000	0.36179	2.845000	0.97973	0.643000	0.83706	TCT		0.537	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			T	30122254	G	T	30122254	3	4	61	1	0	0	0	0	1	0	0	0	16526	942	33	2	599	2	TRIM10	6	30122254	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	245	30122254	140992813	4501	12486										
ABCF1	23	broad.mit.edu	37	chr6	30558400	30558400	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcagagtgttagccaaatCgatggtgactttgaagacta	12	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30558400C>T	ENST00000326195.8	+	25	2572	c.2460C>T	c.(2458-2460)atC>atT	p.I820I	ABCF1_ENST00000396515.4_Silent_p.I213I|ABCF1_ENST00000376545.3_Silent_p.I782I	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	820	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)	p.I820I(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						TTAGCCAAATCGATGGTGACT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	6											275	292	286					6																	30558400		1510	2709	4219	30666379	SO:0001819	synonymous_variant	23			AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.2460C>T	6.37:g.30558400C>T			30666379	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																				0.542	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			T	30558400	C	T	30558400	2	4	61	1	0	0	0	0	0	0	0	1	65	874	31	1		1	ABCF1	6	30558400	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	436146	30558400	140556667	4502	12487										
KIAA1949	170954	broad.mit.edu	37	chr6	30652888	30652888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcggaactgttgccttggGcctcccttgtcagggtctcg	13	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30652888G>A	ENST00000274853.3	-	1	2784	c.908C>T	c.(907-909)gCc>gTc	p.A303V	PPP1R18_ENST00000399199.3_Missense_Mutation_p.A303V|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	303						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A303V(1)									GTTGCCTTGGGCCTCCCTTGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	6											88	107	101					6																	30652888		1431	2652	4083	30760867	SO:0001583	missense	170954			AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29413	protein-coding gene	gene with protein product	"protein phosphatase 1 F-actin cytoskeleton targeting subunit"	610990	"KIAA1949"	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.908C>T	6.37:g.30652888G>A	ENSP00000274853:p.Ala303Val		30760867	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	G	2.456	-0.325176	0.05350	.	.	ENSG00000146112	ENST00000274853;ENST00000399199;ENST00000376424	T;T	0.21734	1.99;1.99	5.27	-3.84	0.04256	.	1.204620	0.06234	N	0.689171	T	0.02610	0.0079	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34428	-0.9829	10	0.02654	T	1	0.5484	6.0357	0.19706	0.3447:0.3544:0.3008:0.0	.	303	Q6NYC8	PPR18_HUMAN	V	303	ENSP00000274853:A303V;ENSP00000382150:A303V	ENSP00000274853:A303V	A	-	2	0	KIAA1949	30760867	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.144000	0.10280	-0.347000	0.08299	0.561000	0.74099	GCC		0.572	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		A	30652888	G	A	30652888	3	1	61	1	0	0	0	0	1	0	0	0	8284	1203	42	3	945	3	KIAA1949	6	30652888	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94488	30652888	140462179	4503	12488										
KIAA1949	170954	broad.mit.edu	37	chr6	30653331	30653331	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactcttgggctccccctatCcccagcctcctctctctggt	6	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30653331C>A	ENST00000274853.3	-	1	2341	c.465G>T	c.(463-465)ggG>ggT	p.G155G	PPP1R18_ENST00000399199.3_Silent_p.G155G|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	155						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G155G(1)									CTCCCCCTATCCCCAGCCTCC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	6											139	155	150					6																	30653331		1200	2507	3707	30761310	SO:0001819	synonymous_variant	170954			AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29413	protein-coding gene	gene with protein product	"protein phosphatase 1 F-actin cytoskeleton targeting subunit"	610990	"KIAA1949"	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.465G>T	6.37:g.30653331C>A			30761310	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Silent	SNP	ENST00000274853.3	37	CCDS43444.1																																																																																				0.627	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		A	30653331	C	A	30653331	2	1	61	1	0	0	0	0	0	0	0	1	8284	842	30	2		2	KIAA1949	6	30653331	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	443	30653331	140461736	4504	12489										
MDC1	9656	broad.mit.edu	37	chr6	30672717	30672717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtggaagtggaaggctCgagcttaggggctgtgggga	20	5	1	0	rs200570441		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30672717C>T	ENST00000376406.3	-	10	4890	c.4243G>A	c.(4243-4245)Gag>Aag	p.E1415K	MDC1_ENST00000376405.2_Missense_Mutation_p.E1151K|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1415	Interaction with the PRKDC complex.|Pro-rich.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)	p.E1415K(1)		breast(2)|kidney(1)|ovary(1)	4						GTGGAAGGCTCGAGCTTAGGG	0.562								Other conserved DNA damage response genes					C|||	1	0.000199681	0	0	5008	,	,		20498	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											91	99	96					6																	30672717		2203	4300	6503	30780696	SO:0001583	missense	9656			D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4243G>A	6.37:g.30672717C>T	ENSP00000365588:p.Glu1415Lys		30780696	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	9.041	0.989607	0.18966	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.05199	3.48;3.48	3.23	0.336	0.15958	.	0.582839	0.12950	N	0.425882	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B;B	0.28258	0.002;0.205	B;B	0.13407	0.0;0.009	T	0.47071	-0.9145	10	0.28530	T	0.3	-0.3845	3.6554	0.08218	0.2435:0.2121:0.5445:0.0	.	1151;1415	Q14676-2;Q14676	.;MDC1_HUMAN	K	1415;1151;1128;981	ENSP00000365588:E1415K;ENSP00000365587:E1151K	ENSP00000365587:E1151K	E	-	1	0	MDC1	30780696	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.144000	0.10280	-0.061000	0.13110	-0.749000	0.03505	GAG		0.562	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		T	30672717	C	T	30672717	3	4	61	1	0	0	0	0	1	0	0	0	9433	893	31	1	2050	1	MDC1	6	30672717	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19386	30672717	140442350	4505	12490										
DPCR1	135656	broad.mit.edu	37	chr6	30920189	30920189	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgctggacagatgggagaGaatgattcattccctgcatg	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30920189G>T	ENST00000462446.1	+	2	3976	c.3948G>T	c.(3946-3948)gaG>gaT	p.E1316D	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.E158D			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	440						integral component of membrane (GO:0016021)		p.E158D(1)|p.E440D(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AGATGGGAGAGAATGATTCAT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	6											101	80	87					6																	30920189		2203	4300	6503	31028168	SO:0001583	missense	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3948G>T	6.37:g.30920189G>T	ENSP00000417182:p.Glu1316Asp		31028168	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	G	12.46	1.943381	0.34283	.	.	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.35605	1.3;1.61	3.78	-0.373	0.12516	.	.	.	.	.	T	0.24967	0.0606	L	0.52573	1.65	0.09310	N	1	D	0.64830	0.994	P	0.57846	0.828	T	0.06661	-1.0814	9	0.87932	D	0	-5.1966	4.0131	0.09631	0.3169:0.1791:0.504:0.0	.	1316	E9PEI6	.	D	1316;440;158	ENSP00000417182:E1316D;ENSP00000305948:E158D	ENSP00000305948:E158D	E	+	3	2	DPCR1	31028168	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.158000	0.10070	-0.234000	0.09782	-0.271000	0.10264	GAG		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		T	30920189	G	T	30920189	3	4	61	1	0	0	0	0	1	0	0	0	4723	933	33	2	3954	2	DPCR1	6	30920189	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	247472	30920189	140194878	4506	12491										
DPCR1	135656	broad.mit.edu	37	chr6	30920862	30920862	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgatggagcagcagaatCttggcatgggccagatccct	12	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:30920862C>A	ENST00000462446.1	+	3	4178	c.4150C>A	c.(4150-4152)Ctt>Att	p.L1384I	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.L226I			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	508						integral component of membrane (GO:0016021)		p.L508I(1)|p.L226I(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GCAGCAGAATCTTGGCATGGG	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	6											138	99	112					6																	30920862		2203	4300	6503	31028841	SO:0001583	missense	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.4150C>A	6.37:g.30920862C>A	ENSP00000417182:p.Leu1384Ile		31028841	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	c	24.4	4.531531	0.85706	.	.	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.52295	0.67;0.78	3.72	2.55	0.30701	.	.	.	.	.	T	0.43919	0.1269	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.21759	-1.0236	9	0.87932	D	0	-9.5808	5.2669	0.15603	0.0:0.7718:0.0:0.2282	.	1384	E9PEI6	.	I	1384;508;226	ENSP00000417182:L1384I;ENSP00000305948:L226I	ENSP00000305948:L226I	L	+	1	0	DPCR1	31028841	0.006000	0.16342	0.169000	0.22859	0.810000	0.45777	-0.142000	0.10311	0.597000	0.29811	0.574000	0.79327	CTT		0.597	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30920862	C	A	30920862	3	1	61	1	0	0	0	0	1	0	0	0	4723	913	32	2	4160	2	DPCR1	6	30920862	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673	30920862	140194205	4507	12492										
CDSN	170679	broad.mit.edu	37	chr6	31084529	31084529	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccataggatttgtctacaGaggtgattgggggacagggc	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31084529G>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.S288Y|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1									p.S288Y(1)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TTTGTCTACAGAGGTGATTGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											36	36	36					6																	31084529		1946	3856	5802	31192508	SO:0001627	intron_variant	1041			AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1861G>T	6.37:g.31084529G>T			31192508	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.571754	0.65765	.	.	ENSG00000204539	ENST00000376288	T	0.12569	2.67	4.76	4.76	0.60689	.	0.000000	0.50627	D	0.000117	T	0.18130	0.0435	L	0.36672	1.1	0.37584	D	0.919912	D	0.76494	0.999	D	0.85130	0.997	T	0.01440	-1.1354	10	0.87932	D	0	-10.3629	13.2439	0.60012	0.0:0.0:1.0:0.0	.	288	Q15517	CDSN_HUMAN	Y	288	ENSP00000365465:S288Y	ENSP00000365465:S288Y	S	-	2	0	CDSN	31192508	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	4.470000	0.60175	2.192000	0.70111	0.549000	0.68633	TCT		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		T	31084529	G	T	31084529	1	4	61	0	1	0	0	0	0	0	0	0	3185	942	33	2		2	CDSN	6	31084529	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163667	31084529	140030538	4508	12493										
CCHCR1	54535	broad.mit.edu	37	chr6	31118749	31118749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctacctcagctgcttccGaagcagctcggcctccctct	7	19	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31118749G>A	ENST00000376266.5	-	5	807	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	CCHCR1_ENST00000396268.3_Missense_Mutation_p.R318W|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R282W|CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R229W	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	229					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R318W(1)|p.R229W(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						AGCTGCTTCCGAAGCAGCTCG	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	6											128	154	145					6																	31118749		1509	2707	4216	31226728	SO:0001583	missense	54535			AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.685C>T	6.37:g.31118749G>A	ENSP00000365442:p.Arg229Trp		31226728	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	g	15.79	2.938693	0.52972	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.04360	3.64;3.64;3.64;3.64	4.63	2.18	0.27775	.	1.134070	0.06794	N	0.787524	T	0.08758	0.0217	M	0.65975	2.015	0.09310	N	1	D;D;D;D;D	0.89917	0.999;0.998;0.998;1.0;1.0	D;P;P;D;D	0.64595	0.927;0.88;0.896;0.927;0.917	T	0.26608	-1.0098	10	0.72032	D	0.01	-4.8282	10.392	0.44179	0.0:0.0:0.5463:0.4537	.	229;229;229;282;318	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	W	318;229;229;229;282	ENSP00000379566:R318W;ENSP00000365442:R229W;ENSP00000379561:R229W;ENSP00000401039:R282W	ENSP00000365442:R229W	R	-	1	2	CCHCR1	31226728	0.105000	0.21958	0.030000	0.17652	0.756000	0.42949	1.672000	0.37523	0.712000	0.32039	0.274000	0.19336	CGG		0.622	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		A	31118749	G	A	31118749	3	1	61	1	0	0	0	0	1	0	0	0	2883	1057	37	1	1719	1	CCHCR1	6	31118749	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34220	31118749	139996318	4509	12494										
MICB	4277	broad.mit.edu	37	chr6	31474903	31474903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatatcacactgacctggCgtcaggatggggtatctttg	13	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31474903C>T	ENST00000252229.6	+	4	797	c.718C>T	c.(718-720)Cgt>Tgt	p.R240C	MICB_ENST00000399150.3_Missense_Mutation_p.R197C|MICB_ENST00000538442.1_Missense_Mutation_p.R208C	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B									p.R240C(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						ACTGACCTGGCGTCAGGATGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											59	63	62					6																	31474903		1380	2619	3999	31582882	SO:0001583	missense	4277				CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"Immunoglobulin superfamily / C1-set domain containing"	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.718C>T	6.37:g.31474903C>T	ENSP00000252229:p.Arg240Cys		31582882		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.576952	0.28092	.	.	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.14022	2.54;2.54;2.54	2.73	0.86	0.19042	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.944910	0.03628	U	0.237521	T	0.21267	0.0512	M	0.82630	2.6	0.27540	N	0.950812	D;P;P	0.89917	1.0;0.764;0.942	D;B;B	0.87578	0.998;0.359;0.396	T	0.01734	-1.1285	10	0.87932	D	0	.	2.5125	0.04660	0.2314:0.4854:0.0:0.2832	.	208;197;240	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	C	208;197;240	ENSP00000442345:R208C;ENSP00000382103:R197C;ENSP00000252229:R240C	ENSP00000252229:R240C	R	+	1	0	MICB	31582882	0.010000	0.17322	0.057000	0.19452	0.096000	0.18686	-0.414000	0.07114	0.053000	0.16036	0.305000	0.20034	CGT		0.582	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931		T	31474903	C	T	31474903	3	4	61	1	0	0	0	0	1	0	0	0	9605	768	27	1	732	1	MICB	6	31474903	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	356154	31474903	139640164	4510	12495										
BAT1	7919	broad.mit.edu	37	chr6	31504294	31504294	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgagctgttcaagcatcTtatcacattcatccaaaata	4	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31504294T>G	ENST00000396172.1	-	5	1229	c.599A>C	c.(598-600)aAg>aCg	p.K200T	SNORD117_ENST00000364915.1_RNA|DDX39B_ENST00000376177.2_Missense_Mutation_p.K200T|DDX39B_ENST00000417556.2_Missense_Mutation_p.K215T|DDX39B_ENST00000458640.1_Missense_Mutation_p.K200T|DDX39B_ENST00000415382.2_Missense_Mutation_p.K122T|DDX39B_ENST00000453105.2_Missense_Mutation_p.K153T|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	200	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)	p.K200T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TTCAAGCATCTTATCACATTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	101	100					6																	31504294		1509	2709	4218	31612273	SO:0001583	missense	7919			Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.599A>C	6.37:g.31504294T>G	ENSP00000379475:p.Lys200Thr		31612273	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	37	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373056	0.82573	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000415382;ENST00000431908;ENST00000427214;ENST00000453105;ENST00000428098;ENST00000419338;ENST00000456662	D;T;T;T;T;T;T;T;T;T;T	0.92397	-3.03;3.57;3.57;3.57;3.57;3.57;1.0;2.45;1.0;1.0;2.45	5.4	5.4	0.78164	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.058359	0.64402	D	0.000004	D	0.91425	0.7294	L	0.37800	1.135	0.80722	D	1	P;P;D;P;D;P	0.56968	0.777;0.777;0.978;0.563;0.974;0.788	P;P;P;P;D;P	0.62955	0.721;0.798;0.786;0.497;0.909;0.456	D	0.92876	0.6319	10	0.66056	D	0.02	-22.611	13.6578	0.62348	0.0:0.0:0.0:1.0	.	122;153;122;220;200;200	B4DIZ8;B4DIJ6;B4DP52;Q59G92;Q13838;Q5STU3	.;.;.;.;DX39B_HUMAN;.	T	200;200;200;215;122;122;200;153;200;200;200	ENSP00000365347:K200T;ENSP00000416269:K200T;ENSP00000379475:K200T;ENSP00000412582:K215T;ENSP00000392669:K122T;ENSP00000408000:K122T;ENSP00000399371:K200T;ENSP00000400328:K153T;ENSP00000392672:K200T;ENSP00000410313:K200T;ENSP00000416350:K200T	ENSP00000365347:K200T	K	-	2	0	DDX39B	31612273	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.594000	0.82698	2.161000	0.67846	0.528000	0.53228	AAG		0.473	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		G	31504294	T	G	31504294	3	3	61	1	0	0	0	0	1	0	0	0	1319	1609	56	4	715	4	BAT1	6	31504294	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	29391	31504294	139610773	4511	12496										
BAT1	7919	broad.mit.edu	37	chr6	31508301	31508301	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcattgtccacatcgttCtctgccataactgggccggc	9	14	2	0	rs371622727		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31508301C>T	ENST00000396172.1	-	2	639	c.9G>A	c.(7-9)gaG>gaA	p.E3E	ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|DDX39B_ENST00000449074.2_Silent_p.E3E|DDX39B-AS1_ENST00000420520.1_RNA|DDX39B_ENST00000376177.2_Silent_p.E3E|DDX39B-AS1_ENST00000416684.1_RNA|DDX39B_ENST00000417556.2_Silent_p.E3E|DDX39B_ENST00000458640.1_Silent_p.E3E|DDX39B_ENST00000415382.2_5'UTR|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000453105.2_5'UTR|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	3					ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)	p.E3E(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						CCACATCGTTCTCTGCCATAA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	6											71	65	67					6																	31508301		2203	4300	6503	31616280	SO:0001819	synonymous_variant	7919			Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.9G>A	6.37:g.31508301C>T			31616280	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Silent	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																				0.547	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		T	31508301	C	T	31508301	2	4	61	1	0	0	0	0	0	0	0	1	1319	912	32	3		3	BAT1	6	31508301	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4007	31508301	139606766	4512	12497										
ATP6V1G2	534	broad.mit.edu	37	chr6	31513262	31513262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagctgggccaggacacGctctcggtttctctgctggg	14	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31513262G>A	ENST00000303892.5	-	3	564	c.280C>T	c.(280-282)Cgt>Tgt	p.R94C	NFKBIL1_ENST00000376145.4_5'Flank|ATP6V1G2-DDX39B_ENST00000475917.1_Intron|ATP6V1G2_ENST00000376151.4_Missense_Mutation_p.R54C|DDX39B-AS1_ENST00000420520.1_RNA|NFKBIL1_ENST00000376148.4_5'Flank|ATP6V1G2_ENST00000483251.1_Missense_Mutation_p.R53C|DDX39B-AS1_ENST00000416684.1_RNA|ATP6V1G2_ENST00000483170.1_5'UTR|ATP6V1G2-DDX39B_ENST00000376185.1_Intron	NM_130463.3|NM_138282.2	NP_569730.1|NP_612139.1	O95670	VATG2_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2	94					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)	p.R94C(1)		breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						GCCAGGACACGCTCTCGGTTT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											53	48	50					6																	31513262		2203	4300	6503	31621241	SO:0001583	missense	534			Y14768	CCDS4698.1, CCDS4699.1, CCDS56413.1	6p21.3	2011-03-29	2006-01-13	2002-05-10	ENSG00000213760	ENSG00000213760		"ATPases / V-type"	862	protein-coding gene	gene with protein product		606853	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 2"	ATP6G, ATP6G2		10202016	Standard	NM_138282		Approved	Vma10, NG38, Em:AC004181.3	uc003nua.3	O95670	OTTHUMG00000166618	ENST00000303892.5:c.280C>T	6.37:g.31513262G>A	ENSP00000302194:p.Arg94Cys		31621241	B5MEF0|Q2L6F8|Q5HYU8|Q5RJ63	Missense_Mutation	SNP	ENST00000303892.5	37	CCDS4698.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.651670	0.67472	.	.	ENSG00000213760	ENST00000376151;ENST00000303892;ENST00000483251;ENST00000415099	T;T;T;T	0.45668	0.89;0.92;0.92;0.92	4.81	3.0	0.34707	.	0.320980	0.25854	U	0.027879	T	0.27933	0.0688	L	0.46157	1.445	0.27837	N	0.941246	P	0.49783	0.928	P	0.53062	0.717	T	0.07424	-1.0773	10	0.62326	D	0.03	-3.7461	5.2228	0.15377	0.1871:0.1698:0.643:0.0	.	94	O95670	VATG2_HUMAN	C	54;94;53;134	ENSP00000365321:R54C;ENSP00000302194:R94C;ENSP00000419698:R53C;ENSP00000390148:R134C	ENSP00000302194:R94C	R	-	1	0	ATP6V1G2	31621241	0.995000	0.38212	0.576000	0.28549	0.992000	0.81027	1.688000	0.37690	1.245000	0.43885	0.655000	0.94253	CGT		0.647	ATP6V1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076399.3	NM_130463		A	31513262	G	A	31513262	3	1	61	1	0	0	0	0	1	0	0	0	1188	1087	38	1	80	1	ATP6V1G2	6	31513262	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4961	31513262	139601805	4513	12498										
BAT2	7916	broad.mit.edu	37	chr6	31593584	31593584	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagatgtatcccccatatCtcccgttccctccgccctat	4	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31593584C>A	ENST00000376033.2	+	8	1009	c.775C>A	c.(775-777)Ctc>Atc	p.L259I	PRRC2A_ENST00000469577.1_3'UTR|SNORA38_ENST00000363946.1_RNA|PRRC2A_ENST00000376007.4_Missense_Mutation_p.L259I	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	259	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L259I(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TCCCCCATATCTCCCGTTCCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	76	81					6																	31593584		1511	2709	4220	31701563	SO:0001583	missense	7916			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.775C>A	6.37:g.31593584C>A	ENSP00000365201:p.Leu259Ile		31701563	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902422	0.33628	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.01787	4.64;4.64	4.98	4.98	0.66077	.	0.000000	0.45126	D	0.000381	T	0.02688	0.0081	L	0.48642	1.525	0.44789	D	0.997798	D	0.62365	0.991	P	0.58820	0.846	T	0.49872	-0.8893	10	0.87932	D	0	-19.3667	10.726	0.46068	0.0:0.912:0.0:0.088	.	259	P48634	PRC2A_HUMAN	I	259	ENSP00000365175:L259I;ENSP00000365201:L259I	ENSP00000365175:L259I	L	+	1	0	PRRC2A	31701563	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.852000	0.48310	2.605000	0.88082	0.655000	0.94253	CTC		0.562	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		A	31593584	C	A	31593584	3	1	61	1	0	0	0	0	1	0	0	0	1320	913	32	2	801	2	BAT2	6	31593584	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80322	31593584	139521483	4514	12499										
BAT2	7916	broad.mit.edu	37	chr6	31599457	31599457	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccccacccaatggaaatCtttcccctgccccaaggctt	6	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31599457C>A	ENST00000376033.2	+	16	3241	c.3007C>A	c.(3007-3009)Ctt>Att	p.L1003I	PRRC2A_ENST00000376007.4_Missense_Mutation_p.L1003I	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1003	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L1003I(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CAATGGAAATCTTTCCCCTGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											16	19	18					6																	31599457		1506	2709	4215	31707436	SO:0001583	missense	7916			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3007C>A	6.37:g.31599457C>A	ENSP00000365201:p.Leu1003Ile		31707436	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	8.201	0.798181	0.16397	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01981	4.52;4.52	5.2	4.34	0.51931	.	0.000000	0.46145	D	0.000307	T	0.00580	0.0019	N	0.14661	0.345	0.24179	N	0.995591	B	0.25719	0.132	B	0.20184	0.028	T	0.48703	-0.9012	10	0.87932	D	0	-16.0634	6.4097	0.21684	0.2778:0.636:0.0:0.0862	.	1003	P48634	PRC2A_HUMAN	I	1003;992;1003;1003;228	ENSP00000365175:L1003I;ENSP00000365201:L1003I	ENSP00000365175:L1003I	L	+	1	0	PRRC2A	31707436	0.997000	0.39634	0.980000	0.43619	0.957000	0.61999	3.543000	0.53633	1.445000	0.47624	0.655000	0.94253	CTT		0.592	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		A	31599457	C	A	31599457	3	1	61	1	0	0	0	0	1	0	0	0	1320	913	32	2	3065	2	BAT2	6	31599457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5873	31599457	139515610	4515	12500										
BAT3	7917	broad.mit.edu	37	chr6	31609993	31609993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcccgagcccccagggagCccagcagggagctgagcaca	14	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31609993C>T	ENST00000375964.6	-	15	2454	c.2141G>A	c.(2140-2142)gGc>gAc	p.G714D	BAG6_ENST00000404765.2_Missense_Mutation_p.G744D|BAG6_ENST00000362049.6_Missense_Mutation_p.G708D|BAG6_ENST00000439687.2_Missense_Mutation_p.G582D|BAG6_ENST00000375976.4_Missense_Mutation_p.G708D|BAG6_ENST00000211379.5_Missense_Mutation_p.G708D|BAG6_ENST00000470875.1_5'UTR	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	714					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)	p.G708D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CCCCAGGGAGCCCAGCAGGGA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											39	39	39					6																	31609993		1509	2709	4218	31717972	SO:0001583	missense	7917			M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2141G>A	6.37:g.31609993C>T	ENSP00000365131:p.Gly714Asp		31717972	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	37	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891288	0.91889	.	.	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049	T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3	5.75	5.75	0.90469	.	0.048960	0.85682	D	0.000000	T	0.48554	0.1506	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.87578	0.949;0.985;0.996;0.998	T	0.42682	-0.9437	10	0.59425	D	0.04	.	18.7781	0.91920	0.0:1.0:0.0:0.0	.	582;708;714;708	E7EMZ4;F8VXY4;P46379;P46379-2	.;.;BAG6_HUMAN;.	D	708;714;708;744;582;708	ENSP00000365143:G708D;ENSP00000365131:G714D;ENSP00000211379:G708D;ENSP00000384494:G744D;ENSP00000402856:G582D;ENSP00000354875:G708D	ENSP00000211379:G708D	G	-	2	0	BAG6	31717972	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.307000	0.72815	2.731000	0.93534	0.650000	0.86243	GGC		0.607	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		T	31609993	C	T	31609993	3	4	61	1	0	0	0	0	1	0	0	0	1323	739	26	3	1301	3	BAT3	6	31609993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10536	31609993	139505074	4516	12501										
APOM	55937	broad.mit.edu	37	chr6	31625862	31625862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctgtgagctgtccaataActgacctgtaacttcatcta	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31625862A>G	ENST00000375916.3	+	6	1059	c.563A>G	c.(562-564)aAc>aGc	p.N188S	C6orf47-AS1_ENST00000422049.1_RNA|APOM_ENST00000375920.4_Missense_Mutation_p.N116S	NM_019101.2	NP_061974.2	O95445	APOM_HUMAN	apolipoprotein M	188				LTPRNQEACELSNN -> VDS (in Ref. 2; CAB51604). {ECO:0000305}.	cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|response to glucose (GO:0009749)|reverse cholesterol transport (GO:0043691)	discoidal high-density lipoprotein particle (GO:0034365)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|lipid transporter activity (GO:0005319)|phospholipid binding (GO:0005543)	p.N188S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(1)	7						CTGTCCAATAACTGACCTGTA	0.517																																					Colon(39;129 858 13764 41453 42617)											1	Substitution - Missense(1)	large_intestine(1)	6											180	170	173					6																	31625862		2203	4300	6503	31733841	SO:0001583	missense	55937			AJ245434	CCDS4710.1, CCDS59004.1	6p21	2014-01-22			ENSG00000204444	ENSG00000204444		"Apolipoproteins", "Lipocalins"	13916	protein-coding gene	gene with protein product		606907				10531326, 11418126	Standard	NM_019101		Approved	ApoM, G3a, NG20	uc003nvl.3	O95445	OTTHUMG00000031250	ENST00000375916.3:c.563A>G	6.37:g.31625862A>G	ENSP00000365081:p.Asn188Ser		31733841	B0UX98|Q5SRP4|Q9P046|Q9UMP6	Missense_Mutation	SNP	ENST00000375916.3	37	CCDS4710.1	.	.	.	.	.	.	.	.	.	.	A	2.178	-0.388350	0.04932	.	.	ENSG00000204444	ENST00000375920;ENST00000375916	.	.	.	4.75	2.32	0.28847	Calycin-like (1);	0.870478	0.10307	N	0.690485	T	0.04137	0.0115	N	0.08118	0	0.21652	N	0.99961	B	0.02656	0.0	B	0.01281	0.0	T	0.43972	-0.9358	9	0.08179	T	0.78	-0.3355	3.8653	0.09013	0.7144:0.0:0.1003:0.1853	.	188	O95445	APOM_HUMAN	S	116;188	.	ENSP00000365081:N188S	N	+	2	0	APOM	31733841	0.878000	0.30173	0.666000	0.29783	0.045000	0.14185	1.200000	0.32247	0.314000	0.23086	-0.695000	0.03696	AAC		0.517	APOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076527.3	NM_019101		G	31625862	A	G	31625862	3	3	61	1	0	0	0	0	1	0	0	0	812	43	2	4	585	4	APOM	6	31625862	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	15869	31625862	139489205	4517	12502										
C6orf47	57827	broad.mit.edu	37	chr6	31627614	31627614	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagtcacttcctgaattCtccgaggagctgtccacccg	8	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31627614C>A	ENST00000375911.1	-	1	935	c.111G>T	c.(109-111)gaG>gaT	p.E37D	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	37						cytoplasm (GO:0005737)		p.E37D(1)		NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						TTCCTGAATTCTCCGAGGAGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											39	37	37					6																	31627614		1510	2708	4218	31735593	SO:0001583	missense	57827			AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.111G>T	6.37:g.31627614C>A	ENSP00000365076:p.Glu37Asp		31735593	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Missense_Mutation	SNP	ENST00000375911.1	37	CCDS34399.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977915	0.74360	.	.	ENSG00000204439	ENST00000375911;ENST00000538106	T	0.43688	0.94	5.44	3.68	0.42216	.	0.000000	0.47093	D	0.000242	T	0.43634	0.1256	M	0.62723	1.935	0.25802	N	0.984497	D	0.76494	0.999	D	0.80764	0.994	T	0.34403	-0.9830	10	0.87932	D	0	-19.7986	8.1562	0.31171	0.0:0.8213:0.0:0.1787	.	37	O95873	CF047_HUMAN	D	37	ENSP00000365076:E37D	ENSP00000365076:E37D	E	-	3	2	C6orf47	31735593	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.985000	0.40668	0.873000	0.35799	0.655000	0.94253	GAG		0.607	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		A	31627614	C	A	31627614	3	1	61	1	0	0	0	0	1	0	0	0	2370	912	32	2	777	2	C6orf47	6	31627614	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1752	31627614	139487453	4518	12503										
DDAH2	23564	broad.mit.edu	37	chr6	31696520	31696520	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggctttgcggactccatcGaccttaggataggagaagag	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31696520G>A	ENST00000375789.2	-	2	930	c.300C>T	c.(298-300)gtC>gtT	p.V100V	DDAH2_ENST00000480913.1_5'UTR|DDAH2_ENST00000375787.2_Silent_p.V100V|DDAH2_ENST00000375792.3_Silent_p.V100V			O95865	DDAH2_HUMAN	dimethylarginine dimethylaminohydrolase 2	100					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|negative regulation of apoptotic process (GO:0043066)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of nitric oxide biosynthetic process (GO:0045429)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)	p.V100V(1)		endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	11					L-Citrulline(DB00155)	GGACTCCATCGACCTTAGGAT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	6											58	56	57					6																	31696520		1510	2709	4219	31804499	SO:0001819	synonymous_variant	23564			AF070667	CCDS4718.1	6p21	2010-02-17			ENSG00000213722	ENSG00000213722	3.5.3.18		2716	protein-coding gene	gene with protein product		604744				10493931	Standard	XM_005248974		Approved		uc003nwq.3	O95865	OTTHUMG00000031212	ENST00000375789.2:c.300C>T	6.37:g.31696520G>A			31804499	A2BEZ7	Silent	SNP	ENST00000375789.2	37	CCDS4718.1	.	.	.	.	.	.	.	.	.	.	G	8.462	0.855636	0.17106	.	.	ENSG00000213722	ENST00000437288	.	.	.	4.99	-5.88	0.02290	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.5478	8.0	0.30291	0.3915:0.4489:0.1595:0.0	.	.	.	.	X	6	.	.	R	-	1	2	DDAH2	31804499	0.227000	0.23707	0.950000	0.38849	0.926000	0.56050	-0.834000	0.04391	-1.114000	0.02977	-0.345000	0.07892	CGA		0.567	DDAH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076432.2			A	31696520	G	A	31696520	2	1	61	1	0	0	0	0	0	0	0	1	4328	1045	37	1		1	DDAH2	6	31696520	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68906	31696520	139418547	4519	12504										
C6orf26	401251	broad.mit.edu	37	chr6	31731208	31731208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctacgcaggatgcaggCtctggagagagaacaggatg	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31731208C>T	ENST00000425424.1	+	2	190	c.131C>T	c.(130-132)gCt>gTt	p.A44V	VWA7_ENST00000467576.1_5'Flank|SAPCD1-AS1_ENST00000419679.1_RNA|MSH5_ENST00000534153.4_3'UTR|MSH5-SAPCD1_ENST00000493662.2_3'UTR|SAPCD1_ENST00000415669.2_Missense_Mutation_p.A44V			Q5SSQ6	SAPC1_HUMAN	suppressor APC domain containing 1	44								p.A44V(1)									AGGATGCAGGCTCTGGAGAGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	76	76					6																	31731208		1511	2708	4219	31839187	SO:0001583	missense	401251				CCDS34411.1	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000228727	ENSG00000228727			13938	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 26"	C6orf26			Standard	NM_001039651		Approved	NG23		Q5SSQ6	OTTHUMG00000031131	ENST00000425424.1:c.131C>T	6.37:g.31731208C>T	ENSP00000413372:p.Ala44Val		31839187	A2ABF2|A2ABS9|Q9Y335	Missense_Mutation	SNP	ENST00000425424.1	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.195637	0.78902	.	.	ENSG00000228727	ENST00000433778;ENST00000415669;ENST00000425424	T;T	0.81330	-1.48;-1.48	4.41	4.41	0.53225	.	.	.	.	.	D	0.84179	0.5415	.	.	.	0.30640	N	0.756515	D	0.89917	1.0	D	0.67725	0.953	T	0.79757	-0.1669	8	0.59425	D	0.04	-3.8138	12.6963	0.57005	0.0:1.0:0.0:0.0	.	44	Q5SSQ6-2	.	V	44	ENSP00000411948:A44V;ENSP00000413372:A44V	ENSP00000411948:A44V	A	+	2	0	C6orf26	31839187	0.977000	0.34250	1.000000	0.80357	0.964000	0.63967	1.222000	0.32515	2.432000	0.82394	0.655000	0.94253	GCT		0.592	SAPCD1-203	KNOWN	basic	protein_coding	protein_coding		NM_001039651		T	31731208	C	T	31731208	3	4	61	1	0	0	0	0	1	0	0	0	2367	797	28	3	137	3	C6orf26	6	31731208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34688	31731208	139383859	4520	12505										
C2	717	broad.mit.edu	37	chr6	31895546	31895546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccatgggcccactgatggTtcttttttgcctgctgttcc	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31895546T>C	ENST00000299367.5	+	1	293	c.17T>C	c.(16-18)gTt>gCt	p.V6A	C2_ENST00000418949.2_Missense_Mutation_p.V6A|C2_ENST00000469372.1_Intron|CFB_ENST00000556679.1_Missense_Mutation_p.V6A|CFB_ENST00000477310.1_Missense_Mutation_p.V6A|C2_ENST00000452323.2_Intron|CFB_ENST00000456570.1_Missense_Mutation_p.V6A|C2_ENST00000442278.2_Missense_Mutation_p.V6A	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	6					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V6A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		CCACTGATGGTTCTTTTTTGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											228	270	255					6																	31895546		1511	2709	4220	32003525	SO:0001583	missense	717				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.17T>C	6.37:g.31895546T>C	ENSP00000299367:p.Val6Ala		32003525	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	37	CCDS4728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.953|8.953	0.968718|0.968718	0.18659|0.18659	.|.	.|.	ENSG00000166278|ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000383177|ENST00000413154;ENST00000299367;ENST00000442278;ENST00000447952;ENST00000418949;ENST00000556679;ENST00000456570;ENST00000477310	.|T;T;D;T;T;D;D;T	.|0.88975	.|1.45;-1.4;-2.45;1.26;1.27;-1.52;-1.52;-1.35	5.75|5.75	2.91|2.91	0.33838|0.33838	.|.	.|0.425540	.|0.17372	.|N	.|0.176622	T|T	0.52885|0.52885	0.1762|0.1762	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.001;0.001;0.0;0.001;0.001	T|T	0.48055|0.48055	-0.9068|-0.9068	4|9	.|0.07813	.|T	.|0.8	-0.3984|-0.3984	5.6526|5.6526	0.17625|0.17625	0.0:0.6453:0.0:0.3547|0.0:0.6453:0.0:0.3547	.|.	.|6;6;6;6;6	.|B4E1Z4;E9PFN7;B4DV20;P06681;Q8N6L6	.|.;.;.;CO2_HUMAN;.	L|A	3|6	.|ENSP00000403325:V6A;ENSP00000299367:V6A;ENSP00000395683:V6A;ENSP00000391354:V6A;ENSP00000406190:V6A;ENSP00000451848:V6A;ENSP00000410815:V6A;ENSP00000418996:V6A	.|ENSP00000299367:V6A	F|V	+|+	1|2	0|0	C2|CFB;C2;XXbac-BPG116M5.17	32003525|32003525	0.037000|0.037000	0.19845|0.19845	0.024000|0.024000	0.17045|0.17045	0.716000|0.716000	0.41182|0.41182	-0.002000|-0.002000	0.12924|0.12924	0.719000|0.719000	0.32188|0.32188	0.533000|0.533000	0.62120|0.62120	TTC|GTT		0.582	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			C	31895546	T	C	31895546	3	2	61	1	0	0	0	0	1	0	0	0	2080	1725	60	4	96	4	C2	6	31895546	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	164338	31895546	139219521	4521	12506										
C2	717	broad.mit.edu	37	chr6	31905145	31905145	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgcggccttaaacagtgtCtatctcatgatgaacaacca	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31905145C>A	ENST00000299367.5	+	8	1314	c.1038C>A	c.(1036-1038)gtC>gtA	p.V346V	C2_ENST00000469372.1_Silent_p.V100V|CFB_ENST00000556679.1_Silent_p.V193V|CFB_ENST00000477310.1_Silent_p.V164V|C2_ENST00000452323.2_Silent_p.V132V|CFB_ENST00000456570.1_Silent_p.V193V|C2_ENST00000442278.2_Silent_p.V214V	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	346	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V346V(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		TAAACAGTGTCTATCTCATGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	6											201	196	198					6																	31905145		1511	2709	4220	32013124	SO:0001819	synonymous_variant	717				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1038C>A	6.37:g.31905145C>A			32013124	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Silent	SNP	ENST00000299367.5	37	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	C	1.646	-0.515179	0.04200	.	.	ENSG00000166278	ENST00000383177	.	.	.	4.97	0.925	0.19424	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20140	-1.0284	4	.	.	.	-30.3314	4.9528	0.14023	0.1459:0.604:0.0:0.2501	.	.	.	.	Y	120	.	.	S	+	2	0	C2	32013124	0.919000	0.31177	0.260000	0.24451	0.148000	0.21650	0.000000	0.12993	0.277000	0.22141	0.544000	0.68410	TCT		0.478	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31905145	C	A	31905145	2	1	61	1	0	0	0	0	0	0	0	1	2080	900	32	2		2	C2	6	31905145	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9599	31905145	139209922	4522	12507										
C2	717	broad.mit.edu	37	chr6	31910803	31910803	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaatgagctagggtccaaGaaggatggtgagaggcatgc	16	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31910803G>T	ENST00000299367.5	+	10	1563	c.1287G>T	c.(1285-1287)aaG>aaT	p.K429N	C2_ENST00000469372.1_Missense_Mutation_p.K183N|CFB_ENST00000556679.1_Missense_Mutation_p.K276N|CFB_ENST00000425368.2_5'Flank|CFB_ENST00000477310.1_Intron|C2_ENST00000452323.2_Missense_Mutation_p.K215N|CFB_ENST00000456570.1_Missense_Mutation_p.K276N|C2_ENST00000442278.2_Missense_Mutation_p.K297N	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	429	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.K429N(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		TAGGGTCCAAGAAGGATGGTG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											311	321	317					6																	31910803		1511	2709	4220	32018782	SO:0001583	missense	717				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1287G>T	6.37:g.31910803G>T	ENSP00000299367:p.Lys429Asn		32018782	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	37	CCDS4728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.094810|4.094810	0.76870|0.76870	.|.	.|.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255|ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570|ENST00000383177	D;D;D;D;D;D;D|.	0.83755|.	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76|.	5.8|5.8	4.04|4.04	0.47022|0.47022	von Willebrand factor, type A (3);|.	0.000000|.	0.41294|.	D|.	0.000915|.	T|T	0.43033|0.43033	0.1229|0.1229	M|M	0.64080|0.64080	1.96|1.96	0.33369|0.33369	D|D	0.573329|0.573329	D;D;D;D;D;D;D;P;P|.	0.63046|.	0.976;0.977;0.992;0.987;0.987;0.984;0.977;0.921;0.952|.	P;P;P;P;P;P;P;P;P|.	0.57911|.	0.62;0.763;0.804;0.763;0.829;0.65;0.763;0.694;0.629|.	T|T	0.40664|0.40664	-0.9551|-0.9551	10|5	0.72032|.	D|.	0.01|.	-21.662|-21.662	9.9729|9.9729	0.41765|0.41765	0.1587:0.0:0.8413:0.0|0.1587:0.0:0.8413:0.0	.|.	276;400;215;183;297;114;297;429;216|.	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0|.	.;.;.;.;.;.;.;CO2_HUMAN;.|.	N|I	183;216;216;215;429;114;297;276;276|203	ENSP00000418923:K183N;ENSP00000417482:K216N;ENSP00000392322:K215N;ENSP00000299367:K429N;ENSP00000395683:K297N;ENSP00000451848:K276N;ENSP00000410815:K276N|.	ENSP00000299367:K429N|.	K|R	+|+	3|2	2|0	CFB;C2;XXbac-BPG116M5.17|C2	32018782|32018782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	3.267000|3.267000	0.51577|0.51577	0.820000|0.820000	0.34516|0.34516	0.455000|0.455000	0.32223|0.32223	AAG|AGA		0.537	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			T	31910803	G	T	31910803	3	4	61	1	0	0	0	0	1	0	0	0	2080	933	33	2	1402	2	C2	6	31910803	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5658	31910803	139204264	4523	12508										
C2	717	broad.mit.edu	37	chr6	31911277	31911277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcttccgcgatggcaacGaccactccctgtggagggtc	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31911277G>A	ENST00000299367.5	+	12	1816	c.1540G>A	c.(1540-1542)Gac>Aac	p.D514N	C2_ENST00000469372.1_Missense_Mutation_p.D268N|CFB_ENST00000556679.1_Missense_Mutation_p.D361N|CFB_ENST00000425368.2_5'Flank|CFB_ENST00000477310.1_Missense_Mutation_p.D285N|C2_ENST00000452323.2_Missense_Mutation_p.D300N|CFB_ENST00000456570.1_Missense_Mutation_p.D361N|C2_ENST00000442278.2_Missense_Mutation_p.D382N	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	514	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.D514N(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		CGATGGCAACGACCACTCCCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	6											92	105	100					6																	31911277		1510	2709	4219	32019256	SO:0001583	missense	717				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1540G>A	6.37:g.31911277G>A	ENSP00000299367:p.Asp514Asn		32019256	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	37	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572499	0.45798	.	.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570;ENST00000477310	T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	5.11	2.62	0.31277	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.352908	0.20603	N	0.089119	T	0.07098	0.0180	L	0.31664	0.95	0.26837	N	0.968463	B;B;B;B;B;B;B;B;B	0.17667	0.003;0.018;0.004;0.023;0.003;0.008;0.005;0.001;0.018	B;B;B;B;B;B;B;B;B	0.13407	0.002;0.008;0.003;0.006;0.002;0.005;0.008;0.001;0.009	T	0.35101	-0.9802	10	0.16896	T	0.51	-7.4961	8.9805	0.35961	0.254:0.0:0.746:0.0	.	361;485;300;268;382;199;382;514;301	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0	.;.;.;.;.;.;.;CO2_HUMAN;.	N	268;301;301;300;514;199;382;361;361;285	ENSP00000418923:D268N;ENSP00000417482:D301N;ENSP00000392322:D300N;ENSP00000299367:D514N;ENSP00000395683:D382N;ENSP00000451848:D361N;ENSP00000410815:D361N;ENSP00000418996:D285N	ENSP00000299367:D514N	D	+	1	0	CFB;C2;XXbac-BPG116M5.17	32019256	0.542000	0.26426	0.881000	0.34555	0.291000	0.27294	1.005000	0.29834	0.907000	0.36646	0.563000	0.77884	GAC		0.627	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31911277	G	A	31911277	3	1	61	1	0	0	0	0	1	0	0	0	2080	1058	37	1	1663	1	C2	6	31911277	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	474	31911277	139203790	4524	12509										
C2	717	broad.mit.edu	37	chr6	31911991	31911991	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgaacattaaccttaaGatgggagtggaggtgagggt	14	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31911991G>T	ENST00000299367.5	+	15	2166	c.1890G>T	c.(1888-1890)aaG>aaT	p.K630N	C2_ENST00000469372.1_Missense_Mutation_p.K384N|CFB_ENST00000556679.1_Missense_Mutation_p.K477N|CFB_ENST00000425368.2_5'Flank|C2_ENST00000468407.1_3'UTR|CFB_ENST00000477310.1_Missense_Mutation_p.K401N|C2_ENST00000452323.2_Missense_Mutation_p.K416N|CFB_ENST00000456570.1_Missense_Mutation_p.K477N|C2_ENST00000442278.2_Missense_Mutation_p.K498N	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	630	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.K630N(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		TTAACCTTAAGATGGGAGTGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	79	81					6																	31911991		1510	2709	4219	32019970	SO:0001583	missense	717				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1890G>T	6.37:g.31911991G>T	ENSP00000299367:p.Lys630Asn		32019970	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	37	CCDS4728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.71|17.71	3.457274|3.457274	0.63401|0.63401	.|.	.|.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570;ENST00000477310|ENST00000383177	T;T;T;T;T;T;T;T|.	0.28895|.	1.59;1.59;1.59;1.59;1.59;1.59;1.59;1.59|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.205306|.	0.24470|.	N|.	0.038254|.	T|T	0.47469|0.47469	0.1447|0.1447	M|M	0.70903|0.70903	2.155|2.155	0.26195|0.26195	N|N	0.979533|0.979533	D;D;D;D;D;D;D;D;D|.	0.89917|.	0.99;0.999;1.0;0.999;0.999;0.999;0.999;0.976;0.991|.	D;D;D;D;D;D;D;D;D|.	0.79784|.	0.93;0.993;0.99;0.993;0.993;0.989;0.993;0.959;0.936|.	T|T	0.43877|0.43877	-0.9364|-0.9364	10|5	0.87932|.	D|.	0|.	-16.7601|-16.7601	14.4085|14.4085	0.67099|0.67099	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	477;601;416;384;498;315;498;630;417|.	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0|.	.;.;.;.;.;.;.;CO2_HUMAN;.|.	N|I	384;417;416;630;315;498;477;477;401|404	ENSP00000418923:K384N;ENSP00000417482:K417N;ENSP00000392322:K416N;ENSP00000299367:K630N;ENSP00000395683:K498N;ENSP00000451848:K477N;ENSP00000410815:K477N;ENSP00000418996:K401N|.	ENSP00000299367:K630N|.	K|R	+|+	3|2	2|0	CFB;C2;XXbac-BPG116M5.17|C2	32019970|32019970	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.427000|0.427000	0.31564|0.31564	4.868000|4.868000	0.63021|0.63021	2.493000|2.493000	0.84123|0.84123	0.563000|0.563000	0.77884|0.77884	AAG|AGA		0.498	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			T	31911991	G	T	31911991	3	4	61	1	0	0	0	0	1	0	0	0	2080	933	33	2	2025	2	C2	6	31911991	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	714	31911991	139203076	4525	12510										
CFB	629	broad.mit.edu	37	chr6	31914358	31914358	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaagactcaagaccaaaaGactgtcaggaaggcagagtg	12	8	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31914358G>T	ENST00000425368.2	+	2	786	c.273G>T	c.(271-273)aaG>aaT	p.K91N	CFB_ENST00000556679.1_Missense_Mutation_p.K593N|CFB_ENST00000477310.1_Intron|CFB_ENST00000456570.1_Missense_Mutation_p.K593N	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	91	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)	p.K91N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						AAGACCAAAAGACTGTCAGGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	51	57					6																	31914358		1511	2708	4219	32022337	SO:0001583	missense	629			L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.273G>T	6.37:g.31914358G>T	ENSP00000416561:p.Lys91Asn		32022337	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	.	.	.	.	.	.	.	.	.	.	G	8.348	0.830236	0.16749	.	.	ENSG00000243649;ENSG00000243649;ENSG00000243649;ENSG00000244255	ENST00000556679;ENST00000475617;ENST00000425368;ENST00000456570	D;T;T;D	0.82433	-1.61;2.4;-1.48;-1.61	5.17	3.39	0.38822	Sushi/SCR/CCP (1);	0.120167	0.37623	N	0.002007	T	0.77955	0.4208	M	0.65975	2.015	0.37439	D	0.914325	D;B;B;B	0.67145	0.996;0.242;0.008;0.047	P;B;B;B	0.54544	0.755;0.032;0.002;0.006	T	0.74919	-0.3500	10	0.26408	T	0.33	-7.2198	8.1055	0.30883	0.1875:0.0:0.8125:0.0	.	91;593;91;91	B4E1Z1;B4E1Z4;P00751;P00751-2	.;.;CFAB_HUMAN;.	N	593;91;91;593	ENSP00000451848:K593N;ENSP00000420090:K91N;ENSP00000416561:K91N;ENSP00000410815:K593N	ENSP00000416561:K91N	K	+	3	2	CFB;XXbac-BPG116M5.17	32022337	0.996000	0.38824	0.185000	0.23176	0.104000	0.19210	2.751000	0.47508	0.598000	0.29829	-0.671000	0.03813	AAG		0.567	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		T	31914358	G	T	31914358	3	4	61	1	0	0	0	0	1	0	0	0	3284	933	33	2	279	2	CFB	6	31914358	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2367	31914358	139200709	4526	12511										
CFB	629	broad.mit.edu	37	chr6	31919009	31919009	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaaggaggtctacatcaaGaatggggataaggtgagaaa	15	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:31919009G>T	ENST00000425368.2	+	15	2457	c.1944G>T	c.(1942-1944)aaG>aaT	p.K648N	CFB_ENST00000556679.1_Missense_Mutation_p.K1150N|CFB_ENST00000477310.1_Missense_Mutation_p.K999N|CFB_ENST00000456570.1_Missense_Mutation_p.K1150N	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	648	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)	p.K648N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						TCTACATCAAGAATGGGGATA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	83	83					6																	31919009		1511	2709	4220	32026988	SO:0001583	missense	629			L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.1944G>T	6.37:g.31919009G>T	ENSP00000416561:p.Lys648Asn		32026988	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.60|18.60	3.659782|3.659782	0.67586|0.67586	.|.	.|.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000243649	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310|ENST00000483004	T;T;T;T|.	0.29917|.	1.55;1.55;1.55;1.55|.	5.53|5.53	4.66|4.66	0.58398|0.58398	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.000000|.	0.49305|.	D|.	0.000144|.	T|T	0.38585|0.38585	0.1046|0.1046	L|L	0.35288|0.35288	1.05|1.05	0.51482|0.51482	D|D	0.999926|0.999926	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.30031|0.30031	-0.9992|-0.9992	10|5	0.72032|.	D|.	0.01|.	-30.1475|-30.1475	11.505|11.505	0.50461|0.50461	0.0843:0.0:0.9157:0.0|0.0843:0.0:0.9157:0.0	.|.	1150;648|.	B4E1Z4;P00751|.	.;CFAB_HUMAN|.	N|I	1150;648;1150;999|189	ENSP00000451848:K1150N;ENSP00000416561:K648N;ENSP00000410815:K1150N;ENSP00000418996:K999N|.	ENSP00000416561:K648N|.	K|R	+|+	3|2	2|0	CFB;XXbac-BPG116M5.17|CFB	32026988|32026988	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.891000|0.891000	0.51852|0.51852	0.828000|0.828000	0.27435|0.27435	1.339000|1.339000	0.45563|0.45563	-0.218000|-0.218000	0.12543|0.12543	AAG|AGA		0.502	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		T	31919009	G	T	31919009	3	4	61	1	0	0	0	0	1	0	0	0	3284	933	33	2	2002	2	CFB	6	31919009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4651	31919009	139196058	4527	12512										
TNXB	7148	broad.mit.edu	37	chr6	32015689	32015689	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactggaccacgaaggagtcGaattcgccctcagggaccgt	12	12	1	0	rs146798373	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32015689G>A	ENST00000375244.3	-	30	10347	c.10146C>T	c.(10144-10146)ttC>ttT	p.F3382F	TNXB_ENST00000375247.2_Silent_p.F3380F|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3427	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.F3447F(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGAAGGAGTCGAATTCGCCCT	0.652													G|||	2	0.000399361	8e-04	0	5008	,	,		19561	0.001		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	6											46	56	53					6																	32015689		1466	2666	4132	32123667	SO:0001819	synonymous_variant	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10146C>T	6.37:g.32015689G>A			32123667	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																					0.652	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32015689	G	A	32015689	2	1	61	1	0	0	0	0	0	0	0	1	16385	1049	37	1		1	TNXB	6	32015689	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96680	32015689	139099378	4528	12513										
TNXB	7148	broad.mit.edu	37	chr6	32037419	32037419	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtgggcagggtccaggCccggcacgctgacctccctg	14	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32037419C>G	ENST00000375244.3	-	15	5699	c.5498G>C	c.(5497-5499)gGc>gCc	p.G1833A	TNXB_ENST00000375247.2_Missense_Mutation_p.G1833A			P22105	TENX_HUMAN	tenascin XB	1915	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.G1920A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGGGTCCAGGCCCGGCACGCT	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	6											23	29	27					6																	32037419		2173	4279	6452	32145397	SO:0001583	missense	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5498G>C	6.37:g.32037419C>G	ENSP00000364393:p.Gly1833Ala		32145397	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	13.90	2.376290	0.42105	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.07327	3.2;3.2	5.5	3.72	0.42706	.	0.446584	0.19087	N	0.123091	T	0.09247	0.0228	H	0.94847	3.59	0.21416	N	0.999697	P	0.48162	0.906	P	0.47134	0.539	T	0.35871	-0.9771	10	0.16896	T	0.51	.	7.5744	0.27926	0.0:0.7379:0.0:0.2621	.	1833	P22105-3	.	A	1833	ENSP00000364393:G1833A;ENSP00000364396:G1833A	ENSP00000364393:G1833A	G	-	2	0	TNXB	32145397	0.817000	0.29147	0.974000	0.42286	0.592000	0.36648	0.629000	0.24538	0.700000	0.31782	-0.218000	0.12543	GGC		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		G	32037419	C	G	32037419	3	3	61	1	0	0	0	0	1	0	0	0	16385	739	26	5	9335	5	TNXB	6	32037419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21730	32037419	139077648	4529	12514										
FKBPL	63943	broad.mit.edu	37	chr6	32096866	32096866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagcccgtccatagcatCgggcagctccttcagggttc	12	13	1	1	rs368026293		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32096866C>T	ENST00000375156.3	-	2	962	c.692G>A	c.(691-693)cGa>cAa	p.R231Q	ATF6B_ENST00000375201.4_5'Flank|ATF6B_ENST00000468502.1_5'Flank|ATF6B_ENST00000375203.3_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	231					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R231Q(1)									TCCATAGCATCGGGCAGCTCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	GLN/ARG	0,4406		0,0,2203	66	72	70		692	4.4	1	6		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	FKBPL	NM_022110.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	231/350	32096866	1,13005	2203	4300	6503	32204844	SO:0001583	missense	63943			AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"Tetratricopeptide (TTC) repeat domain containing"	13949	protein-coding gene	gene with protein product	"WAF-1/CIP1 stabilizing protein 39"		"FK506-binding protein like"			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.692G>A	6.37:g.32096866C>T	ENSP00000364298:p.Arg231Gln		32204844	A8K5V3|B0UYX8|Q9H5G3	Missense_Mutation	SNP	ENST00000375156.3	37	CCDS4738.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600807	0.66332	0.0	1.16E-4	ENSG00000204315	ENST00000375156	T	0.58940	0.3	5.24	4.38	0.52667	Tetratricopeptide-like helical (1);	0.787900	0.10933	N	0.618171	T	0.25306	0.0615	N	0.21142	0.635	0.33192	D	0.551022	P	0.40180	0.705	B	0.38954	0.286	T	0.01839	-1.1263	10	0.16896	T	0.51	-4.454	11.7339	0.51755	0.0:0.9152:0.0:0.0848	.	231	Q9UIM3	FKBPL_HUMAN	Q	231	ENSP00000364298:R231Q	ENSP00000364298:R231Q	R	-	2	0	FKBPL	32204844	0.913000	0.31002	1.000000	0.80357	0.949000	0.60115	1.952000	0.40343	1.444000	0.47605	0.561000	0.74099	CGA		0.587	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2			T	32096866	C	T	32096866	3	4	61	1	0	0	0	0	1	0	0	0	5935	884	31	1	361	1	FKBPL	6	32096866	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59447	32096866	139018201	4530	12515										
PPT2	9374	broad.mit.edu	37	chr6	32130687	32130687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagcctggcactccaaccGtaccctttatgagacctgca	7	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32130687G>A	ENST00000324816.6	+	9	1437	c.869G>A	c.(868-870)cGt>cAt	p.R290H	EGFL8_ENST00000333845.6_5'Flank|EGFL8_ENST00000395512.1_5'Flank|PPT2-EGFL8_ENST00000453656.2_Intron|PPT2_ENST00000437001.2_Intron|PPT2_ENST00000395523.1_Missense_Mutation_p.R290H|PPT2_ENST00000375137.2_Missense_Mutation_p.R290H|PPT2-EGFL8_ENST00000422437.1_Intron|PPT2_ENST00000445576.2_Intron|PPT2_ENST00000361568.2_Missense_Mutation_p.R296H|PPT2_ENST00000375143.2_Missense_Mutation_p.R290H			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	290					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)	p.R296H(1)		NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CACTCCAACCGTACCCTTTAT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	150	146					6																	32130687		2203	4300	6503	32238665	SO:0001583	missense	9374			AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.869G>A	6.37:g.32130687G>A	ENSP00000320528:p.Arg290His		32238665	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	37	CCDS4742.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.646223	0.47258	.	.	ENSG00000221988	ENST00000361568;ENST00000395523;ENST00000324816;ENST00000375137;ENST00000375143	D;D;D;D;D	0.91686	-2.89;-2.88;-2.88;-2.88;-2.88	5.63	2.79	0.32731	.	0.354936	0.30260	N	0.010040	T	0.62998	0.2474	N	0.02539	-0.55	0.80722	D	1	B;B	0.19706	0.038;0.038	B;B	0.06405	0.002;0.002	T	0.56739	-0.7929	10	0.37606	T	0.19	-7.5675	6.5205	0.22272	0.0844:0.0:0.5831:0.3325	.	290;296	Q9UMR5;B0S872	PPT2_HUMAN;.	H	296;290;290;290;290	ENSP00000354608:R296H;ENSP00000378894:R290H;ENSP00000320528:R290H;ENSP00000364279:R290H;ENSP00000364285:R290H	ENSP00000320528:R290H	R	+	2	0	PPT2	32238665	0.791000	0.28800	0.957000	0.39632	0.983000	0.72400	1.338000	0.33873	0.281000	0.22233	0.655000	0.94253	CGT		0.552	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		A	32130687	G	A	32130687	3	1	61	1	0	0	0	0	1	0	0	0	12446	1145	40	1	921	1	PPT2	6	32130687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33821	32130687	138984380	4531	12516										
NOTCH4	4855	broad.mit.edu	37	chr6	32166818	32166818	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctccatgctctcggcgtcGacgccggatgagctggagga	15	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32166818G>A	ENST00000375023.3	-	24	4558	c.4420C>T	c.(4420-4422)Cga>Tga	p.R1474*	NOTCH4_ENST00000443903.2_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1474	Poly-Arg.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.R1474*(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCTCGGCGTCGACGCCGGATG	0.682																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											48	60	56					6																	32166818		1508	2707	4215	32274796	SO:0001587	stop_gained	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4420C>T	6.37:g.32166818G>A	ENSP00000364163:p.Arg1474*		32274796	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Nonsense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	42	9.476191	0.99181	.	.	ENSG00000204301	ENST00000375023	.	.	.	4.9	1.85	0.25348	.	0.000000	0.38492	N	0.001677	.	.	.	.	.	.	0.45183	D	0.998194	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0752	0.53638	0.0:0.0:0.5468:0.4531	.	.	.	.	X	1474	.	ENSP00000364163:R1474X	R	-	1	2	NOTCH4	32274796	0.979000	0.34478	0.018000	0.16275	0.231000	0.25187	2.953000	0.49105	0.725000	0.32318	0.555000	0.69702	CGA		0.682	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32166818	G	A	32166818	4	1	61	1	0	0	0	0	0	1	0	0	10582	1066	37	1	1619	1	NOTCH4	6	32166818	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36131	32166818	138948249	4532	12517										
NOTCH4	4855	broad.mit.edu	37	chr6	32183113	32183113	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggtccttacatatctgCttgggctggcacaggttggg	13	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32183113C>T	ENST00000375023.3	-	12	2049	c.1911G>A	c.(1909-1911)aaG>aaA	p.K637K	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	637	EGF-like 16. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.K637K(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TACATATCTGCTTGGGCTGGC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	6											99	70	80					6																	32183113		1511	2709	4220	32291091	SO:0001819	synonymous_variant	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1911G>A	6.37:g.32183113C>T			32291091	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																				0.577	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32183113	C	T	32183113	2	4	61	1	0	0	0	0	0	0	0	1	10582	796	28	3		3	NOTCH4	6	32183113	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16295	32183113	138931954	4533	12518										
NOTCH4	4855	broad.mit.edu	37	chr6	32184750	32184750	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaggggcagaggcaaaaGaaggctcctggaagatcaag	15	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32184750G>T	ENST00000375023.3	-	11	1971	c.1833C>A	c.(1831-1833)ttC>ttA	p.F611L	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	611	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.F611L(2)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						AGAGGCAAAAGAAGGCTCCTG	0.537																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	6											102	85	91					6																	32184750		1511	2709	4220	32292728	SO:0001583	missense	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1833C>A	6.37:g.32184750G>T	ENSP00000364163:p.Phe611Leu		32292728	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167467	0.78339	.	.	ENSG00000204301	ENST00000375023	D	0.93488	-3.23	4.07	3.18	0.36537	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.42548	D	0.000688	D	0.95884	0.8660	M	0.88241	2.94	0.80722	D	1	D;D	0.62365	0.99;0.991	D;D	0.83275	0.996;0.928	D	0.95755	0.8795	10	0.72032	D	0.01	.	10.0793	0.42379	0.1024:0.0:0.8976:0.0	.	611;611	Q6P3V5;Q99466	.;NOTC4_HUMAN	L	611	ENSP00000364163:F611L	ENSP00000364163:F611L	F	-	3	2	NOTCH4	32292728	0.996000	0.38824	0.445000	0.26908	0.992000	0.81027	3.465000	0.53064	1.018000	0.39521	0.563000	0.77884	TTC		0.537	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32184750	G	T	32184750	3	4	61	1	0	0	0	0	1	0	0	0	10582	933	33	2	4258	2	NOTCH4	6	32184750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1637	32184750	138930317	4534	12519										
C6orf10	10665	broad.mit.edu	37	chr6	32260813	32260813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgccttcgcccttttcGagccttttgatttttcacca	5	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32260813G>A	ENST00000447241.2	-	23	1809	c.1637C>T	c.(1636-1638)tCg>tTg	p.S546L	C6orf10_ENST00000375007.4_Missense_Mutation_p.S544L|C6orf10_ENST00000375015.4_Missense_Mutation_p.S545L|C6orf10_ENST00000533191.1_Missense_Mutation_p.S544L|C6orf10_ENST00000442822.2_Intron|C6orf10_ENST00000527965.1_Missense_Mutation_p.S530L	NM_006781.3	NP_006772.3	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	546	Lys-rich.					integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.S546L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						CGCCCTTTTCGAGCCTTTTGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											122	131	128					6																	32260813		1511	2709	4220	32368791	SO:0001583	missense	10665			U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296			13922	protein-coding gene	gene with protein product	"testis specific basic protein"					10803852	Standard	XM_005248810		Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000447241.2:c.1637C>T	6.37:g.32260813G>A	ENSP00000415517:p.Ser546Leu		32368791	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	Missense_Mutation	SNP	ENST00000447241.2	37	CCDS34422.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.726286	0.30593	.	.	ENSG00000204296	ENST00000447241;ENST00000375015;ENST00000533191;ENST00000527965;ENST00000375007;ENST00000375002;ENST00000305725	T;T;T;T;T	0.03717	3.84;3.84;3.83;3.84;3.84	3.44	1.06	0.20224	.	.	.	.	.	T	0.03305	0.0096	L	0.47716	1.5	0.09310	N	1	D	0.71674	0.998	D	0.72982	0.979	T	0.40664	-0.9551	9	0.32370	T	0.25	.	3.9093	0.09196	0.1856:0.0:0.3124:0.502	.	546	Q5SRN2	CF010_HUMAN	L	546;545;544;530;544;543;543	ENSP00000415517:S546L;ENSP00000364155:S545L;ENSP00000431199:S544L;ENSP00000435103:S530L;ENSP00000364146:S544L	ENSP00000303292:S543L	S	-	2	0	C6orf10	32368791	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.992000	0.29667	0.216000	0.20781	-0.262000	0.10625	TCG		0.333	C6orf10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076178.4	NM_006781		A	32260813	G	A	32260813	3	1	61	1	0	0	0	0	1	0	0	0	2323	1059	37	1	58	1	C6orf10	6	32260813	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76063	32260813	138854254	4535	12520										
C6orf10	10665	broad.mit.edu	37	chr6	32317571	32317571	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaaagaagaatgagttCtgtttgtcccagggagaact	10	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32317571C>A	ENST00000447241.2	-	9	467	c.295G>T	c.(295-297)Gaa>Taa	p.E99*	C6orf10_ENST00000375007.4_Nonsense_Mutation_p.E97*|C6orf10_ENST00000375015.4_Intron|C6orf10_ENST00000533191.1_Intron|C6orf10_ENST00000442822.2_Intron|C6orf10_ENST00000527965.1_Intron	NM_006781.3	NP_006772.3	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	99						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.E99*(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						AGAATGAGTTCTGTTTGTCCC	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											159	153	155					6																	32317571		1511	2709	4220	32425549	SO:0001587	stop_gained	10665			U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296			13922	protein-coding gene	gene with protein product	"testis specific basic protein"					10803852	Standard	XM_005248810		Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000447241.2:c.295G>T	6.37:g.32317571C>A	ENSP00000415517:p.Glu99*		32425549	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	Nonsense_Mutation	SNP	ENST00000447241.2	37	CCDS34422.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780899	0.70222	.	.	ENSG00000204296	ENST00000447241;ENST00000375007;ENST00000534588	.	.	.	3.65	-2.65	0.06095	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4774	0.11750	0.0:0.2509:0.3212:0.4279	.	.	.	.	X	99;97;99	.	.	E	-	1	0	C6orf10	32425549	0.000000	0.05858	0.000000	0.03702	0.460000	0.32559	-0.776000	0.04674	-0.659000	0.05359	-0.182000	0.12963	GAA		0.368	C6orf10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076178.4	NM_006781		A	32317571	C	A	32317571	4	1	61	1	0	0	0	0	0	1	0	0	2323	922	32	2	1160	2	C6orf10	6	32317571	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56758	32317571	138797496	4536	12521										
BTNL2	56244	broad.mit.edu	37	chr6	32364160	32364160	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtccattcacttttaaaGaagctgttaaatagagtgga	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32364160G>T	ENST00000374993.1	-	5	733	c.734C>A	c.(733-735)tCt>tAt	p.S245Y	BTNL2_ENST00000374995.3_Missense_Mutation_p.S151Y|BTNL2_ENST00000414363.1_Missense_Mutation_p.S35Y|BTNL2_ENST00000429232.2_Missense_Mutation_p.S152Y|BTNL2_ENST00000544175.1_5'UTR|BTNL2_ENST00000540315.1_Missense_Mutation_p.S35Y|BTNL2_ENST00000454136.3_Missense_Mutation_p.S245Y|HCG23_ENST00000426643.1_RNA	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	245	Ig-like V-type 3.					integral component of membrane (GO:0016021)		p.S245Y(1)		central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CACTTTTAAAGAAGCTGTTAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	6											40	41	41					6																	32364160		1510	2708	4218	32472138	SO:0001583	missense	56244			AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.734C>A	6.37:g.32364160G>T	ENSP00000364132:p.Ser245Tyr		32472138	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		.	.	.	.	.	.	.	.	.	.	g	9.240	1.038089	0.19669	.	.	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000429232	T;T;T;T;T	0.10192	4.09;4.23;3.68;4.25;2.9	5.16	-0.193	0.13244	Immunoglobulin-like (1);	0.149392	0.31884	N	0.006905	T	0.11623	0.0283	M	0.75264	2.295	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.961;0.982	T	0.06391	-1.0829	10	0.59425	D	0.04	.	2.5114	0.04658	0.2395:0.1221:0.5013:0.1371	.	35;245	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	Y	245;151;35;245;35;152	ENSP00000364134:S151Y;ENSP00000390512:S35Y;ENSP00000364132:S245Y;ENSP00000444714:S35Y;ENSP00000411166:S152Y	ENSP00000364132:S245Y	S	-	2	0	BTNL2	32472138	0.272000	0.24172	0.147000	0.22382	0.081000	0.17604	1.477000	0.35431	0.096000	0.17463	-0.878000	0.02970	TCT		0.428	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		T	32364160	G	T	32364160	3	4	61	1	0	0	0	0	1	0	0	0	1568	942	33	2	641	2	BTNL2	6	32364160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46589	32364160	138750907	4537	12522										
HLA-DRA	3122	broad.mit.edu	37	chr6	32411076	32411076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcaatgtcacgtggcttcGaaatggaaaacctgtcacca	10	10	3	0	rs138462914		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32411076G>A	ENST00000374982.5	+	3	441	c.368G>A	c.(367-369)cGa>cAa	p.R123Q	HLA-DRA_ENST00000395388.2_Missense_Mutation_p.R148Q			P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	148	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.R148Q(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						ACGTGGCTTCGAAATGGAAAA	0.527									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of				G|||	1	0.000199681	0	0	5008	,	,		21476	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	GLN/ARG	0,3022		0,0,1511	150	132	138		443	-6.2	0	6	dbSNP_134	138	1,5417		0,1,2708	yes	missense	HLA-DRA	NM_019111.4	43	0,1,4219	AA,AG,GG		0.0185,0.0,0.0118	benign	148/255	32411076	1,8439	1511	2709	4220	32519054	SO:0001583	missense	3122	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000374982.5:c.368G>A	6.37:g.32411076G>A	ENSP00000364121:p.Arg123Gln		32519054	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000374982.5	37		.	.	.	.	.	.	.	.	.	.	.	12.97	2.098481	0.37048	0.0	1.85E-4	ENSG00000204287	ENST00000395388;ENST00000374982	T;T	0.00626	6.13;6.13	5.59	-6.22	0.02058	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.686460	0.02872	N	0.131730	T	0.00468	0.0015	M	0.75150	2.29	0.09310	N	1	B;B	0.16166	0.016;0.009	B;B	0.21360	0.034;0.004	T	0.33548	-0.9864	10	0.48119	T	0.1	.	14.6496	0.68786	0.4293:0.0:0.5707:0.0	.	123;148	Q30118;P01903	.;DRA_HUMAN	Q	148;123	ENSP00000378786:R148Q;ENSP00000364121:R123Q	ENSP00000364121:R123Q	R	+	2	0	HLA-DRA	32519054	0.000000	0.05858	0.002000	0.10522	0.649000	0.38597	-0.189000	0.09629	-1.318000	0.02289	-1.006000	0.02489	CGA		0.527	HLA-DRA-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000076587.3	NM_019111		A	32411076	G	A	32411076	3	1	61	1	0	0	0	0	1	0	0	0	7228	1058	37	1	453	1	HLA-DRA	6	32411076	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46916	32411076	138703991	4538	12523										
HLA-DRB5	3127	broad.mit.edu	37	chr6	32487369	32487369	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accattcacagagcagaccaGgaggttgtggtgctgcaggg	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32487369G>T	ENST00000374975.3	-	3	492	c.430C>A	c.(430-432)Ctg>Atg	p.L144M		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5									p.L144M(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GAGCAGACCAGGAGGTTGTGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											38	45	43					6																	32487369		1910	4097	6007	32595347	SO:0001583	missense	3127				CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.430C>A	6.37:g.32487369G>T	ENSP00000364114:p.Leu144Met		32595347		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	16.28	3.079278	0.55753	.	.	ENSG00000198502	ENST00000374975	T	0.35236	1.32	4.69	3.82	0.43975	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.248014	0.34338	N	0.004042	T	0.61085	0.2319	H	0.97611	4.04	0.39383	D	0.966285	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;1.0	T	0.69383	-0.5160	10	0.87932	D	0	.	6.0755	0.19913	0.0958:0.0:0.7182:0.186	.	71;144	Q29973;Q30154	.;DRB5_HUMAN	M	144	ENSP00000364114:L144M	ENSP00000364114:L144M	L	-	1	2	HLA-DRB5	32595347	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.119000	0.31258	1.354000	0.45846	0.556000	0.70494	CTG		0.532	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		T	32487369	G	T	32487369	3	4	61	1	0	0	0	0	1	0	0	0	7230	991	35	2	386	2	HLA-DRB5	6	32487369	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76293	32487369	138627698	4539	12524										
HLA-DRB1	3123	broad.mit.edu	37	chr6	32549556	32549556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactcacagagcagaccaGgaggttgtggtgctgcaggg	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32549556G>T	ENST00000360004.5	-	3	535	c.430C>A	c.(430-432)Ctg>Atg	p.L144M		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	144	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)		p.L144M(1)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GAGCAGACCAGGAGGTTGTGG	0.522										Multiple Myeloma(14;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	6											100	121	114					6																	32549556		1511	2709	4220	32657534	SO:0001583	missense	3123			AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.430C>A	6.37:g.32549556G>T	ENSP00000353099:p.Leu144Met		32657534	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	15.80	2.939495	0.52972	.	.	ENSG00000196126	ENST00000360004	T	0.21361	2.01	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.248014	0.34338	N	0.004042	T	0.50000	0.1590	H	0.97682	4.055	0.38849	D	0.956237	D	0.89917	1.0	D	0.97110	1.0	T	0.64664	-0.6354	10	0.87932	D	0	.	9.1917	0.37204	0.0:0.0:0.7829:0.2171	.	144	P01911	2B1F_HUMAN	M	144	ENSP00000353099:L144M	ENSP00000353099:L144M	L	-	1	2	HLA-DRB1	32657534	0.999000	0.42202	1.000000	0.80357	0.984000	0.73092	1.020000	0.30027	1.883000	0.54544	0.453000	0.30009	CTG		0.522	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32549556	G	T	32549556	3	4	61	1	0	0	0	0	1	0	0	0	7229	991	35	2	386	2	HLA-DRB1	6	32549556	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62187	32549556	138565511	4540	12525										
HLA-DQA2	3118	broad.mit.edu	37	chr6	32713027	32713027	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatggagacgaggagttCtatgtggacctggagacgaa	15	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32713027C>A	ENST00000374940.3	+	2	276	c.174C>A	c.(172-174)ttC>ttA	p.F58L		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	58	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)	p.F58L(1)		endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	ACGAGGAGTTCTATGTGGACC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											188	181	184					6																	32713027		1511	2709	4220	32821005	SO:0001583	missense	3118				CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.174C>A	6.37:g.32713027C>A	ENSP00000364076:p.Phe58Leu		32821005	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	9.272	1.045915	0.19748	.	.	ENSG00000237541	ENST00000374940	T	0.01422	4.91	3.2	2.31	0.28768	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.285984	0.35555	U	0.003140	T	0.00967	0.0032	M	0.80508	2.5	0.28286	N	0.923772	B	0.27997	0.197	B	0.30251	0.113	T	0.38929	-0.9638	10	0.72032	D	0.01	.	6.2146	0.20648	0.0:0.8523:0.0:0.1477	.	58	P01906	DQA2_HUMAN	L	58	ENSP00000364076:F58L	ENSP00000364076:F58L	F	+	3	2	HLA-DQA2	32821005	0.724000	0.28038	0.638000	0.29380	0.007000	0.05969	0.082000	0.14847	0.655000	0.30866	0.390000	0.25778	TTC		0.488	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		A	32713027	C	A	32713027	3	1	61	1	0	0	0	0	1	0	0	0	7226	912	32	2	180	2	HLA-DQA2	6	32713027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163471	32713027	138402040	4541	12526										
TAP2	6891	broad.mit.edu	37	chr6	32798533	32798533	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatgtaggagaaaaccttCtctgcagctcccacgttgct	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32798533C>A	ENST00000452392.2	-	8	1496	c.1323G>T	c.(1321-1323)gaG>gaT	p.E441D	TAP2_ENST00000374899.4_Missense_Mutation_p.E441D|TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374897.2_Missense_Mutation_p.E441D			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.E441D(1)								Vitamin E(DB00163)	AGAAAACCTTCTCTGCAGCTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											63	51	55					6																	32798533		1511	2709	4220	32906511	SO:0001583	missense	6891			M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"ATP binding cassette transporters / subfamily B"	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1323G>T	6.37:g.32798533C>A	ENSP00000391806:p.Glu441Asp		32906511	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		.	.	.	.	.	.	.	.	.	.	C	11.76	1.733321	0.30684	.	.	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.82344	-1.6;-1.6;-1.6	5.58	3.79	0.43588	ABC transporter, transmembrane domain, type 1 (1);	0.762005	0.11178	N	0.591237	T	0.65407	0.2688	L	0.39326	1.205	0.24009	N	0.996181	P;P;P;P	0.51351	0.94;0.944;0.944;0.944	P;B;B;P	0.46110	0.497;0.367;0.367;0.504	T	0.52208	-0.8606	9	0.13853	T	0.58	-27.6708	11.3768	0.49733	0.0:0.791:0.1308:0.0782	.	441;442;441;441	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	D	441	ENSP00000364034:E441D;ENSP00000364032:E441D;ENSP00000391806:E441D	ENSP00000364032:E441D	E	-	3	2	XXbac-BPG246D15.9;TAP2	32906511	0.154000	0.22792	0.936000	0.37596	0.037000	0.13140	0.427000	0.21379	0.294000	0.22547	-0.836000	0.03065	GAG		0.517	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544		A	32798533	C	A	32798533	3	1	61	1	0	0	0	0	1	0	0	0	15590	912	32	2	842	2	TAP2	6	32798533	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85506	32798533	138316534	4542	12527										
TAP1	6890	broad.mit.edu	37	chr6	32815404	32815404	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccataggcaatattttCttgaagacttcttccaaata	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32815404C>A	ENST00000354258.4	-	9	2130	c.1969G>T	c.(1969-1971)Gaa>Taa	p.E657*	PSMB9_ENST00000395330.1_Intron|TAPSAR1_ENST00000453426.1_lincRNA|PSMB8_ENST00000374881.2_5'Flank|TAP1_ENST00000425148.2_Nonsense_Mutation_p.E396*	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	657	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.E657*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	GCAATATTTTCTTGAAGACTT	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											103	99	100					6																	32815404		2203	4300	6503	32923382	SO:0001587	stop_gained	6890				CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1969G>T	6.37:g.32815404C>A	ENSP00000346206:p.Glu657*		32923382	Q16149|Q96CP4	Nonsense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	C	42	9.367215	0.99150	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	.	.	.	5.72	5.72	0.89469	.	0.000000	0.51477	D	0.000083	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-10.315	15.3873	0.74711	0.0:1.0:0.0:0.0	.	.	.	.	X	657;396	.	ENSP00000346206:E657X	E	-	1	0	TAP1	32923382	0.995000	0.38212	0.964000	0.40570	0.973000	0.67179	3.384000	0.52478	2.706000	0.92434	0.643000	0.83706	GAA		0.473	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		A	32815404	C	A	32815404	4	1	61	1	0	0	0	0	0	1	0	0	15589	922	32	2	469	2	TAP1	6	32815404	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16871	32815404	138299663	4543	12528										
TAP1	6890	broad.mit.edu	37	chr6	32818213	32818213	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctcgttggcaaagcttcGaactgtaggcatggccgaca	11	12	0	0	rs143800384		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32818213G>A	ENST00000354258.4	-	5	1473	c.1312C>T	c.(1312-1314)Cga>Tga	p.R438*	PSMB9_ENST00000395330.1_Intron|TAP1_ENST00000425148.2_Nonsense_Mutation_p.R177*	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	438	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Involved in peptide-binding site.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.R438*(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	GCAAAGCTTCGAACTGTAGGC	0.532													G|||	1	0.000199681	0	0	5008	,	,		20485	0		0	False		,,,				2504	0.001															2	Substitution - Nonsense(2)	large_intestine(2)	6	GRCh37	CM066242	TAP1	M	rs143800384	G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	88	91	90		1312	3.7	1	6	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained	TAP1	NM_000593.5		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		438/809	32818213	3,13003	2203	4300	6503	32926191	SO:0001587	stop_gained	6890				CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1312C>T	6.37:g.32818213G>A	ENSP00000346206:p.Arg438*		32926191	Q16149|Q96CP4	Nonsense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	G	40	8.369631	0.98781	2.27E-4	2.33E-4	ENSG00000168394	ENST00000354258;ENST00000425148	.	.	.	5.72	3.73	0.42828	.	0.329018	0.21658	N	0.071066	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.5546	12.5898	0.56437	0.0:0.0:0.6139:0.3861	.	.	.	.	X	438;177	.	ENSP00000346206:R438X	R	-	1	2	TAP1	32926191	1.000000	0.71417	0.959000	0.39883	0.901000	0.52897	3.935000	0.56560	1.401000	0.46761	0.643000	0.83706	CGA		0.532	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		A	32818213	G	A	32818213	4	1	61	1	0	0	0	0	0	1	0	0	15589	1066	37	1	1142	1	TAP1	6	32818213	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2809	32818213	138296854	4544	12529										
TAP1	6890	broad.mit.edu	37	chr6	32819981	32819981	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacgtggcccatggtgttgTtatagatcccgtcacccacg	11	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32819981T>G	ENST00000354258.4	-	3	1090	c.929A>C	c.(928-930)aAc>aCc	p.N310T	PSMB9_ENST00000374859.2_5'Flank|PSMB9_ENST00000395330.1_Intron|PSMB9_ENST00000453265.2_5'Flank|TAP1_ENST00000425148.2_Missense_Mutation_p.N49T	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	310	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.N310T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CATGGTGTTGTTATAGATCCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											102	90	94					6																	32819981		1510	2709	4219	32927959	SO:0001583	missense	6890				CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.929A>C	6.37:g.32819981T>G	ENSP00000346206:p.Asn310Thr		32927959	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	T	5.364	0.252400	0.10185	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.88664	-2.41;-2.41	4.88	4.88	0.63580	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	.	.	.	.	T	0.80560	0.4646	L	0.40543	1.245	0.48288	D	0.99962	P	0.34815	0.47	P	0.44623	0.455	T	0.77975	-0.2385	9	0.11485	T	0.65	-6.4503	12.502	0.55960	0.0:0.0:0.0:1.0	.	310	Q03518	TAP1_HUMAN	T	310;49	ENSP00000346206:N310T;ENSP00000401919:N49T	ENSP00000346206:N310T	N	-	2	0	TAP1	32927959	0.998000	0.40836	0.982000	0.44146	0.090000	0.18270	2.931000	0.48932	2.037000	0.60232	0.450000	0.29827	AAC		0.542	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		G	32819981	T	G	32819981	3	3	61	1	0	0	0	0	1	0	0	0	15589	1725	60	4	1533	4	TAP1	6	32819981	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1768	32819981	138295086	4545	12530										
HLA-DMB	3109	broad.mit.edu	37	chr6	32906624	32906624	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcaaggggccatcttattCtcctctggatcccagcaggt	10	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32906624C>A	ENST00000418107.2	-	2	436	c.174G>T	c.(172-174)gaG>gaT	p.E58D	AL645941.1_ENST00000390777.1_RNA|HLA-DMB_ENST00000416244.2_Missense_Mutation_p.E58D|XXbac-BPG181M17.5_ENST00000429234.1_Missense_Mutation_p.E90D	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	58	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|MHC class II protein complex assembly (GO:0002399)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001190)|positive regulation of T cell proliferation (GO:0042102)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)	p.E58D(1)		breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						CCATCTTATTCTCCTCTGGAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	121	119					6																	32906624		1511	2709	4220	33014602	SO:0001583	missense	3109				CCDS4760.1	6p21.3	2014-05-16			ENSG00000242574	ENSG00000242574		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4935	protein-coding gene	gene with protein product		142856				1922365	Standard	NM_002118		Approved	D6S221E, RING7	uc003ocl.2	P28068	OTTHUMG00000031176	ENST00000418107.2:c.174G>T	6.37:g.32906624C>A	ENSP00000398890:p.Glu58Asp		33014602	O77936|Q13012|Q29751|Q58ZE2|Q5SNZ8|Q5STC4|Q9XRX2	Missense_Mutation	SNP	ENST00000418107.2	37	CCDS4760.1	.	.	.	.	.	.	.	.	.	.	C	6.257	0.415447	0.11870	.	.	ENSG00000242574;ENSG00000242574;ENSG00000242574;ENSG00000248993	ENST00000446948;ENST00000418107;ENST00000416244;ENST00000429234	T;T;T	0.00342	8.03;8.03;8.03	5.07	2.07	0.26955	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	1.410940	0.04511	N	0.382938	T	0.00073	0.0002	L	0.60455	1.87	0.09310	N	1	B;B;P	0.34587	0.029;0.039;0.458	B;B;B	0.29077	0.032;0.024;0.098	T	0.21518	-1.0243	9	.	.	.	.	4.0491	0.09786	0.1966:0.6054:0.0:0.1979	.	58;58;67	E9PD01;P28068;Q59F83	.;DMB_HUMAN;.	D	58;58;58;90	ENSP00000398890:E58D;ENSP00000391010:E58D;ENSP00000412457:E90D	.	E	-	3	2	XXbac-BPG181M17.5;HLA-DMB	33014602	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	0.070000	0.14573	0.718000	0.32166	0.637000	0.83480	GAG		0.512	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	NM_002118		A	32906624	C	A	32906624	3	1	61	1	0	0	0	0	1	0	0	0	7220	912	32	2	637	2	HLA-DMB	6	32906624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86643	32906624	138208443	4546	12531										
BRD2	6046	broad.mit.edu	37	chr6	32948370	32948370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgcagcgaatgagaaaAcagagtcatcctctgcacag	10	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32948370A>G	ENST00000374825.4	+	13	3982	c.2281A>G	c.(2281-2283)Aca>Gca	p.T761A	BRD2_ENST00000443797.2_Missense_Mutation_p.T641A|BRD2_ENST00000449085.2_Missense_Mutation_p.T714A|BRD2_ENST00000395287.1_Missense_Mutation_p.T796A|BRD2_ENST00000374831.4_Missense_Mutation_p.T761A|BRD2_ENST00000395289.2_Missense_Mutation_p.T796A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	761					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)	p.T796A(1)		central_nervous_system(3)|stomach(2)	5						GAATGAGAAAACAGAGTCATC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											90	81	85					6																	32948370		1511	2709	4220	33056348	SO:0001583	missense	6046			X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2281A>G	6.37:g.32948370A>G	ENSP00000363958:p.Thr761Ala		33056348	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	37	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	A	7.568	0.666043	0.14710	.	.	ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25	6.01	3.66	0.41972	.	0.273019	0.26620	N	0.023378	T	0.01523	0.0049	N	0.04959	-0.14	0.29613	N	0.846807	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46679	-0.9174	10	0.05959	T	0.93	-9.9294	5.2418	0.15475	0.6818:0.0:0.3182:0.0	.	796;761	A2AAU0;P25440	.;BRD2_HUMAN	A	761;761;796;641;796;714	ENSP00000363958:T761A;ENSP00000363964:T761A;ENSP00000378704:T796A;ENSP00000413495:T641A;ENSP00000378702:T796A;ENSP00000409145:T714A	ENSP00000363958:T761A	T	+	1	0	BRD2	33056348	0.998000	0.40836	0.994000	0.49952	0.973000	0.67179	1.721000	0.38032	1.088000	0.41272	0.523000	0.50628	ACA		0.463	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32948370	A	G	32948370	3	3	61	1	0	0	0	0	1	0	0	0	1505	43	2	4	2327	4	BRD2	6	32948370	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	41746	32948370	138166697	4547	12532										
HLA-DOA	3111	broad.mit.edu	37	chr6	32975122	32975122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggcgcatccaggccccaGtgctccacctggcagtcata	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:32975122G>T	ENST00000229829.5	-	3	654	c.579C>A	c.(577-579)caC>caA	p.H193Q	HLA-DOA_ENST00000450833.2_Missense_Mutation_p.H163Q|HLA-DOA_ENST00000495532.1_5'Flank	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	193	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)	p.H193Q(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						CCAGGCCCCAGTGCTCCACCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	113	108					6																	32975122		1511	2709	4220	33083100	SO:0001583	missense	3111			M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.579C>A	6.37:g.32975122G>T	ENSP00000229829:p.His193Gln		33083100	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Missense_Mutation	SNP	ENST00000229829.5	37	CCDS4763.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016058	0.75161	.	.	ENSG00000204252	ENST00000229829;ENST00000450833	T;T	0.06142	3.34;3.34	4.51	4.51	0.55191	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.35537	0.0935	H	0.98996	4.395	0.46678	D	0.999152	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.60647	-0.7222	10	0.87932	D	0	.	15.1456	0.72647	0.0:0.0:1.0:0.0	.	163;193	B4DW77;P06340	.;DOA_HUMAN	Q	193;163	ENSP00000229829:H193Q;ENSP00000403896:H163Q	ENSP00000229829:H193Q	H	-	3	2	HLA-DOA	33083100	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.191000	0.58372	2.501000	0.84356	0.650000	0.86243	CAC		0.587	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119		T	32975122	G	T	32975122	3	4	61	1	0	0	0	0	1	0	0	0	7221	1020	36	2	185	2	HLA-DOA	6	32975122	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26752	32975122	138139945	4548	12533										
HLA-DPB1	3115	broad.mit.edu	37	chr6	33048540	33048540	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctacaaccgggaggagttCgcgcgcttcgacagcgacgt	13	12	1	0	rs41555415		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33048540C>T	ENST00000418931.2	+	2	308	c.192C>T	c.(190-192)ttC>ttT	p.F64F	HLA-DPB1_ENST00000535465.1_Silent_p.F64F|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	64	Beta-1.		F -> L (in allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*15:02, allele DPB1*17:02, allele DPB1*19:02, allele DPB1*21:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*34:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*44:01, allele DPB1*48:01, allele DPB1*58:01, allele DPB1*62:01, allele DPB1*63:01, allele DPB1*95:01 and allele DPB1*97:01; dbSNP:rs9277348).|F -> Y (in allele DPB1*01:01, allele DPB1*01:02, allele DPB1*09:02, allele DPB1*11:01, allele DPB1*13:01, allele DPB1*15:01, allele DPB1*20:02, allele DPB1*21:02, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*39:01, allele DPB1*40:01, allele DPB1*49:01, allele DPB1*53:01, allele DPB1*65:01, allele DPB1*74:01, allele DPB1*85:01, allele DPB1*89:01 and allele DPB1*96:01; dbSNP:rs1042117).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.F64F(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGGAGGAGTTCGCGCGCTTCG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	6											69	69	69					6																	33048540		1511	2709	4220	33156518	SO:0001819	synonymous_variant	3115				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.192C>T	6.37:g.33048540C>T			33156518	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	.	.	.	.	.	.	.	.	.	.	C	0.788	-0.760016	0.03019	.	.	ENSG00000223865	ENST00000416804	.	.	.	3.94	1.15	0.20763	.	.	.	.	.	T	0.09949	0.0244	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.30794	-0.9966	4	.	.	.	.	4.4029	0.11395	0.0:0.4218:0.3666:0.2116	rs41555415	.	.	.	L	31	.	.	S	+	2	0	HLA-DPB1	33156518	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	0.264000	0.18497	0.451000	0.26802	-0.134000	0.14843	TCG		0.607	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		T	33048540	C	T	33048540	2	4	61	1	0	0	0	0	0	0	0	1	7224	883	31	1		1	HLA-DPB1	6	33048540	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73418	33048540	138066527	4549	12534										
HSD17B8	7923	broad.mit.edu	37	chr6	33173617	33173617	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccacagacatgggatccgCtgtaactctgtcctcccagg	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33173617C>A	ENST00000374662.3	+	6	606	c.579C>A	c.(577-579)cgC>cgA	p.R193R	MIR219-1_ENST00000362166.1_RNA|HSD17B8_ENST00000469186.1_3'UTR|RING1_ENST00000374656.4_5'Flank	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	193				R -> P (in Ref. 5; BAA11529). {ECO:0000305}.	androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.R193R(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						ATGGGATCCGCTGTAACTCTG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											123	125	124					6																	33173617		1509	2708	4217	33281595	SO:0001819	synonymous_variant	7923			D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	3554	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 30C, member 1"	601417	"FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.579C>A	6.37:g.33173617C>A			33281595	A6NLX7|Q5STP7|Q9UIQ1	Silent	SNP	ENST00000374662.3	37	CCDS4769.1																																																																																				0.582	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234		A	33173617	C	A	33173617	2	1	61	1	0	0	0	0	0	0	0	1	7410	784	28	2		2	HSD17B8	6	33173617	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125077	33173617	137941450	4550	12535										
VPS52	6293	broad.mit.edu	37	chr6	33237315	33237315	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttgtgtagagatgctatAttctcactctcttgaatatc	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33237315A>G	ENST00000445902.2	-	5	542	c.324T>C	c.(322-324)aaT>aaC	p.N108N	RPS18_ENST00000439602.2_5'Flank|RPS18_ENST00000474973.1_5'Flank|VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000436044.2_5'UTR|VPS52_ENST00000478934.1_5'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	108					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.N108N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GAGATGCTATATTCTCACTCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6											133	127	129					6																	33237315		1511	2709	4220	33345293	SO:0001819	synonymous_variant	6293			AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"SAC2 suppressor of actin mutations 2-like (yeast)", "vacuolar protein sorting 52 (yeast)"	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.324T>C	6.37:g.33237315A>G			33345293	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																				0.443	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		G	33237315	A	G	33237315	2	3	61	1	0	0	0	0	0	0	0	1	17254	446	16	4		4	VPS52	6	33237315	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	63698	33237315	137877752	4551	12536										
WDR46	9277	broad.mit.edu	37	chr6	33255438	33255438	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatctcgcacataagcttCtttgttacccaatcaagggc	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33255438C>A	ENST00000374617.4	-	7	1037	c.681G>T	c.(679-681)aaG>aaT	p.K227N	PFDN6_ENST00000374606.5_5'Flank|WDR46_ENST00000477718.1_5'UTR|PFDN6_ENST00000463584.1_5'Flank|PFDN6_ENST00000395131.1_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000374610.2_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	227							poly(A) RNA binding (GO:0044822)	p.K227N(1)		NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						ACATAAGCTTCTTTGTTACCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	76	79					6																	33255438		2203	4300	6503	33363416	SO:0001583	missense	9277			Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"WD repeat domain containing"	13923	protein-coding gene	gene with protein product		611440	"chromosome 6 open reading frame 11"	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.681G>T	6.37:g.33255438C>A	ENSP00000363746:p.Lys227Asn		33363416	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	37	CCDS4772.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.538144	0.65085	.	.	ENSG00000227057	ENST00000374617;ENST00000444176	T;T	0.16597	5.05;2.33	4.56	1.62	0.23740	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.22781	0.0550	M	0.78223	2.4	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	0.972;1.0	T	0.04825	-1.0924	10	0.27082	T	0.32	-25.4543	7.6767	0.28490	0.0:0.6854:0.0:0.3146	.	173;227	B4DP15;O15213	.;WDR46_HUMAN	N	227;154	ENSP00000363746:K227N;ENSP00000405568:K154N	ENSP00000363746:K227N	K	-	3	2	WDR46	33363416	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	1.219000	0.32479	0.486000	0.27676	0.549000	0.68633	AAG		0.582	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452		A	33255438	C	A	33255438	3	1	61	1	0	0	0	0	1	0	0	0	17339	912	32	2	1187	2	WDR46	6	33255438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18123	33255438	137859629	4552	12537										
WDR46	9277	broad.mit.edu	37	chr6	33255751	33255751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaccttaccttccagttCgagagtagtttagtctgtag	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33255751C>T	ENST00000374617.4	-	6	970	c.614G>A	c.(613-615)cGa>cAa	p.R205Q	PFDN6_ENST00000374606.5_5'Flank|WDR46_ENST00000477718.1_5'UTR|PFDN6_ENST00000463584.1_5'Flank|PFDN6_ENST00000395131.1_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000374610.2_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	205							poly(A) RNA binding (GO:0044822)	p.R205Q(1)		NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						CCTTCCAGTTCGAGAGTAGTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											189	196	193					6																	33255751		2203	4300	6503	33363729	SO:0001583	missense	9277			Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"WD repeat domain containing"	13923	protein-coding gene	gene with protein product		611440	"chromosome 6 open reading frame 11"	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.614G>A	6.37:g.33255751C>T	ENSP00000363746:p.Arg205Gln		33363729	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	37	CCDS4772.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.576537	0.45902	.	.	ENSG00000227057	ENST00000374617;ENST00000444176	T;T	0.16897	5.03;2.31	4.76	2.97	0.34412	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.250259	0.37669	N	0.001987	T	0.09291	0.0229	M	0.81682	2.555	0.37099	D	0.899788	B;B	0.28026	0.198;0.122	B;B	0.19946	0.018;0.027	T	0.02519	-1.1147	10	0.44086	T	0.13	-0.8314	8.1852	0.31335	0.0:0.7524:0.1591:0.0885	.	151;205	B4DP15;O15213	.;WDR46_HUMAN	Q	205;132	ENSP00000363746:R205Q;ENSP00000405568:R132Q	ENSP00000363746:R205Q	R	-	2	0	WDR46	33363729	0.823000	0.29233	0.996000	0.52242	0.927000	0.56198	1.360000	0.34125	0.601000	0.29879	0.549000	0.68633	CGA		0.448	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452		T	33255751	C	T	33255751	3	4	61	1	0	0	0	0	1	0	0	0	17339	884	31	1	1258	1	WDR46	6	33255751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	313	33255751	137859316	4553	12538										
SYNGAP1	8831	broad.mit.edu	37	chr6	33405452	33405452	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaccatgccaggacaacaGccgccgggtagacaatgtgc	11	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33405452G>T	ENST00000418600.2	+	8	871	c.770G>T	c.(769-771)aGc>aTc	p.S257I	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.S198I|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.S257I	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	257	C2.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.S257I(1)|p.S242I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CAGGACAACAGCCGCCGGGTA	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	6											166	185	179					6																	33405452		2203	4300	6503	33513430	SO:0001583	missense	8831			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.770G>T	6.37:g.33405452G>T	ENSP00000403636:p.Ser257Ile		33513430	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	18.21	3.573050	0.65765	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.93247	-3.19;-3.19;-3.19	4.51	4.51	0.55191	SynGAP C2 domain, N-terminal (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.95214	0.8448	M	0.67953	2.075	0.58432	D	0.999998	D;D;B	0.76494	0.998;0.999;0.077	D;D;B	0.83275	0.991;0.996;0.053	D	0.94897	0.8053	10	0.49607	T	0.09	.	14.7891	0.69827	0.0:0.0:1.0:0.0	.	257;257;257	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	I	257;257;257;198	ENSP00000293748:S257I;ENSP00000403636:S257I;ENSP00000412475:S198I	ENSP00000293748:S257I	S	+	2	0	SYNGAP1	33513430	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.660000	0.83776	2.341000	0.79615	0.655000	0.94253	AGC		0.552	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33405452	G	T	33405452	3	4	61	1	0	0	0	0	1	0	0	0	15486	971	34	2	800	2	SYNGAP1	6	33405452	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149701	33405452	137709615	4554	12539										
SYNGAP1	8831	broad.mit.edu	37	chr6	33405818	33405818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatctgggggcatgggttCgggagggggagggggctcgg	26	5	1	0	rs371883908		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33405818C>T	ENST00000418600.2	+	8	1237	c.1136C>T	c.(1135-1137)tCg>tTg	p.S379L	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.S320L|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.S379L	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	379					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.S364L(1)|p.S379L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGCATGGGTTCGGGAGGGGGA	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	6						C	LEU/SER	0,4096		0,0,2048	9	12	11		1136	4.4	0.8	6		11	1,7985		0,1,3992	no	missense	SYNGAP1	NM_006772.2	145	0,1,6040	TT,TC,CC		0.0125,0.0,0.0083	possibly-damaging	379/1344	33405818	1,12081	2048	3993	6041	33513796	SO:0001583	missense	8831			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1136C>T	6.37:g.33405818C>T	ENSP00000403636:p.Ser379Leu		33513796	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	12.93	2.084260	0.36758	0.0	1.25E-4	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.89681	-2.55;-2.55;-2.55	4.4	4.4	0.53042	.	0.000000	0.32430	U	0.006107	D	0.84606	0.5509	L	0.29908	0.895	0.42590	D	0.993247	B;B;B;D	0.69078	0.015;0.009;0.026;0.997	B;B;B;P	0.54590	0.002;0.005;0.005;0.756	D	0.87237	0.2264	10	0.72032	D	0.01	.	12.3364	0.55069	0.0:1.0:0.0:0.0	.	379;379;379;379	Q96PV0;Q96PV0-2;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.;.	L	379;379;379;320	ENSP00000293748:S379L;ENSP00000403636:S379L;ENSP00000412475:S320L	ENSP00000293748:S379L	S	+	2	0	SYNGAP1	33513796	.	.	0.830000	0.32933	0.532000	0.34746	.	.	2.251000	0.74343	0.650000	0.86243	TCG		0.652	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33405818	C	T	33405818	3	4	61	1	0	0	0	0	1	0	0	0	15486	893	31	1	1166	1	SYNGAP1	6	33405818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366	33405818	137709249	4555	12540										
SYNGAP1	8831	broad.mit.edu	37	chr6	33411044	33411044	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacggcggctggcatgcgCctcagccagatgggtgtcac	14	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33411044C>A	ENST00000418600.2	+	15	2816	c.2715C>A	c.(2713-2715)cgC>cgA	p.R905R	SYNGAP1_ENST00000428982.2_Silent_p.R846R|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.R905R	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	905					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.R905R(1)|p.R890R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CTGGCATGCGCCTCAGCCAGA	0.662																																																2	Substitution - coding silent(2)	large_intestine(2)	6											70	68	69					6																	33411044		2203	4300	6503	33519022	SO:0001819	synonymous_variant	8831			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.2715C>A	6.37:g.33411044C>A			33519022	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																				0.662	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33411044	C	A	33411044	2	1	61	1	0	0	0	0	0	0	0	1	15486	726	26	2		2	SYNGAP1	6	33411044	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5226	33411044	137704023	4556	12541										
C6orf125	84300	broad.mit.edu	37	chr6	33669152	33669152	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtagtttgaatggagtcGcgctaagctctcgtacatct	11	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33669152G>A	ENST00000607484.1	-	2	224	c.184C>T	c.(184-186)Cga>Tga	p.R62*	UQCC2_ENST00000374214.3_Intron	NM_032340.3	NP_115716.1	Q9BRT2	UQCC2_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 2	62					regulation of insulin secretion (GO:0050796)|regulation of oxidative phosphorylation (GO:0002082)|regulation of skeletal muscle cell differentiation (GO:2001014)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R62*(1)									GAATGGAGTCGCGCTAAGCTC	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											178	166	170					6																	33669152		2203	4300	6503	33777130	SO:0001587	stop_gained	84300				CCDS4784.1	6p21.31	2013-09-20	2013-09-20	2013-09-20	ENSG00000137288	ENSG00000137288		"Mitochondrial respiratory chain complex assembly factors"	21237	protein-coding gene	gene with protein product	"cytochrome B protein synthesis 6 homolog (S. cerevisiae)"	614461	"chromosome 6 open reading frame 125", "mitochondrial nucleoid factor 1"	C6orf125, MNF1		19643811	Standard	NM_032340		Approved	MGC14833, bA6B20.2, M19, Cbp6	uc003ofa.2	Q9BRT2	OTTHUMG00000014534	ENST00000607484.1:c.184C>T	6.37:g.33669152G>A	ENSP00000476140:p.Arg62*		33777130	B2R4I0	Nonsense_Mutation	SNP	ENST00000607484.1	37	CCDS4784.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637385	0.87760	.	.	ENSG00000137288	ENST00000374231	.	.	.	6.02	3.09	0.35607	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9392	0.70980	0.0:0.0:0.3467:0.6532	.	.	.	.	X	62	.	ENSP00000363348:R62X	R	-	1	2	C6orf125	33777130	1.000000	0.71417	0.952000	0.39060	0.931000	0.56810	0.902000	0.28459	0.310000	0.22990	-0.169000	0.13324	CGA		0.473	UQCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040207.2	NM_032340		A	33669152	G	A	33669152	4	1	61	1	0	0	0	0	0	1	0	0	2331	1095	38	1	208	1	C6orf125	6	33669152	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	258108	33669152	137445915	4557	12542										
IP6K3	117283	broad.mit.edu	37	chr6	33690771	33690771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagagagctggaatagaagCggtatgaactctggctccta	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:33690771C>T	ENST00000293756.4	-	6	1285	c.959G>A	c.(958-960)cGc>cAc	p.R320H	IP6K3_ENST00000451316.1_Missense_Mutation_p.R320H	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	320					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.R320H(1)		skin(1)	1						GGAATAGAAGCGGTATGAACT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	64	63					6																	33690771		2203	4300	6503	33798749	SO:0001583	missense	117283			AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.959G>A	6.37:g.33690771C>T	ENSP00000293756:p.Arg320His		33798749	Q96MQ9	Missense_Mutation	SNP	ENST00000293756.4	37	CCDS34435.1	.	.	.	.	.	.	.	.	.	.	C	34	5.359293	0.95854	.	.	ENSG00000161896	ENST00000451316;ENST00000293756	T;T	0.16324	2.35;2.35	5.99	5.99	0.97316	.	0.176453	0.40469	N	0.001089	T	0.39517	0.1081	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.07888	-1.0749	10	0.51188	T	0.08	-46.5309	20.0728	0.97731	0.0:1.0:0.0:0.0	.	320	Q96PC2	IP6K3_HUMAN	H	320	ENSP00000398861:R320H;ENSP00000293756:R320H	ENSP00000293756:R320H	R	-	2	0	IP6K3	33798749	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.840000	0.97914	0.655000	0.94253	CGC		0.597	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		T	33690771	C	T	33690771	3	4	61	1	0	0	0	0	1	0	0	0	7811	768	27	1	277	1	IP6K3	6	33690771	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21619	33690771	137424296	4558	12543										
SNRPC	6631	broad.mit.edu	37	chr6	34730475	34730475	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcagagcctgattgacaAaacaagtatgtttcaatctc	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:34730475A>C	ENST00000244520.5	+	3	293	c.155A>C	c.(154-156)aAa>aCa	p.K52T	SNRPC_ENST00000474635.1_3'UTR|SNRPC_ENST00000374018.1_Missense_Mutation_p.K11T|SNRPC_ENST00000374017.3_Missense_Mutation_p.K73T	NM_003093.2	NP_003084.1			small nuclear ribonucleoprotein polypeptide C									p.K52T(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	6						CTGATTGACAAAACAAGTATG	0.403																																					NSCLC(131;576 1831 5287 11175 13324)											1	Substitution - Missense(1)	large_intestine(1)	6											79	69	72					6																	34730475		2203	4300	6503	34838453	SO:0001583	missense	6631				CCDS34436.1	6p21	2014-03-06			ENSG00000124562	ENSG00000124562			11157	protein-coding gene	gene with protein product		603522				2971157, 8532530	Standard	NR_029472		Approved	U1-C, Yhc1	uc003ojt.2	P09234	OTTHUMG00000014555	ENST00000244520.5:c.155A>C	6.37:g.34730475A>C	ENSP00000244520:p.Lys52Thr		34838453		Missense_Mutation	SNP	ENST00000244520.5	37	CCDS34436.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.788947	0.90367	.	.	ENSG00000124562	ENST00000244520;ENST00000374018;ENST00000374017	T;T;T	0.32023	1.47;1.47;1.47	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.26919	0.0659	M	0.69823	2.125	0.80722	D	1	P	0.48998	0.918	B	0.43701	0.428	T	0.04373	-1.0956	10	0.32370	T	0.25	.	16.4837	0.84171	1.0:0.0:0.0:0.0	.	52	P09234	RU1C_HUMAN	T	52;11;73	ENSP00000244520:K52T;ENSP00000363130:K11T;ENSP00000363129:K73T	ENSP00000244520:K52T	K	+	2	0	SNRPC	34838453	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.818000	0.91991	2.371000	0.80710	0.533000	0.62120	AAA		0.403	SNRPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040255.1	NM_003093		C	34730475	A	C	34730475	3	2	61	1	0	0	0	0	1	0	0	0	14900	14	1	4	165	4	SNRPC	6	34730475	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1039704	34730475	136384592	4559	12544										
UHRF1BP1	54887	broad.mit.edu	37	chr6	34802535	34802535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataacttggcaaacactccGaattgaggcagatgctacag	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:34802535G>A	ENST00000192788.5	+	6	737	c.566G>A	c.(565-567)cGa>cAa	p.R189Q	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.R189Q	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	189							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.R189Q(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CAAACACTCCGAATTGAGGCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	6											140	138	139					6																	34802535		1918	4130	6048	34910513	SO:0001583	missense	54887			AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.566G>A	6.37:g.34802535G>A	ENSP00000192788:p.Arg189Gln		34910513	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	G	31	5.104064	0.94245	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.12984	2.63;2.63	4.56	3.69	0.42338	.	0.000000	0.64402	D	0.000002	T	0.28863	0.0716	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.16808	-1.0390	10	0.87932	D	0	-2.5876	12.5072	0.55987	0.0807:0.0:0.9193:0.0	.	189	Q6BDS2	URFB1_HUMAN	Q	189	ENSP00000192788:R189Q;ENSP00000400628:R189Q	ENSP00000192788:R189Q	R	+	2	0	UHRF1BP1	34910513	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	9.593000	0.98250	1.151000	0.42436	0.655000	0.94253	CGA		0.418	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		A	34802535	G	A	34802535	3	1	61	1	0	0	0	0	1	0	0	0	17008	1058	37	1	588	1	UHRF1BP1	6	34802535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72060	34802535	136312532	4560	12545										
UHRF1BP1	54887	broad.mit.edu	37	chr6	34838694	34838694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccagctgtgggccttcGctttgaggtggggcctggag	18	10	0	1	rs76166303	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:34838694G>A	ENST00000192788.5	+	18	3953	c.3782G>A	c.(3781-3783)cGc>cAc	p.R1261H	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.R1261H	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1261							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.R1261H(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GTGGGCCTTCGCTTTGAGGTG	0.502													G|||	4	0.000798722	0.003	0	5008	,	,		19991	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	HIS/ARG	8,3864		0,8,1928	71	71	71		3782	5.3	1	6	dbSNP_131	71	0,8296		0,0,4148	yes	missense	UHRF1BP1	NM_017754.3	29	0,8,6076	AA,AG,GG		0.0,0.2066,0.0657	probably-damaging	1261/1441	34838694	8,12160	1936	4148	6084	34946672	SO:0001583	missense	54887			AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.3782G>A	6.37:g.34838694G>A	ENSP00000192788:p.Arg1261His		34946672	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	33	5.251664	0.95305	0.002066	0.0	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.18810	2.19;2.21	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.41143	0.1146	M	0.71036	2.16	0.48040	D	0.999571	D	0.89917	1.0	D	0.87578	0.998	T	0.38908	-0.9639	10	0.87932	D	0	-14.0054	18.9033	0.92452	0.0:0.0:1.0:0.0	.	1261	Q6BDS2	URFB1_HUMAN	H	1261	ENSP00000192788:R1261H;ENSP00000400628:R1261H	ENSP00000192788:R1261H	R	+	2	0	UHRF1BP1	34946672	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.304000	0.59104	2.427000	0.82271	0.655000	0.94253	CGC		0.502	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		A	34838694	G	A	34838694	3	1	61	1	0	0	0	0	1	0	0	0	17008	1087	38	1	3852	1	UHRF1BP1	6	34838694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36159	34838694	136276373	4561	12546										
ZNF76	7629	broad.mit.edu	37	chr6	35255511	35255511	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtggctgtgccatcggaGagcaccatcctggccgtaca	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35255511G>T	ENST00000373953.3	+	5	587	c.321G>T	c.(319-321)gaG>gaT	p.E107D	ZNF76_ENST00000440666.2_Missense_Mutation_p.E81D|ZNF76_ENST00000339411.5_Missense_Mutation_p.E107D	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	107					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E107D(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						TGCCATCGGAGAGCACCATCC	0.607																																					Esophageal Squamous(52;92 1039 20612 23956 34676)											1	Substitution - Missense(1)	large_intestine(1)	6											109	93	98					6																	35255511		2203	4300	6503	35363489	SO:0001583	missense	7629			M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.321G>T	6.37:g.35255511G>T	ENSP00000363064:p.Glu107Asp		35363489	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.326832	0.00017	.	.	ENSG00000065029	ENST00000469195;ENST00000448999;ENST00000373953;ENST00000417184;ENST00000440666;ENST00000339411	T;T;T;T	0.09350	2.99;3.01;3.01;3.03	5.17	-2.42	0.06542	.	0.485962	0.17210	N	0.182756	T	0.00936	0.0031	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40098	-0.9581	10	0.08837	T	0.75	.	9.0388	0.36305	0.0:0.4465:0.2599:0.2935	.	107;107;107;107	B7Z851;B7Z991;P36508-2;P36508	.;.;.;ZNF76_HUMAN	D	107;107;107;107;81;107	ENSP00000419106:E107D;ENSP00000363064:E107D;ENSP00000392243:E81D;ENSP00000344097:E107D	ENSP00000229405:E107D	E	+	3	2	ZNF76	35363489	0.414000	0.25408	0.000000	0.03702	0.000000	0.00434	-0.001000	0.12947	-1.012000	0.03387	-4.439000	0.00006	GAG		0.607	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35255511	G	T	35255511	3	4	61	1	0	0	0	0	1	0	0	0	18174	933	33	2	335	2	ZNF76	6	35255511	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	416817	35255511	135859556	4562	12547										
ZNF76	7629	broad.mit.edu	37	chr6	35259412	35259412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatccgcaaggtacatgtgCgcacccacacaggcgagagg	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35259412C>T	ENST00000373953.3	+	9	1095	c.829C>T	c.(829-831)Cgc>Tgc	p.R277C	ZNF76_ENST00000440666.2_Missense_Mutation_p.R251C|ZNF76_ENST00000339411.5_Missense_Mutation_p.R277C	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	277					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R277C(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						GGTACATGTGCGCACCCACAC	0.602																																					Esophageal Squamous(52;92 1039 20612 23956 34676)											1	Substitution - Missense(1)	large_intestine(1)	6											84	73	77					6																	35259412		2203	4300	6503	35367390	SO:0001583	missense	7629			M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.829C>T	6.37:g.35259412C>T	ENSP00000363064:p.Arg277Cys		35367390	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	C	33	5.252317	0.95336	.	.	ENSG00000065029	ENST00000469195;ENST00000448999;ENST00000373953;ENST00000417184;ENST00000440666;ENST00000339411	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.1	5.1	0.69264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000339	T	0.51753	0.1693	M	0.87827	2.91	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.59941	-0.7359	10	0.87932	D	0	.	17.7212	0.88351	0.0:1.0:0.0:0.0	.	277;277;277	B7Z851;P36508-2;P36508	.;.;ZNF76_HUMAN	C	277;277;277;277;251;277	ENSP00000419106:R277C;ENSP00000363064:R277C;ENSP00000392243:R251C;ENSP00000344097:R277C	ENSP00000344097:R277C	R	+	1	0	ZNF76	35367390	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.827000	0.69300	2.652000	0.90054	0.655000	0.94253	CGC		0.602	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35259412	C	T	35259412	3	4	61	1	0	0	0	0	1	0	0	0	18174	768	27	1	859	1	ZNF76	6	35259412	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3901	35259412	135855655	4563	12548										
RPL10A	4736	broad.mit.edu	37	chr6	35438370	35438370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccaggtgttatgtctggCtgtagctgttggtcacgtga	13	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35438370C>T	ENST00000322203.6	+	6	524	c.497C>T	c.(496-498)gCt>gTt	p.A166V	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	166					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A166V(1)		breast(1)|large_intestine(2)|ovary(1)	4						TTATGTCTGGCTGTAGCTGTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											166	154	158					6																	35438370		2203	4300	6503	35546348	SO:0001583	missense	4736			U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.497C>T	6.37:g.35438370C>T	ENSP00000363018:p.Ala166Val		35546348	B2R801|P52859|P53025|Q5TZT6|Q8J013	Missense_Mutation	SNP	ENST00000322203.6	37	CCDS4806.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.223273	0.79464	.	.	ENSG00000198755	ENST00000322203	T	0.44881	0.91	4.67	4.67	0.58626	Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.47525	0.1450	M	0.86420	2.815	0.80722	D	1	P	0.39576	0.679	B	0.43990	0.438	T	0.60875	-0.7176	10	0.87932	D	0	.	16.1695	0.81793	0.0:1.0:0.0:0.0	.	166	P62906	RL10A_HUMAN	V	166	ENSP00000363018:A166V	ENSP00000363018:A166V	A	+	2	0	RPL10A	35546348	1.000000	0.71417	0.983000	0.44433	0.713000	0.41058	7.683000	0.84093	2.139000	0.66308	0.561000	0.74099	GCT		0.517	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		T	35438370	C	T	35438370	3	4	61	1	0	0	0	0	1	0	0	0	13592	797	28	3	519	3	RPL10A	6	35438370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178958	35438370	135676697	4564	12549										
FKBP5	2289	broad.mit.edu	37	chr6	35587936	35587936	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagagttgcattcgagggAattttagggagactgccagc	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35587936A>C	ENST00000539068.1	-	4	568	c.366T>G	c.(364-366)atT>atG	p.I122M	FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Missense_Mutation_p.I122M|FKBP5_ENST00000357266.4_Missense_Mutation_p.I122M|FKBP5_ENST00000536438.1_Missense_Mutation_p.I122M	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	122	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.I122M(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						CATTCGAGGGAATTTTAGGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											138	118	125					6																	35587936		2203	4300	6503	35695914	SO:0001583	missense	2289			U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"Tetratricopeptide (TTC) repeat domain containing"	3721	protein-coding gene	gene with protein product		602623	"FK506-binding protein 5"			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.366T>G	6.37:g.35587936A>C	ENSP00000441205:p.Ile122Met		35695914	F5H7R1|Q59EB8|Q5TGM6	Missense_Mutation	SNP	ENST00000539068.1	37	CCDS4808.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093365	0.76756	.	.	ENSG00000096060	ENST00000536438;ENST00000357266;ENST00000539068;ENST00000337746;ENST00000543400;ENST00000542713;ENST00000373875	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.75	-0.396	0.12427	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.058128	0.64402	D	0.000003	T	0.80874	0.4707	H	0.98487	4.245	0.47441	D	0.999424	D;D	0.89917	1.0;0.971	D;P	0.85130	0.997;0.856	D	0.83586	0.0120	10	0.87932	D	0	-6.2849	10.5262	0.44950	0.3835:0.0:0.6165:0.0	.	122;122	F5H7R1;Q13451	.;FKBP5_HUMAN	M	122;122;122;122;85;122;120	ENSP00000444810:I122M;ENSP00000349811:I122M;ENSP00000441205:I122M;ENSP00000442340:I122M	ENSP00000338160:I122M	I	-	3	3	FKBP5	35695914	0.999000	0.42202	0.997000	0.53966	0.994000	0.84299	0.652000	0.24888	-0.070000	0.12908	0.528000	0.53228	ATT		0.463	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			C	35587936	A	C	35587936	3	2	61	1	0	0	0	0	1	0	0	0	5930	242	9	4	1097	4	FKBP5	6	35587936	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	149566	35587936	135527131	4565	12550										
C6orf127	340204	broad.mit.edu	37	chr6	35755728	35755728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagaaatggcttagcatcGcctatggccgttgtcagaaa	11	8	1	2	rs201001742		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35755728G>A	ENST00000373861.5	+	3	401	c.307G>A	c.(307-309)Gcc>Acc	p.A103T	CLPSL1_ENST00000542261.1_Missense_Mutation_p.A102T			A2RUU4	COLL1_HUMAN	colipase-like 1	103					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)	p.A103T(1)									GCTTAGCATCGCCTATGGCCG	0.488													G|||	1	0.000199681	0	0.0014	5008	,	,		26916	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											169	169	169					6																	35755728		2026	4197	6223	35863706	SO:0001583	missense	340204				CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 127"	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.307G>A	6.37:g.35755728G>A	ENSP00000362968:p.Ala103Thr		35863706	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Missense_Mutation	SNP	ENST00000373861.5	37	CCDS43456.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.566951	0.00895	.	.	ENSG00000204140	ENST00000373861;ENST00000373860;ENST00000542261	T;T	0.31510	1.49;1.49	2.69	-0.0658	0.13767	.	1.242570	0.06409	U	0.720168	T	0.03959	0.0111	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.39522	-0.9610	10	0.18276	T	0.48	.	4.6867	0.12760	0.6908:0.0:0.3092:0.0	.	103	A2RUU4	CF127_HUMAN	T	103;103;102	ENSP00000362968:A103T;ENSP00000438478:A102T	ENSP00000362967:A103T	A	+	1	0	C6orf127	35863706	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	0.045000	0.15804	-0.423000	0.05987	GCC		0.488	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886		A	35755728	G	A	35755728	3	1	61	1	0	0	0	0	1	0	0	0	2333	1087	38	1	317	1	C6orf127	6	35755728	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167792	35755728	135359339	4566	12551										
CLPS	1208	broad.mit.edu	37	chr6	35765035	35765035	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcataggccacagagagggCgacaagcaggaggatcagga	16	8	1	1	rs529464575		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35765035C>T	ENST00000259938.2	-	1	53	c.31G>A	c.(31-33)Gcc>Acc	p.A11T		NM_001832.3	NP_001823.1	P04118	COL_HUMAN	colipase, pancreatic	11					lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme activator activity (GO:0008047)	p.A11T(1)		large_intestine(2)|lung(2)|prostate(1)	5						ACAGAGAGGGCGACAAGCAGG	0.602													C|||	1	0.000199681	0	0	5008	,	,		27577	0.001		0	False		,,,				2504	0				Melanoma(167;2962 3494 37796)											1	Substitution - Missense(1)	large_intestine(1)	6											119	106	111					6																	35765035		2203	4300	6503	35873013	SO:0001583	missense	1208				CCDS4811.1, CCDS75437.1, CCDS75438.1	6p21.31	2012-02-06			ENSG00000137392	ENSG00000137392			2085	protein-coding gene	gene with protein product		120105				2045105	Standard	NM_001832		Approved		uc003ole.2	P04118	OTTHUMG00000014578	ENST00000259938.2:c.31G>A	6.37:g.35765035C>T	ENSP00000259938:p.Ala11Thr		35873013	Q5T9G7|Q5U809	Missense_Mutation	SNP	ENST00000259938.2	37	CCDS4811.1	.	.	.	.	.	.	.	.	.	.	C	3.218	-0.160092	0.06502	.	.	ENSG00000137392	ENST00000259938;ENST00000541088	T	0.28454	1.61	4.92	-0.933	0.10431	.	0.990985	0.08205	N	0.981612	T	0.04003	0.0112	N	0.13098	0.295	0.09310	N	1	B;B	0.17667	0.021;0.023	B;B	0.08055	0.002;0.003	T	0.41963	-0.9479	10	0.14252	T	0.57	-12.623	3.582	0.07957	0.3158:0.2414:0.0:0.4427	.	11;11	G3V1M8;P04118	.;COL_HUMAN	T	11	ENSP00000259938:A11T	ENSP00000259938:A11T	A	-	1	0	CLPS	35873013	0.000000	0.05858	0.009000	0.14445	0.179000	0.23085	-2.520000	0.00951	-0.033000	0.13736	0.655000	0.94253	GCC		0.602	CLPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040312.1	NM_001832		T	35765035	C	T	35765035	3	4	61	1	0	0	0	0	1	0	0	0	3559	768	27	1	319	1	CLPS	6	35765035	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9307	35765035	135350032	4567	12552										
LHFPL5	222662	broad.mit.edu	37	chr6	35773483	35773483	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggcccaggaggcagccaaGatctaccataccaactatgt	9	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35773483G>T	ENST00000373853.1	+	1	414	c.36G>T	c.(34-36)aaG>aaT	p.K12N	LHFPL5_ENST00000360215.1_Missense_Mutation_p.K12N			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	12					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)		p.K12N(1)		endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						AGGCAGCCAAGATCTACCATA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											110	98	102					6																	35773483		2203	4300	6503	35881461	SO:0001583	missense	222662			BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"deafness, autosomal recessive 67"	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.36G>T	6.37:g.35773483G>T	ENSP00000362960:p.Lys12Asn		35881461	B3KX66	Missense_Mutation	SNP	ENST00000373853.1	37	CCDS4812.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861737	0.51482	.	.	ENSG00000197753	ENST00000373853;ENST00000360215	T;T	0.78246	-1.16;-1.16	5.54	4.66	0.58398	.	0.147155	0.64402	D	0.000013	T	0.58061	0.2096	M	0.67397	2.05	0.39213	D	0.963352	B	0.32968	0.392	B	0.26770	0.073	T	0.64478	-0.6398	10	0.54805	T	0.06	-28.319	6.5667	0.22515	0.1843:0.1486:0.667:0.0	.	12	Q8TAF8	TMHS_HUMAN	N	12	ENSP00000362960:K12N;ENSP00000353346:K12N	ENSP00000353346:K12N	K	+	3	2	LHFPL5	35881461	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	3.122000	0.50446	1.300000	0.44818	0.542000	0.68232	AAG		0.612	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548		T	35773483	G	T	35773483	3	4	61	1	0	0	0	0	1	0	0	0	8791	933	33	2	38	2	LHFPL5	6	35773483	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8448	35773483	135341584	4568	12553										
SRPK1	6732	broad.mit.edu	37	chr6	35837432	35837432	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgttataggtgtacaaGagtctgtttcttgagatgtg	12	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35837432G>T	ENST00000373825.2	-	11	1523	c.1238C>A	c.(1237-1239)tCt>tAt	p.S413Y	SRPK1_ENST00000423325.2_Missense_Mutation_p.S397Y|SRPK1_ENST00000373822.1_Missense_Mutation_p.S306Y					SRSF protein kinase 1									p.S413Y(1)		endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						AGGTGTACAAGAGTCTGTTTC	0.418																																					NSCLC(31;67 978 16289 24856 26454)											1	Substitution - Missense(1)	large_intestine(1)	6											176	165	168					6																	35837432		1984	4157	6141	35945410	SO:0001583	missense	6732			U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"SR protein kinase 1", "serine/arginine-rich splicing factor kinase 1"	601939	"SFRS protein kinase 1"			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1238C>A	6.37:g.35837432G>T	ENSP00000362931:p.Ser413Tyr		35945410		Missense_Mutation	SNP	ENST00000373825.2	37	CCDS47415.1	.	.	.	.	.	.	.	.	.	.	G	5.337	0.247585	0.10130	.	.	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822	T;T;T;T	0.29917	1.56;1.55;1.55;1.61	5.66	5.66	0.87406	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.32466	0.0830	M	0.67700	2.07	0.38478	D	0.947655	P;P	0.44429	0.835;0.826	P;P	0.49561	0.615;0.467	T	0.04767	-1.0928	9	0.48119	T	0.1	-11.2859	13.563	0.61802	0.0739:0.0:0.9261:0.0	.	397;413	B4DS61;Q96SB4	.;SRPK1_HUMAN	Y	413;429;397;306	ENSP00000362931:S413Y;ENSP00000354674:S429Y;ENSP00000391069:S397Y;ENSP00000362928:S306Y	ENSP00000354674:S429Y	S	-	2	0	SRPK1	35945410	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.120000	0.41968	2.832000	0.97577	0.655000	0.94253	TCT		0.418	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137		T	35837432	G	T	35837432	3	4	61	1	0	0	0	0	1	0	0	0	15198	942	33	2	753	2	SRPK1	6	35837432	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63949	35837432	135277635	4569	12554										
SLC26A8	116369	broad.mit.edu	37	chr6	35965661	35965661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgggctcactttcagaaCgttgatcagcagagcactca	10	10	4	3	rs199595123		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:35965661C>T	ENST00000490799.1	-	5	834	c.481G>A	c.(481-483)Gtt>Att	p.V161I	SLC26A8_ENST00000355574.2_Missense_Mutation_p.V161I|SLC26A8_ENST00000394602.2_Missense_Mutation_p.V161I	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8									p.V161I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						ACTTTCAGAACGTTGATCAGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											122	108	113					6																	35965661		2203	4300	6503	36073639	SO:0001583	missense	116369			AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.481G>A	6.37:g.35965661C>T	ENSP00000417638:p.Val161Ile		36073639		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866742	0.32977	.	.	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	D;D;D	0.91996	-2.95;-2.95;-2.95	5.82	4.95	0.65309	.	0.200900	0.35013	N	0.003510	D	0.85388	0.5685	N	0.21373	0.66	0.32838	D	0.504994	B;D	0.55605	0.341;0.972	B;P	0.53224	0.031;0.721	D	0.85512	0.1198	10	0.46703	T	0.11	.	10.741	0.46154	0.0:0.9127:0.0:0.0873	.	161;161	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	I	161	ENSP00000417638:V161I;ENSP00000378100:V161I;ENSP00000347778:V161I	ENSP00000347778:V161I	V	-	1	0	SLC26A8	36073639	0.953000	0.32496	0.995000	0.50966	0.193000	0.23685	1.480000	0.35464	1.453000	0.47775	0.650000	0.86243	GTT		0.443	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			T	35965661	C	T	35965661	3	4	61	1	0	0	0	0	1	0	0	0	14560	536	19	1	2495	1	SLC26A8	6	35965661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128229	35965661	135149406	4570	12555										
BRPF3	27154	broad.mit.edu	37	chr6	36168316	36168316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taactgcccaggatatcaccGaatgcaatagtaacaaggaa	8	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:36168316G>A	ENST00000357641.6	+	2	470	c.217G>A	c.(217-219)Gaa>Aaa	p.E73K	BRPF3_ENST00000543502.1_Missense_Mutation_p.E73K|BRPF3_ENST00000534400.1_Missense_Mutation_p.E73K|BRPF3_ENST00000443324.2_Missense_Mutation_p.E73K|BRPF3_ENST00000534694.1_Missense_Mutation_p.E73K|BRPF3_ENST00000339717.7_Missense_Mutation_p.E73K	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	73					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)	p.E73K(1)		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						GGATATCACCGAATGCAATAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	90	92					6																	36168316		2203	4300	6503	36276294	SO:0001583	missense	27154			AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.217G>A	6.37:g.36168316G>A	ENSP00000350267:p.Glu73Lys		36276294	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	37	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169648	0.57584	.	.	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000534694;ENST00000446974;ENST00000454960;ENST00000543502;ENST00000443324;ENST00000534400	T;T;T;T;T;T;T;T	0.50001	0.87;0.87;0.87;0.76;0.87;0.87;0.87;0.87	5.43	5.43	0.79202	Enhancer of polycomb-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62962	0.2471	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.995;0.995;0.996	T	0.62599	-0.6820	10	0.49607	T	0.09	.	19.3065	0.94164	0.0:0.0:1.0:0.0	.	73;73;73	B7ZLN5;Q17RB6;Q9ULD4	.;.;BRPF3_HUMAN	K	73	ENSP00000350267:E73K;ENSP00000345419:E73K;ENSP00000434501:E73K;ENSP00000410669:E73K;ENSP00000413655:E73K;ENSP00000445352:E73K;ENSP00000387368:E73K;ENSP00000436504:E73K	ENSP00000345419:E73K	E	+	1	0	BRPF3	36276294	1.000000	0.71417	0.972000	0.41901	0.993000	0.82548	9.411000	0.97342	2.563000	0.86464	0.551000	0.68910	GAA		0.463	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		A	36168316	G	A	36168316	3	1	61	1	0	0	0	0	1	0	0	0	1524	1059	37	1	219	1	BRPF3	6	36168316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202655	36168316	134946751	4571	12556										
BRPF3	27154	broad.mit.edu	37	chr6	36182072	36182072	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcctctccagccagcatCgaggaagagcgccactcccg	10	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:36182072C>T	ENST00000357641.6	+	8	3151	c.2898C>T	c.(2896-2898)atC>atT	p.I966I	BRPF3_ENST00000543502.1_Intron|BRPF3_ENST00000534400.1_Silent_p.I966I|BRPF3_ENST00000443324.2_Intron|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000339717.7_Intron	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	966					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)	p.I966I(1)		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						CAGCCAGCATCGAGGAAGAGC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	6											35	41	39					6																	36182072		2201	4298	6499	36290050	SO:0001819	synonymous_variant	27154			AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.2898C>T	6.37:g.36182072C>T			36290050	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Silent	SNP	ENST00000357641.6	37	CCDS34437.1																																																																																				0.622	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		T	36182072	C	T	36182072	2	4	61	1	0	0	0	0	0	0	0	1	1524	874	31	1		1	BRPF3	6	36182072	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13756	36182072	134932995	4572	12557										
KCTD20	222658	broad.mit.edu	37	chr6	36447474	36447474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgacttcaacactatccGatgtcaagatctgagtaagt	7	8	3	3	rs182729907		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:36447474G>A	ENST00000373731.2	+	5	1035	c.644G>A	c.(643-645)cGa>cAa	p.R215Q	KCTD20_ENST00000536244.1_Missense_Mutation_p.R70Q|KCTD20_ENST00000544295.1_Intron|KCTD20_ENST00000474988.1_Intron|KCTD20_ENST00000449081.2_Intron	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	215					protein homooligomerization (GO:0051260)			p.R215Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						AACACTATCCGATGTCAAGAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	70	72					6																	36447474		2203	4300	6503	36555452	SO:0001583	missense	222658			BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.644G>A	6.37:g.36447474G>A	ENSP00000362836:p.Arg215Gln		36555452	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085069	0.55861	.	.	ENSG00000112078	ENST00000373731;ENST00000536244	T;T	0.81247	-1.47;-1.47	4.72	3.76	0.43208	BTB/POZ-like (1);BTB/POZ fold (2);	0.178769	0.34700	N	0.003742	T	0.48241	0.1489	L	0.31578	0.945	0.80722	D	1	P	0.42161	0.772	B	0.33392	0.163	T	0.58008	-0.7712	10	0.40728	T	0.16	-9.9284	3.8347	0.08889	0.3323:0.0:0.6677:0.0	.	215	Q7Z5Y7	KCD20_HUMAN	Q	215;70	ENSP00000362836:R215Q;ENSP00000439118:R70Q	ENSP00000362836:R215Q	R	+	2	0	KCTD20	36555452	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.204000	0.72143	2.448000	0.82819	0.591000	0.81541	CGA		0.378	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		A	36447474	G	A	36447474	3	1	61	1	0	0	0	0	1	0	0	0	8129	1058	37	1	658	1	KCTD20	6	36447474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	265402	36447474	134667593	4573	12558										
STK38	11329	broad.mit.edu	37	chr6	36493413	36493413	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcaccttttctaacttCttttgtctaaaacaaacaaa	1	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:36493413C>A	ENST00000229812.7	-	3	423	c.138G>T	c.(136-138)aaG>aaT	p.K46N		NM_007271.2	NP_009202.1			serine/threonine kinase 38									p.K46N(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTTCTAACTTCTTTTGTCTAA	0.313																																					Colon(180;997 3561 16158)											1	Substitution - Missense(1)	large_intestine(1)	6											203	172	182					6																	36493413		2202	4299	6501	36601391	SO:0001583	missense	11329				CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.138G>T	6.37:g.36493413C>A	ENSP00000229812:p.Lys46Asn		36601391		Missense_Mutation	SNP	ENST00000229812.7	37	CCDS4822.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193828	0.38707	.	.	ENSG00000112079	ENST00000229812	T	0.44482	0.92	5.69	5.69	0.88448	.	0.045886	0.85682	D	0.000000	T	0.22166	0.0534	L	0.35644	1.08	0.80722	D	1	B	0.32781	0.384	B	0.31337	0.128	T	0.05616	-1.0874	10	0.17369	T	0.5	.	19.8165	0.96571	0.0:1.0:0.0:0.0	.	46	Q15208	STK38_HUMAN	N	46	ENSP00000229812:K46N	ENSP00000229812:K46N	K	-	3	2	STK38	36601391	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.525000	0.60559	2.683000	0.91414	0.655000	0.94253	AAG		0.313	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		A	36493413	C	A	36493413	3	1	61	1	0	0	0	0	1	0	0	0	15342	912	32	2	1307	2	STK38	6	36493413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45939	36493413	134621654	4574	12559										
C6orf89	221477	broad.mit.edu	37	chr6	36887430	36887430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccctcccttccagtgccGaagacattgtcagtctgtgg	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:36887430G>A	ENST00000480824.2	+	8	1196	c.902G>A	c.(901-903)cGa>cAa	p.R301Q	C6orf89_ENST00000510325.2_Missense_Mutation_p.R195Q|C6orf89_ENST00000359359.2_Missense_Mutation_p.R195Q|C6orf89_ENST00000355190.3_Missense_Mutation_p.R308Q|C6orf89_ENST00000373685.1_Missense_Mutation_p.R301Q			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	301					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R308Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TTCCAGTGCCGAAGACATTGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											109	94	99					6																	36887430		2203	4300	6503	36995408	SO:0001583	missense	221477			AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"bombesin receptor activated protein"					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.902G>A	6.37:g.36887430G>A	ENSP00000475947:p.Arg301Gln		36995408	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000480824.2	37		.	.	.	.	.	.	.	.	.	.	G	21.9	4.219593	0.79464	.	.	ENSG00000198663	ENST00000359359;ENST00000510325;ENST00000355190;ENST00000373685	.	.	.	6.17	5.31	0.75309	.	0.207438	0.42682	N	0.000662	T	0.37972	0.1023	L	0.39397	1.21	0.42308	D	0.992208	D;D	0.67145	0.996;0.99	P;P	0.50537	0.643;0.525	T	0.25293	-1.0136	9	0.32370	T	0.25	0.1827	11.6356	0.51202	0.081:0.0:0.919:0.0	.	301;308	Q6UWU4;Q6UWU4-2	CF089_HUMAN;.	Q	195;195;308;301	.	ENSP00000347322:R308Q	R	+	2	0	C6orf89	36995408	0.997000	0.39634	1.000000	0.80357	0.759000	0.43091	0.985000	0.29578	1.630000	0.50440	0.655000	0.94253	CGA		0.512	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		A	36887430	G	A	36887430	3	1	61	1	0	0	0	0	1	0	0	0	2379	1058	37	1	949	1	C6orf89	6	36887430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	394017	36887430	134227637	4575	12560										
FTSJD2	23070	broad.mit.edu	37	chr6	37430662	37430662	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgttcgggattacctcttCgcagtgaatattaaactcaa	8	8	2	1	rs542774031		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:37430662C>T	ENST00000373451.4	+	13	1547	c.1383C>T	c.(1381-1383)ttC>ttT	p.F461F		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	461					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.F461F(1)									ATTACCTCTTCGCAGTGAATA	0.512													C|||	1	0.000199681	0	0	5008	,	,		21541	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	6											211	174	186					6																	37430662		2203	4300	6503	37538640	SO:0001819	synonymous_variant	23070			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1383C>T	6.37:g.37430662C>T			37538640	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																				0.512	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		T	37430662	C	T	37430662	2	4	61	1	0	0	0	0	0	0	0	1	6110	883	31	1		1	FTSJD2	6	37430662	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	543232	37430662	133684405	4576	12561										
FTSJD2	23070	broad.mit.edu	37	chr6	37443954	37443954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaagcctagtcggcccGacatgaatcccatcaggtga	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:37443954G>A	ENST00000373451.4	+	20	2253	c.2089G>A	c.(2089-2091)Gac>Aac	p.D697N		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	697					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.D697N(1)									TAGTCGGCCCGACATGAATCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	6											122	116	118					6																	37443954		2203	4300	6503	37551932	SO:0001583	missense	23070			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.2089G>A	6.37:g.37443954G>A	ENSP00000362550:p.Asp697Asn		37551932	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	37	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.508422	0.85282	.	.	ENSG00000137200	ENST00000373451;ENST00000373420;ENST00000452299	D	0.84516	-1.86	5.39	5.39	0.77823	.	0.082444	0.85682	D	0.000000	T	0.76535	0.4001	M	0.75264	2.295	0.80722	D	1	P	0.43938	0.822	B	0.23419	0.046	T	0.82378	-0.0487	10	0.52906	T	0.07	-14.88	17.8968	0.88891	0.0:0.0:1.0:0.0	.	697	Q8N1G2	MTR1_HUMAN	N	697;104;41	ENSP00000362550:D697N	ENSP00000362519:D104N	D	+	1	0	FTSJD2	37551932	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.285000	0.95894	2.812000	0.96745	0.555000	0.69702	GAC		0.547	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		A	37443954	G	A	37443954	3	1	61	1	0	0	0	0	1	0	0	0	6110	1058	37	1	2163	1	FTSJD2	6	37443954	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13292	37443954	133671113	4577	12562										
MDGA1	266727	broad.mit.edu	37	chr6	37619980	37619980	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcgtgccggcttgccattCttgaaccactggtaggtcac	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:37619980C>A	ENST00000434837.3	-	7	2297	c.1119G>T	c.(1117-1119)aaG>aaT	p.K373N	MDGA1_ENST00000505425.1_Missense_Mutation_p.K373N|MDGA1_ENST00000297153.7_Missense_Mutation_p.K373N	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	373	Ig-like 4.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.K373N(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GCTTGCCATTCTTGAACCACT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											77	82	80					6																	37619980		2118	4226	6344	37727958	SO:0001583	missense	266727			AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.1119G>T	6.37:g.37619980C>A	ENSP00000402584:p.Lys373Asn		37727958	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459233	0.84317	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.20463	2.07;2.07;2.07	5.25	4.37	0.52481	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000066	T	0.40522	0.1120	M	0.87682	2.9	0.52099	D	0.999943	D	0.89917	1.0	D	0.87578	0.998	T	0.50617	-0.8807	10	0.87932	D	0	.	11.9734	0.53075	0.0:0.9154:0.0:0.0846	.	373	Q8NFP4	MDGA1_HUMAN	N	373	ENSP00000402584:K373N;ENSP00000297153:K373N;ENSP00000422042:K373N	ENSP00000297153:K373N	K	-	3	2	MDGA1	37727958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.628000	0.37060	1.186000	0.42985	0.655000	0.94253	AAG		0.582	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			A	37619980	C	A	37619980	3	1	61	1	0	0	0	0	1	0	0	0	9436	912	32	2	1792	2	MDGA1	6	37619980	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	176026	37619980	133495087	4578	12563										
MDGA1	266727	broad.mit.edu	37	chr6	37626117	37626117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcgtgcgtgcaatacgctCgatgcgcagcgtctcgttga	13	12	1	1	rs199521705		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:37626117C>T	ENST00000434837.3	-	3	1464	c.286G>A	c.(286-288)Gag>Aag	p.E96K	MDGA1_ENST00000505425.1_Missense_Mutation_p.E96K|MDGA1_ENST00000297153.7_Missense_Mutation_p.E96K	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	96	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.E96K(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GCAATACGCTCGATGCGCAGC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	76	73					6																	37626117		2125	4221	6346	37734095	SO:0001583	missense	266727			AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.286G>A	6.37:g.37626117C>T	ENSP00000402584:p.Glu96Lys		37734095	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.150253	0.57151	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425;ENST00000515437;ENST00000508399	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000132	T	0.42743	0.1216	N	0.14661	0.345	0.40412	D	0.979756	D	0.61697	0.99	P	0.51229	0.663	T	0.47005	-0.9150	10	0.06365	T	0.9	.	17.8109	0.88616	0.0:1.0:0.0:0.0	.	96	Q8NFP4	MDGA1_HUMAN	K	96;96;96;40;40	ENSP00000402584:E96K;ENSP00000297153:E96K;ENSP00000422042:E96K;ENSP00000421510:E40K;ENSP00000427645:E40K	ENSP00000297153:E96K	E	-	1	0	MDGA1	37734095	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.063000	0.57499	2.515000	0.84797	0.655000	0.94253	GAG		0.652	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37626117	C	T	37626117	3	4	61	1	0	0	0	0	1	0	0	0	9436	893	31	1	2641	1	MDGA1	6	37626117	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6137	37626117	133488950	4579	12564										
DNAH8	1769	broad.mit.edu	37	chr6	38738325	38738325	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgaagctttttgcaaaaGactggagaaggtaagcatta	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38738325G>T	ENST00000359357.3	+	10	1357	c.1103G>T	c.(1102-1104)aGa>aTa	p.R368I	DNAH8_ENST00000449981.2_Missense_Mutation_p.R585I|DNAH8_ENST00000441566.1_Missense_Mutation_p.R368I			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	368					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R368I(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTTTGCAAAAGACTGGAGAAG	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	6											41	40	40					6																	38738325		2203	4300	6503	38846303	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1103G>T	6.37:g.38738325G>T	ENSP00000352312:p.Arg368Ile		38846303	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.183734	0.78677	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.65364	-0.15;-0.15;-0.15	5.27	5.27	0.74061	Dynein heavy chain, domain-1 (1);	0.059450	0.64402	D	0.000007	T	0.78735	0.4330	M	0.87682	2.9	0.80722	D	1	D	0.67145	0.996	D	0.76575	0.988	T	0.80538	-0.1338	10	0.51188	T	0.08	.	17.022	0.86436	0.0:0.0:1.0:0.0	.	368	Q96JB1	DYH8_HUMAN	I	573;573;368;368	ENSP00000333363:R573I;ENSP00000352312:R368I;ENSP00000402294:R368I	ENSP00000333363:R573I	R	+	2	0	DNAH8	38846303	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.545000	0.60698	2.624000	0.88883	0.643000	0.83706	AGA		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38738325	G	T	38738325	3	4	61	1	0	0	0	0	1	0	0	0	4618	942	33	2	1133	2	DNAH8	6	38738325	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1112208	38738325	132376742	4580	12565										
DNAH8	1769	broad.mit.edu	37	chr6	38754599	38754599	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagttgctggttaatttCgatcccaaaattttggaagt	11	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38754599C>T	ENST00000359357.3	+	16	2057	c.1803C>T	c.(1801-1803)ttC>ttT	p.F601F	DNAH8_ENST00000449981.2_Silent_p.F818F|DNAH8_ENST00000441566.1_Silent_p.F601F			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	601					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.F601F(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGGTTAATTTCGATCCCAAAA	0.358																																																2	Substitution - coding silent(2)	large_intestine(2)	6											89	89	89					6																	38754599		2203	4300	6503	38862577	SO:0001819	synonymous_variant	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1803C>T	6.37:g.38754599C>T			38862577	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																					0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38754599	C	T	38754599	2	4	61	1	0	0	0	0	0	0	0	1	4618	883	31	1		1	DNAH8	6	38754599	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16274	38754599	132360468	4581	12566										
DNAH8	1769	broad.mit.edu	37	chr6	38758142	38758142	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagcttctttcaagaagtCgaattagttttggatatgtt	9	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38758142C>T	ENST00000359357.3	+	18	2345	c.2091C>T	c.(2089-2091)gtC>gtT	p.V697V	DNAH8_ENST00000449981.2_Silent_p.V914V|DNAH8_ENST00000441566.1_Silent_p.V697V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	697					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V697V(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTCAAGAAGTCGAATTAGTTT	0.333																																																2	Substitution - coding silent(2)	large_intestine(2)	6											126	119	121					6																	38758142		2203	4300	6503	38866120	SO:0001819	synonymous_variant	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2091C>T	6.37:g.38758142C>T			38866120	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																					0.333	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38758142	C	T	38758142	2	4	61	1	0	0	0	0	0	0	0	1	4618	871	31	1		1	DNAH8	6	38758142	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3543	38758142	132356925	4582	12567										
DNAH8	1769	broad.mit.edu	37	chr6	38775483	38775483	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaatgaaaagaagaatatTtgttgcaaggcaagttgaaa	9	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38775483T>G	ENST00000359357.3	+	22	2851	c.2597T>G	c.(2596-2598)tTt>tGt	p.F866C	DNAH8_ENST00000449981.2_Missense_Mutation_p.F1083C|DNAH8_ENST00000441566.1_Missense_Mutation_p.F866C			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	866					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.F866C(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGAAGAATATTTGTTGCAAGG	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	6											95	95	95					6																	38775483		2203	4298	6501	38883461	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2597T>G	6.37:g.38775483T>G	ENSP00000352312:p.Phe866Cys		38883461	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	T	14.00	2.403758	0.42613	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.25085	1.86;1.85;1.82	6.07	4.91	0.64330	.	0.431769	0.27668	N	0.018345	T	0.16981	0.0408	L	0.50333	1.59	0.38610	D	0.950873	B	0.31640	0.333	B	0.42087	0.375	T	0.04811	-1.0925	10	0.38643	T	0.18	.	9.9806	0.41811	0.0:0.0773:0.0:0.9227	.	866	Q96JB1	DYH8_HUMAN	C	1071;1071;866;866	ENSP00000333363:F1071C;ENSP00000352312:F866C;ENSP00000402294:F866C	ENSP00000333363:F1071C	F	+	2	0	DNAH8	38883461	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.457000	0.45005	1.121000	0.41925	0.528000	0.53228	TTT		0.299	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38775483	T	G	38775483	3	3	61	1	0	0	0	0	1	0	0	0	4618	1841	64	4	2675	4	DNAH8	6	38775483	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	17341	38775483	132339584	4583	12568										
DNAH8	1769	broad.mit.edu	37	chr6	38831813	38831813	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtgttgatttaaatccaGaatttggaatcttcttaacg	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38831813G>T	ENST00000359357.3	+	43	6078	c.5824G>T	c.(5824-5826)Gaa>Taa	p.E1942*	DNAH8_ENST00000449981.2_Nonsense_Mutation_p.E2159*|DNAH8_ENST00000441566.1_Nonsense_Mutation_p.E1942*			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1942	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1942*(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTTAAATCCAGAATTTGGAAT	0.289																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											67	68	68					6																	38831813		2202	4300	6502	38939791	SO:0001587	stop_gained	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5824G>T	6.37:g.38831813G>T	ENSP00000352312:p.Glu1942*		38939791	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Nonsense_Mutation	SNP	ENST00000359357.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	49|49	15.901193|15.901193	0.99848|0.99848	.|.	.|.	ENSG00000124721|ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566|ENST00000394393	.|.	.|.	.|.	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.70911	.|0.3278	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69323	.|-0.5175	.|3	0.25751|.	T|.	0.34|.	.|.	19.3403|19.3403	0.94337|0.94337	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|H	2147;2147;1942;1942|23	.|.	ENSP00000333363:E2147X|.	E|Q	+|+	1|3	0|2	DNAH8|DNAH8	38939791|38939791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.813000|9.813000	0.99286|0.99286	2.582000|2.582000	0.87167|0.87167	0.491000|0.491000	0.48974|0.48974	GAA|CAG		0.289	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38831813	G	T	38831813	4	4	61	1	0	0	0	0	0	1	0	0	4618	943	33	2	5986	2	DNAH8	6	38831813	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56330	38831813	132283254	4584	12569										
DNAH8	1769	broad.mit.edu	37	chr6	38840734	38840734	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggatgccatctggattgaGaacttaaattccgttttgga	11	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38840734G>T	ENST00000359357.3	+	49	6893	c.6639G>T	c.(6637-6639)gaG>gaT	p.E2213D	DNAH8_ENST00000449981.2_Missense_Mutation_p.E2430D|DNAH8_ENST00000441566.1_Missense_Mutation_p.E2177D			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2213	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E2213D(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TCTGGATTGAGAACTTAAATT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	6											76	77	77					6																	38840734		2203	4300	6503	38948712	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6639G>T	6.37:g.38840734G>T	ENSP00000352312:p.Glu2213Asp		38948712	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	18.83	3.707774	0.68615	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	D;D;D	0.97041	-4.22;-4.22;-4.22	5.78	0.954	0.19595	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	D	0.98235	0.9416	H	0.94264	3.515	0.51012	D	0.999909	D	0.89917	1.0	D	0.97110	1.0	D	0.97887	1.0295	10	0.87932	D	0	.	9.312	0.37910	0.4111:0.0:0.5889:0.0	.	2213	Q96JB1	DYH8_HUMAN	D	2418;2418;2213;2177	ENSP00000333363:E2418D;ENSP00000352312:E2213D;ENSP00000402294:E2177D	ENSP00000333363:E2418D	E	+	3	2	DNAH8	38948712	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	1.607000	0.36836	0.089000	0.17243	-0.140000	0.14226	GAG		0.368	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38840734	G	T	38840734	3	4	61	1	0	0	0	0	1	0	0	0	4618	933	33	2	6825	2	DNAH8	6	38840734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8921	38840734	132274333	4585	12570										
DNAH8	1769	broad.mit.edu	37	chr6	38950164	38950164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggatggaatattccctacGaattcaattctgctgacttt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:38950164G>A	ENST00000359357.3	+	84	12480	c.12226G>A	c.(12226-12228)Gaa>Aaa	p.E4076K	DNAH8_ENST00000441566.1_Missense_Mutation_p.E4040K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4076	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E4076K(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TATTCCCTACGAATTCAATTC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	6											183	181	182					6																	38950164		2203	4300	6503	39058142	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12226G>A	6.37:g.38950164G>A	ENSP00000352312:p.Glu4076Lys		39058142	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	36	5.902336	0.97087	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.11495	2.77;2.77;2.77	6.17	6.17	0.99709	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	H	0.98111	4.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65565	-0.6137	10	0.59425	D	0.04	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	4040;4076	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	K	4281;4076;4040	ENSP00000333363:E4281K;ENSP00000352312:E4076K;ENSP00000402294:E4040K	ENSP00000333363:E4281K	E	+	1	0	DNAH8	39058142	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.673000	0.98631	2.941000	0.99782	0.655000	0.94253	GAA		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38950164	G	A	38950164	3	1	61	1	0	0	0	0	1	0	0	0	4618	1059	37	1	12552	1	DNAH8	6	38950164	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109430	38950164	132164903	4586	12571										
GLP1R	2740	broad.mit.edu	37	chr6	39024224	39024224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatggcgagaataccgaCgccagtgccagcgctccctg	12	13	0	2	rs201675748		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39024224C>T	ENST00000373256.4	+	2	173	c.130C>T	c.(130-132)Cgc>Tgc	p.R44C		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	44			R -> H (in dbSNP:rs2295006). {ECO:0000269|Ref.7}.		activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.R44C(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	AGAATACCGACGCCAGTGCCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	57	61					6																	39024224		2203	4300	6503	39132202	SO:0001583	missense	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.130C>T	6.37:g.39024224C>T	ENSP00000362353:p.Arg44Cys		39132202	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657449	0.67586	.	.	ENSG00000112164	ENST00000373256	T	0.52983	0.64	5.53	5.53	0.82687	.	0.663516	0.14585	N	0.310599	T	0.35508	0.0934	L	0.50333	1.59	0.19300	N	0.999979	D	0.54207	0.965	P	0.46049	0.502	T	0.24225	-1.0166	10	0.46703	T	0.11	.	14.9658	0.71193	0.0:1.0:0.0:0.0	.	44	P43220	GLP1R_HUMAN	C	44	ENSP00000362353:R44C	ENSP00000362353:R44C	R	+	1	0	GLP1R	39132202	0.007000	0.16637	0.313000	0.25210	0.869000	0.49853	1.806000	0.38892	2.587000	0.87381	0.655000	0.94253	CGC		0.617	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			T	39024224	C	T	39024224	3	4	61	1	0	0	0	0	1	0	0	0	6472	536	19	1	136	1	GLP1R	6	39024224	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74060	39024224	132090843	4587	12572										
GLP1R	2740	broad.mit.edu	37	chr6	39040720	39040720	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgtccgtcttcatcaagGacgcagccctgaagtggatg	11	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39040720G>T	ENST00000373256.4	+	6	635	c.592G>T	c.(592-594)Gac>Tac	p.D198Y		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	198					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.D198Y(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	CTTCATCAAGGACGCAGCCCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											197	156	170					6																	39040720		2203	4300	6503	39148698	SO:0001583	missense	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.592G>T	6.37:g.39040720G>T	ENSP00000362353:p.Asp198Tyr		39148698	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991818	0.93106	.	.	ENSG00000112164	ENST00000373256	T	0.48522	0.81	5.71	5.71	0.89125	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000002	T	0.66528	0.2798	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68899	-0.5287	10	0.87932	D	0	.	19.8599	0.96779	0.0:0.0:1.0:0.0	.	198	P43220	GLP1R_HUMAN	Y	198	ENSP00000362353:D198Y	ENSP00000362353:D198Y	D	+	1	0	GLP1R	39148698	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	9.773000	0.98989	2.710000	0.92621	0.655000	0.94253	GAC		0.582	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			T	39040720	G	T	39040720	3	4	61	1	0	0	0	0	1	0	0	0	6472	1174	41	2	614	2	GLP1R	6	39040720	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16496	39040720	132074347	4588	12573										
KCNK5	8645	broad.mit.edu	37	chr6	39159259	39159259	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgatctgcttgatgaggtCgttgtaggtctcttccttct	10	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39159259C>A	ENST00000359534.3	-	5	1245	c.907G>T	c.(907-909)Gac>Tac	p.D303Y		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	303					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.D303Y(1)|p.D303N(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						TTGATGAGGTCGTTGTAGGTC	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	6											128	131	130					6																	39159259		2203	4300	6503	39267237	SO:0001583	missense	8645			AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.907G>T	6.37:g.39159259C>A	ENSP00000352527:p.Asp303Tyr		39267237	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.639635	0.87760	.	.	ENSG00000164626	ENST00000359534	T	0.26067	1.76	5.7	5.7	0.88788	.	2.194870	0.01375	N	0.012711	T	0.42291	0.1196	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.31833	-0.9929	10	0.87932	D	0	.	19.8471	0.96713	0.0:1.0:0.0:0.0	.	303	O95279	KCNK5_HUMAN	Y	303	ENSP00000352527:D303Y	ENSP00000352527:D303Y	D	-	1	0	KCNK5	39267237	1.000000	0.71417	0.989000	0.46669	0.924000	0.55760	7.487000	0.81328	2.688000	0.91661	0.655000	0.94253	GAC		0.627	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740		A	39159259	C	A	39159259	3	1	61	1	0	0	0	0	1	0	0	0	8090	884	31	2	596	2	KCNK5	6	39159259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118539	39159259	131955808	4589	12574										
KIF6	221458	broad.mit.edu	37	chr6	39325111	39325111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagatgtctggagaaatgGcttcgtgtgatcgagtgaat	14	5	2	4	rs372001923		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39325111G>A	ENST00000287152.7	-	19	2216	c.2122C>T	c.(2122-2124)Cca>Tca	p.P708S	KIF6_ENST00000229913.5_Missense_Mutation_p.P159S|KIF6_ENST00000394362.1_Missense_Mutation_p.P159S|KIF6_ENST00000373215.3_Missense_Mutation_p.P691S|KIF6_ENST00000373216.3_Missense_Mutation_p.P708S|KIF6_ENST00000538893.1_Missense_Mutation_p.P652S|KIF6_ENST00000541946.1_Missense_Mutation_p.P159S|KIF6_ENST00000373213.4_Missense_Mutation_p.P547S	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	708					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P708S(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						TGGAGAAATGGCTTCGTGTGA	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	6											176	157	164					6																	39325111		2203	4300	6503	39433089	SO:0001583	missense	221458			AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.2122C>T	6.37:g.39325111G>A	ENSP00000287152:p.Pro708Ser		39433089	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.784|8.784	0.929036|0.929036	0.18131|0.18131	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000540362|ENST00000287152;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946	.|T;T;T;T;T;T;T;T	.|0.72051	.|-0.48;1.44;-0.48;-0.33;1.46;-0.5;-0.62;1.49	4.0|4.0	2.08|2.08	0.27032|0.27032	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34048	.|0.0884	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.14805	.|0.011;0.001;0.002;0.006	.|B;B;B;B	.|0.14578	.|0.011;0.002;0.007;0.005	.|T	.|0.20706	.|-1.0267	.|9	.|0.34782	.|T	.|0.22	.|.	5.0487|5.0487	0.14497|0.14497	0.304:0.0:0.696:0.0|0.304:0.0:0.696:0.0	.|.	.|691;652;708;708	.|E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.|.;.;.;KIF6_HUMAN	.|S	-1|708;159;708;547;159;691;652;159	.|ENSP00000287152:P708S;ENSP00000377889:P159S;ENSP00000362312:P708S;ENSP00000362309:P547S;ENSP00000229913:P159S;ENSP00000362311:P691S;ENSP00000441435:P652S;ENSP00000439064:P159S	.|ENSP00000229913:P159S	.|P	-|-	.|1	.|0	KIF6|KIF6	39433089|39433089	0.000000|0.000000	0.05858|0.05858	0.025000|0.025000	0.17156|0.17156	0.010000|0.010000	0.07245|0.07245	-0.017000|-0.017000	0.12590|0.12590	0.569000|0.569000	0.29329|0.29329	0.655000|0.655000	0.94253|0.94253	.|CCA		0.453	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		A	39325111	G	A	39325111	3	1	61	1	0	0	0	0	1	0	0	0	8329	1203	42	3	342	3	KIF6	6	39325111	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165852	39325111	131789956	4590	12575										
KIF6	221458	broad.mit.edu	37	chr6	39507841	39507841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtcctgggcctgtgagGgagctgaggatagtcgcatt	16	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39507841G>A	ENST00000287152.7	-	13	1677	c.1583C>T	c.(1582-1584)cCc>cTc	p.P528L	KIF6_ENST00000373215.3_Missense_Mutation_p.P528L|KIF6_ENST00000373216.3_Missense_Mutation_p.P528L|KIF6_ENST00000538893.1_Intron|KIF6_ENST00000373213.4_Missense_Mutation_p.P367L	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	528					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P528L(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GGCCTGTGAGGGAGCTGAGGA	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	6											216	219	218					6																	39507841		2203	4300	6503	39615819	SO:0001583	missense	221458			AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1583C>T	6.37:g.39507841G>A	ENSP00000287152:p.Pro528Leu		39615819	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.62|12.62	1.991538|1.991538	0.35131|0.35131	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373213;ENST00000373215|ENST00000458470	T;T;T;T|T	0.71341|0.72725	-0.56;-0.53;-0.36;-0.51|-0.68	6.04|6.04	5.17|5.17	0.71159|0.71159	.|.	.|.	.|.	.|.	.|.	T|T	0.48554|0.48554	0.1506|0.1506	L|L	0.50333|0.50333	1.59|1.59	0.28625|0.28625	N|N	0.907995|0.907995	B;B;B|.	0.18166|.	0.003;0.026;0.002|.	B;B;B|.	0.17433|.	0.009;0.018;0.004|.	T|T	0.45131|0.45131	-0.9282|-0.9282	9|7	0.21540|0.09843	T|T	0.41|0.71	.|.	11.6642|11.6642	0.51364|0.51364	0.0821:0.0:0.9179:0.0|0.0821:0.0:0.9179:0.0	.|.	528;528;528|.	E7EUN7;Q6ZMV9-3;Q6ZMV9|.	.;.;KIF6_HUMAN|.	L|S	528;528;367;528|420	ENSP00000287152:P528L;ENSP00000362312:P528L;ENSP00000362309:P367L;ENSP00000362311:P528L|ENSP00000409417:P420S	ENSP00000287152:P528L|ENSP00000409417:P420S	P|P	-|-	2|1	0|0	KIF6|KIF6	39615819|39615819	0.007000|0.007000	0.16637|0.16637	0.126000|0.126000	0.21872|0.21872	0.082000|0.082000	0.17680|0.17680	1.568000|1.568000	0.36418|0.36418	1.540000|1.540000	0.49301|0.49301	0.563000|0.563000	0.77884|0.77884	CCC|CCT		0.478	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		A	39507841	G	A	39507841	3	1	61	1	0	0	0	0	1	0	0	0	8329	1232	43	3	905	3	KIF6	6	39507841	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182730	39507841	131607226	4591	12576										
DAAM2	23500	broad.mit.edu	37	chr6	39869137	39869137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatgcagccagacgaattCtttggcatctttgatacctt	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:39869137C>A	ENST00000398904.2	+	24	3053	c.2871C>A	c.(2869-2871)ttC>ttA	p.F957L	DAAM2_ENST00000274867.4_Missense_Mutation_p.F957L|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.F956L			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	957	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.F956L(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAGACGAATTCTTTGGCATCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											146	148	147					6																	39869137		2054	4203	6257	39977115	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.2871C>A	6.37:g.39869137C>A	ENSP00000381876:p.Phe957Leu		39977115	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.200304	0.79015	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.22539	1.95;1.95;1.95	5.5	3.37	0.38596	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.056331	0.64402	D	0.000001	T	0.25791	0.0628	M	0.73319	2.225	0.80722	D	1	D;P	0.55385	0.971;0.666	P;P	0.57911	0.829;0.562	T	0.03641	-1.1017	10	0.66056	D	0.02	.	9.5385	0.39237	0.0:0.7456:0.0:0.2544	.	956;957	G5EA45;Q86T65	.;DAAM2_HUMAN	L	957;957;956	ENSP00000274867:F957L;ENSP00000381876:F957L;ENSP00000437808:F956L	ENSP00000274867:F957L	F	+	3	2	DAAM2	39977115	1.000000	0.71417	0.998000	0.56505	0.925000	0.55904	1.075000	0.30716	1.309000	0.44985	0.655000	0.94253	TTC		0.582	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39869137	C	A	39869137	3	1	61	1	0	0	0	0	1	0	0	0	4222	912	32	2	2958	2	DAAM2	6	39869137	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	361296	39869137	131245930	4592	12577										
UNC5CL	222643	broad.mit.edu	37	chr6	41002622	41002622	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggcaggtgctgccttgaGacctcattttctagttgggg	14	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:41002622G>T	ENST00000373164.1	-	1	252	c.192C>A	c.(190-192)gtC>gtA	p.V64V	UNC5CL_ENST00000470102.1_5'Flank|UNC5CL_ENST00000244565.3_Silent_p.V64V			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	64					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)	p.V64V(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCTGCCTTGAGACCTCATTTT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											159	140	146					6																	41002622		2203	4300	6503	41110600	SO:0001819	synonymous_variant	222643			BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.192C>A	6.37:g.41002622G>T			41110600	Q5TGU1	Silent	SNP	ENST00000373164.1	37	CCDS4847.1																																																																																				0.582	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		T	41002622	G	T	41002622	2	4	61	1	0	0	0	0	0	0	0	1	17034	929	33	2		2	UNC5CL	6	41002622	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1133485	41002622	130112445	4593	12578										
TREM2	54209	broad.mit.edu	37	chr6	41127535	41127535	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacccatcgctgtacctggaGatgctgtgctccacatgggc	12	13	0	1	rs546844731		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:41127535G>T	ENST00000373113.3	-	3	570	c.477C>A	c.(475-477)atC>atA	p.I159I	TREM2_ENST00000373122.4_Silent_p.I159I|TREM2_ENST00000338469.3_Silent_p.I159I	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	159					axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.I159I(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGTACCTGGAGATGCTGTGCT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	6											66	63	64					6																	41127535		2203	4300	6503	41235513	SO:0001819	synonymous_variant	54209			AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"Immunoglobulin superfamily / V-set domain containing"	17761	protein-coding gene	gene with protein product		605086	"triggering receptor expressed on myeloid cells 2a"			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.477C>A	6.37:g.41127535G>T			41235513	Q8N5H8|Q8WYN6	Silent	SNP	ENST00000373113.3	37	CCDS4852.1																																																																																				0.602	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965		T	41127535	G	T	41127535	2	4	61	1	0	0	0	0	0	0	0	1	16511	932	33	2		2	TREM2	6	41127535	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	124913	41127535	129987532	4594	12579										
TREML4	285852	broad.mit.edu	37	chr6	41196546	41196546	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccctatcagcccaaatCctggtgtcagcagacatctc	9	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:41196546C>A	ENST00000341495.2	+	2	262	c.158C>A	c.(157-159)tCc>tAc	p.S53Y	TREML4_ENST00000448827.2_Missense_Mutation_p.S53Y	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	53	Ig-like V-type.					extracellular region (GO:0005576)		p.S53Y(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					CAGCCCAAATCCTGGTGTCAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											87	83	85					6																	41196546		2203	4300	6503	41304524	SO:0001583	missense	285852			AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"Immunoglobulin superfamily / V-set domain containing"	30807	protein-coding gene	gene with protein product	"TREM like transcript 4"	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.158C>A	6.37:g.41196546C>A	ENSP00000342570:p.Ser53Tyr		41304524	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.230404	0.39399	.	.	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.64085	-0.08;-0.08	4.35	1.37	0.22104	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.24084	0.0583	N	0.03115	-0.41	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.33727	-0.9857	9	0.02654	T	1	-1.8341	2.9787	0.05946	0.1816:0.5391:0.1765:0.1027	.	53	Q6UXN2	TRML4_HUMAN	Y	53	ENSP00000342570:S53Y;ENSP00000418078:S53Y	ENSP00000342570:S53Y	S	+	2	0	TREML4	41304524	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	-0.555000	0.05999	0.425000	0.26087	0.591000	0.81541	TCC		0.527	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			A	41196546	C	A	41196546	3	1	61	1	0	0	0	0	1	0	0	0	16514	855	30	2	164	2	TREML4	6	41196546	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69011	41196546	129918521	4595	12580										
PRICKLE4	29964	broad.mit.edu	37	chr6	41754642	41754642	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatccagtccccagcaggaGaaccgacctggggacaaagc	13	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:41754642G>T	ENST00000394260.1	+	5	810	c.810G>T	c.(808-810)gaG>gaT	p.E270D	PRICKLE4_ENST00000458694.1_Missense_Mutation_p.E310D|TOMM6_ENST00000398884.3_5'Flank|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.E310D			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	270						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.E310D(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCCAGCAGGAGAACCGACCTG	0.627											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	6											91	104	100					6																	41754642		2203	4300	6503	41862620	SO:0001583	missense	29964			AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"chromosome 6 open reading frame 49"	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.810G>T	6.37:g.41754642G>T	ENSP00000377803:p.Glu270Asp	903	41862620	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		.	.	.	.	.	.	.	.	.	.	G	6.136	0.393382	0.11638	.	.	ENSG00000124593	ENST00000458694;ENST00000394263;ENST00000394260	D;D;D	0.84730	-1.89;-1.89;-1.89	3.58	-0.483	0.12075	.	0.165275	0.28527	N	0.015038	T	0.49592	0.1566	N	0.20986	0.625	0.27833	N	0.94137	B	0.02656	0.0	B	0.09377	0.004	T	0.43669	-0.9377	10	0.18276	T	0.48	-6.5822	7.2191	0.25977	0.4311:0.0:0.5689:0.0	.	310	Q2TBC4-3	.	D	310;310;270	ENSP00000404911:E310D;ENSP00000377806:E310D;ENSP00000377803:E270D	ENSP00000335185:E310D	E	+	3	2	PRICKLE4	41862620	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-0.007000	0.12810	-0.268000	0.09312	-1.069000	0.02264	GAG		0.627	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		T	41754642	G	T	41754642	3	4	61	1	0	0	0	0	1	0	0	0	12523	933	33	2	952	2	PRICKLE4	6	41754642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	558096	41754642	129360425	4596	12581										
TAF8	129685	broad.mit.edu	37	chr6	42036321	42036321	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaacagacagacacagaGaaccttgctcttcatatcag	8	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42036321G>T	ENST00000372977.3	+	7	774	c.756G>T	c.(754-756)gaG>gaT	p.E252D	TAF8_ENST00000456846.2_Missense_Mutation_p.E252D|TAF8_ENST00000494547.1_Missense_Mutation_p.E252D|TAF8_ENST00000465926.1_Missense_Mutation_p.E176D|TAF8_ENST00000372982.4_Missense_Mutation_p.E252D	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	252					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)		p.E252D(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			CAGACACAGAGAACCTTGCTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											178	187	184					6																	42036321		2073	4204	6277	42144299	SO:0001583	missense	129685			AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa", "taube nuss homolog (mouse)"	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	ENST00000372977.3:c.756G>T	6.37:g.42036321G>T	ENSP00000362068:p.Glu252Asp		42144299	Q5T0K1|Q8N4R9|Q96M52	Missense_Mutation	SNP	ENST00000372977.3	37	CCDS43462.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476974	0.44044	.	.	ENSG00000137413	ENST00000456846;ENST00000494547;ENST00000372982;ENST00000372977;ENST00000465926	.	.	.	6.05	4.27	0.50696	.	0.044468	0.85682	D	0.000000	T	0.25754	0.0627	L	0.28556	0.865	0.80722	D	1	B;B;B;B	0.22683	0.005;0.01;0.073;0.002	B;B;B;B	0.20767	0.003;0.009;0.031;0.003	T	0.09751	-1.0660	9	0.18710	T	0.47	-31.0245	12.0482	0.53491	0.1392:0.0:0.8608:0.0	.	176;252;252;252	B4DZU5;Q7Z7C8-2;Q7Z7C8-4;Q7Z7C8	.;.;.;TAF8_HUMAN	D	252;252;252;252;176	.	ENSP00000362068:E252D	E	+	3	2	TAF8	42144299	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.612000	0.54142	1.580000	0.49851	0.650000	0.86243	GAG		0.527	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572		T	42036321	G	T	42036321	3	4	61	1	0	0	0	0	1	0	0	0	15573	933	33	2	782	2	TAF8	6	42036321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281679	42036321	129078746	4597	12582										
GUCA1A	2978	broad.mit.edu	37	chr6	42141420	42141420	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgccaccagtggtacaaGaagttcatgactgagtgccc	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42141420G>T	ENST00000394237.1	+	3	1045	c.69G>T	c.(67-69)aaG>aaT	p.K23N	GUCA1A_ENST00000372958.1_Missense_Mutation_p.K23N|GUCA1A_ENST00000053469.4_Missense_Mutation_p.K23N|GUCA1A_ENST00000541991.1_Missense_Mutation_p.K23N			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	23	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.K23N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	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)			AGTGGTACAAGAAGTTCATGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											148	123	131					6																	42141420		2203	4300	6503	42249398	SO:0001583	missense	2978				CCDS4864.1	6p21.1	2013-06-06			ENSG00000048545	ENSG00000048545		"EF-hand domain containing"	4678	protein-coding gene	gene with protein product	"cone dystrophy 3"	600364	"chromosome 6 open reading frame 131"	GUCA, GUCA1, C6orf131		9425234	Standard	NM_000409		Approved	GCAP, GCAP1, COD3, dJ139D8.6, CORD14	uc003orx.3	P43080	OTTHUMG00000014696	ENST00000394237.1:c.69G>T	6.37:g.42141420G>T	ENSP00000377784:p.Lys23Asn		42249398	B3KWT4|Q7Z6T1|Q9NU14	Missense_Mutation	SNP	ENST00000394237.1	37	CCDS4864.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384971	0.42308	.	.	ENSG00000048545	ENST00000418175;ENST00000541991;ENST00000372965;ENST00000053469;ENST00000394237;ENST00000372958	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	5.75	3.96	0.45880	EF-hand-like domain (1);	0.111694	0.64402	D	0.000007	T	0.68384	0.2995	M	0.75150	2.29	0.50632	D	0.999888	D	0.71674	0.998	P	0.57468	0.821	T	0.73936	-0.3825	10	0.87932	D	0	.	10.0034	0.41942	0.1631:0.0:0.8369:0.0	.	23	P43080	GUC1A_HUMAN	N	23;23;19;23;23;23	ENSP00000388438:K23N;ENSP00000437476:K23N;ENSP00000053469:K23N;ENSP00000377784:K23N;ENSP00000362049:K23N	ENSP00000053469:K23N	K	+	3	2	GUCA1A	42249398	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.544000	0.53640	1.426000	0.47256	0.655000	0.94253	AAG		0.592	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1			T	42141420	G	T	42141420	3	4	61	1	0	0	0	0	1	0	0	0	6909	933	33	2	71	2	GUCA1A	6	42141420	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105099	42141420	128973647	4598	12583										
UBR2	23304	broad.mit.edu	37	chr6	42574351	42574351	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggtctgttcgatatggaGattttcagtattgtgagcaa	12	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42574351G>T	ENST00000372899.1	+	7	1084	c.826G>T	c.(826-828)Gat>Tat	p.D276Y	UBR2_ENST00000372903.2_Missense_Mutation_p.D276Y|UBR2_ENST00000372901.1_Missense_Mutation_p.D276Y	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	276					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D276Y(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCGATATGGAGATTTTCAGTA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	76	75					6																	42574351		2203	4287	6490	42682329	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.826G>T	6.37:g.42574351G>T	ENSP00000361990:p.Asp276Tyr		42682329	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.251146	0.80135	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73897	-0.79;0.19;0.19	5.48	5.48	0.80851	Adaptor protein ClpS, core (1);Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like (2);	0.047740	0.85682	D	0.000000	T	0.66228	0.2768	L	0.38175	1.15	0.80722	D	1	B;P	0.42296	0.162;0.775	B;P	0.45343	0.315;0.477	T	0.70655	-0.4812	10	0.56958	D	0.05	-1.5858	19.3648	0.94458	0.0:0.0:1.0:0.0	.	276;276	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	Y	276	ENSP00000361994:D276Y;ENSP00000361990:D276Y;ENSP00000361992:D276Y	ENSP00000361990:D276Y	D	+	1	0	UBR2	42682329	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	9.421000	0.97455	2.569000	0.86673	0.557000	0.71058	GAT		0.259	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		T	42574351	G	T	42574351	3	4	61	1	0	0	0	0	1	0	0	0	16942	942	33	2	852	2	UBR2	6	42574351	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	432931	42574351	128540716	4599	12584										
UBR2	23304	broad.mit.edu	37	chr6	42600420	42600420	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctttacaagccttcaaatTtaggagagtacagagcctta	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42600420T>G	ENST00000372899.1	+	12	1670	c.1412T>G	c.(1411-1413)tTt>tGt	p.F471C	UBR2_ENST00000372883.3_5'UTR|UBR2_ENST00000372901.1_Missense_Mutation_p.F471C	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	471					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F471C(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GCCTTCAAATTTAGGAGAGTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	75	75					6																	42600420		2203	4300	6503	42708398	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1412T>G	6.37:g.42600420T>G	ENSP00000361990:p.Phe471Cys		42708398	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430800	0.83776	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.65732	-0.17;-0.17	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.74504	0.3725	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.984	T	0.75554	-0.3277	10	0.38643	T	0.18	-12.9727	15.4672	0.75409	0.0:0.0:0.0:1.0	.	471;471	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	C	471	ENSP00000361990:F471C;ENSP00000361992:F471C	ENSP00000361990:F471C	F	+	2	0	UBR2	42708398	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.651000	0.83577	2.104000	0.64026	0.533000	0.62120	TTT		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42600420	T	G	42600420	3	3	61	1	0	0	0	0	1	0	0	0	16942	1841	64	4	1604	4	UBR2	6	42600420	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26069	42600420	128514647	4600	12585										
UBR2	23304	broad.mit.edu	37	chr6	42658815	42658815	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagcgattcaagaagatTcagaagctctggcaccaaca	9	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42658815T>G	ENST00000372899.1	+	47	5430	c.5172T>G	c.(5170-5172)atT>atG	p.I1724M	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Missense_Mutation_p.I1724M	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1724					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I1724M(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCAAGAAGATTCAGAAGCTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											106	104	105					6																	42658815		2203	4300	6503	42766793	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.5172T>G	6.37:g.42658815T>G	ENSP00000361990:p.Ile1724Met		42766793	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.063586	0.76187	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.52295	0.67;0.67	5.76	-7.72	0.01250	.	0.000000	0.85682	D	0.000000	T	0.29458	0.0734	N	0.17631	0.505	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.992	D;D;D	0.74674	0.984;0.975;0.923	T	0.57562	-0.7790	10	0.62326	D	0.03	-17.5919	9.3931	0.38386	0.2108:0.5362:0.0:0.2529	.	312;1724;1724	B3KXG6;Q8IWV8-4;Q8IWV8	.;.;UBR2_HUMAN	M	1724	ENSP00000361990:I1724M;ENSP00000361992:I1724M	ENSP00000361990:I1724M	I	+	3	3	UBR2	42766793	0.131000	0.22433	0.809000	0.32408	0.998000	0.95712	-0.544000	0.06077	-1.273000	0.02424	0.528000	0.53228	ATT		0.403	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42658815	T	G	42658815	3	3	61	1	0	0	0	0	1	0	0	0	16942	1771	62	4	5504	4	UBR2	6	42658815	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	58395	42658815	128456252	4601	12586										
KIAA0240	23506	broad.mit.edu	37	chr6	42797492	42797492	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgctgtccacttagtgtCtgggcagacatttgctgcct	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42797492C>A	ENST00000314073.5	+	6	1597	c.1421C>A	c.(1420-1422)tCt>tAt	p.S474Y	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.S474Y			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	474								p.S474Y(1)									CACTTAGTGTCTGGGCAGACA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											130	116	121					6																	42797492		2203	4300	6503	42905470	SO:0001583	missense	23506			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.1421C>A	6.37:g.42797492C>A	ENSP00000313933:p.Ser474Tyr		42905470	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429122	0.62844	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.50277	0.75;0.75	5.77	5.77	0.91146	.	0.162830	0.44902	D	0.000420	T	0.49643	0.1569	L	0.51422	1.61	0.53005	D	0.999962	D;P;P	0.69078	0.997;0.946;0.955	D;P;P	0.80764	0.994;0.808;0.714	T	0.40421	-0.9564	10	0.02654	T	1	-7.7862	20.3627	0.98863	0.0:1.0:0.0:0.0	.	474;474;474	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	Y	474	ENSP00000313933:S474Y;ENSP00000377723:S474Y	ENSP00000313933:S474Y	S	+	2	0	KIAA0240	42905470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.759000	0.62227	2.885000	0.99019	0.655000	0.94253	TCT		0.502	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		A	42797492	C	A	42797492	3	1	61	1	0	0	0	0	1	0	0	0	8185	913	32	2	1435	2	KIAA0240	6	42797492	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138677	42797492	128317575	4602	12587										
PEX6	5190	broad.mit.edu	37	chr6	42936079	42936079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacgcagcacagccatcacaCgggcatcctcacccagccca	8	19	2	0	rs201061728		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42936079C>T	ENST00000304611.8	-	7	1706	c.1637G>A	c.(1636-1638)cGt>cAt	p.R546H	PEX6_ENST00000244546.4_Missense_Mutation_p.R546H	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	546					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R546H(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			AGCCATCACACGGGCATCCTC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	HIS/ARG	0,4406		0,0,2203	47	50	49		1637	5	1	6		49	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PEX6	NM_000287.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	546/981	42936079	1,13005	2203	4300	6503	43044057	SO:0001583	missense	5190			U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"ATPases / AAA-type"	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.1637G>A	6.37:g.42936079C>T	ENSP00000303511:p.Arg546His		43044057	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413303	0.62511	0.0	1.16E-4	ENSG00000124587	ENST00000304611;ENST00000244546	D;D	0.94046	-3.34;-3.34	6.08	5.04	0.67666	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.047618	0.85682	D	0.000000	D	0.88786	0.6531	M	0.62016	1.91	0.44754	D	0.997753	B	0.32425	0.371	B	0.31614	0.133	D	0.88694	0.3211	10	0.54805	T	0.06	-12.2189	13.2209	0.59887	0.0:0.9129:0.0:0.0871	.	546	Q13608	PEX6_HUMAN	H	546	ENSP00000303511:R546H;ENSP00000244546:R546H	ENSP00000244546:R546H	R	-	2	0	PEX6	43044057	0.997000	0.39634	0.997000	0.53966	0.979000	0.70002	3.865000	0.56033	2.894000	0.99253	0.655000	0.94253	CGT		0.657	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		T	42936079	C	T	42936079	3	4	61	1	0	0	0	0	1	0	0	0	11781	536	19	1	1349	1	PEX6	6	42936079	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138587	42936079	128178988	4603	12588										
MEA1	4201	broad.mit.edu	37	chr6	42980278	42980278	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcttcccactgggcatccGatatctcccgagcccaggca	8	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42980278G>A	ENST00000244711.3	-	4	642	c.488C>T	c.(487-489)tCg>tTg	p.S163L	KLHDC3_ENST00000244670.8_5'Flank|KLHDC3_ENST00000326974.4_5'Flank	NM_014623.2	NP_055438.1	Q16626	MEA1_HUMAN	male-enhanced antigen 1	163					cell differentiation (GO:0030154)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)		p.S163L(1)		central_nervous_system(1)|large_intestine(3)|lung(1)|skin(1)	6			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTGGGCATCCGATATCTCCCG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											102	102	102					6																	42980278		2203	4300	6503	43088256	SO:0001583	missense	4201				CCDS4879.1	6p21.3-p21.1	2008-08-15	2005-06-02	2005-06-02	ENSG00000124733	ENSG00000124733			6986	protein-coding gene	gene with protein product		143170	"male-enhanced antigen"	MEA		2813404, 12444059	Standard	NM_014623		Approved		uc003otk.3	Q16626	OTTHUMG00000014717	ENST00000244711.3:c.488C>T	6.37:g.42980278G>A	ENSP00000244711:p.Ser163Leu		43088256	Q5TC36|Q9BV01	Missense_Mutation	SNP	ENST00000244711.3	37	CCDS4879.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.632967	0.87660	.	.	ENSG00000124733	ENST00000244711	T	0.54866	0.55	6.17	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.29850	0.0746	L	0.34521	1.04	0.58432	D	0.999994	B	0.26775	0.159	B	0.23852	0.049	T	0.28299	-1.0048	10	0.87932	D	0	-8.8802	15.3678	0.74538	0.0671:0.0:0.9329:0.0	.	163	Q16626	MEA1_HUMAN	L	163	ENSP00000244711:S163L	ENSP00000244711:S163L	S	-	2	0	MEA1	43088256	1.000000	0.71417	0.662000	0.29724	0.996000	0.88848	7.109000	0.77062	1.630000	0.50440	0.655000	0.94253	TCG		0.567	MEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040574.2			A	42980278	G	A	42980278	3	1	61	1	0	0	0	0	1	0	0	0	9450	1059	37	1	73	1	MEA1	6	42980278	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44199	42980278	128134789	4604	12589										
C6orf153	88745	broad.mit.edu	37	chr6	42992793	42992793	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggactaagacgtacaaacaAttggtagctggaaatagtcc	11	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42992793A>C	ENST00000244496.5	+	2	211	c.201A>C	c.(199-201)caA>caC	p.Q67H		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	67					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.Q67H(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						CGTACAAACAATTGGTAGCTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											136	116	123					6																	42992793		2203	4300	6503	43100771	SO:0001583	missense	88745			BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.201A>C	6.37:g.42992793A>C	ENSP00000244496:p.Gln67His		43100771	Q9BRF6|Q9P0C8	Missense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577598	0.28180	.	.	ENSG00000124541	ENST00000244496	T	0.46451	0.87	4.82	-5.45	0.02616	.	0.376667	0.26594	N	0.023506	T	0.09905	0.0243	N	0.24115	0.695	0.19575	N	0.999969	P	0.45283	0.855	B	0.41510	0.359	T	0.27157	-1.0082	10	0.62326	D	0.03	.	6.5772	0.22573	0.2084:0.0:0.5059:0.2858	.	67	Q96EU6	RRP36_HUMAN	H	67	ENSP00000244496:Q67H	ENSP00000244496:Q67H	Q	+	3	2	RRP36	43100771	0.000000	0.05858	0.124000	0.21820	0.263000	0.26337	-1.860000	0.01656	-0.839000	0.04212	-0.379000	0.06801	CAA		0.458	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		C	42992793	A	C	42992793	3	2	61	1	0	0	0	0	1	0	0	0	2344	98	4	4	207	4	C6orf153	6	42992793	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12515	42992793	128122274	4605	12590										
C6orf153	88745	broad.mit.edu	37	chr6	42993034	42993034	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagccaagatccgagtaccAtttttacgtcaggttgttcc	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:42993034A>G	ENST00000244496.5	+	3	322	c.312A>G	c.(310-312)ccA>ccG	p.P104P		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	104					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P104P(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						TCCGAGTACCATTTTTACGTC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	6											113	110	111					6																	42993034		2203	4300	6503	43101012	SO:0001819	synonymous_variant	88745			BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.312A>G	6.37:g.42993034A>G			43101012	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	37	CCDS34453.1																																																																																				0.507	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		G	42993034	A	G	42993034	2	3	61	1	0	0	0	0	0	0	0	1	2344	204	8	4		4	C6orf153	6	42993034	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	241	42993034	128122033	4606	12591										
PTK7	5754	broad.mit.edu	37	chr6	43109416	43109416	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccctgcagatgggagcagCctcccagagtgggtgacaga	14	12	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43109416C>T	ENST00000230419.4	+	11	1850	c.1629C>T	c.(1627-1629)agC>agT	p.S543S	PTK7_ENST00000352931.2_Silent_p.S543S|PTK7_ENST00000481273.1_Silent_p.S551S|PTK7_ENST00000345201.2_Silent_p.S503S|PTK7_ENST00000349241.2_Silent_p.S413S	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	543	Ig-like C2-type 6.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S543S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			ATGGGAGCAGCCTCCCAGAGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	6											118	117	117					6																	43109416		2203	4300	6503	43217394	SO:0001819	synonymous_variant	5754			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1629C>T	6.37:g.43109416C>T			43217394	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1																																																																																				0.557	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			T	43109416	C	T	43109416	2	4	61	1	0	0	0	0	0	0	0	1	12800	738	26	3		3	PTK7	6	43109416	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116382	43109416	128005651	4607	12592										
PTK7	5754	broad.mit.edu	37	chr6	43127601	43127601	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcctggagggtgacttCtctaccaagtctgatgtctg	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43127601C>A	ENST00000230419.4	+	19	3170	c.2949C>A	c.(2947-2949)ttC>ttA	p.F983L	PTK7_ENST00000352931.2_Missense_Mutation_p.F927L|PTK7_ENST00000481273.1_Missense_Mutation_p.F991L|PTK7_ENST00000345201.2_Missense_Mutation_p.F943L|PTK7_ENST00000349241.2_Missense_Mutation_p.F853L	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	983	Interaction with CTNNB1.|Protein kinase; inactive. {ECO:0000255|PROSITE-ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.F983L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGGTGACTTCTCTACCAAGT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											148	116	127					6																	43127601		2203	4300	6503	43235579	SO:0001583	missense	5754			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2949C>A	6.37:g.43127601C>A	ENSP00000230419:p.Phe983Leu		43235579	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	SNP	ENST00000230419.4	37	CCDS4884.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.868890|3.868890	0.72065|0.72065	.|.	.|.	ENSG00000112655|ENSG00000112655	ENST00000230419;ENST00000325774;ENST00000349241;ENST00000352931;ENST00000345201;ENST00000481273;ENST00000473339|ENST00000489707	D;D;D;D;D;D|.	0.88896|.	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44|.	5.59|5.59	3.82|3.82	0.43975|0.43975	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.053035|.	0.85682|.	D|.	0.000000|.	T|T	0.45677|0.45677	0.1354|0.1354	L|L	0.48362|0.48362	1.52|1.52	0.58432|0.58432	D|D	0.999999|0.999999	P;B;P;B;P;B;P|.	0.43578|.	0.642;0.025;0.767;0.383;0.811;0.383;0.587|.	P;B;P;B;B;B;B|.	0.47376|.	0.53;0.016;0.545;0.219;0.227;0.219;0.268|.	T|T	0.40194|0.40194	-0.9576|-0.9576	10|5	0.40728|.	T|.	0.16|.	.|.	12.3187|12.3187	0.54973|0.54973	0.0:0.8619:0.0:0.1381|0.0:0.8619:0.0:0.1381	.|.	991;309;328;853;943;927;983|.	E9PFZ5;F8W9X8;B3KP36;Q13308-3;Q13308-2;Q13308-4;Q13308|.	.;.;.;.;.;.;PTK7_HUMAN|.	L|Y	983;309;853;927;943;991;251|278	ENSP00000230419:F983L;ENSP00000325462:F853L;ENSP00000326029:F927L;ENSP00000325992:F943L;ENSP00000418754:F991L;ENSP00000420186:F251L|.	ENSP00000230419:F983L|.	F|S	+|+	3|2	2|0	PTK7|PTK7	43235579|43235579	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.948000|0.948000	0.59901|0.59901	3.237000|3.237000	0.51344|0.51344	0.834000|0.834000	0.34852|0.34852	-0.229000|-0.229000	0.12294|0.12294	TTC|TCT		0.592	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			A	43127601	C	A	43127601	3	1	61	1	0	0	0	0	1	0	0	0	12800	912	32	2	3023	2	PTK7	6	43127601	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18185	43127601	127987466	4608	12593										
CUL9	23113	broad.mit.edu	37	chr6	43164514	43164514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactcagggatagcaccaaGaacagaacctatgcctacca	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43164514G>T	ENST00000252050.4	+	11	2801	c.2717G>T	c.(2716-2718)aGa>aTa	p.R906I	CUL9_ENST00000372647.2_Missense_Mutation_p.R906I|CUL9_ENST00000354495.3_Missense_Mutation_p.R796I	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	906					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.R906I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ATAGCACCAAGAACAGAACCT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											190	156	168					6																	43164514		2203	4300	6503	43272492	SO:0001583	missense	23113			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2717G>T	6.37:g.43164514G>T	ENSP00000252050:p.Arg906Ile		43272492	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.182807	0.38511	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.74002	-0.8;-0.79;-0.69	5.61	5.61	0.85477	Armadillo-type fold (1);	1.074150	0.07014	N	0.825604	T	0.44201	0.1282	N	0.08118	0	0.29945	N	0.820769	P;B;B	0.44578	0.838;0.001;0.001	B;B;B	0.37550	0.253;0.0;0.0	T	0.47873	-0.9083	10	0.52906	T	0.07	-17.5939	15.1351	0.72558	0.0:0.0:1.0:0.0	.	796;906;906	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	I	906;796;906	ENSP00000252050:R906I;ENSP00000346490:R796I;ENSP00000361730:R906I	ENSP00000252050:R906I	R	+	2	0	CUL9	43272492	0.995000	0.38212	1.000000	0.80357	0.236000	0.25371	4.240000	0.58701	2.656000	0.90262	0.655000	0.94253	AGA		0.532	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43164514	G	T	43164514	3	4	61	1	0	0	0	0	1	0	0	0	4067	942	33	2	2755	2	CUL9	6	43164514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36913	43164514	127950553	4609	12594										
TTBK1	84630	broad.mit.edu	37	chr6	43221049	43221049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaggaccatgtgtgcaggTtcattggctgtggcaggaac	16	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43221049T>C	ENST00000259750.4	+	4	360	c.277T>C	c.(277-279)Ttc>Ctc	p.F93L	TTBK1_ENST00000304139.5_Missense_Mutation_p.F42L	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	93	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F93L(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			TGTGTGCAGGTTCATTGGCTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											162	134	143					6																	43221049		2203	4300	6503	43329027	SO:0001583	missense	84630			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.277T>C	6.37:g.43221049T>C	ENSP00000259750:p.Phe93Leu		43329027	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.151114	0.57151	.	.	ENSG00000146216	ENST00000393984;ENST00000259750;ENST00000304139	T	0.14766	2.48	4.76	2.19	0.27852	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063358	0.64402	D	0.000004	T	0.10465	0.0256	L	0.27053	0.805	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	T	0.08371	-1.0725	10	0.54805	T	0.06	.	6.0023	0.19527	0.1445:0.0848:0.0:0.7706	.	93	Q5TCY1	TTBK1_HUMAN	L	42;93;42	ENSP00000259750:F93L	ENSP00000259750:F93L	F	+	1	0	TTBK1	43329027	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.588000	0.82629	0.618000	0.30179	0.379000	0.24179	TTC		0.532	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			C	43221049	T	C	43221049	3	2	61	1	0	0	0	0	1	0	0	0	16716	1725	60	4	287	4	TTBK1	6	43221049	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	56535	43221049	127894018	4610	12595										
TTBK1	84630	broad.mit.edu	37	chr6	43222820	43222820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggtttcgaggaacggttCgctatgcctcagtcaatgcc	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43222820C>T	ENST00000259750.4	+	7	693	c.610C>T	c.(610-612)Cgc>Tgc	p.R204C	TTBK1_ENST00000304139.5_Missense_Mutation_p.R153C	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	204	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R204C(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			AGGAACGGTTCGCTATGCCTC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	105	117					6																	43222820		2203	4300	6503	43330798	SO:0001583	missense	84630			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.610C>T	6.37:g.43222820C>T	ENSP00000259750:p.Arg204Cys		43330798	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.375935	0.82682	.	.	ENSG00000146216	ENST00000393984;ENST00000259750;ENST00000304139	T	0.06608	3.28	4.83	4.83	0.62350	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28234	0.0697	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.42172	-0.9467	10	0.87932	D	0	.	11.8928	0.52638	0.1748:0.8252:0.0:0.0	.	204	Q5TCY1	TTBK1_HUMAN	C	153;204;153	ENSP00000259750:R204C	ENSP00000259750:R204C	R	+	1	0	TTBK1	43330798	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	5.551000	0.67274	2.242000	0.73789	0.655000	0.94253	CGC		0.622	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43222820	C	T	43222820	3	4	61	1	0	0	0	0	1	0	0	0	16716	884	31	1	632	1	TTBK1	6	43222820	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1771	43222820	127892247	4611	12596										
TTBK1	84630	broad.mit.edu	37	chr6	43223519	43223519	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcaccggatgctgctgaaGcacatgccgtcagagttcca	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43223519G>A	ENST00000259750.4	+	9	869	c.786G>A	c.(784-786)aaG>aaA	p.K262K	TTBK1_ENST00000304139.5_Silent_p.K211K	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	262	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K262K(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			TGCTGCTGAAGCACATGCCGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	6											186	136	153					6																	43223519		2203	4300	6503	43331497	SO:0001819	synonymous_variant	84630			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.786G>A	6.37:g.43223519G>A			43331497	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																				0.597	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43223519	G	A	43223519	2	1	61	1	0	0	0	0	0	0	0	1	16716	962	34	3		3	TTBK1	6	43223519	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	699	43223519	127891548	4612	12597										
SLC22A7	10864	broad.mit.edu	37	chr6	43266468	43266468	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtacgaccactcagaattCtcctctaccattgcaactga	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43266468C>A	ENST00000372585.5	+	1	467	c.372C>A	c.(370-372)ttC>ttA	p.F124L	SLC22A7_ENST00000487175.1_3'UTR|SLC22A7_ENST00000372589.3_Missense_Mutation_p.F124L|SLC22A7_ENST00000372574.3_Missense_Mutation_p.F124L	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	124					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.F124L(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	ACTCAGAATTCTCCTCTACCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											62	65	64					6																	43266468		2203	4300	6503	43374446	SO:0001583	missense	10864			AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.372C>A	6.37:g.43266468C>A	ENSP00000361666:p.Phe124Leu		43374446	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	37	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.267368	0.80469	.	.	ENSG00000137204	ENST00000449231;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T	0.79141	0.69;-1.24;-1.24;-1.24	5.63	3.85	0.44370	Major facilitator superfamily domain (1);	0.227866	0.46145	D	0.000304	T	0.78355	0.4270	M	0.61703	1.905	0.40706	D	0.982528	D;D;D	0.60160	0.987;0.983;0.983	D;P;P	0.63381	0.914;0.86;0.86	T	0.80417	-0.1391	10	0.72032	D	0.01	.	10.1217	0.42625	0.0:0.8362:0.0:0.1638	.	124;124;124	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	L	124	ENSP00000411818:F124L;ENSP00000361670:F124L;ENSP00000361666:F124L;ENSP00000361655:F124L	ENSP00000361655:F124L	F	+	3	2	SLC22A7	43374446	0.900000	0.30661	1.000000	0.80357	0.931000	0.56810	0.757000	0.26433	0.736000	0.32559	0.563000	0.77884	TTC		0.552	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			A	43266468	C	A	43266468	3	1	61	1	0	0	0	0	1	0	0	0	14496	912	32	2	374	2	SLC22A7	6	43266468	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42949	43266468	127848599	4613	12598										
ZNF318	24149	broad.mit.edu	37	chr6	43325277	43325277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagatcgtatggagtagcCtttgagtttttctcgattcc	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43325277C>A	ENST00000361428.2	-	3	852	c.775G>T	c.(775-777)Ggc>Tgc	p.G259C	ZNF318_ENST00000318149.3_Missense_Mutation_p.G259C	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	259					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.G259C(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			ATGGAGTAGCCTTTGAGTTTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	105	107					6																	43325277		2203	4300	6503	43433255	SO:0001583	missense	24149			AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.775G>T	6.37:g.43325277C>A	ENSP00000354964:p.Gly259Cys		43433255	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	37	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330320	0.60743	.	.	ENSG00000171467	ENST00000318149;ENST00000361428	T;T	0.03496	3.91;3.91	5.62	2.12	0.27331	.	0.980070	0.08370	N	0.956332	T	0.01489	0.0048	N	0.08118	0	0.26524	N	0.97439	D	0.63880	0.993	P	0.53360	0.724	T	0.50423	-0.8830	10	0.72032	D	0.01	-0.0173	7.6053	0.28100	0.0:0.4965:0.0:0.5035	.	259	Q5VUA4	ZN318_HUMAN	C	259	ENSP00000323032:G259C;ENSP00000354964:G259C	ENSP00000323032:G259C	G	-	1	0	ZNF318	43433255	0.961000	0.32948	0.977000	0.42913	0.990000	0.78478	0.799000	0.27028	0.103000	0.17682	0.555000	0.69702	GGC		0.458	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		A	43325277	C	A	43325277	3	1	61	1	0	0	0	0	1	0	0	0	17875	681	24	2	6096	2	ZNF318	6	43325277	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58809	43325277	127789790	4614	12599										
XPO5	57510	broad.mit.edu	37	chr6	43521127	43521127	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttctctatttagtgttcGaaacatctgggtgataacac	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43521127G>A	ENST00000265351.7	-	14	1765	c.1555C>T	c.(1555-1557)Cga>Tga	p.R519*	XPO5_ENST00000424378.2_5'UTR	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	519					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.R519*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TTTAGTGTTCGAAACATCTGG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											65	64	64					6																	43521127		1888	4109	5997	43629105	SO:0001587	stop_gained	57510			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1555C>T	6.37:g.43521127G>A	ENSP00000265351:p.Arg519*		43629105	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Nonsense_Mutation	SNP	ENST00000265351.7	37	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	G	38	7.134127	0.98085	.	.	ENSG00000124571	ENST00000265351;ENST00000436943;ENST00000372252;ENST00000372258;ENST00000439465	.	.	.	5.36	4.47	0.54385	.	0.139039	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-3.8447	15.2204	0.73306	0.0:0.0:0.8581:0.1419	.	.	.	.	X	519;224;59;59;147	.	ENSP00000265351:R519X	R	-	1	2	XPO5	43629105	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	4.857000	0.62939	1.209000	0.43321	0.655000	0.94253	CGA		0.388	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		A	43521127	G	A	43521127	4	1	61	1	0	0	0	0	0	1	0	0	17487	1066	37	1	2135	1	XPO5	6	43521127	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	195850	43521127	127593940	4615	12600										
POLH	5429	broad.mit.edu	37	chr6	43581501	43581501	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgagcagtgacccaagttCtctgccaaaggtgccagtta	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43581501C>A	ENST00000372236.4	+	11	1644	c.1349C>A	c.(1348-1350)tCt>tAt	p.S450Y	POLH_ENST00000535400.1_Missense_Mutation_p.S388Y|POLH_ENST00000372226.1_3'UTR	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.S450Y(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GACCCAAGTTCTCTGCCAAAG	0.507								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																																							1	Substitution - Missense(1)	large_intestine(1)	6											89	92	91					6																	43581501		2203	4300	6503	43689479	SO:0001583	missense	5429	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.1349C>A	6.37:g.43581501C>A	ENSP00000361310:p.Ser450Tyr		43689479	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	C	8.631	0.893635	0.17613	.	.	ENSG00000170734	ENST00000372236;ENST00000535400	T;T	0.60424	0.32;0.19	5.41	2.4	0.29515	.	0.865218	0.10555	N	0.660914	T	0.39118	0.1066	M	0.63843	1.955	0.80722	D	1	B;B	0.16396	0.004;0.017	B;B	0.15484	0.013;0.009	T	0.40440	-0.9563	10	0.37606	T	0.19	-25.4071	13.0809	0.59114	0.0:0.5039:0.4961:0.0	.	388;450	B4DG64;Q9Y253	.;POLH_HUMAN	Y	450;388	ENSP00000361310:S450Y;ENSP00000442102:S388Y	ENSP00000361310:S450Y	S	+	2	0	POLH	43689479	0.017000	0.18338	0.639000	0.29394	0.471000	0.32888	0.596000	0.24044	0.735000	0.32537	-0.440000	0.05779	TCT		0.507	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502		A	43581501	C	A	43581501	3	1	61	1	0	0	0	0	1	0	0	0	12233	913	32	2	1387	2	POLH	6	43581501	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60374	43581501	127533566	4616	12601										
RSPH9	221421	broad.mit.edu	37	chr6	43623416	43623416	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacccacccatgtcaatCggacctttgaaggtgagttc	10	11	1	2	rs139002825		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43623416C>T	ENST00000372163.4	+	3	564	c.511C>T	c.(511-513)Cgg>Tgg	p.R171W	RSPH9_ENST00000372165.4_Missense_Mutation_p.R156W	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	171					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)		p.R171W(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CCATGTCAATCGGACCTTTGA	0.572									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	6						C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	131	134	133		466,511	4.6	1	6	dbSNP_134	133	0,8600		0,0,4300	no	missense,missense	RSPH9	NM_001193341.1,NM_152732.4	101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	156/307,171/277	43623416	1,13005	2203	4300	6503	43731394	SO:0001583	missense	221421	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"mitochondrial ribosomal protein S18A-like 1", "chromosome 6 open reading frame 206"	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.511C>T	6.37:g.43623416C>T	ENSP00000361236:p.Arg171Trp		43731394	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	37	CCDS4905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.87|18.87	3.714898|3.714898	0.68844|0.68844	2.27E-4|2.27E-4	0.0|0.0	ENSG00000172426|ENSG00000172426	ENST00000372165;ENST00000372163;ENST00000372154|ENST00000417236	T|.	0.48201|.	0.82|.	5.58|5.58	4.63|4.63	0.57726|0.57726	.|.	0.054900|.	0.64402|.	D|.	0.000001|.	T|T	0.67869|0.67869	0.2939|0.2939	M|M	0.79475|0.79475	2.455|2.455	0.48632|0.48632	D|D	0.999684|0.999684	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.975;0.996|.	T|T	0.69083|0.69083	-0.5239|-0.5239	10|5	0.72032|.	D|.	0.01|.	-17.4249|-17.4249	12.6176|12.6176	0.56586|0.56586	0.1981:0.8019:0.0:0.0|0.1981:0.8019:0.0:0.0	.|.	156;171|.	Q96NH9;Q9H1X1|.	.;RSPH9_HUMAN|.	W|L	156;171;139|95	ENSP00000361236:R171W|.	ENSP00000361227:R139W|.	R|S	+|+	1|2	2|0	RSPH9|RSPH9	43731394|43731394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.927000|0.927000	0.56198|0.56198	2.384000|2.384000	0.44362|0.44362	2.613000|2.613000	0.88420|0.88420	0.591000|0.591000	0.81541|0.81541	CGG|TCG		0.572	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732		T	43623416	C	T	43623416	3	4	61	1	0	0	0	0	1	0	0	0	13745	875	31	1	521	1	RSPH9	6	43623416	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41915	43623416	127491651	4617	12602										
RSPH9	221421	broad.mit.edu	37	chr6	43638535	43638535	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttatctcagggtcctggaGcatccagatggagaggggca	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43638535G>T	ENST00000372163.4	+	5	733	c.680G>T	c.(679-681)aGc>aTc	p.S227I	RSPH9_ENST00000372165.4_Missense_Mutation_p.E244D	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	227					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)		p.S227I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GGGTCCTGGAGCATCCAGATG	0.637									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	6											73	63	67					6																	43638535		2203	4300	6503	43746513	SO:0001583	missense	221421	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"mitochondrial ribosomal protein S18A-like 1", "chromosome 6 open reading frame 206"	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.680G>T	6.37:g.43638535G>T	ENSP00000361236:p.Ser227Ile		43746513	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	37	CCDS4905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.8|27.8	4.862024|4.862024	0.91433|0.91433	.|.	.|.	ENSG00000172426|ENSG00000172426	ENST00000372165|ENST00000372163	.|T	.|0.17691	.|2.26	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.059957|.	0.64402|.	D|.	0.000003|.	T|T	0.33147|0.33147	0.0853|0.0853	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|D	0.89917|0.65815	1.0|0.995	D|D	0.83275|0.66602	0.996|0.945	T|T	0.00809|0.00809	-1.1557|-1.1557	8|8	0.08179|0.48119	T|T	0.78|0.1	-13.3297|-13.3297	17.9218|17.9218	0.88969|0.88969	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	244|227	Q96NH9|Q9H1X1	.|RSPH9_HUMAN	D|I	244|227	.|ENSP00000361236:S227I	ENSP00000361238:E244D|ENSP00000361236:S227I	E|S	+|+	3|2	2|0	RSPH9|RSPH9	43746513|43746513	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.914000|0.914000	0.54420|0.54420	4.874000|4.874000	0.63064|0.63064	2.837000|2.837000	0.97791|0.97791	0.655000|0.655000	0.94253|0.94253	GAG|AGC		0.637	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732		T	43638535	G	T	43638535	3	4	61	1	0	0	0	0	1	0	0	0	13745	971	34	2	698	2	RSPH9	6	43638535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15119	43638535	127476532	4618	12603										
MRPS18A	55168	broad.mit.edu	37	chr6	43642962	43642962	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagttggggtttgctcttCggaacaactccttcaggaag	12	8	2	1	rs571547048		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:43642962C>T	ENST00000372133.3	-	5	434	c.423G>A	c.(421-423)ccG>ccA	p.P141P	MRPS18A_ENST00000372116.1_Intron	NM_018135.3	NP_060605.1	Q9NVS2	RT18A_HUMAN	mitochondrial ribosomal protein S18A	141					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)	p.P141P(1)		kidney(3)|large_intestine(1)	4	all_cancers(18;6.56e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000479)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0102)|OV - Ovarian serous cystadenocarcinoma(102;0.137)			GTTTGCTCTTCGGAACAACTC	0.552													C|||	1	0.000199681	0	0	5008	,	,		19248	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											139	132	134					6																	43642962		2203	4300	6503	43750940	SO:0001819	synonymous_variant	55168			AB049952	CCDS4906.1, CCDS55006.1	6p21.3	2012-09-13			ENSG00000096080	ENSG00000096080		"Mitochondrial ribosomal proteins / small subunits"	14515	protein-coding gene	gene with protein product		611981				11279123, 11543634	Standard	NM_018135		Approved	FLJ10548, MRPS18-3	uc003ovy.2	Q9NVS2	OTTHUMG00000014750	ENST00000372133.3:c.423G>A	6.37:g.43642962C>T			43750940	A6XND3|Q5QPA4	Silent	SNP	ENST00000372133.3	37	CCDS4906.1																																																																																				0.552	MRPS18A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040697.1	NM_018135		T	43642962	C	T	43642962	2	4	61	1	0	0	0	0	0	0	0	1	9858	871	31	1		1	MRPS18A	6	43642962	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4427	43642962	127472105	4619	12604										
TMEM63B	55362	broad.mit.edu	37	chr6	44108077	44108077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagacacacctccaagatgCgctacaaggaggatgatctg	11	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:44108077C>T	ENST00000259746.9	+	9	874	c.691C>T	c.(691-693)Cgc>Tgc	p.R231C	TMEM63B_ENST00000527188.1_3'UTR|TMEM63B_ENST00000323267.6_Missense_Mutation_p.R231C			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	231					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.R231C(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CTCCAAGATGCGCTACAAGGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	83	94					6																	44108077		2202	4300	6502	44216055	SO:0001583	missense	55362			BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.691C>T	6.37:g.44108077C>T	ENSP00000259746:p.Arg231Cys		44216055	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	37	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644971	0.87859	.	.	ENSG00000137216	ENST00000259746;ENST00000323267	T;T	0.37915	1.17;1.17	4.45	4.45	0.53987	.	0.053599	0.85682	D	0.000000	T	0.39708	0.1088	L	0.50333	1.59	0.80722	D	1	P;D;D	0.76494	0.917;0.998;0.999	P;P;P	0.56700	0.707;0.696;0.804	T	0.37079	-0.9721	10	0.72032	D	0.01	.	16.264	0.82565	0.0:1.0:0.0:0.0	.	231;231;231	Q5T3F8-3;Q5T3F8;Q5T3F8-2	.;TM63B_HUMAN;.	C	231	ENSP00000259746:R231C;ENSP00000327154:R231C	ENSP00000259746:R231C	R	+	1	0	TMEM63B	44216055	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.650000	0.61440	2.317000	0.78254	0.561000	0.74099	CGC		0.587	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		T	44108077	C	T	44108077	3	4	61	1	0	0	0	0	1	0	0	0	16230	768	27	1	721	1	TMEM63B	6	44108077	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	465115	44108077	127006990	4620	12605										
CAPN11	11131	broad.mit.edu	37	chr6	44140733	44140733	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaccggctgcccacaaaGaatgacaagctggtgtttgt	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:44140733G>T	ENST00000398776.1	+	6	623	c.585G>T	c.(583-585)aaG>aaT	p.K195N	CAPN11_ENST00000542245.1_Missense_Mutation_p.K195N	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	195	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)	p.K195N(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGCCCACAAAGAATGACAAGC	0.547											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	6											47	51	50					6																	44140733		2167	4272	6439	44248711	SO:0001583	missense	11131			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.585G>T	6.37:g.44140733G>T	ENSP00000381758:p.Lys195Asn	921	44248711	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745566	0.49151	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.89123	-2.47;-2.47	4.16	1.37	0.22104	Peptidase C2, calpain, catalytic domain (3);	0.149441	0.31542	N	0.007480	D	0.88265	0.6390	M	0.75615	2.305	0.23959	N	0.996347	D	0.67145	0.996	D	0.66351	0.943	T	0.79940	-0.1591	10	0.45353	T	0.12	.	7.5342	0.27700	0.3642:0.0:0.6358:0.0	.	195	Q9UMQ6	CAN11_HUMAN	N	195	ENSP00000381758:K195N;ENSP00000441078:K195N	ENSP00000381758:K195N	K	+	3	2	CAPN11	44248711	1.000000	0.71417	0.035000	0.18076	0.694000	0.40290	2.356000	0.44116	0.516000	0.28340	0.609000	0.83330	AAG		0.547	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			T	44140733	G	T	44140733	3	4	61	1	0	0	0	0	1	0	0	0	2630	933	33	2	607	2	CAPN11	6	44140733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32656	44140733	126974334	4621	12606										
HSP90AB1	3326	broad.mit.edu	37	chr6	44218276	44218276	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatgacatcacccaagaGgagtatggagaattctacaa	9	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:44218276G>T	ENST00000371554.1	+	6	1111	c.897G>T	c.(895-897)gaG>gaT	p.E299D	HSP90AB1_ENST00000371646.5_Missense_Mutation_p.E299D|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.E299D			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	299					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.E299D(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCACCCAAGAGGAGTATGGAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											91	85	87					6																	44218276		2203	4300	6503	44326254	SO:0001583	missense	3326			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.897G>T	6.37:g.44218276G>T	ENSP00000360609:p.Glu299Asp		44326254	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.283226	0.40394	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.11604	2.76;2.76;2.76	4.41	2.19	0.27852	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.64402	U	0.000002	T	0.04998	0.0134	L	0.58428	1.81	0.80722	D	1	B;B;B	0.13145	0.001;0.007;0.006	B;B;B	0.21546	0.01;0.035;0.018	T	0.08351	-1.0726	10	0.48119	T	0.1	-17.9711	8.4362	0.32789	0.3542:0.0:0.6458:0.0	.	261;289;299	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	D	299	ENSP00000360709:E299D;ENSP00000325875:E299D;ENSP00000360609:E299D	ENSP00000325875:E299D	E	+	3	2	HSP90AB1	44326254	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.190000	0.32126	0.859000	0.35456	0.460000	0.39030	GAG		0.423	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		T	44218276	G	T	44218276	3	4	61	1	0	0	0	0	1	0	0	0	7423	991	35	2	915	2	HSP90AB1	6	44218276	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77543	44218276	126896791	4622	12607										
HSP90AB1	3326	broad.mit.edu	37	chr6	44221324	44221324	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgcgtctcgcatggaaGaagtcgattaggttaggagt	15	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:44221324G>T	ENST00000371554.1	+	12	2378	c.2164G>T	c.(2164-2166)Gaa>Taa	p.E722*	HSP90AB1_ENST00000371646.5_Nonsense_Mutation_p.E722*|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000353801.3_Nonsense_Mutation_p.E722*			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	722					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.E722*(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCGCATGGAAGAAGTCGATTA	0.542											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	6											70	73	72					6																	44221324		2203	4300	6503	44329302	SO:0001587	stop_gained	3326			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2164G>T	6.37:g.44221324G>T	ENSP00000360609:p.Glu722*	922	44329302	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Nonsense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	G	40	8.017993	0.98613	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	.	.	.	3.91	3.91	0.45181	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.49582	D	0.999803	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.342	16.4352	0.83873	0.0:0.0:1.0:0.0	.	.	.	.	X	722	.	ENSP00000325875:E722X	E	+	1	0	HSP90AB1	44329302	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.605000	0.98321	2.188000	0.69820	0.609000	0.83330	GAA		0.542	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		T	44221324	G	T	44221324	4	4	61	1	0	0	0	0	0	1	0	0	7423	943	33	2	2206	2	HSP90AB1	6	44221324	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3048	44221324	126893743	4623	12608										
RUNX2	860	broad.mit.edu	37	chr6	45515041	45515041	+	Nonstop_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgtttggcgaccatattGaaattcctcagcagtggccc	9	11	2	1	rs104893994		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:45515041G>T	ENST00000371438.1	+	8	1923	c.1565G>T	c.(1564-1566)tGa>tTa	p.*522L	RUNX2_ENST00000371432.3_Nonstop_Mutation_p.*486L|RUNX2_ENST00000359524.5_Nonstop_Mutation_p.*508L|RUNX2_ENST00000541979.1_Nonstop_Mutation_p.*568L|RUNX2_ENST00000465038.2_Nonstop_Mutation_p.*522L|RUNX2_ENST00000576263.1_Intron|RUNX2_ENST00000352853.5_Nonstop_Mutation_p.*590L|RUNX2_ENST00000371436.6_Nonstop_Mutation_p.*500L	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	0					BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.*522L(1)|p.*590L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CGACCATATTGAAATTCCTCA	0.433																																																2	Nonstop extension(2)	large_intestine(2)	6	GRCh37	CM021322	RUNX2	M	rs104893994						77	82	81					6																	45515041		2202	4300	6502	45623019	SO:0001578	stop_lost	860			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.1565G>T	6.37:g.45515041G>T	ENSP00000360493:p.*522Leuext*23		45623019	O14614|O14615|O95181	Nonstop_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211401	0.79240	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9052	0.97004	0.0:0.0:1.0:0.0	.	.	.	.	L	522;590;568;522;500;508;486	.	.	X	+	2	2	RUNX2	45623019	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.586000	0.82596	2.776000	0.95493	0.655000	0.94253	TGA		0.433	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		T	45515041	G	T	45515041	4	4	61	1	0	0	0	0	0	0	0	0	13785	1285	45	2	1611	2	RUNX2	6	45515041	Nonstop_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1293717	45515041	125600026	4624	12609										
CLIC5	53405	broad.mit.edu	37	chr6	45922972	45922972	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgccgatgctttctccatCgattccagcctggaaagaag	10	11	1	1	rs145250435	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:45922972C>T	ENST00000185206.6	-	2	702	c.550G>A	c.(550-552)Gat>Aat	p.D184N	CLIC5_ENST00000544153.1_Missense_Mutation_p.D25N|CLIC5_ENST00000339561.6_Missense_Mutation_p.D25N	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	184					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)	p.D25N(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						CTTTCTCCATCGATTCCAGCC	0.493													C|||	2	0.000399361	0	0	5008	,	,		20573	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											96	79	85					6																	45922972		2203	4300	6503	46030950	SO:0001583	missense	53405			AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"Ion channels / Chloride channels : Intracellular"	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.550G>A	6.37:g.45922972C>T	ENSP00000185206:p.Asp184Asn		46030950	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Missense_Mutation	SNP	ENST00000185206.6	37	CCDS47438.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	34	5.389985	0.95988	.	.	ENSG00000112782	ENST00000185206;ENST00000339561;ENST00000544153	T;T;T	0.42131	0.98;0.98;0.98	5.36	5.36	0.76844	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	N	0.19112	0.55	0.80722	D	1	D;D;D	0.67145	0.996;0.976;0.996	P;P;P	0.58970	0.849;0.53;0.803	T	0.39881	-0.9592	10	0.72032	D	0.01	.	18.2208	0.89901	0.0:1.0:0.0:0.0	.	25;184;25	Q8NBY3;Q9NZA1;Q53G01	.;CLIC5_HUMAN;.	N	184;25;25	ENSP00000185206:D184N;ENSP00000344165:D25N;ENSP00000439195:D25N	ENSP00000185206:D184N	D	-	1	0	CLIC5	46030950	1.000000	0.71417	0.916000	0.36221	0.978000	0.69477	7.448000	0.80631	2.676000	0.91093	0.650000	0.86243	GAT		0.493	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1			T	45922972	C	T	45922972	3	4	61	1	0	0	0	0	1	0	0	0	3535	884	31	1	702	1	CLIC5	6	45922972	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	407931	45922972	125192095	4625	12610										
ENPP5	59084	broad.mit.edu	37	chr6	46135742	46135742	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcaacaatcccatgattCtctgcaaagaggccagttac	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46135742C>A	ENST00000371383.2	-	3	518	c.258G>T	c.(256-258)gaG>gaT	p.E86D	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.E86D					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)									p.E86D(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						TCCCATGATTCTCTGCAAAGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											63	60	61					6																	46135742		2203	4300	6503	46243701	SO:0001583	missense	59084			AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.258G>T	6.37:g.46135742C>A	ENSP00000360436:p.Glu86Asp		46243701		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278440	0.59758	.	.	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.73789	-0.78;-0.78	5.51	3.75	0.43078	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.76492	0.3995	M	0.67397	2.05	0.37443	D	0.914503	D;D	0.71674	0.998;0.998	D;D	0.70016	0.967;0.967	T	0.79337	-0.1845	10	0.87932	D	0	-21.9521	8.7386	0.34543	0.0:0.6526:0.0:0.3474	.	86;86	A8K9X7;Q9UJA9	.;ENPP5_HUMAN	D	86	ENSP00000360436:E86D;ENSP00000230565:E86D	ENSP00000230565:E86D	E	-	3	2	ENPP5	46243701	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.910000	0.28571	0.815000	0.34398	-0.229000	0.12294	GAG		0.338	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2			A	46135742	C	A	46135742	3	1	61	1	0	0	0	0	1	0	0	0	5146	912	32	2	1187	2	ENPP5	6	46135742	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212770	46135742	124979325	4626	12611										
CYP39A1	51302	broad.mit.edu	37	chr6	46518128	46518128	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttgtttatattcaattCggcattgcccttccggctgg	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46518128C>T	ENST00000275016.2	-	12	1588	c.1385G>A	c.(1384-1386)cGa>cAa	p.R462Q		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	462					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)	p.R462Q(1)	EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						ATATTCAATTCGGCATTGCCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											133	138	136					6																	46518128		2203	4300	6503	46626087	SO:0001583	missense	51302			AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.1385G>A	6.37:g.46518128C>T	ENSP00000275016:p.Arg462Gln		46626087	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.667797	0.47677	.	.	ENSG00000146233	ENST00000275016	D	0.85171	-1.95	5.82	3.11	0.35812	.	0.328524	0.24909	N	0.034625	T	0.58163	0.2103	L	0.47716	1.5	0.20975	N	0.999813	P;P	0.44659	0.722;0.84	B;B	0.36666	0.138;0.23	T	0.53457	-0.8436	10	0.13470	T	0.59	-1.274	8.0835	0.30758	0.0:0.7505:0.0:0.2495	.	442;462	B7Z786;Q9NYL5	.;CP39A_HUMAN	Q	462	ENSP00000275016:R462Q	ENSP00000275016:R462Q	R	-	2	0	CYP39A1	46626087	0.428000	0.25522	0.433000	0.26760	0.991000	0.79684	0.603000	0.24149	0.395000	0.25257	0.655000	0.94253	CGA		0.468	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			T	46518128	C	T	46518128	3	4	61	1	0	0	0	0	1	0	0	0	4183	884	31	1	28	1	CYP39A1	6	46518128	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382386	46518128	124596939	4627	12612										
PLA2G7	7941	broad.mit.edu	37	chr6	46672344	46672344	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgtaacatgatgtgttGattggttgtgttaatgttgg	13	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46672344G>T	ENST00000274793.7	-	12	1475	c.1279C>A	c.(1279-1281)Caa>Aaa	p.Q427K	PLA2G7_ENST00000537365.1_Missense_Mutation_p.Q427K	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	427					cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)	p.Q427K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			ATGATGTGTTGATTGGTTGTG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											118	107	111					6																	46672344		2202	4300	6502	46780303	SO:0001583	missense	7941			U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.1279C>A	6.37:g.46672344G>T	ENSP00000274793:p.Gln427Lys		46780303	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417344	0.11870	.	.	ENSG00000146070	ENST00000274793;ENST00000537365	T;T	0.40756	1.02;1.02	4.27	1.17	0.20885	.	1.093960	0.06891	N	0.804198	T	0.08537	0.0212	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24799	-1.0150	10	0.05351	T	0.99	.	0.9838	0.01442	0.1571:0.1913:0.364:0.2876	.	427	Q13093	PAFA_HUMAN	K	427	ENSP00000274793:Q427K;ENSP00000445666:Q427K	ENSP00000274793:Q427K	Q	-	1	0	PLA2G7	46780303	0.006000	0.16342	0.002000	0.10522	0.003000	0.03518	0.632000	0.24583	0.419000	0.25927	0.561000	0.74099	CAA		0.313	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1			T	46672344	G	T	46672344	3	4	61	1	0	0	0	0	1	0	0	0	12040	1299	45	2	50	2	PLA2G7	6	46672344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154216	46672344	124442723	4628	12613										
GPR116	221395	broad.mit.edu	37	chr6	46823752	46823752	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatctccttgatattggaGaactcatagaaaacacaggt	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46823752G>T	ENST00000283296.7	-	20	4208	c.3920C>A	c.(3919-3921)tCt>tAt	p.S1307Y	GPR116_ENST00000545669.1_Missense_Mutation_p.S736Y|GPR116_ENST00000265417.7_Missense_Mutation_p.S1307Y|GPR116_ENST00000456426.2_Missense_Mutation_p.S1165Y|GPR116_ENST00000362015.4_Missense_Mutation_p.S1287Y	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1307					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S1307Y(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TGATATTGGAGAACTCATAGA	0.418																																					NSCLC(59;410 1274 8751 36715 50546)											1	Substitution - Missense(1)	large_intestine(1)	6											56	50	52					6																	46823752		2203	4296	6499	46931711	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3920C>A	6.37:g.46823752G>T	ENSP00000283296:p.Ser1307Tyr		46931711	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060150	0.36373	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45	5.42	5.42	0.78866	.	0.101172	0.44902	D	0.000420	T	0.16214	0.0390	N	0.08118	0	0.32277	N	0.568073	B;B;P;B;P	0.34864	0.241;0.091;0.473;0.335;0.473	B;B;B;B;B	0.30943	0.082;0.039;0.069;0.122;0.069	T	0.08576	-1.0715	10	0.27785	T	0.31	-15.8516	13.4976	0.61434	0.0:0.0:0.8441:0.1559	.	736;862;1287;1165;1307	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	Y	1307;1307;1287;1165;678;1307;736	ENSP00000283296:S1307Y;ENSP00000354563:S1287Y;ENSP00000412866:S1165Y;ENSP00000265417:S1307Y;ENSP00000441581:S736Y	ENSP00000265417:S1307Y	S	-	2	0	GPR116	46931711	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.156000	0.58138	2.702000	0.92279	0.650000	0.86243	TCT		0.418	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		T	46823752	G	T	46823752	3	4	61	1	0	0	0	0	1	0	0	0	6653	942	33	2	128	2	GPR116	6	46823752	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151408	46823752	124291315	4629	12614										
GPR116	221395	broad.mit.edu	37	chr6	46828469	46828469	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgtcatcatttctgaatTtacttgggttggaactgttg	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46828469T>G	ENST00000283296.7	-	16	2650	c.2362A>C	c.(2362-2364)Aat>Cat	p.N788H	GPR116_ENST00000545669.1_Missense_Mutation_p.N217H|GPR116_ENST00000265417.7_Missense_Mutation_p.N788H|GPR116_ENST00000456426.2_Missense_Mutation_p.N646H|GPR116_ENST00000362015.4_Missense_Mutation_p.N788H	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	788					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N788H(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			ATTTCTGAATTTACTTGGGTT	0.423																																					NSCLC(59;410 1274 8751 36715 50546)											1	Substitution - Missense(1)	large_intestine(1)	6											133	130	131					6																	46828469		2203	4300	6503	46936428	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2362A>C	6.37:g.46828469T>G	ENSP00000283296:p.Asn788His		46936428	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.897675	0.52121	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.30714	1.57;1.96;1.59;1.57;1.52	5.68	5.68	0.88126	.	0.188825	0.36778	N	0.002401	T	0.35799	0.0944	L	0.60455	1.87	0.27796	N	0.942644	D;D;D;D;D	0.63880	0.98;0.966;0.981;0.993;0.981	P;P;P;P;P	0.62649	0.804;0.702;0.635;0.905;0.635	T	0.29488	-1.0010	10	0.66056	D	0.02	-18.0487	12.3287	0.55026	0.0:0.0:0.0:1.0	.	217;343;788;646;788	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	H	788;788;788;646;159;788;217	ENSP00000283296:N788H;ENSP00000354563:N788H;ENSP00000412866:N646H;ENSP00000265417:N788H;ENSP00000441581:N217H	ENSP00000265417:N788H	N	-	1	0	GPR116	46936428	0.993000	0.37304	0.993000	0.49108	0.511000	0.34104	1.289000	0.33307	2.172000	0.68678	0.533000	0.62120	AAT		0.423	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		G	46828469	T	G	46828469	3	3	61	1	0	0	0	0	1	0	0	0	6653	1841	64	4	1702	4	GPR116	6	46828469	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4717	46828469	124286598	4630	12615										
GPR116	221395	broad.mit.edu	37	chr6	46856116	46856116	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcggtaatttggtcagtgTtattcccatgaattggaaaa	10	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:46856116T>G	ENST00000283296.7	-	4	572	c.284A>C	c.(283-285)aAc>aCc	p.N95T	GPR116_ENST00000265417.7_Missense_Mutation_p.N95T|GPR116_ENST00000478711.1_5'UTR|GPR116_ENST00000456426.2_Missense_Mutation_p.N95T|GPR116_ENST00000362015.4_Missense_Mutation_p.N95T	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	95					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N95T(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TTGGTCAGTGTTATTCCCATG	0.383																																					NSCLC(59;410 1274 8751 36715 50546)											1	Substitution - Missense(1)	large_intestine(1)	6											141	134	137					6																	46856116		2203	4300	6503	46964075	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.284A>C	6.37:g.46856116T>G	ENSP00000283296:p.Asn95Thr		46964075	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	T	1.093	-0.663496	0.03428	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.25414	1.83;2.21;1.8;1.83	5.66	-5.18	0.02840	.	1.597120	0.03495	N	0.217172	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.30208	-0.9986	10	0.23891	T	0.37	-0.3031	9.2403	0.37493	0.0:0.5926:0.1292:0.2782	.	95;95;95	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	T	95	ENSP00000283296:N95T;ENSP00000354563:N95T;ENSP00000412866:N95T;ENSP00000265417:N95T	ENSP00000265417:N95T	N	-	2	0	GPR116	46964075	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-1.023000	0.03607	-0.466000	0.06943	-0.290000	0.09829	AAC		0.383	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		G	46856116	T	G	46856116	3	3	61	1	0	0	0	0	1	0	0	0	6653	1725	60	4	3828	4	GPR116	6	46856116	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27647	46856116	124258951	4631	12616										
TNFRSF21	27242	broad.mit.edu	37	chr6	47200581	47200581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcttgactccaataatttCgaatagccggtctagtttgt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:47200581C>T	ENST00000296861.2	-	6	2281	c.1888G>A	c.(1888-1890)Gaa>Aaa	p.E630K		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	630					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)		p.E630K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			CCAATAATTTCGAATAGCCGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6											109	120	116					6																	47200581		2203	4300	6503	47308540	SO:0001583	missense	27242			AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1888G>A	6.37:g.47200581C>T	ENSP00000296861:p.Glu630Lys		47308540	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	C	32	5.125369	0.94429	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.70282	-0.47	5.95	5.95	0.96441	.	0.045975	0.85682	D	0.000000	T	0.70254	0.3203	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	P	0.62435	0.902	T	0.74200	-0.3742	10	0.87932	D	0	.	18.5737	0.91147	0.0:1.0:0.0:0.0	.	630	O75509	TNR21_HUMAN	K	630;319	ENSP00000296861:E630K	ENSP00000296861:E630K	E	-	1	0	TNFRSF21	47308540	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	GAA		0.493	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		T	47200581	C	T	47200581	3	4	61	1	0	0	0	0	1	0	0	0	16334	893	31	1	83	1	TNFRSF21	6	47200581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344465	47200581	123914486	4632	12617										
GPR115	221393	broad.mit.edu	37	chr6	47681856	47681856	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcatcccaagccattaGcatagctttcccaaccttgg	6	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:47681856G>T	ENST00000283303.2	+	6	1133	c.875G>T	c.(874-876)aGc>aTc	p.S292I	GPR115_ENST00000327753.3_Missense_Mutation_p.S292I|RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Missense_Mutation_p.S349I	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	292					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S292I(1)		NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						CAAGCCATTAGCATAGCTTTC	0.468																																					GBM(22;431 510 9010 26644 32828)											1	Substitution - Missense(1)	large_intestine(1)	6											55	58	57					6																	47681856		2203	4300	6503	47789815	SO:0001583	missense	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.875G>T	6.37:g.47681856G>T	ENSP00000283303:p.Ser292Ile		47789815	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Missense_Mutation	SNP	ENST00000283303.2	37	CCDS4922.2	.	.	.	.	.	.	.	.	.	.	G	8.560	0.877515	0.17395	.	.	ENSG00000153294	ENST00000371220;ENST00000327753;ENST00000283303	T;T;T	0.37752	1.42;1.18;1.18	5.19	1.12	0.20585	.	0.697449	0.14950	N	0.288947	T	0.26159	0.0638	M	0.77486	2.375	0.09310	N	1	P	0.45283	0.855	B	0.43413	0.419	T	0.11792	-1.0573	10	0.72032	D	0.01	-0.9993	12.0708	0.53616	0.0:0.5071:0.3625:0.1304	.	292	Q8IZF3	GP115_HUMAN	I	349;292;292	ENSP00000360264:S349I;ENSP00000328319:S292I;ENSP00000283303:S292I	ENSP00000283303:S292I	S	+	2	0	GPR115	47789815	0.311000	0.24536	0.128000	0.21923	0.655000	0.38815	1.829000	0.39121	-0.020000	0.14032	0.655000	0.94253	AGC		0.468	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		T	47681856	G	T	47681856	3	4	61	1	0	0	0	0	1	0	0	0	6652	971	34	2	893	2	GPR115	6	47681856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	481275	47681856	123433211	4633	12618										
MUT	4594	broad.mit.edu	37	chr6	49419385	49419385	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtccctccaaatactgctgCcattgcttctattgcagtac	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:49419385C>A	ENST00000274813.3	-	6	1253	c.1126G>T	c.(1126-1128)Gca>Tca	p.A376S		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	376					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)	p.A376S(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AATACTGCTGCCATTGCTTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											79	71	73					6																	49419385		2203	4300	6503	49527344	SO:0001583	missense	4594				CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"methylmalonyl Coenzyme A mutase"			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1126G>T	6.37:g.49419385C>A	ENSP00000274813:p.Ala376Ser		49527344	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449372	0.84101	.	.	ENSG00000146085	ENST00000274813	D	0.98835	-5.17	5.05	5.05	0.67936	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Cobalamin (vitamin B12)-dependent enzyme, catalytic subdomain (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.98429	0.9477	M	0.61703	1.905	0.80722	D	1	B	0.32338	0.365	P	0.50934	0.654	D	0.99795	1.1033	10	0.44086	T	0.13	-16.6432	17.3928	0.87437	0.0:1.0:0.0:0.0	.	376	P22033	MUTA_HUMAN	S	376	ENSP00000274813:A376S	ENSP00000274813:A376S	A	-	1	0	MUT	49527344	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.347000	0.79759	0.467000	0.42956	GCA		0.373	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			A	49419385	C	A	49419385	3	1	61	1	0	0	0	0	1	0	0	0	10021	739	26	2	1158	2	MUT	6	49419385	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1737529	49419385	121695682	4634	12619										
CRISP1	167	broad.mit.edu	37	chr6	49808636	49808636	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatagtgacaaacgtagaGatatcgaggtgatccttgtt	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:49808636G>T	ENST00000335847.4	-	6	609	c.508C>A	c.(508-510)Ctc>Atc	p.L170I	CRISP1_ENST00000355791.2_Missense_Mutation_p.L170I|CRISP1_ENST00000505118.1_Missense_Mutation_p.L170I|CRISP1_ENST00000329411.5_Missense_Mutation_p.L170I|CRISP1_ENST00000536021.1_Missense_Mutation_p.L170I|CRISP1_ENST00000507853.1_Missense_Mutation_p.L170I	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	170	SCP.				binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)	p.L170I(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					CAAACGTAGAGATATCGAGGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	90	93					6																	49808636		2203	4300	6503	49916595	SO:0001583	missense	167			D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.508C>A	6.37:g.49808636G>T	ENSP00000338276:p.Leu170Ile		49916595	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	37	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.896164	0.33442	.	.	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	4.8	-4.55	0.03441	Allergen V5/Tpx-1-related, conserved site (1);CAP domain (3);	1.107840	0.06749	N	0.779711	T	0.02418	0.0074	L	0.43646	1.37	0.09310	N	1	B;P	0.40660	0.011;0.726	B;B	0.42138	0.01;0.377	T	0.26360	-1.0105	9	.	.	.	.	5.6769	0.17753	0.4068:0.0:0.3859:0.2073	.	170;170	P54107-2;P54107	.;CRIS1_HUMAN	I	170	ENSP00000425020:L170I;ENSP00000338276:L170I;ENSP00000348044:L170I;ENSP00000331317:L170I;ENSP00000427589:L170I;ENSP00000441798:L170I	.	L	-	1	0	CRISP1	49916595	0.048000	0.20356	0.001000	0.08648	0.001000	0.01503	0.027000	0.13621	-1.352000	0.02194	-3.020000	0.00074	CTC		0.348	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		T	49808636	G	T	49808636	3	4	61	1	0	0	0	0	1	0	0	0	3885	942	33	2	253	2	CRISP1	6	49808636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	389251	49808636	121306431	4635	12620										
DEFB114	245928	broad.mit.edu	37	chr6	49928133	49928133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgtaacgtttggtgcaacGatcagcattcaccaaggtac	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:49928133G>A	ENST00000322066.3	-	2	81	c.82C>T	c.(82-84)Cgt>Tgt	p.R28C		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	28					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)	p.R28C(1)		kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TTGGTGCAACGATCAGCATTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	89	93					6																	49928133		2203	4299	6502	50036092	SO:0001583	missense	245928			DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"Defensins, beta"	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.82C>T	6.37:g.49928133G>A	ENSP00000312702:p.Arg28Cys		50036092	Q8NES9	Missense_Mutation	SNP	ENST00000322066.3	37	CCDS34474.1	.	.	.	.	.	.	.	.	.	.	G	7.567	0.665989	0.14710	.	.	ENSG00000177684	ENST00000322066	T	0.14516	2.5	3.55	1.57	0.23409	.	0.497156	0.15401	N	0.264318	T	0.14570	0.0352	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.64595	0.927	T	0.04360	-1.0957	8	.	.	.	-6.758	8.1693	0.31245	0.0:0.0:0.5073:0.4927	.	28	Q30KQ6	DB114_HUMAN	C	28	ENSP00000312702:R28C	.	R	-	1	0	DEFB114	50036092	0.004000	0.15560	0.001000	0.08648	0.481000	0.33189	1.070000	0.30653	0.383000	0.24910	0.650000	0.86243	CGT		0.353	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499		A	49928133	G	A	49928133	3	1	61	1	0	0	0	0	1	0	0	0	4413	1058	37	1	130	1	DEFB114	6	49928133	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119497	49928133	121186934	4636	12621										
TFAP2D	83741	broad.mit.edu	37	chr6	50718949	50718949	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtaaagaattccaagacCtcttgagccaagatagatca	7	9	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:50718949C>A	ENST00000008391.3	+	7	1279	c.1051C>A	c.(1051-1053)Ctc>Atc	p.L351I	TFAP2D_ENST00000492804.1_3'UTR	NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.L351I(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					ATTCCAAGACCTCTTGAGCCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	83	85					6																	50718949		2203	4299	6502	50826908	SO:0001583	missense	83741			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1051C>A	6.37:g.50718949C>A	ENSP00000008391:p.Leu351Ile		50826908		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068889	0.76301	.	.	ENSG00000008197	ENST00000008391	D	0.96992	-4.2	5.48	4.61	0.57282	Transcription factor AP-2, C-terminal (1);	0.000000	0.64402	D	0.000001	D	0.94282	0.8163	L	0.50993	1.605	0.58432	D	0.999999	P	0.41498	0.752	P	0.46917	0.531	D	0.94334	0.7564	10	0.51188	T	0.08	-12.8213	13.6818	0.62489	0.0:0.9258:0.0:0.0742	.	351	Q7Z6R9	AP2D_HUMAN	I	351	ENSP00000008391:L351I	ENSP00000008391:L351I	L	+	1	0	TFAP2D	50826908	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.774000	0.55341	2.574000	0.86865	0.484000	0.47621	CTC		0.343	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		A	50718949	C	A	50718949	3	1	61	1	0	0	0	0	1	0	0	0	15829	681	24	2	1077	2	TFAP2D	6	50718949	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	790816	50718949	120396118	4637	12622										
TFAP2B	7021	broad.mit.edu	37	chr6	50791466	50791466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccccggagggactaccactCggtccgccggccggacgtgc	14	18	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:50791466C>T	ENST00000393655.3	+	2	597	c.428C>T	c.(427-429)tCg>tTg	p.S143L	TFAP2B_ENST00000263046.4_Missense_Mutation_p.S152L|TFAP2B_ENST00000489228.1_3'UTR	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	143					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.S143L(2)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					GACTACCACTCGGTCCGCCGG	0.716																																					Pancreas(116;1373 2332 5475 10752)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6											10	12	11					6																	50791466		2184	4284	6468	50899425	SO:0001583	missense	7021			X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.428C>T	6.37:g.50791466C>T	ENSP00000377265:p.Ser143Leu		50899425	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	C	17.83	3.486240	0.63962	.	.	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;T;D	0.97378	-4.36;-1.12;-4.35	5.43	4.57	0.56435	.	0.272626	0.36591	N	0.002515	D	0.89065	0.6609	N	0.14661	0.345	0.52501	D	0.999955	B	0.24368	0.102	B	0.12837	0.008	D	0.87059	0.2152	10	0.72032	D	0.01	-1.5245	13.9744	0.64262	0.0:0.927:0.0:0.073	.	143	Q92481	AP2B_HUMAN	L	143;141;152	ENSP00000377265:S143L;ENSP00000342252:S141L;ENSP00000263046:S152L	ENSP00000263046:S152L	S	+	2	0	TFAP2B	50899425	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	4.027000	0.57239	1.303000	0.44873	0.563000	0.77884	TCG		0.716	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		T	50791466	C	T	50791466	3	4	61	1	0	0	0	0	1	0	0	0	15827	893	31	1	434	1	TFAP2B	6	50791466	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72517	50791466	120323601	4638	12623										
TFAP2B	7021	broad.mit.edu	37	chr6	50796339	50796339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatattcacagtcagttgAagatgccaataacagcggca	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:50796339A>T	ENST00000393655.3	+	3	717	c.548A>T	c.(547-549)gAa>gTa	p.E183V	TFAP2B_ENST00000263046.4_Missense_Mutation_p.E192V	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	183					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.E183V(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					CAGTCAGTTGAAGATGCCAAT	0.338																																					Pancreas(116;1373 2332 5475 10752)											1	Substitution - Missense(1)	large_intestine(1)	6											112	110	111					6																	50796339		2203	4300	6503	50904298	SO:0001583	missense	7021			X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.548A>T	6.37:g.50796339A>T	ENSP00000377265:p.Glu183Val		50904298	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	A	14.05	2.418426	0.42918	.	.	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;D;D	0.83250	-1.7;-1.7;-1.7	5.9	5.9	0.94986	.	0.076902	0.56097	D	0.000033	T	0.77624	0.4158	M	0.67397	2.05	0.80722	D	1	P	0.48911	0.917	B	0.44315	0.446	T	0.77024	-0.2741	10	0.25106	T	0.35	-15.5372	16.3317	0.83023	1.0:0.0:0.0:0.0	.	183	Q92481	AP2B_HUMAN	V	183;181;192	ENSP00000377265:E183V;ENSP00000342252:E181V;ENSP00000263046:E192V	ENSP00000263046:E192V	E	+	2	0	TFAP2B	50904298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.815000	0.91973	2.264000	0.75181	0.533000	0.62120	GAA		0.338	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		T	50796339	A	T	50796339	3	4	61	1	0	0	0	0	1	0	0	0	15827	246	9	5	558	5	TFAP2B	6	50796339	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4873	50796339	120318728	4639	12624										
TFAP2B	7021	broad.mit.edu	37	chr6	50803903	50803903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctgctcagttcaacttCgaagtacaaagtaactgtgg	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:50803903C>T	ENST00000393655.3	+	4	900	c.731C>T	c.(730-732)tCg>tTg	p.S244L	TFAP2B_ENST00000263046.4_Missense_Mutation_p.S253L	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	244					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.S244L(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					AGTTCAACTTCGAAGTACAAA	0.537																																					Pancreas(116;1373 2332 5475 10752)											1	Substitution - Missense(1)	large_intestine(1)	6											70	68	69					6																	50803903		2203	4300	6503	50911862	SO:0001583	missense	7021			X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.731C>T	6.37:g.50803903C>T	ENSP00000377265:p.Ser244Leu		50911862	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989448	0.74589	.	.	ENSG00000008196	ENST00000393655;ENST00000263046	D;D	0.97811	-4.55;-4.55	5.44	5.44	0.79542	Transcription factor AP-2, C-terminal (1);	0.119560	0.64402	D	0.000018	D	0.98979	0.9652	M	0.90252	3.1	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	D	0.99764	1.1022	10	0.87932	D	0	-5.3343	19.2724	0.94016	0.0:1.0:0.0:0.0	.	244	Q92481	AP2B_HUMAN	L	244;253	ENSP00000377265:S244L;ENSP00000263046:S253L	ENSP00000263046:S253L	S	+	2	0	TFAP2B	50911862	1.000000	0.71417	1.000000	0.80357	0.607000	0.37147	7.818000	0.86416	2.561000	0.86390	0.650000	0.86243	TCG		0.537	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		T	50803903	C	T	50803903	3	4	61	1	0	0	0	0	1	0	0	0	15827	893	31	1	745	1	TFAP2B	6	50803903	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7564	50803903	120311164	4640	12625										
PKHD1	5314	broad.mit.edu	37	chr6	51484119	51484119	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctccttccagttcccagtCtcttgcaggtacacctgctg	7	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51484119C>A	ENST00000371117.3	-	67	12260	c.11985G>T	c.(11983-11985)gaG>gaT	p.E3995D	RP3-335N17.2_ENST00000589278.2_RNA|RP3-335N17.2_ENST00000587000.1_RNA|RP3-335N17.2_ENST00000454361.1_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3995					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E3995D(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGTTCCCAGTCTCTTGCAGGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	69	71					6																	51484119		2203	4300	6503	51592078	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11985G>T	6.37:g.51484119C>A	ENSP00000360158:p.Glu3995Asp		51592078	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.186908	0.57909	.	.	ENSG00000170927	ENST00000371117	D	0.91237	-2.81	4.83	2.02	0.26589	.	0.000000	0.47852	D	0.000205	D	0.90442	0.7007	M	0.66939	2.045	0.32910	D	0.514356	D	0.63880	0.993	D	0.70016	0.967	D	0.88064	0.2796	10	0.87932	D	0	.	7.3426	0.26646	0.0:0.6988:0.0:0.3012	.	3995	P08F94	PKHD1_HUMAN	D	3995	ENSP00000360158:E3995D	ENSP00000360158:E3995D	E	-	3	2	PKHD1	51592078	0.211000	0.23529	0.497000	0.27552	0.859000	0.49053	0.391000	0.20784	0.578000	0.29487	0.655000	0.94253	GAG		0.572	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51484119	C	A	51484119	3	1	61	1	0	0	0	0	1	0	0	0	12002	912	32	2	243	2	PKHD1	6	51484119	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	680216	51484119	119630948	4641	12626										
PKHD1	5314	broad.mit.edu	37	chr6	51523790	51523790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactgagtaactagtaaggCcccgatagtcatattcagaa	9	8	2	3	rs200358765		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51523790C>T	ENST00000371117.3	-	61	11409	c.11134G>A	c.(11134-11136)Gcc>Acc	p.A3712T		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3712					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.A3712T(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ACTAGTAAGGCCCCGATAGTC	0.388													C|||	1	0.000199681	0	0	5008	,	,		18485	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											129	128	128					6																	51523790		2203	4300	6503	51631749	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11134G>A	6.37:g.51523790C>T	ENSP00000360158:p.Ala3712Thr		51631749	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	9.835	1.189543	0.21954	.	.	ENSG00000170927	ENST00000371117	D	0.86497	-2.13	5.8	4.84	0.62591	.	0.338429	0.28865	N	0.013891	T	0.70116	0.3187	L	0.49350	1.555	0.47778	D	0.99951	B	0.10296	0.003	B	0.12156	0.007	T	0.67309	-0.5703	10	0.30078	T	0.28	.	5.2549	0.15542	0.1594:0.6552:0.0:0.1854	.	3712	P08F94	PKHD1_HUMAN	T	3712	ENSP00000360158:A3712T	ENSP00000360158:A3712T	A	-	1	0	PKHD1	51631749	0.643000	0.27269	0.966000	0.40874	0.595000	0.36748	1.058000	0.30504	1.283000	0.44513	0.655000	0.94253	GCC		0.388	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51523790	C	T	51523790	3	4	61	1	0	0	0	0	1	0	0	0	12002	739	26	3	1118	3	PKHD1	6	51523790	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39671	51523790	119591277	4642	12627										
PKHD1	5314	broad.mit.edu	37	chr6	51524480	51524480	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccccaatagaaaaaagcGcaaaacttgaggagtttgat	9	7	0	3	rs148617572		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51524480G>A	ENST00000371117.3	-	61	10719	c.10444C>T	c.(10444-10446)Cgc>Tgc	p.R3482C		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3482			R -> C (in ARPKD). {ECO:0000269|PubMed:12506140, ECO:0000269|PubMed:15108281}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.R3482C(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGAAAAAAGCGCAAAACTTGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6	GRCh37	CM032336	PKHD1	M	rs148617572	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	76	78	78		10444	3.9	0.5	6	dbSNP_134	78	0,8600		0,0,4300	no	missense	PKHD1	NM_138694.3	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	3482/4075	51524480	1,13005	2203	4300	6503	51632439	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10444C>T	6.37:g.51524480G>A	ENSP00000360158:p.Arg3482Cys		51632439	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201621	0.58234	2.27E-4	0.0	ENSG00000170927	ENST00000371117	D	0.94184	-3.37	5.72	3.89	0.44902	.	0.341409	0.25765	N	0.028456	D	0.90045	0.6891	L	0.34521	1.04	0.29128	N	0.879818	D	0.89917	1.0	P	0.57846	0.828	D	0.86300	0.1679	10	0.66056	D	0.02	.	13.3409	0.60545	0.0:0.0:0.4578:0.5422	.	3482	P08F94	PKHD1_HUMAN	C	3482	ENSP00000360158:R3482C	ENSP00000360158:R3482C	R	-	1	0	PKHD1	51632439	0.999000	0.42202	0.472000	0.27241	0.911000	0.54048	2.559000	0.45888	0.717000	0.32145	0.655000	0.94253	CGC		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51524480	G	A	51524480	3	1	61	1	0	0	0	0	1	0	0	0	12002	1087	38	1	1808	1	PKHD1	6	51524480	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	690	51524480	119590587	4643	12628										
PKHD1	5314	broad.mit.edu	37	chr6	51640637	51640637	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtcaatatgaattccattCatacggtcacaaaagactcc	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51640637C>A	ENST00000371117.3	-	54	8798	c.8523G>T	c.(8521-8523)atG>atT	p.M2841I	PKHD1_ENST00000340994.4_Missense_Mutation_p.M2841I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2841	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.M2841I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAATTCCATTCATACGGTCAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	75	75					6																	51640637		2203	4299	6502	51748596	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8523G>T	6.37:g.51640637C>A	ENSP00000360158:p.Met2841Ile		51748596	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050007	0.19827	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.86956	-1.98;-2.19	5.63	-4.58	0.03410	G8 domain (2);	0.741661	0.13003	N	0.421530	T	0.45756	0.1358	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45556	-0.9253	10	0.33940	T	0.23	.	3.5785	0.07943	0.3191:0.423:0.1666:0.0913	.	2841;2841;2841	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	2841	ENSP00000360158:M2841I;ENSP00000341097:M2841I	ENSP00000341097:M2841I	M	-	3	0	PKHD1	51748596	0.002000	0.14202	0.000000	0.03702	0.508000	0.34012	-0.199000	0.09491	-0.805000	0.04404	0.313000	0.20887	ATG		0.338	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51640637	C	A	51640637	3	1	61	1	0	0	0	0	1	0	0	0	12002	826	29	2	3796	2	PKHD1	6	51640637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116157	51640637	119474430	4644	12629										
PKHD1	5314	broad.mit.edu	37	chr6	51640698	51640698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagaagcttttgttcctttTctaagggattttctaaagta	7	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51640698T>C	ENST00000371117.3	-	54	8737	c.8462A>G	c.(8461-8463)gAa>gGa	p.E2821G	PKHD1_ENST00000340994.4_Missense_Mutation_p.E2821G	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2821	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E2821G(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TTGTTCCTTTTCTAAGGGATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	67	67					6																	51640698		2203	4299	6502	51748657	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8462A>G	6.37:g.51640698T>C	ENSP00000360158:p.Glu2821Gly		51748657	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.055442	0.36277	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.89617	-2.54;-2.54	5.63	3.16	0.36331	G8 domain (2);	0.648906	0.15549	N	0.256504	T	0.76919	0.4055	M	0.65975	2.015	0.09310	N	1	B;B;B	0.22003	0.063;0.013;0.003	B;B;B	0.23018	0.043;0.017;0.007	T	0.66968	-0.5789	10	0.35671	T	0.21	.	8.55	0.33447	0.0:0.1543:0.0:0.8457	.	2821;2821;2821	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	G	2821	ENSP00000360158:E2821G;ENSP00000341097:E2821G	ENSP00000341097:E2821G	E	-	2	0	PKHD1	51748657	0.961000	0.32948	0.560000	0.28344	0.935000	0.57460	1.349000	0.33998	0.386000	0.24997	0.260000	0.18958	GAA		0.338	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51640698	T	C	51640698	3	2	61	1	0	0	0	0	1	0	0	0	12002	1783	62	4	3857	4	PKHD1	6	51640698	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	61	51640698	119474369	4645	12630										
PKHD1	5314	broad.mit.edu	37	chr6	51712645	51712645	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgacctggtgatggaaGaaatggaaaagacagaccca	12	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51712645G>T	ENST00000371117.3	-	50	8310	c.8035C>A	c.(8035-8037)Ctt>Att	p.L2679I	PKHD1_ENST00000340994.4_Missense_Mutation_p.L2679I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2679					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.L2679I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGTGATGGAAGAAATGGAAAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	6											149	135	140					6																	51712645		2203	4300	6503	51820604	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8035C>A	6.37:g.51712645G>T	ENSP00000360158:p.Leu2679Ile		51820604	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	7.843	0.722255	0.15372	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87334	-2.05;-2.24	5.47	4.58	0.56647	.	0.567197	0.16951	N	0.192881	T	0.71567	0.3355	L	0.40543	1.245	0.09310	N	1	P;P;P	0.39424	0.666;0.673;0.483	B;B;B	0.39706	0.162;0.307;0.122	T	0.61959	-0.6955	10	0.18710	T	0.47	.	11.3979	0.49854	0.0738:0.1292:0.797:0.0	.	2679;2679;2679	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	2679	ENSP00000360158:L2679I;ENSP00000341097:L2679I	ENSP00000341097:L2679I	L	-	1	0	PKHD1	51820604	0.397000	0.25270	0.361000	0.25849	0.121000	0.20230	2.197000	0.42696	2.720000	0.93068	0.650000	0.86243	CTT		0.483	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51712645	G	T	51712645	3	4	61	1	0	0	0	0	1	0	0	0	12002	942	33	2	4300	2	PKHD1	6	51712645	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71947	51712645	119402422	4646	12631										
PKHD1	5314	broad.mit.edu	37	chr6	51732787	51732787	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaagcaagaatgtgacttCtgtttttcccagacagagac	9	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51732787C>A	ENST00000371117.3	-	48	7882	c.7607G>T	c.(7606-7608)aGa>aTa	p.R2536I	PKHD1_ENST00000340994.4_Missense_Mutation_p.R2536I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2536					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.R2536I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AATGTGACTTCTGTTTTTCCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											88	82	84					6																	51732787		2203	4299	6502	51840746	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7607G>T	6.37:g.51732787C>A	ENSP00000360158:p.Arg2536Ile		51840746	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.663418	0.29515	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87103	-2.0;-2.21	5.67	3.87	0.44632	.	0.636295	0.16798	N	0.199106	T	0.70789	0.3264	L	0.44542	1.39	0.30788	N	0.741281	P;P;P	0.46277	0.761;0.875;0.855	B;B;B	0.40534	0.135;0.332;0.187	T	0.67055	-0.5767	10	0.87932	D	0	.	6.8874	0.24209	0.0:0.7044:0.1451:0.1505	.	2536;2536;2536	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	2536	ENSP00000360158:R2536I;ENSP00000341097:R2536I	ENSP00000341097:R2536I	R	-	2	0	PKHD1	51840746	0.611000	0.26992	0.208000	0.23602	0.685000	0.39939	0.980000	0.29513	0.742000	0.32697	-0.282000	0.10007	AGA		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51732787	C	A	51732787	3	1	61	1	0	0	0	0	1	0	0	0	12002	913	32	2	4736	2	PKHD1	6	51732787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20142	51732787	119382280	4647	12632										
PKHD1	5314	broad.mit.edu	37	chr6	51735425	51735425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttttaatcccagatgacaTacacagacttccctgtgatt	6	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51735425T>C	ENST00000371117.3	-	47	7638	c.7363A>G	c.(7363-7365)Atg>Gtg	p.M2455V	PKHD1_ENST00000340994.4_Missense_Mutation_p.M2455V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2455					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.M2455V(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CCAGATGACATACACAGACTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											106	103	104					6																	51735425		2203	4300	6503	51843384	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7363A>G	6.37:g.51735425T>C	ENSP00000360158:p.Met2455Val		51843384	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447023	0.63178	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87029	-2.01;-2.2	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.91057	0.7186	M	0.72479	2.2	0.36083	D	0.842948	D;D;D	0.67145	0.983;0.984;0.996	P;P;D	0.70227	0.829;0.879;0.968	D	0.92277	0.5830	10	0.54805	T	0.06	.	15.4114	0.74923	0.0:0.0:0.0:1.0	.	2455;2455;2455	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	V	2455	ENSP00000360158:M2455V;ENSP00000341097:M2455V	ENSP00000341097:M2455V	M	-	1	0	PKHD1	51843384	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.219000	0.65262	2.233000	0.73108	0.533000	0.62120	ATG		0.333	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51735425	T	C	51735425	3	2	61	1	0	0	0	0	1	0	0	0	12002	1406	49	4	4984	4	PKHD1	6	51735425	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2638	51735425	119379642	4648	12633										
PKHD1	5314	broad.mit.edu	37	chr6	51777270	51777270	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttccactgatgatgacaaCttcatccccagggttccagt	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51777270C>A	ENST00000371117.3	-	38	6501	c.6226G>T	c.(6226-6228)Gtt>Ttt	p.V2076F	PKHD1_ENST00000340994.4_Missense_Mutation_p.V2076F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2076					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.V2076F(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ATGATGACAACTTCATCCCCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6											179	163	169					6																	51777270		2203	4300	6503	51885229	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.6226G>T	6.37:g.51777270C>A	ENSP00000360158:p.Val2076Phe		51885229	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574086	0.86542	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.93247	-3.19;-3.19	5.99	5.99	0.97316	.	0.889096	0.09735	N	0.762686	D	0.91540	0.7328	L	0.61218	1.895	0.31061	N	0.714091	P;P;P	0.50710	0.877;0.938;0.877	B;B;P	0.45037	0.368;0.435;0.467	D	0.88334	0.2970	10	0.72032	D	0.01	.	15.9758	0.80063	0.0:1.0:0.0:0.0	.	2076;2076;2076	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	F	2076	ENSP00000360158:V2076F;ENSP00000341097:V2076F	ENSP00000341097:V2076F	V	-	1	0	PKHD1	51885229	1.000000	0.71417	0.979000	0.43373	0.948000	0.59901	2.682000	0.46934	2.847000	0.97988	0.655000	0.94253	GTT		0.478	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51777270	C	A	51777270	3	1	61	1	0	0	0	0	1	0	0	0	12002	565	20	2	6157	2	PKHD1	6	51777270	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41845	51777270	119337797	4649	12634										
PKHD1	5314	broad.mit.edu	37	chr6	51875137	51875137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccccagcgtttccgtatCtcagtaatcttgacggtaat	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51875137C>A	ENST00000371117.3	-	35	5996	c.5721G>T	c.(5719-5721)gaG>gaT	p.E1907D	PKHD1_ENST00000340994.4_Missense_Mutation_p.E1907D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1907					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E1907D(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GTTTCCGTATCTCAGTAATCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											141	125	130					6																	51875137		2203	4300	6503	51983096	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5721G>T	6.37:g.51875137C>A	ENSP00000360158:p.Glu1907Asp		51983096	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638812	0.47153	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88354	-2.17;-2.37	5.53	4.65	0.58169	.	0.071141	0.64402	D	0.000019	D	0.86464	0.5939	L	0.32530	0.975	0.32774	N	0.503348	D;D	0.69078	0.997;0.988	P;P	0.62184	0.899;0.76	D	0.86984	0.2106	10	0.56958	D	0.05	.	13.3876	0.60805	0.0:0.9232:0.0:0.0768	.	1907;1907	P08F94-2;P08F94	.;PKHD1_HUMAN	D	1907	ENSP00000360158:E1907D;ENSP00000341097:E1907D	ENSP00000341097:E1907D	E	-	3	2	PKHD1	51983096	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.214000	0.51161	1.307000	0.44944	0.557000	0.71058	GAG		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51875137	C	A	51875137	3	1	61	1	0	0	0	0	1	0	0	0	12002	912	32	2	6674	2	PKHD1	6	51875137	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97867	51875137	119239930	4650	12635										
PKHD1	5314	broad.mit.edu	37	chr6	51918880	51918880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagtcacaggtggtattCtttaccatgttttgaaagcc	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51918880C>A	ENST00000371117.3	-	20	2195	c.1920G>T	c.(1918-1920)aaG>aaT	p.K640N	PKHD1_ENST00000340994.4_Missense_Mutation_p.K640N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	640					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.K640N(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGGTGGTATTCTTTACCATGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6											143	117	126					6																	51918880		2203	4300	6503	52026839	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1920G>T	6.37:g.51918880C>A	ENSP00000360158:p.Lys640Asn		52026839	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754618	0.31046	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87729	-2.09;-2.29	5.36	5.36	0.76844	.	0.162599	0.42548	D	0.000683	T	0.74321	0.3701	M	0.64997	1.995	0.31366	N	0.680748	B;P	0.39480	0.347;0.675	B;B	0.30782	0.12;0.111	T	0.76903	-0.2787	10	0.54805	T	0.06	.	9.8404	0.40996	0.0:0.8427:0.0:0.1573	.	640;640	P08F94-2;P08F94	.;PKHD1_HUMAN	N	640	ENSP00000360158:K640N;ENSP00000341097:K640N	ENSP00000341097:K640N	K	-	3	2	PKHD1	52026839	0.959000	0.32827	0.987000	0.45799	0.136000	0.21042	0.725000	0.25970	2.516000	0.84829	0.591000	0.81541	AAG		0.493	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51918880	C	A	51918880	3	1	61	1	0	0	0	0	1	0	0	0	12002	912	32	2	10535	2	PKHD1	6	51918880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43743	51918880	119196187	4651	12636										
PKHD1	5314	broad.mit.edu	37	chr6	51929780	51929780	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggtggtgagcctcacatCttttcctggagcccgagtgg	15	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:51929780C>A	ENST00000371117.3	-	13	1224	c.949G>T	c.(949-951)Gat>Tat	p.D317Y	PKHD1_ENST00000340994.4_Missense_Mutation_p.D317Y	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	317	IPT/TIG 3.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.D317Y(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGCCTCACATCTTTTCCTGGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											98	97	97					6																	51929780		2203	4300	6503	52037739	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.949G>T	6.37:g.51929780C>A	ENSP00000360158:p.Asp317Tyr		52037739	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	7.945	0.743665	0.15642	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87729	-2.08;-2.29	5.77	3.04	0.35103	Cell surface receptor IPT/TIG (1);	0.642544	0.15132	N	0.278769	T	0.66015	0.2747	N	0.22421	0.69	0.09310	N	1	P;P	0.40834	0.683;0.73	B;B	0.41440	0.163;0.357	T	0.59107	-0.7516	10	0.56958	D	0.05	.	6.8385	0.23949	0.0:0.6607:0.1269:0.2125	.	317;317	P08F94-2;P08F94	.;PKHD1_HUMAN	Y	317	ENSP00000360158:D317Y;ENSP00000341097:D317Y	ENSP00000341097:D317Y	D	-	1	0	PKHD1	52037739	0.000000	0.05858	0.334000	0.25495	0.311000	0.27955	-0.229000	0.09098	0.454000	0.26884	-0.137000	0.14449	GAT		0.448	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51929780	C	A	51929780	3	1	61	1	0	0	0	0	1	0	0	0	12002	913	32	2	11534	2	PKHD1	6	51929780	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10900	51929780	119185287	4652	12637										
MCM3	4172	broad.mit.edu	37	chr6	52141212	52141212	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagacattttgtcaaattCatcaatgcaaaccacgcctc	5	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52141212C>A	ENST00000229854.7	-	9	1304	c.1228G>T	c.(1228-1230)Gaa>Taa	p.E410*	MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000419835.2_Nonsense_Mutation_p.E364*|MCM3_ENST00000596288.1_Nonsense_Mutation_p.E455*			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	410	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.E410*(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					TTGTCAAATTCATCAATGCAA	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											89	72	77					6																	52141212		2203	4300	6503	52249171	SO:0001587	stop_gained	4172			X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1228G>T	6.37:g.52141212C>A	ENSP00000229854:p.Glu410*		52249171	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Nonsense_Mutation	SNP	ENST00000229854.7	37		.	.	.	.	.	.	.	.	.	.	C	38	6.683601	0.97759	.	.	ENSG00000112118	ENST00000229854;ENST00000419835	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-23.8408	18.7743	0.91904	0.0:1.0:0.0:0.0	.	.	.	.	X	410;364	.	ENSP00000229854:E410X	E	-	1	0	MCM3	52249171	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.651000	0.83577	2.669000	0.90835	0.655000	0.94253	GAA		0.532	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			A	52141212	C	A	52141212	4	1	61	1	0	0	0	0	0	1	0	0	9417	835	29	2	1234	2	MCM3	6	52141212	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211432	52141212	118973855	4653	12638										
MCM3	4172	broad.mit.edu	37	chr6	52146962	52146962	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcggacgactttgggacGaactagagaacctagggatg	14	8	0	1	rs371347878		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52146962G>A	ENST00000229854.7	-	4	488	c.412C>T	c.(412-414)Cgt>Tgt	p.R138C	MCM3_ENST00000476448.1_5'Flank|MCM3_ENST00000419835.2_Missense_Mutation_p.R92C|MCM3_ENST00000596288.1_Missense_Mutation_p.R183C			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	138					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.R138C(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					ACTTTGGGACGAACTAGAGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	CYS/ARG	0,4406		0,0,2203	137	125	129		412	5.7	1	6		129	1,8599	1.2+/-3.3	0,1,4299	no	missense	MCM3	NM_002388.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	138/809	52146962	1,13005	2203	4300	6503	52254921	SO:0001583	missense	4172			X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.412C>T	6.37:g.52146962G>A	ENSP00000229854:p.Arg138Cys		52254921	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	37		.	.	.	.	.	.	.	.	.	.	G	29.4	5.004579	0.93287	0.0	1.16E-4	ENSG00000112118	ENST00000229854;ENST00000419835	T;T	0.05447	3.44;3.44	5.69	5.69	0.88448	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.32556	0.0833	H	0.95079	3.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.959;0.993	T	0.49062	-0.8978	10	0.62326	D	0.03	-9.1986	19.8155	0.96566	0.0:0.0:1.0:0.0	.	92;138	B4DUQ9;P25205	.;MCM3_HUMAN	C	138;92	ENSP00000229854:R138C;ENSP00000388647:R92C	ENSP00000229854:R138C	R	-	1	0	MCM3	52254921	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	7.803000	0.85983	2.691000	0.91804	0.563000	0.77884	CGT		0.478	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			A	52146962	G	A	52146962	3	1	61	1	0	0	0	0	1	0	0	0	9417	1058	37	1	2070	1	MCM3	6	52146962	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5750	52146962	118968105	4654	12639										
EFHC1	114327	broad.mit.edu	37	chr6	52303219	52303219	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacagcatgtctgtcataGagcctgttgtagaaaattct	9	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52303219G>T	ENST00000371068.5	+	3	506	c.403G>T	c.(403-405)Gag>Tag	p.E135*	EFHC1_ENST00000433625.2_Nonsense_Mutation_p.E44*|EFHC1_ENST00000491749.1_3'UTR|EFHC1_ENST00000538167.1_Nonsense_Mutation_p.E116*	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	135	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)	p.E135*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					GTCTGTCATAGAGCCTGTTGT	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											61	62	62					6																	52303219		2203	4300	6503	52411178	SO:0001587	stop_gained	114327			AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.403G>T	6.37:g.52303219G>T	ENSP00000360107:p.Glu135*		52411178	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Nonsense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530879	0.96446	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.5359	0.95254	0.0:0.0:1.0:0.0	.	.	.	.	X	135;44;116	.	ENSP00000360107:E135X	E	+	1	0	EFHC1	52411178	1.000000	0.71417	0.982000	0.44146	0.995000	0.86356	7.897000	0.87356	2.617000	0.88574	0.655000	0.94253	GAG		0.423	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		T	52303219	G	T	52303219	4	4	61	1	0	0	0	0	0	1	0	0	4957	943	33	2	423	2	EFHC1	6	52303219	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	156257	52303219	118811848	4655	12640										
EFHC1	114327	broad.mit.edu	37	chr6	52318904	52318904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcaaaggtccttcgattCtatgcaatctgggatgatac	8	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52318904C>A	ENST00000371068.5	+	5	838	c.735C>A	c.(733-735)ttC>ttA	p.F245L	EFHC1_ENST00000433625.2_Missense_Mutation_p.F154L|EFHC1_ENST00000538167.1_Missense_Mutation_p.F226L	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	245	DM10 2. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)	p.F245L(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TCCTTCGATTCTATGCAATCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											130	118	122					6																	52318904		2203	4300	6503	52426863	SO:0001583	missense	114327			AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.735C>A	6.37:g.52318904C>A	ENSP00000360107:p.Phe245Leu		52426863	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725480	0.68959	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.80653	-1.11;-1.35;-1.4	5.87	3.15	0.36227	Uncharacterised domain DM10 (2);	0.042830	0.85682	D	0.000000	D	0.90954	0.7156	H	0.95884	3.735	0.46437	D	0.999041	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.75484	0.983;0.967;0.986	D	0.93273	0.6653	10	0.87932	D	0	-17.5269	15.0862	0.72155	0.0:0.87:0.0:0.13	.	226;154;245	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	L	245;154;226	ENSP00000360107:F245L;ENSP00000416492:F154L;ENSP00000444521:F226L	ENSP00000360107:F245L	F	+	3	2	EFHC1	52426863	1.000000	0.71417	0.999000	0.59377	0.907000	0.53573	1.149000	0.31626	0.396000	0.25283	-1.287000	0.01368	TTC		0.403	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		A	52318904	C	A	52318904	3	1	61	1	0	0	0	0	1	0	0	0	4957	912	32	2	763	2	EFHC1	6	52318904	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15685	52318904	118796163	4656	12641										
EFHC1	114327	broad.mit.edu	37	chr6	52318995	52318995	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatgatacggtggaaattCgagaggtccacgaacggaat	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52318995C>T	ENST00000371068.5	+	5	929	c.826C>T	c.(826-828)Cga>Tga	p.R276*	EFHC1_ENST00000433625.2_Nonsense_Mutation_p.R185*|EFHC1_ENST00000538167.1_Nonsense_Mutation_p.R257*	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	276	DM10 2. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)	p.R276*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					GGTGGAAATTCGAGAGGTCCA	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											179	162	167					6																	52318995		2203	4300	6503	52426954	SO:0001587	stop_gained	114327			AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.826C>T	6.37:g.52318995C>T	ENSP00000360107:p.Arg276*		52426954	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Nonsense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	C	38	6.971522	0.97971	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	.	.	.	5.87	4.99	0.66335	.	0.250637	0.40469	N	0.001087	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-0.2299	14.2317	0.65898	0.2703:0.7297:0.0:0.0	.	.	.	.	X	276;185;257	.	ENSP00000360107:R276X	R	+	1	2	EFHC1	52426954	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.974000	0.29436	1.460000	0.47911	0.591000	0.81541	CGA		0.448	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		T	52318995	C	T	52318995	4	4	61	1	0	0	0	0	0	1	0	0	4957	876	31	1	854	1	EFHC1	6	52318995	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91	52318995	118796072	4657	12642										
TRAM2	9697	broad.mit.edu	37	chr6	52400622	52400622	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatactgaggtaaaataaatAgaaaggcagtcttggctgtg	11	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52400622A>C	ENST00000182527.3	-	2	142	c.143T>G	c.(142-144)cTa>cGa	p.L48R		NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN	translocation associated membrane protein 2	48					collagen biosynthetic process (GO:0032964)|protein transport (GO:0015031)	integral component of membrane (GO:0016021)		p.L48R(1)		endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13	Lung NSC(77;0.109)					TAAAATAAATAGAAAGGCAGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	95	96					6																	52400622		2203	4300	6503	52508581	SO:0001583	missense	9697			D31762	CCDS34477.1	6p21.1-p12	2008-02-05			ENSG00000065308	ENSG00000065308			16855	protein-coding gene	gene with protein product		608485				7584044, 10594243	Standard	NM_012288		Approved	KIAA0057	uc003paq.3	Q15035	OTTHUMG00000014850	ENST00000182527.3:c.143T>G	6.37:g.52400622A>C	ENSP00000182527:p.Leu48Arg		52508581	A8K6T6	Missense_Mutation	SNP	ENST00000182527.3	37	CCDS34477.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.229468	0.79688	.	.	ENSG00000065308	ENST00000182527	.	.	.	5.14	5.14	0.70334	TRAM1-like protein (1);	0.074317	0.53938	D	0.000048	T	0.58075	0.2097	M	0.61703	1.905	0.58432	D	0.999999	D	0.54047	0.964	P	0.58077	0.832	T	0.57849	-0.7740	9	0.31617	T	0.26	.	12.788	0.57518	1.0:0.0:0.0:0.0	.	48	Q15035	TRAM2_HUMAN	R	48	.	ENSP00000182527:L48R	L	-	2	0	TRAM2	52508581	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.240000	0.65378	2.071000	0.62044	0.533000	0.62120	CTA		0.453	TRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040910.1	NM_012288		C	52400622	A	C	52400622	3	2	61	1	0	0	0	0	1	0	0	0	16493	420	15	4	1009	4	TRAM2	6	52400622	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	81627	52400622	118714445	4658	12643										
GSTA3	2940	broad.mit.edu	37	chr6	52768485	52768485	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcttaccatttcttaacTttcccaaatcttctgcagat	3	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52768485T>G	ENST00000211122.3	-	3	193	c.128A>C	c.(127-129)aAg>aCg	p.K43T	GSTA3_ENST00000370968.1_5'UTR	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	43	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)	p.K43T(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	ATTTCTTAACTTTCCCAAATC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											124	120	121					6																	52768485		2202	4300	6502	52876444	SO:0001583	missense	2940			AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"Glutathione S-transferases / Soluble"	4628	protein-coding gene	gene with protein product		605449	"glutathione S-transferase A3"			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.128A>C	6.37:g.52768485T>G	ENSP00000211122:p.Lys43Thr		52876444	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.843116	0.32606	.	.	ENSG00000174156	ENST00000211122	T	0.08807	3.05	3.94	2.77	0.32553	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.171641	0.49916	D	0.000140	T	0.09423	0.0232	M	0.82433	2.59	0.24266	N	0.995261	P	0.39940	0.696	P	0.48141	0.568	T	0.04090	-1.0978	10	0.87932	D	0	.	9.0867	0.36586	0.0:0.0902:0.0:0.9098	.	43	Q16772	GSTA3_HUMAN	T	43	ENSP00000211122:K43T	ENSP00000211122:K43T	K	-	2	0	GSTA3	52876444	0.979000	0.34478	0.005000	0.12908	0.048000	0.14542	3.442000	0.52900	0.678000	0.31325	-0.262000	0.10625	AAG		0.368	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1			G	52768485	T	G	52768485	3	3	61	1	0	0	0	0	1	0	0	0	6853	1609	56	4	560	4	GSTA3	6	52768485	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	367863	52768485	118346582	4659	12644										
ICK	22858	broad.mit.edu	37	chr6	52876668	52876668	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgggtgggggcactgtttCctgtgcccacaggctcagag	15	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52876668C>A	ENST00000350082.5	-	11	1737	c.1391G>T	c.(1390-1392)gGa>gTa	p.G464V	ICK_ENST00000356971.3_Missense_Mutation_p.G464V	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	464					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.G464V(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GGCACTGTTTCCTGTGCCCAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											98	99	99					6																	52876668		2203	4300	6503	52984627	SO:0001583	missense	22858			AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.1391G>T	6.37:g.52876668C>A	ENSP00000263043:p.Gly464Val		52984627	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Missense_Mutation	SNP	ENST00000350082.5	37	CCDS4949.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.179790	0.38511	.	.	ENSG00000112144	ENST00000350082;ENST00000356971	T;T	0.72167	-0.63;-0.63	5.66	5.66	0.87406	.	0.111999	0.64402	D	0.000008	T	0.51719	0.1691	L	0.46157	1.445	0.80722	D	1	B	0.27765	0.188	B	0.26864	0.074	T	0.55438	-0.8141	10	0.44086	T	0.13	-3.5697	12.9995	0.58667	0.0:0.9265:0.0:0.0735	.	464	Q9UPZ9	ICK_HUMAN	V	464	ENSP00000263043:G464V;ENSP00000349458:G464V	ENSP00000263043:G464V	G	-	2	0	ICK	52984627	1.000000	0.71417	0.951000	0.38953	0.450000	0.32258	2.174000	0.42482	2.665000	0.90641	0.561000	0.74099	GGA		0.542	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513		A	52876668	C	A	52876668	3	1	61	1	0	0	0	0	1	0	0	0	7505	855	30	2	523	2	ICK	6	52876668	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108183	52876668	118238399	4660	12645										
FBXO9	26268	broad.mit.edu	37	chr6	52958696	52958696	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaaggactgatgcaattCtactgggtcactatcgcttg	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:52958696C>A	ENST00000244426.6	+	10	1175	c.1003C>A	c.(1003-1005)Cta>Ata	p.L335I	RN7SL244P_ENST00000493405.2_RNA|FBXO9_ENST00000323557.7_Missense_Mutation_p.L325I|FBXO9_ENST00000370939.3_Missense_Mutation_p.L291I	NM_012347.4	NP_036479.1	Q9UK97	FBX9_HUMAN	F-box protein 9	335					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|protein ubiquitination (GO:0016567)|regulation of TOR signaling (GO:0032006)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.L335I(1)		kidney(1)|large_intestine(4)|lung(1)|pancreas(2)|skin(1)	9	Lung NSC(77;0.103)					TGATGCAATTCTACTGGGTCA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	6											45	39	41					6																	52958696		1805	4028	5833	53066655	SO:0001583	missense	26268			AF155114	CCDS55022.1, CCDS55023.1, CCDS55024.1	6p12.3-p11.2	2004-06-15	2004-06-15		ENSG00000112146	ENSG00000112146		"F-boxes /  "other""	13588	protein-coding gene	gene with protein product		609091	"F-box only protein 9"			10531035, 10531037	Standard	NM_012347		Approved	FBX9, NY-REN-57	uc021zao.1	Q9UK97	OTTHUMG00000014869	ENST00000244426.6:c.1003C>A	6.37:g.52958696C>A	ENSP00000244426:p.Leu335Ile		53066655	A6NFW3|B3KMM6|O75986|Q59EH8|Q6PKH7|Q9NT57|Q9Y593	Missense_Mutation	SNP	ENST00000244426.6	37	CCDS55023.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.43|12.43|12.43	1.934180|1.934180|1.934180	0.34096|0.34096|0.34096	.|.|.	.|.|.	ENSG00000112146|ENSG00000112146|ENSG00000112146	ENST00000473318|ENST00000370939;ENST00000323557;ENST00000244426|ENST00000484436	.|T;T;T|.	.|0.79845|.	.|-1.3;-1.31;-1.31|.	5.53|5.53|5.53	3.75|3.75|3.75	0.43078|0.43078|0.43078	.|F-box domain, Skp2-like (1);|.	.|0.068182|.	.|0.64402|.	.|D|.	.|0.000011|.	T|T|T	0.66597|0.66597|0.66597	0.2805|0.2805|0.2805	M|M|M	0.82517|0.82517|0.82517	2.595|2.595|2.595	0.50467|0.50467|0.50467	D|D|D	0.999875|0.999875|0.999875	.|D;D;D|.	.|0.60160|.	.|0.987;0.972;0.969|.	.|P;P;P|.	.|0.59889|.	.|0.865;0.757;0.489|.	T|T|T	0.70163|0.70163|0.70163	-0.4947|-0.4947|-0.4947	5|10|5	.|0.46703|.	.|T|.	.|0.11|.	-9.5132|-9.5132|-9.5132	10.9906|10.9906|10.9906	0.47547|0.47547|0.47547	0.0:0.7853:0.0:0.2147|0.0:0.7853:0.0:0.2147|0.0:0.7853:0.0:0.2147	.|.|.	.|325;442;335|.	.|Q9UK97-2;Q59EH8;Q9UK97|.	.|.;.;FBX9_HUMAN|.	L|I|Y	33|291;325;335|45	.|ENSP00000359977:L291I;ENSP00000326968:L325I;ENSP00000244426:L335I|.	.|ENSP00000244426:L335I|.	F|L|S	+|+|+	3|1|2	2|2|0	FBXO9|FBXO9|FBXO9	53066655|53066655|53066655	0.998000|0.998000|0.998000	0.40836|0.40836|0.40836	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.565000|0.565000|0.565000	0.35776|0.35776|0.35776	0.592000|0.592000|0.592000	0.23984|0.23984|0.23984	1.343000|1.343000|1.343000	0.45638|0.45638|0.45638	-0.363000|-0.363000|-0.363000	0.07495|0.07495|0.07495	TTC|CTA|TCT		0.308	FBXO9-002	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040950.3			A	52958696	C	A	52958696	3	1	61	1	0	0	0	0	1	0	0	0	5781	912	32	2	1048	2	FBXO9	6	52958696	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82028	52958696	118156371	4661	12646										
LRRC1	55227	broad.mit.edu	37	chr6	53769233	53769233	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaacttgaatgcagacagAaataaattagtgtccttacc	7	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:53769233A>C	ENST00000370888.1	+	10	1240	c.963A>C	c.(961-963)agA>agC	p.R321S		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	321						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R321S(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		ATGCAGACAGAAATAAATTAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	85	86					6																	53769233		1822	4071	5893	53877192	SO:0001583	missense	55227			AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.963A>C	6.37:g.53769233A>C	ENSP00000359925:p.Arg321Ser		53877192	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107398	0.77096	.	.	ENSG00000137269	ENST00000370888	T	0.54866	0.55	5.5	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.32285	0.0824	N	0.05592	-0.015	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.27123	-1.0083	10	0.24483	T	0.36	.	7.447	0.27217	0.8313:0.0:0.1687:0.0	.	321	Q9BTT6	LRRC1_HUMAN	S	321	ENSP00000359925:R321S	ENSP00000359925:R321S	R	+	3	2	LRRC1	53877192	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.663000	0.46774	0.917000	0.36895	0.528000	0.53228	AGA		0.279	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		C	53769233	A	C	53769233	3	2	61	1	0	0	0	0	1	0	0	0	8995	243	9	4	1001	4	LRRC1	6	53769233	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	810537	53769233	117345834	4662	12647										
TINAG	27283	broad.mit.edu	37	chr6	54173366	54173366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgtggaccggatataaGatcttaatcttctcttatct	7	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:54173366G>T	ENST00000259782.4	+	1	114	c.18G>T	c.(16-18)aaG>aaT	p.K6N	TINAG_ENST00000370864.3_5'Flank|TINAG_ENST00000370869.3_Intron|TINAG_ENST00000486436.1_Intron	NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	6					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.K6N(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			CCGGATATAAGATCTTAATCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											47	46	46					6																	54173366		2203	4300	6503	54281325	SO:0001583	missense	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.18G>T	6.37:g.54173366G>T	ENSP00000259782:p.Lys6Asn		54281325	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.906938	0.33628	.	.	ENSG00000137251	ENST00000339741;ENST00000259782	T	0.67345	-0.26	5.49	1.68	0.24146	.	0.283721	0.31071	N	0.008313	T	0.39860	0.1094	L	0.50333	1.59	0.58432	D	0.999999	B;B	0.27559	0.09;0.181	B;B	0.24155	0.051;0.03	T	0.39418	-0.9615	10	0.59425	D	0.04	.	7.9011	0.29736	0.3546:0.0:0.6454:0.0	.	6;6	Q9UJW2;Q7Z477	TINAG_HUMAN;.	N	6	ENSP00000259782:K6N	ENSP00000259782:K6N	K	+	3	2	TINAG	54281325	0.750000	0.28316	0.980000	0.43619	0.855000	0.48748	1.162000	0.31786	0.377000	0.24735	0.655000	0.94253	AAG		0.408	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54173366	G	T	54173366	3	4	61	1	0	0	0	0	1	0	0	0	15960	933	33	2	20	2	TINAG	6	54173366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	404133	54173366	116941701	4663	12648										
TINAG	27283	broad.mit.edu	37	chr6	54254624	54254624	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggaaagtcatggggagaGaatggctatttcaggattct	15	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:54254624G>T	ENST00000259782.4	+	11	1428	c.1332G>T	c.(1330-1332)gaG>gaT	p.E444D		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	444					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.E444D(1)|p.E444E(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			CATGGGGAGAGAATGGCTATT	0.393																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	6											132	130	131					6																	54254624		2203	4300	6503	54362583	SO:0001583	missense	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1332G>T	6.37:g.54254624G>T	ENSP00000259782:p.Glu444Asp		54362583	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.863652	0.71949	.	.	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.85556	-2.0	5.89	4.1	0.47936	Peptidase C1A, papain C-terminal (2);	0.000000	0.64402	D	0.000002	D	0.83866	0.5347	L	0.46885	1.475	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82727	-0.0314	10	0.36615	T	0.2	.	9.2285	0.37421	0.1681:0.0:0.8319:0.0	.	444	Q9UJW2	TINAG_HUMAN	D	303;444;123	ENSP00000259782:E444D	ENSP00000259782:E444D	E	+	3	2	TINAG	54362583	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.137000	0.42130	0.821000	0.34540	-0.218000	0.12543	GAG		0.393	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54254624	G	T	54254624	3	4	61	1	0	0	0	0	1	0	0	0	15960	933	33	2	1374	2	TINAG	6	54254624	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81258	54254624	116860443	4664	12649										
FAM83B	222584	broad.mit.edu	37	chr6	54792319	54792319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctagaatattcgagtgcGaacagtaaaaggccaagatt	9	6	1	2	rs76434524	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:54792319G>A	ENST00000306858.7	+	4	739	c.623G>A	c.(622-624)cGa>cAa	p.R208Q		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	208								p.R208Q(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					ATTCGAGTGCGAACAGTAAAA	0.313													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		12276	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	GLN/ARG	16,4388	20.2+/-43.8	0,16,2186	73	77	76		623	5.9	1	6	dbSNP_131	76	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM83B	NM_001010872.1	43	0,18,6484	AA,AG,GG		0.0233,0.3633,0.1384	probably-damaging	208/1012	54792319	18,12986	2202	4300	6502	54900278	SO:0001583	missense	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.623G>A	6.37:g.54792319G>A	ENSP00000304078:p.Arg208Gln		54900278	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	35	5.537151	0.96460	0.003633	2.33E-4	ENSG00000168143	ENST00000306858	T	0.22336	1.96	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.48607	0.1509	M	0.84511	2.7	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.52139	-0.8615	10	0.72032	D	0.01	-18.9956	20.3931	0.98965	0.0:0.0:1.0:0.0	.	208	Q5T0W9	FA83B_HUMAN	Q	208	ENSP00000304078:R208Q	ENSP00000304078:R208Q	R	+	2	0	FAM83B	54900278	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.439000	0.97543	2.824000	0.97209	0.655000	0.94253	CGA		0.313	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		A	54792319	G	A	54792319	3	1	61	1	0	0	0	0	1	0	0	0	5653	1058	37	1	633	1	FAM83B	6	54792319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	537695	54792319	116322748	4665	12650										
FAM83B	222584	broad.mit.edu	37	chr6	54805889	54805889	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagatttgctgaaaagttCtaaaagcatgcacaatgtga	9	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:54805889C>A	ENST00000306858.7	+	5	2236	c.2120C>A	c.(2119-2121)tCt>tAt	p.S707Y	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	707								p.S707Y(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					CTGAAAAGTTCTAAAAGCATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											90	92	91					6																	54805889		2203	4300	6503	54913848	SO:0001583	missense	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2120C>A	6.37:g.54805889C>A	ENSP00000304078:p.Ser707Tyr		54913848	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	7.876	0.729146	0.15507	.	.	ENSG00000168143	ENST00000306858	T	0.34275	1.37	5.55	2.78	0.32641	.	11.160900	0.00166	N	0.000000	T	0.27765	0.0683	M	0.65975	2.015	0.39101	D	0.961283	P	0.42785	0.79	B	0.40782	0.34	T	0.25779	-1.0122	10	0.59425	D	0.04	-12.6889	10.8617	0.46831	0.0:0.5604:0.3743:0.0654	.	707	Q5T0W9	FA83B_HUMAN	Y	707	ENSP00000304078:S707Y	ENSP00000304078:S707Y	S	+	2	0	FAM83B	54913848	0.520000	0.26250	0.844000	0.33320	0.511000	0.34104	0.787000	0.26858	0.382000	0.24878	-0.150000	0.13652	TCT		0.388	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		A	54805889	C	A	54805889	3	1	61	1	0	0	0	0	1	0	0	0	5653	913	32	2	2134	2	FAM83B	6	54805889	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13570	54805889	116309178	4666	12651										
FAM83B	222584	broad.mit.edu	37	chr6	54806507	54806507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacccctgaaagaagacctaCttcttctccaaggccaacgt	6	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:54806507C>A	ENST00000306858.7	+	5	2854	c.2738C>A	c.(2737-2739)aCt>aAt	p.T913N	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	913								p.T913N(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					AGAAGACCTACTTCTTCTCCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	100	103					6																	54806507		2203	4300	6503	54914466	SO:0001583	missense	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2738C>A	6.37:g.54806507C>A	ENSP00000304078:p.Thr913Asn		54914466	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	5.255	0.232510	0.09969	.	.	ENSG00000168143	ENST00000306858	T	0.07114	3.22	5.24	4.37	0.52481	.	2.791760	0.01197	N	0.007461	T	0.03348	0.0097	L	0.40543	1.245	0.09310	N	1	B	0.23735	0.09	B	0.21360	0.034	T	0.41752	-0.9491	10	0.26408	T	0.33	-1.9391	11.1085	0.48218	0.0:0.8371:0.0:0.1629	.	913	Q5T0W9	FA83B_HUMAN	N	913	ENSP00000304078:T913N	ENSP00000304078:T913N	T	+	2	0	FAM83B	54914466	0.011000	0.17503	0.022000	0.16811	0.046000	0.14306	2.015000	0.40961	1.345000	0.45676	0.655000	0.94253	ACT		0.463	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		A	54806507	C	A	54806507	3	1	61	1	0	0	0	0	1	0	0	0	5653	565	20	2	2752	2	FAM83B	6	54806507	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	618	54806507	116308560	4667	12652										
HCRTR2	3062	broad.mit.edu	37	chr6	55039580	55039580	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgggtacatcatcgtgttCgtcgtggctctcattgggaa	13	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55039580C>T	ENST00000370862.3	+	1	531	c.195C>T	c.(193-195)ttC>ttT	p.F65F		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	65					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)	p.F65F(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TCATCGTGTTCGTCGTGGCTC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	6											122	103	110					6																	55039580		2203	4300	6503	55147539	SO:0001819	synonymous_variant	3062			AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.195C>T	6.37:g.55039580C>T			55147539	Q5VTM0	Silent	SNP	ENST00000370862.3	37	CCDS4956.1																																																																																				0.597	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			T	55039580	C	T	55039580	2	4	61	1	0	0	0	0	0	0	0	1	7023	883	31	1		1	HCRTR2	6	55039580	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233073	55039580	116075487	4668	12653										
HCRTR2	3062	broad.mit.edu	37	chr6	55113600	55113600	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagtccctttgcaaagtGattccttatctacaggtaat	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55113600G>T	ENST00000370862.3	+	2	723	c.387G>T	c.(385-387)gtG>gtT	p.V129V		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	129					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)	p.V129V(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TTTGCAAAGTGATTCCTTATC	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6											222	210	214					6																	55113600		2203	4299	6502	55221559	SO:0001819	synonymous_variant	3062			AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.387G>T	6.37:g.55113600G>T			55221559	Q5VTM0	Silent	SNP	ENST00000370862.3	37	CCDS4956.1																																																																																				0.423	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			T	55113600	G	T	55113600	2	4	61	1	0	0	0	0	0	0	0	1	7023	1277	45	2		2	HCRTR2	6	55113600	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74020	55113600	116001467	4669	12654										
GFRAL	389400	broad.mit.edu	37	chr6	55264003	55264003	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaccctgtctaatgtcaaAggcatggcattgtatacaag	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55264003A>C	ENST00000340465.2	+	7	1064	c.978A>C	c.(976-978)aaA>aaC	p.K326N		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	326					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K326N(1)		NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CTAATGTCAAAGGCATGGCAT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	6											37	37	37					6																	55264003		2203	4292	6495	55371962	SO:0001583	missense	389400			AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.978A>C	6.37:g.55264003A>C	ENSP00000343636:p.Lys326Asn		55371962	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	37	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.942180	0.34283	.	.	ENSG00000187871	ENST00000340465	T	0.39787	1.06	5.79	3.41	0.39046	.	0.641614	0.14166	N	0.337044	T	0.22936	0.0554	L	0.27053	0.805	0.09310	N	0.999999	D	0.59767	0.986	P	0.58660	0.843	T	0.07309	-1.0779	10	0.22109	T	0.4	-2.6064	7.4661	0.27322	0.8303:0.0:0.1697:0.0	.	326	Q6UXV0	GFRAL_HUMAN	N	326	ENSP00000343636:K326N	ENSP00000343636:K326N	K	+	3	2	GFRAL	55371962	0.056000	0.20664	0.026000	0.17262	0.041000	0.13682	0.873000	0.28052	0.466000	0.27193	0.533000	0.62120	AAA		0.284	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		C	55264003	A	C	55264003	3	2	61	1	0	0	0	0	1	0	0	0	6371	69	3	4	1004	4	GFRAL	6	55264003	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	150403	55264003	115851064	4670	12655										
HMGCLL1	54511	broad.mit.edu	37	chr6	55300533	55300533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgcaaataaagtcaccaGcttccatcactttgtataga	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55300533G>A	ENST00000398661.2	-	10	1171	c.1040C>T	c.(1039-1041)gCt>gTt	p.A347V	HMGCLL1_ENST00000274901.4_Missense_Mutation_p.A317V|HMGCLL1_ENST00000508459.1_Missense_Mutation_p.A151V|HMGCLL1_ENST00000507223.1_5'UTR|HMGCLL1_ENST00000370850.2_Missense_Mutation_p.A214V|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.A285V	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	347					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.A347V(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			AAAGTCACCAGCTTCCATCAC	0.388																																					Ovarian(35;840 893 7837 15538 42887)											1	Substitution - Missense(1)	large_intestine(1)	6											117	116	117					6																	55300533		1849	4081	5930	55408492	SO:0001583	missense	54511			AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.1040C>T	6.37:g.55300533G>A	ENSP00000381654:p.Ala347Val		55408492	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	37	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.788618	0.70337	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000508459;ENST00000308161	D;D;D;D;D	0.98120	-4.73;-4.73;-4.44;-4.73;-4.73	5.36	5.36	0.76844	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.97732	0.9256	L	0.45285	1.41	0.80722	D	1	D;D;B;B;P	0.76494	0.999;0.997;0.429;0.351;0.464	D;D;B;B;B	0.78314	0.991;0.967;0.263;0.062;0.028	D	0.97498	1.0058	10	0.39692	T	0.17	-16.0533	19.0955	0.93249	0.0:0.0:1.0:0.0	.	151;214;285;317;347	B7Z4D4;B7Z212;F8W793;Q8TB92-2;Q8TB92	.;.;.;.;HMGC2_HUMAN	V	317;347;214;151;285	ENSP00000274901:A317V;ENSP00000381654:A347V;ENSP00000359887:A214V;ENSP00000424309:A151V;ENSP00000309737:A285V	ENSP00000274901:A317V	A	-	2	0	HMGCLL1	55408492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.511000	0.84671	0.655000	0.94253	GCT		0.388	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383		A	55300533	G	A	55300533	3	1	61	1	0	0	0	0	1	0	0	0	7251	971	34	3	76	3	HMGCLL1	6	55300533	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36530	55300533	115814534	4671	12656										
HMGCLL1	54511	broad.mit.edu	37	chr6	55360281	55360281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgacagtgaacagcaagaGcacctggtgggatttctttc	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55360281G>A	ENST00000398661.2	-	8	952	c.821C>T	c.(820-822)gCt>gTt	p.A274V	HMGCLL1_ENST00000274901.4_Missense_Mutation_p.A244V|HMGCLL1_ENST00000508459.1_Intron|HMGCLL1_ENST00000370850.2_Missense_Mutation_p.A141V|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.A212V	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	274					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.A274V(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			AACAGCAAGAGCACCTGGTGG	0.428																																					Ovarian(35;840 893 7837 15538 42887)											1	Substitution - Missense(1)	large_intestine(1)	6											145	131	136					6																	55360281		1896	4117	6013	55468240	SO:0001583	missense	54511			AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.821C>T	6.37:g.55360281G>A	ENSP00000381654:p.Ala274Val		55468240	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	37	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116870	0.56505	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000308161	D;D;D;D	0.98178	-4.77;-4.77;-4.73;-4.77	5.62	5.62	0.85841	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.98723	0.9571	M	0.72118	2.19	0.80722	D	1	D;P;P;P	0.89917	1.0;0.611;0.923;0.938	D;B;B;P	0.83275	0.996;0.29;0.335;0.595	D	0.98583	1.0651	10	0.40728	T	0.16	-18.3909	19.6685	0.95901	0.0:0.0:1.0:0.0	.	141;212;244;274	B7Z212;F8W793;Q8TB92-2;Q8TB92	.;.;.;HMGC2_HUMAN	V	244;274;141;212	ENSP00000274901:A244V;ENSP00000381654:A274V;ENSP00000359887:A141V;ENSP00000309737:A212V	ENSP00000274901:A244V	A	-	2	0	HMGCLL1	55468240	1.000000	0.71417	0.977000	0.42913	0.743000	0.42351	9.776000	0.99001	2.639000	0.89480	0.655000	0.94253	GCT		0.428	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383		A	55360281	G	A	55360281	3	1	61	1	0	0	0	0	1	0	0	0	7251	971	34	3	303	3	HMGCLL1	6	55360281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59748	55360281	115754786	4672	12657										
BMP5	653	broad.mit.edu	37	chr6	55638897	55638897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgagagctggatttattgCggttttgattttttcgtttg	12	3	0	2	rs371743666		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:55638897C>T	ENST00000370830.3	-	4	1675	c.977G>A	c.(976-978)cGc>cAc	p.R326H	BMP5_ENST00000446683.2_Missense_Mutation_p.R326H	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	326					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)	p.R326H(1)|p.R326L(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GGATTTATTGCGGTTTTGATT	0.473																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6						C	HIS/ARG	0,4406		0,0,2203	186	161	169		977	5.7	1	6		169	2,8598	2.2+/-6.3	0,2,4298	no	missense	BMP5	NM_021073.2	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	326/455	55638897	2,13004	2203	4300	6503	55746856	SO:0001583	missense	653				CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"Bone morphogenetic proteins", "Endogenous ligands"	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.977G>A	6.37:g.55638897C>T	ENSP00000359866:p.Arg326His		55746856	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	37	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	C	34	5.299688	0.95574	0.0	2.33E-4	ENSG00000112175	ENST00000370830;ENST00000446683	T;T	0.75367	-0.93;-0.62	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.76821	0.4041	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.73949	-0.3821	10	0.34782	T	0.22	.	19.9351	0.97137	0.0:1.0:0.0:0.0	.	326;326	B4E0Y4;P22003	.;BMP5_HUMAN	H	326	ENSP00000359866:R326H;ENSP00000391818:R326H	ENSP00000359866:R326H	R	-	2	0	BMP5	55746856	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.703000	0.92315	0.655000	0.94253	CGC		0.473	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			T	55638897	C	T	55638897	3	4	61	1	0	0	0	0	1	0	0	0	1464	768	27	1	403	1	BMP5	6	55638897	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	278616	55638897	115476170	4673	12658										
COL21A1	81578	broad.mit.edu	37	chr6	56035610	56035610	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattttcttgactttaaatCtttgagtagacacaaataca	4	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56035610C>A	ENST00000244728.5	-	5	1260	c.863G>T	c.(862-864)aGa>aTa	p.R288I	COL21A1_ENST00000535941.1_Missense_Mutation_p.R288I|COL21A1_ENST00000370819.1_Missense_Mutation_p.R288I	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	288	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.R288I(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			GACTTTAAATCTTTGAGTAGA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	6											66	58	61					6																	56035610		1817	4073	5890	56143569	SO:0001583	missense	81578			AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.863G>T	6.37:g.56035610C>A	ENSP00000244728:p.Arg288Ile		56143569	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.581578	0.46006	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	T;T;T	0.02216	4.39;4.39;4.39	4.66	4.66	0.58398	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.64402	D	0.000017	T	0.10121	0.0248	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.991	T	0.02581	-1.1138	10	0.87932	D	0	.	17.5385	0.87840	0.0:1.0:0.0:0.0	.	288;288	Q96P44-3;Q96P44	.;COLA1_HUMAN	I	288	ENSP00000244728:R288I;ENSP00000359855:R288I;ENSP00000444384:R288I	ENSP00000244728:R288I	R	-	2	0	COL21A1	56143569	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.359000	0.52292	2.126000	0.65437	0.591000	0.81541	AGA		0.333	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	56035610	C	A	56035610	3	1	61	1	0	0	0	0	1	0	0	0	3686	913	32	2	2114	2	COL21A1	6	56035610	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	396713	56035610	115079457	4674	12659										
COL21A1	81578	broad.mit.edu	37	chr6	56044469	56044469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagacgaaggcttgttggCaatagctctaagttcggcat	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56044469C>T	ENST00000244728.5	-	3	944	c.547G>A	c.(547-549)Gcc>Acc	p.A183T	COL21A1_ENST00000535941.1_Missense_Mutation_p.A183T|COL21A1_ENST00000370819.1_Missense_Mutation_p.A183T	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	183	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A183T(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			GGCTTGTTGGCAATAGCTCTA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	6											88	81	83					6																	56044469		1902	4133	6035	56152428	SO:0001583	missense	81578			AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.547G>A	6.37:g.56044469C>T	ENSP00000244728:p.Ala183Thr		56152428	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.982169	0.74474	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	D;D;D	0.87650	-2.28;-2.28;-2.28	4.66	4.66	0.58398	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000021	D	0.92028	0.7474	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.92935	0.6367	10	0.72032	D	0.01	.	17.9099	0.88930	0.0:1.0:0.0:0.0	.	183;183	Q96P44-3;Q96P44	.;COLA1_HUMAN	T	183	ENSP00000244728:A183T;ENSP00000359855:A183T;ENSP00000444384:A183T	ENSP00000244728:A183T	A	-	1	0	COL21A1	56152428	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.524000	0.81866	2.283000	0.76528	0.585000	0.79938	GCC		0.393	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	56044469	C	T	56044469	3	4	61	1	0	0	0	0	1	0	0	0	3686	710	25	3	2438	3	COL21A1	6	56044469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8859	56044469	115070598	4675	12660										
COL21A1	81578	broad.mit.edu	37	chr6	56044618	56044618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctatcttagtcagaaatCgtgaggacttggcaaaaagg	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56044618C>T	ENST00000244728.5	-	3	795	c.398G>A	c.(397-399)cGa>cAa	p.R133Q	COL21A1_ENST00000535941.1_Missense_Mutation_p.R133Q|COL21A1_ENST00000370819.1_Missense_Mutation_p.R133Q	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	133	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.R133Q(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			AGTCAGAAATCGTGAGGACTT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	6											94	90	91					6																	56044618		1989	4169	6158	56152577	SO:0001583	missense	81578			AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.398G>A	6.37:g.56044618C>T	ENSP00000244728:p.Arg133Gln		56152577	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379664	0.82682	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370817	D;D;D;D	0.98889	-4.4;-4.4;-4.4;-5.21	4.75	4.75	0.60458	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000021	D	0.98833	0.9606	M	0.67700	2.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.99320	1.0906	10	0.46703	T	0.11	.	18.1172	0.89559	0.0:1.0:0.0:0.0	.	133;133	Q96P44-3;Q96P44	.;COLA1_HUMAN	Q	133	ENSP00000244728:R133Q;ENSP00000359855:R133Q;ENSP00000444384:R133Q;ENSP00000359853:R133Q	ENSP00000244728:R133Q	R	-	2	0	COL21A1	56152577	1.000000	0.71417	0.936000	0.37596	0.994000	0.84299	7.500000	0.81588	2.331000	0.79229	0.650000	0.86243	CGA		0.448	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	56044618	C	T	56044618	3	4	61	1	0	0	0	0	1	0	0	0	3686	884	31	1	2587	1	COL21A1	6	56044618	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149	56044618	115070449	4676	12661										
DST	667	broad.mit.edu	37	chr6	56357099	56357099	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaccactttttcccatcGactttgtacactgataagta	5	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56357099G>A	ENST00000361203.3	-	80	19730	c.19723C>T	c.(19723-19725)Cga>Tga	p.R6575*	DST_ENST00000370769.4_Nonsense_Mutation_p.R6686*|DST_ENST00000244364.6_Nonsense_Mutation_p.R4272*|DST_ENST00000370788.2_Nonsense_Mutation_p.R4489*|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Nonsense_Mutation_p.R6360*|DST_ENST00000421834.2_Nonsense_Mutation_p.R4598*|DST_ENST00000370754.5_Nonsense_Mutation_p.R6864*|DST_ENST00000340834.4_5'Flank			Q03001	DYST_HUMAN	dystonin	6575					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R6686*(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTTTCCCATCGACTTTGTACA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											142	130	134					6																	56357099		1861	4091	5952	56465058	SO:0001587	stop_gained	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.19723C>T	6.37:g.56357099G>A	ENSP00000354508:p.Arg6575*		56465058	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	58	32.432126	0.99980	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	.	.	.	5.54	4.61	0.57282	.	0.000000	0.42548	D	0.000683	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5389	0.76024	0.0:0.0:0.7928:0.2072	.	.	.	.	X	4272;6864;6686;4598;6360;4489;6575	.	ENSP00000244364:R4272X	R	-	1	2	DST	56465058	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.223000	0.58587	2.758000	0.94735	0.591000	0.81541	CGA		0.383	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56357099	G	A	56357099	4	1	61	1	0	0	0	0	0	1	0	0	4794	1066	37	1	2777	1	DST	6	56357099	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	312481	56357099	114757968	4677	12662										
DST	667	broad.mit.edu	37	chr6	56362797	56362797	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaattagatcatttcctgCtttattaacggcttccactg	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56362797C>A	ENST00000361203.3	-	76	18998	c.18991G>T	c.(18991-18993)Gca>Tca	p.A6331S	DST_ENST00000370769.4_Missense_Mutation_p.A6442S|DST_ENST00000244364.6_Missense_Mutation_p.A4028S|DST_ENST00000370788.2_Missense_Mutation_p.A4245S|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Missense_Mutation_p.A6116S|DST_ENST00000421834.2_Missense_Mutation_p.A4354S|DST_ENST00000370754.5_Missense_Mutation_p.A6620S|DST_ENST00000340834.4_5'UTR			Q03001	DYST_HUMAN	dystonin	6330					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.A6442S(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCATTTCCTGCTTTATTAACG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											193	179	183					6																	56362797		1888	4118	6006	56470756	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.18991G>T	6.37:g.56362797C>A	ENSP00000354508:p.Ala6331Ser		56470756	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	23.5	4.427030	0.83667	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.8	5.8	0.92144	.	0.000000	0.51477	D	0.000096	T	0.63094	0.2482	M	0.71581	2.175	0.30539	N	0.7666189999999999	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.993	D;D;D;D;D	0.91635	0.998;0.999;0.998;0.998;0.993	T	0.55774	-0.8088	9	0.30854	T	0.27	.	20.0503	0.97624	0.0:1.0:0.0:0.0	.	4354;6442;6620;6440;4028	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	S	4028;6620;6442;4354;6116;4245;6331	ENSP00000244364:A4028S;ENSP00000359790:A6620S;ENSP00000359805:A6442S;ENSP00000400883:A4354S;ENSP00000393645:A6116S;ENSP00000359824:A4245S;ENSP00000354508:A6331S	ENSP00000244364:A4028S	A	-	1	0	DST	56470756	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.461000	0.80834	2.736000	0.93811	0.591000	0.81541	GCA		0.373	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56362797	C	A	56362797	3	1	61	1	0	0	0	0	1	0	0	0	4794	797	28	2	3525	2	DST	6	56362797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5698	56362797	114752270	4678	12663										
DST	667	broad.mit.edu	37	chr6	56417040	56417040	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccataccaacaggaccttgtGactcttcatgttcttcggct	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56417040G>T	ENST00000361203.3	-	57	15924	c.15917C>A	c.(15916-15918)tCa>tAa	p.S5306*	DST_ENST00000370769.4_Nonsense_Mutation_p.S5308*|DST_ENST00000244364.6_Nonsense_Mutation_p.S2894*|DST_ENST00000370788.2_Nonsense_Mutation_p.S3220*|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Nonsense_Mutation_p.S4982*|DST_ENST00000421834.2_Nonsense_Mutation_p.S3220*|DST_ENST00000370754.5_Nonsense_Mutation_p.S5486*			Q03001	DYST_HUMAN	dystonin	5306					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.S5308*(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGGACCTTGTGACTCTTCATG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											95	92	93					6																	56417040		1840	4087	5927	56524999	SO:0001587	stop_gained	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15917C>A	6.37:g.56417040G>T	ENSP00000354508:p.Ser5306*		56524999	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	56	25.960887	0.99967	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	.	.	.	5.88	5.88	0.94601	.	0.000000	0.44688	D	0.000437	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2314	0.98350	0.0:0.0:1.0:0.0	.	.	.	.	X	2894;5486;5308;3220;4982;3220;5306	.	ENSP00000244364:S2894X	S	-	2	0	DST	56524999	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	9.476000	0.97823	2.789000	0.95967	0.591000	0.81541	TCA		0.388	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56417040	G	T	56417040	4	4	61	1	0	0	0	0	0	1	0	0	4794	1294	45	2	7006	2	DST	6	56417040	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54243	56417040	114698027	4679	12664										
DST	667	broad.mit.edu	37	chr6	56417396	56417396	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcatcatcaaactctgcGaactgagaaaacatttctcg	6	10	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56417396G>A	ENST00000361203.3	-	57	15568	c.15561C>T	c.(15559-15561)ttC>ttT	p.F5187F	DST_ENST00000370769.4_Silent_p.F5189F|DST_ENST00000244364.6_Silent_p.F2775F|DST_ENST00000370788.2_Silent_p.F3101F|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Silent_p.F4863F|DST_ENST00000421834.2_Silent_p.F3101F|DST_ENST00000370754.5_Silent_p.F5367F			Q03001	DYST_HUMAN	dystonin	5187					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.F5189F(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAAACTCTGCGAACTGAGAAA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	6											58	54	55					6																	56417396		1872	4107	5979	56525355	SO:0001819	synonymous_variant	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15561C>T	6.37:g.56417396G>A			56525355	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																					0.408	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56417396	G	A	56417396	2	1	61	1	0	0	0	0	0	0	0	1	4794	1049	37	1		1	DST	6	56417396	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356	56417396	114697671	4680	12665										
DST	667	broad.mit.edu	37	chr6	56418058	56418058	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtctatccatggccagaGagtctctacttgctctttat	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56418058G>T	ENST00000361203.3	-	57	14906	c.14899C>A	c.(14899-14901)Ctc>Atc	p.L4967I	DST_ENST00000370769.4_Missense_Mutation_p.L4969I|DST_ENST00000244364.6_Missense_Mutation_p.L2555I|DST_ENST00000370788.2_Missense_Mutation_p.L2881I|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Missense_Mutation_p.L4643I|DST_ENST00000421834.2_Missense_Mutation_p.L2881I|DST_ENST00000370754.5_Missense_Mutation_p.L5147I			Q03001	DYST_HUMAN	dystonin	4967					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.L4969I(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CATGGCCAGAGAGTCTCTACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											180	181	181					6																	56418058		1828	4072	5900	56526017	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.14899C>A	6.37:g.56418058G>T	ENSP00000354508:p.Leu4967Ile		56526017	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	13.02	2.111151	0.37242	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.76	3.96	0.45880	.	0.000000	0.42420	D	0.000704	T	0.36880	0.0983	M	0.68317	2.08	0.24566	N	0.99395	B;P;P;B;P	0.47545	0.108;0.897;0.897;0.379;0.63	B;P;P;B;B	0.54346	0.025;0.749;0.593;0.048;0.347	T	0.39078	-0.9631	9	0.44086	T	0.13	.	6.3993	0.21630	0.2013:0.0:0.6657:0.133	.	2881;4969;5147;4967;2555	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	I	2555;5147;4969;2881;4643;2881;4967	ENSP00000244364:L2555I;ENSP00000359790:L5147I;ENSP00000359805:L4969I;ENSP00000400883:L2881I;ENSP00000393645:L4643I;ENSP00000359824:L2881I;ENSP00000354508:L4967I	ENSP00000244364:L2555I	L	-	1	0	DST	56526017	1.000000	0.71417	0.112000	0.21494	0.980000	0.70556	5.468000	0.66743	1.576000	0.49790	0.655000	0.94253	CTC		0.368	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56418058	G	T	56418058	3	4	61	1	0	0	0	0	1	0	0	0	4794	942	33	2	8024	2	DST	6	56418058	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	662	56418058	114697009	4681	12666										
DST	667	broad.mit.edu	37	chr6	56418217	56418217	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacccttgtgtttttaataAcagattttcaccttctgcaa	5	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56418217A>C	ENST00000361203.3	-	57	14747	c.14740T>G	c.(14740-14742)Tta>Gta	p.L4914V	DST_ENST00000370769.4_Missense_Mutation_p.L4916V|DST_ENST00000244364.6_Missense_Mutation_p.L2502V|DST_ENST00000370788.2_Missense_Mutation_p.L2828V|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Missense_Mutation_p.L4590V|DST_ENST00000421834.2_Missense_Mutation_p.L2828V|DST_ENST00000370754.5_Missense_Mutation_p.L5094V			Q03001	DYST_HUMAN	dystonin	4914					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.L4916V(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GTTTTTAATAACAGATTTTCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	105	107					6																	56418217		1818	4085	5903	56526176	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.14740T>G	6.37:g.56418217A>C	ENSP00000354508:p.Leu4914Val		56526176	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	12.26	1.885035	0.33255	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23;1.23	5.61	1.85	0.25348	.	0.000000	0.38005	N	0.001858	T	0.40979	0.1139	M	0.76574	2.34	0.30609	N	0.759733	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.996;0.999;0.999;0.998;0.99	T	0.35101	-0.9802	9	0.33940	T	0.23	.	9.1933	0.37213	0.6466:0.0:0.3534:0.0	.	2828;4916;5094;4914;2502	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	V	2502;5094;4916;2828;4590;2828;4914	ENSP00000244364:L2502V;ENSP00000359790:L5094V;ENSP00000359805:L4916V;ENSP00000400883:L2828V;ENSP00000393645:L4590V;ENSP00000359824:L2828V;ENSP00000354508:L4914V	ENSP00000244364:L2502V	L	-	1	2	DST	56526176	0.994000	0.37717	0.709000	0.30452	0.961000	0.63080	2.560000	0.45896	0.141000	0.18875	0.533000	0.62120	TTA		0.333	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56418217	A	C	56418217	3	2	61	1	0	0	0	0	1	0	0	0	4794	40	2	4	8183	4	DST	6	56418217	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	159	56418217	114696850	4682	12667										
DST	667	broad.mit.edu	37	chr6	56443634	56443634	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgttttctggatatcattCttggctggaagtaaagatcc	10	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56443634C>T	ENST00000361203.3	-	46	12379	c.12372G>A	c.(12370-12372)aaG>aaA	p.K4124K	DST_ENST00000370769.4_Silent_p.K4126K|DST_ENST00000244364.6_Silent_p.K1712K|DST_ENST00000370788.2_Silent_p.K2038K|DST_ENST00000312431.6_Silent_p.K4124K|DST_ENST00000446842.2_Silent_p.K3800K|DST_ENST00000421834.2_Silent_p.K2038K|DST_ENST00000370754.5_Silent_p.K4304K			Q03001	DYST_HUMAN	dystonin	4124					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.K4126K(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GGATATCATTCTTGGCTGGAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	6											78	79	79					6																	56443634		1846	4096	5942	56551593	SO:0001819	synonymous_variant	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.12372G>A	6.37:g.56443634C>T			56551593	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																					0.398	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56443634	C	T	56443634	2	4	61	1	0	0	0	0	0	0	0	1	4794	912	32	3		3	DST	6	56443634	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25417	56443634	114671433	4683	12668										
DST	667	broad.mit.edu	37	chr6	56480713	56480713	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattactaattcacactgtcGcagctgctgggcaaacccct	8	13	1	0	rs201023684		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56480713G>A	ENST00000370765.6	-	24	7659	c.7552C>T	c.(7552-7554)Cga>Tga	p.R2518*	DST_ENST00000370769.4_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1814					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R2518*(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCACACTGTCGCAGCTGCTGG	0.458																																																2	Substitution - Nonsense(2)	large_intestine(2)	6						G	stop/ARG,	0,4406		0,0,2203	81	83	82		7552,	4.1	1	6		82	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained,intron	DST	NM_001723.5,NM_015548.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	2518/2650,	56480713	1,13005	2203	4300	6503	56588672	SO:0001587	stop_gained	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7552C>T	6.37:g.56480713G>A	ENSP00000359801:p.Arg2518*		56588672	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	G	47	13.524804	0.99747	0.0	1.16E-4	ENSG00000151914	ENST00000370765	.	.	.	5.94	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1.000000	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	14.8795	0.70522	0.0:0.0:0.6272:0.3728	.	.	.	.	X	2518	.	ENSP00000359801:R2518X	R	-	1	2	DST	56588672	1.000000	0.71417	0.993000	0.49108	0.945000	0.59286	4.776000	0.62354	0.809000	0.34255	0.557000	0.71058	CGA		0.458	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		A	56480713	G	A	56480713	4	1	61	1	0	0	0	0	0	1	0	0	4794	1095	38	1	12847	1	DST	6	56480713	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37079	56480713	114634354	4684	12669										
DST	667	broad.mit.edu	37	chr6	56481658	56481658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagcctaattctgaattCggggtcaacaactcctttaa	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56481658C>T	ENST00000370765.6	-	24	6714	c.6607G>A	c.(6607-6609)Gaa>Aaa	p.E2203K	DST_ENST00000370769.4_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1619					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.E2203K(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATTCTGAATTCGGGGTCAACA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	6											58	62	61					6																	56481658		2203	4300	6503	56589617	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.6607G>A	6.37:g.56481658C>T	ENSP00000359801:p.Glu2203Lys		56589617	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143802	0.57044	.	.	ENSG00000151914	ENST00000370765	T	0.76578	-1.03	5.77	5.77	0.91146	.	.	.	.	.	T	0.62380	0.2423	.	.	.	0.09310	N	0.999993	P	0.43909	0.821	B	0.37550	0.253	T	0.63765	-0.6563	7	0.29301	T	0.29	.	20.3472	0.98799	0.0:1.0:0.0:0.0	.	2203	Q03001-3	.	K	2203	ENSP00000359801:E2203K	ENSP00000359801:E2203K	E	-	1	0	DST	56589617	0.995000	0.38212	0.998000	0.56505	0.905000	0.53344	3.173000	0.50839	2.890000	0.99128	0.650000	0.86243	GAA		0.388	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56481658	C	T	56481658	3	4	61	1	0	0	0	0	1	0	0	0	4794	893	31	1	13792	1	DST	6	56481658	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	945	56481658	114633409	4685	12670										
DST	667	broad.mit.edu	37	chr6	56483424	56483424	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgttgaagctgtctttcaAgttctttaatgtttgtttca	7	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56483424A>C	ENST00000370765.6	-	23	5515	c.5408T>G	c.(5407-5409)cTt>cGt	p.L1803R	DST_ENST00000370769.4_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	6536					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.L1803R(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGTCTTTCAAGTTCTTTAAT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	6											156	146	149					6																	56483424		2203	4300	6503	56591383	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.5408T>G	6.37:g.56483424A>C	ENSP00000359801:p.Leu1803Arg		56591383	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	A	13.13	2.145046	0.37825	.	.	ENSG00000151914	ENST00000370765	T	0.36340	1.26	5.21	5.21	0.72293	.	.	.	.	.	T	0.28863	0.0716	.	.	.	0.27540	N	0.950815	D	0.55172	0.97	P	0.47981	0.563	T	0.35450	-0.9788	7	0.87932	D	0	.	10.629	0.45525	0.8569:0.0:0.0:0.1431	.	1803	Q03001-3	.	R	1803	ENSP00000359801:L1803R	ENSP00000359801:L1803R	L	-	2	0	DST	56591383	0.927000	0.31430	0.974000	0.42286	0.803000	0.45373	3.574000	0.53863	2.095000	0.63458	0.528000	0.53228	CTT		0.378	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		C	56483424	A	C	56483424	3	2	61	1	0	0	0	0	1	0	0	0	4794	72	3	4	14995	4	DST	6	56483424	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1766	56483424	114631643	4686	12671										
DST	667	broad.mit.edu	37	chr6	56499632	56499632	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtcacagatagctttgatCggaatagaagttttgagtgg	12	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56499632C>T	ENST00000361203.3	-	21	2680	c.2673G>A	c.(2671-2673)ccG>ccA	p.P891P	DST_ENST00000370769.4_Silent_p.P891P|DST_ENST00000244364.6_Silent_p.P565P|DST_ENST00000370788.2_Silent_p.P891P|DST_ENST00000312431.6_Silent_p.P891P|DST_ENST00000446842.2_Silent_p.P565P|DST_ENST00000421834.2_Silent_p.P891P|DST_ENST00000370754.5_Silent_p.P1069P|DST_ENST00000518935.1_Silent_p.P565P|DST_ENST00000370765.6_Silent_p.P565P			Q03001	DYST_HUMAN	dystonin	891	SH3.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.P565P(2)|p.P891P(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TAGCTTTGATCGGAATAGAAG	0.348																																																3	Substitution - coding silent(3)	large_intestine(3)	6											225	227	226					6																	56499632		2203	4300	6503	56607591	SO:0001819	synonymous_variant	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.2673G>A	6.37:g.56499632C>T			56607591	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																					0.348	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56499632	C	T	56499632	2	4	61	1	0	0	0	0	0	0	0	1	4794	871	31	1		1	DST	6	56499632	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16208	56499632	114615435	4687	12672										
DST	667	broad.mit.edu	37	chr6	56505357	56505357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttgctgtacacagaagAacattcgttccttaaggcca	7	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56505357A>G	ENST00000361203.3	-	14	1448	c.1441T>C	c.(1441-1443)Tct>Cct	p.S481P	DST_ENST00000370769.4_Missense_Mutation_p.S481P|DST_ENST00000244364.6_Missense_Mutation_p.S155P|DST_ENST00000370788.2_Missense_Mutation_p.S481P|DST_ENST00000312431.6_Missense_Mutation_p.S481P|DST_ENST00000446842.2_Missense_Mutation_p.S155P|DST_ENST00000421834.2_Missense_Mutation_p.S481P|DST_ENST00000370754.5_Missense_Mutation_p.S659P|DST_ENST00000518935.1_Missense_Mutation_p.S155P|DST_ENST00000370765.6_Missense_Mutation_p.S155P			Q03001	DYST_HUMAN	dystonin	481					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.S155P(2)|p.S659P(1)|p.S481P(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACACAGAAGAACATTCGTTC	0.393																																																4	Substitution - Missense(4)	large_intestine(4)	6											100	98	98					6																	56505357		2203	4300	6503	56613316	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1441T>C	6.37:g.56505357A>G	ENSP00000354508:p.Ser481Pro		56613316	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	17.90	3.502847	0.64298	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935;ENST00000449297	D;D;D;D;D;D;D;D;D;D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55;-3.55	5.65	4.46	0.54185	.	0.000000	0.53938	D	0.000046	D	0.94066	0.8098	L	0.53249	1.67	0.33136	D	0.543702	D;D;D;D;D;P;D;D;P;P	0.89917	0.966;0.966;0.998;0.966;0.999;0.954;0.998;1.0;0.938;0.813	P;B;D;P;D;P;D;D;B;B	0.80764	0.598;0.422;0.986;0.502;0.943;0.548;0.976;0.994;0.422;0.245	D	0.94121	0.7379	9	0.59425	D	0.04	.	8.1458	0.31110	0.7259:0.1403:0.0:0.1339	.	510;481;481;659;597;155;155;155;481;155	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	P	155;659;481;481;155;481;481;481;155;521;155;155;659	ENSP00000244364:S155P;ENSP00000359790:S659P;ENSP00000359805:S481P;ENSP00000400883:S481P;ENSP00000393645:S155P;ENSP00000307959:S481P;ENSP00000359824:S481P;ENSP00000354508:S481P;ENSP00000404924:S155P;ENSP00000431030:S521P;ENSP00000359801:S155P;ENSP00000431003:S155P;ENSP00000393082:S659P	ENSP00000244364:S155P	S	-	1	0	DST	56613316	1.000000	0.71417	0.994000	0.49952	0.683000	0.39861	6.792000	0.75125	1.118000	0.41863	0.533000	0.62120	TCT		0.393	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56505357	A	G	56505357	3	3	61	1	0	0	0	0	1	0	0	0	4794	246	9	4	20016	4	DST	6	56505357	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5725	56505357	114609710	4688	12673										
BEND6	221336	broad.mit.edu	37	chr6	56879960	56879960	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagtcacccagtttgaaGaattggttggtatggccgag	13	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56879960G>T	ENST00000370746.3	+	4	597	c.328G>T	c.(328-330)Gaa>Taa	p.E110*	BEND6_ENST00000484701.1_3'UTR|BEND6_ENST00000545789.1_Nonsense_Mutation_p.E12*|BEND6_ENST00000370750.2_3'UTR	NM_152731.2	NP_689944.2	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6	110					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		RNA polymerase II transcription corepressor activity (GO:0001106)	p.E110*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	17						CCAGTTTGAAGAATTGGTTGG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											102	99	100					6																	56879960		1935	4130	6065	56987919	SO:0001587	stop_gained	221336			AK054724	CCDS43476.1	6p12.1	2012-11-22	2008-10-03	2008-10-03	ENSG00000151917	ENSG00000151917		"BEN domain containing"	20871	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 65"	C6orf65			Standard	NM_152731		Approved	FLJ30162, bA203B9.1	uc010kab.3	Q5SZJ8	OTTHUMG00000014914	ENST00000370746.3:c.328G>T	6.37:g.56879960G>T	ENSP00000359782:p.Glu110*		56987919	Q4G0W8|Q8N662|Q96NS6	Nonsense_Mutation	SNP	ENST00000370746.3	37	CCDS43476.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.913136	0.92178	.	.	ENSG00000151917	ENST00000322055;ENST00000370746;ENST00000545789	.	.	.	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.7276	15.4347	0.75137	0.0:0.0:1.0:0.0	.	.	.	.	X	110;110;12	.	ENSP00000322773:E110X	E	+	1	0	BEND6	56987919	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.990000	0.56965	2.547000	0.85894	0.467000	0.42956	GAA		0.428	BEND6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041032.4	NM_152731		T	56879960	G	T	56879960	4	4	61	1	0	0	0	0	0	1	0	0	1403	943	33	2	338	2	BEND6	6	56879960	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	374603	56879960	114235107	4689	12674										
KIAA1586	57691	broad.mit.edu	37	chr6	56918189	56918189	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcagaacatattgcaaaaGaaatgaagatgaagatattt	8	3	0	6	rs370357858		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56918189G>T	ENST00000370733.4	+	4	1099	c.892G>T	c.(892-894)Gaa>Taa	p.E298*	KIAA1586_ENST00000545356.1_Nonsense_Mutation_p.E271*	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	298							nucleic acid binding (GO:0003676)	p.E298*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TATTGCAAAAGAAATGAAGAT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											37	40	39					6																	56918189		2202	4294	6496	57026148	SO:0001587	stop_gained	57691			AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.892G>T	6.37:g.56918189G>T	ENSP00000359768:p.Glu298*		57026148	A8K4M3|Q8IW25	Nonsense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	26.1	4.708435	0.89018	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	.	.	.	3.82	2.91	0.33838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	8.5206	0.33273	0.0:0.0:0.7686:0.2314	.	.	.	.	X	298;271	.	ENSP00000359768:E298X	E	+	1	0	KIAA1586	57026148	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.833000	0.27504	0.889000	0.36185	0.467000	0.42956	GAA		0.323	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		T	56918189	G	T	56918189	4	4	61	1	0	0	0	0	0	1	0	0	8266	943	33	2	906	2	KIAA1586	6	56918189	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38229	56918189	114196878	4690	12675										
KIAA1586	57691	broad.mit.edu	37	chr6	56918626	56918626	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaatcatttaaaaatattTattgataaaatttattctat	1	2	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:56918626T>C	ENST00000370733.4	+	4	1536	c.1329T>C	c.(1327-1329)ttT>ttC	p.F443F	KIAA1586_ENST00000545356.1_Silent_p.F416F	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	443							nucleic acid binding (GO:0003676)	p.F443F(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			taaaaatatttattgataaaa	0.239																																																1	Substitution - coding silent(1)	large_intestine(1)	6											7	7	7					6																	56918626		1899	4022	5921	57026585	SO:0001819	synonymous_variant	57691			AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.1329T>C	6.37:g.56918626T>C			57026585	A8K4M3|Q8IW25	Silent	SNP	ENST00000370733.4	37	CCDS34480.1																																																																																				0.239	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		C	56918626	T	C	56918626	2	2	61	1	0	0	0	0	0	0	0	1	8266	1751	61	4		4	KIAA1586	6	56918626	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	437	56918626	114196441	4691	12676										
ZNF451	26036	broad.mit.edu	37	chr6	57006239	57006239	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaatcatttccatcagaGtttcaaactgggtggtatgt	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:57006239G>T	ENST00000370706.4	+	8	1086	c.842G>T	c.(841-843)aGt>aTt	p.S281I	ZNF451_ENST00000491832.2_Missense_Mutation_p.S281I|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.S281I|RP11-203B9.4_ENST00000416069.2_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S281I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TTCCATCAGAGTTTCAAACTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											102	94	97					6																	57006239		2203	4300	6503	57114198	SO:0001583	missense	26036			AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.842G>T	6.37:g.57006239G>T	ENSP00000359740:p.Ser281Ile		57114198	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	37	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973611	0.34848	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.07567	3.18;3.18;3.18	5.67	0.254	0.15557	.	0.735164	0.14104	N	0.341196	T	0.02156	0.0067	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.08055	0.002;0.001;0.003;0.001	T	0.37384	-0.9708	10	0.22109	T	0.4	-0.5228	2.2229	0.03977	0.1527:0.3803:0.2373:0.2296	.	281;281;281;281	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	I	281	ENSP00000359740:S281I;ENSP00000350083:S281I;ENSP00000421645:S281I	ENSP00000350083:S281I	S	+	2	0	ZNF451	57114198	0.978000	0.34361	0.986000	0.45419	0.990000	0.78478	0.276000	0.18716	0.015000	0.14971	0.585000	0.79938	AGT		0.348	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		T	57006239	G	T	57006239	3	4	61	1	0	0	0	0	1	0	0	0	17961	1029	36	2	872	2	ZNF451	6	57006239	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87613	57006239	114108828	4692	12677										
RAB23	51715	broad.mit.edu	37	chr6	57075096	57075096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaatgcctttgcaatatCgctgaatcatacttgatttt	5	7	1	2	rs376394715		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:57075096C>T	ENST00000317483.3	-	2	702	c.83G>A	c.(82-84)cGa>cAa	p.R28Q	RAB23_ENST00000468148.1_Missense_Mutation_p.R28Q	NM_016277.3	NP_057361.3	Q9ULC3	RAB23_HUMAN	RAB23, member RAS oncogene family	28					autophagic vacuole assembly (GO:0000045)|cellular defense response (GO:0006968)|cilium assembly (GO:0042384)|craniofacial suture morphogenesis (GO:0097094)|embryonic digit morphogenesis (GO:0042733)|GTP catabolic process (GO:0006184)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription factor import into nucleus (GO:0042992)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|small GTPase mediated signal transduction (GO:0007264)|spinal cord dorsal/ventral patterning (GO:0021513)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R28Q(1)		kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	8	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TTTGCAATATCGCTGAATCAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	216	195	202		83,83	5.6	1	6		202	0,8600		0,0,4300	no	missense,missense	RAB23	NM_016277.3,NM_183227.1	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	28/238,28/238	57075096	1,13005	2203	4300	6503	57183055	SO:0001583	missense	51715			AB034244	CCDS4962.1	6p12.1	2008-05-15			ENSG00000112210	ENSG00000112210		"RAB, member RAS oncogene"	14263	protein-coding gene	gene with protein product		606144					Standard	NM_016277		Approved		uc003pdt.3	Q9ULC3	OTTHUMG00000014918	ENST00000317483.3:c.83G>A	6.37:g.57075096C>T	ENSP00000320413:p.Arg28Gln		57183055	B2R9I5|Q68DJ6|Q8NI06|Q9P023	Missense_Mutation	SNP	ENST00000317483.3	37	CCDS4962.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.581682	0.86748	2.27E-4	0.0	ENSG00000112210	ENST00000317483;ENST00000468148	D;D	0.81739	-1.53;-1.53	5.55	5.55	0.83447	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.86577	0.5966	L	0.58969	1.84	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	D	0.87361	0.2344	10	0.87932	D	0	-0.0328	19.4985	0.95083	0.0:1.0:0.0:0.0	.	28	Q9ULC3	RAB23_HUMAN	Q	28	ENSP00000320413:R28Q;ENSP00000417610:R28Q	ENSP00000320413:R28Q	R	-	2	0	RAB23	57183055	1.000000	0.71417	0.980000	0.43619	0.280000	0.26924	7.814000	0.86154	2.602000	0.87976	0.655000	0.94253	CGA		0.378	RAB23-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041042.1			T	57075096	C	T	57075096	3	4	61	1	0	0	0	0	1	0	0	0	12947	884	31	1	654	1	RAB23	6	57075096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68857	57075096	114039971	4693	12678										
PRIM2	5558	broad.mit.edu	37	chr6	57183364	57183364	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaaacatatctttaataGaatttgaaaacttggctatt	5	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:57183364G>T	ENST00000607273.1	+	2	208	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	PRIM2_ENST00000389488.2_3'UTR	NM_000947.3	NP_000938.2	P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	41					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)	p.E41*(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATCTTTAATAGAATTTGAAAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											34	33	33					6																	57183364		1821	4076	5897	57291323	SO:0001587	stop_gained	5558				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000607273.1:c.121G>T	6.37:g.57183364G>T	ENSP00000475738:p.Glu41*		57291323	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Nonsense_Mutation	SNP	ENST00000607273.1	37																																																																																					0.368	PRIM2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000947		T	57183364	G	T	57183364	4	4	61	1	0	0	0	0	0	1	0	0	12525	943	33	2	123	2	PRIM2	6	57183364	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108268	57183364	113931703	4694	12679										
PRIM2	5558	broad.mit.edu	37	chr6	57472420	57472420	+	3'UTR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttgcagtcatacaagatCtctcctggagggataagcca	10	9	2	1	rs377484942		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:57472420C>A	ENST00000389488.2	+	0	1296				PRIM2_ENST00000607273.1_3'UTR			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)						DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)	p.I403I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CATACAAGATCTCTCCTGGAG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		1,4033		0,1,2016	190	177	181		1209	-0.4	0.7	6		181	0,8392		0,0,4196	no	coding-synonymous	PRIM2	XM_003403439.1		0,1,6212	AA,AC,CC		0.0,0.0248,0.0080		403/510	57472420	1,12425	2017	4196	6213	57580379	SO:0001624	3_prime_UTR_variant	5558				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.*1293C>A	6.37:g.57472420C>A			57580379	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Silent	SNP	ENST00000389488.2	37																																																																																					0.443	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000043468.3	NM_000947		A	57472420	C	A	57472420	1	1	61	0	1	0	0	0	0	0	0	0	12525	903	32	2		2	PRIM2	6	57472420	3'UTR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289056	57472420	113642647	4695	12680										
KHDRBS2	202559	broad.mit.edu	37	chr6	62688056	62688056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcaaacacttcaattaatAcatgaagctcatcactcaag	5	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:62688056A>G	ENST00000281156.4	-	4	676	c.398T>C	c.(397-399)gTa>gCa	p.V133A		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	133	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)	p.V133A(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TTCAATTAATACATGAAGCTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											121	109	113					6																	62688056		2203	4300	6503	62746015	SO:0001583	missense	202559			BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"Sam68-like mammalian protein 1"	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.398T>C	6.37:g.62688056A>G	ENSP00000281156:p.Val133Ala		62746015	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.658472	0.88154	.	.	ENSG00000112232	ENST00000281156;ENST00000539571	T	0.57107	0.42	5.46	5.46	0.80206	K Homology (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.71230	-0.4654	10	0.87932	D	0	-3.77	15.5442	0.76081	1.0:0.0:0.0:0.0	.	133	Q5VWX1	KHDR2_HUMAN	A	133	ENSP00000281156:V133A	ENSP00000281156:V133A	V	-	2	0	KHDRBS2	62746015	1.000000	0.71417	0.989000	0.46669	0.991000	0.79684	9.339000	0.96797	2.078000	0.62432	0.528000	0.53228	GTA		0.383	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		G	62688056	A	G	62688056	3	3	61	1	0	0	0	0	1	0	0	0	8168	391	14	4	675	4	KHDRBS2	6	62688056	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5215636	62688056	108427011	4696	12681										
PTP4A1	7803	broad.mit.edu	37	chr6	64288417	64288417	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactactcttgtggagaaaGaaggtatccatgttcttgta	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:64288417G>T	ENST00000370651.3	+	3	1334	c.181G>T	c.(181-183)Gaa>Taa	p.E61*	PTP4A1_ENST00000370650.2_Nonsense_Mutation_p.E61*	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	61					cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.E61*(1)		large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			TGTGGAGAAAGAAGGTATCCA	0.303																																					Pancreas(91;1019 1502 28028 38110 51645)											1	Substitution - Nonsense(1)	large_intestine(1)	6											85	81	83					6																	64288417		2203	4291	6494	64346376	SO:0001587	stop_gained	7803			U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.181G>T	6.37:g.64288417G>T	ENSP00000359685:p.Glu61*		64346376	B2R6C8|O00648|Q49A54	Nonsense_Mutation	SNP	ENST00000370651.3	37	CCDS4965.1	.	.	.	.	.	.	.	.	.	.	G	35	5.454413	0.96223	.	.	ENSG00000112245	ENST00000370651;ENST00000370650;ENST00000370644	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-34.8605	20.33	0.98713	0.0:0.0:1.0:0.0	.	.	.	.	X	61	.	ENSP00000359678:E61X	E	+	1	0	PTP4A1	64346376	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.764000	0.85297	2.810000	0.96702	0.585000	0.79938	GAA		0.303	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2			T	64288417	G	T	64288417	4	4	61	1	0	0	0	0	0	1	0	0	12805	943	33	2	187	2	PTP4A1	6	64288417	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1600361	64288417	106826650	4697	12682										
PHF3	23469	broad.mit.edu	37	chr6	64401724	64401724	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgggcgaggaagacaaaGaatatgtctgtgtaaaatgt	13	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:64401724G>T	ENST00000262043.3	+	5	2627	c.2287G>T	c.(2287-2289)Gaa>Taa	p.E763*	PHF3_ENST00000393387.1_Nonsense_Mutation_p.E763*			Q92576	PHF3_HUMAN	PHD finger protein 3	763					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.E763*(1)		breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GGAAGACAAAGAATATGTCTG	0.413																																					GBM(135;136 1820 29512 34071 46235)											1	Substitution - Nonsense(1)	large_intestine(1)	6											156	157	156					6																	64401724		2203	4300	6503	64459683	SO:0001587	stop_gained	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2287G>T	6.37:g.64401724G>T	ENSP00000262043:p.Glu763*		64459683	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Nonsense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	G	38	7.188887	0.98121	.	.	ENSG00000118482	ENST00000506783;ENST00000481385;ENST00000515594;ENST00000262043;ENST00000494284;ENST00000393387	.	.	.	5.11	5.11	0.69529	.	0.000000	0.40908	D	0.000996	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-25.403	18.8994	0.92435	0.0:0.0:1.0:0.0	.	.	.	.	X	577;675;32;763;716;763	.	ENSP00000262043:E763X	E	+	1	0	PHF3	64459683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.542000	0.82095	2.536000	0.85505	0.585000	0.79938	GAA		0.413	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			T	64401724	G	T	64401724	4	4	61	1	0	0	0	0	0	1	0	0	11867	943	33	2	2301	2	PHF3	6	64401724	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113307	64401724	106713343	4698	12683										
PHF3	23469	broad.mit.edu	37	chr6	64421526	64421526	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgttgggcttaattattCgtcagaaactgaagcgacag	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:64421526C>T	ENST00000262043.3	+	16	4382	c.4042C>T	c.(4042-4044)Cgt>Tgt	p.R1348C	PHF3_ENST00000393387.1_Missense_Mutation_p.R1348C			Q92576	PHF3_HUMAN	PHD finger protein 3	1348					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R1348C(1)		breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			CTTAATTATTCGTCAGAAACT	0.378																																					GBM(135;136 1820 29512 34071 46235)											1	Substitution - Missense(1)	large_intestine(1)	6											83	88	87					6																	64421526		2195	4289	6484	64479485	SO:0001583	missense	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.4042C>T	6.37:g.64421526C>T	ENSP00000262043:p.Arg1348Cys		64479485	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099894	0.56183	.	.	ENSG00000118482	ENST00000515594;ENST00000262043;ENST00000393387	T;T;T	0.51574	0.7;1.98;1.98	5.88	5.88	0.94601	.	0.443356	0.17105	N	0.186848	T	0.35970	0.0950	L	0.41492	1.28	0.80722	D	1	P	0.38677	0.642	B	0.42361	0.385	T	0.09292	-1.0681	10	0.23891	T	0.37	-4.162	20.2884	0.98536	0.0:1.0:0.0:0.0	.	1348	Q92576	PHF3_HUMAN	C	617;1348;1348	ENSP00000425338:R617C;ENSP00000262043:R1348C;ENSP00000377048:R1348C	ENSP00000262043:R1348C	R	+	1	0	PHF3	64479485	1.000000	0.71417	0.994000	0.49952	0.816000	0.46133	4.445000	0.60007	2.791000	0.96007	0.650000	0.86243	CGT		0.378	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			T	64421526	C	T	64421526	3	4	61	1	0	0	0	0	1	0	0	0	11867	884	31	1	4100	1	PHF3	6	64421526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19802	64421526	106693541	4699	12684										
PHF3	23469	broad.mit.edu	37	chr6	64422599	64422599	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagttgtgttctgcagaGaaaaactcgtgtgttcagca	11	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:64422599G>T	ENST00000262043.3	+	16	5455	c.5115G>T	c.(5113-5115)gaG>gaT	p.E1705D	PHF3_ENST00000393387.1_Missense_Mutation_p.E1705D			Q92576	PHF3_HUMAN	PHD finger protein 3	1705					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.E1705D(1)		breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GTTCTGCAGAGAAAAACTCGT	0.418																																					GBM(135;136 1820 29512 34071 46235)											1	Substitution - Missense(1)	large_intestine(1)	6											59	59	59					6																	64422599		2203	4300	6503	64480558	SO:0001583	missense	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.5115G>T	6.37:g.64422599G>T	ENSP00000262043:p.Glu1705Asp		64480558	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	G	8.992	0.978025	0.18812	.	.	ENSG00000118482	ENST00000262043;ENST00000393387	T;T	0.22336	1.96;1.96	5.97	3.23	0.37069	.	0.000000	0.40064	N	0.001188	T	0.17195	0.0413	L	0.32530	0.975	0.35870	D	0.828184	D	0.76494	0.999	D	0.78314	0.991	T	0.02877	-1.1099	9	.	.	.	-18.1246	6.5729	0.22549	0.3587:0.0:0.6413:0.0	.	1705	Q92576	PHF3_HUMAN	D	1705	ENSP00000262043:E1705D;ENSP00000377048:E1705D	.	E	+	3	2	PHF3	64480558	1.000000	0.71417	0.997000	0.53966	0.432000	0.31715	1.251000	0.32862	1.544000	0.49359	0.655000	0.94253	GAG		0.418	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			T	64422599	G	T	64422599	3	4	61	1	0	0	0	0	1	0	0	0	11867	933	33	2	5173	2	PHF3	6	64422599	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1073	64422599	106692468	4700	12685										
EYS	346007	broad.mit.edu	37	chr6	66205145	66205145	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaccagcaatctctgtaGaagtccaagcagatgttttc	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:66205145G>T	ENST00000370621.3	-	4	685	c.159C>A	c.(157-159)ttC>ttA	p.F53L	EYS_ENST00000393380.2_Missense_Mutation_p.F53L|EYS_ENST00000370616.2_Missense_Mutation_p.F53L|EYS_ENST00000370618.3_Missense_Mutation_p.F53L|EYS_ENST00000342421.5_Missense_Mutation_p.F53L|EYS_ENST00000503581.1_Missense_Mutation_p.F53L			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	53					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.F53L(2)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AATCTCTGTAGAAGTCCAAGC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	6											108	107	107					6																	66205145		2203	4300	6503	66261866	SO:0001583	missense	346007				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.159C>A	6.37:g.66205145G>T	ENSP00000359655:p.Phe53Leu		66261866	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	G	10.21	1.287438	0.23478	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.89552	-1.52;-1.51;-1.51;-2.53;-2.48;-2.48	5.13	1.12	0.20585	.	.	.	.	.	T	0.60830	0.2299	N	0.14661	0.345	0.09310	N	1	B;B;B	0.28419	0.211;0.069;0.041	B;B;B	0.26094	0.066;0.035;0.026	T	0.55528	-0.8127	9	0.66056	D	0.02	.	3.8543	0.08968	0.2272:0.0:0.4621:0.3107	.	53;53;53	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	L	53	ENSP00000424243:F53L;ENSP00000359655:F53L;ENSP00000359650:F53L;ENSP00000377042:F53L;ENSP00000341818:F53L;ENSP00000359652:F53L	ENSP00000341818:F53L	F	-	3	2	EYS	66261866	0.000000	0.05858	0.000000	0.03702	0.626000	0.37791	0.067000	0.14510	0.223000	0.20920	0.591000	0.81541	TTC		0.398	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	66205145	G	T	66205145	3	4	61	1	0	0	0	0	1	0	0	0	5345	933	33	2	9397	2	EYS	6	66205145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1782546	66205145	104909922	4701	12686										
BAI3	577	broad.mit.edu	37	chr6	69666022	69666022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcagctgcccatggaggCtccgaatgcagagggccatg	14	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:69666022C>T	ENST00000370598.1	+	7	2123	c.1302C>T	c.(1300-1302)ggC>ggT	p.G434G		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	434	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G434G(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CCCATGGAGGCTCCGAATGCA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	6											72	65	67					6																	69666022		2203	4300	6503	69722743	SO:0001819	synonymous_variant	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1302C>T	6.37:g.69666022C>T			69722743	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																				0.557	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69666022	C	T	69666022	2	4	61	1	0	0	0	0	0	0	0	1	1301	784	28	3		3	BAI3	6	69666022	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3460877	69666022	101449045	4702	12687										
BAI3	577	broad.mit.edu	37	chr6	70048824	70048824	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtcagatgagtgagcctCatagcggtttgacgctcaaa	12	9	3	4	rs370985736		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:70048824C>A	ENST00000370598.1	+	25	4026	c.3205C>A	c.(3205-3207)Cat>Aat	p.H1069N	BAI3_ENST00000238918.8_Missense_Mutation_p.H275N|BAI3_ENST00000546190.1_Missense_Mutation_p.H33N	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1069					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.H1069N(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GAGTGAGCCTCATAGCGGTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											219	217	217					6																	70048824		2203	4300	6503	70105545	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3205C>A	6.37:g.70048824C>A	ENSP00000359630:p.His1069Asn		70105545	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521971	0.64747	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.42900	2.11;2.71;0.96	6.16	6.16	0.99307	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.29914	0.0748	N	0.05441	-0.05	0.58432	D	0.999999	D;D;P	0.62365	0.991;0.991;0.925	D;D;D	0.76575	0.988;0.988;0.954	T	0.05131	-1.0904	10	0.02654	T	1	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	275;1069;1069	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	N	1069;275;33	ENSP00000359630:H1069N;ENSP00000238918:H275N;ENSP00000441821:H33N	ENSP00000238918:H275N	H	+	1	0	BAI3	70105545	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.037000	0.70956	2.937000	0.99478	0.650000	0.86243	CAT		0.408	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	70048824	C	A	70048824	3	1	61	1	0	0	0	0	1	0	0	0	1301	826	29	2	3295	2	BAI3	6	70048824	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382802	70048824	101066243	4703	12688										
BAI3	577	broad.mit.edu	37	chr6	70092801	70092801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaactttggacagatttCgggatataccaaatacaagc	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:70092801C>T	ENST00000370598.1	+	31	5175	c.4354C>T	c.(4354-4356)Cgg>Tgg	p.R1452W	BAI3_ENST00000238918.8_Missense_Mutation_p.R658W|BAI3_ENST00000546190.1_Missense_Mutation_p.R416W	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1452					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1452W(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GGACAGATTTCGGGATATACC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	92	92					6																	70092801		2203	4299	6502	70149522	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4354C>T	6.37:g.70092801C>T	ENSP00000359630:p.Arg1452Trp		70149522	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253697	0.80135	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.14266	2.52;2.52;2.52	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	L	0.55990	1.75	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.928	T	0.01093	-1.1454	10	0.87932	D	0	.	19.9675	0.97275	0.0:1.0:0.0:0.0	.	658;1452	B7Z356;O60242	.;BAI3_HUMAN	W	1452;658;416	ENSP00000359630:R1452W;ENSP00000238918:R658W;ENSP00000441821:R416W	ENSP00000238918:R658W	R	+	1	2	BAI3	70149522	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.713000	0.68415	2.709000	0.92574	0.655000	0.94253	CGG		0.383	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	70092801	C	T	70092801	3	4	61	1	0	0	0	0	1	0	0	0	1301	875	31	1	4468	1	BAI3	6	70092801	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43977	70092801	101022266	4704	12689										
LMBRD1	55788	broad.mit.edu	37	chr6	70411350	70411350	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactgtttgtagtaaaggCaaaagcatattcagtggatt	9	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:70411350C>T	ENST00000370577.3	-	11	1297	c.1068G>A	c.(1066-1068)ttG>ttA	p.L356L	LMBRD1_ENST00000370570.1_Silent_p.L283L	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	356					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.L356L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						GTAGTAAAGGCAAAAGCATAT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	6											54	55	55					6																	70411350		2198	4285	6483	70468071	SO:0001819	synonymous_variant	55788			AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1068G>A	6.37:g.70411350C>T			70468071	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Silent	SNP	ENST00000370577.3	37	CCDS4969.1																																																																																				0.318	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		T	70411350	C	T	70411350	2	4	61	1	0	0	0	0	0	0	0	1	8866	709	25	3		3	LMBRD1	6	70411350	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	318549	70411350	100703717	4705	12690										
COL19A1	1310	broad.mit.edu	37	chr6	70847624	70847624	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtctgttggccctaaaggAcaaaaaggagaacctgtaag	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:70847624A>G	ENST00000322773.4	+	19	1533	c.1431A>G	c.(1429-1431)ggA>ggG	p.G477G	COL19A1_ENST00000393344.1_Silent_p.G99G	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	477	Collagen-like 4.|Triple-helical region 3 (COL3).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.G477G(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GCCCTAAAGGACAAAAAGGAG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	6											142	142	142					6																	70847624		2203	4300	6503	70904345	SO:0001819	synonymous_variant	1310				CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1431A>G	6.37:g.70847624A>G			70904345	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																				0.403	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			G	70847624	A	G	70847624	2	3	61	1	0	0	0	0	0	0	0	1	3682	262	10	4		4	COL19A1	6	70847624	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	436274	70847624	100267443	4706	12691										
FAM135A	57579	broad.mit.edu	37	chr6	71235542	71235542	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaaattcaagcattaaaGaccctttacaatttgttttt	3	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:71235542G>T	ENST00000418814.2	+	15	3369	c.2755G>T	c.(2755-2757)Gac>Tac	p.D919Y	FAM135A_ENST00000370479.3_Missense_Mutation_p.D706Y|FAM135A_ENST00000457062.2_Missense_Mutation_p.D706Y|FAM135A_ENST00000361499.3_Missense_Mutation_p.D723Y|FAM135A_ENST00000505868.1_Missense_Mutation_p.D919Y|FAM135A_ENST00000505769.1_Intron	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	919								p.D706Y(1)		breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						AAGCATTAAAGACCCTTTACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											62	66	64					6																	71235542		2203	4298	6501	71292263	SO:0001583	missense	57579			AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.2755G>T	6.37:g.71235542G>T	ENSP00000410768:p.Asp919Tyr		71292263	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.546685	0.45383	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T	0.19669	2.15;2.14;2.14;2.13;2.14	5.96	5.96	0.96718	.	0.290992	0.40144	N	0.001163	T	0.36991	0.0987	M	0.64997	1.995	0.47905	D	0.999544	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.986;0.959;0.999;0.994	T	0.04333	-1.0959	10	0.66056	D	0.02	.	15.9476	0.79806	0.0:0.0:0.8645:0.1355	.	919;919;723;706	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	Y	919;706;706;723;919	ENSP00000410768:D919Y;ENSP00000359510:D706Y;ENSP00000409201:D706Y;ENSP00000354913:D723Y;ENSP00000423307:D919Y	ENSP00000354913:D723Y	D	+	1	0	FAM135A	71292263	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.966000	0.63715	2.826000	0.97356	0.655000	0.94253	GAC		0.358	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		T	71235542	G	T	71235542	3	4	61	1	0	0	0	0	1	0	0	0	5464	942	33	2	2883	2	FAM135A	6	71235542	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	387918	71235542	99879525	4707	12692										
SMAP1	60682	broad.mit.edu	37	chr6	71464750	71464750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatcttccagagaactttcGaagaccacagacagatcagt	7	11	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:71464750G>A	ENST00000370455.3	+	3	568	c.320G>A	c.(319-321)cGa>cAa	p.R107Q	SMAP1_ENST00000370452.3_Missense_Mutation_p.R107Q|SMAP1_ENST00000422334.2_Missense_Mutation_p.R107Q|SMAP1_ENST00000316999.5_Missense_Mutation_p.R107Q	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	107	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R107Q(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						GAGAACTTTCGAAGACCACAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	6											135	149	144					6																	71464750		2202	4295	6497	71521471	SO:0001583	missense	60682			AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"ADP-ribosylation factor GTPase activating proteins"	19651	protein-coding gene	gene with protein product		611372	"stromal membrane-associated protein 1", "stromal membrane-associated GTPase-activating protein 1"			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.320G>A	6.37:g.71464750G>A	ENSP00000359484:p.Arg107Gln		71521471	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Missense_Mutation	SNP	ENST00000370455.3	37	CCDS43478.1	.	.	.	.	.	.	.	.	.	.	G	33	5.238049	0.95240	.	.	ENSG00000112305	ENST00000370452;ENST00000316999;ENST00000370455;ENST00000370442;ENST00000422334	T;T;T;T	0.41400	1.01;1.01;1.01;1.0	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	L	0.33293	1	0.80722	D	1	D;D;D;D	0.89917	0.972;1.0;1.0;0.992	P;D;D;P	0.80764	0.487;0.994;0.994;0.832	T	0.47045	-0.9147	10	0.56958	D	0.05	-11.0745	18.5994	0.91242	0.0:0.0:1.0:0.0	.	107;107;107;107	A8K333;Q8IYB5-3;Q8IYB5-2;Q8IYB5	.;.;.;SMAP1_HUMAN	Q	107;107;107;19;107	ENSP00000359481:R107Q;ENSP00000313382:R107Q;ENSP00000359484:R107Q;ENSP00000398541:R107Q	ENSP00000313382:R107Q	R	+	2	0	SMAP1	71521471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.007000	0.93597	2.695000	0.91970	0.644000	0.83932	CGA		0.279	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305		A	71464750	G	A	71464750	3	1	61	1	0	0	0	0	1	0	0	0	14803	1058	37	1	330	1	SMAP1	6	71464750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229208	71464750	99650317	4708	12693										
OGFRL1	79627	broad.mit.edu	37	chr6	72011203	72011203	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatgaagctcttgtggaGaatactattcccaatattaa	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:72011203G>T	ENST00000370435.4	+	7	941	c.807G>T	c.(805-807)gaG>gaT	p.E269D	RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	269						membrane (GO:0016020)	receptor activity (GO:0004872)	p.E269D(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						CTCTTGTGGAGAATACTATTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											87	101	97					6																	72011203		2203	4300	6503	72067924	SO:0001583	missense	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.807G>T	6.37:g.72011203G>T	ENSP00000359464:p.Glu269Asp		72067924	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.360806	0.41801	.	.	ENSG00000119900	ENST00000370435	T	0.46819	0.86	6.04	0.136	0.14780	Opioid growth factor receptor (OGFr) conserved domain (1);	0.290315	0.39615	N	0.001315	T	0.28333	0.0700	N	0.20986	0.625	0.31372	N	0.679996	D	0.69078	0.997	D	0.64042	0.921	T	0.13522	-1.0506	10	0.35671	T	0.21	-23.0941	6.8913	0.24230	0.5768:0.1177:0.3055:0.0	.	269	Q5TC84	OGRL1_HUMAN	D	269	ENSP00000359464:E269D	ENSP00000359464:E269D	E	+	3	2	OGFRL1	72067924	1.000000	0.71417	0.994000	0.49952	0.210000	0.24377	0.926000	0.28804	0.150000	0.19136	-0.440000	0.05779	GAG		0.358	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		T	72011203	G	T	72011203	3	4	61	1	0	0	0	0	1	0	0	0	10875	933	33	2	833	2	OGFRL1	6	72011203	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	546453	72011203	99103864	4709	12694										
OGFRL1	79627	broad.mit.edu	37	chr6	72011393	72011393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaatgtcttcccctctcGcctccagtcataacagtcaa	5	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:72011393G>A	ENST00000370435.4	+	7	1131	c.997G>A	c.(997-999)Gcc>Acc	p.A333T	RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	333						membrane (GO:0016020)	receptor activity (GO:0004872)	p.A333T(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						TTCCCCTCTCGCCTCCAGTCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											44	48	47					6																	72011393		2203	4300	6503	72068114	SO:0001583	missense	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.997G>A	6.37:g.72011393G>A	ENSP00000359464:p.Ala333Thr		72068114	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	G	9.270	1.045502	0.19748	.	.	ENSG00000119900	ENST00000370435	T	0.43294	0.95	6.04	-4.03	0.04021	.	1.652800	0.02784	N	0.121203	T	0.04679	0.0127	N	0.03154	-0.405	0.09310	N	1	B	0.18166	0.026	B	0.08055	0.003	T	0.08269	-1.0730	10	0.15066	T	0.55	6.2185	4.8729	0.13642	0.5217:0.0945:0.2874:0.0964	.	333	Q5TC84	OGRL1_HUMAN	T	333	ENSP00000359464:A333T	ENSP00000359464:A333T	A	+	1	0	OGFRL1	72068114	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-1.212000	0.02994	-1.291000	0.02368	0.563000	0.77884	GCC		0.463	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		A	72011393	G	A	72011393	3	1	61	1	0	0	0	0	1	0	0	0	10875	1087	38	1	1023	1	OGFRL1	6	72011393	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190	72011393	99103674	4710	12695										
OGFRL1	79627	broad.mit.edu	37	chr6	72011675	72011675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtatctcctgagaataacGaagaaggtggaaatgataac	11	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:72011675G>A	ENST00000370435.4	+	7	1413	c.1279G>A	c.(1279-1281)Gaa>Aaa	p.E427K	RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	427						membrane (GO:0016020)	receptor activity (GO:0004872)	p.E427K(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						TGAGAATAACGAAGAAGGTGG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	6											95	104	101					6																	72011675		2203	4300	6503	72068396	SO:0001583	missense	79627				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.1279G>A	6.37:g.72011675G>A	ENSP00000359464:p.Glu427Lys		72068396	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	G	2.915	-0.224478	0.06061	.	.	ENSG00000119900	ENST00000370435	T	0.46451	0.87	5.5	3.7	0.42460	.	0.400623	0.21222	N	0.078132	T	0.15132	0.0365	L	0.45581	1.43	0.09310	N	1	B	0.27971	0.196	B	0.22601	0.04	T	0.11012	-1.0605	10	0.32370	T	0.25	-3.9537	9.0796	0.36542	0.0817:0.1489:0.7694:0.0	.	427	Q5TC84	OGRL1_HUMAN	K	427	ENSP00000359464:E427K	ENSP00000359464:E427K	E	+	1	0	OGFRL1	72068396	0.997000	0.39634	0.004000	0.12327	0.001000	0.01503	2.881000	0.48538	0.681000	0.31386	-0.302000	0.09304	GAA		0.378	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		A	72011675	G	A	72011675	3	1	61	1	0	0	0	0	1	0	0	0	10875	1059	37	1	1305	1	OGFRL1	6	72011675	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282	72011675	99103392	4711	12696										
RIMS1	22999	broad.mit.edu	37	chr6	72960629	72960629	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacttatttttcagtgataAaagtaaaaggaggaccaaaa	7	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:72960629A>C	ENST00000521978.1	+	14	2378	c.2378A>C	c.(2377-2379)aAa>aCa	p.K793T	RIMS1_ENST00000523963.1_Missense_Mutation_p.K267T|RIMS1_ENST00000348717.5_Missense_Mutation_p.K793T|RIMS1_ENST00000520567.1_Missense_Mutation_p.K793T|RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000425662.2_Missense_Mutation_p.K186T|RIMS1_ENST00000264839.7_Missense_Mutation_p.K793T|RIMS1_ENST00000401910.3_Missense_Mutation_p.K267T|RIMS1_ENST00000491071.2_Missense_Mutation_p.K793T|RIMS1_ENST00000517960.1_Missense_Mutation_p.K793T|RIMS1_ENST00000517827.1_Missense_Mutation_p.K252T|RIMS1_ENST00000518273.1_Missense_Mutation_p.K793T|RIMS1_ENST00000522291.1_Missense_Mutation_p.K793T	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	793	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.K793T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TTCAGTGATAAAAGTAAAAGG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	6											48	45	46					6																	72960629		1763	3987	5750	73017350	SO:0001583	missense	22999			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2378A>C	6.37:g.72960629A>C	ENSP00000428417:p.Lys793Thr		73017350	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.952979|3.952979	0.73902|0.73902	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000517433	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.77358|.	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09|.	5.79|5.79	5.79|5.79	0.91817|0.91817	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.079753|.	0.52532|.	D|.	0.000070|.	T|.	0.62889|.	0.2465|.	L|L	0.58354|0.58354	1.805|1.805	0.80722|0.80722	D|D	1|1	B;P;P;D;P;P;D;D;P;P;P;D|.	0.71674|.	0.265;0.685;0.654;0.991;0.889;0.931;0.998;0.994;0.938;0.608;0.6;0.998|.	P;P;P;D;D;D;D;D;D;P;P;D|.	0.91635|.	0.695;0.74;0.623;0.978;0.97;0.945;0.999;0.973;0.973;0.906;0.52;0.999|.	T|.	0.62671|.	-0.6805|.	10|.	0.87932|.	D|.	0|.	-16.1102|-16.1102	16.1056|16.1056	0.81220|0.81220	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	252;267;793;252;267;793;46;793;793;46;793;793|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	T|Y	793;793;793;793;793;793;793;793;793;793;793;793;267;267;186;186;252;18|366	ENSP00000430101:K793T;ENSP00000275037:K793T;ENSP00000264839:K793T;ENSP00000429959:K793T;ENSP00000430408:K793T;ENSP00000430502:K793T;ENSP00000430932:K793T;ENSP00000428417:K793T;ENSP00000385649:K267T;ENSP00000428328:K267T;ENSP00000411235:K186T;ENSP00000389503:K186T;ENSP00000428367:K252T;ENSP00000359448:K18T|.	ENSP00000264839:K793T|.	K|X	+|+	2|3	0|2	RIMS1|RIMS1	73017350|73017350	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	7.536000|7.536000	0.82023|0.82023	2.207000|2.207000	0.71202|0.71202	0.477000|0.477000	0.44152|0.44152	AAA|TAA		0.294	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72960629	A	C	72960629	3	2	61	1	0	0	0	0	1	0	0	0	13404	14	1	4	2595	4	RIMS1	6	72960629	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	948954	72960629	98154438	4712	12697										
C6orf150	115004	broad.mit.edu	37	chr6	74135015	74135015	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgctttgtcagaaattCcttacttcttttgtcaatta	4	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:74135015C>A	ENST00000370315.3	-	5	1598	c.1504G>T	c.(1504-1506)Gaa>Taa	p.E502*	MB21D1_ENST00000370318.1_Intron	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	502					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.E502*(1)		central_nervous_system(1)|large_intestine(4)|lung(1)	6						GTCAGAAATTCCTTACTTCTT	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											40	41	40					6																	74135015		2203	4300	6503	74191736	SO:0001587	stop_gained	115004			BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1504G>T	6.37:g.74135015C>A	ENSP00000359339:p.Glu502*		74191736	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Nonsense_Mutation	SNP	ENST00000370315.3	37	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085170	0.55861	.	.	ENSG00000164430	ENST00000370315;ENST00000296913	.	.	.	5.8	3.97	0.46021	.	0.971053	0.08458	N	0.942775	.	.	.	.	.	.	0.50039	D	0.999849	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-3.5136	3.8313	0.08876	0.1349:0.5909:0.1305:0.1437	.	.	.	.	X	502;485	.	ENSP00000296913:E485X	E	-	1	0	MB21D1	74191736	0.004000	0.15560	0.699000	0.30290	0.296000	0.27459	0.017000	0.13399	1.466000	0.48025	0.650000	0.86243	GAA		0.299	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		A	74135015	C	A	74135015	4	1	61	1	0	0	0	0	0	1	0	0	2343	864	30	2	68	2	C6orf150	6	74135015	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1174386	74135015	96980052	4713	12698										
SLC17A5	26503	broad.mit.edu	37	chr6	74325059	74325059	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataaggctaaaaattctgcGaacacataaagttgaaaaat	6	5	1	1	rs150686745		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:74325059G>A	ENST00000355773.5	-	8	1358	c.1090C>T	c.(1090-1092)Cgc>Tgc	p.R364C	SLC17A5_ENST00000393019.3_3'UTR	NM_012434.4	NP_036566.1	Q9NRA2	S17A5_HUMAN	solute carrier family 17 (acidic sugar transporter), member 5	364					amino acid transport (GO:0006865)|anion transport (GO:0006820)|ion transport (GO:0006811)|proton transport (GO:0015992)|sialic acid transport (GO:0015739)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	sialic acid transmembrane transporter activity (GO:0015136)|sugar:proton symporter activity (GO:0005351)	p.R364C(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAAATTCTGCGAACACATAAA	0.343																																																3	Substitution - Missense(3)	skin(2)|large_intestine(1)	6											95	90	92					6																	74325059		2203	4300	6503	74381780	SO:0001583	missense	26503			AJ387747	CCDS4981.1	6q13	2013-07-18	2013-07-18		ENSG00000119899	ENSG00000119899		"Solute carriers"	10933	protein-coding gene	gene with protein product		604322	"sialic acid storage disease", "solute carrier family 17 (anion/sugar transporter), member 5"	SIASD		10581036, 8198127	Standard	NM_012434		Approved	AST, SD, ISSD, NSD, SIALIN, SLD	uc003phn.4	Q9NRA2	OTTHUMG00000015039	ENST00000355773.5:c.1090C>T	6.37:g.74325059G>A	ENSP00000348019:p.Arg364Cys		74381780	Q5SZ76|Q8NBR5|Q9UGH0	Missense_Mutation	SNP	ENST00000355773.5	37	CCDS4981.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698436	0.68386	.	.	ENSG00000119899	ENST00000355773	T	0.66638	-0.22	4.83	4.83	0.62350	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.85583	0.5730	H	0.97611	4.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90051	0.4149	10	0.87932	D	0	.	12.9623	0.58466	0.0:0.0:0.8381:0.1619	.	426;364	E1P537;Q9NRA2	.;S17A5_HUMAN	C	364	ENSP00000348019:R364C	ENSP00000348019:R364C	R	-	1	0	SLC17A5	74381780	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.386000	0.59620	2.221000	0.72209	0.561000	0.74099	CGC		0.343	SLC17A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041228.1			A	74325059	G	A	74325059	3	1	61	1	0	0	0	0	1	0	0	0	14457	1058	37	1	413	1	SLC17A5	6	74325059	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190044	74325059	96790008	4714	12699										
CD109	135228	broad.mit.edu	37	chr6	74521964	74521964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacggcagttaatatttccGcaaatggttttggatttgct	9	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:74521964G>A	ENST00000287097.5	+	29	3851	c.3739G>A	c.(3739-3741)Gca>Aca	p.A1247T	CD109_ENST00000422508.2_Missense_Mutation_p.A1170T|CD109_ENST00000437994.2_Missense_Mutation_p.A1230T			Q6YHK3	CD109_HUMAN	CD109 molecule	1247					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)	p.A1247P(1)|p.A1247T(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAATATTTCCGCAAATGGTTT	0.333																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											155	145	149					6																	74521964		2203	4300	6503	74578685	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3739G>A	6.37:g.74521964G>A	ENSP00000287097:p.Ala1247Thr		74578685	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700429	0.48307	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.31247	1.64;1.73;1.5	5.25	5.25	0.73442	.	0.110181	0.64402	D	0.000009	T	0.23926	0.0579	M	0.63169	1.94	0.52501	D	0.999957	B;P;B	0.37594	0.428;0.601;0.133	B;B;B	0.35278	0.087;0.199;0.052	T	0.06373	-1.0830	10	0.48119	T	0.1	.	19.0112	0.92874	0.0:0.0:1.0:0.0	.	1170;1230;1247	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	T	1230;1170;1247	ENSP00000388062:A1230T;ENSP00000404475:A1170T;ENSP00000287097:A1247T	ENSP00000287097:A1247T	A	+	1	0	CD109	74578685	1.000000	0.71417	0.895000	0.35142	0.479000	0.33129	4.895000	0.63214	2.727000	0.93392	0.563000	0.77884	GCA		0.333	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		A	74521964	G	A	74521964	3	1	61	1	0	0	0	0	1	0	0	0	2969	1087	38	1	3853	1	CD109	6	74521964	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196905	74521964	96593103	4715	12700										
CD109	135228	broad.mit.edu	37	chr6	74528222	74528222	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacagtgaagaaagtggaAtatgatcatggaaaactcaa	11	4	2	4	rs563120651		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:74528222A>G	ENST00000287097.5	+	31	4135	c.4023A>G	c.(4021-4023)gaA>gaG	p.E1341E	CD109_ENST00000422508.2_Silent_p.E1264E|CD109_ENST00000437994.2_Silent_p.E1324E			Q6YHK3	CD109_HUMAN	CD109 molecule	1341					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)	p.E1341E(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGAAAGTGGAATATGATCATG	0.398													A|||	1	0.000199681	0	0	5008	,	,		17098	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											98	100	99					6																	74528222		2203	4300	6503	74584943	SO:0001819	synonymous_variant	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.4023A>G	6.37:g.74528222A>G			74584943	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																				0.398	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		G	74528222	A	G	74528222	2	3	61	1	0	0	0	0	0	0	0	1	2969	98	4	4		4	CD109	6	74528222	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6258	74528222	96586845	4716	12701										
COL12A1	1303	broad.mit.edu	37	chr6	75818809	75818809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgttatatttccagcttcCttgatgtctttttctataat	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75818809C>A	ENST00000322507.8	-	52	8334	c.8025G>T	c.(8023-8025)aaG>aaT	p.K2675N	COL12A1_ENST00000483888.2_Missense_Mutation_p.K2675N|COL12A1_ENST00000345356.6_Missense_Mutation_p.K1511N|COL12A1_ENST00000416123.2_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2675	Laminin G-like.|Nonhelical region (NC3).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.K2675N(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCCAGCTTCCTTGATGTCTT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	91	92					6																	75818809		1801	4068	5869	75875529	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8025G>T	6.37:g.75818809C>A	ENSP00000325146:p.Lys2675Asn		75875529	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533170	0.27387	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000345356;ENST00000483888	T;T;T;T	0.02085	4.46;4.46;4.46;4.46	5.75	1.86	0.25419	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.095146	0.64402	D	0.000002	T	0.00637	0.0021	L	0.35644	1.08	0.37331	D	0.909965	B;B	0.28026	0.198;0.125	B;B	0.27608	0.081;0.037	T	0.52689	-0.8542	10	0.16896	T	0.51	.	4.594	0.12320	0.1397:0.4671:0.0:0.3931	.	1511;2675	Q99715-2;Q99715	.;COCA1_HUMAN	N	2675;313;1511;2675	ENSP00000325146:K2675N;ENSP00000399812:K313N;ENSP00000305147:K1511N;ENSP00000421216:K2675N	ENSP00000325146:K2675N	K	-	3	2	COL12A1	75875529	0.908000	0.30866	0.997000	0.53966	0.984000	0.73092	-0.000000	0.12993	0.047000	0.15862	0.650000	0.86243	AAG		0.313	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75818809	C	A	75818809	3	1	61	1	0	0	0	0	1	0	0	0	3675	680	24	2	1226	2	COL12A1	6	75818809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1290587	75818809	95296258	4717	12702										
COL12A1	1303	broad.mit.edu	37	chr6	75834909	75834909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagcataaacattcacatCgtaggtggtgctgggattga	12	6	1	2	rs368397177		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75834909C>T	ENST00000322507.8	-	40	6850	c.6541G>A	c.(6541-6543)Gat>Aat	p.D2181N	COL12A1_ENST00000483888.2_Missense_Mutation_p.D2181N|COL12A1_ENST00000345356.6_Missense_Mutation_p.D1017N|COL12A1_ENST00000416123.2_Missense_Mutation_p.D2181N	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2181	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.D2181N(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACATTCACATCGTAGGTGGTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	ASN/ASP,ASN/ASP	0,3840		0,0,1920	131	129	130		6541,3049	5.4	1	6		130	1,8277		0,1,4138	no	missense,missense	COL12A1	NM_004370.5,NM_080645.2	23,23	0,1,6058	TT,TC,CC		0.0121,0.0,0.0083	probably-damaging,probably-damaging	2181/3064,1017/1900	75834909	1,12117	1920	4139	6059	75891629	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.6541G>A	6.37:g.75834909C>T	ENSP00000325146:p.Asp2181Asn		75891629	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	34	5.358107	0.95854	0.0	1.21E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.42	5.42	0.78866	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.17408	0.0418	N	0.15975	0.35	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	T	0.16247	-1.0409	10	0.26408	T	0.33	.	19.5792	0.95459	0.0:1.0:0.0:0.0	.	1017;2181	Q99715-2;Q99715	.;COCA1_HUMAN	N	2181;2181;1017;2181;2181	ENSP00000325146:D2181N;ENSP00000305147:D1017N;ENSP00000412864:D2181N;ENSP00000421216:D2181N	ENSP00000325146:D2181N	D	-	1	0	COL12A1	75891629	1.000000	0.71417	0.992000	0.48379	0.980000	0.70556	7.445000	0.80570	2.718000	0.92993	0.591000	0.81541	GAT		0.403	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75834909	C	T	75834909	3	4	61	1	0	0	0	0	1	0	0	0	3675	884	31	1	2758	1	COL12A1	6	75834909	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16100	75834909	95280158	4718	12703										
COL12A1	1303	broad.mit.edu	37	chr6	75862100	75862100	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttccacaatacgagaaaTgaaactcctcacggttctaa	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75862100T>G	ENST00000322507.8	-	18	3973	c.3664A>C	c.(3664-3666)Att>Ctt	p.I1222L	COL12A1_ENST00000483888.2_Missense_Mutation_p.I1222L|COL12A1_ENST00000345356.6_Missense_Mutation_p.I58L|COL12A1_ENST00000416123.2_Missense_Mutation_p.I1222L	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1222	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.I1222L(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATACGAGAAATGAAACTCCTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	64	65					6																	75862100		1918	4129	6047	75918820	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3664A>C	6.37:g.75862100T>G	ENSP00000325146:p.Ile1222Leu		75918820	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.150263	0.57151	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7	5.74	5.74	0.90152	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000001	T	0.54743	0.1877	N	0.03983	-0.305	0.52099	D	0.99994	B;B	0.10296	0.001;0.003	B;B	0.21546	0.002;0.035	T	0.56282	-0.8005	10	0.36615	T	0.2	.	16.0502	0.80755	0.0:0.0:0.0:1.0	.	58;1222	Q99715-2;Q99715	.;COCA1_HUMAN	L	1222;1222;58;1222;1222	ENSP00000325146:I1222L;ENSP00000305147:I58L;ENSP00000412864:I1222L;ENSP00000421216:I1222L	ENSP00000325146:I1222L	I	-	1	0	COL12A1	75918820	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.895000	0.69814	2.197000	0.70478	0.528000	0.53228	ATT		0.448	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75862100	T	G	75862100	3	3	61	1	0	0	0	0	1	0	0	0	3675	1464	51	4	5723	4	COL12A1	6	75862100	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27191	75862100	95252967	4719	12704										
COL12A1	1303	broad.mit.edu	37	chr6	75866076	75866076	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtcgctttaacactgtCgaagtgactgtggggggcac	14	8	0	2	rs369168979		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75866076C>T	ENST00000322507.8	-	15	3456	c.3147G>A	c.(3145-3147)tcG>tcA	p.S1049S	COL12A1_ENST00000483888.2_Silent_p.S1049S|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.S1049S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1049	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.S1049S(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTAACACTGTCGAAGTGACTG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	6											199	185	189					6																	75866076		1960	4148	6108	75922796	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3147G>A	6.37:g.75866076C>T			75922796	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.493	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75866076	C	T	75866076	2	4	61	1	0	0	0	0	0	0	0	1	3675	871	31	1		1	COL12A1	6	75866076	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3976	75866076	95248991	4720	12705										
COL12A1	1303	broad.mit.edu	37	chr6	75875478	75875478	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtctttagtaactaaatCttgaggagaaccacgttcta	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75875478C>A	ENST00000322507.8	-	14	3037	c.2728G>T	c.(2728-2730)Gat>Tat	p.D910Y	COL12A1_ENST00000483888.2_Missense_Mutation_p.D910Y|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.D910Y	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	910	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.D910Y(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GTAACTAAATCTTGAGGAGAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											82	74	76					6																	75875478		1830	4097	5927	75932198	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2728G>T	6.37:g.75875478C>A	ENSP00000325146:p.Asp910Tyr		75932198	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	10.40	1.340546	0.24339	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.58797	0.31;0.31;0.31	5.3	1.47	0.22746	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.200461	0.33916	N	0.004422	T	0.53318	0.1789	M	0.73962	2.25	0.22468	N	0.999076	P	0.46912	0.886	P	0.59487	0.858	T	0.51309	-0.8722	10	0.72032	D	0.01	.	5.7142	0.17950	0.0:0.4879:0.1312:0.3809	.	910	Q99715	COCA1_HUMAN	Y	910	ENSP00000325146:D910Y;ENSP00000412864:D910Y;ENSP00000421216:D910Y	ENSP00000325146:D910Y	D	-	1	0	COL12A1	75932198	0.003000	0.15002	0.097000	0.21041	0.459000	0.32528	0.049000	0.14099	-0.020000	0.14032	0.563000	0.77884	GAT		0.363	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75875478	C	A	75875478	3	1	61	1	0	0	0	0	1	0	0	0	3675	913	32	2	6675	2	COL12A1	6	75875478	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9402	75875478	95239589	4721	12706										
COL12A1	1303	broad.mit.edu	37	chr6	75887466	75887466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttcatatttcgtgtctgGaatcaagttctccagtgttc	7	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:75887466G>T	ENST00000322507.8	-	12	2659	c.2350C>A	c.(2350-2352)Cca>Aca	p.P784T	COL12A1_ENST00000483888.2_Missense_Mutation_p.P784T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.P784T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	784	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.P784T(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCGTGTCTGGAATCAAGTTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											291	283	285					6																	75887466		1872	4105	5977	75944186	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2350C>A	6.37:g.75887466G>T	ENSP00000325146:p.Pro784Thr		75944186	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208300	0.79240	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.68479	-0.33;-0.33;-0.33	5.73	5.73	0.89815	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000002	T	0.81959	0.4933	M	0.93978	3.48	0.51012	D	0.9999	P;P	0.52170	0.951;0.907	P;P	0.54460	0.753;0.735	D	0.86301	0.1680	10	0.87932	D	0	.	19.8863	0.96913	0.0:0.0:1.0:0.0	.	784;784	D6RGG3;Q99715	.;COCA1_HUMAN	T	784	ENSP00000325146:P784T;ENSP00000412864:P784T;ENSP00000421216:P784T	ENSP00000325146:P784T	P	-	1	0	COL12A1	75944186	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	7.367000	0.79558	2.688000	0.91661	0.650000	0.86243	CCA		0.413	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75887466	G	T	75887466	3	4	61	1	0	0	0	0	1	0	0	0	3675	1174	41	2	7061	2	COL12A1	6	75887466	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11988	75887466	95227601	4722	12707										
FILIP1	27145	broad.mit.edu	37	chr6	76023073	76023073	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcttcctggaaggatttCcgtatgaatacagctggcgt	10	8	1	1	rs267601126		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76023073C>T	ENST00000237172.7	-	5	2805	c.2475G>A	c.(2473-2475)cgG>cgA	p.R825R	FILIP1_ENST00000393004.2_Silent_p.R825R|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Silent_p.R726R	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	825								p.R825R(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GGAAGGATTTCCGTATGAATA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	6											149	162	158					6																	76023073		2203	4300	6503	76079793	SO:0001819	synonymous_variant	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2475G>A	6.37:g.76023073C>T			76079793	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	37	CCDS4984.1																																																																																				0.463	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		T	76023073	C	T	76023073	2	4	61	1	0	0	0	0	0	0	0	1	5913	842	30	3		3	FILIP1	6	76023073	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135607	76023073	95091994	4723	12708										
FILIP1	27145	broad.mit.edu	37	chr6	76023382	76023382	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttaagagcttgtacttcGgcttttaagtctcgactttt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76023382G>A	ENST00000237172.7	-	5	2496	c.2166C>T	c.(2164-2166)gcC>gcT	p.A722A	FILIP1_ENST00000393004.2_Silent_p.A722A|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Silent_p.A623A	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	722								p.A722A(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						CTTGTACTTCGGCTTTTAAGT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	6											124	131	129					6																	76023382		2203	4300	6503	76080102	SO:0001819	synonymous_variant	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2166C>T	6.37:g.76023382G>A			76080102	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	37	CCDS4984.1																																																																																				0.393	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023382	G	A	76023382	2	1	61	1	0	0	0	0	0	0	0	1	5913	1103	39	1		1	FILIP1	6	76023382	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	309	76023382	95091685	4724	12709										
SENP6	26054	broad.mit.edu	37	chr6	76376478	76376478	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgacagaactaacagaagaGaaagcatatctcctcagcct	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76376478G>T	ENST00000447266.2	+	10	1523	c.1045G>T	c.(1045-1047)Gaa>Taa	p.E349*	SENP6_ENST00000370014.3_Nonsense_Mutation_p.E349*|SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000370010.2_Nonsense_Mutation_p.E342*|SENP6_ENST00000327284.8_Nonsense_Mutation_p.E342*	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	349					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)	p.E349*(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TAACAGAAGAGAAAGCATATC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											93	91	91					6																	76376478		1926	4163	6089	76433198	SO:0001587	stop_gained	26054				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1045G>T	6.37:g.76376478G>T	ENSP00000402527:p.Glu349*		76433198	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Nonsense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923825	0.73213	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000424947	.	.	.	5.32	5.32	0.75619	.	0.134612	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-7.1971	19.3602	0.94434	0.0:0.0:1.0:0.0	.	.	.	.	X	342;349;198;342;349;239	.	ENSP00000321820:E342X	E	+	1	0	SENP6	76433198	1.000000	0.71417	0.998000	0.56505	0.026000	0.11368	5.690000	0.68241	2.656000	0.90262	0.650000	0.86243	GAA		0.348	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		T	76376478	G	T	76376478	4	4	61	1	0	0	0	0	0	1	0	0	14087	943	33	2	1083	2	SENP6	6	76376478	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	353096	76376478	94738589	4725	12710										
MYO6	4646	broad.mit.edu	37	chr6	76538325	76538325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgatatagtaaagacagaAtttatgtaagtattttacct	6	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76538325A>C	ENST00000369977.3	+	4	395	c.256A>C	c.(256-258)Att>Ctt	p.I86L	MYO6_ENST00000369981.3_Missense_Mutation_p.I86L|MYO6_ENST00000369975.1_Missense_Mutation_p.I86L|MYO6_ENST00000369985.4_Missense_Mutation_p.I86L	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	86	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.I86L(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TAAAGACAGAATTTATGTAAG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	93	91					6																	76538325		2203	4298	6501	76595045	SO:0001583	missense	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.256A>C	6.37:g.76538325A>C	ENSP00000358994:p.Ile86Leu		76595045	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.953154	0.92660	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	H	0.94847	3.59	0.80722	D	1	D;B	0.64830	0.994;0.429	D;P	0.87578	0.998;0.855	D	0.92904	0.6342	10	0.87932	D	0	.	15.6234	0.76829	1.0:0.0:0.0:0.0	.	86;86	Q9UM54-2;Q9UM54-1	.;.	L	86	ENSP00000358998:I86L;ENSP00000359002:I86L;ENSP00000358994:I86L;ENSP00000358992:I86L	ENSP00000358992:I86L	I	+	1	0	MYO6	76595045	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.700000	0.91322	2.097000	0.63578	0.460000	0.39030	ATT		0.289	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		C	76538325	A	C	76538325	3	2	61	1	0	0	0	0	1	0	0	0	10111	101	4	4	266	4	MYO6	6	76538325	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	161847	76538325	94576742	4726	12711										
MYO6	4646	broad.mit.edu	37	chr6	76540162	76540162	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaacattctgattgcagtGaatccatactttgacatacc	6	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76540162G>T	ENST00000369977.3	+	5	430	c.291G>T	c.(289-291)gtG>gtT	p.V97V	MYO6_ENST00000369981.3_Silent_p.V97V|MYO6_ENST00000369975.1_Silent_p.V97V|MYO6_ENST00000369985.4_Silent_p.V97V	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	97	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.V97V(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TGATTGCAGTGAATCCATACT	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	6											106	108	107					6																	76540162		2203	4299	6502	76596882	SO:0001819	synonymous_variant	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.291G>T	6.37:g.76540162G>T			76596882	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																				0.313	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		T	76540162	G	T	76540162	2	4	61	1	0	0	0	0	0	0	0	1	10111	1277	45	2		2	MYO6	6	76540162	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1837	76540162	94574905	4727	12712										
MYO6	4646	broad.mit.edu	37	chr6	76542652	76542652	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcaaaacagaaaatacaaAatttgttctaaggtgagtat	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76542652A>C	ENST00000369977.3	+	6	624	c.485A>C	c.(484-486)aAa>aCa	p.K162T	MYO6_ENST00000369981.3_Missense_Mutation_p.K162T|MYO6_ENST00000369975.1_Missense_Mutation_p.K162T|MYO6_ENST00000369985.4_Missense_Mutation_p.K162T	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	162	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.K162T(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		GAAAATACAAAATTTGTTCTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	79	78					6																	76542652		2203	4300	6503	76599372	SO:0001583	missense	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.485A>C	6.37:g.76542652A>C	ENSP00000358994:p.Lys162Thr		76599372	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507097	0.85282	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.97182	0.9079	H	0.98351	4.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.98847	1.0757	10	0.87932	D	0	.	15.8146	0.78589	1.0:0.0:0.0:0.0	.	162;162	Q9UM54-2;Q9UM54-1	.;.	T	162	ENSP00000358998:K162T;ENSP00000359002:K162T;ENSP00000358994:K162T;ENSP00000358992:K162T	ENSP00000358992:K162T	K	+	2	0	MYO6	76599372	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.932000	0.92897	2.193000	0.70182	0.528000	0.53228	AAA		0.413	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		C	76542652	A	C	76542652	3	2	61	1	0	0	0	0	1	0	0	0	10111	14	1	4	503	4	MYO6	6	76542652	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2490	76542652	94572415	4728	12713										
MYO6	4646	broad.mit.edu	37	chr6	76589596	76589596	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcacgagcttcatttcatGaactctacaacatgtacaaa	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76589596G>T	ENST00000369977.3	+	21	2276	c.2137G>T	c.(2137-2139)Gaa>Taa	p.E713*	MYO6_ENST00000462633.1_3'UTR|MYO6_ENST00000369985.4_Nonsense_Mutation_p.E713*|MYO6_ENST00000369975.1_Nonsense_Mutation_p.E713*|MYO6_ENST00000369981.3_Nonsense_Mutation_p.E713*	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	713	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.E713*(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TTCATTTCATGAACTCTACAA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											161	149	153					6																	76589596		2203	4300	6503	76646316	SO:0001587	stop_gained	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2137G>T	6.37:g.76589596G>T	ENSP00000358994:p.Glu713*		76646316	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Nonsense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	40	8.458401	0.98820	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.2649	0.93982	0.0:0.0:1.0:0.0	.	.	.	.	X	713	.	ENSP00000358992:E713X	E	+	1	0	MYO6	76646316	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	9.392000	0.97252	2.632000	0.89209	0.655000	0.94253	GAA		0.388	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		T	76589596	G	T	76589596	4	4	61	1	0	0	0	0	0	1	0	0	10111	1291	45	2	2215	2	MYO6	6	76589596	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46944	76589596	94525471	4729	12714										
IMPG1	3617	broad.mit.edu	37	chr6	76660319	76660319	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagagctcggtactccagaGagctcttgttgaacaggtcg	12	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:76660319G>T	ENST00000369950.3	-	13	1973	c.1784C>A	c.(1783-1785)tCt>tAt	p.S595Y	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1									p.S595Y(1)		breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GTACTCCAGAGAGCTCTTGTT	0.483																																					Pancreas(37;839 1141 2599 26037)											1	Substitution - Missense(1)	large_intestine(1)	6											46	41	43					6																	76660319		2203	4300	6503	76717039	SO:0001583	missense	3617			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1784C>A	6.37:g.76660319G>T	ENSP00000358966:p.Ser595Tyr		76717039		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017421	0.93404	.	.	ENSG00000112706	ENST00000369950	T	0.63417	-0.04	5.87	5.87	0.94306	SEA (2);	0.000000	0.64402	D	0.000010	T	0.78547	0.4300	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79657	-0.1712	10	0.87932	D	0	.	20.2245	0.98337	0.0:0.0:1.0:0.0	.	595	Q17R60	IMPG1_HUMAN	Y	595	ENSP00000358966:S595Y	ENSP00000358966:S595Y	S	-	2	0	IMPG1	76717039	1.000000	0.71417	0.989000	0.46669	0.961000	0.63080	9.476000	0.97823	2.770000	0.95276	0.650000	0.86243	TCT		0.483	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		T	76660319	G	T	76660319	3	4	61	1	0	0	0	0	1	0	0	0	7749	942	33	2	629	2	IMPG1	6	76660319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70723	76660319	94454748	4730	12715										
HTR1B	3351	broad.mit.edu	37	chr6	78172346	78172346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacgtggacccgggggagtCggttatcagctgggctcggg	20	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:78172346C>T	ENST00000369947.2	-	1	1144	c.775G>A	c.(775-777)Gac>Aac	p.D259N		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	259					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.D259N(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CCGGGGGAGTCGGTTATCAGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	79	75					6																	78172346		2203	4300	6503	78229065	SO:0001583	missense	3351			BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5287	protein-coding gene	gene with protein product		182131	"5-hydroxytryptamine (serotonin) receptor 1B"			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.775G>A	6.37:g.78172346C>T	ENSP00000358963:p.Asp259Asn		78229065	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	C	8.378	0.836844	0.16891	.	.	ENSG00000135312	ENST00000369947	T	0.62498	0.02	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.114032	0.64402	D	0.000019	T	0.21761	0.0524	N	0.02192	-0.645	0.48395	D	0.999644	B	0.22346	0.068	B	0.22753	0.041	T	0.17715	-1.0360	9	.	.	.	.	17.7254	0.88364	0.0:1.0:0.0:0.0	.	259	P28222	5HT1B_HUMAN	N	259	ENSP00000358963:D259N	.	D	-	1	0	HTR1B	78229065	0.989000	0.36119	0.965000	0.40720	0.418000	0.31294	2.743000	0.47442	2.661000	0.90470	0.555000	0.69702	GAC		0.597	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		T	78172346	C	T	78172346	3	4	61	1	0	0	0	0	1	0	0	0	7458	884	31	1	401	1	HTR1B	6	78172346	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1512027	78172346	92942721	4731	12716										
PHIP	55023	broad.mit.edu	37	chr6	79655764	79655764	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagcttttgtaataaaagtCtttgcagctgaagaagtaga	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:79655764C>A	ENST00000275034.4	-	38	4751	c.4584G>T	c.(4582-4584)aaG>aaT	p.K1528N	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1528					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.K1528N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TAATAAAAGTCTTTGCAGCTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	104	107					6																	79655764		2203	4300	6503	79712483	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4584G>T	6.37:g.79655764C>A	ENSP00000275034:p.Lys1528Asn		79712483	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381842	0.42207	.	.	ENSG00000146247	ENST00000275034;ENST00000355098	T	0.41758	0.99	6.17	2.4	0.29515	.	0.144593	0.49305	D	0.000141	T	0.31765	0.0807	L	0.27053	0.805	0.45161	D	0.998172	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	T	0.06917	-1.0800	9	.	.	.	-18.2043	9.004	0.36100	0.0:0.6459:0.0:0.3541	.	1528;1528	A7J992;Q8WWQ0	.;PHIP_HUMAN	N	1528;254	ENSP00000275034:K1528N	.	K	-	3	2	PHIP	79712483	0.997000	0.39634	0.991000	0.47740	0.747000	0.42532	0.236000	0.17967	0.470000	0.27294	-0.137000	0.14449	AAG		0.368	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79655764	C	A	79655764	3	1	61	1	0	0	0	0	1	0	0	0	11873	912	32	2	893	2	PHIP	6	79655764	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1483418	79655764	91459303	4732	12717										
PHIP	55023	broad.mit.edu	37	chr6	79680570	79680570	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatttttccgggccatttcGacataggcttcatgtccttg	8	10	1	0	rs140757402		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:79680570G>A	ENST00000275034.4	-	25	3092	c.2925C>T	c.(2923-2925)gtC>gtT	p.V975V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	975	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.V975V(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GGGCCATTTCGACATAGGCTT	0.328																																																2	Substitution - coding silent(2)	large_intestine(2)	6											91	87	88					6																	79680570		2202	4299	6501	79737289	SO:0001819	synonymous_variant	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2925C>T	6.37:g.79680570G>A			79737289	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																				0.328	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79680570	G	A	79680570	2	1	61	1	0	0	0	0	0	0	0	1	11873	1045	37	1		1	PHIP	6	79680570	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24806	79680570	91434497	4733	12718										
PHIP	55023	broad.mit.edu	37	chr6	79728820	79728820	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttaccagcactaaaagaaGaacagatcatttgaactcca	5	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:79728820G>T	ENST00000275034.4	-	10	1147	c.980C>A	c.(979-981)tCt>tAt	p.S327Y		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	327					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.S327Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		ACTAAAAGAAGAACAGATCAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											127	142	137					6																	79728820		2203	4300	6503	79785539	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.980C>A	6.37:g.79728820G>T	ENSP00000275034:p.Ser327Tyr		79785539	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274930	0.59649	.	.	ENSG00000146247	ENST00000275034	T	0.16897	2.31	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.078821	0.53938	D	0.000045	T	0.28632	0.0709	M	0.80183	2.485	0.80722	D	1	D;D	0.61697	0.99;0.99	P;P	0.54664	0.758;0.758	T	0.07347	-1.0777	9	.	.	.	-13.9372	17.2352	0.86997	0.0:0.0:1.0:0.0	.	327;327	A7J992;Q8WWQ0	.;PHIP_HUMAN	Y	327	ENSP00000275034:S327Y	.	S	-	2	0	PHIP	79785539	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.690000	0.98676	2.370000	0.80446	0.557000	0.71058	TCT		0.343	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			T	79728820	G	T	79728820	3	4	61	1	0	0	0	0	1	0	0	0	11873	942	33	2	4609	2	PHIP	6	79728820	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48250	79728820	91386247	4734	12719										
LCA5	167691	broad.mit.edu	37	chr6	80223217	80223217	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaacttattcagggctttCtcctgtctgtactgaagcct	7	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:80223217C>A	ENST00000392959.1	-	4	1043	c.432G>T	c.(430-432)gaG>gaT	p.E144D	LCA5_ENST00000369846.4_Missense_Mutation_p.E144D|LCA5_ENST00000467898.3_Missense_Mutation_p.E144D	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	144					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)	p.E144D(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TCAGGGCTTTCTCCTGTCTGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	89	91					6																	80223217		2203	4299	6502	80279936	SO:0001583	missense	167691				CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.432G>T	6.37:g.80223217C>A	ENSP00000376686:p.Glu144Asp		80279936	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274881	0.80580	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.78707	-1.2;-1.2	6.07	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.80732	0.4679	L	0.45581	1.43	0.45046	D	0.998067	P;D	0.89917	0.923;1.0	P;D	0.91635	0.752;0.999	D	0.84100	0.0395	10	0.87932	D	0	-16.3685	14.5253	0.67884	0.0:0.9303:0.0:0.0697	.	144;144	B4DRL2;Q86VQ0	.;LCA5_HUMAN	D	144	ENSP00000358861:E144D;ENSP00000376686:E144D	ENSP00000358861:E144D	E	-	3	2	LCA5	80279936	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.143000	0.42187	1.586000	0.49944	0.655000	0.94253	GAG		0.353	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80223217	C	A	80223217	3	1	61	1	0	0	0	0	1	0	0	0	8678	912	32	2	1685	2	LCA5	6	80223217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	494397	80223217	90891850	4735	12720										
TTK	7272	broad.mit.edu	37	chr6	80717691	80717691	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcgcttcccccagataAatatggccaaaatgagagtt	9	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:80717691A>C	ENST00000369798.2	+	3	416	c.305A>C	c.(304-306)aAa>aCa	p.K102T	TTK_ENST00000230510.3_Missense_Mutation_p.K102T|TTK_ENST00000509894.1_Missense_Mutation_p.K102T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	102					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.K86T(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CCCCCAGATAAATATGGCCAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	62	62					6																	80717691		2202	4300	6502	80774410	SO:0001583	missense	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.305A>C	6.37:g.80717691A>C	ENSP00000358813:p.Lys102Thr		80774410	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579681	0.86645	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000502580;ENST00000511260;ENST00000504040	D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.66	5.66	0.87406	.	0.041197	0.85682	D	0.000000	D	0.92312	0.7561	M	0.63843	1.955	0.45554	D	0.998505	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.93357	0.6723	10	0.87932	D	0	.	15.3831	0.74676	1.0:0.0:0.0:0.0	.	102;102	P33981;A8K8U5	TTK_HUMAN;.	T	102	ENSP00000422936:K102T;ENSP00000230510:K102T;ENSP00000358813:K102T;ENSP00000424851:K102T;ENSP00000421636:K102T;ENSP00000427483:K102T	ENSP00000230510:K102T	K	+	2	0	TTK	80774410	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.127000	0.71642	2.285000	0.76669	0.533000	0.62120	AAA		0.338	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			C	80717691	A	C	80717691	3	2	61	1	0	0	0	0	1	0	0	0	16760	14	1	4	311	4	TTK	6	80717691	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	494474	80717691	90397376	4736	12721										
TTK	7272	broad.mit.edu	37	chr6	80718160	80718160	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggccagagcaaactgcaaGaaatttgcttttgttcatat	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:80718160G>T	ENST00000369798.2	+	4	531	c.420G>T	c.(418-420)aaG>aaT	p.K140N	TTK_ENST00000230510.3_Missense_Mutation_p.K140N|TTK_ENST00000509894.1_Missense_Mutation_p.K140N	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	140					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.K124N(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CAAACTGCAAGAAATTTGCTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											79	72	74					6																	80718160		2203	4299	6502	80774879	SO:0001583	missense	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.420G>T	6.37:g.80718160G>T	ENSP00000358813:p.Lys140Asn		80774879	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.471785	0.84533	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000511260;ENST00000504040	T;T;T;D;T	0.90197	1.36;1.36;1.36;-2.63;1.36	6.01	6.01	0.97437	Tetratricopeptide-like helical (1);	0.096695	0.64402	D	0.000001	D	0.92835	0.7721	M	0.63843	1.955	0.46823	D	0.999215	D;D	0.89917	1.0;0.999	D;D	0.69142	0.962;0.947	D	0.93166	0.6562	10	0.87932	D	0	.	12.7696	0.57412	0.074:0.0:0.926:0.0	.	140;140	P33981;A8K8U5	TTK_HUMAN;.	N	140	ENSP00000422936:K140N;ENSP00000230510:K140N;ENSP00000358813:K140N;ENSP00000421636:K140N;ENSP00000427483:K140N	ENSP00000230510:K140N	K	+	3	2	TTK	80774879	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.759000	0.55227	2.861000	0.98227	0.650000	0.86243	AAG		0.299	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			T	80718160	G	T	80718160	3	4	61	1	0	0	0	0	1	0	0	0	16760	933	33	2	430	2	TTK	6	80718160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	469	80718160	90396907	4737	12722										
TTK	7272	broad.mit.edu	37	chr6	80737719	80737719	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacttgccactccacttcaAaatttacaggttcgataagc	5	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:80737719A>C	ENST00000369798.2	+	13	1623	c.1512A>C	c.(1510-1512)caA>caC	p.Q504H	TTK_ENST00000230510.3_Missense_Mutation_p.Q503H|TTK_ENST00000509894.1_Missense_Mutation_p.Q503H	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	504					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.Q488H(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CTCCACTTCAAAATTTACAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	84	86					6																	80737719		2203	4300	6503	80794438	SO:0001583	missense	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1512A>C	6.37:g.80737719A>C	ENSP00000358813:p.Gln504His		80794438	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.432205	0.25813	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	T;T;T	0.69561	-0.41;-0.41;-0.4	5.99	-9.55	0.00569	.	0.307454	0.36338	N	0.002660	T	0.57710	0.2072	M	0.62723	1.935	0.22719	N	0.998814	D;D	0.54397	0.966;0.966	P;P	0.55785	0.525;0.784	T	0.74156	-0.3756	10	0.48119	T	0.1	.	19.6097	0.95600	0.3018:0.0:0.6982:0.0	.	504;503	P33981;A8K8U5	TTK_HUMAN;.	H	503;503;504	ENSP00000422936:Q503H;ENSP00000230510:Q503H;ENSP00000358813:Q504H	ENSP00000230510:Q503H	Q	+	3	2	TTK	80794438	0.003000	0.15002	0.002000	0.10522	0.005000	0.04900	-0.985000	0.03751	-1.964000	0.01012	-0.899000	0.02877	CAA		0.373	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			C	80737719	A	C	80737719	3	2	61	1	0	0	0	0	1	0	0	0	16760	11	1	4	1558	4	TTK	6	80737719	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	19559	80737719	90377348	4738	12723										
TTK	7272	broad.mit.edu	37	chr6	80744798	80744798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgatagttaccggaacGaaatagcttatttgaataaa	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:80744798G>A	ENST00000369798.2	+	15	1822	c.1711G>A	c.(1711-1713)Gaa>Aaa	p.E571K	TTK_ENST00000230510.3_Missense_Mutation_p.E570K|TTK_ENST00000509894.1_Missense_Mutation_p.E570K	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	571	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.E555K(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		TTACCGGAACGAAATAGCTTA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	82	80					6																	80744798		2200	4288	6488	80801517	SO:0001583	missense	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1711G>A	6.37:g.80744798G>A	ENSP00000358813:p.Glu571Lys		80801517	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	33	5.241982	0.95272	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	D;D;D	0.84873	-1.91;-1.91;-1.91	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90878	0.7134	M	0.69463	2.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91278	0.5049	10	0.87932	D	0	.	18.7461	0.91794	0.0:0.0:1.0:0.0	.	571;570	P33981;A8K8U5	TTK_HUMAN;.	K	570;570;571	ENSP00000422936:E570K;ENSP00000230510:E570K;ENSP00000358813:E571K	ENSP00000230510:E570K	E	+	1	0	TTK	80801517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.677000	0.91161	0.557000	0.71058	GAA		0.284	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			A	80744798	G	A	80744798	3	1	61	1	0	0	0	0	1	0	0	0	16760	1059	37	1	1765	1	TTK	6	80744798	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7079	80744798	90370269	4739	12724										
IBTK	25998	broad.mit.edu	37	chr6	82927752	82927752	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcttgcgtaacaaataGaatttcatttctatttaaag	4	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:82927752G>T	ENST00000306270.7	-	10	1900	c.1351C>A	c.(1351-1353)Cta>Ata	p.L451I	IBTK_ENST00000510291.1_Missense_Mutation_p.L451I|IBTK_ENST00000503631.1_Missense_Mutation_p.L451I	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	451					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.L451I(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GTAACAAATAGAATTTCATTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											93	91	91					6																	82927752		2203	4300	6503	82984471	SO:0001583	missense	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.1351C>A	6.37:g.82927752G>T	ENSP00000305721:p.Leu451Ile		82984471	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.856756	0.32791	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.31510	1.79;1.49;1.8	5.5	1.3	0.21679	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);	0.157992	0.49916	D	0.000124	T	0.07188	0.0182	L	0.47716	1.5	0.32266	N	0.569556	P;P;P;P	0.44986	0.518;0.847;0.798;0.847	B;B;B;B	0.42343	0.079;0.254;0.384;0.254	T	0.21655	-1.0239	10	0.02654	T	1	-3.8747	4.9501	0.14009	0.3061:0.0:0.4909:0.203	.	451;451;451;451	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	I	451	ENSP00000305721:L451I;ENSP00000422762:L451I;ENSP00000426405:L451I	ENSP00000305721:L451I	L	-	1	2	IBTK	82984471	1.000000	0.71417	0.777000	0.31699	0.319000	0.28217	2.352000	0.44080	0.170000	0.19704	0.462000	0.41574	CTA		0.378	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		T	82927752	G	T	82927752	3	4	61	1	0	0	0	0	1	0	0	0	7497	933	33	2	2790	2	IBTK	6	82927752	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2182954	82927752	88187315	4740	12725										
DOPEY1	23033	broad.mit.edu	37	chr6	83818631	83818631	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttatttttttaatagttCtggattatttcctcttcttg	4	6	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:83818631C>T	ENST00000349129.2	+	5	583	c.323C>T	c.(322-324)tCt>tTt	p.S108F	DOPEY1_ENST00000369739.3_Missense_Mutation_p.S108F|DOPEY1_ENST00000237163.5_Missense_Mutation_p.S108F|DOPEY1_ENST00000536812.1_Missense_Mutation_p.S108F	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	108					protein transport (GO:0015031)			p.S108F(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TTTAATAGTTCTGGATTATTT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	6											79	82	81					6																	83818631		2203	4300	6503	83875350	SO:0001583	missense	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.323C>T	6.37:g.83818631C>T	ENSP00000195654:p.Ser108Phe		83875350	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371278	0.82573	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000536812;ENST00000369739	T;T;T	0.25085	1.82;1.82;1.82	5.74	5.74	0.90152	Dopey, N-terminal (1);	0.121781	0.64402	D	0.000019	T	0.42653	0.1212	M	0.71036	2.16	0.80722	D	1	D;P;P	0.76494	0.999;0.813;0.813	D;P;P	0.87578	0.998;0.707;0.707	T	0.03807	-1.1002	10	0.18710	T	0.47	.	20.3557	0.98840	0.0:1.0:0.0:0.0	.	108;108;108	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	F	108	ENSP00000195654:S108F;ENSP00000237163:S108F;ENSP00000358754:S108F	ENSP00000237163:S108F	S	+	2	0	DOPEY1	83875350	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.439000	0.80444	2.890000	0.99128	0.585000	0.79938	TCT		0.289	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83818631	C	T	83818631	3	4	61	1	0	0	0	0	1	0	0	0	4718	913	32	3	333	3	DOPEY1	6	83818631	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	890879	83818631	87296436	4741	12726										
DOPEY1	23033	broad.mit.edu	37	chr6	83847934	83847934	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctgccatcaaagccatCttgaaaactaaccctatagc	4	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:83847934C>T	ENST00000349129.2	+	21	4433	c.4173C>T	c.(4171-4173)atC>atT	p.I1391I	DOPEY1_ENST00000369739.3_Silent_p.I1382I|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Silent_p.I1372I	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1391					protein transport (GO:0015031)			p.I1391I(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCAAAGCCATCTTGAAAACTA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	6											130	138	135					6																	83847934		2203	4300	6503	83904653	SO:0001819	synonymous_variant	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.4173C>T	6.37:g.83847934C>T			83904653	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																				0.383	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83847934	C	T	83847934	2	4	61	1	0	0	0	0	0	0	0	1	4718	903	32	3		3	DOPEY1	6	83847934	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29303	83847934	87267133	4742	12727										
RWDD2A	112611	broad.mit.edu	37	chr6	83905834	83905834	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacctgcgccttttccattCttttgaagagttactccttg	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:83905834C>A	ENST00000369724.4	+	3	927	c.722C>A	c.(721-723)tCt>tAt	p.S241Y	RWDD2A_ENST00000539997.1_Missense_Mutation_p.S187Y|PGM3_ENST00000506587.1_5'Flank|PGM3_ENST00000283977.4_5'Flank|PGM3_ENST00000513973.1_5'Flank|PGM3_ENST00000512866.1_5'Flank	NM_033411.3	NP_219479.2	Q9UIY3	RWD2A_HUMAN	RWD domain containing 2A	241								p.S241Y(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	5		all_cancers(76;2.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00217)		BRCA - Breast invasive adenocarcinoma(397;0.045)		CTTTTCCATTCTTTTGAAGAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	110	111					6																	83905834		2203	4300	6503	83962553	SO:0001583	missense	112611			BC010930	CCDS4998.1	6q15	2012-12-07	2007-07-17	2007-07-17	ENSG00000013392	ENSG00000013392			21385	protein-coding gene	gene with protein product			"RWD domain containing 2"	RWDD2			Standard	NM_033411		Approved	MGC13523, dJ747H23.2	uc003pjx.4	Q9UIY3	OTTHUMG00000015109	ENST00000369724.4:c.722C>A	6.37:g.83905834C>A	ENSP00000358739:p.Ser241Tyr		83962553	B4DIQ3|E1P548|Q2M3R3|Q96FH1	Missense_Mutation	SNP	ENST00000369724.4	37	CCDS4998.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.961331	0.34565	.	.	ENSG00000013392	ENST00000369724;ENST00000539997	.	.	.	5.38	3.58	0.41010	Domain of unknown function DUF1115 (1);	0.470309	0.21566	N	0.072498	T	0.32823	0.0842	L	0.34521	1.04	0.31654	N	0.646395	P	0.50710	0.938	P	0.52109	0.69	T	0.16041	-1.0416	9	0.59425	D	0.04	-15.5297	11.2611	0.49083	0.0:0.698:0.236:0.066	.	241	Q9UIY3	RWD2A_HUMAN	Y	241;187	.	ENSP00000358739:S241Y	S	+	2	0	RWDD2A	83962553	0.960000	0.32886	0.988000	0.46212	0.012000	0.07955	1.726000	0.38085	1.512000	0.48834	-0.127000	0.14921	TCT		0.433	RWDD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041348.2	NM_033411		A	83905834	C	A	83905834	3	1	61	1	0	0	0	0	1	0	0	0	13792	913	32	2	728	2	RWDD2A	6	83905834	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57900	83905834	87209233	4743	12728										
ME1	4199	broad.mit.edu	37	chr6	83921740	83921740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtactatacatctgggagCggacaaatgcttctttgttt	9	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:83921740C>T	ENST00000369705.3	-	14	1738	c.1622G>A	c.(1621-1623)cGc>cAc	p.R541H	ME1_ENST00000543031.1_Missense_Mutation_p.R466H|ME1_ENST00000541327.1_Missense_Mutation_p.R375H	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	541				R -> S (in Ref. 2; AAB01380). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)	p.R541H(1)		NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		CATCTGGGAGCGGACAAATGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											149	139	142					6																	83921740		2203	4300	6503	83978459	SO:0001583	missense	4199			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.1622G>A	6.37:g.83921740C>T	ENSP00000358719:p.Arg541His		83978459	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Missense_Mutation	SNP	ENST00000369705.3	37	CCDS34492.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043223	0.36085	.	.	ENSG00000065833	ENST00000369705;ENST00000540036;ENST00000541327;ENST00000543031	T;T;T	0.45276	0.9;0.9;0.9	5.86	-2.94	0.05581	NAD(P)-binding domain (1);	0.438549	0.28694	N	0.014444	T	0.14570	0.0352	M	0.64997	1.995	0.36442	D	0.86553	B	0.12013	0.005	B	0.09377	0.004	T	0.04551	-1.0943	10	0.87932	D	0	11.1751	1.8393	0.03147	0.2895:0.4039:0.0985:0.2081	.	541	P48163	MAOX_HUMAN	H	541;201;375;466	ENSP00000358719:R541H;ENSP00000439912:R375H;ENSP00000446114:R466H	ENSP00000358719:R541H	R	-	2	0	ME1	83978459	0.827000	0.29292	0.008000	0.14137	0.649000	0.38597	0.115000	0.15540	-1.062000	0.03181	-0.172000	0.13284	CGC		0.373	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1			T	83921740	C	T	83921740	3	4	61	1	0	0	0	0	1	0	0	0	9447	768	27	1	100	1	ME1	6	83921740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15906	83921740	87193327	4744	12729										
PRSS35	167681	broad.mit.edu	37	chr6	84233542	84233542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagacaggtgtatggcaccGacagcaggttcagcatcttg	13	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84233542G>A	ENST00000369700.3	+	2	559	c.382G>A	c.(382-384)Gac>Aac	p.D128N	PRSS35_ENST00000536636.1_Missense_Mutation_p.D128N	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	128	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.D128N(1)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		GTATGGCACCGACAGCAGGTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											95	89	91					6																	84233542		2203	4300	6503	84290261	SO:0001583	missense	167681			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.382G>A	6.37:g.84233542G>A	ENSP00000358714:p.Asp128Asn		84290261	A8K7B3|Q9BQP6	Missense_Mutation	SNP	ENST00000369700.3	37	CCDS4999.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.762738	0.89932	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.44482	0.92;0.92	5.53	5.53	0.82687	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65298	-0.6202	10	0.87932	D	0	-33.23	19.4726	0.94969	0.0:0.0:1.0:0.0	.	128	Q8N3Z0	PRS35_HUMAN	N	128	ENSP00000440870:D128N;ENSP00000358714:D128N	ENSP00000358714:D128N	D	+	1	0	PRSS35	84290261	1.000000	0.71417	0.985000	0.45067	0.773000	0.43773	9.476000	0.97823	2.618000	0.88619	0.561000	0.74099	GAC		0.463	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		A	84233542	G	A	84233542	3	1	61	1	0	0	0	0	1	0	0	0	12658	1058	37	1	384	1	PRSS35	6	84233542	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	311802	84233542	86881525	4745	12730										
PRSS35	167681	broad.mit.edu	37	chr6	84233685	84233685	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgtgttcatgatggaaaGgactatgtcaaagggagtaa	12	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84233685G>T	ENST00000369700.3	+	2	702	c.525G>T	c.(523-525)aaG>aaT	p.K175N	PRSS35_ENST00000536636.1_Missense_Mutation_p.K175N	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	175	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.K175N(1)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		ATGATGGAAAGGACTATGTCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	104	103					6																	84233685		2203	4300	6503	84290404	SO:0001583	missense	167681			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.525G>T	6.37:g.84233685G>T	ENSP00000358714:p.Lys175Asn		84290404	A8K7B3|Q9BQP6	Missense_Mutation	SNP	ENST00000369700.3	37	CCDS4999.1	.	.	.	.	.	.	.	.	.	.	G	7.546	0.661605	0.14645	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.41065	1.01;1.01	5.78	-0.439	0.12264	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.202093	0.50627	N	0.000111	T	0.11879	0.0289	N	0.25957	0.775	0.51767	D	0.999933	B	0.11235	0.004	B	0.12156	0.007	T	0.10941	-1.0608	10	0.62326	D	0.03	-15.7743	6.9128	0.24344	0.2464:0.3336:0.42:0.0	.	175	Q8N3Z0	PRS35_HUMAN	N	175	ENSP00000440870:K175N;ENSP00000358714:K175N	ENSP00000358714:K175N	K	+	3	2	PRSS35	84290404	1.000000	0.71417	0.010000	0.14722	0.046000	0.14306	1.335000	0.33839	-0.415000	0.07484	0.561000	0.74099	AAG		0.478	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		T	84233685	G	T	84233685	3	4	61	1	0	0	0	0	1	0	0	0	12658	991	35	2	527	2	PRSS35	6	84233685	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143	84233685	86881382	4746	12731										
PRSS35	167681	broad.mit.edu	37	chr6	84234054	84234054	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacttggaatcagcccaacGatcaagaaaatgcctggtgg	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84234054G>A	ENST00000369700.3	+	2	1071	c.894G>A	c.(892-894)acG>acA	p.T298T	PRSS35_ENST00000536636.1_Silent_p.T298T	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	298	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.T298T(2)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		TCAGCCCAACGATCAAGAAAA	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	6											100	97	98					6																	84234054		2203	4300	6503	84290773	SO:0001819	synonymous_variant	167681			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.894G>A	6.37:g.84234054G>A			84290773	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																				0.478	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		A	84234054	G	A	84234054	2	1	61	1	0	0	0	0	0	0	0	1	12658	1045	37	1		1	PRSS35	6	84234054	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	369	84234054	86881013	4747	12732										
SNAP91	9892	broad.mit.edu	37	chr6	84304185	84304185	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaggggcctccccaggaGaagctgcaaaggcatcttgg	14	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84304185G>T	ENST00000439399.2	-	17	1656	c.1340C>A	c.(1339-1341)tCt>tAt	p.S447Y	SNAP91_ENST00000521743.1_Missense_Mutation_p.S447Y|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000195649.6_Missense_Mutation_p.S447Y|SNAP91_ENST00000521485.1_Missense_Mutation_p.S447Y|SNAP91_ENST00000428679.2_Missense_Mutation_p.S447Y|SNAP91_ENST00000520302.1_Missense_Mutation_p.S445Y|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000369694.2_Missense_Mutation_p.S447Y	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	447	Ala-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)	p.S447Y(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		CTCCCCAGGAGAAGCTGCAAA	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	6											17	17	17					6																	84304185		1762	3971	5733	84360904	SO:0001583	missense	9892			AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1340C>A	6.37:g.84304185G>T	ENSP00000400459:p.Ser447Tyr		84360904	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	37	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.121766	0.77436	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000520302;ENST00000521743	T;T;T;T;T;T;T	0.16897	2.32;2.31;2.31;2.32;2.32;2.33;2.31	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	L	0.60455	1.87	0.80722	D	1	D;D;D	0.65815	0.995;0.995;0.995	D;D;D	0.75484	0.986;0.986;0.986	T	0.03673	-1.1014	10	0.87932	D	0	-21.8005	19.942	0.97168	0.0:0.0:1.0:0.0	.	445;447;445	E5RI02;O60641;E1P549	.;AP180_HUMAN;.	Y	447;447;447;447;447;445;447	ENSP00000429776:S447Y;ENSP00000358708:S447Y;ENSP00000400459:S447Y;ENSP00000195649:S447Y;ENSP00000412492:S447Y;ENSP00000428511:S445Y;ENSP00000428215:S447Y	ENSP00000195649:S447Y	S	-	2	0	SNAP91	84360904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.218000	0.89768	2.714000	0.92807	0.561000	0.74099	TCT		0.473	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84304185	G	T	84304185	3	4	61	1	0	0	0	0	1	0	0	0	14870	942	33	2	1435	2	SNAP91	6	84304185	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70131	84304185	86810882	4748	12733										
SNAP91	9892	broad.mit.edu	37	chr6	84375235	84375235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctactgtttgttgcccGctcaaagagagtgtcggcca	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84375235G>A	ENST00000439399.2	-	3	512	c.196C>T	c.(196-198)Cgg>Tgg	p.R66W	SNAP91_ENST00000521743.1_Missense_Mutation_p.R66W|SNAP91_ENST00000520213.1_Missense_Mutation_p.R66W|SNAP91_ENST00000195649.6_Missense_Mutation_p.R66W|SNAP91_ENST00000521485.1_Missense_Mutation_p.R66W|SNAP91_ENST00000428679.2_Missense_Mutation_p.R66W|SNAP91_ENST00000520302.1_Missense_Mutation_p.R66W|SNAP91_ENST00000437520.1_Missense_Mutation_p.R66W|SNAP91_ENST00000369694.2_Missense_Mutation_p.R66W	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	66	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)	p.R66W(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TTTGTTGCCCGCTCAAAGAGA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	6											173	166	168					6																	84375235		1880	4099	5979	84431954	SO:0001583	missense	9892			AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.196C>T	6.37:g.84375235G>A	ENSP00000400459:p.Arg66Trp		84431954	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	37	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.088126	0.76642	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931;ENST00000519779;ENST00000518309;ENST00000369690;ENST00000523484;ENST00000519825	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.6	3.53	0.40419	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.73337	0.3574	H	0.96269	3.795	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.84076	0.0382	10	0.87932	D	0	-8.475	15.2687	0.73683	0.0:0.0:0.6923:0.3077	.	66;66;66;66	O60641-3;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	W	66	ENSP00000429776:R66W;ENSP00000358708:R66W;ENSP00000400459:R66W;ENSP00000195649:R66W;ENSP00000412492:R66W;ENSP00000413277:R66W;ENSP00000428511:R66W;ENSP00000428215:R66W;ENSP00000428026:R66W;ENSP00000430071:R66W;ENSP00000429429:R66W;ENSP00000430441:R66W;ENSP00000358704:R66W;ENSP00000427959:R66W;ENSP00000431055:R66W	ENSP00000195649:R66W	R	-	1	2	SNAP91	84431954	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.005000	0.29834	1.480000	0.48289	-0.311000	0.09066	CGG		0.378	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			A	84375235	G	A	84375235	3	1	61	1	0	0	0	0	1	0	0	0	14870	1086	38	1	2631	1	SNAP91	6	84375235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71050	84375235	86739832	4749	12734										
CYB5R4	51167	broad.mit.edu	37	chr6	84665135	84665135	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggacaaatccaaagttCtcgtctgcatttgtggacca	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84665135C>A	ENST00000369681.5	+	15	1605	c.1465C>A	c.(1465-1467)Ctc>Atc	p.L489I		NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	489					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)	p.L489I(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ATCCAAAGTTCTCGTCTGCAT	0.403																																					Esophageal Squamous(86;1289 1332 25971 40349 52675)											1	Substitution - Missense(1)	large_intestine(1)	6											84	82	83					6																	84665135		2203	4300	6503	84721854	SO:0001583	missense	51167			AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"NADPH cytochrome B5 oxidoreductase"	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.1465C>A	6.37:g.84665135C>A	ENSP00000358695:p.Leu489Ile		84721854	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091808	0.55968	.	.	ENSG00000065615	ENST00000369681	D	0.87029	-2.2	5.23	3.4	0.38934	Oxidoreductase FAD/NAD(P)-binding (1);	0.268822	0.40908	D	0.000988	D	0.84831	0.5559	M	0.81497	2.545	0.80722	D	1	B	0.31859	0.343	B	0.43155	0.41	D	0.83486	0.0067	10	0.59425	D	0.04	.	8.89	0.35427	0.0:0.7642:0.1511:0.0847	.	489	Q7L1T6	NB5R4_HUMAN	I	489	ENSP00000358695:L489I	ENSP00000358695:L489I	L	+	1	0	CYB5R4	84721854	0.984000	0.35163	0.925000	0.36789	0.513000	0.34164	2.307000	0.43682	0.545000	0.28902	0.460000	0.39030	CTC		0.403	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230		A	84665135	C	A	84665135	3	1	61	1	0	0	0	0	1	0	0	0	4135	913	32	2	1523	2	CYB5R4	6	84665135	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289900	84665135	86449932	4750	12735										
KIAA1009	22832	broad.mit.edu	37	chr6	84859327	84859327	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagctactttggaagaaGaattttctactgcattttgg	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84859327G>T	ENST00000403245.3	-	24	3839	c.3725C>A	c.(3724-3726)tCt>tAt	p.S1242Y	KIAA1009_ENST00000257766.4_Missense_Mutation_p.S1166Y|KIAA1009_ENST00000461137.1_5'UTR	NM_014895.2	NP_055710.2												p.S1242Y(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		TTTGGAAGAAGAATTTTCTAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											149	147	148					6																	84859327		2203	4300	6503	84916046	SO:0001583	missense	22832																														ENST00000403245.3:c.3725C>A	6.37:g.84859327G>T	ENSP00000385215:p.Ser1242Tyr		84916046		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271141	0.80469	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.22945	1.93;1.93	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	M	0.76002	2.32	0.51767	D	0.999933	D	0.63880	0.993	D	0.63192	0.912	T	0.45804	-0.9236	10	0.72032	D	0.01	-4.8016	19.008	0.92859	0.0:0.0:1.0:0.0	.	1242	Q5TB80	QN1_HUMAN	Y	1166;1242	ENSP00000257766:S1166Y;ENSP00000385215:S1242Y	ENSP00000257766:S1166Y	S	-	2	0	KIAA1009	84916046	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.216000	0.89764	2.470000	0.83445	0.460000	0.39030	TCT		0.363	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84859327	G	T	84859327	3	4	61	1	0	0	0	0	1	0	0	0	8224	942	33	2	502	2	KIAA1009	6	84859327	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194192	84859327	86255740	4751	12736										
KIAA1009	22832	broad.mit.edu	37	chr6	84872918	84872918	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctttcttcattttttcGaagtctacttcaagagcttg	5	10	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84872918G>A	ENST00000403245.3	-	19	2571	c.2457C>T	c.(2455-2457)ttC>ttT	p.F819F	KIAA1009_ENST00000257766.4_Silent_p.F743F|KIAA1009_ENST00000461137.1_5'UTR	NM_014895.2	NP_055710.2												p.F819F(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		TCATTTTTTCGAAGTCTACTT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	6											234	213	220					6																	84872918		2203	4300	6503	84929637	SO:0001819	synonymous_variant	22832																														ENST00000403245.3:c.2457C>T	6.37:g.84872918G>A			84929637		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																				0.333	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			A	84872918	G	A	84872918	2	1	61	1	0	0	0	0	0	0	0	1	8224	1049	37	1		1	KIAA1009	6	84872918	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13591	84872918	86242149	4752	12737										
KIAA1009	22832	broad.mit.edu	37	chr6	84884463	84884463	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccttggcttgaagaatatAattatcttgattcaatttga	6	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84884463A>C	ENST00000403245.3	-	15	2122	c.2008T>G	c.(2008-2010)Tat>Gat	p.Y670D	KIAA1009_ENST00000257766.4_Missense_Mutation_p.Y594D|KIAA1009_ENST00000461137.1_5'UTR	NM_014895.2	NP_055710.2												p.Y670D(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		TGAAGAATATAATTATCTTGA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	6											49	43	45					6																	84884463		2198	4289	6487	84941182	SO:0001583	missense	22832																														ENST00000403245.3:c.2008T>G	6.37:g.84884463A>C	ENSP00000385215:p.Tyr670Asp		84941182		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835768	0.71373	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.33865	1.39;1.39	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.53769	0.1817	M	0.77616	2.38	0.44337	D	0.997224	D	0.89917	1.0	D	0.91635	0.999	T	0.57051	-0.7877	10	0.48119	T	0.1	-2.833	15.8594	0.79009	1.0:0.0:0.0:0.0	.	670	Q5TB80	QN1_HUMAN	D	594;670	ENSP00000257766:Y594D;ENSP00000385215:Y670D	ENSP00000257766:Y594D	Y	-	1	0	KIAA1009	84941182	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.398000	0.73244	2.211000	0.71520	0.460000	0.39030	TAT		0.284	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			C	84884463	A	C	84884463	3	2	61	1	0	0	0	0	1	0	0	0	8224	362	13	4	2255	4	KIAA1009	6	84884463	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11545	84884463	86230604	4753	12738										
KIAA1009	22832	broad.mit.edu	37	chr6	84925545	84925545	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggttccactgctcttaaGaaattgaatcttttcagcag	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84925545G>T	ENST00000403245.3	-	4	382	c.268C>A	c.(268-270)Ctt>Att	p.L90I	KIAA1009_ENST00000257766.4_Missense_Mutation_p.L14I	NM_014895.2	NP_055710.2												p.L90I(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		CTGCTCTTAAGAAATTGAATC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											53	49	50					6																	84925545		2201	4293	6494	84982264	SO:0001583	missense	22832																														ENST00000403245.3:c.268C>A	6.37:g.84925545G>T	ENSP00000385215:p.Leu90Ile		84982264		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094255	0.36952	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.19394	2.15;2.17	5.54	3.72	0.42706	.	0.432524	0.21913	N	0.067276	T	0.11239	0.0274	M	0.67953	2.075	0.09310	N	1	P;P	0.45827	0.763;0.867	B;P	0.44897	0.288;0.463	T	0.08868	-1.0701	10	0.32370	T	0.25	-10.6225	6.3434	0.21335	0.2065:0.0:0.657:0.1365	.	90;90	Q5TB80;C9JFM9	QN1_HUMAN;.	I	14;90	ENSP00000257766:L14I;ENSP00000385215:L90I	ENSP00000257766:L14I	L	-	1	0	KIAA1009	84982264	1.000000	0.71417	0.993000	0.49108	0.895000	0.52256	2.344000	0.44010	1.477000	0.48234	0.655000	0.94253	CTT		0.353	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84925545	G	T	84925545	3	4	61	1	0	0	0	0	1	0	0	0	8224	942	33	2	4039	2	KIAA1009	6	84925545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41082	84925545	86189522	4754	12739										
KIAA1009	22832	broad.mit.edu	37	chr6	84936057	84936057	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaaaatataaacttacctCtttcataaactgttcaaact	1	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:84936057C>A	ENST00000403245.3	-	2	169	c.55G>T	c.(55-57)Gag>Tag	p.E19*	KIAA1009_ENST00000257766.4_Intron	NM_014895.2	NP_055710.2												p.E19*(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		AAACTTACCTCTTTCATAAAC	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											59	57	58					6																	84936057		1820	4051	5871	84992776	SO:0001587	stop_gained	22832																														ENST00000403245.3:c.55G>T	6.37:g.84936057C>A	ENSP00000385215:p.Glu19*		84992776		Nonsense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	C	37	6.452178	0.97577	.	.	ENSG00000135315	ENST00000403245	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.8399	15.8007	0.78453	0.0:1.0:0.0:0.0	.	.	.	.	X	19	.	ENSP00000385215:E19X	E	-	1	0	KIAA1009	84992776	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.308000	0.59129	2.467000	0.83353	0.561000	0.74099	GAG		0.338	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			A	84936057	C	A	84936057	4	1	61	1	0	0	0	0	0	1	0	0	8224	922	32	2	4260	2	KIAA1009	6	84936057	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10512	84936057	86179010	4755	12740										
TBX18	9096	broad.mit.edu	37	chr6	85466570	85466570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctgccaccatccatttcGaactgtggtaaacataccta	5	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:85466570G>A	ENST00000369663.5	-	4	954	c.617C>T	c.(616-618)tCg>tTg	p.S206L	TBX18_ENST00000606521.1_5'UTR|TBX18_ENST00000606784.1_Missense_Mutation_p.S48L	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	206					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S206L(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CATCCATTTCGAACTGTGGTA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											109	86	94					6																	85466570		2203	4300	6503	85523289	SO:0001583	missense	9096			AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.617C>T	6.37:g.85466570G>A	ENSP00000358677:p.Ser206Leu		85523289	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.069191	0.76301	.	.	ENSG00000112837	ENST00000416980;ENST00000369663	T	0.81330	-1.48	6.06	6.06	0.98353	p53-like transcription factor, DNA-binding (1);	0.095323	0.64402	D	0.000001	D	0.93327	0.7873	H	0.96365	3.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94238	0.7482	10	0.87932	D	0	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	122;206	Q8IW86;O95935	.;TBX18_HUMAN	L	121;206	ENSP00000358677:S206L	ENSP00000358677:S206L	S	-	2	0	TBX18	85523289	1.000000	0.71417	0.998000	0.56505	0.043000	0.13939	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	TCG		0.488	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		A	85466570	G	A	85466570	3	1	61	1	0	0	0	0	1	0	0	0	15692	1059	37	1	1226	1	TBX18	6	85466570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	530513	85466570	85648497	4756	12741										
NT5E	4907	broad.mit.edu	37	chr6	86194984	86194984	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaagaggtgcctgctggGaagtacccattcatagtcac	10	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:86194984G>A	ENST00000257770.3	+	4	832	c.783G>A	c.(781-783)ggG>ggA	p.G261G	NT5E_ENST00000369651.3_Silent_p.G261G	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	261					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.G261G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	TGCCTGCTGGGAAGTACCCAT	0.502																																					Melanoma(140;797 1765 2035 2752 18208)											1	Substitution - coding silent(1)	large_intestine(1)	6											102	87	92					6																	86194984		2203	4300	6503	86251703	SO:0001819	synonymous_variant	4907			X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"CD molecules"	8021	protein-coding gene	gene with protein product		129190	"5' nucleotidase (CD73)"	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.783G>A	6.37:g.86194984G>A			86251703	B3KQI8|O75520|Q5W116	Silent	SNP	ENST00000257770.3	37	CCDS5002.1	.	.	.	.	.	.	.	.	.	.	G	9.416	1.081738	0.20309	.	.	ENSG00000135318	ENST00000416334	T	0.66280	-0.2	5.63	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.51652	0.1687	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64050	-0.6498	7	0.87932	D	0	-15.3447	2.3625	0.04310	0.1318:0.1432:0.4772:0.2478	.	.	.	.	E	26	ENSP00000414674:G26E	ENSP00000414674:G26E	G	+	2	0	NT5E	86251703	0.032000	0.19561	1.000000	0.80357	0.996000	0.88848	0.224000	0.17738	2.646000	0.89796	0.462000	0.41574	GGA		0.502	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1			A	86194984	G	A	86194984	2	1	61	1	0	0	0	0	0	0	0	1	10724	1161	41	3		3	NT5E	6	86194984	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	728414	86194984	84920083	4757	12742										
SNX14	57231	broad.mit.edu	37	chr6	86235847	86235847	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttaaattgacttaccaaGatttacatctggtagtatct	5	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:86235847G>T	ENST00000314673.3	-	21	2280	c.2104C>A	c.(2104-2106)Ctt>Att	p.L702I	SNX14_ENST00000505648.1_Missense_Mutation_p.L650I|SNX14_ENST00000369627.2_Missense_Mutation_p.L693I|SNX14_ENST00000513865.1_Intron|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000346348.3_Missense_Mutation_p.L649I	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	702					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)	p.L702I(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		GACTTACCAAGATTTACATCT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	6											27	27	27					6																	86235847		2201	4299	6500	86292566	SO:0001583	missense	57231			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.2104C>A	6.37:g.86235847G>T	ENSP00000313121:p.Leu702Ile		86292566	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Missense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290582	0.59976	.	.	ENSG00000135317	ENST00000346348;ENST00000369628;ENST00000314673;ENST00000505648;ENST00000369627;ENST00000515216;ENST00000418862	T;T;T;T;T	0.27402	1.74;1.7;1.72;1.67;1.75	4.87	4.87	0.63330	.	0.156448	0.43579	D	0.000542	T	0.23330	0.0564	L	0.38175	1.15	0.54753	D	0.999988	D;P;P;D	0.57571	0.98;0.947;0.941;0.965	P;P;P;P	0.54460	0.753;0.58;0.571;0.69	T	0.01420	-1.1359	10	0.33141	T	0.24	.	11.5218	0.50555	0.0828:0.0:0.9172:0.0	.	693;649;702;650	Q9Y5W7-4;Q9Y5W7-2;Q9Y5W7;Q9Y5W7-3	.;.;SNX14_HUMAN;.	I	649;159;702;650;693;620;67	ENSP00000257769:L649I;ENSP00000313121:L702I;ENSP00000427380:L650I;ENSP00000358641:L693I;ENSP00000425630:L620I	ENSP00000313121:L702I	L	-	1	0	SNX14	86292566	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.403000	0.79983	2.228000	0.72767	0.655000	0.94253	CTT		0.323	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		T	86235847	G	T	86235847	3	4	61	1	0	0	0	0	1	0	0	0	14922	942	33	2	772	2	SNX14	6	86235847	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40863	86235847	84879220	4758	12743										
SNX14	57231	broad.mit.edu	37	chr6	86252950	86252950	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacattctccaaaagggaaaGaacatgttcatatgcttcaa	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:86252950G>T	ENST00000314673.3	-	14	1515	c.1339C>A	c.(1339-1341)Ctt>Att	p.L447I	SNX14_ENST00000505648.1_Missense_Mutation_p.L395I|SNX14_ENST00000369627.2_Missense_Mutation_p.L447I|SNX14_ENST00000513865.1_Intron|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000346348.3_Missense_Mutation_p.L403I	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	447	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)	p.L447I(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		AAAAGGGAAAGAACATGTTCA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	100	98					6																	86252950		2203	4293	6496	86309669	SO:0001583	missense	57231			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.1339C>A	6.37:g.86252950G>T	ENSP00000313121:p.Leu447Ile		86309669	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Missense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867453	0.51588	.	.	ENSG00000135317	ENST00000346348;ENST00000314673;ENST00000505648;ENST00000369627;ENST00000515216	T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89	5.63	5.63	0.86233	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.22551	0.0544	L	0.60455	1.87	0.58432	D	0.999999	P;P;P;P	0.44521	0.837;0.837;0.784;0.743	B;B;P;B	0.46796	0.392;0.392;0.527;0.392	T	0.00827	-1.1550	10	0.37606	T	0.19	-15.9525	13.9212	0.63933	0.0726:0.0:0.9274:0.0	.	447;403;447;395	Q9Y5W7-4;Q9Y5W7-2;Q9Y5W7;Q9Y5W7-3	.;.;SNX14_HUMAN;.	I	403;447;395;447;374	ENSP00000257769:L403I;ENSP00000313121:L447I;ENSP00000427380:L395I;ENSP00000358641:L447I;ENSP00000425630:L374I	ENSP00000313121:L447I	L	-	1	0	SNX14	86309669	1.000000	0.71417	1.000000	0.80357	0.220000	0.24768	6.370000	0.73114	2.660000	0.90430	0.313000	0.20887	CTT		0.303	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		T	86252950	G	T	86252950	3	4	61	1	0	0	0	0	1	0	0	0	14922	942	33	2	1565	2	SNX14	6	86252950	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17103	86252950	84862117	4759	12744										
SYNCRIP	10492	broad.mit.edu	37	chr6	86333742	86333742	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgttccttggttttactcTtaggaatagagcccacaaaa	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:86333742T>G	ENST00000369622.3	-	7	1255	c.755A>C	c.(754-756)aAg>aCg	p.K252T	SYNCRIP_ENST00000355238.6_Missense_Mutation_p.K252T	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	252	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K252T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		GGTTTTACTCTTAGGAATAGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	97	98					6																	86333742		2203	4300	6503	86390461	SO:0001583	missense	10492			AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.755A>C	6.37:g.86333742T>G	ENSP00000358635:p.Lys252Thr		86390461	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	37	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	T	32	5.186358	0.94885	.	.	ENSG00000135316	ENST00000355238;ENST00000369622	T;T	0.16196	2.36;2.36	5.85	5.85	0.93711	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	M	0.73430	2.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.99;1.0;0.997;0.971;1.0;0.976;0.99	D;D;D;P;D;P;D	0.97110	0.909;0.999;0.98;0.899;1.0;0.852;0.909	T	0.20273	-1.0280	10	0.87932	D	0	.	16.2444	0.82434	0.0:0.0:0.0:1.0	.	252;252;154;100;252;252;252	O60506;O60506-2;B7Z645;O60506-5;O60506-4;O60506-3;B2R8Z8	HNRPQ_HUMAN;.;.;.;.;.;.	T	252	ENSP00000347380:K252T;ENSP00000358635:K252T	ENSP00000347380:K252T	K	-	2	0	SYNCRIP	86390461	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.233000	0.73108	0.455000	0.32223	AAG		0.343	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		G	86333742	T	G	86333742	3	3	61	1	0	0	0	0	1	0	0	0	15483	1609	56	4	1182	4	SYNCRIP	6	86333742	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	80792	86333742	84781325	4760	12745										
SYNCRIP	10492	broad.mit.edu	37	chr6	86350232	86350232	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaccgtcttcattgaattCttttaaagcttcaatagctc	5	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:86350232C>A	ENST00000369622.3	-	3	699	c.199G>T	c.(199-201)Gaa>Taa	p.E67*	SYNCRIP_ENST00000355238.6_Nonsense_Mutation_p.E67*	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	67					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E67*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		TCATTGAATTCTTTTAAAGCT	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											70	70	70					6																	86350232		2203	4294	6497	86406951	SO:0001587	stop_gained	10492			AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.199G>T	6.37:g.86350232C>A	ENSP00000358635:p.Glu67*		86406951	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Nonsense_Mutation	SNP	ENST00000369622.3	37	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	C	37	6.373811	0.97515	.	.	ENSG00000135316	ENST00000355238;ENST00000369622;ENST00000444272	.	.	.	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.4659	0.90755	0.0:1.0:0.0:0.0	.	.	.	.	X	67	.	ENSP00000347380:E67X	E	-	1	0	SYNCRIP	86406951	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.461000	0.80834	2.329000	0.79093	0.655000	0.94253	GAA		0.294	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		A	86350232	C	A	86350232	4	1	61	1	0	0	0	0	0	1	0	0	15483	922	32	2	1754	2	SYNCRIP	6	86350232	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16490	86350232	84764835	4761	12746										
HTR1E	3354	broad.mit.edu	37	chr6	87725304	87725304	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagcatcatctacattgtCatggatcgctggaagcttgg	11	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87725304C>A	ENST00000305344.5	+	2	955	c.252C>A	c.(250-252)gtC>gtA	p.V84V		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	84					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.V84V(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	TCTACATTGTCATGGATCGCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	6											164	139	148					6																	87725304		2203	4300	6503	87782023	SO:0001819	synonymous_variant	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.252C>A	6.37:g.87725304C>A			87782023	E1P503|Q9P1Y1	Silent	SNP	ENST00000305344.5	37	CCDS5006.1																																																																																				0.567	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		A	87725304	C	A	87725304	2	1	61	1	0	0	0	0	0	0	0	1	7460	813	29	2		2	HTR1E	6	87725304	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1375072	87725304	83389763	4762	12747										
HTR1E	3354	broad.mit.edu	37	chr6	87726062	87726062	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggctcggttatgtgaattCtctgatcaaccctctgctct	9	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87726062C>A	ENST00000305344.5	+	2	1713	c.1010C>A	c.(1009-1011)tCt>tAt	p.S337Y		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	337					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.S337Y(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	TATGTGAATTCTCTGATCAAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	124	121					6																	87726062		2203	4300	6503	87782781	SO:0001583	missense	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.1010C>A	6.37:g.87726062C>A	ENSP00000307766:p.Ser337Tyr		87782781	E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	37	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772164	0.69992	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.79845	-1.31;-1.31	4.61	4.61	0.57282	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000008	D	0.93913	0.8052	H	0.99074	4.42	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96837	0.9615	10	0.87932	D	0	.	17.4189	0.87508	0.0:1.0:0.0:0.0	.	337	P28566	5HT1E_HUMAN	Y	337	ENSP00000307766:S337Y;ENSP00000358597:S337Y	ENSP00000307766:S337Y	S	+	2	0	HTR1E	87782781	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.320000	0.79064	2.119000	0.64992	0.407000	0.27541	TCT		0.438	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		A	87726062	C	A	87726062	3	1	61	1	0	0	0	0	1	0	0	0	7460	913	32	2	1012	2	HTR1E	6	87726062	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	758	87726062	83389005	4763	12748										
ZNF292	23036	broad.mit.edu	37	chr6	87943060	87943060	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgaatgaatttttagctTttgagggtcccatcttgttg	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87943060T>G	ENST00000369577.3	+	5	599	c.556T>G	c.(556-558)Ttt>Gtt	p.F186V	ZNF292_ENST00000339907.4_Missense_Mutation_p.F181V	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	186						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.F186V(1)|p.F41V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		ATTTTTAGCTTTTGAGGGTCC	0.294																																																2	Substitution - Missense(2)	large_intestine(2)	6											53	50	51					6																	87943060		1805	4071	5876	87999779	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.556T>G	6.37:g.87943060T>G	ENSP00000358590:p.Phe186Val		87999779	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	9.499	1.102685	0.20632	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.06849	3.28;3.25	5.36	5.36	0.76844	.	0.201128	0.50627	D	0.000119	T	0.01800	0.0057	N	0.08118	0	0.36651	D	0.877381	B	0.19445	0.036	B	0.15484	0.013	T	0.47774	-0.9091	10	0.15952	T	0.53	.	15.658	0.77158	0.0:0.0:0.0:1.0	.	186	O60281	ZN292_HUMAN	V	186;181	ENSP00000358590:F186V;ENSP00000342847:F181V	ENSP00000342847:F181V	F	+	1	0	ZNF292	87999779	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.261000	0.51530	2.158000	0.67659	0.460000	0.39030	TTT		0.294	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87943060	T	G	87943060	3	3	61	1	0	0	0	0	1	0	0	0	17865	1841	64	4	574	4	ZNF292	6	87943060	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	216998	87943060	83172007	4764	12749										
ZNF292	23036	broad.mit.edu	37	chr6	87965425	87965425	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgtaaaaagggctttaAgtactttaaaaatttaattg	6	2	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87965425A>C	ENST00000369577.3	+	8	2121	c.2078A>C	c.(2077-2079)aAg>aCg	p.K693T	ZNF292_ENST00000339907.4_Missense_Mutation_p.K688T	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	693						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.K693T(1)|p.K548T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAGGGCTTTAAGTACTTTAAA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	6											35	33	34					6																	87965425		1808	4060	5868	88022144	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.2078A>C	6.37:g.87965425A>C	ENSP00000358590:p.Lys693Thr		88022144	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.459647	0.63401	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.51817	0.69;0.69	5.96	5.96	0.96718	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.48732	0.1516	L	0.27944	0.81	0.54753	D	0.999986	D	0.89917	1.0	D	0.91635	0.999	T	0.54456	-0.8291	10	0.54805	T	0.06	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	693	O60281	ZN292_HUMAN	T	693;688	ENSP00000358590:K693T;ENSP00000342847:K688T	ENSP00000342847:K688T	K	+	2	0	ZNF292	88022144	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.284000	0.76573	0.528000	0.53228	AAG		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		C	87965425	A	C	87965425	3	2	61	1	0	0	0	0	1	0	0	0	17865	72	3	4	2108	4	ZNF292	6	87965425	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22365	87965425	83149642	4765	12750										
ZNF292	23036	broad.mit.edu	37	chr6	87966676	87966676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatgtactcgaacctataAttcttcacagagtattggga	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87966676A>G	ENST00000369577.3	+	8	3372	c.3329A>G	c.(3328-3330)aAt>aGt	p.N1110S	ZNF292_ENST00000339907.4_Missense_Mutation_p.N1105S	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1110						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.N1110S(1)|p.N965S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CGAACCTATAATTCTTCACAG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	6											53	49	51					6																	87966676		1868	4101	5969	88023395	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.3329A>G	6.37:g.87966676A>G	ENSP00000358590:p.Asn1110Ser		88023395	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.438034	0.43326	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.06528	3.29;3.3	5.55	5.55	0.83447	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.081171	0.85682	D	0.000000	T	0.10551	0.0258	L	0.46157	1.445	0.35468	D	0.79712	D	0.69078	0.997	D	0.75020	0.985	T	0.18587	-1.0332	10	0.29301	T	0.29	.	15.6783	0.77344	1.0:0.0:0.0:0.0	.	1110	O60281	ZN292_HUMAN	S	1110;1105	ENSP00000358590:N1110S;ENSP00000342847:N1105S	ENSP00000342847:N1105S	N	+	2	0	ZNF292	88023395	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	6.024000	0.70857	2.111000	0.64477	0.482000	0.46254	AAT		0.433	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87966676	A	G	87966676	3	3	61	1	0	0	0	0	1	0	0	0	17865	101	4	4	3359	4	ZNF292	6	87966676	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1251	87966676	83148391	4766	12751										
ZNF292	23036	broad.mit.edu	37	chr6	87970293	87970293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatcaaagtctaaacatCgggggaccaagcacagcaga	9	9	2	1	rs201424493		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:87970293C>T	ENST00000369577.3	+	8	6989	c.6946C>T	c.(6946-6948)Cgg>Tgg	p.R2316W	ZNF292_ENST00000339907.4_Missense_Mutation_p.R2311W	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2316						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R2171W(1)|p.R2316W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GTCTAAACATCGGGGGACCAA	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	6						C	TRP/ARG	1,3737		0,1,1868	38	40	39		6946	4.7	1	6		39	1,8181		0,1,4090	yes	missense	ZNF292	NM_015021.1	101	0,2,5958	TT,TC,CC		0.0122,0.0268,0.0168	probably-damaging	2316/2724	87970293	2,11918	1869	4091	5960	88027012	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6946C>T	6.37:g.87970293C>T	ENSP00000358590:p.Arg2316Trp		88027012	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.697272	0.30142	2.68E-4	1.22E-4	ENSG00000188994	ENST00000369577;ENST00000339907;ENST00000496806	T;T;T	0.50001	3.18;3.19;0.76	5.62	4.74	0.60224	.	0.153517	0.53938	D	0.000044	T	0.52948	0.1766	M	0.63428	1.95	0.33668	D	0.610622	D	0.89917	1.0	D	0.65573	0.936	T	0.62666	-0.6806	10	0.87932	D	0	.	13.0434	0.58913	0.437:0.563:0.0:0.0	.	2316	O60281	ZN292_HUMAN	W	2316;2311;234	ENSP00000358590:R2316W;ENSP00000342847:R2311W;ENSP00000428857:R234W	ENSP00000342847:R2311W	R	+	1	2	ZNF292	88027012	0.019000	0.18553	0.994000	0.49952	0.393000	0.30537	0.183000	0.16919	1.359000	0.45940	0.585000	0.79938	CGG		0.373	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		T	87970293	C	T	87970293	3	4	61	1	0	0	0	0	1	0	0	0	17865	875	31	1	6976	1	ZNF292	6	87970293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3617	87970293	83144774	4767	12752										
C6orf162	57150	broad.mit.edu	37	chr6	88049912	88049912	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatctacatgcaatacaaGagaataaaaaggacctctat	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88049912G>T	ENST00000392863.1	+	4	303	c.214G>T	c.(214-216)Gag>Tag	p.E72*	SMIM8_ENST00000608525.1_Intron|SMIM8_ENST00000608868.1_Nonsense_Mutation_p.E72*|RP1-102H19.8_ENST00000448282.2_Intron|SMIM8_ENST00000608353.1_Nonsense_Mutation_p.E72*|SMIM8_ENST00000229570.5_Nonsense_Mutation_p.E72*	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	72						integral component of membrane (GO:0016021)		p.E72*(1)									TGCAATACAAGAGAATAAAAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											120	121	121					6																	88049912		2203	4300	6503	88106631	SO:0001587	stop_gained	57150			AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 162"	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.214G>T	6.37:g.88049912G>T	ENSP00000376603:p.Glu72*		88106631	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Nonsense_Mutation	SNP	ENST00000392863.1	37	CCDS34496.1	.	.	.	.	.	.	.	.	.	.	G	34	5.319453	0.95682	.	.	ENSG00000111850	ENST00000392863;ENST00000229570	.	.	.	5.56	5.56	0.83823	.	0.090676	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.005	19.9052	0.97004	0.0:0.0:1.0:0.0	.	.	.	.	X	72	.	ENSP00000229570:E72X	E	+	1	0	C6orf162	88106631	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.322000	0.96357	2.776000	0.95493	0.655000	0.94253	GAG		0.373	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425		T	88049912	G	T	88049912	4	4	61	1	0	0	0	0	0	1	0	0	2346	943	33	2	220	2	C6orf162	6	88049912	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79619	88049912	83065155	4768	12753										
C6orf165	154313	broad.mit.edu	37	chr6	88140810	88140810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttttcccagaaacaacaGcaaattttgataaactgtta	6	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88140810G>A	ENST00000507897.1	+	10	1302	c.1219G>A	c.(1219-1221)Gca>Aca	p.A407T	C6ORF165_ENST00000369562.4_Missense_Mutation_p.A407T			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	407								p.A407T(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		AGAAACAACAGCAAATTTTGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											91	85	87					6																	88140810		2203	4300	6503	88197529	SO:0001583	missense	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1219G>A	6.37:g.88140810G>A	ENSP00000426769:p.Ala407Thr		88197529	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751820	0.49362	.	.	ENSG00000213204	ENST00000369562	T	0.31247	1.5	5.51	5.51	0.81932	.	0.211314	0.49916	D	0.000135	T	0.15912	0.0383	L	0.43701	1.375	0.49915	D	0.999837	B	0.32031	0.352	B	0.30105	0.111	T	0.04242	-1.0966	10	0.17832	T	0.49	.	19.0404	0.92997	0.0:0.0:1.0:0.0	.	407	Q8IYR0	CF165_HUMAN	T	407	ENSP00000358575:A407T	ENSP00000358575:A407T	A	+	1	0	C6orf165	88197529	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.849000	0.55910	2.589000	0.87451	0.591000	0.81541	GCA		0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		A	88140810	G	A	88140810	3	1	61	1	0	0	0	0	1	0	0	0	2347	971	34	3	1253	3	C6orf165	6	88140810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90898	88140810	82974257	4769	12754										
SLC35A1	10559	broad.mit.edu	37	chr6	88187167	88187167	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagctttaagatacacaaGgacatcagacaaagaactct	6	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88187167G>T	ENST00000369552.4	+	2	131	c.104G>T	c.(103-105)aGg>aTg	p.R35M	SLC35A1_ENST00000369556.3_Missense_Mutation_p.R35M|SLC35A1_ENST00000369557.5_Missense_Mutation_p.R35M|C6orf165_ENST00000507897.1_3'UTR|SLC35A1_ENST00000464978.1_3'UTR|SLC35A1_ENST00000544441.1_5'UTR|C6orf165_ENST00000506888.1_3'UTR	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	35					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|CMP-N-acetylneuraminate transport (GO:0015782)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456)|sugar:proton symporter activity (GO:0005351)	p.R35M(1)		breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		AGATACACAAGGACATCAGAC	0.373																																					NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)											1	Substitution - Missense(1)	large_intestine(1)	6											112	106	108					6																	88187167		2203	4300	6503	88243886	SO:0001583	missense	10559			D87969	CCDS5010.1, CCDS55043.1	6q15	2013-05-22			ENSG00000164414	ENSG00000164414		"Solute carriers"	11021	protein-coding gene	gene with protein product		605634	"solute carrier family 35 (UDP-galactose transporter), member 1"			9010752, 9644260	Standard	NM_006416		Approved	CMPST, hCST	uc011dzj.2	P78382	OTTHUMG00000015177	ENST00000369552.4:c.104G>T	6.37:g.88187167G>T	ENSP00000358565:p.Arg35Met		88243886	Q5W1L8	Missense_Mutation	SNP	ENST00000369552.4	37	CCDS5010.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178174	0.94846	.	.	ENSG00000164414	ENST00000369556;ENST00000369552;ENST00000429605;ENST00000369557;ENST00000369544	T	0.53206	0.63	5.62	5.62	0.85841	.	0.000000	0.85682	U	0.000000	T	0.73249	0.3563	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.979;0.991	T	0.79383	-0.1826	10	0.87932	D	0	-31.8085	19.6689	0.95903	0.0:0.0:1.0:0.0	.	35;35	P78382;Q5W1L8	S35A1_HUMAN;.	M	35;35;35;35;16	ENSP00000358565:R35M	ENSP00000358557:R16M	R	+	2	0	SLC35A1	88243886	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.642000	0.89623	0.655000	0.94253	AGG		0.373	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1			T	88187167	G	T	88187167	3	4	61	1	0	0	0	0	1	0	0	0	14607	1000	35	2	110	2	SLC35A1	6	88187167	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46357	88187167	82927900	4770	12755										
RARS2	57038	broad.mit.edu	37	chr6	88258320	88258320	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacttacctatgatggtaGaacgcaaatgtccaacatga	7	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88258320G>T	ENST00000369536.5	-	6	485	c.440C>A	c.(439-441)tCt>tAt	p.S147Y		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	147					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.S147Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		TATGATGGTAGAACGCAAATG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	75	77					6																	88258320		2203	4300	6503	88315039	SO:0001583	missense	57038			AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.440C>A	6.37:g.88258320G>T	ENSP00000358549:p.Ser147Tyr		88315039	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.3|22.3	4.269413|4.269413	0.80469|0.80469	.|.	.|.	ENSG00000146282|ENSG00000146282	ENST00000451155|ENST00000369536;ENST00000369523	.|T	.|0.68624	.|-0.34	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	.|0.049401	.|0.85682	.|D	.|0.000000	D|D	0.88355|0.88355	0.6414|0.6414	H|H	0.98199|0.98199	4.17|4.17	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.91913|0.91913	0.5541|0.5541	5|10	.|0.87932	.|D	.|0	.|.	18.8048|18.8048	0.92032|0.92032	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|147	.|Q5T160	.|SYRM_HUMAN	I|Y	175|147;174	.|ENSP00000358549:S147Y	.|ENSP00000358536:S174Y	L|S	-|-	1|2	2|0	RARS2|RARS2	88315039|88315039	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.887000|7.887000	0.87295|0.87295	2.803000|2.803000	0.96430|0.96430	0.650000|0.650000	0.86243|0.86243	CTA|TCT		0.299	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88258320	G	T	88258320	3	4	61	1	0	0	0	0	1	0	0	0	13096	942	33	2	1356	2	RARS2	6	88258320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71153	88258320	82856747	4771	12756										
ORC3L	23595	broad.mit.edu	37	chr6	88331076	88331076	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacatgtctttcagctttCtctattagagcatttctatt	4	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88331076C>A	ENST00000392844.3	+	10	1040	c.992C>A	c.(991-993)tCt>tAt	p.S331Y	ORC3_ENST00000546266.1_Missense_Mutation_p.S188Y|ORC3_ENST00000417380.2_Missense_Mutation_p.S278Y|ORC3_ENST00000257789.4_Missense_Mutation_p.S331Y	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	331					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)	p.S331Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						TTTCAGCTTTCTCTATTAGAG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											87	90	89					6																	88331076		2202	4297	6499	88387795	SO:0001583	missense	23595			AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"origin recognition complex, subunit 3 (yeast homolog)-like", "origin recognition complex, subunit 3-like (yeast)", "origin recognition complex, subunit 3 honolog (yeast)"	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.992C>A	6.37:g.88331076C>A	ENSP00000376586:p.Ser331Tyr		88387795	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Missense_Mutation	SNP	ENST00000392844.3	37	CCDS43486.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697727	0.68386	.	.	ENSG00000135336	ENST00000392844;ENST00000257789;ENST00000546266;ENST00000417380	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.51	5.51	0.81932	.	0.241113	0.45361	D	0.000373	T	0.32376	0.0827	M	0.67953	2.075	0.53005	D	0.99996	D;D;D;D;D	0.69078	0.987;0.997;0.971;0.993;0.996	D;D;D;D;D	0.71656	0.934;0.974;0.934;0.968;0.946	T	0.02042	-1.1224	10	0.72032	D	0.01	-1.1534	16.2993	0.82801	0.0:0.859:0.141:0.0	.	331;331;269;331;331	B7ZAI3;B7Z8A5;B4E014;Q9UBD5;Q9UBD5-2	.;.;.;ORC3_HUMAN;.	Y	331;331;188;278	ENSP00000376586:S331Y;ENSP00000257789:S331Y;ENSP00000444695:S188Y;ENSP00000390176:S278Y	ENSP00000257789:S331Y	S	+	2	0	ORC3	88387795	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	5.684000	0.68197	2.738000	0.93877	0.655000	0.94253	TCT		0.313	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2			A	88331076	C	A	88331076	3	1	61	1	0	0	0	0	1	0	0	0	11294	913	32	2	1030	2	ORC3L	6	88331076	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72756	88331076	82783991	4772	12757										
SPACA1	81833	broad.mit.edu	37	chr6	88767422	88767422	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatgccgtggaccaacaGattgtggctgtgagttgaat	13	6	0	4	rs557931381		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88767422G>T	ENST00000237201.1	+	3	475	c.358G>T	c.(358-360)Gat>Tat	p.D120Y		NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	120					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)		p.D120Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		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;0.11)		TGGACCAACAGATTGTGGCTG	0.438													G|||	1	0.000199681	0	0	5008	,	,		16753	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											103	101	102					6																	88767422		2203	4300	6503	88824141	SO:0001583	missense	81833			AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.358G>T	6.37:g.88767422G>T	ENSP00000237201:p.Asp120Tyr		88824141		Missense_Mutation	SNP	ENST00000237201.1	37	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757374	0.49468	.	.	ENSG00000118434	ENST00000237201	T	0.22336	1.96	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.39911	0.1096	M	0.67953	2.075	0.44104	D	0.996872	D	0.89917	1.0	D	0.91635	0.999	T	0.16335	-1.0406	10	0.87932	D	0	-30.5078	18.0854	0.89456	0.0:0.0:1.0:0.0	.	120	Q9HBV2	SACA1_HUMAN	Y	120	ENSP00000237201:D120Y	ENSP00000237201:D120Y	D	+	1	0	SPACA1	88824141	1.000000	0.71417	0.821000	0.32701	0.122000	0.20287	5.831000	0.69330	2.776000	0.95493	0.655000	0.94253	GAT		0.438	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			T	88767422	G	T	88767422	3	4	61	1	0	0	0	0	1	0	0	0	15009	942	33	2	368	2	SPACA1	6	88767422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436346	88767422	82347645	4773	12758										
SPACA1	81833	broad.mit.edu	37	chr6	88769240	88769240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtcaccccttggctttcGagtgtgacacactggataat	9	10	1	1	rs371980319		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88769240G>A	ENST00000237201.1	+	5	661	c.544G>A	c.(544-546)Gag>Aag	p.E182K	SPACA1_ENST00000462690.1_3'UTR	NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	182					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)		p.E182K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		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;0.11)		CTTGGCTTTCGAGTGTGACAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	LYS/GLU	0,4406		0,0,2203	95	93	94		544	0.2	0.1	6		94	1,8599	1.2+/-3.3	0,1,4299	no	missense	SPACA1	NM_030960.2	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	182/295	88769240	1,13005	2203	4300	6503	88825959	SO:0001583	missense	81833			AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.544G>A	6.37:g.88769240G>A	ENSP00000237201:p.Glu182Lys		88825959		Missense_Mutation	SNP	ENST00000237201.1	37	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	G	9.495	1.101589	0.20632	0.0	1.16E-4	ENSG00000118434	ENST00000237201	T	0.23348	1.91	5.5	0.191	0.15130	.	0.524214	0.18693	N	0.133781	T	0.12689	0.0308	L	0.51422	1.61	0.09310	N	1	B	0.32876	0.388	B	0.29524	0.103	T	0.16100	-1.0414	10	0.56958	D	0.05	-4.2235	21.0354	0.99944	0.0:0.5717:0.4283:0.0	.	182	Q9HBV2	SACA1_HUMAN	K	182	ENSP00000237201:E182K	ENSP00000237201:E182K	E	+	1	0	SPACA1	88825959	0.267000	0.24122	0.105000	0.21289	0.367000	0.29736	0.465000	0.22004	-0.215000	0.10063	-0.810000	0.03169	GAG		0.348	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88769240	G	A	88769240	3	1	61	1	0	0	0	0	1	0	0	0	15009	1059	37	1	562	1	SPACA1	6	88769240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1818	88769240	82345827	4774	12759										
CNR1	1268	broad.mit.edu	37	chr6	88854070	88854070	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgggtgccacgctgaatCatgcggacggcgtggctgtg	16	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88854070C>A	ENST00000537554.1	-	2	4486	c.924G>T	c.(922-924)atG>atT	p.M308I	CNR1_ENST00000468898.1_Missense_Mutation_p.M275I|CNR1_ENST00000369499.2_Missense_Mutation_p.M308I|CNR1_ENST00000549716.1_Missense_Mutation_p.M247I|CNR1_ENST00000428600.2_Missense_Mutation_p.M308I|CNR1_ENST00000369501.2_Missense_Mutation_p.M308I|CNR1_ENST00000549890.1_Missense_Mutation_p.M308I|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000535130.1_Missense_Mutation_p.M308I	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	308					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)	p.M308I(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		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)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	CACGCTGAATCATGCGGACGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	6											107	98	101					6																	88854070		2203	4300	6503	88910789	SO:0001583	missense	1268			AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.924G>T	6.37:g.88854070C>A	ENSP00000441046:p.Met308Ile		88910789	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	37	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679175	0.68042	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57;-0.57;-0.57;-0.57	6.05	6.05	0.98169	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.68714	0.3031	N	0.12182	0.205	0.80722	D	1	D;D	0.56746	0.962;0.977	D;P	0.66716	0.946;0.905	T	0.75297	-0.3367	10	0.87932	D	0	.	20.6086	0.99469	0.0:1.0:0.0:0.0	.	275;308	P21554-3;P21554	.;CNR1_HUMAN	I	308;308;308;308;308;275;308;247	ENSP00000358513:M308I;ENSP00000442689:M308I;ENSP00000441046:M308I;ENSP00000358511:M308I;ENSP00000446819:M308I;ENSP00000420188:M275I;ENSP00000412192:M308I;ENSP00000449549:M247I	ENSP00000358511:M308I	M	-	3	0	CNR1	88910789	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	7.818000	0.86416	2.880000	0.98712	0.655000	0.94253	ATG		0.547	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			A	88854070	C	A	88854070	3	1	61	1	0	0	0	0	1	0	0	0	3637	826	29	2	498	2	CNR1	6	88854070	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84830	88854070	82260997	4775	12760										
CNR1	1268	broad.mit.edu	37	chr6	88854250	88854250	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcccaggagaggcagcacGgcgatcacaatggctatggt	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:88854250G>A	ENST00000537554.1	-	2	4306	c.744C>T	c.(742-744)gcC>gcT	p.A248A	CNR1_ENST00000468898.1_Silent_p.A215A|CNR1_ENST00000369499.2_Silent_p.A248A|CNR1_ENST00000549716.1_Silent_p.A187A|CNR1_ENST00000428600.2_Silent_p.A248A|CNR1_ENST00000369501.2_Silent_p.A248A|CNR1_ENST00000549890.1_Silent_p.A248A|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000535130.1_Silent_p.A248A	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	248					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)	p.A248A(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		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)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	GAGGCAGCACGGCGATCACAA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	6											84	77	79					6																	88854250		2203	4300	6503	88910969	SO:0001819	synonymous_variant	1268			AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.744C>T	6.37:g.88854250G>A			88910969	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																				0.532	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			A	88854250	G	A	88854250	2	1	61	1	0	0	0	0	0	0	0	1	3637	1103	39	1		1	CNR1	6	88854250	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180	88854250	82260817	4776	12761										
GABRR1	2569	broad.mit.edu	37	chr6	89890095	89890095	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcaccgagaggaacacGaacacaaagctgacccagag	10	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:89890095G>A	ENST00000454853.2	-	9	1172	c.1062C>T	c.(1060-1062)ttC>ttT	p.F354F	GABRR1_ENST00000369451.3_Silent_p.F267F|GABRR1_ENST00000435811.1_Silent_p.F337F	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	354					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.F348F(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	AGAGGAACACGAACACAAAGC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	6											157	120	133					6																	89890095		2203	4300	6503	89946814	SO:0001819	synonymous_variant	2569				CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.1062C>T	6.37:g.89890095G>A			89946814	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Silent	SNP	ENST00000454853.2	37	CCDS5019.2																																																																																				0.577	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			A	89890095	G	A	89890095	2	1	61	1	0	0	0	0	0	0	0	1	6195	1049	37	1		1	GABRR1	6	89890095	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1035845	89890095	81224972	4777	12762										
GABRR1	2569	broad.mit.edu	37	chr6	89927009	89927009	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccccaccacaaaagaaaGatgccaaatctcatatttgg	5	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:89927009G>T	ENST00000454853.2	-	1	143	c.33C>A	c.(31-33)atC>atA	p.I11I	GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000481493.1_5'Flank|GABRR1_ENST00000435811.1_Silent_p.I11I	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	11					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.I5I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	ACAAAAGAAAGATGCCAAATC	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	6											72	66	68					6																	89927009		2203	4300	6503	89983728	SO:0001819	synonymous_variant	2569				CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.33C>A	6.37:g.89927009G>T			89983728	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Silent	SNP	ENST00000454853.2	37	CCDS5019.2																																																																																				0.448	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			T	89927009	G	T	89927009	2	4	61	1	0	0	0	0	0	0	0	1	6195	932	33	2		2	GABRR1	6	89927009	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36914	89927009	81188058	4778	12763										
GABRR2	2570	broad.mit.edu	37	chr6	89977750	89977750	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagctctccagctccaaaGaacaggtctgggagtccagg	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:89977750G>T	ENST00000402938.3	-	5	711	c.578C>A	c.(577-579)tCt>tAt	p.S193Y	GABRR2_ENST00000602808.1_5'Flank|GABRR2_ENST00000602399.1_Missense_Mutation_p.S218Y	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	193					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S193Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	CAGCTCCAAAGAACAGGTCTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											103	90	94					6																	89977750		2203	4300	6503	90034469	SO:0001583	missense	2570				CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4091	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 2"	137162	"gamma-aminobutyric acid (GABA) receptor, rho 2"			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.578C>A	6.37:g.89977750G>T	ENSP00000386029:p.Ser193Tyr		90034469	A2BDE4|Q9H153	Missense_Mutation	SNP	ENST00000402938.3	37	CCDS5020.3	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843729	0.91197	.	.	ENSG00000111886	ENST00000402938	.	.	.	5.91	5.91	0.95273	Neurotransmitter-gated ion-channel ligand-binding (3);	0.105102	0.64402	D	0.000002	T	0.68026	0.2956	L	0.54908	1.71	0.80722	D	1	D	0.53885	0.963	P	0.58266	0.836	T	0.63157	-0.6700	8	.	.	.	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	218	P28476	GBRR2_HUMAN	Y	218	.	.	S	-	2	0	GABRR2	90034469	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.776000	0.99001	2.808000	0.96608	0.655000	0.94253	TCT		0.473	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3			T	89977750	G	T	89977750	3	4	61	1	0	0	0	0	1	0	0	0	6196	942	33	2	839	2	GABRR2	6	89977750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50741	89977750	81137317	4779	12764										
ANKRD6	22881	broad.mit.edu	37	chr6	90315788	90315788	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagtcagccaagctgctCattaaagcaggagccaacgt	10	12	2	0	rs182815222		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90315788C>T	ENST00000522441.1	+	5	1022	c.381C>T	c.(379-381)ctC>ctT	p.L127L	ANKRD6_ENST00000369408.5_Silent_p.L127L|ANKRD6_ENST00000520886.2_3'UTR|ANKRD6_ENST00000447838.2_Silent_p.L127L|ANKRD6_ENST00000520793.1_Intron|ANKRD6_ENST00000339746.4_Silent_p.L127L|ANKRD6_ENST00000485637.1_Silent_p.L127L	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	127					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L127L(1)		NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		CCAAGCTGCTCATTAAAGCAG	0.532													C|||	1	0.000199681	0	0	5008	,	,		21846	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											54	54	54					6																	90315788		2057	4194	6251	90372507	SO:0001819	synonymous_variant	22881			AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"Ankyrin repeat domain containing"	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.381C>T	6.37:g.90315788C>T			90372507	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1																																																																																				0.532	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1			T	90315788	C	T	90315788	2	4	61	1	0	0	0	0	0	0	0	1	685	813	29	3		3	ANKRD6	6	90315788	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	338038	90315788	80799279	4780	12765										
MDN1	23195	broad.mit.edu	37	chr6	90381987	90381987	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacagctcggagatggcagAaattattttctgcacgtgca	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90381987A>C	ENST00000369393.3	-	82	13841	c.13726T>G	c.(13726-13728)Tct>Gct	p.S4576A	MDN1_ENST00000468568.1_5'UTR|MDN1_ENST00000428876.1_Missense_Mutation_p.S4576A|RP1-122O8.7_ENST00000438877.1_RNA			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4576					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.S4576A(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAGATGGCAGAAATTATTTTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	6											121	110	114					6																	90381987		2203	4300	6503	90438708	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13726T>G	6.37:g.90381987A>C	ENSP00000358400:p.Ser4576Ala		90438708	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.751342	0.49257	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.28666	1.6;1.6	6.06	6.06	0.98353	.	0.230014	0.38778	N	0.001572	T	0.14700	0.0355	M	0.63428	1.95	0.32818	D	0.502397	P	0.44006	0.824	B	0.34418	0.182	T	0.22208	-1.0223	10	0.12766	T	0.61	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	4576	Q9NU22	MDN1_HUMAN	A	4576	ENSP00000358400:S4576A;ENSP00000413970:S4576A	ENSP00000358400:S4576A	S	-	1	0	MDN1	90438708	1.000000	0.71417	0.968000	0.41197	0.906000	0.53458	5.131000	0.64751	2.324000	0.78689	0.533000	0.62120	TCT		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90381987	A	C	90381987	3	2	61	1	0	0	0	0	1	0	0	0	9445	246	9	4	3148	4	MDN1	6	90381987	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	66199	90381987	80733080	4781	12766										
MDN1	23195	broad.mit.edu	37	chr6	90394621	90394621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttttctaggggggaacGaagttccacaattttggcct	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90394621G>A	ENST00000369393.3	-	71	11918	c.11803C>T	c.(11803-11805)Cgt>Tgt	p.R3935C	MDN1_ENST00000428876.1_Missense_Mutation_p.R3935C			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3935					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.R3935C(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGGGGGGAACGAAGTTCCACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											53	56	55					6																	90394621		2203	4300	6503	90451342	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11803C>T	6.37:g.90394621G>A	ENSP00000358400:p.Arg3935Cys		90451342	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407615	0.62399	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.53423	0.62;0.62	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.69602	0.3129	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72246	-0.4349	10	0.72032	D	0.01	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	3935	Q9NU22	MDN1_HUMAN	C	3935	ENSP00000358400:R3935C;ENSP00000413970:R3935C	ENSP00000358400:R3935C	R	-	1	0	MDN1	90451342	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.272000	0.72575	2.783000	0.95769	0.655000	0.94253	CGT		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90394621	G	A	90394621	3	1	61	1	0	0	0	0	1	0	0	0	9445	1058	37	1	5115	1	MDN1	6	90394621	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12634	90394621	80720446	4782	12767										
MDN1	23195	broad.mit.edu	37	chr6	90403822	90403822	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgagagtagctgacaacGacttcatcttccaggtctct	10	10	3	2	rs116213908		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90403822G>A	ENST00000369393.3	-	62	9967	c.9852C>T	c.(9850-9852)gtC>gtT	p.V3284V	MDN1_ENST00000428876.1_Silent_p.V3284V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3284					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.V3284V(2)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGCTGACAACGACTTCATCTT	0.443													G|||	1	0.000199681	0	0	5008	,	,		22788	0.001		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	6						G		0,4406		0,0,2203	179	140	153		9852	-6.4	0	6	dbSNP_132	153	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MDN1	NM_014611.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		3284/5597	90403822	1,13005	2203	4300	6503	90460543	SO:0001819	synonymous_variant	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9852C>T	6.37:g.90403822G>A			90460543	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																				0.443	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90403822	G	A	90403822	2	1	61	1	0	0	0	0	0	0	0	1	9445	1045	37	1		1	MDN1	6	90403822	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9201	90403822	80711245	4783	12768										
MDN1	23195	broad.mit.edu	37	chr6	90406124	90406124	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgttagtccaaagcatcGaactgatgtcctggagctgc	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90406124G>A	ENST00000369393.3	-	60	9453	c.9338C>T	c.(9337-9339)tCg>tTg	p.S3113L	MDN1_ENST00000428876.1_Missense_Mutation_p.S3113L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3113					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.S3113L(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CCAAAGCATCGAACTGATGTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	81	84					6																	90406124		2203	4300	6503	90462845	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9338C>T	6.37:g.90406124G>A	ENSP00000358400:p.Ser3113Leu		90462845	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730536	0.30684	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03212	4.01;4.01	5.44	4.55	0.56014	.	0.214038	0.39083	N	0.001472	T	0.00845	0.0028	N	0.14661	0.345	0.35700	D	0.815532	B	0.11235	0.004	B	0.04013	0.001	T	0.41716	-0.9493	10	0.08599	T	0.76	.	13.3593	0.60646	0.0792:0.0:0.9208:0.0	.	3113	Q9NU22	MDN1_HUMAN	L	3113	ENSP00000358400:S3113L;ENSP00000413970:S3113L	ENSP00000358400:S3113L	S	-	2	0	MDN1	90462845	0.999000	0.42202	0.054000	0.19295	0.464000	0.32679	3.581000	0.53914	1.229000	0.43630	0.650000	0.86243	TCG		0.512	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90406124	G	A	90406124	3	1	61	1	0	0	0	0	1	0	0	0	9445	1059	37	1	7624	1	MDN1	6	90406124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2302	90406124	80708943	4784	12769										
MDN1	23195	broad.mit.edu	37	chr6	90421896	90421896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccagtaagtattcacttCgactgcattgaatttcaggt	8	8	2	1	rs200448957		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90421896C>T	ENST00000369393.3	-	49	7625	c.7510G>A	c.(7510-7512)Gaa>Aaa	p.E2504K	MDN1_ENST00000428876.1_Missense_Mutation_p.E2504K			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2504					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.E2504K(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTATTCACTTCGACTGCATTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	151	154	153		7510	3	0	6		153	0,8600		0,0,4300	no	missense	MDN1	NM_014611.1	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	2504/5597	90421896	1,13005	2203	4300	6503	90478617	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.7510G>A	6.37:g.90421896C>T	ENSP00000358400:p.Glu2504Lys		90478617	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870955	0.33069	2.27E-4	0.0	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03358	3.96;3.96	5.86	2.99	0.34606	.	0.415320	0.25860	N	0.027823	T	0.00815	0.0027	N	0.19112	0.55	0.26986	N	0.965244	B	0.21688	0.059	B	0.08055	0.003	T	0.47586	-0.9106	10	0.17369	T	0.5	.	11.2019	0.48747	0.0:0.6969:0.238:0.0651	.	2504	Q9NU22	MDN1_HUMAN	K	2504	ENSP00000358400:E2504K;ENSP00000413970:E2504K	ENSP00000358400:E2504K	E	-	1	0	MDN1	90478617	0.030000	0.19436	0.017000	0.16124	0.924000	0.55760	0.999000	0.29757	0.757000	0.33036	0.563000	0.77884	GAA		0.408	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90421896	C	T	90421896	3	4	61	1	0	0	0	0	1	0	0	0	9445	893	31	1	9496	1	MDN1	6	90421896	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15772	90421896	80693171	4785	12770										
MDN1	23195	broad.mit.edu	37	chr6	90440577	90440577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactatcttggcaagcctctTgattagaaatttcagacatt	6	8	3	3	rs552155845		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90440577T>C	ENST00000369393.3	-	35	5123	c.5008A>G	c.(5008-5010)Aag>Gag	p.K1670E	MDN1_ENST00000428876.1_Missense_Mutation_p.K1670E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1670					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.K1670E(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GCAAGCCTCTTGATTAGAAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											110	103	105					6																	90440577		2203	4300	6503	90497298	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.5008A>G	6.37:g.90440577T>C	ENSP00000358400:p.Lys1670Glu		90497298	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	6.787	0.514219	0.12944	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03004	4.08;4.08	5.51	5.51	0.81932	.	0.175288	0.50627	D	0.000114	T	0.00637	0.0021	N	0.16066	0.365	0.33083	D	0.53694	B	0.15719	0.014	B	0.13407	0.009	T	0.47328	-0.9126	10	0.02654	T	1	.	5.9083	0.19014	0.0:0.2054:0.0:0.7946	.	1670	Q9NU22	MDN1_HUMAN	E	1670	ENSP00000358400:K1670E;ENSP00000413970:K1670E	ENSP00000358400:K1670E	K	-	1	0	MDN1	90497298	0.933000	0.31639	0.995000	0.50966	0.276000	0.26787	1.062000	0.30555	2.086000	0.62901	0.477000	0.44152	AAG		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90440577	T	C	90440577	3	2	61	1	0	0	0	0	1	0	0	0	9445	1821	63	4	12054	4	MDN1	6	90440577	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18681	90440577	80674490	4786	12771										
MDN1	23195	broad.mit.edu	37	chr6	90481315	90481315	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtatcactttgttgattCatattgacaaccctcaaacg	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90481315C>A	ENST00000369393.3	-	15	2224	c.2109G>T	c.(2107-2109)atG>atT	p.M703I	MDN1_ENST00000428876.1_Missense_Mutation_p.M703I			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	703					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.M703I(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTTGTTGATTCATATTGACAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											116	110	112					6																	90481315		2203	4300	6503	90538036	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.2109G>T	6.37:g.90481315C>A	ENSP00000358400:p.Met703Ile		90538036	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894822	0.72639	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.41065	1.01;1.01;1.01	5.4	5.4	0.78164	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.49592	0.1566	L	0.40543	1.245	0.80722	D	1	D;P	0.63880	0.993;0.88	D;P	0.67103	0.949;0.876	T	0.47649	-0.9101	10	0.56958	D	0.05	.	19.5833	0.95478	0.0:1.0:0.0:0.0	.	630;703	Q5T795;Q9NU22	.;MDN1_HUMAN	I	703;703;630	ENSP00000358400:M703I;ENSP00000413970:M703I;ENSP00000409664:M630I	ENSP00000358400:M703I	M	-	3	0	MDN1	90538036	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.858000	0.75461	2.699000	0.92147	0.637000	0.83480	ATG		0.348	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90481315	C	A	90481315	3	1	61	1	0	0	0	0	1	0	0	0	9445	826	29	2	15033	2	MDN1	6	90481315	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40738	90481315	80633752	4787	12772										
MDN1	23195	broad.mit.edu	37	chr6	90503860	90503860	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcactattaaatatcttCttaagaaatgataacttgtg	4	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90503860C>A	ENST00000369393.3	-	4	736	c.621G>T	c.(619-621)aaG>aaT	p.K207N	MDN1_ENST00000428876.1_Missense_Mutation_p.K207N			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	207					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.K207N(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TAAATATCTTCTTAAGAAATG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											61	64	63					6																	90503860		2203	4300	6503	90560581	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.621G>T	6.37:g.90503860C>A	ENSP00000358400:p.Lys207Asn		90560581	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.736065	0.30774	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.28666	1.6;1.6;1.6	5.32	4.46	0.54185	.	0.229124	0.42682	D	0.000663	T	0.11067	0.0270	N	0.24115	0.695	0.37019	D	0.896129	B;B	0.28552	0.215;0.08	B;B	0.28784	0.094;0.029	T	0.05084	-1.0907	10	0.41790	T	0.15	.	13.9464	0.64086	0.0:0.9268:0.0:0.0732	.	207;207	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	N	207	ENSP00000358400:K207N;ENSP00000413970:K207N;ENSP00000409664:K207N	ENSP00000358400:K207N	K	-	3	2	MDN1	90560581	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.268000	0.58883	1.243000	0.43853	-0.262000	0.10625	AAG		0.328	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90503860	C	A	90503860	3	1	61	1	0	0	0	0	1	0	0	0	9445	912	32	2	16565	2	MDN1	6	90503860	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22545	90503860	80611207	4788	12773										
CASP8AP2	9994	broad.mit.edu	37	chr6	90571915	90571915	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatacagttaaaacaaaaGatcttaaatctagatctcca	4	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90571915G>T	ENST00000551025.1	+	0	1924									caspase 8 associated protein 2									p.D163Y(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TAAAACAAAAGATCTTAAATC	0.299																																					Colon(187;1656 2025 17045 31481 39901)											1	Substitution - Missense(1)	large_intestine(1)	6											73	67	69					6																	90571915		1825	4087	5912	90628636			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90571915G>T			90628636		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.299	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90571915	G	T	90571915	1	4	61	0	1	0	0	0	0	0	0	0	2684	942	33	2		2	CASP8AP2	6	90571915	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68055	90571915	80543152	4789	12774										
CASP8AP2	9994	broad.mit.edu	37	chr6	90572336	90572336	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagactgaaagcaaaagttCgaagtttaaaagtaactcag	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90572336C>T	ENST00000551025.1	+	0	2345									caspase 8 associated protein 2									p.S303L(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AGCAAAAGTTCGAAGTTTAAA	0.423																																					Colon(187;1656 2025 17045 31481 39901)											1	Substitution - Missense(1)	large_intestine(1)	6											127	130	129					6																	90572336		1872	4118	5990	90629057			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90572336C>T			90629057		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.423	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90572336	C	T	90572336	1	4	61	0	1	0	0	0	0	0	0	0	2684	893	31	1		1	CASP8AP2	6	90572336	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	421	90572336	80542731	4790	12775										
CASP8AP2	9994	broad.mit.edu	37	chr6	90578192	90578192	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcaaatattagacaattCtttgcaggctgatactgtag	8	7	2	2	rs377357235		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90578192C>A	ENST00000551025.1	+	0	6620									caspase 8 associated protein 2									p.S1728Y(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TTAGACAATTCTTTGCAGGCT	0.373																																					Colon(187;1656 2025 17045 31481 39901)											1	Substitution - Missense(1)	large_intestine(1)	6						C	TYR/SER,TYR/SER,TYR/SER	1,3725		0,1,1862	81	75	77		5183,5183,5183	3.3	0.9	6		77	0,8192		0,0,4096	no	missense,missense,missense	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	144,144,144	0,1,5958	AA,AC,CC		0.0,0.0268,0.0084	possibly-damaging,possibly-damaging,possibly-damaging	1728/1967,1728/1967,1728/1967	90578192	1,11917	1863	4096	5959	90634913			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90578192C>A			90634913		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.373	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90578192	C	A	90578192	1	1	61	0	1	0	0	0	0	0	0	0	2684	913	32	2		2	CASP8AP2	6	90578192	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5856	90578192	80536875	4791	12776										
GJA10	84694	broad.mit.edu	37	chr6	90604651	90604651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgaaaggatgtctgctgcGtacttatgtcttacacatct	8	9	4	1	rs150298953		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90604651G>A	ENST00000369352.1	+	1	464	c.464G>A	c.(463-465)cGt>cAt	p.R155H		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	155					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.R155H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		TGTCTGCTGCGTACTTATGTC	0.438													G|||	1	0.000199681	0	0	5008	,	,		20784	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	131	126	128		464	3.1	1	6	dbSNP_134	128	0,8600		0,0,4300	yes	missense	GJA10	NM_032602.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	155/544	90604651	1,13005	2203	4300	6503	90661372	SO:0001583	missense	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.464G>A	6.37:g.90604651G>A	ENSP00000358358:p.Arg155His		90661372	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002443	0.74932	2.27E-4	0.0	ENSG00000135355	ENST00000369352	D	0.97906	-4.6	4.91	3.14	0.36123	.	0.117649	0.64402	D	0.000011	D	0.97235	0.9096	M	0.62723	1.935	0.45704	D	0.998613	D	0.89917	1.0	D	0.71184	0.972	D	0.95831	0.8858	10	0.34782	T	0.22	.	11.3055	0.49332	0.1479:0.0:0.8521:0.0	.	155	Q969M2	CXA10_HUMAN	H	155	ENSP00000358358:R155H	ENSP00000358358:R155H	R	+	2	0	GJA10	90661372	1.000000	0.71417	0.981000	0.43875	0.995000	0.86356	5.475000	0.66787	0.684000	0.31448	0.563000	0.77884	CGT		0.438	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		A	90604651	G	A	90604651	3	1	61	1	0	0	0	0	1	0	0	0	6421	1145	40	1	466	1	GJA10	6	90604651	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26459	90604651	80510416	4792	12777										
GJA10	84694	broad.mit.edu	37	chr6	90605388	90605388	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaggtgagcctctcacaGatcttcatagtcactgcaga	8	13	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90605388G>T	ENST00000369352.1	+	1	1201	c.1201G>T	c.(1201-1203)Gat>Tat	p.D401Y	Y_RNA_ENST00000517082.1_RNA	NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	188					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.D401Y(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GCCTCTCACAGATCTTCATAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											72	72	72					6																	90605388		2203	4300	6503	90662109	SO:0001583	missense	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.1201G>T	6.37:g.90605388G>T	ENSP00000358358:p.Asp401Tyr		90662109	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.742826	0.89573	.	.	ENSG00000135355	ENST00000369352	D	0.98792	-5.14	5.6	4.68	0.58851	.	1.492200	0.03891	N	0.278628	D	0.98327	0.9445	M	0.61703	1.905	0.36407	D	0.863484	D	0.56521	0.976	P	0.53185	0.72	D	0.93682	0.6999	10	0.62326	D	0.03	.	14.2298	0.65885	0.0:0.0:0.8501:0.1499	.	401	Q969M2	CXA10_HUMAN	Y	401	ENSP00000358358:D401Y	ENSP00000358358:D401Y	D	+	1	0	GJA10	90662109	0.010000	0.17322	0.684000	0.30055	0.430000	0.31655	1.461000	0.35255	2.652000	0.90054	0.563000	0.77884	GAT		0.552	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90605388	G	T	90605388	3	4	61	1	0	0	0	0	1	0	0	0	6421	942	33	2	1203	2	GJA10	6	90605388	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	737	90605388	80509679	4793	12778										
GJA10	84694	broad.mit.edu	37	chr6	90605508	90605508	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagattgttgtctgaaaagCgacatctgcacagtgactca	9	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:90605508C>T	ENST00000369352.1	+	1	1321	c.1321C>T	c.(1321-1323)Cga>Tga	p.R441*	Y_RNA_ENST00000517082.1_RNA	NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	0					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.R441*(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GTCTGAAAAGCGACATCTGCA	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											123	119	120					6																	90605508		2203	4300	6503	90662229	SO:0001587	stop_gained	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.1321C>T	6.37:g.90605508C>T	ENSP00000358358:p.Arg441*		90662229	B2R722|B3KVQ2|Q5TA63|Q96KG0	Nonsense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970792	0.92919	.	.	ENSG00000135355	ENST00000369352	.	.	.	4.92	4.05	0.47172	.	1.180480	0.06368	N	0.713024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	8.5486	0.33438	0.0854:0.3947:0.5199:0.0	.	.	.	.	X	441	.	ENSP00000358358:R441X	R	+	1	2	GJA10	90662229	0.998000	0.40836	1.000000	0.80357	0.969000	0.65631	1.399000	0.34566	1.201000	0.43203	-0.344000	0.07964	CGA		0.532	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90605508	C	T	90605508	4	4	61	1	0	0	0	0	0	1	0	0	6421	760	27	1	1323	1	GJA10	6	90605508	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120	90605508	80509559	4794	12779										
MAP3K7	6885	broad.mit.edu	37	chr6	91256990	91256990	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttacctgtggttgcggcGatcctagcttctatttcaga	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:91256990G>A	ENST00000369329.3	-	11	1358	c.1197C>T	c.(1195-1197)atC>atT	p.I399I	MAP3K7_ENST00000369320.1_Silent_p.I80I|MAP3K7_ENST00000369332.3_Silent_p.I399I|MAP3K7_ENST00000369327.3_Silent_p.I399I|MAP3K7_ENST00000369325.3_Silent_p.I399I	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	399					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)	p.I399I(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		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)		TGGTTGCGGCGATCCTAGCTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	6											195	197	196					6																	91256990		2203	4300	6503	91313711	SO:0001819	synonymous_variant	6885			AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1197C>T	6.37:g.91256990G>A			91313711	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Silent	SNP	ENST00000369329.3	37	CCDS5028.1																																																																																				0.473	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		A	91256990	G	A	91256990	2	1	61	1	0	0	0	0	0	0	0	1	9285	1048	37	1		1	MAP3K7	6	91256990	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	651482	91256990	79858077	4795	12780										
MAP3K7	6885	broad.mit.edu	37	chr6	91257801	91257801	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttcaacaattttgattCtaagcgcttaatagtatcat	4	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:91257801C>A	ENST00000369329.3	-	10	1206	c.1045G>T	c.(1045-1047)Gaa>Taa	p.E349*	MAP3K7_ENST00000369320.1_Nonsense_Mutation_p.E30*|MAP3K7_ENST00000369332.3_Nonsense_Mutation_p.E349*|MAP3K7_ENST00000369327.3_Nonsense_Mutation_p.E349*|MAP3K7_ENST00000369325.3_Nonsense_Mutation_p.E349*	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	349					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)	p.E349*(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		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)		AATTTTGATTCTAAGCGCTTA	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											163	157	159					6																	91257801		2203	4299	6502	91314522	SO:0001587	stop_gained	6885			AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1045G>T	6.37:g.91257801C>A	ENSP00000358335:p.Glu349*		91314522	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Nonsense_Mutation	SNP	ENST00000369329.3	37	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	C	37	6.282638	0.97440	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327;ENST00000369320;ENST00000450832	.	.	.	6.07	6.07	0.98685	.	0.100388	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.6525	0.99598	0.0:1.0:0.0:0.0	.	.	.	.	X	349;349;349;349;30;276	.	ENSP00000358326:E30X	E	-	1	0	MAP3K7	91314522	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.474000	0.60203	2.890000	0.99128	0.585000	0.79938	GAA		0.348	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		A	91257801	C	A	91257801	4	1	61	1	0	0	0	0	0	1	0	0	9285	922	32	2	807	2	MAP3K7	6	91257801	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	811	91257801	79857266	4796	12781										
MAP3K7	6885	broad.mit.edu	37	chr6	91281450	91281450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcctctcagattcacttTctatttgtttaatagcaaca	3	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:91281450T>C	ENST00000369329.3	-	2	358	c.197A>G	c.(196-198)gAa>gGa	p.E66G	MAP3K7_ENST00000369332.3_Missense_Mutation_p.E66G|MAP3K7_ENST00000369327.3_Missense_Mutation_p.E66G|MAP3K7_ENST00000369325.3_Missense_Mutation_p.E66G	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	66	Interaction with MAPK8IP1. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)	p.E66G(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		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)		AGATTCACTTTCTATTTGTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	6											155	141	146					6																	91281450		2203	4299	6502	91338171	SO:0001583	missense	6885			AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.197A>G	6.37:g.91281450T>C	ENSP00000358335:p.Glu66Gly		91338171	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Missense_Mutation	SNP	ENST00000369329.3	37	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	T	18.93	3.726924	0.69074	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327;ENST00000450832	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.57	5.57	0.84162	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77498	0.4139	N	0.26042	0.785	0.80722	D	1	P;B;D;B	0.59357	0.87;0.133;0.985;0.307	B;B;P;B	0.55615	0.244;0.064;0.78;0.106	T	0.79115	-0.1936	10	0.38643	T	0.18	.	15.7394	0.77876	0.0:0.0:0.0:1.0	.	66;66;66;66	O43318-4;O43318-2;O43318-3;O43318	.;.;.;M3K7_HUMAN	G	66	ENSP00000358338:E66G;ENSP00000358335:E66G;ENSP00000358331:E66G;ENSP00000358333:E66G	ENSP00000358331:E66G	E	-	2	0	MAP3K7	91338171	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.789000	0.85783	2.122000	0.65172	0.455000	0.32223	GAA		0.333	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		C	91281450	T	C	91281450	3	2	61	1	0	0	0	0	1	0	0	0	9285	1783	62	4	1687	4	MAP3K7	6	91281450	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	23649	91281450	79833617	4797	12782										
EPHA7	2045	broad.mit.edu	37	chr6	93956553	93956553	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagactatttgggtttcGaatcattttgtctagaattc	7	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:93956553G>A	ENST00000369303.4	-	15	2867	c.2683C>T	c.(2683-2685)Cga>Tga	p.R895*		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	895					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.R895*(2)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TTTGGGTTTCGAATCATTTTG	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											135	129	131					6																	93956553		2203	4300	6503	94013274	SO:0001587	stop_gained	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2683C>T	6.37:g.93956553G>A	ENSP00000358309:p.Arg895*		94013274	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Nonsense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	40	8.444810	0.98815	.	.	ENSG00000135333	ENST00000369303	.	.	.	5.74	2.52	0.30459	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5944	0.84792	0.0:0.0:0.609:0.391	.	.	.	.	X	895	.	ENSP00000358309:R895X	R	-	1	2	EPHA7	94013274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.145000	0.50623	0.700000	0.31782	0.591000	0.81541	CGA		0.413	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93956553	G	A	93956553	4	1	61	1	0	0	0	0	0	1	0	0	5185	1066	37	1	325	1	EPHA7	6	93956553	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2675103	93956553	77158514	4798	12783										
FUT9	10690	broad.mit.edu	37	chr6	96651688	96651688	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaaatccatacctacggGcaagcatttggagaatatgt	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:96651688G>A	ENST00000302103.5	+	3	983	c.657G>A	c.(655-657)ggG>ggA	p.G219G		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	219					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.G219G(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		ATACCTACGGGCAAGCATTTG	0.363																																					Melanoma(98;1369 1476 6592 22940 26587)											1	Substitution - coding silent(1)	large_intestine(1)	6											53	52	53					6																	96651688		2203	4300	6503	96758409	SO:0001819	synonymous_variant	10690			AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.657G>A	6.37:g.96651688G>A			96758409	Q5T0W4	Silent	SNP	ENST00000302103.5	37	CCDS5033.1																																																																																				0.363	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		A	96651688	G	A	96651688	2	1	61	1	0	0	0	0	0	0	0	1	6130	1190	42	3		3	FUT9	6	96651688	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2695135	96651688	74463379	4799	12784										
KIAA0776	23376	broad.mit.edu	37	chr6	96990864	96990864	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaaaagatgatgatagTgatgatgaatctcaatcatc	10	4	2	7	rs144746493		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:96990864T>G	ENST00000369278.4	+	12	1440	c.1374T>G	c.(1372-1374)agT>agG	p.S458R		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	458					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.S458R(1)									ATGATGATAGTGATGATGAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	98	99					6																	96990864		2203	4300	6503	97097585	SO:0001583	missense	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1374T>G	6.37:g.96990864T>G	ENSP00000358283:p.Ser458Arg		97097585	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	T	8.507	0.865650	0.17250	.	.	ENSG00000014123	ENST00000369278	T	0.49432	0.78	5.92	2.33	0.28932	.	0.171277	0.64402	D	0.000003	T	0.20414	0.0491	L	0.60455	1.87	0.51012	D	0.999908	B	0.34103	0.437	B	0.29942	0.109	T	0.04029	-1.0983	10	0.21014	T	0.42	-3.417	8.6607	0.34091	0.0:0.2163:0.0:0.7837	.	458	O94874	UFL1_HUMAN	R	458	ENSP00000358283:S458R	ENSP00000358283:S458R	S	+	3	2	KIAA0776	97097585	0.997000	0.39634	1.000000	0.80357	0.145000	0.21501	0.281000	0.18810	0.502000	0.28037	0.533000	0.62120	AGT		0.383	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		G	96990864	T	G	96990864	3	3	61	1	0	0	0	0	1	0	0	0	8214	1693	59	4	1420	4	KIAA0776	6	96990864	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	339176	96990864	74124203	4800	12785										
KIAA0776	23376	broad.mit.edu	37	chr6	96997643	96997643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcttcggatttaatgatgGcagtagacgatcctgcagcc	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:96997643G>A	ENST00000369278.4	+	15	1852	c.1786G>A	c.(1786-1788)Gca>Aca	p.A596T		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	596					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.A596T(1)									TTTAATGATGGCAGTAGACGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	123	129					6																	96997643		2203	4300	6503	97104364	SO:0001583	missense	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1786G>A	6.37:g.96997643G>A	ENSP00000358283:p.Ala596Thr		97104364	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697285	0.48202	.	.	ENSG00000014123	ENST00000369278	T	0.46063	0.88	5.64	4.76	0.60689	.	0.153604	0.64402	D	0.000014	T	0.12220	0.0297	L	0.28740	0.885	0.44899	D	0.997919	B	0.24721	0.11	B	0.16722	0.016	T	0.08207	-1.0733	10	0.15499	T	0.54	-12.7801	8.5182	0.33259	0.0834:0.0:0.7608:0.1559	.	596	O94874	UFL1_HUMAN	T	596	ENSP00000358283:A596T	ENSP00000358283:A596T	A	+	1	0	KIAA0776	97104364	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.819000	0.39022	1.350000	0.45770	0.655000	0.94253	GCA		0.383	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		A	96997643	G	A	96997643	3	1	61	1	0	0	0	0	1	0	0	0	8214	1203	42	3	1844	3	KIAA0776	6	96997643	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6779	96997643	74117424	4801	12786										
FHL5	9457	broad.mit.edu	37	chr6	97063641	97063641	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctccggaatggacactgAcatctaggagacagtccttg	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:97063641A>C	ENST00000326771.2	+	7	1228	c.848A>C	c.(847-849)gAc>gCc	p.D283A	FHL5_ENST00000541107.1_Missense_Mutation_p.D283A	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	283	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.D283A(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ATGGACACTGACATCTAGGAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	67	68					6																	97063641		2203	4300	6503	97170362	SO:0001583	missense	9457			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.848A>C	6.37:g.97063641A>C	ENSP00000326022:p.Asp283Ala		97170362	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.590306	0.46214	.	.	ENSG00000112214	ENST00000541107;ENST00000326771	T;T	0.58060	0.36;0.36	5.12	3.97	0.46021	Zinc finger, LIM-type (1);	0.000000	0.42548	D	0.000681	T	0.16557	0.0398	N	0.14661	0.345	0.31106	N	0.71048	B	0.23377	0.084	B	0.17979	0.02	T	0.07849	-1.0751	10	0.87932	D	0	.	8.4933	0.33112	0.9119:0.0:0.0881:0.0	.	283	Q5TD97	FHL5_HUMAN	A	283	ENSP00000442357:D283A;ENSP00000326022:D283A	ENSP00000326022:D283A	D	+	2	0	FHL5	97170362	1.000000	0.71417	0.190000	0.23270	0.021000	0.10359	2.727000	0.47311	0.974000	0.38366	-0.256000	0.11100	GAC		0.448	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		C	97063641	A	C	97063641	3	2	61	1	0	0	0	0	1	0	0	0	5900	275	10	4	866	4	FHL5	6	97063641	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	65998	97063641	74051426	4802	12787										
GPR63	81491	broad.mit.edu	37	chr6	97246362	97246362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatattcacaccaccgtccGatgttccccacacacataga	4	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:97246362G>A	ENST00000229955.3	-	2	1591	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	GPR63_ENST00000417980.1_Missense_Mutation_p.R416W|RP3-417O22.3_ENST00000442184.1_RNA	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	416						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.R416W(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		ACCACCGTCCGATGTTCCCCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											143	116	125					6																	97246362		2203	4300	6503	97353083	SO:0001583	missense	81491			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.1246C>T	6.37:g.97246362G>A	ENSP00000229955:p.Arg416Trp		97353083	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456555	0.63401	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.63580	-0.05;-0.05;-0.05	5.35	3.42	0.39159	.	0.000000	0.64402	D	0.000001	T	0.56093	0.1962	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.65063	-0.6259	10	0.87932	D	0	-7.7627	13.2629	0.60115	0.0:0.0:0.5948:0.4051	.	416	Q9BZJ6	GPR63_HUMAN	W	440;416;416;416	ENSP00000393170:R416W;ENSP00000229955:R416W;ENSP00000358273:R416W	ENSP00000229955:R416W	R	-	1	2	GPR63	97353083	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.194000	0.65125	1.373000	0.46208	0.650000	0.86243	CGG		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			A	97246362	G	A	97246362	3	1	61	1	0	0	0	0	1	0	0	0	6724	1057	37	1	17	1	GPR63	6	97246362	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182721	97246362	73868705	4803	12788										
GPR63	81491	broad.mit.edu	37	chr6	97246901	97246901	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataagcctggtagcctggaTtggttgtgtacccaaacaca	10	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:97246901T>G	ENST00000229955.3	-	2	1052	c.707A>C	c.(706-708)aAt>aCt	p.N236T	GPR63_ENST00000417980.1_Missense_Mutation_p.N236T	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.N236T(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		GTAGCCTGGATTGGTTGTGTA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	6											78	83	81					6																	97246901		2203	4300	6503	97353622	SO:0001583	missense	81491			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.707A>C	6.37:g.97246901T>G	ENSP00000229955:p.Asn236Thr		97353622	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	T	2.300	-0.360312	0.05103	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.33438	1.41;1.41;1.41	5.2	2.81	0.32909	GPCR, rhodopsin-like superfamily (1);	0.405452	0.26532	N	0.023854	T	0.11196	0.0273	L	0.57536	1.79	0.09310	N	1	B	0.14805	0.011	B	0.23852	0.049	T	0.32929	-0.9888	10	0.21540	T	0.41	-5.6066	7.9392	0.29948	0.0:0.2967:0.0:0.7033	.	236	Q9BZJ6	GPR63_HUMAN	T	260;236;236;236	ENSP00000393170:N236T;ENSP00000229955:N236T;ENSP00000358273:N236T	ENSP00000229955:N236T	N	-	2	0	GPR63	97353622	0.404000	0.25328	0.002000	0.10522	0.942000	0.58702	2.529000	0.45632	0.399000	0.25367	-0.256000	0.11100	AAT		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			G	97246901	T	G	97246901	3	3	61	1	0	0	0	0	1	0	0	0	6724	1493	52	4	556	4	GPR63	6	97246901	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	539	97246901	73868166	4804	12789										
KLHL32	114792	broad.mit.edu	37	chr6	97561953	97561953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcaaggtcaaggaacttCggtacttcaatcctgttgat	9	9	3	1	rs35641414		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:97561953C>T	ENST00000369261.4	+	7	1285	c.922C>T	c.(922-924)Cgg>Tgg	p.R308W	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Missense_Mutation_p.R239W|KLHL32_ENST00000536676.1_Missense_Mutation_p.R272W	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	308								p.R308W(1)		breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		CAAGGAACTTCGGTACTTCAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	80	80					6																	97561953		2203	4300	6503	97668674	SO:0001583	missense	114792			AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.922C>T	6.37:g.97561953C>T	ENSP00000358265:p.Arg308Trp		97668674	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.243638	0.79912	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.66280	-0.2;-0.2;-0.2	5.5	5.5	0.81552	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.67021	0.2849	L	0.42245	1.32	0.80722	D	1	D;D;B;D	0.89917	1.0;1.0;0.033;1.0	D;D;B;D	0.81914	0.93;0.993;0.003;0.995	T	0.69412	-0.5152	10	0.87932	D	0	.	14.4399	0.67309	0.1471:0.8529:0.0:0.0	.	239;272;308;308	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	W	308;272;239	ENSP00000358265:R308W;ENSP00000440382:R272W;ENSP00000441527:R239W	ENSP00000358265:R308W	R	+	1	2	KLHL32	97668674	1.000000	0.71417	0.982000	0.44146	0.939000	0.58152	5.439000	0.66556	2.854000	0.98071	0.655000	0.94253	CGG		0.527	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97561953	C	T	97561953	3	4	61	1	0	0	0	0	1	0	0	0	8407	875	31	1	944	1	KLHL32	6	97561953	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	315052	97561953	73553114	4805	12790										
C6orf167	253714	broad.mit.edu	37	chr6	97715856	97715856	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacttgccagattcataaaCtgatgaccatatacaacttg	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:97715856C>T	ENST00000275053.4	-	8	985	c.720G>A	c.(718-720)caG>caA	p.Q240Q	MMS22L_ENST00000506256.1_5'UTR|MMS22L_ENST00000369251.2_Silent_p.Q240Q	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	240					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)		p.Q240Q(1)		breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						GATTCATAAACTGATGACCAT	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	6											76	72	73					6																	97715856		2203	4299	6502	97822577	SO:0001819	synonymous_variant	253714				CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.720G>A	6.37:g.97715856C>T			97822577	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Silent	SNP	ENST00000275053.4	37	CCDS5039.1																																																																																				0.308	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		T	97715856	C	T	97715856	2	4	61	1	0	0	0	0	0	0	0	1	2348	564	20	3		3	C6orf167	6	97715856	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153903	97715856	73399211	4806	12791										
POU3F2	5454	broad.mit.edu	37	chr6	99283719	99283719	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcaagaacatgtgcaagCtgaagcctttgttgaacaag	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99283719C>T	ENST00000328345.5	+	1	1140	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	324	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L324L(1)		endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		CATGTGCAAGCTGAAGCCTTT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	6											135	137	136					6																	99283719		2203	4300	6503	99390440	SO:0001819	synonymous_variant	5454			Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.970C>T	6.37:g.99283719C>T			99390440	Q14960|Q86V54|Q9UJL0	Silent	SNP	ENST00000328345.5	37	CCDS5040.1																																																																																				0.587	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			T	99283719	C	T	99283719	2	4	61	1	0	0	0	0	0	0	0	1	12306	796	28	3		3	POU3F2	6	99283719	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1567863	99283719	71831348	4807	12792										
POU3F2	5454	broad.mit.edu	37	chr6	99283793	99283793	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacgagcatagacaagatCgcagcgcaagggcgcaagcg	13	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99283793C>T	ENST00000328345.5	+	1	1214	c.1044C>T	c.(1042-1044)atC>atT	p.I348I		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	348					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I348I(1)		endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		TAGACAAGATCGCAGCGCAAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	6											84	92	89					6																	99283793		2203	4300	6503	99390514	SO:0001819	synonymous_variant	5454			Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.1044C>T	6.37:g.99283793C>T			99390514	Q14960|Q86V54|Q9UJL0	Silent	SNP	ENST00000328345.5	37	CCDS5040.1																																																																																				0.592	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			T	99283793	C	T	99283793	2	4	61	1	0	0	0	0	0	0	0	1	12306	874	31	1		1	POU3F2	6	99283793	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74	99283793	71831274	4808	12793										
FBXL4	26235	broad.mit.edu	37	chr6	99323498	99323498	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacacccagaagccagttCtgctattccattctcagtaa	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99323498C>A	ENST00000369244.2	-	9	1923	c.1495G>T	c.(1495-1497)Gaa>Taa	p.E499*	FBXL4_ENST00000229971.1_Nonsense_Mutation_p.E499*	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	499					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.E499*(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		GAAGCCAGTTCTGCTATTCCA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											85	83	84					6																	99323498		2203	4300	6503	99430219	SO:0001587	stop_gained	26235			AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1495G>T	6.37:g.99323498C>A	ENSP00000358247:p.Glu499*		99430219	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Nonsense_Mutation	SNP	ENST00000369244.2	37	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	C	40	8.468081	0.98825	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	.	.	.	5.82	4.9	0.64082	.	0.044485	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	16.388	0.83522	0.0:0.8684:0.1316:0.0	.	.	.	.	X	499	.	ENSP00000229971:E499X	E	-	1	0	FBXL4	99430219	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.550000	0.67268	2.754000	0.94517	0.591000	0.81541	GAA		0.507	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			A	99323498	C	A	99323498	4	1	61	1	0	0	0	0	0	1	0	0	5740	922	32	2	378	2	FBXL4	6	99323498	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39705	99323498	71791569	4809	12794										
C6orf168	84553	broad.mit.edu	37	chr6	99739652	99739652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtgtccaaagacagtggCgtcaagagtggaaagcttgg	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99739652C>T	ENST00000389677.5	-	5	1150	c.868G>A	c.(868-870)Gcc>Acc	p.A290T	FAXC_ENST00000538471.1_Missense_Mutation_p.A10T	NM_032511.2	NP_115900.1	Q5TGI0	FAXC_HUMAN	failed axon connections homolog (Drosophila)	290						integral component of membrane (GO:0016021)		p.A290T(1)									AAGACAGTGGCGTCAAGAGTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											191	176	181					6																	99739652		2203	4300	6503	99846373	SO:0001583	missense	84553			BC011583	CCDS34500.1	6q16.3	2012-02-07	2012-02-07	2012-02-07	ENSG00000146267	ENSG00000146267			20742	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 168"	C6orf168		12477932	Standard	NM_032511		Approved	MGC2817, dJ273F20	uc003ppj.4	Q5TGI0	OTTHUMG00000015261	ENST00000389677.5:c.868G>A	6.37:g.99739652C>T	ENSP00000374328:p.Ala290Thr		99846373	B3KU39|Q96F61|Q96LU3|Q9BR58|Q9BSS2	Missense_Mutation	SNP	ENST00000389677.5	37	CCDS34500.1	.	.	.	.	.	.	.	.	.	.	C	34	5.348593	0.95807	.	.	ENSG00000146267	ENST00000389677;ENST00000538471	T;T	0.50548	0.74;0.74	5.87	5.87	0.94306	Glutathione S-transferase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.68293	0.2985	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71560	-0.4556	10	0.62326	D	0.03	-21.4558	17.99	0.89165	0.0:1.0:0.0:0.0	.	290	Q5TGI0	CF168_HUMAN	T	290;10	ENSP00000374328:A290T;ENSP00000445267:A10T	ENSP00000374328:A290T	A	-	1	0	C6orf168	99846373	1.000000	0.71417	0.973000	0.42090	0.981000	0.71138	7.137000	0.77295	2.774000	0.95407	0.643000	0.83706	GCC		0.512	FAXC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041589.4	NM_032511		T	99739652	C	T	99739652	3	4	61	1	0	0	0	0	1	0	0	0	2349	768	27	1	369	1	C6orf168	6	99739652	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	416154	99739652	71375415	4810	12795										
C6orf168	84553	broad.mit.edu	37	chr6	99790884	99790884	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatgcaaaataatagcatCtttagagtcaatctcttgct	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99790884C>T	ENST00000389677.5	-	2	574	c.292G>A	c.(292-294)Gat>Aat	p.D98N	FAXC_ENST00000538471.1_5'Flank	NM_032511.2	NP_115900.1	Q5TGI0	FAXC_HUMAN	failed axon connections homolog (Drosophila)	98						integral component of membrane (GO:0016021)		p.D98N(1)									ATAATAGCATCTTTAGAGTCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											145	127	133					6																	99790884		2203	4300	6503	99897605	SO:0001583	missense	84553			BC011583	CCDS34500.1	6q16.3	2012-02-07	2012-02-07	2012-02-07	ENSG00000146267	ENSG00000146267			20742	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 168"	C6orf168		12477932	Standard	NM_032511		Approved	MGC2817, dJ273F20	uc003ppj.4	Q5TGI0	OTTHUMG00000015261	ENST00000389677.5:c.292G>A	6.37:g.99790884C>T	ENSP00000374328:p.Asp98Asn		99897605	B3KU39|Q96F61|Q96LU3|Q9BR58|Q9BSS2	Missense_Mutation	SNP	ENST00000389677.5	37	CCDS34500.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634299	0.87660	.	.	ENSG00000146267	ENST00000389677	.	.	.	5.6	4.74	0.60224	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.55800	0.1943	M	0.67397	2.05	0.80722	D	1	P	0.51537	0.946	P	0.53313	0.723	T	0.56890	-0.7904	9	0.33141	T	0.24	-12.6342	14.4026	0.67060	0.0:0.929:0.0:0.071	.	98	Q5TGI0	CF168_HUMAN	N	98	.	ENSP00000374328:D98N	D	-	1	0	C6orf168	99897605	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	1.379000	0.46325	0.655000	0.94253	GAT		0.358	FAXC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041589.4	NM_032511		T	99790884	C	T	99790884	3	4	61	1	0	0	0	0	1	0	0	0	2349	913	32	3	957	3	C6orf168	6	99790884	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51232	99790884	71324183	4811	12796										
SFRS18	25957	broad.mit.edu	37	chr6	99849089	99849089	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctagccctattgctctctAttttaattctgcgagaatag	6	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99849089A>T	ENST00000369239.5	-	12	1949	c.1745T>A	c.(1744-1746)aTa>aAa	p.I582K	PNISR_ENST00000438806.1_Missense_Mutation_p.I582K	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	582						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I582K(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						ATTGCTCTCTATTTTAATTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	121	119					6																	99849089		2203	4300	6503	99955810	SO:0001583	missense	25957			AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1745T>A	6.37:g.99849089A>T	ENSP00000358242:p.Ile582Lys		99955810	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	37	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	A	3.210	-0.161857	0.06502	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	.	.	.	5.49	1.65	0.23941	.	0.460942	0.22918	N	0.054055	T	0.10852	0.0265	N	0.14661	0.345	0.37544	D	0.918437	B	0.06786	0.001	B	0.04013	0.001	T	0.25117	-1.0141	9	0.05436	T	0.98	.	8.1264	0.31001	0.4017:0.5137:0.0846:0.0	.	582	Q8TF01	PNISR_HUMAN	K	582	.	ENSP00000358242:I582K	I	-	2	0	PNISR	99955810	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.983000	0.49345	1.004000	0.39156	0.472000	0.43445	ATA		0.403	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		T	99849089	A	T	99849089	3	4	61	1	0	0	0	0	1	0	0	0	14211	449	16	5	676	5	SFRS18	6	99849089	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	58205	99849089	71265978	4812	12797										
USP45	85015	broad.mit.edu	37	chr6	99894322	99894322	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattttctaatacattttcgGtcatgaattagttgactctg	6	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:99894322G>A	ENST00000327681.6	-	14	1858	c.1326C>T	c.(1324-1326)gaC>gaT	p.D442D	USP45_ENST00000500704.2_Silent_p.D442D|USP45_ENST00000369233.2_Silent_p.D394D|USP45_ENST00000539675.1_Intron|USP45_ENST00000392738.2_Silent_p.D122D	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	442	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.D442D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		TACATTTTCGGTCATGAATTA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	6											32	31	31					6																	99894322		2203	4300	6503	100001043	SO:0001819	synonymous_variant	85015			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1326C>T	6.37:g.99894322G>A			100001043	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	37	CCDS34501.1																																																																																				0.323	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		A	99894322	G	A	99894322	2	1	61	1	0	0	0	0	0	0	0	1	17116	1252	44	3		3	USP45	6	99894322	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45233	99894322	71220745	4813	12798										
MCHR2	84539	broad.mit.edu	37	chr6	100403892	100403892	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaccagccctgttgaacaGataatcccaatcatggaagg	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:100403892G>T	ENST00000281806.2	-	2	446	c.132C>A	c.(130-132)atC>atA	p.I44I	MCHR2_ENST00000369212.2_Silent_p.I44I	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I44I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		CTGTTGAACAGATAATCCCAA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	6											116	108	110					6																	100403892		2203	4300	6503	100510613	SO:0001819	synonymous_variant	84539			AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"GPCR / Class A : MCH receptors"	20867	protein-coding gene	gene with protein product		606111	"G protein-coupled receptor 145"	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.132C>A	6.37:g.100403892G>T			100510613	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Silent	SNP	ENST00000281806.2	37	CCDS5044.1																																																																																				0.388	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503		T	100403892	G	T	100403892	2	4	61	1	0	0	0	0	0	0	0	1	9413	932	33	2		2	MCHR2	6	100403892	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	509570	100403892	70711175	4814	12799										
MCHR2	84539	broad.mit.edu	37	chr6	100403984	100403984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggatttgtttaaaagttCggcagaggtgttccaacaag	11	7	0	1	rs142259467		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:100403984C>T	ENST00000281806.2	-	2	354	c.40G>A	c.(40-42)Gaa>Aaa	p.E14K	MCHR2_ENST00000369212.2_Missense_Mutation_p.E14K	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E14K(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TTTAAAAGTTCGGCAGAGGTG	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	6											144	145	145					6																	100403984		2203	4300	6503	100510705	SO:0001583	missense	84539			AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"GPCR / Class A : MCH receptors"	20867	protein-coding gene	gene with protein product		606111	"G protein-coupled receptor 145"	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.40G>A	6.37:g.100403984C>T	ENSP00000281806:p.Glu14Lys		100510705	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Missense_Mutation	SNP	ENST00000281806.2	37	CCDS5044.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320291	0.41096	.	.	ENSG00000152034	ENST00000445970;ENST00000281806;ENST00000369212	T;T;T	0.69306	-0.39;-0.39;-0.39	4.86	3.98	0.46160	.	0.459428	0.18287	N	0.145830	T	0.25306	0.0615	L	0.27053	0.805	0.23325	N	0.9979	B	0.27853	0.191	B	0.15052	0.012	T	0.10245	-1.0638	10	0.06099	T	0.92	.	11.704	0.51587	0.0:0.9058:0.0:0.0942	.	14	Q969V1	MCHR2_HUMAN	K	14	ENSP00000403490:E14K;ENSP00000281806:E14K;ENSP00000358214:E14K	ENSP00000281806:E14K	E	-	1	0	MCHR2	100510705	0.715000	0.27946	0.967000	0.41034	0.528000	0.34623	1.606000	0.36826	2.386000	0.81285	0.561000	0.74099	GAA		0.388	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503		T	100403984	C	T	100403984	3	4	61	1	0	0	0	0	1	0	0	0	9413	893	31	1	1002	1	MCHR2	6	100403984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92	100403984	70711083	4815	12800										
ASCC3	10973	broad.mit.edu	37	chr6	101214448	101214448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaacaacatacctgagttCgtaaaatttcacttttggac	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:101214448C>T	ENST00000369162.2	-	10	2074	c.1730G>A	c.(1729-1731)cGa>cAa	p.R577Q	ASCC3_ENST00000522650.1_Missense_Mutation_p.R577Q	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	577	Helicase ATP-binding 1. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.R577Q(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TACCTGAGTTCGTAAAATTTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	111	112					6																	101214448		2203	4300	6503	101321169	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.1730G>A	6.37:g.101214448C>T	ENSP00000358159:p.Arg577Gln		101321169	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.079089	0.55753	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.35048	1.33;1.33	5.3	5.3	0.74995	DEAD-like helicase (2);ATPase, AAA+ type, core (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.11196	0.0273	N	0.11427	0.14	0.80722	D	1	P;B	0.40250	0.709;0.307	B;B	0.33890	0.172;0.069	T	0.06215	-1.0839	10	0.23302	T	0.38	.	19.3125	0.94195	0.0:1.0:0.0:0.0	.	577;577	E7EW23;Q8N3C0	.;HELC1_HUMAN	Q	577	ENSP00000358159:R577Q;ENSP00000430769:R577Q	ENSP00000358159:R577Q	R	-	2	0	ASCC3	101321169	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.445000	0.80570	2.636000	0.89361	0.591000	0.81541	CGA		0.318	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101214448	C	T	101214448	3	4	61	1	0	0	0	0	1	0	0	0	1034	884	31	1	5010	1	ASCC3	6	101214448	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	810464	101214448	69900619	4816	12801										
ASCC3	10973	broad.mit.edu	37	chr6	101248365	101248365	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttagcattttctcctaaaAtttttttacaattgtctaag	4	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:101248365A>T	ENST00000369162.2	-	6	1282	c.938T>A	c.(937-939)aTt>aAt	p.I313N	ASCC3_ENST00000522650.1_Missense_Mutation_p.I313N	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	313					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.I313N(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TTCTCCTAAAATTTTTTTACA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	6											46	44	45					6																	101248365		2200	4298	6498	101355086	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.938T>A	6.37:g.101248365A>T	ENSP00000358159:p.Ile313Asn		101355086	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457177	0.26161	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.49139	0.79;0.79	5.51	5.51	0.81932	.	0.467407	0.22701	N	0.056693	T	0.14270	0.0345	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.09840	-1.0656	10	0.17369	T	0.5	.	15.6243	0.76840	1.0:0.0:0.0:0.0	.	313;313	E7EW23;Q8N3C0	.;HELC1_HUMAN	N	313	ENSP00000358159:I313N;ENSP00000430769:I313N	ENSP00000358159:I313N	I	-	2	0	ASCC3	101355086	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.640000	0.54350	2.091000	0.63221	0.459000	0.35465	ATT		0.303	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101248365	A	T	101248365	3	4	61	1	0	0	0	0	1	0	0	0	1034	101	4	5	5818	5	ASCC3	6	101248365	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33917	101248365	69866702	4817	12802										
ASCC3	10973	broad.mit.edu	37	chr6	101296492	101296492	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgtttgatagcctttgtTtccttgtgaccaacagagtc	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:101296492T>G	ENST00000369162.2	-	4	677	c.333A>C	c.(331-333)gaA>gaC	p.E111D	ASCC3_ENST00000522650.1_Missense_Mutation_p.E111D	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	111					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.E111D(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TAGCCTTTGTTTCCTTGTGAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											69	70	69					6																	101296492		2203	4299	6502	101403213	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.333A>C	6.37:g.101296492T>G	ENSP00000358159:p.Glu111Asp		101403213	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.580444	0.46006	.	.	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723	T;T;T	0.61742	0.29;0.08;0.51	5.85	2.67	0.31697	.	0.000000	0.85682	D	0.000000	T	0.61664	0.2365	M	0.61703	1.905	0.80722	D	1	D;D;P	0.76494	0.999;0.999;0.842	D;D;B	0.78314	0.991;0.991;0.237	T	0.65738	-0.6095	10	0.66056	D	0.02	.	10.9099	0.47103	0.0:0.7029:0.0:0.2971	.	111;111;111	Q4G1A0;E7EW23;Q8N3C0	.;.;HELC1_HUMAN	D	111	ENSP00000358159:E111D;ENSP00000430769:E111D;ENSP00000320777:E111D	ENSP00000320777:E111D	E	-	3	2	ASCC3	101403213	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.775000	0.26689	0.800000	0.34041	-0.242000	0.12053	GAA		0.398	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		G	101296492	T	G	101296492	3	3	61	1	0	0	0	0	1	0	0	0	1034	1838	64	4	6431	4	ASCC3	6	101296492	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	48127	101296492	69818575	4818	12803										
GRIK2	2898	broad.mit.edu	37	chr6	102074301	102074301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccatcttcgggccttcAcacagctcatcagcaaacgc	8	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:102074301A>G	ENST00000421544.1	+	3	820	c.330A>G	c.(328-330)tcA>tcG	p.S110S	GRIK2_ENST00000369137.3_Silent_p.S110S|GRIK2_ENST00000318991.6_Silent_p.S110S|GRIK2_ENST00000369138.1_Silent_p.S110S|GRIK2_ENST00000413795.1_Silent_p.S110S|GRIK2_ENST00000369134.4_Silent_p.S61S|GRIK2_ENST00000358361.3_Silent_p.S110S	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	110					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.S110S(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TCGGGCCTTCACACAGCTCAT	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	6											171	172	172					6																	102074301		2203	4300	6503	102180994	SO:0001819	synonymous_variant	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.330A>G	6.37:g.102074301A>G			102180994	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																				0.532	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102074301	A	G	102074301	2	3	61	1	0	0	0	0	0	0	0	1	6795	146	6	4		4	GRIK2	6	102074301	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	777809	102074301	69040766	4819	12804										
HACE1	57531	broad.mit.edu	37	chr6	105233165	105233165	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctattaaaactagccattcAtctaacgagtgccaaagcaa	6	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105233165A>G	ENST00000262903.4	-	12	1380	c.1104T>C	c.(1102-1104)gaT>gaC	p.D368D	HACE1_ENST00000369125.2_Silent_p.D368D|HACE1_ENST00000517995.1_5'Flank	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	368					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.D368D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CTAGCCATTCATCTAACGAGT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	6											60	62	61					6																	105233165		2203	4300	6503	105339858	SO:0001819	synonymous_variant	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.1104T>C	6.37:g.105233165A>G			105339858	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Silent	SNP	ENST00000262903.4	37	CCDS5050.1																																																																																				0.323	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		G	105233165	A	G	105233165	2	3	61	1	0	0	0	0	0	0	0	1	6961	214	8	4		4	HACE1	6	105233165	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3158864	105233165	65881902	4820	12805										
HACE1	57531	broad.mit.edu	37	chr6	105259193	105259193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaatatcatacctgcaagCaaagtacaatggagttgctc	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105259193C>T	ENST00000262903.4	-	7	886	c.610G>A	c.(610-612)Gct>Act	p.A204T	HACE1_ENST00000369125.2_Missense_Mutation_p.A204T	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	204					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.A204T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TACCTGCAAGCAAAGTACAAT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	6											95	91	92					6																	105259193		2203	4300	6503	105365886	SO:0001583	missense	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.610G>A	6.37:g.105259193C>T	ENSP00000262903:p.Ala204Thr		105365886	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.099103	0.76983	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645	T;T;T	0.81163	-1.46;-1.46;-1.46	5.31	5.31	0.75309	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.90810	0.7114	M	0.90425	3.115	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.80764	0.989;0.994	D	0.92484	0.5995	10	0.87932	D	0	.	18.5746	0.91150	0.0:1.0:0.0:0.0	.	204;204	E9PGP0;Q8IYU2	.;HACE1_HUMAN	T	204;204;160	ENSP00000262903:A204T;ENSP00000358121:A204T;ENSP00000429765:A160T	ENSP00000262903:A204T	A	-	1	0	HACE1	105365886	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.350000	0.73017	2.451000	0.82905	0.563000	0.77884	GCT		0.303	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		T	105259193	C	T	105259193	3	4	61	1	0	0	0	0	1	0	0	0	6961	710	25	3	2191	3	HACE1	6	105259193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26028	105259193	65855874	4821	12806										
HACE1	57531	broad.mit.edu	37	chr6	105291167	105291167	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatttactcatacatttCttctgcctgaaaagaaaaaa	3	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105291167C>A	ENST00000262903.4	-	5	609	c.333G>T	c.(331-333)aaG>aaT	p.K111N	HACE1_ENST00000369125.2_Missense_Mutation_p.K111N|RP11-809N15.2_ENST00000422930.2_RNA	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	111					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.K111N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TCATACATTTCTTCTGCCTGA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	6											108	121	117					6																	105291167		2202	4297	6499	105397860	SO:0001583	missense	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.333G>T	6.37:g.105291167C>A	ENSP00000262903:p.Lys111Asn		105397860	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954823	0.73902	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645;ENST00000524020	T;T;T;T	0.71817	-0.17;-0.17;-0.6;-0.17	5.92	5.02	0.67125	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.72479	0.3465	L	0.49699	1.58	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.78314	0.991;0.991	T	0.77011	-0.2746	10	0.72032	D	0.01	.	10.6671	0.45736	0.0:0.8271:0.0:0.1729	.	111;111	E9PGP0;Q8IYU2	.;HACE1_HUMAN	N	111;111;111;77	ENSP00000262903:K111N;ENSP00000358121:K111N;ENSP00000429765:K111N;ENSP00000427901:K77N	ENSP00000262903:K111N	K	-	3	2	HACE1	105397860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.221000	0.42917	1.422000	0.47177	0.650000	0.86243	AAG		0.289	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		A	105291167	C	A	105291167	3	1	61	1	0	0	0	0	1	0	0	0	6961	912	32	2	2476	2	HACE1	6	105291167	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31974	105291167	65823900	4822	12807										
LIN28B	389421	broad.mit.edu	37	chr6	105526629	105526629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagcaaagcaaaaaggggCcttcagttcaaaaaaggaaa	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105526629C>T	ENST00000345080.4	+	4	927	c.724C>T	c.(724-726)Cct>Tct	p.P242S		NM_001004317.3	NP_001004317.1	Q6ZN17	LN28B_HUMAN	lin-28 homolog B (C. elegans)	242					miRNA catabolic process (GO:0010587)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.P242S(1)		large_intestine(1)|lung(10)|ovary(1)	12		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				CAAAAAGGGGCCTTCAGTTCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	75	75					6																	105526629		2203	4300	6503	105633322	SO:0001583	missense	389421			AK131411	CCDS34504.1	6q21	2010-04-06			ENSG00000187772	ENSG00000187772			32207	protein-coding gene	gene with protein product		611044					Standard	NM_001004317		Approved	FLJ16517, CSDD2	uc003pqv.2	Q6ZN17	OTTHUMG00000015290	ENST00000345080.4:c.724C>T	6.37:g.105526629C>T	ENSP00000344401:p.Pro242Ser		105633322	A1L165|B2RPN6|Q5TCM4	Missense_Mutation	SNP	ENST00000345080.4	37	CCDS34504.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.456537	0.84317	.	.	ENSG00000187772	ENST00000345080	.	.	.	6.02	6.02	0.97574	.	0.049098	0.85682	D	0.000000	T	0.72128	0.3422	L	0.46157	1.445	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.71826	-0.4475	9	0.66056	D	0.02	-8.1618	20.5407	0.99260	0.0:1.0:0.0:0.0	.	242	Q6ZN17	LN28B_HUMAN	S	242	.	ENSP00000344401:P242S	P	+	1	0	LIN28B	105633322	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.462000	0.60121	2.865000	0.98341	0.655000	0.94253	CCT		0.463	LIN28B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041646.2	NM_001004317		T	105526629	C	T	105526629	3	4	61	1	0	0	0	0	1	0	0	0	8830	739	26	3	738	3	LIN28B	6	105526629	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235462	105526629	65588438	4823	12808										
BVES	11149	broad.mit.edu	37	chr6	105564709	105564709	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttctcttgaccagcatAaaaatctgcagttatcatct	4	10	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105564709A>C	ENST00000314641.5	-	6	899	c.683T>G	c.(682-684)tTa>tGa	p.L228*	BVES_ENST00000336775.5_Nonsense_Mutation_p.L228*|BVES_ENST00000446408.2_Nonsense_Mutation_p.L228*	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	228					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)	p.L228*(1)		NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TGACCAGCATAAAAATCTGCA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											59	56	57					6																	105564709		2203	4293	6496	105671402	SO:0001587	stop_gained	11149			AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.683T>G	6.37:g.105564709A>C	ENSP00000313172:p.Leu228*		105671402	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Nonsense_Mutation	SNP	ENST00000314641.5	37	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	A	38	6.644138	0.97730	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.4858	16.3809	0.83461	1.0:0.0:0.0:0.0	.	.	.	.	X	228	.	ENSP00000313172:L228X	L	-	2	0	BVES	105671402	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.326000	0.78906	0.528000	0.53228	TTA		0.323	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		C	105564709	A	C	105564709	4	2	61	1	0	0	0	0	0	1	0	0	1578	372	13	4	411	4	BVES	6	105564709	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	38080	105564709	65550358	4824	12809										
PREP	5550	broad.mit.edu	37	chr6	105733372	105733372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacctcacctttatgccacGtctctccatattcgccacct	3	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:105733372G>A	ENST00000369110.3	-	12	1730	c.1538C>T	c.(1537-1539)aCg>aTg	p.T513M		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	513					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.T513M(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	TTTATGCCACGTCTCTCCATA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											148	127	134					6																	105733372		2203	4300	6503	105840065	SO:0001583	missense	5550				CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1538C>T	6.37:g.105733372G>A	ENSP00000358106:p.Thr513Met		105840065	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.229398	0.58777	.	.	ENSG00000085377	ENST00000369110	T	0.31247	1.5	6.02	4.25	0.50352	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.043963	0.85682	N	0.000000	T	0.31979	0.0814	M	0.64260	1.97	0.58432	D	0.999999	D	0.58620	0.983	P	0.55222	0.771	T	0.13255	-1.0516	10	0.62326	D	0.03	-5.4864	11.9869	0.53153	0.0651:0.1223:0.8126:0.0	.	513	P48147	PPCE_HUMAN	M	513	ENSP00000358106:T513M	ENSP00000358106:T513M	T	-	2	0	PREP	105840065	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.348000	0.73009	0.873000	0.35799	0.650000	0.86243	ACG		0.453	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			A	105733372	G	A	105733372	3	1	61	1	0	0	0	0	1	0	0	0	12508	1145	40	1	610	1	PREP	6	105733372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168663	105733372	65381695	4825	12810										
PRDM1	639	broad.mit.edu	37	chr6	106555185	106555185	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtggtcagaaaagagaaaGaagaaactggcctgaaagtg	13	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:106555185G>T	ENST00000369096.4	+	7	2536	c.2302G>T	c.(2302-2304)Gaa>Taa	p.E768*	PRDM1_ENST00000369091.2_Nonsense_Mutation_p.E732*|PRDM1_ENST00000369089.3_Nonsense_Mutation_p.E634*	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	768					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E732*(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		AAAAGAGAAAGAAGAAACTGG	0.488			"D, N, Mis, F, S"		DLBCL																																		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	1	Substitution - Nonsense(1)	large_intestine(1)	6											81	87	85					6																	106555185		2203	4300	6503	106661878	SO:0001587	stop_gained	639				CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.2302G>T	6.37:g.106555185G>T	ENSP00000358092:p.Glu768*		106661878	B2REA6|E1P5E0|Q86WM7	Nonsense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	39	7.806516	0.98501	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	.	.	.	5.78	5.78	0.91487	.	0.147080	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-25.3936	20.0137	0.97470	0.0:0.0:1.0:0.0	.	.	.	.	X	732;768;731;634	.	ENSP00000358085:E634X	E	+	1	0	PRDM1	106661878	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.501000	0.90501	2.734000	0.93682	0.563000	0.77884	GAA		0.488	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106555185	G	T	106555185	4	4	61	1	0	0	0	0	0	1	0	0	12484	943	33	2	2341	2	PRDM1	6	106555185	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	821813	106555185	64559882	4826	12811										
ATG5	9474	broad.mit.edu	37	chr6	106727584	106727584	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatcttttttctgcatttCattgattacttgacttttat	5	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:106727584C>A	ENST00000369076.3	-	5	753	c.430G>T	c.(430-432)Gaa>Taa	p.E144*	ATG5_ENST00000369070.1_Nonsense_Mutation_p.E66*|ATG5_ENST00000360666.4_Intron|ATG5_ENST00000343245.3_Nonsense_Mutation_p.E144*	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	144					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)		p.E144*(1)		endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		TTCTGCATTTCATTGATTACT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											118	109	112					6																	106727584		2203	4300	6503	106834277	SO:0001587	stop_gained	9474			Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.430G>T	6.37:g.106727584C>A	ENSP00000358072:p.Glu144*		106834277	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Nonsense_Mutation	SNP	ENST00000369076.3	37	CCDS5055.1	.	.	.	.	.	.	.	.	.	.	C	41	8.749738	0.98939	.	.	ENSG00000057663	ENST00000369076;ENST00000343245;ENST00000369070	.	.	.	6.07	6.07	0.98685	.	0.043646	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-0.3837	20.6593	0.99626	0.0:1.0:0.0:0.0	.	.	.	.	X	144;144;66	.	ENSP00000343313:E144X	E	-	1	0	ATG5	106834277	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.580000	0.67464	2.885000	0.99019	0.655000	0.94253	GAA		0.313	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		A	106727584	C	A	106727584	4	1	61	1	0	0	0	0	0	1	0	0	1101	835	29	2	413	2	ATG5	6	106727584	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	172399	106727584	64387483	4827	12812										
AIM1	202	broad.mit.edu	37	chr6	106967178	106967178	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccaagacacactgacattCgaggccaaaggaatactcct	8	13	0	2	rs558701608	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:106967178C>T	ENST00000369066.3	+	2	1358	c.871C>T	c.(871-873)Cga>Tga	p.R291*		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.R291*(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CACTGACATTCGAGGCCAAAG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											56	56	56					6																	106967178		2203	4300	6503	107073871	SO:0001587	stop_gained	202			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.871C>T	6.37:g.106967178C>T	ENSP00000358062:p.Arg291*		107073871	Q6P2P0|Q9BTM3	Nonsense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	C	39	7.436096	0.98282	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	.	.	.	5.73	5.73	0.89815	.	0.232228	0.22390	N	0.060695	.	.	.	.	.	.	0.30402	N	0.779886	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.438	0.44448	0.0:0.8515:0.0:0.1485	.	.	.	.	X	699;291	.	ENSP00000285105:R699X	R	+	1	2	AIM1	107073871	0.966000	0.33281	0.222000	0.23844	0.200000	0.23975	2.622000	0.46427	2.709000	0.92574	0.655000	0.94253	CGA		0.433	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			T	106967178	C	T	106967178	4	4	61	1	0	0	0	0	0	1	0	0	430	876	31	1	877	1	AIM1	6	106967178	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	239594	106967178	64147889	4828	12813										
AIM1	202	broad.mit.edu	37	chr6	106968528	106968528	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattcacgaagaccatttaGaaaaggtgtttgatcccaaa	7	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:106968528G>T	ENST00000369066.3	+	2	2708	c.2221G>T	c.(2221-2223)Gaa>Taa	p.E741*		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.E741*(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AGACCATTTAGAAAAGGTGTT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											61	65	63					6																	106968528		2203	4300	6503	107075221	SO:0001587	stop_gained	202			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2221G>T	6.37:g.106968528G>T	ENSP00000358062:p.Glu741*		107075221	Q6P2P0|Q9BTM3	Nonsense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	45	12.000447	0.99626	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	.	.	.	6.16	6.16	0.99307	.	0.385177	0.27266	N	0.020143	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	X	1149;741	.	ENSP00000285105:E1149X	E	+	1	0	AIM1	107075221	1.000000	0.71417	0.999000	0.59377	0.879000	0.50718	7.927000	0.87577	2.937000	0.99478	0.650000	0.86243	GAA		0.453	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			T	106968528	G	T	106968528	4	4	61	1	0	0	0	0	0	1	0	0	430	943	33	2	2227	2	AIM1	6	106968528	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1350	106968528	64146539	4829	12814										
RTN4IP1	84816	broad.mit.edu	37	chr6	107019952	107019952	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggaactttagaaaaaggAaaggtttgttcaataactgg	10	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:107019952A>G	ENST00000369063.3	-	9	1575	c.1110T>C	c.(1108-1110)ttT>ttC	p.F370F	RTN4IP1_ENST00000539449.1_3'UTR|RTN4IP1_ENST00000498091.1_5'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	370						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.F370F(1)		breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TAGAAAAAGGAAAGGTTTGTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	6											111	113	112					6																	107019952		2203	4300	6503	107126645	SO:0001819	synonymous_variant	84816			AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1110T>C	6.37:g.107019952A>G			107126645	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																				0.383	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1			G	107019952	A	G	107019952	2	3	61	1	0	0	0	0	0	0	0	1	13766	243	9	4		4	RTN4IP1	6	107019952	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	51424	107019952	64095115	4830	12815										
QRSL1	55278	broad.mit.edu	37	chr6	107113791	107113791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaaaacaagtacagtttCctgttattcaacttcaagaa	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:107113791C>T	ENST00000369046.4	+	11	1605	c.1501C>T	c.(1501-1503)Cct>Tct	p.P501S		NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1									p.P501S(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		AGTACAGTTTCCTGTTATTCA	0.383																																					NSCLC(192;2127 2142 11668 26277 49545)											1	Substitution - Missense(1)	large_intestine(1)	6											57	54	55					6																	107113791		2203	4300	6503	107220484	SO:0001583	missense	55278			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"glutamyl-tRNA(Gln) amidotransferase, subunit A"					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.1501C>T	6.37:g.107113791C>T	ENSP00000358042:p.Pro501Ser		107220484		Missense_Mutation	SNP	ENST00000369046.4	37	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.150805	0.57151	.	.	ENSG00000130348	ENST00000369046	T	0.43688	0.94	5.74	5.74	0.90152	.	0.100169	0.64402	D	0.000001	T	0.17365	0.0417	N	0.20766	0.605	0.80722	D	1	B	0.23316	0.083	B	0.19391	0.025	T	0.04551	-1.0943	10	0.54805	T	0.06	-16.3761	13.1603	0.59540	0.0:0.9272:0.0:0.0728	.	501	Q9H0R6	GATA_HUMAN	S	501	ENSP00000358042:P501S	ENSP00000358042:P501S	P	+	1	0	QRSL1	107220484	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.912000	0.63335	2.711000	0.92665	0.561000	0.74099	CCT		0.383	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292		T	107113791	C	T	107113791	3	4	61	1	0	0	0	0	1	0	0	0	12918	855	30	3	1543	3	QRSL1	6	107113791	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93839	107113791	64001276	4831	12816										
PDSS2	57107	broad.mit.edu	37	chr6	107475967	107475967	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcacacctttgccagctttGattctttctcgcaactgtta	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:107475967G>T	ENST00000369037.4	-	8	1333	c.1056C>A	c.(1054-1056)atC>atA	p.I352I	PDSS2_ENST00000453874.2_Silent_p.I250I	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	352					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.I352I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		TGCCAGCTTTGATTCTTTCTC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	6											62	57	59					6																	107475967		2203	4300	6503	107582660	SO:0001819	synonymous_variant	57107			AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"chromosome 6 open reading frame 210"	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.1056C>A	6.37:g.107475967G>T			107582660	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Silent	SNP	ENST00000369037.4	37	CCDS5059.1																																																																																				0.453	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381		T	107475967	G	T	107475967	2	4	61	1	0	0	0	0	0	0	0	1	11725	1280	45	2		2	PDSS2	6	107475967	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	362176	107475967	63639100	4832	12817										
SOBP	55084	broad.mit.edu	37	chr6	107955698	107955699	+	Frame_Shift_Ins	INS	-	-	C													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacgtcagcgactccaagINSccccccaacgggttctccag							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:107955698_107955699insC	ENST00000317357.5	+	6	2309_2310	c.1650_1651insC	c.(1651-1653)cccfs	p.P551fs		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)									p.N553fs*184(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		GCGACTCCAAGCCCCCCAACGG	0.693																																																1	Insertion - Frameshift(1)	large_intestine(1)	6																																								108062392	SO:0001589	frameshift_variant	55084			AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.1656dupC	6.37:g.107955704_107955704dupC	ENSP00000318900:p.Pro551fs		108062391		Frame_Shift_Ins	INS	ENST00000317357.5	37	CCDS43488.1																																																																																				0.693	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		C	107955699	-	C	107955698	7	5	61	1	0	1	1	0	0	0	0	0	14949	962	34	0	1672	0	SOBP	6	107955698	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	479731	107955698	63159369	4833	12818										
SCML4	256380	broad.mit.edu	37	chr6	108066254	108066254	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcatcgcacaggaggcttCggcacagcttggcgaggaag	16	10	1	0	rs555376188		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:108066254C>T	ENST00000369020.3	-	5	826	c.581G>A	c.(580-582)cGa>cAa	p.R194Q	SCML4_ENST00000369021.3_Missense_Mutation_p.R165Q|SCML4_ENST00000369022.2_Missense_Mutation_p.R136Q|SCML4_ENST00000479803.1_5'Flank	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R165Q(2)		endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CAGGAGGCTTCGGCACAGCTT	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	6											65	55	59					6																	108066254		2203	4300	6503	108172947	SO:0001583	missense	256380				CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.581G>A	6.37:g.108066254C>T	ENSP00000358016:p.Arg194Gln		108172947	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900077	0.52227	.	.	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.38	3.44	0.39384	.	0.169399	0.53938	N	0.000054	T	0.14700	0.0355	L	0.37750	1.13	0.58432	D	0.999999	B;B;P	0.39003	0.393;0.327;0.654	B;B;B	0.35312	0.081;0.053;0.2	T	0.03662	-1.1015	10	0.11794	T	0.64	.	12.8262	0.57721	0.0:0.8468:0.0:0.1532	.	194;194;165	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	Q	136;194;165;165	ENSP00000358018:R136Q;ENSP00000358016:R194Q;ENSP00000358017:R165Q;ENSP00000404688:R165Q	ENSP00000358016:R194Q	R	-	2	0	SCML4	108172947	1.000000	0.71417	0.996000	0.52242	0.946000	0.59487	2.326000	0.43849	1.475000	0.48197	0.655000	0.94253	CGA		0.587	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		T	108066254	C	T	108066254	3	4	61	1	0	0	0	0	1	0	0	0	13948	884	31	1	679	1	SCML4	6	108066254	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110556	108066254	63048813	4834	12819										
SNX3	8724	broad.mit.edu	37	chr6	108535732	108535732	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgctccagcccttgttttCtttcctcaataaaattgtca	4	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:108535732C>A	ENST00000230085.8	-	3	691	c.353G>T	c.(352-354)aGa>aTa	p.R118I	SNX3_ENST00000349379.5_Missense_Mutation_p.R96I|SNX3_ENST00000426155.2_Missense_Mutation_p.R86I	NM_003795.4	NP_003786.1	O60493	SNX3_HUMAN	sorting nexin 3	118	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				hemoglobin biosynthetic process (GO:0042541)|intracellular protein transport (GO:0006886)|intralumenal vesicle formation (GO:0070676)|membrane invagination (GO:0010324)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein transport (GO:0051224)|negative regulation of viral entry into host cell (GO:0046597)|regulation of cellular protein metabolic process (GO:0032268)|regulation of intracellular protein transport (GO:0033157)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein phosphatase binding (GO:0019903)	p.R118I(1)		large_intestine(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		CCCTTGTTTTCTTTCCTCAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											96	85	89					6																	108535732		2203	4300	6503	108642425	SO:0001583	missense	8724			AF034546	CCDS5064.1, CCDS5065.1, CCDS75501.1	6q21	2010-08-05			ENSG00000112335	ENSG00000112335		"Sorting nexins"	11174	protein-coding gene	gene with protein product		605930				9819414	Standard	XM_005267192		Approved	Grd19	uc003psh.3	O60493	OTTHUMG00000015323	ENST00000230085.8:c.353G>T	6.37:g.108535732C>A	ENSP00000230085:p.Arg118Ile		108642425	A8K0B1|E1P5E4|E1P5E5|O60718|Q4TT29|Q4TT31|Q5JXJ7|Q5JXJ8|Q96AP9|Q9C0J5|Q9NU45	Missense_Mutation	SNP	ENST00000230085.8	37	CCDS5064.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530541	0.85706	.	.	ENSG00000112335	ENST00000230085;ENST00000426155;ENST00000349379	T;T;T	0.64085	-0.08;-0.08;-0.08	5.46	5.46	0.80206	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	D	0.86883	0.6040	H	0.99712	4.72	0.80722	D	1	D;D	0.62365	0.989;0.991	D;D	0.71870	0.951;0.975	D	0.92039	0.5639	10	0.87932	D	0	-21.0364	14.5159	0.67818	0.0:0.9274:0.0:0.0726	.	86;118	O60493-2;O60493	.;SNX3_HUMAN	I	118;86;96	ENSP00000230085:R118I;ENSP00000401779:R86I;ENSP00000296991:R96I	ENSP00000230085:R118I	R	-	2	0	SNX3	108642425	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.033000	0.70925	2.562000	0.86427	0.462000	0.41574	AGA		0.393	SNX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041717.1			A	108535732	C	A	108535732	3	1	61	1	0	0	0	0	1	0	0	0	14936	913	32	2	143	2	SNX3	6	108535732	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	469478	108535732	62579335	4835	12820										
LACE1	246269	broad.mit.edu	37	chr6	108723252	108723252	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtaccattcatagcagtCttgaaggtaaaaacaaatca	6	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:108723252C>A	ENST00000368977.4	+	7	987	c.801C>A	c.(799-801)gtC>gtA	p.V267V		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	267						mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.V267V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		TCATAGCAGTCTTGAAGGTAA	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	6											36	35	35					6																	108723252		2199	4291	6490	108829945	SO:0001819	synonymous_variant	246269			AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"ATPase family gene 1 homolog (S. cerevisiae)"					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.801C>A	6.37:g.108723252C>A			108829945	Q8N6A3	Silent	SNP	ENST00000368977.4	37	CCDS5067.1	.	.	.	.	.	.	.	.	.	.	C	8.112	0.779009	0.16120	.	.	ENSG00000135537	ENST00000421954	.	.	.	5.03	1.9	0.25705	.	.	.	.	.	T	0.42314	0.1197	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30621	-0.9972	4	.	.	.	-10.2509	8.618	0.33845	0.0:0.4637:0.4453:0.0911	.	.	.	.	Y	135	.	.	S	+	2	0	LACE1	108829945	0.956000	0.32656	1.000000	0.80357	0.931000	0.56810	0.138000	0.16016	0.571000	0.29365	0.579000	0.79373	TCT		0.308	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	NM_145315		A	108723252	C	A	108723252	2	1	61	1	0	0	0	0	0	0	0	1	8617	900	32	2		2	LACE1	6	108723252	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187520	108723252	62391815	4836	12821										
ARMC2	84071	broad.mit.edu	37	chr6	109220944	109220944	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcagaaatagaagtagacGaagtcttttggaatacaagg	11	5	1	3	rs6911885	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109220944G>A	ENST00000392644.4	+	7	964	c.796G>A	c.(796-798)Gaa>Aaa	p.E266K	ARMC2_ENST00000368972.3_Missense_Mutation_p.E101K	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	266								p.E259K(1)		endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		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)		AGAAGTAGACGAAGTCTTTTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	55	58	57		796	5.7	0.8	6	dbSNP_116	57	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARMC2	NM_032131.4	56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	266/868	109220944	2,13004	2203	4300	6503	109327637	SO:0001583	missense	84071			BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"Armadillo repeat containing"	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.796G>A	6.37:g.109220944G>A	ENSP00000376417:p.Glu266Lys		109327637	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	37	CCDS5069.2	.	.	.	.	.	.	.	.	.	.	G	11.16	1.555730	0.27827	2.27E-4	1.16E-4	ENSG00000118690	ENST00000368972;ENST00000392644	T;T	0.56275	0.47;0.47	5.65	5.65	0.86999	Armadillo-like helical (1);	0.433276	0.25616	N	0.029447	T	0.28433	0.0703	L	0.55481	1.735	0.29837	N	0.829578	B	0.30193	0.272	B	0.15052	0.012	T	0.08330	-1.0727	10	0.31617	T	0.26	.	12.6187	0.56592	0.0791:0.0:0.9209:0.0	rs6911885;rs6911885	266	Q8NEN0	ARMC2_HUMAN	K	101;266	ENSP00000357968:E101K;ENSP00000376417:E266K	ENSP00000357968:E101K	E	+	1	0	ARMC2	109327637	0.996000	0.38824	0.826000	0.32828	0.328000	0.28507	4.015000	0.57152	2.821000	0.97095	0.650000	0.86243	GAA		0.358	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		A	109220944	G	A	109220944	3	1	61	1	0	0	0	0	1	0	0	0	952	1059	37	1	818	1	ARMC2	6	109220944	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	497692	109220944	61894123	4837	12822										
ARMC2	84071	broad.mit.edu	37	chr6	109232174	109232174	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagcaggaatgagaagaatGattctttgattcaaaatgac	9	4	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109232174G>T	ENST00000392644.4	+	9	1264	c.1096G>T	c.(1096-1098)Gat>Tat	p.D366Y	ARMC2_ENST00000368972.3_Missense_Mutation_p.D201Y	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	366								p.D359Y(1)		endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		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)		TGAGAAGAATGATTCTTTGAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											51	51	51					6																	109232174		2203	4298	6501	109338867	SO:0001583	missense	84071			BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"Armadillo repeat containing"	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.1096G>T	6.37:g.109232174G>T	ENSP00000376417:p.Asp366Tyr		109338867	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	37	CCDS5069.2	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966431	0.53507	.	.	ENSG00000118690	ENST00000368972;ENST00000392644	T;T	0.48201	0.82;0.82	5.28	5.28	0.74379	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	M	0.83483	2.645	0.54753	D	0.999989	P	0.37122	0.583	B	0.32342	0.144	T	0.51896	-0.8647	10	0.52906	T	0.07	.	15.3039	0.73976	0.0:0.0:0.8597:0.1403	.	366	Q8NEN0	ARMC2_HUMAN	Y	201;366	ENSP00000357968:D201Y;ENSP00000376417:D366Y	ENSP00000357968:D201Y	D	+	1	0	ARMC2	109338867	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.276000	0.65580	2.441000	0.82636	0.655000	0.94253	GAT		0.338	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		T	109232174	G	T	109232174	3	4	61	1	0	0	0	0	1	0	0	0	952	1290	45	2	1126	2	ARMC2	6	109232174	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11230	109232174	61882893	4838	12823										
ARMC2	84071	broad.mit.edu	37	chr6	109294665	109294665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcacagcagcttctaaaccGaattcagagacatcacacct	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109294665G>A	ENST00000392644.4	+	18	2720	c.2552G>A	c.(2551-2553)cGa>cAa	p.R851Q	ARMC2_ENST00000368972.3_Missense_Mutation_p.R686Q	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	851								p.R844Q(1)|p.R844P(1)		endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		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)		CTTCTAAACCGAATTCAGAGA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	6											172	168	169					6																	109294665		2203	4300	6503	109401358	SO:0001583	missense	84071			BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"Armadillo repeat containing"	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.2552G>A	6.37:g.109294665G>A	ENSP00000376417:p.Arg851Gln		109401358	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	37	CCDS5069.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125547	0.77436	.	.	ENSG00000118690	ENST00000368972;ENST00000392644	T;T	0.35048	1.33;1.35	5.16	4.27	0.50696	.	0.326060	0.29473	N	0.012058	T	0.32224	0.0822	L	0.32530	0.975	0.40379	D	0.979425	D	0.76494	0.999	P	0.58970	0.849	T	0.07462	-1.0771	10	0.66056	D	0.02	-1.487	11.4828	0.50335	0.1424:0.0:0.8576:0.0	.	851	Q8NEN0	ARMC2_HUMAN	Q	686;851	ENSP00000357968:R686Q;ENSP00000376417:R851Q	ENSP00000357968:R686Q	R	+	2	0	ARMC2	109401358	0.991000	0.36638	0.966000	0.40874	0.966000	0.64601	3.656000	0.54467	2.677000	0.91161	0.655000	0.94253	CGA		0.448	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		A	109294665	G	A	109294665	3	1	61	1	0	0	0	0	1	0	0	0	952	1058	37	1	2618	1	ARMC2	6	109294665	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62491	109294665	61820402	4839	12824										
PPIL6	285755	broad.mit.edu	37	chr6	109752505	109752505	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaactgaccattaacaaaaGaaatcacagaggaagaatat	7	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109752505G>T	ENST00000521072.2	-	3	855	c.275C>A	c.(274-276)tCt>tAt	p.S92Y	PPIL6_ENST00000524031.1_5'Flank|AL109947.1_ENST00000459391.1_RNA|PPIL6_ENST00000424445.2_Missense_Mutation_p.S60Y|PPIL6_ENST00000440797.2_Missense_Mutation_p.S92Y	NM_173672.4	NP_775943.1	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 6	92					protein folding (GO:0006457)		peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.S92Y(1)		large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		ATTAACAAAAGAAATCACAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	72	73					6																	109752505		2203	4300	6503	109859198	SO:0001583	missense	285755				CCDS5074.1, CCDS47466.1, CCDS47466.2, CCDS69169.1	6q21	2009-11-18			ENSG00000185250	ENSG00000185250			21557	protein-coding gene	gene with protein product	"radial spoke 12 homolog (Chlamydomonas)"						Standard	NM_173672		Approved	bA425D10.6, MGC41939, dJ919F19.1, RSPH12	uc010kdp.3	Q8IXY8	OTTHUMG00000036593	ENST00000521072.2:c.275C>A	6.37:g.109752505G>T	ENSP00000427929:p.Ser92Tyr		109859198	A9NIU0|A9NIU9|E7EX15	Missense_Mutation	SNP	ENST00000521072.2	37	CCDS5074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.50|11.50	1.656060|1.656060	0.29425|0.29425	.|.	.|.	ENSG00000185250|ENSG00000185250	ENST00000520723;ENST00000518648|ENST00000424445;ENST00000440797;ENST00000521072;ENST00000417394	.|T;T;T;T	.|0.30714	.|2.1;2.11;2.11;1.52	5.26|5.26	4.39|4.39	0.52855|0.52855	.|.	.|0.108693	.|0.64402	.|D	.|0.000005	T|T	0.11281|0.11281	0.0275|0.0275	N|N	0.19112|0.19112	0.55|0.55	0.34160|0.34160	D|D	0.668536|0.668536	.|P;P;P	.|0.47302	.|0.824;0.893;0.824	.|B;B;B	.|0.39738	.|0.242;0.308;0.242	T|T	0.02774|0.02774	-1.1112|-1.1112	5|10	.|0.87932	.|D	.|0	-10.7778|-10.7778	14.5991|14.5991	0.68427|0.68427	0.0:0.8457:0.1543:0.0|0.0:0.8457:0.1543:0.0	.|.	.|92;60;92	.|A9NIU9;E7EX15;Q8IXY8	.|.;.;PPIL6_HUMAN	L|Y	31;39|60;92;92;49	.|ENSP00000407731:S60Y;ENSP00000392257:S92Y;ENSP00000427929:S92Y;ENSP00000411731:S49Y	.|ENSP00000411731:S49Y	F|S	-|-	3|2	2|0	PPIL6|PPIL6	109859198|109859198	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.270000|0.270000	0.26580|0.26580	4.103000|4.103000	0.57783|0.57783	1.198000|1.198000	0.43158|0.43158	-0.165000|-0.165000	0.13383|0.13383	TTC|TCT		0.403	PPIL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089003.4			T	109752505	G	T	109752505	3	4	61	1	0	0	0	0	1	0	0	0	12365	942	33	2	766	2	PPIL6	6	109752505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	457840	109752505	61362562	4840	12825										
ZBTB24	9841	broad.mit.edu	37	chr6	109788857	109788857	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatctgcaaaactttaccGatggattctgatgtgggtct	9	7	3	1	rs387907106		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109788857G>A	ENST00000230122.3	-	6	1536	c.1369C>T	c.(1369-1371)Cga>Tga	p.R457*	MICAL1_ENST00000368952.4_5'Flank	NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	457					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R457*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		AAACTTTACCGATGGATTCTG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											101	99	100					6																	109788857		2203	4300	6503	109895550	SO:0001630	splice_region_variant	9841			AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1370+1C>T	6.37:g.109788857G>A			109895550	Q17RC6|Q5TED5|Q8N455	Nonsense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	G	38	7.280252	0.98182	.	.	ENSG00000112365	ENST00000230122	.	.	.	5.71	4.83	0.62350	.	0.058878	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-11.9129	13.0125	0.58739	0.0:0.0:0.5577:0.4423	.	.	.	.	X	457	.	ENSP00000230122:R457X	R	-	1	2	ZBTB24	109895550	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.381000	0.44336	1.397000	0.46682	0.650000	0.86243	CGA		0.388	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	Nonsense_Mutation	A	109788857	G	A	109788857	5	1	61	1	0	0	0	0	0	0	1	0	17570	1072	37	1	732	1	ZBTB24	6	109788857	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36352	109788857	61326210	4841	12826										
AKD1	221264	broad.mit.edu	37	chr6	109962806	109962806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggttcagatatttaagtCgatccataacaatctagatt	6	6	2	2	rs148448147	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109962806C>T	ENST00000424296.2	-	10	924	c.848G>A	c.(847-849)cGa>cAa	p.R283Q	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Missense_Mutation_p.R283Q|AK9_ENST00000368948.2_Missense_Mutation_p.R283Q	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	283	Adenylate kinase 1.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.R283Q(2)									ATATTTAAGTCGATCCATAAC	0.348													C|||	3	0.000599042	0.0023	0	5008	,	,		19792	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	6						C	GLN/ARG,GLN/ARG	17,4389	24.3+/-50.5	0,17,2186	105	96	99		848,848	3.7	0.6	6	dbSNP_134	99	0,8598		0,0,4299	yes	missense,missense	AKD1	NM_001145128.2,NM_145025.4	43,43	0,17,6485	TT,TC,CC		0.0,0.3858,0.1307	probably-damaging,probably-damaging	283/1912,283/422	109962806	17,12987	2203	4299	6502	110069499	SO:0001583	missense	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.848G>A	6.37:g.109962806C>T	ENSP00000410186:p.Arg283Gln		110069499	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.29	1.593716	0.28445	0.003858	0.0	ENSG00000155085	ENST00000424296;ENST00000368948;ENST00000285397;ENST00000448084	T;T;T;T	0.69806	-0.43;-0.34;-0.28;0.55	5.44	3.65	0.41850	.	0.183932	0.44688	N	0.000436	T	0.37571	0.1008	L	0.40543	1.245	0.26402	N	0.97641	D;P	0.57899	0.981;0.854	B;B	0.41510	0.359;0.187	T	0.14282	-1.0478	9	.	.	.	-6.5868	9.6202	0.39716	0.0:0.8365:0.0:0.1635	.	283;283	Q5TCS8-2;Q5TCS8	.;AKD1_HUMAN	Q	283;283;283;206	ENSP00000410186:R283Q;ENSP00000357944:R283Q;ENSP00000285397:R283Q;ENSP00000407510:R206Q	.	R	-	2	0	AKD1	110069499	0.519000	0.26242	0.631000	0.29282	0.272000	0.26649	1.281000	0.33214	1.303000	0.44873	0.650000	0.86243	CGA		0.348	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		T	109962806	C	T	109962806	3	4	61	1	0	0	0	0	1	0	0	0	460	884	31	1	5027	1	AKD1	6	109962806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173949	109962806	61152261	4842	12827										
AKD1	221264	broad.mit.edu	37	chr6	109996917	109996917	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaatatatctgcaaaaGgatactcttctgtcttctct	4	10	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:109996917G>T	ENST00000424296.2	-	2	108	c.32C>A	c.(31-33)cCt>cAt	p.P11H	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Missense_Mutation_p.P11H|AK9_ENST00000368948.2_Missense_Mutation_p.P11H	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	11					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.P11H(2)									ATCTGCAAAAGGATACTCTTC	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	6											63	66	65					6																	109996917		2203	4294	6497	110103610	SO:0001583	missense	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.32C>A	6.37:g.109996917G>T	ENSP00000410186:p.Pro11His		110103610	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.563284	0.65538	.	.	ENSG00000155085	ENST00000424296;ENST00000368948;ENST00000285397;ENST00000532976	T;T;T;T	0.72282	-0.48;-0.64;-0.38;-0.46	5.15	5.15	0.70609	.	0.224630	0.46145	D	0.000301	T	0.74756	0.3758	M	0.61703	1.905	0.80722	D	1	D;D	0.69078	0.963;0.997	P;P	0.58013	0.73;0.831	T	0.74000	-0.3805	9	.	.	.	-9.2772	17.768	0.88484	0.0:0.0:1.0:0.0	.	11;11	Q5TCS8-2;Q5TCS8	.;AKD1_HUMAN	H	11	ENSP00000410186:P11H;ENSP00000357944:P11H;ENSP00000285397:P11H;ENSP00000436325:P11H	.	P	-	2	0	AKD1	110103610	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	6.012000	0.70767	2.567000	0.86603	0.591000	0.81541	CCT		0.328	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		T	109996917	G	T	109996917	3	4	61	1	0	0	0	0	1	0	0	0	460	1000	35	2	5875	2	AKD1	6	109996917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34111	109996917	61118150	4843	12828										
GPR6	2830	broad.mit.edu	37	chr6	110301377	110301377	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagtccaaagtgcccttTcgttccaggtctcccagcga	8	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:110301377T>G	ENST00000275169.3	+	1	1080	c.1062T>G	c.(1060-1062)ttT>ttG	p.F354L	GPR6_ENST00000414000.2_Missense_Mutation_p.F369L	NM_005284.3	NP_005275.1	P46095	GPR6_HUMAN	G protein-coupled receptor 6	354					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.F354L(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;1.64e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;2.83e-05)|all_lung(197;0.00016)|Lung NSC(302;0.000318)|Colorectal(196;0.0488)		BRCA - Breast invasive adenocarcinoma(108;8.01e-05)|Epithelial(106;8.76e-05)|all cancers(137;0.000197)|OV - Ovarian serous cystadenocarcinoma(136;0.0307)		AAGTGCCCTTTCGTTCCAGGT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											102	105	104					6																	110301377		2203	4300	6503	110408070	SO:0001583	missense	2830				CCDS5079.1, CCDS69172.1	6q21	2012-08-21				ENSG00000146360		"GPCR / Class A : Orphans"	4515	protein-coding gene	gene with protein product		600553				8530049	Standard	NM_001286099		Approved		uc003ptu.3	P46095	OTTHUMG00000015354	ENST00000275169.3:c.1062T>G	6.37:g.110301377T>G	ENSP00000275169:p.Phe354Leu		110408070	B4DHS9|J3KQR3|Q17RJ7|Q5SYL0	Missense_Mutation	SNP	ENST00000275169.3	37	CCDS5079.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222420	0.39300	.	.	ENSG00000146360	ENST00000428489;ENST00000414000;ENST00000275169	T;T	0.36340	1.26;1.26	4.93	4.05	0.47172	.	0.235104	0.37136	N	0.002239	T	0.08044	0.0201	N	0.17474	0.49	0.53005	D	0.99996	P;B	0.48089	0.905;0.002	B;B	0.40825	0.341;0.004	T	0.05903	-1.0857	10	0.11182	T	0.66	.	7.4603	0.27291	0.0:0.7186:0.0:0.2814	.	369;354	B4DHS9;P46095	.;GPR6_HUMAN	L	332;369;354	ENSP00000406986:F369L;ENSP00000275169:F354L	ENSP00000275169:F354L	F	+	3	2	GPR6	110408070	0.995000	0.38212	1.000000	0.80357	0.903000	0.53119	0.421000	0.21280	1.276000	0.44395	-0.242000	0.12053	TTT		0.592	GPR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041774.1			G	110301377	T	G	110301377	3	3	61	1	0	0	0	0	1	0	0	0	6721	1780	62	4	1064	4	GPR6	6	110301377	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	304460	110301377	60813690	4844	12829										
WASF1	8936	broad.mit.edu	37	chr6	110429816	110429816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataggcaaagtcttgcgatCgaaaagctgctggtcttgaa	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:110429816C>T	ENST00000392589.1	-	6	1173	c.337G>A	c.(337-339)Gat>Aat	p.D113N	WASF1_ENST00000359451.2_Missense_Mutation_p.D113N|WASF1_ENST00000392588.1_Missense_Mutation_p.D113N|WASF1_ENST00000392587.2_Missense_Mutation_p.D113N|WASF1_ENST00000392586.1_Missense_Mutation_p.D113N	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	113					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)	p.D113N(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		GTCTTGCGATCGAAAAGCTGC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	92	95					6																	110429816		2203	4300	6503	110536509	SO:0001583	missense	8936			D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.337G>A	6.37:g.110429816C>T	ENSP00000376368:p.Asp113Asn		110536509	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.372774	0.82573	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451;ENST00000444391;ENST00000265601;ENST00000368938	T;T;T;T;T;T;T;T	0.41400	1.01;1.01;1.01;1.01;1.01;1.01;1.0;1.0	6.06	6.06	0.98353	.	0.133860	0.64402	D	0.000002	T	0.16557	0.0398	L	0.34521	1.04	0.48830	D	0.999717	P	0.35493	0.505	B	0.21360	0.034	T	0.03684	-1.1013	10	0.23891	T	0.37	.	16.0477	0.80731	0.0:0.8667:0.1333:0.0	.	113	Q92558	WASF1_HUMAN	N	113	ENSP00000376365:D113N;ENSP00000376366:D113N;ENSP00000376368:D113N;ENSP00000376367:D113N;ENSP00000352425:D113N;ENSP00000407041:D113N;ENSP00000265601:D113N;ENSP00000357934:D113N	ENSP00000265601:D113N	D	-	1	0	WASF1	110536509	0.999000	0.42202	0.989000	0.46669	0.964000	0.63967	2.962000	0.49176	2.880000	0.98712	0.650000	0.86243	GAT		0.368	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		T	110429816	C	T	110429816	3	4	61	1	0	0	0	0	1	0	0	0	17292	884	31	1	1366	1	WASF1	6	110429816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128439	110429816	60685251	4845	12830										
SLC22A16	85413	broad.mit.edu	37	chr6	110763546	110763546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaaccagattagccaaaCggtaagtgtccttttcgtaa	9	8	0	2	rs149834139		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:110763546C>T	ENST00000368919.3	-	4	1150	c.1084G>A	c.(1084-1086)Gtt>Att	p.V362I	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000330550.4_Missense_Mutation_p.V328I|SLC22A16_ENST00000439654.1_Missense_Mutation_p.V362I	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	362					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)	p.V362I(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	ATTAGCCAAACGGTAAGTGTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	6						C	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	117	115	116		1084	-6.7	0	6	dbSNP_134	116	0,8600		0,0,4300	yes	missense	SLC22A16	NM_033125.2	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	362/578	110763546	2,13004	2203	4300	6503	110870239	SO:0001583	missense	85413				CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1084G>A	6.37:g.110763546C>T	ENSP00000357915:p.Val362Ile		110870239	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	C	6.957	0.546545	0.13312	4.54E-4	0.0	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	T;T;T;T;T;T	0.73681	0.36;0.36;0.36;0.36;0.36;-0.77	4.78	-6.67	0.01783	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.881639	0.09911	N	0.739817	T	0.19525	0.0469	N	0.20483	0.58	0.24646	N	0.993546	B;B	0.33000	0.393;0.108	B;B	0.24006	0.05;0.029	T	0.26326	-1.0106	10	0.02654	T	1	.	7.2502	0.26146	0.0:0.3758:0.27:0.3542	.	362;328	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	I	362;279;328;362;192;319	ENSP00000357915:V362I;ENSP00000395642:V279I;ENSP00000328583:V328I;ENSP00000408799:V362I;ENSP00000409306:V192I;ENSP00000416310:V319I	ENSP00000328583:V328I	V	-	1	0	SLC22A16	110870239	0.036000	0.19791	0.000000	0.03702	0.112000	0.19704	0.163000	0.16520	-1.787000	0.01268	0.655000	0.94253	GTT		0.418	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		T	110763546	C	T	110763546	3	4	61	1	0	0	0	0	1	0	0	0	14484	536	19	1	669	1	SLC22A16	6	110763546	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	333730	110763546	60351521	4846	12831										
CDK19	23097	broad.mit.edu	37	chr6	110948235	110948235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccatgacactaaatatccGatccagttgatcatgatgaa	6	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:110948235G>A	ENST00000368911.3	-	7	939	c.760C>T	c.(760-762)Cgg>Tgg	p.R254W	CDK19_ENST00000323817.3_Missense_Mutation_p.R194W|CDK19_ENST00000413605.2_Missense_Mutation_p.R130W	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R254W(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						CTAAATATCCGATCCAGTTGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											120	114	116					6																	110948235		2203	4300	6503	111054928	SO:0001583	missense	23097			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"Cyclin-dependent kinases"	19338	protein-coding gene	gene with protein product		614720	"cyclin-dependent kinase (CDC2-like) 11", "cell division cycle 2-like 6 (CDK8-like)"	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.760C>T	6.37:g.110948235G>A	ENSP00000357907:p.Arg254Trp		111054928	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.528512	0.64860	.	.	ENSG00000155111	ENST00000368911;ENST00000323817;ENST00000392576;ENST00000413605;ENST00000457688	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.11	4.23	0.50019	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71970	0.3403	L	0.53617	1.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.76934	-0.2775	10	0.87932	D	0	-25.4413	14.9032	0.70696	0.0:0.0:0.8555:0.1445	.	130;254	B4DUB1;Q9BWU1	.;CDK19_HUMAN	W	254;194;193;130;194	ENSP00000357907:R254W;ENSP00000317665:R194W;ENSP00000410604:R130W;ENSP00000415621:R194W	ENSP00000317665:R194W	R	-	1	2	CDK19	111054928	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	4.263000	0.58853	1.146000	0.42352	-0.538000	0.04264	CGG		0.328	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076		A	110948235	G	A	110948235	3	1	61	1	0	0	0	0	1	0	0	0	3141	1057	37	1	776	1	CDK19	6	110948235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184689	110948235	60166832	4847	12832										
CDK19	23097	broad.mit.edu	37	chr6	110948306	110948306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagtgaaaaataggttccGaagtcaacaattcagcaaat	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:110948306G>A	ENST00000368911.3	-	7	868	c.689C>T	c.(688-690)tCg>tTg	p.S230L	CDK19_ENST00000323817.3_Missense_Mutation_p.S170L|CDK19_ENST00000413605.2_Missense_Mutation_p.S106L	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.S230L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						AATAGGTTCCGAAGTCAACAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											106	104	104					6																	110948306		2203	4300	6503	111054999	SO:0001583	missense	23097			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"Cyclin-dependent kinases"	19338	protein-coding gene	gene with protein product		614720	"cyclin-dependent kinase (CDC2-like) 11", "cell division cycle 2-like 6 (CDK8-like)"	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.689C>T	6.37:g.110948306G>A	ENSP00000357907:p.Ser230Leu		111054999	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892511	0.52121	.	.	ENSG00000155111	ENST00000368911;ENST00000323817;ENST00000392576;ENST00000413605;ENST00000457688	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36744	0.0978	N	0.00859	-1.14	0.80722	D	1	D;P	0.62365	0.991;0.891	P;B	0.58780	0.845;0.34	T	0.59873	-0.7372	10	0.26408	T	0.33	-29.8161	18.8613	0.92273	0.0:0.0:1.0:0.0	.	106;230	B4DUB1;Q9BWU1	.;CDK19_HUMAN	L	230;170;169;106;170	ENSP00000357907:S230L;ENSP00000317665:S170L;ENSP00000410604:S106L;ENSP00000415621:S170L	ENSP00000317665:S170L	S	-	2	0	CDK19	111054999	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.476000	0.97823	2.464000	0.83262	0.455000	0.32223	TCG		0.353	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076		A	110948306	G	A	110948306	3	1	61	1	0	0	0	0	1	0	0	0	3141	1059	37	1	847	1	CDK19	6	110948306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71	110948306	60166761	4848	12833										
AMD1	262	broad.mit.edu	37	chr6	111210151	111210151	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggttcccctgttgaagCttgctagggattacagtggg	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111210151C>A	ENST00000368885.3	+	3	625	c.289C>A	c.(289-291)Ctt>Att	p.L97I	AMD1_ENST00000368882.3_Intron|AMD1_ENST00000451850.2_Intron|AMD1_ENST00000368876.1_Missense_Mutation_p.L28I|AMD1_ENST00000368877.5_Missense_Mutation_p.L68I	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	97					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)	p.L97I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	CCTGTTGAAGCTTGCTAGGGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	90	93					6																	111210151		2203	4300	6503	111316844	SO:0001583	missense	262			M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.289C>A	6.37:g.111210151C>A	ENSP00000357880:p.Leu97Ile		111316844	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Missense_Mutation	SNP	ENST00000368885.3	37	CCDS5086.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822211	0.90873	.	.	ENSG00000123505	ENST00000368885;ENST00000368877;ENST00000368876	.	.	.	5.55	5.55	0.83447	S-adenosylmethionine decarboxylase, core (2);	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	L	0.45228	1.405	0.80722	D	1	P;P	0.47191	0.891;0.614	P;P	0.56960	0.81;0.775	T	0.56123	-0.8031	9	0.27082	T	0.32	.	19.5083	0.95130	0.0:1.0:0.0:0.0	.	68;97	A6NNH3;P17707	.;DCAM_HUMAN	I	97;68;28	.	ENSP00000357870:L28I	L	+	1	0	AMD1	111316844	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.635000	0.67841	2.611000	0.88343	0.591000	0.81541	CTT		0.403	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			A	111210151	C	A	111210151	3	1	61	1	0	0	0	0	1	0	0	0	566	797	28	2	299	2	AMD1	6	111210151	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	261845	111210151	59904916	4849	12834										
RPF2	84154	broad.mit.edu	37	chr6	111306257	111306257	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttgagaagagagaaccGaaactcaatgaaaatattaa	7	6	1	4	rs370938715		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111306257G>A	ENST00000441448.2	+	2	164	c.72G>A	c.(70-72)ccG>ccA	p.P24P		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	24						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P24P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						AGAGAGAACCGAAACTCAATG	0.338													G|||	1	0.000199681	8e-04	0	5008	,	,		17698	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						G		1,4405	2.1+/-5.4	0,1,2202	87	100	95		72	-6	1	6		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RPF2	NM_032194.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		24/307	111306257	2,13004	2203	4300	6503	111412950	SO:0001819	synonymous_variant	84154			AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"ribosomal processing factor 2 homolog (S. cerevisiae)"		"brix domain containing 1"	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.72G>A	6.37:g.111306257G>A			111412950	Q5VXN1|Q8N4A1	Silent	SNP	ENST00000441448.2	37	CCDS5088.1																																																																																				0.338	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194		A	111306257	G	A	111306257	2	1	61	1	0	0	0	0	0	0	0	1	13584	1045	37	1		1	RPF2	6	111306257	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96106	111306257	59808810	4850	12835										
REV3L	5980	broad.mit.edu	37	chr6	111672895	111672895	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctggcacccgagagatCatccgacataagtcaatact	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111672895C>A	ENST00000358835.3	-	20	7738	c.7284G>T	c.(7282-7284)atG>atT	p.M2428I	REV3L_ENST00000435970.1_Missense_Mutation_p.M2350I|REV3L_ENST00000368805.1_Missense_Mutation_p.M2428I|REV3L_ENST00000368802.3_Missense_Mutation_p.M2428I			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2428					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.M2350I(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCCGAGAGATCATCCGACATA	0.388								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											92	80	84					6																	111672895		2203	4300	6503	111779588	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7284G>T	6.37:g.111672895C>A	ENSP00000351697:p.Met2428Ile		111779588	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934145	0.73442	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.40476	3.05;3.05;3.05;1.03	4.83	4.83	0.62350	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.136421	0.50627	D	0.000112	T	0.35393	0.0930	L	0.39245	1.2	0.41594	D	0.988813	P	0.38978	0.652	P	0.48063	0.565	T	0.13737	-1.0498	10	0.35671	T	0.21	-5.2963	17.9332	0.89005	0.0:1.0:0.0:0.0	.	2428	O60673	DPOLZ_HUMAN	I	2428;2428;2428;2350;501	ENSP00000357792:M2428I;ENSP00000357795:M2428I;ENSP00000351697:M2428I;ENSP00000402003:M2350I	ENSP00000351697:M2428I	M	-	3	0	REV3L	111779588	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.073000	0.50057	2.217000	0.71921	0.585000	0.79938	ATG		0.388	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111672895	C	A	111672895	3	1	61	1	0	0	0	0	1	0	0	0	13277	826	29	2	2164	2	REV3L	6	111672895	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366638	111672895	59442172	4851	12836										
REV3L	5980	broad.mit.edu	37	chr6	111688541	111688541	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagccaatgaaggcagctcCtctactggtgatgagggtct	12	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111688541C>A	ENST00000358835.3	-	15	6904	c.6450G>T	c.(6448-6450)gaG>gaT	p.E2150D	REV3L_ENST00000435970.1_Missense_Mutation_p.E2072D|REV3L_ENST00000368805.1_Missense_Mutation_p.E2150D|REV3L_ENST00000368802.3_Missense_Mutation_p.E2150D			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2150					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.E2072D(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AAGGCAGCTCCTCTACTGGTG	0.443								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											91	91	91					6																	111688541		2203	4300	6503	111795234	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6450G>T	6.37:g.111688541C>A	ENSP00000351697:p.Glu2150Asp		111795234	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	10.20	1.285321	0.23478	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.01548	4.88;4.88;4.88;4.78	5.73	1.4	0.22301	Ribonuclease H-like (1);	0.880504	0.10012	N	0.727013	T	0.00328	0.0010	N	0.12182	0.205	0.22305	N	0.999213	B	0.02656	0.0	B	0.04013	0.001	T	0.40979	-0.9534	10	0.13108	T	0.6	-0.4527	2.7196	0.05197	0.2034:0.4248:0.0:0.3718	.	2150	O60673	DPOLZ_HUMAN	D	2150;2150;2150;2072;223	ENSP00000357792:E2150D;ENSP00000357795:E2150D;ENSP00000351697:E2150D;ENSP00000402003:E2072D	ENSP00000351697:E2150D	E	-	3	2	REV3L	111795234	0.529000	0.26322	0.766000	0.31476	0.206000	0.24218	0.364000	0.20325	0.436000	0.26393	-0.136000	0.14681	GAG		0.443	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111688541	C	A	111688541	3	1	61	1	0	0	0	0	1	0	0	0	13277	680	24	2	3018	2	REV3L	6	111688541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15646	111688541	59426526	4852	12837										
REV3L	5980	broad.mit.edu	37	chr6	111693893	111693893	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaaagttgccataatttCttccctacttgggggggaca	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111693893C>A	ENST00000358835.3	-	14	6119	c.5665G>T	c.(5665-5667)Gaa>Taa	p.E1889*	REV3L_ENST00000435970.1_Nonsense_Mutation_p.E1811*|REV3L_ENST00000368805.1_Nonsense_Mutation_p.E1889*|REV3L_ENST00000368802.3_Nonsense_Mutation_p.E1889*			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1889	Mediates interaction with MAD2L2.				DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.E1811*(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GCCATAATTTCTTCCCTACTT	0.433								DNA polymerases (catalytic subunits)																																								1	Substitution - Nonsense(1)	large_intestine(1)	6											147	155	152					6																	111693893		2203	4300	6503	111800586	SO:0001587	stop_gained	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5665G>T	6.37:g.111693893C>A	ENSP00000351697:p.Glu1889*		111800586	O43214|Q5TC33	Nonsense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	50	16.963013	0.99876	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	.	.	.	6.03	6.03	0.97812	.	0.279939	0.38326	N	0.001734	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-7.2869	20.5568	0.99304	0.0:1.0:0.0:0.0	.	.	.	.	X	1889;1889;1889;1811	.	ENSP00000351697:E1889X	E	-	1	0	REV3L	111800586	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.440000	0.80464	2.861000	0.98227	0.655000	0.94253	GAA		0.433	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111693893	C	A	111693893	4	1	61	1	0	0	0	0	0	1	0	0	13277	922	32	2	3807	2	REV3L	6	111693893	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5352	111693893	59421174	4853	12838										
REV3L	5980	broad.mit.edu	37	chr6	111695024	111695024	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggtgttgacacatttcGatttttacactgagaaagtg	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111695024G>A	ENST00000358835.3	-	14	4988	c.4534C>T	c.(4534-4536)Cga>Tga	p.R1512*	REV3L_ENST00000435970.1_Nonsense_Mutation_p.R1434*|REV3L_ENST00000368805.1_Nonsense_Mutation_p.R1512*|REV3L_ENST00000368802.3_Nonsense_Mutation_p.R1512*			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1512					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.R1434*(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GACACATTTCGATTTTTACAC	0.353								DNA polymerases (catalytic subunits)																																								1	Substitution - Nonsense(1)	large_intestine(1)	6											171	166	168					6																	111695024		2203	4300	6503	111801717	SO:0001587	stop_gained	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4534C>T	6.37:g.111695024G>A	ENSP00000351697:p.Arg1512*		111801717	O43214|Q5TC33	Nonsense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	G	48	14.507187	0.99798	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	.	.	.	6.04	5.17	0.71159	.	0.635768	0.13924	N	0.353398	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.3473	8.1816	0.31313	0.0723:0.0:0.5815:0.3462	.	.	.	.	X	1512;1512;1512;1434	.	ENSP00000351697:R1512X	R	-	1	2	REV3L	111801717	0.997000	0.39634	0.983000	0.44433	0.942000	0.58702	2.717000	0.47227	1.559000	0.49555	0.563000	0.77884	CGA		0.353	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111695024	G	A	111695024	4	1	61	1	0	0	0	0	0	1	0	0	13277	1066	37	1	4938	1	REV3L	6	111695024	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1131	111695024	59420043	4854	12839										
REV3L	5980	broad.mit.edu	37	chr6	111695977	111695977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtttatttgtctgatttCgtttgttccttttcttagta	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111695977C>T	ENST00000358835.3	-	14	4035	c.3581G>A	c.(3580-3582)cGa>cAa	p.R1194Q	REV3L_ENST00000435970.1_Missense_Mutation_p.R1116Q|REV3L_ENST00000368805.1_Missense_Mutation_p.R1194Q|REV3L_ENST00000368802.3_Missense_Mutation_p.R1194Q			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1194					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.R1116Q(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TGTCTGATTTCGTTTGTTCCT	0.338								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											90	89	89					6																	111695977		2203	4300	6503	111802670	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.3581G>A	6.37:g.111695977C>T	ENSP00000351697:p.Arg1194Gln		111802670	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848445	0.32699	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01474	4.94;4.94;4.94;4.85	5.54	5.54	0.83059	Ribonuclease H-like (1);	0.581231	0.16598	N	0.207462	T	0.00666	0.0022	L	0.44542	1.39	0.29515	N	0.853917	P	0.44006	0.824	B	0.30105	0.111	T	0.52704	-0.8540	10	0.36615	T	0.2	.	9.0681	0.36475	0.1571:0.7674:0.0:0.0755	.	1194	O60673	DPOLZ_HUMAN	Q	1194;1194;1194;1116	ENSP00000357792:R1194Q;ENSP00000357795:R1194Q;ENSP00000351697:R1194Q;ENSP00000402003:R1116Q	ENSP00000351697:R1194Q	R	-	2	0	REV3L	111802670	0.989000	0.36119	1.000000	0.80357	0.999000	0.98932	1.623000	0.37008	2.764000	0.94973	0.655000	0.94253	CGA		0.338	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111695977	C	T	111695977	3	4	61	1	0	0	0	0	1	0	0	0	13277	884	31	1	5891	1	REV3L	6	111695977	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	953	111695977	59419090	4855	12840										
REV3L	5980	broad.mit.edu	37	chr6	111697683	111697683	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaaagatccagggtatttCatagaataagtgctttcgtt	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111697683C>A	ENST00000358835.3	-	14	2329	c.1875G>T	c.(1873-1875)atG>atT	p.M625I	REV3L_ENST00000435970.1_Missense_Mutation_p.M547I|REV3L_ENST00000368805.1_Missense_Mutation_p.M625I|REV3L_ENST00000368802.3_Missense_Mutation_p.M625I			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	625					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.M547I(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CAGGGTATTTCATAGAATAAG	0.333								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											58	62	61					6																	111697683		2196	4296	6492	111804376	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.1875G>T	6.37:g.111697683C>A	ENSP00000351697:p.Met625Ile		111804376	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	6.656	0.489498	0.12641	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01446	4.97;4.97;4.97;4.88	5.31	2.55	0.30701	Ribonuclease H-like (1);	2.133630	0.02441	N	0.084599	T	0.00608	0.0020	L	0.29908	0.895	0.24072	N	0.995978	B	0.02656	0.0	B	0.01281	0.0	T	0.46965	-0.9153	10	0.26408	T	0.33	-11.3494	6.3012	0.21113	0.0:0.5865:0.1285:0.285	.	625	O60673	DPOLZ_HUMAN	I	625;625;625;547	ENSP00000357792:M625I;ENSP00000357795:M625I;ENSP00000351697:M625I;ENSP00000402003:M547I	ENSP00000351697:M625I	M	-	3	0	REV3L	111804376	0.966000	0.33281	0.999000	0.59377	0.739000	0.42172	0.215000	0.17562	0.623000	0.30267	0.563000	0.77884	ATG		0.333	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111697683	C	A	111697683	3	1	61	1	0	0	0	0	1	0	0	0	13277	826	29	2	7597	2	REV3L	6	111697683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1706	111697683	59417384	4856	12841										
REV3L	5980	broad.mit.edu	37	chr6	111702606	111702606	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataaggttcaaaattgcttCttcattaataagagcttctt	5	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111702606C>A	ENST00000358835.3	-	11	1592	c.1138G>T	c.(1138-1140)Gaa>Taa	p.E380*	REV3L_ENST00000435970.1_Nonsense_Mutation_p.E302*|REV3L_ENST00000368805.1_Nonsense_Mutation_p.E380*|REV3L_ENST00000368802.3_Nonsense_Mutation_p.E380*			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	380					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.E302*(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AAAATTGCTTCTTCATTAATA	0.338								DNA polymerases (catalytic subunits)																																								1	Substitution - Nonsense(1)	large_intestine(1)	6											111	107	108					6																	111702606		2203	4300	6503	111809299	SO:0001587	stop_gained	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.1138G>T	6.37:g.111702606C>A	ENSP00000351697:p.Glu380*		111809299	O43214|Q5TC33	Nonsense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	45	11.598683	0.99580	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	.	.	.	4.85	4.85	0.62838	.	0.168624	0.40908	D	0.000988	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	18.3301	0.90265	0.0:1.0:0.0:0.0	.	.	.	.	X	380;380;380;302	.	ENSP00000351697:E380X	E	-	1	0	REV3L	111809299	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.748000	0.74877	2.404000	0.81709	0.591000	0.81541	GAA		0.338	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111702606	C	A	111702606	4	1	61	1	0	0	0	0	0	1	0	0	13277	922	32	2	8346	2	REV3L	6	111702606	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4923	111702606	59412461	4857	12842										
REV3L	5980	broad.mit.edu	37	chr6	111709211	111709211	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaccacttacacagagaAatcattctgtttgagaattt	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111709211A>C	ENST00000358835.3	-	9	1394	c.940T>G	c.(940-942)Ttc>Gtc	p.F314V	REV3L_ENST00000435970.1_Missense_Mutation_p.F236V|REV3L_ENST00000368805.1_Missense_Mutation_p.F314V|REV3L_ENST00000368802.3_Missense_Mutation_p.F314V			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	314					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.F236V(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TACACAGAGAAATCATTCTGT	0.289								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	6											46	49	48					6																	111709211		2203	4295	6498	111815904	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.940T>G	6.37:g.111709211A>C	ENSP00000351697:p.Phe314Val		111815904	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	16.74	3.206713	0.58343	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.35	5.35	0.76521	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.18841	0.0452	L	0.59436	1.845	0.38355	D	0.944432	P	0.48407	0.91	B	0.42462	0.388	T	0.04509	-1.0946	10	0.39692	T	0.17	.	10.5319	0.44981	0.9242:0.0:0.0758:0.0	.	314	O60673	DPOLZ_HUMAN	V	314;314;314;236	ENSP00000357792:F314V;ENSP00000357795:F314V;ENSP00000351697:F314V;ENSP00000402003:F236V	ENSP00000351697:F314V	F	-	1	0	REV3L	111815904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.284000	0.72652	2.017000	0.59298	0.482000	0.46254	TTC		0.289	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111709211	A	C	111709211	3	2	61	1	0	0	0	0	1	0	0	0	13277	14	1	4	8552	4	REV3L	6	111709211	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6605	111709211	59405856	4858	12843										
TRAF3IP2	10758	broad.mit.edu	37	chr6	111913115	111913115	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtgagcttgagaaaagtCtccggaggaattgtgaagca	14	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:111913115C>A	ENST00000340026.6	-	3	796	c.202G>T	c.(202-204)Gac>Tac	p.D68Y	TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.D59Y|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.D59Y|TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2-AS1_ENST00000532353.1_RNA			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	68	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)			p.D68Y(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		TGAGAAAAGTCTCCGGAGGAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											105	106	106					6																	111913115		2203	4300	6503	112019808	SO:0001583	missense	10758			AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.202G>T	6.37:g.111913115C>A	ENSP00000345984:p.Asp68Tyr		112019808	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	C	6.770	0.510914	0.12883	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.37584	1.2;1.2;1.19	5.49	3.64	0.41730	.	0.422253	0.22976	N	0.053376	T	0.24198	0.0586	L	0.51422	1.61	0.22819	N	0.998696	P;P;P	0.51351	0.745;0.944;0.745	P;P;B	0.53006	0.522;0.715;0.303	T	0.05162	-1.0902	10	0.46703	T	0.11	-40.548	5.9042	0.18984	0.0:0.6701:0.1586:0.1713	.	68;59;59	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	Y	68;59;68;59	ENSP00000357750:D59Y;ENSP00000345984:D68Y;ENSP00000352889:D59Y	ENSP00000345984:D68Y	D	-	1	0	TRAF3IP2	112019808	0.001000	0.12720	0.123000	0.21794	0.019000	0.09904	0.740000	0.26188	1.322000	0.45245	0.511000	0.50034	GAC		0.517	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			A	111913115	C	A	111913115	3	1	61	1	0	0	0	0	1	0	0	0	16481	913	32	2	1554	2	TRAF3IP2	6	111913115	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203904	111913115	59201952	4859	12844										
FYN	2534	broad.mit.edu	37	chr6	112041099	112041099	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcccccggctgcgtggaaGttgttgtagttggggatgga	18	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112041099G>T	ENST00000354650.3	-	4	762	c.156C>A	c.(154-156)aaC>aaA	p.N52K	FYN_ENST00000356013.2_Missense_Mutation_p.N52K|FYN_ENST00000538466.1_Missense_Mutation_p.N52K|FYN_ENST00000368682.3_Missense_Mutation_p.N52K|FYN_ENST00000229471.4_Missense_Mutation_p.N52K|FYN_ENST00000368678.4_Missense_Mutation_p.N52K|FYN_ENST00000368667.2_Missense_Mutation_p.N52K|FYN_ENST00000229470.5_Missense_Mutation_p.N52K	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	52					activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.N52K(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	CTGCGTGGAAGTTGTTGTAGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	6											116	95	102					6																	112041099		2203	4300	6503	112147792	SO:0001583	missense	2534			AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"SH2 domain containing"	4037	protein-coding gene	gene with protein product		137025	"FYN oncogene related to SRC, FGR, YES"			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.156C>A	6.37:g.112041099G>T	ENSP00000346671:p.Asn52Lys		112147792	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Missense_Mutation	SNP	ENST00000354650.3	37	CCDS5094.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.465213	0.63513	.	.	ENSG00000010810	ENST00000368682;ENST00000354650;ENST00000229471;ENST00000368667;ENST00000368678;ENST00000229470;ENST00000356013;ENST00000538466;ENST00000544792;ENST00000462856;ENST00000520518;ENST00000517419;ENST00000518295;ENST00000523238;ENST00000524310;ENST00000523574;ENST00000462598;ENST00000518630;ENST00000523570;ENST00000484067;ENST00000521062;ENST00000487824	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.74632	-0.76;-0.68;-0.83;-0.68;-0.76;-0.86;-0.83;-0.76;-0.39;0.38;1.0;1.37;1.38;1.25;1.31;1.59;0.98;0.98	5.55	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	M	0.61703	1.905	0.80722	D	1	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.10450	0.002;0.005;0.005	T	0.66791	-0.5834	10	0.72032	D	0.01	.	13.8129	0.63274	0.0732:0.0:0.9268:0.0	.	52;52;52	P06241;P06241-3;E1P556	FYN_HUMAN;.;.	K	52	ENSP00000357671:N52K;ENSP00000346671:N52K;ENSP00000229471:N52K;ENSP00000357656:N52K;ENSP00000357667:N52K;ENSP00000229470:N52K;ENSP00000348295:N52K;ENSP00000440646:N52K;ENSP00000427993:N52K;ENSP00000429294:N52K;ENSP00000429866:N52K;ENSP00000428695:N52K;ENSP00000430364:N52K;ENSP00000428493:N52K;ENSP00000429992:N52K;ENSP00000429590:N52K;ENSP00000429813:N52K;ENSP00000428045:N52K	ENSP00000229470:N52K	N	-	3	2	FYN	112147792	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.651000	0.83577	2.621000	0.88768	0.561000	0.74099	AAC		0.602	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			T	112041099	G	T	112041099	3	4	61	1	0	0	0	0	1	0	0	0	6145	1020	36	2	1661	2	FYN	6	112041099	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127984	112041099	59073968	4860	12845										
WISP3	8838	broad.mit.edu	37	chr6	112390774	112390774	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatcttgtgtgtgtcagaGaaactgcagagaacctggag	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112390774G>T	ENST00000368666.2	+	5	1302	c.1016G>T	c.(1015-1017)aGa>aTa	p.R339I	WISP3_ENST00000361714.1_Missense_Mutation_p.R357I|TUBE1_ENST00000604814.1_5'Flank|WISP3_ENST00000230529.5_Missense_Mutation_p.R339I|WISP3_ENST00000409166.1_Missense_Mutation_p.R115I|WISP3_ENST00000368663.3_Missense_Mutation_p.R316I|WISP3_ENST00000604763.1_Missense_Mutation_p.R339I	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	339	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)		p.R357I(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GTGTGTCAGAGAAACTGCAGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											84	81	82					6																	112390774		2203	4300	6503	112497467	SO:0001583	missense	8838			AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.1016G>T	6.37:g.112390774G>T	ENSP00000357655:p.Arg339Ile		112497467	Q3KR29|Q5H8W4|Q6UXH6	Missense_Mutation	SNP	ENST00000368666.2	37	CCDS5098.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951592	0.53186	.	.	ENSG00000112761	ENST00000368666;ENST00000230529;ENST00000541491;ENST00000361714;ENST00000368663;ENST00000409166	T;T;T;T;D	0.81739	-1.27;-1.27;-1.27;-1.26;-1.53	5.33	4.34	0.51931	Cystine knot (1);Cystine knot, C-terminal (2);	0.096626	0.64402	D	0.000001	T	0.71392	0.3334	L	0.56769	1.78	0.58432	D	0.999995	P;P	0.50710	0.935;0.938	P;P	0.50314	0.505;0.637	T	0.69529	-0.5121	10	0.23302	T	0.38	-11.1563	7.1587	0.25652	0.2657:0.0:0.7343:0.0	.	357;339	O95389-2;O95389	.;WISP3_HUMAN	I	339;339;115;357;316;115	ENSP00000357655:R339I;ENSP00000230529:R339I;ENSP00000354734:R357I;ENSP00000357652:R316I;ENSP00000386467:R115I	ENSP00000230529:R339I	R	+	2	0	WISP3	112497467	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.845000	0.39279	2.506000	0.84524	0.467000	0.42956	AGA		0.348	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880		T	112390774	G	T	112390774	3	4	61	1	0	0	0	0	1	0	0	0	17414	942	33	2	1088	2	WISP3	6	112390774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	349675	112390774	58724293	4861	12846										
TUBE1	51175	broad.mit.edu	37	chr6	112394052	112394052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtgtttggggtctgcccGaagcagctggtgatctttac	13	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112394052G>A	ENST00000368662.5	-	10	1081	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W	TUBE1_ENST00000604814.1_5'UTR	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	335					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R335W(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		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)	Vinblastine(DB00570)	GGGTCTGCCCGAAGCAGCTGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											113	120	117					6																	112394052		2203	4300	6503	112500745	SO:0001583	missense	51175			AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.1003C>T	6.37:g.112394052G>A	ENSP00000357651:p.Arg335Trp		112500745	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	37	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.362841	0.82353	.	.	ENSG00000074935	ENST00000368662	D	0.81821	-1.54	6.06	6.06	0.98353	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.408588	0.26514	N	0.023946	T	0.80808	0.4694	L	0.46157	1.445	0.80722	D	1	D	0.53745	0.962	P	0.51453	0.67	T	0.81974	-0.0687	10	0.87932	D	0	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	335	Q9UJT0	TBE_HUMAN	W	335	ENSP00000357651:R335W	ENSP00000357651:R335W	R	-	1	2	TUBE1	112500745	1.000000	0.71417	0.241000	0.24154	0.701000	0.40568	7.636000	0.83301	2.879000	0.98667	0.650000	0.86243	CGG		0.373	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		A	112394052	G	A	112394052	3	1	61	1	0	0	0	0	1	0	0	0	16803	1057	37	1	436	1	TUBE1	6	112394052	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3278	112394052	58721015	4862	12847										
TUBE1	51175	broad.mit.edu	37	chr6	112397237	112397237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagaacttgaagtaaccaGactctttggcttcacagttg	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112397237G>T	ENST00000368662.5	-	8	793	c.715C>A	c.(715-717)Ctg>Atg	p.L239M	TUBE1_ENST00000604814.1_5'UTR	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	239					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.L239M(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		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)	Vinblastine(DB00570)	GAAGTAACCAGACTCTTTGGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											160	173	168					6																	112397237		2203	4300	6503	112503930	SO:0001583	missense	51175			AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.715C>A	6.37:g.112397237G>T	ENSP00000357651:p.Leu239Met		112503930	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	37	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931165	0.52866	.	.	ENSG00000074935	ENST00000368658;ENST00000368662;ENST00000441191	T	0.78816	-1.21	5.92	4.09	0.47781	Tubulin/FtsZ, GTPase domain (3);	0.125198	0.53938	D	0.000046	T	0.49287	0.1548	N	0.08118	0	0.80722	D	1	P	0.51240	0.943	P	0.46718	0.525	T	0.61372	-0.7076	10	0.62326	D	0.03	.	7.828	0.29326	0.2829:0.0:0.7171:0.0	.	239	Q9UJT0	TBE_HUMAN	M	195;239;195	ENSP00000357651:L239M	ENSP00000357647:L195M	L	-	1	2	TUBE1	112503930	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.576000	0.36504	1.434000	0.47414	0.650000	0.86243	CTG		0.398	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		T	112397237	G	T	112397237	3	4	61	1	0	0	0	0	1	0	0	0	16803	933	33	2	732	2	TUBE1	6	112397237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3185	112397237	58717830	4863	12848										
LAMA4	3910	broad.mit.edu	37	chr6	112457365	112457365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttgagctttctttaacGtatcttcaagatgcacaggg	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112457365G>A	ENST00000230538.7	-	25	3771	c.3374C>T	c.(3373-3375)aCg>aTg	p.T1125M	LAMA4_ENST00000389463.4_Missense_Mutation_p.T1118M|LAMA4_ENST00000522006.1_Missense_Mutation_p.T1118M|LAMA4_ENST00000424408.2_Missense_Mutation_p.T1118M	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1125	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)	p.T1118M(1)		NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		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)		TTTCTTTAACGTATCTTCAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											137	122	127					6																	112457365		2203	4300	6503	112564058	SO:0001583	missense	3910				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.3374C>T	6.37:g.112457365G>A	ENSP00000230538:p.Thr1125Met		112564058	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	g	17.31	3.357414	0.61293	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.93	5.07	0.68467	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.202649	0.51477	N	0.000086	T	0.70745	0.3259	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60886	0.88;0.809	T	0.80106	-0.1521	10	0.59425	D	0.04	.	15.3825	0.74669	0.0666:0.0:0.9334:0.0	.	1125;1118	Q16363;Q16363-2	LAMA4_HUMAN;.	M	1125;1118;1118;1118	ENSP00000230538:T1125M;ENSP00000429488:T1118M;ENSP00000374114:T1118M;ENSP00000416470:T1118M	ENSP00000230538:T1125M	T	-	2	0	LAMA4	112564058	1.000000	0.71417	0.896000	0.35187	0.415000	0.31203	5.135000	0.64777	1.527000	0.49086	-0.119000	0.15052	ACG		0.363	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112457365	G	A	112457365	3	1	61	1	0	0	0	0	1	0	0	0	8630	1145	40	1	2157	1	LAMA4	6	112457365	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60128	112457365	58657702	4864	12849										
LAMA4	3910	broad.mit.edu	37	chr6	112480078	112480078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgcataaatccctgacGcattctaaagaaaaaaattt	4	8	2	2	rs137893207		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112480078G>A	ENST00000230538.7	-	14	2070	c.1673C>T	c.(1672-1674)gCg>gTg	p.A558V	LAMA4_ENST00000389463.4_Missense_Mutation_p.A551V|RP1-142L7.5_ENST00000585373.1_RNA|LAMA4_ENST00000522006.1_Missense_Mutation_p.A551V|LAMA4_ENST00000424408.2_Missense_Mutation_p.A551V|RP1-142L7.5_ENST00000425503.1_RNA	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	558	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)	p.A551V(2)		NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		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)		AATCCCTGACGCATTCTAAAG	0.303													G|||	1	0.000199681	8e-04	0	5008	,	,		16725	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	6						G	VAL/ALA,VAL/ALA,VAL/ALA	0,4404		0,0,2202	95	86	89		1673,1652,1652	5.7	1	6	dbSNP_134	89	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	64,64,64	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign	558/1824,551/1817,551/1817	112480078	2,13002	2202	4300	6502	112586771	SO:0001583	missense	3910				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.1673C>T	6.37:g.112480078G>A	ENSP00000230538:p.Ala558Val		112586771	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.996	0.754395	0.15778	0.0	2.33E-4	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.12672	2.68;2.66;2.66;2.66	5.68	5.68	0.88126	.	0.251709	0.39210	N	0.001423	T	0.02610	0.0079	N	0.12182	0.205	0.80722	D	1	B;B	0.27971	0.123;0.196	B;B	0.19148	0.008;0.024	T	0.17653	-1.0362	10	0.05959	T	0.93	.	16.695	0.85333	0.0:0.0:1.0:0.0	.	558;551	Q16363;Q16363-2	LAMA4_HUMAN;.	V	558;551;551;551	ENSP00000230538:A558V;ENSP00000429488:A551V;ENSP00000374114:A551V;ENSP00000416470:A551V	ENSP00000230538:A558V	A	-	2	0	LAMA4	112586771	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	2.197000	0.42696	2.668000	0.90789	0.591000	0.81541	GCG		0.303	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112480078	G	A	112480078	3	1	61	1	0	0	0	0	1	0	0	0	8630	1087	38	1	3902	1	LAMA4	6	112480078	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22713	112480078	58634989	4865	12850										
RFPL4B	442247	broad.mit.edu	37	chr6	112671465	112671465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttctggatcagcatgaaGgcaggagcaatccatgctaa	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:112671465G>T	ENST00000441065.2	+	3	867	c.555G>T	c.(553-555)aaG>aaT	p.K185N	RP11-506B6.6_ENST00000585611.1_RNA|RP11-506B6.6_ENST00000590673.1_RNA|RP11-506B6.6_ENST00000587816.1_RNA	NM_001013734.2	NP_001013756.2	Q6ZWI9	RFPLB_HUMAN	ret finger protein-like 4B	185	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.K185N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	14		all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209)		all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244)		TCAGCATGAAGGCAGGAGCAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	72	73					6																	112671465		2203	4300	6503	112778158	SO:0001583	missense	442247			AK122906	CCDS34515.1	6q21	2007-04-24			ENSG00000251258	ENSG00000251258		"RING-type (C3HC4) zinc fingers"	33264	protein-coding gene	gene with protein product							Standard	NM_001013734		Approved	RNF211	uc003pvx.1	Q6ZWI9	OTTHUMG00000015390	ENST00000441065.2:c.555G>T	6.37:g.112671465G>T	ENSP00000423391:p.Lys185Asn		112778158	A2RU91	Missense_Mutation	SNP	ENST00000441065.2	37	CCDS34515.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615629	0.28801	.	.	ENSG00000251258	ENST00000441065	T	0.61040	0.14	4.38	0.242	0.15498	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.214318	0.23545	N	0.047037	T	0.23410	0.0566	L	0.45470	1.425	0.09310	N	1	B	0.22541	0.071	B	0.29663	0.105	T	0.25606	-1.0127	10	0.28530	T	0.3	.	4.3258	0.11039	0.2711:0.0:0.537:0.1919	.	185	Q6ZWI9	RFPLB_HUMAN	N	185	ENSP00000423391:K185N	ENSP00000423391:K185N	K	+	3	2	RFPL4B	112778158	0.000000	0.05858	0.001000	0.08648	0.228000	0.25075	0.581000	0.23819	0.012000	0.14892	0.655000	0.94253	AAG		0.532	RFPL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041885.2	NM_001013734		T	112671465	G	T	112671465	3	4	61	1	0	0	0	0	1	0	0	0	13293	991	35	2	557	2	RFPL4B	6	112671465	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191387	112671465	58443602	4866	12851										
HS3ST5	222537	broad.mit.edu	37	chr6	114378562	114378562	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgccaggcacttattaaaGataatattaaaccgcaagca	6	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:114378562G>A	ENST00000312719.5	-	5	2088	c.900C>T	c.(898-900)atC>atT	p.I300I	RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000523087.1_RNA|HS3ST5_ENST00000411826.1_Silent_p.I300I|RP3-399L15.3_ENST00000519270.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	300					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.I300I(3)		breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		ACTTATTAAAGATAATATTAA	0.418																																																3	Substitution - coding silent(3)	large_intestine(1)|lung(1)|endometrium(1)	6											61	66	64					6																	114378562		2203	4300	6503	114485255	SO:0001819	synonymous_variant	222537			AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.900C>T	6.37:g.114378562G>A			114485255	A8K1J2|Q52LI2|Q8N285	Silent	SNP	ENST00000312719.5	37	CCDS34517.1																																																																																				0.418	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		A	114378562	G	A	114378562	2	1	61	1	0	0	0	0	0	0	0	1	7389	932	33	3		3	HS3ST5	6	114378562	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1707097	114378562	56736505	4867	12852										
HS3ST5	222537	broad.mit.edu	37	chr6	114378706	114378706	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaggcgatctccatcgacGacatgaaattgctcaattgg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:114378706G>T	ENST00000312719.5	-	5	1944	c.756C>A	c.(754-756)gtC>gtA	p.V252V	RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000523087.1_RNA|HS3ST5_ENST00000411826.1_Silent_p.V252V|RP3-399L15.3_ENST00000519270.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	252					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.V252V(1)		breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CTCCATCGACGACATGAAATT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6											171	165	167					6																	114378706		2203	4300	6503	114485399	SO:0001819	synonymous_variant	222537			AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.756C>A	6.37:g.114378706G>T			114485399	A8K1J2|Q52LI2|Q8N285	Silent	SNP	ENST00000312719.5	37	CCDS34517.1																																																																																				0.423	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		T	114378706	G	T	114378706	2	4	61	1	0	0	0	0	0	0	0	1	7389	1045	37	2		2	HS3ST5	6	114378706	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144	114378706	56736361	4868	12853										
TSPYL1	7259	broad.mit.edu	37	chr6	116600075	116600075	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagttccttcacctctaAattggttatgtaccttaaca	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116600075A>C	ENST00000368608.3	-	1	991	c.919T>G	c.(919-921)Tta>Gta	p.L307V	DSE_ENST00000452085.3_5'Flank|DSE_ENST00000540275.1_Intron|RP1-93H18.1_ENST00000449314.1_lincRNA	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	307					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.L307V(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		TTCACCTCTAAATTGGTTATG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											118	124	122					6																	116600075		2203	4300	6503	116706768	SO:0001583	missense	7259			AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"TSPY-like"	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.919T>G	6.37:g.116600075A>C	ENSP00000357597:p.Leu307Val		116706768	O75885|Q5TFE6	Missense_Mutation	SNP	ENST00000368608.3	37	CCDS34518.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379147	0.61735	.	.	ENSG00000189241	ENST00000368608	T	0.33216	1.42	4.27	-0.422	0.12329	.	0.000000	0.28659	N	0.014571	T	0.25382	0.0617	L	0.41906	1.305	0.44946	D	0.997968	D	0.89917	1.0	D	0.87578	0.998	T	0.06917	-1.0800	10	0.42905	T	0.14	-3.741	7.2473	0.26129	0.4826:0.0:0.5174:0.0	.	307	Q9H0U9	TSYL1_HUMAN	V	307	ENSP00000357597:L307V	ENSP00000357597:L307V	L	-	1	2	TSPYL1	116706768	0.923000	0.31300	0.988000	0.46212	0.989000	0.77384	0.138000	0.16016	-0.058000	0.13177	0.379000	0.24179	TTA		0.453	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1			C	116600075	A	C	116600075	3	2	61	1	0	0	0	0	1	0	0	0	16699	11	1	4	398	4	TSPYL1	6	116600075	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2221369	116600075	54514992	4869	12854										
DSE	29940	broad.mit.edu	37	chr6	116720488	116720488	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgtcagcctacatcacCgacgagaacccagaagttat	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116720488C>T	ENST00000331677.3	+	3	519	c.75C>T	c.(73-75)acC>acT	p.T25T	DSE_ENST00000452085.3_Silent_p.T25T|DSE_ENST00000540275.1_3'UTR|DSE_ENST00000359564.2_Silent_p.T25T|DSE_ENST00000537543.1_Silent_p.T44T			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	25			T -> I (in dbSNP:rs10485183).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)	p.T25T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		CCTACATCACCGACGAGAACC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	6											89	78	81					6																	116720488		2203	4300	6503	116827181	SO:0001819	synonymous_variant	29940			AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.75C>T	6.37:g.116720488C>T			116827181	Q5R3K6	Silent	SNP	ENST00000331677.3	37	CCDS5107.1																																																																																				0.512	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116720488	C	T	116720488	2	4	61	1	0	0	0	0	0	0	0	1	4785	639	23	1		1	DSE	6	116720488	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120413	116720488	54394579	4870	12855										
DSE	29940	broad.mit.edu	37	chr6	116747871	116747871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgaagtgattgccaatgCctcagggtatatgtatgaaa	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116747871C>A	ENST00000331677.3	+	4	995	c.551C>A	c.(550-552)gCc>gAc	p.A184D	DSE_ENST00000452085.3_Missense_Mutation_p.A184D|DSE_ENST00000606265.1_3'UTR|DSE_ENST00000359564.2_Missense_Mutation_p.A184D|DSE_ENST00000537543.1_Missense_Mutation_p.A203D			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	184					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)	p.A184D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		ATTGCCAATGCCTCAGGGTAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	100	104					6																	116747871		2203	4300	6503	116854564	SO:0001583	missense	29940			AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.551C>A	6.37:g.116747871C>A	ENSP00000332151:p.Ala184Asp		116854564	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686356	0.68157	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	6.06	4.23	0.50019	.	0.154369	0.64402	D	0.000018	T	0.21674	0.0522	L	0.59436	1.845	0.58432	D	0.999999	P;P	0.43231	0.801;0.693	P;B	0.49332	0.607;0.354	T	0.01225	-1.1413	9	.	.	.	-11.8466	12.1131	0.53850	0.0:0.8577:0.0:0.1423	.	203;184	B7Z765;Q9UL01	.;DSE_HUMAN	D	184;203;184;184	ENSP00000404049:A184D;ENSP00000441152:A203D;ENSP00000332151:A184D;ENSP00000352567:A184D	.	A	+	2	0	DSE	116854564	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.128000	0.42045	0.838000	0.34948	0.655000	0.94253	GCC		0.463	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		A	116747871	C	A	116747871	3	1	61	1	0	0	0	0	1	0	0	0	4785	739	26	2	557	2	DSE	6	116747871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27383	116747871	54367196	4871	12856										
FAM26F	441168	broad.mit.edu	37	chr6	116784651	116784651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgtttctttgagggctCgcatccaaaagaatataaca	7	7	1	2	rs557482432		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116784651C>T	ENST00000368605.1	+	3	826	c.731C>T	c.(730-732)tCg>tTg	p.S244L	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Missense_Mutation_p.S72L	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	244					ion transport (GO:0006811)	integral component of membrane (GO:0016021)		p.S244L(1)		large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		TTTGAGGGCTCGCATCCAAAA	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		18324	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											124	126	125					6																	116784651		2203	4300	6503	116891344	SO:0001583	missense	441168			AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 187"	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.731C>T	6.37:g.116784651C>T	ENSP00000357594:p.Ser244Leu		116891344	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673276	0.29693	.	.	ENSG00000188820	ENST00000368606;ENST00000368605;ENST00000368604	T;T;T	0.17370	2.28;2.28;2.28	5.11	-0.172	0.13327	.	0.709020	0.12631	N	0.452187	T	0.04003	0.0112	L	0.47716	1.5	0.09310	N	1	B	0.28667	0.219	B	0.21360	0.034	T	0.37314	-0.9711	10	0.38643	T	0.18	-4.0028	5.1432	0.14971	0.2869:0.5098:0.0:0.2033	.	244	Q5R3K3	FA26F_HUMAN	L	72;244;87	ENSP00000357595:S72L;ENSP00000357594:S244L;ENSP00000357593:S87L	ENSP00000357593:S87L	S	+	2	0	FAM26F	116891344	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.767000	0.26575	-0.255000	0.09486	-0.897000	0.02905	TCG		0.398	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919		T	116784651	C	T	116784651	3	4	61	1	0	0	0	0	1	0	0	0	5570	893	31	1	737	1	FAM26F	6	116784651	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36780	116784651	54330416	4872	12857										
RWDD1	51389	broad.mit.edu	37	chr6	116892815	116892815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctaccctgactccttcAcaggtgactcccgcggccgc	8	19	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116892815A>G	ENST00000466444.2	+	1	286	c.70A>G	c.(70-72)Aca>Gca	p.T24A	RWDD1_ENST00000392526.1_5'UTR|RWDD1_ENST00000517800.1_3'UTR|RWDD1_ENST00000487832.2_5'UTR	NM_015952.2	NP_057036.2	Q9H446	RWDD1_HUMAN	RWD domain containing 1	24	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.							p.T24A(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)	12		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		TGACTCCTTCACAGGTGACTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											40	32	34					6																	116892815		2203	4299	6502	116999508	SO:0001583	missense	51389			AF092134	CCDS34520.1, CCDS43496.1	6q13-q22.33	2012-12-07			ENSG00000111832	ENSG00000111832			20993	protein-coding gene	gene with protein product						10810093	Standard	NM_016104		Approved	PTD013	uc003pxd.3	Q9H446	OTTHUMG00000015441	ENST00000466444.2:c.70A>G	6.37:g.116892815A>G	ENSP00000420357:p.Thr24Ala		116999508	A8K3W2|A8MT24|Q9Y313|Q9Y6B3	Missense_Mutation	SNP	ENST00000466444.2	37	CCDS34520.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.738477	0.69304	.	.	ENSG00000111832	ENST00000466444	T	0.40756	1.02	5.88	5.88	0.94601	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	T	0.38268	0.1034	M	0.77313	2.365	0.80722	D	1	B	0.17852	0.024	B	0.36666	0.23	T	0.35674	-0.9779	10	0.27082	T	0.32	-0.4468	13.8241	0.63340	1.0:0.0:0.0:0.0	.	24	Q9H446	RWDD1_HUMAN	A	24	ENSP00000420357:T24A	ENSP00000420357:T24A	T	+	1	0	RWDD1	116999508	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.107000	0.64603	2.246000	0.74042	0.533000	0.62120	ACA		0.647	RWDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041952.2	NM_015952		G	116892815	A	G	116892815	3	3	61	1	0	0	0	0	1	0	0	0	13791	159	6	4	72	4	RWDD1	6	116892815	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	108164	116892815	54222252	4873	12858										
RSPH4A	345895	broad.mit.edu	37	chr6	116938122	116938122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaccacctcagtcggacagGaccacgagtgtgattcctga	11	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116938122G>T	ENST00000229554.5	+	1	473	c.336G>T	c.(334-336)agG>agT	p.R112S	RSPH4A_ENST00000368581.4_Missense_Mutation_p.R112S|RSPH4A_ENST00000368580.4_Missense_Mutation_p.R112S	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	112					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)		p.R112S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGTCGGACAGGACCACGAGTG	0.552									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	6											64	66	65					6																	116938122		2203	4300	6503	117044815	SO:0001583	missense	345895	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"radial spokehead-like 3"	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.336G>T	6.37:g.116938122G>T	ENSP00000229554:p.Arg112Ser		117044815	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996477	0.35226	.	.	ENSG00000111834	ENST00000368581;ENST00000229554;ENST00000368580	T;T;T	0.66638	-0.22;1.43;1.35	5.53	2.68	0.31781	.	0.530412	0.18057	N	0.153078	T	0.23532	0.0569	N	0.19112	0.55	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.10450	0.005;0.002	T	0.17961	-1.0352	10	0.26408	T	0.33	-7.0196	5.0845	0.14675	0.19:0.1692:0.6407:0.0	.	112;112	Q5TD94-3;Q5TD94	.;RSH4A_HUMAN	S	112	ENSP00000357570:R112S;ENSP00000229554:R112S;ENSP00000357569:R112S	ENSP00000229554:R112S	R	+	3	2	RSPH4A	117044815	0.001000	0.12720	0.001000	0.08648	0.014000	0.08584	0.699000	0.25586	0.389000	0.25086	0.655000	0.94253	AGG		0.552	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892		T	116938122	G	T	116938122	3	4	61	1	0	0	0	0	1	0	0	0	13743	1165	41	2	338	2	RSPH4A	6	116938122	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45307	116938122	54176945	4874	12859										
RSPH4A	345895	broad.mit.edu	37	chr6	116949371	116949371	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacccacgtcagtcctctaGgattttatcagtttggtgaa	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:116949371G>T	ENST00000229554.5	+	3	1638	c.1501G>T	c.(1501-1503)Gga>Tga	p.G501*	RSPH4A_ENST00000368581.4_Nonsense_Mutation_p.G501*|RSPH4A_ENST00000368580.4_Intron	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	501					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)		p.G501*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CAGTCCTCTAGGATTTTATCA	0.463									Kartagener syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	6											65	68	67					6																	116949371		2203	4300	6503	117056064	SO:0001587	stop_gained	345895	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"radial spokehead-like 3"	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1501G>T	6.37:g.116949371G>T	ENSP00000229554:p.Gly501*		117056064	B4DSI1|Q3KP24|Q5TD95	Nonsense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	.	.	.	.	.	.	.	.	.	.	G	38	7.195125	0.98129	.	.	ENSG00000111834	ENST00000368581;ENST00000229554;ENST00000447842	.	.	.	5.74	5.74	0.90152	.	0.100592	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.7375	17.4199	0.87512	0.0:0.0:1.0:0.0	.	.	.	.	X	501;501;296	.	ENSP00000229554:G501X	G	+	1	0	RSPH4A	117056064	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.273000	0.95719	2.707000	0.92482	0.655000	0.94253	GGA		0.463	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892		T	116949371	G	T	116949371	4	4	61	1	0	0	0	0	0	1	0	0	13743	1001	35	2	1511	2	RSPH4A	6	116949371	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11249	116949371	54165696	4875	12860										
KPNA5	3841	broad.mit.edu	37	chr6	117023265	117023265	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaaactggggctgttccGatttttatcaaacttcttaa	7	7	2	1	rs374140887		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117023265G>A	ENST00000368564.1	+	6	667	c.519G>A	c.(517-519)ccG>ccA	p.P173P	KPNA5_ENST00000356348.1_Silent_p.P173P			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	170	NLS binding site (major). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)	p.P173P(1)		breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		GGGCTGTTCCGATTTTTATCA	0.348													G|||	1	0.000199681	0	0	5008	,	,		17552	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											109	109	109					6																	117023265		2203	4300	6503	117129958	SO:0001819	synonymous_variant	3841			AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"Importins", "Armadillo repeat containing"	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.519G>A	6.37:g.117023265G>A			117129958	B2RAI5|Q86X23	Silent	SNP	ENST00000368564.1	37	CCDS5111.1																																																																																				0.348	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269		A	117023265	G	A	117023265	2	1	61	1	0	0	0	0	0	0	0	1	8454	1045	37	1		1	KPNA5	6	117023265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73894	117023265	54091802	4876	12861										
GPRC6A	222545	broad.mit.edu	37	chr6	117130538	117130538	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttatttctgagtacccaGaacctatgacagccttaact	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117130538G>T	ENST00000310357.3	-	2	458	c.437C>A	c.(436-438)tCt>tAt	p.S146Y	GPRC6A_ENST00000530250.1_Missense_Mutation_p.S146Y|GPRC6A_ENST00000368549.3_Missense_Mutation_p.S146Y	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	146					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S146Y(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGAGTACCCAGAACCTATGAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											90	87	88					6																	117130538		2203	4300	6503	117237231	SO:0001583	missense	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.437C>A	6.37:g.117130538G>T	ENSP00000309493:p.Ser146Tyr		117237231	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551354	0.65311	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.83250	-1.7;-1.7;-1.7	4.86	4.86	0.63082	Extracellular ligand-binding receptor (1);	0.236875	0.32287	N	0.006305	T	0.65091	0.2658	N	0.24115	0.695	0.27806	N	0.94231	P;P;P	0.46277	0.875;0.683;0.754	B;B;B	0.43445	0.309;0.243;0.42	T	0.65504	-0.6152	10	0.59425	D	0.04	.	13.1878	0.59691	0.0:0.0:0.8407:0.1593	.	146;146;146	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	Y	146	ENSP00000309493:S146Y;ENSP00000357537:S146Y;ENSP00000433465:S146Y	ENSP00000309493:S146Y	S	-	2	0	GPRC6A	117237231	0.998000	0.40836	1.000000	0.80357	0.936000	0.57629	4.511000	0.60462	2.531000	0.85337	0.585000	0.79938	TCT		0.423	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117130538	G	T	117130538	3	4	61	1	0	0	0	0	1	0	0	0	6749	942	33	2	2363	2	GPRC6A	6	117130538	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107273	117130538	53984529	4877	12862										
GPRC6A	222545	broad.mit.edu	37	chr6	117150134	117150134	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaggctgtgaagtagcaaGaataatcacaaagcaggtaa	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117150134G>T	ENST00000310357.3	-	1	64	c.43C>A	c.(43-45)Ctt>Att	p.L15I	GPRC6A_ENST00000530250.1_Missense_Mutation_p.L15I|GPRC6A_ENST00000368549.3_Missense_Mutation_p.L15I	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	15					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L15I(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		GAAGTAGCAAGAATAATCACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	102	101					6																	117150134		2203	4300	6503	117256827	SO:0001583	missense	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.43C>A	6.37:g.117150134G>T	ENSP00000309493:p.Leu15Ile		117256827	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.998213	0.35226	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.91011	-2.55;-2.77;-2.76	5.18	-0.128	0.13506	.	0.934464	0.09040	N	0.857425	T	0.60117	0.2244	N	0.08118	0	0.09310	N	1	P;P;B	0.38078	0.617;0.51;0.376	B;B;B	0.37144	0.242;0.154;0.141	T	0.58719	-0.7587	10	0.21014	T	0.42	.	4.9839	0.14180	0.5774:0.0:0.2641:0.1585	.	15;15;15	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	I	15	ENSP00000309493:L15I;ENSP00000357537:L15I;ENSP00000433465:L15I	ENSP00000309493:L15I	L	-	1	0	GPRC6A	117256827	0.969000	0.33509	0.918000	0.36340	0.895000	0.52256	0.658000	0.24979	0.062000	0.16340	-0.136000	0.14681	CTT		0.393	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117150134	G	T	117150134	3	4	61	1	0	0	0	0	1	0	0	0	6749	942	33	2	2761	2	GPRC6A	6	117150134	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19596	117150134	53964933	4878	12863										
RFX6	222546	broad.mit.edu	37	chr6	117232115	117232115	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagggtggcttcactcgtaaAtattcgcttagctcaaaaac	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117232115A>C	ENST00000332958.2	+	7	706	c.690A>C	c.(688-690)aaA>aaC	p.K230N	RFX6_ENST00000471966.1_3'UTR	NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	230					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)	p.K230N(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						TCACTCGTAAATATTCGCTTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	101	100					6																	117232115		2203	4300	6503	117338808	SO:0001583	missense	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.690A>C	6.37:g.117232115A>C	ENSP00000332208:p.Lys230Asn		117338808	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054176	0.75960	.	.	ENSG00000185002	ENST00000332958	T	0.57752	0.38	5.77	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	L	0.44542	1.39	0.58432	D	0.999993	D	0.89917	1.0	D	0.71184	0.972	T	0.54536	-0.8279	10	0.45353	T	0.12	-24.8661	11.8778	0.52558	0.9317:0.0:0.0683:0.0	.	230	Q8HWS3	RFX6_HUMAN	N	230	ENSP00000332208:K230N	ENSP00000332208:K230N	K	+	3	2	RFX6	117338808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.179000	0.58290	1.114000	0.41781	0.533000	0.62120	AAA		0.343	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		C	117232115	A	C	117232115	3	2	61	1	0	0	0	0	1	0	0	0	13304	98	4	4	716	4	RFX6	6	117232115	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	81981	117232115	53882952	4879	12864										
RFX6	222546	broad.mit.edu	37	chr6	117250120	117250120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatctccagttgcatgtcGaactccagtcctaggtaaat	7	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117250120G>A	ENST00000332958.2	+	18	2613	c.2597G>A	c.(2596-2598)cGa>cAa	p.R866Q		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	866					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)	p.R866Q(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						GTTGCATGTCGAACTCCAGTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											112	99	103					6																	117250120		2203	4300	6503	117356813	SO:0001583	missense	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.2597G>A	6.37:g.117250120G>A	ENSP00000332208:p.Arg866Gln		117356813	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583543	0.65992	.	.	ENSG00000185002	ENST00000332958	T	0.56776	0.44	5.63	5.63	0.86233	.	0.406919	0.25762	N	0.028472	T	0.28333	0.0700	L	0.29908	0.895	0.46478	D	0.999069	B	0.33135	0.399	B	0.16289	0.015	T	0.10474	-1.0628	10	0.41790	T	0.15	-17.6006	20.0442	0.97604	0.0:0.0:1.0:0.0	.	866	Q8HWS3	RFX6_HUMAN	Q	866	ENSP00000332208:R866Q	ENSP00000332208:R866Q	R	+	2	0	RFX6	117356813	1.000000	0.71417	0.999000	0.59377	0.797000	0.45037	4.649000	0.61433	2.814000	0.96858	0.655000	0.94253	CGA		0.403	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117250120	G	A	117250120	3	1	61	1	0	0	0	0	1	0	0	0	13304	1058	37	1	2667	1	RFX6	6	117250120	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18005	117250120	53864947	4880	12865										
ROS1	6098	broad.mit.edu	37	chr6	117629975	117629975	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagatcatcaggacaatttCttggtggctccagtctccct	8	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117629975C>A	ENST00000368508.3	-	41	6749	c.6551G>T	c.(6550-6552)aGa>aTa	p.R2184I	ROS1_ENST00000368507.3_Missense_Mutation_p.R2178I	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R2184I(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGGACAATTTCTTGGTGGCTC	0.383			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - Missense(2)	large_intestine(2)	6											91	85	87					6																	117629975		2203	4300	6503	117736668	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6551G>T	6.37:g.117629975C>A	ENSP00000357494:p.Arg2184Ile		117736668	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.451709	0.43531	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.83075	-1.68;-1.68	5.05	2.09	0.27110	.	0.380247	0.25358	N	0.031246	T	0.55000	0.1893	N	0.16307	0.4	0.25383	N	0.988597	P	0.46142	0.873	P	0.49192	0.602	T	0.52815	-0.8525	10	0.34782	T	0.22	.	1.664	0.02798	0.1443:0.4507:0.141:0.2639	.	2184	P08922	ROS1_HUMAN	I	2184;2178	ENSP00000357494:R2184I;ENSP00000357493:R2178I	ENSP00000357493:R2178I	R	-	2	0	ROS1	117736668	0.001000	0.12720	1.000000	0.80357	0.990000	0.78478	1.002000	0.29796	0.626000	0.30322	0.650000	0.86243	AGA		0.383	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117629975	C	A	117629975	3	1	61	1	0	0	0	0	1	0	0	0	13568	913	32	2	504	2	ROS1	6	117629975	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	379855	117629975	53485092	4881	12866										
ROS1	6098	broad.mit.edu	37	chr6	117658398	117658398	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcttataaaccaccactaCtctgacattatatgaagtat	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117658398C>A	ENST00000368508.3	-	31	5383	c.5185G>T	c.(5185-5187)Gta>Tta	p.V1729L	ROS1_ENST00000368507.3_Missense_Mutation_p.V1723L|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1729	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V1729L(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ACCACCACTACTCTGACATTA	0.358			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - Missense(2)	large_intestine(2)	6											131	127	128					6																	117658398		2203	4299	6502	117765091	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.5185G>T	6.37:g.117658398C>A	ENSP00000357494:p.Val1729Leu		117765091	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	8.983	0.975894	0.18736	.	.	ENSG00000047936	ENST00000368508;ENST00000368507;ENST00000403284	T;T;T	0.72282	-0.64;-0.64;-0.18	4.6	3.73	0.42828	.	0.341802	0.24901	N	0.034690	T	0.42426	0.1202	L	0.32530	0.975	0.80722	D	1	P	0.36412	0.552	B	0.42462	0.388	T	0.39231	-0.9624	10	0.08837	T	0.75	.	9.2176	0.37358	0.0:0.8963:0.0:0.1037	.	1729	P08922	ROS1_HUMAN	L	1729;1723;36	ENSP00000357494:V1729L;ENSP00000357493:V1723L;ENSP00000384647:V36L	ENSP00000357493:V1723L	V	-	1	0	ROS1	117765091	0.409000	0.25368	0.686000	0.30086	0.911000	0.54048	1.280000	0.33202	1.256000	0.44068	0.655000	0.94253	GTA		0.358	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117658398	C	A	117658398	3	1	61	1	0	0	0	0	1	0	0	0	13568	565	20	2	1910	2	ROS1	6	117658398	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28423	117658398	53456669	4882	12867										
ROS1	6098	broad.mit.edu	37	chr6	117663577	117663577	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttacctccatttttagttTttccccaaatctcttttcct	1	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117663577T>G	ENST00000368508.3	-	28	4853	c.4655A>C	c.(4654-4656)aAa>aCa	p.K1552T	ROS1_ENST00000368507.3_Missense_Mutation_p.K1546T|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1552	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K1552T(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ATTTTTAGTTTTTCCCCAAAT	0.318			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - Missense(2)	large_intestine(2)	6											127	136	133					6																	117663577		2202	4300	6502	117770270	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4655A>C	6.37:g.117663577T>G	ENSP00000357494:p.Lys1552Thr		117770270	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	9.180	1.023334	0.19433	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.51071	0.72;0.72	5.32	2.7	0.31948	.	0.274767	0.30695	N	0.009062	T	0.11537	0.0281	N	0.11560	0.145	0.80722	D	1	B	0.12630	0.006	B	0.11329	0.006	T	0.06006	-1.0851	10	0.24483	T	0.36	.	9.2525	0.37564	0.0:0.0:0.3549:0.6451	.	1552	P08922	ROS1_HUMAN	T	1552;1546	ENSP00000357494:K1552T;ENSP00000357493:K1546T	ENSP00000357493:K1546T	K	-	2	0	ROS1	117770270	0.996000	0.38824	1.000000	0.80357	0.984000	0.73092	0.509000	0.22707	0.947000	0.37659	0.459000	0.35465	AAA		0.318	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117663577	T	G	117663577	3	3	61	1	0	0	0	0	1	0	0	0	13568	1841	64	4	2452	4	ROS1	6	117663577	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5179	117663577	53451490	4883	12868										
ROS1	6098	broad.mit.edu	37	chr6	117681131	117681131	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatatctaaaaaaactatCttgttaccaagaagagttat	4	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117681131C>A	ENST00000368508.3	-	23	3687	c.3489G>T	c.(3487-3489)aaG>aaT	p.K1163N	ROS1_ENST00000368507.3_Missense_Mutation_p.K1158N|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1163					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K1163N(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AAAAAACTATCTTGTTACCAA	0.358			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	2	Substitution - Missense(2)	large_intestine(2)	6											89	86	87					6																	117681131		2203	4300	6503	117787824	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3489G>T	6.37:g.117681131C>A	ENSP00000357494:p.Lys1163Asn		117787824	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.310009	0.23821	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91180	-2.8;-2.8	4.62	3.74	0.42951	.	0.195708	0.35555	N	0.003131	D	0.82632	0.5079	L	0.51422	1.61	0.80722	D	1	P	0.37781	0.608	B	0.37943	0.261	T	0.83299	-0.0029	10	0.48119	T	0.1	.	12.8997	0.58119	0.0:0.8362:0.1638:0.0	.	1163	P08922	ROS1_HUMAN	N	1163;1158	ENSP00000357494:K1163N;ENSP00000357493:K1158N	ENSP00000357493:K1158N	K	-	3	2	ROS1	117787824	0.993000	0.37304	0.846000	0.33378	0.276000	0.26787	0.643000	0.24750	1.235000	0.43724	0.655000	0.94253	AAG		0.358	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117681131	C	A	117681131	3	1	61	1	0	0	0	0	1	0	0	0	13568	912	32	2	3638	2	ROS1	6	117681131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17554	117681131	53433936	4884	12869										
GOPC	57120	broad.mit.edu	37	chr6	117896422	117896422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaacagctatatgtctacGaagggcttcattctcttttc	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:117896422G>A	ENST00000368498.2	-	4	643	c.568C>T	c.(568-570)Cgt>Tgt	p.R190C	GOPC_ENST00000535237.1_Missense_Mutation_p.R190C|GOPC_ENST00000467125.1_5'Flank|GOPC_ENST00000052569.6_Missense_Mutation_p.R182C	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	190					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)	p.R190C(1)	GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		ATATGTCTACGAAGGGCTTCA	0.408			O	ROS1	glioblastoma																																		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	1	Substitution - Missense(1)	large_intestine(1)	6											140	122	128					6																	117896422		2203	4300	6503	118003115	SO:0001583	missense	57120			AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.568C>T	6.37:g.117896422G>A	ENSP00000357484:p.Arg190Cys		118003115	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	37	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.570760	0.86542	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	D;T;T	0.84730	-1.89;2.04;0.74	5.65	4.75	0.60458	.	0.000000	0.85682	D	0.000000	D	0.90287	0.6962	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.98	D	0.90890	0.4760	10	0.72032	D	0.01	-20.0627	16.0078	0.80374	0.0:0.0:0.8651:0.1349	.	182;190	Q9HD26-2;Q9HD26	.;GOPC_HUMAN	C	182;190;190	ENSP00000052569:R182C;ENSP00000357484:R190C;ENSP00000445690:R190C	ENSP00000052569:R182C	R	-	1	0	GOPC	118003115	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.001000	0.88508	2.660000	0.90430	0.591000	0.81541	CGT		0.408	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		A	117896422	G	A	117896422	3	1	61	1	0	0	0	0	1	0	0	0	6593	1058	37	1	844	1	GOPC	6	117896422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215291	117896422	53218645	4885	12870										
SLC35F1	222553	broad.mit.edu	37	chr6	118475625	118475625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggagatgttaatctctgTggccctaggccaggtgttat	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:118475625T>C	ENST00000360388.4	+	2	392	c.191T>C	c.(190-192)gTg>gCg	p.V64A		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	64					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.V64A(1)		breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		TTAATCTCTGTGGCCCTAGGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											168	159	162					6																	118475625		2203	4300	6503	118582318	SO:0001583	missense	222553			BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"Solute carriers"	21483	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 169"	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.191T>C	6.37:g.118475625T>C	ENSP00000353557:p.Val64Ala		118582318	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	T	19.48	3.836039	0.71373	.	.	ENSG00000196376	ENST00000360388	.	.	.	6.02	6.02	0.97574	.	0.071450	0.56097	D	0.000032	T	0.52092	0.1713	L	0.49126	1.545	0.48236	D	0.999615	B	0.30914	0.3	B	0.37198	0.243	T	0.59423	-0.7457	9	0.72032	D	0.01	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	64	Q5T1Q4	S35F1_HUMAN	A	64	.	ENSP00000353557:V64A	V	+	2	0	SLC35F1	118582318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.967000	0.76079	2.311000	0.77944	0.533000	0.62120	GTG		0.423	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044		C	118475625	T	C	118475625	3	2	61	1	0	0	0	0	1	0	0	0	14625	1696	59	4	197	4	SLC35F1	6	118475625	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	579203	118475625	52639442	4886	12871										
SLC35F1	222553	broad.mit.edu	37	chr6	118596708	118596708	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgggaagaatacatcatcCgaactctgagccgagtggaa	11	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:118596708C>T	ENST00000360388.4	+	5	925	c.724C>T	c.(724-726)Cga>Tga	p.R242*		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	242					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.R242*(1)		breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		ATACATCATCCGAACTCTGAG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											113	111	112					6																	118596708		2203	4300	6503	118703401	SO:0001587	stop_gained	222553			BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"Solute carriers"	21483	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 169"	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.724C>T	6.37:g.118596708C>T	ENSP00000353557:p.Arg242*		118703401	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Nonsense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	C	37	6.554281	0.97658	.	.	ENSG00000196376	ENST00000360388	.	.	.	5.07	5.07	0.68467	.	0.144445	0.44285	D	0.000480	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	13.9102	0.63862	0.1521:0.8479:0.0:0.0	.	.	.	.	X	242	.	ENSP00000353557:R242X	R	+	1	2	SLC35F1	118703401	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.769000	0.68865	2.780000	0.95670	0.655000	0.94253	CGA		0.423	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044		T	118596708	C	T	118596708	4	4	61	1	0	0	0	0	0	1	0	0	14625	644	23	1	742	1	SLC35F1	6	118596708	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121083	118596708	52518359	4887	12872										
SLC35F1	222553	broad.mit.edu	37	chr6	118606379	118606379	+	Frame_Shift_Del	DEL	T	T	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggctttagtgcctgcatgTttggtctctacagctttatg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:118606379delT	ENST00000360388.4	+	7	1081	c.880delT	c.(880-882)tttfs	p.F294fs		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	294					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.F294fs*11(1)		breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		TGCCTGCATGTTTGGTCTCTA	0.527											OREG0017635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Deletion - Frameshift(1)	large_intestine(1)	6											260	252	255					6																	118606379		2203	4300	6503	118713072	SO:0001589	frameshift_variant	222553			BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"Solute carriers"	21483	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 169"	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.880delT	6.37:g.118606379delT	ENSP00000353557:p.Phe294fs	1489	118713072	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Frame_Shift_Del	DEL	ENST00000360388.4	37	CCDS34524.1																																																																																				0.527	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044		-	118606379	T	-	118606379	7	5	61	1	0	1	0	1	0	0	0	0	14625	1725	60	0	906	0	SLC35F1	6	118606379	Frame_Shift_Del	DEL	T	TCGA-AG-A002-01A-01W-A00K-09	9671	118606379	52508688	4888	12873										
PLN	5350	broad.mit.edu	37	chr6	118880208	118880208	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtctcatcttaatatgtCtcttgctgatctgtatcatc	5	10	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:118880208C>T	ENST00000357525.5	+	2	316	c.124C>T	c.(124-126)Ctc>Ttc	p.L42F	CEP85L_ENST00000368488.5_Intron|CEP85L_ENST00000419517.2_Intron|CEP85L_ENST00000392500.3_Intron|CEP85L_ENST00000368491.3_Intron|CEP85L_ENST00000360290.3_Intron	NM_002667.3	NP_002658.1	P26678	PPLA_HUMAN	phospholamban	42					adrenergic receptor signaling pathway involved in heart process (GO:0086023)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cardiac muscle tissue development (GO:0048738)|cytosolic calcium ion homeostasis (GO:0051480)|negative regulation of ATPase activity (GO:0032780)|negative regulation of calcium ion binding (GO:1901877)|negative regulation of calcium ion import (GO:0090281)|negative regulation of calcium ion import into sarcoplasmic reticulum (GO:1902081)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium-transporting ATPase activity (GO:1901895)|negative regulation of catalytic activity (GO:0043086)|negative regulation of heart rate (GO:0010459)|protein homooligomerization (GO:0051260)|regulation of calcium ion transport (GO:0051924)|regulation of calcium-transporting ATPase activity (GO:1901894)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart contraction (GO:0008016)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of the force of heart contraction by cardiac conduction (GO:0086092)|relaxation of cardiac muscle (GO:0055119)|response to testosterone (GO:0033574)|response to zinc ion (GO:0010043)	calcium ion-transporting ATPase complex (GO:0090534)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|vesicle (GO:0031982)	ATPase binding (GO:0051117)|ATPase inhibitor activity (GO:0042030)|calcium channel regulator activity (GO:0005246)|enzyme inhibitor activity (GO:0004857)|identical protein binding (GO:0042802)	p.L42F(1)		large_intestine(1)|lung(3)	4		all_cancers(87;0.0916)|all_epithelial(87;0.131)		GBM - Glioblastoma multiforme(226;0.0325)|all cancers(137;0.154)|OV - Ovarian serous cystadenocarcinoma(136;0.176)		CTTAATATGTCTCTTGCTGAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											190	173	179					6																	118880208		2203	4300	6503	118986901	SO:0001583	missense	5350				CCDS5120.1	6q22.1	2014-09-17			ENSG00000198523	ENSG00000198523			9080	protein-coding gene	gene with protein product		172405		PLB		1828805	Standard	NM_002667		Approved	CMD1P	uc003pye.3	P26678	OTTHUMG00000015462	ENST00000357525.5:c.124C>T	6.37:g.118880208C>T	ENSP00000350132:p.Leu42Phe		118986901		Missense_Mutation	SNP	ENST00000357525.5	37	CCDS5120.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024610	0.54683	.	.	ENSG00000198523	ENST00000357525	D	0.92149	-2.98	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000003	D	0.95790	0.8630	.	.	.	0.58432	D	0.999999	D	0.63880	0.993	D	0.68943	0.961	D	0.96045	0.9027	9	0.87932	D	0	-12.2407	19.1001	0.93270	0.0:1.0:0.0:0.0	.	42	P26678	PPLA_HUMAN	F	42	ENSP00000350132:L42F	ENSP00000350132:L42F	L	+	1	0	PLN	118986901	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	6.473000	0.73572	2.514000	0.84764	0.655000	0.94253	CTC		0.413	PLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041993.1	NM_002667		T	118880208	C	T	118880208	3	4	61	1	0	0	0	0	1	0	0	0	12131	913	32	3	126	3	PLN	6	118880208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	273829	118880208	52234859	4889	12874										
FAM184A	79632	broad.mit.edu	37	chr6	119296213	119296213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgttggttagattcacttCgtattctgagaatttctttc	7	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:119296213C>T	ENST00000338891.7	-	13	3187	c.2744G>A	c.(2743-2745)cGa>cAa	p.R915Q	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Missense_Mutation_p.R795Q|FAM184A_ENST00000368475.4_Missense_Mutation_p.R795Q|FAM184A_ENST00000521531.1_Missense_Mutation_p.R915Q	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	915						extracellular space (GO:0005615)		p.R915Q(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						AGATTCACTTCGTATTCTGAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											153	133	139					6																	119296213		1854	4098	5952	119337912	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2744G>A	6.37:g.119296213C>T	ENSP00000342604:p.Arg915Gln		119337912	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673085	0.67928	.	.	ENSG00000111879	ENST00000521043;ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.30182	2.32;2.34;1.55;1.54	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	M	0.72894	2.215	0.80722	D	1	D;D;D	0.64830	0.98;0.994;0.991	P;P;P	0.53593	0.467;0.73;0.576	T	0.06197	-1.0840	10	0.39692	T	0.17	-10.2862	14.7443	0.69480	0.0:0.9286:0.0:0.0714	.	915;795;915	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	Q	78;915;795;795;915	ENSP00000342604:R915Q;ENSP00000326608:R795Q;ENSP00000357460:R795Q;ENSP00000430442:R915Q	ENSP00000342604:R915Q	R	-	2	0	FAM184A	119337912	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.746000	0.68681	2.705000	0.92388	0.650000	0.86243	CGA		0.368	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119296213	C	T	119296213	3	4	61	1	0	0	0	0	1	0	0	0	5527	884	31	1	702	1	FAM184A	6	119296213	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	416005	119296213	51818854	4890	12875										
FAM184A	79632	broad.mit.edu	37	chr6	119301401	119301401	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatgttgctcctctaattCttcaagctcttgcgtaagcc	7	12	4	1	rs368304565		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:119301401C>A	ENST00000338891.7	-	10	2646	c.2203G>T	c.(2203-2205)Gaa>Taa	p.E735*	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Nonsense_Mutation_p.E615*|FAM184A_ENST00000368475.4_Nonsense_Mutation_p.E615*|FAM184A_ENST00000521531.1_Nonsense_Mutation_p.E735*	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	735						extracellular space (GO:0005615)		p.E735*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TCCTCTAATTCTTCAAGCTCT	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											141	130	133					6																	119301401		1894	4132	6026	119343100	SO:0001587	stop_gained	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2203G>T	6.37:g.119301401C>A	ENSP00000342604:p.Glu735*		119343100	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Nonsense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	44	10.892873	0.99484	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	.	.	.	6.17	5.31	0.75309	.	0.100426	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-8.5402	15.5968	0.76590	0.0:0.9345:0.0:0.0655	.	.	.	.	X	735;615;615;735	.	ENSP00000342604:E735X	E	-	1	0	FAM184A	119343100	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	7.267000	0.78462	1.627000	0.50400	0.655000	0.94253	GAA		0.428	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119301401	C	A	119301401	4	1	61	1	0	0	0	0	0	1	0	0	5527	922	32	2	1255	2	FAM184A	6	119301401	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5188	119301401	51813666	4891	12876										
FAM184A	79632	broad.mit.edu	37	chr6	119324102	119324102	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactttcttctgccatgaatCtcttgctgcatttttctctc	4	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:119324102C>A	ENST00000338891.7	-	9	2493	c.2050G>T	c.(2050-2052)Gat>Tat	p.D684Y	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Missense_Mutation_p.D564Y|FAM184A_ENST00000368475.4_Missense_Mutation_p.D564Y|FAM184A_ENST00000521531.1_Missense_Mutation_p.D684Y	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	684						extracellular space (GO:0005615)		p.D684Y(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TGCCATGAATCTCTTGCTGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											165	162	163					6																	119324102		1864	4105	5969	119365801	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2050G>T	6.37:g.119324102C>A	ENSP00000342604:p.Asp684Tyr		119365801	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644365	0.87859	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.97	5.97	0.96955	.	0.098155	0.64402	D	0.000001	T	0.48786	0.1519	L	0.44542	1.39	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.76071	0.987;0.964;0.986	T	0.43458	-0.9390	10	0.66056	D	0.02	-15.4749	20.4238	0.99064	0.0:1.0:0.0:0.0	.	684;564;684	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	Y	684;564;564;684	ENSP00000342604:D684Y;ENSP00000326608:D564Y;ENSP00000357460:D564Y;ENSP00000430442:D684Y	ENSP00000342604:D684Y	D	-	1	0	FAM184A	119365801	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.467000	0.73547	2.834000	0.97654	0.650000	0.86243	GAT		0.373	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119324102	C	A	119324102	3	1	61	1	0	0	0	0	1	0	0	0	5527	913	32	2	1412	2	FAM184A	6	119324102	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22701	119324102	51790965	4892	12877										
FAM184A	79632	broad.mit.edu	37	chr6	119338090	119338090	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataatattcttgctgagttCtctttgcttcatttactttc	4	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:119338090C>T	ENST00000338891.7	-	5	1795	c.1352G>A	c.(1351-1353)aGa>aAa	p.R451K	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Missense_Mutation_p.R331K|FAM184A_ENST00000522284.1_Missense_Mutation_p.R331K|FAM184A_ENST00000368475.4_Missense_Mutation_p.R331K|FAM184A_ENST00000521531.1_Missense_Mutation_p.R451K	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	451						extracellular space (GO:0005615)		p.R451I(1)|p.R451K(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TTGCTGAGTTCTCTTTGCTTC	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	6											87	82	84					6																	119338090		1804	4066	5870	119379789	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1352G>A	6.37:g.119338090C>T	ENSP00000342604:p.Arg451Lys		119379789	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.867|4.867	0.161138|0.161138	0.09287|0.09287	.|.	.|.	ENSG00000111879|ENSG00000111879	ENST00000448815|ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	.|T;T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61;1.61	4.94|4.94	2.79|2.79	0.32731|0.32731	.|.	.|0.391115	.|0.27122	.|N	.|0.020840	T|T	0.03011|0.03011	0.0089|0.0089	N|N	0.02539|0.02539	-0.55|-0.55	0.21184|0.21184	N|N	0.999763|0.999763	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.0;0.0;0.001	T|T	0.46555|0.46555	-0.9183|-0.9183	5|10	.|0.15499	.|T	.|0.54	-5.8195|-5.8195	7.6499|7.6499	0.28342|0.28342	0.0:0.1432:0.0:0.8568|0.0:0.1432:0.0:0.8568	.|.	.|451;331;451	.|Q8NB25-2;F8W8D6;Q8NB25	.|.;.;F184A_HUMAN	K|K	37|451;331;331;451;331	.|ENSP00000342604:R451K;ENSP00000326608:R331K;ENSP00000357460:R331K;ENSP00000430442:R451K;ENSP00000429826:R331K	.|ENSP00000342604:R451K	E|R	-|-	1|2	0|0	FAM184A|FAM184A	119379789|119379789	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.896000|0.896000	0.52359|0.52359	2.652000|2.652000	0.46682|0.46682	0.344000|0.344000	0.23847|0.23847	-0.424000|-0.424000	0.05967|0.05967	GAA|AGA		0.328	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119338090	C	T	119338090	3	4	61	1	0	0	0	0	1	0	0	0	5527	913	32	3	2126	3	FAM184A	6	119338090	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13988	119338090	51776977	4893	12878										
MAN1A1	4121	broad.mit.edu	37	chr6	119510835	119510835	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacatgtactcacatgttcGattatatgattcatgacaag	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:119510835G>A	ENST00000368468.3	-	10	1981	c.1540C>T	c.(1540-1542)Cga>Tga	p.R514*		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	514					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.R514*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		TCACATGTTCGATTATATGAT	0.453																																					Ovarian(136;8 1825 12608 33541 47587)											1	Substitution - Nonsense(1)	large_intestine(1)	6											138	137	137					6																	119510835		2203	4300	6503	119552534	SO:0001587	stop_gained	4121			AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.1540C>T	6.37:g.119510835G>A	ENSP00000357453:p.Arg514*		119552534	E7EU32|Q6P052|Q9NU44|Q9UJI3	Nonsense_Mutation	SNP	ENST00000368468.3	37	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	G	38	7.201029	0.98132	.	.	ENSG00000111885	ENST00000368468	.	.	.	5.11	4.24	0.50183	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2159	15.0397	0.71781	0.0:0.0:0.8567:0.1433	.	.	.	.	X	514	.	ENSP00000357453:R514X	R	-	1	2	MAN1A1	119552534	1.000000	0.71417	0.977000	0.42913	0.121000	0.20230	6.399000	0.73248	1.130000	0.42092	-0.152000	0.13540	CGA		0.453	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		A	119510835	G	A	119510835	4	1	61	1	0	0	0	0	0	1	0	0	9240	1066	37	1	437	1	MAN1A1	6	119510835	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172745	119510835	51604232	4894	12879										
C6orf170	221322	broad.mit.edu	37	chr6	121412019	121412019	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaggaaaacttgcagatCttgagtctgagtgtgctgta	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121412019C>A	ENST00000398212.2	-	31	3683	c.3634G>T	c.(3634-3636)Gat>Tat	p.D1212Y	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Missense_Mutation_p.D1253Y	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1212	Rab-GAP TBC.				cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.D1212Y(1)									ACTTGCAGATCTTGAGTCTGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											135	129	131					6																	121412019		1847	4101	5948	121453718	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3634G>T	6.37:g.121412019C>A	ENSP00000381270:p.Asp1212Tyr		121453718	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283027	0.80692	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.27890	1.64;1.64	5.17	5.17	0.71159	Rab-GAP/TBC domain (1);	0.052010	0.85682	D	0.000000	T	0.47358	0.1441	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.46911	-0.9157	10	0.87932	D	0	.	17.8272	0.88669	0.0:1.0:0.0:0.0	.	1212	Q96NH3	BROMI_HUMAN	Y	1253;1212	ENSP00000275159:D1253Y;ENSP00000381270:D1212Y	ENSP00000275159:D1253Y	D	-	1	0	C6orf170	121453718	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.647000	0.67923	2.679000	0.91253	0.585000	0.79938	GAT		0.338	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121412019	C	A	121412019	3	1	61	1	0	0	0	0	1	0	0	0	2350	913	32	2	147	2	C6orf170	6	121412019	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1901184	121412019	49703048	4895	12880										
C6orf170	221322	broad.mit.edu	37	chr6	121427278	121427278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatatactggatggatgCcagattctacagtgtcatta	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121427278C>T	ENST00000398212.2	-	30	3405	c.3356G>A	c.(3355-3357)gGc>gAc	p.G1119D	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Missense_Mutation_p.G1160D	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1119	Rab-GAP TBC.				cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.G1119D(1)									TGGATGGATGCCAGATTCTAC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											171	161	164					6																	121427278		1821	4080	5901	121468977	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3356G>A	6.37:g.121427278C>T	ENSP00000381270:p.Gly1119Asp		121468977	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.765987	0.49574	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.19806	2.12;2.12	5.06	4.13	0.48395	Rab-GAP/TBC domain (1);	0.109401	0.64402	D	0.000009	T	0.30479	0.0766	L	0.59436	1.845	0.49051	D	0.999745	D	0.76494	0.999	D	0.70227	0.968	T	0.00647	-1.1628	10	0.29301	T	0.29	.	15.3958	0.74790	0.0:0.8602:0.1398:0.0	.	1119	Q96NH3	BROMI_HUMAN	D	1160;1119	ENSP00000275159:G1160D;ENSP00000381270:G1119D	ENSP00000275159:G1160D	G	-	2	0	C6orf170	121468977	1.000000	0.71417	0.997000	0.53966	0.257000	0.26127	3.684000	0.54671	2.775000	0.95449	0.650000	0.86243	GGC		0.299	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121427278	C	T	121427278	3	4	61	1	0	0	0	0	1	0	0	0	2350	739	26	3	429	3	C6orf170	6	121427278	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15259	121427278	49687789	4896	12881										
C6orf170	221322	broad.mit.edu	37	chr6	121576485	121576485	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtacttacatgttttgggaTtcctggcttactgaagaaac	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121576485T>C	ENST00000398212.2	-	17	2056	c.2007A>G	c.(2005-2007)gaA>gaG	p.E669E	TBC1D32_ENST00000275159.6_Silent_p.E669E	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	669					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.E669E(1)									TGTTTTGGGATTCCTGGCTTA	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	6											59	58	58					6																	121576485		1791	4055	5846	121618184	SO:0001819	synonymous_variant	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2007A>G	6.37:g.121576485T>C			121618184	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																				0.279	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		C	121576485	T	C	121576485	2	2	61	1	0	0	0	0	0	0	0	1	2350	1490	52	4		4	C6orf170	6	121576485	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	149207	121576485	49538582	4897	12882										
C6orf170	221322	broad.mit.edu	37	chr6	121577429	121577429	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattatatgagcacctgtaGgactaaaagatgatacctga	8	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121577429G>T	ENST00000398212.2	-	16	1785	c.1736C>A	c.(1735-1737)cCt>cAt	p.P579H	TBC1D32_ENST00000275159.6_Missense_Mutation_p.P579H	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	579					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.P579H(1)									AGCACCTGTAGGACTAAAAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											32	29	30					6																	121577429		1818	4084	5902	121619128	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1736C>A	6.37:g.121577429G>T	ENSP00000381270:p.Pro579His		121619128	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340614	0.24339	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.18502	2.21;2.21	5.21	0.243	0.15503	.	0.683081	0.15074	N	0.282024	T	0.08358	0.0208	L	0.54323	1.7	0.09310	N	1	P;B	0.36315	0.547;0.005	B;B	0.43331	0.416;0.011	T	0.22800	-1.0206	10	0.72032	D	0.01	-8.9712	5.6096	0.17398	0.404:0.0:0.4722:0.1238	.	579;579	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	H	579	ENSP00000275159:P579H;ENSP00000381270:P579H	ENSP00000275159:P579H	P	-	2	0	C6orf170	121619128	0.998000	0.40836	0.616000	0.29078	0.552000	0.35366	0.957000	0.29215	0.026000	0.15269	-0.136000	0.14681	CCT		0.353	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121577429	G	T	121577429	3	4	61	1	0	0	0	0	1	0	0	0	2350	1000	35	2	2105	2	C6orf170	6	121577429	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	944	121577429	49537638	4898	12883										
C6orf170	221322	broad.mit.edu	37	chr6	121624817	121624817	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaatgcaaaaaagtagatCggatccaaaatcttttgtga	7	6	1	2	rs374800522		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121624817C>T	ENST00000398212.2	-	9	1075	c.1026G>A	c.(1024-1026)ccG>ccA	p.P342P	TBC1D32_ENST00000275159.6_Silent_p.P342P	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	342					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.P342P(2)									AAAAGTAGATCGGATCCAAAA	0.323																																																2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	6											95	87	90					6																	121624817		1810	4074	5884	121666516	SO:0001819	synonymous_variant	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1026G>A	6.37:g.121624817C>T			121666516	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																				0.323	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121624817	C	T	121624817	2	4	61	1	0	0	0	0	0	0	0	1	2350	871	31	1		1	C6orf170	6	121624817	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47388	121624817	49490250	4899	12884										
C6orf170	221322	broad.mit.edu	37	chr6	121642797	121642797	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctttagattcttgagttCttttagtgacctgctgtaca	7	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121642797C>A	ENST00000398212.2	-	2	348	c.299G>T	c.(298-300)aGa>aTa	p.R100I	TBC1D32_ENST00000275159.6_Missense_Mutation_p.R100I	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	100					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.R100I(1)									TTCTTGAGTTCTTTTAGTGAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											259	239	245					6																	121642797		1894	4117	6011	121684496	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.299G>T	6.37:g.121642797C>A	ENSP00000381270:p.Arg100Ile		121684496	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	9.866	1.197545	0.22037	.	.	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.19806	2.12;2.12;2.12	5.44	2.25	0.28309	.	0.381500	0.27345	N	0.019797	T	0.08044	0.0201	L	0.54323	1.7	0.42155	D	0.991578	B	0.28584	0.216	B	0.23852	0.049	T	0.06180	-1.0841	10	0.72032	D	0.01	-5.8151	5.8378	0.18617	0.1452:0.5505:0.0:0.3043	.	100	Q96NH3	BROMI_HUMAN	I	100	ENSP00000275159:R100I;ENSP00000381270:R100I;ENSP00000397993:R100I	ENSP00000275159:R100I	R	-	2	0	C6orf170	121684496	0.650000	0.27331	0.961000	0.40146	0.306000	0.27790	0.665000	0.25083	0.642000	0.30620	0.609000	0.83330	AGA		0.403	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121642797	C	A	121642797	3	1	61	1	0	0	0	0	1	0	0	0	2350	913	32	2	3598	2	C6orf170	6	121642797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17980	121642797	49472270	4900	12885										
GJA1	2697	broad.mit.edu	37	chr6	121768295	121768295	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgtgttctatgtgatgcGaaaggaagagaaactgaaca	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121768295G>A	ENST00000282561.3	+	2	459	c.302G>A	c.(301-303)cGa>cAa	p.R101Q		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	101					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.R101Q(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	TATGTGATGCGAAAGGAAGAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	73	76					6																	121768295		2203	4300	6503	121809994	SO:0001583	missense	2697			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.302G>A	6.37:g.121768295G>A	ENSP00000282561:p.Arg101Gln		121809994	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661625	0.88154	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	D	0.99089	-5.41	5.32	4.45	0.53987	Connexin, N-terminal (1);	0.190029	0.41500	D	0.000861	D	0.96800	0.8955	M	0.62154	1.92	0.51012	D	0.999903	P	0.38565	0.637	B	0.35550	0.205	D	0.96731	0.9539	10	0.66056	D	0.02	.	13.8968	0.63778	0.0734:0.0:0.9265:0.0	.	101	P17302	CXA1_HUMAN	Q	85;101	ENSP00000282561:R101Q	ENSP00000282561:R101Q	R	+	2	0	GJA1	121809994	1.000000	0.71417	0.333000	0.25482	0.700000	0.40528	9.813000	0.99286	1.264000	0.44198	0.460000	0.39030	CGA		0.443	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		A	121768295	G	A	121768295	3	1	61	1	0	0	0	0	1	0	0	0	6420	1058	37	1	304	1	GJA1	6	121768295	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125498	121768295	49346772	4901	12886										
GJA1	2697	broad.mit.edu	37	chr6	121768540	121768540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatggattcagcttgagtGctgtttacacttgcaaaaga	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121768540G>A	ENST00000282561.3	+	2	704	c.547G>A	c.(547-549)Gct>Act	p.A183T		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	183					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.A183T(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	CAGCTTGAGTGCTGTTTACAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	111	114					6																	121768540		2203	4300	6503	121810239	SO:0001583	missense	2697			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.547G>A	6.37:g.121768540G>A	ENSP00000282561:p.Ala183Thr		121810239	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689605	0.48097	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	D	0.95554	-3.74	5.81	5.81	0.92471	Gap junction protein, cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	D	0.91597	0.7345	L	0.37750	1.13	0.58432	D	0.999999	B	0.32862	0.387	B	0.35859	0.212	D	0.90333	0.4353	10	0.45353	T	0.12	.	20.0796	0.97766	0.0:0.0:1.0:0.0	.	183	P17302	CXA1_HUMAN	T	167;183	ENSP00000282561:A183T	ENSP00000282561:A183T	A	+	1	0	GJA1	121810239	1.000000	0.71417	0.357000	0.25798	0.088000	0.18126	6.539000	0.73856	2.758000	0.94735	0.460000	0.39030	GCT		0.488	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		A	121768540	G	A	121768540	3	1	61	1	0	0	0	0	1	0	0	0	6420	1319	46	3	549	3	GJA1	6	121768540	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	245	121768540	49346527	4902	12887										
GJA1	2697	broad.mit.edu	37	chr6	121768668	121768668	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtccctggccttgaatatCattgaactcttctatgtttt	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121768668C>A	ENST00000282561.3	+	2	832	c.675C>A	c.(673-675)atC>atA	p.I225I		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	225					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.I225I(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	CCTTGAATATCATTGAACTCT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	6											140	140	140					6																	121768668		2203	4300	6503	121810367	SO:0001819	synonymous_variant	2697			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.675C>A	6.37:g.121768668C>A			121810367	B2R5U9|Q6FHU1|Q9Y5I8	Silent	SNP	ENST00000282561.3	37	CCDS5123.1																																																																																				0.522	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		A	121768668	C	A	121768668	2	1	61	1	0	0	0	0	0	0	0	1	6420	816	29	2		2	GJA1	6	121768668	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128	121768668	49346399	4903	12888										
GJA1	2697	broad.mit.edu	37	chr6	121769011	121769011	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccttttgatttccccgatGataaccagaattctaaaaaa	5	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:121769011G>T	ENST00000282561.3	+	2	1175	c.1018G>T	c.(1018-1020)Gat>Tat	p.D340Y		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	340					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.D340Y(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	TTTCCCCGATGATAACCAGAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6											65	69	68					6																	121769011		2203	4300	6503	121810710	SO:0001583	missense	2697			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.1018G>T	6.37:g.121769011G>T	ENSP00000282561:p.Asp340Tyr		121810710	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.798592	0.50208	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	T	0.79352	-1.26	4.75	4.75	0.60458	.	1.387560	0.04996	N	0.468186	T	0.74619	0.3740	N	0.24115	0.695	0.58432	D	0.999999	P	0.35793	0.521	P	0.48901	0.594	T	0.65450	-0.6165	10	0.72032	D	0.01	.	18.2902	0.90127	0.0:0.0:1.0:0.0	.	340	P17302	CXA1_HUMAN	Y	324;340	ENSP00000282561:D340Y	ENSP00000282561:D340Y	D	+	1	0	GJA1	121810710	1.000000	0.71417	0.994000	0.49952	0.899000	0.52679	9.066000	0.93949	2.625000	0.88918	0.484000	0.47621	GAT		0.493	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		T	121769011	G	T	121769011	3	4	61	1	0	0	0	0	1	0	0	0	6420	1290	45	2	1020	2	GJA1	6	121769011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	343	121769011	49346056	4904	12889										
SERINC1	57515	broad.mit.edu	37	chr6	122774931	122774931	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgcataccaacatctCgagttcccttcttccatttt	3	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:122774931C>T	ENST00000339697.4	-	5	657	c.573G>A	c.(571-573)tcG>tcA	p.S191S		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	191					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)	p.S191S(1)		endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		ACCAACATCTCGAGTTCCCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	6											152	133	139					6																	122774931		2203	4300	6503	122816630	SO:0001819	synonymous_variant	57515			AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"tumor differentially expressed 2"	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.573G>A	6.37:g.122774931C>T			122816630	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Silent	SNP	ENST00000339697.4	37	CCDS5125.1																																																																																				0.383	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		T	122774931	C	T	122774931	2	4	61	1	0	0	0	0	0	0	0	1	14116	871	31	1		1	SERINC1	6	122774931	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1005920	122774931	48340136	4905	12890										
SMPDL3A	10924	broad.mit.edu	37	chr6	123126129	123126129	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaatgagagaatactatAatgagaaattgatagatatt	8	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:123126129A>C	ENST00000368440.4	+	6	991	c.814A>C	c.(814-816)Aat>Cat	p.N272H	SMPDL3A_ENST00000539041.1_Missense_Mutation_p.N141H	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	272					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)	p.N272H(1)		breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		AGAATACTATAATGAGAAATT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											107	108	108					6																	123126129		2203	4300	6503	123167828	SO:0001583	missense	10924			AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594			17389	protein-coding gene	gene with protein product	"acid sphingomyelinase-like phosphodiesterase 3a"	610728				12442002	Standard	XM_005266798		Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.814A>C	6.37:g.123126129A>C	ENSP00000357425:p.Asn272His		123167828	B7Z729|Q8WV13	Missense_Mutation	SNP	ENST00000368440.4	37	CCDS5128.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.301149	0.60195	.	.	ENSG00000172594	ENST00000368440;ENST00000539041	D;D	0.90788	-2.73;-2.73	5.7	5.7	0.88788	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.94545	0.8243	M	0.81179	2.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94614	0.7807	10	0.51188	T	0.08	-30.6155	15.9645	0.79956	1.0:0.0:0.0:0.0	.	272	Q92484	ASM3A_HUMAN	H	272;141	ENSP00000357425:N272H;ENSP00000442152:N141H	ENSP00000357425:N272H	N	+	1	0	SMPDL3A	123167828	1.000000	0.71417	0.983000	0.44433	0.217000	0.24651	8.962000	0.93254	2.174000	0.68829	0.533000	0.62120	AAT		0.363	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714		C	123126129	A	C	123126129	3	2	61	1	0	0	0	0	1	0	0	0	14845	362	13	4	836	4	SMPDL3A	6	123126129	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	351198	123126129	47988938	4906	12891										
CLVS2	134829	broad.mit.edu	37	chr6	123332304	123332304	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagctattgaaggcctgcaGgtaggatatggaaattacct	11	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:123332304G>T	ENST00000275162.5	+	3	1899	c.564G>T	c.(562-564)caG>caT	p.Q188H	CLVS2_ENST00000368438.1_Splice_Site_p.Q42H	NM_001010852.3	NP_001010852.2	Q5SYC1	CLVS2_HUMAN	clavesin 2	188	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)	p.Q188H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	40						AAGGCCTGCAGGTAGGATATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	83	88					6																	123332304		2203	4300	6503	123374003	SO:0001630	splice_region_variant	134829			AK095527	CCDS34525.1	6q22.31	2009-10-14	2009-10-14	2009-10-14	ENSG00000146352	ENSG00000146352			23046	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 212", "chromosome 6 open reading frame 213", "retinaldehyde binding protein 1-like 2"	C6orf212, C6orf213, RLBP1L2		19651769	Standard	NM_001010852		Approved	bA160A10.4	uc003pzi.1	Q5SYC1	OTTHUMG00000015495	ENST00000275162.5:c.564+1G>T	6.37:g.123332304G>T			123374003	B3KTG5|B4DHL0|C8UZT4|Q5SYC0	Missense_Mutation	SNP	ENST00000275162.5	37	CCDS34525.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591504	0.66219	.	.	ENSG00000146352	ENST00000275162;ENST00000368438	D;D	0.87571	-2.27;-2.27	5.07	5.07	0.68467	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.88097	0.6345	M	0.89353	3.025	0.80722	D	1	B	0.18863	0.031	B	0.28385	0.089	D	0.86841	0.2017	10	0.66056	D	0.02	-21.3705	18.6278	0.91347	0.0:0.0:1.0:0.0	.	188	Q5SYC1	CLVS2_HUMAN	H	188;42	ENSP00000275162:Q188H;ENSP00000357423:Q42H	ENSP00000275162:Q188H	Q	+	3	2	CLVS2	123374003	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.578000	0.98200	2.625000	0.88918	0.585000	0.79938	CAG		0.373	CLVS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042042.2	NM_001010852	Missense_Mutation	T	123332304	G	T	123332304	5	4	61	1	0	0	0	0	0	0	1	0	3578	1014	35	2	570	2	CLVS2	6	123332304	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206175	123332304	47782763	4907	12892										
TRDN	10345	broad.mit.edu	37	chr6	123539774	123539774	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgttgcttctgtcctggaGaatttgcttgaccagagctc	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:123539774G>T	ENST00000398178.3	-	41	2183	c.2162C>A	c.(2161-2163)tCt>tAt	p.S721Y	TRDN_ENST00000334268.4_Missense_Mutation_p.S713Y	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	721					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)	p.S721Y(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CTGTCCTGGAGAATTTGCTTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											128	116	120					6																	123539774		1886	4108	5994	123581473	SO:0001583	missense	10345			U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.2162C>A	6.37:g.123539774G>T	ENSP00000381240:p.Ser721Tyr		123581473	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389057	0.42410	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.32023	1.48;1.47	4.94	4.94	0.65067	.	0.197503	0.25461	N	0.030504	T	0.22898	0.0553	L	0.27053	0.805	0.80722	D	1	P	0.48407	0.91	P	0.51487	0.671	T	0.03017	-1.1082	10	0.87932	D	0	-1.6955	14.0166	0.64527	0.0:0.0:1.0:0.0	.	721	Q13061	TRDN_HUMAN	Y	721;723;713	ENSP00000381240:S721Y;ENSP00000333984:S713Y	ENSP00000333984:S713Y	S	-	2	0	TRDN	123581473	1.000000	0.71417	0.756000	0.31282	0.092000	0.18411	4.951000	0.63610	2.439000	0.82584	0.655000	0.94253	TCT		0.438	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	123539774	G	T	123539774	3	4	61	1	0	0	0	0	1	0	0	0	16508	942	33	2	31	2	TRDN	6	123539774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207470	123539774	47575293	4908	12893										
HEY2	23493	broad.mit.edu	37	chr6	126080403	126080403	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgcggcttgtgtctcatCtcagcacttgcgccacccag	12	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126080403C>A	ENST00000368364.3	+	5	666	c.469C>A	c.(469-471)Ctc>Atc	p.L157I	HEY2_ENST00000368365.1_Missense_Mutation_p.L111I	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	157	Orange. {ECO:0000255|PROSITE- ProRule:PRU00380}.				anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.L157I(1)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		TGTGTCTCATCTCAGCACTTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	69	71					6																	126080403		2203	4300	6503	126122096	SO:0001583	missense	23493			AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"Basic helix-loop-helix proteins"	4881	protein-coding gene	gene with protein product		604674	"hairy/enhancer-of-split related with YRPW motif 2"			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.469C>A	6.37:g.126080403C>A	ENSP00000357348:p.Leu157Ile		126122096		Missense_Mutation	SNP	ENST00000368364.3	37	CCDS5131.1	.	.	.	.	.	.	.	.	.	.	C	36	5.812505	0.96975	.	.	ENSG00000135547	ENST00000368365;ENST00000368364	T;T	0.79749	-1.3;-1.3	5.64	5.64	0.86602	Orange subgroup (1);Orange (2);	0.078608	0.51477	D	0.000081	D	0.91888	0.7432	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92987	0.6411	10	0.72032	D	0.01	-24.6888	19.7025	0.96060	0.0:1.0:0.0:0.0	.	157	Q9UBP5	HEY2_HUMAN	I	111;157	ENSP00000357349:L111I;ENSP00000357348:L157I	ENSP00000357348:L157I	L	+	1	0	HEY2	126122096	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.731000	0.84895	2.664000	0.90586	0.561000	0.74099	CTC		0.647	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1			A	126080403	C	A	126080403	3	1	61	1	0	0	0	0	1	0	0	0	7100	913	32	2	487	2	HEY2	6	126080403	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2540629	126080403	45034664	4909	12894										
NCOA7	135112	broad.mit.edu	37	chr6	126210166	126210166	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaggatatcaacccattCagtaagttcaaatctatcaa	5	8	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126210166C>A	ENST00000368357.3	+	10	1318	c.966C>A	c.(964-966)ttC>ttA	p.F322L	NCOA7_ENST00000392477.2_Missense_Mutation_p.F322L|NCOA7_ENST00000229634.9_Missense_Mutation_p.F207L	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	322					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)	p.F322L(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		TCAACCCATTCAGTAAGTTCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											107	112	110					6																	126210166		2203	4300	6503	126251859	SO:0001583	missense	135112			AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.966C>A	6.37:g.126210166C>A	ENSP00000357341:p.Phe322Leu		126251859	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047570	0.75846	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.37915	2.62;2.62;2.66;1.17	5.61	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.28896	0.0717	L	0.36672	1.1	0.50467	D	0.999879	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.80764	0.994;0.994;0.94	T	0.06303	-1.0834	10	0.17832	T	0.49	.	9.0626	0.36444	0.0:0.7626:0.0:0.2374	.	311;311;322	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	L	322;322;207;120	ENSP00000357341:F322L;ENSP00000376269:F322L;ENSP00000229634:F207L;ENSP00000389186:F120L	ENSP00000229634:F207L	F	+	3	2	NCOA7	126251859	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.753000	0.55180	0.749000	0.32854	0.591000	0.81541	TTC		0.443	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		A	126210166	C	A	126210166	3	1	61	1	0	0	0	0	1	0	0	0	10265	825	29	2	996	2	NCOA7	6	126210166	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	129763	126210166	44904901	4910	12895										
NCOA7	135112	broad.mit.edu	37	chr6	126210984	126210984	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcccggtaaaactgaactCttctacagaagcaaatgtga	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126210984C>A	ENST00000368357.3	+	10	2136	c.1784C>A	c.(1783-1785)tCt>tAt	p.S595Y	NCOA7_ENST00000392477.2_Missense_Mutation_p.S595Y|NCOA7_ENST00000229634.9_Missense_Mutation_p.S480Y	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	595					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)	p.S595Y(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		AAACTGAACTCTTCTACAGAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											59	63	62					6																	126210984		2203	4300	6503	126252677	SO:0001583	missense	135112			AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1784C>A	6.37:g.126210984C>A	ENSP00000357341:p.Ser595Tyr		126252677	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	7.621	0.676892	0.14841	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.42	3.59	0.41128	.	0.971136	0.08466	N	0.941758	T	0.14227	0.0344	L	0.27053	0.805	0.09310	N	1	B;P;P	0.42649	0.0;0.786;0.681	B;P;B	0.47251	0.001;0.542;0.254	T	0.27191	-1.0081	10	0.72032	D	0.01	1.0312	7.4467	0.27215	0.3014:0.6229:0.0:0.0757	.	584;584;595	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	Y	595;595;480;393	ENSP00000357341:S595Y;ENSP00000376269:S595Y;ENSP00000229634:S480Y;ENSP00000389186:S393Y	ENSP00000229634:S480Y	S	+	2	0	NCOA7	126252677	0.000000	0.05858	0.001000	0.08648	0.372000	0.29890	0.949000	0.29109	0.613000	0.30089	0.655000	0.94253	TCT		0.453	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		A	126210984	C	A	126210984	3	1	61	1	0	0	0	0	1	0	0	0	10265	913	32	2	1814	2	NCOA7	6	126210984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	818	126210984	44904083	4911	12896										
HINT3	135114	broad.mit.edu	37	chr6	126296098	126296098	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagttggtttatagagtCaattcctattggtttatcac	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126296098C>A	ENST00000229633.5	+	4	692	c.495C>A	c.(493-495)gtC>gtA	p.V165V		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	165						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)	p.V165V(1)		endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		TTTATAGAGTCAATTCCTATT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	6											160	149	153					6																	126296098		2203	4300	6503	126337791	SO:0001819	synonymous_variant	135114			AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.495C>A	6.37:g.126296098C>A			126337791	B3KQ91|Q8N0Y9	Silent	SNP	ENST00000229633.5	37	CCDS5133.1																																																																																				0.363	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571		A	126296098	C	A	126296098	2	1	61	1	0	0	0	0	0	0	0	1	7134	813	29	2		2	HINT3	6	126296098	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85114	126296098	44818969	4912	12897										
TRMT11	60487	broad.mit.edu	37	chr6	126332553	126332553	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcacatattttgatgcaatCattactgatcgtaagtttat	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126332553C>A	ENST00000334379.5	+	9	1036	c.915C>A	c.(913-915)atC>atA	p.I305I	TRMT11_ENST00000368332.3_Silent_p.I305I	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	305					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)	p.I305I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		TTGATGCAATCATTACTGATC	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	6											81	68	73					6																	126332553		2203	4300	6503	126374246	SO:0001819	synonymous_variant	60487			AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 75"	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.915C>A	6.37:g.126332553C>A			126374246	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Silent	SNP	ENST00000334379.5	37	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	C	8.722	0.914615	0.17907	.	.	ENSG00000066651	ENST00000453993	.	.	.	5.49	2.59	0.31030	.	.	.	.	.	T	0.39627	0.1085	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26780	-1.0093	4	.	.	.	-5.4922	6.2129	0.20640	0.1265:0.6484:0.0:0.2251	.	.	.	.	N	104	.	.	H	+	1	0	TRMT11	126374246	0.999000	0.42202	1.000000	0.80357	0.970000	0.65996	0.734000	0.26101	0.620000	0.30215	-0.345000	0.07892	CAT		0.333	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820		A	126332553	C	A	126332553	2	1	61	1	0	0	0	0	0	0	0	1	16602	816	29	2		2	TRMT11	6	126332553	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36455	126332553	44782514	4913	12898										
CENPW	387103	broad.mit.edu	37	chr6	126667416	126667416	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggacaaacgcttgtgcGagtaaatgtagagtcattaa	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:126667416G>A	ENST00000368328.4	+	2	292	c.192G>A	c.(190-192)gcG>gcA	p.A64A	CENPW_ENST00000368325.1_Silent_p.A79A|CENPW_ENST00000368326.1_Missense_Mutation_p.R51Q			Q5EE01	CENPW_HUMAN	centromere protein W	64					CENP-A containing nucleosome assembly (GO:0034080)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|kinetochore (GO:0000776)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A64A(2)		kidney(2)|large_intestine(1)|lung(3)	6						ACGCTTGTGCGAGTAAATGTA	0.373																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	6											115	110	112					6																	126667416		2203	4300	6503	126709109	SO:0001819	synonymous_variant	387103			BC039556	CCDS34529.1, CCDS69196.1, CCDS75516.1	6q22.32	2013-11-05	2010-04-16	2010-04-16	ENSG00000203760	ENSG00000203760			21488	protein-coding gene	gene with protein product	"cancer-upregulated gene 2"	611264	"chromosome 6 open reading frame 173"	C6orf173		17610844, 19070575	Standard	NM_001286524		Approved	CUG2	uc003qao.3	Q5EE01	OTTHUMG00000015518	ENST00000368328.4:c.192G>A	6.37:g.126667416G>A			126709109	A6NIR0|A6NJC2	Silent	SNP	ENST00000368328.4	37	CCDS34529.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.567507	0.28003	.	.	ENSG00000203760	ENST00000368326	.	.	.	5.61	1.85	0.25348	.	.	.	.	.	T	0.49660	0.1570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53258	-0.8464	5	0.87932	D	0	-4.8312	6.7698	0.23587	0.38:0.0:0.62:0.0	.	.	.	.	Q	51	.	ENSP00000357309:R51Q	R	+	2	0	CENPW	126709109	1.000000	0.71417	0.944000	0.38274	0.569000	0.35902	1.863000	0.39459	0.308000	0.22923	-0.244000	0.11960	CGA		0.373	CENPW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042104.1			A	126667416	G	A	126667416	2	1	61	1	0	0	0	0	0	0	0	1	3250	1045	37	1		1	CENPW	6	126667416	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334863	126667416	44447651	4914	12899										
KIAA0408	9729	broad.mit.edu	37	chr6	127768124	127768124	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctgttctaaatacagttCtgttaaattcatcagtcttt	4	7	6	0	rs267600792		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:127768124C>T	ENST00000483725.3	-	5	1676	c.1340G>A	c.(1339-1341)aGa>aAa	p.R447K	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	447								p.R447K(1)		endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		AAATACAGTTCTGTTAAATTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	71	70					6																	127768124		2203	4300	6503	127809817	SO:0001583	missense	9729			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1340G>A	6.37:g.127768124C>T	ENSP00000435150:p.Arg447Lys		127809817	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.905602	0.92107	.	.	ENSG00000189367	ENST00000465254;ENST00000483725	T	0.59906	0.23	5.18	5.18	0.71444	.	0.000000	0.41605	U	0.000853	T	0.69967	0.3170	M	0.66939	2.045	0.46725	D	0.999176	D	0.89917	1.0	D	0.85130	0.997	T	0.73892	-0.3839	10	0.87932	D	0	-13.2877	16.8826	0.86067	0.0:1.0:0.0:0.0	.	447	Q6ZU52	K0408_HUMAN	K	36;447	ENSP00000435150:R447K	ENSP00000436178:R36K	R	-	2	0	KIAA0408	127809817	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.589000	0.74080	2.410000	0.81850	0.655000	0.94253	AGA		0.413	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		T	127768124	C	T	127768124	3	4	61	1	0	0	0	0	1	0	0	0	8195	913	32	3	752	3	KIAA0408	6	127768124	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1100708	127768124	43346943	4915	12900										
KIAA0408	9729	broad.mit.edu	37	chr6	127768215	127768215	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaagtgggctactgctctCtgctactgaggagctacagt	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:127768215C>T	ENST00000483725.3	-	5	1585	c.1249G>A	c.(1249-1251)Gag>Aag	p.E417K	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	417								p.E417K(1)		endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		CTACTGCTCTCTGCTACTGAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	69	68					6																	127768215		2203	4300	6503	127809908	SO:0001583	missense	9729			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1249G>A	6.37:g.127768215C>T	ENSP00000435150:p.Glu417Lys		127809908	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	C	1.137	-0.650626	0.03506	.	.	ENSG00000189367	ENST00000465254;ENST00000483725	T	0.29655	1.56	5.38	2.58	0.30949	.	0.663482	0.11386	U	0.569350	T	0.06826	0.0174	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36866	-0.9730	10	0.44086	T	0.13	0.098	5.2513	0.15522	0.0757:0.2785:0.5123:0.1335	.	417	Q6ZU52	K0408_HUMAN	K	6;417	ENSP00000435150:E417K	ENSP00000436178:E6K	E	-	1	0	KIAA0408	127809908	0.041000	0.20044	0.003000	0.11579	0.002000	0.02628	0.902000	0.28459	0.237000	0.21200	-0.165000	0.13383	GAG		0.413	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		T	127768215	C	T	127768215	3	4	61	1	0	0	0	0	1	0	0	0	8195	922	32	3	843	3	KIAA0408	6	127768215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91	127768215	43346852	4916	12901										
KIAA0408	9729	broad.mit.edu	37	chr6	127770989	127770989	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatggttagaccgctttcGaatttcctcttgaaagctgc	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:127770989G>A	ENST00000483725.3	-	4	892	c.556C>T	c.(556-558)Cga>Tga	p.R186*	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	186								p.R186*(1)		endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		GACCGCTTTCGAATTTCCTCT	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											125	123	124					6																	127770989		2203	4300	6503	127812682	SO:0001587	stop_gained	9729			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.556C>T	6.37:g.127770989G>A	ENSP00000435150:p.Arg186*		127812682	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Nonsense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	G	39	7.343593	0.98224	.	.	ENSG00000189367	ENST00000483725;ENST00000487331	.	.	.	5.71	4.82	0.62117	.	0.445152	0.17657	U	0.166443	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6788	15.7786	0.78243	0.0:0.0:0.8627:0.1373	.	.	.	.	X	186;198	.	ENSP00000435150:R186X	R	-	1	2	KIAA0408	127812682	0.997000	0.39634	0.963000	0.40424	0.996000	0.88848	2.953000	0.49105	1.353000	0.45828	0.655000	0.94253	CGA		0.363	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		A	127770989	G	A	127770989	4	1	61	1	0	0	0	0	0	1	0	0	8195	1066	37	1	1540	1	KIAA0408	6	127770989	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2774	127770989	43344078	4917	12902										
C6orf174	387104	broad.mit.edu	37	chr6	127797080	127797080	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcctgcagggcctcggtCttggcgttgtcgtggtgccg	15	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:127797080C>A	ENST00000525778.1	-	6	2836	c.2091G>T	c.(2089-2091)aaG>aaT	p.K697N	SOGA3_ENST00000556132.1_Missense_Mutation_p.K697N|SOGA3_ENST00000368268.2_Missense_Mutation_p.K697N|SOGA3_ENST00000465909.2_Missense_Mutation_p.K697N|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Missense_Mutation_p.K697N			Q5TF21	SOGA3_HUMAN	SOGA family member 3	697					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.K697N(1)									GGGCCTCGGTCTTGGCGTTGT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	82	79					6																	127797080		2192	4295	6487	127838773	SO:0001583	missense	387104			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2091G>T	6.37:g.127797080C>A	ENSP00000434570:p.Lys697Asn		127838773		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977737	0.53720	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.33865	1.39;1.39;1.39;1.4	5.22	4.35	0.52113	.	0.257134	0.45606	D	0.000358	T	0.34861	0.0912	L	0.57536	1.79	0.53688	D	0.999973	P	0.43633	0.813	P	0.52710	0.707	T	0.08680	-1.0710	10	0.35671	T	0.21	-26.6774	13.3714	0.60715	0.0:0.9242:0.0:0.0758	.	697	Q5TF21	CF174_HUMAN	N	697	ENSP00000451768:K697N;ENSP00000357251:K697N;ENSP00000434570:K697N;ENSP00000435559:K697N	ENSP00000435559:K697N	K	-	3	2	C6orf174	127838773	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.485000	0.45250	1.207000	0.43291	0.561000	0.74099	AAG		0.632	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		A	127797080	C	A	127797080	3	1	61	1	0	0	0	0	1	0	0	0	2351	912	32	2	760	2	C6orf174	6	127797080	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26091	127797080	43317987	4918	12903										
C6orf174	387104	broad.mit.edu	37	chr6	127836142	127836142	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaggcatcctcctcgaaGaaagtgtccctcatctcgtc	8	14	2	2	rs371537730		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:127836142G>T	ENST00000525778.1	-	3	1897	c.1152C>A	c.(1150-1152)ttC>ttA	p.F384L	SOGA3_ENST00000556132.1_Missense_Mutation_p.F384L|SOGA3_ENST00000368268.2_Missense_Mutation_p.F384L|SOGA3_ENST00000465909.2_Missense_Mutation_p.F384L|SOGA3_ENST00000481848.2_Missense_Mutation_p.F384L			Q5TF21	SOGA3_HUMAN	SOGA family member 3	384					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.F384L(1)									CCTCCTCGAAGAAAGTGTCCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6											190	190	190					6																	127836142		2124	4243	6367	127877835	SO:0001583	missense	387104			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1152C>A	6.37:g.127836142G>T	ENSP00000434570:p.Phe384Leu		127877835		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682952	0.88542	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	5.65	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.24967	0.0606	M	0.77103	2.36	0.48762	D	0.999709	P	0.46859	0.885	P	0.49799	0.622	T	0.02257	-1.1187	10	0.72032	D	0.01	-13.9869	10.8309	0.46659	0.1462:0.0:0.8538:0.0	.	384	Q5TF21	CF174_HUMAN	L	384	ENSP00000451768:F384L;ENSP00000357251:F384L;ENSP00000434570:F384L;ENSP00000435559:F384L	ENSP00000435559:F384L	F	-	3	2	C6orf174	127877835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.812000	0.69194	2.666000	0.90696	0.557000	0.71058	TTC		0.562	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		T	127836142	G	T	127836142	3	4	61	1	0	0	0	0	1	0	0	0	2351	933	33	2	1711	2	C6orf174	6	127836142	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39062	127836142	43278925	4919	12904										
THEMIS	387357	broad.mit.edu	37	chr6	128150625	128150625	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtggatactcacatttCatcacaccttgaatttcata	4	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:128150625C>A	ENST00000368248.2	-	3	853	c.705G>T	c.(703-705)atG>atT	p.M235I	THEMIS_ENST00000543064.1_Missense_Mutation_p.M235I|THEMIS_ENST00000368250.1_Missense_Mutation_p.M156I|THEMIS_ENST00000537166.1_Missense_Mutation_p.M200I	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	235	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.M235I(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						ACTCACATTTCATCACACCTT	0.373																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											99	95	96					6																	128150625		2203	4300	6503	128192318	SO:0001583	missense	387357			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.705G>T	6.37:g.128150625C>A	ENSP00000357231:p.Met235Ile		128192318	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	37	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.890145	0.52014	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	6.14	5.27	0.74061	.	0.216084	0.49916	D	0.000122	T	0.09774	0.0240	M	0.77313	2.365	0.26814	N	0.968934	P;P	0.40000	0.617;0.698	B;B	0.36845	0.173;0.234	T	0.06881	-1.0802	10	0.42905	T	0.14	-17.0971	15.4432	0.75204	0.0:0.9339:0.0:0.0661	.	235;235	F5H1J9;Q8N1K5	.;THMS1_HUMAN	I	156;235;235;200	ENSP00000357233:M156I;ENSP00000439594:M235I;ENSP00000357231:M235I;ENSP00000439863:M200I	ENSP00000357231:M235I	M	-	3	0	THEMIS	128192318	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.475000	0.53136	1.612000	0.50221	0.650000	0.86243	ATG		0.373	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		A	128150625	C	A	128150625	3	1	61	1	0	0	0	0	1	0	0	0	15899	826	29	2	1357	2	THEMIS	6	128150625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314483	128150625	42964442	4920	12905										
THEMIS	387357	broad.mit.edu	37	chr6	128150791	128150791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcctttagagtgtaaataCgttcatcttcacactcgtag	6	10	4	1	rs537149882	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:128150791C>T	ENST00000368248.2	-	3	687	c.539G>A	c.(538-540)cGt>cAt	p.R180H	THEMIS_ENST00000543064.1_Missense_Mutation_p.R180H|THEMIS_ENST00000368250.1_Missense_Mutation_p.R101H|THEMIS_ENST00000537166.1_Missense_Mutation_p.R145H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	180	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R180H(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						AGTGTAAATACGTTCATCTTC	0.363													C|||	3	0.000599042	0	0	5008	,	,		21536	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	6											139	134	136					6																	128150791		2203	4300	6503	128192484	SO:0001583	missense	387357			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.539G>A	6.37:g.128150791C>T	ENSP00000357231:p.Arg180His		128192484	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	37	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.251022	0.22880	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	6.14	3.78	0.43462	.	0.402393	0.27388	N	0.019586	T	0.01092	0.0036	N	0.01048	-1.04	0.22896	N	0.998599	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.48352	-0.9043	10	0.15952	T	0.53	-7.4055	9.137	0.36879	0.0:0.2076:0.0:0.7924	.	180;180	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	101;180;180;145	ENSP00000357233:R101H;ENSP00000439594:R180H;ENSP00000357231:R180H;ENSP00000439863:R145H	ENSP00000357231:R180H	R	-	2	0	THEMIS	128192484	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.782000	0.38654	0.573000	0.29400	-0.312000	0.09012	CGT		0.363	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		T	128150791	C	T	128150791	3	4	61	1	0	0	0	0	1	0	0	0	15899	536	19	1	1523	1	THEMIS	6	128150791	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166	128150791	42964276	4921	12906										
THEMIS	387357	broad.mit.edu	37	chr6	128176286	128176286	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagtaattttaatcacttCtcctgttgaaaaacagcatt	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:128176286C>A	ENST00000368248.2	-	2	287	c.139G>T	c.(139-141)Gaa>Taa	p.E47*	THEMIS_ENST00000543064.1_Nonsense_Mutation_p.E47*|THEMIS_ENST00000368250.1_5'UTR|THEMIS_ENST00000537166.1_Nonsense_Mutation_p.E12*	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	47	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E47*(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TTAATCACTTCTCCTGTTGAA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											77	76	76					6																	128176286		2203	4300	6503	128217979	SO:0001587	stop_gained	387357			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.139G>T	6.37:g.128176286C>A	ENSP00000357231:p.Glu47*		128217979	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Nonsense_Mutation	SNP	ENST00000368248.2	37	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	37	6.493518	0.97612	.	.	ENSG00000172673	ENST00000543064;ENST00000368248;ENST00000537166	.	.	.	5.73	5.73	0.89815	.	0.067569	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-19.9145	19.8863	0.96913	0.0:1.0:0.0:0.0	.	.	.	.	X	47;47;12	.	ENSP00000357231:E47X	E	-	1	0	THEMIS	128217979	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.652000	0.67959	2.688000	0.91661	0.650000	0.86243	GAA		0.323	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		A	128176286	C	A	128176286	4	1	61	1	0	0	0	0	0	1	0	0	15899	922	32	2	1927	2	THEMIS	6	128176286	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25495	128176286	42938781	4922	12907										
LAMA2	3908	broad.mit.edu	37	chr6	129712699	129712699	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgagacgaggcctttgagaGaaatttggaagggcttcaga	14	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:129712699G>T	ENST00000421865.2	+	36	5184	c.5135G>T	c.(5134-5136)aGa>aTa	p.R1712I		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1712	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R1712I(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCCTTTGAGAGAAATTTGGAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											100	112	108					6																	129712699		2203	4300	6503	129754392	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5135G>T	6.37:g.129712699G>T	ENSP00000400365:p.Arg1712Ile		129754392	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959517	0.34565	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.10192	2.9	6.06	1.86	0.25419	Laminin I (1);	0.200765	0.51477	D	0.000088	T	0.01592	0.0051	N	0.12182	0.205	0.44085	D	0.996849	B;B	0.14012	0.009;0.009	B;B	0.14578	0.011;0.011	T	0.40289	-0.9571	10	0.36615	T	0.2	.	2.6986	0.05142	0.4547:0.0:0.3359:0.2095	.	1712;1712	A6NF00;P24043	.;LAMA2_HUMAN	I	1712	ENSP00000400365:R1712I	ENSP00000346769:R1712I	R	+	2	0	LAMA2	129754392	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	2.120000	0.41968	0.459000	0.27016	-0.158000	0.13435	AGA		0.368	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129712699	G	T	129712699	3	4	61	1	0	0	0	0	1	0	0	0	8628	942	33	2	5277	2	LAMA2	6	129712699	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1536413	129712699	41402368	4923	12908										
LAMA2	3908	broad.mit.edu	37	chr6	129813150	129813150	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttgggggtgctccacctgAatttcaaccttccccactca	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:129813150A>C	ENST00000421865.2	+	57	8052	c.8003A>C	c.(8002-8004)gAa>gCa	p.E2668A	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2668	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.E2668A(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCTCCACCTGAATTTCAACCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	83	82					6																	129813150		2203	4300	6503	129854843	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8003A>C	6.37:g.129813150A>C	ENSP00000400365:p.Glu2668Ala		129854843	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	3.238	-0.155965	0.06544	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.80123	-1.34	5.55	5.55	0.83447	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.231876	0.49916	D	0.000130	T	0.72439	0.3460	M	0.61703	1.905	0.39353	D	0.965783	B;B	0.29212	0.237;0.237	B;B	0.37731	0.257;0.257	T	0.71938	-0.4441	9	.	.	.	.	13.0338	0.58859	0.8661:0.1339:0.0:0.0	.	2669;2668	A6NF00;P24043	.;LAMA2_HUMAN	A	2668;2667;2668;686	ENSP00000400365:E2668A	.	E	+	2	0	LAMA2	129854843	1.000000	0.71417	0.984000	0.44739	0.075000	0.17131	2.947000	0.49058	2.233000	0.73108	0.533000	0.62120	GAA		0.398	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129813150	A	C	129813150	3	2	61	1	0	0	0	0	1	0	0	0	8628	246	9	4	8229	4	LAMA2	6	129813150	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	100451	129813150	41301917	4924	12909										
LAMA2	3908	broad.mit.edu	37	chr6	129824404	129824404	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatgatccccaccaaaatCaatgatggccagtggcacaa	7	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:129824404C>A	ENST00000421865.2	+	60	8575	c.8526C>A	c.(8524-8526)atC>atA	p.I2842I		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2842	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.I2842I(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCACCAAAATCAATGATGGCC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	6											81	76	78					6																	129824404		2203	4300	6503	129866097	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8526C>A	6.37:g.129824404C>A			129866097	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.493	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129824404	C	A	129824404	2	1	61	1	0	0	0	0	0	0	0	1	8628	816	29	2		2	LAMA2	6	129824404	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11254	129824404	41290663	4925	12910										
ARHGAP18	93663	broad.mit.edu	37	chr6	129963089	129963089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatcctgggaaattgatCgatcaaatggaggcttctcc	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:129963089C>T	ENST00000368149.2	-	2	276	c.188G>A	c.(187-189)cGa>cAa	p.R63Q		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18									p.R63Q(1)		NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GGAAATTGATCGATCAAATGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											143	140	141					6																	129963089		2203	4300	6503	130004782	SO:0001583	missense	93663			AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"Rho GTPase activating proteins"	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.188G>A	6.37:g.129963089C>T	ENSP00000357131:p.Arg63Gln		130004782		Missense_Mutation	SNP	ENST00000368149.2	37	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.198859	0.38806	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.89	5.0	0.66597	.	0.305297	0.25042	N	0.033587	T	0.44664	0.1304	M	0.81497	2.545	0.41605	D	0.988874	P;P	0.42456	0.78;0.629	B;B	0.35073	0.138;0.195	T	0.53479	-0.8433	8	.	.	.	.	13.8728	0.63629	0.0:0.9234:0.0:0.0766	.	63;63	A9UK01;Q8N392	.;RHG18_HUMAN	Q	18;63	.	.	R	-	2	0	ARHGAP18	130004782	1.000000	0.71417	0.687000	0.30102	0.065000	0.16274	2.615000	0.46368	1.426000	0.47256	0.655000	0.94253	CGA		0.388	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515		T	129963089	C	T	129963089	3	4	61	1	0	0	0	0	1	0	0	0	868	884	31	1	1859	1	ARHGAP18	6	129963089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138685	129963089	41151978	4926	12911										
TMEM200A	114801	broad.mit.edu	37	chr6	130762628	130762628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaataattccattggggagtCgttgtcgagtcagtacaagt	12	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:130762628C>T	ENST00000296978.3	+	3	1932	c.1061C>T	c.(1060-1062)tCg>tTg	p.S354L	TMEM200A_ENST00000392429.1_Missense_Mutation_p.S354L|TMEM200A_ENST00000545622.1_Missense_Mutation_p.S354L	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	354						integral component of membrane (GO:0016021)		p.S354L(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		ATTGGGGAGTCGTTGTCGAGT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	6											85	83	84					6																	130762628		2203	4300	6503	130804321	SO:0001583	missense	114801			AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"KIAA1913"	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.1061C>T	6.37:g.130762628C>T	ENSP00000296978:p.Ser354Leu		130804321	Q96PX5	Missense_Mutation	SNP	ENST00000296978.3	37	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.602463	0.28534	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.93	5.93	0.95920	.	0.129722	0.53938	D	0.000057	T	0.34629	0.0904	L	0.29908	0.895	0.50171	D	0.999853	B	0.32781	0.384	B	0.21546	0.035	T	0.23226	-1.0194	9	0.44086	T	0.13	-8.4043	20.3368	0.98748	0.0:1.0:0.0:0.0	.	354	Q86VY9	T200A_HUMAN	L	354	.	ENSP00000296978:S354L	S	+	2	0	TMEM200A	130804321	0.989000	0.36119	0.939000	0.37840	0.078000	0.17371	2.876000	0.48498	2.805000	0.96524	0.655000	0.94253	TCG		0.517	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913		T	130762628	C	T	130762628	3	4	61	1	0	0	0	0	1	0	0	0	16162	893	31	1	1063	1	TMEM200A	6	130762628	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	799539	130762628	40352439	4927	12912										
ARG1	383	broad.mit.edu	37	chr6	131894434	131894434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcagagcatgagcgccaaGtccagaaccatagggattat	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131894434G>A	ENST00000368087.3	+	1	151	c.12G>A	c.(10-12)aaG>aaA	p.K4K	ARG1_ENST00000356962.2_Silent_p.K4K|ARG1_ENST00000498260.1_3'UTR			P05089	ARGI1_HUMAN	arginase 1	4					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|liver development (GO:0001889)|lung development (GO:0030324)|mammary gland involution (GO:0060056)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of endothelial cell proliferation (GO:0001938)|protein homotrimerization (GO:0070207)|regulation of L-arginine import (GO:0010963)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to herbicide (GO:0009635)|response to manganese ion (GO:0010042)|response to methylmercury (GO:0051597)|response to selenium ion (GO:0010269)|response to vitamin A (GO:0033189)|response to vitamin E (GO:0033197)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	arginase activity (GO:0004053)|manganese ion binding (GO:0030145)	p.K4K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|skin(3)	14	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)	TGAGCGCCAAGTCCAGAACCA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6											105	100	102					6																	131894434		2203	4300	6503	131936127	SO:0001819	synonymous_variant	383				CCDS5145.1, CCDS59038.1	6q23	2013-05-01	2013-05-01		ENSG00000118520	ENSG00000118520	3.5.3.1		663	protein-coding gene	gene with protein product		608313	"arginase, liver"			22959135	Standard	NM_000045		Approved		uc003qcp.2	P05089	OTTHUMG00000015566	ENST00000368087.3:c.12G>A	6.37:g.131894434G>A			131936127	A6NEA0|Q5JWT5|Q5JWT6|Q8TE72|Q9BS50	Silent	SNP	ENST00000368087.3	37	CCDS5145.1																																																																																				0.423	ARG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042223.1			A	131894434	G	A	131894434	2	1	61	1	0	0	0	0	0	0	0	1	857	1020	36	3		3	ARG1	6	131894434	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1131806	131894434	39220633	4928	12913										
MED23	9439	broad.mit.edu	37	chr6	131913540	131913540	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taactcactggtagggcagtGatgatcaaaccaattgcatt	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131913540G>T	ENST00000368068.3	-	25	3638	c.3459C>A	c.(3457-3459)atC>atA	p.I1153I	MED23_ENST00000368060.3_Silent_p.I1153I|MED23_ENST00000354577.4_Silent_p.I1159I|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000403834.3_Silent_p.I1159I|MED23_ENST00000545957.1_Silent_p.I794I|MED23_ENST00000368058.1_Silent_p.I1159I	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1153					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.I1159I(1)|p.I1153I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		GTAGGGCAGTGATGATCAAAC	0.373																																																2	Substitution - coding silent(2)	large_intestine(2)	6											159	147	151					6																	131913540		2203	4300	6503	131955233	SO:0001819	synonymous_variant	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.3459C>A	6.37:g.131913540G>T			131955233	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Silent	SNP	ENST00000368068.3	37	CCDS5147.1																																																																																				0.373	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			T	131913540	G	T	131913540	2	4	61	1	0	0	0	0	0	0	0	1	9471	1280	45	2		2	MED23	6	131913540	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19106	131913540	39201527	4929	12914										
MED23	9439	broad.mit.edu	37	chr6	131915359	131915359	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacaccagccctgcggtcGattatccttcagagagccaa	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131915359G>A	ENST00000368068.3	-	23	3291	c.3112C>T	c.(3112-3114)Cga>Tga	p.R1038*	MED23_ENST00000368060.3_Nonsense_Mutation_p.R1038*|MED23_ENST00000354577.4_Nonsense_Mutation_p.R1044*|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000403834.3_Nonsense_Mutation_p.R1044*|MED23_ENST00000545957.1_Nonsense_Mutation_p.R679*|MED23_ENST00000368058.1_Nonsense_Mutation_p.R1044*	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1038					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.R1038*(1)|p.R1044*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		CCCTGCGGTCGATTATCCTTC	0.458																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											113	95	101					6																	131915359		2203	4300	6503	131957052	SO:0001587	stop_gained	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.3112C>T	6.37:g.131915359G>A	ENSP00000357047:p.Arg1038*		131957052	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Nonsense_Mutation	SNP	ENST00000368068.3	37	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	G	39	7.597745	0.98381	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957	.	.	.	6.17	4.37	0.52481	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.4923	14.4851	0.67611	0.0:0.0:0.6142:0.3857	.	.	.	.	X	1044;1038;1044;1038;1044;679	.	ENSP00000346588:R1044X	R	-	1	2	MED23	131957052	1.000000	0.71417	0.997000	0.53966	0.908000	0.53690	5.550000	0.67268	0.904000	0.36572	-0.152000	0.13540	CGA		0.458	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			A	131915359	G	A	131915359	4	1	61	1	0	0	0	0	0	1	0	0	9471	1066	37	1	1029	1	MED23	6	131915359	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1819	131915359	39199708	4930	12915										
MED23	9439	broad.mit.edu	37	chr6	131917670	131917670	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actagtaccttgtgataattCatgtgcttggtgtgccagtc	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131917670C>A	ENST00000368068.3	-	21	2945	c.2766G>T	c.(2764-2766)atG>atT	p.M922I	MED23_ENST00000368060.3_Missense_Mutation_p.M922I|MED23_ENST00000354577.4_Missense_Mutation_p.M928I|MED23_ENST00000479213.1_5'Flank|MED23_ENST00000403834.3_Missense_Mutation_p.M928I|MED23_ENST00000545957.1_Missense_Mutation_p.M563I|MED23_ENST00000368058.1_Missense_Mutation_p.M928I	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	922					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.M928I(1)|p.M922I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TGTGATAATTCATGTGCTTGG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	6											172	168	170					6																	131917670		2203	4300	6503	131959363	SO:0001583	missense	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.2766G>T	6.37:g.131917670C>A	ENSP00000357047:p.Met922Ile		131959363	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	37	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.388363	0.61956	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957	T;T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95;-0.95	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.59756	0.2217	L	0.43152	1.355	0.80722	D	1	B;B;B	0.27791	0.189;0.189;0.157	B;B;B	0.27380	0.079;0.079;0.047	T	0.56619	-0.7949	10	0.25751	T	0.34	-13.4342	20.5373	0.99239	0.0:1.0:0.0:0.0	.	563;922;928	B4E3G4;Q9ULK4;Q9ULK4-3	.;MED23_HUMAN;.	I	928;922;928;922;928;563	ENSP00000346588:M928I;ENSP00000357047:M922I;ENSP00000384536:M928I;ENSP00000357039:M922I;ENSP00000357037:M928I;ENSP00000439977:M563I	ENSP00000346588:M928I	M	-	3	0	MED23	131959363	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	ATG		0.378	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			A	131917670	C	A	131917670	3	1	61	1	0	0	0	0	1	0	0	0	9471	826	29	2	1383	2	MED23	6	131917670	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2311	131917670	39197397	4931	12916										
MED23	9439	broad.mit.edu	37	chr6	131939626	131939626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaattacaaatggcacccGaattatttacaactggcaga	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131939626G>A	ENST00000368068.3	-	9	880	c.701C>T	c.(700-702)tCg>tTg	p.S234L	MED23_ENST00000539158.1_Missense_Mutation_p.S234L|MED23_ENST00000368060.3_Missense_Mutation_p.S234L|MED23_ENST00000354577.4_Missense_Mutation_p.S234L|MED23_ENST00000540546.1_Missense_Mutation_p.S234L|MED23_ENST00000403834.3_Missense_Mutation_p.S234L|MED23_ENST00000368058.1_Missense_Mutation_p.S234L|MED23_ENST00000368053.4_Missense_Mutation_p.S234L	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	234					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.S234L(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		AATGGCACCCGAATTATTTAC	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	6											90	82	84					6																	131939626		2203	4300	6503	131981319	SO:0001583	missense	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.701C>T	6.37:g.131939626G>A	ENSP00000357047:p.Ser234Leu		131981319	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	37	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722434	0.89298	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000368053;ENST00000540546;ENST00000539158	T;T;T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	5.49	5.49	0.81192	.	0.108809	0.64402	D	0.000006	T	0.77857	0.4193	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.976;0.971	D;P;P	0.66847	0.947;0.611;0.476	T	0.74247	-0.3727	10	0.27082	T	0.32	-0.0088	19.3773	0.94517	0.0:0.0:1.0:0.0	.	234;234;234	Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;MED23_HUMAN;.	L	234	ENSP00000346588:S234L;ENSP00000357047:S234L;ENSP00000384536:S234L;ENSP00000357039:S234L;ENSP00000357037:S234L;ENSP00000357032:S234L;ENSP00000437818:S234L;ENSP00000445072:S234L	ENSP00000346588:S234L	S	-	2	0	MED23	131981319	1.000000	0.71417	0.951000	0.38953	0.960000	0.62799	7.515000	0.81761	2.583000	0.87209	0.650000	0.86243	TCG		0.358	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			A	131939626	G	A	131939626	3	1	61	1	0	0	0	0	1	0	0	0	9471	1059	37	1	3518	1	MED23	6	131939626	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21956	131939626	39175441	4932	12917										
ENPP3	5169	broad.mit.edu	37	chr6	131996245	131996245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgacagcaatgtatcaagGtttaaaagccgctacctact	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:131996245G>A	ENST00000414305.1	+	10	1116	c.788G>A	c.(787-789)gGt>gAt	p.G263D	ENPP3_ENST00000357639.3_Missense_Mutation_p.G263D|ENPP3_ENST00000427148.2_3'UTR|ENPP3_ENST00000358229.5_Missense_Mutation_p.G263D|ENPP3_ENST00000543135.1_Missense_Mutation_p.G229D			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	263	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.G263D(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		ATGTATCAAGGTTTAAAAGCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											96	92	93					6																	131996245		2203	4300	6503	132037938	SO:0001583	missense	5169			AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.788G>A	6.37:g.131996245G>A	ENSP00000406261:p.Gly263Asp		132037938	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	37	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358077	0.82243	.	.	ENSG00000154269	ENST00000414305;ENST00000357639;ENST00000543135;ENST00000358229	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	5.64	5.64	0.86602	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.64402	D	0.000002	D	0.86180	0.5871	M	0.85945	2.785	0.80722	D	1	P	0.35944	0.529	B	0.44163	0.443	D	0.87421	0.2382	10	0.62326	D	0.03	-20.7115	18.4893	0.90841	0.0:0.0:1.0:0.0	.	263	O14638	ENPP3_HUMAN	D	263;263;229;263	ENSP00000406261:G263D;ENSP00000350265:G263D;ENSP00000440810:G229D;ENSP00000350964:G263D	ENSP00000350265:G263D	G	+	2	0	ENPP3	132037938	0.963000	0.33076	0.987000	0.45799	0.764000	0.43329	1.579000	0.36536	2.654000	0.90174	0.542000	0.68232	GGT		0.403	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			A	131996245	G	A	131996245	3	1	61	1	0	0	0	0	1	0	0	0	5144	1261	44	3	822	3	ENPP3	6	131996245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56619	131996245	39118822	4933	12918										
ENPP1	5167	broad.mit.edu	37	chr6	132179887	132179887	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcactacagcattgtcacCgtaagctctgcatttcaact	5	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132179887C>T	ENST00000360971.2	+	7	815	c.795C>T	c.(793-795)acC>acT	p.T265T		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	265	Phosphodiesterase.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)	p.T213T(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GCATTGTCACCGTAAGCTCTG	0.323																																					Colon(104;336 1535 5856 11019 33782)											1	Substitution - coding silent(1)	large_intestine(1)	6											124	111	116					6																	132179887		2203	4300	6503	132221580	SO:0001630	splice_region_variant	5167			M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.795+1C>T	6.37:g.132179887C>T			132221580	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Silent	SNP	ENST00000360971.2	37	CCDS5150.2																																																																																				0.323	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2		Silent	T	132179887	C	T	132179887	5	4	61	1	0	0	0	0	0	0	1	0	5142	666	23	1	821	1	ENPP1	6	132179887	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	183642	132179887	38935180	4934	12919										
MOXD1	26002	broad.mit.edu	37	chr6	132618355	132618355	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacaagcaagttgatggaGaaatctctgtgcagggaaga	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132618355G>T	ENST00000367963.3	-	12	1897	c.1779C>A	c.(1777-1779)ttC>ttA	p.F593L	MOXD1_ENST00000336749.3_Missense_Mutation_p.F525L	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	593						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.F525L(1)|p.F593L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		AGTTGATGGAGAAATCTCTGT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	6											150	134	139					6																	132618355		2203	4300	6503	132660048	SO:0001583	missense	26002			AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1779C>A	6.37:g.132618355G>T	ENSP00000356940:p.Phe593Leu		132660048	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	G	6.233	0.411130	0.11812	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.43294	0.97;0.95	5.7	1.33	0.21861	.	1.363200	0.04540	N	0.388044	T	0.06371	0.0164	N	0.11560	0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18903	-1.0322	10	0.11485	T	0.65	0.728	2.7927	0.05392	0.1622:0.2427:0.4563:0.1388	.	593;525	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	L	593;525	ENSP00000356940:F593L;ENSP00000336998:F525L	ENSP00000336998:F525L	F	-	3	2	MOXD1	132660048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.685000	0.25378	0.329000	0.23460	0.591000	0.81541	TTC		0.438	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		T	132618355	G	T	132618355	3	4	61	1	0	0	0	0	1	0	0	0	9750	933	33	2	66	2	MOXD1	6	132618355	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	438468	132618355	38496712	4935	12920										
MOXD1	26002	broad.mit.edu	37	chr6	132618927	132618927	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggttaaaaagagcttaccGaccactcagcattgtctgtc	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132618927G>A	ENST00000367963.3	-	11	1794	c.1676C>T	c.(1675-1677)tCg>tTg	p.S559L	MOXD1_ENST00000336749.3_Splice_Site_p.S491L	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	559						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.S491L(1)|p.S559L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		AGAGCTTACCGACCACTCAGC	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	6											120	111	114					6																	132618927		2203	4300	6503	132660620	SO:0001630	splice_region_variant	26002			AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1677+1C>T	6.37:g.132618927G>A			132660620	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.817598	0.70912	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.49432	0.78;0.78	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000002	T	0.33673	0.0871	M	0.70595	2.14	0.80722	D	1	P;P	0.52170	0.84;0.951	B;B	0.34590	0.054;0.186	T	0.33317	-0.9873	10	0.29301	T	0.29	-12.6328	18.8014	0.92018	0.0:0.0:1.0:0.0	.	559;491	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	L	559;491	ENSP00000356940:S559L;ENSP00000336998:S491L	ENSP00000336998:S491L	S	-	2	0	MOXD1	132660620	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.383000	0.66219	2.882000	0.98803	0.655000	0.94253	TCG		0.418	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529	Missense_Mutation	A	132618927	G	A	132618927	5	1	61	1	0	0	0	0	0	0	1	0	9750	1072	37	1	173	1	MOXD1	6	132618927	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	572	132618927	38496140	4936	12921										
MOXD1	26002	broad.mit.edu	37	chr6	132641803	132641803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatctttcgtgttgtagcGacactcagtaattaggttat	8	7	3	0	rs138817081	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132641803G>A	ENST00000367963.3	-	9	1448	c.1330C>T	c.(1330-1332)Cgc>Tgc	p.R444C	MOXD1_ENST00000489128.1_5'UTR|MOXD1_ENST00000336749.3_Missense_Mutation_p.R376C	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	444						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.R444C(1)|p.R376C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		GTGTTGTAGCGACACTCAGTA	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	6						G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	80	78	79		1330	4.7	1	6	dbSNP_134	79	0,8600		0,0,4300	no	missense	MOXD1	NM_015529.2	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging	444/614	132641803	2,13004	2203	4300	6503	132683496	SO:0001583	missense	26002			AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1330C>T	6.37:g.132641803G>A	ENSP00000356940:p.Arg444Cys		132683496	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	G	14.10	2.435217	0.43224	4.54E-4	0.0	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.76448	-1.02;-1.02	5.58	4.65	0.58169	PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);	0.224065	0.37053	N	0.002280	T	0.59851	0.2224	L	0.39898	1.24	0.80722	D	1	B;B	0.18741	0.017;0.03	B;B	0.18561	0.022;0.005	T	0.58381	-0.7646	10	0.38643	T	0.18	-23.7408	15.2453	0.73502	0.0:0.0:0.8588:0.1411	.	444;376	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	C	444;376	ENSP00000356940:R444C;ENSP00000336998:R376C	ENSP00000336998:R376C	R	-	1	0	MOXD1	132683496	0.995000	0.38212	1.000000	0.80357	0.948000	0.59901	2.749000	0.47492	2.782000	0.95742	0.563000	0.77884	CGC		0.308	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		A	132641803	G	A	132641803	3	1	61	1	0	0	0	0	1	0	0	0	9750	1058	37	1	527	1	MOXD1	6	132641803	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22876	132641803	38473264	4937	12922										
MOXD1	26002	broad.mit.edu	37	chr6	132695900	132695900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttttcaactctctatttGcatttgtaaaataatcctgt	3	8	2	0	rs146200701		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132695900G>A	ENST00000367963.3	-	2	399	c.281C>T	c.(280-282)gCa>gTa	p.A94V	MOXD1_ENST00000336749.3_Missense_Mutation_p.A26V	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	94	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.A94V(1)|p.A26V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		CTCTCTATTTGCATTTGTAAA	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	6						G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	115	111	112		281	1.6	1	6	dbSNP_134	112	0,8598		0,0,4299	no	missense	MOXD1	NM_015529.2	64	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	benign	94/614	132695900	2,13002	2203	4299	6502	132737593	SO:0001583	missense	26002			AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.281C>T	6.37:g.132695900G>A	ENSP00000356940:p.Ala94Val		132737593	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	G	15.05	2.718399	0.48622	4.54E-4	0.0	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.77098	-1.07;-1.07	5.62	1.63	0.23807	DOMON domain (3);	0.495547	0.20972	N	0.082368	T	0.65238	0.2672	M	0.73962	2.25	0.80722	D	1	B;B	0.27765	0.188;0.082	B;B	0.39119	0.291;0.035	T	0.64947	-0.6287	10	0.45353	T	0.12	-28.3031	3.5679	0.07907	0.1357:0.0986:0.4567:0.309	.	94;26	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	V	94;26	ENSP00000356940:A94V;ENSP00000336998:A26V	ENSP00000336998:A26V	A	-	2	0	MOXD1	132737593	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.715000	0.25822	0.727000	0.32360	-0.136000	0.14681	GCA		0.328	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		A	132695900	G	A	132695900	3	1	61	1	0	0	0	0	1	0	0	0	9750	1319	46	3	1604	3	MOXD1	6	132695900	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54097	132695900	38419167	4938	12923										
TAAR9	134860	broad.mit.edu	37	chr6	132860310	132860310	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcctccttatgtttatgaGattttagtttggtgtgttta	8	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132860310G>T	ENST00000434551.1	+	0	882					NM_175057.3	NP_778227.3	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9 (gene/pseudogene)						G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)					Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		ATGTTTATGAGATTTTAGTTT	0.348																																					Colon(10;433 445 15992 45047 47213)											0			6											99	92	94					6																	132860310		1858	4110	5968	132902003			134860			AF380189	CCDS75520.1	6q23.2	2013-10-02	2010-03-12	2005-02-24	ENSG00000237110	ENSG00000237110		"GPCR / Class A : Trace amine associated receptors"	20977	protein-coding gene	gene with protein product		608282	"trace amine receptor 3", "trace amine associated receptor 9"	TRAR3		15718104	Standard	NM_175057		Approved	TA3, TAR3	uc011eci.2	Q96RI9	OTTHUMG00000015578		6.37:g.132860310G>T			132902003		Missense_Mutation	SNP	ENST00000434551.1	37																																																																																					0.348	TAAR9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000042254.2	NM_175057		T	132860310	G	T	132860310	1	4	61	0	1	0	0	0	0	0	0	0	15533	933	33	2		2	TAAR9	6	132860310	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164410	132860310	38254757	4939	12924										
TAAR9	134860	broad.mit.edu	37	chr6	132860453	132860453	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaacaactaatttattttCtgaagaagtagagacagatt	7	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132860453C>A	ENST00000434551.1	+	0	1025					NM_175057.3	NP_778227.3	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9 (gene/pseudogene)						G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)					Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		AATTTATTTTCTGAAGAAGTA	0.338																																					Colon(10;433 445 15992 45047 47213)											0			6											39	34	36					6																	132860453		1829	4081	5910	132902146			134860			AF380189	CCDS75520.1	6q23.2	2013-10-02	2010-03-12	2005-02-24	ENSG00000237110	ENSG00000237110		"GPCR / Class A : Trace amine associated receptors"	20977	protein-coding gene	gene with protein product		608282	"trace amine receptor 3", "trace amine associated receptor 9"	TRAR3		15718104	Standard	NM_175057		Approved	TA3, TAR3	uc011eci.2	Q96RI9	OTTHUMG00000015578		6.37:g.132860453C>A			132902146		Missense_Mutation	SNP	ENST00000434551.1	37																																																																																					0.338	TAAR9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000042254.2	NM_175057		A	132860453	C	A	132860453	1	1	61	0	1	0	0	0	0	0	0	0	15533	913	32	2		2	TAAR9	6	132860453	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	143	132860453	38254614	4940	12925										
TAAR8	83551	broad.mit.edu	37	chr6	132874763	132874763	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaatcctttgatttatgCtctattttatccttggttta	5	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132874763C>T	ENST00000275200.1	+	1	932	c.932C>T	c.(931-933)gCt>gTt	p.A311V		NM_053278.1	NP_444508.1	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	311					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.A311V(1)		endometrium(3)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)		TTGATTTATGCTCTATTTTAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											108	113	111					6																	132874763		2203	4300	6503	132916456	SO:0001583	missense	83551			AF380193	CCDS5154.1	6q23.2	2014-05-14	2005-02-23	2005-02-24	ENSG00000146385	ENSG00000146385		"GPCR / Class A : Trace amine associated receptors"	14964	protein-coding gene	gene with protein product		606927	"trace amine receptor 5"	GPR102, TRAR5		11574155, 15718104	Standard	NM_053278		Approved	TA5, TAR5	uc011ecj.2	Q969N4	OTTHUMG00000015586	ENST00000275200.1:c.932C>T	6.37:g.132874763C>T	ENSP00000275200:p.Ala311Val		132916456	Q5VUQ0	Missense_Mutation	SNP	ENST00000275200.1	37	CCDS5154.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.153058	0.57259	.	.	ENSG00000146385	ENST00000275200	T	0.38560	1.13	4.58	3.64	0.41730	.	0.104931	0.34853	N	0.003632	T	0.52789	0.1756	M	0.78285	2.405	0.31668	N	0.644742	P	0.47841	0.901	P	0.61397	0.888	T	0.49390	-0.8945	10	0.39692	T	0.17	-13.0216	16.093	0.81102	0.0:0.8042:0.1958:0.0	.	311	Q969N4	TAAR8_HUMAN	V	311	ENSP00000275200:A311V	ENSP00000275200:A311V	A	+	2	0	TAAR8	132916456	0.045000	0.20229	1.000000	0.80357	0.930000	0.56654	0.481000	0.22260	2.524000	0.85096	0.561000	0.74099	GCT		0.328	TAAR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042262.1	NM_053278		T	132874763	C	T	132874763	3	4	61	1	0	0	0	0	1	0	0	0	15532	797	28	3	934	3	TAAR8	6	132874763	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14310	132874763	38240304	4941	12926										
TAAR6	319100	broad.mit.edu	37	chr6	132891697	132891697	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctggcctgcgctgatttCttggtgggtgtgactgtgat	14	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132891697C>A	ENST00000275198.1	+	1	237	c.237C>A	c.(235-237)ttC>ttA	p.F79L		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	79					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.F79L(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		GCGCTGATTTCTTGGTGGGTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	6											173	155	161					6																	132891697		2203	4300	6503	132933390	SO:0001583	missense	319100			AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"GPCR / Class A : Trace amine associated receptors"	20978	protein-coding gene	gene with protein product		608923	"trace amine receptor 4"	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.237C>A	6.37:g.132891697C>A	ENSP00000275198:p.Phe79Leu		132933390	Q5VUQ4	Missense_Mutation	SNP	ENST00000275198.1	37	CCDS5155.1	.	.	.	.	.	.	.	.	.	.	C	5.616	0.298388	0.10622	.	.	ENSG00000146383	ENST00000275198;ENST00000539228	T	0.26660	1.72	4.99	-7.05	0.01573	GPCR, rhodopsin-like superfamily (1);	0.111853	0.36854	N	0.002379	T	0.03095	0.0091	N	0.16037	0.36	0.19775	N	0.999959	B	0.06786	0.001	B	0.15484	0.013	T	0.36504	-0.9745	10	0.13853	T	0.58	-2.972	12.2446	0.54563	0.0:0.3646:0.0788:0.5566	.	79	Q96RI8	TAAR6_HUMAN	L	79;62	ENSP00000275198:F79L	ENSP00000275198:F79L	F	+	3	2	TAAR6	132933390	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-3.477000	0.00458	-1.580000	0.01644	-0.253000	0.11424	TTC		0.507	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067		A	132891697	C	A	132891697	3	1	61	1	0	0	0	0	1	0	0	0	15531	912	32	2	239	2	TAAR6	6	132891697	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16934	132891697	38223370	4942	12927										
TAAR6	319100	broad.mit.edu	37	chr6	132892150	132892150	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctagacgacaggcgaaaaaGatagaaaatactggtagcaa	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132892150G>T	ENST00000275198.1	+	1	690	c.690G>T	c.(688-690)aaG>aaT	p.K230N		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	230					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.K230N(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		AGGCGAAAAAGATAGAAAATA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											60	61	60					6																	132892150		2203	4300	6503	132933843	SO:0001583	missense	319100			AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"GPCR / Class A : Trace amine associated receptors"	20978	protein-coding gene	gene with protein product		608923	"trace amine receptor 4"	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.690G>T	6.37:g.132892150G>T	ENSP00000275198:p.Lys230Asn		132933843	Q5VUQ4	Missense_Mutation	SNP	ENST00000275198.1	37	CCDS5155.1	.	.	.	.	.	.	.	.	.	.	G	3.055	-0.194434	0.06259	.	.	ENSG00000146383	ENST00000275198;ENST00000539228	T	0.73363	-0.74	4.87	-0.0908	0.13663	GPCR, rhodopsin-like superfamily (1);	0.262894	0.27513	N	0.019034	T	0.41166	0.1147	L	0.58925	1.835	0.19300	N	0.99998	B	0.14438	0.01	B	0.23852	0.049	T	0.33650	-0.9860	10	0.28530	T	0.3	-12.1813	1.251	0.01982	0.2585:0.1091:0.4091:0.2234	.	230	Q96RI8	TAAR6_HUMAN	N	230;213	ENSP00000275198:K230N	ENSP00000275198:K230N	K	+	3	2	TAAR6	132933843	0.000000	0.05858	0.014000	0.15608	0.174000	0.22865	-0.327000	0.07955	-0.217000	0.10033	0.650000	0.86243	AAG		0.413	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067		T	132892150	G	T	132892150	3	4	61	1	0	0	0	0	1	0	0	0	15531	933	33	2	692	2	TAAR6	6	132892150	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	453	132892150	38222917	4943	12928										
TAAR1	134864	broad.mit.edu	37	chr6	132967108	132967108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagttgtttttcacacagGaaatattaattatattgtgg	7	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:132967108G>A	ENST00000275216.1	-	1	34	c.35C>T	c.(34-36)tCc>tTc	p.S12F		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	12					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.S12F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	TTTCACACAGGAAATATTAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											160	162	162					6																	132967108		2203	4299	6502	133008801	SO:0001583	missense	134864			AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"GPCR / Class A : Trace amine associated receptors"	17734	protein-coding gene	gene with protein product		609333	"trace amine receptor 1"	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.35C>T	6.37:g.132967108G>A	ENSP00000275216:p.Ser12Phe		133008801	Q2M1W5|Q3MIH8|Q5VUQ1	Missense_Mutation	SNP	ENST00000275216.1	37	CCDS5158.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775913	0.70107	.	.	ENSG00000146399	ENST00000275216	T	0.57907	0.37	5.51	4.65	0.58169	.	0.058444	0.64402	D	0.000002	T	0.66237	0.2769	M	0.80332	2.49	0.46396	D	0.999022	D	0.89917	1.0	D	0.72982	0.979	T	0.73603	-0.3930	10	0.87932	D	0	-14.1303	14.2441	0.65975	0.0719:0.0:0.9281:0.0	.	12	Q96RJ0	TAAR1_HUMAN	F	12	ENSP00000275216:S12F	ENSP00000275216:S12F	S	-	2	0	TAAR1	133008801	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	3.871000	0.56077	1.333000	0.45449	0.555000	0.69702	TCC		0.378	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327		A	132967108	G	A	132967108	3	1	61	1	0	0	0	0	1	0	0	0	15528	1174	41	3	988	3	TAAR1	6	132967108	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74958	132967108	38147959	4944	12929										
VNN1	8876	broad.mit.edu	37	chr6	133004348	133004348	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttgcttgtgctgtgagGcctgatgaagcatttgatgc	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:133004348G>A	ENST00000367928.4	-	7	1486	c.1473C>T	c.(1471-1473)ggC>ggT	p.G491G		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	491					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)	p.G491G(1)		NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		GTGCTGTGAGGCCTGATGAAG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	6											147	134	138					6																	133004348		2203	4300	6503	133046041	SO:0001819	synonymous_variant	8876			AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1473C>T	6.37:g.133004348G>A			133046041	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Silent	SNP	ENST00000367928.4	37	CCDS5159.1																																																																																				0.393	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			A	133004348	G	A	133004348	2	1	61	1	0	0	0	0	0	0	0	1	17222	1190	42	3		3	VNN1	6	133004348	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37240	133004348	38110719	4945	12930										
VNN2	8875	broad.mit.edu	37	chr6	133072586	133072586	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatccacctctgaaaggaGaagttttcccaactctgtct	7	11	3	3	rs35700463		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:133072586G>T	ENST00000326499.6	-	5	1022	c.898C>A	c.(898-900)Ctc>Atc	p.L300I	RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525270.1_Missense_Mutation_p.L247I|VNN2_ENST00000525289.1_Intron|VNN2_ENST00000526192.1_5'Flank	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	300	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)	p.L300I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCTGAAAGGAGAAGTTTTCCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	72	73					6																	133072586		2202	4286	6488	133114279	SO:0001583	missense	8875			AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"Vanins"	12706	protein-coding gene	gene with protein product	"pantetheinase"	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.898C>A	6.37:g.133072586G>T	ENSP00000322276:p.Leu300Ile		133114279	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Missense_Mutation	SNP	ENST00000326499.6	37	CCDS5161.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.360228	0.24598	.	.	ENSG00000112303	ENST00000326499;ENST00000525270	D;D	0.88431	-2.38;-2.38	5.56	2.68	0.31781	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.102660	0.42172	D	0.000754	T	0.77039	0.4072	L	0.57536	1.79	0.27367	N	0.955808	P	0.42203	0.773	B	0.42214	0.38	T	0.67593	-0.5631	10	0.33141	T	0.24	-13.3196	7.2964	0.26395	0.1169:0.0:0.5383:0.3448	.	300	O95498	VNN2_HUMAN	I	300;247	ENSP00000322276:L300I;ENSP00000436822:L247I	ENSP00000322276:L300I	L	-	1	0	VNN2	133114279	0.000000	0.05858	0.007000	0.13788	0.023000	0.10783	-0.351000	0.07711	0.760000	0.33108	0.609000	0.83330	CTC		0.428	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2			T	133072586	G	T	133072586	3	4	61	1	0	0	0	0	1	0	0	0	17223	942	33	2	676	2	VNN2	6	133072586	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68238	133072586	38042481	4946	12931										
EYA4	2070	broad.mit.edu	37	chr6	133767875	133767875	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcagcagcacatcagttaCtacaaatgggacaggaggta	10	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:133767875C>A	ENST00000367895.5	+	4	655	c.191C>A	c.(190-192)aCt>aAt	p.T64N	EYA4_ENST00000531901.1_Missense_Mutation_p.T64N|EYA4_ENST00000430974.2_Missense_Mutation_p.T64N|EYA4_ENST00000431403.2_Missense_Mutation_p.T64N|EYA4_ENST00000452339.2_Missense_Mutation_p.T64N|EYA4_ENST00000355286.6_Missense_Mutation_p.T64N|EYA4_ENST00000525849.1_Missense_Mutation_p.T64N|EYA4_ENST00000355167.3_Missense_Mutation_p.T64N	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	64					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)	p.T64N(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		ACATCAGTTACTACAAATGGG	0.393																																					Melanoma(57;398 1237 3528 4702 7415)											1	Substitution - Missense(1)	large_intestine(1)	6											115	106	109					6																	133767875		2203	4300	6503	133809568	SO:0001583	missense	2070			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.191C>A	6.37:g.133767875C>A	ENSP00000356870:p.Thr64Asn		133809568	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453515	0.84209	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	T;T;D;D;T;D;T;D	0.87179	-0.31;-0.31;-2.22;-2.22;0.09;-2.22;0.09;-2.22	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.89832	0.6829	L	0.47716	1.5	0.80722	D	1	D;D;D;D;D;D	0.76494	0.993;0.997;0.998;0.999;0.992;0.997	D;P;D;D;D;D	0.76575	0.956;0.854;0.973;0.988;0.931;0.959	D	0.89361	0.3668	10	0.45353	T	0.12	-2.1598	18.5374	0.91015	0.0:1.0:0.0:0.0	.	64;64;64;64;64;64	F2Z2Y1;E7ESD5;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;.;EYA4_HUMAN	N	64	ENSP00000395916:T64N;ENSP00000388670:T64N;ENSP00000356870:T64N;ENSP00000347294:T64N;ENSP00000347434:T64N;ENSP00000432770:T64N;ENSP00000433219:T64N;ENSP00000404558:T64N	ENSP00000347294:T64N	T	+	2	0	EYA4	133809568	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.256000	0.78350	2.418000	0.82041	0.591000	0.81541	ACT		0.393	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		A	133767875	C	A	133767875	3	1	61	1	0	0	0	0	1	0	0	0	5344	565	20	2	201	2	EYA4	6	133767875	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	695289	133767875	37347192	4947	12932										
EYA4	2070	broad.mit.edu	37	chr6	133827283	133827283	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttggactccgcatggaaGaaatgatttttaatcttgct	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:133827283G>T	ENST00000367895.5	+	14	1695	c.1231G>T	c.(1231-1233)Gaa>Taa	p.E411*	EYA4_ENST00000531901.1_Nonsense_Mutation_p.E417*|EYA4_ENST00000430974.2_Nonsense_Mutation_p.E363*|EYA4_ENST00000431403.2_Nonsense_Mutation_p.E411*|EYA4_ENST00000452339.2_Nonsense_Mutation_p.E357*|RP3-323P13.2_ENST00000607033.1_RNA|EYA4_ENST00000355286.6_Nonsense_Mutation_p.E388*|RP3-323P13.2_ENST00000451017.1_RNA|EYA4_ENST00000525849.1_Nonsense_Mutation_p.E388*|EYA4_ENST00000355167.3_Nonsense_Mutation_p.E411*	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	411					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)	p.E411*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		CCGCATGGAAGAAATGATTTT	0.338																																					Melanoma(57;398 1237 3528 4702 7415)											1	Substitution - Nonsense(1)	large_intestine(1)	6											80	81	81					6																	133827283		2203	4300	6503	133868976	SO:0001587	stop_gained	2070			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.1231G>T	6.37:g.133827283G>T	ENSP00000356870:p.Glu411*		133868976	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Nonsense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	G	41	8.933363	0.99008	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	.	.	.	5.63	3.75	0.43078	.	0.087568	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-12.114	11.1147	0.48254	0.0687:0.0:0.8029:0.1284	.	.	.	.	X	357;363;411;411;388;417;388;411	.	ENSP00000347294:E411X	E	+	1	0	EYA4	133868976	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	7.271000	0.78506	1.523000	0.49018	0.650000	0.86243	GAA		0.338	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		T	133827283	G	T	133827283	4	4	61	1	0	0	0	0	0	1	0	0	5344	943	33	2	1281	2	EYA4	6	133827283	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59408	133827283	37287784	4948	12933										
SLC2A12	154091	broad.mit.edu	37	chr6	134328047	134328047	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctgatcccaccaggaaaGatctcgctgagcaccagcca	8	16	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:134328047G>T	ENST00000275230.5	-	3	1625	c.1470C>A	c.(1468-1470)atC>atA	p.I490I		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	490					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.I490I(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		CACCAGGAAAGATCTCGCTGA	0.507																																					Melanoma(122;1663 1672 14489 35294 41228)											1	Substitution - coding silent(1)	large_intestine(1)	6											111	93	99					6																	134328047		2203	4300	6503	134369740	SO:0001819	synonymous_variant	154091			AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.1470C>A	6.37:g.134328047G>T			134369740	B3KV17|Q7Z6U3|Q96MR8	Silent	SNP	ENST00000275230.5	37	CCDS5169.1																																																																																				0.507	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			T	134328047	G	T	134328047	2	4	61	1	0	0	0	0	0	0	0	1	14578	932	33	2		2	SLC2A12	6	134328047	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	500764	134328047	36787020	4949	12934										
SGK1	6446	broad.mit.edu	37	chr6	134492033	134492033	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttaattaaggagaagaaGacatgactcttaatctccat	7	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:134492033G>T	ENST00000237305.7	-	11	1147	c.1059C>A	c.(1057-1059)gtC>gtA	p.V353V	SGK1_ENST00000475719.2_Silent_p.V309V|SGK1_ENST00000528577.1_Silent_p.V381V|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Silent_p.V343V|SGK1_ENST00000413996.3_Silent_p.V367V|SGK1_ENST00000367858.5_Silent_p.V448V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	353	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.V353V(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGGAGAAGAAGACATGACTCT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	6											100	108	105					6																	134492033		2203	4300	6503	134533726	SO:0001819	synonymous_variant	6446			AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.1059C>A	6.37:g.134492033G>T			134533726	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																				0.418	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134492033	G	T	134492033	2	4	61	1	0	0	0	0	0	0	0	1	14244	929	33	2		2	SGK1	6	134492033	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163986	134492033	36623034	4950	12935										
SGK1	6446	broad.mit.edu	37	chr6	134498882	134498882	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggattacttctggaggCtggaggtagagcccagttat	15	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:134498882C>T	ENST00000237305.7	-	0	0				SGK1_ENST00000475719.2_5'Flank|SGK1_ENST00000528577.1_Missense_Mutation_p.A27T|SGK1_ENST00000367857.5_5'Flank|SGK1_ENST00000413996.3_5'Flank|SGK1_ENST00000367858.5_Intron	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.A27T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		CTTCTGGAGGCTGGAGGTAGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	109	112					6																	134498882		1568	3582	5150	134540575	SO:0001631	upstream_gene_variant	6446			AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613		6.37:g.134498882C>T	Exception_encountered		134540575	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.030485	0.54790	.	.	ENSG00000118515	ENST00000528577	T	0.72167	-0.63	5.84	-1.0	0.10196	.	.	.	.	.	T	0.29914	0.0748	.	.	.	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.20075	-1.0286	8	0.31617	T	0.26	.	6.3804	0.21531	0.0:0.1824:0.157:0.6606	.	27	O00141-5	.	T	27	ENSP00000434450:A27T	ENSP00000434450:A27T	A	-	1	0	SGK1	134540575	0.964000	0.33143	0.000000	0.03702	0.514000	0.34195	-0.193000	0.09573	-0.406000	0.07588	0.655000	0.94253	GCC		0.498	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134498882	C	T	134498882	1	4	61	0	1	0	0	0	0	0	0	0	14244	797	28	3		3	SGK1	6	134498882	5'Flank	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6849	134498882	36616185	4951	12936										
MYB	4602	broad.mit.edu	37	chr6	135511466	135511466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacagatgggcagaaatcGcaaagctactgcctggacgg	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:135511466G>A	ENST00000367814.4	+	5	694	c.508G>A	c.(508-510)Gca>Aca	p.A170T	MYB_ENST00000442647.2_Missense_Mutation_p.A170T|MYB_ENST00000527615.1_Missense_Mutation_p.A170T|MYB_ENST00000534044.1_Missense_Mutation_p.A170T|MYB_ENST00000525369.1_Missense_Mutation_p.A170T|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000528774.1_Missense_Mutation_p.A170T|MYB_ENST00000316528.8_Missense_Mutation_p.A170T|MYB_ENST00000341911.5_Missense_Mutation_p.A170T|MYB_ENST00000420123.2_Missense_Mutation_p.A146T|MYB_ENST00000534121.1_Missense_Mutation_p.A170T|MYB_ENST00000533624.1_Missense_Mutation_p.A170T	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	170	HTH myb-type 3. {ECO:0000255|PROSITE- ProRule:PRU00625}.|Interaction with HIPK2 and NLK. {ECO:0000250}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A170T(2)		breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GGCAGAAATCGCAAAGCTACT	0.418			T	NFIB	adenoid cystic carcinoma																																		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	2	Substitution - Missense(2)	large_intestine(2)	6											55	58	57					6																	135511466		2203	4300	6503	135553159	SO:0001583	missense	4602				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.508G>A	6.37:g.135511466G>A	ENSP00000356788:p.Ala170Thr		135553159	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037006	0.93630	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624;ENST00000430686	T;T;T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	5.93	5.93	0.95920	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.74061	0.3667	M	0.86028	2.79	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;P;D;D;D	0.77004	0.983;0.961;0.983;0.975;0.974;0.802;0.983;0.949;0.989	T	0.76817	-0.2819	10	0.87932	D	0	-14.1146	20.3311	0.98718	0.0:0.0:1.0:0.0	.	170;170;170;170;170;170;170;170;170	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	T	170;170;170;170;170;170;146;170;170;170;170;170;124	ENSP00000339992:A170T;ENSP00000410825:A170T;ENSP00000326328:A170T;ENSP00000356788:A170T;ENSP00000433227:A170T;ENSP00000435938:A170T;ENSP00000434723:A170T;ENSP00000432851:A170T;ENSP00000435055:A170T;ENSP00000436605:A170T	ENSP00000237302:A170T	A	+	1	0	MYB	135553159	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.797000	0.96272	0.655000	0.94253	GCA		0.418	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			A	135511466	G	A	135511466	3	1	61	1	0	0	0	0	1	0	0	0	10037	1087	38	1	526	1	MYB	6	135511466	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1012584	135511466	35603601	4952	12937										
AHI1	54806	broad.mit.edu	37	chr6	135621647	135621647	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttgcttactgtgtcataGattctgagcctagtctgaag	10	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:135621647G>T	ENST00000367800.4	-	25	3692	c.3476C>A	c.(3475-3477)tCt>tAt	p.S1159Y	AHI1_ENST00000457866.2_Missense_Mutation_p.S1159Y|AHI1_ENST00000417892.2_3'UTR|RP3-388E23.2_ENST00000444302.1_RNA	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1159					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)		p.S1159Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CTGTGTCATAGATTCTGAGCC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	6											121	111	114					6																	135621647		1820	4076	5896	135663340	SO:0001583	missense	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3476C>A	6.37:g.135621647G>T	ENSP00000356774:p.Ser1159Tyr		135663340	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.414|3.414	-0.119543|-0.119543	0.06838|0.06838	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367799|ENST00000367800;ENST00000457866;ENST00000265602	.|T;T;T	.|0.58358	.|0.34;0.34;0.34	5.78|5.78	3.99|3.99	0.46301|0.46301	.|.	.|0.395100	.|0.24178	.|N	.|0.040833	T|T	0.21801|0.21801	0.0525|0.0525	N|N	0.14661|0.14661	0.345|0.345	0.19775|0.19775	N|N	0.999953|0.999953	.|D;P	.|0.56521	.|0.976;0.79	.|P;B	.|0.47744	.|0.556;0.365	T|T	0.04191|0.04191	-1.0970|-1.0970	5|10	.|0.51188	.|T	.|0.08	-0.204|-0.204	7.8284|7.8284	0.29328|0.29328	0.0856:0.1634:0.751:0.0|0.0856:0.1634:0.751:0.0	.|.	.|1159;1159	.|Q8N157;Q4FD35	.|AHI1_HUMAN;.	I|Y	659|1159	.|ENSP00000356774:S1159Y;ENSP00000388650:S1159Y;ENSP00000265602:S1159Y	.|ENSP00000265602:S1159Y	L|S	-|-	1|2	2|0	AHI1|AHI1	135663340|135663340	0.574000|0.574000	0.26684|0.26684	0.002000|0.002000	0.10522|0.10522	0.117000|0.117000	0.20001|0.20001	2.024000|2.024000	0.41049|0.41049	0.800000|0.800000	0.34041|0.34041	-0.181000|-0.181000	0.13052|0.13052	CTA|TCT		0.318	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		T	135621647	G	T	135621647	3	4	61	1	0	0	0	0	1	0	0	0	413	942	33	2	126	2	AHI1	6	135621647	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110181	135621647	35493420	4953	12938										
AHI1	54806	broad.mit.edu	37	chr6	135778680	135778680	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgctcatcaaccacatgaAtttttaccattgggtgagaa	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:135778680A>C	ENST00000367800.4	-	7	1319	c.1103T>G	c.(1102-1104)aTt>aGt	p.I368S	AHI1_ENST00000457866.2_Missense_Mutation_p.I368S|AHI1_ENST00000327035.6_Missense_Mutation_p.I368S	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	368	Interaction with HAP1.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)		p.I368S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		AACCACATGAATTTTTACCAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											99	90	93					6																	135778680		1851	4093	5944	135820373	SO:0001583	missense	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.1103T>G	6.37:g.135778680A>C	ENSP00000356774:p.Ile368Ser		135820373	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.423745	0.83667	.	.	ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000265602;ENST00000327035;ENST00000367801	T;T;T;T	0.64618	-0.04;-0.04;-0.04;-0.11	5.48	5.48	0.80851	.	0.054681	0.64402	D	0.000001	T	0.72439	0.3460	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.975	T	0.76987	-0.2755	10	0.87932	D	0	-20.5623	15.5818	0.76448	1.0:0.0:0.0:0.0	.	368;368	Q8N157-2;Q8N157	.;AHI1_HUMAN	S	368	ENSP00000356774:I368S;ENSP00000388650:I368S;ENSP00000265602:I368S;ENSP00000322478:I368S	ENSP00000265602:I368S	I	-	2	0	AHI1	135820373	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.474000	0.90413	2.077000	0.62373	0.455000	0.32223	ATT		0.338	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135778680	A	C	135778680	3	2	61	1	0	0	0	0	1	0	0	0	413	101	4	4	2628	4	AHI1	6	135778680	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	157033	135778680	35336387	4954	12939										
AHI1	54806	broad.mit.edu	37	chr6	135811801	135811801	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaagttttttcttcagtTttttcttttcacgcattaga	5	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:135811801T>G	ENST00000367800.4	-	3	311	c.95A>C	c.(94-96)aAa>aCa	p.K32T	AHI1_ENST00000531527.1_5'Flank|AHI1_ENST00000488690.2_Missense_Mutation_p.K32T|AHI1_ENST00000534469.1_Missense_Mutation_p.K32T|AHI1_ENST00000457866.2_Missense_Mutation_p.K32T|AHI1_ENST00000367798.2_Missense_Mutation_p.K32T|AHI1_ENST00000327035.6_Missense_Mutation_p.K32T|AHI1_ENST00000528103.1_Missense_Mutation_p.K32T	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	32					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)		p.K32T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TTTCTTCAGTTTTTTCTTTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											202	187	192					6																	135811801		1824	4073	5897	135853494	SO:0001583	missense	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.95A>C	6.37:g.135811801T>G	ENSP00000356774:p.Lys32Thr		135853494	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	T	9.160	1.018519	0.19355	.	.	ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000265602;ENST00000327035;ENST00000367801;ENST00000524469;ENST00000488690;ENST00000367798;ENST00000528103;ENST00000534469	T;T;T;T;T	0.57907	0.96;0.96;0.96;0.96;0.37	4.97	2.51	0.30379	.	0.344757	0.24474	N	0.038216	T	0.40272	0.1110	L	0.54323	1.7	0.38647	D	0.951754	P;P	0.44429	0.835;0.745	P;B	0.49999	0.628;0.425	T	0.41734	-0.9492	10	0.87932	D	0	-14.1057	6.3116	0.21169	0.0:0.2284:0.0:0.7716	.	32;32	Q8N157-2;Q8N157	.;AHI1_HUMAN	T	32	ENSP00000356774:K32T;ENSP00000388650:K32T;ENSP00000265602:K32T;ENSP00000322478:K32T;ENSP00000433063:K32T	ENSP00000265602:K32T	K	-	2	0	AHI1	135853494	0.992000	0.36948	0.993000	0.49108	0.165000	0.22458	1.329000	0.33770	0.732000	0.32470	0.455000	0.32223	AAA		0.353	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		G	135811801	T	G	135811801	3	3	61	1	0	0	0	0	1	0	0	0	413	1841	64	4	3652	4	AHI1	6	135811801	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33121	135811801	35303266	4955	12940										
BCLAF1	9774	broad.mit.edu	37	chr6	136589371	136589371	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatggtgagttttaaattCttcttctctttccttcttac	4	9	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:136589371C>A	ENST00000531224.1	-	10	2578	c.2326G>T	c.(2326-2328)Gaa>Taa	p.E776*	BCLAF1_ENST00000392348.2_Nonsense_Mutation_p.E774*|BCLAF1_ENST00000353331.4_Nonsense_Mutation_p.E774*|BCLAF1_ENST00000530767.1_Nonsense_Mutation_p.E603*|BCLAF1_ENST00000527536.1_Nonsense_Mutation_p.E776*|BCLAF1_ENST00000527759.1_Nonsense_Mutation_p.E774*|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000031135.9_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	776					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.E776*(2)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		GTTTTAAATTCTTCTTCTCTT	0.383																																					Colon(142;1534 1789 5427 7063 28491)											2	Substitution - Nonsense(2)	large_intestine(2)	6											175	162	167					6																	136589371		2203	4300	6503	136631064	SO:0001587	stop_gained	9774			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2326G>T	6.37:g.136589371C>A	ENSP00000435210:p.Glu776*		136631064	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Nonsense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.208172|9.208172	0.99101|0.99101	.|.	.|.	ENSG00000029363|ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348|ENST00000534762	.|.	.|.	.|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.64402|.	D|.	0.000007|.	.|T	.|0.54791	.|0.1880	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54523	.|-0.8281	.|4	0.12430|.	T|.	0.62|.	-11.1231|-11.1231	12.4947|12.4947	0.55921|0.55921	0.0:0.9235:0.0:0.0765|0.0:0.9235:0.0:0.0765	.|.	.|.	.|.	.|.	X|I	776;774;776;603;774;774|42	.|.	ENSP00000229446:E774X|.	E|R	-|-	1|2	0|0	BCLAF1|BCLAF1	136631064|136631064	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	3.166000|3.166000	0.50785|0.50785	2.549000|2.549000	0.85964|0.85964	0.484000|0.484000	0.47621|0.47621	GAA|AGA		0.383	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136589371	C	A	136589371	4	1	61	1	0	0	0	0	0	1	0	0	1384	922	32	2	452	2	BCLAF1	6	136589371	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	777570	136589371	34525696	4956	12941										
BCLAF1	9774	broad.mit.edu	37	chr6	136597534	136597534	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaatctagagcttcctgatCttcccattctccctctgccc	5	16	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:136597534C>A	ENST00000531224.1	-	5	1381	c.1129G>T	c.(1129-1131)Gat>Tat	p.D377Y	BCLAF1_ENST00000392348.2_Missense_Mutation_p.D375Y|BCLAF1_ENST00000353331.4_Missense_Mutation_p.D375Y|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000527536.1_Missense_Mutation_p.D377Y|BCLAF1_ENST00000527759.1_Missense_Mutation_p.D375Y	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	377					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.D377Y(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		GCTTCCTGATCTTCCCATTCT	0.423																																					Colon(142;1534 1789 5427 7063 28491)											1	Substitution - Missense(1)	large_intestine(1)	6											222	239	233					6																	136597534		2203	4297	6500	136639227	SO:0001583	missense	9774			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1129G>T	6.37:g.136597534C>A	ENSP00000435210:p.Asp377Tyr		136639227	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608099	0.46527	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4;2.4	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000008	T	0.11067	0.0270	N	0.22421	0.69	0.80722	D	1	P;P;P	0.41848	0.763;0.763;0.763	P;P;P	0.44359	0.447;0.447;0.447	T	0.05007	-1.0912	10	0.45353	T	0.12	-14.1837	19.8217	0.96599	0.0:1.0:0.0:0.0	.	375;375;377	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	Y	377;375;377;375;375;377	ENSP00000435210:D377Y;ENSP00000229446:D375Y;ENSP00000435441:D377Y;ENSP00000434826:D375Y;ENSP00000376159:D375Y;ENSP00000431734:D377Y	ENSP00000229446:D375Y	D	-	1	0	BCLAF1	136639227	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.194000	0.58393	2.775000	0.95449	0.650000	0.86243	GAT		0.423	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136597534	C	A	136597534	3	1	61	1	0	0	0	0	1	0	0	0	1384	913	32	2	1669	2	BCLAF1	6	136597534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8163	136597534	34517533	4957	12942										
MAP7	9053	broad.mit.edu	37	chr6	136686974	136686974	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagggctcattggcaactTtctgaggttccttctcagga	12	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:136686974T>G	ENST00000354570.3	-	10	1582	c.1172A>C	c.(1171-1173)aAa>aCa	p.K391T	RP3-406A7.3_ENST00000571188.1_RNA|MAP7_ENST00000432797.2_Missense_Mutation_p.K245T|MAP7_ENST00000544465.1_Missense_Mutation_p.K376T|MAP7_ENST00000454590.1_Missense_Mutation_p.K413T|MAP7_ENST00000438100.2_Missense_Mutation_p.K376T	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	391	Pro-rich.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.K391T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		ATTGGCAACTTTCTGAGGTTC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	88	87					6																	136686974		2203	4300	6503	136728667	SO:0001583	missense	9053			X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.1172A>C	6.37:g.136686974T>G	ENSP00000346581:p.Lys391Thr		136728667	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	37	CCDS5178.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.761260	0.31137	.	.	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100;ENST00000432797;ENST00000345567	T;T;T;T;T	0.05025	3.51;3.51;3.51;3.51;3.51	5.72	1.88	0.25563	.	0.572415	0.16822	N	0.198132	T	0.01905	0.0060	L	0.48362	1.52	0.32402	N	0.551785	B;B;B;B;B;B;B	0.23377	0.007;0.007;0.011;0.007;0.084;0.021;0.012	B;B;B;B;B;B;B	0.21917	0.006;0.006;0.015;0.006;0.037;0.037;0.011	T	0.45220	-0.9276	10	0.25106	T	0.35	-5.4656	7.2384	0.26082	0.0:0.0705:0.2769:0.6526	.	376;413;376;413;297;354;391	B7Z290;B7ZB64;F5H1E2;E9PCP3;F8W783;Q14244-2;Q14244	.;.;.;.;.;.;MAP7_HUMAN	T	391;413;376;376;245;297	ENSP00000346581:K391T;ENSP00000414712:K413T;ENSP00000445737:K376T;ENSP00000400790:K376T;ENSP00000414879:K245T	ENSP00000344217:K297T	K	-	2	0	MAP7	136728667	0.503000	0.26115	0.080000	0.20451	0.998000	0.95712	0.661000	0.25023	0.084000	0.17077	0.528000	0.53228	AAA		0.552	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		G	136686974	T	G	136686974	3	3	61	1	0	0	0	0	1	0	0	0	9296	1841	64	4	1113	4	MAP7	6	136686974	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	89440	136686974	34428093	4958	12943										
MAP3K5	4217	broad.mit.edu	37	chr6	136958511	136958511	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctgtgcttctccccttCtcttcggtaatggtgttcac	7	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:136958511C>A	ENST00000359015.4	-	14	2328	c.1968G>T	c.(1966-1968)gaG>gaT	p.E656D	RP3-325F22.3_ENST00000432477.1_RNA|MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	656					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)	p.E656D(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TTCTCCCCTTCTCTTCGGTAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											171	137	148					6																	136958511		2203	4300	6503	137000204	SO:0001583	missense	4217			U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.1968G>T	6.37:g.136958511C>A	ENSP00000351908:p.Glu656Asp		137000204	A6NIA0|B4DGB2|Q5THN3|Q99461	Missense_Mutation	SNP	ENST00000359015.4	37	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	C	7.299	0.612666	0.14066	.	.	ENSG00000197442	ENST00000359015;ENST00000367768	T	0.69685	-0.42	5.69	2.43	0.29744	.	0.193032	0.53938	D	0.000059	T	0.30135	0.0755	L	0.54323	1.7	0.80722	D	1	B;B	0.29378	0.243;0.009	B;B	0.28465	0.09;0.007	T	0.39231	-0.9624	10	0.02654	T	1	.	5.3151	0.15850	0.0:0.5877:0.1668:0.2454	.	736;656	Q59GL6;Q99683	.;M3K5_HUMAN	D	656;736	ENSP00000351908:E656D	ENSP00000351908:E656D	E	-	3	2	MAP3K5	137000204	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.218000	0.17622	0.857000	0.35407	0.591000	0.81541	GAG		0.378	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			A	136958511	C	A	136958511	3	1	61	1	0	0	0	0	1	0	0	0	9283	912	32	2	2224	2	MAP3K5	6	136958511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271537	136958511	34156556	4959	12944										
IL20RA	53832	broad.mit.edu	37	chr6	137323365	137323365	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatacatcactgctttttCccagtaaactcatatcctga	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:137323365C>A	ENST00000316649.5	-	7	1227	c.992G>T	c.(991-993)gGa>gTa	p.G331V	RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Missense_Mutation_p.G220V|IL20RA_ENST00000541547.1_Missense_Mutation_p.G282V|IL20RA_ENST00000468393.1_5'Flank	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	331					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)		p.G331V(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		ACTGCTTTTTCCCAGTAAACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											52	56	55					6																	137323365		2203	4300	6503	137365058	SO:0001583	missense	53832			AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.992G>T	6.37:g.137323365C>A	ENSP00000314976:p.Gly331Val		137365058	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.822423	0.50739	.	.	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.60299	0.47;1.94;0.2	5.75	0.346	0.16017	.	0.970208	0.08522	N	0.933340	T	0.21227	0.0511	L	0.29908	0.895	0.21064	N	0.999797	P;P	0.49961	0.899;0.93	B;B	0.41571	0.299;0.36	T	0.08994	-1.0695	10	0.14656	T	0.56	-3.5397	9.1654	0.37048	0.0:0.3572:0.0:0.6428	.	220;331	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	V	331;220;282	ENSP00000314976:G331V;ENSP00000356722:G220V;ENSP00000437843:G282V	ENSP00000314976:G331V	G	-	2	0	IL20RA	137365058	0.000000	0.05858	0.015000	0.15790	0.181000	0.23173	-0.479000	0.06567	0.131000	0.18576	-0.471000	0.05019	GGA		0.433	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		A	137323365	C	A	137323365	3	1	61	1	0	0	0	0	1	0	0	0	7689	855	30	2	673	2	IL20RA	6	137323365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	364854	137323365	33791702	4960	12945										
IFNGR1	3459	broad.mit.edu	37	chr6	137525525	137525525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaatgtaacaggtagtttCgggatcataatcgacttcct	8	9	1	0	rs146687518		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:137525525C>T	ENST00000367739.4	-	4	611	c.490G>A	c.(490-492)Gaa>Aaa	p.E164K	IFNGR1_ENST00000478333.1_5'Flank|IFNGR1_ENST00000543628.1_Missense_Mutation_p.E136K|IFNGR1_ENST00000367735.2_Missense_Mutation_p.E154K	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	164					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)	p.E164K(1)		central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CAGGTAGTTTCGGGATCATAA	0.373													C|||	1	0.000199681	0	0	5008	,	,		21320	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	6						C	LYS/GLU	0,4406		0,0,2203	181	161	168		490	5.4	0	6	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFNGR1	NM_000416.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	164/490	137525525	1,13005	2203	4300	6503	137567218	SO:0001583	missense	3459				CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.490G>A	6.37:g.137525525C>T	ENSP00000356713:p.Glu164Lys		137567218	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	37	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.945598	0.53079	0.0	1.16E-4	ENSG00000027697	ENST00000367739;ENST00000418947;ENST00000543628;ENST00000458076;ENST00000367735;ENST00000414770	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.36	5.36	0.76844	Interferon gamma receptor, poxvirus/mammal (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.662303	0.15694	N	0.249281	T	0.28499	0.0705	L	0.60455	1.87	0.09310	N	1	D;P;D	0.55605	0.972;0.936;0.959	B;B;B	0.42214	0.158;0.143;0.38	T	0.16394	-1.0404	10	0.51188	T	0.08	-6.404	14.5865	0.68328	0.0:1.0:0.0:0.0	.	154;136;164	B4DFT7;F5H5M7;P15260	.;.;INGR1_HUMAN	K	164;164;136;130;154;154	ENSP00000356713:E164K;ENSP00000443282:E136K;ENSP00000389249:E130K;ENSP00000356709:E154K;ENSP00000394230:E154K	ENSP00000356709:E154K	E	-	1	0	IFNGR1	137567218	0.042000	0.20092	0.008000	0.14137	0.001000	0.01503	1.921000	0.40035	2.494000	0.84150	0.655000	0.94253	GAA		0.373	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			T	137525525	C	T	137525525	3	4	61	1	0	0	0	0	1	0	0	0	7570	893	31	1	995	1	IFNGR1	6	137525525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	202160	137525525	33589542	4961	12946										
KIAA1244	57221	broad.mit.edu	37	chr6	138576826	138576826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggactccatgaagcccGtgctccagtccctctaccac	8	17	1	1	rs141449825		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:138576826G>A	ENST00000251691.4	+	10	1190	c.1024G>A	c.(1024-1026)Gtg>Atg	p.V342M		NM_020340.4	NP_065073.3			KIAA1244									p.V271M(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CATGAAGCCCGTGCTCCAGTC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	23	23	23		1024	4.8	0.9	6	dbSNP_134	23	0,8600		0,0,4300	no	missense	KIAA1244	NM_020340.4	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	342/2178	138576826	1,13005	2203	4300	6503	138618519	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1024G>A	6.37:g.138576826G>A	ENSP00000251691:p.Val342Met		138618519		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775065	0.70107	2.27E-4	0.0	ENSG00000112379	ENST00000251691	T	0.05258	3.47	5.68	4.82	0.62117	.	0.059279	0.64402	D	0.000002	T	0.02970	0.0088	L	0.46157	1.445	0.53688	D	0.999979	P	0.35077	0.483	B	0.21546	0.035	T	0.32025	-0.9922	10	0.87932	D	0	-27.7221	14.7436	0.69474	0.0695:0.0:0.9305:0.0	.	342	Q5TH69	BIG3_HUMAN	M	342	ENSP00000251691:V342M	ENSP00000251691:V342M	V	+	1	0	KIAA1244	138618519	1.000000	0.71417	0.920000	0.36463	0.951000	0.60555	8.007000	0.88571	1.420000	0.47138	0.655000	0.94253	GTG		0.617	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138576826	G	A	138576826	3	1	61	1	0	0	0	0	1	0	0	0	8238	1145	40	1	1062	1	KIAA1244	6	138576826	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1051301	138576826	32538241	4962	12947										
KIAA1244	57221	broad.mit.edu	37	chr6	138584581	138584581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaggccaccggtccctgcGaactgccgccctgtctctaa	9	18	1	0	rs374061664		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:138584581G>A	ENST00000251691.4	+	12	2127	c.1961G>A	c.(1960-1962)cGa>cAa	p.R654Q		NM_020340.4	NP_065073.3			KIAA1244									p.R583Q(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CGGTCCCTGCGAACTGCCGCC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	58	66	64		1961	5.5	0.9	6		64	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1244	NM_020340.4	43	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	654/2178	138584581	2,13004	2203	4300	6503	138626274	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1961G>A	6.37:g.138584581G>A	ENSP00000251691:p.Arg654Gln		138626274		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	31	5.088112	0.94100	2.27E-4	1.16E-4	ENSG00000112379	ENST00000251691	T	0.24350	1.86	5.47	5.47	0.80525	SEC7-like (1);	0.616769	0.14049	N	0.344886	T	0.41511	0.1162	L	0.57536	1.79	0.53005	D	0.99996	D	0.76494	0.999	D	0.72625	0.978	T	0.06391	-1.0829	10	0.40728	T	0.16	-1.0	19.3197	0.94233	0.0:0.0:1.0:0.0	.	654	Q5TH69	BIG3_HUMAN	Q	654	ENSP00000251691:R654Q	ENSP00000251691:R654Q	R	+	2	0	KIAA1244	138626274	1.000000	0.71417	0.918000	0.36340	0.945000	0.59286	9.496000	0.97967	2.569000	0.86673	0.655000	0.94253	CGA		0.617	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138584581	G	A	138584581	3	1	61	1	0	0	0	0	1	0	0	0	8238	1058	37	1	2007	1	KIAA1244	6	138584581	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7755	138584581	32530486	4963	12948										
KIAA1244	57221	broad.mit.edu	37	chr6	138635034	138635034	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagtcagccagcagtgagGatggaattgaatcagtcctg	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:138635034G>T	ENST00000251691.4	+	26	4469	c.4303G>T	c.(4303-4305)Gat>Tat	p.D1435Y		NM_020340.4	NP_065073.3			KIAA1244									p.D1364Y(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAGCAGTGAGGATGGAATTGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											119	103	108					6																	138635034		2203	4300	6503	138676727	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.4303G>T	6.37:g.138635034G>T	ENSP00000251691:p.Asp1435Tyr		138676727		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	24.2	4.505142	0.85282	.	.	ENSG00000112379	ENST00000251691	T	0.05786	3.39	5.03	5.03	0.67393	.	0.058672	0.64402	D	0.000002	T	0.14657	0.0354	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	T	0.01245	-1.1407	10	0.87932	D	0	-21.8746	18.3612	0.90375	0.0:0.0:1.0:0.0	.	1435	Q5TH69	BIG3_HUMAN	Y	1435	ENSP00000251691:D1435Y	ENSP00000251691:D1435Y	D	+	1	0	KIAA1244	138676727	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.648000	0.91062	2.342000	0.79632	0.655000	0.94253	GAT		0.438	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		T	138635034	G	T	138635034	3	4	61	1	0	0	0	0	1	0	0	0	8238	1174	41	2	4405	2	KIAA1244	6	138635034	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50453	138635034	32480033	4964	12949										
KIAA1244	57221	broad.mit.edu	37	chr6	138656288	138656288	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctccaccgggagctcccTcagtgtctcggtgagagacg	14	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:138656288T>G	ENST00000251691.4	+	33	6471	c.6305T>G	c.(6304-6306)cTc>cGc	p.L2102R		NM_020340.4	NP_065073.3			KIAA1244									p.L2031R(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GGGAGCTCCCTCAGTGTCTCG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6											14	15	15					6																	138656288		2203	4300	6503	138697981	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.6305T>G	6.37:g.138656288T>G	ENSP00000251691:p.Leu2102Arg		138697981		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	T	11.20	1.569701	0.28003	.	.	ENSG00000112379	ENST00000251691;ENST00000367706	T	0.18338	2.22	5.76	3.37	0.38596	.	0.355744	0.30193	N	0.010194	T	0.03651	0.0104	N	0.17082	0.46	0.38703	D	0.953035	B	0.06786	0.001	B	0.06405	0.002	T	0.31530	-0.9940	10	0.18710	T	0.47	-26.3311	12.8316	0.57748	0.0:0.0:0.2989:0.7011	.	2102	Q5TH69	BIG3_HUMAN	R	2102;143	ENSP00000251691:L2102R	ENSP00000251691:L2102R	L	+	2	0	KIAA1244	138697981	1.000000	0.71417	0.923000	0.36655	0.914000	0.54420	3.749000	0.55150	0.439000	0.26476	0.418000	0.28097	CTC		0.642	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138656288	T	G	138656288	3	3	61	1	0	0	0	0	1	0	0	0	8238	1551	54	4	6435	4	KIAA1244	6	138656288	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	21254	138656288	32458779	4965	12950										
HEBP2	23593	broad.mit.edu	37	chr6	138734054	138734054	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtgcccaaaagaatcaaGaacaacttttgacattagca	6	9	1	3	rs34750897		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:138734054G>T	ENST00000607197.1	+	4	734	c.457G>T	c.(457-459)Gaa>Taa	p.E153*	HEBP2_ENST00000448741.1_Missense_Mutation_p.K124N|HEBP2_ENST00000367697.3_Missense_Mutation_p.K113N	NM_014320.2	NP_055135.1	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	153					negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)		p.E153*(1)		endometrium(1)|large_intestine(1)|lung(3)	5	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		AAAGAATCAAGAACAACTTTT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											151	148	149					6																	138734054		2203	4300	6503	138775747	SO:0001587	stop_gained	23593			AF117616	CCDS5191.1	6q24	2008-08-29	2002-09-23	2002-09-27	ENSG00000051620	ENSG00000051620			15716	protein-coding gene	gene with protein product		605825	"chromosome 6 open reading frame 34"	C6orf34		10640688, 17098234	Standard	NM_014320		Approved	SOUL	uc003qhw.1	Q9Y5Z4	OTTHUMG00000015671	ENST00000607197.1:c.457G>T	6.37:g.138734054G>T	ENSP00000475750:p.Glu153*		138775747	Q96P57	Nonsense_Mutation	SNP	ENST00000607197.1	37	CCDS5191.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.757065|6.757065	0.97817|0.97817	.|.	.|.	ENSG00000051620|ENSG00000051620	ENST00000058691|ENST00000448741;ENST00000367697	.|T;T	.|0.22539	.|1.95;1.95	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.269694|.	0.41500|.	D|.	0.000880|.	.|T	.|0.31670	.|0.0804	.|.	.|.	.|.	0.34908|0.34908	D|D	0.747142|0.747142	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.06607	.|-1.0817	.|6	0.10636|0.72032	T|D	0.68|0.01	.|.	16.855|16.855	0.86003|0.86003	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs34750897|rs34750897	.|.	.|.	.|.	X|N	153|124;113	.|ENSP00000392101:K124N;ENSP00000356670:K113N	ENSP00000058691:E153X|ENSP00000356670:K113N	E|K	+|+	1|3	0|2	HEBP2|HEBP2	138775747|138775747	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	6.328000|6.328000	0.72915|0.72915	2.720000|2.720000	0.93068|0.93068	0.563000|0.563000	0.77884|0.77884	GAA|AAG		0.373	HEBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042426.2			T	138734054	G	T	138734054	4	4	61	1	0	0	0	0	0	1	0	0	7058	943	33	2	471	2	HEBP2	6	138734054	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77766	138734054	32381013	4966	12951										
ECT2L	345930	broad.mit.edu	37	chr6	139202164	139202164	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaactcttacagagtgagaGaaaatacgtgcagatactgg	11	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:139202164G>T	ENST00000423192.1	+	14	1897	c.1736G>T	c.(1735-1737)aGa>aTa	p.R579I	RP3-509I19.6_ENST00000572284.1_RNA|ECT2L_ENST00000541398.1_Missense_Mutation_p.R510I|ECT2L_ENST00000367682.2_Missense_Mutation_p.R579I			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	579	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R579I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CAGAGTGAGAGAAAATACGTG	0.433			"N, Splice, Mis"		ETP ALL																																		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	1	Substitution - Missense(1)	large_intestine(1)	6											110	103	105					6																	139202164		1922	4148	6070	139243857	SO:0001583	missense	345930				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1736G>T	6.37:g.139202164G>T	ENSP00000387388:p.Arg579Ile		139243857	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.712313	0.68730	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.67523	-0.27;-0.27;-0.27	5.53	5.53	0.82687	Dbl homology (DH) domain (5);	0.260319	0.22934	U	0.053861	T	0.72170	0.3427	M	0.61703	1.905	0.51767	D	0.999937	D;D	0.89917	0.999;1.0	D;D	0.79108	0.992;0.986	T	0.73994	-0.3807	10	0.52906	T	0.07	-4.9585	10.4802	0.44689	0.0887:0.0:0.9113:0.0	.	510;579	F5H7S9;Q008S8	.;ECT2L_HUMAN	I	579;579;510	ENSP00000387388:R579I;ENSP00000356655:R579I;ENSP00000442307:R510I	ENSP00000356655:R579I	R	+	2	0	ECT2L	139243857	0.998000	0.40836	0.956000	0.39512	0.887000	0.51463	2.746000	0.47467	2.609000	0.88269	0.655000	0.94253	AGA		0.433	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139202164	G	T	139202164	3	4	61	1	0	0	0	0	1	0	0	0	4913	942	33	2	1786	2	ECT2L	6	139202164	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	468110	139202164	31912903	4967	12952										
ECT2L	345930	broad.mit.edu	37	chr6	139210149	139210149	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttcattgctgtgatgaaGaaataagtttctctttaagg	8	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:139210149G>T	ENST00000423192.1	+	19	2556	c.2395G>T	c.(2395-2397)Gaa>Taa	p.E799*	ECT2L_ENST00000541398.1_Nonsense_Mutation_p.E653*|ECT2L_ENST00000367682.2_Nonsense_Mutation_p.E799*			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	799							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E799*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CTGTGATGAAGAAATAAGTTT	0.368			"N, Splice, Mis"		ETP ALL																																		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	1	Substitution - Nonsense(1)	large_intestine(1)	6											93	94	94					6																	139210149		1868	4111	5979	139251842	SO:0001587	stop_gained	345930				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.2395G>T	6.37:g.139210149G>T	ENSP00000387388:p.Glu799*		139251842	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Nonsense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	G	39	7.476814	0.98309	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	.	.	.	4.86	3.98	0.46160	.	0.658638	0.11349	U	0.573192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-0.0845	7.1675	0.25700	0.2072:0.0:0.7928:0.0	.	.	.	.	X	799;799;653	.	ENSP00000356655:E799X	E	+	1	0	ECT2L	139251842	1.000000	0.71417	0.979000	0.43373	0.986000	0.74619	2.268000	0.43338	1.165000	0.42670	0.561000	0.74099	GAA		0.368	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139210149	G	T	139210149	4	4	61	1	0	0	0	0	0	1	0	0	4913	943	33	2	2465	2	ECT2L	6	139210149	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7985	139210149	31904918	4968	12953										
ECT2L	345930	broad.mit.edu	37	chr6	139223644	139223644	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcttttacagatgtcaaGaatgcatttattcttcaggg	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:139223644G>A	ENST00000423192.1	+	21	2756	c.2595G>A	c.(2593-2595)aaG>aaA	p.K865K	ECT2L_ENST00000541398.1_Silent_p.K719K|ECT2L_ENST00000367682.2_Silent_p.K865K			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	865							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K865K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CAGATGTCAAGAATGCATTTA	0.303			"N, Splice, Mis"		ETP ALL																																		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	1	Substitution - coding silent(1)	large_intestine(1)	6											79	76	77					6																	139223644		1805	4075	5880	139265337	SO:0001819	synonymous_variant	345930				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.2595G>A	6.37:g.139223644G>A			139265337	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	37	CCDS43508.1																																																																																				0.303	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		A	139223644	G	A	139223644	2	1	61	1	0	0	0	0	0	0	0	1	4913	933	33	3		3	ECT2L	6	139223644	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13495	139223644	31891423	4969	12954										
REPS1	85021	broad.mit.edu	37	chr6	139229911	139229911	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgattttaatcttcttcGaacaggtttaggtggtggag	11	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:139229911G>A	ENST00000450536.2	-	18	2684	c.2110C>T	c.(2110-2112)Cga>Tga	p.R704*	REPS1_ENST00000415951.2_Nonsense_Mutation_p.R645*|REPS1_ENST00000258062.5_Nonsense_Mutation_p.R703*|REPS1_ENST00000409812.2_Nonsense_Mutation_p.R613*|REPS1_ENST00000367663.4_Nonsense_Mutation_p.R677*			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	704	Interaction with RALBP1. {ECO:0000250}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)	p.R651*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		AATCTTCTTCGAACAGGTTTA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											164	148	154					6																	139229911		2203	4300	6503	139271604	SO:0001587	stop_gained	85021				CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.2110C>T	6.37:g.139229911G>A	ENSP00000392065:p.Arg704*		139271604	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Nonsense_Mutation	SNP	ENST00000450536.2	37		.	.	.	.	.	.	.	.	.	.	G	37	6.449137	0.97577	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	.	.	.	5.35	2.57	0.30868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.3038	8.537	0.33368	0.0679:0.0:0.5428:0.3893	.	.	.	.	X	704;677;662;613;703;645;652	.	ENSP00000258062:R703X	R	-	1	2	REPS1	139271604	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	3.200000	0.51051	0.373000	0.24621	-0.291000	0.09656	CGA		0.378	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			A	139229911	G	A	139229911	4	1	61	1	0	0	0	0	0	1	0	0	13265	1066	37	1	292	1	REPS1	6	139229911	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6267	139229911	31885156	4970	12955										
GPR126	57211	broad.mit.edu	37	chr6	142726906	142726906	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagaatttaagtccagaaGattctgtattagttagaaga	9	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:142726906G>T	ENST00000230173.6	+	15	2685	c.2209G>T	c.(2209-2211)Gat>Tat	p.D737Y	GPR126_ENST00000296932.8_Missense_Mutation_p.D709Y|GPR126_ENST00000367608.2_Missense_Mutation_p.D709Y|GPR126_ENST00000367609.3_Missense_Mutation_p.D737Y	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	737					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D708Y(1)|p.D737Y(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		AAGTCCAGAAGATTCTGTATT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	6											91	86	88					6																	142726906		1825	4077	5902	142768599	SO:0001583	missense	57211			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.2209G>T	6.37:g.142726906G>T	ENSP00000230173:p.Asp737Tyr		142768599	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.442327	0.63067	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.27402	1.67;1.67;1.68;1.67	5.79	4.92	0.64577	.	0.577602	0.17629	N	0.167463	T	0.40297	0.1111	L	0.56769	1.78	0.41804	D	0.989936	D;D;D;D	0.63046	0.992;0.983;0.992;0.986	D;P;D;P	0.64144	0.922;0.898;0.922;0.838	T	0.39663	-0.9603	10	0.87932	D	0	.	14.8813	0.70534	0.0688:0.0:0.9312:0.0	.	709;737;709;737	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;GP126_HUMAN	Y	737;709;709;737	ENSP00000230173:D737Y;ENSP00000356580:D709Y;ENSP00000296932:D709Y;ENSP00000356581:D737Y	ENSP00000230173:D737Y	D	+	1	0	GPR126	142768599	1.000000	0.71417	0.943000	0.38184	0.773000	0.43773	2.858000	0.48356	1.431000	0.47355	-0.140000	0.14226	GAT		0.363	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142726906	G	T	142726906	3	4	61	1	0	0	0	0	1	0	0	0	6660	942	33	2	2267	2	GPR126	6	142726906	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3496995	142726906	28388161	4971	12956										
GPR126	57211	broad.mit.edu	37	chr6	142738465	142738465	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagaaacaacaatgaagtCtatggaaaagaaagttatgg	10	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:142738465C>A	ENST00000230173.6	+	21	3470	c.2994C>A	c.(2992-2994)gtC>gtA	p.V998V	GPR126_ENST00000296932.8_Silent_p.V970V|GPR126_ENST00000367608.2_Silent_p.V970V|GPR126_ENST00000367609.3_Silent_p.V998V	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	998					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V998V(1)|p.V969V(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		ACAATGAAGTCTATGGAAAAG	0.353																																																2	Substitution - coding silent(2)	large_intestine(2)	6											118	107	111					6																	142738465		1830	4091	5921	142780158	SO:0001819	synonymous_variant	57211			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.2994C>A	6.37:g.142738465C>A			142780158	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Silent	SNP	ENST00000230173.6	37	CCDS47490.1																																																																																				0.353	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			A	142738465	C	A	142738465	2	1	61	1	0	0	0	0	0	0	0	1	6660	900	32	2		2	GPR126	6	142738465	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11559	142738465	28376602	4972	12957										
HIVEP2	3097	broad.mit.edu	37	chr6	143074678	143074678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctgtttcatcaacagccGaggagaggagggagtgctag	15	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143074678G>A	ENST00000367604.1	-	9	7546	c.6907C>T	c.(6907-6909)Cgg>Tgg	p.R2303W	HIVEP2_ENST00000367603.2_Missense_Mutation_p.R2303W|RP1-67K17.3_ENST00000437067.1_RNA|HIVEP2_ENST00000012134.2_Missense_Mutation_p.R2303W			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	2303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R2303W(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ATCAACAGCCGAGGAGAGGAG	0.512																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - Missense(1)	large_intestine(1)	6											90	92	91					6																	143074678		2013	4183	6196	143116371	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.6907C>T	6.37:g.143074678G>A	ENSP00000356576:p.Arg2303Trp		143116371	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.368137	0.24771	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02472	4.28;4.28;4.28	5.78	3.99	0.46301	.	0.450941	0.25987	N	0.027028	T	0.00695	0.0023	L	0.34521	1.04	0.27789	N	0.942907	D	0.54047	0.964	B	0.32805	0.153	T	0.50825	-0.8782	10	0.54805	T	0.06	-12.0397	5.0456	0.14483	0.2171:0.0:0.6173:0.1657	.	2303	P31629	ZEP2_HUMAN	W	2303	ENSP00000356576:R2303W;ENSP00000356575:R2303W;ENSP00000012134:R2303W	ENSP00000012134:R2303W	R	-	1	2	HIVEP2	143116371	1.000000	0.71417	0.999000	0.59377	0.465000	0.32709	2.468000	0.45102	1.434000	0.47414	0.655000	0.94253	CGG		0.512	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			A	143074678	G	A	143074678	3	1	61	1	0	0	0	0	1	0	0	0	7208	1057	37	1	437	1	HIVEP2	6	143074678	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336213	143074678	28040389	4973	12958										
HIVEP2	3097	broad.mit.edu	37	chr6	143091958	143091958	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgctcagagggcgtttcAgttgacttactgctctggtc	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143091958A>C	ENST00000367604.1	-	4	4557	c.3918T>G	c.(3916-3918)acT>acG	p.T1306T	HIVEP2_ENST00000367603.2_Silent_p.T1306T|HIVEP2_ENST00000012134.2_Silent_p.T1306T			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T1306T(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		AGGGCGTTTCAGTTGACTTAC	0.498																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - coding silent(1)	large_intestine(1)	6											169	169	169					6																	143091958		1937	4131	6068	143133651	SO:0001819	synonymous_variant	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.3918T>G	6.37:g.143091958A>C			143133651	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																				0.498	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143091958	A	C	143091958	2	2	61	1	0	0	0	0	0	0	0	1	7208	175	7	4		4	HIVEP2	6	143091958	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	17280	143091958	28023109	4974	12959										
HIVEP2	3097	broad.mit.edu	37	chr6	143094200	143094200	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagtgacttcctctcaaaGaaggaggaatagttagatta	10	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143094200G>T	ENST00000367604.1	-	4	2315	c.1676C>A	c.(1675-1677)tCt>tAt	p.S559Y	HIVEP2_ENST00000367603.2_Missense_Mutation_p.S559Y|HIVEP2_ENST00000012134.2_Missense_Mutation_p.S559Y			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S559Y(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TCCTCTCAAAGAAGGAGGAAT	0.468																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - Missense(1)	large_intestine(1)	6											90	89	89					6																	143094200		1902	4127	6029	143135893	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1676C>A	6.37:g.143094200G>T	ENSP00000356576:p.Ser559Tyr		143135893	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512071	0.44660	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.12039	2.72;2.72;2.72	5.48	5.48	0.80851	.	0.374019	0.31624	N	0.007324	T	0.10078	0.0247	L	0.53249	1.67	0.30671	N	0.753345	D	0.56521	0.976	P	0.44732	0.459	T	0.02098	-1.1214	10	0.72032	D	0.01	-21.5276	14.217	0.65800	0.0:0.0:0.8507:0.1493	.	559	P31629	ZEP2_HUMAN	Y	559	ENSP00000356576:S559Y;ENSP00000356575:S559Y;ENSP00000012134:S559Y	ENSP00000012134:S559Y	S	-	2	0	HIVEP2	143135893	0.981000	0.34729	1.000000	0.80357	0.996000	0.88848	3.893000	0.56243	2.566000	0.86566	0.655000	0.94253	TCT		0.468	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143094200	G	T	143094200	3	4	61	1	0	0	0	0	1	0	0	0	7208	942	33	2	5688	2	HIVEP2	6	143094200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2242	143094200	28020867	4975	12960										
ADAT2	134637	broad.mit.edu	37	chr6	143759816	143759816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaggaacttcagtattttCgagggcttctttggcctgaa	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143759816C>T	ENST00000237283.8	-	2	126	c.112G>A	c.(112-114)Gaa>Aaa	p.E38K	ADAT2_ENST00000606514.1_5'UTR|AL031320.1_ENST00000595616.1_Intron	NM_182503.2	NP_872309.2	Q7Z6V5	ADAT2_HUMAN	adenosine deaminase, tRNA-specific 2	38					tRNA wobble adenosine to inosine editing (GO:0002100)		tRNA-specific adenosine deaminase activity (GO:0008251)|zinc ion binding (GO:0008270)	p.E38K(1)		endometrium(2)|large_intestine(3)|lung(3)	8				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)		TCAGTATTTTCGAGGGCTTCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											153	136	141					6																	143759816		1864	4095	5959	143801509	SO:0001583	missense	134637			BC037955	CCDS43511.1, CCDS69219.1	6q24.2	2014-01-28	2011-05-19	2007-08-16	ENSG00000189007	ENSG00000189007			21172	protein-coding gene	gene with protein product	tRNA-specific adenosine deaminase 2 homolog (S. cerevisiae)	615388	"deaminase domain containing 1", "adenosine deaminase, tRNA-specific 2, TAD2 homolog (S. cerevisiae)"	DEADC1		12457566	Standard	NM_182503		Approved	dJ20N2.1, TAD2	uc003qjj.3	Q7Z6V5	OTTHUMG00000015725	ENST00000237283.8:c.112G>A	6.37:g.143759816C>T	ENSP00000237283:p.Glu38Lys		143801509	A6NL12|B3KWY3|Q7Z327|Q8IY39	Missense_Mutation	SNP	ENST00000237283.8	37	CCDS43511.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577853	0.28180	.	.	ENSG00000189007	ENST00000237283	T	0.39592	1.07	5.89	5.03	0.67393	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.269079	0.42682	N	0.000677	T	0.07324	0.0185	N	0.04245	-0.25	0.80722	D	1	B	0.18166	0.026	B	0.14578	0.011	T	0.19289	-1.0310	10	0.07644	T	0.81	-10.9942	10.9233	0.47178	0.0:0.8581:0.0:0.1419	.	38	Q7Z6V5	ADAT2_HUMAN	K	38	ENSP00000237283:E38K	ENSP00000237283:E38K	E	-	1	0	ADAT2	143801509	0.996000	0.38824	0.517000	0.27799	0.677000	0.39632	2.248000	0.43160	1.507000	0.48752	0.563000	0.77884	GAA		0.393	ADAT2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042517.1	XM_059727		T	143759816	C	T	143759816	3	4	61	1	0	0	0	0	1	0	0	0	285	893	31	1	483	1	ADAT2	6	143759816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	665616	143759816	27355251	4976	12961										
PEX3	8504	broad.mit.edu	37	chr6	143780306	143780306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatacattgcccaagcacGacgacaatatcattttgaaa	6	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143780306G>A	ENST00000367591.4	+	2	221	c.158G>A	c.(157-159)cGa>cAa	p.R53Q		NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	53					peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.R53Q(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		GCCCAAGCACGACGACAATAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	6											126	121	122					6																	143780306		2203	4300	6503	143821999	SO:0001583	missense	8504			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.158G>A	6.37:g.143780306G>A	ENSP00000356563:p.Arg53Gln		143821999	Q6FGP5	Missense_Mutation	SNP	ENST00000367591.4	37	CCDS5199.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426895	0.96131	.	.	ENSG00000034693	ENST00000367591	T	0.39229	1.09	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.47563	0.1452	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.83275	0.703;0.996	T	0.30937	-0.9961	10	0.07482	T	0.82	-12.4305	19.6691	0.95903	0.0:0.0:1.0:0.0	.	53;53	B4DV31;P56589	.;PEX3_HUMAN	Q	53	ENSP00000356563:R53Q	ENSP00000356563:R53Q	R	+	2	0	PEX3	143821999	1.000000	0.71417	0.948000	0.38648	0.879000	0.50718	9.343000	0.97047	2.721000	0.93114	0.591000	0.81541	CGA		0.353	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1			A	143780306	G	A	143780306	3	1	61	1	0	0	0	0	1	0	0	0	11778	1058	37	1	164	1	PEX3	6	143780306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20490	143780306	27334761	4977	12962										
PEX3	8504	broad.mit.edu	37	chr6	143792154	143792154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatgctggttgttcttttgCgggtccagttaaacataatt	10	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:143792154C>T	ENST00000367591.4	+	5	451	c.388C>T	c.(388-390)Cgg>Tgg	p.R130W		NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	130	Interaction with PEX19.				peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.R130W(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		TGTTCTTTTGCGGGTCCAGTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											143	135	138					6																	143792154		2203	4300	6503	143833847	SO:0001583	missense	8504			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.388C>T	6.37:g.143792154C>T	ENSP00000356563:p.Arg130Trp		143833847	Q6FGP5	Missense_Mutation	SNP	ENST00000367591.4	37	CCDS5199.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975325	0.74360	.	.	ENSG00000034693	ENST00000344281;ENST00000367592;ENST00000367591	T;T	0.59772	0.24;0.24	5.48	3.64	0.41730	.	0.000000	0.85682	D	0.000000	T	0.70675	0.3251	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77099	-0.2713	10	0.87932	D	0	-11.0984	14.5306	0.67923	0.2593:0.7407:0.0:0.0	.	130;130	B4DV31;P56589	.;PEX3_HUMAN	W	86;86;130	ENSP00000356564:R86W;ENSP00000356563:R130W	ENSP00000344195:R86W	R	+	1	2	PEX3	143833847	1.000000	0.71417	0.973000	0.42090	0.983000	0.72400	1.779000	0.38624	0.630000	0.30394	0.591000	0.81541	CGG		0.363	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1			T	143792154	C	T	143792154	3	4	61	1	0	0	0	0	1	0	0	0	11778	759	27	1	406	1	PEX3	6	143792154	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11848	143792154	27322913	4978	12963										
PHACTR2	9749	broad.mit.edu	37	chr6	144074943	144074943	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgggcacatgatacccatCggagaggaatctacccgaga	11	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144074943C>T	ENST00000427704.2	+	4	445	c.315C>T	c.(313-315)atC>atT	p.I105I	PHACTR2_ENST00000440869.2_Silent_p.I116I|PHACTR2_ENST00000367584.4_Silent_p.I173I|PHACTR2_ENST00000397980.3_Silent_p.I116I|PHACTR2_ENST00000305766.6_Silent_p.I105I|PHACTR2_ENST00000367582.3_Silent_p.I116I	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	105							protein phosphatase inhibitor activity (GO:0004864)	p.I105I(1)|p.I116I(1)		NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		TGATACCCATCGGAGAGGAAT	0.408																																					Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)											2	Substitution - coding silent(2)	large_intestine(2)	6											88	80	82					6																	144074943		1814	4082	5896	144116636	SO:0001819	synonymous_variant	9749			AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.315C>T	6.37:g.144074943C>T			144116636	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	37	CCDS47492.1																																																																																				0.408	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		T	144074943	C	T	144074943	2	4	61	1	0	0	0	0	0	0	0	1	11841	874	31	1		1	PHACTR2	6	144074943	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	282789	144074943	27040124	4979	12964										
PHACTR2	9749	broad.mit.edu	37	chr6	144086576	144086576	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaataacttctcacctgtcCtcagacacaacaacttctgg	4	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144086576C>T	ENST00000427704.2	+	6	970	c.840C>T	c.(838-840)tcC>tcT	p.S280S	PHACTR2_ENST00000440869.2_Silent_p.S291S|PHACTR2_ENST00000367584.4_Silent_p.S268S|PHACTR2_ENST00000305766.6_Silent_p.S200S|PHACTR2_ENST00000367582.3_Silent_p.S211S	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	280							protein phosphatase inhibitor activity (GO:0004864)	p.S291S(1)|p.S200S(1)		NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		CTCACCTGTCCTCAGACACAA	0.512																																					Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)											2	Substitution - coding silent(2)	large_intestine(2)	6											89	94	93					6																	144086576		1990	4184	6174	144128269	SO:0001819	synonymous_variant	9749			AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.840C>T	6.37:g.144086576C>T			144128269	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	37	CCDS47492.1																																																																																				0.512	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		T	144086576	C	T	144086576	2	4	61	1	0	0	0	0	0	0	0	1	11841	668	24	3		3	PHACTR2	6	144086576	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11633	144086576	27028491	4980	12965										
PLAGL1	5325	broad.mit.edu	37	chr6	144263204	144263204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagctacttgcaagcccgTtctgggcagaagctcctaaa	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144263204T>C	ENST00000360537.2	-	5	2662	c.749A>G	c.(748-750)aAc>aGc	p.N250S	PLAGL1_ENST00000367571.1_Missense_Mutation_p.N250S|PLAGL1_ENST00000416623.1_Missense_Mutation_p.N250S|PLAGL1_ENST00000354765.2_Missense_Mutation_p.N250S|PLAGL1_ENST00000367572.1_Missense_Mutation_p.N198S|PLAGL1_ENST00000429150.1_Missense_Mutation_p.N250S|PLAGL1_ENST00000444202.1_Missense_Mutation_p.N250S|PLAGL1_ENST00000392307.1_Missense_Mutation_p.N198S|PLAGL1_ENST00000437412.1_Missense_Mutation_p.N198S|PLAGL1_ENST00000392309.1_Missense_Mutation_p.N250S			Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1	250					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.N250S(1)		endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(3)|stomach(2)	13				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)		TGCAAGCCCGTTCTGGGCAGA	0.602											OREG0017707	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	6											93	97	95					6																	144263204		2203	4300	6503	144304897	SO:0001583	missense	5325			U81992	CCDS5202.1, CCDS5203.1	6q24-q25	2013-01-08			ENSG00000118495	ENSG00000118495		"Zinc fingers, C2H2-type"	9046	protein-coding gene	gene with protein product		603044				9722527, 9671765	Standard	NM_006718		Approved	ZAC, LOT1	uc003qkf.3	Q9UM63	OTTHUMG00000015738	ENST00000360537.2:c.749A>G	6.37:g.144263204T>C	ENSP00000353734:p.Asn250Ser	1685	144304897	B2RBA4|B2RCM8|E1P595|E1P597|O76019|Q7Z3V8|Q92981|Q96JR9|Q9UIZ0	Missense_Mutation	SNP	ENST00000360537.2	37	CCDS5202.1	.	.	.	.	.	.	.	.	.	.	T	2.750	-0.260340	0.05791	.	.	ENSG00000118495	ENST00000360537;ENST00000354765;ENST00000444202;ENST00000429150;ENST00000392309;ENST00000416623;ENST00000437412;ENST00000392307;ENST00000451709;ENST00000367572;ENST00000367571	T;T;T;T;T;T;T;T;T;T	0.10192	2.9;2.9;2.9;2.9;2.9;2.9;3.96;3.96;3.96;2.9	5.39	2.94	0.34122	.	0.263495	0.32343	N	0.006227	T	0.01695	0.0054	N	0.24115	0.695	0.23882	N	0.996578	B	0.12630	0.006	B	0.16722	0.016	T	0.47861	-0.9084	10	0.07990	T	0.79	-9.7547	9.4522	0.38734	0.0:0.1352:0.0:0.8648	.	250	Q9UM63	PLAL1_HUMAN	S	250;250;250;250;250;250;198;198;39;198;250	ENSP00000353734:N250S;ENSP00000346810:N250S;ENSP00000400929:N250S;ENSP00000398409:N250S;ENSP00000376125:N250S;ENSP00000400060:N250S;ENSP00000392418:N198S;ENSP00000376124:N198S;ENSP00000356544:N198S;ENSP00000356543:N250S	ENSP00000346810:N250S	N	-	2	0	PLAGL1	144304897	1.000000	0.71417	0.228000	0.23943	0.847000	0.48162	5.408000	0.66368	0.335000	0.23614	0.402000	0.26972	AAC		0.602	PLAGL1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042541.1			C	144263204	T	C	144263204	3	2	61	1	0	0	0	0	1	0	0	0	12050	1725	60	4	646	4	PLAGL1	6	144263204	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	176628	144263204	26851863	4981	12966										
STX11	8676	broad.mit.edu	37	chr6	144508154	144508154	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcgcgcatttcgcgggcGcagtacaacgcgctcaccct	13	15	1	0	rs544924911		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144508154G>A	ENST00000367568.4	+	2	573	c.390G>A	c.(388-390)gcG>gcA	p.A130A		NM_003764.3	NP_003755.2	O75558	STX11_HUMAN	syntaxin 11	130					cytotoxic T cell degranulation (GO:0043316)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|natural killer cell degranulation (GO:0043320)|neutrophil degranulation (GO:0043312)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	SNAP receptor activity (GO:0005484)	p.A130A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	12				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		TTTCGCGGGCGCAGTACAACG	0.667									Familial Hemophagocytic Lymphohistiocytosis																																							1	Substitution - coding silent(1)	large_intestine(1)	6											26	24	24					6																	144508154		2203	4300	6503	144549847	SO:0001819	synonymous_variant	8676	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AF044309	CCDS5205.1	6q24.1	2014-09-17			ENSG00000135604	ENSG00000135604			11429	protein-coding gene	gene with protein product		605014				9553086	Standard	NM_003764		Approved		uc003qks.4	O75558	OTTHUMG00000015739	ENST00000367568.4:c.390G>A	6.37:g.144508154G>A			144549847	E1P598|O75378|O95148|Q5TCL6	Silent	SNP	ENST00000367568.4	37	CCDS5205.1																																																																																				0.667	STX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042544.1			A	144508154	G	A	144508154	2	1	61	1	0	0	0	0	0	0	0	1	15376	1074	38	1		1	STX11	6	144508154	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244950	144508154	26606913	4982	12967										
STX11	8676	broad.mit.edu	37	chr6	144508523	144508523	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaacgtacaaaagacggtCgactacaccggccaggccaa	9	14	1	1	rs369303487		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144508523C>T	ENST00000367568.4	+	2	942	c.759C>T	c.(757-759)gtC>gtT	p.V253V		NM_003764.3	NP_003755.2	O75558	STX11_HUMAN	syntaxin 11	253	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				cytotoxic T cell degranulation (GO:0043316)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|natural killer cell degranulation (GO:0043320)|neutrophil degranulation (GO:0043312)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	SNAP receptor activity (GO:0005484)	p.V253V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	12				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		AAAAGACGGTCGACTACACCG	0.622									Familial Hemophagocytic Lymphohistiocytosis																																							1	Substitution - coding silent(1)	large_intestine(1)	6											59	47	51					6																	144508523		2203	4300	6503	144550216	SO:0001819	synonymous_variant	8676	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AF044309	CCDS5205.1	6q24.1	2014-09-17			ENSG00000135604	ENSG00000135604			11429	protein-coding gene	gene with protein product		605014				9553086	Standard	NM_003764		Approved		uc003qks.4	O75558	OTTHUMG00000015739	ENST00000367568.4:c.759C>T	6.37:g.144508523C>T			144550216	E1P598|O75378|O95148|Q5TCL6	Silent	SNP	ENST00000367568.4	37	CCDS5205.1																																																																																				0.622	STX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042544.1			T	144508523	C	T	144508523	2	4	61	1	0	0	0	0	0	0	0	1	15376	871	31	1		1	STX11	6	144508523	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	369	144508523	26606544	4983	12968										
UTRN	7402	broad.mit.edu	37	chr6	144757231	144757231	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggagcaggatgatatttCtgatgatgttgaagaagtca	12	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144757231C>A	ENST00000367545.3	+	9	1016	c.1016C>A	c.(1015-1017)tCt>tAt	p.S339Y		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	339	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.S339Y(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GATGATATTTCTGATGATGTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											159	142	148					6																	144757231		2203	4300	6503	144798924	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1016C>A	6.37:g.144757231C>A	ENSP00000356515:p.Ser339Tyr		144798924	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960034	0.92791	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.53640	0.61	5.77	5.77	0.91146	.	0.000000	0.53938	D	0.000054	T	0.72495	0.3467	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76280	-0.3017	10	0.87932	D	0	.	20.3473	0.98799	0.0:1.0:0.0:0.0	.	339	P46939	UTRO_HUMAN	Y	339	ENSP00000356515:S339Y	ENSP00000356499:S339Y	S	+	2	0	UTRN	144798924	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.687000	0.84139	2.884000	0.98904	0.655000	0.94253	TCT		0.473	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144757231	C	A	144757231	3	1	61	1	0	0	0	0	1	0	0	0	17143	913	32	2	1050	2	UTRN	6	144757231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	248708	144757231	26357836	4984	12969										
UTRN	7402	broad.mit.edu	37	chr6	144768443	144768443	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaactaagtgtcagtgttCgacgtctggctgtaagtgat	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144768443C>T	ENST00000367545.3	+	14	1711	c.1711C>T	c.(1711-1713)Cga>Tga	p.R571*		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	571	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R571*(2)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TGTCAGTGTTCGACGTCTGGC	0.383																																																2	Substitution - Nonsense(2)	large_intestine(1)|breast(1)	6											118	104	109					6																	144768443		2203	4300	6503	144810136	SO:0001587	stop_gained	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1711C>T	6.37:g.144768443C>T	ENSP00000356515:p.Arg571*		144810136	Q5SYY1|Q5SZ57|Q9UJ40	Nonsense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	38	7.240768	0.98157	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	.	.	.	5.85	4.98	0.66077	.	0.000000	0.44902	D	0.000415	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7217	0.40306	0.1401:0.7897:0.0:0.0702	.	.	.	.	X	571	.	ENSP00000356499:R571X	R	+	1	2	UTRN	144810136	1.000000	0.71417	0.110000	0.21437	0.686000	0.39977	4.662000	0.61525	1.470000	0.48102	0.561000	0.74099	CGA		0.383	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144768443	C	T	144768443	4	4	61	1	0	0	0	0	0	1	0	0	17143	876	31	1	1765	1	UTRN	6	144768443	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11212	144768443	26346624	4985	12970										
UTRN	7402	broad.mit.edu	37	chr6	144768895	144768895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggattctttggttcagaGactagaagattcctccaacc	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144768895G>T	ENST00000367545.3	+	15	1880	c.1880G>T	c.(1879-1881)aGa>aTa	p.R627I		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	627	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R627I(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TTGGTTCAGAGACTAGAAGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											113	113	113					6																	144768895		2203	4300	6503	144810588	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1880G>T	6.37:g.144768895G>T	ENSP00000356515:p.Arg627Ile		144810588	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517226	0.85495	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.36157	1.27	5.87	4.99	0.66335	.	0.101083	0.43919	D	0.000501	T	0.25158	0.0611	L	0.44542	1.39	0.80722	D	1	P	0.52316	0.952	P	0.50896	0.653	T	0.06303	-1.0834	10	0.51188	T	0.08	.	5.9329	0.19148	0.2468:0.0:0.7532:0.0	.	627	P46939	UTRO_HUMAN	I	627	ENSP00000356515:R627I	ENSP00000356499:R627I	R	+	2	0	UTRN	144810588	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.975000	0.63777	2.941000	0.99782	0.655000	0.94253	AGA		0.368	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144768895	G	T	144768895	3	4	61	1	0	0	0	0	1	0	0	0	17143	942	33	2	1938	2	UTRN	6	144768895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	452	144768895	26346172	4986	12971										
UTRN	7402	broad.mit.edu	37	chr6	144772609	144772609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagatgcaagacacttccGaaatgaaaaagaagttgaag	10	5	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144772609G>A	ENST00000367545.3	+	17	2176	c.2176G>A	c.(2176-2178)Gaa>Aaa	p.E726K		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	726	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E726K(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AGACACTTCCGAAATGAAAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											88	84	85					6																	144772609		2203	4300	6503	144814302	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2176G>A	6.37:g.144772609G>A	ENSP00000356515:p.Glu726Lys		144814302	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.100637	0.37048	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.61742	0.08	5.99	5.99	0.97316	.	0.543702	0.16825	N	0.198016	T	0.30230	0.0758	L	0.38175	1.15	0.80722	D	1	P	0.38110	0.618	B	0.24541	0.054	T	0.23084	-1.0198	10	0.42905	T	0.14	.	14.0646	0.64821	0.0771:0.0:0.9229:0.0	.	726	P46939	UTRO_HUMAN	K	726	ENSP00000356515:E726K	ENSP00000356499:E726K	E	+	1	0	UTRN	144814302	1.000000	0.71417	0.895000	0.35142	0.023000	0.10783	4.616000	0.61197	2.847000	0.97988	0.655000	0.94253	GAA		0.348	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144772609	G	A	144772609	3	1	61	1	0	0	0	0	1	0	0	0	17143	1059	37	1	2242	1	UTRN	6	144772609	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3714	144772609	26342458	4987	12972										
UTRN	7402	broad.mit.edu	37	chr6	144783844	144783844	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattacataaacttgcagaaGaaacaaaggctctggagaaa	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144783844G>T	ENST00000367545.3	+	22	2908	c.2908G>T	c.(2908-2910)Gaa>Taa	p.E970*		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	970					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E970*(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACTTGCAGAAGAAACAAAGGC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											52	59	56					6																	144783844		2201	4298	6499	144825537	SO:0001587	stop_gained	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2908G>T	6.37:g.144783844G>T	ENSP00000356515:p.Glu970*		144825537	Q5SYY1|Q5SZ57|Q9UJ40	Nonsense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	40	8.413451	0.98801	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	.	.	.	5.36	4.48	0.54585	.	0.118708	0.37483	N	0.002067	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	16.0496	0.80745	0.0:0.1345:0.8655:0.0	.	.	.	.	X	970	.	ENSP00000356499:E970X	E	+	1	0	UTRN	144825537	1.000000	0.71417	0.999000	0.59377	0.709000	0.40893	4.769000	0.62300	1.221000	0.43506	-0.176000	0.13171	GAA		0.328	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144783844	G	T	144783844	4	4	61	1	0	0	0	0	0	1	0	0	17143	943	33	2	2994	2	UTRN	6	144783844	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11235	144783844	26331223	4988	12973										
UTRN	7402	broad.mit.edu	37	chr6	144795803	144795803	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgaaggaaatagagactAatcttcgaagtggtccagtt	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144795803A>C	ENST00000367545.3	+	24	3244	c.3244A>C	c.(3244-3246)Aat>Cat	p.N1082H		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1082					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.N1082H(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AATAGAGACTAATCTTCGAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											105	105	105					6																	144795803		2203	4300	6503	144837496	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.3244A>C	6.37:g.144795803A>C	ENSP00000356515:p.Asn1082His		144837496	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	0.089	-1.170605	0.01660	.	.	ENSG00000152818	ENST00000367545	T	0.51071	0.72	5.68	0.263	0.15602	.	1.103270	0.06912	N	0.807875	T	0.16128	0.0388	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31752	-0.9932	10	0.46703	T	0.11	.	5.5389	0.17028	0.5218:0.2515:0.2267:0.0	.	1082	P46939	UTRO_HUMAN	H	1082	ENSP00000356515:N1082H	ENSP00000356515:N1082H	N	+	1	0	UTRN	144837496	0.000000	0.05858	0.015000	0.15790	0.041000	0.13682	-0.313000	0.08103	0.062000	0.16340	0.460000	0.39030	AAT		0.363	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			C	144795803	A	C	144795803	3	2	61	1	0	0	0	0	1	0	0	0	17143	362	13	4	3338	4	UTRN	6	144795803	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11959	144795803	26319264	4989	12974										
UTRN	7402	broad.mit.edu	37	chr6	144843278	144843278	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacactgctatttacgaaGacttctcttttcaggaagac	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:144843278G>T	ENST00000367545.3	+	39	5704	c.5704G>T	c.(5704-5706)Gac>Tac	p.D1902Y		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1902					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.D1902Y(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TATTTACGAAGACTTCTCTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											122	114	117					6																	144843278		2203	4300	6503	144884971	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.5704G>T	6.37:g.144843278G>T	ENSP00000356515:p.Asp1902Tyr		144884971	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759231	0.49468	.	.	ENSG00000152818	ENST00000367545	T	0.63580	-0.05	5.51	4.61	0.57282	.	0.107611	0.40818	N	0.001012	T	0.47820	0.1466	M	0.72894	2.215	0.80722	D	1	P	0.45474	0.859	B	0.39419	0.299	T	0.59606	-0.7423	10	0.62326	D	0.03	.	9.8873	0.41268	0.0731:0.1396:0.7872:0.0	.	1902	P46939	UTRO_HUMAN	Y	1902	ENSP00000356515:D1902Y	ENSP00000356515:D1902Y	D	+	1	0	UTRN	144884971	1.000000	0.71417	0.981000	0.43875	0.377000	0.30045	6.073000	0.71245	2.593000	0.87608	0.491000	0.48974	GAC		0.378	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144843278	G	T	144843278	3	4	61	1	0	0	0	0	1	0	0	0	17143	942	33	2	5858	2	UTRN	6	144843278	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47475	144843278	26271789	4990	12975										
SHPRH	257218	broad.mit.edu	37	chr6	146243422	146243422	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcaaatagagaacttacGtgttggaaaatagctttgat	8	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146243422G>A	ENST00000367505.2	-	20	4046	c.3782C>T	c.(3781-3783)aCa>aTa	p.T1261I	SHPRH_ENST00000275233.7_Splice_Site_p.T1261I|SHPRH_ENST00000367503.3_Splice_Site_p.T1265I|SHPRH_ENST00000438092.2_Splice_Site_p.T1265I			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1261					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T1265I(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GAGAACTTACGTGTTGGAAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	6											74	70	71					6																	146243422		1816	4058	5874	146285115	SO:0001630	splice_region_variant	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3782+1C>T	6.37:g.146243422G>A			146285115	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912772	0.72983	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74947	-0.89;-0.89;-0.88;-0.89	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.79581	0.4470	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.91635	0.657;0.998;0.999	T	0.78863	-0.2036	9	.	.	.	-17.3411	14.6902	0.69080	0.0:0.1456:0.8544:0.0	.	460;1261;1265	B3KX98;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	I	1261;1265;1265;1261	ENSP00000356475:T1261I;ENSP00000356473:T1265I;ENSP00000412797:T1265I;ENSP00000275233:T1261I	.	T	-	2	0	SHPRH	146285115	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.302000	0.65733	2.423000	0.82170	0.655000	0.94253	ACA		0.313	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	Missense_Mutation	A	146243422	G	A	146243422	5	1	61	1	0	0	0	0	0	0	1	0	14328	1159	40	1	1330	1	SHPRH	6	146243422	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1400144	146243422	24871645	4991	12976										
SHPRH	257218	broad.mit.edu	37	chr6	146264506	146264506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattgaacacgaggcttacGatctatctgatcaagttcac	8	10	4	2	rs369914151		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146264506G>A	ENST00000367505.2	-	9	2275	c.2011C>T	c.(2011-2013)Cgt>Tgt	p.R671C	SHPRH_ENST00000275233.7_Missense_Mutation_p.R671C|SHPRH_ENST00000367503.3_Missense_Mutation_p.R671C|SHPRH_ENST00000438092.2_Missense_Mutation_p.R671C			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	671					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R671C(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		CGAGGCTTACGATCTATCTGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	CYS/ARG,CYS/ARG	0,3950		0,0,1975	112	106	108		2011,2011	-0.6	0	6		108	1,8321		0,1,4160	no	missense,missense	SHPRH	NM_001042683.2,NM_173082.3	180,180	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign,benign	671/1684,671/1660	146264506	1,12271	1975	4161	6136	146306199	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.2011C>T	6.37:g.146264506G>A	ENSP00000356475:p.Arg671Cys		146306199	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	11.38	1.622288	0.28889	0.0	1.2E-4	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.46	-0.575	0.11734	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);DEAD-like helicase (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	1.190550	0.05905	N	0.630643	T	0.27454	0.0674	L	0.27053	0.805	0.23056	N	0.998361	B;B;B;B	0.14012	0.001;0.003;0.002;0.009	B;B;B;B	0.09377	0.001;0.002;0.002;0.004	T	0.31613	-0.9937	10	0.38643	T	0.18	3.442	10.7864	0.46407	0.6361:0.0:0.3639:0.0	.	560;671;671;560	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	C	671;671;671;671;560	ENSP00000356475:R671C;ENSP00000356473:R671C;ENSP00000412797:R671C;ENSP00000275233:R671C	ENSP00000275233:R671C	R	-	1	0	SHPRH	146306199	0.992000	0.36948	0.001000	0.08648	0.806000	0.45545	2.755000	0.47540	-0.092000	0.12417	-0.142000	0.14014	CGT		0.418	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146264506	G	A	146264506	3	1	61	1	0	0	0	0	1	0	0	0	14328	1058	37	1	3172	1	SHPRH	6	146264506	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21084	146264506	24850561	4992	12977										
SHPRH	257218	broad.mit.edu	37	chr6	146264908	146264908	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccctgattttctagtttCtttctgaattttccttggac	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146264908C>A	ENST00000367505.2	-	9	1873	c.1609G>T	c.(1609-1611)Gaa>Taa	p.E537*	SHPRH_ENST00000275233.7_Nonsense_Mutation_p.E537*|SHPRH_ENST00000367503.3_Nonsense_Mutation_p.E537*|SHPRH_ENST00000438092.2_Nonsense_Mutation_p.E537*			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	537					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E537*(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTTCTAGTTTCTTTCTGAATT	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											70	66	67					6																	146264908		1821	4084	5905	146306601	SO:0001587	stop_gained	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1609G>T	6.37:g.146264908C>A	ENSP00000356475:p.Glu537*		146306601	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Nonsense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	41	8.688860	0.98916	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	.	.	.	5.62	4.74	0.60224	.	0.288858	0.31082	N	0.008292	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-15.0477	10.6835	0.45828	0.0:0.8396:0.0:0.1604	.	.	.	.	X	537;537;537;537;426	.	ENSP00000275233:E537X	E	-	1	0	SHPRH	146306601	0.999000	0.42202	1.000000	0.80357	0.887000	0.51463	1.529000	0.35996	2.822000	0.97130	0.650000	0.86243	GAA		0.333	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146264908	C	A	146264908	4	1	61	1	0	0	0	0	0	1	0	0	14328	922	32	2	3574	2	SHPRH	6	146264908	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402	146264908	24850159	4993	12978										
SHPRH	257218	broad.mit.edu	37	chr6	146267402	146267402	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcttttggttcaaattCgatattctggatttctgtct	6	6	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146267402C>T	ENST00000367505.2	-	7	1552	c.1288G>A	c.(1288-1290)Gaa>Aaa	p.E430K	SHPRH_ENST00000275233.7_Missense_Mutation_p.E430K|SHPRH_ENST00000367503.3_Missense_Mutation_p.E430K|SHPRH_ENST00000438092.2_Missense_Mutation_p.E430K			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	430					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E430K(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GGTTCAAATTCGATATTCTGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											183	160	167					6																	146267402		1820	4067	5887	146309095	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1288G>A	6.37:g.146267402C>T	ENSP00000356475:p.Glu430Lys		146309095	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511743	0.85389	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.74632	-0.86;-0.86;-0.84;-0.86	5.33	5.33	0.75918	DEAD-like helicase (1);	0.282690	0.29106	N	0.013140	T	0.75532	0.3862	L	0.47716	1.5	0.42336	D	0.992317	P;D;P;D	0.64830	0.938;0.971;0.926;0.994	B;P;B;P	0.55785	0.294;0.619;0.382;0.784	T	0.78518	-0.2173	10	0.72032	D	0.01	-21.6379	18.9987	0.92824	0.0:1.0:0.0:0.0	.	319;430;430;319	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	K	430;430;430;430;319	ENSP00000356475:E430K;ENSP00000356473:E430K;ENSP00000412797:E430K;ENSP00000275233:E430K	ENSP00000275233:E430K	E	-	1	0	SHPRH	146309095	1.000000	0.71417	0.844000	0.33320	0.531000	0.34715	6.253000	0.72453	2.494000	0.84150	0.561000	0.74099	GAA		0.338	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146267402	C	T	146267402	3	4	61	1	0	0	0	0	1	0	0	0	14328	893	31	1	3903	1	SHPRH	6	146267402	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2494	146267402	24847665	4994	12979										
GRM1	2911	broad.mit.edu	37	chr6	146350902	146350902	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagggtggaggccatgttCcacacgttggataagatcaa	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146350902C>T	ENST00000282753.1	+	1	484	c.249C>T	c.(247-249)ttC>ttT	p.F83F	GRM1_ENST00000361719.2_Silent_p.F83F|GRM1_ENST00000492807.2_Silent_p.F83F|GRM1_ENST00000507907.1_Silent_p.F83F|GRM1_ENST00000392299.2_Silent_p.F83F|GRM1_ENST00000355289.4_Silent_p.F83F			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	83					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.F83F(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		AGGCCATGTTCCACACGTTGG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	6											70	60	64					6																	146350902		2203	4300	6503	146392595	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.249C>T	6.37:g.146350902C>T			146392595	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																				0.607	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146350902	C	T	146350902	2	4	61	1	0	0	0	0	0	0	0	1	6817	854	30	3		3	GRM1	6	146350902	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83500	146350902	24764165	4995	12980										
GRM1	2911	broad.mit.edu	37	chr6	146351112	146351112	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccccccaggcaggactaaGaagcccattgcgggagtgat	12	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146351112G>T	ENST00000282753.1	+	1	694	c.459G>T	c.(457-459)aaG>aaT	p.K153N	GRM1_ENST00000361719.2_Missense_Mutation_p.K153N|GRM1_ENST00000492807.2_Missense_Mutation_p.K153N|GRM1_ENST00000507907.1_Missense_Mutation_p.K153N|GRM1_ENST00000392299.2_Missense_Mutation_p.K153N|GRM1_ENST00000355289.4_Missense_Mutation_p.K153N			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	153					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.K153N(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCAGGACTAAGAAGCCCATTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											68	72	71					6																	146351112		2203	4300	6503	146392805	SO:0001583	missense	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.459G>T	6.37:g.146351112G>T	ENSP00000282753:p.Lys153Asn		146392805	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109863	0.56398	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	5.69	3.59	0.41128	Extracellular ligand-binding receptor (1);	0.096714	0.64402	D	0.000001	T	0.79179	0.4402	L	0.45581	1.43	0.54753	D	0.999985	B;P;B;B	0.51147	0.38;0.942;0.433;0.38	B;P;P;B	0.51777	0.425;0.679;0.456;0.425	T	0.80513	-0.1349	10	0.54805	T	0.06	.	8.9963	0.36055	0.3291:0.0:0.6709:0.0	.	153;153;148;153	F8W805;Q13255;Q59HC2;Q13255-2	.;GRM1_HUMAN;.;.	N	153	ENSP00000354896:K153N;ENSP00000376119:K153N;ENSP00000424095:K153N;ENSP00000282753:K153N;ENSP00000347437:K153N;ENSP00000425599:K153N	ENSP00000282753:K153N	K	+	3	2	GRM1	146392805	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	2.207000	0.42788	1.405000	0.46838	0.561000	0.74099	AAG		0.557	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146351112	G	T	146351112	3	4	61	1	0	0	0	0	1	0	0	0	6817	933	33	2	461	2	GRM1	6	146351112	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210	146351112	24763955	4996	12981										
GRM1	2911	broad.mit.edu	37	chr6	146720611	146720611	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgggagcaactacaagatCatcacaacttgctttgcagt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146720611C>A	ENST00000282753.1	+	7	2671	c.2436C>A	c.(2434-2436)atC>atA	p.I812I	GRM1_ENST00000361719.2_Silent_p.I812I|GRM1_ENST00000492807.2_Silent_p.I812I|GRM1_ENST00000507907.1_Silent_p.I812I|GRM1_ENST00000392299.2_Silent_p.I812I|GRM1_ENST00000355289.4_Silent_p.I812I			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	812					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.I812I(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		ACTACAAGATCATCACAACTT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	6											160	129	140					6																	146720611		2203	4300	6503	146762304	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2436C>A	6.37:g.146720611C>A			146762304	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																				0.463	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		A	146720611	C	A	146720611	2	1	61	1	0	0	0	0	0	0	0	1	6817	816	29	2		2	GRM1	6	146720611	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	369499	146720611	24394456	4997	12982										
RAB32	10981	broad.mit.edu	37	chr6	146875640	146875640	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcctagtggagaagattCttgtaaaccaccaaagcttt	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:146875640C>A	ENST00000367495.3	+	3	756	c.577C>A	c.(577-579)Ctt>Att	p.L193I		NM_006834.3	NP_006825.1	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	193	PKA-RII subunit binding domain.				antigen processing and presentation (GO:0019882)|endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome maturation (GO:0090382)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)	p.L193I(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	8		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		GGAGAAGATTCTTGTAAACCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	99	99					6																	146875640		2203	4300	6503	146917333	SO:0001583	missense	10981			U71127	CCDS5210.1	6q24.2	2010-08-20			ENSG00000118508	ENSG00000118508		"RAB, member RAS oncogene", "A-kinase anchor proteins"	9772	protein-coding gene	gene with protein product		612906					Standard	NM_006834		Approved		uc003qln.1	Q13637	OTTHUMG00000015755	ENST00000367495.3:c.577C>A	6.37:g.146875640C>A	ENSP00000356465:p.Leu193Ile		146917333		Missense_Mutation	SNP	ENST00000367495.3	37	CCDS5210.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.709783	0.68730	.	.	ENSG00000118508	ENST00000367495	T	0.80653	-1.4	5.8	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	L	0.35288	1.05	0.80722	D	1	B	0.28128	0.201	B	0.39119	0.291	T	0.70565	-0.4837	10	0.48119	T	0.1	-20.1965	14.2916	0.66281	0.0:0.9294:0.0:0.0706	.	193	Q13637	RAB32_HUMAN	I	193	ENSP00000356465:L193I	ENSP00000356465:L193I	L	+	1	0	RAB32	146917333	1.000000	0.71417	0.886000	0.34754	0.971000	0.66376	3.627000	0.54252	2.735000	0.93741	0.655000	0.94253	CTT		0.383	RAB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042579.1	NM_006834		A	146875640	C	A	146875640	3	1	61	1	0	0	0	0	1	0	0	0	12958	913	32	2	587	2	RAB32	6	146875640	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	155029	146875640	24239427	4998	12983										
STXBP5	134957	broad.mit.edu	37	chr6	147560406	147560406	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttaaattttgcagagaaaGgtaagaattctcccagttat	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:147560406G>T	ENST00000321680.6	+	4	431	c.431G>T	c.(430-432)aGg>aTg	p.R144M	STXBP5_ENST00000367480.3_Splice_Site_p.R144M|STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000367481.3_Splice_Site_p.R144M|STXBP5_ENST00000546097.1_Splice_Site_p.R144M	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	144					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)	p.R144M(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGCAGAGAAAGGTAAGAATTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	81	83					6																	147560406		2203	4300	6503	147602099	SO:0001630	splice_region_variant	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.431+1G>T	6.37:g.147560406G>T			147602099	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835878	0.91117	.	.	ENSG00000164506	ENST00000367481;ENST00000546097;ENST00000321680;ENST00000367480	T;T;T;T	0.66638	1.54;4.96;1.54;-0.22	5.33	5.33	0.75918	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82449	0.5039	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.981	D	0.84745	0.0753	10	0.87932	D	0	.	19.3925	0.94590	0.0:0.0:1.0:0.0	.	144;144	Q5T5C0-2;Q5T5C0	.;STXB5_HUMAN	M	144	ENSP00000356451:R144M;ENSP00000441479:R144M;ENSP00000321826:R144M;ENSP00000356450:R144M	ENSP00000321826:R144M	R	+	2	0	STXBP5	147602099	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.223000	0.95203	2.664000	0.90586	0.563000	0.77884	AGG		0.373	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		Missense_Mutation	T	147560406	G	T	147560406	5	4	61	1	0	0	0	0	0	0	1	0	15395	1014	35	2	445	2	STXBP5	6	147560406	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	684766	147560406	23554661	4999	12984										
STXBP5	134957	broad.mit.edu	37	chr6	147583481	147583481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtgataatccaatggacGagggaaaggtagaatttttt	11	3	0	2	rs367614502		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:147583481G>A	ENST00000321680.6	+	6	622	c.622G>A	c.(622-624)Gag>Aag	p.E208K	STXBP5_ENST00000367480.3_Missense_Mutation_p.E208K|STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000367481.3_Missense_Mutation_p.E208K|STXBP5_ENST00000546097.1_Missense_Mutation_p.E208K	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	208					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)	p.E208K(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TCCAATGGACGAGGGAAAGGT	0.284													G|||	1	0.000199681	0	0	5008	,	,		12301	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	6						G	LYS/GLU,LYS/GLU	1,4377		0,1,2188	22	23	23		622,622	5.2	1	6		23	0,8546		0,0,4273	no	missense,missense	STXBP5	NM_001127715.2,NM_139244.4	56,56	0,1,6461	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging,probably-damaging	208/1152,208/1116	147583481	1,12923	2189	4273	6462	147625174	SO:0001583	missense	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.622G>A	6.37:g.147583481G>A	ENSP00000321826:p.Glu208Lys		147625174	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868282	0.91587	2.28E-4	0.0	ENSG00000164506	ENST00000367481;ENST00000546097;ENST00000321680;ENST00000367480	T;T;T;T	0.64085	1.56;4.99;1.56;-0.08	5.19	5.19	0.71726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.65048	0.2654	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79108	0.992;0.911	T	0.60291	-0.7292	10	0.08179	T	0.78	.	18.6689	0.91502	0.0:0.0:1.0:0.0	.	208;208	Q5T5C0-2;Q5T5C0	.;STXB5_HUMAN	K	208	ENSP00000356451:E208K;ENSP00000441479:E208K;ENSP00000321826:E208K;ENSP00000356450:E208K	ENSP00000321826:E208K	E	+	1	0	STXBP5	147625174	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.392000	0.97252	2.583000	0.87209	0.655000	0.94253	GAG		0.284	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			A	147583481	G	A	147583481	3	1	61	1	0	0	0	0	1	0	0	0	15395	1059	37	1	644	1	STXBP5	6	147583481	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23075	147583481	23531586	5000	12985										
STXBP5	134957	broad.mit.edu	37	chr6	147632635	147632635	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttcttctagaaaaggatTtagtacttatagaccttgca	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:147632635T>G	ENST00000321680.6	+	11	1117	c.1117T>G	c.(1117-1119)Tta>Gta	p.L373V	STXBP5_ENST00000367480.3_Missense_Mutation_p.L373V|STXBP5_ENST00000179882.6_Missense_Mutation_p.L44V|STXBP5_ENST00000367481.3_Missense_Mutation_p.L373V	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	373					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)	p.L373V(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		AGAAAAGGATTTAGTACTTAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	6											124	125	125					6																	147632635		2203	4299	6502	147674328	SO:0001583	missense	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1117T>G	6.37:g.147632635T>G	ENSP00000321826:p.Leu373Val		147674328	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845040	0.71603	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.20200	3.01;3.01;2.09;2.38	5.64	4.47	0.54385	WD40 repeat-like-containing domain (2);Lethal giant larvae homologue 2 (1);	0.000000	0.64402	D	0.000001	T	0.36248	0.0960	M	0.80746	2.51	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.87578	0.99;0.998;0.994	T	0.36407	-0.9749	10	0.87932	D	0	.	11.38	0.49752	0.0:0.071:0.0:0.929	.	373;373;44	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	V	373;373;373;44	ENSP00000356451:L373V;ENSP00000321826:L373V;ENSP00000356450:L373V;ENSP00000179882:L44V	ENSP00000179882:L44V	L	+	1	2	STXBP5	147674328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.320000	0.51991	0.965000	0.38133	0.459000	0.35465	TTA		0.323	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			G	147632635	T	G	147632635	3	3	61	1	0	0	0	0	1	0	0	0	15395	1838	64	4	1159	4	STXBP5	6	147632635	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	49154	147632635	23482432	5001	12986										
SASH1	23328	broad.mit.edu	37	chr6	148848723	148848723	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaatacagcagctctgtCtctgagcaggtatgcagcta	9	9	2	1	rs368513083		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:148848723C>A	ENST00000367467.3	+	12	1894	c.1419C>A	c.(1417-1419)gtC>gtA	p.V473V		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	473					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.V473V(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCAGCTCTGTCTCTGAGCAGG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	6											114	116	115					6																	148848723		2203	4300	6503	148890416	SO:0001819	synonymous_variant	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1419C>A	6.37:g.148848723C>A			148890416	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																				0.423	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148848723	C	A	148848723	2	1	61	1	0	0	0	0	0	0	0	1	13885	900	32	2		2	SASH1	6	148848723	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1216088	148848723	22266344	5002	12987										
SASH1	23328	broad.mit.edu	37	chr6	148865259	148865259	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcccagcccctggagcaaGactctgctgtcgacaatgca	11	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:148865259G>T	ENST00000367467.3	+	18	3128	c.2653G>T	c.(2653-2655)Gac>Tac	p.D885Y		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	885					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.D885Y(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		CCTGGAGCAAGACTCTGCTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											129	142	137					6																	148865259		2203	4300	6503	148906952	SO:0001583	missense	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.2653G>T	6.37:g.148865259G>T	ENSP00000356437:p.Asp885Tyr		148906952	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	G	6.469	0.454623	0.12283	.	.	ENSG00000111961	ENST00000367467;ENST00000535767;ENST00000537769	T	0.38240	1.15	5.21	3.4	0.38934	.	0.723087	0.13565	N	0.378500	T	0.08714	0.0216	L	0.36672	1.1	0.09310	N	1	B;B	0.28512	0.214;0.214	B;B	0.34873	0.191;0.094	T	0.40421	-0.9564	10	0.05620	T	0.96	-6.6203	4.7248	0.12936	0.1599:0.2052:0.6349:0.0	.	866;885	Q6P4R9;O94885	.;SASH1_HUMAN	Y	885;646;295	ENSP00000356437:D885Y	ENSP00000356437:D885Y	D	+	1	0	SASH1	148906952	0.000000	0.05858	0.002000	0.10522	0.148000	0.21650	0.687000	0.25407	1.183000	0.42943	0.650000	0.86243	GAC		0.537	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		T	148865259	G	T	148865259	3	4	61	1	0	0	0	0	1	0	0	0	13885	942	33	2	2723	2	SASH1	6	148865259	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16536	148865259	22249808	5003	12988										
ZC3H12D	340152	broad.mit.edu	37	chr6	149783045	149783045	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtaggtgtgtcctctgtCcctgaaccagtcaacagcca	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:149783045C>A	ENST00000409806.3	-	3	685	c.367G>T	c.(367-369)Gac>Tac	p.D123Y	ZC3H12D_ENST00000416573.2_Missense_Mutation_p.D123Y|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.D123Y|ZC3H12D_ENST00000409948.1_Missense_Mutation_p.D123Y|ZC3H12D_ENST00000542614.1_Missense_Mutation_p.D123Y			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	123					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.D123Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		TGTCCTCTGTCCCTGAACCAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	85	84					6																	149783045		1991	4168	6159	149824738	SO:0001583	missense	340152					6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"Zinc fingers, CCCH-type domain containing"	21175	protein-coding gene	gene with protein product	"MCP induced protein 4"	611106	"chromosome 6 open reading frame 95"	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.367G>T	6.37:g.149783045C>A	ENSP00000386616:p.Asp123Tyr		149824738	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		.	.	.	.	.	.	.	.	.	.	C	22.7	4.320023	0.81469	.	.	ENSG00000178199	ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614;ENST00000409948	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.19	5.19	0.71726	Ribonuclease Zc3h12a-like (1);	0.325480	0.31797	N	0.007048	T	0.52125	0.1715	M	0.65498	2.005	0.41431	D	0.987867	D;P	0.58970	0.984;0.81	P;P	0.60541	0.876;0.647	T	0.55438	-0.8141	10	0.87932	D	0	-17.1924	15.2987	0.73931	0.0:0.8599:0.1401:0.0	.	123;123	A2A288;B7WNU7	ZC12D_HUMAN;.	Y	123	ENSP00000374592:D123Y;ENSP00000408686:D123Y;ENSP00000386616:D123Y;ENSP00000440813:D123Y;ENSP00000387062:D123Y	ENSP00000374592:D123Y	D	-	1	0	ZC3H12D	149824738	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.326000	0.59241	2.709000	0.92574	0.563000	0.77884	GAC		0.473	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360		A	149783045	C	A	149783045	3	1	61	1	0	0	0	0	1	0	0	0	17603	855	30	2	1232	2	ZC3H12D	6	149783045	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	917786	149783045	21332022	5004	12989										
KATNA1	11104	broad.mit.edu	37	chr6	149916262	149916262	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttttttaaagccatctcGaaatcctccatagttgtagg	6	10	1	0	rs375745597		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:149916262G>A	ENST00000335647.5	-	10	1430	c.1386C>T	c.(1384-1386)ttC>ttT	p.F462F	KATNA1_ENST00000494504.1_5'Flank|SNORA2_ENST00000365473.1_RNA|KATNA1_ENST00000367411.2_Silent_p.F462F|RP1-12G14.7_ENST00000419134.1_RNA|KATNA1_ENST00000335643.8_3'UTR					katanin p60 (ATPase containing) subunit A 1									p.F462F(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		AAGCCATCTCGAAATCCTCCA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	0,4406		0,0,2203	135	127	130		,1386	-1.2	1	6		130	4,8596	4.3+/-15.6	0,4,4296	no	utr-3,coding-synonymous	KATNA1	NM_001204076.1,NM_007044.3	,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,	,462/492	149916262	4,13002	2203	4300	6503	149957955	SO:0001819	synonymous_variant	11104			AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.1386C>T	6.37:g.149916262G>A			149957955		Silent	SNP	ENST00000335647.5	37	CCDS5217.1																																																																																				0.398	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		A	149916262	G	A	149916262	2	1	61	1	0	0	0	0	0	0	0	1	8005	1049	37	1		1	KATNA1	6	149916262	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133217	149916262	21198805	5005	12990										
LATS1	9113	broad.mit.edu	37	chr6	150001395	150001395	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagaacatctttctttcGaagagtttttgttgcataca	7	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:150001395G>A	ENST00000543571.1	-	5	2756	c.2209C>T	c.(2209-2211)Cga>Tga	p.R737*	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Nonsense_Mutation_p.R737*	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1									p.R737*(1)		central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TCTTTCTTTCGAAGAGTTTTT	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											102	101	102					6																	150001395		2203	4300	6503	150043088	SO:0001587	stop_gained	9113			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2209C>T	6.37:g.150001395G>A	ENSP00000437550:p.Arg737*		150043088		Nonsense_Mutation	SNP	ENST00000543571.1	37	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	G	40	8.165884	0.98686	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	.	.	.	5.64	5.64	0.86602	.	0.000000	0.48286	D	0.000196	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9906	0.64364	0.0:0.0:0.7498:0.2502	.	.	.	.	X	737	.	.	R	-	1	2	LATS1	150043088	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.999000	0.63934	2.812000	0.96745	0.557000	0.71058	CGA		0.378	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		A	150001395	G	A	150001395	4	1	61	1	0	0	0	0	0	1	0	0	8668	1066	37	1	1199	1	LATS1	6	150001395	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85133	150001395	21113672	5006	12991										
PCMT1	5110	broad.mit.edu	37	chr6	150117635	150117635	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcccctgttgtaccccaggCggtgagtcgggattttttct	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:150117635C>T	ENST00000367380.5	+	6	710	c.503C>T	c.(502-504)gCg>gTg	p.A168V	PCMT1_ENST00000544496.1_Splice_Site_p.A133V|RP11-350J20.5_ENST00000455607.2_RNA|PCMT1_ENST00000464889.1_Splice_Site_p.A226V|PCMT1_ENST00000367378.1_Splice_Site_p.A226V|PCMT1_ENST00000367384.2_Splice_Site_p.A226V	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase	168				A -> P (in Ref. 10; AA sequence). {ECO:0000305}.	protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.A168V(1)		kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		GTACCCCAGGCGGTGAGTCGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											110	108	109					6																	150117635		2203	4300	6503	150159328	SO:0001630	splice_region_variant	5110				CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.504+1C>T	6.37:g.150117635C>T			150159328	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Missense_Mutation	SNP	ENST00000367380.5	37		.	.	.	.	.	.	.	.	.	.	C	23.0	4.356982	0.82243	.	.	ENSG00000120265	ENST00000367384;ENST00000367378;ENST00000464889;ENST00000367380;ENST00000544496	T;T;T;T;T	0.50001	0.87;0.87;0.87;0.87;0.76	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.39200	0.1069	M	0.64260	1.97	0.80722	D	1	B;D;P	0.59767	0.329;0.986;0.7	B;B;B	0.41466	0.206;0.358;0.108	T	0.43956	-0.9359	10	0.48119	T	0.1	-15.813	19.4376	0.94804	0.0:1.0:0.0:0.0	.	133;168;168	B7Z972;P22061-2;P22061	.;.;PIMT_HUMAN	V	226;226;226;168;133	ENSP00000356354:A226V;ENSP00000356348:A226V;ENSP00000420813:A226V;ENSP00000356350:A168V;ENSP00000438247:A133V	ENSP00000356348:A226V	A	+	2	0	PCMT1	150159328	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.731000	0.84895	2.605000	0.88082	0.563000	0.77884	GCG		0.408	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Missense_Mutation	T	150117635	C	T	150117635	5	4	61	1	0	0	0	0	0	0	1	0	11616	782	27	1	699	1	PCMT1	6	150117635	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116240	150117635	20997432	5007	12992										
RAET1E	135250	broad.mit.edu	37	chr6	150210578	150210578	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgaaatacttttccagCcctctgtctttcttccatgt	4	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:150210578C>T	ENST00000357183.4	-	3	660	c.528G>A	c.(526-528)ggG>ggA	p.G176G	RAET1E_ENST00000532335.1_Silent_p.G176G|RAET1E_ENST00000367363.3_Silent_p.G140G|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000529948.1_Silent_p.G176G|RAET1E-AS1_ENST00000605899.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	176	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)	p.G176G(1)		cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		ACTTTTCCAGCCCTCTGTCTT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	6											168	157	161					6																	150210578		2203	4300	6503	150252271	SO:0001819	synonymous_variant	135250			AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.528G>A	6.37:g.150210578C>T			150252271	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Silent	SNP	ENST00000357183.4	37	CCDS5221.1																																																																																				0.473	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165		T	150210578	C	T	150210578	2	4	61	1	0	0	0	0	0	0	0	1	13036	726	26	3		3	RAET1E	6	150210578	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92943	150210578	20904489	5008	12993										
MTHFD1L	25902	broad.mit.edu	37	chr6	151243371	151243371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtggaaggagatggcttCgtgaacagcagcacaggcgg	17	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151243371C>T	ENST00000367321.3	+	10	1289	c.1015C>T	c.(1015-1017)Cgt>Tgt	p.R339C		NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	339	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)	p.R339C(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		GAGATGGCTTCGTGAACAGCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	6											235	192	207					6																	151243371		2203	4300	6503	151285064	SO:0001583	missense	25902			BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.1015C>T	6.37:g.151243371C>T	ENSP00000356290:p.Arg339Cys		151285064	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	37	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558607	0.65538	.	.	ENSG00000120254	ENST00000367321;ENST00000441122	T;T	0.45276	2.71;0.9	5.26	3.44	0.39384	.	0.165679	0.53938	D	0.000056	T	0.14442	0.0349	L	0.29908	0.895	0.25026	N	0.991306	D;P;D	0.64830	0.994;0.93;0.994	B;B;B	0.43123	0.409;0.39;0.409	T	0.05852	-1.0860	10	0.72032	D	0.01	.	5.6733	0.17735	0.1293:0.5516:0.2474:0.0717	.	340;94;339	B7ZM99;B2RD24;Q6UB35	.;.;C1TM_HUMAN	C	339;10	ENSP00000356290:R339C;ENSP00000407070:R10C	ENSP00000356290:R339C	R	+	1	0	MTHFD1L	151285064	0.070000	0.21116	0.175000	0.22980	0.992000	0.81027	0.898000	0.28404	1.191000	0.43056	0.650000	0.86243	CGT		0.483	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		T	151243371	C	T	151243371	3	4	61	1	0	0	0	0	1	0	0	0	9958	884	31	1	1053	1	MTHFD1L	6	151243371	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1032793	151243371	19871696	5009	12994										
MTHFD1L	25902	broad.mit.edu	37	chr6	151330992	151330992	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgctgacatcggaatggaGaaattcttcaacatcaagtg	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151330992G>T	ENST00000367321.3	+	21	2437	c.2163G>T	c.(2161-2163)gaG>gaT	p.E721D	MTHFD1L_ENST00000478643.1_3'UTR	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	721	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)	p.E721D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TCGGAATGGAGAAATTCTTCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	6											145	138	141					6																	151330992		2203	4300	6503	151372685	SO:0001583	missense	25902			BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.2163G>T	6.37:g.151330992G>T	ENSP00000356290:p.Glu721Asp		151372685	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	37	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520042	0.85495	.	.	ENSG00000120254	ENST00000367321	T	0.33654	1.4	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.74053	0.3666	H	0.99525	4.61	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.998	D	0.87231	0.2260	10	0.87932	D	0	.	17.0632	0.86553	0.0:0.0:1.0:0.0	.	722;476;721	B7ZM99;B2RD24;Q6UB35	.;.;C1TM_HUMAN	D	721	ENSP00000356290:E721D	ENSP00000356290:E721D	E	+	3	2	MTHFD1L	151372685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.757000	0.62213	2.010000	0.58986	0.650000	0.86243	GAG		0.498	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		T	151330992	G	T	151330992	3	4	61	1	0	0	0	0	1	0	0	0	9958	933	33	2	2245	2	MTHFD1L	6	151330992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87621	151330992	19784075	5010	12995										
AKAP12	9590	broad.mit.edu	37	chr6	151672474	151672474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagctgcagaaactgcagGgccattgggtgccgaagaag	15	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151672474G>T	ENST00000253332.1	+	3	3137	c.2948G>T	c.(2947-2949)gGg>gTg	p.G983V	AKAP12_ENST00000354675.6_Missense_Mutation_p.G885V|AKAP12_ENST00000359755.5_Missense_Mutation_p.G878V|AKAP12_ENST00000402676.2_Missense_Mutation_p.G983V			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	983					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.G983V(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAAACTGCAGGGCCATTGGGT	0.572																																					Melanoma(141;1616 1805 10049 24534 51979)											1	Substitution - Missense(1)	large_intestine(1)	6											67	66	66					6																	151672474		2203	4300	6503	151714167	SO:0001583	missense	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2948G>T	6.37:g.151672474G>T	ENSP00000253332:p.Gly983Val		151714167	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.781012	0.31502	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07114	3.22;3.22;3.22;3.22	5.04	1.38	0.22167	.	0.833475	0.10066	N	0.720366	T	0.02380	0.0073	L	0.40543	1.245	0.26411	N	0.976258	P;P;P	0.41265	0.744;0.744;0.627	B;B;B	0.38327	0.271;0.211;0.139	T	0.45234	-0.9275	10	0.35671	T	0.21	.	7.6098	0.28124	0.7577:0.0:0.2423:0.0	.	878;885;983	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	V	983;983;885;878	ENSP00000384537:G983V;ENSP00000253332:G983V;ENSP00000346702:G885V;ENSP00000352794:G878V	ENSP00000253332:G983V	G	+	2	0	AKAP12	151714167	0.490000	0.26012	0.007000	0.13788	0.013000	0.08279	0.816000	0.27267	0.007000	0.14760	-0.379000	0.06801	GGG		0.572	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151672474	G	T	151672474	3	4	61	1	0	0	0	0	1	0	0	0	448	1232	43	2	2987	2	AKAP12	6	151672474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	341482	151672474	19442593	5011	12996										
AKAP12	9590	broad.mit.edu	37	chr6	151672668	151672668	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtcctccaggcagtggcaGaaaaagtgaaagaggaatcc	13	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151672668G>A	ENST00000253332.1	+	3	3331	c.3142G>A	c.(3142-3144)Gaa>Aaa	p.E1048K	AKAP12_ENST00000354675.6_Missense_Mutation_p.E950K|AKAP12_ENST00000359755.5_Missense_Mutation_p.E943K|AKAP12_ENST00000402676.2_Missense_Mutation_p.E1048K			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1048					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.E1048K(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GGCAGTGGCAGAAAAAGTGAA	0.587																																					Melanoma(141;1616 1805 10049 24534 51979)											1	Substitution - Missense(1)	large_intestine(1)	6											49	53	52					6																	151672668		2203	4300	6503	151714361	SO:0001583	missense	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3142G>A	6.37:g.151672668G>A	ENSP00000253332:p.Glu1048Lys		151714361	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.491826	0.84962	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	5.26	5.26	0.73747	.	0.162443	0.29522	N	0.011904	T	0.18045	0.0433	L	0.32530	0.975	0.48975	D	0.999733	D;D;D	0.76494	0.999;0.999;0.999	D;D;P	0.65443	0.935;0.935;0.862	T	0.02115	-1.1211	10	0.37606	T	0.19	.	18.8893	0.92392	0.0:0.0:1.0:0.0	.	943;950;1048	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	K	1048;1048;950;943	ENSP00000384537:E1048K;ENSP00000253332:E1048K;ENSP00000346702:E950K;ENSP00000352794:E943K	ENSP00000253332:E1048K	E	+	1	0	AKAP12	151714361	1.000000	0.71417	0.973000	0.42090	0.616000	0.37450	8.968000	0.93407	2.462000	0.83206	0.455000	0.32223	GAA		0.587	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			A	151672668	G	A	151672668	3	1	61	1	0	0	0	0	1	0	0	0	448	943	33	3	3181	3	AKAP12	6	151672668	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194	151672668	19442399	5012	12997										
AKAP12	9590	broad.mit.edu	37	chr6	151673370	151673370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagacgtaccatttttcGaaggacttgaggggtctata	10	8	1	2	rs368517285		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151673370G>A	ENST00000253332.1	+	3	4033	c.3844G>A	c.(3844-3846)Gaa>Aaa	p.E1282K	AKAP12_ENST00000354675.6_Missense_Mutation_p.E1184K|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1177K|AKAP12_ENST00000402676.2_Missense_Mutation_p.E1282K			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1282					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.E1282K(3)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		ACCATTTTTCGAAGGACTTGA	0.458																																					Melanoma(141;1616 1805 10049 24534 51979)											3	Substitution - Missense(3)	large_intestine(2)|skin(1)	6						G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	82	79	80		3550,3844	-1.4	0	6		80	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AKAP12	NM_144497.2,NM_005100.3	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	1184/1685,1282/1783	151673370	1,13005	2203	4300	6503	151715063	SO:0001583	missense	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3844G>A	6.37:g.151673370G>A	ENSP00000253332:p.Glu1282Lys		151715063	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	8.059	0.767736	0.15983	0.0	1.16E-4	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	4.48	-1.38	0.09027	.	1.166780	0.06567	N	0.747894	T	0.00967	0.0032	N	0.12746	0.255	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.48885	-0.8995	10	0.18710	T	0.47	.	1.0087	0.01492	0.3548:0.1151:0.3179:0.2122	.	1177;1184;1282	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	K	1282;1282;1184;1177	ENSP00000384537:E1282K;ENSP00000253332:E1282K;ENSP00000346702:E1184K;ENSP00000352794:E1177K	ENSP00000253332:E1282K	E	+	1	0	AKAP12	151715063	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.435000	0.21510	-0.217000	0.10033	-0.252000	0.11476	GAA		0.458	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			A	151673370	G	A	151673370	3	1	61	1	0	0	0	0	1	0	0	0	448	1059	37	1	3883	1	AKAP12	6	151673370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	702	151673370	19441697	5013	12998										
AKAP12	9590	broad.mit.edu	37	chr6	151673522	151673522	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaagtctcctccatccccCgtggagagagagatggtagt	12	11	1	2	rs142473808		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151673522C>T	ENST00000253332.1	+	3	4185	c.3996C>T	c.(3994-3996)ccC>ccT	p.P1332P	AKAP12_ENST00000354675.6_Silent_p.P1234P|AKAP12_ENST00000359755.5_Silent_p.P1227P|AKAP12_ENST00000402676.2_Silent_p.P1332P			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1332					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.P1332P(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		CTCCATCCCCCGTGGAGAGAG	0.478													C|||	1	0.000199681	0	0	5008	,	,		22842	0.001		0	False		,,,				2504	0				Melanoma(141;1616 1805 10049 24534 51979)											1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	1,4405	2.1+/-5.4	0,1,2202	93	89	90		3996,3702	-1.5	0	6	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	AKAP12	NM_005100.3,NM_144497.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	1332/1783,1234/1685	151673522	1,13005	2203	4300	6503	151715215	SO:0001819	synonymous_variant	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3996C>T	6.37:g.151673522C>T			151715215	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Silent	SNP	ENST00000253332.1	37	CCDS5229.1																																																																																				0.478	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151673522	C	T	151673522	2	4	61	1	0	0	0	0	0	0	0	1	448	639	23	1		1	AKAP12	6	151673522	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152	151673522	19441545	5014	12999										
ZBTB2	57621	broad.mit.edu	37	chr6	151694683	151694683	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttgaagtatacatcgccGattgcaaccgtgcagtcaca	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151694683G>A	ENST00000325144.4	-	2	230	c.90C>T	c.(88-90)atC>atT	p.I30I		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	30	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I30I(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		ATACATCGCCGATTGCAACCG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	6											145	135	138					6																	151694683		2203	4300	6503	151736376	SO:0001819	synonymous_variant	57621			BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.90C>T	6.37:g.151694683G>A			151736376	A8K7C7|Q5SZ81|Q9P245	Silent	SNP	ENST00000325144.4	37	CCDS5231.1																																																																																				0.408	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		A	151694683	G	A	151694683	2	1	61	1	0	0	0	0	0	0	0	1	17567	1048	37	1		1	ZBTB2	6	151694683	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21161	151694683	19420384	5015	13000										
C6orf97	80129	broad.mit.edu	37	chr6	151857562	151857562	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcaactttggtcaaatTtgaatgtgctcagtctgagg	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151857562T>G	ENST00000239374.7	+	2	266	c.167T>G	c.(166-168)tTt>tGt	p.F56C	CCDC170_ENST00000367290.5_Missense_Mutation_p.F56C|CCDC170_ENST00000544131.1_3'UTR	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	56								p.F56C(1)									TTGGTCAAATTTGAATGTGCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	6											86	83	84					6																	151857562		1909	4123	6032	151899255	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.167T>G	6.37:g.151857562T>G	ENSP00000239374:p.Phe56Cys		151899255	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756574	0.49362	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.08546	3.08;3.08	5.8	5.8	0.92144	.	0.264750	0.36778	N	0.002410	T	0.14184	0.0343	M	0.75447	2.3	0.29565	N	0.850368	D	0.76494	0.999	D	0.69654	0.965	T	0.11916	-1.0568	10	0.39692	T	0.17	-8.6959	9.6723	0.40019	0.2597:0.0:0.0:0.7403	.	56	Q8IYT3	CF097_HUMAN	C	56	ENSP00000239374:F56C;ENSP00000356259:F56C	ENSP00000239374:F56C	F	+	2	0	C6orf97	151899255	1.000000	0.71417	0.988000	0.46212	0.528000	0.34623	4.450000	0.60041	2.216000	0.71823	0.528000	0.53228	TTT		0.443	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		G	151857562	T	G	151857562	3	3	61	1	0	0	0	0	1	0	0	0	2380	1841	64	4	173	4	C6orf97	6	151857562	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162879	151857562	19257505	5016	13001										
C6orf97	80129	broad.mit.edu	37	chr6	151859200	151859200	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaagacctccgatccaaGatgctttctaaagaagtctc	6	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151859200G>T	ENST00000239374.7	+	3	306	c.207G>T	c.(205-207)aaG>aaT	p.K69N	CCDC170_ENST00000367290.5_Missense_Mutation_p.K69N|CCDC170_ENST00000544131.1_3'UTR	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	69								p.K69N(1)									TCCGATCCAAGATGCTTTCTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	6											61	56	58					6																	151859200		1812	4085	5897	151900893	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.207G>T	6.37:g.151859200G>T	ENSP00000239374:p.Lys69Asn		151900893	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.810948	0.50421	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09817	2.94;2.94	5.53	2.63	0.31362	.	0.053556	0.64402	D	0.000001	T	0.07188	0.0182	M	0.75447	2.3	0.26627	N	0.972534	P	0.45827	0.867	P	0.46629	0.522	T	0.14254	-1.0479	10	0.59425	D	0.04	-42.1112	5.8804	0.18852	0.3638:0.1269:0.5093:0.0	.	69	Q8IYT3	CF097_HUMAN	N	69	ENSP00000239374:K69N;ENSP00000356259:K69N	ENSP00000239374:K69N	K	+	3	2	C6orf97	151900893	0.997000	0.39634	1.000000	0.80357	0.961000	0.63080	0.769000	0.26604	0.235000	0.21160	0.650000	0.86243	AAG		0.358	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		T	151859200	G	T	151859200	3	4	61	1	0	0	0	0	1	0	0	0	2380	933	33	2	217	2	C6orf97	6	151859200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1638	151859200	19255867	5017	13002										
C6orf97	80129	broad.mit.edu	37	chr6	151894594	151894594	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattttggagaagattcgaGaaatggacagccgggaagaa	13	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151894594G>A	ENST00000239374.7	+	6	1159	c.1060G>A	c.(1060-1062)Gaa>Aaa	p.E354K	CCDC170_ENST00000367290.5_Missense_Mutation_p.E354K	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	354								p.E354K(1)									GAAGATTCGAGAAATGGACAG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	6											51	53	52					6																	151894594		1923	4128	6051	151936287	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1060G>A	6.37:g.151894594G>A	ENSP00000239374:p.Glu354Lys		151936287	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.973921	0.74246	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09255	3.0;3.0	5.55	5.55	0.83447	.	0.105878	0.64402	D	0.000006	T	0.08802	0.0218	M	0.76574	2.34	0.49130	D	0.999751	P	0.38110	0.618	B	0.29862	0.108	T	0.03922	-1.0992	10	0.49607	T	0.09	-23.9043	18.0488	0.89341	0.0:0.0:1.0:0.0	.	354	Q8IYT3	CF097_HUMAN	K	354	ENSP00000239374:E354K;ENSP00000356259:E354K	ENSP00000239374:E354K	E	+	1	0	C6orf97	151936287	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	4.929000	0.63455	2.776000	0.95493	0.643000	0.83706	GAA		0.493	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		A	151894594	G	A	151894594	3	1	61	1	0	0	0	0	1	0	0	0	2380	943	33	3	1082	3	C6orf97	6	151894594	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35394	151894594	19220473	5018	13003										
C6orf97	80129	broad.mit.edu	37	chr6	151936783	151936783	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaagacactaaaaaaatCtctggaagaagcagaaaaga	8	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:151936783C>A	ENST00000239374.7	+	10	2015	c.1916C>A	c.(1915-1917)tCt>tAt	p.S639Y	RNU6-813P_ENST00000384691.1_RNA|CCDC170_ENST00000367290.5_Missense_Mutation_p.S646Y	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	639								p.S639Y(1)									CTAAAAAAATCTCTGGAAGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											131	128	129					6																	151936783		1822	4076	5898	151978476	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1916C>A	6.37:g.151936783C>A	ENSP00000239374:p.Ser639Tyr		151978476	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487687	0.84854	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09538	2.97;2.97	5.95	5.95	0.96441	.	0.178650	0.47852	D	0.000203	T	0.22742	0.0549	M	0.68317	2.08	0.38968	D	0.958687	D	0.65815	0.995	P	0.59643	0.861	T	0.00229	-1.1898	10	0.54805	T	0.06	0.1688	20.3967	0.98985	0.0:1.0:0.0:0.0	.	639	Q8IYT3	CF097_HUMAN	Y	639;646	ENSP00000239374:S639Y;ENSP00000356259:S646Y	ENSP00000239374:S639Y	S	+	2	0	C6orf97	151978476	0.229000	0.23729	0.967000	0.41034	0.970000	0.65996	2.508000	0.45450	2.829000	0.97493	0.655000	0.94253	TCT		0.383	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		A	151936783	C	A	151936783	3	1	61	1	0	0	0	0	1	0	0	0	2380	913	32	2	1954	2	C6orf97	6	151936783	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42189	151936783	19178284	5019	13004										
SYNE1	23345	broad.mit.edu	37	chr6	152551733	152551733	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgatctccaattcgatgCtgttgttttagtctcttttc	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152551733C>T	ENST00000367255.5	-	115	21745	c.21144G>A	c.(21142-21144)caG>caA	p.Q7048Q	SYNE1_ENST00000423061.1_Silent_p.Q6977Q|SYNE1_ENST00000265368.4_Silent_p.Q7048Q|SYNE1_ENST00000356820.4_Silent_p.Q1572Q|SYNE1_ENST00000341594.5_Silent_p.Q6660Q|SYNE1_ENST00000448038.1_Silent_p.Q6977Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7048					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.Q7048Q(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CAATTCGATGCTGTTGTTTTA	0.398										HNSCC(10;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	6											254	212	226					6																	152551733		2203	4300	6503	152593426	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.21144G>A	6.37:g.152551733C>T			152593426	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.398	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152551733	C	T	152551733	2	4	61	1	0	0	0	0	0	0	0	1	15484	796	28	3		3	SYNE1	6	152551733	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	614950	152551733	18563334	5020	13005										
SYNE1	23345	broad.mit.edu	37	chr6	152565708	152565708	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgcatggacggctgctcGacctgtagcttgtcaccacg	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152565708G>A	ENST00000367255.5	-	106	20257	c.19656C>T	c.(19654-19656)gtC>gtT	p.V6552V	SYNE1_ENST00000423061.1_Silent_p.V6481V|SYNE1_ENST00000265368.4_Silent_p.V6552V|SYNE1_ENST00000356820.4_Silent_p.V1076V|SYNE1_ENST00000341594.5_Silent_p.V6164V|SYNE1_ENST00000448038.1_Silent_p.V6481V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6552					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V6552V(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACGGCTGCTCGACCTGTAGCT	0.453										HNSCC(10;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	6											173	155	161					6																	152565708		2203	4300	6503	152607401	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.19656C>T	6.37:g.152565708G>A			152607401	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152565708	G	A	152565708	2	1	61	1	0	0	0	0	0	0	0	1	15484	1045	37	1		1	SYNE1	6	152565708	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13975	152565708	18549359	5021	13006										
SYNE1	23345	broad.mit.edu	37	chr6	152615173	152615173	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccaatcccggttcataGaactcctgggatgcggatgt	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152615173G>T	ENST00000367255.5	-	94	18373	c.17772C>A	c.(17770-17772)ttC>ttA	p.F5924L	SYNE1_ENST00000423061.1_Missense_Mutation_p.F5853L|SYNE1_ENST00000265368.4_Missense_Mutation_p.F5924L|SYNE1_ENST00000356820.4_Missense_Mutation_p.F448L|SYNE1_ENST00000341594.5_Missense_Mutation_p.F5536L|SYNE1_ENST00000448038.1_Missense_Mutation_p.F5853L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5924					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.F5924L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCGGTTCATAGAACTCCTGGG	0.493										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											103	94	97					6																	152615173		2203	4300	6503	152656866	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.17772C>A	6.37:g.152615173G>T	ENSP00000356224:p.Phe5924Leu		152656866	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	0.007	-2.016964	0.00418	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000540663;ENST00000537033	T;T;T;T;T;T;T	0.39406	1.17;1.14;1.08;1.21;1.22;2.91;1.17	4.69	1.82	0.25136	.	0.614797	0.14259	N	0.330946	T	0.05823	0.0152	N	0.04508	-0.205	0.24662	N	0.99346	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.44937	-0.9295	10	0.13108	T	0.6	.	8.8784	0.35358	0.1365:0.3697:0.4938:0.0	.	339;5924;5924;5853	B7ZBD0;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	L	5924;5853;5924;5853;5536;448;99;146	ENSP00000356224:F5924L;ENSP00000396024:F5853L;ENSP00000265368:F5924L;ENSP00000390975:F5853L;ENSP00000341887:F5536L;ENSP00000349276:F448L;ENSP00000437411:F99L	ENSP00000265368:F5924L	F	-	3	2	SYNE1	152656866	0.984000	0.35163	0.776000	0.31678	0.123000	0.20343	0.244000	0.18124	-0.187000	0.10516	-1.273000	0.01405	TTC		0.493	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152615173	G	T	152615173	3	4	61	1	0	0	0	0	1	0	0	0	15484	933	33	2	8906	2	SYNE1	6	152615173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49465	152615173	18499894	5022	13007										
SYNE1	23345	broad.mit.edu	37	chr6	152642463	152642463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagacctaagtacttctcCttctgttcttctgccatttt	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152642463C>A	ENST00000367255.5	-	84	16747	c.16146G>T	c.(16144-16146)aaG>aaT	p.K5382N	SYNE1_ENST00000423061.1_Missense_Mutation_p.K5311N|SYNE1_ENST00000265368.4_Missense_Mutation_p.K5382N|SYNE1_ENST00000356820.4_5'Flank|SYNE1_ENST00000341594.5_Missense_Mutation_p.K5055N|SYNE1_ENST00000448038.1_Missense_Mutation_p.K5311N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5382					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.K5382N(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGTACTTCTCCTTCTGTTCTT	0.388										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											112	106	108					6																	152642463		2203	4300	6503	152684156	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16146G>T	6.37:g.152642463C>A	ENSP00000356224:p.Lys5382Asn		152684156	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	10.30	1.312540	0.23908	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.59906	0.32;0.27;0.23;0.27;0.45	5.38	1.04	0.20106	.	0.118890	0.38663	N	0.001619	T	0.36468	0.0968	L	0.51422	1.61	0.80722	D	1	P;P;P;P	0.47762	0.9;0.704;0.704;0.804	B;B;B;B	0.42522	0.39;0.165;0.165;0.311	T	0.34004	-0.9846	10	0.62326	D	0.03	.	11.1891	0.48675	0.0:0.6418:0.0:0.3581	.	5382;5382;5382;5311	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	N	5382;5311;5382;5311;5055	ENSP00000356224:K5382N;ENSP00000396024:K5311N;ENSP00000265368:K5382N;ENSP00000390975:K5311N;ENSP00000341887:K5055N	ENSP00000265368:K5382N	K	-	3	2	SYNE1	152684156	0.999000	0.42202	0.960000	0.40013	0.741000	0.42261	0.717000	0.25851	0.259000	0.21709	-0.150000	0.13652	AAG		0.388	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152642463	C	A	152642463	3	1	61	1	0	0	0	0	1	0	0	0	15484	680	24	2	10572	2	SYNE1	6	152642463	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27290	152642463	18472604	5023	13008										
SYNE1	23345	broad.mit.edu	37	chr6	152642938	152642938	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaacccaacatttcacaGaattgatctgagtctccacc	5	14	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152642938G>T	ENST00000367255.5	-	83	16602	c.16001C>A	c.(16000-16002)tCt>tAt	p.S5334Y	SYNE1_ENST00000423061.1_Missense_Mutation_p.S5263Y|SYNE1_ENST00000265368.4_Missense_Mutation_p.S5334Y|SYNE1_ENST00000341594.5_Missense_Mutation_p.S5007Y|SYNE1_ENST00000448038.1_Missense_Mutation_p.S5263Y	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5334					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S5334Y(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACATTTCACAGAATTGATCTG	0.398										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											172	162	166					6																	152642938		2203	4300	6503	152684631	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16001C>A	6.37:g.152642938G>T	ENSP00000356224:p.Ser5334Tyr		152684631	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	12.30	1.897790	0.33535	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.55930	0.58;0.58;0.49;0.58;0.66	5.53	5.53	0.82687	.	0.230089	0.31082	N	0.008285	T	0.49064	0.1535	M	0.62723	1.935	0.80722	D	1	D;P;P;P	0.61080	0.989;0.793;0.793;0.868	P;B;B;B	0.53649	0.731;0.176;0.176;0.397	T	0.55921	-0.8064	10	0.52906	T	0.07	.	8.6015	0.33747	0.0825:0.0:0.7628:0.1547	.	5334;5334;5334;5263	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Y	5334;5263;5334;5263;5007	ENSP00000356224:S5334Y;ENSP00000396024:S5263Y;ENSP00000265368:S5334Y;ENSP00000390975:S5263Y;ENSP00000341887:S5007Y	ENSP00000265368:S5334Y	S	-	2	0	SYNE1	152684631	0.278000	0.24230	0.995000	0.50966	0.978000	0.69477	3.692000	0.54727	2.605000	0.88082	0.655000	0.94253	TCT		0.398	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152642938	G	T	152642938	3	4	61	1	0	0	0	0	1	0	0	0	15484	942	33	2	10721	2	SYNE1	6	152642938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	475	152642938	18472129	5024	13009										
SYNE1	23345	broad.mit.edu	37	chr6	152650912	152650912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctccatccagctctgagaGctcagcgaggctgtgttcta	11	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152650912G>A	ENST00000367255.5	-	78	15509	c.14908C>T	c.(14908-14910)Ctc>Ttc	p.L4970F	SYNE1_ENST00000423061.1_Missense_Mutation_p.L4899F|SYNE1_ENST00000265368.4_Missense_Mutation_p.L4970F|SYNE1_ENST00000341594.5_Missense_Mutation_p.L4717F|SYNE1_ENST00000448038.1_Missense_Mutation_p.L4899F	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4970					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L4970F(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCTCTGAGAGCTCAGCGAGG	0.468										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											154	157	156					6																	152650912		2203	4300	6503	152692605	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.14908C>T	6.37:g.152650912G>A	ENSP00000356224:p.Leu4970Phe		152692605	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287068	0.59867	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	6.03	6.03	0.97812	.	0.000000	0.52532	D	0.000065	T	0.73401	0.3582	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.997;0.998	D;P;P;D	0.71870	0.975;0.889;0.889;0.944	T	0.71034	-0.4709	10	0.51188	T	0.08	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	4970;4970;4970;4899	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	F	4970;4899;4970;4899;4717	ENSP00000356224:L4970F;ENSP00000396024:L4899F;ENSP00000265368:L4970F;ENSP00000390975:L4899F;ENSP00000341887:L4717F	ENSP00000265368:L4970F	L	-	1	0	SYNE1	152692605	1.000000	0.71417	0.770000	0.31555	0.940000	0.58332	6.177000	0.71961	2.861000	0.98227	0.655000	0.94253	CTC		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152650912	G	A	152650912	3	1	61	1	0	0	0	0	1	0	0	0	15484	971	34	3	11834	3	SYNE1	6	152650912	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7974	152650912	18464155	5025	13010										
SYNE1	23345	broad.mit.edu	37	chr6	152651968	152651968	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctgcagcgtaagtagaaGattttcatattctggagatt	9	6	3	3	rs147125369		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152651968G>T	ENST00000367255.5	-	78	14453	c.13852C>A	c.(13852-13854)Ctt>Att	p.L4618I	SYNE1_ENST00000423061.1_Missense_Mutation_p.L4547I|SYNE1_ENST00000265368.4_Missense_Mutation_p.L4618I|SYNE1_ENST00000341594.5_Missense_Mutation_p.L4365I|SYNE1_ENST00000448038.1_Missense_Mutation_p.L4547I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4618					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L4618I(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTAAGTAGAAGATTTTCATAT	0.393										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6						G	ILE/LEU,ILE/LEU	0,4406		0,0,2203	164	165	165		13639,13852	6	0.4	6	dbSNP_134	165	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	5,5	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	4547/8750,4618/8798	152651968	1,13005	2203	4300	6503	152693661	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.13852C>A	6.37:g.152651968G>T	ENSP00000356224:p.Leu4618Ile		152693661	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271828	0.59649	0.0	1.16E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54866	1.34;1.34;1.34;1.34;0.55	6.03	6.03	0.97812	.	0.000000	0.56097	D	0.000030	T	0.64692	0.2621	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.996;0.998	T	0.53975	-0.8362	10	0.17369	T	0.5	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	4618;4618;4618;4547	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	I	4618;4547;4618;4547;4365	ENSP00000356224:L4618I;ENSP00000396024:L4547I;ENSP00000265368:L4618I;ENSP00000390975:L4547I;ENSP00000341887:L4365I	ENSP00000265368:L4618I	L	-	1	0	SYNE1	152693661	1.000000	0.71417	0.430000	0.26722	0.893000	0.52053	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	CTT		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152651968	G	T	152651968	3	4	61	1	0	0	0	0	1	0	0	0	15484	942	33	2	12890	2	SYNE1	6	152651968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1056	152651968	18463099	5026	13011										
SYNE1	23345	broad.mit.edu	37	chr6	152680581	152680581	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctgtaactcagcacttCttcatttaataactagagag	7	9	3	1	rs550171329		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152680581C>T	ENST00000367255.5	-	65	10913	c.10312G>A	c.(10312-10314)Gaa>Aaa	p.E3438K	SYNE1_ENST00000423061.1_Missense_Mutation_p.E3445K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E3438K|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000448038.1_Missense_Mutation_p.E3445K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3438					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E3438K(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCAGCACTTCTTCATTTAAT	0.413										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											94	85	88					6																	152680581		2203	4300	6503	152722274	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10312G>A	6.37:g.152680581C>T	ENSP00000356224:p.Glu3438Lys		152722274	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	21.9	4.209986	0.79240	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	4.78	4.78	0.61160	.	0.000000	0.56097	D	0.000024	T	0.59569	0.2203	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.74674	0.968;0.968;0.968;0.984	T	0.55817	-0.8081	10	0.27082	T	0.32	.	18.1974	0.89828	0.0:1.0:0.0:0.0	.	3438;3438;3438;3445	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	3438;3445;3438;3445	ENSP00000356224:E3438K;ENSP00000396024:E3445K;ENSP00000265368:E3438K;ENSP00000390975:E3445K	ENSP00000265368:E3438K	E	-	1	0	SYNE1	152722274	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.445000	0.80570	2.354000	0.79902	0.650000	0.86243	GAA		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152680581	C	T	152680581	3	4	61	1	0	0	0	0	1	0	0	0	15484	922	32	3	16482	3	SYNE1	6	152680581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28613	152680581	18434486	5027	13012										
SYNE1	23345	broad.mit.edu	37	chr6	152690652	152690652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctggcagatcatagaggCgattgctgctttcatggacc	12	9	2	2	rs146769373	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152690652C>T	ENST00000367255.5	-	60	10206	c.9605G>A	c.(9604-9606)cGc>cAc	p.R3202H	SYNE1_ENST00000423061.1_Missense_Mutation_p.R3209H|SYNE1_ENST00000265368.4_Missense_Mutation_p.R3202H|SYNE1_ENST00000341594.5_Missense_Mutation_p.R3241H|SYNE1_ENST00000448038.1_Missense_Mutation_p.R3209H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3202					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R3202H(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATCATAGAGGCGATTGCTGCT	0.512										HNSCC(10;0.0054)			C|||	9	0.00179712	0.0053	0.0014	5008	,	,		18257	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	6						C	HIS/ARG,HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	140	121	127		9626,9605	5.4	1	6	dbSNP_134	127	0,8600		0,0,4300	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	29,29	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging,probably-damaging	3209/8750,3202/8798	152690652	3,13003	2203	4300	6503	152732345	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9605G>A	6.37:g.152690652C>T	ENSP00000356224:p.Arg3202His		152732345	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	8|8	0.003663003663003663|0.003663003663003663	7|7	0.014227642276422764|0.014227642276422764	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.4|21.4	4.136295|4.136295	0.77662|0.77662	6.81E-4|6.81E-4	0.0|0.0	ENSG00000131018|ENSG00000131018	ENST00000454018|ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.|T;T;T;T;T	.|0.35048	.|1.33;1.33;1.33;1.33;1.33	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.56097	.|D	.|0.000022	T|T	0.43411|0.43411	0.1246|0.1246	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0	T|T	0.17018|0.17018	-1.0383|-1.0383	5|10	.|0.36615	.|T	.|0.2	.|.	19.1929|19.1929	0.93674|0.93674	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3202;319;3202;3209	.|Q8NF91;B7ZBC4;E7EQI5;Q8NF91-4	.|SYNE1_HUMAN;.;.;.	T|H	319|3202;3209;3202;3209;3241	.|ENSP00000356224:R3202H;ENSP00000396024:R3209H;ENSP00000265368:R3202H;ENSP00000390975:R3209H;ENSP00000341887:R3241H	.|ENSP00000265368:R3202H	A|R	-|-	1|2	0|0	SYNE1|SYNE1	152732345|152732345	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.472000|0.472000	0.32918|0.32918	5.766000|5.766000	0.68843|0.68843	2.540000|2.540000	0.85666|0.85666	0.551000|0.551000	0.68910|0.68910	GCC|CGC		0.512	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152690652	C	T	152690652	3	4	61	1	0	0	0	0	1	0	0	0	15484	768	27	1	17209	1	SYNE1	6	152690652	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10071	152690652	18424415	5028	13013										
SYNE1	23345	broad.mit.edu	37	chr6	152694198	152694198	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagattctttttggtggaGatttgaatgaaaatttttcc	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152694198G>T	ENST00000367255.5	-	59	10082	c.9481C>A	c.(9481-9483)Ctc>Atc	p.L3161I	SYNE1_ENST00000423061.1_Missense_Mutation_p.L3168I|SYNE1_ENST00000265368.4_Missense_Mutation_p.L3161I|SYNE1_ENST00000341594.5_Missense_Mutation_p.L3200I|SYNE1_ENST00000448038.1_Missense_Mutation_p.L3168I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3161					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L3161I(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTTGGTGGAGATTTGAATGA	0.388										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											196	207	203					6																	152694198		2203	4300	6503	152735891	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9481C>A	6.37:g.152694198G>T	ENSP00000356224:p.Leu3161Ile		152735891	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.2|28.2	4.901477|4.901477	0.92035|0.92035	.|.	.|.	ENSG00000131018|ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594|ENST00000469439	T;T;T;T;T|.	0.36878|.	1.23;1.23;1.23;1.23;1.23|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.000000|.	0.56097|.	D|.	0.000030|.	T|T	0.72382|0.72382	0.3453|0.3453	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.997;0.997;0.997;0.999|.	T|T	0.68735|0.68735	-0.5330|-0.5330	10|5	0.08837|.	T|.	0.75|.	.|.	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3161;278;3161;3168|.	Q8NF91;B7ZBC4;E7EQI5;Q8NF91-4|.	SYNE1_HUMAN;.;.;.|.	I|Y	3161;3168;3161;3168;3200|25	ENSP00000356224:L3161I;ENSP00000396024:L3168I;ENSP00000265368:L3161I;ENSP00000390975:L3168I;ENSP00000341887:L3200I|.	ENSP00000265368:L3161I|.	L|S	-|-	1|2	0|0	SYNE1|SYNE1	152735891|152735891	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	7.489000|7.489000	0.81451|0.81451	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	CTC|TCT		0.388	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152694198	G	T	152694198	3	4	61	1	0	0	0	0	1	0	0	0	15484	942	33	2	17337	2	SYNE1	6	152694198	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3546	152694198	18420869	5029	13014										
SYNE1	23345	broad.mit.edu	37	chr6	152697995	152697995	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaagttcattcagctgaGacttgagatcctctgttcta	8	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152697995G>A	ENST00000367255.5	-	57	9663	c.9062C>T	c.(9061-9063)tCt>tTt	p.S3021F	SYNE1_ENST00000423061.1_Missense_Mutation_p.S3028F|SYNE1_ENST00000265368.4_Missense_Mutation_p.S3021F|SYNE1_ENST00000341594.5_Missense_Mutation_p.S3060F|SYNE1_ENST00000448038.1_Missense_Mutation_p.S3028F	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3021					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S3021F(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATTCAGCTGAGACTTGAGATC	0.408										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											91	85	87					6																	152697995		2203	4300	6503	152739688	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9062C>T	6.37:g.152697995G>A	ENSP00000356224:p.Ser3021Phe		152739688	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.011175|4.011175	0.75046|0.75046	.|.	.|.	ENSG00000131018|ENSG00000131018	ENST00000454018|ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.|T;T;T;T;T	.|0.56941	.|0.53;0.55;0.43;0.55;0.65	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.208444	.|0.33792	.|N	.|0.004546	T|T	0.32556|0.32556	0.0833|0.0833	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P	.|0.50710	.|0.855;0.898;0.883;0.898;0.938	.|B;B;B;B;P	.|0.47705	.|0.365;0.352;0.341;0.352;0.555	T|T	0.09751|0.09751	-1.0660|-1.0660	5|10	.|0.10377	.|T	.|0.69	.|.	19.3499|19.3499	0.94379|0.94379	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|3004;3021;138;3021;3028	.|B3W695;Q8NF91;B7ZBC4;E7EQI5;Q8NF91-4	.|.;SYNE1_HUMAN;.;.;.	F|F	138|3021;3028;3021;3028;3060	.|ENSP00000356224:S3021F;ENSP00000396024:S3028F;ENSP00000265368:S3021F;ENSP00000390975:S3028F;ENSP00000341887:S3060F	.|ENSP00000265368:S3021F	L|S	-|-	1|2	0|0	SYNE1|SYNE1	152739688|152739688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.180000|5.180000	0.65048|0.65048	2.585000|2.585000	0.87301|0.87301	0.650000|0.650000	0.86243|0.86243	CTC|TCT		0.408	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152697995	G	A	152697995	3	1	61	1	0	0	0	0	1	0	0	0	15484	942	33	3	17764	3	SYNE1	6	152697995	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3797	152697995	18417072	5030	13015										
SYNE1	23345	broad.mit.edu	37	chr6	152702484	152702484	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttgcaccaatctctctgGaatctatcagctcctgtaat	7	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152702484G>T	ENST00000367255.5	-	56	9267	c.8666C>A	c.(8665-8667)tCc>tAc	p.S2889Y	SYNE1-AS1_ENST00000412161.1_RNA|SYNE1_ENST00000423061.1_Missense_Mutation_p.S2896Y|SYNE1_ENST00000265368.4_Missense_Mutation_p.S2889Y|SYNE1_ENST00000341594.5_Missense_Mutation_p.S2928Y|SYNE1_ENST00000448038.1_Missense_Mutation_p.S2896Y	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2889					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S2889Y(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AATCTCTCTGGAATCTATCAG	0.517										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											116	118	118					6																	152702484		2203	4300	6503	152744177	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.8666C>A	6.37:g.152702484G>T	ENSP00000356224:p.Ser2889Tyr		152744177	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.4|23.4	4.408908|4.408908	0.83340|0.83340	.|.	.|.	ENSG00000131018|ENSG00000131018	ENST00000454018|ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.|T;T;T;T;T	.|0.57907	.|0.46;0.49;0.37;0.5;0.58	6.01|6.01	6.01|6.01	0.97437|0.97437	.|.	.|0.000000	.|0.64402	.|D	.|0.000008	T|T	0.69593|0.69593	0.3128|0.3128	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.78314	.|0.972;0.979;0.979;0.991	T|T	0.69146|0.69146	-0.5222|-0.5222	5|10	.|0.62326	.|D	.|0.03	.|.	20.5211|20.5211	0.99222|0.99222	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2872;2889;2889;2896	.|B3W695;Q8NF91;E7EQI5;Q8NF91-4	.|.;SYNE1_HUMAN;.;.	T|Y	6|2889;2896;2889;2896;2928	.|ENSP00000356224:S2889Y;ENSP00000396024:S2896Y;ENSP00000265368:S2889Y;ENSP00000390975:S2896Y;ENSP00000341887:S2928Y	.|ENSP00000265368:S2889Y	P|S	-|-	1|2	0|0	SYNE1|SYNE1	152744177|152744177	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.196000|9.196000	0.94978|0.94978	2.861000|2.861000	0.98227|0.98227	0.650000|0.650000	0.86243|0.86243	CCA|TCC		0.517	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152702484	G	T	152702484	3	4	61	1	0	0	0	0	1	0	0	0	15484	1174	41	2	18164	2	SYNE1	6	152702484	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4489	152702484	18412583	5031	13016										
SYNE1	23345	broad.mit.edu	37	chr6	152708384	152708384	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggtggtcaagcaggacGaacttctctttcagacctgg	13	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152708384G>A	ENST00000367255.5	-	54	8911	c.8310C>T	c.(8308-8310)ttC>ttT	p.F2770F	SYNE1_ENST00000423061.1_Silent_p.F2777F|SYNE1_ENST00000265368.4_Silent_p.F2770F|SYNE1_ENST00000341594.5_Silent_p.F2809F|SYNE1_ENST00000448038.1_Silent_p.F2777F	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2770					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.F2770F(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CAAGCAGGACGAACTTCTCTT	0.483										HNSCC(10;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	6											265	230	242					6																	152708384		2203	4300	6503	152750077	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.8310C>T	6.37:g.152708384G>A			152750077	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152708384	G	A	152708384	2	1	61	1	0	0	0	0	0	0	0	1	15484	1049	37	1		1	SYNE1	6	152708384	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5900	152708384	18406683	5032	13017										
SYNE1	23345	broad.mit.edu	37	chr6	152716698	152716699	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaactttatgaacttcaINStttttcttctcaggaatgtg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152716698_152716699insT	ENST00000367255.5	-	51	8265_8266	c.7664_7665insA	c.(7663-7665)aatfs	p.N2555fs	SYNE1_ENST00000423061.1_Frame_Shift_Ins_p.N2562fs|SYNE1_ENST00000265368.4_Frame_Shift_Ins_p.N2555fs|SYNE1_ENST00000341594.5_Frame_Shift_Ins_p.N2594fs|SYNE1_ENST00000448038.1_Frame_Shift_Ins_p.N2562fs	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2555					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.N2555fs*2(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TATGAACTTCATTTTTCTTCTC	0.396										HNSCC(10;0.0054)																																						2	Insertion - Frameshift(2)	large_intestine(2)	6																																								152758392	SO:0001589	frameshift_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.7665dupA	6.37:g.152716703_152716703dupT	ENSP00000356224:p.Asn2555fs		152758391	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Frame_Shift_Ins	INS	ENST00000367255.5	37	CCDS5236.2																																																																																				0.396	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152716699	-	T	152716698	7	5	61	1	0	1	1	0	0	0	0	0	15484	214	8	0	19185	0	SYNE1	6	152716698	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	8314	152716698	18398369	5033	13018										
SYNE1	23345	broad.mit.edu	37	chr6	152823852	152823852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acataggtcataatagatttCtcatctggtttatccacatc	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152823852C>A	ENST00000367255.5	-	10	1405	c.804G>T	c.(802-804)gaG>gaT	p.E268D	SYNE1_ENST00000367248.3_Missense_Mutation_p.E275D|SYNE1_ENST00000423061.1_Missense_Mutation_p.E275D|SYNE1_ENST00000265368.4_Missense_Mutation_p.E268D|SYNE1_ENST00000466159.2_Missense_Mutation_p.E268D|SYNE1_ENST00000341594.5_Missense_Mutation_p.E268D|SYNE1_ENST00000367253.4_Missense_Mutation_p.E268D|SYNE1_ENST00000448038.1_Missense_Mutation_p.E275D|SYNE1_ENST00000413186.2_Missense_Mutation_p.E268D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	268	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E268D(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TAATAGATTTCTCATCTGGTT	0.343										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											135	123	127					6																	152823852		2203	4300	6503	152865545	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.804G>T	6.37:g.152823852C>A	ENSP00000356224:p.Glu268Asp		152865545	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043571	0.36085	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	D;D;D;D;D;D;D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01	4.83	2.03	0.26663	Calponin homology domain (5);	0.272343	0.25166	U	0.032639	D	0.96664	0.8911	M	0.84156	2.68	0.80722	D	1	B;B;B;B;D	0.67145	0.005;0.44;0.01;0.44;0.996	B;B;B;B;D	0.65987	0.015;0.356;0.019;0.356;0.94	D	0.95639	0.8696	10	0.87932	D	0	.	7.6866	0.28544	0.0:0.6126:0.0:0.3874	.	268;268;268;268;275	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	D	268;275;268;275;268;268;275;268;268;268	ENSP00000356224:E268D;ENSP00000396024:E275D;ENSP00000265368:E268D;ENSP00000390975:E275D;ENSP00000341887:E268D;ENSP00000356222:E268D;ENSP00000356217:E275D;ENSP00000414510:E268D;ENSP00000446021:E268D;ENSP00000441264:E268D	ENSP00000265368:E268D	E	-	3	2	SYNE1	152865545	0.969000	0.33509	1.000000	0.80357	0.938000	0.57974	0.140000	0.16056	0.454000	0.26884	-0.162000	0.13425	GAG		0.343	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152823852	C	A	152823852	3	1	61	1	0	0	0	0	1	0	0	0	15484	912	32	2	26210	2	SYNE1	6	152823852	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107154	152823852	18291215	5034	13019										
SYNE1	23345	broad.mit.edu	37	chr6	152841605	152841605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcttacctttcttccttCgaggaacttgagtgccgtgc	8	13	2	1	rs187117263		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:152841605C>T	ENST00000367255.5	-	6	899	c.298G>A	c.(298-300)Gaa>Aaa	p.E100K	SYNE1_ENST00000367248.3_Missense_Mutation_p.E100K|SYNE1_ENST00000423061.1_Missense_Mutation_p.E100K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E100K|SYNE1_ENST00000466159.2_Missense_Mutation_p.E100K|SYNE1_ENST00000341594.5_Missense_Mutation_p.E100K|SYNE1_ENST00000367253.4_Missense_Mutation_p.E100K|SYNE1_ENST00000448038.1_Missense_Mutation_p.E100K|SYNE1_ENST00000413186.2_Missense_Mutation_p.E100K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	100	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E100K(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTCTTCCTTCGAGGAACTTG	0.443										HNSCC(10;0.0054)			C|||	1	0.000199681	8e-04	0	5008	,	,		17625	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	6											141	140	140					6																	152841605		2203	4300	6503	152883298	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.298G>A	6.37:g.152841605C>T	ENSP00000356224:p.Glu100Lys		152883298	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	34	5.321335	0.95682	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	D;D;D;D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	5.45	5.45	0.79879	Calponin homology domain (5);	0.000000	0.64402	D	0.000010	D	0.91157	0.7215	N	0.02412	-0.56	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.998;1.0;0.999	D;D;P;D;D	0.70716	0.97;0.945;0.88;0.945;0.909	D	0.93930	0.7213	10	0.49607	T	0.09	.	19.6439	0.95769	0.0:1.0:0.0:0.0	.	100;100;100;100;100	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	K	100	ENSP00000356224:E100K;ENSP00000396024:E100K;ENSP00000265368:E100K;ENSP00000390975:E100K;ENSP00000341887:E100K;ENSP00000356222:E100K;ENSP00000356217:E100K;ENSP00000414510:E100K;ENSP00000446021:E100K;ENSP00000441264:E100K	ENSP00000265368:E100K	E	-	1	0	SYNE1	152883298	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.187000	0.77730	2.716000	0.92895	0.650000	0.86243	GAA		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152841605	C	T	152841605	3	4	61	1	0	0	0	0	1	0	0	0	15484	893	31	1	26757	1	SYNE1	6	152841605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17753	152841605	18273462	5035	13020										
FBXO5	26271	broad.mit.edu	37	chr6	153296106	153296106	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatgtctgagtccccttcGaaagagttcgctgagaatat	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:153296106G>A	ENST00000229758.3	-	2	812	c.754C>T	c.(754-756)Cga>Tga	p.R252*	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Nonsense_Mutation_p.R206*	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	252	F-box.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.R252*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		AGTCCCCTTCGAAAGAGTTCG	0.358																																					NSCLC(121;372 1757 17721 17977 29669)											1	Substitution - Nonsense(1)	large_intestine(1)	6											120	123	122					6																	153296106		2203	4300	6503	153337799	SO:0001587	stop_gained	26271			AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"F-boxes /  "other""	13584	protein-coding gene	gene with protein product		606013	"F-box only protein 5"			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.754C>T	6.37:g.153296106G>A	ENSP00000229758:p.Arg252*		153337799	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Nonsense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	.	.	.	.	.	.	.	.	.	.	G	33	5.289943	0.95546	.	.	ENSG00000112029	ENST00000229758;ENST00000367241	.	.	.	6.07	3.21	0.36854	.	0.667620	0.16246	N	0.222939	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0089	12.7641	0.57383	0.0:0.2354:0.6422:0.1224	.	.	.	.	X	252;206	.	ENSP00000229758:R252X	R	-	1	2	FBXO5	153337799	0.987000	0.35691	0.736000	0.30914	0.595000	0.36748	1.566000	0.36396	0.383000	0.24910	0.655000	0.94253	CGA		0.358	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1			A	153296106	G	A	153296106	4	1	61	1	0	0	0	0	0	1	0	0	5777	1066	37	1	605	1	FBXO5	6	153296106	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	454501	153296106	17818961	5036	13021										
MTRF1L	54516	broad.mit.edu	37	chr6	153311183	153311183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatctgtgacccggttctgTggaaaattatatgttcttat	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:153311183T>C	ENST00000367233.5	-	7	989	c.990A>G	c.(988-990)ccA>ccG	p.P330P	MTRF1L_ENST00000367231.5_3'UTR|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_3'UTR|RP1-101K10.6_ENST00000442269.1_RNA	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	330						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)	p.P330P(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		CCCGGTTCTGTGGAAAATTAT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	6											68	69	69					6																	153311183		2202	4295	6497	153352876	SO:0001819	synonymous_variant	54516			BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.990A>G	6.37:g.153311183T>C			153352876	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Silent	SNP	ENST00000367233.5	37	CCDS5243.1																																																																																				0.358	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		C	153311183	T	C	153311183	2	2	61	1	0	0	0	0	0	0	0	1	9990	1683	59	4		4	MTRF1L	6	153311183	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	15077	153311183	17803884	5037	13022										
RGS17	26575	broad.mit.edu	37	chr6	153345514	153345514	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagccagaaaagtaggttCtcttcactgtattctgttcg	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:153345514C>A	ENST00000367225.2	-	3	351	c.327G>T	c.(325-327)gaG>gaT	p.E109D	RGS17_ENST00000206262.1_Missense_Mutation_p.E109D			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	109	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.E109D(1)		cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		AAAGTAGGTTCTCTTCACTGT	0.388																																					Esophageal Squamous(78;500 1236 6775 24364 49058)											1	Substitution - Missense(1)	large_intestine(1)	6											106	98	101					6																	153345514		2203	4300	6503	153387207	SO:0001583	missense	26575			AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"Regulators of G-protein signaling"	14088	protein-coding gene	gene with protein product		607191	"regulator of G-protein signalling 17"			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.327G>T	6.37:g.153345514C>A	ENSP00000356194:p.Glu109Asp		153387207	Q5TF49|Q8TD61|Q9UJS8	Missense_Mutation	SNP	ENST00000367225.2	37	CCDS5244.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714552	0.48622	.	.	ENSG00000091844	ENST00000367225;ENST00000206262	T;T	0.37058	1.22;1.22	6.03	4.26	0.50523	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.044972	0.85682	D	0.000000	T	0.30039	0.0752	M	0.84326	2.69	0.80722	D	1	B	0.23377	0.084	B	0.32583	0.148	T	0.24225	-1.0166	10	0.66056	D	0.02	.	9.8584	0.41098	0.0:0.7936:0.0:0.2064	.	109	Q9UGC6	RGS17_HUMAN	D	109	ENSP00000356194:E109D;ENSP00000206262:E109D	ENSP00000206262:E109D	E	-	3	2	RGS17	153387207	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.155000	0.42301	0.877000	0.35895	0.655000	0.94253	GAG		0.388	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2			A	153345514	C	A	153345514	3	1	61	1	0	0	0	0	1	0	0	0	13336	912	32	2	313	2	RGS17	6	153345514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34331	153345514	17769553	5038	13023										
RBM16	22828	broad.mit.edu	37	chr6	155095158	155095158	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactataaaccacccatttcGaaagcgaaaatgacccaaat	5	11	0	1	rs559874211	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155095158G>A	ENST00000367178.3	+	2	642	c.66G>A	c.(64-66)tcG>tcA	p.S22S	SCAF8_ENST00000367186.4_Silent_p.S88S|SCAF8_ENST00000417268.1_Silent_p.S22S|SCAF8_ENST00000461219.1_3'UTR	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	22	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)	p.S22S(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						CACCCATTTCGAAAGCGAAAA	0.303													G|||	2	0.000399361	0.0015	0	5008	,	,		17849	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											126	128	127					6																	155095158		2203	4300	6503	155136850	SO:0001819	synonymous_variant	22828			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.66G>A	6.37:g.155095158G>A			155136850	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Silent	SNP	ENST00000367178.3	37	CCDS5247.1																																																																																				0.303	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		A	155095158	G	A	155095158	2	1	61	1	0	0	0	0	0	0	0	1	13155	1045	37	1		1	RBM16	6	155095158	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1749644	155095158	16019909	5039	13024										
RBM16	22828	broad.mit.edu	37	chr6	155109056	155109056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccattgtgcgacaatcccGacatcagtttggtcaagaaa	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155109056G>A	ENST00000367178.3	+	4	797	c.221G>A	c.(220-222)cGa>cAa	p.R74Q	SCAF8_ENST00000367186.4_Missense_Mutation_p.R140Q|SCAF8_ENST00000417268.1_Missense_Mutation_p.R74Q|SCAF8_ENST00000461219.1_3'UTR	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	74	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)	p.R74Q(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						CGACAATCCCGACATCAGTTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											159	150	153					6																	155109056		2203	4300	6503	155150748	SO:0001583	missense	22828			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.221G>A	6.37:g.155109056G>A	ENSP00000356146:p.Arg74Gln		155150748	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605672	0.87157	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.42513	0.97;0.97;0.97	5.27	5.27	0.74061	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);Domain of unknown function DUF618 (1);	0.000000	0.64402	U	0.000003	T	0.57315	0.2045	M	0.62266	1.93	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.998;0.998;0.995;0.998	T	0.56511	-0.7967	10	0.51188	T	0.08	.	19.2563	0.93947	0.0:0.0:1.0:0.0	.	119;140;152;74	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	Q	74;74;140	ENSP00000356146:R74Q;ENSP00000413098:R74Q;ENSP00000356154:R140Q	ENSP00000356146:R74Q	R	+	2	0	SCAF8	155150748	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.813000	0.99286	2.621000	0.88768	0.655000	0.94253	CGA		0.383	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		A	155109056	G	A	155109056	3	1	61	1	0	0	0	0	1	0	0	0	13155	1058	37	1	235	1	RBM16	6	155109056	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13898	155109056	16006011	5040	13025										
RBM16	22828	broad.mit.edu	37	chr6	155141455	155141455	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcatgattgatcaggagActgtaaatactggtaagaat	12	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155141455A>G	ENST00000367178.3	+	15	2356	c.1780A>G	c.(1780-1782)Act>Gct	p.T594A	SCAF8_ENST00000367186.4_Missense_Mutation_p.T660A|SCAF8_ENST00000417268.1_Missense_Mutation_p.T594A	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	594					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)	p.T594A(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						TGATCAGGAGACTGTAAATAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	78	77					6																	155141455		2203	4300	6503	155183147	SO:0001583	missense	22828			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.1780A>G	6.37:g.155141455A>G	ENSP00000356146:p.Thr594Ala		155183147	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463580	0.84425	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.67698	-0.25;-0.25;-0.28	5.33	5.33	0.75918	.	0.071533	0.56097	U	0.000039	T	0.69415	0.3108	M	0.81802	2.56	0.80722	D	1	P;P;P;P	0.51351	0.894;0.944;0.807;0.944	B;P;B;P	0.49708	0.437;0.62;0.294;0.62	T	0.75516	-0.3290	10	0.59425	D	0.04	.	15.6101	0.76710	1.0:0.0:0.0:0.0	.	639;660;672;594	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	A	594;594;660	ENSP00000356146:T594A;ENSP00000413098:T594A;ENSP00000356154:T660A	ENSP00000356146:T594A	T	+	1	0	SCAF8	155183147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.142000	0.66516	0.533000	0.62120	ACT		0.368	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		G	155141455	A	G	155141455	3	3	61	1	0	0	0	0	1	0	0	0	13155	275	10	4	1838	4	RBM16	6	155141455	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	32399	155141455	15973612	5041	13026										
TIAM2	26230	broad.mit.edu	37	chr6	155458622	155458622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggatctgctctttgagaaGgaacagggggtggtccggaa	16	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155458622G>T	ENST00000461783.3	+	7	2779	c.1506G>T	c.(1504-1506)aaG>aaT	p.K502N	TIAM2_ENST00000360366.4_Missense_Mutation_p.K502N|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000529824.2_Missense_Mutation_p.K502N|TIAM2_ENST00000456144.1_Missense_Mutation_p.K502N|TIAM2_ENST00000318981.5_Missense_Mutation_p.K502N			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	502					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K502N(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TCTTTGAGAAGGAACAGGGGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	76	74					6																	155458622		2203	4300	6503	155500314	SO:0001583	missense	26230				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.1506G>T	6.37:g.155458622G>T	ENSP00000437188:p.Lys502Asn		155500314	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.774439	0.70107	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.06371	3.42;3.31;3.38;3.42;3.43;3.38	6.08	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.12732	0.0309	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00099	-1.2068	10	0.42905	T	0.14	.	8.5601	0.33505	0.1492:0.1271:0.7237:0.0	.	502;502	Q8IVF5-2;Q8IVF5	.;TIAM2_HUMAN	N	502;748;502;502;502;502;502	ENSP00000437188:K502N;ENSP00000434901:K502N;ENSP00000407746:K502N;ENSP00000327315:K502N;ENSP00000353528:K502N;ENSP00000433348:K502N	ENSP00000327315:K502N	K	+	3	2	TIAM2	155500314	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	1.286000	0.33273	2.894000	0.99253	0.655000	0.94253	AAG		0.552	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155458622	G	T	155458622	3	4	61	1	0	0	0	0	1	0	0	0	15930	991	35	2	1512	2	TIAM2	6	155458622	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	317167	155458622	15656445	5042	13027										
TIAM2	26230	broad.mit.edu	37	chr6	155578058	155578058	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcacttctgccccattaaaCgaaaagccaacagcaccaag	7	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155578058C>T	ENST00000461783.3	+	29	6182	c.4909C>T	c.(4909-4911)Cga>Tga	p.R1637*	TIAM2_ENST00000456877.2_Nonsense_Mutation_p.R949*|TIAM2_ENST00000360366.4_Nonsense_Mutation_p.R1661*|TIAM2_ENST00000275246.7_Nonsense_Mutation_p.R562*|TIAM2_ENST00000367174.2_Nonsense_Mutation_p.R1013*|TIAM2_ENST00000529824.2_Nonsense_Mutation_p.R1666*|TIAM2_ENST00000456144.1_Nonsense_Mutation_p.R1666*|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000318981.5_Nonsense_Mutation_p.R1637*|TIAM2_ENST00000528391.2_Nonsense_Mutation_p.R981*			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1637					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1637*(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CCCCATTAAACGAAAAGCCAA	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											61	59	59					6																	155578058		2203	4300	6503	155619750	SO:0001587	stop_gained	26230				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4909C>T	6.37:g.155578058C>T	ENSP00000437188:p.Arg1637*		155619750	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Nonsense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	42	9.451428	0.99175	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8027	0.69926	0.1434:0.8566:0.0:0.0	.	.	.	.	X	1637;1883;1666;1637;1013;1661;1666;949;981;562	.	ENSP00000275246:R562X	R	+	1	2	TIAM2	155619750	1.000000	0.71417	0.964000	0.40570	0.990000	0.78478	3.270000	0.51600	2.775000	0.95449	0.655000	0.94253	CGA		0.587	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155578058	C	T	155578058	4	4	61	1	0	0	0	0	0	1	0	0	15930	528	19	1	5003	1	TIAM2	6	155578058	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119436	155578058	15537009	5043	13028										
NOX3	50508	broad.mit.edu	37	chr6	155750078	155750078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggggtgccactccagcGaagatatggctgggcactgc	15	10	0	2	rs376763861		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155750078G>A	ENST00000159060.2	-	9	1097	c.995C>T	c.(994-996)tCg>tTg	p.S332L		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	332	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.S332L(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		CCACTCCAGCGAAGATATGGC	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		17050	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	76	77	77		995	-0.9	0	6		77	0,8600		0,0,4300	no	missense	NOX3	NM_015718.2	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	332/569	155750078	1,13005	2203	4300	6503	155791770	SO:0001583	missense	50508			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.995C>T	6.37:g.155750078G>A	ENSP00000159060:p.Ser332Leu		155791770	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	2.526	-0.309681	0.05458	2.27E-4	0.0	ENSG00000074771	ENST00000159060	D	0.92299	-3.01	5.78	-0.917	0.10485	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	2.308480	0.01620	N	0.022967	T	0.61022	0.2314	N	0.05414	-0.055	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.67241	-0.5720	10	0.07813	T	0.8	0.0623	4.1018	0.10017	0.0714:0.2634:0.3351:0.3301	.	332	Q9HBY0	NOX3_HUMAN	L	332	ENSP00000159060:S332L	ENSP00000159060:S332L	S	-	2	0	NOX3	155791770	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-0.429000	0.06982	0.056000	0.16144	0.557000	0.71058	TCG		0.577	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			A	155750078	G	A	155750078	3	1	61	1	0	0	0	0	1	0	0	0	10588	1059	37	1	731	1	NOX3	6	155750078	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172020	155750078	15364989	5044	13029										
NOX3	50508	broad.mit.edu	37	chr6	155775979	155775979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgaatgaaataaggtttCgactgacaggtattagaatt	9	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:155775979C>T	ENST00000159060.2	-	3	323	c.221G>A	c.(220-222)cGa>cAa	p.R74Q		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	74	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.R74Q(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AATAAGGTTTCGACTGACAGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	6											65	64	64					6																	155775979		2203	4299	6502	155817671	SO:0001583	missense	50508			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.221G>A	6.37:g.155775979C>T	ENSP00000159060:p.Arg74Gln		155817671	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364222	0.82463	.	.	ENSG00000074771	ENST00000159060	D	0.98633	-5.04	5.91	5.05	0.67936	Flavoprotein transmembrane component (1);	0.000000	0.51477	D	0.000085	D	0.97879	0.9303	M	0.93550	3.43	0.40176	D	0.977237	P	0.39847	0.691	B	0.34180	0.177	D	0.98321	1.0528	10	0.87932	D	0	-11.3805	15.2862	0.73831	0.0:0.9327:0.0:0.0673	.	74	Q9HBY0	NOX3_HUMAN	Q	74	ENSP00000159060:R74Q	ENSP00000159060:R74Q	R	-	2	0	NOX3	155817671	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.321000	0.72881	1.509000	0.48786	0.650000	0.86243	CGA		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			T	155775979	C	T	155775979	3	4	61	1	0	0	0	0	1	0	0	0	10588	884	31	1	1529	1	NOX3	6	155775979	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25901	155775979	15339088	5045	13030										
ARID1B	57492	broad.mit.edu	37	chr6	157431621	157431621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaggtagtcagatgcctcCgcagccacccgggagccagt	12	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:157431621C>T	ENST00000350026.5	+	6	2259	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	ARID1B_ENST00000346085.5_Missense_Mutation_p.P766L|RP1-137K2.2_ENST00000442936.1_RNA|ARID1B_ENST00000275248.4_Missense_Mutation_p.P695L|ARID1B_ENST00000367148.1_Missense_Mutation_p.P753L	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	753	Ser-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.P695L(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CAGATGCCTCCGCAGCCACCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											103	92	96					6																	157431621		2203	4300	6503	157473313	SO:0001583	missense	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2258C>T	6.37:g.157431621C>T	ENSP00000055163:p.Pro753Leu		157473313	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	18.90	3.720898	0.68959	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000535255;ENST00000319584	T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03	5.37	5.37	0.77165	.	0.127860	0.53938	D	0.000052	T	0.26629	0.0651	L	0.49778	1.585	0.58432	D	0.999999	D;D;D;D	0.67145	0.98;0.993;0.996;0.996	P;P;P;P	0.54100	0.689;0.557;0.742;0.742	T	0.02208	-1.1195	10	0.87932	D	0	.	19.1266	0.93388	0.0:1.0:0.0:0.0	.	137;753;766;695	F5H333;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	L	766;753;753;695;174;137;175	ENSP00000344546:P766L;ENSP00000055163:P753L;ENSP00000356116:P753L;ENSP00000275248:P695L;ENSP00000313006:P175L	ENSP00000275248:P695L	P	+	2	0	ARID1B	157473313	0.993000	0.37304	0.732000	0.30844	0.500000	0.33767	5.652000	0.67959	2.493000	0.84123	0.655000	0.94253	CCG		0.512	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157431621	C	T	157431621	3	4	61	1	0	0	0	0	1	0	0	0	914	652	23	1	2323	1	ARID1B	6	157431621	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1655642	157431621	13683446	5046	13031										
SNX9	51429	broad.mit.edu	37	chr6	158317968	158317968	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggctggagcccaaagaaAcacaaacactcccaacaact	9	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158317968A>C	ENST00000392185.3	+	5	581	c.410A>C	c.(409-411)aAc>aCc	p.N137T		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	137					cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.N137T(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		GCCCAAAGAAACACAAACACT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	75	72					6																	158317968		2203	4300	6503	158237956	SO:0001583	missense	51429			AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.410A>C	6.37:g.158317968A>C	ENSP00000376024:p.Asn137Thr		158237956	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	37	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.170238	0.00315	.	.	ENSG00000130340	ENST00000539592;ENST00000392185	T	0.44881	0.91	0.235	-0.47	0.12131	.	1.243050	0.05569	N	0.570822	T	0.06735	0.0172	N	0.04508	-0.205	0.33477	D	0.587009	B	0.02656	0.0	B	0.06405	0.002	T	0.31138	-0.9954	9	0.12430	T	0.62	.	.	.	.	.	137	Q9Y5X1	SNX9_HUMAN	T	137	ENSP00000376024:N137T	ENSP00000376024:N137T	N	+	2	0	SNX9	158237956	0.989000	0.36119	0.009000	0.14445	0.273000	0.26683	-0.560000	0.05964	0.308000	0.22923	0.313000	0.20887	AAC		0.637	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			C	158317968	A	C	158317968	3	2	61	1	0	0	0	0	1	0	0	0	14946	43	2	4	428	4	SNX9	6	158317968	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	886347	158317968	12797099	5047	13032										
SYNJ2	8871	broad.mit.edu	37	chr6	158514049	158514049	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggggcagccaaaccagaGaccccacaggcgcccccact	11	19	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158514049G>T	ENST00000355585.4	+	26	3732	c.3657G>T	c.(3655-3657)gaG>gaT	p.E1219D	SYNJ2_ENST00000367112.1_Missense_Mutation_p.E304D|SYNJ2_ENST00000367122.2_Missense_Mutation_p.E1174D|SYNJ2_ENST00000367121.3_Missense_Mutation_p.E1219D	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1219	Pro-rich.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.E1219D(1)		biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CCAAACCAGAGACCCCACAGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											48	53	52					6																	158514049		2203	4300	6503	158434037	SO:0001583	missense	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.3657G>T	6.37:g.158514049G>T	ENSP00000347792:p.Glu1219Asp		158434037	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	G	2.038	-0.420645	0.04734	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000367112	D;D;D;T	0.94330	-3.1;-3.4;-3.16;0.8	3.72	-1.58	0.08479	.	0.973778	0.08375	N	0.955494	T	0.71854	0.3389	L	0.34521	1.04	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.58457	-0.7633	10	0.13470	T	0.59	.	3.2877	0.06937	0.187:0.3504:0.3534:0.1092	.	614;1219;1219	B4DLC4;O15056;O15056-3	.;SYNJ2_HUMAN;.	D	1174;1219;1219;304	ENSP00000356089:E1174D;ENSP00000356088:E1219D;ENSP00000347792:E1219D;ENSP00000356079:E304D	ENSP00000347792:E1219D	E	+	3	2	SYNJ2	158434037	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.052000	0.11865	-0.645000	0.05458	-0.321000	0.08615	GAG		0.607	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158514049	G	T	158514049	3	4	61	1	0	0	0	0	1	0	0	0	15492	933	33	2	3759	2	SYNJ2	6	158514049	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196081	158514049	12601018	5048	13033										
SERAC1	84947	broad.mit.edu	37	chr6	158532439	158532439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagcttcacgaatgaattGtaaagtacgctggtacaaaa	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158532439G>T	ENST00000367104.3	-	17	2055	c.1924C>A	c.(1924-1926)Caa>Aaa	p.Q642K	SERAC1_ENST00000367102.2_3'UTR	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	642					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)	p.Q642K(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		CGAATGAATTGTAAAGTACGC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											117	109	112					6																	158532439		2203	4300	6503	158452427	SO:0001583	missense	84947			BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.1924C>A	6.37:g.158532439G>T	ENSP00000356071:p.Gln642Lys		158452427	Q49AT1|Q5VTX3|Q6PKF3	Missense_Mutation	SNP	ENST00000367104.3	37	CCDS5255.1	.	.	.	.	.	.	.	.	.	.	.	11.98	1.799654	0.31869	.	.	ENSG00000122335	ENST00000367104	D	0.95342	-3.68	5.67	4.75	0.60458	.	0.103621	0.64402	D	0.000002	T	0.80523	0.4639	N	0.20986	0.625	0.80722	D	1	B	0.10296	0.003	B	0.12156	0.007	T	0.71130	-0.4682	10	0.07813	T	0.8	-10.8553	13.9304	0.63991	0.0:0.0:0.775:0.225	.	642	Q96JX3	SRAC1_HUMAN	K	642	ENSP00000356071:Q642K	ENSP00000356071:Q642K	Q	-	1	0	SERAC1	158452427	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.644000	0.67902	0.445000	0.26639	0.528000	0.53228	CAA		0.363	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861		T	158532439	G	T	158532439	3	4	61	1	0	0	0	0	1	0	0	0	14111	1386	48	2	44	2	SERAC1	6	158532439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18390	158532439	12582628	5049	13034										
TULP4	56995	broad.mit.edu	37	chr6	158902147	158902147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctacccatcagccggcaacGagcggctgcactgcaccatg	11	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158902147G>A	ENST00000367097.3	+	8	2669	c.1312G>A	c.(1312-1314)Gag>Aag	p.E438K	TULP4_ENST00000367094.2_Missense_Mutation_p.E438K	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	438					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E438K(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		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)		AGCCGGCAACGAGCGGCTGCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											69	73	72					6																	158902147		2203	4300	6503	158822135	SO:0001583	missense	56995				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1312G>A	6.37:g.158902147G>A	ENSP00000356064:p.Glu438Lys		158822135	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911129	0.92178	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.64438	-0.1;-0.1	5.31	5.31	0.75309	Tumour necrosis factor-like (1);	0.000000	0.85682	D	0.000000	T	0.68081	0.2962	L	0.47716	1.5	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.77557	0.981;0.98;0.99	T	0.63849	-0.6544	10	0.31617	T	0.26	-35.684	18.9788	0.92747	0.0:0.0:1.0:0.0	.	438;438;438	B4E202;Q9NRJ4-2;Q9NRJ4	.;.;TULP4_HUMAN	K	438	ENSP00000356064:E438K;ENSP00000356061:E438K	ENSP00000356061:E438K	E	+	1	0	TULP4	158822135	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	9.275000	0.95738	2.491000	0.84063	0.561000	0.74099	GAG		0.597	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158902147	G	A	158902147	3	1	61	1	0	0	0	0	1	0	0	0	16816	1059	37	1	1342	1	TULP4	6	158902147	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	369708	158902147	12212920	5050	13035										
TULP4	56995	broad.mit.edu	37	chr6	158910647	158910647	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgggaacagcttgatttCtactgtgatcgacagctgca	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158910647C>A	ENST00000367097.3	+	9	2871	c.1514C>A	c.(1513-1515)tCt>tAt	p.S505Y	TULP4_ENST00000367094.2_Missense_Mutation_p.S505Y	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	505					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S505Y(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		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)		AGCTTGATTTCTACTGTGATC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	6											144	134	137					6																	158910647		2203	4300	6503	158830635	SO:0001583	missense	56995				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1514C>A	6.37:g.158910647C>A	ENSP00000356064:p.Ser505Tyr		158830635	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	C	34	5.329205	0.95733	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.63417	-0.04;0.78	5.57	5.57	0.84162	.	0.055415	0.85682	D	0.000000	T	0.62986	0.2473	L	0.39898	1.24	0.58432	D	0.999993	D;D	0.62365	0.974;0.991	P;P	0.55871	0.748;0.786	T	0.66416	-0.5929	10	0.72032	D	0.01	-21.4308	19.5417	0.95277	0.0:1.0:0.0:0.0	.	505;505	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	Y	505	ENSP00000356064:S505Y;ENSP00000356061:S505Y	ENSP00000356061:S505Y	S	+	2	0	TULP4	158830635	1.000000	0.71417	0.005000	0.12908	0.937000	0.57800	7.371000	0.79600	2.614000	0.88457	0.655000	0.94253	TCT		0.428	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158910647	C	A	158910647	3	1	61	1	0	0	0	0	1	0	0	0	16816	913	32	2	1548	2	TULP4	6	158910647	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8500	158910647	12204420	5051	13036										
TULP4	56995	broad.mit.edu	37	chr6	158919770	158919770	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatctcccagaagttcggaAaatttccatggactatatta	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:158919770A>G	ENST00000367097.3	+	12	3297	c.1940A>G	c.(1939-1941)aAa>aGa	p.K647R	TULP4_ENST00000367094.2_Missense_Mutation_p.K647R	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	647					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K647R(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		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)		GAAGTTCGGAAAATTTCCATG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	116	115					6																	158919770		2203	4300	6503	158839758	SO:0001583	missense	56995				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1940A>G	6.37:g.158919770A>G	ENSP00000356064:p.Lys647Arg		158839758	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.466288	0.84425	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	D;D	0.85484	-1.99;-1.99	5.77	5.77	0.91146	Tubby, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.66336	0.2779	N	0.17474	0.49	0.58432	D	0.999998	P;P	0.47762	0.675;0.9	B;B	0.43413	0.218;0.419	T	0.69412	-0.5152	10	0.19147	T	0.46	-31.5574	14.6668	0.68915	1.0:0.0:0.0:0.0	.	647;647	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	R	647	ENSP00000356064:K647R;ENSP00000356061:K647R	ENSP00000356061:K647R	K	+	2	0	TULP4	158839758	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	8.762000	0.91711	2.199000	0.70637	0.533000	0.62120	AAA		0.413	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		G	158919770	A	G	158919770	3	3	61	1	0	0	0	0	1	0	0	0	16816	14	1	4	1986	4	TULP4	6	158919770	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9123	158919770	12195297	5052	13037										
SYTL3	94120	broad.mit.edu	37	chr6	159166581	159166581	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgctaatgtcactggaGaaatagaatttgccattcat	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159166581G>T	ENST00000297239.9	+	11	1119	c.925G>T	c.(925-927)Gaa>Taa	p.E309*	SYTL3_ENST00000360448.3_Nonsense_Mutation_p.E241*|SYTL3_ENST00000367081.3_Nonsense_Mutation_p.E35*			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	309	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)	p.E241*(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		TGTCACTGGAGAAATAGAATT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											86	83	84					6																	159166581		2203	4300	6503	159086569	SO:0001587	stop_gained	94120			AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.925G>T	6.37:g.159166581G>T	ENSP00000297239:p.Glu309*		159086569	Q496J4|Q496J6|Q5U3B9	Nonsense_Mutation	SNP	ENST00000297239.9	37	CCDS56458.1	.	.	.	.	.	.	.	.	.	.	G	40	8.515929	0.98845	.	.	ENSG00000164674	ENST00000360448;ENST00000543689;ENST00000297239;ENST00000367081	.	.	.	5.51	5.51	0.81932	.	0.179153	0.47852	D	0.000205	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	19.4315	0.94772	0.0:0.0:1.0:0.0	.	.	.	.	X	241;309;309;35	.	ENSP00000297239:E309X	E	+	1	0	SYTL3	159086569	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.629000	0.83207	2.600000	0.87896	0.655000	0.94253	GAA		0.343	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1			T	159166581	G	T	159166581	4	4	61	1	0	0	0	0	0	1	0	0	15523	943	33	2	747	2	SYTL3	6	159166581	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246811	159166581	11948486	5053	13038										
TAGAP	117289	broad.mit.edu	37	chr6	159457356	159457356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtctcaggcagaagccgcGggctgtttggttgtgggttt	18	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159457356G>A	ENST00000367066.3	-	10	2030	c.1699C>T	c.(1699-1701)Cgc>Tgc	p.R567C	RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.R389C|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	567					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R567C(2)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CAGAAGCCGCGGGCTGTTTGG	0.597																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6											60	67	65					6																	159457356		2202	4299	6501	159377344	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1699C>T	6.37:g.159457356G>A	ENSP00000356033:p.Arg567Cys		159377344	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883882	0.33255	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000539071	T;T	0.17854	2.25;2.51	5.54	-1.25	0.09405	.	1.289820	0.05495	N	0.557396	T	0.02083	0.0065	N	0.08118	0	0.09310	N	1	P	0.47302	0.893	B	0.35182	0.197	T	0.32640	-0.9899	10	0.72032	D	0.01	-0.0297	4.4677	0.11698	0.1279:0.4598:0.2155:0.1968	.	567	Q8N103	TAGAP_HUMAN	C	567;389;232	ENSP00000356033:R567C;ENSP00000322650:R389C	ENSP00000322650:R389C	R	-	1	0	TAGAP	159377344	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.253000	0.08794	-0.616000	0.05671	0.655000	0.94253	CGC		0.597	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159457356	G	A	159457356	3	1	61	1	0	0	0	0	1	0	0	0	15576	1116	39	1	500	1	TAGAP	6	159457356	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	290775	159457356	11657711	5054	13039										
TAGAP	117289	broad.mit.edu	37	chr6	159461769	159461769	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttactgtttcagggcctcGattctgtcctcctcgtcctg	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159461769G>A	ENST00000367066.3	-	7	904	c.573C>T	c.(571-573)atC>atT	p.I191I	RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_Silent_p.I13I|TAGAP_ENST00000338313.5_Silent_p.I191I|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	191	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.I191I(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TCAGGGCCTCGATTCTGTCCT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	6											195	175	182					6																	159461769		2203	4300	6503	159381757	SO:0001819	synonymous_variant	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.573C>T	6.37:g.159461769G>A			159381757	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Silent	SNP	ENST00000367066.3	37	CCDS5261.1																																																																																				0.498	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159461769	G	A	159461769	2	1	61	1	0	0	0	0	0	0	0	1	15576	1048	37	1		1	TAGAP	6	159461769	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4413	159461769	11653298	5055	13040										
TAGAP	117289	broad.mit.edu	37	chr6	159462392	159462392	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttgaactcaccttaaaGaccacagcgaggaggtgcac	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159462392G>T	ENST00000367066.3	-	6	802	c.471C>A	c.(469-471)gtC>gtA	p.V157V	RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_5'UTR|TAGAP_ENST00000338313.5_Silent_p.V157V|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	157	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.V157V(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TCACCTTAAAGACCACAGCGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	6											94	86	89					6																	159462392		2203	4300	6503	159382380	SO:0001819	synonymous_variant	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.471C>A	6.37:g.159462392G>T			159382380	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Silent	SNP	ENST00000367066.3	37	CCDS5261.1																																																																																				0.562	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159462392	G	T	159462392	2	4	61	1	0	0	0	0	0	0	0	1	15576	929	33	2		2	TAGAP	6	159462392	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	623	159462392	11652675	5056	13041										
FNDC1	84624	broad.mit.edu	37	chr6	159642721	159642721	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccctaacaaagcgaaaGatttcaggtatgtttctaag	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159642721G>T	ENST00000297267.9	+	6	959	c.759G>T	c.(757-759)aaG>aaT	p.K253N	FNDC1_ENST00000480856.1_3'UTR|FNDC1_ENST00000340366.6_Missense_Mutation_p.K253N	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	253	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K253N(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CAAAGCGAAAGATTTCAGGTA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											101	110	107					6																	159642721		1951	4142	6093	159562709	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.759G>T	6.37:g.159642721G>T	ENSP00000297267:p.Lys253Asn		159562709	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.21|14.21	2.468197|2.468197	0.43839|0.43839	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.08807	.|3.05;3.99	6.17|6.17	1.98|1.98	0.26296|0.26296	.|Fibronectin, type III (1);	.|0.111909	.|0.64402	.|D	.|0.000011	T|T	0.07052|0.07052	0.0179|0.0179	L|L	0.36672|0.36672	1.1|1.1	0.28380|0.28380	N|N	0.919585|0.919585	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.975	T|T	0.15093|0.15093	-1.0449|-1.0449	5|10	.|0.46703	.|T	.|0.11	-34.0927|-34.0927	6.5326|6.5326	0.22336|0.22336	0.5231:0.0:0.4769:0.0|0.5231:0.0:0.4769:0.0	.|.	.|253;253	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	Y|N	212|253	.|ENSP00000297267:K253N;ENSP00000342460:K253N	.|ENSP00000297267:K253N	D|K	+|+	1|3	0|2	FNDC1|FNDC1	159562709|159562709	1.000000|1.000000	0.71417|0.71417	0.658000|0.658000	0.29665|0.29665	0.810000|0.810000	0.45777|0.45777	1.578000|1.578000	0.36525|0.36525	0.492000|0.492000	0.27815|0.27815	0.655000|0.655000	0.94253|0.94253	GAT|AAG		0.473	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159642721	G	T	159642721	3	4	61	1	0	0	0	0	1	0	0	0	5987	933	33	2	781	2	FNDC1	6	159642721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180329	159642721	11472346	5057	13042										
FNDC1	84624	broad.mit.edu	37	chr6	159653331	159653331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgctgccccgaagggaagGcgtagataagcctggctttt	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159653331G>A	ENST00000297267.9	+	11	1987	c.1787G>A	c.(1786-1788)gGc>gAc	p.G596D	FNDC1_ENST00000340366.6_Missense_Mutation_p.G533D	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	596					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G596D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CGAAGGGAAGGCGTAGATAAG	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	6											20	25	24					6																	159653331		2021	4176	6197	159573321	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1787G>A	6.37:g.159653331G>A	ENSP00000297267:p.Gly596Asp		159573321	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.374576	0.24857	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.07114	3.22;4.02	5.16	0.405	0.16361	.	1.461170	0.03812	N	0.266102	T	0.01523	0.0049	L	0.29908	0.895	0.09310	N	1	P;B	0.43938	0.822;0.294	B;B	0.38225	0.268;0.084	T	0.36114	-0.9761	10	0.09590	T	0.72	-0.7005	4.9225	0.13876	0.1017:0.4461:0.3351:0.1171	.	533;596	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	D	596;533	ENSP00000297267:G596D;ENSP00000342460:G533D	ENSP00000297267:G596D	G	+	2	0	FNDC1	159573321	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.022000	0.13511	0.141000	0.18875	0.655000	0.94253	GGC		0.706	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159653331	G	A	159653331	3	1	61	1	0	0	0	0	1	0	0	0	5987	1203	42	3	1829	3	FNDC1	6	159653331	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10610	159653331	11461736	5058	13043										
FNDC1	84624	broad.mit.edu	37	chr6	159653499	159653499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactcagacgaagatgagcGcgctgtgggctccctccacc	13	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159653499G>A	ENST00000297267.9	+	11	2155	c.1955G>A	c.(1954-1956)cGc>cAc	p.R652H	FNDC1_ENST00000340366.6_Missense_Mutation_p.R589H	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	652					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R652H(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GAAGATGAGCGCGCTGTGGGC	0.677																																																2	Substitution - Missense(2)	large_intestine(2)	6											30	35	33					6																	159653499		2050	4170	6220	159573489	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1955G>A	6.37:g.159653499G>A	ENSP00000297267:p.Arg652His		159573489	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	g	11.03	1.517544	0.27123	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.08282	3.11;3.87	4.06	-5.09	0.02920	.	1.251300	0.05499	N	0.558041	T	0.01092	0.0036	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.002	B;B	0.06405	0.002;0.0	T	0.46275	-0.9203	10	0.49607	T	0.09	2.5948	0.4558	0.00508	0.3328:0.2595:0.123:0.2847	.	589;652	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	H	652;589	ENSP00000297267:R652H;ENSP00000342460:R589H	ENSP00000297267:R652H	R	+	2	0	FNDC1	159573489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.235000	0.01202	-0.707000	0.05022	-1.718000	0.00708	CGC		0.677	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159653499	G	A	159653499	3	1	61	1	0	0	0	0	1	0	0	0	5987	1087	38	1	1997	1	FNDC1	6	159653499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	159653499	11461568	5059	13044										
FNDC1	84624	broad.mit.edu	37	chr6	159655446	159655446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctgtccttgcgccagaGgatgatgcatgccagattcc	12	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159655446G>T	ENST00000297267.9	+	11	4102	c.3902G>T	c.(3901-3903)aGg>aTg	p.R1301M	FNDC1_ENST00000340366.6_Missense_Mutation_p.R1238M	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1301					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1301M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TTGCGCCAGAGGATGATGCAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	6											28	30	29					6																	159655446		2065	4154	6219	159575436	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3902G>T	6.37:g.159655446G>T	ENSP00000297267:p.Arg1301Met		159575436	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.46|14.46	2.542860|2.542860	0.45280|0.45280	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.13089	.|2.62;3.41	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.340357	.|0.27591	.|N	.|0.018700	T|T	0.18964|0.18964	0.0455|0.0455	L|L	0.34521|0.34521	1.04|1.04	0.35252|0.35252	D|D	0.778758|0.778758	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.98	T|T	0.01390|0.01390	-1.1367|-1.1367	5|10	.|0.72032	.|D	.|0.01	-24.0719|-24.0719	15.5087|15.5087	0.75764|0.75764	0.0:0.1386:0.8613:0.0|0.0:0.1386:0.8613:0.0	.|.	.|1238;1301	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	D|M	1196|1301;1238	.|ENSP00000297267:R1301M;ENSP00000342460:R1238M	.|ENSP00000297267:R1301M	E|R	+|+	3|2	2|0	FNDC1|FNDC1	159575436|159575436	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.425000|0.425000	0.31504|0.31504	4.356000|4.356000	0.59430|0.59430	2.612000|2.612000	0.88384|0.88384	0.650000|0.650000	0.86243|0.86243	GAG|AGG		0.587	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159655446	G	T	159655446	3	4	61	1	0	0	0	0	1	0	0	0	5987	1000	35	2	3944	2	FNDC1	6	159655446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1947	159655446	11459621	5060	13045										
FNDC1	84624	broad.mit.edu	37	chr6	159667987	159667987	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctacggaagaggcctacgTtatatatgatgaaggtacaa	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159667987T>A	ENST00000297267.9	+	15	4876	c.4676T>A	c.(4675-4677)gTt>gAt	p.V1559D	FNDC1_ENST00000340366.6_Missense_Mutation_p.V1496D	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1559					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V1559D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GAGGCCTACGTTATATATGAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	6											131	125	127					6																	159667987		1896	4125	6021	159587977	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4676T>A	6.37:g.159667987T>A	ENSP00000297267:p.Val1559Asp		159587977	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550953	0.45383	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.11277	2.79;3.59	5.54	4.38	0.52667	.	0.151509	0.43579	D	0.000545	T	0.15739	0.0379	M	0.62723	1.935	0.39635	D	0.970233	D	0.71674	0.998	D	0.74023	0.982	T	0.01349	-1.1378	9	.	.	.	-10.0047	9.5659	0.39398	0.0:0.0803:0.0:0.9197	.	1559	Q4ZHG4	FNDC1_HUMAN	D	1559;1496	ENSP00000297267:V1559D;ENSP00000342460:V1496D	.	V	+	2	0	FNDC1	159587977	0.933000	0.31639	0.000000	0.03702	0.382000	0.30200	1.611000	0.36879	0.936000	0.37367	0.482000	0.46254	GTT		0.423	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159667987	T	A	159667987	3	1	61	1	0	0	0	0	1	0	0	0	5987	1725	60	5	4734	5	FNDC1	6	159667987	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12541	159667987	11447080	5061	13046										
FNDC1	84624	broad.mit.edu	37	chr6	159682295	159682295	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcggtctcatttgtcaccGaatcaggtatgaatgacttc	8	10	3	2	rs560595190		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:159682295G>A	ENST00000297267.9	+	19	5448	c.5248G>A	c.(5248-5250)Gaa>Aaa	p.E1750K	FNDC1_ENST00000340366.6_Missense_Mutation_p.E1687K	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1750	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E1750K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		ATTTGTCACCGAATCAGGTAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											104	97	99					6																	159682295		1834	4084	5918	159602285	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.5248G>A	6.37:g.159682295G>A	ENSP00000297267:p.Glu1750Lys		159602285	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.0|23.0	4.365498|4.365498	0.82463|0.82463	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.09817|.	2.94;3.79|.	5.81|5.81	5.81|5.81	0.92471|0.92471	Fibronectin, type III (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.66356|0.66356	0.2781|0.2781	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.61327|0.61327	-0.7085|-0.7085	9|5	.|.	.|.	.|.	-26.527|-26.527	20.073|20.073	0.97731|0.97731	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1750|.	Q4ZHG4|.	FNDC1_HUMAN|.	K|Q	1750;1687|1645	ENSP00000297267:E1750K;ENSP00000342460:E1687K|.	.|.	E|R	+|+	1|2	0|0	FNDC1|FNDC1	159602285|159602285	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.240000|0.240000	0.25518|0.25518	9.424000|9.424000	0.97464|0.97464	2.750000|2.750000	0.94351|0.94351	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.343	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159682295	G	A	159682295	3	1	61	1	0	0	0	0	1	0	0	0	5987	1059	37	1	5322	1	FNDC1	6	159682295	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14308	159682295	11432772	5062	13047										
PNLDC1	154197	broad.mit.edu	37	chr6	160225025	160225025	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccattcttgtaacttctatCtcttccctacaacgtttggg	5	13	3	0	rs138958903		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160225025C>T	ENST00000610273.1	+	5	415	c.244C>T	c.(244-246)Ctc>Ttc	p.L82F	PNLDC1_ENST00000609334.1_3'UTR|PNLDC1_ENST00000392167.3_Missense_Mutation_p.L93F	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	82						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.L82F(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TAACTTCTATCTCTTCCCTAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											139	142	141					6																	160225025		2203	4300	6503	160145015	SO:0001583	missense	154197			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.244C>T	6.37:g.160225025C>T	ENSP00000476448:p.Leu82Phe		160145015	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.228784	0.79576	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	T;T	0.23950	1.88;1.88	5.47	5.47	0.80525	Ribonuclease H-like (1);	0.000000	0.53938	D	0.000048	T	0.47581	0.1453	M	0.79805	2.47	0.43444	D	0.995628	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	T	0.52343	-0.8588	10	0.87932	D	0	.	16.4851	0.84182	0.0:1.0:0.0:0.0	.	93;82	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	F	82;93	ENSP00000275275:L82F;ENSP00000376007:L93F	ENSP00000275275:L82F	L	+	1	0	PNLDC1	160145015	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.709000	0.61867	2.553000	0.86117	0.655000	0.94253	CTC		0.393	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160225025	C	T	160225025	3	4	61	1	0	0	0	0	1	0	0	0	12179	913	32	3	258	3	PNLDC1	6	160225025	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	542730	160225025	10890042	5063	13048										
PNLDC1	154197	broad.mit.edu	37	chr6	160225665	160225665	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactgggaactggagagttCgcaggtatggcctgtttctc	14	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160225665C>T	ENST00000610273.1	+	6	595	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C	PNLDC1_ENST00000609334.1_3'UTR|PNLDC1_ENST00000392167.3_Missense_Mutation_p.R153C	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	142						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.R142C(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTGGAGAGTTCGCAGGTATGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											98	94	95					6																	160225665		2203	4300	6503	160145655	SO:0001583	missense	154197			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.424C>T	6.37:g.160225665C>T	ENSP00000476448:p.Arg142Cys		160145655	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	9.866	1.197597	0.22037	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.28	4.41	0.53225	Ribonuclease H-like (1);	0.207467	0.34200	N	0.004166	T	0.24314	0.0589	L	0.27053	0.805	0.47441	D	0.999428	B;B	0.19706	0.038;0.022	B;B	0.17722	0.007;0.019	T	0.10706	-1.0618	9	0.38643	T	0.18	.	7.8886	0.29665	0.0:0.805:0.0:0.195	.	153;142	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	C	142;153	.	ENSP00000275275:R142C	R	+	1	0	PNLDC1	160145655	0.761000	0.28439	0.958000	0.39756	0.399000	0.30720	1.163000	0.31798	1.215000	0.43411	0.655000	0.94253	CGC		0.473	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160225665	C	T	160225665	3	4	61	1	0	0	0	0	1	0	0	0	12179	884	31	1	442	1	PNLDC1	6	160225665	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	640	160225665	10889402	5064	13049										
PNLDC1	154197	broad.mit.edu	37	chr6	160232740	160232740	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcccctcagaaagctaCgatcaatttaagcagaatat	5	9	2	2	rs181607194		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160232740C>T	ENST00000610273.1	+	11	999	c.828C>T	c.(826-828)taC>taT	p.Y276Y	PNLDC1_ENST00000392167.3_Silent_p.Y287Y	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	276						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.Y276Y(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CAGAAAGCTACGATCAATTTA	0.408													C|||	1	0.000199681	0	0.0014	5008	,	,		18669	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											110	108	109					6																	160232740		2203	4300	6503	160152730	SO:0001819	synonymous_variant	154197			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.828C>T	6.37:g.160232740C>T			160152730	Q5TAP7|Q8N7X5	Silent	SNP	ENST00000610273.1	37	CCDS5271.1																																																																																				0.408	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160232740	C	T	160232740	2	4	61	1	0	0	0	0	0	0	0	1	12179	547	19	1		1	PNLDC1	6	160232740	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7075	160232740	10882327	5065	13050										
PNLDC1	154197	broad.mit.edu	37	chr6	160240086	160240086	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaccataagtttcagaatCtctgcaagtttgatgtcagg	8	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160240086C>A	ENST00000610273.1	+	17	1504	c.1333C>A	c.(1333-1335)Ctc>Atc	p.L445I	PNLDC1_ENST00000392167.3_Missense_Mutation_p.L456I	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	445						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.L445I(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GTTTCAGAATCTCTGCAAGTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											103	99	101					6																	160240086		2203	4300	6503	160160076	SO:0001583	missense	154197			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1333C>A	6.37:g.160240086C>A	ENSP00000476448:p.Leu445Ile		160160076	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	5.111	0.206135	0.09704	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	4.57	2.78	0.32641	.	0.137105	0.31102	N	0.008250	T	0.10981	0.0268	L	0.27053	0.805	0.27208	N	0.95998	B;B	0.22146	0.065;0.018	B;B	0.23716	0.048;0.023	T	0.19647	-1.0299	9	0.36615	T	0.2	.	5.9447	0.19211	0.0:0.6722:0.158:0.1698	.	456;445	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	I	445;456	.	ENSP00000275275:L445I	L	+	1	0	PNLDC1	160160076	0.009000	0.17119	0.997000	0.53966	0.057000	0.15508	0.207000	0.17395	0.537000	0.28751	-0.379000	0.06801	CTC		0.517	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		A	160240086	C	A	160240086	3	1	61	1	0	0	0	0	1	0	0	0	12179	913	32	2	1395	2	PNLDC1	6	160240086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7346	160240086	10874981	5066	13051										
IGF2R	3482	broad.mit.edu	37	chr6	160453696	160453696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacttgttctctgagcggCgagcagcaggatgtctccat	11	10	2	1	rs201732709		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160453696C>T	ENST00000356956.1	+	8	1144	c.996C>T	c.(994-996)ggC>ggT	p.G332G		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	332					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.G332G(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CTCTGAGCGGCGAGCAGCAGG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		3,4403	6.2+/-15.9	0,3,2200	93	89	90		996	-5.2	0	6		90	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	IGF2R	NM_000876.2		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		332/2492	160453696	4,13002	2203	4300	6503	160373686	SO:0001819	synonymous_variant	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.996C>T	6.37:g.160453696C>T			160373686	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																				0.512	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		T	160453696	C	T	160453696	2	4	61	1	0	0	0	0	0	0	0	1	7597	755	27	1		1	IGF2R	6	160453696	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213610	160453696	10661371	5067	13052										
IGF2R	3482	broad.mit.edu	37	chr6	160485885	160485885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctacttgtttgagtggcGaacgcagtatgcctgcccac	10	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160485885G>A	ENST00000356956.1	+	29	4215	c.4067G>A	c.(4066-4068)cGa>cAa	p.R1356Q		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1356					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.R1356Q(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTGAGTGGCGAACGCAGTAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											165	145	152					6																	160485885		2203	4300	6503	160405875	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4067G>A	6.37:g.160485885G>A	ENSP00000349437:p.Arg1356Gln		160405875	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323756	0.60634	.	.	ENSG00000197081	ENST00000356956	T	0.02140	4.43	5.19	4.32	0.51571	Mannose-6-phosphate receptor, binding (1);	0.246858	0.36665	N	0.002476	T	0.01387	0.0045	M	0.70842	2.15	0.34975	D	0.753543	D	0.60575	0.988	P	0.46275	0.51	T	0.53781	-0.8390	10	0.14656	T	0.56	-14.7369	4.8397	0.13483	0.2178:0.1728:0.6094:0.0	.	1356	P11717	MPRI_HUMAN	Q	1356	ENSP00000349437:R1356Q	ENSP00000349437:R1356Q	R	+	2	0	IGF2R	160405875	1.000000	0.71417	0.422000	0.26621	0.980000	0.70556	3.619000	0.54196	1.199000	0.43173	0.655000	0.94253	CGA		0.383	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		A	160485885	G	A	160485885	3	1	61	1	0	0	0	0	1	0	0	0	7597	1058	37	1	4181	1	IGF2R	6	160485885	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32189	160485885	10629182	5068	13053										
SLC22A3	6581	broad.mit.edu	37	chr6	160858073	160858073	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacttgtcatgcgcctggGaattatagggggcaacctct	13	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160858073G>T	ENST00000275300.2	+	7	1270	c.1118G>T	c.(1117-1119)gGa>gTa	p.G373V	SLC22A3_ENST00000392145.1_Missense_Mutation_p.G373V	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	373					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)	p.G373V(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	ATGCGCCTGGGAATTATAGGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											123	132	129					6																	160858073		2203	4300	6503	160778063	SO:0001583	missense	6581			AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"Solute carriers"	10967	protein-coding gene	gene with protein product		604842	"solute carrier family 22 (extraneuronal monoamine transporter), member 3"			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1118G>T	6.37:g.160858073G>T	ENSP00000275300:p.Gly373Val		160778063	Q5SYN6|Q9UP02	Missense_Mutation	SNP	ENST00000275300.2	37	CCDS5277.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006408	0.74932	.	.	ENSG00000146477	ENST00000275300;ENST00000392145	T;T	0.57273	0.41;0.41	5.83	5.83	0.93111	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.68476	0.3005	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70073	-0.4972	10	0.72032	D	0.01	.	18.2967	0.90148	0.0:0.0:1.0:0.0	.	373	O75751	S22A3_HUMAN	V	373	ENSP00000275300:G373V;ENSP00000375989:G373V	ENSP00000275300:G373V	G	+	2	0	SLC22A3	160778063	1.000000	0.71417	0.042000	0.18584	0.998000	0.95712	8.972000	0.93424	2.756000	0.94617	0.655000	0.94253	GGA		0.468	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977		T	160858073	G	T	160858073	3	4	61	1	0	0	0	0	1	0	0	0	14492	1174	41	2	1144	2	SLC22A3	6	160858073	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	372188	160858073	10256994	5069	13054										
LPA	4018	broad.mit.edu	37	chr6	160952893	160952893	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatgtatttgtccttctcGaagcaaaccagaggccctcc	7	12	1	1	rs531254436		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160952893G>A	ENST00000316300.5	-	39	6035	c.5991C>T	c.(5989-5991)ttC>ttT	p.F1997F	LPA_ENST00000447678.1_Silent_p.F1997F			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4505	Kringle 18. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.F1997F(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TGTCCTTCTCGAAGCAAACCA	0.468													G|||	1	0.000199681	0	0	5008	,	,		18694	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	6											105	100	102					6																	160952893		2203	4300	6503	160872883	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.5991C>T	6.37:g.160952893G>A			160872883	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.468	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	160952893	G	A	160952893	2	1	61	1	0	0	0	0	0	0	0	1	8932	1049	37	1		1	LPA	6	160952893	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94820	160952893	10162174	5070	13055										
LPA	4018	broad.mit.edu	37	chr6	160962147	160962147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaaacgtacttcttcaaGcagtgagcagcagtcagcac	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:160962147G>A	ENST00000316300.5	-	35	5630	c.5586C>T	c.(5584-5586)tgC>tgT	p.C1862C	LPA_ENST00000447678.1_Silent_p.C1862C			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4370	Kringle 17. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.C1862C(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	ACTTCTTCAAGCAGTGAGCAG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	6											92	97	95					6																	160962147		2203	4300	6503	160882137	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.5586C>T	6.37:g.160962147G>A			160882137	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.473	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	160962147	G	A	160962147	2	1	61	1	0	0	0	0	0	0	0	1	8932	963	34	3		3	LPA	6	160962147	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9254	160962147	10152920	5071	13056										
LPA	4018	broad.mit.edu	37	chr6	161006106	161006106	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtataatgggatcctccGatgccaatgtggtgtcatag	11	7	1	0	rs370130400		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:161006106G>T	ENST00000316300.5	-	26	4305	c.4261C>A	c.(4261-4263)Cgg>Agg	p.R1421R	LPA_ENST00000447678.1_Silent_p.R1421R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3929	Kringle 13. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.R1421R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGGATCCTCCGATGCCAATGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6											216	214	215					6																	161006106		2176	4295	6471	160926096	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4261C>A	6.37:g.161006106G>T			160926096	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161006106	G	T	161006106	2	4	61	1	0	0	0	0	0	0	0	1	8932	1057	37	2		2	LPA	6	161006106	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43959	161006106	10108961	5072	13057										
LPA	4018	broad.mit.edu	37	chr6	161010695	161010695	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgagcctcgataactctgTccatcaccatggtagcagtc	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:161010695T>C	ENST00000316300.5	-	24	3881	c.3837A>G	c.(3835-3837)ggA>ggG	p.G1279G	LPA_ENST00000447678.1_Silent_p.G1279G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3787	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.G1279G(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GATAACTCTGTCCATCACCAT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	6											153	158	157					6																	161010695		2185	4296	6481	160930685	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3837A>G	6.37:g.161010695T>C			160930685	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.473	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		C	161010695	T	C	161010695	2	2	61	1	0	0	0	0	0	0	0	1	8932	1654	58	4		4	LPA	6	161010695	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4589	161010695	10104372	5073	13058										
PLG	5340	broad.mit.edu	37	chr6	161137753	161137753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccttggtgtttcaccaccGaccccaacaagcgctgggaa	11	14	1	0	rs532027310		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:161137753G>A	ENST00000308192.9	+	7	808	c.745G>A	c.(745-747)Gac>Aac	p.D249N		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	249	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D249N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	TTTCACCACCGACCCCAACAA	0.488													G|||	1	0.000199681	0	0.0014	5008	,	,		18241	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											69	65	66					6																	161137753		2203	4300	6503	161057743	SO:0001583	missense	5340			M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.745G>A	6.37:g.161137753G>A	ENSP00000308938:p.Asp249Asn		161057743	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	G	8.624	0.892139	0.17613	.	.	ENSG00000122194	ENST00000308192	T	0.64085	-0.08	5.26	-0.578	0.11724	Kringle (4);Kringle-like fold (1);	0.172675	0.26832	U	0.022271	T	0.22551	0.0544	L	0.28014	0.82	0.09310	N	1	B	0.17268	0.021	B	0.19148	0.024	T	0.31110	-0.9955	10	0.27785	T	0.31	.	9.4995	0.39008	0.5999:0.0:0.4001:0.0	.	249	P00747	PLMN_HUMAN	N	249	ENSP00000308938:D249N	ENSP00000308938:D249N	D	+	1	0	PLG	161057743	0.000000	0.05858	0.029000	0.17559	0.661000	0.39034	0.480000	0.22244	-0.075000	0.12798	-0.440000	0.05779	GAC		0.488	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161137753	G	A	161137753	3	1	61	1	0	0	0	0	1	0	0	0	12117	1058	37	1	775	1	PLG	6	161137753	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127058	161137753	9977314	5074	13059										
AGPAT4	56895	broad.mit.edu	37	chr6	161587403	161587403	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggcgcgcgggtccgtgaaGatggtgcattccgtgcccga	16	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:161587403G>T	ENST00000320285.4	-	3	437	c.225C>A	c.(223-225)atC>atA	p.I75I	AGPAT4_ENST00000366906.5_Silent_p.I13I|AGPAT4_ENST00000366905.3_Silent_p.I75I|AGPAT4_ENST00000366908.5_Silent_p.I75I|AGPAT4_ENST00000457520.2_Intron|AGPAT4_ENST00000366911.5_Intron	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	75					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.I75I(1)		endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		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)		GGTCCGTGAAGATGGTGCATT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	6											90	79	83					6																	161587403		2203	4300	6503	161507393	SO:0001819	synonymous_variant	56895			AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20885	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, delta"	614795	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.225C>A	6.37:g.161587403G>T			161507393	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1																																																																																				0.527	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133		T	161587403	G	T	161587403	2	4	61	1	0	0	0	0	0	0	0	1	389	932	33	2		2	AGPAT4	6	161587403	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	449650	161587403	9527664	5075	13060										
PARK2	5071	broad.mit.edu	37	chr6	161990401	161990401	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacctgctcttctcccaGaatcctgaagtgatggagct	8	13	3	3	rs138920699	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:161990401G>T	ENST00000366898.1	-	8	1021	c.919C>A	c.(919-921)Ctg>Atg	p.L307M	PARK2_ENST00000366894.1_Missense_Mutation_p.L116M|PARK2_ENST00000366892.1_Missense_Mutation_p.L307M|PARK2_ENST00000338468.3_Missense_Mutation_p.L116M|PARK2_ENST00000366896.1_Missense_Mutation_p.L158M|PARK2_ENST00000366897.1_Missense_Mutation_p.L279M	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	307					adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)	p.L307M(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TCTTCTCCCAGAATCCTGAAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6	GRCh37	CM063012	PARK2	M	rs138920699						116	109	112					6																	161990401		2203	4300	6503	161910391	SO:0001583	missense	5071				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.919C>A	6.37:g.161990401G>T	ENSP00000355865:p.Leu307Met		161910391	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.695842	0.68386	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892	D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	5.11	5.11	0.69529	.	0.000000	0.64402	D	0.000004	D	0.95768	0.8623	M	0.83953	2.67	0.45541	D	0.998498	D;D;D;D;D	0.89917	1.0;0.998;0.998;0.998;1.0	D;D;P;P;D	0.91635	0.999;0.994;0.906;0.906;0.987	D	0.95931	0.8938	10	0.59425	D	0.04	.	16.7149	0.85395	0.0:0.0:1.0:0.0	.	326;158;279;307;116	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	M	307;279;158;116;116;116;307	ENSP00000355865:L307M;ENSP00000355863:L279M;ENSP00000355862:L158M;ENSP00000355860:L116M;ENSP00000343589:L116M;ENSP00000355858:L307M	ENSP00000343589:L116M	L	-	1	2	PARK2	161910391	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	6.444000	0.73452	2.383000	0.81215	0.643000	0.83706	CTG		0.473	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			T	161990401	G	T	161990401	3	4	61	1	0	0	0	0	1	0	0	0	11480	933	33	2	498	2	PARK2	6	161990401	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	402998	161990401	9124666	5076	13061										
PACRG	135138	broad.mit.edu	37	chr6	163735866	163735866	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcatgcaccagtgaactcCggagacggcattgactacag	11	11	0	3	rs191922264	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:163735866C>T	ENST00000337019.3	+	7	962	c.738C>T	c.(736-738)tcC>tcT	p.S246S	PACRG_ENST00000366889.2_Silent_p.S207S|PACRG_ENST00000366888.2_Silent_p.S207S	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	246					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)		p.S246S(1)		endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		CAGTGAACTCCGGAGACGGCA	0.498													C|||	2	0.000399361	0	0.0029	5008	,	,		20219	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											93	85	87					6																	163735866		2203	4300	6503	163655856	SO:0001819	synonymous_variant	135138			AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.738C>T	6.37:g.163735866C>T			163655856	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Silent	SNP	ENST00000337019.3	37	CCDS5284.1																																																																																				0.498	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410		T	163735866	C	T	163735866	2	4	61	1	0	0	0	0	0	0	0	1	11401	639	23	1		1	PACRG	6	163735866	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1745465	163735866	7379201	5077	13062										
QKI	9444	broad.mit.edu	37	chr6	163876327	163876327	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaaattagcagagtacgGaaagacatgtacaatgacac	9	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:163876327G>T	ENST00000361752.3	+	2	710	c.159G>T	c.(157-159)cgG>cgT	p.R53R	QKI_ENST00000392127.2_Silent_p.R53R|QKI_ENST00000275262.7_Silent_p.R53R|QKI_ENST00000361195.2_Silent_p.R53R|QKI_ENST00000453779.2_Silent_p.R53R|QKI_ENST00000424802.3_Silent_p.R53R	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	53					long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R53R(1)		central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		GCAGAGTACGGAAAGACATGT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	6											115	111	112					6																	163876327		2203	4300	6503	163796317	SO:0001819	synonymous_variant	9444			AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531			21100	protein-coding gene	gene with protein product		609590	"quaking homolog, KH domain RNA binding (mouse)"			10535969	Standard	NM_006775		Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.159G>T	6.37:g.163876327G>T			163796317	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	Silent	SNP	ENST00000361752.3	37	CCDS5285.1																																																																																				0.373	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043016.2	NM_006775		T	163876327	G	T	163876327	2	4	61	1	0	0	0	0	0	0	0	1	12910	1161	41	2		2	QKI	6	163876327	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140461	163876327	7238740	5078	13063										
C6orf118	168090	broad.mit.edu	37	chr6	165713964	165713964	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggctgcacgtgcaaatTttctggagctcctggaggaa	15	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:165713964T>A	ENST00000230301.8	-	3	785	c.765A>T	c.(763-765)aaA>aaT	p.K255N	C6orf118_ENST00000543069.1_Missense_Mutation_p.K151N	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	255								p.K255N(1)		breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		ACGTGCAAATTTTCTGGAGCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											118	136	130					6																	165713964		2203	4300	6503	165633954	SO:0001583	missense	168090				CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.765A>T	6.37:g.165713964T>A	ENSP00000230301:p.Lys255Asn		165633954	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.651636	0.29336	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.19532	2.46;2.14	5.02	-6.44	0.01920	.	0.260506	0.31347	N	0.007812	T	0.14442	0.0349	M	0.67397	2.05	0.27970	N	0.936431	D	0.76494	0.999	D	0.69479	0.964	T	0.04537	-1.0944	10	0.62326	D	0.03	.	1.0767	0.01634	0.2295:0.3261:0.2341:0.2103	.	255	Q5T5N4	CF118_HUMAN	N	255;151	ENSP00000230301:K255N;ENSP00000439288:K151N	ENSP00000230301:K255N	K	-	3	2	C6orf118	165633954	0.000000	0.05858	0.666000	0.29783	0.017000	0.09413	-1.463000	0.02361	-1.659000	0.01488	-0.408000	0.06270	AAA		0.453	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165713964	T	A	165713964	3	1	61	1	0	0	0	0	1	0	0	0	2329	1838	64	5	672	5	C6orf118	6	165713964	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1837637	165713964	5401103	5079	13064										
PDE10A	10846	broad.mit.edu	37	chr6	165756884	165756884	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatcaaggacatacctcaGcccagaattctgcatatata	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:165756884G>T	ENST00000366882.1	-	20	2217	c.2063C>A	c.(2062-2064)gCt>gAt	p.A688D	PDE10A_ENST00000354448.4_Missense_Mutation_p.A688D|PDE10A_ENST00000539869.2_Missense_Mutation_p.A698D			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	688					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.A688D(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	ACATACCTCAGCCCAGAATTC	0.363																																					Esophageal Squamous(22;308 615 5753 12038 40624)											1	Substitution - Missense(1)	large_intestine(1)	6											107	103	104					6																	165756884		2203	4300	6503	165676874	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.2063C>A	6.37:g.165756884G>T	ENSP00000355847:p.Ala688Asp		165676874	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	G	14.89	2.671025	0.47781	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.81078	-1.45;-1.45	5.67	5.67	0.87782	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.046666	0.85682	D	0.000000	T	0.63965	0.2556	N	0.10782	0.045	0.80722	D	1	P;B	0.45986	0.87;0.002	P;B	0.49276	0.605;0.003	T	0.65549	-0.6141	10	0.15499	T	0.54	.	19.3597	0.94432	0.0:0.0:1.0:0.0	.	698;688	Q9ULW9;Q9Y233	.;PDE10_HUMAN	D	688;716;698;688;687	ENSP00000355847:A688D;ENSP00000346435:A688D	ENSP00000341187:A698D	A	-	2	0	PDE10A	165676874	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.975000	0.93437	2.671000	0.90904	0.585000	0.79938	GCT		0.363	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165756884	G	T	165756884	3	4	61	1	0	0	0	0	1	0	0	0	11661	971	34	2	292	2	PDE10A	6	165756884	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42920	165756884	5358183	5080	13065										
PDE10A	10846	broad.mit.edu	37	chr6	165809816	165809816	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatacttacaattcaatttCtttgcagagacgcacgggaa	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:165809816C>A	ENST00000366882.1	-	15	1535	c.1381G>T	c.(1381-1383)Gaa>Taa	p.E461*	PDE10A_ENST00000354448.4_Nonsense_Mutation_p.E461*|PDE10A_ENST00000539869.2_Nonsense_Mutation_p.E471*			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	461					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.E461*(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AATTCAATTTCTTTGCAGAGA	0.388																																					Esophageal Squamous(22;308 615 5753 12038 40624)											1	Substitution - Nonsense(1)	large_intestine(1)	6											160	139	146					6																	165809816		2203	4300	6503	165729806	SO:0001587	stop_gained	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1381G>T	6.37:g.165809816C>A	ENSP00000355847:p.Glu461*		165729806	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Nonsense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.599085	0.96614	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	.	.	.	5.46	4.58	0.56647	.	0.473959	0.25071	N	0.033363	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	15.6303	0.76904	0.1385:0.8615:0.0:0.0	.	.	.	.	X	461;489;471;461;460	.	ENSP00000341187:E471X	E	-	1	0	PDE10A	165729806	1.000000	0.71417	0.067000	0.19924	0.444000	0.32077	7.463000	0.80869	1.292000	0.44672	0.650000	0.86243	GAA		0.388	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			A	165809816	C	A	165809816	4	1	61	1	0	0	0	0	0	1	0	0	11661	922	32	2	994	2	PDE10A	6	165809816	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52932	165809816	5305251	5081	13066										
RPS6KA2	6196	broad.mit.edu	37	chr6	166914411	166914411	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctcttcatccaggaggaTgctaaaagaaagggagagaa	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:166914411T>C	ENST00000265678.4	-	7	791	c.568A>G	c.(568-570)Atc>Gtc	p.I190V	RPS6KA2_ENST00000510118.1_Splice_Site_p.I215V|RPS6KA2_ENST00000366863.2_Splice_Site_p.I36V|RPS6KA2_ENST00000405189.3_Splice_Site_p.I101V|RPS6KA2_ENST00000481261.2_Splice_Site_p.I101V|RPS6KA2_ENST00000503859.1_Splice_Site_p.I198V	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	190	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.I190V(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TCCAGGAGGATGCTAAAAGAA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	6											71	67	68					6																	166914411		2203	4300	6503	166834401	SO:0001630	splice_region_variant	6196			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.567-1A>G	6.37:g.166914411T>C			166834401	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	37	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.414091	0.42817	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189;ENST00000366863;ENST00000507350	T;T;T;T;T;T;T	0.72942	1.42;1.42;1.42;1.42;1.42;-0.7;1.42	4.38	4.38	0.52667	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70159	0.3192	L	0.39514	1.22	0.80722	D	1	B;B;P	0.49447	0.205;0.082;0.924	B;B;D	0.68765	0.248;0.077;0.96	T	0.72286	-0.4338	10	0.45353	T	0.12	.	13.0844	0.59132	0.0:0.0:0.0:1.0	.	215;198;190	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	V	190;215;198;101;101;36;101	ENSP00000265678:I190V;ENSP00000422435:I215V;ENSP00000427015:I198V;ENSP00000422484:I101V;ENSP00000386050:I101V;ENSP00000355828:I36V;ENSP00000422197:I101V	ENSP00000265678:I190V	I	-	1	0	RPS6KA2	166834401	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	6.902000	0.75699	1.739000	0.51704	0.460000	0.39030	ATC		0.572	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	Missense_Mutation	C	166914411	T	C	166914411	5	2	61	1	0	0	0	0	0	0	1	0	13688	1478	51	4	1693	4	RPS6KA2	6	166914411	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1104595	166914411	4200656	5082	13067										
RPS6KA2	6196	broad.mit.edu	37	chr6	167271690	167271690	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaacgtgtatagttacttCttctgcagtgtcttctgtgg	9	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167271690C>A	ENST00000510118.1	-	2	461	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	RPS6KA2_ENST00000503859.1_Nonsense_Mutation_p.E41*|RP11-514O12.4_ENST00000507747.1_Missense_Mutation_p.K164N			Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	0					axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.E41*(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ATAGTTACTTCTTCTGCAGTG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											267	219	236					6																	167271690		2203	4300	6503	167191680	SO:0001587	stop_gained	6196			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000510118.1:c.121G>T	6.37:g.167271690C>A	ENSP00000422435:p.Glu41*		167191680	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Nonsense_Mutation	SNP	ENST00000510118.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.93|15.93	2.979605|2.979605	0.53827|0.53827	.|.	.|.	ENSG00000071242|ENSG00000249141	ENST00000510118;ENST00000503859;ENST00000506565|ENST00000507747	.|.	.|.	.|.	4.74|4.74	4.74|4.74	0.60224|0.60224	.|.	0.462954|.	0.22443|.	N|.	0.059987|.	.|T	.|0.55273	.|0.1910	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54403	.|-0.8299	.|4	0.07482|.	T|.	0.82|.	.|.	13.0924|13.0924	0.59172|0.59172	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	41|164	.|.	ENSP00000427015:E41X|.	E|K	-|-	1|3	0|2	RPS6KA2|RP11-514O12.4	167191680|167191680	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.270000|0.270000	0.26580|0.26580	1.551000|1.551000	0.36233|0.36233	2.458000|2.458000	0.83093|0.83093	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.433	RPS6KA2-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000362836.2	NM_021135		A	167271690	C	A	167271690	4	1	61	1	0	0	0	0	0	1	0	0	13688	922	32	2	2291	2	RPS6KA2	6	167271690	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	357279	167271690	3843377	5083	13068										
RNASET2	8635	broad.mit.edu	37	chr6	167344591	167344591	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatactctggcaagggcatCtttaaaatctgcaacctgat	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167344591C>A	ENST00000508775.1	-	8	1027	c.508G>T	c.(508-510)Gat>Tat	p.D170Y	RNASET2_ENST00000476238.2_Missense_Mutation_p.D170Y|RNASET2_ENST00000366855.6_Missense_Mutation_p.D132Y|RP11-514O12.4_ENST00000507747.1_Intron|RNASET2_ENST00000496851.2_5'Flank	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	170					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)	p.D170Y(1)		large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		GCAAGGGCATCTTTAAAATCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	6											149	147	148					6																	167344591		2203	4300	6503	167264581	SO:0001583	missense	8635			AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.508G>T	6.37:g.167344591C>A	ENSP00000426455:p.Asp170Tyr		167264581	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Missense_Mutation	SNP	ENST00000508775.1	37	CCDS5295.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554675	0.27739	.	.	ENSG00000026297	ENST00000366855;ENST00000508775;ENST00000428859;ENST00000476238;ENST00000478180	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	4.5	3.47	0.39725	.	0.428900	0.27841	N	0.017623	T	0.79209	0.4407	M	0.75150	2.29	0.40781	D	0.983174	D;D	0.61697	0.99;0.98	D;P	0.67103	0.949;0.747	T	0.81109	-0.1082	10	0.66056	D	0.02	-17.3238	3.9528	0.09377	0.0:0.683:0.0:0.317	.	220;170	C9JIU8;O00584	.;RNT2_HUMAN	Y	132;170;220;170;170	ENSP00000424947:D132Y;ENSP00000426455:D170Y;ENSP00000422846:D170Y;ENSP00000426059:D170Y	ENSP00000424947:D132Y	D	-	1	0	RNASET2	167264581	0.998000	0.40836	0.807000	0.32361	0.027000	0.11550	1.288000	0.33296	2.045000	0.60652	0.563000	0.77884	GAT		0.393	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730		A	167344591	C	A	167344591	3	1	61	1	0	0	0	0	1	0	0	0	13455	913	32	2	270	2	RNASET2	6	167344591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72901	167344591	3770476	5084	13069										
FGFR1OP	11116	broad.mit.edu	37	chr6	167447412	167447412	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtattggtgaagagataGaagaagacctttctgtggaa	12	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167447412G>T	ENST00000366847.4	+	12	1309	c.1078G>T	c.(1078-1080)Gaa>Taa	p.E360*	RP11-517H2.6_ENST00000609590.1_RNA|FGFR1OP_ENST00000349556.4_Nonsense_Mutation_p.E340*	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	360					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.E340*(1)		large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		TGAAGAGATAGAAGAAGACCT	0.338			T	FGFR1	"MPD, NHL"																																		Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	1	Substitution - Nonsense(1)	large_intestine(1)	6											98	99	99					6																	167447412		2203	4299	6502	167367402	SO:0001587	stop_gained	11116			Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066			17012	protein-coding gene	gene with protein product		605392				9949182, 10373756	Standard	NM_007045		Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.1078G>T	6.37:g.167447412G>T	ENSP00000355812:p.Glu360*		167367402	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	Nonsense_Mutation	SNP	ENST00000366847.4	37	CCDS5296.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939314	0.92526	.	.	ENSG00000213066	ENST00000366847;ENST00000420493;ENST00000349556	.	.	.	5.13	5.13	0.70059	.	0.125962	0.51477	U	0.000083	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-23.5135	17.5512	0.87876	0.0:0.0:1.0:0.0	.	.	.	.	X	360;313;340	.	ENSP00000230248:E340X	E	+	1	0	FGFR1OP	167367402	1.000000	0.71417	0.366000	0.25914	0.988000	0.76386	5.944000	0.70219	2.366000	0.80165	0.650000	0.86243	GAA		0.338	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043099.2	NM_007045		T	167447412	G	T	167447412	4	4	61	1	0	0	0	0	0	1	0	0	5883	943	33	2	1124	2	FGFR1OP	6	167447412	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102821	167447412	3667655	5085	13070										
GPR31	2853	broad.mit.edu	37	chr6	167570744	167570744	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcattgcagaacacgatGaggccaaaggggaggacaaa	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167570744G>T	ENST00000366834.1	-	1	1073	c.576C>A	c.(574-576)ctC>ctA	p.L192L		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	192					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L192L(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		AGAACACGATGAGGCCAAAGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											92	99	96					6																	167570744		2203	4300	6503	167490734	SO:0001819	synonymous_variant	2853			U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.576C>A	6.37:g.167570744G>T			167490734	B0M0K2|Q4VBL3|Q9NQ20	Silent	SNP	ENST00000366834.1	37	CCDS5299.1																																																																																				0.582	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		T	167570744	G	T	167570744	2	4	61	1	0	0	0	0	0	0	0	1	6707	1277	45	2		2	GPR31	6	167570744	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123332	167570744	3544323	5086	13071										
GPR31	2853	broad.mit.edu	37	chr6	167571106	167571106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaggctcaggtagaaggCggccaggaaaggcaggcacg	18	9	1	1	rs200346870		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167571106C>T	ENST00000366834.1	-	1	711	c.214G>A	c.(214-216)Gcc>Acc	p.A72T		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	72					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A72T(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		AGGTAGAAGGCGGCCAGGAAA	0.657													C|||	1	0.000199681	0	0	5008	,	,		17905	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											38	33	35					6																	167571106		2202	4299	6501	167491096	SO:0001583	missense	2853			U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.214G>A	6.37:g.167571106C>T	ENSP00000355799:p.Ala72Thr		167491096	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	37	CCDS5299.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	0.021	-1.430632	0.01117	.	.	ENSG00000120436	ENST00000366834	T	0.37915	1.17	3.54	-1.9	0.07665	GPCR, rhodopsin-like superfamily (1);	0.695757	0.11786	N	0.529700	T	0.08223	0.0205	L	0.43701	1.375	0.09310	N	1	B	0.32731	0.382	B	0.25506	0.061	T	0.26189	-1.0110	10	0.22109	T	0.4	-5.3889	5.6258	0.17482	0.1312:0.5408:0.0:0.328	.	72	O00270	GPR31_HUMAN	T	72	ENSP00000355799:A72T	ENSP00000355799:A72T	A	-	1	0	GPR31	167491096	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.872000	0.04219	-0.063000	0.13065	-0.671000	0.03813	GCC		0.657	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		T	167571106	C	T	167571106	3	4	61	1	0	0	0	0	1	0	0	0	6707	768	27	1	748	1	GPR31	6	167571106	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	362	167571106	3543961	5087	13072										
TTLL2	83887	broad.mit.edu	37	chr6	167752266	167752266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccctcccaggcgaggccGcccaacaccaacactggaga	9	18	0	1	rs200446307	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167752266G>A	ENST00000239587.5	+	2	267	c.179G>A	c.(178-180)cGc>cAc	p.R60H		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	60					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)	p.R60H(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AGGCGAGGCCGCCCAACACCA	0.572													g|||	3	0.000599042	0.0015	0	5008	,	,		18206	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	6											89	61	70					6																	167752266		2203	4300	6503	167672256	SO:0001583	missense	83887			AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.179G>A	6.37:g.167752266G>A	ENSP00000239587:p.Arg60His		167672256	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	5.998	0.368011	0.11352	.	.	ENSG00000120440	ENST00000239587	T	0.02890	4.12	1.57	0.361	0.16107	.	.	.	.	.	T	0.00300	0.0009	N	0.03608	-0.345	0.09310	N	1	P	0.40107	0.703	B	0.18263	0.021	T	0.31081	-0.9956	9	0.15066	T	0.55	.	4.4473	0.11604	0.0:0.0:0.3896:0.6104	.	60	Q9BWV7	TTLL2_HUMAN	H	60	ENSP00000239587:R60H	ENSP00000239587:R60H	R	+	2	0	TTLL2	167672256	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.560000	0.05964	0.102000	0.17638	0.299000	0.19835	CGC		0.572	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167752266	G	A	167752266	3	1	61	1	0	0	0	0	1	0	0	0	16767	1087	38	1	185	1	TTLL2	6	167752266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	181160	167752266	3362801	5088	13073										
TTLL2	83887	broad.mit.edu	37	chr6	167754239	167754239	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcggtttgccacggaaaAgtttgacctcagtaatttgc	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:167754239A>C	ENST00000239587.5	+	3	939	c.851A>C	c.(850-852)aAg>aCg	p.K284T		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	284	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)	p.K284T(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCCACGGAAAAGTTTGACCTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	6											160	165	163					6																	167754239		2203	4300	6503	167674229	SO:0001583	missense	83887			AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.851A>C	6.37:g.167754239A>C	ENSP00000239587:p.Lys284Thr		167674229	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.001698	0.35320	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.08193	3.12	3.59	3.59	0.41128	.	0.080583	0.45606	D	0.000351	T	0.19765	0.0475	M	0.83603	2.65	0.39486	D	0.967965	D	0.89917	1.0	D	0.79784	0.993	T	0.01800	-1.1271	10	0.72032	D	0.01	.	11.4294	0.50032	1.0:0.0:0.0:0.0	.	284	Q9BWV7	TTLL2_HUMAN	T	284;211	ENSP00000239587:K284T	ENSP00000239587:K284T	K	+	2	0	TTLL2	167674229	1.000000	0.71417	0.063000	0.19743	0.043000	0.13939	4.854000	0.62918	1.620000	0.50308	0.397000	0.26171	AAG		0.398	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		C	167754239	A	C	167754239	3	2	61	1	0	0	0	0	1	0	0	0	16767	72	3	4	861	4	TTLL2	6	167754239	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1973	167754239	3360828	5089	13074										
MLLT4	4301	broad.mit.edu	37	chr6	168311795	168311795	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttagaacacaggatgcttCtgggcctgagctgatactac	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:168311795C>A	ENST00000447894.2	+	14	1784	c.1784C>A	c.(1783-1785)tCt>tAt	p.S595Y	MLLT4_ENST00000392108.3_Missense_Mutation_p.S595Y|MLLT4_ENST00000344191.4_Missense_Mutation_p.S595Y|MLLT4_ENST00000392112.1_Missense_Mutation_p.S579Y|MLLT4_ENST00000351017.4_Missense_Mutation_p.S595Y|MLLT4_ENST00000400822.3_Missense_Mutation_p.S594Y|MLLT4_ENST00000366806.2_Missense_Mutation_p.S595Y			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	595					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.S579Y(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		CAGGATGCTTCTGGGCCTGAG	0.363			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	1	Substitution - Missense(1)	large_intestine(1)	6											144	141	142					6																	168311795		2203	4300	6503	168054644	SO:0001583	missense	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1784C>A	6.37:g.168311795C>A	ENSP00000404595:p.Ser595Tyr		168054644	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.14|10.14	1.268871|1.268871	0.23136|0.23136	.|.	.|.	ENSG00000130396|ENSG00000130396	ENST00000423229|ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.|T;T;T;T;T;T;T	.|0.04502	.|3.81;3.72;3.81;3.81;3.61;3.71;3.71	5.3|5.3	3.53|3.53	0.40419|0.40419	.|.	.|0.958916	.|0.08673	.|N	.|0.910684	T|T	0.00998|0.00998	0.0033|0.0033	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.21821	.|0.011;0.037;0.061;0.061	.|B;B;B;B	.|0.26614	.|0.042;0.043;0.071;0.071	T|T	0.49762|0.49762	-0.8905|-0.8905	5|10	.|0.56958	.|D	.|0.05	-4.3227|-4.3227	5.7862|5.7862	0.18334|0.18334	0.1375:0.6381:0.0:0.2244|0.1375:0.6381:0.0:0.2244	.|.	.|293;594;595;579	.|Q96C95;P55196-5;P55196-6;P55196-2	.|.;.;.;.	L|Y	293|595;595;595;595;579;595;594;595	.|ENSP00000341118:S595Y;ENSP00000252692:S595Y;ENSP00000375956:S595Y;ENSP00000355771:S595Y;ENSP00000375960:S579Y;ENSP00000383623:S594Y;ENSP00000404595:S595Y	.|ENSP00000345834:S595Y	F|S	+|+	3|2	2|0	MLLT4|MLLT4	168054644|168054644	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.928000|0.928000	0.56348|0.56348	-0.371000|-0.371000	0.07513|0.07513	0.638000|0.638000	0.30545|0.30545	0.591000|0.591000	0.81541|0.81541	TTC|TCT		0.363	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		A	168311795	C	A	168311795	3	1	61	1	0	0	0	0	1	0	0	0	9659	913	32	2	1838	2	MLLT4	6	168311795	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	557556	168311795	2803272	5090	13075										
MLLT4	4301	broad.mit.edu	37	chr6	168312121	168312121	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagagcgcacacataaagtCattgcagtcgtcaacaagat	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:168312121C>A	ENST00000447894.2	+	15	1989	c.1989C>A	c.(1987-1989)gtC>gtA	p.V663V	MLLT4_ENST00000392108.3_Silent_p.V663V|MLLT4_ENST00000344191.4_Silent_p.V663V|MLLT4_ENST00000392112.1_Silent_p.V647V|MLLT4_ENST00000351017.4_Silent_p.V663V|MLLT4_ENST00000400822.3_Silent_p.V662V|MLLT4_ENST00000366806.2_Silent_p.V663V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	663					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.V647V(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		CACATAAAGTCATTGCAGTCG	0.483			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	6											105	91	96					6																	168312121		2203	4300	6503	168054970	SO:0001819	synonymous_variant	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1989C>A	6.37:g.168312121C>A			168054970	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	C	8.232	0.804798	0.16467	.	.	ENSG00000130396	ENST00000423229	.	.	.	5.5	3.7	0.42460	.	.	.	.	.	T	0.47619	0.1455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	0.5846	10.1366	0.42710	0.0:0.7213:0.1359:0.1428	.	.	.	.	N	362	.	.	H	+	1	0	MLLT4	168054970	1.000000	0.71417	0.977000	0.42913	0.744000	0.42396	1.979000	0.40608	0.651000	0.30788	0.467000	0.42956	CAT		0.483	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		A	168312121	C	A	168312121	2	1	61	1	0	0	0	0	0	0	0	1	9659	813	29	2		2	MLLT4	6	168312121	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	326	168312121	2802946	5091	13076										
MLLT4	4301	broad.mit.edu	37	chr6	168351893	168351893	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgttcccaagaagaacttCgagaagataaagcttaccaa	7	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:168351893C>T	ENST00000447894.2	+	29	3838	c.3838C>T	c.(3838-3840)Cga>Tga	p.R1280*	MLLT4_ENST00000392108.3_Nonsense_Mutation_p.R1280*|MLLT4_ENST00000344191.4_Nonsense_Mutation_p.R1280*|MLLT4_ENST00000392112.1_Nonsense_Mutation_p.R1263*|MLLT4_ENST00000351017.4_Nonsense_Mutation_p.R1287*|MLLT4_ENST00000400822.3_Nonsense_Mutation_p.R1279*|MLLT4_ENST00000366806.2_Nonsense_Mutation_p.R1280*			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1280					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.R1264*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		AGAAGAACTTCGAGAAGATAA	0.378			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	1	Substitution - Nonsense(1)	large_intestine(1)	6											68	70	69					6																	168351893		2203	4300	6503	168094742	SO:0001587	stop_gained	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3838C>T	6.37:g.168351893C>T	ENSP00000404595:p.Arg1280*		168094742	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Nonsense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	C	40	8.019383	0.98613	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.	.	.	5.5	2.46	0.29980	.	0.304658	0.25604	N	0.029535	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2537	15.7486	0.77967	0.5748:0.4252:0.0:0.0	.	.	.	.	X	1280;1287;1280;1280;1263;1280;1279;1280	.	ENSP00000345834:R1280X	R	+	1	2	MLLT4	168094742	0.052000	0.20516	0.082000	0.20525	0.267000	0.26476	0.256000	0.18351	0.722000	0.32252	-0.182000	0.12963	CGA		0.378	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168351893	C	T	168351893	4	4	61	1	0	0	0	0	0	1	0	0	9659	876	31	1	3952	1	MLLT4	6	168351893	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39772	168351893	2763174	5092	13077										
FRMD1	79981	broad.mit.edu	37	chr6	168464367	168464367	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcctccttggggctcaGgccctggcgctcacggtgca	14	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:168464367G>T	ENST00000283309.6	-	6	782	c.718C>A	c.(718-720)Ctg>Atg	p.L240M	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.L172M|FRMD1_ENST00000537786.1_Missense_Mutation_p.L11M	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	240	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)		p.L240M(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TTGGGGCTCAGGCCCTGGCGC	0.642																																					GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)											1	Substitution - Missense(1)	large_intestine(1)	6											89	75	80					6																	168464367		2203	4300	6503	168207216	SO:0001583	missense	79981				CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.718C>A	6.37:g.168464367G>T	ENSP00000283309:p.Leu240Met		168207216	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	G	7.527	0.657943	0.14645	.	.	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.81163	-1.46;-1.46;0.93	2.83	0.801	0.18679	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.104953	0.38837	U	0.001558	T	0.61324	0.2338	L	0.46741	1.465	0.09310	N	1	P;P;P;P	0.46395	0.771;0.877;0.851;0.771	P;P;P;P	0.54026	0.673;0.74;0.623;0.673	T	0.58645	-0.7600	10	0.08599	T	0.76	.	5.4427	0.16517	0.1932:0.0:0.6507:0.156	.	152;240;172;112	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	M	240;172;11	ENSP00000283309:L240M;ENSP00000414115:L172M;ENSP00000440078:L11M	ENSP00000283309:L240M	L	-	1	2	FRMD1	168207216	0.078000	0.21339	0.267000	0.24556	0.229000	0.25112	0.305000	0.19254	0.398000	0.25338	-0.680000	0.03767	CTG		0.642	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		T	168464367	G	T	168464367	3	4	61	1	0	0	0	0	1	0	0	0	6068	991	35	2	955	2	FRMD1	6	168464367	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112474	168464367	2650700	5093	13078										
THBS2	7058	broad.mit.edu	37	chr6	169623400	169623400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctccttgccttgatggcGaatgacccagttgggatcaa	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:169623400G>A	ENST00000366787.3	-	19	3193	c.2944C>T	c.(2944-2946)Cgc>Tgc	p.R982C	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	982	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R982C(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		CCTTGATGGCGAATGACCCAG	0.557																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Missense(1)	large_intestine(1)	6											102	91	95					6																	169623400		2203	4300	6503	169365325	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2944C>T	6.37:g.169623400G>A	ENSP00000355751:p.Arg982Cys		169365325	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822508	0.71028	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.95412	-3.7	4.73	4.73	0.59995	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.41938	U	0.000797	D	0.97093	0.9050	M	0.71581	2.175	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.97517	1.0070	10	0.59425	D	0.04	-34.6025	17.7107	0.88321	0.0:0.0:1.0:0.0	.	982	P35442	TSP2_HUMAN	C	982;240	ENSP00000355751:R982C	ENSP00000355751:R982C	R	-	1	0	THBS2	169365325	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.720000	0.54933	2.150000	0.67090	0.471000	0.43371	CGC		0.557	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		A	169623400	G	A	169623400	3	1	61	1	0	0	0	0	1	0	0	0	15893	1058	37	1	594	1	THBS2	6	169623400	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1159033	169623400	1491667	5094	13079										
THBS2	7058	broad.mit.edu	37	chr6	169629749	169629749	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcaaagtcttcctgcccaGaatttggcagatgggggcag	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:169629749G>T	ENST00000366787.3	-	15	2426	c.2177C>A	c.(2176-2178)tCt>tAt	p.S726Y	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	726					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.S726Y(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		TTCCTGCCCAGAATTTGGCAG	0.483																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Missense(1)	large_intestine(1)	6											160	140	147					6																	169629749		2203	4300	6503	169371674	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2177C>A	6.37:g.169629749G>T	ENSP00000355751:p.Ser726Tyr		169371674	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557130	0.86231	.	.	ENSG00000186340	ENST00000366787	D	0.97906	-4.6	4.51	4.51	0.55191	.	0.000000	0.40385	U	0.001101	D	0.98998	0.9658	M	0.92833	3.35	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.99712	1.1007	10	0.87932	D	0	-26.1935	17.5907	0.87995	0.0:0.0:1.0:0.0	.	726	P35442	TSP2_HUMAN	Y	726	ENSP00000355751:S726Y	ENSP00000355751:S726Y	S	-	2	0	THBS2	169371674	1.000000	0.71417	0.729000	0.30791	0.949000	0.60115	9.159000	0.94728	2.211000	0.71520	0.579000	0.79373	TCT		0.483	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169629749	G	T	169629749	3	4	61	1	0	0	0	0	1	0	0	0	15893	942	33	2	1377	2	THBS2	6	169629749	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6349	169629749	1485318	5095	13080										
THBS2	7058	broad.mit.edu	37	chr6	169648592	169648592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtgctcgtagaagggctCgtccagagcgaagctgtcta	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:169648592C>T	ENST00000366787.3	-	4	778	c.529G>A	c.(529-531)Gag>Aag	p.E177K		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	177	Heparin-binding. {ECO:0000255}.|Laminin G-like.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.E177K(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		TAGAAGGGCTCGTCCAGAGCG	0.612																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Missense(1)	large_intestine(1)	6											77	74	75					6																	169648592		2203	4300	6503	169390517	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.529G>A	6.37:g.169648592C>T	ENSP00000355751:p.Glu177Lys		169390517	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636439	0.87760	.	.	ENSG00000186340	ENST00000366787	T	0.02216	4.39	4.5	4.5	0.54988	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.41396	U	0.000888	T	0.04861	0.0131	M	0.69823	2.125	0.49299	D	0.999771	D	0.89917	1.0	D	0.80764	0.994	T	0.47484	-0.9114	10	0.06891	T	0.86	-50.2577	17.5714	0.87935	0.0:1.0:0.0:0.0	.	177	P35442	TSP2_HUMAN	K	177	ENSP00000355751:E177K	ENSP00000355751:E177K	E	-	1	0	THBS2	169390517	1.000000	0.71417	0.999000	0.59377	0.582000	0.36321	5.608000	0.67654	2.204000	0.70986	0.563000	0.77884	GAG		0.612	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169648592	C	T	169648592	3	4	61	1	0	0	0	0	1	0	0	0	15893	893	31	1	3069	1	THBS2	6	169648592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18843	169648592	1466475	5096	13081										
WDR27	253769	broad.mit.edu	37	chr6	170062510	170062510	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcacttgtagagggaagCtggctttcttctagggacag	14	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170062510C>T	ENST00000448612.1	-	9	1024	c.915G>A	c.(913-915)caG>caA	p.Q305Q	WDR27_ENST00000333572.6_Silent_p.Q305Q|WDR27_ENST00000423258.1_Silent_p.Q178Q|WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000420344.2_3'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	275						nucleus (GO:0005634)		p.Q305Q(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		TAGAGGGAAGCTGGCTTTCTT	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	6											94	96	95					6																	170062510		1910	4146	6056	169804435	SO:0001819	synonymous_variant	253769			AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.915G>A	6.37:g.170062510C>T			169804435	A5PLM8|C9JGV0|Q5T066	Silent	SNP	ENST00000448612.1	37	CCDS47520.2																																																																																				0.448	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		T	170062510	C	T	170062510	2	4	61	1	0	0	0	0	0	0	0	1	17324	796	28	3		3	WDR27	6	170062510	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	413918	170062510	1052557	5097	13082										
PHF10	55274	broad.mit.edu	37	chr6	170105399	170105399	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaagctccattgtcataTccaggcaagaaggatggcct	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170105399T>C	ENST00000339209.4	-	11	1364	c.1241A>G	c.(1240-1242)gAt>gGt	p.D414G	PHF10_ENST00000366780.4_Missense_Mutation_p.D412G|C6orf120_ENST00000332290.2_3'UTR	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	414					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)	p.D326G(1)		endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CATTGTCATATCCAGGCAAGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	6											107	90	96					6																	170105399		2203	4299	6502	169847324	SO:0001583	missense	55274			AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1241A>G	6.37:g.170105399T>C	ENSP00000341805:p.Asp414Gly		169847324	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	37	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896198	0.72639	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.85861	-2.04;-2.04	5.97	5.97	0.96955	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.88596	0.6479	L	0.54323	1.7	0.80722	D	1	D;B	0.71674	0.998;0.256	D;B	0.81914	0.995;0.348	D	0.89307	0.3630	10	0.54805	T	0.06	-30.2833	15.6316	0.76912	0.0:0.0:0.0:1.0	.	412;414	Q8WUB8-2;Q8WUB8	.;PHF10_HUMAN	G	412;414	ENSP00000355743:D412G;ENSP00000341805:D414G	ENSP00000341805:D414G	D	-	2	0	PHF10	169847324	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.457000	0.80775	2.288000	0.76882	0.533000	0.62120	GAT		0.363	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		C	170105399	T	C	170105399	3	2	61	1	0	0	0	0	1	0	0	0	11852	1435	50	4	263	4	PHF10	6	170105399	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	42889	170105399	1009668	5098	13083										
DLL1	28514	broad.mit.edu	37	chr6	170597420	170597420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggcatcgtcccggggacGgcagaaaacggagcagccct	15	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170597420G>A	ENST00000366756.3	-	4	910	c.577C>T	c.(577-579)Cgt>Tgt	p.R193C	FAM120B_ENST00000540480.1_5'Flank	NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	193	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.R193C(1)		NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		TCCCGGGGACGGCAGAAAACG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	6											84	70	74					6																	170597420		2203	4300	6503	170439345	SO:0001583	missense	28514			AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.577C>T	6.37:g.170597420G>A	ENSP00000355718:p.Arg193Cys		170439345	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	37	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634615	0.47049	.	.	ENSG00000198719	ENST00000366756	T	0.03330	3.97	4.35	3.39	0.38822	Delta/Serrate/lag-2 (DSL) protein (3);	0.058856	0.64402	N	0.000003	T	0.17152	0.0412	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.989;1.0	T	0.07424	-1.0773	10	0.87932	D	0	.	14.7455	0.69488	0.0:0.0:0.8456:0.1544	.	193;193	B5M0B3;O00548	.;DLL1_HUMAN	C	193	ENSP00000355718:R193C	ENSP00000355718:R193C	R	-	1	0	DLL1	170439345	1.000000	0.71417	0.995000	0.50966	0.198000	0.23893	4.167000	0.58209	2.258000	0.74832	0.462000	0.41574	CGT		0.627	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			A	170597420	G	A	170597420	3	1	61	1	0	0	0	0	1	0	0	0	4577	1116	39	1	1626	1	DLL1	6	170597420	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	492021	170597420	517647	5099	13084										
DLL1	28514	broad.mit.edu	37	chr6	170597466	170597466	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtagtgttcgtcacacacGaagcggtaggagtacttgag	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170597466G>A	ENST00000366756.3	-	4	864	c.531C>T	c.(529-531)ttC>ttT	p.F177F	FAM120B_ENST00000540480.1_5'Flank	NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	177	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.F177F(1)		NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		CGTCACACACGAAGCGGTAGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	6											79	65	70					6																	170597466		2203	4300	6503	170439391	SO:0001819	synonymous_variant	28514			AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.531C>T	6.37:g.170597466G>A			170439391	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Silent	SNP	ENST00000366756.3	37	CCDS5313.1																																																																																				0.652	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			A	170597466	G	A	170597466	2	1	61	1	0	0	0	0	0	0	0	1	4577	1049	37	1		1	DLL1	6	170597466	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46	170597466	517601	5100	13085										
FAM120B	84498	broad.mit.edu	37	chr6	170626643	170626643	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagatattggtatactccAgaatcttggatctgcggtgg	11	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170626643A>T	ENST00000476287.1	+	2	273	c.165A>T	c.(163-165)ccA>ccT	p.P55P	FAM120B_ENST00000540480.1_Silent_p.P67P|FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000537664.1_Silent_p.P78P	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	55					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P55P(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GGTATACTCCAGAATCTTGGA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6											173	161	165					6																	170626643		2203	4300	6503	170468568	SO:0001819	synonymous_variant	84498			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.165A>T	6.37:g.170626643A>T			170468568	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																				0.443	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		T	170626643	A	T	170626643	2	4	61	1	0	0	0	0	0	0	0	1	5433	175	7	5		5	FAM120B	6	170626643	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29177	170626643	488424	5101	13086										
FAM120B	84498	broad.mit.edu	37	chr6	170667322	170667322	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccttttcaggtggacacGctttgcctggaggatttgca	12	9	1	0	rs150094606		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170667322G>A	ENST00000476287.1	+	6	2307	c.2199G>A	c.(2197-2199)acG>acA	p.T733T	FAM120B_ENST00000252510.9_Silent_p.T65T|FAM120B_ENST00000537664.1_Silent_p.T756T|FAM120B_ENST00000540480.1_Silent_p.T745T	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	733					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.T733T(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AGGTGGACACGCTTTGCCTGG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G		1,4403	2.1+/-5.4	0,1,2201	111	83	92		2199	-9	0	6	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous	FAM120B	NM_032448.1		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		733/911	170667322	1,13003	2202	4300	6502	170509247	SO:0001819	synonymous_variant	84498			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2199G>A	6.37:g.170667322G>A			170509247	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																				0.443	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		A	170667322	G	A	170667322	2	1	61	1	0	0	0	0	0	0	0	1	5433	1074	38	1		1	FAM120B	6	170667322	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40679	170667322	447745	5102	13087										
FAM120B	84498	broad.mit.edu	37	chr6	170697567	170697567	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttatgctgtggaggttCttttagaacaaaatgtgagt	13	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170697567C>A	ENST00000476287.1	+	7	2584	c.2476C>A	c.(2476-2478)Ctt>Att	p.L826I	FAM120B_ENST00000252510.9_Missense_Mutation_p.L158I|FAM120B_ENST00000537664.1_Missense_Mutation_p.L849I|FAM120B_ENST00000540480.1_Missense_Mutation_p.L838I	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	826					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.L826I(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TGTGGAGGTTCTTTTAGAACA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	74	74					6																	170697567		2203	4300	6503	170539492	SO:0001583	missense	84498			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2476C>A	6.37:g.170697567C>A	ENSP00000417970:p.Leu826Ile		170539492	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159520	0.78226	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287;ENST00000252510	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.51	5.51	0.81932	.	0.085279	0.47093	D	0.000251	T	0.48857	0.1523	N	0.24115	0.695	0.38138	D	0.938373	D;D	0.55605	0.972;0.972	P;P	0.60541	0.876;0.876	T	0.50215	-0.8854	10	0.46703	T	0.11	-23.9951	17.5538	0.87885	0.0:1.0:0.0:0.0	.	826;826	Q96EK7;F2Z2E1	F120B_HUMAN;.	I	838;849;826;158	ENSP00000444125:L838I;ENSP00000440125:L849I;ENSP00000417970:L826I;ENSP00000252510:L158I	ENSP00000252510:L158I	L	+	1	0	FAM120B	170539492	0.989000	0.36119	0.085000	0.20634	0.140000	0.21249	3.905000	0.56333	2.745000	0.94114	0.655000	0.94253	CTT		0.438	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		A	170697567	C	A	170697567	3	1	61	1	0	0	0	0	1	0	0	0	5433	913	32	2	2498	2	FAM120B	6	170697567	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30245	170697567	417500	5103	13088										
PDCD2	5134	broad.mit.edu	37	chr6	170886650	170886650	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggctttaagatgcctttaCggtgtatctgttacatcctg	9	8	1	1	rs377450946		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr6:170886650C>T	ENST00000541970.1	-	6	1110	c.1032G>A	c.(1030-1032)ccG>ccA	p.P344P	PDCD2_ENST00000392090.2_Silent_p.P311P	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	344					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)	p.P344P(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		GATGCCTTTACGGTGTATCTG	0.398																																					Colon(60;1476 1726 39478)											1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	2,4404	4.2+/-10.8	0,2,2201	77	74	75		933,1032	-8.6	0	6		75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PDCD2	NM_001199462.1,NM_002598.3	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	311/312,344/345	170886650	2,13004	2203	4300	6503	170728575	SO:0001819	synonymous_variant	5134			AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"Zinc fingers, MYND-type"	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.1032G>A	6.37:g.170886650C>T			170728575	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	37	CCDS5316.1																																																																																				0.398	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		T	170886650	C	T	170886650	2	4	61	1	0	0	0	0	0	0	0	1	11650	523	19	1		1	PDCD2	6	170886650	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	189083	170886650	228417	5104	13089										
NUDT1	29886	broad.mit.edu	37	chr7	2289561	2289561	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccagatcgtgtttgagttCgtgggcgagcctgagctcat	15	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:2289561C>T	ENST00000222990.3	-	0	4727				NUDT1_ENST00000397048.1_Silent_p.F97F|NUDT1_ENST00000356714.1_Silent_p.F74F|NUDT1_ENST00000397049.1_Silent_p.F97F|NUDT1_ENST00000487426.1_3'UTR|NUDT1_ENST00000397046.1_Silent_p.F74F|NUDT1_ENST00000339737.2_Silent_p.F74F|NUDT1_ENST00000343985.4_Silent_p.F97F	NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8						early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.F97F(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		TGTTTGAGTTCGTGGGCGAGC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	7											261	195	217					7																	2289561		2203	4300	6503	2256087	SO:0001628	intergenic_variant	4521			AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"Sorting nexins"	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512		7.37:g.2289561C>T			2256087	A4D207|Q96I67	Silent	SNP	ENST00000222990.3	37	CCDS5331.1																																																																																				0.657	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			T	2289561	C	T	2289561	1	4	61	0	1	0	0	0	0	0	0	0	10756	883	31	1		1	NUDT1	7	2289561	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		2289561	156849102	5105	13090										
EIF3B	8662	broad.mit.edu	37	chr7	2411432	2411432	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgttgtcacaaattttgaAattttccgaatgagggagaa	11	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:2411432A>C	ENST00000360876.4	+	11	1691	c.1635A>C	c.(1633-1635)gaA>gaC	p.E545D	EIF3B_ENST00000397011.2_Missense_Mutation_p.E545D	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B									p.E545D(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		CAAATTTTGAAATTTTCCGAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											111	109	110					7																	2411432		2203	4300	6503	2377958	SO:0001583	missense	8662			U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"RNA binding motif (RRM) containing"	3280	protein-coding gene	gene with protein product		603917	"eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1635A>C	7.37:g.2411432A>C	ENSP00000354125:p.Glu545Asp		2377958		Missense_Mutation	SNP	ENST00000360876.4	37	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.320654	0.81469	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	T;T	0.05513	3.43;3.43	5.62	3.05	0.35203	Translation initiation factor 2A, beta propellor-like domain (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.22282	0.0537	M	0.84511	2.7	0.48288	D	0.999628	D	0.56746	0.977	D	0.64687	0.928	T	0.00249	-1.1879	10	0.72032	D	0.01	-38.8577	7.6369	0.28272	0.7301:0.0:0.2699:0.0	.	545	P55884	EIF3B_HUMAN	D	545;545;545;469	ENSP00000354125:E545D;ENSP00000380206:E545D	ENSP00000316638:E545D	E	+	3	2	EIF3B	2377958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.482000	0.45224	0.325000	0.23359	0.533000	0.62120	GAA		0.413	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			C	2411432	A	C	2411432	3	2	61	1	0	0	0	0	1	0	0	0	5024	11	1	4	1677	4	EIF3B	7	2411432	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	121871	2411432	156727231	5106	13091										
CHST12	55501	broad.mit.edu	37	chr7	2473318	2473318	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagactctggacgaggaCgccgcgcagctgctgcagct	15	13	1	1	rs148612060		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:2473318C>T	ENST00000258711.6	+	2	1179	c.1044C>T	c.(1042-1044)gaC>gaT	p.D348D		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	348					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)	p.D348D(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		TGGACGAGGACGCCGCGCAGC	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	7											39	40	39					7																	2473318		2203	4300	6503	2439844	SO:0001819	synonymous_variant	55501			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.1044C>T	7.37:g.2473318C>T			2439844	A4D1Z9|Q502W3|Q9NXY7	Silent	SNP	ENST00000258711.6	37	CCDS5333.1																																																																																				0.672	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		T	2473318	C	T	2473318	2	4	61	1	0	0	0	0	0	0	0	1	3406	535	19	1		1	CHST12	7	2473318	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61886	2473318	156665345	5107	13092										
SDK1	221935	broad.mit.edu	37	chr7	4002368	4002368	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcctcgatacaaagtgctCgccagcggaggcctgcgcat	11	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4002368C>T	ENST00000404826.2	+	9	1453	c.1314C>T	c.(1312-1314)ctC>ctT	p.L438L	SDK1_ENST00000389531.3_Silent_p.L438L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	438	Ig-like C2-type 4.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L438L(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ACAAAGTGCTCGCCAGCGGAG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	7											48	44	45					7																	4002368		2203	4300	6503	3968894	SO:0001819	synonymous_variant	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1314C>T	7.37:g.4002368C>T			3968894	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.582	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4002368	C	T	4002368	2	4	61	1	0	0	0	0	0	0	0	1	14005	871	31	1		1	SDK1	7	4002368	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1529050	4002368	155136295	5108	13093										
SDK1	221935	broad.mit.edu	37	chr7	4006968	4006968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatatcgctccagtgttcaCccagcggccagtggacacca	10	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4006968C>T	ENST00000404826.2	+	10	1587	c.1448C>T	c.(1447-1449)aCc>aTc	p.T483I	SDK1_ENST00000389531.3_Missense_Mutation_p.T483I	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	483	Ig-like C2-type 5.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T483I(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CCAGTGTTCACCCAGCGGCCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											100	99	99					7																	4006968		2203	4300	6503	3973494	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1448C>T	7.37:g.4006968C>T	ENSP00000385899:p.Thr483Ile		3973494	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	7.216	0.596475	0.13875	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.68624	-0.34;-0.34	5.65	2.89	0.33648	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.508988	0.18332	N	0.144456	T	0.43188	0.1236	N	0.10685	0.025	0.30814	N	0.738517	B	0.14438	0.01	B	0.17979	0.02	T	0.35574	-0.9783	10	0.22706	T	0.39	.	9.9246	0.41485	0.0:0.7161:0.0:0.2839	.	483	Q7Z5N4	SDK1_HUMAN	I	483	ENSP00000385899:T483I;ENSP00000374182:T483I	ENSP00000374182:T483I	T	+	2	0	SDK1	3973494	0.991000	0.36638	0.023000	0.16930	0.468000	0.32798	2.899000	0.48679	0.336000	0.23639	0.655000	0.94253	ACC		0.552	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4006968	C	T	4006968	3	4	61	1	0	0	0	0	1	0	0	0	14005	507	18	3	1486	3	SDK1	7	4006968	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4600	4006968	155131695	5109	13094										
SDK1	221935	broad.mit.edu	37	chr7	4152939	4152939	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatttcgaatgaagcaagtGaacattgttgggccgagccc	12	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4152939G>T	ENST00000404826.2	+	24	3592	c.3453G>T	c.(3451-3453)gtG>gtT	p.V1151V	SDK1_ENST00000389531.3_Silent_p.V1151V	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1151	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V1151V(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGAAGCAAGTGAACATTGTTG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	7											197	207	203					7																	4152939		2203	4300	6503	4119465	SO:0001819	synonymous_variant	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3453G>T	7.37:g.4152939G>T			4119465	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.537	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4152939	G	T	4152939	2	4	61	1	0	0	0	0	0	0	0	1	14005	1277	45	2		2	SDK1	7	4152939	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	145971	4152939	154985724	5110	13095										
SDK1	221935	broad.mit.edu	37	chr7	4169639	4169639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaggcctgcgcaagttcGtgctctacgagctccaggtg	14	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4169639G>A	ENST00000404826.2	+	27	4178	c.4039G>A	c.(4039-4041)Gtg>Atg	p.V1347M	SDK1_ENST00000389531.3_Missense_Mutation_p.V1347M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1347	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V1347M(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCGCAAGTTCGTGCTCTACGA	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	7											55	52	53					7																	4169639		2203	4300	6503	4136165	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4039G>A	7.37:g.4169639G>A	ENSP00000385899:p.Val1347Met		4136165	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617835	0.87359	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.56941	0.43;0.43	5.73	5.73	0.89815	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.172787	0.39687	N	0.001286	T	0.66187	0.2764	L	0.39147	1.195	0.40805	D	0.983372	D;D	0.89917	0.973;1.0	P;D	0.67548	0.476;0.952	T	0.67546	-0.5643	10	0.66056	D	0.02	.	19.9025	0.96993	0.0:0.0:1.0:0.0	.	1347;1347	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	M	1347	ENSP00000385899:V1347M;ENSP00000374182:V1347M	ENSP00000374182:V1347M	V	+	1	0	SDK1	4136165	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.197000	0.77814	2.722000	0.93159	0.655000	0.94253	GTG		0.657	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4169639	G	A	4169639	3	1	61	1	0	0	0	0	1	0	0	0	14005	1145	40	1	4145	1	SDK1	7	4169639	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16700	4169639	154969024	5111	13096										
FOXK1	221937	broad.mit.edu	37	chr7	4780517	4780517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaagatccagttcacgtcGctctatcacaaagaagaggc	8	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4780517G>A	ENST00000328914.4	+	2	609	c.609G>A	c.(607-609)tcG>tcA	p.S203S	FOXK1_ENST00000446823.1_Silent_p.S40S	NM_001037165.1	NP_001032242.1			forkhead box K1									p.S203S(1)|p.S29S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		AGTTCACGTCGCTCTATCACA	0.612																																																2	Substitution - coding silent(2)	large_intestine(2)	7											173	176	175					7																	4780517		2203	4300	6503	4747043	SO:0001819	synonymous_variant	221937			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.609G>A	7.37:g.4780517G>A			4747043		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																				0.612	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			A	4780517	G	A	4780517	2	1	61	1	0	0	0	0	0	0	0	1	6033	1074	38	1		1	FOXK1	7	4780517	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	610878	4780517	154358146	5112	13097										
RADIL	55698	broad.mit.edu	37	chr7	4871799	4871799	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcttctctgctagttctTtggttttctcctacaattac	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4871799T>G	ENST00000399583.3	-	5	1614	c.1427A>C	c.(1426-1428)aAa>aCa	p.K476T	RADIL_ENST00000536091.1_Missense_Mutation_p.K476T|RADIL_ENST00000538469.1_Missense_Mutation_p.K236T	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	476					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.K476T(1)		NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TGCTAGTTCTTTGGTTTTCTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	97	94					7																	4871799		1999	4194	6193	4838325	SO:0001583	missense	55698			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1427A>C	7.37:g.4871799T>G	ENSP00000382492:p.Lys476Thr		4838325	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.491741	0.64074	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000536091;ENST00000538469	T;T;T	0.42513	0.97;1.19;0.97	5.15	3.97	0.46021	.	0.132615	0.49916	D	0.000135	T	0.49830	0.1580	M	0.64630	1.985	0.31880	N	0.618528	D	0.63880	0.993	P	0.55455	0.776	T	0.58239	-0.7671	10	0.41790	T	0.15	-7.535	7.948	0.29998	0.0:0.0954:0.0:0.9046	.	476	Q96JH8	RADIL_HUMAN	T	476;447;210;476;236	ENSP00000382492:K476T;ENSP00000442533:K476T;ENSP00000442966:K236T	ENSP00000320946:K447T	K	-	2	0	RADIL	4838325	1.000000	0.71417	0.998000	0.56505	0.887000	0.51463	2.404000	0.44539	0.782000	0.33613	0.454000	0.30748	AAA		0.527	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		G	4871799	T	G	4871799	3	3	61	1	0	0	0	0	1	0	0	0	13034	1841	64	4	1844	4	RADIL	7	4871799	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	91282	4871799	154266864	5113	13098										
PAPOLB	56903	broad.mit.edu	37	chr7	4899668	4899668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagcgtgaggaatactttCgtttaatgcaacccctgaac	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4899668C>T	ENST00000404991.1	-	1	1957	c.1771G>A	c.(1771-1773)Gaa>Aaa	p.E591K	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	591					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.E591K(1)		kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		GGAATACTTTCGTTTAATGCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7											95	98	97					7																	4899668		2123	4267	6390	4866194	SO:0001583	missense	56903			AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1771G>A	7.37:g.4899668C>T	ENSP00000384700:p.Glu591Lys		4866194	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	37		.	.	.	.	.	.	.	.	.	.	C	2.179	-0.388133	0.04932	.	.	ENSG00000218823	ENST00000404991	.	.	.	4.48	3.6	0.41247	.	.	.	.	.	T	0.25382	0.0617	L	0.34521	1.04	0.21579	N	0.999632	D	0.55385	0.971	B	0.41174	0.349	T	0.04413	-1.0953	8	0.15952	T	0.53	.	10.8626	0.46835	0.0:0.9071:0.0:0.0929	.	592	A4D1Z6	.	K	591	.	ENSP00000384700:E591K	E	-	1	0	PAPOLB	4866194	0.998000	0.40836	0.024000	0.17045	0.027000	0.11550	5.030000	0.64128	1.491000	0.48482	0.591000	0.81541	GAA		0.458	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		T	4899668	C	T	4899668	3	4	61	1	0	0	0	0	1	0	0	0	11461	893	31	1	143	1	PAPOLB	7	4899668	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27869	4899668	154238995	5114	13099										
PAPOLB	56903	broad.mit.edu	37	chr7	4901283	4901283	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagttcctcttcctcttcGaagaccccgaagggcctgag	10	14	2	2	rs368004972		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:4901283G>A	ENST00000404991.1	-	1	342	c.156C>T	c.(154-156)ttC>ttT	p.F52F	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	52					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.F52F(1)		kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		CTTCCTCTTCGAAGACCCCGA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	7											26	26	26					7																	4901283		1912	4150	6062	4867809	SO:0001819	synonymous_variant	56903			AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.156C>T	7.37:g.4901283G>A			4867809	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																					0.502	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		A	4901283	G	A	4901283	2	1	61	1	0	0	0	0	0	0	0	1	11461	1049	37	1		1	PAPOLB	7	4901283	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1615	4901283	154237380	5115	13100										
TNRC18	84629	broad.mit.edu	37	chr7	5396890	5396890	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctggtcgctggccatcttCttcttcttaatctttagctg	7	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:5396890C>A	ENST00000430969.1	-	16	5199	c.4851G>T	c.(4849-4851)aaG>aaT	p.K1617N	TNRC18_ENST00000399537.4_Missense_Mutation_p.K1617N	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1617							chromatin binding (GO:0003682)	p.K1617N(2)|p.K672N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGGCCATCTTCTTCTTCTTAA	0.512																																																3	Substitution - Missense(3)	large_intestine(3)	7											41	42	42					7																	5396890		1994	4176	6170	5363416	SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4851G>T	7.37:g.5396890C>A	ENSP00000395538:p.Lys1617Asn		5363416	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	c	14.81	2.645245	0.47258	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.51071	2.5;2.49;0.72	5.25	4.36	0.52297	.	0.000000	0.41500	D	0.000862	T	0.62319	0.2418	M	0.65498	2.005	0.33686	D	0.612705	D	0.89917	1.0	D	0.69307	0.963	T	0.73279	-0.4033	10	0.62326	D	0.03	.	9.3801	0.38309	0.0:0.8353:0.0:0.1647	.	1617	O15417	TNC18_HUMAN	N	1617;1617;672;107	ENSP00000382452:K1617N;ENSP00000395538:K1617N;ENSP00000395990:K107N	ENSP00000382452:K1617N	K	-	3	2	TNRC18	5363416	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.913000	0.28611	1.186000	0.42985	0.561000	0.74099	AAG		0.512	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5396890	C	A	5396890	3	1	61	1	0	0	0	0	1	0	0	0	16378	912	32	2	4115	2	TNRC18	7	5396890	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	495607	5396890	153741773	5116	13101										
RNF216	54476	broad.mit.edu	37	chr7	5778927	5778927	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattcagatcataataattCttaaaatgaattatttcctc	2	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:5778927C>A	ENST00000425013.2	-	5	1154	c.930G>T	c.(928-930)aaG>aaT	p.K310N	RNF216_ENST00000389902.3_Missense_Mutation_p.K367N	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	310					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.K367N(1)	FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		CATAATAATTCTTAAAATGAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	7											46	50	49					7																	5778927		2200	4295	6495	5745453	SO:0001583	missense	54476			AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.930G>T	7.37:g.5778927C>A	ENSP00000404602:p.Lys310Asn		5745453	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	37	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.390116	0.61956	.	.	ENSG00000011275	ENST00000425013;ENST00000389902;ENST00000458425	T;T	0.48836	0.85;0.8	5.96	3.8	0.43715	.	0.215843	0.39834	N	0.001253	T	0.59362	0.2188	L	0.58101	1.795	0.34773	D	0.733967	P;D	0.76494	0.48;0.999	B;D	0.71414	0.203;0.973	T	0.67126	-0.5749	10	0.49607	T	0.09	-17.5886	8.0634	0.30646	0.0:0.7177:0.0:0.2823	.	310;367	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	N	310;367;122	ENSP00000404602:K310N;ENSP00000374552:K367N	ENSP00000374552:K367N	K	-	3	2	RNF216	5745453	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.731000	0.26058	0.619000	0.30197	-0.142000	0.14014	AAG		0.274	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		A	5778927	C	A	5778927	3	1	61	1	0	0	0	0	1	0	0	0	13517	912	32	2	1722	2	RNF216	7	5778927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382037	5778927	153359736	5117	13102										
DAGLB	221955	broad.mit.edu	37	chr7	6449620	6449620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttgctgaattccgcttCgtgtgaccacttggcgctat	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6449620C>T	ENST00000297056.6	-	15	2036	c.1867G>A	c.(1867-1869)Gaa>Aaa	p.E623K	DAGLB_ENST00000425398.2_Missense_Mutation_p.E494K|DAGLB_ENST00000436575.1_Missense_Mutation_p.E582K	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	623					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.E623K(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		AATTCCGCTTCGTGTGACCAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											109	108	108					7																	6449620		2203	4300	6503	6416145	SO:0001583	missense	221955			AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1867G>A	7.37:g.6449620C>T	ENSP00000297056:p.Glu623Lys		6416145	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	37	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	.	33	5.285609	0.95517	.	.	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575	T;T;T	0.44083	0.94;0.93;0.94	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.64527	0.2606	M	0.76838	2.35	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.71656	0.918;0.963;0.92;0.974	T	0.59369	-0.7467	10	0.15066	T	0.55	-32.3817	19.4545	0.94882	0.0:1.0:0.0:0.0	.	494;437;623;320	B4DQU0;B4DQQ6;Q8NCG7;B3KRA0	.;.;DGLB_HUMAN;.	K	623;494;582	ENSP00000297056:E623K;ENSP00000391171:E494K;ENSP00000404785:E582K	ENSP00000297056:E623K	E	-	1	0	DAGLB	6416145	1.000000	0.71417	0.138000	0.22173	0.992000	0.81027	5.574000	0.67424	2.590000	0.87494	0.650000	0.86243	GAA		0.592	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		T	6449620	C	T	6449620	3	4	61	1	0	0	0	0	1	0	0	0	4233	893	31	1	155	1	DAGLB	7	6449620	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	670693	6449620	152689043	5118	13103										
KDELR2	11014	broad.mit.edu	37	chr7	6513837	6513837	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatagatgtgttatacaatGaaataaatgaagtaaaaaga	7	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6513837G>T	ENST00000258739.4	-	2	354	c.170C>A	c.(169-171)tCa>tAa	p.S57*	KDELR2_ENST00000463747.1_Intron|DAGLB_ENST00000436575.1_Intron|KDELR2_ENST00000490996.1_Nonsense_Mutation_p.S57*	NM_006854.3	NP_006845.1	P33947	ERD22_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	57					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	KDEL sequence binding (GO:0005046)	p.S57*(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GTTATACAATGAAATAAATGA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											95	93	94					7																	6513837		2203	4300	6503	6480362	SO:0001587	stop_gained	11014			X63745	CCDS5351.1, CCDS43550.1	7p	2008-05-02			ENSG00000136240	ENSG00000136240			6305	protein-coding gene	gene with protein product		609024				1316805, 1325562	Standard	NM_006854		Approved	ELP-1, ERD2.2	uc003sqe.4	P33947	OTTHUMG00000023103	ENST00000258739.4:c.170C>A	7.37:g.6513837G>T	ENSP00000258739:p.Ser57*		6480362	A4D2P4|Q6IPC5|Q96E30	Nonsense_Mutation	SNP	ENST00000258739.4	37	CCDS5351.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998682	0.93227	.	.	ENSG00000136240	ENST00000258739;ENST00000490996	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4036	20.3931	0.98965	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000258739:S57X	S	-	2	0	KDELR2	6480362	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.756000	0.98918	2.824000	0.97209	0.655000	0.94253	TCA		0.388	KDELR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059424.2			T	6513837	G	T	6513837	4	4	61	1	0	0	0	0	0	1	0	0	8141	1294	45	2	659	2	KDELR2	7	6513837	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64217	6513837	152624826	5119	13104										
ZDHHC4	55146	broad.mit.edu	37	chr7	6621309	6621309	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcattaccttttccatacGaggtatttctctttcagagt	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6621309G>A	ENST00000396706.2	+	4	632	c.189G>A	c.(187-189)acG>acA	p.T63T	ZDHHC4_ENST00000396709.1_Silent_p.T63T|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000335965.6_Silent_p.T63T|ZDHHC4_ENST00000396713.2_Silent_p.T63T|ZDHHC4_ENST00000396707.2_Silent_p.T63T|ZDHHC4_ENST00000405731.3_Silent_p.T63T			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	63						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.T63T(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TTTTCCATACGAGGTATTTCT	0.373																																																2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	7											124	121	122					7																	6621309		2203	4300	6503	6587834	SO:0001819	synonymous_variant	55146			AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"Zinc fingers, DHHC-type"	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.189G>A	7.37:g.6621309G>A			6587834	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Silent	SNP	ENST00000396706.2	37	CCDS5352.1																																																																																				0.373	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106		A	6621309	G	A	6621309	2	1	61	1	0	0	0	0	0	0	0	1	17656	1045	37	1		1	ZDHHC4	7	6621309	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107472	6621309	152517354	5120	13105										
ZNF12	7559	broad.mit.edu	37	chr7	6730955	6730955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcctttgtgtattctccGatgtctacaaagggctgagt	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6730955G>A	ENST00000405858.1	-	5	2159	c.1618C>T	c.(1618-1620)Cgg>Tgg	p.R540W	AC073343.2_ENST00000577401.1_RNA|ZNF12_ENST00000404360.1_Missense_Mutation_p.R466W|ZNF12_ENST00000342651.5_Missense_Mutation_p.R502W|AC073343.13_ENST00000366167.2_RNA	NM_006956.2|NM_016265.3	NP_008887.2|NP_057349.2	P17014	ZNF12_HUMAN	zinc finger protein 12	540					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R540W(1)		NS(2)|endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(3)	16		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		TGTATTCTCCGATGTCTACAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											51	57	55					7																	6730955		2163	4286	6449	6697480	SO:0001583	missense	7559			X52334, AB021643	CCDS47538.1, CCDS47539.1	7p21.1	2013-01-08	2005-06-09		ENSG00000164631	ENSG00000164631		"Zinc fingers, C2H2-type", "-"	12902	protein-coding gene	gene with protein product		194536	"zinc finger protein 325"	ZNF325			Standard	NM_016265		Approved	KOX3, GIOT-3	uc003sqt.1	P17014	OTTHUMG00000151910	ENST00000405858.1:c.1618C>T	7.37:g.6730955G>A	ENSP00000385939:p.Arg540Trp		6697480	A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	Missense_Mutation	SNP	ENST00000405858.1	37	CCDS47538.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.478010	0.44044	.	.	ENSG00000164631	ENST00000404360;ENST00000405858;ENST00000342651;ENST00000399476	T;T;T	0.18810	2.19;2.19;2.19	4.0	4.0	0.46444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.232242	0.22419	N	0.060303	T	0.41050	0.1142	M	0.71871	2.18	0.19945	N	0.999941	D;D	0.69078	0.997;0.995	P;P	0.60173	0.87;0.707	T	0.17531	-1.0366	10	0.66056	D	0.02	.	14.4017	0.67050	0.0:0.0:1.0:0.0	.	540;502	P17014;P17014-5	ZNF12_HUMAN;.	W	466;540;502;598	ENSP00000384405:R466W;ENSP00000385939:R540W;ENSP00000344745:R502W	ENSP00000344745:R502W	R	-	1	2	ZNF12	6697480	0.121000	0.22262	0.080000	0.20451	0.894000	0.52154	1.316000	0.33620	2.521000	0.84997	0.655000	0.94253	CGG		0.388	ZNF12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324373.2	NM_016265		A	6730955	G	A	6730955	3	1	61	1	0	0	0	0	1	0	0	0	17757	1057	37	1	479	1	ZNF12	7	6730955	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109646	6730955	152407708	5121	13106										
RSPH10B	728194	broad.mit.edu	37	chr7	6797528	6797528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaagatgccagccaatacGaagagtccattctgaccaaa	8	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6797528G>A	ENST00000403107.1	+	2	607	c.220G>A	c.(220-222)Gaa>Aaa	p.E74K	RSPH10B2_ENST00000433859.2_Missense_Mutation_p.E74K|RSPH10B2_ENST00000404077.1_Missense_Mutation_p.E74K|RSPH10B2_ENST00000359718.3_5'UTR|RSPH10B2_ENST00000297186.3_Missense_Mutation_p.E74K			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)	74								p.E74K(2)		breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						CAGCCAATACGAAGAGTCCAT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	7											190	208	202					7																	6797528		2165	4267	6432	6764053	SO:0001583	missense	222967				CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	ENST00000403107.1:c.220G>A	7.37:g.6797528G>A	ENSP00000384766:p.Glu74Lys		6764053	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000403107.1	37	CCDS43552.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.230860	0.58777	.	.	ENSG00000169402	ENST00000403107;ENST00000404077;ENST00000297186;ENST00000433859	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	2.65	2.65	0.31530	.	0.194531	0.33553	N	0.004798	T	0.63248	0.2495	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	P	0.61070	0.883	T	0.64183	-0.6467	10	0.41790	T	0.15	.	11.0959	0.48143	0.0:0.0:1.0:0.0	.	74	B2RC85	R10B2_HUMAN	K	74	ENSP00000384766:E74K;ENSP00000386102:E74K;ENSP00000297186:E74K;ENSP00000416710:E74K	ENSP00000297186:E74K	E	+	1	0	RSPH10B2	6764053	1.000000	0.71417	0.949000	0.38748	0.542000	0.35054	4.909000	0.63314	1.494000	0.48533	0.392000	0.25879	GAA		0.468	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697		A	6797528	G	A	6797528	3	1	61	1	0	0	0	0	1	0	0	0	13740	1059	37	1	2911	1	RSPH10B	7	6797528	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66573	6797528	152341135	5122	13107										
C7orf28B	221960	broad.mit.edu	37	chr7	6851690	6851690	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggttcaagggtccggtaaGaaatcttaaaagcaagaaca	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:6851690G>T	ENST00000316731.8	-	10	1419	c.847C>A	c.(847-849)Ctt>Att	p.L283I	CCZ1B_ENST00000538180.1_Missense_Mutation_p.L140I	NM_198097.3	NP_932765.1	P86790	CCZ1B_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog B (S. cerevisiae)	283						lysosome (GO:0005764)|membrane (GO:0016020)		p.L283I(1)									GGTCCGGTAAGAAATCTTAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											27	27	27					7																	6851690		2136	4267	6403	6818215	SO:0001583	missense	221960			BC010130	CCDS5354.1	7p22.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000146574	ENSG00000146574			21717	protein-coding gene	gene with protein product	"similar to CGI-43 protein"		"chromosome 7 open reading frame 28B"	C7orf28B		12477932	Standard	NM_198097		Approved	DKFZP586I1023, H_NH0577018.2, MGC19819	uc003sqx.2	P86790	OTTHUMG00000152441	ENST00000316731.8:c.847C>A	7.37:g.6851690G>T	ENSP00000314544:p.Leu283Ile		6818215	A2RU45|O95766|Q9UG65|Q9Y359	Missense_Mutation	SNP	ENST00000316731.8	37	CCDS5354.1	.	.	.	.	.	.	.	.	.	.	G	0.022	-1.410398	0.01145	.	.	ENSG00000146574	ENST00000316731;ENST00000538180	.	.	.	2.6	2.6	0.31112	.	0.000000	0.85682	D	0.000000	T	0.37376	0.1001	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.08617	-1.0713	6	0.07813	T	0.8	-15.0487	10.9885	0.47537	0.0:0.0:1.0:0.0	.	.	.	.	I	283;140	.	ENSP00000314544:L283I	L	-	1	0	C7orf28B	6818215	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	4.351000	0.59398	1.460000	0.47911	0.184000	0.17185	CTT		0.393	CCZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246858.1	NM_198097		T	6851690	G	T	6851690	3	4	61	1	0	0	0	0	1	0	0	0	2390	942	33	2	625	2	C7orf28B	7	6851690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54162	6851690	152286973	5123	13108										
COL28A1	340267	broad.mit.edu	37	chr7	7412930	7412930	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtgccttcccccagataCtgcatgttgtccacagccaa	7	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:7412930C>A	ENST00000399429.3	-	32	2747	c.2607G>T	c.(2605-2607)caG>caT	p.Q869H		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	869	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q869H(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCCCCAGATACTGCATGTTGT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											95	91	92					7																	7412930		2033	4196	6229	7379455	SO:0001583	missense	340267			AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2607G>T	7.37:g.7412930C>A	ENSP00000382356:p.Gln869His		7379455	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	8.695	0.908268	0.17833	.	.	ENSG00000215018	ENST00000399429	T	0.78816	-1.21	4.33	3.45	0.39498	von Willebrand factor, type A (3);	0.997979	0.08106	U	0.996938	T	0.74566	0.3733	L	0.39633	1.23	0.33969	D	0.646584	B	0.34241	0.444	P	0.44477	0.451	T	0.73294	-0.4028	10	0.42905	T	0.14	-1.634	4.6654	0.12662	0.1438:0.6091:0.1594:0.0878	.	869	Q2UY09	COSA1_HUMAN	H	869	ENSP00000382356:Q869H	ENSP00000382356:Q869H	Q	-	3	2	COL28A1	7379455	0.180000	0.23148	1.000000	0.80357	0.997000	0.91878	-0.431000	0.06965	1.171000	0.42768	0.655000	0.94253	CAG		0.478	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		A	7412930	C	A	7412930	3	1	61	1	0	0	0	0	1	0	0	0	3692	564	20	2	786	2	COL28A1	7	7412930	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	561240	7412930	151725733	5124	13109										
COL28A1	340267	broad.mit.edu	37	chr7	7413101	7413101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttaatgatctgaaagttCtctggccccacgctttctga	7	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:7413101C>A	ENST00000399429.3	-	32	2576	c.2436G>T	c.(2434-2436)gaG>gaT	p.E812D		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	812	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E812D(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TCTGAAAGTTCTCTGGCCCCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											88	89	89					7																	7413101		1870	4105	5975	7379626	SO:0001583	missense	340267			AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2436G>T	7.37:g.7413101C>A	ENSP00000382356:p.Glu812Asp		7379626	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	5.939	0.357276	0.11239	.	.	ENSG00000215018	ENST00000399429	T	0.77750	-1.12	4.44	0.428	0.16499	von Willebrand factor, type A (3);	1.724680	0.04671	U	0.410691	T	0.65460	0.2693	N	0.25380	0.74	0.25030	N	0.991273	B	0.16396	0.017	B	0.29267	0.1	T	0.48980	-0.8986	10	0.31617	T	0.26	-6.1376	2.726	0.05214	0.1137:0.2905:0.3783:0.2175	.	812	Q2UY09	COSA1_HUMAN	D	812	ENSP00000382356:E812D	ENSP00000382356:E812D	E	-	3	2	COL28A1	7379626	0.000000	0.05858	0.027000	0.17364	0.795000	0.44927	-1.796000	0.01750	-0.036000	0.13669	-0.140000	0.14226	GAG		0.473	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		A	7413101	C	A	7413101	3	1	61	1	0	0	0	0	1	0	0	0	3692	912	32	2	957	2	COL28A1	7	7413101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171	7413101	151725562	5125	13110										
MIOS	54468	broad.mit.edu	37	chr7	7613247	7613247	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatgaatgtacggaagaaGaaaatgataattctttagaa	8	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:7613247G>T	ENST00000340080.4	+	4	1562	c.1141G>T	c.(1141-1143)Gaa>Taa	p.E381*	MIOS_ENST00000405785.1_Nonsense_Mutation_p.E381*	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	381						lysosomal membrane (GO:0005765)		p.E381*(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TACGGAAGAAGAAAATGATAA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											77	74	75					7																	7613247		1832	4083	5915	7579772	SO:0001587	stop_gained	54468				CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.1141G>T	7.37:g.7613247G>T	ENSP00000339881:p.Glu381*		7579772	B2RTV6|O75216|Q7L551|Q9H092	Nonsense_Mutation	SNP	ENST00000340080.4	37	CCDS43554.1	.	.	.	.	.	.	.	.	.	.	G	38	7.264776	0.98175	.	.	ENSG00000164654	ENST00000340080;ENST00000405785	.	.	.	5.49	5.49	0.81192	.	0.109397	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-27.987	19.7592	0.96308	0.0:0.0:1.0:0.0	.	.	.	.	X	381	.	ENSP00000339881:E381X	E	+	1	0	MIOS	7579772	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.306000	0.78905	2.736000	0.93811	0.650000	0.86243	GAA		0.398	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		T	7613247	G	T	7613247	4	4	61	1	0	0	0	0	0	1	0	0	9619	943	33	2	1143	2	MIOS	7	7613247	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	200146	7613247	151525416	5126	13111										
GLCCI1	113263	broad.mit.edu	37	chr7	8043541	8043541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcactttctgtagcggAcaaggcaaaatctcagcaag	8	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:8043541A>G	ENST00000223145.5	+	2	1018	c.461A>G	c.(460-462)gAc>gGc	p.D154G	GLCCI1_ENST00000474269.1_3'UTR|RPA3-AS1_ENST00000469183.1_3'UTR	NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	154						cytoplasm (GO:0005737)		p.D154G(1)		endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		TCTGTAGCGGACAAGGCAAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											101	95	97					7																	8043541		2203	4300	6503	8010066	SO:0001583	missense	113263			BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.461A>G	7.37:g.8043541A>G	ENSP00000223145:p.Asp154Gly		8010066	A4D103|Q96FD0	Missense_Mutation	SNP	ENST00000223145.5	37	CCDS34601.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844504	0.51164	.	.	ENSG00000106415	ENST00000223145;ENST00000414914;ENST00000430798	.	.	.	4.75	4.75	0.60458	.	0.290368	0.32655	N	0.005805	T	0.61565	0.2357	L	0.34521	1.04	0.51767	D	0.99993	D	0.63880	0.993	P	0.60789	0.879	T	0.57648	-0.7775	9	0.25106	T	0.35	-8.8037	15.0225	0.71640	1.0:0.0:0.0:0.0	.	154	Q86VQ1	GLCI1_HUMAN	G	154;42;42	.	ENSP00000223145:D154G	D	+	2	0	GLCCI1	8010066	1.000000	0.71417	1.000000	0.80357	0.390000	0.30446	8.676000	0.91199	2.087000	0.62958	0.456000	0.33151	GAC		0.373	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426		G	8043541	A	G	8043541	3	3	61	1	0	0	0	0	1	0	0	0	6451	275	10	4	467	4	GLCCI1	7	8043541	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	430294	8043541	151095122	5127	13112										
GLCCI1	113263	broad.mit.edu	37	chr7	8124633	8124633	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtgagcgagtgaaggtCtttgaggaaatggcgtaagt	17	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:8124633C>A	ENST00000223145.5	+	7	1841	c.1284C>A	c.(1282-1284)gtC>gtA	p.V428V		NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	428						cytoplasm (GO:0005737)		p.V428V(1)		endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		GAGTGAAGGTCTTTGAGGAAA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	7											141	142	141					7																	8124633		2203	4300	6503	8091158	SO:0001819	synonymous_variant	113263			BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.1284C>A	7.37:g.8124633C>A			8091158	A4D103|Q96FD0	Silent	SNP	ENST00000223145.5	37	CCDS34601.1																																																																																				0.448	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426		A	8124633	C	A	8124633	2	1	61	1	0	0	0	0	0	0	0	1	6451	900	32	2		2	GLCCI1	7	8124633	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81092	8124633	151014030	5128	13113										
NDUFA4	4697	broad.mit.edu	37	chr7	10978469	10978469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacaatgccagacgcaagaGatacagtgttgctccagtag	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:10978469G>T	ENST00000339600.5	-	2	295	c.97C>A	c.(97-99)Ctc>Atc	p.L33I	NDUFA4_ENST00000492822.1_5'Flank|RP5-855F16.1_ENST00000604183.1_lincRNA	NM_002489.3	NP_002480.1	O00483	NDUA4_HUMAN	NDUFA4, mitochondrial complex associated	33					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrial respiratory chain complex IV (GO:0005751)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|protein complex binding (GO:0032403)	p.L33I(1)		large_intestine(2)|lung(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)		AGACGCAAGAGATACAGTGTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	92	91					7																	10978469		2203	4300	6503	10944994	SO:0001583	missense	4697			U94586	CCDS5357.1	7p21.3	2014-07-30	2014-07-30		ENSG00000189043	ENSG00000189043			7687	protein-coding gene	gene with protein product	"complex I 9kDa subunit", "NADH-ubiquinone oxidoreductase MLRQ subunit"	603833	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4 (9kD, MLRQ)", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa"			9352085	Standard	NM_002489		Approved	MLRQ, CI-9k	uc003srx.2	O00483	OTTHUMG00000023880	ENST00000339600.5:c.97C>A	7.37:g.10978469G>T	ENSP00000339720:p.Leu33Ile		10944994	A4D109|Q6FHN5	Missense_Mutation	SNP	ENST00000339600.5	37	CCDS5357.1	.	.	.	.	.	.	.	.	.	.	G	6.176	0.400735	0.11696	.	.	ENSG00000189043	ENST00000339600	T	0.81078	-1.45	4.97	0.917	0.19380	.	0.387478	0.26899	N	0.021930	T	0.62159	0.2405	.	.	.	0.21740	N	0.999567	B	0.10296	0.003	B	0.10450	0.005	T	0.42258	-0.9462	9	0.25106	T	0.35	-0.1184	3.7917	0.08722	0.1481:0.413:0.348:0.091	.	33	O00483	NDUA4_HUMAN	I	33	ENSP00000339720:L33I	ENSP00000339720:L33I	L	-	1	0	NDUFA4	10944994	0.935000	0.31712	0.441000	0.26858	0.024000	0.10985	-0.066000	0.11598	0.050000	0.15949	-0.211000	0.12701	CTC		0.373	NDUFA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207507.3	NM_002489		T	10978469	G	T	10978469	3	4	61	1	0	0	0	0	1	0	0	0	10297	942	33	2	160	2	NDUFA4	7	10978469	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2853836	10978469	148160194	5129	13114										
PHF14	9678	broad.mit.edu	37	chr7	11062550	11062550	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtagcctttggagatattGacaaattacgaccagtaaca	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:11062550G>T	ENST00000403050.3	+	6	1713	c.1261G>T	c.(1261-1263)Gac>Tac	p.D421Y	PHF14_ENST00000445996.2_Missense_Mutation_p.D136Y	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	421					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.D421Y(1)		NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		TGGAGATATTGACAAATTACG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											99	91	93					7																	11062550		1867	4112	5979	11029075	SO:0001583	missense	9678			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1261G>T	7.37:g.11062550G>T	ENSP00000385795:p.Asp421Tyr		11029075	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524108	0.85600	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	T;T	0.14022	2.54;2.54	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.47040	0.1424	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;0.997	D;D;D;D	0.79784	0.971;0.975;0.993;0.972	T	0.52837	-0.8522	10	0.62326	D	0.03	.	19.6736	0.95921	0.0:0.0:1.0:0.0	.	136;136;421;421	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	Y	421;136	ENSP00000385795:D421Y;ENSP00000403907:D136Y	ENSP00000385795:D421Y	D	+	1	0	PHF14	11029075	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.660000	0.90430	0.650000	0.86243	GAC		0.348	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		T	11062550	G	T	11062550	3	4	61	1	0	0	0	0	1	0	0	0	11856	1290	45	2	1283	2	PHF14	7	11062550	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84081	11062550	148076113	5130	13115										
THSD7A	221981	broad.mit.edu	37	chr7	11464376	11464376	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcccgcatattcacaaaGgtcaccttgcagatgctcca	6	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:11464376G>T	ENST00000423059.4	-	16	3581	c.3330C>A	c.(3328-3330)acC>acA	p.T1110T	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1110	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T1110T(1)		NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TATTCACAAAGGTCACCTTGC	0.478										HNSCC(18;0.044)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											207	194	198					7																	11464376		1994	4187	6181	11430901	SO:0001819	synonymous_variant	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.3330C>A	7.37:g.11464376G>T			11430901		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																				0.478	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11464376	G	T	11464376	2	4	61	1	0	0	0	0	0	0	0	1	15918	987	35	2		2	THSD7A	7	11464376	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	401826	11464376	147674287	5131	13116										
SCIN	85477	broad.mit.edu	37	chr7	12665401	12665401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaggtaaagatgctaatCcccaagagaggaaggctgca	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:12665401C>T	ENST00000297029.5	+	7	1008	c.907C>T	c.(907-909)Ccc>Tcc	p.P303S	SCIN_ENST00000473722.1_3'UTR|SCIN_ENST00000445618.2_Missense_Mutation_p.P56S|SCIN_ENST00000519209.1_Missense_Mutation_p.P56S	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	303	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.P303S(2)		endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AGATGCTAATCCCCAAGAGAG	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	7											73	69	70					7																	12665401		1814	4087	5901	12631926	SO:0001583	missense	85477			AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.907C>T	7.37:g.12665401C>T	ENSP00000297029:p.Pro303Ser		12631926	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	C	9.738	1.164178	0.21538	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.56103	0.48;0.48;0.48	5.68	4.79	0.61399	Gelsolin domain (1);	0.174673	0.51477	D	0.000092	T	0.41673	0.1169	L	0.38649	1.16	0.44508	D	0.997458	B	0.02656	0.0	B	0.15052	0.012	T	0.22417	-1.0217	10	0.15952	T	0.53	-4.2362	13.6789	0.62472	0.281:0.719:0.0:0.0	.	303	Q9Y6U3	ADSV_HUMAN	S	303;56;56	ENSP00000297029:P303S;ENSP00000430997:P56S;ENSP00000390189:P56S	ENSP00000297029:P303S	P	+	1	0	SCIN	12631926	0.829000	0.29322	1.000000	0.80357	0.989000	0.77384	1.559000	0.36320	1.389000	0.46526	0.467000	0.42956	CCC		0.348	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		T	12665401	C	T	12665401	3	4	61	1	0	0	0	0	1	0	0	0	13942	855	30	3	933	3	SCIN	7	12665401	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1201025	12665401	146473262	5132	13117										
ETV1	2115	broad.mit.edu	37	chr7	13971370	13971370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggttcagaaagctggcggcGaaatctagggaataagagag	16	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:13971370G>A	ENST00000430479.1	-	9	1226	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	ETV1_ENST00000405218.2_Missense_Mutation_p.R187C|ETV1_ENST00000343495.5_Missense_Mutation_p.R169C|ETV1_ENST00000403685.1_Missense_Mutation_p.R169C|ETV1_ENST00000405192.2_Missense_Mutation_p.R187C|ETV1_ENST00000399357.3_Missense_Mutation_p.R84C|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000242066.5_Missense_Mutation_p.R169C|ETV1_ENST00000420159.2_Missense_Mutation_p.R129C|ETV1_ENST00000403527.1_Missense_Mutation_p.R147C|ETV1_ENST00000405358.4_Missense_Mutation_p.R201C	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	187					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R187C(1)	TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						AGCTGGCGGCGAAATCTAGGG	0.448			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	1	Substitution - Missense(1)	large_intestine(1)	7											74	74	74					7																	13971370		1952	4136	6088	13937895	SO:0001583	missense	2115				CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"ets variant gene 1"			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.559C>T	7.37:g.13971370G>A	ENSP00000405327:p.Arg187Cys		13937895	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	G	32	5.188457	0.94923	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956;ENST00000443608	T;T;T;T;T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	6.13	6.13	0.99165	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.000000	0.40302	N	0.001135	T	0.50326	0.1609	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.959;0.931;0.981;0.995;0.999;0.997;0.953;0.959	T	0.25433	-1.0132	10	0.51188	T	0.08	.	20.8401	0.99726	0.0:0.0:1.0:0.0	.	198;169;201;129;84;147;129;187	Q59GA7;P50549-2;B5MCT2;F5GXR2;B7Z9P2;E9PHB1;B7Z618;P50549	.;.;.;.;.;.;.;ETV1_HUMAN	C	187;169;169;129;84;187;201;147;187;169;129;84	ENSP00000405327:R187C;ENSP00000242066:R169C;ENSP00000340853:R169C;ENSP00000411626:R129C;ENSP00000382293:R84C;ENSP00000385381:R187C;ENSP00000384085:R201C;ENSP00000384138:R147C;ENSP00000385551:R187C;ENSP00000385686:R169C;ENSP00000393078:R129C;ENSP00000394710:R84C	ENSP00000242066:R169C	R	-	1	0	ETV1	13937895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.266000	0.78452	2.932000	0.99384	0.644000	0.83932	CGC		0.448	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		A	13971370	G	A	13971370	3	1	61	1	0	0	0	0	1	0	0	0	5290	1058	37	1	898	1	ETV1	7	13971370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1305969	13971370	145167293	5133	13118										
DGKB	1607	broad.mit.edu	37	chr7	14613907	14613907	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctcatctttgtcattaGgtatgacttcaaacttccac	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:14613907G>T	ENST00000403951.2	-	20	2122	c.1703C>A	c.(1702-1704)cCt>cAt	p.P568H	DGKB_ENST00000444700.2_Missense_Mutation_p.P549H|DGKB_ENST00000406247.3_Missense_Mutation_p.P568H|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000258767.5_Missense_Mutation_p.P568H|DGKB_ENST00000399322.3_Missense_Mutation_p.P568H|DGKB_ENST00000407950.1_Missense_Mutation_p.P560H|DGKB_ENST00000402815.1_Missense_Mutation_p.P567H			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	568	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.P568H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TTTGTCATTAGGTATGACTTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											230	214	219					7																	14613907		1898	4116	6014	14580432	SO:0001583	missense	1607			AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"EF-hand domain containing"	2850	protein-coding gene	gene with protein product		604070	"diacylglycerol kinase, beta (90kD)"	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1703C>A	7.37:g.14613907G>T	ENSP00000385780:p.Pro568His		14580432	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716879	0.89205	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.81163	-1.37;-1.37;-1.37;-1.37;-1.37;-1.36;-1.46	5.54	5.54	0.83059	Diacylglycerol kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90889	0.7137	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.89917	1.0;0.995;0.995;0.999	D;D;D;D	0.74023	0.982;0.929;0.952;0.923	D	0.91107	0.4919	10	0.52906	T	0.07	.	19.4712	0.94963	0.0:0.0:1.0:0.0	.	567;549;568;568	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	H	568;568;568;567;560;549;568	ENSP00000385780:P568H;ENSP00000382260:P568H;ENSP00000258767:P568H;ENSP00000384909:P567H;ENSP00000385031:P560H;ENSP00000388451:P549H;ENSP00000386066:P568H	ENSP00000258767:P568H	P	-	2	0	DGKB	14580432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.597000	0.87782	0.561000	0.74099	CCT		0.373	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		T	14613907	G	T	14613907	3	4	61	1	0	0	0	0	1	0	0	0	4477	1000	35	2	754	2	DGKB	7	14613907	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	642537	14613907	144524756	5134	13119										
DGKB	1607	broad.mit.edu	37	chr7	14775701	14775701	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcttactttttaccattGgactagaatgaggaaacttg	9	7	0	2	rs367918629		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:14775701G>T	ENST00000403951.2	-	5	706	c.287C>A	c.(286-288)cCa>cAa	p.P96Q	DGKB_ENST00000444700.2_Missense_Mutation_p.P89Q|DGKB_ENST00000406247.3_Missense_Mutation_p.P96Q|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000258767.5_Missense_Mutation_p.P96Q|DGKB_ENST00000399322.3_Missense_Mutation_p.P96Q|DGKB_ENST00000407950.1_Missense_Mutation_p.P89Q|DGKB_ENST00000402815.1_Missense_Mutation_p.P96Q			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	96					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.P96Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TTTTACCATTGGACTAGAATG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	GLN/PRO,GLN/PRO	0,3674		0,0,1837	52	52	52		287,287	5.8	1	7		52	1,8181		0,1,4090	no	missense,missense	DGKB	NM_145695.2,NM_004080.2	76,76	0,1,5927	TT,TG,GG		0.0122,0.0,0.0084	benign,benign	96/774,96/805	14775701	1,11855	1837	4091	5928	14742226	SO:0001583	missense	1607			AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"EF-hand domain containing"	2850	protein-coding gene	gene with protein product		604070	"diacylglycerol kinase, beta (90kD)"	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.287C>A	7.37:g.14775701G>T	ENSP00000385780:p.Pro96Gln		14742226	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.190246	0.58017	0.0	1.22E-4	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.81	5.81	0.92471	.	1.269500	0.05290	N	0.520845	T	0.52322	0.1727	M	0.72118	2.19	0.49915	D	0.999835	B;B;B;B	0.28378	0.209;0.169;0.169;0.142	B;B;B;B	0.32149	0.141;0.059;0.141;0.025	T	0.46638	-0.9177	10	0.15952	T	0.53	.	18.8376	0.92169	0.0:0.0:1.0:0.0	.	96;89;96;96	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	Q	96;96;96;96;89;89;96	ENSP00000385780:P96Q;ENSP00000382260:P96Q;ENSP00000258767:P96Q;ENSP00000384909:P96Q;ENSP00000385031:P89Q;ENSP00000388451:P89Q;ENSP00000386066:P96Q	ENSP00000258767:P96Q	P	-	2	0	DGKB	14742226	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	6.113000	0.71553	2.739000	0.93911	0.563000	0.77884	CCA		0.348	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		T	14775701	G	T	14775701	3	4	61	1	0	0	0	0	1	0	0	0	4477	1348	47	2	2230	2	DGKB	7	14775701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161794	14775701	144362962	5135	13120										
TMEM195	392636	broad.mit.edu	37	chr7	15427072	15427072	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaagtcttggtttacctgGaccccatcccggtcccttaa	7	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:15427072G>T	ENST00000342526.3	-	9	1085	c.916C>A	c.(916-918)Cca>Aca	p.P306T		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	306					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.P306T(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						GGTTTACCTGGACCCCATCCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											122	122	122					7																	15427072		2203	4300	6503	15393597	SO:0001583	missense	392636				CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"Fatty acid hydroxylase domain containing"	33784	protein-coding gene	gene with protein product		613738	"transmembrane protein 195"	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.916C>A	7.37:g.15427072G>T	ENSP00000341662:p.Pro306Thr		15393597	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535715	0.85812	.	.	ENSG00000187546	ENST00000342526	T	0.36699	1.24	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.62073	0.2398	M	0.87617	2.895	0.80722	D	1	P	0.52316	0.952	P	0.55615	0.78	T	0.67654	-0.5615	10	0.56958	D	0.05	-8.5947	19.4557	0.94886	0.0:0.0:1.0:0.0	.	306	Q6ZNB7	ALKMO_HUMAN	T	306	ENSP00000341662:P306T	ENSP00000341662:P306T	P	-	1	0	AGMO	15393597	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.720000	0.84759	2.599000	0.87857	0.655000	0.94253	CCA		0.408	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320		T	15427072	G	T	15427072	3	4	61	1	0	0	0	0	1	0	0	0	16156	1174	41	2	441	2	TMEM195	7	15427072	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	651371	15427072	143711591	5136	13121										
TMEM195	392636	broad.mit.edu	37	chr7	15430525	15430525	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtctatgcaataacgatTtctgcctatgagacaaaata	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:15430525T>C	ENST00000342526.3	-	7	851	c.682A>G	c.(682-684)Aat>Gat	p.N228D		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	228					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.N228D(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						CAATAACGATTTCTGCCTATG	0.234																																																1	Substitution - Missense(1)	large_intestine(1)	7											25	26	26					7																	15430525		2154	4264	6418	15397050	SO:0001583	missense	392636				CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"Fatty acid hydroxylase domain containing"	33784	protein-coding gene	gene with protein product		613738	"transmembrane protein 195"	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.682A>G	7.37:g.15430525T>C	ENSP00000341662:p.Asn228Asp		15397050	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.156719	0.78114	.	.	ENSG00000187546	ENST00000342526	T	0.33654	1.4	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.50309	0.1608	L	0.56769	1.78	0.54753	D	0.999987	D	0.60575	0.988	P	0.56648	0.803	T	0.50906	-0.8772	10	0.49607	T	0.09	-9.958	15.224	0.73336	0.0:0.0:0.0:1.0	.	228	Q6ZNB7	ALKMO_HUMAN	D	228	ENSP00000341662:N228D	ENSP00000341662:N228D	N	-	1	0	AGMO	15397050	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.885000	0.75606	2.055000	0.61198	0.482000	0.46254	AAT		0.234	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320		C	15430525	T	C	15430525	3	2	61	1	0	0	0	0	1	0	0	0	16156	1841	64	4	683	4	TMEM195	7	15430525	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3453	15430525	143708138	5137	13122										
ISPD	729920	broad.mit.edu	37	chr7	16348234	16348234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacactcagttccaaattCcaagtcatagtcactacact	3	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:16348234C>T	ENST00000407010.2	-	4	702	c.703G>A	c.(703-705)Gaa>Aaa	p.E235K	ISPD_ENST00000399310.3_Missense_Mutation_p.E185K	NM_001101426.3	NP_001094896.1	A4D126	ISPD_HUMAN	isoprenoid synthase domain containing	235					axon guidance (GO:0007411)|isoprenoid biosynthetic process (GO:0008299)|protein O-linked mannosylation (GO:0035269)		nucleotidyltransferase activity (GO:0016779)	p.E235K(2)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9						GTTCCAAATTCCAAGTCATAG	0.378										Multiple Myeloma(15;0.18)																																						2	Substitution - Missense(2)	large_intestine(2)	7											109	105	106					7																	16348234		1908	4134	6042	16314759	SO:0001583	missense	729920			AK124805		7p21.2	2010-03-19			ENSG00000214960	ENSG00000214960			37276	protein-coding gene	gene with protein product	"notch1-induced protein", "4-diphosphocytidyl-2C-methyl-D-erythritol synthase homolog (Arabidopsis)"	614631				11181995	Standard	NM_001101417		Approved	hCG_1745121, IspD, Nip	uc010ktx.2	A4D126	OTTHUMG00000152447	ENST00000407010.2:c.703G>A	7.37:g.16348234C>T	ENSP00000385478:p.Glu235Lys		16314759	A8MU35|H9KVB2	Missense_Mutation	SNP	ENST00000407010.2	37		.	.	.	.	.	.	.	.	.	.	C	26.0	4.699307	0.88830	.	.	ENSG00000214960	ENST00000407010;ENST00000399310	D;D	0.87103	-2.21;-1.98	5.32	5.32	0.75619	4-diphosphocytidyl-2C-methyl-D-erythritol synthase (1);	0.213545	0.38436	U	0.001691	D	0.89876	0.6842	L	0.33339	1.005	0.53688	D	0.999973	D	0.60160	0.987	D	0.65573	0.936	D	0.89424	0.3712	10	0.44086	T	0.13	-16.1336	19.358	0.94422	0.0:1.0:0.0:0.0	.	235	A4D126	ISPD_HUMAN	K	235;185	ENSP00000385478:E235K;ENSP00000382249:E185K	ENSP00000382249:E185K	E	-	1	0	ISPD	16314759	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.273000	0.72581	2.661000	0.90470	0.655000	0.94253	GAA		0.378	ISPD-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000326252.4	NM_001101426		T	16348234	C	T	16348234	3	4	61	1	0	0	0	0	1	0	0	0	7885	864	30	3	680	3	ISPD	7	16348234	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	917709	16348234	142790429	5138	13123										
BZW2	28969	broad.mit.edu	37	chr7	16714053	16714053	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagatgaaaaagagaaattCgaacccacagtcttcaggga	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:16714053C>T	ENST00000433922.2	+	3	253	c.75C>T	c.(73-75)ttC>ttT	p.F25F	BZW2_ENST00000405202.1_5'UTR|BZW2_ENST00000432311.1_3'UTR|BZW2_ENST00000452975.2_Silent_p.F25F|BZW2_ENST00000258761.3_Silent_p.F25F	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	25					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)		p.F25F(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		AAGAGAAATTCGAACCCACAG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	7											84	84	84					7																	16714053		2203	4300	6503	16680578	SO:0001819	synonymous_variant	28969			AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.75C>T	7.37:g.16714053C>T			16680578	A4D123|Q3B779|Q96JW5|Q9H3F7	Silent	SNP	ENST00000433922.2	37	CCDS5362.1																																																																																				0.333	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038		T	16714053	C	T	16714053	2	4	61	1	0	0	0	0	0	0	0	1	1582	883	31	1		1	BZW2	7	16714053	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	365819	16714053	142424610	5139	13124										
BZW2	28969	broad.mit.edu	37	chr7	16745690	16745690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttctctcctagaatccGaatcggaaggtgaggaaaat	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:16745690G>A	ENST00000433922.2	+	12	1415	c.1237G>A	c.(1237-1239)Gaa>Aaa	p.E413K	AC073333.8_ENST00000418907.1_RNA|BZW2_ENST00000407633.1_Missense_Mutation_p.E219K|BZW2_ENST00000405202.1_Missense_Mutation_p.E337K|BZW2_ENST00000258761.3_Missense_Mutation_p.E413K	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	413	W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)		p.E413K(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		CCTAGAATCCGAATCGGAAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											129	126	127					7																	16745690		2203	4300	6503	16712215	SO:0001583	missense	28969			AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.1237G>A	7.37:g.16745690G>A	ENSP00000397249:p.Glu413Lys		16712215	A4D123|Q3B779|Q96JW5|Q9H3F7	Missense_Mutation	SNP	ENST00000433922.2	37	CCDS5362.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440280	0.63067	.	.	ENSG00000136261	ENST00000258761;ENST00000433922;ENST00000405202;ENST00000407633	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.55	5.55	0.83447	eIF4-gamma/eIF5/eIF2-epsilon (2);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	D	0.94788	0.8317	H	0.94462	3.54	0.80722	D	1	D	0.61080	0.989	D	0.71656	0.974	D	0.95406	0.8494	10	0.66056	D	0.02	-36.6725	19.8667	0.96806	0.0:0.0:1.0:0.0	.	413	Q9Y6E2	BZW2_HUMAN	K	413;413;337;219	ENSP00000258761:E413K;ENSP00000397249:E413K;ENSP00000385577:E337K;ENSP00000384617:E219K	ENSP00000258761:E413K	E	+	1	0	BZW2	16712215	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	6.733000	0.74796	2.773000	0.95371	0.655000	0.94253	GAA		0.418	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038		A	16745690	G	A	16745690	3	1	61	1	0	0	0	0	1	0	0	0	1582	1059	37	1	1279	1	BZW2	7	16745690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31637	16745690	142392973	5140	13125										
AHR	196	broad.mit.edu	37	chr7	17369639	17369639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaccgagctgaatttcagCgtcagctacactgggcatta	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:17369639C>T	ENST00000242057.4	+	5	1157	c.514C>T	c.(514-516)Cgt>Tgt	p.R172C		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	172	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R172C(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TGAATTTCAGCGTCAGCTACA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											86	87	86					7																	17369639		2203	4300	6503	17336164	SO:0001583	missense	196			L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.514C>T	7.37:g.17369639C>T	ENSP00000242057:p.Arg172Cys		17336164	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076620	0.55753	.	.	ENSG00000106546	ENST00000242057	T	0.19394	2.15	5.92	5.03	0.67393	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.45216	0.1331	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	T	0.41360	-0.9513	10	0.45353	T	0.12	.	16.4323	0.83853	0.1325:0.8675:0.0:0.0	.	172	P35869	AHR_HUMAN	C	172	ENSP00000242057:R172C	ENSP00000242057:R172C	R	+	1	0	AHR	17336164	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.205000	0.72148	1.477000	0.48234	0.655000	0.94253	CGT		0.373	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		T	17369639	C	T	17369639	3	4	61	1	0	0	0	0	1	0	0	0	416	768	27	1	532	1	AHR	7	17369639	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	623949	17369639	141769024	5141	13126										
AHR	196	broad.mit.edu	37	chr7	17379658	17379658	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactacttctagtttagaaGattttgtcacttgtttacaa	5	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:17379658G>T	ENST00000242057.4	+	10	2852	c.2209G>T	c.(2209-2211)Gat>Tat	p.D737Y		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	737					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D737Y(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TAGTTTAGAAGATTTTGTCAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	7											113	108	110					7																	17379658		2203	4300	6503	17346183	SO:0001583	missense	196			L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.2209G>T	7.37:g.17379658G>T	ENSP00000242057:p.Asp737Tyr		17346183	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.284160	0.59867	.	.	ENSG00000106546	ENST00000242057	T	0.56275	0.47	5.25	4.37	0.52481	.	0.399738	0.27886	N	0.017455	T	0.64238	0.2580	M	0.76328	2.33	0.42388	D	0.992517	P	0.44659	0.84	P	0.49502	0.613	T	0.71321	-0.4628	10	0.72032	D	0.01	.	16.1502	0.81611	0.0:0.1334:0.8665:0.0	.	737	P35869	AHR_HUMAN	Y	737	ENSP00000242057:D737Y	ENSP00000242057:D737Y	D	+	1	0	AHR	17346183	1.000000	0.71417	0.993000	0.49108	0.883000	0.51084	3.697000	0.54764	1.443000	0.47586	-0.156000	0.13503	GAT		0.423	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		T	17379658	G	T	17379658	3	4	61	1	0	0	0	0	1	0	0	0	416	942	33	2	2247	2	AHR	7	17379658	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10019	17379658	141759005	5142	13127										
SNX13	23161	broad.mit.edu	37	chr7	17854462	17854462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctgcttacttaccttgcGagcaaaatccccttttcctt	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:17854462G>A	ENST00000409389.1	-	20	2264	c.2092C>T	c.(2092-2094)Cgc>Tgc	p.R698C	SNX13_ENST00000428135.3_Missense_Mutation_p.R687C|SNX13_ENST00000496855.1_5'UTR			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	698					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.R687C(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					CTTACCTTGCGAGCAAAATCC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											85	81	82					7																	17854462		1856	4095	5951	17820987	SO:0001583	missense	23161			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.2092C>T	7.37:g.17854462G>A	ENSP00000386705:p.Arg698Cys		17820987	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	G	24.1	4.492210	0.84962	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.21734	1.99;2.28	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.44871	0.1314	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.964;0.917;0.993	T	0.20806	-1.0264	10	0.52906	T	0.07	-5.9617	14.844	0.70246	0.0:0.0:0.8562:0.1437	.	484;698;687	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	C	698;687;735	ENSP00000386705:R698C;ENSP00000398789:R687C	ENSP00000242044:R735C	R	-	1	0	SNX13	17820987	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.469000	0.80959	2.737000	0.93849	0.563000	0.77884	CGC		0.388	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		A	17854462	G	A	17854462	3	1	61	1	0	0	0	0	1	0	0	0	14921	1058	37	1	842	1	SNX13	7	17854462	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	474804	17854462	141284201	5143	13128										
SNX13	23161	broad.mit.edu	37	chr7	17879586	17879586	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccactgtcatccaaaaGaatagatgtgcttgacctcc	6	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:17879586G>T	ENST00000409389.1	-	13	1375	c.1203C>A	c.(1201-1203)ttC>ttA	p.F401L	SNX13_ENST00000428135.3_Missense_Mutation_p.F401L			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	401	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.F401L(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TCATCCAAAAGAATAGATGTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											115	103	106					7																	17879586		1888	4120	6008	17846111	SO:0001583	missense	23161			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1203C>A	7.37:g.17879586G>T	ENSP00000386705:p.Phe401Leu		17846111	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	G	17.35	3.366600	0.61513	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.01767	4.65;4.65	5.25	5.25	0.73442	.	0.000000	0.64402	U	0.000001	T	0.03095	0.0091	N	0.20530	0.585	0.80722	D	1	D;B;D	0.62365	0.959;0.444;0.991	P;B;P	0.59424	0.696;0.374;0.857	T	0.68618	-0.5361	10	0.22706	T	0.39	-6.5791	10.4533	0.44535	0.1207:0.0:0.8793:0.0	.	198;401;401	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	L	401;401;449	ENSP00000386705:F401L;ENSP00000398789:F401L	ENSP00000242044:F449L	F	-	3	2	SNX13	17846111	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.857000	0.55972	2.595000	0.87683	0.557000	0.71058	TTC		0.398	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		T	17879586	G	T	17879586	3	4	61	1	0	0	0	0	1	0	0	0	14921	933	33	2	1726	2	SNX13	7	17879586	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25124	17879586	141259077	5144	13129										
HDAC9	9734	broad.mit.edu	37	chr7	18631236	18631236	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaatggaaaaaatcattcCgtgagccgccatcccaagct	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:18631236C>T	ENST00000432645.2	+	4	504	c.504C>T	c.(502-504)tcC>tcT	p.S168S	HDAC9_ENST00000406072.1_Silent_p.S199S|HDAC9_ENST00000524023.1_Silent_p.S137S|HDAC9_ENST00000405010.3_Silent_p.S168S|HDAC9_ENST00000417496.2_Silent_p.S210S|HDAC9_ENST00000441542.2_Silent_p.S171S|HDAC9_ENST00000456174.2_Silent_p.S140S|HDAC9_ENST00000428307.2_Silent_p.S168S|HDAC9_ENST00000401921.1_Silent_p.S171S|HDAC9_ENST00000406451.4_Silent_p.S168S	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	168					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.S171S(2)|p.S168S(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AAAATCATTCCGTGAGCCGCC	0.463																																																3	Substitution - coding silent(3)	large_intestine(3)	7											84	86	85					7																	18631236		1952	4151	6103	18597761	SO:0001819	synonymous_variant	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.504C>T	7.37:g.18631236C>T			18597761	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																				0.463	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18631236	C	T	18631236	2	4	61	1	0	0	0	0	0	0	0	1	7035	639	23	1		1	HDAC9	7	18631236	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	751650	18631236	140507427	5145	13130										
TWISTNB	221830	broad.mit.edu	37	chr7	19738023	19738023	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcactgtgttttcttttCttttttttctttttatggtc	4	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:19738023C>A	ENST00000222567.5	-	4	1003	c.933G>T	c.(931-933)aaG>aaT	p.K311N		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	311	Lys-rich.				transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)	p.K311N(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						GTTTTCTTTTCTTTTTTTTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	118	113					7																	19738023		2200	4298	6498	19704548	SO:0001583	missense	221830			AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.933G>T	7.37:g.19738023C>A	ENSP00000222567:p.Lys311Asn		19704548	A0PJ45|B7Z724	Missense_Mutation	SNP	ENST00000222567.5	37	CCDS34606.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036899	0.75617	.	.	ENSG00000105849	ENST00000222567	.	.	.	5.84	4.96	0.65561	.	0.093402	0.85682	D	0.000000	T	0.66107	0.2756	L	0.60455	1.87	0.49582	D	0.999809	D	0.56035	0.974	P	0.53450	0.726	T	0.70238	-0.4927	9	0.72032	D	0.01	-16.0885	14.7917	0.69846	0.0:0.9309:0.0:0.0691	.	311	Q3B726	RPA43_HUMAN	N	311	.	ENSP00000222567:K311N	K	-	3	2	TWISTNB	19704548	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.915000	0.39976	1.475000	0.48197	0.484000	0.47621	AAG		0.383	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			A	19738023	C	A	19738023	3	1	61	1	0	0	0	0	1	0	0	0	16824	912	32	2	87	2	TWISTNB	7	19738023	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1106787	19738023	139400640	5146	13131										
TWISTNB	221830	broad.mit.edu	37	chr7	19744435	19744435	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggttcagggcagaaaatAacaaaatcggcttcaatgtt	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:19744435A>C	ENST00000222567.5	-	2	433	c.363T>G	c.(361-363)gtT>gtG	p.V121V	MIR3146_ENST00000580367.1_RNA	NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	121					transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)	p.V121V(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						GGCAGAAAATAACAAAATCGG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	7											75	75	75					7																	19744435		2203	4300	6503	19710960	SO:0001819	synonymous_variant	221830			AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.363T>G	7.37:g.19744435A>C			19710960	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																				0.353	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			C	19744435	A	C	19744435	2	2	61	1	0	0	0	0	0	0	0	1	16824	349	13	4		4	TWISTNB	7	19744435	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6412	19744435	139394228	5147	13132										
MACC1	346389	broad.mit.edu	37	chr7	20199715	20199715	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagatggaaatattatttCtcttcctgttatttcttagt	5	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20199715C>A	ENST00000400331.5	-	5	577	c.269G>T	c.(268-270)aGa>aTa	p.R90I	MACC1_ENST00000332878.4_Missense_Mutation_p.R90I|MACC1_ENST00000589011.1_Missense_Mutation_p.R90I	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	90					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R90I(1)		endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						AATATTATTTCTCTTCCTGTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											42	45	44					7																	20199715		2203	4300	6503	20166240	SO:0001583	missense	346389				CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.269G>T	7.37:g.20199715C>A	ENSP00000383185:p.Arg90Ile		20166240	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	C	4.014	-0.000069	0.07819	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.10192	2.9;2.9	5.97	-1.17	0.09648	.	0.956548	0.08831	N	0.887326	T	0.12944	0.0314	L	0.57536	1.79	0.24652	N	0.993518	B	0.14438	0.01	B	0.09377	0.004	T	0.34675	-0.9819	10	0.66056	D	0.02	-5.5534	11.8978	0.52665	0.0:0.4423:0.0:0.5577	.	90	Q6ZN28	MACC1_HUMAN	I	90	ENSP00000383185:R90I;ENSP00000328410:R90I	ENSP00000328410:R90I	R	-	2	0	MACC1	20166240	0.290000	0.24343	0.010000	0.14722	0.247000	0.25773	0.479000	0.22228	-0.130000	0.11599	0.585000	0.79938	AGA		0.338	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20199715	C	A	20199715	3	1	61	1	0	0	0	0	1	0	0	0	9173	913	32	2	2301	2	MACC1	7	20199715	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455280	20199715	138938948	5148	13133										
ITGB8	3696	broad.mit.edu	37	chr7	20441524	20441524	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtagatgaaacttttctaGattccaagtgtttccagtgt	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20441524G>T	ENST00000222573.4	+	10	2146	c.1462G>T	c.(1462-1464)Gat>Tat	p.D488Y	ITGB8_ENST00000537992.1_Missense_Mutation_p.D353Y	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	488	Cysteine-rich tandem repeats.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)	p.D488Y(2)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AACTTTTCTAGATTCCAAGTG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	7											167	172	170					7																	20441524		2203	4300	6503	20408049	SO:0001583	missense	3696				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1462G>T	7.37:g.20441524G>T	ENSP00000222573:p.Asp488Tyr		20408049	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	37	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.557262	0.65425	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.90620	-2.7;-2.59	5.66	5.66	0.87406	.	0.070102	0.64402	D	0.000020	D	0.92857	0.7728	L	0.59436	1.845	0.46725	D	0.99917	D	0.56521	0.976	P	0.53185	0.72	D	0.92918	0.6353	10	0.66056	D	0.02	.	20.1156	0.97930	0.0:0.0:1.0:0.0	.	488	P26012	ITB8_HUMAN	Y	353;488	ENSP00000441561:D353Y;ENSP00000222573:D488Y	ENSP00000222573:D488Y	D	+	1	0	ITGB8	20408049	1.000000	0.71417	0.189000	0.23252	0.805000	0.45488	7.964000	0.87933	2.824000	0.97209	0.655000	0.94253	GAT		0.383	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		T	20441524	G	T	20441524	3	4	61	1	0	0	0	0	1	0	0	0	7922	942	33	2	1500	2	ITGB8	7	20441524	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241809	20441524	138697139	5149	13134										
ABCB5	340273	broad.mit.edu	37	chr7	20687254	20687254	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagctgcctttcatattTtccaggttattgataaggta	10	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20687254T>G	ENST00000404938.2	+	10	1730	c.1078T>G	c.(1078-1080)Ttc>Gtc	p.F360V	ABCB5_ENST00000406935.1_5'UTR|ABCB5_ENST00000443026.2_5'UTR|ABCB5_ENST00000258738.6_5'UTR|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	360					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CTTTCATATTTTCCAGGTTAT	0.383																																																0			7											58	52	54					7																	20687254		1564	3581	5145	20653779	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1078T>G	7.37:g.20687254T>G	ENSP00000384881:p.Phe360Val		20653779	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477616	0.84640	.	.	ENSG00000004846	ENST00000404938	D	0.82081	-1.57	4.09	4.09	0.47781	.	.	.	.	.	D	0.91888	0.7432	M	0.91249	3.19	0.80722	D	1	D	0.76494	0.999	D	0.71870	0.975	D	0.93419	0.6775	9	0.87932	D	0	.	12.8739	0.57980	0.0:0.0:0.0:1.0	.	360	A7BKA4	.	V	360	ENSP00000384881:F360V	ENSP00000384881:F360V	F	+	1	0	ABCB5	20653779	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.258000	0.78371	2.087000	0.62958	0.533000	0.62120	TTC		0.383	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20687254	T	G	20687254	3	3	61	1	0	0	0	0	1	0	0	0	44	1841	64	4	1112	4	ABCB5	7	20687254	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	245730	20687254	138451409	5150	13135										
ABCB5	340273	broad.mit.edu	37	chr7	20689690	20689690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagtctggagagacagtcGccttggtcggtctcaatggc	13	9	2	1	rs372984477		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20689690G>A	ENST00000404938.2	+	12	1904	c.1252G>A	c.(1252-1254)Gcc>Acc	p.A418T	ABCB5_ENST00000406935.1_5'UTR|ABCB5_ENST00000443026.2_5'UTR|ABCB5_ENST00000258738.6_5'UTR|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	418	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AGAGACAGTCGCCTTGGTCGG	0.438																																																0			7						G	THR/ALA,,,	1,3135		0,1,1567	89	78	81		1252,,,	5.1	1	7		81	1,7163		0,1,3581	no	missense,utr-5,utr-5,utr-5	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	58,,,	0,2,5148	AA,AG,GG		0.014,0.0319,0.0194	probably-damaging,,,	418/1258,,,	20689690	2,10298	1568	3582	5150	20656215	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1252G>A	7.37:g.20689690G>A	ENSP00000384881:p.Ala418Thr		20656215	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	34	5.354245	0.95830	3.19E-4	1.4E-4	ENSG00000004846	ENST00000404938	D	0.93859	-3.3	5.14	5.14	0.70334	.	.	.	.	.	D	0.96917	0.8993	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97238	0.9889	9	0.87932	D	0	.	18.4761	0.90793	0.0:0.0:1.0:0.0	.	418	A7BKA4	.	T	418	ENSP00000384881:A418T	ENSP00000384881:A418T	A	+	1	0	ABCB5	20656215	1.000000	0.71417	0.985000	0.45067	0.835000	0.47333	7.758000	0.85224	2.775000	0.95449	0.650000	0.86243	GCC		0.438	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		A	20689690	G	A	20689690	3	1	61	1	0	0	0	0	1	0	0	0	44	1087	38	1	1294	1	ABCB5	7	20689690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2436	20689690	138448973	5151	13136										
ABCB5	340273	broad.mit.edu	37	chr7	20738058	20738058	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgaagtctctctattaaAaattttaaagttaaacaagc	4	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20738058A>C	ENST00000404938.2	+	17	2691	c.2039A>C	c.(2038-2040)aAa>aCa	p.K680T	ABCB5_ENST00000258738.6_Missense_Mutation_p.K235T	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	680					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)	p.K235T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TCTCTATTAAAAATTTTAAAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7											54	57	56					7																	20738058		2201	4295	6496	20704583	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2039A>C	7.37:g.20738058A>C	ENSP00000384881:p.Lys680Thr		20704583	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.810299	0.32053	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.81499	-1.5;-1.5	5.55	4.36	0.52297	ABC transporter, transmembrane domain, type 1 (1);	0.083397	0.47455	N	0.000230	T	0.71273	0.3320	L	0.31476	0.935	0.37196	D	0.90416	B;B	0.24533	0.105;0.052	B;B	0.28784	0.04;0.094	T	0.70572	-0.4835	10	0.51188	T	0.08	.	11.0134	0.47675	0.8436:0.1564:0.0:0.0	.	680;235	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	T	680;235	ENSP00000384881:K680T;ENSP00000258738:K235T	ENSP00000258738:K235T	K	+	2	0	ABCB5	20704583	1.000000	0.71417	1.000000	0.80357	0.436000	0.31835	2.457000	0.45005	0.995000	0.38917	0.482000	0.46254	AAA		0.343	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		C	20738058	A	C	20738058	3	2	61	1	0	0	0	0	1	0	0	0	44	14	1	4	2142	4	ABCB5	7	20738058	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	48368	20738058	138400605	5152	13137										
ABCB5	340273	broad.mit.edu	37	chr7	20784912	20784912	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggctccgttcccaaataGcaatcgttcctcaagagcct	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:20784912G>T	ENST00000404938.2	+	26	3932	c.3280G>T	c.(3280-3282)Gca>Tca	p.A1094S	ABCB5_ENST00000258738.6_Missense_Mutation_p.A649S	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	1094	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)	p.A649S(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TTCCCAAATAGCAATCGTTCC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7											149	137	141					7																	20784912		2203	4300	6503	20751437	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.3280G>T	7.37:g.20784912G>T	ENSP00000384881:p.Ala1094Ser		20751437	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989537	0.53934	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.93247	-3.19;-3.19	5.32	4.39	0.52855	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.56097	D	0.000031	D	0.91603	0.7347	L	0.42529	1.33	0.38401	D	0.945654	B;B	0.32781	0.024;0.384	B;B	0.39935	0.042;0.314	D	0.91827	0.5472	10	0.46703	T	0.11	.	15.5679	0.76309	0.0:0.1382:0.8618:0.0	.	1094;649	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	S	1094;649	ENSP00000384881:A1094S;ENSP00000258738:A649S	ENSP00000258738:A649S	A	+	1	0	ABCB5	20751437	1.000000	0.71417	0.929000	0.37066	0.417000	0.31264	7.778000	0.85637	2.642000	0.89623	0.655000	0.94253	GCA		0.458	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		T	20784912	G	T	20784912	3	4	61	1	0	0	0	0	1	0	0	0	44	971	34	2	3419	2	ABCB5	7	20784912	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46854	20784912	138353751	5153	13138										
DNAH11	8701	broad.mit.edu	37	chr7	21628830	21628830	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccttattcctacagatttTtgggcaatcctgatcacgct	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21628830T>G	ENST00000409508.3	+	12	2009	c.1978T>G	c.(1978-1980)Ttg>Gtg	p.L660V	DNAH11_ENST00000328843.6_Missense_Mutation_p.L660V	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	660	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L660V(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						CTACAGATTTTTGGGCAATCC	0.279									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											77	73	74					7																	21628830		1809	4071	5880	21595355	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.1978T>G	7.37:g.21628830T>G	ENSP00000475939:p.Leu660Val		21595355	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	1.474	-0.559100	0.03967	.	.	ENSG00000105877	ENST00000328843	T	0.56776	0.44	5.58	0.557	0.17260	Dynein heavy chain, domain-1 (1);	1.409190	0.04988	N	0.466883	T	0.36082	0.0954	.	.	.	0.22412	N	0.999128	B	0.12630	0.006	B	0.14578	0.011	T	0.19614	-1.0300	9	0.41790	T	0.15	.	1.2699	0.02019	0.1354:0.2325:0.1405:0.4917	.	660	Q96DT5	DYH11_HUMAN	V	660	ENSP00000330671:L660V	ENSP00000330671:L660V	L	+	1	2	DNAH11	21595355	0.085000	0.21516	0.130000	0.21974	0.015000	0.08874	-0.056000	0.11787	-0.124000	0.11724	-1.123000	0.02005	TTG		0.279	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21628830	T	G	21628830	3	3	61	1	0	0	0	0	1	0	0	0	4610	1838	64	4	2024	4	DNAH11	7	21628830	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	843918	21628830	137509833	5154	13139										
DNAH11	8701	broad.mit.edu	37	chr7	21640664	21640664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtatgttcaaatgagcAaatttgaggactttagagtg	10	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21640664A>G	ENST00000409508.3	+	17	3323	c.3292A>G	c.(3292-3294)Aaa>Gaa	p.K1098E	DNAH11_ENST00000328843.6_Missense_Mutation_p.K1098E	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1098	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K1098E(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TCAAATGAGCAAATTTGAGGA	0.338									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											125	118	120					7																	21640664		1834	4092	5926	21607189	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3292A>G	7.37:g.21640664A>G	ENSP00000475939:p.Lys1098Glu		21607189	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	A	1.379	-0.584037	0.03827	.	.	ENSG00000105877	ENST00000328843	T	0.21932	1.98	5.43	5.43	0.79202	.	0.441505	0.24783	N	0.035633	T	0.08582	0.0213	.	.	.	0.32825	D	0.503266	B	0.29716	0.255	B	0.24974	0.057	T	0.12785	-1.0534	9	0.02654	T	1	.	10.4006	0.44227	0.854:0.0:0.0:0.146	.	1098	Q96DT5	DYH11_HUMAN	E	1098	ENSP00000330671:K1098E	ENSP00000330671:K1098E	K	+	1	0	DNAH11	21607189	0.999000	0.42202	1.000000	0.80357	0.235000	0.25334	0.965000	0.29319	2.073000	0.62155	0.460000	0.39030	AAA		0.338	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21640664	A	G	21640664	3	3	61	1	0	0	0	0	1	0	0	0	4610	131	5	4	3358	4	DNAH11	7	21640664	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11834	21640664	137497999	5155	13140										
DNAH11	8701	broad.mit.edu	37	chr7	21641066	21641066	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagattccggacttcagagaGaattaaatgaaggtgatcat	10	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21641066G>T	ENST00000409508.3	+	18	3509	c.3478G>T	c.(3478-3480)Gaa>Taa	p.E1160*	DNAH11_ENST00000328843.6_Nonsense_Mutation_p.E1160*	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1160	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1160*(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ACTTCAGAGAGAATTAAATGA	0.348									Kartagener syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	7											85	84	84					7																	21641066		1825	4083	5908	21607591	SO:0001587	stop_gained	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3478G>T	7.37:g.21641066G>T	ENSP00000475939:p.Glu1160*		21607591	Q9UJ82	Nonsense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	41	8.673600	0.98910	.	.	ENSG00000105877	ENST00000328843	.	.	.	5.7	2.85	0.33270	.	0.616552	0.15736	N	0.247141	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	6.8676	0.24102	0.1518:0.267:0.5813:0.0	.	.	.	.	X	1160	.	ENSP00000330671:E1160X	E	+	1	0	DNAH11	21607591	0.096000	0.21769	0.803000	0.32268	0.583000	0.36354	0.735000	0.26115	0.316000	0.23135	0.650000	0.86243	GAA		0.348	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21641066	G	T	21641066	4	4	61	1	0	0	0	0	0	1	0	0	4610	943	33	2	3548	2	DNAH11	7	21641066	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	402	21641066	137497597	5156	13141										
DNAH11	8701	broad.mit.edu	37	chr7	21646160	21646160	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaatgtattttgtttgaCgtaagctagttaccaagttt	7	4	0	1	rs190062687	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21646160C>T	ENST00000409508.3	+	19	3796	c.3765C>T	c.(3763-3765)gaC>gaT	p.D1255D	DNAH11_ENST00000328843.6_Splice_Site_p.D1255D	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1255	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D1255D(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTTTGTTTGACGTAAGCTAGT	0.313									Kartagener syndrome				C|||	5	0.000998403	0.0038	0	5008	,	,		18077	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C		13,3649		0,13,1818	68	64	65		3765	4.4	1	7		65	1,8177		0,1,4088	yes	coding-synonymous-near-splice	DNAH11	NM_003777.3		0,14,5906	TT,TC,CC		0.0122,0.355,0.1182		1255/4524	21646160	14,11826	1831	4089	5920	21612685	SO:0001630	splice_region_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3765+1C>T	7.37:g.21646160C>T			21612685	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.313	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	Silent	T	21646160	C	T	21646160	5	4	61	1	0	0	0	0	0	0	1	0	4610	550	19	1	3839	1	DNAH11	7	21646160	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5094	21646160	137492503	5157	13142										
DNAH11	8701	broad.mit.edu	37	chr7	21654843	21654843	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgaaacagtgtcgcaaaGaaataaaattgctcaaggga	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21654843G>T	ENST00000409508.3	+	21	3995	c.3964G>T	c.(3964-3966)Gaa>Taa	p.E1322*	DNAH11_ENST00000328843.6_Nonsense_Mutation_p.E1322*	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1322	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1322*(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTGTCGCAAAGAAATAAAATT	0.353									Kartagener syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	7											139	132	134					7																	21654843		1850	4099	5949	21621368	SO:0001587	stop_gained	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3964G>T	7.37:g.21654843G>T	ENSP00000475939:p.Glu1322*		21621368	Q9UJ82	Nonsense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	44	11.167547	0.99525	.	.	ENSG00000105877	ENST00000328843	.	.	.	5.37	5.37	0.77165	.	0.304292	0.34484	N	0.003926	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	16.4715	0.84112	0.0:0.1309:0.8691:0.0	.	.	.	.	X	1322	.	ENSP00000330671:E1322X	E	+	1	0	DNAH11	21621368	1.000000	0.71417	0.458000	0.27068	0.988000	0.76386	7.829000	0.86735	2.659000	0.90383	0.655000	0.94253	GAA		0.353	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21654843	G	T	21654843	4	4	61	1	0	0	0	0	0	1	0	0	4610	943	33	2	4046	2	DNAH11	7	21654843	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8683	21654843	137483820	5158	13143										
DNAH11	8701	broad.mit.edu	37	chr7	21721203	21721203	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattacacttttgctgggaGaacttccacctggagacaga	10	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21721203G>A	ENST00000409508.3	+	31	5399	c.5368G>A	c.(5368-5370)Gaa>Aaa	p.E1790K	DNAH11_ENST00000328843.6_Missense_Mutation_p.E1795K	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1795	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1795K(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTTGCTGGGAGAACTTCCACC	0.403									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											107	99	101					7																	21721203		1877	4124	6001	21687728	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5368G>A	7.37:g.21721203G>A	ENSP00000475939:p.Glu1790Lys		21687728	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	19.29	3.799307	0.70567	.	.	ENSG00000105877	ENST00000328843	T	0.57436	0.4	5.39	5.39	0.77823	.	0.130967	0.56097	D	0.000025	T	0.44685	0.1305	.	.	.	0.58432	D	0.999999	P	0.40909	0.732	B	0.40199	0.322	T	0.25117	-1.0141	9	0.13470	T	0.59	.	19.1182	0.93351	0.0:0.0:1.0:0.0	.	1795	Q96DT5	DYH11_HUMAN	K	1795	ENSP00000330671:E1795K	ENSP00000330671:E1795K	E	+	1	0	DNAH11	21687728	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.234000	0.58658	2.665000	0.90641	0.585000	0.79938	GAA		0.403	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21721203	G	A	21721203	3	1	61	1	0	0	0	0	1	0	0	0	4610	943	33	3	5505	3	DNAH11	7	21721203	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66360	21721203	137417460	5159	13144										
DNAH11	8701	broad.mit.edu	37	chr7	21726808	21726808	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaacagagaccaccaaaGacctaggacgtgcccttggc	11	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21726808G>T	ENST00000409508.3	+	33	5744	c.5713G>T	c.(5713-5715)Gac>Tac	p.D1905Y	DNAH11_ENST00000328843.6_Missense_Mutation_p.D1912Y	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1912	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D1912Y(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GACCACCAAAGACCTAGGACG	0.423									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											91	93	92					7																	21726808		1879	4124	6003	21693333	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5713G>T	7.37:g.21726808G>T	ENSP00000475939:p.Asp1905Tyr		21693333	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	17.23	3.337674	0.60963	.	.	ENSG00000105877	ENST00000328843	T	0.15718	2.4	5.84	5.84	0.93424	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.42361	-0.9456	9	0.87932	D	0	.	19.7538	0.96281	0.0:0.0:1.0:0.0	.	1912	Q96DT5	DYH11_HUMAN	Y	1912	ENSP00000330671:D1912Y	ENSP00000330671:D1912Y	D	+	1	0	DNAH11	21693333	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	9.756000	0.98918	2.769000	0.95229	0.563000	0.77884	GAC		0.423	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21726808	G	T	21726808	3	4	61	1	0	0	0	0	1	0	0	0	4610	942	33	2	5865	2	DNAH11	7	21726808	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5605	21726808	137411855	5160	13145										
DNAH11	8701	broad.mit.edu	37	chr7	21727071	21727071	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatgagttcaaccgaatCtctgtggaagttctgtcagt	10	7	4	2	rs377208329		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21727071C>A	ENST00000409508.3	+	34	5881	c.5850C>A	c.(5848-5850)atC>atA	p.I1950I	DNAH11_ENST00000328843.6_Silent_p.I1957I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1957	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I1957I(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TCAACCGAATCTCTGTGGAAG	0.448									Kartagener syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	7											75	79	78					7																	21727071		2197	4299	6496	21693596	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5850C>A	7.37:g.21727071C>A			21693596	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.448	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21727071	C	A	21727071	2	1	61	1	0	0	0	0	0	0	0	1	4610	903	32	2		2	DNAH11	7	21727071	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	263	21727071	137411592	5161	13146										
DNAH11	8701	broad.mit.edu	37	chr7	21730393	21730393	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatggtagatttgtatttCttggggaagctatcacactg	10	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21730393C>A	ENST00000409508.3	+	35	5966	c.5935C>A	c.(5935-5937)Ctt>Att	p.L1979I	DNAH11_ENST00000328843.6_Missense_Mutation_p.L1986I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1986	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L1986I(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATTTGTATTTCTTGGGGAAGC	0.353									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											157	150	152					7																	21730393		1827	4090	5917	21696918	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5935C>A	7.37:g.21730393C>A	ENSP00000475939:p.Leu1979Ile		21696918	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	25.3	4.626065	0.87560	.	.	ENSG00000105877	ENST00000328843	T	0.12774	2.65	6.17	6.17	0.99709	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	.	.	.	0.49687	D	0.999813	D	0.89917	1.0	D	0.87578	0.998	T	0.08229	-1.0732	9	0.56958	D	0.05	.	20.4898	0.99202	0.0:1.0:0.0:0.0	.	1986	Q96DT5	DYH11_HUMAN	I	1986	ENSP00000330671:L1986I	ENSP00000330671:L1986I	L	+	1	0	DNAH11	21696918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.983000	0.40648	2.941000	0.99782	0.655000	0.94253	CTT		0.353	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21730393	C	A	21730393	3	1	61	1	0	0	0	0	1	0	0	0	4610	913	32	2	6095	2	DNAH11	7	21730393	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3322	21730393	137408270	5162	13147										
DNAH11	8701	broad.mit.edu	37	chr7	21813410	21813410	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaaagactctattagcctTttcatggcacatgttcacac	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21813410T>G	ENST00000409508.3	+	56	9160	c.9129T>G	c.(9127-9129)ctT>ctG	p.L3043L	DNAH11_ENST00000328843.6_Silent_p.L3050L	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3050	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L3050L(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						CTATTAGCCTTTTCATGGCAC	0.343									Kartagener syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	7											57	52	53					7																	21813410		1846	4105	5951	21779935	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.9129T>G	7.37:g.21813410T>G			21779935	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.343	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21813410	T	G	21813410	2	3	61	1	0	0	0	0	0	0	0	1	4610	1828	64	4		4	DNAH11	7	21813410	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	83017	21813410	137325253	5163	13148										
DNAH11	8701	broad.mit.edu	37	chr7	21857893	21857893	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcatcttaattgaaaatCtcgaggaaacgatagatcca	7	7	3	2	rs370350252		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21857893C>A	ENST00000409508.3	+	65	10658	c.10627C>A	c.(10627-10629)Ctc>Atc	p.L3543I	DNAH11_ENST00000328843.6_Missense_Mutation_p.L3550I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3550	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L3550I(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						AATTGAAAATCTCGAGGAAAC	0.333									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											95	87	90					7																	21857893		1836	4078	5914	21824418	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10627C>A	7.37:g.21857893C>A	ENSP00000475939:p.Leu3543Ile		21824418	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	5.447	0.267496	0.10294	.	.	ENSG00000105877	ENST00000328843	T	0.24723	1.84	5.48	4.6	0.57074	.	0.066895	0.64402	D	0.000010	T	0.17534	0.0421	.	.	.	0.38288	D	0.942617	P	0.39094	0.659	B	0.43413	0.419	T	0.04203	-1.0969	9	0.05721	T	0.95	.	12.0134	0.53301	0.1436:0.7332:0.1233:0.0	.	3550	Q96DT5	DYH11_HUMAN	I	3550	ENSP00000330671:L3550I	ENSP00000330671:L3550I	L	+	1	0	DNAH11	21824418	0.997000	0.39634	0.995000	0.50966	0.927000	0.56198	0.935000	0.28924	1.300000	0.44818	0.644000	0.83932	CTC		0.333	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21857893	C	A	21857893	3	1	61	1	0	0	0	0	1	0	0	0	4610	913	32	2	10907	2	DNAH11	7	21857893	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44483	21857893	137280770	5164	13149										
DNAH11	8701	broad.mit.edu	37	chr7	21892120	21892120	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaaaatgattttaaaatTgagctcaagtatctggaaga	7	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21892120T>G	ENST00000409508.3	+	67	10963	c.10932T>G	c.(10930-10932)atT>atG	p.I3644M	DNAH11_ENST00000328843.6_Missense_Mutation_p.I3651M	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3651	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I3651M(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATTTTAAAATTGAGCTCAAGT	0.378									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											86	86	86					7																	21892120		1864	4093	5957	21858645	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10932T>G	7.37:g.21892120T>G	ENSP00000475939:p.Ile3644Met		21858645	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	16.75|16.75	3.208686|3.208686	0.58343|0.58343	.|.	.|.	ENSG00000105877|ENSG00000105877	ENST00000328843|ENST00000421290	T|.	0.55413|.	0.52|.	6.14|6.14	-10.3|-10.3	0.00346|0.00346	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.43875|.	0.1267|.	.|.	.|.	.|.	0.49483|0.49483	D|D	0.999794|0.999794	D|.	0.76494|.	0.999|.	D|.	0.75020|.	0.985|.	T|.	0.53129|.	-0.8482|.	9|.	0.51188|.	T|.	0.08|.	.|.	7.2173|7.2173	0.25967|0.25967	0.3109:0.3648:0.0:0.3243|0.3109:0.3648:0.0:0.3243	.|.	3651|.	Q96DT5|.	DYH11_HUMAN|.	M|G	3651|39	ENSP00000330671:I3651M|.	ENSP00000330671:I3651M|.	I|X	+|+	3|1	3|0	DNAH11|DNAH11	21858645|21858645	0.199000|0.199000	0.23386|0.23386	0.783000|0.783000	0.31826|0.31826	0.411000|0.411000	0.31082|0.31082	-0.427000|-0.427000	0.06999|0.06999	-1.615000|-1.615000	0.01573|0.01573	-0.253000|-0.253000	0.11424|0.11424	ATT|TGA		0.378	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21892120	T	G	21892120	3	3	61	1	0	0	0	0	1	0	0	0	4610	1800	63	4	11220	4	DNAH11	7	21892120	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34227	21892120	137246543	5165	13150										
CDCA7L	55536	broad.mit.edu	37	chr7	21945991	21945991	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttctctagagcaaacttCtcaggaggccgcgcactccg	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21945991C>A	ENST00000406877.3	-	6	1116	c.837G>T	c.(835-837)gaG>gaT	p.E279D	CDCA7L_ENST00000373934.4_Missense_Mutation_p.E233D|CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000356195.5_Missense_Mutation_p.E245D	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	279					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.E279D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						GAGCAAACTTCTCAGGAGGCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	100	97					7																	21945991		2203	4300	6503	21912516	SO:0001583	missense	55536				CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.837G>T	7.37:g.21945991C>A	ENSP00000383986:p.Glu279Asp		21912516	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Missense_Mutation	SNP	ENST00000406877.3	37	CCDS5374.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052853	0.55218	.	.	ENSG00000164649	ENST00000356195;ENST00000406877;ENST00000373934	T;T;T	0.49139	0.81;0.79;0.82	5.63	3.79	0.43588	.	0.050184	0.85682	D	0.000000	T	0.46171	0.1379	M	0.73598	2.24	0.51012	D	0.999906	B;B;B	0.20887	0.049;0.008;0.015	B;B;B	0.19391	0.015;0.01;0.025	T	0.41395	-0.9511	10	0.28530	T	0.3	-7.2211	10.95	0.47323	0.0:0.789:0.0:0.211	.	233;279;278	C9K0Y1;Q96GN5;Q96GN5-2	.;CDA7L_HUMAN;.	D	245;279;233	ENSP00000348523:E245D;ENSP00000383986:E279D;ENSP00000363045:E233D	ENSP00000348523:E245D	E	-	3	2	CDCA7L	21912516	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.298000	0.33412	1.363000	0.46019	0.655000	0.94253	GAG		0.507	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719		A	21945991	C	A	21945991	3	1	61	1	0	0	0	0	1	0	0	0	3097	912	32	2	547	2	CDCA7L	7	21945991	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53871	21945991	137192672	5166	13151										
CDCA7L	55536	broad.mit.edu	37	chr7	21947910	21947910	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaattgtttttttctcattCtgtaagcgtgcgctagaaaa	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:21947910C>A	ENST00000406877.3	-	4	798	c.519G>T	c.(517-519)caG>caT	p.Q173H	CDCA7L_ENST00000373934.4_Missense_Mutation_p.Q127H|CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000356195.5_Missense_Mutation_p.Q139H	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	173					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.Q173H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						TTTTCTCATTCTGTAAGCGTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											91	82	85					7																	21947910		2203	4300	6503	21914435	SO:0001583	missense	55536				CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.519G>T	7.37:g.21947910C>A	ENSP00000383986:p.Gln173His		21914435	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Missense_Mutation	SNP	ENST00000406877.3	37	CCDS5374.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.345626	0.61073	.	.	ENSG00000164649	ENST00000356195;ENST00000406877;ENST00000373934;ENST00000457951	T;T;T;T	0.47528	0.93;0.92;0.93;0.84	5.95	0.17	0.15021	.	0.647404	0.14263	N	0.330669	T	0.33731	0.0873	L	0.36672	1.1	0.20074	N	0.999935	P;P;P;P	0.48640	0.815;0.776;0.913;0.884	B;B;B;B	0.43536	0.243;0.187;0.339;0.423	T	0.20940	-1.0260	10	0.66056	D	0.02	-11.9295	3.5798	0.07947	0.2186:0.5176:0.1065:0.1573	.	173;127;173;172	A8K8X5;C9K0Y1;Q96GN5;Q96GN5-2	.;.;CDA7L_HUMAN;.	H	139;173;127;126	ENSP00000348523:Q139H;ENSP00000383986:Q173H;ENSP00000363045:Q127H;ENSP00000406616:Q126H	ENSP00000348523:Q139H	Q	-	3	2	CDCA7L	21914435	0.922000	0.31269	0.337000	0.25536	0.077000	0.17291	0.473000	0.22132	0.412000	0.25729	-0.169000	0.13324	CAG		0.433	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719		A	21947910	C	A	21947910	3	1	61	1	0	0	0	0	1	0	0	0	3097	912	32	2	873	2	CDCA7L	7	21947910	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1919	21947910	137190753	5167	13152										
IL6	3569	broad.mit.edu	37	chr7	22767227	22767227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaattcggtacatcctcGacggcatctcagccctgaga	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:22767227G>A	ENST00000404625.1	+	3	643	c.184G>A	c.(184-186)Gac>Aac	p.D62N	IL6_ENST00000420258.2_Missense_Mutation_p.D116N|AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000406575.1_Missense_Mutation_p.D62N|IL6_ENST00000401630.3_Missense_Mutation_p.D39N|IL6_ENST00000407492.1_Intron|IL6_ENST00000401651.1_Intron|IL6_ENST00000258743.5_Missense_Mutation_p.D62N			P05231	IL6_HUMAN	interleukin 6	62					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)	p.D62N(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	GTACATCCTCGACGGCATCTC	0.597																																					Esophageal Squamous(47;342 1214 13936 33513)											1	Substitution - Missense(1)	large_intestine(1)	7											95	91	92					7																	22767227		2203	4300	6503	22733752	SO:0001583	missense	3569			M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.184G>A	7.37:g.22767227G>A	ENSP00000385675:p.Asp62Asn		22733752	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	37	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640591	0.47153	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000401630;ENST00000406575	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.73	-11.5	0.00074	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.791630	0.00678	N	0.000679	T	0.10380	0.0254	L	0.47716	1.5	0.09310	N	1	D;P;B	0.59767	0.986;0.842;0.424	B;B;B	0.42798	0.398;0.184;0.046	T	0.46442	-0.9191	10	0.16420	T	0.52	7.5021	1.9144	0.03294	0.4706:0.1792:0.1025:0.2477	.	116;62;62	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	N	62;62;62;116;39;62	ENSP00000385675:D62N;ENSP00000405150:D62N;ENSP00000258743:D62N;ENSP00000405994:D116N;ENSP00000384928:D39N;ENSP00000385227:D62N	ENSP00000258743:D62N	D	+	1	0	IL6	22733752	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.562000	0.02156	-2.556000	0.00476	-1.130000	0.01982	GAC		0.597	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		A	22767227	G	A	22767227	3	1	61	1	0	0	0	0	1	0	0	0	7722	1058	37	1	190	1	IL6	7	22767227	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	819317	22767227	136371436	5168	13153										
FAM126A	84668	broad.mit.edu	37	chr7	23000877	23000877	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatggctctggatataattCtagctgggctctgtatataa	9	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23000877C>A	ENST00000432176.2	-	9	1040	c.808G>T	c.(808-810)Gaa>Taa	p.E270*	FAM126A_ENST00000498833.1_5'UTR|FAM126A_ENST00000409923.1_Nonsense_Mutation_p.E270*	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	270					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)	p.E270*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						GGATATAATTCTAGCTGGGCT	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											73	79	77					7																	23000877		2203	4298	6501	22967402	SO:0001587	stop_gained	84668			BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"down regulated by Ctnnb1, a"	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.808G>T	7.37:g.23000877C>A	ENSP00000403396:p.Glu270*		22967402	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Nonsense_Mutation	SNP	ENST00000432176.2	37	CCDS5377.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.022799|7.022799	0.98010|0.98010	.|.	.|.	ENSG00000122591|ENSG00000122591	ENST00000432176;ENST00000409923|ENST00000440481	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.046278|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.72032|.	D|.	0.01|.	-6.7447|-6.7447	18.9288|18.9288	0.92556|0.92556	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|Y	270|321	.|.	ENSP00000386246:E270X|.	E|X	-|-	1|3	0|2	FAM126A|FAM126A	22967402|22967402	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.111000|7.111000	0.77077|0.77077	2.482000|2.482000	0.83794|0.83794	0.650000|0.650000	0.86243|0.86243	GAA|TAG		0.299	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581		A	23000877	C	A	23000877	4	1	61	1	0	0	0	0	0	1	0	0	5445	922	32	2	769	2	FAM126A	7	23000877	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233650	23000877	136137786	5169	13154										
KLHL7	55975	broad.mit.edu	37	chr7	23191755	23191755	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatggcacaagacctagaaGaaagaaacatgactaccgca	9	9	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23191755G>T	ENST00000339077.5	+	7	1106	c.863G>T	c.(862-864)aGa>aTa	p.R288I	KLHL7_ENST00000545443.1_Missense_Mutation_p.R266I|KLHL7_ENST00000322231.7_Missense_Mutation_p.R266I|KLHL7_ENST00000409689.1_Missense_Mutation_p.R240I|KLHL7_ENST00000542558.1_Missense_Mutation_p.R63I|KLHL7_ENST00000539124.1_Missense_Mutation_p.R212I	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	288					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.R266I(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGACCTAGAAGAAAGAAACAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											136	129	131					7																	23191755		2203	4300	6503	23158280	SO:0001583	missense	55975				CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.863G>T	7.37:g.23191755G>T	ENSP00000343273:p.Arg288Ile		23158280	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	37	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	G	34	5.364248	0.95877	.	.	ENSG00000122550	ENST00000538858;ENST00000536369;ENST00000322231;ENST00000339077;ENST00000539124;ENST00000542558;ENST00000409689;ENST00000545443;ENST00000414163	T;T;T;T;T;T;T	0.79247	-0.62;-0.61;-0.58;-0.78;-0.6;-0.62;-1.25	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.70237	0.3201	L	0.34521	1.04	0.80722	D	1	P;P;B	0.38922	0.651;0.651;0.112	B;B;B	0.33196	0.159;0.081;0.031	T	0.73017	-0.4115	10	0.59425	D	0.04	.	20.139	0.98050	0.0:0.0:1.0:0.0	.	63;288;266	B7Z3P9;Q8IXQ5;Q8IXQ5-2	.;KLHL7_HUMAN;.	I	129;254;266;288;212;63;240;266;56	ENSP00000322958:R266I;ENSP00000343273:R288I;ENSP00000441136:R212I;ENSP00000442367:R63I;ENSP00000386263:R240I;ENSP00000442366:R266I;ENSP00000404181:R56I	ENSP00000322958:R266I	R	+	2	0	KLHL7	23158280	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.835000	0.92100	2.764000	0.94973	0.655000	0.94253	AGA		0.408	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		T	23191755	G	T	23191755	3	4	61	1	0	0	0	0	1	0	0	0	8415	942	33	2	952	2	KLHL7	7	23191755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190878	23191755	135946908	5170	13155										
GPNMB	10457	broad.mit.edu	37	chr7	23299726	23299726	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacgggcatatgttcccatCgcacaagtgaaagatgtgta	12	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23299726C>T	ENST00000381990.2	+	5	830	c.669C>T	c.(667-669)atC>atT	p.I223I	GPNMB_ENST00000258733.4_Silent_p.I223I|GPNMB_ENST00000539136.1_Silent_p.I124I|GPNMB_ENST00000453162.2_Silent_p.I165I	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	223					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)	p.I223I(2)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			ATGTTCCCATCGCACAAGTGA	0.463																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	7											166	150	155					7																	23299726		2203	4300	6503	23266251	SO:0001819	synonymous_variant	10457			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.669C>T	7.37:g.23299726C>T			23266251	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																				0.463	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		T	23299726	C	T	23299726	2	4	61	1	0	0	0	0	0	0	0	1	6640	874	31	1		1	GPNMB	7	23299726	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107971	23299726	135838937	5171	13156										
C7orf30	115416	broad.mit.edu	37	chr7	23349030	23349030	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaaatctatgaattagaGaaattatggaccctacgttc	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23349030G>T	ENST00000466681.1	+	4	726	c.573G>T	c.(571-573)gaG>gaT	p.E191D		NM_138446.1	NP_612455.1	Q96EH3	MASU1_HUMAN	mitochondrial assembly of ribosomal large subunit 1	191					negative regulation of mitochondrial translation (GO:0070130)|ribosomal large subunit biogenesis (GO:0042273)	mitochondrion (GO:0005739)		p.E191D(1)									ATGAATTAGAGAAATTATGGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											145	140	141					7																	23349030		2203	4300	6503	23315555	SO:0001583	missense	115416			BC012331	CCDS5381.1	7p15.3	2013-05-24	2012-02-20	2012-02-20	ENSG00000156928	ENSG00000156928			21721	protein-coding gene	gene with protein product		614624	"chromosome 7 open reading frame 30"	C7orf30		22238376, 22238375	Standard	NM_138446		Approved	mtRsfA	uc003swd.1	Q96EH3	OTTHUMG00000128443	ENST00000466681.1:c.573G>T	7.37:g.23349030G>T	ENSP00000419370:p.Glu191Asp		23315555	A4D154	Missense_Mutation	SNP	ENST00000466681.1	37	CCDS5381.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.212175	0.79240	.	.	ENSG00000156928	ENST00000466681	.	.	.	5.61	2.82	0.32997	.	0.000000	0.85682	D	0.000000	T	0.76292	0.3967	M	0.76838	2.35	0.46521	D	0.999088	D	0.89917	1.0	D	0.91635	0.999	T	0.77143	-0.2696	9	0.87932	D	0	-16.5236	9.9494	0.41630	0.275:0.0:0.725:0.0	.	191	Q96EH3	CG030_HUMAN	D	191	.	ENSP00000419370:E191D	E	+	3	2	C7orf30	23315555	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.312000	0.33574	0.741000	0.32674	0.591000	0.81541	GAG		0.388	MALSU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250241.2	NM_138446		T	23349030	G	T	23349030	3	4	61	1	0	0	0	0	1	0	0	0	2392	933	33	2	587	2	C7orf30	7	23349030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49304	23349030	135789633	5172	13157										
IGF2BP3	10643	broad.mit.edu	37	chr7	23385660	23385660	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttattatgagctaaaatCttcaaggggatctcttctgt	8	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23385660C>A	ENST00000258729.3	-	8	1196	c.840G>T	c.(838-840)aaG>aaT	p.K280N		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	280	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)	p.K280N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						GAGCTAAAATCTTCAAGGGGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	7											97	95	96					7																	23385660		2203	4300	6503	23352185	SO:0001583	missense	10643			AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.840G>T	7.37:g.23385660C>A	ENSP00000258729:p.Lys280Asn		23352185	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Missense_Mutation	SNP	ENST00000258729.3	37	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341445	0.81911	.	.	ENSG00000136231	ENST00000258729	T	0.31247	1.5	6.07	6.07	0.98685	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.62744	0.2453	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68727	-0.5332	10	0.87932	D	0	-2.1077	13.793	0.63152	0.0:0.9304:0.0:0.0696	.	280	O00425	IF2B3_HUMAN	N	280	ENSP00000258729:K280N	ENSP00000258729:K280N	K	-	3	2	IGF2BP3	23352185	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.153000	0.42282	2.890000	0.99128	0.650000	0.86243	AAG		0.323	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		A	23385660	C	A	23385660	3	1	61	1	0	0	0	0	1	0	0	0	7596	912	32	2	931	2	IGF2BP3	7	23385660	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36630	23385660	135753003	5173	13158										
C7orf46	340277	broad.mit.edu	37	chr7	23724180	23724180	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatatgaagaatacaaaaGaaaagttttacctctgcgct	7	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23724180G>T	ENST00000344962.4	+	2	217	c.128G>T	c.(127-129)aGa>aTa	p.R43I	FAM221A_ENST00000409994.3_Intron|FAM221A_ENST00000409653.1_Intron|FAM221A_ENST00000409192.3_Missense_Mutation_p.R43I	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	43								p.R43I(1)									GAATACAAAAGAAAAGTTTTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											73	75	74					7																	23724180		2203	4300	6503	23690705	SO:0001583	missense	340277				CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 46"	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.128G>T	7.37:g.23724180G>T	ENSP00000342576:p.Arg43Ile		23690705	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	37	CCDS5385.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.043280	0.55003	.	.	ENSG00000188732	ENST00000409192;ENST00000344962	T;T	0.17528	2.27;2.27	5.63	0.317	0.15861	.	0.523738	0.22100	N	0.064621	T	0.08492	0.0211	L	0.29908	0.895	0.58432	D	0.999999	P;P	0.40144	0.624;0.704	B;B	0.28916	0.096;0.096	T	0.19321	-1.0309	10	0.87932	D	0	-8.0321	5.8845	0.18874	0.4452:0.1314:0.4233:0.0	.	43;43	A4D161-2;A4D161	.;CG046_HUMAN	I	43	ENSP00000386927:R43I;ENSP00000342576:R43I	ENSP00000342576:R43I	R	+	2	0	C7orf46	23690705	0.995000	0.38212	0.996000	0.52242	0.995000	0.86356	0.436000	0.21526	0.282000	0.22254	0.555000	0.69702	AGA		0.373	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136		T	23724180	G	T	23724180	3	4	61	1	0	0	0	0	1	0	0	0	2402	942	33	2	134	2	C7orf46	7	23724180	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	338520	23724180	135414483	5174	13159										
STK31	56164	broad.mit.edu	37	chr7	23811892	23811892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttgaaaagagtaatttgGaagaggtaaggaaacagttg	14	1	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:23811892G>A	ENST00000355870.3	+	15	2079	c.1960G>A	c.(1960-1962)Gaa>Aaa	p.E654K	STK31_ENST00000433467.2_Missense_Mutation_p.E654K|STK31_ENST00000428484.1_Missense_Mutation_p.E631K|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.E631K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	654						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)	p.E654K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GAGTAATTTGGAAGAGGTAAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	7											74	77	76					7																	23811892		2203	4293	6496	23778417	SO:0001583	missense	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1960G>A	7.37:g.23811892G>A	ENSP00000348132:p.Glu654Lys		23778417	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903392	0.92035	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	D;T;D;D	0.85013	-1.93;-0.1;-1.89;-1.89	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.91713	0.7380	M	0.66939	2.045	0.49915	D	0.999832	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.92335	0.5877	10	0.66056	D	0.02	-14.8818	18.3042	0.90175	0.0:0.0:1.0:0.0	.	654;654	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	654;654;631;631	ENSP00000348132:E654K;ENSP00000411852:E654K;ENSP00000346660:E631K;ENSP00000406146:E631K	ENSP00000346660:E631K	E	+	1	0	STK31	23778417	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.127000	0.71642	2.423000	0.82170	0.557000	0.71058	GAA		0.333	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		A	23811892	G	A	23811892	3	1	61	1	0	0	0	0	1	0	0	0	15335	1175	41	3	2018	3	STK31	7	23811892	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87712	23811892	135326771	5175	13160										
OSBPL3	26031	broad.mit.edu	37	chr7	24892208	24892208	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagctgcttcagtttctctCtctccgctgacatgatatta	6	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:24892208C>A	ENST00000313367.2	-	11	1524	c.1073G>T	c.(1072-1074)aGa>aTa	p.R358I	OSBPL3_ENST00000396431.1_Missense_Mutation_p.R327I|OSBPL3_ENST00000409069.1_Missense_Mutation_p.R327I|OSBPL3_ENST00000352860.1_Missense_Mutation_p.R327I|OSBPL3_ENST00000396429.1_Missense_Mutation_p.R358I|OSBPL3_ENST00000353930.1_Missense_Mutation_p.R358I|OSBPL3_ENST00000431825.2_Missense_Mutation_p.R327I	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	358					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.R358I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CAGTTTCTCTCTCTCCGCTGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											92	76	81					7																	24892208		2203	4300	6503	24858733	SO:0001583	missense	26031			AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1073G>T	7.37:g.24892208C>A	ENSP00000315410:p.Arg358Ile		24858733	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234772	0.79800	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.54479	1.98;0.71;0.57;1.78;0.71;0.57;1.78	5.16	4.28	0.50868	.	0.046336	0.85682	D	0.000000	T	0.69495	0.3117	M	0.68593	2.085	0.58432	D	0.999996	D;D;D;D;D;P	0.89917	1.0;0.959;0.993;0.997;0.999;0.843	D;P;D;D;D;P	0.91635	0.999;0.908;0.956;0.975;0.979;0.531	T	0.72093	-0.4394	10	0.59425	D	0.04	-16.1599	13.747	0.62881	0.0:0.9259:0.0:0.0741	.	327;358;327;327;358;358	Q9H4L5-8;Q9H4L5-7;Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;.;.;OSBL3_HUMAN	I	358;327;358;327;327;358;327	ENSP00000315410:R358I;ENSP00000315331:R327I;ENSP00000315277:R358I;ENSP00000389779:R327I;ENSP00000379708:R327I;ENSP00000379706:R358I;ENSP00000386953:R327I	ENSP00000315410:R358I	R	-	2	0	OSBPL3	24858733	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.589000	0.46145	1.184000	0.42957	0.561000	0.74099	AGA		0.413	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			A	24892208	C	A	24892208	3	1	61	1	0	0	0	0	1	0	0	0	11310	913	32	2	1642	2	OSBPL3	7	24892208	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1080316	24892208	134246455	5176	13161										
NFE2L3	9603	broad.mit.edu	37	chr7	26217629	26217629	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagcatgaggaaaatgaaGaaagggtgtcagcccagaag	13	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:26217629G>T	ENST00000056233.3	+	2	896	c.637G>T	c.(637-639)Gaa>Taa	p.E213*		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	213					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.E213*(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GGAAAATGAAGAAAGGGTGTC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											87	85	86					7																	26217629		2203	4300	6503	26184154	SO:0001587	stop_gained	9603			AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.637G>T	7.37:g.26217629G>T	ENSP00000056233:p.Glu213*		26184154	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Nonsense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	G	34	5.398957	0.96030	.	.	ENSG00000050344	ENST00000056233	.	.	.	4.52	1.71	0.24356	.	0.774862	0.11555	N	0.552341	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	0.438	4.952	0.14019	0.0:0.3644:0.3602:0.2754	.	.	.	.	X	213	.	ENSP00000056233:E213X	E	+	1	0	NFE2L3	26184154	0.770000	0.28543	0.003000	0.11579	0.394000	0.30568	1.095000	0.30964	0.391000	0.25143	0.655000	0.94253	GAA		0.413	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			T	26217629	G	T	26217629	4	4	61	1	0	0	0	0	0	1	0	0	10400	943	33	2	643	2	NFE2L3	7	26217629	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1325421	26217629	132921034	5177	13162										
HOXA2	3199	broad.mit.edu	37	chr7	27140770	27140770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccccagagacgctaagggCttgctcaaagagcgtcttct	12	12	3	2	rs372854321		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27140770C>T	ENST00000222718.5	-	2	1016	c.706G>A	c.(706-708)Gcc>Acc	p.A236T	HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000428939.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	236					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A236T(1)		breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						ACGCTAAGGGCTTGCTCAAAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	106	98	100		706	4.6	1	7		100	0,8600		0,0,4300	no	missense	HOXA2	NM_006735.3	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	236/377	27140770	1,13005	2203	4300	6503	27107295	SO:0001583	missense	3199				CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.706G>A	7.37:g.27140770C>T	ENSP00000222718:p.Ala236Thr		27107295	A1L4K3|B2RMW3	Missense_Mutation	SNP	ENST00000222718.5	37	CCDS5403.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.727486	0.30593	2.27E-4	0.0	ENSG00000105996	ENST00000222718	T	0.09445	2.98	5.45	4.55	0.56014	.	0.065629	0.64402	D	0.000012	T	0.14399	0.0348	M	0.61703	1.905	0.49915	D	0.999834	B	0.12013	0.005	B	0.17433	0.018	T	0.03684	-1.1013	10	0.23302	T	0.38	.	15.9223	0.79586	0.0:0.8642:0.1358:0.0	.	236	O43364	HXA2_HUMAN	T	236	ENSP00000222718:A236T	ENSP00000222718:A236T	A	-	1	0	HOXA2	27107295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.966000	0.49208	1.382000	0.46385	0.655000	0.94253	GCC		0.527	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			T	27140770	C	T	27140770	3	4	61	1	0	0	0	0	1	0	0	0	7313	797	28	3	428	3	HOXA2	7	27140770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	923141	27140770	131997893	5178	13163										
HOXA2	3199	broad.mit.edu	37	chr7	27141985	27141985	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggaggaggaatcagtgtCgagtgtgaaagcgtcgaggt	17	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27141985C>T	ENST00000222718.5	-	1	445	c.135G>A	c.(133-135)tcG>tcA	p.S45S	HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000428939.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	45					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S45S(1)		breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						GAATCAGTGTCGAGTGTGAAA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	7											97	109	105					7																	27141985		2203	4300	6503	27108510	SO:0001819	synonymous_variant	3199				CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.135G>A	7.37:g.27141985C>T			27108510	A1L4K3|B2RMW3	Silent	SNP	ENST00000222718.5	37	CCDS5403.1																																																																																				0.597	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			T	27141985	C	T	27141985	2	4	61	1	0	0	0	0	0	0	0	1	7313	871	31	1		1	HOXA2	7	27141985	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1215	27141985	131996678	5179	13164										
HOXA3	3200	broad.mit.edu	37	chr7	27147599	27147599	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatggtggccggtaaggtCcgtgtaggtggggtgcggct	21	6	0	0	rs371241609		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27147599C>T	ENST00000396352.4	-	3	1466	c.1267G>A	c.(1267-1269)Gac>Aac	p.D423N	HOXA3_ENST00000317201.2_Missense_Mutation_p.D423N|HOXA3_ENST00000521401.1_5'Flank|HOXA-AS2_ENST00000518088.1_RNA	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	423					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D423N(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						CCGGTAAGGTCCGTGTAGGTG	0.687																																					Esophageal Squamous(136;1368 1743 5685 7935 50360)											1	Substitution - Missense(1)	large_intestine(1)	7						C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	46	54	51		1267,1267	5.6	1	7		51	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	HOXA3	NM_030661.4,NM_153631.2	23,23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	423/444,423/444	27147599	1,13005	2203	4300	6503	27114124	SO:0001583	missense	3200				CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.1267G>A	7.37:g.27147599C>T	ENSP00000379640:p.Asp423Asn		27114124	A4D181	Missense_Mutation	SNP	ENST00000396352.4	37	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996011	0.54147	0.0	1.16E-4	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.89485	-2.52;-2.52	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.95297	0.8474	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95508	0.8583	10	0.87932	D	0	.	19.6081	0.95588	0.0:1.0:0.0:0.0	.	423	O43365	HXA3_HUMAN	N	423;423;265	ENSP00000379640:D423N;ENSP00000324884:D423N	ENSP00000324884:D423N	D	-	1	0	HOXA3	27114124	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	7.482000	0.81143	2.652000	0.90054	0.591000	0.81541	GAC		0.687	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			T	27147599	C	T	27147599	3	4	61	1	0	0	0	0	1	0	0	0	7314	855	30	3	68	3	HOXA3	7	27147599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5614	27147599	131991064	5180	13165										
HOXA3	3200	broad.mit.edu	37	chr7	27148158	27148158	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcgattctggaaccagatCttgatctggcgctcagtgag	13	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27148158C>A	ENST00000396352.4	-	3	907	c.708G>T	c.(706-708)aaG>aaT	p.K236N	HOXA3_ENST00000317201.2_Missense_Mutation_p.K236N|HOXA3_ENST00000521401.1_5'Flank|HOXA-AS2_ENST00000518088.1_RNA	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	236					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K236N(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						GGAACCAGATCTTGATCTGGC	0.587																																					Esophageal Squamous(136;1368 1743 5685 7935 50360)											1	Substitution - Missense(1)	large_intestine(1)	7											147	131	136					7																	27148158		2203	4300	6503	27114683	SO:0001583	missense	3200				CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.708G>T	7.37:g.27148158C>A	ENSP00000379640:p.Lys236Asn		27114683	A4D181	Missense_Mutation	SNP	ENST00000396352.4	37	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.985000	0.35036	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.96913	-4.17;-4.17	4.85	2.9	0.33743	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.046295	0.85682	D	0.000000	D	0.98432	0.9478	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97570	1.0104	10	0.87932	D	0	.	6.5591	0.22476	0.0:0.6944:0.0:0.3056	.	236	O43365	HXA3_HUMAN	N	236;236;78	ENSP00000379640:K236N;ENSP00000324884:K236N	ENSP00000324884:K236N	K	-	3	2	HOXA3	27114683	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.125000	0.42016	1.276000	0.44395	-0.136000	0.14681	AAG		0.587	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			A	27148158	C	A	27148158	3	1	61	1	0	0	0	0	1	0	0	0	7314	912	32	2	627	2	HOXA3	7	27148158	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	559	27148158	131990505	5181	13166										
HOXA6	3203	broad.mit.edu	37	chr7	27185425	27185425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcgttggcgatctcgatgCggcggcgccgtgtcaggtag	18	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27185425C>T	ENST00000222728.3	-	2	578	c.554G>A	c.(553-555)cGc>cAc	p.R185H	HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA5_ENST00000222726.3_5'Flank|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA6_ENST00000521478.1_5'UTR|HOXA-AS3_ENST00000518947.2_RNA	NM_024014.3	NP_076919.1	P31267	HXA6_HUMAN	homeobox A6	185					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R185H(1)		central_nervous_system(1)|large_intestine(5)|lung(3)|ovary(1)	10						GATCTCGATGCGGCGGCGCCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											164	151	155					7																	27185425		2203	4300	6503	27151950	SO:0001583	missense	3203				CCDS5407.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106006	ENSG00000106006		"Homeoboxes / ANTP class : HOXL subclass"	5107	protein-coding gene	gene with protein product		142951	"homeo box A6"	HOX1B, HOX1		1973146, 1358459	Standard	NM_024014		Approved		uc003syo.2	P31267	OTTHUMG00000023216	ENST00000222728.3:c.554G>A	7.37:g.27185425C>T	ENSP00000222728:p.Arg185His		27151950	A4D192|Q2M3G3|Q9UPM0	Missense_Mutation	SNP	ENST00000222728.3	37	CCDS5407.1	.	.	.	.	.	.	.	.	.	.	C	36	5.880790	0.97062	.	.	ENSG00000106006	ENST00000222728	D	0.97505	-4.41	5.36	5.36	0.76844	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99089	0.9687	H	0.96833	3.89	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99222	1.0879	10	0.87932	D	0	.	19.0808	0.93180	0.0:1.0:0.0:0.0	.	185	P31267	HXA6_HUMAN	H	185	ENSP00000222728:R185H	ENSP00000222728:R185H	R	-	2	0	HOXA6	27151950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.511000	0.84671	0.561000	0.74099	CGC		0.602	HOXA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358697.1			T	27185425	C	T	27185425	3	4	61	1	0	0	0	0	1	0	0	0	7317	768	27	1	151	1	HOXA6	7	27185425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37267	27185425	131953238	5182	13167										
HOXA13	3209	broad.mit.edu	37	chr7	27237978	27237978	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgtattcccgttcaagttCttttaattgcaccttggtat	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27237978C>A	ENST00000222753.4	-	2	1034	c.1006G>T	c.(1006-1008)Gaa>Taa	p.E336*	HOTTIP_ENST00000521028.2_RNA|HOTTIP_ENST00000605136.1_RNA|HOTTIP_ENST00000421733.1_RNA|HOXA13_ENST00000518136.3_5'Flank|HOTTIP_ENST00000472494.1_RNA	NM_000522.4	NP_000513.2	P31271	HXA13_HUMAN	homeobox A13	336					artery morphogenesis (GO:0048844)|branching involved in prostate gland morphogenesis (GO:0060442)|embryonic forelimb morphogenesis (GO:0035115)|endothelial cell fate specification (GO:0060847)|endothelial cell morphogenesis (GO:0001886)|inner ear development (GO:0048839)|male genitalia development (GO:0030539)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of BMP signaling pathway (GO:0030510)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|ventricular septum development (GO:0003281)	intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E336*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	6						CGTTCAAGTTCTTTTAATTGC	0.502			T	NUP98	AML						OREG0003748	type=REGULATORY REGION|Gene=HOXA13|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																											Dom	yes		7	7p15-p14.2	3209	homeo box A13		L	1	Substitution - Nonsense(1)	large_intestine(1)	7											189	186	187					7																	27237978		2203	4300	6503	27204503	SO:0001587	stop_gained	3209				CCDS5412.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106031	ENSG00000106031		"Homeoboxes / ANTP class : HOXL subclass"	5102	protein-coding gene	gene with protein product		142959	"homeo box A13"	HOX1J, HOX1		1973146, 1358459	Standard	NM_000522		Approved		uc003szb.1	P31271	OTTHUMG00000023438	ENST00000222753.4:c.1006G>T	7.37:g.27237978C>A	ENSP00000222753:p.Glu336*	792	27204503	A4D188|O43371	Nonsense_Mutation	SNP	ENST00000222753.4	37	CCDS5412.1	.	.	.	.	.	.	.	.	.	.	C	36	5.873165	0.97049	.	.	ENSG00000106031	ENST00000222753	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1476	0.93475	0.0:1.0:0.0:0.0	.	.	.	.	X	336	.	ENSP00000222753:E336X	E	-	1	0	HOXA13	27204503	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	6.092000	0.71414	2.609000	0.88269	0.563000	0.77884	GAA		0.502	HOXA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358752.3			A	27237978	C	A	27237978	4	1	61	1	0	0	0	0	0	1	0	0	7312	922	32	2	164	2	HOXA13	7	27237978	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52553	27237978	131900685	5183	13168										
TAX1BP1	8887	broad.mit.edu	37	chr7	27809319	27809319	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattgagaaaaccatgaaaGaaaaagaagaactgttaaag	8	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27809319G>T	ENST00000396319.2	+	5	566	c.478G>T	c.(478-480)Gaa>Taa	p.E160*	TAX1BP1_ENST00000433216.2_Nonsense_Mutation_p.E3*|TAX1BP1_ENST00000494033.1_3'UTR|TAX1BP1_ENST00000265393.6_Nonsense_Mutation_p.E160*|TAX1BP1_ENST00000543117.1_Nonsense_Mutation_p.E160*|TAX1BP1_ENST00000409980.1_Nonsense_Mutation_p.E160*	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	160					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.E160*(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			AACCATGAAAGAAAAAGAAGA	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											46	46	46					7																	27809319		2202	4298	6500	27775844	SO:0001587	stop_gained	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.478G>T	7.37:g.27809319G>T	ENSP00000379612:p.Glu160*		27775844	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Nonsense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	G	38	6.880543	0.97908	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319	.	.	.	5.57	4.67	0.58626	.	0.000000	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.569	15.5706	0.76333	0.0:0.0:0.861:0.139	.	.	.	.	X	160;160;160;3;160	.	ENSP00000265393:E160X	E	+	1	0	TAX1BP1	27775844	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.443000	0.80521	1.306000	0.44926	0.650000	0.86243	GAA		0.294	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		T	27809319	G	T	27809319	4	4	61	1	0	0	0	0	0	1	0	0	15633	943	33	2	492	2	TAX1BP1	7	27809319	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	571341	27809319	131329344	5184	13169										
TAX1BP1	8887	broad.mit.edu	37	chr7	27824920	27824920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcaattgaaaaagaaaccGaattagacaggtatttctca	7	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27824920G>A	ENST00000396319.2	+	6	839	c.751G>A	c.(751-753)Gaa>Aaa	p.E251K	TAX1BP1_ENST00000433216.2_Missense_Mutation_p.E94K|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.E251K|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.E251K|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.E251K	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	251					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.E251K(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			AAAAGAAACCGAATTAGACAG	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	7											63	62	62					7																	27824920		2203	4300	6503	27791445	SO:0001583	missense	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.751G>A	7.37:g.27824920G>A	ENSP00000379612:p.Glu251Lys		27791445	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	G	34	5.341971	0.95783	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319	T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45	5.89	5.89	0.94794	.	0.238942	0.28694	N	0.014457	T	0.41581	0.1165	M	0.73217	2.22	0.80722	D	1	D;D;D	0.71674	0.976;0.998;0.985	P;P;P	0.60117	0.597;0.869;0.793	T	0.13282	-1.0515	10	0.72032	D	0.01	-12.8135	20.2572	0.98426	0.0:0.0:1.0:0.0	.	94;251;251	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	K	251;251;251;94;251	ENSP00000444811:E251K;ENSP00000265393:E251K;ENSP00000386515:E251K;ENSP00000391907:E94K;ENSP00000379612:E251K	ENSP00000265393:E251K	E	+	1	0	TAX1BP1	27791445	1.000000	0.71417	0.994000	0.49952	0.833000	0.47200	7.130000	0.77235	2.793000	0.96121	0.650000	0.86243	GAA		0.284	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		A	27824920	G	A	27824920	3	1	61	1	0	0	0	0	1	0	0	0	15633	1059	37	1	769	1	TAX1BP1	7	27824920	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15601	27824920	131313743	5185	13170										
TAX1BP1	8887	broad.mit.edu	37	chr7	27831747	27831747	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaacgtacgagacagaacGatggcagacctgcatactgc	11	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27831747G>A	ENST00000396319.2	+	9	1249	c.1161G>A	c.(1159-1161)acG>acA	p.T387T	TAX1BP1_ENST00000433216.2_Silent_p.T230T|TAX1BP1_ENST00000265393.6_Silent_p.T387T|TAX1BP1_ENST00000543117.1_Silent_p.T387T|TAX1BP1_ENST00000409980.1_Silent_p.T387T	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	387	Oligomerization.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.T387T(2)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			GAGACAGAACGATGGCAGACC	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	7											106	96	99					7																	27831747		2203	4300	6503	27798272	SO:0001819	synonymous_variant	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1161G>A	7.37:g.27831747G>A			27798272	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	37	CCDS5415.1																																																																																				0.443	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		A	27831747	G	A	27831747	2	1	61	1	0	0	0	0	0	0	0	1	15633	1045	37	1		1	TAX1BP1	7	27831747	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6827	27831747	131306916	5186	13171										
TAX1BP1	8887	broad.mit.edu	37	chr7	27835788	27835788	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtctgtgaaatgaccaaaGaaattgctgacaaaacagaa	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27835788G>T	ENST00000396319.2	+	12	1676	c.1588G>T	c.(1588-1590)Gaa>Taa	p.E530*	TAX1BP1_ENST00000433216.2_Nonsense_Mutation_p.E373*|TAX1BP1_ENST00000265393.6_Nonsense_Mutation_p.E530*|TAX1BP1_ENST00000543117.1_Nonsense_Mutation_p.E530*|TAX1BP1_ENST00000409980.1_Nonsense_Mutation_p.E530*	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	530					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.E530*(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			AATGACCAAAGAAATTGCTGA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											85	95	92					7																	27835788		2203	4300	6503	27802313	SO:0001587	stop_gained	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1588G>T	7.37:g.27835788G>T	ENSP00000379612:p.Glu530*		27802313	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Nonsense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	G	36	5.626590	0.96671	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	.	.	.	5.91	5.91	0.95273	.	0.113488	0.38436	N	0.001693	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-24.2624	17.0175	0.86423	0.0:0.0:1.0:0.0	.	.	.	.	X	530;530;530;373;530;85	.	ENSP00000265393:E530X	E	+	1	0	TAX1BP1	27802313	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.265000	0.58865	2.802000	0.96397	0.655000	0.94253	GAA		0.328	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		T	27835788	G	T	27835788	4	4	61	1	0	0	0	0	0	1	0	0	15633	943	33	2	1630	2	TAX1BP1	7	27835788	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4041	27835788	131302875	5187	13172										
TAX1BP1	8887	broad.mit.edu	37	chr7	27856611	27856611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctgcagccagcctgctcGaaactttagtcggcctgatg	11	12	1	1	rs377595038		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:27856611G>A	ENST00000396319.2	+	15	2127	c.2039G>A	c.(2038-2040)cGa>cAa	p.R680Q	TAX1BP1_ENST00000433216.2_Missense_Mutation_p.R481Q|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.R638Q|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.R638Q|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.R704Q	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	680					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.R680Q(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CAGCCTGCTCGAAACTTTAGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	89	90					7																	27856611		2203	4300	6503	27823136	SO:0001583	missense	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.2039G>A	7.37:g.27856611G>A	ENSP00000379612:p.Arg680Gln		27823136	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	G	33	5.257992	0.95368	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	T;T;T;T;T	0.54479	1.86;1.86;2.44;0.57;1.75	5.91	5.91	0.95273	.	0.000000	0.45867	D	0.000331	T	0.72423	0.3458	M	0.69823	2.125	0.46376	D	0.999011	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.93;0.983;0.987	T	0.65796	-0.6081	10	0.26408	T	0.33	-9.3254	20.2963	0.98556	0.0:0.0:1.0:0.0	.	481;680;638	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	Q	638;638;704;481;680;217	ENSP00000444811:R638Q;ENSP00000265393:R638Q;ENSP00000386515:R704Q;ENSP00000391907:R481Q;ENSP00000379612:R680Q	ENSP00000265393:R638Q	R	+	2	0	TAX1BP1	27823136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.801000	0.69115	2.813000	0.96785	0.655000	0.94253	CGA		0.453	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		A	27856611	G	A	27856611	3	1	61	1	0	0	0	0	1	0	0	0	15633	1058	37	1	2093	1	TAX1BP1	7	27856611	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20823	27856611	131282052	5188	13173										
CREB5	9586	broad.mit.edu	37	chr7	28527810	28527810	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatttatgaggaatccaaGatgaatttggagcaggagag	13	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:28527810G>T	ENST00000357727.2	+	2	411	c.21G>T	c.(19-21)aaG>aaT	p.K7N	CREB5_ENST00000409603.1_5'Flank|CREB5_ENST00000396300.2_5'UTR|CREB5_ENST00000396299.2_Intron	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	7					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K7N(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						AGGAATCCAAGATGAATTTGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											109	111	110					7																	28527810		2203	4300	6503	28494335	SO:0001583	missense	9586			L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.21G>T	7.37:g.28527810G>T	ENSP00000350359:p.Lys7Asn		28494335	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	37	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180615	0.78677	.	.	ENSG00000146592	ENST00000357727	T	0.65364	-0.15	6.08	6.08	0.98989	.	0.142964	0.52532	D	0.000071	T	0.47875	0.1469	N	0.08118	0	0.80722	D	1	B	0.19583	0.037	B	0.11329	0.006	T	0.42155	-0.9468	10	0.62326	D	0.03	-28.6856	20.6634	0.99662	0.0:0.0:1.0:0.0	.	7	Q02930	CREB5_HUMAN	N	7	ENSP00000350359:K7N	ENSP00000350359:K7N	K	+	3	2	CREB5	28494335	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.411000	0.97342	2.894000	0.99253	0.655000	0.94253	AAG		0.512	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		T	28527810	G	T	28527810	3	4	61	1	0	0	0	0	1	0	0	0	3866	933	33	2	27	2	CREB5	7	28527810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	671199	28527810	130610853	5189	13174										
CREB5	9586	broad.mit.edu	37	chr7	28547353	28547353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagaggagagcagcaagCgggtaggtttgcttggatgg	19	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:28547353C>T	ENST00000357727.2	+	4	679	c.289C>T	c.(289-291)Cgg>Tgg	p.R97W	CREB5_ENST00000409603.1_Missense_Mutation_p.R64W|CREB5_ENST00000396300.2_Missense_Mutation_p.R90W|CREB5_ENST00000396299.2_Missense_Mutation_p.R64W	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	97					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R97W(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						GAGCAGCAAGCGGGTAGGTTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	7											87	93	91					7																	28547353		2203	4300	6503	28513878	SO:0001583	missense	9586			L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.289C>T	7.37:g.28547353C>T	ENSP00000350359:p.Arg97Trp		28513878	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	37	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.061267	0.55432	.	.	ENSG00000146592	ENST00000396299;ENST00000424599;ENST00000357727;ENST00000396300;ENST00000409603	T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39	5.49	3.49	0.39957	.	0.055994	0.64402	D	0.000001	T	0.35364	0.0929	L	0.54323	1.7	0.80722	D	1	D	0.63880	0.993	B	0.44315	0.446	T	0.25187	-1.0139	10	0.52906	T	0.07	-22.8426	11.4148	0.49945	0.546:0.4539:0.0:0.0	.	97	Q02930	CREB5_HUMAN	W	64;90;97;90;64	ENSP00000379593:R64W;ENSP00000394088:R90W;ENSP00000350359:R97W;ENSP00000379594:R90W;ENSP00000387197:R64W	ENSP00000350359:R97W	R	+	1	2	CREB5	28513878	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.586000	0.46119	1.303000	0.44873	0.655000	0.94253	CGG		0.567	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		T	28547353	C	T	28547353	3	4	61	1	0	0	0	0	1	0	0	0	3866	759	27	1	303	1	CREB5	7	28547353	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19543	28547353	130591310	5190	13175										
CREB5	9586	broad.mit.edu	37	chr7	28725814	28725814	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcctcagtgatgtccatgaGgtttgtttttaattttattt	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:28725814G>T	ENST00000357727.2	+	6	854				CREB5_ENST00000409603.1_Intron|CREB5_ENST00000396300.2_Intron|CREB5_ENST00000396299.2_Intron|CREB5_ENST00000396298.2_Splice_Site_p.R16M	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R16M(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						ATGTCCATGAGGTTTGTTTTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											165	150	155					7																	28725814		1871	4102	5973	28692339	SO:0001627	intron_variant	9586			L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.465-32556G>T	7.37:g.28725814G>T			28692339	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	37	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845209	0.51164	.	.	ENSG00000146592	ENST00000396298	T	0.64085	-0.08	6.17	6.17	0.99709	.	.	.	.	.	T	0.60405	0.2266	N	0.02011	-0.69	0.45172	D	0.998186	D;D	0.76494	0.999;0.99	D;D	0.81914	0.995;0.962	T	0.73375	-0.4002	9	0.52906	T	0.07	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	16;16	B7Z4Z1;B4DU13	.;.	M	16	ENSP00000379592:R16M	ENSP00000379592:R16M	R	+	2	0	CREB5	28692339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.094000	0.76944	2.941000	0.99782	0.655000	0.94253	AGG		0.413	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		T	28725814	G	T	28725814	1	4	61	0	1	0	0	0	0	0	0	0	3866	1014	35	2		2	CREB5	7	28725814	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178461	28725814	130412849	5191	13176										
CPVL	54504	broad.mit.edu	37	chr7	29070308	29070308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatcctttccagtccatgCccatcaaggagcgctctgtc	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:29070308C>T	ENST00000409850.1	-	16	1851	c.1205G>A	c.(1204-1206)gGc>gAc	p.G402D	CPVL_ENST00000396276.3_Missense_Mutation_p.G402D|CPVL_ENST00000265394.5_Missense_Mutation_p.G402D			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	402						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)	p.G402D(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						CCAGTCCATGCCCATCAAGGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											138	135	136					7																	29070308		2203	4300	6503	29036833	SO:0001583	missense	54504			AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"carboxypeptidase WUG", "vitellogenic carboxypeptidase-like protein", "CP-Mac carboxypeptidase"	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.1205G>A	7.37:g.29070308C>T	ENSP00000387164:p.Gly402Asp		29036833	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	C	6.225	0.409683	0.11812	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000455893;ENST00000409850	D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97	5.71	3.89	0.44902	.	0.441828	0.26341	N	0.024935	T	0.70971	0.3285	N	0.12569	0.235	0.26936	N	0.966341	B	0.33000	0.393	B	0.35971	0.215	T	0.59820	-0.7382	10	0.13853	T	0.58	1.8027	10.8978	0.47034	0.074:0.1348:0.7912:0.0	.	402	Q9H3G5	CPVL_HUMAN	D	402;402;67;402	ENSP00000265394:G402D;ENSP00000379572:G402D;ENSP00000403580:G67D;ENSP00000387164:G402D	ENSP00000265394:G402D	G	-	2	0	CPVL	29036833	1.000000	0.71417	0.990000	0.47175	0.079000	0.17450	4.614000	0.61183	1.404000	0.46819	-0.353000	0.07706	GGC		0.473	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		T	29070308	C	T	29070308	3	4	61	1	0	0	0	0	1	0	0	0	3841	739	26	3	233	3	CPVL	7	29070308	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344494	29070308	130068355	5192	13177										
WIPF3	644150	broad.mit.edu	37	chr7	29915483	29915483	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttgcgaagggcagatcCgaaaggccggagtgcgctgt	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:29915483C>T	ENST00000409290.1	+	2	128	c.128C>T	c.(127-129)cCg>cTg	p.P43L	WIPF3_ENST00000409123.1_Missense_Mutation_p.P43L|WIPF3_ENST00000242140.5_Missense_Mutation_p.P43L	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	43					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)		p.P43L(1)		breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						AGGGCAGATCCGAAAGGCCGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	7											64	72	69					7																	29915483		2108	4242	6350	29882008	SO:0001583	missense	644150			AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.128C>T	7.37:g.29915483C>T	ENSP00000386878:p.Pro43Leu		29882008	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050013	0.19827	.	.	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.46451	0.87;0.87;0.87	5.22	1.54	0.23209	.	0.466636	0.18447	N	0.140941	T	0.26521	0.0648	L	0.35854	1.095	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.10800	-1.0614	10	0.36615	T	0.2	.	3.3734	0.07229	0.1887:0.5393:0.0:0.272	.	43	A6NGB9	WIPF3_HUMAN	L	43	ENSP00000386790:P43L;ENSP00000386878:P43L;ENSP00000242140:P43L	ENSP00000242140:P43L	P	+	2	0	WIPF3	29882008	0.000000	0.05858	0.250000	0.24296	0.520000	0.34377	0.406000	0.21032	0.854000	0.35336	0.643000	0.83706	CCG		0.517	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			T	29915483	C	T	29915483	3	4	61	1	0	0	0	0	1	0	0	0	17409	652	23	1	134	1	WIPF3	7	29915483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	845175	29915483	129223180	5193	13178										
FKBP14	55033	broad.mit.edu	37	chr7	30058686	30058686	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggatcttggtccatttcGaatctccaggagatcaatat	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30058686G>A	ENST00000222803.5	-	3	578	c.403C>T	c.(403-405)Cga>Tga	p.R135*	AC007285.6_ENST00000419103.1_RNA|AC007285.6_ENST00000422239.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	135	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.|PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R135*(1)		breast(1)|large_intestine(2)|lung(2)	5						GGTCCATTTCGAATCTCCAGG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											109	111	110					7																	30058686		2203	4300	6503	30025211	SO:0001587	stop_gained	55033			AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"EF-hand domain containing"	18625	protein-coding gene	gene with protein product		614505	"FK506 binding protein 14 (22 kDa)"			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.403C>T	7.37:g.30058686G>A	ENSP00000222803:p.Arg135*		30025211		Nonsense_Mutation	SNP	ENST00000222803.5	37	CCDS5423.1	.	.	.	.	.	.	.	.	.	.	G	37	6.200192	0.97371	.	.	ENSG00000106080	ENST00000222803	.	.	.	5.74	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-3.1929	12.2885	0.54805	0.0:0.0:0.5857:0.4143	.	.	.	.	X	135	.	ENSP00000222803:R135X	R	-	1	2	FKBP14	30025211	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.969000	0.40510	1.390000	0.46547	0.591000	0.81541	CGA		0.388	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946		A	30058686	G	A	30058686	4	1	61	1	0	0	0	0	0	1	0	0	5923	1066	37	1	240	1	FKBP14	7	30058686	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143203	30058686	129079977	5194	13179										
PLEKHA8	84725	broad.mit.edu	37	chr7	30092382	30092382	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatggaaataaatggtgaGgaagaaatcctaatgaaaaa	9	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30092382G>T	ENST00000449726.1	+	7	1046	c.696G>T	c.(694-696)gaG>gaT	p.E232D	PLEKHA8_ENST00000396259.1_Missense_Mutation_p.E232D|PLEKHA8_ENST00000258679.7_Missense_Mutation_p.E232D|PLEKHA8_ENST00000396257.2_Missense_Mutation_p.E232D	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	232				E -> G (in Ref. 4; BAB14449). {ECO:0000305}.	ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)	p.E232D(2)		breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						TAAATGGTGAGGAAGAAATCC	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	7											28	29	29					7																	30092382		2193	4288	6481	30058907	SO:0001583	missense	84725			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.696G>T	7.37:g.30092382G>T	ENSP00000397947:p.Glu232Asp		30058907	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Missense_Mutation	SNP	ENST00000449726.1	37	CCDS56473.1	.	.	.	.	.	.	.	.	.	.	G	4.279	0.050893	0.08243	.	.	ENSG00000106086	ENST00000258679;ENST00000449726;ENST00000396257;ENST00000396259;ENST00000440706	.	.	.	5.95	1.87	0.25490	.	1.008340	0.07958	N	0.981967	T	0.15219	0.0367	N	0.08118	0	0.20196	N	0.999923	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.31833	-0.9929	9	0.13470	T	0.59	-28.6246	1.7616	0.02993	0.1344:0.1666:0.1441:0.5548	.	232;232;232;232	Q96JA3-2;Q96JA3;Q96JA3-3;B4DH00	.;PKHA8_HUMAN;.;.	D	232;232;232;232;258	.	ENSP00000258679:E232D	E	+	3	2	PLEKHA8	30058907	0.993000	0.37304	0.999000	0.59377	0.782000	0.44232	0.233000	0.17911	0.500000	0.27991	-0.266000	0.10368	GAG		0.313	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		T	30092382	G	T	30092382	3	4	61	1	0	0	0	0	1	0	0	0	12093	991	35	2	722	2	PLEKHA8	7	30092382	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33696	30092382	129046281	5195	13180										
PLEKHA8	84725	broad.mit.edu	37	chr7	30094454	30094454	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaggcaaagaagttatccCaactttctttagtaccatga	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30094454C>A	ENST00000449726.1	+	8	1276	c.926C>A	c.(925-927)cCa>cAa	p.P309Q	PLEKHA8_ENST00000396259.1_Missense_Mutation_p.P309Q|PLEKHA8_ENST00000258679.7_Missense_Mutation_p.P309Q|PLEKHA8_ENST00000396257.2_Missense_Mutation_p.P309Q	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	309					ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)	p.P309Q(1)		breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						GAAGTTATCCCAACTTTCTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											165	157	160					7																	30094454		2203	4300	6503	30060979	SO:0001583	missense	84725			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.926C>A	7.37:g.30094454C>A	ENSP00000397947:p.Pro309Gln		30060979	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Missense_Mutation	SNP	ENST00000449726.1	37	CCDS56473.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284475	0.23392	.	.	ENSG00000106086	ENST00000258679;ENST00000449726;ENST00000396257;ENST00000396259;ENST00000440706	.	.	.	5.96	4.03	0.46877	Glycolipid transfer protein domain (1);	0.335640	0.32401	N	0.006146	T	0.23451	0.0567	N	0.03608	-0.345	0.33848	D	0.632255	B;B;B;B	0.19583	0.008;0.005;0.037;0.006	B;B;B;B	0.15052	0.007;0.002;0.012;0.001	T	0.21143	-1.0254	9	0.42905	T	0.14	-14.8007	10.533	0.44988	0.1529:0.7135:0.1336:0.0	.	309;309;309;309	Q96JA3-2;Q96JA3;Q96JA3-3;B4DH00	.;PKHA8_HUMAN;.;.	Q	309;309;309;309;335	.	ENSP00000258679:P309Q	P	+	2	0	PLEKHA8	30060979	0.858000	0.29795	1.000000	0.80357	0.984000	0.73092	1.672000	0.37523	2.830000	0.97506	0.655000	0.94253	CCA		0.403	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		A	30094454	C	A	30094454	3	1	61	1	0	0	0	0	1	0	0	0	12093	594	21	2	956	2	PLEKHA8	7	30094454	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2072	30094454	129044209	5196	13181										
NOD1	10392	broad.mit.edu	37	chr7	30492330	30492330	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagctgaacatgcggcagcGaaagtggaagaagaatttga	14	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30492330G>A	ENST00000222823.4	-	6	1228	c.703C>T	c.(703-705)Cgc>Tgc	p.R235C	NOD1_ENST00000423334.2_Intron	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	235	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)	p.R235C(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						ATGCGGCAGCGAAAGTGGAAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	7											70	75	73					7																	30492330		2203	4300	6503	30458855	SO:0001583	missense	10392			AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"Nucleotide-binding domain and leucine rich repeat containing"	16390	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1", "NLR family, CARD domain containing 1"	605980	"caspase recruitment domain family, member 4"	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.703C>T	7.37:g.30492330G>A	ENSP00000222823:p.Arg235Cys		30458855	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457232	0.43634	.	.	ENSG00000106100	ENST00000222823	T	0.78003	-1.14	5.64	4.75	0.60458	NACHT nucleoside triphosphatase (1);	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87415	0.2378	10	0.56958	D	0.05	.	10.7004	0.45924	0.0:0.1431:0.7083:0.1486	.	235	Q9Y239	NOD1_HUMAN	C	235	ENSP00000222823:R235C	ENSP00000222823:R235C	R	-	1	0	NOD1	30458855	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	3.862000	0.56009	1.350000	0.45770	0.655000	0.94253	CGC		0.607	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30492330	G	A	30492330	3	1	61	1	0	0	0	0	1	0	0	0	10547	1058	37	1	2194	1	NOD1	7	30492330	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	397876	30492330	128646333	5197	13182										
CRHR2	1395	broad.mit.edu	37	chr7	30693116	30693116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgctgtggaagctgatcCgtgtgggtgatgtagggatg	18	4	0	3	rs143322026		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30693116C>T	ENST00000471646.1	-	12	1613	c.1196G>A	c.(1195-1197)cGg>cAg	p.R399Q	CRHR2_ENST00000341843.4_Missense_Mutation_p.R385Q|CRHR2_ENST00000506074.2_3'UTR|CRHR2_ENST00000348438.4_Missense_Mutation_p.R426Q	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	399					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)	p.R399Q(2)|p.R399L(1)|p.R385L(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GAAGCTGATCCGTGTGGGTGA	0.642																																																4	Substitution - Missense(4)	lung(2)|large_intestine(1)|skin(1)	7											180	162	168					7																	30693116		2203	4300	6503	30659641	SO:0001583	missense	1395				CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.1196G>A	7.37:g.30693116C>T	ENSP00000418722:p.Arg399Gln		30659641	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	37	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956674	0.92726	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843	T;T;T	0.44482	0.92;1.07;0.94	4.45	3.56	0.40772	.	0.050721	0.64402	D	0.000001	T	0.55593	0.1930	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.76494	0.996;0.999;0.992;0.996	P;P;P;P	0.62491	0.716;0.903;0.723;0.716	T	0.53858	-0.8379	10	0.37606	T	0.19	.	10.868	0.46866	0.0:0.9042:0.0:0.0958	.	398;426;385;399	B3SXT0;Q13324-2;Q13324-3;Q13324	.;.;.;CRFR2_HUMAN	Q	399;426;385	ENSP00000418722:R399Q;ENSP00000340943:R426Q;ENSP00000344304:R385Q	ENSP00000344304:R385Q	R	-	2	0	CRHR2	30659641	0.423000	0.25482	0.643000	0.29450	0.892000	0.51952	4.938000	0.63519	1.008000	0.39264	0.461000	0.40582	CGG		0.642	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3			T	30693116	C	T	30693116	3	4	61	1	0	0	0	0	1	0	0	0	3878	652	23	1	43	1	CRHR2	7	30693116	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200786	30693116	128445547	5198	13183										
CRHR2	1395	broad.mit.edu	37	chr7	30694688	30694688	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagtagaagacagacacGaagaaaccctggaaaggagg	13	7	0	4	rs552742156		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30694688G>A	ENST00000471646.1	-	11	1479	c.1062C>T	c.(1060-1062)ttC>ttT	p.F354F	CRHR2_ENST00000341843.4_Silent_p.F340F|CRHR2_ENST00000506074.2_Silent_p.F354F|CRHR2_ENST00000348438.4_Silent_p.F381F	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	354					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)	p.F354F(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGACAGACACGAAGAAACCCT	0.602													G|||	1	0.000199681	8e-04	0	5008	,	,		17415	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											78	67	71					7																	30694688		2203	4300	6503	30661213	SO:0001819	synonymous_variant	1395				CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.1062C>T	7.37:g.30694688G>A			30661213	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Silent	SNP	ENST00000471646.1	37	CCDS5429.1																																																																																				0.602	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3			A	30694688	G	A	30694688	2	1	61	1	0	0	0	0	0	0	0	1	3878	1049	37	1		1	CRHR2	7	30694688	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1572	30694688	128443975	5199	13184										
INMT	11185	broad.mit.edu	37	chr7	30793369	30793369	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctccaaggggacacgctGattgacattggctcaggtcc	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30793369G>T	ENST00000013222.5	+	2	193	c.177G>T	c.(175-177)ctG>ctT	p.L59L	INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Silent_p.L58L|INMT_ENST00000409539.1_Silent_p.L58L	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	59					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)	p.L59L(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						GGGACACGCTGATTGACATTG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	7											279	257	264					7																	30793369		2203	4300	6503	30759894	SO:0001819	synonymous_variant	11185				CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.177G>T	7.37:g.30793369G>T			30759894	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																				0.542	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774		T	30793369	G	T	30793369	2	4	61	1	0	0	0	0	0	0	0	1	7766	1277	45	2		2	INMT	7	30793369	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98681	30793369	128345294	5200	13185										
INMT	11185	broad.mit.edu	37	chr7	30793498	30793498	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggctgaagaaggagccGggggcctatgactggacccc	16	10	0	3	rs147050778		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:30793498G>A	ENST00000013222.5	+	2	322	c.306G>A	c.(304-306)ccG>ccA	p.P102P	INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Silent_p.P101P|INMT_ENST00000409539.1_Silent_p.P101P	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	102					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)	p.P102P(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						AGAAGGAGCCGGGGGCCTATG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	7						G	,	0,4406		0,0,2203	90	99	96		303,306	-7.4	0.2	7	dbSNP_134	96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	101/263,102/264	30793498	1,13005	2203	4300	6503	30760023	SO:0001819	synonymous_variant	11185				CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.306G>A	7.37:g.30793498G>A			30760023	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																				0.572	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774		A	30793498	G	A	30793498	2	1	61	1	0	0	0	0	0	0	0	1	7766	1103	39	1		1	INMT	7	30793498	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129	30793498	128345165	5201	13186										
ADCYAP1R1	117	broad.mit.edu	37	chr7	31123784	31123784	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgagccggaactgcacGgaggatggctggtcggaacc	18	9	0	1	rs375886816		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:31123784G>A	ENST00000304166.4	+	7	646	c.357G>A	c.(355-357)acG>acA	p.T119T	ADCYAP1R1_ENST00000409363.1_Silent_p.T98T|ADCYAP1R1_ENST00000396211.2_Silent_p.T119T|ADCYAP1R1_ENST00000409489.1_Silent_p.T119T	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	119					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.T119T(1)		endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						GGAACTGCACGGAGGATGGCT	0.498																																					Ovarian(44;225 1186 2158 11092)											1	Substitution - coding silent(1)	large_intestine(1)	7						G	,,,	0,4406		0,0,2203	173	166	169		357,357,357,294	-11.3	0	7		169	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADCYAP1R1	NM_001118.4,NM_001199635.1,NM_001199636.1,NM_001199637.1	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	119/469,119/497,119/496,98/448	31123784	1,13005	2203	4300	6503	31090309	SO:0001819	synonymous_variant	117				CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.357G>A	7.37:g.31123784G>A			31090309	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Silent	SNP	ENST00000304166.4	37	CCDS5433.1																																																																																				0.498	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		A	31123784	G	A	31123784	2	1	61	1	0	0	0	0	0	0	0	1	303	1103	39	1		1	ADCYAP1R1	7	31123784	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	330286	31123784	128014879	5202	13187										
CCDC129	223075	broad.mit.edu	37	chr7	31617622	31617622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtgagtgccgccaaagaGcatcgaagaagaatgggtaa	13	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:31617622G>T	ENST00000407970.3	+	8	782	c.744G>T	c.(742-744)gaG>gaT	p.E248D	CCDC129_ENST00000319386.3_Intron|CCDC129_ENST00000451887.2_Missense_Mutation_p.E274D|CCDC129_ENST00000409210.1_Missense_Mutation_p.E156D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	248								p.E248D(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CCGCCAAAGAGCATCGAAGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	7											73	66	68					7																	31617622		2203	4300	6503	31584147	SO:0001583	missense	223075			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.744G>T	7.37:g.31617622G>T	ENSP00000384416:p.Glu248Asp		31584147	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	11.38	1.622743	0.28889	.	.	ENSG00000180347	ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T	0.19250	2.42;2.41;2.16	5.38	-2.93	0.05598	.	.	.	.	.	T	0.18002	0.0432	M	0.61703	1.905	0.09310	N	1	B;B;B	0.32653	0.037;0.379;0.379	B;B;B	0.28553	0.012;0.091;0.091	T	0.18335	-1.0340	8	.	.	.	-17.6219	9.0103	0.36137	0.672:0.1312:0.1968:0.0	.	274;258;248	F5H3V5;F5H2J8;Q6ZRS4	.;.;CC129_HUMAN	D	248;274;258;156	ENSP00000384416:E248D;ENSP00000395835:E274D;ENSP00000387214:E156D	.	E	+	3	2	CCDC129	31584147	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-1.319000	0.02702	-0.398000	0.07679	-0.136000	0.14681	GAG		0.488	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31617622	G	T	31617622	3	4	61	1	0	0	0	0	1	0	0	0	2770	962	34	2	770	2	CCDC129	7	31617622	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	493838	31617622	127521041	5203	13188										
CCDC129	223075	broad.mit.edu	37	chr7	31682786	31682786	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtctcaaaggtcacctgGaaatgatcatactcaagaca	8	9	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:31682786G>T	ENST00000407970.3	+	11	1840	c.1802G>T	c.(1801-1803)gGa>gTa	p.G601V	CCDC129_ENST00000319386.3_Missense_Mutation_p.G453V|CCDC129_ENST00000451887.2_Missense_Mutation_p.G627V|CCDC129_ENST00000409210.1_Missense_Mutation_p.G509V	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	601								p.G601V(1)|p.G453V(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGGTCACCTGGAAATGATCAT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	7											128	129	128					7																	31682786		2203	4300	6503	31649311	SO:0001583	missense	223075			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1802G>T	7.37:g.31682786G>T	ENSP00000384416:p.Gly601Val		31649311	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893069	0.52121	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.19938	2.11;2.38;2.38;2.12	6.02	3.24	0.37175	.	0.729121	0.12823	N	0.436311	T	0.40247	0.1109	M	0.67953	2.075	0.09310	N	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.996	D;D;D;D	0.68192	0.956;0.956;0.956;0.931	T	0.12915	-1.0529	10	0.48119	T	0.1	-27.4258	8.4062	0.32616	0.2439:0.0:0.7561:0.0	.	627;611;601;453	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	V	453;601;627;611;509	ENSP00000313062:G453V;ENSP00000384416:G601V;ENSP00000395835:G627V;ENSP00000387214:G509V	ENSP00000313062:G453V	G	+	2	0	CCDC129	31649311	0.000000	0.05858	0.003000	0.11579	0.189000	0.23516	0.065000	0.14466	0.427000	0.26145	0.655000	0.94253	GGA		0.488	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31682786	G	T	31682786	3	4	61	1	0	0	0	0	1	0	0	0	2770	1174	41	2	1840	2	CCDC129	7	31682786	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65164	31682786	127455877	5204	13189										
CCDC129	223075	broad.mit.edu	37	chr7	31691556	31691556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctattatttacttgcagggaGgaggccgagcaactgcaaac	11	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:31691556G>T	ENST00000407970.3	+	13	2753	c.2715G>T	c.(2713-2715)gaG>gaT	p.E905D	CCDC129_ENST00000319386.3_Missense_Mutation_p.E757D|CCDC129_ENST00000451887.2_Missense_Mutation_p.E931D|CCDC129_ENST00000409210.1_Missense_Mutation_p.E813D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	905								p.E905D(1)|p.E757D(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CTTGCAGGGAGGAGGCCGAGC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	7											58	53	54					7																	31691556		2203	4299	6502	31658081	SO:0001583	missense	223075			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2715G>T	7.37:g.31691556G>T	ENSP00000384416:p.Glu905Asp		31658081	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588365	0.46110	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.21	2.13	0.27403	.	0.252828	0.28006	N	0.016967	T	0.42314	0.1197	M	0.71581	2.175	0.26791	N	0.969395	D;D;D;D	0.60575	0.986;0.987;0.987;0.988	P;P;P;P	0.57009	0.737;0.811;0.811;0.794	T	0.27157	-1.0082	10	0.51188	T	0.08	-4.7803	6.482	0.22067	0.3653:0.0:0.6347:0.0	.	931;915;905;757	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	D	757;905;931;915;813	ENSP00000313062:E757D;ENSP00000384416:E905D;ENSP00000395835:E931D;ENSP00000387214:E813D	ENSP00000313062:E757D	E	+	3	2	CCDC129	31658081	1.000000	0.71417	0.998000	0.56505	0.299000	0.27559	0.665000	0.25083	0.112000	0.17975	-0.367000	0.07326	GAG		0.453	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31691556	G	T	31691556	3	4	61	1	0	0	0	0	1	0	0	0	2770	991	35	2	2761	2	CCDC129	7	31691556	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8770	31691556	127447107	5205	13190										
PDE1C	5137	broad.mit.edu	37	chr7	31862779	31862779	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatagtcaacggagatgacaGaattgttgatcggggcactt	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:31862779G>T	ENST00000396191.1	-	14	1945	c.1490C>A	c.(1489-1491)tCt>tAt	p.S497Y	PDE1C_ENST00000396184.3_Missense_Mutation_p.S497Y|PDE1C_ENST00000321453.7_Missense_Mutation_p.S497Y|PDE1C_ENST00000396193.1_Missense_Mutation_p.S557Y|PDE1C_ENST00000396182.2_Missense_Mutation_p.S497Y|PDE1C_ENST00000479980.1_5'Flank	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	497	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.S497Y(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GGAGATGACAGAATTGTTGAT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	7											138	121	126					7																	31862779		2203	4300	6503	31829304	SO:0001583	missense	5137			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1490C>A	7.37:g.31862779G>T	ENSP00000379494:p.Ser497Tyr		31829304	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365021	0.61513	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.75154	-0.89;-0.91;-0.91;-0.86;-0.86	5.91	5.0	0.66597	.	0.791890	0.12092	N	0.500306	T	0.80221	0.4583	L	0.34521	1.04	0.52501	D	0.99995	D;P;P	0.54397	0.966;0.89;0.929	D;P;P	0.64237	0.923;0.823;0.624	T	0.79427	-0.1808	10	0.87932	D	0	.	16.1278	0.81406	0.0:0.0:0.8657:0.1343	.	497;557;497	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	Y	557;497;497;497;497	ENSP00000379496:S557Y;ENSP00000379494:S497Y;ENSP00000318105:S497Y;ENSP00000379487:S497Y;ENSP00000379485:S497Y	ENSP00000318105:S497Y	S	-	2	0	PDE1C	31829304	1.000000	0.71417	0.751000	0.31187	0.220000	0.24768	4.915000	0.63355	2.808000	0.96608	0.655000	0.94253	TCT		0.468	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			T	31862779	G	T	31862779	3	4	61	1	0	0	0	0	1	0	0	0	11666	942	33	2	430	2	PDE1C	7	31862779	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171223	31862779	127275884	5206	13191										
AVL9	23080	broad.mit.edu	37	chr7	32591904	32591904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaaggatcccaagtatatCttggtaagtaactgacttac	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:32591904C>A	ENST00000318709.4	+	6	747	c.526C>A	c.(526-528)Ctt>Att	p.L176I	AVL9_ENST00000404479.1_Missense_Mutation_p.L176I|AVL9_ENST00000409301.1_Missense_Mutation_p.L176I	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	176					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)		p.L176I(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CCAAGTATATCTTGGTAAGTA	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	7											45	47	46					7																	32591904		2203	4296	6499	32558429	SO:0001583	missense	23080			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.526C>A	7.37:g.32591904C>A	ENSP00000315568:p.Leu176Ile		32558429	Q92573	Missense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.123306	0.56613	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.61299	0.2336	L	0.52126	1.63	0.80722	D	1	D;B;D	0.89917	1.0;0.34;0.957	D;B;P	0.87578	0.998;0.155;0.545	T	0.54430	-0.8295	9	.	.	.	2.0499	20.1057	0.97893	0.0:1.0:0.0:0.0	.	176;176;176	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	I	176;176;176;176;107	ENSP00000315568:L176I;ENSP00000387011:L176I;ENSP00000385242:L176I;ENSP00000395134:L107I	.	L	+	1	0	AVL9	32558429	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.262000	0.78410	2.827000	0.97445	0.650000	0.86243	CTT		0.318	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		A	32591904	C	A	32591904	3	1	61	1	0	0	0	0	1	0	0	0	1229	913	32	2	548	2	AVL9	7	32591904	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	729125	32591904	126546759	5207	13192										
KBTBD2	25948	broad.mit.edu	37	chr7	32909951	32909951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacataacttgtaaacttttTctgcttgggggctgtaacag	9	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:32909951T>C	ENST00000304056.4	-	4	1577	c.878A>G	c.(877-879)gAa>gGa	p.E293G	AVL9_ENST00000404479.1_Intron|KBTBD2_ENST00000485611.1_5'Flank	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	293								p.E293G(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			GTAAACTTTTTCTGCTTGGGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											93	86	88					7																	32909951		2203	4300	6503	32876476	SO:0001583	missense	25948			AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"BTB/POZ domain containing"	21751	protein-coding gene	gene with protein product			"BTB and kelch domain containing 1"	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.878A>G	7.37:g.32909951T>C	ENSP00000302586:p.Glu293Gly		32876476	A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Missense_Mutation	SNP	ENST00000304056.4	37	CCDS34614.1	.	.	.	.	.	.	.	.	.	.	T	7.573	0.667106	0.14710	.	.	ENSG00000170852	ENST00000304056;ENST00000537125	T	0.63255	-0.03	5.74	5.74	0.90152	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	N	0.11364	0.135	0.58432	D	0.999999	B	0.12630	0.006	B	0.09377	0.004	T	0.34675	-0.9819	10	0.17369	T	0.5	.	16.3305	0.83010	0.0:0.0:0.0:1.0	.	293	Q8IY47	KBTB2_HUMAN	G	293;100	ENSP00000302586:E293G	ENSP00000302586:E293G	E	-	2	0	KBTBD2	32876476	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.249000	0.72427	2.317000	0.78254	0.459000	0.35465	GAA		0.408	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224		C	32909951	T	C	32909951	3	2	61	1	0	0	0	0	1	0	0	0	8014	1783	62	4	997	4	KBTBD2	7	32909951	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	318047	32909951	126228712	5208	13193										
FKBP9	11328	broad.mit.edu	37	chr7	33042434	33042434	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaaggatggcaacggaGaagtcctcctggaagaggta	14	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:33042434G>T	ENST00000242209.4	+	9	1688	c.1519G>T	c.(1519-1521)Gaa>Taa	p.E507*	RNU6-388P_ENST00000517012.1_RNA|FKBP9_ENST00000538443.1_Nonsense_Mutation_p.E369*|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Nonsense_Mutation_p.E560*|FKBP9_ENST00000490776.2_Nonsense_Mutation_p.E275*	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	507	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.E507*(1)|p.E275*(1)		central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			TGGCAACGGAGAAGTCCTCCT	0.552																																																2	Substitution - Nonsense(2)	large_intestine(2)	7											94	68	77					7																	33042434		2203	4300	6503	33008959	SO:0001587	stop_gained	11328			AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.1519G>T	7.37:g.33042434G>T	ENSP00000242209:p.Glu507*		33008959	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Nonsense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	G	39	7.721551	0.98453	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443;ENST00000490776	.	.	.	4.8	4.8	0.61643	.	0.176270	0.49305	D	0.000159	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-13.2163	17.8793	0.88835	0.0:0.0:1.0:0.0	.	.	.	.	X	507;560;369;275	.	ENSP00000242209:E507X	E	+	1	0	FKBP9	33008959	0.999000	0.42202	0.997000	0.53966	0.984000	0.73092	1.580000	0.36547	2.228000	0.72767	0.555000	0.69702	GAA		0.552	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		T	33042434	G	T	33042434	4	4	61	1	0	0	0	0	0	1	0	0	5934	943	33	2	1553	2	FKBP9	7	33042434	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132483	33042434	126096229	5209	13194										
NPSR1	387129	broad.mit.edu	37	chr7	34874019	34874019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtatggcattgtgatccGaactatttggattaaaagca	9	6	0	1	rs116249859	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:34874019G>A	ENST00000360581.1	+	6	832	c.704G>A	c.(703-705)cGa>cAa	p.R235Q	NPSR1_ENST00000381539.3_Missense_Mutation_p.R235Q|NPSR1_ENST00000531252.1_Missense_Mutation_p.R224Q|NPSR1_ENST00000359791.1_Missense_Mutation_p.R235Q|NPSR1_ENST00000381542.1_Missense_Mutation_p.R169Q	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	235						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)	p.R235Q(4)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	ATTGTGATCCGAACTATTTGG	0.438													G|||	4	0.000798722	0	0	5008	,	,		21671	0.004		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	7											197	169	179					7																	34874019		2203	4300	6503	34840544	SO:0001583	missense	387129			AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.704G>A	7.37:g.34874019G>A	ENSP00000353788:p.Arg235Gln		34840544	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	21.6	4.168595	0.78339	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	4.75	3.87	0.44632	GPCR, rhodopsin-like superfamily (1);	0.193094	0.29260	N	0.012678	T	0.56572	0.1994	M	0.64080	1.96	0.40488	D	0.980513	D;D;D;P;D;P	0.89917	1.0;1.0;1.0;0.892;1.0;0.911	D;P;D;P;P;P	0.66716	0.946;0.801;0.91;0.474;0.801;0.541	T	0.55405	-0.8146	10	0.31617	T	0.26	-5.4177	11.8755	0.52544	0.0859:0.0:0.9141:0.0	.	169;224;169;235;235;235	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	Q	235;169;235;224;235	ENSP00000353788:R235Q;ENSP00000370953:R169Q;ENSP00000352839:R235Q;ENSP00000433258:R224Q;ENSP00000370950:R235Q	ENSP00000352839:R235Q	R	+	2	0	NPSR1	34840544	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.383000	0.44354	1.212000	0.43366	0.555000	0.69702	CGA		0.438	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		A	34874019	G	A	34874019	3	1	61	1	0	0	0	0	1	0	0	0	10631	1058	37	1	726	1	NPSR1	7	34874019	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1831585	34874019	124264644	5210	13195										
DPY19L1	23333	broad.mit.edu	37	chr7	34985293	34985293	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaccttacatgtgtctgTtgtttagctaagacacccca	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:34985293T>A	ENST00000310974.4	-	16	1455	c.1311A>T	c.(1309-1311)caA>caT	p.Q437H		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	437						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.Q437H(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						CATGTGTCTGTTGTTTAGCTA	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	7											52	49	50					7																	34985293		1795	4045	5840	34951818	SO:0001583	missense	23333			AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1311A>T	7.37:g.34985293T>A	ENSP00000308695:p.Gln437His		34951818	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102479	0.56183	.	.	ENSG00000173852	ENST00000310974	T	0.55588	0.51	5.37	-5.47	0.02600	.	1.181040	0.05974	N	0.642855	T	0.29491	0.0735	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.29549	-1.0008	10	0.49607	T	0.09	-1.5431	9.5252	0.39160	0.1396:0.6328:0.0:0.2276	.	437	Q2PZI1	D19L1_HUMAN	H	437	ENSP00000308695:Q437H	ENSP00000308695:Q437H	Q	-	3	2	DPY19L1	34951818	0.887000	0.30362	0.424000	0.26647	0.989000	0.77384	-0.592000	0.05747	-0.844000	0.04184	0.482000	0.46254	CAA		0.264	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			A	34985293	T	A	34985293	3	1	61	1	0	0	0	0	1	0	0	0	4751	1722	60	5	744	5	DPY19L1	7	34985293	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	111274	34985293	124153370	5211	13196										
DPY19L1	23333	broad.mit.edu	37	chr7	34989478	34989478	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaaatccttataactaaaGaattttgatgttagtaagtt	5	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:34989478G>T	ENST00000310974.4	-	14	1278	c.1134C>A	c.(1132-1134)ttC>ttA	p.F378L		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	378						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.F378L(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TATAACTAAAGAATTTTGATG	0.294																																																2	Substitution - Missense(2)	large_intestine(2)	7											35	33	34					7																	34989478		1800	4058	5858	34956003	SO:0001583	missense	23333			AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1134C>A	7.37:g.34989478G>T	ENSP00000308695:p.Phe378Leu		34956003	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137422	0.37728	.	.	ENSG00000173852	ENST00000310974;ENST00000446375	T;T	0.54279	0.58;0.58	5.09	5.09	0.68999	.	0.048832	0.85682	D	0.000000	T	0.59649	0.2209	L	0.49571	1.57	0.53005	D	0.999961	D	0.57257	0.979	D	0.74023	0.982	T	0.55211	-0.8176	10	0.14656	T	0.56	-18.1179	7.7651	0.28976	0.1814:0.0:0.8186:0.0	.	378	Q2PZI1	D19L1_HUMAN	L	378;148	ENSP00000308695:F378L;ENSP00000400510:F148L	ENSP00000308695:F378L	F	-	3	2	DPY19L1	34956003	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.226000	0.51254	2.508000	0.84585	0.591000	0.81541	TTC		0.294	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			T	34989478	G	T	34989478	3	4	61	1	0	0	0	0	1	0	0	0	4751	933	33	2	929	2	DPY19L1	7	34989478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4185	34989478	124149185	5212	13197										
HERPUD2	64224	broad.mit.edu	37	chr7	35712883	35712883	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaccaatctctgatccttCgtcaactaagaaatgggaca	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:35712883C>T	ENST00000396081.1	-	2	957	c.153G>A	c.(151-153)acG>acA	p.T51T	HERPUD2_ENST00000311350.3_Silent_p.T51T	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	51	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T51T(1)		kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						TCTGATCCTTCGTCAACTAAG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	7											99	96	97					7																	35712883		2203	4300	6503	35679408	SO:0001819	synonymous_variant	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.153G>A	7.37:g.35712883C>T			35679408	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	37	CCDS5446.1																																																																																				0.373	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35712883	C	T	35712883	2	4	61	1	0	0	0	0	0	0	0	1	7085	871	31	1		1	HERPUD2	7	35712883	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	723405	35712883	123425780	5213	13198										
EEPD1	80820	broad.mit.edu	37	chr7	36194158	36194158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtatatcggtggcttcaaGaaggtggaggacctggcatt	15	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36194158G>T	ENST00000242108.4	+	2	943	c.225G>T	c.(223-225)aaG>aaT	p.K75N	EEPD1_ENST00000534978.1_Missense_Mutation_p.K75N	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1	75					DNA repair (GO:0006281)		DNA binding (GO:0003677)	p.K75N(1)		endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|skin(1)	18						GTGGCTTCAAGAAGGTGGAGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											95	93	94					7																	36194158		2203	4300	6503	36160683	SO:0001583	missense	80820			AK027386	CCDS34619.1	7p14.2	2007-12-07	2007-12-07		ENSG00000122547	ENSG00000122547			22223	protein-coding gene	gene with protein product							Standard	NM_030636		Approved	KIAA1706	uc003tfa.3	Q7L9B9	OTTHUMG00000154904	ENST00000242108.4:c.225G>T	7.37:g.36194158G>T	ENSP00000242108:p.Lys75Asn		36160683	Q96K64|Q9C0F7	Missense_Mutation	SNP	ENST00000242108.4	37	CCDS34619.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263072	0.59431	.	.	ENSG00000122547	ENST00000242108;ENST00000534978	T;T	0.26067	1.76;1.76	5.68	2.88	0.33553	RuvA domain 2-like (1);Competence protein ComEA, helix-hairpin-helix domain (1);	0.114193	0.64402	D	0.000013	T	0.37046	0.0989	L	0.39692	1.235	0.50171	D	0.999857	D	0.71674	0.998	D	0.69824	0.966	T	0.04191	-1.0970	10	0.59425	D	0.04	-34.1453	9.5317	0.39198	0.2731:0.0:0.7269:0.0	.	75	Q7L9B9	EEPD1_HUMAN	N	75	ENSP00000242108:K75N;ENSP00000442692:K75N	ENSP00000242108:K75N	K	+	3	2	EEPD1	36160683	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.828000	0.39111	0.327000	0.23409	-0.258000	0.10820	AAG		0.602	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	NM_030636		T	36194158	G	T	36194158	3	4	61	1	0	0	0	0	1	0	0	0	4943	933	33	2	227	2	EEPD1	7	36194158	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	481275	36194158	122944505	5214	13199										
KIAA0895	23366	broad.mit.edu	37	chr7	36373755	36373755	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggaggttgttaatacctCgaaaataatgtgtacctatg	10	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36373755C>T	ENST00000297063.6	-	5	1066	c.1016G>A	c.(1015-1017)cGa>cAa	p.R339Q	KIAA0895_ENST00000480192.1_5'UTR|KIAA0895_ENST00000317020.6_Missense_Mutation_p.R288Q|KIAA0895_ENST00000338533.5_Missense_Mutation_p.R326Q|KIAA0895_ENST00000440378.1_Missense_Mutation_p.R336Q|KIAA0895_ENST00000436884.1_Missense_Mutation_p.R236Q|KIAA0895_ENST00000453212.1_Missense_Mutation_p.R94Q	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	339								p.R339Q(1)|p.R326Q(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GTTAATACCTCGAAAATAATG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	7											127	112	116					7																	36373755		1884	4111	5995	36340280	SO:0001583	missense	23366			BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.1016G>A	7.37:g.36373755C>T	ENSP00000297063:p.Arg339Gln		36340280	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	C	34	5.408539	0.96051	.	.	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212;ENST00000431396	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.82967	0.5152	M	0.80616	2.505	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.997;0.997	D	0.85736	0.1334	9	0.72032	D	0.01	-19.495	18.1516	0.89676	0.0:1.0:0.0:0.0	.	336;236;339;326;288	B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;K0895_HUMAN;.;.	Q	339;326;288;336;236;94;94	.	ENSP00000297063:R339Q	R	-	2	0	KIAA0895	36340280	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.391000	0.79828	2.371000	0.80710	0.650000	0.86243	CGA		0.383	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		T	36373755	C	T	36373755	3	4	61	1	0	0	0	0	1	0	0	0	8218	884	31	1	558	1	KIAA0895	7	36373755	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179597	36373755	122764908	5215	13200										
KIAA0895	23366	broad.mit.edu	37	chr7	36396676	36396676	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtcaatatacaaaatttCttcccagaaaagtcatctcc	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36396676C>A	ENST00000297063.6	-	3	752	c.702G>T	c.(700-702)aaG>aaT	p.K234N	KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000415803.2_Missense_Mutation_p.K221N|KIAA0895_ENST00000317020.6_Missense_Mutation_p.K183N|KIAA0895_ENST00000338533.5_Missense_Mutation_p.K221N|KIAA0895_ENST00000440378.1_Missense_Mutation_p.K183N|KIAA0895_ENST00000436884.1_Missense_Mutation_p.K83N|KIAA0895_ENST00000453212.1_Intron	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	234								p.K234N(1)|p.K221N(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TACAAAATTTCTTCCCAGAAA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	7											99	93	95					7																	36396676		1830	4088	5918	36363201	SO:0001583	missense	23366			BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.702G>T	7.37:g.36396676C>A	ENSP00000297063:p.Lys234Asn		36363201	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.133850	0.56828	.	.	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000415803;ENST00000429651	.	.	.	5.65	2.37	0.29283	.	0.192719	0.51477	D	0.000100	T	0.66509	0.2796	L	0.57536	1.79	0.45239	D	0.998247	D;P;P;D;D;D;D	0.69078	0.976;0.835;0.954;0.997;0.973;0.98;0.96	P;B;P;D;P;P;P	0.65874	0.743;0.443;0.478;0.939;0.544;0.663;0.663	T	0.64575	-0.6375	9	0.87932	D	0	-19.6699	8.1868	0.31343	0.0:0.7042:0.1217:0.1741	.	183;183;83;221;234;221;183	B4DGN6;B7ZLT4;B4DF35;Q8NCT3-4;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;.;.;K0895_HUMAN;.;.	N	234;221;183;183;83;221;101	.	ENSP00000297063:K234N	K	-	3	2	KIAA0895	36363201	0.988000	0.35896	0.998000	0.56505	0.983000	0.72400	0.642000	0.24735	0.170000	0.19704	-0.253000	0.11424	AAG		0.393	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		A	36396676	C	A	36396676	3	1	61	1	0	0	0	0	1	0	0	0	8218	912	32	2	880	2	KIAA0895	7	36396676	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22921	36396676	122741987	5216	13201										
KIAA0895	23366	broad.mit.edu	37	chr7	36397083	36397083	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttccagttgtgaaaatgtCttttagcactcccgaggaca	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36397083C>A	ENST00000297063.6	-	3	345	c.295G>T	c.(295-297)Gac>Tac	p.D99Y	KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000415803.2_Missense_Mutation_p.D86Y|KIAA0895_ENST00000317020.6_Missense_Mutation_p.D48Y|KIAA0895_ENST00000338533.5_Missense_Mutation_p.D86Y|KIAA0895_ENST00000440378.1_Missense_Mutation_p.D48Y|KIAA0895_ENST00000436884.1_5'UTR|KIAA0895_ENST00000453212.1_Intron	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	99								p.D86Y(1)|p.D99Y(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GTGAAAATGTCTTTTAGCACT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	7											120	103	108					7																	36397083		1864	4102	5966	36363608	SO:0001583	missense	23366			BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.295G>T	7.37:g.36397083C>A	ENSP00000297063:p.Asp99Tyr		36363608	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630637	0.67015	.	.	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000415803	.	.	.	5.78	5.78	0.91487	.	0.170688	0.64402	D	0.000007	T	0.75376	0.3841	L	0.54323	1.7	0.58432	D	0.999991	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999	T	0.76708	-0.2860	9	0.87932	D	0	-29.9617	15.1295	0.72511	0.0:0.9309:0.0:0.0691	.	48;48;86;99;86;48	B4DGN6;B7ZLT4;Q8NCT3-4;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;.;K0895_HUMAN;.;.	Y	99;86;48;48;86	.	ENSP00000297063:D99Y	D	-	1	0	KIAA0895	36363608	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	4.166000	0.58203	2.724000	0.93272	0.563000	0.77884	GAC		0.378	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		A	36397083	C	A	36397083	3	1	61	1	0	0	0	0	1	0	0	0	8218	913	32	2	1287	2	KIAA0895	7	36397083	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	407	36397083	122741580	5217	13202										
ANLN	54443	broad.mit.edu	37	chr7	36478829	36478829	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggtcccctttttatcttCtttggaaggtcatatttatt	7	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36478829C>A	ENST00000265748.2	+	21	3121	c.2900C>A	c.(2899-2901)tCt>tAt	p.S967Y	ANLN_ENST00000396068.2_Missense_Mutation_p.S930Y	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	967	Localization to the cleavage furrow.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.S967Y(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						TTTTTATCTTCTTTGGAAGGT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	7											108	108	108					7																	36478829		2202	4297	6499	36445354	SO:0001583	missense	54443			AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.2900C>A	7.37:g.36478829C>A	ENSP00000265748:p.Ser967Tyr		36445354	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	37	CCDS5447.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.80|15.80|15.80	2.940600|2.940600|2.940600	0.52972|0.52972|0.52972	.|.|.	.|.|.	ENSG00000011426|ENSG00000011426|ENSG00000011426	ENST00000428612|ENST00000457743|ENST00000265748;ENST00000396068	.|.|T;T	.|.|0.11821	.|.|2.74;2.74	5.22|5.22|5.22	5.22|5.22|5.22	0.72569|0.72569|0.72569	.|.|.	.|.|0.204155	.|.|0.52532	.|.|D	.|.|0.000061	T|T|T	0.10165|0.10165|0.10165	0.0249|0.0249|0.0249	N|N|N	0.08118|0.08118|0.08118	0|0|0	0.27636|0.27636|0.27636	N|N|N	0.947882|0.947882|0.947882	.|.|B;B;B;B	.|.|0.29270	.|.|0.13;0.155;0.24;0.155	.|.|B;B;B;B	.|.|0.32393	.|.|0.081;0.069;0.145;0.069	T|T|T	0.25328|0.25328|0.25328	-1.0135|-1.0135|-1.0135	5|5|10	.|.|0.87932	.|.|D	.|.|0	-0.3251|-0.3251|-0.3251	17.6987|17.6987|17.6987	0.88289|0.88289|0.88289	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|844;929;930;967	.|.|B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.|.|.;.;.;ANLN_HUMAN	L|I|Y	131|189|967;930	.|.|ENSP00000265748:S967Y;ENSP00000379380:S930Y	.|.|ENSP00000265748:S967Y	F|L|S	+|+|+	3|1|2	2|0|0	ANLN|ANLN|ANLN	36445354|36445354|36445354	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.991000|0.991000|0.991000	0.47740|0.47740|0.47740	0.903000|0.903000|0.903000	0.53119|0.53119|0.53119	5.215000|5.215000|5.215000	0.65241|0.65241|0.65241	2.578000|2.578000|2.578000	0.87016|0.87016|0.87016	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTT|TCT		0.299	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		A	36478829	C	A	36478829	3	1	61	1	0	0	0	0	1	0	0	0	694	913	32	2	2982	2	ANLN	7	36478829	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81746	36478829	122659834	5218	13203										
AOAH	313	broad.mit.edu	37	chr7	36671659	36671659	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaatttaattttctggcaGatcttggccaaaaccgggag	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36671659G>T	ENST00000258749.5	-	6	903	c.504C>A	c.(502-504)atC>atA	p.I168I	AOAH_ENST00000535891.1_Silent_p.I136I|AOAH_ENST00000431169.1_Silent_p.I168I	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	168					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.I168I(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						TTTTCTGGCAGATCTTGGCCA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	7											53	55	54					7																	36671659		2203	4300	6503	36638184	SO:0001819	synonymous_variant	313			BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.504C>A	7.37:g.36671659G>T			36638184	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																				0.358	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637		T	36671659	G	T	36671659	2	4	61	1	0	0	0	0	0	0	0	1	726	932	33	2		2	AOAH	7	36671659	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192830	36671659	122467004	5219	13204										
ELMO1	9844	broad.mit.edu	37	chr7	36917663	36917663	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctccctgaggactctcttCtaagtctccgtaatgcagga	8	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:36917663C>T	ENST00000310758.4	-	19	2421	c.1774G>A	c.(1774-1776)Gaa>Aaa	p.E592K	ELMO1_ENST00000396045.3_Missense_Mutation_p.E112K|ELMO1_ENST00000341056.3_Missense_Mutation_p.E294K|ELMO1_ENST00000448602.1_Missense_Mutation_p.E592K|ELMO1_ENST00000396040.2_Missense_Mutation_p.E112K|ELMO1_ENST00000442504.1_Missense_Mutation_p.E592K	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	592	PH.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)	p.E592K(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GGACTCTCTTCTAAGTCTCCG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											97	85	89					7																	36917663		2203	4300	6503	36884188	SO:0001583	missense	9844			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1774G>A	7.37:g.36917663C>T	ENSP00000312185:p.Glu592Lys		36884188	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	37	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.900058	0.92035	.	.	ENSG00000155849	ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602	T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64	5.81	5.81	0.92471	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.51363	0.1670	M	0.82517	2.595	0.80722	D	1	P	0.37466	0.596	B	0.26969	0.075	T	0.57382	-0.7821	10	0.39692	T	0.17	.	20.0833	0.97789	0.0:1.0:0.0:0.0	.	592	Q92556	ELMO1_HUMAN	K	294;112;592;496;112;592;592	ENSP00000342142:E294K;ENSP00000379360:E112K;ENSP00000312185:E592K;ENSP00000379355:E112K;ENSP00000406952:E592K;ENSP00000394458:E592K	ENSP00000312185:E592K	E	-	1	0	ELMO1	36884188	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.399000	0.79935	2.756000	0.94617	0.655000	0.94253	GAA		0.478	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		T	36917663	C	T	36917663	3	4	61	1	0	0	0	0	1	0	0	0	5078	922	32	3	425	3	ELMO1	7	36917663	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	246004	36917663	122221000	5220	13205										
TARP	6966	broad.mit.edu	37	chr7	38304975	38304975	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttattggaggaaagataatTtcttgatcaactccgttttt	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:38304975T>G	ENST00000443402.2	-	0	304					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											GAAAGATAATTTCTTGATCAA	0.353																																																0			7											132	124	127					7																	38304975		1837	4095	5932	38271500			445347			M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"T cell receptors / TRG locus"	12275	other	T cell receptor gene	"T-cell receptor, gamma, constant region C1"	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38304975T>G			38271500		Missense_Mutation	SNP	ENST00000443402.2	37																																																																																					0.353	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336		G	38304975	T	G	38304975	1	3	61	0	1	0	0	0	0	0	0	0	15597	1838	64	4		4	TARP	7	38304975	RNA	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1387312	38304975	120833688	5221	13206										
AMPH	273	broad.mit.edu	37	chr7	38433672	38433672	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaccctcagtggtttcaGttccaattttggcctcctct	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:38433672G>T	ENST00000356264.2	-	18	1756	c.1541C>A	c.(1540-1542)aCt>aAt	p.T514N	AMPH_ENST00000471913.1_5'UTR|AMPH_ENST00000428293.2_Missense_Mutation_p.T472N|AMPH_ENST00000325590.5_Missense_Mutation_p.T472N	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	514					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.T514N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						AGTGGTTTCAGTTCCAATTTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											167	144	152					7																	38433672		2203	4300	6503	38400197	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1541C>A	7.37:g.38433672G>T	ENSP00000348602:p.Thr514Asn		38400197	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.039|9.039	0.989163|0.989163	0.18966|0.18966	.|.	.|.	ENSG00000078053|ENSG00000078053	ENST00000441628|ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	.|T;T;T	.|0.60672	.|0.18;0.25;0.17	5.93|5.93	-0.261|-0.261	0.12963|0.12963	.|.	.|1.069620	.|0.07195	.|N	.|0.856379	T|T	0.33760|0.33760	0.0874|0.0874	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.27882	.|0.051;0.001;0.002;0.192	.|B;B;B;B	.|0.22880	.|0.042;0.002;0.001;0.017	T|T	0.13282|0.13282	-1.0515|-1.0515	5|10	.|0.13108	.|T	.|0.6	0.2458|0.2458	1.6019|1.6019	0.02675|0.02675	0.2237:0.2599:0.3825:0.1339|0.2237:0.2599:0.3825:0.1339	.|.	.|560;472;514;402	.|Q8NFL6;P49418-2;P49418;Q8NFL4	.|.;.;AMPH_HUMAN;.	K|N	396|472;514;472;416	.|ENSP00000317441:T472N;ENSP00000348602:T514N;ENSP00000390734:T472N	.|ENSP00000317441:T472N	N|T	-|-	3|2	2|0	AMPH|AMPH	38400197|38400197	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	0.745000|0.745000	0.26259|0.26259	-0.337000|-0.337000	0.08426|0.08426	-0.300000|-0.300000	0.09419|0.09419	AAC|ACT		0.602	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		T	38433672	G	T	38433672	3	4	61	1	0	0	0	0	1	0	0	0	588	1029	36	2	562	2	AMPH	7	38433672	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128697	38433672	120704991	5222	13207										
POU6F2	11281	broad.mit.edu	37	chr7	39125630	39125630	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacactcccagcaagctcttCggtaagtctgtctaggtatt	9	11	3	0	rs530262963	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:39125630C>T	ENST00000403058.1	+	3	343	c.189C>T	c.(187-189)ttC>ttT	p.F63F	POU6F2_ENST00000518318.2_Splice_Site_p.F63F|POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Splice_Site_p.F55F|POU6F2_ENST00000464276.2_Splice_Site_p.F55F	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	63					central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F63F(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						GCAAGCTCTTCGGTAAGTCTG	0.507													C|||	7	0.00139776	0	0	5008	,	,		15948	0		0	False		,,,				2504	0.0072															1	Substitution - coding silent(1)	large_intestine(1)	7											90	78	82					7																	39125630		2203	4300	6503	39092155	SO:0001630	splice_region_variant	11281			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.190+1C>T	7.37:g.39125630C>T			39092155	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	37	CCDS34620.2																																																																																				0.507	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	Silent	T	39125630	C	T	39125630	5	4	61	1	0	0	0	0	0	0	1	0	12316	898	31	1	195	1	POU6F2	7	39125630	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	691958	39125630	120013033	5223	13208										
POU6F2	11281	broad.mit.edu	37	chr7	39379257	39379257	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagctacctcatccctgaaCtcccagctccagcagctcca	6	18	1	1	rs147178262		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:39379257C>A	ENST00000403058.1	+	6	682	c.528C>A	c.(526-528)aaC>aaA	p.N176K	POU6F2_ENST00000518318.2_Missense_Mutation_p.N176K|POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Missense_Mutation_p.N168K	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	176	Gln-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N176K(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CATCCCTGAACTCCCAGCTCc	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7											24	23	23					7																	39379257		2164	4255	6419	39345782	SO:0001583	missense	11281			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.528C>A	7.37:g.39379257C>A	ENSP00000384004:p.Asn176Lys		39345782	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420953	0.42918	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.86230	0.97;-2.09	4.81	3.79	0.43588	.	1.437400	0.05624	U	0.580404	D	0.88503	0.6454	L	0.39898	1.24	0.32267	N	0.569393	D;P	0.60160	0.987;0.608	P;B	0.58077	0.832;0.079	T	0.82434	-0.0459	10	0.72032	D	0.01	.	6.5853	0.22616	0.0:0.7016:0.0:0.2984	.	176;176	P78424-2;P78424	.;PO6F2_HUMAN	K	176	ENSP00000384004:N176K;ENSP00000430514:N176K	ENSP00000384004:N176K	N	+	3	2	POU6F2	39345782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.032000	0.41127	2.200000	0.70718	0.557000	0.71058	AAC		0.587	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		A	39379257	C	A	39379257	3	1	61	1	0	0	0	0	1	0	0	0	12316	564	20	2	546	2	POU6F2	7	39379257	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253627	39379257	119759406	5224	13209										
RALA	5898	broad.mit.edu	37	chr7	39745749	39745749	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatttaatgagagaaattCgagcgagaaagatggaagac	12	3	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:39745749C>T	ENST00000005257.2	+	5	906	c.526C>T	c.(526-528)Cga>Tga	p.R176*	AC004837.5_ENST00000435766.1_RNA|RALA_ENST00000468201.1_3'UTR	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	176					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R176*(2)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						GAGAGAAATTCGAGCGAGAAA	0.318																																																2	Substitution - Nonsense(2)	large_intestine(1)|skin(1)	7											57	62	60					7																	39745749		2202	4298	6500	39712274	SO:0001587	stop_gained	5898				CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"RAS-like protein A", "Ras-related protein Ral-A", "Ras family small GTP binding protein RALA", "ras related GTP binding protein A"	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.526C>T	7.37:g.39745749C>T	ENSP00000005257:p.Arg176*		39712274	A4D1W3	Nonsense_Mutation	SNP	ENST00000005257.2	37	CCDS5460.1	.	.	.	.	.	.	.	.	.	.	C	37	6.625501	0.97714	.	.	ENSG00000006451	ENST00000005257	.	.	.	5.93	5.0	0.66597	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3985	0.67027	0.2164:0.7836:0.0:0.0	.	.	.	.	X	176	.	ENSP00000005257:R176X	R	+	1	2	RALA	39712274	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.962000	0.56766	2.803000	0.96430	0.585000	0.79938	CGA		0.318	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402		T	39745749	C	T	39745749	4	4	61	1	0	0	0	0	0	1	0	0	13047	876	31	1	540	1	RALA	7	39745749	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366492	39745749	119392914	5225	13210										
INHBA	3624	broad.mit.edu	37	chr7	41729665	41729665	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatgaggaaaggtctgtgCgactgctccttttcctcatc	10	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:41729665C>T	ENST00000242208.4	-	3	1110	c.864G>A	c.(862-864)tcG>tcA	p.S288S	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Silent_p.S288S	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	288					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.S288S(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						AAGGTCTGTGCGActgctcct	0.582										TSP Lung(11;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											76	76	76					7																	41729665		2203	4300	6503	41696190	SO:0001819	synonymous_variant	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.864G>A	7.37:g.41729665C>T			41696190	Q14599	Silent	SNP	ENST00000242208.4	37	CCDS5464.1																																																																																				0.582	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			T	41729665	C	T	41729665	2	4	61	1	0	0	0	0	0	0	0	1	7762	755	27	1		1	INHBA	7	41729665	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1983916	41729665	117408998	5226	13211										
INHBA	3624	broad.mit.edu	37	chr7	41729879	41729879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacagggaagacatgccagGtgctcttccgagcgtctact	12	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:41729879G>A	ENST00000242208.4	-	3	896	c.650C>T	c.(649-651)aCc>aTc	p.T217I	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.T217I	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	217					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.T217S(1)|p.T217I(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GACATGCCAGGTGCTCTTCCG	0.582										TSP Lung(11;0.080)																																						2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7											62	57	59					7																	41729879		2203	4300	6503	41696404	SO:0001583	missense	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.650C>T	7.37:g.41729879G>A	ENSP00000242208:p.Thr217Ile		41696404	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	21.3	4.126255	0.77549	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.65916	-0.18;-0.18	6.06	6.06	0.98353	Transforming growth factor-beta, N-terminal (1);	0.155706	0.64402	D	0.000014	T	0.65004	0.2650	N	0.22421	0.69	0.43191	D	0.995022	D	0.63880	0.993	P	0.62560	0.904	T	0.60525	-0.7246	10	0.28530	T	0.3	-24.7588	16.0307	0.80574	0.0:0.1335:0.8665:0.0	.	217	P08476	INHBA_HUMAN	I	217	ENSP00000242208:T217I;ENSP00000397197:T217I	ENSP00000242208:T217I	T	-	2	0	INHBA	41696404	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.911000	0.63328	2.882000	0.98803	0.655000	0.94253	ACC		0.582	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			A	41729879	G	A	41729879	3	1	61	1	0	0	0	0	1	0	0	0	7762	1261	44	3	634	3	INHBA	7	41729879	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214	41729879	117408784	5227	13212										
GLI3	2737	broad.mit.edu	37	chr7	42005025	42005025	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggttgctgttctccccgaGggtctgatagcccccagcag	14	13	2	1	rs112234184		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:42005025G>T	ENST00000395925.3	-	15	3730	c.3646C>A	c.(3646-3648)Ctc>Atc	p.L1216I	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1216					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L1216I(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TTCTCCCCGAGGGTCTGATAG	0.647									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							1	Substitution - Missense(1)	large_intestine(1)	7											49	57	54					7																	42005025		2203	4300	6503	41971550	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3646C>A	7.37:g.42005025G>T	ENSP00000379258:p.Leu1216Ile		41971550	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685715	0.68157	.	.	ENSG00000106571	ENST00000395925	T	0.14022	2.54	5.64	5.64	0.86602	.	0.295527	0.34314	N	0.004067	T	0.16385	0.0394	N	0.22421	0.69	0.80722	D	1	D	0.54964	0.969	P	0.49683	0.619	T	0.04930	-1.0917	10	0.21014	T	0.42	.	19.6945	0.96019	0.0:0.0:1.0:0.0	.	1216	P10071	GLI3_HUMAN	I	1216	ENSP00000379258:L1216I	ENSP00000379258:L1216I	L	-	1	0	GLI3	41971550	0.960000	0.32886	0.032000	0.17829	0.030000	0.12068	4.088000	0.57678	2.644000	0.89710	0.609000	0.83330	CTC		0.647	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42005025	G	T	42005025	3	4	61	1	0	0	0	0	1	0	0	0	6459	1000	35	2	1100	2	GLI3	7	42005025	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	275146	42005025	117133638	5228	13213										
GLI3	2737	broad.mit.edu	37	chr7	42017211	42017211	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatcagaggcatttgagaaAgccttgttgcaaccttcgtg	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:42017211A>C	ENST00000395925.3	-	12	1842	c.1758T>G	c.(1756-1758)gcT>gcG	p.A586A	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	586					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A586A(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CATTTGAGAAAGCCTTGTTGC	0.463									Pallister-Hall syndrome;Greig Cephalopolysyndactyly		OREG0018015	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	7											252	206	222					7																	42017211		2203	4300	6503	41983736	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1758T>G	7.37:g.42017211A>C		905	41983736	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.463	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		C	42017211	A	C	42017211	2	2	61	1	0	0	0	0	0	0	0	1	6459	59	3	4		4	GLI3	7	42017211	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12186	42017211	117121452	5229	13214										
GLI3	2737	broad.mit.edu	37	chr7	42079828	42079828	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgacagcctggggctggaGaatctggtgcctgttatata	14	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:42079828G>T	ENST00000395925.3	-	7	921	c.837C>A	c.(835-837)ttC>ttA	p.F279L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	279					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F279L(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TGGGGCTGGAGAATCTGGTGC	0.463									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							1	Substitution - Missense(1)	large_intestine(1)	7											112	107	109					7																	42079828		2203	4300	6503	42046353	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.837C>A	7.37:g.42079828G>T	ENSP00000379258:p.Phe279Leu		42046353	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836019	0.71373	.	.	ENSG00000106571	ENST00000395925	T	0.69685	-0.42	5.96	-0.219	0.13135	.	0.000000	0.85682	D	0.000000	T	0.64549	0.2608	L	0.43923	1.385	0.80722	D	1	P	0.51147	0.942	P	0.57057	0.812	T	0.60974	-0.7156	10	0.54805	T	0.06	.	5.616	0.17432	0.5319:0.1462:0.3219:0.0	.	279	P10071	GLI3_HUMAN	L	279	ENSP00000379258:F279L	ENSP00000379258:F279L	F	-	3	2	GLI3	42046353	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	1.852000	0.39348	0.103000	0.17682	0.655000	0.94253	TTC		0.463	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42079828	G	T	42079828	3	4	61	1	0	0	0	0	1	0	0	0	6459	933	33	2	3941	2	GLI3	7	42079828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62617	42079828	117058835	5230	13215										
C7orf25	79020	broad.mit.edu	37	chr7	42949774	42949774	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttactcttttgcacacatcGaccttaatttctgttggaaa	5	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:42949774G>T	ENST00000350427.4	-	2	1001	c.726C>A	c.(724-726)gtC>gtA	p.V242V	PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000447342.1_Silent_p.V242V|C7orf25_ENST00000438029.1_Silent_p.V242V|C7orf25_ENST00000431882.2_Silent_p.V300V			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	242								p.V242V(1)		endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TGCACACATCGACCTTAATTT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	7											105	106	106					7																	42949774		2203	4300	6503	42916299	SO:0001819	synonymous_variant	79020			BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.726C>A	7.37:g.42949774G>T			42916299	A4D1V2|J3KR36|Q9H779	Silent	SNP	ENST00000350427.4	37	CCDS5466.1																																																																																				0.413	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		T	42949774	G	T	42949774	2	4	61	1	0	0	0	0	0	0	0	1	2386	1045	37	2		2	C7orf25	7	42949774	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	869946	42949774	116188889	5231	13216										
HECW1	23072	broad.mit.edu	37	chr7	43540370	43540370	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgtgatgcggatctggtCattttgctgaggtagggggc	16	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43540370C>A	ENST00000395891.2	+	20	4115	c.3510C>A	c.(3508-3510)gtC>gtA	p.V1170V	HECW1_ENST00000453890.1_Silent_p.V1136V	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1170					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.V1149V(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CGGATCTGGTCATTTTGCTGA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	7											184	179	181					7																	43540370		1912	4133	6045	43506895	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3510C>A	7.37:g.43540370C>A			43506895	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.498	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43540370	C	A	43540370	2	1	61	1	0	0	0	0	0	0	0	1	7063	813	29	2		2	HECW1	7	43540370	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	590596	43540370	115598293	5232	13217										
HECW1	23072	broad.mit.edu	37	chr7	43548598	43548598	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggcccctcgcgggagttCttcttccttctgtctcagga	11	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43548598C>A	ENST00000395891.2	+	24	4502	c.3897C>A	c.(3895-3897)ttC>ttA	p.F1299L	HECW1_ENST00000453890.1_Missense_Mutation_p.F1265L|AC011738.4_ENST00000436105.1_RNA	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1299	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.F1278L(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CGCGGGAGTTCTTCTTCCTTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	7											138	135	136					7																	43548598		1886	4116	6002	43515123	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3897C>A	7.37:g.43548598C>A	ENSP00000379228:p.Phe1299Leu		43515123	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791224	0.70452	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.51071	0.72;0.72	5.92	5.05	0.67936	HECT (3);	0.000000	0.85682	D	0.000000	T	0.63426	0.2510	M	0.86573	2.825	0.80722	D	1	B;P	0.50443	0.257;0.935	B;P	0.49361	0.117;0.608	T	0.72516	-0.4269	10	0.87932	D	0	.	14.9559	0.71113	0.0:0.9318:0.0:0.0682	.	1265;1299	B4DH42;Q76N89	.;HECW1_HUMAN	L	1299;1265;1299	ENSP00000379228:F1299L;ENSP00000407774:F1265L	ENSP00000265522:F1299L	F	+	3	2	HECW1	43515123	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	6.045000	0.71020	1.515000	0.48885	0.555000	0.69702	TTC		0.547	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43548598	C	A	43548598	3	1	61	1	0	0	0	0	1	0	0	0	7063	912	32	2	3983	2	HECW1	7	43548598	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8228	43548598	115590065	5233	13218										
HECW1	23072	broad.mit.edu	37	chr7	43580825	43580825	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtaccttcttgacgctttCttcacgaggcccttctacaa	6	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43580825C>T	ENST00000395891.2	+	25	4688	c.4083C>T	c.(4081-4083)ttC>ttT	p.F1361F	HECW1_ENST00000453890.1_Silent_p.F1327F	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1361	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.F1340F(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TTGACGCTTTCTTCACGAGGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	7											159	153	155					7																	43580825		2000	4169	6169	43547350	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4083C>T	7.37:g.43580825C>T			43547350	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	10.60	1.394923	0.25205	.	.	ENSG00000002746	ENST00000429529	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	T	0.76912	0.4054	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74315	-0.3705	4	.	.	.	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	.	.	.	F	85	.	.	S	+	2	0	HECW1	43547350	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.759000	0.68785	2.757000	0.94681	0.563000	0.77884	TCT		0.542	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		T	43580825	C	T	43580825	2	4	61	1	0	0	0	0	0	0	0	1	7063	912	32	3		3	HECW1	7	43580825	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32227	43580825	115557838	5234	13219										
HECW1	23072	broad.mit.edu	37	chr7	43581490	43581490	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgatttgagtgacctgGaatatttggatgaggaattc	12	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43581490G>T	ENST00000395891.2	+	26	4746	c.4141G>T	c.(4141-4143)Gaa>Taa	p.E1381*	HECW1_ENST00000453890.1_Nonsense_Mutation_p.E1347*	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1381	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.E1360*(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GAGTGACCTGGAATATTTGGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											139	125	129					7																	43581490		1860	4122	5982	43548015	SO:0001587	stop_gained	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4141G>T	7.37:g.43581490G>T	ENSP00000379228:p.Glu1381*		43548015	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Nonsense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	45|45	12.058539|12.058539	0.99631|0.99631	.|.	.|.	ENSG00000002746|ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522|ENST00000429529	.|.	.|.	.|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80330	.|0.4603	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77736	.|-0.2476	.|3	0.87932|.	D|.	0|.	.|.	20.3747|20.3747	0.98911|0.98911	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|C	1381;1347;1381|104	.|.	ENSP00000265522:E1381X|.	E|W	+|+	1|3	0|0	HECW1|HECW1	43548015|43548015	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.467000|9.467000	0.97671|0.97671	2.817000|2.817000	0.96982|0.96982	0.563000|0.563000	0.77884|0.77884	GAA|TGG		0.418	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		T	43581490	G	T	43581490	4	4	61	1	0	0	0	0	0	1	0	0	7063	1175	41	2	4235	2	HECW1	7	43581490	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	665	43581490	115557173	5235	13220										
STK17A	9263	broad.mit.edu	37	chr7	43663458	43663458	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagtcggctgttgatttCatcaggacacttttagttaa	9	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43663458C>A	ENST00000319357.5	+	6	1070	c.891C>A	c.(889-891)ttC>ttA	p.F297L		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	297	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F297L(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						CTGTTGATTTCATCAGGACAC	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	88	88					7																	43663458		2203	4295	6498	43629983	SO:0001583	missense	9263			AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"death-associated protein kinase-related 1"	604726	"serine/threonine kinase 17a (apoptosis-inducing)"			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.891C>A	7.37:g.43663458C>A	ENSP00000319192:p.Phe297Leu		43629983	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	37	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016875	0.54576	.	.	ENSG00000164543	ENST00000319357	T	0.59224	0.28	4.82	3.95	0.45737	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49916	D	0.000122	T	0.60881	0.2303	N	0.20610	0.595	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60546	-0.7242	10	0.38643	T	0.18	.	13.3053	0.60349	0.0:0.9228:0.0:0.0772	.	297	Q9UEE5	ST17A_HUMAN	L	297	ENSP00000319192:F297L	ENSP00000319192:F297L	F	+	3	2	STK17A	43629983	1.000000	0.71417	0.998000	0.56505	0.082000	0.17680	3.608000	0.54109	0.999000	0.39023	-0.232000	0.12228	TTC		0.269	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		A	43663458	C	A	43663458	3	1	61	1	0	0	0	0	1	0	0	0	15329	825	29	2	913	2	STK17A	7	43663458	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81968	43663458	115475205	5236	13221										
URGCP	55665	broad.mit.edu	37	chr7	43917434	43917434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcacccccgaggagggaTcatggccgttctgctgcatt	12	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:43917434T>C	ENST00000453200.1	-	6	2121	c.1628A>G	c.(1627-1629)gAt>gGt	p.D543G	URGCP_ENST00000443736.1_Missense_Mutation_p.D500G|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000447717.3_Missense_Mutation_p.D500G|URGCP_ENST00000336086.6_Missense_Mutation_p.D500G|URGCP_ENST00000402306.3_Missense_Mutation_p.D534G|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000223341.7_Missense_Mutation_p.D500G			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	543					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.D500G(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CGAGGAGGGATCATGGCCGTT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	7											38	43	41					7																	43917434		2028	4172	6200	43883959	SO:0001583	missense	55665				CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1628A>G	7.37:g.43917434T>C	ENSP00000396918:p.Asp543Gly		43883959	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	T	0.689	-0.795095	0.02862	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89	5.69	2.01	0.26516	.	0.562852	0.19228	N	0.119481	T	0.05777	0.0151	N	0.20574	0.59	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.08055	0.003;0.003	T	0.39292	-0.9621	10	0.23891	T	0.37	-14.1427	5.3309	0.15932	0.0:0.1603:0.1514:0.6883	.	534;543	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	G	500;500;534;500;543;500	ENSP00000223341:D500G;ENSP00000336872:D500G;ENSP00000384955:D534G;ENSP00000392136:D500G;ENSP00000396918:D543G;ENSP00000402803:D500G	ENSP00000223341:D500G	D	-	2	0	URGCP	43883959	0.024000	0.19004	0.003000	0.11579	0.013000	0.08279	1.282000	0.33226	0.408000	0.25621	0.533000	0.62120	GAT		0.632	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		C	43917434	T	C	43917434	3	2	61	1	0	0	0	0	1	0	0	0	17066	1435	50	4	1171	4	URGCP	7	43917434	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	253976	43917434	115221229	5237	13222										
SPDYE1	285955	broad.mit.edu	37	chr7	44040655	44040655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacacagtggcctggtttCtttactcagcccctggggta	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44040655C>A	ENST00000258704.3	+	1	168	c.31C>A	c.(31-33)Ctt>Att	p.L11I	RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA|AC004951.6_ENST00000447643.1_lincRNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	11								p.L11I(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						GGCCTGGTTTCTTTACTCAGC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	7											2	2	2					7																	44040655		712	1551	2263	44007180	SO:0001583	missense	285955			AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"Speedy homologs"	16408	protein-coding gene	gene with protein product	"Speedy E"		"Williams Beuren syndrome chromosome region 19", "speedy homolog E1 (Xenopus laevis)"	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.31C>A	7.37:g.44040655C>A	ENSP00000258704:p.Leu11Ile		44007180	Q9NTH5	Missense_Mutation	SNP	ENST00000258704.3	37	CCDS5475.1	.	.	.	.	.	.	.	.	.	.	.	8.647	0.897231	0.17686	.	.	ENSG00000136206	ENST00000258704	.	.	.	.	.	.	.	.	.	.	.	T	0.20577	0.0495	L	0.36672	1.1	0.09310	N	1	P	0.35700	0.516	B	0.20384	0.029	T	0.09729	-1.0661	6	0.35671	T	0.21	.	.	.	.	.	11	Q8NFV5	SPDE1_HUMAN	I	11	.	ENSP00000258704:L11I	L	+	1	0	SPDYE1	44007180	0.960000	0.32886	0.394000	0.26270	0.363000	0.29612	0.633000	0.24598	0.400000	0.25396	0.399000	0.26434	CTT		0.557	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064		A	44040655	C	A	44040655	3	1	61	1	0	0	0	0	1	0	0	0	15068	913	32	2	33	2	SPDYE1	7	44040655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123221	44040655	115098008	5238	13223										
PGAM2	5224	broad.mit.edu	37	chr7	44104787	44104787	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcgaaggagcgcctccaGatcttcacctgctcctcccc	8	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44104787G>T	ENST00000297283.3	-	1	399	c.342C>A	c.(340-342)atC>atA	p.I114I	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	114				KI -> RS (in Ref. 3; AAA60072). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)	p.I114I(1)		large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						AGCGCCTCCAGATCTTCACCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	7											62	60	60					7																	44104787		2203	4300	6503	44071312	SO:0001819	synonymous_variant	5224				CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.342C>A	7.37:g.44104787G>T			44071312		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																				0.627	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			T	44104787	G	T	44104787	2	4	61	1	0	0	0	0	0	0	0	1	11805	932	33	2		2	PGAM2	7	44104787	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64132	44104787	115033876	5239	13224										
AEBP1	165	broad.mit.edu	37	chr7	44153269	44153269	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgcggagggctacaccccGagcgccaagacctgcaatgt	12	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44153269G>A	ENST00000223357.3	+	21	3191	c.2886G>A	c.(2884-2886)ccG>ccA	p.P962P	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Silent_p.P537P	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	962	Interaction with PTEN. {ECO:0000250}.|Required for transcriptional repression. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.P962P(1)		NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GCTACACCCCGAGCGCCAAGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	7											86	84	84					7																	44153269		2203	4300	6503	44119794	SO:0001819	synonymous_variant	165			D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.2886G>A	7.37:g.44153269G>A			44119794	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Silent	SNP	ENST00000223357.3	37	CCDS5476.1																																																																																				0.607	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44153269	G	A	44153269	2	1	61	1	0	0	0	0	0	0	0	1	349	1045	37	1		1	AEBP1	7	44153269	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48482	44153269	114985394	5240	13225										
MYL7	58498	broad.mit.edu	37	chr7	44180602	44180602	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgttcaaacatggaaaaGacgttggaagaaccacgttg	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44180602G>T	ENST00000223364.3	-	2	101	c.75C>A	c.(73-75)gtC>gtA	p.V25V	MYL7_ENST00000434895.1_5'UTR|MYL7_ENST00000458240.1_5'UTR	NM_021223.2	NP_067046.1	Q01449	MLRA_HUMAN	myosin, light chain 7, regulatory	25						A band (GO:0031672)|dendritic spine (GO:0043197)|myosin complex (GO:0016459)	calcium ion binding (GO:0005509)	p.V25V(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	12						ACATGGAAAAGACGTTGGAAG	0.607																																																2	Substitution - coding silent(2)	large_intestine(2)	7											106	104	104					7																	44180602		2203	4300	6503	44147127	SO:0001819	synonymous_variant	58498			M94547	CCDS5478.1	7p21-p11.2	2013-01-10	2006-09-29		ENSG00000106631	ENSG00000106631		"Myosins / Light chain", "EF-hand domain containing"	21719	protein-coding gene	gene with protein product		613993	"myosin, light polypeptide 7, regulatory"			8207020	Standard	NM_021223		Approved	MYLC2A, MYL2A	uc003tkg.3	Q01449	OTTHUMG00000023125	ENST00000223364.3:c.75C>A	7.37:g.44180602G>T			44147127	B2R4L3	Silent	SNP	ENST00000223364.3	37	CCDS5478.1																																																																																				0.607	MYL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059446.4	NM_021223		T	44180602	G	T	44180602	2	4	61	1	0	0	0	0	0	0	0	1	10083	929	33	2		2	MYL7	7	44180602	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27333	44180602	114958061	5241	13226										
GCK	2645	broad.mit.edu	37	chr7	44198715	44198715	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccttgtgacatccatcGccatctctccgaggggctaa	10	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44198715G>A	ENST00000403799.3	-	2	515				GCK_ENST00000476008.1_Intron|GCK_ENST00000345378.2_Missense_Mutation_p.A2V|GCK_ENST00000437084.1_Intron|GCK_ENST00000395796.3_5'UTR	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)						calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)	p.A2V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						GACATCCATCGCCATCTCTCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											134	121	126					7																	44198715		2203	4300	6503	44165240	SO:0001627	intron_variant	2645			AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.46-5653C>T	7.37:g.44198715G>A			44165240	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	37	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	G	8.831	0.939839	0.18281	.	.	ENSG00000106633	ENST00000345378	D	0.97404	-4.37	3.05	2.17	0.27698	.	2.388090	0.02053	N	0.050199	D	0.92260	0.7545	.	.	.	0.09310	N	0.999999	B	0.21452	0.056	B	0.10450	0.005	D	0.85420	0.1142	9	0.15952	T	0.53	-5.6747	6.1893	0.20516	0.1417:0.0:0.8583:0.0	.	2	P35557-2	.	V	2	ENSP00000223366:A2V	ENSP00000223366:A2V	A	-	2	0	GCK	44165240	0.107000	0.21998	0.010000	0.14722	0.073000	0.16967	1.208000	0.32345	0.843000	0.35070	0.462000	0.41574	GCG		0.592	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			A	44198715	G	A	44198715	1	1	61	0	1	0	0	0	0	0	0	0	6313	1087	38	1		1	GCK	7	44198715	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18113	44198715	114939948	5242	13227										
YKT6	10652	broad.mit.edu	37	chr7	44247771	44247771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgactaaagtgcaggccGaactagatgagaccaaaatc	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44247771G>A	ENST00000223369.2	+	5	520	c.433G>A	c.(433-435)Gaa>Aaa	p.E145K	YKT6_ENST00000496112.1_Missense_Mutation_p.E145K|YKT6_ENST00000447123.1_3'UTR	NM_006555.3	NP_006546.1	O15498	YKT6_HUMAN	YKT6 v-SNARE homolog (S. cerevisiae)	145	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				ER to Golgi vesicle-mediated transport (GO:0006888)|metabolic process (GO:0008152)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle docking involved in exocytosis (GO:0006904)|vesicle targeting (GO:0006903)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|SNARE complex (GO:0031201)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|SNAP receptor activity (GO:0005484)	p.E145K(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7						AGTGCAGGCCGAACTAGATGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	68	72					7																	44247771		2203	4300	6503	44214296	SO:0001583	missense	10652			BC007319	CCDS5482.1	7p13	2006-07-07			ENSG00000106636	ENSG00000106636			16959	protein-coding gene	gene with protein product	"R-SNARE"	606209				15479160, 15544955	Standard	NM_006555		Approved		uc003tkm.3	O15498	OTTHUMG00000129089	ENST00000223369.2:c.433G>A	7.37:g.44247771G>A	ENSP00000223369:p.Glu145Lys		44214296	B4DR94|Q53F01|Q6FGU9|Q6IB15	Missense_Mutation	SNP	ENST00000223369.2	37	CCDS5482.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922328	0.92319	.	.	ENSG00000106636	ENST00000496112;ENST00000223369	T	0.48201	0.82	6.06	5.19	0.71726	Synaptobrevin (2);	0.042768	0.85682	N	0.000000	T	0.61299	0.2336	M	0.70842	2.15	0.80722	D	1	D;D	0.69078	0.994;0.997	P;P	0.55303	0.463;0.773	T	0.66933	-0.5798	10	0.87932	D	0	-7.4861	14.1628	0.65457	0.0725:0.0:0.9275:0.0	.	145;145	B4DR94;O15498	.;YKT6_HUMAN	K	145	ENSP00000223369:E145K	ENSP00000223369:E145K	E	+	1	0	YKT6	44214296	1.000000	0.71417	0.543000	0.28128	0.938000	0.57974	8.817000	0.91985	1.578000	0.49821	0.650000	0.86243	GAA		0.488	YKT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251125.2	NM_006555		A	44247771	G	A	44247771	3	1	61	1	0	0	0	0	1	0	0	0	17525	1059	37	1	451	1	YKT6	7	44247771	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49056	44247771	114890892	5243	13228										
DDX56	54606	broad.mit.edu	37	chr7	44612328	44612328	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctactaccacatctggcttCtccatcagcacagctctgga	6	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44612328C>A	ENST00000258772.5	-	4	505	c.399G>T	c.(397-399)gaG>gaT	p.E133D	DDX56_ENST00000485367.1_5'UTR|DDX56_ENST00000431640.1_Missense_Mutation_p.E133D	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	133	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.E133D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CATCTGGCTTCTCCATCAGCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	7											95	90	92					7																	44612328		2203	4300	6503	44578853	SO:0001583	missense	54606			AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.399G>T	7.37:g.44612328C>A	ENSP00000258772:p.Glu133Asp		44578853	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	37	CCDS5492.1	.	.	.	.	.	.	.	.	.	.	.	22.2	4.257885	0.80246	.	.	ENSG00000136271	ENST00000258772;ENST00000431640	T;T	0.42131	0.98;0.98	5.48	3.66	0.41972	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.30885	0.0779	L	0.28014	0.82	0.54753	D	0.999986	B;B	0.25048	0.117;0.026	B;B	0.35770	0.21;0.085	T	0.04885	-1.0920	10	0.11182	T	0.66	-39.4064	10.9224	0.47171	0.0:0.836:0.0:0.164	.	133;133	C9JV95;Q9NY93	.;DDX56_HUMAN	D	133	ENSP00000258772:E133D;ENSP00000393488:E133D	ENSP00000258772:E133D	E	-	3	2	DDX56	44578853	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.868000	0.48436	1.468000	0.48064	-0.136000	0.14681	GAG		0.517	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		A	44612328	C	A	44612328	3	1	61	1	0	0	0	0	1	0	0	0	4380	912	32	2	1288	2	DDX56	7	44612328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	364557	44612328	114526335	5244	13229										
H2AFV	94239	broad.mit.edu	37	chr7	44875157	44875157	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatggtagccttgataagaGaatccaactcttcatcacca	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44875157G>T	ENST00000308153.4	-	4	387	c.296C>A	c.(295-297)tCt>tAt	p.S99Y	H2AFV_ENST00000349299.3_Missense_Mutation_p.S61Y|H2AFV_ENST00000350771.3_Missense_Mutation_p.S73Y|H2AFV_ENST00000437072.1_Missense_Mutation_p.S61Y|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000222690.6_Missense_Mutation_p.S99Y|H2AFV_ENST00000446531.1_Missense_Mutation_p.S99Y|H2AFV_ENST00000521529.1_Intron	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	99						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S99Y(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						CTTGATAAGAGAATCCAACTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	7											116	92	100					7																	44875157		2203	4300	6503	44841682	SO:0001583	missense	94239			AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"Histones / Replication-independent"	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.296C>A	7.37:g.44875157G>T	ENSP00000308405:p.Ser99Tyr		44841682	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630555	0.87660	.	.	ENSG00000105968	ENST00000222690;ENST00000437072;ENST00000349299;ENST00000308153;ENST00000350771;ENST00000446531	D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.68	5.68	0.88126	Histone-fold (2);Histone H2A (1);	.	.	.	.	D	0.89649	0.6776	M	0.64404	1.975	0.80722	D	1	P;D;D;P	0.65815	0.529;0.975;0.995;0.904	B;P;P;B	0.56751	0.281;0.805;0.615;0.396	D	0.90292	0.4323	9	0.72032	D	0.01	-11.8079	17.2793	0.87124	0.0:0.0:1.0:0.0	.	73;61;99;99	A6NKY0;A6NFA8;Q71UI9;A6NN01	.;.;H2AV_HUMAN;.	Y	99;61;61;99;73;99	ENSP00000222690:S99Y;ENSP00000397115:S61Y;ENSP00000342714:S61Y;ENSP00000308405:S99Y;ENSP00000340708:S73Y;ENSP00000406901:S99Y	ENSP00000222690:S99Y	S	-	2	0	H2AFV	44841682	1.000000	0.71417	0.969000	0.41365	0.995000	0.86356	9.179000	0.94861	2.698000	0.92095	0.585000	0.79938	TCT		0.428	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412		T	44875157	G	T	44875157	3	4	61	1	0	0	0	0	1	0	0	0	6948	942	33	2	122	2	H2AFV	7	44875157	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	262829	44875157	114263506	5245	13230										
PURB	5814	broad.mit.edu	37	chr7	44924203	44924203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggtaggacggcttcacctCgctcactcgcagaaacaccc	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:44924203C>T	ENST00000395699.2	-	1	757	c.745G>A	c.(745-747)Gag>Aag	p.E249K	RP4-673M15.1_ENST00000608450.1_RNA|MIR4657_ENST00000578157.1_RNA	NM_033224.3	NP_150093.1	Q96QR8	PURB_HUMAN	purine-rich element binding protein B	249					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of myeloid cell differentiation (GO:0045637)|transcription, DNA-templated (GO:0006351)	DNA replication factor A complex (GO:0005662)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)	p.E249K(1)		large_intestine(2)|lung(3)|prostate(1)|skin(1)	7						GGCTTCACCTCGCTCACTCGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	7											119	125	123					7																	44924203		2203	4300	6503	44890728	SO:0001583	missense	5814				CCDS5499.1	7p13	2008-07-18			ENSG00000146676	ENSG00000146676			9702	protein-coding gene	gene with protein product		608887				1448097	Standard	NM_033224		Approved	PURBETA	uc003tme.3	Q96QR8	OTTHUMG00000023578	ENST00000395699.2:c.745G>A	7.37:g.44924203C>T	ENSP00000379051:p.Glu249Lys		44890728	A4D2L7	Missense_Mutation	SNP	ENST00000395699.2	37	CCDS5499.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153276	0.94645	.	.	ENSG00000146676	ENST00000395699	T	0.47869	0.83	4.27	4.27	0.50696	.	0.072925	0.52532	U	0.000061	T	0.73830	0.3637	M	0.91300	3.195	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.80930	-0.1162	10	0.87932	D	0	.	14.5813	0.68292	0.0:1.0:0.0:0.0	.	249	Q96QR8	PURB_HUMAN	K	249	ENSP00000379051:E249K	ENSP00000379051:E249K	E	-	1	0	PURB	44890728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.567000	0.82357	2.362000	0.80069	0.591000	0.81541	GAG		0.567	PURB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251332.2	NM_033224		T	44924203	C	T	44924203	3	4	61	1	0	0	0	0	1	0	0	0	12865	893	31	1	197	1	PURB	7	44924203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49046	44924203	114214460	5246	13231										
ADCY1	107	broad.mit.edu	37	chr7	45662327	45662327	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgagctcttcggcaagttCgatgaattagccacggtaag	11	8	1	2	rs143472730		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:45662327C>T	ENST00000297323.7	+	4	1027	c.1005C>T	c.(1003-1005)ttC>ttT	p.F335F	ADCY1_ENST00000432715.1_Silent_p.F110F	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	335					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.F335F(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCGGCAAGTTCGATGAATTAG	0.488													C|||	1	0.000199681	0	0	5008	,	,		20567	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C		0,4406		0,0,2203	94	83	86		1005	-0.6	1	7	dbSNP_134	86	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADCY1	NM_021116.2		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		335/1120	45662327	3,13003	2203	4300	6503	45628852	SO:0001819	synonymous_variant	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1005C>T	7.37:g.45662327C>T			45628852	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																				0.488	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45662327	C	T	45662327	2	4	61	1	0	0	0	0	0	0	0	1	292	883	31	1		1	ADCY1	7	45662327	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	738124	45662327	113476336	5247	13232										
TNS3	64759	broad.mit.edu	37	chr7	47342587	47342587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgaagccttggaaaagtCgggaaggacatttgggaagg	15	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47342587C>T	ENST00000398879.1	-	22	3784	c.3418G>A	c.(3418-3420)Gac>Aac	p.D1140N	TNS3_ENST00000355730.3_Missense_Mutation_p.D900N|TNS3_ENST00000311160.9_Missense_Mutation_p.D1140N			Q68CZ2	TENS3_HUMAN	tensin 3	1140					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.D1140N(1)		NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						TTGGAAAAGTCGGGAAGGACA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	7											77	84	82					7																	47342587		1954	4144	6098	47309112	SO:0001583	missense	64759			AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3418G>A	7.37:g.47342587C>T	ENSP00000381854:p.Asp1140Asn		47309112	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	C	19.31	3.803047	0.70682	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.98474	-3.3;-3.3;-3.82;-4.95	5.56	5.56	0.83823	.	0.115999	0.56097	D	0.000033	D	0.98852	0.9612	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99826	1.1050	10	0.72032	D	0.01	-38.1981	17.0298	0.86458	0.0:1.0:0.0:0.0	.	1140	Q68CZ2	TENS3_HUMAN	N	1140;1250;1140;900;596;1243	ENSP00000312143:D1140N;ENSP00000381854:D1140N;ENSP00000347968:D900N;ENSP00000414358:D1243N	ENSP00000312143:D1140N	D	-	1	0	TNS3	47309112	1.000000	0.71417	0.611000	0.29010	0.009000	0.06853	7.097000	0.76967	2.615000	0.88500	0.484000	0.47621	GAC		0.597	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47342587	C	T	47342587	3	4	61	1	0	0	0	0	1	0	0	0	16383	884	31	1	959	1	TNS3	7	47342587	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1680260	47342587	111796076	5248	13233										
C7orf65	401335	broad.mit.edu	37	chr7	47698549	47698549	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcctgcagcatttaaaaAatgcagagaagtgttcagag	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47698549A>C	ENST00000408988.2	+	3	214	c.179A>C	c.(178-180)aAa>aCa	p.K60T		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	60										endometrium(1)|lung(2)	3						GCATTTAAAAAATGCAGAGAA	0.488																																																0			7											48	46	47					7																	47698549		1568	3582	5150	47665074	SO:0001583	missense	401335				CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.179A>C	7.37:g.47698549A>C	ENSP00000386198:p.Lys60Thr		47665074	A4D2F8	Missense_Mutation	SNP	ENST00000408988.2	37	CCDS43580.1	.	.	.	.	.	.	.	.	.	.	A	7.006	0.555786	0.13436	.	.	ENSG00000221845	ENST00000408988	.	.	.	0.881	0.881	0.19166	.	.	.	.	.	T	0.27594	0.0678	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.09707	-1.0662	8	0.87932	D	0	.	4.0544	0.09810	1.0:0.0:0.0:0.0	.	60	Q6ZTY9	CG065_HUMAN	T	60	.	ENSP00000386198:K60T	K	+	2	0	C7orf65	47665074	0.000000	0.05858	0.006000	0.13384	0.148000	0.21650	-0.401000	0.07232	0.641000	0.30601	0.324000	0.21423	AAA		0.488	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065		C	47698549	A	C	47698549	3	2	61	1	0	0	0	0	1	0	0	0	2417	14	1	4	189	4	C7orf65	7	47698549	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	355962	47698549	111440114	5249	13234										
PKD1L1	168507	broad.mit.edu	37	chr7	47847885	47847885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgaggtccataaatgctCggcaaagtcctctgtgaaac	12	9	1	2	rs147668180	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47847885C>T	ENST00000289672.2	-	52	7837	c.7787G>A	c.(7786-7788)cGa>cAa	p.R2596Q	C7orf69_ENST00000418326.2_Intron|C7orf69_ENST00000258776.4_Intron|PKD1L1_ENST00000462350.1_5'Flank	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2596					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R2596Q(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CATAAATGCTCGGCAAAGTCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	7											159	130	140					7																	47847885		2203	4300	6503	47814410	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7787G>A	7.37:g.47847885C>T	ENSP00000289672:p.Arg2596Gln		47814410	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	c	0.008	-1.874281	0.00542	.	.	ENSG00000158683	ENST00000289672	T	0.70164	-0.46	4.98	-0.414	0.12359	Polycystin cation channel, PKD1/PKD2 (1);	0.569907	0.14863	N	0.293989	T	0.30696	0.0773	N	0.03608	-0.345	0.09310	N	0.999997	B	0.09022	0.002	B	0.06405	0.002	T	0.27502	-1.0072	10	0.02654	T	1	-1.0356	4.31	0.10965	0.1502:0.3473:0.0:0.5025	.	2596	Q8TDX9	PK1L1_HUMAN	Q	2596	ENSP00000289672:R2596Q	ENSP00000289672:R2596Q	R	-	2	0	PKD1L1	47814410	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.305000	0.08188	-0.346000	0.08312	-0.285000	0.09966	CGA		0.517	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47847885	C	T	47847885	3	4	61	1	0	0	0	0	1	0	0	0	11995	884	31	1	786	1	PKD1L1	7	47847885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149336	47847885	111290778	5250	13235										
PKD1L1	168507	broad.mit.edu	37	chr7	47886498	47886498	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagttcactttttcaggaGaagtccctggttgtggagag	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47886498G>T	ENST00000289672.2	-	32	5182	c.5132C>A	c.(5131-5133)tCt>tAt	p.S1711Y		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1711	GPS.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S1711F(1)|p.S1711Y(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TTTTTCAGGAGAAGTCCCTGG	0.433																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7											97	92	93					7																	47886498		2203	4300	6503	47853023	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5132C>A	7.37:g.47886498G>T	ENSP00000289672:p.Ser1711Tyr		47853023	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.256851	0.39896	.	.	ENSG00000158683	ENST00000289672	T	0.22336	1.96	5.07	2.24	0.28232	.	0.525001	0.17793	N	0.161835	T	0.12220	0.0297	L	0.27053	0.805	0.24298	N	0.995136	P	0.48016	0.904	B	0.38264	0.269	T	0.14035	-1.0487	10	0.87932	D	0	-11.2487	6.4218	0.21748	0.3834:0.0:0.6166:0.0	.	1711	Q8TDX9	PK1L1_HUMAN	Y	1711	ENSP00000289672:S1711Y	ENSP00000289672:S1711Y	S	-	2	0	PKD1L1	47853023	0.798000	0.28890	0.917000	0.36280	0.986000	0.74619	0.608000	0.24223	0.523000	0.28482	0.563000	0.77884	TCT		0.433	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47886498	G	T	47886498	3	4	61	1	0	0	0	0	1	0	0	0	11995	942	33	2	3521	2	PKD1L1	7	47886498	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38613	47886498	111252165	5251	13236										
PKD1L1	168507	broad.mit.edu	37	chr7	47925648	47925648	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccccactactctgcagaaGggaacttaagcaaacgtttg	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47925648G>T	ENST00000289672.2	-	18	2891	c.2841C>A	c.(2839-2841)ccC>ccA	p.P947P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	947	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.P947P(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CTCTGCAGAAGGGAACTTAAG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	7											47	48	48					7																	47925648		2203	4300	6503	47892173	SO:0001819	synonymous_variant	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2841C>A	7.37:g.47925648G>T			47892173	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																				0.433	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47925648	G	T	47925648	2	4	61	1	0	0	0	0	0	0	0	1	11995	987	35	2		2	PKD1L1	7	47925648	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39150	47925648	111213015	5252	13237										
PKD1L1	168507	broad.mit.edu	37	chr7	47933555	47933555	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaggtggtcctggagaaGaataggtgtgtgccctcgga	17	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47933555G>T	ENST00000289672.2	-	15	2423	c.2373C>A	c.(2371-2373)ttC>ttA	p.F791L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	791	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.F791L(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TCCTGGAGAAGAATAGGTGTG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											92	66	75					7																	47933555		2203	4300	6503	47900080	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2373C>A	7.37:g.47933555G>T	ENSP00000289672:p.Phe791Leu		47900080	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	g	10.90	1.482192	0.26598	.	.	ENSG00000158683	ENST00000289672	T	0.68765	-0.35	5.23	0.0841	0.14436	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.000000	0.64402	D	0.000003	T	0.61689	0.2367	L	0.45581	1.43	0.09310	N	0.999996	D	0.52996	0.957	P	0.53490	0.727	T	0.52548	-0.8561	10	0.29301	T	0.29	-26.3625	5.4535	0.16578	0.3271:0.138:0.5349:0.0	.	791	Q8TDX9	PK1L1_HUMAN	L	791	ENSP00000289672:F791L	ENSP00000289672:F791L	F	-	3	2	PKD1L1	47900080	0.037000	0.19845	0.162000	0.22713	0.051000	0.14879	0.004000	0.13106	0.242000	0.21303	-0.284000	0.09977	TTC		0.602	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47933555	G	T	47933555	3	4	61	1	0	0	0	0	1	0	0	0	11995	933	33	2	6348	2	PKD1L1	7	47933555	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7907	47933555	111205108	5253	13238										
PKD1L1	168507	broad.mit.edu	37	chr7	47944114	47944114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccagagctgaggagggggAcgtgagccgattggccacaa	16	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47944114A>G	ENST00000289672.2	-	12	1842	c.1792T>C	c.(1792-1794)Tcc>Ccc	p.S598P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	598	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S598P(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GAGGAGGGGGACGTGAGCCGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	80	89					7																	47944114		2203	4300	6503	47910639	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1792T>C	7.37:g.47944114A>G	ENSP00000289672:p.Ser598Pro		47910639	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	A	10.52	1.374311	0.24857	.	.	ENSG00000158683	ENST00000289672	T	0.69926	-0.44	5.12	3.95	0.45737	PKD/Chitinase domain (1);PKD domain (2);	0.169710	0.37348	N	0.002125	T	0.76147	0.3947	M	0.68952	2.095	0.09310	N	1	D	0.71674	0.998	D	0.66351	0.943	T	0.66736	-0.5848	10	0.52906	T	0.07	-33.7065	9.7112	0.40247	0.6625:0.3375:0.0:0.0	.	598	Q8TDX9	PK1L1_HUMAN	P	598	ENSP00000289672:S598P	ENSP00000289672:S598P	S	-	1	0	PKD1L1	47910639	0.140000	0.22579	0.002000	0.10522	0.092000	0.18411	1.448000	0.35112	0.886000	0.36113	0.477000	0.44152	TCC		0.542	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		G	47944114	A	G	47944114	3	3	61	1	0	0	0	0	1	0	0	0	11995	275	10	4	6941	4	PKD1L1	7	47944114	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10559	47944114	111194549	5254	13239										
PKD1L1	168507	broad.mit.edu	37	chr7	47947723	47947723	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagcacttcatcttcatgGacactgctggagttcatgaa	8	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47947723G>A	ENST00000289672.2	-	9	1403	c.1353C>T	c.(1351-1353)gtC>gtT	p.V451V		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	451					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.V451V(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CATCTTCATGGACACTGCTGG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	7											120	105	110					7																	47947723		2203	4300	6503	47914248	SO:0001819	synonymous_variant	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1353C>T	7.37:g.47947723G>A			47914248	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																				0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47947723	G	A	47947723	2	1	61	1	0	0	0	0	0	0	0	1	11995	1161	41	3		3	PKD1L1	7	47947723	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3609	47947723	111190940	5255	13240										
PKD1L1	168507	broad.mit.edu	37	chr7	47968801	47968801	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggacaccatgcaccttacCttttgagtactggtggtagg	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:47968801C>A	ENST00000289672.2	-	7	1110	c.1060G>T	c.(1060-1062)Ggt>Tgt	p.G354C		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	354					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.G354C(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TGCACCTTACCTTTTGAGTAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											102	95	97					7																	47968801		2203	4300	6503	47935326	SO:0001630	splice_region_variant	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1060+1G>T	7.37:g.47968801C>A			47935326	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.054571	0.36277	.	.	ENSG00000158683	ENST00000289672	T	0.21543	2.0	4.11	4.11	0.48088	.	2587.440000	0.00465	U	0.000103	T	0.26340	0.0643	N	0.08118	0	0.28496	N	0.914244	D	0.62365	0.991	P	0.58454	0.839	T	0.46582	-0.9181	9	.	.	.	.	12.077	0.53649	0.0:1.0:0.0:0.0	.	354	Q8TDX9	PK1L1_HUMAN	C	354	ENSP00000289672:G354C	.	G	-	1	0	PKD1L1	47935326	0.999000	0.42202	0.928000	0.36995	0.014000	0.08584	2.819000	0.48049	2.295000	0.77249	0.579000	0.79373	GGT		0.512	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	Missense_Mutation	A	47968801	C	A	47968801	5	1	61	1	0	0	0	0	0	0	1	0	11995	695	24	2	7693	2	PKD1L1	7	47968801	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21078	47968801	111169862	5256	13241										
ABCA13	154664	broad.mit.edu	37	chr7	48259035	48259035	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaagacctggcagaggaAattcatggaatgatggacaa	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48259035A>C	ENST00000435803.1	+	4	396	c.372A>C	c.(370-372)gaA>gaC	p.E124D		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	124					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E124D(1)|p.E69D(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGGCAGAGGAAATTCATGGAA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	7											102	97	99					7																	48259035		1839	4087	5926	48229581	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.372A>C	7.37:g.48259035A>C	ENSP00000411096:p.Glu124Asp		48229581	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.358226	0.24598	.	.	ENSG00000179869	ENST00000435803	D	0.85861	-2.04	5.58	-9.6	0.00553	.	0.833401	0.10272	N	0.694655	T	0.64768	0.2628	N	0.16478	0.41	0.09310	N	0.999999	B;B	0.11235	0.002;0.004	B;B	0.11329	0.006;0.003	T	0.49263	-0.8958	10	0.29301	T	0.29	.	6.326	0.21244	0.2294:0.5427:0.1422:0.0857	.	124;124	Q86UQ4;Q86UQ4-2	ABCAD_HUMAN;.	D	124	ENSP00000411096:E124D	ENSP00000409268:E124D	E	+	3	2	ABCA13	48229581	0.001000	0.12720	0.001000	0.08648	0.428000	0.31595	-0.788000	0.04614	-1.164000	0.02790	0.533000	0.62120	GAA		0.403	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48259035	A	C	48259035	3	2	61	1	0	0	0	0	1	0	0	0	31	11	1	4	215	4	ABCA13	7	48259035	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	290234	48259035	110879628	5257	13242										
ABCA13	154664	broad.mit.edu	37	chr7	48280567	48280567	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgaagaagagagcaagcCctggaaggtggtggaagctc	16	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48280567C>A	ENST00000435803.1	+	10	1190	c.1166C>A	c.(1165-1167)cCc>cAc	p.P389H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	389					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.P389H(1)|p.P334H(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GAGAGCAAGCCCTGGAAGGTG	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	7											132	133	133					7																	48280567		2048	4204	6252	48251113	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1166C>A	7.37:g.48280567C>A	ENSP00000411096:p.Pro389His		48251113	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768256	0.49680	.	.	ENSG00000179869	ENST00000435803	D	0.91464	-2.85	5.5	3.69	0.42338	.	0.276231	0.25954	N	0.027224	D	0.89424	0.6711	L	0.27053	0.805	0.09310	N	0.999994	D	0.71674	0.998	P	0.61397	0.888	T	0.81531	-0.0890	10	0.87932	D	0	.	8.1417	0.31086	0.0:0.8152:0.0:0.1848	.	389	Q86UQ4	ABCAD_HUMAN	H	389	ENSP00000411096:P389H	ENSP00000411096:P389H	P	+	2	0	ABCA13	48251113	0.000000	0.05858	0.006000	0.13384	0.100000	0.18952	0.082000	0.14847	0.678000	0.31325	0.655000	0.94253	CCC		0.493	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48280567	C	A	48280567	3	1	61	1	0	0	0	0	1	0	0	0	31	623	22	2	1033	2	ABCA13	7	48280567	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21532	48280567	110858096	5258	13243										
ABCA13	154664	broad.mit.edu	37	chr7	48280633	48280633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacagcttgtcagcagatgGcccaaaagataatcatacat	8	9	2	3	rs557664531		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48280633G>A	ENST00000435803.1	+	10	1256	c.1232G>A	c.(1231-1233)gGc>gAc	p.G411D		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	411					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.G411D(1)|p.G356D(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCAGCAGATGGCCCAAAAGAT	0.443													G|||	1	0.000199681	0	0	5008	,	,		19719	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	7											151	149	150					7																	48280633		2026	4195	6221	48251179	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1232G>A	7.37:g.48280633G>A	ENSP00000411096:p.Gly411Asp		48251179	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.812816	0.50527	.	.	ENSG00000179869	ENST00000435803	D	0.89196	-2.48	5.36	-3.0E-4	0.14038	.	0.785759	0.10983	N	0.612505	D	0.84138	0.5406	L	0.27053	0.805	0.09310	N	1	D	0.64830	0.994	P	0.54544	0.755	T	0.73209	-0.4055	10	0.66056	D	0.02	.	1.111	0.01704	0.287:0.1919:0.383:0.1381	.	411	Q86UQ4	ABCAD_HUMAN	D	411	ENSP00000411096:G411D	ENSP00000411096:G411D	G	+	2	0	ABCA13	48251179	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	-0.007000	0.12810	-0.011000	0.14247	0.655000	0.94253	GGC		0.443	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48280633	G	A	48280633	3	1	61	1	0	0	0	0	1	0	0	0	31	1203	42	3	1099	3	ABCA13	7	48280633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66	48280633	110858030	5259	13244										
ABCA13	154664	broad.mit.edu	37	chr7	48285536	48285536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgccgcctggaaactccaGcatatggggtggtctccagg	13	11	1	0	rs369781498		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48285536G>A	ENST00000435803.1	+	13	1592	c.1568G>A	c.(1567-1569)aGc>aAc	p.S523N		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	523					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S523N(1)|p.S468N(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GGAAACTCCAGCATATGGGGT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	7											83	78	80					7																	48285536		1873	4104	5977	48256082	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1568G>A	7.37:g.48285536G>A	ENSP00000411096:p.Ser523Asn		48256082	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094425	0.36952	.	.	ENSG00000179869	ENST00000435803	D	0.88124	-2.34	4.81	3.8	0.43715	.	0.970605	0.08459	N	0.942633	T	0.78660	0.4318	L	0.27053	0.805	0.20638	N	0.999879	B	0.22604	0.072	B	0.18871	0.023	T	0.67177	-0.5736	10	0.72032	D	0.01	.	5.205	0.15285	0.1888:0.0:0.8112:0.0	.	523	Q86UQ4	ABCAD_HUMAN	N	523	ENSP00000411096:S523N	ENSP00000411096:S523N	S	+	2	0	ABCA13	48256082	0.006000	0.16342	0.005000	0.12908	0.068000	0.16541	1.567000	0.36407	2.196000	0.70406	0.655000	0.94253	AGC		0.453	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48285536	G	A	48285536	3	1	61	1	0	0	0	0	1	0	0	0	31	971	34	3	1447	3	ABCA13	7	48285536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4903	48285536	110853127	5260	13245										
ABCA13	154664	broad.mit.edu	37	chr7	48311961	48311961	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttaagtgaggctataataActagtctccatgaatttgga	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48311961A>C	ENST00000435803.1	+	17	2722	c.2698A>C	c.(2698-2700)Act>Cct	p.T900P		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	900					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.T900P(1)|p.T845P(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GGCTATAATAACTAGTCTCCA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	7											97	96	97					7																	48311961		1856	4098	5954	48282507	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.2698A>C	7.37:g.48311961A>C	ENSP00000411096:p.Thr900Pro		48282507	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	5.347	0.249405	0.10130	.	.	ENSG00000179869	ENST00000435803	D	0.85484	-1.99	5.46	0.0515	0.14298	.	1.038830	0.07640	N	0.930190	T	0.70263	0.3204	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.57952	-0.7722	10	0.66056	D	0.02	.	7.6631	0.28415	0.4883:0.4365:0.0752:0.0	.	900	Q86UQ4	ABCAD_HUMAN	P	900	ENSP00000411096:T900P	ENSP00000411096:T900P	T	+	1	0	ABCA13	48282507	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.542000	0.23222	-0.136000	0.11475	0.528000	0.53228	ACT		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48311961	A	C	48311961	3	2	61	1	0	0	0	0	1	0	0	0	31	43	2	4	2593	4	ABCA13	7	48311961	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	26425	48311961	110826702	5261	13246										
ABCA13	154664	broad.mit.edu	37	chr7	48313251	48313251	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcactgagctaagagaaGcaatagtatttcttagaaat	7	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48313251G>T	ENST00000435803.1	+	17	4012	c.3988G>T	c.(3988-3990)Gca>Tca	p.A1330S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1330					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.A1275S(1)|p.A1330S(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCTAAGAGAAGCAATAGTATT	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	7											25	26	25					7																	48313251		1811	4052	5863	48283797	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.3988G>T	7.37:g.48313251G>T	ENSP00000411096:p.Ala1330Ser		48283797	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	9.950	1.219883	0.22373	.	.	ENSG00000179869	ENST00000435803	D	0.85556	-2.0	5.37	3.02	0.34903	.	0.267738	0.26359	N	0.024826	T	0.71400	0.3335	N	0.22421	0.69	0.80722	D	1	B	0.25667	0.131	B	0.22386	0.039	T	0.59075	-0.7522	9	.	.	.	.	7.5144	0.27592	0.8254:0.0:0.1746:0.0	.	1330	Q86UQ4	ABCAD_HUMAN	S	1330	ENSP00000411096:A1330S	.	A	+	1	0	ABCA13	48283797	0.242000	0.23868	0.211000	0.23655	0.430000	0.31655	2.035000	0.41155	0.442000	0.26555	-0.484000	0.04775	GCA		0.279	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48313251	G	T	48313251	3	4	61	1	0	0	0	0	1	0	0	0	31	971	34	2	3883	2	ABCA13	7	48313251	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1290	48313251	110825412	5262	13247										
ABCA13	154664	broad.mit.edu	37	chr7	48314155	48314155	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaaagctacaggtcttgGtattcaactgataagggatg	11	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48314155G>T	ENST00000435803.1	+	17	4916	c.4892G>T	c.(4891-4893)gGt>gTt	p.G1631V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1631					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.G1631V(1)|p.G1576V(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ACAGGTCTTGGTATTCAACTG	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	7											180	172	174					7																	48314155		1869	4096	5965	48284701	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4892G>T	7.37:g.48314155G>T	ENSP00000411096:p.Gly1631Val		48284701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	7.149	0.583322	0.13749	.	.	ENSG00000179869	ENST00000435803	D	0.86562	-2.14	5.43	-0.743	0.11105	.	1.016150	0.07887	N	0.970466	T	0.78052	0.4223	L	0.47716	1.5	0.09310	N	1	B	0.21905	0.062	B	0.18871	0.023	T	0.59894	-0.7368	9	.	.	.	.	0.2822	0.00246	0.2444:0.1636:0.2926:0.2994	.	1631	Q86UQ4	ABCAD_HUMAN	V	1631	ENSP00000411096:G1631V	.	G	+	2	0	ABCA13	48284701	0.002000	0.14202	0.000000	0.03702	0.151000	0.21798	1.334000	0.33827	-0.021000	0.14009	0.563000	0.77884	GGT		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48314155	G	T	48314155	3	4	61	1	0	0	0	0	1	0	0	0	31	1261	44	2	4787	2	ABCA13	7	48314155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	904	48314155	110824508	5263	13248										
ABCA13	154664	broad.mit.edu	37	chr7	48314899	48314899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgttcaaatgaaagctcccGaatggaaataactaggaaag	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48314899G>A	ENST00000435803.1	+	17	5660	c.5636G>A	c.(5635-5637)cGa>cAa	p.R1879Q		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1879					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1879Q(1)|p.R1824L(1)|p.R1879L(1)|p.R1824Q(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GAAAGCTCCCGAATGGAAATA	0.403																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	7											60	61	61					7																	48314899		1814	4073	5887	48285445	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5636G>A	7.37:g.48314899G>A	ENSP00000411096:p.Arg1879Gln		48285445	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	1.447	-0.565947	0.03910	.	.	ENSG00000179869	ENST00000435803	T	0.20738	2.05	6.16	-4.9	0.03094	.	1.687590	0.03791	N	0.262930	T	0.04998	0.0134	N	0.00729	-1.24	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.30592	-0.9973	9	.	.	.	.	4.8921	0.13731	0.2606:0.1049:0.5302:0.1044	.	1879	Q86UQ4	ABCAD_HUMAN	Q	1879	ENSP00000411096:R1879Q	.	R	+	2	0	ABCA13	48285445	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.385000	0.02540	-0.595000	0.05828	-0.300000	0.09419	CGA		0.403	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48314899	G	A	48314899	3	1	61	1	0	0	0	0	1	0	0	0	31	1058	37	1	5531	1	ABCA13	7	48314899	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	744	48314899	110823764	5264	13249										
ABCA13	154664	broad.mit.edu	37	chr7	48315394	48315394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtttagaagcattatcaaGttttattgaaaaaagtgaaa	7	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48315394G>T	ENST00000435803.1	+	17	6155	c.6131G>T	c.(6130-6132)aGt>aTt	p.S2044I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2044					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S2044I(1)|p.S1989I(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCATTATCAAGTTTTATTGAA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											32	30	31					7																	48315394		1829	4082	5911	48285940	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.6131G>T	7.37:g.48315394G>T	ENSP00000411096:p.Ser2044Ile		48285940	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	8.186	0.794944	0.16327	.	.	ENSG00000179869	ENST00000435803	T	0.15603	2.41	4.65	-2.5	0.06384	.	0.883493	0.09483	N	0.796038	T	0.12263	0.0298	L	0.44542	1.39	0.09310	N	1	B	0.22003	0.063	B	0.21360	0.034	T	0.36089	-0.9762	9	.	.	.	.	6.2943	0.21077	0.4705:0.2465:0.283:0.0	.	2044	Q86UQ4	ABCAD_HUMAN	I	2044	ENSP00000411096:S2044I	.	S	+	2	0	ABCA13	48285940	0.001000	0.12720	0.000000	0.03702	0.042000	0.13812	-0.664000	0.05292	-0.586000	0.05898	-2.630000	0.00154	AGT		0.358	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48315394	G	T	48315394	3	4	61	1	0	0	0	0	1	0	0	0	31	1029	36	2	6026	2	ABCA13	7	48315394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	495	48315394	110823269	5265	13250										
ABCA13	154664	broad.mit.edu	37	chr7	48431626	48431626	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggagcttggtgtgtgtccGcagcaggacatcctgttgga	15	8	0	0	rs372260479		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48431626G>A	ENST00000435803.1	+	38	11787	c.11763G>A	c.(11761-11763)ccG>ccA	p.P3921P		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3921	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.P3921P(1)|p.P3866P(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GTGTGTGTCCGCAGCAGGACA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	7						G		6,4058		0,6,2026	121	125	123		11763	-10.6	0	7		123	0,8362		0,0,4181	no	coding-synonymous	ABCA13	NM_152701.3		0,6,6207	AA,AG,GG		0.0,0.1476,0.0483		3921/5059	48431626	6,12420	2032	4181	6213	48402172	SO:0001819	synonymous_variant	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11763G>A	7.37:g.48431626G>A			48402172	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																				0.552	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48431626	G	A	48431626	2	1	61	1	0	0	0	0	0	0	0	1	31	1074	38	1		1	ABCA13	7	48431626	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116232	48431626	110707037	5266	13251										
ABCA13	154664	broad.mit.edu	37	chr7	48452009	48452009	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttacatccctgataaaGatctatattccacaagcatt	5	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48452009G>T	ENST00000435803.1	+	41	12312	c.12288G>T	c.(12286-12288)aaG>aaT	p.K4096N		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4096					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.K4096N(1)|p.K4041N(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CCCTGATAAAGATCTATATTC	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	7											47	45	46					7																	48452009		1880	4117	5997	48422555	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12288G>T	7.37:g.48452009G>T	ENSP00000411096:p.Lys4096Asn		48422555	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	7.498	0.651989	0.14580	.	.	ENSG00000179869	ENST00000435803	D	0.83673	-1.75	4.98	4.98	0.66077	.	0.142695	0.32473	N	0.006058	T	0.77903	0.4200	L	0.33189	0.99	0.80722	D	1	B;B	0.20988	0.05;0.023	B;B	0.23716	0.048;0.014	T	0.75291	-0.3369	10	0.59425	D	0.04	.	17.2325	0.86988	0.0:0.0:1.0:0.0	.	1798;4096	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	N	4096	ENSP00000411096:K4096N	ENSP00000411096:K4096N	K	+	3	2	ABCA13	48422555	1.000000	0.71417	0.041000	0.18516	0.004000	0.04260	3.924000	0.56476	2.288000	0.76882	0.555000	0.69702	AAG		0.438	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48452009	G	T	48452009	3	4	61	1	0	0	0	0	1	0	0	0	31	933	33	2	12279	2	ABCA13	7	48452009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20383	48452009	110686654	5267	13252										
ABCA13	154664	broad.mit.edu	37	chr7	48547482	48547482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcagcctggagagcatccGtcagtgtggagtggccctct	14	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48547482G>A	ENST00000435803.1	+	50	13385	c.13361G>A	c.(13360-13362)cGt>cAt	p.R4454H	ABCA13_ENST00000544596.1_Missense_Mutation_p.R184H	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4454					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R4454H(1)|p.R4399H(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GAGAGCATCCGTCAGTGTGGA	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	7											63	65	65					7																	48547482		2139	4257	6396	48518028	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13361G>A	7.37:g.48547482G>A	ENSP00000411096:p.Arg4454His		48518028	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260620	0.80246	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.87334	-2.24;-2.24;-2.24	5.5	5.5	0.81552	.	0.000000	0.51477	D	0.000085	D	0.93141	0.7816	M	0.76574	2.34	0.47214	D	0.999352	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.975;0.992;0.999	D	0.93715	0.7027	10	0.87932	D	0	.	16.5419	0.84395	0.0:0.0:1.0:0.0	.	184;2156;4454	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	H	4454;227;184	ENSP00000411096:R4454H;ENSP00000391042:R227H;ENSP00000442634:R184H	ENSP00000391042:R227H	R	+	2	0	ABCA13	48518028	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	4.292000	0.59031	2.556000	0.86216	0.650000	0.86243	CGT		0.552	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48547482	G	A	48547482	3	1	61	1	0	0	0	0	1	0	0	0	31	1145	40	1	13388	1	ABCA13	7	48547482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95473	48547482	110591181	5268	13253										
ABCA13	154664	broad.mit.edu	37	chr7	48563975	48563975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccttagtaaacattatcGacgctttttccagaatatta	4	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48563975G>A	ENST00000435803.1	+	54	14207	c.14183G>A	c.(14182-14184)cGa>cAa	p.R4728Q	ABCA13_ENST00000544596.1_Missense_Mutation_p.R458Q	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4728	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R4673Q(1)|p.R4728Q(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAACATTATCGACGCTTTTTC	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	7											110	111	111					7																	48563975		1827	4089	5916	48534521	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14183G>A	7.37:g.48563975G>A	ENSP00000411096:p.Arg4728Gln		48534521	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	0.671	-0.801885	0.02841	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.87412	-2.0;-2.25;-2.21	5.59	-1.52	0.08637	ABC transporter-like (1);	1.451940	0.04585	N	0.395644	T	0.74053	0.3666	N	0.17474	0.49	0.09310	N	1	B;B;B	0.24963	0.013;0.115;0.026	B;B;B	0.15870	0.006;0.014;0.002	T	0.58284	-0.7663	10	0.17832	T	0.49	.	6.6363	0.22885	0.457:0.1241:0.4189:0.0	.	458;2430;4728	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	Q	4728;501;458	ENSP00000411096:R4728Q;ENSP00000391042:R501Q;ENSP00000442634:R458Q	ENSP00000391042:R501Q	R	+	2	0	ABCA13	48534521	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.182000	0.09726	-0.323000	0.08602	-0.345000	0.07892	CGA		0.348	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48563975	G	A	48563975	3	1	61	1	0	0	0	0	1	0	0	0	31	1058	37	1	14226	1	ABCA13	7	48563975	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16493	48563975	110574688	5269	13254										
ABCA13	154664	broad.mit.edu	37	chr7	48626792	48626792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttacacctcgaagcccacGcggacaaacctgtggccacc	9	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48626792G>A	ENST00000435803.1	+	57	14572	c.14548G>A	c.(14548-14550)Gcg>Acg	p.A4850T	ABCA13_ENST00000544596.1_Missense_Mutation_p.A580T	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4850	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.A4850T(1)|p.A4795T(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CGAAGCCCACGCGGACAAACC	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	7											43	47	46					7																	48626792		2026	4190	6216	48597338	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14548G>A	7.37:g.48626792G>A	ENSP00000411096:p.Ala4850Thr		48597338	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534926	0.27475	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.94000	-3.33;-3.33;-3.33	5.71	4.72	0.59763	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.760684	0.11485	N	0.559299	D	0.91895	0.7434	M	0.87827	2.91	0.09310	N	1	B;P;P	0.35894	0.156;0.524;0.526	B;B;B	0.28784	0.04;0.079;0.094	D	0.87452	0.2402	10	0.66056	D	0.02	.	5.3099	0.15825	0.2323:0.0:0.7677:0.0	.	580;2552;4850	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	T	4850;623;580	ENSP00000411096:A4850T;ENSP00000391042:A623T;ENSP00000442634:A580T	ENSP00000391042:A623T	A	+	1	0	ABCA13	48597338	0.122000	0.22280	0.167000	0.22817	0.153000	0.21895	2.313000	0.43735	2.683000	0.91414	0.650000	0.86243	GCG		0.562	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48626792	G	A	48626792	3	1	61	1	0	0	0	0	1	0	0	0	31	1087	38	1	14603	1	ABCA13	7	48626792	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62817	48626792	110511871	5270	13255										
ABCA13	154664	broad.mit.edu	37	chr7	48634409	48634409	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcggtgctgacctcccacaGgtgagttccagtttctcttg	11	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:48634409G>A	ENST00000435803.1	+	58	14768	c.14744G>A	c.(14743-14745)aGc>aAc	p.S4915N	ABCA13_ENST00000544596.1_Splice_Site_p.S645N	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4915	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S4915N(1)|p.S4860N(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ACCTCCCACAGGTGAGTTCCA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	7																																								48604955	SO:0001630	splice_region_variant	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14744+1G>A	7.37:g.48634409G>A			48604955	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522224	0.85600	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.97888	-4.59;-4.59;-4.59	5.7	5.7	0.88788	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.64402	D	0.000014	D	0.97620	0.9220	L	0.31578	0.945	0.47698	D	0.999496	D;D;D	0.89917	0.995;1.0;1.0	D;D;D	0.76575	0.975;0.988;0.963	D	0.98735	1.0714	10	0.66056	D	0.02	.	17.3203	0.87234	0.0:0.0:1.0:0.0	.	645;2617;4915	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	N	4915;688;645	ENSP00000411096:S4915N;ENSP00000391042:S688N;ENSP00000442634:S645N	ENSP00000391042:S688N	S	+	2	0	ABCA13	48604955	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	8.303000	0.89955	2.672000	0.90937	0.563000	0.77884	AGC		0.493	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	Missense_Mutation	A	48634409	G	A	48634409	5	1	61	1	0	0	0	0	0	0	1	0	31	1014	35	3	14803	3	ABCA13	7	48634409	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7617	48634409	110504254	5271	13256										
COBL	23242	broad.mit.edu	37	chr7	51152969	51152969	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggcgctcgccgcttcttCttctgtaaatcaatctgtga	9	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:51152969C>A	ENST00000265136.7	-	7	1155	c.990G>T	c.(988-990)aaG>aaT	p.K330N	COBL_ENST00000395540.2_Missense_Mutation_p.K330N|COBL_ENST00000441453.1_Missense_Mutation_p.K330N|COBL_ENST00000395542.2_Missense_Mutation_p.K355N	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	330	Pro-rich.				actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)	p.K330N(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GCCGCTTCTTCTTCTGTAAAT	0.493																																					NSCLC(189;2119 2138 12223 30818 34679)											1	Substitution - Missense(1)	large_intestine(1)	7											105	88	94					7																	51152969		2203	4300	6503	51120463	SO:0001583	missense	23242			AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.990G>T	7.37:g.51152969C>A	ENSP00000265136:p.Lys330Asn		51120463	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.996991|3.996991	0.74818|0.74818	.|.	.|.	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000395540;ENST00000441453	.|T;T;T;T;T;T	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58	5.46|5.46	-2.08|-2.08	0.07254|0.07254	.|Cordon-bleu domain (1);	.|0.167217	.|0.29293	.|N	.|0.012578	.|T	.|0.60919	.|0.2306	L|L	0.53249|0.53249	1.67|1.67	0.32277|0.32277	N|N	0.568033|0.568033	.|D;P;D;D;D	.|0.76494	.|0.998;0.897;0.996;0.999;0.999	.|D;P;P;D;D	.|0.68765	.|0.923;0.548;0.866;0.96;0.933	.|T	.|0.66304	.|-0.5957	.|10	.|0.52906	.|T	.|0.07	.|.	11.9345|11.9345	0.52866|0.52866	0.0:0.289:0.0:0.711|0.0:0.289:0.0:0.711	.|.	.|330;330;330;330;355	.|O75128-3;O75128-5;O75128-7;O75128;O75128-2	.|.;.;.;COBL_HUMAN;.	X|N	249|330;222;158;355;330;330	.|ENSP00000265136:K330N;ENSP00000401204:K222N;ENSP00000413498:K158N;ENSP00000378912:K355N;ENSP00000378910:K330N;ENSP00000399500:K330N	.|ENSP00000265136:K330N	E|K	-|-	1|3	0|2	COBL|COBL	51120463|51120463	0.931000|0.931000	0.31567|0.31567	0.978000|0.978000	0.43139|0.43139	0.964000|0.964000	0.63967|0.63967	-0.248000|-0.248000	0.08854|0.08854	-0.484000|-0.484000	0.06763|0.06763	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.493	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		A	51152969	C	A	51152969	3	1	61	1	0	0	0	0	1	0	0	0	3659	912	32	2	2823	2	COBL	7	51152969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2518560	51152969	107985694	5272	13257										
VSTM2A	222008	broad.mit.edu	37	chr7	54617553	54617553	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtccaaggcaatgacatCtcccacaagcttcagatttc	6	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:54617553C>A	ENST00000407838.3	+	4	730	c.324C>A	c.(322-324)atC>atA	p.I108I	VSTM2A_ENST00000404951.1_Silent_p.I108I|VSTM2A_ENST00000302287.3_Silent_p.I108I|VSTM2A_ENST00000498834.1_3'UTR|VSTM2A_ENST00000402026.2_Silent_p.I107I|VSTM2A_ENST00000402613.3_Silent_p.I108I	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	108	Ig-like V-type.					extracellular region (GO:0005576)		p.I107I(2)|p.I108I(1)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			GCAATGACATCTCCCACAAGC	0.408																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	7											43	41	42					7																	54617553		2203	4300	6503	54585047	SO:0001819	synonymous_variant	222008			BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"Immunoglobulin superfamily / V-set domain containing"	28499	protein-coding gene	gene with protein product			"V-set and transmembrane domain containing 2"	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.324C>A	7.37:g.54617553C>A			54585047	A4D2E9|B5MC94	Silent	SNP	ENST00000407838.3	37	CCDS5512.2																																																																																				0.408	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546		A	54617553	C	A	54617553	2	1	61	1	0	0	0	0	0	0	0	1	17269	903	32	2		2	VSTM2A	7	54617553	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3464584	54617553	104521110	5273	13258										
EGFR	1956	broad.mit.edu	37	chr7	55211097	55211097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagaggaaatatgtactacGaaaattcctatgccttagca	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:55211097G>A	ENST00000275493.2	+	3	517	c.340G>A	c.(340-342)Gaa>Aaa	p.E114K	EGFR_ENST00000420316.2_Missense_Mutation_p.E114K|EGFR_ENST00000455089.1_Missense_Mutation_p.E114K|EGFR_ENST00000342916.3_Missense_Mutation_p.E114K|EGFR_ENST00000344576.2_Missense_Mutation_p.E114K|EGFR_ENST00000442591.1_Missense_Mutation_p.E114K|EGFR_ENST00000454757.2_Missense_Mutation_p.E61K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	114			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.E114K(2)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TATGTACTACGAAAATTCCTA	0.458		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	2	Substitution - Missense(2)	large_intestine(2)	7											113	113	113					7																	55211097		2203	4300	6503	55178591	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.340G>A	7.37:g.55211097G>A	ENSP00000275493:p.Glu114Lys		55178591	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364338	0.41902	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000450046;ENST00000454757	T;T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	5.31	5.31	0.75309	EGF receptor, L domain (1);	0.141063	0.64402	D	0.000006	T	0.69033	0.3066	L	0.37800	1.135	0.58432	D	0.999996	B;B;P;B;B	0.36249	0.142;0.019;0.545;0.04;0.036	B;B;B;B;B	0.28638	0.066;0.016;0.092;0.021;0.017	T	0.71652	-0.4528	10	0.52906	T	0.07	.	11.4126	0.49933	0.0839:0.0:0.9161:0.0	.	114;114;114;114;114	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	K	114;114;114;114;114;114;61;61	ENSP00000415559:E114K;ENSP00000342376:E114K;ENSP00000345973:E114K;ENSP00000413843:E114K;ENSP00000275493:E114K;ENSP00000410031:E114K;ENSP00000413354:E61K;ENSP00000395243:E61K	ENSP00000275493:E114K	E	+	1	0	EGFR	55178591	1.000000	0.71417	0.943000	0.38184	0.083000	0.17756	4.824000	0.62701	2.656000	0.90262	0.655000	0.94253	GAA		0.458	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55211097	G	A	55211097	3	1	61	1	0	0	0	0	1	0	0	0	4978	1059	37	1	350	1	EGFR	7	55211097	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	593544	55211097	103927566	5274	13259										
LANCL2	55915	broad.mit.edu	37	chr7	55499000	55499000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatttgaacttgactcttCgaagagggattaaaaggtgc	11	6	1	3	rs372359047		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:55499000C>T	ENST00000254770.2	+	9	1918	c.1340C>T	c.(1339-1341)tCg>tTg	p.S447L		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	447					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.S447L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			CTTGACTCTTCGAAGAGGGAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	LEU/SER	0,4406		0,0,2203	77	72	74		1340	2.8	0	7		74	1,8599		0,1,4299	no	missense	LANCL2	NM_018697.3	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	447/451	55499000	1,13005	2203	4300	6503	55466494	SO:0001583	missense	55915			AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"testis-specific adriamycin sensitivity protein", "G protein-coupled receptor 69B"	612919	"LanC (bacterial lantibiotic synthetase component C)-like 2"	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.1340C>T	7.37:g.55499000C>T	ENSP00000254770:p.Ser447Leu		55466494	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Missense_Mutation	SNP	ENST00000254770.2	37	CCDS5517.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.255988	0.22965	0.0	1.16E-4	ENSG00000132434	ENST00000254770	T	0.30448	1.53	5.79	2.78	0.32641	.	1.359230	0.04657	N	0.408184	T	0.20941	0.0504	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26503	-1.0101	10	0.09843	T	0.71	.	2.0557	0.03581	0.1504:0.3918:0.2919:0.166	.	447	Q9NS86	LANC2_HUMAN	L	447	ENSP00000254770:S447L	ENSP00000254770:S447L	S	+	2	0	LANCL2	55466494	0.000000	0.05858	0.010000	0.14722	0.946000	0.59487	0.610000	0.24253	0.740000	0.32651	0.563000	0.77884	TCG		0.448	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697		T	55499000	C	T	55499000	3	4	61	1	0	0	0	0	1	0	0	0	8643	893	31	1	1374	1	LANCL2	7	55499000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	287903	55499000	103639663	5275	13260										
VOPP1	81552	broad.mit.edu	37	chr7	55540571	55540571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggccttcactacctgttCgtacgggggcggaggcgtgt	15	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:55540571C>T	ENST00000285279.5	-	5	696	c.496G>A	c.(496-498)Gaa>Aaa	p.E166K	VOPP1_ENST00000433959.1_Missense_Mutation_p.E157K|VOPP1_ENST00000428097.1_Missense_Mutation_p.E99K|VOPP1_ENST00000428648.1_Missense_Mutation_p.E99K|VOPP1_ENST00000453256.1_Missense_Mutation_p.E99K|VOPP1_ENST00000545390.1_Missense_Mutation_p.E163K|VOPP1_ENST00000418904.1_Missense_Mutation_p.E149K|VOPP1_ENST00000427700.1_Missense_Mutation_p.E164K|VOPP1_ENST00000454227.1_Missense_Mutation_p.E103K	NM_001284282.1|NM_030796.3	NP_001271211.1|NP_110423.3	Q96AW1	VOPP1_HUMAN	vesicular, overexpressed in cancer, prosurvival protein 1	166					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|integral component of organelle membrane (GO:0031301)	signal transducer activity (GO:0004871)	p.R128Q(1)		endometrium(1)|lung(4)	5						ACTACCTGTTCGTACGGGGGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	7											3	3	3					7																	55540571		1499	3492	4991	55508065	SO:0001583	missense	81552				CCDS47588.1, CCDS64654.1, CCDS64656.1	7p11.2	2010-06-22			ENSG00000154978	ENSG00000154978			34518	protein-coding gene	gene with protein product	"Glioblastoma-amplified secreted protein", "EGFR-coamplified and overexpressed protein"	611915				15735698	Standard	NM_030796		Approved	ECop, GASP, FLJ20532, DKFZp564K0822	uc003tqs.3	Q96AW1	OTTHUMG00000156124	ENST00000285279.5:c.496G>A	7.37:g.55540571C>T	ENSP00000285279:p.Glu166Lys		55508065	B0AZU1|B2RAT4|B3KS72|C9JWR3|Q6FIE3|Q8NBN8|Q96RE5|Q9H0W4	Missense_Mutation	SNP	ENST00000285279.5	37	CCDS47588.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178050	0.94846	.	.	ENSG00000154978	ENST00000285279;ENST00000428648;ENST00000433959;ENST00000545390;ENST00000428097;ENST00000418904;ENST00000454227;ENST00000453256;ENST00000427700	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	T	0.66829	0.2829	L	0.29908	0.895	0.42879	D	0.99416	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	D;D;D;D	0.76575	0.97;0.988;0.988;0.988	T	0.70583	-0.4832	8	0.87932	D	0	-9.9258	16.8455	0.85979	0.0:1.0:0.0:0.0	.	149;163;166;157	C9JWR3;B0AZU1;Q96AW1;B3KS72	.;.;VOPP1_HUMAN;.	K	166;99;157;163;99;149;103;99;164	.	ENSP00000285279:E166K	E	-	1	0	VOPP1	55508065	1.000000	0.71417	0.944000	0.38274	0.968000	0.65278	5.448000	0.66612	2.554000	0.86153	0.650000	0.86243	GAA		0.612	VOPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343074.1	NM_030796		T	55540571	C	T	55540571	3	4	61	1	0	0	0	0	1	0	0	0	17224	893	31	1	26	1	VOPP1	7	55540571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41571	55540571	103598092	5276	13261										
SEPT14	346288	broad.mit.edu	37	chr7	55863771	55863771	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatcattttaagatgctcGaacttgtcctgcagctgtga	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:55863771G>A	ENST00000388975.3	-	10	1250	c.1134C>T	c.(1132-1134)ttC>ttT	p.F378F		NM_207366.2	NP_997249.2	Q6ZU15	SEP14_HUMAN	septin 14	378					cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.F378F(1)|p.F167F(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|skin(2)	23	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TAAGATGCTCGAACTTGTCCT	0.378																																																2	Substitution - coding silent(2)	large_intestine(2)	7											22	25	24					7																	55863771		1123	2160	3283	55831265	SO:0001819	synonymous_variant	346288			AK126048	CCDS5519.2	7p11.2	2013-01-21			ENSG00000154997	ENSG00000154997		"Septins"	33280	protein-coding gene	gene with protein product		612140					Standard	NM_207366		Approved	FLJ44060	uc003tqz.2	Q6ZU15	OTTHUMG00000129341	ENST00000388975.3:c.1134C>T	7.37:g.55863771G>A			55831265	A6NCC2|B4DXD6	Silent	SNP	ENST00000388975.3	37	CCDS5519.2																																																																																				0.378	SEPT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251489.2	NM_207366		A	55863771	G	A	55863771	2	1	61	1	0	0	0	0	0	0	0	1	14100	1049	37	1		1	SEPT14	7	55863771	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	323200	55863771	103274892	5277	13262										
SEPT14	346288	broad.mit.edu	37	chr7	55874887	55874887	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttttttcttttagattTtccatattggtacaaagaag	8	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:55874887T>G	ENST00000388975.3	-	8	998	c.882A>C	c.(880-882)gaA>gaC	p.E294D		NM_207366.2	NP_997249.2	Q6ZU15	SEP14_HUMAN	septin 14	294	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.E294D(1)|p.E83D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|skin(2)	23	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTTTTAGATTTTCCATATTGG	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											111	106	108					7																	55874887		2203	4300	6503	55842381	SO:0001583	missense	346288			AK126048	CCDS5519.2	7p11.2	2013-01-21			ENSG00000154997	ENSG00000154997		"Septins"	33280	protein-coding gene	gene with protein product		612140					Standard	NM_207366		Approved	FLJ44060	uc003tqz.2	Q6ZU15	OTTHUMG00000129341	ENST00000388975.3:c.882A>C	7.37:g.55874887T>G	ENSP00000373627:p.Glu294Asp		55842381	A6NCC2|B4DXD6	Missense_Mutation	SNP	ENST00000388975.3	37	CCDS5519.2	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991928	0.54041	.	.	ENSG00000154997	ENST00000388975	D	0.83506	-1.73	3.24	-0.473	0.12112	.	0.150124	0.42420	D	0.000711	D	0.84638	0.5516	L	0.45470	1.425	0.34314	D	0.685838	D	0.89917	1.0	D	0.91635	0.999	D	0.84345	0.0529	10	0.72032	D	0.01	.	7.3584	0.26731	0.0:0.5462:0.0:0.4538	.	294	Q6ZU15	SEP14_HUMAN	D	294	ENSP00000373627:E294D	ENSP00000373627:E294D	E	-	3	2	SEPT14	55842381	1.000000	0.71417	0.979000	0.43373	0.933000	0.57130	1.174000	0.31932	-0.087000	0.12528	0.455000	0.32223	GAA		0.358	SEPT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251489.2	NM_207366		G	55874887	T	G	55874887	3	3	61	1	0	0	0	0	1	0	0	0	14100	1838	64	4	428	4	SEPT14	7	55874887	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11116	55874887	103263776	5278	13263										
ZNF713	349075	broad.mit.edu	37	chr7	56006916	56006916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagaagccttgagtgtaaTaaatttgcagaaaactgtaa	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:56006916T>C	ENST00000429591.2	+	4	548	c.510T>C	c.(508-510)aaT>aaC	p.N170N	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N170N(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TTGAGTGTAATAAATTTGCAG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7											57	58	58					7																	56006916		2203	4300	6503	55974410	SO:0001819	synonymous_variant	349075			AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"Zinc fingers, C2H2-type", "-"	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.510T>C	7.37:g.56006916T>C			55974410		Silent	SNP	ENST00000429591.2	37	CCDS34639.1																																																																																				0.378	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		C	56006916	T	C	56006916	2	2	61	1	0	0	0	0	0	0	0	1	18156	1403	49	4		4	ZNF713	7	56006916	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	132029	56006916	103131747	5279	13264										
MRPS17	51373	broad.mit.edu	37	chr7	56022703	56022703	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgttccacgagcaaaGcatgtgaaacatgaactggc	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:56022703G>A	ENST00000285298.4	+	3	354	c.225G>A	c.(223-225)aaG>aaA	p.K75K	MRPS17_ENST00000426595.1_Silent_p.K170K	NM_015969.2	NP_057053.1	Q9Y2R5	RT17_HUMAN	mitochondrial ribosomal protein S17	75					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.K75K(1)		kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CACGAGCAAAGCATGTGAAAC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	7											172	173	173					7																	56022703		2203	4300	6503	55990197	SO:0001819	synonymous_variant	51373			AB051352	CCDS5520.1	7p11-q11.21	2012-09-13			ENSG00000239789	ENSG00000239789		"Mitochondrial ribosomal proteins / small subunits"	14047	protein-coding gene	gene with protein product	"28S ribosomal protein S17, mitochondrial"	611980				11279123	Standard	NM_015969		Approved	HSPC011, RPMS17, MRP-S17	uc003trd.3	Q9Y2R5	OTTHUMG00000023153	ENST00000285298.4:c.225G>A	7.37:g.56022703G>A			55990197	Q86X15	Silent	SNP	ENST00000285298.4	37	CCDS5520.1																																																																																				0.458	MRPS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251527.2	NM_015969		A	56022703	G	A	56022703	2	1	61	1	0	0	0	0	0	0	0	1	9857	962	34	3		3	MRPS17	7	56022703	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15787	56022703	103115960	5280	13265										
CCT6A	908	broad.mit.edu	37	chr7	56126155	56126155	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagggttaaaaaaataataGaactgaaaaggaaagtctgt	9	2	1	2	rs370382749		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:56126155G>T	ENST00000275603.4	+	7	1045	c.826G>T	c.(826-828)Gaa>Taa	p.E276*	SNORA15_ENST00000384439.1_RNA|SNORA22_ENST00000383876.1_RNA|CCT6A_ENST00000335503.3_Nonsense_Mutation_p.E231*|CCT6A_ENST00000540286.1_Nonsense_Mutation_p.E245*	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	276					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.E276*(1)		breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AAAAATAATAGAACTGAAAAG	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											46	51	50					7																	56126155		2201	4294	6495	56093649	SO:0001587	stop_gained	908			M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"Heat Shock Proteins / Chaperonins"	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.826G>T	7.37:g.56126155G>T	ENSP00000275603:p.Glu276*		56093649	A6NCD2|Q3KP28|Q75LP4|Q96S46	Nonsense_Mutation	SNP	ENST00000275603.4	37	CCDS5523.1	.	.	.	.	.	.	.	.	.	.	G	36	5.913000	0.97099	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	.	.	.	5.66	5.66	0.87406	.	0.369326	0.32401	N	0.006155	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-1.6602	18.3139	0.90210	0.0:0.0:1.0:0.0	.	.	.	.	X	276;231;245;134	.	ENSP00000275603:E276X	E	+	1	0	CCT6A	56093649	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.950000	0.63603	2.667000	0.90743	0.491000	0.48974	GAA		0.308	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762		T	56126155	G	T	56126155	4	4	61	1	0	0	0	0	0	1	0	0	2963	943	33	2	852	2	CCT6A	7	56126155	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103452	56126155	103012508	5281	13266										
ZNF680	340252	broad.mit.edu	37	chr7	63982511	63982511	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcacatttgtaagaattCtctctagtgtgaattcttat	5	8	4	2	rs145625716	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:63982511C>A	ENST00000309683.6	-	4	772	c.621G>T	c.(619-621)gaG>gaT	p.E207D	ZNF680_ENST00000476563.1_5'UTR	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E207D(1)		breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				TGTAAGAATTCTCTCTAGTGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	63	64	63		621	0	0	7	dbSNP_134	63	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF680	NM_178558.4	45	0,7,6496	AA,AC,CC		0.0698,0.0227,0.0538	benign	207/531	63982511	7,12999	2203	4300	6503	63619946	SO:0001583	missense	340252			AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"Zinc fingers, C2H2-type", "-"	26897	protein-coding gene	gene with protein product	"hypothetical protein FLJ90430"					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.621G>T	7.37:g.63982511C>A	ENSP00000309330:p.Glu207Asp		63619946	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	37	CCDS34644.1	.	.	.	.	.	.	.	.	.	.	c	8.706	0.910809	0.17833	2.27E-4	6.98E-4	ENSG00000173041	ENST00000309683	T	0.19806	2.12	1.36	0.0327	0.14176	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16854	0.0405	L	0.49571	1.57	0.80722	D	1	B	0.32350	0.366	B	0.34824	0.19	T	0.07271	-1.0781	9	0.51188	T	0.08	.	3.7845	0.08694	0.0:0.6731:0.0:0.3269	.	207	Q8NEM1	ZN680_HUMAN	D	207	ENSP00000309330:E207D	ENSP00000309330:E207D	E	-	3	2	ZNF680	63619946	0.939000	0.31865	0.002000	0.10522	0.010000	0.07245	0.005000	0.13129	-0.178000	0.10672	0.491000	0.48974	GAG		0.338	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558		A	63982511	C	A	63982511	3	1	61	1	0	0	0	0	1	0	0	0	18126	912	32	2	975	2	ZNF680	7	63982511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7856356	63982511	95156152	5282	13267										
ZNF107	51427	broad.mit.edu	37	chr7	64166725	64166725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcttttcattttgcccaaGacctttggccagagcagaac	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64166725G>T	ENST00000395391.1	+	4	1418	c.43G>T	c.(43-45)Gac>Tac	p.D15Y	ZNF107_ENST00000423627.1_Missense_Mutation_p.D15Y|ZNF107_ENST00000344930.3_Missense_Mutation_p.D15Y			Q9UII5	ZN107_HUMAN	zinc finger protein 107	15					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D15Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TTTTGCCCAAGACCTTTGGCC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	7											49	50	49					7																	64166725		2201	4298	6499	63804160	SO:0001583	missense	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.43G>T	7.37:g.64166725G>T	ENSP00000378789:p.Asp15Tyr		63804160		Missense_Mutation	SNP	ENST00000395391.1	37	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	14.14	2.446895	0.43429	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T;T	0.11277	4.21;2.79;2.79;2.79	1.2	0.147	0.14838	.	.	.	.	.	T	0.14356	0.0347	M	0.85777	2.775	0.26318	N	0.977711	B	0.31009	0.303	B	0.31337	0.128	T	0.27839	-1.0062	9	0.54805	T	0.06	.	2.9933	0.05990	0.36:0.0:0.64:0.0	.	15	Q9UII5	ZN107_HUMAN	Y	15	ENSP00000353234:D15Y;ENSP00000343443:D15Y;ENSP00000400037:D15Y;ENSP00000378789:D15Y	ENSP00000343443:D15Y	D	+	1	0	ZNF107	63804160	0.000000	0.05858	0.277000	0.24703	0.498000	0.33706	0.030000	0.13688	0.570000	0.29347	0.305000	0.20034	GAC		0.308	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		T	64166725	G	T	64166725	3	4	61	1	0	0	0	0	1	0	0	0	17754	942	33	2	49	2	ZNF107	7	64166725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184214	64166725	94971938	5283	13268										
ZNF107	51427	broad.mit.edu	37	chr7	64166954	64166954	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgataaattttcaaattCaaatagatataagagaagac	5	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64166954C>T	ENST00000395391.1	+	4	1647	c.272C>T	c.(271-273)tCa>tTa	p.S91L	ZNF107_ENST00000423627.1_Missense_Mutation_p.S91L|ZNF107_ENST00000344930.3_Missense_Mutation_p.S91L			Q9UII5	ZN107_HUMAN	zinc finger protein 107	91					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S91L(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TTTTCAAATTCAAATAGATAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	7											33	33	33					7																	64166954		2203	4298	6501	63804389	SO:0001583	missense	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.272C>T	7.37:g.64166954C>T	ENSP00000378789:p.Ser91Leu		63804389		Missense_Mutation	SNP	ENST00000395391.1	37	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	2.376	-0.343208	0.05243	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T;T	0.17054	4.17;2.3;2.3;2.3	0.916	-0.222	0.13122	.	.	.	.	.	T	0.04092	0.0114	N	0.00380	-1.58	0.09310	N	1	B	0.33266	0.404	B	0.43445	0.42	T	0.40776	-0.9545	9	0.02654	T	1	.	3.3357	0.07100	0.0:0.3785:0.0:0.6215	.	91	Q9UII5	ZN107_HUMAN	L	91	ENSP00000353234:S91L;ENSP00000343443:S91L;ENSP00000400037:S91L;ENSP00000378789:S91L	ENSP00000343443:S91L	S	+	2	0	ZNF107	63804389	0.000000	0.05858	0.209000	0.23619	0.204000	0.24138	0.289000	0.18957	0.300000	0.22699	0.305000	0.20034	TCA		0.313	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		T	64166954	C	T	64166954	3	4	61	1	0	0	0	0	1	0	0	0	17754	838	29	3	278	3	ZNF107	7	64166954	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	229	64166954	94971709	5284	13269										
ZNF107	51427	broad.mit.edu	37	chr7	64167711	64167711	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaccagttctcaactctTactagacataagataattca	3	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64167711T>G	ENST00000395391.1	+	4	2404	c.1029T>G	c.(1027-1029)ctT>ctG	p.L343L	ZNF107_ENST00000423627.1_Silent_p.L343L|ZNF107_ENST00000344930.3_Silent_p.L343L			Q9UII5	ZN107_HUMAN	zinc finger protein 107	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L343L(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TCTCAACTCTTACTAGACATA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	7											29	31	31					7																	64167711		2153	4270	6423	63805146	SO:0001819	synonymous_variant	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.1029T>G	7.37:g.64167711T>G			63805146		Silent	SNP	ENST00000395391.1	37	CCDS5527.1																																																																																				0.338	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		G	64167711	T	G	64167711	2	3	61	1	0	0	0	0	0	0	0	1	17754	1741	61	4		4	ZNF107	7	64167711	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	757	64167711	94970952	5285	13270										
ZNF107	51427	broad.mit.edu	37	chr7	64168118	64168118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggcaaagcttttaaccGattctcaacccttactaaac	5	11	1	0	rs370014833		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64168118G>A	ENST00000395391.1	+	4	2811	c.1436G>A	c.(1435-1437)cGa>cAa	p.R479Q	ZNF107_ENST00000423627.1_Missense_Mutation_p.R479Q|ZNF107_ENST00000344930.3_Missense_Mutation_p.R479Q			Q9UII5	ZN107_HUMAN	zinc finger protein 107	479					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R479Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				GCTTTTAACCGATTCTCAACC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	GLN/ARG,GLN/ARG	0,4400		0,0,2200	27	29	28		1436,1436	1.3	0.3	7		28	1,8589		0,1,4294	no	missense,missense	ZNF107	NM_001013746.1,NM_016220.3	43,43	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	479/784,479/784	64168118	1,12989	2200	4295	6495	63805553	SO:0001583	missense	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.1436G>A	7.37:g.64168118G>A	ENSP00000378789:p.Arg479Gln		63805553		Missense_Mutation	SNP	ENST00000395391.1	37	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	0.720	-0.783979	0.02907	0.0	1.16E-4	ENSG00000196247	ENST00000344930;ENST00000423627;ENST00000395391	T;T;T	0.35973	1.28;1.28;1.28	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15696	0.0378	N	0.20845	0.615	0.09310	N	1	P	0.36837	0.571	B	0.21546	0.035	T	0.11227	-1.0596	8	.	.	.	.	4.552	0.12117	0.0:0.0:0.6247:0.3752	.	479	Q9UII5	ZN107_HUMAN	Q	479	ENSP00000343443:R479Q;ENSP00000400037:R479Q;ENSP00000378789:R479Q	.	R	+	2	0	ZNF107	63805553	0.000000	0.05858	0.278000	0.24718	0.596000	0.36781	-2.160000	0.01279	0.635000	0.30488	0.313000	0.20887	CGA		0.353	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		A	64168118	G	A	64168118	3	1	61	1	0	0	0	0	1	0	0	0	17754	1058	37	1	1442	1	ZNF107	7	64168118	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	407	64168118	94970545	5286	13271										
ZNF273	10793	broad.mit.edu	37	chr7	64388677	64388677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaattgtgaagaatgtgGcaaaggctttagtatattct	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64388677G>A	ENST00000476120.1	+	4	1042	c.971G>A	c.(970-972)gGc>gAc	p.G324D	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.G259D	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G324D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				GAAGAATGTGGCAAAGGCTTT	0.338																																					Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)											1	Substitution - Missense(1)	large_intestine(1)	7											35	39	38					7																	64388677		2203	4298	6501	64026112	SO:0001583	missense	10793			X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.971G>A	7.37:g.64388677G>A	ENSP00000418719:p.Gly324Asp		64026112	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	13.82	2.350753	0.41599	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.58358	0.34;0.34	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37183	0.0994	N	0.20328	0.56	0.41841	D	0.99012	P	0.34977	0.478	B	0.39503	0.301	T	0.17745	-1.0359	9	0.59425	D	0.04	.	7.3527	0.26700	0.0:0.0:1.0:0.0	.	324	Q14593	ZN273_HUMAN	D	324;259	ENSP00000418719:G324D;ENSP00000324518:G259D	ENSP00000324518:G259D	G	+	2	0	ZNF273	64026112	0.998000	0.40836	0.349000	0.25694	0.348000	0.29142	1.731000	0.38135	0.202000	0.20498	0.205000	0.17691	GGC		0.338	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			A	64388677	G	A	64388677	3	1	61	1	0	0	0	0	1	0	0	0	17847	1203	42	3	985	3	ZNF273	7	64388677	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	220559	64388677	94749986	5287	13272										
ZNF117	51351	broad.mit.edu	37	chr7	64439395	64439395	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctcttcagtatgaattCtcttatgtctaataaggtgt	7	6	4	1	rs368230173		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64439395C>A	ENST00000282869.6	-	4	1838	c.554G>T	c.(553-555)aGa>aTa	p.R185I		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	185					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R185I(2)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGTATGAATTCTCTTATGTCT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	7						C	ILE/ARG	1,4307		0,1,2153	48	51	50		554	1.2	0	7		50	0,8552		0,0,4276	no	missense	ZNF117	NM_015852.3	97	0,1,6429	AA,AC,CC		0.0,0.0232,0.0078	benign	185/484	64439395	1,12859	2154	4276	6430	64076830	SO:0001583	missense	51351			M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"Zinc fingers, C2H2-type"	12897	protein-coding gene	gene with protein product		194624	"zinc finger protein 117 (HPF9)"			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.554G>T	7.37:g.64439395C>A	ENSP00000282869:p.Arg185Ile		64076830	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	.	.	.	.	.	.	.	.	.	.	.	11.16	1.557908	0.27827	2.32E-4	0.0	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.02446	4.29	1.2	1.2	0.21068	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03011	0.0089	L	0.48877	1.53	0.44275	D	0.997138	B	0.19583	0.037	B	0.18561	0.022	T	0.44922	-0.9296	9	0.27082	T	0.32	.	7.8438	0.29414	0.0:1.0:0.0:0.0	.	185	Q03924	ZN117_HUMAN	I	185	ENSP00000282869:R185I	ENSP00000282869:R185I	R	-	2	0	ZNF117	64076830	0.000000	0.05858	0.024000	0.17045	0.630000	0.37929	-0.129000	0.10515	0.598000	0.29829	0.205000	0.17691	AGA		0.353	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498		A	64439395	C	A	64439395	3	1	61	1	0	0	0	0	1	0	0	0	17756	913	32	2	901	2	ZNF117	7	64439395	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50718	64439395	94699268	5288	13273										
ZNF117	51351	broad.mit.edu	37	chr7	64439479	64439479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttttctccagtatgaattCtcttatgtttattaagggtt	7	5	2	1	rs371560994		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64439479C>A	ENST00000282869.6	-	4	1754	c.470G>T	c.(469-471)aGa>aTa	p.R157I		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	157					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R157I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGTATGAATTCTCTTATGTTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											52	54	53					7																	64439479		2135	4265	6400	64076914	SO:0001583	missense	51351			M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"Zinc fingers, C2H2-type"	12897	protein-coding gene	gene with protein product		194624	"zinc finger protein 117 (HPF9)"			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.470G>T	7.37:g.64439479C>A	ENSP00000282869:p.Arg157Ile		64076914	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	.	.	.	.	.	.	.	.	.	.	.	10.57	1.386552	0.25031	.	.	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.24908	1.83	1.39	1.39	0.22231	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20901	0.0503	M	0.71296	2.17	0.43029	D	0.994596	P	0.38978	0.652	B	0.33392	0.163	T	0.05194	-1.0900	9	0.32370	T	0.25	.	4.764	0.13123	0.364:0.636:0.0:0.0	.	157	Q03924	ZN117_HUMAN	I	157	ENSP00000282869:R157I	ENSP00000282869:R157I	R	-	2	0	ZNF117	64076914	0.000000	0.05858	0.002000	0.10522	0.253000	0.25986	-4.997000	0.00161	0.731000	0.32448	0.205000	0.17691	AGA		0.348	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498		A	64439479	C	A	64439479	3	1	61	1	0	0	0	0	1	0	0	0	17756	913	32	2	985	2	ZNF117	7	64439479	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84	64439479	94699184	5289	13274										
ZNF92	168374	broad.mit.edu	37	chr7	64864629	64864629	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagataatttatactggagaGaaaccctacaaatatgaaga	7	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:64864629G>T	ENST00000328747.7	+	4	1801	c.1602G>T	c.(1600-1602)gaG>gaT	p.E534D	ZNF92_ENST00000357512.2_Missense_Mutation_p.E502D|ZNF92_ENST00000450302.2_Missense_Mutation_p.E465D|ZNF92_ENST00000431504.1_Missense_Mutation_p.E458D	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	534					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E534D(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				ATACTGGAGAGAAACCCTACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											42	49	47					7																	64864629		2202	4300	6502	64502064	SO:0001583	missense	168374			M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.1602G>T	7.37:g.64864629G>T	ENSP00000332595:p.Glu534Asp		64502064	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	37	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772412	0.31411	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	0.418	0.418	0.16429	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25158	0.0611	M	0.61703	1.905	0.33307	D	0.565642	B;P	0.34864	0.023;0.473	B;B	0.42361	0.062;0.385	T	0.38993	-0.9635	9	0.56958	D	0.05	.	6.6212	0.22804	1.0E-4:0.0:0.9999:0.0	.	502;534	Q03936-3;Q03936	.;ZNF92_HUMAN	D	534;458;502;465	ENSP00000332595:E534D;ENSP00000400495:E458D;ENSP00000350113:E502D;ENSP00000396126:E465D	ENSP00000332595:E534D	E	+	3	2	ZNF92	64502064	0.987000	0.35691	0.174000	0.22961	0.176000	0.22953	0.292000	0.19011	0.452000	0.26830	0.460000	0.39030	GAG		0.358	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		T	64864629	G	T	64864629	3	4	61	1	0	0	0	0	1	0	0	0	18240	933	33	2	1616	2	ZNF92	7	64864629	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	425150	64864629	94274034	5290	13275										
C7orf42	55069	broad.mit.edu	37	chr7	66410016	66410016	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacttgtgtgtatcagaGaatgaaaccctcaagcatct	9	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:66410016G>T	ENST00000341567.4	+	3	468	c.213G>T	c.(211-213)gaG>gaT	p.E71D		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	71						integral component of membrane (GO:0016021)		p.E71D(1)									GTGTATCAGAGAATGAAACCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											84	77	79					7																	66410016		2203	4300	6503	66047451	SO:0001583	missense	55069				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.213G>T	7.37:g.66410016G>T	ENSP00000340668:p.Glu71Asp		66047451	Q53H07|Q96FR2	Missense_Mutation	SNP	ENST00000341567.4	37	CCDS5536.1	.	.	.	.	.	.	.	.	.	.	G	9.663	1.144710	0.21288	.	.	ENSG00000106609	ENST00000341567;ENST00000413593;ENST00000424964;ENST00000418375	.	.	.	5.84	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	N	0.14661	0.345	0.52099	D	0.999948	B	0.06786	0.001	B	0.08055	0.003	T	0.07654	-1.0761	9	0.17369	T	0.5	-9.7594	8.6716	0.34154	0.1922:0.0:0.8078:0.0	.	71	Q9NWD8	CG042_HUMAN	D	71	.	ENSP00000340668:E71D	E	+	3	2	C7orf42	66047451	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	3.522000	0.53480	0.713000	0.32060	0.561000	0.74099	GAG		0.502	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		T	66410016	G	T	66410016	3	4	61	1	0	0	0	0	1	0	0	0	2398	933	33	2	219	2	C7orf42	7	66410016	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1545387	66410016	92728647	5291	13276										
WBSCR17	64409	broad.mit.edu	37	chr7	70880999	70880999	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggctggaaggtggctacCgggcaggtcactggcttctt	17	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:70880999C>T	ENST00000333538.5	+	4	1348	c.714C>T	c.(712-714)acC>acT	p.T238T	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	238	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.T238T(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AGGTGGCTACCGGGCAGGTCA	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	7											84	71	75					7																	70880999		2203	4300	6503	70518935	SO:0001819	synonymous_variant	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.714C>T	7.37:g.70880999C>T			70518935	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																				0.567	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	70880999	C	T	70880999	2	4	61	1	0	0	0	0	0	0	0	1	17304	639	23	1		1	WBSCR17	7	70880999	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4470983	70880999	88257664	5292	13277										
WBSCR17	64409	broad.mit.edu	37	chr7	71142268	71142268	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacacagcaatattgtatCcgtgccatggctggggacca	10	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:71142268C>A	ENST00000333538.5	+	9	2111	c.1477C>A	c.(1477-1479)Ccg>Acg	p.P493T	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	493	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.P493T(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AATATTGTATCCGTGCCATGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	7											190	188	189					7																	71142268		2203	4300	6503	70780204	SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1477C>A	7.37:g.71142268C>A	ENSP00000329654:p.Pro493Thr		70780204	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561876	0.65538	.	.	ENSG00000185274	ENST00000333538	T	0.26957	1.7	5.35	5.35	0.76521	Ricin B-related lectin (1);Ricin B lectin (3);	0.346611	0.34628	N	0.003804	T	0.48150	0.1484	M	0.73217	2.22	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	T	0.28996	-1.0026	10	0.11182	T	0.66	.	18.2305	0.89934	0.0:1.0:0.0:0.0	.	493	Q6IS24	GLTL3_HUMAN	T	493	ENSP00000329654:P493T	ENSP00000329654:P493T	P	+	1	0	WBSCR17	70780204	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.203000	0.77864	2.779000	0.95612	0.650000	0.86243	CCG		0.537	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71142268	C	A	71142268	3	1	61	1	0	0	0	0	1	0	0	0	17304	855	30	2	1511	2	WBSCR17	7	71142268	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	261269	71142268	87996395	5293	13278										
CALN1	83698	broad.mit.edu	37	chr7	71275379	71275379	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggctctcttcctcattGataatgatgttctcaatgtc	6	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:71275379G>T	ENST00000329008.5	-	5	772	c.474C>A	c.(472-474)atC>atA	p.I158I	CALN1_ENST00000395275.2_Silent_p.I200I|CALN1_ENST00000405452.2_Silent_p.I158I|CALN1_ENST00000431984.1_Silent_p.I158I|CALN1_ENST00000395276.2_Silent_p.I158I|CALN1_ENST00000412588.1_Silent_p.I200I	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)	p.I158I(1)		biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				CTTCCTCATTGATAATGATGT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	7											212	171	185					7																	71275379		2203	4300	6503	70913315	SO:0001819	synonymous_variant	83698			AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166		"EF-hand domain containing"	13248	protein-coding gene	gene with protein product	"calcium-binding protein CABP8"	607176				11286509	Standard	NM_031468		Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.474C>A	7.37:g.71275379G>T			70913315	J3KQA7	Silent	SNP	ENST00000329008.5	37	CCDS5541.1																																																																																				0.507	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320044.2	NM_031468		T	71275379	G	T	71275379	2	4	61	1	0	0	0	0	0	0	0	1	2597	1280	45	2		2	CALN1	7	71275379	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133111	71275379	87863284	5294	13279										
CALN1	83698	broad.mit.edu	37	chr7	71488747	71488747	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattcatcaaaatccacctgGccatcccctgcaaggagaag	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:71488747G>A	ENST00000329008.5	-	4	568	c.270C>T	c.(268-270)ggC>ggT	p.G90G	CALN1_ENST00000395275.2_Silent_p.G132G|CALN1_ENST00000405452.2_Silent_p.G90G|CALN1_ENST00000431984.1_Silent_p.G90G|CALN1_ENST00000395276.2_Silent_p.G90G|CALN1_ENST00000412588.1_Silent_p.G132G	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	90	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)	p.G90G(1)		biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				AATCCACCTGGCCATCCCCTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	7											107	89	95					7																	71488747		2203	4300	6503	71126683	SO:0001819	synonymous_variant	83698			AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166		"EF-hand domain containing"	13248	protein-coding gene	gene with protein product	"calcium-binding protein CABP8"	607176				11286509	Standard	NM_031468		Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.270C>T	7.37:g.71488747G>A			71126683	J3KQA7	Silent	SNP	ENST00000329008.5	37	CCDS5541.1																																																																																				0.448	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320044.2	NM_031468		A	71488747	G	A	71488747	2	1	61	1	0	0	0	0	0	0	0	1	2597	1190	42	3		3	CALN1	7	71488747	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213368	71488747	87649916	5295	13280										
TRIM50	135892	broad.mit.edu	37	chr7	72732851	72732851	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtggtggtcctcattgccGaactgttccagcacacactc	9	13	1	0	rs568335787		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:72732851G>A	ENST00000333149.2	-	4	896	c.696C>T	c.(694-696)ttC>ttT	p.F232F	TRIM50_ENST00000453152.1_Silent_p.F232F	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	232						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.F232F(4)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						CCTCATTGCCGAACTGTTCCA	0.657													G|||	1	0.000199681	0	0	5008	,	,		17354	0.001		0	False		,,,				2504	0															4	Substitution - coding silent(4)	large_intestine(2)|skin(2)	7											140	128	132					7																	72732851		2203	4300	6503	72370787	SO:0001819	synonymous_variant	135892			AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19017	protein-coding gene	gene with protein product		612548	"tripartite motif-containing 50A", "tripartite motif-containing 50"	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.696C>T	7.37:g.72732851G>A			72370787	Q86XT3	Silent	SNP	ENST00000333149.2	37	CCDS34654.1																																																																																				0.657	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125		A	72732851	G	A	72732851	2	1	61	1	0	0	0	0	0	0	0	1	16566	1049	37	1		1	TRIM50	7	72732851	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1244104	72732851	86405812	5296	13281										
BAZ1B	9031	broad.mit.edu	37	chr7	72907227	72907227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatgaagtaggaagttttCgtggcgatctacgtgctctg	12	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:72907227C>T	ENST00000339594.4	-	5	934	c.596G>A	c.(595-597)cGa>cAa	p.R199Q	BAZ1B_ENST00000404251.1_Missense_Mutation_p.R199Q	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	199	Mediates the tyrosine-protein kinase activity.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.R199Q(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGGAAGTTTTCGTGGCGATCT	0.323																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											1	Substitution - Missense(1)	large_intestine(1)	7											134	128	130					7																	72907227		2202	4300	6502	72545163	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.596G>A	7.37:g.72907227C>T	ENSP00000342434:p.Arg199Gln		72545163	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	C	34	5.326375	0.95708	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.60040	0.22;0.22	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.62962	0.2471	L	0.32530	0.975	0.53005	D	0.999968	D	0.76494	0.999	P	0.61275	0.886	T	0.54323	-0.8311	10	0.14252	T	0.57	-5.1657	18.4101	0.90549	0.0:1.0:0.0:0.0	.	199	Q9UIG0	BAZ1B_HUMAN	Q	199	ENSP00000342434:R199Q;ENSP00000385442:R199Q	ENSP00000342434:R199Q	R	-	2	0	BAZ1B	72545163	0.998000	0.40836	0.992000	0.48379	0.986000	0.74619	5.239000	0.65371	2.690000	0.91761	0.585000	0.79938	CGA		0.323	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		T	72907227	C	T	72907227	3	4	61	1	0	0	0	0	1	0	0	0	1331	884	31	1	3915	1	BAZ1B	7	72907227	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174376	72907227	86231436	5297	13282										
WBSCR22	114049	broad.mit.edu	37	chr7	73098102	73098102	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctttttcgcagttttaTgacgagacagaagcccggaa	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:73098102T>C	ENST00000265758.2	+	2	112	c.54T>C	c.(52-54)taT>taC	p.Y18Y	WBSCR22_ENST00000423497.1_Silent_p.Y18Y|WBSCR22_ENST00000464615.1_Intron|DNAJC30_ENST00000395176.2_5'Flank|WBSCR22_ENST00000423166.2_Missense_Mutation_p.M9T	NM_017528.4	NP_059998.2	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	18					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.Y18Y(1)		autonomic_ganglia(1)|large_intestine(2)|lung(9)|prostate(1)	13		Lung NSC(55;0.0908)|all_lung(88;0.198)				CGCAGTTTTATGACGAGACAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	7											73	83	79					7																	73098102		2203	4300	6503	72736038	SO:0001819	synonymous_variant	114049			AF420248	CCDS5557.1, CCDS56490.1	7q11.23	2012-06-12			ENSG00000071462	ENSG00000071462			16405	protein-coding gene	gene with protein product	"metastasis-related methyltransferase 1"	615733				12073013, 11978965, 21148752	Standard	NM_001202560		Approved	MGC19709, MGC2022, MGC5140, PP3381, WBMT, MERM1	uc003tyt.3	O43709	OTTHUMG00000023306	ENST00000265758.2:c.54T>C	7.37:g.73098102T>C			72736038	A8K501|C9K060|Q96P12|Q9BQ58|Q9HBP9	Silent	SNP	ENST00000265758.2	37	CCDS5557.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480111	0.26598	.	.	ENSG00000071462	ENST00000423166	.	.	.	5.3	0.678	0.17969	.	.	.	.	.	T	0.41811	0.1175	.	.	.	0.24665	N	0.993446	.	.	.	.	.	.	T	0.39313	-0.9620	5	0.87932	D	0	-7.9303	7.5458	0.27766	0.0:0.584:0.0:0.416	.	.	.	.	T	9	.	ENSP00000397056:M9T	M	+	2	0	WBSCR22	72736038	1.000000	0.71417	0.938000	0.37757	0.035000	0.12851	0.973000	0.29422	-0.055000	0.13244	-0.371000	0.07208	ATG		0.592	WBSCR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252303.1			C	73098102	T	C	73098102	2	2	61	1	0	0	0	0	0	0	0	1	17305	1471	51	4		4	WBSCR22	7	73098102	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	190875	73098102	86040561	5298	13283										
LAT2	7462	broad.mit.edu	37	chr7	73636006	73636006	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattacaactgggggcggttCtcgaagcccccagaaggtga	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:73636006C>T	ENST00000460943.1	+	10	1261	c.372C>T	c.(370-372)ttC>ttT	p.F124F	LAT2_ENST00000275635.7_Silent_p.F124F|LAT2_ENST00000398475.1_Silent_p.F124F|LAT2_ENST00000344995.5_Silent_p.F124F	NM_032464.2	NP_115853.2	Q9UHI5	LAT2_HUMAN	linker for activation of T cells family, member 2	0					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)	p.F124F(1)|p.F124L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6					L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	GGGGGCGGTTCTCGAAGCCCC	0.587																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	7											92	99	97					7																	73636006		1874	4105	5979	73273942	SO:0001819	synonymous_variant	7462			AF257135	CCDS5566.2	7q11.23	2011-11-01	2005-04-26	2005-04-26	ENSG00000086730	ENSG00000086730			12749	protein-coding gene	gene with protein product	"linker for activation of B cells", "non-T cell activation linker", "linker for activation of T cells, transmembrane adaptor 2"	605719	"Williams-Beuren syndrome chromosome region 5"	WBSCR15, WBSCR5		8812460, 12514734	Standard	NM_032464		Approved	WSCR5, HSPC046, LAB, NTAL	uc003uai.3	Q9GZY6	OTTHUMG00000130151	ENST00000460943.1:c.372C>T	7.37:g.73636006C>T			73273942	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000460943.1	37	CCDS5566.2																																																																																				0.587	LAT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277062.1			T	73636006	C	T	73636006	2	4	61	1	0	0	0	0	0	0	0	1	8667	912	32	3		3	LAT2	7	73636006	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	537904	73636006	85502657	5299	13284										
HIP1	3092	broad.mit.edu	37	chr7	75168733	75168733	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttctgcaattcattttCtagctctagcaccctaacct	3	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:75168733C>A	ENST00000336926.6	-	30	2997	c.2971G>T	c.(2971-2973)Gaa>Taa	p.E991*	HIP1_ENST00000434438.2_Nonsense_Mutation_p.E940*	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	991	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)	p.E993*(1)		breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AATTCATTTTCTAGCTCTAGC	0.418			T	PDGFRB	CMML																																		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	1	Substitution - Nonsense(1)	large_intestine(1)	7											208	208	208					7																	75168733		2203	4300	6503	75006669	SO:0001587	stop_gained	3092			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2971G>T	7.37:g.75168733C>A	ENSP00000336747:p.Glu991*		75006669	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Nonsense_Mutation	SNP	ENST00000336926.6	37	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	C	41	8.815001	0.98964	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-23.8834	17.8985	0.88896	0.0:1.0:0.0:0.0	.	.	.	.	X	991;940	.	ENSP00000336747:E991X	E	-	1	0	HIP1	75006669	1.000000	0.71417	0.981000	0.43875	0.996000	0.88848	7.488000	0.81441	2.652000	0.90054	0.655000	0.94253	GAA		0.418	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75168733	C	A	75168733	4	1	61	1	0	0	0	0	0	1	0	0	7135	922	32	2	150	2	HIP1	7	75168733	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1532727	75168733	83969930	5300	13285										
HIP1	3092	broad.mit.edu	37	chr7	75211410	75211410	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagttgttcacgtcactttCtccagcctcgtccagctggc	8	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:75211410C>A	ENST00000336926.6	-	6	549	c.523G>T	c.(523-525)Gaa>Taa	p.E175*	RN7SL642P_ENST00000581382.1_RNA|HIP1_ENST00000434438.2_Nonsense_Mutation_p.E175*	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	175					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)	p.E175*(1)		breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						ACGTCACTTTCTCCAGCCTCG	0.562			T	PDGFRB	CMML																																		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	1	Substitution - Nonsense(1)	large_intestine(1)	7											91	68	76					7																	75211410		2203	4300	6503	75049346	SO:0001587	stop_gained	3092			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.523G>T	7.37:g.75211410C>A	ENSP00000336747:p.Glu175*		75049346	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Nonsense_Mutation	SNP	ENST00000336926.6	37	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776885	0.90195	.	.	ENSG00000127946	ENST00000336926;ENST00000434438;ENST00000420909	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-27.3923	18.1538	0.89686	0.0:1.0:0.0:0.0	.	.	.	.	X	175;175;146	.	ENSP00000336747:E175X	E	-	1	0	HIP1	75049346	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	7.459000	0.80802	2.530000	0.85305	0.561000	0.74099	GAA		0.562	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75211410	C	A	75211410	4	1	61	1	0	0	0	0	0	1	0	0	7135	922	32	2	2694	2	HIP1	7	75211410	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42677	75211410	83927253	5301	13286										
STYXL1	51657	broad.mit.edu	37	chr7	75659820	75659820	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtaaagctctgttggttCacataaaagcaaaccaggca	9	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:75659820C>A	ENST00000248600.1	-	2	364	c.22G>T	c.(22-24)Gaa>Taa	p.E8*	STYXL1_ENST00000360591.3_Nonsense_Mutation_p.E8*|STYXL1_ENST00000340062.5_Nonsense_Mutation_p.E8*|STYXL1_ENST00000359697.3_Nonsense_Mutation_p.E8*|STYXL1_ENST00000451157.1_Nonsense_Mutation_p.E8*|STYXL1_ENST00000431581.1_Nonsense_Mutation_p.E8*|STYXL1_ENST00000460184.2_5'UTR	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	8					intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E8*(1)		endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						TCTGTTGGTTCACATAAAAGC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											109	94	99					7																	75659820		2203	4300	6503	75497756	SO:0001587	stop_gained	51657			AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.22G>T	7.37:g.75659820C>A	ENSP00000248600:p.Glu8*		75497756	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Nonsense_Mutation	SNP	ENST00000248600.1	37	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	C	37	6.197748	0.97367	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000340062;ENST00000404050;ENST00000360591;ENST00000431581;ENST00000451157	.	.	.	5.62	5.62	0.85841	.	0.188792	0.46145	D	0.000312	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-27.2304	10.5614	0.45148	0.0:0.9123:0.0:0.0877	.	.	.	.	X	8	.	ENSP00000248600:E8X	E	-	1	0	STYXL1	75497756	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	3.442000	0.52900	2.652000	0.90054	0.650000	0.86243	GAA		0.373	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086		A	75659820	C	A	75659820	4	1	61	1	0	0	0	0	0	1	0	0	15400	835	29	2	951	2	STYXL1	7	75659820	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	448410	75659820	83478843	5302	13287										
MDH2	4191	broad.mit.edu	37	chr7	75689759	75689759	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtacaaccccaacaaaatCttcggcgtgacgaccctgga	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:75689759C>A	ENST00000315758.5	+	5	592	c.498C>A	c.(496-498)atC>atA	p.I166I	MDH2_ENST00000432020.2_Intron|MDH2_ENST00000443006.1_Silent_p.I59I	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	166					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)	p.I166I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CCAACAAAATCTTCGGCGTGA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	7											151	123	132					7																	75689759		2203	4300	6503	75527695	SO:0001819	synonymous_variant	4191				CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.498C>A	7.37:g.75689759C>A			75527695	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	37	CCDS5581.1																																																																																				0.517	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1			A	75689759	C	A	75689759	2	1	61	1	0	0	0	0	0	0	0	1	9440	903	32	2		2	MDH2	7	75689759	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29939	75689759	83448904	5303	13288										
SRRM3	222183	broad.mit.edu	37	chr7	75894123	75894123	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaaaagagaagaacaaaGagaagaagaggtaagcgccc	12	5	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:75894123G>T	ENST00000326382.8	+	9	922	c.715G>T	c.(715-717)Gag>Tag	p.E239*	SRRM3_ENST00000388802.4_Nonsense_Mutation_p.E239*	NM_001110199.1	NP_001103669.1	A6NNA2	SRRM3_HUMAN	serine/arginine repetitive matrix 3	239	Arg-rich.|Lys-rich.|Ser-rich.							p.E239*(1)		NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)	8						GAAGAACAAAGAgaagaagag	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											116	117	117					7																	75894123		1568	3582	5150	75732059	SO:0001587	stop_gained	222183			AK092590		7q11.23	2014-02-12			ENSG00000177679	ENSG00000177679			26729	protein-coding gene	gene with protein product							Standard	NM_001291831		Approved	FLJ37078	uc010ldi.2	A6NNA2	OTTHUMG00000130489	ENST00000326382.8:c.715G>T	7.37:g.75894123G>T	ENSP00000325298:p.Glu239*		75732059	A6ND75	Nonsense_Mutation	SNP	ENST00000326382.8	37		.	.	.	.	.	.	.	.	.	.	G	38	7.122563	0.98077	.	.	ENSG00000177679	ENST00000388802;ENST00000326382	.	.	.	4.23	4.23	0.50019	.	0.416092	0.19940	N	0.102675	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-20.941	13.8229	0.63333	0.0:0.0:1.0:0.0	.	.	.	.	X	239	.	ENSP00000325298:E239X	E	+	1	0	SRRM3	75732059	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.220000	0.51207	2.361000	0.80049	0.555000	0.69702	GAG		0.552	SRRM3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000252889.2	NM_001110199		T	75894123	G	T	75894123	4	4	61	1	0	0	0	0	0	1	0	0	15209	943	33	2	745	2	SRRM3	7	75894123	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	204364	75894123	83244540	5304	13289										
FGL2	10875	broad.mit.edu	37	chr7	76826265	76826265	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttcttttgcctattgcGtagtagtcagagcaatcttt	8	9	3	1	rs566096585		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:76826265G>A	ENST00000248598.5	-	2	683	c.651C>T	c.(649-651)taC>taT	p.Y217Y	RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	217	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)		p.Y217Y(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TGCCTATTGCGTAGTAGTCAG	0.398													G|||	1	0.000199681	0	0	5008	,	,		21238	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											72	69	70					7																	76826265		2201	4289	6490	76664201	SO:0001819	synonymous_variant	10875			Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.651C>T	7.37:g.76826265G>A			76664201		Silent	SNP	ENST00000248598.5	37	CCDS5591.1																																																																																				0.398	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		A	76826265	G	A	76826265	2	1	61	1	0	0	0	0	0	0	0	1	5892	1140	40	1		1	FGL2	7	76826265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	932142	76826265	82312398	5305	13290										
CCDC146	57639	broad.mit.edu	37	chr7	76911946	76911946	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaatatccaagagaagatGaaactaaatggagaaattga	8	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:76911946G>T	ENST00000285871.4	+	15	2119	c.1992G>T	c.(1990-1992)atG>atT	p.M664I	CCDC146_ENST00000431197.1_Missense_Mutation_p.M378I|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	664								p.M664I(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AAGAGAAGATGAAACTAAATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	39	39					7																	76911946		2203	4300	6503	76749882	SO:0001583	missense	57639			BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1992G>T	7.37:g.76911946G>T	ENSP00000285871:p.Met664Ile		76749882	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860080	0.32884	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.38401	1.14;1.14	5.24	4.35	0.52113	.	0.450082	0.28828	N	0.014002	T	0.21509	0.0518	N	0.16602	0.42	0.34831	D	0.739715	B;B	0.10296	0.001;0.003	B;B	0.09377	0.004;0.003	T	0.17198	-1.0377	10	0.33141	T	0.24	-5.9984	9.2009	0.37258	0.0754:0.0:0.7806:0.144	.	378;664	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	I	664;378	ENSP00000285871:M664I;ENSP00000413885:M378I	ENSP00000285871:M664I	M	+	3	0	AC007000.1	76749882	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.270000	0.51600	1.307000	0.44944	0.655000	0.94253	ATG		0.358	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		T	76911946	G	T	76911946	3	4	61	1	0	0	0	0	1	0	0	0	2786	1290	45	2	2046	2	CCDC146	7	76911946	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85681	76911946	82226717	5306	13291										
CCDC146	57639	broad.mit.edu	37	chr7	76916810	76916810	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctggagaaggatttcatCtatgagcaggtctccaggct	12	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:76916810C>A	ENST00000285871.4	+	17	2458	c.2331C>A	c.(2329-2331)atC>atA	p.I777I	CCDC146_ENST00000431197.1_Silent_p.I491I|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	777								p.I777I(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AGGATTTCATCTATGAGCAGG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	7											81	80	80					7																	76916810		2203	4300	6503	76754746	SO:0001819	synonymous_variant	57639			BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.2331C>A	7.37:g.76916810C>A			76754746	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																				0.473	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		A	76916810	C	A	76916810	2	1	61	1	0	0	0	0	0	0	0	1	2786	903	32	2		2	CCDC146	7	76916810	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4864	76916810	82221853	5307	13292										
PTPN12	5782	broad.mit.edu	37	chr7	77256279	77256279	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaattgaacagatagataAaaaattggaacgaaatttaa	6	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77256279A>C	ENST00000248594.6	+	13	1555	c.1283A>C	c.(1282-1284)aAa>aCa	p.K428T	PTPN12_ENST00000435495.2_Missense_Mutation_p.K298T|PTPN12_ENST00000415482.2_Missense_Mutation_p.K309T	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	428	Interaction with TGFB1I1. {ECO:0000250}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)	p.K428T(1)		breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CAGATAGATAAAAAATTGGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											38	41	40					7																	77256279		2199	4299	6498	77094215	SO:0001583	missense	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1283A>C	7.37:g.77256279A>C	ENSP00000248594:p.Lys428Thr		77094215	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784099	0.70222	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.08807	3.63;3.05;3.05	6.17	6.17	0.99709	.	0.291855	0.39687	N	0.001293	T	0.22205	0.0535	M	0.72353	2.195	0.46336	D	0.998992	P	0.51933	0.949	P	0.52267	0.694	T	0.00138	-1.2002	10	0.72032	D	0.01	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	428	Q05209	PTN12_HUMAN	T	428;309;309;298	ENSP00000248594:K428T;ENSP00000392429:K309T;ENSP00000397991:K298T	ENSP00000248594:K428T	K	+	2	0	PTPN12	77094215	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.117000	0.57877	2.371000	0.80710	0.533000	0.62120	AAA		0.358	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			C	77256279	A	C	77256279	3	2	61	1	0	0	0	0	1	0	0	0	12816	14	1	4	1333	4	PTPN12	7	77256279	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	339469	77256279	81882384	5308	13293										
PTPN12	5782	broad.mit.edu	37	chr7	77268548	77268548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgtaggttttggtaatcGatgtggaaaacccaaaggac	11	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77268548G>A	ENST00000248594.6	+	18	2566	c.2294G>A	c.(2293-2295)cGa>cAa	p.R765Q	PTPN12_ENST00000435495.2_Missense_Mutation_p.R635Q|PTPN12_ENST00000415482.2_Missense_Mutation_p.R646Q	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	765					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)	p.R765Q(2)		breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TTTGGTAATCGATGTGGAAAA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	7											141	138	139					7																	77268548		2203	4300	6503	77106484	SO:0001583	missense	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.2294G>A	7.37:g.77268548G>A	ENSP00000248594:p.Arg765Gln		77106484	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850011	0.71603	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000435495	T;T;T	0.23950	2.44;1.89;1.88	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	M	0.73962	2.25	0.40187	D	0.977363	D	0.89917	1.0	D	0.79108	0.992	T	0.54866	-0.8229	10	0.87932	D	0	.	14.0096	0.64488	0.0:0.0:0.8487:0.1513	.	765	Q05209	PTN12_HUMAN	Q	765;646;635	ENSP00000248594:R765Q;ENSP00000392429:R646Q;ENSP00000397991:R635Q	ENSP00000248594:R765Q	R	+	2	0	PTPN12	77106484	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.548000	0.67255	2.590000	0.87494	0.579000	0.79373	CGA		0.388	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			A	77268548	G	A	77268548	3	1	61	1	0	0	0	0	1	0	0	0	12816	1058	37	1	2364	1	PTPN12	7	77268548	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12269	77268548	81870115	5309	13294										
RSBN1L	222194	broad.mit.edu	37	chr7	77365830	77365830	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagaatggagaagtaaaGattttgctgaaaagtaagtt	11	1	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77365830G>T	ENST00000334955.8	+	2	717	c.690G>T	c.(688-690)aaG>aaT	p.K230N	RSBN1L_ENST00000445288.1_5'UTR	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	230	Lys-rich.					nucleus (GO:0005634)		p.K230N(1)		central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						gagaagtaaagaTTTTGCTGA	0.249																																																1	Substitution - Missense(1)	large_intestine(1)	7											87	92	91					7																	77365830		1793	4061	5854	77203766	SO:0001583	missense	222194			AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.690G>T	7.37:g.77365830G>T	ENSP00000334040:p.Lys230Asn		77203766	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.528642	0.44969	.	.	ENSG00000187257	ENST00000334955	T	0.08807	3.05	3.93	3.05	0.35203	.	0.085303	0.53938	D	0.000053	T	0.09069	0.0224	L	0.44542	1.39	0.80722	D	1	P	0.41265	0.744	B	0.44044	0.439	T	0.26360	-1.0105	10	0.29301	T	0.29	-3.8103	7.7731	0.29021	0.1135:0.0:0.8865:0.0	.	230	Q6PCB5	RSBNL_HUMAN	N	230	ENSP00000334040:K230N	ENSP00000334040:K230N	K	+	3	2	RSBN1L	77203766	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	0.971000	0.29396	1.232000	0.43678	-0.150000	0.13652	AAG		0.249	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		T	77365830	G	T	77365830	3	4	61	1	0	0	0	0	1	0	0	0	13734	933	33	2	696	2	RSBN1L	7	77365830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97282	77365830	81772833	5310	13295										
RSBN1L	222194	broad.mit.edu	37	chr7	77379339	77379339	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatggagatattgggaaaGaaagatatagagacaacgac	11	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77379339G>T	ENST00000334955.8	+	3	1329	c.1302G>T	c.(1300-1302)aaG>aaT	p.K434N	RSBN1L_ENST00000445288.1_Missense_Mutation_p.K164N	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	434						nucleus (GO:0005634)		p.K434N(1)		central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TATTGGGAAAGAAAGATATAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	68	71					7																	77379339		1799	4064	5863	77217275	SO:0001583	missense	222194			AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.1302G>T	7.37:g.77379339G>T	ENSP00000334040:p.Lys434Asn		77217275	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522398	0.64747	.	.	ENSG00000187257	ENST00000334955;ENST00000445288	.	.	.	5.95	4.14	0.48551	.	0.000000	0.85682	D	0.000000	T	0.74527	0.3728	L	0.57536	1.79	0.54753	D	0.999988	D	0.89917	1.0	D	0.87578	0.998	T	0.77289	-0.2643	9	0.72032	D	0.01	-19.3473	13.0844	0.59132	0.1316:0.0:0.8684:0.0	.	434	Q6PCB5	RSBNL_HUMAN	N	434;164	.	ENSP00000334040:K434N	K	+	3	2	RSBN1L	77217275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.690000	0.74567	1.532000	0.49169	0.655000	0.94253	AAG		0.299	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		T	77379339	G	T	77379339	3	4	61	1	0	0	0	0	1	0	0	0	13734	933	33	2	1312	2	RSBN1L	7	77379339	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13509	77379339	81759324	5311	13296										
TMEM60	85025	broad.mit.edu	37	chr7	77423409	77423409	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgttccagtttagcacaGagtgcgaggcagaaggctaa	12	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77423409G>T	ENST00000257663.3	-	2	658	c.282C>A	c.(280-282)ctC>ctA	p.L94L		NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	94						integral component of membrane (GO:0016021)		p.L94L(1)		endometrium(1)|large_intestine(1)|lung(2)	4						GTTTAGCACAGAGTGCGAGGC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	7											147	141	143					7																	77423409		2203	4300	6503	77261345	SO:0001819	synonymous_variant	85025			AF260336	CCDS5593.1	7q11.23	2005-07-25	2005-07-25	2005-07-25	ENSG00000135211	ENSG00000135211			21754	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 35"	C7orf35			Standard	NM_032936		Approved	DC32	uc003ugn.3	Q9H2L4	OTTHUMG00000130689	ENST00000257663.3:c.282C>A	7.37:g.77423409G>T			77261345	A4D1C3|Q86UM0	Silent	SNP	ENST00000257663.3	37	CCDS5593.1																																																																																				0.418	TMEM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253185.2	NM_032936		T	77423409	G	T	77423409	2	4	61	1	0	0	0	0	0	0	0	1	16226	929	33	2		2	TMEM60	7	77423409	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44070	77423409	81715254	5312	13297										
PHTF2	57157	broad.mit.edu	37	chr7	77558637	77558637	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatatagagatgacccttTtcatcaggttggtttatggt	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77558637T>G	ENST00000248550.7	+	11	1407	c.1331T>G	c.(1330-1332)tTt>tGt	p.F444C	PHTF2_ENST00000422959.2_Missense_Mutation_p.F410C|PHTF2_ENST00000307305.8_Missense_Mutation_p.F406C|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000416283.2_Missense_Mutation_p.F410C|PHTF2_ENST00000275575.7_Missense_Mutation_p.F406C|PHTF2_ENST00000424760.1_Missense_Mutation_p.F406C			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F444C(1)|p.F410C(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						GATGACCCTTTTCATCAGGTT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											131	125	127					7																	77558637		1849	4102	5951	77396573	SO:0001583	missense	57157			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1331T>G	7.37:g.77558637T>G	ENSP00000248550:p.Phe444Cys		77396573	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	T	21.7	4.193909	0.78902	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.77205	0.4096	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0;1.0;1.0	D;P;D;D;D;D;D	0.87578	0.998;0.891;0.976;0.998;0.997;0.982;0.987	T	0.78922	-0.2013	9	0.62326	D	0.03	-20.3122	15.9998	0.80285	0.0:0.0:0.0:1.0	.	248;406;269;410;444;406;406	Q8WVD6;Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;.;PHTF2_HUMAN;.;.	C	410;410;406;406;406;410;444	.	ENSP00000248550:F444C	F	+	2	0	PHTF2	77396573	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.481000	0.81124	2.189000	0.69895	0.533000	0.62120	TTT		0.358	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77558637	T	G	77558637	3	3	61	1	0	0	0	0	1	0	0	0	11894	1841	64	4	1321	4	PHTF2	7	77558637	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	135228	77558637	81580026	5313	13298										
PHTF2	57157	broad.mit.edu	37	chr7	77569515	77569515	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcatttggttctaatgaaGatgtcatagttctttctatg	8	5	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77569515G>T	ENST00000248550.7	+	13	1712	c.1636G>T	c.(1636-1638)Gat>Tat	p.D546Y	PHTF2_ENST00000422959.2_Missense_Mutation_p.D512Y|PHTF2_ENST00000307305.8_Missense_Mutation_p.D508Y|PHTF2_ENST00000416283.2_Missense_Mutation_p.D512Y|PHTF2_ENST00000275575.7_Missense_Mutation_p.D508Y|PHTF2_ENST00000424760.1_Missense_Mutation_p.D508Y			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	546					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D546Y(1)|p.D512Y(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TTCTAATGAAGATGTCATAGT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											143	132	135					7																	77569515		1850	4100	5950	77407451	SO:0001583	missense	57157			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1636G>T	7.37:g.77569515G>T	ENSP00000248550:p.Asp546Tyr		77407451	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	G	19.78	3.891845	0.72524	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.74943	0.3783	L	0.43152	1.355	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.999;1.0;0.994;0.989;0.995	D;D;D;P;P;P	0.91635	0.964;0.939;0.999;0.852;0.788;0.862	T	0.73411	-0.3991	9	0.48119	T	0.1	-17.3746	19.9854	0.97342	0.0:0.0:1.0:0.0	.	307;508;512;546;508;508	Q8WVD6;Q8N3S3-4;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;PHTF2_HUMAN;.;.	Y	512;512;508;508;508;512;546	.	ENSP00000248550:D546Y	D	+	1	0	PHTF2	77407451	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.802000	0.85969	2.722000	0.93159	0.557000	0.71058	GAT		0.358	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		T	77569515	G	T	77569515	3	4	61	1	0	0	0	0	1	0	0	0	11894	942	33	2	1634	2	PHTF2	7	77569515	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10878	77569515	81569148	5314	13299										
MAGI2	9863	broad.mit.edu	37	chr7	77885532	77885532	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccccagatgaagccataGacacattgtcatcatggacg	10	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77885532G>T	ENST00000354212.4	-	10	2028	c.1775C>A	c.(1774-1776)tCt>tAt	p.S592Y	MAGI2_ENST00000535697.1_Missense_Mutation_p.S429Y|MAGI2_ENST00000522391.1_Missense_Mutation_p.S592Y|MAGI2_ENST00000536571.1_Missense_Mutation_p.S424Y|MAGI2_ENST00000419488.1_Missense_Mutation_p.S592Y	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	592					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.S592Y(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGAAGCCATAGACACATTGTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	81	84					7																	77885532		2203	4300	6503	77723468	SO:0001583	missense	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1775C>A	7.37:g.77885532G>T	ENSP00000346151:p.Ser592Tyr		77723468	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911439	0.72983	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.85	5.85	0.93711	PDZ/DHR/GLGF (1);	0.000000	0.35677	U	0.003059	T	0.71467	0.3343	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.993;0.998;0.998;0.997;0.998	D;D;D;D;D;D	0.78314	0.987;0.964;0.991;0.991;0.935;0.991	T	0.73560	-0.3944	10	0.87932	D	0	.	19.1657	0.93557	0.0:0.0:1.0:0.0	.	429;424;592;592;592;592	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	Y	592;592;592;592;424;429	ENSP00000405766:S592Y;ENSP00000346151:S592Y;ENSP00000428389:S592Y;ENSP00000441584:S424Y;ENSP00000441603:S429Y	ENSP00000346151:S592Y	S	-	2	0	MAGI2	77723468	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.863000	0.87023	2.771000	0.95319	0.561000	0.74099	TCT		0.532	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		T	77885532	G	T	77885532	3	4	61	1	0	0	0	0	1	0	0	0	9221	942	33	2	2644	2	MAGI2	7	77885532	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	316017	77885532	81253131	5315	13300										
MAGI2	9863	broad.mit.edu	37	chr7	77998491	77998491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaacataataagtgccaTaaatgggatcatcgattttt	6	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:77998491T>C	ENST00000354212.4	-	7	1338	c.1085A>G	c.(1084-1086)tAt>tGt	p.Y362C	MAGI2_ENST00000535697.1_Missense_Mutation_p.Y199C|MAGI2_ENST00000522391.1_Missense_Mutation_p.Y362C|MAGI2_ENST00000536571.1_Missense_Mutation_p.Y194C|MAGI2_ENST00000419488.1_Missense_Mutation_p.Y362C	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	362	Interaction with DDN.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.Y362C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				ATAAGTGCCATAAATGGGATC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	7											67	68	68					7																	77998491		2202	4300	6502	77836427	SO:0001583	missense	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1085A>G	7.37:g.77998491T>C	ENSP00000346151:p.Tyr362Cys		77836427	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630029	0.67015	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	5.95	5.95	0.96441	WW/Rsp5/WWP (6);	0.000000	0.33650	U	0.004697	D	0.92648	0.7664	M	0.90369	3.11	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.982;0.998;0.999	D	0.93945	0.7227	10	0.87932	D	0	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	199;194;362;362	F5GWH1;F5GWK7;Q86UL8-2;Q86UL8	.;.;.;MAGI2_HUMAN	C	362;362;362;362;194;199	ENSP00000405766:Y362C;ENSP00000346151:Y362C;ENSP00000428389:Y362C;ENSP00000441584:Y194C;ENSP00000441603:Y199C	ENSP00000346151:Y362C	Y	-	2	0	MAGI2	77836427	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.258000	0.78371	2.279000	0.76181	0.533000	0.62120	TAT		0.279	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	77998491	T	C	77998491	3	2	61	1	0	0	0	0	1	0	0	0	9221	1406	49	4	3346	4	MAGI2	7	77998491	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	112959	77998491	81140172	5316	13301										
MAGI2	9863	broad.mit.edu	37	chr7	79082603	79082603	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctcatggactttgctagTccagtggcttttctttttca	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:79082603T>G	ENST00000354212.4	-	1	287	c.34A>C	c.(34-36)Act>Cct	p.T12P	MAGI2_ENST00000522391.1_Missense_Mutation_p.T12P|MAGI2-AS3_ENST00000414797.1_RNA|MAGI2-AS3_ENST00000424477.1_RNA|MAGI2-AS3_ENST00000429408.1_RNA|MAGI2-AS3_ENST00000448195.1_RNA|MAGI2_ENST00000419488.1_Missense_Mutation_p.T12P|MAGI2-AS3_ENST00000446159.1_RNA|MAGI2-AS3_ENST00000426835.1_RNA|MAGI2-AS3_ENST00000422093.1_RNA|MAGI2-AS3_ENST00000451809.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	12					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.T12P(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				ACTTTGCTAGTCCAGTGGCTT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											86	98	94					7																	79082603		2203	4300	6503	78920539	SO:0001583	missense	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.34A>C	7.37:g.79082603T>G	ENSP00000346151:p.Thr12Pro		78920539	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.043893	0.75732	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11495	2.88;2.88;2.77	5.17	5.17	0.71159	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.30135	0.0755	M	0.72894	2.215	0.80722	D	1	D;D	0.71674	0.998;0.981	D;P	0.65010	0.931;0.69	T	0.02307	-1.1179	9	0.59425	D	0.04	.	14.1738	0.65527	0.0:0.0:0.0:1.0	.	12;12	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	P	12	ENSP00000405766:T12P;ENSP00000346151:T12P;ENSP00000428389:T12P	ENSP00000346151:T12P	T	-	1	0	MAGI2	78920539	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.860000	0.86993	1.943000	0.56356	0.402000	0.26972	ACT		0.582	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	79082603	T	G	79082603	3	3	61	1	0	0	0	0	1	0	0	0	9221	1667	58	4	4421	4	MAGI2	7	79082603	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1084112	79082603	80056060	5317	13302										
GNAI1	2770	broad.mit.edu	37	chr7	79840352	79840352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcttcgaaggagtgacgGcgatcatcttctgtgtagca	12	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:79840352G>A	ENST00000351004.3	+	6	1031	c.658G>A	c.(658-660)Gcg>Acg	p.A220T	GNAI1_ENST00000457358.2_Missense_Mutation_p.A168T	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	220					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.A220T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AGGAGTGACGGCGATCATCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	7											166	136	146					7																	79840352		2203	4300	6503	79678288	SO:0001583	missense	2770			AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.658G>A	7.37:g.79840352G>A	ENSP00000343027:p.Ala220Thr		79678288	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	37	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	G	31	5.061085	0.93846	.	.	ENSG00000127955	ENST00000351004;ENST00000457358	D;D	0.91407	-2.84;-2.84	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.95494	0.8536	M	0.82433	2.59	0.80722	D	1	P	0.50272	0.933	D	0.63033	0.91	D	0.94758	0.7933	9	.	.	.	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	220	P63096	GNAI1_HUMAN	T	220;168	ENSP00000343027:A220T;ENSP00000410572:A168T	.	A	+	1	0	GNAI1	79678288	1.000000	0.71417	0.995000	0.50966	0.914000	0.54420	7.820000	0.86633	2.685000	0.91497	0.650000	0.86243	GCG		0.428	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		A	79840352	G	A	79840352	3	1	61	1	0	0	0	0	1	0	0	0	6524	1203	42	3	680	3	GNAI1	7	79840352	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	757749	79840352	79298311	5318	13303										
GNAT3	346562	broad.mit.edu	37	chr7	80141148	80141148	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtagcagctttacggttCttgcatctcgctcagcatcc	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:80141148C>A	ENST00000398291.3	-	1	188	c.95G>T	c.(94-96)aGa>aTa	p.R32I	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	32					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)	p.R32I(2)		endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						CTTTACGGTTCTTGCATCTCG	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	7											91	92	92					7																	80141148		2022	4183	6205	79979084	SO:0001583	missense	346562				CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.95G>T	7.37:g.80141148C>A	ENSP00000381339:p.Arg32Ile		79979084	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	37	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497409	0.64186	.	.	ENSG00000214415	ENST00000398291	D	0.89681	-2.55	5.17	5.17	0.71159	.	0.059984	0.64402	U	0.000002	D	0.94771	0.8312	M	0.92970	3.365	0.53005	D	0.999964	D	0.55385	0.971	P	0.62740	0.906	D	0.95280	0.8385	9	.	.	.	.	11.3325	0.49484	0.0:0.9143:0.0:0.0857	.	32	A8MTJ3	GNAT3_HUMAN	I	32	ENSP00000381339:R32I	.	R	-	2	0	GNAT3	79979084	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	3.235000	0.51328	2.570000	0.86706	0.655000	0.94253	AGA		0.373	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		A	80141148	C	A	80141148	3	1	61	1	0	0	0	0	1	0	0	0	6533	913	32	2	999	2	GNAT3	7	80141148	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	300796	80141148	78997515	5319	13304										
SEMA3C	10512	broad.mit.edu	37	chr7	80394557	80394557	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactttttgcacagtaccccGatctaaattaaaaaaagaag	5	9	1	1	rs147463830		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:80394557G>A	ENST00000265361.3	-	13	1918	c.1357C>T	c.(1357-1359)Cgg>Tgg	p.R453W	SEMA3C_ENST00000544525.1_Missense_Mutation_p.R471W|SEMA3C_ENST00000419255.2_Missense_Mutation_p.R453W	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	453	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R453W(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						ACAGTACCCCGATCTAAATTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	69	70	70		1357	5.7	1	7	dbSNP_134	70	0,8600		0,0,4300	no	missense	SEMA3C	NM_006379.3	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	453/752	80394557	1,13005	2203	4300	6503	80232493	SO:0001583	missense	10512			AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1357C>T	7.37:g.80394557G>A	ENSP00000265361:p.Arg453Trp		80232493	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.638796	0.67130	2.27E-4	0.0	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.11712	2.75;2.75;2.75	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.226724	0.44902	D	0.000418	T	0.25044	0.0608	L	0.50333	1.59	0.80722	D	1	D;D	0.64830	0.992;0.994	P;P	0.61722	0.828;0.893	T	0.00035	-1.2262	10	0.66056	D	0.02	.	14.8863	0.70572	0.0:0.0:0.8565:0.1434	.	471;453	F5H1Z7;Q99985	.;SEM3C_HUMAN	W	453;453;471	ENSP00000265361:R453W;ENSP00000411193:R453W;ENSP00000445649:R471W	ENSP00000265361:R453W	R	-	1	2	SEMA3C	80232493	0.999000	0.42202	1.000000	0.80357	0.542000	0.35054	3.186000	0.50942	2.830000	0.97506	0.585000	0.79938	CGG		0.358	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		A	80394557	G	A	80394557	3	1	61	1	0	0	0	0	1	0	0	0	14063	1057	37	1	922	1	SEMA3C	7	80394557	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253409	80394557	78744106	5320	13305										
HGF	3082	broad.mit.edu	37	chr7	81336625	81336625	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagaagggaaacactgtcGtgcagtaagaacccaactct	10	11	1	2	rs527951814		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:81336625G>A	ENST00000222390.5	-	14	1823	c.1597C>T	c.(1597-1599)Cga>Tga	p.R533*	HGF_ENST00000457544.2_Nonsense_Mutation_p.R528*	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	533	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)	p.R533*(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						AAACACTGTCGTGCAGTAAGA	0.353													G|||	1	0.000199681	0	0.0014	5008	,	,		17341	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	7											97	94	95					7																	81336625		2202	4300	6502	81174561	SO:0001587	stop_gained	3082				CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1597C>T	7.37:g.81336625G>A	ENSP00000222390:p.Arg533*		81174561	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Nonsense_Mutation	SNP	ENST00000222390.5	37	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	G	37	6.319659	0.97471	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	.	.	.	5.57	1.72	0.24424	.	0.089431	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	13.3645	0.60676	0.0:0.0:0.3927:0.6073	.	.	.	.	X	533;528	.	ENSP00000222390:R533X	R	-	1	2	HGF	81174561	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	2.367000	0.44213	0.106000	0.17784	-0.485000	0.04761	CGA		0.353	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		A	81336625	G	A	81336625	4	1	61	1	0	0	0	0	0	1	0	0	7106	1153	40	1	609	1	HGF	7	81336625	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	942068	81336625	77802038	5321	13306										
HGF	3082	broad.mit.edu	37	chr7	81346553	81346553	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaactgtacttacaacgaGaaatagggcaataatcccaa	6	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:81346553G>T	ENST00000222390.5	-	11	1626	c.1400C>A	c.(1399-1401)tCt>tAt	p.S467Y	HGF_ENST00000457544.2_Missense_Mutation_p.S462Y	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	467	Kringle 4. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)	p.S467Y(2)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CTTACAACGAGAAATAGGGCA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	7											172	141	152					7																	81346553		2203	4300	6503	81184489	SO:0001583	missense	3082				CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1400C>A	7.37:g.81346553G>T	ENSP00000222390:p.Ser467Tyr		81184489	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	37	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960355	0.53400	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	T;T	0.63417	-0.04;-0.04	6.02	5.14	0.70334	Kringle (4);Kringle-like fold (1);	0.218049	0.48767	D	0.000168	T	0.72170	0.3427	M	0.83483	2.645	0.80722	D	1	B;B	0.28933	0.191;0.228	B;B	0.39531	0.2;0.302	T	0.74506	-0.3643	10	0.72032	D	0.01	.	15.4479	0.75248	0.0664:0.0:0.9336:0.0	.	462;467	P14210-3;P14210	.;HGF_HUMAN	Y	467;462	ENSP00000222390:S467Y;ENSP00000391238:S462Y	ENSP00000222390:S467Y	S	-	2	0	HGF	81184489	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.353000	0.59411	1.548000	0.49413	0.650000	0.86243	TCT		0.378	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81346553	G	T	81346553	3	4	61	1	0	0	0	0	1	0	0	0	7106	942	33	2	818	2	HGF	7	81346553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9928	81346553	77792110	5322	13307										
HGF	3082	broad.mit.edu	37	chr7	81372780	81372780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attatcatcaaagcccttgtCgggatatctgcaaaccacac	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:81372780C>T	ENST00000222390.5	-	7	980	c.754G>A	c.(754-756)Gac>Aac	p.D252N	HGF_ENST00000457544.2_Missense_Mutation_p.D247N|HGF_ENST00000444829.2_Missense_Mutation_p.D252N|HGF_ENST00000453411.1_Missense_Mutation_p.D247N	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	252	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)	p.D252N(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						AAGCCCTTGTCGGGATATCTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											79	74	76					7																	81372780		2203	4300	6503	81210716	SO:0001583	missense	3082				CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.754G>A	7.37:g.81372780C>T	ENSP00000222390:p.Asp252Asn		81210716	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	37	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.234665	0.58886	.	.	ENSG00000019991	ENST00000222390;ENST00000457544;ENST00000444829;ENST00000453411;ENST00000394769	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.75	5.75	0.90469	Kringle (4);Kringle-like fold (1);	0.087572	0.85682	D	0.000000	T	0.47192	0.1432	N	0.25992	0.78	0.80722	D	1	B;B;B;B	0.23058	0.009;0.079;0.029;0.036	B;B;B;B	0.19946	0.01;0.023;0.016;0.027	T	0.38112	-0.9676	10	0.15952	T	0.53	.	13.1841	0.59672	0.0:0.9273:0.0:0.0727	.	247;252;247;252	P14210-5;P14210-2;P14210-3;P14210	.;.;.;HGF_HUMAN	N	252;247;252;247;252	ENSP00000222390:D252N;ENSP00000391238:D247N;ENSP00000389854:D252N;ENSP00000408270:D247N	ENSP00000222390:D252N	D	-	1	0	HGF	81210716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.439000	0.52878	2.724000	0.93272	0.655000	0.94253	GAC		0.498	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81372780	C	T	81372780	3	4	61	1	0	0	0	0	1	0	0	0	7106	884	31	1	1492	1	HGF	7	81372780	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26227	81372780	77765883	5323	13308										
CACNA2D1	781	broad.mit.edu	37	chr7	81667423	81667423	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcaaaagcaaaactaaaGcccttcttataatctgtaat	4	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:81667423G>T	ENST00000356253.5	-	11	1263	c.1008C>A	c.(1006-1008)ggC>ggA	p.G336G	CACNA2D1_ENST00000356860.3_Silent_p.G336G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	336	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G336G(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CAAAACTaaagcccttcttat	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	7											153	152	152					7																	81667423		2203	4300	6503	81505359	SO:0001819	synonymous_variant	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1008C>A	7.37:g.81667423G>T			81505359	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																					0.328	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				T	81667423	G	T	81667423	2	4	61	1	0	0	0	0	0	0	0	1	2554	958	34	2		2	CACNA2D1	7	81667423	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	294643	81667423	77471240	5324	13309										
PCLO	27445	broad.mit.edu	37	chr7	82389990	82389990	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggacttagactgaatcGaaaagtttcattaaacgaag	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82389990G>A	ENST00000333891.9	-	24	15590	c.15253C>T	c.(15253-15255)Cga>Tga	p.R5085*		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.R5085*(4)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGACTGAATCGAAAAGTTTCA	0.323																																																4	Substitution - Nonsense(4)	large_intestine(4)	7											134	132	132					7																	82389990		1827	4069	5896	82227926	SO:0001587	stop_gained	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.15253C>T	7.37:g.82389990G>A	ENSP00000334319:p.Arg5085*		82227926		Nonsense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	56	26.706062	0.99969	.	.	ENSG00000186472	ENST00000333891	.	.	.	5.25	2.84	0.33178	.	0.000000	0.42821	U	0.000656	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.2602	0.54647	0.0:0.0:0.4373:0.5627	.	.	.	.	X	5085	.	ENSP00000334319:R5085X	R	-	1	2	PCLO	82227926	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	2.265000	0.43311	0.301000	0.22738	-0.485000	0.04761	CGA		0.323	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82389990	G	A	82389990	4	1	61	1	0	0	0	0	0	1	0	0	11614	1066	37	1	183	1	PCLO	7	82389990	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	722567	82389990	76748673	5325	13310										
PCLO	27445	broad.mit.edu	37	chr7	82545358	82545358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcataaggggttggttgcGaatcacttcatagtttgagg	12	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82545358G>A	ENST00000333891.9	-	7	12281	c.11944C>T	c.(11944-11946)Cgc>Tgc	p.R3982C	PCLO_ENST00000423517.2_Missense_Mutation_p.R3982C|PCLO_ENST00000437081.1_Missense_Mutation_p.R702C	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.R3982C(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GGTTGGTTGCGAATCACTTCA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	7											389	368	374					7																	82545358		1926	4131	6057	82383294	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.11944C>T	7.37:g.82545358G>A	ENSP00000334319:p.Arg3982Cys		82383294		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751592	0.49257	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.18016	2.24;2.24	5.85	5.85	0.93711	.	.	.	.	.	T	0.39489	0.1080	M	0.61703	1.905	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.925;0.982;0.982	T	0.06588	-1.0818	9	0.87932	D	0	.	14.9344	0.70941	0.0:0.0:0.857:0.143	.	3913;3982;3982	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	C	3982;3982;702	ENSP00000334319:R3982C;ENSP00000388393:R3982C	ENSP00000334319:R3982C	R	-	1	0	PCLO	82383294	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.725000	0.54970	2.767000	0.95098	0.563000	0.77884	CGC		0.388	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82545358	G	A	82545358	3	1	61	1	0	0	0	0	1	0	0	0	11614	1058	37	1	3577	1	PCLO	7	82545358	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155368	82545358	76593305	5326	13311										
PCLO	27445	broad.mit.edu	37	chr7	82580119	82580119	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaaggtgttgcttcataGactgcagctcctccaacttt	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82580119G>T	ENST00000333891.9	-	6	10122	c.9785C>A	c.(9784-9786)tCt>tAt	p.S3262Y	PCLO_ENST00000423517.2_Missense_Mutation_p.S3262Y|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S3262Y(2)|p.S3193Y(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGCTTCATAGACTGCAGCTC	0.478																																																3	Substitution - Missense(3)	large_intestine(3)	7											122	115	118					7																	82580119		1940	4160	6100	82418055	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9785C>A	7.37:g.82580119G>T	ENSP00000334319:p.Ser3262Tyr		82418055		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	7.957	0.746186	0.15710	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19669	2.13;2.13	5.59	5.59	0.84812	.	.	.	.	.	T	0.46541	0.1398	M	0.63843	1.955	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.999	P;D;D	0.73380	0.862;0.98;0.98	T	0.38866	-0.9641	9	0.87932	D	0	.	19.1751	0.93600	0.0:0.0:1.0:0.0	.	3193;3262;3262	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	Y	3193;3262;3262	ENSP00000334319:S3262Y;ENSP00000388393:S3262Y	ENSP00000334319:S3262Y	S	-	2	0	PCLO	82418055	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.501000	0.66950	2.634000	0.89283	0.563000	0.77884	TCT		0.478	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82580119	G	T	82580119	3	4	61	1	0	0	0	0	1	0	0	0	11614	942	33	2	5740	2	PCLO	7	82580119	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34761	82580119	76558544	5327	13312										
PCLO	27445	broad.mit.edu	37	chr7	82580718	82580718	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcattcttgctgtggaataCtgtggggtactaatcccagc	11	9	2	0	rs560117236		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82580718C>A	ENST00000333891.9	-	6	9523	c.9186G>T	c.(9184-9186)caG>caT	p.Q3062H	PCLO_ENST00000423517.2_Missense_Mutation_p.Q3062H|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.Q3062H(2)|p.Q2993H(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTGTGGAATACTGTGGGGTAC	0.453																																																3	Substitution - Missense(3)	large_intestine(3)	7											103	96	98					7																	82580718		1910	4130	6040	82418654	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9186G>T	7.37:g.82580718C>A	ENSP00000334319:p.Gln3062His		82418654		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	5.154	0.213964	0.09810	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.18016	2.24;2.25	5.37	3.57	0.40892	.	.	.	.	.	T	0.32971	0.0847	M	0.63843	1.955	0.80722	D	1	D;D;D	0.71674	0.976;0.998;0.998	P;D;D	0.64595	0.735;0.927;0.927	T	0.02743	-1.1116	9	0.87932	D	0	.	8.6359	0.33948	0.0:0.709:0.0:0.291	.	2993;3062;3062	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	H	2993;3062;3062	ENSP00000334319:Q3062H;ENSP00000388393:Q3062H	ENSP00000334319:Q3062H	Q	-	3	2	PCLO	82418654	0.146000	0.22672	1.000000	0.80357	0.996000	0.88848	-0.438000	0.06905	0.653000	0.30826	0.563000	0.77884	CAG		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82580718	C	A	82580718	3	1	61	1	0	0	0	0	1	0	0	0	11614	564	20	2	6339	2	PCLO	7	82580718	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	599	82580718	76557945	5328	13313										
PCLO	27445	broad.mit.edu	37	chr7	82581542	82581542	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagactcatccattgttacGactgttctgtgagacttggt	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82581542G>A	ENST00000333891.9	-	5	9064	c.8727C>T	c.(8725-8727)gtC>gtT	p.V2909V	PCLO_ENST00000423517.2_Silent_p.V2909V|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.V2909V(2)|p.V2840V(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCATTGTTACGACTGTTCTGT	0.448																																																3	Substitution - coding silent(3)	large_intestine(3)	7											207	196	199					7																	82581542		1965	4152	6117	82419478	SO:0001819	synonymous_variant	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8727C>T	7.37:g.82581542G>A			82419478		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82581542	G	A	82581542	2	1	61	1	0	0	0	0	0	0	0	1	11614	1045	37	1		1	PCLO	7	82581542	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	824	82581542	76557121	5329	13314										
PCLO	27445	broad.mit.edu	37	chr7	82582694	82582694	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggtgtatatctgttggTttttgtgtagttgttggaag	15	1	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82582694T>C	ENST00000333891.9	-	5	7912	c.7575A>G	c.(7573-7575)aaA>aaG	p.K2525K	PCLO_ENST00000423517.2_Silent_p.K2525K|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.K2525K(2)|p.K2456K(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TATCTGTTGGTTTTTGTGTAG	0.433																																																3	Substitution - coding silent(3)	large_intestine(3)	7											107	104	105					7																	82582694		1922	4131	6053	82420630	SO:0001819	synonymous_variant	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7575A>G	7.37:g.82582694T>C			82420630		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82582694	T	C	82582694	2	2	61	1	0	0	0	0	0	0	0	1	11614	1722	60	4		4	PCLO	7	82582694	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1152	82582694	76555969	5330	13315										
PCLO	27445	broad.mit.edu	37	chr7	82583589	82583589	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaaaataagttgatgaaGaaatttcctcagaatcttca	7	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82583589G>T	ENST00000333891.9	-	5	7017	c.6680C>A	c.(6679-6681)tCt>tAt	p.S2227Y	PCLO_ENST00000423517.2_Missense_Mutation_p.S2227Y	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S2227Y(2)|p.S2158Y(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGTTGATGAAGAAATTTCCTC	0.398																																																3	Substitution - Missense(3)	large_intestine(3)	7											54	52	52					7																	82583589		1833	4092	5925	82421525	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6680C>A	7.37:g.82583589G>T	ENSP00000334319:p.Ser2227Tyr		82421525		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	5.990	0.366520	0.11352	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17854	2.25;2.25	5.5	5.5	0.81552	.	.	.	.	.	T	0.13157	0.0319	L	0.36672	1.1	0.80722	D	1	P;P	0.35328	0.495;0.495	B;B	0.31337	0.128;0.128	T	0.03068	-1.1076	9	0.87932	D	0	.	8.4397	0.32808	0.0825:0.2065:0.711:0.0	.	2227;2227	Q9Y6V0-5;Q9Y6V0-6	.;.	Y	2158;2227;2227	ENSP00000334319:S2227Y;ENSP00000388393:S2227Y	ENSP00000334319:S2227Y	S	-	2	0	PCLO	82421525	0.506000	0.26139	1.000000	0.80357	0.938000	0.57974	3.440000	0.52886	2.575000	0.86900	0.650000	0.86243	TCT		0.398	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82583589	G	T	82583589	3	4	61	1	0	0	0	0	1	0	0	0	11614	942	33	2	8849	2	PCLO	7	82583589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	895	82583589	76555074	5331	13316										
PCLO	27445	broad.mit.edu	37	chr7	82584117	82584117	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcctttcttcttctgtaGaagttaccatagtacccagg	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82584117G>T	ENST00000333891.9	-	5	6489	c.6152C>A	c.(6151-6153)tCt>tAt	p.S2051Y	PCLO_ENST00000423517.2_Missense_Mutation_p.S2051Y	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S2051Y(2)|p.S1982Y(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTCTTCTGTAGAAGTTACCAT	0.423																																																3	Substitution - Missense(3)	large_intestine(3)	7											80	75	76					7																	82584117		1890	4113	6003	82422053	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6152C>A	7.37:g.82584117G>T	ENSP00000334319:p.Ser2051Tyr		82422053		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	2.779	-0.253960	0.05829	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19532	2.14;2.15	5.64	5.64	0.86602	.	.	.	.	.	T	0.41834	0.1176	L	0.51422	1.61	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.67548	0.952;0.952	T	0.14896	-1.0456	9	0.87932	D	0	.	17.8784	0.88831	0.0:0.0:1.0:0.0	.	2051;2051	Q9Y6V0-5;Q9Y6V0-6	.;.	Y	1982;2051;2051	ENSP00000334319:S2051Y;ENSP00000388393:S2051Y	ENSP00000334319:S2051Y	S	-	2	0	PCLO	82422053	.	.	0.472000	0.27241	0.331000	0.28603	.	.	2.660000	0.90430	0.561000	0.74099	TCT		0.423	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82584117	G	T	82584117	3	4	61	1	0	0	0	0	1	0	0	0	11614	942	33	2	9377	2	PCLO	7	82584117	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	528	82584117	76554546	5332	13317										
PCLO	27445	broad.mit.edu	37	chr7	82584797	82584797	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagattactaggtggtgtCtttggcctttcccttcttct	10	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82584797C>A	ENST00000333891.9	-	5	5809	c.5472G>T	c.(5470-5472)aaG>aaT	p.K1824N	PCLO_ENST00000423517.2_Missense_Mutation_p.K1824N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.K1824N(2)|p.K1755N(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TAGGTGGTGTCTTTGGCCTTT	0.428																																																3	Substitution - Missense(3)	large_intestine(3)	7											258	238	244					7																	82584797		1880	4108	5988	82422733	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5472G>T	7.37:g.82584797C>A	ENSP00000334319:p.Lys1824Asn		82422733		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	8.918	0.960266	0.18507	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.37915	1.17;1.19	5.33	3.51	0.40186	.	.	.	.	.	T	0.43545	0.1252	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.39881	-0.9592	9	0.87932	D	0	.	9.4202	0.38546	0.0:0.7754:0.0:0.2246	.	1824;1824	Q9Y6V0-5;Q9Y6V0-6	.;.	N	1755;1824;1824	ENSP00000334319:K1824N;ENSP00000388393:K1824N	ENSP00000334319:K1824N	K	-	3	2	PCLO	82422733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.373000	0.44266	1.247000	0.43917	0.655000	0.94253	AAG		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82584797	C	A	82584797	3	1	61	1	0	0	0	0	1	0	0	0	11614	912	32	2	10057	2	PCLO	7	82584797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	680	82584797	76553866	5333	13318										
PCLO	27445	broad.mit.edu	37	chr7	82585272	82585272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagctcaattgttttaaatCggcgtagccctcctcctcca	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82585272C>T	ENST00000333891.9	-	5	5334	c.4997G>A	c.(4996-4998)cGa>cAa	p.R1666Q	PCLO_ENST00000423517.2_Missense_Mutation_p.R1666Q	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.R1666Q(2)|p.R1597Q(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGTTTTAAATCGGCGTAGCCC	0.373																																																3	Substitution - Missense(3)	large_intestine(3)	7											110	102	105					7																	82585272		1861	4100	5961	82423208	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4997G>A	7.37:g.82585272C>T	ENSP00000334319:p.Arg1666Gln		82423208		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.542433	0.27563	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.24723	1.84;1.85	5.31	5.31	0.75309	.	.	.	.	.	T	0.51736	0.1692	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.64144	0.922;0.922	T	0.56019	-0.8048	9	0.87932	D	0	.	18.9766	0.92740	0.0:1.0:0.0:0.0	.	1666;1666	Q9Y6V0-5;Q9Y6V0-6	.;.	Q	1597;1666;1666	ENSP00000334319:R1666Q;ENSP00000388393:R1666Q	ENSP00000334319:R1666Q	R	-	2	0	PCLO	82423208	0.856000	0.29760	0.643000	0.29450	0.904000	0.53231	3.107000	0.50329	2.478000	0.83669	0.650000	0.86243	CGA		0.373	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82585272	C	T	82585272	3	4	61	1	0	0	0	0	1	0	0	0	11614	884	31	1	10532	1	PCLO	7	82585272	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	475	82585272	76553391	5334	13319										
PCLO	27445	broad.mit.edu	37	chr7	82585906	82585906	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttccaaggtttcagataAactctgagttttctcttggt	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82585906A>C	ENST00000333891.9	-	5	4700	c.4363T>G	c.(4363-4365)Tta>Gta	p.L1455V	PCLO_ENST00000423517.2_Missense_Mutation_p.L1455V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.L1455V(2)|p.L1386V(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTTTCAGATAAACTCTGAGTT	0.368																																																3	Substitution - Missense(3)	large_intestine(3)	7											107	99	102					7																	82585906		1808	4075	5883	82423842	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4363T>G	7.37:g.82585906A>C	ENSP00000334319:p.Leu1455Val		82423842		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	1.929	-0.446444	0.04604	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19250	2.16;2.17	5.48	-4.93	0.03066	.	.	.	.	.	T	0.14442	0.0349	L	0.54323	1.7	0.09310	N	1	B;B	0.31548	0.328;0.328	B;B	0.27380	0.079;0.079	T	0.20405	-1.0276	9	0.87932	D	0	.	2.2844	0.04123	0.3562:0.3094:0.2344:0.1	.	1455;1455	Q9Y6V0-5;Q9Y6V0-6	.;.	V	1386;1455;1455	ENSP00000334319:L1455V;ENSP00000388393:L1455V	ENSP00000334319:L1455V	L	-	1	2	PCLO	82423842	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	0.075000	0.14686	-1.281000	0.02399	-0.309000	0.09137	TTA		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82585906	A	C	82585906	3	2	61	1	0	0	0	0	1	0	0	0	11614	11	1	4	11166	4	PCLO	7	82585906	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	634	82585906	76552757	5335	13320										
PCLO	27445	broad.mit.edu	37	chr7	82586071	82586071	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggctggaagggctgctttCttgtgaaaaagagtcctttt	14	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82586071C>A	ENST00000333891.9	-	5	4535	c.4198G>T	c.(4198-4200)Gaa>Taa	p.E1400*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.E1400*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.E1400*(2)|p.E1331*(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GGGCTGCTTTCTTGTGAAAAA	0.403																																																3	Substitution - Nonsense(3)	large_intestine(3)	7											91	85	86					7																	82586071		1837	4088	5925	82424007	SO:0001587	stop_gained	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4198G>T	7.37:g.82586071C>A	ENSP00000334319:p.Glu1400*		82424007		Nonsense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	46	12.717255	0.99690	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.9855	0.97347	0.0:1.0:0.0:0.0	.	.	.	.	X	1331;1400;1400	.	ENSP00000334319:E1400X	E	-	1	0	PCLO	82424007	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.017000	0.70805	2.715000	0.92844	0.655000	0.94253	GAA		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82586071	C	A	82586071	4	1	61	1	0	0	0	0	0	1	0	0	11614	922	32	2	11331	2	PCLO	7	82586071	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165	82586071	76552592	5336	13321										
PCLO	27445	broad.mit.edu	37	chr7	82785548	82785548	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagttctggactttgattCtttcaagctaatagtggaag	9	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82785548C>A	ENST00000333891.9	-	2	746	c.409G>T	c.(409-411)Gaa>Taa	p.E137*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.E137*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.E137*(3)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GACTTTGATTCTTTCAAGCTA	0.448																																																3	Substitution - Nonsense(3)	large_intestine(3)	7											107	108	107					7																	82785548		1850	4106	5956	82623484	SO:0001587	stop_gained	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.409G>T	7.37:g.82785548C>A	ENSP00000334319:p.Glu137*		82623484		Nonsense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	41	8.657743	0.98903	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.992	0.80214	0.0:0.8655:0.1345:0.0	.	.	.	.	X	137	.	ENSP00000334319:E137X	E	-	1	0	PCLO	82623484	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.008000	0.63991	2.665000	0.90641	0.655000	0.94253	GAA		0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82785548	C	A	82785548	4	1	61	1	0	0	0	0	0	1	0	0	11614	922	32	2	15132	2	PCLO	7	82785548	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	199477	82785548	76353115	5337	13322										
SEMA3E	9723	broad.mit.edu	37	chr7	82997280	82997280	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtctggcaaaaataggtCccagcatctgatttgtgtaa	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:82997280C>T	ENST00000307792.3	-	17	2417	c.1950G>A	c.(1948-1950)ggG>ggA	p.G650G	SEMA3E_ENST00000427262.1_Silent_p.G590G	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	650	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.G650G(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				AAAAATAGGTCCCAGCATCTG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	7											126	118	120					7																	82997280		2203	4300	6503	82835216	SO:0001819	synonymous_variant	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1950G>A	7.37:g.82997280C>T			82835216	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																				0.418	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	82997280	C	T	82997280	2	4	61	1	0	0	0	0	0	0	0	1	14065	842	30	3		3	SEMA3E	7	82997280	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211732	82997280	76141383	5338	13323										
SEMA3E	9723	broad.mit.edu	37	chr7	83016343	83016343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgagctgcatttccatgtCgaacatcttgtctccggaaa	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83016343C>T	ENST00000307792.3	-	15	2158	c.1691G>A	c.(1690-1692)cGa>cAa	p.R564Q	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R504Q	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	564					axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R564Q(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				ATTTCCATGTCGAACATCTTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	76	80					7																	83016343		2203	4300	6503	82854279	SO:0001583	missense	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1691G>A	7.37:g.83016343C>T	ENSP00000303212:p.Arg564Gln		82854279	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	35	5.446225	0.96187	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.22134	1.97;1.97	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.36286	-0.9754	10	0.51188	T	0.08	.	19.6817	0.95967	0.0:1.0:0.0:0.0	.	564	O15041	SEM3E_HUMAN	Q	564;504;564	ENSP00000303212:R564Q;ENSP00000405052:R504Q	ENSP00000303212:R564Q	R	-	2	0	SEMA3E	82854279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.319000	0.65835	2.653000	0.90120	0.650000	0.86243	CGA		0.363	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	83016343	C	T	83016343	3	4	61	1	0	0	0	0	1	0	0	0	14065	884	31	1	648	1	SEMA3E	7	83016343	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19063	83016343	76122320	5339	13324										
SEMA3E	9723	broad.mit.edu	37	chr7	83035288	83035288	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaaaatatgtgtcaattcCattcattcctggtactgagc	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83035288C>A	ENST00000307792.3	-	8	1368	c.901G>T	c.(901-903)Gga>Tga	p.G301*	SEMA3E_ENST00000427262.1_Nonsense_Mutation_p.G241*	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	301	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.G301*(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GTGTCAATTCCATTCATTCCT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											155	142	146					7																	83035288		2203	4300	6503	82873224	SO:0001587	stop_gained	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.901G>T	7.37:g.83035288C>A	ENSP00000303212:p.Gly301*		82873224	B4E1P1|Q75M94|Q75M97	Nonsense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	36	5.923584	0.97110	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	.	.	.	5.73	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.9684	0.71213	0.0:0.9314:0.0:0.0685	.	.	.	.	X	301;241;301	.	ENSP00000303212:G301X	G	-	1	0	SEMA3E	82873224	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	6.059000	0.71133	1.426000	0.47256	-0.143000	0.13931	GGA		0.353	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83035288	C	A	83035288	4	1	61	1	0	0	0	0	0	1	0	0	14065	603	21	2	1466	2	SEMA3E	7	83035288	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18945	83035288	76103375	5340	13325										
SEMA3E	9723	broad.mit.edu	37	chr7	83095896	83095896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatagtgatgcaaaacccGaacataatttgcacattcac	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83095896G>A	ENST00000307792.3	-	4	825	c.358C>T	c.(358-360)Cgg>Tgg	p.R120W	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R60W	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	120	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R120W(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGCAAAACCCGAACATAATTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											130	111	117					7																	83095896		2203	4300	6503	82933832	SO:0001583	missense	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.358C>T	7.37:g.83095896G>A	ENSP00000303212:p.Arg120Trp		82933832	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.022523	0.75275	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	T;T;T	0.31510	1.49;1.49;1.49	5.48	4.58	0.56647	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.139535	0.47852	D	0.000217	T	0.66247	0.2770	H	0.94183	3.505	0.42590	D	0.993243	D	0.89917	1.0	D	0.91635	0.999	T	0.77632	-0.2515	10	0.87932	D	0	.	14.4761	0.67546	0.0:0.0:0.8517:0.1483	.	120	O15041	SEM3E_HUMAN	W	120;60;120;60	ENSP00000303212:R120W;ENSP00000405052:R60W;ENSP00000412867:R60W	ENSP00000303212:R120W	R	-	1	2	SEMA3E	82933832	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	4.003000	0.57061	1.290000	0.44636	0.650000	0.86243	CGG		0.388	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83095896	G	A	83095896	3	1	61	1	0	0	0	0	1	0	0	0	14065	1057	37	1	2025	1	SEMA3E	7	83095896	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60608	83095896	76042767	5341	13326										
SEMA3A	10371	broad.mit.edu	37	chr7	83592543	83592543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttttcgctcttcatttCgcctctggaattgccaatag	6	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83592543C>T	ENST00000265362.4	-	16	2152	c.1838G>A	c.(1837-1839)cGa>cAa	p.R613Q	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R613Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	613	Ig-like C2-type.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.R613Q(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTCTTCATTTCGCCTCTGGAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											187	187	187					7																	83592543		2203	4300	6503	83430479	SO:0001583	missense	10371			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1838G>A	7.37:g.83592543C>T	ENSP00000265362:p.Arg613Gln		83430479		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740001	0.30865	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.01527	4.8;4.8	5.9	4.91	0.64330	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.355176	0.32624	N	0.005858	T	0.00724	0.0024	N	0.01705	-0.755	0.31357	N	0.681812	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.14252	T	0.57	.	3.4603	0.07531	0.0:0.5419:0.2844:0.1737	.	613	Q14563	SEM3A_HUMAN	Q	613	ENSP00000265362:R613Q;ENSP00000415260:R613Q	ENSP00000265362:R613Q	R	-	2	0	SEMA3A	83430479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.637000	0.46553	2.802000	0.96397	0.650000	0.86243	CGA		0.403	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83592543	C	T	83592543	3	4	61	1	0	0	0	0	1	0	0	0	14061	884	31	1	485	1	SEMA3A	7	83592543	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	496647	83592543	75546120	5342	13327										
SEMA3A	10371	broad.mit.edu	37	chr7	83739791	83739791	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagccagcgttacctcagGatgatgtccaatttcaatgt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83739791G>T	ENST00000265362.4	-	4	762	c.448C>A	c.(448-450)Cct>Act	p.P150T	SEMA3A_ENST00000436949.1_Missense_Mutation_p.P150T	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	150	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.P150T(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						GTTACCTCAGGATGATGTCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	90	91					7																	83739791		2203	4300	6503	83577727	SO:0001583	missense	10371			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.448C>A	7.37:g.83739791G>T	ENSP00000265362:p.Pro150Thr		83577727		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.919097	0.33908	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.20738	2.05;2.05	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.516702	0.23107	N	0.051843	T	0.14227	0.0344	N	0.12887	0.27	0.46849	D	0.999221	B	0.09022	0.002	B	0.11329	0.006	T	0.16012	-1.0417	10	0.10902	T	0.67	.	20.3046	0.98621	0.0:0.0:1.0:0.0	.	150	Q14563	SEM3A_HUMAN	T	150	ENSP00000265362:P150T;ENSP00000415260:P150T	ENSP00000265362:P150T	P	-	1	0	SEMA3A	83577727	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.728000	0.62000	2.878000	0.98634	0.650000	0.86243	CCT		0.368	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83739791	G	T	83739791	3	4	61	1	0	0	0	0	1	0	0	0	14061	1174	41	2	1923	2	SEMA3A	7	83739791	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147248	83739791	75398872	5343	13328										
SEMA3A	10371	broad.mit.edu	37	chr7	83764139	83764139	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccttgatattaaccaggtCgaatgaaaatatgtgatcct	7	7	0	3	rs376684446		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:83764139C>T	ENST00000265362.4	-	2	555	c.241G>A	c.(241-243)Gac>Aac	p.D81N	SEMA3A_ENST00000436949.1_Missense_Mutation_p.D81N	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	81	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.D81N(2)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						TTAACCAGGTCGAATGAAAAT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											99	96	97					7																	83764139		2203	4300	6503	83602075	SO:0001583	missense	10371			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.241G>A	7.37:g.83764139C>T	ENSP00000265362:p.Asp81Asn		83602075		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	c	4.150	0.026195	0.08054	.	.	ENSG00000075213	ENST00000265362;ENST00000436949;ENST00000420047	T;T;T	0.22134	1.97;1.97;1.97	4.79	3.62	0.41486	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.213570	0.56097	N	0.000034	T	0.07234	0.0183	N	0.02916	-0.46	0.26223	N	0.979132	B	0.02656	0.0	B	0.04013	0.001	T	0.37502	-0.9703	10	0.02654	T	1	.	10.7511	0.46209	0.0:0.0765:0.0:0.9235	.	81	Q14563	SEM3A_HUMAN	N	81	ENSP00000265362:D81N;ENSP00000415260:D81N;ENSP00000391900:D81N	ENSP00000265362:D81N	D	-	1	0	SEMA3A	83602075	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.414000	0.44627	0.757000	0.33036	-0.600000	0.04104	GAC		0.358	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83764139	C	T	83764139	3	4	61	1	0	0	0	0	1	0	0	0	14061	884	31	1	2138	1	SEMA3A	7	83764139	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24348	83764139	75374524	5344	13329										
SEMA3D	223117	broad.mit.edu	37	chr7	84628811	84628811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtgatgtcttcgatttCgtttcttcttcatttcctgc	6	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:84628811C>T	ENST00000284136.6	-	17	2322	c.2279G>A	c.(2278-2280)cGa>cAa	p.R760Q	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	760	Arg/Lys-rich (basic).				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R760Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TCTTCGATTTCGTTTCTTCTT	0.453																																					Ovarian(63;442 1191 17318 29975 31528)											1	Substitution - Missense(1)	large_intestine(1)	7											180	146	158					7																	84628811		2203	4300	6503	84466747	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2279G>A	7.37:g.84628811C>T	ENSP00000284136:p.Arg760Gln		84466747	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.155987	0.78114	.	.	ENSG00000153993	ENST00000284136	T	0.36699	1.24	5.93	5.93	0.95920	.	0.114181	0.56097	D	0.000021	T	0.63070	0.2480	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62581	-0.6824	10	0.66056	D	0.02	.	20.3409	0.98764	0.0:1.0:0.0:0.0	.	760	O95025	SEM3D_HUMAN	Q	760	ENSP00000284136:R760Q	ENSP00000284136:R760Q	R	-	2	0	SEMA3D	84466747	1.000000	0.71417	0.980000	0.43619	0.271000	0.26615	7.224000	0.78042	2.814000	0.96858	0.655000	0.94253	CGA		0.453	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		T	84628811	C	T	84628811	3	4	61	1	0	0	0	0	1	0	0	0	14064	884	31	1	58	1	SEMA3D	7	84628811	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	864672	84628811	74509852	5345	13330										
SEMA3D	223117	broad.mit.edu	37	chr7	84727225	84727225	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctaagagaagagtttgaaAatccagtccttctgatgaac	8	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:84727225A>C	ENST00000284136.6	-	2	251	c.208T>G	c.(208-210)Ttt>Gtt	p.F70V	SEMA3D_ENST00000444867.1_Missense_Mutation_p.F70V	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	70	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.F70V(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						AGAGTTTGAAAATCCAGTCCT	0.373																																					Ovarian(63;442 1191 17318 29975 31528)											1	Substitution - Missense(1)	large_intestine(1)	7											103	107	106					7																	84727225		2203	4300	6503	84565161	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.208T>G	7.37:g.84727225A>C	ENSP00000284136:p.Phe70Val		84565161	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502033	0.85176	.	.	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.11277	2.79;2.79	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.046039	0.85682	D	0.000000	T	0.27731	0.0682	L	0.60845	1.875	0.58432	D	0.999999	D;D	0.63880	0.993;0.98	P;P	0.61275	0.886;0.783	T	0.00609	-1.1646	10	0.72032	D	0.01	.	16.0068	0.80367	1.0:0.0:0.0:0.0	.	70;70	C9JYT6;O95025	.;SEM3D_HUMAN	V	70	ENSP00000284136:F70V;ENSP00000401366:F70V	ENSP00000284136:F70V	F	-	1	0	SEMA3D	84565161	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.232000	0.89796	2.241000	0.73720	0.482000	0.46254	TTT		0.373	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		C	84727225	A	C	84727225	3	2	61	1	0	0	0	0	1	0	0	0	14064	14	1	4	2189	4	SEMA3D	7	84727225	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	98414	84727225	74411438	5346	13331										
KIAA1324L	222223	broad.mit.edu	37	chr7	86541520	86541520	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaactctgattttctttTtcatggtagaaaaagcagtc	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:86541520T>C	ENST00000450689.2	-	15	2222	c.2037A>G	c.(2035-2037)gaA>gaG	p.E679E	KIAA1324L_ENST00000297222.6_Silent_p.E439E|KIAA1324L_ENST00000444627.1_Intron|KIAA1324L_ENST00000416314.1_Silent_p.E512E|KIAA1324L_ENST00000490995.1_5'Flank	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	679						integral component of membrane (GO:0016021)		p.E439E(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					GATTTTCTTTTTCATGGTAGA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	7											117	119	119					7																	86541520		2203	4300	6503	86379456	SO:0001819	synonymous_variant	222223			AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.2037A>G	7.37:g.86541520T>C			86379456	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Silent	SNP	ENST00000450689.2	37	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	T	8.960	0.970244	0.18659	.	.	ENSG00000164659	ENST00000423294	.	.	.	5.76	-8.13	0.01073	.	.	.	.	.	T	0.51295	0.1666	.	.	.	0.54753	D	0.999983	.	.	.	.	.	.	T	0.59679	-0.7409	4	.	.	.	.	11.1891	0.48675	0.0865:0.6616:0.1275:0.1244	.	.	.	.	E	640	.	.	K	-	1	0	KIAA1324L	86379456	0.076000	0.21285	0.911000	0.35937	0.984000	0.73092	-0.651000	0.05372	-1.120000	0.02953	-0.467000	0.05162	AAA		0.373	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		C	86541520	T	C	86541520	2	2	61	1	0	0	0	0	0	0	0	1	8245	1838	64	4		4	KIAA1324L	7	86541520	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1814295	86541520	72597143	5347	13332										
KIAA1324L	222223	broad.mit.edu	37	chr7	86544125	86544125	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggtgtaagcttgtttttCtttggttccaccccacgatt	9	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:86544125C>A	ENST00000450689.2	-	13	1830	c.1645G>T	c.(1645-1647)Gaa>Taa	p.E549*	KIAA1324L_ENST00000297222.6_Nonsense_Mutation_p.E309*|KIAA1324L_ENST00000444627.1_Nonsense_Mutation_p.E549*|KIAA1324L_ENST00000416314.1_Nonsense_Mutation_p.E382*|KIAA1324L_ENST00000490995.1_5'UTR	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	549						integral component of membrane (GO:0016021)		p.E309*(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					GCTTGTTTTTCTTTGGTTCCA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											196	167	177					7																	86544125		2203	4300	6503	86382061	SO:0001587	stop_gained	222223			AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1645G>T	7.37:g.86544125C>A	ENSP00000413445:p.Glu549*		86382061	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Nonsense_Mutation	SNP	ENST00000450689.2	37	CCDS47632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.484358|7.484358	0.98312|0.98312	.|.	.|.	ENSG00000164659|ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314|ENST00000423294	.|.	.|.	.|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.096355|.	0.64402|.	D|.	0.000001|.	.|T	.|0.76622	.|0.4013	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73911	.|-0.3833	.|3	0.07482|.	T|.	0.82|.	.|.	19.3629|19.3629	0.94448|0.94448	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	549;309;549;382|509	.|.	ENSP00000297222:E309X|.	E|R	-|-	1|2	0|0	KIAA1324L|KIAA1324L	86382061|86382061	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	4.168000|4.168000	0.58216|0.58216	2.817000|2.817000	0.96982|0.96982	0.563000|0.563000	0.77884|0.77884	GAA|AGA		0.343	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		A	86544125	C	A	86544125	4	1	61	1	0	0	0	0	0	1	0	0	8245	922	32	2	1484	2	KIAA1324L	7	86544125	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2605	86544125	72594538	5348	13333										
KIAA1324L	222223	broad.mit.edu	37	chr7	86554959	86554959	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggctccgttcctgctggAcatggtctacattctacagg	11	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:86554959A>G	ENST00000450689.2	-	10	1469	c.1284T>C	c.(1282-1284)tgT>tgC	p.C428C	KIAA1324L_ENST00000297222.6_Silent_p.C188C|KIAA1324L_ENST00000444627.1_Silent_p.C428C|KIAA1324L_ENST00000416314.1_Silent_p.C261C	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	428						integral component of membrane (GO:0016021)		p.C188C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					TTCCTGCTGGACATGGTCTAC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	7											108	99	102					7																	86554959		2203	4300	6503	86392895	SO:0001819	synonymous_variant	222223			AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1284T>C	7.37:g.86554959A>G			86392895	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Silent	SNP	ENST00000450689.2	37	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	A	1.407	-0.576581	0.03854	.	.	ENSG00000164659	ENST00000423294	.	.	.	5.7	0.204	0.15199	.	.	.	.	.	T	0.56062	0.1960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49818	-0.8899	4	.	.	.	.	9.594	0.39563	0.6092:0.0:0.3908:0.0	.	.	.	.	P	389	.	.	S	-	1	0	KIAA1324L	86392895	0.989000	0.36119	0.975000	0.42487	0.125000	0.20455	0.417000	0.21214	0.114000	0.18032	0.459000	0.35465	TCC		0.403	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		G	86554959	A	G	86554959	2	3	61	1	0	0	0	0	0	0	0	1	8245	273	10	4		4	KIAA1324L	7	86554959	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10834	86554959	72583704	5349	13334										
DMTF1	9988	broad.mit.edu	37	chr7	86811606	86811606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgctaggaagaagtgcatCttctgtcaaagatcggtgcc	13	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:86811606C>A	ENST00000394703.5	+	12	1336	c.773C>A	c.(772-774)tCt>tAt	p.S258Y	DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000432937.2_Missense_Mutation_p.S170Y|DMTF1_ENST00000331242.7_Missense_Mutation_p.S258Y|DMTF1_ENST00000413276.2_Missense_Mutation_p.S258Y|DMTF1_ENST00000411766.2_3'UTR	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	258	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Myb-like 1. {ECO:0000255|PROSITE- ProRule:PRU00133}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S258Y(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					AGAAGTGCATCTTCTGTCAAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											156	141	146					7																	86811606		2203	4300	6503	86649542	SO:0001583	missense	9988			AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.773C>A	7.37:g.86811606C>A	ENSP00000378193:p.Ser258Tyr		86649542	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	37	CCDS5601.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.232419	0.79688	.	.	ENSG00000135164	ENST00000331242;ENST00000413276;ENST00000432937;ENST00000394703	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.76	4.89	0.63831	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);MYB-like (1);	0.047647	0.85682	D	0.000000	T	0.47340	0.1440	L	0.50333	1.59	0.80722	D	1	D	0.69078	0.997	D	0.69824	0.966	T	0.45644	-0.9247	10	0.02654	T	1	-12.1014	14.1857	0.65605	0.0:0.9284:0.0:0.0716	.	258	Q9Y222	DMTF1_HUMAN	Y	258;258;170;258	ENSP00000332171:S258Y;ENSP00000402627:S258Y;ENSP00000412532:S170Y;ENSP00000378193:S258Y	ENSP00000332171:S258Y	S	+	2	0	DMTF1	86649542	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	1.582000	0.49881	0.650000	0.86243	TCT		0.483	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		A	86811606	C	A	86811606	3	1	61	1	0	0	0	0	1	0	0	0	4603	913	32	2	803	2	DMTF1	7	86811606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	256647	86811606	72327057	5350	13335										
CROT	54677	broad.mit.edu	37	chr7	87021885	87021885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgatttttaatacagcttCgtgagcggcagcaaaagatg	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87021885C>T	ENST00000331536.3	+	15	1614	c.1429C>T	c.(1429-1431)Cgt>Tgt	p.R477C	CROT_ENST00000442291.1_Missense_Mutation_p.R477C|CROT_ENST00000419147.2_Missense_Mutation_p.R505C	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	477					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)	p.R477C(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	AATACAGCTTCGTGAGCGGCA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7											107	115	112					7																	87021885		2201	4299	6500	86859821	SO:0001583	missense	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.1429C>T	7.37:g.87021885C>T	ENSP00000331981:p.Arg477Cys		86859821	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550215	0.27652	.	.	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.89343	-2.5;-2.5;-2.5	5.93	-0.0817	0.13701	.	0.920708	0.09500	N	0.793789	T	0.77922	0.4203	N	0.19112	0.55	0.09310	N	1	B;B	0.30021	0.265;0.265	B;B	0.21360	0.034;0.023	T	0.63659	-0.6587	10	0.54805	T	0.06	0.242	7.2846	0.26330	0.0:0.3357:0.3099:0.3544	.	505;477	E7EQF2;Q9UKG9	.;OCTC_HUMAN	C	505;477;477	ENSP00000413575:R505C;ENSP00000331981:R477C;ENSP00000411983:R477C	ENSP00000331981:R477C	R	+	1	0	CROT	86859821	0.000000	0.05858	0.001000	0.08648	0.816000	0.46133	0.052000	0.14163	-0.309000	0.08779	0.655000	0.94253	CGT		0.343	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		T	87021885	C	T	87021885	3	4	61	1	0	0	0	0	1	0	0	0	3900	884	31	1	1567	1	CROT	7	87021885	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	210279	87021885	72116778	5351	13336										
CROT	54677	broad.mit.edu	37	chr7	87022054	87022054	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcattgcaggatttgatCgtcaccttttaggtctctta	8	8	3	1	rs374151013		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87022054C>T	ENST00000331536.3	+	16	1698	c.1513C>T	c.(1513-1515)Cgt>Tgt	p.R505C	CROT_ENST00000442291.1_Missense_Mutation_p.R505C|CROT_ENST00000419147.2_Missense_Mutation_p.R533C	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	505					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)	p.R505C(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	AGGATTTGATCGTCACCTTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	99	101	100		1597,1513	5.9	1	7		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CROT	NM_001143935.1,NM_021151.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	533/641,505/613	87022054	1,13005	2203	4300	6503	86859990	SO:0001583	missense	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.1513C>T	7.37:g.87022054C>T	ENSP00000331981:p.Arg505Cys		86859990	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422409	0.83559	0.0	1.16E-4	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.92545	-3.06;-3.06;-3.06	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.97377	0.9142	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97485	1.0050	10	0.66056	D	0.02	-22.1656	20.3465	0.98790	0.0:1.0:0.0:0.0	.	533;505	E7EQF2;Q9UKG9	.;OCTC_HUMAN	C	533;505;505	ENSP00000413575:R533C;ENSP00000331981:R505C;ENSP00000411983:R505C	ENSP00000331981:R505C	R	+	1	0	CROT	86859990	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.072000	0.71238	2.798000	0.96311	0.655000	0.94253	CGT		0.353	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		T	87022054	C	T	87022054	3	4	61	1	0	0	0	0	1	0	0	0	3900	884	31	1	1655	1	CROT	7	87022054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	169	87022054	72116609	5352	13337										
ABCB4	5244	broad.mit.edu	37	chr7	87035805	87035805	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttgcttcttgaccatcGagaagctgaaaaccaaagtc	7	10	2	3	rs561612231		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87035805G>A	ENST00000265723.4	-	26	3417	c.3306C>T	c.(3304-3306)ctC>ctT	p.L1102L	ABCB4_ENST00000358400.3_Silent_p.L1048L|ABCB4_ENST00000545634.1_Silent_p.L1095L|ABCB4_ENST00000453593.1_Silent_p.L1048L|ABCB4_ENST00000359206.3_Silent_p.L1095L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	1102	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.L1095L(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	CTTGACCATCGAGAAGCTGAA	0.408													G|||	1	0.000199681	0	0	5008	,	,		20158	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											63	62	62					7																	87035805		2203	4300	6503	86873741	SO:0001819	synonymous_variant	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.3306C>T	7.37:g.87035805G>A			86873741	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																				0.408	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		A	87035805	G	A	87035805	2	1	61	1	0	0	0	0	0	0	0	1	43	1045	37	1		1	ABCB4	7	87035805	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13751	87035805	72102858	5353	13338										
ABCB4	5244	broad.mit.edu	37	chr7	87060767	87060767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttccttcttcatcagttCgctgtggcttccttgctcca	6	16	3	0	rs370195624		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87060767C>T	ENST00000265723.4	-	15	1957	c.1846G>A	c.(1846-1848)Gaa>Aaa	p.E616K	ABCB4_ENST00000358400.3_Missense_Mutation_p.E616K|ABCB4_ENST00000545634.1_Missense_Mutation_p.E616K|ABCB4_ENST00000453593.1_Missense_Mutation_p.E616K|ABCB4_ENST00000359206.3_Missense_Mutation_p.E616K	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	616	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.E616K(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TTCATCAGTTCGCTGTGGCTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	214	182	193		1846,1846,1846	5.5	0.7	7		193	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ABCB4	NM_000443.3,NM_018849.2,NM_018850.2	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	616/1280,616/1287,616/1233	87060767	1,13005	2203	4300	6503	86898703	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1846G>A	7.37:g.87060767C>T	ENSP00000265723:p.Glu616Lys		86898703	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.031373	0.54790	0.0	1.16E-4	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82	5.49	5.49	0.81192	ABC transporter-like (1);	0.152222	0.56097	D	0.000021	T	0.66499	0.2795	L	0.43598	1.365	0.58432	D	0.999999	P;B;B	0.41232	0.743;0.277;0.181	B;B;B	0.35727	0.209;0.111;0.052	T	0.71543	-0.4561	10	0.62326	D	0.03	-15.5791	14.57	0.68205	0.0:0.9278:0.0:0.0722	.	616;616;616	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	K	616	ENSP00000352135:E616K;ENSP00000351172:E616K;ENSP00000265723:E616K;ENSP00000392983:E616K;ENSP00000437465:E616K	ENSP00000265723:E616K	E	-	1	0	ABCB4	86898703	0.927000	0.31430	0.711000	0.30485	0.727000	0.41649	1.982000	0.40638	2.580000	0.87095	0.591000	0.81541	GAA		0.453	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87060767	C	T	87060767	3	4	61	1	0	0	0	0	1	0	0	0	43	893	31	1	2070	1	ABCB4	7	87060767	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24962	87060767	72077896	5354	13339										
ABCB4	5244	broad.mit.edu	37	chr7	87082277	87082277	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactctgttagccgcgtattGagttcagtggtgtcgttgat	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87082277G>T	ENST00000265723.4	-	6	630	c.519C>A	c.(517-519)ctC>ctA	p.L173L	ABCB4_ENST00000358400.3_Silent_p.L173L|ABCB4_ENST00000545634.1_Silent_p.L173L|ABCB4_ENST00000453593.1_Silent_p.L173L|ABCB4_ENST00000359206.3_Silent_p.L173L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	173	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.L173L(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	GCCGCGTATTGAGTTCAGTGG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	7											115	105	108					7																	87082277		2203	4300	6503	86920213	SO:0001819	synonymous_variant	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.519C>A	7.37:g.87082277G>T			86920213	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																				0.363	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87082277	G	T	87082277	2	4	61	1	0	0	0	0	0	0	0	1	43	1277	45	2		2	ABCB4	7	87082277	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21510	87082277	72056386	5355	13340										
ABCB1	5243	broad.mit.edu	37	chr7	87133758	87133758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctttgtccagggcttctTggacaacctattccataatc	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87133758T>C	ENST00000265724.3	-	29	4061	c.3644A>G	c.(3643-3645)cAa>cGa	p.Q1215R	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Missense_Mutation_p.Q1151R	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	1215	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.Q1215R(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CAGGGCTTCTTGGACAACCTA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	77	78					7																	87133758		2203	4300	6503	86971694	SO:0001583	missense	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.3644A>G	7.37:g.87133758T>C	ENSP00000265724:p.Gln1215Arg		86971694	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.785386	0.90282	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.83163	-1.69;-1.69	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.87657	0.6232	L	0.41824	1.3	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	D	0.88881	0.3339	10	0.87932	D	0	-15.6491	15.3408	0.74296	0.0:0.0:0.0:1.0	.	1151;1215	B5AK60;P08183	.;MDR1_HUMAN	R	996;1215;1151	ENSP00000265724:Q1215R;ENSP00000444095:Q1151R	ENSP00000265724:Q1215R	Q	-	2	0	ABCB1	86971694	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.001000	0.88508	2.216000	0.71823	0.533000	0.62120	CAA		0.453	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		C	87133758	T	C	87133758	3	2	61	1	0	0	0	0	1	0	0	0	40	1812	63	4	202	4	ABCB1	7	87133758	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	51481	87133758	72004905	5356	13341										
ABCB1	5243	broad.mit.edu	37	chr7	87150174	87150174	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacggttcggaagttttCtattgcttcagtagcgatct	9	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87150174C>A	ENST00000265724.3	-	23	3121	c.2704G>T	c.(2704-2706)Gaa>Taa	p.E902*	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Nonsense_Mutation_p.E838*	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	902	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.E902*(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CGGAAGTTTTCTATTGCTTCA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											105	95	99					7																	87150174		2203	4300	6503	86988110	SO:0001587	stop_gained	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2704G>T	7.37:g.87150174C>A	ENSP00000265724:p.Glu902*		86988110	A8K294|B5AK60|Q12755|Q14812	Nonsense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	45	11.829727	0.99607	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	.	.	.	5.28	5.28	0.74379	.	0.157536	0.56097	D	0.000034	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-28.0919	18.9356	0.92584	0.0:1.0:0.0:0.0	.	.	.	.	X	683;902;838	.	ENSP00000265724:E902X	E	-	1	0	ABCB1	86988110	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.153000	0.58118	2.467000	0.83353	0.655000	0.94253	GAA		0.398	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87150174	C	A	87150174	4	1	61	1	0	0	0	0	0	1	0	0	40	922	32	2	1166	2	ABCB1	7	87150174	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16416	87150174	71988489	5357	13342										
ABCB1	5243	broad.mit.edu	37	chr7	87165857	87165857	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatcaaaccaactcacatCctgtggcacagaaaatgatt	6	11	3	2	rs41305517		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87165857C>A	ENST00000265724.3	-	21	2815	c.2398G>T	c.(2398-2400)Gat>Tat	p.D800Y	ABCB1_ENST00000543898.1_Splice_Site_p.D736Y	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	800	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.D800Y(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CAACTCACATCCTGTGGCACA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	7											130	119	122					7																	87165857		2203	4300	6503	87003793	SO:0001630	splice_region_variant	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2398-1G>T	7.37:g.87165857C>A			87003793	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935785	0.92458	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.92545	-3.06;-3.06	5.64	5.64	0.86602	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.101468	0.64402	D	0.000003	D	0.97448	0.9165	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.97912	1.0309	10	0.87932	D	0	-28.9982	20.0627	0.97684	0.0:1.0:0.0:0.0	.	736;800	B5AK60;P08183	.;MDR1_HUMAN	Y	581;800;736	ENSP00000265724:D800Y;ENSP00000444095:D736Y	ENSP00000265724:D800Y	D	-	1	0	ABCB1	87003793	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.319000	0.79040	2.807000	0.96579	0.591000	0.81541	GAT		0.453	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	Missense_Mutation	A	87165857	C	A	87165857	5	1	61	1	0	0	0	0	0	0	1	0	40	869	30	2	1480	2	ABCB1	7	87165857	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15683	87165857	71972806	5358	13343										
ABCB1	5243	broad.mit.edu	37	chr7	87183219	87183219	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctttctttatcccaattCttttagcttcttctaaattt	2	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87183219C>A	ENST00000265724.3	-	10	1274	c.857G>T	c.(856-858)aGa>aTa	p.R286I	ABCB1_ENST00000543898.1_Missense_Mutation_p.R222I	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	286	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.R286I(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TATCCCAATTCTTTTAGCTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											168	160	163					7																	87183219		2203	4300	6503	87021155	SO:0001583	missense	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.857G>T	7.37:g.87183219C>A	ENSP00000265724:p.Arg286Ile		87021155	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.200353	0.38905	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.82984	-1.67;-1.67	5.55	3.37	0.38596	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.390808	0.30830	N	0.008792	T	0.80497	0.4634	L	0.41079	1.255	0.53005	D	0.999969	B;P	0.40875	0.032;0.731	B;P	0.51453	0.003;0.67	T	0.77859	-0.2431	10	0.44086	T	0.13	-10.6552	5.4902	0.16771	0.0:0.5921:0.157:0.2509	.	222;286	B5AK60;P08183	.;MDR1_HUMAN	I	67;286;222	ENSP00000265724:R286I;ENSP00000444095:R222I	ENSP00000265724:R286I	R	-	2	0	ABCB1	87021155	0.241000	0.23857	1.000000	0.80357	0.998000	0.95712	0.716000	0.25836	1.478000	0.48253	0.655000	0.94253	AGA		0.353	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87183219	C	A	87183219	3	1	61	1	0	0	0	0	1	0	0	0	40	913	32	2	3065	2	ABCB1	7	87183219	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17362	87183219	71955444	5359	13344										
SLC25A40	55972	broad.mit.edu	37	chr7	87476354	87476354	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactttcttgctgacaaatcGatgcagttccacgtaagaaa	7	9	1	2	rs201629378		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87476354G>A	ENST00000341119.5	-	8	887	c.541C>T	c.(541-543)Cga>Tga	p.R181*		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	181					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.R181*(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					CTGACAAATCGATGCAGTTCC	0.408													G|||	1	0.000199681	0	0	5008	,	,		16040	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	7						G	stop/ARG	0,4406		0,0,2203	152	156	155		541	4.6	0	7		155	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	SLC25A40	NM_018843.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		181/339	87476354	1,13005	2203	4300	6503	87314290	SO:0001587	stop_gained	55972			AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"Solute carriers"	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.541C>T	7.37:g.87476354G>A	ENSP00000344831:p.Arg181*		87314290	A8K483|D6W5P6|Q53GB1|Q9UHR1	Nonsense_Mutation	SNP	ENST00000341119.5	37	CCDS5610.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	38	6.744380	0.97805	0.0	1.16E-4	ENSG00000075303	ENST00000341119	.	.	.	5.54	4.64	0.57946	.	1.312210	0.04912	N	0.453353	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	7.1554	0.25635	0.0697:0.1251:0.6759:0.1294	.	.	.	.	X	181	.	ENSP00000344831:R181X	R	-	1	2	SLC25A40	87314290	0.000000	0.05858	0.030000	0.17652	0.901000	0.52897	-0.018000	0.12568	1.298000	0.44778	0.650000	0.86243	CGA		0.408	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		A	87476354	G	A	87476354	4	1	61	1	0	0	0	0	0	1	0	0	14542	1066	37	1	495	1	SLC25A40	7	87476354	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293135	87476354	71662309	5360	13345										
DBF4	10926	broad.mit.edu	37	chr7	87525823	87525823	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtggtgcacaaaaaacaaGaagtaagtattttgtgatct	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87525823G>T	ENST00000265728.1	+	7	1136	c.632G>T	c.(631-633)aGa>aTa	p.R211I		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	211					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R211I(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				CAAAAAACAAGAAGTAAGTAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	90	90					7																	87525823		2203	4300	6503	87363759	SO:0001583	missense	10926			AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.632G>T	7.37:g.87525823G>T	ENSP00000265728:p.Arg211Ile		87363759	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684860	0.47991	.	.	ENSG00000006634	ENST00000265728	T	0.12361	2.69	5.02	-0.386	0.12466	.	0.482690	0.22565	N	0.058411	T	0.16938	0.0407	L	0.50333	1.59	0.45261	D	0.998262	D	0.56035	0.974	P	0.50896	0.653	T	0.02691	-1.1123	10	0.66056	D	0.02	-9.7966	8.3541	0.32321	0.6722:0.0:0.3278:0.0	.	211	Q9UBU7	DBF4A_HUMAN	I	211	ENSP00000265728:R211I	ENSP00000265728:R211I	R	+	2	0	DBF4	87363759	0.998000	0.40836	0.998000	0.56505	0.941000	0.58515	0.195000	0.17155	0.022000	0.15160	0.591000	0.81541	AGA		0.294	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		T	87525823	G	T	87525823	3	4	61	1	0	0	0	0	1	0	0	0	4254	942	33	2	658	2	DBF4	7	87525823	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49469	87525823	71612840	5361	13346										
DBF4	10926	broad.mit.edu	37	chr7	87536595	87536595	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggaattgcaacatatttCtcagaaagattgccaggaag	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87536595C>A	ENST00000265728.1	+	12	1646	c.1142C>A	c.(1141-1143)tCt>tAt	p.S381Y		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	381					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.S381Y(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				CAACATATTTCTCAGAAAGAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											91	101	97					7																	87536595		2203	4299	6502	87374531	SO:0001583	missense	10926			AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1142C>A	7.37:g.87536595C>A	ENSP00000265728:p.Ser381Tyr		87374531	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	C	8.980	0.975155	0.18736	.	.	ENSG00000006634	ENST00000265728	T	0.36878	1.23	5.66	2.73	0.32206	.	0.400881	0.24258	N	0.040104	T	0.26340	0.0643	L	0.29908	0.895	0.24347	N	0.994932	P;P	0.46277	0.875;0.766	B;B	0.42882	0.401;0.246	T	0.06734	-1.0810	10	0.41790	T	0.15	-1.493	8.8184	0.35009	0.0:0.6371:0.2859:0.077	.	157;381	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	Y	381	ENSP00000265728:S381Y	ENSP00000265728:S381Y	S	+	2	0	DBF4	87374531	0.985000	0.35326	0.779000	0.31741	0.182000	0.23217	1.196000	0.32198	0.274000	0.22072	0.655000	0.94253	TCT		0.373	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		A	87536595	C	A	87536595	3	1	61	1	0	0	0	0	1	0	0	0	4254	913	32	2	1188	2	DBF4	7	87536595	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10772	87536595	71602068	5362	13347										
DBF4	10926	broad.mit.edu	37	chr7	87537311	87537311	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccggtacagtctttactaGacttgtttcagactagtgaa	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87537311G>T	ENST00000265728.1	+	12	2362	c.1858G>T	c.(1858-1860)Gac>Tac	p.D620Y		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	620					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.D620Y(1)|p.D620N(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				GTCTTTACTAGACTTGTTTCA	0.328																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	7											53	58	57					7																	87537311		2203	4298	6501	87375247	SO:0001583	missense	10926			AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1858G>T	7.37:g.87537311G>T	ENSP00000265728:p.Asp620Tyr		87375247	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.502003	0.64298	.	.	ENSG00000006634	ENST00000265728	T	0.34275	1.37	5.13	5.13	0.70059	.	0.273852	0.30556	N	0.009372	T	0.44808	0.1311	L	0.27053	0.805	0.36640	D	0.876785	D;D	0.71674	0.998;0.996	D;P	0.65573	0.936;0.862	T	0.54569	-0.8274	10	0.72032	D	0.01	-5.5978	13.3965	0.60856	0.0:0.1572:0.8428:0.0	.	396;620	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	Y	620	ENSP00000265728:D620Y	ENSP00000265728:D620Y	D	+	1	0	DBF4	87375247	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.654000	0.61469	2.386000	0.81285	0.650000	0.86243	GAC		0.328	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		T	87537311	G	T	87537311	3	4	61	1	0	0	0	0	1	0	0	0	4254	942	33	2	1904	2	DBF4	7	87537311	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	716	87537311	71601352	5363	13348										
ADAM22	53616	broad.mit.edu	37	chr7	87763720	87763720	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtattatctcagacaaaaGaaagttagcaagtggtaagt	10	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87763720G>T	ENST00000265727.7	+	13	1233	c.1154G>T	c.(1153-1155)aGa>aTa	p.R385I	ADAM22_ENST00000315984.7_Missense_Mutation_p.R385I|ADAM22_ENST00000398201.4_Missense_Mutation_p.R385I|ADAM22_ENST00000398204.4_Missense_Mutation_p.R385I|ADAM22_ENST00000398209.3_Missense_Mutation_p.R385I			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	385	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R385I(2)		endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TCAGACAAAAGAAAGTTAGCA	0.284																																																2	Substitution - Missense(2)	large_intestine(2)	7											84	83	84					7																	87763720		1802	4065	5867	87601656	SO:0001583	missense	53616			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1154G>T	7.37:g.87763720G>T	ENSP00000265727:p.Arg385Ile		87601656	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	37	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225094	0.39300	.	.	ENSG00000008277	ENST00000398204;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.56	3.7	0.42460	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.152198	0.64402	D	0.000013	T	0.41096	0.1144	N	0.12746	0.255	0.58432	D	0.999995	B;B;B;B	0.28055	0.199;0.166;0.199;0.043	B;B;B;B	0.26094	0.066;0.039;0.066;0.033	T	0.20140	-1.0284	10	0.38643	T	0.18	.	9.5513	0.39313	0.0707:0.2729:0.6564:0.0	.	437;385;385;385	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2	.;.;ADA22_HUMAN;.	I	385;385;385;385;385;352	ENSP00000381262:R385I;ENSP00000381260:R385I;ENSP00000265727:R385I;ENSP00000315900:R385I;ENSP00000381267:R385I;ENSP00000381261:R352I	ENSP00000265727:R385I	R	+	2	0	ADAM22	87601656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.509000	0.60448	0.670000	0.31165	0.650000	0.86243	AGA		0.284	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87763720	G	T	87763720	3	4	61	1	0	0	0	0	1	0	0	0	244	942	33	2	1204	2	ADAM22	7	87763720	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226409	87763720	71374943	5364	13349										
ADAM22	53616	broad.mit.edu	37	chr7	87782624	87782624	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaagacaaagacacatgGatacagtgcaacaaacggtg	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87782624G>T	ENST00000265727.7	+	21	1849	c.1770G>T	c.(1768-1770)tgG>tgT	p.W590C	ADAM22_ENST00000315984.7_Missense_Mutation_p.W590C|ADAM22_ENST00000398201.4_Missense_Mutation_p.W590C|ADAM22_ENST00000398204.4_Missense_Mutation_p.W590C|ADAM22_ENST00000398209.3_Missense_Mutation_p.W590C			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	590	Cys-rich.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.W590C(2)		endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AAGACACATGGATACAGTGCA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	7											116	118	117					7																	87782624		2003	4168	6171	87620560	SO:0001583	missense	53616			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1770G>T	7.37:g.87782624G>T	ENSP00000265727:p.Trp590Cys		87620560	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	37	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325140	0.81580	.	.	ENSG00000008277	ENST00000398204;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	5.7	5.7	0.88788	ADAM, cysteine-rich (2);	0.057724	0.85682	D	0.000000	T	0.51686	0.1689	M	0.81239	2.535	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	T	0.54410	-0.8298	10	0.87932	D	0	.	18.5979	0.91235	0.0:0.0:1.0:0.0	.	642;590;590;590	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2	.;.;ADA22_HUMAN;.	C	590;590;590;590;590;557	ENSP00000381262:W590C;ENSP00000381260:W590C;ENSP00000265727:W590C;ENSP00000315900:W590C;ENSP00000381267:W590C;ENSP00000381261:W557C	ENSP00000265727:W590C	W	+	3	0	ADAM22	87620560	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.286000	0.95898	2.688000	0.91661	0.655000	0.94253	TGG		0.428	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87782624	G	T	87782624	3	4	61	1	0	0	0	0	1	0	0	0	244	1183	41	2	1852	2	ADAM22	7	87782624	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18904	87782624	71356039	5365	13350										
ADAM22	53616	broad.mit.edu	37	chr7	87785260	87785260	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaatatcccaaggcttggaGaactcgatggtgaaatcaca	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87785260G>A	ENST00000265727.7	+	22	1925	c.1846G>A	c.(1846-1848)Gaa>Aaa	p.E616K	ADAM22_ENST00000315984.7_Missense_Mutation_p.E616K|ADAM22_ENST00000398201.4_Missense_Mutation_p.E616K|ADAM22_ENST00000398204.4_Missense_Mutation_p.E616K|ADAM22_ENST00000398209.3_Missense_Mutation_p.E616K			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	616	Cys-rich.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E616K(2)		endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AAGGCTTGGAGAACTCGATGG	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	7											210	198	202					7																	87785260		1862	4108	5970	87623196	SO:0001583	missense	53616			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1846G>A	7.37:g.87785260G>A	ENSP00000265727:p.Glu616Lys		87623196	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	37	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.800686	0.90538	.	.	ENSG00000008277	ENST00000398204;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96	5.35	5.35	0.76521	ADAM, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.39118	0.1066	L	0.43701	1.375	0.80722	D	1	B;B;B;D	0.64830	0.312;0.266;0.312;0.994	B;B;B;D	0.77557	0.15;0.093;0.15;0.99	T	0.01819	-1.1267	10	0.27082	T	0.32	.	18.169	0.89739	0.0:0.0:1.0:0.0	.	668;616;616;616	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2	.;.;ADA22_HUMAN;.	K	616;616;616;616;616;583	ENSP00000381262:E616K;ENSP00000381260:E616K;ENSP00000265727:E616K;ENSP00000315900:E616K;ENSP00000381267:E616K;ENSP00000381261:E583K	ENSP00000265727:E616K	E	+	1	0	ADAM22	87623196	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.700000	0.91322	2.650000	0.89964	0.655000	0.94253	GAA		0.363	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		A	87785260	G	A	87785260	3	1	61	1	0	0	0	0	1	0	0	0	244	943	33	3	1932	3	ADAM22	7	87785260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2636	87785260	71353403	5366	13351										
SRI	6717	broad.mit.edu	37	chr7	87838696	87838696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcaggcgatgtagtcgtCgaaggtgatctttccattgg	14	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87838696C>T	ENST00000265729.2	-	6	521	c.469G>A	c.(469-471)Gac>Aac	p.D157N	SRI_ENST00000394641.3_Missense_Mutation_p.D142N|SRI_ENST00000419179.1_Missense_Mutation_p.D117N|SRI_ENST00000490437.1_Missense_Mutation_p.D114N|SRI_ENST00000431660.1_Missense_Mutation_p.D142N	NM_003130.3	NP_003121.1	P30626	SORCN_HUMAN	sorcin	157	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				action potential (GO:0001508)|calcium ion transport (GO:0006816)|cytoplasmic sequestering of transcription factor (GO:0042994)|heart development (GO:0007507)|intracellular sequestering of iron ion (GO:0006880)|muscle organ development (GO:0007517)|negative regulation of heart rate (GO:0010459)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|proteolysis (GO:0006508)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart contraction (GO:0008016)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of relaxation of muscle (GO:1901077)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of striated muscle contraction (GO:0006942)|signal transduction (GO:0007165)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|ion channel binding (GO:0044325)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)	p.D157N(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(14;0.00202)					ATGTAGTCGTCGAAGGTGATC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											185	153	164					7																	87838696		2203	4300	6503	87676632	SO:0001583	missense	6717			M32886	CCDS5612.1, CCDS47638.1, CCDS59063.1	7q21.1	2014-09-17			ENSG00000075142	ENSG00000075142		"EF-hand domain containing"	11292	protein-coding gene	gene with protein product		182520				2901906	Standard	NM_001256891		Approved		uc003ujq.2	P30626	OTTHUMG00000157267	ENST00000265729.2:c.469G>A	7.37:g.87838696C>T	ENSP00000265729:p.Asp157Asn		87676632	A8MTH6|B4DKK2|D6W5Q0	Missense_Mutation	SNP	ENST00000265729.2	37	CCDS5612.1	.	.	.	.	.	.	.	.	.	.	C	36	5.789257	0.96945	.	.	ENSG00000075142	ENST00000265729;ENST00000419179;ENST00000490437;ENST00000394641;ENST00000431660	T;T;T;T;T	0.73469	-0.75;0.81;-0.75;-0.75;-0.75	5.87	5.87	0.94306	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.87767	0.6260	M	0.81802	2.56	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.966;1.0;1.0;1.0	D	0.87800	0.2624	10	0.62326	D	0.03	.	20.1861	0.98216	0.0:1.0:0.0:0.0	.	142;117;114;142;157	B4DKK2;B4DHQ6;C9J0K6;A8MTH6;P30626	.;.;.;.;SORCN_HUMAN	N	157;117;114;142;142	ENSP00000265729:D157N;ENSP00000397609:D117N;ENSP00000418512:D114N;ENSP00000378137:D142N;ENSP00000391148:D142N	ENSP00000265729:D157N	D	-	1	0	SRI	87676632	1.000000	0.71417	0.984000	0.44739	0.973000	0.67179	7.729000	0.84864	2.774000	0.95407	0.655000	0.94253	GAC		0.433	SRI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253680.1	NM_003130		T	87838696	C	T	87838696	3	4	61	1	0	0	0	0	1	0	0	0	15188	884	31	1	139	1	SRI	7	87838696	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53436	87838696	71299967	5367	13352										
STEAP4	79689	broad.mit.edu	37	chr7	87912071	87912071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaccaagccaagctgctttCggcaaagcatccagtggtca	9	13	1	0	rs377052757		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87912071C>T	ENST00000380079.4	-	3	970	c.869G>A	c.(868-870)cGa>cAa	p.R290Q	AC003991.3_ENST00000434733.1_RNA|AC003991.3_ENST00000447758.1_RNA|STEAP4_ENST00000414498.1_Missense_Mutation_p.R290Q|STEAP4_ENST00000301959.5_Intron|AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000600908.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	290	Ferric oxidoreductase.				copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)	p.R290Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					AAGCTGCTTTCGGCAAAGCAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	GLN/ARG,GLN/ARG,	0,3964		0,0,1982	76	75	75		869,869,	6.1	1	7		75	1,8311		0,1,4155	no	missense,missense,intron	STEAP4	NM_001205315.1,NM_024636.3,NM_001205316.1	43,43,	0,1,6137	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging,	290/460,290/460,	87912071	1,12275	1982	4156	6138	87750007	SO:0001583	missense	79689			AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.869G>A	7.37:g.87912071C>T	ENSP00000369419:p.Arg290Gln		87750007	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Missense_Mutation	SNP	ENST00000380079.4	37	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	C	36	5.693123	0.96793	0.0	1.2E-4	ENSG00000127954	ENST00000380079;ENST00000414498	D;D	0.92595	-3.07;-3.07	6.08	6.08	0.98989	Flavoprotein transmembrane component (1);	0.000000	0.85682	D	0.000000	D	0.97210	0.9088	M	0.91090	3.175	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97158	0.9836	10	0.87932	D	0	-12.647	20.6721	0.99693	0.0:1.0:0.0:0.0	.	290;290	C9JS50;Q687X5	.;STEA4_HUMAN	Q	290	ENSP00000369419:R290Q;ENSP00000394399:R290Q	ENSP00000369419:R290Q	R	-	2	0	STEAP4	87750007	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.818000	0.86416	2.894000	0.99253	0.591000	0.81541	CGA		0.473	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		T	87912071	C	T	87912071	3	4	61	1	0	0	0	0	1	0	0	0	15319	884	31	1	522	1	STEAP4	7	87912071	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73375	87912071	71226592	5368	13353										
STEAP4	79689	broad.mit.edu	37	chr7	87912292	87912292	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtctcttataacacaataGaaaaacaagaagacacacag	5	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:87912292G>T	ENST00000380079.4	-	3	749	c.648C>A	c.(646-648)ttC>ttA	p.F216L	AC003991.3_ENST00000434733.1_RNA|AC003991.3_ENST00000447758.1_RNA|STEAP4_ENST00000414498.1_Missense_Mutation_p.F216L|STEAP4_ENST00000301959.5_Intron|AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000600908.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	216					copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)	p.F216L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					TAACACAATAGAAAAACAAGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											85	82	82					7																	87912292		1887	4108	5995	87750228	SO:0001583	missense	79689			AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.648C>A	7.37:g.87912292G>T	ENSP00000369419:p.Phe216Leu		87750228	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Missense_Mutation	SNP	ENST00000380079.4	37	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	G	0.266	-0.995927	0.02145	.	.	ENSG00000127954	ENST00000380079;ENST00000414498	T;T	0.07567	3.51;3.18	6.08	2.9	0.33743	.	0.565371	0.22033	N	0.065575	T	0.02807	0.0084	N	0.10707	0.03	0.35501	D	0.799771	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.34204	-0.9838	10	0.02654	T	1	-0.3657	3.818	0.08824	0.126:0.272:0.4703:0.1317	.	216;216	C9JS50;Q687X5	.;STEA4_HUMAN	L	216	ENSP00000369419:F216L;ENSP00000394399:F216L	ENSP00000369419:F216L	F	-	3	2	STEAP4	87750228	1.000000	0.71417	0.981000	0.43875	0.316000	0.28119	0.770000	0.26618	1.545000	0.49373	0.591000	0.81541	TTC		0.368	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		T	87912292	G	T	87912292	3	4	61	1	0	0	0	0	1	0	0	0	15319	933	33	2	743	2	STEAP4	7	87912292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	221	87912292	71226371	5369	13354										
ZNF804B	219578	broad.mit.edu	37	chr7	88962858	88962858	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggtccaccatgccaaatCgacaccaattacaatcagac	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:88962858C>T	ENST00000333190.4	+	4	1171	c.562C>T	c.(562-564)Cga>Tga	p.R188*		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	188							metal ion binding (GO:0046872)	p.R188*(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CATGCCAAATCGACACCAATT	0.418										HNSCC(36;0.09)																																						1	Substitution - Nonsense(1)	large_intestine(1)	7											115	111	112					7																	88962858		2203	4300	6503	88800794	SO:0001587	stop_gained	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.562C>T	7.37:g.88962858C>T	ENSP00000329638:p.Arg188*		88800794	B2RTV2|Q7Z714|Q96MN7	Nonsense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	40	8.148229	0.98678	.	.	ENSG00000182348	ENST00000333190	.	.	.	5.3	4.4	0.53042	.	0.129990	0.33938	N	0.004408	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2873	12.2014	0.54328	0.5044:0.4956:0.0:0.0	.	.	.	.	X	188	.	ENSP00000329638:R188X	R	+	1	2	ZNF804B	88800794	0.025000	0.19082	0.909000	0.35828	0.973000	0.67179	0.855000	0.27805	1.437000	0.47472	0.650000	0.86243	CGA		0.418	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88962858	C	T	88962858	4	4	61	1	0	0	0	0	0	1	0	0	18210	876	31	1	576	1	ZNF804B	7	88962858	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1050566	88962858	70175805	5370	13355										
ZNF804B	219578	broad.mit.edu	37	chr7	88962921	88962921	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtactgcaaacatcttcaGatctcagcaatgcaaatcac	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:88962921G>T	ENST00000333190.4	+	4	1234	c.625G>T	c.(625-627)Gat>Tat	p.D209Y		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	209							metal ion binding (GO:0046872)	p.D209Y(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AACATCTTCAGATCTCAGCAA	0.388										HNSCC(36;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	7											93	91	92					7																	88962921		2203	4300	6503	88800857	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.625G>T	7.37:g.88962921G>T	ENSP00000329638:p.Asp209Tyr		88800857	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	g	9.898	1.205992	0.22205	.	.	ENSG00000182348	ENST00000333190	T	0.05786	3.39	5.3	-0.631	0.11526	.	0.547615	0.17710	N	0.164625	T	0.04543	0.0124	L	0.44542	1.39	0.09310	N	0.999999	B	0.25048	0.117	B	0.21546	0.035	T	0.35425	-0.9789	10	0.39692	T	0.17	-1.0691	1.7839	0.03038	0.3894:0.0993:0.3443:0.167	.	209	A4D1E1	Z804B_HUMAN	Y	209	ENSP00000329638:D209Y	ENSP00000329638:D209Y	D	+	1	0	ZNF804B	88800857	0.410000	0.25376	0.903000	0.35520	0.922000	0.55478	0.353000	0.20130	-0.302000	0.08869	-0.127000	0.14921	GAT		0.388	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88962921	G	T	88962921	3	4	61	1	0	0	0	0	1	0	0	0	18210	942	33	2	639	2	ZNF804B	7	88962921	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63	88962921	70175742	5371	13356										
ZNF804B	219578	broad.mit.edu	37	chr7	88966213	88966213	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaaatccagccacaacttCtatcatccacttgaatcctt	2	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:88966213C>A	ENST00000333190.4	+	4	4526	c.3917C>A	c.(3916-3918)tCt>tAt	p.S1306Y		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1306							metal ion binding (GO:0046872)	p.S1306Y(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GCCACAACTTCTATCATCCAC	0.433										HNSCC(36;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	7											182	179	180					7																	88966213		2203	4300	6503	88804149	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3917C>A	7.37:g.88966213C>A	ENSP00000329638:p.Ser1306Tyr		88804149	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480468	0.63849	.	.	ENSG00000182348	ENST00000333190	T	0.07688	3.17	5.5	4.59	0.56863	.	0.094804	0.47455	D	0.000231	T	0.24509	0.0594	L	0.60455	1.87	0.31672	N	0.64425	D	0.76494	0.999	D	0.68192	0.956	T	0.01440	-1.1354	10	0.87932	D	0	-16.4743	15.9404	0.79750	0.135:0.865:0.0:0.0	.	1306	A4D1E1	Z804B_HUMAN	Y	1306	ENSP00000329638:S1306Y	ENSP00000329638:S1306Y	S	+	2	0	ZNF804B	88804149	0.994000	0.37717	0.977000	0.42913	0.929000	0.56500	5.022000	0.64078	2.854000	0.98071	0.655000	0.94253	TCT		0.433	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88966213	C	A	88966213	3	1	61	1	0	0	0	0	1	0	0	0	18210	913	32	2	3931	2	ZNF804B	7	88966213	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3292	88966213	70172450	5372	13357										
STEAP1	26872	broad.mit.edu	37	chr7	89790367	89790367	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttttataaaattccaatCctggtcatcaacaaagtctt	3	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89790367C>A	ENST00000297205.2	+	3	533	c.333C>A	c.(331-333)atC>atA	p.I111I	STEAP2-AS1_ENST00000478318.2_RNA	NM_012449.2	NP_036581.1	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the prostate 1	111					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|transmembrane transport (GO:0055085)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	channel activity (GO:0015267)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|transporter activity (GO:0005215)	p.I111I(1)		kidney(2)|large_intestine(3)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	14	all_hematologic(106;0.112)					AAATTCCAATCCTGGTCATCA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											62	64	64					7																	89790367		2203	4296	6499	89628303	SO:0001819	synonymous_variant	26872			AF186249	CCDS5614.1	7q21	2011-08-31	2005-02-21	2005-02-24	ENSG00000164647	ENSG00000164647		"Serine peptidases / Serine peptidases"	11378	protein-coding gene	gene with protein product		604415	"six transmembrane epithelial antigen of the prostate"	STEAP			Standard	NM_012449		Approved	PRSS24	uc003ujx.3	Q9UHE8	OTTHUMG00000023006	ENST00000297205.2:c.333C>A	7.37:g.89790367C>A			89628303	A4D1E0|O95034	Silent	SNP	ENST00000297205.2	37	CCDS5614.1																																																																																				0.388	STEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059327.3	NM_012449		A	89790367	C	A	89790367	2	1	61	1	0	0	0	0	0	0	0	1	15316	845	30	2		2	STEAP1	7	89790367	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	824154	89790367	69348296	5373	13358										
STEAP2	261729	broad.mit.edu	37	chr7	89854682	89854682	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgttgctatacacagaGaacattatacctccctgtgg	7	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89854682G>T	ENST00000287908.3	+	2	679	c.286G>T	c.(286-288)Gaa>Taa	p.E96*	STEAP2_ENST00000394622.2_Nonsense_Mutation_p.E96*|STEAP2_ENST00000402625.2_Nonsense_Mutation_p.E96*|STEAP2_ENST00000394632.1_Nonsense_Mutation_p.E96*|STEAP2_ENST00000394621.2_Nonsense_Mutation_p.E96*|STEAP2_ENST00000394629.2_Nonsense_Mutation_p.E96*|STEAP2_ENST00000394626.1_Nonsense_Mutation_p.E96*	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	96					copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.E96*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					TATACACAGAGAACATTATAC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											139	133	135					7																	89854682		2203	4300	6503	89692618	SO:0001587	stop_gained	261729			AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"prostate cancer associated protein 1", "six transmembrane epithelial antigen of the prostate 2"	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.286G>T	7.37:g.89854682G>T	ENSP00000287908:p.Glu96*		89692618	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Nonsense_Mutation	SNP	ENST00000287908.3	37	CCDS5615.1	.	.	.	.	.	.	.	.	.	.	G	35	5.414312	0.96092	.	.	ENSG00000157214	ENST00000428074;ENST00000287908;ENST00000394626;ENST00000394622;ENST00000394632;ENST00000394624;ENST00000394621;ENST00000402625;ENST00000394629	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-17.9308	20.1142	0.97922	0.0:0.0:1.0:0.0	.	.	.	.	X	96	.	ENSP00000287908:E96X	E	+	1	0	STEAP2	89692618	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.862000	0.87013	2.765000	0.95021	0.650000	0.86243	GAA		0.383	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999		T	89854682	G	T	89854682	4	4	61	1	0	0	0	0	0	1	0	0	15317	943	33	2	288	2	STEAP2	7	89854682	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64315	89854682	69283981	5374	13359										
C7orf63	79846	broad.mit.edu	37	chr7	89900867	89900867	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagcgagttcatcatacaAgattcaaatggctgaagttg	10	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89900867A>C	ENST00000389297.4	+	7	811	c.560A>C	c.(559-561)aAg>aCg	p.K187T	C7orf63_ENST00000316089.8_Missense_Mutation_p.K187T|C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000497910.1_Missense_Mutation_p.K169T|AC002064.4_ENST00000420245.1_RNA	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		187								p.K187T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TCATCATACAAGATTCAAATG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	98	100					7																	89900867		1852	4097	5949	89738803	SO:0001583	missense	79846																														ENST00000389297.4:c.560A>C	7.37:g.89900867A>C	ENSP00000373948:p.Lys187Thr		89738803	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	A	20.9	4.067207	0.76301	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000457170	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	6.11	6.11	0.99139	.	0.110364	0.64402	D	0.000013	T	0.66268	0.2772	M	0.76002	2.32	0.43069	D	0.994708	D;D;D	0.89917	0.963;0.992;1.0	P;P;D	0.91635	0.631;0.73;0.999	T	0.69705	-0.5073	10	0.72032	D	0.01	-12.3223	16.7021	0.85357	1.0:0.0:0.0:0.0	.	169;187;185	A5D8W1-5;A5D8W1;A5D8W1-4	.;CG063_HUMAN;.	T	187;187;169;127	ENSP00000373948:K187T;ENSP00000321753:K187T;ENSP00000419549:K169T;ENSP00000392365:K127T	ENSP00000321753:K187T	K	+	2	0	C7orf63	89738803	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.617000	0.67716	2.343000	0.79666	0.533000	0.62120	AAG		0.333	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			C	89900867	A	C	89900867	3	2	61	1	0	0	0	0	1	0	0	0	2415	72	3	4	586	4	C7orf63	7	89900867	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	46185	89900867	69237796	5375	13360										
C7orf63	79846	broad.mit.edu	37	chr7	89901131	89901131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgatgaaagcacaagcagCcagtggaatctgtactcacc	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89901131C>A	ENST00000389297.4	+	8	970	c.719C>A	c.(718-720)gCc>gAc	p.A240D	C7orf63_ENST00000316089.8_Missense_Mutation_p.A240D|C7orf63_ENST00000463311.1_Intron|C7orf63_ENST00000497910.1_Missense_Mutation_p.A222D|AC002064.4_ENST00000420245.1_RNA	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		240								p.A240D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GCACAAGCAGCCAGTGGAATC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	7											25	25	25					7																	89901131		1806	4055	5861	89739067	SO:0001583	missense	79846																														ENST00000389297.4:c.719C>A	7.37:g.89901131C>A	ENSP00000373948:p.Ala240Asp		89739067	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.650939|4.650939	0.87958|0.87958	.|.	.|.	ENSG00000105792|ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000457170|ENST00000418199	T;T;T;T|.	0.50001|.	0.77;0.77;0.76;0.77|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78910|0.78910	0.4358|0.4358	M|M	0.78049|0.78049	2.395|2.395	0.53005|0.53005	D|D	0.999965|0.999965	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.75020|.	0.985;0.982|.	T|T	0.77576|0.77576	-0.2536|-0.2536	10|5	0.66056|.	D|.	0.02|.	-6.5983|-6.5983	20.1454|20.1454	0.98074|0.98074	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	222;240|.	A5D8W1-5;A5D8W1|.	.;CG063_HUMAN|.	D|T	240;240;222;180|42	ENSP00000373948:A240D;ENSP00000321753:A240D;ENSP00000419549:A222D;ENSP00000392365:A180D|.	ENSP00000321753:A240D|.	A|P	+|+	2|1	0|0	C7orf63|C7orf63	89739067|89739067	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.276000|6.276000	0.72601|0.72601	2.748000|2.748000	0.94277|0.94277	0.650000|0.650000	0.86243|0.86243	GCC|CCA		0.313	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			A	89901131	C	A	89901131	3	1	61	1	0	0	0	0	1	0	0	0	2415	739	26	2	749	2	C7orf63	7	89901131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	264	89901131	69237532	5376	13361										
C7orf63	79846	broad.mit.edu	37	chr7	89929334	89929334	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggagaaaggaggaaaaaGaactaggagtaaaacgtgat	14	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89929334G>T	ENST00000389297.4	+	17	2262	c.2011G>T	c.(2011-2013)Gaa>Taa	p.E671*	C7orf63_ENST00000316089.8_Nonsense_Mutation_p.E671*|C7orf63_ENST00000497910.1_Nonsense_Mutation_p.E653*	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		671								p.E671*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GGAGGAAAAAGAACTAGGAGT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											86	84	85					7																	89929334		1815	4081	5896	89767270	SO:0001587	stop_gained	79846																														ENST00000389297.4:c.2011G>T	7.37:g.89929334G>T	ENSP00000373948:p.Glu671*		89767270	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Nonsense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876121	0.72180	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	.	.	.	5.81	4.92	0.64577	.	0.245199	0.40064	N	0.001184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-26.6468	15.1734	0.72894	0.0683:0.0:0.9317:0.0	.	.	.	.	X	671;671;653;254	.	ENSP00000321753:E671X	E	+	1	0	C7orf63	89767270	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.799000	0.69101	2.746000	0.94184	0.655000	0.94253	GAA		0.323	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			T	89929334	G	T	89929334	4	4	61	1	0	0	0	0	0	1	0	0	2415	943	33	2	2077	2	C7orf63	7	89929334	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28203	89929334	69209329	5377	13362										
C7orf63	79846	broad.mit.edu	37	chr7	89939470	89939470	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacggatattgctcttaaaaAactgcccattcgaggaggag	10	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:89939470A>C	ENST00000389297.4	+	23	2995	c.2744A>C	c.(2743-2745)aAa>aCa	p.K915T	C7orf63_ENST00000316089.8_Missense_Mutation_p.K869T|AC002064.5_ENST00000445784.1_lincRNA|C7orf63_ENST00000497910.1_Missense_Mutation_p.K897T	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		915								p.K869T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GCTCTTAAAAAACTGCCCATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											110	102	105					7																	89939470		1884	4105	5989	89777406	SO:0001583	missense	79846																														ENST00000389297.4:c.2744A>C	7.37:g.89939470A>C	ENSP00000373948:p.Lys915Thr		89777406	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.21|14.21	2.468540|2.468540	0.43839|0.43839	.|.	.|.	ENSG00000105792|ENSG00000105792	ENST00000412839;ENST00000445156|ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	T;T|T;T;T;T	0.58358|0.26067	0.34;0.4|2.34;2.33;2.34;1.76	5.83|5.83	0.503|0.503	0.16940|0.16940	.|.	0.219974|0.219974	0.39341|0.39341	N|N	0.001395|0.001395	T|T	0.18923|0.18923	0.0454|0.0454	L|L	0.50919|0.50919	1.6|1.6	0.28625|0.28625	N|N	0.907969|0.907969	.|B;B	.|0.23990	.|0.095;0.061	.|B;B	.|0.20184	.|0.017;0.028	T|T	0.11891|0.11891	-1.0569|-1.0569	8|10	0.87932|0.54805	D|T	0|0.06	-10.4608|-10.4608	5.322|5.322	0.15885|0.15885	0.4617:0.151:0.3873:0.0|0.4617:0.151:0.3873:0.0	.|.	.|897;915	.|A5D8W1-5;A5D8W1	.|.;CG063_HUMAN	N|T	143;66|915;869;897;452	ENSP00000415818:K143N;ENSP00000414772:K66N|ENSP00000373948:K915T;ENSP00000321753:K869T;ENSP00000419549:K897T;ENSP00000391571:K452T	ENSP00000415818:K143N|ENSP00000321753:K869T	K|K	+|+	3|2	2|0	C7orf63|C7orf63	89777406|89777406	0.247000|0.247000	0.23920|0.23920	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	0.623000|0.623000	0.24447|0.24447	0.462000|0.462000	0.27095|0.27095	0.533000|0.533000	0.62120|0.62120	AAA|AAA		0.438	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			C	89939470	A	C	89939470	3	2	61	1	0	0	0	0	1	0	0	0	2415	14	1	4	2834	4	C7orf63	7	89939470	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10136	89939470	69199193	5378	13363										
GTPBP10	85865	broad.mit.edu	37	chr7	90014304	90014304	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactggagaaggaatcgaaGaattaaagaattgtataaga	10	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:90014304G>A	ENST00000222511.6	+	10	1066	c.1000G>A	c.(1000-1002)Gaa>Aaa	p.E334K	GTPBP10_ENST00000257659.8_Missense_Mutation_p.E255K	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	334	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)	p.E334K(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						AGGAATCGAAGAATTAAAGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											103	102	103					7																	90014304		2203	4300	6503	89852240	SO:0001583	missense	85865				CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.1000G>A	7.37:g.90014304G>A	ENSP00000222511:p.Glu334Lys		89852240	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	37	CCDS5617.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149805	0.57151	.	.	ENSG00000105793	ENST00000257659;ENST00000222511	T;T	0.19394	2.15;2.15	5.74	4.87	0.63330	.	0.437829	0.28082	N	0.016675	T	0.26122	0.0637	M	0.83012	2.62	0.80722	D	1	B;B	0.28258	0.023;0.205	B;B	0.18263	0.016;0.021	T	0.04216	-1.0968	9	.	.	.	-11.7086	10.566	0.45173	0.1456:0.0:0.8544:0.0	.	255;334	A4D1E9-2;A4D1E9	.;GTPBA_HUMAN	K	255;334	ENSP00000257659:E255K;ENSP00000222511:E334K	.	E	+	1	0	GTPBP10	89852240	0.983000	0.35010	0.978000	0.43139	0.952000	0.60782	2.189000	0.42621	1.424000	0.47217	0.655000	0.94253	GAA		0.358	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107		A	90014304	G	A	90014304	3	1	61	1	0	0	0	0	1	0	0	0	6900	943	33	3	1038	3	GTPBP10	7	90014304	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74834	90014304	69124359	5379	13364										
CLDN12	9069	broad.mit.edu	37	chr7	90042592	90042592	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtattgtacatgcaaatCtttgccttctcctttctggc	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:90042592C>A	ENST00000287916.4	+	3	889	c.602C>A	c.(601-603)tCt>tAt	p.S201Y	CTB-13L3.1_ENST00000480135.1_RNA|CLDN12_ENST00000394605.2_Missense_Mutation_p.S201Y|CLDN12_ENST00000535571.1_Missense_Mutation_p.S201Y	NM_001185073.2|NM_012129.4	NP_001172002.1|NP_036261.1	P56749	CLD12_HUMAN	claudin 12	201					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.S201Y(1)		breast(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)	15						ACATGCAAATCTTTGCCTTCT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											213	206	208					7																	90042592		2203	4300	6503	89880528	SO:0001583	missense	9069			AJ250713	CCDS5618.1	7q21	2008-07-18			ENSG00000157224	ENSG00000157224		"Claudins"	2034	protein-coding gene	gene with protein product		611232					Standard	NM_001185072		Approved		uc003ukr.3	P56749	OTTHUMG00000156612	ENST00000287916.4:c.602C>A	7.37:g.90042592C>A	ENSP00000287916:p.Ser201Tyr		89880528	D6W5Q4|Q7LDZ0	Missense_Mutation	SNP	ENST00000287916.4	37	CCDS5618.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.382338	0.42207	.	.	ENSG00000157224	ENST00000496677;ENST00000287916;ENST00000535571;ENST00000394605	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.45	5.45	0.79879	.	0.307999	0.35585	N	0.003120	T	0.64011	0.2560	N	0.19112	0.55	0.41404	D	0.987691	P	0.37276	0.589	B	0.38056	0.264	T	0.69472	-0.5136	10	0.72032	D	0.01	-20.1441	16.0609	0.80838	0.0:0.8569:0.1431:0.0	.	201	P56749	CLD12_HUMAN	Y	201	ENSP00000419053:S201Y;ENSP00000287916:S201Y;ENSP00000443476:S201Y;ENSP00000378103:S201Y	ENSP00000287916:S201Y	S	+	2	0	CLDN12	89880528	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.475000	0.53136	2.838000	0.97847	0.655000	0.94253	TCT		0.438	CLDN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059221.1	NM_012129		A	90042592	C	A	90042592	3	1	61	1	0	0	0	0	1	0	0	0	3480	913	32	2	604	2	CLDN12	7	90042592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28288	90042592	69096071	5380	13365										
MTERF	7978	broad.mit.edu	37	chr7	91503015	91503015	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccagcatttaccaattCtttgattcgactttttaaag	5	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91503015C>A	ENST00000351870.3	-	3	1186	c.1093G>T	c.(1093-1095)Gaa>Taa	p.E365*	MTERF_ENST00000419292.1_Nonsense_Mutation_p.E345*|MTERF_ENST00000406735.2_Nonsense_Mutation_p.E345*	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		365					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.E365*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			TTTACCAATTCTTTGATTCGA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											85	84	84					7																	91503015		2202	4300	6502	91340951	SO:0001587	stop_gained	7978																														ENST00000351870.3:c.1093G>T	7.37:g.91503015C>A	ENSP00000248643:p.Glu365*		91340951	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Nonsense_Mutation	SNP	ENST00000351870.3	37	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446783	0.84101	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735	.	.	.	4.89	4.89	0.63831	.	0.230728	0.33290	N	0.005069	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-8.5804	17.7051	0.88306	0.0:1.0:0.0:0.0	.	.	.	.	X	345;365;345	.	ENSP00000248643:E365X	E	-	1	0	MTERF	91340951	1.000000	0.71417	0.910000	0.35882	0.804000	0.45430	6.749000	0.74883	2.652000	0.90054	0.591000	0.81541	GAA		0.323	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			A	91503015	C	A	91503015	4	1	61	1	0	0	0	0	0	1	0	0	9948	922	32	2	110	2	MTERF	7	91503015	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1460423	91503015	67635648	5381	13366										
MTERF	7978	broad.mit.edu	37	chr7	91503330	91503330	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaaattgaaagttgaccGtaagaattcaatgttagctt	8	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91503330G>A	ENST00000351870.3	-	3	871	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W	MTERF_ENST00000481516.1_5'Flank|MTERF_ENST00000419292.1_Missense_Mutation_p.R240W|MTERF_ENST00000406735.2_Missense_Mutation_p.R240W	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		260					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.R260W(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			AAAGTTGACCGTAAGAATTCA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											50	51	51					7																	91503330		2203	4300	6503	91341266	SO:0001583	missense	7978																														ENST00000351870.3:c.778C>T	7.37:g.91503330G>A	ENSP00000248643:p.Arg260Trp		91341266	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Missense_Mutation	SNP	ENST00000351870.3	37	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304974	0.60305	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735	T;T;T	0.13420	2.59;2.59;2.59	4.83	3.86	0.44501	.	0.278953	0.29185	N	0.012898	T	0.11537	0.0281	N	0.19112	0.55	0.19300	N	0.999976	D	0.64830	0.994	P	0.45558	0.485	T	0.11567	-1.0582	10	0.72032	D	0.01	-2.0299	13.4966	0.61430	0.0:0.0:0.8426:0.1573	.	260	Q99551	MTERF_HUMAN	W	240;260;240	ENSP00000414116:R240W;ENSP00000248643:R260W;ENSP00000384986:R240W	ENSP00000248643:R260W	R	-	1	2	MTERF	91341266	0.999000	0.42202	1.000000	0.80357	0.954000	0.61252	3.194000	0.51005	2.613000	0.88420	0.585000	0.79938	CGG		0.393	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			A	91503330	G	A	91503330	3	1	61	1	0	0	0	0	1	0	0	0	9948	1144	40	1	425	1	MTERF	7	91503330	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315	91503330	67635333	5382	13367										
MTERF	7978	broad.mit.edu	37	chr7	91503394	91503394	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagataaaagggtttttaaaAattatctttctgacaaaatc	5	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91503394A>C	ENST00000351870.3	-	3	807	c.714T>G	c.(712-714)atT>atG	p.I238M	MTERF_ENST00000481516.1_5'Flank|MTERF_ENST00000419292.1_Missense_Mutation_p.I218M|MTERF_ENST00000406735.2_Missense_Mutation_p.I218M	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		238					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.I238M(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			GGTTTTTAAAAATTATCTTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	44	43					7																	91503394		2202	4299	6501	91341330	SO:0001583	missense	7978																														ENST00000351870.3:c.714T>G	7.37:g.91503394A>C	ENSP00000248643:p.Ile238Met		91341330	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Missense_Mutation	SNP	ENST00000351870.3	37	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124978	0.56613	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735	T;T;T	0.12569	2.67;2.67;2.67	4.94	3.81	0.43845	.	0.136472	0.45867	D	0.000332	T	0.31295	0.0792	M	0.66939	2.045	0.40905	D	0.98418	D	0.56287	0.975	D	0.70487	0.969	T	0.03957	-1.0989	10	0.72032	D	0.01	-9.7823	9.646	0.39868	0.9139:0.0:0.0861:0.0	.	238	Q99551	MTERF_HUMAN	M	218;238;218	ENSP00000414116:I218M;ENSP00000248643:I238M;ENSP00000384986:I218M	ENSP00000248643:I238M	I	-	3	3	MTERF	91341330	0.999000	0.42202	0.994000	0.49952	0.920000	0.55202	0.728000	0.26013	2.158000	0.67659	0.477000	0.44152	ATT		0.388	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			C	91503394	A	C	91503394	3	2	61	1	0	0	0	0	1	0	0	0	9948	10	1	4	489	4	MTERF	7	91503394	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	64	91503394	67635269	5383	13368										
AKAP9	10142	broad.mit.edu	37	chr7	91631398	91631398	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgactcttcaaatcaatGaacttcaaaaagaaattgaa	4	6	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91631398G>T	ENST00000359028.2	+	9	2428	c.2203G>T	c.(2203-2205)Gaa>Taa	p.E735*	AKAP9_ENST00000356239.3_Nonsense_Mutation_p.E723*|AKAP9_ENST00000358100.2_Nonsense_Mutation_p.E735*			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	735	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.E723*(1)|p.E735*(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCAAATCAATGAACTTCAAAA	0.284			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - Nonsense(2)	large_intestine(2)	7																																								91469334	SO:0001587	stop_gained	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.2203G>T	7.37:g.91631398G>T	ENSP00000351922:p.Glu735*		91469334	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Nonsense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	G	39	7.823574	0.98510	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	.	.	.	5.73	5.73	0.89815	.	0.000000	0.42821	D	0.000656	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.5094	0.67774	0.0701:0.0:0.9299:0.0	.	.	.	.	X	723;735;735;735;735	.	ENSP00000348573:E723X	E	+	1	0	AKAP9	91469334	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.445000	0.73456	2.881000	0.98747	0.650000	0.86243	GAA		0.284	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		T	91631398	G	T	91631398	4	4	61	1	0	0	0	0	0	1	0	0	459	1291	45	2	2197	2	AKAP9	7	91631398	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128004	91631398	67507265	5384	13369										
AKAP9	10142	broad.mit.edu	37	chr7	91709403	91709403	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagaagctattggagggCaatgagaaaaaacagagaga	12	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91709403C>A	ENST00000359028.2	+	32	8217	c.7992C>A	c.(7990-7992)ggC>ggA	p.G2664G	AKAP9_ENST00000356239.3_Silent_p.G2652G|AKAP9_ENST00000358100.2_Silent_p.G2664G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2664	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.G2664G(1)|p.G2652G(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTGGAGGGCAATGAGAAAA	0.303			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - coding silent(2)	large_intestine(2)	7											19	21	20					7																	91709403		2055	4222	6277	91547339	SO:0001819	synonymous_variant	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.7992C>A	7.37:g.91709403C>A			91547339	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																					0.303	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91709403	C	A	91709403	2	1	61	1	0	0	0	0	0	0	0	1	459	697	25	2		2	AKAP9	7	91709403	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78005	91709403	67429260	5385	13370										
AKAP9	10142	broad.mit.edu	37	chr7	91726945	91726945	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagaactagaaattgggttCttcaacagaaaatagaagga	9	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91726945C>A	ENST00000359028.2	+	42	10681	c.10456C>A	c.(10456-10458)Ctt>Att	p.L3486I	AKAP9_ENST00000356239.3_Missense_Mutation_p.L3482I|AKAP9_ENST00000358100.2_Missense_Mutation_p.L3432I			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3486					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.L3486I(2)|p.L3482I(2)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAATTGGGTTCTTCAACAGAA	0.353			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	4	Substitution - Missense(4)	large_intestine(4)	7											80	81	81					7																	91726945		2203	4300	6503	91564881	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10456C>A	7.37:g.91726945C>A	ENSP00000351922:p.Leu3486Ile		91564881	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	C	11.70	1.715644	0.30413	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.04654	3.68;3.68;3.69;3.58	5.32	4.43	0.53597	.	0.000000	0.37577	N	0.002028	T	0.10637	0.0260	M	0.75447	2.3	0.30182	N	0.80032	D;B;B;P;P	0.53885	0.963;0.087;0.404;0.539;0.539	P;B;B;B;B	0.48454	0.578;0.063;0.082;0.17;0.17	T	0.04855	-1.0922	10	0.59425	D	0.04	.	8.4654	0.32953	0.1541:0.7682:0.0:0.0777	.	757;3486;3486;3482;3474	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	I	3482;3486;3432;3486;1328	ENSP00000348573:L3482I;ENSP00000351922:L3486I;ENSP00000350813:L3432I;ENSP00000378042:L1328I	ENSP00000348573:L3482I	L	+	1	0	AKAP9	91564881	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	1.693000	0.37742	1.349000	0.45751	0.585000	0.79938	CTT		0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91726945	C	A	91726945	3	1	61	1	0	0	0	0	1	0	0	0	459	913	32	2	10610	2	AKAP9	7	91726945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17542	91726945	67411718	5386	13371										
ANKIB1	54467	broad.mit.edu	37	chr7	91936790	91936790	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggagcccttcatcctcgCttggcacgccccacagaaga	10	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:91936790C>A	ENST00000265742.3	+	3	682	c.306C>A	c.(304-306)cgC>cgA	p.R102R		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	102							zinc ion binding (GO:0008270)	p.R102R(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTCATCCTCGCTTGGCACGCC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	7											104	102	102					7																	91936790		1928	4137	6065	91774726	SO:0001819	synonymous_variant	54467			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.306C>A	7.37:g.91936790C>A			91774726	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																				0.418	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			A	91936790	C	A	91936790	2	1	61	1	0	0	0	0	0	0	0	1	630	784	28	2		2	ANKIB1	7	91936790	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	209845	91936790	67201873	5387	13372										
ANKIB1	54467	broad.mit.edu	37	chr7	92027925	92027925	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaacatcatggcttggtttCatgacatgaaccctcagagt	9	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92027925C>A	ENST00000265742.3	+	20	3308	c.2932C>A	c.(2932-2934)Cat>Aat	p.H978N		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	978							zinc ion binding (GO:0008270)	p.H978N(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GGCTTGGTTTCATGACATGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	7											123	120	121					7																	92027925		2014	4186	6200	91865861	SO:0001583	missense	54467			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2932C>A	7.37:g.92027925C>A	ENSP00000265742:p.His978Asn		91865861	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520174	0.64747	.	.	ENSG00000001629	ENST00000265742	T	0.10860	2.83	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.25975	0.0633	L	0.32530	0.975	0.80722	D	1	D;B	0.89917	1.0;0.034	D;B	0.87578	0.998;0.012	T	0.00520	-1.1692	10	0.87932	D	0	.	19.6142	0.95626	0.0:1.0:0.0:0.0	.	330;978	Q4VBX8;Q9P2G1	.;AKIB1_HUMAN	N	978	ENSP00000265742:H978N	ENSP00000265742:H978N	H	+	1	0	ANKIB1	91865861	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.587000	0.67510	2.941000	0.99782	0.655000	0.94253	CAT		0.488	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			A	92027925	C	A	92027925	3	1	61	1	0	0	0	0	1	0	0	0	630	826	29	2	3006	2	ANKIB1	7	92027925	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91135	92027925	67110738	5388	13373										
PEX1	5189	broad.mit.edu	37	chr7	92129040	92129040	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacacttataaaattcattCtactctctcgtgcaattacc	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92129040C>A	ENST00000248633.4	-	16	2791	c.2696G>T	c.(2695-2697)aGa>aTa	p.R899I	PEX1_ENST00000438045.1_Missense_Mutation_p.R577I|PEX1_ENST00000428214.1_Missense_Mutation_p.R842I|PEX1_ENST00000541751.1_3'UTR	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	899					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R899I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	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)			AAAATTCATTCTACTCTCTCG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											146	145	145					7																	92129040		2203	4300	6503	91966976	SO:0001583	missense	5189			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.2696G>T	7.37:g.92129040C>A	ENSP00000248633:p.Arg899Ile		91966976	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	37	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270193	0.80469	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	D;D;D	0.95001	-3.58;-3.58;-3.58	5.51	5.51	0.81932	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.153798	0.64402	D	0.000015	D	0.96034	0.8708	M	0.74389	2.26	0.80722	D	1	B;B;B	0.30526	0.204;0.243;0.283	B;B;B	0.43838	0.433;0.159;0.173	D	0.95272	0.8378	10	0.66056	D	0.02	-6.3529	19.4363	0.94796	0.0:1.0:0.0:0.0	.	577;691;899	E9PE75;B4DER6;O43933	.;.;PEX1_HUMAN	I	577;899;842	ENSP00000410438:R577I;ENSP00000248633:R899I;ENSP00000394413:R842I	ENSP00000248633:R899I	R	-	2	0	PEX1	91966976	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.445000	0.80570	2.606000	0.88127	0.650000	0.86243	AGA		0.348	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		A	92129040	C	A	92129040	3	1	61	1	0	0	0	0	1	0	0	0	11766	913	32	2	1191	2	PEX1	7	92129040	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101115	92129040	67009623	5389	13374										
PEX1	5189	broad.mit.edu	37	chr7	92129115	92129115	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacaacagtattcctgttCtttgtcgtatgggcaagttt	8	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92129115C>A	ENST00000248633.4	-	16	2716	c.2621G>T	c.(2620-2622)aGa>aTa	p.R874I	PEX1_ENST00000438045.1_Missense_Mutation_p.R552I|PEX1_ENST00000428214.1_Missense_Mutation_p.R817I|PEX1_ENST00000541751.1_3'UTR	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	874					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R874I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	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)			TATTCCTGTTCTTTGTCGTAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											129	126	127					7																	92129115		2203	4300	6503	91967051	SO:0001583	missense	5189			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.2621G>T	7.37:g.92129115C>A	ENSP00000248633:p.Arg874Ile		91967051	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	37	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.655521	0.88056	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	D;D;D	0.94793	-3.52;-3.52;-3.52	5.51	5.51	0.81932	ATPase, AAA+ type, core (1);	0.045170	0.85682	D	0.000000	D	0.97241	0.9098	M	0.89163	3.01	0.80722	D	1	P;P;P	0.46784	0.88;0.884;0.84	P;P;P	0.55391	0.775;0.453;0.461	D	0.97437	1.0019	10	0.59425	D	0.04	-20.835	19.4363	0.94796	0.0:1.0:0.0:0.0	.	552;666;874	E9PE75;B4DER6;O43933	.;.;PEX1_HUMAN	I	552;874;817	ENSP00000410438:R552I;ENSP00000248633:R874I;ENSP00000394413:R817I	ENSP00000248633:R874I	R	-	2	0	PEX1	91967051	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.692000	0.68256	2.606000	0.88127	0.650000	0.86243	AGA		0.363	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		A	92129115	C	A	92129115	3	1	61	1	0	0	0	0	1	0	0	0	11766	913	32	2	1266	2	PEX1	7	92129115	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75	92129115	67009548	5390	13375										
C7orf64	84060	broad.mit.edu	37	chr7	92161754	92161754	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggatgaacagagtttcttCggtggattgcttcatgtgtg	13	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92161754C>T	ENST00000265732.5	+	3	380	c.339C>T	c.(337-339)ttC>ttT	p.F113F	RBM48_ENST00000481551.1_Silent_p.F113F	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	113	RRM.					nucleus (GO:0005634)	RNA binding (GO:0003723)	p.F113F(1)									AGAGTTTCTTCGGTGGATTGC	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	7											158	146	150					7																	92161754		1823	4091	5914	91999690	SO:0001819	synonymous_variant	84060			AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.339C>T	7.37:g.92161754C>T			91999690	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Silent	SNP	ENST00000265732.5	37	CCDS43615.1																																																																																				0.353	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		T	92161754	C	T	92161754	2	4	61	1	0	0	0	0	0	0	0	1	2416	883	31	1		1	C7orf64	7	92161754	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32639	92161754	66976909	5391	13376										
C7orf64	84060	broad.mit.edu	37	chr7	92164267	92164267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaacggcgaatttaattCggcataaacttaaagaggta	8	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92164267C>T	ENST00000265732.5	+	4	1041	c.1000C>T	c.(1000-1002)Cgg>Tgg	p.R334W	RBM48_ENST00000481551.1_Missense_Mutation_p.R334W	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	334						nucleus (GO:0005634)	RNA binding (GO:0003723)	p.R334W(1)									GAATTTAATTCGGCATAAACT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	39	39					7																	92164267		1817	4072	5889	92002203	SO:0001583	missense	84060			AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.1000C>T	7.37:g.92164267C>T	ENSP00000265732:p.Arg334Trp		92002203	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Missense_Mutation	SNP	ENST00000265732.5	37	CCDS43615.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.698692	0.30142	.	.	ENSG00000127993	ENST00000265732;ENST00000481551;ENST00000450580	.	.	.	5.11	3.23	0.37069	.	0.101210	0.64402	N	0.000005	T	0.69106	0.3074	L	0.52126	1.63	0.58432	D	0.999999	D;P	0.89917	1.0;0.7	D;B	0.91635	0.999;0.095	T	0.70802	-0.4773	9	0.87932	D	0	2.5305	12.8541	0.57876	0.4276:0.5724:0.0:0.0	.	334;334	B7Z2K5;Q5RL73	.;CG064_HUMAN	W	334	.	ENSP00000265732:R334W	R	+	1	2	C7orf64	92002203	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	1.099000	0.31013	0.688000	0.31529	0.467000	0.42956	CGG		0.338	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		T	92164267	C	T	92164267	3	4	61	1	0	0	0	0	1	0	0	0	2416	875	31	1	1014	1	C7orf64	7	92164267	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2513	92164267	66974396	5392	13377										
SAMD9	54809	broad.mit.edu	37	chr7	92731949	92731949	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaggcatgttctgctaaAtccaaaagagcaattagatc	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92731949A>C	ENST00000379958.2	-	3	3731	c.3462T>G	c.(3460-3462)gaT>gaG	p.D1154E		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1154						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.D1154E(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GTTCTGCTAAATCCAAAAGAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											206	209	208					7																	92731949		2203	4300	6503	92569885	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3462T>G	7.37:g.92731949A>C	ENSP00000369292:p.Asp1154Glu		92569885	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.443596	0.00178	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.20200	2.09;2.9	4.39	-8.78	0.00824	.	0.706571	0.12751	N	0.442173	T	0.04861	0.0131	N	0.02315	-0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	10	0.02654	T	1	0.0896	10.6564	0.45678	0.186:0.1033:0.0:0.7108	.	1154	Q5K651	SAMD9_HUMAN	E	1154	ENSP00000369292:D1154E;ENSP00000414529:D1154E	ENSP00000369292:D1154E	D	-	3	2	SAMD9	92569885	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-4.104000	0.00294	-1.608000	0.01587	0.418000	0.28097	GAT		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92731949	A	C	92731949	3	2	61	1	0	0	0	0	1	0	0	0	13863	98	4	4	1311	4	SAMD9	7	92731949	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	567682	92731949	66406714	5393	13378										
SAMD9	54809	broad.mit.edu	37	chr7	92732492	92732492	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagtagttcccacattcGatgacctctgtttttatcag	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92732492G>A	ENST00000379958.2	-	3	3188	c.2919C>T	c.(2917-2919)atC>atT	p.I973I		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	973						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.I973I(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCCCACATTCGATGACCTCTG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											126	123	124					7																	92732492		2203	4300	6503	92570428	SO:0001819	synonymous_variant	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2919C>T	7.37:g.92732492G>A			92570428	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																				0.388	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92732492	G	A	92732492	2	1	61	1	0	0	0	0	0	0	0	1	13863	1048	37	1		1	SAMD9	7	92732492	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	543	92732492	66406171	5394	13379										
SAMD9	54809	broad.mit.edu	37	chr7	92733306	92733306	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttttgacaaaaggtgaaGaataactttcagaagagaag	9	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92733306G>T	ENST00000379958.2	-	3	2374	c.2105C>A	c.(2104-2106)tCt>tAt	p.S702Y		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	702						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.S702Y(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AAAAGGTGAAGAATAACTTTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7											153	152	152					7																	92733306		2203	4299	6502	92571242	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2105C>A	7.37:g.92733306G>T	ENSP00000369292:p.Ser702Tyr		92571242	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.755328	0.31046	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.25579	1.79;2.6	4.51	4.51	0.55191	.	0.402817	0.21581	N	0.072254	T	0.46347	0.1388	M	0.62723	1.935	0.26375	N	0.976836	D	0.65815	0.995	P	0.62885	0.908	T	0.34825	-0.9813	10	0.66056	D	0.02	.	15.9256	0.79615	0.0:0.0:1.0:0.0	.	702	Q5K651	SAMD9_HUMAN	Y	702	ENSP00000369292:S702Y;ENSP00000414529:S702Y	ENSP00000369292:S702Y	S	-	2	0	SAMD9	92571242	0.000000	0.05858	0.884000	0.34674	0.379000	0.30106	0.728000	0.26013	2.335000	0.79485	0.609000	0.83330	TCT		0.343	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		T	92733306	G	T	92733306	3	4	61	1	0	0	0	0	1	0	0	0	13863	942	33	2	2668	2	SAMD9	7	92733306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	814	92733306	66405357	5395	13380										
SAMD9	54809	broad.mit.edu	37	chr7	92733781	92733781	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccacagaggacagtaataGaaataccaccaaaaacttcc	5	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92733781G>T	ENST00000379958.2	-	3	1899	c.1630C>A	c.(1630-1632)Cta>Ata	p.L544I		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	544						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.L544I(1)|p.L544V(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GACAGTAATAGAAATACCACC	0.398																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	7											85	88	87					7																	92733781		2203	4299	6502	92571717	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1630C>A	7.37:g.92733781G>T	ENSP00000369292:p.Leu544Ile		92571717	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	G	9.016	0.983656	0.18889	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.38560	1.13;1.13	4.25	1.64	0.23874	.	0.149206	0.26907	U	0.021894	T	0.33352	0.0860	L	0.46885	1.475	0.22500	N	0.999046	P	0.41673	0.759	B	0.43052	0.406	T	0.17379	-1.0371	10	0.52906	T	0.07	.	3.5359	0.07794	0.353:0.0:0.4724:0.1746	.	544	Q5K651	SAMD9_HUMAN	I	544	ENSP00000369292:L544I;ENSP00000414529:L544I	ENSP00000369292:L544I	L	-	1	2	SAMD9	92571717	0.979000	0.34478	0.771000	0.31576	0.360000	0.29518	0.165000	0.16564	0.232000	0.21100	0.603000	0.83216	CTA		0.398	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		T	92733781	G	T	92733781	3	4	61	1	0	0	0	0	1	0	0	0	13863	933	33	2	3143	2	SAMD9	7	92733781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	475	92733781	66404882	5396	13381										
SAMD9	54809	broad.mit.edu	37	chr7	92734110	92734110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatacagcaaaccatttaAtttccttcaggaaatctaag	4	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92734110A>C	ENST00000379958.2	-	3	1570	c.1301T>G	c.(1300-1302)aTt>aGt	p.I434S		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	434						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.I434S(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AAACCATTTAATTTCCTTCAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											43	44	44					7																	92734110		2202	4300	6502	92572046	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1301T>G	7.37:g.92734110A>C	ENSP00000369292:p.Ile434Ser		92572046	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492238	0.64074	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.14516	2.5;2.5	4.06	4.06	0.47325	.	0.092996	0.41194	U	0.000929	T	0.29321	0.0730	M	0.62723	1.935	0.39814	D	0.972744	D	0.69078	0.997	P	0.60789	0.879	T	0.08638	-1.0712	10	0.87932	D	0	-8.4804	12.2328	0.54497	1.0:0.0:0.0:0.0	.	434	Q5K651	SAMD9_HUMAN	S	434	ENSP00000369292:I434S;ENSP00000414529:I434S	ENSP00000369292:I434S	I	-	2	0	SAMD9	92572046	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	8.733000	0.91539	1.821000	0.53095	0.491000	0.48974	ATT		0.348	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92734110	A	C	92734110	3	2	61	1	0	0	0	0	1	0	0	0	13863	101	4	4	3472	4	SAMD9	7	92734110	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	329	92734110	66404553	5397	13382										
SAMD9L	219285	broad.mit.edu	37	chr7	92761456	92761456	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtatacctcattttcagaaGaaccatataatcaataaaaa	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92761456G>T	ENST00000318238.4	-	5	5045	c.3829C>A	c.(3829-3831)Ctt>Att	p.L1277I	SAMD9L_ENST00000437805.1_Missense_Mutation_p.L1277I|SAMD9L_ENST00000411955.1_Missense_Mutation_p.L1277I	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1277					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.L1277I(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			ATTTTCAGAAGAACCATATAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	7											70	73	72					7																	92761456		2198	4297	6495	92599392	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.3829C>A	7.37:g.92761456G>T	ENSP00000326247:p.Leu1277Ile		92599392	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	9.098	1.003535	0.19121	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.23754	1.89;1.89;1.89	4.77	2.63	0.31362	.	0.541604	0.16997	N	0.191061	T	0.22589	0.0545	L	0.53249	1.67	0.09310	N	0.999994	P	0.38078	0.617	B	0.37144	0.242	T	0.11717	-1.0576	10	0.54805	T	0.06	-2.1519	6.5989	0.22689	0.4797:0.0:0.5203:0.0	.	1277	Q8IVG5	SAM9L_HUMAN	I	1277	ENSP00000326247:L1277I;ENSP00000405760:L1277I;ENSP00000408796:L1277I	ENSP00000326247:L1277I	L	-	1	0	SAMD9L	92599392	0.694000	0.27738	0.908000	0.35775	0.855000	0.48748	1.168000	0.31859	0.514000	0.28300	0.467000	0.42956	CTT		0.318	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		T	92761456	G	T	92761456	3	4	61	1	0	0	0	0	1	0	0	0	13864	942	33	2	929	2	SAMD9L	7	92761456	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27346	92761456	66377207	5398	13383										
SAMD9L	219285	broad.mit.edu	37	chr7	92761865	92761865	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaacagtaatgctcctacaGtttttgttcccatccaacca	4	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92761865G>A	ENST00000318238.4	-	5	4636	c.3420C>T	c.(3418-3420)aaC>aaT	p.N1140N	SAMD9L_ENST00000437805.1_Silent_p.N1140N|SAMD9L_ENST00000411955.1_Silent_p.N1140N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1140					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.N1140N(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGCTCCTACAGTTTTTGTTCC	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	7											114	118	116					7																	92761865		2203	4299	6502	92599801	SO:0001819	synonymous_variant	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.3420C>T	7.37:g.92761865G>A			92599801	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Silent	SNP	ENST00000318238.4	37	CCDS34681.1																																																																																				0.383	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92761865	G	A	92761865	2	1	61	1	0	0	0	0	0	0	0	1	13864	1020	36	3		3	SAMD9L	7	92761865	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	409	92761865	66376798	5399	13384										
SAMD9L	219285	broad.mit.edu	37	chr7	92762490	92762490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaattgtagagtcagtaAcataagagctgagtaaagcc	10	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92762490A>G	ENST00000318238.4	-	5	4011	c.2795T>C	c.(2794-2796)gTt>gCt	p.V932A	SAMD9L_ENST00000437805.1_Missense_Mutation_p.V932A|SAMD9L_ENST00000411955.1_Missense_Mutation_p.V932A	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	932					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.V932A(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			AGAGTCAGTAACATAAGAGCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											93	88	90					7																	92762490		2203	4299	6502	92600426	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.2795T>C	7.37:g.92762490A>G	ENSP00000326247:p.Val932Ala		92600426	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.452664	0.43531	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.28255	1.62;1.62;1.62	5.22	5.22	0.72569	.	0.279479	0.28166	N	0.016341	T	0.41604	0.1166	M	0.65498	2.005	0.45087	D	0.998101	P	0.51791	0.948	P	0.47827	0.558	T	0.44847	-0.9301	10	0.87932	D	0	-16.596	14.9182	0.70815	1.0:0.0:0.0:0.0	.	932	Q8IVG5	SAM9L_HUMAN	A	932	ENSP00000326247:V932A;ENSP00000405760:V932A;ENSP00000408796:V932A	ENSP00000326247:V932A	V	-	2	0	SAMD9L	92600426	1.000000	0.71417	0.476000	0.27291	0.001000	0.01503	5.948000	0.70249	2.193000	0.70182	0.383000	0.25322	GTT		0.383	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		G	92762490	A	G	92762490	3	3	61	1	0	0	0	0	1	0	0	0	13864	43	2	4	1963	4	SAMD9L	7	92762490	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	625	92762490	66376173	5400	13385										
SAMD9L	219285	broad.mit.edu	37	chr7	92764009	92764009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtgctttatttggtttgGatggcatttatttgttacaa	9	3	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92764009G>A	ENST00000318238.4	-	5	2492	c.1276C>T	c.(1276-1278)Cca>Tca	p.P426S	SAMD9L_ENST00000437805.1_Missense_Mutation_p.P426S|SAMD9L_ENST00000411955.1_Missense_Mutation_p.P426S	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	426					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.P426S(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			ATTTGGTTTGGATGGCATTTA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											98	102	101					7																	92764009		2203	4299	6502	92601945	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1276C>T	7.37:g.92764009G>A	ENSP00000326247:p.Pro426Ser		92601945	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514820	0.44763	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.16597	2.33;2.33;2.33	4.74	3.86	0.44501	.	0.154759	0.42548	D	0.000683	T	0.19685	0.0473	M	0.65498	2.005	0.39922	D	0.97416	P	0.36683	0.565	B	0.35655	0.207	T	0.05338	-1.0891	10	0.32370	T	0.25	-11.4075	12.6483	0.56748	0.0813:0.0:0.9187:0.0	.	426	Q8IVG5	SAM9L_HUMAN	S	426	ENSP00000326247:P426S;ENSP00000405760:P426S;ENSP00000408796:P426S	ENSP00000326247:P426S	P	-	1	0	SAMD9L	92601945	1.000000	0.71417	0.623000	0.29173	0.588000	0.36517	5.492000	0.66893	1.226000	0.43582	-0.384000	0.06662	CCA		0.348	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92764009	G	A	92764009	3	1	61	1	0	0	0	0	1	0	0	0	13864	1174	41	3	3482	3	SAMD9L	7	92764009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1519	92764009	66374654	5401	13386										
SAMD9L	219285	broad.mit.edu	37	chr7	92764081	92764081	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtctcggtttcctatgaGaagtttaaccagctttagtc	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92764081G>T	ENST00000318238.4	-	5	2420	c.1204C>A	c.(1204-1206)Ctc>Atc	p.L402I	SAMD9L_ENST00000437805.1_Missense_Mutation_p.L402I|SAMD9L_ENST00000411955.1_Missense_Mutation_p.L402I	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	402					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.L402I(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTCCTATGAGAAGTTTAACC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											156	158	157					7																	92764081		2203	4299	6502	92602017	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1204C>A	7.37:g.92764081G>T	ENSP00000326247:p.Leu402Ile		92602017	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.033940	0.35893	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.12879	2.64;2.64;2.64	4.74	2.91	0.33838	.	0.104633	0.33875	N	0.004462	T	0.10508	0.0257	L	0.39397	1.21	0.34792	D	0.735819	P	0.40619	0.724	B	0.39152	0.292	T	0.20306	-1.0279	10	0.51188	T	0.08	-5.9358	5.1712	0.15110	0.1765:0.0:0.6592:0.1643	.	402	Q8IVG5	SAM9L_HUMAN	I	402	ENSP00000326247:L402I;ENSP00000405760:L402I;ENSP00000408796:L402I	ENSP00000326247:L402I	L	-	1	0	SAMD9L	92602017	0.872000	0.30054	0.990000	0.47175	0.969000	0.65631	1.322000	0.33689	0.591000	0.29711	0.460000	0.39030	CTC		0.358	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		T	92764081	G	T	92764081	3	4	61	1	0	0	0	0	1	0	0	0	13864	942	33	2	3554	2	SAMD9L	7	92764081	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72	92764081	66374582	5402	13387										
HEPACAM2	253012	broad.mit.edu	37	chr7	92825175	92825175	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacatctggaaaagcaacaAattcatatattccgaagtca	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:92825175A>C	ENST00000394468.2	-	8	1318	c.1241T>G	c.(1240-1242)tTt>tGt	p.F414C	HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000453812.2_Missense_Mutation_p.F437C|HEPACAM2_ENST00000341723.4_Missense_Mutation_p.F402C|HEPACAM2_ENST00000440868.1_Missense_Mutation_p.L394V	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	414					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)		p.F402C(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						AAAAGCAACAAATTCATATAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											119	116	117					7																	92825175		2203	4300	6503	92663111	SO:0001583	missense	253012			AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1241T>G	7.37:g.92825175A>C	ENSP00000377980:p.Phe414Cys		92663111	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Missense_Mutation	SNP	ENST00000394468.2	37	CCDS43616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.56|15.56	2.869048|2.869048	0.51588|0.51588	.|.	.|.	ENSG00000188175|ENSG00000188175	ENST00000394468;ENST00000341723;ENST00000453812|ENST00000440868	T;T;T|T	0.60171|0.59772	0.21;0.25;0.25|0.24	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.46580|0.46580	0.1400|0.1400	L|L	0.36672|0.36672	1.1|1.1	0.49130|0.49130	D|D	0.999755|0.999755	D;D;D|P	0.89917|0.37525	1.0;1.0;1.0|0.598	D;D;D|B	0.91635|0.34824	0.998;0.998;0.999|0.19	T|T	0.46925|0.46925	-0.9156|-0.9156	10|9	0.02654|0.37606	T|T	1|0.19	-23.0595|-23.0595	13.5382|13.5382	0.61657|0.61657	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	437;414;402|394	E9PDV5;A8MVW5;A8MVW5-2|C9JN07	.;HECA2_HUMAN;.|.	C|V	414;402;437|394	ENSP00000377980:F414C;ENSP00000340532:F402C;ENSP00000390204:F437C|ENSP00000389592:L394V	ENSP00000340532:F402C|ENSP00000389592:L394V	F|L	-|-	2|1	0|2	HEPACAM2|HEPACAM2	92663111|92663111	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.420000|5.420000	0.66441|0.66441	2.174000|2.174000	0.68829|0.68829	0.528000|0.528000	0.53228|0.53228	TTT|TTG		0.388	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		C	92825175	A	C	92825175	3	2	61	1	0	0	0	0	1	0	0	0	7074	14	1	4	159	4	HEPACAM2	7	92825175	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	61094	92825175	66313488	5403	13388										
CALCR	799	broad.mit.edu	37	chr7	93090197	93090197	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggatgatgataatcataGaattcagaatgtaagtaaga	11	2	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:93090197G>T	ENST00000394441.1	-	7	899	c.584C>A	c.(583-585)tCt>tAt	p.S195Y	CALCR_ENST00000359558.2_Missense_Mutation_p.S229Y|CALCR_ENST00000360249.4_Missense_Mutation_p.S211Y|CALCR_ENST00000426151.1_Missense_Mutation_p.S195Y|CALCR_ENST00000421592.1_Missense_Mutation_p.S211Y	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	229					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.S195Y(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	GATAATCATAGAATTCAGAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											140	137	138					7																	93090197		2203	4300	6503	92928133	SO:0001583	missense	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.584C>A	7.37:g.93090197G>T	ENSP00000377959:p.Ser195Tyr		92928133	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.599969	0.66332	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.47869	0.83;1.04;1.04;1.04;1.04	5.44	5.44	0.79542	.	.	.	.	.	T	0.72661	0.3488	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.76334	-0.2997	9	0.87932	D	0	.	18.4169	0.90574	0.0:0.0:1.0:0.0	.	229;195	F5H605;A4D1G6	.;.	Y	229;211;211;195;195	ENSP00000352561:S229Y;ENSP00000353385:S211Y;ENSP00000399552:S211Y;ENSP00000377959:S195Y;ENSP00000389295:S195Y	ENSP00000352561:S229Y	S	-	2	0	CALCR	92928133	1.000000	0.71417	0.706000	0.30403	0.314000	0.28054	8.491000	0.90468	2.719000	0.93026	0.555000	0.69702	TCT		0.408	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		T	93090197	G	T	93090197	3	4	61	1	0	0	0	0	1	0	0	0	2585	942	33	2	868	2	CALCR	7	93090197	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	265022	93090197	66048466	5404	13389										
COL1A2	1278	broad.mit.edu	37	chr7	94041406	94041406	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggttcccctggaaatatCggccccgctggaaaagaagg	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:94041406C>T	ENST00000297268.6	+	24	1848	c.1377C>T	c.(1375-1377)atC>atT	p.I459I		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	459					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.I459I(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTGGAAATATCGGCCCCGCTG	0.378										HNSCC(75;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											91	86	88					7																	94041406		2203	4300	6503	93879342	SO:0001819	synonymous_variant	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1377C>T	7.37:g.94041406C>T			93879342	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																				0.378	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94041406	C	T	94041406	2	4	61	1	0	0	0	0	0	0	0	1	3684	874	31	1		1	COL1A2	7	94041406	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	951209	94041406	65097257	5405	13390										
CASD1	64921	broad.mit.edu	37	chr7	94167039	94167039	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtcttcattagaaataCttttacaatctttctgcaaa	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:94167039C>A	ENST00000297273.4	+	9	1386	c.1099C>A	c.(1099-1101)Ctt>Att	p.L367I		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	367						integral component of membrane (GO:0016021)		p.L367I(1)		NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	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)			ATTAGAAATACTTTTACAATC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											107	121	116					7																	94167039		2203	4300	6503	94004975	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1099C>A	7.37:g.94167039C>A	ENSP00000297273:p.Leu367Ile		94004975	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999446	0.35320	.	.	ENSG00000127995	ENST00000297273	T	0.46451	0.87	5.52	3.62	0.41486	.	0.178751	0.49916	D	0.000126	T	0.37237	0.0996	L	0.55213	1.73	0.43652	D	0.996067	B;B	0.14012	0.009;0.009	B;B	0.21151	0.033;0.033	T	0.18808	-1.0325	10	0.26408	T	0.33	.	11.949	0.52944	0.0:0.8094:0.122:0.0685	.	367;367	Q8WZ77;Q96PB1	.;CASD1_HUMAN	I	367	ENSP00000297273:L367I	ENSP00000297273:L367I	L	+	1	0	CASD1	94004975	0.999000	0.42202	1.000000	0.80357	0.730000	0.41778	1.469000	0.35343	1.481000	0.48307	0.591000	0.81541	CTT		0.348	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		A	94167039	C	A	94167039	3	1	61	1	0	0	0	0	1	0	0	0	2670	565	20	2	1133	2	CASD1	7	94167039	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125633	94167039	64971624	5406	13391										
CASD1	64921	broad.mit.edu	37	chr7	94174866	94174866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcaataggttttatttCgtctcaatttcctggtagtg	7	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:94174866C>T	ENST00000297273.4	+	12	1773	c.1486C>T	c.(1486-1488)Cgt>Tgt	p.R496C		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	496						integral component of membrane (GO:0016021)		p.R496C(2)		NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	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)			GGTTTTATTTCGTCTCAATTT	0.358																																																2	Substitution - Missense(2)	cervix(1)|large_intestine(1)	7											173	150	158					7																	94174866		2203	4299	6502	94012802	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1486C>T	7.37:g.94174866C>T	ENSP00000297273:p.Arg496Cys		94012802	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.187546	0.78789	.	.	ENSG00000127995	ENST00000297273	T	0.57752	0.38	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.77096	0.4080	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.63957	0.92;0.92	T	0.82914	-0.0221	10	0.87932	D	0	.	18.7033	0.91629	0.0:1.0:0.0:0.0	.	496;496	Q8WZ77;Q96PB1	.;CASD1_HUMAN	C	496	ENSP00000297273:R496C	ENSP00000297273:R496C	R	+	1	0	CASD1	94012802	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.823000	0.69272	2.489000	0.83994	0.491000	0.48974	CGT		0.358	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		T	94174866	C	T	94174866	3	4	61	1	0	0	0	0	1	0	0	0	2670	884	31	1	1532	1	CASD1	7	94174866	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7827	94174866	64963797	5407	13392										
PPP1R9A	55607	broad.mit.edu	37	chr7	94539496	94539496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcacaggaatgcatatcGaactgagtttcaggcactga	9	10	2	2	rs140272671		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:94539496G>A	ENST00000433881.1	+	2	603	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	PPP1R9A_ENST00000424654.1_Missense_Mutation_p.R24Q|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.R24Q|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.R24Q|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.R24Q|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.R24Q			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	24	Actin-binding.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)		p.R24Q(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			AATGCATATCGAACTGAGTTT	0.473										HNSCC(28;0.073)																																						1	Substitution - Missense(1)	large_intestine(1)	7											53	53	53					7																	94539496		2203	4300	6503	94377432	SO:0001583	missense	55607			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.71G>A	7.37:g.94539496G>A	ENSP00000398870:p.Arg24Gln		94377432	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	37	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265260	0.59431	.	.	ENSG00000158528	ENST00000413325;ENST00000433360;ENST00000340694;ENST00000424654;ENST00000422324;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.15017	2.46;2.48;2.46;2.48;2.46;2.46	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.44561	0.1299	M	0.72118	2.19	0.41414	D	0.987754	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.978;0.997;0.997;0.965;0.949	T	0.22765	-1.0207	10	0.52906	T	0.07	.	19.8016	0.96509	0.0:0.0:1.0:0.0	.	24;24;24;24;24	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	Q	24	ENSP00000405514:R24Q;ENSP00000344524:R24Q;ENSP00000411342:R24Q;ENSP00000398870:R24Q;ENSP00000289495:R24Q;ENSP00000402893:R24Q	ENSP00000289495:R24Q	R	+	2	0	PPP1R9A	94377432	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.597000	0.82733	2.770000	0.95276	0.655000	0.94253	CGA		0.473	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		A	94539496	G	A	94539496	3	1	61	1	0	0	0	0	1	0	0	0	12412	1058	37	1	73	1	PPP1R9A	7	94539496	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	364630	94539496	64599167	5408	13393										
PON3	5446	broad.mit.edu	37	chr7	94992147	94992147	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctacatcagctacataGacatacctttgaagtaaatg	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:94992147G>T	ENST00000265627.5	-	7	712	c.702C>A	c.(700-702)gtC>gtA	p.V234V	PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Intron|PON3_ENST00000451904.1_Silent_p.V234V	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	234					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)	p.V234V(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	CAGCTACATAGACATACCTTT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	7											172	147	155					7																	94992147		2203	4300	6503	94830083	SO:0001819	synonymous_variant	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.702C>A	7.37:g.94992147G>T			94830083	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																				0.373	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		T	94992147	G	T	94992147	2	4	61	1	0	0	0	0	0	0	0	1	12281	929	33	2		2	PON3	7	94992147	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	452651	94992147	64146516	5409	13394										
ASB4	51666	broad.mit.edu	37	chr7	95125342	95125342	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacaactccaagttccattCtctgtgccaagcaattggtt	7	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95125342C>A	ENST00000325885.5	+	2	531	c.460C>A	c.(460-462)Ctc>Atc	p.L154I	ASB4_ENST00000428113.1_Missense_Mutation_p.L154I|ASB4_ENST00000257621.4_3'UTR	NM_016116.2	NP_057200.1	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box containing 4	154					intracellular signal transduction (GO:0035556)|positive regulation of vasculogenesis (GO:2001214)|protein autoubiquitination (GO:0051865)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)	p.L154I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|pancreas(1)|prostate(1)|skin(2)	20	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			AAGTTCCATTCTCTGTGCCAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											144	127	132					7																	95125342		2203	4300	6503	94963278	SO:0001583	missense	51666			AF156779	CCDS5641.1, CCDS5642.1	7q21-q22	2013-01-10	2011-01-25		ENSG00000005981	ENSG00000005981		"Ankyrin repeat domain containing"	16009	protein-coding gene	gene with protein product		605761	"ankyrin repeat and SOCS box-containing 4"				Standard	NM_145872		Approved	ASB-4	uc011kij.2	Q9Y574	OTTHUMG00000153960	ENST00000325885.5:c.460C>A	7.37:g.95125342C>A	ENSP00000321388:p.Leu154Ile		94963278	A4D1H6|O14586|Q14D68|Q8TBT2	Missense_Mutation	SNP	ENST00000325885.5	37	CCDS5641.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.191275	0.38707	.	.	ENSG00000005981	ENST00000325885;ENST00000428113	T;T	0.64260	-0.09;-0.09	5.35	3.42	0.39159	Ankyrin repeat-containing domain (3);	0.446032	0.25484	N	0.030347	T	0.44519	0.1297	N	0.12961	0.28	0.27118	N	0.962201	B;B	0.19583	0.003;0.037	B;B	0.21917	0.005;0.037	T	0.44967	-0.9293	10	0.52906	T	0.07	-17.4091	11.5333	0.50622	0.1276:0.6248:0.2475:0.0	.	154;154	Q9Y574;Q14D68	ASB4_HUMAN;.	I	154	ENSP00000321388:L154I;ENSP00000397070:L154I	ENSP00000321388:L154I	L	+	1	0	ASB4	94963278	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.154000	0.50693	1.378000	0.46305	0.655000	0.94253	CTC		0.463	ASB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333225.2	NM_016116		A	95125342	C	A	95125342	3	1	61	1	0	0	0	0	1	0	0	0	1026	913	32	2	466	2	ASB4	7	95125342	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133195	95125342	64013321	5410	13395										
PDK4	5166	broad.mit.edu	37	chr7	95222119	95222119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatacggttcatgtaaaatCgatccaagaaatattgaaga	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95222119C>T	ENST00000005178.5	-	4	679	c.482G>A	c.(481-483)cGa>cAa	p.R161Q		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	161	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.	Interaction with the other subunit in the homodimer.			cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.R161Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			CATGTAAAATCGATCCAAGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											145	140	141					7																	95222119		2203	4300	6503	95060055	SO:0001583	missense	5166			U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.482G>A	7.37:g.95222119C>T	ENSP00000005178:p.Arg161Gln		95060055		Missense_Mutation	SNP	ENST00000005178.5	37	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	C	36	5.833411	0.97003	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.34667	1.35	5.75	5.75	0.90469	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.72187	0.3429	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78404	-0.2217	10	0.72032	D	0.01	.	20.3271	0.98704	0.0:1.0:0.0:0.0	.	161	Q16654	PDK4_HUMAN	Q	161;125	ENSP00000005178:R161Q	ENSP00000005178:R161Q	R	-	2	0	PDK4	95060055	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	CGA		0.383	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		T	95222119	C	T	95222119	3	4	61	1	0	0	0	0	1	0	0	0	11709	884	31	1	785	1	PDK4	7	95222119	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96777	95222119	63916544	5411	13396										
DYNC1I1	1780	broad.mit.edu	37	chr7	95657515	95657515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtcggtctgcttcgcccGtttccatcctaacttggtgg	11	12	1	0	rs376275541		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95657515G>A	ENST00000324972.6	+	11	1242	c.1049G>A	c.(1048-1050)cGt>cAt	p.R350H	DYNC1I1_ENST00000447467.2_Missense_Mutation_p.R333H|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.R333H|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.R313H|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.R313H|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.R330H	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	350					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)	p.R350H(2)		NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			TGCTTCGCCCGTTTCCATCCT	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						G	HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	241	212	222		998,938,1049	5	1	7		222	0,8600		0,0,4300	no	missense,missense,missense	DYNC1I1	NM_001135556.1,NM_001135557.1,NM_004411.4	29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	333/629,313/609,350/646	95657515	1,13005	2203	4300	6503	95495451	SO:0001583	missense	1780			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1049G>A	7.37:g.95657515G>A	ENSP00000320130:p.Arg350His		95495451	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611195	0.87258	2.27E-4	0.0	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32	5.04	5.04	0.67666	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.057497	0.64402	D	0.000002	T	0.19127	0.0459	L	0.55990	1.75	0.50813	D	0.999896	D;D;D;D;D	0.61080	0.962;0.978;0.978;0.962;0.989	P;P;P;P;P	0.59056	0.628;0.851;0.795;0.714;0.541	T	0.00062	-1.2156	10	0.72032	D	0.01	-10.2341	18.9501	0.92638	0.0:0.0:1.0:0.0	.	333;330;333;350;313	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	H	333;350;313;330;313;333	ENSP00000392337:R333H;ENSP00000320130:R350H;ENSP00000438377:R313H;ENSP00000398118:R330H;ENSP00000352348:R313H;ENSP00000412444:R333H	ENSP00000320130:R350H	R	+	2	0	DYNC1I1	95495451	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.128000	0.50492	2.788000	0.95919	0.585000	0.79938	CGT		0.512	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		A	95657515	G	A	95657515	3	1	61	1	0	0	0	0	1	0	0	0	4853	1145	40	1	1087	1	DYNC1I1	7	95657515	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	435396	95657515	63481148	5412	13397										
DYNC1I1	1780	broad.mit.edu	37	chr7	95657632	95657632	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttatcagctgctgcacacaCggtaatgcaaacttttgcca	7	12	1	0	rs546629907		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95657632C>T	ENST00000324972.6	+	11	1359	c.1166C>T	c.(1165-1167)aCg>aTg	p.T389M	DYNC1I1_ENST00000447467.2_Splice_Site_p.T372M|DYNC1I1_ENST00000457059.1_Splice_Site_p.T372M|DYNC1I1_ENST00000359388.4_Splice_Site_p.T352M|DYNC1I1_ENST00000537881.1_Splice_Site_p.T352M|DYNC1I1_ENST00000437599.1_Splice_Site_p.T369M	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	389					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)	p.T389M(1)		NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			GCTGCACACACGGTAATGCAA	0.493													C|||	1	0.000199681	0	0	5008	,	,		19607	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	7											107	90	95					7																	95657632		2203	4300	6503	95495568	SO:0001630	splice_region_variant	1780			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1167+1C>T	7.37:g.95657632C>T			95495568	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901329	0.52227	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-1.04	5.03	4.15	0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89458	0.6721	M	0.88181	2.935	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.999;0.996;0.95	D	0.91817	0.5464	10	0.87932	D	0	-7.5132	15.3555	0.74423	0.1406:0.8594:0.0:0.0	.	372;369;372;389;352	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	M	372;389;352;369;352;372	ENSP00000392337:T372M;ENSP00000320130:T389M;ENSP00000438377:T352M;ENSP00000398118:T369M;ENSP00000352348:T352M;ENSP00000412444:T372M	ENSP00000320130:T389M	T	+	2	0	DYNC1I1	95495568	1.000000	0.71417	0.888000	0.34837	0.005000	0.04900	7.651000	0.83577	1.484000	0.48361	-0.175000	0.13238	ACG		0.493	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	Missense_Mutation	T	95657632	C	T	95657632	5	4	61	1	0	0	0	0	0	0	1	0	4853	550	19	1	1204	1	DYNC1I1	7	95657632	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117	95657632	63481031	5413	13398										
SLC25A13	10165	broad.mit.edu	37	chr7	95799394	95799394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgctgcaagtgggaccGaaccatctttgtgcataaat	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95799394G>A	ENST00000265631.5	-	13	1410	c.1274C>T	c.(1273-1275)tCg>tTg	p.S425L	SLC25A13_ENST00000416240.2_Missense_Mutation_p.S426L|SLC25A13_ENST00000542654.1_Missense_Mutation_p.S317L			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	425					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)	p.S425L(1)		breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	AAGTGGGACCGAACCATCTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											115	118	117					7																	95799394		2203	4300	6503	95637330	SO:0001583	missense	10165			AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1274C>T	7.37:g.95799394G>A	ENSP00000265631:p.Ser425Leu		95637330	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864638	0.51482	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.77750	-1.12;-1.12;-1.12	4.92	4.92	0.64577	Mitochondrial carrier domain (2);	0.967373	0.08499	N	0.936803	T	0.72277	0.3440	L	0.38175	1.15	0.49798	D	0.999823	P;P;P	0.39131	0.456;0.661;0.661	B;B;B	0.33568	0.103;0.166;0.166	T	0.69228	-0.5200	10	0.41790	T	0.15	-10.7135	18.6919	0.91586	0.0:0.0:1.0:0.0	.	317;426;425	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	L	425;426;317	ENSP00000265631:S425L;ENSP00000400101:S426L;ENSP00000440484:S317L	ENSP00000265631:S425L	S	-	2	0	SLC25A13	95637330	1.000000	0.71417	0.985000	0.45067	0.986000	0.74619	6.307000	0.72815	2.729000	0.93468	0.467000	0.42956	TCG		0.353	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		A	95799394	G	A	95799394	3	1	61	1	0	0	0	0	1	0	0	0	14512	1059	37	1	777	1	SLC25A13	7	95799394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141762	95799394	63339269	5414	13399										
SLC25A13	10165	broad.mit.edu	37	chr7	95820524	95820524	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaatccattaaaataggaGaaactaacttgatgggatgt	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:95820524G>T	ENST00000265631.5	-	7	787	c.651C>A	c.(649-651)ttC>ttA	p.F217L	SLC25A13_ENST00000416240.2_Missense_Mutation_p.F217L|SLC25A13_ENST00000542654.1_Missense_Mutation_p.F109L			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	217					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)	p.F217L(1)		breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	TAAAATAGGAGAAACTAACTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											112	111	111					7																	95820524		2203	4300	6503	95658460	SO:0001583	missense	10165			AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.651C>A	7.37:g.95820524G>T	ENSP00000265631:p.Phe217Leu		95658460	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783155	0.70222	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	D;D;D	0.81579	-1.51;-1.51;-1.51	5.18	5.18	0.71444	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.86180	0.5871	M	0.87269	2.87	0.80722	D	1	D;P;P	0.55172	0.97;0.949;0.949	P;P;P	0.55577	0.779;0.607;0.607	D	0.86203	0.1620	10	0.49607	T	0.09	-14.4697	6.4815	0.22065	0.207:0.0:0.793:0.0	.	109;217;217	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	L	217;217;109	ENSP00000265631:F217L;ENSP00000400101:F217L;ENSP00000440484:F109L	ENSP00000265631:F217L	F	-	3	2	SLC25A13	95658460	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.669000	0.54561	2.868000	0.98415	0.557000	0.71058	TTC		0.353	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		T	95820524	G	T	95820524	3	4	61	1	0	0	0	0	1	0	0	0	14512	933	33	2	1427	2	SLC25A13	7	95820524	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21130	95820524	63318139	5415	13400										
DLX5	1749	broad.mit.edu	37	chr7	96650234	96650234	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgagcgagcgggacgaGccctggggctcccacaccgc	16	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:96650234G>C	ENST00000222598.4	-	3	1157	c.684C>G	c.(682-684)ggC>ggG	p.G228G	DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	228					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.G228G(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					AGCGGGACGAGCCCTGGGGCT	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	7											70	62	65					7																	96650234		2203	4300	6503	96488170	SO:0001819	synonymous_variant	1749				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.684C>G	7.37:g.96650234G>C			96488170	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																				0.642	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			C	96650234	G	C	96650234	2	2	61	1	0	0	0	0	0	0	0	1	4585	958	34	5		5	DLX5	7	96650234	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	829710	96650234	62488429	5416	13401										
DLX5	1749	broad.mit.edu	37	chr7	96651537	96651537	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaggcggccagctcggcgCgttccggcaaggcgaggtac	18	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:96651537C>T	ENST00000222598.4	-	2	973	c.500G>A	c.(499-501)cGc>cAc	p.R167H	DLX5_ENST00000486603.2_Missense_Mutation_p.R167H|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	167					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.R167H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CAGCTCGGCGCGTTCCGGCAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	7											99	100	99					7																	96651537		2203	4300	6503	96489473	SO:0001583	missense	1749				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.500G>A	7.37:g.96651537C>T	ENSP00000222598:p.Arg167His		96489473	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	37	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	C	35	5.580266	0.96565	.	.	ENSG00000105880	ENST00000222598	D	0.97529	-4.42	5.41	5.41	0.78517	Homeobox, eukaryotic (1);Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	H	0.97415	4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99047	1.0826	10	0.87932	D	0	-13.4354	18.9868	0.92773	0.0:1.0:0.0:0.0	.	167;167	B7Z4P3;P56178	.;DLX5_HUMAN	H	167	ENSP00000222598:R167H	ENSP00000222598:R167H	R	-	2	0	DLX5	96489473	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.582000	0.82546	2.816000	0.96949	0.563000	0.77884	CGC		0.557	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			T	96651537	C	T	96651537	3	4	61	1	0	0	0	0	1	0	0	0	4585	768	27	1	377	1	DLX5	7	96651537	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1303	96651537	62487126	5417	13402										
LMTK2	22853	broad.mit.edu	37	chr7	97800937	97800937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcagaggatggcgtgcGaggtcgccgcggggctggcc	20	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:97800937G>A	ENST00000297293.5	+	7	1035	c.742G>A	c.(742-744)Gag>Aag	p.E248K		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	248	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)	p.E248K(2)		NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	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)					GATGGCGTGCGAGGTCGCCGC	0.667																																																2	Substitution - Missense(2)	large_intestine(2)	7											42	41	41					7																	97800937		2203	4300	6503	97638873	SO:0001583	missense	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.742G>A	7.37:g.97800937G>A	ENSP00000297293:p.Glu248Lys		97638873	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896283	0.72639	.	.	ENSG00000164715	ENST00000297293	T	0.63744	-0.06	5.1	5.1	0.69264	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.048675	0.85682	D	0.000000	T	0.76898	0.4052	M	0.75615	2.305	0.46927	D	0.999258	D	0.76494	0.999	D	0.74348	0.983	T	0.79329	-0.1848	10	0.87932	D	0	.	12.1567	0.54081	0.0:0.1726:0.8274:0.0	.	248	Q8IWU2	LMTK2_HUMAN	K	248	ENSP00000297293:E248K	ENSP00000297293:E248K	E	+	1	0	LMTK2	97638873	1.000000	0.71417	0.959000	0.39883	0.406000	0.30931	4.079000	0.57613	2.542000	0.85734	0.655000	0.94253	GAG		0.667	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97800937	G	A	97800937	3	1	61	1	0	0	0	0	1	0	0	0	8883	1059	37	1	768	1	LMTK2	7	97800937	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1149400	97800937	61337726	5418	13403										
LMTK2	22853	broad.mit.edu	37	chr7	97823561	97823561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgaaggagccggacatcGaagggaagtacctggggaaa	16	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:97823561G>A	ENST00000297293.5	+	11	4077	c.3784G>A	c.(3784-3786)Gaa>Aaa	p.E1262K		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1262					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)	p.E1262K(2)		NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	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)					GCCGGACATCGAAGGGAAGTA	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	7											76	76	76					7																	97823561		2203	4300	6503	97661497	SO:0001583	missense	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3784G>A	7.37:g.97823561G>A	ENSP00000297293:p.Glu1262Lys		97661497	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.779854	0.90195	.	.	ENSG00000164715	ENST00000297293	D	0.85484	-1.99	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.92596	0.7648	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.92342	0.5882	10	0.72032	D	0.01	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	1262	Q8IWU2	LMTK2_HUMAN	K	1262	ENSP00000297293:E1262K	ENSP00000297293:E1262K	E	+	1	0	LMTK2	97661497	1.000000	0.71417	0.767000	0.31495	0.269000	0.26545	9.414000	0.97362	2.894000	0.99253	0.655000	0.94253	GAA		0.597	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97823561	G	A	97823561	3	1	61	1	0	0	0	0	1	0	0	0	8883	1059	37	1	3826	1	LMTK2	7	97823561	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22624	97823561	61315102	5419	13404										
BAIAP2L1	55971	broad.mit.edu	37	chr7	97949421	97949421	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctccagctcatggataatCtctttgtggaattttttaaa	6	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:97949421C>T	ENST00000005260.8	-	5	512	c.297G>A	c.(295-297)gaG>gaA	p.E99E	BAIAP2L1_ENST00000462558.1_5'UTR|RP11-307C18.1_ENST00000610062.1_RNA	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	99	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.E99E(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			CATGGATAATCTCTTTGTGGA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	7											116	109	111					7																	97949421		2203	4300	6503	97787357	SO:0001819	synonymous_variant	55971			AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.297G>A	7.37:g.97949421C>T			97787357	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																				0.373	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		T	97949421	C	T	97949421	2	4	61	1	0	0	0	0	0	0	0	1	1303	912	32	3		3	BAIAP2L1	7	97949421	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125860	97949421	61189242	5420	13405										
TMEM130	222865	broad.mit.edu	37	chr7	98453722	98453722	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccacctcttcccactcCgccaccactttgagcttcac	5	20	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98453722C>T	ENST00000416379.2	-	4	640	c.636G>A	c.(634-636)gcG>gcA	p.A212A	TMEM130_ENST00000345589.4_Silent_p.A110A|TMEM130_ENST00000339375.4_Silent_p.A212A|TMEM130_ENST00000546258.1_Silent_p.A193A|TMEM130_ENST00000450876.1_Silent_p.A128A			Q8N3G9	TM130_HUMAN	transmembrane protein 130	212	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A212A(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CTTCCCACTCCGCCACCACTT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	7											88	80	83					7																	98453722		2203	4300	6503	98291658	SO:0001819	synonymous_variant	222865				CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.636G>A	7.37:g.98453722C>T			98291658	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Silent	SNP	ENST00000416379.2	37	CCDS47650.1																																																																																				0.587	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		T	98453722	C	T	98453722	2	4	61	1	0	0	0	0	0	0	0	1	16082	639	23	1		1	TMEM130	7	98453722	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	504301	98453722	60684941	5421	13406										
TRRAP	8295	broad.mit.edu	37	chr7	98548513	98548513	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtaggttctgcagcatatCttgaatcctgctttcttgta	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98548513C>A	ENST00000359863.4	+	38	5537	c.5328C>A	c.(5326-5328)atC>atA	p.I1776I	TRRAP_ENST00000446306.3_Silent_p.I1757I|TRRAP_ENST00000355540.3_Silent_p.I1758I	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1776					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.I1758I(1)|p.I1776I(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGCAGCATATCTTGAATCCTG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	7											159	169	166					7																	98548513		2203	4300	6503	98386449	SO:0001819	synonymous_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.5328C>A	7.37:g.98548513C>A			98386449	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	3.564	-0.088977	0.07097	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.6	1.6	0.23607	.	.	.	.	.	T	0.54647	0.1871	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44329	-0.9335	4	.	.	.	.	7.0407	0.25019	0.1193:0.614:0.0:0.2667	.	.	.	.	Y	1498	.	.	S	+	2	0	TRRAP	98386449	1.000000	0.71417	0.998000	0.56505	0.522000	0.34438	1.742000	0.38248	0.283000	0.22279	-1.538000	0.00913	TCT		0.433	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98548513	C	A	98548513	2	1	61	1	0	0	0	0	0	0	0	1	16641	903	32	2		2	TRRAP	7	98548513	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94791	98548513	60590150	5422	13407										
TRRAP	8295	broad.mit.edu	37	chr7	98575945	98575945	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgggaagaccactggattCggtaagccaaacacagtgct	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98575945C>T	ENST00000359863.4	+	56	8685	c.8476C>T	c.(8476-8478)Cga>Tga	p.R2826*	TRRAP_ENST00000446306.3_Splice_Site_p.R2808*|TRRAP_ENST00000355540.3_Splice_Site_p.R2808*	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2826	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R2808*(1)|p.R2826*(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CCACTGGATTCGGTAAGCCAA	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	7											95	84	88					7																	98575945		2203	4300	6503	98413881	SO:0001630	splice_region_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8477+1C>T	7.37:g.98575945C>T			98413881	A4D265|O75218|Q9Y631|Q9Y6H4	Nonsense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	50	17.289499	0.99883	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	.	.	.	6.06	4.18	0.49190	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3176	0.74092	0.2464:0.7536:0.0:0.0	.	.	.	.	X	2826;2808;2807	.	ENSP00000347733:R2808X	R	+	1	2	TRRAP	98413881	1.000000	0.71417	0.925000	0.36789	0.942000	0.58702	4.957000	0.63652	0.812000	0.34326	0.655000	0.94253	CGA		0.433	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	Nonsense_Mutation	T	98575945	C	T	98575945	5	4	61	1	0	0	0	0	0	0	1	0	16641	898	31	1	8636	1	TRRAP	7	98575945	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27432	98575945	60562718	5423	13408										
TRRAP	8295	broad.mit.edu	37	chr7	98576486	98576486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtcctggagtgcgcctggCgggtgtccaactggactgcc	15	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98576486C>T	ENST00000359863.4	+	57	8781	c.8572C>T	c.(8572-8574)Cgg>Tgg	p.R2858W	TRRAP_ENST00000446306.3_Missense_Mutation_p.R2840W|TRRAP_ENST00000355540.3_Missense_Mutation_p.R2840W	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2858	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R2858W(1)|p.R2840W(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTGCGCCTGGCGGGTGTCCAA	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	7											65	68	67					7																	98576486		2203	4300	6503	98414422	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8572C>T	7.37:g.98576486C>T	ENSP00000352925:p.Arg2858Trp		98414422	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611893	0.87258	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.72835	-0.69;-0.69	6.03	1.55	0.23275	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	M	0.91090	3.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.89389	0.3687	10	0.87932	D	0	.	15.723	0.77728	0.6104:0.3896:0.0:0.0	.	2840;2579;2858	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	W	2858;2840;2839	ENSP00000352925:R2858W;ENSP00000347733:R2840W	ENSP00000347733:R2840W	R	+	1	2	TRRAP	98414422	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.247000	0.51422	0.360000	0.24265	0.655000	0.94253	CGG		0.622	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98576486	C	T	98576486	3	4	61	1	0	0	0	0	1	0	0	0	16641	759	27	1	8736	1	TRRAP	7	98576486	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541	98576486	60562177	5424	13409										
SMURF1	57154	broad.mit.edu	37	chr7	98643392	98643392	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccgttttttcaagtctttCggtcgcatcttcattatctg	7	10	5	0	rs142287239		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98643392C>T	ENST00000361125.1	-	12	1582	c.1263G>A	c.(1261-1263)ccG>ccA	p.P421P	SMURF1_ENST00000361368.2_Silent_p.P395P|AC004893.11_ENST00000468960.2_RNA|AC004893.11_ENST00000482799.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	421	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)	p.P421P(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCAAGTCTTTCGGTCGCATCT	0.438													C|||	1	0.000199681	8e-04	0	5008	,	,		17246	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C	,,	2,4404	4.2+/-10.8	0,2,2201	142	124	130		1185,1263,1185	-6.9	0.1	7	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SMURF1	NM_001199847.1,NM_020429.2,NM_181349.2	,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,	395/729,421/758,395/732	98643392	2,13004	2203	4300	6503	98481328	SO:0001819	synonymous_variant	57154			AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1263G>A	7.37:g.98643392C>T			98481328	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																				0.438	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		T	98643392	C	T	98643392	2	4	61	1	0	0	0	0	0	0	0	1	14856	871	31	1		1	SMURF1	7	98643392	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66906	98643392	60495271	5425	13410										
SMURF1	57154	broad.mit.edu	37	chr7	98647331	98647331	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagttcacactgttaaggtCtctaccaaaatggaagatac	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:98647331C>A	ENST00000361125.1	-	10	1205	c.886G>T	c.(886-888)Gac>Tac	p.D296Y	SMURF1_ENST00000480055.1_5'Flank|SMURF1_ENST00000361368.2_Splice_Site_p.D270Y|AC004893.11_ENST00000468960.2_RNA|AC004893.11_ENST00000482799.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	296					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)	p.D296Y(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			CTGTTAAGGTCTCTACCAAAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											84	77	79					7																	98647331		2203	4300	6503	98485267	SO:0001630	splice_region_variant	57154			AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.885-1G>T	7.37:g.98647331C>A			98485267	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	37	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906815	0.92107	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.48201	1.11;0.82	5.46	5.46	0.80206	.	0.527164	0.15948	N	0.236863	T	0.52805	0.1757	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.77557	0.987;0.99;0.973	T	0.63765	-0.6563	10	0.66056	D	0.02	.	19.321	0.94240	0.0:1.0:0.0:0.0	.	270;296;270	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	Y	270;296	ENSP00000355326:D270Y;ENSP00000354621:D296Y	ENSP00000354621:D296Y	D	-	1	0	SMURF1	98485267	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.557000	0.86248	0.563000	0.77884	GAC		0.438	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	Missense_Mutation	A	98647331	C	A	98647331	5	1	61	1	0	0	0	0	0	0	1	0	14856	927	32	2	1427	2	SMURF1	7	98647331	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3939	98647331	60491332	5426	13411										
ZNF655	79027	broad.mit.edu	37	chr7	99171198	99171198	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagcattcataccaaagaGaactcatgaatgtaatgaag	8	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99171198G>T	ENST00000394163.2	+	3	1650	c.1467G>T	c.(1465-1467)gaG>gaT	p.E489D	GS1-259H13.10_ENST00000455905.1_Intron|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000425063.1_3'UTR|ZNF655_ENST00000493277.1_Missense_Mutation_p.E524D|ZNF655_ENST00000424881.1_Missense_Mutation_p.E524D|ZNF655_ENST00000252713.4_Missense_Mutation_p.E489D|ZNF655_ENST00000419215.2_3'UTR	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	489					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E489D(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					ATACCAAAGAGAACTCATGAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	75	75					7																	99171198		2203	4300	6503	99009134	SO:0001583	missense	79027			AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"Zinc fingers, C2H2-type", "-"	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.1467G>T	7.37:g.99171198G>T	ENSP00000377718:p.Glu489Asp		99009134	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Missense_Mutation	SNP	ENST00000394163.2	37	CCDS5669.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210167	0.58343	.	.	ENSG00000197343	ENST00000252713;ENST00000493277;ENST00000424881;ENST00000394163	T;T;T;T	0.06371	3.38;3.31;3.31;3.38	4.69	3.81	0.43845	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43260	D	0.000588	T	0.12220	0.0297	L	0.58669	1.825	0.80722	D	1	D;P	0.53619	0.961;0.935	P;P	0.49597	0.616;0.575	T	0.01416	-1.1360	10	0.72032	D	0.01	-5.1093	11.2745	0.49159	0.092:0.0:0.908:0.0	.	524;489	Q8N720-3;Q8N720	.;ZN655_HUMAN	D	489;524;524;489	ENSP00000252713:E489D;ENSP00000419135:E524D;ENSP00000393876:E524D;ENSP00000377718:E489D	ENSP00000252713:E489D	E	+	3	2	ZNF655	99009134	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.965000	0.40471	1.296000	0.44742	0.655000	0.94253	GAG		0.398	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494		T	99171198	G	T	99171198	3	4	61	1	0	0	0	0	1	0	0	0	18107	933	33	2	2004	2	ZNF655	7	99171198	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	523867	99171198	59967465	5427	13412										
ZNF498	221785	broad.mit.edu	37	chr7	99227017	99227017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccatccccctgcctgacGaagtcaaaacccacagctcc	7	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99227017G>A	ENST00000394152.2	+	8	1336	c.1009G>A	c.(1009-1011)Gaa>Aaa	p.E337K	ZSCAN25_ENST00000262941.6_Missense_Mutation_p.E265K|ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.E337K	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	337					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E337K(1)									CCTGCCTGACGAAGTCAAAAC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	7											56	49	51					7																	99227017		2203	4300	6503	99064953	SO:0001583	missense	221785			AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1009G>A	7.37:g.99227017G>A	ENSP00000377708:p.Glu337Lys		99064953	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	G	0.355	-0.942440	0.02322	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08370	3.14;3.14;3.1	3.89	2.98	0.34508	.	0.610047	0.14670	N	0.305382	T	0.04272	0.0118	N	0.11756	0.17	0.19575	N	0.999963	B;B	0.25743	0.133;0.082	B;B	0.19666	0.026;0.012	T	0.41378	-0.9512	10	0.09338	T	0.73	-13.4289	10.2562	0.43399	0.1013:0.0:0.8987:0.0	.	265;337	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	K	337;337;265	ENSP00000377708:E337K;ENSP00000334800:E337K;ENSP00000262941:E265K	ENSP00000262941:E265K	E	+	1	0	ZNF498	99064953	0.002000	0.14202	0.453000	0.27007	0.191000	0.23601	0.992000	0.29667	1.178000	0.42870	0.561000	0.74099	GAA		0.632	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		A	99227017	G	A	99227017	3	1	61	1	0	0	0	0	1	0	0	0	17986	1059	37	1	1027	1	ZNF498	7	99227017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55819	99227017	59911646	5428	13413										
CYP3A7	1551	broad.mit.edu	37	chr7	99319924	99319924	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagaatactcacccccaGacttttctatactttttata	2	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99319924G>T	ENST00000336374.2	-	3	215	c.213C>A	c.(211-213)gtC>gtA	p.V71V		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	71			V -> A (in dbSNP:rs45580339).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.V71V(1)		autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CTCACCCCCAGACTTTTCTAT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	7											85	83	83					7																	99319924		2203	4300	6503	99157860	SO:0001819	synonymous_variant	1551			AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"Cytochrome P450s"	2640	protein-coding gene	gene with protein product		605340	"cytochrome P450, subfamily IIIA, polypeptide 7"			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.213C>A	7.37:g.99319924G>T			99157860	A4D288|Q9H241	Silent	SNP	ENST00000336374.2	37	CCDS5673.1																																																																																				0.393	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			T	99319924	G	T	99319924	2	4	61	1	0	0	0	0	0	0	0	1	4187	929	33	2		2	CYP3A7	7	99319924	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92907	99319924	59818739	5429	13414										
CYP3A7	1551	broad.mit.edu	37	chr7	99328750	99328750	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaattccaagcttcttaaAaagtccatgtgtacgggttc	9	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99328750A>C	ENST00000336374.2	-	2	99	c.97T>G	c.(97-99)Ttt>Gtt	p.F33V		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	33					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.F33V(1)		autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AGCTTCTTAAAAAGTCCATGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											100	94	96					7																	99328750		2203	4300	6503	99166686	SO:0001583	missense	1551			AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"Cytochrome P450s"	2640	protein-coding gene	gene with protein product		605340	"cytochrome P450, subfamily IIIA, polypeptide 7"			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.97T>G	7.37:g.99328750A>C	ENSP00000337450:p.Phe33Val		99166686	A4D288|Q9H241	Missense_Mutation	SNP	ENST00000336374.2	37	CCDS5673.1	.	.	.	.	.	.	.	.	.	.	A	11.61	1.690692	0.29962	.	.	ENSG00000160870	ENST00000292414;ENST00000336374	T	0.22539	1.95	3.52	2.35	0.29111	.	0.000000	0.85682	D	0.000000	T	0.35595	0.0937	M	0.61703	1.905	0.40848	D	0.98372	D	0.63880	0.993	D	0.68765	0.96	T	0.11155	-1.0599	10	0.87932	D	0	.	5.4933	0.16789	0.8663:0.0:0.1337:0.0	.	33	P24462	CP3A7_HUMAN	V	33	ENSP00000337450:F33V	ENSP00000292414:F33V	F	-	1	0	CYP3A7	99166686	0.993000	0.37304	0.538000	0.28064	0.087000	0.18053	3.461000	0.53035	0.536000	0.28733	0.418000	0.28097	TTT		0.433	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			C	99328750	A	C	99328750	3	2	61	1	0	0	0	0	1	0	0	0	4187	14	1	4	1462	4	CYP3A7	7	99328750	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8826	99328750	59809913	5430	13415										
CYP3A43	64816	broad.mit.edu	37	chr7	99447172	99447172	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttttactctactcagtttCtttggggcctacaccatgga	8	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99447172C>A	ENST00000354829.2	+	7	628	c.525C>A	c.(523-525)ttC>ttA	p.F175L	CYP3A43_ENST00000222382.5_Missense_Mutation_p.F175L|CYP3A43_ENST00000312017.5_Missense_Mutation_p.F175L|CYP3A43_ENST00000417625.1_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000342499.4_Missense_Mutation_p.L38I|CYP3A43_ENST00000415413.1_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	175			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.F175L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TACTCAGTTTCTTTGGGGCCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											181	158	166					7																	99447172		2203	4300	6503	99285108	SO:0001583	missense	64816			AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.525C>A	7.37:g.99447172C>A	ENSP00000346887:p.Phe175Leu		99285108	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.123|9.123	1.009380|1.009380	0.19277|0.19277	.|.	.|.	ENSG00000021461|ENSG00000021461	ENST00000354829;ENST00000312017;ENST00000222382|ENST00000342499;ENST00000379654	T;T;T|T	0.65732|0.78126	-0.17;-0.17;-0.17|-1.15	2.98|2.98	-0.341|-0.341	0.12639|0.12639	.|.	0.934586|.	0.08847|.	U|.	0.884971|.	T|T	0.50188|0.50188	0.1601|0.1601	N|N	0.11673|0.11673	0.155|0.155	0.09310|0.09310	N|N	1|1	B;B;B|B	0.10296|0.28713	0.003;0.001;0.001|0.22	B;B;B|B	0.11329|0.22880	0.003;0.006;0.006|0.042	T|T	0.31475|0.31475	-0.9942|-0.9942	10|9	0.20046|0.20519	T|T	0.44|0.43	.|.	2.3026|2.3026	0.04166|0.04166	0.1758:0.3573:0.3467:0.1202|0.1758:0.3573:0.3467:0.1202	.|.	175;175;175|38	Q9HB55-3;Q75MK2;Q9HB55|F8W6L8	.;.;CP343_HUMAN|.	L|I	175|38;69	ENSP00000346887:F175L;ENSP00000312110:F175L;ENSP00000222382:F175L|ENSP00000345351:L38I	ENSP00000222382:F175L|ENSP00000345351:L38I	F|L	+|+	3|1	2|0	CYP3A43|CYP3A43	99285108|99285108	0.000000|0.000000	0.05858|0.05858	0.110000|0.110000	0.21437|0.21437	0.552000|0.552000	0.35366|0.35366	-2.050000|-2.050000	0.01404|0.01404	-0.246000|-0.246000	0.09611|0.09611	0.205000|0.205000	0.17691|0.17691	TTC|CTT		0.408	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			A	99447172	C	A	99447172	3	1	61	1	0	0	0	0	1	0	0	0	4185	912	32	2	551	2	CYP3A43	7	99447172	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118422	99447172	59691491	5431	13416										
CYP3A43	64816	broad.mit.edu	37	chr7	99459347	99459347	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacgagagtctgcaagaaaGatattgaaatcaatggagtg	11	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99459347G>T	ENST00000354829.2	+	11	1241	c.1138G>T	c.(1138-1140)Gat>Tat	p.D380Y	CYP3A43_ENST00000222382.5_Missense_Mutation_p.D380Y|CYP3A43_ENST00000312017.5_Missense_Mutation_p.D380Y|CYP3A43_ENST00000417625.1_Missense_Mutation_p.D270Y|CYP3A43_ENST00000444905.1_Missense_Mutation_p.D127Y|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000342499.4_Missense_Mutation_p.D240Y|CYP3A43_ENST00000415413.1_Missense_Mutation_p.D169Y	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	380			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.D380Y(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	CTGCAAGAAAGATATTGAAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											129	114	119					7																	99459347		2203	4300	6503	99297283	SO:0001583	missense	64816			AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.1138G>T	7.37:g.99459347G>T	ENSP00000346887:p.Asp380Tyr		99297283	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342422	0.24339	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000342499;ENST00000444905;ENST00000415413;ENST00000312017;ENST00000222382	T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.1;-1.11;-1.11	2.71	2.71	0.32032	.	0.682067	0.13722	N	0.367283	D	0.90631	0.7062	H	0.98256	4.185	0.47621	D	0.999477	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.998	D;D;D;D;D	0.75484	0.965;0.986;0.968;0.98;0.949	D	0.89429	0.3715	10	0.87932	D	0	.	5.6216	0.17459	0.1528:0.0:0.8472:0.0	.	270;240;380;380;380	Q495Y1;F8W6L8;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;.;CP343_HUMAN	Y	380;270;240;127;169;380;380	ENSP00000346887:D380Y;ENSP00000416581:D270Y;ENSP00000345351:D240Y;ENSP00000405557:D127Y;ENSP00000401521:D169Y;ENSP00000312110:D380Y;ENSP00000222382:D380Y	ENSP00000222382:D380Y	D	+	1	0	CYP3A43	99297283	0.073000	0.21202	0.998000	0.56505	0.046000	0.14306	1.210000	0.32370	1.821000	0.53095	0.404000	0.27445	GAT		0.443	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			T	99459347	G	T	99459347	3	4	61	1	0	0	0	0	1	0	0	0	4185	942	33	2	1180	2	CYP3A43	7	99459347	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12175	99459347	59679316	5432	13417										
OR2AE1	81392	broad.mit.edu	37	chr7	99473800	99473800	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccggagagtataaatcagaGaattcaatgtgggcgtaatg	12	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99473800G>T	ENST00000316368.2	-	1	880	c.857C>A	c.(856-858)tCt>tAt	p.S286Y		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S286Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					ATAAATCAGAGAATTCAATGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	7											112	116	115					7																	99473800		2203	4300	6503	99311736	SO:0001583	missense	81392			AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.857C>A	7.37:g.99473800G>T	ENSP00000313936:p.Ser286Tyr		99311736	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.267677	0.23136	.	.	ENSG00000244623	ENST00000316368	T	0.37752	1.18	3.56	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.201466	0.24843	N	0.035141	T	0.20577	0.0495	N	0.08118	0	0.23232	N	0.998078	B	0.17465	0.022	B	0.08055	0.003	T	0.28839	-1.0031	10	0.87932	D	0	.	13.4395	0.61104	0.0:0.0:1.0:0.0	.	286	Q8NHA4	O2AE1_HUMAN	Y	286	ENSP00000313936:S286Y	ENSP00000313936:S286Y	S	-	2	0	OR2AE1	99311736	1.000000	0.71417	0.203000	0.23512	0.174000	0.22865	6.648000	0.74359	2.285000	0.76669	0.385000	0.25706	TCT		0.458	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			T	99473800	G	T	99473800	3	4	61	1	0	0	0	0	1	0	0	0	11014	942	33	2	118	2	OR2AE1	7	99473800	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14453	99473800	59664863	5433	13418										
TRIM4	89122	broad.mit.edu	37	chr7	99506410	99506410	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaaactccgtgctgattCtcattcgctgactctttatc	6	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99506410C>A	ENST00000355947.2	-	4	722	c.593G>T	c.(592-594)aGa>aTa	p.R198I	TRIM4_ENST00000354241.5_Missense_Mutation_p.R172I|TRIM4_ENST00000349062.2_Missense_Mutation_p.R172I	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	198					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.R198I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				CGTGCTGATTCTCATTCGCTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											131	121	124					7																	99506410		2203	4300	6503	99344346	SO:0001583	missense	89122			AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16275	protein-coding gene	gene with protein product	"tripartite motif protein TRIM4", "tripartite motif protein 4"		"tripartite motif-containing 4"			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.593G>T	7.37:g.99506410C>A	ENSP00000348216:p.Arg198Ile		99344346	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	37	CCDS5679.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.09|14.09	2.431779|2.431779	0.43122|0.43122	.|.	.|.	ENSG00000146833|ENSG00000146833	ENST00000447480|ENST00000355947;ENST00000349062;ENST00000542799;ENST00000354241	.|T;T;T	.|0.03441	.|3.93;3.93;3.93	2.68|2.68	-0.426|-0.426	0.12314|0.12314	.|.	.|.	.|.	.|.	.|.	T|T	0.09774|0.09774	0.0240|0.0240	M|M	0.64404|0.64404	1.975|1.975	0.09310|0.09310	N|N	1|1	.|D;D;D	.|0.69078	.|0.982;0.997;0.995	.|P;D;D	.|0.78314	.|0.838;0.991;0.979	T|T	0.27088|0.27088	-1.0084|-1.0084	5|9	.|0.39692	.|T	.|0.17	.|.	1.1148|1.1148	0.01712|0.01712	0.2333:0.3941:0.2285:0.144|0.2333:0.3941:0.2285:0.144	.|.	.|172;172;198	.|Q9C037-3;Q9C037-2;Q9C037	.|.;.;TRIM4_HUMAN	D|I	73|198;172;28;172	.|ENSP00000348216:R198I;ENSP00000275736:R172I;ENSP00000346186:R172I	.|ENSP00000275736:R172I	E|R	-|-	3|2	2|0	TRIM4|TRIM4	99344346|99344346	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.814000|0.814000	0.46013|0.46013	0.028000|0.028000	0.13644|0.13644	-0.092000|-0.092000	0.12417|0.12417	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.433	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		A	99506410	C	A	99506410	3	1	61	1	0	0	0	0	1	0	0	0	16554	913	32	2	925	2	TRIM4	7	99506410	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32610	99506410	59632253	5434	13419										
AZGP1	563	broad.mit.edu	37	chr7	99565994	99565994	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtaatatttccagaatgCtccgctgcttctgttattct	6	9	2	1	rs372477471		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99565994C>G	ENST00000292401.4	-	3	533	c.397G>C	c.(397-399)Gca>Cca	p.A133P	AZGP1_ENST00000483612.1_5'Flank|AZGP1_ENST00000411734.1_Missense_Mutation_p.A130P	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	133					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)	p.A133P(1)|p.A133T(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TTCCAGAATGCTCCGCTGCTT	0.498																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	7											210	226	221					7																	99565994		2203	4300	6503	99403930	SO:0001583	missense	563			BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"Immunoglobulin superfamily / C1-set domain containing"	910	protein-coding gene	gene with protein product		194460	"alpha-2-glycoprotein 1, zinc"			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.397G>C	7.37:g.99565994C>G	ENSP00000292401:p.Ala133Pro		99403930	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	37	CCDS5680.1	.	.	.	.	.	.	.	.	.	.	C	8.046	0.764929	0.15914	.	.	ENSG00000160862	ENST00000292401;ENST00000411734	T;T	0.00784	5.7;5.7	2.76	-0.41	0.12374	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.626440	0.12130	U	0.496886	T	0.02119	0.0066	M	0.85197	2.74	0.09310	N	1	P	0.36199	0.543	P	0.44623	0.455	T	0.22730	-1.0208	10	0.87932	D	0	.	5.9834	0.19419	0.1539:0.6314:0.0:0.2147	.	133	P25311	ZA2G_HUMAN	P	133;130	ENSP00000292401:A133P;ENSP00000396093:A130P	ENSP00000292401:A133P	A	-	1	0	AZGP1	99403930	0.500000	0.26091	0.006000	0.13384	0.011000	0.07611	2.734000	0.47368	-0.717000	0.04955	-2.281000	0.00270	GCA		0.498	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185		G	99565994	C	G	99565994	3	3	61	1	0	0	0	0	1	0	0	0	1240	797	28	5	507	5	AZGP1	7	99565994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59584	99565994	59572669	5435	13420										
ZSCAN21	7589	broad.mit.edu	37	chr7	99661644	99661644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctaccccaggagagagaCgttatatatgtgctgaatgt	10	8	0	3	rs201249540		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99661644C>T	ENST00000292450.4	+	4	990	c.826C>T	c.(826-828)Cgt>Tgt	p.R276C	ZSCAN21_ENST00000456748.2_Intron|ZSCAN21_ENST00000477297.1_Intron|ZSCAN21_ENST00000543588.1_Intron	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	276					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R276C(1)		breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			AGGAGAGAGACGTTATATATG	0.438													C|||	1	0.000199681	0	0	5008	,	,		21946	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						C	CYS/ARG	0,4406		0,0,2203	77	74	75		826	3.7	1	7		75	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZSCAN21	NM_145914.2	180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	276/474	99661644	2,13004	2203	4300	6503	99499580	SO:0001583	missense	7589			AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.826C>T	7.37:g.99661644C>T	ENSP00000292450:p.Arg276Cys		99499580	A4D2A6|D6W5T9|Q9H0B5	Missense_Mutation	SNP	ENST00000292450.4	37	CCDS5681.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436633	0.62955	0.0	2.33E-4	ENSG00000166529	ENST00000292450;ENST00000379635	T	0.01043	5.41	4.61	3.67	0.42095	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42682	D	0.000680	T	0.02083	0.0065	L	0.49778	1.585	0.80722	D	1	D	0.69078	0.997	P	0.47299	0.543	T	0.65882	-0.6060	10	0.44086	T	0.13	.	12.6978	0.57014	0.0:0.8324:0.1676:0.0	.	276	Q9Y5A6	ZSC21_HUMAN	C	276;251	ENSP00000292450:R276C	ENSP00000292450:R276C	R	+	1	0	ZSCAN21	99499580	0.026000	0.19158	1.000000	0.80357	0.959000	0.62525	2.212000	0.42835	2.571000	0.86741	0.655000	0.94253	CGT		0.438	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		T	99661644	C	T	99661644	3	4	61	1	0	0	0	0	1	0	0	0	18272	536	19	1	836	1	ZSCAN21	7	99661644	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95650	99661644	59477019	5436	13421										
ZNF3	7551	broad.mit.edu	37	chr7	99669833	99669833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttcagtcctggtctcacGatctgacacaataaaaaatg	6	9	3	1	rs573869420		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99669833G>A	ENST00000424697.1	-	6	580	c.274C>T	c.(274-276)Cgt>Tgt	p.R92C	ZNF3_ENST00000303915.6_Missense_Mutation_p.R92C|ZNF3_ENST00000413658.2_Intron|ZNF3_ENST00000299667.4_Missense_Mutation_p.R92C	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	92	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.R92C(2)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CTGGTCTCACGATCTGACACA	0.388													G|||	1	0.000199681	0	0	5008	,	,		21934	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|skin(1)	7																																								99507769	SO:0001583	missense	7551			AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.274C>T	7.37:g.99669833G>A	ENSP00000415358:p.Arg92Cys		99507769	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	37	CCDS43619.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274018	0.23221	.	.	ENSG00000166526	ENST00000424697;ENST00000303915;ENST00000299667;ENST00000412947;ENST00000449785;ENST00000428683;ENST00000441298;ENST00000415068	T;T;T;T;T;T;T;T	0.00776	5.71;5.71;5.71;5.71;5.71;5.71;5.71;5.71	5.16	4.27	0.50696	Krueppel-associated box (3);	0.243063	0.29355	N	0.012389	T	0.00440	0.0014	N	0.02111	-0.68	0.32639	N	0.520906	P;P	0.51537	0.946;0.83	B;B	0.37422	0.249;0.092	T	0.67409	-0.5678	10	0.37606	T	0.19	-13.0518	12.1402	0.53994	0.0:0.6607:0.3392:0.0	.	75;92	B3KRP4;P17036	.;ZNF3_HUMAN	C	92;92;92;56;92;92;56;92	ENSP00000415358:R92C;ENSP00000306372:R92C;ENSP00000299667:R92C;ENSP00000416088:R56C;ENSP00000405970:R92C;ENSP00000388042:R92C;ENSP00000394113:R56C;ENSP00000416686:R92C	ENSP00000299667:R92C	R	-	1	0	ZNF3	99507769	0.001000	0.12720	1.000000	0.80357	0.857000	0.48899	-0.174000	0.09839	1.407000	0.46875	-0.540000	0.04249	CGT		0.388	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		A	99669833	G	A	99669833	3	1	61	1	0	0	0	0	1	0	0	0	17868	1058	37	1	1199	1	ZNF3	7	99669833	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8189	99669833	59468830	5437	13422										
MCM7	4176	broad.mit.edu	37	chr7	99690684	99690684	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgctgctctgcctcagaGaaccggacacttcggccccc	10	18	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99690684G>T	ENST00000303887.5	-	15	2676	c.2031C>A	c.(2029-2031)ttC>ttA	p.F677L	MIR25_ENST00000384816.1_RNA|MIR106B_ENST00000385301.1_RNA|MCM7_ENST00000343023.6_Missense_Mutation_p.F347L|MCM7_ENST00000354230.3_Missense_Mutation_p.F501L|MIR93_ENST00000385024.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	677	Interaction with ATRIP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.F501L(1)|p.F677L(1)		endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTGCCTCAGAGAACCGGACAC	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	7											73	66	68					7																	99690684		2203	4300	6503	99528620	SO:0001583	missense	4176				CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.2031C>A	7.37:g.99690684G>T	ENSP00000307288:p.Phe677Leu		99528620	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	G	3.070	-0.191323	0.06299	.	.	ENSG00000166508	ENST00000343023;ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T;T	0.59906	3.16;0.23;0.23	5.98	-2.12	0.07165	.	0.213700	0.46442	D	0.000292	T	0.23210	0.0561	N	0.02539	-0.55	0.33681	D	0.612152	B	0.02656	0.0	B	0.01281	0.0	T	0.45220	-0.9276	10	0.02654	T	1	-18.7491	12.6668	0.56846	0.3839:0.0:0.6161:0.0	.	677	P33993	MCM7_HUMAN	L	347;677;614;570;501	ENSP00000344006:F347L;ENSP00000307288:F677L;ENSP00000346171:F501L	ENSP00000307288:F677L	F	-	3	2	MCM7	99528620	0.992000	0.36948	0.932000	0.37286	0.544000	0.35116	0.550000	0.23345	-0.357000	0.08175	-0.218000	0.12543	TTC		0.557	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			T	99690684	G	T	99690684	3	4	61	1	0	0	0	0	1	0	0	0	9422	933	33	2	132	2	MCM7	7	99690684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20851	99690684	59447979	5438	13423										
MCM7	4176	broad.mit.edu	37	chr7	99695355	99695355	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaagctgccagcttttcGtagaaatcctcctctgtaga	8	10	1	3	rs146340949	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99695355G>A	ENST00000303887.5	-	9	1644	c.999C>T	c.(997-999)taC>taT	p.Y333Y	MCM7_ENST00000343023.6_Intron|MCM7_ENST00000354230.3_Silent_p.Y157Y	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	333	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.Y333Y(1)|p.Y157Y(1)		endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCAGCTTTTCGTAGAAATCCT	0.502													G|||	2	0.000399361	0	0	5008	,	,		20510	0.002		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	7											171	170	170					7																	99695355		2203	4300	6503	99533291	SO:0001819	synonymous_variant	4176				CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.999C>T	7.37:g.99695355G>A			99533291	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Silent	SNP	ENST00000303887.5	37	CCDS5683.1																																																																																				0.502	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			A	99695355	G	A	99695355	2	1	61	1	0	0	0	0	0	0	0	1	9422	1140	40	1		1	MCM7	7	99695355	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4671	99695355	59443308	5439	13424										
STAG3	10734	broad.mit.edu	37	chr7	99796515	99796515	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgggtggaagagagcaaCgccagagcccaggcgcccag	16	11	0	3	rs539912996		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99796515C>T	ENST00000426455.1	+	14	1809	c.1402C>T	c.(1402-1404)Cgc>Tgc	p.R468C	STAG3_ENST00000317296.5_Missense_Mutation_p.R468C|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.R410C	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	468					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.R468C(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAGAGAGCAACGCCAGAGCCC	0.537													C|||	1	0.000199681	0	0	5008	,	,		16772	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7											114	114	114					7																	99796515		2203	4300	6503	99634451	SO:0001583	missense	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1402C>T	7.37:g.99796515C>T	ENSP00000400359:p.Arg468Cys		99634451	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	12.04	1.818867	0.32145	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000317296	T;T;T	0.25749	1.78;1.8;1.78	5.75	4.87	0.63330	Armadillo-type fold (1);	1.147120	0.06612	N	0.755773	T	0.37598	0.1009	M	0.67397	2.05	0.09310	N	0.999999	D;B	0.65815	0.995;0.1	P;B	0.48677	0.586;0.042	T	0.24870	-1.0148	10	0.87932	D	0	-0.7305	7.782	0.29070	0.1609:0.7572:0.0:0.0819	.	410;468	B4DZ10;Q9UJ98	.;STAG3_HUMAN	C	468;410;426;468	ENSP00000400359:R468C;ENSP00000377586:R410C;ENSP00000319318:R468C	ENSP00000319318:R468C	R	+	1	0	STAG3	99634451	0.441000	0.25626	0.508000	0.27688	0.212000	0.24457	2.315000	0.43752	1.572000	0.49736	0.650000	0.86243	CGC		0.537	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		T	99796515	C	T	99796515	3	4	61	1	0	0	0	0	1	0	0	0	15283	536	19	1	1452	1	STAG3	7	99796515	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101160	99796515	59342148	5440	13425										
STAG3	10734	broad.mit.edu	37	chr7	99797196	99797196	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggagagcacactgataGaaatccttgtgtccagtgcc	11	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99797196G>T	ENST00000426455.1	+	16	2013	c.1606G>T	c.(1606-1608)Gaa>Taa	p.E536*	STAG3_ENST00000317296.5_Nonsense_Mutation_p.E536*|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Nonsense_Mutation_p.E478*	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	536					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.E536*(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CACACTGATAGAAATCCTTGT	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											27	29	28					7																	99797196		2203	4300	6503	99635132	SO:0001587	stop_gained	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1606G>T	7.37:g.99797196G>T	ENSP00000400359:p.Glu536*		99635132	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Nonsense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	42	9.212975	0.99103	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000317296	.	.	.	6.16	5.28	0.74379	.	0.000000	0.52532	D	0.000077	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.9121	14.7787	0.69749	0.0:0.0:0.8547:0.1453	.	.	.	.	X	536;478;494;536	.	ENSP00000319318:E536X	E	+	1	0	STAG3	99635132	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.168000	0.71908	1.606000	0.50161	0.650000	0.86243	GAA		0.567	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		T	99797196	G	T	99797196	4	4	61	1	0	0	0	0	0	1	0	0	15283	943	33	2	1664	2	STAG3	7	99797196	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681	99797196	59341467	5441	13426										
STAG3	10734	broad.mit.edu	37	chr7	99801705	99801705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagcaaggcagattgaccGaagtcattgttcccgaatcc	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99801705G>A	ENST00000426455.1	+	26	3169	c.2762G>A	c.(2761-2763)cGa>cAa	p.R921Q	STAG3_ENST00000317296.5_Missense_Mutation_p.R921Q|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.R863Q	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	921					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.R921Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CAGATTGACCGAAGTCATTGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											166	135	145					7																	99801705		2203	4300	6503	99639641	SO:0001583	missense	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2762G>A	7.37:g.99801705G>A	ENSP00000400359:p.Arg921Gln		99639641	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	18.41	3.618467	0.66787	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.22743	1.94;1.94;1.94	5.71	4.83	0.62350	.	0.174834	0.26944	N	0.021716	T	0.26159	0.0638	L	0.46614	1.455	0.80722	D	1	B;D;P	0.63046	0.243;0.992;0.676	B;P;B	0.50570	0.09;0.644;0.139	T	0.02238	-1.1190	10	0.87932	D	0	-7.404	8.9533	0.35803	0.167:0.0:0.833:0.0	.	863;921;921	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	Q	921;863;921	ENSP00000400359:R921Q;ENSP00000377586:R863Q;ENSP00000319318:R921Q	ENSP00000319318:R921Q	R	+	2	0	STAG3	99639641	0.992000	0.36948	0.884000	0.34674	0.911000	0.54048	2.625000	0.46452	1.428000	0.47296	0.655000	0.94253	CGA		0.507	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		A	99801705	G	A	99801705	3	1	61	1	0	0	0	0	1	0	0	0	15283	1058	37	1	2860	1	STAG3	7	99801705	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4509	99801705	59336958	5442	13427										
STAG3	10734	broad.mit.edu	37	chr7	99809443	99809443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttatggaagaggacgagGaagaagagttagaaatccag	14	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99809443G>A	ENST00000426455.1	+	32	3948	c.3541G>A	c.(3541-3543)Gaa>Aaa	p.E1181K	STAG3_ENST00000317296.5_Missense_Mutation_p.E1181K|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.E1123K	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	1181	Poly-Glu.				chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.E1181K(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGAGGACGAGGAAGAAGAGTT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											118	103	108					7																	99809443		2203	4300	6503	99647379	SO:0001583	missense	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.3541G>A	7.37:g.99809443G>A	ENSP00000400359:p.Glu1181Lys		99647379	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	g	12.80	2.045524	0.36085	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000379577;ENST00000317296;ENST00000412190	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.14	4.14	0.48551	.	0.384248	0.18924	N	0.127416	T	0.31071	0.0785	M	0.63843	1.955	0.80722	D	1	P;B;P	0.34522	0.455;0.319;0.455	B;B;B	0.32211	0.099;0.081;0.142	T	0.27536	-1.0071	10	0.87932	D	0	-2.4298	12.2062	0.54353	0.0:0.0:1.0:0.0	.	1123;1182;1181	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	K	1181;1123;844;202;1181;140	ENSP00000400359:E1181K;ENSP00000377586:E1123K;ENSP00000319318:E1181K;ENSP00000395039:E140K	ENSP00000319318:E1181K	E	+	1	0	STAG3	99647379	0.584000	0.26766	0.330000	0.25442	0.409000	0.31022	2.122000	0.41987	2.606000	0.88127	0.561000	0.74099	GAA		0.502	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		A	99809443	G	A	99809443	3	1	61	1	0	0	0	0	1	0	0	0	15283	1175	41	3	3663	3	STAG3	7	99809443	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7738	99809443	59329220	5443	13428										
PILRB	29990	broad.mit.edu	37	chr7	99957093	99957093	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagggttgcattggctgtCgctgtgctcaaaactgtcat	11	9	3	0	rs371268553		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99957093C>T	ENST00000452089.1	+	8	1647	c.588C>T	c.(586-588)gtC>gtT	p.V196V	PILRB_ENST00000448382.1_Missense_Mutation_p.R249C|PILRB_ENST00000444073.1_Silent_p.V196V|PILRB_ENST00000609309.1_Silent_p.V196V|PILRB_ENST00000610247.1_Silent_p.V196V|STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	196					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)		p.V196V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CATTGGCTGTCGCTGTGCTCA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	7											100	109	106					7																	99957093		2201	4300	6501	99795029	SO:0001819	synonymous_variant	29990			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"Immunoglobulin superfamily / V-set domain containing"	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.588C>T	7.37:g.99957093C>T			99795029	Q69YF9|Q9HBS0	Silent	SNP	ENST00000452089.1	37	CCDS43622.1	.	.	.	.	.	.	.	.	.	.	C	5.077	0.199872	0.09652	.	.	ENSG00000121716	ENST00000444874;ENST00000448382	.	.	.	2.32	-2.98	0.05513	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23084	-1.0198	6	.	.	.	.	6.1239	0.20167	0.0:0.4128:0.0:0.5872	.	127	Q9UKJ0-2	.	C	127;249	.	.	R	+	1	0	PILRB	99795029	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.414000	0.00237	-0.557000	0.06126	-0.275000	0.10095	CGC		0.547	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238		T	99957093	C	T	99957093	2	4	61	1	0	0	0	0	0	0	0	1	11957	884	31	1		1	PILRB	7	99957093	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147650	99957093	59181570	5444	13429										
PILRA	29992	broad.mit.edu	37	chr7	99987612	99987612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtcacacagggcaaacgaCgctcagactcttggcacata	11	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99987612C>T	ENST00000198536.2	+	3	768	c.556C>T	c.(556-558)Cgc>Tgc	p.R186C	PILRA_ENST00000453419.1_Intron|PILRA_ENST00000350573.2_Intron|PILRA_ENST00000394000.2_Intron	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	186					signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R186C(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGCAAACGACGCTCAGACTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											156	122	133					7																	99987612		2203	4300	6503	99825548	SO:0001583	missense	29992			AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"Immunoglobulin superfamily / V-set domain containing"	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.556C>T	7.37:g.99987612C>T	ENSP00000198536:p.Arg186Cys		99825548	Q8NHI1	Missense_Mutation	SNP	ENST00000198536.2	37	CCDS5691.1	.	.	.	.	.	.	.	.	.	.	C	9.355	1.066487	0.20067	.	.	ENSG00000085514	ENST00000198536	T	0.18338	2.22	2.8	0.359	0.16088	.	1.222400	0.05765	N	0.605562	T	0.06096	0.0158	N	0.08118	0	0.09310	N	1	P	0.46277	0.875	B	0.32211	0.142	T	0.20338	-1.0278	9	.	.	.	.	3.2664	0.06867	0.5906:0.265:0.1445:0.0	.	186	Q9UKJ1	PILRA_HUMAN	C	186	ENSP00000198536:R186C	.	R	+	1	0	PILRA	99825548	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.165000	0.16564	0.066000	0.16515	-1.105000	0.02106	CGC		0.582	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439		T	99987612	C	T	99987612	3	4	61	1	0	0	0	0	1	0	0	0	11956	536	19	1	566	1	PILRA	7	99987612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30519	99987612	59151051	5445	13430										
ZCWPW1	55063	broad.mit.edu	37	chr7	99998815	99998815	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtcaggggttcccggtgtCtgggctcttctttcgcagat	15	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:99998815C>A	ENST00000398027.2	-	18	2016	c.1769G>T	c.(1768-1770)aGa>aTa	p.R590I	ZCWPW1_ENST00000324725.6_Missense_Mutation_p.R419I|ZCWPW1_ENST00000360951.4_Missense_Mutation_p.D520Y|ZCWPW1_ENST00000490721.1_Missense_Mutation_p.R419I	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	590							zinc ion binding (GO:0008270)	p.R590I(1)		breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTCCCGGTGTCTGGGCTCTTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											46	47	47					7																	99998815		1889	4110	5999	99836751	SO:0001583	missense	55063			AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1769G>T	7.37:g.99998815C>A	ENSP00000381109:p.Arg590Ile		99836751	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	37	CCDS43623.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.66|13.66|13.66	2.304924|2.304924|2.304924	0.40795|0.40795|0.40795	.|.|.	.|.|.	ENSG00000078487|ENSG00000233389|ENSG00000078487	ENST00000360951;ENST00000471336|ENST00000449355|ENST00000398027;ENST00000490721;ENST00000324725	T;T|.|T;T;T	0.59906|.|0.46819	0.69;0.23|.|0.88;0.86;0.86	4.75|4.75|4.75	-4.39|-4.39|-4.39	0.03611|0.03611|0.03611	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	0.19287|0.19287|0.19287	0.0463|0.0463|0.0463	N|N|N	0.14661|0.14661|0.14661	0.345|0.345|0.345	0.09310|0.09310|0.09310	N|N|N	1|1|1	P|.|B;B;B	0.35982|.|0.30763	0.531|.|0.196;0.294;0.141	B|.|B;B;B	0.30646|.|0.21151	0.118|.|0.014;0.022;0.033	T|T|T	0.14035|0.14035|0.14035	-1.0487|-1.0487|-1.0487	8|5|8	.|.|.	.|.|.	.|.|.	5.7155|5.7155|5.7155	1.8897|1.8897|1.8897	0.03245|0.03245|0.03245	0.1225:0.1961:0.3611:0.3203|0.1225:0.1961:0.3611:0.3203|0.1225:0.1961:0.3611:0.3203	.|.|.	520|.|551;590;419	B4DUQ2|.|B4DXS7;Q9H0M4;Q9H0M4-4	.|.|.;ZCPW1_HUMAN;.	Y|M|I	520;242|29|590;419;419	ENSP00000354210:D520Y;ENSP00000418351:D242Y|.|ENSP00000381109:R590I;ENSP00000419187:R419I;ENSP00000314880:R419I	.|.|.	D|L|R	-|+|-	1|1|2	0|2|0	ZCWPW1|AC005071.3|ZCWPW1	99836751|99836751|99836751	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.001000|0.001000|0.001000	0.01503|0.01503|0.01503	-1.091000|-1.091000|-1.091000	0.03369|0.03369|0.03369	-0.814000|-0.814000|-0.814000	0.04352|0.04352|0.04352	-0.176000|-0.176000|-0.176000	0.13171|0.13171|0.13171	GAC|CTG|AGA		0.572	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		A	99998815	C	A	99998815	3	1	61	1	0	0	0	0	1	0	0	0	17636	913	32	2	181	2	ZCWPW1	7	99998815	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11203	99998815	59139848	5446	13431										
MEPCE	56257	broad.mit.edu	37	chr7	100030747	100030747	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtcgtcgtatggcaagaGaaagactcttacagtgagtt	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100030747G>T	ENST00000310512.2	+	2	2265	c.1877G>T	c.(1876-1878)aGa>aTa	p.R626I	PPP1R35_ENST00000476185.1_5'Flank|RP11-758P17.2_ENST00000492523.1_RNA|MEPCE_ENST00000414441.1_Missense_Mutation_p.R157I	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	626	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.R626I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TATGGCAAGAGAAAGACTCTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											62	59	60					7																	100030747		2203	4300	6503	99868683	SO:0001583	missense	56257			AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"bin3, bicoid-interacting 3, homolog (Drosophila)"	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.1877G>T	7.37:g.100030747G>T	ENSP00000308546:p.Arg626Ile		99868683	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	37	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038929	0.75617	.	.	ENSG00000146834	ENST00000414441;ENST00000425355;ENST00000310512	T	0.40756	1.02	5.37	5.37	0.77165	Bin3-type S-adenosyl-L-methionine binding domain (1);Bicoid-interacting 3 (1);	0.000000	0.85682	D	0.000000	T	0.65565	0.2703	M	0.79258	2.445	0.80722	D	1	D	0.71674	0.998	D	0.68621	0.959	T	0.68595	-0.5367	10	0.66056	D	0.02	-24.8873	16.9485	0.86237	0.0:0.0:1.0:0.0	.	626	Q7L2J0	MEPCE_HUMAN	I	157;157;626	ENSP00000400875:R157I	ENSP00000308546:R626I	R	+	2	0	MEPCE	99868683	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	5.965000	0.70387	2.677000	0.91161	0.462000	0.41574	AGA		0.602	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			T	100030747	G	T	100030747	3	4	61	1	0	0	0	0	1	0	0	0	9507	942	33	2	1883	2	MEPCE	7	100030747	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31932	100030747	59107916	5447	13432										
AGFG2	3268	broad.mit.edu	37	chr7	100148030	100148030	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttttaggtttgccggaaGatttggttgggtctgtttga	13	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100148030G>T	ENST00000300176.4	+	3	449	c.327G>T	c.(325-327)aaG>aaT	p.K109N	AGFG2_ENST00000262935.4_Missense_Mutation_p.K109N	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	109	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.K109N(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TTTGCCGGAAGATTTGGTTGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											130	133	132					7																	100148030		2203	4300	6503	99985966	SO:0001583	missense	3268			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.327G>T	7.37:g.100148030G>T	ENSP00000300176:p.Lys109Asn		99985966	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.838026	0.50951	.	.	ENSG00000106351	ENST00000300176;ENST00000262935	T;T	0.44881	0.91;0.91	6.14	4.32	0.51571	.	0.155894	0.64402	D	0.000018	T	0.54679	0.1873	L	0.48218	1.51	0.38971	D	0.958757	P;D	0.76494	0.544;0.999	B;D	0.74674	0.234;0.984	T	0.56226	-0.8014	10	0.49607	T	0.09	-9.994	11.6413	0.51235	0.146:0.0:0.854:0.0	.	109;109	O95081-2;O95081	.;AGFG2_HUMAN	N	109	ENSP00000300176:K109N;ENSP00000262935:K109N	ENSP00000262935:K109N	K	+	3	2	AGFG2	99985966	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.872000	0.39549	0.912000	0.36772	0.650000	0.86243	AAG		0.378	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		T	100148030	G	T	100148030	3	4	61	1	0	0	0	0	1	0	0	0	381	933	33	2	337	2	AGFG2	7	100148030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117283	100148030	58990633	5448	13433										
ZAN	7455	broad.mit.edu	37	chr7	100334193	100334193	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacgatgaagactgggttcGagccagtgggccctctccca	13	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100334193G>A	ENST00000348028.3	+	0	359				ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R65Q(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GACTGGGTTCGAGCCAGTGGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	78	79					7																	100334193		1821	3877	5698	100172129			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100334193G>A			100172129	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	G	16.87	3.242684	0.58995	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.02498	4.27;4.27;4.27	4.7	3.81	0.43845	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.29009	N	0.013438	T	0.12689	0.0308	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.959;0.976	T	0.00607	-1.1647	10	0.52906	T	0.07	.	11.4809	0.50324	0.0:0.1826:0.8174:0.0	.	65;65	F5H0T8;Q9Y493	.;ZAN_HUMAN	Q	65	ENSP00000445943:R65Q;ENSP00000445091:R65Q;ENSP00000444427:R65Q	ENSP00000423579:R65Q	R	+	2	0	ZAN	100172129	0.061000	0.20836	0.424000	0.26647	0.314000	0.28054	1.349000	0.33998	1.284000	0.44531	0.561000	0.74099	CGA		0.617	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		A	100334193	G	A	100334193	1	1	61	0	1	0	0	0	0	0	0	0	17553	1058	37	1		1	ZAN	7	100334193	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186163	100334193	58804470	5449	13434										
ZAN	7455	broad.mit.edu	37	chr7	100365562	100365562	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaactttgggctccaagttCgctacgacgggagccacttg	12	12	0	0	rs574171826	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100365562C>T	ENST00000348028.3	+	0	5134				ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1657C(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCTCCAAGTTCGCTACGACGG	0.612													C|||	2	0.000399361	0	0	5008	,	,		18318	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	7											56	62	60					7																	100365562		2089	4200	6289	100203498			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100365562C>T			100203498	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	C	17.98	3.519749	0.64634	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213	T;T;T;T	0.60171	0.21;0.21;0.21;0.21	4.77	4.77	0.60923	von Willebrand factor, type D domain (3);	0.000000	0.43747	D	0.000533	T	0.78898	0.4356	M	0.89601	3.045	0.37020	D	0.896133	D;D	0.89917	1.0;1.0	D;D	0.69824	0.942;0.966	D	0.85328	0.1088	10	0.66056	D	0.02	.	13.9911	0.64367	0.0:1.0:0.0:0.0	.	1657;1657	F5H0T8;Q9Y493	.;ZAN_HUMAN	C	1657;1657;1657;234	ENSP00000445943:R1657C;ENSP00000445091:R1657C;ENSP00000444427:R1657C;ENSP00000441117:R234C	ENSP00000423579:R1657C	R	+	1	0	ZAN	100203498	0.000000	0.05858	0.828000	0.32881	0.044000	0.14063	0.390000	0.20768	2.586000	0.87340	0.655000	0.94253	CGC		0.612	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100365562	C	T	100365562	1	4	61	0	1	0	0	0	0	0	0	0	17553	884	31	1		1	ZAN	7	100365562	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31369	100365562	58773101	5450	13435										
ZAN	7455	broad.mit.edu	37	chr7	100366278	100366278	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaacctgcgccccgacaGaaagcttgcaggcgattcca	10	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100366278G>T	ENST00000348028.3	+	0	5252				ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1696I(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CGCCCCGACAGAAAGCTTGCA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	7											28	28	28					7																	100366278		1864	4101	5965	100204214			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100366278G>T			100204214	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	G	15.59	2.878882	0.51801	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213	T;T;T;T	0.22134	2.47;2.47;2.45;1.97	4.62	-7.18	0.01505	von Willebrand factor, type D domain (2);	1.381740	0.04845	N	0.441344	T	0.15349	0.0370	N	0.19112	0.55	0.09310	N	1	P;P	0.47762	0.878;0.9	B;P	0.45712	0.359;0.491	T	0.38779	-0.9645	10	0.59425	D	0.04	.	9.6794	0.40061	0.18:0.0:0.7007:0.1193	.	1696;1696	F5H0T8;Q9Y493	.;ZAN_HUMAN	I	1696;1696;1696;273	ENSP00000445943:R1696I;ENSP00000445091:R1696I;ENSP00000444427:R1696I;ENSP00000441117:R273I	ENSP00000423579:R1696I	R	+	2	0	ZAN	100204214	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.042000	0.12063	-1.559000	0.01688	-0.345000	0.07892	AGA		0.607	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100366278	G	T	100366278	1	4	61	0	1	0	0	0	0	0	0	0	17553	942	33	2		2	ZAN	7	100366278	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	716	100366278	58772385	5451	13436										
EPHB4	2050	broad.mit.edu	37	chr7	100401167	100401167	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggacactggccaagatTttcttctggtgtcccgccag	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100401167T>G	ENST00000358173.3	-	17	3348	c.2880A>C	c.(2878-2880)aaA>aaC	p.K960N	EPHB4_ENST00000360620.3_Missense_Mutation_p.K908N	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	960	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K960N(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					TGGCCAAGATTTTCTTCTGGT	0.627																																					GBM(200;2113 3072 25865 52728)											1	Substitution - Missense(1)	large_intestine(1)	7											41	41	41					7																	100401167		2203	4300	6503	100239103	SO:0001583	missense	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.2880A>C	7.37:g.100401167T>G	ENSP00000350896:p.Lys960Asn		100239103	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435343	0.62955	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.61980	0.06;0.06	4.64	-0.382	0.12481	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.52532	D	0.000080	T	0.68915	0.3053	M	0.92880	3.355	0.45528	D	0.998485	P;P	0.46784	0.884;0.884	B;P	0.45794	0.287;0.493	T	0.70876	-0.4753	10	0.87932	D	0	.	7.8528	0.29464	0.0:0.3819:0.0:0.6181	.	908;960	Q96L35;P54760	.;EPHB4_HUMAN	N	908;960	ENSP00000353833:K908N;ENSP00000350896:K960N	ENSP00000350896:K960N	K	-	3	2	EPHB4	100239103	0.988000	0.35896	0.998000	0.56505	0.990000	0.78478	0.251000	0.18257	-0.075000	0.12798	0.374000	0.22700	AAA		0.627	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		G	100401167	T	G	100401167	3	3	61	1	0	0	0	0	1	0	0	0	5190	1838	64	4	87	4	EPHB4	7	100401167	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34889	100401167	58737496	5452	13437										
EPHB4	2050	broad.mit.edu	37	chr7	100411306	100411306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatactgtccgtgtttgtccGaatattctgcttctctccca	7	12	2	0	rs60537976		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100411306G>A	ENST00000358173.3	-	10	2192	c.1724C>T	c.(1723-1725)tCg>tTg	p.S575L	EPHB4_ENST00000360620.3_Missense_Mutation_p.S575L|EPHB4_ENST00000477446.1_5'Flank	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	575					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S575L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTGTTTGTCCGAATATTCTGC	0.493																																					GBM(200;2113 3072 25865 52728)											1	Substitution - Missense(1)	large_intestine(1)	7											380	352	362					7																	100411306		2203	4300	6503	100249242	SO:0001583	missense	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.1724C>T	7.37:g.100411306G>A	ENSP00000350896:p.Ser575Leu		100249242	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881491	0.51908	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.11712	2.75;2.75	5.5	5.5	0.81552	.	0.000000	0.47852	D	0.000220	T	0.08179	0.0204	L	0.42632	1.34	0.43637	D	0.996033	P;D	0.56035	0.93;0.974	B;B	0.34489	0.095;0.184	T	0.32348	-0.9910	10	0.23891	T	0.37	.	12.586	0.56419	0.0:0.1672:0.8328:0.0	rs60537976	575;575	Q96L35;P54760	.;EPHB4_HUMAN	L	575	ENSP00000353833:S575L;ENSP00000350896:S575L	ENSP00000350896:S575L	S	-	2	0	EPHB4	100249242	1.000000	0.71417	0.880000	0.34516	0.691000	0.40173	4.102000	0.57776	2.577000	0.86979	0.655000	0.94253	TCG		0.493	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100411306	G	A	100411306	3	1	61	1	0	0	0	0	1	0	0	0	5190	1059	37	1	1271	1	EPHB4	7	100411306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10139	100411306	58727357	5453	13438										
ACHE	43	broad.mit.edu	37	chr7	100490005	100490005	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagtcgctgggcgaagatTttctcctctgccgtgtagtt	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100490005T>G	ENST00000412389.1	-	2	1658	c.1503A>C	c.(1501-1503)aaA>aaC	p.K501N	ACHE_ENST00000241069.5_Missense_Mutation_p.K501N|ACHE_ENST00000428317.1_Missense_Mutation_p.K501N|ACHE_ENST00000302913.4_Missense_Mutation_p.K501N|ACHE_ENST00000411582.1_Missense_Mutation_p.K501N|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000419336.2_Missense_Mutation_p.K413N			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	501					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)	p.K501N(1)		large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GGGCGAAGATTTTCTCCTCTG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	7											51	49	50					7																	100490005		2203	4300	6503	100327941	SO:0001583	missense	43				CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1503A>C	7.37:g.100490005T>G	ENSP00000394976:p.Lys501Asn		100327941	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	T	1.831	-0.469884	0.04445	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000411582;ENST00000422451	T;T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31;-0.31	3.81	1.37	0.22104	Carboxylesterase, type B (1);	0.372421	0.27193	N	0.020498	T	0.50735	0.1633	L	0.53780	1.695	0.09310	N	0.999999	B;B;B	0.34372	0.027;0.451;0.062	B;B;B	0.25614	0.018;0.06;0.062	T	0.32188	-0.9916	10	0.26408	T	0.33	.	6.4117	0.21694	0.0:0.2222:0.0:0.7778	.	413;501;501	P22303-3;P22303-2;P22303	.;.;ACES_HUMAN	N	413;501;501;501;501;501;501	ENSP00000403474:K413N;ENSP00000241069:K501N;ENSP00000414858:K501N;ENSP00000303211:K501N;ENSP00000394976:K501N;ENSP00000404865:K501N	ENSP00000241069:K501N	K	-	3	2	ACHE	100327941	0.000000	0.05858	0.880000	0.34516	0.568000	0.35870	0.071000	0.14594	0.176000	0.19873	0.402000	0.26972	AAA		0.622	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		G	100490005	T	G	100490005	3	3	61	1	0	0	0	0	1	0	0	0	141	1838	64	4	488	4	ACHE	7	100490005	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	78699	100490005	58648658	5454	13439										
MUC17	140453	broad.mit.edu	37	chr7	100677393	100677393	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcacacctgtgaccaattCtactgaagcccgttcgtctc	7	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100677393C>A	ENST00000306151.4	+	3	2760	c.2696C>A	c.(2695-2697)tCt>tAt	p.S899Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	899	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.S899Y(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GTGACCAATTCTACTGAAGCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											304	293	297					7																	100677393		2203	4300	6503	100464113	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2696C>A	7.37:g.100677393C>A	ENSP00000302716:p.Ser899Tyr		100464113	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	4.169	0.029955	0.08101	.	.	ENSG00000169876	ENST00000306151	T	0.02682	4.2	1.19	1.19	0.21007	.	.	.	.	.	T	0.03827	0.0108	L	0.29908	0.895	0.09310	N	1	D	0.54964	0.969	P	0.50490	0.642	T	0.50406	-0.8832	9	0.28530	T	0.3	.	8.4004	0.32583	0.0:1.0:0.0:0.0	.	899	Q685J3	MUC17_HUMAN	Y	899	ENSP00000302716:S899Y	ENSP00000302716:S899Y	S	+	2	0	MUC17	100464113	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.238000	0.18004	1.000000	0.39049	0.134000	0.15878	TCT		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100677393	C	A	100677393	3	1	61	1	0	0	0	0	1	0	0	0	10004	913	32	2	2706	2	MUC17	7	100677393	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187388	100677393	58461270	5455	13440										
MUC17	140453	broad.mit.edu	37	chr7	100678532	100678532	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactagtgaaggaagtactCtattaacaagtatacctgtc	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100678532C>A	ENST00000306151.4	+	3	3899	c.3835C>A	c.(3835-3837)Cta>Ata	p.L1279I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1279	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.L1279I(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGGAAGTACTCTATTAACAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											277	267	270					7																	100678532		2203	4300	6503	100465252	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3835C>A	7.37:g.100678532C>A	ENSP00000302716:p.Leu1279Ile		100465252	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.671	-0.801948	0.02841	.	.	ENSG00000169876	ENST00000306151	T	0.02837	4.14	0.471	-0.942	0.10398	.	.	.	.	.	T	0.01254	0.0041	N	0.03608	-0.345	0.09310	N	1	B	0.23377	0.084	B	0.13407	0.009	T	0.46762	-0.9168	8	0.35671	T	0.21	.	.	.	.	.	1279	Q685J3	MUC17_HUMAN	I	1279	ENSP00000302716:L1279I	ENSP00000302716:L1279I	L	+	1	2	MUC17	100465252	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.497000	0.00969	-0.556000	0.06134	0.134000	0.15878	CTA		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100678532	C	A	100678532	3	1	61	1	0	0	0	0	1	0	0	0	10004	912	32	2	3845	2	MUC17	7	100678532	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1139	100678532	58460131	5456	13441										
MUC17	140453	broad.mit.edu	37	chr7	100680945	100680945	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattctactgaagccagttCatctgcaaccgctgaaggta	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100680945C>T	ENST00000306151.4	+	3	6312	c.6248C>T	c.(6247-6249)tCa>tTa	p.S2083L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2083	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.S2083L(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GAAGCCAGTTCATCTGCAACC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											172	171	171					7																	100680945		2203	4300	6503	100467665	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6248C>T	7.37:g.100680945C>T	ENSP00000302716:p.Ser2083Leu		100467665	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	3.627	-0.076438	0.07184	.	.	ENSG00000169876	ENST00000306151	T	0.02606	4.23	0.942	-0.252	0.12999	.	.	.	.	.	T	0.01627	0.0052	L	0.29908	0.895	0.09310	N	1	P	0.38110	0.618	B	0.25759	0.063	T	0.48592	-0.9022	9	0.13108	T	0.6	.	5.9269	0.19118	0.3055:0.6945:0.0:0.0	.	2083	Q685J3	MUC17_HUMAN	L	2083	ENSP00000302716:S2083L	ENSP00000302716:S2083L	S	+	2	0	MUC17	100467665	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.049000	0.14099	-0.058000	0.13177	0.134000	0.15878	TCA		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100680945	C	T	100680945	3	4	61	1	0	0	0	0	1	0	0	0	10004	838	29	3	6258	3	MUC17	7	100680945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2413	100680945	58457718	5457	13442										
TRIM56	81844	broad.mit.edu	37	chr7	100732537	100732537	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagcccccaggggcatttCgtggggtcggactggcagca	15	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100732537C>T	ENST00000306085.6	+	3	2241	c.1944C>T	c.(1942-1944)ttC>ttT	p.F648F		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	648					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F648F(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					AGGGGCATTTCGTGGGGTCGG	0.652																																					Ovarian(89;1092 1379 22756 38989 39611)											1	Substitution - coding silent(1)	large_intestine(1)	7											100	108	106					7																	100732537		1894	4099	5993	100519257	SO:0001819	synonymous_variant	81844			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1944C>T	7.37:g.100732537C>T			100519257	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																				0.652	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		T	100732537	C	T	100732537	2	4	61	1	0	0	0	0	0	0	0	1	16570	883	31	1		1	TRIM56	7	100732537	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51592	100732537	58406126	5458	13443										
SERPINE1	5054	broad.mit.edu	37	chr7	100771897	100771897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctccagctgacaacaggaGgagaaacccagcagcagatt	11	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100771897G>A	ENST00000223095.4	+	2	380	c.223G>A	c.(223-225)Gga>Aga	p.G75R	SERPINE1_ENST00000445463.2_Missense_Mutation_p.G60R	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	75				G -> V (in Ref. 7; CAA31208). {ECO:0000305}.	angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G75R(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GACAACAGGAGGAGAAACCCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											54	52	53					7																	100771897		2203	4300	6503	100558617	SO:0001583	missense	5054			M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"Serine (or cysteine) peptidase inhibitors"	8583	protein-coding gene	gene with protein product	"plasminogen activator inhibitor, type I"	173360	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.223G>A	7.37:g.100771897G>A	ENSP00000223095:p.Gly75Arg		100558617	B7Z4S0|F8WD53	Missense_Mutation	SNP	ENST00000223095.4	37	CCDS5711.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.106267	0.77096	.	.	ENSG00000106366	ENST00000223095;ENST00000445463;ENST00000441467	T;T	0.31510	1.49;1.49	5.71	5.71	0.89125	Serpin domain (3);	0.000000	0.85682	D	0.000000	T	0.67988	0.2952	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77127	-0.2702	10	0.87932	D	0	.	17.3615	0.87351	0.0:0.0:1.0:0.0	.	60;75	F8WD53;P05121	.;PAI1_HUMAN	R	75;60;60	ENSP00000223095:G75R;ENSP00000396766:G60R	ENSP00000223095:G75R	G	+	1	0	SERPINE1	100558617	1.000000	0.71417	0.257000	0.24404	0.368000	0.29767	5.802000	0.69122	2.709000	0.92574	0.655000	0.94253	GGA		0.582	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		A	100771897	G	A	100771897	3	1	61	1	0	0	0	0	1	0	0	0	14148	1001	35	3	225	3	SERPINE1	7	100771897	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39360	100771897	58366766	5459	13444										
SERPINE1	5054	broad.mit.edu	37	chr7	100777074	100777074	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctgccccttatgaaaaaGaggtgcctctctctgccctc	8	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:100777074G>T	ENST00000223095.4	+	5	956	c.799G>T	c.(799-801)Gag>Tag	p.E267*	SERPINE1_ENST00000445463.2_Nonsense_Mutation_p.E252*	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	267					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E267*(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TTATGAAAAAGAGGTGCCTCT	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											184	153	164					7																	100777074		2203	4300	6503	100563794	SO:0001587	stop_gained	5054			M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"Serine (or cysteine) peptidase inhibitors"	8583	protein-coding gene	gene with protein product	"plasminogen activator inhibitor, type I"	173360	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.799G>T	7.37:g.100777074G>T	ENSP00000223095:p.Glu267*		100563794	B7Z4S0|F8WD53	Nonsense_Mutation	SNP	ENST00000223095.4	37	CCDS5711.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124529	0.77436	.	.	ENSG00000106366	ENST00000223095;ENST00000445463;ENST00000536888	.	.	.	5.67	2.86	0.33363	.	0.408932	0.26341	N	0.024930	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	7.7566	0.28927	0.1383:0.2701:0.5916:0.0	.	.	.	.	X	267;252;44	.	ENSP00000223095:E267X	E	+	1	0	SERPINE1	100563794	0.997000	0.39634	0.126000	0.21872	0.236000	0.25371	1.708000	0.37899	0.323000	0.23307	-1.268000	0.01426	GAG		0.572	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		T	100777074	G	T	100777074	4	4	61	1	0	0	0	0	0	1	0	0	14148	943	33	2	813	2	SERPINE1	7	100777074	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5177	100777074	58361589	5460	13445										
EMID2	136227	broad.mit.edu	37	chr7	101063297	101063297	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacacggacggtgtcctgCcaggtgcagaatggctcgga	16	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:101063297C>T	ENST00000397927.3	+	0	411				COL26A1_ENST00000313669.7_RNA|COL26A1_ENST00000528707.1_RNA	NM_001278563.1	NP_001265492.1	Q96A83	COQA1_HUMAN	collagen, type XXVI, alpha 1						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.C66C(1)									CGGTGTCCTGCCAGGTGCAGA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	7											32	41	38					7																	101063297		2098	4229	6327	100850017			136227			AJ416091	CCDS64739.1	7q22.1	2013-01-16	2013-01-16	2013-01-16	ENSG00000160963	ENSG00000160963		"Collagens", "EMI domain containing"	18038	protein-coding gene	gene with protein product	"Emu2 gene"	608927	"EMI domain containing 2"	EMID2		12221002, 12145293	Standard	NM_001278563		Approved	Emu2, EMI6	uc003uyo.1	Q96A83	OTTHUMG00000150033		7.37:g.101063297C>T			100850017	Q32M90	Silent	SNP	ENST00000397927.3	37																																																																																					0.642	COL26A1-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000315898.2	NM_133457		T	101063297	C	T	101063297	1	4	61	0	1	0	0	0	0	0	0	0	5105	747	26	3		3	EMID2	7	101063297	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	286223	101063297	58075366	5461	13446										
MYL10	93408	broad.mit.edu	37	chr7	101265464	101265464	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcctccagttcctcgttCttgacattgatgcggcctgt	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:101265464C>A	ENST00000223167.4	-	5	543	c.366G>T	c.(364-366)aaG>aaT	p.K122N		NM_138403.4	NP_612412.2	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	122						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)	p.K122N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	12						GTTCCTCGTTCTTGACATTGA	0.597																																					Esophageal Squamous(24;575 709 17516 40384 51639)											1	Substitution - Missense(1)	large_intestine(1)	7											96	79	85					7																	101265464		2203	4300	6503	101052184	SO:0001583	missense	93408			BC002778	CCDS34713.1	7q22.1	2013-01-10			ENSG00000106436	ENSG00000106436		"Myosins / Light chain", "EF-hand domain containing"	29825	protein-coding gene	gene with protein product						1628631	Standard	NM_138403		Approved	MGC3479, MYLC2PL, PLRLC	uc003uyr.3	Q9BUA6	OTTHUMG00000157137	ENST00000223167.4:c.366G>T	7.37:g.101265464C>A	ENSP00000223167:p.Lys122Asn		101052184		Missense_Mutation	SNP	ENST00000223167.4	37	CCDS34713.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709692	0.30322	.	.	ENSG00000106436	ENST00000223167	T	0.78595	-1.19	4.28	2.44	0.29823	EF-hand-like domain (1);	0.246159	0.35013	N	0.003502	T	0.77485	0.4137	L	0.31420	0.93	0.37654	D	0.922513	P	0.46142	0.873	P	0.62014	0.897	T	0.75357	-0.3346	10	0.37606	T	0.19	.	9.3975	0.38412	0.0:0.82:0.0:0.18	.	122	Q9BUA6	MYL10_HUMAN	N	122	ENSP00000223167:K122N	ENSP00000223167:K122N	K	-	3	2	MYL10	101052184	1.000000	0.71417	0.988000	0.46212	0.021000	0.10359	0.876000	0.28092	0.382000	0.24878	0.460000	0.39030	AAG		0.597	MYL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347575.1	NM_138403		A	101265464	C	A	101265464	3	1	61	1	0	0	0	0	1	0	0	0	10074	912	32	2	330	2	MYL10	7	101265464	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	202167	101265464	57873199	5462	13447										
CUX1	1523	broad.mit.edu	37	chr7	101925170	101925170	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaagatggcgcgcaccatCggcttcttctacacactgtt	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:101925170C>T	ENST00000437600.4	+	21	2206	c.1854C>T	c.(1852-1854)atC>atT	p.I618I	CUX1_ENST00000292538.4_Silent_p.I620I|CUX1_ENST00000393824.3_Silent_p.I581I|CUX1_ENST00000547394.2_Silent_p.I604I|CUX1_ENST00000425244.2_Silent_p.I574I|CUX1_ENST00000560541.1_3'UTR	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	0					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.I620I(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CGCGCACCATCGGCTTCTTCT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	7											100	75	84					7																	101925170		2203	4300	6503	101711890	SO:0001819	synonymous_variant	1523			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1854C>T	7.37:g.101925170C>T			101711890	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000437600.4	37	CCDS47672.1																																																																																				0.652	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913		T	101925170	C	T	101925170	2	4	61	1	0	0	0	0	0	0	0	1	4070	874	31	1		1	CUX1	7	101925170	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	659706	101925170	57213493	5463	13448										
FBXL13	222235	broad.mit.edu	37	chr7	102518869	102518869	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcttgcaggaccatcaaGaaattgctttagtcccatat	7	10	1	1	rs199732318		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:102518869G>T	ENST00000313221.4	-	15	1843	c.1417C>A	c.(1417-1419)Ctt>Att	p.L473I	FBXL13_ENST00000379305.3_Missense_Mutation_p.L473I|FBXL13_ENST00000455112.2_Missense_Mutation_p.L473I|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000393772.2_Missense_Mutation_p.L473I|FBXL13_ENST00000379308.3_Missense_Mutation_p.L473I|FBXL13_ENST00000436908.1_Missense_Mutation_p.L473I|FBXL13_ENST00000379306.3_Intron	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	473								p.L473I(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						GGACCATCAAGAAATTGCTTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	ILE/LEU,ILE/LEU	0,4406		0,0,2203	107	97	100		1417,1417	3.5	1	7		100	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	FBXL13	NM_001111038.1,NM_145032.3	5,5	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	benign,benign	473/691,473/736	102518869	2,13004	2203	4300	6503	102306105	SO:0001583	missense	222235			BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.1417C>A	7.37:g.102518869G>T	ENSP00000321927:p.Leu473Ile		102306105	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Missense_Mutation	SNP	ENST00000313221.4	37	CCDS5726.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	12.40	1.925894	0.34002	0.0	2.33E-4	ENSG00000161040	ENST00000393772;ENST00000379308;ENST00000349747;ENST00000379305;ENST00000436908;ENST00000313221;ENST00000455112	T;T;T;T;T;T	0.54279	4.44;0.6;4.44;0.58;0.58;0.6	5.38	3.55	0.40652	.	0.265332	0.30869	N	0.008716	T	0.43166	0.1235	L	0.38953	1.18	0.80722	D	1	B;P;B	0.52842	0.346;0.956;0.118	B;P;B	0.47044	0.335;0.535;0.141	T	0.25537	-1.0129	10	0.35671	T	0.21	.	6.3781	0.21519	0.1715:0.1935:0.635:0.0	.	473;473;473	Q8NEE6-3;Q8NEE6-2;Q8NEE6	.;.;FXL13_HUMAN	I	473;473;194;473;473;473;473	ENSP00000377367:L473I;ENSP00000368610:L473I;ENSP00000368607:L473I;ENSP00000388608:L473I;ENSP00000321927:L473I;ENSP00000391550:L473I	ENSP00000321927:L473I	L	-	1	0	FBXL13	102306105	0.997000	0.39634	0.998000	0.56505	0.858000	0.48976	0.366000	0.20365	1.266000	0.44231	0.655000	0.94253	CTT		0.343	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		T	102518869	G	T	102518869	3	4	61	1	0	0	0	0	1	0	0	0	5728	942	33	2	814	2	FBXL13	7	102518869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	593699	102518869	56619794	5464	13449										
LRRC17	10234	broad.mit.edu	37	chr7	102584932	102584932	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttactatgaagaatgccccAaagacaagttaccagcatat	7	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:102584932A>C	ENST00000339431.4	+	4	1499	c.1204A>C	c.(1204-1206)Aaa>Caa	p.K402Q	FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000436908.1_Intron|LRRC17_ENST00000249377.4_3'UTR|FBXL13_ENST00000379306.3_Intron|LRRC17_ENST00000485478.1_3'UTR	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	402	LRRCT 2.				bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)		p.K402Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						AGAATGCCCCAAAGACAAGTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	85	87					7																	102584932		2203	4300	6503	102372168	SO:0001583	missense	10234			U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.1204A>C	7.37:g.102584932A>C	ENSP00000344242:p.Lys402Gln		102372168	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.550653	0.86127	.	.	ENSG00000128606	ENST00000339431	T	0.60424	0.19	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000013	T	0.44477	0.1295	N	0.24115	0.695	0.80722	D	1	P	0.45902	0.868	B	0.39876	0.312	T	0.37911	-0.9685	10	0.27082	T	0.32	-24.8285	16.1303	0.81428	1.0:0.0:0.0:0.0	.	402	Q8N6Y2	LRC17_HUMAN	Q	402	ENSP00000344242:K402Q	ENSP00000344242:K402Q	K	+	1	0	LRRC17	102372168	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.421000	0.66447	2.218000	0.71995	0.533000	0.62120	AAA		0.393	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		C	102584932	A	C	102584932	3	2	61	1	0	0	0	0	1	0	0	0	9002	131	5	4	1232	4	LRRC17	7	102584932	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	66063	102584932	56553731	5465	13450										
NAPEPLD	222236	broad.mit.edu	37	chr7	102760469	102760469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgtgcacggggaacgacGaaatcgctttggacccatgt	12	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:102760469G>A	ENST00000417955.1	-	3	650	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C	NAPEPLD_ENST00000455523.2_Missense_Mutation_p.R239C|NAPEPLD_ENST00000341533.4_Missense_Mutation_p.R166C|NAPEPLD_ENST00000465647.1_Missense_Mutation_p.R166C|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.R166C			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	166					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)	p.R166C(2)		endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GGGGAACGACGAAATCGCTTT	0.473																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	7											200	171	180					7																	102760469		2203	4300	6503	102547705	SO:0001583	missense	222236			BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.496C>T	7.37:g.102760469G>A	ENSP00000407112:p.Arg166Cys		102547705	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.178881	0.57692	.	.	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523	D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38	5.93	4.12	0.48240	.	0.045078	0.85682	N	0.000000	D	0.92512	0.7622	M	0.72576	2.205	0.80722	D	1	B;B	0.33022	0.394;0.072	B;B	0.36244	0.22;0.052	D	0.90344	0.4361	10	0.48119	T	0.1	-35.9257	13.5805	0.61901	0.1144:0.0:0.8856:0.0	.	239;166	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	C	166;166;166;166;239	ENSP00000340093:R166C;ENSP00000407112:R166C;ENSP00000419188:R166C;ENSP00000392775:R166C;ENSP00000414364:R239C	ENSP00000340093:R166C	R	-	1	0	NAPEPLD	102547705	1.000000	0.71417	0.031000	0.17742	0.908000	0.53690	3.762000	0.55250	0.840000	0.34995	0.591000	0.81541	CGT		0.473	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990		A	102760469	G	A	102760469	3	1	61	1	0	0	0	0	1	0	0	0	10193	1058	37	1	697	1	NAPEPLD	7	102760469	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	175537	102760469	56378194	5466	13451										
SLC26A5	375611	broad.mit.edu	37	chr7	103038399	103038399	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctagaggaagtgttccaacGacatccacattgtatgattc	8	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103038399G>A	ENST00000306312.3	-	9	1212	c.951C>T	c.(949-951)gtC>gtT	p.V317V	SLC26A5_ENST00000432958.2_Silent_p.V317V|SLC26A5_ENST00000339444.6_Silent_p.V317V|SLC26A5_ENST00000393727.1_Silent_p.V317V|SLC26A5_ENST00000356767.4_Silent_p.V317V|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000393723.1_Silent_p.V317V|SLC26A5_ENST00000393730.1_Silent_p.V317V|SLC26A5_ENST00000393729.1_Silent_p.V280V|SLC26A5_ENST00000393735.2_Silent_p.V317V	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	317					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)	p.V317V(1)		endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						GTGTTCCAACGACATCCACAT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7											148	130	136					7																	103038399		2203	4300	6503	102825635	SO:0001819	synonymous_variant	375611			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.951C>T	7.37:g.103038399G>A			102825635	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																				0.378	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		A	103038399	G	A	103038399	2	1	61	1	0	0	0	0	0	0	0	1	14557	1045	37	1		1	SLC26A5	7	103038399	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	277930	103038399	56100264	5467	13452										
SLC26A5	375611	broad.mit.edu	37	chr7	103061222	103061222	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccctgtgcttatgcctgaGaccaagtcacccaacacata	6	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103061222G>T	ENST00000306312.3	-	4	516	c.255C>A	c.(253-255)gtC>gtA	p.V85V	SLC26A5_ENST00000432958.2_Silent_p.V85V|SLC26A5_ENST00000339444.6_Silent_p.V85V|SLC26A5_ENST00000393727.1_Silent_p.V85V|SLC26A5_ENST00000356767.4_Silent_p.V85V|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000393723.1_Silent_p.V85V|SLC26A5_ENST00000393730.1_Silent_p.V85V|SLC26A5_ENST00000393729.1_Silent_p.V85V|SLC26A5_ENST00000393735.2_Silent_p.V85V	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	85					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)	p.V85V(1)		endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTATGCCTGAGACCAAGTCAC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	7											133	132	132					7																	103061222		2203	4300	6503	102848458	SO:0001819	synonymous_variant	375611			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.255C>A	7.37:g.103061222G>T			102848458	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																				0.408	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		T	103061222	G	T	103061222	2	4	61	1	0	0	0	0	0	0	0	1	14557	929	33	2		2	SLC26A5	7	103061222	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22823	103061222	56077441	5468	13453										
RELN	5649	broad.mit.edu	37	chr7	103151406	103151406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccatcaggggagtcacaGaatctttctactgtacaatc	7	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103151406G>T	ENST00000428762.1	-	51	8325	c.8166C>A	c.(8164-8166)ttC>ttA	p.F2722L	RELN_ENST00000343529.5_Missense_Mutation_p.F2722L|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Missense_Mutation_p.F2722L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2722					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.F2722L(2)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGGAGTCACAGAATCTTTCTA	0.418																																					NSCLC(146;835 1944 15585 22231 52158)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	7											127	104	112					7																	103151406		2203	4300	6503	102938642	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.8166C>A	7.37:g.103151406G>T	ENSP00000392423:p.Phe2722Leu		102938642	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719835	0.48728	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.19938	2.11;2.11;2.11	5.65	2.85	0.33270	Neuraminidase (2);	0.000000	0.85682	D	0.000000	T	0.38904	0.1058	M	0.64404	1.975	0.47778	D	0.999512	D;B	0.76494	0.999;0.077	D;B	0.81914	0.995;0.056	T	0.06588	-1.0818	10	0.39692	T	0.17	.	10.4919	0.44756	0.2852:0.0:0.7148:0.0	.	2722;2722	P78509-2;P78509	.;RELN_HUMAN	L	2722;2722;2722;239;2722	ENSP00000392423:F2722L;ENSP00000345694:F2722L;ENSP00000388446:F2722L	ENSP00000345694:F2722L	F	-	3	2	RELN	102938642	1.000000	0.71417	0.997000	0.53966	0.201000	0.24016	4.579000	0.60936	0.743000	0.32719	-0.148000	0.13756	TTC		0.418	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103151406	G	T	103151406	3	4	61	1	0	0	0	0	1	0	0	0	13257	933	33	2	2276	2	RELN	7	103151406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90184	103151406	55987257	5469	13454										
RELN	5649	broad.mit.edu	37	chr7	103183303	103183303	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccaccactcattaataaGaatctatcagattctagctg	4	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103183303G>T	ENST00000428762.1	-	43	6705	c.6546C>A	c.(6544-6546)ttC>ttA	p.F2182L	RELN_ENST00000343529.5_Missense_Mutation_p.F2182L|RELN_ENST00000424685.2_Missense_Mutation_p.F2182L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2182					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.F2182L(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TCATTAATAAGAATCTATCAG	0.363																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											79	80	80					7																	103183303		2203	4300	6503	102970539	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6546C>A	7.37:g.103183303G>T	ENSP00000392423:p.Phe2182Leu		102970539	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.633927	0.67130	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.32272	1.46;1.46;1.46	5.79	3.99	0.46301	Neuraminidase (1);	0.111902	0.64402	D	0.000007	T	0.43389	0.1245	L	0.44542	1.39	0.48087	D	0.999588	D;D	0.89917	1.0;0.998	D;D	0.73380	0.98;0.939	T	0.29212	-1.0019	10	0.72032	D	0.01	.	8.7515	0.34618	0.2845:0.0:0.7155:0.0	.	2182;2182	P78509-2;P78509	.;RELN_HUMAN	L	2182	ENSP00000392423:F2182L;ENSP00000345694:F2182L;ENSP00000388446:F2182L	ENSP00000345694:F2182L	F	-	3	2	RELN	102970539	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	3.420000	0.52735	0.785000	0.33685	0.591000	0.81541	TTC		0.363	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103183303	G	T	103183303	3	4	61	1	0	0	0	0	1	0	0	0	13257	933	33	2	3928	2	RELN	7	103183303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31897	103183303	55955360	5470	13455										
RELN	5649	broad.mit.edu	37	chr7	103194238	103194238	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtttacattatttccatcGataatgaagtcatcaacaat	4	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103194238G>A	ENST00000428762.1	-	39	5997	c.5838C>T	c.(5836-5838)atC>atT	p.I1946I	RELN_ENST00000343529.5_Silent_p.I1946I|RELN_ENST00000424685.2_Silent_p.I1946I	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1946					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.I1946I(2)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TATTTCCATCGATAATGAAGT	0.363																																					NSCLC(146;835 1944 15585 22231 52158)											2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	7											151	142	145					7																	103194238		2203	4300	6503	102981474	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5838C>T	7.37:g.103194238G>A			102981474	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.363	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103194238	G	A	103194238	2	1	61	1	0	0	0	0	0	0	0	1	13257	1048	37	1		1	RELN	7	103194238	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10935	103194238	55944425	5471	13456										
RELN	5649	broad.mit.edu	37	chr7	103198423	103198423	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacttactttttgctataAatctaagtgaaaactggaca	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103198423A>C	ENST00000428762.1	-	37	5762	c.5603T>G	c.(5602-5604)tTt>tGt	p.F1868C	RELN_ENST00000343529.5_Missense_Mutation_p.F1868C|RELN_ENST00000424685.2_Missense_Mutation_p.F1868C	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1868					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.F1868C(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTTTGCTATAAATCTAAGTGA	0.318																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											60	62	61					7																	103198423		2197	4286	6483	102985659	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5603T>G	7.37:g.103198423A>C	ENSP00000392423:p.Phe1868Cys		102985659	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.435175	0.62955	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.31769	1.48;1.48;1.48	5.77	4.62	0.57501	Neuraminidase (1);	0.052456	0.85682	D	0.000000	T	0.49949	0.1587	L	0.60455	1.87	0.50632	D	0.999883	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.987	T	0.51020	-0.8758	10	0.87932	D	0	.	11.9144	0.52757	0.9321:0.0:0.0679:0.0	.	1868;1868	P78509-2;P78509	.;RELN_HUMAN	C	1868	ENSP00000392423:F1868C;ENSP00000345694:F1868C;ENSP00000388446:F1868C	ENSP00000345694:F1868C	F	-	2	0	RELN	102985659	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	1.125000	0.41998	0.533000	0.62120	TTT		0.318	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103198423	A	C	103198423	3	2	61	1	0	0	0	0	1	0	0	0	13257	14	1	4	4895	4	RELN	7	103198423	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4185	103198423	55940240	5472	13457										
RELN	5649	broad.mit.edu	37	chr7	103202398	103202398	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgaaccgggtcctgggaGaactaaccaaaaaaaaaaaa	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103202398G>T	ENST00000428762.1	-	35	5372	c.5213C>A	c.(5212-5214)tCt>tAt	p.S1738Y	RELN_ENST00000343529.5_Missense_Mutation_p.S1738Y|RELN_ENST00000424685.2_Missense_Mutation_p.S1738Y	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1738					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.S1738Y(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGTCCTGGGAGAACTAACCAA	0.433																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											38	32	34					7																	103202398		2203	4300	6503	102989634	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5213C>A	7.37:g.103202398G>T	ENSP00000392423:p.Ser1738Tyr		102989634	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603329	0.87157	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.27104	1.69;1.69;1.69	5.78	5.78	0.91487	Neuraminidase (1);	0.000000	0.85682	D	0.000000	T	0.58133	0.2101	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.988	T	0.61715	-0.7006	10	0.87932	D	0	.	20.0118	0.97458	0.0:0.0:1.0:0.0	.	1738;1738	P78509-2;P78509	.;RELN_HUMAN	Y	1738	ENSP00000392423:S1738Y;ENSP00000345694:S1738Y;ENSP00000388446:S1738Y	ENSP00000345694:S1738Y	S	-	2	0	RELN	102989634	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.209000	0.95087	2.744000	0.94065	0.563000	0.77884	TCT		0.433	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103202398	G	T	103202398	3	4	61	1	0	0	0	0	1	0	0	0	13257	942	33	2	5293	2	RELN	7	103202398	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3975	103202398	55936265	5473	13458										
RELN	5649	broad.mit.edu	37	chr7	103205756	103205756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaaggtagacagtgatccGcttccaattctggaatcttt	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103205756G>A	ENST00000428762.1	-	34	5338	c.5179C>T	c.(5179-5181)Cgg>Tgg	p.R1727W	RELN_ENST00000343529.5_Missense_Mutation_p.R1727W|RELN_ENST00000424685.2_Missense_Mutation_p.R1727W	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1727					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.R1727W(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACAGTGATCCGCTTCCAATTC	0.438																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											123	111	115					7																	103205756		2203	4300	6503	102992992	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5179C>T	7.37:g.103205756G>A	ENSP00000392423:p.Arg1727Trp		102992992	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.381839	0.82792	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.55588	1.31;0.51;1.31	6.02	4.09	0.47781	Neuraminidase (1);	0.053048	0.64402	D	0.000001	T	0.73760	0.3628	M	0.84585	2.705	0.50467	D	0.999879	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.78889	-0.2026	10	0.87932	D	0	.	12.891	0.58071	0.0:0.0:0.4962:0.5038	.	1727;1727	P78509-2;P78509	.;RELN_HUMAN	W	1727	ENSP00000392423:R1727W;ENSP00000345694:R1727W;ENSP00000388446:R1727W	ENSP00000345694:R1727W	R	-	1	2	RELN	102992992	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.045000	0.49838	1.518000	0.48934	0.655000	0.94253	CGG		0.438	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103205756	G	A	103205756	3	1	61	1	0	0	0	0	1	0	0	0	13257	1086	38	1	5331	1	RELN	7	103205756	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3358	103205756	55932907	5474	13459										
RELN	5649	broad.mit.edu	37	chr7	103207092	103207092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccgttgcaggtgtcttcGcgtcctgtggcaggtcaatg	14	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103207092G>A	ENST00000428762.1	-	32	4862	c.4703C>T	c.(4702-4704)gCg>gTg	p.A1568V	RELN_ENST00000343529.5_Missense_Mutation_p.A1568V|RELN_ENST00000424685.2_Missense_Mutation_p.A1568V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1568					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.A1568V(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGGTGTCTTCGCGTCCTGTGG	0.468																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											117	101	106					7																	103207092		2203	4300	6503	102994328	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.4703C>T	7.37:g.103207092G>A	ENSP00000392423:p.Ala1568Val		102994328	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128338	0.94473	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.34072	1.38;1.38;1.38	5.95	5.95	0.96441	.	0.053931	0.64402	D	0.000001	T	0.49795	0.1578	M	0.80332	2.49	0.58432	D	0.999998	D;D	0.63880	0.993;0.992	P;B	0.44518	0.452;0.266	T	0.58940	-0.7547	10	0.87932	D	0	.	20.3719	0.98893	0.0:0.0:1.0:0.0	.	1568;1568	P78509-2;P78509	.;RELN_HUMAN	V	1568	ENSP00000392423:A1568V;ENSP00000345694:A1568V;ENSP00000388446:A1568V	ENSP00000345694:A1568V	A	-	2	0	RELN	102994328	1.000000	0.71417	0.975000	0.42487	0.881000	0.50899	9.189000	0.94928	2.826000	0.97356	0.491000	0.48974	GCG		0.468	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103207092	G	A	103207092	3	1	61	1	0	0	0	0	1	0	0	0	13257	1087	38	1	5815	1	RELN	7	103207092	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1336	103207092	55931571	5475	13460										
RELN	5649	broad.mit.edu	37	chr7	103230147	103230147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttctctggagtttccttcGcatcctttgcctgcagaagc	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103230147G>A	ENST00000428762.1	-	28	4200	c.4041C>T	c.(4039-4041)tgC>tgT	p.C1347C	RELN_ENST00000343529.5_Silent_p.C1347C|RELN_ENST00000424685.2_Silent_p.C1347C	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1347					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.C1347C(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGTTTCCTTCGCATCCTTTGC	0.473																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - coding silent(1)	large_intestine(1)	7											197	175	183					7																	103230147		2203	4300	6503	103017383	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.4041C>T	7.37:g.103230147G>A			103017383	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.473	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103230147	G	A	103230147	2	1	61	1	0	0	0	0	0	0	0	1	13257	1079	38	1		1	RELN	7	103230147	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23055	103230147	55908516	5476	13461										
RELN	5649	broad.mit.edu	37	chr7	103293089	103293089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaacaggcaagacatggaAaaagtctacagcccagacat	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103293089A>G	ENST00000428762.1	-	14	1831	c.1672T>C	c.(1672-1674)Ttc>Ctc	p.F558L	RELN_ENST00000343529.5_Missense_Mutation_p.F558L|RELN_ENST00000424685.2_Missense_Mutation_p.F558L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	558					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.F558L(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AAGACATGGAAAAAGTCTACA	0.443																																					NSCLC(146;835 1944 15585 22231 52158)											1	Substitution - Missense(1)	large_intestine(1)	7											159	155	157					7																	103293089		2203	4300	6503	103080325	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.1672T>C	7.37:g.103293089A>G	ENSP00000392423:p.Phe558Leu		103080325	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	13.90	2.374641	0.42105	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.19394	2.16;2.15;2.16	5.67	5.67	0.87782	.	0.096403	0.64402	D	0.000001	T	0.15132	0.0365	L	0.27053	0.805	0.36774	D	0.883946	B;B	0.20780	0.037;0.048	B;B	0.18561	0.022;0.022	T	0.16100	-1.0414	10	0.24483	T	0.36	.	12.1139	0.53854	0.8569:0.1431:0.0:0.0	.	558;558	P78509-2;P78509	.;RELN_HUMAN	L	558	ENSP00000392423:F558L;ENSP00000345694:F558L;ENSP00000388446:F558L	ENSP00000345694:F558L	F	-	1	0	RELN	103080325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.306000	0.59117	2.288000	0.76882	0.533000	0.62120	TTC		0.443	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103293089	A	G	103293089	3	3	61	1	0	0	0	0	1	0	0	0	13257	14	1	4	8918	4	RELN	7	103293089	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	62942	103293089	55845574	5477	13462										
LHFPL3	375612	broad.mit.edu	37	chr7	103969335	103969335	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcggaactcgcgggccatCggcgtgctgtgggccatctt	16	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:103969335C>T	ENST00000401970.2	+	1	188	c.66C>T	c.(64-66)atC>atT	p.I22I	LHFPL3_ENST00000535008.1_Silent_p.I36I|LHFPL3_ENST00000543266.1_Silent_p.I36I|LHFPL3_ENST00000424859.1_Silent_p.I22I			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	36						integral component of membrane (GO:0016021)		p.I36I(1)		kidney(1)|large_intestine(2)|lung(6)	9						CGCGGGCCATCGGCGTGCTGT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	7											65	78	74					7																	103969335		2201	4300	6501	103756571	SO:0001819	synonymous_variant	375612			AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000401970.2:c.66C>T	7.37:g.103969335C>T			103756571	A1L383|A4D0Q5	Silent	SNP	ENST00000401970.2	37																																																																																					0.672	LHFPL3-002	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000348284.1	NM_199000		T	103969335	C	T	103969335	2	4	61	1	0	0	0	0	0	0	0	1	8789	874	31	1		1	LHFPL3	7	103969335	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	676246	103969335	55169328	5478	13463										
MLL5	55904	broad.mit.edu	37	chr7	104717764	104717764	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttagagccatatacaaaaGaataagaaaattcttaaatc	4	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104717764G>T	ENST00000311117.3	+	11	1559	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N	KMT2E_ENST00000476671.1_Missense_Mutation_p.K338N|KMT2E_ENST00000334877.4_Missense_Mutation_p.K338N|KMT2E_ENST00000257745.4_Missense_Mutation_p.K338N|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	338	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.K338N(1)									ATATACAAAAGAATAAGAAAA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	7											32	34	34					7																	104717764		2200	4292	6492	104505000	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.1014G>T	7.37:g.104717764G>T	ENSP00000312379:p.Lys338Asn		104505000	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278460	0.40294	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95918	-2.99;-2.62;-2.99;-3.85;-3.34	5.62	4.66	0.58398	SET domain (1);	0.046412	0.85682	D	0.000000	D	0.95974	0.8689	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.999;0.993	D;D	0.78314	0.991;0.974	D	0.95085	0.8217	10	0.59425	D	0.04	.	7.687	0.28546	0.2777:0.0:0.7223:0.0	.	338;338	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	N	338;338;338;338;338;196;338;272	ENSP00000312379:K338N;ENSP00000335599:K338N;ENSP00000257745:K338N;ENSP00000419883:K196N;ENSP00000417888:K338N	ENSP00000257745:K338N	K	+	3	2	MLL5	104505000	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.869000	0.48444	1.170000	0.42753	0.655000	0.94253	AAG		0.294	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104717764	G	T	104717764	3	4	61	1	0	0	0	0	1	0	0	0	9654	933	33	2	1048	2	MLL5	7	104717764	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	748429	104717764	54420899	5479	13464										
MLL5	55904	broad.mit.edu	37	chr7	104746355	104746355	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcagcaattttacataGatttaattcaccctgtcaag	4	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104746355G>T	ENST00000311117.3	+	19	3046	c.2501G>T	c.(2500-2502)aGa>aTa	p.R834I	KMT2E_ENST00000334877.4_Missense_Mutation_p.R834I|KMT2E_ENST00000257745.4_Missense_Mutation_p.R834I|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	834					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R834I(1)									ATTTTACATAGATTTAATTCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											83	89	87					7																	104746355		2202	4300	6502	104533591	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2501G>T	7.37:g.104746355G>T	ENSP00000312379:p.Arg834Ile		104533591	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.728651	0.30593	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	D;D;D	0.91740	-2.9;-2.54;-2.9	5.81	3.67	0.42095	.	0.204155	0.46758	D	0.000273	D	0.84456	0.5476	L	0.34521	1.04	0.80722	D	1	B	0.12630	0.006	B	0.09377	0.004	T	0.78026	-0.2365	10	0.35671	T	0.21	.	5.3875	0.16226	0.1173:0.1288:0.622:0.132	.	834	Q8IZD2	MLL5_HUMAN	I	834;834;834;754;834	ENSP00000312379:R834I;ENSP00000335599:R834I;ENSP00000257745:R834I	ENSP00000257745:R834I	R	+	2	0	MLL5	104533591	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.572000	0.53849	1.440000	0.47531	0.655000	0.94253	AGA		0.363	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104746355	G	T	104746355	3	4	61	1	0	0	0	0	1	0	0	0	9654	942	33	2	2567	2	MLL5	7	104746355	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28591	104746355	54392308	5480	13465										
MLL5	55904	broad.mit.edu	37	chr7	104747133	104747133	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacggataaaatcagatgatGaaacttgtagaaatggttat	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104747133G>T	ENST00000311117.3	+	20	3306	c.2761G>T	c.(2761-2763)Gaa>Taa	p.E921*	KMT2E_ENST00000334877.4_Nonsense_Mutation_p.E921*|KMT2E_ENST00000257745.4_Nonsense_Mutation_p.E921*|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	921					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E921*(1)									ATCAGATGATGAAACTTGTAG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											136	141	140					7																	104747133		2203	4300	6503	104534369	SO:0001587	stop_gained	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2761G>T	7.37:g.104747133G>T	ENSP00000312379:p.Glu921*		104534369	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Nonsense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	43	10.191776	0.99355	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	.	.	.	5.1	5.1	0.69264	.	0.147654	0.45126	D	0.000382	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.5067	0.90900	0.0:0.0:1.0:0.0	.	.	.	.	X	921;921;921;841;921	.	ENSP00000257745:E921X	E	+	1	0	MLL5	104534369	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	6.778000	0.75043	2.374000	0.81015	0.585000	0.79938	GAA		0.433	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104747133	G	T	104747133	4	4	61	1	0	0	0	0	0	1	0	0	9654	1291	45	2	2831	2	MLL5	7	104747133	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	778	104747133	54391530	5481	13466										
MLL5	55904	broad.mit.edu	37	chr7	104747620	104747620	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttatatacagaatatttCttccccagaaagttctccag	4	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104747620C>A	ENST00000311117.3	+	21	3400	c.2855C>A	c.(2854-2856)tCt>tAt	p.S952Y	KMT2E_ENST00000334877.4_Missense_Mutation_p.S952Y|KMT2E_ENST00000257745.4_Missense_Mutation_p.S952Y|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_Missense_Mutation_p.S7Y	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	952					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.S952Y(1)									CAGAATATTTCTTCCCCAGAA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	44	43					7																	104747620		2095	4230	6325	104534856	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2855C>A	7.37:g.104747620C>A	ENSP00000312379:p.Ser952Tyr		104534856	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.232734	0.79688	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.94576	-3.46;-2.92;-3.46;0.28	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000014	D	0.95730	0.8611	L	0.34521	1.04	0.54753	D	0.999983	D	0.71674	0.998	D	0.78314	0.991	D	0.96008	0.8999	10	0.66056	D	0.02	.	19.6958	0.96026	0.0:1.0:0.0:0.0	.	952	Q8IZD2	MLL5_HUMAN	Y	952;952;952;872;952;7	ENSP00000312379:S952Y;ENSP00000335599:S952Y;ENSP00000257745:S952Y;ENSP00000333986:S7Y	ENSP00000257745:S952Y	S	+	2	0	MLL5	104534856	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.970000	0.70431	2.748000	0.94277	0.591000	0.81541	TCT		0.254	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			A	104747620	C	A	104747620	3	1	61	1	0	0	0	0	1	0	0	0	9654	913	32	2	2929	2	MLL5	7	104747620	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	487	104747620	54391043	5482	13467										
MLL5	55904	broad.mit.edu	37	chr7	104747950	104747950	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacaggcagtgtcctggaGaaaaggaacctgtgtcagac	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104747950G>T	ENST00000311117.3	+	22	3591	c.3046G>T	c.(3046-3048)Gaa>Taa	p.E1016*	KMT2E_ENST00000334877.4_Nonsense_Mutation_p.E1016*|KMT2E_ENST00000257745.4_Nonsense_Mutation_p.E1016*|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_Nonsense_Mutation_p.E71*	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1016					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E1016*(1)									GTGTCCTGGAGAAAAGGAACC	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											97	98	98					7																	104747950		2203	4300	6503	104535186	SO:0001587	stop_gained	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3046G>T	7.37:g.104747950G>T	ENSP00000312379:p.Glu1016*		104535186	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Nonsense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	57	29.144492	0.99975	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	.	.	.	6.03	6.03	0.97812	.	0.135877	0.48767	D	0.000162	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	.	.	.	X	1016;1016;1016;936;1016;71	.	ENSP00000257745:E1016X	E	+	1	0	MLL5	104535186	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.611000	0.67674	2.854000	0.98071	0.655000	0.94253	GAA		0.473	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104747950	G	T	104747950	4	4	61	1	0	0	0	0	0	1	0	0	9654	943	33	2	3124	2	MLL5	7	104747950	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	330	104747950	54390713	5483	13468										
MLL5	55904	broad.mit.edu	37	chr7	104748203	104748203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggttggaggaggcttccGaataagtgagtcaaagtgcc	16	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104748203G>A	ENST00000311117.3	+	22	3844	c.3299G>A	c.(3298-3300)cGa>cAa	p.R1100Q	KMT2E_ENST00000334877.4_Missense_Mutation_p.R1100Q|SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000257745.4_Missense_Mutation_p.R1100Q|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_Missense_Mutation_p.R155Q	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1100					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R1100Q(1)									GGAGGCTTCCGAATAAGTGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											91	89	89					7																	104748203		2203	4300	6503	104535439	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3299G>A	7.37:g.104748203G>A	ENSP00000312379:p.Arg1100Gln		104535439	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.993480	0.93167	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.95821	-3.82;-3.1;-3.82;-0.12	5.85	5.85	0.93711	.	0.160745	0.40144	N	0.001167	D	0.91157	0.7215	L	0.34521	1.04	0.43122	D	0.994849	P	0.40107	0.703	B	0.23716	0.048	D	0.91184	0.4978	10	0.49607	T	0.09	.	20.1649	0.98147	0.0:0.0:1.0:0.0	.	1100	Q8IZD2	MLL5_HUMAN	Q	1100;1100;1100;1020;1100;155	ENSP00000312379:R1100Q;ENSP00000335599:R1100Q;ENSP00000257745:R1100Q;ENSP00000333986:R155Q	ENSP00000257745:R1100Q	R	+	2	0	MLL5	104535439	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	6.540000	0.73861	2.753000	0.94483	0.655000	0.94253	CGA		0.473	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			A	104748203	G	A	104748203	3	1	61	1	0	0	0	0	1	0	0	0	9654	1058	37	1	3377	1	MLL5	7	104748203	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253	104748203	54390460	5484	13469										
MLL5	55904	broad.mit.edu	37	chr7	104750798	104750798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacttctcagtgatcaccGaaaagataaagatagtggta	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104750798G>A	ENST00000311117.3	+	24	4372	c.3827G>A	c.(3826-3828)cGa>cAa	p.R1276Q	KMT2E_ENST00000334877.4_Missense_Mutation_p.R1276Q|SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000257745.4_Missense_Mutation_p.R1276Q|KMT2E_ENST00000334914.7_Missense_Mutation_p.R331Q	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1276					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R1276Q(1)									AGTGATCACCGAAAAGATAAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											131	135	134					7																	104750798		2203	4300	6503	104538034	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3827G>A	7.37:g.104750798G>A	ENSP00000312379:p.Arg1276Gln		104538034	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	34	5.317638	0.95682	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.94793	-3.52;-2.84;-3.52;0.09	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000016	D	0.93141	0.7816	L	0.32530	0.975	0.47476	D	0.999435	D	0.67145	0.996	P	0.53006	0.715	D	0.90694	0.4615	10	0.11794	T	0.64	.	18.8917	0.92407	0.0:0.0:1.0:0.0	.	1276	Q8IZD2	MLL5_HUMAN	Q	1276;1276;1276;1196;1276;331	ENSP00000312379:R1276Q;ENSP00000335599:R1276Q;ENSP00000257745:R1276Q;ENSP00000333986:R331Q	ENSP00000257745:R1276Q	R	+	2	0	MLL5	104538034	1.000000	0.71417	0.978000	0.43139	0.982000	0.71751	8.569000	0.90744	2.468000	0.83385	0.561000	0.74099	CGA		0.398	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			A	104750798	G	A	104750798	3	1	61	1	0	0	0	0	1	0	0	0	9654	1058	37	1	3913	1	MLL5	7	104750798	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2595	104750798	54387865	5485	13470										
SRPK2	6733	broad.mit.edu	37	chr7	104844078	104844078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcttggcacatcaccttTgcagtagtccgcagggtcct	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104844078T>C	ENST00000393651.3	-	3	313	c.226A>G	c.(226-228)Aaa>Gaa	p.K76E	SRPK2_ENST00000357311.3_Missense_Mutation_p.K65E|SRPK2_ENST00000489828.1_Missense_Mutation_p.K65E	NM_182692.1	NP_872634.1			SRSF protein kinase 2									p.K65E(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						ACATCACCTTTGCAGTAGTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											148	121	130					7																	104844078		2203	4300	6503	104631314	SO:0001583	missense	6733			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.226A>G	7.37:g.104844078T>C	ENSP00000377262:p.Lys76Glu		104631314		Missense_Mutation	SNP	ENST00000393651.3	37	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.125377	0.56721	.	.	ENSG00000135250	ENST00000393651;ENST00000357311;ENST00000489828;ENST00000482897;ENST00000460391	T;T;T;T;T	0.32515	1.45;1.47;1.47;3.35;2.9	6.04	4.89	0.63831	.	0.050786	0.85682	N	0.000000	T	0.27765	0.0683	L	0.48260	1.515	0.58432	D	0.999994	B;B	0.12013	0.005;0.0	B;B	0.08055	0.003;0.0	T	0.04708	-1.0932	10	0.62326	D	0.03	.	10.5688	0.45188	0.0:0.0732:0.0:0.9268	.	76;65	P78362-2;P78362	.;SRPK2_HUMAN	E	76;65;65;113;65	ENSP00000377262:K76E;ENSP00000349863:K65E;ENSP00000419791:K65E;ENSP00000419240:K113E;ENSP00000417357:K65E	ENSP00000349863:K65E	K	-	1	0	SRPK2	104631314	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	7.348000	0.79366	1.111000	0.41721	-0.379000	0.06801	AAA		0.582	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		C	104844078	T	C	104844078	3	2	61	1	0	0	0	0	1	0	0	0	15199	1821	63	4	1929	4	SRPK2	7	104844078	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	93280	104844078	54294585	5486	13471										
SRPK2	6733	broad.mit.edu	37	chr7	104909273	104909273	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctgaagaggacgacttCtcagagttaactgacatcag	9	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:104909273C>A	ENST00000357311.3	-	1	189	c.18G>T	c.(16-18)gaG>gaT	p.E6D	SRPK2_ENST00000393651.3_Intron|SRPK2_ENST00000489828.1_Missense_Mutation_p.E6D	NM_001278273.1|NM_182691.1	NP_001265202.1|NP_872633.1			SRSF protein kinase 2									p.E6D(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						AGGACGACTTCTCAGAGTTAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	7											117	106	109					7																	104909273		2203	4300	6503	104696509	SO:0001583	missense	6733			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000357311.3:c.18G>T	7.37:g.104909273C>A	ENSP00000349863:p.Glu6Asp		104696509		Missense_Mutation	SNP	ENST00000357311.3	37	CCDS5735.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507658	0.44558	.	.	ENSG00000135250	ENST00000357311;ENST00000489828;ENST00000460391	T;T;T	0.31769	1.48;1.48;2.93	5.5	5.5	0.81552	.	.	.	.	.	T	0.33818	0.0876	N	0.08118	0	0.35320	D	0.784659	P	0.52842	0.956	P	0.62184	0.899	T	0.40175	-0.9577	9	0.25106	T	0.35	.	18.741	0.91773	0.0:1.0:0.0:0.0	.	6	P78362	SRPK2_HUMAN	D	6	ENSP00000349863:E6D;ENSP00000419791:E6D;ENSP00000417357:E6D	ENSP00000349863:E6D	E	-	3	2	SRPK2	104696509	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.698000	0.54771	2.734000	0.93682	0.650000	0.86243	GAG		0.383	SRPK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348716.1	NM_182691		A	104909273	C	A	104909273	3	1	61	1	0	0	0	0	1	0	0	0	15199	912	32	2	2108	2	SRPK2	7	104909273	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65195	104909273	54229390	5487	13472										
PUS7	54517	broad.mit.edu	37	chr7	105105785	105105785	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctttgggtagataacatcGaaaccaggcaagggcattac	11	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:105105785G>A	ENST00000356362.2	-	13	1816	c.1602C>T	c.(1600-1602)ttC>ttT	p.F534F	PUS7_ENST00000469408.1_Silent_p.F534F	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	534	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)	p.F534F(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						AGATAACATCGAAACCAGGCA	0.343																																					Colon(138;2387 3051 17860)											2	Substitution - coding silent(2)	large_intestine(2)	7											116	106	110					7																	105105785		2203	4300	6503	104893021	SO:0001819	synonymous_variant	54517			AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.1602C>T	7.37:g.105105785G>A			104893021	Q75MG4|Q9NX19	Silent	SNP	ENST00000356362.2	37	CCDS34725.1																																																																																				0.343	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		A	105105785	G	A	105105785	2	1	61	1	0	0	0	0	0	0	0	1	12870	1049	37	1		1	PUS7	7	105105785	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196512	105105785	54032878	5488	13473										
PUS7	54517	broad.mit.edu	37	chr7	105131992	105131992	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctctctacttacttgagAacagcaatttcttgaactgt	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:105131992A>C	ENST00000356362.2	-	7	1129	c.915T>G	c.(913-915)gtT>gtG	p.V305V	PUS7_ENST00000469408.1_Silent_p.V305V	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	305					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)	p.V305V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						CTTACTTGAGAACAGCAATTT	0.378																																					Colon(138;2387 3051 17860)											1	Substitution - coding silent(1)	large_intestine(1)	7											145	129	134					7																	105131992		2203	4300	6503	104919228	SO:0001819	synonymous_variant	54517			AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.915T>G	7.37:g.105131992A>C			104919228	Q75MG4|Q9NX19	Silent	SNP	ENST00000356362.2	37	CCDS34725.1																																																																																				0.378	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		C	105131992	A	C	105131992	2	2	61	1	0	0	0	0	0	0	0	1	12870	233	9	4		4	PUS7	7	105131992	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	26207	105131992	54006671	5489	13474										
RINT1	60561	broad.mit.edu	37	chr7	105195543	105195543	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttacagaaggacttagtaGatgattttaggatacgatta	10	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:105195543G>T	ENST00000257700.2	+	11	1771	c.1540G>T	c.(1540-1542)Gat>Tat	p.D514Y		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	514	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.D514Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GGACTTAGTAGATGATTTTAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											146	146	146					7																	105195543		2203	4300	6503	104982779	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.1540G>T	7.37:g.105195543G>T	ENSP00000257700:p.Asp514Tyr		104982779	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.969326	0.92855	.	.	ENSG00000135249	ENST00000257700	T	0.35421	1.31	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.65134	-0.6242	10	0.66056	D	0.02	-26.117	20.5373	0.99239	0.0:0.0:1.0:0.0	.	514	Q6NUQ1	RINT1_HUMAN	Y	514	ENSP00000257700:D514Y	ENSP00000257700:D514Y	D	+	1	0	RINT1	104982779	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.606000	0.90888	2.857000	0.98124	0.650000	0.86243	GAT		0.388	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		T	105195543	G	T	105195543	3	4	61	1	0	0	0	0	1	0	0	0	13413	942	33	2	1582	2	RINT1	7	105195543	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63551	105195543	53943120	5490	13475										
CDHR3	222256	broad.mit.edu	37	chr7	105671275	105671275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactatctttgatggagaagCcatagatccaggtaattaag	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:105671275C>T	ENST00000317716.9	+	18	2422	c.2342C>T	c.(2341-2343)gCc>gTc	p.A781V	CDHR3_ENST00000542731.1_Missense_Mutation_p.A781V|CDHR3_ENST00000478080.1_Missense_Mutation_p.A693V|CDHR3_ENST00000343407.5_3'UTR|CDHR3_ENST00000470188.1_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	781					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A781V(2)		breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GATGGAGAAGCCATAGATCCA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	7											123	118	120					7																	105671275		1924	4135	6059	105458511	SO:0001583	missense	222256			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.2342C>T	7.37:g.105671275C>T	ENSP00000325954:p.Ala781Val		105458511	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789194	0.49997	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.67171	-0.25;-0.22;-0.22	5.48	4.59	0.56863	.	0.000000	0.64402	D	0.000002	T	0.81555	0.4847	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.83225	-0.0066	10	0.87932	D	0	-17.7751	17.4033	0.87466	0.0:0.9332:0.0:0.0668	.	768;781	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	V	781;781;693	ENSP00000439766:A781V;ENSP00000325954:A781V;ENSP00000417771:A693V	ENSP00000325954:A781V	A	+	2	0	CDHR3	105458511	0.997000	0.39634	0.883000	0.34634	0.416000	0.31233	3.804000	0.55568	0.688000	0.31529	-1.134000	0.01955	GCC		0.408	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		T	105671275	C	T	105671275	3	4	61	1	0	0	0	0	1	0	0	0	3126	739	26	3	2412	3	CDHR3	7	105671275	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	475732	105671275	53467388	5491	13476										
PIK3CG	5294	broad.mit.edu	37	chr7	106508721	106508721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattaaggtctcacccgacGacacccccggcgccatcctg	8	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:106508721G>A	ENST00000359195.3	+	2	1025	c.715G>A	c.(715-717)Gac>Aac	p.D239N	PIK3CG_ENST00000440650.2_Missense_Mutation_p.D239N|PIK3CG_ENST00000496166.1_Missense_Mutation_p.D239N	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	239	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D239N(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CTCACCCGACGACACCCCCGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	94	92					7																	106508721		2203	4300	6503	106295957	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.715G>A	7.37:g.106508721G>A	ENSP00000352121:p.Asp239Asn		106295957	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842888	0.32606	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.70399	-0.48;-0.48;-0.48	5.5	5.5	0.81552	Phosphoinositide 3-kinase, ras-binding (2);	0.043367	0.85682	D	0.000000	T	0.69342	0.3100	M	0.66939	2.045	0.80722	D	1	P	0.37207	0.587	B	0.34385	0.181	T	0.67473	-0.5662	10	0.23891	T	0.37	-33.7791	19.7537	0.96281	0.0:0.0:1.0:0.0	.	239	P48736	PK3CG_HUMAN	N	239	ENSP00000392258:D239N;ENSP00000419260:D239N;ENSP00000352121:D239N	ENSP00000352121:D239N	D	+	1	0	PIK3CG	106295957	1.000000	0.71417	0.953000	0.39169	0.183000	0.23260	7.799000	0.85936	2.736000	0.93811	0.591000	0.81541	GAC		0.537	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			A	106508721	G	A	106508721	3	1	61	1	0	0	0	0	1	0	0	0	11947	1058	37	1	717	1	PIK3CG	7	106508721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	837446	106508721	52629942	5492	13477										
PIK3CG	5294	broad.mit.edu	37	chr7	106513010	106513010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgaaccataccatgataGcgcccttgccagatttctgc	7	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:106513010G>A	ENST00000359195.3	+	3	2334	c.2024G>A	c.(2023-2025)aGc>aAc	p.S675N	PIK3CG_ENST00000440650.2_Missense_Mutation_p.S675N|PIK3CG_ENST00000496166.1_Missense_Mutation_p.S675N	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	675	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S675N(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						TACCATGATAGCGCCCTTGCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											207	197	200					7																	106513010		2203	4300	6503	106300246	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2024G>A	7.37:g.106513010G>A	ENSP00000352121:p.Ser675Asn		106300246	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.883098	0.72410	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.70749	-0.51;-0.51;-0.51	5.62	5.62	0.85841	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.82421	0.5033	M	0.63208	1.945	0.80722	D	1	D	0.60575	0.988	D	0.67900	0.954	T	0.80256	-0.1458	10	0.41790	T	0.15	-19.2247	20.024	0.97514	0.0:0.0:1.0:0.0	.	675	P48736	PK3CG_HUMAN	N	675	ENSP00000392258:S675N;ENSP00000419260:S675N;ENSP00000352121:S675N	ENSP00000352121:S675N	S	+	2	0	PIK3CG	106300246	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.420000	0.97426	2.809000	0.96659	0.655000	0.94253	AGC		0.398	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			A	106513010	G	A	106513010	3	1	61	1	0	0	0	0	1	0	0	0	11947	971	34	3	2030	3	PIK3CG	7	106513010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4289	106513010	52625653	5493	13478										
PIK3CG	5294	broad.mit.edu	37	chr7	106526602	106526602	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctatttcatattgacttCgggcacattcttgggaatta	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:106526602C>T	ENST00000359195.3	+	10	3205	c.2895C>T	c.(2893-2895)ttC>ttT	p.F965F	PIK3CG_ENST00000440650.2_Silent_p.F965F|PIK3CG_ENST00000496166.1_Silent_p.F965F	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	965	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F965F(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						ATATTGACTTCGGGCACATTC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											109	104	106					7																	106526602		2203	4300	6503	106313838	SO:0001819	synonymous_variant	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2895C>T	7.37:g.106526602C>T			106313838	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	CCDS5739.1																																																																																				0.388	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			T	106526602	C	T	106526602	2	4	61	1	0	0	0	0	0	0	0	1	11947	883	31	1		1	PIK3CG	7	106526602	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13592	106526602	52612061	5494	13479										
HBP1	26959	broad.mit.edu	37	chr7	106822912	106822912	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacatcaagaatacccaagAtcatcttggaaccaaaatac	4	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:106822912A>C	ENST00000222574.4	+	3	450	c.264A>C	c.(262-264)agA>agC	p.R88S	HBP1_ENST00000468410.1_Missense_Mutation_p.R88S|HBP1_ENST00000485846.1_Missense_Mutation_p.R88S	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	88					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.R88S(1)		large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						AATACCCAAGATCATCTTGGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											102	89	94					7																	106822912		2203	4300	6503	106610148	SO:0001583	missense	26959			BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.264A>C	7.37:g.106822912A>C	ENSP00000222574:p.Arg88Ser		106610148	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	37	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.038078	0.54896	.	.	ENSG00000105856	ENST00000468410;ENST00000464009;ENST00000222574;ENST00000497535;ENST00000485846;ENST00000479011;ENST00000498408	D;D;D	0.98968	-5.28;-5.28;-5.28	5.86	3.53	0.40419	.	0.251282	0.43747	D	0.000539	D	0.94374	0.8191	N	0.19112	0.55	0.42186	D	0.991704	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.11329	0.003;0.006;0.003	D	0.89418	0.3708	10	0.30854	T	0.27	-5.1436	4.5473	0.12087	0.5609:0.0:0.4391:0.0	.	98;88;88	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	S	88;88;88;88;88;88;80	ENSP00000420500:R88S;ENSP00000222574:R88S;ENSP00000418738:R88S	ENSP00000222574:R88S	R	+	3	2	HBP1	106610148	1.000000	0.71417	0.988000	0.46212	0.852000	0.48524	2.332000	0.43903	1.052000	0.40392	0.533000	0.62120	AGA		0.443	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		C	106822912	A	C	106822912	3	2	61	1	0	0	0	0	1	0	0	0	7006	330	12	4	270	4	HBP1	7	106822912	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	296310	106822912	52315751	5495	13480										
HBP1	26959	broad.mit.edu	37	chr7	106830716	106830716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctacctcctggacaccccGatgccattaattttgatgat	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:106830716G>A	ENST00000222574.4	+	8	1207	c.1021G>A	c.(1021-1023)Gat>Aat	p.D341N	HBP1_ENST00000461963.1_Intron|HBP1_ENST00000485846.1_Missense_Mutation_p.D341N|HBP1_ENST00000468410.1_Missense_Mutation_p.D341N|CTA-363E19.2_ENST00000607036.1_RNA	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	341	AXH. {ECO:0000255|PROSITE- ProRule:PRU00496}.				cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.D341N(1)		large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						TGGACACCCCGATGCCATTAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											230	208	215					7																	106830716		2203	4300	6503	106617952	SO:0001583	missense	26959			BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.1021G>A	7.37:g.106830716G>A	ENSP00000222574:p.Asp341Asn		106617952	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	37	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904948	0.92035	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.99353	-5.77;-5.77;-5.77	5.37	5.37	0.77165	Ataxin-1/HBP1 module (AXH) (1);	0.045776	0.85682	D	0.000000	D	0.99193	0.9720	L	0.60455	1.87	0.54753	D	0.999989	D;D;D	0.76494	0.976;0.999;0.998	P;D;P	0.66847	0.786;0.947;0.848	D	0.99871	1.1096	10	0.62326	D	0.03	-9.8201	19.1082	0.93305	0.0:0.0:1.0:0.0	.	351;341;341	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	N	341;341;341;333	ENSP00000420500:D341N;ENSP00000222574:D341N;ENSP00000418738:D341N	ENSP00000222574:D341N	D	+	1	0	HBP1	106617952	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.817000	0.86213	2.524000	0.85096	0.561000	0.74099	GAT		0.363	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		A	106830716	G	A	106830716	3	1	61	1	0	0	0	0	1	0	0	0	7006	1058	37	1	1047	1	HBP1	7	106830716	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7804	106830716	52307947	5496	13481										
COG5	10466	broad.mit.edu	37	chr7	107053042	107053042	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatcattttctatcacttCtattccagaaagatctattc	3	9	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107053042C>A	ENST00000347053.3	-	7	717	c.667G>T	c.(667-669)Gaa>Taa	p.E223*	COG5_ENST00000297135.3_Nonsense_Mutation_p.E223*|COG5_ENST00000475638.2_5'UTR|COG5_ENST00000393603.2_Nonsense_Mutation_p.E223*	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	223					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.E223*(1)		breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						TCTATCACTTCTATTCCAGAA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											49	49	49					7																	107053042		2203	4300	6503	106840278	SO:0001587	stop_gained	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.667G>T	7.37:g.107053042C>A	ENSP00000334703:p.Glu223*		106840278	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Nonsense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937674	0.92458	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	.	.	.	4.47	4.47	0.54385	.	0.122356	0.53938	D	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-16.2897	17.5112	0.87760	0.0:1.0:0.0:0.0	.	.	.	.	X	223	.	ENSP00000297135:E223X	E	-	1	0	COG5	106840278	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	5.453000	0.66645	2.190000	0.69967	0.561000	0.74099	GAA		0.328	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			A	107053042	C	A	107053042	4	1	61	1	0	0	0	0	0	1	0	0	3667	922	32	2	1983	2	COG5	7	107053042	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222326	107053042	52085621	5497	13482										
GPR22	2845	broad.mit.edu	37	chr7	107114856	107114856	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgctctcatttgctgtttCcatgaggcttgtgtatcttt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107114856C>T	ENST00000304402.4	+	3	1694	c.351C>T	c.(349-351)ttC>ttT	p.F117F	COG5_ENST00000297135.3_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000393603.2_Intron|COG5_ENST00000475638.2_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	117					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.F117F(1)		large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						TTTGCTGTTTCCATGAGGCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	7											119	116	117					7																	107114856		2203	4299	6502	106902092	SO:0001819	synonymous_variant	2845			U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.351C>T	7.37:g.107114856C>T			106902092	O14554	Silent	SNP	ENST00000304402.4	37	CCDS5744.1																																																																																				0.383	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			T	107114856	C	T	107114856	2	4	61	1	0	0	0	0	0	0	0	1	6702	854	30	3		3	GPR22	7	107114856	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61814	107114856	52023807	5498	13483										
SLC26A4	5172	broad.mit.edu	37	chr7	107303845	107303845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcttagtgacgtcatttCgggagttagtactgggctag	14	7	1	1	rs370588279		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107303845C>T	ENST00000265715.3	+	3	493	c.269C>T	c.(268-270)tCg>tTg	p.S90L	SLC26A4-AS1_ENST00000591896.1_RNA|SLC26A4-AS1_ENST00000587899.1_RNA|SLC26A4-AS1_ENST00000449741.1_RNA|SLC26A4-AS1_ENST00000440512.1_RNA	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	90			S -> L (in DFNB4). {ECO:0000269|PubMed:12676893}.		chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.S90L(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GACGTCATTTCGGGAGTTAGT	0.507									Pendred syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7	GRCh37	CM030956	SLC26A4	M							159	129	139					7																	107303845		2203	4300	6503	107091081	SO:0001583	missense	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.269C>T	7.37:g.107303845C>T	ENSP00000265715:p.Ser90Leu		107091081	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927841	0.73327	.	.	ENSG00000091137	ENST00000265715;ENST00000440056	D;D	0.92048	-2.96;-2.96	4.8	4.8	0.61643	.	0.000000	0.64402	D	0.000001	D	0.97328	0.9126	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.98342	1.0539	10	0.87932	D	0	.	17.9844	0.89152	0.0:1.0:0.0:0.0	.	90	O43511	S26A4_HUMAN	L	90	ENSP00000265715:S90L;ENSP00000394760:S90L	ENSP00000265715:S90L	S	+	2	0	SLC26A4	107091081	1.000000	0.71417	0.851000	0.33527	0.511000	0.34104	6.092000	0.71414	2.655000	0.90218	0.591000	0.81541	TCG		0.507	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		T	107303845	C	T	107303845	3	4	61	1	0	0	0	0	1	0	0	0	14556	893	31	1	275	1	SLC26A4	7	107303845	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	188989	107303845	51834818	5499	13484										
SLC26A4	5172	broad.mit.edu	37	chr7	107336382	107336382	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatttttttccctaggttaTctgggtgtttacgtgtatag	9	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107336382T>G	ENST00000265715.3	+	13	1666	c.1442T>G	c.(1441-1443)aTc>aGc	p.I481S	SLC26A4_ENST00000543100.1_Missense_Mutation_p.I50S|SLC26A4_ENST00000541474.1_Missense_Mutation_p.I42S|SLC26A4_ENST00000480841.1_3'UTR|SLC26A4_ENST00000544569.1_Missense_Mutation_p.I68S	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	481					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.I481S(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						CCCTAGGTTATCTGGGTGTTT	0.373									Pendred syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											228	222	224					7																	107336382		2203	4300	6503	107123618	SO:0001583	missense	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1442T>G	7.37:g.107336382T>G	ENSP00000265715:p.Ile481Ser		107123618	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611445	0.87258	.	.	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.95588	-3.4;-3.75;-3.4;-3.4	6.06	6.06	0.98353	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.96670	0.8913	M	0.80422	2.495	0.53005	D	0.999965	P;P;P	0.48407	0.89;0.91;0.89	P;P;P	0.50754	0.472;0.628;0.649	D	0.96907	0.9664	10	0.66056	D	0.02	.	16.607	0.84832	0.0:0.0:0.0:1.0	.	42;68;481	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	S	481;42;68;50	ENSP00000265715:I481S;ENSP00000439743:I42S;ENSP00000437427:I68S;ENSP00000441209:I50S	ENSP00000265715:I481S	I	+	2	0	SLC26A4	107123618	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.501000	0.66950	2.319000	0.78375	0.523000	0.50628	ATC		0.373	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		G	107336382	T	G	107336382	3	3	61	1	0	0	0	0	1	0	0	0	14556	1435	50	4	1488	4	SLC26A4	7	107336382	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32537	107336382	51802281	5500	13485										
CBLL1	79872	broad.mit.edu	37	chr7	107389430	107389430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagcaaacaaagcgaaacCtgcaccgcgaactcaaagaa	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107389430C>T	ENST00000440859.3	+	2	586	c.119C>T	c.(118-120)cCt>cTt	p.P40L	CBLL1_ENST00000222597.2_Missense_Mutation_p.P40L|CBLL1_ENST00000415884.2_Missense_Mutation_p.P40L	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	40					negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P40L(1)		endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						AAAGCGAAACCTGCACCGCGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											128	129	128					7																	107389430		2203	4300	6503	107176666	SO:0001583	missense	79872			AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.119C>T	7.37:g.107389430C>T	ENSP00000401277:p.Pro40Leu		107176666	B7ZM03|Q8TAJ4|Q9H5S6	Missense_Mutation	SNP	ENST00000440859.3	37	CCDS5747.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212806	0.79352	.	.	ENSG00000105879	ENST00000440859;ENST00000222597	T;T	0.30714	1.53;1.52	4.92	4.92	0.64577	.	0.132408	0.52532	D	0.000080	T	0.45276	0.1334	L	0.53249	1.67	0.80722	D	1	D;B	0.57571	0.98;0.042	P;B	0.54856	0.762;0.046	T	0.37361	-0.9709	10	0.45353	T	0.12	.	18.1098	0.89532	0.0:1.0:0.0:0.0	.	40;40	B7ZM03;Q75N03	.;HAKAI_HUMAN	L	40	ENSP00000401277:P40L;ENSP00000222597:P40L	ENSP00000222597:P40L	P	+	2	0	CBLL1	107176666	1.000000	0.71417	0.787000	0.31911	0.871000	0.50021	7.217000	0.77982	2.262000	0.75019	0.467000	0.42956	CCT		0.433	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		T	107389430	C	T	107389430	3	4	61	1	0	0	0	0	1	0	0	0	2709	681	24	3	125	3	CBLL1	7	107389430	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53048	107389430	51749233	5501	13486										
CBLL1	79872	broad.mit.edu	37	chr7	107393862	107393862	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttttctcagaaggatTtgattataatgaagaagaac	7	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107393862T>G	ENST00000440859.3	+	3	655	c.188T>G	c.(187-189)tTt>tGt	p.F63C	CBLL1_ENST00000222597.2_Missense_Mutation_p.F62C|CBLL1_ENST00000415884.2_Missense_Mutation_p.F63C	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	63					negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F63C(1)		endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						TCAGAAGGATTTGATTATAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	7											56	62	60					7																	107393862		2203	4300	6503	107181098	SO:0001583	missense	79872			AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.188T>G	7.37:g.107393862T>G	ENSP00000401277:p.Phe63Cys		107181098	B7ZM03|Q8TAJ4|Q9H5S6	Missense_Mutation	SNP	ENST00000440859.3	37	CCDS5747.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.814077	0.50527	.	.	ENSG00000105879	ENST00000440859;ENST00000222597;ENST00000420796;ENST00000415884;ENST00000417616	T;T;T	0.36520	1.27;1.35;1.25	5.67	5.67	0.87782	.	0.057163	0.64402	D	0.000001	T	0.54791	0.1880	L	0.55481	1.735	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.81914	0.995;0.947	T	0.49661	-0.8916	10	0.32370	T	0.25	-1.5684	15.9124	0.79482	0.0:0.0:0.0:1.0	.	62;63	B7ZM03;Q75N03	.;HAKAI_HUMAN	C	63;62;13;13;9	ENSP00000401277:F63C;ENSP00000222597:F62C;ENSP00000410615:F13C	ENSP00000222597:F62C	F	+	2	0	CBLL1	107181098	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.339000	0.79282	2.164000	0.68074	0.460000	0.39030	TTT		0.348	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		G	107393862	T	G	107393862	3	3	61	1	0	0	0	0	1	0	0	0	2709	1841	64	4	198	4	CBLL1	7	107393862	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4432	107393862	51744801	5502	13487										
SLC26A3	1811	broad.mit.edu	37	chr7	107431525	107431525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagcactgtgactgatgCcgccgccgccaccctcaccc	9	18	1	3	rs369893693		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107431525C>T	ENST00000340010.5	-	5	722	c.538G>A	c.(538-540)Gca>Aca	p.A180T	SLC26A3_ENST00000422236.2_Missense_Mutation_p.A145T	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	180					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)	p.A180T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						GTGACTGATGCCGCCGCCGCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											81	71	74					7																	107431525		2203	4300	6503	107218761	SO:0001583	missense	1811			L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.538G>A	7.37:g.107431525C>T	ENSP00000345873:p.Ala180Thr		107218761		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545078	0.45280	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.93189	-3.14;-3.18	5.69	3.78	0.43462	.	.	.	.	.	D	0.89143	0.6631	L	0.43923	1.385	0.09310	N	0.999992	B;B	0.29590	0.164;0.25	B;B	0.29077	0.098;0.067	T	0.78927	-0.2011	9	0.25751	T	0.34	.	10.2461	0.43341	0.136:0.7937:0.0:0.0703	.	145;180	G5E9U3;P40879	.;S26A3_HUMAN	T	145;180	ENSP00000415817:A145T;ENSP00000345873:A180T	ENSP00000345873:A180T	A	-	1	0	SLC26A3	107218761	0.389000	0.25205	0.271000	0.24616	0.005000	0.04900	0.987000	0.29603	1.409000	0.46915	0.591000	0.81541	GCA		0.478	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		T	107431525	C	T	107431525	3	4	61	1	0	0	0	0	1	0	0	0	14555	739	26	3	1824	3	SLC26A3	7	107431525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37663	107431525	51707138	5503	13488										
LAMB4	22798	broad.mit.edu	37	chr7	107696177	107696177	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacacgttccctctgaggtCtttgaagtctgcctcacaga	9	12	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107696177C>A	ENST00000388781.3	-	25	3738	c.3655G>T	c.(3655-3657)Gac>Tac	p.D1219Y	LAMB4_ENST00000205386.4_Missense_Mutation_p.D1219Y|LAMB4_ENST00000388780.3_Missense_Mutation_p.D1219Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1219	Domain II.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.D1219Y(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CCTCTGAGGTCTTTGAAGTCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											79	80	79					7																	107696177		2203	4300	6503	107483413	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.3655G>T	7.37:g.107696177C>A	ENSP00000373433:p.Asp1219Tyr		107483413	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.037479	0.35989	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.34667	1.35;1.35;1.8;1.42	5.02	3.14	0.36123	.	0.621077	0.13418	N	0.389391	T	0.23330	0.0564	N	0.14661	0.345	0.80722	D	1	B;B	0.32425	0.238;0.371	B;B	0.35770	0.21;0.169	T	0.09487	-1.0672	10	0.59425	D	0.04	.	8.154	0.31158	0.0:0.7001:0.1437:0.1562	.	1219;1219	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	Y	1219;1219;245;1219	ENSP00000205386:D1219Y;ENSP00000373433:D1219Y;ENSP00000416562:D245Y;ENSP00000373432:D1219Y	ENSP00000205386:D1219Y	D	-	1	0	LAMB4	107483413	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	1.542000	0.36137	1.346000	0.45694	0.655000	0.94253	GAC		0.433	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107696177	C	A	107696177	3	1	61	1	0	0	0	0	1	0	0	0	8635	913	32	2	1670	2	LAMB4	7	107696177	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	264652	107696177	51442486	5504	13489										
LAMB4	22798	broad.mit.edu	37	chr7	107706349	107706349	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaagaaggatttccataGtaaccatcaatacacctgtc	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107706349G>T	ENST00000388781.3	-	21	2777	c.2694C>A	c.(2692-2694)taC>taA	p.Y898*	LAMB4_ENST00000205386.4_Nonsense_Mutation_p.Y898*|LAMB4_ENST00000388780.3_Nonsense_Mutation_p.Y898*	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	898	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.Y898*(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GATTTCCATAGTAACCATCAA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											126	124	125					7																	107706349		2203	4300	6503	107493585	SO:0001587	stop_gained	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2694C>A	7.37:g.107706349G>T	ENSP00000373433:p.Tyr898*		107493585	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Nonsense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	G	42	9.684229	0.99238	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	.	.	.	4.69	4.69	0.59074	.	0.000000	0.46758	D	0.000278	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.1077	0.53821	0.0908:0.0:0.9092:0.0	.	.	.	.	X	898	.	ENSP00000205386:Y898X	Y	-	3	2	LAMB4	107493585	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.730000	0.62015	2.606000	0.88127	0.563000	0.77884	TAC		0.418	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		T	107706349	G	T	107706349	4	4	61	1	0	0	0	0	0	1	0	0	8635	1024	36	2	2647	2	LAMB4	7	107706349	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10172	107706349	51432314	5505	13490										
LAMB4	22798	broad.mit.edu	37	chr7	107743535	107743535	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttgagcgggtccctgtaGaagaggggtctgcagcggtc	17	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:107743535G>A	ENST00000388781.3	-	10	1217	c.1134C>T	c.(1132-1134)ttC>ttT	p.F378F	LAMB4_ENST00000418464.1_Silent_p.F378F|LAMB4_ENST00000205386.4_Silent_p.F378F|LAMB4_ENST00000414450.2_Silent_p.F378F|LAMB4_ENST00000388780.3_Silent_p.F378F	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	378	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.F378F(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GGTCCCTGTAGAAGAGGGGTC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	7											65	58	60					7																	107743535		2203	4300	6503	107530771	SO:0001819	synonymous_variant	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1134C>T	7.37:g.107743535G>A			107530771	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																				0.602	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107743535	G	A	107743535	2	1	61	1	0	0	0	0	0	0	0	1	8635	933	33	3		3	LAMB4	7	107743535	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37186	107743535	51395128	5506	13491										
PNPLA8	50640	broad.mit.edu	37	chr7	108119795	108119795	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcatgcatagctaatgccGaagggttattcagaagcaaa	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:108119795G>A	ENST00000422087.1	-	11	2313	c.1907C>T	c.(1906-1908)tCg>tTg	p.S636L	PNPLA8_ENST00000257694.8_Missense_Mutation_p.S636L|PNPLA8_ENST00000436062.1_Missense_Mutation_p.S636L|PNPLA8_ENST00000426128.2_Missense_Mutation_p.S574L|PNPLA8_ENST00000388728.5_Missense_Mutation_p.S574L|PNPLA8_ENST00000453144.1_Missense_Mutation_p.S536L	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	636	Patatin.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)	p.S636L(1)		breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						AGCTAATGCCGAAGGGTTATT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											126	105	112					7																	108119795		2203	4300	6503	107907031	SO:0001583	missense	50640			AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.1907C>T	7.37:g.108119795G>A	ENSP00000410804:p.Ser636Leu		107907031	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454645	0.63290	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085	T;T;T;T;T;T	0.76839	-1.05;-0.8;-1.05;-1.05;-1.05;-1.05	5.61	5.61	0.85477	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.192970	0.45606	D	0.000354	T	0.72590	0.3479	L	0.39085	1.19	0.25701	N	0.985588	P	0.51653	0.947	P	0.44561	0.453	T	0.70212	-0.4934	10	0.56958	D	0.05	.	15.1498	0.72689	0.0:0.1407:0.8593:0.0	.	636	Q9NP80	PLPL8_HUMAN	L	571;636;574;636;536;636;536	ENSP00000257694:S636L;ENSP00000373380:S574L;ENSP00000410804:S636L;ENSP00000387789:S536L;ENSP00000406779:S636L;ENSP00000402274:S536L	ENSP00000257694:S636L	S	-	2	0	PNPLA8	107907031	1.000000	0.71417	0.981000	0.43875	0.301000	0.27625	4.643000	0.61390	2.614000	0.88457	0.655000	0.94253	TCG		0.413	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		A	108119795	G	A	108119795	3	1	61	1	0	0	0	0	1	0	0	0	12202	1059	37	1	449	1	PNPLA8	7	108119795	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	376260	108119795	51018868	5507	13492										
PNPLA8	50640	broad.mit.edu	37	chr7	108142960	108142960	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccaccatcaattgagaGaattcggattcctctccctt	5	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:108142960G>T	ENST00000422087.1	-	6	1739	c.1333C>A	c.(1333-1335)Ctc>Atc	p.L445I	PNPLA8_ENST00000257694.8_Missense_Mutation_p.L445I|PNPLA8_ENST00000436062.1_Missense_Mutation_p.L445I|PNPLA8_ENST00000426128.2_Missense_Mutation_p.L445I|PNPLA8_ENST00000388728.5_Missense_Mutation_p.L445I|PNPLA8_ENST00000453144.1_Missense_Mutation_p.L345I|PNPLA8_ENST00000483879.1_5'UTR	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	445	Patatin.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)	p.L445I(1)		breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TCAATTGAGAGAATTCGGATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											119	117	118					7																	108142960		2203	4300	6503	107930196	SO:0001583	missense	50640			AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.1333C>A	7.37:g.108142960G>T	ENSP00000410804:p.Leu445Ile		107930196	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	G	34	5.311761	0.95655	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085	D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	6.02	6.02	0.97574	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.000000	0.85682	D	0.000000	D	0.96269	0.8783	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95959	0.8960	10	0.72032	D	0.01	.	20.5269	0.99230	0.0:0.0:1.0:0.0	.	445	Q9NP80	PLPL8_HUMAN	I	445;445;445;445;345;445;345	ENSP00000394988:L445I;ENSP00000257694:L445I;ENSP00000373380:L445I;ENSP00000410804:L445I;ENSP00000387789:L345I;ENSP00000406779:L445I;ENSP00000402274:L345I	ENSP00000257694:L445I	L	-	1	0	PNPLA8	107930196	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.987000	0.88182	2.859000	0.98148	0.591000	0.81541	CTC		0.388	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		T	108142960	G	T	108142960	3	4	61	1	0	0	0	0	1	0	0	0	12202	942	33	2	1043	2	PNPLA8	7	108142960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23165	108142960	50995703	5508	13493										
DNAJB9	4189	broad.mit.edu	37	chr7	108212277	108212277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcttaggtgtgccaaaatCggcatcagagcgccaaatca	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:108212277C>T	ENST00000249356.3	+	2	653	c.107C>T	c.(106-108)tCg>tTg	p.S36L	DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000313516.5_5'Flank|THAP5_ENST00000415914.3_5'Flank|THAP5_ENST00000438865.1_5'Flank|THAP5_ENST00000493722.1_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	36	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)	p.S36L(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						GTGCCAAAATCGGCATCAGAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											103	113	109					7																	108212277		2203	4300	6503	107999513	SO:0001583	missense	4189			AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"Heat shock proteins / DNAJ (HSP40)"	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.107C>T	7.37:g.108212277C>T	ENSP00000249356:p.Ser36Leu		107999513		Missense_Mutation	SNP	ENST00000249356.3	37	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442874	0.63067	.	.	ENSG00000128590	ENST00000249356	T	0.74737	-0.87	5.34	4.46	0.54185	Heat shock protein DnaJ, N-terminal (5);	0.181794	0.47093	D	0.000259	T	0.68026	0.2956	L	0.50993	1.605	0.30498	N	0.770694	D	0.55172	0.97	P	0.45406	0.479	T	0.69120	-0.5229	9	.	.	.	.	7.0934	0.25297	0.2672:0.6486:0.0:0.0842	.	36	Q9UBS3	DNJB9_HUMAN	L	36	ENSP00000249356:S36L	.	S	+	2	0	DNAJB9	107999513	1.000000	0.71417	0.591000	0.28745	0.995000	0.86356	4.349000	0.59385	1.245000	0.43885	0.563000	0.77884	TCG		0.413	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			T	108212277	C	T	108212277	3	4	61	1	0	0	0	0	1	0	0	0	4638	893	31	1	109	1	DNAJB9	7	108212277	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69317	108212277	50926386	5509	13494										
DNAJB9	4189	broad.mit.edu	37	chr7	108213709	108213709	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagtacagactgaaaataGatttcatggatctagcaagc	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:108213709G>T	ENST00000249356.3	+	3	1130	c.584G>T	c.(583-585)aGa>aTa	p.R195I	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	195					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)	p.R195I(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						ACTGAAAATAGATTTCATGGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											120	119	119					7																	108213709		2203	4300	6503	108000945	SO:0001583	missense	4189			AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"Heat shock proteins / DNAJ (HSP40)"	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.584G>T	7.37:g.108213709G>T	ENSP00000249356:p.Arg195Ile		108000945		Missense_Mutation	SNP	ENST00000249356.3	37	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.489376	0.84962	.	.	ENSG00000128590	ENST00000249356	T	0.60797	0.16	5.86	5.86	0.93980	.	0.039585	0.85682	D	0.000000	T	0.64438	0.2598	M	0.64997	1.995	0.80722	D	1	P	0.48911	0.917	P	0.47470	0.548	T	0.62914	-0.6753	9	.	.	.	.	19.1901	0.93663	0.0:0.0:1.0:0.0	.	195	Q9UBS3	DNJB9_HUMAN	I	195	ENSP00000249356:R195I	.	R	+	2	0	DNAJB9	108000945	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.425000	0.73370	2.776000	0.95493	0.655000	0.94253	AGA		0.373	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			T	108213709	G	T	108213709	3	4	61	1	0	0	0	0	1	0	0	0	4638	942	33	2	590	2	DNAJB9	7	108213709	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1432	108213709	50924954	5510	13495										
LRRN3	54674	broad.mit.edu	37	chr7	110764715	110764715	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaataataccacaacactTatggcctgtcttggaggcct	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:110764715T>G	ENST00000422987.3	+	2	2718	c.1887T>G	c.(1885-1887)ctT>ctG	p.L629L	IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000308478.5_Silent_p.L629L|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000437687.1_Intron|LRRN3_ENST00000451085.1_Silent_p.L629L|IMMP2L_ENST00000447215.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	629					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L629L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CCACAACACTTATGGCCTGTC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	7											74	74	74					7																	110764715		2203	4300	6503	110551951	SO:0001819	synonymous_variant	54674			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1887T>G	7.37:g.110764715T>G			110551951	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																				0.413	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110764715	T	G	110764715	2	3	61	1	0	0	0	0	0	0	0	1	9065	1741	61	4		4	LRRN3	7	110764715	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2551006	110764715	48373948	5511	13496										
DOCK4	9732	broad.mit.edu	37	chr7	111387366	111387366	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattaactgcagcatctataActccattcaggcacatagtc	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:111387366A>C	ENST00000437633.1	-	42	4779	c.4523T>G	c.(4522-4524)gTt>gGt	p.V1508G	DOCK4_ENST00000494651.2_Missense_Mutation_p.V391G|DOCK4_ENST00000428084.1_Missense_Mutation_p.V1517G	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1508	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.V1505G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				AGCATCTATAACTCCATTCAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											109	105	106					7																	111387366		2000	4184	6184	111174602	SO:0001583	missense	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4523T>G	7.37:g.111387366A>C	ENSP00000404179:p.Val1508Gly		111174602	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.511645|4.511645	0.85389|0.85389	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000423057;ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	.|T;T;T	.|0.17854	.|2.25;2.25;2.25	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.45617|0.45617	0.1351|0.1351	M|M	0.83223|0.83223	2.63|2.63	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.71674	.|0.996;0.998;0.998;0.998;0.995	.|D;D;D;D;D	.|0.74023	.|0.979;0.974;0.982;0.982;0.962	T|T	0.51411|0.51411	-0.8709|-0.8709	5|10	.|0.87932	.|D	.|0	.|.	15.3585|15.3585	0.74448|0.74448	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|415;391;1553;1508;1517	.|B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2	.|.;.;.;DOCK4_HUMAN;.	V|G	969;1541|1496;1517;391;1508;1505	.|ENSP00000410746:V1517G;ENSP00000440944:V391G;ENSP00000404179:V1508G	.|ENSP00000345432:V1505G	L|V	-|-	1|2	2|0	DOCK4|DOCK4	111174602|111174602	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	9.139000|9.139000	0.94554|0.94554	2.218000|2.218000	0.71995|0.71995	0.533000|0.533000	0.62120|0.62120	TTA|GTT		0.398	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111387366	A	C	111387366	3	2	61	1	0	0	0	0	1	0	0	0	4700	43	2	4	1421	4	DOCK4	7	111387366	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	622651	111387366	47751297	5512	13497										
DOCK4	9732	broad.mit.edu	37	chr7	111508204	111508204	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatacttaaaaatgtattCttgtgccttaaaaatacaat	3	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:111508204C>A	ENST00000437633.1	-	22	2372	c.2116G>T	c.(2116-2118)Gaa>Taa	p.E706*	DOCK4_ENST00000428084.1_Nonsense_Mutation_p.E706*|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	706					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.E694*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				AAAATGTATTCTTGTGCCTTA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											35	37	36					7																	111508204		1814	4082	5896	111295440	SO:0001587	stop_gained	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2116G>T	7.37:g.111508204C>A	ENSP00000404179:p.Glu706*		111295440	O14584|O94824|Q8NB45	Nonsense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.745099|7.745099	0.98465|0.98465	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250|ENST00000423057;ENST00000445943	.|.	.|.	.|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76772	.|0.4034	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74188	.|-0.3746	.|4	0.49607|.	T|.	0.09|.	.|.	20.0822|20.0822	0.97779|0.97779	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	694;706;706;694;705|157;693	.|.	ENSP00000345432:E694X|.	E|K	-|-	1|3	0|2	DOCK4|DOCK4	111295440|111295440	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.805000|0.805000	0.45488|0.45488	7.445000|7.445000	0.80570|0.80570	2.826000|2.826000	0.97356|0.97356	0.563000|0.563000	0.77884|0.77884	GAA|AAG		0.373	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111508204	C	A	111508204	4	1	61	1	0	0	0	0	0	1	0	0	4700	922	32	2	3908	2	DOCK4	7	111508204	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120838	111508204	47630459	5513	13498										
DOCK4	9732	broad.mit.edu	37	chr7	111629206	111629206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagccggtggaagagatCgccttcattacgctaagaaa	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:111629206C>T	ENST00000437633.1	-	6	584	c.328G>A	c.(328-330)Gat>Aat	p.D110N	DOCK4_ENST00000428084.1_Missense_Mutation_p.D110N|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	110					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.D98N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TGGAAGAGATCGCCTTCATTA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											79	77	77					7																	111629206		2027	4187	6214	111416442	SO:0001583	missense	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.328G>A	7.37:g.111629206C>T	ENSP00000404179:p.Asp110Asn		111416442	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.717479	0.68844	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.02863	4.13;4.13	5.46	5.46	0.80206	.	0.047905	0.85682	D	0.000000	T	0.04952	0.0133	L	0.49126	1.545	0.80722	D	1	B;B;B;B	0.25850	0.065;0.136;0.065;0.029	B;B;B;B	0.16722	0.014;0.01;0.016;0.006	T	0.40213	-0.9575	10	0.46703	T	0.11	.	18.6769	0.91531	0.0:1.0:0.0:0.0	.	110;110;110;110	A4D0S8;Q149N6;Q149N5;Q8N1I0	.;.;.;DOCK4_HUMAN	N	98;110;110;98;109	ENSP00000410746:D110N;ENSP00000404179:D110N	ENSP00000345432:D98N	D	-	1	0	DOCK4	111416442	1.000000	0.71417	0.971000	0.41717	0.956000	0.61745	7.726000	0.84824	2.706000	0.92434	0.655000	0.94253	GAT		0.512	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111629206	C	T	111629206	3	4	61	1	0	0	0	0	1	0	0	0	4700	884	31	1	5760	1	DOCK4	7	111629206	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121002	111629206	47509457	5514	13499										
IFRD1	3475	broad.mit.edu	37	chr7	112102102	112102102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaatatcttcactaaatCctatctcaaagagaaagaca	5	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:112102102C>A	ENST00000403825.3	+	7	926	c.665C>A	c.(664-666)tCc>tAc	p.S222Y	IFRD1_ENST00000535603.1_Missense_Mutation_p.S172Y|IFRD1_ENST00000005558.4_Missense_Mutation_p.S222Y|IFRD1_ENST00000486688.1_3'UTR	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	222					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)		p.S222Y(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						TTCACTAAATCCTATCTCAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											111	106	108					7																	112102102		2203	4300	6503	111889338	SO:0001583	missense	3475			Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.665C>A	7.37:g.112102102C>A	ENSP00000384477:p.Ser222Tyr		111889338	B7Z5G1|O75234|Q5U013|Q9BVE4	Missense_Mutation	SNP	ENST00000403825.3	37	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396057	0.83011	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000535603	T;T;T	0.51071	0.72;0.72;0.75	5.84	5.84	0.93424	Interferon-related developmental regulator, N-terminal (1);Armadillo-type fold (1);	0.290344	0.40640	N	0.001053	T	0.63498	0.2516	M	0.77486	2.375	0.58432	D	0.999995	P	0.42620	0.785	P	0.52159	0.691	T	0.65537	-0.6144	10	0.62326	D	0.03	-8.9464	14.9211	0.70838	0.1431:0.8569:0.0:0.0	.	222	O00458	IFRD1_HUMAN	Y	222;222;172	ENSP00000005558:S222Y;ENSP00000384477:S222Y;ENSP00000439188:S172Y	ENSP00000005558:S222Y	S	+	2	0	IFRD1	111889338	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.543000	0.60684	2.775000	0.95449	0.655000	0.94253	TCC		0.353	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		A	112102102	C	A	112102102	3	1	61	1	0	0	0	0	1	0	0	0	7574	855	30	2	691	2	IFRD1	7	112102102	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	472896	112102102	47036561	5515	13500										
IFRD1	3475	broad.mit.edu	37	chr7	112112836	112112836	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagtcaaatgaattccttCgaaatgtatttgaacttgga	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:112112836C>T	ENST00000403825.3	+	11	1447	c.1186C>T	c.(1186-1188)Cga>Tga	p.R396*	IFRD1_ENST00000535603.1_Nonsense_Mutation_p.R346*|IFRD1_ENST00000005558.4_Nonsense_Mutation_p.R396*	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	396				R -> E (in Ref. 1; CAA71366). {ECO:0000305}.	adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)		p.R396*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						TGAATTCCTTCGAAATGTATT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											119	118	118					7																	112112836		2203	4300	6503	111900072	SO:0001587	stop_gained	3475			Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1186C>T	7.37:g.112112836C>T	ENSP00000384477:p.Arg396*		111900072	B7Z5G1|O75234|Q5U013|Q9BVE4	Nonsense_Mutation	SNP	ENST00000403825.3	37	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	C	37	6.477943	0.97598	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000536259;ENST00000535603;ENST00000462155	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.2822	14.5242	0.67875	0.1467:0.8532:0.0:0.0	.	.	.	.	X	396;396;131;346;59	.	ENSP00000005558:R396X	R	+	1	2	IFRD1	111900072	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.083000	0.41615	2.762000	0.94881	0.650000	0.86243	CGA		0.358	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		T	112112836	C	T	112112836	4	4	61	1	0	0	0	0	0	1	0	0	7574	876	31	1	1228	1	IFRD1	7	112112836	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10734	112112836	47025827	5516	13501										
TMEM168	64418	broad.mit.edu	37	chr7	112415338	112415338	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggattccaatggcaaaacGattagaaacatgctcaagaa	8	7	1	2	rs201379399		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:112415338G>A	ENST00000312814.6	-	3	1724	c.1164C>T	c.(1162-1164)atC>atT	p.I388I	TMEM168_ENST00000480969.1_5'UTR|TMEM168_ENST00000454074.1_Silent_p.I388I	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	388						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.I388I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						ATGGCAAAACGATTAGAAACA	0.368													G|||	1	0.000199681	0	0	5008	,	,		16681	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											89	77	81					7																	112415338		2203	4300	6503	112202574	SO:0001819	synonymous_variant	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1164C>T	7.37:g.112415338G>A			112202574	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Silent	SNP	ENST00000312814.6	37	CCDS5757.1																																																																																				0.368	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		A	112415338	G	A	112415338	2	1	61	1	0	0	0	0	0	0	0	1	16122	1048	37	1		1	TMEM168	7	112415338	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	302502	112415338	46723325	5517	13502										
TMEM168	64418	broad.mit.edu	37	chr7	112424870	112424870	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactaaagcaataacgcagtGatttacacatgtaaccagca	7	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:112424870G>T	ENST00000312814.6	-	2	571	c.11C>A	c.(10-12)tCa>tAa	p.S4*	TMEM168_ENST00000454074.1_Nonsense_Mutation_p.S4*	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	4						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.S4*(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						ATAACGCAGTGATTTACACAT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											55	49	51					7																	112424870		2203	4300	6503	112212106	SO:0001587	stop_gained	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.11C>A	7.37:g.112424870G>T	ENSP00000323068:p.Ser4*		112212106	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Nonsense_Mutation	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	G	38	7.148165	0.98096	.	.	ENSG00000146802	ENST00000312814;ENST00000454074	.	.	.	5.2	5.2	0.72013	.	0.084481	0.49916	D	0.000130	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-21.5454	19.1034	0.93283	0.0:0.0:1.0:0.0	.	.	.	.	X	4	.	ENSP00000323068:S4X	S	-	2	0	TMEM168	112212106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.867000	0.75511	2.571000	0.86741	0.650000	0.86243	TCA		0.388	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		T	112424870	G	T	112424870	4	4	61	1	0	0	0	0	0	1	0	0	16122	1294	45	2	2098	2	TMEM168	7	112424870	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9532	112424870	46713793	5518	13503										
PPP1R3A	5506	broad.mit.edu	37	chr7	113519535	113519535	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctttcttggtcatgtaAgattgtttggaaattttttc	7	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:113519535A>C	ENST00000284601.3	-	4	1680	c.1612T>G	c.(1612-1614)Tta>Gta	p.L538V		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	538					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.L538V(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TGGTCATGTAAGATTGTTTGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											98	88	91					7																	113519535		2203	4300	6503	113306771	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1612T>G	7.37:g.113519535A>C	ENSP00000284601:p.Leu538Val		113306771	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.869912	0.33069	.	.	ENSG00000154415	ENST00000284601	T	0.16457	2.34	6.02	3.51	0.40186	.	0.946937	0.08812	N	0.890108	T	0.16041	0.0386	L	0.57536	1.79	0.09310	N	1	B	0.34015	0.435	B	0.24974	0.057	T	0.21280	-1.0250	10	0.44086	T	0.13	-0.6216	6.3716	0.21485	0.6765:0.1654:0.0:0.1581	.	538	Q16821	PPR3A_HUMAN	V	538	ENSP00000284601:L538V	ENSP00000284601:L538V	L	-	1	2	PPP1R3A	113306771	0.022000	0.18835	0.004000	0.12327	0.133000	0.20885	1.519000	0.35888	1.082000	0.41137	0.533000	0.62120	TTA		0.373	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113519535	A	C	113519535	3	2	61	1	0	0	0	0	1	0	0	0	12405	69	3	4	1760	4	PPP1R3A	7	113519535	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1094665	113519535	45619128	5519	13504										
FOXP2	93986	broad.mit.edu	37	chr7	114304367	114304367	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttacctttgctaagtaatCctggactgataaataatgca	7	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:114304367C>T	ENST00000393494.2	+	16	2158	c.1879C>T	c.(1879-1881)Cct>Tct	p.P627S	FOXP2_ENST00000393498.2_Missense_Mutation_p.P606S|FOXP2_ENST00000403559.4_Missense_Mutation_p.P644S|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000393491.3_Missense_Mutation_p.P442S|FOXP2_ENST00000350908.4_Missense_Mutation_p.P627S|FOXP2_ENST00000393489.3_Missense_Mutation_p.P535S|FOXP2_ENST00000408937.3_Missense_Mutation_p.P652S			O15409	FOXP2_HUMAN	forkhead box P2	627					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P652S(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						GCTAAGTAATCCTGGACTGAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											88	79	82					7																	114304367		2203	4300	6503	114091603	SO:0001583	missense	93986			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1879C>T	7.37:g.114304367C>T	ENSP00000377132:p.Pro627Ser		114091603	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189465	0.38707	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	D;D;D;D;D;D	0.91945	-2.68;-2.67;-2.68;-2.68;-2.76;-2.94	5.57	5.57	0.84162	.	0.100076	0.64402	D	0.000001	D	0.91260	0.7245	L	0.46157	1.445	0.80722	D	1	B;B;P;B;B	0.41710	0.295;0.025;0.76;0.295;0.137	B;B;P;B;B	0.46510	0.068;0.026;0.519;0.068;0.057	D	0.90967	0.4817	10	0.48119	T	0.1	.	14.3901	0.66973	0.1477:0.8523:0.0:0.0	.	626;644;442;627;652	B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4	.;.;.;FOXP2_HUMAN;.	S	627;652;644;627;604;535;442	ENSP00000377132:P627S;ENSP00000386200:P652S;ENSP00000385069:P644S;ENSP00000265436:P627S;ENSP00000377129:P535S;ENSP00000377130:P442S	ENSP00000265436:P627S	P	+	1	0	FOXP2	114091603	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.341000	0.59335	2.614000	0.88457	0.655000	0.94253	CCT		0.403	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		T	114304367	C	T	114304367	3	4	61	1	0	0	0	0	1	0	0	0	6046	855	30	3	2104	3	FOXP2	7	114304367	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	784832	114304367	44834296	5520	13505										
CAPZA2	830	broad.mit.edu	37	chr7	116528223	116528223	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattcatgcccctcctggaGaatttaatgaggttttcaat	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:116528223G>T	ENST00000361183.3	+	2	221	c.82G>T	c.(82-84)Gaa>Taa	p.E28*	CAPZA2_ENST00000458284.2_Nonsense_Mutation_p.E28*|CAPZA2_ENST00000490693.1_Nonsense_Mutation_p.E28*	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	28					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.E28*(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			CCCTCCTGGAGAATTTAATGA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											92	95	94					7																	116528223		2203	4298	6501	116315459	SO:0001587	stop_gained	830				CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"F-actin capping protein alpha-2 subunit"	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.82G>T	7.37:g.116528223G>T	ENSP00000354947:p.Glu28*		116315459	B4DG50	Nonsense_Mutation	SNP	ENST00000361183.3	37	CCDS5768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	23.9|23.9	4.471051|4.471051	0.84533|0.84533	.|.	.|.	ENSG00000198898|ENSG00000198898	ENST00000464223;ENST00000484325|ENST00000361183;ENST00000458284;ENST00000490693	.|.	.|.	.|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.81574|.	0.4851|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.82973|.	-0.0191|.	5|.	0.87932|0.87932	D|D	0|0	-19.3167|-19.3167	18.9609|18.9609	0.92677|0.92677	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	D|X	5|28	.|.	ENSP00000420640:E5D|ENSP00000354947:E28X	E|E	+|+	3|1	2|0	CAPZA2|CAPZA2	116315459|116315459	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.490000|7.490000	0.81461|0.81461	2.776000|2.776000	0.95493|0.95493	0.586000|0.586000	0.80456|0.80456	GAG|GAA		0.338	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136		T	116528223	G	T	116528223	4	4	61	1	0	0	0	0	0	1	0	0	2647	943	33	2	88	2	CAPZA2	7	116528223	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2223856	116528223	42610440	5521	13506										
CAPZA2	830	broad.mit.edu	37	chr7	116556135	116556135	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagtgcaaacagcaaaaGaatttataaagattgtagaa	8	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:116556135G>T	ENST00000361183.3	+	9	818	c.679G>T	c.(679-681)Gaa>Taa	p.E227*	CAPZA2_ENST00000458284.2_3'UTR	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	227					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.E227*(2)		endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			AACAGCAAAAGAATTTATAAA	0.224																																																2	Substitution - Nonsense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	7											20	22	21					7																	116556135		2184	4272	6456	116343371	SO:0001587	stop_gained	830				CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"F-actin capping protein alpha-2 subunit"	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.679G>T	7.37:g.116556135G>T	ENSP00000354947:p.Glu227*		116343371	B4DG50	Nonsense_Mutation	SNP	ENST00000361183.3	37	CCDS5768.1	.	.	.	.	.	.	.	.	.	.	G	37	5.991878	0.97179	.	.	ENSG00000198898	ENST00000361183	.	.	.	5.55	5.55	0.83447	.	0.051784	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-11.7075	19.5113	0.95142	0.0:0.0:1.0:0.0	.	.	.	.	X	227	.	ENSP00000354947:E227X	E	+	1	0	CAPZA2	116343371	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.607000	0.98328	2.612000	0.88384	0.591000	0.81541	GAA		0.224	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136		T	116556135	G	T	116556135	4	4	61	1	0	0	0	0	0	1	0	0	2647	943	33	2	713	2	CAPZA2	7	116556135	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27912	116556135	42582528	5522	13507										
ASZ1	136991	broad.mit.edu	37	chr7	117023053	117023053	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattacctaaaaatgtgatCtttttctctatcagaatctg	4	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117023053C>A	ENST00000284629.2	-	7	861	c.799G>T	c.(799-801)Gat>Tat	p.D267Y		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1									p.D267Y(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			AAAATGTGATCTTTTTCTCTA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	7											60	60	60					7																	117023053		2192	4267	6459	116810289	SO:0001583	missense	136991			AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	1350	protein-coding gene	gene with protein product		605797	"ankyrin-like 1"	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.799G>T	7.37:g.117023053C>A	ENSP00000284629:p.Asp267Tyr		116810289		Missense_Mutation	SNP	ENST00000284629.2	37	CCDS5772.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.354888	0.61293	.	.	ENSG00000154438	ENST00000284629	T	0.68479	-0.33	5.71	5.71	0.89125	.	0.363222	0.32386	N	0.006163	T	0.76378	0.3979	M	0.65975	2.015	0.37634	D	0.9218	D;D	0.62365	0.991;0.991	P;P	0.56700	0.804;0.804	T	0.80576	-0.1321	10	0.59425	D	0.04	-38.4327	15.3667	0.74529	0.0:1.0:0.0:0.0	.	267;267	B7ZM20;Q8WWH4	.;ASZ1_HUMAN	Y	267	ENSP00000284629:D267Y	ENSP00000284629:D267Y	D	-	1	0	ASZ1	116810289	0.992000	0.36948	1.000000	0.80357	0.802000	0.45316	3.124000	0.50461	2.707000	0.92482	0.650000	0.86243	GAT		0.259	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768		A	117023053	C	A	117023053	3	1	61	1	0	0	0	0	1	0	0	0	1070	913	32	2	656	2	ASZ1	7	117023053	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	466918	117023053	42115610	5523	13508										
CFTR	1080	broad.mit.edu	37	chr7	117188741	117188741	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacaaaacaataacaataGaaaaacttctaatggtgatg	5	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117188741G>T	ENST00000003084.6	+	10	1388	c.1256G>T	c.(1255-1257)aGa>aTa	p.R419I	CFTR_ENST00000454343.1_Intron	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	419					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.R419I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	AATAACAATAGAAAAACTTCT	0.333									Cystic Fibrosis																																							1	Substitution - Missense(1)	large_intestine(1)	7											20	21	21					7																	117188741		2199	4291	6490	116975977	SO:0001583	missense	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1256G>T	7.37:g.117188741G>T	ENSP00000003084:p.Arg419Ile		116975977	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	G	6.593	0.477753	0.12521	.	.	ENSG00000001626	ENST00000003084;ENST00000426809	D;D	0.92699	-3.03;-3.09	4.85	2.87	0.33458	ABC transporter, transmembrane domain, type 1 (1);	0.468223	0.25971	N	0.027126	D	0.87120	0.6098	L	0.34521	1.04	0.21220	N	0.99976	B	0.15719	0.014	B	0.22601	0.04	T	0.76846	-0.2808	10	0.35671	T	0.21	-3.9783	14.0016	0.64437	0.0:0.0:0.7296:0.2704	.	419	P13569	CFTR_HUMAN	I	419;389	ENSP00000003084:R419I;ENSP00000389119:R389I	ENSP00000003084:R419I	R	+	2	0	CFTR	116975977	1.000000	0.71417	0.003000	0.11579	0.034000	0.12701	3.332000	0.52083	1.143000	0.42306	0.650000	0.86243	AGA		0.333	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117188741	G	T	117188741	3	4	61	1	0	0	0	0	1	0	0	0	3300	942	33	2	1294	2	CFTR	7	117188741	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165688	117188741	41949922	5524	13509										
CFTR	1080	broad.mit.edu	37	chr7	117227869	117227869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgagtggaggtcaacgagCaagaatttctttagcaaggt	12	6	2	2	rs121909022		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117227869C>A	ENST00000003084.6	+	12	1793	c.1661C>A	c.(1660-1662)gCa>gAa	p.A554E	CFTR_ENST00000454343.1_Missense_Mutation_p.A493E	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	554	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.A554E(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GGTCAACGAGCAAGAATTTCT	0.343									Cystic Fibrosis																																							1	Substitution - Missense(1)	large_intestine(1)	7	GRCh37	CM930113	CFTR	M	rs121909022						96	96	96					7																	117227869		2203	4300	6503	117015105	SO:0001583	missense	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1661C>A	7.37:g.117227869C>A	ENSP00000003084:p.Ala554Glu		117015105	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046947	0.93740	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.90133	-2.62;-2.62;-2.62	5.27	5.27	0.74061	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.94935	0.8362	M	0.68317	2.08	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95170	0.8289	9	0.87932	D	0	-16.8806	19.2582	0.93955	0.0:1.0:0.0:0.0	.	554	P13569	CFTR_HUMAN	E	554;493;524	ENSP00000003084:A554E;ENSP00000403677:A493E;ENSP00000389119:A524E	ENSP00000003084:A554E	A	+	2	0	CFTR	117015105	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.088000	0.64486	2.622000	0.88805	0.655000	0.94253	GCA		0.343	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		A	117227869	C	A	117227869	3	1	61	1	0	0	0	0	1	0	0	0	3300	710	25	2	1707	2	CFTR	7	117227869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39128	117227869	41910794	5525	13510										
CFTR	1080	broad.mit.edu	37	chr7	117250675	117250675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcttttattatgttgagaGcatatttcctccaaacctca	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117250675G>A	ENST00000003084.6	+	19	3223	c.3091G>A	c.(3091-3093)Gca>Aca	p.A1031T	CFTR_ENST00000454343.1_Missense_Mutation_p.A970T|AC000111.6_ENST00000456270.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1031	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.A1031T(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TATGTTGAGAGCATATTTCCT	0.383									Cystic Fibrosis																																							1	Substitution - Missense(1)	large_intestine(1)	7											126	112	117					7																	117250675		2203	4300	6503	117037911	SO:0001583	missense	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.3091G>A	7.37:g.117250675G>A	ENSP00000003084:p.Ala1031Thr		117037911	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806461	0.31961	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.90900	-2.75;-2.75;-2.75	6.16	5.28	0.74379	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.249428	0.47455	D	0.000233	D	0.89104	0.6620	L	0.41236	1.265	0.35645	D	0.811275	B	0.21225	0.053	B	0.38655	0.278	D	0.87581	0.2484	10	0.23302	T	0.38	-3.2963	14.5361	0.67960	0.0:0.0:0.7333:0.2667	.	1031	P13569	CFTR_HUMAN	T	1031;970;1001	ENSP00000003084:A1031T;ENSP00000403677:A970T;ENSP00000389119:A1001T	ENSP00000003084:A1031T	A	+	1	0	CFTR	117037911	1.000000	0.71417	0.697000	0.30258	0.105000	0.19272	3.680000	0.54641	1.591000	0.50007	0.650000	0.86243	GCA		0.383	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		A	117250675	G	A	117250675	3	1	61	1	0	0	0	0	1	0	0	0	3300	971	34	3	3165	3	CFTR	7	117250675	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22806	117250675	41887988	5526	13511										
CFTR	1080	broad.mit.edu	37	chr7	117282581	117282581	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaaggagaaatccagatCgatggtgtgtcttgggattc	13	6	1	3	rs1800129		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117282581C>T	ENST00000003084.6	+	23	3939	c.3807C>T	c.(3805-3807)atC>atT	p.I1269I	CFTR_ENST00000454343.1_Silent_p.I1208I|AC000111.6_ENST00000456270.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1269	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.I1269I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	AAATCCAGATCGATGGTGTGT	0.438									Cystic Fibrosis																																							1	Substitution - coding silent(1)	large_intestine(1)	7											128	125	126					7																	117282581		2203	4300	6503	117069817	SO:0001819	synonymous_variant	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.3807C>T	7.37:g.117282581C>T			117069817	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																				0.438	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117282581	C	T	117282581	2	4	61	1	0	0	0	0	0	0	0	1	3300	874	31	1		1	CFTR	7	117282581	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31906	117282581	41856082	5527	13512										
CTTNBP2	83992	broad.mit.edu	37	chr7	117365280	117365280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttcttgaactctgggtgCgatgacgccattccacagct	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117365280C>T	ENST00000160373.3	-	18	4178	c.4087G>A	c.(4087-4089)Gca>Aca	p.A1363T		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1363					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.A1363T(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ACTCTGGGTGCGATGACGCCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											180	173	175					7																	117365280		2203	4300	6503	117152516	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4087G>A	7.37:g.117365280C>T	ENSP00000160373:p.Ala1363Thr		117152516	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.29|16.29	3.082939|3.082939	0.55861|0.55861	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000160373|ENST00000446636	D|.	0.89050|.	-2.46|.	5.72|5.72	3.93|3.93	0.45458|0.45458	.|.	0.209915|.	0.51477|.	N|.	0.000093|.	T|T	0.75867|0.75867	0.3908|0.3908	M|M	0.84585|0.84585	2.705|2.705	0.36210|0.36210	D|D	0.851305|0.851305	D|.	0.76494|.	0.999|.	P|.	0.59825|.	0.864|.	T|T	0.81982|0.81982	-0.0683|-0.0683	10|5	0.49607|.	T|.	0.09|.	-0.4431|-0.4431	12.5805|12.5805	0.56388|0.56388	0.0:0.8654:0.0:0.1346|0.0:0.8654:0.0:0.1346	.|.	1363|.	Q8WZ74|.	CTTB2_HUMAN|.	T|H	1363|850	ENSP00000160373:A1363T|.	ENSP00000160373:A1363T|.	A|R	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117152516|117152516	1.000000|1.000000	0.71417|0.71417	0.093000|0.093000	0.20910|0.20910	0.185000|0.185000	0.23345|0.23345	4.579000|4.579000	0.60936|0.60936	0.889000|0.889000	0.36185|0.36185	-0.137000|-0.137000	0.14449|0.14449	GCA|CGC		0.478	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117365280	C	T	117365280	3	4	61	1	0	0	0	0	1	0	0	0	4051	768	27	1	928	1	CTTNBP2	7	117365280	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82699	117365280	41773383	5528	13513										
CTTNBP2	83992	broad.mit.edu	37	chr7	117368182	117368182	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccaggaactacaggacaaGacaggaaatattttggtcca	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117368182G>T	ENST00000160373.3	-	17	4107	c.4016C>A	c.(4015-4017)tCt>tAt	p.S1339Y		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1339					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.S1339Y(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TACAGGACAAGACAGGAAATA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	96	94					7																	117368182		2203	4300	6503	117155418	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4016C>A	7.37:g.117368182G>T	ENSP00000160373:p.Ser1339Tyr		117155418	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686344	0.88639	.	.	ENSG00000077063	ENST00000160373	D	0.90676	-2.71	5.43	5.43	0.79202	.	0.152363	0.64402	D	0.000009	D	0.95465	0.8527	M	0.87547	2.89	0.58432	D	0.999998	D	0.57899	0.981	P	0.59288	0.855	D	0.95812	0.8842	10	0.87932	D	0	-2.4272	19.5983	0.95549	0.0:0.0:1.0:0.0	.	1339	Q8WZ74	CTTB2_HUMAN	Y	1339	ENSP00000160373:S1339Y	ENSP00000160373:S1339Y	S	-	2	0	CTTNBP2	117155418	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.873000	0.92357	2.704000	0.92352	0.650000	0.86243	TCT		0.488	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117368182	G	T	117368182	3	4	61	1	0	0	0	0	1	0	0	0	4051	942	33	2	1003	2	CTTNBP2	7	117368182	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2902	117368182	41770481	5529	13514										
CTTNBP2	83992	broad.mit.edu	37	chr7	117417776	117417776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagaagcttgaggctgtccAcattaccagtgtccacagct	9	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117417776A>G	ENST00000160373.3	-	8	2658	c.2567T>C	c.(2566-2568)gTg>gCg	p.V856A		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	856					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.V856A(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GAGGCTGTCCACATTACCAGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											72	74	74					7																	117417776		2203	4300	6503	117205012	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2567T>C	7.37:g.117417776A>G	ENSP00000160373:p.Val856Ala		117205012	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957734	0.53400	.	.	ENSG00000077063	ENST00000160373	T	0.53857	0.6	5.46	5.46	0.80206	Ankyrin repeat-containing domain (3);	0.165679	0.52532	D	0.000065	T	0.42449	0.1203	N	0.16307	0.4	0.43467	D	0.995674	P	0.45768	0.866	P	0.44597	0.454	T	0.36040	-0.9764	10	0.35671	T	0.21	-18.8457	15.8249	0.78690	1.0:0.0:0.0:0.0	.	856	Q8WZ74	CTTB2_HUMAN	A	856	ENSP00000160373:V856A	ENSP00000160373:V856A	V	-	2	0	CTTNBP2	117205012	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.438000	0.59961	2.197000	0.70478	0.528000	0.53228	GTG		0.443	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117417776	A	G	117417776	3	3	61	1	0	0	0	0	1	0	0	0	4051	159	6	4	2488	4	CTTNBP2	7	117417776	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	49594	117417776	41720887	5530	13515										
CTTNBP2	83992	broad.mit.edu	37	chr7	117431351	117431351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccaggcacccacctgagaCgtggccagggctgaaacggc	15	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117431351C>T	ENST00000160373.3	-	4	1990	c.1899G>A	c.(1897-1899)acG>acA	p.T633T	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	633					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.T633T(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CCACCTGAGACGTGGCCAGGG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	7											83	76	78					7																	117431351		2203	4300	6503	117218587	SO:0001819	synonymous_variant	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1899G>A	7.37:g.117431351C>T			117218587	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	C	5.590	0.293679	0.10567	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.74	0.556	0.17253	.	.	.	.	.	T	0.53610	0.1807	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41395	-0.9511	4	.	.	.	-1.2485	6.9355	0.24464	0.1105:0.4548:0.0:0.4347	.	.	.	.	I	162	.	.	V	-	1	0	CTTNBP2	117218587	0.381000	0.25140	0.997000	0.53966	0.981000	0.71138	-0.402000	0.07223	-0.038000	0.13624	-1.119000	0.02030	GTC		0.552	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117431351	C	T	117431351	2	4	61	1	0	0	0	0	0	0	0	1	4051	523	19	1		1	CTTNBP2	7	117431351	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13575	117431351	41707312	5531	13516										
CTTNBP2	83992	broad.mit.edu	37	chr7	117432385	117432385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagatatggaaaccaaacGcctatcttttgtcttccgtg	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117432385G>A	ENST00000160373.3	-	4	956	c.865C>T	c.(865-867)Cgt>Tgt	p.R289C	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	289					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.R289C(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GAAACCAAACGCCTATCTTTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											144	126	132					7																	117432385		2203	4300	6503	117219621	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.865C>T	7.37:g.117432385G>A	ENSP00000160373:p.Arg289Cys		117219621	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917573	0.33815	.	.	ENSG00000077063	ENST00000160373	T	0.65916	-0.18	5.67	5.67	0.87782	.	0.315545	0.39475	N	0.001359	T	0.67392	0.2888	M	0.82630	2.6	0.47065	D	0.9993	D	0.53885	0.963	P	0.44860	0.462	T	0.73541	-0.3950	10	0.66056	D	0.02	-4.5801	11.8781	0.52558	0.0:0.1226:0.7354:0.1419	.	289	Q8WZ74	CTTB2_HUMAN	C	289	ENSP00000160373:R289C	ENSP00000160373:R289C	R	-	1	0	CTTNBP2	117219621	0.973000	0.33851	0.996000	0.52242	0.215000	0.24574	1.474000	0.35398	2.831000	0.97527	0.650000	0.86243	CGT		0.443	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117432385	G	A	117432385	3	1	61	1	0	0	0	0	1	0	0	0	4051	1087	38	1	4206	1	CTTNBP2	7	117432385	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1034	117432385	41706278	5532	13517										
ANKRD7	56311	broad.mit.edu	37	chr7	117876899	117876899	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtttagtaaagcttcttCttcagcaaggtgtggaatta	9	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:117876899C>A	ENST00000265224.4	+	5	786	c.631C>A	c.(631-633)Ctt>Att	p.L211I	ANKRD7_ENST00000417525.1_Missense_Mutation_p.L158I|ANKRD7_ENST00000477532.1_3'UTR|ANKRD7_ENST00000357099.4_Missense_Mutation_p.L231I|ANKRD7_ENST00000433239.1_Missense_Mutation_p.L158I	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	211					male gonad development (GO:0008584)	nucleus (GO:0005634)		p.L231I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						AAAGCTTCTTCTTCAGCAAGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											238	221	226					7																	117876899		1893	4116	6009	117664135	SO:0001583	missense	56311			D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.631C>A	7.37:g.117876899C>A	ENSP00000265224:p.Leu211Ile		117664135	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	37	CCDS43638.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043113	0.36085	.	.	ENSG00000106013	ENST00000357099;ENST00000265224;ENST00000417525;ENST00000433239	T;T;T;T	0.57907	1.38;1.38;0.37;0.37	4.57	4.57	0.56435	Ankyrin repeat-containing domain (3);	0.000000	0.42294	D	0.000727	T	0.57917	0.2086	M	0.64404	1.975	0.33095	D	0.538406	D	0.65815	0.995	P	0.55965	0.788	T	0.60845	-0.7182	10	0.02654	T	1	-6.8665	14.4335	0.67266	0.0:1.0:0.0:0.0	.	211	Q92527	ANKR7_HUMAN	I	231;211;158;158	ENSP00000349612:L231I;ENSP00000265224:L211I;ENSP00000395595:L158I;ENSP00000388473:L158I	ENSP00000265224:L211I	L	+	1	0	ANKRD7	117664135	0.999000	0.42202	0.998000	0.56505	0.157000	0.22087	2.512000	0.45485	2.260000	0.74910	0.305000	0.20034	CTT		0.398	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		A	117876899	C	A	117876899	3	1	61	1	0	0	0	0	1	0	0	0	686	913	32	2	649	2	ANKRD7	7	117876899	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	444514	117876899	41261764	5533	13518										
C7orf58	79974	broad.mit.edu	37	chr7	120740099	120740099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcgtgcattcattcattCgacgggcacagtttggaatc	10	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:120740099C>T	ENST00000310396.5	+	7	1336	c.869C>T	c.(868-870)tCg>tTg	p.S290L	CPED1_ENST00000423795.1_Missense_Mutation_p.S70L|CPED1_ENST00000450913.2_Missense_Mutation_p.S290L	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	290						endoplasmic reticulum (GO:0005783)		p.S290L(1)									TTCATTCATTCGACGGGCACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	7											157	134	141					7																	120740099		2203	4300	6503	120527335	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.869C>T	7.37:g.120740099C>T	ENSP00000309772:p.Ser290Leu		120527335	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380134	0.82682	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.58	5.58	0.84498	.	0.403623	0.25804	N	0.028184	T	0.65668	0.2713	M	0.76002	2.32	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.996;0.997	T	0.67469	-0.5663	10	0.62326	D	0.03	.	16.4822	0.84160	0.0:1.0:0.0:0.0	.	70;290;290	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	L	290;290;290;70;70	ENSP00000309772:S290L;ENSP00000398082:S290L;ENSP00000406122:S290L;ENSP00000415573:S70L;ENSP00000391952:S70L	ENSP00000309772:S290L	S	+	2	0	C7orf58	120527335	0.997000	0.39634	0.993000	0.49108	0.729000	0.41735	4.585000	0.60977	2.641000	0.89580	0.585000	0.79938	TCG		0.428	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120740099	C	T	120740099	3	4	61	1	0	0	0	0	1	0	0	0	2411	893	31	1	891	1	C7orf58	7	120740099	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2863200	120740099	38398564	5534	13519										
C7orf58	79974	broad.mit.edu	37	chr7	120782146	120782146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccatctatagagaagaccGcccaagtctgcccttgtttg	8	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:120782146G>A	ENST00000310396.5	+	16	2473	c.2006G>A	c.(2005-2007)cGc>cAc	p.R669H	CPED1_ENST00000423795.1_Missense_Mutation_p.R449H|CPED1_ENST00000450913.2_Missense_Mutation_p.R669H	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	669						endoplasmic reticulum (GO:0005783)		p.R669H(1)									AGAGAAGACCGCCCAAGTCTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											189	170	176					7																	120782146		2203	4299	6502	120569382	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2006G>A	7.37:g.120782146G>A	ENSP00000309772:p.Arg669His		120569382	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	G	32	5.145084	0.94603	.	.	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.31510	1.85;1.49;1.51	5.77	5.77	0.91146	.	0.116384	0.56097	D	0.000024	T	0.51686	0.1689	L	0.43152	1.355	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.994	D;D;P	0.91635	0.999;0.999;0.619	T	0.47736	-0.9094	10	0.87932	D	0	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	449;669;669	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	H	669;669;449	ENSP00000309772:R669H;ENSP00000406122:R669H;ENSP00000415573:R449H	ENSP00000309772:R669H	R	+	2	0	C7orf58	120569382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.103000	0.77014	2.885000	0.99019	0.655000	0.94253	CGC		0.433	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		A	120782146	G	A	120782146	3	1	61	1	0	0	0	0	1	0	0	0	2411	1087	38	1	2064	1	C7orf58	7	120782146	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42047	120782146	38356517	5535	13520										
C7orf58	79974	broad.mit.edu	37	chr7	120876862	120876862	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacagtctgaactaaaaaGatgtccatctggggacatga	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:120876862G>T	ENST00000310396.5	+	17	2617	c.2150G>T	c.(2149-2151)aGa>aTa	p.R717I	CPED1_ENST00000423795.1_Missense_Mutation_p.R497I|CPED1_ENST00000450913.2_Missense_Mutation_p.R717I	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	717						endoplasmic reticulum (GO:0005783)		p.R717I(1)									GAACTAAAAAGATGTCCATCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	91	92					7																	120876862		2203	4300	6503	120664098	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2150G>T	7.37:g.120876862G>T	ENSP00000309772:p.Arg717Ile		120664098	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	G	8.020	0.759339	0.15846	.	.	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.19806	2.33;2.12;2.13	5.86	-4.01	0.04045	.	0.896444	0.09754	N	0.760194	T	0.03651	0.0104	N	0.00436	-1.5	0.09310	N	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.15066	T	0.55	.	2.9795	0.05948	0.1763:0.4435:0.1365:0.2437	.	497;717;717	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	I	717;717;497	ENSP00000309772:R717I;ENSP00000406122:R717I;ENSP00000415573:R497I	ENSP00000309772:R717I	R	+	2	0	C7orf58	120664098	0.029000	0.19370	0.001000	0.08648	0.715000	0.41141	0.014000	0.13333	-0.795000	0.04462	-0.225000	0.12378	AGA		0.358	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120876862	G	T	120876862	3	4	61	1	0	0	0	0	1	0	0	0	2411	942	33	2	2212	2	C7orf58	7	120876862	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94716	120876862	38261801	5536	13521										
PTPRZ1	5803	broad.mit.edu	37	chr7	121651648	121651648	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaagttacttcagctaccGagagtgataaggtgcccttg	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121651648G>A	ENST00000393386.2	+	12	2959	c.2548G>A	c.(2548-2550)Gag>Aag	p.E850K	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	850					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E850K(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTCAGCTACCGAGAGTGATAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											135	126	129					7																	121651648		2203	4300	6503	121438884	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2548G>A	7.37:g.121651648G>A	ENSP00000377047:p.Glu850Lys		121438884	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.190780	0.38707	.	.	ENSG00000106278	ENST00000393386	T	0.48836	0.8	5.71	3.81	0.43845	.	0.459334	0.21658	N	0.071069	T	0.38585	0.1046	M	0.63428	1.95	0.80722	D	1	P	0.41710	0.76	B	0.30943	0.122	T	0.40646	-0.9552	10	0.52906	T	0.07	.	9.8396	0.40991	0.0735:0.1382:0.7883:0.0	.	850	P23471	PTPRZ_HUMAN	K	850	ENSP00000377047:E850K	ENSP00000377047:E850K	E	+	1	0	PTPRZ1	121438884	1.000000	0.71417	0.927000	0.36925	0.883000	0.51084	2.369000	0.44231	1.428000	0.47296	-0.128000	0.14901	GAG		0.478	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121651648	G	A	121651648	3	1	61	1	0	0	0	0	1	0	0	0	12851	1059	37	1	2594	1	PTPRZ1	7	121651648	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	774786	121651648	37487015	5537	13522										
PTPRZ1	5803	broad.mit.edu	37	chr7	121652624	121652624	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttatgagacctcagcttCttttagtactgaagtattgc	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121652624C>A	ENST00000393386.2	+	12	3935	c.3524C>A	c.(3523-3525)tCt>tAt	p.S1175Y	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1175					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S1175Y(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ACCTCAGCTTCTTTTAGTACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											209	206	207					7																	121652624		2203	4300	6503	121439860	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3524C>A	7.37:g.121652624C>A	ENSP00000377047:p.Ser1175Tyr		121439860	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791758	0.50102	.	.	ENSG00000106278	ENST00000393386	T	0.45668	0.89	5.51	5.51	0.81932	.	0.797182	0.11326	N	0.575544	T	0.46619	0.1402	L	0.54323	1.7	0.80722	D	1	P	0.49447	0.924	P	0.44732	0.459	T	0.47509	-0.9112	10	0.72032	D	0.01	.	14.2663	0.66121	0.1489:0.8511:0.0:0.0	.	1175	P23471	PTPRZ_HUMAN	Y	1175	ENSP00000377047:S1175Y	ENSP00000377047:S1175Y	S	+	2	0	PTPRZ1	121439860	0.999000	0.42202	1.000000	0.80357	0.965000	0.64279	2.775000	0.47702	2.573000	0.86826	0.555000	0.69702	TCT		0.433	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121652624	C	A	121652624	3	1	61	1	0	0	0	0	1	0	0	0	12851	913	32	2	3570	2	PTPRZ1	7	121652624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	976	121652624	37486039	5538	13523										
PTPRZ1	5803	broad.mit.edu	37	chr7	121694029	121694029	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcataccatcaaggatttCtggaggatgatatgggacca	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121694029C>A	ENST00000393386.2	+	26	6729	c.6318C>A	c.(6316-6318)ttC>ttA	p.F2106L	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.F1239L	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2106	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.F2106L(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCAAGGATTTCTGGAGGATGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											197	188	191					7																	121694029		2203	4300	6503	121481265	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6318C>A	7.37:g.121694029C>A	ENSP00000377047:p.Phe2106Leu		121481265	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576083	0.65878	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.39056	1.1;1.1	5.67	3.87	0.44632	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.64402	D	0.000001	T	0.66336	0.2779	M	0.91510	3.215	0.58432	D	0.999997	B;P;P	0.51351	0.233;0.944;0.891	B;P;P	0.59948	0.104;0.823;0.866	T	0.73353	-0.4009	10	0.62326	D	0.03	.	11.587	0.50925	0.0:0.8574:0.0:0.1426	.	1245;1239;2106	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	L	2106;1239	ENSP00000377047:F2106L;ENSP00000410000:F1239L	ENSP00000377047:F2106L	F	+	3	2	PTPRZ1	121481265	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.607000	0.46300	1.397000	0.46682	0.591000	0.81541	TTC		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121694029	C	A	121694029	3	1	61	1	0	0	0	0	1	0	0	0	12851	912	32	2	6420	2	PTPRZ1	7	121694029	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41405	121694029	37444634	5539	13524										
AASS	10157	broad.mit.edu	37	chr7	121733115	121733115	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttacctcttttccaattCttttagtgctggtgtgatgt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121733115C>A	ENST00000393376.1	-	15	1848	c.1753G>T	c.(1753-1755)Gaa>Taa	p.E585*	AASS_ENST00000417368.2_Nonsense_Mutation_p.E585*|AASS_ENST00000473553.1_5'UTR			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	585	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.E585*(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTTTCCAATTCTTTTAGTGCT	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											164	170	168					7																	121733115		2203	4300	6503	121520351	SO:0001587	stop_gained	10157			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.1753G>T	7.37:g.121733115C>A	ENSP00000377040:p.Glu585*		121520351	O95462	Nonsense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	C	39	7.354968	0.98231	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-22.0805	20.2544	0.98414	0.0:1.0:0.0:0.0	.	.	.	.	X	585	.	ENSP00000351834:E585X	E	-	1	0	AASS	121520351	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	4.451000	0.60047	2.885000	0.99019	0.655000	0.94253	GAA		0.378	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		A	121733115	C	A	121733115	4	1	61	1	0	0	0	0	0	1	0	0	24	922	32	2	1063	2	AASS	7	121733115	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39086	121733115	37405548	5540	13525										
FEZF1	389549	broad.mit.edu	37	chr7	121943719	121943719	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacttcgcaagtgaaaactTtgggcttggcattaggagag	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121943719T>G	ENST00000442488.2	-	1	840	c.773A>C	c.(772-774)aAa>aCa	p.K258T	FEZF1_ENST00000427185.2_Missense_Mutation_p.K208T|FEZF1-AS1_ENST00000428449.1_RNA|FEZF1-AS1_ENST00000437317.1_RNA|FEZF1_ENST00000331178.4_Missense_Mutation_p.K258T	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	258					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.K258T(1)		breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						AGTGAAAACTTTGGGCTTGGC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											124	136	132					7																	121943719		2203	4300	6503	121730955	SO:0001583	missense	389549			AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"Zinc fingers, C2H2-type"	22788	protein-coding gene	gene with protein product		613301	"zinc finger protein 312B"	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.773A>C	7.37:g.121943719T>G	ENSP00000411145:p.Lys258Thr		121730955	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	t	19.92	3.916708	0.73098	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.08370	3.2;3.1;3.2	4.8	4.8	0.61643	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	L	0.42245	1.32	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.991;0.996	T	0.00583	-1.1659	10	0.87932	D	0	-11.9512	14.8686	0.70437	0.0:0.0:0.0:1.0	.	258;208	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	T	258;258;208	ENSP00000411145:K258T;ENSP00000332777:K258T;ENSP00000392727:K208T	ENSP00000332777:K258T	K	-	2	0	FEZF1	121730955	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.435000	0.80391	2.160000	0.67779	0.445000	0.29226	AAA		0.507	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613		G	121943719	T	G	121943719	3	3	61	1	0	0	0	0	1	0	0	0	5844	1841	64	4	670	4	FEZF1	7	121943719	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	210604	121943719	37194944	5541	13526										
CADPS2	93664	broad.mit.edu	37	chr7	121985693	121985693	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatatcttggttttgccGaacaaacataatataggtgt	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:121985693G>A	ENST00000449022.2	-	28	3566	c.3547C>T	c.(3547-3549)Cgg>Tgg	p.R1183W	RP5-1101C3.1_ENST00000482375.1_RNA|RP5-1101C3.1_ENST00000593910.1_RNA|CADPS2_ENST00000313070.7_Missense_Mutation_p.R1142W|RP5-1101C3.1_ENST00000602012.1_RNA|CADPS2_ENST00000334010.7_Missense_Mutation_p.R1181W|CADPS2_ENST00000412584.2_Missense_Mutation_p.R1142W|RP5-1101C3.1_ENST00000591140.1_RNA|RP5-1101C3.1_ENST00000602199.1_RNA	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	1183					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.R1180W(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TGGTTTTGCCGAACAAACATA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											176	167	170					7																	121985693		1819	4080	5899	121772929	SO:0001583	missense	93664				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.3547C>T	7.37:g.121985693G>A	ENSP00000398481:p.Arg1183Trp		121772929	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.8|28.8	4.950930|4.950930	0.92660|0.92660	.|.	.|.	ENSG00000081803|ENSG00000081803	ENST00000360097;ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022|ENST00000397721	T;T;T;T|.	0.34472|.	1.36;1.36;1.36;1.36|.	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83372|0.83372	0.5240|0.5240	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.85130|.	0.996;0.997;0.996;0.997|.	T|T	0.82868|0.82868	-0.0244|-0.0244	10|5	0.87932|.	D|.	0|.	-16.7106|-16.7106	20.6634|20.6634	0.99662|0.99662	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1187;1142;1183;1137|.	B7ZM57;Q86UW7-2;Q86UW7;Q86UW7-3|.	.;.;CAPS2_HUMAN;.|.	W|L	356;1142;1181;1188;1109;1142;1183|785	ENSP00000325581:R1142W;ENSP00000333940:R1181W;ENSP00000400401:R1142W;ENSP00000398481:R1183W|.	ENSP00000325581:R1142W|.	R|S	-|-	1|2	2|0	CADPS2|CADPS2	121772929|121772929	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.695000|7.695000	0.84257|0.84257	2.894000|2.894000	0.99253|0.99253	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.373	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		A	121985693	G	A	121985693	3	1	61	1	0	0	0	0	1	0	0	0	2577	1057	37	1	355	1	CADPS2	7	121985693	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41974	121985693	37152970	5542	13527										
CADPS2	93664	broad.mit.edu	37	chr7	122047704	122047704	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactgtaaataaagcccaaAatttctctgcatgttcagcc	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122047704A>C	ENST00000449022.2	-	20	2655	c.2636T>G	c.(2635-2637)tTt>tGt	p.F879C	RP5-1101C3.1_ENST00000593910.1_RNA|CADPS2_ENST00000313070.7_Missense_Mutation_p.F873C|CADPS2_ENST00000334010.7_Missense_Mutation_p.F877C|CADPS2_ENST00000412584.2_Missense_Mutation_p.F873C|RP5-1101C3.1_ENST00000591140.1_RNA	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	879	Interaction with DRD2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.F876C(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TAAAGCCCAAAATTTCTCTGC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											56	55	56					7																	122047704		1940	4148	6088	121834940	SO:0001583	missense	93664				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.2636T>G	7.37:g.122047704A>C	ENSP00000398481:p.Phe879Cys		121834940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	23.5|23.5|23.5	4.427043|4.427043|4.427043	0.83667|0.83667|0.83667	.|.|.	.|.|.	ENSG00000081803|ENSG00000081803|ENSG00000081803	ENST00000360097;ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022|ENST00000462699|ENST00000397721	T;T;T;T|.|.	0.57907|.|.	0.41;0.4;0.41;0.37|.|.	5.44|5.44|5.44	5.44|5.44|5.44	0.79542|0.79542|0.79542	Calcium-dependent secretion activator (1);|.|.	0.000000|0.000000|.	0.85682|0.85682|.	D|D|.	0.000000|0.000000|.	T|T|T	0.74650|0.74650|0.74650	0.3744|0.3744|0.3744	M|M|M	0.73598|0.73598|0.73598	2.24|2.24|2.24	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0;0.999|.|.	D;D;D;D|.|.	0.97110|.|.	0.999;1.0;0.999;0.995|.|.	T|T|T	0.75419|0.75419|0.75419	-0.3324|-0.3324|-0.3324	10|7|5	0.87932|0.87932|.	D|D|.	0|0|.	-17.3102|-17.3102|-17.3102	15.5078|15.5078|15.5078	0.75753|0.75753|0.75753	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	883;873;879;873|.|.	B7ZM57;Q86UW7-2;Q86UW7;Q86UW7-3|.|.	.;.;CAPS2_HUMAN;.|.|.	C|V|M	52;873;877;884;840;873;879|73|521	ENSP00000325581:F873C;ENSP00000333940:F877C;ENSP00000400401:F873C;ENSP00000398481:F879C|.|.	ENSP00000325581:F873C|ENSP00000419418:F73V|.	F|F|I	-|-|-	2|1|3	0|0|3	CADPS2|CADPS2|CADPS2	121834940|121834940|121834940	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.926000|0.926000|0.926000	0.56050|0.56050|0.56050	9.307000|9.307000|9.307000	0.96226|0.96226|0.96226	2.069000|2.069000|2.069000	0.61940|0.61940|0.61940	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TTT|TTT|ATT		0.388	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		C	122047704	A	C	122047704	3	2	61	1	0	0	0	0	1	0	0	0	2577	14	1	4	1317	4	CADPS2	7	122047704	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	62011	122047704	37090959	5543	13528										
RNF148	378925	broad.mit.edu	37	chr7	122342077	122342077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcatccccttctttgagaActcgcagttgaagctggtca	8	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122342077A>G	ENST00000434824.1	-	1	944	c.728T>C	c.(727-729)gTt>gCt	p.V243A	RNF133_ENST00000340112.2_5'Flank|CADPS2_ENST00000449022.2_Intron|RNF148_ENST00000447240.1_3'UTR|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	243						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.V243A(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						TTCTTTGAGAACTCGCAGTTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	7											102	94	97					7																	122342077		1904	4127	6031	122129313	SO:0001583	missense	378925			BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.728T>C	7.37:g.122342077A>G	ENSP00000388207:p.Val243Ala		122129313	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	37	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.432785	0.25813	.	.	ENSG00000235631	ENST00000434824	T	0.04275	3.66	5.37	5.37	0.77165	.	.	.	.	.	T	0.06280	0.0162	L	0.55481	1.735	0.80722	D	1	B	0.29988	0.264	B	0.26864	0.074	T	0.31280	-0.9949	9	0.33141	T	0.24	.	10.9018	0.47056	0.8593:0.0:0.0:0.1407	.	243	Q8N7C7	RN148_HUMAN	A	243	ENSP00000388207:V243A	ENSP00000388207:V243A	V	-	2	0	RNF148	122129313	0.922000	0.31269	1.000000	0.80357	0.626000	0.37791	2.114000	0.41911	2.031000	0.59945	0.459000	0.35465	GTT		0.423	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		G	122342077	A	G	122342077	3	3	61	1	0	0	0	0	1	0	0	0	13486	43	2	4	193	4	RNF148	7	122342077	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	294373	122342077	36796586	5544	13529										
RNF148	378925	broad.mit.edu	37	chr7	122342791	122342791	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgcgtcgaaggggtaattCtaaggaagctcatgcctcca	11	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122342791C>A	ENST00000434824.1	-	1	230	c.14G>T	c.(13-15)aGa>aTa	p.R5I	CADPS2_ENST00000449022.2_Intron|RNF148_ENST00000447240.1_Missense_Mutation_p.R5I|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	5						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R5I(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						AGGGGTAATTCTAAGGAAGCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											22	20	21					7																	122342791		1860	4097	5957	122130027	SO:0001583	missense	378925			BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.14G>T	7.37:g.122342791C>A	ENSP00000388207:p.Arg5Ile		122130027	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	37	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	C	0.529	-0.858662	0.02610	.	.	ENSG00000235631	ENST00000434824;ENST00000447240	T	0.04603	3.59	5.4	2.56	0.30785	.	.	.	.	.	T	0.05044	0.0135	L	0.40543	1.245	0.09310	N	1	B;B	0.34015	0.372;0.435	B;B	0.34385	0.181;0.088	T	0.38178	-0.9673	9	0.72032	D	0.01	.	5.7986	0.18401	0.0:0.6655:0.1589:0.1756	.	5;5	C9JVJ0;Q8N7C7	.;RN148_HUMAN	I	5	ENSP00000388207:R5I	ENSP00000388207:R5I	R	-	2	0	RNF148	122130027	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.286000	0.08399	0.242000	0.21303	0.555000	0.69702	AGA		0.393	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		A	122342791	C	A	122342791	3	1	61	1	0	0	0	0	1	0	0	0	13486	913	32	2	907	2	RNF148	7	122342791	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	714	122342791	36795872	5545	13530										
TAS2R16	50833	broad.mit.edu	37	chr7	122635175	122635175	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactgatactgatgaaaatTttcaagtttgtcagttacag	8	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122635175T>G	ENST00000249284.2	-	1	579	c.514A>C	c.(514-516)Aat>Cat	p.N172H		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	172			N -> K (associated with susceptibility to alcoholism; dbSNP:rs846664). {ECO:0000269|PubMed:16385453}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)	p.N172H(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TGATGAAAATTTTCAAGTTTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											158	144	148					7																	122635175		2203	4300	6503	122422411	SO:0001583	missense	50833			AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.514A>C	7.37:g.122635175T>G	ENSP00000249284:p.Asn172His		122422411	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	37	CCDS5785.1	.	.	.	.	.	.	.	.	.	.	T	9.188	1.025189	0.19433	.	.	ENSG00000128519	ENST00000249284	T	0.37411	1.2	4.45	-2.11	0.07187	.	2.895720	0.01993	N	0.045711	T	0.19208	0.0461	N	0.08118	0	0.09310	N	1	B	0.21452	0.056	B	0.18561	0.022	T	0.19745	-1.0296	10	0.46703	T	0.11	.	4.9846	0.14183	0.0:0.3993:0.1765:0.4242	.	172	Q9NYV7	T2R16_HUMAN	H	172	ENSP00000249284:N172H	ENSP00000249284:N172H	N	-	1	0	TAS2R16	122422411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.847000	0.04331	-0.218000	0.10018	0.533000	0.62120	AAT		0.408	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945		G	122635175	T	G	122635175	3	3	61	1	0	0	0	0	1	0	0	0	15608	1841	64	4	365	4	TAS2R16	7	122635175	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	292384	122635175	36503488	5546	13531										
TAS2R16	50833	broad.mit.edu	37	chr7	122635343	122635343	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctccacctcagccagaGaaagatgtgatgggtgaaag	11	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122635343G>T	ENST00000249284.2	-	1	411	c.346C>A	c.(346-348)Ctc>Atc	p.L116I		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	116					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)	p.L116I(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CTCAGCCAGAGAAAGATGTGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											80	78	79					7																	122635343		2203	4300	6503	122422579	SO:0001583	missense	50833			AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.346C>A	7.37:g.122635343G>T	ENSP00000249284:p.Leu116Ile		122422579	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	37	CCDS5785.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.796358	0.31777	.	.	ENSG00000128519	ENST00000249284	T	0.01854	4.6	4.02	1.19	0.21007	.	0.270973	0.30584	N	0.009303	T	0.10423	0.0255	M	0.86420	2.815	0.22827	N	0.998689	D	0.76494	0.999	D	0.72625	0.978	T	0.03354	-1.1045	10	0.66056	D	0.02	.	5.7284	0.18026	0.3486:0.0:0.6514:0.0	.	116	Q9NYV7	T2R16_HUMAN	I	116	ENSP00000249284:L116I	ENSP00000249284:L116I	L	-	1	0	TAS2R16	122422579	0.968000	0.33430	0.659000	0.29680	0.176000	0.22953	-0.193000	0.09573	0.464000	0.27142	0.655000	0.94253	CTC		0.398	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945		T	122635343	G	T	122635343	3	4	61	1	0	0	0	0	1	0	0	0	15608	942	33	2	533	2	TAS2R16	7	122635343	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	122635343	36503320	5547	13532										
SLC13A1	6561	broad.mit.edu	37	chr7	122768993	122768993	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaccaaggtcacaatttCttgatacctgtggaaaaatt	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122768993C>A	ENST00000194130.2	-	10	1078	c.1039G>T	c.(1039-1041)Gaa>Taa	p.E347*	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	347					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.E347*(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	GTCACAATTTCTTGATACCTG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											69	61	63					7																	122768993		2203	4300	6503	122556229	SO:0001587	stop_gained	6561				CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.1039G>T	7.37:g.122768993C>A	ENSP00000194130:p.Glu347*		122556229	Q9H5Z0	Nonsense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	C	38	6.663946	0.97743	.	.	ENSG00000081800	ENST00000194130	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	0.0243	19.2443	0.93896	0.0:1.0:0.0:0.0	.	.	.	.	X	347	.	ENSP00000194130:E347X	E	-	1	0	SLC13A1	122556229	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.481000	0.73608	2.797000	0.96272	0.563000	0.77884	GAA		0.423	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		A	122768993	C	A	122768993	4	1	61	1	0	0	0	0	0	1	0	0	14428	922	32	2	772	2	SLC13A1	7	122768993	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133650	122768993	36369670	5548	13533										
SLC13A1	6561	broad.mit.edu	37	chr7	122811867	122811867	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccattttcagagcaattCtcttgtgcaaattccatttt	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122811867C>A	ENST00000194130.2	-	3	359	c.320G>T	c.(319-321)aGa>aTa	p.R107I	SLC13A1_ENST00000539873.1_Missense_Mutation_p.R43I	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	107					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.R107I(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	CAGAGCAATTCTCTTGTGCAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											225	201	209					7																	122811867		2203	4300	6503	122599103	SO:0001583	missense	6561				CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.320G>T	7.37:g.122811867C>A	ENSP00000194130:p.Arg107Ile		122599103	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084461	0.94100	.	.	ENSG00000081800	ENST00000194130;ENST00000539873	T;T	0.14516	2.5;2.5	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.53626	0.1808	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68739	-0.5329	10	0.87932	D	0	.	18.7118	0.91659	0.0:1.0:0.0:0.0	.	107	Q9BZW2	S13A1_HUMAN	I	107;43	ENSP00000194130:R107I;ENSP00000441309:R43I	ENSP00000194130:R107I	R	-	2	0	SLC13A1	122599103	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.759000	0.85235	2.739000	0.93911	0.563000	0.77884	AGA		0.378	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		A	122811867	C	A	122811867	3	1	61	1	0	0	0	0	1	0	0	0	14428	913	32	2	1519	2	SLC13A1	7	122811867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42874	122811867	36326796	5549	13534										
SLC13A1	6561	broad.mit.edu	37	chr7	122839996	122839996	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaatgtaactgaagaatTtcattgtcctgagcaggtgg	11	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:122839996T>G	ENST00000194130.2	-	1	44	c.5A>C	c.(4-6)aAa>aCa	p.K2T		NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	2					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.K2T(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	ACTGAAGAATTTCATTGTCCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	7											106	83	91					7																	122839996		2202	4300	6502	122627232	SO:0001583	missense	6561				CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.5A>C	7.37:g.122839996T>G	ENSP00000194130:p.Lys2Thr		122627232	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	T	8.142	0.785467	0.16189	.	.	ENSG00000081800	ENST00000194130	T	0.67171	-0.25	5.73	5.73	0.89815	.	0.556413	0.19398	N	0.115260	T	0.66733	0.2819	L	0.60455	1.87	0.80722	D	1	D	0.59767	0.986	P	0.47206	0.541	T	0.64334	-0.6432	10	0.24483	T	0.36	.	13.4061	0.60913	0.0:0.0:0.0:1.0	.	2	Q9BZW2	S13A1_HUMAN	T	2	ENSP00000194130:K2T	ENSP00000194130:K2T	K	-	2	0	SLC13A1	122627232	1.000000	0.71417	0.931000	0.37212	0.085000	0.17905	4.578000	0.60929	2.197000	0.70478	0.533000	0.62120	AAA		0.423	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		G	122839996	T	G	122839996	3	3	61	1	0	0	0	0	1	0	0	0	14428	1841	64	4	1842	4	SLC13A1	7	122839996	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	28129	122839996	36298667	5550	13535										
IQUB	154865	broad.mit.edu	37	chr7	123136907	123136907	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttctgtcttcttaaattCtctacgaagattttagcatg	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123136907C>T	ENST00000466202.1	-	7	1653	c.1077G>A	c.(1075-1077)gaG>gaA	p.E359E	IQUB_ENST00000434450.1_Silent_p.E359E|IQUB_ENST00000324698.6_Silent_p.E359E	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	359	IQ.				cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.E359E(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						TTCTTAAATTCTCTACGAAGA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	7											109	98	101					7																	123136907		2202	4299	6501	122924143	SO:0001819	synonymous_variant	154865			AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1077G>A	7.37:g.123136907C>T			122924143	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																				0.338	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		T	123136907	C	T	123136907	2	4	61	1	0	0	0	0	0	0	0	1	7841	912	32	3		3	IQUB	7	123136907	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296911	123136907	36001756	5551	13536										
LMOD2	442721	broad.mit.edu	37	chr7	123296065	123296065	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtaaatacgaatccatCgacgaggatgaactcctcgc	8	12	1	1	rs542588014		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123296065C>T	ENST00000458573.2	+	1	205	c.48C>T	c.(46-48)atC>atT	p.I16I	LMOD2_ENST00000456238.2_Silent_p.I16I	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	16	Glu-rich.|Tropomyosin-binding. {ECO:0000250}.					cytoskeleton (GO:0005856)		p.I16I(1)									ACGAATCCATCGACGAGGATG	0.547													C|||	1	0.000199681	0	0	5008	,	,		20017	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											40	42	42					7																	123296065		2000	4175	6175	123083301	SO:0001819	synonymous_variant	442721			AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.48C>T	7.37:g.123296065C>T			123083301	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	37	CCDS47693.1																																																																																				0.547	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			T	123296065	C	T	123296065	2	4	61	1	0	0	0	0	0	0	0	1	8881	874	31	1		1	LMOD2	7	123296065	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159158	123296065	35842598	5552	13537										
LMOD2	442721	broad.mit.edu	37	chr7	123302482	123302482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcgagtccaacttcataaCgggaaaggggatcctggcca	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123302482C>T	ENST00000458573.2	+	2	999	c.842C>T	c.(841-843)aCg>aTg	p.T281M	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	281						cytoskeleton (GO:0005856)		p.T281M(2)									AACTTCATAACGGGAAAGGGG	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	7											90	89	89					7																	123302482		2138	4243	6381	123089718	SO:0001583	missense	442721			AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.842C>T	7.37:g.123302482C>T	ENSP00000411932:p.Thr281Met		123089718	A4D0W9|A4D0Y2|Q8WVJ8	Missense_Mutation	SNP	ENST00000458573.2	37	CCDS47693.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169637	0.78452	.	.	ENSG00000170807	ENST00000458573;ENST00000444702;ENST00000332074	D	0.93076	-3.16	5.35	5.35	0.76521	.	.	.	.	.	D	0.97340	0.9130	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97832	1.0263	9	0.87932	D	0	-11.2761	19.4255	0.94740	0.0:1.0:0.0:0.0	.	281	Q6P5Q4	LMOD2_HUMAN	M	281;241;252	ENSP00000411932:T281M	ENSP00000405123:T252M	T	+	2	0	LMOD2	123089718	0.998000	0.40836	1.000000	0.80357	0.965000	0.64279	3.890000	0.56220	2.648000	0.89879	0.591000	0.81541	ACG		0.552	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			T	123302482	C	T	123302482	3	4	61	1	0	0	0	0	1	0	0	0	8881	536	19	1	848	1	LMOD2	7	123302482	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6417	123302482	35836181	5553	13538										
WASL	8976	broad.mit.edu	37	chr7	123336703	123336703	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttttcccttcttcttttCtttggtatgggagatgttgt	9	7	3	1	rs3209159		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123336703C>A	ENST00000223023.4	-	6	891	c.559G>T	c.(559-561)Gaa>Taa	p.E187*		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	187					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)	p.E187*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTCTTCTTTTCTTTGGTATGG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											158	145	149					7																	123336703		2203	4300	6503	123123939	SO:0001587	stop_gained	8976			D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.559G>T	7.37:g.123336703C>A	ENSP00000223023:p.Glu187*		123123939	A1JUI9|Q7Z746	Nonsense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	C	39	7.517875	0.98332	.	.	ENSG00000106299	ENST00000223023	.	.	.	5.97	5.97	0.96955	.	0.151890	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.6209	20.4251	0.99070	0.0:1.0:0.0:0.0	.	.	.	.	X	187	.	ENSP00000223023:E187X	E	-	1	0	WASL	123123939	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.494000	0.60347	2.829000	0.97493	0.650000	0.86243	GAA		0.353	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		A	123336703	C	A	123336703	4	1	61	1	0	0	0	0	0	1	0	0	17296	922	32	2	982	2	WASL	7	123336703	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34221	123336703	35801960	5554	13539										
WASL	8976	broad.mit.edu	37	chr7	123346375	123346375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggtctgtaactgcttttCgaaatttttttgcttcttct	6	7	3	0	rs200364266		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123346375C>T	ENST00000223023.4	-	4	724	c.392G>A	c.(391-393)cGa>cAa	p.R131Q		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	131	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)	p.R131Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AACTGCTTTTCGAAATTTTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											66	65	66					7																	123346375		2203	4300	6503	123133611	SO:0001583	missense	8976			D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.392G>A	7.37:g.123346375C>T	ENSP00000223023:p.Arg131Gln		123133611	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566379	0.65651	.	.	ENSG00000106299	ENST00000223023	D	0.98701	-5.08	5.59	5.59	0.84812	EVH1 (3);Pleckstrin homology-type (1);	0.062086	0.64402	D	0.000004	D	0.96519	0.8864	L	0.39245	1.2	0.58432	D	0.999999	B	0.10296	0.003	B	0.11329	0.006	D	0.93616	0.6943	10	0.30854	T	0.27	-13.9486	14.1736	0.65527	0.0:0.9283:0.0:0.0717	.	131	O00401	WASL_HUMAN	Q	131	ENSP00000223023:R131Q	ENSP00000223023:R131Q	R	-	2	0	WASL	123133611	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.437000	0.59955	2.783000	0.95769	0.655000	0.94253	CGA		0.363	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		T	123346375	C	T	123346375	3	4	61	1	0	0	0	0	1	0	0	0	17296	884	31	1	1157	1	WASL	7	123346375	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9672	123346375	35792288	5555	13540										
HYAL4	23553	broad.mit.edu	37	chr7	123508381	123508381	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttgttcaaccagtacaTctcacttcatggctccttat	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123508381T>A	ENST00000223026.4	+	3	692	c.54T>A	c.(52-54)caT>caA	p.H18Q	HYAL4_ENST00000476325.1_Missense_Mutation_p.H18Q	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	18					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.H18Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						AACCAGTACATCTCACTTCAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											126	134	131					7																	123508381		2202	4300	6502	123295617	SO:0001583	missense	23553			AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.54T>A	7.37:g.123508381T>A	ENSP00000223026:p.His18Gln		123295617	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.974277	0.34848	.	.	ENSG00000106302	ENST00000489978;ENST00000488323;ENST00000223026;ENST00000476325	T;T	0.16743	2.32;2.32	5.2	4.0	0.46444	.	0.276152	0.35291	N	0.003301	T	0.07818	0.0196	N	0.08118	0	0.27959	N	0.936865	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.004	T	0.22417	-1.0217	10	0.32370	T	0.25	-1.682	6.0243	0.19646	0.1638:0.0:0.1706:0.6656	.	18;18	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	Q	18	ENSP00000223026:H18Q;ENSP00000417186:H18Q	ENSP00000223026:H18Q	H	+	3	2	HYAL4	123295617	0.104000	0.21937	0.925000	0.36789	0.799000	0.45148	0.272000	0.18644	0.869000	0.35703	0.533000	0.62120	CAT		0.338	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		A	123508381	T	A	123508381	3	1	61	1	0	0	0	0	1	0	0	0	7487	1432	50	5	56	5	HYAL4	7	123508381	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162006	123508381	35630282	5556	13541										
HYAL4	23553	broad.mit.edu	37	chr7	123509053	123509053	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgcccagaagacgaagtCttgaggaacaatgagctctc	10	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123509053C>A	ENST00000223026.4	+	3	1364	c.726C>A	c.(724-726)gtC>gtA	p.V242V	HYAL4_ENST00000476325.1_Silent_p.V242V	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	242					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.V242V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						AAGACGAAGTCTTGAGGAACA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	7											87	90	89					7																	123509053		2203	4300	6503	123296289	SO:0001819	synonymous_variant	23553			AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.726C>A	7.37:g.123509053C>A			123296289	D0VXG1|Q9UL99|Q9Y6T9	Silent	SNP	ENST00000223026.4	37	CCDS5789.1																																																																																				0.453	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		A	123509053	C	A	123509053	2	1	61	1	0	0	0	0	0	0	0	1	7487	900	32	2		2	HYAL4	7	123509053	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	672	123509053	35629610	5557	13542										
SPAM1	6677	broad.mit.edu	37	chr7	123595075	123595075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttgtgtatacatttggcGaaactgttgctctgggtgct	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123595075G>A	ENST00000439500.1	+	5	1592	c.979G>A	c.(979-981)Gaa>Aaa	p.E327K	SPAM1_ENST00000223028.7_Missense_Mutation_p.E327K|SPAM1_ENST00000460182.1_Missense_Mutation_p.E327K|SPAM1_ENST00000402183.2_Missense_Mutation_p.E327K|SPAM1_ENST00000340011.5_Missense_Mutation_p.E327K	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	327					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)	p.E327K(2)		breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TACATTTGGCGAAACTGTTGC	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	7											218	215	216					7																	123595075		2203	4300	6503	123382311	SO:0001583	missense	6677			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.979G>A	7.37:g.123595075G>A	ENSP00000402123:p.Glu327Lys		123382311	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.441893	0.83993	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79	6.02	6.02	0.97574	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.050751	0.85682	N	0.000000	T	0.63768	0.2539	M	0.92459	3.31	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71140	-0.4679	10	0.87932	D	0	-69.3012	19.5352	0.95251	0.0:0.0:1.0:0.0	.	327;327	Q8TC30;P38567	.;HYALP_HUMAN	K	327	ENSP00000386028:E327K;ENSP00000417934:E327K;ENSP00000345849:E327K;ENSP00000402123:E327K;ENSP00000223028:E327K	ENSP00000223028:E327K	E	+	1	0	SPAM1	123382311	1.000000	0.71417	0.992000	0.48379	0.237000	0.25408	6.989000	0.76219	2.850000	0.98022	0.650000	0.86243	GAA		0.373	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			A	123595075	G	A	123595075	3	1	61	1	0	0	0	0	1	0	0	0	15025	1059	37	1	985	1	SPAM1	7	123595075	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86022	123595075	35543588	5558	13543										
SPAM1	6677	broad.mit.edu	37	chr7	123599597	123599597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaatccttacataatcaaCgtcacactagcagccaaaat	4	12	2	1	rs373230630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:123599597C>T	ENST00000439500.1	+	6	1717	c.1104C>T	c.(1102-1104)aaC>aaT	p.N368N	SPAM1_ENST00000223028.7_Silent_p.N368N|SPAM1_ENST00000460182.1_Silent_p.N368N|SPAM1_ENST00000402183.2_Silent_p.N368N|SPAM1_ENST00000340011.5_Silent_p.N368N	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	368					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)	p.N368N(2)		breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ACATAATCAACGTCACACTAG	0.383																																																2	Substitution - coding silent(2)	large_intestine(2)	7											98	91	93					7																	123599597		2203	4300	6503	123386833	SO:0001819	synonymous_variant	6677			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1104C>T	7.37:g.123599597C>T			123386833	Q8TC30	Silent	SNP	ENST00000439500.1	37	CCDS5791.1																																																																																				0.383	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			T	123599597	C	T	123599597	2	4	61	1	0	0	0	0	0	0	0	1	15025	535	19	1		1	SPAM1	7	123599597	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4522	123599597	35539066	5559	13544										
GRM8	2918	broad.mit.edu	37	chr7	126173578	126173578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggagcacgtaactaagttCgcgtcctgaagccctcacga	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:126173578C>T	ENST00000339582.2	-	9	2666	c.1858G>A	c.(1858-1860)Gaa>Aaa	p.E620K	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000444921.2_Missense_Mutation_p.E620K|GRM8_ENST00000358373.3_Missense_Mutation_p.E620K			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	620					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.E620K(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				TAACTAAGTTCGCGTCCTGAA	0.458										HNSCC(24;0.065)																																						1	Substitution - Missense(1)	large_intestine(1)	7											114	110	112					7																	126173578		2203	4300	6503	125960814	SO:0001583	missense	2918				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1858G>A	7.37:g.126173578C>T	ENSP00000344173:p.Glu620Lys		125960814	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.964732	0.92791	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.89270	-2.49;-2.49;-2.49	5.73	5.73	0.89815	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96185	0.8756	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	D	0.96773	0.9570	10	0.87932	D	0	.	18.8976	0.92430	0.0:1.0:0.0:0.0	.	620;620	O00222-2;O00222	.;GRM8_HUMAN	K	620	ENSP00000344173:E620K;ENSP00000409790:E620K;ENSP00000351142:E620K	ENSP00000344173:E620K	E	-	1	0	GRM8	125960814	1.000000	0.71417	0.964000	0.40570	0.923000	0.55619	7.811000	0.86092	2.723000	0.93209	0.643000	0.83706	GAA		0.458	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			T	126173578	C	T	126173578	3	4	61	1	0	0	0	0	1	0	0	0	6824	893	31	1	930	1	GRM8	7	126173578	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2573981	126173578	32965085	5560	13545										
GRM8	2918	broad.mit.edu	37	chr7	126542725	126542725	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcggcttctaaagtatcGatcaaatcctatttcaaagg	7	8	3	0	rs554849639		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:126542725G>A	ENST00000339582.2	-	6	1835	c.1027C>T	c.(1027-1029)Cga>Tga	p.R343*	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000405249.1_Nonsense_Mutation_p.R343*|GRM8_ENST00000444921.2_Nonsense_Mutation_p.R343*|GRM8_ENST00000358373.3_Nonsense_Mutation_p.R343*			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	343			R -> Q (in dbSNP:rs13309334). {ECO:0000269|PubMed:12853948}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.R343*(2)|p.R343G(2)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CTAAAGTATCGATCAAATCCT	0.348										HNSCC(24;0.065)																																						4	Substitution - Nonsense(2)|Substitution - Missense(2)	large_intestine(2)|endometrium(2)	7											61	61	61					7																	126542725		2202	4300	6502	126329961	SO:0001587	stop_gained	2918				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1027C>T	7.37:g.126542725G>A	ENSP00000344173:p.Arg343*		126329961	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Nonsense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	36	5.810558	0.96975	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	.	.	.	4.88	4.88	0.63580	.	0.073633	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.7604	0.57361	0.0:0.0:0.8247:0.1753	.	.	.	.	X	343	.	ENSP00000344173:R343X	R	-	1	2	GRM8	126329961	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.986000	0.56937	2.251000	0.74343	0.511000	0.50034	CGA		0.348	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			A	126542725	G	A	126542725	4	1	61	1	0	0	0	0	0	1	0	0	6824	1066	37	1	1773	1	GRM8	7	126542725	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	369147	126542725	32595938	5561	13546										
GRM8	2918	broad.mit.edu	37	chr7	126746620	126746620	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccctcagaagccagtgtCgaaacataattccatcccag	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:126746620C>T	ENST00000339582.2	-	3	1465	c.657G>A	c.(655-657)tcG>tcA	p.S219S	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000405249.1_Silent_p.S219S|GRM8_ENST00000444921.2_Silent_p.S219S|GRM8_ENST00000358373.3_Silent_p.S219S			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	219					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.S219S(4)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				AAGCCAGTGTCGAAACATAAT	0.493										HNSCC(24;0.065)																																						4	Substitution - coding silent(4)	large_intestine(3)|ovary(1)	7											137	119	125					7																	126746620		2203	4300	6503	126533856	SO:0001819	synonymous_variant	2918				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.657G>A	7.37:g.126746620C>T			126533856	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	37	CCDS5794.1																																																																																				0.493	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			T	126746620	C	T	126746620	2	4	61	1	0	0	0	0	0	0	0	1	6824	871	31	1		1	GRM8	7	126746620	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203895	126746620	32392043	5562	13547										
ZNF800	168850	broad.mit.edu	37	chr7	127026120	127026120	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaacattcatacctgatcGaaagcactcaattatttgtt	4	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127026120G>A	ENST00000393313.1	-	3	742	c.151C>T	c.(151-153)Cga>Tga	p.R51*	ZNF800_ENST00000393312.1_Nonsense_Mutation_p.R51*|ZNF800_ENST00000265827.3_Nonsense_Mutation_p.R51*			Q2TB10	ZN800_HUMAN	zinc finger protein 800	51					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R51*(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						ATACCTGATCGAAAGCACTCA	0.313																																																2	Substitution - Nonsense(2)	large_intestine(2)	7											101	95	97					7																	127026120		2203	4300	6503	126813356	SO:0001587	stop_gained	168850			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.151C>T	7.37:g.127026120G>A	ENSP00000376989:p.Arg51*		126813356	Q9HBN0	Nonsense_Mutation	SNP	ENST00000393313.1	37	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	G	37	6.520801	0.97633	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312;ENST00000434602;ENST00000436992;ENST00000439506	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.6257	18.2091	0.89864	0.0:0.0:1.0:0.0	.	.	.	.	X	51	.	ENSP00000265827:R51X	R	-	1	2	ZNF800	126813356	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.254000	0.78329	2.546000	0.85860	0.655000	0.94253	CGA		0.313	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		A	127026120	G	A	127026120	4	1	61	1	0	0	0	0	0	1	0	0	18208	1066	37	1	1859	1	ZNF800	7	127026120	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	279500	127026120	32112543	5563	13548										
GCC1	79571	broad.mit.edu	37	chr7	127224309	127224309	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgattcttctcatctcGaatggcctgcagttcacttt	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127224309G>A	ENST00000321407.2	-	1	1352	c.928C>T	c.(928-930)Cga>Tga	p.R310*	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	310					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.R310*(1)		breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TTCTCATCTCGAATGGCCTGC	0.527											OREG0003809	type=REGULATORY REGION|Gene=GCC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Nonsense(1)	large_intestine(1)	7											102	98	99					7																	127224309		2203	4300	6503	127011545	SO:0001587	stop_gained	79571			AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.928C>T	7.37:g.127224309G>A	ENSP00000318821:p.Arg310*	1555	127011545	Q9H6N7	Nonsense_Mutation	SNP	ENST00000321407.2	37	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	G	40	7.991232	0.98599	.	.	ENSG00000179562	ENST00000321407	.	.	.	5.91	5.01	0.66863	.	0.338213	0.31312	N	0.007876	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-4.2572	12.3341	0.55056	0.0:0.0:0.831:0.169	.	.	.	.	X	310	.	ENSP00000318821:R310X	R	-	1	2	GCC1	127011545	0.962000	0.33011	1.000000	0.80357	0.761000	0.43186	4.020000	0.57189	1.463000	0.47967	0.655000	0.94253	CGA		0.527	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		A	127224309	G	A	127224309	4	1	61	1	0	0	0	0	0	1	0	0	6305	1066	37	1	1407	1	GCC1	7	127224309	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198189	127224309	31914354	5564	13549										
PAX4	5078	broad.mit.edu	37	chr7	127253509	127253509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagagctcactcaccctcaCcgtgtcctcaggcagagagg	11	15	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127253509C>T	ENST00000341640.2	-	5	821	c.616G>A	c.(616-618)Gtg>Atg	p.V206M	PAX4_ENST00000463946.1_Missense_Mutation_p.V204M|PAX4_ENST00000338516.3_Missense_Mutation_p.V214M|PAX4_ENST00000378740.2_Missense_Mutation_p.V206M	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	214					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.V206M(1)		cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CTCACCCTCACCGTGTCCTCA	0.582																																					Ovarian(113;737 1605 7858 27720 34092)											1	Substitution - Missense(1)	large_intestine(1)	7											63	65	64					7																	127253509		2203	4300	6503	127040745	SO:0001583	missense	5078				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.616G>A	7.37:g.127253509C>T	ENSP00000339906:p.Val206Met		127040745	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.688040	0.68271	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740;ENST00000463946	D;D;D	0.98550	-4.99;-4.99;-4.99	4.9	4.9	0.64082	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.093158	0.44097	D	0.000491	D	0.99149	0.9706	H	0.96547	3.84	0.43662	D	0.996083	D;D;D;D	0.89917	0.982;0.998;0.993;1.0	D;D;D;D	0.79784	0.945;0.958;0.968;0.993	D	0.98971	1.0801	10	0.87932	D	0	.	9.8831	0.41245	0.0:0.9051:0.0:0.0949	.	206;204;214;204	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	M	206;214;214;204	ENSP00000339906:V206M;ENSP00000344297:V214M;ENSP00000451923:V204M	ENSP00000344297:V214M	V	-	1	0	PAX4	127040745	0.990000	0.36364	0.959000	0.39883	0.756000	0.42949	2.605000	0.46283	2.661000	0.90470	0.650000	0.86243	GTG		0.582	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			T	127253509	C	T	127253509	3	4	61	1	0	0	0	0	1	0	0	0	11512	507	18	3	435	3	PAX4	7	127253509	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29200	127253509	31885154	5565	13550										
PAX4	5078	broad.mit.edu	37	chr7	127254558	127254558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgacctgagccgtgtgcaCggtagtccctggtcctcctg	14	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127254558C>T	ENST00000341640.2	-	3	595	c.390G>A	c.(388-390)ccG>ccA	p.P130P	PAX4_ENST00000463946.1_Silent_p.P128P|PAX4_ENST00000338516.3_Silent_p.P138P|PAX4_ENST00000378740.2_Silent_p.P130P	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	138	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.P130P(1)		cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GCCGTGTGCACGGTAGTCCCT	0.547																																					Ovarian(113;737 1605 7858 27720 34092)											1	Substitution - coding silent(1)	large_intestine(1)	7											103	74	84					7																	127254558		2203	4300	6503	127041794	SO:0001819	synonymous_variant	5078				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.390G>A	7.37:g.127254558C>T			127041794	O95161|Q6B0H0	Silent	SNP	ENST00000341640.2	37	CCDS5797.1																																																																																				0.547	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			T	127254558	C	T	127254558	2	4	61	1	0	0	0	0	0	0	0	1	11512	523	19	1		1	PAX4	7	127254558	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1049	127254558	31884105	5566	13551										
SND1	27044	broad.mit.edu	37	chr7	127544815	127544815	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagagctattaagaatggCaaaggattgcatagcaagaa	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127544815C>T	ENST00000354725.3	+	14	1664	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	490	TNase-like 3. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)	p.G490G(1)		central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						TTAAGAATGGCAAAGGATTGC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	7											149	137	141					7																	127544815		2203	4300	6503	127332051	SO:0001819	synonymous_variant	27044				CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"Tudor domain containing"	30646	protein-coding gene	gene with protein product	"p100 EBNA2 co-activator", "Tudor-SN"	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.1470C>T	7.37:g.127544815C>T			127332051	Q13122|Q96AG0	Silent	SNP	ENST00000354725.3	37	CCDS34747.1																																																																																				0.453	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		T	127544815	C	T	127544815	2	4	61	1	0	0	0	0	0	0	0	1	14881	697	25	3		3	SND1	7	127544815	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	290257	127544815	31593848	5567	13552										
LRRC4	64101	broad.mit.edu	37	chr7	127669478	127669478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaagttcaaggtgccgtCgttgaggacagagatccttg	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127669478C>T	ENST00000249363.3	-	2	1473	c.1216G>A	c.(1216-1218)Gac>Aac	p.D406N	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	406	Ig-like.				postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.D406N(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		AAGGTGCCGTCGTTGAGGACA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	7											113	95	101					7																	127669478		2203	4300	6503	127456714	SO:0001583	missense	64101			AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"Immunoglobulin superfamily / I-set domain containing"	15586	protein-coding gene	gene with protein product		610486	"leucine-rich repeat-containing 4"			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1216G>A	7.37:g.127669478C>T	ENSP00000249363:p.Asp406Asn		127456714	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	37	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.231418	0.58777	.	.	ENSG00000128594	ENST00000249363	T	0.40756	1.02	4.4	4.4	0.53042	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.50137	0.1598	L	0.36672	1.1	0.58432	D	0.999999	D	0.67145	0.996	D	0.63488	0.915	T	0.40270	-0.9572	10	0.30854	T	0.27	.	14.5186	0.67835	0.0:1.0:0.0:0.0	.	406	Q9HBW1	LRRC4_HUMAN	N	406	ENSP00000249363:D406N	ENSP00000249363:D406N	D	-	1	0	LRRC4	127456714	1.000000	0.71417	0.260000	0.24451	0.878000	0.50629	7.638000	0.83328	2.268000	0.75426	0.655000	0.94253	GAC		0.577	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		T	127669478	C	T	127669478	3	4	61	1	0	0	0	0	1	0	0	0	9026	884	31	1	749	1	LRRC4	7	127669478	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124663	127669478	31469185	5568	13553										
LEP	3952	broad.mit.edu	37	chr7	127894714	127894714	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacagcctggggggtgtCctggaagcttcaggctactc	15	10	1	0	rs372892330		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:127894714C>T	ENST00000308868.4	+	3	453	c.402C>T	c.(400-402)gtC>gtT	p.V134V		NM_000230.2	NP_000221.1	P41159	LEP_HUMAN	leptin	134					adipose tissue development (GO:0060612)|adult feeding behavior (GO:0008343)|bile acid metabolic process (GO:0008206)|bone mineralization involved in bone maturation (GO:0035630)|cellular response to L-ascorbic acid (GO:0071298)|cellular response to retinoic acid (GO:0071300)|central nervous system neuron development (GO:0021954)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|fatty acid beta-oxidation (GO:0006635)|female pregnancy (GO:0007565)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process (GO:0006114)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|leptin-mediated signaling pathway (GO:0033210)|leukocyte tethering or rolling (GO:0050901)|negative regulation of apoptotic process (GO:0043066)|negative regulation of appetite (GO:0032099)|negative regulation of cartilage development (GO:0061037)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of glutamine transport (GO:2000486)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vasoconstriction (GO:0045906)|ovulation from ovarian follicle (GO:0001542)|placenta development (GO:0001890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of developmental growth (GO:0048639)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of ion transport (GO:0043270)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of blood pressure (GO:0008217)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis (GO:0006111)|regulation of insulin secretion (GO:0050796)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of lipoprotein lipid oxidation (GO:0060587)|regulation of steroid biosynthetic process (GO:0050810)|response to dietary excess (GO:0002021)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to vitamin E (GO:0033197)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.V134V(1)		endometrium(1)|large_intestine(2)|lung(5)	8						TGGGGGGTGTCCTGGAAGCTT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	7						C		1,4405	2.1+/-5.4	0,1,2202	35	36	36		402	4.8	0.9	7		36	0,8600		0,0,4300	no	coding-synonymous	LEP	NM_000230.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		134/168	127894714	1,13005	2203	4300	6503	127681950	SO:0001819	synonymous_variant	3952				CCDS5800.1	7q31	2008-03-06	2008-03-06		ENSG00000174697	ENSG00000174697			6553	protein-coding gene	gene with protein product		164160	"leptin (murine obesity homolog)", "leptin (obesity homolog, mouse)"	OBS, OB		1686014, 16932309	Standard	NM_000230		Approved		uc003vml.2	P41159	OTTHUMG00000157564	ENST00000308868.4:c.402C>T	7.37:g.127894714C>T			127681950	O15158|Q56A88	Silent	SNP	ENST00000308868.4	37	CCDS5800.1																																																																																				0.632	LEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349174.1			T	127894714	C	T	127894714	2	4	61	1	0	0	0	0	0	0	0	1	8749	842	30	3		3	LEP	7	127894714	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	225236	127894714	31243949	5569	13554										
METTL2B	55798	broad.mit.edu	37	chr7	128119309	128119309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattggctttttaccgaattCcctgagctggcacctagcca	8	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128119309C>A	ENST00000262432.8	+	3	337	c.300C>A	c.(298-300)ttC>ttA	p.F100L	METTL2B_ENST00000480046.1_Missense_Mutation_p.F35L|RP11-212P7.3_ENST00000462662.1_RNA	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	100					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)	p.F100L(1)		breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TTACCGAATTCCCTGAGCTGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											59	60	59					7																	128119309		2203	4297	6500	127906545	SO:0001583	missense	55798			AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.300C>A	7.37:g.128119309C>A	ENSP00000262432:p.Phe100Leu		127906545	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	37	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	C	16.12	3.034083	0.54896	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.03124	4.04;4.04;4.04	2.86	0.16	0.14972	.	0.000000	0.85682	D	0.000000	T	0.12433	0.0302	M	0.87381	2.88	0.50039	D	0.999845	D;D	0.62365	0.991;0.972	P;P	0.57548	0.823;0.728	T	0.01280	-1.1397	10	0.87932	D	0	-3.2708	6.4034	0.21650	0.0:0.614:0.0:0.386	.	35;100	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	L	94;100;35	ENSP00000418634:F94L;ENSP00000262432:F100L;ENSP00000418402:F35L	ENSP00000262432:F100L	F	+	3	2	METTL2B	127906545	0.994000	0.37717	0.994000	0.49952	0.590000	0.36582	0.393000	0.20817	0.100000	0.17581	0.405000	0.27470	TTC		0.393	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		A	128119309	C	A	128119309	3	1	61	1	0	0	0	0	1	0	0	0	9530	854	30	2	310	2	METTL2B	7	128119309	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	224595	128119309	31019354	5570	13555										
FAM71F2	346653	broad.mit.edu	37	chr7	128315725	128315725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtacctgaggctgatttCcaggtcactaagcccgggaa	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128315725C>A	ENST00000480462.1	+	2	283	c.177C>A	c.(175-177)ttC>ttA	p.F59L	FAM71F2_ENST00000477515.1_Missense_Mutation_p.F59L|FAM71F2_ENST00000378704.3_Intron|FAM71F2_ENST00000460349.1_Intron			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	59								p.F59L(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						AGGCTGATTTCCAGGTCACTA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											52	55	54					7																	128315725		1988	4171	6159	128102961	SO:0001583	missense	346653			BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"family with sequence similarity 137, member B"	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.177C>A	7.37:g.128315725C>A	ENSP00000420140:p.Phe59Leu		128102961	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	.	.	.	.	.	.	.	.	.	.	C	0.217	-1.031917	0.02029	.	.	ENSG00000205085	ENST00000480462;ENST00000477515	T;T	0.29142	3.41;1.58	4.67	0.799	0.18667	.	.	.	.	.	T	0.16214	0.0390	N	0.08118	0	0.58432	D	0.999997	P	0.46784	0.884	B	0.43838	0.433	T	0.06215	-1.0839	9	0.87932	D	0	-7.5279	6.9166	0.24363	0.0:0.6402:0.0:0.3598	.	59	Q6NXP2	F71F2_HUMAN	L	59	ENSP00000420140:F59L;ENSP00000419649:F59L	ENSP00000419649:F59L	F	+	3	2	FAM71F2	128102961	0.552000	0.26505	0.793000	0.32043	0.221000	0.24807	-0.200000	0.09478	0.288000	0.22398	0.557000	0.71058	TTC		0.572	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			A	128315725	C	A	128315725	3	1	61	1	0	0	0	0	1	0	0	0	5632	854	30	2	183	2	FAM71F2	7	128315725	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	196416	128315725	30822938	5571	13556										
FAM71F2	346653	broad.mit.edu	37	chr7	128317694	128317694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagggttaggacagtgaccGaaaagatctactatctgaag	12	6	2	4	rs200938500		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128317694G>A	ENST00000480462.1	+	3	548	c.442G>A	c.(442-444)Gaa>Aaa	p.E148K	FAM71F2_ENST00000378704.3_Missense_Mutation_p.E139K|FAM71F2_ENST00000477515.1_Intron|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	148								p.E148K(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						GACAGTGACCGAAAAGATCTA	0.498													G|||	1	0.000199681	8e-04	0	5008	,	,		13672	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7											51	53	53					7																	128317694		1957	4175	6132	128104930	SO:0001583	missense	346653			BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"family with sequence similarity 137, member B"	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.442G>A	7.37:g.128317694G>A	ENSP00000420140:p.Glu148Lys		128104930	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.25	3.341256	0.60963	.	.	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	5.6	5.6	0.85130	.	0.000000	0.49916	D	0.000130	T	0.45316	0.1336	M	0.68593	2.085	0.36831	D	0.886919	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.50285	-0.8846	10	0.56958	D	0.05	-9.5975	15.1095	0.72343	0.0:0.0:1.0:0.0	.	139;148	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	K	139;148;139;139	ENSP00000418907:E139K;ENSP00000420140:E148K;ENSP00000367976:E139K;ENSP00000401654:E139K	ENSP00000367976:E139K	E	+	1	0	FAM71F2	128104930	0.906000	0.30813	0.699000	0.30290	0.298000	0.27526	3.289000	0.51747	2.628000	0.89032	0.650000	0.86243	GAA		0.498	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			A	128317694	G	A	128317694	3	1	61	1	0	0	0	0	1	0	0	0	5632	1059	37	1	452	1	FAM71F2	7	128317694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1969	128317694	30820969	5572	13557										
CALU	813	broad.mit.edu	37	chr7	128394424	128394424	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatttacgaggatgtagaGcgacagtggaaggggcatga	17	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128394424G>T	ENST00000249364.4	+	3	432	c.330G>T	c.(328-330)gaG>gaT	p.E110D	CALU_ENST00000479257.1_Missense_Mutation_p.E118D|CALU_ENST00000542996.2_Intron|CALU_ENST00000538546.1_Intron|CALU_ENST00000535623.1_Missense_Mutation_p.E118D|CALU_ENST00000449187.2_Intron|CALU_ENST00000535011.2_Missense_Mutation_p.E110D	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	110	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)	p.E110D(1)		kidney(2)|large_intestine(3)|lung(5)	10						AGGATGTAGAGCGACAGTGGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											136	117	123					7																	128394424		2203	4300	6503	128181660	SO:0001583	missense	813			AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"EF-hand domain containing"	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.330G>T	7.37:g.128394424G>T	ENSP00000249364:p.Glu110Asp		128181660	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	37	CCDS5805.1	.	.	.	.	.	.	.	.	.	.	G	9.802	1.180828	0.21787	.	.	ENSG00000128595	ENST00000535623;ENST00000538394;ENST00000535011;ENST00000249364;ENST00000479257	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.96	4.14	0.48551	EF-hand-like domain (1);	0.049750	0.85682	D	0.000000	T	0.45377	0.1339	N	0.04705	-0.18	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34204	-0.9838	10	0.12103	T	0.63	-15.8581	10.9339	0.47235	0.1551:0.0:0.8449:0.0	.	110	O43852	CALU_HUMAN	D	118;110;110;110;118	ENSP00000439139:E118D;ENSP00000442110:E110D;ENSP00000249364:E110D;ENSP00000420381:E118D	ENSP00000249364:E110D	E	+	3	2	CALU	128181660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.916000	0.28651	1.521000	0.48983	0.655000	0.94253	GAG		0.478	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219		T	128394424	G	T	128394424	3	4	61	1	0	0	0	0	1	0	0	0	2600	962	34	2	336	2	CALU	7	128394424	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76730	128394424	30744239	5573	13558										
CCDC136	64753	broad.mit.edu	37	chr7	128441290	128441290	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgttagagcatgagaaaGaaagcgaacttaaggaaata	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128441290G>T	ENST00000297788.4	+	4	764	c.397G>T	c.(397-399)Gaa>Taa	p.E133*	CCDC136_ENST00000378685.4_Nonsense_Mutation_p.E183*|CCDC136_ENST00000464832.1_Nonsense_Mutation_p.E183*|CCDC136_ENST00000487361.1_Nonsense_Mutation_p.E133*	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	133	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.E133*(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						GCATGAGAAAGAAAGCGAACT	0.488																																																2	Substitution - Nonsense(2)	large_intestine(2)	7											75	74	74					7																	128441290		1948	4157	6105	128228526	SO:0001587	stop_gained	64753				CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.397G>T	7.37:g.128441290G>T	ENSP00000297788:p.Glu133*		128228526	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Nonsense_Mutation	SNP	ENST00000297788.4	37	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.236453|6.236453	0.97399|0.97399	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000485998;ENST00000378685;ENST00000464832;ENST00000487361;ENST00000297788;ENST00000397697;ENST00000320524|ENST00000494552	.|T	.|0.57752	.|0.38	5.65|5.65	4.74|4.74	0.60224|0.60224	.|.	0.157561|.	0.56097|.	D|.	0.000031|.	.|T	.|0.65821	.|0.2728	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.75731	.|-0.3215	.|5	0.37606|0.66056	T|D	0.19|0.02	-6.9233|-6.9233	14.0126|14.0126	0.64507|0.64507	0.0:0.1527:0.8473:0.0|0.0:0.1527:0.8473:0.0	.|.	.|.	.|.	.|.	X|N	133;183;183;133;133;133;133|9	.|ENSP00000417931:K9N	ENSP00000297788:E133X|ENSP00000417931:K9N	E|K	+|+	1|3	0|2	CCDC136|CCDC136	128228526|128228526	1.000000|1.000000	0.71417|0.71417	0.399000|0.399000	0.26333|0.26333	0.381000|0.381000	0.30169|0.30169	5.994000|5.994000	0.70623|0.70623	1.325000|1.325000	0.45301|0.45301	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.488	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128441290	G	T	128441290	4	4	61	1	0	0	0	0	0	1	0	0	2776	943	33	2	411	2	CCDC136	7	128441290	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46866	128441290	30697373	5574	13559										
CCDC136	64753	broad.mit.edu	37	chr7	128451962	128451962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggaggctcctagaggagCggaagaggctgcaggcagac	18	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128451962C>T	ENST00000297788.4	+	13	2504	c.2137C>T	c.(2137-2139)Cgg>Tgg	p.R713W	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	713						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.R713W(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CCTAGAGGAGCGGAAGAGGCT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	7											64	66	66					7																	128451962		1919	4141	6060	128239198	SO:0001583	missense	64753				CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.2137C>T	7.37:g.128451962C>T	ENSP00000297788:p.Arg713Trp		128239198	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	37	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059376	0.55325	.	.	ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672	T;T	0.57595	0.39;0.39	5.93	5.04	0.67666	.	0.334859	0.25951	N	0.027241	T	0.48857	0.1523	M	0.71581	2.175	0.30602	N	0.760458	P;B;B	0.36599	0.56;0.308;0.2	B;B;B	0.30179	0.112;0.067;0.046	T	0.60234	-0.7303	10	0.59425	D	0.04	-15.005	11.3654	0.49668	0.0:0.9159:0.0:0.0841	.	713;713;713	Q96JN2-4;Q96JN2-2;Q96JN2	.;.;CC136_HUMAN	W	713;713;713;304	ENSP00000297788:R713W;ENSP00000417991:R304W	ENSP00000297788:R713W	R	+	1	2	CCDC136	128239198	0.674000	0.27549	0.999000	0.59377	0.991000	0.79684	1.806000	0.38892	1.494000	0.48533	0.561000	0.74099	CGG		0.567	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128451962	C	T	128451962	3	4	61	1	0	0	0	0	1	0	0	0	2776	759	27	1	2187	1	CCDC136	7	128451962	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10672	128451962	30686701	5575	13560										
FLNC	2318	broad.mit.edu	37	chr7	128483556	128483556	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcagggacagccaagggCgaggttgtgcgggactttga	17	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128483556C>T	ENST00000325888.8	+	18	2997	c.2736C>T	c.(2734-2736)ggC>ggT	p.G912G	FLNC_ENST00000346177.6_Silent_p.G912G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	912					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.G912G(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CAGCCAAGGGCGAGGTTGTGC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	7											90	101	97					7																	128483556		2149	4244	6393	128270792	SO:0001819	synonymous_variant	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.2736C>T	7.37:g.128483556C>T			128270792	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																				0.592	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128483556	C	T	128483556	2	4	61	1	0	0	0	0	0	0	0	1	5954	755	27	1		1	FLNC	7	128483556	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31594	128483556	30655107	5576	13561										
FLNC	2318	broad.mit.edu	37	chr7	128492797	128492797	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgaagcgcctgcccaacCggcacattggtgagcgtggg	15	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:128492797C>A	ENST00000325888.8	+	36	6256	c.5995C>A	c.(5995-5997)Cgg>Agg	p.R1999R	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.R1966R	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1999					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.R1999R(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CCTGCCCAACCGGCACATTGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	7											42	47	45					7																	128492797		2021	4183	6204	128280033	SO:0001819	synonymous_variant	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.5995C>A	7.37:g.128492797C>A			128280033	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																				0.652	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128492797	C	A	128492797	2	1	61	1	0	0	0	0	0	0	0	1	5954	643	23	2		2	FLNC	7	128492797	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9241	128492797	30645866	5577	13562										
AHCYL2	23382	broad.mit.edu	37	chr7	129040170	129040170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagggagagtcagaagatgActtttggtggtgtatcgata	15	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129040170A>G	ENST00000325006.3	+	6	917	c.863A>G	c.(862-864)gAc>gGc	p.D288G	AHCYL2_ENST00000531335.2_Missense_Mutation_p.D207G|AHCYL2_ENST00000490911.1_Missense_Mutation_p.D185G|AHCYL2_ENST00000446212.1_Missense_Mutation_p.D186G|AHCYL2_ENST00000446544.2_Missense_Mutation_p.D287G|AHCYL2_ENST00000474594.1_Missense_Mutation_p.D185G	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	288					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)	p.D288G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						TCAGAAGATGACTTTTGGTGG	0.448																																					Pancreas(160;1736 1964 29875 40941 45605)											1	Substitution - Missense(1)	large_intestine(1)	7											194	190	191					7																	129040170		2203	4300	6503	128827406	SO:0001583	missense	23382			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"S-adenosylhomocysteine hydrolase-like 2"				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.863A>G	7.37:g.129040170A>G	ENSP00000315931:p.Asp288Gly		128827406	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	30|30	5.051686|5.051686	0.93793|0.93793	.|.	.|.	ENSG00000158467|ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911|ENST00000466924	T;T;T;T;T;T|.	0.77098|.	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76615|0.76615	0.4012|0.4012	M|M	0.82517|0.82517	2.595|2.595	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D;D|.	0.65815|.	0.969;0.969;0.995;0.969;0.993|.	P;P;D;P;P|.	0.65773|.	0.896;0.896;0.938;0.896;0.898|.	T|T	0.78984|0.78984	-0.1988|-0.1988	10|5	0.87932|.	D|.	0|.	-13.2448|-13.2448	13.7453|13.7453	0.62872|0.62872	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	185;186;288;185;287|.	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2|.	.;.;SAHH3_HUMAN;.;.|.	G|A	288;287;207;185;186;185|195	ENSP00000315931:D288G;ENSP00000413639:D287G;ENSP00000431787:D207G;ENSP00000420459:D185G;ENSP00000405267:D186G;ENSP00000420801:D185G|.	ENSP00000315931:D288G|.	D|T	+|+	2|1	0|0	AHCYL2|AHCYL2	128827406|128827406	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.884000|8.884000	0.92432|0.92432	1.980000|1.980000	0.57719|0.57719	0.460000|0.460000	0.39030|0.39030	GAC|ACT		0.448	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1			G	129040170	A	G	129040170	3	3	61	1	0	0	0	0	1	0	0	0	411	275	10	4	1007	4	AHCYL2	7	129040170	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	547373	129040170	30098493	5578	13563										
AHCYL2	23382	broad.mit.edu	37	chr7	129045015	129045015	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtcaccaaacagaaatTtgacaacctctactgttgcc	5	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129045015T>G	ENST00000325006.3	+	8	1157	c.1103T>G	c.(1102-1104)tTt>tGt	p.F368C	AHCYL2_ENST00000531335.2_Missense_Mutation_p.F287C|AHCYL2_ENST00000490911.1_Missense_Mutation_p.F265C|AHCYL2_ENST00000446212.1_Missense_Mutation_p.F266C|AHCYL2_ENST00000446544.2_Missense_Mutation_p.F367C|AHCYL2_ENST00000474594.1_Missense_Mutation_p.F265C|RNU7-16P_ENST00000516471.1_RNA	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	368					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)	p.F368C(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						AAACAGAAATTTGACAACCTC	0.418																																					Pancreas(160;1736 1964 29875 40941 45605)											1	Substitution - Missense(1)	large_intestine(1)	7											198	190	193					7																	129045015		2203	4300	6503	128832251	SO:0001583	missense	23382			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"S-adenosylhomocysteine hydrolase-like 2"				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1103T>G	7.37:g.129045015T>G	ENSP00000315931:p.Phe368Cys		128832251	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.689860|4.689860	0.88735|0.88735	.|.	.|.	ENSG00000158467|ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911|ENST00000466924	D;D;D;D;D;D|.	0.82526|.	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87233|0.87233	0.6126|0.6126	H|H	0.96365|0.96365	3.81|3.81	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.91635|.	0.998;0.998;0.999;0.998;0.998|.	D|D	0.90960|0.90960	0.4812|0.4812	10|5	0.87932|.	D|.	0|.	-13.6816|-13.6816	14.1334|14.1334	0.65270|0.65270	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	265;266;368;265;367|.	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2|.	.;.;SAHH3_HUMAN;.;.|.	C|V	368;367;287;265;266;265|275	ENSP00000315931:F368C;ENSP00000413639:F367C;ENSP00000431787:F287C;ENSP00000420459:F265C;ENSP00000405267:F266C;ENSP00000420801:F265C|.	ENSP00000315931:F368C|.	F|L	+|+	2|1	0|2	AHCYL2|AHCYL2	128832251|128832251	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.739000|7.739000	0.84976|0.84976	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	TTT|TTG		0.418	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1			G	129045015	T	G	129045015	3	3	61	1	0	0	0	0	1	0	0	0	411	1841	64	4	1255	4	AHCYL2	7	129045015	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4845	129045015	30093648	5579	13564										
NRF1	4899	broad.mit.edu	37	chr7	129357071	129357071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctcaggtggaacaaaatTgggccacgttacagggaggt	14	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129357071T>C	ENST00000393232.1	+	9	1195	c.1078T>C	c.(1078-1080)Tgg>Cgg	p.W360R	NRF1_ENST00000353868.4_Missense_Mutation_p.W294R|NRF1_ENST00000311967.2_Missense_Mutation_p.W360R|NRF1_ENST00000223190.4_Missense_Mutation_p.W360R|NRF1_ENST00000393231.3_Missense_Mutation_p.W360R|NRF1_ENST00000393230.2_Missense_Mutation_p.W360R|NRF1_ENST00000539636.1_Missense_Mutation_p.W199R	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	360	Required for transcriptional activation.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.W360R(1)		breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						GGAACAAAATTGGGCCACGTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	7											68	66	67					7																	129357071		2203	4300	6503	129144307	SO:0001583	missense	4899			L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"alpha palindromic-binding protein"	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.1078T>C	7.37:g.129357071T>C	ENSP00000376924:p.Trp360Arg		129144307	A8K4C6|B4DDV6|Q15305|Q96AN2	Missense_Mutation	SNP	ENST00000393232.1	37	CCDS5813.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186166	0.78789	.	.	ENSG00000106459	ENST00000393232;ENST00000353868;ENST00000539636;ENST00000223190;ENST00000311967;ENST00000393230;ENST00000393231	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.63426	0.2510	N	0.22421	0.69	0.80722	D	1	P;D	0.61697	0.907;0.99	B;D	0.72982	0.246;0.979	T	0.65479	-0.6158	9	0.46703	T	0.11	-7.1233	14.8785	0.70513	0.0:0.0:0.0:1.0	.	360;360	Q96AN2;Q16656	.;NRF1_HUMAN	R	360;294;199;360;360;360;360	.	ENSP00000223190:W360R	W	+	1	0	NRF1	129144307	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.694000	0.84235	2.115000	0.64714	0.529000	0.55759	TGG		0.468	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110		C	129357071	T	C	129357071	3	2	61	1	0	0	0	0	1	0	0	0	10677	1812	63	4	1108	4	NRF1	7	129357071	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	312056	129357071	29781592	5580	13565										
ZC3HC1	51530	broad.mit.edu	37	chr7	129658533	129658533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacagagattcccactgccGaaatattcggaatactttcc	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129658533G>A	ENST00000358303.4	-	10	1564	c.1480C>T	c.(1480-1482)Cgg>Tgg	p.R494W	ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R451W|RP11-306G20.1_ENST00000480018.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.R423W|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R473W	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	494					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.R494W(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TCCCACTGCCGAAATATTCGG	0.398																																					Melanoma(115;540 1606 16325 28853 48167)											1	Substitution - Missense(1)	large_intestine(1)	7											96	101	99					7																	129658533		2203	4300	6503	129445769	SO:0001583	missense	51530			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1480C>T	7.37:g.129658533G>A	ENSP00000351052:p.Arg494Trp		129445769	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215685	0.79352	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503	T;T;T;T	0.56611	1.12;0.57;1.14;0.45	6.17	6.17	0.99709	.	0.067008	0.64402	D	0.000008	T	0.70395	0.3219	L	0.59436	1.845	0.52501	D	0.999951	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.994;0.994	T	0.70339	-0.4899	10	0.87932	D	0	-19.2943	17.5987	0.88020	0.0:0.0:1.0:0.0	.	423;494;451	Q86WB0-3;Q86WB0;C9J0I9	.;NIPA_HUMAN;.	W	494;423;473;451	ENSP00000351052:R494W;ENSP00000353933:R423W;ENSP00000309301:R473W;ENSP00000418533:R451W	ENSP00000309301:R473W	R	-	1	2	ZC3HC1	129445769	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	5.019000	0.64060	2.941000	0.99782	0.655000	0.94253	CGG		0.398	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		A	129658533	G	A	129658533	3	1	61	1	0	0	0	0	1	0	0	0	17616	1057	37	1	32	1	ZC3HC1	7	129658533	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	301462	129658533	29480130	5581	13566										
ZC3HC1	51530	broad.mit.edu	37	chr7	129668806	129668806	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagtgacaaaggctttgaAaacgatctaggaattcacta	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129668806A>C	ENST00000358303.4	-	5	641	c.557T>G	c.(556-558)tTt>tGt	p.F186C	ZC3HC1_ENST00000481503.1_Missense_Mutation_p.F186C|RNA5SP245_ENST00000364239.1_RNA|RP11-306G20.1_ENST00000480018.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.F186C|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.F165C	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	186	F-box-like.				mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.F186C(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					AAGGCTTTGAAAACGATCTAG	0.453																																					Melanoma(115;540 1606 16325 28853 48167)											1	Substitution - Missense(1)	large_intestine(1)	7											65	63	64					7																	129668806		2203	4300	6503	129456042	SO:0001583	missense	51530			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.557T>G	7.37:g.129668806A>C	ENSP00000351052:p.Phe186Cys		129456042	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.407280	0.62399	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503	T;T;T;T	0.43294	1.5;0.95;1.52;1.02	5.82	5.82	0.92795	Zinc finger, C3HC-like (1);	0.177391	0.52532	D	0.000064	T	0.51312	0.1667	N	0.25890	0.77	0.51767	D	0.999934	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.85130	0.992;0.997;0.914	T	0.48547	-0.9026	10	0.35671	T	0.21	-24.1432	15.0031	0.71489	1.0:0.0:0.0:0.0	.	186;186;186	Q86WB0-3;Q86WB0;C9J0I9	.;NIPA_HUMAN;.	C	186;186;165;186	ENSP00000351052:F186C;ENSP00000353933:F186C;ENSP00000309301:F165C;ENSP00000418533:F186C	ENSP00000309301:F165C	F	-	2	0	ZC3HC1	129456042	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.456000	0.73501	2.229000	0.72834	0.523000	0.50628	TTT		0.453	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		C	129668806	A	C	129668806	3	2	61	1	0	0	0	0	1	0	0	0	17616	14	1	4	975	4	ZC3HC1	7	129668806	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10273	129668806	29469857	5582	13567										
ZC3HC1	51530	broad.mit.edu	37	chr7	129691182	129691182	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaacccctacggcaaacgCttgtccctcacagggcgccg	9	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129691182C>A	ENST00000358303.4	-	1	109	c.25G>T	c.(25-27)Gcg>Tcg	p.A9S	ZC3HC1_ENST00000481503.1_Missense_Mutation_p.A9S|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.A9S|ZC3HC1_ENST00000311873.5_5'UTR	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	9					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.A9S(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					ACGGCAAACGCTTGTCCCTCA	0.592																																					Melanoma(115;540 1606 16325 28853 48167)											1	Substitution - Missense(1)	large_intestine(1)	7											51	53	52					7																	129691182		2203	4300	6503	129478418	SO:0001583	missense	51530			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.25G>T	7.37:g.129691182C>A	ENSP00000351052:p.Ala9Ser		129478418	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	C	7.610	0.674647	0.14841	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000481503;ENST00000480193	T;T;T	0.44881	1.5;0.92;0.91	5.2	2.21	0.28008	.	0.837369	0.10454	N	0.672712	T	0.18045	0.0433	N	0.03608	-0.345	0.21220	N	0.999755	B	0.02656	0.0	B	0.04013	0.001	T	0.22103	-1.0226	10	0.30854	T	0.27	-0.01	4.4121	0.11438	0.1428:0.5635:0.2088:0.0849	.	9	Q86WB0	NIPA_HUMAN	S	9	ENSP00000351052:A9S;ENSP00000353933:A9S;ENSP00000418533:A9S	ENSP00000351052:A9S	A	-	1	0	ZC3HC1	129478418	0.000000	0.05858	0.001000	0.08648	0.087000	0.18053	-0.627000	0.05521	0.249000	0.21456	0.561000	0.74099	GCG		0.592	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		A	129691182	C	A	129691182	3	1	61	1	0	0	0	0	1	0	0	0	17616	797	28	2	1523	2	ZC3HC1	7	129691182	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22376	129691182	29447481	5583	13568										
CPA5	93979	broad.mit.edu	37	chr7	129987642	129987642	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcctggccaaagatgagaAgcagctttcacttctcgggg	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:129987642A>C	ENST00000485477.1	+	3	1281	c.152A>C	c.(151-153)aAg>aCg	p.K51T	CPA5_ENST00000466363.2_Missense_Mutation_p.K51T|CPA5_ENST00000461828.1_Missense_Mutation_p.K51T|CPA5_ENST00000393213.3_Missense_Mutation_p.K51T|CPA5_ENST00000474905.1_Missense_Mutation_p.K51T|CPA5_ENST00000355388.3_Missense_Mutation_p.K51T|CPA5_ENST00000431780.2_Missense_Mutation_p.K51T			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	51						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.K51T(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					AAAGATGAGAAGCAGCTTTCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	70	71					7																	129987642		2203	4300	6503	129774878	SO:0001583	missense	93979			AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.152A>C	7.37:g.129987642A>C	ENSP00000420237:p.Lys51Thr		129774878	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.485704	0.26686	.	.	ENSG00000158525	ENST00000355388;ENST00000463587;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49	5.63	-1.42	0.08913	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.806159	0.11253	N	0.583444	T	0.07503	0.0189	L	0.34521	1.04	0.29834	N	0.829772	B;B	0.20988	0.05;0.007	B;B	0.18561	0.022;0.014	T	0.37384	-0.9708	9	.	.	.	.	1.1113	0.01704	0.3936:0.2983:0.164:0.1441	.	51;51	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	T	51	ENSP00000347549:K51T;ENSP00000420060:K51T;ENSP00000418183:K51T;ENSP00000419025:K51T;ENSP00000420237:K51T;ENSP00000393045:K51T;ENSP00000417314:K51T;ENSP00000376907:K51T	.	K	+	2	0	CPA5	129774878	0.999000	0.42202	0.945000	0.38365	0.818000	0.46254	0.944000	0.29043	-0.151000	0.11176	-0.313000	0.08912	AAG		0.582	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		C	129987642	A	C	129987642	3	2	61	1	0	0	0	0	1	0	0	0	3799	72	3	4	158	4	CPA5	7	129987642	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	296460	129987642	29151021	5584	13569										
CPA5	93979	broad.mit.edu	37	chr7	130001023	130001023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgtaatggagcattccGatattgtctcaaaaattcag	7	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130001023G>A	ENST00000485477.1	+	6	1601	c.472G>A	c.(472-474)Gat>Aat	p.D158N	CPA5_ENST00000466363.2_Missense_Mutation_p.D158N|CPA5_ENST00000461828.1_Missense_Mutation_p.D158N|CPA5_ENST00000393213.3_Missense_Mutation_p.D158N|CPA5_ENST00000474905.1_Missense_Mutation_p.D158N|CPA5_ENST00000355388.3_Missense_Mutation_p.D158N|CPA5_ENST00000431780.2_Missense_Mutation_p.D158N			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	158						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.D158N(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					GGAGCATTCCGATATTGTCTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											106	97	100					7																	130001023		2203	4300	6503	129788259	SO:0001583	missense	93979			AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.472G>A	7.37:g.130001023G>A	ENSP00000420237:p.Asp158Asn		129788259	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	G	1.468	-0.560517	0.03939	.	.	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93;3.93;3.93	6.17	0.237	0.15475	Peptidase M14, carboxypeptidase A (2);	0.285799	0.30547	N	0.009398	T	0.01661	0.0053	N	0.04090	-0.28	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.49390	-0.8945	9	.	.	.	.	8.9112	0.35555	0.5259:0.0:0.4741:0.0	.	158;158	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	N	158	ENSP00000347549:D158N;ENSP00000418183:D158N;ENSP00000419025:D158N;ENSP00000420237:D158N;ENSP00000393045:D158N;ENSP00000417314:D158N;ENSP00000376907:D158N	.	D	+	1	0	CPA5	129788259	0.039000	0.19947	0.788000	0.31933	0.323000	0.28346	0.478000	0.22212	0.191000	0.20236	-0.700000	0.03674	GAT		0.418	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		A	130001023	G	A	130001023	3	1	61	1	0	0	0	0	1	0	0	0	3799	1058	37	1	490	1	CPA5	7	130001023	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13381	130001023	29137640	5585	13570										
TSGA14	95681	broad.mit.edu	37	chr7	130042563	130042563	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaggggcagtcaggataaGgtttgtctttggtatggggc	18	4	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130042563G>T	ENST00000223208.5	-	7	770	c.500C>A	c.(499-501)cCt>cAt	p.P167H	CEP41_ENST00000541543.1_Missense_Mutation_p.P151H|CEP41_ENST00000343969.5_Missense_Mutation_p.P167H	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	167					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)		p.P167H(1)									GTCAGGATAAGGTTTGTCTTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											314	278	290					7																	130042563		2203	4300	6503	129829799	SO:0001583	missense	95681			AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"testis specific, 14"	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.500C>A	7.37:g.130042563G>T	ENSP00000223208:p.Pro167His		129829799	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.838610	0.91117	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000492389;ENST00000472739;ENST00000477003;ENST00000475282	D;D;D;D;D;D;D	0.89939	-2.59;-2.25;-2.56;-2.22;-2.24;-2.31;-2.26	5.83	5.83	0.93111	Rhodanese-like (2);	0.000000	0.85682	D	0.000000	D	0.94212	0.8142	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.976;0.995	D	0.94023	0.7294	10	0.62326	D	0.03	-14.2869	18.7012	0.91620	0.0:0.0:1.0:0.0	.	151;167;167	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	H	167;151;167;132;132;164;132	ENSP00000223208:P167H;ENSP00000445888:P151H;ENSP00000342738:P167H;ENSP00000419192:P132H;ENSP00000417593:P132H;ENSP00000420670:P164H;ENSP00000418363:P132H	ENSP00000223208:P167H	P	-	2	0	TSGA14	129829799	1.000000	0.71417	0.995000	0.50966	0.940000	0.58332	7.910000	0.87451	2.763000	0.94921	0.563000	0.77884	CCT		0.483	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		T	130042563	G	T	130042563	3	4	61	1	0	0	0	0	1	0	0	0	16660	1000	35	2	641	2	TSGA14	7	130042563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41540	130042563	29096100	5586	13571										
MEST	4232	broad.mit.edu	37	chr7	130135349	130135349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcacttacaagggactgcGtatcttctaccaaggtaaga	8	9	3	1	rs561353737		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130135349G>A	ENST00000223215.4	+	2	388	c.167G>A	c.(166-168)cGt>cAt	p.R56H	MIR335_ENST00000362173.1_RNA|MEST_ENST00000341441.5_Missense_Mutation_p.R47H|MEST_ENST00000437945.1_Missense_Mutation_p.R56H|MEST_ENST00000378576.4_Missense_Mutation_p.R47H|MEST_ENST00000416162.2_Missense_Mutation_p.R47H|hsa-mir-335_ENST00000604666.1_RNA|MEST_ENST00000393187.1_Missense_Mutation_p.R47H	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	56					mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.R56H(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					AAGGGACTGCGTATCTTCTAC	0.502													G|||	1	0.000199681	0	0	5008	,	,		19354	0		0	False		,,,				2504	0.001				Colon(126;2182 2305 6517 35181)											1	Substitution - Missense(1)	large_intestine(1)	7											79	65	70					7																	130135349		2203	4300	6503	129922585	SO:0001583	missense	4232				CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"Paternally-expressed gene 1"	601029	"mesoderm specific transcript (mouse) homolog", "mesoderm specific transcript homolog (mouse)"			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.167G>A	7.37:g.130135349G>A	ENSP00000223215:p.Arg56His		129922585	B2R6S1|O14973|O15007|Q6AI49|Q92571	Missense_Mutation	SNP	ENST00000223215.4	37	CCDS5822.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089848	0.36855	.	.	ENSG00000106484	ENST00000341441;ENST00000427521;ENST00000416162;ENST00000378576;ENST00000399874;ENST00000433159;ENST00000393187;ENST00000421001;ENST00000223215;ENST00000437945;ENST00000437637;ENST00000458161	T;T;T;T;T;T;T;T;T;T;T	0.04603	3.59;3.59;3.59;3.59;3.59;3.59;3.59;3.59;3.59;3.59;3.59	5.4	2.63	0.31362	.	0.520095	0.23575	N	0.046709	T	0.03477	0.0100	N	0.17082	0.46	0.28282	N	0.92393	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.30416	-0.9979	10	0.56958	D	0.05	.	9.1357	0.36872	0.3555:0.0:0.6445:0.0	.	56;56;47	C9JW74;Q5EB52;Q5EB52-3	.;MEST_HUMAN;.	H	47;47;47;47;47;47;47;47;56;56;47;47	ENSP00000342749:R47H;ENSP00000409505:R47H;ENSP00000408933:R47H;ENSP00000367839:R47H;ENSP00000390589:R47H;ENSP00000409768:R47H;ENSP00000376884:R47H;ENSP00000407222:R47H;ENSP00000223215:R56H;ENSP00000401657:R56H;ENSP00000393709:R47H	ENSP00000223215:R56H	R	+	2	0	MEST	129922585	0.996000	0.38824	0.999000	0.59377	0.983000	0.72400	2.598000	0.46223	0.348000	0.23949	0.655000	0.94253	CGT		0.502	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402		A	130135349	G	A	130135349	3	1	61	1	0	0	0	0	1	0	0	0	9514	1145	40	1	173	1	MEST	7	130135349	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92786	130135349	29003314	5587	13572										
MEST	4232	broad.mit.edu	37	chr7	130139729	130139729	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacaggtatctttcctgaGactcaccgtccactccttct	5	15	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130139729G>T	ENST00000223215.4	+	7	770	c.549G>T	c.(547-549)gaG>gaT	p.E183D	MEST_ENST00000341441.5_Missense_Mutation_p.E174D|MEST_ENST00000437945.1_Missense_Mutation_p.E183D|MEST_ENST00000378576.4_Missense_Mutation_p.E174D|MEST_ENST00000462132.1_3'UTR|MEST_ENST00000416162.2_Missense_Mutation_p.E174D|hsa-mir-335_ENST00000604666.1_RNA|MEST_ENST00000393187.1_Missense_Mutation_p.E174D	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	183					mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.E183D(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					TCTTTCCTGAGACTCACCGTC	0.398																																					Colon(126;2182 2305 6517 35181)											1	Substitution - Missense(1)	large_intestine(1)	7											104	94	97					7																	130139729		2203	4300	6503	129926965	SO:0001583	missense	4232				CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"Paternally-expressed gene 1"	601029	"mesoderm specific transcript (mouse) homolog", "mesoderm specific transcript homolog (mouse)"			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.549G>T	7.37:g.130139729G>T	ENSP00000223215:p.Glu183Asp		129926965	B2R6S1|O14973|O15007|Q6AI49|Q92571	Missense_Mutation	SNP	ENST00000223215.4	37	CCDS5822.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611577	0.87258	.	.	ENSG00000106484	ENST00000341441;ENST00000427521;ENST00000416162;ENST00000378576;ENST00000393187;ENST00000421001;ENST00000223215;ENST00000437945	T;T;T;T;T;T;T;T	0.67171	-0.2;-0.2;-0.25;-0.25;-0.2;-0.2;-0.2;-0.2	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.78904	0.4357	L	0.56199	1.76	0.53688	D	0.999972	P;D;D;D	0.76494	0.84;0.999;0.999;0.997	P;D;D;D	0.80764	0.773;0.994;0.994;0.921	T	0.76222	-0.3038	10	0.41790	T	0.15	-23.4574	17.8994	0.88899	0.0:0.0:1.0:0.0	.	169;183;183;174	B4DQW6;C9JW74;Q5EB52;Q5EB52-3	.;.;MEST_HUMAN;.	D	174;174;174;174;174;174;183;183	ENSP00000342749:E174D;ENSP00000409505:E174D;ENSP00000408933:E174D;ENSP00000367839:E174D;ENSP00000376884:E174D;ENSP00000407222:E174D;ENSP00000223215:E183D;ENSP00000401657:E183D	ENSP00000223215:E183D	E	+	3	2	MEST	129926965	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.242000	0.43106	2.825000	0.97269	0.644000	0.83932	GAG		0.398	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402		T	130139729	G	T	130139729	3	4	61	1	0	0	0	0	1	0	0	0	9514	933	33	2	575	2	MEST	7	130139729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4380	130139729	28998934	5588	13573										
TSGA13	114960	broad.mit.edu	37	chr7	130356607	130356607	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatacttcccttcgctcttGaaatcattgtcagtggaaaa	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130356607G>A	ENST00000456951.1	-	8	1403	c.552C>T	c.(550-552)ttC>ttT	p.F184F	TSGA13_ENST00000356588.3_Silent_p.F184F			Q96PP4	TSG13_HUMAN	testis specific, 13	184								p.F184F(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					CTTCGCTCTTGAAATCATTGT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											137	134	135					7																	130356607		2203	4300	6503	130007147	SO:0001819	synonymous_variant	114960			AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.552C>T	7.37:g.130356607G>A			130007147	B3KSC9	Silent	SNP	ENST00000456951.1	37	CCDS5824.1																																																																																				0.388	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933		A	130356607	G	A	130356607	2	1	61	1	0	0	0	0	0	0	0	1	16659	1281	45	3		3	TSGA13	7	130356607	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216878	130356607	28782056	5589	13574										
TSGA13	114960	broad.mit.edu	37	chr7	130357634	130357634	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcaaagggaagattggtTtcagcttagatcttaacttt	9	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:130357634T>G	ENST00000456951.1	-	7	1321	c.470A>C	c.(469-471)aAa>aCa	p.K157T	TSGA13_ENST00000356588.3_Missense_Mutation_p.K157T			Q96PP4	TSG13_HUMAN	testis specific, 13	157								p.K157T(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					GAAGATTGGTTTCAGCTTAGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											207	193	198					7																	130357634		2203	4300	6503	130008174	SO:0001583	missense	114960			AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.470A>C	7.37:g.130357634T>G	ENSP00000406047:p.Lys157Thr		130008174	B3KSC9	Missense_Mutation	SNP	ENST00000456951.1	37	CCDS5824.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887585	0.33348	.	.	ENSG00000213265	ENST00000456951;ENST00000418126;ENST00000356588	.	.	.	5.31	4.16	0.48862	.	0.000000	0.53938	D	0.000058	T	0.41696	0.1170	L	0.34521	1.04	0.09310	N	1	P	0.44946	0.846	P	0.52267	0.694	T	0.21143	-1.0254	9	0.56958	D	0.05	-20.373	8.3009	0.32014	0.0:0.0911:0.0:0.9089	.	157	Q96PP4	TSG13_HUMAN	T	157	.	ENSP00000348996:K157T	K	-	2	0	TSGA13	130008174	0.935000	0.31712	0.309000	0.25155	0.050000	0.14768	0.837000	0.27558	0.946000	0.37632	-0.274000	0.10170	AAA		0.443	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933		G	130357634	T	G	130357634	3	3	61	1	0	0	0	0	1	0	0	0	16659	1841	64	4	369	4	TSGA13	7	130357634	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1027	130357634	28781029	5590	13575										
MKLN1	4289	broad.mit.edu	37	chr7	131084165	131084165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtgattttgatgcttgcGaagagttgattgaaaaggct	14	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:131084165G>A	ENST00000352689.6	+	6	716	c.676G>A	c.(676-678)Gaa>Aaa	p.E226K	MKLN1_ENST00000421797.2_Missense_Mutation_p.E134K	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	226	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)		p.E226K(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					TGATGCTTGCGAAGAGTTGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	7											182	179	180					7																	131084165		2203	4300	6503	130734705	SO:0001583	missense	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.676G>A	7.37:g.131084165G>A	ENSP00000323527:p.Glu226Lys		130734705	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	37	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203236	0.95033	.	.	ENSG00000128585	ENST00000421797;ENST00000352689	T;T	0.58797	1.34;0.31	6.02	5.14	0.70334	CTLH, C-terminal LisH motif (1);	0.000000	0.85682	D	0.000000	T	0.72503	0.3468	M	0.76170	2.325	0.80722	D	1	D;P;D	0.67145	0.996;0.868;0.958	P;B;B	0.60886	0.88;0.328;0.263	T	0.76410	-0.2969	10	0.66056	D	0.02	-20.612	14.2351	0.65922	0.0707:0.0:0.9293:0.0	.	226;203;134	Q9UL63;B4DG30;C9J7E8	MKLN1_HUMAN;.;.	K	134;226	ENSP00000398094:E134K;ENSP00000323527:E226K	ENSP00000323527:E226K	E	+	1	0	MKLN1	130734705	1.000000	0.71417	0.858000	0.33744	0.950000	0.60333	9.785000	0.99042	1.560000	0.49568	0.650000	0.86243	GAA		0.353	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		A	131084165	G	A	131084165	3	1	61	1	0	0	0	0	1	0	0	0	9633	1059	37	1	731	1	MKLN1	7	131084165	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	726531	131084165	28054498	5591	13576										
MKLN1	4289	broad.mit.edu	37	chr7	131148084	131148084	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagggaagaaaatgttaGaaattcattctggatttatg	10	2	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:131148084G>T	ENST00000352689.6	+	13	1674	c.1634G>T	c.(1633-1635)aGa>aTa	p.R545I	MKLN1_ENST00000498778.1_3'UTR|MKLN1_ENST00000421797.2_Missense_Mutation_p.R453I	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	545					signal transduction (GO:0007165)	cytoplasm (GO:0005737)		p.R545I(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					GAAAATGTTAGAAATTCATTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	109	108					7																	131148084		2203	4299	6502	130798624	SO:0001583	missense	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1634G>T	7.37:g.131148084G>T	ENSP00000323527:p.Arg545Ile		130798624	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	37	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620864	0.87460	.	.	ENSG00000128585	ENST00000421797;ENST00000352689;ENST00000388758	T;T	0.73152	-0.72;-0.72	5.93	5.93	0.95920	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.74921	0.3780	L	0.33485	1.01	0.80722	D	1	B;D;P;D	0.61697	0.044;0.981;0.944;0.99	B;P;P;P	0.60886	0.017;0.491;0.497;0.88	T	0.68217	-0.5467	10	0.19590	T	0.45	-20.2923	19.3216	0.94243	0.0:0.0:1.0:0.0	.	545;522;453;35	Q9UL63;B4DG30;C9J7E8;F8W7E8	MKLN1_HUMAN;.;.;.	I	453;545;35	ENSP00000398094:R453I;ENSP00000323527:R545I	ENSP00000323527:R545I	R	+	2	0	MKLN1	130798624	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.444000	0.97578	2.818000	0.97014	0.591000	0.81541	AGA		0.358	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		T	131148084	G	T	131148084	3	4	61	1	0	0	0	0	1	0	0	0	9633	942	33	2	1717	2	MKLN1	7	131148084	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63919	131148084	27990579	5592	13577										
PLXNA4	91584	broad.mit.edu	37	chr7	131831322	131831322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacaccatcttgctcccccGgtccccctccttctggtctc	6	20	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:131831322G>A	ENST00000359827.3	-	28	5964	c.5002C>T	c.(5002-5004)Cgg>Tgg	p.R1668W	PLXNA4_ENST00000321063.4_Missense_Mutation_p.R1668W			Q9HCM2	PLXA4_HUMAN	plexin A4	1668					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R1668W(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTGCTCCCCCGGTCCCCCTCC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	7											202	216	211					7																	131831322		2182	4298	6480	131481862	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.5002C>T	7.37:g.131831322G>A	ENSP00000352882:p.Arg1668Trp		131481862	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.581281	0.86748	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.15952	2.38;2.38	5.8	4.89	0.63831	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.057652	0.64402	D	0.000001	T	0.49115	0.1538	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60031	-0.7342	10	0.87932	D	0	.	13.6924	0.62553	0.0:0.0:0.7194:0.2806	.	1668	Q9HCM2	PLXA4_HUMAN	W	1668	ENSP00000323194:R1668W;ENSP00000352882:R1668W	ENSP00000323194:R1668W	R	-	1	2	PLXNA4	131481862	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.520000	0.60524	1.405000	0.46838	0.561000	0.74099	CGG		0.572	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131831322	G	A	131831322	3	1	61	1	0	0	0	0	1	0	0	0	12153	1115	39	1	702	1	PLXNA4	7	131831322	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	683238	131831322	27307341	5593	13578										
PLXNA4	91584	broad.mit.edu	37	chr7	131844364	131844364	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggacctcggggctgttggCattgtctgggctgacacagc	16	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:131844364C>A	ENST00000359827.3	-	25	5490	c.4528G>T	c.(4528-4530)Gcc>Tcc	p.A1510S	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A1510S			Q9HCM2	PLXA4_HUMAN	plexin A4	1510					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.A1510S(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GGGCTGTTGGCATTGTCTGGG	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	7											217	222	220					7																	131844364		2189	4300	6489	131494904	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4528G>T	7.37:g.131844364C>A	ENSP00000352882:p.Ala1510Ser		131494904	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.160329	0.38119	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.10860	2.83;2.83	5.21	4.33	0.51752	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.264822	0.39909	N	0.001235	T	0.04907	0.0132	N	0.04297	-0.235	0.26339	N	0.977395	B	0.10296	0.003	B	0.08055	0.003	T	0.38866	-0.9641	10	0.12766	T	0.61	.	11.8895	0.52620	0.0:0.8541:0.0:0.1459	.	1510	Q9HCM2	PLXA4_HUMAN	S	1510	ENSP00000323194:A1510S;ENSP00000352882:A1510S	ENSP00000323194:A1510S	A	-	1	0	PLXNA4	131494904	0.998000	0.40836	0.900000	0.35374	0.993000	0.82548	3.793000	0.55484	1.185000	0.42971	0.650000	0.86243	GCC		0.527	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131844364	C	A	131844364	3	1	61	1	0	0	0	0	1	0	0	0	12153	710	25	2	1188	2	PLXNA4	7	131844364	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13042	131844364	27294299	5594	13579										
PLXNA4	91584	broad.mit.edu	37	chr7	131865380	131865380	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgatgaggttgggggactCgcagagcagctggacatctg	17	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:131865380C>T	ENST00000359827.3	-	19	4566	c.3604G>A	c.(3604-3606)Gag>Aag	p.E1202K	PLXNA4_ENST00000321063.4_Missense_Mutation_p.E1202K			Q9HCM2	PLXA4_HUMAN	plexin A4	1202	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.E1202K(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTGGGGGACTCGCAGAGCAGC	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	7											60	65	63					7																	131865380		2125	4249	6374	131515920	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3604G>A	7.37:g.131865380C>T	ENSP00000352882:p.Glu1202Lys		131515920	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755039	0.89843	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.76578	-1.03;-1.03	5.38	5.38	0.77491	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.88047	0.6332	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.85654	0.1284	10	0.25751	T	0.34	.	19.1282	0.93394	0.0:1.0:0.0:0.0	.	1202	Q9HCM2	PLXA4_HUMAN	K	1202	ENSP00000323194:E1202K;ENSP00000352882:E1202K	ENSP00000323194:E1202K	E	-	1	0	PLXNA4	131515920	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.792000	0.85828	2.551000	0.86045	0.561000	0.74099	GAG		0.617	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131865380	C	T	131865380	3	4	61	1	0	0	0	0	1	0	0	0	12153	893	31	1	2136	1	PLXNA4	7	131865380	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21016	131865380	27273283	5595	13580										
PLXNA4	91584	broad.mit.edu	37	chr7	132174090	132174090	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtgcccacaaaggccagAgagtggttcttgtagacata	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:132174090A>C	ENST00000359827.3	-	3	2294	c.1332T>G	c.(1330-1332)tcT>tcG	p.S444S	PLXNA4_ENST00000423507.2_Silent_p.S444S|PLXNA4_ENST00000321063.4_Silent_p.S444S|PLXNA4_ENST00000378539.5_Silent_p.S444S			Q9HCM2	PLXA4_HUMAN	plexin A4	444	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.S444S(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CAAAGGCCAGAGAGTGGTTCT	0.542																																																2	Substitution - coding silent(2)	large_intestine(2)	7											125	102	109					7																	132174090		2203	4300	6503	131824630	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1332T>G	7.37:g.132174090A>C			131824630	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.542	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	132174090	A	C	132174090	2	2	61	1	0	0	0	0	0	0	0	1	12153	291	11	4		4	PLXNA4	7	132174090	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	308710	132174090	26964573	5596	13581										
PLXNA4	91584	broad.mit.edu	37	chr7	132192420	132192420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccagggatttcattttccGcttctggcccttggagaaga	10	10	2	2	rs115629766	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:132192420G>A	ENST00000359827.3	-	2	1995	c.1033C>T	c.(1033-1035)Cgg>Tgg	p.R345W	PLXNA4_ENST00000423507.2_Missense_Mutation_p.R345W|PLXNA4_ENST00000321063.4_Missense_Mutation_p.R345W|PLXNA4_ENST00000378539.5_Missense_Mutation_p.R345W			Q9HCM2	PLXA4_HUMAN	plexin A4	345	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R345W(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTCATTTTCCGCTTCTGGCCC	0.562													G|||	12	0.00239617	0.0083	0	5008	,	,		21559	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	7						G	TRP/ARG,TRP/ARG,TRP/ARG	17,4389	23.3+/-48.9	0,17,2186	73	70	71		1033,1033,1033	3	1	7	dbSNP_133	71	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	101,101,101	0,18,6485	AA,AG,GG		0.0116,0.3858,0.1384	probably-damaging,probably-damaging,probably-damaging	345/493,345/1895,345/523	132192420	18,12988	2203	4300	6503	131842960	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1033C>T	7.37:g.132192420G>A	ENSP00000352882:p.Arg345Trp		131842960	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	G	16.77	3.214054	0.58452	0.003858	1.16E-4	ENSG00000221866	ENST00000321063;ENST00000359827;ENST00000423507;ENST00000378539	T;T;T;T	0.04809	3.55;3.55;3.55;3.55	5.96	3.03	0.35002	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	U	0.000004	T	0.11153	0.0272	L	0.51422	1.61	0.54753	D	0.999989	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.74348	0.972;0.983;0.948	T	0.00591	-1.1655	10	0.59425	D	0.04	.	15.5096	0.75769	0.0:0.0:0.4027:0.5973	.	345;345;345	Q9HCM2-2;A4D1N6;Q9HCM2	.;.;PLXA4_HUMAN	W	345	ENSP00000323194:R345W;ENSP00000352882:R345W;ENSP00000392772:R345W;ENSP00000367800:R345W	ENSP00000323194:R345W	R	-	1	2	PLXNA4	131842960	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.235000	0.32671	0.804000	0.34136	0.655000	0.94253	CGG		0.562	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	132192420	G	A	132192420	3	1	61	1	0	0	0	0	1	0	0	0	12153	1086	38	1	5089	1	PLXNA4	7	132192420	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18330	132192420	26946243	5597	13582										
PLXNA4	91584	broad.mit.edu	37	chr7	132193345	132193345	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgacaaatgaccgctgCttctgggacagcggggctgg	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:132193345C>T	ENST00000359827.3	-	2	1070	c.108G>A	c.(106-108)aaG>aaA	p.K36K	PLXNA4_ENST00000423507.2_Silent_p.K36K|PLXNA4_ENST00000321063.4_Silent_p.K36K|PLXNA4_ENST00000378539.5_Silent_p.K36K			Q9HCM2	PLXA4_HUMAN	plexin A4	36	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.K36K(3)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ATGACCGCTGCTTCTGGGACA	0.607																																																3	Substitution - coding silent(3)	large_intestine(3)	7											33	32	32					7																	132193345		2203	4300	6503	131843885	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.108G>A	7.37:g.132193345C>T			131843885	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.607	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	132193345	C	T	132193345	2	4	61	1	0	0	0	0	0	0	0	1	12153	796	28	3		3	PLXNA4	7	132193345	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	925	132193345	26945318	5598	13583										
EXOC4	60412	broad.mit.edu	37	chr7	133041122	133041122	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacatcaaggaagatttaGaattggatccagaggaaaac	11	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:133041122G>T	ENST00000253861.4	+	6	831	c.802G>T	c.(802-804)Gaa>Taa	p.E268*	EXOC4_ENST00000539845.1_Nonsense_Mutation_p.E167*|EXOC4_ENST00000393161.2_Nonsense_Mutation_p.E268*	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	268					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)	p.E268*(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GGAAGATTTAGAATTGGATCC	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											66	68	67					7																	133041122		2203	4300	6503	132691662	SO:0001587	stop_gained	60412			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.802G>T	7.37:g.133041122G>T	ENSP00000253861:p.Glu268*		132691662	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Nonsense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	42	9.474326	0.99181	.	.	ENSG00000131558	ENST00000253861;ENST00000393161;ENST00000539845	.	.	.	5.51	4.6	0.57074	.	0.591478	0.17700	N	0.164958	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	16.422	0.83766	0.0:0.1317:0.8683:0.0	.	.	.	.	X	268;268;167	.	ENSP00000253861:E268X	E	+	1	0	EXOC4	132691662	1.000000	0.71417	0.897000	0.35233	0.974000	0.67602	7.210000	0.77924	1.400000	0.46741	0.650000	0.86243	GAA		0.388	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		T	133041122	G	T	133041122	4	4	61	1	0	0	0	0	0	1	0	0	5319	943	33	2	824	2	EXOC4	7	133041122	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	847777	133041122	26097541	5599	13584										
EXOC4	60412	broad.mit.edu	37	chr7	133682251	133682251	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttacctttcagtgctttCtcctgctcaagacagccaca	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:133682251C>A	ENST00000253861.4	+	15	2242	c.2213C>A	c.(2212-2214)tCt>tAt	p.S738Y	EXOC4_ENST00000541309.1_Missense_Mutation_p.S26Y|EXOC4_ENST00000545148.1_Missense_Mutation_p.S348Y|EXOC4_ENST00000539845.1_Missense_Mutation_p.S637Y	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	738					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)	p.S738Y(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				TCAGTGCTTTCTCCTGCTCAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											112	94	100					7																	133682251		2203	4300	6503	133332791	SO:0001583	missense	60412			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2213C>A	7.37:g.133682251C>A	ENSP00000253861:p.Ser738Tyr		133332791	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.751246	0.49257	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.43	5.43	0.79202	.	0.055443	0.85682	D	0.000000	T	0.56396	0.1982	L	0.47716	1.5	0.47374	D	0.999402	P;B;P	0.45283	0.846;0.061;0.855	B;B;B	0.41813	0.367;0.047;0.135	T	0.61407	-0.7069	9	0.59425	D	0.04	.	18.8686	0.92303	0.0:1.0:0.0:0.0	.	270;348;738	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	Y	738;357;637;348;26	.	ENSP00000253861:S738Y	S	+	2	0	EXOC4	133332791	0.996000	0.38824	0.998000	0.56505	0.699000	0.40488	2.694000	0.47035	2.549000	0.85964	0.655000	0.94253	TCT		0.418	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		A	133682251	C	A	133682251	3	1	61	1	0	0	0	0	1	0	0	0	5319	913	32	2	2280	2	EXOC4	7	133682251	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	641129	133682251	25456412	5600	13585										
LRGUK	136332	broad.mit.edu	37	chr7	133842872	133842872	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaataagatcacgacaaTtaatggcttaaacaagttac	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:133842872T>G	ENST00000285928.2	+	6	824	c.755T>G	c.(754-756)aTt>aGt	p.I252S		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	252						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)	p.I252S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ATCACGACAATTAATGGCTTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	7											135	119	124					7																	133842872		2203	4300	6503	133493412	SO:0001583	missense	136332			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.755T>G	7.37:g.133842872T>G	ENSP00000285928:p.Ile252Ser		133493412	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397425	0.62177	.	.	ENSG00000155530	ENST00000285928	T	0.32023	1.47	5.47	5.47	0.80525	.	0.061993	0.64402	D	0.000007	T	0.58090	0.2098	M	0.91090	3.175	0.19945	N	0.999945	D	0.56287	0.975	P	0.56163	0.793	T	0.62296	-0.6884	10	0.87932	D	0	-13.5898	14.535	0.67953	0.0:0.0:0.0:1.0	.	252	Q96M69	LRGUK_HUMAN	S	252	ENSP00000285928:I252S	ENSP00000285928:I252S	I	+	2	0	LRGUK	133493412	0.933000	0.31639	0.005000	0.12908	0.002000	0.02628	3.840000	0.55843	2.079000	0.62486	0.455000	0.32223	ATT		0.343	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		G	133842872	T	G	133842872	3	3	61	1	0	0	0	0	1	0	0	0	8972	1493	52	4	777	4	LRGUK	7	133842872	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160621	133842872	25295791	5601	13586										
AKR1B1	231	broad.mit.edu	37	chr7	134132059	134132059	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagatcttaccttaaagttCtcagcaatgcgttctggtgt	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:134132059C>A	ENST00000285930.4	-	8	895	c.816G>T	c.(814-816)gaG>gaT	p.E272D	AKR1B1_ENST00000489022.1_5'Flank	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	272				IAE -> EAA (in Ref. 16; AA sequence). {ECO:0000305}.	C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)	p.E272D(1)		kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	CCTTAAAGTTCTCAGCAATGC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											159	114	129					7																	134132059		2203	4300	6503	133782599	SO:0001583	missense	231			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.816G>T	7.37:g.134132059C>A	ENSP00000285930:p.Glu272Asp		133782599	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Missense_Mutation	SNP	ENST00000285930.4	37	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.647699	0.47258	.	.	ENSG00000085662	ENST00000285930	T	0.25912	1.77	5.12	4.24	0.50183	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.090641	0.85682	D	0.000000	T	0.26304	0.0642	L	0.52905	1.665	0.50171	D	0.999857	B	0.19200	0.034	B	0.21917	0.037	T	0.06972	-1.0797	10	0.66056	D	0.02	.	11.2447	0.48990	0.0:0.915:0.0:0.085	.	272	P15121	ALDR_HUMAN	D	272	ENSP00000285930:E272D	ENSP00000285930:E272D	E	-	3	2	AKR1B1	133782599	0.998000	0.40836	1.000000	0.80357	0.922000	0.55478	0.694000	0.25512	1.289000	0.44618	0.561000	0.74099	GAG		0.572	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		A	134132059	C	A	134132059	3	1	61	1	0	0	0	0	1	0	0	0	466	912	32	2	146	2	AKR1B1	7	134132059	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289187	134132059	25006604	5602	13587										
CALD1	800	broad.mit.edu	37	chr7	134618822	134618822	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcagacagctgtcctaaaGaaacaggtacagtaaacatt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:134618822G>A	ENST00000361675.2	+	5	1531	c.1302G>A	c.(1300-1302)aaG>aaA	p.K434K	CALD1_ENST00000361388.2_Intron|CALD1_ENST00000393118.2_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000422748.1_Intron|CALD1_ENST00000361901.2_Intron			Q05682	CALD1_HUMAN	caldesmon 1	434					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)	p.K434K(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						CTGTCCTAAAGAAACAGGTAC	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	7											110	115	113					7																	134618822		2203	4300	6503	134269362	SO:0001819	synonymous_variant	800			M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1302G>A	7.37:g.134618822G>A			134269362	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Silent	SNP	ENST00000361675.2	37	CCDS5835.1																																																																																				0.383	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		A	134618822	G	A	134618822	2	1	61	1	0	0	0	0	0	0	0	1	2587	933	33	3		3	CALD1	7	134618822	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	486763	134618822	24519841	5603	13588										
CALD1	800	broad.mit.edu	37	chr7	134632379	134632379	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaccgagagcgaagagttCgagaagctcaaacagaagca	13	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:134632379C>T	ENST00000361675.2	+	8	1882	c.1653C>T	c.(1651-1653)ttC>ttT	p.F551F	CALD1_ENST00000361388.2_Silent_p.F322F|CALD1_ENST00000393118.2_Silent_p.F316F|CALD1_ENST00000495522.1_Silent_p.F316F|CALD1_ENST00000543443.1_Silent_p.F301F|CALD1_ENST00000424922.1_Silent_p.F290F|CALD1_ENST00000417172.1_Silent_p.F296F|CALD1_ENST00000422748.1_Silent_p.F322F|CALD1_ENST00000361901.2_Silent_p.F296F			Q05682	CALD1_HUMAN	caldesmon 1	551					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)	p.F551F(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GCGAAGAGTTCGAGAAGCTCA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	7											29	29	29					7																	134632379		2186	4279	6465	134282919	SO:0001819	synonymous_variant	800			M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1653C>T	7.37:g.134632379C>T			134282919	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Silent	SNP	ENST00000361675.2	37	CCDS5835.1																																																																																				0.607	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		T	134632379	C	T	134632379	2	4	61	1	0	0	0	0	0	0	0	1	2587	883	31	1		1	CALD1	7	134632379	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13557	134632379	24506284	5604	13589										
WDR91	29062	broad.mit.edu	37	chr7	134889139	134889139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaggacaggaagcccacacGaggtgactgggagagggagg	19	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:134889139G>A	ENST00000354475.4	-	6	803	c.772C>T	c.(772-774)Cgt>Tgt	p.R258C	AC009542.2_ENST00000595902.1_RNA|WDR91_ENST00000423565.1_Missense_Mutation_p.R223C|WDR91_ENST00000485942.1_5'UTR|WDR91_ENST00000344400.5_Missense_Mutation_p.R258C	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	258								p.R258C(2)		breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						AAGCCCACACGAGGTGACTGG	0.582																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	7											72	57	62					7																	134889139		2203	4300	6503	134539679	SO:0001583	missense	29062			AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.772C>T	7.37:g.134889139G>A	ENSP00000346466:p.Arg258Cys		134539679	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.730242	0.69074	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.66460	1.36;-0.21;0.37	5.4	4.43	0.53597	.	0.358038	0.29192	N	0.012878	T	0.59676	0.2211	L	0.27053	0.805	0.09310	N	0.999995	D	0.63880	0.993	P	0.46885	0.53	T	0.59490	-0.7445	10	0.72032	D	0.01	-1.775	15.2136	0.73247	0.0:0.0:0.8504:0.1496	.	258	A4D1P6	WDR91_HUMAN	C	258;258;223	ENSP00000340877:R258C;ENSP00000346466:R258C;ENSP00000392555:R223C	ENSP00000340877:R258C	R	-	1	0	WDR91	134539679	0.962000	0.33011	0.421000	0.26609	0.949000	0.60115	3.733000	0.55029	2.548000	0.85928	0.655000	0.94253	CGT		0.582	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134889139	G	A	134889139	3	1	61	1	0	0	0	0	1	0	0	0	17378	1058	37	1	1511	1	WDR91	7	134889139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	256760	134889139	24249524	5605	13590										
NUP205	23165	broad.mit.edu	37	chr7	135255879	135255879	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctatggggtccttacaaaGacatttggcataaagtggga	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:135255879G>T	ENST00000285968.6	+	2	81	c.55G>T	c.(55-57)Gac>Tac	p.D19Y	NUP205_ENST00000489493.1_3'UTR|NUP205_ENST00000440390.2_5'UTR	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	19					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.D19Y(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TCCTTACAAAGACATTTGGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											81	84	83					7																	135255879		2203	4300	6503	134906419	SO:0001583	missense	23165			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.55G>T	7.37:g.135255879G>T	ENSP00000285968:p.Asp19Tyr		134906419	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.485159	0.84854	.	.	ENSG00000155561	ENST00000285968	T	0.33654	1.4	5.21	5.21	0.72293	.	0.049889	0.85682	D	0.000000	T	0.51669	0.1688	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.54563	-0.8275	10	0.87932	D	0	-9.6087	18.7467	0.91795	0.0:0.0:1.0:0.0	.	19	Q92621	NU205_HUMAN	Y	19	ENSP00000285968:D19Y	ENSP00000285968:D19Y	D	+	1	0	NUP205	134906419	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.490000	0.97952	2.446000	0.82766	0.591000	0.81541	GAC		0.373	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			T	135255879	G	T	135255879	3	4	61	1	0	0	0	0	1	0	0	0	10790	942	33	2	61	2	NUP205	7	135255879	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	366740	135255879	23882784	5606	13591										
SLC13A4	26266	broad.mit.edu	37	chr7	135390916	135390916	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttggagttgcccgccacGagctgctcgtcctcagcact	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:135390916G>A	ENST00000354042.4	-	4	1187	c.498C>T	c.(496-498)ctC>ctT	p.L166L	RP11-644N4.1_ENST00000609370.1_RNA	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	166					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.L166L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						TGCCCGCCACGAGCTGCTCGT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	7											106	90	95					7																	135390916		2203	4300	6503	135041456	SO:0001819	synonymous_variant	26266			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.498C>T	7.37:g.135390916G>A			135041456	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																				0.612	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		A	135390916	G	A	135390916	2	1	61	1	0	0	0	0	0	0	0	1	14431	1045	37	1		1	SLC13A4	7	135390916	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135037	135390916	23747747	5607	13592										
CHRM2	1129	broad.mit.edu	37	chr7	136699817	136699817	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattcagcttggcctgtgctGaccttatcataggtgttttc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:136699817G>T	ENST00000445907.2	+	3	733	c.205G>T	c.(205-207)Gac>Tac	p.D69Y	hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.D69Y|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.D69Y|CHRM2_ENST00000453373.1_Missense_Mutation_p.D69Y|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.D69Y|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.D69Y	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	69					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.D69Y(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GGCCTGTGCTGACCTTATCAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											225	192	203					7																	136699817		2203	4300	6503	136350357	SO:0001583	missense	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.205G>T	7.37:g.136699817G>T	ENSP00000399745:p.Asp69Tyr		136350357	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783528	0.70222	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	5.4	5.4	0.78164	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97294	0.9115	H	0.99143	4.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99019	1.0817	10	0.87932	D	0	-5.2158	19.2407	0.93881	0.0:0.0:1.0:0.0	.	69	P08172	ACM2_HUMAN	Y	69	ENSP00000399745:D69Y;ENSP00000415386:D69Y;ENSP00000319984:D69Y;ENSP00000380733:D69Y;ENSP00000384937:D69Y;ENSP00000384401:D69Y	ENSP00000319984:D69Y	D	+	1	0	CHRM2	136350357	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.766000	0.98957	2.546000	0.85860	0.644000	0.83932	GAC		0.473	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136699817	G	T	136699817	3	4	61	1	0	0	0	0	1	0	0	0	3383	1290	45	2	207	2	CHRM2	7	136699817	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1308901	136699817	22438846	5608	13593										
CHRM2	1129	broad.mit.edu	37	chr7	136700369	136700369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacatgcccagcagtgacGatggcctggagcacaacaaa	10	12	0	1	rs140681489		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:136700369G>A	ENST00000445907.2	+	3	1285	c.757G>A	c.(757-759)Gat>Aat	p.D253N	hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.D253N|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.D253N|CHRM2_ENST00000453373.1_Missense_Mutation_p.D253N|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.D253N|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.D253N	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	253					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.D253N(2)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAGCAGTGACGATGGCCTGGA	0.512													G|||	1	0.000199681	8e-04	0	5008	,	,		19435	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	7						G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	3,4403	8.1+/-20.4	0,3,2200	57	59	59		757,757,757,757,757,757,757,757	4.5	0.4	7	dbSNP_134	59	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense	CHRM2	NM_000739.2,NM_001006626.1,NM_001006627.1,NM_001006628.1,NM_001006629.1,NM_001006630.1,NM_001006631.1,NM_001006632.1	23,23,23,23,23,23,23,23	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign,benign,benign,benign,benign,benign,benign,benign	253/467,253/467,253/467,253/467,253/467,253/467,253/467,253/467	136700369	3,13003	2203	4300	6503	136350909	SO:0001583	missense	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.757G>A	7.37:g.136700369G>A	ENSP00000399745:p.Asp253Asn		136350909	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	3.934	-0.015654	0.07681	6.81E-4	0.0	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11	5.4	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.411149	0.25795	N	0.028256	T	0.42471	0.1204	N	0.25485	0.75	0.38338	D	0.94398	B	0.26483	0.15	B	0.22753	0.041	T	0.34700	-0.9818	10	0.16896	T	0.51	-0.2836	13.8766	0.63655	0.0731:0.0:0.9269:0.0	.	253	P08172	ACM2_HUMAN	N	253	ENSP00000399745:D253N;ENSP00000415386:D253N;ENSP00000319984:D253N;ENSP00000380733:D253N;ENSP00000384937:D253N;ENSP00000384401:D253N	ENSP00000319984:D253N	D	+	1	0	CHRM2	136350909	0.225000	0.23685	0.438000	0.26821	0.326000	0.28443	2.051000	0.41307	1.290000	0.44636	0.655000	0.94253	GAT		0.512	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			A	136700369	G	A	136700369	3	1	61	1	0	0	0	0	1	0	0	0	3383	1058	37	1	759	1	CHRM2	7	136700369	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	552	136700369	22438294	5609	13594										
PTN	5764	broad.mit.edu	37	chr7	136912820	136912820	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttcttcttcttagattCtgctgtgattacaaaaaaga	5	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:136912820C>T	ENST00000348225.2	-	5	881	c.454G>A	c.(454-456)Gaa>Aaa	p.E152K	PTN_ENST00000393083.2_3'UTR	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	152					bone mineralization (GO:0030282)|learning (GO:0007612)|negative regulation of catalytic activity (GO:0043086)|nervous system development (GO:0007399)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	heparin binding (GO:0008201)|protein phosphatase inhibitor activity (GO:0004864)	p.E152K(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23						TTCTTAGATTCTGCTGTGATT	0.358																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7											179	157	164					7																	136912820		2202	4299	6501	136563360	SO:0001583	missense	5764			M57399	CCDS5844.1	7q33	2014-01-30	2008-07-31		ENSG00000105894	ENSG00000105894		"Endogenous ligands"	9630	protein-coding gene	gene with protein product	"heparin binding growth factor 8"	162095	"neurite growth-promoting factor 1"	NEGF1		1457401, 1768439	Standard	NM_002825		Approved	HBNF, HBGF8	uc003vtq.2	P21246	OTTHUMG00000155709	ENST00000348225.2:c.454G>A	7.37:g.136912820C>T	ENSP00000341170:p.Glu152Lys		136563360	Q5U0B0|Q6ICQ5|Q9UCC6	Missense_Mutation	SNP	ENST00000348225.2	37	CCDS5844.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315472	0.23908	.	.	ENSG00000105894	ENST00000348225	.	.	.	5.79	5.79	0.91817	Midkine heparin-binding growth factor, C-terminal (1);	0.109566	0.64402	D	0.000009	T	0.60051	0.2239	N	0.14661	0.345	0.80722	D	1	P	0.51057	0.941	D	0.71414	0.973	T	0.55023	-0.8205	9	0.18276	T	0.48	-11.1496	17.1805	0.86853	0.0:1.0:0.0:0.0	.	152	P21246	PTN_HUMAN	K	152	.	ENSP00000341170:E152K	E	-	1	0	PTN	136563360	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	4.390000	0.59646	2.750000	0.94351	0.561000	0.74099	GAA		0.358	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825		T	136912820	C	T	136912820	3	4	61	1	0	0	0	0	1	0	0	0	12803	922	32	3	56	3	PTN	7	136912820	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212451	136912820	22225843	5610	13595										
DGKI	9162	broad.mit.edu	37	chr7	137237203	137237203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccgaatcatagctggggCcaacctacagggctccccat	10	14	1	0	rs370315489		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:137237203C>T	ENST00000288490.5	-	20	2059	c.2059G>A	c.(2059-2061)Gcc>Acc	p.A687T	DGKI_ENST00000446122.1_Missense_Mutation_p.A687T|DGKI_ENST00000424189.2_Missense_Mutation_p.A687T|DGKI_ENST00000453654.2_Missense_Mutation_p.A387T	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	687					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.A687T(1)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						ATAGCTGGGGCCAACCTACAG	0.517													C|||	1	0.000199681	8e-04	0	5008	,	,		18872	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	150	133	139		2059	5.4	1	7		139	0,8600		0,0,4300	no	missense	DGKI	NM_004717.2	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	687/1066	137237203	1,13005	2203	4300	6503	136887743	SO:0001583	missense	9162			AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2059G>A	7.37:g.137237203C>T	ENSP00000288490:p.Ala687Thr		136887743	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026601	0.93518	2.27E-4	0.0	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.39406	1.08;1.08;1.08	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.46367	0.1389	M	0.65498	2.005	0.80722	D	1	P;P	0.42010	0.564;0.768	B;B	0.39379	0.11;0.298	T	0.44544	-0.9321	10	0.36615	T	0.2	.	19.6391	0.95749	0.0:1.0:0.0:0.0	.	387;687	E9PFX6;O75912	.;DGKI_HUMAN	T	387;635;687;687;687	ENSP00000392161:A387T;ENSP00000288490:A687T;ENSP00000399131:A687T	ENSP00000288490:A687T	A	-	1	0	DGKI	136887743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.715000	0.92844	0.655000	0.94253	GCC		0.517	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137237203	C	T	137237203	3	4	61	1	0	0	0	0	1	0	0	0	4482	739	26	3	1198	3	DGKI	7	137237203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	324383	137237203	21901460	5611	13596										
CREB3L2	64764	broad.mit.edu	37	chr7	137588741	137588741	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgtattctttcttctttCtcctactttcctgagcagaa	4	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:137588741C>A	ENST00000330387.6	-	7	1289	c.938G>T	c.(937-939)aGa>aTa	p.R313I	CREB3L2_ENST00000456390.1_Missense_Mutation_p.R313I	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	313	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.R313I(1)	FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TTTCTTCTTTCTCCTACTTTC	0.468			T	FUS	fibromyxoid sarcoma						OREG0018352	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	1	Substitution - Missense(1)	large_intestine(1)	7											113	107	109					7																	137588741		2203	4300	6503	137239281	SO:0001583	missense	64764			AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"basic leucine zipper proteins"	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.938G>T	7.37:g.137588741C>A	ENSP00000329140:p.Arg313Ile	1634	137239281	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	37	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	C	34	5.393673	0.96009	.	.	ENSG00000182158	ENST00000330387;ENST00000456390	T;T	0.77098	-1.07;-1.07	5.32	5.32	0.75619	Basic-leucine zipper (bZIP) transcription factor (3);Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.91304	0.7258	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.991;0.998	D	0.93276	0.6656	10	0.87932	D	0	0.1841	17.9295	0.88992	0.0:1.0:0.0:0.0	.	313;313	Q70SY1-2;Q70SY1	.;CR3L2_HUMAN	I	313	ENSP00000329140:R313I;ENSP00000403550:R313I	ENSP00000329140:R313I	R	-	2	0	CREB3L2	137239281	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.076000	0.76806	2.625000	0.88918	0.655000	0.94253	AGA		0.468	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071		A	137588741	C	A	137588741	3	1	61	1	0	0	0	0	1	0	0	0	3863	913	32	2	648	2	CREB3L2	7	137588741	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	351538	137588741	21549922	5612	13597										
TRIM24	8805	broad.mit.edu	37	chr7	138262238	138262238	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtcatgctggagccaattCgaataaaacaagaaaacagt	9	7	1	1	rs201997143		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138262238C>T	ENST00000343526.4	+	14	2376	c.2161C>T	c.(2161-2163)Cga>Tga	p.R721*	TRIM24_ENST00000415680.2_Nonsense_Mutation_p.R687*			O15164	TIF1A_HUMAN	tripartite motif containing 24	721					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R721*(2)|p.R687*(2)		breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						GGAGCCAATTCGAATAAAACA	0.423																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)											4	Substitution - Nonsense(4)	large_intestine(4)	7											87	85	86					7																	138262238		2203	4300	6503	137912778	SO:0001587	stop_gained	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.2161C>T	7.37:g.138262238C>T	ENSP00000340507:p.Arg721*		137912778	A4D1R7|A4D1R8|O95854	Nonsense_Mutation	SNP	ENST00000343526.4	37	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	C	39	7.705403	0.98444	.	.	ENSG00000122779	ENST00000343526;ENST00000536822;ENST00000415680	.	.	.	5.67	4.71	0.59529	.	0.102507	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-15.1556	13.2383	0.59982	0.2643:0.7357:0.0:0.0	.	.	.	.	X	721;632;687	.	ENSP00000340507:R721X	R	+	1	2	TRIM24	137912778	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.972000	0.49256	2.661000	0.90470	0.460000	0.39030	CGA		0.423	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		T	138262238	C	T	138262238	4	4	61	1	0	0	0	0	0	1	0	0	16538	876	31	1	2215	1	TRIM24	7	138262238	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673497	138262238	20876425	5613	13598										
ATP6V0A4	50617	broad.mit.edu	37	chr7	138447176	138447176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatcagctaaattggtttCcgtctgaaagtcaaagcact	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138447176C>T	ENST00000310018.2	-	7	703	c.421G>A	c.(421-423)Gaa>Aaa	p.E141K	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.E141K|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.E141K|ATP6V0A4_ENST00000483139.1_5'UTR	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	141					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.E141K(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						AAATTGGTTTCCGTCTGAAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											98	91	93					7																	138447176		2203	4300	6503	138097716	SO:0001583	missense	50617			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.421G>A	7.37:g.138447176C>T	ENSP00000308122:p.Glu141Lys		138097716	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447856	0.63178	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.85861	-2.04;-2.04;-2.04	6.17	6.17	0.99709	.	0.341865	0.27491	N	0.019127	D	0.83746	0.5321	L	0.59436	1.845	0.54753	D	0.999981	B	0.16802	0.019	B	0.19666	0.026	T	0.77253	-0.2656	10	0.16420	T	0.52	-19.0985	19.8676	0.96824	0.0:1.0:0.0:0.0	.	141	Q9HBG4	VPP4_HUMAN	K	141	ENSP00000308122:E141K;ENSP00000376774:E141K;ENSP00000253856:E141K	ENSP00000308122:E141K	E	-	1	0	ATP6V0A4	138097716	0.998000	0.40836	0.997000	0.53966	0.968000	0.65278	4.875000	0.63072	2.941000	0.99782	0.655000	0.94253	GAA		0.393	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		T	138447176	C	T	138447176	3	4	61	1	0	0	0	0	1	0	0	0	1171	864	30	3	2165	3	ATP6V0A4	7	138447176	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	184938	138447176	20691487	5614	13599										
ATP6V0A4	50617	broad.mit.edu	37	chr7	138455976	138455976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaacacatctcctcgcttCgaaacacagacaccatcttg	4	15	2	1	rs147512254		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138455976C>T	ENST00000310018.2	-	3	299	c.17G>A	c.(16-18)cGa>cAa	p.R6Q	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.R6Q|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.R6Q|ATP6V0A4_ENST00000483139.1_5'UTR	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	6					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.R6Q(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						CTCCTCGCTTCGAAACACAGA	0.433													C|||	1	0.000199681	8e-04	0	5008	,	,		16732	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7						C	GLN/ARG,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	147	144	145		17,17,17	4.8	1	7	dbSNP_134	145	0,8600		0,0,4300	yes	missense,missense,missense	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	43,43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging,probably-damaging	6/841,6/841,6/841	138455976	2,13004	2203	4300	6503	138106516	SO:0001583	missense	50617			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.17G>A	7.37:g.138455976C>T	ENSP00000308122:p.Arg6Gln		138106516	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	33	5.243612	0.95272	4.54E-4	0.0	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.91351	-2.83;-2.83;-2.83	4.76	4.76	0.60689	.	0.000000	0.64402	D	0.000017	D	0.97353	0.9134	H	0.98507	4.25	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.99010	1.0814	10	0.87932	D	0	-15.7712	16.9469	0.86232	0.0:1.0:0.0:0.0	.	6	Q9HBG4	VPP4_HUMAN	Q	6	ENSP00000308122:R6Q;ENSP00000376774:R6Q;ENSP00000253856:R6Q	ENSP00000308122:R6Q	R	-	2	0	ATP6V0A4	138106516	1.000000	0.71417	0.992000	0.48379	0.951000	0.60555	7.446000	0.80609	2.454000	0.82982	0.557000	0.71058	CGA		0.433	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		T	138455976	C	T	138455976	3	4	61	1	0	0	0	0	1	0	0	0	1171	884	31	1	2585	1	ATP6V0A4	7	138455976	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8800	138455976	20682687	5615	13600										
KIAA1549	57670	broad.mit.edu	37	chr7	138566238	138566238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagaggtcctggcagtggCgctggctcatgaataatcaa	12	9	3	2	rs377023001		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138566238C>T	ENST00000422774.1	-	11	4173	c.4125G>A	c.(4123-4125)gcG>gcA	p.A1375A	KIAA1549_ENST00000440172.1_Silent_p.A1375A|KIAA1549_ENST00000242365.4_Silent_p.A1325A			Q9HCM3	K1549_HUMAN	KIAA1549	1375						integral component of membrane (GO:0016021)		p.A1375A(1)|p.A1325A(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CTGGCAGTGGCGCTGGCTCAT	0.507			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	2	Substitution - coding silent(2)	large_intestine(2)	7						C	,	1,4167		0,1,2083	116	121	119		4125,4125	-11.5	0	7		119	0,8434		0,0,4217	no	coding-synonymous,coding-synonymous	KIAA1549	NM_001164665.1,NM_020910.2	,	0,1,6300	TT,TC,CC		0.0,0.024,0.0079	,	1375/1951,1375/1935	138566238	1,12601	2084	4217	6301	138216778	SO:0001819	synonymous_variant	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4125G>A	7.37:g.138566238C>T			138216778	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																				0.507	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138566238	C	T	138566238	2	4	61	1	0	0	0	0	0	0	0	1	8265	755	27	1		1	KIAA1549	7	138566238	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110262	138566238	20572425	5616	13601										
KIAA1549	57670	broad.mit.edu	37	chr7	138566325	138566325	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcccttcacactagggatCtgcagctgaaacatacacac	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138566325C>A	ENST00000422774.1	-	11	4086	c.4038G>T	c.(4036-4038)caG>caT	p.Q1346H	KIAA1549_ENST00000440172.1_Missense_Mutation_p.Q1346H|KIAA1549_ENST00000242365.4_Missense_Mutation_p.Q1296H			Q9HCM3	K1549_HUMAN	KIAA1549	1346						integral component of membrane (GO:0016021)		p.Q1296H(1)|p.Q1346H(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CACTAGGGATCTGCAGCTGAA	0.478			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	2	Substitution - Missense(2)	large_intestine(2)	7											53	55	54					7																	138566325		2056	4206	6262	138216865	SO:0001583	missense	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4038G>T	7.37:g.138566325C>A	ENSP00000416040:p.Gln1346His		138216865	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332628	0.81801	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.28895	1.59;1.59;1.61	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.53045	0.1772	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.998	T	0.53906	-0.8372	10	0.87932	D	0	.	12.8586	0.57901	0.0:0.9217:0.0:0.0783	.	1346;130;1346;130	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	H	1346;1296;1346	ENSP00000406661:Q1346H;ENSP00000242365:Q1296H;ENSP00000416040:Q1346H	ENSP00000242365:Q1296H	Q	-	3	2	KIAA1549	138216865	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.577000	0.60922	2.716000	0.92895	0.655000	0.94253	CAG		0.478	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138566325	C	A	138566325	3	1	61	1	0	0	0	0	1	0	0	0	8265	912	32	2	1854	2	KIAA1549	7	138566325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87	138566325	20572338	5617	13602										
KIAA1549	57670	broad.mit.edu	37	chr7	138603353	138603353	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcacagtggggtatgttCttggagagatggtttcttct	13	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138603353C>A	ENST00000422774.1	-	2	1067	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	KIAA1549_ENST00000440172.1_Missense_Mutation_p.R340I|KIAA1549_ENST00000242365.4_Missense_Mutation_p.R290I			Q9HCM3	K1549_HUMAN	KIAA1549	340						integral component of membrane (GO:0016021)		p.R290I(1)|p.R340I(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GGGGTATGTTCTTGGAGAGAT	0.507			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	2	Substitution - Missense(2)	large_intestine(2)	7											200	210	207					7																	138603353		2144	4253	6397	138253893	SO:0001583	missense	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1019G>T	7.37:g.138603353C>A	ENSP00000416040:p.Arg340Ile		138253893	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.778393	0.49786	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.27256	1.68;1.69;1.68	4.42	1.48	0.22813	.	1.027140	0.07759	N	0.949804	T	0.21550	0.0519	N	0.24115	0.695	0.09310	N	1	P;P	0.47677	0.838;0.899	B;P	0.48141	0.364;0.568	T	0.18555	-1.0333	10	0.36615	T	0.2	.	5.5938	0.17315	0.0:0.6283:0.186:0.1857	.	340;340	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	I	340;290;340	ENSP00000406661:R340I;ENSP00000242365:R290I;ENSP00000416040:R340I	ENSP00000242365:R290I	R	-	2	0	KIAA1549	138253893	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	0.312000	0.19397	0.455000	0.26910	0.555000	0.69702	AGA		0.507	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138603353	C	A	138603353	3	1	61	1	0	0	0	0	1	0	0	0	8265	913	32	2	4909	2	KIAA1549	7	138603353	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37028	138603353	20535310	5618	13603										
KIAA1549	57670	broad.mit.edu	37	chr7	138603675	138603675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtgcgaaaagctgaccGaaaggtgtggaaatgactgg	16	5	0	3	rs369822469		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138603675G>A	ENST00000422774.1	-	2	745	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	KIAA1549_ENST00000440172.1_Missense_Mutation_p.R233W|KIAA1549_ENST00000242365.4_Missense_Mutation_p.R183W			Q9HCM3	K1549_HUMAN	KIAA1549	233						integral component of membrane (GO:0016021)		p.R233W(1)|p.R183W(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						AAAGCTGACCGAAAGGTGTGG	0.493			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	2	Substitution - Missense(2)	large_intestine(2)	7						G	TRP/ARG,TRP/ARG	0,4210		0,0,2105	133	142	139		697,697	-2.7	0	7		139	1,8427		0,1,4213	no	missense,missense	KIAA1549	NM_020910.2,NM_001164665.1	101,101	0,1,6318	AA,AG,GG		0.0119,0.0,0.0079	benign,benign	233/1935,233/1951	138603675	1,12637	2105	4214	6319	138254215	SO:0001583	missense	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.697C>T	7.37:g.138603675G>A	ENSP00000416040:p.Arg233Trp		138254215	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.142881	0.37825	0.0	1.19E-4	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.31510	1.49;1.49;1.49	4.68	-2.71	0.05986	.	2.073320	0.02184	N	0.060777	T	0.15219	0.0367	N	0.04508	-0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.27123	-1.0083	10	0.56958	D	0.05	.	6.1846	0.20490	0.4504:0.2679:0.2817:0.0	.	233;233	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	W	233;183;233	ENSP00000406661:R233W;ENSP00000242365:R183W;ENSP00000416040:R233W	ENSP00000242365:R183W	R	-	1	2	KIAA1549	138254215	0.000000	0.05858	0.000000	0.03702	0.177000	0.22998	-0.694000	0.05115	-0.670000	0.05282	0.561000	0.74099	CGG		0.493	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138603675	G	A	138603675	3	1	61	1	0	0	0	0	1	0	0	0	8265	1057	37	1	5231	1	KIAA1549	7	138603675	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	322	138603675	20534988	5619	13604										
ZC3HAV1	56829	broad.mit.edu	37	chr7	138732482	138732482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggagggctcgtgtacGttatatttccttcagtaaac	12	7	1	0	rs542431197		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138732482G>A	ENST00000242351.5	-	13	2883	c.2567C>T	c.(2566-2568)aCg>aTg	p.T856M	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.T978M	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	856	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.T856M(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						GCTCGTGTACGTTATATTTCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											145	144	144					7																	138732482		2203	4300	6503	138383022	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2567C>T	7.37:g.138732482G>A	ENSP00000242351:p.Thr856Met		138383022	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636410	0.29068	.	.	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.14266	2.52;2.52	5.23	-10.5	0.00291	Poly(ADP-ribose) polymerase, catalytic domain (2);	1.464130	0.04338	N	0.353519	T	0.08313	0.0207	L	0.41824	1.3	0.09310	N	1	B	0.17465	0.022	B	0.06405	0.002	T	0.20405	-1.0276	10	0.44086	T	0.13	.	3.17	0.06549	0.4969:0.1605:0.2051:0.1375	.	856	Q7Z2W4	ZCCHV_HUMAN	M	856;978	ENSP00000242351:T856M;ENSP00000418385:T978M	ENSP00000242351:T856M	T	-	2	0	ZC3HAV1	138383022	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.239000	0.00268	-2.456000	0.00539	-0.300000	0.09419	ACG		0.433	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		A	138732482	G	A	138732482	3	1	61	1	0	0	0	0	1	0	0	0	17614	1145	40	1	145	1	ZC3HAV1	7	138732482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128807	138732482	20406181	5620	13605										
ZC3HAV1	56829	broad.mit.edu	37	chr7	138764331	138764331	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatatttctctgtgaccGctgctagtgcttttgtaatt	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138764331G>A	ENST00000242351.5	-	4	1672	c.1356C>T	c.(1354-1356)agC>agT	p.S452S	ZC3HAV1_ENST00000464606.1_Silent_p.S452S|ZC3HAV1_ENST00000471652.1_Silent_p.S452S	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	452					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.S452S(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CTCTGTGACCGCTGCTAGTGC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	7											112	110	110					7																	138764331		2203	4300	6503	138414871	SO:0001819	synonymous_variant	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1356C>T	7.37:g.138764331G>A			138414871	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	37	CCDS5851.1																																																																																				0.478	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		A	138764331	G	A	138764331	2	1	61	1	0	0	0	0	0	0	0	1	17614	1078	38	1		1	ZC3HAV1	7	138764331	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31849	138764331	20374332	5621	13606										
ZC3HAV1	56829	broad.mit.edu	37	chr7	138774441	138774441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgttcagtccagagagttCgtgatttttcaggactttga	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138774441C>T	ENST00000242351.5	-	2	689	c.373G>A	c.(373-375)Gaa>Aaa	p.E125K	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.E125K|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.E125K	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	125	N-terminal domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.E125K(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CCAGAGAGTTCGTGATTTTTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											121	109	113					7																	138774441		2203	4300	6503	138424981	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.373G>A	7.37:g.138774441C>T	ENSP00000242351:p.Glu125Lys		138424981	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	9.494	1.101481	0.20632	.	.	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652	T;T;T	0.44881	0.91;0.91;0.91	4.21	3.25	0.37280	.	0.790188	0.10801	N	0.632688	T	0.34135	0.0887	N	0.21448	0.665	0.09310	N	1	P;D	0.61080	0.669;0.989	B;P	0.47626	0.138;0.552	T	0.11179	-1.0598	10	0.59425	D	0.04	.	8.7002	0.34320	0.2266:0.7734:0.0:0.0	.	125;125	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	K	125	ENSP00000242351:E125K;ENSP00000418385:E125K;ENSP00000419855:E125K	ENSP00000242351:E125K	E	-	1	0	ZC3HAV1	138424981	0.159000	0.22864	0.120000	0.21714	0.160000	0.22226	0.748000	0.26305	2.337000	0.79520	0.650000	0.86243	GAA		0.403	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		T	138774441	C	T	138774441	3	4	61	1	0	0	0	0	1	0	0	0	17614	893	31	1	2387	1	ZC3HAV1	7	138774441	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10110	138774441	20364222	5622	13607										
TTC26	79989	broad.mit.edu	37	chr7	138819507	138819507	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggagctactttcaaaaaGagatttcactggagctatta	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138819507G>T	ENST00000464848.1	+	2	190	c.110G>T	c.(109-111)aGa>aTa	p.R37I	TTC26_ENST00000430935.1_Missense_Mutation_p.R37I|TTC26_ENST00000495038.1_Missense_Mutation_p.R37I|TTC26_ENST00000481482.1_3'UTR|TTC26_ENST00000343187.4_Missense_Mutation_p.R37I|TTC26_ENST00000474035.2_Missense_Mutation_p.R37I|TTC26_ENST00000478836.2_Missense_Mutation_p.R37I			A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26	37					cilium assembly (GO:0042384)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle B (GO:0030992)|primary cilium (GO:0072372)		p.R37I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	24						CTTTCAAAAAGAGATTTCACT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											82	75	78					7																	138819507		2203	4300	6503	138470047	SO:0001583	missense	79989			AK022633	CCDS5852.1, CCDS55172.1, CCDS55173.1, CCDS75665.1	7q34	2013-01-11			ENSG00000105948	ENSG00000105948		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	21882	protein-coding gene	gene with protein product							Standard	NM_001144920		Approved	FLJ12571, dyf-13, DYF13	uc003vus.2	A0AVF1	OTTHUMG00000157472	ENST00000464848.1:c.110G>T	7.37:g.138819507G>T	ENSP00000419279:p.Arg37Ile		138470047	A4D1S3|B7Z5M0|C9J2N7|F8W724|Q9H9S8|Q9NTC0	Missense_Mutation	SNP	ENST00000464848.1	37	CCDS5852.1	.	.	.	.	.	.	.	.	.	.	G	32	5.166540	0.94768	.	.	ENSG00000105948	ENST00000430935;ENST00000495038;ENST00000474035;ENST00000478836;ENST00000464848;ENST00000343187	T;T;T;T;T	0.57907	0.41;1.5;1.11;0.44;0.37	6.06	6.06	0.98353	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.80019	0.4547	M	0.91196	3.185	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.99;0.994;0.999;0.995;0.99;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.962;0.975;0.994;0.979;0.962;1.0;0.999	T	0.83148	-0.0105	10	0.87932	D	0	.	19.3958	0.94607	0.0:0.0:1.0:0.0	.	37;37;37;37;37;37;37	B7Z2T3;F8W724;C9J2N7;B7Z6R6;A0AVF1;B7Z5M0;Q96CU4	.;.;.;.;TTC26_HUMAN;.;.	I	37	ENSP00000410655:R37I;ENSP00000418788:R37I;ENSP00000419178:R37I;ENSP00000419279:R37I;ENSP00000339135:R37I	ENSP00000339135:R37I	R	+	2	0	TTC26	138470047	1.000000	0.71417	0.963000	0.40424	0.996000	0.88848	7.139000	0.77314	2.879000	0.98667	0.650000	0.86243	AGA		0.438	TTC26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348919.2	NM_024926		T	138819507	G	T	138819507	3	4	61	1	0	0	0	0	1	0	0	0	16734	942	33	2	116	2	TTC26	7	138819507	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45066	138819507	20319156	5623	13608										
TTC26	79989	broad.mit.edu	37	chr7	138863338	138863338	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggcaataccagtgagggCgaagaggtgggtatctgctt	15	7	1	2	rs138889631		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:138863338C>T	ENST00000464848.1	+	14	1316	c.1236C>T	c.(1234-1236)ggC>ggT	p.G412G	TTC26_ENST00000430935.1_Silent_p.G412G|TTC26_ENST00000495038.1_Silent_p.G281G|TTC26_ENST00000343187.4_Silent_p.G381G|TTC26_ENST00000478836.2_Silent_p.G305G			A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26	412					cilium assembly (GO:0042384)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle B (GO:0030992)|primary cilium (GO:0072372)		p.G412G(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	24						CCAGTGAGGGCGAAGAGGTGG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7						C	,,	2,4404	4.2+/-10.8	0,2,2201	116	110	112		1236,1143,1236	-2.1	1	7	dbSNP_134	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC26	NM_001144920.1,NM_001144923.1,NM_024926.2	,,	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	,,	412/488,381/524,412/555	138863338	4,13002	2203	4300	6503	138513878	SO:0001819	synonymous_variant	79989			AK022633	CCDS5852.1, CCDS55172.1, CCDS55173.1, CCDS75665.1	7q34	2013-01-11			ENSG00000105948	ENSG00000105948		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	21882	protein-coding gene	gene with protein product							Standard	NM_001144920		Approved	FLJ12571, dyf-13, DYF13	uc003vus.2	A0AVF1	OTTHUMG00000157472	ENST00000464848.1:c.1236C>T	7.37:g.138863338C>T			138513878	A4D1S3|B7Z5M0|C9J2N7|F8W724|Q9H9S8|Q9NTC0	Silent	SNP	ENST00000464848.1	37	CCDS5852.1																																																																																				0.378	TTC26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348919.2	NM_024926		T	138863338	C	T	138863338	2	4	61	1	0	0	0	0	0	0	0	1	16734	755	27	1		1	TTC26	7	138863338	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43831	138863338	20275325	5624	13609										
LUC7L2	100996928	broad.mit.edu	37	chr7	139106997	139106997	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcacctcgtgacagagatCggaaagataagaagcggtcc	12	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:139106997C>T	ENST00000354926.4	+	10	1444	c.1090C>T	c.(1090-1092)Cgg>Tgg	p.R364W	LUC7L2_ENST00000541515.3_Missense_Mutation_p.R430W|C7orf55-LUC7L2_ENST00000541170.3_Missense_Mutation_p.R361W|C7orf55-LUC7L2_ENST00000263545.6_Missense_Mutation_p.R363W|C7orf55-LUC7L2_ENST00000482860.1_3'UTR	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough									p.R364W(1)									TGACAGAGATCGGAAAGATAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	7											124	126	125					7																	139106997		1932	4136	6068	138757537	SO:0001583	missense	51631				CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.1090C>T	7.37:g.139106997C>T	ENSP00000347005:p.Arg364Trp		138757537		Missense_Mutation	SNP	ENST00000354926.4	37	CCDS43656.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.534109	0.45073	.	.	ENSG00000146963	ENST00000541170;ENST00000541515;ENST00000545899;ENST00000354926;ENST00000263545	T;T;T;T	0.30714	3.28;1.52;3.28;3.28	6.03	2.87	0.33458	.	0.302789	0.33040	N	0.005360	T	0.20170	0.0485	L	0.57536	1.79	0.40138	D	0.976804	P;P;B;B	0.51537	0.946;0.946;0.3;0.199	B;B;B;B	0.31390	0.129;0.129;0.085;0.039	T	0.38329	-0.9666	9	0.56958	D	0.05	-0.0644	5.5622	0.17150	0.1357:0.5394:0.2365:0.0884	.	430;361;363;364	B7Z4Q3;B7Z500;Q9Y383-2;Q9Y383	.;.;.;LC7L2_HUMAN	W	361;430;364;364;363	ENSP00000441604:R361W;ENSP00000440222:R430W;ENSP00000347005:R364W;ENSP00000263545:R363W	ENSP00000263545:R363W	R	+	1	2	LUC7L2	138757537	0.961000	0.32948	1.000000	0.80357	0.994000	0.84299	1.067000	0.30616	0.832000	0.34804	0.557000	0.71058	CGG		0.453	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			T	139106997	C	T	139106997	3	4	61	1	0	0	0	0	1	0	0	0	9112	875	31	1	1128	1	LUC7L2	7	139106997	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	243659	139106997	20031666	5625	13610										
JHDM1D	80853	broad.mit.edu	37	chr7	139790922	139790922	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaacgtgcatggccatttCtgttcaacttaaggatcttc	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:139790922C>A	ENST00000397560.2	-	20	2895	c.2798G>T	c.(2797-2799)aGa>aTa	p.R933I		NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		933					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.R933I(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					ATGGCCATTTCTGTTCAACTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	7											169	165	166					7																	139790922		1927	4139	6066	139437391	SO:0001583	missense	80853																														ENST00000397560.2:c.2798G>T	7.37:g.139790922C>A	ENSP00000380692:p.Arg933Ile		139437391	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	37	CCDS43658.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.074385	0.76415	.	.	ENSG00000006459	ENST00000397560	T	0.26223	1.75	5.81	5.81	0.92471	.	0.087536	0.45126	U	0.000386	T	0.53802	0.1819	M	0.70275	2.135	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53613	-0.8414	10	0.87932	D	0	-12.0452	20.0557	0.97650	0.0:1.0:0.0:0.0	.	933	Q6ZMT4	KDM7_HUMAN	I	933	ENSP00000380692:R933I	ENSP00000380692:R933I	R	-	2	0	JHDM1D	139437391	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.306000	0.72810	2.741000	0.93983	0.591000	0.81541	AGA		0.468	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			A	139790922	C	A	139790922	3	1	61	1	0	0	0	0	1	0	0	0	7969	913	32	2	31	2	JHDM1D	7	139790922	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	683925	139790922	19347741	5626	13611										
SLC37A3	84255	broad.mit.edu	37	chr7	140043303	140043303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttggatgagctcctggCgacccaagtccgcagaaata	10	12	0	2	rs557916487		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:140043303C>T	ENST00000326232.9	-	13	1438	c.1235G>A	c.(1234-1236)cGc>cAc	p.R412H	SLC37A3_ENST00000340308.3_Intron|SLC37A3_ENST00000447932.2_Missense_Mutation_p.R396H	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	412					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.R412H(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					GAGCTCCTGGCGACCCAAGTC	0.458													C|||	1	0.000199681	0	0.0014	5008	,	,		17859	0		0	False		,,,				2504	0				Esophageal Squamous(133;211 1716 4665 11387 37873)											1	Substitution - Missense(1)	large_intestine(1)	7											102	89	94					7																	140043303		2203	4300	6503	139689772	SO:0001583	missense	84255			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"Solute carriers"	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.1235G>A	7.37:g.140043303C>T	ENSP00000321498:p.Arg412His		139689772	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.97|16.97	3.267583|3.267583	0.59540|0.59540	.|.	.|.	ENSG00000157800|ENSG00000157800	ENST00000485538;ENST00000477006|ENST00000447932;ENST00000326232;ENST00000498469	.|T;T;T	.|0.46819	.|2.52;2.5;0.86	5.51|5.51	3.38|3.38	0.38709|0.38709	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.098119	.|0.64402	.|N	.|0.000002	T|T	0.40719|0.40719	0.1128|0.1128	L|L	0.39566|0.39566	1.225|1.225	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.30824	.|0.122;0.296;0.131	.|B;B;B	.|0.33960	.|0.049;0.173;0.023	T|T	0.38845|0.38845	-0.9642|-0.9642	5|10	.|0.45353	.|T	.|0.12	-36.7665|-36.7665	13.2165|13.2165	0.59863|0.59863	0.0:0.8489:0.0:0.1511|0.0:0.8489:0.0:0.1511	.|.	.|396;412;24	.|Q8NCC5-2;Q8NCC5;B3KX37	.|.;SPX3_HUMAN;.	T|H	10;50|396;412;51	.|ENSP00000397481:R396H;ENSP00000321498:R412H;ENSP00000418158:R51H	.|ENSP00000321498:R412H	A|R	-|-	1|2	0|0	SLC37A3|SLC37A3	139689772|139689772	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	4.878000|4.878000	0.63093|0.63093	1.330000|1.330000	0.45394|0.45394	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.458	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		T	140043303	C	T	140043303	3	4	61	1	0	0	0	0	1	0	0	0	14636	768	27	1	410	1	SLC37A3	7	140043303	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252381	140043303	19095360	5627	13612										
DENND2A	27147	broad.mit.edu	37	chr7	140246737	140246737	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttttccacctcatccaaGatctgcaagggtcagaaaag	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:140246737G>T	ENST00000275884.6	-	12	2457	c.2040C>A	c.(2038-2040)atC>atA	p.I680I	DENND2A_ENST00000537639.1_Silent_p.I680I|DENND2A_ENST00000492720.1_Silent_p.I680I|DENND2A_ENST00000496613.1_Silent_p.I680I			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	680	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.I680I(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CCTCATCCAAGATCTGCAAGG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	7											61	63	63					7																	140246737		1956	4177	6133	139893206	SO:0001819	synonymous_variant	27147			AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2040C>A	7.37:g.140246737G>T			139893206	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																				0.527	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		T	140246737	G	T	140246737	2	4	61	1	0	0	0	0	0	0	0	1	4440	932	33	2		2	DENND2A	7	140246737	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203434	140246737	18891926	5628	13613										
DENND2A	27147	broad.mit.edu	37	chr7	140266970	140266970	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacaaccacaaagtactcGaagagctgcctctcctggta	8	13	1	1	rs200641456		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:140266970G>A	ENST00000275884.6	-	8	2112	c.1695C>T	c.(1693-1695)ttC>ttT	p.F565F	DENND2A_ENST00000537639.1_Silent_p.F565F|DENND2A_ENST00000492720.1_Silent_p.F565F|DENND2A_ENST00000496613.1_Silent_p.F565F			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	565					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.F565F(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CAAAGTACTCGAAGAGCTGCC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	7											37	42	40					7																	140266970		1920	4137	6057	139913439	SO:0001819	synonymous_variant	27147			AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1695C>T	7.37:g.140266970G>A			139913439	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																				0.592	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140266970	G	A	140266970	2	1	61	1	0	0	0	0	0	0	0	1	4440	1049	37	1		1	DENND2A	7	140266970	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20233	140266970	18871693	5629	13614										
DENND2A	27147	broad.mit.edu	37	chr7	140285476	140285476	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagcgaccatgtaactcGatgtcctcataagggttctc	10	11	2	0	rs544674444		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:140285476G>A	ENST00000275884.6	-	4	1575	c.1158C>T	c.(1156-1158)atC>atT	p.I386I	DENND2A_ENST00000537639.1_Silent_p.I386I|DENND2A_ENST00000492720.1_Silent_p.I386I|DENND2A_ENST00000496613.1_Silent_p.I386I			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	386					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.I386I(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CATGTAACTCGATGTCCTCAT	0.488													G|||	1	0.000199681	0	0.0014	5008	,	,		22956	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											174	174	174					7																	140285476		1978	4166	6144	139931945	SO:0001819	synonymous_variant	27147			AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1158C>T	7.37:g.140285476G>A			139931945	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																				0.488	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140285476	G	A	140285476	2	1	61	1	0	0	0	0	0	0	0	1	4440	1048	37	1		1	DENND2A	7	140285476	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18506	140285476	18853187	5630	13615										
BRAF	673	broad.mit.edu	37	chr7	140501331	140501331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttcgacaaaagtcacaAaatgctaaggtgaaaaacgt	8	7	1	1	rs397509343		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:140501331A>C	ENST00000288602.6	-	6	801	c.741T>G	c.(739-741)ttT>ttG	p.F247L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	247					activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F247L(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AAAAGTCACAAAATGCTAAGG	0.378		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	1	Substitution - Missense(1)	large_intestine(1)	7											47	44	45					7																	140501331		2203	4300	6503	140147800	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.741T>G	7.37:g.140501331A>C	ENSP00000288602:p.Phe247Leu		140147800	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.950970	0.92660	.	.	ENSG00000157764	ENST00000288602	D	0.93659	-3.26	5.43	3.08	0.35506	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.000000	0.85682	D	0.000000	D	0.93000	0.7772	M	0.87682	2.9	0.58432	D	0.999999	P	0.43542	0.81	B	0.43950	0.437	D	0.91268	0.5042	10	0.87932	D	0	.	4.5974	0.12336	0.5182:0.0:0.4818:0.0	.	247	P15056	BRAF_HUMAN	L	247	ENSP00000288602:F247L	ENSP00000288602:F247L	F	-	3	2	BRAF	140147800	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.373000	0.52394	0.905000	0.36596	0.459000	0.35465	TTT		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140501331	A	C	140501331	3	2	61	1	0	0	0	0	1	0	0	0	1499	11	1	4	1611	4	BRAF	7	140501331	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	215855	140501331	18637332	5631	13616										
AGK	55750	broad.mit.edu	37	chr7	141341072	141341072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctcagactcatcaagccTctatctcatacacgggacct	7	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141341072T>C	ENST00000355413.4	+	12	1011	c.751T>C	c.(751-753)Tct>Cct	p.S251P	AGK_ENST00000535825.1_Intron|AGK_ENST00000473247.1_Missense_Mutation_p.S223P	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	251					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.S251P(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					TCATCAAGCCTCTATCTCATA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											68	65	66					7																	141341072		2203	4300	6503	140987541	SO:0001583	missense	55750			BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.751T>C	7.37:g.141341072T>C	ENSP00000347581:p.Ser251Pro		140987541	Q75KN1|Q96GC3|Q9NP48	Missense_Mutation	SNP	ENST00000355413.4	37	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179407	0.78564	.	.	ENSG00000006530	ENST00000355413;ENST00000473247	T;T	0.13089	2.62;2.62	5.51	5.51	0.81932	.	0.098369	0.64402	D	0.000001	T	0.20861	0.0502	M	0.70595	2.14	0.80722	D	1	P	0.47910	0.902	B	0.44278	0.445	T	0.01661	-1.1301	10	0.34782	T	0.22	.	13.4302	0.61051	0.0:0.0:0.0:1.0	.	251	Q53H12	AGK_HUMAN	P	251;223	ENSP00000347581:S251P;ENSP00000420776:S223P	ENSP00000347581:S251P	S	+	1	0	AGK	140987541	0.997000	0.39634	0.995000	0.50966	0.974000	0.67602	1.563000	0.36364	2.225000	0.72522	0.528000	0.53228	TCT		0.443	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		C	141341072	T	C	141341072	3	2	61	1	0	0	0	0	1	0	0	0	383	1551	54	4	793	4	AGK	7	141341072	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	839741	141341072	17797591	5632	13617										
TAS2R4	50832	broad.mit.edu	37	chr7	141478295	141478295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaatgagtaaagatgcttCggttattctatttctctgct	7	8	3	2	rs368599194		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141478295C>T	ENST00000247881.2	+	1	54	c.7C>T	c.(7-9)Cgg>Tgg	p.R3W	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	3			R -> Q (in dbSNP:rs2233995).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.R3W(1)		endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		AAAGATGCTTCGGTTATTCTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	63	60	61		7	-0.5	0	7		61	1,8599	1.2+/-3.3	0,1,4299	no	missense	TAS2R4	NM_016944.1	101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	3/300	141478295	2,13004	2203	4300	6503	141124764	SO:0001583	missense	50832			AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.7C>T	7.37:g.141478295C>T	ENSP00000247881:p.Arg3Trp		141124764	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	.	.	.	.	.	.	.	.	.	.	C	3.801	-0.041773	0.07452	2.27E-4	1.16E-4	ENSG00000127364	ENST00000247881	T	0.00784	5.7	5.91	-0.509	0.11977	.	3.248150	0.00682	N	0.000693	T	0.00845	0.0028	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49224	-0.8962	10	0.51188	T	0.08	.	4.5145	0.11928	0.1075:0.4139:0.3378:0.1407	.	3	Q9NYW5	TA2R4_HUMAN	W	3	ENSP00000247881:R3W	ENSP00000247881:R3W	R	+	1	2	TAS2R4	141124764	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.062000	0.11674	-0.681000	0.05204	-1.822000	0.00598	CGG		0.368	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1			T	141478295	C	T	141478295	3	4	61	1	0	0	0	0	1	0	0	0	15616	875	31	1	9	1	TAS2R4	7	141478295	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137223	141478295	17660368	5633	13618										
TAS2R4	50832	broad.mit.edu	37	chr7	141478396	141478396	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaattgcaaaacttgggtCaaaagccatagaatctcctc	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141478396C>A	ENST00000247881.2	+	1	155	c.108C>A	c.(106-108)gtC>gtA	p.V36V	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	36					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.V36V(1)		endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		AAACTTGGGTCAAAAGCCATA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7											148	146	147					7																	141478396		2203	4300	6503	141124865	SO:0001819	synonymous_variant	50832			AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.108C>A	7.37:g.141478396C>A			141124865	Q645W5|Q75MV8	Silent	SNP	ENST00000247881.2	37	CCDS5868.1																																																																																				0.378	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1			A	141478396	C	A	141478396	2	1	61	1	0	0	0	0	0	0	0	1	15616	813	29	2		2	TAS2R4	7	141478396	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101	141478396	17660267	5634	13619										
TAS2R5	54429	broad.mit.edu	37	chr7	141490821	141490821	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaaggctcacatcactgcGctgaagtccttgggctgctt	11	13	2	1	rs148483148		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141490821G>A	ENST00000247883.4	+	1	805	c.660G>A	c.(658-660)gcG>gcA	p.A220A		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	220					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.A220A(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					ACATCACTGCGCTGAAGTCCT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	7						C		1,4405		0,1,2202	192	174	180		660	-1.2	0.9	7	dbSNP_134	180	0,8600		0,0,4300	no	coding-synonymous	TAS2R5	NM_018980.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		220/300	141490821	1,13005	2203	4300	6503	141137290	SO:0001819	synonymous_variant	54429			AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.660G>A	7.37:g.141490821G>A			141137290	Q645W0|Q75MV7	Silent	SNP	ENST00000247883.4	37	CCDS5869.1																																																																																				0.517	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1			A	141490821	G	A	141490821	2	1	61	1	0	0	0	0	0	0	0	1	15622	1074	38	1		1	TAS2R5	7	141490821	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12425	141490821	17647842	5635	13620										
OR9A4	130075	broad.mit.edu	37	chr7	141618707	141618707	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactctagtgccactgaatTttatctccttggcttccctg	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141618707T>G	ENST00000548136.1	+	1	91	c.32T>G	c.(31-33)tTt>tGt	p.F11C	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F11C(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					GCCACTGAATTTTATCTCCTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											220	221	221					7																	141618707		2072	4222	6294	141265176	SO:0001583	missense	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.32T>G	7.37:g.141618707T>G	ENSP00000448789:p.Phe11Cys		141265176	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	37	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.916575	0.33815	.	.	ENSG00000258083	ENST00000548136	T	0.04603	3.59	3.88	3.88	0.44766	.	.	.	.	.	T	0.29223	0.0727	H	0.95504	3.68	0.38785	D	0.954843	D	0.89917	1.0	D	0.85130	0.997	T	0.43893	-0.9363	9	0.87932	D	0	-34.9457	10.9854	0.47518	0.0:0.0:0.0:1.0	.	11	Q8NGU2	OR9A4_HUMAN	C	11	ENSP00000448789:F11C	ENSP00000386148:F11C	F	+	2	0	OR9A4	141265176	0.984000	0.35163	0.989000	0.46669	0.065000	0.16274	3.388000	0.52509	1.754000	0.51921	0.523000	0.50628	TTT		0.378	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		G	141618707	T	G	141618707	3	3	61	1	0	0	0	0	1	0	0	0	11280	1841	64	4	34	4	OR9A4	7	141618707	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	127886	141618707	17519956	5636	13621										
OR9A4	130075	broad.mit.edu	37	chr7	141618903	141618903	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctggtcacaaccataatCgtccccgtgatgctttgggg	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141618903C>T	ENST00000548136.1	+	1	287	c.228C>T	c.(226-228)atC>atT	p.I76I	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I76I(2)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					CAACCATAATCGTCCCCGTGA	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	7											121	125	124					7																	141618903		2203	4300	6503	141265372	SO:0001819	synonymous_variant	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.228C>T	7.37:g.141618903C>T			141265372	B9EGV6|Q6IFI4	Silent	SNP	ENST00000548136.1	37	CCDS43661.1																																																																																				0.507	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		T	141618903	C	T	141618903	2	4	61	1	0	0	0	0	0	0	0	1	11280	874	31	1		1	OR9A4	7	141618903	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	196	141618903	17519760	5637	13622										
OR9A4	130075	broad.mit.edu	37	chr7	141619011	141619011	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtggggacaacagagttCgcattacttggagcaatggc	14	8	0	1	rs73529456	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141619011C>T	ENST00000548136.1	+	1	395	c.336C>T	c.(334-336)ttC>ttT	p.F112F	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F112F(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					CAACAGAGTTCGCATTACTTG	0.483													C|||	130	0.0259585	0.0961	0.0043	5008	,	,		19569	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C		328,4076		17,294,1891	119	119	119		336	-2.4	0	7	dbSNP_130	119	1,8599		0,1,4299	no	coding-synonymous	OR9A4	NM_001001656.1		17,295,6190	TT,TC,CC		0.0116,7.4478,2.53		112/315	141619011	329,12675	2202	4300	6502	141265480	SO:0001819	synonymous_variant	130075				CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.336C>T	7.37:g.141619011C>T			141265480	B9EGV6|Q6IFI4	Silent	SNP	ENST00000548136.1	37	CCDS43661.1																																																																																				0.483	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		T	141619011	C	T	141619011	2	4	61	1	0	0	0	0	0	0	0	1	11280	883	31	1		1	OR9A4	7	141619011	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108	141619011	17519652	5638	13623										
TAS2R38	5726	broad.mit.edu	37	chr7	141672591	141672591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcctcaacttggcattgCctgagatcaggatggctgca	10	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141672591C>T	ENST00000547270.1	-	1	982	c.899G>A	c.(898-900)gGc>gAc	p.G300D		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	300					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.G300D(1)		NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					CTTGGCATTGCCTGAGATCAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											79	69	72					7																	141672591		2203	4300	6503	141319060	SO:0001583	missense	5726			AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.899G>A	7.37:g.141672591C>T	ENSP00000448219:p.Gly300Asp		141319060	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Missense_Mutation	SNP	ENST00000547270.1	37	CCDS34765.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595803	0.46318	.	.	ENSG00000257138	ENST00000547270	T	0.37411	1.2	5.01	5.01	0.66863	.	0.207947	0.39985	N	0.001205	T	0.52837	0.1759	M	0.80616	2.505	0.31448	N	0.671095	P	0.46912	0.886	P	0.51550	0.673	T	0.64719	-0.6341	10	0.87932	D	0	.	14.0093	0.64486	0.0:1.0:0.0:0.0	.	300	P59533	T2R38_HUMAN	D	300	ENSP00000448219:G300D	ENSP00000331291:G300D	G	-	2	0	TAS2R38	141319060	0.009000	0.17119	0.908000	0.35775	0.037000	0.13140	1.290000	0.33319	2.769000	0.95229	0.655000	0.94253	GGC		0.552	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		T	141672591	C	T	141672591	3	4	61	1	0	0	0	0	1	0	0	0	15614	739	26	3	106	3	TAS2R38	7	141672591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53580	141672591	17466072	5639	13624										
MGAM	8972	broad.mit.edu	37	chr7	141705375	141705375	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttactactttggagattgtGctcagtgttcttctgcttgt	9	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141705375G>C	ENST00000549489.2	+	2	140	c.45G>C	c.(43-45)gtG>gtC	p.V15V	MGAM_ENST00000475668.2_Silent_p.V15V	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	15					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.V15V(3)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGGAGATTGTGCTCAGTGTTC	0.318																																																3	Substitution - coding silent(3)	large_intestine(3)	7											112	105	107					7																	141705375		1843	4094	5937	141351844	SO:0001819	synonymous_variant	8972			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.45G>C	7.37:g.141705375G>C			141351844	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																				0.318	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141705375	G	C	141705375	2	2	61	1	0	0	0	0	0	0	0	1	9571	1306	46	5		5	MGAM	7	141705375	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32784	141705375	17433288	5640	13625										
MGAM	8972	broad.mit.edu	37	chr7	141720869	141720869	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatatcagacatctaatCgtttccactttaaggttgta	6	8	2	2	rs146995745	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141720869C>T	ENST00000549489.2	+	5	639	c.544C>T	c.(544-546)Cgt>Tgt	p.R182C	MGAM_ENST00000475668.2_Missense_Mutation_p.R182C	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	182					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R182C(3)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACATCTAATCGTTTCCACTT	0.343													C|||	2	0.000399361	0.0015	0	5008	,	,		16611	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	7											94	85	87					7																	141720869		1830	4080	5910	141367338	SO:0001583	missense	8972			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.544C>T	7.37:g.141720869C>T	ENSP00000447378:p.Arg182Cys		141367338	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	19.18	3.778201	0.70107	.	.	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000475668;ENST00000548812	T;D	0.81739	-1.46;-1.53	5.22	5.22	0.72569	Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.49916	D	0.000121	D	0.90390	0.6992	M	0.88512	2.96	0.58432	D	0.999999	D	0.71674	0.998	D	0.64042	0.921	D	0.91960	0.5578	10	0.87932	D	0	.	16.3173	0.82932	0.0:1.0:0.0:0.0	.	182	O43451	MGA_HUMAN	C	182;182;182;59	ENSP00000419372:R182C;ENSP00000447378:R182C	ENSP00000316431:R59C	R	+	1	0	MGAM	141367338	1.000000	0.71417	0.739000	0.30968	0.977000	0.68977	6.584000	0.74057	2.711000	0.92665	0.563000	0.77884	CGT		0.343	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141720869	C	T	141720869	3	4	61	1	0	0	0	0	1	0	0	0	9571	884	31	1	558	1	MGAM	7	141720869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15494	141720869	17417794	5641	13626										
MGAM	8972	broad.mit.edu	37	chr7	141754683	141754683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccatttgggattgaaattCgccggaagagtacaggcact	11	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141754683C>T	ENST00000549489.2	+	27	3384	c.3289C>T	c.(3289-3291)Cgc>Tgc	p.R1097C	MGAM_ENST00000475668.2_Missense_Mutation_p.R1097C	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1097	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R1097C(2)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GATTGAAATTCGCCGGAAGAG	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	7											77	74	75					7																	141754683		1884	4098	5982	141401152	SO:0001583	missense	8972			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3289C>T	7.37:g.141754683C>T	ENSP00000447378:p.Arg1097Cys		141401152	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.277063	0.23307	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	T	0.13538	2.58	4.24	2.15	0.27550	Glycoside hydrolase-type carbohydrate-binding (1);	0.774326	0.10690	N	0.645363	T	0.42291	0.1196	M	0.90759	3.145	0.19300	N	0.999978	D	0.89917	1.0	D	0.78314	0.991	T	0.14282	-1.0478	10	0.49607	T	0.09	.	10.2669	0.43460	0.4981:0.5019:0.0:0.0	.	1097	O43451	MGA_HUMAN	C	1097;1097;974	ENSP00000447378:R1097C	ENSP00000316431:R974C	R	+	1	0	MGAM	141401152	0.019000	0.18553	0.004000	0.12327	0.026000	0.11368	1.486000	0.35530	0.682000	0.31407	0.460000	0.39030	CGC		0.498	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141754683	C	T	141754683	3	4	61	1	0	0	0	0	1	0	0	0	9571	884	31	1	3391	1	MGAM	7	141754683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33814	141754683	17383980	5642	13627										
MGAM	8972	broad.mit.edu	37	chr7	141794584	141794584	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttctttcaagatgctgAatatgagatgtgtgttcgct	12	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141794584A>C	ENST00000549489.2	+	40	4786	c.4691A>C	c.(4690-4692)gAa>gCa	p.E1564A	MGAM_ENST00000475668.2_Missense_Mutation_p.E2460A	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1564	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.E1564A(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CAAGATGCTGAATATGAGATG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	7											70	68	69					7																	141794584		1880	4109	5989	141441053	SO:0001583	missense	8972			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4691A>C	7.37:g.141794584A>C	ENSP00000447378:p.Glu1564Ala		141441053	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	A	18.96	3.734668	0.69189	.	.	ENSG00000257335	ENST00000549489;ENST00000475668	D	0.93019	-3.15	5.37	5.37	0.77165	Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.94843	0.8334	M	0.88031	2.925	0.09310	N	1	B	0.23854	0.092	B	0.37144	0.242	D	0.89774	0.3956	9	0.48119	T	0.1	.	10.2991	0.43642	0.7217:0.2783:0.0:0.0	.	1564	O43451	MGA_HUMAN	A	1564;2461	ENSP00000447378:E1564A	ENSP00000373973:E1564A	E	+	2	0	MGAM	141441053	0.009000	0.17119	0.986000	0.45419	0.955000	0.61496	2.585000	0.46111	2.154000	0.67381	0.533000	0.62120	GAA		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141794584	A	C	141794584	3	2	61	1	0	0	0	0	1	0	0	0	9571	246	9	4	4845	4	MGAM	7	141794584	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	39901	141794584	17344079	5643	13628										
TRYX3	136541	broad.mit.edu	37	chr7	141952068	141952068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttggattacattttcaatCcagggtatatagtaaaaaat	6	4	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:141952068C>A	ENST00000552471.1	-	5	1018	c.699G>T	c.(697-699)tgG>tgT	p.W233C	PRSS58_ENST00000547058.2_Missense_Mutation_p.W233C			Q8IYP2	PRS58_HUMAN	protease, serine, 58	233	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.W233C(1)		kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						CATTTTCAATCCAGGGTATAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											62	72	69					7																	141952068		2203	4300	6503	141598546	SO:0001583	missense	136541				CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"Serine peptidases / Serine peptidases"	39125	protein-coding gene	gene with protein product	"trypsin X3"						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.699G>T	7.37:g.141952068C>A	ENSP00000446916:p.Trp233Cys		141598546	B3KVJ6|D3DXD2	Missense_Mutation	SNP	ENST00000552471.1	37	CCDS5871.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354814	0.41700	.	.	ENSG00000258223	ENST00000547058;ENST00000552471	D;D	0.94758	-3.51;-3.51	5.24	5.24	0.73138	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.98153	0.9390	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98824	1.0748	9	0.87932	D	0	.	14.1973	0.65679	0.0:1.0:0.0:0.0	.	233	Q8IYP2	PRS58_HUMAN	C	233	ENSP00000447588:W233C;ENSP00000446916:W233C	ENSP00000307206:W233C	W	-	3	0	PRSS58	141598546	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	3.484000	0.53201	2.723000	0.93209	0.655000	0.94253	TGG		0.388	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317		A	141952068	C	A	141952068	3	1	61	1	0	0	0	0	1	0	0	0	16644	856	30	2	30	2	TRYX3	7	141952068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157484	141952068	17186595	5644	13629										
TRPV6	55503	broad.mit.edu	37	chr7	142583228	142583228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgctccataggcagagaaTtagccctttctccttgggca	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142583228T>C	ENST00000359396.3	-	1	279	c.34A>G	c.(34-36)Att>Gtt	p.I12V	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	12					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)	p.I12V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					AGGCAGAGAATTAGCCCTTTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	7											105	108	107					7																	142583228		2203	4300	6503	142293350	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.34A>G	7.37:g.142583228T>C	ENSP00000352358:p.Ile12Val		142293350	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	T	3.929	-0.016497	0.07681	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.76709	-1.04	3.54	-0.966	0.10320	.	0.670897	0.13610	N	0.375214	T	0.63034	0.2477	L	0.40543	1.245	0.23816	N	0.996766	B	0.02656	0.0	B	0.04013	0.001	T	0.51764	-0.8664	10	0.46703	T	0.11	-2.4877	4.3236	0.11029	0.0:0.1209:0.4068:0.4723	.	12	Q9H1D0	TRPV6_HUMAN	V	12	ENSP00000352358:I12V	ENSP00000310825:I12V	I	-	1	0	TRPV6	142293350	0.908000	0.30866	0.946000	0.38457	0.978000	0.69477	0.083000	0.14871	0.075000	0.16796	0.317000	0.21355	ATT		0.612	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		C	142583228	T	C	142583228	3	2	61	1	0	0	0	0	1	0	0	0	16640	1493	52	4	2203	4	TRPV6	7	142583228	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	631160	142583228	16555435	5645	13630										
TRPV5	56302	broad.mit.edu	37	chr7	142605700	142605700	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaaaatggtagacctcctCtccatccccctcactaaggt	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142605700C>A	ENST00000265310.1	-	15	2518	c.2170G>T	c.(2170-2172)Gag>Tag	p.E724*		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	724	Involved in Ca(2+)-dependent inactivation. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.E724*(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TAGACCTCCTCTCCATCCCCC	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											111	106	108					7																	142605700		2203	4300	6503	142315822	SO:0001587	stop_gained	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.2170G>T	7.37:g.142605700C>A	ENSP00000265310:p.Glu724*		142315822	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Nonsense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.235500	0.58886	.	.	ENSG00000127412	ENST00000265310;ENST00000439304	.	.	.	4.99	4.99	0.66335	.	0.421997	0.23842	N	0.044025	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-15.5316	15.5865	0.76489	0.0:1.0:0.0:0.0	.	.	.	.	X	724;669	.	ENSP00000265310:E724X	E	-	1	0	TRPV5	142315822	0.994000	0.37717	1.000000	0.80357	0.098000	0.18820	4.634000	0.61325	2.615000	0.88500	0.655000	0.94253	GAG		0.562	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142605700	C	A	142605700	4	1	61	1	0	0	0	0	0	1	0	0	16639	922	32	2	23	2	TRPV5	7	142605700	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22472	142605700	16532963	5646	13631										
TRPV5	56302	broad.mit.edu	37	chr7	142606708	142606708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacccacagatcccggagcGaggccacaggcagcgaggca	14	15	0	1	rs148001669		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142606708G>A	ENST00000265310.1	-	14	2191	c.1843C>T	c.(1843-1845)Cgc>Tgc	p.R615C		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	615					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R615C(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					ATCCCGGAGCGAGGCCACAGG	0.592																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	78	69	72		1843	4.8	1	7	dbSNP_134	72	0,8600		0,0,4300	no	missense	TRPV5	NM_019841.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	615/730	142606708	1,13005	2203	4300	6503	142316830	SO:0001583	missense	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1843C>T	7.37:g.142606708G>A	ENSP00000265310:p.Arg615Cys		142316830	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182709	0.78677	2.27E-4	0.0	ENSG00000127412	ENST00000265310;ENST00000439304	D;D	0.82711	-1.58;-1.64	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.82162	0.4977	M	0.83384	2.64	0.80722	D	1	B	0.33318	0.408	B	0.26693	0.072	D	0.84228	0.0465	10	0.87932	D	0	-14.5709	12.4738	0.55801	0.0:0.0:0.833:0.167	.	615	Q9NQA5	TRPV5_HUMAN	C	615;560	ENSP00000265310:R615C;ENSP00000406361:R560C	ENSP00000265310:R615C	R	-	1	0	TRPV5	142316830	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.932000	0.63476	2.672000	0.90937	0.655000	0.94253	CGC		0.592	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142606708	G	A	142606708	3	1	61	1	0	0	0	0	1	0	0	0	16639	1058	37	1	354	1	TRPV5	7	142606708	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1008	142606708	16531955	5647	13632										
TRPV5	56302	broad.mit.edu	37	chr7	142622661	142622661	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggatggtgatgtctcgaGaatgagtgcggttgccacca	16	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142622661G>T	ENST00000265310.1	-	8	1433	c.1085C>A	c.(1084-1086)tCt>tAt	p.S362Y	TRPV5_ENST00000442623.1_Missense_Mutation_p.S362Y	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	362					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S362Y(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					GATGTCTCGAGAATGAGTGCG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											109	97	101					7																	142622661		2203	4300	6503	142332783	SO:0001583	missense	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1085C>A	7.37:g.142622661G>T	ENSP00000265310:p.Ser362Tyr		142332783	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845596	0.51164	.	.	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	D;D;D	0.85556	-2.0;-2.0;-2.0	5.18	3.22	0.36961	.	1.130910	0.06361	N	0.711692	D	0.84488	0.5483	L	0.56769	1.78	0.09310	N	0.999997	P;P	0.37663	0.604;0.604	P;B	0.46510	0.519;0.332	T	0.69606	-0.5100	10	0.12766	T	0.61	-2.0212	5.047	0.14488	0.0874:0.154:0.6191:0.1396	.	362;362	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	Y	362;307;362	ENSP00000265310:S362Y;ENSP00000406361:S307Y;ENSP00000406572:S362Y	ENSP00000265310:S362Y	S	-	2	0	TRPV5	142332783	0.156000	0.22821	0.108000	0.21378	0.971000	0.66376	0.953000	0.29162	1.287000	0.44583	0.655000	0.94253	TCT		0.512	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142622661	G	T	142622661	3	4	61	1	0	0	0	0	1	0	0	0	16639	942	33	2	1136	2	TRPV5	7	142622661	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15953	142622661	16516002	5648	13633										
TRPV5	56302	broad.mit.edu	37	chr7	142626211	142626211	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcaaaggacaaagggtgCtcccctgtggacacagagag	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142626211C>A	ENST00000265310.1	-	5	840	c.492G>T	c.(490-492)gaG>gaT	p.E164D	TRPV5_ENST00000442623.1_Missense_Mutation_p.E164D	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	164					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.E164D(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					ACAAAGGGTGCTCCCCTGTGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											62	50	54					7																	142626211		2203	4300	6503	142336333	SO:0001583	missense	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.492G>T	7.37:g.142626211C>A	ENSP00000265310:p.Glu164Asp		142336333	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695053	0.68386	.	.	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	T;T;T	0.64085	-0.08;-0.08;-0.08	4.2	3.3	0.37823	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.66376	0.2783	L	0.38692	1.165	0.58432	D	0.999999	P;D	0.71674	0.945;0.998	P;D	0.76071	0.818;0.987	T	0.66771	-0.5839	10	0.72032	D	0.01	-7.3749	7.496	0.27490	0.0:0.7728:0.0:0.2272	.	164;164	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	D	164;158;164	ENSP00000265310:E164D;ENSP00000406361:E158D;ENSP00000406572:E164D	ENSP00000265310:E164D	E	-	3	2	TRPV5	142336333	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.307000	0.33516	1.092000	0.41356	0.462000	0.41574	GAG		0.592	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142626211	C	A	142626211	3	1	61	1	0	0	0	0	1	0	0	0	16639	796	28	2	1741	2	TRPV5	7	142626211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3550	142626211	16512452	5649	13634										
KEL	3792	broad.mit.edu	37	chr7	142638474	142638474	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgagtgtcgtgagagtcCtgggggctgggcttcctaca	16	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142638474C>T	ENST00000355265.2	-	19	2538	c.2064G>A	c.(2062-2064)caG>caA	p.Q688Q		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	688					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.Q688Q(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CGTGAGAGTCCTGGGGGCTGG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	7											99	102	101					7																	142638474		2203	4300	6503	142348596	SO:0001819	synonymous_variant	3792			BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.2064G>A	7.37:g.142638474C>T			142348596	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																				0.617	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		T	142638474	C	T	142638474	2	4	61	1	0	0	0	0	0	0	0	1	8163	680	24	3		3	KEL	7	142638474	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12263	142638474	16500189	5650	13635										
KEL	3792	broad.mit.edu	37	chr7	142649704	142649704	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaccaccagccctaagatCatgtggctctgcagaaagtc	9	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142649704C>A	ENST00000355265.2	-	10	1569	c.1095G>T	c.(1093-1095)atG>atT	p.M365I	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	365					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.M365I(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					GCCCTAAGATCATGTGGCTCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	76	81					7																	142649704		2203	4300	6503	142359826	SO:0001583	missense	3792			BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1095G>T	7.37:g.142649704C>A	ENSP00000347409:p.Met365Ile		142359826	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730283	0.48939	.	.	ENSG00000197993	ENST00000355265	T	0.72725	-0.68	5.55	4.68	0.58851	Peptidase M13 (1);	0.073826	0.56097	N	0.000021	T	0.64125	0.2570	L	0.55481	1.735	0.42035	D	0.991043	B	0.13145	0.007	B	0.12837	0.008	T	0.62105	-0.6924	10	0.42905	T	0.14	0.0014	10.2354	0.43280	0.0:0.9115:0.0:0.0885	.	365	P23276	KELL_HUMAN	I	365	ENSP00000347409:M365I	ENSP00000347409:M365I	M	-	3	0	KEL	142359826	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.792000	0.47837	1.594000	0.50039	0.655000	0.94253	ATG		0.527	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		A	142649704	C	A	142649704	3	1	61	1	0	0	0	0	1	0	0	0	8163	826	29	2	1143	2	KEL	7	142649704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11230	142649704	16488959	5651	13636										
OR9A2	135924	broad.mit.edu	37	chr7	142724124	142724124	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaatgtcactaaatagaaGaaaaagaatatagcaaaaag	6	3	1	3	rs142788435		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142724124G>T	ENST00000350513.2	-	1	158	c.96C>A	c.(94-96)ttC>ttA	p.F32L		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F32F(1)|p.F32L(1)		central_nervous_system(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					CTAAATAGAAGAAAAAGAATA	0.433																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|skin(1)	7											88	91	90					7																	142724124		2203	4300	6503	142434246	SO:0001583	missense	135924				CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"GPCR / Class A : Olfactory receptors"	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.96C>A	7.37:g.142724124G>T	ENSP00000316518:p.Phe32Leu		142434246	B9EH51|Q6IF71|Q8NGD9	Missense_Mutation	SNP	ENST00000350513.2	37	CCDS34767.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.666359	0.00105	.	.	ENSG00000179468	ENST00000350513	T	0.00424	7.45	3.93	1.98	0.26296	.	0.232593	0.21933	N	0.066986	T	0.00109	0.0003	N	0.03930	-0.32	0.19300	N	0.999972	B	0.06786	0.001	B	0.08055	0.003	T	0.40979	-0.9534	10	0.02654	T	1	-12.9894	2.5182	0.04674	0.1068:0.192:0.5032:0.198	.	32	Q8NGT5	OR9A2_HUMAN	L	32	ENSP00000316518:F32L	ENSP00000316518:F32L	F	-	3	2	OR9A2	142434246	0.000000	0.05858	0.033000	0.17914	0.017000	0.09413	-0.155000	0.10115	0.373000	0.24621	-0.516000	0.04426	TTC		0.433	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1			T	142724124	G	T	142724124	3	4	61	1	0	0	0	0	1	0	0	0	11279	933	33	2	840	2	OR9A2	7	142724124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74420	142724124	16414539	5652	13637										
PIP	5304	broad.mit.edu	37	chr7	142832372	142832372	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgcttgcagttcaaacaGaattgaaagaatgcatggtg	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142832372G>T	ENST00000291009.3	+	2	221	c.181G>T	c.(181-183)Gaa>Taa	p.E61*		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	61					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)	p.E61*(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		AGTTCAAACAGAATTGAAAGA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											59	54	56					7																	142832372		2203	4299	6502	142542494	SO:0001587	stop_gained	5304				CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"prolactin-inducible protein"	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.181G>T	7.37:g.142832372G>T	ENSP00000291009:p.Glu61*		142542494	A0A963|A0A9C3|A0A9F3|A4D2I1	Nonsense_Mutation	SNP	ENST00000291009.3	37	CCDS34768.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312045	0.40895	.	.	ENSG00000159763	ENST00000291009	.	.	.	4.55	-0.609	0.11608	.	0.979395	0.08363	N	0.957405	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	4.501	0.11863	0.2837:0.3277:0.3886:0.0	.	.	.	.	X	61	.	ENSP00000291009:E61X	E	+	1	0	PIP	142542494	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.735000	0.04888	-0.215000	0.10063	-0.142000	0.14014	GAA		0.378	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652		T	142832372	G	T	142832372	4	4	61	1	0	0	0	0	0	1	0	0	11966	943	33	2	187	2	PIP	7	142832372	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108248	142832372	16306291	5653	13638										
TAS2R40	259286	broad.mit.edu	37	chr7	142919225	142919225	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatatccaagttcaaggtCaccttcactttggtggtctc	8	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:142919225C>A	ENST00000408947.3	+	1	96	c.54C>A	c.(52-54)gtC>gtA	p.V18V	AC073342.1_ENST00000595842.1_Missense_Mutation_p.D46Y	NM_176882.1	NP_795363.1	P59535	T2R40_HUMAN	taste receptor, type 2, member 40	18					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.V18V(2)		kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8	Melanoma(164;0.059)					AGTTCAAGGTCACCTTCACTT	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	7											110	112	111					7																	142919225		2033	4181	6214	142629347	SO:0001819	synonymous_variant	259286			AF494229	CCDS43662.1	7q34	2012-08-22	2003-12-16		ENSG00000221937	ENSG00000221937		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18885	protein-coding gene	gene with protein product		613964	"G protein-coupled receptor 60"	GPR60		12379855	Standard	NM_176882		Approved		uc011ksx.2	P59535	OTTHUMG00000152638	ENST00000408947.3:c.54C>A	7.37:g.142919225C>A			142629347	A4D2I2|Q645W6	Silent	SNP	ENST00000408947.3	37	CCDS43662.1																																																																																				0.502	TAS2R40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327097.1			A	142919225	C	A	142919225	2	1	61	1	0	0	0	0	0	0	0	1	15617	813	29	2		2	TAS2R40	7	142919225	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86853	142919225	16219438	5654	13639										
CLCN1	1180	broad.mit.edu	37	chr7	143017790	143017790	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggacaggtggtgagaaGaaaattaggggaagacggga	18	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143017790G>A	ENST00000343257.2	+	3	422	c.335G>A	c.(334-336)aGa>aAa	p.R112K		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	112					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R112K(1)		breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					GTGGTGAGAAGAAAATTAGGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	7											163	133	143					7																	143017790		2203	4300	6503	142727912	SO:0001583	missense	1180			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.335G>A	7.37:g.143017790G>A	ENSP00000339867:p.Arg112Lys		142727912	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	37	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	.	13.99	2.401945	0.42613	.	.	ENSG00000188037	ENST00000343257	D	0.92805	-3.11	4.99	4.99	0.66335	Chloride channel, core (2);	0.115950	0.64402	D	0.000016	D	0.86740	0.6005	L	0.47190	1.495	0.30307	N	0.788861	B	0.13145	0.007	B	0.06405	0.002	T	0.76761	-0.2840	10	0.15066	T	0.55	.	9.5235	0.39149	0.096:0.0:0.904:0.0	.	112	P35523	CLCN1_HUMAN	K	112	ENSP00000339867:R112K	ENSP00000339867:R112K	R	+	2	0	CLCN1	142727912	.	.	0.694000	0.30210	0.896000	0.52359	.	.	2.333000	0.79357	0.650000	0.86243	AGA		0.448	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143017790	G	A	143017790	3	1	61	1	0	0	0	0	1	0	0	0	3468	942	33	3	345	3	CLCN1	7	143017790	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98565	143017790	16120873	5655	13640										
CLCN1	1180	broad.mit.edu	37	chr7	143028407	143028407	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaccagcttttgctgccatCgggtcagtggggttacctgc	12	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143028407C>T	ENST00000343257.2	+	9	1149	c.1062C>T	c.(1060-1062)atC>atT	p.I354I		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	354					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.I354I(1)		breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TTGCTGCCATCGGGTCAGTGG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	7											120	108	112					7																	143028407		2203	4300	6503	142738529	SO:0001819	synonymous_variant	1180			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.1062C>T	7.37:g.143028407C>T			142738529	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																				0.527	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		T	143028407	C	T	143028407	2	4	61	1	0	0	0	0	0	0	0	1	3468	874	31	1		1	CLCN1	7	143028407	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10617	143028407	16110256	5656	13641										
CLCN1	1180	broad.mit.edu	37	chr7	143039197	143039197	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatcatccaggtcaagaaGctaccctacttgcctgacct	7	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143039197G>T	ENST00000343257.2	+	15	1845	c.1758G>T	c.(1756-1758)aaG>aaT	p.K586N		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	586					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.K586N(1)		breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AGGTCAAGAAGCTACCCTACT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											81	74	76					7																	143039197		2203	4300	6503	142749319	SO:0001583	missense	1180			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.1758G>T	7.37:g.143039197G>T	ENSP00000339867:p.Lys586Asn		142749319	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	37	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457330	0.84317	.	.	ENSG00000188037	ENST00000343257	D	0.92752	-3.1	6.04	5.15	0.70609	Chloride channel, core (2);	0.088817	0.85682	D	0.000000	D	0.94621	0.8266	L	0.58428	1.81	0.58432	D	0.999992	D	0.89917	1.0	D	0.73708	0.981	D	0.93938	0.7220	10	0.51188	T	0.08	.	14.7504	0.69522	0.0686:0.0:0.9314:0.0	.	586	P35523	CLCN1_HUMAN	N	586	ENSP00000339867:K586N	ENSP00000339867:K586N	K	+	3	2	CLCN1	142749319	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.780000	0.75063	2.873000	0.98535	0.643000	0.83706	AAG		0.552	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		T	143039197	G	T	143039197	3	4	61	1	0	0	0	0	1	0	0	0	3468	962	34	2	1816	2	CLCN1	7	143039197	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10790	143039197	16099466	5657	13642										
FAM131B	9715	broad.mit.edu	37	chr7	143054021	143054021	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcaatgagggactgatcGctggcttcccaggcatctga	14	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143054021G>A	ENST00000409408.1	-	6	2329	c.621C>T	c.(619-621)agC>agT	p.S207S	FAM131B_ENST00000409346.1_Silent_p.S207S|FAM131B_ENST00000443739.2_Silent_p.S235S|FAM131B_ENST00000409222.3_Silent_p.S207S|FAM131B_ENST00000409578.1_Silent_p.S223S			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	207								p.S207S(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					GGGACTGATCGCTGGCTTCCC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	7											64	59	61					7																	143054021		2203	4300	6503	142764143	SO:0001819	synonymous_variant	9715			BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.621C>T	7.37:g.143054021G>A			142764143	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Silent	SNP	ENST00000409408.1	37	CCDS5882.1																																																																																				0.562	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690		A	143054021	G	A	143054021	2	1	61	1	0	0	0	0	0	0	0	1	5456	1078	38	1		1	FAM131B	7	143054021	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14824	143054021	16084642	5658	13643										
ZYX	7791	broad.mit.edu	37	chr7	143080204	143080204	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagttttctccagtgactcCtaagtttactcctgtggctt	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143080204C>A	ENST00000322764.5	+	5	1157	c.812C>A	c.(811-813)cCt>cAt	p.P271H	ZYX_ENST00000449423.2_Missense_Mutation_p.P184H|AC093673.5_ENST00000429630.1_RNA|ZYX_ENST00000392910.2_Missense_Mutation_p.P114H|ZYX_ENST00000477373.1_3'UTR	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	271					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P271H(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					CCAGTGACTCCTAAGTTTACT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											112	138	129					7																	143080204		2203	4300	6503	142790326	SO:0001583	missense	7791			X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.812C>A	7.37:g.143080204C>A	ENSP00000324422:p.Pro271His		142790326	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	C	9.241	1.038405	0.19669	.	.	ENSG00000159840	ENST00000322764;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T	0.55052	0.67;0.6;0.55;0.54	4.25	3.35	0.38373	.	0.086968	0.47093	N	0.000241	T	0.63522	0.2518	M	0.63428	1.95	0.09310	N	1	D;D	0.71674	0.998;0.997	P;P	0.61397	0.888;0.841	T	0.55927	-0.8063	10	0.59425	D	0.04	.	10.4387	0.44452	0.35:0.65:0.0:0.0	.	184;271	B4DQR8;Q15942	.;ZYX_HUMAN	H	271;239;184;114	ENSP00000324422:P271H;ENSP00000346417:P239H;ENSP00000394158:P184H;ENSP00000376642:P114H	ENSP00000324422:P271H	P	+	2	0	ZYX	142790326	0.667000	0.27484	0.883000	0.34634	0.155000	0.21991	2.758000	0.47565	0.749000	0.32854	-0.182000	0.12963	CCT		0.572	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461		A	143080204	C	A	143080204	3	1	61	1	0	0	0	0	1	0	0	0	18293	681	24	2	826	2	ZYX	7	143080204	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26183	143080204	16058459	5659	13644										
EPHA1	2041	broad.mit.edu	37	chr7	143095468	143095468	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccagggcttcggggccgGgaccccgcccaggtcagctc	15	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143095468G>A	ENST00000275815.3	-	7	1496	c.1410C>T	c.(1408-1410)tcC>tcT	p.S470S		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	470	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.S470S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				TTCGGGGCCGGGACCCCGCCC	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	7											48	51	50					7																	143095468		2203	4300	6503	142805590	SO:0001819	synonymous_variant	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1410C>T	7.37:g.143095468G>A			142805590	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																				0.602	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143095468	G	A	143095468	2	1	61	1	0	0	0	0	0	0	0	1	5178	1219	43	3		3	EPHA1	7	143095468	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15264	143095468	16043195	5660	13645										
TAS2R60	338398	broad.mit.edu	37	chr7	143140577	143140577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacatggttctaggatcttCggtgactgacaagaaggcca	11	10	2	3	rs144050978		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143140577C>T	ENST00000332690.1	+	1	32	c.32C>T	c.(31-33)tCg>tTg	p.S11L	EPHA1-AS1_ENST00000429289.1_RNA	NM_177437.1	NP_803186.1	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	11					sensory perception of bitter taste (GO:0050913)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S11L(1)		breast(1)|kidney(1)|large_intestine(2)|lung(17)|prostate(1)|skin(7)|urinary_tract(2)	31	Melanoma(164;0.172)					CTAGGATCTTCGGTGACTGAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	202	189	193		32	-9.4	0	7	dbSNP_134	193	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TAS2R60	NM_177437.1	145	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	11/319	143140577	2,13004	2203	4300	6503	142850699	SO:0001583	missense	338398			AY114094	CCDS5885.1	7q35	2014-07-10			ENSG00000185899	ENSG00000185899		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	20639	protein-coding gene	gene with protein product		613968				12584440	Standard	NM_177437		Approved	T2R60	uc011ktg.2	P59551	OTTHUMG00000154891	ENST00000332690.1:c.32C>T	7.37:g.143140577C>T	ENSP00000327724:p.Ser11Leu		142850699	A4D2G8|Q645W8|Q7RTR7	Missense_Mutation	SNP	ENST00000332690.1	37	CCDS5885.1	.	.	.	.	.	.	.	.	.	.	C	9.204	1.029302	0.19512	2.27E-4	1.16E-4	ENSG00000185899	ENST00000332690	T	0.38401	1.14	4.72	-9.43	0.00607	.	2.502070	0.02146	N	0.057611	T	0.15003	0.0362	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12889	-1.0530	10	0.36615	T	0.2	.	3.9768	0.09478	0.2212:0.1192:0.0858:0.5739	.	11	P59551	T2R60_HUMAN	L	11	ENSP00000327724:S11L	ENSP00000327724:S11L	S	+	2	0	TAS2R60	142850699	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.115000	0.01328	-2.448000	0.00545	-0.812000	0.03155	TCG		0.498	TAS2R60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337541.1			T	143140577	C	T	143140577	3	4	61	1	0	0	0	0	1	0	0	0	15624	893	31	1	34	1	TAS2R60	7	143140577	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45109	143140577	15998086	5661	13646										
TAS2R41	259287	broad.mit.edu	37	chr7	143175841	143175841	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaacctcaagcttcgaagCgtgttctcgcagctcctgtt	9	13	2	0	rs202050176		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143175841C>T	ENST00000408916.1	+	1	876	c.876C>T	c.(874-876)agC>agT	p.S292S	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	292					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S292S(1)		endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					AGCTTCGAAGCGTGTTCTCGC	0.517													C|||	1	0.000199681	8e-04	0	5008	,	,		21194	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						C		0,4126		0,0,2063	106	98	101		876	-3.9	0	7		101	1,8391		0,1,4195	no	coding-synonymous	TAS2R41	NM_176883.2		0,1,6258	TT,TC,CC		0.0119,0.0,0.0080		292/308	143175841	1,12517	2063	4196	6259	142885963	SO:0001819	synonymous_variant	259287			AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.876C>T	7.37:g.143175841C>T			142885963	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Silent	SNP	ENST00000408916.1	37	CCDS43663.1																																																																																				0.517	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175841	C	T	143175841	2	4	61	1	0	0	0	0	0	0	0	1	15618	767	27	1		1	TAS2R41	7	143175841	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35264	143175841	15962822	5662	13647										
LOC441294	441294	broad.mit.edu	37	chr7	143270136	143270136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagtggaggaaaattaccGaatagaggaagaagagaagc	13	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143270136G>A	ENST00000420911.2	+	1	1243	c.1226G>A	c.(1225-1227)cGa>cAa	p.R409Q	RNU6-162P_ENST00000516228.1_RNA	NM_001008747.1	NP_001008747.1	A4D2H0	CTGEF_HUMAN	CTAGE family, member 15	409						integral component of membrane (GO:0016021)											GAAAATTACCGAATAGAGGAA	0.378																																																0			7											33	36	35					7																	143270136		1646	3652	5298	142980258	SO:0001583	missense	441294				CCDS64788.1	7q35	2013-02-25	2013-02-25	2013-02-25	ENSG00000176227	ENSG00000271079			37295	protein-coding gene	gene with protein product			"CTAGE family, member 15, pseudogene"	CTAGE15P			Standard	NM_001008747		Approved		uc011kth.3	A4D2H0	OTTHUMG00000153233	ENST00000420911.2:c.1226G>A	7.37:g.143270136G>A	ENSP00000474204:p.Arg409Gln		142980258	A6H8Z8	Missense_Mutation	SNP	ENST00000420911.2	37																																																																																					0.378	CTAGE15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330280.2	NM_001008747		A	143270136	G	A	143270136	3	1	61	1	0	0	0	0	1	0	0	0	8908	1058	37	1	1228	1	LOC441294	7	143270136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94295	143270136	15868527	5663	13648										
FAM115C	285966	broad.mit.edu	37	chr7	143417173	143417173	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgctgcaaggcgtacagtGacaaggaggctaagcagctg	14	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143417173G>T	ENST00000441159.2	+	3	1087	c.1021G>T	c.(1021-1023)Gac>Tac	p.D341Y	FAM115C_ENST00000409703.3_Missense_Mutation_p.D177Y|FAM115C_ENST00000357344.4_Missense_Mutation_p.D341Y|FAM115C_ENST00000425618.2_Missense_Mutation_p.D60Y|FAM115C_ENST00000444908.2_Missense_Mutation_p.D341Y|FAM115C_ENST00000411935.1_Missense_Mutation_p.D177Y|FAM115C_ENST00000411497.2_Missense_Mutation_p.D60Y			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	341					hematopoietic progenitor cell differentiation (GO:0002244)			p.D341Y(1)		endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						GGCGTACAGTGACAAGGAGGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											65	68	67					7																	143417173		2147	4288	6435	143048106	SO:0001583	missense	285966			AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"family with sequence similarity 139, member A"	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.1021G>T	7.37:g.143417173G>T	ENSP00000404265:p.Asp341Tyr		143048106	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Missense_Mutation	SNP	ENST00000441159.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	13.87|13.87	2.366962|2.366962	0.41902|0.41902	.|.	.|.	ENSG00000170379|ENSG00000170379	ENST00000444908;ENST00000411497;ENST00000357344;ENST00000441159;ENST00000411935;ENST00000409703;ENST00000425618|ENST00000518791	T;T;T;T;T;T;T|.	0.21361|.	2.01;2.01;2.01;2.01;2.01;2.01;2.01|.	3.58|3.58	2.69|2.69	0.31865|0.31865	.|.	0.250346|.	0.45361|.	D|.	0.000377|.	T|.	0.70692|.	0.3253|.	M|M	0.88377|0.88377	2.95|2.95	0.33587|0.33587	D|D	0.600564|0.600564	D;D;D;D|.	0.89917|.	1.0;0.998;0.996;0.999|.	D;D;P;D|.	0.78314|.	0.991;0.928;0.838;0.967|.	T|.	0.77384|.	-0.2608|.	10|.	0.87932|.	D|.	0|.	-16.0425|-16.0425	7.4885|7.4885	0.27447|0.27447	0.1292:0.0:0.8708:0.0|0.1292:0.0:0.8708:0.0	.|.	177;341;60;341|.	A6NFQ2-3;A6NFQ2;Q8N1I1;A6NFQ2-2|.	.;F115C_HUMAN;.;.|.	Y|L	341;60;341;341;177;177;60|155	ENSP00000412724:D341Y;ENSP00000390603:D60Y;ENSP00000349902:D341Y;ENSP00000404265:D341Y;ENSP00000389100:D177Y;ENSP00000386405:D177Y;ENSP00000441099:D60Y|.	ENSP00000349902:D341Y|.	D|X	+|+	1|2	0|2	FAM115C|FAM115C	143048106|143048106	0.890000|0.890000	0.30428|0.30428	0.043000|0.043000	0.18650|0.18650	0.808000|0.808000	0.45660|0.45660	4.487000|4.487000	0.60293|0.60293	0.788000|0.788000	0.33755|0.33755	0.411000|0.411000	0.27672|0.27672	GAC|TGA		0.602	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330287.1	NM_173678		T	143417173	G	T	143417173	3	4	61	1	0	0	0	0	1	0	0	0	5422	1290	45	2	1162	2	FAM115C	7	143417173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147037	143417173	15721490	5664	13649										
FAM115C	285966	broad.mit.edu	37	chr7	143421714	143421714	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctccagagcgagagaggaGaatcaaggcccacctgggaa	13	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143421714G>T	ENST00000441159.2	+	7	2495	c.2429G>T	c.(2428-2430)aGa>aTa	p.R810I	FAM115C_ENST00000409703.3_Missense_Mutation_p.R706I|FAM115C_ENST00000357344.4_Missense_Mutation_p.R810I|FAM115C_ENST00000425618.2_Missense_Mutation_p.R529I|FAM115C_ENST00000444908.2_Missense_Mutation_p.R810I|FAM115C_ENST00000411935.1_Missense_Mutation_p.R706I|FAM115C_ENST00000411497.2_Missense_Mutation_p.R529I			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	810	Peptidase M60.				hematopoietic progenitor cell differentiation (GO:0002244)			p.R810I(1)		endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						CGAGAGAGGAGAATCAAGGCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	7											25	25	25					7																	143421714		2202	4296	6498	143052647	SO:0001583	missense	285966			AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"family with sequence similarity 139, member A"	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.2429G>T	7.37:g.143421714G>T	ENSP00000404265:p.Arg810Ile		143052647	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Missense_Mutation	SNP	ENST00000441159.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.66|14.66	2.603140|2.603140	0.46423|0.46423	.|.	.|.	ENSG00000170379|ENSG00000170379	ENST00000518791|ENST00000444908;ENST00000411497;ENST00000357344;ENST00000441159;ENST00000411935;ENST00000409703;ENST00000425618	.|.	.|.	.|.	4.23|4.23	4.23|4.23	0.50019|0.50019	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81168|0.81168	0.4766|0.4766	M|M	0.88640|0.88640	2.97|2.97	0.40087|0.40087	D|D	0.976206|0.976206	.|D;D;D;D	.|0.89917	.|0.961;0.999;1.0;1.0	.|P;D;D;D	.|0.97110	.|0.848;0.992;1.0;0.995	D|D	0.84417|0.84417	0.0569|0.0569	5|9	.|0.46703	.|T	.|0.11	-32.1436|-32.1436	14.4736|14.4736	0.67533|0.67533	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|706;810;529;810	.|A6NFQ2-3;A6NFQ2;Q8N1I1;A6NFQ2-2	.|.;F115C_HUMAN;.;.	D|I	624|810;529;810;810;706;706;529	.|.	.|ENSP00000349902:R810I	E|R	+|+	3|2	2|0	FAM115C|FAM115C	143052647|143052647	1.000000|1.000000	0.71417|0.71417	0.126000|0.126000	0.21872|0.21872	0.005000|0.005000	0.04900|0.04900	5.328000|5.328000	0.65887|0.65887	2.078000|2.078000	0.62432|0.62432	0.411000|0.411000	0.27672|0.27672	GAG|AGA		0.567	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330287.1	NM_173678		T	143421714	G	T	143421714	3	4	61	1	0	0	0	0	1	0	0	0	5422	942	33	2	2770	2	FAM115C	7	143421714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4541	143421714	15716949	5665	13650										
CTAGE6P	340307	broad.mit.edu	37	chr7	143453459	143453459	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggctagctttctataggtCtccagctgttcagtggcacg	11	10	3	0	rs536781747		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143453459C>A	ENST00000470691.2	-	1	1330	c.1293G>T	c.(1291-1293)gaG>gaT	p.E431D	RNU6-267P_ENST00000516714.1_RNA	NM_178561.4	NP_848656.2	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	431						integral component of membrane (GO:0016021)						Melanoma(164;0.0903)					TTCTATAGGTCTCCAGCTGTT	0.388																																																0			7											107	98	101					7																	143453459		1930	4157	6087	143084392	SO:0001583	missense	340307			BC043153	CCDS64790.1	7q35	2013-05-22	2013-02-25	2013-02-25	ENSG00000271321	ENSG00000271321			28644	protein-coding gene	gene with protein product			"CTAGE family, member 6, pseudogene"	CTAGE6P		12477932	Standard	NM_178561		Approved	MGC41943	uc003wdk.4	Q86UF2	OTTHUMG00000157770	ENST00000470691.2:c.1293G>T	7.37:g.143453459C>A	ENSP00000474388:p.Glu431Asp		143084392	A4FU29|Q3ZCM5	Missense_Mutation	SNP	ENST00000470691.2	37																																																																																					0.388	CTAGE6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349580.2	NM_178561		A	143453459	C	A	143453459	3	1	61	1	0	0	0	0	1	0	0	0	4001	912	32	2	1044	2	CTAGE6P	7	143453459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31745	143453459	15685204	5666	13651										
CTAGE6P	340307	broad.mit.edu	37	chr7	143453582	143453582	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatttcatcttcttgataGaattcagtcattattttaag	4	6	6	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143453582G>T	ENST00000470691.2	-	1	1207	c.1170C>A	c.(1168-1170)ttC>ttA	p.F390L	RNU6-267P_ENST00000516714.1_RNA	NM_178561.4	NP_848656.2	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	390						integral component of membrane (GO:0016021)						Melanoma(164;0.0903)					CTTCTTGATAGAATTCAGTCA	0.313																																																0			7											90	73	78					7																	143453582		1905	4167	6072	143084515	SO:0001583	missense	340307			BC043153	CCDS64790.1	7q35	2013-05-22	2013-02-25	2013-02-25	ENSG00000271321	ENSG00000271321			28644	protein-coding gene	gene with protein product			"CTAGE family, member 6, pseudogene"	CTAGE6P		12477932	Standard	NM_178561		Approved	MGC41943	uc003wdk.4	Q86UF2	OTTHUMG00000157770	ENST00000470691.2:c.1170C>A	7.37:g.143453582G>T	ENSP00000474388:p.Phe390Leu		143084515	A4FU29|Q3ZCM5	Missense_Mutation	SNP	ENST00000470691.2	37																																																																																					0.313	CTAGE6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349580.2	NM_178561		T	143453582	G	T	143453582	3	4	61	1	0	0	0	0	1	0	0	0	4001	933	33	2	1167	2	CTAGE6P	7	143453582	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123	143453582	15685081	5667	13652										
OR2F1	26211	broad.mit.edu	37	chr7	143657246	143657246	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccacactcccatgtatttCtttctcaccaacctctccct	1	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143657246C>A	ENST00000392899.1	+	1	220	c.183C>A	c.(181-183)ttC>ttA	p.F61L	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	61					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F61L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					CCATGTATTTCTTTCTCACCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											274	262	266					7																	143657246		2203	4298	6501	143288179	SO:0001583	missense	26211			U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.183C>A	7.37:g.143657246C>A	ENSP00000376633:p.Phe61Leu		143288179	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.689365	0.48097	.	.	ENSG00000213215	ENST00000392899	T	0.00551	6.65	5.65	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000029	T	0.00815	0.0027	M	0.83012	2.62	0.39113	D	0.961519	B	0.14438	0.01	B	0.13407	0.009	T	0.52704	-0.8540	10	0.87932	D	0	-53.3045	5.6131	0.17416	0.1559:0.6842:0.0:0.1599	.	61	Q13607	OR2F1_HUMAN	L	61	ENSP00000376633:F61L	ENSP00000376633:F61L	F	+	3	2	OR2F1	143288179	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	0.446000	0.21694	0.946000	0.37632	0.655000	0.94253	TTC		0.498	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			A	143657246	C	A	143657246	3	1	61	1	0	0	0	0	1	0	0	0	11027	912	32	2	185	2	OR2F1	7	143657246	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203664	143657246	15481417	5668	13653										
OR2F1	26211	broad.mit.edu	37	chr7	143657768	143657768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtccagagaaggaagaaaGaaagctttccacacgtgtgc	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143657768G>T	ENST00000392899.1	+	1	742	c.705G>T	c.(703-705)aaG>aaT	p.K235N	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	235					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K235N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					AAGGAAGAAAGAAAGCTTTCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											183	158	167					7																	143657768		2203	4300	6503	143288701	SO:0001583	missense	26211			U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.705G>T	7.37:g.143657768G>T	ENSP00000376633:p.Lys235Asn		143288701	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511243	0.44660	.	.	ENSG00000213215	ENST00000392899	T	0.00495	6.99	5.53	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.358433	0.24072	N	0.041820	T	0.00784	0.0026	L	0.46614	1.455	0.29098	N	0.881648	P	0.34587	0.458	P	0.48141	0.568	T	0.21965	-1.0230	10	0.62326	D	0.03	-4.5588	9.0966	0.36642	0.077:0.4362:0.4869:0.0	.	235	Q13607	OR2F1_HUMAN	N	235	ENSP00000376633:K235N	ENSP00000376633:K235N	K	+	3	2	OR2F1	143288701	0.056000	0.20664	0.461000	0.27105	0.673000	0.39480	0.251000	0.18257	0.430000	0.26230	0.655000	0.94253	AAG		0.502	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			T	143657768	G	T	143657768	3	4	61	1	0	0	0	0	1	0	0	0	11027	933	33	2	707	2	OR2F1	7	143657768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	522	143657768	15480895	5669	13654										
OR6B1	135946	broad.mit.edu	37	chr7	143701794	143701794	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacaggaaagcagaaagcGttctccacttgtgcctccca	8	15	1	1	rs150940478	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143701794G>A	ENST00000408922.2	+	1	773	c.705G>A	c.(703-705)gcG>gcA	p.A235A		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A235A(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					AGCAGAAAGCGTTCTCCACTT	0.463													G|||	5	0.000998403	0.0038	0	5008	,	,		24020	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						G		2,4064		0,2,2031	197	188	191		705	-7.8	0.7	7	dbSNP_134	191	0,8368		0,0,4184	no	coding-synonymous	OR6B1	NM_001005281.1		0,2,6215	AA,AG,GG		0.0,0.0492,0.0161		235/312	143701794	2,12432	2033	4184	6217	143332727	SO:0001819	synonymous_variant	135946				CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"GPCR / Class A : Olfactory receptors"	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.705G>A	7.37:g.143701794G>A			143332727	A4D2G2|B9EH47|Q6IFP6|Q96R38	Silent	SNP	ENST00000408922.2	37	CCDS43667.1																																																																																				0.463	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1			A	143701794	G	A	143701794	2	1	61	1	0	0	0	0	0	0	0	1	11218	1132	40	1		1	OR6B1	7	143701794	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44026	143701794	15436869	5670	13655										
OR2A2	442361	broad.mit.edu	37	chr7	143806690	143806690	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagcatggaaggcaaccaGacatggatcacagacatcac	10	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143806690G>T	ENST00000408979.2	+	1	84	c.15G>T	c.(13-15)caG>caT	p.Q5H		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	5			Q -> K (in dbSNP:rs10230228).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q5H(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					AAGGCAACCAGACATGGATCA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											108	105	106					7																	143806690		2009	4188	6197	143437623	SO:0001583	missense	442361				CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"GPCR / Class A : Olfactory receptors"	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.15G>T	7.37:g.143806690G>T	ENSP00000386209:p.Gln5His		143437623	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.645927	0.29246	.	.	ENSG00000221989	ENST00000408979	T	0.00649	5.98	3.61	2.71	0.32032	.	.	.	.	.	T	0.00608	0.0020	N	0.21508	0.67	0.09310	N	1	B	0.22604	0.072	B	0.23018	0.043	T	0.47774	-0.9091	9	0.49607	T	0.09	.	6.8737	0.24135	0.1329:0.0:0.8671:0.0	.	5	Q6IF42	OR2A2_HUMAN	H	5	ENSP00000386209:Q5H	ENSP00000386209:Q5H	Q	+	3	2	OR2A2	143437623	0.000000	0.05858	0.991000	0.47740	0.994000	0.84299	-0.419000	0.07071	0.842000	0.35045	0.609000	0.83330	CAG		0.507	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1			T	143806690	G	T	143806690	3	4	61	1	0	0	0	0	1	0	0	0	11008	933	33	2	17	2	OR2A2	7	143806690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104896	143806690	15331973	5671	13656										
OR2A2	442361	broad.mit.edu	37	chr7	143806972	143806972	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgttccatgcataatgcaGacttttttgtatttggcttt	7	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:143806972G>T	ENST00000408979.2	+	1	366	c.297G>T	c.(295-297)caG>caT	p.Q99H		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q99H(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					GCATAATGCAGACTTTTTTGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	7											230	211	217					7																	143806972		2021	4211	6232	143437905	SO:0001583	missense	442361				CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"GPCR / Class A : Olfactory receptors"	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.297G>T	7.37:g.143806972G>T	ENSP00000386209:p.Gln99His		143437905	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	.	.	.	.	.	.	.	.	.	.	G	8.270	0.813243	0.16537	.	.	ENSG00000221989	ENST00000408979	T	0.00472	7.19	3.61	0.638	0.17742	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02012	0.0063	H	0.96691	3.865	0.29634	N	0.845217	D	0.89917	1.0	D	0.75484	0.986	T	0.12016	-1.0564	9	0.87932	D	0	-11.8729	6.2082	0.20613	0.4976:0.0:0.5024:0.0	.	99	Q6IF42	OR2A2_HUMAN	H	99	ENSP00000386209:Q99H	ENSP00000386209:Q99H	Q	+	3	2	OR2A2	143437905	0.525000	0.26290	0.016000	0.15963	0.013000	0.08279	0.454000	0.21827	0.006000	0.14734	-0.192000	0.12808	CAG		0.428	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1			T	143806972	G	T	143806972	3	4	61	1	0	0	0	0	1	0	0	0	11008	933	33	2	299	2	OR2A2	7	143806972	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282	143806972	15331691	5672	13657										
OR2A1	346528	broad.mit.edu	37	chr7	144015544	144015544	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgagttttggacacagCgaatgtctcctgctggtgct	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:144015544C>T	ENST00000408951.1	+	1	327	c.327C>T	c.(325-327)agC>agT	p.S109S	OR2A1-AS1_ENST00000475089.1_RNA|OR2A1-AS1_ENST00000488041.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000496968.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000493539.1_RNA|OR2A1-AS1_ENST00000486094.1_RNA|OR2A1-AS1_ENST00000478925.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000467944.1_RNA	NM_001005287.1	NP_001005287.1	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A, member 1	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S109S(1)		large_intestine(1)|lung(3)|skin(2)	6	Melanoma(164;0.14)					TTGGACACAGCGAATGTCTCC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	7											107	124	118					7																	144015544		2202	4294	6496	143646477	SO:0001819	synonymous_variant	441295				CCDS43673.1	7q35	2013-09-20			ENSG00000221970	ENSG00000221970		"GPCR / Class A : Olfactory receptors"	8229	protein-coding gene	gene with protein product							Standard	NM_001005287		Approved		uc011kub.2	Q8NGT9	OTTHUMG00000158005	ENST00000408951.1:c.327C>T	7.37:g.144015544C>T			143646477	Q6IF44|Q96R46	Silent	SNP	ENST00000408951.1	37	CCDS43673.1																																																																																				0.567	OR2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349985.1			T	144015544	C	T	144015544	2	4	61	1	0	0	0	0	0	0	0	1	11005	767	27	1		1	OR2A1	7	144015544	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	208572	144015544	15123119	5673	13658										
TPK1	27010	broad.mit.edu	37	chr7	144288524	144288524	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttgactcactggttggaGcaggtagatcagcgattcct	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:144288524G>T	ENST00000360057.3	-	7	595	c.493C>A	c.(493-495)Ctc>Atc	p.L165I	TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Intron|TPK1_ENST00000549981.1_Missense_Mutation_p.L48I|TPK1_ENST00000378099.3_Intron	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	165					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)	p.L165I(1)		large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	ACTGGTTGGAGCAGGTAGATC	0.418																																					Ovarian(45;88 1034 2073 5829 28455)											1	Substitution - Missense(1)	large_intestine(1)	7											141	141	141					7																	144288524		2203	4300	6503	143919457	SO:0001583	missense	27010			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.493C>A	7.37:g.144288524G>T	ENSP00000353165:p.Leu165Ile		143919457	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.284940	0.80803	.	.	ENSG00000196511	ENST00000360057;ENST00000549981;ENST00000552881	T;D	0.90004	-1.29;-2.6	5.78	5.78	0.91487	Thiamin pyrophosphokinase, vitamin B1-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.93304	0.7866	M	0.82923	2.615	0.80722	D	1	D	0.60160	0.987	P	0.56434	0.798	D	0.91959	0.5577	10	0.31617	T	0.26	-7.0755	17.5062	0.87746	0.0:0.0:1.0:0.0	.	165	Q9H3S4	TPK1_HUMAN	I	165;48;165	ENSP00000353165:L165I;ENSP00000448655:L165I	ENSP00000353165:L165I	L	-	1	0	TPK1	143919457	1.000000	0.71417	1.000000	0.80357	0.548000	0.35241	8.218000	0.89768	2.749000	0.94314	0.655000	0.94253	CTC		0.418	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		T	144288524	G	T	144288524	3	4	61	1	0	0	0	0	1	0	0	0	16444	971	34	2	250	2	TPK1	7	144288524	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272980	144288524	14850139	5674	13659										
TPK1	27010	broad.mit.edu	37	chr7	144320270	144320270	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatattacctttaagtcttTttcttctatcttcttttgga	3	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:144320270T>G	ENST00000360057.3	-	6	445	c.343A>C	c.(343-345)Aaa>Caa	p.K115Q	TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Missense_Mutation_p.K110Q|TPK1_ENST00000549981.1_5'UTR|TPK1_ENST00000378099.3_Missense_Mutation_p.K115Q	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	115					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)	p.K115Q(1)		large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	TTTAAGTCTTTTTCTTCTATC	0.318																																					Ovarian(45;88 1034 2073 5829 28455)											1	Substitution - Missense(1)	large_intestine(1)	7											168	179	175					7																	144320270		2203	4300	6503	143951203	SO:0001583	missense	27010			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.343A>C	7.37:g.144320270T>G	ENSP00000353165:p.Lys115Gln		143951203	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.406519	0.25378	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099;ENST00000552881	D;T;D;D	0.83163	-1.69;-1.13;-1.64;-1.69	5.78	4.63	0.57726	Thiamin pyrophosphokinase, catalytic domain (3);	0.229182	0.51477	D	0.000085	T	0.72526	0.3471	L	0.42008	1.315	0.80722	D	1	B;B;B	0.32128	0.158;0.006;0.357	B;B;B	0.30316	0.046;0.002;0.114	T	0.64309	-0.6438	10	0.12766	T	0.61	-13.7889	8.6143	0.33822	0.0:0.0861:0.0:0.9139	.	115;115;110	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	Q	115;110;115;115	ENSP00000353165:K115Q;ENSP00000438813:K110Q;ENSP00000367339:K115Q;ENSP00000448655:K115Q	ENSP00000353165:K115Q	K	-	1	0	TPK1	143951203	0.080000	0.21391	0.970000	0.41538	0.361000	0.29550	2.302000	0.43637	1.034000	0.39945	0.533000	0.62120	AAA		0.318	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		G	144320270	T	G	144320270	3	3	61	1	0	0	0	0	1	0	0	0	16444	1850	64	4	404	4	TPK1	7	144320270	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31746	144320270	14818393	5675	13660										
TPK1	27010	broad.mit.edu	37	chr7	144380018	144380018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctttctctctctccttCggtgatatcatataagcggt	6	11	3	1	rs200717734		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:144380018C>T	ENST00000360057.3	-	4	271	c.169G>A	c.(169-171)Gaa>Aaa	p.E57K	TPK1_ENST00000538212.2_Silent_p.P11P|TPK1_ENST00000549981.1_5'UTR|TPK1_ENST00000378099.3_Missense_Mutation_p.E57K	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	57					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)	p.E57K(1)|p.E57Q(1)		large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	CTCTCTCCTTCGGTGATATCA	0.393													C|||	1	0.000199681	0	0	5008	,	,		19760	0		0.001	False		,,,				2504	0				Ovarian(45;88 1034 2073 5829 28455)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7						C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	203	200	201		169,169	4.2	0.7	7		201	0,8600		0,0,4300	no	missense,missense	TPK1	NM_001042482.1,NM_022445.3	56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	57/195,57/244	144380018	1,13005	2203	4300	6503	144010951	SO:0001583	missense	27010			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.169G>A	7.37:g.144380018C>T	ENSP00000353165:p.Glu57Lys		144010951	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	16.12	3.031891	0.54790	2.27E-4	0.0	ENSG00000196511	ENST00000360057;ENST00000378099;ENST00000552881	D;D;D	0.82526	-1.62;-1.62;-1.62	6.02	4.21	0.49690	Thiamin pyrophosphokinase, catalytic domain (3);	0.258640	0.44688	D	0.000429	T	0.68054	0.2959	L	0.35487	1.065	0.80722	D	1	B;B	0.28667	0.219;0.173	B;B	0.23275	0.035;0.045	T	0.59343	-0.7472	10	0.06099	T	0.92	-13.4417	8.7148	0.34405	0.0:0.7694:0.1505:0.0801	.	57;57	F5GZG6;Q9H3S4	.;TPK1_HUMAN	K	57	ENSP00000353165:E57K;ENSP00000367339:E57K;ENSP00000448655:E57K	ENSP00000353165:E57K	E	-	1	0	TPK1	144010951	0.785000	0.28726	0.725000	0.30721	0.978000	0.69477	1.162000	0.31786	0.874000	0.35823	0.655000	0.94253	GAA		0.393	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		T	144380018	C	T	144380018	3	4	61	1	0	0	0	0	1	0	0	0	16444	893	31	1	586	1	TPK1	7	144380018	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59748	144380018	14758645	5676	13661										
CNTNAP2	26047	broad.mit.edu	37	chr7	146471468	146471468	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgccaagataaacaagaGaggaggtaagccaaattttg	10	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:146471468G>T	ENST00000361727.3	+	2	719	c.203G>T	c.(202-204)aGa>aTa	p.R68I		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	68	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.R68I(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ATAAACAAGAGAGGAGGTAAG	0.383										HNSCC(39;0.1)																																						1	Substitution - Missense(1)	large_intestine(1)	7											59	58	58					7																	146471468		2203	4300	6503	146102401	SO:0001583	missense	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.203G>T	7.37:g.146471468G>T	ENSP00000354778:p.Arg68Ile		146102401	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447692	0.84101	.	.	ENSG00000174469	ENST00000361727	D	0.98192	-4.78	5.74	5.74	0.90152	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.42821	D	0.000654	D	0.98707	0.9566	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	D	0.99814	1.1043	10	0.87932	D	0	.	17.4268	0.87528	0.0:0.0:1.0:0.0	.	68	Q9UHC6	CNTP2_HUMAN	I	68	ENSP00000354778:R68I	ENSP00000354778:R68I	R	+	2	0	CNTNAP2	146102401	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	8.817000	0.91985	2.714000	0.92807	0.650000	0.86243	AGA		0.383	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	146471468	G	T	146471468	3	4	61	1	0	0	0	0	1	0	0	0	3653	942	33	2	209	2	CNTNAP2	7	146471468	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2091450	146471468	12667195	5677	13662										
CNTNAP2	26047	broad.mit.edu	37	chr7	146829507	146829507	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtcactttgcggataaTttgggcaatgtggagattga	12	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:146829507T>C	ENST00000361727.3	+	8	1770	c.1254T>C	c.(1252-1254)aaT>aaC	p.N418N		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	418	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		N -> D. {ECO:0000269|PubMed:18179895}.		adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.N418N(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TTGCGGATAATTTGGGCAATG	0.483										HNSCC(39;0.1)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											124	110	115					7																	146829507		2203	4300	6503	146460440	SO:0001819	synonymous_variant	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1254T>C	7.37:g.146829507T>C			146460440	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																				0.483	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			C	146829507	T	C	146829507	2	2	61	1	0	0	0	0	0	0	0	1	3653	1490	52	4		4	CNTNAP2	7	146829507	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	358039	146829507	12309156	5678	13663										
CNTNAP2	26047	broad.mit.edu	37	chr7	147675053	147675053	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcagaagccaaattgagCgtaggtcctctgcgctgcca	12	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:147675053C>T	ENST00000361727.3	+	15	2871	c.2355C>T	c.(2353-2355)agC>agT	p.S785S		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	785	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.S785S(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CCAAATTGAGCGTAGGTCCTC	0.478										HNSCC(39;0.1)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											139	119	126					7																	147675053		2203	4300	6503	147305986	SO:0001819	synonymous_variant	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.2355C>T	7.37:g.147675053C>T			147305986	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																				0.478	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	147675053	C	T	147675053	2	4	61	1	0	0	0	0	0	0	0	1	3653	767	27	1		1	CNTNAP2	7	147675053	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	845546	147675053	11463610	5679	13664										
C7orf33	202865	broad.mit.edu	37	chr7	148312419	148312419	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcgtaatccacatgtagGtacgtgggcatgaagtaaga	11	7	1	2	rs141656152	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148312419G>A	ENST00000307003.2	+	3	821	c.460G>A	c.(460-462)Gta>Ata	p.V154I		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	154								p.V154I(1)		central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CCACATGTAGGTACGTGGGCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											125	120	122					7																	148312419		2203	4300	6503	147943352	SO:0001630	splice_region_variant	202865			BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.460-1G>A	7.37:g.148312419G>A			147943352		Missense_Mutation	SNP	ENST00000307003.2	37	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	G	4.083	0.013400	0.07912	.	.	ENSG00000170279	ENST00000307003	.	.	.	2.02	-2.21	0.06973	.	.	.	.	.	T	0.12987	0.0315	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.15870	0.014	T	0.23583	-1.0184	7	.	.	.	.	0.4748	0.00538	0.2528:0.1962:0.3519:0.1991	.	154	Q8WU49	CG033_HUMAN	I	154	.	.	V	+	1	0	C7orf33	147943352	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.812000	0.04496	-0.734000	0.04843	0.655000	0.94253	GTA		0.418	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	Missense_Mutation	A	148312419	G	A	148312419	5	1	61	1	0	0	0	0	0	0	1	0	2394	1275	44	3	470	3	C7orf33	7	148312419	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	637366	148312419	10826244	5680	13665										
ZNF425	155054	broad.mit.edu	37	chr7	148801486	148801486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaactccttctgcctgtCgtggactctggtgtggcagg	15	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148801486C>T	ENST00000378061.2	-	4	1609	c.1477G>A	c.(1477-1479)Gac>Aac	p.D493N		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	493					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D493N(1)		breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TTCTGCCTGTCGTGGACTCTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	7											50	43	45					7																	148801486		2200	4292	6492	148432419	SO:0001583	missense	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1477G>A	7.37:g.148801486C>T	ENSP00000367300:p.Asp493Asn		148432419	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	0.867	-0.733254	0.03135	.	.	ENSG00000204947	ENST00000378061	T	0.14640	2.49	2.74	-1.9	0.07665	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07052	0.0179	N	0.11892	0.195	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33879	-0.9851	9	0.62326	D	0.03	.	7.0521	0.25079	0.0:0.3014:0.0:0.6986	.	493	Q6IV72	ZN425_HUMAN	N	493	ENSP00000367300:D493N	ENSP00000367300:D493N	D	-	1	0	ZNF425	148432419	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.727000	0.04931	-0.520000	0.06435	-0.140000	0.14226	GAC		0.627	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148801486	C	T	148801486	3	4	61	1	0	0	0	0	1	0	0	0	17938	884	31	1	785	1	ZNF425	7	148801486	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	489067	148801486	10337177	5681	13666										
ZNF425	155054	broad.mit.edu	37	chr7	148802653	148802653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtcctgggagttccttCgtcatctggagcagaaagaa	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148802653C>T	ENST00000378061.2	-	4	442	c.310G>A	c.(310-312)Gaa>Aaa	p.E104K		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	104					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E104K(1)		breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GGAGTTCCTTCGTCATCTGGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											71	68	69					7																	148802653		2203	4299	6502	148433586	SO:0001583	missense	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.310G>A	7.37:g.148802653C>T	ENSP00000367300:p.Glu104Lys		148433586	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	7.720	0.697039	0.15106	.	.	ENSG00000204947	ENST00000378061;ENST00000483014	T;T	0.07021	3.23;5.01	2.45	-0.788	0.10939	.	.	.	.	.	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47420	-0.9119	9	0.07813	T	0.8	.	6.4447	0.21869	0.0:0.168:0.5049:0.3271	.	104	Q6IV72	ZN425_HUMAN	K	104;126	ENSP00000367300:E104K;ENSP00000420379:E126K	ENSP00000367300:E104K	E	-	1	0	ZNF425	148433586	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.042000	0.12063	-0.387000	0.07809	-2.406000	0.00223	GAA		0.368	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148802653	C	T	148802653	3	4	61	1	0	0	0	0	1	0	0	0	17938	893	31	1	1952	1	ZNF425	7	148802653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1167	148802653	10336010	5682	13667										
ZNF398	57541	broad.mit.edu	37	chr7	148876724	148876724	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacactcaaggaccacctccGttcaggccacaatggaggct	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148876724G>A	ENST00000475153.1	+	6	2027	c.1760G>A	c.(1759-1761)cGt>cAt	p.R587H	ZNF398_ENST00000540950.1_Missense_Mutation_p.R592H|ZNF398_ENST00000426851.2_Missense_Mutation_p.R416H|ZNF398_ENST00000335901.4_Missense_Mutation_p.R416H|ZNF398_ENST00000491174.1_Missense_Mutation_p.R416H|ZNF398_ENST00000483892.1_Missense_Mutation_p.R416H|ZNF398_ENST00000420008.2_Missense_Mutation_p.R416H			Q8TD17	ZN398_HUMAN	zinc finger protein 398	587					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R587H(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			GACCACCTCCGTTCAGGCCAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											63	66	65					7																	148876724		2203	4300	6503	148507657	SO:0001583	missense	57541			AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"Zinc fingers, C2H2-type", "-"	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.1760G>A	7.37:g.148876724G>A	ENSP00000420418:p.Arg587His		148507657	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Missense_Mutation	SNP	ENST00000475153.1	37	CCDS5894.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.888810	0.72524	.	.	ENSG00000197024	ENST00000426851;ENST00000420008;ENST00000475153;ENST00000483892;ENST00000491174;ENST00000540950;ENST00000335901	T;T;T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93;2.93;2.93	5.22	5.22	0.72569	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000124	T	0.26159	0.0638	L	0.48174	1.505	0.36725	D	0.881398	P;D	0.89917	0.627;1.0	B;D	0.72338	0.065;0.977	T	0.05733	-1.0867	10	0.87932	D	0	-22.5846	14.3573	0.66745	0.0:0.0:1.0:0.0	.	592;587	B4DXA9;Q8TD17	.;ZN398_HUMAN	H	416;416;587;416;416;592;416	ENSP00000389972:R416H;ENSP00000416751:R416H;ENSP00000420418:R587H;ENSP00000418564:R416H;ENSP00000419391:R416H;ENSP00000439340:R592H;ENSP00000338984:R416H	ENSP00000338984:R416H	R	+	2	0	ZNF398	148507657	0.166000	0.22962	0.884000	0.34674	0.970000	0.65996	1.607000	0.36836	2.454000	0.82982	0.650000	0.86243	CGT		0.592	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352722.2			A	148876724	G	A	148876724	3	1	61	1	0	0	0	0	1	0	0	0	17924	1145	40	1	1782	1	ZNF398	7	148876724	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74071	148876724	10261939	5683	13668										
ZNF282	8427	broad.mit.edu	37	chr7	148903889	148903889	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataacaaccttgttaaggaGaactacaaaaccctcatgtc	5	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148903889G>T	ENST00000262085.3	+	3	792	c.687G>T	c.(685-687)gaG>gaT	p.E229D	ZNF282_ENST00000479907.1_Missense_Mutation_p.E229D	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	229	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E229D(1)		endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TTGTTAAGGAGAACTACAAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	7											201	172	182					7																	148903889		2203	4300	6503	148534822	SO:0001583	missense	8427			D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.687G>T	7.37:g.148903889G>T	ENSP00000262085:p.Glu229Asp		148534822	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	37	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.727790	0.48833	.	.	ENSG00000170265	ENST00000430197;ENST00000262085;ENST00000479907	T;T	0.03920	3.76;3.76	5.69	2.75	0.32379	Krueppel-associated box (4);	0.000000	0.50627	D	0.000112	T	0.06371	0.0164	L	0.49513	1.565	0.32935	D	0.517693	P;P;P;P	0.42961	0.65;0.795;0.795;0.656	P;B;B;B	0.45099	0.469;0.396;0.396;0.396	T	0.23190	-1.0195	10	0.14252	T	0.57	-21.0492	9.27	0.37666	0.0768:0.2734:0.6498:0.0	.	229;180;201;229	B4DRI5;Q86YG2;Q7Z2V4;Q9UDV7	.;.;.;ZN282_HUMAN	D	144;229;229	ENSP00000262085:E229D;ENSP00000418840:E229D	ENSP00000262085:E229D	E	+	3	2	ZNF282	148534822	0.993000	0.37304	1.000000	0.80357	0.963000	0.63663	0.481000	0.22260	0.727000	0.32360	0.655000	0.94253	GAG		0.463	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		T	148903889	G	T	148903889	3	4	61	1	0	0	0	0	1	0	0	0	17858	933	33	2	697	2	ZNF282	7	148903889	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27165	148903889	10234774	5684	13669										
ZNF212	7988	broad.mit.edu	37	chr7	148947257	148947257	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaatccatcagcacaggaGaaaacgacgctccacacctt	6	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148947257G>A	ENST00000335870.2	+	2	160	c.32G>A	c.(31-33)aGa>aAa	p.R11K		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	11					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.R11K(1)		endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			CAGCACAGGAGAAAACGACGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											65	67	67					7																	148947257		2203	4300	6503	148578190	SO:0001583	missense	7988			U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"Zinc fingers, C2H2-type", "-"	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.32G>A	7.37:g.148947257G>A	ENSP00000338572:p.Arg11Lys		148578190	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	37	CCDS5896.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306260	0.23736	.	.	ENSG00000170260	ENST00000335870	T	0.06371	3.31	5.45	4.57	0.56435	.	0.472529	0.19855	N	0.104554	T	0.03651	0.0104	L	0.27053	0.805	0.23192	N	0.998142	P	0.37466	0.596	B	0.29785	0.107	T	0.29366	-1.0014	10	0.06365	T	0.9	-12.6355	10.4696	0.44629	0.0899:0.0:0.9101:0.0	.	11	Q9UDV6	ZN212_HUMAN	K	11	ENSP00000338572:R11K	ENSP00000338572:R11K	R	+	2	0	ZNF212	148578190	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	3.085000	0.50151	1.331000	0.45412	-0.217000	0.12591	AGA		0.433	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		A	148947257	G	A	148947257	3	1	61	1	0	0	0	0	1	0	0	0	17807	942	33	3	38	3	ZNF212	7	148947257	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43368	148947257	10191406	5685	13670										
ZNF212	7988	broad.mit.edu	37	chr7	148947581	148947581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgtggagaacctgctgcGcaacaggaacttctggatcc	12	11	1	1	rs553396170		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:148947581G>A	ENST00000335870.2	+	2	484	c.356G>A	c.(355-357)cGc>cAc	p.R119H		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.R119H(1)		endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			AACCTGCTGCGCAACAGGAAC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	7											67	85	79					7																	148947581		2203	4300	6503	148578514	SO:0001583	missense	7988			U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"Zinc fingers, C2H2-type", "-"	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.356G>A	7.37:g.148947581G>A	ENSP00000338572:p.Arg119His		148578514	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	37	CCDS5896.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139468	0.77775	.	.	ENSG00000170260	ENST00000335870	T	0.12361	2.69	5.95	5.95	0.96441	.	0.000000	0.48767	D	0.000180	T	0.21674	0.0522	M	0.61703	1.905	0.27543	N	0.950727	P	0.48350	0.909	P	0.44897	0.463	T	0.09684	-1.0663	10	0.72032	D	0.01	-23.0334	15.879	0.79189	0.0:0.0:1.0:0.0	.	119	Q9UDV6	ZN212_HUMAN	H	119	ENSP00000338572:R119H	ENSP00000338572:R119H	R	+	2	0	ZNF212	148578514	0.082000	0.21442	0.930000	0.37139	0.996000	0.88848	1.774000	0.38573	2.826000	0.97356	0.563000	0.77884	CGC		0.617	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		A	148947581	G	A	148947581	3	1	61	1	0	0	0	0	1	0	0	0	17807	1087	38	1	362	1	ZNF212	7	148947581	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	324	148947581	10191082	5686	13671										
ZNF467	168544	broad.mit.edu	37	chr7	149467551	149467551	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcacacccccagtgctctCtcttccctagaagaggacat	8	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:149467551C>A	ENST00000302017.3	-	3	542	c.129G>T	c.(127-129)gaG>gaT	p.E43D	ZNF467_ENST00000484747.1_Missense_Mutation_p.E43D	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	43					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E43D(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCAGTGCTCTCTCTTCCCTAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	7											69	69	69					7																	149467551		2203	4300	6503	149098484	SO:0001583	missense	168544			BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"Zinc fingers, C2H2-type"	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.129G>T	7.37:g.149467551C>A	ENSP00000304769:p.Glu43Asp		149098484		Missense_Mutation	SNP	ENST00000302017.3	37	CCDS5899.1	.	.	.	.	.	.	.	.	.	.	c	8.524	0.869513	0.17322	.	.	ENSG00000181444	ENST00000484747;ENST00000302017	T	0.08282	3.11	4.38	-1.87	0.07737	.	.	.	.	.	T	0.03220	0.0094	N	0.04880	-0.145	0.09310	N	1	B;B	0.17667	0.001;0.023	B;B	0.15484	0.001;0.013	T	0.48043	-0.9069	9	0.15066	T	0.55	-4.5603	6.3068	0.21143	0.0:0.2132:0.5385:0.2483	.	43;43	Q7Z7K2;C9JAX3	ZN467_HUMAN;.	D	43	ENSP00000304769:E43D	ENSP00000304769:E43D	E	-	3	2	ZNF467	149098484	0.000000	0.05858	0.005000	0.12908	0.490000	0.33462	-0.926000	0.03988	-0.230000	0.09840	0.651000	0.88453	GAG		0.582	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		A	149467551	C	A	149467551	3	1	61	1	0	0	0	0	1	0	0	0	17966	912	32	2	1670	2	ZNF467	7	149467551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	519970	149467551	9671112	5687	13672										
SSPO	23145	broad.mit.edu	37	chr7	149502521	149502521	+	RNA	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttcggctggacgccctgGacttcctggtcctcctgctc	12	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:149502521G>T	ENST00000378016.2	+	0	8334							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGACGCCCTGGACTTCCTGGT	0.662																																																0			7											44	50	48					7																	149502521		1954	4142	6096	149133454			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149502521G>T			149133454	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.662	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149502521	G	T	149502521	1	4	61	0	1	0	0	0	0	0	0	0	15228	1183	41	2		2	SSPO	7	149502521	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34970	149502521	9636142	5688	13673										
ZNF862	643641	broad.mit.edu	37	chr7	149557786	149557786	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttacacggggccttttaaaGtggagactttaaaataccat	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:149557786G>T	ENST00000223210.4	+	7	1782	c.1537G>T	c.(1537-1539)Gtg>Ttg	p.V513L	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.V513L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						GCCTTTTAAAGTGGAGACTTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											66	71	69					7																	149557786		1975	4141	6116	149188719	SO:0001583	missense	643641			AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.1537G>T	7.37:g.149557786G>T	ENSP00000223210:p.Val513Leu		149188719	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	37	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359506	0.61403	.	.	ENSG00000106479	ENST00000223210	T	0.01034	5.42	5.19	5.19	0.71726	Zinc finger, TTF-type (1);	0.000000	0.47093	D	0.000241	T	0.03827	0.0108	L	0.60845	1.875	0.29217	N	0.87417	D	0.64830	0.994	D	0.72625	0.978	T	0.33574	-0.9863	10	0.30854	T	0.27	-30.6054	14.2328	0.65906	0.0:0.0:1.0:0.0	.	513	O60290	ZN862_HUMAN	L	513	ENSP00000223210:V513L	ENSP00000223210:V513L	V	+	1	0	ZNF862	149188719	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.800000	0.55537	2.431000	0.82371	0.655000	0.94253	GTG		0.473	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		T	149557786	G	T	149557786	3	4	61	1	0	0	0	0	1	0	0	0	18234	1029	36	2	1563	2	ZNF862	7	149557786	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55265	149557786	9580877	5689	13674										
GIMAP8	155038	broad.mit.edu	37	chr7	150164277	150164277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcaagactatgagggccGatactgcattttcaacaaca	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150164277G>A	ENST00000307271.3	+	2	1065	c.491G>A	c.(490-492)cGa>cAa	p.R164Q		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	164	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.R164Q(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TATGAGGGCCGATACTGCATT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											123	116	119					7																	150164277		2203	4300	6503	149795210	SO:0001583	missense	155038			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.491G>A	7.37:g.150164277G>A	ENSP00000305107:p.Arg164Gln		149795210		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.524339	0.64747	.	.	ENSG00000171115	ENST00000307271	T	0.22134	1.97	4.38	3.5	0.40072	AIG1 (1);	0.411941	0.17950	N	0.156556	T	0.30634	0.0771	M	0.83483	2.645	0.09310	N	1	D	0.58970	0.984	P	0.46172	0.506	T	0.23940	-1.0174	10	0.54805	T	0.06	.	8.11	0.30909	0.1109:0.0:0.8891:0.0	.	164	Q8ND71	GIMA8_HUMAN	Q	164	ENSP00000305107:R164Q	ENSP00000305107:R164Q	R	+	2	0	GIMAP8	149795210	0.254000	0.23992	0.008000	0.14137	0.041000	0.13682	2.654000	0.46699	1.084000	0.41184	0.585000	0.79938	CGA		0.443	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		A	150164277	G	A	150164277	3	1	61	1	0	0	0	0	1	0	0	0	6405	1058	37	1	493	1	GIMAP8	7	150164277	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	606491	150164277	8974386	5690	13675										
GIMAP7	168537	broad.mit.edu	37	chr7	150217169	150217169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagaggaaatctttgattCtagaattgctgcccaagctg	11	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150217169C>A	ENST00000313543.4	+	2	264	c.107C>A	c.(106-108)tCt>tAt	p.S36Y		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	36	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)	p.S36Y(1)		breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATCTTTGATTCTAGAATTGCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											64	59	61					7																	150217169		2203	4300	6503	149848102	SO:0001583	missense	168537			BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"GTPases, IMAP"	22404	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 7"					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.107C>A	7.37:g.150217169C>A	ENSP00000315474:p.Ser36Tyr		149848102		Missense_Mutation	SNP	ENST00000313543.4	37	CCDS5903.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.752299	0.49362	.	.	ENSG00000179144	ENST00000313543	T	0.11712	2.75	5.09	3.2	0.36748	AIG1 (1);	0.073692	0.56097	D	0.000022	T	0.32645	0.0836	H	0.97265	3.97	0.09310	N	1	D	0.61697	0.99	P	0.51324	0.666	T	0.43196	-0.9406	10	0.66056	D	0.02	.	7.2545	0.26168	0.0:0.7389:0.169:0.0921	.	36	Q8NHV1	GIMA7_HUMAN	Y	36	ENSP00000315474:S36Y	ENSP00000315474:S36Y	S	+	2	0	GIMAP7	149848102	0.008000	0.16893	0.142000	0.22268	0.026000	0.11368	1.482000	0.35486	1.391000	0.46566	0.655000	0.94253	TCT		0.502	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236		A	150217169	C	A	150217169	3	1	61	1	0	0	0	0	1	0	0	0	6404	913	32	2	109	2	GIMAP7	7	150217169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52892	150217169	8921494	5691	13676										
GIMAP7	168537	broad.mit.edu	37	chr7	150217460	150217460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggtcatcttgttcactcGcaaagaagagttggagggcc	12	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150217460G>A	ENST00000313543.4	+	2	555	c.398G>A	c.(397-399)cGc>cAc	p.R133H		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	133	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)	p.R133H(1)		breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTGTTCACTCGCAAAGAAGAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	7											76	70	72					7																	150217460		2203	4300	6503	149848393	SO:0001583	missense	168537			BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"GTPases, IMAP"	22404	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 7"					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.398G>A	7.37:g.150217460G>A	ENSP00000315474:p.Arg133His		149848393		Missense_Mutation	SNP	ENST00000313543.4	37	CCDS5903.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.403021	0.25291	.	.	ENSG00000179144	ENST00000313543	T	0.61627	0.09	5.09	1.8	0.24995	AIG1 (1);	0.243508	0.33477	N	0.004866	T	0.31796	0.0808	N	0.20328	0.56	0.09310	N	0.999997	B	0.29886	0.26	B	0.22386	0.039	T	0.16778	-1.0391	10	0.11794	T	0.64	.	6.4482	0.21887	0.3691:0.0:0.6309:0.0	.	133	Q8NHV1	GIMA7_HUMAN	H	133	ENSP00000315474:R133H	ENSP00000315474:R133H	R	+	2	0	GIMAP7	149848393	0.002000	0.14202	0.983000	0.44433	0.681000	0.39784	1.138000	0.31491	0.171000	0.19730	-0.150000	0.13652	CGC		0.537	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236		A	150217460	G	A	150217460	3	1	61	1	0	0	0	0	1	0	0	0	6404	1087	38	1	400	1	GIMAP7	7	150217460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	291	150217460	8921203	5692	13677										
GIMAP5	55340	broad.mit.edu	37	chr7	150439899	150439899	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacagcaatgacctcttCttggatgcccagctgctcca	7	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150439899C>A	ENST00000358647.3	+	3	1039	c.672C>A	c.(670-672)ttC>ttA	p.F224L	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	224	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)	p.F224L(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGACCTCTTCTTGGATGCCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											58	56	56					7																	150439899		2203	4300	6503	150070832	SO:0001583	missense	55340			AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"GTPases, IMAP"	18005	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 5"	608086	"immune associated nucleotide 4 like 1 (mouse)"	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.672C>A	7.37:g.150439899C>A	ENSP00000351473:p.Phe224Leu		150070832	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Missense_Mutation	SNP	ENST00000358647.3	37	CCDS5907.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.421569	0.43020	.	.	ENSG00000196329	ENST00000358647;ENST00000447239	T	0.05447	3.44	4.25	4.25	0.50352	AIG1 (1);	0.310848	0.36066	N	0.002813	T	0.14614	0.0353	L	0.60067	1.865	0.09310	N	1	D	0.63046	0.992	P	0.56612	0.802	T	0.04242	-1.0966	10	0.35671	T	0.21	.	12.016	0.53313	0.0:1.0:0.0:0.0	.	224	Q96F15	GIMA5_HUMAN	L	224;260	ENSP00000351473:F224L	ENSP00000351473:F224L	F	+	3	2	GIMAP5	150070832	0.002000	0.14202	0.766000	0.31476	0.008000	0.06430	0.258000	0.18387	2.211000	0.71520	0.650000	0.86243	TTC		0.602	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384		A	150439899	C	A	150439899	3	1	61	1	0	0	0	0	1	0	0	0	6402	912	32	2	678	2	GIMAP5	7	150439899	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	222439	150439899	8698764	5693	13678										
TMEM176B	28959	broad.mit.edu	37	chr7	150491123	150491123	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagctgagacacactccaaGaacacaactcacaaccccca	4	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150491123G>T	ENST00000447204.2	-	3	613	c.241C>A	c.(241-243)Ctt>Att	p.L81I	TMEM176B_ENST00000450753.2_Intron|TMEM176B_ENST00000492607.1_Missense_Mutation_p.L81I|TMEM176B_ENST00000326442.5_Missense_Mutation_p.L81I|TMEM176B_ENST00000434545.1_Missense_Mutation_p.L81I|TMEM176B_ENST00000429904.2_Missense_Mutation_p.L81I	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	81					cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.L81I(1)		cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CACACTCCAAGAACACAACTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	7											264	224	238					7																	150491123		2203	4300	6503	150122056	SO:0001583	missense	28959			AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.241C>A	7.37:g.150491123G>T	ENSP00000410269:p.Leu81Ile		150122056	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	.	.	.	.	.	.	.	.	.	.	g	8.478	0.859156	0.17178	.	.	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000528038	T;T;T;T;T	0.03745	3.82;3.82;3.82;3.82;3.82	4.93	2.06	0.26882	.	0.360695	0.22132	N	0.064162	T	0.10078	0.0247	M	0.82056	2.57	0.20307	N	0.999919	D	0.53312	0.959	P	0.53689	0.732	T	0.09250	-1.0683	10	0.72032	D	0.01	-3.5484	4.8405	0.13487	0.1861:0.0:0.6459:0.168	.	81	Q3YBM2	T176B_HUMAN	I	81	ENSP00000419258:L81I;ENSP00000318409:L81I;ENSP00000410269:L81I;ENSP00000413531:L81I;ENSP00000397810:L81I	ENSP00000318409:L81I	L	-	1	0	TMEM176B	150122056	0.004000	0.15560	0.409000	0.26459	0.003000	0.03518	0.124000	0.15728	0.487000	0.27698	-0.339000	0.08088	CTT		0.592	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020		T	150491123	G	T	150491123	3	4	61	1	0	0	0	0	1	0	0	0	16132	942	33	2	591	2	TMEM176B	7	150491123	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51224	150491123	8647540	5694	13679										
ABP1	26	broad.mit.edu	37	chr7	150553724	150553724	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtccaagaaggagctgaggCtgcagccctccagtaccacc	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150553724C>T	ENST00000493429.1	+	4	750	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	AOC1_ENST00000467291.1_Silent_p.L56L|AOC1_ENST00000360937.4_Silent_p.L56L|AOC1_ENST00000416793.2_Silent_p.L56L			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	56					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.L56L(1)								Amiloride(DB00594)	GGAGCTGAGGCTGCAGCCCTC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	7											115	119	118					7																	150553724		2092	4236	6328	150184657	SO:0001819	synonymous_variant	26			AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.166C>T	7.37:g.150553724C>T			150184657	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																				0.562	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		T	150553724	C	T	150553724	2	4	61	1	0	0	0	0	0	0	0	1	98	796	28	3		3	ABP1	7	150553724	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62601	150553724	8584939	5695	13680										
ATG9B	285973	broad.mit.edu	37	chr7	150720253	150720253	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacattgtaatccacgcatcGaaggaggaaggttgtgaagg	13	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150720253G>A	ENST00000377974.2	-	4	775	c.700C>T	c.(700-702)Cga>Tga	p.R234*	ATG9B_ENST00000605938.1_Nonsense_Mutation_p.R234*|ATG9B_ENST00000444312.1_5'UTR|ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000605952.1_Nonsense_Mutation_p.R234*			Q674R7	ATG9B_HUMAN	autophagy related 9B	234					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)		p.R234*(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCACGCATCGAAGGAGGAAG	0.537																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											242	245	244					7																	150720253		2044	4198	6242	150351186	SO:0001587	stop_gained	285973			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"nitric oxide synthase 3 antisense", "ATG9 autophagy related 9 homolog B (S. cerevisiae)"	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.700C>T	7.37:g.150720253G>A	ENSP00000475005:p.Arg234*		150351186	A1A5D3|Q6JRW5|Q8N8I8	Nonsense_Mutation	SNP	ENST00000377974.2	37		.	.	.	.	.	.	.	.	.	.	G	15.24	2.774114	0.49786	.	.	ENSG00000248602	ENST00000377974;ENST00000397266;ENST00000545613	.	.	.	5.42	4.44	0.53790	.	0.107611	0.64402	D	0.000006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-41.8169	11.6032	0.51015	0.0947:0.0:0.9053:0.0	.	.	.	.	X	234	.	ENSP00000444232:R234X	R	-	1	2	AC010973.1	150351186	0.990000	0.36364	0.736000	0.30914	0.938000	0.57974	0.364000	0.20325	1.120000	0.41904	0.655000	0.94253	CGA		0.537	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173681		A	150720253	G	A	150720253	4	1	61	1	0	0	0	0	0	1	0	0	1104	1066	37	1	2113	1	ATG9B	7	150720253	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166529	150720253	8418410	5696	13681										
ABCB8	11194	broad.mit.edu	37	chr7	150733024	150733024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaatgtgcggactgtgcGtgccttcgccatggagcaac	15	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150733024G>A	ENST00000297504.6	+	8	1100	c.1034G>A	c.(1033-1035)cGt>cAt	p.R345H	ABCB8_ENST00000477719.1_Missense_Mutation_p.R328H|ABCB8_ENST00000477092.1_Missense_Mutation_p.R328H|ABCB8_ENST00000498578.1_Missense_Mutation_p.R328H|ABCB8_ENST00000358849.4_Missense_Mutation_p.R328H|ABCB8_ENST00000542328.1_Missense_Mutation_p.R240H|ABCB8_ENST00000356058.4_Missense_Mutation_p.R365H			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	345	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.R328Q(2)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CGGACTGTGCGTGCCTTCGCC	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	7											82	66	71					7																	150733024		2203	4300	6503	150363957	SO:0001583	missense	11194			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1034G>A	7.37:g.150733024G>A	ENSP00000297504:p.Arg345His		150363957	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		.	.	.	.	.	.	.	.	.	.	G	16.64	3.178349	0.57692	.	.	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73;-1.64;-1.64;-1.64	5.34	5.34	0.76211	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.115170	0.56097	D	0.000030	D	0.97548	0.9197	M	0.86573	2.825	0.53688	D	0.999977	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.83275	0.988;0.993;0.996;0.988;0.996;0.996	D	0.97688	1.0177	10	0.72032	D	0.01	1.4811	10.0475	0.42195	0.0917:0.0:0.9083:0.0	.	240;328;345;328;328;365	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;.;ABCB8_HUMAN;.;.;.	H	328;311;345;240;328;365;328;328	ENSP00000351717:R328H;ENSP00000297504:R345H;ENSP00000438776:R240H;ENSP00000418271:R328H;ENSP00000348353:R365H;ENSP00000419891:R328H;ENSP00000419558:R328H	ENSP00000297504:R345H	R	+	2	0	ABCB8	150363957	1.000000	0.71417	0.398000	0.26321	0.180000	0.23129	4.994000	0.63901	2.504000	0.84457	0.561000	0.74099	CGT		0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		A	150733024	G	A	150733024	3	1	61	1	0	0	0	0	1	0	0	0	47	1145	40	1	1009	1	ABCB8	7	150733024	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12771	150733024	8405639	5697	13682										
ABCF2	10061	broad.mit.edu	37	chr7	150916218	150916218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctcctccagctctagccGcgtcttcacgtactgatcat	7	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:150916218G>A	ENST00000287844.2	-	8	1058	c.949C>T	c.(949-951)Cgg>Tgg	p.R317W	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Missense_Mutation_p.R317W	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	317	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)	p.R317W(1)|p.R317fs*63(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCTCTAGCCGCGTCTTCACG	0.498																																																2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(1)|breast(1)	7											192	168	176					7																	150916218		2203	4300	6503	150547151	SO:0001583	missense	10061			AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.949C>T	7.37:g.150916218G>A	ENSP00000287844:p.Arg317Trp		150547151	O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	37	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153778	0.78114	.	.	ENSG00000033050	ENST00000222388;ENST00000287844	D;D	0.93247	-3.15;-3.19	5.36	5.36	0.76844	ABC transporter-like (1);	0.226040	0.44902	D	0.000411	D	0.98207	0.9407	H	0.98701	4.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.99643	1.0989	10	0.87932	D	0	-2.6723	16.2682	0.82601	0.0:0.0:1.0:0.0	.	317;317	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	W	317	ENSP00000222388:R317W;ENSP00000287844:R317W	ENSP00000222388:R317W	R	-	1	2	ABCF2	150547151	1.000000	0.71417	0.976000	0.42696	0.734000	0.41952	6.698000	0.74608	2.496000	0.84212	0.563000	0.77884	CGG		0.498	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		A	150916218	G	A	150916218	3	1	61	1	0	0	0	0	1	0	0	0	66	1086	38	1	995	1	ABCF2	7	150916218	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	183194	150916218	8222445	5698	13683										
NUB1	51667	broad.mit.edu	37	chr7	151064178	151064178	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgctttaaaaattgttaCggagaaaatcatcagagact	7	5	2	2	rs373895352		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151064178C>T	ENST00000355851.4	+	9	1031	c.954C>T	c.(952-954)taC>taT	p.Y318Y	NUB1_ENST00000413040.2_Silent_p.Y342Y|NUB1_ENST00000566856.1_Silent_p.Y318Y|NUB1_ENST00000568733.1_Silent_p.Y342Y	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	318					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.Y318Y(1)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AAAATTGTTACGGAGAAAATC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7											66	65	65					7																	151064178		1841	4090	5931	150695111	SO:0001819	synonymous_variant	51667			AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"NEDD8 ultimate buster-1"	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.954C>T	7.37:g.151064178C>T			150695111	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37																																																																																					0.378	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118		T	151064178	C	T	151064178	2	4	61	1	0	0	0	0	0	0	0	1	10745	547	19	1		1	NUB1	7	151064178	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147960	151064178	8074485	5699	13684										
WDR86	349136	broad.mit.edu	37	chr7	151097322	151097322	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaaggtcacatagctttCatgtcctgcagatgagggac	12	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151097322C>T	ENST00000334493.6	-	2	599	c.169G>A	c.(169-171)Gaa>Aaa	p.E57K	WDR86_ENST00000469830.2_Missense_Mutation_p.E57K|WDR86_ENST00000477459.1_5'UTR	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	57										breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACATAGCTTTCATGTCCTGCA	0.557																																																0			7											37	39	38					7																	151097322		2155	4245	6400	150728255	SO:0001583	missense	349136			AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"WD repeat domain containing"	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.169G>A	7.37:g.151097322C>T	ENSP00000335522:p.Glu57Lys		150728255	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Missense_Mutation	SNP	ENST00000334493.6	37	CCDS5925.2	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523702	0.27299	.	.	ENSG00000187260	ENST00000334493;ENST00000469830	T;T	0.62364	0.03;0.03	5.0	5.0	0.66597	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.65893	0.2735	L	0.33293	1	0.31600	N	0.652817	D;P;P	0.76494	0.999;0.9;0.932	D;P;B	0.81914	0.995;0.472;0.321	T	0.61931	-0.6961	9	0.17369	T	0.5	-16.0588	10.5266	0.44952	0.0:0.9104:0.0:0.0896	.	57;57;15	B4DJF1;Q86TI4;D3DX12	.;WDR86_HUMAN;.	K	57	ENSP00000335522:E57K;ENSP00000419162:E57K	ENSP00000335522:E57K	E	-	1	0	WDR86	150728255	0.993000	0.37304	0.991000	0.47740	0.718000	0.41266	3.139000	0.50577	2.311000	0.77944	0.585000	0.79938	GAA		0.557	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285		T	151097322	C	T	151097322	3	4	61	1	0	0	0	0	1	0	0	0	17374	835	29	3	981	3	WDR86	7	151097322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33144	151097322	8041341	5700	13685										
PRKAG2	51422	broad.mit.edu	37	chr7	151262838	151262838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaggcagagctgatattCgtctttccacaaatatgttc	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151262838C>T	ENST00000287878.4	-	12	1871	c.1367G>A	c.(1366-1368)cGa>cAa	p.R456Q	PRKAG2_ENST00000492843.1_Missense_Mutation_p.R332Q|PRKAG2_ENST00000392801.2_Missense_Mutation_p.R412Q|PRKAG2_ENST00000433631.2_Missense_Mutation_p.R331Q|PRKAG2_ENST00000418337.2_Missense_Mutation_p.R215Q	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	456	CBS 3. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)	p.R456Q(3)|p.R331Q(3)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	AGCTGATATTCGTCTTTCCAC	0.433																																																6	Substitution - Missense(6)	endometrium(4)|large_intestine(2)	7											237	201	213					7																	151262838		2203	4300	6503	150893771	SO:0001583	missense	51422			AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.1367G>A	7.37:g.151262838C>T	ENSP00000287878:p.Arg456Gln		150893771	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	37	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	C	32	5.140044	0.94560	.	.	ENSG00000106617	ENST00000418337;ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	6.06	6.06	0.98353	Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (3);	0.000000	0.85682	D	0.000000	D	0.94241	0.8151	M	0.75150	2.29	0.80722	D	1	P;D	0.54207	0.85;0.965	B;P	0.45610	0.281;0.487	D	0.94392	0.7615	10	0.66056	D	0.02	.	19.609	0.95594	0.0:1.0:0.0:0.0	.	331;456	B7Z6X8;Q9UGJ0	.;AAKG2_HUMAN	Q	215;456;332;331;412	ENSP00000387386:R215Q;ENSP00000287878:R456Q;ENSP00000419577:R332Q;ENSP00000406544:R331Q;ENSP00000376549:R412Q	ENSP00000287878:R456Q	R	-	2	0	PRKAG2	150893771	1.000000	0.71417	0.968000	0.41197	0.996000	0.88848	7.538000	0.82048	2.882000	0.98803	0.655000	0.94253	CGA		0.433	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		T	151262838	C	T	151262838	3	4	61	1	0	0	0	0	1	0	0	0	12535	884	31	1	362	1	PRKAG2	7	151262838	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165516	151262838	7875825	5701	13686										
GALNTL5	168391	broad.mit.edu	37	chr7	151699925	151699925	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatagatgtcattgatgataGaactctggagtataagccct	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151699925G>T	ENST00000392800.2	+	6	1039	c.785G>T	c.(784-786)aGa>aTa	p.R262I	GALNTL5_ENST00000431418.2_Missense_Mutation_p.R262I|GALNTL5_ENST00000483959.1_3'UTR	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	262					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.R262I(2)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		ATTGATGATAGAACTCTGGAG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	7											158	157	157					7																	151699925		2203	4300	6503	151330858	SO:0001583	missense	168391			AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.785G>T	7.37:g.151699925G>T	ENSP00000376548:p.Arg262Ile		151330858	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.751109	0.31046	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.59772	0.24;0.24	4.83	-8.69	0.00855	Glycosyl transferase, family 2 (1);	2.837350	0.00918	N	0.002546	T	0.33847	0.0877	N	0.20574	0.59	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.15983	-1.0418	10	0.72032	D	0.01	.	0.6247	0.00784	0.2543:0.3124:0.2024:0.2308	.	13;262	A8MZD3;Q7Z4T8	.;GLTL5_HUMAN	I	262	ENSP00000392582:R262I;ENSP00000376548:R262I	ENSP00000376548:R262I	R	+	2	0	GALNTL5	151330858	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.746000	0.26275	-1.305000	0.02327	-0.884000	0.02946	AGA		0.463	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		T	151699925	G	T	151699925	3	4	61	1	0	0	0	0	1	0	0	0	6244	942	33	2	803	2	GALNTL5	7	151699925	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	437087	151699925	7438738	5702	13687										
MLL3	58508	broad.mit.edu	37	chr7	151873758	151873758	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctaatgtctgaattatcaGatttctcattagcaagtaaa	6	7	3	2	rs372187941		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151873758G>A	ENST00000262189.6	-	38	8998	c.8780C>T	c.(8779-8781)tCt>tTt	p.S2927F	KMT2C_ENST00000355193.2_Missense_Mutation_p.S2927F	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2927					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S2927F(2)									TGAATTATCAGATTTCTCATT	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	7											70	76	74					7																	151873758		2203	4300	6503	151504691	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8780C>T	7.37:g.151873758G>A	ENSP00000262189:p.Ser2927Phe		151504691	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	7.997	0.754465	0.15778	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85013	-1.93;-1.92	5.24	2.24	0.28232	.	0.517985	0.16095	N	0.229882	T	0.78923	0.4360	L	0.27053	0.805	0.47183	D	0.999347	P;P;B	0.43169	0.8;0.573;0.374	P;B;B	0.45037	0.467;0.256;0.366	T	0.71206	-0.4661	10	0.11182	T	0.66	.	16.1271	0.81402	0.0:0.3893:0.6107:0.0	.	2927;1988;2927	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	F	2927	ENSP00000262189:S2927F;ENSP00000347325:S2927F	ENSP00000262189:S2927F	S	-	2	0	MLL3	151504691	1.000000	0.71417	0.022000	0.16811	0.486000	0.33341	4.936000	0.63506	0.553000	0.29044	0.650000	0.86243	TCT		0.463	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151873758	G	A	151873758	3	1	61	1	0	0	0	0	1	0	0	0	9652	942	33	3	6043	3	MLL3	7	151873758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173833	151873758	7264905	5703	13688										
MLL3	58508	broad.mit.edu	37	chr7	151874515	151874515	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctgggtggttatctgtaAattatcagacgttgtttcag	12	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151874515A>C	ENST00000262189.6	-	38	8241	c.8023T>G	c.(8023-8025)Tta>Gta	p.L2675V	KMT2C_ENST00000355193.2_Missense_Mutation_p.L2675V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2675					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L2675V(2)									GTTATCTGTAAATTATCAGAC	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	7											77	76	76					7																	151874515		2203	4300	6503	151505448	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8023T>G	7.37:g.151874515A>C	ENSP00000262189:p.Leu2675Val		151505448	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.559|2.559	-0.302231|-0.302231	0.05495|0.05495	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193	.|D;D	.|0.83075	.|-1.65;-1.68	5.63|5.63	3.17|3.17	0.36434|0.36434	.|.	.|0.237808	.|0.21743	.|N	.|0.069785	T|T	0.76765|0.76765	0.4033|0.4033	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	.|P;P;B	.|0.42941	.|0.595;0.794;0.186	.|B;B;B	.|0.43052	.|0.123;0.406;0.075	T|T	0.67833|0.67833	-0.5568|-0.5568	5|10	.|0.18710	.|T	.|0.47	.|.	4.3625|4.3625	0.11210|0.11210	0.6154:0.0:0.136:0.2486|0.6154:0.0:0.136:0.2486	.|.	.|2675;1736;2675	.|Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	.|MLL3_HUMAN;.;.	C|V	180|2675	.|ENSP00000262189:L2675V;ENSP00000347325:L2675V	.|ENSP00000262189:L2675V	F|L	-|-	2|1	0|2	MLL3|MLL3	151505448|151505448	0.036000|0.036000	0.19791|0.19791	0.100000|0.100000	0.21137|0.21137	0.541000|0.541000	0.35023|0.35023	0.452000|0.452000	0.21795|0.21795	0.375000|0.375000	0.24679|0.24679	-0.341000|-0.341000	0.08007|0.08007	TTT|TTA		0.433	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151874515	A	C	151874515	3	2	61	1	0	0	0	0	1	0	0	0	9652	11	1	4	6800	4	MLL3	7	151874515	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	757	151874515	7264148	5704	13689										
MLL3	58508	broad.mit.edu	37	chr7	151880121	151880121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaaaggatctttaaaaaGctccgaatcaatacgagagc	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151880121G>A	ENST00000262189.6	-	35	5421	c.5203C>T	c.(5203-5205)Ctt>Ttt	p.L1735F	KMT2C_ENST00000355193.2_Missense_Mutation_p.L1735F	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1735	Gln-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L1735F(2)									TCTTTAAAAAGCTCCGAATCA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	7											231	232	232					7																	151880121		2203	4300	6503	151511054	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5203C>T	7.37:g.151880121G>A	ENSP00000262189:p.Leu1735Phe		151511054	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.707936	0.48412	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.88586	-2.39;-2.4	4.7	2.79	0.32731	.	0.000000	0.40554	N	0.001077	D	0.91153	0.7214	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.997;0.998	D	0.88052	0.2788	10	0.25751	T	0.34	.	13.7154	0.62693	0.0:0.0:0.7186:0.2813	.	1735;796	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	F	1735	ENSP00000262189:L1735F;ENSP00000347325:L1735F	ENSP00000262189:L1735F	L	-	1	0	MLL3	151511054	1.000000	0.71417	0.597000	0.28824	0.714000	0.41099	5.381000	0.66208	0.602000	0.29896	0.563000	0.77884	CTT		0.358	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151880121	G	A	151880121	3	1	61	1	0	0	0	0	1	0	0	0	9652	971	34	3	9632	3	MLL3	7	151880121	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5606	151880121	7258542	5705	13690										
MLL3	58508	broad.mit.edu	37	chr7	151884543	151884543	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcacttgccattggattAaaggctgaatttttatccct	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151884543A>C	ENST00000262189.6	-	33	5030	c.4812T>G	c.(4810-4812)ttT>ttG	p.F1604L	KMT2C_ENST00000355193.2_Missense_Mutation_p.F1604L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1604					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.F1604L(2)									CCATTGGATTAAAGGCTGAAT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	7											129	134	132					7																	151884543		2203	4300	6503	151515476	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.4812T>G	7.37:g.151884543A>C	ENSP00000262189:p.Phe1604Leu		151515476	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331292	0.24167	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.89939	-2.56;-2.59	5.62	1.76	0.24704	.	0.000000	0.44688	U	0.000431	D	0.89577	0.6755	M	0.74258	2.255	0.41373	D	0.987501	B;D	0.59767	0.012;0.986	B;P	0.53035	0.006;0.716	D	0.87233	0.2261	10	0.66056	D	0.02	.	5.7455	0.18118	0.5682:0.1353:0.2965:0.0	.	1604;665	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	L	1604	ENSP00000262189:F1604L;ENSP00000347325:F1604L	ENSP00000262189:F1604L	F	-	3	2	MLL3	151515476	1.000000	0.71417	0.117000	0.21633	0.806000	0.45545	1.268000	0.33062	0.506000	0.28125	0.472000	0.43445	TTT		0.348	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151884543	A	C	151884543	3	2	61	1	0	0	0	0	1	0	0	0	9652	359	13	4	10031	4	MLL3	7	151884543	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4422	151884543	7254120	5706	13691										
MLL3	58508	broad.mit.edu	37	chr7	151945455	151945455	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagagtgacagattccatGactaattttggaggccttga	12	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:151945455G>T	ENST00000262189.6	-	14	2282	c.2064C>A	c.(2062-2064)gtC>gtA	p.V688V	KMT2C_ENST00000355193.2_Silent_p.V688V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	688					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.V688V(2)									CAGATTCCATGACTAATTTTG	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	7											73	69	70					7																	151945455		2203	4300	6503	151576388	SO:0001819	synonymous_variant	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2064C>A	7.37:g.151945455G>T			151576388	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																				0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151945455	G	T	151945455	2	4	61	1	0	0	0	0	0	0	0	1	9652	1277	45	2		2	MLL3	7	151945455	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60912	151945455	7193208	5707	13692										
ACTR3B	57180	broad.mit.edu	37	chr7	152522209	152522209	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggcgcccgctgtataaggTatgagctgcctgggtaaggt	16	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:152522209T>C	ENST00000256001.8	+	9	1085		c.e9+2		ACTR3B_ENST00000537264.1_Splice_Site|ACTR3B_ENST00000377776.3_Splice_Site|ACTR3B_ENST00000397282.2_Splice_Site	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)							cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.?(1)		breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		CTGTATAAGGTATGAGCTGCC	0.423																																																1	Unknown(1)	large_intestine(1)	7											81	74	76					7																	152522209		2203	4300	6503	152153142	SO:0001630	splice_region_variant	57180				CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627			17256	protein-coding gene	gene with protein product						10806390	Standard	NM_001040135		Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.951+2T>C	7.37:g.152522209T>C			152153142	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Splice_Site	SNP	ENST00000256001.8	37	CCDS5934.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.795422	0.50208	.	.	ENSG00000133627	ENST00000377776;ENST00000256001;ENST00000397282;ENST00000537264	.	.	.	3.85	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1363	0.53972	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACTR3B	152153142	1.000000	0.71417	0.988000	0.46212	0.550000	0.35303	5.800000	0.69108	1.536000	0.49237	0.402000	0.26972	.		0.423	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445	Intron	C	152522209	T	C	152522209	5	2	61	1	0	0	0	0	0	0	1	0	213	1652	57	4	987	4	ACTR3B	7	152522209	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	576754	152522209	6616454	5708	13693										
HTR5A	3361	broad.mit.edu	37	chr7	154863040	154863040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccgctactggtccatcaCgcgccacatggaatacacgc	10	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:154863040C>T	ENST00000287907.2	+	1	1007	c.431C>T	c.(430-432)aCg>aTg	p.T144M	HTR5A-AS1_ENST00000493904.1_5'UTR|HTR5A-AS1_ENST00000395731.2_De_novo_Start_InFrame|HTR5A-AS1_ENST00000543018.1_De_novo_Start_InFrame	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	144					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)	p.T144M(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	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)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TGGTCCATCACGCGCCACATG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	7											89	66	74					7																	154863040		2203	4300	6503	154493973	SO:0001583	missense	3361				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.431C>T	7.37:g.154863040C>T	ENSP00000287907:p.Thr144Met		154493973	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920092	0.73098	.	.	ENSG00000157219	ENST00000287907	T	0.38401	1.14	4.75	3.83	0.44106	GPCR, rhodopsin-like superfamily (1);	0.097522	0.64402	D	0.000001	T	0.42944	0.1225	M	0.80982	2.52	0.80722	D	1	P	0.47034	0.889	B	0.40940	0.344	T	0.58792	-0.7574	10	0.87932	D	0	.	15.0903	0.72188	0.0:0.8586:0.1414:0.0	.	144	P47898	5HT5A_HUMAN	M	144	ENSP00000287907:T144M	ENSP00000287907:T144M	T	+	2	0	HTR5A	154493973	1.000000	0.71417	0.965000	0.40720	0.835000	0.47333	4.545000	0.60698	2.465000	0.83290	0.655000	0.94253	ACG		0.637	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154863040	C	T	154863040	3	4	61	1	0	0	0	0	1	0	0	0	7471	536	19	1	433	1	HTR5A	7	154863040	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2340831	154863040	4275623	5709	13694										
HTR5A	3361	broad.mit.edu	37	chr7	154863232	154863232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgttctccaccgtaggcgCcttctacctgccgctctgtg	10	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:154863232C>T	ENST00000287907.2	+	1	1199	c.623C>T	c.(622-624)gCc>gTc	p.A208V	HTR5A-AS1_ENST00000493904.1_5'UTR|HTR5A-AS1_ENST00000395731.2_5'UTR|HTR5A-AS1_ENST00000543018.1_5'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	208					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)	p.A208V(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	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)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	ACCGTAGGCGCCTTCTACCTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	7											75	67	70					7																	154863232		2203	4300	6503	154494165	SO:0001583	missense	3361				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.623C>T	7.37:g.154863232C>T	ENSP00000287907:p.Ala208Val		154494165	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300532	0.95601	.	.	ENSG00000157219	ENST00000287907	T	0.72394	-0.65	4.77	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82715	0.5097	M	0.65677	2.01	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.84939	0.0864	10	0.87932	D	0	.	18.0029	0.89202	0.0:1.0:0.0:0.0	.	208	P47898	5HT5A_HUMAN	V	208	ENSP00000287907:A208V	ENSP00000287907:A208V	A	+	2	0	HTR5A	154494165	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.328000	0.79160	2.489000	0.83994	0.655000	0.94253	GCC		0.612	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154863232	C	T	154863232	3	4	61	1	0	0	0	0	1	0	0	0	7471	739	26	3	625	3	HTR5A	7	154863232	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192	154863232	4275431	5710	13695										
RBM33	155435	broad.mit.edu	37	chr7	155537703	155537703	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatcgcttaaagatagaaGaacagaaacgcctaagagaa	8	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:155537703G>T	ENST00000401878.3	+	14	2584	c.2386G>T	c.(2386-2388)Gaa>Taa	p.E796*	RBM33_ENST00000341148.3_5'Flank	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	796							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E796*(2)		breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		AAAGATAGAAGAACAGAAACG	0.463																																																2	Substitution - Nonsense(2)	large_intestine(2)	7											26	27	27					7																	155537703		2203	4300	6503	155230464	SO:0001587	stop_gained	155435			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.2386G>T	7.37:g.155537703G>T	ENSP00000384160:p.Glu796*		155230464	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Nonsense_Mutation	SNP	ENST00000401878.3	37	CCDS5941.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.861024|8.861024	0.98980|0.98980	.|.	.|.	ENSG00000184863|ENSG00000184863	ENST00000401878|ENST00000392761	.|.	.|.	.|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.64402|.	D|.	0.000003|.	.|T	.|0.77082	.|0.4078	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73990	.|-0.3808	.|4	0.49607|.	T|.	0.09|.	.|.	20.3931|20.3931	0.98965|0.98965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	796|567	.|.	ENSP00000384160:E796X|.	E|K	+|+	1|3	0|2	RBM33|RBM33	155230464|155230464	1.000000|1.000000	0.71417|0.71417	0.914000|0.914000	0.36105|0.36105	0.990000|0.990000	0.78478|0.78478	9.027000|9.027000	0.93706|0.93706	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.463	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		T	155537703	G	T	155537703	4	4	61	1	0	0	0	0	0	1	0	0	13167	943	33	2	2440	2	RBM33	7	155537703	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	674471	155537703	3600960	5711	13696										
NOM1	64434	broad.mit.edu	37	chr7	156743316	156743316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaacagggggaagaaaaGgaaaagggagcgcaggagaa	19	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:156743316G>T	ENST00000275820.3	+	1	900	c.885G>T	c.(883-885)aaG>aaT	p.K295N		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	295	Glu-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K295N(1)		endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		gggaagaaaaggaaaagggag	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	7											69	54	59					7																	156743316		2173	4251	6424	156436077	SO:0001583	missense	64434			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.885G>T	7.37:g.156743316G>T	ENSP00000275820:p.Lys295Asn		156436077	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	G	9.951	1.220216	0.22457	.	.	ENSG00000146909	ENST00000275820	T	0.12255	2.7	4.19	-8.37	0.00976	.	3.361950	0.01584	N	0.021255	T	0.05090	0.0136	N	0.08118	0	0.09310	N	1	B	0.23490	0.086	B	0.20767	0.031	T	0.26710	-1.0095	10	0.16420	T	0.52	-0.2287	3.9116	0.09205	0.2376:0.1925:0.4739:0.0961	.	295	Q5C9Z4	NOM1_HUMAN	N	295	ENSP00000275820:K295N	ENSP00000275820:K295N	K	+	3	2	NOM1	156436077	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.184000	0.03076	-1.475000	0.01876	0.650000	0.86243	AAG		0.512	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		T	156743316	G	T	156743316	3	4	61	1	0	0	0	0	1	0	0	0	10561	991	35	2	887	2	NOM1	7	156743316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1205613	156743316	2395347	5712	13697										
NOM1	64434	broad.mit.edu	37	chr7	156745276	156745276	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggctgaagaaacatgtaAaaggtctacttaacaggtga	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:156745276A>C	ENST00000275820.3	+	2	1111	c.1096A>C	c.(1096-1098)Aaa>Caa	p.K366Q		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	366	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K366Q(1)		endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GAAACATGTAAAAGGTCTACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											108	98	101					7																	156745276		2203	4300	6503	156438037	SO:0001583	missense	64434			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1096A>C	7.37:g.156745276A>C	ENSP00000275820:p.Lys366Gln		156438037	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.864080	0.32884	.	.	ENSG00000146909	ENST00000275820	T	0.25414	1.8	4.69	0.619	0.17630	MIF4G-like, type 3 (2);Armadillo-type fold (1);	0.282275	0.38837	N	0.001542	T	0.29288	0.0729	L	0.43923	1.385	0.40477	D	0.980407	P	0.46064	0.872	P	0.54706	0.759	T	0.02958	-1.1089	10	0.39692	T	0.17	-15.755	6.7862	0.23675	0.556:0.3002:0.0:0.1438	.	366	Q5C9Z4	NOM1_HUMAN	Q	366	ENSP00000275820:K366Q	ENSP00000275820:K366Q	K	+	1	0	NOM1	156438037	1.000000	0.71417	0.025000	0.17156	0.017000	0.09413	4.970000	0.63742	-0.145000	0.11294	0.456000	0.33151	AAA		0.408	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		C	156745276	A	C	156745276	3	2	61	1	0	0	0	0	1	0	0	0	10561	15	1	4	1102	4	NOM1	7	156745276	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1960	156745276	2393387	5713	13698										
UBE3C	9690	broad.mit.edu	37	chr7	157000177	157000177	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatcatcccactcttttatCtttttagctccttgtttagt	4	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:157000177C>A	ENST00000348165.5	+	12	1864	c.1504C>A	c.(1504-1506)Ctt>Att	p.L502I		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	502					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L502I(1)		central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		ACTCTTTTATCTTTTTAGCTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	7											149	145	146					7																	157000177		2203	4300	6503	156692938	SO:0001583	missense	9690			AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.1504C>A	7.37:g.157000177C>A	ENSP00000309198:p.Leu502Ile		156692938	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	37	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092097	0.76756	.	.	ENSG00000009335	ENST00000348165	T	0.48836	0.8	5.26	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.60222	0.2252	M	0.67953	2.075	0.80722	D	1	P;D	0.56968	0.604;0.978	B;P	0.55871	0.209;0.786	T	0.63690	-0.6580	10	0.54805	T	0.06	.	13.9691	0.64228	0.0:0.9262:0.0:0.0738	.	502;502	Q15386;Q15386-2	UBE3C_HUMAN;.	I	502	ENSP00000309198:L502I	ENSP00000309198:L502I	L	+	1	0	UBE3C	156692938	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	5.520000	0.67080	1.208000	0.43306	0.655000	0.94253	CTT		0.378	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		A	157000177	C	A	157000177	3	1	61	1	0	0	0	0	1	0	0	0	16921	913	32	2	1550	2	UBE3C	7	157000177	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	254901	157000177	2138486	5714	13699										
PTPRN2	5799	broad.mit.edu	37	chr7	157341694	157341694	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgctccagggtcgctgcGatatcaatctctttagcacc	9	12	2	0	rs370473762		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:157341694G>A	ENST00000389418.4	-	22	2931	c.2922C>T	c.(2920-2922)atC>atT	p.I974I	PTPRN2_ENST00000389416.4_Silent_p.I957I|PTPRN2_ENST00000404321.2_Silent_p.I997I|PTPRN2_ENST00000409483.1_Silent_p.I936I|PTPRN2_ENST00000389413.3_Silent_p.I945I	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	974	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.I974I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	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)		GGGTCGCTGCGATATCAATCT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	7							,,	0,4406		0,0,2203	146	126	133		2922,2871,2835	3	1	7		133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	974/1016,957/999,945/987	157341694	1,13005	2203	4300	6503	157034455	SO:0001819	synonymous_variant	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2922C>T	7.37:g.157341694G>A			157034455	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																				0.532	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			A	157341694	G	A	157341694	2	1	61	1	0	0	0	0	0	0	0	1	12845	1048	37	1		1	PTPRN2	7	157341694	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	341517	157341694	1796969	5715	13700										
PTPRN2	5799	broad.mit.edu	37	chr7	157926383	157926383	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcactctctgtctgtcacGatgtagccccgcgcctcttc	7	17	5	0	rs201964824	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:157926383G>A	ENST00000389418.4	-	9	1551	c.1542C>T	c.(1540-1542)atC>atT	p.I514I	PTPRN2_ENST00000389416.4_Silent_p.I497I|PTPRN2_ENST00000404321.2_Silent_p.I537I|PTPRN2_ENST00000409483.1_Silent_p.I476I|PTPRN2_ENST00000389413.3_Silent_p.I514I	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	514					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.I514I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	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)		TGTCTGTCACGATGTAGCCCC	0.657													G|||	2	0.000399361	0	0	5008	,	,		15886	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											59	63	62					7																	157926383		2202	4300	6502	157619144	SO:0001819	synonymous_variant	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1542C>T	7.37:g.157926383G>A			157619144	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																				0.657	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			A	157926383	G	A	157926383	2	1	61	1	0	0	0	0	0	0	0	1	12845	1048	37	1		1	PTPRN2	7	157926383	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	584689	157926383	1212280	5716	13701										
VIPR2	7434	broad.mit.edu	37	chr7	158835801	158835801	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtccttgaccagcactgaGatggctctcaggatgaagga	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr7:158835801G>T	ENST00000262178.2	-	6	707	c.522C>A	c.(520-522)atC>atA	p.I174I	VIPR2_ENST00000402066.1_Silent_p.I315I|VIPR2_ENST00000377633.3_Silent_p.I158I	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	174					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.I174I(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CCAGCACTGAGATGGCTCTCA	0.577																																					Pancreas(154;1876 1931 2329 17914 20079)											1	Substitution - coding silent(1)	large_intestine(1)	7											141	113	123					7																	158835801		2203	4300	6503	158528562	SO:0001819	synonymous_variant	7434			CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.522C>A	7.37:g.158835801G>T			158528562	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1																																																																																				0.577	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		T	158835801	G	T	158835801	2	4	61	1	0	0	0	0	0	0	0	1	17210	932	33	2		2	VIPR2	7	158835801	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	909418	158835801	302862	5717	13702										
FBXO25	26260	broad.mit.edu	37	chr8	382885	382885	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggtaatttttattctaGgtttttatcgtgaaaaatgg	8	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:382885G>T	ENST00000276326.5	+	4	357		c.e4-1		FBXO25_ENST00000382824.1_Intron|FBXO25_ENST00000352684.2_Intron|FBXO25_ENST00000350302.3_Splice_Site	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25						protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.?(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		TTTTATTCTAGGTTTTTATCG	0.249																																																1	Unknown(1)	large_intestine(1)	8											26	26	26					8																	382885		2180	4250	6430	372885	SO:0001630	splice_region_variant	26260			AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"F-boxes /  "other""	13596	protein-coding gene	gene with protein product		609098	"F-box only protein 25"			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.239-1G>T	8.37:g.382885G>T			372885	Q6PJ83|Q7Z4V4|Q9UKB8	Splice_Site	SNP	ENST00000276326.5	37	CCDS5953.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.947391	0.53186	.	.	ENSG00000147364	ENST00000518240;ENST00000350302;ENST00000276326;ENST00000447233	.	.	.	4.36	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3924	0.49822	0.0:0.0:0.8173:0.1827	.	.	.	.	.	-1	.	.	.	+	.	.	FBXO25	372885	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.388000	0.79795	0.920000	0.36970	0.449000	0.29647	.		0.249	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173	Intron	T	382885	G	T	382885	5	4	61	1	0	0	0	0	0	0	1	0	5755	1014	35	2	248	2	FBXO25	8	382885	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		382885	145981137	5718	13703										
CLN8	2055	broad.mit.edu	37	chr8	1719650	1719650	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccatctctttgcctttCttgggtttcttggctgcttg	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:1719650C>A	ENST00000331222.4	+	2	677	c.430C>A	c.(430-432)Ctt>Att	p.L144I		NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	144	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				adult walking behavior (GO:0007628)|age-dependent response to oxidative stress (GO:0001306)|associative learning (GO:0008306)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|ceramide biosynthetic process (GO:0046513)|ceramide metabolic process (GO:0006672)|cholesterol metabolic process (GO:0008203)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|lipid biosynthetic process (GO:0008610)|lipid transport (GO:0006869)|lysosome organization (GO:0007040)|mitochondrial membrane organization (GO:0007006)|musculoskeletal movement (GO:0050881)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteolysis (GO:0045861)|negative regulation of transferase activity (GO:0051348)|nervous system development (GO:0007399)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|phospholipid metabolic process (GO:0006644)|photoreceptor cell maintenance (GO:0045494)|protein catabolic process (GO:0030163)|regulation of cell size (GO:0008361)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic motor neuron differentiation (GO:0021523)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.L144I(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		CTTTGCCTTTCTTGGGTTTCT	0.478																																					Pancreas(155;338 1942 6138 10888 50612)											2	Substitution - Missense(2)	large_intestine(2)	8											142	144	143					8																	1719650		2203	4300	6503	1707057	SO:0001583	missense	2055			AF123761	CCDS5956.1	8p23.3	2014-09-17			ENSG00000182372	ENSG00000182372			2079	protein-coding gene	gene with protein product		607837	"chromosome 8 open reading frame 61"	EPMR, C8orf61		10508524	Standard	NM_018941		Approved	FLJ39417	uc003wpo.4	Q9UBY8	OTTHUMG00000090343	ENST00000331222.4:c.430C>A	8.37:g.1719650C>A	ENSP00000328182:p.Leu144Ile		1707057	Q86U71|Q96I95	Missense_Mutation	SNP	ENST00000331222.4	37	CCDS5956.1	.	.	.	.	.	.	.	.	.	.	C	5.702	0.314027	0.10789	.	.	ENSG00000182372	ENST00000331222	D	0.85339	-1.97	5.06	2.28	0.28536	TRAM/LAG1/CLN8 homology domain (3);	0.596654	0.14779	U	0.298906	T	0.81014	0.4735	M	0.65975	2.015	0.09310	N	1	P	0.35793	0.521	B	0.35182	0.197	T	0.68150	-0.5485	9	.	.	.	-11.9042	6.9163	0.24361	0.0:0.6079:0.1594:0.2327	.	144	Q9UBY8	CLN8_HUMAN	I	144	ENSP00000328182:L144I	.	L	+	1	0	CLN8	1707057	0.992000	0.36948	0.023000	0.16930	0.064000	0.16182	1.500000	0.35682	0.166000	0.19597	0.455000	0.32223	CTT		0.478	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941		A	1719650	C	A	1719650	3	1	61	1	0	0	0	0	1	0	0	0	3552	913	32	2	432	2	CLN8	8	1719650	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1336765	1719650	144644372	5719	13704										
ARHGEF10	9639	broad.mit.edu	37	chr8	1876686	1876686	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcttcaacgtggaatctCgcatcctgtgcatgctgtac	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:1876686C>T	ENST00000398564.1	+	24	2866	c.2866C>T	c.(2866-2868)Cgc>Tgc	p.R956C	ARHGEF10_ENST00000520359.1_Missense_Mutation_p.R893C|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.R931C|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.R927C|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.R955C			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	956					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R956C(1)|p.R708C(1)		endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CGTGGAATCTCGCATCCTGTG	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	8											154	144	148					8																	1876686		2203	4300	6503	1864093	SO:0001583	missense	9639			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.2866C>T	8.37:g.1876686C>T	ENSP00000381571:p.Arg956Cys		1864093	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	C	20.3	3.968642	0.74131	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.07;-0.07	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78027	0.4219	L	0.56124	1.755	0.80722	D	1	D;P	0.89917	1.0;0.525	D;B	0.91635	0.999;0.15	T	0.77515	-0.2559	10	0.48119	T	0.1	-43.5395	15.1195	0.72432	0.1421:0.8579:0.0:0.0	.	893;931	O15013-7;O15013-5	.;.	C	931;893;955;956;927;575	ENSP00000340297:R931C;ENSP00000427909:R893C;ENSP00000431012:R955C;ENSP00000381571:R956C;ENSP00000262112:R927C;ENSP00000427768:R575C	ENSP00000262112:R927C	R	+	1	0	ARHGEF10	1864093	0.999000	0.42202	0.409000	0.26459	0.656000	0.38851	4.257000	0.58816	2.590000	0.87494	0.655000	0.94253	CGC		0.562	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1876686	C	T	1876686	3	4	61	1	0	0	0	0	1	0	0	0	894	884	31	1	2881	1	ARHGEF10	8	1876686	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157036	1876686	144487336	5720	13705										
MYOM2	9172	broad.mit.edu	37	chr8	2020460	2020460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattccgtacacgcacttcGacgtccagtttttggagaag	10	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:2020460G>A	ENST00000262113.4	+	9	970	c.829G>A	c.(829-831)Gac>Aac	p.D277N	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	277	Ig-like C2-type 2.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.D277N(1)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CACGCACTTCGACGTCCAGTT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	8											101	85	90					8																	2020460		2203	4300	6503	2007867	SO:0001583	missense	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.829G>A	8.37:g.2020460G>A	ENSP00000262113:p.Asp277Asn		2007867	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.023464	0.35701	.	.	ENSG00000036448	ENST00000262113	T	0.50813	0.73	5.13	5.13	0.70059	Immunoglobulin-like (1);	0.135403	0.49916	D	0.000130	T	0.38134	0.1029	L	0.28740	0.885	0.80722	D	1	B	0.29232	0.238	B	0.18871	0.023	T	0.22521	-1.0214	10	0.48119	T	0.1	.	18.5987	0.91239	0.0:0.0:1.0:0.0	.	277	P54296	MYOM2_HUMAN	N	277	ENSP00000262113:D277N	ENSP00000262113:D277N	D	+	1	0	MYOM2	2007867	1.000000	0.71417	0.780000	0.31762	0.358000	0.29455	5.304000	0.65744	2.373000	0.80994	0.655000	0.94253	GAC		0.562	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		A	2020460	G	A	2020460	3	1	61	1	0	0	0	0	1	0	0	0	10122	1058	37	1	859	1	MYOM2	8	2020460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143774	2020460	144343562	5721	13706										
CSMD1	64478	broad.mit.edu	37	chr8	2820008	2820008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgcaggtgggttgtatgCcgctccacgtgccgtcagct	13	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:2820008C>T	ENST00000520002.1	-	62	10166	c.9611G>A	c.(9610-9612)gGc>gAc	p.G3204D	CSMD1_ENST00000400186.3_Missense_Mutation_p.G3027D|CSMD1_ENST00000542608.1_Missense_Mutation_p.G3026D|CSMD1_ENST00000602557.1_Missense_Mutation_p.G3204D|CSMD1_ENST00000602723.1_Missense_Mutation_p.G3027D|CSMD1_ENST00000537824.1_Missense_Mutation_p.G3203D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3204	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.G3203D(1)|p.G2932D(1)		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)		GGGTTGTATGCCGCTCCACGT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	8											65	63	64					8																	2820008		1923	4141	6064	2807415	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9611G>A	8.37:g.2820008C>T	ENSP00000430733:p.Gly3204Asp		2807415	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	18.03	3.532377	0.64972	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.6	5.6	0.85130	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.57710	0.2072	M	0.83852	2.665	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.62039	-0.6938	10	0.72032	D	0.01	.	19.6087	0.95589	0.0:1.0:0.0:0.0	.	3204;3204;3026	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	D	3027;3204;3065;3203;3026	ENSP00000383047:G3027D;ENSP00000430733:G3204D;ENSP00000441462:G3203D;ENSP00000446243:G3026D	ENSP00000320445:G3065D	G	-	2	0	CSMD1	2807415	1.000000	0.71417	0.150000	0.22450	0.004000	0.04260	7.638000	0.83328	2.639000	0.89480	0.655000	0.94253	GGC		0.473	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2820008	C	T	2820008	3	4	61	1	0	0	0	0	1	0	0	0	3950	739	26	3	1126	3	CSMD1	8	2820008	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	799548	2820008	143544014	5722	13707										
CSMD1	64478	broad.mit.edu	37	chr8	2887015	2887015	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgttctgagagctgagcttCaatgctggggcaagcgaccg	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:2887015C>A	ENST00000520002.1	-	52	8239	c.7684G>T	c.(7684-7686)Gaa>Taa	p.E2562*	CSMD1_ENST00000400186.3_Nonsense_Mutation_p.E2562*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.E2561*|CSMD1_ENST00000602557.1_Nonsense_Mutation_p.E2562*|CSMD1_ENST00000602723.1_Nonsense_Mutation_p.E2562*|CSMD1_ENST00000537824.1_Nonsense_Mutation_p.E2561*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2562	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.E2561*(1)|p.E2290*(1)		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)		AGCTGAGCTTCAATGCTGGGG	0.478																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											45	43	44					8																	2887015		1978	4168	6146	2874422	SO:0001587	stop_gained	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7684G>T	8.37:g.2887015C>A	ENSP00000430733:p.Glu2562*		2874422	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	50|50	16.419515|16.419515	0.99863|0.99863	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	.|.	.|.	.|.	4.88|4.88	4.0|4.0	0.46444|0.46444	.|.	0.260617|.	0.29799|.	N|.	0.011170|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.11794|.	T|.	0.64|.	.|.	15.2383|15.2383	0.73450|0.73450	0.0:0.859:0.141:0.0|0.0:0.859:0.141:0.0	.|.	.|.	.|.	.|.	X|L	2562;2562;2423;2561;2561|1978	.|.	ENSP00000320445:E2423X|.	E|X	-|-	1|2	0|2	CSMD1|CSMD1	2874422|2874422	0.998000|0.998000	0.40836|0.40836	0.018000|0.018000	0.16275|0.16275	0.031000|0.031000	0.12232|0.12232	2.975000|2.975000	0.49281|0.49281	1.272000|1.272000	0.44329|0.44329	0.591000|0.591000	0.81541|0.81541	GAA|TGA		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2887015	C	A	2887015	4	1	61	1	0	0	0	0	0	1	0	0	3950	835	29	2	3093	2	CSMD1	8	2887015	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67007	2887015	143477007	5723	13708										
CSMD1	64478	broad.mit.edu	37	chr8	3000022	3000022	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatccttgccggttttgcGaatggtcactataaaagtgg	10	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:3000022G>A	ENST00000520002.1	-	42	6764	c.6209C>T	c.(6208-6210)tCg>tTg	p.S2070L	CSMD1_ENST00000400186.3_Missense_Mutation_p.S2070L|CSMD1_ENST00000542608.1_Missense_Mutation_p.S2069L|CSMD1_ENST00000539096.1_Missense_Mutation_p.S2069L|CSMD1_ENST00000602557.1_Missense_Mutation_p.S2070L|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Missense_Mutation_p.S2070L|CSMD1_ENST00000537824.1_Missense_Mutation_p.S2069L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2070	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.S2069L(1)|p.S1798L(1)		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)		CCGGTTTTGCGAATGGTCACT	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	8											70	76	74					8																	3000022		1971	4172	6143	2987429	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6209C>T	8.37:g.3000022G>A	ENSP00000430733:p.Ser2070Leu		2987429	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	27.8	4.865823	0.91511	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	5.24	5.24	0.73138	CUB (5);	0.000000	0.64402	D	0.000005	T	0.55800	0.1943	M	0.89478	3.035	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.999;0.997	T	0.64499	-0.6393	10	0.87932	D	0	.	19.2056	0.93729	0.0:0.0:1.0:0.0	.	2070;2070;2069	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	L	2070;2070;1931;2069;2069;2069	ENSP00000383047:S2070L;ENSP00000430733:S2070L;ENSP00000441462:S2069L;ENSP00000446243:S2069L;ENSP00000441675:S2069L	ENSP00000320445:S1931L	S	-	2	0	CSMD1	2987429	1.000000	0.71417	0.630000	0.29268	0.555000	0.35460	9.585000	0.98223	2.605000	0.88082	0.591000	0.81541	TCG		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3000022	G	A	3000022	3	1	61	1	0	0	0	0	1	0	0	0	3950	1059	37	1	4608	1	CSMD1	8	3000022	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113007	3000022	143364000	5724	13709										
CSMD1	64478	broad.mit.edu	37	chr8	3205575	3205575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggtggatgcccttgccgGcttctgtttctattttatag	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:3205575G>A	ENST00000520002.1	-	23	3971	c.3416C>T	c.(3415-3417)gCc>gTc	p.A1139V	CSMD1_ENST00000400186.3_Missense_Mutation_p.A1139V|CSMD1_ENST00000542608.1_Missense_Mutation_p.A1138V|CSMD1_ENST00000539096.1_Missense_Mutation_p.A1138V|CSMD1_ENST00000602557.1_Missense_Mutation_p.A1139V|CSMD1_ENST00000602723.1_Missense_Mutation_p.A1139V|CSMD1_ENST00000537824.1_Missense_Mutation_p.A1138V			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1139	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.A867V(1)|p.A867D(1)|p.A1138D(1)|p.A1138V(1)		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)		GCCCTTGCCGGCTTCTGTTTC	0.383																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	8											67	60	62					8																	3205575		1813	4067	5880	3192982	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3416C>T	8.37:g.3205575G>A	ENSP00000430733:p.Ala1139Val		3192982	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	13.79	2.341929	0.41498	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.64	5.64	0.86602	CUB (5);	0.153691	0.45361	D	0.000378	T	0.36386	0.0965	L	0.39633	1.23	0.28185	N	0.928004	D;P;P	0.89917	1.0;0.656;0.614	D;P;P	0.83275	0.996;0.601;0.46	T	0.07158	-1.0787	10	0.54805	T	0.06	.	19.7076	0.96081	0.0:0.0:1.0:0.0	.	1139;1139;1139	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	V	1139;1139;1001;1138;1138;1138	ENSP00000383047:A1139V;ENSP00000430733:A1139V;ENSP00000441462:A1138V;ENSP00000446243:A1138V;ENSP00000441675:A1138V	ENSP00000320445:A1001V	A	-	2	0	CSMD1	3192982	0.994000	0.37717	0.308000	0.25141	0.083000	0.17756	5.045000	0.64220	2.642000	0.89623	0.650000	0.86243	GCC		0.383	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3205575	G	A	3205575	3	1	61	1	0	0	0	0	1	0	0	0	3950	1203	42	3	7477	3	CSMD1	8	3205575	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205553	3205575	143158447	5725	13710										
CSMD1	64478	broad.mit.edu	37	chr8	3855477	3855477	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagaaatcatatccttcttCtagctgaaagtcagtgaaga	7	7	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:3855477C>A	ENST00000520002.1	-	5	1321	c.766G>T	c.(766-768)Gaa>Taa	p.E256*	CSMD1_ENST00000400186.3_Nonsense_Mutation_p.E256*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.E256*|CSMD1_ENST00000539096.1_Nonsense_Mutation_p.E256*|CSMD1_ENST00000602557.1_Nonsense_Mutation_p.E256*|CSMD1_ENST00000602723.1_Nonsense_Mutation_p.E256*|CSMD1_ENST00000537824.1_Nonsense_Mutation_p.E256*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	256	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.E256*(1)		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)		TATCCTTCTTCTAGCTGAAAG	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											56	57	57					8																	3855477		2072	4241	6313	3842885	SO:0001587	stop_gained	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.766G>T	8.37:g.3855477C>A	ENSP00000430733:p.Glu256*		3842885	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	41	8.865694	0.98982	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.	.	.	5.54	5.54	0.83059	.	0.000000	0.26711	U	0.022882	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-23.2611	18.4741	0.90785	0.0:1.0:0.0:0.0	.	.	.	.	X	256;256;118;256;256;256	.	ENSP00000320445:E118X	E	-	1	0	CSMD1	3842885	1.000000	0.71417	0.953000	0.39169	0.831000	0.47069	7.626000	0.83164	2.600000	0.87896	0.563000	0.77884	GAA		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3855477	C	A	3855477	4	1	61	1	0	0	0	0	0	1	0	0	3950	922	32	2	10005	2	CSMD1	8	3855477	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	649902	3855477	142508545	5726	13711										
MFHAS1	9258	broad.mit.edu	37	chr8	8750004	8750004	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagtgagctggttgtgatCcacgtccagggtgcgcaggc	17	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:8750004C>A	ENST00000276282.6	-	1	1151	c.565G>T	c.(565-567)Gat>Tat	p.D189Y		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	189								p.D189Y(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TGGTTGTGATCCACGTCCAGG	0.677																																					Melanoma(103;1201 2045 17515 28966)											1	Substitution - Missense(1)	large_intestine(1)	8											21	25	24					8																	8750004		2197	4294	6491	8787414	SO:0001583	missense	9258			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.565G>T	8.37:g.8750004C>A	ENSP00000276282:p.Asp189Tyr		8787414	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764070	0.69878	.	.	ENSG00000147324	ENST00000276282	T	0.57752	0.38	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.65302	0.2678	L	0.37897	1.145	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67444	-0.5669	10	0.62326	D	0.03	.	17.9146	0.88945	0.0:1.0:0.0:0.0	.	189	Q9Y4C4	MFHA1_HUMAN	Y	189	ENSP00000276282:D189Y	ENSP00000276282:D189Y	D	-	1	0	MFHAS1	8787414	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.604000	0.82830	2.456000	0.83038	0.563000	0.77884	GAT		0.677	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		A	8750004	C	A	8750004	3	1	61	1	0	0	0	0	1	0	0	0	9551	855	30	2	2605	2	MFHAS1	8	8750004	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4894527	8750004	137614018	5727	13712										
ERI1	90459	broad.mit.edu	37	chr8	8869118	8869118	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagaagctgatgctgaaAgagagcaattttgctgacag	12	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:8869118A>T	ENST00000523898.1	+	4	1033	c.354A>T	c.(352-354)aaA>aaT	p.K118N	ERI1_ENST00000519292.1_Missense_Mutation_p.K118N|ERI1_ENST00000250263.7_Missense_Mutation_p.K118N			Q8IV48	ERI1_HUMAN	exoribonuclease 1	118					gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)	p.K118N(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						TGATGCTGAAAGAGAGCAATT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	8											83	83	83					8																	8869118		2203	4300	6503	8906528	SO:0001583	missense	90459			BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"Enhanced RNAi three prime mRNA exonucleases"	23994	protein-coding gene	gene with protein product	"exoribonuclease 1", "enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"	608739	"three prime histone mRNA exonuclease 1"	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.354A>T	8.37:g.8869118A>T	ENSP00000429615:p.Lys118Asn		8906528	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	37	CCDS5972.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.794007	0.50102	.	.	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.48201	0.82;0.82;0.82	5.79	2.17	0.27698	.	0.405934	0.29260	N	0.012675	T	0.31451	0.0797	L	0.36672	1.1	0.44587	D	0.997553	B	0.26577	0.153	B	0.19148	0.024	T	0.07121	-1.0789	10	0.38643	T	0.18	-16.6596	6.1455	0.20283	0.4844:0.0:0.5156:0.0	.	118	Q8IV48	ERI1_HUMAN	N	118	ENSP00000429615:K118N;ENSP00000250263:K118N;ENSP00000430190:K118N	ENSP00000250263:K118N	K	+	3	2	ERI1	8906528	1.000000	0.71417	0.993000	0.49108	0.972000	0.66771	1.788000	0.38714	0.476000	0.27440	0.451000	0.29950	AAA		0.348	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332		T	8869118	A	T	8869118	3	4	61	1	0	0	0	0	1	0	0	0	5240	69	3	5	364	5	ERI1	8	8869118	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	119114	8869118	137494904	5728	13713										
PRSS55	203074	broad.mit.edu	37	chr8	10387083	10387083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcacaggggggatggaggCggaggtgggtgagtttccgt	20	5	1	1	rs144558050		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10387083C>T	ENST00000328655.3	+	2	261	c.221C>T	c.(220-222)gCg>gTg	p.A74V	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Missense_Mutation_p.A74V	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	74	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.A74V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GGGATGGAGGCGGAGGTGGGT	0.517													C|||	1	0.000199681	0	0	5008	,	,		18508	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	220	217	218		221,221	3.2	0.9	8	dbSNP_134	218	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	PRSS55	NM_001197020.1,NM_198464.3	64,64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	74/277,74/353	10387083	2,13004	2203	4300	6503	10424493	SO:0001583	missense	203074			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.221C>T	8.37:g.10387083C>T	ENSP00000333003:p.Ala74Val		10424493	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.770965	0.49680	0.0	2.33E-4	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.94417	-3.42;-3.42	4.05	3.18	0.36537	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.94434	0.8209	L	0.35644	1.08	0.40607	D	0.981638	D	0.89917	1.0	D	0.91635	0.999	D	0.93518	0.6859	9	0.62326	D	0.03	.	8.0557	0.30604	0.0:0.8904:0.0:0.1096	.	74	Q6UWB4	PRS55_HUMAN	V	74	ENSP00000333003:A74V;ENSP00000430459:A74V	ENSP00000333003:A74V	A	+	2	0	PRSS55	10424493	0.928000	0.31464	0.903000	0.35520	0.129000	0.20672	1.921000	0.40035	1.291000	0.44653	-0.215000	0.12644	GCG		0.517	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		T	10387083	C	T	10387083	3	4	61	1	0	0	0	0	1	0	0	0	12668	768	27	1	227	1	PRSS55	8	10387083	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1517965	10387083	135976939	5729	13714										
PRSS55	203074	broad.mit.edu	37	chr8	10396121	10396121	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgttggtgaactacaacCtctggatcgagaaagtgacc	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10396121C>A	ENST00000328655.3	+	5	917	c.877C>A	c.(877-879)Ctc>Atc	p.L293I	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Intron	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	293	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.L293I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GAACTACAACCTCTGGATCGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	8											110	115	114					8																	10396121		2203	4300	6503	10433531	SO:0001583	missense	203074			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.877C>A	8.37:g.10396121C>A	ENSP00000333003:p.Leu293Ile		10433531	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	8.853	0.945163	0.18356	.	.	ENSG00000184647	ENST00000328655	D	0.92805	-3.11	4.2	-1.35	0.09114	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.398600	0.02386	N	0.079274	T	0.81754	0.4889	N	0.14661	0.345	0.09310	N	1	P	0.37573	0.6	B	0.32465	0.146	T	0.74090	-0.3777	10	0.59425	D	0.04	.	1.3548	0.02180	0.1599:0.3275:0.3127:0.1998	.	293	Q6UWB4	PRS55_HUMAN	I	293	ENSP00000333003:L293I	ENSP00000333003:L293I	L	+	1	0	PRSS55	10433531	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.210000	0.17455	-0.401000	0.07644	-1.113000	0.02065	CTC		0.537	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10396121	C	A	10396121	3	1	61	1	0	0	0	0	1	0	0	0	12668	681	24	2	895	2	PRSS55	8	10396121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9038	10396121	135967901	5730	13715										
PRSS55	203074	broad.mit.edu	37	chr8	10396185	10396185	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagagaaaaggaggacttCtgtcaaacagaaacctatgg	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10396185C>A	ENST00000328655.3	+	5	981	c.941C>A	c.(940-942)tCt>tAt	p.S314Y	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Intron	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	314						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.S314Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						AGGAGGACTTCTGTCAAACAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	8											106	117	113					8																	10396185		2203	4300	6503	10433595	SO:0001583	missense	203074			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.941C>A	8.37:g.10396185C>A	ENSP00000333003:p.Ser314Tyr		10433595	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.713379	0.30413	.	.	ENSG00000184647	ENST00000328655	D	0.88975	-2.45	3.36	-2.45	0.06481	.	2.889210	0.01692	N	0.026710	T	0.80330	0.4603	L	0.27053	0.805	0.09310	N	1	P	0.52316	0.952	P	0.45881	0.496	T	0.70479	-0.4860	10	0.02654	T	1	.	4.4886	0.11803	0.0:0.3583:0.1686:0.4731	.	314	Q6UWB4	PRS55_HUMAN	Y	314	ENSP00000333003:S314Y	ENSP00000333003:S314Y	S	+	2	0	PRSS55	10433595	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.320000	0.19540	-0.569000	0.06030	-0.345000	0.07892	TCT		0.562	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10396185	C	A	10396185	3	1	61	1	0	0	0	0	1	0	0	0	12668	913	32	2	959	2	PRSS55	8	10396185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64	10396185	135967837	5731	13716										
RP1L1	94137	broad.mit.edu	37	chr8	10465689	10465689	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggcctctacatcttctgaCtctggctgggcttcctcttc	9	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10465689C>A	ENST00000382483.3	-	4	6142	c.5919G>T	c.(5917-5919)gaG>gaT	p.E1973D		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2053	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.E1973D(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CATCTTCTGACTCTGGCTGGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	8											151	171	164					8																	10465689		2014	4187	6201	10503099	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5919G>T	8.37:g.10465689C>A	ENSP00000371923:p.Glu1973Asp		10503099	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	4.612	0.113674	0.08831	.	.	ENSG00000183638	ENST00000382483	T	0.04862	3.54	1.24	0.184	0.15086	.	.	.	.	.	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	P	0.51933	0.949	B	0.37304	0.246	T	0.43877	-0.9364	9	0.15952	T	0.53	.	5.981	0.19407	0.0:0.7886:0.0:0.2114	.	1973	A6NKC6	.	D	1973	ENSP00000371923:E1973D	ENSP00000371923:E1973D	E	-	3	2	RP1L1	10503099	0.000000	0.05858	0.046000	0.18839	0.107000	0.19398	-0.294000	0.08309	0.535000	0.28714	0.305000	0.20034	GAG		0.602	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10465689	C	A	10465689	3	1	61	1	0	0	0	0	1	0	0	0	13570	564	20	2	1287	2	RP1L1	8	10465689	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69504	10465689	135898333	5732	13717										
RP1L1	94137	broad.mit.edu	37	chr8	10468304	10468304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccatgggcctagacacttCgggcacgctgctgggccggc	16	14	0	1	rs575772322		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10468304C>T	ENST00000382483.3	-	4	3527	c.3304G>A	c.(3304-3306)Gaa>Aaa	p.E1102K		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1102					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.E1102K(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTAGACACTTCGGGCACGCTG	0.647													C|||	1	0.000199681	0	0	5008	,	,		17897	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	8											49	56	54					8																	10468304		1922	4147	6069	10505714	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3304G>A	8.37:g.10468304C>T	ENSP00000371923:p.Glu1102Lys		10505714	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201370	0.79015	.	.	ENSG00000183638	ENST00000382483	D	0.81579	-1.51	4.57	4.57	0.56435	.	0.000000	0.33591	U	0.004745	D	0.84620	0.5512	L	0.32530	0.975	0.36611	D	0.875188	D	0.89917	1.0	D	0.79108	0.992	D	0.88760	0.3256	10	0.87932	D	0	-23.7293	16.5031	0.84262	0.0:1.0:0.0:0.0	.	1102	A6NKC6	.	K	1102	ENSP00000371923:E1102K	ENSP00000371923:E1102K	E	-	1	0	RP1L1	10505714	0.998000	0.40836	0.947000	0.38551	0.718000	0.41266	4.067000	0.57527	2.330000	0.79161	0.561000	0.74099	GAA		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10468304	C	T	10468304	3	4	61	1	0	0	0	0	1	0	0	0	13570	893	31	1	3902	1	RP1L1	8	10468304	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2615	10468304	135895718	5733	13718										
RP1L1	94137	broad.mit.edu	37	chr8	10469845	10469845	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgcgtctctgcctgcaggTcgtcactccttaaagatgaa	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10469845T>C	ENST00000382483.3	-	4	1986	c.1763A>G	c.(1762-1764)gAc>gGc	p.D588G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	588					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.D588G(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGCCTGCAGGTCGTCACTCCT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	8											73	83	80					8																	10469845		2097	4219	6316	10507255	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1763A>G	8.37:g.10469845T>C	ENSP00000371923:p.Asp588Gly		10507255	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.604566	0.28623	.	.	ENSG00000183638	ENST00000382483	T	0.05382	3.45	4.34	-4.33	0.03677	.	0.688754	0.11976	N	0.511272	T	0.03348	0.0097	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.42189	-0.9466	10	0.30078	T	0.28	-5.0173	6.1792	0.20461	0.1645:0.5292:0.0:0.3064	.	588	A6NKC6	.	G	588	ENSP00000371923:D588G	ENSP00000371923:D588G	D	-	2	0	RP1L1	10507255	0.000000	0.05858	0.001000	0.08648	0.180000	0.23129	-0.501000	0.06398	-0.377000	0.07930	0.374000	0.22700	GAC		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			C	10469845	T	C	10469845	3	2	61	1	0	0	0	0	1	0	0	0	13570	1667	58	4	5443	4	RP1L1	8	10469845	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1541	10469845	135894177	5734	13719										
RP1L1	94137	broad.mit.edu	37	chr8	10470381	10470381	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaggcatgcaggggattCgtccagatttcatacttggg	15	7	1	1	rs201081190		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10470381C>T	ENST00000382483.3	-	4	1450	c.1227G>A	c.(1225-1227)acG>acA	p.T409T		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	409					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.T409T(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCAGGGGATTCGTCCAGATTT	0.672													C|||	1	0.000199681	0	0	5008	,	,		16313	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											41	48	46					8																	10470381		1965	4136	6101	10507791	SO:0001819	synonymous_variant	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1227G>A	8.37:g.10470381C>T			10507791	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10470381	C	T	10470381	2	4	61	1	0	0	0	0	0	0	0	1	13570	871	31	1		1	RP1L1	8	10470381	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	536	10470381	135893641	5735	13720										
SOX7	83595	broad.mit.edu	37	chr8	10583419	10583419	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtgttcaaatactggtcGaattcattgcgatccatgtc	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:10583419G>A	ENST00000304501.1	-	2	1074	c.996C>T	c.(994-996)ttC>ttT	p.F332F	SOX7_ENST00000554914.1_Silent_p.F384F|SOX7_ENST00000553390.1_Silent_p.F384F	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	332	Sox C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00849}.				endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.F332F(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		AATACTGGTCGAATTCATTGC	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	8											94	85	88					8																	10583419		2203	4300	6503	10620829	SO:0001819	synonymous_variant	83595			AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"SRY (sex determining region Y)-boxes"	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.996C>T	8.37:g.10583419G>A			10620829	B4DKV0|Q53YD0	Silent	SNP	ENST00000304501.1	37	CCDS5977.1																																																																																				0.622	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1			A	10583419	G	A	10583419	2	1	61	1	0	0	0	0	0	0	0	1	14993	1049	37	1		1	SOX7	8	10583419	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113038	10583419	135780603	5736	13721										
MTMR9	66036	broad.mit.edu	37	chr8	11162452	11162452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcgatgatgaagctcttCggaaggtagctacatttcga	10	9	1	2	rs144999294		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11162452C>T	ENST00000221086.3	+	4	993	c.520C>T	c.(520-522)Cgg>Tgg	p.R174W	MTMR9_ENST00000526292.1_Missense_Mutation_p.R89W	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	174	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)	p.R174W(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TGAAGCTCTTCGGAAGGTAGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	TRP/ARG	0,4406		0,0,2203	224	183	197		520	3	1	8	dbSNP_134	197	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MTMR9	NM_015458.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	174/550	11162452	1,13005	2203	4300	6503	11199862	SO:0001583	missense	66036			AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	14596	protein-coding gene	gene with protein product		606260	"myotubularin related protein 8"	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.520C>T	8.37:g.11162452C>T	ENSP00000221086:p.Arg174Trp		11199862	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	37	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198304	0.58126	0.0	1.16E-4	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.93133	-3.17;-3.17	4.99	2.98	0.34508	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.373441	0.28182	N	0.016298	D	0.94036	0.8089	M	0.70108	2.13	0.45318	D	0.998311	D	0.59767	0.986	P	0.51453	0.67	D	0.94285	0.7523	10	0.66056	D	0.02	.	14.1335	0.65270	0.27:0.73:0.0:0.0	.	174	Q96QG7	MTMR9_HUMAN	W	174;89	ENSP00000221086:R174W;ENSP00000433239:R89W	ENSP00000221086:R174W	R	+	1	2	MTMR9	11199862	0.124000	0.22315	1.000000	0.80357	0.612000	0.37316	0.602000	0.24134	1.251000	0.43983	0.563000	0.77884	CGG		0.453	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		T	11162452	C	T	11162452	3	4	61	1	0	0	0	0	1	0	0	0	9980	875	31	1	534	1	MTMR9	8	11162452	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	579033	11162452	135201570	5737	13722										
FAM167A	83648	broad.mit.edu	37	chr8	11282088	11282088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattttcagcttgttgatgtCgccacgcaggcgcatgagct	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11282088C>T	ENST00000528897.1	-	3	1058	c.439G>A	c.(439-441)Gac>Aac	p.D147N	FAM167A_ENST00000531564.1_5'UTR|FAM167A_ENST00000284486.4_Missense_Mutation_p.D147N|C8orf12_ENST00000529305.1_Intron|FAM167A_ENST00000534308.1_Missense_Mutation_p.D147N|C8orf12_ENST00000284481.3_Intron			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	147								p.D147N(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						TTGTTGATGTCGCCACGCAGG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	8											108	81	90					8																	11282088		2203	4300	6503	11319498	SO:0001583	missense	83648				CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"chromosome 8 open reading frame 13"	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.439G>A	8.37:g.11282088C>T	ENSP00000436655:p.Asp147Asn		11319498	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559895	0.86335	.	.	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897	T;T;T	0.32988	1.43;1.43;1.43	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.46048	-0.9219	10	0.66056	D	0.02	-6.6204	17.3188	0.87231	0.0:1.0:0.0:0.0	.	147	Q96KS9	F167A_HUMAN	N	147	ENSP00000284486:D147N;ENSP00000432232:D147N;ENSP00000436655:D147N	ENSP00000284486:D147N	D	-	1	0	FAM167A	11319498	1.000000	0.71417	0.957000	0.39632	0.412000	0.31113	7.124000	0.77185	2.558000	0.86282	0.555000	0.69702	GAC		0.627	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1			T	11282088	C	T	11282088	3	4	61	1	0	0	0	0	1	0	0	0	5499	884	31	1	209	1	FAM167A	8	11282088	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119636	11282088	135081934	5738	13723										
FDFT1	2222	broad.mit.edu	37	chr8	11679323	11679323	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgccgacatttgccggaGaatgggcattgggatggcag	16	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11679323G>T	ENST00000220584.4	+	4	668	c.446G>T	c.(445-447)aGa>aTa	p.R149I	FDFT1_ENST00000528643.1_Missense_Mutation_p.R64I|FDFT1_ENST00000443614.2_Intron|FDFT1_ENST00000525777.1_Missense_Mutation_p.R64I|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000538689.1_Missense_Mutation_p.R38I|FDFT1_ENST00000528812.1_Missense_Mutation_p.R85I|FDFT1_ENST00000530664.1_Missense_Mutation_p.R85I|FDFT1_ENST00000525900.1_Missense_Mutation_p.R142I	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	149					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)	p.R149I(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		ATTTGCCGGAGAATGGGCATT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	8											211	196	201					8																	11679323		2203	4300	6503	11716732	SO:0001583	missense	2222			X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"squalene synthase"	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.446G>T	8.37:g.11679323G>T	ENSP00000220584:p.Arg149Ile		11716732	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Missense_Mutation	SNP	ENST00000220584.4	37	CCDS5985.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214121	0.58452	.	.	ENSG00000079459	ENST00000538689;ENST00000530337;ENST00000220584;ENST00000525900;ENST00000528812;ENST00000530664;ENST00000528643;ENST00000525777	T;T;T;T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.17	0.299	0.15771	Terpenoid synthase (2);	0.534882	0.20319	N	0.094680	T	0.75989	0.3925	M	0.82132	2.575	0.52501	D	0.999953	D;P;P	0.60160	0.987;0.825;0.825	P;B;P	0.53185	0.72;0.402;0.506	T	0.75442	-0.3316	10	0.87932	D	0	-15.2207	8.8002	0.34905	0.5841:0.0:0.4159:0.0	.	206;142;149	B4DND3;E9PNM1;P37268	.;.;FDFT_HUMAN	I	38;149;149;142;85;85;64;64	ENSP00000444248:R38I;ENSP00000431852:R149I;ENSP00000220584:R149I;ENSP00000434714:R142I;ENSP00000431749:R85I;ENSP00000432331:R85I;ENSP00000431649:R64I;ENSP00000436069:R64I	ENSP00000220584:R149I	R	+	2	0	FDFT1	11716732	1.000000	0.71417	0.123000	0.21794	0.610000	0.37248	2.038000	0.41184	-0.084000	0.12595	-0.367000	0.07326	AGA		0.423	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2			T	11679323	G	T	11679323	3	4	61	1	0	0	0	0	1	0	0	0	5821	942	33	2	460	2	FDFT1	8	11679323	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	397235	11679323	134684699	5739	13724										
CTSB	1508	broad.mit.edu	37	chr8	11702690	11702690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagccaccacttctgattCgattccacagtgatcctgtc	6	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11702690C>T	ENST00000353047.6	-	10	1217	c.964G>A	c.(964-966)Gaa>Aaa	p.E322K	CTSB_ENST00000533455.1_Missense_Mutation_p.E322K|CTSB_ENST00000534510.1_Missense_Mutation_p.E322K|CTSB_ENST00000530640.2_Missense_Mutation_p.E322K|CTSB_ENST00000531089.1_Missense_Mutation_p.E322K|CTSB_ENST00000345125.3_Missense_Mutation_p.E322K|CTSB_ENST00000434271.1_Missense_Mutation_p.E322K|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000453527.2_Missense_Mutation_p.E322K|CTSB_ENST00000415599.2_3'UTR	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	322					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.E322K(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		ACTTCTGATTCGATTCCACAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	8											88	79	82					8																	11702690		2203	4300	6503	11740099	SO:0001583	missense	1508			M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.964G>A	8.37:g.11702690C>T	ENSP00000345672:p.Glu322Lys		11740099	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	C	36	5.667128	0.96745	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	D;D;D;D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09;-2.09;-2.09;-2.09	6.07	6.07	0.98685	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96617	0.8896	H	0.98559	4.265	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97523	1.0074	10	0.87932	D	0	.	19.6321	0.95713	0.0:1.0:0.0:0.0	.	259;322;322;259	B3KUJ8;A8K2H4;P07858;F5H2P9	.;.;CATB_HUMAN;.	K	322;259;322;322;322;322;322;322;322;228	ENSP00000415889:E322K;ENSP00000345672:E322K;ENSP00000435105:E322K;ENSP00000433215:E322K;ENSP00000409917:E322K;ENSP00000342070:E322K;ENSP00000432244:E322K;ENSP00000434217:E322K	ENSP00000342070:E322K	E	-	1	0	CTSB	11740099	1.000000	0.71417	0.320000	0.25306	0.982000	0.71751	7.550000	0.82173	2.884000	0.98904	0.655000	0.94253	GAA		0.488	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		T	11702690	C	T	11702690	3	4	61	1	0	0	0	0	1	0	0	0	4036	893	31	1	59	1	CTSB	8	11702690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23367	11702690	134661332	5740	13725										
CTSB	1508	broad.mit.edu	37	chr8	11705293	11705293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggccgggagccgttgaCgtggtgctcacagggaggga	21	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11705293C>T	ENST00000353047.6	-	7	824	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	CTSB_ENST00000533455.1_Missense_Mutation_p.V191I|CTSB_ENST00000534510.1_Missense_Mutation_p.V191I|CTSB_ENST00000530640.2_Missense_Mutation_p.V191I|CTSB_ENST00000531089.1_Missense_Mutation_p.V191I|CTSB_ENST00000345125.3_Missense_Mutation_p.V191I|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000434271.1_Missense_Mutation_p.V191I|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000453527.2_Missense_Mutation_p.V191I|CTSB_ENST00000415599.2_3'UTR	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	191					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.V191I(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		GAGCCGTTGACGTGGTGCTCA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	8											77	77	77					8																	11705293		2203	4300	6503	11742702	SO:0001583	missense	1508			M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.571G>A	8.37:g.11705293C>T	ENSP00000345672:p.Val191Ile		11742702	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428761	0.83667	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	D;D;D;D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81	5.03	5.03	0.67393	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87585	0.6214	L	0.50333	1.59	0.80722	D	1	D;B;B;B;P	0.57899	0.981;0.118;0.054;0.051;0.571	P;B;B;B;B	0.54174	0.744;0.046;0.025;0.035;0.113	D	0.87913	0.2698	10	0.48119	T	0.1	.	17.3323	0.87268	0.0:1.0:0.0:0.0	.	128;191;97;191;128	B3KUJ8;A8K2H4;B4DMY4;P07858;F5H2P9	.;.;.;CATB_HUMAN;.	I	191;128;191;191;191;191;191;191;191;97	ENSP00000415889:V191I;ENSP00000345672:V191I;ENSP00000435105:V191I;ENSP00000433215:V191I;ENSP00000409917:V191I;ENSP00000342070:V191I;ENSP00000432244:V191I;ENSP00000434217:V191I	ENSP00000342070:V191I	V	-	1	0	CTSB	11742702	1.000000	0.71417	0.991000	0.47740	0.962000	0.63368	3.155000	0.50700	2.304000	0.77564	0.561000	0.74099	GTC		0.622	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		T	11705293	C	T	11705293	3	4	61	1	0	0	0	0	1	0	0	0	4036	536	19	1	464	1	CTSB	8	11705293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2603	11705293	134658729	5741	13726										
DEFB135	613209	broad.mit.edu	37	chr8	11841933	11841933	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtttctcttggcaggtaGaagtggacccaatgtctaca	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11841933G>A	ENST00000382208.2	+	2	68	c.68G>A	c.(67-69)aGa>aAa	p.R23K		NM_001033017.2	NP_001028189.2	Q30KP9	DB135_HUMAN	defensin, beta 135	23					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.R23K(1)		endometrium(1)|large_intestine(2)|prostate(1)	4						TTGGCAGGTAGAAGTGGACCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	76	77					8																	11841933		1914	4124	6038	11879342	SO:0001583	missense	613209			DQ012025	CCDS43710.1	8p23.1	2009-05-27			ENSG00000205883	ENSG00000205883		"Defensins, beta"	32400	protein-coding gene	gene with protein product						16033865	Standard	NM_001033017		Approved		uc003wuw.1	Q30KP9	OTTHUMG00000158719	ENST00000382208.2:c.68G>A	8.37:g.11841933G>A	ENSP00000371643:p.Arg23Lys		11879342	Q4QY37	Missense_Mutation	SNP	ENST00000382208.2	37	CCDS43710.1	.	.	.	.	.	.	.	.	.	.	G	8.692	0.907611	0.17833	.	.	ENSG00000205883	ENST00000382208	.	.	.	3.34	0.458	0.16670	.	0.493260	0.15283	N	0.270554	T	0.23492	0.0568	.	.	.	0.09310	N	0.999994	B	0.17038	0.02	B	0.11329	0.006	T	0.13335	-1.0513	8	0.32370	T	0.25	-6.4888	3.4358	0.07445	0.251:0.2174:0.5316:0.0	.	23	Q30KP9	DB135_HUMAN	K	23	.	ENSP00000371643:R23K	R	+	2	0	DEFB135	11879342	0.988000	0.35896	0.410000	0.26471	0.004000	0.04260	0.158000	0.16422	0.072000	0.16694	0.561000	0.74099	AGA		0.383	DEFB135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351888.1	NM_001033017		A	11841933	G	A	11841933	3	1	61	1	0	0	0	0	1	0	0	0	4430	942	33	3	74	3	DEFB135	8	11841933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136640	11841933	134522089	5742	13727										
DEFB134	613211	broad.mit.edu	37	chr8	11853730	11853730	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggatcccaaaggaaaaGaaagacaaacacaacaagga	8	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11853730G>T	ENST00000526438.1	-	1	91	c.31C>A	c.(31-33)Ctt>Att	p.L11I	DEFB134_ENST00000382205.4_Missense_Mutation_p.L11I	NM_001033019.1	NP_001028191.1	Q4QY38	DB134_HUMAN	defensin, beta 134	11					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.L11I(1)		kidney(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.159)		CAAAGGAAAAGAAAGACAAAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	8											142	142	142					8																	11853730		2203	4300	6503	11891139	SO:0001583	missense	613211			AY621331, DQ012024	CCDS34847.1	8p23.1	2010-04-15			ENSG00000205882	ENSG00000205882		"Defensins, beta"	32399	protein-coding gene	gene with protein product						16033865	Standard	NM_001033019		Approved		uc011kxn.2	Q4QY38	OTTHUMG00000158718	ENST00000526438.1:c.31C>A	8.37:g.11853730G>T	ENSP00000435010:p.Leu11Ile		11891139	A1L4A4	Missense_Mutation	SNP	ENST00000526438.1	37	CCDS34847.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331280	0.24167	.	.	ENSG00000205882	ENST00000526438;ENST00000382205	.	.	.	3.15	2.26	0.28386	.	0.000000	0.29572	N	0.011777	T	0.20780	0.0500	.	.	.	0.09310	N	1	P	0.52842	0.956	B	0.42386	0.386	T	0.08868	-1.0701	8	0.37606	T	0.19	-11.4769	6.0915	0.19997	0.1427:0.0:0.8573:0.0	.	11	Q4QY38	DB134_HUMAN	I	11	.	ENSP00000371640:L11I	L	-	1	0	DEFB134	11891139	0.020000	0.18652	0.023000	0.16930	0.026000	0.11368	0.432000	0.21461	0.892000	0.36259	0.655000	0.94253	CTT		0.478	DEFB134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351887.2	NM_001033019		T	11853730	G	T	11853730	3	4	61	1	0	0	0	0	1	0	0	0	4429	942	33	2	176	2	DEFB134	8	11853730	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11797	11853730	134510292	5743	13728										
USP17L2	377630	broad.mit.edu	37	chr8	11995777	11995777	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatccacagtgaacatgaGaaattcatgggcatcttcct	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:11995777G>T	ENST00000333796.3	-	1	809	c.493C>A	c.(493-495)Ctc>Atc	p.L165I	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	165	USP.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.L165I(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GTGAACATGAGAAATTCATGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	8											2	2	2					8																	11995777		647	1526	2173	12033186	SO:0001583	missense	377630			BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.493C>A	8.37:g.11995777G>T	ENSP00000333329:p.Leu165Ile		12033186		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078962	0.36662	.	.	ENSG00000223443	ENST00000333796	T	0.38887	1.11	0.745	-0.335	0.12662	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.56097	D	0.000026	T	0.56124	0.1964	M	0.80332	2.49	0.29301	N	0.868703	D	0.71674	0.998	D	0.77557	0.99	T	0.51896	-0.8647	10	0.87932	D	0	.	3.3559	0.07169	0.3198:0.0:0.6802:0.0	.	165	Q6R6M4	U17L2_HUMAN	I	165	ENSP00000333329:L165I	ENSP00000333329:L165I	L	-	1	0	USP17L2	12033186	1.000000	0.71417	0.326000	0.25389	0.112000	0.19704	1.659000	0.37387	-0.078000	0.12730	-0.365000	0.07479	CTC		0.522	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		T	11995777	G	T	11995777	3	4	61	1	0	0	0	0	1	0	0	0	17088	942	33	2	1103	2	USP17L2	8	11995777	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142047	11995777	134368245	5744	13729										
LONRF1	91694	broad.mit.edu	37	chr8	12586510	12586510	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccaactgtatcaaccacaGaccttccgtccggtaagaaa	6	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:12586510G>A	ENST00000398246.3	-	10	1979	c.1910C>T	c.(1909-1911)tCt>tTt	p.S637F	LONRF1_ENST00000525024.1_Missense_Mutation_p.S63F|LONRF1_ENST00000533751.1_Missense_Mutation_p.S280F|MIR3926-2_ENST00000578598.1_RNA	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	637	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.S637F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		ATCAACCACAGACCTTCCGTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	8											132	121	124					8																	12586510		1841	4088	5929	12630881	SO:0001583	missense	91694			AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.1910C>T	8.37:g.12586510G>A	ENSP00000381298:p.Ser637Phe		12630881	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Missense_Mutation	SNP	ENST00000398246.3	37	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	G	26.9	4.784136	0.90282	.	.	ENSG00000154359	ENST00000398246;ENST00000525024;ENST00000533751;ENST00000524526	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.04	5.04	0.67666	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.000000	0.85682	D	0.000000	T	0.62744	0.2453	M	0.73217	2.22	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.77557	0.984;0.99	T	0.55573	-0.8120	10	0.15066	T	0.55	-17.9999	19.2731	0.94018	0.0:0.0:1.0:0.0	.	626;637	Q17RB8-2;Q17RB8	.;LONF1_HUMAN	F	637;63;280;240	ENSP00000381298:S637F;ENSP00000436770:S63F;ENSP00000432130:S280F;ENSP00000433327:S240F	ENSP00000381298:S637F	S	-	2	0	LONRF1	12630881	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.733000	0.93635	0.557000	0.71058	TCT		0.363	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		A	12586510	G	A	12586510	3	1	61	1	0	0	0	0	1	0	0	0	8923	942	33	3	423	3	LONRF1	8	12586510	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	590733	12586510	133777512	5745	13730										
LONRF1	91694	broad.mit.edu	37	chr8	12594230	12594230	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatgcagagagaacactcGaaatctgagacatcgattaa	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:12594230G>A	ENST00000398246.3	-	6	1500	c.1431C>T	c.(1429-1431)ttC>ttT	p.F477F	LONRF1_ENST00000530693.1_5'Flank|LONRF1_ENST00000533751.1_Silent_p.F120F	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	477							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.F477F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		GAGAACACTCGAAATCTGAGA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	8											75	70	71					8																	12594230		1819	4071	5890	12638601	SO:0001819	synonymous_variant	91694			AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.1431C>T	8.37:g.12594230G>A			12638601	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Silent	SNP	ENST00000398246.3	37	CCDS5987.2																																																																																				0.313	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		A	12594230	G	A	12594230	2	1	61	1	0	0	0	0	0	0	0	1	8923	1049	37	1		1	LONRF1	8	12594230	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7720	12594230	133769792	5746	13731										
DLC1	10395	broad.mit.edu	37	chr8	13251148	13251148	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagaagacaaatttactcGtgtctgatttactgaaatgg	9	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:13251148G>A	ENST00000276297.4	-	4	1637	c.1228C>T	c.(1228-1230)Cga>Tga	p.R410*	DLC1_ENST00000316609.5_Nonsense_Mutation_p.R410*|DLC1_ENST00000511869.1_Nonsense_Mutation_p.R410*	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	410					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.R410L(3)|p.R410*(2)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AAATTTACTCGTGTCTGATTT	0.423																																																5	Substitution - Missense(3)|Substitution - Nonsense(2)	lung(3)|large_intestine(2)	8											163	152	156					8																	13251148		2203	4300	6503	13295519	SO:0001587	stop_gained	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1228C>T	8.37:g.13251148G>A	ENSP00000276297:p.Arg410*		13295519	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Nonsense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	G	35	5.488499	0.96323	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	.	.	.	4.78	3.89	0.44902	.	1.162670	0.06418	N	0.721807	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	13.0033	0.58690	0.0:0.0:0.8382:0.1618	.	.	.	.	X	410	.	ENSP00000276297:R410X	R	-	1	2	DLC1	13295519	0.269000	0.24143	0.003000	0.11579	0.365000	0.29674	2.706000	0.47135	1.347000	0.45714	0.650000	0.86243	CGA		0.423	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	13251148	G	A	13251148	4	1	61	1	0	0	0	0	0	1	0	0	4561	1153	40	1	3503	1	DLC1	8	13251148	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	656918	13251148	133112874	5747	13732										
DLC1	10395	broad.mit.edu	37	chr8	13357214	13357214	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaaaacctgtttatcatCtgtaaggcataaatcagcat	5	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:13357214C>T	ENST00000276297.4	-	2	776	c.367G>A	c.(367-369)Gat>Aat	p.D123N	DLC1_ENST00000316609.5_Missense_Mutation_p.D123N|DLC1_ENST00000511869.1_Missense_Mutation_p.D123N	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	123					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.D123N(2)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGTTTATCATCTGTAAGGCAT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	8											182	183	183					8																	13357214		2203	4300	6503	13401585	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.367G>A	8.37:g.13357214C>T	ENSP00000276297:p.Asp123Asn		13401585	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	0.390	-0.923840	0.02377	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.12465	3.62;2.68;2.7	5.03	3.08	0.35506	.	0.307446	0.23591	N	0.046544	T	0.05686	0.0149	N	0.16656	0.425	0.09310	N	1	B;B;B	0.21147	0.002;0.052;0.0	B;B;B	0.15052	0.006;0.012;0.001	T	0.39860	-0.9593	10	0.06757	T	0.87	.	4.3886	0.11328	0.1606:0.5447:0.0:0.2947	.	123;123;123	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	N	123	ENSP00000276297:D123N;ENSP00000321034:D123N;ENSP00000425878:D123N	ENSP00000276297:D123N	D	-	1	0	DLC1	13401585	0.004000	0.15560	0.744000	0.31058	0.229000	0.25112	0.567000	0.23608	1.467000	0.48044	0.655000	0.94253	GAT		0.428	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	13357214	C	T	13357214	3	4	61	1	0	0	0	0	1	0	0	0	4561	913	32	3	4372	3	DLC1	8	13357214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106066	13357214	133006808	5748	13733										
SGCZ	137868	broad.mit.edu	37	chr8	14412244	14412244	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatagtggtacttaccacAgtgaaattcataactttcaa	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:14412244A>C	ENST00000382080.1	-	2	946	c.231T>G	c.(229-231)acT>acG	p.T77T	SGCZ_ENST00000421524.2_Silent_p.T64T	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	64					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)		p.T77T(1)		NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TACTTACCACAGTGAAATTCA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	8											107	96	100					8																	14412244		2203	4300	6503	14456615	SO:0001819	synonymous_variant	137868			AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.231T>G	8.37:g.14412244A>C			14456615	Q6REU0	Silent	SNP	ENST00000382080.1	37	CCDS5992.2																																																																																				0.328	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		C	14412244	A	C	14412244	2	2	61	1	0	0	0	0	0	0	0	1	14241	175	7	4		4	SGCZ	8	14412244	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1055030	14412244	131951778	5749	13734										
TUSC3	7991	broad.mit.edu	37	chr8	15480697	15480697	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttataaaggcaccacctcgaAactattccatgattgttatg	6	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:15480697A>C	ENST00000503731.1	+	2	395	c.247A>C	c.(247-249)Aac>Cac	p.N83H	TUSC3_ENST00000503191.1_3'UTR|TUSC3_ENST00000506802.1_Missense_Mutation_p.N83H|TUSC3_ENST00000382020.4_Missense_Mutation_p.N83H|TUSC3_ENST00000509380.1_Missense_Mutation_p.N83H	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	83	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)	p.N83H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		ACCACCTCGAAACTATTCCAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											83	85	85					8																	15480697		2203	4300	6503	15525068	SO:0001583	missense	7991			AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.247A>C	8.37:g.15480697A>C	ENSP00000424544:p.Asn83His		15525068	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	37	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.670154	0.88348	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.59	5.59	0.84812	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.039879	0.85682	D	0.000000	T	0.70081	0.3183	M	0.88105	2.93	0.80722	D	1	D;D;D;D;D;D	0.89917	0.996;1.0;0.997;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.991;0.998;0.994;0.999;0.998;0.998	T	0.76258	-0.3025	10	0.66056	D	0.02	-18.1985	15.2531	0.73564	1.0:0.0:0.0:0.0	.	83;83;83;83;83;83	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	H	83	ENSP00000371450:N83H;ENSP00000425777:N83H;ENSP00000423426:N83H;ENSP00000424544:N83H	ENSP00000221167:N83H	N	+	1	0	TUSC3	15525068	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.962000	0.93254	2.263000	0.75096	0.528000	0.53228	AAC		0.373	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		C	15480697	A	C	15480697	3	2	61	1	0	0	0	0	1	0	0	0	16818	14	1	4	253	4	TUSC3	8	15480697	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1068453	15480697	130883325	5750	13735										
FGF20	26281	broad.mit.edu	37	chr8	16850811	16850811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctccctaaagatgcattCggaagtaagtttctcctgaa	8	10	1	2	rs201317229		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:16850811C>T	ENST00000180166.5	-	3	554	c.406G>A	c.(406-408)Gaa>Aaa	p.E136K		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	136					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)		p.E136K(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		AAGATGCATTCGGAAGTAAGT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	LYS/GLU	0,4406		0,0,2203	116	121	120		406	5.8	1	8		120	2,8598	1.2+/-3.3	0,2,4298	no	missense	FGF20	NM_019851.2	56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	136/212	16850811	2,13004	2203	4300	6503	16895182	SO:0001583	missense	26281			AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.406G>A	8.37:g.16850811C>T	ENSP00000180166:p.Glu136Lys		16895182	B2RPH5	Missense_Mutation	SNP	ENST00000180166.5	37	CCDS5998.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.6|29.6	5.018103|5.018103	0.93404|0.93404	0.0|0.0	2.33E-4|2.33E-4	ENSG00000078579|ENSG00000078579	ENST00000180166|ENST00000519941	T|.	0.74632|.	-0.86|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86083|0.86083	0.5848|0.5848	M|M	0.89785|0.89785	3.06|3.06	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.74674|.	0.984|.	D|D	0.87025|0.87025	0.2131|0.2131	10|5	0.87932|.	D|.	0|.	.|.	20.5471|20.5471	0.99284|0.99284	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	136|.	Q9NP95|.	FGF20_HUMAN|.	K|Q	136|37	ENSP00000180166:E136K|.	ENSP00000180166:E136K|.	E|R	-|-	1|2	0|0	FGF20|FGF20	16895182|16895182	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.818000|7.818000	0.86416|0.86416	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.328	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1			T	16850811	C	T	16850811	3	4	61	1	0	0	0	0	1	0	0	0	5868	893	31	1	233	1	FGF20	8	16850811	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1370114	16850811	129513211	5751	13736										
ZDHHC2	51201	broad.mit.edu	37	chr8	17063200	17063200	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattttcaaattataagttCtttctccttttcttggctta	5	7	4	0	rs368763365		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17063200C>A	ENST00000262096.8	+	7	1208	c.513C>A	c.(511-513)ttC>ttA	p.F171L		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	171					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.F171L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		ATTATAAGTTCTTTCTCCTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	LEU/PHE	0,3662		0,0,1831	273	265	268		513	2.5	1	8		268	1,8151		0,1,4075	no	missense	ZDHHC2	NM_016353.4	22	0,1,5906	AA,AC,CC		0.0123,0.0,0.0085	possibly-damaging	171/368	17063200	1,11813	1831	4076	5907	17107571	SO:0001583	missense	51201			AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.513C>A	8.37:g.17063200C>A	ENSP00000262096:p.Phe171Leu		17107571	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923710	0.73213	0.0	1.23E-4	ENSG00000104219	ENST00000262096;ENST00000522184	T;T	0.24723	1.84;1.84	5.72	2.46	0.29980	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.38904	0.1058	M	0.77712	2.385	0.58432	D	0.999998	P	0.52463	0.953	P	0.54174	0.744	T	0.23976	-1.0173	10	0.87932	D	0	-3.422	6.9507	0.24544	0.0:0.3837:0.0:0.6163	.	171	Q9UIJ5	ZDHC2_HUMAN	L	171;126	ENSP00000262096:F171L;ENSP00000430317:F126L	ENSP00000262096:F171L	F	+	3	2	ZDHHC2	17107571	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.059000	0.49947	0.707000	0.31934	0.563000	0.77884	TTC		0.333	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		A	17063200	C	A	17063200	3	1	61	1	0	0	0	0	1	0	0	0	17649	912	32	2	539	2	ZDHHC2	8	17063200	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212389	17063200	129300822	5752	13737										
ZDHHC2	51201	broad.mit.edu	37	chr8	17063278	17063278	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacagtattttatcaaattTtggacagtaagtcattaact	5	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17063278T>G	ENST00000262096.8	+	7	1286	c.591T>G	c.(589-591)ttT>ttG	p.F197L		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	197					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.F197L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TTATCAAATTTTGGACAGTAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	8											165	157	159					8																	17063278		1806	4064	5870	17107649	SO:0001583	missense	51201			AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.591T>G	8.37:g.17063278T>G	ENSP00000262096:p.Phe197Leu		17107649	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.496131	0.85069	.	.	ENSG00000104219	ENST00000262096	T	0.22134	1.97	5.5	0.484	0.16825	.	0.098186	0.64402	D	0.000001	T	0.32194	0.0821	L	0.41236	1.265	0.80722	D	1	D	0.63046	0.992	D	0.76071	0.987	T	0.02263	-1.1186	10	0.66056	D	0.02	-4.0304	10.4127	0.44303	0.0:0.335:0.0:0.665	.	197	Q9UIJ5	ZDHC2_HUMAN	L	197	ENSP00000262096:F197L	ENSP00000262096:F197L	F	+	3	2	ZDHHC2	17107649	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	0.222000	0.17699	0.145000	0.18977	0.460000	0.39030	TTT		0.303	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		G	17063278	T	G	17063278	3	3	61	1	0	0	0	0	1	0	0	0	17649	1838	64	4	617	4	ZDHHC2	8	17063278	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	78	17063278	129300744	5753	13738										
MTUS1	57509	broad.mit.edu	37	chr8	17510988	17510988	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagcgatttcttttctatTtcatggcctttcttaatttc	4	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17510988T>G	ENST00000262102.6	-	11	3458	c.3234A>C	c.(3232-3234)gaA>gaC	p.E1078D	MTUS1_ENST00000400046.1_Missense_Mutation_p.E150D|MTUS1_ENST00000381861.3_Missense_Mutation_p.E325D|MTUS1_ENST00000381869.3_Missense_Mutation_p.E1024D|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000544260.1_Missense_Mutation_p.E223D|MTUS1_ENST00000297488.6_Missense_Mutation_p.E244D|MTUS1_ENST00000519263.1_Missense_Mutation_p.E1024D	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1078					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E325D(1)|p.E244D(1)|p.E1078D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TCTTTTCTATTTCATGGCCTT	0.343																																																3	Substitution - Missense(3)	large_intestine(3)	8											66	60	62					8																	17510988		1797	4073	5870	17555268	SO:0001583	missense	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.3234A>C	8.37:g.17510988T>G	ENSP00000262102:p.Glu1078Asp		17555268	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551627	0.65311	.	.	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.36157	1.34;1.27;1.96;1.27;1.34;1.34;1.34	5.32	-0.0713	0.13744	.	0.212382	0.49305	D	0.000144	T	0.36413	0.0966	M	0.68593	2.085	0.42186	D	0.991709	P;P;B;B	0.36768	0.569;0.569;0.039;0.257	B;B;B;B	0.43413	0.353;0.419;0.047;0.147	T	0.15954	-1.0419	10	0.49607	T	0.09	-27.9494	5.9782	0.19393	0.0:0.2793:0.1278:0.5929	.	1024;1078;325;244	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	D	1024;223;150;244;325;1078;1024	ENSP00000371293:E1024D;ENSP00000445738:E223D;ENSP00000382921:E150D;ENSP00000297488:E244D;ENSP00000371285:E325D;ENSP00000262102:E1078D;ENSP00000430167:E1024D	ENSP00000262102:E1078D	E	-	3	2	MTUS1	17555268	0.518000	0.26234	0.899000	0.35326	0.939000	0.58152	0.656000	0.24948	0.380000	0.24823	0.383000	0.25322	GAA		0.343	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17510988	T	G	17510988	3	3	61	1	0	0	0	0	1	0	0	0	9995	1838	64	4	598	4	MTUS1	8	17510988	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	447710	17510988	128853034	5754	13739										
MTUS1	57509	broad.mit.edu	37	chr8	17573355	17573355	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatcctgaggaaccattCtgaaatgctggttttggagg	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17573355C>A	ENST00000262102.6	-	5	2729	c.2505G>T	c.(2503-2505)caG>caT	p.Q835H	MTUS1_ENST00000381861.3_Missense_Mutation_p.Q82H|MTUS1_ENST00000381869.3_Missense_Mutation_p.Q781H|MTUS1_ENST00000544260.1_5'UTR|MTUS1_ENST00000519263.1_Missense_Mutation_p.Q781H	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	835					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Q835H(1)|p.Q82H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AGGAACCATTCTGAAATGCTG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	8											150	145	147					8																	17573355		1831	4086	5917	17617635	SO:0001583	missense	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2505G>T	8.37:g.17573355C>A	ENSP00000262102:p.Gln835His		17617635	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300105	0.60195	.	.	ENSG00000129422	ENST00000381869;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T	0.36520	3.08;2.35;1.25;3.08	4.85	-8.68	0.00859	.	0.825208	0.11400	N	0.567975	T	0.49712	0.1573	M	0.63428	1.95	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;P	0.67548	0.935;0.952;0.904	T	0.71663	-0.4525	10	0.72032	D	0.01	-15.9992	16.4248	0.83810	0.0:0.7331:0.0951:0.1718	.	781;835;82	Q9ULD2-2;Q9ULD2;Q9ULD2-6	.;MTUS1_HUMAN;.	H	781;82;835;781	ENSP00000371293:Q781H;ENSP00000371285:Q82H;ENSP00000262102:Q835H;ENSP00000430167:Q781H	ENSP00000262102:Q835H	Q	-	3	2	MTUS1	17617635	0.137000	0.22531	0.894000	0.35097	0.948000	0.59901	-1.339000	0.02652	-1.224000	0.02581	-1.021000	0.02439	CAG		0.383	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17573355	C	A	17573355	3	1	61	1	0	0	0	0	1	0	0	0	9995	912	32	2	1476	2	MTUS1	8	17573355	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62367	17573355	128790667	5755	13740										
MTUS1	57509	broad.mit.edu	37	chr8	17611493	17611493	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcttcctgattcgatttCacggcagatgttgttcttgg	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17611493C>A	ENST00000262102.6	-	2	2048	c.1824G>T	c.(1822-1824)gtG>gtT	p.V608V	MTUS1_ENST00000381869.3_Silent_p.V608V|MTUS1_ENST00000381862.3_Silent_p.V608V|MTUS1_ENST00000519263.1_Silent_p.V608V	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	608					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V608V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		GATTCGATTTCACGGCAGATG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	8											177	165	169					8																	17611493		1898	4117	6015	17655773	SO:0001819	synonymous_variant	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1824G>T	8.37:g.17611493C>A			17655773	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																				0.433	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17611493	C	A	17611493	2	1	61	1	0	0	0	0	0	0	0	1	9995	813	29	2		2	MTUS1	8	17611493	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38138	17611493	128752529	5756	13741										
MTUS1	57509	broad.mit.edu	37	chr8	17612008	17612008	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaacagaaaaggttacttTtgtgggttctaggactggtg	13	4	1	2	rs374391254		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17612008T>G	ENST00000262102.6	-	2	1533	c.1309A>C	c.(1309-1311)Aaa>Caa	p.K437Q	MTUS1_ENST00000381869.3_Missense_Mutation_p.K437Q|MTUS1_ENST00000381862.3_Missense_Mutation_p.K437Q|MTUS1_ENST00000519263.1_Missense_Mutation_p.K437Q	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	437					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K437Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AAGGTTACTTTTGTGGGTTCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											130	125	126					8																	17612008		1890	4116	6006	17656288	SO:0001583	missense	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1309A>C	8.37:g.17612008T>G	ENSP00000262102:p.Lys437Gln		17656288	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	4.692	0.128735	0.08981	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.17213	3.31;3.32;3.31;2.29	5.0	-1.95	0.07548	.	0.453433	0.21105	N	0.080088	T	0.06690	0.0171	N	0.08118	0	0.09310	N	1	B;B;B	0.17852	0.024;0.01;0.01	B;B;B	0.18871	0.023;0.023;0.023	T	0.24297	-1.0164	10	0.39692	T	0.17	-3.2763	5.9483	0.19232	0.0:0.2687:0.2286:0.5027	.	437;437;437	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	Q	437	ENSP00000371293:K437Q;ENSP00000262102:K437Q;ENSP00000430167:K437Q;ENSP00000371286:K437Q	ENSP00000262102:K437Q	K	-	1	0	MTUS1	17656288	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	0.028000	0.13644	-0.389000	0.07786	-0.274000	0.10170	AAA		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17612008	T	G	17612008	3	3	61	1	0	0	0	0	1	0	0	0	9995	1850	64	4	2878	4	MTUS1	8	17612008	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	515	17612008	128752014	5757	13742										
MTUS1	57509	broad.mit.edu	37	chr8	17613105	17613105	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaccctgaaggcttaaaGaaatattttcaccagtaact	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17613105G>T	ENST00000262102.6	-	2	436	c.212C>A	c.(211-213)tCt>tAt	p.S71Y	MTUS1_ENST00000381869.3_Missense_Mutation_p.S71Y|MTUS1_ENST00000381862.3_Missense_Mutation_p.S71Y|MTUS1_ENST00000519263.1_Missense_Mutation_p.S71Y	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	71					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S71Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AAGGCTTAAAGAAATATTTTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											130	122	124					8																	17613105		1855	4100	5955	17657385	SO:0001583	missense	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.212C>A	8.37:g.17613105G>T	ENSP00000262102:p.Ser71Tyr		17657385	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	g	15.70	2.910797	0.52439	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.26373	2.7;2.74;2.7;1.74	3.98	3.98	0.46160	.	1.154810	0.06452	N	0.727851	T	0.37812	0.1017	L	0.27053	0.805	0.09310	N	1	D;D;D	0.76494	0.999;0.99;0.99	D;D;D	0.66979	0.948;0.912;0.912	T	0.36040	-0.9764	10	0.87932	D	0	-0.5216	9.896	0.41318	0.0997:0.0:0.9003:0.0	.	71;71;71	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	Y	71	ENSP00000371293:S71Y;ENSP00000262102:S71Y;ENSP00000430167:S71Y;ENSP00000371286:S71Y	ENSP00000262102:S71Y	S	-	2	0	MTUS1	17657385	0.415000	0.25416	0.027000	0.17364	0.147000	0.21601	1.089000	0.30890	2.495000	0.84180	0.558000	0.71614	TCT		0.388	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17613105	G	T	17613105	3	4	61	1	0	0	0	0	1	0	0	0	9995	942	33	2	3975	2	MTUS1	8	17613105	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1097	17613105	128750917	5758	13743										
PCM1	5108	broad.mit.edu	37	chr8	17813059	17813059	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaccggttgtcaatggaGaatccaatagcctcacatca	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17813059G>T	ENST00000519253.1	+	10	1620	c.1369G>T	c.(1369-1371)Gaa>Taa	p.E457*	PCM1_ENST00000325083.8_Nonsense_Mutation_p.E457*|PCM1_ENST00000518537.1_Nonsense_Mutation_p.E496*|PCM1_ENST00000524226.1_Nonsense_Mutation_p.E457*			Q15154	PCM1_HUMAN	pericentriolar material 1	457					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.E457*(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGTCAATGGAGAATCCAATAG	0.463			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Nonsense(1)	large_intestine(1)	8											92	86	88					8																	17813059		1930	4132	6062	17857339	SO:0001587	stop_gained	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.1369G>T	8.37:g.17813059G>T	ENSP00000431099:p.Glu457*		17857339	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Nonsense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	G	27.3	4.820691	0.90873	.	.	ENSG00000078674	ENST00000325083;ENST00000325126;ENST00000517730;ENST00000518537;ENST00000519253;ENST00000524226	.	.	.	4.88	4.88	0.63580	.	0.412335	0.30219	N	0.010125	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-18.6479	18.9274	0.92550	0.0:0.0:1.0:0.0	.	.	.	.	X	457;496;496;496;457;457	.	ENSP00000327077:E457X	E	+	1	0	PCM1	17857339	1.000000	0.71417	0.996000	0.52242	0.537000	0.34900	7.037000	0.76531	2.645000	0.89757	0.655000	0.94253	GAA		0.463	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17813059	G	T	17813059	4	4	61	1	0	0	0	0	0	1	0	0	11615	943	33	2	1399	2	PCM1	8	17813059	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199954	17813059	128550963	5759	13744										
PCM1	5108	broad.mit.edu	37	chr8	17814153	17814153	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagattgaatgagctaagaGaattagttcattattatgaa	9	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17814153G>T	ENST00000519253.1	+	11	1764	c.1513G>T	c.(1513-1515)Gaa>Taa	p.E505*	PCM1_ENST00000325083.8_Nonsense_Mutation_p.E505*|PCM1_ENST00000524226.1_Nonsense_Mutation_p.E505*			Q15154	PCM1_HUMAN	pericentriolar material 1	505					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.E505*(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGAGCTAAGAGAATTAGTTCA	0.308			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Nonsense(1)	large_intestine(1)	8											54	52	53					8																	17814153		1832	4091	5923	17858433	SO:0001587	stop_gained	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.1513G>T	8.37:g.17814153G>T	ENSP00000431099:p.Glu505*		17858433	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Nonsense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	G	37	6.229246	0.97394	.	.	ENSG00000078674	ENST00000325083;ENST00000517730;ENST00000519253;ENST00000524226	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-19.1497	18.4789	0.90804	0.0:0.0:1.0:0.0	.	.	.	.	X	505;544;505;505	.	ENSP00000327077:E505X	E	+	1	0	PCM1	17858433	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.751000	0.98889	2.529000	0.85273	0.650000	0.86243	GAA		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17814153	G	T	17814153	4	4	61	1	0	0	0	0	0	1	0	0	11615	943	33	2	1547	2	PCM1	8	17814153	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1094	17814153	128549869	5760	13745										
PCM1	5108	broad.mit.edu	37	chr8	17823673	17823673	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacaaatcaatcagctaaaGaaacagcttgattttagtgt	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17823673G>T	ENST00000519253.1	+	19	3272	c.3021G>T	c.(3019-3021)aaG>aaT	p.K1007N	PCM1_ENST00000325083.8_Missense_Mutation_p.K1007N|PCM1_ENST00000524226.1_Missense_Mutation_p.K1008N			Q15154	PCM1_HUMAN	pericentriolar material 1	1007					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.K1007N(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		ATCAGCTAAAGAAACAGCTTG	0.358			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Missense(1)	large_intestine(1)	8											102	100	101					8																	17823673		1861	4102	5963	17867953	SO:0001583	missense	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3021G>T	8.37:g.17823673G>T	ENSP00000431099:p.Lys1007Asn		17867953	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	G	19.71	3.877577	0.72294	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.20200	2.09;2.09;2.09	5.61	3.82	0.43975	.	0.091151	0.85682	D	0.000000	T	0.20007	0.0481	L	0.27053	0.805	0.80722	D	1	P;P;P	0.49783	0.928;0.928;0.928	P;P;P	0.49922	0.626;0.626;0.626	T	0.01480	-1.1344	10	0.48119	T	0.1	-18.6511	8.5869	0.33664	0.2883:0.0:0.7117:0.0	.	1007;1008;1007	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	N	1007;1007;1008	ENSP00000327077:K1007N;ENSP00000431099:K1007N;ENSP00000430521:K1008N	ENSP00000327077:K1007N	K	+	3	2	PCM1	17867953	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	4.151000	0.58105	0.858000	0.35431	0.655000	0.94253	AAG		0.358	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17823673	G	T	17823673	3	4	61	1	0	0	0	0	1	0	0	0	11615	933	33	2	3087	2	PCM1	8	17823673	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9520	17823673	128540349	5761	13746										
PCM1	5108	broad.mit.edu	37	chr8	17829995	17829995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatcaattagatacaaacGgaagaagacgccagtttgat	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17829995G>A	ENST00000519253.1	+	23	3993	c.3742G>A	c.(3742-3744)Gga>Aga	p.G1248R	PCM1_ENST00000325083.8_Missense_Mutation_p.G1248R|PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000524226.1_Missense_Mutation_p.G1249R			Q15154	PCM1_HUMAN	pericentriolar material 1	1248					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.G1248R(1)|p.G1248*(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		AGATACAAACGGAAGAAGACG	0.368			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	8											100	94	96					8																	17829995		1856	4097	5953	17874275	SO:0001583	missense	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3742G>A	8.37:g.17829995G>A	ENSP00000431099:p.Gly1248Arg		17874275	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	G	0.003	-2.470773	0.00167	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.04758	3.8;3.8;3.56	4.46	0.659	0.17861	.	0.483859	0.26535	N	0.023826	T	0.01222	0.0040	N	0.00926	-1.1	0.48571	D	0.999679	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.04013	0.0;0.001;0.0;0.001	T	0.49916	-0.8888	10	0.17832	T	0.49	-0.4574	1.4089	0.02287	0.4419:0.2698:0.1575:0.1308	.	110;1248;1249;1248	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	R	1248;1248;1249	ENSP00000327077:G1248R;ENSP00000431099:G1248R;ENSP00000430521:G1249R	ENSP00000327077:G1248R	G	+	1	0	PCM1	17874275	0.117000	0.22190	0.093000	0.20910	0.076000	0.17211	0.201000	0.17276	0.014000	0.14944	0.313000	0.20887	GGA		0.368	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		A	17829995	G	A	17829995	3	1	61	1	0	0	0	0	1	0	0	0	11615	1117	39	1	3824	1	PCM1	8	17829995	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6322	17829995	128534027	5762	13747										
PCM1	5108	broad.mit.edu	37	chr8	17843510	17843510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagagccatgaaaaaggaGaaaatgtaaagtcagtaaac	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17843510G>T	ENST00000519253.1	+	26	4575	c.4324G>T	c.(4324-4326)Gaa>Taa	p.E1442*	PCM1_ENST00000325083.8_Nonsense_Mutation_p.E1442*|PCM1_ENST00000327578.8_Nonsense_Mutation_p.E141*|PCM1_ENST00000524226.1_Nonsense_Mutation_p.E1388*			Q15154	PCM1_HUMAN	pericentriolar material 1	1442	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.E1442*(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGAAAAAGGAGAAAATGTAAA	0.328			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Nonsense(1)	large_intestine(1)	8											71	67	69					8																	17843510		1833	4069	5902	17887790	SO:0001587	stop_gained	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.4324G>T	8.37:g.17843510G>T	ENSP00000431099:p.Glu1442*		17887790	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Nonsense_Mutation	SNP	ENST00000519253.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.613438|7.613438	0.98390|0.98390	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000522275|ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578	.|.	.|.	.|.	4.5|4.5	2.7|2.7	0.31948|0.31948	.|.	0.738380|0.738380	0.13794|0.13794	N|N	0.362277|0.362277	T|.	0.40297|.	0.1111|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.46803|.	-0.9165|.	4|.	.|0.30854	.|T	.|0.27	-3.3058|-3.3058	6.0453|6.0453	0.19755|0.19755	0.1585:0.0:0.6911:0.1504|0.1585:0.0:0.6911:0.1504	.|.	.|.	.|.	.|.	D|X	181|1442;1442;1388;141	.|.	.|ENSP00000327077:E1442X	E|E	+|+	3|1	2|0	PCM1|PCM1	17887790|17887790	0.999000|0.999000	0.42202|0.42202	0.154000|0.154000	0.22540|0.22540	0.697000|0.697000	0.40408|0.40408	5.140000|5.140000	0.64807|0.64807	0.628000|0.628000	0.30357|0.30357	0.650000|0.650000	0.86243|0.86243	GAG|GAA		0.328	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17843510	G	T	17843510	4	4	61	1	0	0	0	0	0	1	0	0	11615	943	33	2	4418	2	PCM1	8	17843510	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13515	17843510	128520512	5763	13748										
PCM1	5108	broad.mit.edu	37	chr8	17872095	17872095	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttcttttgatgacagatGaccaaaataactgtcctgtg	7	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17872095G>T	ENST00000519253.1	+	36	5814	c.5563G>T	c.(5563-5565)Gac>Tac	p.D1855Y	PCM1_ENST00000325083.8_Missense_Mutation_p.D1863Y|PCM1_ENST00000327578.8_Missense_Mutation_p.D562Y|PCM1_ENST00000524226.1_Intron			Q15154	PCM1_HUMAN	pericentriolar material 1	1863				PLEREATSKNDQ -> HWNEKPLVKMTK (in Ref. 1; AAA60120). {ECO:0000305}.	centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.D1863Y(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GATGACAGATGACCAAAATAA	0.343			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	1	Substitution - Missense(1)	large_intestine(1)	8											81	76	77					8																	17872095		1842	4090	5932	17916375	SO:0001583	missense	5108				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5563G>T	8.37:g.17872095G>T	ENSP00000431099:p.Asp1855Tyr		17916375	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.87|16.87	3.240848|3.240848	0.58995|0.58995	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000327578|ENST00000522275	T;T;T|.	0.20332|.	3.45;3.45;2.08|.	5.32|5.32	3.54|3.54	0.40534|0.40534	.|.	.|.	.|.	.|.	.|.	T|T	0.51143|0.51143	0.1657|0.1657	L|L	0.34521|0.34521	1.04|1.04	0.38660|0.38660	D|D	0.952069|0.952069	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;0.993;1.0|.	D;D;D;D;P;D|.	0.87578|.	0.998;0.998;0.998;0.998;0.891;0.998|.	T|T	0.48570|0.48570	-0.9024|-0.9024	9|5	0.87932|.	D|.	0|.	1.9891|1.9891	10.3989|10.3989	0.44218|0.44218	0.1501:0.0:0.8499:0.0|0.1501:0.0:0.8499:0.0	.|.	1855;1863;662;1855;1808;1863|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;Q15154|.	.;.;.;.;.;PCM1_HUMAN|.	Y|I	1863;1855;562|602	ENSP00000327077:D1863Y;ENSP00000431099:D1855Y;ENSP00000328332:D562Y|.	ENSP00000327077:D1863Y|.	D|M	+|+	1|3	0|0	PCM1|PCM1	17916375|17916375	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.409000|1.409000	0.34680|0.34680	0.945000|0.945000	0.37605|0.37605	0.655000|0.655000	0.94253|0.94253	GAC|ATG		0.343	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17872095	G	T	17872095	3	4	61	1	0	0	0	0	1	0	0	0	11615	1290	45	2	5721	2	PCM1	8	17872095	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28585	17872095	128491927	5764	13749										
ASAH1	427	broad.mit.edu	37	chr8	17915088	17915088	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcccgcaggtaagtttcGaattgacctttggtaacatc	9	10	0	1	rs375983141		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:17915088G>A	ENST00000262097.6	-	14	1454	c.1143C>T	c.(1141-1143)ttC>ttT	p.F381F	ASAH1_ENST00000314146.10_Silent_p.F375F|ASAH1_ENST00000417108.2_Silent_p.F291F|ASAH1_ENST00000381733.4_Silent_p.F397F|ASAH1_ENST00000520781.1_Silent_p.F356F	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	381					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)	p.F397F(1)|p.F381F(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		GGTAAGTTTCGAATTGACCTT	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	8						G	,,	0,4406		0,0,2203	113	97	102		1125,1191,1143	3.1	0.1	8		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	375/390,397/412,381/396	17915088	1,13005	2203	4300	6503	17959368	SO:0001819	synonymous_variant	427			U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.1143C>T	8.37:g.17915088G>A			17959368	E9PDS0|Q6W898|Q96AS2	Silent	SNP	ENST00000262097.6	37	CCDS6006.1																																																																																				0.438	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315		A	17915088	G	A	17915088	2	1	61	1	0	0	0	0	0	0	0	1	1007	1049	37	1		1	ASAH1	8	17915088	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42993	17915088	128448934	5765	13750										
PSD3	23362	broad.mit.edu	37	chr8	18725290	18725290	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccatcacgatgccaccatCtgcagacacactcaggatat	7	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:18725290C>A	ENST00000327040.8	-	4	1630	c.1528G>T	c.(1528-1530)Gat>Tat	p.D510Y	PSD3_ENST00000523619.1_Missense_Mutation_p.D445Y|PSD3_ENST00000440756.2_Missense_Mutation_p.D510Y	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	510					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.D510Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		ATGCCACCATCTGCAGACACA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	8											188	187	187					8																	18725290		2136	4246	6382	18769570	SO:0001583	missense	23362			AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.1528G>T	8.37:g.18725290C>A	ENSP00000324127:p.Asp510Tyr		18769570	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160888	0.57368	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000523619	T;T;T	0.13420	2.6;2.6;2.59	5.28	5.28	0.74379	.	0.229124	0.30185	N	0.010204	T	0.13756	0.0333	L	0.29908	0.895	0.38696	D	0.952882	P	0.44344	0.833	B	0.41271	0.352	T	0.02909	-1.1095	10	0.87932	D	0	.	16.7614	0.85513	0.0:1.0:0.0:0.0	.	510	E9KL50	.	Y	510;510;445	ENSP00000324127:D510Y;ENSP00000401704:D510Y;ENSP00000430640:D445Y	ENSP00000324127:D510Y	D	-	1	0	PSD3	18769570	0.996000	0.38824	0.886000	0.34754	0.843000	0.47879	3.722000	0.54948	2.637000	0.89404	0.585000	0.79938	GAT		0.527	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		A	18725290	C	A	18725290	3	1	61	1	0	0	0	0	1	0	0	0	12682	913	32	2	1703	2	PSD3	8	18725290	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	810202	18725290	127638732	5766	13751										
PSD3	23362	broad.mit.edu	37	chr8	18729413	18729413	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcagtgatgtctcaaaatCtataggatgctgggtctctc	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:18729413C>A	ENST00000327040.8	-	3	1063	c.961G>T	c.(961-963)Gat>Tat	p.D321Y	PSD3_ENST00000523619.1_Missense_Mutation_p.D256Y|PSD3_ENST00000440756.2_Missense_Mutation_p.D321Y	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	321					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.D321Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		GTCTCAAAATCTATAGGATGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	8											156	161	159					8																	18729413		2034	4191	6225	18773693	SO:0001583	missense	23362			AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.961G>T	8.37:g.18729413C>A	ENSP00000324127:p.Asp321Tyr		18773693	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	C	4.469	0.086862	0.08583	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000523619	T;T;T	0.14766	2.5;2.49;2.48	5.78	3.69	0.42338	.	1.489460	0.03961	N	0.290042	T	0.13628	0.0330	L	0.27053	0.805	0.09310	N	1	P	0.39576	0.679	B	0.41723	0.365	T	0.25676	-1.0125	10	0.48119	T	0.1	.	6.0582	0.19822	0.0:0.6953:0.1789:0.1258	.	321	E9KL50	.	Y	321;321;256	ENSP00000324127:D321Y;ENSP00000401704:D321Y;ENSP00000430640:D256Y	ENSP00000324127:D321Y	D	-	1	0	PSD3	18773693	0.003000	0.15002	0.000000	0.03702	0.016000	0.09150	1.669000	0.37492	0.566000	0.29273	0.655000	0.94253	GAT		0.493	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		A	18729413	C	A	18729413	3	1	61	1	0	0	0	0	1	0	0	0	12682	913	32	2	2274	2	PSD3	8	18729413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4123	18729413	127634609	5767	13752										
SH2D4A	63898	broad.mit.edu	37	chr8	19231124	19231124	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggagcagctaccacttcGagcgggctaccagaaaacct	11	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:19231124G>A	ENST00000265807.3	+	8	1412	c.1001G>A	c.(1000-1002)cGa>cAa	p.R334Q	SH2D4A_ENST00000519207.1_Missense_Mutation_p.R334Q|SH2D4A_ENST00000518040.1_Missense_Mutation_p.R289Q	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	334					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)	p.R334Q(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		CTACCACTTCGAGCGGGCTAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	8											90	69	76					8																	19231124		2203	4300	6503	19275404	SO:0001583	missense	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.1001G>A	8.37:g.19231124G>A	ENSP00000265807:p.Arg334Gln		19275404	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.668107	0.67814	.	.	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;T;T	0.21031	2.03;2.03;2.03	5.99	5.11	0.69529	.	0.427284	0.21398	N	0.075191	T	0.43678	0.1258	M	0.75447	2.3	0.37667	D	0.922987	D;D	0.89917	1.0;1.0	D;D	0.67231	0.925;0.95	T	0.51560	-0.8690	10	0.62326	D	0.03	.	10.9292	0.47207	0.0851:0.0:0.9149:0.0	.	289;334	B4DDR1;Q9H788	.;SH24A_HUMAN	Q	334;289;334	ENSP00000265807:R334Q;ENSP00000429482:R289Q;ENSP00000428684:R334Q	ENSP00000265807:R334Q	R	+	2	0	SH2D4A	19275404	1.000000	0.71417	0.725000	0.30721	0.261000	0.26267	3.611000	0.54132	1.533000	0.49186	0.655000	0.94253	CGA		0.502	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		A	19231124	G	A	19231124	3	1	61	1	0	0	0	0	1	0	0	0	14272	1058	37	1	1077	1	SH2D4A	8	19231124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	501711	19231124	127132898	5768	13753										
SLC18A1	6570	broad.mit.edu	37	chr8	20005552	20005552	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccctgcattggggccaatGagaccaaaaatattgtgagc	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:20005552G>T	ENST00000276373.5	-	13	1442	c.1176C>A	c.(1174-1176)ctC>ctA	p.L392L	SLC18A1_ENST00000440926.1_Silent_p.L392L|SLC18A1_ENST00000381608.4_Silent_p.L392L|SLC18A1_ENST00000265808.7_Silent_p.L360L|SLC18A1_ENST00000437980.1_Silent_p.L392L|SLC18A1_ENST00000519026.1_Silent_p.L360L	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	392			L -> V (in dbSNP:rs17092104).		monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)	p.L392L(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TGGGGCCAATGAGACCAAAAA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	8											80	69	73					8																	20005552		2203	4300	6503	20049832	SO:0001819	synonymous_variant	6570				CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"Solute carriers"	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.1176C>A	8.37:g.20005552G>T			20049832	E9PDJ5|Q9BRE4	Silent	SNP	ENST00000276373.5	37	CCDS6013.1																																																																																				0.502	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1			T	20005552	G	T	20005552	2	4	61	1	0	0	0	0	0	0	0	1	14462	1277	45	2		2	SLC18A1	8	20005552	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	774428	20005552	126358470	5769	13754										
LZTS1	11178	broad.mit.edu	37	chr8	20110323	20110323	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcctccagcgcggggccGaagctggtcttctccctctc	11	17	4	0	rs139017329		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:20110323G>A	ENST00000381569.1	-	3	1476	c.1119C>T	c.(1117-1119)ttC>ttT	p.F373F	LZTS1_ENST00000522290.1_Silent_p.F373F|LZTS1_ENST00000265801.6_Silent_p.F373F			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	373					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F373F(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GCGCGGGGCCGAAGCTGGTCT	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	8						G		3,4403		0,3,2200	33	35	35		1119	-8.3	0.7	8	dbSNP_134	35	1,8599		0,1,4299	no	coding-synonymous	LZTS1	NM_021020.2		0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308		373/597	20110323	4,13002	2203	4300	6503	20154603	SO:0001819	synonymous_variant	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1119C>T	8.37:g.20110323G>A			20154603	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																				0.647	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		A	20110323	G	A	20110323	2	1	61	1	0	0	0	0	0	0	0	1	9168	1049	37	1		1	LZTS1	8	20110323	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104771	20110323	126253699	5770	13755										
LZTS1	11178	broad.mit.edu	37	chr8	20112507	20112507	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgtagaagaagtcttcGctcttgcccattttggagct	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:20112507G>A	ENST00000381569.1	-	2	543	c.186C>T	c.(184-186)agC>agT	p.S62S	LZTS1_ENST00000522290.1_Silent_p.S62S|LZTS1_ENST00000265801.6_Silent_p.S62S			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	62					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S62S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		AGAAGTCTTCGCTCTTGCCCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	8											98	91	93					8																	20112507		2203	4300	6503	20156787	SO:0001819	synonymous_variant	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.186C>T	8.37:g.20112507G>A			20156787	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																				0.597	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		A	20112507	G	A	20112507	2	1	61	1	0	0	0	0	0	0	0	1	9168	1078	38	1		1	LZTS1	8	20112507	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2184	20112507	126251515	5771	13756										
EPB49	2039	broad.mit.edu	37	chr8	21927802	21927802	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaaccagccagccaaaatCgaaaccgactactggccatg	7	16	0	0	rs148314902	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:21927802C>T	ENST00000523266.1	+	8	1023	c.561C>T	c.(559-561)atC>atT	p.I187I	DMTN_ENST00000519907.1_Silent_p.I187I|DMTN_ENST00000523782.2_Silent_p.I162I|DMTN_ENST00000265800.5_Silent_p.I187I|DMTN_ENST00000432128.1_Silent_p.I187I|DMTN_ENST00000443491.2_Silent_p.I162I|DMTN_ENST00000381470.3_Silent_p.I187I|DMTN_ENST00000415253.1_Silent_p.I187I|DMTN_ENST00000517600.1_Silent_p.I147I|DMTN_ENST00000358242.3_Silent_p.I187I	NM_001978.2	NP_001969.2	Q08495	DEMA_HUMAN	dematin actin binding protein	187					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|actin filament capping (GO:0051693)|actin filament reorganization (GO:0090527)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cytoskeleton organization (GO:0007010)|erythrocyte development (GO:0048821)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of platelet aggregation (GO:1901731)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of wound healing (GO:0090303)|protein complex assembly (GO:0006461)|protein secretion by platelet (GO:0070560)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)|regulation of lamellipodium assembly (GO:0010591)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection membrane (GO:0031253)|cortical cytoskeleton (GO:0030863)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|protein self-association (GO:0043621)|receptor binding (GO:0005102)|spectrin binding (GO:0030507)	p.I187I(1)									CAGCCAAAATCGAAACCGACT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	8						C	,,,,,	4,4402	8.1+/-20.4	0,4,2199	94	95	94		561,561,561,561,486,561	-5.3	0.9	8	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EPB49	NM_001114135.2,NM_001114136.1,NM_001114137.1,NM_001114138.1,NM_001114139.1,NM_001978.2	,,,,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,,,,	187/406,187/406,187/384,187/384,162/359,187/406	21927802	4,13002	2203	4300	6503	21983748	SO:0001819	synonymous_variant	2039			U28389	CCDS6020.1, CCDS47820.1, CCDS47821.1	8p21.1	2013-05-03	2013-05-03	2013-05-03	ENSG00000158856	ENSG00000158856			3382	protein-coding gene	gene with protein product		125305	"erythrocyte membrane protein band 4.9 (dematin)"	EPB49		8341682, 12011427	Standard	NM_001978		Approved	DMT		Q08495	OTTHUMG00000097087	ENST00000523266.1:c.561C>T	8.37:g.21927802C>T			21983748	A8K0T5|B3KP70|B3KRH3|E9PEJ0|Q13215|Q9BRE3	Silent	SNP	ENST00000523266.1	37	CCDS6020.1																																																																																				0.597	DMTN-009	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375178.1	NM_001978		T	21927802	C	T	21927802	2	4	61	1	0	0	0	0	0	0	0	1	5172	874	31	1		1	EPB49	8	21927802	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1815295	21927802	124436220	5772	13757										
PIWIL2	55124	broad.mit.edu	37	chr8	22138714	22138714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgaaacgggaaatgcttCcatcaggtatgtggaaaact	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22138714C>T	ENST00000454009.2	+	3	789	c.280C>T	c.(280-282)Cca>Tca	p.P94S	PIWIL2_ENST00000521356.1_Missense_Mutation_p.P94S|PIWIL2_ENST00000356766.6_Missense_Mutation_p.P94S	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	94					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.P94S(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		GGAAATGCTTCCATCAGGTAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											73	72	72					8																	22138714		2203	4300	6503	22194659	SO:0001583	missense	55124			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.280C>T	8.37:g.22138714C>T	ENSP00000406956:p.Pro94Ser		22194659	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.360692	0.24598	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.04454	3.65;3.62;3.65	5.69	-1.88	0.07713	.	1.015470	0.07868	N	0.967381	T	0.03220	0.0094	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.47433	-0.9118	10	0.59425	D	0.04	.	0.6919	0.00893	0.1608:0.2509:0.2268:0.3615	.	94;94	E7ECA4;Q8TC59	.;PIWL2_HUMAN	S	94	ENSP00000349208:P94S;ENSP00000428267:P94S;ENSP00000406956:P94S	ENSP00000349208:P94S	P	+	1	0	PIWIL2	22194659	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.014000	0.13333	-0.203000	0.10251	-0.150000	0.13652	CCA		0.408	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			T	22138714	C	T	22138714	3	4	61	1	0	0	0	0	1	0	0	0	11989	855	30	3	286	3	PIWIL2	8	22138714	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	210912	22138714	124225308	5773	13758										
PIWIL2	55124	broad.mit.edu	37	chr8	22161708	22161708	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgggaaagagatcacattCttggaatactacaggtagca	11	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22161708C>A	ENST00000454009.2	+	11	1865	c.1356C>A	c.(1354-1356)ttC>ttA	p.F452L	PIWIL2_ENST00000521356.1_Missense_Mutation_p.F452L|PIWIL2_ENST00000356766.6_Missense_Mutation_p.F452L	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	452	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.F452L(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		AGATCACATTCTTGGAATACT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											156	132	140					8																	22161708		2203	4300	6503	22217653	SO:0001583	missense	55124			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.1356C>A	8.37:g.22161708C>A	ENSP00000406956:p.Phe452Leu		22217653	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098293	0.76870	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.15139	2.45;2.45;2.45	5.87	3.05	0.35203	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	M	0.73319	2.225	0.80722	D	1	D;D	0.59767	0.986;0.969	P;P	0.59889	0.865;0.811	T	0.02070	-1.1219	10	0.44086	T	0.13	-20.1399	10.439	0.44452	0.0:0.7773:0.0:0.2227	.	452;452	E7ECA4;Q8TC59	.;PIWL2_HUMAN	L	452	ENSP00000349208:F452L;ENSP00000428267:F452L;ENSP00000406956:F452L	ENSP00000349208:F452L	F	+	3	2	PIWIL2	22217653	0.894000	0.30519	1.000000	0.80357	0.983000	0.72400	0.292000	0.19011	0.448000	0.26722	0.655000	0.94253	TTC		0.453	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			A	22161708	C	A	22161708	3	1	61	1	0	0	0	0	1	0	0	0	11989	912	32	2	1394	2	PIWIL2	8	22161708	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22994	22161708	124202314	5774	13759										
PPP3CC	5533	broad.mit.edu	37	chr8	22368602	22368602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttccttttttgttaggtcGaatcaaatattcggaacagg	8	6	1	0	rs61756434	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22368602G>A	ENST00000240139.5	+	5	815	c.488G>A	c.(487-489)cGa>cAa	p.R163Q	PPP3CC_ENST00000518852.1_Missense_Mutation_p.R163Q|PPP3CC_ENST00000397775.3_Missense_Mutation_p.R163Q|PPP3CC_ENST00000289963.8_Missense_Mutation_p.R163Q	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	163					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.R163Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		TTGTTAGGTCGAATCAAATAT	0.398													G|||	28	0.00559105	0.0197	0.0029	5008	,	,		18702	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						G	GLN/ARG	77,4329	68.7+/-106.4	0,77,2126	178	160	166		488	4.1	1	8	dbSNP_129	166	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PPP3CC	NM_005605.4	43	0,78,6425	AA,AG,GG		0.0116,1.7476,0.5997	possibly-damaging	163/513	22368602	78,12928	2203	4300	6503	22424547	SO:0001583	missense	5533				CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9316	protein-coding gene	gene with protein product	"calcineurin A gamma", "protein phosphatase 2B, catalytic subunit, gamma isoform"	114107	"protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)", "protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.488G>A	8.37:g.22368602G>A	ENSP00000240139:p.Arg163Gln		22424547	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	7|7	0.003205128205128205|0.003205128205128205	6|6	0.012195121951219513|0.012195121951219513	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.44|14.44	2.536496|2.536496	0.45176|0.45176	0.017476|0.017476	1.16E-4|1.16E-4	ENSG00000120910|ENSG00000120910	ENST00000522034;ENST00000521651|ENST00000518852;ENST00000240139;ENST00000289963;ENST00000397775	.|T;T;T;T	.|0.05649	.|3.41;3.41;3.41;3.41	5.91|5.91	4.1|4.1	0.47936|0.47936	.|Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	.|0.189068	.|0.45606	.|N	.|0.000348	T|T	0.01254|0.01254	0.0041|0.0041	N|N	0.04508|0.04508	-0.205|-0.205	0.37229|0.37229	D|D	0.905619|0.905619	.|B;B;B;B	.|0.19445	.|0.036;0.012;0.003;0.006	.|B;B;B;B	.|0.13407	.|0.009;0.005;0.009;0.009	T|T	0.49943|0.49943	-0.8885|-0.8885	5|10	.|0.19590	.|T	.|0.45	-1.2201|-1.2201	6.4732|6.4732	0.22020|0.22020	0.1498:0.0:0.7018:0.1484|0.1498:0.0:0.7018:0.1484	rs61756434|rs61756434	.|163;163;163;163	.|B4DRT5;P48454-2;P48454;G3V111	.|.;.;PP2BC_HUMAN;.	K|Q	13;40|163	.|ENSP00000429379:R163Q;ENSP00000240139:R163Q;ENSP00000289963:R163Q;ENSP00000380878:R163Q	.|ENSP00000240139:R163Q	E|R	+|+	1|2	0|0	PPP3CC|PPP3CC	22424547|22424547	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.098000|3.098000	0.50259|0.50259	0.805000|0.805000	0.34159|0.34159	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.398	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605		A	22368602	G	A	22368602	3	1	61	1	0	0	0	0	1	0	0	0	12433	1058	37	1	506	1	PPP3CC	8	22368602	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206894	22368602	123995420	5775	13760										
PPP3CC	5533	broad.mit.edu	37	chr8	22389769	22389769	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcgtaaggagatcatcagGaataagatcagagccattgg	12	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22389769G>A	ENST00000240139.5	+	11	1500	c.1173G>A	c.(1171-1173)agG>agA	p.R391R	PPP3CC_ENST00000397775.3_Silent_p.R400R|PPP3CC_ENST00000289963.8_Silent_p.R391R	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	391					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.R391R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		AGATCATCAGGAATAAGATCA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	8											154	143	147					8																	22389769		2203	4300	6503	22445714	SO:0001819	synonymous_variant	5533				CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9316	protein-coding gene	gene with protein product	"calcineurin A gamma", "protein phosphatase 2B, catalytic subunit, gamma isoform"	114107	"protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)", "protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.1173G>A	8.37:g.22389769G>A			22445714	B4DRT5|Q9BSS6|Q9H4M5	Silent	SNP	ENST00000240139.5	37	CCDS34859.1																																																																																				0.383	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605		A	22389769	G	A	22389769	2	1	61	1	0	0	0	0	0	0	0	1	12433	1165	41	3		3	PPP3CC	8	22389769	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21167	22389769	123974253	5776	13761										
KIAA1967	57805	broad.mit.edu	37	chr8	22470548	22470548	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgatgactatgactccaaGaaacgcaaacagcgggctgg	12	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22470548G>T	ENST00000308511.4	+	8	852	c.603G>T	c.(601-603)aaG>aaT	p.K201N	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Missense_Mutation_p.K201N|CCAR2_ENST00000520861.1_5'UTR			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	201					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)	p.K201N(1)									ATGACTCCAAGAAACGCAAAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	8											112	94	100					8																	22470548		2203	4300	6503	22526493	SO:0001583	missense	57805			AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.603G>T	8.37:g.22470548G>T	ENSP00000310670:p.Lys201Asn		22526493	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693734	0.88735	.	.	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000522599	T;T;T	0.46819	1.43;1.43;0.86	5.87	5.87	0.94306	.	0.126709	0.52532	D	0.000080	T	0.46288	0.1385	N	0.08118	0	0.80722	D	1	D	0.62365	0.991	P	0.58013	0.831	T	0.53837	-0.8382	10	0.62326	D	0.03	-39.3796	17.4969	0.87720	0.0:0.0:1.0:0.0	.	201	Q8N163	K1967_HUMAN	N	201;201;19	ENSP00000310670:K201N;ENSP00000373930:K201N;ENSP00000429739:K19N	ENSP00000310670:K201N	K	+	3	2	KIAA1967	22526493	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.648000	0.46647	2.941000	0.99782	0.655000	0.94253	AAG		0.478	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		T	22470548	G	T	22470548	3	4	61	1	0	0	0	0	1	0	0	0	8286	933	33	2	629	2	KIAA1967	8	22470548	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80779	22470548	123893474	5777	13762										
RHOBTB2	23221	broad.mit.edu	37	chr8	22864340	22864340	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagcgtggtggcccagttCggcatcaaggacgtctttga	13	11	2	1	rs370461878		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22864340C>T	ENST00000251822.6	+	5	1119	c.582C>T	c.(580-582)ttC>ttT	p.F194F	RHOBTB2_ENST00000519685.1_Silent_p.F216F|RP11-875O11.1_ENST00000523884.1_RNA|RP11-875O11.1_ENST00000502083.2_RNA|RHOBTB2_ENST00000522948.1_Silent_p.F201F	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	194	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.F194F(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		TGGCCCAGTTCGGCATCAAGG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	8						C	,,	0,4406		0,0,2203	100	92	95		648,603,582	-4.9	1	8		95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RHOBTB2	NM_001160036.1,NM_001160037.1,NM_015178.2	,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,	216/750,201/735,194/728	22864340	2,13004	2203	4300	6503	22920285	SO:0001819	synonymous_variant	23221			AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"BTB/POZ domain containing"	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.582C>T	8.37:g.22864340C>T			22920285	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Silent	SNP	ENST00000251822.6	37	CCDS6034.1																																																																																				0.612	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2			T	22864340	C	T	22864340	2	4	61	1	0	0	0	0	0	0	0	1	13371	883	31	1		1	RHOBTB2	8	22864340	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	393792	22864340	123499682	5778	13763										
RHOBTB2	23221	broad.mit.edu	37	chr8	22864634	22864634	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccacctcttcctccaagttCtatgacctgttcctcatgga	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22864634C>A	ENST00000251822.6	+	5	1413	c.876C>A	c.(874-876)ttC>ttA	p.F292L	RHOBTB2_ENST00000519685.1_Missense_Mutation_p.F314L|RP11-875O11.1_ENST00000523884.1_RNA|RP11-875O11.1_ENST00000502083.2_RNA|RHOBTB2_ENST00000522948.1_Missense_Mutation_p.F299L	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	292	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.F292L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		CCTCCAAGTTCTATGACCTGT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	8											95	93	94					8																	22864634		2203	4300	6503	22920579	SO:0001583	missense	23221			AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"BTB/POZ domain containing"	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.876C>A	8.37:g.22864634C>A	ENSP00000251822:p.Phe292Leu		22920579	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Missense_Mutation	SNP	ENST00000251822.6	37	CCDS6034.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445769	0.63178	.	.	ENSG00000008853	ENST00000519685;ENST00000522948;ENST00000251822	T;T;T	0.56776	0.44;0.44;0.44	5.34	4.46	0.54185	BTB/POZ-like (2);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.67126	0.2860	M	0.71036	2.16	0.54753	D	0.999989	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.998;0.998	T	0.67964	-0.5534	10	0.59425	D	0.04	.	7.2551	0.26171	0.0:0.7426:0.0:0.2574	.	299;292;314	E9PEI7;Q9BYZ6;E9PBU2	.;RHBT2_HUMAN;.	L	314;299;292	ENSP00000427926:F314L;ENSP00000429141:F299L;ENSP00000251822:F292L	ENSP00000251822:F292L	F	+	3	2	RHOBTB2	22920579	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.378000	0.34328	1.224000	0.43551	0.655000	0.94253	TTC		0.637	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2			A	22864634	C	A	22864634	3	1	61	1	0	0	0	0	1	0	0	0	13371	912	32	2	975	2	RHOBTB2	8	22864634	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294	22864634	123499388	5779	13764										
TNFRSF10B	8795	broad.mit.edu	37	chr8	22884762	22884762	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaagatactcacgatctCattgaggacattgtcctcag	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22884762C>A	ENST00000276431.4	-	7	1104	c.820G>T	c.(820-822)Gag>Tag	p.E274*	TNFRSF10B_ENST00000347739.3_Nonsense_Mutation_p.E245*|TNFRSF10B_ENST00000519910.1_5'Flank|TNFRSF10B_ENST00000542226.1_Nonsense_Mutation_p.E94*	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	274					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)	p.E274*(1)		NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		CTCACGATCTCATTGAGGACA	0.562																																					GBM(94;1064 1342 1839 21060 42553)											1	Substitution - Nonsense(1)	large_intestine(1)	8											91	85	87					8																	22884762		2203	4300	6503	22940707	SO:0001587	stop_gained	8795			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.820G>T	8.37:g.22884762C>A	ENSP00000276431:p.Glu274*		22940707	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Nonsense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	c	17.13	3.310220	0.60414	.	.	ENSG00000120889	ENST00000276431;ENST00000347739;ENST00000542226	.	.	.	2.28	-0.993	0.10228	.	7739.210000	0.00166	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	4.4657	0.11687	0.0:0.3901:0.4575:0.1524	.	.	.	.	X	274;245;94	.	ENSP00000276431:E274X	E	-	1	0	TNFRSF10B	22940707	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.358000	0.07641	-0.259000	0.09432	-0.282000	0.10007	GAG		0.562	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187		A	22884762	C	A	22884762	4	1	61	1	0	0	0	0	0	1	0	0	16320	835	29	2	514	2	TNFRSF10B	8	22884762	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20128	22884762	123479260	5780	13765										
TNFRSF10B	8795	broad.mit.edu	37	chr8	22886063	22886063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattctttgtggacacattCgatgtcactccagggtgtac	10	9	2	1	rs139403599		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22886063C>T	ENST00000276431.4	-	5	813	c.529G>A	c.(529-531)Gaa>Aaa	p.E177K	TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.E177K|TNFRSF10B_ENST00000519910.1_5'UTR|TNFRSF10B_ENST00000542226.1_Missense_Mutation_p.E26K	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	177					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)	p.E177K(1)		NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		TGGACACATTCGATGTCACTC	0.572																																					GBM(94;1064 1342 1839 21060 42553)											1	Substitution - Missense(1)	large_intestine(1)	8						C	LYS/GLU,LYS/GLU	0,4406		0,0,2203	157	138	144		529,529	-6.3	0	8	dbSNP_134	144	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TNFRSF10B	NM_003842.4,NM_147187.2	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	177/441,177/412	22886063	1,13005	2203	4300	6503	22942008	SO:0001583	missense	8795			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.529G>A	8.37:g.22886063C>T	ENSP00000276431:p.Glu177Lys		22942008	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	c	1.187	-0.636445	0.03557	0.0	1.16E-4	ENSG00000120889	ENST00000276431;ENST00000347739;ENST00000542226	T;T;T	0.29655	1.56;1.56;1.56	4.41	-6.27	0.02026	TNFR/CD27/30/40/95 cysteine-rich region (3);	1.121670	0.07117	N	0.843293	T	0.07908	0.0198	N	0.02345	-0.59	0.09310	N	1	B;B;B;B	0.16802	0.009;0.004;0.011;0.019	B;B;B;B	0.06405	0.001;0.0;0.002;0.001	T	0.37056	-0.9722	10	0.02654	T	1	.	5.697	0.17861	0.0:0.267:0.42:0.313	.	26;177;177;177	B7Z588;B5BU36;O14763;O14763-2	.;.;TR10B_HUMAN;.	K	177;177;26	ENSP00000276431:E177K;ENSP00000317859:E177K;ENSP00000443386:E26K	ENSP00000276431:E177K	E	-	1	0	TNFRSF10B	22942008	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.429000	0.06982	-0.593000	0.05844	-1.254000	0.01491	GAA		0.572	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187		T	22886063	C	T	22886063	3	4	61	1	0	0	0	0	1	0	0	0	16320	893	31	1	813	1	TNFRSF10B	8	22886063	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1301	22886063	123477959	5781	13766										
TNFRSF10B	8795	broad.mit.edu	37	chr8	22887181	22887181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccggaaggtgccttcttCgcactgacacactgtgtttc	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:22887181C>T	ENST00000276431.4	-	4	702	c.418G>A	c.(418-420)Gaa>Aaa	p.E140K	TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.E140K|TNFRSF10B_ENST00000519910.1_5'UTR|TNFRSF10B_ENST00000542226.1_5'UTR	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	140					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)	p.E140K(1)		NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		GTGCCTTCTTCGCACTGACAC	0.557																																					GBM(94;1064 1342 1839 21060 42553)											1	Substitution - Missense(1)	large_intestine(1)	8											99	75	83					8																	22887181		2203	4300	6503	22943126	SO:0001583	missense	8795			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.418G>A	8.37:g.22887181C>T	ENSP00000276431:p.Glu140Lys		22943126	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	c	0.204	-1.041859	0.01997	.	.	ENSG00000120889	ENST00000276431;ENST00000347739	T;D	0.81821	-1.4;-1.54	3.93	1.5	0.22942	TNFR/CD27/30/40/95 cysteine-rich region (3);	0.202418	0.40640	N	0.001050	T	0.54663	0.1872	N	0.12746	0.255	0.09310	N	0.999995	B;B;B	0.25563	0.129;0.129;0.102	B;B;B	0.17098	0.011;0.017;0.01	T	0.45789	-0.9237	10	0.02654	T	1	.	7.3877	0.26893	0.0:0.1243:0.0:0.8757	.	140;140;140	B5BU36;O14763;O14763-2	.;TR10B_HUMAN;.	K	140	ENSP00000276431:E140K;ENSP00000317859:E140K	ENSP00000276431:E140K	E	-	1	0	TNFRSF10B	22943126	0.421000	0.25465	0.005000	0.12908	0.003000	0.03518	0.173000	0.16724	0.201000	0.20466	-1.084000	0.02203	GAA		0.557	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187		T	22887181	C	T	22887181	3	4	61	1	0	0	0	0	1	0	0	0	16320	893	31	1	928	1	TNFRSF10B	8	22887181	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1118	22887181	123476841	5782	13767										
TNFRSF10D	8793	broad.mit.edu	37	chr8	23002047	23002047	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttggatttcctgctcagaGacctgggtgggctgcaagta	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:23002047G>T	ENST00000312584.3	-	7	964	c.870C>A	c.(868-870)gtC>gtA	p.V290V		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	290					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.V290V(2)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		CCTGCTCAGAGACCTGGGTGG	0.577																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	8											98	91	93					8																	23002047		2203	4300	6503	23057992	SO:0001819	synonymous_variant	8793			AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"Tumor necrosis factor receptor superfamily", "CD molecules"	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.870C>A	8.37:g.23002047G>T			23057992	B2R8W0|Q9Y6Q4	Silent	SNP	ENST00000312584.3	37	CCDS6038.1																																																																																				0.577	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			T	23002047	G	T	23002047	2	4	61	1	0	0	0	0	0	0	0	1	16322	929	33	2		2	TNFRSF10D	8	23002047	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114866	23002047	123361975	5783	13768										
LOXL2	4017	broad.mit.edu	37	chr8	23198598	23198598	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtccagtgcttgtcacagAtctgcttccaggtcttgccc	9	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:23198598A>C	ENST00000389131.3	-	4	1019	c.650T>G	c.(649-651)aTc>aGc	p.I217S	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	217	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)	p.I217S(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		CTTGTCACAGATCTGCTTCCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	8											202	158	173					8																	23198598		2203	4300	6503	23254543	SO:0001583	missense	4017			U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.650T>G	8.37:g.23198598A>C	ENSP00000373783:p.Ile217Ser		23254543	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	37	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.762170	0.89932	.	.	ENSG00000134013	ENST00000389131	T	0.64085	-0.08	5.68	5.68	0.88126	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.250952	0.46145	D	0.000302	T	0.82051	0.4953	M	0.90309	3.105	0.58432	D	0.999999	P	0.47106	0.89	D	0.66979	0.948	D	0.85385	0.1122	10	0.87932	D	0	.	13.3028	0.60334	1.0:0.0:0.0:0.0	.	217	Q9Y4K0	LOXL2_HUMAN	S	217	ENSP00000373783:I217S	ENSP00000373783:I217S	I	-	2	0	LOXL2	23254543	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.229000	0.95273	2.156000	0.67533	0.533000	0.62120	ATC		0.557	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			C	23198598	A	C	23198598	3	2	61	1	0	0	0	0	1	0	0	0	8929	333	12	4	1718	4	LOXL2	8	23198598	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	196551	23198598	123165424	5784	13769										
ADAM28	10863	broad.mit.edu	37	chr8	24157544	24157544	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtggtttatcctataaGacttcatccactgcataaaa	6	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:24157544G>T	ENST00000265769.4	+	2	214	c.104G>T	c.(103-105)aGa>aTa	p.R35I	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000540823.1_5'UTR|ADAM28_ENST00000437154.2_Missense_Mutation_p.R35I|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	35					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R35I(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TATCCTATAAGACTTCATCCA	0.368																																					NSCLC(193;488 2149 22258 34798 40734)											1	Substitution - Missense(1)	large_intestine(1)	8											100	106	104					8																	24157544		2203	4300	6503	24213489	SO:0001583	missense	10863			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.104G>T	8.37:g.24157544G>T	ENSP00000265769:p.Arg35Ile		24213489	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486345	0.44147	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.07908	3.15;3.15	4.31	3.43	0.39272	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.22666	0.0547	M	0.76574	2.34	0.80722	D	1	D;P	0.71674	0.998;0.753	D;P	0.68483	0.958;0.511	T	0.00276	-1.1855	9	0.51188	T	0.08	.	7.4033	0.26977	0.1154:0.0:0.8846:0.0	.	35;35	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	I	35	ENSP00000265769:R35I;ENSP00000393699:R35I	ENSP00000265769:R35I	R	+	2	0	ADAM28	24213489	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	1.630000	0.37081	2.393000	0.81446	0.313000	0.20887	AGA		0.368	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		T	24157544	G	T	24157544	3	4	61	1	0	0	0	0	1	0	0	0	246	942	33	2	110	2	ADAM28	8	24157544	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	958946	24157544	122206478	5785	13770										
ADAM28	10863	broad.mit.edu	37	chr8	24181448	24181448	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcaagcttcaccttggaGaatttttctaaatggagggg	11	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:24181448G>T	ENST00000265769.4	+	9	932	c.822G>T	c.(820-822)gaG>gaT	p.E274D	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000540823.1_Missense_Mutation_p.E41D|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000437154.2_Missense_Mutation_p.E274D|ADAM28_ENST00000397649.3_Missense_Mutation_p.E21D|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	274	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E274D(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TCACCTTGGAGAATTTTTCTA	0.383																																					NSCLC(193;488 2149 22258 34798 40734)											1	Substitution - Missense(1)	large_intestine(1)	8											112	114	113					8																	24181448		2203	4299	6502	24237393	SO:0001583	missense	10863			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.822G>T	8.37:g.24181448G>T	ENSP00000265769:p.Glu274Asp		24237393	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	4.884	0.164349	0.09287	.	.	ENSG00000042980	ENST00000265769;ENST00000397649;ENST00000540823;ENST00000437154	T;T;T;T	0.08546	3.08;3.08;3.08;3.08	5.41	1.03	0.20045	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.07188	0.0182	N	0.13198	0.31	0.26859	N	0.967994	B;D;B	0.54047	0.1;0.964;0.03	B;P;B	0.54856	0.06;0.762;0.022	T	0.25502	-1.0130	9	0.11485	T	0.65	.	5.2422	0.15477	0.4612:0.3506:0.1882:0.0	.	41;274;274	B4DDY3;Q9UKQ2;Q9UKQ2-2	.;ADA28_HUMAN;.	D	274;21;41;274	ENSP00000265769:E274D;ENSP00000380770:E21D;ENSP00000443743:E41D;ENSP00000393699:E274D	ENSP00000265769:E274D	E	+	3	2	ADAM28	24237393	0.982000	0.34865	0.998000	0.56505	0.905000	0.53344	0.131000	0.15870	-0.009000	0.14296	-0.269000	0.10298	GAG		0.383	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		T	24181448	G	T	24181448	3	4	61	1	0	0	0	0	1	0	0	0	246	933	33	2	856	2	ADAM28	8	24181448	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23904	24181448	122182574	5786	13771										
ADAM7	8756	broad.mit.edu	37	chr8	24342814	24342814	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggctctactcacatgtGcaaggaatttcttatccagg	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:24342814G>A	ENST00000175238.6	+	10	983	c.900G>A	c.(898-900)gtG>gtA	p.V300V	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Silent_p.V72V|ADAM7_ENST00000380789.1_Silent_p.V300V	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	300	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V300V(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		ACTCACATGTGCAAGGAATTT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	8											153	147	149					8																	24342814		2203	4300	6503	24398704	SO:0001819	synonymous_variant	8756			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.900G>A	8.37:g.24342814G>A			24398704	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	37	CCDS6045.1																																																																																				0.353	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		A	24342814	G	A	24342814	2	1	61	1	0	0	0	0	0	0	0	1	251	1306	46	3		3	ADAM7	8	24342814	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161366	24342814	122021208	5787	13772										
ADAM7	8756	broad.mit.edu	37	chr8	24346751	24346751	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attataagccaacatgcatgCtcaacattccatttccttac	3	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:24346751C>A	ENST00000175238.6	+	12	1254	c.1171C>A	c.(1171-1173)Ctc>Atc	p.L391I	RP11-624C23.1_ENST00000523578.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.L163I|ADAM7_ENST00000380789.1_Missense_Mutation_p.L391I	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	391	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L391I(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AACATGCATGCTCAACATTCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	8											156	131	140					8																	24346751		2203	4300	6503	24402641	SO:0001583	missense	8756			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1171C>A	8.37:g.24346751C>A	ENSP00000175238:p.Leu391Ile		24402641	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.422186	0.43020	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.33654	1.4;1.4;1.4	5.74	-5.17	0.02849	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.856720	0.03110	N	0.162370	T	0.37732	0.1014	M	0.73319	2.225	0.09310	N	1	P;P	0.43578	0.811;0.811	P;P	0.45660	0.489;0.489	T	0.42310	-0.9459	10	0.27785	T	0.31	.	3.6903	0.08343	0.2057:0.5327:0.1026:0.159	.	163;391	E5RK87;Q9H2U9	.;ADAM7_HUMAN	I	391;391;163;206	ENSP00000175238:L391I;ENSP00000370166:L391I;ENSP00000430400:L163I	ENSP00000175238:L391I	L	+	1	0	ADAM7	24402641	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.650000	0.05378	-1.099000	0.03034	-0.878000	0.02970	CTC		0.398	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		A	24346751	C	A	24346751	3	1	61	1	0	0	0	0	1	0	0	0	251	797	28	2	1217	2	ADAM7	8	24346751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3937	24346751	122017271	5788	13773										
NEFM	4741	broad.mit.edu	37	chr8	24773148	24773148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagctggaaaatgagcttCggggcacaaagtgggaaatg	15	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:24773148C>T	ENST00000221166.5	+	2	1893	c.1111C>T	c.(1111-1113)Cgg>Tgg	p.R371W	NEFM_ENST00000518131.1_Missense_Mutation_p.R371W|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000433454.2_5'UTR|GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000437366.2_Missense_Mutation_p.R371W			P07197	NFM_HUMAN	neurofilament, medium polypeptide	371	Coil 2B.|Rod.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)	p.R371W(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		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)		AAATGAGCTTCGGGGCACAAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8											142	131	134					8																	24773148		2203	4300	6503	24829053	SO:0001583	missense	4741			BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"Intermediate filaments type IV"	7734	protein-coding gene	gene with protein product		162250	"neurofilament, medium polypeptide 150kDa"	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.1111C>T	8.37:g.24773148C>T	ENSP00000221166:p.Arg371Trp		24829053	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	37	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872270	0.91587	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366	D;D;D	0.89552	-2.53;-2.53;-2.53	5.36	4.42	0.53409	Filament (1);	0.000000	0.40469	N	0.001099	D	0.94351	0.8184	M	0.86953	2.85	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	D	0.94596	0.7792	10	0.87932	D	0	.	11.4449	0.50116	0.3592:0.6408:0.0:0.0	.	371;371	E7EMV2;P07197	.;NFM_HUMAN	W	371	ENSP00000221166:R371W;ENSP00000427872:R371W;ENSP00000410137:R371W	ENSP00000221166:R371W	R	+	1	2	NEFM	24829053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.350000	0.59392	2.508000	0.84585	0.591000	0.81541	CGG		0.507	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		T	24773148	C	T	24773148	3	4	61	1	0	0	0	0	1	0	0	0	10347	875	31	1	1117	1	NEFM	8	24773148	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426397	24773148	121590874	5789	13774										
DOCK5	80005	broad.mit.edu	37	chr8	25230131	25230131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctctggggaggtcttcgCcctcctggtcagcagcctct	12	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:25230131C>T	ENST00000276440.7	+	35	3625	c.3581C>T	c.(3580-3582)gCc>gTc	p.A1194V		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1194					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1194V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GAGGTCTTCGCCCTCCTGGTC	0.537																																					Pancreas(145;34 1887 3271 10937 30165)											1	Substitution - Missense(1)	large_intestine(1)	8											81	73	76					8																	25230131		2203	4300	6503	25286048	SO:0001583	missense	80005				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3581C>T	8.37:g.25230131C>T	ENSP00000276440:p.Ala1194Val		25286048	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	C	2.537	-0.307127	0.05458	.	.	ENSG00000147459	ENST00000276440	T	0.34072	1.38	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.12732	0.0309	N	0.00666	-1.275	0.58432	D	0.999995	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.34054	-0.9844	10	0.02654	T	1	.	19.5183	0.95174	0.0:1.0:0.0:0.0	.	1184;969;1194	D3DSS6;Q68DL4;Q9H7D0	.;.;DOCK5_HUMAN	V	1194	ENSP00000276440:A1194V	ENSP00000276440:A1194V	A	+	2	0	DOCK5	25286048	0.957000	0.32711	0.123000	0.21794	0.151000	0.21798	2.220000	0.42908	2.633000	0.89246	0.655000	0.94253	GCC		0.537	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25230131	C	T	25230131	3	4	61	1	0	0	0	0	1	0	0	0	4701	739	26	3	3719	3	DOCK5	8	25230131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	456983	25230131	121133891	5790	13775										
PPP2R2A	5520	broad.mit.edu	37	chr8	26227731	26227731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacataaccctagaagcatcGcgggaaaacaataagcctcg	9	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:26227731G>A	ENST00000380737.3	+	10	1475	c.1146G>A	c.(1144-1146)tcG>tcA	p.S382S	PPP2R2A_ENST00000315985.7_Silent_p.S392S	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	382					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)	p.S382S(1)		kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		TAGAAGCATCGCGGGAAAACA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	8											79	76	77					8																	26227731		2203	4300	6503	26283648	SO:0001819	synonymous_variant	5520			M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1146G>A	8.37:g.26227731G>A			26283648	B2RBU8|B4E1T7|P50409|Q00007	Silent	SNP	ENST00000380737.3	37	CCDS34867.1																																																																																				0.418	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		A	26227731	G	A	26227731	2	1	61	1	0	0	0	0	0	0	0	1	12418	1074	38	1		1	PPP2R2A	8	26227731	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	997600	26227731	120136291	5791	13776										
DPYSL2	1808	broad.mit.edu	37	chr8	26505251	26505251	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgcattgctgtgggatccGatgccgacctggtcatctgg	14	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:26505251G>A	ENST00000311151.5	+	11	1628	c.1216G>A	c.(1216-1218)Gat>Aat	p.D406N	DPYSL2_ENST00000521913.1_Missense_Mutation_p.D370N|DPYSL2_ENST00000523027.1_Missense_Mutation_p.D370N	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	406					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)	p.D406N(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		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)		TGTGGGATCCGATGCCGACCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	8											99	90	93					8																	26505251		2203	4300	6503	26561168	SO:0001583	missense	1808			D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.1216G>A	8.37:g.26505251G>A	ENSP00000309539:p.Asp406Asn		26561168	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	37	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688418	0.96784	.	.	ENSG00000092964	ENST00000545637;ENST00000521913;ENST00000311151;ENST00000522745;ENST00000523027	D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69	5.22	5.22	0.72569	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.96753	0.8940	M	0.93594	3.435	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.993;0.996	D	0.97240	0.9890	10	0.87932	D	0	-22.4912	19.3296	0.94280	0.0:0.0:1.0:0.0	.	406;462	Q16555;Q59GB4	DPYL2_HUMAN;.	N	45;370;406;406;370	ENSP00000427985:D370N;ENSP00000309539:D406N;ENSP00000428909:D406N;ENSP00000431117:D370N	ENSP00000309539:D406N	D	+	1	0	DPYSL2	26561168	1.000000	0.71417	0.948000	0.38648	0.948000	0.59901	9.601000	0.98297	2.873000	0.98535	0.563000	0.77884	GAT		0.537	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		A	26505251	G	A	26505251	3	1	61	1	0	0	0	0	1	0	0	0	4758	1058	37	1	1258	1	DPYSL2	8	26505251	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	277520	26505251	119858771	5792	13777										
STMN4	81551	broad.mit.edu	37	chr8	27099209	27099209	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaccctgagctcttctttCtctccagtcagcactgtctt	5	16	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:27099209C>A	ENST00000265770.7	-	4	246				STMN4_ENST00000350889.4_Nonsense_Mutation_p.E59*|STMN4_ENST00000519997.1_Intron|STMN4_ENST00000519614.1_Intron|STMN4_ENST00000523048.1_Nonsense_Mutation_p.E59*|STMN4_ENST00000522908.1_Nonsense_Mutation_p.E59*			Q9H169	STMN4_HUMAN	stathmin-like 4						regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)		p.E59*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	GCTCTTCTTTCTCTCCAGTCA	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											133	109	117					8																	27099209		2203	4300	6503	27155126	SO:0001627	intron_variant	81551				CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.110-430G>T	8.37:g.27099209C>A			27155126	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Nonsense_Mutation	SNP	ENST00000265770.7	37		.	.	.	.	.	.	.	.	.	.	C	19.28	3.796327	0.70567	.	.	ENSG00000015592	ENST00000350889;ENST00000523048;ENST00000522908	.	.	.	4.8	3.92	0.45320	.	0.146705	0.31566	N	0.007434	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-12.6319	9.6492	0.39886	0.0:0.9006:0.0:0.0994	.	.	.	.	X	59	.	ENSP00000342538:E59X	E	-	1	0	STMN4	27155126	1.000000	0.71417	1.000000	0.80357	0.455000	0.32408	2.138000	0.42140	1.333000	0.45449	0.462000	0.41574	GAA		0.607	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		A	27099209	C	A	27099209	1	1	61	0	1	0	0	0	0	0	0	0	15350	922	32	2		2	STMN4	8	27099209	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	593958	27099209	119264813	5793	13778										
PTK2B	2185	broad.mit.edu	37	chr8	27312077	27312077	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaccctgcggaagctcatCgggagcgtggatgatctcct	13	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:27312077C>T	ENST00000397501.1	+	35	3571	c.2763C>T	c.(2761-2763)atC>atT	p.I921I	PTK2B_ENST00000346049.5_Silent_p.I921I|PTK2B_ENST00000338238.4_Silent_p.I879I|PTK2B_ENST00000420218.2_Silent_p.I879I|PTK2B_ENST00000544172.1_Silent_p.I921I|PTK2B_ENST00000517339.1_Silent_p.I879I	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	921	Focal adhesion targeting (FAT).|Interaction with TGFB1I1. {ECO:0000250}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)	p.I921I(2)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		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)	Leflunomide(DB01097)	GGAAGCTCATCGGGAGCGTGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	8											89	68	75					8																	27312077		2203	4300	6503	27367994	SO:0001819	synonymous_variant	2185			U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2763C>T	8.37:g.27312077C>T			27367994	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																				0.597	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		T	27312077	C	T	27312077	2	4	61	1	0	0	0	0	0	0	0	1	12798	874	31	1		1	PTK2B	8	27312077	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212868	27312077	119051945	5794	13779										
CHRNA2	1135	broad.mit.edu	37	chr8	27321066	27321066	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagcaccgaaatgcacagCgtgatcttctcgccgcagtc	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:27321066C>T	ENST00000520933.2	-	5	1047	c.894G>A	c.(892-894)acG>acA	p.T298T	CHRNA2_ENST00000240132.2_Silent_p.T283T|CHRNA2_ENST00000407991.1_Silent_p.T298T			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	298					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.T298T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	AAATGCACAGCGTGATCTTCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	8											225	171	190					8																	27321066		2203	4300	6503	27376983	SO:0001819	synonymous_variant	1135			U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.894G>A	8.37:g.27321066C>T			27376983	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	37	CCDS6059.1																																																																																				0.587	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			T	27321066	C	T	27321066	2	4	61	1	0	0	0	0	0	0	0	1	3389	755	27	1		1	CHRNA2	8	27321066	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8989	27321066	119042956	5795	13780										
CHRNA2	1135	broad.mit.edu	37	chr8	27324848	27324848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcgcagtttgtagtcgCtccactcctgtgtgtgggga	13	11	0	0	rs541282922		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:27324848C>T	ENST00000520933.2	-	4	500	c.347G>A	c.(346-348)aGc>aAc	p.S116N	CHRNA2_ENST00000240132.2_Missense_Mutation_p.S101N|CHRNA2_ENST00000407991.1_Missense_Mutation_p.S116N			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	116					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.S116N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	TTTGTAGTCGCTCCACTCCTG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	8											95	94	94					8																	27324848		2203	4300	6503	27380765	SO:0001583	missense	1135			U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.347G>A	8.37:g.27324848C>T	ENSP00000429616:p.Ser116Asn		27380765	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	C	0.322	-0.961233	0.02249	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	T;T;T	0.76839	-1.05;-1.05;0.98	5.52	-5.63	0.02474	Neurotransmitter-gated ion-channel ligand-binding (3);	0.389394	0.32671	N	0.005783	T	0.28566	0.0707	N	0.00123	-2.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.004	T	0.52064	-0.8625	10	0.02654	T	1	.	10.9824	0.47501	0.0:0.165:0.1102:0.7248	.	101;116	B4DK19;Q15822	.;ACHA2_HUMAN	N	116;116;101	ENSP00000385026:S116N;ENSP00000429616:S116N;ENSP00000240132:S101N	ENSP00000240132:S101N	S	-	2	0	CHRNA2	27380765	0.000000	0.05858	0.014000	0.15608	0.327000	0.28475	-0.570000	0.05895	-1.367000	0.02152	-0.345000	0.07892	AGC		0.552	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			T	27324848	C	T	27324848	3	4	61	1	0	0	0	0	1	0	0	0	3389	797	28	3	1254	3	CHRNA2	8	27324848	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3782	27324848	119039174	5796	13781										
CLU	1191	broad.mit.edu	37	chr8	27457480	27457480	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgacctggagggattcgtcGagctcccgccgcagcttagc	14	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:27457480G>A	ENST00000316403.10	-	7	1386	c.981C>T	c.(979-981)ctC>ctT	p.L327L	CLU_ENST00000560366.1_Silent_p.L379L|CLU_ENST00000546343.1_Silent_p.L338L|CLU_ENST00000405140.3_Silent_p.L327L|CLU_ENST00000523500.1_Silent_p.L327L			P10909	CLUS_HUMAN	clusterin	327					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)	p.L379L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		GGGATTCGTCGAGCTCCCGCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	8											72	65	67					8																	27457480		2203	4300	6503	27513397	SO:0001819	synonymous_variant	1191			M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"complement lysis inhibitor", "sulfated glycoprotein 2", "testosterone-repressed prostate message 2", "apolipoprotein J"	185430	"clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.981C>T	8.37:g.27457480G>A			27513397	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.134|6.134	0.392998|0.392998	0.11638|0.11638	.|.	.|.	ENSG00000120885|ENSG00000120885	ENST00000522098|ENST00000521770	.|.	.|.	.|.	5.62|5.62	-6.93|-6.93	0.01638|0.01638	.|.	.|.	.|.	.|.	.|.	.|T	.|0.44095	.|0.1277	.|.	.|.	.|.	0.48288|0.48288	D|D	0.999624|0.999624	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.49351	.|-0.8949	.|4	.|.	.|.	.|.	-26.3671|-26.3671	4.9001|4.9001	0.13769|0.13769	0.4186:0.1364:0.372:0.073|0.4186:0.1364:0.372:0.073	.|.	.|.	.|.	.|.	X|L	190|18	.|.	.|.	R|S	-|-	1|2	2|0	CLU|CLU	27513397|27513397	0.028000|0.028000	0.19301|0.19301	0.046000|0.046000	0.18839|0.18839	0.003000|0.003000	0.03518|0.03518	-0.952000|-0.952000	0.03881|0.03881	-0.712000|-0.712000	0.04988|0.04988	-0.955000|-0.955000	0.02649|0.02649	CGA|TCG		0.552	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		A	27457480	G	A	27457480	2	1	61	1	0	0	0	0	0	0	0	1	3574	1045	37	1		1	CLU	8	27457480	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132632	27457480	118906542	5797	13782										
FBXO16	157574	broad.mit.edu	37	chr8	28309877	28309877	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttctcccctgagttattCttctttcttaaagaggaaga	7	9	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28309877C>A	ENST00000380254.2	-	6	772	c.624G>T	c.(622-624)aaG>aaT	p.K208N	RP11-181B11.2_ENST00000523935.1_RNA|FBXO16_ENST00000518734.1_Missense_Mutation_p.K196N|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Missense_Mutation_p.K196N|RP11-181B11.2_ENST00000518819.1_RNA	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	208								p.K208N(1)		large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		CTGAGTTATTCTTCTTTCTTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	8											90	93	92					8																	28309877		2203	4300	6503	28365796	SO:0001583	missense	157574			AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"F-boxes /  "other""	13618	protein-coding gene	gene with protein product		608519	"F-box only protein 16"			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.624G>T	8.37:g.28309877C>A	ENSP00000369604:p.Lys208Asn		28365796	Q3T1B2|Q3T1B3|Q3T1B4	Missense_Mutation	SNP	ENST00000380254.2	37	CCDS6068.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.45|11.45	1.643698|1.643698	0.29246|0.29246	.|.	.|.	ENSG00000214050|ENSG00000214050	ENST00000380254;ENST00000346498;ENST00000518734;ENST00000517673|ENST00000518248	T;T;T;T|.	0.52754|.	2.34;2.28;2.32;0.65|.	5.49|5.49	4.61|4.61	0.57282|0.57282	.|.	0.338424|.	0.23640|.	U|.	0.046030|.	T|T	0.62744|0.62744	0.2453|0.2453	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	P;P;P|.	0.40144|.	0.698;0.704;0.554|.	B;B;B|.	0.35550|.	0.205;0.203;0.159|.	T|T	0.61302|0.61302	-0.7090|-0.7090	10|5	0.72032|.	D|.	0.01|.	-13.088|-13.088	9.5753|9.5753	0.39454|0.39454	0.0:0.8378:0.0:0.1622|0.0:0.8378:0.0:0.1622	.|.	196;196;208|.	Q3T1B3;Q3T1B2;Q8IX29|.	.;.;FBX16_HUMAN|.	N|I	208;196;196;153|53	ENSP00000369604:K208N;ENSP00000341416:K196N;ENSP00000429687:K196N;ENSP00000429390:K153N|.	ENSP00000341416:K196N|.	K|R	-|-	3|2	2|0	FBXO16|FBXO16	28365796|28365796	1.000000|1.000000	0.71417|0.71417	0.905000|0.905000	0.35620|0.35620	0.288000|0.288000	0.27193|0.27193	3.181000|3.181000	0.50903|0.50903	1.300000|1.300000	0.44818|0.44818	0.591000|0.591000	0.81541|0.81541	AAG|AGA		0.433	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366		A	28309877	C	A	28309877	3	1	61	1	0	0	0	0	1	0	0	0	5748	912	32	2	270	2	FBXO16	8	28309877	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	852397	28309877	118054145	5798	13783										
FZD3	7976	broad.mit.edu	37	chr8	28360642	28360642	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttgaggatgtgccaaGatttgccttataatactacc	7	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28360642G>T	ENST00000240093.3	+	3	590	c.112G>T	c.(112-114)Gat>Tat	p.D38Y	FZD3_ENST00000537916.1_Missense_Mutation_p.D38Y|MIR4288_ENST00000582598.1_RNA	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	38	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.D38Y(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		GATGTGCCAAGATTTGCCTTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											230	202	211					8																	28360642		2203	4300	6503	28416561	SO:0001583	missense	7976			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.112G>T	8.37:g.28360642G>T	ENSP00000240093:p.Asp38Tyr		28416561	A8K615	Missense_Mutation	SNP	ENST00000240093.3	37	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529181	0.64860	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	T;T	0.81163	-1.46;-1.46	5.68	5.68	0.88126	Frizzled domain (5);	0.163608	0.53938	D	0.000045	D	0.86859	0.6034	M	0.68952	2.095	0.80722	D	1	P	0.48350	0.909	P	0.57776	0.827	D	0.85892	0.1429	9	.	.	.	.	16.4948	0.84237	0.0:0.0:1.0:0.0	.	38	Q9NPG1	FZD3_HUMAN	Y	38	ENSP00000437489:D38Y;ENSP00000240093:D38Y	.	D	+	1	0	FZD3	28416561	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.483000	0.97937	2.676000	0.91093	0.561000	0.74099	GAT		0.413	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		T	28360642	G	T	28360642	3	4	61	1	0	0	0	0	1	0	0	0	6150	942	33	2	114	2	FZD3	8	28360642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50765	28360642	118003380	5799	13784										
FZD3	7976	broad.mit.edu	37	chr8	28385376	28385376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttttgttggcctctacGatgttgatgcattgagatat	11	5	1	2	rs372290611		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28385376G>A	ENST00000240093.3	+	5	1577	c.1099G>A	c.(1099-1101)Gat>Aat	p.D367N	FZD3_ENST00000537916.1_Missense_Mutation_p.D367N|RNA5SP259_ENST00000365541.1_RNA	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	367					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.D367N(2)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TGGCCTCTACGATGTTGATGC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	8						G	ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	144	141	142		1099,1099	5.1	1	8		142	0,8600		0,0,4300	no	missense,missense	FZD3	NM_017412.3,NM_145866.1	23,23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	367/667,367/667	28385376	1,13005	2203	4300	6503	28441295	SO:0001583	missense	7976			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1099G>A	8.37:g.28385376G>A	ENSP00000240093:p.Asp367Asn		28441295	A8K615	Missense_Mutation	SNP	ENST00000240093.3	37	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.478444	0.44044	2.27E-4	0.0	ENSG00000104290	ENST00000537916;ENST00000240093	T;T	0.81415	-1.49;-1.49	5.11	5.11	0.69529	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.74786	0.3762	L	0.38649	1.16	0.80722	D	1	P	0.40970	0.734	B	0.40825	0.341	T	0.73142	-0.4076	10	0.25751	T	0.34	.	17.0794	0.86594	0.0:0.0:1.0:0.0	.	367	Q9NPG1	FZD3_HUMAN	N	367	ENSP00000437489:D367N;ENSP00000240093:D367N	ENSP00000240093:D367N	D	+	1	0	FZD3	28441295	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.877000	0.63086	2.371000	0.80710	0.563000	0.77884	GAT		0.443	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		A	28385376	G	A	28385376	3	1	61	1	0	0	0	0	1	0	0	0	6150	1058	37	1	1109	1	FZD3	8	28385376	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24734	28385376	117978646	5800	13785										
FZD3	7976	broad.mit.edu	37	chr8	28385478	28385478	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatatccctaaacagagttCgaattgagattccattagaa	6	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28385478C>T	ENST00000240093.3	+	5	1679	c.1201C>T	c.(1201-1203)Cga>Tga	p.R401*	FZD3_ENST00000537916.1_Nonsense_Mutation_p.R401*|RNA5SP259_ENST00000365541.1_RNA	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	401					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R401*(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		AAACAGAGTTCGAATTGAGAT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											136	136	136					8																	28385478		2203	4300	6503	28441397	SO:0001587	stop_gained	7976			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1201C>T	8.37:g.28385478C>T	ENSP00000240093:p.Arg401*		28441397	A8K615	Nonsense_Mutation	SNP	ENST00000240093.3	37	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	C	42	9.652083	0.99230	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.8242	0.88660	0.0:1.0:0.0:0.0	.	.	.	.	X	401	.	ENSP00000240093:R401X	R	+	1	2	FZD3	28441397	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.549000	0.85964	0.563000	0.77884	CGA		0.403	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		T	28385478	C	T	28385478	4	4	61	1	0	0	0	0	0	1	0	0	6150	876	31	1	1211	1	FZD3	8	28385478	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102	28385478	117978544	5801	13786										
EXTL3	2137	broad.mit.edu	37	chr8	28575042	28575042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtggtgccaaagcctcGtgttaccgaggttcatttcc	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28575042G>A	ENST00000220562.4	+	3	2368	c.1466G>A	c.(1465-1467)cGt>cAt	p.R489H	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Missense_Mutation_p.R105H	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	489					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.R489H(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CCAAAGCCTCGTGTTACCGAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	8											62	62	62					8																	28575042		2203	4300	6503	28630961	SO:0001583	missense	2137			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1466G>A	8.37:g.28575042G>A	ENSP00000220562:p.Arg489His		28630961	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	37	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.137020	0.56936	.	.	ENSG00000012232	ENST00000523149;ENST00000220562	D;D	0.97811	-4.55;-4.55	5.8	5.8	0.92144	.	0.052123	0.85682	D	0.000000	D	0.98661	0.9551	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99289	1.0898	10	0.59425	D	0.04	-15.0215	20.0522	0.97631	0.0:0.0:1.0:0.0	.	489	O43909	EXTL3_HUMAN	H	105;489	ENSP00000428691:R105H;ENSP00000220562:R489H	ENSP00000220562:R489H	R	+	2	0	EXTL3	28630961	1.000000	0.71417	0.089000	0.20774	0.241000	0.25554	9.853000	0.99521	2.737000	0.93849	0.563000	0.77884	CGT		0.607	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		A	28575042	G	A	28575042	3	1	61	1	0	0	0	0	1	0	0	0	5340	1145	40	1	1468	1	EXTL3	8	28575042	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189564	28575042	117788980	5802	13787										
INTS9	55756	broad.mit.edu	37	chr8	28638404	28638404	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagtggaccacgtccccGaagcggagggaagggtgccc	16	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28638404G>A	ENST00000521022.1	-	12	1287	c.1206C>T	c.(1204-1206)ttC>ttT	p.F402F	INTS9_ENST00000521777.1_Silent_p.F378F|INTS9_ENST00000521070.1_5'UTR|INTS9_ENST00000416984.2_Silent_p.F381F|INTS9_ENST00000397363.4_Silent_p.F296F	NM_018250.3	NP_060720.2	Q9NV88	INT9_HUMAN	integrator complex subunit 9	402					snRNA processing (GO:0016180)	cytoplasm (GO:0005737)|integrator complex (GO:0032039)|nucleus (GO:0005634)		p.F402F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(2)	19		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		CCACGTCCCCGAAGCGGAGGG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	8											69	66	67					8																	28638404		2203	4300	6503	28694323	SO:0001819	synonymous_variant	55756			BC025267	CCDS34873.1, CCDS55215.1, CCDS55216.1	8p21.1	2008-02-05			ENSG00000104299	ENSG00000104299			25592	protein-coding gene	gene with protein product		611352				16239144	Standard	NM_001172562		Approved	FLJ10871, CPSF2L, RC-74	uc011lav.2	Q9NV88	OTTHUMG00000164030	ENST00000521022.1:c.1206C>T	8.37:g.28638404G>A			28694323	B7Z560|B7Z6M5|O00224|Q8TB16	Silent	SNP	ENST00000521022.1	37	CCDS34873.1																																																																																				0.493	INTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376846.1	NM_018250		A	28638404	G	A	28638404	2	1	61	1	0	0	0	0	0	0	0	1	7806	1049	37	1		1	INTS9	8	28638404	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63362	28638404	117725618	5803	13788										
KIF13B	23303	broad.mit.edu	37	chr8	28967560	28967560	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgccattcttgctaatgCttcccgttcttccactccct	6	16	2	0	rs553766326		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:28967560C>A	ENST00000524189.1	-	33	3996	c.3958G>T	c.(3958-3960)Gca>Tca	p.A1320S	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1320					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)	p.A1320S(1)		endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CTTGCTAATGCTTCCCGTTCT	0.473													C|||	1	0.000199681	0	0	5008	,	,		19960	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											46	43	44					8																	28967560		1996	4173	6169	29023479	SO:0001583	missense	23303			AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3958G>T	8.37:g.28967560C>A	ENSP00000427900:p.Ala1320Ser		29023479	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	0.097	-1.157762	0.01686	.	.	ENSG00000197892	ENST00000524189	T	0.74209	-0.82	5.13	3.19	0.36642	.	0.208574	0.49916	D	0.000138	T	0.46092	0.1375	N	0.03983	-0.305	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.43458	-0.9390	10	0.02654	T	1	.	11.8375	0.52333	0.0:0.8896:0.0:0.1104	.	1320	F8VPJ2	.	S	1320	ENSP00000427900:A1320S	ENSP00000427900:A1320S	A	-	1	0	KIF13B	29023479	1.000000	0.71417	0.799000	0.32177	0.010000	0.07245	2.901000	0.48695	0.611000	0.30052	0.650000	0.86243	GCA		0.473	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			A	28967560	C	A	28967560	3	1	61	1	0	0	0	0	1	0	0	0	8296	797	28	2	1554	2	KIF13B	8	28967560	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	329156	28967560	117396462	5804	13789										
KIF13B	23303	broad.mit.edu	37	chr8	29033633	29033633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatatggaacaaatttattCttgtttttgccagcactctg	7	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:29033633C>A	ENST00000524189.1	-	10	935	c.897G>T	c.(895-897)aaG>aaT	p.K299N	KIF13B_ENST00000521515.1_Missense_Mutation_p.K299N	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	299	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)	p.K299N(1)		endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CAAATTTATTCTTGTTTTTGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	8											79	74	76					8																	29033633		1896	4114	6010	29089552	SO:0001583	missense	23303			AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.897G>T	8.37:g.29033633C>A	ENSP00000427900:p.Lys299Asn		29089552	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.514844	0.85389	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	T;T	0.75938	-0.98;-0.98	5.44	4.52	0.55395	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.83709	0.5313	M	0.70108	2.13	0.80722	D	1	D;D;D	0.89917	0.992;1.0;0.964	P;D;P	0.79784	0.903;0.993;0.749	D	0.84947	0.0869	10	0.72032	D	0.01	.	11.2553	0.49050	0.0:0.9054:0.0:0.0946	.	285;299;299	C9JK41;Q9NQT8;F8VPJ2	.;KI13B_HUMAN;.	N	299	ENSP00000427900:K299N;ENSP00000429201:K299N	ENSP00000429201:K299N	K	-	3	2	KIF13B	29089552	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.896000	0.56266	1.374000	0.46228	0.655000	0.94253	AAG		0.418	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			A	29033633	C	A	29033633	3	1	61	1	0	0	0	0	1	0	0	0	8296	912	32	2	4707	2	KIF13B	8	29033633	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66073	29033633	117330389	5805	13790										
RBPMS	11030	broad.mit.edu	37	chr8	30361947	30361947	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctcagttcattgccagaGagccatgtaagtcgatctac	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30361947G>T	ENST00000320203.4	+	5	973	c.391G>T	c.(391-393)Gag>Tag	p.E131*	RBPMS_ENST00000339877.4_Nonsense_Mutation_p.E131*|RBPMS_ENST00000287771.5_Nonsense_Mutation_p.E131*|RBPMS_ENST00000397323.4_Nonsense_Mutation_p.E131*|RBPMS_ENST00000520161.1_Nonsense_Mutation_p.E27*|RBPMS_ENST00000517860.1_Nonsense_Mutation_p.E131*|RBPMS_ENST00000520191.1_Nonsense_Mutation_p.E27*|RBPMS_ENST00000519647.1_Nonsense_Mutation_p.E27*|RBPMS_ENST00000538486.1_Nonsense_Mutation_p.E131*	NM_006867.2	NP_006858.1	Q93062	RBPMS_HUMAN	RNA binding protein with multiple splicing	131					positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.E131*(1)		autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)		CATTGCCAGAGAGCCATGTAA	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											121	103	109					8																	30361947		2203	4300	6503	30481489	SO:0001587	stop_gained	11030			D84110	CCDS6077.1, CCDS34875.1, CCDS34876.1	8p12	2013-06-07			ENSG00000157110	ENSG00000157110		"RNA binding motif (RRM) containing"	19097	protein-coding gene	gene with protein product		601558				8855282	Standard	NM_001008710		Approved	HERMES	uc003xib.3	Q93062	OTTHUMG00000163845	ENST00000320203.4:c.391G>T	8.37:g.30361947G>T	ENSP00000318102:p.Glu131*		30481489	D3DSU9|Q92516|Q92517|Q92518|Q96J26	Nonsense_Mutation	SNP	ENST00000320203.4	37	CCDS6077.1	.	.	.	.	.	.	.	.	.	.	G	42	9.290611	0.99127	.	.	ENSG00000157110	ENST00000538486;ENST00000397323;ENST00000339877;ENST00000320203;ENST00000287771;ENST00000517860;ENST00000520161;ENST00000523115;ENST00000519647;ENST00000520191	.	.	.	5.65	5.65	0.86999	.	0.057039	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-16.8346	17.2626	0.87075	0.0:0.0:1.0:0.0	.	.	.	.	X	131;131;131;131;131;131;27;27;27;27	.	ENSP00000287771:E131X	E	+	1	0	RBPMS	30481489	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.475000	0.97721	2.941000	0.99782	0.655000	0.94253	GAG		0.458	RBPMS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376357.2			T	30361947	G	T	30361947	4	4	61	1	0	0	0	0	0	1	0	0	13200	943	33	2	409	2	RBPMS	8	30361947	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1328314	30361947	116002075	5806	13791										
PPP2CB	5516	broad.mit.edu	37	chr8	30651555	30651555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaataccccatccaccacGatcatctggatctgaccata	5	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30651555G>A	ENST00000221138.4	-	5	1066	c.616C>T	c.(616-618)Cgt>Tgt	p.R206C	PPP2CB_ENST00000518564.1_Intron	NM_001009552.1	NP_001009552.1	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta isozyme	206					apoptotic mitochondrial changes (GO:0008637)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of Ras protein signal transduction (GO:0046580)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|regulation of gene expression (GO:0010468)|response to antibiotic (GO:0046677)|response to endoplasmic reticulum stress (GO:0034976)|response to hydrogen peroxide (GO:0042542)	chromosome, centromeric region (GO:0000775)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.R206C(1)		breast(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	9				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	CATCCACCACGATCATCTGGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	53	58					8																	30651555		2203	4300	6503	30771097	SO:0001583	missense	5516				CCDS6079.1	8p12	2011-05-24	2010-03-05		ENSG00000104695	ENSG00000104695	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9300	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, beta isoform"	176916	"protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform"			8383590	Standard	NM_001009552		Approved	PP2Abeta	uc003xik.3	P62714	OTTHUMG00000163949	ENST00000221138.4:c.616C>T	8.37:g.30651555G>A	ENSP00000221138:p.Arg206Cys		30771097	D3DSV4|P11082|Q6FHK5	Missense_Mutation	SNP	ENST00000221138.4	37	CCDS6079.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370387	0.61624	.	.	ENSG00000104695	ENST00000221138;ENST00000406655;ENST00000520334;ENST00000518243	T;T;T	0.42131	0.98;0.98;0.98	4.99	4.1	0.47936	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.43942	0.1270	M	0.77486	2.375	0.80722	D	1	B	0.24043	0.096	B	0.09377	0.004	T	0.51772	-0.8663	10	0.72032	D	0.01	-29.5685	12.7918	0.57539	0.0807:0.0:0.9193:0.0	.	206	P62714	PP2AB_HUMAN	C	206;206;44;159	ENSP00000221138:R206C;ENSP00000430758:R44C;ENSP00000428618:R159C	ENSP00000221138:R206C	R	-	1	0	PPP2CB	30771097	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.647000	0.83462	2.455000	0.83008	0.655000	0.94253	CGT		0.423	PPP2CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376527.2	NM_001009552		A	30651555	G	A	30651555	3	1	61	1	0	0	0	0	1	0	0	0	12415	1058	37	1	325	1	PPP2CB	8	30651555	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	289608	30651555	115712467	5807	13792										
PPP2CB	5516	broad.mit.edu	37	chr8	30657062	30657062	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaatttcaataatcatacCtttaatgctacaagaagagt	5	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30657062C>A	ENST00000221138.4	-	2	762	c.312G>T	c.(310-312)aaG>aaT	p.K104N	PPP2CB_ENST00000520500.1_5'Flank|PPP2CB_ENST00000518564.1_Intron	NM_001009552.1	NP_001009552.1	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta isozyme	104					apoptotic mitochondrial changes (GO:0008637)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of Ras protein signal transduction (GO:0046580)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|regulation of gene expression (GO:0010468)|response to antibiotic (GO:0046677)|response to endoplasmic reticulum stress (GO:0034976)|response to hydrogen peroxide (GO:0042542)	chromosome, centromeric region (GO:0000775)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.K104N(1)		breast(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	9				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	ATAATCATACCTTTAATGCTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	83	83					8																	30657062		2203	4300	6503	30776604	SO:0001630	splice_region_variant	5516				CCDS6079.1	8p12	2011-05-24	2010-03-05		ENSG00000104695	ENSG00000104695	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9300	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, beta isoform"	176916	"protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform"			8383590	Standard	NM_001009552		Approved	PP2Abeta	uc003xik.3	P62714	OTTHUMG00000163949	ENST00000221138.4:c.312+1G>T	8.37:g.30657062C>A			30776604	D3DSV4|P11082|Q6FHK5	Missense_Mutation	SNP	ENST00000221138.4	37	CCDS6079.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178680	0.78564	.	.	ENSG00000104695	ENST00000221138;ENST00000406655;ENST00000518243;ENST00000520056	T;T;T	0.10099	2.91;2.91;2.91	4.23	4.23	0.50019	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.62097	0.2400	H	0.99998	5.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84939	0.0864	9	.	.	.	-0.1905	16.5695	0.84607	0.0:1.0:0.0:0.0	.	104	P62714	PP2AB_HUMAN	N	104;104;57;39	ENSP00000221138:K104N;ENSP00000428618:K57N;ENSP00000428866:K39N	.	K	-	3	2	PPP2CB	30776604	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.942000	0.63547	2.046000	0.60703	0.655000	0.94253	AAG		0.338	PPP2CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376527.2	NM_001009552	Missense_Mutation	A	30657062	C	A	30657062	5	1	61	1	0	0	0	0	0	0	1	0	12415	695	24	2	641	2	PPP2CB	8	30657062	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5507	30657062	115706960	5808	13793										
TEX15	56154	broad.mit.edu	37	chr8	30700271	30700271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaccaaagcatacctcgaAacctctgtttgtctagtttc	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30700271A>G	ENST00000256246.2	-	1	6337	c.6263T>C	c.(6262-6264)tTt>tCt	p.F2088S		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2088					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.F2088S(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CATACCTCGAAACCTCTGTTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	8											60	60	60					8																	30700271		2203	4300	6503	30819813	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.6263T>C	8.37:g.30700271A>G	ENSP00000256246:p.Phe2088Ser		30819813		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	A	17.35	3.367279	0.61513	.	.	ENSG00000133863	ENST00000256246	T	0.17213	2.29	5.43	5.43	0.79202	.	0.000000	0.56097	D	0.000027	T	0.37128	0.0992	L	0.59436	1.845	0.40273	D	0.978312	D	0.71674	0.998	D	0.67548	0.952	T	0.18681	-1.0329	10	0.87932	D	0	.	14.4533	0.67399	1.0:0.0:0.0:0.0	.	2088	Q9BXT5	TEX15_HUMAN	S	2088	ENSP00000256246:F2088S	ENSP00000256246:F2088S	F	-	2	0	TEX15	30819813	1.000000	0.71417	0.996000	0.52242	0.956000	0.61745	4.113000	0.57851	2.065000	0.61736	0.477000	0.44152	TTT		0.348	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30700271	A	G	30700271	3	3	61	1	0	0	0	0	1	0	0	0	15818	14	1	4	2122	4	TEX15	8	30700271	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	43209	30700271	115663751	5809	13794										
TEX15	56154	broad.mit.edu	37	chr8	30701203	30701203	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatacatagtatgaattCttttccctttttgtttcttc	4	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30701203C>A	ENST00000256246.2	-	1	5405	c.5331G>T	c.(5329-5331)aaG>aaT	p.K1777N		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1777					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.K1777N(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGTATGAATTCTTTTCCCTTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	62	64					8																	30701203		2203	4300	6503	30820745	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5331G>T	8.37:g.30701203C>A	ENSP00000256246:p.Lys1777Asn		30820745		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.644652	0.00792	.	.	ENSG00000133863	ENST00000256246	T	0.07021	3.23	5.55	-4.83	0.03161	.	0.353914	0.23446	N	0.048089	T	0.01558	0.0050	N	0.00621	-1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38972	-0.9636	10	0.87932	D	0	.	0.8176	0.01105	0.1682:0.2158:0.2915:0.3245	.	1777	Q9BXT5	TEX15_HUMAN	N	1777	ENSP00000256246:K1777N	ENSP00000256246:K1777N	K	-	3	2	TEX15	30820745	0.000000	0.05858	0.016000	0.15963	0.938000	0.57974	-1.416000	0.02467	-0.393000	0.07739	-0.262000	0.10625	AAG		0.328	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30701203	C	A	30701203	3	1	61	1	0	0	0	0	1	0	0	0	15818	912	32	2	3054	2	TEX15	8	30701203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	932	30701203	115662819	5810	13795										
TEX15	56154	broad.mit.edu	37	chr8	30701385	30701385	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcataccaaagcaagcttcGcaatgttggttcaccttcta	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30701385G>A	ENST00000256246.2	-	1	5223	c.5149C>T	c.(5149-5151)Cga>Tga	p.R1717*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1717					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.R1717*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGCAAGCTTCGCAATGTTGGT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											142	133	136					8																	30701385		2203	4300	6503	30820927	SO:0001587	stop_gained	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5149C>T	8.37:g.30701385G>A	ENSP00000256246:p.Arg1717*		30820927		Nonsense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	44	11.233117	0.99534	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.69	4.79	0.61399	.	0.000000	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.4557	0.55702	0.0:0.0:0.6716:0.3283	.	.	.	.	X	1717	.	ENSP00000256246:R1717X	R	-	1	2	TEX15	30820927	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.381000	0.52455	1.323000	0.45263	0.563000	0.77884	CGA		0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30701385	G	A	30701385	4	1	61	1	0	0	0	0	0	1	0	0	15818	1095	38	1	3236	1	TEX15	8	30701385	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182	30701385	115662637	5811	13796										
TEX15	56154	broad.mit.edu	37	chr8	30701628	30701628	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttagacaaaccttagtttCttcctgtagaatctgcaaag	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30701628C>A	ENST00000256246.2	-	1	4980	c.4906G>T	c.(4906-4908)Gaa>Taa	p.E1636*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1636					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.E1636*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ACCTTAGTTTCTTCCTGTAGA	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											51	51	51					8																	30701628		2203	4299	6502	30821170	SO:0001587	stop_gained	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.4906G>T	8.37:g.30701628C>A	ENSP00000256246:p.Glu1636*		30821170		Nonsense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	C	44	10.733387	0.99458	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.92	4.04	0.47022	.	0.209741	0.33477	N	0.004880	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.2895	0.37778	0.1289:0.4481:0.423:0.0	.	.	.	.	X	1636	.	ENSP00000256246:E1636X	E	-	1	0	TEX15	30821170	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.505000	0.35736	1.440000	0.47531	0.655000	0.94253	GAA		0.358	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30701628	C	A	30701628	4	1	61	1	0	0	0	0	0	1	0	0	15818	922	32	2	3479	2	TEX15	8	30701628	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	243	30701628	115662394	5812	13797										
TEX15	56154	broad.mit.edu	37	chr8	30701882	30701882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaatgtcaagtcagactgcGagtctttactaactttaatt	7	7	3	1	rs140180655		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30701882G>A	ENST00000256246.2	-	1	4726	c.4652C>T	c.(4651-4653)tCg>tTg	p.S1551L		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1551					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.S1551L(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GTCAGACTGCGAGTCTTTACT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	189	189	189		4652	1.6	0	8	dbSNP_134	189	0,8600		0,0,4300	no	missense	TEX15	NM_031271.3	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	1551/2790	30701882	1,13005	2203	4300	6503	30821424	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.4652C>T	8.37:g.30701882G>A	ENSP00000256246:p.Ser1551Leu		30821424		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721886	0.30503	2.27E-4	0.0	ENSG00000133863	ENST00000256246	T	0.11930	2.73	5.47	1.6	0.23607	.	0.631705	0.14770	N	0.299434	T	0.13500	0.0327	M	0.61703	1.905	0.09310	N	1	B	0.20887	0.049	B	0.14578	0.011	T	0.24476	-1.0159	10	0.87932	D	0	.	5.0005	0.14262	0.2554:0.1525:0.5921:0.0	.	1551	Q9BXT5	TEX15_HUMAN	L	1551	ENSP00000256246:S1551L	ENSP00000256246:S1551L	S	-	2	0	TEX15	30821424	0.013000	0.17824	0.000000	0.03702	0.012000	0.07955	0.491000	0.22419	0.076000	0.16826	0.655000	0.94253	TCG		0.383	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30701882	G	A	30701882	3	1	61	1	0	0	0	0	1	0	0	0	15818	1059	37	1	3733	1	TEX15	8	30701882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	254	30701882	115662140	5813	13798										
TEX15	56154	broad.mit.edu	37	chr8	30703414	30703414	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggtcacaactttcccaGaaattattgcatattattgc	6	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30703414G>T	ENST00000256246.2	-	1	3194	c.3120C>A	c.(3118-3120)ttC>ttA	p.F1040L	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1040					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.F1040L(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AACTTTCCCAGAAATTATTGC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8											69	74	72					8																	30703414		2203	4295	6498	30822956	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3120C>A	8.37:g.30703414G>T	ENSP00000256246:p.Phe1040Leu		30822956		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420917	0.62622	.	.	ENSG00000133863	ENST00000256246	T	0.10288	2.89	5.71	-2.23	0.06930	.	0.191953	0.37136	N	0.002229	T	0.06234	0.0161	L	0.42245	1.32	0.30103	N	0.807278	P	0.40619	0.724	B	0.34452	0.183	T	0.18335	-1.0340	10	0.87932	D	0	.	3.067	0.06218	0.463:0.1102:0.3148:0.112	.	1040	Q9BXT5	TEX15_HUMAN	L	1040	ENSP00000256246:F1040L	ENSP00000256246:F1040L	F	-	3	2	TEX15	30822956	0.997000	0.39634	0.976000	0.42696	0.896000	0.52359	0.104000	0.15313	-0.148000	0.11234	-0.444000	0.05651	TTC		0.328	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			T	30703414	G	T	30703414	3	4	61	1	0	0	0	0	1	0	0	0	15818	933	33	2	5265	2	TEX15	8	30703414	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1532	30703414	115660608	5814	13799										
TEX15	56154	broad.mit.edu	37	chr8	30704275	30704275	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttttgtgtagaggaataAaaatagttactttccttaga	8	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30704275A>C	ENST00000256246.2	-	1	2333	c.2259T>G	c.(2257-2259)ttT>ttG	p.F753L	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	753					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.F753L(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TAGAGGAATAAAAATAGTTAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	8											91	90	90					8																	30704275		2203	4300	6503	30823817	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2259T>G	8.37:g.30704275A>C	ENSP00000256246:p.Phe753Leu		30823817		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.375905	0.24857	.	.	ENSG00000133863	ENST00000256246	T	0.09445	2.98	5.78	0.598	0.17512	.	0.757705	0.11905	N	0.518275	T	0.05960	0.0155	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.36114	-0.9761	10	0.87932	D	0	.	3.5206	0.07740	0.5809:0.0:0.2604:0.1588	.	753	Q9BXT5	TEX15_HUMAN	L	753	ENSP00000256246:F753L	ENSP00000256246:F753L	F	-	3	2	TEX15	30823817	0.001000	0.12720	0.000000	0.03702	0.008000	0.06430	0.479000	0.22228	0.082000	0.17018	0.533000	0.62120	TTT		0.363	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30704275	A	C	30704275	3	2	61	1	0	0	0	0	1	0	0	0	15818	11	1	4	6126	4	TEX15	8	30704275	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	861	30704275	115659747	5815	13800										
TEX15	56154	broad.mit.edu	37	chr8	30704934	30704934	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaaatttagtagaaaattCttcagaactcaaaatttcta	4	5	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30704934C>A	ENST00000256246.2	-	1	1674	c.1600G>T	c.(1600-1602)Gaa>Taa	p.E534*	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	534					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.E534*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GTAGAAAATTCTTCAGAACTC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											60	61	61					8																	30704934		2202	4292	6494	30824476	SO:0001587	stop_gained	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.1600G>T	8.37:g.30704934C>A	ENSP00000256246:p.Glu534*		30824476		Nonsense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	C	37	6.225998	0.97394	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.49	2.15	0.27550	.	0.419100	0.20593	N	0.089301	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.5775	0.17231	0.0:0.6167:0.1635:0.2197	.	.	.	.	X	534	.	ENSP00000256246:E534X	E	-	1	0	TEX15	30824476	0.125000	0.22332	0.742000	0.31022	0.709000	0.40893	0.262000	0.18460	0.776000	0.33473	0.650000	0.86243	GAA		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30704934	C	A	30704934	4	1	61	1	0	0	0	0	0	1	0	0	15818	922	32	2	6785	2	TEX15	8	30704934	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	659	30704934	115659088	5816	13801										
TEX15	56154	broad.mit.edu	37	chr8	30705600	30705600	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttatcctttatggtagatgTagaagattttgttatttcta	7	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30705600T>C	ENST00000256246.2	-	1	1008	c.934A>G	c.(934-936)Aca>Gca	p.T312A	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	312					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.T312A(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ATGGTAGATGTAGAAGATTTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	8											52	53	53					8																	30705600		2203	4299	6502	30825142	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.934A>G	8.37:g.30705600T>C	ENSP00000256246:p.Thr312Ala		30825142		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	2.895	-0.228860	0.06022	.	.	ENSG00000133863	ENST00000256246	T	0.08896	3.04	5.46	0.251	0.15540	.	0.969624	0.08473	N	0.940676	T	0.04861	0.0131	N	0.17082	0.46	0.09310	N	1	B	0.11235	0.004	B	0.15052	0.012	T	0.44345	-0.9334	10	0.87932	D	0	.	1.2603	0.02000	0.1357:0.2304:0.1411:0.4928	.	312	Q9BXT5	TEX15_HUMAN	A	312	ENSP00000256246:T312A	ENSP00000256246:T312A	T	-	1	0	TEX15	30825142	0.000000	0.05858	0.000000	0.03702	0.410000	0.31052	-0.272000	0.08560	-0.109000	0.12044	0.528000	0.53228	ACA		0.348	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30705600	T	C	30705600	3	2	61	1	0	0	0	0	1	0	0	0	15818	1638	57	4	7451	4	TEX15	8	30705600	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	666	30705600	115658422	5817	13802										
WRN	7486	broad.mit.edu	37	chr8	30938555	30938555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaattagagaacatgaaGttttaattcacgttgaagat	7	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30938555G>A	ENST00000298139.5	+	9	1261	c.1012G>A	c.(1012-1014)Gtt>Att	p.V338I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	338					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)	p.V338I(1)		central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AGAACATGAAGTTTTAATTCA	0.358			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												Ovarian(18;161 598 2706 14834 27543)	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	8											101	99	100					8																	30938555		2203	4299	6502	31058097	SO:0001583	missense	7486	Familial Cancer Database	WS, Adult Progeria		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1012G>A	8.37:g.30938555G>A	ENSP00000298139:p.Val338Ile		31058097	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	4.631	0.117272	0.08881	.	.	ENSG00000165392	ENST00000298139	T	0.42131	0.98	4.75	-4.41	0.03590	.	1.361190	0.04758	N	0.425723	T	0.10165	0.0249	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10222	-1.0639	10	0.21540	T	0.41	0.3763	0.6418	0.00812	0.2561:0.1195:0.2593:0.3651	.	338	Q14191	WRN_HUMAN	I	338	ENSP00000298139:V338I	ENSP00000298139:V338I	V	+	1	0	WRN	31058097	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.653000	0.05360	-0.467000	0.06932	-1.111000	0.02071	GTT		0.358	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	30938555	G	A	30938555	3	1	61	1	0	0	0	0	1	0	0	0	17442	1029	36	3	1042	3	WRN	8	30938555	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232955	30938555	115425467	5818	13803										
WRN	7486	broad.mit.edu	37	chr8	30941264	30941264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgtcctatgtaattgagaGtgatgaagatttagaaatgg	11	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30941264G>A	ENST00000298139.5	+	10	1568	c.1319G>A	c.(1318-1320)aGt>aAt	p.S440N		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	440	2 X 27 AA tandem repeats of H-L-S-P-N-D- N-E-N-D-T-S-Y-V-I-E-S-D-E-D-L-E-M-E-M-L- K.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)	p.S440N(1)		central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		GTAATTGAGAGTGATGAAGAT	0.254			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												Ovarian(18;161 598 2706 14834 27543)	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	8											78	77	77					8																	30941264		2202	4280	6482	31060806	SO:0001583	missense	7486	Familial Cancer Database	WS, Adult Progeria		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1319G>A	8.37:g.30941264G>A	ENSP00000298139:p.Ser440Asn		31060806	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	g	11.33	1.607963	0.28623	.	.	ENSG00000165392	ENST00000298139	T	0.49720	0.77	4.25	4.25	0.50352	.	0.235594	0.43416	D	0.000574	T	0.66819	0.2828	M	0.71581	2.175	0.42118	D	0.991418	D	0.71674	0.998	D	0.75484	0.986	T	0.71185	-0.4667	10	0.54805	T	0.06	7.0616	15.2089	0.73202	0.0:0.0:1.0:0.0	.	440	Q14191	WRN_HUMAN	N	440	ENSP00000298139:S440N	ENSP00000298139:S440N	S	+	2	0	WRN	31060806	1.000000	0.71417	0.996000	0.52242	0.244000	0.25665	6.757000	0.74924	1.916000	0.55485	0.305000	0.20034	AGT		0.254	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	30941264	G	A	30941264	3	1	61	1	0	0	0	0	1	0	0	0	17442	1029	36	3	1353	3	WRN	8	30941264	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2709	30941264	115422758	5819	13804										
WRN	7486	broad.mit.edu	37	chr8	30948015	30948015	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattcattcagtattagaaGaaagaagagataatgttgct	9	3	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:30948015G>T	ENST00000298139.5	+	14	1936	c.1687G>T	c.(1687-1689)Gaa>Taa	p.E563*		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	563	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)	p.E563*(1)		central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AGTATTAGAAGAAAGAAGAGA	0.289			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												Ovarian(18;161 598 2706 14834 27543)	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	1	Substitution - Nonsense(1)	large_intestine(1)	8											72	79	76					8																	30948015		2202	4291	6493	31067557	SO:0001587	stop_gained	7486	Familial Cancer Database	WS, Adult Progeria		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1687G>T	8.37:g.30948015G>T	ENSP00000298139:p.Glu563*		31067557	A1KYY9	Nonsense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	42	9.781993	0.99263	.	.	ENSG00000165392	ENST00000298139	.	.	.	5.46	5.46	0.80206	.	0.056024	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-25.7162	17.8791	0.88834	0.0:0.0:1.0:0.0	.	.	.	.	X	563	.	ENSP00000298139:E563X	E	+	1	0	WRN	31067557	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.604000	0.61112	2.579000	0.87056	0.650000	0.86243	GAA		0.289	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			T	30948015	G	T	30948015	4	4	61	1	0	0	0	0	0	1	0	0	17442	943	33	2	1737	2	WRN	8	30948015	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6751	30948015	115416007	5820	13805										
NRG1	3084	broad.mit.edu	37	chr8	32505545	32505545	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtatttgtggacaagatCtttgaatatgactctcctac	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:32505545C>A	ENST00000405005.3	+	5	502				NRG1_ENST00000520502.2_Silent_p.I103I|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000356819.4_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.I103I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TGGACAAGATCTTTGAATATG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	8											115	115	115					8																	32505545		2203	4300	6503	32625087	SO:0001627	intron_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31142C>A	8.37:g.32505545C>A			32625087	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Silent	SNP	ENST00000405005.3	37	CCDS6085.1																																																																																				0.542	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			A	32505545	C	A	32505545	1	1	61	0	1	0	0	0	0	0	0	0	10678	903	32	2		2	NRG1	8	32505545	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1557530	32505545	113858477	5821	13806										
NRG1	3084	broad.mit.edu	37	chr8	32621575	32621575	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggatgaggagtatgaAacgacccaagagtacgagcc	15	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:32621575A>C	ENST00000405005.3	+	12	1578	c.1578A>C	c.(1576-1578)gaA>gaC	p.E526D	RP11-1002K11.1_ENST00000607314.1_lincRNA|NRG1_ENST00000287842.3_Missense_Mutation_p.E523D|NRG1_ENST00000338921.4_Missense_Mutation_p.E534D|NRG1_ENST00000539990.1_Missense_Mutation_p.E369D|NRG1_ENST00000287845.5_Missense_Mutation_p.E497D|NRG1_ENST00000519301.1_Missense_Mutation_p.E476D|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Missense_Mutation_p.E531D			Q02297	NRG1_HUMAN	neuregulin 1	526					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.E531D(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		AGGAGTATGAAACGACCCAAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	8											67	60	62					8																	32621575		2203	4300	6503	32741117	SO:0001583	missense	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.1578A>C	8.37:g.32621575A>C	ENSP00000384620:p.Glu526Asp		32741117	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.756083	0.49362	.	.	ENSG00000157168	ENST00000519301;ENST00000523534;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000539990	T;T;T;T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11	5.75	-0.907	0.10521	Neuregulin 1-related, C-terminal (1);	0.057749	0.64402	D	0.000002	T	0.62974	0.2472	L	0.45352	1.415	0.40701	D	0.982486	D;B;B;D;B;D;B	0.71674	0.997;0.257;0.192;0.988;0.257;0.998;0.159	D;B;B;P;B;D;B	0.83275	0.994;0.147;0.34;0.778;0.23;0.996;0.23	T	0.59311	-0.7478	9	.	.	.	-17.9413	11.0886	0.48102	0.5135:0.0:0.4865:0.0	.	369;497;531;534;523;526;531	B7Z1E3;F8W9E3;Q7RTW4;Q02297-2;Q02297-7;Q02297;Q02297-6	.;.;.;.;.;NRG1_HUMAN;.	D	476;599;534;531;526;497;523;526;369	ENSP00000429582:E476D;ENSP00000429067:E599D;ENSP00000343395:E534D;ENSP00000349275:E531D;ENSP00000287840:E526D;ENSP00000287845:E497D;ENSP00000287842:E523D;ENSP00000384620:E526D;ENSP00000439276:E369D	.	E	+	3	2	NRG1	32741117	1.000000	0.71417	0.969000	0.41365	0.905000	0.53344	1.034000	0.30204	-0.101000	0.12219	0.374000	0.22700	GAA		0.547	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			C	32621575	A	C	32621575	3	2	61	1	0	0	0	0	1	0	0	0	10678	11	1	4	3349	4	NRG1	8	32621575	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116030	32621575	113742447	5822	13807										
FUT10	84750	broad.mit.edu	37	chr8	33246541	33246541	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatacactcaaatgcatcGatgtaattgtcctggttgac	7	10	1	1	rs202141953		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33246541G>A	ENST00000327671.5	-	4	1783	c.1152C>T	c.(1150-1152)atC>atT	p.I384I	FUT10_ENST00000518672.1_Silent_p.I356I|FUT10_ENST00000335589.3_Silent_p.I322I|FUT10_ENST00000524021.1_Silent_p.I356I|FUT10_ENST00000518076.1_5'UTR	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	384					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.I384I(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CAAATGCATCGATGTAATTGT	0.498													G|||	1	0.000199681	0	0.0014	5008	,	,		22150	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											250	211	224					8																	33246541		2203	4300	6503	33366083	SO:0001819	synonymous_variant	84750			AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1152C>T	8.37:g.33246541G>A			33366083	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																				0.498	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		A	33246541	G	A	33246541	2	1	61	1	0	0	0	0	0	0	0	1	6121	1048	37	1		1	FUT10	8	33246541	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	624966	33246541	113117481	5823	13808										
FUT10	84750	broad.mit.edu	37	chr8	33310889	33310889	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgtccaattcccattttCttttcctgttgaaggtcaat	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33310889C>A	ENST00000327671.5	-	3	852	c.221G>T	c.(220-222)aGa>aTa	p.R74I	FUT10_ENST00000518672.1_Missense_Mutation_p.R46I|FUT10_ENST00000335589.3_5'UTR|FUT10_ENST00000524021.1_Missense_Mutation_p.R46I|FUT10_ENST00000518076.1_5'UTR	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	74					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.R74I(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		TTCCCATTTTCTTTTCCTGTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											111	105	107					8																	33310889		2203	4300	6503	33430431	SO:0001583	missense	84750			AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.221G>T	8.37:g.33310889C>A	ENSP00000332757:p.Arg74Ile		33430431	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	37	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790893	0.31685	.	.	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021	T;T;T	0.25250	1.81;1.81;1.81	5.58	-5.81	0.02340	.	3.053280	0.00766	N	0.001164	T	0.18045	0.0433	L	0.29908	0.895	0.09310	N	0.999998	B;B;B;B;B;B	0.27416	0.178;0.015;0.037;0.064;0.025;0.018	B;B;B;B;B;B	0.28385	0.089;0.057;0.047;0.047;0.038;0.079	T	0.19031	-1.0318	10	0.34782	T	0.22	0.8794	7.7534	0.28911	0.0:0.2908:0.4624:0.2468	.	124;116;74;46;74;116	B4E056;B4DLS4;Q6P4F1-5;Q6P4F1-4;Q6P4F1;E7EU36	.;.;.;.;FUT10_HUMAN;.	I	74;116;46;46	ENSP00000332757:R74I;ENSP00000430428:R46I;ENSP00000429870:R46I	ENSP00000332757:R74I	R	-	2	0	FUT10	33430431	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.997000	0.03705	-0.957000	0.03627	-0.302000	0.09304	AGA		0.453	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		A	33310889	C	A	33310889	3	1	61	1	0	0	0	0	1	0	0	0	6121	913	32	2	1230	2	FUT10	8	33310889	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64348	33310889	113053133	5824	13809										
MAK16	84549	broad.mit.edu	37	chr8	33346629	33346629	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcacccaatacctaattCgaattagaaaacttacacta	3	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33346629C>T	ENST00000360128.6	+	5	821	c.364C>T	c.(364-366)Cga>Tga	p.R122*	TTI2_ENST00000519356.1_Intron	NM_032509.3	NP_115898.2	Q9BXY0	MAK16_HUMAN	MAK16 homolog (S. cerevisiae)	122						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R122*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	8						ATACCTAATTCGAATTAGAAA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											103	100	101					8																	33346629		2203	4300	6503	33466171	SO:0001587	stop_gained	84549			AF251062	CCDS6089.1	8p12	2011-10-13	2008-06-04	2008-06-04	ENSG00000198042	ENSG00000198042		"RNA binding motif (RRM) containing"	13703	protein-coding gene	gene with protein product			"RNA binding motif protein 13"	RBM13			Standard	NM_032509		Approved	MAK16L	uc003xjj.3	Q9BXY0	OTTHUMG00000163957	ENST00000360128.6:c.364C>T	8.37:g.33346629C>T	ENSP00000353246:p.Arg122*		33466171	B2RB44|Q5U5T1|Q86UC4|Q96SY6	Nonsense_Mutation	SNP	ENST00000360128.6	37	CCDS6089.1	.	.	.	.	.	.	.	.	.	.	C	41	8.770487	0.98948	.	.	ENSG00000198042	ENST00000360128	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8121	20.1743	0.98175	0.0:1.0:0.0:0.0	.	.	.	.	X	122	.	ENSP00000353246:R122X	R	+	1	2	MAK16	33466171	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.651000	0.54431	2.873000	0.98535	0.561000	0.74099	CGA		0.343	MAK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376559.3	NM_032509		T	33346629	C	T	33346629	4	4	61	1	0	0	0	0	0	1	0	0	9228	876	31	1	382	1	MAK16	8	33346629	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35740	33346629	113017393	5825	13810										
C8orf41	80185	broad.mit.edu	37	chr8	33361027	33361027	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcaggtccatcataaacCtccagataaccaatgatgac	5	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33361027C>A	ENST00000431156.2	-	6	1797	c.1179G>T	c.(1177-1179)gaG>gaT	p.E393D	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.E362D|TTI2_ENST00000360742.5_Missense_Mutation_p.E393D	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	393								p.E393D(1)									CATCATAAACCTCCAGATAAC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											177	179	178					8																	33361027		2203	4300	6503	33480569	SO:0001583	missense	80185			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1179G>T	8.37:g.33361027C>A	ENSP00000411169:p.Glu393Asp		33480569	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.987653	0.74589	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.78364	-1.17;-1.17;-1.17	6.03	1.3	0.21679	.	0.059957	0.64402	D	0.000005	D	0.85544	0.5721	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.84499	0.0615	10	0.66056	D	0.02	-26.8976	10.1222	0.42627	0.0:0.5242:0.0:0.4758	.	393;362	Q6NXR4;E5RIH5	TTI2_HUMAN;.	D	393;393;382;362	ENSP00000353971:E393D;ENSP00000411169:E393D;ENSP00000428401:E362D	ENSP00000353971:E393D	E	-	3	2	C8orf41	33480569	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.724000	0.25954	0.301000	0.22738	-0.150000	0.13652	GAG		0.453	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33361027	C	A	33361027	3	1	61	1	0	0	0	0	1	0	0	0	2433	680	24	2	359	2	C8orf41	8	33361027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14398	33361027	113002995	5826	13811										
C8orf41	80185	broad.mit.edu	37	chr8	33369892	33369892	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgctacctgccccagtgtCtccggcattccgcggagccg	11	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33369892C>A	ENST00000431156.2	-	2	858	c.240G>T	c.(238-240)gaG>gaT	p.E80D	SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000520636.1_Missense_Mutation_p.E80D|TTI2_ENST00000360742.5_Missense_Mutation_p.E80D	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	80								p.E80D(1)									GCCCCAGTGTCTCCGGCATTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	71	70					8																	33369892		2203	4300	6503	33489434	SO:0001583	missense	80185			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.240G>T	8.37:g.33369892C>A	ENSP00000411169:p.Glu80Asp		33489434	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576293	0.28092	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397;ENST00000523305	T;T;T;T	0.57907	0.39;0.39;0.37;0.52	4.55	1.69	0.24217	.	1.051700	0.07570	N	0.918366	T	0.49609	0.1567	M	0.75447	2.3	0.09310	N	1	P;B;P	0.38535	0.635;0.231;0.608	B;B;B	0.35413	0.173;0.107;0.202	T	0.35847	-0.9772	10	0.36615	T	0.2	-5.9882	6.4854	0.22085	0.0:0.6099:0.1348:0.2552	.	80;80;80	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	D	80	ENSP00000353971:E80D;ENSP00000411169:E80D;ENSP00000428401:E80D;ENSP00000428569:E80D	ENSP00000353971:E80D	E	-	3	2	C8orf41	33489434	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.779000	0.04659	0.183000	0.20059	-0.797000	0.03246	GAG		0.542	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33369892	C	A	33369892	3	1	61	1	0	0	0	0	1	0	0	0	2433	912	32	2	1314	2	C8orf41	8	33369892	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8865	33369892	112994130	5827	13812										
C8orf41	80185	broad.mit.edu	37	chr8	33369964	33369964	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtggcttctattagatcAccgaggtctttaagaactgc	9	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:33369964A>G	ENST00000431156.2	-	2	786	c.168T>C	c.(166-168)ggT>ggC	p.G56G	SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000520636.1_Silent_p.G56G|TTI2_ENST00000360742.5_Silent_p.G56G	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	56								p.G56G(1)									CTATTAGATCACCGAGGTCTT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	8											72	73	73					8																	33369964		2203	4300	6503	33489506	SO:0001819	synonymous_variant	80185			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.168T>C	8.37:g.33369964A>G			33489506	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																				0.532	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		G	33369964	A	G	33369964	2	3	61	1	0	0	0	0	0	0	0	1	2433	146	6	4		4	C8orf41	8	33369964	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72	33369964	112994058	5828	13813										
UNC5D	137970	broad.mit.edu	37	chr8	35584025	35584025	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctttggccatttagggggGcgcttagtaatgccaaatac	12	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:35584025G>A	ENST00000404895.2	+	10	1987	c.1659G>A	c.(1657-1659)ggG>ggA	p.G553G	UNC5D_ENST00000453357.2_Silent_p.G548G|UNC5D_ENST00000420357.1_Silent_p.G486G|UNC5D_ENST00000449677.1_Silent_p.G129G|UNC5D_ENST00000287272.2_Silent_p.G484G|UNC5D_ENST00000416672.1_Silent_p.G558G	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	553	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.G548G(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ATTTAGGGGGGCGCTTAGTAA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	8																																								35703567	SO:0001819	synonymous_variant	137970			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1659G>A	8.37:g.35584025G>A			35703567	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																				0.418	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			A	35584025	G	A	35584025	2	1	61	1	0	0	0	0	0	0	0	1	17035	1190	42	3		3	UNC5D	8	35584025	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2214061	35584025	110779997	5829	13814										
KCNU1	157855	broad.mit.edu	37	chr8	36662796	36662796	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctttagtttctattttgGattgagggtaagtacctatt	8	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:36662796G>T	ENST00000399881.3	+	4	498	c.461G>T	c.(460-462)gGa>gTa	p.G154V		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	154					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.G154V(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTCTATTTTGGATTGAGGGTA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	8											163	143	150					8																	36662796		1859	4095	5954	36781954	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.461G>T	8.37:g.36662796G>T	ENSP00000382770:p.Gly154Val		36781954		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.917513	0.73098	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	T;T	0.53857	0.6;0.6	5.46	5.46	0.80206	Ion transport (1);	0.000000	0.64402	U	0.000020	T	0.55657	0.1934	N	0.10874	0.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59343	-0.7472	10	0.33940	T	0.23	-5.3528	18.0747	0.89423	0.0:0.0:1.0:0.0	.	154	A8MYU2	KCNU1_HUMAN	V	154	ENSP00000429951:G154V;ENSP00000382770:G154V	ENSP00000382770:G154V	G	+	2	0	KCNU1	36781954	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.178000	0.89690	2.572000	0.86782	0.655000	0.94253	GGA		0.398	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36662796	G	T	36662796	3	4	61	1	0	0	0	0	1	0	0	0	8114	1174	41	2	475	2	KCNU1	8	36662796	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1078771	36662796	109701226	5830	13815										
KCNU1	157855	broad.mit.edu	37	chr8	36693822	36693822	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttatatagggtgctctCtatcaagaactatgattcta	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:36693822C>T	ENST00000399881.3	+	13	1341	c.1304C>T	c.(1303-1305)tCt>tTt	p.S435F		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	435	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.S435F(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGGGTGCTCTCTATCAAGAAC	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	8											140	133	135					8																	36693822		1827	4079	5906	36812980	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1304C>T	8.37:g.36693822C>T	ENSP00000382770:p.Ser435Phe		36812980		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049503	0.55218	.	.	ENSG00000215262	ENST00000399881	T	0.70282	-0.47	5.6	4.71	0.59529	NAD(P)-binding domain (1);	0.000000	0.35151	U	0.003416	D	0.84074	0.5392	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.86779	0.1978	10	0.87932	D	0	-4.1264	16.6359	0.85059	0.0:0.87:0.13:0.0	.	435	A8MYU2	KCNU1_HUMAN	F	435	ENSP00000382770:S435F	ENSP00000382770:S435F	S	+	2	0	KCNU1	36812980	0.998000	0.40836	0.929000	0.37066	0.298000	0.27526	4.151000	0.58105	1.466000	0.48025	0.650000	0.86243	TCT		0.348	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36693822	C	T	36693822	3	4	61	1	0	0	0	0	1	0	0	0	8114	913	32	3	1354	3	KCNU1	8	36693822	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31026	36693822	109670200	5831	13816										
KCNU1	157855	broad.mit.edu	37	chr8	36766859	36766859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagtcaaagtataagtttCggaaccatattgtagcatgt	9	6	1	0	rs199759602		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:36766859C>T	ENST00000399881.3	+	21	2174	c.2137C>T	c.(2137-2139)Cgg>Tgg	p.R713W		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	713	Segment S9.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R713W(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GTATAAGTTTCGGAACCATAT	0.468													C|||	1	0.000199681	8e-04	0	5008	,	,		16879	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	8						C	TRP/ARG	8,3754		0,8,1873	219	212	214		2137	4.9	0.9	8		214	0,8242		0,0,4121	yes	missense	KCNU1	NM_001031836.2	101	0,8,5994	TT,TC,CC		0.0,0.2127,0.0666	probably-damaging	713/1150	36766859	8,11996	1881	4121	6002	36886017	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2137C>T	8.37:g.36766859C>T	ENSP00000382770:p.Arg713Trp		36886017		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.245906	0.39697	0.002127	0.0	ENSG00000215262	ENST00000399881	T	0.32272	1.46	5.8	4.93	0.64822	.	0.758151	0.10676	U	0.646924	T	0.32675	0.0837	L	0.54323	1.7	0.80722	D	1	B	0.23490	0.086	B	0.15052	0.012	T	0.06972	-1.0797	10	0.66056	D	0.02	-2.6227	12.8229	0.57704	0.0:0.9241:0.0:0.0759	.	713	A8MYU2	KCNU1_HUMAN	W	713	ENSP00000382770:R713W	ENSP00000382770:R713W	R	+	1	2	KCNU1	36886017	0.998000	0.40836	0.914000	0.36105	0.011000	0.07611	2.455000	0.44988	1.468000	0.48064	-0.136000	0.14681	CGG		0.468	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36766859	C	T	36766859	3	4	61	1	0	0	0	0	1	0	0	0	8114	875	31	1	2219	1	KCNU1	8	36766859	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73037	36766859	109597163	5832	13817										
KCNU1	157855	broad.mit.edu	37	chr8	36766989	36766989	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacatagtgttcattgggtCtctggactatctacagagag	12	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:36766989C>A	ENST00000399881.3	+	21	2304	c.2267C>A	c.(2266-2268)tCt>tAt	p.S756Y		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	756					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.S756Y(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTCATTGGGTCTCTGGACTAT	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	8											152	151	151					8																	36766989		1866	4097	5963	36886147	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2267C>A	8.37:g.36766989C>A	ENSP00000382770:p.Ser756Tyr		36886147		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.090332	0.55968	.	.	ENSG00000215262	ENST00000399881	T	0.51817	0.69	5.8	5.8	0.92144	.	0.362164	0.20856	U	0.084426	T	0.66208	0.2766	M	0.76328	2.33	0.80722	D	1	D	0.76494	0.999	P	0.60789	0.879	T	0.68739	-0.5329	10	0.87932	D	0	-9.3302	15.2998	0.73940	0.1406:0.8594:0.0:0.0	.	756	A8MYU2	KCNU1_HUMAN	Y	756	ENSP00000382770:S756Y	ENSP00000382770:S756Y	S	+	2	0	KCNU1	36886147	0.965000	0.33210	0.675000	0.29917	0.537000	0.34900	3.441000	0.52893	2.745000	0.94114	0.655000	0.94253	TCT		0.438	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36766989	C	A	36766989	3	1	61	1	0	0	0	0	1	0	0	0	8114	913	32	2	2349	2	KCNU1	8	36766989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130	36766989	109597033	5833	13818										
KCNU1	157855	broad.mit.edu	37	chr8	36793332	36793332	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagagtagaacaaacagtaTtatatcatctcagatacctt	5	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:36793332T>G	ENST00000399881.3	+	27	3381	c.3344T>G	c.(3343-3345)aTt>aGt	p.I1115S		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	1115					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.I1115S(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		ACAAACAGTATTATATCATCT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	8											125	122	123					8																	36793332		1871	4098	5969	36912490	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.3344T>G	8.37:g.36793332T>G	ENSP00000382770:p.Ile1115Ser		36912490		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	T	1.346	-0.592809	0.03771	.	.	ENSG00000215262	ENST00000399881	T	0.34859	1.34	3.45	-6.89	0.01660	.	.	.	.	.	T	0.09247	0.0228	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13575	-1.0504	9	0.02654	T	1	.	1.2882	0.02055	0.1494:0.272:0.3022:0.2764	.	1115	A8MYU2	KCNU1_HUMAN	S	1115	ENSP00000382770:I1115S	ENSP00000382770:I1115S	I	+	2	0	KCNU1	36912490	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.006000	0.12833	-3.730000	0.00114	-3.039000	0.00071	ATT		0.378	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		G	36793332	T	G	36793332	3	3	61	1	0	0	0	0	1	0	0	0	8114	1493	52	4	3450	4	KCNU1	8	36793332	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26343	36793332	109570690	5834	13819										
ERLIN2	11160	broad.mit.edu	37	chr8	37609217	37609217	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaggagactgagaagaaGatttcagaaattgaaggtaa	13	2	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:37609217G>T	ENST00000276461.5	+	10	790	c.723G>T	c.(721-723)aaG>aaT	p.K241N	ERLIN2_ENST00000519638.1_Missense_Mutation_p.K241N	NM_007175.6	NP_009106.1	O94905	ERLN2_HUMAN	ER lipid raft associated 2	241	Interaction with ERLIN1.				cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)		p.K241N(1)		NS(1)|large_intestine(1)|lung(5)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CTGAGAAGAAGATTTCAGAAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	8											105	94	98					8																	37609217		2203	4300	6503	37728375	SO:0001583	missense	11160			AY358108	CCDS6095.1, CCDS34879.1	8p11.2	2012-11-23	2007-01-26	2007-01-26	ENSG00000147475	ENSG00000147475			1356	protein-coding gene	gene with protein product		611605	"chromosome 8 open reading frame 2", "SPFH domain family, member 2"	C8orf2, SPFH2, Erlin-2		10449903, 15897872, 16835267	Standard	NM_007175		Approved	NET32, SPG18	uc003xke.4	O94905	OTTHUMG00000164005	ENST00000276461.5:c.723G>T	8.37:g.37609217G>T	ENSP00000276461:p.Lys241Asn		37728375	A0JLQ1|A8K5S9|B4DM38|D3DSW0|Q6NW21|Q86VS6|Q86W49	Missense_Mutation	SNP	ENST00000276461.5	37	CCDS6095.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227537	0.58668	.	.	ENSG00000147475	ENST00000276461;ENST00000521644;ENST00000519638	T;T;T	0.66995	-0.24;-0.24;-0.24	5.87	4.99	0.66335	.	0.248188	0.45126	D	0.000390	T	0.56804	0.2010	L	0.58510	1.815	0.53005	D	0.999963	B	0.32968	0.392	B	0.27608	0.081	T	0.54403	-0.8299	9	.	.	.	-14.0602	8.9042	0.35512	0.2061:0.0:0.7939:0.0	.	241	O94905	ERLN2_HUMAN	N	241	ENSP00000276461:K241N;ENSP00000429621:K241N;ENSP00000428112:K241N	.	K	+	3	2	ERLIN2	37728375	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.225000	0.32551	2.941000	0.99782	0.655000	0.94253	AAG		0.527	ERLIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376712.2	NM_007175		T	37609217	G	T	37609217	3	4	61	1	0	0	0	0	1	0	0	0	5246	933	33	2	796	2	ERLIN2	8	37609217	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	815885	37609217	108754805	5835	13820										
RAB11FIP1	80223	broad.mit.edu	37	chr8	37720419	37720419	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttctgctgatttacatCtttcctgcttttttgccaac	4	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:37720419C>A	ENST00000330843.4	-	6	3858	c.3846G>T	c.(3844-3846)aaG>aaT	p.K1282N	RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.K648N|RAB11FIP1_ENST00000522727.1_Missense_Mutation_p.K500N|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	1282	Necessary for interaction with RAB4A and RAB11A, subcellular location and endosomal recycling.				protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.K1282N(1)		NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGATTTACATCTTTCCTGCTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											151	140	144					8																	37720419		2203	4300	6503	37839577	SO:0001583	missense	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.3846G>T	8.37:g.37720419C>A	ENSP00000331342:p.Lys1282Asn		37839577	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605310	0.66445	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000522727	T;T;T	0.53206	1.25;1.2;0.63	6.16	3.43	0.39272	.	0.000000	0.64402	D	0.000005	T	0.64483	0.2602	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.998;0.995	T	0.64896	-0.6299	10	0.72032	D	0.01	-29.5194	11.6195	0.51108	0.0:0.8087:0.0:0.1913	.	500;648;1282	E7EX40;Q6WKZ4-3;Q6WKZ4	.;.;RFIP1_HUMAN	N	648;1282;500	ENSP00000287263:K648N;ENSP00000331342:K1282N;ENSP00000430009:K500N	ENSP00000287263:K648N	K	-	3	2	RAB11FIP1	37839577	1.000000	0.71417	0.998000	0.56505	0.583000	0.36354	1.884000	0.39668	0.485000	0.27652	0.650000	0.86243	AAG		0.498	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		A	37720419	C	A	37720419	3	1	61	1	0	0	0	0	1	0	0	0	12930	912	32	2	9	2	RAB11FIP1	8	37720419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111202	37720419	108643603	5836	13821										
RAB11FIP1	80223	broad.mit.edu	37	chr8	37728914	37728914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaattttcaactctaccagCggagccctctgctgtggctt	8	12	3	0	rs201773104		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:37728914C>T	ENST00000330843.4	-	4	3418	c.3406G>A	c.(3406-3408)Gct>Act	p.A1136T	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	1136					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.A1136T(1)		NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			ACTCTACCAGCGGAGCCCTCT	0.542											OREG0018713	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											109	118	115					8																	37728914		2203	4300	6503	37848072	SO:0001583	missense	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.3406G>A	8.37:g.37728914C>T	ENSP00000331342:p.Ala1136Thr	872	37848072	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.313623	0.23908	.	.	ENSG00000156675	ENST00000330843	T	0.41758	0.99	5.29	0.0514	0.14297	.	0.867765	0.09895	N	0.741866	T	0.12987	0.0315	N	0.11106	0.095	0.20926	N	0.999823	P;B	0.48350	0.909;0.41	B;B	0.32149	0.141;0.017	T	0.09335	-1.0679	10	0.11182	T	0.66	-1.0042	1.2767	0.02032	0.2411:0.4183:0.1345:0.2061	.	465;1136	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	T	1136	ENSP00000331342:A1136T	ENSP00000331342:A1136T	A	-	1	0	RAB11FIP1	37848072	0.003000	0.15002	0.106000	0.21319	0.878000	0.50629	0.172000	0.16704	-0.054000	0.13266	0.555000	0.69702	GCT		0.542	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37728914	C	T	37728914	3	4	61	1	0	0	0	0	1	0	0	0	12930	768	27	1	457	1	RAB11FIP1	8	37728914	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8495	37728914	108635108	5837	13822										
RAB11FIP1	80223	broad.mit.edu	37	chr8	37732508	37732508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtccttggtggaagattCggagagctgcctgtcagaag	16	7	1	3	rs116955940		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:37732508C>T	ENST00000330843.4	-	3	1159	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.E383K|RAB11FIP1_ENST00000522727.1_Missense_Mutation_p.E235K|RAB11FIP1_ENST00000524118.1_Missense_Mutation_p.E235K|RAB11FIP1_ENST00000523182.1_5'Flank	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	383					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.E383K(1)		NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			GTGGAAGATTCGGAGAGCTGC	0.567													C|||	1	0.000199681	0	0	5008	,	,		17594	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											58	59	59					8																	37732508		2203	4300	6503	37851666	SO:0001583	missense	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.1147G>A	8.37:g.37732508C>T	ENSP00000331342:p.Glu383Lys		37851666	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.353	0.831394	0.16820	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000522727;ENST00000524118	T;T;T;T	0.31769	2.24;2.7;1.5;1.48	4.68	4.68	0.58851	.	0.365246	0.23420	N	0.048361	T	0.24661	0.0598	L	0.57536	1.79	0.09310	N	1	P;B;P;B	0.48230	0.659;0.109;0.907;0.267	B;B;B;B	0.37304	0.056;0.039;0.246;0.025	T	0.29181	-1.0020	10	0.07325	T	0.83	-10.147	13.3886	0.60809	0.0:0.8422:0.1578:0.0	.	235;235;383;383	E7EX40;Q6WKZ4-2;Q6WKZ4-3;Q6WKZ4	.;.;.;RFIP1_HUMAN	K	383;383;235;235	ENSP00000287263:E383K;ENSP00000331342:E383K;ENSP00000430009:E235K;ENSP00000430680:E235K	ENSP00000287263:E383K	E	-	1	0	RAB11FIP1	37851666	0.009000	0.17119	0.010000	0.14722	0.009000	0.06853	2.163000	0.42377	2.148000	0.66965	0.563000	0.77884	GAA		0.567	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37732508	C	T	37732508	3	4	61	1	0	0	0	0	1	0	0	0	12930	893	31	1	2720	1	RAB11FIP1	8	37732508	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3594	37732508	108631514	5838	13823										
RAB11FIP1	80223	broad.mit.edu	37	chr8	37734711	37734711	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacgaagcagcactttttCtggctttgaagtcggcagga	14	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:37734711C>T	ENST00000330843.4	-	2	742	c.730G>A	c.(730-732)Gaa>Aaa	p.E244K	RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.E244K|RAB11FIP1_ENST00000522727.1_Missense_Mutation_p.E96K|RAB11FIP1_ENST00000524118.1_Missense_Mutation_p.E96K	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	244					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.E244K(1)		NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			AGCACTTTTTCTGGCTTTGAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8											160	151	154					8																	37734711		2203	4300	6503	37853869	SO:0001583	missense	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.730G>A	8.37:g.37734711C>T	ENSP00000331342:p.Glu244Lys		37853869	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.139671	0.37728	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000522727;ENST00000524118	T;T;T;T	0.33438	2.17;2.58;1.43;1.41	5.63	5.63	0.86233	.	0.419375	0.23670	N	0.045735	T	0.21307	0.0513	L	0.31752	0.955	0.09310	N	1	B;B;P;P	0.35272	0.156;0.302;0.493;0.454	B;B;B;B	0.31101	0.037;0.085;0.124;0.078	T	0.15378	-1.0439	10	0.15066	T	0.55	-22.2235	15.0256	0.71667	0.0:0.8589:0.1411:0.0	.	96;96;244;244	E7EX40;Q6WKZ4-2;Q6WKZ4-3;Q6WKZ4	.;.;.;RFIP1_HUMAN	K	244;244;96;96	ENSP00000287263:E244K;ENSP00000331342:E244K;ENSP00000430009:E96K;ENSP00000430680:E96K	ENSP00000287263:E244K	E	-	1	0	RAB11FIP1	37853869	0.056000	0.20664	0.992000	0.48379	0.013000	0.08279	2.565000	0.45939	2.644000	0.89710	0.655000	0.94253	GAA		0.483	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37734711	C	T	37734711	3	4	61	1	0	0	0	0	1	0	0	0	12930	922	32	3	3141	3	RAB11FIP1	8	37734711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2203	37734711	108629311	5839	13824										
DDHD2	23259	broad.mit.edu	37	chr8	38091916	38091916	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaatccttgaaaggaaaAggttgtaatgggagagttgt	12	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:38091916A>G	ENST00000397166.2	+	3	750	c.225A>G	c.(223-225)aaA>aaG	p.K75K	DDHD2_ENST00000520272.2_Silent_p.K75K	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	75	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.K75K(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TGAAAGGAAAAGGTTGTAATG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	8											149	159	155					8																	38091916		2203	4300	6503	38211073	SO:0001819	synonymous_variant	23259			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"Sterile alpha motif (SAM) domain containing"	29106	protein-coding gene	gene with protein product		615003	"SAM, WWE and DDHD domain containing 1"	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.225A>G	8.37:g.38091916A>G			38211073	B3KWV2|B3KXB5|Q9H8X7	Silent	SNP	ENST00000397166.2	37	CCDS34883.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.821596	0.50633	.	.	ENSG00000085788	ENST00000528358	.	.	.	5.79	2.01	0.26516	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7652	0.34698	0.6832:0.0:0.3168:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DDHD2	38211073	0.989000	0.36119	0.929000	0.37066	0.930000	0.56654	0.686000	0.25392	0.099000	0.17552	0.533000	0.62120	.		0.388	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291		G	38091916	A	G	38091916	2	3	61	1	0	0	0	0	0	0	0	1	4333	69	3	4		4	DDHD2	8	38091916	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	357205	38091916	108272106	5840	13825										
LETM2	137994	broad.mit.edu	37	chr8	38257839	38257839	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagttggaactagcaaaatTtcttcaagaaaccatgacag	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:38257839T>G	ENST00000379957.4	+	5	822	c.695T>G	c.(694-696)tTt>tGt	p.F232C	RP11-350N15.3_ENST00000533301.1_RNA|LETM2_ENST00000297720.5_Missense_Mutation_p.F137C|LETM2_ENST00000524874.1_Missense_Mutation_p.F184C|LETM2_ENST00000527710.1_Missense_Mutation_p.F18C|LETM2_ENST00000523983.2_Missense_Mutation_p.F185C	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	232	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.F137C(1)		NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			CTAGCAAAATTTCTTCAAGAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	70	73					8																	38257839		2203	4300	6503	38376996	SO:0001583	missense	137994			AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"EF-hand domain containing"	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.695T>G	8.37:g.38257839T>G	ENSP00000369291:p.Phe232Cys		38376996	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	37		.	.	.	.	.	.	.	.	.	.	T	24.7	4.559302	0.86335	.	.	ENSG00000165046	ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000527710	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.77	5.77	0.91146	LETM1-like (1);	0.000000	0.85682	D	0.000000	T	0.77805	0.4185	H	0.94385	3.53	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.84542	0.0639	10	0.87932	D	0	-15.1134	16.0892	0.81080	0.0:0.0:0.0:1.0	.	29;232;184	B7Z7T4;Q2VYF4;E9PMA4	.;LETM2_HUMAN;.	C	137;184;232;185;18	ENSP00000297720:F137C;ENSP00000431211:F184C;ENSP00000369291:F232C;ENSP00000428765:F185C;ENSP00000434867:F18C	ENSP00000297720:F137C	F	+	2	0	LETM2	38376996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.584000	0.82572	2.208000	0.71279	0.454000	0.30748	TTT		0.398	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652		G	38257839	T	G	38257839	3	3	61	1	0	0	0	0	1	0	0	0	8757	1841	64	4	416	4	LETM2	8	38257839	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	165923	38257839	108106183	5841	13826										
FGFR1	2260	broad.mit.edu	37	chr8	38273413	38273413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggccagatactccatgCctcgggccacctggtaggcg	14	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:38273413C>T	ENST00000447712.2	-	13	2770	c.1829G>A	c.(1828-1830)gGc>gAc	p.G610D	FGFR1_ENST00000356207.5_Missense_Mutation_p.G521D|FGFR1_ENST00000341462.5_Missense_Mutation_p.G610D|FGFR1_ENST00000397103.1_Missense_Mutation_p.G521D|FGFR1_ENST00000335922.5_Missense_Mutation_p.G600D|FGFR1_ENST00000532791.1_Missense_Mutation_p.G608D|FGFR1_ENST00000397113.2_Missense_Mutation_p.G608D|FGFR1_ENST00000397091.5_Missense_Mutation_p.G608D|FGFR1_ENST00000326324.6_Missense_Mutation_p.G519D|FGFR1_ENST00000397108.4_Missense_Mutation_p.G608D|FGFR1_ENST00000425967.3_Missense_Mutation_p.G641D	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.G610D(3)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	ATACTCCATGCCTCGGGCCAC	0.617		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	3	Substitution - Missense(3)	large_intestine(3)	8											50	57	55					8																	38273413		2183	4293	6476	38392570	SO:0001583	missense	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.1829G>A	8.37:g.38273413C>T	ENSP00000400162:p.Gly610Asp		38392570	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	37	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	C	35	5.544553	0.96488	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108	D;D;D;D;D;D;D;D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69;-3.69;-3.69;-3.69;-3.69;-3.69;-3.69;-3.69	5.4	5.4	0.78164	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98782	0.9590	H	0.98027	4.13	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99391	1.0925	10	0.87932	D	0	.	19.5496	0.95312	0.0:1.0:0.0:0.0	.	519;519;610;600;608	P11362-14;P11362-4;P11362;P11362-20;P11362-2	.;.;FGFR1_HUMAN;.;.	D	608;641;610;610;610;608;608;521;600;519;521;608	ENSP00000380280:G608D;ENSP00000393312:G641D;ENSP00000400162:G610D;ENSP00000340636:G610D;ENSP00000432972:G608D;ENSP00000380302:G608D;ENSP00000348537:G521D;ENSP00000337247:G600D;ENSP00000327229:G519D;ENSP00000380292:G521D;ENSP00000380297:G608D	ENSP00000311337:G610D	G	-	2	0	FGFR1	38392570	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.688000	0.91661	0.655000	0.94253	GGC		0.617	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	38273413	C	T	38273413	3	4	61	1	0	0	0	0	1	0	0	0	5882	739	26	3	663	3	FGFR1	8	38273413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15574	38273413	108090609	5842	13827										
ADAM9	8754	broad.mit.edu	37	chr8	38865471	38865471	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggagattaactagagaaaGaagagaagcccctaggccct	11	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:38865471G>T	ENST00000487273.2	+	2	242	c.164G>T	c.(163-165)aGa>aTa	p.R55I	ADAM9_ENST00000481513.1_Missense_Mutation_p.R55I|ADAM9_ENST00000466936.1_Missense_Mutation_p.R55I	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	55				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R55I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ACTAGAGAAAGAAGAGAAGCC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											62	64	63					8																	38865471		2203	4296	6499	38984628	SO:0001583	missense	8754			U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.164G>T	8.37:g.38865471G>T	ENSP00000419446:p.Arg55Ile		38984628	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	37	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849235	0.91277	.	.	ENSG00000168615	ENST00000466936;ENST00000481513;ENST00000487273	T;T;T	0.06849	3.25;3.25;3.25	6.04	6.04	0.98038	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.60957	1.885	0.80722	D	1	D;D;D	0.76494	0.979;0.999;0.969	D;D;D	0.76575	0.917;0.988;0.925	T	0.00027	-1.2303	10	0.37606	T	0.19	.	16.0949	0.81114	0.0:0.0:1.0:0.0	.	55;55;55	Q13443;C9J6H5;C9JPM3	ADAM9_HUMAN;.;.	I	55	ENSP00000420257:R55I;ENSP00000417066:R55I;ENSP00000419446:R55I	ENSP00000369249:R55I	R	+	2	0	ADAM9	38984628	0.998000	0.40836	0.995000	0.50966	0.993000	0.82548	1.434000	0.34958	2.873000	0.98535	0.563000	0.77884	AGA		0.313	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			T	38865471	G	T	38865471	3	4	61	1	0	0	0	0	1	0	0	0	253	942	33	2	170	2	ADAM9	8	38865471	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	592058	38865471	107498551	5843	13828										
ADAM9	8754	broad.mit.edu	37	chr8	38948860	38948860	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagtgacacctcccagaGaagttgtaagtataaaatga	8	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:38948860G>T	ENST00000487273.2	+	20	2371	c.2293G>T	c.(2293-2295)Gaa>Taa	p.E765*		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	765				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.E765*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ACCTCCCAGAGAAGTTGTAAG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											80	86	84					8																	38948860		2203	4300	6503	39068017	SO:0001587	stop_gained	8754			U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.2293G>T	8.37:g.38948860G>T	ENSP00000419446:p.Glu765*		39068017	B7ZLN7|Q10718|Q8NFM6	Nonsense_Mutation	SNP	ENST00000487273.2	37	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	36	5.939291	0.97128	.	.	ENSG00000168615	ENST00000487273	.	.	.	4.67	1.77	0.24775	.	1.042410	0.07504	N	0.907770	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	6.7269	0.23361	0.0957:0.3456:0.5587:0.0	.	.	.	.	X	765	.	ENSP00000419446:E765X	E	+	1	0	ADAM9	39068017	0.996000	0.38824	0.813000	0.32504	0.440000	0.31957	1.274000	0.33132	0.258000	0.21686	-0.662000	0.03851	GAA		0.353	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			T	38948860	G	T	38948860	4	4	61	1	0	0	0	0	0	1	0	0	253	943	33	2	2371	2	ADAM9	8	38948860	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83389	38948860	107415162	5844	13829										
ADAM32	203102	broad.mit.edu	37	chr8	39091459	39091459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttgtacctaccctactcGaaagcctttccatcaagaaa	5	12	1	1	rs199669397	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39091459G>A	ENST00000379907.4	+	16	1803	c.1676G>A	c.(1675-1677)cGa>cAa	p.R559Q	ADAM32_ENST00000437682.2_Missense_Mutation_p.R460Q|ADAM32_ENST00000519315.1_Missense_Mutation_p.R453Q	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	559						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R558Q(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		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)			TACCCTACTCGAAAGCCTTTC	0.323													G|||	2	0.000399361	0	0.0029	5008	,	,		12863	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	8						G	GLN/ARG	1,3655		0,1,1827	82	70	73		1676	-6.4	0	8		73	2,8162		0,2,4080	yes	missense	ADAM32	NM_145004.5	43	0,3,5907	AA,AG,GG		0.0245,0.0274,0.0254	benign	559/788	39091459	3,11817	1828	4082	5910	39210616	SO:0001583	missense	203102			BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1676G>A	8.37:g.39091459G>A	ENSP00000369238:p.Arg559Gln		39210616	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	10.24	1.294779	0.23564	2.74E-4	2.45E-4	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.21543	2.0;2.0;2.0	4.91	-6.44	0.01920	ADAM, cysteine-rich (2);	1.949330	0.03863	N	0.274390	T	0.05456	0.0144	N	0.17764	0.52	0.09310	N	1	P;P;B	0.35944	0.488;0.529;0.335	B;B;B	0.26770	0.073;0.025;0.069	T	0.19745	-1.0296	10	0.16896	T	0.51	.	1.9638	0.03391	0.4264:0.22:0.2424:0.1111	.	460;453;559	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	Q	460;453;559	ENSP00000405978:R460Q;ENSP00000429422:R453Q;ENSP00000369238:R559Q	ENSP00000369238:R559Q	R	+	2	0	ADAM32	39210616	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.258000	0.08733	-1.871000	0.01138	-0.157000	0.13467	CGA		0.323	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		A	39091459	G	A	39091459	3	1	61	1	0	0	0	0	1	0	0	0	249	1058	37	1	1738	1	ADAM32	8	39091459	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142599	39091459	107272563	5845	13830										
ADAM18	8749	broad.mit.edu	37	chr8	39496048	39496048	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtatgcaataaaagctatGatgcaggtattgctatggta	10	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39496048G>T	ENST00000265707.5	+	10	937	c.892G>T	c.(892-894)Gat>Tat	p.D298Y	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.D274Y	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	298	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D298Y(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			TAAAAGCTATGATGCAGGTAT	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	111	112					8																	39496048		2203	4297	6500	39615205	SO:0001583	missense	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.892G>T	8.37:g.39496048G>T	ENSP00000265707:p.Asp298Tyr		39615205	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	9.064	0.995181	0.19043	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.09911	2.93;2.93	5.5	2.61	0.31194	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.755238	0.11784	N	0.529894	T	0.19087	0.0458	L	0.54323	1.7	0.09310	N	1	P;P	0.51537	0.933;0.946	P;P	0.56163	0.689;0.793	T	0.10019	-1.0648	10	0.87932	D	0	.	5.3379	0.15967	0.1704:0.0:0.6693:0.1603	.	274;298	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	Y	298;274;230	ENSP00000265707:D298Y;ENSP00000369195:D274Y	ENSP00000265707:D298Y	D	+	1	0	ADAM18	39615205	0.000000	0.05858	0.006000	0.13384	0.050000	0.14768	-0.027000	0.12371	0.880000	0.35969	0.644000	0.83932	GAT		0.269	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39496048	G	T	39496048	3	4	61	1	0	0	0	0	1	0	0	0	239	1290	45	2	930	2	ADAM18	8	39496048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	404589	39496048	106867974	5846	13831										
ADAM18	8749	broad.mit.edu	37	chr8	39502863	39502863	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttttattttagtatccaGatgcaataggtttggaggga	11	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39502863G>T	ENST00000265707.5	+	11	961	c.916G>T	c.(916-918)Gat>Tat	p.D306Y	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.D282Y	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	306	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D306Y(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			TTAGTATCCAGATGCAATAGG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	8											107	101	103					8																	39502863		2203	4300	6503	39622020	SO:0001583	missense	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.916G>T	8.37:g.39502863G>T	ENSP00000265707:p.Asp306Tyr		39622020	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.938471	0.34189	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.10668	2.85;2.85	5.19	4.24	0.50183	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.509560	0.16625	N	0.206330	T	0.19725	0.0474	L	0.53249	1.67	0.80722	D	1	P;P	0.51537	0.933;0.946	P;P	0.56163	0.689;0.793	T	0.00158	-1.1976	10	0.66056	D	0.02	.	7.8067	0.29206	0.113:0.0:0.887:0.0	.	282;306	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	Y	306;282;238	ENSP00000265707:D306Y;ENSP00000369195:D282Y	ENSP00000265707:D306Y	D	+	1	0	ADAM18	39622020	0.976000	0.34144	0.939000	0.37840	0.091000	0.18340	2.104000	0.41815	2.689000	0.91719	0.591000	0.81541	GAT		0.289	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39502863	G	T	39502863	3	4	61	1	0	0	0	0	1	0	0	0	239	942	33	2	958	2	ADAM18	8	39502863	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6815	39502863	106861159	5847	13832										
ADAM18	8749	broad.mit.edu	37	chr8	39505882	39505883	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgccagtggtagaaagaINStttttagcaactgcagcatg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39505882_39505883insT	ENST00000265707.5	+	12	1111_1112	c.1066_1067insT	c.(1066-1068)attfs	p.I356fs	ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Frame_Shift_Ins_p.I332fs	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	356	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S358fs*1(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			TGGTAGAAAGATTTTTAGCAAC	0.332																																																1	Insertion - Frameshift(1)	large_intestine(1)	8																																								39625040	SO:0001589	frameshift_variant	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1071dupT	8.37:g.39505887_39505887dupT	ENSP00000265707:p.Ile356fs		39625039	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Frame_Shift_Ins	INS	ENST00000265707.5	37	CCDS6113.1																																																																																				0.332	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39505883	-	T	39505882	7	5	61	1	0	1	1	0	0	0	0	0	239	333	12	0	1112	0	ADAM18	8	39505882	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	3019	39505882	106858140	5848	13833										
ADAM18	8749	broad.mit.edu	37	chr8	39525568	39525568	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattgatccagagtgtgatTttacagagtactgcaatgga	11	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39525568T>G	ENST00000265707.5	+	14	1423	c.1378T>G	c.(1378-1380)Ttt>Gtt	p.F460V	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.F436V	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	460	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F460V(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			AGAGTGTGATTTTACAGAGTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											201	192	195					8																	39525568		2203	4300	6503	39644725	SO:0001583	missense	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1378T>G	8.37:g.39525568T>G	ENSP00000265707:p.Phe460Val		39644725	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.685828	0.68157	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.10763	2.84;2.84	5.36	4.18	0.49190	Blood coagulation inhibitor, Disintegrin (5);	0.000000	0.48767	D	0.000170	T	0.14657	0.0354	L	0.45470	1.425	0.80722	D	1	P;P	0.42248	0.733;0.774	P;P	0.48654	0.45;0.585	T	0.00710	-1.1599	10	0.51188	T	0.08	.	8.0116	0.30357	0.0:0.0921:0.0:0.9079	.	436;460	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	V	460;436;392	ENSP00000265707:F460V;ENSP00000369195:F436V	ENSP00000265707:F460V	F	+	1	0	ADAM18	39644725	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	1.672000	0.37523	2.257000	0.74773	0.459000	0.35465	TTT		0.388	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		G	39525568	T	G	39525568	3	3	61	1	0	0	0	0	1	0	0	0	239	1841	64	4	1432	4	ADAM18	8	39525568	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19686	39525568	106838454	5849	13834										
ADAM18	8749	broad.mit.edu	37	chr8	39537696	39537696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctccatgagatcagatgGaacagacaatgcctatgtgg	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39537696G>A	ENST00000265707.5	+	16	1817	c.1772G>A	c.(1771-1773)gGa>gAa	p.G591E	ADAM18_ENST00000541111.1_Missense_Mutation_p.G5E|ADAM18_ENST00000379866.1_Missense_Mutation_p.G567E	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	591	Cys-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.G591E(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			AGATCAGATGGAACAGACAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											88	82	84					8																	39537696		2203	4300	6503	39656853	SO:0001583	missense	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1772G>A	8.37:g.39537696G>A	ENSP00000265707:p.Gly591Glu		39656853	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	1.539	-0.542200	0.04053	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111;ENST00000522198	T;T;T	0.28666	5.36;4.91;1.6	3.85	3.85	0.44370	ADAM, cysteine-rich (1);	0.000000	0.35615	N	0.003093	T	0.22627	0.0546	L	0.46741	1.465	0.32333	N	0.560776	B;B	0.15141	0.01;0.012	B;B	0.20577	0.018;0.03	T	0.19516	-1.0303	10	0.02654	T	1	.	11.5792	0.50881	0.0:0.0:1.0:0.0	.	567;591	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	E	591;567;5;523	ENSP00000265707:G591E;ENSP00000369195:G567E;ENSP00000444729:G5E	ENSP00000265707:G591E	G	+	2	0	ADAM18	39656853	0.896000	0.30565	0.983000	0.44433	0.860000	0.49131	0.603000	0.24149	2.451000	0.82905	0.563000	0.77884	GGA		0.353	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		A	39537696	G	A	39537696	3	1	61	1	0	0	0	0	1	0	0	0	239	1174	41	3	1834	3	ADAM18	8	39537696	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12128	39537696	106826326	5850	13835										
ADAM2	2515	broad.mit.edu	37	chr8	39645689	39645689	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtaataactcattagcttCtccagtggttgcaattttat	7	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39645689C>T	ENST00000265708.4	-	9	827	c.724G>A	c.(724-726)Gaa>Aaa	p.E242K	ADAM2_ENST00000347580.4_Missense_Mutation_p.E223K|ADAM2_ENST00000521880.1_Missense_Mutation_p.E242K|ADAM2_ENST00000379853.2_Intron	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	242	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E242K(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		TCATTAGCTTCTCCAGTGGTT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	8											94	95	94					8																	39645689		2203	4291	6494	39764846	SO:0001583	missense	2515			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.724G>A	8.37:g.39645689C>T	ENSP00000265708:p.Glu242Lys		39764846	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.191491	0.38707	.	.	ENSG00000104755	ENST00000347580;ENST00000265708;ENST00000521880	T;T;T	0.09538	2.97;2.97;2.97	4.57	2.74	0.32292	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.10121	0.0248	L	0.43152	1.355	0.21782	N	0.999545	B;B;B	0.19073	0.009;0.026;0.033	B;B;B	0.29176	0.099;0.087;0.099	T	0.38714	-0.9648	8	.	.	.	.	5.7646	0.18219	0.1918:0.7061:0.0:0.1022	.	242;223;242	B4DWY7;Q99965-2;Q99965	.;.;ADAM2_HUMAN	K	223;242;242	ENSP00000343854:E223K;ENSP00000265708:E242K;ENSP00000429352:E242K	.	E	-	1	0	ADAM2	39764846	1.000000	0.71417	0.996000	0.52242	0.717000	0.41224	2.058000	0.41374	0.456000	0.26937	0.460000	0.39030	GAA		0.289	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		T	39645689	C	T	39645689	3	4	61	1	0	0	0	0	1	0	0	0	241	922	32	3	1531	3	ADAM2	8	39645689	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107993	39645689	106718333	5851	13836										
ADAM2	2515	broad.mit.edu	37	chr8	39678604	39678604	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatctgctttcttatgttTtacttggtaaattacatgtt	5	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39678604T>G	ENST00000265708.4	-	6	533	c.430A>C	c.(430-432)Aaa>Caa	p.K144Q	ADAM2_ENST00000347580.4_Missense_Mutation_p.K144Q|ADAM2_ENST00000521880.1_Missense_Mutation_p.K144Q|ADAM2_ENST00000379853.2_Missense_Mutation_p.K144Q|ADAM2_ENST00000523181.1_5'UTR	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	144					adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.K144Q(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		TTCTTATGTTTTACTTGGTAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	8											74	74	74					8																	39678604		2203	4296	6499	39797761	SO:0001583	missense	2515			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.430A>C	8.37:g.39678604T>G	ENSP00000265708:p.Lys144Gln		39797761	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.937752	0.34189	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.02280	4.97;4.36;5.22;5.18	5.47	5.47	0.80525	.	.	.	.	.	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	P;D;P;P	0.58970	0.672;0.984;0.779;0.672	B;P;P;P	0.61070	0.41;0.883;0.688;0.49	T	0.55379	-0.8150	8	.	.	.	.	8.1325	0.31035	0.0:0.0893:0.0:0.9107	.	144;144;144;144	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	Q	144	ENSP00000343854:K144Q;ENSP00000369182:K144Q;ENSP00000265708:K144Q;ENSP00000429352:K144Q	.	K	-	1	0	ADAM2	39797761	0.042000	0.20092	0.008000	0.14137	0.004000	0.04260	0.660000	0.25009	2.076000	0.62316	0.533000	0.62120	AAA		0.328	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		G	39678604	T	G	39678604	3	3	61	1	0	0	0	0	1	0	0	0	241	1850	64	4	1837	4	ADAM2	8	39678604	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32915	39678604	106685418	5852	13837										
IDO2	169355	broad.mit.edu	37	chr8	39806779	39806779	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctttcttcttccagattCtctggtaaggatagagcctt	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:39806779C>T	ENST00000389060.4	+	1	95	c.95C>T	c.(94-96)tCt>tTt	p.S32F	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Missense_Mutation_p.S45F|RP11-44K6.3_ENST00000517623.1_RNA			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	32					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)	p.S45F(1)|p.S32C(1)|p.S45C(1)|p.S32F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						CTTCCAGATTCTCTGGTAAGG	0.383																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	8											54	51	52					8																	39806779		1867	4100	5967	39925936	SO:0001583	missense	169355			AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.95C>T	8.37:g.39806779C>T	ENSP00000426447:p.Ser32Phe		39925936	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		.	.	.	.	.	.	.	.	.	.	-	15.46	2.838796	0.51057	.	.	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.43294	0.95;0.95	4.92	4.92	0.64577	.	0.064020	0.64402	D	0.000007	T	0.22437	0.0541	N	0.14661	0.345	0.25213	N	0.989962	P	0.41345	0.746	B	0.31812	0.136	T	0.14035	-1.0487	9	.	.	.	.	13.5172	0.61547	0.0:1.0:0.0:0.0	.	45	F5H5G0	.	F	45;32	ENSP00000443432:S45F;ENSP00000426447:S32F	.	S	+	2	0	IDO2	39925936	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.550000	0.53691	2.550000	0.86006	0.645000	0.84053	TCT		0.383	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		T	39806779	C	T	39806779	3	4	61	1	0	0	0	0	1	0	0	0	7523	913	32	3	140	3	IDO2	8	39806779	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128175	39806779	106557243	5853	13838										
ZMAT4	79698	broad.mit.edu	37	chr8	40683097	40683097	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaacgctgtccttacctcGtagtgggccacacgctgcga	12	13	0	0	rs375382251		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:40683097G>A	ENST00000297737.6	-	2	245	c.99C>T	c.(97-99)taC>taT	p.Y33Y	ZMAT4_ENST00000523823.1_5'UTR|ZMAT4_ENST00000315769.7_Silent_p.Y33Y	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	33						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Y33Y(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			TCCTTACCTCGTAGTGGGCCA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	8						G	,	3,4337		0,3,2167	49	41	44		99,99	-0.4	1	8		44	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous	ZMAT4	NM_001135731.1,NM_024645.2	,	0,3,6390	AA,AG,GG		0.0,0.0691,0.0235	,	33/154,33/230	40683097	3,12783	2170	4223	6393	40802254	SO:0001819	synonymous_variant	79698			AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.99C>T	8.37:g.40683097G>A			40802254	Q8WUT8	Silent	SNP	ENST00000297737.6	37	CCDS34885.1																																																																																				0.522	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40683097	G	A	40683097	2	1	61	1	0	0	0	0	0	0	0	1	17733	1140	40	1		1	ZMAT4	8	40683097	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	876318	40683097	105680925	5854	13839										
AGPAT6	137964	broad.mit.edu	37	chr8	41467286	41467286	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgagctctctgacattttCtacttttgccggaaaggaat	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41467286C>T	ENST00000396987.3	+	4	1275	c.348C>T	c.(346-348)ttC>ttT	p.F116F	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	116					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.F116F(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			CTGACATTTTCTACTTTTGCC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	8											104	97	99					8																	41467286		2203	4300	6503	41586443	SO:0001819	synonymous_variant	137964			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.348C>T	8.37:g.41467286C>T			41586443	Q86V89	Silent	SNP	ENST00000396987.3	37	CCDS6117.1																																																																																				0.463	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		T	41467286	C	T	41467286	2	4	61	1	0	0	0	0	0	0	0	1	391	912	32	3		3	AGPAT6	8	41467286	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	784189	41467286	104896736	5855	13840										
ANK1	286	broad.mit.edu	37	chr8	41559121	41559121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtctcagggaaactcattCgatgcttatcactgactaac	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41559121C>T	ENST00000347528.4	-	22	2491	c.2408G>A	c.(2407-2409)cGa>cAa	p.R803Q	ANK1_ENST00000396942.1_Missense_Mutation_p.R803Q|ANK1_ENST00000396945.1_Missense_Mutation_p.R803Q|ANK1_ENST00000352337.4_Missense_Mutation_p.R803Q|ANK1_ENST00000289734.7_Missense_Mutation_p.R803Q|ANK1_ENST00000379758.2_Missense_Mutation_p.R803Q|ANK1_ENST00000265709.8_Missense_Mutation_p.R836Q	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	803	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R803Q(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	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)			GAAACTCATTCGATGCTTATC	0.488											OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											120	110	113					8																	41559121		2203	4300	6503	41678278	SO:0001583	missense	286			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2408G>A	8.37:g.41559121C>T	ENSP00000339620:p.Arg803Gln	902	41678278	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.639923	0.87760	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4;2.4;2.4	5.97	5.07	0.68467	Ankyrin repeat-containing domain (1);	0.060741	0.64402	D	0.000003	T	0.33990	0.0882	M	0.81239	2.535	0.58432	D	0.999999	D;D;B;D;D;D	0.71674	0.985;0.998;0.24;0.987;0.974;0.978	P;B;B;B;P;B	0.49683	0.619;0.419;0.011;0.343;0.619;0.251	T	0.33574	-0.9863	10	0.54805	T	0.06	.	16.5849	0.84725	0.1392:0.8608:0.0:0.0	.	836;803;803;803;803;111	P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.;.;ANK1_HUMAN;.;.;.	Q	803;803;803;803;803;803;836;803	ENSP00000339620:R803Q;ENSP00000289734:R803Q;ENSP00000369082:R803Q;ENSP00000380149:R803Q;ENSP00000380147:R803Q;ENSP00000309131:R803Q;ENSP00000265709:R836Q	ENSP00000265709:R836Q	R	-	2	0	ANK1	41678278	0.999000	0.42202	0.997000	0.53966	0.735000	0.41995	2.165000	0.42396	1.454000	0.47793	0.655000	0.94253	CGA		0.488	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41559121	C	T	41559121	3	4	61	1	0	0	0	0	1	0	0	0	620	884	31	1	3675	1	ANK1	8	41559121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91835	41559121	104804901	5856	13841										
MYST3	7994	broad.mit.edu	37	chr8	41790573	41790573	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcccagtgcttccagatTctggtatctccatgatcata	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41790573T>G	ENST00000396930.3	-	18	5708	c.5165A>C	c.(5164-5166)gAa>gCa	p.E1722A	KAT6A_ENST00000406337.1_Missense_Mutation_p.E1722A|KAT6A_ENST00000265713.2_Missense_Mutation_p.E1722A	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1722	Interaction with PML.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E1722A(1)									GCTTCCAGATTCTGGTATCTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	8											109	114	112					8																	41790573		2203	4300	6503	41909730	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.5165A>C	8.37:g.41790573T>G	ENSP00000380136:p.Glu1722Ala		41909730	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	8.337	0.827840	0.16749	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.72725	-0.68;-0.68;-0.68	5.63	4.46	0.54185	.	0.148147	0.46145	D	0.000303	T	0.60051	0.2239	L	0.34521	1.04	0.53688	D	0.999971	B	0.24483	0.104	B	0.27608	0.081	T	0.53885	-0.8375	10	0.33141	T	0.24	-11.9704	12.0549	0.53529	0.1293:0.0:0.0:0.8706	.	1722	Q92794	KAT6A_HUMAN	A	1722	ENSP00000265713:E1722A;ENSP00000385888:E1722A;ENSP00000380136:E1722A	ENSP00000265713:E1722A	E	-	2	0	KAT6A	41909730	1.000000	0.71417	0.359000	0.25824	0.886000	0.51366	5.912000	0.69948	0.942000	0.37525	0.528000	0.53228	GAA		0.542	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41790573	T	G	41790573	3	3	61	1	0	0	0	0	1	0	0	0	10134	1783	62	4	853	4	MYST3	8	41790573	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	231452	41790573	104573449	5857	13842										
MYST3	7994	broad.mit.edu	37	chr8	41791516	41791516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcctcctcttttaattCgattaactcttccttagtgt	3	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41791516C>T	ENST00000396930.3	-	18	4765	c.4222G>A	c.(4222-4224)Gaa>Aaa	p.E1408K	KAT6A_ENST00000406337.1_Missense_Mutation_p.E1408K|KAT6A_ENST00000265713.2_Missense_Mutation_p.E1408K	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1408					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E1408K(1)									TCTTTTAATTCGATTAACTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	8											103	96	98					8																	41791516		2203	4300	6503	41910673	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4222G>A	8.37:g.41791516C>T	ENSP00000380136:p.Glu1408Lys		41910673	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999255	0.35226	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.60299	0.2;0.2;0.2	5.97	5.09	0.68999	.	0.000000	0.64402	D	0.000001	T	0.56963	0.2021	N	0.24115	0.695	0.33902	D	0.638645	D	0.58620	0.983	P	0.57468	0.821	T	0.60214	-0.7307	10	0.10902	T	0.67	-17.4461	17.4623	0.87623	0.0:0.876:0.124:0.0	.	1408	Q92794	KAT6A_HUMAN	K	1408	ENSP00000265713:E1408K;ENSP00000385888:E1408K;ENSP00000380136:E1408K	ENSP00000265713:E1408K	E	-	1	0	KAT6A	41910673	1.000000	0.71417	0.013000	0.15412	0.022000	0.10575	4.752000	0.62176	1.520000	0.48965	0.655000	0.94253	GAA		0.502	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		T	41791516	C	T	41791516	3	4	61	1	0	0	0	0	1	0	0	0	10134	893	31	1	1796	1	MYST3	8	41791516	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	943	41791516	104572506	5858	13843										
MYST3	7994	broad.mit.edu	37	chr8	41798926	41798926	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttctactgaataagaatCttgttctttgttctcatgag	6	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41798926C>A	ENST00000396930.3	-	16	3016	c.2473G>T	c.(2473-2475)Gat>Tat	p.D825Y	KAT6A_ENST00000406337.1_Missense_Mutation_p.D825Y|KAT6A_ENST00000265713.2_Missense_Mutation_p.D825Y	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	825					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.D825Y(1)									GAATAAGAATCTTGTTCTTTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	8											66	64	65					8																	41798926		2203	4300	6503	41918083	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.2473G>T	8.37:g.41798926C>A	ENSP00000380136:p.Asp825Tyr		41918083	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234852	0.39498	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.60424	0.19;0.19;0.19	5.67	5.67	0.87782	.	0.168787	0.40222	N	0.001143	T	0.52917	0.1764	N	0.24115	0.695	0.40658	D	0.982105	P	0.48503	0.911	P	0.46585	0.521	T	0.59563	-0.7431	10	0.72032	D	0.01	-14.6466	17.9519	0.89056	0.0:1.0:0.0:0.0	.	825	Q92794	KAT6A_HUMAN	Y	825;825;825;405	ENSP00000265713:D825Y;ENSP00000385888:D825Y;ENSP00000380136:D825Y	ENSP00000265713:D825Y	D	-	1	0	KAT6A	41918083	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.038000	0.64177	2.666000	0.90696	0.655000	0.94253	GAT		0.363	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41798926	C	A	41798926	3	1	61	1	0	0	0	0	1	0	0	0	10134	913	32	2	3553	2	MYST3	8	41798926	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7410	41798926	104565096	5859	13844										
MYST3	7994	broad.mit.edu	37	chr8	41806765	41806765	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacagaaatattattctttCtgtaaatctcattggcagga	7	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:41806765C>A	ENST00000396930.3	-	11	2258	c.1715G>T	c.(1714-1716)aGa>aTa	p.R572I	KAT6A_ENST00000406337.1_Missense_Mutation_p.R572I|KAT6A_ENST00000265713.2_Missense_Mutation_p.R572I|KAT6A_ENST00000485568.1_Missense_Mutation_p.R572I	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	572	Catalytic.|Interaction with PML.|Interaction with RUNX1-1.|MYST-type HAT.|Mediates interaction with BRPF1, required for histone H3 acetyltransferase activity.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R572I(1)									ATTATTCTTTCTGTAAATCTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											57	46	50					8																	41806765		2188	4279	6467	41925922	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1715G>T	8.37:g.41806765C>A	ENSP00000380136:p.Arg572Ile		41925922	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826328	0.50739	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721;ENST00000485568	T;T;T;D	0.87571	-0.23;-0.23;-0.23;-2.27	5.24	4.37	0.52481	.	0.280549	0.29444	N	0.012134	D	0.93680	0.7981	M	0.88310	2.945	0.80722	D	1	D;D	0.69078	0.988;0.997	P;D	0.65874	0.847;0.939	D	0.94658	0.7845	10	0.87932	D	0	-6.8087	14.1526	0.65395	0.0:0.9273:0.0:0.0727	.	572;572	A5PLL3;Q92794	.;KAT6A_HUMAN	I	572;572;572;152;572	ENSP00000265713:R572I;ENSP00000385888:R572I;ENSP00000380136:R572I;ENSP00000430606:R572I	ENSP00000265713:R572I	R	-	2	0	KAT6A	41925922	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.818000	0.86416	1.351000	0.45789	0.591000	0.81541	AGA		0.353	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41806765	C	A	41806765	3	1	61	1	0	0	0	0	1	0	0	0	10134	913	32	2	4331	2	MYST3	8	41806765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7839	41806765	104557257	5860	13845										
PLAT	5327	broad.mit.edu	37	chr8	42037541	42037541	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtgcggaccacgctgctCtcctgggcacagcgggacga	14	14	1	0	rs540586282		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42037541C>A	ENST00000220809.4	-	12	1522	c.1266G>T	c.(1264-1266)gaG>gaT	p.E422D	PLAT_ENST00000429089.2_Missense_Mutation_p.E422D|PLAT_ENST00000429710.2_Missense_Mutation_p.E296D|PLAT_ENST00000352041.3_Missense_Mutation_p.E376D|PLAT_ENST00000519510.1_Missense_Mutation_p.E359D|PLAT_ENST00000524009.1_Missense_Mutation_p.E333D|PLAT_ENST00000270189.6_Intron	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	422	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)	p.E422D(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	CCACGCTGCTCTCCTGGGCAC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	8											35	27	30					8																	42037541		2203	4299	6502	42156698	SO:0001583	missense	5327				CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.1266G>T	8.37:g.42037541C>A	ENSP00000220809:p.Glu422Asp		42156698	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	37	CCDS6126.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.365345	0.24684	.	.	ENSG00000104368	ENST00000429089;ENST00000220809;ENST00000352041;ENST00000519510;ENST00000429710;ENST00000524009	D;D;D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41;-2.41;-2.41	5.39	0.863	0.19062	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.239889	0.49305	D	0.000146	T	0.80763	0.4685	L	0.42632	1.34	0.80722	D	1	B;B;B;B;B;B	0.15930	0.01;0.01;0.011;0.015;0.007;0.011	B;B;B;B;B;B	0.23419	0.015;0.015;0.038;0.046;0.017;0.031	T	0.66248	-0.5971	10	0.25106	T	0.35	.	4.5426	0.12066	0.0:0.4525:0.1681:0.3794	.	296;333;359;422;376;422	B4DNJ1;B4DN26;B4DV92;B8ZX62;P00750-3;P00750	.;.;.;.;.;TPA_HUMAN	D	422;422;376;359;296;333	ENSP00000392045:E422D;ENSP00000220809:E422D;ENSP00000270188:E376D;ENSP00000428886:E359D;ENSP00000407861:E296D;ENSP00000429401:E333D	ENSP00000220809:E422D	E	-	3	2	PLAT	42156698	0.987000	0.35691	0.982000	0.44146	0.018000	0.09664	0.182000	0.16900	0.316000	0.23135	0.655000	0.94253	GAG		0.677	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930		A	42037541	C	A	42037541	3	1	61	1	0	0	0	0	1	0	0	0	12052	912	32	2	434	2	PLAT	8	42037541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230776	42037541	104326481	5861	13846										
IKBKB	3551	broad.mit.edu	37	chr8	42176850	42176850	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaattccatggcttccatgtCtcagcagctcaaggccaagt	9	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42176850C>A	ENST00000520810.1	+	14	1613	c.1427C>A	c.(1426-1428)tCt>tAt	p.S476Y	IKBKB_ENST00000416505.2_Missense_Mutation_p.S417Y|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.S474Y|IKBKB_ENST00000522785.1_3'UTR|IKBKB_ENST00000379708.3_Missense_Mutation_p.S253Y	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	476	Leucine-zipper.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)	p.S476Y(1)		breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	GCTTCCATGTCTCAGCAGCTC	0.493											OREG0018747	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											109	101	104					8																	42176850		2203	4300	6503	42296007	SO:0001583	missense	3551			AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1427C>A	8.37:g.42176850C>A	ENSP00000430684:p.Ser476Tyr	906	42296007	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	C	7.777	0.708716	0.15239	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.76186	-0.91;-1.0;-0.82;2.79	5.95	5.95	0.96441	.	0.239442	0.46442	D	0.000297	T	0.59004	0.2162	L	0.32530	0.975	0.33145	D	0.544893	B;B;B;B;B	0.30455	0.001;0.019;0.28;0.007;0.003	B;B;B;B;B	0.27500	0.001;0.049;0.08;0.022;0.013	T	0.59091	-0.7519	10	0.02654	T	1	-11.7506	13.2201	0.59883	0.0:0.9269:0.0:0.0731	.	417;474;253;427;476	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920	.;.;.;.;IKKB_HUMAN	Y	476;417;474;253	ENSP00000430684:S476Y;ENSP00000404920:S417Y;ENSP00000430868:S474Y;ENSP00000369030:S253Y	ENSP00000369030:S253Y	S	+	2	0	IKBKB	42296007	0.995000	0.38212	0.997000	0.53966	0.992000	0.81027	3.105000	0.50314	2.817000	0.96982	0.563000	0.77884	TCT		0.493	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42176850	C	A	42176850	3	1	61	1	0	0	0	0	1	0	0	0	7632	913	32	2	1477	2	IKBKB	8	42176850	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139309	42176850	104187172	5862	13847										
POLB	5423	broad.mit.edu	37	chr8	42214718	42214718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgaaaaaagaattcctCgtgaagagatgttacaaatg	8	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42214718C>T	ENST00000265421.4	+	8	624	c.454C>T	c.(454-456)Cgt>Tgt	p.R152C	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	152					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)	p.R152C(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	AAGAATTCCTCGTGAAGAGAT	0.299								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	8											62	67	66					8																	42214718		2203	4297	6500	42333875	SO:0001583	missense	5423				CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.454C>T	8.37:g.42214718C>T	ENSP00000265421:p.Arg152Cys		42333875	B2RC78|Q3KP48|Q6FI34	Missense_Mutation	SNP	ENST00000265421.4	37	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.868392|3.868392	0.72065|0.72065	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000532157;ENST00000265421;ENST00000518925|ENST00000521290	T;T|.	0.51325|.	0.71;0.71|.	5.93|5.93	4.98|4.98	0.66077|0.66077	DNA-directed DNA polymerase X (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85944|0.85944	0.5815|0.5815	M|M	0.93978|0.93978	3.48|3.48	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|D	0.89026|0.89026	0.3438|0.3438	10|5	0.87932|.	D|.	0|.	2.3915|2.3915	15.4411|15.4411	0.75184|0.75184	0.1481:0.8518:0.0:0.0|0.1481:0.8518:0.0:0.0	.|.	152;152|.	Q53EV2;P06746|.	.;DPOLB_HUMAN|.	C|L	38;152;187|82	ENSP00000265421:R152C;ENSP00000430784:R187C|.	ENSP00000265421:R152C|.	R|S	+|+	1|2	0|0	POLB|POLB	42333875|42333875	0.969000|0.969000	0.33509|0.33509	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	1.398000|1.398000	0.34554|0.34554	2.805000|2.805000	0.96524|0.96524	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.299	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		T	42214718	C	T	42214718	3	4	61	1	0	0	0	0	1	0	0	0	12220	884	31	1	484	1	POLB	8	42214718	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37868	42214718	104149304	5863	13848										
POLB	5423	broad.mit.edu	37	chr8	42229092	42229092	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttgcaggagttgcaggaGaacccctgccagtggatagt	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42229092G>T	ENST00000265421.4	+	14	1095	c.925G>T	c.(925-927)Gaa>Taa	p.E309*	POLB_ENST00000538005.1_Nonsense_Mutation_p.E155*|POLB_ENST00000521492.1_Nonsense_Mutation_p.E28*	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	309					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)	p.E309*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	AGTTGCAGGAGAACCCCTGCC	0.448								DNA polymerases (catalytic subunits)																																								1	Substitution - Nonsense(1)	large_intestine(1)	8											41	44	43					8																	42229092		2203	4300	6503	42348249	SO:0001587	stop_gained	5423				CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.925G>T	8.37:g.42229092G>T	ENSP00000265421:p.Glu309*		42348249	B2RC78|Q3KP48|Q6FI34	Nonsense_Mutation	SNP	ENST00000265421.4	37	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.401068|7.401068	0.98262|0.98262	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000265421;ENST00000538005;ENST00000521492|ENST00000521290;ENST00000518579;ENST00000517393	.|.	.|.	.|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.226696|.	0.47093|.	D|.	0.000244|.	.|T	.|0.74589	.|0.3736	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71866	.|-0.4463	.|4	0.42905|.	T|.	0.14|.	-0.3598|-0.3598	17.8336|17.8336	0.88689|0.88689	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	309;155;28|210;189;56	.|.	ENSP00000265421:E309X|.	E|R	+|+	1|2	0|0	POLB|POLB	42348249|42348249	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.800000|0.800000	0.45204|0.45204	9.688000|9.688000	0.98670|0.98670	2.803000|2.803000	0.96430|0.96430	0.585000|0.585000	0.79938|0.79938	GAA|AGA		0.448	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		T	42229092	G	T	42229092	4	4	61	1	0	0	0	0	0	1	0	0	12220	943	33	2	979	2	POLB	8	42229092	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14374	42229092	104134930	5864	13849										
CHRNB3	1142	broad.mit.edu	37	chr8	42563941	42563941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttatcagaaatgggtccGccctgtattacattctaatg	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42563941G>A	ENST00000289957.2	+	2	262	c.134G>A	c.(133-135)cGc>cAc	p.R45H	RP11-412B14.1_ENST00000527318.1_RNA	NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	45					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)	p.R45H(1)		endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AAATGGGTCCGCCCTGTATTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											118	114	115					8																	42563941		2203	4300	6503	42683098	SO:0001583	missense	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.134G>A	8.37:g.42563941G>A	ENSP00000289957:p.Arg45His		42683098	Q15827	Missense_Mutation	SNP	ENST00000289957.2	37	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	31	5.083844	0.94050	.	.	ENSG00000147432	ENST00000289957	T	0.62498	0.02	5.74	5.74	0.90152	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.82235	0.4993	M	0.87038	2.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83921	0.0301	9	.	.	.	.	17.4865	0.87689	0.0:0.0:1.0:0.0	.	45	Q05901	ACHB3_HUMAN	H	45	ENSP00000289957:R45H	.	R	+	2	0	CHRNB3	42683098	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	9.022000	0.93678	2.745000	0.94114	0.650000	0.86243	CGC		0.408	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			A	42563941	G	A	42563941	3	1	61	1	0	0	0	0	1	0	0	0	3398	1087	38	1	140	1	CHRNB3	8	42563941	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334849	42563941	103800081	5865	13850										
CHRNB3	1142	broad.mit.edu	37	chr8	42586825	42586825	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagtgctgacggccgcttCgaaggctccctgatgaccaa	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42586825C>T	ENST00000289957.2	+	5	503	c.375C>T	c.(373-375)ttC>ttT	p.F125F		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	125					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)	p.F125F(2)		endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	ACGGCCGCTTCGAAGGCTCCC	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	8											49	48	48					8																	42586825		2203	4300	6503	42705982	SO:0001819	synonymous_variant	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.375C>T	8.37:g.42586825C>T			42705982	Q15827	Silent	SNP	ENST00000289957.2	37	CCDS6134.1																																																																																				0.507	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			T	42586825	C	T	42586825	2	4	61	1	0	0	0	0	0	0	0	1	3398	883	31	1		1	CHRNB3	8	42586825	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22884	42586825	103777197	5866	13851										
CHRNB3	1142	broad.mit.edu	37	chr8	42587025	42587025	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcaatgaaaatgtcgacaGaaaagacttcttcgataacg	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42587025G>T	ENST00000289957.2	+	5	703	c.575G>T	c.(574-576)aGa>aTa	p.R192I		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	192					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)	p.R192I(1)		endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AATGTCGACAGAAAAGACTTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											85	81	82					8																	42587025		2203	4300	6503	42706182	SO:0001583	missense	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.575G>T	8.37:g.42587025G>T	ENSP00000289957:p.Arg192Ile		42706182	Q15827	Missense_Mutation	SNP	ENST00000289957.2	37	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	16.24	3.068760	0.55539	.	.	ENSG00000147432	ENST00000289957	T	0.78126	-1.15	5.58	5.58	0.84498	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.78761	0.4334	N	0.21282	0.65	0.80722	D	1	D	0.53745	0.962	P	0.60789	0.879	T	0.80471	-0.1368	10	0.59425	D	0.04	.	14.3706	0.66836	0.0:0.0:0.8162:0.1838	.	192	Q05901	ACHB3_HUMAN	I	192	ENSP00000289957:R192I	ENSP00000289957:R192I	R	+	2	0	CHRNB3	42706182	0.865000	0.29922	0.885000	0.34714	0.428000	0.31595	2.150000	0.42254	2.637000	0.89404	0.650000	0.86243	AGA		0.453	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			T	42587025	G	T	42587025	3	4	61	1	0	0	0	0	1	0	0	0	3398	942	33	2	593	2	CHRNB3	8	42587025	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	200	42587025	103776997	5867	13852										
HOOK3	84376	broad.mit.edu	37	chr8	42761366	42761366	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaccgtggaagatttaacGaatggggttgtgatggccca	14	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42761366G>A	ENST00000307602.4	+	2	308	c.108G>A	c.(106-108)acG>acA	p.T36T		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	36	Sufficient for interaction with microtubules.				cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.T36T(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			AAGATTTAACGAATGGGGTTG	0.408			T	RET	papillary thyroid																																		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - coding silent(1)	large_intestine(1)	8											127	130	129					8																	42761366		2203	4300	6503	42880523	SO:0001819	synonymous_variant	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.108G>A	8.37:g.42761366G>A			42880523	D3DSY8|Q8NBH0|Q9BY13	Silent	SNP	ENST00000307602.4	37	CCDS6139.1																																																																																				0.408	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		A	42761366	G	A	42761366	2	1	61	1	0	0	0	0	0	0	0	1	7305	1045	37	1		1	HOOK3	8	42761366	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	174341	42761366	103602656	5868	13853										
HOOK3	84376	broad.mit.edu	37	chr8	42841933	42841933	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatgaactggagacagaGaataggtagagtattatagg	13	2	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42841933G>T	ENST00000307602.4	+	15	1727	c.1527G>T	c.(1525-1527)gaG>gaT	p.E509D		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	509					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.E509D(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			TGGAGACAGAGAATAGGTAGA	0.418			T	RET	papillary thyroid																																		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - Missense(1)	large_intestine(1)	8											111	119	116					8																	42841933		2203	4300	6503	42961090	SO:0001583	missense	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.1527G>T	8.37:g.42841933G>T	ENSP00000305699:p.Glu509Asp		42961090	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	37	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.227575	0.39399	.	.	ENSG00000168172	ENST00000307602	T	0.19105	2.17	5.07	0.124	0.14714	.	0.097389	0.64402	D	0.000002	T	0.18087	0.0434	L	0.55481	1.735	0.53688	D	0.999978	B	0.15473	0.013	B	0.20955	0.032	T	0.07462	-1.0771	10	0.31617	T	0.26	-19.2221	9.5839	0.39504	0.5143:0.0:0.4857:0.0	.	509	Q86VS8	HOOK3_HUMAN	D	509	ENSP00000305699:E509D	ENSP00000305699:E509D	E	+	3	2	HOOK3	42961090	0.992000	0.36948	0.997000	0.53966	0.871000	0.50021	0.255000	0.18333	0.197000	0.20387	-0.261000	0.10672	GAG		0.418	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		T	42841933	G	T	42841933	3	4	61	1	0	0	0	0	1	0	0	0	7305	933	33	2	1585	2	HOOK3	8	42841933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80567	42841933	103522089	5869	13854										
HOOK3	84376	broad.mit.edu	37	chr8	42852746	42852746	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagttgaagaattacaaaAatctttacaggatcaaggct	7	6	2	2	rs149673072	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:42852746A>C	ENST00000307602.4	+	16	1786	c.1586A>C	c.(1585-1587)aAa>aCa	p.K529T		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	529					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.K529T(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			GAATTACAAAAATCTTTACAG	0.333			T	RET	papillary thyroid								A|||	2	0.000399361	0	0	5008	,	,		18133	0.002		0	False		,,,				2504	0						Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - Missense(1)	large_intestine(1)	8											76	78	77					8																	42852746		2203	4300	6503	42971903	SO:0001583	missense	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.1586A>C	8.37:g.42852746A>C	ENSP00000305699:p.Lys529Thr		42971903	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	37	CCDS6139.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	A	20.8	4.054205	0.75960	.	.	ENSG00000168172	ENST00000307602;ENST00000533539	T;T	0.27557	1.66;1.66	5.29	5.29	0.74685	.	0.091585	0.64402	D	0.000001	T	0.48732	0.1516	L	0.49126	1.545	0.58432	D	0.999998	D	0.76494	0.999	D	0.81914	0.995	T	0.35400	-0.9790	10	0.33141	T	0.24	-29.4011	15.1843	0.72986	1.0:0.0:0.0:0.0	.	529	Q86VS8	HOOK3_HUMAN	T	529;5	ENSP00000305699:K529T;ENSP00000433953:K5T	ENSP00000305699:K529T	K	+	2	0	HOOK3	42971903	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	5.028000	0.64115	2.134000	0.65973	0.533000	0.62120	AAA		0.333	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		C	42852746	A	C	42852746	3	2	61	1	0	0	0	0	1	0	0	0	7305	14	1	4	1648	4	HOOK3	8	42852746	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10813	42852746	103511276	5870	13855										
KIAA0146	23514	broad.mit.edu	37	chr8	48586409	48586409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaatgttcggtgaagtgCacttggagttcaccatgtcg	14	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:48586409C>T	ENST00000297423.4	+	11	1975	c.1591C>T	c.(1591-1593)Cac>Tac	p.H531Y	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000517693.1_Missense_Mutation_p.H6Y|SPIDR_ENST00000518074.1_Missense_Mutation_p.H471Y|SPIDR_ENST00000541342.1_Missense_Mutation_p.H461Y	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	531					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)		p.H531Y(1)									CGGTGAAGTGCACTTGGAGTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											165	169	167					8																	48586409		1953	4141	6094	48748962	SO:0001583	missense	23514			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1591C>T	8.37:g.48586409C>T	ENSP00000297423:p.His531Tyr		48748962	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	C	6.355	0.433545	0.12045	.	.	ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362	.	.	.	5.34	1.02	0.19986	.	0.430708	0.25294	N	0.031701	T	0.22589	0.0545	N	0.16656	0.425	0.09310	N	1	B;B;B;B;B;B;B;B	0.12013	0.002;0.002;0.005;0.004;0.002;0.004;0.004;0.004	B;B;B;B;B;B;B;B	0.14578	0.006;0.006;0.011;0.004;0.006;0.004;0.006;0.004	T	0.14531	-1.0469	9	0.30854	T	0.27	.	7.3377	0.26619	0.0:0.5707:0.0:0.4293	.	21;36;471;461;531;220;6;531	B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B4DEV5;B4DFT3;B3KP42;Q14159	.;.;.;.;.;.;.;K0146_HUMAN	Y	531;471;461;36;6;6	.	ENSP00000297423:H531Y	H	+	1	0	KIAA0146	48748962	0.003000	0.15002	0.003000	0.11579	0.482000	0.33219	0.187000	0.16998	-0.119000	0.11830	0.591000	0.81541	CAC		0.468	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48586409	C	T	48586409	3	4	61	1	0	0	0	0	1	0	0	0	8178	710	25	3	1633	3	KIAA0146	8	48586409	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5733663	48586409	97777613	5871	13856										
PRKDC	5591	broad.mit.edu	37	chr8	48749969	48749969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcatggctccagaaatttCgaataattaatctgaaaagc	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:48749969C>T	ENST00000314191.2	-	58	7618	c.7562G>A	c.(7561-7563)cGa>cAa	p.R2521Q	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Missense_Mutation_p.R2521Q	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2522	KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.R2522Q(1)|p.R2521Q(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	CCAGAAATTTCGAATAATTAA	0.383								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											2	Substitution - Missense(2)	large_intestine(2)	8											36	34	35					8																	48749969		1833	4080	5913	48912522	SO:0001583	missense	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.7562G>A	8.37:g.48749969C>T	ENSP00000313420:p.Arg2521Gln		48912522	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	C	16.07	3.019846	0.54576	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.02258	4.44;4.37	5.79	4.92	0.64577	.	0.000000	0.64402	D	0.000001	T	0.02047	0.0064	L	0.38531	1.155	0.53688	D	0.999972	P;P	0.47350	0.894;0.79	B;B	0.31337	0.128;0.128	T	0.66548	-0.5896	10	0.31617	T	0.26	.	13.9256	0.63961	0.0:0.9274:0.0:0.0726	.	2521;2522	E7EUY0;P78527	.;PRKDC_HUMAN	Q	2521	ENSP00000313420:R2521Q;ENSP00000345182:R2521Q	ENSP00000313420:R2521Q	R	-	2	0	PRKDC	48912522	1.000000	0.71417	0.996000	0.52242	0.732000	0.41865	7.487000	0.81328	1.459000	0.47892	-0.229000	0.12294	CGA		0.383	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		T	48749969	C	T	48749969	3	4	61	1	0	0	0	0	1	0	0	0	12555	884	31	1	4941	1	PRKDC	8	48749969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163560	48749969	97614053	5872	13857										
PRKDC	5591	broad.mit.edu	37	chr8	48840366	48840366	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggctctaacatcgagttCaatgatgttgtgtggcaagg	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:48840366C>A	ENST00000314191.2	-	20	2280	c.2224G>T	c.(2224-2226)Gaa>Taa	p.E742*	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Nonsense_Mutation_p.E742*	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	742					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.E742*(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	ACATCGAGTTCAATGATGTTG	0.448								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											2	Substitution - Nonsense(2)	large_intestine(2)	8											124	130	128					8																	48840366		2027	4177	6204	49002919	SO:0001587	stop_gained	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.2224G>T	8.37:g.48840366C>A	ENSP00000313420:p.Glu742*		49002919	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Nonsense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	C	29.0	4.967554	0.92855	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.35	3.5	0.40072	.	0.575230	0.18362	N	0.143560	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	5.7097	0.17929	0.0:0.6246:0.0:0.3754	.	.	.	.	X	742	.	ENSP00000313420:E742X	E	-	1	0	PRKDC	49002919	1.000000	0.71417	0.997000	0.53966	0.047000	0.14425	3.011000	0.49567	1.354000	0.45846	0.563000	0.77884	GAA		0.448	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		A	48840366	C	A	48840366	4	1	61	1	0	0	0	0	0	1	0	0	12555	835	29	2	10429	2	PRKDC	8	48840366	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90397	48840366	97523656	5873	13858										
EFCAB1	79645	broad.mit.edu	37	chr8	49641672	49641672	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcacagccagttcatagtCtgcaaaagacagcttcccat	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:49641672C>A	ENST00000262103.3	-	5	585	c.505G>T	c.(505-507)Gac>Tac	p.D169Y	EFCAB1_ENST00000523092.1_Missense_Mutation_p.D117Y|EFCAB1_ENST00000521002.1_Splice_Site|EFCAB1_ENST00000433756.1_Missense_Mutation_p.D117Y	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	169	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.D169Y(1)		endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				AGTTCATAGTCTGCAAAAGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	8											115	99	104					8																	49641672		2203	4300	6503	49804225	SO:0001583	missense	79645				CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.505G>T	8.37:g.49641672C>A	ENSP00000262103:p.Asp169Tyr		49804225	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	37	CCDS6145.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.6|21.6	4.180572|4.180572	0.78677|0.78677	.|.	.|.	ENSG00000034239|ENSG00000034239	ENST00000433756;ENST00000262103;ENST00000450553;ENST00000523092|ENST00000523008;ENST00000522254	T;T;T|.	0.74842|.	-0.88;-0.88;-0.88|.	5.22|5.22	5.22|5.22	0.72569|0.72569	EF-hand-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87517|0.87517	0.6197|0.6197	H|H	0.96333|0.96333	3.805|3.805	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|D	0.91062|0.91062	0.4886|0.4886	9|5	.|.	.|.	.|.	.|.	16.3211|16.3211	0.82951|0.82951	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	117;169|.	Q9HAE3-2;Q9HAE3|.	.;EFCB1_HUMAN|.	Y|I	117;169;169;117|35;86	ENSP00000400873:D117Y;ENSP00000262103:D169Y;ENSP00000430765:D117Y|.	.|.	D|R	-|-	1|2	0|0	EFCAB1|EFCAB1	49804225|49804225	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.352000|7.352000	0.79404|0.79404	2.710000|2.710000	0.92621|0.92621	0.555000|0.555000	0.69702|0.69702	GAC|AGA		0.428	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		A	49641672	C	A	49641672	3	1	61	1	0	0	0	0	1	0	0	0	4944	913	32	2	138	2	EFCAB1	8	49641672	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	801306	49641672	96722350	5874	13859										
C8orf22	492307	broad.mit.edu	37	chr8	49986642	49986642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtttcttcagttagttCtttaactagctctgattctg	7	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:49986642C>A	ENST00000303202.8	+	3	253	c.80C>A	c.(79-81)tCt>tAt	p.S27Y	C8orf22_ENST00000517663.1_Missense_Mutation_p.S27Y|C8orf22_ENST00000399653.4_Missense_Mutation_p.S27Y|C8orf22_ENST00000522267.1_Missense_Mutation_p.S27Y	NM_001256598.1	NP_001243527.1	Q8WWR9	PDPFL_HUMAN	chromosome 8 open reading frame 22	27					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)			p.S27Y(1)|p.S27F(1)		large_intestine(1)|lung(7)|prostate(1)	9		all_cancers(86;0.0452)|all_epithelial(80;0.000863)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				TCAGTTAGTTCTTTAACTAGC	0.318																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	8											103	98	100					8																	49986642		1836	4093	5929	50149195	SO:0001583	missense	492307			BC017981	CCDS47854.1, CCDS59101.1, CCDS59102.1	8q11.21	2012-04-11			ENSG00000168333	ENSG00000168333			31745	protein-coding gene	gene with protein product							Standard	NM_001007176		Approved		uc031tba.1	Q8WWR9	OTTHUMG00000164217	ENST00000303202.8:c.80C>A	8.37:g.49986642C>A	ENSP00000304926:p.Ser27Tyr		50149195	G3V137|Q8WVI1	Missense_Mutation	SNP	ENST00000303202.8	37	CCDS59101.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.420823	0.25639	.	.	ENSG00000168333	ENST00000517663;ENST00000522267;ENST00000399653;ENST00000303202	.	.	.	4.06	4.06	0.47325	.	0.000000	0.43747	U	0.000526	T	0.64057	0.2564	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.55477	-0.8135	7	.	.	.	-16.5602	11.7297	0.51730	0.0:1.0:0.0:0.0	.	27	Q8WWR9-2	.	Y	27	.	.	S	+	2	0	C8orf22	50149195	0.224000	0.23674	0.017000	0.16124	0.074000	0.17049	1.796000	0.38794	1.803000	0.52742	0.467000	0.42956	TCT		0.318	C8orf22-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377837.1	NM_001007176		A	49986642	C	A	49986642	3	1	61	1	0	0	0	0	1	0	0	0	2425	913	32	2	86	2	C8orf22	8	49986642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344970	49986642	96377380	5875	13860										
SNTG1	54212	broad.mit.edu	37	chr8	51415350	51415350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcaggttcaggttcttCggaatgctggagaagaagtg	13	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:51415350C>T	ENST00000522124.1	+	9	1037	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	SNTG1_ENST00000517473.1_Missense_Mutation_p.R126W|SNTG1_ENST00000518864.1_Missense_Mutation_p.R126W|SNTG1_ENST00000276467.5_Missense_Mutation_p.R126W	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	126	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)	p.R126W(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				TCAGGTTCTTCGGAATGCTGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	8											67	65	66					8																	51415350		2203	4300	6503	51577903	SO:0001583	missense	54212			AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481			13740	protein-coding gene	gene with protein product		608714				10747910	Standard	NM_018967		Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.376C>T	8.37:g.51415350C>T	ENSP00000429842:p.Arg126Trp		51577903	Q2M3Q0|Q9NY98	Missense_Mutation	SNP	ENST00000522124.1	37	CCDS6147.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243550	0.58995	.	.	ENSG00000147481	ENST00000518864;ENST00000522124;ENST00000517473;ENST00000276467	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	4.86	2.98	0.34508	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.70092	-0.4967	10	0.87932	D	0	.	11.7228	0.51691	0.464:0.536:0.0:0.0	.	126;126	Q9NSN8-2;Q9NSN8	.;SNTG1_HUMAN	W	126	ENSP00000429276:R126W;ENSP00000429842:R126W;ENSP00000431123:R126W;ENSP00000276467:R126W	ENSP00000276467:R126W	R	+	1	2	SNTG1	51577903	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.413000	0.44618	0.502000	0.28037	0.655000	0.94253	CGG		0.338	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377964.1			T	51415350	C	T	51415350	3	4	61	1	0	0	0	0	1	0	0	0	14911	875	31	1	402	1	SNTG1	8	51415350	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1428708	51415350	94948672	5876	13861										
SNTG1	54212	broad.mit.edu	37	chr8	51617192	51617192	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaccgacggaaacagtgCttcaccgtgcagtctgagtc	12	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:51617192C>A	ENST00000522124.1	+	16	1732	c.1071C>A	c.(1069-1071)tgC>tgA	p.C357*	SNTG1_ENST00000517473.1_Nonsense_Mutation_p.C357*|SNTG1_ENST00000518864.1_Nonsense_Mutation_p.C357*|SNTG1_ENST00000276467.5_Nonsense_Mutation_p.C357*	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	357	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)	p.C357*(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GGAAACAGTGCTTCACCGTGC	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											149	123	132					8																	51617192		2203	4300	6503	51779745	SO:0001587	stop_gained	54212			AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481			13740	protein-coding gene	gene with protein product		608714				10747910	Standard	NM_018967		Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.1071C>A	8.37:g.51617192C>A	ENSP00000429842:p.Cys357*		51779745	Q2M3Q0|Q9NY98	Nonsense_Mutation	SNP	ENST00000522124.1	37	CCDS6147.1	.	.	.	.	.	.	.	.	.	.	C	37	6.392568	0.97529	.	.	ENSG00000147481	ENST00000518864;ENST00000522124;ENST00000517473;ENST00000276467	.	.	.	5.19	3.39	0.38822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2713	10.1549	0.42816	0.0:0.773:0.0:0.227	.	.	.	.	X	357	.	ENSP00000276467:C357X	C	+	3	2	SNTG1	51779745	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	1.811000	0.38942	0.680000	0.31366	0.643000	0.83706	TGC		0.547	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377964.1			A	51617192	C	A	51617192	4	1	61	1	0	0	0	0	0	1	0	0	14911	805	28	2	1125	2	SNTG1	8	51617192	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201842	51617192	94746830	5877	13862										
PXDNL	137902	broad.mit.edu	37	chr8	52233367	52233367	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaatgcagtgagtgcagtCttctttcatccagcgctcct	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:52233367C>A	ENST00000356297.4	-	22	4337	c.4237G>T	c.(4237-4239)Gac>Tac	p.D1413Y	RP11-401H2.1_ENST00000521294.1_RNA|PXDNL_ENST00000543296.1_3'UTR	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1413	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D1413Y(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGAGTGCAGTCTTCTTTCATC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8											131	143	139					8																	52233367		1933	4132	6065	52395920	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.4237G>T	8.37:g.52233367C>A	ENSP00000348645:p.Asp1413Tyr		52395920	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.02|12.02	1.814101|1.814101	0.32053|0.32053	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297|ENST00000522933	T|.	0.64803|.	-0.12|.	4.26|4.26	4.26|4.26	0.50523|0.50523	von Willebrand factor, type C (3);|.	.|.	.|.	.|.	.|.	T|T	0.55114|0.55114	0.1900|0.1900	L|L	0.38649|0.38649	1.16|1.16	0.80722|0.80722	D|D	1|1	P|.	0.42993|.	0.797|.	P|.	0.56163|.	0.793|.	T|T	0.51865|0.51865	-0.8651|-0.8651	9|5	0.56958|.	D|.	0.05|.	.|.	12.1739|12.1739	0.54173|0.54173	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1413|.	A1KZ92|.	PXDNL_HUMAN|.	Y|N	1413|486	ENSP00000348645:D1413Y|.	ENSP00000348645:D1413Y|.	D|K	-|-	1|3	0|2	PXDNL|PXDNL	52395920|52395920	0.766000|0.766000	0.28496|0.28496	0.233000|0.233000	0.24025|0.24025	0.014000|0.014000	0.08584|0.08584	3.302000|3.302000	0.51849|0.51849	1.911000|1.911000	0.55334|0.55334	0.655000|0.655000	0.94253|0.94253	GAC|AAG		0.507	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52233367	C	A	52233367	3	1	61	1	0	0	0	0	1	0	0	0	12885	913	32	2	162	2	PXDNL	8	52233367	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	616175	52233367	94130655	5878	13863										
PXDNL	137902	broad.mit.edu	37	chr8	52320912	52320912	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatcccaccttccttgattAttctggacggtgaaaagagc	8	11	1	3	rs370901923		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:52320912A>G	ENST00000356297.4	-	17	3372	c.3272T>C	c.(3271-3273)aTa>aCa	p.I1091T	PXDNL_ENST00000543296.1_Missense_Mutation_p.I1091T	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1091					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.I1091T(1)|p.I290T(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TTCCTTGATTATTCTGGACGG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	8											59	61	60					8																	52320912		1872	4107	5979	52483465	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3272T>C	8.37:g.52320912A>G	ENSP00000348645:p.Ile1091Thr		52483465	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.78|10.78	1.446942|1.446942	0.25987|0.25987	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.74002|.	-0.8;-0.8|.	3.82|3.82	2.64|2.64	0.31445|0.31445	.|.	0.103768|.	0.41001|.	D|.	0.000971|.	T|.	0.68559|.	0.3014|.	M|M	0.85945|0.85945	2.785|2.785	0.36215|0.36215	D|D	0.85158|0.85158	D|.	0.55172|.	0.97|.	D|.	0.63877|.	0.919|.	T|.	0.71606|.	-0.4542|.	10|.	0.87932|.	D|.	0|.	.|.	7.1373|7.1373	0.25535|0.25535	0.885:0.0:0.115:0.0|0.885:0.0:0.115:0.0	.|.	1091|.	A1KZ92|.	PXDNL_HUMAN|.	T|Q	1091|210	ENSP00000348645:I1091T;ENSP00000444865:I1091T|.	ENSP00000348645:I1091T|.	I|X	-|-	2|1	0|0	PXDNL|PXDNL	52483465|52483465	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.001000|0.001000	0.01503|0.01503	7.897000|7.897000	0.87356|0.87356	0.356000|0.356000	0.24157|0.24157	-0.250000|-0.250000	0.11733|0.11733	ATA|TAA		0.517	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52320912	A	G	52320912	3	3	61	1	0	0	0	0	1	0	0	0	12885	449	16	4	1147	4	PXDNL	8	52320912	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	87545	52320912	94043110	5879	13864										
PXDNL	137902	broad.mit.edu	37	chr8	52336225	52336225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtcagggaaccctgcgtCgtagatagtcagcgtgcctt	13	11	2	1	rs180899557		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:52336225C>T	ENST00000356297.4	-	14	1805	c.1705G>A	c.(1705-1707)Gac>Aac	p.D569N	PXDNL_ENST00000543296.1_Missense_Mutation_p.D569N	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	569	Ig-like C2-type 4.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D569N(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AACCCTGCGTCGTAGATAGTC	0.478													C|||	0	0	0	0	5008	,	,		15174	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	ASN/ASP	4,4328		0,4,2162	115	125	122		1705	3.5	0	8		122	1,8537		0,1,4268	yes	missense	PXDNL	NM_144651.4	23	0,5,6430	TT,TC,CC		0.0117,0.0923,0.0389	possibly-damaging	569/1464	52336225	5,12865	2166	4269	6435	52498778	SO:0001583	missense	137902				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1705G>A	8.37:g.52336225C>T	ENSP00000348645:p.Asp569Asn		52498778	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	4.806	0.149785	0.09185	9.23E-4	1.17E-4	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.75154	-0.91;-0.91	4.43	3.52	0.40303	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42877	0.1222	N	0.01473	-0.845	0.21527	N	0.999657	B	0.33739	0.422	B	0.31495	0.131	T	0.30707	-0.9969	9	0.09590	T	0.72	.	9.7459	0.40446	0.2074:0.7926:0.0:0.0	.	569	A1KZ92	PXDNL_HUMAN	N	569	ENSP00000348645:D569N;ENSP00000444865:D569N	ENSP00000348645:D569N	D	-	1	0	PXDNL	52498778	0.979000	0.34478	0.005000	0.12908	0.002000	0.02628	3.200000	0.51051	0.907000	0.36646	0.650000	0.86243	GAC		0.478	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52336225	C	T	52336225	3	4	61	1	0	0	0	0	1	0	0	0	12885	884	31	1	2726	1	PXDNL	8	52336225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15313	52336225	94027797	5880	13865										
PCMTD1	115294	broad.mit.edu	37	chr8	52744111	52744111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaagtgttctgtccagttCgcataatctgtgttaactat	7	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:52744111C>T	ENST00000360540.5	-	6	1005	c.599G>A	c.(598-600)cGa>cAa	p.R200Q	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.R124Q|PCMTD1_ENST00000522514.1_Missense_Mutation_p.R200Q	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	200						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.R200Q(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CTGTCCAGTTCGCATAATCTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	8											120	105	110					8																	52744111		2203	4300	6503	52906664	SO:0001583	missense	115294				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.599G>A	8.37:g.52744111C>T	ENSP00000353739:p.Arg200Gln		52906664	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.8|28.8	4.953493|4.953493	0.92660|0.92660	.|.	.|.	ENSG00000168300|ENSG00000168300	ENST00000519554|ENST00000360540;ENST00000544451;ENST00000522514	.|T;T;T	.|0.47177	.|0.85;0.85;0.85	5.45|5.45	4.55|4.55	0.56014|0.56014	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.73225|0.73225	0.3560|0.3560	M|M	0.90252|0.90252	3.1|3.1	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P;D	.|0.89917	.|0.998;0.681;1.0	.|D;B;D	.|0.87578	.|0.988;0.071;0.998	T|T	0.79327|0.79327	-0.1849|-0.1849	5|10	.|0.87932	.|D	.|0	-15.0532|-15.0532	13.3667|13.3667	0.60689|0.60689	0.0:0.9211:0.0:0.0789|0.0:0.9211:0.0:0.0789	.|.	.|70;124;200	.|B4E2B4;F5H1M8;Q96MG8	.|.;.;PCMD1_HUMAN	K|Q	92|200;124;200	.|ENSP00000353739:R200Q;ENSP00000444026:R124Q;ENSP00000428099:R200Q	.|ENSP00000353739:R200Q	E|R	-|-	1|2	0|0	PCMTD1|PCMTD1	52906664|52906664	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.626000|7.626000	0.83164|0.83164	1.231000|1.231000	0.43661|0.43661	0.557000|0.557000	0.71058|0.71058	GAA|CGA		0.358	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		T	52744111	C	T	52744111	3	4	61	1	0	0	0	0	1	0	0	0	11617	884	31	1	482	1	PCMTD1	8	52744111	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	407886	52744111	93619911	5881	13866										
PCMTD1	115294	broad.mit.edu	37	chr8	52746175	52746175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagctccacaataaattCgatcatactgatgactgtca	5	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:52746175C>T	ENST00000360540.5	-	5	891	c.485G>A	c.(484-486)cGa>cAa	p.R162Q	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.R86Q|PCMTD1_ENST00000522514.1_Missense_Mutation_p.R162Q	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	162						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.R162Q(2)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				ACAATAAATTCGATCATACTG	0.363																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	8											144	129	134					8																	52746175		2203	4300	6503	52908728	SO:0001583	missense	115294				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.485G>A	8.37:g.52746175C>T	ENSP00000353739:p.Arg162Gln		52908728	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.5|27.5	4.836588|4.836588	0.91117|0.91117	.|.	.|.	ENSG00000168300|ENSG00000168300	ENST00000519554|ENST00000360540;ENST00000544451;ENST00000522514	.|T;T;T	.|0.41400	.|1.0;1.0;1.0	5.2|5.2	3.38|3.38	0.38709|0.38709	.|.	.|0.124846	.|0.56097	.|D	.|0.000034	T|T	0.68118|0.68118	0.2966|0.2966	M|M	0.89534|0.89534	3.04|3.04	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;P;D	.|0.89917	.|0.998;0.998;0.545;1.0	.|D;D;B;D	.|0.97110	.|0.992;0.992;0.039;1.0	T|T	0.74200|0.74200	-0.3742|-0.3742	5|10	.|0.59425	.|D	.|0.04	-42.8563|-42.8563	12.0488|12.0488	0.53495|0.53495	0.0:0.8575:0.0:0.1425|0.0:0.8575:0.0:0.1425	.|.	.|79;32;86;162	.|Q658R8;B4E2B4;F5H1M8;Q96MG8	.|.;.;.;PCMD1_HUMAN	K|Q	54|162;86;162	.|ENSP00000353739:R162Q;ENSP00000444026:R86Q;ENSP00000428099:R162Q	.|ENSP00000353739:R162Q	E|R	-|-	1|2	0|0	PCMTD1|PCMTD1	52908728|52908728	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	6.060000|6.060000	0.71141|0.71141	1.195000|1.195000	0.43115|0.43115	0.591000|0.591000	0.81541|0.81541	GAA|CGA		0.363	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		T	52746175	C	T	52746175	3	4	61	1	0	0	0	0	1	0	0	0	11617	884	31	1	600	1	PCMTD1	8	52746175	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2064	52746175	93617847	5882	13867										
ST18	9705	broad.mit.edu	37	chr8	53028876	53028876	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaaggcttgaaatgagagCttggcttagacctgccagct	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:53028876C>T	ENST00000276480.7	-	25	3645	c.2962G>A	c.(2962-2964)Gct>Act	p.A988T		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	988					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A988T(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				GAAATGAGAGCTTGGCTTAGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											223	165	185					8																	53028876		2203	4300	6503	53191429	SO:0001583	missense	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2962G>A	8.37:g.53028876C>T	ENSP00000276480:p.Ala988Thr		53191429	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	36	5.932401	0.97116	.	.	ENSG00000147488	ENST00000276480	T	0.48836	0.8	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.68375	0.2994	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.65602	-0.6128	10	0.46703	T	0.11	-15.4891	20.0735	0.97734	0.0:1.0:0.0:0.0	.	988	O60284	ST18_HUMAN	T	988	ENSP00000276480:A988T	ENSP00000276480:A988T	A	-	1	0	ST18	53191429	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	6.009000	0.70745	2.745000	0.94114	0.655000	0.94253	GCT		0.448	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028876	C	T	53028876	3	4	61	1	0	0	0	0	1	0	0	0	15251	797	28	3	189	3	ST18	8	53028876	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	282701	53028876	93335146	5883	13868										
ST18	9705	broad.mit.edu	37	chr8	53038698	53038698	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgagaggacatccagatAagctgtgaaaatagaaattg	10	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:53038698A>C	ENST00000276480.7	-	23	3352	c.2669T>G	c.(2668-2670)tTa>tGa	p.L890*		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	890					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.L890*(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				ACATCCAGATAAGCTGTGAAA	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											142	122	129					8																	53038698		2203	4300	6503	53201251	SO:0001587	stop_gained	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2669T>G	8.37:g.53038698A>C	ENSP00000276480:p.Leu890*		53201251	Q17RY1	Nonsense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	A	46	12.380587	0.99662	.	.	ENSG00000147488	ENST00000276480	.	.	.	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6512	16.1063	0.81225	1.0:0.0:0.0:0.0	.	.	.	.	X	890	.	ENSP00000276480:L890X	L	-	2	0	ST18	53201251	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	8.750000	0.91623	2.205000	0.71048	0.528000	0.53228	TTA		0.348	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			C	53038698	A	C	53038698	4	2	61	1	0	0	0	0	0	1	0	0	15251	372	13	4	490	4	ST18	8	53038698	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9822	53038698	93325324	5884	13869										
RB1CC1	9821	broad.mit.edu	37	chr8	53569748	53569748	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcagtttcctttattaGtccgtcaagtttaccttcat	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:53569748G>T	ENST00000025008.5	-	15	3164	c.2641C>A	c.(2641-2643)Cta>Ata	p.L881I	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Missense_Mutation_p.L881I|RB1CC1_ENST00000539297.1_Missense_Mutation_p.L881I	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	881					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.L881I(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TCCTTTATTAGTCCGTCAAGT	0.274																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - Missense(1)	large_intestine(1)	8											37	42	40					8																	53569748		2179	4257	6436	53732301	SO:0001583	missense	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2641C>A	8.37:g.53569748G>T	ENSP00000025008:p.Leu881Ile		53732301	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678005	0.47886	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.04406	3.63;3.63;3.63	5.38	3.2	0.36748	.	0.077566	0.53938	D	0.000053	T	0.06735	0.0172	L	0.34521	1.04	0.40030	D	0.975527	D;D	0.59767	0.986;0.976	P;P	0.55713	0.782;0.609	T	0.45381	-0.9265	10	0.31617	T	0.26	-8.6832	4.3385	0.11097	0.4553:0.0:0.5447:0.0	.	881;881	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	I	881	ENSP00000025008:L881I;ENSP00000396067:L881I;ENSP00000445960:L881I	ENSP00000025008:L881I	L	-	1	2	RB1CC1	53732301	0.986000	0.35501	0.275000	0.24674	0.915000	0.54546	2.254000	0.43214	1.398000	0.46701	0.563000	0.77884	CTA		0.274	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53569748	G	T	53569748	3	4	61	1	0	0	0	0	1	0	0	0	13136	1020	36	2	2183	2	RB1CC1	8	53569748	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	531050	53569748	92794274	5885	13870										
RB1CC1	9821	broad.mit.edu	37	chr8	53596476	53596476	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtaggtacacactcttcGatctgcagccatgcattctc	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:53596476G>A	ENST00000025008.5	-	4	692	c.169C>T	c.(169-171)Cga>Tga	p.R57*	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Nonsense_Mutation_p.R57*|RB1CC1_ENST00000539297.1_Nonsense_Mutation_p.R57*	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	57					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.R57*(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CACACTCTTCGATCTGCAGCC	0.448																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - Nonsense(1)	large_intestine(1)	8											130	103	113					8																	53596476		2203	4300	6503	53759029	SO:0001587	stop_gained	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.169C>T	8.37:g.53596476G>A	ENSP00000025008:p.Arg57*		53759029	Q86YR4|Q8WVU9|Q92601	Nonsense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	G	39	7.436678	0.98282	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297;ENST00000518710;ENST00000517963	.	.	.	4.99	3.14	0.36123	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.8293	13.2393	0.59987	0.0:0.0:0.4052:0.5948	.	.	.	.	X	57;57;57;5;53	.	ENSP00000025008:R57X	R	-	1	2	RB1CC1	53759029	1.000000	0.71417	0.968000	0.41197	0.965000	0.64279	1.930000	0.40124	0.572000	0.29383	-0.319000	0.08680	CGA		0.448	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		A	53596476	G	A	53596476	4	1	61	1	0	0	0	0	0	1	0	0	13136	1066	37	1	4699	1	RB1CC1	8	53596476	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26728	53596476	92767546	5886	13871										
OPRK1	4986	broad.mit.edu	37	chr8	54142010	54142010	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttttcatcaagaaaggcGtagagaatgggattcaggct	12	5	3	2	rs77333617		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:54142010G>A	ENST00000265572.3	-	4	1287	c.990C>T	c.(988-990)taC>taT	p.Y330Y	RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000524278.1_Silent_p.Y241Y|OPRK1_ENST00000520287.1_Silent_p.Y330Y	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	330					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)	p.Y330Y(1)		NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CAAGAAAGGCGTAGAGAATGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	8						G		0,4406		0,0,2203	80	73	75		990	-4.5	1	8	dbSNP_131	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OPRK1	NM_000912.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		330/381	54142010	1,13005	2203	4300	6503	54304563	SO:0001819	synonymous_variant	4986				CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.990C>T	8.37:g.54142010G>A			54304563	E5RHC9|Q499G4	Silent	SNP	ENST00000265572.3	37	CCDS6152.1																																																																																				0.517	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			A	54142010	G	A	54142010	2	1	61	1	0	0	0	0	0	0	0	1	10916	1140	40	1		1	OPRK1	8	54142010	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	545534	54142010	92222012	5887	13872										
RGS20	8601	broad.mit.edu	37	chr8	54866734	54866734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcattccgtgaattcctccGaacagaattcagtgaggaaa	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:54866734G>A	ENST00000297313.3	+	5	934	c.842G>A	c.(841-843)cGa>cAa	p.R281Q	RGS20_ENST00000522225.1_Missense_Mutation_p.R15Q|RGS20_ENST00000344277.6_Missense_Mutation_p.R166Q|RGS20_ENST00000517405.1_3'UTR|RGS20_ENST00000276500.4_Missense_Mutation_p.R134Q	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	281	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R281Q(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			GAATTCCTCCGAACAGAATTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	8											75	74	74					8																	54866734		2203	4300	6503	55029287	SO:0001583	missense	8601			AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.842G>A	8.37:g.54866734G>A	ENSP00000297313:p.Arg281Gln		55029287	Q96BG9	Missense_Mutation	SNP	ENST00000297313.3	37	CCDS6155.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876302	0.72180	.	.	ENSG00000147509	ENST00000297313;ENST00000344277;ENST00000522225;ENST00000276500	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	4.78	3.91	0.45181	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.49236	0.1545	M	0.64404	1.975	0.58432	D	0.999999	P;D;D;D;D	0.64830	0.693;0.987;0.994;0.994;0.99	B;P;D;D;P	0.63597	0.289;0.887;0.916;0.916;0.79	T	0.52495	-0.8568	10	0.72032	D	0.01	.	13.3209	0.60432	0.077:0.0:0.923:0.0	.	45;73;134;166;281	O76081-4;O76081-3;O76081-6;O76081-2;O76081	.;.;.;.;RGS20_HUMAN	Q	281;166;15;134	ENSP00000297313:R281Q;ENSP00000344630:R166Q;ENSP00000430627:R15Q;ENSP00000276500:R134Q	ENSP00000276500:R134Q	R	+	2	0	RGS20	55029287	1.000000	0.71417	0.389000	0.26208	0.384000	0.30261	9.813000	0.99286	1.133000	0.42147	0.563000	0.77884	CGA		0.433	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			A	54866734	G	A	54866734	3	1	61	1	0	0	0	0	1	0	0	0	13340	1058	37	1	933	1	RGS20	8	54866734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	724724	54866734	91497288	5888	13873										
TCEA1	6917	broad.mit.edu	37	chr8	54900682	54900682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggacttaccccctgttCgaagagctgcagcaagcatc	9	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:54900682C>T	ENST00000521604.2	-	5	861	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000522635.1_Intron|TCEA1_ENST00000396401.3_Missense_Mutation_p.R132Q	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	153	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R153Q(1)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			ACCCCCTGTTCGAAGAGCTGC	0.478			T	PLAG1	salivary adenoma																																		Dom	yes		8	8q11.2	6917	"transcription elongation factor A (SII), 1"		E	1	Substitution - Missense(1)	large_intestine(1)	8											75	76	76					8																	54900682		2090	4217	6307	55063235	SO:0001583	missense	6917			X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"General transcription factors"	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.458G>A	8.37:g.54900682C>T	ENSP00000428426:p.Arg153Gln		55063235	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	37	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.537366	0.27475	.	.	ENSG00000187735	ENST00000396401;ENST00000521604	T;T	0.41400	1.0;1.0	5.49	4.6	0.57074	Transcription elongation factor S-IIM (1);Transcription elongation factor S-II, central domain (4);	0.192988	0.44902	D	0.000419	T	0.14313	0.0346	N	0.01464	-0.85	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.11329	0.006;0.004	T	0.21690	-1.0238	10	0.09084	T	0.74	-8.5502	8.7074	0.34363	0.0:0.7861:0.0:0.2139	.	132;153	P23193-2;P23193	.;TCEA1_HUMAN	Q	132;153	ENSP00000395483:R132Q;ENSP00000428426:R153Q	ENSP00000395483:R132Q	R	-	2	0	TCEA1	55063235	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	2.836000	0.48183	2.749000	0.94314	0.491000	0.48974	CGA		0.478	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756		T	54900682	C	T	54900682	3	4	61	1	0	0	0	0	1	0	0	0	15706	884	31	1	471	1	TCEA1	8	54900682	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33948	54900682	91463340	5889	13874										
TCEA1	6917	broad.mit.edu	37	chr8	54906286	54906286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggttctttcttcttttCgtcaaggtctttctcagttg	8	9	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:54906286C>T	ENST00000521604.2	-	4	665	c.262G>A	c.(262-264)Gaa>Aaa	p.E88K	TCEA1_ENST00000520534.1_Missense_Mutation_p.E88K|TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000522635.1_Intron|TCEA1_ENST00000396401.3_Missense_Mutation_p.E67K	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	88					DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E88K(2)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			TTCTTCTTTTCGTCAAGGTCT	0.353			T	PLAG1	salivary adenoma																																		Dom	yes		8	8q11.2	6917	"transcription elongation factor A (SII), 1"		E	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	8											199	184	189					8																	54906286		1823	4086	5909	55068839	SO:0001583	missense	6917			X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"General transcription factors"	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.262G>A	8.37:g.54906286C>T	ENSP00000428426:p.Glu88Lys		55068839	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	37	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.077841	0.55753	.	.	ENSG00000187735	ENST00000396401;ENST00000521604;ENST00000520534	.	.	.	4.89	4.89	0.63831	Transcription factor IIS, N-terminal (2);	0.294524	0.36815	N	0.002382	T	0.50990	0.1648	L	0.34521	1.04	0.80722	D	1	B;B	0.21381	0.055;0.003	B;B	0.19946	0.027;0.002	T	0.47686	-0.9098	9	0.10111	T	0.7	-27.0655	18.4354	0.90643	0.0:1.0:0.0:0.0	.	67;88	P23193-2;P23193	.;TCEA1_HUMAN	K	67;88;88	.	ENSP00000395483:E67K	E	-	1	0	TCEA1	55068839	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.016000	0.76393	2.407000	0.81776	0.591000	0.81541	GAA		0.353	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756		T	54906286	C	T	54906286	3	4	61	1	0	0	0	0	1	0	0	0	15706	893	31	1	671	1	TCEA1	8	54906286	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5604	54906286	91457736	5890	13875										
RP1	6101	broad.mit.edu	37	chr8	55534069	55534069	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtcacccagagcttcgaGgcatttctacagcacctgac	10	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55534069G>T	ENST00000220676.1	+	2	691	c.543G>T	c.(541-543)gaG>gaT	p.E181D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	181	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.E181D(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			AGAGCTTCGAGGCATTTCTAC	0.632																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											117	119	119					8																	55534069		2203	4300	6503	55696622	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.543G>T	8.37:g.55534069G>T	ENSP00000220676:p.Glu181Asp		55696622		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.982217	0.53827	.	.	ENSG00000104237	ENST00000220676	D	0.89810	-2.57	5.14	3.3	0.37823	Doublecortin domain (5);	0.113744	0.39020	N	0.001492	D	0.82770	0.5109	L	0.47716	1.5	0.35719	D	0.816995	P	0.42908	0.793	B	0.40602	0.334	T	0.82196	-0.0577	10	0.32370	T	0.25	-8.972	6.7467	0.23466	0.1596:0.1437:0.6967:0.0	.	181	P56715	RP1_HUMAN	D	181	ENSP00000220676:E181D	ENSP00000220676:E181D	E	+	3	2	RP1	55696622	0.901000	0.30685	0.925000	0.36789	0.570000	0.35934	0.124000	0.15728	1.145000	0.42336	0.650000	0.86243	GAG		0.632	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55534069	G	T	55534069	3	4	61	1	0	0	0	0	1	0	0	0	13569	991	35	2	545	2	RP1	8	55534069	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	627783	55534069	90829953	5891	13876										
RP1	6101	broad.mit.edu	37	chr8	55537349	55537349	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaaagtacttggccttaGaaaagaatgattctcagaat	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55537349G>T	ENST00000220676.1	+	4	1055	c.907G>T	c.(907-909)Gaa>Taa	p.E303*		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	303					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.E303*(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			CTTGGCCTTAGAAAAGAATGA	0.318																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Nonsense(1)	large_intestine(1)	8											61	66	64					8																	55537349		2202	4298	6500	55699902	SO:0001587	stop_gained	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.907G>T	8.37:g.55537349G>T	ENSP00000220676:p.Glu303*		55699902		Nonsense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530276	0.96446	.	.	ENSG00000104237	ENST00000220676	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	12.1332	0.53955	0.0782:0.0:0.9218:0.0	.	.	.	.	X	303	.	ENSP00000220676:E303X	E	+	1	0	RP1	55699902	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.216000	0.51176	2.432000	0.82394	0.655000	0.94253	GAA		0.318	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55537349	G	T	55537349	4	4	61	1	0	0	0	0	0	1	0	0	13569	943	33	2	917	2	RP1	8	55537349	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3280	55537349	90826673	5892	13877										
RP1	6101	broad.mit.edu	37	chr8	55538311	55538312	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaataactctggaactgacINSaaaaatatttctgaggctcc							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55538311_55538312insA	ENST00000220676.1	+	4	2017_2018	c.1869_1870insA	c.(1870-1872)aaafs	p.K624fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	624					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.N625fs*4(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			CTGGAACTGACAAAAATATTTC	0.371																																					Colon(91;1014 1389 7634 14542 40420)											1	Insertion - Frameshift(1)	large_intestine(1)	8																																								55700865	SO:0001589	frameshift_variant	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.1874dupA	8.37:g.55538316_55538316dupA	ENSP00000220676:p.Lys624fs		55700864		Frame_Shift_Ins	INS	ENST00000220676.1	37	CCDS6160.1																																																																																				0.371	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55538312	-	A	55538311	7	5	61	1	0	1	1	0	0	0	0	0	13569	477	17	0	1879	0	RP1	8	55538311	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	962	55538311	90825711	5893	13878										
RP1	6101	broad.mit.edu	37	chr8	55539536	55539536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtcacagtcagctattAatgatcataatactaaaagt	5	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55539536A>G	ENST00000220676.1	+	4	3242	c.3094A>G	c.(3094-3096)Aat>Gat	p.N1032D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1032					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.N1032D(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			GTCAGCTATTAATGATCATAA	0.383																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											160	175	170					8																	55539536		2203	4300	6503	55702089	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3094A>G	8.37:g.55539536A>G	ENSP00000220676:p.Asn1032Asp		55702089		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	0.211	-1.036591	0.02013	.	.	ENSG00000104237	ENST00000220676	T	0.21031	2.03	5.65	-1.55	0.08558	.	0.779574	0.11892	N	0.519542	T	0.04861	0.0131	N	0.01482	-0.84	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.38329	-0.9666	10	0.18710	T	0.47	.	0.4381	0.00482	0.3682:0.2019:0.1247:0.3053	.	1032	P56715	RP1_HUMAN	D	1032	ENSP00000220676:N1032D	ENSP00000220676:N1032D	N	+	1	0	RP1	55702089	0.000000	0.05858	0.001000	0.08648	0.117000	0.20001	0.086000	0.14935	0.191000	0.20236	0.533000	0.62120	AAT		0.383	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55539536	A	G	55539536	3	3	61	1	0	0	0	0	1	0	0	0	13569	362	13	4	3104	4	RP1	8	55539536	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1225	55539536	90824486	5894	13879										
RP1	6101	broad.mit.edu	37	chr8	55540919	55540919	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagcaagccactgaagaaTtaatccaagaagaggtagag	12	6	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55540919T>A	ENST00000220676.1	+	4	4625	c.4477T>A	c.(4477-4479)Tta>Ata	p.L1493I		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1493					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.L1493I(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			CACTGAAGAATTAATCCAAGA	0.313																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											44	49	47					8																	55540919		2198	4297	6495	55703472	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4477T>A	8.37:g.55540919T>A	ENSP00000220676:p.Leu1493Ile		55703472		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	3.590	-0.083787	0.07141	.	.	ENSG00000104237	ENST00000220676	T	0.66460	-0.21	5.48	-3.75	0.04372	.	1.715750	0.03490	N	0.216436	T	0.52468	0.1736	L	0.36672	1.1	0.09310	N	1	B	0.24258	0.1	B	0.21708	0.036	T	0.40869	-0.9540	10	0.41790	T	0.15	.	5.2068	0.15295	0.2255:0.3327:0.0:0.4419	.	1493	P56715	RP1_HUMAN	I	1493	ENSP00000220676:L1493I	ENSP00000220676:L1493I	L	+	1	2	RP1	55703472	0.009000	0.17119	0.000000	0.03702	0.088000	0.18126	0.043000	0.13971	-0.201000	0.10284	0.533000	0.62120	TTA		0.313	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55540919	T	A	55540919	3	1	61	1	0	0	0	0	1	0	0	0	13569	1490	52	5	4487	5	RP1	8	55540919	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1383	55540919	90823103	5895	13880										
RP1	6101	broad.mit.edu	37	chr8	55541631	55541631	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacaaaatgatgatagcaGaatcctcacagacatagagg	8	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:55541631G>T	ENST00000220676.1	+	4	5337	c.5189G>T	c.(5188-5190)aGa>aTa	p.R1730I		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1730					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.R1730I(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			GATGATAGCAGAATCCTCACA	0.403																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											123	117	119					8																	55541631		2203	4300	6503	55704184	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5189G>T	8.37:g.55541631G>T	ENSP00000220676:p.Arg1730Ile		55704184		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	8.534	0.871773	0.17322	.	.	ENSG00000104237	ENST00000220676	T	0.25250	1.81	5.93	4.11	0.48088	.	0.112539	0.39544	N	0.001332	T	0.23766	0.0575	L	0.59436	1.845	0.26259	N	0.978606	B	0.34372	0.451	B	0.31869	0.137	T	0.25745	-1.0123	10	0.87932	D	0	-18.5254	8.2939	0.31973	0.0637:0.1145:0.7031:0.1187	.	1730	P56715	RP1_HUMAN	I	1730	ENSP00000220676:R1730I	ENSP00000220676:R1730I	R	+	2	0	RP1	55704184	0.651000	0.27340	0.023000	0.16930	0.047000	0.14425	0.802000	0.27069	1.495000	0.48549	0.655000	0.94253	AGA		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55541631	G	T	55541631	3	4	61	1	0	0	0	0	1	0	0	0	13569	942	33	2	5199	2	RP1	8	55541631	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	712	55541631	90822391	5896	13881										
TGS1	96764	broad.mit.edu	37	chr8	56686217	56686217	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgcgtggcggaaatgtttCtcttcattgaggagcgggag	16	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:56686217C>A	ENST00000260129.5	+	1	517	c.40C>A	c.(40-42)Ctc>Atc	p.L14I	TMEM68_ENST00000522576.1_5'Flank|TMEM68_ENST00000523073.1_5'Flank|TMEM68_ENST00000519784.1_5'Flank|TMEM68_ENST00000434581.2_5'Flank|TMEM68_ENST00000521229.1_5'Flank|TMEM68_ENST00000334667.2_5'Flank	NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	14					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)	p.L14I(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			GGAAATGTTTCTCTTCATTGA	0.547																																					Esophageal Squamous(34;275 823 4842 34837 48447)											1	Substitution - Missense(1)	large_intestine(1)	8											134	132	132					8																	56686217		2203	4300	6503	56848771	SO:0001583	missense	96764			AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.40C>A	8.37:g.56686217C>A	ENSP00000260129:p.Leu14Ile		56848771	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821286	0.50633	.	.	ENSG00000137574	ENST00000260129	T	0.14766	2.48	4.97	4.1	0.47936	.	0.237231	0.36303	N	0.002661	T	0.18425	0.0442	M	0.73962	2.25	0.29313	N	0.867902	P	0.48294	0.908	B	0.41860	0.368	T	0.15122	-1.0448	10	0.59425	D	0.04	-4.6848	10.5623	0.45152	0.0:0.9104:0.0:0.0896	.	14	Q96RS0	TGS1_HUMAN	I	14	ENSP00000260129:L14I	ENSP00000260129:L14I	L	+	1	0	TGS1	56848771	0.932000	0.31603	0.856000	0.33681	0.597000	0.36814	1.910000	0.39927	1.455000	0.47813	0.655000	0.94253	CTC		0.547	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		A	56686217	C	A	56686217	3	1	61	1	0	0	0	0	1	0	0	0	15876	913	32	2	42	2	TGS1	8	56686217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1144586	56686217	89677805	5897	13882										
TGS1	96764	broad.mit.edu	37	chr8	56699470	56699470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacagagccaattagattCctgtacaagtcatgatggtc	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:56699470C>T	ENST00000260129.5	+	4	1490	c.1013C>T	c.(1012-1014)tCc>tTc	p.S338F		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	338					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)	p.S338F(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CAATTAGATTCCTGTACAAGT	0.403																																					Esophageal Squamous(34;275 823 4842 34837 48447)											1	Substitution - Missense(1)	large_intestine(1)	8											76	71	73					8																	56699470		2203	4300	6503	56862024	SO:0001583	missense	96764			AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1013C>T	8.37:g.56699470C>T	ENSP00000260129:p.Ser338Phe		56862024	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	C	7.285	0.609864	0.14066	.	.	ENSG00000137574	ENST00000260129	T	0.16897	2.31	5.57	0.356	0.16074	.	0.803369	0.11641	N	0.543762	T	0.17408	0.0418	M	0.63428	1.95	0.09310	N	1	P;P	0.45902	0.868;0.868	B;B	0.39805	0.24;0.31	T	0.12091	-1.0561	10	0.62326	D	0.03	-0.0067	8.4292	0.32746	0.0:0.3326:0.5228:0.1446	.	338;338	B2RBJ7;Q96RS0	.;TGS1_HUMAN	F	338	ENSP00000260129:S338F	ENSP00000260129:S338F	S	+	2	0	TGS1	56862024	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.081000	0.14823	-0.002000	0.14469	0.655000	0.94253	TCC		0.403	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		T	56699470	C	T	56699470	3	4	61	1	0	0	0	0	1	0	0	0	15876	855	30	3	1027	3	TGS1	8	56699470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13253	56699470	89664552	5898	13883										
TGS1	96764	broad.mit.edu	37	chr8	56725651	56725651	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaataatattgtttattttCttccaagaaatgctgatatt	4	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:56725651C>A	ENST00000260129.5	+	12	2890	c.2413C>A	c.(2413-2415)Ctt>Att	p.L805I		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	805	Sufficient for catalytic activity.				7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)	p.L805I(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			TGTTTATTTTCTTCCAAGAAA	0.323																																					Esophageal Squamous(34;275 823 4842 34837 48447)											1	Substitution - Missense(1)	large_intestine(1)	8											54	54	54					8																	56725651		2201	4298	6499	56888205	SO:0001583	missense	96764			AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.2413C>A	8.37:g.56725651C>A	ENSP00000260129:p.Leu805Ile		56888205	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020952	0.93462	.	.	ENSG00000137574	ENST00000260129	T	0.69175	-0.38	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.86260	0.5890	M	0.91612	3.225	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.88545	0.3112	10	0.66056	D	0.02	-18.1781	19.6223	0.95663	0.0:1.0:0.0:0.0	.	805	Q96RS0	TGS1_HUMAN	I	805	ENSP00000260129:L805I	ENSP00000260129:L805I	L	+	1	0	TGS1	56888205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.402000	0.52608	2.635000	0.89317	0.650000	0.86243	CTT		0.323	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		A	56725651	C	A	56725651	3	1	61	1	0	0	0	0	1	0	0	0	15876	913	32	2	2459	2	TGS1	8	56725651	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26181	56725651	89638371	5899	13884										
PLAG1	5324	broad.mit.edu	37	chr8	57080001	57080001	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcagatgatctttccggtGaaacattttctcacaataat	5	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:57080001G>T	ENST00000316981.3	-	5	783	c.304C>A	c.(304-306)Cac>Aac	p.H102N	PLAG1_ENST00000423799.2_Missense_Mutation_p.H20N|PLAG1_ENST00000429357.2_Missense_Mutation_p.H102N	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	102	Decreased nuclear import with localization in the nucleus but also in the cytoplasm.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H102N(1)	CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			TCTTTCCGGTGAAACATTTTC	0.383			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	1	Substitution - Missense(1)	large_intestine(1)	8											90	75	80					8																	57080001		2203	4300	6503	57242555	SO:0001583	missense	5324			U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.304C>A	8.37:g.57080001G>T	ENSP00000325546:p.His102Asn		57242555	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	37	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663703	0.47572	.	.	ENSG00000181690	ENST00000316981;ENST00000423799;ENST00000429357	T;T;T	0.75260	2.3;-0.92;2.3	5.82	5.82	0.92795	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.043426	0.85682	N	0.000000	T	0.73361	0.3577	N	0.05158	-0.105	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.72083	-0.4397	10	0.18276	T	0.48	-18.9289	20.0812	0.97776	0.0:0.0:1.0:0.0	.	102	Q6DJT9	PLAG1_HUMAN	N	102;20;102	ENSP00000325546:H102N;ENSP00000404067:H20N;ENSP00000416537:H102N	ENSP00000325546:H102N	H	-	1	0	PLAG1	57242555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.744000	0.94065	0.585000	0.79938	CAC		0.383	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		T	57080001	G	T	57080001	3	4	61	1	0	0	0	0	1	0	0	0	12049	1290	45	2	1202	2	PLAG1	8	57080001	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	354350	57080001	89284021	5900	13885										
SDR16C5	195814	broad.mit.edu	37	chr8	57219241	57219241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggacatacttaccctgtaGtacaaccttcaaacattcca	4	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:57219241G>A	ENST00000303749.3	-	5	1341	c.704C>T	c.(703-705)aCt>aTt	p.T235I	SDR16C5_ENST00000396721.2_Missense_Mutation_p.T191I|SDR16C5_ENST00000522671.1_Missense_Mutation_p.T235I	NM_138969.2	NP_620419.2	Q8N3Y7	RDHE2_HUMAN	short chain dehydrogenase/reductase family 16C, member 5	235					detection of light stimulus involved in visual perception (GO:0050908)|keratinocyte proliferation (GO:0043616)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	retinol dehydrogenase activity (GO:0004745)	p.T235I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)	16						TTACCCTGTAGTACAACCTTC	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	8											69	69	69					8																	57219241		2203	4300	6503	57381795	SO:0001583	missense	195814				CCDS6167.1	8q12.1	2011-09-20			ENSG00000170786	ENSG00000170786	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	30311	protein-coding gene	gene with protein product		608989				12372410	Standard	NM_138969		Approved	RDHE2, RDH-E2	uc003xsy.1	Q8N3Y7	OTTHUMG00000164311	ENST00000303749.3:c.704C>T	8.37:g.57219241G>A	ENSP00000307607:p.Thr235Ile		57381795	B4DGK2|Q330K3|Q8TDV9|Q96LX1	Missense_Mutation	SNP	ENST00000303749.3	37	CCDS6167.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.367936	0.24771	.	.	ENSG00000170786	ENST00000396721;ENST00000303749;ENST00000522671	D;D;T	0.89270	-2.49;-2.49;0.75	5.55	4.65	0.58169	NAD(P)-binding domain (1);	0.641961	0.16942	N	0.193226	D	0.85741	0.5767	L	0.52266	1.64	0.09310	N	1	B;B;B	0.19935	0.024;0.04;0.007	B;B;B	0.24701	0.034;0.055;0.015	T	0.77078	-0.2721	10	0.49607	T	0.09	.	10.2693	0.43473	0.0:0.2351:0.5682:0.1967	.	191;235;235	Q8N3Y7-2;G3V145;Q8N3Y7	.;.;RDHE2_HUMAN	I	191;235;235	ENSP00000379947:T191I;ENSP00000307607:T235I;ENSP00000431010:T235I	ENSP00000307607:T235I	T	-	2	0	SDR16C5	57381795	0.002000	0.14202	0.379000	0.26080	0.856000	0.48823	1.270000	0.33086	1.291000	0.44653	0.655000	0.94253	ACT		0.284	SDR16C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378235.1	NM_138969		A	57219241	G	A	57219241	3	1	61	1	0	0	0	0	1	0	0	0	14008	1029	36	3	237	3	SDR16C5	8	57219241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139240	57219241	89144781	5901	13886										
FAM110B	90362	broad.mit.edu	37	chr8	59059479	59059479	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctcccaagcccaaaatCgcagccatcgcctccatgaa	6	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59059479C>T	ENST00000361488.3	+	5	1570	c.690C>T	c.(688-690)atC>atT	p.I230I	FAM110B_ENST00000520369.1_Intron	NM_147189.2	NP_671722.1	Q8TC76	F110B_HUMAN	family with sequence similarity 110, member B	230						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.I230I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				AGCCCAAAATCGCAGCCATCG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	8											78	84	82					8																	59059479		2203	4300	6503	59222033	SO:0001819	synonymous_variant	90362			U79298	CCDS6170.1	8q12.1	2007-06-21	2007-03-21	2007-03-21		ENSG00000169122			28587	protein-coding gene	gene with protein product		611394	"chromosome 8 open reading frame 72"	C8orf72		8619474, 9110174, 17499476	Standard	XM_005251324		Approved	MGC39325	uc003xtj.1	Q8TC76		ENST00000361488.3:c.690C>T	8.37:g.59059479C>T			59222033	Q5BM08|Q9Y4K2	Silent	SNP	ENST00000361488.3	37	CCDS6170.1																																																																																				0.627	FAM110B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378095.2	NM_147189		T	59059479	C	T	59059479	2	4	61	1	0	0	0	0	0	0	0	1	5413	874	31	1		1	FAM110B	8	59059479	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1840238	59059479	87304543	5902	13887										
UBXN2B	137886	broad.mit.edu	37	chr8	59358570	59358570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtgccaacaacaaaaaTtcaaatcaggttagcagatg	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59358570T>A	ENST00000399598.2	+	7	898	c.776T>A	c.(775-777)aTt>aAt	p.I259N		NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	259	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.I259N(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						ACAACAAAAATTCAAATCAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											133	118	123					8																	59358570		1854	4088	5942	59521124	SO:0001583	missense	137886			AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"UBX domain containing"	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.776T>A	8.37:g.59358570T>A	ENSP00000382507:p.Ile259Asn		59521124	B3KWZ3	Missense_Mutation	SNP	ENST00000399598.2	37	CCDS43741.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.541145	0.85917	.	.	ENSG00000215114	ENST00000399598	T	0.56941	0.43	5.3	5.3	0.74995	UBX (3);	0.151143	0.29822	U	0.011119	T	0.79323	0.4426	H	0.95780	3.72	0.54753	D	0.999985	D	0.53885	0.963	D	0.64595	0.927	D	0.85473	0.1174	10	0.87932	D	0	-4.5069	14.163	0.65459	0.0:0.0:0.0:1.0	.	259	Q14CS0	UBX2B_HUMAN	N	259	ENSP00000382507:I259N	ENSP00000382507:I259N	I	+	2	0	UBXN2B	59521124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.607000	0.82883	2.157000	0.67596	0.529000	0.55759	ATT		0.373	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619		A	59358570	T	A	59358570	3	1	61	1	0	0	0	0	1	0	0	0	16955	1493	52	5	802	5	UBXN2B	8	59358570	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	299091	59358570	87005452	5903	13888										
CYP7A1	1581	broad.mit.edu	37	chr8	59409435	59409435	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggctggaaagactttgtcGaattgcttgaagttgtcaag	13	5	1	2	rs370087640		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59409435G>A	ENST00000301645.3	-	3	773	c.636C>T	c.(634-636)ttC>ttT	p.F212F		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	212					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cholesterol catabolic process (GO:0006707)|cholesterol homeostasis (GO:0042632)|regulation of bile acid biosynthetic process (GO:0070857)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	cholesterol 7-alpha-monooxygenase activity (GO:0008123)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.F212F(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(1)|urinary_tract(1)	34		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				AGACTTTGTCGAATTGCTTGA	0.478									Neonatal Giant Cell Hepatitis																																							1	Substitution - coding silent(1)	large_intestine(1)	8						G		1,4405	2.1+/-5.4	0,1,2202	141	138	139		636	0.8	0.9	8		139	0,8600		0,0,4300	no	coding-synonymous	CYP7A1	NM_000780.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		212/505	59409435	1,13005	2203	4300	6503	59571989	SO:0001819	synonymous_variant	1581	Familial Cancer Database	Neonatal Hemochromatosis	M89803	CCDS6171.1	8q11-q12	2010-05-04	2003-01-14		ENSG00000167910	ENSG00000167910	1.14.13.17	"Cytochrome P450s"	2651	protein-coding gene	gene with protein product	"cholesterol 7 alpha-monooxygenase"	118455	"cytochrome P450, subfamily VIIA (cholesterol 7 alpha-monooxygenase), polypeptide 1"	CYP7		1358792	Standard	NM_000780		Approved		uc003xtm.4	P22680	OTTHUMG00000164301	ENST00000301645.3:c.636C>T	8.37:g.59409435G>A			59571989	P78454|Q3MIL8|Q7KZ19	Silent	SNP	ENST00000301645.3	37	CCDS6171.1																																																																																				0.478	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		A	59409435	G	A	59409435	2	1	61	1	0	0	0	0	0	0	0	1	4202	1049	37	1		1	CYP7A1	8	59409435	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50865	59409435	86954587	5904	13889										
NSMAF	8439	broad.mit.edu	37	chr8	59514652	59514652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgttccttatttagggcccCtactggcttactgagatccc	8	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59514652C>T	ENST00000038176.3	-	14	1302	c.1090G>A	c.(1090-1092)Ggg>Agg	p.G364R	NSMAF_ENST00000519858.1_5'UTR|NSMAF_ENST00000427130.2_Missense_Mutation_p.G395R	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	364	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.G364R(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TTTAGGGCCCCTACTGGCTTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	116	115					8																	59514652		2203	4300	6503	59677206	SO:0001583	missense	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1090G>A	8.37:g.59514652C>T	ENSP00000038176:p.Gly364Arg		59677206	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.821753	0.90873	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	D;D	0.82344	-1.6;-1.6	5.96	5.09	0.68999	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.94315	0.8173	H	0.97465	4.01	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96161	0.9115	9	.	.	.	.	15.1623	0.72793	0.0:0.9325:0.0:0.0675	.	395;364;364	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	R	364;395	ENSP00000038176:G364R;ENSP00000411012:G395R	.	G	-	1	0	NSMAF	59677206	1.000000	0.71417	0.992000	0.48379	0.835000	0.47333	7.513000	0.81739	1.523000	0.49018	0.655000	0.94253	GGG		0.413	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		T	59514652	C	T	59514652	3	4	61	1	0	0	0	0	1	0	0	0	10705	681	24	3	1735	3	NSMAF	8	59514652	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105217	59514652	86849370	5905	13890										
NSMAF	8439	broad.mit.edu	37	chr8	59547919	59547919	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcctatttttatacagtCtctcaaaggaatctggataa	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59547919C>A	ENST00000038176.3	-	4	453	c.241G>T	c.(241-243)Gac>Tac	p.D81Y	NSMAF_ENST00000427130.2_Missense_Mutation_p.D112Y	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	81					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.D81Y(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TTTATACAGTCTCTCAAAGGA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	8											73	76	75					8																	59547919		2203	4294	6497	59710473	SO:0001583	missense	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.241G>T	8.37:g.59547919C>A	ENSP00000038176:p.Asp81Tyr		59710473	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.590518	0.66219	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.55760	0.51;0.5	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	M	0.68593	2.085	0.52099	D	0.99994	D;P;B	0.89917	1.0;0.777;0.397	D;B;B	0.91635	0.999;0.297;0.057	T	0.70135	-0.4955	9	.	.	.	.	17.8311	0.88683	0.0:1.0:0.0:0.0	.	112;81;81	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	Y	81;112	ENSP00000038176:D81Y;ENSP00000411012:D112Y	.	D	-	1	0	NSMAF	59710473	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.939000	0.63526	2.640000	0.89533	0.591000	0.81541	GAC		0.294	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		A	59547919	C	A	59547919	3	1	61	1	0	0	0	0	1	0	0	0	10705	913	32	2	2624	2	NSMAF	8	59547919	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33267	59547919	86816103	5906	13891										
TOX	9760	broad.mit.edu	37	chr8	59750740	59750740	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcccttgatggcggcctgaGtatcacgaaagaataacgca	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:59750740G>T	ENST00000361421.1	-	5	1044	c.824C>A	c.(823-825)aCt>aAt	p.T275N		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	275						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T275N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GGCGGCCTGAGTATCACGAAA	0.458																																					Pancreas(161;610 1969 17913 21374 22725)											1	Substitution - Missense(1)	large_intestine(1)	8											119	116	117					8																	59750740		2203	4300	6503	59913294	SO:0001583	missense	9760				CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.824C>A	8.37:g.59750740G>T	ENSP00000354842:p.Thr275Asn		59913294	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959368	0.92726	.	.	ENSG00000198846	ENST00000361421;ENST00000456290	D	0.97870	-4.58	5.59	5.59	0.84812	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	N	0.20304	0.555	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97063	0.9772	9	.	.	.	.	19.5961	0.95538	0.0:0.0:1.0:0.0	.	275	O94900	TOX_HUMAN	N	275;33	ENSP00000354842:T275N	.	T	-	2	0	TOX	59913294	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.869000	0.99810	2.621000	0.88768	0.591000	0.81541	ACT		0.458	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59750740	G	T	59750740	3	4	61	1	0	0	0	0	1	0	0	0	16417	1029	36	2	776	2	TOX	8	59750740	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202821	59750740	86613282	5907	13892										
CHD7	55636	broad.mit.edu	37	chr8	61693684	61693684	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacagcagccacaacaaaaGaagaagaaaaagaaaaacaa	7	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:61693684G>T	ENST00000423902.2	+	3	2270	c.1791G>T	c.(1789-1791)aaG>aaT	p.K597N	CHD7_ENST00000525508.1_Missense_Mutation_p.K597N|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	597	Lys-rich.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.K597N(2)|p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		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)			CACAACAAAAGAAGAAGAAAA	0.423																																																3	Substitution - Missense(2)|Insertion - In frame(1)	large_intestine(2)|lung(1)	8											43	44	44					8																	61693684		1883	4108	5991	61856238	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.1791G>T	8.37:g.61693684G>T	ENSP00000392028:p.Lys597Asn		61856238	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958599	0.53400	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	D;T	0.83837	-1.77;-1.45	5.23	2.42	0.29668	.	0.000000	0.48286	D	0.000189	T	0.80839	0.4700	L	0.29908	0.895	0.41711	D	0.989453	D	0.62365	0.991	P	0.55011	0.766	T	0.79579	-0.1745	10	0.59425	D	0.04	-25.7198	10.8251	0.46627	0.2097:0.0:0.7903:0.0	.	597	Q9P2D1	CHD7_HUMAN	N	597	ENSP00000392028:K597N;ENSP00000436027:K597N	ENSP00000307304:K597N	K	+	3	2	CHD7	61856238	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	3.818000	0.55678	0.286000	0.22352	-0.145000	0.13849	AAG		0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61693684	G	T	61693684	3	4	61	1	0	0	0	0	1	0	0	0	3336	933	33	2	1797	2	CHD7	8	61693684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1942944	61693684	84670338	5908	13893										
CHD7	55636	broad.mit.edu	37	chr8	61693775	61693775	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtggggtagataaccaaGaactaaataggaactcactg	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:61693775G>T	ENST00000423902.2	+	3	2361	c.1882G>T	c.(1882-1884)Gaa>Taa	p.E628*	CHD7_ENST00000525508.1_Nonsense_Mutation_p.E628*|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	628	Lys-rich.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.E628*(2)|p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		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)			AGATAACCAAGAACTAAATAG	0.398																																																3	Substitution - Nonsense(2)|Insertion - In frame(1)	large_intestine(2)|lung(1)	8											44	43	44					8																	61693775		1823	4071	5894	61856329	SO:0001587	stop_gained	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.1882G>T	8.37:g.61693775G>T	ENSP00000392028:p.Glu628*		61856329	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Nonsense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	40	8.463363	0.98822	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	.	.	.	5.23	4.35	0.52113	.	0.142434	0.32703	N	0.005742	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-21.176	10.9161	0.47137	0.1651:0.0:0.8349:0.0	.	.	.	.	X	628	.	ENSP00000307304:E628X	E	+	1	0	CHD7	61856329	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.199000	0.72112	1.336000	0.45506	0.650000	0.86243	GAA		0.398	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61693775	G	T	61693775	4	4	61	1	0	0	0	0	0	1	0	0	3336	943	33	2	1888	2	CHD7	8	61693775	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91	61693775	84670247	5909	13894										
CHD7	55636	broad.mit.edu	37	chr8	61735155	61735155	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgaaaggaatccatggCccttttttagtaattgcccc	7	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:61735155C>T	ENST00000423902.2	+	12	3530	c.3051C>T	c.(3049-3051)ggC>ggT	p.G1017G	CHD7_ENST00000525508.1_Silent_p.G1017G|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1017	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.G1017G(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		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)			GAATCCATGGCCCTTTTTTAG	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	8											170	165	167					8																	61735155		1844	4086	5930	61897709	SO:0001819	synonymous_variant	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.3051C>T	8.37:g.61735155C>T			61897709	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																				0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61735155	C	T	61735155	2	4	61	1	0	0	0	0	0	0	0	1	3336	726	26	3		3	CHD7	8	61735155	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41380	61735155	84628867	5910	13895										
ASPH	444	broad.mit.edu	37	chr8	62496558	62496558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaatagtcttatcaaatTtatttaaaagtttaggcttc	4	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:62496558T>G	ENST00000379454.4	-	15	1194	c.1007A>C	c.(1006-1008)aAa>aCa	p.K336T	ASPH_ENST00000541428.1_Missense_Mutation_p.K307T|ASPH_ENST00000523897.1_5'UTR	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	336					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)	p.K336T(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CTTATCAAATTTATTTAAAAG	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	8											49	51	50					8																	62496558		2202	4295	6497	62659112	SO:0001583	missense	444			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.1007A>C	8.37:g.62496558T>G	ENSP00000368767:p.Lys336Thr		62659112	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	37	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.456469	0.43634	.	.	ENSG00000198363	ENST00000389213;ENST00000541428;ENST00000379454;ENST00000522349	T;T;T	0.54675	1.24;1.22;0.56	5.37	5.37	0.77165	Tetratricopeptide-like helical (1);	0.052984	0.64402	D	0.000001	T	0.59390	0.2190	L	0.29908	0.895	0.80722	D	1	B;D;B	0.69078	0.117;0.997;0.071	B;D;B	0.63283	0.063;0.913;0.048	T	0.61237	-0.7103	10	0.49607	T	0.09	-23.3693	15.6639	0.77209	0.0:0.0:0.0:1.0	.	307;317;336	F5H667;F8W7A9;Q12797	.;.;ASPH_HUMAN	T	317;307;336;89	ENSP00000437864:K307T;ENSP00000368767:K336T;ENSP00000429718:K89T	ENSP00000368767:K336T	K	-	2	0	ASPH	62659112	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.715000	0.61909	2.158000	0.67659	0.455000	0.32223	AAA		0.254	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		G	62496558	T	G	62496558	3	3	61	1	0	0	0	0	1	0	0	0	1054	1841	64	4	1313	4	ASPH	8	62496558	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	761403	62496558	83867464	5911	13896										
TTPA	7274	broad.mit.edu	37	chr8	63978615	63978615	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtgattagacttactcGaaatacgtcataagctgtaa	9	6	1	2	rs121917851		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:63978615G>A	ENST00000260116.4	-	3	431	c.400C>T	c.(400-402)Cga>Tga	p.R134*	TTPA_ENST00000521138.1_Intron	NM_000370.3	NP_000361.1	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	134	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)	p.R134*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	AGACTTACTCGAAATACGTCA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	8	GRCh37	CM981965	TTPA	M	rs121917851						73	67	69					8																	63978615		2203	4300	6503	64141169	SO:0001587	stop_gained	7274			BC058000	CCDS6178.1	8q12.3	2007-07-18	2007-07-16			ENSG00000137561			12404	protein-coding gene	gene with protein product		600415	"ataxia (Friedreich-like) with vitamin E deficiency"	AVED		7719340, 7887897	Standard	NM_000370		Approved		uc003xux.2	P49638		ENST00000260116.4:c.400C>T	8.37:g.63978615G>A	ENSP00000260116:p.Arg134*		64141169	Q71V64	Nonsense_Mutation	SNP	ENST00000260116.4	37	CCDS6178.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521383	0.96416	.	.	ENSG00000137561	ENST00000260116	.	.	.	5.54	5.54	0.83059	.	0.048816	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4812	0.95011	0.0:0.0:1.0:0.0	.	.	.	.	X	134	.	ENSP00000260116:R134X	R	-	1	2	TTPA	64141169	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.786000	0.62425	2.600000	0.87896	0.655000	0.94253	CGA		0.373	TTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378460.1	NM_000370		A	63978615	G	A	63978615	4	1	61	1	0	0	0	0	0	1	0	0	16776	1066	37	1	448	1	TTPA	8	63978615	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1482057	63978615	82385407	5912	13897										
TRIM55	84675	broad.mit.edu	37	chr8	67047301	67047301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctactgtctgaactgcGaagtacccacctgctctctg	7	14	3	1	rs138811034	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67047301G>A	ENST00000315962.4	+	3	791	c.418G>A	c.(418-420)Gaa>Aaa	p.E140K	TRIM55_ENST00000353317.5_Missense_Mutation_p.E140K|TRIM55_ENST00000350034.4_Missense_Mutation_p.E140K|TRIM55_ENST00000276573.7_Missense_Mutation_p.E140K	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	140					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.E140K(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			TCTGAACTGCGAAGTACCCAC	0.522													G|||	2	0.000399361	0	0.0014	5008	,	,		22453	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	204	164	177		418,418,418,418	5.5	1	8	dbSNP_134	177	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense,missense,missense	TRIM55	NM_033058.2,NM_184085.1,NM_184086.1,NM_184087.1	56,56,56,56	0,16,6487	AA,AG,GG		0.1744,0.0227,0.123	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	140/541,140/549,140/453,140/242	67047301	16,12990	2203	4300	6503	67209855	SO:0001583	missense	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.418G>A	8.37:g.67047301G>A	ENSP00000323913:p.Glu140Lys		67209855	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	32	5.116955	0.94385	2.27E-4	0.001744	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573;ENST00000350034	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.51	5.51	0.81932	Zinc finger, B-box (3);	0.153105	0.64402	D	0.000020	T	0.49406	0.1555	L	0.39566	1.225	0.41635	D	0.989042	P;P;D;P	0.56968	0.884;0.947;0.978;0.735	B;P;P;B	0.52514	0.325;0.576;0.701;0.18	T	0.44205	-0.9343	10	0.45353	T	0.12	.	19.41	0.94667	0.0:0.0:1.0:0.0	.	140;140;140;140	Q9BYV6-4;Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;.;TRI55_HUMAN;.	K	140	ENSP00000323913:E140K;ENSP00000297348:E140K;ENSP00000276573:E140K;ENSP00000332302:E140K	ENSP00000276573:E140K	E	+	1	0	TRIM55	67209855	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.030000	0.88816	2.580000	0.87095	0.655000	0.94253	GAA		0.522	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		A	67047301	G	A	67047301	3	1	61	1	0	0	0	0	1	0	0	0	16569	1059	37	1	428	1	TRIM55	8	67047301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3068686	67047301	79316721	5913	13898										
TRIM55	84675	broad.mit.edu	37	chr8	67064656	67064656	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcggagaaggagaaaaaGaaggagaaggagaagtggga	19	1	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67064656G>T	ENST00000315962.4	+	8	1403	c.1030G>T	c.(1030-1032)Gaa>Taa	p.E344*	TRIM55_ENST00000353317.5_Nonsense_Mutation_p.E344*|TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Nonsense_Mutation_p.E344*	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	344					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.E344*(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			aggagaaaaagaaggagaagg	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											42	39	40					8																	67064656		2203	4300	6503	67227210	SO:0001587	stop_gained	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1030G>T	8.37:g.67064656G>T	ENSP00000323913:p.Glu344*		67227210	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Nonsense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.797665	0.90538	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	.	.	.	5.07	3.16	0.36331	.	0.586799	0.18167	N	0.149570	.	.	.	.	.	.	0.29534	N	0.852557	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	9.2147	0.37339	0.1931:0.0:0.8069:0.0	.	.	.	.	X	344	.	ENSP00000276573:E344X	E	+	1	0	TRIM55	67227210	0.676000	0.27567	0.004000	0.12327	0.125000	0.20455	2.804000	0.47931	0.566000	0.29273	0.585000	0.79938	GAA		0.413	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		T	67064656	G	T	67064656	4	4	61	1	0	0	0	0	0	1	0	0	16569	943	33	2	1060	2	TRIM55	8	67064656	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17355	67064656	79299366	5914	13899										
ADHFE1	137872	broad.mit.edu	37	chr8	67372616	67372616	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgctccggaaattcttattCgatctggatgttgatgatgg	11	7	2	2	rs369719961		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67372616C>T	ENST00000396623.3	+	13	1267	c.1236C>T	c.(1234-1236)ttC>ttT	p.F412F	ADHFE1_ENST00000496501.1_3'UTR|ADHFE1_ENST00000415254.1_Silent_p.F364F|C8orf46_ENST00000482608.2_3'UTR	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	412					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)	p.F364F(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		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)			AATTCTTATTCGATCTGGATG	0.537											OREG0018808	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - coding silent(2)	large_intestine(2)	8											108	105	106					8																	67372616		2203	4300	6503	67535170	SO:0001819	synonymous_variant	137872			AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"Alcohol dehydrogenases"	16354	protein-coding gene	gene with protein product	"hydroxyacid-oxoacid transhydrogenase"	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.1236C>T	8.37:g.67372616C>T		1099	67535170	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Silent	SNP	ENST00000396623.3	37	CCDS6190.2																																																																																				0.537	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650		T	67372616	C	T	67372616	2	4	61	1	0	0	0	0	0	0	0	1	314	883	31	1		1	ADHFE1	8	67372616	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	307960	67372616	78991406	5915	13900										
VCPIP1	80124	broad.mit.edu	37	chr8	67546899	67546899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttgtttctgtattcaaaTtttcagtaccaccagttaaa	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67546899T>G	ENST00000310421.4	-	3	3764	c.3506A>C	c.(3505-3507)aAt>aCt	p.N1169T		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	1169					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)	p.N1169T(1)		breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			TGTATTCAAATTTTCAGTACC	0.448																																					NSCLC(179;265 2915 6144 43644)											1	Substitution - Missense(1)	large_intestine(1)	8											106	102	104					8																	67546899		2203	4300	6503	67709453	SO:0001583	missense	80124			AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.3506A>C	8.37:g.67546899T>G	ENSP00000309031:p.Asn1169Thr		67709453	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	37	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	T	8.405	0.842926	0.16963	.	.	ENSG00000175073	ENST00000310421	T	0.29917	1.55	5.59	5.59	0.84812	.	0.265423	0.37906	N	0.001887	T	0.17831	0.0428	N	0.12182	0.205	0.30845	N	0.73524	B	0.16166	0.016	B	0.15870	0.014	T	0.08086	-1.0739	10	0.41790	T	0.15	-17.9356	10.1563	0.42825	0.0:0.0745:0.0:0.9255	.	1169	Q96JH7	VCIP1_HUMAN	T	1169	ENSP00000309031:N1169T	ENSP00000309031:N1169T	N	-	2	0	VCPIP1	67709453	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.978000	0.29488	2.121000	0.65114	0.482000	0.46254	AAT		0.448	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			G	67546899	T	G	67546899	3	3	61	1	0	0	0	0	1	0	0	0	17181	1493	52	4	166	4	VCPIP1	8	67546899	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	174283	67546899	78817123	5916	13901										
VCPIP1	80124	broad.mit.edu	37	chr8	67547158	67547158	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactactccaggagctattcGaataagctcactattactag	6	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67547158G>A	ENST00000310421.4	-	3	3505	c.3247C>T	c.(3247-3249)Cga>Tga	p.R1083*		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	1083					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)	p.R1083*(1)		breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			GGAGCTATTCGAATAAGCTCA	0.403																																					NSCLC(179;265 2915 6144 43644)											1	Substitution - Nonsense(1)	large_intestine(1)	8											87	88	88					8																	67547158		2203	4300	6503	67709712	SO:0001587	stop_gained	80124			AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.3247C>T	8.37:g.67547158G>A	ENSP00000309031:p.Arg1083*		67709712	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Nonsense_Mutation	SNP	ENST00000310421.4	37	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	G	41	8.972623	0.99021	.	.	ENSG00000175073	ENST00000310421	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5482	15.3963	0.74798	0.0:0.0:0.8608:0.1392	.	.	.	.	X	1083	.	ENSP00000309031:R1083X	R	-	1	2	VCPIP1	67709712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.226000	0.78060	2.894000	0.99253	0.591000	0.81541	CGA		0.403	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			A	67547158	G	A	67547158	4	1	61	1	0	0	0	0	0	1	0	0	17181	1066	37	1	425	1	VCPIP1	8	67547158	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259	67547158	78816864	5917	13902										
SGK3	23678	broad.mit.edu	37	chr8	67710789	67710789	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacaggtttataaagttCtggtttcagtgggaagaagt	11	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67710789C>A	ENST00000396596.1	+	3	323	c.109C>A	c.(109-111)Ctg>Atg	p.L37M	SGK3_ENST00000520976.1_Missense_Mutation_p.L37M|SGK3_ENST00000345714.4_Missense_Mutation_p.L37M|SGK3_ENST00000522398.1_Missense_Mutation_p.L37M|SGK3_ENST00000521198.2_Missense_Mutation_p.L37M|C8orf44-SGK3_ENST00000519289.1_Missense_Mutation_p.L37M	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	37	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.L37M(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TTATAAAGTTCTGGTTTCAGT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	8											154	168	163					8																	67710789		2203	4300	6503	67873343	SO:0001583	missense	23678				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"serum/glucocorticoid regulated kinase-like"	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.109C>A	8.37:g.67710789C>A	ENSP00000379842:p.Leu37Met		67873343	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Missense_Mutation	SNP	ENST00000396596.1	37	CCDS6195.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815577	0.32145	.	.	ENSG00000104205	ENST00000519289;ENST00000521198;ENST00000262211;ENST00000522398;ENST00000522629;ENST00000520976;ENST00000396596;ENST00000518388;ENST00000345714	T;T;T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07	5.56	2.39	0.29439	Phox homologous domain (5);	0.166595	0.41396	D	0.000898	T	0.17238	0.0414	N	0.08118	0	0.37499	D	0.916672	B;B	0.30068	0.225;0.267	B;B	0.27380	0.047;0.079	T	0.07158	-1.0787	9	0.33940	T	0.23	.	2.7252	0.05212	0.2038:0.401:0.0:0.3953	.	37;37	Q96BR1-2;Q96BR1	.;SGK3_HUMAN	M	37	ENSP00000429022:L37M;ENSP00000430463:L37M;ENSP00000430256:L37M;ENSP00000429606:L37M;ENSP00000430691:L37M;ENSP00000379842:L37M;ENSP00000428972:L37M;ENSP00000331816:L37M	ENSP00000262211:L37M	L	+	1	2	SGK3	67873343	0.671000	0.27521	1.000000	0.80357	0.997000	0.91878	0.547000	0.23299	0.705000	0.31890	0.650000	0.86243	CTG		0.284	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3			A	67710789	C	A	67710789	3	1	61	1	0	0	0	0	1	0	0	0	14249	912	32	2	115	2	SGK3	8	67710789	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163631	67710789	78653233	5918	13903										
C8orf45	157777	broad.mit.edu	37	chr8	67808431	67808431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcagaagcatcacagtgTacatcccaggaaagaagttt	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:67808431T>C	ENST00000422365.2	+	11	1477	c.1306T>C	c.(1306-1308)Tac>Cac	p.Y436H	MCMDC2_ENST00000396592.3_Missense_Mutation_p.Y436H|MCMDC2_ENST00000541540.1_Missense_Mutation_p.Y373H|MCMDC2_ENST00000313616.5_Missense_Mutation_p.Y436H	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	436					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.Y431H(1)		endometrium(2)|kidney(2)|lung(5)	9						CATCACAGTGTACATCCCAGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											199	176	184					8																	67808431		2203	4300	6503	67970985	SO:0001583	missense	157777			BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 45"	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.1306T>C	8.37:g.67808431T>C	ENSP00000413632:p.Tyr436His		67970985	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034227	0.75617	.	.	ENSG00000178460	ENST00000379356;ENST00000396592;ENST00000422365;ENST00000313616;ENST00000541540	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	6.03	4.88	0.63580	.	0.162993	0.53938	N	0.000055	T	0.26085	0.0636	L	0.36672	1.1	0.27152	N	0.961371	B;B;B	0.15930	0.015;0.004;0.004	B;B;B	0.18561	0.022;0.003;0.003	T	0.18085	-1.0348	10	0.56958	D	0.05	-2.8366	11.874	0.52537	0.0:0.0676:0.0:0.9324	.	373;436;436	Q4G0Z9-4;Q4G0Z9;B4DXX4	.;CH045_HUMAN;.	H	308;436;436;436;373	ENSP00000379837:Y436H;ENSP00000413632:Y436H;ENSP00000317234:Y436H;ENSP00000445629:Y373H	ENSP00000317234:Y436H	Y	+	1	0	C8orf45	67970985	1.000000	0.71417	0.940000	0.37924	0.899000	0.52679	5.431000	0.66507	1.104000	0.41587	0.533000	0.62120	TAC		0.368	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		C	67808431	T	C	67808431	3	2	61	1	0	0	0	0	1	0	0	0	2436	1638	57	4	1344	4	C8orf45	8	67808431	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	97642	67808431	78555591	5919	13904										
CSPP1	79848	broad.mit.edu	37	chr8	68007717	68007717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaactagatgatgaaatcGaattaaggaatagaagaatt	9	3	0	5	rs201451280		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68007717G>A	ENST00000262210.5	+	6	731	c.700G>A	c.(700-702)Gaa>Aaa	p.E234K	CSPP1_ENST00000412460.1_5'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	269					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.E234K(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			TGATGAAATCGAATTAAGGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	LYS/GLU	3,3643		0,3,1820	94	85	88		700	5.9	1	8		88	1,8163		0,1,4081	yes	missense	CSPP1	NM_024790.6	56	0,4,5901	AA,AG,GG		0.0122,0.0823,0.0339	probably-damaging	234/1222	68007717	4,11806	1823	4082	5905	68170271	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.700G>A	8.37:g.68007717G>A	ENSP00000262210:p.Glu234Lys		68170271	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287331	0.80803	8.23E-4	1.22E-4	ENSG00000104218	ENST00000262210;ENST00000389042	T	0.75938	-0.98	5.95	5.95	0.96441	.	0.249218	0.18598	U	0.136540	D	0.84844	0.5562	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.79108	0.927;0.992;0.992	D	0.83615	0.0136	10	0.48119	T	0.1	-16.5399	15.8179	0.78618	0.0:0.1352:0.8648:0.0	.	234;269;269	Q1MSJ5-1;Q1MSJ5;F8W7C3	.;CSPP1_HUMAN;.	K	234;269	ENSP00000262210:E234K	ENSP00000262210:E234K	E	+	1	0	CSPP1	68170271	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	4.639000	0.61361	2.821000	0.97095	0.650000	0.86243	GAA		0.383	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		A	68007717	G	A	68007717	3	1	61	1	0	0	0	0	1	0	0	0	3968	1059	37	1	835	1	CSPP1	8	68007717	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199286	68007717	78356305	5920	13905										
CSPP1	79848	broad.mit.edu	37	chr8	68049832	68049832	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagggatgcaaaaggaaatCtgataagtacgttatttcta	9	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68049832C>A	ENST00000262210.5	+	15	1985	c.1954C>A	c.(1954-1956)Ctg>Atg	p.L652M	CSPP1_ENST00000412460.1_Missense_Mutation_p.L358M	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	687					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.L652M(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			AAAAGGAAATCTGATAAGTAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	8											99	95	96					8																	68049832		1830	4079	5909	68212386	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.1954C>A	8.37:g.68049832C>A	ENSP00000262210:p.Leu652Met		68212386	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.551668	0.65311	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.70749	-0.51;-0.51;-0.51	5.36	1.51	0.23008	.	0.000000	0.56097	D	0.000034	T	0.78142	0.4237	L	0.55990	1.75	0.37023	D	0.896317	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.79897	-0.1609	10	0.62326	D	0.03	-7.7696	11.1815	0.48631	0.0:0.747:0.0:0.253	.	358;652;687;687	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5;F8W7C3	.;.;CSPP1_HUMAN;.	M	652;687;358;358	ENSP00000262210:L652M;ENSP00000415782:L358M;ENSP00000430092:L358M	ENSP00000262210:L652M	L	+	1	2	CSPP1	68212386	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.825000	0.39081	0.342000	0.23796	0.460000	0.39030	CTG		0.333	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		A	68049832	C	A	68049832	3	1	61	1	0	0	0	0	1	0	0	0	3968	912	32	2	2125	2	CSPP1	8	68049832	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42115	68049832	78314190	5921	13906										
CSPP1	79848	broad.mit.edu	37	chr8	68066353	68066353	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagcaagaattatacaaGaattttcttcgtttccaggt	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68066353G>T	ENST00000262210.5	+	17	2239	c.2208G>T	c.(2206-2208)aaG>aaT	p.K736N	CSPP1_ENST00000412460.1_Missense_Mutation_p.K391N	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	771					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.K736N(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			AATTATACAAGAATTTTCTTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	8											90	85	87					8																	68066353		1808	4076	5884	68228907	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.2208G>T	8.37:g.68066353G>T	ENSP00000262210:p.Lys736Asn		68228907	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541573	0.85917	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.46819	0.86;1.23;1.23	5.77	5.77	0.91146	.	0.100554	0.64402	D	0.000003	T	0.66327	0.2778	L	0.50333	1.59	0.46901	D	0.999244	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.996;0.984;0.984	T	0.65985	-0.6035	10	0.87932	D	0	-26.0877	19.9508	0.97198	0.0:0.0:1.0:0.0	.	391;736;771;771	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5;F8W7C3	.;.;CSPP1_HUMAN;.	N	736;771;391;391	ENSP00000262210:K736N;ENSP00000415782:K391N;ENSP00000430092:K391N	ENSP00000262210:K736N	K	+	3	2	CSPP1	68228907	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.405000	0.44548	2.890000	0.99128	0.585000	0.79938	AAG		0.348	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		T	68066353	G	T	68066353	3	4	61	1	0	0	0	0	1	0	0	0	3968	933	33	2	2387	2	CSPP1	8	68066353	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16521	68066353	78297669	5922	13907										
ARFGEF1	10565	broad.mit.edu	37	chr8	68150614	68150614	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcatcaggagcctgatCttttgttccagtaagagatc	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68150614C>A	ENST00000262215.3	-	22	3642	c.3253G>T	c.(3253-3255)Gat>Tat	p.D1085Y	ARFGEF1_ENST00000518230.1_5'UTR|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.D539Y	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1085					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.D1085Y(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GGAGCCTGATCTTTTGTTCCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	8											103	95	98					8																	68150614		2203	4300	6503	68313168	SO:0001583	missense	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.3253G>T	8.37:g.68150614C>A	ENSP00000262215:p.Asp1085Tyr		68313168	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808870	0.70797	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.21191	2.85;2.02	5.49	5.49	0.81192	Armadillo-type fold (1);	0.050719	0.85682	D	0.000000	T	0.15349	0.0370	N	0.14661	0.345	0.80722	D	1	P;B;B	0.47545	0.897;0.0;0.234	B;B;B	0.38921	0.285;0.004;0.195	T	0.03717	-1.1010	10	0.62326	D	0.03	.	19.3565	0.94416	0.0:1.0:0.0:0.0	.	1085;563;539	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	Y	539;1085	ENSP00000428429:D539Y;ENSP00000262215:D1085Y	ENSP00000262215:D1085Y	D	-	1	0	ARFGEF1	68313168	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.571000	0.86741	0.655000	0.94253	GAT		0.398	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68150614	C	A	68150614	3	1	61	1	0	0	0	0	1	0	0	0	852	913	32	2	2368	2	ARFGEF1	8	68150614	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84261	68150614	78213408	5923	13908										
ARFGEF1	10565	broad.mit.edu	37	chr8	68165794	68165794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatactcttcaggaaggtCtttactgtcattgatacctc	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68165794C>A	ENST00000262215.3	-	18	2979	c.2590G>T	c.(2590-2592)Gac>Tac	p.D864Y	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.D318Y	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	864					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.D864Y(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCAGGAAGGTCTTTACTGTCA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	8											167	149	155					8																	68165794		2201	4299	6500	68328348	SO:0001583	missense	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.2590G>T	8.37:g.68165794C>A	ENSP00000262215:p.Asp864Tyr		68328348	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801821	0.90538	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.57907	0.37;0.37	5.97	5.97	0.96955	SEC7-like, alpha orthogonal bundle (1);Armadillo-type fold (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	D	0.85716	0.5761	H	0.99273	4.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.91017	0.4854	10	0.87932	D	0	.	20.4171	0.99027	0.0:1.0:0.0:0.0	.	864;318	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	Y	318;864	ENSP00000428429:D318Y;ENSP00000262215:D864Y	ENSP00000262215:D864Y	D	-	1	0	ARFGEF1	68328348	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.804000	0.85993	2.832000	0.97577	0.585000	0.79938	GAC		0.289	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68165794	C	A	68165794	3	1	61	1	0	0	0	0	1	0	0	0	852	913	32	2	3047	2	ARFGEF1	8	68165794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15180	68165794	78198228	5924	13909										
ARFGEF1	10565	broad.mit.edu	37	chr8	68179400	68179400	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatcatttactagtctttCaaatatattggctgcattta	5	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:68179400C>A	ENST00000262215.3	-	12	2127	c.1738G>T	c.(1738-1740)Gaa>Taa	p.E580*	ARFGEF1_ENST00000520381.1_Nonsense_Mutation_p.E34*	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	580					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.E580*(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			ACTAGTCTTTCAAATATATTG	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											75	76	75					8																	68179400		2202	4293	6495	68341954	SO:0001587	stop_gained	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.1738G>T	8.37:g.68179400C>A	ENSP00000262215:p.Glu580*		68341954	Q9NV46|Q9UFV2|Q9UNL0	Nonsense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	44	10.852585	0.99478	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	19.7032	0.96063	0.0:1.0:0.0:0.0	.	.	.	.	X	34;580	.	ENSP00000262215:E580X	E	-	1	0	ARFGEF1	68341954	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.663000	0.90544	0.650000	0.86243	GAA		0.308	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68179400	C	A	68179400	4	1	61	1	0	0	0	0	0	1	0	0	852	835	29	2	3923	2	ARFGEF1	8	68179400	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13606	68179400	78184622	5925	13910										
SULF1	23213	broad.mit.edu	37	chr8	70512880	70512880	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaatatggataaacactgGattatgcagtacacaggacc	8	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:70512880G>T	ENST00000260128.4	+	9	1494	c.777G>T	c.(775-777)tgG>tgT	p.W259C	SULF1_ENST00000458141.2_Missense_Mutation_p.W259C|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000419716.3_Missense_Mutation_p.W259C|SULF1_ENST00000402687.4_Missense_Mutation_p.W259C	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	259					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.W259C(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			ATAAACACTGGATTATGCAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											136	130	132					8																	70512880		2203	4300	6503	70675434	SO:0001583	missense	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.777G>T	8.37:g.70512880G>T	ENSP00000260128:p.Trp259Cys		70675434	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720785	0.89205	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	D;D;D;D	0.99176	-5.52;-5.52;-5.52;-5.52	6.02	6.02	0.97574	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.96333	3.805	0.80722	D	1	B	0.30482	0.281	P	0.49708	0.62	D	0.97606	1.0126	10	0.87932	D	0	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	259	Q8IWU6	SULF1_HUMAN	C	259	ENSP00000403040:W259C;ENSP00000260128:W259C;ENSP00000385704:W259C;ENSP00000390315:W259C	ENSP00000260128:W259C	W	+	3	0	SULF1	70675434	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	TGG		0.368	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70512880	G	T	70512880	3	4	61	1	0	0	0	0	1	0	0	0	15409	1183	41	2	795	2	SULF1	8	70512880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2333480	70512880	75851142	5926	13911										
SULF1	23213	broad.mit.edu	37	chr8	70540458	70540458	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagaaattaaagagccatCttcacccattcaagtaagta	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:70540458C>A	ENST00000260128.4	+	18	2812	c.2095C>A	c.(2095-2097)Ctt>Att	p.L699I	SULF1_ENST00000458141.2_Missense_Mutation_p.L699I|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000419716.3_Missense_Mutation_p.L699I|SULF1_ENST00000402687.4_Missense_Mutation_p.L699I	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	699					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.L699I(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AAAGAGCCATCTTCACCCATT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	8											105	111	109					8																	70540458		2203	4300	6503	70703012	SO:0001583	missense	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2095C>A	8.37:g.70540458C>A	ENSP00000260128:p.Leu699Ile		70703012	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.785506	0.70337	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.14	5.14	0.70334	Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.30727	0.0774	M	0.70275	2.135	0.41055	D	0.985333	B	0.26602	0.154	B	0.25759	0.063	T	0.12630	-1.0540	10	0.56958	D	0.05	.	13.5752	0.61870	0.1554:0.8446:0.0:0.0	.	699	Q8IWU6	SULF1_HUMAN	I	699	ENSP00000403040:L699I;ENSP00000260128:L699I;ENSP00000385704:L699I;ENSP00000390315:L699I	ENSP00000260128:L699I	L	+	1	0	SULF1	70703012	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	3.289000	0.51747	2.371000	0.80710	0.563000	0.77884	CTT		0.428	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		A	70540458	C	A	70540458	3	1	61	1	0	0	0	0	1	0	0	0	15409	913	32	2	2149	2	SULF1	8	70540458	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27578	70540458	75823564	5927	13912										
SLCO5A1	81796	broad.mit.edu	37	chr8	70585523	70585523	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagagcatgcaggtggtgtCaatgactgctccaaagtaga	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:70585523C>A	ENST00000260126.4	-	10	2834	c.2128G>T	c.(2128-2130)Gac>Tac	p.D710Y	SLCO5A1_ENST00000530307.1_Missense_Mutation_p.D655Y|SLCO5A1_ENST00000524945.1_Nonstop_Mutation_p.*688L	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	710						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.D710Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			CAGGTGGTGTCAATGACTGCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											139	138	139					8																	70585523		2203	4300	6503	70748077	SO:0001583	missense	81796			AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.2128G>T	8.37:g.70585523C>A	ENSP00000260126:p.Asp710Tyr		70748077	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	37	CCDS6205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.183128|4.183128	0.78677|0.78677	.|.	.|.	ENSG00000137571|ENSG00000137571	ENST00000260126;ENST00000530307|ENST00000524945	T;T|.	0.73897|.	-0.79;-0.79|.	5.63|5.63	5.63|5.63	0.86233|0.86233	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.76758|.	0.4032|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|.	0.74203|.	-0.3741|.	9|.	0.87932|.	D|.	0|.	.|.	20.0572|20.0572	0.97657|0.97657	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	655;710|.	E9PKK5;Q9H2Y9|.	.;SO5A1_HUMAN|.	Y|L	710;655|688	ENSP00000260126:D710Y;ENSP00000431611:D655Y|.	ENSP00000260126:D710Y|.	D|X	-|-	1|2	0|2	SLCO5A1|SLCO5A1	70748077|70748077	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.967000|0.967000	0.64934|0.64934	7.661000|7.661000	0.83786|0.83786	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAC|TGA		0.468	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70585523	C	A	70585523	3	1	61	1	0	0	0	0	1	0	0	0	14768	838	29	2	422	2	SLCO5A1	8	70585523	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45065	70585523	75778499	5928	13913										
NCOA2	10499	broad.mit.edu	37	chr8	71068844	71068844	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctccccatatagtccaaAacagtcttttgagtccaagc	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:71068844A>G	ENST00000452400.2	-	11	1937	c.1756T>C	c.(1756-1758)Ttt>Ctt	p.F586L	NCOA2_ENST00000524223.1_5'UTR	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	586					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)	p.F586L(1)	PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TATAGTCCAAAACAGTCTTTT	0.498			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	1	Substitution - Missense(1)	large_intestine(1)	8											115	111	113					8																	71068844		1889	4128	6017	71231398	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.1756T>C	8.37:g.71068844A>G	ENSP00000399968:p.Phe586Leu		71231398	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	A	8.248	0.808462	0.16467	.	.	ENSG00000140396	ENST00000452400	T	0.01414	4.92	5.93	5.93	0.95920	.	0.097389	0.64402	D	0.000001	T	0.02047	0.0064	L	0.32530	0.975	0.80722	D	1	P	0.49559	0.925	P	0.45753	0.492	T	0.71787	-0.4487	10	0.10902	T	0.67	.	16.3766	0.83401	1.0:0.0:0.0:0.0	.	586	Q15596	NCOA2_HUMAN	L	586	ENSP00000399968:F586L	ENSP00000399968:F586L	F	-	1	0	NCOA2	71231398	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.839000	0.69395	2.263000	0.75096	0.533000	0.62120	TTT		0.498	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			G	71068844	A	G	71068844	3	3	61	1	0	0	0	0	1	0	0	0	10260	14	1	4	2690	4	NCOA2	8	71068844	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	483321	71068844	75295178	5929	13914										
TRAM1	23471	broad.mit.edu	37	chr8	71520329	71520329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctcaaacatgagccccaGcaggaagaccatcgccacac	7	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:71520329G>A	ENST00000262213.2	-	1	275	c.106C>T	c.(106-108)Ctg>Ttg	p.L36L	RP11-382J12.1_ENST00000499227.2_5'Flank|TRAM1_ENST00000521425.1_5'Flank|TRAM1_ENST00000521049.1_5'UTR|TRAM1_ENST00000536748.1_Silent_p.L5L	NM_014294.5	NP_055109.1	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	36					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L36L(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	17			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			ATGAGCCCCAGCAGGAAGACC	0.657																																					Ovarian(85;984 1334 5116 12432 40638)											1	Substitution - coding silent(1)	large_intestine(1)	8											45	44	45					8																	71520329		2203	4300	6503	71682883	SO:0001819	synonymous_variant	23471			X63679	CCDS6207.1	8q13.1	2004-01-22			ENSG00000067167	ENSG00000067167			20568	protein-coding gene	gene with protein product		605190				1315422	Standard	NM_014294		Approved	TRAM, TRAMP	uc003xyo.2	Q15629	OTTHUMG00000164428	ENST00000262213.2:c.106C>T	8.37:g.71520329G>A			71682883	B4E0K2	Silent	SNP	ENST00000262213.2	37	CCDS6207.1																																																																																				0.657	TRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378738.1	NM_014294		A	71520329	G	A	71520329	2	1	61	1	0	0	0	0	0	0	0	1	16491	962	34	3		3	TRAM1	8	71520329	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	451485	71520329	74843693	5930	13915										
XKR9	389668	broad.mit.edu	37	chr8	71593401	71593401	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagatttttccatgaaggAcagtatgtttttagtgcttt	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:71593401A>G	ENST00000408926.3	+	3	642	c.108A>G	c.(106-108)ggA>ggG	p.G36G	XKR9_ENST00000520030.1_Silent_p.G36G|XKR9_ENST00000520273.1_Intron	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	36						integral component of membrane (GO:0016021)		p.G36G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			TCCATGAAGGACAGTATGTTT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	8											255	250	252					8																	71593401		2203	4300	6503	71755955	SO:0001819	synonymous_variant	389668			AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 9"				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.108A>G	8.37:g.71593401A>G			71755955	B2RNS9|B9EH74	Silent	SNP	ENST00000408926.3	37	CCDS34905.1																																																																																				0.333	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		G	71593401	A	G	71593401	2	3	61	1	0	0	0	0	0	0	0	1	17478	262	10	4		4	XKR9	8	71593401	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73072	71593401	74770621	5931	13916										
XKR9	389668	broad.mit.edu	37	chr8	71646602	71646602	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaaacaaaatgtgatgaAattgatggaaaaccagttct	9	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:71646602A>C	ENST00000408926.3	+	5	1599	c.1065A>C	c.(1063-1065)gaA>gaC	p.E355D	XKR9_ENST00000520030.1_Missense_Mutation_p.E355D|XKR9_ENST00000520273.1_Intron	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	355						integral component of membrane (GO:0016021)		p.E355D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			AATGTGATGAAATTGATGGAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	8											40	43	42					8																	71646602		2196	4297	6493	71809156	SO:0001583	missense	389668			AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 9"				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.1065A>C	8.37:g.71646602A>C	ENSP00000386141:p.Glu355Asp		71809156	B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	37	CCDS34905.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.549101	0.65311	.	.	ENSG00000221947	ENST00000408926;ENST00000520030	.	.	.	4.98	3.81	0.43845	.	0.412925	0.25668	N	0.029092	T	0.57359	0.2048	M	0.69823	2.125	0.39563	D	0.969159	P	0.42871	0.792	B	0.42798	0.398	T	0.57010	-0.7884	9	0.25106	T	0.35	-9.7431	12.1017	0.53788	0.8565:0.1435:0.0:0.0	.	355	Q5GH70	XKR9_HUMAN	D	355	.	ENSP00000386141:E355D	E	+	3	2	XKR9	71809156	0.997000	0.39634	0.755000	0.31263	0.973000	0.67179	3.821000	0.55700	0.912000	0.36772	0.455000	0.32223	GAA		0.274	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		C	71646602	A	C	71646602	3	2	61	1	0	0	0	0	1	0	0	0	17478	11	1	4	1075	4	XKR9	8	71646602	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	53201	71646602	74717420	5932	13917										
TRPA1	8989	broad.mit.edu	37	chr8	72967727	72967727	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actactttatcatgtccattCtttgctgccagatggagagg	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:72967727C>A	ENST00000262209.4	-	12	1680	c.1473G>T	c.(1471-1473)aaG>aaT	p.K491N	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	491					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.K491N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CATGTCCATTCTTTGCTGCCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											64	64	64					8																	72967727		2203	4299	6502	73130281	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1473G>T	8.37:g.72967727C>A	ENSP00000262209:p.Lys491Asn		73130281	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519230	0.64634	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.65549	-0.16;-0.16	5.4	-2.45	0.06481	Ankyrin repeat-containing domain (4);	0.183825	0.64402	D	0.000020	T	0.62466	0.2430	L	0.35487	1.065	0.36142	D	0.846886	D	0.67145	0.996	P	0.61275	0.886	T	0.66771	-0.5839	10	0.52906	T	0.07	-27.3158	13.7681	0.63008	0.0:0.62:0.0:0.38	.	491	O75762	TRPA1_HUMAN	N	343;491	ENSP00000428151:K343N;ENSP00000262209:K491N	ENSP00000262209:K491N	K	-	3	2	TRPA1	73130281	0.845000	0.29573	0.988000	0.46212	0.939000	0.58152	-0.165000	0.09968	-0.460000	0.07003	-0.312000	0.09012	AAG		0.388	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72967727	C	A	72967727	3	1	61	1	0	0	0	0	1	0	0	0	16617	912	32	2	1950	2	TRPA1	8	72967727	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1321125	72967727	73396295	5933	13918										
TRPA1	8989	broad.mit.edu	37	chr8	72967957	72967957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtgatttcttatctttgCttttggaatgaatggacaca	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:72967957C>A	ENST00000262209.4	-	11	1535	c.1328G>T	c.(1327-1329)aGc>aTc	p.S443I	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	443					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.S443I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTTATCTTTGCTTTTGGAATG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											35	35	35					8																	72967957		2203	4294	6497	73130511	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1328G>T	8.37:g.72967957C>A	ENSP00000262209:p.Ser443Ile		73130511	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.828454	0.71143	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.72394	-0.65;-0.65	5.4	5.4	0.78164	Ankyrin repeat-containing domain (4);	0.082611	0.85682	D	0.000000	T	0.80308	0.4599	M	0.69248	2.105	0.51233	D	0.999914	P	0.44260	0.83	P	0.53360	0.724	T	0.81066	-0.1101	10	0.56958	D	0.05	-11.8752	19.1513	0.93491	0.0:1.0:0.0:0.0	.	443	O75762	TRPA1_HUMAN	I	295;443	ENSP00000428151:S295I;ENSP00000262209:S443I	ENSP00000262209:S443I	S	-	2	0	TRPA1	73130511	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	2.497000	0.45354	2.521000	0.84997	0.650000	0.86243	AGC		0.403	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72967957	C	A	72967957	3	1	61	1	0	0	0	0	1	0	0	0	16617	797	28	2	2099	2	TRPA1	8	72967957	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230	72967957	73396065	5934	13919										
TRPA1	8989	broad.mit.edu	37	chr8	72981383	72981383	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttcaatttggtttttttCtacagcacaatgcagagggg	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:72981383C>A	ENST00000262209.4	-	3	526	c.319G>T	c.(319-321)Gaa>Taa	p.E107*		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	107					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.E107*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TGGTTTTTTTCTACAGCACAA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											158	165	163					8																	72981383		2203	4300	6503	73143937	SO:0001587	stop_gained	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.319G>T	8.37:g.72981383C>A	ENSP00000262209:p.Glu107*		73143937	A6NIN6	Nonsense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	38	6.657439	0.97739	.	.	ENSG00000104321	ENST00000262209	.	.	.	5.74	4.81	0.61882	.	0.432367	0.28653	N	0.014597	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-7.9419	6.2588	0.20889	0.0:0.5374:0.352:0.1106	.	.	.	.	X	107	.	ENSP00000262209:E107X	E	-	1	0	TRPA1	73143937	0.997000	0.39634	0.998000	0.56505	0.846000	0.48090	1.760000	0.38430	2.715000	0.92844	0.655000	0.94253	GAA		0.388	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72981383	C	A	72981383	4	1	61	1	0	0	0	0	0	1	0	0	16617	922	32	2	3140	2	TRPA1	8	72981383	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13426	72981383	73382639	5935	13920										
TRPA1	8989	broad.mit.edu	37	chr8	72984052	72984052	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtcacatctttttaatttCttttgcttattaaagttttg	4	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:72984052C>A	ENST00000262209.4	-	2	369	c.162G>T	c.(160-162)aaG>aaT	p.K54N		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	54					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.K54N(2)|p.K54K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TTTTTAATTTCTTTTGCTTAT	0.353																																																3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(3)	8											131	117	121					8																	72984052		2203	4300	6503	73146606	SO:0001583	missense	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.162G>T	8.37:g.72984052C>A	ENSP00000262209:p.Lys54Asn		73146606	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	3.640	-0.073760	0.07184	.	.	ENSG00000104321	ENST00000262209	T	0.39406	1.08	5.08	-5.05	0.02955	.	0.706131	0.13537	N	0.380516	T	0.20820	0.0501	L	0.38531	1.155	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.18085	-1.0348	10	0.22109	T	0.4	-4.2979	1.1527	0.01789	0.1479:0.2877:0.246:0.3184	.	54	O75762	TRPA1_HUMAN	N	54	ENSP00000262209:K54N	ENSP00000262209:K54N	K	-	3	2	TRPA1	73146606	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	-0.652000	0.05366	-0.581000	0.05937	0.563000	0.77884	AAG		0.353	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72984052	C	A	72984052	3	1	61	1	0	0	0	0	1	0	0	0	16617	912	32	2	3301	2	TRPA1	8	72984052	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2669	72984052	73379970	5936	13921										
KCNB2	9312	broad.mit.edu	37	chr8	73480176	73480176	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcttcgagactgcaacacAcacgagagcctcctggaagt	10	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:73480176A>G	ENST00000523207.1	+	2	795	c.207A>G	c.(205-207)acA>acG	p.T69T		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	69					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.T69T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	ACTGCAACACACACGAGAGCC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	8											81	79	80					8																	73480176		2203	4300	6503	73642730	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.207A>G	8.37:g.73480176A>G			73642730	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.522	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73480176	A	G	73480176	2	3	61	1	0	0	0	0	0	0	0	1	8034	146	6	4		4	KCNB2	8	73480176	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	496124	73480176	72883846	5937	13922										
KCNB2	9312	broad.mit.edu	37	chr8	73848677	73848677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaaggatgaagatgctAccaagttcaccagtatccct	9	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:73848677A>G	ENST00000523207.1	+	3	1675	c.1087A>G	c.(1087-1089)Acc>Gcc	p.T363A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	363					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.T363A(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TGAAGATGCTACCAAGTTCAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	8											119	121	120					8																	73848677		2203	4300	6503	74011231	SO:0001583	missense	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1087A>G	8.37:g.73848677A>G	ENSP00000430846:p.Thr363Ala		74011231	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.998586	0.74818	.	.	ENSG00000182674	ENST00000523207	D	0.98701	-5.08	5.58	5.58	0.84498	Ion transport (1);	0.000000	0.38959	N	0.001508	D	0.97804	0.9279	L	0.53561	1.675	0.58432	D	0.999994	P	0.42123	0.771	P	0.45276	0.475	D	0.98660	1.0683	10	0.72032	D	0.01	.	15.7481	0.77962	1.0:0.0:0.0:0.0	.	363	Q92953	KCNB2_HUMAN	A	363	ENSP00000430846:T363A	ENSP00000430846:T363A	T	+	1	0	KCNB2	74011231	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.339000	0.96797	2.121000	0.65114	0.533000	0.62120	ACC		0.428	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73848677	A	G	73848677	3	3	61	1	0	0	0	0	1	0	0	0	8034	391	14	4	1093	4	KCNB2	8	73848677	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	368501	73848677	72515345	5938	13923										
TERF1	7013	broad.mit.edu	37	chr8	73933027	73933027	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgaagaaatacagaattTaattaaaattcaggtatgaa	6	3	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:73933027T>C	ENST00000276603.5	+	3	547	c.524T>C	c.(523-525)tTa>tCa	p.L175S	RNU6-285P_ENST00000410556.1_RNA|TERF1_ENST00000276602.6_Missense_Mutation_p.L175S	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	175	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)	p.L175S(1)		central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			ATACAGAATTTAATTAAAATT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	8											17	16	16					8																	73933027		2184	4276	6460	74095581	SO:0001583	missense	7013			U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.524T>C	8.37:g.73933027T>C	ENSP00000276603:p.Leu175Ser		74095581	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	37	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367082	0.61513	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000518874;ENST00000517390	.	.	.	4.82	4.82	0.62117	Telomere repeat-binding factor, dimerisation domain (4);	0.000000	0.64402	D	0.000003	T	0.75917	0.3915	M	0.68952	2.095	0.53005	D	0.999969	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78708	-0.2099	9	0.87932	D	0	.	12.1853	0.54234	0.0:0.0:0.0:1.0	.	175;175	P54274-2;P54274	.;TERF1_HUMAN	S	175;175;143;71	.	ENSP00000276602:L175S	L	+	2	0	TERF1	74095581	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	4.388000	0.59633	1.927000	0.55829	0.383000	0.25322	TTA		0.289	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		C	73933027	T	C	73933027	3	2	61	1	0	0	0	0	1	0	0	0	15800	1764	61	4	534	4	TERF1	8	73933027	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	84350	73933027	72430995	5939	13924										
C8orf84	157869	broad.mit.edu	37	chr8	73979589	73979589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccatctatataaaaataAaactgtgaacagctggacaa	5	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:73979589A>G	ENST00000297354.6	-	5	986	c.782T>C	c.(781-783)tTt>tCt	p.F261S	SBSPON_ENST00000519697.1_5'UTR	NM_153225.3	NP_694957.3	Q8IVN8	SBSPO_HUMAN	somatomedin B and thrombospondin, type 1 domain containing	261					immune response (GO:0006955)	proteinaceous extracellular matrix (GO:0005578)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.F256S(1)									TATAAAAATAAAACTGTGAAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											66	64	65					8																	73979589		1811	4069	5880	74142143	SO:0001583	missense	157869				CCDS43747.2	8q21.11	2013-08-07	2012-05-15	2012-05-15	ENSG00000164764	ENSG00000164764			30362	protein-coding gene	gene with protein product	"RPE spondin", "rpe-spondin"		"chromosome 8 open reading frame 84"	C8orf84		12107410	Standard	NM_153225		Approved	RPESP	uc003xzf.3	Q8IVN8	OTTHUMG00000157144	ENST00000297354.6:c.782T>C	8.37:g.73979589A>G	ENSP00000297354:p.Phe261Ser		74142143	A8KAA5|Q96J64	Missense_Mutation	SNP	ENST00000297354.6	37	CCDS43747.2	.	.	.	.	.	.	.	.	.	.	A	25.4	4.635003	0.87760	.	.	ENSG00000164764	ENST00000297354	T	0.23754	1.89	5.99	5.99	0.97316	.	0.055258	0.85682	D	0.000000	T	0.55049	0.1896	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60073	-0.7334	10	0.87932	D	0	-22.3614	16.1945	0.82018	1.0:0.0:0.0:0.0	.	261	Q8IVN8	RPESP_HUMAN	S	261	ENSP00000297354:F261S	ENSP00000297354:F261S	F	-	2	0	C8orf84	74142143	1.000000	0.71417	0.930000	0.37139	0.965000	0.64279	7.820000	0.86633	2.295000	0.77249	0.524000	0.50904	TTT		0.353	SBSPON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347584.2	NM_153225		G	73979589	A	G	73979589	3	3	61	1	0	0	0	0	1	0	0	0	2446	14	1	4	16	4	C8orf84	8	73979589	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	46562	73979589	72384433	5940	13925										
TMEM70	54968	broad.mit.edu	37	chr8	74893415	74893415	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtttctcttattctacGagtctgattggccttacatt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:74893415G>A	ENST00000312184.5	+	3	415	c.342G>A	c.(340-342)acG>acA	p.T114T	Y_RNA_ENST00000365350.1_RNA|TMEM70_ENST00000517439.1_3'UTR	NM_001040613.2|NM_017866.5	NP_001035703.1|NP_060336.3	Q9BUB7	TMM70_HUMAN	transmembrane protein 70	114					mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)		p.T114T(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8	Breast(64;0.0311)		Epithelial(68;0.0186)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0564)			CTTATTCTACGAGTCTGATTG	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	8											101	98	99					8																	74893415		2203	4300	6503	75055969	SO:0001819	synonymous_variant	54968			BC002748	CCDS6215.1, CCDS47876.1	8q21.11	2013-05-23				ENSG00000175606			26050	protein-coding gene	gene with protein product		612418				21945727, 22986587	Standard	NM_017866		Approved	FLJ20533	uc003yab.3	Q9BUB7		ENST00000312184.5:c.342G>A	8.37:g.74893415G>A			75055969	E9PDY9|Q9NWY5	Silent	SNP	ENST00000312184.5	37	CCDS6215.1																																																																																				0.318	TMEM70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379028.1	NM_017866		A	74893415	G	A	74893415	2	1	61	1	0	0	0	0	0	0	0	1	16238	1045	37	1		1	TMEM70	8	74893415	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	913826	74893415	71470607	5941	13926										
PI15	51050	broad.mit.edu	37	chr8	75757461	75757461	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccccagatgtcctatgaGatgttttggtcccatgtgca	9	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:75757461G>T	ENST00000260113.2	+	4	670	c.491G>T	c.(490-492)aGa>aTa	p.R164I	RP11-758M4.4_ENST00000522914.1_RNA|PI15_ENST00000523773.1_Missense_Mutation_p.R164I|RP11-758M4.4_ENST00000518128.1_RNA|RP11-758M4.4_ENST00000523860.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	164	SCP.					extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)	p.R164I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			TGTCCTATGAGATGTTTTGGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											211	191	198					8																	75757461		2203	4300	6503	75920016	SO:0001583	missense	51050			D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"protease inhibitor 15"			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.491G>T	8.37:g.75757461G>T	ENSP00000260113:p.Arg164Ile		75920016	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	37	CCDS6218.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452063	0.84209	.	.	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.07444	3.19;3.19	5.27	5.27	0.74061	CAP domain (3);	0.049628	0.85682	D	0.000000	T	0.21103	0.0508	M	0.71206	2.165	0.80722	D	1	P	0.52316	0.952	P	0.50490	0.642	T	0.00254	-1.1874	10	0.52906	T	0.07	.	19.0772	0.93168	0.0:0.0:1.0:0.0	.	164	O43692	PI15_HUMAN	I	164	ENSP00000260113:R164I;ENSP00000428567:R164I	ENSP00000260113:R164I	R	+	2	0	PI15	75920016	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.159000	0.71856	2.725000	0.93324	0.557000	0.71058	AGA		0.368	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		T	75757461	G	T	75757461	3	4	61	1	0	0	0	0	1	0	0	0	11899	942	33	2	501	2	PI15	8	75757461	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	864046	75757461	70606561	5942	13927										
HNF4G	3174	broad.mit.edu	37	chr8	76471263	76471263	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatctacttcaggaaatgCtattaggtggtgagtacatt	9	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:76471263C>T	ENST00000354370.1	+	9	1243	c.973C>T	c.(973-975)Cta>Tta	p.L325L	HNF4G_ENST00000396423.2_Silent_p.L362L			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	325					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.L325L(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			TCAGGAAATGCTATTAGGTGG	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	8											65	68	67					8																	76471263		2203	4300	6503	76633818	SO:0001819	synonymous_variant	3174				CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"Nuclear hormone receptors"	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.973C>T	8.37:g.76471263C>T			76633818	Q7Z2V9|Q9UH81|Q9UIS6	Silent	SNP	ENST00000354370.1	37																																																																																					0.328	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		T	76471263	C	T	76471263	2	4	61	1	0	0	0	0	0	0	0	1	7275	796	28	3		3	HNF4G	8	76471263	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	713802	76471263	69892759	5943	13928										
ZFHX4	79776	broad.mit.edu	37	chr8	77616880	77616880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgcttctgcacctatgtCgttctacccacagatcatca	6	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77616880C>T	ENST00000521891.2	+	2	1005	c.557C>T	c.(556-558)tCg>tTg	p.S186L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S186L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S186L|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S186L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.S186L(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GCACCTATGTCGTTCTACCCA	0.483										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											74	72	73					8																	77616880		2000	4177	6177	77779435	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.557C>T	8.37:g.77616880C>T	ENSP00000430497:p.Ser186Leu		77779435	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270925	0.40194	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.42	5.42	0.78866	.	0.196712	0.25055	U	0.033486	T	0.40145	0.1105	L	0.43152	1.355	0.80722	D	1	B;P;P;P	0.49253	0.384;0.519;0.519;0.921	B;B;B;P	0.44897	0.035;0.123;0.077;0.463	T	0.33854	-0.9852	10	0.87932	D	0	.	19.416	0.94700	0.0:1.0:0.0:0.0	.	186;186;186;186	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	L	186	ENSP00000430497:S186L;ENSP00000399605:S186L;ENSP00000050961:S186L;ENSP00000430848:S186L	ENSP00000050961:S186L	S	+	2	0	ZFHX4	77779435	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.609000	0.82925	2.821000	0.97095	0.650000	0.86243	TCG		0.483	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77616880	C	T	77616880	3	4	61	1	0	0	0	0	1	0	0	0	17674	893	31	1	559	1	ZFHX4	8	77616880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1145617	77616880	68747142	5944	13929										
ZFHX4	79776	broad.mit.edu	37	chr8	77617034	77617034	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctccgacacaagagagaGaaagactatctaaccagtga	9	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77617034G>T	ENST00000521891.2	+	2	1159	c.711G>T	c.(709-711)gaG>gaT	p.E237D	ZFHX4_ENST00000050961.6_Missense_Mutation_p.E237D|ZFHX4_ENST00000518282.1_Missense_Mutation_p.E237D|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.E237D	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.E237D(2)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACAAGAGAGAGAAAGACTATC	0.463										HNSCC(33;0.089)																																						2	Substitution - Missense(2)	large_intestine(2)	8											128	120	123					8																	77617034		2060	4214	6274	77779589	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.711G>T	8.37:g.77617034G>T	ENSP00000430497:p.Glu237Asp		77779589	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	8.988	0.977045	0.18812	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.45276	0.9;0.95;0.92;0.91	5.42	4.49	0.54785	.	0.154833	0.29486	U	0.012015	T	0.15652	0.0377	N	0.01705	-0.755	0.36313	D	0.857772	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.001	T	0.20042	-1.0287	10	0.08179	T	0.78	.	11.4082	0.49911	0.0:0.0:0.6568:0.3432	.	237;237;237;237	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	D	237	ENSP00000430497:E237D;ENSP00000399605:E237D;ENSP00000050961:E237D;ENSP00000430848:E237D	ENSP00000050961:E237D	E	+	3	2	ZFHX4	77779589	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.892000	0.39748	2.821000	0.97095	0.650000	0.86243	GAG		0.463	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77617034	G	T	77617034	3	4	61	1	0	0	0	0	1	0	0	0	17674	933	33	2	713	2	ZFHX4	8	77617034	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154	77617034	68746988	5945	13930										
ZFHX4	79776	broad.mit.edu	37	chr8	77618197	77618197	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgacactgtgttggggtcttCgaggtctcttggtggtcata	14	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77618197C>T	ENST00000521891.2	+	2	2322	c.1874C>T	c.(1873-1875)tCg>tTg	p.S625L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S625L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S625L|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S625L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	625					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.S625L(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTGGGGTCTTCGAGGTCTCTT	0.532										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											90	93	92					8																	77618197		2011	4206	6217	77780752	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1874C>T	8.37:g.77618197C>T	ENSP00000430497:p.Ser625Leu		77780752	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	14.69	2.609759	0.46527	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55234	0.54;0.58;0.54;0.53	5.3	5.3	0.74995	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.38959	U	0.001519	T	0.70465	0.3227	L	0.61036	1.89	0.80722	D	1	D;D;D;D	0.76494	0.992;0.996;0.996;0.999	P;P;P;D	0.67103	0.619;0.788;0.788;0.949	T	0.72228	-0.4354	10	0.72032	D	0.01	.	19.15	0.93483	0.0:1.0:0.0:0.0	.	625;625;625;625	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	L	625	ENSP00000430497:S625L;ENSP00000399605:S625L;ENSP00000050961:S625L;ENSP00000430848:S625L	ENSP00000050961:S625L	S	+	2	0	ZFHX4	77780752	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.750000	0.94351	0.655000	0.94253	TCG		0.532	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77618197	C	T	77618197	3	4	61	1	0	0	0	0	1	0	0	0	17674	893	31	1	1876	1	ZFHX4	8	77618197	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1163	77618197	68745825	5946	13931										
ZFHX4	79776	broad.mit.edu	37	chr8	77620100	77620100	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgataaacatatgcagaaAtatcaactggtggctcacat	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77620100A>C	ENST00000521891.2	+	3	3358	c.2910A>C	c.(2908-2910)aaA>aaC	p.K970N	ZFHX4_ENST00000050961.6_Missense_Mutation_p.K944N|ZFHX4_ENST00000518282.1_Missense_Mutation_p.K944N|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K944N	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	944					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.K970N(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATATGCAGAAATATCAACTGG	0.438										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											100	102	101					8																	77620100		2199	4296	6495	77782655	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.2910A>C	8.37:g.77620100A>C	ENSP00000430497:p.Lys970Asn		77782655	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	8.568	0.879440	0.17467	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.19	0.225	0.15325	Zinc finger, U1-type (1);	0.000000	0.45361	U	0.000377	T	0.70842	0.3270	M	0.85041	2.73	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.997;0.997;0.99	T	0.71764	-0.4494	10	0.87932	D	0	.	10.6543	0.45665	0.5641:0.0:0.4359:0.0	.	944;944;970;944	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	N	970;970;944;944;944	ENSP00000430497:K970N;ENSP00000399605:K944N;ENSP00000050961:K944N;ENSP00000430848:K944N	ENSP00000050961:K944N	K	+	3	2	ZFHX4	77782655	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.788000	0.38714	-0.088000	0.12506	-0.359000	0.07587	AAA		0.438	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77620100	A	C	77620100	3	2	61	1	0	0	0	0	1	0	0	0	17674	98	4	4	2916	4	ZFHX4	8	77620100	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1903	77620100	68743922	5947	13932										
ZFHX4	79776	broad.mit.edu	37	chr8	77690553	77690553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggtacaacatgtccgttCggtgaagcatcagcagactg	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77690553C>T	ENST00000521891.2	+	4	3651	c.3203C>T	c.(3202-3204)tCg>tTg	p.S1068L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S1042L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S1042L|ZFHX4_ENST00000517683.1_3'UTR|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S1042L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1042					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.S1068L(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CATGTCCGTTCGGTGAAGCAT	0.507										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											153	159	157					8																	77690553		2043	4198	6241	77853108	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3203C>T	8.37:g.77690553C>T	ENSP00000430497:p.Ser1068Leu		77853108	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	15.51	2.856338	0.51376	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.22	5.22	0.72569	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);	0.000000	0.37857	U	0.001913	T	0.73179	0.3554	M	0.72479	2.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.996	T	0.74426	-0.3669	10	0.66056	D	0.02	.	19.3361	0.94319	0.0:1.0:0.0:0.0	.	1042;1042;1068	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	1068;1068;1042;1042;1042	ENSP00000430497:S1068L;ENSP00000399605:S1042L;ENSP00000050961:S1042L;ENSP00000430848:S1042L	ENSP00000050961:S1042L	S	+	2	0	ZFHX4	77853108	1.000000	0.71417	0.178000	0.23040	0.997000	0.91878	7.609000	0.82925	2.878000	0.98634	0.650000	0.86243	TCG		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77690553	C	T	77690553	3	4	61	1	0	0	0	0	1	0	0	0	17674	893	31	1	3213	1	ZFHX4	8	77690553	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70453	77690553	68673469	5948	13933										
ZFHX4	79776	broad.mit.edu	37	chr8	77764621	77764621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagcagcagccaccacctCcacagcagcagcagcaacag	8	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77764621C>T	ENST00000521891.2	+	10	5912	c.5464C>T	c.(5464-5466)Cca>Tca	p.P1822S	ZFHX4_ENST00000050961.6_Missense_Mutation_p.P1777S|ZFHX4_ENST00000518282.1_Missense_Mutation_p.P1796S|ZFHX4_ENST00000455469.2_Missense_Mutation_p.P1777S	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1777					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.P1822S(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			gccaccacctccacagcagca	0.478										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											24	23	23					8																	77764621		2156	4242	6398	77927176	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.5464C>T	8.37:g.77764621C>T	ENSP00000430497:p.Pro1822Ser		77927176	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.422283	0.00186	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.45276	0.9;0.95;0.91;0.91	2.3	2.3	0.28687	.	0.570420	0.13046	U	0.418085	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	B;B;B	0.12013	0.003;0.005;0.005	B;B;B	0.08055	0.001;0.003;0.003	T	0.21930	-1.0231	10	0.08381	T	0.77	.	8.1556	0.31167	0.0:1.0:0.0:0.0	.	1777;1777;1822	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	S	1822;1822;1777;1777;1796	ENSP00000430497:P1822S;ENSP00000399605:P1777S;ENSP00000050961:P1777S;ENSP00000430848:P1796S	ENSP00000050961:P1777S	P	+	1	0	ZFHX4	77927176	0.000000	0.05858	0.004000	0.12327	0.029000	0.11900	0.539000	0.23175	1.310000	0.45006	0.632000	0.83419	CCA		0.478	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77764621	C	T	77764621	3	4	61	1	0	0	0	0	1	0	0	0	17674	855	30	3	5498	3	ZFHX4	8	77764621	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74068	77764621	68599401	5949	13934										
ZFHX4	79776	broad.mit.edu	37	chr8	77765144	77765144	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaagctttatccaatttCtccatcttctccagaaacgc	4	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77765144C>T	ENST00000521891.2	+	10	6435	c.5987C>T	c.(5986-5988)tCt>tTt	p.S1996F	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S1951F|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S1970F|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S1951F	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1951	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.S1996F(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TATCCAATTTCTCCATCTTCT	0.507										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											44	44	44					8																	77765144		1915	4131	6046	77927699	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.5987C>T	8.37:g.77765144C>T	ENSP00000430497:p.Ser1996Phe		77927699	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361617	0.82353	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51574	0.7;0.75;0.72;0.71	4.06	4.06	0.47325	.	0.000000	0.43110	U	0.000607	T	0.45054	0.1323	L	0.44542	1.39	0.34596	D	0.715987	B;P;P	0.36249	0.41;0.545;0.545	B;B;B	0.38755	0.064;0.281;0.136	T	0.63594	-0.6602	10	0.59425	D	0.04	.	16.8418	0.85971	0.0:1.0:0.0:0.0	.	1951;1951;1996	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	F	1996;1996;1951;1951;1970	ENSP00000430497:S1996F;ENSP00000399605:S1951F;ENSP00000050961:S1951F;ENSP00000430848:S1970F	ENSP00000050961:S1951F	S	+	2	0	ZFHX4	77927699	1.000000	0.71417	0.930000	0.37139	0.993000	0.82548	4.645000	0.61404	2.295000	0.77249	0.435000	0.28638	TCT		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77765144	C	T	77765144	3	4	61	1	0	0	0	0	1	0	0	0	17674	913	32	3	6021	3	ZFHX4	8	77765144	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	523	77765144	68598878	5950	13935										
ZFHX4	79776	broad.mit.edu	37	chr8	77766073	77766073	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactaatgaacggtacattCgaacaagcaacatgcagtac	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77766073C>T	ENST00000521891.2	+	10	7364	c.6916C>T	c.(6916-6918)Cga>Tga	p.R2306*	ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.R2261*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.R2280*|ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.R2261*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R2290*(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACGGTACATTCGAACAAGCAA	0.388										HNSCC(33;0.089)																																						1	Substitution - Nonsense(1)	large_intestine(1)	8											96	93	94					8																	77766073		1944	4150	6094	77928628	SO:0001587	stop_gained	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6916C>T	8.37:g.77766073C>T	ENSP00000430497:p.Arg2306*		77928628	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	48	14.908460	0.99815	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	4.34	2.28	0.28536	.	0.000000	0.37857	U	0.001912	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9636	0.58472	0.2989:0.7011:0.0:0.0	.	.	.	.	X	2306;2290;2261;2261;2280	.	ENSP00000050961:R2261X	R	+	1	2	ZFHX4	77928628	0.756000	0.28383	0.310000	0.25168	0.882000	0.50991	1.523000	0.35932	1.115000	0.41800	0.650000	0.86243	CGA		0.388	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766073	C	T	77766073	4	4	61	1	0	0	0	0	0	1	0	0	17674	876	31	1	6950	1	ZFHX4	8	77766073	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	929	77766073	68597949	5951	13936										
ZFHX4	79776	broad.mit.edu	37	chr8	77767750	77767750	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtctgcgatgacaaatttCtcttttctctcacaagccca	6	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77767750C>A	ENST00000521891.2	+	10	9041	c.8593C>A	c.(8593-8595)Ctc>Atc	p.L2865I	ZFHX4_ENST00000050961.6_Missense_Mutation_p.L2820I|ZFHX4_ENST00000518282.1_Missense_Mutation_p.L2839I|ZFHX4_ENST00000455469.2_Missense_Mutation_p.L2820I	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2820					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.L2849I(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGACAAATTTCTCTTTTCTCT	0.488										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											94	96	95					8																	77767750		1969	4146	6115	77930305	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8593C>A	8.37:g.77767750C>A	ENSP00000430497:p.Leu2865Ile		77930305	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	7.948	0.744269	0.15710	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.49139	0.79;0.84;0.81;0.8	5.25	4.35	0.52113	.	0.000000	0.40144	U	0.001178	T	0.31734	0.0806	N	0.22421	0.69	0.25788	N	0.984655	B;B;B	0.22080	0.038;0.064;0.064	B;B;B	0.30251	0.032;0.07;0.113	T	0.20505	-1.0273	10	0.18276	T	0.48	.	8.0132	0.30365	0.2859:0.641:0.0:0.0731	.	2820;2820;2865	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	I	2865;2849;2820;2820;2839	ENSP00000430497:L2865I;ENSP00000399605:L2820I;ENSP00000050961:L2820I;ENSP00000430848:L2839I	ENSP00000050961:L2820I	L	+	1	0	ZFHX4	77930305	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	3.209000	0.51122	1.397000	0.46682	0.561000	0.74099	CTC		0.488	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77767750	C	A	77767750	3	1	61	1	0	0	0	0	1	0	0	0	17674	913	32	2	8627	2	ZFHX4	8	77767750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1677	77767750	68596272	5952	13937										
ZFHX4	79776	broad.mit.edu	37	chr8	77767842	77767842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagatgacccggatgacaaCgccgaccgcagcgaaacgtc	11	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77767842C>T	ENST00000521891.2	+	10	9133	c.8685C>T	c.(8683-8685)aaC>aaT	p.N2895N	ZFHX4_ENST00000050961.6_Silent_p.N2850N|ZFHX4_ENST00000518282.1_Silent_p.N2869N|ZFHX4_ENST00000455469.2_Silent_p.N2850N	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2850					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.N2879N(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CGGATGACAACGCCGACCGCA	0.498										HNSCC(33;0.089)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											79	79	79					8																	77767842		1984	4161	6145	77930397	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8685C>T	8.37:g.77767842C>T			77930397	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77767842	C	T	77767842	2	4	61	1	0	0	0	0	0	0	0	1	17674	535	19	1		1	ZFHX4	8	77767842	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92	77767842	68596180	5953	13938										
ZFHX4	79776	broad.mit.edu	37	chr8	77768313	77768313	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaagattacttggctccGaccacggttcggcagctgat	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77768313G>A	ENST00000521891.2	+	10	9604	c.9156G>A	c.(9154-9156)ccG>ccA	p.P3052P	ZFHX4_ENST00000050961.6_Silent_p.P3007P|ZFHX4_ENST00000518282.1_Silent_p.P3026P|ZFHX4_ENST00000455469.2_Silent_p.P3007P	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3007	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.P3036P(2)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACTTGGCTCCGACCACGGTTC	0.507										HNSCC(33;0.089)																																						2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	8											102	102	102					8																	77768313		2006	4172	6178	77930868	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9156G>A	8.37:g.77768313G>A			77930868	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77768313	G	A	77768313	2	1	61	1	0	0	0	0	0	0	0	1	17674	1045	37	1		1	ZFHX4	8	77768313	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	471	77768313	68595709	5954	13939										
ZFHX4	79776	broad.mit.edu	37	chr8	77775450	77775450	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactccaccacctccaccacCtcctcctcctcctcctcctt	1	25	0	0	rs199874527		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77775450C>A	ENST00000521891.2	+	11	9948	c.9500C>A	c.(9499-9501)cCt>cAt	p.P3167H	ZFHX4_ENST00000050961.6_Missense_Mutation_p.P3118H|ZFHX4_ENST00000518282.1_Missense_Mutation_p.P3141H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.P3122H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.P3151H(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			cctccaccacctcctcctcct	0.527										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											53	54	53					8																	77775450		2068	4228	6296	77938005	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9500C>A	8.37:g.77775450C>A	ENSP00000430497:p.Pro3167His		77938005	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402460	0.25291	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29	4.28	4.28	0.50868	.	0.000000	0.40554	U	0.001079	D	0.82884	0.5134	L	0.50333	1.59	0.43065	D	0.994693	B	0.11235	0.004	B	0.11329	0.006	T	0.80999	-0.1131	10	0.59425	D	0.04	.	11.1258	0.48317	0.1848:0.8152:0.0:0.0	.	3122	Q86UP3-4	.	H	3167;3151;3122;3118;3141	ENSP00000430497:P3167H;ENSP00000399605:P3122H;ENSP00000050961:P3118H;ENSP00000430848:P3141H	ENSP00000050961:P3118H	P	+	2	0	ZFHX4	77938005	.	.	0.979000	0.43373	0.963000	0.63663	.	.	2.345000	0.79718	0.651000	0.88453	CCT		0.527	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77775450	C	A	77775450	3	1	61	1	0	0	0	0	1	0	0	0	17674	681	24	2	9538	2	ZFHX4	8	77775450	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7137	77775450	68588572	5955	13940										
ZFHX4	79776	broad.mit.edu	37	chr8	77776719	77776719	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctagaagacttagataAttctttggaagtgaaggcta	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:77776719A>C	ENST00000521891.2	+	11	11217	c.10769A>C	c.(10768-10770)aAt>aCt	p.N3590T	ZFHX4_ENST00000050961.6_Missense_Mutation_p.N3541T|ZFHX4_ENST00000518282.1_Missense_Mutation_p.N3564T|ZFHX4_ENST00000455469.2_Missense_Mutation_p.N3545T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3541					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.N3574T(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GACTTAGATAATTCTTTGGAA	0.458										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											48	47	47					8																	77776719		1974	4176	6150	77939274	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.10769A>C	8.37:g.77776719A>C	ENSP00000430497:p.Asn3590Thr		77939274	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	11.31	1.602394	0.28534	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.49720	0.77;0.82;0.79;0.78	4.6	4.6	0.57074	.	0.000000	0.47455	U	0.000227	T	0.60248	0.2254	L	0.57536	1.79	0.50467	D	0.999875	D	0.61697	0.99	P	0.58928	0.848	T	0.64257	-0.6450	10	0.62326	D	0.03	.	14.4505	0.67382	1.0:0.0:0.0:0.0	.	3545	Q86UP3-4	.	T	3590;3574;3545;3541;3564	ENSP00000430497:N3590T;ENSP00000399605:N3545T;ENSP00000050961:N3541T;ENSP00000430848:N3564T	ENSP00000050961:N3541T	N	+	2	0	ZFHX4	77939274	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.664000	0.68045	2.064000	0.61679	0.528000	0.53228	AAT		0.458	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77776719	A	C	77776719	3	2	61	1	0	0	0	0	1	0	0	0	17674	101	4	4	10807	4	ZFHX4	8	77776719	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1269	77776719	68587303	5956	13941										
IL7	3574	broad.mit.edu	37	chr8	79648715	79648715	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaattattctcaccaaactCtttgttggttgggcttcacc	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:79648715C>A	ENST00000263851.4	-	5	1008	c.408G>T	c.(406-408)aaG>aaT	p.K136N	IL7_ENST00000520269.1_Missense_Mutation_p.K92N|IL7_ENST00000519833.1_5'UTR|IL7_ENST00000541183.1_Intron	NM_000880.3|NM_001199886.1|NM_001199887.1	NP_000871.1|NP_001186815.1|NP_001186816.1	P13232	IL7_HUMAN	interleukin 7	136					bone resorption (GO:0045453)|cell-cell signaling (GO:0007267)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|organ morphogenesis (GO:0009887)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell differentiation (GO:0045582)|regulation of gene expression (GO:0010468)|T cell lineage commitment (GO:0002360)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-7 receptor binding (GO:0005139)	p.K136N(1)		endometrium(2)|large_intestine(2)|lung(1)	5						TCACCAAACTCTTTGTTGGTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	8											49	48	48					8																	79648715		2203	4299	6502	79811270	SO:0001583	missense	3574			J04156	CCDS6224.1, CCDS56541.1, CCDS75755.1, CCDS75756.1	8q12-q13	2008-07-03				ENSG00000104432		"Interleukins and interleukin receptors"	6023	protein-coding gene	gene with protein product		146660					Standard	NM_000880		Approved	IL-7	uc003ybg.3	P13232		ENST00000263851.4:c.408G>T	8.37:g.79648715C>A	ENSP00000263851:p.Lys136Asn		79811270	A0N0L3|Q5FBY5|Q5FBY9	Missense_Mutation	SNP	ENST00000263851.4	37	CCDS6224.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.543773	0.27563	.	.	ENSG00000104432	ENST00000263851;ENST00000520269;ENST00000379114	T	0.50001	0.76	3.4	1.55	0.23275	.	0.152965	0.30752	N	0.008959	T	0.47060	0.1425	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.67900	0.89;0.954	T	0.33214	-0.9877	9	.	.	.	.	5.8794	0.18846	0.0:0.7497:0.0:0.2503	.	136;92	P13232;Q5FBY9	IL7_HUMAN;.	N	136;92;89	ENSP00000427750:K92N	.	K	-	3	2	IL7	79811270	0.998000	0.40836	0.998000	0.56505	0.125000	0.20455	0.093000	0.15086	0.429000	0.26202	0.644000	0.83932	AAG		0.323	IL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379429.1			A	79648715	C	A	79648715	3	1	61	1	0	0	0	0	1	0	0	0	7725	912	32	2	133	2	IL7	8	79648715	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1871996	79648715	66715307	5957	13942										
STMN2	11075	broad.mit.edu	37	chr8	80553627	80553627	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagatatggaagtgaagCaaatcaacaaacgtgcctct	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:80553627C>T	ENST00000220876.7	+	3	512	c.130C>T	c.(130-132)Caa>Taa	p.Q44*	STMN2_ENST00000518111.1_Nonsense_Mutation_p.Q44*|STMN2_ENST00000518491.1_Nonsense_Mutation_p.Q33*	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	44	Regulatory/phosphorylation domain. {ECO:0000255}.|SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)	p.Q44*(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			GGAAGTGAAGCAAATCAACAA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											84	81	82					8																	80553627		1940	4156	6096	80716182	SO:0001587	stop_gained	11075				CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"stathmin-like 2"	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.130C>T	8.37:g.80553627C>T	ENSP00000220876:p.Gln44*		80716182	A8K9M2|G3V110|O14952|Q6PK68	Nonsense_Mutation	SNP	ENST00000220876.7	37	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	C	33	5.226091	0.95173	.	.	ENSG00000104435	ENST00000220876;ENST00000414622;ENST00000518111;ENST00000518491	.	.	.	5.68	4.8	0.61643	.	0.114070	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-12.4926	15.1331	0.72542	0.0:0.7325:0.2675:0.0	.	.	.	.	X	44;44;44;33	.	ENSP00000220876:Q44X	Q	+	1	0	STMN2	80716182	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.505000	0.45424	1.380000	0.46344	0.467000	0.42956	CAA		0.403	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029		T	80553627	C	T	80553627	4	4	61	1	0	0	0	0	0	1	0	0	15348	711	25	3	140	3	STMN2	8	80553627	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	904912	80553627	65810395	5958	13943										
ZBTB10	65986	broad.mit.edu	37	chr8	81411785	81411785	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaatagtaggccaaatgaGaactcttattgctatcaact	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:81411785G>A	ENST00000430430.1	+	3	1808	c.1029G>A	c.(1027-1029)gaG>gaA	p.E343E	ZBTB10_ENST00000455036.3_Silent_p.E343E|ZBTB10_ENST00000379091.4_Silent_p.E51E|ZBTB10_ENST00000426744.2_Silent_p.E343E	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E343E(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			GGCCAAATGAGAACTCTTATT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	8											89	91	90					8																	81411785		1882	4122	6004	81574340	SO:0001819	synonymous_variant	65986			AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1029G>A	8.37:g.81411785G>A			81574340	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Silent	SNP	ENST00000430430.1	37	CCDS47880.1																																																																																				0.343	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		A	81411785	G	A	81411785	2	1	61	1	0	0	0	0	0	0	0	1	17562	933	33	3		3	ZBTB10	8	81411785	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	858158	81411785	64952237	5959	13944										
ZBTB10	65986	broad.mit.edu	37	chr8	81412187	81412187	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccagagtctgtagttgtGgactataataatagaaaacc	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:81412187G>A	ENST00000430430.1	+	3	2210	c.1431G>A	c.(1429-1431)gtG>gtA	p.V477V	ZBTB10_ENST00000455036.3_Silent_p.V477V|ZBTB10_ENST00000379091.4_Silent_p.V185V|ZBTB10_ENST00000426744.2_Silent_p.V477V	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	477					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V477V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			CTGTAGTTGTGGACTATAATA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	8											95	95	95					8																	81412187		1807	4079	5886	81574742	SO:0001819	synonymous_variant	65986			AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1431G>A	8.37:g.81412187G>A			81574742	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Silent	SNP	ENST00000430430.1	37	CCDS47880.1																																																																																				0.358	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		A	81412187	G	A	81412187	2	1	61	1	0	0	0	0	0	0	0	1	17562	1335	47	3		3	ZBTB10	8	81412187	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	402	81412187	64951835	5960	13945										
PAG1	55824	broad.mit.edu	37	chr8	81903751	81903751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggtccccactatgctgtCgcggcttcttttccctgaaa	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:81903751C>T	ENST00000220597.4	-	5	850	c.140G>A	c.(139-141)cGa>cAa	p.R47Q		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	47					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)	p.R47Q(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			ACTATGCTGTCGCGGCTTCTT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	8											140	119	126					8																	81903751		2203	4300	6503	82066306	SO:0001583	missense	55824			AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"Csk-binding protein", "transmembrane adaptor protein PAG"	605767	"phosphoprotein associated with glycosphingolipid microdomains 1"			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.140G>A	8.37:g.81903751C>T	ENSP00000220597:p.Arg47Gln		82066306	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	37	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.494039	0.44352	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.13	4.12	0.48240	.	0.160550	0.53938	D	0.000043	T	0.21267	0.0512	L	0.57536	1.79	0.09310	N	1	P	0.46327	0.876	B	0.34652	0.187	T	0.40794	-0.9544	9	0.51188	T	0.08	-23.321	3.3271	0.07071	0.0:0.6059:0.0:0.394	.	47	Q9NWQ8	PAG1_HUMAN	Q	47	.	ENSP00000220597:R47Q	R	-	2	0	PAG1	82066306	0.998000	0.40836	0.020000	0.16555	0.636000	0.38137	1.410000	0.34691	2.374000	0.81015	0.655000	0.94253	CGA		0.488	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		T	81903751	C	T	81903751	3	4	61	1	0	0	0	0	1	0	0	0	11419	884	31	1	1178	1	PAG1	8	81903751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	491564	81903751	64460271	5961	13946										
PAG1	55824	broad.mit.edu	37	chr8	81905453	81905453	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcccagcaggctccccgCgggccccatggcaggagcag	15	17	0	0	rs151324516		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:81905453C>T	ENST00000220597.4	-	4	720	c.10G>A	c.(10-12)Gcg>Acg	p.A4T		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	4				A -> V (in Ref. 4; AAH90931). {ECO:0000305}.	epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)	p.A4T(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			AGGCTCCCCGCGGGCCCCATG	0.597													C|||	1	0.000199681	0	0	5008	,	,		16509	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	THR/ALA	0,4406		0,0,2203	36	37	37		10	-1.4	0	8	dbSNP_134	37	2,8598	2.2+/-6.3	0,2,4298	no	missense	PAG1	NM_018440.3	58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	4/433	81905453	2,13004	2203	4300	6503	82068008	SO:0001583	missense	55824			AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"Csk-binding protein", "transmembrane adaptor protein PAG"	605767	"phosphoprotein associated with glycosphingolipid microdomains 1"			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.10G>A	8.37:g.81905453C>T	ENSP00000220597:p.Ala4Thr		82068008	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	37	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	C	8.753	0.921653	0.17982	0.0	2.33E-4	ENSG00000076641	ENST00000220597	.	.	.	5.48	-1.35	0.09114	.	1.718550	0.03233	N	0.179214	T	0.28101	0.0693	L	0.34521	1.04	0.09310	N	1	B	0.23540	0.087	B	0.11329	0.006	T	0.04427	-1.0952	9	0.19590	T	0.45	-0.0701	3.5452	0.07826	0.2535:0.4545:0.1691:0.1229	.	4	Q9NWQ8	PAG1_HUMAN	T	4	.	ENSP00000220597:A4T	A	-	1	0	PAG1	82068008	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.167000	0.09940	-1.026000	0.03330	-1.193000	0.01689	GCG		0.597	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		T	81905453	C	T	81905453	3	4	61	1	0	0	0	0	1	0	0	0	11419	768	27	1	1312	1	PAG1	8	81905453	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1702	81905453	64458569	5962	13947										
FABP9	646480	broad.mit.edu	37	chr8	82371562	82371562	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgccatgttccgggctgcGaaattcactcctacaagaca	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:82371562G>A	ENST00000379071.2	-	2	139	c.84C>T	c.(82-84)ttC>ttT	p.F28F	RP11-157I4.4_ENST00000524085.2_RNA	NM_001080526.1	NP_001073995.1	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis	28					acrosome assembly (GO:0001675)	acrosomal vesicle (GO:0001669)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.F28F(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6			Epithelial(68;0.186)			TCCGGGCTGCGAAATTCACTC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	8											100	99	99					8																	82371562		2203	4300	6503	82534117	SO:0001819	synonymous_variant	646480					8q21.13	2013-03-01			ENSG00000205186	ENSG00000205186		"Fatty acid binding protein family"	3563	protein-coding gene	gene with protein product						7958448	Standard	NM_001080526		Approved	PERF, T-FABP, PERF15	uc011lfo.2	Q0Z7S8	OTTHUMG00000164601	ENST00000379071.2:c.84C>T	8.37:g.82371562G>A			82534117		Silent	SNP	ENST00000379071.2	37																																																																																					0.393	FABP9-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379367.2	NM_001080526		A	82371562	G	A	82371562	2	1	61	1	0	0	0	0	0	0	0	1	5379	1049	37	1		1	FABP9	8	82371562	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	466109	82371562	63992460	5963	13948										
SLC10A5	347051	broad.mit.edu	37	chr8	82606447	82606447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatcctactgtatatataaGaattgacaggcatcatgatc	6	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:82606447G>T	ENST00000518568.1	-	1	1962	c.761C>A	c.(760-762)tCt>tAt	p.S254Y		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	254						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)	p.S254Y(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						GTATATATAAGAATTGACAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											73	76	75					8																	82606447		2203	4300	6503	82769002	SO:0001583	missense	347051				CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.761C>A	8.37:g.82606447G>T	ENSP00000428612:p.Ser254Tyr		82769002	B2RN26	Missense_Mutation	SNP	ENST00000518568.1	37	CCDS34915.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.190542	0.58017	.	.	ENSG00000253598	ENST00000518568	T	0.12147	2.71	6.01	5.12	0.69794	.	0.123130	0.37261	N	0.002173	T	0.36908	0.0984	M	0.70275	2.135	0.41973	D	0.990769	D	0.89917	1.0	D	0.76071	0.987	T	0.17961	-1.0352	10	0.56958	D	0.05	-12.2582	15.0279	0.71682	0.0:0.143:0.857:0.0	.	254	Q5PT55	NTCP5_HUMAN	Y	254	ENSP00000428612:S254Y	ENSP00000428612:S254Y	S	-	2	0	SLC10A5	82769002	1.000000	0.71417	0.938000	0.37757	0.441000	0.31987	3.847000	0.55895	1.530000	0.49136	0.585000	0.79938	TCT		0.373	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		T	82606447	G	T	82606447	3	4	61	1	0	0	0	0	1	0	0	0	14414	942	33	2	557	2	SLC10A5	8	82606447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	234885	82606447	63757575	5964	13949										
CHMP4C	92421	broad.mit.edu	37	chr8	82670430	82670430	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggaggaattaaataagaaGatgacaaatatccgccttcc	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:82670430G>T	ENST00000297265.4	+	4	730	c.537G>T	c.(535-537)aaG>aaT	p.K179N		NM_152284.3	NP_689497.1	Q96CF2	CHM4C_HUMAN	charged multivesicular body protein 4C	179	Intramolecular interaction with N- terminus. {ECO:0000250}.				abscission (GO:0009838)|cytokinesis checkpoint (GO:0031565)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of cytokinesis (GO:0032466)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|membrane (GO:0016020)|midbody (GO:0030496)	protein homodimerization activity (GO:0042803)	p.K179N(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	10						TAAATAAGAAGATGACAAATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											113	109	111					8																	82670430		2203	4300	6503	82832985	SO:0001583	missense	92421			AK000049	CCDS6233.1	8q21.13	2011-09-21	2011-09-21		ENSG00000164695	ENSG00000164695		"Charged multivesicular body proteins"	30599	protein-coding gene	gene with protein product	"Snf7 homologue associated with Alix 3"	610899	"chromatin modifying protein 4C"			12860994 , 14678797	Standard	NM_152284		Approved	MGC22825, Shax3, VPS32C	uc003ycl.3	Q96CF2	OTTHUMG00000164726	ENST00000297265.4:c.537G>T	8.37:g.82670430G>T	ENSP00000297265:p.Lys179Asn		82832985	B2RBZ1	Missense_Mutation	SNP	ENST00000297265.4	37	CCDS6233.1	.	.	.	.	.	.	.	.	.	.	G	8.409	0.843746	0.16963	.	.	ENSG00000164695	ENST00000297265	T	0.73575	-0.76	6.17	6.17	0.99709	.	0.180931	0.64402	D	0.000006	T	0.55433	0.1920	N	0.13371	0.34	0.34380	D	0.693004	B	0.09022	0.002	B	0.17979	0.02	T	0.58640	-0.7601	10	0.27082	T	0.32	-41.792	8.1392	0.31073	0.1799:0.0:0.8201:0.0	.	179	Q96CF2	CHM4C_HUMAN	N	179	ENSP00000297265:K179N	ENSP00000297265:K179N	K	+	3	2	CHMP4C	82832985	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.612000	0.36889	2.941000	0.99782	0.655000	0.94253	AAG		0.448	CHMP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379927.1	NM_152284		T	82670430	G	T	82670430	3	4	61	1	0	0	0	0	1	0	0	0	3364	933	33	2	551	2	CHMP4C	8	82670430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63983	82670430	63693592	5965	13950										
RALYL	138046	broad.mit.edu	37	chr8	85441609	85441609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caataagaatgaccccaagtCcatcaactcccgtgttttca	5	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:85441609C>T	ENST00000521268.1	+	2	1158	c.53C>T	c.(52-54)tCc>tTc	p.S18F	RALYL_ENST00000518566.1_Missense_Mutation_p.S18F|RALYL_ENST00000521695.1_Missense_Mutation_p.S18F|RALYL_ENST00000522455.1_Missense_Mutation_p.S18F|RALYL_ENST00000517638.1_Missense_Mutation_p.S31F	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	18							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S18F(3)		endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						GACCCCAAGTCCATCAACTCC	0.383																																																3	Substitution - Missense(3)	large_intestine(3)	8											66	71	69					8																	85441609		2013	4203	6216	85604164	SO:0001583	missense	138046				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.53C>T	8.37:g.85441609C>T	ENSP00000430367:p.Ser18Phe		85604164	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	37	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764374	0.89932	.	.	ENSG00000184672	ENST00000522613;ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517988;ENST00000517638;ENST00000522647	T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.71626	0.3362	M	0.88842	2.985	0.80722	D	1	D;D;D	0.71674	0.994;0.993;0.998	D;D;D	0.76575	0.947;0.947;0.988	T	0.77534	-0.2552	10	0.87932	D	0	.	19.2791	0.94044	0.0:1.0:0.0:0.0	.	18;31;18	B3KT61;G3V129;Q86SE5	.;.;RALYL_HUMAN	F	18;18;18;18;18;18;31;18	ENSP00000427787:S18F;ENSP00000430394:S18F;ENSP00000428667:S18F;ENSP00000430367:S18F;ENSP00000430065:S18F;ENSP00000428711:S18F;ENSP00000430128:S31F;ENSP00000429284:S18F	ENSP00000430128:S31F	S	+	2	0	RALYL	85604164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.775000	0.85489	2.630000	0.89119	0.558000	0.71614	TCC		0.383	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			T	85441609	C	T	85441609	3	4	61	1	0	0	0	0	1	0	0	0	13057	855	30	3	98	3	RALYL	8	85441609	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2771179	85441609	60922413	5966	13951										
LRRCC1	85444	broad.mit.edu	37	chr8	86035736	86035736	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaagtgactatggaaacaGaaaagaatgcaatagaaaag	10	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:86035736G>T	ENST00000360375.3	+	7	1168	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	LRRCC1_ENST00000414626.2_Missense_Mutation_p.R320I	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	340					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R340I(1)|p.R320I(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TATGGAAACAGAAAAGAATGC	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	8											83	82	82					8																	86035736		1809	4072	5881	86222988	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1019G>T	8.37:g.86035736G>T	ENSP00000353538:p.Arg340Ile		86222988	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.32|16.32	3.089896|3.089896	0.55968|0.55968	.|.	.|.	ENSG00000133739|ENSG00000133739	ENST00000360375;ENST00000414626|ENST00000426019	T;T|.	0.31510|.	1.49;1.49|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.165663|.	0.28983|.	N|.	0.013506|.	T|T	0.61362|0.61362	0.2341|0.2341	L|L	0.60455|0.60455	1.87|1.87	0.41643|0.41643	D|D	0.98908|0.98908	D;D;D;D|.	0.71674|.	0.998;0.996;0.998;0.979|.	P;P;P;P|.	0.62560|.	0.904;0.875;0.904;0.504|.	T|T	0.61392|0.61392	-0.7072|-0.7072	10|5	0.40728|.	T|.	0.16|.	-17.636|-17.636	8.0298|8.0298	0.30459|0.30459	0.121:0.1454:0.7336:0.0|0.121:0.1454:0.7336:0.0	.|.	247;320;247;340|.	B4DV06;Q9C099-2;E9PE41;Q9C099|.	.;.;.;LRCC1_HUMAN|.	I|I	340;320|247	ENSP00000353538:R340I;ENSP00000394695:R320I|.	ENSP00000353538:R340I|.	R|S	+|+	2|2	0|0	LRRCC1|LRRCC1	86222988|86222988	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	1.396000|1.396000	0.34531|0.34531	2.588000|2.588000	0.87417|0.87417	0.650000|0.650000	0.86243|0.86243	AGA|AGT		0.318	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		T	86035736	G	T	86035736	3	4	61	1	0	0	0	0	1	0	0	0	9055	942	33	2	1045	2	LRRCC1	8	86035736	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	594127	86035736	60328286	5967	13952										
LRRCC1	85444	broad.mit.edu	37	chr8	86047104	86047104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagatggttttgaaaatgTtgcaactgagttagcaaaga	10	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:86047104T>C	ENST00000360375.3	+	13	2140	c.1991T>C	c.(1990-1992)gTt>gCt	p.V664A	LRRCC1_ENST00000414626.2_Missense_Mutation_p.V644A	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	664					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V644A(1)|p.V664A(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TTTGAAAATGTTGCAACTGAG	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	8											62	59	60					8																	86047104		1810	4065	5875	86234356	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1991T>C	8.37:g.86047104T>C	ENSP00000353538:p.Val664Ala		86234356	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.735880	0.49045	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.32023	1.47;1.47	5.71	5.71	0.89125	.	0.000000	0.35555	N	0.003137	T	0.27697	0.0681	L	0.55481	1.735	0.41713	D	0.989465	P;B;P;B	0.45715	0.759;0.208;0.865;0.101	B;B;B;B	0.39503	0.187;0.084;0.301;0.032	T	0.06516	-1.0822	10	0.20519	T	0.43	-11.6347	11.8388	0.52342	0.0:0.07:0.0:0.93	.	571;644;571;664	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	A	664;644	ENSP00000353538:V664A;ENSP00000394695:V644A	ENSP00000353538:V664A	V	+	2	0	LRRCC1	86234356	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.724000	0.47285	2.171000	0.68590	0.533000	0.62120	GTT		0.313	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		C	86047104	T	C	86047104	3	2	61	1	0	0	0	0	1	0	0	0	9055	1725	60	4	2041	4	LRRCC1	8	86047104	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11368	86047104	60316918	5968	13953										
LRRCC1	85444	broad.mit.edu	37	chr8	86053747	86053747	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtattgattctgcaaatTtaaaggtattgtaagtaaaa	8	2	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:86053747T>G	ENST00000360375.3	+	18	3120	c.2971T>G	c.(2971-2973)Tta>Gta	p.L991V	LRRCC1_ENST00000414626.2_Missense_Mutation_p.L971V	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	991					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L971V(1)|p.L991V(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TTCTGCAAATTTAAAGGTATT	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	8											47	46	46					8																	86053747		1824	4083	5907	86240999	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.2971T>G	8.37:g.86053747T>G	ENSP00000353538:p.Leu991Val		86240999	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	T	8.794	0.931390	0.18131	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.30182	1.54;1.54	5.26	1.91	0.25777	.	1.622580	0.04368	N	0.358547	T	0.26702	0.0653	L	0.44542	1.39	0.26462	N	0.975435	B;B;B	0.29301	0.241;0.137;0.231	B;B;B	0.30495	0.116;0.058;0.048	T	0.22452	-1.0216	10	0.34782	T	0.22	1.9955	3.6447	0.08180	0.0988:0.0963:0.4918:0.3131	.	971;898;991	Q9C099-2;E9PE41;Q9C099	.;.;LRCC1_HUMAN	V	991;971	ENSP00000353538:L991V;ENSP00000394695:L971V	ENSP00000353538:L991V	L	+	1	2	LRRCC1	86240999	1.000000	0.71417	0.673000	0.29887	0.227000	0.25037	3.567000	0.53813	0.095000	0.17434	0.528000	0.53228	TTA		0.308	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		G	86053747	T	G	86053747	3	3	61	1	0	0	0	0	1	0	0	0	9055	1838	64	4	3041	4	LRRCC1	8	86053747	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6643	86053747	60310275	5969	13954										
CA3	761	broad.mit.edu	37	chr8	86352106	86352106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaataatgggaagacctgccGagttgtatttgatgatactt	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:86352106G>A	ENST00000285381.2	+	2	283	c.200G>A	c.(199-201)cGa>cAa	p.R67Q	RP11-317J10.2_ENST00000517697.1_RNA|RP11-317J10.2_ENST00000521761.1_RNA	NM_005181.3	NP_005172.1	P07451	CAH3_HUMAN	carbonic anhydrase III, muscle specific	67	Involved in proton transfer.				bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|response to ethanol (GO:0045471)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|nickel cation binding (GO:0016151)|zinc ion binding (GO:0008270)	p.R67Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23					Acetazolamide(DB00819)|Zonisamide(DB00909)	AAGACCTGCCGAGTTGTATTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											100	88	92					8																	86352106		2203	4300	6503	86539358	SO:0001583	missense	761			AJ006473	CCDS6238.1	8q21.2	2012-10-02					4.2.1.1	"Carbonic anhydrases"	1374	protein-coding gene	gene with protein product		114750				6221502	Standard	NM_005181		Approved	Car3, CAIII	uc003ydj.3	P07451		ENST00000285381.2:c.200G>A	8.37:g.86352106G>A	ENSP00000285381:p.Arg67Gln		86539358	B2R867|B3KUC8|O60842	Missense_Mutation	SNP	ENST00000285381.2	37	CCDS6238.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.848026	0.32699	.	.	ENSG00000164879	ENST00000285381;ENST00000426378	T	0.64260	-0.09	5.81	5.81	0.92471	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.137768	0.64402	D	0.000003	T	0.26629	0.0651	N	0.01505	-0.83	0.44417	D	0.99733	D	0.59357	0.985	B	0.31016	0.123	T	0.54248	-0.8322	10	0.02654	T	1	-18.954	19.0778	0.93169	0.0:0.0:1.0:0.0	.	67	P07451	CAH3_HUMAN	Q	67;51	ENSP00000285381:R67Q	ENSP00000285381:R67Q	R	+	2	0	CA3	86539358	0.998000	0.40836	0.996000	0.52242	0.838000	0.47535	4.138000	0.58017	2.741000	0.93983	0.650000	0.86243	CGA		0.413	CA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381090.1	NM_005181		A	86352106	G	A	86352106	3	1	61	1	0	0	0	0	1	0	0	0	2523	1058	37	1	206	1	CA3	8	86352106	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298359	86352106	60011916	5970	13955										
ATP6V0D2	245972	broad.mit.edu	37	chr8	87155128	87155128	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttgaggcattctataAattctgtaagaatcatggtg	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87155128A>C	ENST00000285393.3	+	5	726	c.584A>C	c.(583-585)aAa>aCa	p.K195T	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	195					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)	p.K195T(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						GCATTCTATAAATTCTGTAAG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											153	162	159					8																	87155128		2203	4294	6497	87224244	SO:0001583	missense	245972			AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"ATPases / V-type"	18266	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.584A>C	8.37:g.87155128A>C	ENSP00000285393:p.Lys195Thr		87224244		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.499944	0.44455	.	.	ENSG00000147614	ENST00000285393	T	0.33216	1.42	5.43	2.97	0.34412	.	0.268679	0.38058	N	0.001827	T	0.34948	0.0915	M	0.78223	2.4	0.54753	D	0.999986	B	0.13594	0.008	B	0.13407	0.009	T	0.16100	-1.0414	10	0.45353	T	0.12	-10.5217	12.141	0.53998	0.7339:0.2661:0.0:0.0	.	195	Q8N8Y2	VA0D2_HUMAN	T	195	ENSP00000285393:K195T	ENSP00000285393:K195T	K	+	2	0	ATP6V0D2	87224244	1.000000	0.71417	0.984000	0.44739	0.992000	0.81027	3.411000	0.52672	0.415000	0.25817	0.533000	0.62120	AAA		0.313	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565		C	87155128	A	C	87155128	3	2	61	1	0	0	0	0	1	0	0	0	1175	14	1	4	602	4	ATP6V0D2	8	87155128	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	803022	87155128	59208894	5971	13956										
ATP6V0D2	245972	broad.mit.edu	37	chr8	87162479	87162479	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgttggctcaagcagaaGactttgaccagatgaagaac	12	8	1	6	rs374663729		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87162479G>T	ENST00000285393.3	+	6	920	c.778G>T	c.(778-780)Gac>Tac	p.D260Y	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	260					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)	p.D260Y(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						TCAAGCAGAAGACTTTGACCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	102	106					8																	87162479		2203	4300	6503	87231595	SO:0001583	missense	245972			AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"ATPases / V-type"	18266	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.778G>T	8.37:g.87162479G>T	ENSP00000285393:p.Asp260Tyr		87231595		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	.	.	.	.	.	.	.	.	.	.	G	33	5.212351	0.95069	.	.	ENSG00000147614	ENST00000285393	T	0.39229	1.09	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.77751	0.4177	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83539	0.0095	10	0.87932	D	0	-18.3267	19.8676	0.96824	0.0:0.0:1.0:0.0	.	260	Q8N8Y2	VA0D2_HUMAN	Y	260	ENSP00000285393:D260Y	ENSP00000285393:D260Y	D	+	1	0	ATP6V0D2	87231595	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.771000	0.98977	2.941000	0.99782	0.655000	0.94253	GAC		0.473	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565		T	87162479	G	T	87162479	3	4	61	1	0	0	0	0	1	0	0	0	1175	942	33	2	800	2	ATP6V0D2	8	87162479	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7351	87162479	59201543	5972	13957										
SLC7A13	157724	broad.mit.edu	37	chr8	87242488	87242488	+	Frame_Shift_Del	DEL	T	T	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacactctcttgagctgtaTtttctcccctctatccattg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87242488delT	ENST00000297524.3	-	1	122	c.19delA	c.(19-21)atafs	p.I7fs	SLC7A13_ENST00000419776.2_Frame_Shift_Del_p.I7fs|SLC7A13_ENST00000520624.1_Intron	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	7						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)	p.I7fs*38(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						TTGAGCTGTATTTTCTCCCCT	0.368																																																1	Deletion - Frameshift(1)	large_intestine(1)	8											47	48	47					8																	87242488		2202	4298	6500	87311604	SO:0001589	frameshift_variant	157724			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.19delA	8.37:g.87242488delT	ENSP00000297524:p.Ile7fs		87311604	Q05C37|Q08AH9|Q96N84	Frame_Shift_Del	DEL	ENST00000297524.3	37	CCDS34917.1																																																																																				0.368	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		-	87242488	T	-	87242488	7	5	61	1	0	1	0	1	0	0	0	0	14732	1493	52	0	1409	0	SLC7A13	8	87242488	Frame_Shift_Del	DEL	T	TCGA-AG-A002-01A-01W-A00K-09	80009	87242488	59121534	5973	13958										
WWP1	11059	broad.mit.edu	37	chr8	87437508	87437508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgtggatcataatactcGaactaccacatgggagagac	9	8	1	1	rs267602027		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87437508G>A	ENST00000517970.1	+	10	1425	c.1118G>A	c.(1117-1119)cGa>cAa	p.R373Q	WWP1_ENST00000265428.4_Missense_Mutation_p.R373Q|WWP1_ENST00000341922.2_Missense_Mutation_p.R243Q|WWP1_ENST00000349423.2_Missense_Mutation_p.R155Q	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	373	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R373Q(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CATAATACTCGAACTACCACA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	8											114	96	102					8																	87437508		2203	4299	6502	87506624	SO:0001583	missense	11059			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1118G>A	8.37:g.87437508G>A	ENSP00000427793:p.Arg373Gln		87506624	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.671954	0.67928	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.22	5.22	0.72569	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	T	0.81113	0.4755	L	0.60957	1.885	0.58432	D	0.999998	B;B	0.32604	0.024;0.377	B;B	0.28385	0.049;0.089	T	0.81172	-0.1054	10	0.52906	T	0.07	.	18.7754	0.91910	0.0:0.0:1.0:0.0	.	155;373	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	Q	373;373;243;155	ENSP00000427793:R373Q;ENSP00000265428:R373Q;ENSP00000340564:R243Q;ENSP00000342665:R155Q	ENSP00000265428:R373Q	R	+	2	0	WWP1	87506624	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.765000	0.68834	2.431000	0.82371	0.655000	0.94253	CGA		0.333	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		A	87437508	G	A	87437508	3	1	61	1	0	0	0	0	1	0	0	0	17455	1058	37	1	1148	1	WWP1	8	87437508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	195020	87437508	58926514	5974	13959										
WWP1	11059	broad.mit.edu	37	chr8	87450854	87450854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacttgaggaggcgcttatAtgtaatatttagaggagaag	13	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87450854A>G	ENST00000517970.1	+	17	2097	c.1790A>G	c.(1789-1791)tAt>tGt	p.Y597C	WWP1_ENST00000265428.4_Missense_Mutation_p.Y597C|WWP1_ENST00000341922.2_Missense_Mutation_p.Y467C|WWP1_ENST00000349423.2_Missense_Mutation_p.Y379C	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	597	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.Y597C(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						AGGCGCTTATATGTAATATTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	8											77	80	79					8																	87450854		2203	4300	6503	87519970	SO:0001583	missense	11059			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1790A>G	8.37:g.87450854A>G	ENSP00000427793:p.Tyr597Cys		87519970	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.072802|4.072802	0.76415|0.76415	.|.	.|.	ENSG00000123124|ENSG00000123124	ENST00000520453|ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	.|T;T;T;T	.|0.76316	.|-1.01;-1.01;-1.01;-1.01	5.0|5.0	5.0|5.0	0.66597|0.66597	.|HECT (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87059|0.87059	0.6083|0.6083	M|M	0.77313|0.77313	2.365|2.365	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.66497	.|0.944;0.91	D|D	0.89023|0.89023	0.3436|0.3436	5|10	.|0.87932	.|D	.|0	.|.	14.9977|14.9977	0.71446|0.71446	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|379;597	.|Q9H0M0-6;Q9H0M0	.|.;WWP1_HUMAN	M|C	61|597;597;467;379	.|ENSP00000427793:Y597C;ENSP00000265428:Y597C;ENSP00000340564:Y467C;ENSP00000342665:Y379C	.|ENSP00000265428:Y597C	I|Y	+|+	3|2	3|0	WWP1|WWP1	87519970|87519970	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.915000|5.915000	0.69973|0.69973	1.993000|1.993000	0.58246|0.58246	0.528000|0.528000	0.53228|0.53228	ATA|TAT		0.318	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		G	87450854	A	G	87450854	3	3	61	1	0	0	0	0	1	0	0	0	17455	449	16	4	1848	4	WWP1	8	87450854	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13346	87450854	58913168	5975	13960										
WWP1	11059	broad.mit.edu	37	chr8	87454945	87454945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtctgcagataaatccaGcatcaaccattaatccagac	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87454945G>A	ENST00000517970.1	+	18	2243	c.1936G>A	c.(1936-1938)Gca>Aca	p.A646T	WWP1_ENST00000265428.4_Missense_Mutation_p.A646T|WWP1_ENST00000341922.2_Missense_Mutation_p.A516T|WWP1_ENST00000349423.2_Missense_Mutation_p.A428T	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	646	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.A646T(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						GATAAATCCAGCATCAACCAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	8											134	121	125					8																	87454945		2203	4300	6503	87524061	SO:0001583	missense	11059			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1936G>A	8.37:g.87454945G>A	ENSP00000427793:p.Ala646Thr		87524061	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.9|29.9	5.049454|5.049454	0.93740|0.93740	.|.	.|.	ENSG00000123124|ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423|ENST00000520453	T;T;T;T|.	0.57595|.	0.39;0.39;0.39;0.39|.	5.4|5.4	5.4|5.4	0.78164|0.78164	HECT (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.65606|0.65606	0.2707|0.2707	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.79108|.	0.956;0.992|.	T|T	0.60934|0.60934	-0.7164|-0.7164	10|5	0.34782|.	T|.	0.22|.	.|.	19.1599|19.1599	0.93526|0.93526	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	428;646|.	Q9H0M0-6;Q9H0M0|.	.;WWP1_HUMAN|.	T|N	646;646;516;428|146	ENSP00000427793:A646T;ENSP00000265428:A646T;ENSP00000340564:A516T;ENSP00000342665:A428T|.	ENSP00000265428:A646T|.	A|S	+|+	1|2	0|0	WWP1|WWP1	87524061|87524061	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.813000|9.813000	0.99286|0.99286	2.506000|2.506000	0.84524|0.84524	0.585000|0.585000	0.79938|0.79938	GCA|AGC		0.343	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		A	87454945	G	A	87454945	3	1	61	1	0	0	0	0	1	0	0	0	17455	971	34	3	1998	3	WWP1	8	87454945	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4091	87454945	58909077	5976	13961										
CPNE3	8895	broad.mit.edu	37	chr8	87544749	87544749	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcatagatttcagctgaaGaaataaaagataatagagtg	8	4	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87544749G>T	ENST00000521271.1	+	6	562	c.400G>T	c.(400-402)Gaa>Taa	p.E134*	CPNE3_ENST00000198765.4_Nonsense_Mutation_p.E134*	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	134	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)	p.E134*(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						TTCAGCTGAAGAAATAAAAGA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											104	116	112					8																	87544749		2203	4297	6500	87613865	SO:0001587	stop_gained	8895			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.400G>T	8.37:g.87544749G>T	ENSP00000430934:p.Glu134*		87613865	A8KA47|Q8IYA1	Nonsense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	30|30	5.051278|5.051278	0.93740|0.93740	.|.	.|.	ENSG00000085719|ENSG00000085719	ENST00000198765;ENST00000521271;ENST00000523072;ENST00000523001;ENST00000517771;ENST00000523469|ENST00000517391	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79563	.|0.4467	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77838	.|-0.2439	.|3	0.87932|.	D|.	0|.	-7.43|-7.43	19.604|19.604	0.95574|0.95574	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	134|50	.|.	ENSP00000198765:E134X|.	E|K	+|+	1|3	0|2	CPNE3|CPNE3	87613865|87613865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.827000|9.827000	0.99397|0.99397	2.642000|2.642000	0.89623|0.89623	0.591000|0.591000	0.81541|0.81541	GAA|AAG		0.313	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1			T	87544749	G	T	87544749	4	4	61	1	0	0	0	0	0	1	0	0	3819	943	33	2	414	2	CPNE3	8	87544749	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89804	87544749	58819273	5977	13962										
CPNE3	8895	broad.mit.edu	37	chr8	87567145	87567145	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaactctatggaccaactaAtttttctccaatcataaatc	2	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87567145A>C	ENST00000521271.1	+	15	1349	c.1187A>C	c.(1186-1188)aAt>aCt	p.N396T	CPNE3_ENST00000198765.4_Missense_Mutation_p.N396T	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	396	VWFA.				lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)	p.N396T(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						GGACCAACTAATTTTTCTCCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	8											148	139	142					8																	87567145		2203	4300	6503	87636261	SO:0001583	missense	8895			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.1187A>C	8.37:g.87567145A>C	ENSP00000430934:p.Asn396Thr		87636261	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	.	.	.	.	.	.	.	.	.	.	A	31	5.100294	0.94245	.	.	ENSG00000085719	ENST00000198765;ENST00000521271	T;T	0.26223	1.75;1.75	5.96	5.96	0.96718	von Willebrand factor, type A (1);Copine (1);	0.000000	0.85682	D	0.000000	T	0.61160	0.2325	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70626	-0.4820	10	0.87932	D	0	-11.6927	16.4338	0.83864	1.0:0.0:0.0:0.0	.	396	O75131	CPNE3_HUMAN	T	396	ENSP00000198765:N396T;ENSP00000430934:N396T	ENSP00000198765:N396T	N	+	2	0	CPNE3	87636261	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	9.335000	0.96500	2.270000	0.75569	0.533000	0.62120	AAT		0.428	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1			C	87567145	A	C	87567145	3	2	61	1	0	0	0	0	1	0	0	0	3819	101	4	4	1237	4	CPNE3	8	87567145	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22396	87567145	58796877	5978	13963										
CNGB3	54714	broad.mit.edu	37	chr8	87588277	87588278	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcctttatcttcattttcINStttttgtttatcttcatttt							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87588277_87588278insT	ENST00000320005.5	-	18	2231_2232	c.2184_2185insA	c.(2182-2187)aaagaafs	p.E729fs		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	729					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.E729fs*3(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						tcttcattttctttttgtttat	0.342																																																1	Insertion - Frameshift(1)	large_intestine(1)	8																																								87657394	SO:0001589	frameshift_variant	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2185dupA	8.37:g.87588282_87588282dupT	ENSP00000316605:p.Glu729fs		87657393	C9JA51|Q9NRE9	Frame_Shift_Ins	INS	ENST00000320005.5	37	CCDS6244.1																																																																																				0.342	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87588278	-	T	87588277	7	5	61	1	0	1	1	0	0	0	0	0	3607	922	32	0	248	0	CNGB3	8	87588277	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	21132	87588277	58775745	5979	13964										
CNGB3	54714	broad.mit.edu	37	chr8	87591386	87591386	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggataatgcactagaatttCttggagggtctttttgtcta	10	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87591386C>T	ENST00000320005.5	-	16	1923	c.1876G>A	c.(1876-1878)Gaa>Aaa	p.E626K		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	626					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.E626K(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						ACTAGAATTTCTTGGAGGGTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	8											131	141	138					8																	87591386		2203	4300	6503	87660502	SO:0001583	missense	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1876G>A	8.37:g.87591386C>T	ENSP00000316605:p.Glu626Lys		87660502	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.443993	0.63067	.	.	ENSG00000170289	ENST00000517327;ENST00000320005	D;D	0.96830	-1.69;-4.14	5.71	0.609	0.17575	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.406199	0.24764	N	0.035781	D	0.92580	0.7643	L	0.28608	0.87	0.46927	D	0.999253	B;B	0.26902	0.135;0.163	B;B	0.40477	0.222;0.33	D	0.84495	0.0613	10	0.66056	D	0.02	.	3.291	0.06949	0.1294:0.5624:0.1118:0.1963	.	621;626	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	K	17;626	ENSP00000428329:E17K;ENSP00000316605:E626K	ENSP00000316605:E626K	E	-	1	0	CNGB3	87660502	0.985000	0.35326	0.643000	0.29450	0.846000	0.48090	2.700000	0.47085	-0.168000	0.10853	0.563000	0.77884	GAA		0.438	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87591386	C	T	87591386	3	4	61	1	0	0	0	0	1	0	0	0	3607	922	32	3	565	3	CNGB3	8	87591386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3109	87591386	58772636	5980	13965										
CNGB3	54714	broad.mit.edu	37	chr8	87656094	87656094	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaagtatccagttgttcGaataactctgtcagagagaa	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87656094G>A	ENST00000320005.5	-	10	1110	c.1063C>T	c.(1063-1065)Cga>Tga	p.R355*		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	355					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.R355*(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CCAGTTGTTCGAATAACTCTG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	8	GRCh37	CM050554	CNGB3	M							106	101	103					8																	87656094		2203	4300	6503	87725210	SO:0001587	stop_gained	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1063C>T	8.37:g.87656094G>A	ENSP00000316605:p.Arg355*		87725210	C9JA51|Q9NRE9	Nonsense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	G	37	6.118747	0.97300	.	.	ENSG00000170289	ENST00000320005	.	.	.	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6384	0.95746	0.0:0.0:1.0:0.0	.	.	.	.	X	355	.	ENSP00000316605:R355X	R	-	1	2	CNGB3	87725210	1.000000	0.71417	1.000000	0.80357	0.640000	0.38277	7.381000	0.79718	2.703000	0.92315	0.655000	0.94253	CGA		0.363	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		A	87656094	G	A	87656094	4	1	61	1	0	0	0	0	0	1	0	0	3607	1066	37	1	1402	1	CNGB3	8	87656094	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64708	87656094	58707928	5981	13966										
CNGB3	54714	broad.mit.edu	37	chr8	87666269	87666269	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagaagtcctgtagtgttTccttagctcatttgaatcca	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87666269T>A	ENST00000320005.5	-	7	921	c.874A>T	c.(874-876)Aaa>Taa	p.K292*		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	292					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.K292*(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CTGTAGTGTTTCCTTAGCTCA	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											141	140	141					8																	87666269		2202	4299	6501	87735385	SO:0001587	stop_gained	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.874A>T	8.37:g.87666269T>A	ENSP00000316605:p.Lys292*		87735385	C9JA51|Q9NRE9	Nonsense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	T	34	5.296962	0.95574	.	.	ENSG00000170289	ENST00000320005	.	.	.	5.27	3.9	0.45041	.	0.569470	0.17805	N	0.161409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0734	0.30701	0.0:0.1745:0.0:0.8255	.	.	.	.	X	292	.	ENSP00000316605:K292X	K	-	1	0	CNGB3	87735385	1.000000	0.71417	0.958000	0.39756	0.741000	0.42261	1.891000	0.39738	1.989000	0.58080	0.454000	0.30748	AAA		0.289	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		A	87666269	T	A	87666269	4	1	61	1	0	0	0	0	0	1	0	0	3607	1792	62	5	1603	5	CNGB3	8	87666269	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10175	87666269	58697753	5982	13967										
CNGB3	54714	broad.mit.edu	37	chr8	87683200	87683200	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctggcttcgggtgaggaGagatctccctctaccaactt	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:87683200G>T	ENST00000320005.5	-	4	512	c.465C>A	c.(463-465)ctC>ctA	p.L155L		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	155					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.L155L(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CGGGTGAGGAGAGATCTCCCT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	8											207	207	207					8																	87683200		2203	4300	6503	87752316	SO:0001819	synonymous_variant	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.465C>A	8.37:g.87683200G>T			87752316	C9JA51|Q9NRE9	Silent	SNP	ENST00000320005.5	37	CCDS6244.1																																																																																				0.478	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87683200	G	T	87683200	2	4	61	1	0	0	0	0	0	0	0	1	3607	929	33	2		2	CNGB3	8	87683200	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16931	87683200	58680822	5983	13968										
CNBD1	168975	broad.mit.edu	37	chr8	88365983	88365983	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaccaaaaaagaagttgaGatggcaatcattgaagataa	8	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:88365983G>A	ENST00000518476.1	+	10	1323	c.1272G>A	c.(1270-1272)gaG>gaA	p.E424E		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	424								p.E424E(2)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AAGAAGTTGAGATGGCAATCA	0.318																																																2	Substitution - coding silent(2)	large_intestine(2)	8											87	85	85					8																	88365983		1840	4083	5923	88435099	SO:0001819	synonymous_variant	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1272G>A	8.37:g.88365983G>A			88435099		Silent	SNP	ENST00000518476.1	37	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.348264	0.01266	.	.	ENSG00000176571	ENST00000523299;ENST00000521593	.	.	.	4.98	0.207	0.15214	.	.	.	.	.	T	0.47192	0.1432	.	.	.	0.37203	D	0.904456	.	.	.	.	.	.	T	0.44329	-0.9335	4	.	.	.	-21.5028	6.4362	0.21825	0.5859:0.0:0.4141:0.0	.	.	.	.	K	116;61	.	.	R	+	2	0	CNBD1	88435099	0.432000	0.25554	0.455000	0.27031	0.012000	0.07955	0.211000	0.17474	0.117000	0.18138	-0.377000	0.06932	AGA		0.318	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		A	88365983	G	A	88365983	2	1	61	1	0	0	0	0	0	0	0	1	3597	933	33	3		3	CNBD1	8	88365983	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	682783	88365983	57998039	5984	13969										
DCAF4L2	138009	broad.mit.edu	37	chr8	88885451	88885451	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacagcgcagatcaatgCcaaagatctccccagagcga	8	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:88885451C>T	ENST00000319675.3	-	1	845	c.749G>A	c.(748-750)gGc>gAc	p.G250D		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	250								p.G250D(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CAGATCAATGCCAAAGATCTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	8											122	116	118					8																	88885451		2203	4300	6503	88954567	SO:0001583	missense	138009			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.749G>A	8.37:g.88885451C>T	ENSP00000316496:p.Gly250Asp		88954567		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.534616	0.27475	.	.	ENSG00000176566	ENST00000319675	T	0.70516	-0.49	1.74	0.759	0.18438	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.450948	0.28219	N	0.016145	T	0.51193	0.1660	N	0.14661	0.345	0.22581	N	0.998966	B	0.33512	0.415	B	0.38264	0.269	T	0.42378	-0.9455	10	0.34782	T	0.22	.	7.6675	0.28439	0.0:0.283:0.7169:0.0	.	250	Q8NA75	DC4L2_HUMAN	D	250	ENSP00000316496:G250D	ENSP00000316496:G250D	G	-	2	0	DCAF4L2	88954567	1.000000	0.71417	0.126000	0.21872	0.252000	0.25951	1.814000	0.38972	-0.353000	0.08224	-0.499000	0.04595	GGC		0.512	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		T	88885451	C	T	88885451	3	4	61	1	0	0	0	0	1	0	0	0	4278	739	26	3	442	3	DCAF4L2	8	88885451	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	519468	88885451	57478571	5985	13970										
DCAF4L2	138009	broad.mit.edu	37	chr8	88885807	88885807	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgattcagtgaggcccaGcacatagaattcaccttccg	9	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:88885807G>T	ENST00000319675.3	-	1	489	c.393C>A	c.(391-393)tgC>tgA	p.C131*		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	131								p.C131*(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						GTGAGGCCCAGCACATAGAAT	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											110	103	106					8																	88885807		2203	4300	6503	88954923	SO:0001587	stop_gained	138009			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.393C>A	8.37:g.88885807G>T	ENSP00000316496:p.Cys131*		88954923		Nonsense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295015	0.60086	.	.	ENSG00000176566	ENST00000319675	.	.	.	1.39	1.39	0.22231	.	0.040960	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.7882	0.13236	0.0:0.0:0.6372:0.3628	.	.	.	.	X	131	.	ENSP00000316496:C131X	C	-	3	2	DCAF4L2	88954923	1.000000	0.71417	0.007000	0.13788	0.025000	0.11179	3.747000	0.55134	0.750000	0.32877	0.467000	0.42956	TGC		0.562	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		T	88885807	G	T	88885807	4	4	61	1	0	0	0	0	0	1	0	0	4278	963	34	2	798	2	DCAF4L2	8	88885807	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356	88885807	57478215	5986	13971										
DCAF4L2	138009	broad.mit.edu	37	chr8	88886083	88886083	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctatacggcaatagttggcGaatctgaggaaacctagctg	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:88886083G>A	ENST00000319675.3	-	1	213	c.117C>T	c.(115-117)ttC>ttT	p.F39F		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	39								p.F39F(2)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						AATAGTTGGCGAATCTGAGGA	0.522																																																2	Substitution - coding silent(2)	large_intestine(2)	8											90	81	84					8																	88886083		2203	4300	6503	88955199	SO:0001819	synonymous_variant	138009			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.117C>T	8.37:g.88886083G>A			88955199		Silent	SNP	ENST00000319675.3	37	CCDS6245.1																																																																																				0.522	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88886083	G	A	88886083	2	1	61	1	0	0	0	0	0	0	0	1	4278	1049	37	1		1	DCAF4L2	8	88886083	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	276	88886083	57477939	5987	13972										
MMP16	4325	broad.mit.edu	37	chr8	89128907	89128907	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcggtgtgggggcactgtCggtagaggtcttgtaggtgg	21	5	1	1	rs149503873	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:89128907C>T	ENST00000286614.6	-	6	1193	c.912G>A	c.(910-912)ccG>ccA	p.P304P	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	304					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P304P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGGGCACTGTCGGTAGAGGTC	0.522													C|||	4	0.000798722	0.003	0	5008	,	,		15464	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						C		7,4399	12.9+/-30.5	0,7,2196	200	207	204		912	-6.8	0.4	8	dbSNP_134	204	0,8600		0,0,4300	no	coding-synonymous	MMP16	NM_005941.4		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		304/608	89128907	7,12999	2203	4300	6503	89198023	SO:0001819	synonymous_variant	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.912G>A	8.37:g.89128907C>T			89198023	B2RAN7|Q14824|Q52H48	Silent	SNP	ENST00000286614.6	37	CCDS6246.1																																																																																				0.522	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		T	89128907	C	T	89128907	2	4	61	1	0	0	0	0	0	0	0	1	9685	871	31	1		1	MMP16	8	89128907	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	242824	89128907	57235115	5988	13973										
NBN	4683	broad.mit.edu	37	chr8	90958376	90958376	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaatacctacctttttgaAtttcttgaaattttttagtt	4	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:90958376A>C	ENST00000265433.3	-	13	2216	c.2062T>G	c.(2062-2064)Ttc>Gtc	p.F688V	NBN_ENST00000409330.1_Missense_Mutation_p.F606V	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	688					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)	p.F688V(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			ACCTTTTTGAATTTCTTGAAA	0.308								Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	8											89	90	90					8																	90958376		2202	4298	6500	91027552	SO:0001583	missense	4683			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.2062T>G	8.37:g.90958376A>C	ENSP00000265433:p.Phe688Val		91027552	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.474528	0.84640	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	D;D	0.85861	-1.87;-2.04	5.65	5.65	0.86999	DNA repair Nbs1, C-terminal (1);	0.051901	0.85682	D	0.000000	D	0.91717	0.7381	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92571	0.6066	10	0.87932	D	0	-13.4292	15.8597	0.79012	1.0:0.0:0.0:0.0	.	688;688	A6H8Y5;O60934	.;NBN_HUMAN	V	688;606	ENSP00000265433:F688V;ENSP00000386924:F606V	ENSP00000265433:F688V	F	-	1	0	NBN	91027552	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.488000	0.60300	2.281000	0.76405	0.528000	0.53228	TTC		0.308	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90958376	A	C	90958376	3	2	61	1	0	0	0	0	1	0	0	0	10221	101	4	4	218	4	NBN	8	90958376	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1829469	90958376	55405646	5989	13974										
DECR1	1666	broad.mit.edu	37	chr8	91063963	91063963	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggaattcaacgacctgaGaaaggtaatgcttttgtgtg	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:91063963G>T	ENST00000220764.2	+	9	1032	c.944G>T	c.(943-945)aGa>aTa	p.R315I	DECR1_ENST00000522161.1_Missense_Mutation_p.R306I	NM_001359.1	NP_001350.1	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1, mitochondrial	315					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|NADPH binding (GO:0070402)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.R315I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	15			BRCA - Breast invasive adenocarcinoma(11;0.00953)			AACGACCTGAGAAAGGTAATG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	8											87	91	90					8																	91063963		2203	4300	6503	91133139	SO:0001583	missense	1666			L26050	CCDS6250.1	8q21.3	2011-09-14			ENSG00000104325	ENSG00000104325		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2753	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 18C, member 1"	222745		DECR		7818482, 19027726	Standard	NM_001359		Approved	SDR18C1	uc003yek.1	Q16698	OTTHUMG00000163829	ENST00000220764.2:c.944G>T	8.37:g.91063963G>T	ENSP00000220764:p.Arg315Ile		91133139	B7Z6B8|Q2M304|Q93085	Missense_Mutation	SNP	ENST00000220764.2	37	CCDS6250.1	.	.	.	.	.	.	.	.	.	.	G	9.074	0.997636	0.19043	.	.	ENSG00000104325	ENST00000220764;ENST00000522161	D;D	0.84873	-1.78;-1.91	5.88	1.92	0.25849	.	0.485095	0.23440	N	0.048144	T	0.78910	0.4358	L	0.56769	1.78	0.09310	N	0.999996	B;B	0.20164	0.016;0.042	B;B	0.14578	0.003;0.011	T	0.67469	-0.5663	10	0.44086	T	0.13	.	6.5131	0.22232	0.37:0.1306:0.4994:0.0	.	306;315	B7Z6B8;Q16698	.;DECR_HUMAN	I	315;306	ENSP00000220764:R315I;ENSP00000429779:R306I	ENSP00000220764:R315I	R	+	2	0	DECR1	91133139	0.000000	0.05858	0.347000	0.25668	0.247000	0.25773	-0.219000	0.09228	0.511000	0.28236	0.655000	0.94253	AGA		0.318	DECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375822.1			T	91063963	G	T	91063963	3	4	61	1	0	0	0	0	1	0	0	0	4388	942	33	2	978	2	DECR1	8	91063963	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105587	91063963	55300059	5990	13975										
OTUD6B	51633	broad.mit.edu	37	chr8	92083455	92083455	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggccaagttggaaaaaGaaatggaacagaaacataga	11	4	0	3	rs554642481		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:92083455G>T	ENST00000285420.4	+	2	361	c.262G>T	c.(262-264)Gaa>Taa	p.E88*	GS1-251I9.4_ENST00000522817.1_RNA|GS1-251I9.4_ENST00000524003.1_RNA|OTUD6B_ENST00000404789.3_5'UTR	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	58							cysteine-type peptidase activity (GO:0008234)	p.E88*(1)|p.E58*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			GTTGGAAAAAGAAATGGAACA	0.413																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											137	132	134					8																	92083455		2203	4300	6503	92152631	SO:0001587	stop_gained	51633				CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"OTU domain containing"	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758	ENST00000285420.4:c.262G>T	8.37:g.92083455G>T	ENSP00000285420:p.Glu88*		92152631	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Nonsense_Mutation	SNP	ENST00000285420.4	37	CCDS6253.2	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222704	0.79464	.	.	ENSG00000155100	ENST00000285420	.	.	.	5.73	5.73	0.89815	.	0.140945	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-10.9081	19.9031	0.96996	0.0:0.0:1.0:0.0	.	.	.	.	X	88	.	ENSP00000285420:E88X	E	+	1	0	OTUD6B	92152631	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	9.055000	0.93873	2.710000	0.92621	0.561000	0.74099	GAA		0.413	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023		T	92083455	G	T	92083455	4	4	61	1	0	0	0	0	0	1	0	0	11348	943	33	2	268	2	OTUD6B	8	92083455	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1019492	92083455	54280567	5991	13976										
RUNX1T1	862	broad.mit.edu	37	chr8	93017487	93017487	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgtttggccagtcttgcGcagtggaggagctcacgctg	14	10	3	0	rs138740592	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:93017487G>A	ENST00000523629.1	-	6	1051	c.597C>T	c.(595-597)tgC>tgT	p.C199C	RUNX1T1_ENST00000521553.1_Silent_p.C162C|RUNX1T1_ENST00000518844.1_Silent_p.C172C|RUNX1T1_ENST00000396218.1_Silent_p.C172C|RUNX1T1_ENST00000422361.2_Silent_p.C162C|RUNX1T1_ENST00000265814.3_Silent_p.C199C|RUNX1T1_ENST00000360348.2_Silent_p.C162C|RUNX1T1_ENST00000436581.2_Silent_p.C210C|RUNX1T1_ENST00000520724.1_Silent_p.C162C	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	199	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C199C(1)|p.C162C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CCAGTCTTGCGCAGTGGAGGA	0.562													G|||	2	0.000399361	0	0	5008	,	,		20140	0.001		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	8						G	,,,,,,,,,,,,,,	0,4406		0,0,2203	133	105	115		516,597,597,597,597,597,597,516,537,630,774,516,597,486,486	-2.7	1	8	dbSNP_134	115	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RUNX1T1	NM_001198625.1,NM_001198626.1,NM_001198627.1,NM_001198628.1,NM_001198629.1,NM_001198630.1,NM_001198631.1,NM_001198632.1,NM_001198633.1,NM_001198634.1,NM_001198679.1,NM_004349.3,NM_175634.2,NM_175635.2,NM_175636.2	,,,,,,,,,,,,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,,,,,,,,,,,,	172/578,199/605,199/605,199/605,199/605,199/605,199/605,172/578,179/585,210/616,258/664,172/578,199/605,162/568,162/568	93017487	2,13004	2203	4300	6503	93086663	SO:0001819	synonymous_variant	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.597C>T	8.37:g.93017487G>A			93086663	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Silent	SNP	ENST00000523629.1	37	CCDS6256.1																																																																																				0.562	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93017487	G	A	93017487	2	1	61	1	0	0	0	0	0	0	0	1	13784	1079	38	1		1	RUNX1T1	8	93017487	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	934032	93017487	53346535	5992	13977										
RUNX1T1	862	broad.mit.edu	37	chr8	93023241	93023241	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcaataccttcaaaaatgGgatgacaaaaggtctcagtg	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:93023241G>T	ENST00000523629.1	-	5	1001	c.547C>A	c.(547-549)Cca>Aca	p.P183T	RUNX1T1_ENST00000521553.1_Missense_Mutation_p.P146T|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.P156T|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.P156T|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.P146T|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.P183T|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.P146T|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.P194T|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.P146T	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	183	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P146T(1)|p.P183T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TTCAAAAATGGGATGACAAAA	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	8											140	134	136					8																	93023241		2203	4300	6503	93092417	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.547C>A	8.37:g.93023241G>T	ENSP00000428543:p.Pro183Thr		93092417	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	30	5.052617	0.93793	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844;ENST00000521553;ENST00000518992;ENST00000521054	T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14	5.87	5.87	0.94306	TAFH/NHR1 (3);	0.000000	0.85682	D	0.000000	T	0.79441	0.4446	M	0.81802	2.56	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;0.999	T	0.80137	-0.1508	10	0.87932	D	0	-11.0118	20.5827	0.99408	0.0:0.0:1.0:0.0	.	194;194;156;183;156	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	T	183;156;183;146;146;146;194;156;146;183;146	ENSP00000428543:P183T;ENSP00000379520:P156T;ENSP00000265814:P183T;ENSP00000353504:P146T;ENSP00000390137:P146T;ENSP00000428742:P146T;ENSP00000402257:P194T;ENSP00000430728:P156T;ENSP00000429728:P146T;ENSP00000431094:P183T;ENSP00000427763:P146T	ENSP00000265814:P183T	P	-	1	0	RUNX1T1	93092417	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	CCA		0.358	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	93023241	G	T	93023241	3	4	61	1	0	0	0	0	1	0	0	0	13784	1232	43	2	1299	2	RUNX1T1	8	93023241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5754	93023241	53340781	5993	13978										
FAM92A1	137392	broad.mit.edu	37	chr8	94713527	94713527	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaactgtgccaaatcttCgctgcctatgtgcggaaaac	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:94713527C>T	ENST00000518322.1	+	2	243	c.102C>T	c.(100-102)ttC>ttT	p.F34F	FAM92A1_ENST00000522324.1_Silent_p.F34F|LINC00535_ENST00000501400.1_RNA|FAM92A1_ENST00000423990.2_Silent_p.F34F	NM_145269.3	NP_660312.2	A1XBS5	F92A1_HUMAN	family with sequence similarity 92, member A1	34								p.F34F(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)	7	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GCCAAATCTTCGCTGCCTATG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	8											63	60	61					8																	94713527		1910	4123	6033	94782703	SO:0001819	synonymous_variant	137392				CCDS47892.1, CCDS64933.1	8q22.1	2005-09-22			ENSG00000188343	ENSG00000188343			30452	protein-coding gene	gene with protein product						12477932	Standard	XM_005250783		Approved	FLJ38979	uc022ayd.1	A1XBS5	OTTHUMG00000164238	ENST00000518322.1:c.102C>T	8.37:g.94713527C>T			94782703	A1XBS4|Q32ND3|Q6AHW7|Q8N8R1|Q96L09	Silent	SNP	ENST00000518322.1	37	CCDS47892.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.528149	0.27299	.	.	ENSG00000188343	ENST00000523453	.	.	.	4.38	0.61	0.17580	.	.	.	.	.	T	0.54967	0.1891	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47302	-0.9128	4	.	.	.	-7.0555	8.1902	0.31363	0.0:0.3906:0.0:0.6094	.	.	.	.	C	45	.	.	R	+	1	0	FAM92A1	94782703	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.706000	0.25690	0.260000	0.21731	-0.345000	0.07892	CGC		0.478	FAM92A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377890.4	NM_145269		T	94713527	C	T	94713527	2	4	61	1	0	0	0	0	0	0	0	1	5671	883	31	1		1	FAM92A1	8	94713527	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1690286	94713527	51650495	5994	13979										
RBM12B	389677	broad.mit.edu	37	chr8	94745658	94745658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaagttaacttaacttttCggggcccaactggcctatca	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:94745658C>T	ENST00000399300.2	-	3	3194	c.2981G>A	c.(2980-2982)cGa>cAa	p.R994Q	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Missense_Mutation_p.R874Q	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	994	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R994Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			CTTAACTTTTCGGGGCCCAAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											40	38	39					8																	94745658		1811	4084	5895	94814834	SO:0001583	missense	389677				CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2981G>A	8.37:g.94745658C>T	ENSP00000382239:p.Arg994Gln		94814834	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789441	0.90367	.	.	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.12465	2.68;2.68	5.44	5.44	0.79542	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.673599	0.14098	N	0.341596	T	0.52322	0.1727	M	0.93197	3.39	0.38248	D	0.941511	D	0.89917	1.0	D	0.91635	0.999	T	0.65207	-0.6224	10	0.87932	D	0	-0.5895	19.2621	0.93971	0.0:1.0:0.0:0.0	.	994	Q8IXT5	RB12B_HUMAN	Q	994;874	ENSP00000382239:R994Q;ENSP00000427729:R874Q	ENSP00000382239:R994Q	R	-	2	0	RBM12B	94814834	1.000000	0.71417	0.988000	0.46212	0.811000	0.45836	7.487000	0.81328	2.555000	0.86185	0.563000	0.77884	CGA		0.368	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		T	94745658	C	T	94745658	3	4	61	1	0	0	0	0	1	0	0	0	13151	884	31	1	28	1	RBM12B	8	94745658	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32131	94745658	51618364	5995	13980										
PDP1	54704	broad.mit.edu	37	chr8	94935822	94935822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcctgaagagcttgctcGaatgtacagagatgacatta	9	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:94935822G>A	ENST00000297598.4	+	2	1804	c.1535G>A	c.(1534-1536)cGa>cAa	p.R512Q	PDP1_ENST00000517764.1_Missense_Mutation_p.R512Q|PDP1_ENST00000520728.1_Missense_Mutation_p.R512Q|PDP1_ENST00000396200.3_Missense_Mutation_p.R537Q	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	512					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.R512Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						GAGCTTGCTCGAATGTACAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	8											103	94	97					8																	94935822		2203	4300	6503	95004998	SO:0001583	missense	54704			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1535G>A	8.37:g.94935822G>A	ENSP00000297598:p.Arg512Gln		95004998	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.462699	0.84425	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	6.17	6.17	0.99709	Protein phosphatase 2C-like (4);	0.058646	0.64402	D	0.000002	T	0.41143	0.1146	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.14364	-1.0475	10	0.87932	D	0	-7.9484	20.8794	0.99867	0.0:0.0:1.0:0.0	.	563;512	B4DYX8;Q9P0J1	.;PDP1_HUMAN	Q	512;512;537;512	ENSP00000297598:R512Q;ENSP00000428317:R512Q;ENSP00000379503:R537Q;ENSP00000430380:R512Q	ENSP00000297598:R512Q	R	+	2	0	PDP1	95004998	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.441000	0.97557	2.941000	0.99782	0.655000	0.94253	CGA		0.453	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		A	94935822	G	A	94935822	3	1	61	1	0	0	0	0	1	0	0	0	11716	1058	37	1	1718	1	PDP1	8	94935822	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190164	94935822	51428200	5996	13981										
RAD54B	25788	broad.mit.edu	37	chr8	95404039	95404039	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaggtgggagatatttaTttataatttcttgggttctt	9	2	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95404039T>G	ENST00000336148.5	-	10	1731	c.1607A>C	c.(1606-1608)aAt>aCt	p.N536T		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	536					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)	p.N536T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GAGATATTTATTTATAATTTC	0.383								Direct reversal of damage;Homologous recombination																																								1	Substitution - Missense(1)	large_intestine(1)	8											99	111	107					8																	95404039		2203	4300	6503	95473215	SO:0001583	missense	25788			AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1607A>C	8.37:g.95404039T>G	ENSP00000336606:p.Asn536Thr		95473215	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.314498	0.60524	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.92699	-3.09	4.89	4.89	0.63831	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.83599	0.5289	N	0.12502	0.225	0.80722	D	1	B	0.32283	0.362	B	0.32980	0.156	T	0.81272	-0.1008	10	0.13853	T	0.58	-3.4213	14.8183	0.70052	0.0:0.0:0.0:1.0	.	536	Q9Y620	RA54B_HUMAN	T	536;208	ENSP00000336606:N536T	ENSP00000336606:N536T	N	-	2	0	RAD54B	95473215	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	1.947000	0.56498	0.528000	0.53228	AAT		0.383	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		G	95404039	T	G	95404039	3	3	61	1	0	0	0	0	1	0	0	0	13029	1493	52	4	1149	4	RAD54B	8	95404039	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	468217	95404039	50959983	5997	13982										
RAD54B	25788	broad.mit.edu	37	chr8	95412519	95412519	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctagccatttttgaaattCtttcttccaattattcacca	2	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95412519C>A	ENST00000336148.5	-	7	1241	c.1117G>T	c.(1117-1119)Gaa>Taa	p.E373*		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	373	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)	p.E373*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TTTTGAAATTCTTTCTTCCAA	0.373								Direct reversal of damage;Homologous recombination																																								1	Substitution - Nonsense(1)	large_intestine(1)	8											88	86	87					8																	95412519		2203	4300	6503	95481695	SO:0001587	stop_gained	25788			AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1117G>T	8.37:g.95412519C>A	ENSP00000336606:p.Glu373*		95481695	F6WBS8	Nonsense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	C	39	7.760634	0.98474	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.6825	19.4213	0.94723	0.0:1.0:0.0:0.0	.	.	.	.	X	373;46	.	ENSP00000336606:E373X	E	-	1	0	RAD54B	95481695	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.589000	0.87451	0.655000	0.94253	GAA		0.373	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		A	95412519	C	A	95412519	4	1	61	1	0	0	0	0	0	1	0	0	13029	922	32	2	1651	2	RAD54B	8	95412519	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8480	95412519	50951503	5998	13983										
KIAA1429	25962	broad.mit.edu	37	chr8	95522038	95522038	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctctgcatatctttcatCacctttaatagttccattaa	2	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95522038C>T	ENST00000297591.5	-	15	3832	c.3757G>A	c.(3757-3759)Gat>Aat	p.D1253N	KIAA1429_ENST00000523405.1_5'UTR|KIAA1429_ENST00000437199.1_Missense_Mutation_p.D1253N	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1253					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.D1253N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TATCTTTCATCACCTTTAATA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											97	95	96					8																	95522038		2203	4300	6503	95591214	SO:0001583	missense	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.3757G>A	8.37:g.95522038C>T	ENSP00000297591:p.Asp1253Asn		95591214	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245207	0.80024	.	.	ENSG00000164944	ENST00000297591;ENST00000437199	T;T	0.69685	0.12;-0.42	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.81133	0.4759	M	0.63843	1.955	0.80722	D	1	D	0.67145	0.996	D	0.79784	0.993	T	0.80327	-0.1429	10	0.54805	T	0.06	-19.4204	20.1006	0.97874	0.0:1.0:0.0:0.0	.	1253	Q69YN4	VIR_HUMAN	N	1253	ENSP00000297591:D1253N;ENSP00000395600:D1253N	ENSP00000297591:D1253N	D	-	1	0	KIAA1429	95591214	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.513000	0.73742	2.757000	0.94681	0.561000	0.74099	GAT		0.403	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		T	95522038	C	T	95522038	3	4	61	1	0	0	0	0	1	0	0	0	8252	826	29	3	1721	3	KIAA1429	8	95522038	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109519	95522038	50841984	5999	13984										
KIAA1429	25962	broad.mit.edu	37	chr8	95522784	95522784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgtgccagagaaagagcGaactatttcttggagcaact	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95522784G>A	ENST00000297591.5	-	14	3562	c.3487C>T	c.(3487-3489)Cgc>Tgc	p.R1163C	KIAA1429_ENST00000523405.1_Intron|KIAA1429_ENST00000437199.1_Missense_Mutation_p.R1163C	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1163					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1163C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			GAGAAAGAGCGAACTATTTCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											149	130	136					8																	95522784		2203	4300	6503	95591960	SO:0001583	missense	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.3487C>T	8.37:g.95522784G>A	ENSP00000297591:p.Arg1163Cys		95591960	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477622	0.63849	.	.	ENSG00000164944	ENST00000297591;ENST00000437199	T;T	0.67698	-0.28;-0.28	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.80824	0.4697	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80939	-0.1158	10	0.66056	D	0.02	-8.3847	19.9405	0.97159	0.0:0.0:1.0:0.0	.	1163	Q69YN4	VIR_HUMAN	C	1163	ENSP00000297591:R1163C;ENSP00000395600:R1163C	ENSP00000297591:R1163C	R	-	1	0	KIAA1429	95591960	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.820000	0.62671	2.716000	0.92895	0.650000	0.86243	CGC		0.443	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		A	95522784	G	A	95522784	3	1	61	1	0	0	0	0	1	0	0	0	8252	1058	37	1	1995	1	KIAA1429	8	95522784	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	746	95522784	50841238	6000	13985										
KIAA1429	25962	broad.mit.edu	37	chr8	95523508	95523508	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccttcaagattgaagaaaGaacttcttttaacattaaag	5	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95523508G>T	ENST00000297591.5	-	13	3370	c.3295C>A	c.(3295-3297)Ctt>Att	p.L1099I	KIAA1429_ENST00000523405.1_5'UTR|KIAA1429_ENST00000421249.2_Missense_Mutation_p.L1099I|KIAA1429_ENST00000437199.1_Missense_Mutation_p.L1099I	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1099					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L1099I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ATTGAAGAAAGAACTTCTTTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											48	50	49					8																	95523508		2203	4300	6503	95592684	SO:0001583	missense	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.3295C>A	8.37:g.95523508G>T	ENSP00000297591:p.Leu1099Ile		95592684	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837088	0.50951	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.51574	0.7;0.72;0.71	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.66297	0.2775	L	0.48986	1.54	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.75484	0.986;0.986	T	0.65372	-0.6184	10	0.66056	D	0.02	-12.689	20.327	0.98704	0.0:0.0:1.0:0.0	.	1099;1099	Q69YN4-4;Q69YN4	.;VIR_HUMAN	I	1099	ENSP00000297591:L1099I;ENSP00000395600:L1099I;ENSP00000398390:L1099I	ENSP00000297591:L1099I	L	-	1	0	KIAA1429	95592684	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.061000	0.64319	2.794000	0.96219	0.650000	0.86243	CTT		0.373	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		T	95523508	G	T	95523508	3	4	61	1	0	0	0	0	1	0	0	0	8252	942	33	2	2245	2	KIAA1429	8	95523508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	724	95523508	50840514	6001	13986										
KIAA1429	25962	broad.mit.edu	37	chr8	95539112	95539112	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcccagctttgagctgtcGaacatttaaggcgataggtt	12	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95539112G>A	ENST00000297591.5	-	8	1435	c.1360C>T	c.(1360-1362)Cga>Tga	p.R454*	KIAA1429_ENST00000421249.2_Nonsense_Mutation_p.R454*|KIAA1429_ENST00000437199.1_Nonsense_Mutation_p.R454*	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	454					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R454*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TTGAGCTGTCGAACATTTAAG	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											110	104	106					8																	95539112		2203	4300	6503	95608288	SO:0001587	stop_gained	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1360C>T	8.37:g.95539112G>A	ENSP00000297591:p.Arg454*		95608288	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Nonsense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	38	6.688451	0.97764	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	.	.	.	5.85	2.94	0.34122	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6099	15.3522	0.74399	0.0:0.0:0.6376:0.3624	.	.	.	.	X	454	.	ENSP00000297591:R454X	R	-	1	2	KIAA1429	95608288	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.938000	0.48987	0.777000	0.33496	0.563000	0.77884	CGA		0.458	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		A	95539112	G	A	95539112	4	1	61	1	0	0	0	0	0	1	0	0	8252	1066	37	1	4200	1	KIAA1429	8	95539112	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15604	95539112	50824910	6002	13987										
ESRP1	54845	broad.mit.edu	37	chr8	95704959	95704959	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacagctgctaatcttagCggtgtccctccacagcctgg	9	15	1	0	rs369829287	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95704959C>T	ENST00000433389.2	+	14	2065	c.1875C>T	c.(1873-1875)agC>agT	p.S625S	ESRP1_ENST00000423620.2_Silent_p.S621S|ESRP1_ENST00000358397.5_Silent_p.S621S|ESRP1_ENST00000454170.2_Intron	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	625					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)	p.S625S(2)|p.S621S(1)	ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						CTAATCTTAGCGGTGTCCCTC	0.493													C|||	2	0.000399361	0	0.0029	5008	,	,		19022	0		0	False		,,,				2504	0															3	Substitution - coding silent(3)	large_intestine(3)	8						C	,,,,	1,3823		0,1,1911	92	88	90		1863,,1863,,1875	5.2	1	8		90	0,8216		0,0,4108	no	coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	0,1,6019	TT,TC,CC		0.0,0.0262,0.0083	,,,,	621/678,,621/660,,625/682	95704959	1,12039	1912	4108	6020	95774135	SO:0001819	synonymous_variant	54845			AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"RNA binding motif (RRM) containing"	25966	protein-coding gene	gene with protein product		612959	"RNA binding motif protein 35A"	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.1875C>T	8.37:g.95704959C>T			95774135	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1																																																																																				0.493	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		T	95704959	C	T	95704959	2	4	61	1	0	0	0	0	0	0	0	1	5271	767	27	1		1	ESRP1	8	95704959	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165847	95704959	50659063	6003	13988										
DPY19L4	286148	broad.mit.edu	37	chr8	95796020	95796020	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgatgatcttctcaagaGaaatgaaaatgtaagacatt	8	4	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95796020G>T	ENST00000414645.2	+	17	1937	c.1838G>T	c.(1837-1839)aGa>aTa	p.R613I		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	613						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.R613I(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					CTTCTCAAGAGAAATGAAAAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											90	83	86					8																	95796020		2203	4300	6503	95865196	SO:0001583	missense	286148				CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.1838G>T	8.37:g.95796020G>T	ENSP00000389630:p.Arg613Ile		95865196	Q6ZW32|Q6ZW42|Q7Z329	Missense_Mutation	SNP	ENST00000414645.2	37	CCDS34924.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611000	0.87258	.	.	ENSG00000156162	ENST00000414645	T	0.77620	-1.11	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.88145	0.6358	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89565	0.3809	10	0.87932	D	0	-17.5205	18.5125	0.90921	0.0:0.0:1.0:0.0	.	613	Q7Z388	D19L4_HUMAN	I	613	ENSP00000389630:R613I	ENSP00000389630:R613I	R	+	2	0	DPY19L4	95865196	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.417000	0.90247	2.454000	0.82982	0.650000	0.86243	AGA		0.368	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787		T	95796020	G	T	95796020	3	4	61	1	0	0	0	0	1	0	0	0	4754	942	33	2	1904	2	DPY19L4	8	95796020	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91061	95796020	50568002	6004	13989										
INTS8	55656	broad.mit.edu	37	chr8	95844297	95844297	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatctttatgtccatacGatgagaactctagatttatt	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95844297G>A	ENST00000523731.1	+	6	781	c.648G>A	c.(646-648)acG>acA	p.T216T	INTS8_ENST00000447247.1_Silent_p.T216T	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	216					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.T216T(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					ATGTCCATACGATGAGAACTC	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	8											72	71	71					8																	95844297		2203	4300	6503	95913473	SO:0001819	synonymous_variant	55656			AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.648G>A	8.37:g.95844297G>A			95913473	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	G	7.674	0.687559	0.14973	.	.	ENSG00000164941	ENST00000520526	.	.	.	5.3	-10.6	0.00265	.	.	.	.	.	T	0.42765	0.1217	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53507	-0.8429	4	.	.	.	-32.0142	6.5836	0.22609	0.135:0.2401:0.5147:0.1103	.	.	.	.	Q	38	.	.	R	+	2	0	INTS8	95913473	0.000000	0.05858	0.330000	0.25442	0.964000	0.63967	-4.468000	0.00229	-2.927000	0.00302	-0.982000	0.02568	CGA		0.373	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		A	95844297	G	A	95844297	2	1	61	1	0	0	0	0	0	0	0	1	7805	1045	37	1		1	INTS8	8	95844297	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48277	95844297	50519725	6005	13990										
INTS8	55656	broad.mit.edu	37	chr8	95848808	95848808	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccacaaattcagctgtCtatgaaaatgccagggaaaa	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95848808C>A	ENST00000523731.1	+	7	943	c.810C>A	c.(808-810)gtC>gtA	p.V270V	INTS8_ENST00000447247.1_Silent_p.V270V	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	270					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.V270V(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					ATTCAGCTGTCTATGAAAATG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	8											90	91	91					8																	95848808		2203	4300	6503	95917984	SO:0001819	synonymous_variant	55656			AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.810C>A	8.37:g.95848808C>A			95917984	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	C	7.877	0.729462	0.15507	.	.	ENSG00000164941	ENST00000520526	.	.	.	5.76	1.81	0.25067	.	.	.	.	.	T	0.42494	0.1205	.	.	.	0.49130	D	0.999753	.	.	.	.	.	.	T	0.25779	-1.0122	4	.	.	.	-32.7043	1.2691	0.02017	0.1429:0.3401:0.1388:0.3783	.	.	.	.	Y	92	.	.	S	+	2	0	INTS8	95917984	0.128000	0.22383	0.759000	0.31340	0.989000	0.77384	0.413000	0.21148	0.379000	0.24794	-0.350000	0.07774	TCT		0.358	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		A	95848808	C	A	95848808	2	1	61	1	0	0	0	0	0	0	0	1	7805	900	32	2		2	INTS8	8	95848808	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4511	95848808	50515214	6006	13991										
CCNE2	9134	broad.mit.edu	37	chr8	95895114	95895114	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggctagaatacacagatCtaaaagctaacaggaaaaac	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:95895114C>A	ENST00000520509.1	-	10	1090	c.838G>T	c.(838-840)Gat>Tat	p.D280Y	CCNE2_ENST00000308108.4_Missense_Mutation_p.D280Y|RP11-347C18.5_ENST00000605911.1_RNA|CCNE2_ENST00000396133.3_Missense_Mutation_p.D280Y|CCNE2_ENST00000523476.1_5'Flank			O96020	CCNE2_HUMAN	cyclin E2	280					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)	p.D280Y(1)		cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					ATACACAGATCTAAAAGCTAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											93	90	91					8																	95895114		2203	4300	6503	95964290	SO:0001583	missense	9134			AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.838G>T	8.37:g.95895114C>A	ENSP00000429089:p.Asp280Tyr		95964290	O95439	Missense_Mutation	SNP	ENST00000520509.1	37	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.941779	0.92526	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000542725;ENST00000396133	T;T;T	0.42513	1.38;1.38;0.97	6.06	6.06	0.98353	Cyclin, C-terminal (1);Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.72875	0.3515	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75929	-0.3144	10	0.72032	D	0.01	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	280;280	Q8WUE3;O96020	.;CCNE2_HUMAN	Y	280;280;172;280	ENSP00000429089:D280Y;ENSP00000309181:D280Y;ENSP00000379437:D280Y	ENSP00000309181:D280Y	D	-	1	0	CCNE2	95964290	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	2.880000	0.98712	0.650000	0.86243	GAT		0.373	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702		A	95895114	C	A	95895114	3	1	61	1	0	0	0	0	1	0	0	0	2927	913	32	2	388	2	CCNE2	8	95895114	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46306	95895114	50468908	6007	13992										
MTERFD1	51001	broad.mit.edu	37	chr8	97251734	97251734	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatctaaagcgtttttaaGaatttttcaaagtcctgtac	5	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:97251734G>T	ENST00000287025.3	-	8	1337	c.1239C>A	c.(1237-1239)ttC>ttA	p.F413L	KB-1043D8.6_ENST00000520575.1_RNA|MTERFD1_ENST00000523821.1_3'UTR|MTERFD1_ENST00000522822.1_Missense_Mutation_p.F292L|MTERFD1_ENST00000524341.1_Missense_Mutation_p.F169L	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		413					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)	p.F413L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					GCGTTTTTAAGAATTTTTCAA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	8											39	41	40					8																	97251734		2200	4295	6495	97320910	SO:0001583	missense	51001																														ENST00000287025.3:c.1239C>A	8.37:g.97251734G>T	ENSP00000287025:p.Phe413Leu		97320910	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	37	CCDS6270.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.811475	0.70797	.	.	ENSG00000156469	ENST00000522822;ENST00000524341;ENST00000287025	T;T;T	0.67345	0.2;-0.26;-0.01	5.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.80523	0.4639	M	0.82716	2.605	0.58432	D	0.999999	D	0.76494	0.999	D	0.79784	0.993	T	0.81439	-0.0932	10	0.56958	D	0.05	-15.772	8.8356	0.35111	0.2541:0.0:0.7459:0.0	.	413	Q96E29	MTER1_HUMAN	L	292;169;413	ENSP00000430138:F292L;ENSP00000429267:F169L;ENSP00000287025:F413L	ENSP00000287025:F413L	F	-	3	2	MTERFD1	97320910	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.879000	0.39618	1.368000	0.46115	0.655000	0.94253	TTC		0.284	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1			T	97251734	G	T	97251734	3	4	61	1	0	0	0	0	1	0	0	0	9949	933	33	2	18	2	MTERFD1	8	97251734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1356620	97251734	49112288	6008	13993										
PTDSS1	9791	broad.mit.edu	37	chr8	97316341	97316341	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctagctggacctatgttCgatggtttgaccccaaatct	9	11	1	1	rs142695191	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:97316341C>T	ENST00000517309.1	+	7	1152	c.826C>T	c.(826-828)Cga>Tga	p.R276*	PTDSS1_ENST00000522072.1_Nonsense_Mutation_p.R73*|PTDSS1_ENST00000518776.1_3'UTR|PTDSS1_ENST00000455950.2_Nonsense_Mutation_p.R130*	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	276					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.R276*(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	GACCTATGTTCGATGGTTTGA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											212	206	208					8																	97316341		2203	4300	6503	97385517	SO:0001587	stop_gained	9791			D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.826C>T	8.37:g.97316341C>T	ENSP00000430548:p.Arg276*		97385517	E5RFC5|Q9BUQ5	Nonsense_Mutation	SNP	ENST00000517309.1	37	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	C	38	7.234577	0.98154	.	.	ENSG00000156471	ENST00000517309;ENST00000455950;ENST00000522072	.	.	.	5.81	2.78	0.32641	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4952	13.2206	0.59885	0.5257:0.4743:0.0:0.0	.	.	.	.	X	276;130;73	.	ENSP00000401248:R130X	R	+	1	2	PTDSS1	97385517	1.000000	0.71417	0.158000	0.22627	0.994000	0.84299	4.150000	0.58098	0.246000	0.21394	0.655000	0.94253	CGA		0.468	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2			T	97316341	C	T	97316341	4	4	61	1	0	0	0	0	0	1	0	0	12770	876	31	1	852	1	PTDSS1	8	97316341	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64607	97316341	49047681	6009	13994										
SDC2	6383	broad.mit.edu	37	chr8	97621642	97621642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtggagttattggctttCtctttgcaatttttcttatc	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:97621642C>A	ENST00000302190.4	+	5	1393	c.472C>A	c.(472-474)Ctc>Atc	p.L158I	SDC2_ENST00000522911.1_Missense_Mutation_p.L129I|SDC2_ENST00000518385.1_Missense_Mutation_p.L122I|SDC2_ENST00000519914.1_Missense_Mutation_p.L129I	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	158					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.L158I(1)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	TATTGGCTTTCTCTTTGCAAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											168	152	157					8																	97621642		2203	4300	6503	97690818	SO:0001583	missense	6383			BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"Proteoglycans / Cell Surface : Syndecans", "CD molecules"	10659	protein-coding gene	gene with protein product	"syndecan proteoglycan 2"	142460	"heparan sulfate proteoglycan 1, cell surface-associated"	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.472C>A	8.37:g.97621642C>A	ENSP00000307046:p.Leu158Ile		97690818	B3KQA3|Q6PIS6|Q9H6V1	Missense_Mutation	SNP	ENST00000302190.4	37	CCDS6272.1	.	.	.	.	.	.	.	.	.	.	C	18.64	3.667080	0.67814	.	.	ENSG00000169439	ENST00000302190;ENST00000518385;ENST00000545117;ENST00000546193;ENST00000522911;ENST00000519914;ENST00000521590;ENST00000523877	T;T;T;T;T	0.59224	0.57;0.79;0.66;0.66;0.28	6.05	6.05	0.98169	.	0.060857	0.64402	D	0.000002	T	0.74321	0.3701	L	0.60957	1.885	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.70059	-0.4976	10	0.41790	T	0.15	-12.1489	20.6013	0.99457	0.0:1.0:0.0:0.0	.	158	P34741	SDC2_HUMAN	I	158;122;158;148;129;129;129;129	ENSP00000307046:L158I;ENSP00000429045:L122I;ENSP00000427784:L129I;ENSP00000428256:L129I;ENSP00000429121:L129I	ENSP00000307046:L158I	L	+	1	0	SDC2	97690818	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.066000	0.71185	2.878000	0.98634	0.650000	0.86243	CTC		0.413	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998		A	97621642	C	A	97621642	3	1	61	1	0	0	0	0	1	0	0	0	13989	913	32	2	490	2	SDC2	8	97621642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	305301	97621642	48742380	6010	13995										
MTDH	92140	broad.mit.edu	37	chr8	98718943	98718943	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaagaaagagcttcacttCtaaagtcccaggaaccaatt	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:98718943C>A	ENST00000336273.3	+	8	1565	c.1237C>A	c.(1237-1239)Cta>Ata	p.L413I	MTDH_ENST00000519934.1_Missense_Mutation_p.L357I	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	413	Lung-homing for mammary tumors. {ECO:0000250}.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)	p.L413I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			AGCTTCACTTCTAAAGTCCCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	8											138	142	141					8																	98718943		2203	4300	6503	98788119	SO:0001583	missense	92140			AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"astrocyte elevated gene 1"	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.1237C>A	8.37:g.98718943C>A	ENSP00000338235:p.Leu413Ile		98788119	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	37	CCDS6274.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.370150	0.42003	.	.	ENSG00000147649	ENST00000336273;ENST00000519934;ENST00000521933	T;T	0.47528	0.84;0.85	5.6	3.67	0.42095	.	0.575096	0.16818	N	0.198270	T	0.44329	0.1288	L	0.40543	1.245	0.29629	N	0.845592	D	0.57257	0.979	P	0.51615	0.675	T	0.27262	-1.0079	10	0.19147	T	0.46	-4.7763	8.6223	0.33868	0.1508:0.771:0.0:0.0782	.	413	Q86UE4	LYRIC_HUMAN	I	413;357;83	ENSP00000338235:L413I;ENSP00000428168:L357I	ENSP00000338235:L413I	L	+	1	2	MTDH	98788119	0.668000	0.27493	0.992000	0.48379	0.998000	0.95712	0.567000	0.23608	1.487000	0.48415	0.655000	0.94253	CTA		0.438	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2			A	98718943	C	A	98718943	3	1	61	1	0	0	0	0	1	0	0	0	9947	912	32	2	1267	2	MTDH	8	98718943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1097301	98718943	47645079	6011	13996										
MATN2	4147	broad.mit.edu	37	chr8	99039681	99039681	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgacctggtctttgtgatCgatggatccaagagtcttgg	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:99039681C>T	ENST00000520016.1	+	13	2104	c.1980C>T	c.(1978-1980)atC>atT	p.I660I	MATN2_ENST00000521689.1_Silent_p.I660I|MATN2_ENST00000522025.2_Silent_p.I376I|MATN2_ENST00000524308.1_Silent_p.I619I|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000254898.5_Silent_p.I660I			O00339	MATN2_HUMAN	matrilin 2	660	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.I660I(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TCTTTGTGATCGATGGATCCA	0.403																																																2	Substitution - coding silent(2)	large_intestine(2)	8											92	91	91					8																	99039681		1848	4092	5940	99108857	SO:0001819	synonymous_variant	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1980C>T	8.37:g.99039681C>T			99108857	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	9.014	0.983283	0.18889	.	.	ENSG00000132561	ENST00000518154;ENST00000517321	.	.	.	5.0	-4.97	0.03029	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.2025	10.6386	0.45579	0.0856:0.2617:0.0:0.6527	.	.	.	.	X	443;94	.	.	R	+	1	2	MATN2	99108857	0.697000	0.27767	0.941000	0.38009	0.961000	0.63080	-0.123000	0.10611	-0.961000	0.03609	-0.350000	0.07774	CGA		0.403	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99039681	C	T	99039681	2	4	61	1	0	0	0	0	0	0	0	1	9364	874	31	1		1	MATN2	8	99039681	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	320738	99039681	47324341	6012	13997										
C8orf47	203111	broad.mit.edu	37	chr8	99101670	99101670	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagggacagaggccgagtCtctaaaaggaaatgctgaag	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:99101670C>A	ENST00000318528.3	+	2	784	c.425C>A	c.(424-426)tCt>tAt	p.S142Y	C8orf47_ENST00000545282.1_Intron	NM_173549.2	NP_775820.2	Q6P6B1	ERIC5_HUMAN		142								p.S142Y(1)		kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(2)	13	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			GAGGCCGAGTCTCTAAAAGGA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	8											67	69	68					8																	99101670		2203	4300	6503	99170846	SO:0001583	missense	203111																														ENST00000318528.3:c.425C>A	8.37:g.99101670C>A	ENSP00000315614:p.Ser142Tyr		99170846	G3V1K4|Q8N1L8	Missense_Mutation	SNP	ENST00000318528.3	37	CCDS34929.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.471985	0.26423	.	.	ENSG00000177459	ENST00000318528	T	0.48522	0.81	5.08	4.2	0.49525	.	1.276180	0.05296	N	0.522153	T	0.36717	0.0977	N	0.14661	0.345	0.24977	N	0.991627	B	0.06786	0.001	B	0.10450	0.005	T	0.29852	-0.9998	10	0.72032	D	0.01	1.1802	11.1412	0.48404	0.1836:0.8164:0.0:0.0	.	142	Q6P6B1	CH047_HUMAN	Y	142	ENSP00000315614:S142Y	ENSP00000315614:S142Y	S	+	2	0	C8orf47	99170846	0.000000	0.05858	0.010000	0.14722	0.002000	0.02628	0.192000	0.17096	1.488000	0.48433	0.655000	0.94253	TCT		0.557	C8orf47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380465.1			A	99101670	C	A	99101670	3	1	61	1	0	0	0	0	1	0	0	0	2438	913	32	2	431	2	C8orf47	8	99101670	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61989	99101670	47262352	6013	13998										
HRSP12	10247	broad.mit.edu	37	chr8	99115125	99115125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactgcttcaatttcaattCggctgccctgtgaggaaaat	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:99115125C>T	ENST00000254878.3	-	6	503	c.359G>A	c.(358-360)cGa>cAa	p.R120Q		NM_005836.2	NP_005827.1	P52758	UK114_HUMAN	heat-responsive protein 12	120					regulation of translational termination (GO:0006449)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deaminase activity (GO:0019239)|endonuclease activity (GO:0004519)|poly(A) RNA binding (GO:0044822)	p.R120Q(2)		large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	6	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			AATTTCAATTCGGCTGCCCTG	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	8											129	124	125					8																	99115125		2203	4300	6503	99184301	SO:0001583	missense	10247			BC008418	CCDS6276.1	8q22	2014-05-09			ENSG00000132541	ENSG00000132541			16897	protein-coding gene	gene with protein product	"translational inhibitor p14.5"	602487				8973653, 9405234, 20817725	Standard	NM_005836		Approved	UK114, P14.5, PSP	uc003yii.1	P52758	OTTHUMG00000164670	ENST00000254878.3:c.359G>A	8.37:g.99115125C>T	ENSP00000254878:p.Arg120Gln		99184301	Q6FHU9|Q6IBG0	Missense_Mutation	SNP	ENST00000254878.3	37	CCDS6276.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.57|11.57	1.679388|1.679388	0.29783|0.29783	.|.	.|.	ENSG00000132541|ENSG00000132541	ENST00000521560|ENST00000254878;ENST00000520989	.|.	.|.	.|.	5.36|5.36	3.53|3.53	0.40419|0.40419	.|Endoribonuclease L-PSP/chorismate mutase-like (2);YjgF-like protein, conserved site (1);	.|0.070231	.|0.64402	.|D	.|0.000016	T|T	0.31009|0.31009	0.0783|0.0783	L|L	0.45137|0.45137	1.4|1.4	0.18873|0.18873	N|N	0.999981|0.999981	.|B	.|0.33528	.|0.416	.|B	.|0.31101	.|0.124	T|T	0.15521|0.15521	-1.0434|-1.0434	5|9	.|0.41790	.|T	.|0.15	.|.	7.9431|7.9431	0.29969|0.29969	0.1593:0.758:0.0:0.0826|0.1593:0.758:0.0:0.0826	.|.	.|120	.|P52758	.|UK114_HUMAN	K|Q	110|120;97	.|.	.|ENSP00000254878:R120Q	E|R	-|-	1|2	0|0	HRSP12|HRSP12	99184301|99184301	0.759000|0.759000	0.28416|0.28416	0.008000|0.008000	0.14137|0.14137	0.271000|0.271000	0.26615|0.26615	2.045000|2.045000	0.41250|0.41250	0.720000|0.720000	0.32209|0.32209	0.563000|0.563000	0.77884|0.77884	GAA|CGA		0.368	HRSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379687.1	NM_005836		T	99115125	C	T	99115125	3	4	61	1	0	0	0	0	1	0	0	0	7381	884	31	1	58	1	HRSP12	8	99115125	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13455	99115125	47248897	6014	13999										
KCNS2	3788	broad.mit.edu	37	chr8	99440421	99440421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcgggagttctacttcGaccgcaaccctgagctcttc	9	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:99440421G>A	ENST00000287042.4	+	2	564	c.214G>A	c.(214-216)Gac>Aac	p.D72N	KCNS2_ENST00000521839.1_Missense_Mutation_p.D72N	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	72					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.D72N(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			GTTCTACTTCGACCGCAACCC	0.602																																					Pancreas(138;844 2489 9202 24627)											1	Substitution - Missense(1)	large_intestine(1)	8											129	100	110					8																	99440421		2203	4300	6503	99509597	SO:0001583	missense	3788			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.214G>A	8.37:g.99440421G>A	ENSP00000287042:p.Asp72Asn		99509597	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	g	27.5	4.838245	0.91117	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	T;T	0.66460	-0.21;-0.21	5.4	5.4	0.78164	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.86276	0.5894	M	0.91768	3.24	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	D	0.89176	0.3540	10	0.87932	D	0	.	19.1824	0.93629	0.0:0.0:1.0:0.0	.	72	Q9ULS6	KCNS2_HUMAN	N	72	ENSP00000287042:D72N;ENSP00000430712:D72N	ENSP00000287042:D72N	D	+	1	0	KCNS2	99509597	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	9.866000	0.99616	2.523000	0.85059	0.558000	0.71614	GAC		0.602	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		A	99440421	G	A	99440421	3	1	61	1	0	0	0	0	1	0	0	0	8110	1058	37	1	216	1	KCNS2	8	99440421	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325296	99440421	46923601	6015	14000										
VPS13B	157680	broad.mit.edu	37	chr8	100026025	100026025	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttaaaagatgctggaGtcatatgtaactccaatttt	6	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100026025G>T	ENST00000358544.2	+	2	120	c.9G>T	c.(7-9)gaG>gaT	p.E3D	VPS13B_ENST00000355155.1_Missense_Mutation_p.E3D|RP11-410L14.2_ENST00000521696.1_lincRNA|VPS13B_ENST00000357162.2_Missense_Mutation_p.E3D|VPS13B_ENST00000395996.1_Missense_Mutation_p.E3D|VPS13B_ENST00000441350.2_Missense_Mutation_p.E3D	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3					protein transport (GO:0015031)			p.E3D(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGATGCTGGAGTCATATGTAA	0.443																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											112	106	108					8																	100026025		2203	4300	6503	100095201	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.9G>T	8.37:g.100026025G>T	ENSP00000351346:p.Glu3Asp		100095201	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	33	5.206875	0.95033	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	4.85	3.97	0.46021	.	0.000000	0.85682	D	0.000000	D	0.91590	0.7343	M	0.78801	2.425	0.58432	D	0.999997	D;D;D;D;D	0.89917	0.996;0.999;1.0;1.0;0.996	D;D;D;D;D	0.85130	0.987;0.994;0.997;0.997;0.97	D	0.92425	0.5949	10	0.87932	D	0	.	13.347	0.60580	0.076:0.0:0.924:0.0	.	3;3;3;3;3	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	D	3	ENSP00000347281:E3D;ENSP00000349685:E3D;ENSP00000351346:E3D;ENSP00000379318:E3D;ENSP00000398472:E3D	ENSP00000347281:E3D	E	+	3	2	VPS13B	100095201	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.371000	0.73119	1.258000	0.44101	0.557000	0.71058	GAG		0.443	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100026025	G	T	100026025	3	4	61	1	0	0	0	0	1	0	0	0	17230	1020	36	2	11	2	VPS13B	8	100026025	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	585604	100026025	46337997	6016	14001										
VPS13B	157680	broad.mit.edu	37	chr8	100123355	100123355	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgctgagaaaggttatcAatttttctgactgtacagtt	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100123355A>C	ENST00000358544.2	+	6	721	c.610A>C	c.(610-612)Aat>Cat	p.N204H	VPS13B_ENST00000355155.1_Missense_Mutation_p.N204H|VPS13B_ENST00000357162.2_Missense_Mutation_p.N204H|VPS13B_ENST00000395996.1_Missense_Mutation_p.N204H|VPS13B_ENST00000441350.2_Missense_Mutation_p.N204H	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	204					protein transport (GO:0015031)			p.N204H(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AAAGGTTATCAATTTTTCTGA	0.313																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											69	73	71					8																	100123355		2202	4299	6501	100192531	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.610A>C	8.37:g.100123355A>C	ENSP00000351346:p.Asn204His		100192531	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.536977	0.65085	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	T;T;T;T;D	0.83506	-1.16;-0.49;-0.49;-0.18;-1.73	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.87779	0.6263	L	0.43152	1.355	0.58432	D	0.999992	D;D;D;D;P	0.89917	1.0;0.999;0.998;0.998;0.728	D;D;D;D;B	0.85130	0.997;0.997;0.935;0.929;0.39	D	0.88407	0.3019	10	0.54805	T	0.06	.	15.2793	0.73770	1.0:0.0:0.0:0.0	.	204;204;204;204;204	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	H	204	ENSP00000347281:N204H;ENSP00000349685:N204H;ENSP00000351346:N204H;ENSP00000379318:N204H;ENSP00000398472:N204H	ENSP00000347281:N204H	N	+	1	0	VPS13B	100192531	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.075000	0.94004	2.005000	0.58758	0.454000	0.30748	AAT		0.313	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100123355	A	C	100123355	3	2	61	1	0	0	0	0	1	0	0	0	17230	130	5	4	628	4	VPS13B	8	100123355	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	97330	100123355	46240667	6017	14002										
VPS13B	157680	broad.mit.edu	37	chr8	100160233	100160233	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactacctgtcattatgggaGaaaaggtatattttgtgatt	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100160233G>T	ENST00000358544.2	+	14	2119	c.2008G>T	c.(2008-2010)Gaa>Taa	p.E670*	VPS13B_ENST00000355155.1_Nonsense_Mutation_p.E670*|VPS13B_ENST00000357162.2_Nonsense_Mutation_p.E670*|VPS13B_ENST00000395996.1_Nonsense_Mutation_p.E670*	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	670					protein transport (GO:0015031)			p.E670*(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CATTATGGGAGAAAAGGTATA	0.353																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Nonsense(1)	large_intestine(1)	8											141	141	141					8																	100160233		2203	4300	6503	100229409	SO:0001587	stop_gained	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.2008G>T	8.37:g.100160233G>T	ENSP00000351346:p.Glu670*		100229409	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Nonsense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	37	6.399398	0.97537	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996	.	.	.	5.14	5.14	0.70334	.	0.259163	0.32785	N	0.005660	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	14.0166	0.64527	0.0:0.2774:0.7226:0.0	.	.	.	.	X	670	.	ENSP00000347281:E670X	E	+	1	0	VPS13B	100229409	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	1.322000	0.33689	2.540000	0.85666	0.563000	0.77884	GAA		0.353	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100160233	G	T	100160233	4	4	61	1	0	0	0	0	0	1	0	0	17230	943	33	2	2100	2	VPS13B	8	100160233	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36878	100160233	46203789	6018	14003										
VPS13B	157680	broad.mit.edu	37	chr8	100168971	100168971	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtacactgctatcttaaGgtatgaaaagtgaattttct	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100168971G>A	ENST00000358544.2	+	15	2319	c.2208G>A	c.(2206-2208)aaG>aaA	p.K736K	VPS13B_ENST00000521932.1_3'UTR|VPS13B_ENST00000355155.1_Splice_Site_p.K736K|VPS13B_ENST00000357162.2_Splice_Site_p.K736K|VPS13B_ENST00000395996.1_Splice_Site_p.K736K	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	736					protein transport (GO:0015031)			p.K736K(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GCTATCTTAAGGTATGAAAAG	0.368																																					Colon(161;2205 2542 7338 31318)											1	Substitution - coding silent(1)	large_intestine(1)	8											133	121	125					8																	100168971		2203	4300	6503	100238147	SO:0001630	splice_region_variant	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.2208+1G>A	8.37:g.100168971G>A			100238147	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.368	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	Silent	A	100168971	G	A	100168971	5	1	61	1	0	0	0	0	0	0	1	0	17230	1014	35	3	2304	3	VPS13B	8	100168971	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8738	100168971	46195051	6019	14004										
VPS13B	157680	broad.mit.edu	37	chr8	100286541	100286541	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaccatgggatcaataaaAatttgtgccaaagccccagg	11	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100286541A>C	ENST00000358544.2	+	18	2742	c.2631A>C	c.(2629-2631)aaA>aaC	p.K877N	VPS13B_ENST00000357162.2_Missense_Mutation_p.K877N|VPS13B_ENST00000395996.1_Missense_Mutation_p.K877N	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	877					protein transport (GO:0015031)			p.K877N(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GATCAATAAAAATTTGTGCCA	0.453																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											90	95	93					8																	100286541		2203	4300	6503	100355717	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.2631A>C	8.37:g.100286541A>C	ENSP00000351346:p.Lys877Asn		100355717	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133562	0.77662	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.72942	-0.69;-0.7;-0.4	5.65	5.65	0.86999	.	0.067188	0.64402	D	0.000009	T	0.77928	0.4204	L	0.32530	0.975	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.85130	0.997;0.997;0.994;0.997	T	0.80284	-0.1447	10	0.72032	D	0.01	.	16.1642	0.81743	1.0:0.0:0.0:0.0	.	877;877;877;877	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	N	877	ENSP00000349685:K877N;ENSP00000351346:K877N;ENSP00000379318:K877N	ENSP00000349685:K877N	K	+	3	2	VPS13B	100355717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.880000	0.92407	2.280000	0.76307	0.460000	0.39030	AAA		0.453	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100286541	A	C	100286541	3	2	61	1	0	0	0	0	1	0	0	0	17230	11	1	4	2820	4	VPS13B	8	100286541	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	117570	100286541	46077481	6020	14005										
VPS13B	157680	broad.mit.edu	37	chr8	100712137	100712137	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaatggaagccttagtgTcaaggcaacacaaaaagtac	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100712137T>G	ENST00000358544.2	+	36	6617	c.6506T>G	c.(6505-6507)gTc>gGc	p.V2169G	VPS13B_ENST00000357162.2_Missense_Mutation_p.V2144G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2169					protein transport (GO:0015031)			p.V2169G(1)|p.V2144G(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGCCTTAGTGTCAAGGCAACA	0.423																																					Colon(161;2205 2542 7338 31318)											2	Substitution - Missense(2)	large_intestine(2)	8											52	44	47					8																	100712137		2203	4298	6501	100781313	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6506T>G	8.37:g.100712137T>G	ENSP00000351346:p.Val2169Gly		100781313	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.774418	0.70107	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70631	-0.49;-0.5	5.85	5.85	0.93711	.	0.139046	0.45361	D	0.000361	T	0.74419	0.3714	L	0.50333	1.59	0.80722	D	1	D;P	0.53885	0.963;0.938	P;B	0.50754	0.649;0.446	T	0.77645	-0.2510	10	0.87932	D	0	.	16.2416	0.82411	0.0:0.0:0.0:1.0	.	2144;2169	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	2144;2169	ENSP00000349685:V2144G;ENSP00000351346:V2169G	ENSP00000349685:V2144G	V	+	2	0	VPS13B	100781313	0.995000	0.38212	0.565000	0.28409	0.590000	0.36582	6.345000	0.72995	2.229000	0.72834	0.533000	0.62120	GTC		0.423	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100712137	T	G	100712137	3	3	61	1	0	0	0	0	1	0	0	0	17230	1667	58	4	6838	4	VPS13B	8	100712137	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	425596	100712137	45651885	6021	14006										
VPS13B	157680	broad.mit.edu	37	chr8	100732575	100732575	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttatgattttaaaggtCttctggggtcaagaacattt	8	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100732575C>A	ENST00000358544.2	+	38	6846	c.6735C>A	c.(6733-6735)gtC>gtA	p.V2245V	VPS13B_ENST00000357162.2_Silent_p.V2220V|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2245					protein transport (GO:0015031)			p.V2245V(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTTAAAGGTCTTCTGGGGTC	0.284																																					Colon(161;2205 2542 7338 31318)											1	Substitution - coding silent(1)	large_intestine(1)	8											41	41	41					8																	100732575		2203	4300	6503	100801751	SO:0001819	synonymous_variant	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6735C>A	8.37:g.100732575C>A			100801751	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.284	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100732575	C	A	100732575	2	1	61	1	0	0	0	0	0	0	0	1	17230	900	32	2		2	VPS13B	8	100732575	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20438	100732575	45631447	6022	14007										
VPS13B	157680	broad.mit.edu	37	chr8	100733094	100733094	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacttttatttgacagaatCtttgaaattgcctggggtct	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100733094C>A	ENST00000358544.2	+	39	7055	c.6944C>A	c.(6943-6945)tCt>tAt	p.S2315Y	VPS13B_ENST00000357162.2_Missense_Mutation_p.S2290Y|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2315					protein transport (GO:0015031)			p.S2315Y(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTGACAGAATCTTTGAAATTG	0.323																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											27	28	28					8																	100733094		2200	4298	6498	100802270	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6944C>A	8.37:g.100733094C>A	ENSP00000351346:p.Ser2315Tyr		100802270	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	12.37	1.919082	0.33908	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69685	-0.42;-0.42	5.94	4.16	0.48862	.	0.565355	0.18121	N	0.151040	T	0.54727	0.1876	N	0.24115	0.695	0.80722	D	1	P;P	0.42649	0.786;0.681	B;B	0.40228	0.323;0.172	T	0.51911	-0.8645	10	0.51188	T	0.08	.	14.1716	0.65512	0.1109:0.8284:0.0:0.0607	.	2290;2315	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Y	2290;2315	ENSP00000349685:S2290Y;ENSP00000351346:S2315Y	ENSP00000349685:S2290Y	S	+	2	0	VPS13B	100802270	1.000000	0.71417	0.997000	0.53966	0.708000	0.40852	2.916000	0.48813	0.428000	0.26173	-0.808000	0.03180	TCT		0.323	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100733094	C	A	100733094	3	1	61	1	0	0	0	0	1	0	0	0	17230	913	32	2	7288	2	VPS13B	8	100733094	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	519	100733094	45630928	6023	14008										
RGS22	26166	broad.mit.edu	37	chr8	100975155	100975155	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcttggatcttaagaaGaattctctcctgttctaagg	7	8	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:100975155G>T	ENST00000360863.6	-	25	3861	c.3667C>A	c.(3667-3669)Ctt>Att	p.L1223I	RGS22_ENST00000523287.1_Missense_Mutation_p.L1042I|RGS22_ENST00000523437.1_Missense_Mutation_p.L1211I	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1223					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.L1223I(2)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			ATCTTAAGAAGAATTCTCTCC	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	8											68	65	66					8																	100975155		1802	4062	5864	101044331	SO:0001583	missense	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.3667C>A	8.37:g.100975155G>T	ENSP00000354109:p.Leu1223Ile		101044331	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734532	0.69189	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000517843;ENST00000523437	T;T;T	0.55588	0.55;0.51;0.54	5.03	4.14	0.48551	.	0.000000	0.64402	D	0.000004	T	0.68091	0.2963	M	0.71581	2.175	0.26143	N	0.980251	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.987;0.987;0.994	T	0.59359	-0.7469	10	0.51188	T	0.08	.	11.3655	0.49668	0.0922:0.0:0.9078:0.0	.	1211;1223;1042	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	I	1223;1210;1042;95;1211	ENSP00000354109:L1223I;ENSP00000429382:L1042I;ENSP00000428212:L1211I	ENSP00000354109:L1223I	L	-	1	0	RGS22	101044331	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.430000	0.52807	2.488000	0.83962	0.491000	0.48974	CTT		0.308	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		T	100975155	G	T	100975155	3	4	61	1	0	0	0	0	1	0	0	0	13342	942	33	2	139	2	RGS22	8	100975155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	242061	100975155	45388867	6024	14009										
RGS22	26166	broad.mit.edu	37	chr8	101011531	101011531	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgttcacttgcaagaaAcaatggcagccatacatttt	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101011531A>G	ENST00000360863.6	-	19	3102	c.2908T>C	c.(2908-2910)Ttt>Ctt	p.F970L	RGS22_ENST00000523287.1_Missense_Mutation_p.F789L|RGS22_ENST00000523437.1_Missense_Mutation_p.F958L	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	970	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.F970L(2)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CTTGCAAGAAACAATGGCAGC	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	8											87	82	83					8																	101011531		1846	4101	5947	101080707	SO:0001583	missense	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2908T>C	8.37:g.101011531A>G	ENSP00000354109:p.Phe970Leu		101080707	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.733571	0.89482	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.63744	-0.06;-0.06;-0.06	4.91	4.91	0.64330	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78368	0.4272	M	0.74881	2.28	0.37520	D	0.917499	D;D;D	0.76494	0.999;0.999;0.996	D;D;D	0.83275	0.996;0.996;0.99	D	0.83738	0.0202	10	0.72032	D	0.01	.	14.5442	0.68017	1.0:0.0:0.0:0.0	.	958;970;789	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	L	970;957;789;958	ENSP00000354109:F970L;ENSP00000429382:F789L;ENSP00000428212:F958L	ENSP00000354109:F970L	F	-	1	0	RGS22	101080707	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.208000	0.77907	1.835000	0.53391	0.482000	0.46254	TTT		0.388	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101011531	A	G	101011531	3	3	61	1	0	0	0	0	1	0	0	0	13342	43	2	4	922	4	RGS22	8	101011531	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	36376	101011531	45352491	6025	14010										
RGS22	26166	broad.mit.edu	37	chr8	101018266	101018266	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagctttcttggaaaatgtCtctttatgcaaagcctgtag	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101018266C>A	ENST00000360863.6	-	16	2627	c.2433G>T	c.(2431-2433)gaG>gaT	p.E811D	RGS22_ENST00000519421.1_5'UTR|RGS22_ENST00000523287.1_Missense_Mutation_p.E630D|RGS22_ENST00000523437.1_Missense_Mutation_p.E799D|SNORD77_ENST00000391112.1_RNA	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	811					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.E811D(2)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TGGAAAATGTCTCTTTATGCA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	8											112	108	109					8																	101018266		1828	4093	5921	101087442	SO:0001583	missense	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2433G>T	8.37:g.101018266C>A	ENSP00000354109:p.Glu811Asp		101087442	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.621292	0.28889	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437;ENST00000517828	T;T;T;T	0.50277	1.31;1.3;1.31;0.75	5.83	-1.94	0.07571	.	0.291169	0.32416	N	0.006125	T	0.36690	0.0976	M	0.66939	2.045	0.09310	N	1	B;B;B	0.18166	0.012;0.012;0.026	B;B;B	0.16289	0.007;0.007;0.015	T	0.25257	-1.0137	10	0.51188	T	0.08	.	3.9073	0.09188	0.096:0.3794:0.0945:0.4302	.	799;811;630	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	D	811;799;630;799;126	ENSP00000354109:E811D;ENSP00000429382:E630D;ENSP00000428212:E799D;ENSP00000427754:E126D	ENSP00000354109:E811D	E	-	3	2	RGS22	101087442	0.001000	0.12720	0.018000	0.16275	0.803000	0.45373	-0.690000	0.05138	-0.413000	0.07507	0.591000	0.81541	GAG		0.398	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101018266	C	A	101018266	3	1	61	1	0	0	0	0	1	0	0	0	13342	912	32	2	1409	2	RGS22	8	101018266	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6735	101018266	45345756	6026	14011										
RGS22	26166	broad.mit.edu	37	chr8	101076056	101076056	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatataggagcttaaaaattCttcacatgttgagaaatgca	7	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101076056C>A	ENST00000360863.6	-	8	1134	c.940G>T	c.(940-942)Gaa>Taa	p.E314*	RGS22_ENST00000523287.1_Nonsense_Mutation_p.E133*|RGS22_ENST00000523437.1_Nonsense_Mutation_p.E302*	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	314					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.E314*(2)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CTTAAAAATTCTTCACATGTT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											66	64	65					8																	101076056		1825	4072	5897	101145232	SO:0001587	stop_gained	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.940G>T	8.37:g.101076056C>A	ENSP00000354109:p.Glu314*		101145232	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Nonsense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	38	7.049313	0.98029	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	.	.	.	5.86	4.94	0.65067	.	0.263587	0.37178	N	0.002215	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.672	0.88221	0.0:0.8775:0.1225:0.0	.	.	.	.	X	314;302;133;302	.	ENSP00000354109:E314X	E	-	1	0	RGS22	101145232	1.000000	0.71417	1.000000	0.80357	0.047000	0.14425	2.778000	0.47726	2.937000	0.99478	0.650000	0.86243	GAA		0.363	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101076056	C	A	101076056	4	1	61	1	0	0	0	0	0	1	0	0	13342	922	32	2	2934	2	RGS22	8	101076056	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57790	101076056	45287966	6027	14012										
RGS22	26166	broad.mit.edu	37	chr8	101117607	101117607	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaatgatacttacaaattCttcttctgtaatagttggtg	7	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101117607C>A	ENST00000360863.6	-	2	243	c.49G>T	c.(49-51)Gaa>Taa	p.E17*	RGS22_ENST00000523287.1_5'UTR|RGS22_ENST00000523437.1_Nonsense_Mutation_p.E17*	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	17					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.E17*(2)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CTTACAAATTCTTCTTCTGTA	0.328																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											94	98	97					8																	101117607		1823	4076	5899	101186783	SO:0001587	stop_gained	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.49G>T	8.37:g.101117607C>A	ENSP00000354109:p.Glu17*		101186783	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Nonsense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	c	33	5.194701	0.94960	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523437	.	.	.	4.96	4.05	0.47172	.	1.402410	0.04637	N	0.404745	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	7.8233	0.29300	0.0:0.8791:0.0:0.1209	.	.	.	.	X	17	.	ENSP00000354109:E17X	E	-	1	0	RGS22	101186783	0.594000	0.26849	0.817000	0.32601	0.974000	0.67602	2.115000	0.41921	1.212000	0.43366	0.651000	0.88453	GAA		0.328	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101117607	C	A	101117607	4	1	61	1	0	0	0	0	0	1	0	0	13342	922	32	2	3849	2	RGS22	8	101117607	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41551	101117607	45246415	6028	14013										
FBXO43	286151	broad.mit.edu	37	chr8	101154374	101154374	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgacctgagtgcctttgCgacatcttcaaaatctctgt	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101154374C>T	ENST00000428847.2	-	2	424	c.108G>A	c.(106-108)tcG>tcA	p.S36S		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	36					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.S2S(2)		endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			AGTGCCTTTGCGACATCTTCA	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	8											78	82	81					8																	101154374		2001	4179	6180	101223550	SO:0001819	synonymous_variant	286151			BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.108G>A	8.37:g.101154374C>T			101223550		Silent	SNP	ENST00000428847.2	37	CCDS47904.1																																																																																				0.418	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		T	101154374	C	T	101154374	2	4	61	1	0	0	0	0	0	0	0	1	5771	755	27	1		1	FBXO43	8	101154374	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36767	101154374	45209648	6029	14014										
SPAG1	6674	broad.mit.edu	37	chr8	101243396	101243396	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccatagatgaaaaaacatTtaaagcccttaaggaagaag	7	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101243396T>G	ENST00000388798.2	+	15	2059	c.1868T>G	c.(1867-1869)tTt>tGt	p.F623C	SPAG1_ENST00000251809.3_Missense_Mutation_p.F623C|SPAG1_ENST00000523302.1_3'UTR	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	623					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.F623C(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GAAAAAACATTTAAAGCCCTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	8											73	74	74					8																	101243396		2203	4296	6499	101312572	SO:0001583	missense	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1868T>G	8.37:g.101243396T>G	ENSP00000373450:p.Phe623Cys		101312572	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.487548	0.44249	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.74106	-0.81;-0.81	5.41	4.24	0.50183	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.520245	0.22370	N	0.060946	T	0.74809	0.3765	M	0.62723	1.935	0.58432	D	0.999995	P	0.50819	0.939	P	0.47744	0.556	T	0.74153	-0.3757	10	0.46703	T	0.11	-18.0341	11.0187	0.47705	0.0:0.0743:0.0:0.9257	.	623	Q07617	SPAG1_HUMAN	C	623	ENSP00000251809:F623C;ENSP00000373450:F623C	ENSP00000251809:F623C	F	+	2	0	SPAG1	101312572	1.000000	0.71417	0.106000	0.21319	0.065000	0.16274	7.019000	0.76412	0.991000	0.38814	0.533000	0.62120	TTT		0.308	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		G	101243396	T	G	101243396	3	3	61	1	0	0	0	0	1	0	0	0	15014	1841	64	4	1922	4	SPAG1	8	101243396	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	89022	101243396	45120626	6030	14015										
RNF19A	25897	broad.mit.edu	37	chr8	101271373	101271373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaaccgccagcatgacttCgggtggcactgccatcatcc	10	14	1	2	rs563127836	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101271373C>T	ENST00000519449.1	-	11	2244	c.1928G>A	c.(1927-1929)cGa>cAa	p.R643Q	RNF19A_ENST00000341084.2_Missense_Mutation_p.R643Q|RNF19A_ENST00000523255.1_5'UTR	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	643					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R643Q(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			AGCATGACTTCGGGTGGCACT	0.483											OREG0018897	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	0	0	5008	,	,		20563	0		0	False		,,,				2504	0.0041															1	Substitution - Missense(1)	large_intestine(1)	8											130	115	120					8																	101271373		2203	4300	6503	101340549	SO:0001583	missense	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1928G>A	8.37:g.101271373C>T	ENSP00000428968:p.Arg643Gln	1357	101340549	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163361	0.57476	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.84146	-1.81;-1.81	5.74	5.74	0.90152	.	0.452265	0.22331	N	0.061480	T	0.79936	0.4532	L	0.47716	1.5	0.51482	D	0.999925	P	0.47253	0.892	B	0.35182	0.197	T	0.78481	-0.2187	10	0.21540	T	0.41	.	19.5387	0.95266	0.0:1.0:0.0:0.0	.	643	Q9NV58	RN19A_HUMAN	Q	643	ENSP00000428968:R643Q;ENSP00000342667:R643Q	ENSP00000342667:R643Q	R	-	2	0	RNF19A	101340549	1.000000	0.71417	0.745000	0.31077	0.267000	0.26476	4.542000	0.60677	2.708000	0.92522	0.585000	0.79938	CGA		0.483	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		T	101271373	C	T	101271373	3	4	61	1	0	0	0	0	1	0	0	0	13507	884	31	1	592	1	RNF19A	8	101271373	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27977	101271373	45092649	6031	14016										
RNF19A	25897	broad.mit.edu	37	chr8	101282122	101282122	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatgcaaatctgagatttCtttcatacacaaccaacaaa	3	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101282122C>T	ENST00000519449.1	-	5	1319	c.1003G>A	c.(1003-1005)Gaa>Aaa	p.E335K	RNF19A_ENST00000341084.2_Missense_Mutation_p.E335K|RNF19A_ENST00000523255.1_5'Flank	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	335					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E335K(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			TCTGAGATTTCTTTCATACAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											98	89	92					8																	101282122		2203	4300	6503	101351298	SO:0001583	missense	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1003G>A	8.37:g.101282122C>T	ENSP00000428968:p.Glu335Lys		101351298	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	35	5.435532	0.96150	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	T;T	0.80909	-1.43;-1.43	5.57	5.57	0.84162	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.85212	0.5645	L	0.31065	0.9	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.85928	0.1450	10	0.54805	T	0.06	.	19.1637	0.93544	0.0:1.0:0.0:0.0	.	335	Q9NV58	RN19A_HUMAN	K	335	ENSP00000428968:E335K;ENSP00000342667:E335K	ENSP00000342667:E335K	E	-	1	0	RNF19A	101351298	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.744000	0.85034	2.623000	0.88846	0.585000	0.79938	GAA		0.313	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		T	101282122	C	T	101282122	3	4	61	1	0	0	0	0	1	0	0	0	13507	922	32	3	1541	3	RNF19A	8	101282122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10749	101282122	45081900	6032	14017										
RNF19A	25897	broad.mit.edu	37	chr8	101287231	101287231	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatgaagaacgtatagttCtcaaacgtaagctctgggct	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:101287231C>A	ENST00000519449.1	-	4	1149	c.833G>T	c.(832-834)aGa>aTa	p.R278I	RNF19A_ENST00000341084.2_Missense_Mutation_p.R278I	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	278					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R278I(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			ACGTATAGTTCTCAAACGTAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											85	84	84					8																	101287231		2203	4300	6503	101356407	SO:0001583	missense	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.833G>T	8.37:g.101287231C>A	ENSP00000428968:p.Arg278Ile		101356407	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	34	5.308005	0.95629	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.85258	-1.96;-1.96	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.88897	0.6562	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89568	0.3811	10	0.72032	D	0.01	.	19.2824	0.94057	0.0:1.0:0.0:0.0	.	278	Q9NV58	RN19A_HUMAN	I	278	ENSP00000428968:R278I;ENSP00000342667:R278I	ENSP00000342667:R278I	R	-	2	0	RNF19A	101356407	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.651000	0.83577	2.880000	0.98712	0.650000	0.86243	AGA		0.408	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101287231	C	A	101287231	3	1	61	1	0	0	0	0	1	0	0	0	13507	913	32	2	1715	2	RNF19A	8	101287231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5109	101287231	45076791	6033	14018										
ZNF706	51123	broad.mit.edu	37	chr8	102212326	102212326	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagggtctggcatttgtgtCtaacaaaaaattgtgcaaaa	9	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:102212326C>A	ENST00000520347.1	-	3	3092		c.e3-1		ZNF706_ENST00000518336.1_Splice_Site|ZNF706_ENST00000521272.1_Splice_Site|ZNF706_ENST00000519882.1_Splice_Site|ZNF706_ENST00000517844.1_Splice_Site|ZNF706_ENST00000520984.1_Splice_Site|ZNF706_ENST00000311212.4_Splice_Site|ZNF706_ENST00000519744.1_Intron			Q9Y5V0	ZN706_HUMAN	zinc finger protein 706								metal ion binding (GO:0046872)	p.?(2)		large_intestine(1)|ovary(2)	3	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)		Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)			GCATTTGTGTCTAACAAAAAA	0.368																																																2	Unknown(2)	large_intestine(2)	8											129	118	122					8																	102212326		2203	4300	6503	102281502	SO:0001630	splice_region_variant	51123			AF125099	CCDS6291.1	8q22.3	2005-09-22				ENSG00000120963			24992	protein-coding gene	gene with protein product						11042152	Standard	NM_001042510		Approved	HSPC038	uc031tbv.1	Q9Y5V0		ENST00000520347.1:c.136-1G>T	8.37:g.102212326C>A			102281502	A8K362	Splice_Site	SNP	ENST00000520347.1	37	CCDS6291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.78|18.78	3.696865|3.696865	0.68386|0.68386	.|.	.|.	ENSG00000120963|ENSG00000120963	ENST00000520984;ENST00000311212;ENST00000517844;ENST00000520347;ENST00000519882;ENST00000521272;ENST00000518336|ENST00000519103	.|.	.|.	.|.	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	.|.	.|.	.|.	.|.	.|T	.|0.76535	.|0.4001	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74281	.|-0.3716	.|4	.|.	.|.	.|.	.|.	19.9225|19.9225	0.97093|0.97093	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|I	-1|26	.|.	.|.	.|R	-|-	.|2	.|0	ZNF706|ZNF706	102281502|102281502	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	7.715000|7.715000	0.84713|0.84713	2.780000|2.780000	0.95670|0.95670	0.655000|0.655000	0.94253|0.94253	.|AGA		0.368	ZNF706-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380477.1	NM_016096	Intron	A	102212326	C	A	102212326	5	1	61	1	0	0	0	0	0	0	1	0	18149	927	32	2	99	2	ZNF706	8	102212326	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	925095	102212326	44151696	6034	14019										
GRHL2	79977	broad.mit.edu	37	chr8	102589728	102589728	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcggcagcatacggcgaaGcagagggtccttgacattgg	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:102589728G>A	ENST00000251808.3	+	7	1322	c.984G>A	c.(982-984)aaG>aaA	p.K328K	GRHL2_ENST00000395927.1_Silent_p.K312K	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	328					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K328K(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			ATACGGCGAAGCAGAGGGTCC	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	8											122	101	108					8																	102589728		2203	4300	6503	102658904	SO:0001819	synonymous_variant	79977			AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.984G>A	8.37:g.102589728G>A			102658904	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																				0.483	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		A	102589728	G	A	102589728	2	1	61	1	0	0	0	0	0	0	0	1	6785	962	34	3		3	GRHL2	8	102589728	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	377402	102589728	43774294	6035	14020										
UBR5	51366	broad.mit.edu	37	chr8	103317461	103317461	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaccgcttgctcaagattCattagatattgtcgacaggc	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:103317461C>A	ENST00000520539.1	-	21	3285	c.2679G>T	c.(2677-2679)atG>atT	p.M893I	UBR5_ENST00000521922.1_Missense_Mutation_p.M887I|UBR5_ENST00000220959.4_Missense_Mutation_p.M893I	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	893					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.M893I(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			GCTCAAGATTCATTAGATATT	0.408																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											159	157	158					8																	103317461		2203	4300	6503	103386637	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.2679G>T	8.37:g.103317461C>A	ENSP00000429084:p.Met893Ile		103386637	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.03|12.03	1.816557|1.816557	0.32145|0.32145	.|.	.|.	ENSG00000104517|ENSG00000104517	ENST00000519365|ENST00000520539;ENST00000220959;ENST00000521922	.|T;T;T	.|0.42513	.|0.97;0.97;0.97	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.304265	.|0.35013	.|N	.|0.003511	.|T	.|0.28665	.|0.0710	N|N	0.14661|0.14661	0.345|0.345	0.38095|0.38095	D|D	0.937081|0.937081	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	.|T	.|0.09907	.|-1.0653	.|10	.|0.22109	.|T	.|0.4	.|.	18.0346|18.0346	0.89296|0.89296	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|887;893	.|E7EMW7;O95071	.|.;UBR5_HUMAN	X|I	9|893;893;887	.|ENSP00000429084:M893I;ENSP00000220959:M893I;ENSP00000427819:M887I	.|ENSP00000220959:M893I	E|M	-|-	1|3	0|0	UBR5|UBR5	103386637|103386637	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	3.140000|3.140000	0.50585|0.50585	2.268000|2.268000	0.75426|0.75426	0.305000|0.305000	0.20034|0.20034	GAA|ATG		0.408	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103317461	C	A	103317461	3	1	61	1	0	0	0	0	1	0	0	0	16945	826	29	2	5876	2	UBR5	8	103317461	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	727733	103317461	43046561	6036	14021										
UBR5	51366	broad.mit.edu	37	chr8	103354761	103354761	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggactttgaacaggtgtattCttcttatccaagtttggctc	9	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:103354761C>A	ENST00000520539.1	-	9	1644	c.1038G>T	c.(1036-1038)aaG>aaT	p.K346N	UBR5_ENST00000521922.1_Missense_Mutation_p.K340N|UBR5_ENST00000220959.4_Missense_Mutation_p.K346N	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	346					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.K346N(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			CAGGTGTATTCTTCTTATCCA	0.418																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											192	179	184					8																	103354761		2203	4300	6503	103423937	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.1038G>T	8.37:g.103354761C>A	ENSP00000429084:p.Lys346Asn		103423937	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654420	0.67472	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.49139	0.8;0.8;0.79	5.25	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	L	0.54323	1.7	0.58432	D	0.999994	D;D	0.57899	0.981;0.981	D;D	0.67231	0.95;0.95	T	0.65776	-0.6086	10	0.72032	D	0.01	.	14.1332	0.65268	0.0:0.9273:0.0:0.0727	.	340;346	E7EMW7;O95071	.;UBR5_HUMAN	N	346;346;340	ENSP00000429084:K346N;ENSP00000220959:K346N;ENSP00000427819:K340N	ENSP00000220959:K346N	K	-	3	2	UBR5	103423937	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	4.939000	0.63526	1.345000	0.45676	0.655000	0.94253	AAG		0.418	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103354761	C	A	103354761	3	1	61	1	0	0	0	0	1	0	0	0	16945	912	32	2	7565	2	UBR5	8	103354761	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37300	103354761	43009261	6037	14022										
UBR5	51366	broad.mit.edu	37	chr8	103373836	103373836	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattatatttgttcagcttCtcagaaacttctcgtaacct	4	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:103373836C>A	ENST00000520539.1	-	2	687	c.81G>T	c.(79-81)gaG>gaT	p.E27D	UBR5_ENST00000521922.1_Missense_Mutation_p.E27D|UBR5_ENST00000220959.4_Missense_Mutation_p.E27D	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	27					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.E27D(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			TGTTCAGCTTCTCAGAAACTT	0.284																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											38	38	38					8																	103373836		2198	4287	6485	103443012	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.81G>T	8.37:g.103373836C>A	ENSP00000429084:p.Glu27Asp		103443012	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	8.111	0.778848	0.16120	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.45276	0.91;0.91;0.9	5.98	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.32164	0.0820	N	0.12182	0.205	0.41456	D	0.988011	P;P	0.35745	0.518;0.518	P;P	0.48654	0.585;0.585	T	0.11567	-1.0582	10	0.02654	T	1	.	12.6685	0.56855	0.0:0.8672:0.0:0.1328	.	27;27	E7EMW7;O95071	.;UBR5_HUMAN	D	27	ENSP00000429084:E27D;ENSP00000220959:E27D;ENSP00000427819:E27D	ENSP00000220959:E27D	E	-	3	2	UBR5	103443012	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	0.796000	0.26986	0.881000	0.35993	0.591000	0.81541	GAG		0.284	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103373836	C	A	103373836	3	1	61	1	0	0	0	0	1	0	0	0	16945	912	32	2	8550	2	UBR5	8	103373836	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19075	103373836	42990186	6038	14023										
ODF1	4956	broad.mit.edu	37	chr8	103564039	103564039	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaggcaactgagatgcatCgacgaatttagcacacggtg	11	9	0	1	rs142790437		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:103564039C>T	ENST00000285402.3	+	1	240	c.84C>T	c.(82-84)atC>atT	p.I28I		NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	28					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.I28I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			TGAGATGCATCGACGAATTTA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	8						T		1,4405	2.1+/-5.4	0,1,2202	326	245	273		84	0.6	1	8	dbSNP_134	273	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ODF1	NM_024410.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		28/251	103564039	2,13004	2203	4300	6503	103633215	SO:0001819	synonymous_variant	4956			M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.84C>T	8.37:g.103564039C>T			103633215	Q3SX72	Silent	SNP	ENST00000285402.3	37	CCDS6293.1																																																																																				0.483	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			T	103564039	C	T	103564039	2	4	61	1	0	0	0	0	0	0	0	1	10857	874	31	1		1	ODF1	8	103564039	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	190203	103564039	42799983	6039	14024										
FZD6	8323	broad.mit.edu	37	chr8	104336800	104336800	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagaacaagtccaaagaGacattggattttggtgtcca	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104336800G>T	ENST00000358755.4	+	4	783	c.466G>T	c.(466-468)Gac>Tac	p.D156Y	FZD6_ENST00000522566.1_Missense_Mutation_p.D156Y|FZD6_ENST00000523739.1_Missense_Mutation_p.D124Y|FZD6_ENST00000540287.1_Intron	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	156					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.D156Y(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			AGTCCAAAGAGACATTGGATT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	73	71					8																	104336800		2203	4300	6503	104405976	SO:0001583	missense	8323			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.466G>T	8.37:g.104336800G>T	ENSP00000351605:p.Asp156Tyr		104405976	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.197203	0.79015	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000539487	T;T;T	0.77877	-1.09;-1.09;-1.13	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.88540	0.6464	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.988;0.99	D	0.88552	0.3117	10	0.66056	D	0.02	.	20.0493	0.97618	0.0:0.0:1.0:0.0	.	101;156;156	B4E236;B2R9H9;O60353	.;.;FZD6_HUMAN	Y	156;156;124;101	ENSP00000429055:D156Y;ENSP00000351605:D156Y;ENSP00000429528:D124Y	ENSP00000351605:D156Y	D	+	1	0	FZD6	104405976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.648000	0.83479	2.745000	0.94114	0.491000	0.48974	GAC		0.423	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		T	104336800	G	T	104336800	3	4	61	1	0	0	0	0	1	0	0	0	6153	942	33	2	476	2	FZD6	8	104336800	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	772761	104336800	42027222	6040	14025										
FZD6	8323	broad.mit.edu	37	chr8	104337567	104337567	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaaccaagaaaaactaaaGaaatttatgattcgaattgg	8	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104337567G>T	ENST00000358755.4	+	4	1550	c.1233G>T	c.(1231-1233)aaG>aaT	p.K411N	FZD6_ENST00000522566.1_Missense_Mutation_p.K411N|FZD6_ENST00000523739.1_Missense_Mutation_p.K379N|FZD6_ENST00000540287.1_Missense_Mutation_p.K106N	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	411					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.K411N(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			AAAAACTAAAGAAATTTATGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											141	136	138					8																	104337567		2203	4300	6503	104406743	SO:0001583	missense	8323			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.1233G>T	8.37:g.104337567G>T	ENSP00000351605:p.Lys411Asn		104406743	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679325	0.68042	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000540287;ENST00000539487	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.03	4.25	0.50352	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.86414	0.5927	L	0.41236	1.265	0.58432	D	0.999998	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.91635	0.992;0.999;0.999;0.992	D	0.85039	0.0922	10	0.41790	T	0.15	.	13.0078	0.58715	0.1309:0.0:0.8691:0.0	.	356;106;411;411	B4E236;F5H831;B2R9H9;O60353	.;.;.;FZD6_HUMAN	N	411;411;379;106;356	ENSP00000429055:K411N;ENSP00000351605:K411N;ENSP00000429528:K379N;ENSP00000443757:K106N	ENSP00000351605:K411N	K	+	3	2	FZD6	104406743	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.475000	0.53136	0.882000	0.36016	0.557000	0.71058	AAG		0.403	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		T	104337567	G	T	104337567	3	4	61	1	0	0	0	0	1	0	0	0	6153	933	33	2	1243	2	FZD6	8	104337567	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	767	104337567	42026455	6041	14026										
CTHRC1	115908	broad.mit.edu	37	chr8	104390331	104390331	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacttcggctaaaatgcaGaaatgcatgctgtcagcgtt	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104390331G>A	ENST00000330295.5	+	3	591	c.449G>A	c.(448-450)aGa>aAa	p.R150K	CTHRC1_ENST00000520337.1_Missense_Mutation_p.R136K|CTHRC1_ENST00000520880.1_Missense_Mutation_p.R20K	NM_138455.3	NP_612464.1	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	150					cell migration (GO:0016477)|cochlea morphogenesis (GO:0090103)|establishment of planar polarity involved in neural tube closure (GO:0090177)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|ossification involved in bone remodeling (GO:0043932)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein binding (GO:0032092)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)		p.R150K(1)		endometrium(1)|large_intestine(5)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			CTAAAATGCAGAAATGCATGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											185	180	181					8																	104390331		2203	4300	6503	104459507	SO:0001583	missense	115908			BC014245	CCDS6299.1, CCDS59110.1	8q22.3	2008-08-07			ENSG00000164932	ENSG00000164932			18831	protein-coding gene	gene with protein product		610635				15618538	Standard	NM_138455		Approved		uc003ylk.4	Q96CG8	OTTHUMG00000164887	ENST00000330295.5:c.449G>A	8.37:g.104390331G>A	ENSP00000330523:p.Arg150Lys		104459507	G3V141|Q6UW91|Q8IX63	Missense_Mutation	SNP	ENST00000330295.5	37	CCDS6299.1	.	.	.	.	.	.	.	.	.	.	G	7.753	0.703793	0.15172	.	.	ENSG00000164932	ENST00000330295;ENST00000520337;ENST00000297577;ENST00000520880	T;T	0.62498	0.02;1.01	5.3	3.47	0.39725	.	0.098439	0.64402	D	0.000002	T	0.28665	0.0710	N	0.02916	-0.46	0.29568	N	0.85009	B	0.02656	0.0	B	0.04013	0.001	T	0.27706	-1.0066	10	0.02654	T	1	-22.3828	8.3784	0.32457	0.2707:0.0:0.7293:0.0	.	150	Q96CG8	CTHR1_HUMAN	K	150;136;136;20	ENSP00000330523:R150K;ENSP00000430550:R136K	ENSP00000297577:R136K	R	+	2	0	CTHRC1	104459507	1.000000	0.71417	0.939000	0.37840	0.998000	0.95712	4.373000	0.59537	2.472000	0.83506	0.655000	0.94253	AGA		0.408	CTHRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380792.1	NM_138455		A	104390331	G	A	104390331	3	1	61	1	0	0	0	0	1	0	0	0	4016	942	33	3	459	3	CTHRC1	8	104390331	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52764	104390331	41973691	6042	14027										
SLC25A32	81034	broad.mit.edu	37	chr8	104419968	104419968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaatggtagtcaagcaatGtaaaattccattatatttcg	6	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104419968G>A	ENST00000297578.4	-	2	365	c.199C>T	c.(199-201)Cat>Tat	p.H67Y	SLC25A32_ENST00000543107.1_5'UTR	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	67					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)	p.H67Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	GTCAAGCAATGTAAAATTCCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											161	158	159					8																	104419968		2203	4300	6503	104489144	SO:0001583	missense	81034			AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.199C>T	8.37:g.104419968G>A	ENSP00000297578:p.His67Tyr		104489144	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120883	0.94385	.	.	ENSG00000164933	ENST00000297578;ENST00000424899	T	0.78481	-1.18	6.05	6.05	0.98169	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.89770	0.6811	M	0.85710	2.77	0.80722	D	1	D	0.64830	0.994	D	0.68943	0.961	D	0.89754	0.3942	10	0.66056	D	0.02	-18.7509	20.6013	0.99457	0.0:0.0:1.0:0.0	.	67	Q9H2D1	MFTC_HUMAN	Y	67;51	ENSP00000297578:H67Y	ENSP00000297578:H67Y	H	-	1	0	SLC25A32	104489144	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	9.209000	0.95087	2.878000	0.98634	0.650000	0.86243	CAT		0.413	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		A	104419968	G	A	104419968	3	1	61	1	0	0	0	0	1	0	0	0	14533	1377	48	3	772	3	SLC25A32	8	104419968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29637	104419968	41944054	6043	14028										
DCAF13	25879	broad.mit.edu	37	chr8	104432596	104432596	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtatttgcaaaaccattcCttgcttcgctggatggtcac	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104432596C>A	ENST00000297579.5	+	2	908	c.631C>A	c.(631-633)Ctt>Att	p.L211I	DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000521716.1_Missense_Mutation_p.L55I|DCAF13_ENST00000521971.1_Missense_Mutation_p.L55I|DCAF13_ENST00000519682.1_Missense_Mutation_p.L55I	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	59					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.L211I(1)		NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						AAAACCATTCCTTGCTTCGCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	8											107	99	102					8																	104432596		2203	4300	6503	104501772	SO:0001583	missense	25879			AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.631C>A	8.37:g.104432596C>A	ENSP00000297579:p.Leu211Ile		104501772	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	C	7.520	0.656418	0.14580	.	.	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.61859	0.07;5.01;0.07;0.07	5.2	5.2	0.72013	.	0.363431	0.29389	N	0.012297	T	0.32852	0.0843	N	0.04686	-0.185	0.43874	D	0.996481	B	0.18968	0.032	B	0.22152	0.038	T	0.21690	-1.0238	10	0.12430	T	0.62	-22.0953	10.3178	0.43747	0.1509:0.7032:0.1458:0.0	.	59	B3KME9	.	I	211;55;55;59;55	ENSP00000297579:L211I;ENSP00000430645:L55I;ENSP00000430883:L55I;ENSP00000430411:L55I	ENSP00000297579:L211I	L	+	1	0	DCAF13	104501772	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	2.006000	0.40874	2.420000	0.82092	0.655000	0.94253	CTT		0.458	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		A	104432596	C	A	104432596	3	1	61	1	0	0	0	0	1	0	0	0	4272	681	24	2	637	2	DCAF13	8	104432596	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12628	104432596	41931426	6044	14029										
DCAF13	25879	broad.mit.edu	37	chr8	104433296	104433296	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtactcgcttttgtgggActtcttttttcactgtaagt	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104433296A>G	ENST00000297579.5	+	3	1097	c.820A>G	c.(820-822)Act>Gct	p.T274A	DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000521971.1_Intron|DCAF13_ENST00000519682.1_Missense_Mutation_p.T118A	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	122					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.T274A(1)		NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CTTTTGTGGGACTTCTTTTTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	8											117	108	111					8																	104433296		2203	4300	6503	104502472	SO:0001583	missense	25879			AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.820A>G	8.37:g.104433296A>G	ENSP00000297579:p.Thr274Ala		104502472	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.021534	0.35701	.	.	ENSG00000164934	ENST00000297579;ENST00000519682	T;T	0.60548	0.18;0.18	5.17	3.97	0.46021	.	0.160329	0.56097	D	0.000039	T	0.42314	0.1197	L	0.35249	1.045	0.47065	D	0.999308	B	0.21225	0.053	B	0.23574	0.047	T	0.14364	-1.0475	10	0.11794	T	0.64	-13.5752	9.8191	0.40871	0.7262:0.0:0.0:0.2738	.	122	B3KME9	.	A	274;118	ENSP00000297579:T274A;ENSP00000430411:T118A	ENSP00000297579:T274A	T	+	1	0	DCAF13	104502472	0.995000	0.38212	0.996000	0.52242	0.942000	0.58702	3.866000	0.56040	0.777000	0.33496	0.533000	0.62120	ACT		0.308	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		G	104433296	A	G	104433296	3	3	61	1	0	0	0	0	1	0	0	0	4272	275	10	4	830	4	DCAF13	8	104433296	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	700	104433296	41930726	6045	14030										
RIMS2	9699	broad.mit.edu	37	chr8	104898068	104898068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgatcttattcaatggaaaGaactcgagaggctcagggac	12	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104898068G>T	ENST00000436393.2	+	2	816	c.575G>T	c.(574-576)aGa>aTa	p.R192I	RIMS2_ENST00000507740.1_Missense_Mutation_p.R222I|RIMS2_ENST00000406091.3_Missense_Mutation_p.R414I|RIMS2_ENST00000262231.10_Missense_Mutation_p.R222I			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	445					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.R192I(1)|p.R222I(1)|p.R450I(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TCAATGGAAAGAACTCGAGAG	0.468										HNSCC(12;0.0054)																																						3	Substitution - Missense(3)	large_intestine(3)	8											71	68	69					8																	104898068		1924	4132	6056	104967244	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.575G>T	8.37:g.104898068G>T	ENSP00000390665:p.Arg192Ile		104967244	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	G	28.1	4.890325	0.91889	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11;1.11	5.65	5.65	0.86999	.	.	.	.	.	T	0.63105	0.2483	L	0.54323	1.7	0.80722	D	1	D;D;P;D;D	0.89917	0.999;0.995;0.876;1.0;0.967	D;D;P;D;P	0.87578	0.979;0.987;0.646;0.998;0.761	T	0.63985	-0.6513	9	0.87932	D	0	.	19.7233	0.96151	0.0:0.0:1.0:0.0	.	445;192;222;222;414	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	I	414;445;414;445;222;222;222;222;192	ENSP00000427018:R414I;ENSP00000384892:R414I;ENSP00000425205:R222I;ENSP00000262231:R222I;ENSP00000423559:R222I;ENSP00000386228:R222I;ENSP00000390665:R192I	ENSP00000262231:R222I	R	+	2	0	RIMS2	104967244	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.464000	0.80887	2.653000	0.90120	0.563000	0.77884	AGA		0.468	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		T	104898068	G	T	104898068	3	4	61	1	0	0	0	0	1	0	0	0	13405	942	33	2	1381	2	RIMS2	8	104898068	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	464772	104898068	41465954	6046	14031										
RIMS2	9699	broad.mit.edu	37	chr8	104924320	104924320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctaaagatggagatcgtTtaattggtcgcattttatta	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:104924320T>G	ENST00000436393.2	+	4	1307	c.1066T>G	c.(1066-1068)Tta>Gta	p.L356V	RIMS2_ENST00000507740.1_Missense_Mutation_p.L386V|RIMS2_ENST00000406091.3_Missense_Mutation_p.L578V|RIMS2_ENST00000262231.10_Missense_Mutation_p.L433V			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	656					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.L661V(1)|p.L386V(1)|p.L356V(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TGGAGATCGTTTAATTGGTCG	0.318										HNSCC(12;0.0054)																																						3	Substitution - Missense(3)	large_intestine(3)	8											110	109	109					8																	104924320		1832	4089	5921	104993496	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1066T>G	8.37:g.104924320T>G	ENSP00000390665:p.Leu356Val		104993496	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	T	19.27	3.795646	0.70452	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.25085	1.82;2.29;2.02;2.11;2.0;1.94;2.33	5.92	2.27	0.28462	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.41351	0.1155	L	0.56199	1.76	0.80722	D	1	D;P;P;P;D	0.57571	0.966;0.89;0.941;0.701;0.98	P;D;D;P;D	0.72982	0.888;0.96;0.949;0.853;0.979	T	0.17410	-1.0370	9	0.87932	D	0	.	8.9425	0.35738	0.0:0.2972:0.0:0.7028	.	656;356;433;386;578	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	V	578;609;578;656;386;433;386;386;356	ENSP00000427018:L578V;ENSP00000384892:L578V;ENSP00000425205:L386V;ENSP00000262231:L433V;ENSP00000423559:L386V;ENSP00000386228:L386V;ENSP00000390665:L356V	ENSP00000262231:L433V	L	+	1	2	RIMS2	104993496	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	1.274000	0.33132	0.478000	0.27488	0.528000	0.53228	TTA		0.318	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104924320	T	G	104924320	3	3	61	1	0	0	0	0	1	0	0	0	13405	1838	64	4	1880	4	RIMS2	8	104924320	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26252	104924320	41439702	6047	14032										
RIMS2	9699	broad.mit.edu	37	chr8	105001556	105001556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgtggaacaggggcttcGagggacccgcactatgaccg	15	10	0	1	rs376934485		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:105001556G>A	ENST00000436393.2	+	15	2526	c.2285G>A	c.(2284-2286)cGa>cAa	p.R762Q	RIMS2_ENST00000507740.1_Missense_Mutation_p.R776Q|RIMS2_ENST00000406091.3_Missense_Mutation_p.R984Q|RIMS2_ENST00000262231.10_Missense_Mutation_p.R823Q			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1046					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.R1051Q(1)|p.R776Q(1)|p.R762Q(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CAGGGGCTTCGAGGGACCCGC	0.393										HNSCC(12;0.0054)																																						3	Substitution - Missense(3)	large_intestine(3)	8						G	GLN/ARG,GLN/ARG	1,3741		0,1,1870	132	130	130		2951,2327	5.5	1	8		130	0,8198		0,0,4099	no	missense,missense	RIMS2	NM_001100117.2,NM_014677.4	43,43	0,1,5969	AA,AG,GG		0.0,0.0267,0.0084	probably-damaging,probably-damaging	984/1350,776/1164	105001556	1,11939	1871	4099	5970	105070732	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.2285G>A	8.37:g.105001556G>A	ENSP00000390665:p.Arg762Gln		105070732	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	G	19.95	3.922543	0.73213	2.67E-4	0.0	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T	0.23348	1.91;2.45;2.27;1.99;1.92;2.49	5.54	5.54	0.83059	.	.	.	.	.	T	0.49949	0.1587	L	0.58810	1.83	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.978;1.0;0.984;0.995	D;P;D;P;P	0.79108	0.992;0.453;0.988;0.653;0.609	T	0.46512	-0.9186	9	0.66056	D	0.02	.	19.0702	0.93130	0.0:0.0:1.0:0.0	.	1046;762;823;776;984	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	Q	984;999;984;1046;823;776;776;762	ENSP00000427018:R984Q;ENSP00000384892:R984Q;ENSP00000262231:R823Q;ENSP00000423559:R776Q;ENSP00000386228:R776Q;ENSP00000390665:R762Q	ENSP00000262231:R823Q	R	+	2	0	RIMS2	105070732	1.000000	0.71417	1.000000	0.80357	0.250000	0.25880	6.280000	0.72626	2.617000	0.88574	0.484000	0.47621	CGA		0.393	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		A	105001556	G	A	105001556	3	1	61	1	0	0	0	0	1	0	0	0	13405	1058	37	1	3143	1	RIMS2	8	105001556	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77236	105001556	41362466	6048	14033										
RIMS2	9699	broad.mit.edu	37	chr8	105261749	105261749	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatgatggacaaaaagggAcagctggaggtagaaatcat	14	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:105261749A>G	ENST00000436393.2	+	26	3919	c.3678A>G	c.(3676-3678)ggA>ggG	p.G1226G	RIMS2_ENST00000507740.1_Silent_p.G1022G|RIMS2_ENST00000339750.2_Silent_p.G144G|RIMS2_ENST00000406091.3_Silent_p.G1208G|RIMS2_ENST00000262231.10_Silent_p.G1047G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1270					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.G1022G(1)|p.G1226G(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			ACAAAAAGGGACAGCTGGAGG	0.403										HNSCC(12;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	8											73	76	75					8																	105261749		1864	4088	5952	105330925	SO:0001819	synonymous_variant	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.3678A>G	8.37:g.105261749A>G			105330925	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																					0.403	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	105261749	A	G	105261749	2	3	61	1	0	0	0	0	0	0	0	1	13405	262	10	4		4	RIMS2	8	105261749	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	260193	105261749	41102273	6049	14034										
DPYS	1807	broad.mit.edu	37	chr8	105459659	105459659	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtcaccatgtacagatCtttataggccataaacatct	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:105459659C>A	ENST00000351513.2	-	3	628	c.496G>T	c.(496-498)Gat>Tat	p.D166Y		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	166					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)	p.D166Y(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			ATGTACAGATCTTTATAGGCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											134	123	127					8																	105459659		2203	4300	6503	105528835	SO:0001583	missense	1807			D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.496G>T	8.37:g.105459659C>A	ENSP00000276651:p.Asp166Tyr		105528835		Missense_Mutation	SNP	ENST00000351513.2	37	CCDS6302.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.638527	0.87760	.	.	ENSG00000147647	ENST00000351513;ENST00000521573	D;D	0.91295	-2.82;-2.82	6.02	6.02	0.97574	Amidohydrolase 1 (1);	0.097705	0.64402	D	0.000002	D	0.96617	0.8896	M	0.92122	3.275	0.80722	D	1	D	0.61697	0.99	D	0.67548	0.952	D	0.96595	0.9440	10	0.72032	D	0.01	-21.837	20.547	0.99278	0.0:1.0:0.0:0.0	.	166	Q14117	DPYS_HUMAN	Y	166;113	ENSP00000276651:D166Y;ENSP00000430246:D113Y	ENSP00000276651:D166Y	D	-	1	0	DPYS	105528835	1.000000	0.71417	0.064000	0.19789	0.979000	0.70002	7.487000	0.81328	2.850000	0.98022	0.650000	0.86243	GAT		0.413	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		A	105459659	C	A	105459659	3	1	61	1	0	0	0	0	1	0	0	0	4757	913	32	2	1091	2	DPYS	8	105459659	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	197910	105459659	40904363	6050	14035										
LRP12	29967	broad.mit.edu	37	chr8	105507435	105507435	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaactgtgtttcaaatGatctttgagagtagatggaa	10	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:105507435G>T	ENST00000276654.5	-	6	1691	c.1583C>A	c.(1582-1584)tCa>tAa	p.S528*	LRP12_ENST00000424843.2_Nonsense_Mutation_p.S509*|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	528					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)	p.S528*(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TGTTTCAAATGATCTTTGAGA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											83	89	87					8																	105507435		2203	4300	6503	105576611	SO:0001587	stop_gained	29967			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1583C>A	8.37:g.105507435G>T	ENSP00000276654:p.Ser528*		105576611	A8K137|B4DRQ2	Nonsense_Mutation	SNP	ENST00000276654.5	37	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	G	39	7.568514	0.98365	.	.	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000523007	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.9351	20.244	0.98389	0.0:0.0:1.0:0.0	.	.	.	.	X	509;528;117	.	ENSP00000276654:S528X	S	-	2	0	LRP12	105576611	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.823000	0.86660	2.865000	0.98341	0.655000	0.94253	TCA		0.363	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		T	105507435	G	T	105507435	4	4	61	1	0	0	0	0	0	1	0	0	8983	1294	45	2	1004	2	LRP12	8	105507435	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47776	105507435	40856587	6051	14036										
LRP12	29967	broad.mit.edu	37	chr8	105511579	105511579	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctgaaaccctttctagaGatgttgtcatccgaatgaaa	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:105511579G>T	ENST00000276654.5	-	4	549	c.441C>A	c.(439-441)atC>atA	p.I147I	LRP12_ENST00000424843.2_Silent_p.I128I	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	147	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)	p.I147I(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCTTTCTAGAGATGTTGTCAT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	8											139	140	140					8																	105511579		2203	4300	6503	105580755	SO:0001819	synonymous_variant	29967			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.441C>A	8.37:g.105511579G>T			105580755	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	37	CCDS6303.1																																																																																				0.368	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		T	105511579	G	T	105511579	2	4	61	1	0	0	0	0	0	0	0	1	8983	932	33	2		2	LRP12	8	105511579	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4144	105511579	40852443	6052	14037										
ZFPM2	23414	broad.mit.edu	37	chr8	106814932	106814932	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactatctggcccacaagcaGaatttctgcccggttactgc	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:106814932G>T	ENST00000407775.2	+	8	2872	c.2622G>T	c.(2620-2622)caG>caT	p.Q874H	RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.Q742H|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000378472.4_Missense_Mutation_p.Q605H|ZFPM2_ENST00000517361.1_Missense_Mutation_p.Q742H|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	874					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.Q874H(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CCCACAAGCAGAATTTCTGCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	8											45	43	44					8																	106814932		1947	4142	6089	106884108	SO:0001583	missense	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2622G>T	8.37:g.106814932G>T	ENSP00000384179:p.Gln874His		106884108	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.555960	0.45487	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.65	4.78	0.61160	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	L	0.40543	1.245	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.47302	-0.9128	10	0.56958	D	0.05	.	10.7496	0.46200	0.1448:0.0:0.8552:0.0	.	874	Q8WW38	FOG2_HUMAN	H	874;742;742;605	ENSP00000384179:Q874H;ENSP00000430757:Q742H;ENSP00000428720:Q742H;ENSP00000367733:Q605H	ENSP00000367733:Q605H	Q	+	3	2	ZFPM2	106884108	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.134000	0.57990	1.400000	0.46741	0.655000	0.94253	CAG		0.502	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			T	106814932	G	T	106814932	3	4	61	1	0	0	0	0	1	0	0	0	17697	933	33	2	2652	2	ZFPM2	8	106814932	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1303353	106814932	39549090	6053	14038										
ZFPM2	23414	broad.mit.edu	37	chr8	106815061	106815061	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagcataataaaatgtgaGaaaaatgggaatttgaagca	10	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:106815061G>A	ENST00000407775.2	+	8	3001	c.2751G>A	c.(2749-2751)gaG>gaA	p.E917E	RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000520492.1_Silent_p.E785E|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000378472.4_Silent_p.E648E|ZFPM2_ENST00000517361.1_Silent_p.E785E|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	917					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E917E(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			TAAAATGTGAGAAAAATGGGA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	8											40	39	39					8																	106815061		1887	4117	6004	106884237	SO:0001819	synonymous_variant	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2751G>A	8.37:g.106815061G>A			106884237	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																				0.458	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106815061	G	A	106815061	2	1	61	1	0	0	0	0	0	0	0	1	17697	933	33	3		3	ZFPM2	8	106815061	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129	106815061	39548961	6054	14039										
OXR1	55074	broad.mit.edu	37	chr8	107715281	107715281	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcagctgcaatgtacaaaGaaattttggatagcaaaata	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:107715281G>T	ENST00000442977.2	+	7	925	c.826G>T	c.(826-828)Gaa>Taa	p.E276*	OXR1_ENST00000312046.6_Nonsense_Mutation_p.E268*|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000497705.1_Nonsense_Mutation_p.E208*|OXR1_ENST00000531443.1_Nonsense_Mutation_p.E275*|OXR1_ENST00000517566.2_Nonsense_Mutation_p.E275*|OXR1_ENST00000445937.1_Nonsense_Mutation_p.E275*	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	276					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)	p.E187*(1)|p.E276*(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AATGTACAAAGAAATTTTGGA	0.358																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											102	99	100					8																	107715281		2203	4300	6503	107784457	SO:0001587	stop_gained	55074			AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.826G>T	8.37:g.107715281G>T	ENSP00000405424:p.Glu276*		107784457	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Nonsense_Mutation	SNP	ENST00000442977.2	37	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.455214|4.455214	0.84209|0.84209	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046|ENST00000517455	.|.	.|.	.|.	5.65|5.65	4.78|4.78	0.61160|0.61160	.|.	0.052534|.	0.85682|.	D|.	0.000000|.	.|T	.|0.41511	.|0.1162	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.31052	.|-0.9957	.|5	0.87932|0.02654	D|T	0|1	-9.5961|-9.5961	14.6546|14.6546	0.68823|0.68823	0.0698:0.0:0.9302:0.0|0.0698:0.0:0.9302:0.0	.|.	.|.	.|.	.|.	X|N	275;275;275;276;208;268|191	.|.	ENSP00000311026:E268X|ENSP00000428339:K191N	E|K	+|+	1|3	0|2	OXR1|OXR1	107784457|107784457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.747000|9.747000	0.98863|0.98863	1.527000|1.527000	0.49086|0.49086	0.650000|0.650000	0.86243|0.86243	GAA|AAG		0.358	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		T	107715281	G	T	107715281	4	4	61	1	0	0	0	0	0	1	0	0	11365	943	33	2	1052	2	OXR1	8	107715281	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	900220	107715281	38648741	6055	14040										
OXR1	55074	broad.mit.edu	37	chr8	107718611	107718611	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taattttgtttaatgacagaGatatagatcagctatcagga	8	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:107718611G>T	ENST00000442977.2	+	8	964	c.865G>T	c.(865-867)Gat>Tat	p.D289Y	OXR1_ENST00000312046.6_Splice_Site_p.D281Y|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000497705.1_Splice_Site_p.D221Y|OXR1_ENST00000531443.1_Splice_Site_p.D288Y|OXR1_ENST00000517566.2_Splice_Site_p.D288Y|OXR1_ENST00000445937.1_Splice_Site_p.D288Y	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	289					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)	p.D289Y(1)|p.D200Y(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TAATGACAGAGATATAGATCA	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	8											47	49	48					8																	107718611		2203	4299	6502	107787787	SO:0001630	splice_region_variant	55074			AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.864-1G>T	8.37:g.107718611G>T			107787787	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	37	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.288741|4.288741	0.80914|0.80914	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046|ENST00000519415	T;T;T;T;T;T|.	0.33438|.	2.26;2.26;2.25;2.24;1.41;2.32|.	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.311307|.	0.36444|.	N|.	0.002582|.	T|T	0.59101|0.59101	0.2169|0.2169	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;P;P;D|.	0.54207|.	0.965;0.941;0.782;0.965|.	P;P;P;P|.	0.62298|.	0.9;0.702;0.698;0.9|.	T|T	0.49688|0.49688	-0.8913|-0.8913	10|5	0.72032|.	D|.	0.01|.	-18.7744|-18.7744	20.6721|20.6721	0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	281;289;221;288|.	Q8N573-2;Q8N573;Q8N573-3;Q8N573-5|.	.;OXR1_HUMAN;.;.|.	Y|D	288;288;288;289;221;281|1	ENSP00000402918:D288Y;ENSP00000431966:D288Y;ENSP00000429205:D288Y;ENSP00000405424:D289Y;ENSP00000431014:D221Y;ENSP00000311026:D281Y|.	ENSP00000311026:D281Y|.	D|E	+|+	1|3	0|2	OXR1|OXR1	107787787|107787787	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.789000|0.789000	0.44602|0.44602	8.985000|8.985000	0.93487|0.93487	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GAT|GAG		0.318	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	Missense_Mutation	T	107718611	G	T	107718611	5	4	61	1	0	0	0	0	0	0	1	0	11365	956	33	2	1095	2	OXR1	8	107718611	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3330	107718611	38645411	6056	14041										
ANGPT1	284	broad.mit.edu	37	chr8	108509678	108509678	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggcacattgcccatgttGaatccggttatatcttctcc	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:108509678G>T								ANGPT1 (160928 upstream) : RNA5SP275 (387043 downstream)														p.Q37K(1)									TGCCCATGTTGAATCCGGTTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8											215	175	189					8																	108509678		2203	4300	6503	108578854	SO:0001628	intergenic_variant	284																															8.37:g.108509678G>T			108578854		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	G	23.2	4.389308	0.82902	.	.	ENSG00000154188	ENST00000517746;ENST00000297450	D;D	0.83992	-1.79;-1.79	6.06	6.06	0.98353	.	0.215337	0.38492	N	0.001664	D	0.90676	0.7075	M	0.74647	2.275	0.80722	D	1	D;D	0.57571	0.98;0.98	D;D	0.63192	0.912;0.912	D	0.89071	0.3469	10	0.45353	T	0.12	.	20.6397	0.99537	0.0:0.0:1.0:0.0	.	37;37	Q5HYA0;Q15389	.;ANGP1_HUMAN	K	37	ENSP00000428340:Q37K;ENSP00000297450:Q37K	ENSP00000297450:Q37K	Q	-	1	0	ANGPT1	108578854	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.125000	0.94402	2.880000	0.98712	0.650000	0.86243	CAA	0	0.483									T	108509678	G	T	108509678	1	4	61	0	1	0	0	0	0	0	0	0	610	1299	45	2		2	ANGPT1	8	108509678	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	791067	108509678	37854344	6057	14042										
TTC35	9694	broad.mit.edu	37	chr8	109498750	109498750	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttaattagtttgcaggtCgaagtaagaaggaaaccaaa	9	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:109498750C>T	ENST00000220853.3	+	11	852	c.817C>T	c.(817-819)Cga>Tga	p.R273*	EMC2_ENST00000520294.1_3'UTR	NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	273						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R273*(1)									GTTTGCAGGTCGAAGTAAGAA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											52	52	52					8																	109498750		2203	4300	6503	109567926	SO:0001587	stop_gained	9694			BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.817C>T	8.37:g.109498750C>T	ENSP00000220853:p.Arg273*		109567926	Q8WUE1	Nonsense_Mutation	SNP	ENST00000220853.3	37	CCDS6309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.8|26.8	4.773840|4.773840	0.90108|0.90108	.|.	.|.	ENSG00000104412|ENSG00000104412	ENST00000220853|ENST00000519642	.|.	.|.	.|.	5.95|5.95	5.07|5.07	0.68467|0.68467	.|.	0.105878|.	0.64402|.	D|.	0.000003|.	.|T	.|0.70859	.|0.3272	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70238	.|-0.4927	.|4	0.11182|.	T|.	0.66|.	-6.2049|-6.2049	15.0205|15.0205	0.71627|0.71627	0.0:0.9319:0.0:0.0681|0.0:0.9319:0.0:0.0681	.|.	.|.	.|.	.|.	X|L	273|121	.|.	ENSP00000220853:R273X|.	R|S	+|+	1|2	2|0	TTC35|TTC35	109567926|109567926	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.760000|6.760000	0.74939|0.74939	1.509000|1.509000	0.48786|0.48786	0.563000|0.563000	0.77884|0.77884	CGA|TCG		0.333	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		T	109498750	C	T	109498750	4	4	61	1	0	0	0	0	0	1	0	0	16743	876	31	1	859	1	TTC35	8	109498750	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	989072	109498750	36865272	6058	14043										
TRHR	7201	broad.mit.edu	37	chr8	110100426	110100426	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattccttcagatcctaaaGaaaactctaagacatggaaa	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110100426G>T	ENST00000518632.1	+	2	1036	c.685G>T	c.(685-687)Gaa>Taa	p.E229*	TRHR_ENST00000311762.2_Nonsense_Mutation_p.E229*			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	229					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)	p.E229*(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			AGATCCTAAAGAAAACTCTAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											65	64	64					8																	110100426		2202	4300	6502	110169602	SO:0001587	stop_gained	7201				CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.685G>T	8.37:g.110100426G>T	ENSP00000430711:p.Glu229*		110169602	Q2M339	Nonsense_Mutation	SNP	ENST00000518632.1	37	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	G	37	6.121961	0.97300	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	.	.	.	5.88	5.88	0.94601	.	0.291706	0.43919	D	0.000514	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-6.2639	19.2068	0.93734	0.0:0.0:1.0:0.0	.	.	.	.	X	229	.	ENSP00000309818:E229X	E	+	1	0	TRHR	110169602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.325000	0.79124	2.780000	0.95670	0.655000	0.94253	GAA		0.368	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			T	110100426	G	T	110100426	4	4	61	1	0	0	0	0	0	1	0	0	16520	943	33	2	687	2	TRHR	8	110100426	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	601676	110100426	36263596	6059	14044										
PKHD1L1	93035	broad.mit.edu	37	chr8	110457296	110457296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaatacatggagtgcctgCccagtgccagggaaactgca	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110457296C>T	ENST00000378402.5	+	38	5302	c.5198C>T	c.(5197-5199)gCc>gTc	p.A1733V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1733	IPT/TIG 9.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.A1735V(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GGAGTGCCTGCCCAGTGCCAG	0.428										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	large_intestine(1)	8											164	157	159					8																	110457296		1917	4145	6062	110526472	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5198C>T	8.37:g.110457296C>T	ENSP00000367655:p.Ala1733Val		110526472	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.044768	0.36085	.	.	ENSG00000205038	ENST00000378402	T	0.77358	-1.09	6.17	5.28	0.74379	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.196940	0.44097	D	0.000500	T	0.71888	0.3393	L	0.46741	1.465	0.24681	N	0.993361	B	0.29671	0.254	B	0.36766	0.232	T	0.57991	-0.7715	10	0.07813	T	0.8	.	13.6613	0.62368	0.0:0.704:0.296:0.0	.	1733	Q86WI1	PKHL1_HUMAN	V	1733	ENSP00000367655:A1733V	ENSP00000367655:A1733V	A	+	2	0	PKHD1L1	110526472	0.988000	0.35896	0.970000	0.41538	0.992000	0.81027	2.724000	0.47285	1.587000	0.49959	0.655000	0.94253	GCC		0.428	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110457296	C	T	110457296	3	4	61	1	0	0	0	0	1	0	0	0	12003	739	26	3	5348	3	PKHD1L1	8	110457296	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	356870	110457296	35906726	6060	14045										
PKHD1L1	93035	broad.mit.edu	37	chr8	110457591	110457591	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctgactgtcagcagcccCccagtagcatctctatcacc	6	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110457591C>T	ENST00000378402.5	+	38	5597	c.5493C>T	c.(5491-5493)ccC>ccT	p.P1831P		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1831	IPT/TIG 11.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.P1833P(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCAGCAGCCCCCCAGTAGCAT	0.498										HNSCC(38;0.096)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											77	77	77					8																	110457591		1936	4130	6066	110526767	SO:0001819	synonymous_variant	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5493C>T	8.37:g.110457591C>T			110526767	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																				0.498	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110457591	C	T	110457591	2	4	61	1	0	0	0	0	0	0	0	1	12003	610	22	3		3	PKHD1L1	8	110457591	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	295	110457591	35906431	6061	14046										
PKHD1L1	93035	broad.mit.edu	37	chr8	110471996	110471996	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaattcttacaagaaatattTtaataagaggatctgataat	6	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110471996T>G	ENST00000378402.5	+	47	7281	c.7177T>G	c.(7177-7179)Tta>Gta	p.L2393V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2393					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L2395V(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AAGAAATATTTTAATAAGAGG	0.373										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	large_intestine(1)	8											49	48	48					8																	110471996		1808	4066	5874	110541172	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.7177T>G	8.37:g.110471996T>G	ENSP00000367655:p.Leu2393Val		110541172	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	4.341	0.062793	0.08388	.	.	ENSG00000205038	ENST00000378402	D	0.92249	-3.0	5.37	-0.0824	0.13698	.	0.192857	0.34088	N	0.004275	T	0.70640	0.3247	N	0.02985	-0.445	0.22521	N	0.999026	B	0.06786	0.001	B	0.08055	0.003	T	0.62637	-0.6812	10	0.02654	T	1	.	2.4734	0.04570	0.3806:0.3006:0.0:0.3188	.	2393	Q86WI1	PKHL1_HUMAN	V	2393	ENSP00000367655:L2393V	ENSP00000367655:L2393V	L	+	1	2	PKHD1L1	110541172	0.910000	0.30920	0.939000	0.37840	0.968000	0.65278	0.759000	0.26461	0.012000	0.14892	0.377000	0.23210	TTA		0.373	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110471996	T	G	110471996	3	3	61	1	0	0	0	0	1	0	0	0	12003	1838	64	4	7363	4	PKHD1L1	8	110471996	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	14405	110471996	35892026	6062	14047										
PKHD1L1	93035	broad.mit.edu	37	chr8	110488759	110488759	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagactatgtaattatatCacataacttcactcaaaatc	3	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110488759C>A	ENST00000378402.5	+	52	8884	c.8780C>A	c.(8779-8781)tCa>tAa	p.S2927*		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2927					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.S2929*(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTAATTATATCACATAACTTC	0.279										HNSCC(38;0.096)																																						1	Substitution - Nonsense(1)	large_intestine(1)	8											32	31	31					8																	110488759		1799	4054	5853	110557935	SO:0001587	stop_gained	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.8780C>A	8.37:g.110488759C>A	ENSP00000367655:p.Ser2927*		110557935	Q567P2|Q9UF27	Nonsense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	50	16.894908	0.99874	.	.	ENSG00000205038	ENST00000378402	.	.	.	5.79	4.91	0.64330	.	0.142680	0.47852	D	0.000218	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7584	0.69588	0.0:0.8547:0.1453:0.0	.	.	.	.	X	2927	.	ENSP00000367655:S2927X	S	+	2	0	PKHD1L1	110557935	0.999000	0.42202	0.999000	0.59377	0.994000	0.84299	3.401000	0.52601	1.436000	0.47453	0.585000	0.79938	TCA		0.279	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110488759	C	A	110488759	4	1	61	1	0	0	0	0	0	1	0	0	12003	838	29	2	8986	2	PKHD1L1	8	110488759	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16763	110488759	35875263	6063	14048										
PKHD1L1	93035	broad.mit.edu	37	chr8	110504129	110504129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatgggggaatgccaaccGagtccgagggaatttgattg	14	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110504129G>A	ENST00000378402.5	+	62	10246	c.10142G>A	c.(10141-10143)cGa>cAa	p.R3381Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3381					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R3383Q(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AATGCCAACCGAGTCCGAGGG	0.388										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	large_intestine(1)	8											43	44	44					8																	110504129		1815	4069	5884	110573305	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10142G>A	8.37:g.110504129G>A	ENSP00000367655:p.Arg3381Gln		110573305	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803498	0.31869	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85955	-2.05;-1.84	5.61	4.74	0.60224	Pectin lyase fold/virulence factor (1);	0.366778	0.28247	N	0.016051	T	0.76011	0.3928	L	0.43152	1.355	0.09310	N	0.999996	P	0.40066	0.701	B	0.34346	0.18	T	0.62081	-0.6929	10	0.15499	T	0.54	.	10.8335	0.46673	0.0769:0.1319:0.7912:0.0	.	3381	Q86WI1	PKHL1_HUMAN	Q	3381;309	ENSP00000367655:R3381Q;ENSP00000437376:R309Q	ENSP00000367655:R3381Q	R	+	2	0	PKHD1L1	110573305	0.971000	0.33674	1.000000	0.80357	0.850000	0.48378	0.433000	0.21477	0.737000	0.32582	-1.119000	0.02030	CGA		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110504129	G	A	110504129	3	1	61	1	0	0	0	0	1	0	0	0	12003	1058	37	1	10388	1	PKHD1L1	8	110504129	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15370	110504129	35859893	6064	14049										
PKHD1L1	93035	broad.mit.edu	37	chr8	110520022	110520022	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagaatatgaatgggacGgaaacagccaagtaggaatt	12	5	0	2	rs199559636		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110520022G>A	ENST00000378402.5	+	69	11229	c.11125G>A	c.(11125-11127)Gga>Aga	p.G3709R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3709					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.G3713R(2)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGAATGGGACGGAAACAGCCA	0.433										HNSCC(38;0.096)			G|||	1	0.000199681	0	0	5008	,	,		17590	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	8						G	ARG/GLY	0,3762		0,0,1881	128	120	122		11125	5.4	1	8		122	3,8233		0,3,4115	yes	missense	PKHD1L1	NM_177531.4	125	0,3,5996	AA,AG,GG		0.0364,0.0,0.025	probably-damaging	3709/4244	110520022	3,11995	1881	4118	5999	110589198	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.11125G>A	8.37:g.110520022G>A	ENSP00000367655:p.Gly3709Arg		110589198	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.5	4.158731	0.78226	0.0	3.64E-4	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.87729	-2.29;-2.07	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.90823	0.7118	M	0.83603	2.65	0.38916	D	0.957648	D	0.71674	0.998	P	0.53861	0.736	D	0.92266	0.5821	10	0.87932	D	0	.	10.4689	0.44624	0.0889:0.0:0.9111:0.0	.	3709	Q86WI1	PKHL1_HUMAN	R	3709;637	ENSP00000367655:G3709R;ENSP00000437376:G637R	ENSP00000367655:G3709R	G	+	1	0	PKHD1L1	110589198	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.575000	0.74018	2.678000	0.91216	0.655000	0.94253	GGA		0.433	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110520022	G	A	110520022	3	1	61	1	0	0	0	0	1	0	0	0	12003	1117	39	1	11399	1	PKHD1L1	8	110520022	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15893	110520022	35844000	6065	14050										
PKHD1L1	93035	broad.mit.edu	37	chr8	110527439	110527439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttccacacttcaacgttTggatgtctatgtgaacaact	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110527439T>C	ENST00000378402.5	+	72	11698	c.11594T>C	c.(11593-11595)tTg>tCg	p.L3865S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3865					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L3869S(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTTCAACGTTTGGATGTCTAT	0.318										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	large_intestine(1)	8											103	89	93					8																	110527439		1828	4085	5913	110596615	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.11594T>C	8.37:g.110527439T>C	ENSP00000367655:p.Leu3865Ser		110596615	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.074504	0.76415	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.88431	-2.38;-2.18	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000002	D	0.94069	0.8099	M	0.83012	2.62	0.36424	D	0.864481	D	0.89917	1.0	D	0.76575	0.988	D	0.96432	0.9320	10	0.87932	D	0	.	11.6105	0.51057	0.0:0.0:0.0:1.0	.	3865	Q86WI1	PKHL1_HUMAN	S	3865;793	ENSP00000367655:L3865S;ENSP00000437376:L793S	ENSP00000367655:L3865S	L	+	2	0	PKHD1L1	110596615	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.481000	0.66826	2.012000	0.59069	0.477000	0.44152	TTG		0.318	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110527439	T	C	110527439	3	2	61	1	0	0	0	0	1	0	0	0	12003	1821	63	4	11880	4	PKHD1L1	8	110527439	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7417	110527439	35836583	6066	14051										
PKHD1L1	93035	broad.mit.edu	37	chr8	110530568	110530568	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaagatgacttttatacCtctcacaatctggttaaaaa	5	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110530568C>A	ENST00000378402.5	+	73	11966	c.11862C>A	c.(11860-11862)acC>acA	p.T3954T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3954					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.T3958T(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACTTTTATACCTCTCACAATC	0.363										HNSCC(38;0.096)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											130	129	129					8																	110530568		1845	4084	5929	110599744	SO:0001819	synonymous_variant	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.11862C>A	8.37:g.110530568C>A			110599744	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																				0.363	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110530568	C	A	110530568	2	1	61	1	0	0	0	0	0	0	0	1	12003	668	24	2		2	PKHD1L1	8	110530568	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3129	110530568	35833454	6067	14052										
SYBU	55638	broad.mit.edu	37	chr8	110655129	110655129	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaattcggcttcgagaaatCtccttgtcatgatgctgcac	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:110655129C>A	ENST00000422135.1	-	3	572	c.57G>T	c.(55-57)gaG>gaT	p.E19D	SYBU_ENST00000419099.1_Missense_Mutation_p.E18D|SYBU_ENST00000408908.2_Missense_Mutation_p.E19D|SYBU_ENST00000440310.1_Missense_Mutation_p.E19D|SYBU_ENST00000408889.3_Intron|SYBU_ENST00000276646.9_Missense_Mutation_p.E19D|SYBU_ENST00000533171.1_Missense_Mutation_p.E19D|SYBU_ENST00000433638.1_Missense_Mutation_p.E19D|SYBU_ENST00000533895.1_Missense_Mutation_p.E18D|SYBU_ENST00000446070.2_Missense_Mutation_p.E18D|SYBU_ENST00000528331.1_Intron|SYBU_ENST00000532779.1_Intron|SYBU_ENST00000424158.2_Missense_Mutation_p.E24D|SYBU_ENST00000528647.1_Missense_Mutation_p.E18D|SYBU_ENST00000399066.3_Missense_Mutation_p.E16D|SYBU_ENST00000533065.1_Intron|RP11-422N16.3_ENST00000499579.1_5'Flank	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	19	Sufficient for interaction with KIF5B.				regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.E16D(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						TTCGAGAAATCTCCTTGTCAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8											101	104	103					8																	110655129		1910	4139	6049	110724305	SO:0001583	missense	55638			AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"syntaphilin-like"	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.57G>T	8.37:g.110655129C>A	ENSP00000407118:p.Glu19Asp		110724305	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Missense_Mutation	SNP	ENST00000422135.1	37	CCDS47912.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.053491	0.75960	.	.	ENSG00000147642	ENST00000533895;ENST00000424158;ENST00000399066;ENST00000446070;ENST00000276646;ENST00000528647;ENST00000422135;ENST00000419099;ENST00000433638;ENST00000408908;ENST00000440310;ENST00000533171;ENST00000529190;ENST00000533821;ENST00000534501;ENST00000524720;ENST00000534184;ENST00000528716;ENST00000526302;ENST00000534578;ENST00000527600	.	.	.	5.91	5.91	0.95273	.	0.209202	0.50627	D	0.000110	T	0.65575	0.2704	M	0.62723	1.935	0.80722	D	1	P;P;P	0.52316	0.952;0.952;0.952	P;P;P	0.49085	0.6;0.6;0.6	T	0.68473	-0.5399	9	0.72032	D	0.01	-30.7372	17.7884	0.88545	0.0:1.0:0.0:0.0	.	18;19;16	Q9NX95-3;Q9NX95;Q9NX95-4	.;SYBU_HUMAN;.	D	18;24;16;18;19;18;19;18;19;19;19;19;18;18;19;19;18;19;19;19;19	.	ENSP00000276646:E19D	E	-	3	2	SYBU	110724305	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	3.412000	0.52679	2.804000	0.96469	0.462000	0.41574	GAG		0.483	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		A	110655129	C	A	110655129	3	1	61	1	0	0	0	0	1	0	0	0	15466	912	32	2	1958	2	SYBU	8	110655129	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124561	110655129	35708893	6068	14053										
CSMD3	114788	broad.mit.edu	37	chr8	113249459	113249459	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctattgctcagtgttgcGttaactctcccagtggaagc	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:113249459G>A	ENST00000297405.5	-	67	10831	c.10587C>T	c.(10585-10587)aaC>aaT	p.N3529N	CSMD3_ENST00000455883.2_Silent_p.N3360N|CSMD3_ENST00000352409.3_Silent_p.N3459N|CSMD3_ENST00000343508.3_Silent_p.N3489N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3529						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N3529N(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCAGTGTTGCGTTAACTCTCC	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											215	197	203					8																	113249459		2203	4300	6503	113318635	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10587C>T	8.37:g.113249459G>A			113318635	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113249459	G	A	113249459	2	1	61	1	0	0	0	0	0	0	0	1	3952	1136	40	1		1	CSMD3	8	113249459	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2594330	113249459	33114563	6069	14054										
CSMD3	114788	broad.mit.edu	37	chr8	113293502	113293502	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccatgcaggaataaatgaCtgaactagaaaatgttgtgc	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:113293502C>A	ENST00000297405.5	-	59	9653	c.9409G>T	c.(9409-9411)Gtc>Ttc	p.V3137F	CSMD3_ENST00000455883.2_Missense_Mutation_p.V2968F|CSMD3_ENST00000352409.3_Missense_Mutation_p.V3067F|CSMD3_ENST00000343508.3_Missense_Mutation_p.V3097F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3137	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V3137F(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAATAAATGACTGAACTAGAA	0.433										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											128	112	118					8																	113293502		2203	4300	6503	113362678	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9409G>T	8.37:g.113293502C>A	ENSP00000297405:p.Val3137Phe		113362678	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249846	0.80024	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	5.51	4.58	0.56647	Complement control module (2);Sushi/SCR/CCP (3);	0.338199	0.27327	N	0.019879	D	0.85957	0.5818	M	0.92219	3.285	0.54753	D	0.999985	D;P;B	0.55800	0.973;0.886;0.123	D;P;B	0.63957	0.92;0.772;0.089	D	0.88158	0.2855	10	0.56958	D	0.05	.	13.1108	0.59273	0.0:0.9162:0.0:0.0838	.	2968;3137;3097	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	F	3097;3137;2407;2968;3067	ENSP00000345799:V3097F;ENSP00000297405:V3137F;ENSP00000341558:V2407F;ENSP00000412263:V2968F;ENSP00000343124:V3067F	ENSP00000297405:V3137F	V	-	1	0	CSMD3	113362678	0.999000	0.42202	0.999000	0.59377	0.631000	0.37964	3.980000	0.56895	1.189000	0.43028	0.650000	0.86243	GTC		0.433	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113293502	C	A	113293502	3	1	61	1	0	0	0	0	1	0	0	0	3952	565	20	2	1766	2	CSMD3	8	113293502	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44043	113293502	33070520	6070	14055										
CSMD3	114788	broad.mit.edu	37	chr8	113348978	113348978	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttacaagccaaaaacaatCttgaaagtttggatattcat	5	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:113348978C>A	ENST00000297405.5	-	44	7166	c.6922G>T	c.(6922-6924)Gat>Tat	p.D2308Y	CSMD3_ENST00000455883.2_Missense_Mutation_p.D2204Y|CSMD3_ENST00000352409.3_Missense_Mutation_p.D2238Y|CSMD3_ENST00000343508.3_Missense_Mutation_p.D2268Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2308	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D2308Y(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAAAAACAATCTTGAAAGTTT	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											102	97	99					8																	113348978		2203	4300	6503	113418154	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6922G>T	8.37:g.113348978C>A	ENSP00000297405:p.Asp2308Tyr		113418154	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.795207	0.90453	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	5.64	5.64	0.86602	CUB (5);	0.000000	0.85682	D	0.000000	T	0.76919	0.4055	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.76719	-0.2856	10	0.62326	D	0.03	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2204;2308;2268	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	2268;2308;1578;2204;2238	ENSP00000345799:D2268Y;ENSP00000297405:D2308Y;ENSP00000341558:D1578Y;ENSP00000412263:D2204Y;ENSP00000343124:D2238Y	ENSP00000297405:D2308Y	D	-	1	0	CSMD3	113418154	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.651000	0.83577	2.937000	0.99478	0.650000	0.86243	GAT		0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113348978	C	A	113348978	3	1	61	1	0	0	0	0	1	0	0	0	3952	913	32	2	4313	2	CSMD3	8	113348978	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55476	113348978	33015044	6071	14056										
CSMD3	114788	broad.mit.edu	37	chr8	113651100	113651100	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatcagtaagtagtcatgAtggtcttccaaatgaaaagt	10	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:113651100A>G	ENST00000297405.5	-	21	3595	c.3351T>C	c.(3349-3351)caT>caC	p.H1117H	CSMD3_ENST00000455883.2_Silent_p.H1013H|CSMD3_ENST00000352409.3_Silent_p.H1117H|CSMD3_ENST00000343508.3_Silent_p.H1077H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1117	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.H1117H(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGTAGTCATGATGGTCTTCCA	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											107	100	103					8																	113651100		2203	4300	6503	113720276	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3351T>C	8.37:g.113651100A>G			113720276	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.408	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113651100	A	G	113651100	2	3	61	1	0	0	0	0	0	0	0	1	3952	330	12	4		4	CSMD3	8	113651100	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	302122	113651100	32712922	6072	14057										
CSMD3	114788	broad.mit.edu	37	chr8	113933929	113933929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaggtgatgctctttgcGccctgtaggacataatcttc	10	10	2	2	rs377399711		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:113933929G>A	ENST00000297405.5	-	10	1804	c.1560C>T	c.(1558-1560)ggC>ggT	p.G520G	CSMD3_ENST00000455883.2_Silent_p.G416G|CSMD3_ENST00000352409.3_Silent_p.G520G|CSMD3_ENST00000343508.3_Silent_p.G480G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	520	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G520G(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGCTCTTTGCGCCCTGTAGGA	0.383										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - coding silent(1)	large_intestine(1)	8						G	,,	1,4405	2.1+/-5.4	0,1,2202	113	107	109		1248,1560,1440	-11	0.4	8		109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	416/3539,520/3708,480/3668	113933929	1,13005	2203	4300	6503	114003105	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1560C>T	8.37:g.113933929G>A			114003105	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.383	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113933929	G	A	113933929	2	1	61	1	0	0	0	0	0	0	0	1	3952	1074	38	1		1	CSMD3	8	113933929	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282829	113933929	32430093	6073	14058										
TRPS1	7227	broad.mit.edu	37	chr8	116632271	116632271	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtttctcagaggggggttCtttttccggaccatatctgc	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:116632271C>A	ENST00000220888.5	-	2	174	c.15G>T	c.(13-15)aaG>aaT	p.K5N	TRPS1_ENST00000520276.1_Missense_Mutation_p.K9N|TRPS1_ENST00000519076.1_Missense_Mutation_p.K5N|TRPS1_ENST00000519674.1_Missense_Mutation_p.K5N|TRPS1_ENST00000395715.3_Missense_Mutation_p.K18N			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	5					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K5N(1)|p.K5K(1)|p.K18K(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GAGGGGGGTTCTTTTTCCGGA	0.413									Langer-Giedion syndrome																																							3	Substitution - coding silent(2)|Substitution - Missense(1)	lung(2)|large_intestine(1)	8											57	54	55					8																	116632271		1836	4086	5922	116701446	SO:0001583	missense	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.15G>T	8.37:g.116632271C>A	ENSP00000220888:p.Lys5Asn		116701446	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	C	21.2	4.106276	0.77096	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674;ENST00000395713;ENST00000519815;ENST00000422939	D;D;D;D;T	0.99287	-5.39;-5.35;-5.69;-5.36;0.43	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000001	D	0.98912	0.9631	L	0.27053	0.805	0.80722	D	1	D;D;D	0.76494	0.989;0.981;0.999	D;D;D	0.80764	0.985;0.966;0.994	D	0.99939	1.1387	10	0.87932	D	0	0.0788	20.0966	0.97849	0.0:1.0:0.0:0.0	.	9;5;18	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	N	18;5;5;9;5;18;18;18	ENSP00000379065:K18N;ENSP00000220888:K5N;ENSP00000428910:K5N;ENSP00000428680:K9N;ENSP00000429174:K5N	ENSP00000220888:K5N	K	-	3	2	TRPS1	116701446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.272000	0.78516	2.751000	0.94390	0.650000	0.86243	AAG		0.413	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116632271	C	A	116632271	3	1	61	1	0	0	0	0	1	0	0	0	16633	912	32	2	3850	2	TRPS1	8	116632271	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2698342	116632271	29731751	6074	14059										
UTP23	84294	broad.mit.edu	37	chr8	117783832	117783832	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggagtcaggtcagcttgtCtcagtgcatgagaaagaaag	14	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:117783832C>A	ENST00000309822.2	+	3	602	c.501C>A	c.(499-501)gtC>gtA	p.V167V	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000520733.1_Intron|UTP23_ENST00000357148.3_Intron	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	167					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.V167V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						GTCAGCTTGTCTCAGTGCATG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	8											91	89	90					8																	117783832		2203	4300	6503	117853013	SO:0001819	synonymous_variant	84294				CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 53"	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.501C>A	8.37:g.117783832C>A			117853013	B2RE25|Q96NJ8	Silent	SNP	ENST00000309822.2	37	CCDS6320.1																																																																																				0.383	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334		A	117783832	C	A	117783832	2	1	61	1	0	0	0	0	0	0	0	1	17140	900	32	2		2	UTP23	8	117783832	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1151561	117783832	28580190	6075	14060										
RAD21	5885	broad.mit.edu	37	chr8	117868913	117868913	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatcatcctcatccatatcGtcatgtgcaggctgctctgg	8	12	4	0	rs34653007	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:117868913G>A	ENST00000297338.2	-	7	1073	c.786C>T	c.(784-786)gaC>gaT	p.D262D	RAD21_ENST00000523547.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	262					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.D262D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					CATCCATATCGTCATGTGCAG	0.433													G|||	5	0.000998403	0.003	0.0014	5008	,	,		16204	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						G		42,4364	45.3+/-79.5	0,42,2161	110	112	111		786	3.1	1	8	dbSNP_126	111	0,8600		0,0,4300	no	coding-synonymous	RAD21	NM_006265.2		0,42,6461	AA,AG,GG		0.0,0.9532,0.3229		262/632	117868913	42,12964	2203	4300	6503	117938094	SO:0001819	synonymous_variant	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.786C>T	8.37:g.117868913G>A			117938094	A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	37	CCDS6321.1																																																																																				0.433	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117868913	G	A	117868913	2	1	61	1	0	0	0	0	0	0	0	1	13018	1136	40	1		1	RAD21	8	117868913	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85081	117868913	28495109	6076	14061										
SLC30A8	169026	broad.mit.edu	37	chr8	118183386	118183386	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacaatgaatcaagtaattCtctcagctcatgttgctaca	5	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:118183386C>A	ENST00000456015.2	+	7	943	c.943C>A	c.(943-945)Ctc>Atc	p.L315I	SLC30A8_ENST00000427715.2_Missense_Mutation_p.L266I|SLC30A8_ENST00000521243.1_Missense_Mutation_p.L266I|SLC30A8_ENST00000519688.1_Missense_Mutation_p.L266I	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	315					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.L315I(1)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TCAAGTAATTCTCTCAGCTCA	0.423																																					Ovarian(162;1202 1922 6011 16223 52092)											1	Substitution - Missense(1)	large_intestine(1)	8											190	175	180					8																	118183386		2203	4300	6503	118252567	SO:0001583	missense	169026				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.943C>A	8.37:g.118183386C>A	ENSP00000415011:p.Leu315Ile		118252567	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421794	0.83559	.	.	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.97	4.06	0.47325	.	0.067430	0.64402	N	0.000010	T	0.64897	0.2640	M	0.78344	2.41	0.58432	D	0.999997	D	0.56287	0.975	P	0.61722	0.893	T	0.68059	-0.5509	10	0.54805	T	0.06	-9.4419	12.481	0.55842	0.1686:0.8314:0.0:0.0	.	315	Q8IWU4	ZNT8_HUMAN	I	266;266;266;315	ENSP00000428545:L266I;ENSP00000407505:L266I;ENSP00000431069:L266I;ENSP00000415011:L315I	ENSP00000407505:L266I	L	+	1	0	SLC30A8	118252567	0.988000	0.35896	1.000000	0.80357	0.978000	0.69477	1.404000	0.34623	1.162000	0.42619	0.655000	0.94253	CTC		0.423	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118183386	C	A	118183386	3	1	61	1	0	0	0	0	1	0	0	0	14598	913	32	2	969	2	SLC30A8	8	118183386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314473	118183386	28180636	6077	14062										
SLC30A8	169026	broad.mit.edu	37	chr8	118184848	118184848	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagctttacgatgcactcActcaccattcagatggaatc	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:118184848A>C	ENST00000456015.2	+	8	1038	c.1038A>C	c.(1036-1038)tcA>tcC	p.S346S	SLC30A8_ENST00000427715.2_Silent_p.S297S|SLC30A8_ENST00000521243.1_Silent_p.S297S|SLC30A8_ENST00000519688.1_Silent_p.S297S	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	346					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.S346S(1)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			CGATGCACTCACTCACCATTC	0.498																																					Ovarian(162;1202 1922 6011 16223 52092)											1	Substitution - coding silent(1)	large_intestine(1)	8											149	131	137					8																	118184848		2203	4300	6503	118254029	SO:0001819	synonymous_variant	169026				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.1038A>C	8.37:g.118184848A>C			118254029	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Silent	SNP	ENST00000456015.2	37	CCDS6322.1																																																																																				0.498	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		C	118184848	A	C	118184848	2	2	61	1	0	0	0	0	0	0	0	1	14598	146	6	4		4	SLC30A8	8	118184848	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1462	118184848	28179174	6078	14063										
COLEC10	10584	broad.mit.edu	37	chr8	120118131	120118131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctaacccactgcaggattCggggtggaatgctagccatg	12	12	0	0	rs115273924	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120118131C>T	ENST00000332843.2	+	6	576	c.535C>T	c.(535-537)Cgg>Tgg	p.R179W		NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	179	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.R179W(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			CTGCAGGATTCGGGGTGGAAT	0.502													C|||	15	0.00299521	0.0068	0	5008	,	,		19133	0		0	False		,,,				2504	0.0061															1	Substitution - Missense(1)	large_intestine(1)	8						C	TRP/ARG	14,4392	21.2+/-45.6	0,14,2189	104	82	89		535	5.4	1	8	dbSNP_132	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COLEC10	NM_006438.3	101	0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153	probably-damaging	179/278	120118131	15,12991	2203	4300	6503	120187312	SO:0001583	missense	10584			AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"Collectins"	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.535C>T	8.37:g.120118131C>T	ENSP00000332723:p.Arg179Trp		120187312	Q3SYH6|Q6UW19	Missense_Mutation	SNP	ENST00000332843.2	37	CCDS6327.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	19.52	3.842792	0.71488	0.003177	1.16E-4	ENSG00000184374	ENST00000332843	T	0.18174	2.23	5.39	5.39	0.77823	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.89968	3.075	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	T	0.52638	-0.8549	10	0.48119	T	0.1	-13.3309	13.5562	0.61761	0.2585:0.7415:0.0:0.0	.	179	Q9Y6Z7	COL10_HUMAN	W	179	ENSP00000332723:R179W	ENSP00000332723:R179W	R	+	1	2	COLEC10	120187312	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.341000	0.52151	2.692000	0.91855	0.555000	0.69702	CGG		0.502	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381225.1			T	120118131	C	T	120118131	3	4	61	1	0	0	0	0	1	0	0	0	3716	875	31	1	557	1	COLEC10	8	120118131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1933283	120118131	26245891	6079	14064										
NOV	4856	broad.mit.edu	37	chr8	120435102	120435102	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagtgtctccgcaccaaGaagtcactcaaagccatcca	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120435102G>T	ENST00000259526.3	+	5	1031	c.804G>T	c.(802-804)aaG>aaT	p.K268N	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.K268N(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TCCGCACCAAGAAGTCACTCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	8											75	76	76					8																	120435102		2203	4300	6503	120504283	SO:0001583	missense	4856			X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.804G>T	8.37:g.120435102G>T	ENSP00000259526:p.Lys268Asn		120504283		Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	G	9.395	1.076412	0.20227	.	.	ENSG00000136999	ENST00000259526	D	0.90004	-2.6	5.91	0.697	0.18081	Cystine knot (1);Cystine knot, C-terminal (1);	0.669377	0.16696	N	0.203337	T	0.81908	0.4922	L	0.57536	1.79	0.34344	D	0.689136	B	0.17852	0.024	B	0.16722	0.016	T	0.70733	-0.4791	10	0.28530	T	0.3	-1.8576	1.7317	0.02933	0.2686:0.1189:0.4691:0.1433	.	268	P48745	NOV_HUMAN	N	268	ENSP00000259526:K268N	ENSP00000259526:K268N	K	+	3	2	NOV	120504283	0.314000	0.24563	0.455000	0.27031	0.521000	0.34408	0.232000	0.17891	0.046000	0.15833	-0.142000	0.14014	AAG		0.473	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		T	120435102	G	T	120435102	3	4	61	1	0	0	0	0	1	0	0	0	10584	933	33	2	822	2	NOV	8	120435102	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	316971	120435102	25928920	6080	14065										
ENPP2	5168	broad.mit.edu	37	chr8	120606098	120606098	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttccctcagaggatttgtCatctaggaaaaagaagcaag	9	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120606098C>A	ENST00000075322.6	-	12	1033	c.975G>T	c.(973-975)atG>atT	p.M325I	ENPP2_ENST00000522826.1_Missense_Mutation_p.M325I|ENPP2_ENST00000522167.1_5'Flank|ENPP2_ENST00000427067.2_Missense_Mutation_p.M321I|ENPP2_ENST00000259486.6_Missense_Mutation_p.M377I	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	325					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.M377I(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GAGGATTTGTCATCTAGGAAA	0.413																																					Melanoma(20;305 879 2501 4818 31020)											1	Substitution - Missense(1)	large_intestine(1)	8											216	203	207					8																	120606098		2203	4300	6503	120675279	SO:0001583	missense	5168			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.975G>T	8.37:g.120606098C>A	ENSP00000075322:p.Met325Ile		120675279	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284447	0.59867	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.5	5.5	0.81552	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.118865	0.64402	D	0.000010	T	0.67040	0.2851	L	0.27944	0.81	0.54753	D	0.999985	B;B;B	0.21821	0.024;0.023;0.061	B;B;B	0.23574	0.022;0.016;0.047	T	0.64356	-0.6427	10	0.72032	D	0.01	.	18.7617	0.91855	0.0:1.0:0.0:0.0	.	325;325;377	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	I	377;321;325;325	ENSP00000259486:M377I;ENSP00000403315:M321I;ENSP00000428291:M325I;ENSP00000075322:M325I	ENSP00000075322:M325I	M	-	3	0	ENPP2	120675279	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.709000	0.61867	2.744000	0.94065	0.655000	0.94253	ATG		0.413	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			A	120606098	C	A	120606098	3	1	61	1	0	0	0	0	1	0	0	0	5143	826	29	2	1751	2	ENPP2	8	120606098	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	170996	120606098	25757924	6081	14066										
ENPP2	5168	broad.mit.edu	37	chr8	120629776	120629776	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacggaagccatccacggaGaagatgattaatggagggcg	15	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120629776G>T	ENST00000075322.6	-	6	565	c.507C>A	c.(505-507)ttC>ttA	p.F169L	ENPP2_ENST00000522826.1_Missense_Mutation_p.F169L|ENPP2_ENST00000427067.2_Missense_Mutation_p.F165L|ENPP2_ENST00000259486.6_Missense_Mutation_p.F169L	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	169					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.F169L(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CATCCACGGAGAAGATGATTA	0.368																																					Melanoma(20;305 879 2501 4818 31020)											1	Substitution - Missense(1)	large_intestine(1)	8											66	63	64					8																	120629776		2203	4300	6503	120698957	SO:0001583	missense	5168			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.507C>A	8.37:g.120629776G>T	ENSP00000075322:p.Phe169Leu		120698957	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.778399	0.49786	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322;ENST00000520066	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.95	3.11	0.35812	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.102545	0.64402	D	0.000002	T	0.44561	0.1299	N	0.10664	0.02	0.46901	D	0.999244	B;B;B	0.18310	0.001;0.027;0.002	B;B;B	0.17979	0.007;0.02;0.007	T	0.26643	-1.0097	10	0.54805	T	0.06	.	9.8029	0.40775	0.2975:0.0:0.7025:0.0	.	169;169;169	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	L	169;165;169;169;151	ENSP00000259486:F169L;ENSP00000403315:F165L;ENSP00000428291:F169L;ENSP00000075322:F169L;ENSP00000428304:F151L	ENSP00000075322:F169L	F	-	3	2	ENPP2	120698957	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	1.489000	0.35562	0.363000	0.24346	0.650000	0.86243	TTC		0.368	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120629776	G	T	120629776	3	4	61	1	0	0	0	0	1	0	0	0	5143	933	33	2	2403	2	ENPP2	8	120629776	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23678	120629776	25734246	6082	14067										
ENPP2	5168	broad.mit.edu	37	chr8	120650665	120650665	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatagttttgacacttacCtgtaggaggaccttcctccc	7	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120650665C>T	ENST00000075322.6	-	2	194	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	ENPP2_ENST00000522826.1_Splice_Site_p.V46M|ENPP2_ENST00000427067.2_Splice_Site_p.V42M|ENPP2_ENST00000259486.6_Splice_Site_p.V46M	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	46					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.V46M(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGACACTTACCTGTAGGAGGA	0.333																																					Melanoma(20;305 879 2501 4818 31020)											1	Substitution - Missense(1)	large_intestine(1)	8											112	111	111					8																	120650665		2203	4299	6502	120719846	SO:0001630	splice_region_variant	5168			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.136+1G>A	8.37:g.120650665C>T			120719846	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208605	0.79240	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322;ENST00000520066	T;T;T;T;T	0.74315	-0.74;-0.71;-0.72;-0.71;-0.83	6.17	6.17	0.99709	.	0.525823	0.20502	N	0.091076	T	0.77955	0.4208	L	0.51422	1.61	0.53688	D	0.999979	B;P;P	0.39003	0.232;0.472;0.654	B;B;P	0.46172	0.309;0.224;0.506	T	0.72590	-0.4247	9	.	.	.	.	19.8676	0.96824	0.0:1.0:0.0:0.0	.	46;46;46	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	M	46;42;46;46;46	ENSP00000259486:V46M;ENSP00000403315:V42M;ENSP00000428291:V46M;ENSP00000075322:V46M;ENSP00000428304:V46M	.	V	-	1	0	ENPP2	120719846	1.000000	0.71417	1.000000	0.80357	0.518000	0.34316	5.167000	0.64972	2.941000	0.99782	0.655000	0.94253	GTG		0.333	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		Missense_Mutation	T	120650665	C	T	120650665	5	4	61	1	0	0	0	0	0	0	1	0	5143	695	24	3	2790	3	ENPP2	8	120650665	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20889	120650665	25713357	6083	14068										
TAF2	6873	broad.mit.edu	37	chr8	120793389	120793389	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctagtgaagagtgacttCatggctggtggtcctgtcca	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:120793389C>A	ENST00000378164.2	-	17	2455	c.2157G>T	c.(2155-2157)atG>atT	p.M719I		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	719					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.M719I(2)		NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGAGTGACTTCATGGCTGGTG	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	8											78	82	81					8																	120793389		2203	4300	6503	120862570	SO:0001583	missense	6873			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2157G>T	8.37:g.120793389C>A	ENSP00000367406:p.Met719Ile		120862570	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747527	0.69533	.	.	ENSG00000064313	ENST00000378164	T	0.28454	1.61	5.41	4.54	0.55810	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.39226	0.1070	M	0.71581	2.175	0.80722	D	1	P	0.51351	0.944	P	0.45138	0.471	T	0.45702	-0.9243	10	0.72032	D	0.01	-15.1813	14.4386	0.67301	0.0:0.9291:0.0:0.0709	.	719	Q6P1X5	TAF2_HUMAN	I	719	ENSP00000367406:M719I	ENSP00000367406:M719I	M	-	3	0	TAF2	120862570	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.776000	0.85560	1.438000	0.47492	0.650000	0.86243	ATG		0.343	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		A	120793389	C	A	120793389	3	1	61	1	0	0	0	0	1	0	0	0	15563	826	29	2	1482	2	TAF2	8	120793389	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142724	120793389	25570633	6084	14069										
COL14A1	7373	broad.mit.edu	37	chr8	121211775	121211775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccaccatctagaaatcttCgtgagtctggtgtagaactg	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121211775C>T	ENST00000297848.3	+	8	1117	c.847C>T	c.(847-849)Cgt>Tgt	p.R283C	COL14A1_ENST00000537875.1_Missense_Mutation_p.R283C|COL14A1_ENST00000247781.3_Intron|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.R283C	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.R283C(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TAGAAATCTTCGTGAGTCTGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											160	139	146					8																	121211775		2203	4300	6503	121280956	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.847C>T	8.37:g.121211775C>T	ENSP00000297848:p.Arg283Cys		121280956		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365990	0.61513	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000434620	T;T;T;T	0.81330	-1.48;-1.48;-1.48;0.24	5.55	5.55	0.83447	von Willebrand factor, type A (3);	0.110124	0.64402	D	0.000018	D	0.89739	0.6802	M	0.87547	2.89	0.50039	D	0.999847	D	0.89917	1.0	D	0.65773	0.938	D	0.90716	0.4631	10	0.87932	D	0	.	13.2695	0.60153	0.2711:0.7289:0.0:0.0	.	283	Q05707	COEA1_HUMAN	C	283;283;283;96	ENSP00000443974:R283C;ENSP00000311809:R283C;ENSP00000297848:R283C;ENSP00000409461:R96C	ENSP00000297848:R283C	R	+	1	0	COL14A1	121280956	0.371000	0.25056	1.000000	0.80357	0.819000	0.46315	1.029000	0.30140	2.894000	0.99253	0.655000	0.94253	CGT		0.388	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121211775	C	T	121211775	3	4	61	1	0	0	0	0	1	0	0	0	3677	884	31	1	873	1	COL14A1	8	121211775	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	418386	121211775	25152247	6085	14070										
COL14A1	7373	broad.mit.edu	37	chr8	121216031	121216031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtacaatgttgccgaattcGatctgatgcacacagttgtg	10	8	1	1	rs367633536		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121216031G>A	ENST00000297848.3	+	9	1231	c.961G>A	c.(961-963)Gat>Aat	p.D321N	COL14A1_ENST00000537875.1_Missense_Mutation_p.D321N|COL14A1_ENST00000247781.3_Missense_Mutation_p.D226N|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.D321N	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.D321N(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TGCCGAATTCGATCTGATGCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	ASN/ASP	0,4406		0,0,2203	135	115	122		961	5.2	1	8		122	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL14A1	NM_021110.1	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	321/1797	121216031	1,13005	2203	4300	6503	121285212	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.961G>A	8.37:g.121216031G>A	ENSP00000297848:p.Asp321Asn		121285212		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.11|13.11	2.139838|2.139838	0.37728|0.37728	0.0|0.0	1.16E-4|1.16E-4	ENSG00000187955|ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	T;T;T;T;D|.	0.83837|.	-1.28;-1.28;-1.28;0.5;-1.77|.	5.21|5.21	5.21|5.21	0.72293|0.72293	von Willebrand factor, type A (3);|.	0.157791|.	0.56097|.	D|.	0.000038|.	T|T	0.32763|0.32763	0.0840|0.0840	N|N	0.17082|0.17082	0.46|0.46	0.34557|0.34557	D|D	0.711914|0.711914	B|.	0.18610|.	0.029|.	B|.	0.12837|.	0.008|.	T|T	0.39482|0.39482	-0.9612|-0.9612	10|5	0.15952|.	T|.	0.53|.	.|.	6.2322|6.2322	0.20742|0.20742	0.2138:0.0:0.7862:0.0|0.2138:0.0:0.7862:0.0	.|.	321|.	Q05707|.	COEA1_HUMAN|.	N|Q	321;321;321;226;134|77	ENSP00000443974:D321N;ENSP00000311809:D321N;ENSP00000297848:D321N;ENSP00000247781:D226N;ENSP00000409461:D134N|.	ENSP00000247781:D226N|.	D|R	+|+	1|2	0|0	COL14A1|COL14A1	121285212|121285212	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.616000|0.616000	0.37450|0.37450	7.427000|7.427000	0.80284|0.80284	2.708000|2.708000	0.92522|0.92522	0.655000|0.655000	0.94253|0.94253	GAT|CGA		0.473	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121216031	G	A	121216031	3	1	61	1	0	0	0	0	1	0	0	0	3677	1058	37	1	991	1	COL14A1	8	121216031	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4256	121216031	25147991	6086	14071										
COL14A1	7373	broad.mit.edu	37	chr8	121216100	121216100	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtggaagaacaggacagaGaaattaaaggtaaaatgagt	13	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121216100G>T	ENST00000297848.3	+	9	1300	c.1030G>T	c.(1030-1032)Gaa>Taa	p.E344*	COL14A1_ENST00000537875.1_Nonsense_Mutation_p.E344*|COL14A1_ENST00000247781.3_Nonsense_Mutation_p.E249*|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Nonsense_Mutation_p.E344*	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.E344*(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			ACAGGACAGAGAAATTAAAGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											78	71	73					8																	121216100		2203	4300	6503	121285281	SO:0001587	stop_gained	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1030G>T	8.37:g.121216100G>T	ENSP00000297848:p.Glu344*		121285281		Nonsense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.69|14.69	2.612086|2.612086	0.46631|0.46631	.|.	.|.	ENSG00000187955|ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	.|T	.|0.50277	.|0.75	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.242355|.	0.40818|.	N|.	0.001008|.	.|T	.|0.63546	.|0.2520	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.60954	.|-0.7160	.|5	0.07325|0.39692	T|T	0.83|0.17	.|.	18.7849|18.7849	0.91951|0.91951	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	344;344;344;249;157|100	.|ENSP00000429123:R100I	ENSP00000247781:E249X|ENSP00000429123:R100I	E|R	+|+	1|2	0|0	COL14A1|COL14A1	121285281|121285281	1.000000|1.000000	0.71417|0.71417	0.783000|0.783000	0.31826|0.31826	0.120000|0.120000	0.20174|0.20174	3.717000|3.717000	0.54911|0.54911	2.672000|2.672000	0.90937|0.90937	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.423	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121216100	G	T	121216100	4	4	61	1	0	0	0	0	0	1	0	0	3677	943	33	2	1060	2	COL14A1	8	121216100	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69	121216100	25147922	6087	14072										
COL14A1	7373	broad.mit.edu	37	chr8	121282317	121282317	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtatttatggtggatggAtcctggagcattggagatga	15	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121282317A>G	ENST00000297848.3	+	26	3387	c.3117A>G	c.(3115-3117)ggA>ggG	p.G1039G	COL14A1_ENST00000247781.3_Silent_p.G944G|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.G1039G	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.G1039G(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TGGTGGATGGATCCTGGAGCA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	8											137	124	128					8																	121282317		2203	4299	6502	121351498	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3117A>G	8.37:g.121282317A>G			121351498		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.413	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		G	121282317	A	G	121282317	2	3	61	1	0	0	0	0	0	0	0	1	3677	320	12	4		4	COL14A1	8	121282317	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	66217	121282317	25081705	6088	14073										
COL14A1	7373	broad.mit.edu	37	chr8	121290381	121290381	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagttcactgatgatcccaGaacagaatttaaactaaatg	6	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121290381G>T	ENST00000297848.3	+	27	3515	c.3245G>T	c.(3244-3246)aGa>aTa	p.R1082I	COL14A1_ENST00000247781.3_Missense_Mutation_p.R987I|COL14A1_ENST00000309791.4_Missense_Mutation_p.R1082I	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.R1082I(2)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			GATGATCCCAGAACAGAATTT	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	8											109	114	112					8																	121290381		2203	4300	6503	121359562	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3245G>T	8.37:g.121290381G>T	ENSP00000297848:p.Arg1082Ile		121359562		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375168	0.95923	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	D;D;D	0.84223	-1.82;-1.82;-1.82	5.6	5.6	0.85130	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.93012	0.7776	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93330	0.6700	10	0.72032	D	0.01	.	19.618	0.95643	0.0:0.0:1.0:0.0	.	1082	Q05707	COEA1_HUMAN	I	1082;1082;987	ENSP00000311809:R1082I;ENSP00000297848:R1082I;ENSP00000247781:R987I	ENSP00000247781:R987I	R	+	2	0	COL14A1	121359562	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.741000	0.74837	2.635000	0.89317	0.650000	0.86243	AGA		0.383	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121290381	G	T	121290381	3	4	61	1	0	0	0	0	1	0	0	0	3677	942	33	2	3347	2	COL14A1	8	121290381	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8064	121290381	25073641	6089	14074										
COL14A1	7373	broad.mit.edu	37	chr8	121295928	121295928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaatcagttttctattccGgattcttcctgacactccac	4	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121295928G>A	ENST00000297848.3	+	32	4148	c.3878G>A	c.(3877-3879)cGg>cAg	p.R1293Q	COL14A1_ENST00000247781.3_Missense_Mutation_p.R1198Q|COL14A1_ENST00000309791.4_Missense_Mutation_p.R1293Q	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.R1293Q(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			TTTCTATTCCGGATTCTTCCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											143	133	137					8																	121295928		2203	4300	6503	121365109	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3878G>A	8.37:g.121295928G>A	ENSP00000297848:p.Arg1293Gln		121365109		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	35	5.430627	0.96150	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	T;T;T	0.02258	4.37;4.37;4.37	5.45	5.45	0.79879	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.00168	-1.1963	10	0.87932	D	0	.	19.2777	0.94039	0.0:0.0:1.0:0.0	.	1293	Q05707	COEA1_HUMAN	Q	1293;1293;1198	ENSP00000311809:R1293Q;ENSP00000297848:R1293Q;ENSP00000247781:R1198Q	ENSP00000247781:R1198Q	R	+	2	0	COL14A1	121365109	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.551000	0.86045	0.462000	0.41574	CGG		0.388	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121295928	G	A	121295928	3	1	61	1	0	0	0	0	1	0	0	0	3677	1116	39	1	4000	1	COL14A1	8	121295928	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5547	121295928	25068094	6090	14075										
COL14A1	7373	broad.mit.edu	37	chr8	121327802	121327802	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaaaaggagagaaaggaGatactggccttccaggtcca	13	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121327802G>T	ENST00000297848.3	+	39	4852	c.4582G>T	c.(4582-4584)Gat>Tat	p.D1528Y	COL14A1_ENST00000247781.3_Missense_Mutation_p.D1433Y|COL14A1_ENST00000309791.4_Missense_Mutation_p.D1528Y	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.D1528Y(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			AGAGAAAGGAGATACTGGCCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	8											101	117	112					8																	121327802		2203	4300	6503	121396983	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4582G>T	8.37:g.121327802G>T	ENSP00000297848:p.Asp1528Tyr		121396983		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176102	0.78564	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	D;D;D	0.94330	-3.4;-3.4;-3.4	5.04	5.04	0.67666	.	0.203125	0.51477	D	0.000097	D	0.95265	0.8464	M	0.71581	2.175	0.80722	D	1	P	0.51240	0.943	P	0.55455	0.776	D	0.95566	0.8634	10	0.66056	D	0.02	.	16.2278	0.82311	0.0:0.0:1.0:0.0	.	1528	Q05707	COEA1_HUMAN	Y	1528;1528;1433	ENSP00000311809:D1528Y;ENSP00000297848:D1528Y;ENSP00000247781:D1433Y	ENSP00000247781:D1433Y	D	+	1	0	COL14A1	121396983	1.000000	0.71417	0.984000	0.44739	0.980000	0.70556	6.823000	0.75282	2.498000	0.84270	0.655000	0.94253	GAT		0.388	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121327802	G	T	121327802	3	4	61	1	0	0	0	0	1	0	0	0	3677	942	33	2	4732	2	COL14A1	8	121327802	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31874	121327802	25036220	6091	14076										
COL14A1	7373	broad.mit.edu	37	chr8	121357724	121357724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggccaggctcacctggaGcccctggtgaacaaggaccc	14	14	1	1	rs200266880	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121357724G>T	ENST00000297848.3	+	45	5269	c.4999G>T	c.(4999-5001)Gcc>Tcc	p.A1667S	COL14A1_ENST00000247781.3_Missense_Mutation_p.A1572S|COL14A1_ENST00000309791.4_Missense_Mutation_p.A1667S	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.A1667S(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			CTCACCTGGAGCCCCTGGTGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	8											47	48	48					8																	121357724		2203	4300	6503	121426905	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4999G>T	8.37:g.121357724G>T	ENSP00000297848:p.Ala1667Ser		121426905		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475829	0.26511	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.93547	-3.23;-3.23;-3.23;-3.24	5.75	1.83	0.25207	.	0.326839	0.36854	N	0.002365	D	0.82967	0.5152	N	0.21097	0.63	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.68465	-0.5401	10	0.08837	T	0.75	.	4.779	0.13192	0.5266:0.2715:0.2019:0.0	.	1667	Q05707	COEA1_HUMAN	S	1667;1667;1572;14	ENSP00000311809:A1667S;ENSP00000297848:A1667S;ENSP00000247781:A1572S;ENSP00000403640:A14S	ENSP00000247781:A1572S	A	+	1	0	COL14A1	121426905	0.953000	0.32496	0.999000	0.59377	0.997000	0.91878	0.835000	0.27531	0.441000	0.26529	0.555000	0.69702	GCC		0.642	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121357724	G	T	121357724	3	4	61	1	0	0	0	0	1	0	0	0	3677	971	34	2	5173	2	COL14A1	8	121357724	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29922	121357724	25006298	6092	14077										
MTBP	27085	broad.mit.edu	37	chr8	121457794	121457794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcagaacatgggccagaGgtgtcgtcgggtgagggtac	19	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121457794G>T	ENST00000305949.1	+	1	129	c.84G>T	c.(82-84)gaG>gaT	p.E28D	MRPL13_ENST00000306185.3_5'Flank	NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	28					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)		p.E28D(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			ATGGGCCAGAGGTGTCGTCGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8											80	81	81					8																	121457794		2203	4300	6503	121526975	SO:0001583	missense	27085				CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.84G>T	8.37:g.121457794G>T	ENSP00000303398:p.Glu28Asp		121526975	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590160	0.46214	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.05	2.14	0.27477	.	0.750969	0.12924	N	0.427971	T	0.25158	0.0611	N	0.19112	0.55	0.09310	N	1	B;B	0.25809	0.135;0.135	B;B	0.26416	0.069;0.069	T	0.21211	-1.0252	9	0.20046	T	0.44	-3.1456	8.2108	0.31481	0.2757:0.0:0.7243:0.0	.	28;28	Q96DY7;B4DUR5	MTBP_HUMAN;.	D	28	.	ENSP00000303398:E28D	E	+	3	2	MTBP	121526975	0.000000	0.05858	0.002000	0.10522	0.447000	0.32167	-0.300000	0.08243	0.675000	0.31264	0.448000	0.29417	GAG		0.577	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121457794	G	T	121457794	3	4	61	1	0	0	0	0	1	0	0	0	9942	991	35	2	86	2	MTBP	8	121457794	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100070	121457794	24906228	6093	14078										
MTBP	27085	broad.mit.edu	37	chr8	121530321	121530321	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcaaattaaggaatcaaGatcacagaaacacacacggg	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:121530321G>T	ENST00000305949.1	+	19	2522	c.2477G>T	c.(2476-2478)aGa>aTa	p.R826I		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	826	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)		p.R826I(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			AAGGAATCAAGATCACAGAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	78	80					8																	121530321		2203	4300	6503	121599502	SO:0001583	missense	27085				CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2477G>T	8.37:g.121530321G>T	ENSP00000303398:p.Arg826Ile		121599502	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375674	0.82682	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.79941	0.4533	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80935	-0.1160	9	0.87932	D	0	-25.7391	19.8575	0.96767	0.0:0.0:1.0:0.0	.	826	Q96DY7	MTBP_HUMAN	I	826	.	ENSP00000303398:R826I	R	+	2	0	MTBP	121599502	1.000000	0.71417	0.515000	0.27774	0.996000	0.88848	6.963000	0.76055	2.767000	0.95098	0.563000	0.77884	AGA		0.313	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121530321	G	T	121530321	3	4	61	1	0	0	0	0	1	0	0	0	9942	942	33	2	2551	2	MTBP	8	121530321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72527	121530321	24833701	6094	14079										
HAS2	3037	broad.mit.edu	37	chr8	122626880	122626880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgataatcgcttcgtaggtCatccacaagtgatgtttgtg	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:122626880C>A	ENST00000303924.4	-	4	1665	c.1128G>T	c.(1126-1128)atG>atT	p.M376I		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	376					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)	p.M376I(1)	HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	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)			CTTCGTAGGTCATCCACAAGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	8											170	148	155					8																	122626880		2203	4300	6503	122696061	SO:0001583	missense	3037			U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.1128G>T	8.37:g.122626880C>A	ENSP00000306991:p.Met376Ile		122696061	Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	37	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.224769	0.79576	.	.	ENSG00000170961	ENST00000303924	T	0.58358	0.34	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.70404	0.3220	M	0.76574	2.34	0.80722	D	1	P	0.51240	0.943	P	0.55391	0.775	T	0.71451	-0.4589	10	0.72032	D	0.01	-26.5641	20.5385	0.99246	0.0:1.0:0.0:0.0	.	376	Q92819	HAS2_HUMAN	I	376	ENSP00000306991:M376I	ENSP00000306991:M376I	M	-	3	0	HAS2	122696061	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.801000	0.85960	2.863000	0.98299	0.549000	0.68633	ATG		0.438	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		A	122626880	C	A	122626880	3	1	61	1	0	0	0	0	1	0	0	0	6983	826	29	2	534	2	HAS2	8	122626880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1096559	122626880	23737142	6095	14080										
HAS2	3037	broad.mit.edu	37	chr8	122626944	122626944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctcggaagtaggacttgCtccaacgggtctgctggttt	12	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:122626944C>T	ENST00000303924.4	-	4	1601	c.1064G>A	c.(1063-1065)aGc>aAc	p.S355N		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	355					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)	p.S355N(1)	HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	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)			GTAGGACTTGCTCCAACGGGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	8											162	140	147					8																	122626944		2203	4300	6503	122696125	SO:0001583	missense	3037			U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.1064G>A	8.37:g.122626944C>T	ENSP00000306991:p.Ser355Asn		122696125	Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	37	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076355	0.76415	.	.	ENSG00000170961	ENST00000303924	T	0.59638	0.25	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.27053	0.805	0.80722	D	1	D	0.63046	0.992	D	0.64410	0.925	T	0.59825	-0.7381	10	0.30854	T	0.27	-21.263	20.5385	0.99246	0.0:1.0:0.0:0.0	.	355	Q92819	HAS2_HUMAN	N	355	ENSP00000306991:S355N	ENSP00000306991:S355N	S	-	2	0	HAS2	122696125	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.983000	0.70540	2.863000	0.98299	0.549000	0.68633	AGC		0.448	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		T	122626944	C	T	122626944	3	4	61	1	0	0	0	0	1	0	0	0	6983	797	28	3	598	3	HAS2	8	122626944	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64	122626944	23737078	6096	14081										
WDR67	93594	broad.mit.edu	37	chr8	124153002	124153002	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaaatgattttaacagaAtcttactgaaaatcaagaag	5	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124153002A>T	ENST00000287380.1	+	18	2591	c.2501A>T	c.(2500-2502)aAt>aTt	p.N834I	TBC1D31_ENST00000521676.1_Splice_Site_p.N711I|TBC1D31_ENST00000518805.1_Splice_Site_p.N388I|TBC1D31_ENST00000522420.1_Splice_Site_p.N729I|TBC1D31_ENST00000378080.2_3'UTR|TBC1D31_ENST00000327098.5_Splice_Site_p.N803I|TBC1D31_ENST00000309336.3_Splice_Site_p.N834I	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	834						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)	p.N834I(1)									TTTTAACAGAATCTTACTGAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	8											43	46	45					8																	124153002		2202	4300	6502	124222183	SO:0001630	splice_region_variant	93594			AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2500-1A>T	8.37:g.124153002A>T			124222183	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	37	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	A	8.724	0.915032	0.17907	.	.	ENSG00000156787	ENST00000287380;ENST00000309336;ENST00000327098;ENST00000522420;ENST00000521676;ENST00000518805	D;T;T;D;D;T	0.85411	-1.98;-0.24;-0.28;-1.98;-1.98;1.0	5.76	3.28	0.37604	.	0.963671	0.08669	N	0.911161	T	0.74481	0.3722	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.27625	0.078;0.076;0.183;0.078	B;B;B;B	0.24541	0.013;0.047;0.054;0.035	T	0.66126	-0.6001	10	0.42905	T	0.14	-2.7441	6.1863	0.20500	0.7466:0.0:0.1292:0.1241	.	803;834;729;834	B7ZL19;Q96DN5-2;E7ERK7;Q96DN5	.;.;.;WDR67_HUMAN	I	834;834;803;729;711;388	ENSP00000287380:N834I;ENSP00000308358:N834I;ENSP00000312701:N803I;ENSP00000429334:N729I;ENSP00000430628:N711I;ENSP00000429494:N388I	ENSP00000287380:N834I	N	+	2	0	WDR67	124222183	1.000000	0.71417	0.340000	0.25575	0.330000	0.28571	1.731000	0.38135	0.951000	0.37770	0.482000	0.46254	AAT		0.303	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	Missense_Mutation	T	124153002	A	T	124153002	5	4	61	1	0	0	0	0	0	0	1	0	17358	115	4	5	2571	5	WDR67	8	124153002	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1526058	124153002	22211020	6097	14082										
FAM83A	84985	broad.mit.edu	37	chr8	124204060	124204060	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtcctggtcatcctgatGgatgtgttcacggatgtgga	14	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124204060G>T	ENST00000518448.1	+	3	2512	c.498G>T	c.(496-498)atG>atT	p.M166I	FAM83A_ENST00000546351.1_Intron|FAM83A_ENST00000276699.6_Missense_Mutation_p.M166I|FAM83A_ENST00000318462.6_Missense_Mutation_p.M166I|FAM83A_ENST00000536633.1_Missense_Mutation_p.M166I|FAM83A_ENST00000522648.1_Intron			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	166								p.M166I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TCATCCTGATGGATGTGTTCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	8											210	191	198					8																	124204060		2203	4300	6503	124273241	SO:0001583	missense	84985			BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.498G>T	8.37:g.124204060G>T	ENSP00000428876:p.Met166Ile		124273241	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	.	.	.	.	.	.	.	.	.	.	G	33	5.257459	0.95368	.	.	ENSG00000147689	ENST00000518448;ENST00000536633;ENST00000318462;ENST00000276699	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.51873	0.1700	M	0.89414	3.03	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.994;0.996	T	0.58945	-0.7546	10	0.72032	D	0.01	-44.7437	19.7629	0.96329	0.0:0.0:1.0:0.0	.	166;166	Q86UY5-3;Q86UY5	.;FA83A_HUMAN	I	166	ENSP00000428876:M166I;ENSP00000445218:M166I;ENSP00000323034:M166I;ENSP00000276699:M166I	ENSP00000276699:M166I	M	+	3	0	FAM83A	124273241	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.149000	0.94659	2.666000	0.90696	0.561000	0.74099	ATG		0.557	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899		T	124204060	G	T	124204060	3	4	61	1	0	0	0	0	1	0	0	0	5652	1348	47	2	504	2	FAM83A	8	124204060	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51058	124204060	22159962	6098	14083										
ZHX1	11244	broad.mit.edu	37	chr8	124267657	124267657	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgataggagttttactgataGatattcccgaagaagaaact	9	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124267657G>T	ENST00000522655.1	-	3	1070	c.530C>A	c.(529-531)tCt>tAt	p.S177Y	ZHX1_ENST00000297857.2_Missense_Mutation_p.S177Y|ZHX1_ENST00000395571.3_Missense_Mutation_p.S177Y|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	177					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S177Y(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTACTGATAGATATTCCCGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	8											99	102	101					8																	124267657		2203	4299	6502	124336838	SO:0001583	missense	11244			AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.530C>A	8.37:g.124267657G>T	ENSP00000428821:p.Ser177Tyr		124336838	Q8IWD8	Missense_Mutation	SNP	ENST00000522655.1	37	CCDS6342.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938488	0.73557	.	.	ENSG00000165156	ENST00000297857;ENST00000395571;ENST00000522655	T;T;T	0.52295	0.67;0.67;0.67	5.66	5.66	0.87406	.	0.202573	0.42821	D	0.000644	T	0.58581	0.2132	.	.	.	0.80722	D	1	P	0.52061	0.95	P	0.49752	0.621	T	0.60870	-0.7177	9	0.59425	D	0.04	-3.8755	19.7433	0.96241	0.0:0.0:1.0:0.0	.	177	Q9UKY1	ZHX1_HUMAN	Y	177	ENSP00000297857:S177Y;ENSP00000378938:S177Y;ENSP00000428821:S177Y	ENSP00000297857:S177Y	S	-	2	0	ZHX1	124336838	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.434000	0.97515	2.662000	0.90505	0.555000	0.69702	TCT		0.338	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			T	124267657	G	T	124267657	3	4	61	1	0	0	0	0	1	0	0	0	17714	942	33	2	2095	2	ZHX1	8	124267657	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63597	124267657	22096365	6099	14084										
ATAD2	29028	broad.mit.edu	37	chr8	124348640	124348640	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctctatctggattgtattCtaaggcattactacagatta	6	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124348640C>A	ENST00000287394.5	-	22	3291	c.3184G>T	c.(3184-3186)Gaa>Taa	p.E1062*	ATAD2_ENST00000521903.1_Nonsense_Mutation_p.E380*	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1062	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E1062*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			GGATTGTATTCTAAGGCATTA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											83	80	81					8																	124348640		2203	4299	6502	124417821	SO:0001587	stop_gained	29028			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.3184G>T	8.37:g.124348640C>A	ENSP00000287394:p.Glu1062*		124417821	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Nonsense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	C	41	8.601564	0.98881	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	.	.	.	5.89	5.89	0.94794	.	0.136177	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-26.8847	20.2576	0.98430	0.0:1.0:0.0:0.0	.	.	.	.	X	1062;380	.	ENSP00000287394:E1062X	E	-	1	0	ATAD2	124417821	1.000000	0.71417	1.000000	0.80357	0.590000	0.36582	5.762000	0.68809	2.783000	0.95769	0.655000	0.94253	GAA		0.378	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124348640	C	A	124348640	4	1	61	1	0	0	0	0	0	1	0	0	1072	922	32	2	1016	2	ATAD2	8	124348640	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80983	124348640	22015382	6100	14085										
ATAD2	29028	broad.mit.edu	37	chr8	124349986	124349986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttcttgttcttctagtCgtttcacttcttctgctgtc	5	12	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124349986C>T	ENST00000287394.5	-	21	3037	c.2930G>A	c.(2929-2931)cGa>cAa	p.R977Q	ATAD2_ENST00000521903.1_Missense_Mutation_p.R295Q	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	977					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R977Q(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TTCTTCTAGTCGTTTCACTTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											218	199	205					8																	124349986		2203	4300	6503	124419167	SO:0001583	missense	29028			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.2930G>A	8.37:g.124349986C>T	ENSP00000287394:p.Arg977Gln		124419167	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088604	0.36855	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;D	0.82619	-1.63;-1.63	5.58	1.8	0.24995	Bromodomain (1);	0.625902	0.15622	N	0.252836	T	0.69815	0.3153	L	0.34521	1.04	0.09310	N	0.999997	B	0.25850	0.136	B	0.14023	0.01	T	0.49969	-0.8882	10	0.13470	T	0.59	-0.3591	10.0423	0.42166	0.0:0.5307:0.0:0.4693	.	977	Q6PL18	ATAD2_HUMAN	Q	977;295	ENSP00000287394:R977Q;ENSP00000429213:R295Q	ENSP00000287394:R977Q	R	-	2	0	ATAD2	124419167	0.002000	0.14202	0.028000	0.17463	0.980000	0.70556	0.353000	0.20130	0.114000	0.18032	0.650000	0.86243	CGA		0.408	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124349986	C	T	124349986	3	4	61	1	0	0	0	0	1	0	0	0	1072	884	31	1	1274	1	ATAD2	8	124349986	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1346	124349986	22014036	6101	14086										
ATAD2	29028	broad.mit.edu	37	chr8	124357187	124357187	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaaaactggagcaaatgaAggaatattctgtaataatgt	9	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124357187A>T	ENST00000287394.5	-	19	2762	c.2655T>A	c.(2653-2655)ccT>ccA	p.P885P	RNU6-875P_ENST00000516488.1_RNA|ATAD2_ENST00000521903.1_Silent_p.P203P	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	885					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.P885P(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			GAGCAAATGAAGGAATATTCT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	8											164	152	156					8																	124357187		2203	4300	6503	124426368	SO:0001819	synonymous_variant	29028			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.2655T>A	8.37:g.124357187A>T			124426368	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																				0.403	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124357187	A	T	124357187	2	4	61	1	0	0	0	0	0	0	0	1	1072	59	3	5		5	ATAD2	8	124357187	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7201	124357187	22006835	6102	14087										
FBXO32	114907	broad.mit.edu	37	chr8	124516969	124516969	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgccctttgtctgacaGaattaatcgtttgcggatct	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124516969G>T	ENST00000517956.1	-	8	1044	c.853C>A	c.(853-855)Ctg>Atg	p.L285M	FBXO32_ENST00000443022.2_Missense_Mutation_p.L192M	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	285					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)		p.L285M(1)		autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TTGTCTGACAGAATTAATCGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											106	93	98					8																	124516969		2203	4300	6503	124586150	SO:0001583	missense	114907			AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"F-boxes /  "other""	16731	protein-coding gene	gene with protein product		606604	"F-box only protein 32"			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.853C>A	8.37:g.124516969G>T	ENSP00000428205:p.Leu285Met		124586150	A4KYM0	Missense_Mutation	SNP	ENST00000517956.1	37	CCDS6345.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.815455	0.50527	.	.	ENSG00000156804	ENST00000517956;ENST00000443022	T;T	0.24538	1.85;1.85	5.18	-1.95	0.07548	F-box domain, Skp2-like (1);	0.125441	0.53938	D	0.000046	T	0.27278	0.0669	L	0.36672	1.1	0.41857	D	0.9902	D;P	0.65815	0.995;0.845	D;P	0.66847	0.947;0.73	T	0.21690	-1.0238	10	0.33940	T	0.23	0.2683	2.9992	0.06008	0.4252:0.1137:0.3504:0.1107	.	192;285	A4KYM0;Q969P5	.;FBX32_HUMAN	M	285;192	ENSP00000428205:L285M;ENSP00000390790:L192M	ENSP00000390790:L192M	L	-	1	2	FBXO32	124586150	0.958000	0.32768	0.978000	0.43139	0.984000	0.73092	0.491000	0.22419	-0.490000	0.06707	-0.367000	0.07326	CTG		0.403	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1			T	124516969	G	T	124516969	3	4	61	1	0	0	0	0	1	0	0	0	5761	933	33	2	222	2	FBXO32	8	124516969	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159782	124516969	21847053	6103	14088										
KLHL38	340359	broad.mit.edu	37	chr8	124664387	124664387	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggtggtgccacacaaagaGaacatctgtctcttggcggt	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124664387G>T	ENST00000325995.7	-	1	803	c.780C>A	c.(778-780)ttC>ttA	p.F260L	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	260								p.F260L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CACACAAAGAGAACATCTGTC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	8											74	77	76					8																	124664387		2084	4214	6298	124733568	SO:0001583	missense	340359				CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.780C>A	8.37:g.124664387G>T	ENSP00000321475:p.Phe260Leu		124733568	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	G	8.897	0.955341	0.18507	.	.	ENSG00000175946	ENST00000325995	T	0.70869	-0.52	5.69	-0.165	0.13355	.	0.049614	0.85682	D	0.000000	T	0.60869	0.2302	M	0.75447	2.3	0.43360	D	0.995439	B	0.09022	0.002	B	0.06405	0.002	T	0.54125	-0.8340	10	0.02654	T	1	.	10.3086	0.43695	0.4769:0.0:0.5231:0.0	.	260	Q2WGJ6	KLH38_HUMAN	L	260	ENSP00000321475:F260L	ENSP00000321475:F260L	F	-	3	2	KLHL38	124733568	0.329000	0.24696	0.885000	0.34714	0.323000	0.28346	-0.201000	0.09464	-0.027000	0.13873	0.561000	0.74099	TTC		0.542	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			T	124664387	G	T	124664387	3	4	61	1	0	0	0	0	1	0	0	0	8411	933	33	2	977	2	KLHL38	8	124664387	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147418	124664387	21699635	6104	14089										
KLHL38	340359	broad.mit.edu	37	chr8	124664615	124664615	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagagcccatcatctccGagatagtccctcaactccaa	5	17	3	2	rs116917652		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124664615G>A	ENST00000325995.7	-	1	575	c.552C>T	c.(550-552)ctC>ctT	p.L184L	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	184	BACK.							p.L184L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CATCATCTCCGAGATAGTCCC	0.577													G|||	1	0.000199681	0	0	5008	,	,		20754	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											59	60	59					8																	124664615		2011	4169	6180	124733796	SO:0001819	synonymous_variant	340359				CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.552C>T	8.37:g.124664615G>A			124733796	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																				0.577	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			A	124664615	G	A	124664615	2	1	61	1	0	0	0	0	0	0	0	1	8411	1045	37	1		1	KLHL38	8	124664615	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	228	124664615	21699407	6105	14090										
FAM91A1	157769	broad.mit.edu	37	chr8	124786341	124786341	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttggaaattcacagagaGaatatgaaaagcaggttgtc	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124786341G>T	ENST00000334705.7	+	2	340	c.94G>T	c.(94-96)Gaa>Taa	p.E32*	FAM91A1_ENST00000521166.1_Nonsense_Mutation_p.E32*	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	32								p.E32*(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TTCACAGAGAGAATATGAAAA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											151	153	153					8																	124786341		1814	4077	5891	124855522	SO:0001587	stop_gained	157769			AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.94G>T	8.37:g.124786341G>T	ENSP00000335082:p.Glu32*		124855522	B6YY23|Q658T5|Q8TE89	Nonsense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	G	37	6.336463	0.97485	.	.	ENSG00000176853	ENST00000521166;ENST00000334705;ENST00000395537	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.6963	0.96028	0.0:0.0:1.0:0.0	.	.	.	.	X	32	.	ENSP00000335082:E32X	E	+	1	0	FAM91A1	124855522	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.109000	0.94291	2.659000	0.90383	0.591000	0.81541	GAA		0.338	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		T	124786341	G	T	124786341	4	4	61	1	0	0	0	0	0	1	0	0	5670	943	33	2	100	2	FAM91A1	8	124786341	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121726	124786341	21577681	6106	14091										
FAM91A1	157769	broad.mit.edu	37	chr8	124801946	124801946	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcgtcataacaaagatCtagttgcgcaaactgcacag	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124801946C>A	ENST00000334705.7	+	15	1618	c.1372C>A	c.(1372-1374)Cta>Ata	p.L458I	FAM91A1_ENST00000521166.1_Missense_Mutation_p.L458I	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	458								p.L458I(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TAACAAAGATCTAGTTGCGCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	8											95	84	87					8																	124801946		1885	4107	5992	124871127	SO:0001583	missense	157769			AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.1372C>A	8.37:g.124801946C>A	ENSP00000335082:p.Leu458Ile		124871127	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	C	15.26	2.779375	0.49891	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	T;T	0.34667	1.35;1.35	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.31136	0.0787	L	0.41236	1.265	0.58432	D	0.999997	B;B	0.31318	0.319;0.319	B;B	0.30105	0.111;0.111	T	0.08330	-1.0727	10	0.44086	T	0.13	.	14.3615	0.66773	0.0:0.9259:0.0:0.0741	.	458;458	E7ER68;Q658Y4	.;F91A1_HUMAN	I	458	ENSP00000429491:L458I;ENSP00000335082:L458I	ENSP00000335082:L458I	L	+	1	2	FAM91A1	124871127	0.966000	0.33281	0.991000	0.47740	0.716000	0.41182	2.260000	0.43267	2.577000	0.86979	0.557000	0.71058	CTA		0.353	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		A	124801946	C	A	124801946	3	1	61	1	0	0	0	0	1	0	0	0	5670	912	32	2	1430	2	FAM91A1	8	124801946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15605	124801946	21562076	6107	14092										
FER1L6	654463	broad.mit.edu	37	chr8	124989831	124989831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgaagaaaatctccaacGaacaggatggagacaaaggt	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:124989831G>A	ENST00000522917.1	+	10	1251	c.1045G>A	c.(1045-1047)Gaa>Aaa	p.E349K	FER1L6_ENST00000399018.1_Missense_Mutation_p.E349K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	349						integral component of membrane (GO:0016021)		p.E349K(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AATCTCCAACGAACAGGATGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											87	85	86					8																	124989831		1934	4138	6072	125059012	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1045G>A	8.37:g.124989831G>A	ENSP00000428280:p.Glu349Lys		125059012		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724888	0.89298	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.09255	3.0;3.0	5.53	5.53	0.82687	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000001	T	0.29190	0.0726	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.01182	-1.1426	10	0.19147	T	0.46	.	19.4728	0.94969	0.0:0.0:1.0:0.0	.	349	Q2WGJ9	FR1L6_HUMAN	K	349	ENSP00000428280:E349K;ENSP00000381982:E349K	ENSP00000381982:E349K	E	+	1	0	FER1L6	125059012	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.543000	0.90651	2.608000	0.88229	0.561000	0.74099	GAA		0.468	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	124989831	G	A	124989831	3	1	61	1	0	0	0	0	1	0	0	0	5834	1059	37	1	1079	1	FER1L6	8	124989831	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187885	124989831	21374191	6108	14093										
FER1L6	654463	broad.mit.edu	37	chr8	125033834	125033834	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatcattcagcagcagaaGaaaaagttatctgttgatga	11	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125033834G>T	ENST00000522917.1	+	17	2264	c.2058G>T	c.(2056-2058)aaG>aaT	p.K686N	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.K686N	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	686						integral component of membrane (GO:0016021)		p.K686N(1)|p.K686K(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGCAGCAGAAGAAAAAGTTAT	0.433																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	upper_aerodigestive_tract(1)|large_intestine(1)	8											124	122	122					8																	125033834		1952	4151	6103	125103015	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2058G>T	8.37:g.125033834G>T	ENSP00000428280:p.Lys686Asn		125103015		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.870963	0.51695	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.81415	-1.49;-1.49	5.77	5.77	0.91146	.	0.149392	0.42420	U	0.000707	T	0.75481	0.3855	M	0.63428	1.95	0.44142	D	0.996938	P	0.39576	0.679	B	0.37091	0.241	T	0.71777	-0.4490	10	0.17832	T	0.49	.	12.1325	0.53950	0.0793:0.0:0.9207:0.0	.	686	Q2WGJ9	FR1L6_HUMAN	N	686	ENSP00000428280:K686N;ENSP00000381982:K686N	ENSP00000381982:K686N	K	+	3	2	FER1L6	125103015	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.187000	0.50950	2.727000	0.93392	0.591000	0.81541	AAG		0.433	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125033834	G	T	125033834	3	4	61	1	0	0	0	0	1	0	0	0	5834	933	33	2	2120	2	FER1L6	8	125033834	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44003	125033834	21330188	6109	14094										
FER1L6	654463	broad.mit.edu	37	chr8	125072830	125072830	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgaagaaggtgcagctCctctctgtggatcggcctca	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125072830C>T	ENST00000522917.1	+	24	3233	c.3027C>T	c.(3025-3027)ctC>ctT	p.L1009L	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Silent_p.L1009L	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1009						integral component of membrane (GO:0016021)		p.L1009L(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGGTGCAGCTCCTCTCTGTGG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	8											153	130	138					8																	125072830		2203	4300	6503	125142011	SO:0001819	synonymous_variant	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3027C>T	8.37:g.125072830C>T			125142011		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																				0.562	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125072830	C	T	125072830	2	4	61	1	0	0	0	0	0	0	0	1	5834	842	30	3		3	FER1L6	8	125072830	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38996	125072830	21291192	6110	14095										
FER1L6	654463	broad.mit.edu	37	chr8	125072945	125072945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatccaggcagacgctttcGaagtggtgcgagcttctcac	12	12	1	1	rs200333104		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125072945G>A	ENST00000522917.1	+	24	3348	c.3142G>A	c.(3142-3144)Gaa>Aaa	p.E1048K	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.E1048K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1048	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)		p.E1048K(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGACGCTTTCGAAGTGGTGCG	0.517													G|||	1	0.000199681	0	0	5008	,	,		18406	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											110	106	107					8																	125072945		2203	4300	6503	125142126	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3142G>A	8.37:g.125072945G>A	ENSP00000428280:p.Glu1048Lys		125142126		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.8	4.572111	0.86542	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.81821	-1.54;-1.54	6.06	6.06	0.98353	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.117978	0.56097	U	0.000028	D	0.83852	0.5344	L	0.42245	1.32	0.80722	D	1	D	0.62365	0.991	P	0.55055	0.767	T	0.80984	-0.1138	10	0.34782	T	0.22	-13.0665	20.2159	0.98296	0.0:0.0:1.0:0.0	.	1048	Q2WGJ9	FR1L6_HUMAN	K	1048	ENSP00000428280:E1048K;ENSP00000381982:E1048K	ENSP00000381982:E1048K	E	+	1	0	FER1L6	125142126	1.000000	0.71417	0.946000	0.38457	0.135000	0.20990	9.779000	0.99018	2.882000	0.98803	0.655000	0.94253	GAA		0.517	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125072945	G	A	125072945	3	1	61	1	0	0	0	0	1	0	0	0	5834	1059	37	1	3232	1	FER1L6	8	125072945	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115	125072945	21291077	6111	14096										
TMEM65	157378	broad.mit.edu	37	chr8	125332344	125332344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaaatgtgtactaagacGtgtttgccacatgtcaactt	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125332344G>A	ENST00000297632.6	-	6	1138	c.604C>T	c.(604-606)Cgt>Tgt	p.R202C		NM_194291.2	NP_919267.2	Q6PI78	TMM65_HUMAN	transmembrane protein 65	202						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.R202C(2)		cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	6	Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GTACTAAGACGTGTTTGCCAC	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	8											155	139	144					8																	125332344		2203	4300	6503	125401525	SO:0001583	missense	157378			BC032396	CCDS6348.1	8q24.13	2006-11-24			ENSG00000164983	ENSG00000164983			25203	protein-coding gene	gene with protein product						12477932	Standard	NM_194291		Approved		uc010mdl.3	Q6PI78	OTTHUMG00000165021	ENST00000297632.6:c.604C>T	8.37:g.125332344G>A	ENSP00000297632:p.Arg202Cys		125401525	Q8N5G8|Q8WVK5	Missense_Mutation	SNP	ENST00000297632.6	37	CCDS6348.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.193880	0.78902	.	.	ENSG00000164983	ENST00000297632	T	0.54479	0.57	5.74	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.57946	0.2088	M	0.89214	3.015	0.80722	D	1	P	0.38642	0.641	B	0.33521	0.165	T	0.66783	-0.5836	10	0.72032	D	0.01	.	13.2249	0.59909	0.0737:0.0:0.9263:0.0	.	202	Q6PI78	TMM65_HUMAN	C	202	ENSP00000297632:R202C	ENSP00000297632:R202C	R	-	1	0	TMEM65	125401525	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.650000	0.61440	1.421000	0.47157	0.655000	0.94253	CGT		0.418	TMEM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381464.1	NM_194291		A	125332344	G	A	125332344	3	1	61	1	0	0	0	0	1	0	0	0	16233	1145	40	1	126	1	TMEM65	8	125332344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259399	125332344	21031678	6112	14097										
RNF139	83940	broad.mit.edu	37	chr8	125499053	125499053	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgtgtcatcttttcgtaGacattttcctgtgctgtttg	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125499053G>T	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Missense_Mutation_p.R388I	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.R388I(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TCTTTTCGTAGACATTTTCCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	8											395	379	384					8																	125499053		2203	4300	6503	125568234	SO:0001628	intergenic_variant	11236			AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125499053G>T			125568234	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545912	0.65198	.	.	ENSG00000170881	ENST00000303545	T	0.26957	1.7	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.54743	0.1877	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55879	-0.8071	10	0.51188	T	0.08	-9.9035	19.2104	0.93751	0.0:0.0:1.0:0.0	.	388	Q8WU17	RN139_HUMAN	I	388	ENSP00000304051:R388I	ENSP00000304051:R388I	R	+	2	0	RNF139	125568234	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	9.071000	0.93980	2.590000	0.87494	0.655000	0.94253	AGA		0.393	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		T	125499053	G	T	125499053	1	4	61	0	1	0	0	0	0	0	0	0	13479	942	33	2		2	RNF139	8	125499053	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166709	125499053	20864969	6113	14098										
RNF139	83940	broad.mit.edu	37	chr8	125499824	125499824	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgatgttcaaagagaaaGaaatggagtgattcagcaca	11	4	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:125499824G>T	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Missense_Mutation_p.R645I	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.R645I(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CAAAGAGAAAGAAATGGAGTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	75	76					8																	125499824		2203	4299	6502	125569005	SO:0001628	intergenic_variant	11236			AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125499824G>T			125569005	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.831274	0.32329	.	.	ENSG00000170881	ENST00000303545	T	0.25085	1.82	5.11	5.11	0.69529	.	0.232450	0.33199	N	0.005167	T	0.30039	0.0752	N	0.08118	0	0.47153	D	0.999334	D	0.61697	0.99	D	0.66497	0.944	T	0.23226	-1.0194	10	0.48119	T	0.1	-9.6937	16.421	0.83758	0.0:0.0:1.0:0.0	.	645	Q8WU17	RN139_HUMAN	I	645	ENSP00000304051:R645I	ENSP00000304051:R645I	R	+	2	0	RNF139	125569005	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.249000	0.43169	2.816000	0.96949	0.561000	0.74099	AGA		0.383	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		T	125499824	G	T	125499824	1	4	61	0	1	0	0	0	0	0	0	0	13479	942	33	2		2	RNF139	8	125499824	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	771	125499824	20864198	6114	14099										
TRIB1	10221	broad.mit.edu	37	chr8	126448662	126448662	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaataggaacttcagaccaGattgttccagagtaccagga	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:126448662G>T	ENST00000519576.1	+	2	638	c.375G>T	c.(373-375)caG>caT	p.Q125H	TRIB1_ENST00000311922.3_Missense_Mutation_p.Q356H|TRIB1_ENST00000520847.1_Missense_Mutation_p.Q190H					tribbles pseudokinase 1									p.Q356H(2)		NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			CTTCAGACCAGATTGTTCCAG	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	8											83	85	85					8																	126448662		2203	4300	6503	126517844	SO:0001583	missense	10221			AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"tribbles homolog 1 (Drosophila)"			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000519576.1:c.375G>T	8.37:g.126448662G>T	ENSP00000428879:p.Gln125His		126517844		Missense_Mutation	SNP	ENST00000519576.1	37		.	.	.	.	.	.	.	.	.	.	G	19.07	3.756447	0.69648	.	.	ENSG00000173334	ENST00000311922;ENST00000520847;ENST00000519576	T;T;T	0.48522	0.81;0.83;1.09	5.88	5.88	0.94601	.	0.000000	0.31809	U	0.007024	T	0.58637	0.2136	L	0.36672	1.1	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	T	0.59064	-0.7524	10	0.66056	D	0.02	-21.5236	13.115	0.59295	0.0736:0.0:0.9264:0.0	.	356	Q96RU8	TRIB1_HUMAN	H	356;190;125	ENSP00000312150:Q356H;ENSP00000429063:Q190H;ENSP00000428879:Q125H	ENSP00000312150:Q356H	Q	+	3	2	TRIB1	126517844	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	1.789000	0.38724	2.797000	0.96272	0.561000	0.74099	CAG		0.493	TRIB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000381433.1	NM_025195		T	126448662	G	T	126448662	3	4	61	1	0	0	0	0	1	0	0	0	16522	933	33	2	1078	2	TRIB1	8	126448662	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	948838	126448662	19915360	6115	14100										
GSDMC	56169	broad.mit.edu	37	chr8	130772805	130772805	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaccatcttgaaaggttCtctgttcatcatcatctgag	6	11	7	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:130772805C>A	ENST00000276708.4	-	6	1588	c.707G>T	c.(706-708)aGa>aTa	p.R236I		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	236						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)		p.R236I(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TTGAAAGGTTCTCTGTTCATC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	8											104	101	102					8																	130772805		2203	4300	6503	130841987	SO:0001583	missense	56169			AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"melanoma-derived leucine zipper, extra-nuclear factor"	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.707G>T	8.37:g.130772805C>A	ENSP00000276708:p.Arg236Ile		130841987	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	.	.	.	.	.	.	.	.	.	.	C	8.212	0.800629	0.16397	.	.	ENSG00000147697	ENST00000276708	T	0.25749	1.78	3.69	-1.92	0.07618	.	4.434490	0.00728	N	0.000935	T	0.16727	0.0402	L	0.32530	0.975	0.09310	N	1	B	0.24533	0.105	B	0.19148	0.024	T	0.11446	-1.0587	10	0.37606	T	0.19	.	0.3993	0.00423	0.1818:0.2305:0.1869:0.4008	.	236	Q9BYG8	GSDMC_HUMAN	I	236	ENSP00000276708:R236I	ENSP00000276708:R236I	R	-	2	0	GSDMC	130841987	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.290000	0.08354	-0.320000	0.08640	-0.482000	0.04802	AGA		0.373	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			A	130772805	C	A	130772805	3	1	61	1	0	0	0	0	1	0	0	0	6839	913	32	2	855	2	GSDMC	8	130772805	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4324143	130772805	15591217	6116	14101										
FAM49B	51571	broad.mit.edu	37	chr8	130867925	130867925	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagcaagagcctgctctcGctctagatgctgggtgggag	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:130867925G>A	ENST00000519824.2	-	6	643	c.370C>T	c.(370-372)Cga>Tga	p.R124*	FAM49B_ENST00000401979.2_Nonsense_Mutation_p.R124*|FAM49B_ENST00000519540.1_Nonsense_Mutation_p.R124*|FAM49B_ENST00000517654.1_Nonsense_Mutation_p.R124*|FAM49B_ENST00000523509.1_Nonsense_Mutation_p.R124*|FAM49B_ENST00000522746.1_Nonsense_Mutation_p.R124*|FAM49B_ENST00000518879.1_5'UTR|FAM49B_ENST00000519110.1_Nonsense_Mutation_p.R124*|FAM49B_ENST00000522250.1_5'UTR|FAM49B_ENST00000522941.1_5'UTR	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	124						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)		p.R124*(1)		kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			GCCTGCTCTCGCTCTAGATGC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											86	89	88					8																	130867925		2203	4300	6503	130937107	SO:0001587	stop_gained	51571			AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.370C>T	8.37:g.130867925G>A	ENSP00000429150:p.Arg124*		130937107	Q96AZ5|Q9NW21|Q9NZE7	Nonsense_Mutation	SNP	ENST00000519824.2	37	CCDS6361.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.334678|6.334678	0.97485|0.97485	.|.	.|.	ENSG00000153310|ENSG00000153310	ENST00000311292|ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142	.|.	.|.	.|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.55561|.	0.1928|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41215|.	-0.9521|.	5|.	0.21014|0.07990	T|T	0.42|0.79	-3.992|-3.992	19.848|19.848	0.96722|0.96722	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	78|124	.|.	ENSP00000311651:A78V|ENSP00000384880:R124X	A|R	-|-	2|1	0|2	FAM49B|FAM49B	130937107|130937107	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.004000|8.004000	0.88535|0.88535	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCG|CGA		0.398	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623		A	130867925	G	A	130867925	4	1	61	1	0	0	0	0	0	1	0	0	5595	1095	38	1	632	1	FAM49B	8	130867925	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95120	130867925	15496097	6117	14102										
ASAP1	50807	broad.mit.edu	37	chr8	131104311	131104311	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccgggtggtgggggaggaGgcctcttcttggatagggtg	21	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:131104311G>T	ENST00000518721.1	-	25	2707	c.2480C>A	c.(2479-2481)cCt>cAt	p.P827H	ASAP1_ENST00000357668.1_Missense_Mutation_p.P827H	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	827	Pro-rich.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.P827H(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TGGGGGAGGAGGCCTCTTCTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	84	83					8																	131104311		2203	4300	6503	131173493	SO:0001583	missense	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2480C>A	8.37:g.131104311G>T	ENSP00000429900:p.Pro827His		131173493	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658349	0.88154	.	.	ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721	T;T	0.07021	3.23;3.23	5.3	5.3	0.74995	.	0.563007	0.19187	N	0.120526	T	0.22742	0.0549	L	0.50333	1.59	0.80722	D	1	D;D;D	0.65815	0.992;0.992;0.995	P;P;P	0.60415	0.751;0.751;0.874	T	0.00138	-1.2003	10	0.87932	D	0	.	18.3059	0.90180	0.0:0.0:1.0:0.0	.	827;827;830	B2RNV3;Q9ULH1;Q9ULH1-2	.;ASAP1_HUMAN;.	H	830;827;827	ENSP00000350297:P827H;ENSP00000429900:P827H	ENSP00000344591:P830H	P	-	2	0	ASAP1	131173493	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.722000	0.91452	2.639000	0.89480	0.455000	0.32223	CCT		0.572	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		T	131104311	G	T	131104311	3	4	61	1	0	0	0	0	1	0	0	0	1011	1000	35	2	933	2	ASAP1	8	131104311	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236386	131104311	15259711	6118	14103										
ASAP1	50807	broad.mit.edu	37	chr8	131124416	131124416	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtctgtgcttgtggaaacGaagatctggttggtgaaggc	16	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:131124416G>A	ENST00000518721.1	-	24	2552	c.2325C>T	c.(2323-2325)ttC>ttT	p.F775F	ASAP1_ENST00000357668.1_Silent_p.F775F	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	775					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.F775F(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TTGTGGAAACGAAGATCTGGT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	8											188	170	176					8																	131124416		2203	4300	6503	131193598	SO:0001819	synonymous_variant	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2325C>T	8.37:g.131124416G>A			131193598	B2RNV3	Silent	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	G	9.206	1.029636	0.19512	.	.	ENSG00000153317	ENST00000524124;ENST00000519483	.	.	.	5.82	-2.45	0.06481	.	.	.	.	.	T	0.57725	0.2073	.	.	.	0.47245	D	0.999366	.	.	.	.	.	.	T	0.56195	-0.8019	4	.	.	.	.	11.8286	0.52282	0.6398:0.0:0.3602:0.0	.	.	.	.	C	596;189	.	.	R	-	1	0	ASAP1	131193598	0.942000	0.31987	0.026000	0.17262	0.998000	0.95712	0.162000	0.16501	-0.386000	0.07821	0.655000	0.94253	CGT		0.587	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		A	131124416	G	A	131124416	2	1	61	1	0	0	0	0	0	0	0	1	1011	1049	37	1		1	ASAP1	8	131124416	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20105	131124416	15239606	6119	14104										
ASAP1	50807	broad.mit.edu	37	chr8	131226912	131226912	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attactcccaaacttatcaaGaacttgtgcatagttttctt	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:131226912G>T	ENST00000518721.1	-	5	522	c.295C>A	c.(295-297)Ctt>Att	p.L99I	ASAP1_ENST00000357668.1_Missense_Mutation_p.L99I	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	99					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.L99I(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						AACTTATCAAGAACTTGTGCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	8											70	73	72					8																	131226912		2203	4300	6503	131296094	SO:0001583	missense	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.295C>A	8.37:g.131226912G>T	ENSP00000429900:p.Leu99Ile		131296094	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997427	0.74818	.	.	ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721;ENST00000524367;ENST00000521426	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	5.28	5.28	0.74379	IRSp53/MIM homology domain (IMD) (1);	0.146541	0.46758	D	0.000277	T	0.15176	0.0366	L	0.52206	1.635	0.80722	D	1	D;D	0.53151	0.958;0.958	B;B	0.42386	0.386;0.386	T	0.00605	-1.1648	10	0.59425	D	0.04	.	11.7076	0.51605	0.0809:0.0:0.9191:0.0	.	99;99	B2RNV3;Q9ULH1	.;ASAP1_HUMAN	I	99;99;99;69;92	ENSP00000350297:L99I;ENSP00000429900:L99I;ENSP00000430588:L69I;ENSP00000430917:L92I	ENSP00000344591:L99I	L	-	1	0	ASAP1	131296094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.323000	0.65858	2.637000	0.89404	0.585000	0.79938	CTT		0.363	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		T	131226912	G	T	131226912	3	4	61	1	0	0	0	0	1	0	0	0	1011	942	33	2	3198	2	ASAP1	8	131226912	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102496	131226912	15137110	6120	14105										
ADCY8	114	broad.mit.edu	37	chr8	131792792	131792792	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgcctattgagggactgGacaagtcccaggacaaccgc	11	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:131792792G>A	ENST00000286355.5	-	18	5692	c.3600C>T	c.(3598-3600)gtC>gtT	p.V1200V	ADCY8_ENST00000377928.3_Silent_p.V1069V	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1200					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.V1200V(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TGAGGGACTGGACAAGTCCCA	0.527										HNSCC(32;0.087)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											160	152	155					8																	131792792		2203	4300	6503	131861974	SO:0001819	synonymous_variant	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3600C>T	8.37:g.131792792G>A			131861974		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																				0.527	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131792792	G	A	131792792	2	1	61	1	0	0	0	0	0	0	0	1	300	1161	41	3		3	ADCY8	8	131792792	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	565880	131792792	14571230	6121	14106										
ADCY8	114	broad.mit.edu	37	chr8	131921959	131921959	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgctttatcttacccaggGattcctccagattcgagttt	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:131921959G>A	ENST00000286355.5	-	6	3727	c.1635C>T	c.(1633-1635)atC>atT	p.I545I	ADCY8_ENST00000377928.3_Silent_p.I545I	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	545					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.I545I(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CTTACCCAGGGATTCCTCCAG	0.463										HNSCC(32;0.087)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											233	209	217					8																	131921959		2203	4300	6503	131991141	SO:0001819	synonymous_variant	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1635C>T	8.37:g.131921959G>A			131991141		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																				0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131921959	G	A	131921959	2	1	61	1	0	0	0	0	0	0	0	1	300	1164	41	3		3	ADCY8	8	131921959	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129167	131921959	14442063	6122	14107										
ADCY8	114	broad.mit.edu	37	chr8	132051899	132051899	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgaccaccaccagggcGcagatcactacctcaatgcc	7	17	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:132051899G>A	ENST00000286355.5	-	1	2773	c.681C>T	c.(679-681)tgC>tgT	p.C227C	ADCY8_ENST00000377928.3_Silent_p.C227C	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	227					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.C227C(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CCACCAGGGCGCAGATCACTA	0.627										HNSCC(32;0.087)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											61	58	59					8																	132051899		2203	4300	6503	132121081	SO:0001819	synonymous_variant	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.681C>T	8.37:g.132051899G>A			132121081		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																				0.627	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132051899	G	A	132051899	2	1	61	1	0	0	0	0	0	0	0	1	300	1079	38	1		1	ADCY8	8	132051899	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129940	132051899	14312123	6123	14108										
EFR3A	23167	broad.mit.edu	37	chr8	132982784	132982784	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcgtctcagcgttgaattCgaagcaaatgatttacaggg	11	8	1	2	rs528953018		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:132982784C>T	ENST00000254624.5	+	10	1278	c.1053C>T	c.(1051-1053)ttC>ttT	p.F351F	EFR3A_ENST00000519656.1_Silent_p.F315F|EFR3A_ENST00000334503.4_Silent_p.F351F	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	351						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.F351F(1)|p.S348fs*15(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			GCGTTGAATTCGAAGCAAATG	0.398													C|||	1	0.000199681	0	0	5008	,	,		16804	0		0	False		,,,				2504	0.001															2	Deletion - Frameshift(1)|Substitution - coding silent(1)	large_intestine(1)|breast(1)	8											100	94	96					8																	132982784		2203	4300	6503	133051966	SO:0001819	synonymous_variant	23167			D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1053C>T	8.37:g.132982784C>T			133051966	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																				0.398	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132982784	C	T	132982784	2	4	61	1	0	0	0	0	0	0	0	1	4969	883	31	1		1	EFR3A	8	132982784	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	930885	132982784	13381238	6124	14109										
KCNQ3	3786	broad.mit.edu	37	chr8	133196530	133196530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaaacttcagtcggccccGccagcctttgtatcggcagc	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133196530G>A	ENST00000388996.4	-	3	982	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W	KCNQ3_ENST00000519445.1_Missense_Mutation_p.R188W|KCNQ3_ENST00000521134.1_Missense_Mutation_p.R68W	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	188					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R188W(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	AGTCGGCCCCGCCAGCCTTTG	0.537																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	8											85	87	87					8																	133196530		2203	4300	6503	133265712	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.562C>T	8.37:g.133196530G>A	ENSP00000373648:p.Arg188Trp		133265712	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.304080	0.81136	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.97772	-4.53;-4.53;-4.53	5.87	2.71	0.32032	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97820	0.9284	L	0.49699	1.58	0.51012	D	0.999905	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97820	1.0256	10	0.87932	D	0	-24.2394	13.0159	0.58757	0.0:0.0:0.3351:0.6648	.	188;188	E7ET42;O43525	.;KCNQ3_HUMAN	W	188;68;188;177;67	ENSP00000373648:R188W;ENSP00000429799:R68W;ENSP00000428790:R188W	ENSP00000373648:R188W	R	-	1	2	KCNQ3	133265712	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.634000	0.46528	0.754000	0.32968	0.655000	0.94253	CGG		0.537	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133196530	G	A	133196530	3	1	61	1	0	0	0	0	1	0	0	0	8105	1086	38	1	2108	1	KCNQ3	8	133196530	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213746	133196530	13167492	6125	14110										
PHF20L1	51105	broad.mit.edu	37	chr8	133826884	133826884	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttattatttattcaggcGatttcacctaaacctcaaag	4	8	3	0	rs79154195		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133826884G>A	ENST00000395386.2	+	10	1232	c.933G>A	c.(931-933)gcG>gcA	p.A311A	PHF20L1_ENST00000395390.2_Silent_p.A286A|PHF20L1_ENST00000220847.7_5'UTR	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	311							zinc ion binding (GO:0008270)	p.A285A(2)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			ttattCAGGCGATTTCACCTA	0.323																																																2	Substitution - coding silent(2)	large_intestine(2)	8											43	47	46					8																	133826884		2202	4299	6501	133896066	SO:0001819	synonymous_variant	51105			AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.933G>A	8.37:g.133826884G>A			133896066	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Silent	SNP	ENST00000395386.2	37	CCDS6367.2																																																																																				0.323	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		A	133826884	G	A	133826884	2	1	61	1	0	0	0	0	0	0	0	1	11863	1045	37	1		1	PHF20L1	8	133826884	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	630354	133826884	12537138	6126	14111										
PHF20L1	51105	broad.mit.edu	37	chr8	133851813	133851813	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacacgggctacagctgaaGattggaatactaaagtaagt	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133851813G>T	ENST00000395386.2	+	18	2672	c.2373G>T	c.(2371-2373)aaG>aaT	p.K791N	AF230666.2_ENST00000429151.1_RNA|AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000220847.7_Missense_Mutation_p.K178N|PHF20L1_ENST00000395390.2_Missense_Mutation_p.K766N	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	791							zinc ion binding (GO:0008270)	p.K765N(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TACAGCTGAAGATTGGAATAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	8											93	84	87					8																	133851813		1900	4120	6020	133920995	SO:0001583	missense	51105			AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2373G>T	8.37:g.133851813G>T	ENSP00000378784:p.Lys791Asn		133920995	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576664	0.65878	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	T;T	0.57107	0.46;0.42	5.41	2.64	0.31445	.	0.581136	0.16132	N	0.228130	T	0.69477	0.3115	M	0.75777	2.31	0.43632	D	0.996024	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.69899	-0.5020	10	0.87932	D	0	-33.1945	10.4863	0.44724	0.2141:0.0:0.7859:0.0	.	766;791	F8W9L8;A8MW92	.;P20L1_HUMAN	N	791;178;766	ENSP00000378784:K791N;ENSP00000378788:K766N	ENSP00000220847:K178N	K	+	3	2	PHF20L1	133920995	1.000000	0.71417	0.996000	0.52242	0.911000	0.54048	1.791000	0.38744	0.686000	0.31488	-0.123000	0.14984	AAG		0.423	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		T	133851813	G	T	133851813	3	4	61	1	0	0	0	0	1	0	0	0	11863	933	33	2	2535	2	PHF20L1	8	133851813	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24929	133851813	12512209	6127	14112										
PHF20L1	51105	broad.mit.edu	37	chr8	133856559	133856559	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctaatagaaaaagaagtCgatggtaatttaagaaagaa	9	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133856559C>T	ENST00000395386.2	+	20	3206	c.2907C>T	c.(2905-2907)gtC>gtT	p.V969V	AF230666.2_ENST00000429151.1_RNA|AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000220847.7_Silent_p.V356V|PHF20L1_ENST00000395390.2_Silent_p.V944V	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	969							zinc ion binding (GO:0008270)	p.V943V(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			AAAAAGAAGTCGATGGTAATT	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	8											66	62	63					8																	133856559		1844	4090	5934	133925741	SO:0001819	synonymous_variant	51105			AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2907C>T	8.37:g.133856559C>T			133925741	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Silent	SNP	ENST00000395386.2	37	CCDS6367.2																																																																																				0.338	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		T	133856559	C	T	133856559	2	4	61	1	0	0	0	0	0	0	0	1	11863	871	31	1		1	PHF20L1	8	133856559	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4746	133856559	12507463	6128	14113										
TG	7038	broad.mit.edu	37	chr8	133883794	133883794	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctggggaggccaaagcGatgtgagtttcactgagcgc	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133883794G>A	ENST00000220616.4	+	4	516	c.476G>A	c.(475-477)cGa>cAa	p.R159Q	TG_ENST00000377869.1_Missense_Mutation_p.R159Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	159	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R159Q(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		AGGCCAAAGCGATGTGAGTTT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	8											85	63	71					8																	133883794		2203	4300	6503	133952976	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.476G>A	8.37:g.133883794G>A	ENSP00000220616:p.Arg159Gln		133952976	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615912	0.66672	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.62941	-0.01;-0.01	5.58	2.72	0.32119	Thyroglobulin type-1 (4);	0.287111	0.25683	N	0.029000	T	0.52141	0.1716	L	0.28776	0.89	0.09310	N	1	D	0.63046	0.992	P	0.53102	0.718	T	0.37820	-0.9689	10	0.29301	T	0.29	.	3.1707	0.06551	0.2604:0.0:0.5417:0.1979	.	159	P01266	THYG_HUMAN	Q	159	ENSP00000367100:R159Q;ENSP00000220616:R159Q	ENSP00000220616:R159Q	R	+	2	0	TG	133952976	0.000000	0.05858	0.015000	0.15790	0.364000	0.29643	0.805000	0.27112	0.667000	0.31107	0.460000	0.39030	CGA		0.602	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133883794	G	A	133883794	3	1	61	1	0	0	0	0	1	0	0	0	15852	1058	37	1	490	1	TG	8	133883794	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27235	133883794	12480228	6129	14114										
TG	7038	broad.mit.edu	37	chr8	133899255	133899255	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatggtactatgaataaGccaactgtgggcagctttgg	13	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133899255G>A	ENST00000220616.4	+	9	1678	c.1638G>A	c.(1636-1638)aaG>aaA	p.K546K	TG_ENST00000377869.1_Silent_p.K546K	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	546					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.K546K(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		CTATGAATAAGCCAACTGTGG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	8											69	68	69					8																	133899255		2203	4300	6503	133968437	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1638G>A	8.37:g.133899255G>A			133968437	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																				0.448	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133899255	G	A	133899255	2	1	61	1	0	0	0	0	0	0	0	1	15852	962	34	3		3	TG	8	133899255	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15461	133899255	12464767	6130	14115										
TG	7038	broad.mit.edu	37	chr8	133900543	133900543	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgaggctggccagcaaGatgtcttcccggtgctgtca	13	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133900543G>T	ENST00000220616.4	+	10	2531	c.2491G>T	c.(2491-2493)Gat>Tat	p.D831Y	TG_ENST00000377869.1_Missense_Mutation_p.D831Y	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	831	Thyroglobulin type-1 7. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.D831Y(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		TGGCCAGCAAGATGTCTTCCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	8											81	80	80					8																	133900543		2203	4300	6503	133969725	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2491G>T	8.37:g.133900543G>T	ENSP00000220616:p.Asp831Tyr		133969725	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693326	0.30052	.	.	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.63913	-0.07;-0.07	5.8	1.43	0.22495	Thyroglobulin type-1 (2);	1.260580	0.05140	N	0.494003	T	0.42787	0.1218	N	0.08118	0	0.09310	N	1	B	0.29955	0.263	B	0.27262	0.078	T	0.41161	-0.9524	10	0.66056	D	0.02	.	8.0054	0.30321	0.5202:0.0:0.4798:0.0	.	831	P01266	THYG_HUMAN	Y	831	ENSP00000367100:D831Y;ENSP00000220616:D831Y	ENSP00000220616:D831Y	D	+	1	0	TG	133969725	0.596000	0.26866	0.176000	0.23000	0.835000	0.47333	1.068000	0.30629	0.359000	0.24239	0.650000	0.86243	GAT		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133900543	G	T	133900543	3	4	61	1	0	0	0	0	1	0	0	0	15852	942	33	2	2529	2	TG	8	133900543	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1288	133900543	12463479	6131	14116										
TG	7038	broad.mit.edu	37	chr8	133911103	133911103	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagttggaaacaggctaGatcccaagaaaacccatctc	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:133911103G>T	ENST00000220616.4	+	14	3318	c.3278G>T	c.(3277-3279)aGa>aTa	p.R1093I	TG_ENST00000377869.1_Missense_Mutation_p.R1093I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1093	Thyroglobulin type-1 9. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R1093I(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		AAACAGGCTAGATCCCAAGAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	8											80	68	72					8																	133911103		2203	4300	6503	133980285	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3278G>T	8.37:g.133911103G>T	ENSP00000220616:p.Arg1093Ile		133980285	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.55|11.55	1.671495|1.671495	0.29693|0.29693	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000518505|ENST00000377869;ENST00000220616	.|T;T	.|0.63417	.|-0.04;-0.04	5.74|5.74	0.364|0.364	0.16124|0.16124	.|Thyroglobulin type-1 (4);	.|0.662303	.|0.14290	.|N	.|0.328985	T|T	0.45955|0.45955	0.1368|0.1368	N|N	0.22421|0.22421	0.69|0.69	0.20403|0.20403	N|N	0.999903|0.999903	.|B	.|0.23854	.|0.092	.|B	.|0.25614	.|0.062	T|T	0.41980|0.41980	-0.9478|-0.9478	5|10	.|0.66056	.|D	.|0.02	.|.	9.7565|9.7565	0.40506|0.40506	0.0:0.4467:0.3143:0.239|0.0:0.4467:0.3143:0.239	.|.	.|1093	.|P01266	.|THYG_HUMAN	Y|I	60|1093	.|ENSP00000367100:R1093I;ENSP00000220616:R1093I	.|ENSP00000220616:R1093I	D|R	+|+	1|2	0|0	TG|TG	133980285|133980285	0.007000|0.007000	0.16637|0.16637	0.113000|0.113000	0.21522|0.21522	0.343000|0.343000	0.28985|0.28985	0.035000|0.035000	0.13797|0.13797	0.035000|0.035000	0.15519|0.15519	0.655000|0.655000	0.94253|0.94253	GAT|AGA		0.562	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133911103	G	T	133911103	3	4	61	1	0	0	0	0	1	0	0	0	15852	942	33	2	3332	2	TG	8	133911103	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10560	133911103	12452919	6132	14117										
TG	7038	broad.mit.edu	37	chr8	134042147	134042147	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagacccacatccgaggatTtggcggggaccctcggcgcg	15	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:134042147T>G	ENST00000220616.4	+	41	7158	c.7118T>G	c.(7117-7119)tTt>tGt	p.F2373C	TG_ENST00000519543.1_Missense_Mutation_p.F506C|TG_ENST00000542445.1_Missense_Mutation_p.F743C|TG_ENST00000377869.1_Missense_Mutation_p.F2316C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2373					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.F2373C(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		ATCCGAGGATTTGGCGGGGAC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	8											48	49	48					8																	134042147		2203	4299	6502	134111329	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7118T>G	8.37:g.134042147T>G	ENSP00000220616:p.Phe2373Cys		134111329	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.01|16.01	3.000966|3.000966	0.54254|0.54254	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543|ENST00000519178;ENST00000518108	D;D;D;D|.	0.91351|.	-2.83;-2.83;-2.83;-2.83|.	5.47|5.47	5.47|5.47	0.80525|0.80525	Carboxylesterase, type B (1);|.	0.136288|.	0.49305|.	D|.	0.000153|.	D|D	0.89058|0.89058	0.6607|0.6607	H|H	0.99011|0.99011	4.4|4.4	0.53005|0.53005	D|D	0.999969|0.999969	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.997;1.0;0.999|.	D|D	0.93184|0.93184	0.6577|0.6577	10|5	0.87932|.	D|.	0|.	.|.	14.3795|14.3795	0.66902|0.66902	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	506;743;2373|.	E7EVM0;F5GWW5;P01266|.	.;.;THYG_HUMAN|.	C|M	2316;1179;2373;743;506|828;168	ENSP00000367100:F2316C;ENSP00000220616:F2373C;ENSP00000441693:F743C;ENSP00000430430:F506C|.	ENSP00000220616:F2373C|.	F|I	+|+	2|3	0|3	TG|TG	134111329|134111329	1.000000|1.000000	0.71417|0.71417	0.287000|0.287000	0.24848|0.24848	0.093000|0.093000	0.18481|0.18481	7.302000|7.302000	0.78861|0.78861	2.077000|2.077000	0.62373|0.62373	0.459000|0.459000	0.35465|0.35465	TTT|ATT		0.652	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	134042147	T	G	134042147	3	3	61	1	0	0	0	0	1	0	0	0	15852	1841	64	4	7280	4	TG	8	134042147	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	131044	134042147	12321875	6133	14118										
TG	7038	broad.mit.edu	37	chr8	134107393	134107393	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccatgtcatccagccaaGaagtggtgtcctgcctccgc	10	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:134107393G>T	ENST00000220616.4	+	42	7385	c.7345G>T	c.(7345-7347)Gaa>Taa	p.E2449*	SLA_ENST00000518565.1_Intron|SLA_ENST00000517648.1_Intron|TG_ENST00000519543.1_Nonsense_Mutation_p.E582*|SLA_ENST00000395352.3_Intron|SLA_ENST00000338087.5_Intron|TG_ENST00000542445.1_Nonsense_Mutation_p.E819*|TG_ENST00000377869.1_Nonsense_Mutation_p.E2392*|SLA_ENST00000524345.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2449					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.E2449*(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		ATCCAGCCAAGAAGTGGTGTC	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											167	142	150					8																	134107393		2203	4300	6503	134176575	SO:0001587	stop_gained	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7345G>T	8.37:g.134107393G>T	ENSP00000220616:p.Glu2449*		134176575	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Nonsense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	50|50	16.216117|16.216117	0.99857|0.99857	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543|ENST00000519178	.|.	.|.	.|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.663946|.	0.14924|.	N|.	0.290496|.	.|T	.|0.72534	.|0.3472	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69300	.|-0.5181	.|4	0.39692|.	T|.	0.17|.	.|.	16.144|16.144	0.81551|0.81551	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	2392;1255;2449;819;582|904	.|.	ENSP00000220616:E2449X|.	E|R	+|+	1|2	0|0	TG|TG	134176575|134176575	0.994000|0.994000	0.37717|0.37717	0.622000|0.622000	0.29159|0.29159	0.752000|0.752000	0.42762|0.42762	5.889000|5.889000	0.69766|0.69766	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.577	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	134107393	G	T	134107393	4	4	61	1	0	0	0	0	0	1	0	0	15852	943	33	2	7511	2	TG	8	134107393	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65246	134107393	12256629	6134	14119										
ZFAT	57623	broad.mit.edu	37	chr8	135533133	135533133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaaaaaattacctcccacTtggggtctccatcaatttcc	4	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:135533133T>C	ENST00000377838.3	-	13	3401	c.3227A>G	c.(3226-3228)aAg>aGg	p.K1076R	ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520356.1_Missense_Mutation_p.K1064R|ZFAT_ENST00000523399.1_Missense_Mutation_p.K1014R|ZFAT_ENST00000520727.1_Missense_Mutation_p.K1064R|ZFAT_ENST00000429442.2_Missense_Mutation_p.K1064R|ZFAT_ENST00000520214.1_Missense_Mutation_p.K1064R	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1076					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.K1076R(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	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)			TACCTCCCACTTGGGGTCTCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											63	59	60					8																	135533133		1834	4086	5920	135602315	SO:0001583	missense	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3227A>G	8.37:g.135533133T>C	ENSP00000367069:p.Lys1076Arg		135602315	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.141981	0.77775	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399	T;T;T;T;T;T	0.10763	2.95;2.87;2.84;2.86;2.87;2.88	5.53	4.34	0.51931	.	0.057885	0.64402	D	0.000005	T	0.18800	0.0451	L	0.27053	0.805	0.35394	D	0.791037	D;D;P;P	0.69078	0.997;0.976;0.915;0.941	D;P;B;B	0.73380	0.98;0.541;0.313;0.321	T	0.14811	-1.0459	10	0.42905	T	0.14	-26.2261	11.5415	0.50669	0.0:0.0:0.1501:0.8499	.	195;1014;1064;1076	B7Z741;E9PER3;E9PBN4;Q9P243	.;.;.;ZFAT_HUMAN	R	1064;1064;1064;1076;1064;963;1014	ENSP00000427879:K1064R;ENSP00000427831:K1064R;ENSP00000394501:K1064R;ENSP00000367069:K1076R;ENSP00000428483:K1064R;ENSP00000429091:K1014R	ENSP00000326997:K963R	K	-	2	0	ZFAT	135602315	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.867000	0.48428	0.904000	0.36572	0.524000	0.50904	AAG		0.413	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		C	135533133	T	C	135533133	3	2	61	1	0	0	0	0	1	0	0	0	17671	1609	56	4	520	4	ZFAT	8	135533133	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1425740	135533133	10830889	6135	14120										
ZFAT	57623	broad.mit.edu	37	chr8	135612793	135612793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtttctgaattacgtgGcgtttaaggcagtttttggt	12	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:135612793G>A	ENST00000377838.3	-	7	2535	c.2361C>T	c.(2359-2361)cgC>cgT	p.R787R	ZFAT_ENST00000520356.1_Silent_p.R775R|ZFAT_ENST00000523399.1_Silent_p.R725R|ZFAT_ENST00000520727.1_Silent_p.R775R|ZFAT_ENST00000429442.2_Silent_p.R775R|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520214.1_Silent_p.R775R	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	787					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R775R(1)|p.R787R(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	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)			GAATTACGTGGCGTTTAAGGC	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	8											148	146	146					8																	135612793		1971	4155	6126	135681975	SO:0001819	synonymous_variant	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2361C>T	8.37:g.135612793G>A			135681975	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																				0.428	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		A	135612793	G	A	135612793	2	1	61	1	0	0	0	0	0	0	0	1	17671	1190	42	3		3	ZFAT	8	135612793	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79660	135612793	10751229	6136	14121										
FAM135B	51059	broad.mit.edu	37	chr8	139158255	139158255	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccagggagccccagttCtatgaaagtctttaccagcc	8	14	2	1	rs267601783		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139158255C>A	ENST00000395297.1	-	15	3657	c.3487G>T	c.(3487-3489)Gaa>Taa	p.E1163*		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1163								p.E1163*(4)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGCCCCAGTTCTATGAAAGTC	0.448										HNSCC(54;0.14)																																						4	Substitution - Nonsense(4)	large_intestine(2)|lung(2)	8											88	93	92					8																	139158255		2203	4300	6503	139227437	SO:0001587	stop_gained	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3487G>T	8.37:g.139158255C>A	ENSP00000378710:p.Glu1163*		139227437	B5MDB3|O95879|Q2WGJ7|Q3KP46	Nonsense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	44	11.161224	0.99525	.	.	ENSG00000147724	ENST00000395297	.	.	.	5.81	4.92	0.64577	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-8.7909	15.404	0.74863	0.1401:0.8599:0.0:0.0	.	.	.	.	X	1163	.	ENSP00000378710:E1163X	E	-	1	0	FAM135B	139227437	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.064000	0.71169	1.433000	0.47394	0.655000	0.94253	GAA		0.448	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		A	139158255	C	A	139158255	4	1	61	1	0	0	0	0	0	1	0	0	5465	922	32	2	757	2	FAM135B	8	139158255	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3545462	139158255	7205767	6137	14122										
FAM135B	51059	broad.mit.edu	37	chr8	139165035	139165035	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcagctctggaggggttCttattgctagattttacgtc	12	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139165035C>A	ENST00000395297.1	-	13	1853	c.1683G>T	c.(1681-1683)aaG>aaT	p.K561N		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	561								p.K561N(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGGAGGGGTTCTTATTGCTAG	0.498										HNSCC(54;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	8											97	95	96					8																	139165035		1910	4123	6033	139234217	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1683G>T	8.37:g.139165035C>A	ENSP00000378710:p.Lys561Asn		139234217	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333719	0.60853	.	.	ENSG00000147724	ENST00000395297	T	0.19105	2.17	5.45	3.63	0.41609	.	0.304511	0.36234	N	0.002702	T	0.19765	0.0475	M	0.63428	1.95	0.34727	D	0.72934	P;P;B	0.46142	0.873;0.465;0.028	B;B;B	0.40477	0.33;0.148;0.018	T	0.27536	-1.0071	10	0.33940	T	0.23	-17.4869	7.0029	0.24820	0.0:0.7059:0.1436:0.1505	.	561;561;561	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	N	561	ENSP00000378710:K561N	ENSP00000276737:K561N	K	-	3	2	FAM135B	139234217	0.083000	0.21467	0.671000	0.29857	0.843000	0.47879	0.296000	0.19083	0.763000	0.33175	0.655000	0.94253	AAG		0.498	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		A	139165035	C	A	139165035	3	1	61	1	0	0	0	0	1	0	0	0	5465	912	32	2	2569	2	FAM135B	8	139165035	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6780	139165035	7198987	6138	14123										
FAM135B	51059	broad.mit.edu	37	chr8	139165251	139165251	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcacatgtccatatgattTtgtgtggccacattctcacc	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139165251T>G	ENST00000395297.1	-	13	1637	c.1467A>C	c.(1465-1467)caA>caC	p.Q489H		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	489								p.Q489H(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CCATATGATTTTGTGTGGCCA	0.413										HNSCC(54;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	8											133	125	128					8																	139165251		1934	4143	6077	139234433	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1467A>C	8.37:g.139165251T>G	ENSP00000378710:p.Gln489His		139234433	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877935	0.51801	.	.	ENSG00000147724	ENST00000395297	T	0.14893	2.47	5.75	-7.73	0.01245	.	1.567240	0.03127	N	0.164586	T	0.09555	0.0235	N	0.14661	0.345	0.09310	N	1	P;P;B	0.45348	0.856;0.763;0.328	B;B;B	0.44163	0.443;0.35;0.135	T	0.34725	-0.9817	10	0.46703	T	0.11	-0.0786	4.1504	0.10235	0.0957:0.388:0.2917:0.2246	.	489;489;489	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	H	489	ENSP00000378710:Q489H	ENSP00000276737:Q489H	Q	-	3	2	FAM135B	139234433	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.943000	0.03917	-0.570000	0.06022	0.533000	0.62120	CAA		0.413	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139165251	T	G	139165251	3	3	61	1	0	0	0	0	1	0	0	0	5465	1838	64	4	2785	4	FAM135B	8	139165251	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	216	139165251	7198771	6139	14124										
FAM135B	51059	broad.mit.edu	37	chr8	139165314	139165314	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcatcagaatccatttgGgatggttttatggtagacaa	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139165314G>A	ENST00000395297.1	-	13	1574	c.1404C>T	c.(1402-1404)tcC>tcT	p.S468S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	468								p.S468S(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AATCCATTTGGGATGGTTTTA	0.383										HNSCC(54;0.14)																																						2	Substitution - coding silent(2)	large_intestine(2)	8											98	92	94					8																	139165314		1885	4125	6010	139234496	SO:0001819	synonymous_variant	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1404C>T	8.37:g.139165314G>A			139234496	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																				0.383	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		A	139165314	G	A	139165314	2	1	61	1	0	0	0	0	0	0	0	1	5465	1219	43	3		3	FAM135B	8	139165314	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63	139165314	7198708	6140	14125										
FAM135B	51059	broad.mit.edu	37	chr8	139180246	139180246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggggcatgctagtgaggtActccgagttccggatatcca	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139180246A>G	ENST00000395297.1	-	12	1320	c.1150T>C	c.(1150-1152)Tac>Cac	p.Y384H		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	384								p.Y384H(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CTAGTGAGGTACTCCGAGTTC	0.597										HNSCC(54;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	8											110	119	116					8																	139180246		2115	4231	6346	139249428	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1150T>C	8.37:g.139180246A>G	ENSP00000378710:p.Tyr384His		139249428	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	A	19.71	3.878770	0.72294	.	.	ENSG00000147724	ENST00000395297	D	0.90676	-2.71	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.95421	0.8513	M	0.82716	2.605	0.54753	D	0.999982	D	0.89917	1.0	D	0.87578	0.998	D	0.95854	0.8877	10	0.72032	D	0.01	-23.8834	15.014	0.71570	1.0:0.0:0.0:0.0	.	384	Q49AJ0	F135B_HUMAN	H	384	ENSP00000378710:Y384H	ENSP00000276737:Y384H	Y	-	1	0	FAM135B	139249428	1.000000	0.71417	1.000000	0.80357	0.322000	0.28314	8.217000	0.89766	2.278000	0.76064	0.533000	0.62120	TAC		0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139180246	A	G	139180246	3	3	61	1	0	0	0	0	1	0	0	0	5465	391	14	4	3106	4	FAM135B	8	139180246	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	14932	139180246	7183776	6141	14126										
FAM135B	51059	broad.mit.edu	37	chr8	139189659	139189659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggcctcagaaaaccttCggacctgcagaataaaacaa	8	10	1	3	rs187739434		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139189659C>T	ENST00000395297.1	-	11	1204	c.1034G>A	c.(1033-1035)cGa>cAa	p.R345Q		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	345								p.R345Q(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGAAAACCTTCGGACCTGCAG	0.378										HNSCC(54;0.14)			C|||	1	0.000199681	0	0	5008	,	,		19887	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	8											90	84	86					8																	139189659		1869	4103	5972	139258841	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1034G>A	8.37:g.139189659C>T	ENSP00000378710:p.Arg345Gln		139258841	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	28.8	4.955134	0.92726	.	.	ENSG00000147724	ENST00000395297	T	0.18174	2.23	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.39279	0.1072	L	0.60845	1.875	0.51482	D	0.999928	D	0.89917	1.0	D	0.91635	0.999	T	0.09122	-1.0689	10	0.72032	D	0.01	-5.78	16.1375	0.81497	0.0:1.0:0.0:0.0	.	345	Q49AJ0	F135B_HUMAN	Q	345	ENSP00000378710:R345Q	ENSP00000276737:R345Q	R	-	2	0	FAM135B	139258841	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.307000	0.78920	2.674000	0.91012	0.563000	0.77884	CGA		0.378	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139189659	C	T	139189659	3	4	61	1	0	0	0	0	1	0	0	0	5465	884	31	1	3226	1	FAM135B	8	139189659	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9413	139189659	7174363	6142	14127										
COL22A1	169044	broad.mit.edu	37	chr8	139609183	139609183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctcttcttgaataagccGacgcagggtttccatggatg	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139609183G>A	ENST00000303045.6	-	62	4842	c.4396C>T	c.(4396-4398)Cgg>Tgg	p.R1466W	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.R1446W	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1466	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.R1466W(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGAATAAGCCGACGCAGGGTT	0.522										HNSCC(7;0.00092)																																						1	Substitution - Missense(1)	large_intestine(1)	8											155	157	157					8																	139609183		2203	4300	6503	139678365	SO:0001583	missense	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4396C>T	8.37:g.139609183G>A	ENSP00000303153:p.Arg1466Trp		139678365	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684634	0.47991	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.89939	-2.59;-2.49	4.93	1.53	0.23141	.	0.000000	0.40728	U	0.001032	D	0.92681	0.7674	M	0.70595	2.14	0.46874	D	0.999233	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	D	0.91184	0.4978	10	0.44086	T	0.13	.	12.7493	0.57300	0.0:0.0:0.437:0.563	.	1446;1466	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	W	1466;1446;1159	ENSP00000303153:R1466W;ENSP00000387655:R1446W	ENSP00000303153:R1466W	R	-	1	2	COL22A1	139678365	0.988000	0.35896	0.820000	0.32676	0.976000	0.68499	0.848000	0.27710	0.429000	0.26202	0.467000	0.42956	CGG		0.522	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139609183	G	A	139609183	3	1	61	1	0	0	0	0	1	0	0	0	3687	1057	37	1	500	1	COL22A1	8	139609183	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	419524	139609183	6754839	6143	14128										
COL22A1	169044	broad.mit.edu	37	chr8	139696684	139696684	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccttggttcctaggggtCcagggagtccaggtgatcca	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139696684C>A	ENST00000303045.6	-	39	3442	c.2996G>T	c.(2995-2997)gGa>gTa	p.G999V	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.G999V	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	999	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G999V(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCTAGGGGTCCAGGGAGTCC	0.498										HNSCC(7;0.00092)																																						1	Substitution - Missense(1)	large_intestine(1)	8											121	124	123					8																	139696684		2203	4300	6503	139765866	SO:0001583	missense	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2996G>T	8.37:g.139696684C>A	ENSP00000303153:p.Gly999Val		139765866	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247332	0.22880	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99429	-5.89;-5.77	4.0	4.0	0.46444	.	0.000000	0.47852	U	0.000217	D	0.99680	0.9880	H	0.97852	4.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97524	1.0075	10	0.72032	D	0.01	.	11.4747	0.50291	0.0:1.0:0.0:0.0	.	999;999	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	V	999;999;712	ENSP00000303153:G999V;ENSP00000387655:G999V	ENSP00000303153:G999V	G	-	2	0	COL22A1	139765866	0.981000	0.34729	0.785000	0.31869	0.296000	0.27459	3.286000	0.51724	2.044000	0.60594	0.448000	0.29417	GGA		0.498	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139696684	C	A	139696684	3	1	61	1	0	0	0	0	1	0	0	0	3687	855	30	2	1992	2	COL22A1	8	139696684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87501	139696684	6667338	6144	14129										
COL22A1	169044	broad.mit.edu	37	chr8	139845356	139845356	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattctctctcttccccaaGatttccttcacactgaacaa	2	16	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:139845356G>A	ENST00000303045.6	-	5	1217	c.771C>T	c.(769-771)atC>atT	p.I257I	COL22A1_ENST00000435777.1_Silent_p.I257I	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	257	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.I257I(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCTTCCCCAAGATTTCCTTCA	0.458										HNSCC(7;0.00092)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											129	106	114					8																	139845356		2203	4300	6503	139914538	SO:0001819	synonymous_variant	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.771C>T	8.37:g.139845356G>A			139914538	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																				0.458	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139845356	G	A	139845356	2	1	61	1	0	0	0	0	0	0	0	1	3687	932	33	3		3	COL22A1	8	139845356	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148672	139845356	6518666	6145	14130										
KCNK9	51305	broad.mit.edu	37	chr8	140631216	140631216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgcgcttcagcaggtagCgcacgaaggtgttcatgcgc	13	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:140631216C>T	ENST00000520439.1	-	2	473	c.410G>A	c.(409-411)cGc>cAc	p.R137H	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Missense_Mutation_p.R137H	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	137					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.R137H(1)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CAGCAGGTAGCGCACGAAGGT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	8											113	87	96					8																	140631216		2203	4300	6503	140700398	SO:0001583	missense	51305			AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.410G>A	8.37:g.140631216C>T	ENSP00000430676:p.Arg137His		140700398	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	37	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.123684	0.77436	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.24908	1.83;1.83;1.83	5.85	4.87	0.63330	.	0.125201	0.50627	D	0.000103	T	0.36248	0.0960	M	0.64997	1.995	0.35242	D	0.777873	D	0.65815	0.995	P	0.55161	0.77	T	0.45264	-0.9273	10	0.46703	T	0.11	.	7.916	0.29818	0.0:0.8416:0.0:0.1584	.	137	Q9NPC2	KCNK9_HUMAN	H	137	ENSP00000429847:R137H;ENSP00000302166:R137H;ENSP00000430676:R137H	ENSP00000302166:R137H	R	-	2	0	KCNK9	140700398	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.924000	0.63418	2.753000	0.94483	0.655000	0.94253	CGC		0.582	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		T	140631216	C	T	140631216	3	4	61	1	0	0	0	0	1	0	0	0	8093	768	27	1	718	1	KCNK9	8	140631216	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	785860	140631216	5732806	6146	14131										
TRAPPC9	83696	broad.mit.edu	37	chr8	141449256	141449256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaggcacaggtcccccaCgtgcttccgcatgcggcctt	11	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:141449256C>T	ENST00000438773.2	-	3	758	c.625G>A	c.(625-627)Gtg>Atg	p.V209M	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.V307M|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.V209M	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	209					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)		p.V307M(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						AGGTCCCCCACGTGCTTCCGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	8											100	90	93					8																	141449256		2203	4300	6503	141518438	SO:0001583	missense	83696			BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.625G>A	8.37:g.141449256C>T	ENSP00000405060:p.Val209Met		141518438	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.77|18.77	3.694144|3.694144	0.68386|0.68386	.|.	.|.	ENSG00000167632|ENSG00000167632	ENST00000520857|ENST00000389328;ENST00000389327;ENST00000438773	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75243|0.75243	0.3823|0.3823	L|L	0.54323|0.54323	1.7|1.7	0.43191|0.43191	D|D	0.995022|0.995022	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.74348	.|0.983;0.957;0.968	T|T	0.69873|0.69873	-0.5027|-0.5027	5|9	.|0.25106	.|T	.|0.35	.|.	19.4258|19.4258	0.94741|0.94741	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|209;209;307	.|Q96Q05;Q96Q05-3;Q96Q05-2	.|TPPC9_HUMAN;.;.	H|M	61|307;209;209	.|.	.|ENSP00000373978:V209M	R|V	-|-	2|1	0|0	TRAPPC9|TRAPPC9	141518438|141518438	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.480000|0.480000	0.33159|0.33159	5.653000|5.653000	0.67967|0.67967	2.582000|2.582000	0.87167|0.87167	0.650000|0.650000	0.86243|0.86243	CGT|GTG		0.512	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	141449256	C	T	141449256	3	4	61	1	0	0	0	0	1	0	0	0	16505	536	19	1	2905	1	TRAPPC9	8	141449256	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	818040	141449256	4914766	6147	14132										
DENND3	22898	broad.mit.edu	37	chr8	142185339	142185339	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaaacattcaaagatttCtacaactgctggaaggagac	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:142185339C>A	ENST00000262585.2	+	14	2354	c.2076C>A	c.(2074-2076)ttC>ttA	p.F692L	DENND3_ENST00000519811.1_Missense_Mutation_p.F772L|DENND3_ENST00000424248.1_Missense_Mutation_p.F640L	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	692					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.F692L(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	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)			TCAAAGATTTCTACAACTGCT	0.473											OREG0019025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											105	103	104					8																	142185339		2203	4300	6503	142254521	SO:0001583	missense	22898			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2076C>A	8.37:g.142185339C>A	ENSP00000262585:p.Phe692Leu	1669	142254521	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.240373|4.240373	0.79912|0.79912	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811|ENST00000518668	T;T;T|.	0.45276|.	1.42;0.9;1.37|.	4.64|4.64	3.75|3.75	0.43078|0.43078	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71048|0.71048	0.3294|0.3294	M|M	0.77103|0.77103	2.36|2.36	0.48632|0.48632	D|D	0.999689|0.999689	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.997;0.999;0.997|.	T|T	0.70439|0.70439	-0.4871|-0.4871	10|5	0.87932|.	D|.	0|.	-3.9523|-3.9523	9.5416|9.5416	0.39255|0.39255	0.0:0.8265:0.0:0.1735|0.0:0.8265:0.0:0.1735	.|.	772;640;692|.	E9PF32;A2RUS2-2;A2RUS2|.	.;.;DEND3_HUMAN|.	L|I	692;640;772|697	ENSP00000262585:F692L;ENSP00000410594:F640L;ENSP00000428714:F772L|.	ENSP00000262585:F692L|.	F|L	+|+	3|1	2|2	DENND3|DENND3	142254521|142254521	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.937000|0.937000	0.57800|0.57800	1.695000|1.695000	0.37763|0.37763	1.052000|1.052000	0.40392|0.40392	0.491000|0.491000	0.48974|0.48974	TTC|CTA		0.473	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142185339	C	A	142185339	3	1	61	1	0	0	0	0	1	0	0	0	4443	912	32	2	2126	2	DENND3	8	142185339	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	736083	142185339	4178683	6148	14133										
DENND3	22898	broad.mit.edu	37	chr8	142185478	142185478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctaggcgttggcaagatcGccatgacccagaagcgcctg	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:142185478G>A	ENST00000262585.2	+	14	2493	c.2215G>A	c.(2215-2217)Gcc>Acc	p.A739T	DENND3_ENST00000519811.1_Missense_Mutation_p.A819T|DENND3_ENST00000424248.1_Missense_Mutation_p.A687T	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	739					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.A739T(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	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)			TGGCAAGATCGCCATGACCCA	0.522											OREG0019025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	8											129	115	120					8																	142185478		2203	4300	6503	142254660	SO:0001583	missense	22898			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2215G>A	8.37:g.142185478G>A	ENSP00000262585:p.Ala739Thr	1669	142254660	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.248030|5.248030	0.95305|0.95305	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811|ENST00000518668	T;T;T|.	0.19105|.	2.64;2.17;2.62|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76162|0.76162	0.3949|0.3949	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.996;1.0;1.0|.	T|T	0.76852|0.76852	-0.2806|-0.2806	10|5	0.66056|.	D|.	0.02|.	-6.7346|-6.7346	18.1709|18.1709	0.89745|0.89745	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	819;687;739|.	E9PF32;A2RUS2-2;A2RUS2|.	.;.;DEND3_HUMAN|.	T|H	739;687;819|743	ENSP00000262585:A739T;ENSP00000410594:A687T;ENSP00000428714:A819T|.	ENSP00000262585:A739T|.	A|R	+|+	1|2	0|0	DENND3|DENND3	142254660|142254660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	9.146000|9.146000	0.94640|0.94640	2.289000|2.289000	0.77006|0.77006	0.491000|0.491000	0.48974|0.48974	GCC|CGC		0.522	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142185478	G	A	142185478	3	1	61	1	0	0	0	0	1	0	0	0	4443	1087	38	1	2265	1	DENND3	8	142185478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139	142185478	4178544	6149	14134										
FLJ43860	389690	broad.mit.edu	37	chr8	142505582	142505582	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcatcttgaagccggtGgctaaggttggcaagaaggc	15	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:142505582G>T	ENST00000430863.1	-	0	344					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5									p.A88A(1)									TGAAGCCGGTGGCTAAGGTTG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	8											103	102	103					8																	142505582		2161	4270	6431	142574764			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142505582G>T			142574764		Silent	SNP	ENST00000430863.1	37																																																																																					0.547	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		T	142505582	G	T	142505582	1	4	61	0	1	0	0	0	0	0	0	0	5949	1362	47	2		2	FLJ43860	8	142505582	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	320104	142505582	3858440	6150	14135										
GML	2765	broad.mit.edu	37	chr8	143927988	143927988	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacctactaatcttgaaaGggacatgttacccgatgaag	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:143927988G>T	ENST00000220940.1	+	4	449	c.359G>T	c.(358-360)aGg>aTg	p.R120M		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	120	UPAR/Ly6.				apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)		p.R120M(1)		NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AATCTTGAAAGGGACATGTTA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											111	108	109					8																	143927988		2203	4300	6503	143924990	SO:0001583	missense	2765			D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"GPI anchored molecule like protein", "glycosylphosphatidylinositol anchored molecule like protein"			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.359G>T	8.37:g.143927988G>T	ENSP00000220940:p.Arg120Met		143924990	A0AVF6|O00686|O00731	Missense_Mutation	SNP	ENST00000220940.1	37	CCDS6391.1	.	.	.	.	.	.	.	.	.	.	N	12.33	1.906003	0.33628	.	.	ENSG00000104499	ENST00000220940	T	0.51817	0.69	3.52	-0.415	0.12355	Ly-6 antigen / uPA receptor -like (1);	0.376588	0.19226	N	0.119544	T	0.52980	0.1768	L	0.59436	1.845	0.09310	N	1	D	0.76494	0.999	D	0.64237	0.923	T	0.43081	-0.9413	10	0.87932	D	0	-29.3109	3.6721	0.08277	0.3289:0.1882:0.4829:0.0	.	120	Q99445	GML_HUMAN	M	120	ENSP00000220940:R120M	ENSP00000220940:R120M	R	+	2	0	GML	143924990	0.254000	0.23992	0.023000	0.16930	0.017000	0.09413	-0.051000	0.11885	-0.099000	0.12263	-0.484000	0.04775	AGG		0.443	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066		T	143927988	G	T	143927988	3	4	61	1	0	0	0	0	1	0	0	0	6512	1000	35	2	369	2	GML	8	143927988	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1422406	143927988	2436034	6151	14136										
TOP1MT	116447	broad.mit.edu	37	chr8	144400221	144400221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggtcgtcccgggggtcCttgttctccataaagagctg	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:144400221C>A	ENST00000329245.4	-	9	1216	c.1182G>T	c.(1180-1182)aaG>aaT	p.K394N	TOP1MT_ENST00000521193.1_Missense_Mutation_p.K296N|TOP1MT_ENST00000519148.1_Missense_Mutation_p.K296N|TOP1MT_ENST00000523676.1_Missense_Mutation_p.K296N	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	394					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)	p.K394N(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	CCCGGGGGTCCTTGTTCTCCA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	8											71	78	76					8																	144400221		2203	4300	6503	144471596	SO:0001583	missense	116447			AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1182G>T	8.37:g.144400221C>A	ENSP00000328835:p.Lys394Asn		144471596	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.430152	0.43122	.	.	ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	2.63	-3.87	0.04218	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (1);	0.314508	0.22331	U	0.061466	T	0.74458	0.3719	H	0.97962	4.115	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.988	T	0.76958	-0.2766	10	0.87932	D	0	.	10.7322	0.46104	0.0:0.3079:0.0:0.6921	.	189;394	E7ESI1;Q969P6	.;TOP1M_HUMAN	N	394;296;296;296	ENSP00000328835:K394N;ENSP00000428369:K296N;ENSP00000429169:K296N;ENSP00000429181:K296N	ENSP00000328835:K394N	K	-	3	2	TOP1MT	144471596	0.009000	0.17119	0.001000	0.08648	0.001000	0.01503	-0.257000	0.08745	-0.998000	0.03446	-0.908000	0.02827	AAG		0.567	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		A	144400221	C	A	144400221	3	1	61	1	0	0	0	0	1	0	0	0	16404	680	24	2	647	2	TOP1MT	8	144400221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	472233	144400221	1963801	6152	14137										
PLEC	5339	broad.mit.edu	37	chr8	144993470	144993470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaagcccttggtgtcgtCgctggggtccgccaggacgc	15	12	0	1	rs200293573		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:144993470C>T	ENST00000322810.4	-	32	11099	c.10930G>A	c.(10930-10932)Gac>Aac	p.D3644N	PLEC_ENST00000345136.3_Missense_Mutation_p.D3507N|PLEC_ENST00000527096.1_Missense_Mutation_p.D3530N|PLEC_ENST00000357649.2_Missense_Mutation_p.D3511N|PLEC_ENST00000436759.2_Missense_Mutation_p.D3534N|PLEC_ENST00000354589.3_Missense_Mutation_p.D3507N|PLEC_ENST00000356346.3_Missense_Mutation_p.D3493N|PLEC_ENST00000354958.2_Missense_Mutation_p.D3485N|PLEC_ENST00000398774.2_Missense_Mutation_p.D3475N	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3644	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.D3644N(1)|p.D3534N(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TTGGTGTCGTCGCTGGGGTCC	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	8						C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4154		0,0,2077	77	87	84		10600,10477,10453,10930,10423,10519,10531,10519	3.9	0.7	8		84	1,8391		0,1,4195	no	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	23,23,23,23,23,23,23,23	0,1,6272	TT,TC,CC		0.0119,0.0,0.0080	benign,benign,benign,benign,benign,benign,benign,benign	3534/4575,3493/4534,3485/4526,3644/4685,3475/4516,3507/4548,3511/4552,3507/4548	144993470	1,12545	2077	4196	6273	145065458	SO:0001583	missense	5339			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.10930G>A	8.37:g.144993470C>T	ENSP00000323856:p.Asp3644Asn		145065458	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	9.390	1.075141	0.20227	0.0	1.19E-4	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	4.79	3.92	0.45320	.	0.078423	0.47852	U	0.000219	T	0.75679	0.3882	M	0.84433	2.695	0.47621	D	0.999472	D;D;D;D;D;D;D;D	0.69078	0.997;0.997;0.997;0.995;0.997;0.997;0.997;0.997	P;P;P;B;P;P;P;P	0.51945	0.614;0.614;0.614;0.41;0.685;0.685;0.685;0.685	T	0.77099	-0.2713	10	0.32370	T	0.25	.	13.0824	0.59121	0.0:0.9217:0.0:0.0783	.	3534;3493;3485;3644;3475;3507;3511;3507	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	N	3507;3511;3507;3475;3644;3485;3493;3534;3530	ENSP00000344848:D3507N;ENSP00000350277:D3511N;ENSP00000346602:D3507N;ENSP00000381756:D3475N;ENSP00000323856:D3644N;ENSP00000347044:D3485N;ENSP00000348702:D3493N;ENSP00000388180:D3534N;ENSP00000434583:D3530N	ENSP00000323856:D3644N	D	-	1	0	PLEC	145065458	0.998000	0.40836	0.679000	0.29978	0.137000	0.21094	4.651000	0.61447	1.265000	0.44215	-0.395000	0.06472	GAC		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144993470	C	T	144993470	3	4	61	1	0	0	0	0	1	0	0	0	12083	884	31	1	3128	1	PLEC	8	144993470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	593249	144993470	1370552	6153	14138										
SLC39A4	55630	broad.mit.edu	37	chr8	145640359	145640359	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccagggcgcagctcaccGtgtcccacacactggagctg	11	17	1	0	rs185494598		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:145640359G>A	ENST00000301305.3	-	4	908	c.803C>T	c.(802-804)aCg>aTg	p.T268M	SLC39A4_ENST00000276833.5_Splice_Site_p.T243M|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	268					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)	p.T268M(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-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;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GCAGCTCACCGTGTCCCACAC	0.672													G|||	1	0.000199681	0	0.0014	5008	,	,		17014	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											45	48	47					8																	145640359		2203	4300	6503	145611167	SO:0001630	splice_region_variant	55630			AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.804+1C>T	8.37:g.145640359G>A			145611167	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.58	3.162310	0.57368	.	.	ENSG00000147804	ENST00000276833;ENST00000301305;ENST00000526658	T;T;T	0.59906	0.23;0.23;0.23	5.3	3.34	0.38264	.	3.229310	0.00875	N	0.002075	T	0.72366	0.3451	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.999	P;P	0.61800	0.894;0.854	T	0.58725	-0.7586	10	0.66056	D	0.02	-15.1985	7.8933	0.29691	0.0:0.1779:0.638:0.1841	.	268;243	Q6P5W5;A6NDY5	S39A4_HUMAN;.	M	243;268;174	ENSP00000276833:T243M;ENSP00000301305:T268M;ENSP00000434512:T174M	ENSP00000276833:T243M	T	-	2	0	SLC39A4	145611167	0.996000	0.38824	1.000000	0.80357	0.535000	0.34838	2.299000	0.43611	1.218000	0.43458	0.543000	0.68304	ACG		0.672	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		Missense_Mutation	A	145640359	G	A	145640359	5	1	61	1	0	0	0	0	0	0	1	0	14657	1159	40	1	1176	1	SLC39A4	8	145640359	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	646889	145640359	723663	6154	14139										
ZNF251	90987	broad.mit.edu	37	chr8	145948334	145948334	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcccacaccggccacattcGtacggcttctccccagtgtg	9	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:145948334G>A	ENST00000292562.7	-	5	986	c.711C>T	c.(709-711)taC>taT	p.Y237Y	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y194Y(1)		autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		GGCCACATTCGTACGGCTTCT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	8											60	65	64					8																	145948334		2080	4237	6317	145919143	SO:0001819	synonymous_variant	90987			AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.711C>T	8.37:g.145948334G>A			145919143	Q2M219	Silent	SNP	ENST00000292562.7	37	CCDS47944.1																																																																																				0.433	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		A	145948334	G	A	145948334	2	1	61	1	0	0	0	0	0	0	0	1	17835	1140	40	1		1	ZNF251	8	145948334	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	307975	145948334	415688	6155	14140										
ZNF251	90987	broad.mit.edu	37	chr8	145948443	145948443	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctctctcctgttttatttCtttgaagtctaacaacattt	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:145948443C>A	ENST00000292562.7	-	5	877	c.602G>T	c.(601-603)aGa>aTa	p.R201I	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R158I(1)		autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		TGTTTTATTTCTTTGAAGTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											89	92	91					8																	145948443		1868	4109	5977	145919252	SO:0001583	missense	90987			AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.602G>T	8.37:g.145948443C>A	ENSP00000292562:p.Arg201Ile		145919252	Q2M219	Missense_Mutation	SNP	ENST00000292562.7	37	CCDS47944.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326714	0.60743	.	.	ENSG00000198169	ENST00000292562	T	0.08193	3.12	2.12	2.12	0.27331	.	.	.	.	.	T	0.13586	0.0329	L	0.35644	1.08	0.42899	D	0.994228	D	0.63046	0.992	P	0.62089	0.898	T	0.05178	-1.0901	9	0.52906	T	0.07	.	6.5137	0.22236	0.0:0.8463:0.0:0.1537	.	201	Q9BRH9	ZN251_HUMAN	I	201	ENSP00000292562:R201I	ENSP00000292562:R201I	R	-	2	0	ZNF251	145919252	0.000000	0.05858	0.969000	0.41365	0.987000	0.75469	-0.190000	0.09615	1.466000	0.48025	0.563000	0.77884	AGA		0.403	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		A	145948443	C	A	145948443	3	1	61	1	0	0	0	0	1	0	0	0	17835	913	32	2	1417	2	ZNF251	8	145948443	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109	145948443	415579	6156	14141										
ZNF251	90987	broad.mit.edu	37	chr8	145948711	145948711	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattctggggtttttacttCttcggaaaatttttggttta	8	4	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr8:145948711C>A	ENST00000292562.7	-	5	609	c.334G>T	c.(334-336)Gaa>Taa	p.E112*	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	112					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E69*(1)		autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		GTTTTTACTTCTTCGGAAAAT	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											14	15	15					8																	145948711		1795	4053	5848	145919520	SO:0001587	stop_gained	90987			AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.334G>T	8.37:g.145948711C>A	ENSP00000292562:p.Glu112*		145919520	Q2M219	Nonsense_Mutation	SNP	ENST00000292562.7	37	CCDS47944.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.519153	0.44866	.	.	ENSG00000198169	ENST00000292562	.	.	.	1.97	1.97	0.26223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-0.2649	9.957	0.41673	0.0:1.0:0.0:0.0	.	.	.	.	X	112	.	ENSP00000292562:E112X	E	-	1	0	ZNF251	145919520	0.000000	0.05858	0.332000	0.25469	0.153000	0.21895	0.151000	0.16283	1.384000	0.46424	0.313000	0.20887	GAA		0.393	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		A	145948711	C	A	145948711	4	1	61	1	0	0	0	0	0	1	0	0	17835	922	32	2	1685	2	ZNF251	8	145948711	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	268	145948711	415311	6157	14142										
DOCK8	81704	broad.mit.edu	37	chr9	406981	406981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagatcgccagcatgttcGatctgacttccgagtaccgc	10	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:406981G>A	ENST00000453981.1	+	28	3554	c.3442G>A	c.(3442-3444)Gat>Aat	p.D1148N	DOCK8_ENST00000469391.1_Missense_Mutation_p.D1048N|DOCK8_ENST00000432829.2_Missense_Mutation_p.D1080N|DOCK8_ENST00000382329.1_Missense_Mutation_p.D615N			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1148					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D1148N(1)|p.D1080N(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CAGCATGTTCGATCTGACTTC	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	9											109	106	107					9																	406981		2203	4300	6503	396981	SO:0001583	missense	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.3442G>A	9.37:g.406981G>A	ENSP00000408464:p.Asp1148Asn		396981	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	36	5.690822	0.96793	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.62	5.62	0.85841	.	0.088085	0.85682	D	0.000000	T	0.37210	0.0995	M	0.74258	2.255	0.80722	D	1	D;P;D	0.54397	0.966;0.889;0.958	P;B;P	0.48114	0.533;0.428;0.567	T	0.13415	-1.0510	10	0.49607	T	0.09	.	20.0246	0.97519	0.0:0.0:1.0:0.0	.	1048;615;1148	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	N	1148;1116;1080;1048;615	ENSP00000408464:D1148N;ENSP00000394888:D1080N;ENSP00000419438:D1048N;ENSP00000371766:D615N	ENSP00000287364:D1116N	D	+	1	0	DOCK8	396981	1.000000	0.71417	0.983000	0.44433	0.951000	0.60555	9.603000	0.98315	2.810000	0.96702	0.650000	0.86243	GAT		0.537	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	406981	G	A	406981	3	1	61	1	0	0	0	0	1	0	0	0	4704	1058	37	1	3552	1	DOCK8	9	406981	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		406981	140806450	6158	14143										
DOCK8	81704	broad.mit.edu	37	chr9	439338	439338	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcaggccagtacttcaccGagagtggcctggtaggcctc	14	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:439338G>A	ENST00000453981.1	+	40	5285	c.5173G>A	c.(5173-5175)Gag>Aag	p.E1725K	DOCK8_ENST00000469391.1_Missense_Mutation_p.E1625K|DOCK8_ENST00000432829.2_Missense_Mutation_p.E1657K|DOCK8_ENST00000382329.1_Missense_Mutation_p.E1192K			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1725	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.E1657K(1)|p.E1725K(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GTACTTCACCGAGAGTGGCCT	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	9											71	66	68					9																	439338		2203	4300	6503	429338	SO:0001583	missense	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5173G>A	9.37:g.439338G>A	ENSP00000408464:p.Glu1725Lys		429338	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	34	5.308301	0.95629	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.20881	2.26;2.27;2.25;2.04	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.56307	0.1976	M	0.91300	3.195	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.71184	0.963;0.95;0.972	T	0.66964	-0.5790	10	0.72032	D	0.01	.	18.6173	0.91306	0.0:0.0:1.0:0.0	.	1625;1192;1725	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	K	1725;1693;1657;1625;1192	ENSP00000408464:E1725K;ENSP00000394888:E1657K;ENSP00000419438:E1625K;ENSP00000371766:E1192K	ENSP00000287364:E1693K	E	+	1	0	DOCK8	429338	1.000000	0.71417	0.996000	0.52242	0.738000	0.42128	9.150000	0.94667	2.624000	0.88883	0.655000	0.94253	GAG		0.617	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	439338	G	A	439338	3	1	61	1	0	0	0	0	1	0	0	0	4704	1059	37	1	5331	1	DOCK8	9	439338	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32357	439338	140774093	6159	14144										
DOCK8	81704	broad.mit.edu	37	chr9	441899	441899	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagagaatgtttggaaccTacttccgagttggtttcttt	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:441899T>C	ENST00000453981.1	+	42	5492	c.5380T>C	c.(5380-5382)Tac>Cac	p.Y1794H	DOCK8_ENST00000469391.1_Missense_Mutation_p.Y1694H|DOCK8_ENST00000432829.2_Missense_Mutation_p.Y1726H|DOCK8_ENST00000382329.1_Missense_Mutation_p.Y1261H			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1794	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Y1794H(1)|p.Y1726H(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GTTTGGAACCTACTTCCGAGT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	9											105	102	103					9																	441899		2203	4300	6503	431899	SO:0001583	missense	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5380T>C	9.37:g.441899T>C	ENSP00000408464:p.Tyr1794His		431899	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	T	26.4	4.734248	0.89482	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.55052	0.78;0.78;0.78;0.54	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.78654	0.4317	M	0.91717	3.235	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.83744	0.0205	10	0.87932	D	0	.	16.0399	0.80667	0.0:0.0:0.0:1.0	.	1694;1261;1794	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	H	1794;1762;1726;1694;1261	ENSP00000408464:Y1794H;ENSP00000394888:Y1726H;ENSP00000419438:Y1694H;ENSP00000371766:Y1261H	ENSP00000287364:Y1762H	Y	+	1	0	DOCK8	431899	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.043000	0.71004	2.371000	0.80710	0.533000	0.62120	TAC		0.433	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		C	441899	T	C	441899	3	2	61	1	0	0	0	0	1	0	0	0	4704	1522	53	4	5546	4	DOCK8	9	441899	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2561	441899	140771532	6160	14145										
KANK1	23189	broad.mit.edu	37	chr9	711610	711610	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagctggaggagcaggtgCgaaccatccctgtgctccag	15	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:711610C>T	ENST00000382303.1	+	7	1496	c.844C>T	c.(844-846)Cga>Tga	p.R282*	KANK1_ENST00000382297.2_Nonsense_Mutation_p.R282*|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Nonsense_Mutation_p.R124*	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	282					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.R124*(2)|p.R282*(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		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)		GGAGCAGGTGCGAACCATCCC	0.552																																																4	Substitution - Nonsense(4)	large_intestine(2)|autonomic_ganglia(2)	9											86	81	83					9																	711610		2203	4300	6503	701610	SO:0001587	stop_gained	23189			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.844C>T	9.37:g.711610C>T	ENSP00000371740:p.Arg282*		701610	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Nonsense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	44	10.749810	0.99461	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	.	.	.	5.93	1.47	0.22746	.	0.000000	0.49305	D	0.000149	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-1.3225	15.2745	0.73732	0.7335:0.2665:0.0:0.0	.	.	.	.	X	282;282;282;124	.	ENSP00000346479:R282X	R	+	1	2	KANK1	701610	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	4.504000	0.60414	0.362000	0.24319	0.655000	0.94253	CGA		0.552	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		T	711610	C	T	711610	4	4	61	1	0	0	0	0	0	1	0	0	7997	760	27	1	850	1	KANK1	9	711610	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	269711	711610	140501821	6161	14146										
DMRT3	58524	broad.mit.edu	37	chr9	990838	990838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagtaactctaccagcGtcttcagaagctcgcccgtc	7	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:990838G>A	ENST00000190165.2	+	2	1290	c.1252G>A	c.(1252-1254)Gtc>Atc	p.V418I		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	418					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V418I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CTCTACCAGCGTCTTCAGAAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											85	66	72					9																	990838		2203	4300	6503	980838	SO:0001583	missense	58524			AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"testis-specific protein"	614754	"DMRT-like family A3"	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1252G>A	9.37:g.990838G>A	ENSP00000190165:p.Val418Ile		980838	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209646	0.39003	.	.	ENSG00000064218	ENST00000190165	T	0.30714	1.52	5.22	2.37	0.29283	.	0.145948	0.45361	N	0.000365	T	0.17365	0.0417	L	0.32530	0.975	0.40341	D	0.979033	P	0.36144	0.539	B	0.19148	0.024	T	0.05241	-1.0897	10	0.52906	T	0.07	-20.7237	8.9089	0.35541	0.1365:0.1224:0.7411:0.0	.	418	Q9NQL9	DMRT3_HUMAN	I	418	ENSP00000190165:V418I	ENSP00000190165:V418I	V	+	1	0	DMRT3	980838	0.042000	0.20092	0.602000	0.28890	0.912000	0.54170	1.865000	0.39479	0.208000	0.20626	-0.126000	0.14955	GTC		0.542	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		A	990838	G	A	990838	3	1	61	1	0	0	0	0	1	0	0	0	4598	1145	40	1	1258	1	DMRT3	9	990838	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	279228	990838	140222593	6162	14147										
DMRT2	10655	broad.mit.edu	37	chr9	1056474	1056474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcccagtggaaccaccaaGcaaggacttctgtaattttt	8	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:1056474G>T	ENST00000358146.2	+	3	887	c.887G>T	c.(886-888)aGc>aTc	p.S296I	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.S296I|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.S296I			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	296					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S296I(1)		large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		GAACCACCAAGCAAGGACTTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											82	79	80					9																	1056474		2203	4300	6503	1046474	SO:0001583	missense	10655			AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"terra-like protein"	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.887G>T	9.37:g.1056474G>T	ENSP00000350865:p.Ser296Ile		1046474	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.296846	0.23650	.	.	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.25414	1.8;1.8;1.8	5.53	4.61	0.57282	.	0.234003	0.48767	D	0.000178	T	0.25419	0.0618	L	0.44542	1.39	0.30588	N	0.761822	D;P	0.62365	0.991;0.874	P;B	0.48873	0.593;0.277	T	0.16541	-1.0399	10	0.37606	T	0.19	-9.1326	6.7722	0.23601	0.3169:0.0:0.6831:0.0	.	296;140	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	I	296	ENSP00000371686:S296I;ENSP00000305785:S296I;ENSP00000350865:S296I	ENSP00000305785:S296I	S	+	2	0	DMRT2	1046474	0.980000	0.34600	0.959000	0.39883	0.100000	0.18952	0.893000	0.28336	1.285000	0.44548	0.585000	0.79938	AGC		0.493	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		T	1056474	G	T	1056474	3	4	61	1	0	0	0	0	1	0	0	0	4597	971	34	2	954	2	DMRT2	9	1056474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65636	1056474	140156957	6163	14148										
SMARCA2	6595	broad.mit.edu	37	chr9	2032957	2032957	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaaatgtttcagcccatCgatggtatacatgacaaggg	9	8	1	1	rs148086416	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2032957C>T	ENST00000382203.1	+	3	440	c.231C>T	c.(229-231)atC>atT	p.I77I	SMARCA2_ENST00000382194.1_Silent_p.I77I|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000349721.2_Silent_p.I77I|SMARCA2_ENST00000357248.2_Silent_p.I77I			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	77					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.I77I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		TTCAGCCCATCGATGGTATAC	0.438													C|||	6	0.00119808	0.0015	0.0043	5008	,	,		18138	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9						C	,	1,4405	2.1+/-5.4	0,1,2202	108	97	101		231,231	-11.6	0.2	9	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	77/1591,77/1573	2032957	2,13004	2203	4300	6503	2022957	SO:0001819	synonymous_variant	6595			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.231C>T	9.37:g.2032957C>T			2022957	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																				0.438	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		T	2032957	C	T	2032957	2	4	61	1	0	0	0	0	0	0	0	1	14806	874	31	1		1	SMARCA2	9	2032957	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	976483	2032957	139180474	6164	14149										
SMARCA2	6595	broad.mit.edu	37	chr9	2060894	2060894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaccttttgcagcagaccGatgagtatgtagccaatctg	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2060894G>A	ENST00000382203.1	+	9	1809	c.1600G>A	c.(1600-1602)Gat>Aat	p.D534N	SMARCA2_ENST00000382194.1_Missense_Mutation_p.D534N|SMARCA2_ENST00000349721.2_Missense_Mutation_p.D534N|SMARCA2_ENST00000357248.2_Missense_Mutation_p.D534N			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	534					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.D530N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GCAGCAGACCGATGAGTATGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	96	99					9																	2060894		2203	4300	6503	2050894	SO:0001583	missense	6595			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1600G>A	9.37:g.2060894G>A	ENSP00000371638:p.Asp534Asn		2050894	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	G	35	5.580897	0.96565	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.61426	0.2346	L	0.45137	1.4	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.994;0.985	T	0.53034	-0.8495	10	0.22706	T	0.39	-28.7058	18.8772	0.92343	0.0:0.0:1.0:0.0	.	135;534;534	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	N	534	ENSP00000265773:D534N;ENSP00000349788:D534N;ENSP00000392081:D534N;ENSP00000371638:D534N;ENSP00000371629:D534N	ENSP00000265773:D534N	D	+	1	0	SMARCA2	2050894	1.000000	0.71417	0.843000	0.33291	0.959000	0.62525	9.657000	0.98554	2.673000	0.90976	0.655000	0.94253	GAT		0.463	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2060894	G	A	2060894	3	1	61	1	0	0	0	0	1	0	0	0	14806	1058	37	1	1630	1	SMARCA2	9	2060894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27937	2060894	139152537	6165	14150										
SMARCA2	6595	broad.mit.edu	37	chr9	2086832	2086832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcttgtgttatagattCggtggaaatacatgatagtg	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2086832C>T	ENST00000382203.1	+	18	2739	c.2530C>T	c.(2530-2532)Cgg>Tgg	p.R844W	SMARCA2_ENST00000382194.1_Missense_Mutation_p.R844W|SMARCA2_ENST00000349721.2_Missense_Mutation_p.R844W|SMARCA2_ENST00000357248.2_Missense_Mutation_p.R844W			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	844	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.R840W(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GTTATAGATTCGGTGGAAATA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	77	78					9																	2086832		2203	4300	6503	2076832	SO:0001583	missense	6595			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.2530C>T	9.37:g.2086832C>T	ENSP00000371638:p.Arg844Trp		2076832	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831847	0.91036	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.8	4.9	0.64082	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.96291	0.8790	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.985;0.996;0.998	D	0.96768	0.9566	10	0.87932	D	0	-25.0753	16.4761	0.84132	0.1318:0.8682:0.0:0.0	.	445;844;844	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	W	844	ENSP00000265773:R844W;ENSP00000349788:R844W;ENSP00000371638:R844W;ENSP00000371629:R844W	ENSP00000265773:R844W	R	+	1	2	SMARCA2	2076832	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.019000	0.70818	1.436000	0.47453	0.650000	0.86243	CGG		0.468	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		T	2086832	C	T	2086832	3	4	61	1	0	0	0	0	1	0	0	0	14806	875	31	1	2596	1	SMARCA2	9	2086832	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25938	2086832	139126599	6166	14151										
VLDLR	7436	broad.mit.edu	37	chr9	2648774	2648774	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacctgaatgatgcccaaGacatcattgtctatcatgaa	6	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2648774G>T	ENST00000382100.3	+	14	2424	c.2068G>T	c.(2068-2070)Gac>Tac	p.D690Y	VLDLR_ENST00000382099.2_Missense_Mutation_p.D690Y	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	690					cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.D690Y(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TGATGCCCAAGACATCATTGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											122	110	114					9																	2648774		2203	4300	6503	2638774	SO:0001583	missense	7436				CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.2068G>T	9.37:g.2648774G>T	ENSP00000371532:p.Asp690Tyr		2638774	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991314	0.93106	.	.	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	D;D	0.96651	-4.08;-4.08	5.97	5.97	0.96955	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.56097	D	0.000029	D	0.98801	0.9596	M	0.94142	3.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.998;0.999	D	0.99023	1.0818	10	0.72032	D	0.01	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	690;690;690	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	Y	690;690;569	ENSP00000371532:D690Y;ENSP00000371531:D690Y	ENSP00000371524:D569Y	D	+	1	0	VLDLR	2638774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	2.836000	0.97738	0.655000	0.94253	GAC		0.443	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		T	2648774	G	T	2648774	3	4	61	1	0	0	0	0	1	0	0	0	17214	942	33	2	2122	2	VLDLR	9	2648774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	561942	2648774	138564657	6167	14152										
KCNV2	169522	broad.mit.edu	37	chr9	2729545	2729545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttgggatcattctcaacGggatgcccatttccatcctc	7	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2729545G>A	ENST00000382082.3	+	2	1694	c.1456G>A	c.(1456-1458)Ggg>Agg	p.G486R		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	486					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.G486R(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CATTCTCAACGGGATGCCCAT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	9											139	110	120					9																	2729545		2203	4300	6503	2719545	SO:0001583	missense	169522			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1456G>A	9.37:g.2729545G>A	ENSP00000371514:p.Gly486Arg		2719545	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.597802	0.87055	.	.	ENSG00000168263	ENST00000382082	D	0.97642	-4.47	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.98969	0.9649	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99429	1.0935	10	0.87932	D	0	.	19.47	0.94959	0.0:0.0:1.0:0.0	.	486	Q8TDN2	KCNV2_HUMAN	R	486	ENSP00000371514:G486R	ENSP00000371514:G486R	G	+	1	0	KCNV2	2719545	1.000000	0.71417	0.940000	0.37924	0.985000	0.73830	9.813000	0.99286	2.681000	0.91329	0.655000	0.94253	GGG		0.507	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		A	2729545	G	A	2729545	3	1	61	1	0	0	0	0	1	0	0	0	8116	1116	39	1	1462	1	KCNV2	9	2729545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80771	2729545	138483886	6168	14153										
KIAA0020	9933	broad.mit.edu	37	chr9	2837247	2837247	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgccggctggaatttgttCtttggtgatttgtccccttg	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:2837247C>A	ENST00000397885.2	-	3	443	c.237G>T	c.(235-237)aaG>aaT	p.K79N		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	79						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.K79N(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		GGAATTTGTTCTTTGGTGATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											280	265	270					9																	2837247		1859	4099	5958	2827247	SO:0001583	missense	9933			AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.237G>T	9.37:g.2837247C>A	ENSP00000380982:p.Lys79Asn		2827247	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	21.7	4.194424	0.78902	.	.	ENSG00000080608	ENST00000397885	D	0.86497	-2.13	4.55	4.55	0.56014	.	0.146210	0.45126	D	0.000393	T	0.79003	0.4373	L	0.29908	0.895	0.32546	N	0.533064	B	0.34200	0.441	B	0.28638	0.092	T	0.79112	-0.1937	10	0.18276	T	0.48	-18.0287	17.4585	0.87614	0.0:1.0:0.0:0.0	.	79	Q15397	K0020_HUMAN	N	79	ENSP00000380982:K79N	ENSP00000380982:K79N	K	-	3	2	KIAA0020	2827247	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.331000	0.59273	2.523000	0.85059	0.650000	0.86243	AAG		0.403	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		A	2837247	C	A	2837247	3	1	61	1	0	0	0	0	1	0	0	0	8173	912	32	2	1773	2	KIAA0020	9	2837247	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107702	2837247	138376184	6169	14154										
GLIS3	169792	broad.mit.edu	37	chr9	3856069	3856069	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggctgataggacttcaGgtgtgaacctgatggctgct	13	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:3856069G>A	ENST00000324333.10	-	8	2141	c.1948C>T	c.(1948-1950)Ctg>Ttg	p.L650L	GLIS3_ENST00000381971.3_Silent_p.L805L|GLIS3_ENST00000461870.1_5'UTR	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	650					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L650L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TAGGACTTCAGGTGTGAACCT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	9											161	154	156					9																	3856069		2203	4300	6503	3846069	SO:0001819	synonymous_variant	169792			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.1948C>T	9.37:g.3856069G>A			3846069	B1AL19|Q1PHK5	Silent	SNP	ENST00000324333.10	37	CCDS6451.1																																																																																				0.483	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		A	3856069	G	A	3856069	2	1	61	1	0	0	0	0	0	0	0	1	6467	991	35	3		3	GLIS3	9	3856069	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1018822	3856069	137357362	6170	14155										
GLIS3	169792	broad.mit.edu	37	chr9	4118183	4118183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccgggaactcctccaggCgttcggtcttgaacaggccg	13	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:4118183C>T	ENST00000324333.10	-	3	1023	c.830G>A	c.(829-831)cGc>cAc	p.R277H	GLIS3_ENST00000381971.3_Missense_Mutation_p.R432H	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	277					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R277H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		CTCCTCCAGGCGTTCGGTCTT	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	9											6	8	7					9																	4118183		1691	3386	5077	4108183	SO:0001583	missense	169792			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.830G>A	9.37:g.4118183C>T	ENSP00000325494:p.Arg277His		4108183	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.351725	0.61183	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11385	2.8;2.78	5.51	5.51	0.81932	.	0.000000	0.45606	D	0.000358	T	0.20373	0.0490	M	0.63428	1.95	0.27650	N	0.947427	D;D	0.64830	0.994;0.971	P;B	0.51415	0.669;0.374	T	0.05818	-1.0862	10	0.46703	T	0.11	.	13.1567	0.59522	0.0:0.9169:0.0:0.0831	.	432;277	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	H	277;432	ENSP00000325494:R277H;ENSP00000371398:R432H	ENSP00000325494:R277H	R	-	2	0	GLIS3	4108183	0.988000	0.35896	1.000000	0.80357	0.676000	0.39594	1.035000	0.30216	2.583000	0.87209	0.655000	0.94253	CGC		0.721	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		T	4118183	C	T	4118183	3	4	61	1	0	0	0	0	1	0	0	0	6467	768	27	1	1529	1	GLIS3	9	4118183	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	262114	4118183	137095248	6171	14156										
PPAPDC2	403313	broad.mit.edu	37	chr9	4662720	4662720	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgacctgtggctgtccaaGaagctgggggtgtgcgcggg	18	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:4662720G>T	ENST00000381883.2	+	1	423	c.345G>T	c.(343-345)aaG>aaT	p.K115N	SPATA6L_ENST00000381890.5_Intron|SPATA6L_ENST00000223517.5_Intron|SPATA6L_ENST00000454239.2_Intron|SPATA6L_ENST00000381895.5_Intron|SPATA6L_ENST00000475086.1_Intron	NM_203453.3	NP_982278.3	Q8IY26	PPAC2_HUMAN	phosphatidic acid phosphatase type 2 domain containing 2	115						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.K115N(1)		endometrium(1)|large_intestine(2)|lung(1)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.026)		GGCTGTCCAAGAAGCTGGGGG	0.682											OREG0019084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Melanoma(187;1057 3809 8526)											1	Substitution - Missense(1)	large_intestine(1)	9											35	36	36					9																	4662720		2203	4300	6503	4652720	SO:0001583	missense	403313			AK128369	CCDS34981.1	9p24	2010-04-23			ENSG00000205808	ENSG00000205808			23682	protein-coding gene	gene with protein product	"polyisoprenoid diphosphate phosphatase type 1"	611666				16464866	Standard	NM_203453		Approved	FLJ90191, FLJ46512, PDP1	uc003zin.4	Q8IY26	OTTHUMG00000019466	ENST00000381883.2:c.345G>T	9.37:g.4662720G>T	ENSP00000371307:p.Lys115Asn	620	4652720	B3KY05|Q5JVJ6|Q8NCK9	Missense_Mutation	SNP	ENST00000381883.2	37	CCDS34981.1	.	.	.	.	.	.	.	.	.	.	G	31	5.060166	0.93846	.	.	ENSG00000205808	ENST00000381883;ENST00000537542	T	0.17854	2.25	5.41	5.41	0.78517	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.37732	0.1014	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02933	-1.1092	10	0.72032	D	0.01	-24.7291	16.7297	0.85431	0.0:0.0:1.0:0.0	.	115	Q8IY26	PPAC2_HUMAN	N	115;24	ENSP00000371307:K115N	ENSP00000371307:K115N	K	+	3	2	PPAPDC2	4652720	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.183000	0.72002	2.798000	0.96311	0.655000	0.94253	AAG		0.682	PPAPDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051567.1	NM_203453		T	4662720	G	T	4662720	3	4	61	1	0	0	0	0	1	0	0	0	12326	933	33	2	347	2	PPAPDC2	9	4662720	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	544537	4662720	136550711	6172	14157										
JAK2	3717	broad.mit.edu	37	chr9	5064899	5064899	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggaaattgaacttagctCattaagggaagctttgtctt	9	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5064899C>A	ENST00000381652.3	+	9	1567	c.1073C>A	c.(1072-1074)tCa>tAa	p.S358*	JAK2_ENST00000539801.1_Nonsense_Mutation_p.S358*|JAK2_ENST00000544510.1_Nonsense_Mutation_p.S209*	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	358	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.S358*(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GAACTTAGCTCATTAAGGGAA	0.338		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	1	Substitution - Nonsense(1)	large_intestine(1)	9											95	94	94					9																	5064899		2202	4300	6502	5054899	SO:0001587	stop_gained	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1073C>A	9.37:g.5064899C>A	ENSP00000371067:p.Ser358*		5054899	O14636|O75297	Nonsense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	C	40	8.036297	0.98621	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	.	.	.	4.85	4.85	0.62838	.	0.263641	0.35096	N	0.003448	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8508	18.3218	0.90241	0.0:1.0:0.0:0.0	.	.	.	.	X	358;358;209	.	ENSP00000371067:S358X	S	+	2	0	JAK2	5054899	0.467000	0.25831	1.000000	0.80357	0.918000	0.54935	2.336000	0.43938	2.412000	0.81896	0.313000	0.20887	TCA		0.338	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			A	5064899	C	A	5064899	4	1	61	1	0	0	0	0	0	1	0	0	7959	838	29	2	1099	2	JAK2	9	5064899	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402179	5064899	136148532	6173	14158										
JAK2	3717	broad.mit.edu	37	chr9	5069145	5069145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgaattgttaccagatgGaaactgttcgctcagacaat	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5069145G>A	ENST00000381652.3	+	11	1944	c.1450G>A	c.(1450-1452)Gaa>Aaa	p.E484K	JAK2_ENST00000539801.1_Missense_Mutation_p.E484K|JAK2_ENST00000544510.1_Missense_Mutation_p.E335K	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	484					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.E484K(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTACCAGATGGAAACTGTTCG	0.338		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	1	Substitution - Missense(1)	large_intestine(1)	9											73	73	73					9																	5069145		2203	4299	6502	5059145	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1450G>A	9.37:g.5069145G>A	ENSP00000371067:p.Glu484Lys		5059145	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023325	0.54683	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.25579	1.79;1.79;1.79	4.81	4.81	0.61882	SH2 motif (2);	0.000000	0.85682	D	0.000000	T	0.30916	0.0780	M	0.68317	2.08	0.80722	D	1	P	0.46512	0.879	B	0.40782	0.34	T	0.13899	-1.0492	10	0.30078	T	0.28	-19.2903	17.8943	0.88881	0.0:0.0:1.0:0.0	.	484	O60674	JAK2_HUMAN	K	484;484;335	ENSP00000440387:E484K;ENSP00000371067:E484K;ENSP00000443103:E335K	ENSP00000371067:E484K	E	+	1	0	JAK2	5059145	1.000000	0.71417	1.000000	0.80357	0.165000	0.22458	9.427000	0.97472	2.198000	0.70561	0.591000	0.81541	GAA		0.338	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			A	5069145	G	A	5069145	3	1	61	1	0	0	0	0	1	0	0	0	7959	1175	41	3	1484	3	JAK2	9	5069145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4246	5069145	136144286	6174	14159										
JAK2	3717	broad.mit.edu	37	chr9	5089745	5089745	+	Frame_Shift_Del	DEL	A	A	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggggaggtggtcgctgtAaaaaagcttcagcatagtac							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5089745delA	ENST00000381652.3	+	20	3137	c.2643delA	c.(2641-2643)gtafs	p.V881fs	JAK2_ENST00000539801.1_Frame_Shift_Del_p.V881fs|JAK2_ENST00000544510.1_Frame_Shift_Del_p.V732fs	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	881	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.K883fs*10(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGGTCGCTGTAAAAAAGCTTC	0.433		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	1	Deletion - Frameshift(1)	large_intestine(1)	9											138	125	129					9																	5089745		2203	4300	6503	5079745	SO:0001589	frameshift_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2643delA	9.37:g.5089745delA	ENSP00000371067:p.Val881fs		5079745	O14636|O75297	Frame_Shift_Del	DEL	ENST00000381652.3	37	CCDS6457.1																																																																																				0.433	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			-	5089745	A	-	5089745	7	5	61	1	0	1	0	1	0	0	0	0	7959	349	13	0	2713	0	JAK2	9	5089745	Frame_Shift_Del	DEL	A	TCGA-AG-A002-01A-01W-A00K-09	20600	5089745	136123686	6175	14160										
RLN1	6013	broad.mit.edu	37	chr9	5335270	5335270	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagcaatatttagcaagaGaccttttggtacaaccaatt	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5335270G>T	ENST00000223862.1	-	2	665	c.539C>A	c.(538-540)tCt>tAt	p.S180Y	RLN1_ENST00000223858.4_3'UTR|RLN1_ENST00000487557.2_5'UTR	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	180					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.S180Y(1)		large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		TTTAGCAAGAGACCTTTTGGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	75	77					9																	5335270		2203	4300	6503	5325270	SO:0001583	missense	6013				CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"Endogenous ligands"	10026	protein-coding gene	gene with protein product	"prorelaxin H1"	179730	"relaxin 1 (H1)"				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.539C>A	9.37:g.5335270G>T	ENSP00000223862:p.Ser180Tyr		5325270	Q99936|Q9UQJ1	Missense_Mutation	SNP	ENST00000223862.1	37	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	G	0.181	-1.062124	0.01950	.	.	ENSG00000107018	ENST00000223862	D	0.84442	-1.85	2.62	-5.24	0.02789	Insulin, conserved site (1);Insulin-like (4);	1.070350	0.07374	N	0.886332	T	0.73410	0.3583	L	0.42245	1.32	0.09310	N	1	B	0.13594	0.008	B	0.17433	0.018	T	0.54781	-0.8242	10	0.27785	T	0.31	.	2.1899	0.03896	0.203:0.128:0.4664:0.2027	.	180	P04808	REL1_HUMAN	Y	180	ENSP00000223862:S180Y	ENSP00000223862:S180Y	S	-	2	0	RLN1	5325270	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.250000	0.08830	-1.535000	0.01740	-0.926000	0.02714	TCT		0.383	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1			T	5335270	G	T	5335270	3	4	61	1	0	0	0	0	1	0	0	0	13428	942	33	2	22	2	RLN1	9	5335270	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	245525	5335270	135878161	6176	14161										
CD274	29126	broad.mit.edu	37	chr9	5466805	5466805	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaaaatgtggcatccaaGatacaaactcaaagaagcaa	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5466805G>T	ENST00000381577.3	+	6	912	c.826G>T	c.(826-828)Gat>Tat	p.D276Y	CD274_ENST00000498261.1_3'UTR|CD274_ENST00000381573.4_Missense_Mutation_p.D162Y	NM_014143.3	NP_054862.1	Q9NZQ7	PD1L1_HUMAN	CD274 molecule	276					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D276Y(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		TGGCATCCAAGATACAAACTC	0.348			T	CIITA	"PMBL, Hodgkin Lymphona, "																																		Dom	yes		9	9p24	29126	CD274 molecule		L	1	Substitution - Missense(1)	large_intestine(1)	9											126	120	122					9																	5466805		2203	4300	6503	5456805	SO:0001583	missense	29126			AF177937	CCDS6464.1, CCDS59118.1	9p24.1	2014-01-30	2006-03-28	2005-02-25	ENSG00000120217	ENSG00000120217		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Endogenous ligands"	17635	protein-coding gene	gene with protein product	"B7 homolog 1"	605402	"programmed cell death 1 ligand 1", "CD274 antigen"	PDCD1LG1		11015443, 10581077	Standard	NM_014143		Approved	B7-H, B7H1, PD-L1, PDL1, B7-H1	uc003zje.3	Q9NZQ7	OTTHUMG00000019503	ENST00000381577.3:c.826G>T	9.37:g.5466805G>T	ENSP00000370989:p.Asp276Tyr		5456805	B2RBA2|B4DU27|Q14CJ2|Q2V8D5|Q66RK1|Q6WEX4|Q9NUZ5	Missense_Mutation	SNP	ENST00000381577.3	37	CCDS6464.1	.	.	.	.	.	.	.	.	.	.	G	7.492	0.650921	0.14516	.	.	ENSG00000120217	ENST00000381573;ENST00000381577	T;T	0.38240	1.15;5.18	4.16	2.34	0.29019	.	0.463942	0.19810	N	0.105544	T	0.33177	0.0854	L	0.36672	1.1	0.09310	N	1	D;B	0.58970	0.984;0.303	P;B	0.50440	0.641;0.172	T	0.10520	-1.0626	10	0.72032	D	0.01	-8.3026	6.4937	0.22130	0.2158:0.0:0.7842:0.0	.	162;276	Q2V8D5;Q9NZQ7	.;PD1L1_HUMAN	Y	162;276	ENSP00000370985:D162Y;ENSP00000370989:D276Y	ENSP00000370985:D162Y	D	+	1	0	CD274	5456805	0.008000	0.16893	0.002000	0.10522	0.008000	0.06430	0.629000	0.24538	0.718000	0.32166	-0.258000	0.10820	GAT		0.348	CD274-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051631.2	NM_014143		T	5466805	G	T	5466805	3	4	61	1	0	0	0	0	1	0	0	0	2997	942	33	2	844	2	CD274	9	5466805	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131535	5466805	135746626	6177	14162										
KIAA1432	57589	broad.mit.edu	37	chr9	5772740	5772740	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaatcccaggtccagcttCggtgagtttcttggctattt	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5772740C>T	ENST00000414202.2	+	24	3984	c.3793C>T	c.(3793-3795)Cgg>Tgg	p.R1265W	KIAA1432_ENST00000418622.3_Splice_Site_p.R1186W|KIAA1432_ENST00000449720.2_Splice_Site_p.R1149W	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2												p.R1186W(2)		breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GGTCCAGCTTCGGTGAGTTTC	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	9											51	50	50					9																	5772740		2203	4300	6503	5762740	SO:0001630	splice_region_variant	57589																														ENST00000414202.2:c.3794+1C>T	9.37:g.5772740C>T			5762740		Missense_Mutation	SNP	ENST00000414202.2	37	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.45|19.45	3.829814|3.829814	0.71258|0.71258	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000414202;ENST00000418622;ENST00000449720;ENST00000490816|ENST00000545641	.|.	.|.	.|.	5.66|5.66	3.79|3.79	0.43588|0.43588	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71143|0.71143	0.3305|0.3305	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.69781|0.69781	-0.5052|-0.5052	9|5	0.87932|.	D|.	0|.	-18.0482|-18.0482	14.9079|14.9079	0.70733|0.70733	0.3725:0.6274:0.0:0.0|0.3725:0.6274:0.0:0.0	.|.	1149;1265|.	B7ZM67;Q4ADV7|.	.;RIC1_HUMAN|.	W|L	1265;1186;1149;84|1156	.|.	ENSP00000416696:R1265W|.	R|S	+|+	1|2	2|0	KIAA1432|KIAA1432	5762740|5762740	0.977000|0.977000	0.34250|0.34250	0.977000|0.977000	0.42913|0.42913	0.949000|0.949000	0.60115|0.60115	2.465000|2.465000	0.45075|0.45075	0.718000|0.718000	0.32166|0.32166	0.561000|0.561000	0.74099|0.74099	CGG|TCG		0.438	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		Missense_Mutation	T	5772740	C	T	5772740	5	4	61	1	0	0	0	0	0	0	1	0	8254	898	31	1	3720	1	KIAA1432	9	5772740	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	305935	5772740	135440691	6178	14163										
ERMP1	79956	broad.mit.edu	37	chr9	5812130	5812130	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattggaataccaacctgctCtctgaatggaatctgttaga	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5812130C>A	ENST00000339450.5	-	6	1198	c.1109G>T	c.(1108-1110)aGa>aTa	p.R370I	ERMP1_ENST00000543230.1_5'Flank|ERMP1_ENST00000381506.3_Missense_Mutation_p.R146I|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	370						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.R370I(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		CCAACCTGCTCTCTGAATGGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											146	150	148					9																	5812130		2203	4300	6503	5802130	SO:0001583	missense	79956			AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1109G>T	9.37:g.5812130C>A	ENSP00000340427:p.Arg370Ile		5802130	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	C	34	5.370796	0.95923	.	.	ENSG00000099219	ENST00000339450;ENST00000381506	T	0.49720	0.77	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.67458	0.2895	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67937	-0.5541	10	0.59425	D	0.04	-18.2006	19.4394	0.94811	0.0:1.0:0.0:0.0	.	370	Q7Z2K6	ERMP1_HUMAN	I	370;146	ENSP00000340427:R370I	ENSP00000340427:R370I	R	-	2	0	ERMP1	5802130	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.476000	0.81055	2.581000	0.87130	0.655000	0.94253	AGA		0.343	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		A	5812130	C	A	5812130	3	1	61	1	0	0	0	0	1	0	0	0	5249	913	32	2	1645	2	ERMP1	9	5812130	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39390	5812130	135401301	6179	14164										
MLANA	2315	broad.mit.edu	37	chr9	5897569	5897569	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggccagggccgctgggatCggcatcctgacagtgatcct	15	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5897569C>T	ENST00000381477.3	+	3	250	c.90C>T	c.(88-90)atC>atT	p.I30I	MLANA_ENST00000381476.1_Silent_p.I30I|KIAA2026_ENST00000443149.2_5'Flank|MLANA_ENST00000490518.1_3'UTR|MLANA_ENST00000381471.1_Silent_p.I30I	NM_005511.1	NP_005502.1	Q16655	MAR1_HUMAN	melan-A	30						endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|melanosome (GO:0042470)|trans-Golgi network (GO:0005802)		p.I30I(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	8		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		CCGCTGGGATCGGCATCCTGA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	9											159	146	150					9																	5897569		2203	4300	6503	5887569	SO:0001819	synonymous_variant	2315				CCDS6466.1	9p24.1	2008-02-05			ENSG00000120215	ENSG00000120215			7124	protein-coding gene	gene with protein product		605513					Standard	NM_005511		Approved	MART1	uc003zjo.1	Q16655	OTTHUMG00000019510	ENST00000381477.3:c.90C>T	9.37:g.5897569C>T			5887569	Q6ICU4	Silent	SNP	ENST00000381477.3	37	CCDS6466.1																																																																																				0.448	MLANA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051643.1			T	5897569	C	T	5897569	2	4	61	1	0	0	0	0	0	0	0	1	9641	874	31	1		1	MLANA	9	5897569	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85439	5897569	135315862	6180	14165										
MLANA	2315	broad.mit.edu	37	chr9	5897631	5897631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttggtattgtagaagacGaaatggatacagagccttga	12	5	0	4	rs142544535		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5897631G>A	ENST00000381477.3	+	3	312	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	MLANA_ENST00000381476.1_Missense_Mutation_p.R51Q|KIAA2026_ENST00000443149.2_5'Flank|MLANA_ENST00000490518.1_3'UTR|MLANA_ENST00000381471.1_Missense_Mutation_p.R51Q	NM_005511.1	NP_005502.1	Q16655	MAR1_HUMAN	melan-A	51						endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|melanosome (GO:0042470)|trans-Golgi network (GO:0005802)		p.R51Q(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	8		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		TGTAGAAGACGAAATGGATAC	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	9						G	GLN/ARG	0,4406		0,0,2203	168	155	159		152	5	1	9	dbSNP_134	159	1,8599	1.2+/-3.3	0,1,4299	no	missense	MLANA	NM_005511.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	51/119	5897631	1,13005	2203	4300	6503	5887631	SO:0001583	missense	2315				CCDS6466.1	9p24.1	2008-02-05			ENSG00000120215	ENSG00000120215			7124	protein-coding gene	gene with protein product		605513					Standard	NM_005511		Approved	MART1	uc003zjo.1	Q16655	OTTHUMG00000019510	ENST00000381477.3:c.152G>A	9.37:g.5897631G>A	ENSP00000370886:p.Arg51Gln		5887631	Q6ICU4	Missense_Mutation	SNP	ENST00000381477.3	37	CCDS6466.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.861265	0.32884	0.0	1.16E-4	ENSG00000120215	ENST00000381477;ENST00000381476;ENST00000381471	.	.	.	5.93	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.47967	0.1474	M	0.71581	2.175	0.34257	D	0.679496	P	0.44986	0.847	B	0.34722	0.188	T	0.68116	-0.5494	9	0.87932	D	0	-10.6036	11.0406	0.47829	0.0849:0.0:0.9151:0.0	.	51	Q16655	MAR1_HUMAN	Q	51	.	ENSP00000370880:R51Q	R	+	2	0	MLANA	5887631	1.000000	0.71417	0.993000	0.49108	0.005000	0.04900	2.425000	0.44723	1.512000	0.48834	-0.136000	0.14681	CGA		0.512	MLANA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051643.1			A	5897631	G	A	5897631	3	1	61	1	0	0	0	0	1	0	0	0	9641	1058	37	1	158	1	MLANA	9	5897631	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	5897631	135315800	6181	14166										
KIAA2026	158358	broad.mit.edu	37	chr9	5920353	5920353	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaccaggtgccaaaggtgtActggtattgatgactatttt	11	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5920353A>G	ENST00000399933.3	-	8	5642	c.5643T>C	c.(5641-5643)agT>agC	p.S1881S	KIAA2026_ENST00000381461.2_Silent_p.S1851S	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1881								p.S1056S(1)|p.S1881S(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CCAAAGGTGTACTGGTATTGA	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	9											168	169	169					9																	5920353		1956	4160	6116	5910353	SO:0001819	synonymous_variant	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.5643T>C	9.37:g.5920353A>G			5910353	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																					0.448	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5920353	A	G	5920353	2	3	61	1	0	0	0	0	0	0	0	1	8291	388	14	4		4	KIAA2026	9	5920353	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22722	5920353	135293078	6182	14167										
KIAA2026	158358	broad.mit.edu	37	chr9	5921062	5921062	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttactgctcttgctgaaGaaaccactgattcattaaca	5	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5921062G>T	ENST00000399933.3	-	8	4933	c.4934C>A	c.(4933-4935)tCt>tAt	p.S1645Y	KIAA2026_ENST00000381461.2_Missense_Mutation_p.S1615Y	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1645								p.S1645Y(1)|p.S820Y(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TCTTGCTGAAGAAACCACTGA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	9											100	96	97					9																	5921062		1854	4098	5952	5911062	SO:0001583	missense	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4934C>A	9.37:g.5921062G>T	ENSP00000382815:p.Ser1645Tyr		5911062	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.332870	0.60853	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.65	4.65	0.58169	.	0.227969	0.30473	N	0.009555	T	0.34832	0.0911	L	0.27053	0.805	0.24306	N	0.995101	D	0.54207	0.965	P	0.51135	0.66	T	0.17137	-1.0379	9	0.62326	D	0.03	-8.2055	11.6682	0.51387	0.0941:0.0:0.9059:0.0	.	1645	Q5HYC2	K2026_HUMAN	Y	1645;1615	.	ENSP00000370870:S1615Y	S	-	2	0	KIAA2026	5911062	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	3.023000	0.49666	2.420000	0.82092	0.591000	0.81541	TCT		0.423	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		T	5921062	G	T	5921062	3	4	61	1	0	0	0	0	1	0	0	0	8291	942	33	2	1381	2	KIAA2026	9	5921062	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	709	5921062	135292369	6183	14168										
KIAA2026	158358	broad.mit.edu	37	chr9	5922155	5922155	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacctcgtgtcctaacaaGaattgactgtgaatctctta	6	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5922155G>A	ENST00000399933.3	-	8	3840	c.3841C>T	c.(3841-3843)Ctt>Ttt	p.L1281F	KIAA2026_ENST00000381461.2_Missense_Mutation_p.L1251F	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1281								p.L456F(1)|p.L1281F(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GTCCTAACAAGAATTGACTGT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	9											130	120	123					9																	5922155		1897	4123	6020	5912155	SO:0001583	missense	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3841C>T	9.37:g.5922155G>A	ENSP00000382815:p.Leu1281Phe		5912155	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		.	.	.	.	.	.	.	.	.	.	G	17.38	3.375236	0.61735	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000013	T	0.65923	0.2738	L	0.29908	0.895	0.44816	D	0.99782	D	0.89917	1.0	D	0.91635	0.999	T	0.64655	-0.6356	9	0.34782	T	0.22	-10.3327	17.7075	0.88312	0.0:0.0:1.0:0.0	.	1281	Q5HYC2	K2026_HUMAN	F	1281;1251	.	ENSP00000370870:L1251F	L	-	1	0	KIAA2026	5912155	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.357000	0.79456	2.428000	0.82296	0.555000	0.69702	CTT		0.408	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		A	5922155	G	A	5922155	3	1	61	1	0	0	0	0	1	0	0	0	8291	942	33	3	2474	3	KIAA2026	9	5922155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1093	5922155	135291276	6184	14169										
KIAA2026	158358	broad.mit.edu	37	chr9	5922336	5922336	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgaagcactgggcaaggaGaatgtggctgctgaaactgc	16	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:5922336G>T	ENST00000399933.3	-	8	3659	c.3660C>A	c.(3658-3660)ttC>ttA	p.F1220L	KIAA2026_ENST00000381461.2_Missense_Mutation_p.F1190L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1220								p.F395L(1)|p.F1220L(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TGGGCAAGGAGAATGTGGCTG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	9											99	98	98					9																	5922336		2062	4208	6270	5912336	SO:0001583	missense	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3660C>A	9.37:g.5922336G>T	ENSP00000382815:p.Phe1220Leu		5912336	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		.	.	.	.	.	.	.	.	.	.	G	7.962	0.747100	0.15710	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.99	2.1	0.27182	.	0.533626	0.18448	N	0.140904	T	0.18425	0.0442	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17561	-1.0365	9	0.18276	T	0.48	-1.5147	1.9016	0.03269	0.2181:0.2482:0.4064:0.1273	.	1220	Q5HYC2	K2026_HUMAN	L	1220;1190	.	ENSP00000370870:F1190L	F	-	3	2	KIAA2026	5912336	0.603000	0.26924	0.380000	0.26093	0.705000	0.40729	0.049000	0.14099	0.279000	0.22186	0.555000	0.69702	TTC		0.463	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		T	5922336	G	T	5922336	3	4	61	1	0	0	0	0	1	0	0	0	8291	933	33	2	2655	2	KIAA2026	9	5922336	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	181	5922336	135291095	6185	14170										
RANBP6	26953	broad.mit.edu	37	chr9	6012674	6012674	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctattgctgagatacagttCtctgtagcaatgacattttt	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:6012674C>A	ENST00000259569.5	-	1	2944	c.2934G>T	c.(2932-2934)gaG>gaT	p.E978D	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	978					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E978D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		AGATACAGTTCTCTGTAGCAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											116	108	111					9																	6012674		2203	4300	6503	6002674	SO:0001583	missense	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2934G>T	9.37:g.6012674C>A	ENSP00000259569:p.Glu978Asp		6002674	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	37	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.216163	0.39201	.	.	ENSG00000137040	ENST00000259569	T	0.06768	3.26	4.79	1.98	0.26296	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.11024	0.0269	L	0.47078	1.49	0.58432	D	0.999999	D;D;D	0.59357	0.985;0.985;0.965	P;P;P	0.58013	0.831;0.728;0.62	T	0.36212	-0.9757	10	0.02654	T	1	-10.0109	6.578	0.22577	0.0:0.6266:0.0:0.3734	.	145;566;978	B4E340;B4DTX6;O60518	.;.;RNBP6_HUMAN	D	978	ENSP00000259569:E978D	ENSP00000259569:E978D	E	-	3	2	RANBP6	6002674	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.988000	0.29616	0.490000	0.27771	0.655000	0.94253	GAG		0.363	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		A	6012674	C	A	6012674	3	1	61	1	0	0	0	0	1	0	0	0	13068	912	32	2	387	2	RANBP6	9	6012674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90338	6012674	135200757	6186	14171										
RANBP6	26953	broad.mit.edu	37	chr9	6015324	6015324	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagttcaatcttgacatctCtctgaacatcagcaggcaga	7	11	6	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:6015324C>A	ENST00000259569.5	-	1	294	c.284G>T	c.(283-285)aGa>aTa	p.R95I	RANBP6_ENST00000485372.1_Intron	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	95					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R95I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CTTGACATCTCTCTGAACATC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	85	85					9																	6015324		2203	4300	6503	6005324	SO:0001583	missense	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.284G>T	9.37:g.6015324C>A	ENSP00000259569:p.Arg95Ile		6005324	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	37	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527131	0.27299	.	.	ENSG00000137040	ENST00000259569	T	0.67865	-0.29	4.39	4.39	0.52855	Armadillo-like helical (1);Armadillo-type fold (1);	0.215729	0.46145	D	0.000316	T	0.38241	0.1033	N	0.01874	-0.695	0.44289	D	0.99715	B	0.09022	0.002	B	0.01281	0.0	T	0.31613	-0.9937	10	0.41790	T	0.15	-7.9498	10.7292	0.46087	0.0:0.8073:0.1927:0.0	.	95	O60518	RNBP6_HUMAN	I	95	ENSP00000259569:R95I	ENSP00000259569:R95I	R	-	2	0	RANBP6	6005324	0.997000	0.39634	1.000000	0.80357	0.981000	0.71138	1.794000	0.38774	2.733000	0.93635	0.561000	0.74099	AGA		0.448	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		A	6015324	C	A	6015324	3	1	61	1	0	0	0	0	1	0	0	0	13068	913	32	2	3037	2	RANBP6	9	6015324	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2650	6015324	135198107	6187	14172										
TPD52L3	89882	broad.mit.edu	37	chr9	6330998	6330998	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatcttcaataaatacacGttaaatcaaggaaggaatta	6	5	3	1	rs192550349		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:6330998G>A	ENST00000344545.5	+	0	2572				TPD52L3_ENST00000314556.3_Silent_p.T130T	NM_033516.5	NP_277051	Q96J77	TPD55_HUMAN	tumor protein D52-like 3									p.T130T(2)		large_intestine(1)|lung(9)|skin(1)	11		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0198)|Lung(218;0.1)		ATAAATACACGTTAAATCAAG	0.313													G|||	1	0.000199681	0	0	5008	,	,		20283	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	9											102	101	101					9																	6330998		2202	4298	6500	6320998	SO:0001628	intergenic_variant	89882			AY032877	CCDS34984.1, CCDS34985.1, CCDS34986.1	9p24.1	2008-02-05			ENSG00000170777	ENSG00000170777			23382	protein-coding gene	gene with protein product							Standard	NM_033516		Approved	NYD-SP25	uc003zjw.3	Q96J77	OTTHUMG00000019518		9.37:g.6330998G>A			6320998	Q5TCR3|Q5TCR4|Q5TCR5|Q8N4P5|Q8WWF7|Q96M09	Silent	SNP	ENST00000344545.5	37	CCDS34986.1																																																																																				0.313	TPD52L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051658.1	NM_033516		A	6330998	G	A	6330998	1	1	61	0	1	0	0	0	0	0	0	0	16440	1132	40	1		1	TPD52L3	9	6330998	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315674	6330998	134882433	6188	14173										
GLDC	2731	broad.mit.edu	37	chr9	6604606	6604606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttgttacccccaccattCttccaggcatcattctcacc	3	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:6604606C>A	ENST00000321612.6	-	7	1190	c.1040G>T	c.(1039-1041)aGa>aTa	p.R347I		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	347					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)	p.R347I(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	CCCCACCATTCTTCCAGGCAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	84	82					9																	6604606		2203	4300	6503	6594606	SO:0001583	missense	2731			D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1040G>T	9.37:g.6604606C>A	ENSP00000370737:p.Arg347Ile		6594606	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	37	CCDS34987.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774774	0.90108	.	.	ENSG00000178445	ENST00000321612	D	0.98296	-4.85	5.25	5.25	0.73442	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Glycine cleavage system P-protein, N-terminal (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.99477	0.9814	H	0.98769	4.325	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.98016	1.0368	10	0.87932	D	0	-20.4403	19.1956	0.93686	0.0:1.0:0.0:0.0	.	347	P23378	GCSP_HUMAN	I	347	ENSP00000370737:R347I	ENSP00000370737:R347I	R	-	2	0	GLDC	6594606	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.270000	0.78493	2.615000	0.88500	0.591000	0.81541	AGA		0.458	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6604606	C	A	6604606	3	1	61	1	0	0	0	0	1	0	0	0	6453	913	32	2	2098	2	GLDC	9	6604606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	273608	6604606	134608825	6189	14174										
KDM4C	23081	broad.mit.edu	37	chr9	6880041	6880041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccggagcatggaaaacGacttgaaagactagctcaag	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:6880041G>A	ENST00000381309.3	+	6	1224	c.659G>A	c.(658-660)cGa>cAa	p.R220Q	KDM4C_ENST00000442236.2_Missense_Mutation_p.R39Q|KDM4C_ENST00000536108.1_Missense_Mutation_p.R39Q|KDM4C_ENST00000381306.3_Missense_Mutation_p.R220Q|KDM4C_ENST00000543771.1_Missense_Mutation_p.R220Q|KDM4C_ENST00000535193.1_Missense_Mutation_p.R242Q|KDM4C_ENST00000489243.1_3'UTR	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	220	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)	p.R220Q(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CATGGAAAACGACTTGAAAGA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	9											64	64	64					9																	6880041		2203	4299	6502	6870041	SO:0001583	missense	23081			AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.659G>A	9.37:g.6880041G>A	ENSP00000370710:p.Arg220Gln		6870041	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	36	5.731119	0.96856	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108	T;T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6;-0.6	5.16	5.16	0.70880	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.153645	0.46442	D	0.000287	D	0.83852	0.5344	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.993;0.978;0.992;1.0	D;D;P;B;P;D	0.77557	0.99;0.989;0.768;0.399;0.75;0.962	D	0.85362	0.1108	10	0.87932	D	0	-0.0458	18.8266	0.92122	0.0:0.0:1.0:0.0	.	39;220;220;242;220;220	E7EV17;F5H347;B4E1Y4;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;.;KDM4C_HUMAN;.	Q	242;220;220;220;39;39	ENSP00000442382:R242Q;ENSP00000445427:R220Q;ENSP00000370710:R220Q;ENSP00000370707:R220Q;ENSP00000409353:R39Q;ENSP00000440656:R39Q	ENSP00000370707:R220Q	R	+	2	0	KDM4C	6870041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.040000	0.93783	2.677000	0.91161	0.591000	0.81541	CGA		0.303	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		A	6880041	G	A	6880041	3	1	61	1	0	0	0	0	1	0	0	0	8151	1058	37	1	747	1	KDM4C	9	6880041	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	275435	6880041	134333390	6190	14175										
KDM4C	23081	broad.mit.edu	37	chr9	7013848	7013848	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaattagatgaagtcgttAcatcggagggaaagactaag	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:7013848A>G	ENST00000381309.3	+	14	2594	c.2029A>G	c.(2029-2031)Aca>Gca	p.T677A	KDM4C_ENST00000442236.2_Missense_Mutation_p.T422A|KDM4C_ENST00000536108.1_Missense_Mutation_p.T496A|KDM4C_ENST00000381306.3_Missense_Mutation_p.T677A|KDM4C_ENST00000543771.1_Missense_Mutation_p.T677A|KDM4C_ENST00000428870.2_Missense_Mutation_p.T364A|KDM4C_ENST00000535193.1_Missense_Mutation_p.T699A	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	677					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)	p.T677A(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						TGAAGTCGTTACATCGGAGGG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	115	117					9																	7013848		2203	4300	6503	7003848	SO:0001583	missense	23081			AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2029A>G	9.37:g.7013848A>G	ENSP00000370710:p.Thr677Ala		7003848	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.910849	0.00508	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870;ENST00000420847	T;T;T;T;T;T;T;T	0.17213	2.39;2.4;2.56;2.47;2.78;2.29;3.57;2.84	4.89	-0.839	0.10759	.	1.039740	0.07467	N	0.901564	T	0.06416	0.0165	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.12013	0.005;0.0;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.002;0.002;0.0;0.002	T	0.39121	-0.9629	10	0.07644	T	0.81	.	0.4012	0.00426	0.3739:0.2288:0.1881:0.2091	.	422;677;699;677;677	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	A	699;677;677;677;422;496;364;21	ENSP00000442382:T699A;ENSP00000445427:T677A;ENSP00000370710:T677A;ENSP00000370707:T677A;ENSP00000409353:T422A;ENSP00000440656:T496A;ENSP00000405739:T364A;ENSP00000400127:T21A	ENSP00000370707:T677A	T	+	1	0	KDM4C	7003848	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.136000	0.10405	-0.007000	0.14345	0.477000	0.44152	ACA		0.383	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		G	7013848	A	G	7013848	3	3	61	1	0	0	0	0	1	0	0	0	8151	391	14	4	2149	4	KDM4C	9	7013848	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	133807	7013848	134199583	6191	14176										
PTPRD	5789	broad.mit.edu	37	chr9	8518036	8518036	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccattgtataataaactCtatatccttggatctgtcca	5	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:8518036C>A	ENST00000381196.4	-	18	1898	c.1355G>T	c.(1354-1356)aGa>aTa	p.R452I	PTPRD_ENST00000358503.5_Missense_Mutation_p.R439I|PTPRD_ENST00000540109.1_Missense_Mutation_p.R452I|PTPRD_ENST00000356435.5_Missense_Mutation_p.R452I|PTPRD_ENST00000360074.4_Missense_Mutation_p.R439I|PTPRD_ENST00000397606.3_Missense_Mutation_p.R442I|PTPRD_ENST00000397617.3_Missense_Mutation_p.R442I|PTPRD_ENST00000537002.1_Missense_Mutation_p.R449I|PTPRD_ENST00000397611.3_Missense_Mutation_p.R449I|PTPRD_ENST00000486161.1_Missense_Mutation_p.R452I|PTPRD_ENST00000355233.5_Missense_Mutation_p.R452I	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	452	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R452I(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		ATAATAAACTCTATATCCTTG	0.458										TSP Lung(15;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	9											300	268	279					9																	8518036		2203	4300	6503	8508036	SO:0001583	missense	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1355G>T	9.37:g.8518036C>A	ENSP00000370593:p.Arg452Ile		8508036	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156797	0.57259	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.31	5.31	0.75309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.76183	0.3952	L	0.55481	1.735	0.80722	D	1	P;D;D;D;B;D;D;D;D	0.89917	0.629;0.999;0.999;0.999;0.334;0.997;1.0;0.999;1.0	P;D;D;D;B;D;D;D;D	0.83275	0.604;0.996;0.978;0.996;0.251;0.968;0.995;0.99;0.992	T	0.74447	-0.3662	9	.	.	.	.	18.9787	0.92747	0.0:1.0:0.0:0.0	.	442;446;452;452;449;449;439;452;452	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	I	452;452;439;439;452;442;449;449;452;452;452;442	ENSP00000370593:R452I;ENSP00000348812:R452I;ENSP00000353187:R439I;ENSP00000351293:R439I;ENSP00000347373:R452I;ENSP00000380741:R442I;ENSP00000380735:R449I;ENSP00000440515:R449I;ENSP00000438164:R452I;ENSP00000417093:R452I;ENSP00000380731:R442I	.	R	-	2	0	PTPRD	8508036	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	7.770000	0.85390	2.484000	0.83849	0.467000	0.42956	AGA		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8518036	C	A	8518036	3	1	61	1	0	0	0	0	1	0	0	0	12836	913	32	2	4555	2	PTPRD	9	8518036	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1504188	8518036	132695395	6192	14177										
TYRP1	7306	broad.mit.edu	37	chr9	12704674	12704674	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaccttcacagatgcagtCtttgatgaatggctgaggag	11	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:12704674C>A	ENST00000388918.5	+	6	1359	c.1230C>A	c.(1228-1230)gtC>gtA	p.V410V	TYRP1_ENST00000381136.2_Silent_p.V120V|TYRP1_ENST00000381137.2_Silent_p.V119V|RP11-3L8.3_ENST00000417638.1_RNA	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	410					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.V410V(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		CAGATGCAGTCTTTGATGAAT	0.428									Oculocutaneous Albinism																																							1	Substitution - coding silent(1)	large_intestine(1)	9											126	110	115					9																	12704674		2203	4300	6503	12694674	SO:0001819	synonymous_variant	7306	Familial Cancer Database		L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.1230C>A	9.37:g.12704674C>A			12694674	P78468|P78469|Q13721|Q15679	Silent	SNP	ENST00000388918.5	37	CCDS34990.1																																																																																				0.428	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		A	12704674	C	A	12704674	2	1	61	1	0	0	0	0	0	0	0	1	16856	900	32	2		2	TYRP1	9	12704674	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4186638	12704674	128508757	6193	14178										
MPDZ	8777	broad.mit.edu	37	chr9	13107075	13107075	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacagcaatgatctgatcGccccttttcagacgtccgtc	8	13	2	4	rs200049739	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:13107075G>A	ENST00000319217.7	-	47	6349	c.6102C>T	c.(6100-6102)ggC>ggT	p.G2034G	MPDZ_ENST00000541093.1_Silent_p.G268G|MPDZ_ENST00000381022.2_Silent_p.G2005G|MPDZ_ENST00000381015.4_Silent_p.G2034G|MPDZ_ENST00000447879.1_Silent_p.G2001G|MPDZ_ENST00000538841.1_Silent_p.G893G|MPDZ_ENST00000546205.1_Silent_p.G2048G|MPDZ_ENST00000536827.1_Silent_p.G1972G|MPDZ_ENST00000541718.1_Silent_p.G2005G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	2034	PDZ 13. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.G2006G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGATCTGATCGCCCCTTTTCA	0.448													G|||	4	0.000798722	0.0023	0.0014	5008	,	,		18839	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9						G		11,3913		0,11,1951	183	177	179		6015	-7.1	1	9		179	0,8286		0,0,4143	no	coding-synonymous	MPDZ	NM_003829.3		0,11,6094	AA,AG,GG		0.0,0.2803,0.0901		2005/2042	13107075	11,12199	1962	4143	6105	13097075	SO:0001819	synonymous_variant	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.6102C>T	9.37:g.13107075G>A			13097075	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																					0.448	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13107075	G	A	13107075	2	1	61	1	0	0	0	0	0	0	0	1	9752	1074	38	1		1	MPDZ	9	13107075	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	402401	13107075	128106356	6194	14179										
MPDZ	8777	broad.mit.edu	37	chr9	13126572	13126572	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccagtatctgatctccGactttgagtcgtccatccta	7	13	2	2	rs367937602		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:13126572G>A	ENST00000319217.7	-	34	4822	c.4575C>T	c.(4573-4575)gtC>gtT	p.V1525V	MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000381022.2_Silent_p.V1525V|MPDZ_ENST00000381015.4_Silent_p.V1525V|MPDZ_ENST00000447879.1_Silent_p.V1492V|MPDZ_ENST00000538841.1_Silent_p.V384V|MPDZ_ENST00000546205.1_Silent_p.V1539V|MPDZ_ENST00000536827.1_Silent_p.V1492V|MPDZ_ENST00000541718.1_Silent_p.V1525V	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1525	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.V1525V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TCTGATCTCCGACTTTGAGTC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	9						G		0,3732		0,0,1866	70	66	67		4575	3.9	1	9		67	1,8175		0,1,4087	no	coding-synonymous	MPDZ	NM_003829.3		0,1,5953	AA,AG,GG		0.0122,0.0,0.0084		1525/2042	13126572	1,11907	1866	4088	5954	13116572	SO:0001819	synonymous_variant	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4575C>T	9.37:g.13126572G>A			13116572	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																					0.368	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13126572	G	A	13126572	2	1	61	1	0	0	0	0	0	0	0	1	9752	1045	37	1		1	MPDZ	9	13126572	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19497	13126572	128086859	6195	14180										
MPDZ	8777	broad.mit.edu	37	chr9	13186340	13186340	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggagtgtggtgggtagaGaaaggaatcctccttagcag	15	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:13186340G>T	ENST00000319217.7	-	18	2657	c.2410C>A	c.(2410-2412)Ctc>Atc	p.L804I	MPDZ_ENST00000381022.2_Missense_Mutation_p.L804I|MPDZ_ENST00000381015.4_Missense_Mutation_p.L804I|MPDZ_ENST00000447879.1_Missense_Mutation_p.L804I|MPDZ_ENST00000546205.1_Missense_Mutation_p.L804I|MPDZ_ENST00000536827.1_Missense_Mutation_p.L804I|MPDZ_ENST00000541718.1_Missense_Mutation_p.L804I	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	804					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)	p.L804I(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		GGTGGGTAGAGAAAGGAATCC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	9											46	47	47					9																	13186340		1892	4114	6006	13176340	SO:0001583	missense	8777			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2410C>A	9.37:g.13186340G>T	ENSP00000320006:p.Leu804Ile		13176340	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	G	5.629	0.300822	0.10678	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.10668	2.9;2.85;2.85;2.85;2.89;2.9;2.9	5.24	0.332	0.15938	.	0.386473	0.18025	N	0.154109	T	0.05686	0.0149	N	0.19112	0.55	0.80722	D	1	P;P;P	0.39424	0.544;0.673;0.673	B;B;B	0.36464	0.113;0.165;0.225	T	0.49021	-0.8982	10	0.21540	T	0.41	.	8.0033	0.30310	0.6213:0.0:0.3787:0.0	.	804;804;804	B7ZMI4;O75970-3;O75970-2	.;.;.	I	804;804;804;804;804;804;754;804	ENSP00000320006:L804I;ENSP00000439807:L804I;ENSP00000370410:L804I;ENSP00000444151:L804I;ENSP00000415208:L804I;ENSP00000370403:L804I;ENSP00000446358:L804I	ENSP00000320006:L804I	L	-	1	0	MPDZ	13176340	1.000000	0.71417	0.853000	0.33588	0.180000	0.23129	2.480000	0.45206	0.161000	0.19458	-0.806000	0.03193	CTC		0.463	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		T	13186340	G	T	13186340	3	4	61	1	0	0	0	0	1	0	0	0	9752	942	33	2	3831	2	MPDZ	9	13186340	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59768	13186340	128027091	6196	14181										
NFIB	4781	broad.mit.edu	37	chr9	14307498	14307498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatgtggaagaagtgcctCgatgaatgggtgaaattcat	13	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14307498C>T	ENST00000380959.3	-	2	525	c.52G>A	c.(52-54)Gag>Aag	p.E18K	NFIB_ENST00000380953.1_Missense_Mutation_p.E18K|NFIB_ENST00000397575.3_Missense_Mutation_p.E18K|NFIB_ENST00000397579.2_Missense_Mutation_p.E18K|NFIB_ENST00000380921.3_Missense_Mutation_p.E18K|NFIB_ENST00000397581.2_Missense_Mutation_p.E18K|NFIB_ENST00000380934.4_Missense_Mutation_p.E44K	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	18					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.E18K(2)		central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		AGAAGTGCCTCGATGAATGGG	0.403			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																Esophageal Squamous(132;921 1730 14828 40753 46471)		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	2	Substitution - Missense(2)	large_intestine(2)	9											58	57	58					9																	14307498		2203	4300	6503	14297498	SO:0001583	missense	4781			U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.52G>A	9.37:g.14307498C>T	ENSP00000370346:p.Glu18Lys		14297498	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.512354	0.85389	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000380921	T;T;T;T;T;T	0.56941	0.49;0.53;0.5;0.44;0.43;0.55	5.51	5.51	0.81932	CTF transcription factor/nuclear factor 1, N-terminal (1);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.73118	0.3546	M	0.72894	2.215	0.80722	D	1	D;D;D	0.67145	0.996;0.996;0.996	D;D;D	0.74348	0.974;0.983;0.974	T	0.75569	-0.3272	10	0.87932	D	0	.	19.4366	0.94798	0.0:1.0:0.0:0.0	.	18;18;18	Q5VW27;Q5VW29;O00712	.;.;NFIB_HUMAN	K	44;18;18;18;18;18;18	ENSP00000370321:E44K;ENSP00000370346:E18K;ENSP00000370340:E18K;ENSP00000380705:E18K;ENSP00000380711:E18K;ENSP00000380709:E18K	ENSP00000370308:E18K	E	-	1	0	NFIB	14297498	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.580000	0.87095	0.650000	0.86243	GAG		0.403	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		T	14307498	C	T	14307498	3	4	61	1	0	0	0	0	1	0	0	0	10402	893	31	1	1242	1	NFIB	9	14307498	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1121158	14307498	126905933	6197	14182										
ZDHHC21	340481	broad.mit.edu	37	chr9	14619085	14619085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtctgctgccatggctttCggggcctcgatctacagaag	13	11	2	1	rs61752940	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14619085C>T	ENST00000380916.4	-	10	1143	c.677G>A	c.(676-678)cGa>cAa	p.R226Q		NM_178566.4	NP_848661.1	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21	226					hair follicle development (GO:0001942)|nitric oxide metabolic process (GO:0046209)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)|regulation of nitric-oxide synthase activity (GO:0050999)|sebaceous gland development (GO:0048733)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.R226Q(1)		endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9				GBM - Glioblastoma multiforme(50;4.31e-06)		CCATGGCTTTCGGGGCCTCGA	0.493													C|||	6	0.00119808	0	0	5008	,	,		16863	0.004		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9						C	GLN/ARG	0,4406		0,0,2203	95	91	92		677	5.8	1	9	dbSNP_129	92	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZDHHC21	NM_178566.4	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	226/266	14619085	1,13005	2203	4300	6503	14609085	SO:0001583	missense	340481			AF161360	CCDS6475.1	9p22.3	2010-02-09			ENSG00000175893	ENSG00000175893		"Zinc fingers, DHHC-type"	20750	protein-coding gene	gene with protein product		614605				19956733	Standard	NM_178566		Approved	HSPC097, DNZ1	uc003zlg.2	Q8IVQ6	OTTHUMG00000019573	ENST00000380916.4:c.677G>A	9.37:g.14619085C>T	ENSP00000370303:p.Arg226Gln		14609085	A8KA95|D3DRI7|Q5VWG1	Missense_Mutation	SNP	ENST00000380916.4	37	CCDS6475.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	17.60	3.428798	0.62844	0.0	1.16E-4	ENSG00000175893	ENST00000380916	T	0.47177	0.85	5.82	5.82	0.92795	.	0.066025	0.64402	D	0.000009	T	0.44891	0.1315	N	0.19112	0.55	0.58432	D	0.999996	D	0.64830	0.994	P	0.61201	0.885	T	0.39840	-0.9594	10	0.27082	T	0.32	-5.5419	20.0938	0.97831	0.0:1.0:0.0:0.0	rs61752940	226	Q8IVQ6	ZDH21_HUMAN	Q	226	ENSP00000370303:R226Q	ENSP00000370303:R226Q	R	-	2	0	ZDHHC21	14609085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.324000	0.59228	2.757000	0.94681	0.585000	0.79938	CGA		0.493	ZDHHC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051748.2	NM_178566		T	14619085	C	T	14619085	3	4	61	1	0	0	0	0	1	0	0	0	17651	893	31	1	116	1	ZDHHC21	9	14619085	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	311587	14619085	126594346	6198	14183										
ZDHHC21	340481	broad.mit.edu	37	chr9	14662297	14662297	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtctcatcaaattacacTtgttacataattcccagaac	4	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14662297T>G	ENST00000380916.4	-	6	747	c.281A>C	c.(280-282)aAg>aCg	p.K94T		NM_178566.4	NP_848661.1	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21	94					hair follicle development (GO:0001942)|nitric oxide metabolic process (GO:0046209)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)|regulation of nitric-oxide synthase activity (GO:0050999)|sebaceous gland development (GO:0048733)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.K94T(1)		endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9				GBM - Glioblastoma multiforme(50;4.31e-06)		CAAATTACACTTGTTACATAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	9											65	62	63					9																	14662297		2203	4300	6503	14652297	SO:0001583	missense	340481			AF161360	CCDS6475.1	9p22.3	2010-02-09			ENSG00000175893	ENSG00000175893		"Zinc fingers, DHHC-type"	20750	protein-coding gene	gene with protein product		614605				19956733	Standard	NM_178566		Approved	HSPC097, DNZ1	uc003zlg.2	Q8IVQ6	OTTHUMG00000019573	ENST00000380916.4:c.281A>C	9.37:g.14662297T>G	ENSP00000370303:p.Lys94Thr		14652297	A8KA95|D3DRI7|Q5VWG1	Missense_Mutation	SNP	ENST00000380916.4	37	CCDS6475.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.728018	0.89390	.	.	ENSG00000175893	ENST00000380916	T	0.24538	1.85	5.8	5.8	0.92144	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	N	0.25060	0.705	0.58432	D	0.999998	D	0.62365	0.991	D	0.74023	0.982	T	0.12656	-1.0539	10	0.39692	T	0.17	-13.6178	15.8121	0.78573	0.0:0.0:0.0:1.0	.	94	Q8IVQ6	ZDH21_HUMAN	T	94	ENSP00000370303:K94T	ENSP00000370303:K94T	K	-	2	0	ZDHHC21	14652297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.077000	0.76814	2.206000	0.71126	0.528000	0.53228	AAG		0.393	ZDHHC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051748.2	NM_178566		G	14662297	T	G	14662297	3	3	61	1	0	0	0	0	1	0	0	0	17651	1609	56	4	528	4	ZDHHC21	9	14662297	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	43212	14662297	126551134	6199	14184										
FREM1	158326	broad.mit.edu	37	chr9	14756379	14756379	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacaaaatgtacctgggtcAaactgaatcagtttagatgg	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14756379A>G	ENST00000380880.3	-	29	6183	c.5400T>C	c.(5398-5400)ttT>ttC	p.F1800F	FREM1_ENST00000422223.2_Silent_p.F1800F|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380894.1_Silent_p.F336F|FREM1_ENST00000380881.4_Silent_p.F1801F			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1800	Calx-beta.				cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.F1801F(1)|p.F213F(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TACCTGGGTCAAACTGAATCA	0.343																																																2	Substitution - coding silent(2)	large_intestine(2)	9											57	57	57					9																	14756379		1831	4087	5918	14746379	SO:0001819	synonymous_variant	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.5400T>C	9.37:g.14756379A>G			14746379	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																				0.343	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14756379	A	G	14756379	2	3	61	1	0	0	0	0	0	0	0	1	6063	127	5	4		4	FREM1	9	14756379	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	94082	14756379	126457052	6200	14185										
FREM1	158326	broad.mit.edu	37	chr9	14759770	14759770	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacatttcagagtcattacCtttatacccacaaaggccga	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14759770C>A	ENST00000380880.3	-	28	6117	c.5334G>T	c.(5332-5334)aaG>aaT	p.K1778N	FREM1_ENST00000422223.2_Splice_Site_p.K1778N|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380894.1_Splice_Site_p.K314N|FREM1_ENST00000380881.4_Splice_Site_p.K1779N			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1778	Calx-beta.				cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.K1779N(1)|p.K191N(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GAGTCATTACCTTTATACCCA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	9											122	112	115					9																	14759770		1829	4088	5917	14749770	SO:0001630	splice_region_variant	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.5334+1G>T	9.37:g.14759770C>A			14749770	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.244723	0.59103	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880;ENST00000380892	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.97	5.06	0.68205	Na-Ca exchanger/integrin-beta4 (1);	0.301984	0.40469	N	0.001089	T	0.49847	0.1581	L	0.61387	1.9	0.43508	D	0.995763	D;D	0.59767	0.986;0.962	P;P	0.60345	0.872;0.873	T	0.48222	-0.9054	9	.	.	.	-10.0521	17.0236	0.86440	0.0:0.8727:0.1273:0.0	.	1778;314	Q5H8C1;B7ZBX4	FREM1_HUMAN;.	N	1779;1778;314;1778;191	ENSP00000370263:K1779N;ENSP00000412940:K1778N;ENSP00000370278:K314N;ENSP00000370262:K1778N	.	K	-	3	2	FREM1	14749770	1.000000	0.71417	0.998000	0.56505	0.790000	0.44656	5.240000	0.65378	1.495000	0.48549	0.655000	0.94253	AAG		0.363	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	Missense_Mutation	A	14759770	C	A	14759770	5	1	61	1	0	0	0	0	0	0	1	0	6063	695	24	2	1245	2	FREM1	9	14759770	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3391	14759770	126453661	6201	14186										
FREM1	158326	broad.mit.edu	37	chr9	14801729	14801729	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggctgcttattctcagaGaagtctttgctaaaccccct	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14801729G>T	ENST00000380880.3	-	20	4398	c.3615C>A	c.(3613-3615)ttC>ttA	p.F1205L	FREM1_ENST00000422223.2_Missense_Mutation_p.F1205L|FREM1_ENST00000380881.4_Missense_Mutation_p.F1206L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1205					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.F1206L(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TATTCTCAGAGAAGTCTTTGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											149	148	148					9																	14801729		1999	4177	6176	14791729	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3615C>A	9.37:g.14801729G>T	ENSP00000370262:p.Phe1205Leu		14791729	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	G	7.131	0.579927	0.13686	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.49432	0.78;0.78;0.78	5.51	-9.02	0.00741	.	0.927069	0.09265	N	0.825993	T	0.26810	0.0656	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27400	-1.0075	10	0.09843	T	0.71	-0.2519	6.0892	0.19985	0.3258:0.0975:0.4806:0.0961	.	1205	Q5H8C1	FREM1_HUMAN	L	1206;1205;1205	ENSP00000370263:F1206L;ENSP00000412940:F1205L;ENSP00000370262:F1205L	ENSP00000370257:F1208L	F	-	3	2	FREM1	14791729	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.870000	0.04228	-1.613000	0.01577	-0.469000	0.05056	TTC		0.522	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14801729	G	T	14801729	3	4	61	1	0	0	0	0	1	0	0	0	6063	933	33	2	3046	2	FREM1	9	14801729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41959	14801729	126411702	6202	14187										
FREM1	158326	broad.mit.edu	37	chr9	14816814	14816814	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgctgaatttgtgccatCggtgacctccaagagtaggt	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14816814C>T	ENST00000380880.3	-	15	3385	c.2602G>A	c.(2602-2604)Gat>Aat	p.D868N	FREM1_ENST00000422223.2_Missense_Mutation_p.D868N|FREM1_ENST00000380881.4_Missense_Mutation_p.D869N			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	868					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.D869N(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTTGTGCCATCGgtgacctcc	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											59	62	61					9																	14816814		1857	4098	5955	14806814	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2602G>A	9.37:g.14816814C>T	ENSP00000370262:p.Asp868Asn		14806814	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894312	0.72639	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51325	0.71;0.71;0.71	5.65	5.65	0.86999	.	0.100720	0.64402	D	0.000001	T	0.73426	0.3585	M	0.88704	2.975	0.52501	D	0.999954	D	0.89917	1.0	D	0.97110	1.0	T	0.77517	-0.2558	10	0.87932	D	0	-21.0074	15.093	0.72211	0.0:1.0:0.0:0.0	.	868	Q5H8C1	FREM1_HUMAN	N	869;868;868	ENSP00000370263:D869N;ENSP00000412940:D868N;ENSP00000370262:D868N	ENSP00000370257:D871N	D	-	1	0	FREM1	14806814	1.000000	0.71417	0.998000	0.56505	0.192000	0.23643	5.014000	0.64029	2.941000	0.99782	0.655000	0.94253	GAT		0.428	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14816814	C	T	14816814	3	4	61	1	0	0	0	0	1	0	0	0	6063	884	31	1	4079	1	FREM1	9	14816814	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15085	14816814	126396617	6203	14188										
FREM1	158326	broad.mit.edu	37	chr9	14851562	14851562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctttggaatctgattcGgaattccagctctgatatag	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14851562G>A	ENST00000380880.3	-	6	1655	c.872C>T	c.(871-873)cCg>cTg	p.P291L	FREM1_ENST00000422223.2_Missense_Mutation_p.P291L|RNU6-1260P_ENST00000362944.1_RNA|FREM1_ENST00000380881.4_Missense_Mutation_p.P292L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	291					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.P292L(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		AATCTGATTCGGAATTCCAGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											113	112	112					9																	14851562		1923	4134	6057	14841562	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.872C>T	9.37:g.14851562G>A	ENSP00000370262:p.Pro291Leu		14841562	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351360	0.95830	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.10960	2.82;2.82;2.82	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.37972	0.1023	M	0.80982	2.52	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.02378	-1.1168	10	0.54805	T	0.06	-15.6975	20.7342	0.99715	0.0:0.0:1.0:0.0	.	291	Q5H8C1	FREM1_HUMAN	L	292;291;291	ENSP00000370263:P292L;ENSP00000412940:P291L;ENSP00000370262:P291L	ENSP00000370257:P294L	P	-	2	0	FREM1	14841562	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.476000	0.97823	2.906000	0.99361	0.655000	0.94253	CCG		0.418	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		A	14851562	G	A	14851562	3	1	61	1	0	0	0	0	1	0	0	0	6063	1116	39	1	5845	1	FREM1	9	14851562	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34748	14851562	126361869	6204	14189										
FREM1	158326	broad.mit.edu	37	chr9	14863874	14863874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtgaacatacttgacttCgttgggaaggaaatggcagt	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:14863874C>T	ENST00000380880.3	-	3	1045	c.262G>A	c.(262-264)Gaa>Aaa	p.E88K	FREM1_ENST00000422223.2_Missense_Mutation_p.E88K|FREM1_ENST00000380881.4_Missense_Mutation_p.E88K			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	88					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.E88K(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TACTTGACTTCGTTGGGAAGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											110	106	108					9																	14863874		1949	4140	6089	14853874	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.262G>A	9.37:g.14863874C>T	ENSP00000370262:p.Glu88Lys		14853874	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	32	5.187172	0.94923	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.12255	2.7;2.7;2.7	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.23688	0.0573	M	0.75447	2.3	0.58432	D	0.999999	D	0.55172	0.97	B	0.42555	0.391	T	0.05115	-1.0905	10	0.66056	D	0.02	-18.5681	19.8046	0.96525	0.0:1.0:0.0:0.0	.	88	Q5H8C1	FREM1_HUMAN	K	88	ENSP00000370263:E88K;ENSP00000412940:E88K;ENSP00000370262:E88K	ENSP00000370257:E88K	E	-	1	0	FREM1	14853874	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	7.445000	0.80570	2.748000	0.94277	0.655000	0.94253	GAA		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14863874	C	T	14863874	3	4	61	1	0	0	0	0	1	0	0	0	6063	893	31	1	6467	1	FREM1	9	14863874	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12312	14863874	126349557	6205	14190										
TTC39B	158219	broad.mit.edu	37	chr9	15188039	15188039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatccagttttgttggaaaAcattaatccacattagctcc	6	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:15188039A>G	ENST00000512701.2	-	14	1361	c.1325T>C	c.(1324-1326)gTt>gCt	p.V442A	TTC39B_ENST00000297615.5_Missense_Mutation_p.V373A|TTC39B_ENST00000507993.1_Missense_Mutation_p.V277A|TTC39B_ENST00000355694.2_Missense_Mutation_p.V376A|TTC39B_ENST00000380850.4_Missense_Mutation_p.V429A|TTC39B_ENST00000507285.1_Missense_Mutation_p.V277A			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	442								p.V376A(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						TTGTTGGAAAACATTAATCCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											171	161	164					9																	15188039		2203	4300	6503	15178039	SO:0001583	missense	158219			AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"Tetratricopeptide (TTC) repeat domain containing"	23704	protein-coding gene	gene with protein product		613574	"chromosome 9 open reading frame 52"	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1325T>C	9.37:g.15188039A>G	ENSP00000422496:p.Val442Ala		15178039	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	A	11.33	1.608234	0.28623	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.58	3.29	0.37713	.	0.604156	0.16068	N	0.231136	T	0.14227	0.0344	N	0.02539	-0.55	0.80722	D	1	B;B;B;B;B	0.23128	0.022;0.009;0.08;0.0;0.0	B;B;B;B;B	0.22880	0.007;0.012;0.042;0.007;0.007	T	0.15607	-1.0431	10	0.09084	T	0.74	-2.5935	4.9803	0.14162	0.6791:0.0:0.3209:0.0	.	373;429;442;374;376	F5H705;E9PAQ9;E9PE60;A5PLN1;Q5VTQ0	.;.;.;.;TT39B_HUMAN	A	429;373;376;442;277;277	ENSP00000370231:V429A;ENSP00000297615:V373A;ENSP00000347920:V376A;ENSP00000422496:V442A;ENSP00000426539:V277A;ENSP00000423392:V277A	ENSP00000297615:V373A	V	-	2	0	TTC39B	15178039	1.000000	0.71417	0.018000	0.16275	0.959000	0.62525	6.480000	0.73604	2.120000	0.65058	0.377000	0.23210	GTT		0.363	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574		G	15188039	A	G	15188039	3	3	61	1	0	0	0	0	1	0	0	0	16748	43	2	4	751	4	TTC39B	9	15188039	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	324165	15188039	126025392	6206	14191										
SNAPC3	6619	broad.mit.edu	37	chr9	15423915	15423915	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgttttagccttgataAactgaaatgccttgaggacg	9	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:15423915A>C	ENST00000380821.3	+	2	499	c.323A>C	c.(322-324)aAa>aCa	p.K108T	SNAPC3_ENST00000461041.1_3'UTR	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	108					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K108T(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AGCCTTGATAAACTGAAATGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											184	164	171					9																	15423915		2203	4300	6503	15413915	SO:0001583	missense	6619			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.323A>C	9.37:g.15423915A>C	ENSP00000370200:p.Lys108Thr		15413915	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.551739	0.27739	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.45276	0.9	5.79	4.59	0.56863	.	0.212430	0.49305	D	0.000146	T	0.46737	0.1408	L	0.46157	1.445	0.80722	D	1	D;B	0.63880	0.993;0.006	D;B	0.63033	0.91;0.008	T	0.39313	-0.9620	10	0.09338	T	0.73	-5.9821	8.5057	0.33186	0.8278:0.0:0.0:0.1722	.	79;108	B4DDR9;Q92966	.;SNPC3_HUMAN	T	108;108;79;108	ENSP00000370200:K108T	ENSP00000370185:K108T	K	+	2	0	SNAPC3	15413915	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	2.834000	0.48167	2.208000	0.71279	0.533000	0.62120	AAA		0.408	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		C	15423915	A	C	15423915	3	2	61	1	0	0	0	0	1	0	0	0	14873	14	1	4	329	4	SNAPC3	9	15423915	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	235876	15423915	125789516	6207	14192										
SNAPC3	6619	broad.mit.edu	37	chr9	15444628	15444628	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccataggaaaaaagcctgAaaattcagcagacatgattg	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:15444628A>C	ENST00000380821.3	+	4	682	c.506A>C	c.(505-507)gAa>gCa	p.E169A	SNAPC3_ENST00000380799.1_5'Flank	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	169					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E169A(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAAAAGCCTGAAAATTCAGCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											117	110	112					9																	15444628		2203	4300	6503	15434628	SO:0001583	missense	6619			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.506A>C	9.37:g.15444628A>C	ENSP00000370200:p.Glu169Ala		15434628	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.385037	0.42308	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.46819	0.86	5.35	2.84	0.33178	.	0.460951	0.25211	N	0.032314	T	0.38799	0.1054	L	0.51422	1.61	0.80722	D	1	P;B	0.37207	0.587;0.179	B;B	0.36464	0.225;0.053	T	0.29488	-1.0010	10	0.59425	D	0.04	-9.5194	7.3792	0.26845	0.7802:0.1424:0.0773:0.0	.	140;169	B4DDR9;Q92966	.;SNPC3_HUMAN	A	169;169;140;169	ENSP00000370200:E169A	ENSP00000370185:E169A	E	+	2	0	SNAPC3	15434628	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.648000	0.46647	0.969000	0.38237	-0.297000	0.09499	GAA		0.363	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		C	15444628	A	C	15444628	3	2	61	1	0	0	0	0	1	0	0	0	14873	246	9	4	520	4	SNAPC3	9	15444628	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	20713	15444628	125768803	6208	14193										
C9orf93	203238	broad.mit.edu	37	chr9	15724841	15724841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacactaaatgtgcagaccGagaggctttaataagcactt	8	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:15724841G>A	ENST00000380701.3	+	14	1887	c.1559G>A	c.(1558-1560)cGa>cAa	p.R520Q	CCDC171_ENST00000297641.3_Missense_Mutation_p.R520Q	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	520								p.R520Q(2)									TGTGCAGACCGAGAGGCTTTA	0.393																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	9											122	134	130					9																	15724841		2203	4300	6503	15714841	SO:0001583	missense	203238			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.1559G>A	9.37:g.15724841G>A	ENSP00000370077:p.Arg520Gln		15714841	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035823	0.75617	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.50001	0.76;0.76	5.42	5.42	0.78866	.	0.327625	0.33401	N	0.004954	T	0.25791	0.0628	N	0.14661	0.345	0.80722	D	1	P;P;P	0.52463	0.953;0.953;0.953	B;B;B	0.39152	0.292;0.292;0.292	T	0.06023	-1.0850	10	0.12103	T	0.63	-11.2819	11.1066	0.48207	0.1433:0.0:0.8567:0.0	.	528;520;520	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	Q	520	ENSP00000297641:R520Q;ENSP00000370077:R520Q	ENSP00000297641:R520Q	R	+	2	0	C9orf93	15714841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.356000	0.44116	2.716000	0.92895	0.650000	0.86243	CGA		0.393	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		A	15724841	G	A	15724841	3	1	61	1	0	0	0	0	1	0	0	0	2512	1058	37	1	1609	1	C9orf93	9	15724841	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	280213	15724841	125488590	6209	14194										
C9orf93	203238	broad.mit.edu	37	chr9	15784546	15784546	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttgaaagtgcatgtgaaGaactaaataatgcattactt	8	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:15784546G>T	ENST00000380701.3	+	21	3449	c.3121G>T	c.(3121-3123)Gaa>Taa	p.E1041*	CCDC171_ENST00000297641.3_Nonsense_Mutation_p.E1041*	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1041								p.E1041*(1)									TGCATGTGAAGAACTAAATAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											85	76	80					9																	15784546		2203	4300	6503	15774546	SO:0001587	stop_gained	203238			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3121G>T	9.37:g.15784546G>T	ENSP00000370077:p.Glu1041*		15774546	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Nonsense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	46|46	12.105303|12.105303	0.99636|0.99636	.|.	.|.	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701|ENST00000449575;ENST00000432954	.|.	.|.	.|.	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.050057|.	0.85682|.	D|.	0.000000|.	.|T	.|0.74581	.|0.3735	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73760	.|-0.3881	.|4	0.42905|.	T|.	0.14|.	-6.7623|-6.7623	18.7422|18.7422	0.91777|0.91777	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	1041;308;1041|280;94	.|.	ENSP00000297641:E1041X|.	E|K	+|+	1|3	0|2	C9orf93|C9orf93	15774546|15774546	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.437000|7.437000	0.80417|0.80417	2.500000|2.500000	0.84329|0.84329	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.368	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		T	15784546	G	T	15784546	4	4	61	1	0	0	0	0	0	1	0	0	2512	943	33	2	3199	2	C9orf93	9	15784546	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59705	15784546	125428885	6210	14195										
CNTLN	54875	broad.mit.edu	37	chr9	17143295	17143295	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctttaaggctgataaaGaatttgtatggtctttgtgg	10	3	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:17143295G>A	ENST00000380647.3	+	2	454	c.370G>A	c.(370-372)Gaa>Aaa	p.E124K	CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000380641.4_Missense_Mutation_p.E124K|CNTLN_ENST00000425824.1_Missense_Mutation_p.E124K|CNTLN_ENST00000262360.5_Missense_Mutation_p.E124K			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	124					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.E124K(1)		breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GGCTGATAAAGAATTTGTATG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	9											162	156	158					9																	17143295		1811	4080	5891	17133295	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.370G>A	9.37:g.17143295G>A	ENSP00000370021:p.Glu124Lys		17133295	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	33	5.239362	0.95240	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.89	5.89	0.94794	.	.	.	.	.	T	0.34395	0.0896	L	0.59436	1.845	0.49582	D	0.999801	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.997	T	0.00800	-1.1561	9	0.20046	T	0.44	.	19.0291	0.92948	0.0:0.0:1.0:0.0	.	124;124;124;124	C9J1F9;Q9NXG0-2;Q9NXG0-3;B1AMC8	.;.;.;.	K	124	ENSP00000370021:E124K;ENSP00000392798:E124K;ENSP00000262360:E124K;ENSP00000370015:E124K	ENSP00000262360:E124K	E	+	1	0	CNTLN	17133295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.570000	0.90748	2.783000	0.95769	0.655000	0.94253	GAA		0.318	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17143295	G	A	17143295	3	1	61	1	0	0	0	0	1	0	0	0	3645	943	33	3	376	3	CNTLN	9	17143295	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1358749	17143295	124070136	6211	14196										
CNTLN	54875	broad.mit.edu	37	chr9	17235695	17235695	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaataaatgaccttgtaAaacggaaaattgcagtagat	9	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:17235695A>C	ENST00000380647.3	+	4	658	c.574A>C	c.(574-576)Aaa>Caa	p.K192Q	CNTLN_ENST00000380641.4_Missense_Mutation_p.K192Q|CNTLN_ENST00000425824.1_Missense_Mutation_p.K192Q|CNTLN_ENST00000262360.5_Missense_Mutation_p.K192Q			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	192					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.K192Q(1)		breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		TGACCTTGTAAAACGGAAAAT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	100	100					9																	17235695		1799	4060	5859	17225695	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.574A>C	9.37:g.17235695A>C	ENSP00000370021:p.Lys192Gln		17225695	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	0.780	-0.762565	0.02996	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	5.42	4.25	0.50352	.	.	.	.	.	T	0.07369	0.0186	L	0.43923	1.385	0.26226	N	0.979083	B;B;B	0.29988	0.084;0.084;0.264	B;B;B	0.24006	0.04;0.04;0.05	T	0.30357	-0.9981	9	0.08381	T	0.77	.	11.9713	0.53065	0.552:0.448:0.0:0.0	.	192;192;192	C9J1F9;Q9NXG0-2;Q9NXG0-3	.;.;.	Q	192	ENSP00000370021:K192Q;ENSP00000392798:K192Q;ENSP00000262360:K192Q;ENSP00000370015:K192Q	ENSP00000262360:K192Q	K	+	1	0	CNTLN	17225695	0.997000	0.39634	0.499000	0.27577	0.058000	0.15608	2.182000	0.42556	0.959000	0.37980	0.528000	0.53228	AAA		0.294	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17235695	A	C	17235695	3	2	61	1	0	0	0	0	1	0	0	0	3645	15	1	4	588	4	CNTLN	9	17235695	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	92400	17235695	123977736	6212	14197										
CNTLN	54875	broad.mit.edu	37	chr9	17330716	17330716	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttacaggagaaactaaaGatagcaaatgaaaaactgtc	7	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:17330716G>T	ENST00000380647.3	+	9	1512	c.1428G>T	c.(1426-1428)aaG>aaT	p.K476N	CNTLN_ENST00000425824.1_Missense_Mutation_p.K476N|CNTLN_ENST00000262360.5_Missense_Mutation_p.K476N			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	476					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.K476N(1)		breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGAAACTAAAGATAGCAAATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											130	126	127					9																	17330716		1830	4077	5907	17320716	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1428G>T	9.37:g.17330716G>T	ENSP00000370021:p.Lys476Asn		17320716	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124638	0.56613	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.36157	1.27;1.27;1.27	5.0	3.77	0.43336	.	.	.	.	.	T	0.53061	0.1773	M	0.69823	2.125	0.32769	N	0.504045	D;P;P	0.76494	0.999;0.933;0.933	D;P;P	0.68943	0.961;0.804;0.804	T	0.60556	-0.7240	9	0.33141	T	0.24	.	8.8139	0.34985	0.8199:0.0:0.1801:0.0	.	476;476;476	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	N	476	ENSP00000370021:K476N;ENSP00000392798:K476N;ENSP00000262360:K476N	ENSP00000262360:K476N	K	+	3	2	CNTLN	17320716	0.993000	0.37304	0.997000	0.53966	0.927000	0.56198	0.630000	0.24553	0.743000	0.32719	-0.355000	0.07637	AAG		0.373	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		T	17330716	G	T	17330716	3	4	61	1	0	0	0	0	1	0	0	0	3645	933	33	2	1492	2	CNTLN	9	17330716	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95021	17330716	123882715	6213	14198										
CNTLN	54875	broad.mit.edu	37	chr9	17394581	17394581	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgagaaaaggtcgagaaAattaaaagaagggaataaaa	10	1	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:17394581A>C	ENST00000380647.3	+	15	2213	c.2129A>C	c.(2128-2130)aAa>aCa	p.K710T	CNTLN_ENST00000425824.1_Missense_Mutation_p.K710T|CNTLN_ENST00000262360.5_Missense_Mutation_p.K710T			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	710					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.K710T(1)		breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGGTCGAGAAAATTAAAAGAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	9											27	25	26					9																	17394581		1781	4046	5827	17384581	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2129A>C	9.37:g.17394581A>C	ENSP00000370021:p.Lys710Thr		17384581	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	10.96	1.498840	0.26861	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.19669	2.13;2.13;2.39	5.37	4.19	0.49359	.	.	.	.	.	T	0.33962	0.0881	M	0.64997	1.995	0.27218	N	0.959735	D;P;P	0.67145	0.996;0.95;0.95	D;P;P	0.63793	0.918;0.571;0.571	T	0.14811	-1.0459	9	0.18276	T	0.48	.	6.099	0.20037	0.7738:0.0:0.0851:0.1411	.	710;710;710	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	T	710	ENSP00000370021:K710T;ENSP00000392798:K710T;ENSP00000262360:K710T	ENSP00000262360:K710T	K	+	2	0	CNTLN	17384581	1.000000	0.71417	0.987000	0.45799	0.780000	0.44128	2.091000	0.41691	0.835000	0.34877	-0.417000	0.06048	AAA		0.308	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17394581	A	C	17394581	3	2	61	1	0	0	0	0	1	0	0	0	3645	14	1	4	2217	4	CNTLN	9	17394581	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	63865	17394581	123818850	6214	14199										
FAM154A	158297	broad.mit.edu	37	chr9	18928824	18928824	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcatgcacaaagcgcttCtccacggggtgggccacata	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:18928824C>A	ENST00000380534.4	-	4	930	c.651G>T	c.(649-651)gaG>gaT	p.E217D	FAM154A_ENST00000542071.1_Missense_Mutation_p.E25D|FAM154A_ENST00000380530.1_3'UTR	NM_153707.2	NP_714918.2	Q8IYX7	F154A_HUMAN	family with sequence similarity 154, member A	217								p.E217D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|skin(1)	26				GBM - Glioblastoma multiforme(50;6.53e-16)		CAAAGCGCTTCTCCACGGGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											99	101	101					9																	18928824		2203	4300	6503	18918824	SO:0001583	missense	158297			BC033489	CCDS6487.1, CCDS75819.1, CCDS75820.1	9p22.1	2012-03-23	2008-02-21	2008-02-21	ENSG00000155875	ENSG00000155875			28566	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 138"	C9orf138		12477932	Standard	NM_153707		Approved	MGC35182	uc003zni.2	Q8IYX7	OTTHUMG00000019609	ENST00000380534.4:c.651G>T	9.37:g.18928824C>A	ENSP00000369907:p.Glu217Asp		18918824	Q5VY58	Missense_Mutation	SNP	ENST00000380534.4	37	CCDS6487.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.935250	0.73442	.	.	ENSG00000155875	ENST00000380534;ENST00000542071	T;T	0.16597	2.33;2.33	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000020	T	0.40171	0.1106	M	0.77820	2.39	0.37610	D	0.920903	D	0.76494	0.999	D	0.72338	0.977	T	0.41875	-0.9484	10	0.59425	D	0.04	-27.6989	10.7665	0.46297	0.0:0.913:0.0:0.087	.	217	Q8IYX7	F154A_HUMAN	D	217;25	ENSP00000369907:E217D;ENSP00000438823:E25D	ENSP00000369907:E217D	E	-	3	2	FAM154A	18918824	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.670000	0.37502	2.640000	0.89533	0.650000	0.86243	GAG		0.517	FAM154A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051811.1	NM_153707		A	18928824	C	A	18928824	3	1	61	1	0	0	0	0	1	0	0	0	5479	912	32	2	777	2	FAM154A	9	18928824	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1534243	18928824	122284607	6215	14200										
PLIN2	123	broad.mit.edu	37	chr9	19118436	19118436	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattggcactatacacattCttcctggcaaattcaatcta	5	10	3	1	rs373365753		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:19118436C>A	ENST00000276914.2	-	7	974	c.795G>T	c.(793-795)aaG>aaT	p.K265N	PLIN2_ENST00000411567.1_Missense_Mutation_p.K184N	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	265					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K265N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						TATACACATTCTTCCTGGCAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	ASN/LYS	0,4406		0,0,2203	100	91	94		795	3.8	1	9		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	PLIN2	NM_001122.3	94	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	benign	265/438	19118436	2,13004	2203	4300	6503	19108436	SO:0001583	missense	123			X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.795G>T	9.37:g.19118436C>A	ENSP00000276914:p.Lys265Asn		19108436	Q9BSC3	Missense_Mutation	SNP	ENST00000276914.2	37	CCDS6490.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374172	0.42105	0.0	2.33E-4	ENSG00000147872	ENST00000411567;ENST00000276914	T;T	0.06371	3.31;3.31	5.77	3.84	0.44239	.	0.322809	0.33477	N	0.004870	T	0.12390	0.0301	M	0.82517	2.595	0.48236	D	0.999617	B	0.24618	0.107	B	0.35413	0.202	T	0.01993	-1.1233	10	0.31617	T	0.26	.	7.2755	0.26281	0.0:0.7108:0.1372:0.152	.	265	Q99541	PLIN2_HUMAN	N	184;265	ENSP00000415270:K184N;ENSP00000276914:K265N	ENSP00000276914:K265N	K	-	3	2	PLIN2	19108436	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.548000	0.45794	0.709000	0.31976	-0.355000	0.07637	AAG		0.398	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		A	19118436	C	A	19118436	3	1	61	1	0	0	0	0	1	0	0	0	12121	912	32	2	526	2	PLIN2	9	19118436	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	189612	19118436	122094995	6216	14201										
DENND4C	55667	broad.mit.edu	37	chr9	19346864	19346864	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcagcaaaccccctctcGaactcataaagaacgttcaa	5	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:19346864G>A	ENST00000380432.2	+	18	3275	c.3242G>A	c.(3241-3243)cGa>cAa	p.R1081Q	DENND4C_ENST00000434457.2_Missense_Mutation_p.R1366Q|DENND4C_ENST00000602925.1_Missense_Mutation_p.R1317Q			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1081					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1081Q(2)		breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ACCCCCTCTCGAACTCATAAA	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	9											66	66	66					9																	19346864		2203	4300	6503	19336864	SO:0001583	missense	55667			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3242G>A	9.37:g.19346864G>A	ENSP00000369797:p.Arg1081Gln		19336864	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	15.32	2.797864	0.50208	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.57273	0.41;0.41	5.46	5.46	0.80206	.	2.078500	0.01775	N	0.031421	T	0.56920	0.2018	L	0.59436	1.845	0.20074	N	0.999935	P;B;P;P	0.36048	0.534;0.36;0.534;0.47	B;B;B;B	0.35727	0.209;0.028;0.209;0.024	T	0.51996	-0.8634	10	0.27785	T	0.31	-9.5114	14.5143	0.67809	0.0725:0.0:0.9275:0.0	.	411;1081;263;1081	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	Q	1081;554;263;411;554;263;78	ENSP00000305795:R554Q;ENSP00000443804:R411Q	ENSP00000305795:R554Q	R	+	2	0	DENND4C	19336864	0.978000	0.34361	0.015000	0.15790	0.962000	0.63368	2.299000	0.43611	2.564000	0.86499	0.585000	0.79938	CGA		0.473	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		A	19346864	G	A	19346864	3	1	61	1	0	0	0	0	1	0	0	0	4446	1058	37	1	3312	1	DENND4C	9	19346864	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	228428	19346864	121866567	6217	14202										
MLLT3	4300	broad.mit.edu	37	chr9	20363483	20363483	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatactcacctgcgacttCggctgcctcctctatttaca	6	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:20363483C>T	ENST00000380338.4	-	7	1608	c.1322G>A	c.(1321-1323)cGa>cAa	p.R441Q	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000380321.1_Missense_Mutation_p.R35Q|MLLT3_ENST00000355930.6_Missense_Mutation_p.R35Q|MLLT3_ENST00000429426.2_Missense_Mutation_p.R438Q	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	441					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.R441Q(1)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		CCTGCGACTTCGGCTGCCTCC	0.468			T	MLL	ALL																																		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	1	Substitution - Missense(1)	large_intestine(1)	9											149	130	137					9																	20363483		2203	4300	6503	20353483	SO:0001583	missense	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.1322G>A	9.37:g.20363483C>T	ENSP00000369695:p.Arg441Gln		20353483	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	37	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343300	0.61073	.	.	ENSG00000171843	ENST00000380338;ENST00000355930;ENST00000380323;ENST00000429426;ENST00000540751;ENST00000380321	.	.	.	5.49	5.49	0.81192	.	0.059997	0.64402	D	0.000005	T	0.73305	0.3570	L	0.46157	1.445	0.50313	D	0.999863	D;P	0.64830	0.994;0.48	P;B	0.61201	0.885;0.034	T	0.74124	-0.3766	9	0.62326	D	0.03	-7.049	19.7332	0.96192	0.0:1.0:0.0:0.0	.	438;441	B7Z755;P42568	.;AF9_HUMAN	Q	441;35;35;438;480;35	.	ENSP00000348196:R35Q	R	-	2	0	MLLT3	20353483	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	5.873000	0.69644	2.735000	0.93741	0.643000	0.83706	CGA		0.468	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		T	20363483	C	T	20363483	3	4	61	1	0	0	0	0	1	0	0	0	9658	884	31	1	404	1	MLLT3	9	20363483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1016619	20363483	120849948	6218	14203										
KIAA1797	54914	broad.mit.edu	37	chr9	20820345	20820345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtataggacaaattctacGaataatacaactacttggaa	7	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:20820345G>A	ENST00000380249.1	+	15	1947	c.1583G>A	c.(1582-1584)cGa>cAa	p.R528Q	FOCAD_ENST00000338382.6_Missense_Mutation_p.R528Q|FOCAD_ENST00000605086.1_5'UTR	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	528						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.R528Q(1)									CAAATTCTACGAATAATACAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											100	95	97					9																	20820345		2203	4300	6503	20810345	SO:0001583	missense	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.1583G>A	9.37:g.20820345G>A	ENSP00000369599:p.Arg528Gln		20810345	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.975139	0.34848	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.20069	2.1;2.1	5.65	5.65	0.86999	Domain of unknown function DUF3730 (1);	0.264640	0.39274	N	0.001407	T	0.21801	0.0525	N	0.20685	0.6	0.43000	D	0.994513	D	0.56968	0.978	P	0.47251	0.542	T	0.01215	-1.1416	10	0.44086	T	0.13	-14.8233	19.7777	0.96400	0.0:0.0:1.0:0.0	.	528	Q5VW36	K1797_HUMAN	Q	528	ENSP00000369599:R528Q;ENSP00000344307:R528Q	ENSP00000344307:R528Q	R	+	2	0	KIAA1797	20810345	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	3.759000	0.55227	2.669000	0.90835	0.644000	0.83932	CGA		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20820345	G	A	20820345	3	1	61	1	0	0	0	0	1	0	0	0	8279	1058	37	1	1629	1	KIAA1797	9	20820345	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	456862	20820345	120393086	6219	14204										
IFNA10	3446	broad.mit.edu	37	chr9	21207035	21207035	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcagatcacagcctagaGaacagatggatttgtagctg	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:21207035G>T	ENST00000357374.2	-	1	107	c.62C>A	c.(61-63)tCt>tAt	p.S21Y		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	21					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.S21Y(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		ACAGCCTAGAGAACAGATGGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											46	58	54					9																	21207035		2202	4297	6499	21197035	SO:0001583	missense	3446				CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"Interferons"	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.62C>A	9.37:g.21207035G>T	ENSP00000369566:p.Ser21Tyr		21197035	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	.	.	.	.	.	.	.	.	.	.	-	11.37	1.618452	0.28801	.	.	ENSG00000186803	ENST00000357374	T	0.05717	3.4	3.65	1.69	0.24217	Four-helical cytokine-like, core (1);	0.574821	0.16675	N	0.204194	T	0.15869	0.0382	M	0.93720	3.45	0.09310	N	1	B	0.26775	0.159	B	0.27262	0.078	T	0.10520	-1.0626	10	0.72032	D	0.01	.	11.1174	0.48268	0.0:0.3591:0.6409:0.0	.	21	P01566	IFN10_HUMAN	Y	21	ENSP00000369566:S21Y	ENSP00000369566:S21Y	S	-	2	0	IFNA10	21197035	0.000000	0.05858	0.008000	0.14137	0.329000	0.28539	0.090000	0.15025	0.139000	0.18822	0.499000	0.49734	TCT		0.493	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171		T	21207035	G	T	21207035	3	4	61	1	0	0	0	0	1	0	0	0	7553	942	33	2	511	2	IFNA10	9	21207035	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	386690	21207035	120006396	6220	14205										
IFNA14	3448	broad.mit.edu	37	chr9	21239629	21239629	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaatttttctaggagggtCtcatcccaagcagcagatga	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:21239629C>T	ENST00000380222.2	-	1	349	c.306G>A	c.(304-306)gaG>gaA	p.E102E		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	102					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)	p.E102E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CTAGGAGGGTCTCATCCCAAG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9											111	114	113					9																	21239629		2203	4300	6503	21229629	SO:0001819	synonymous_variant	3448				CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"Interferons"	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.306G>A	9.37:g.21239629C>T			21229629	Q5VZ56|Q7M4S1	Silent	SNP	ENST00000380222.2	37	CCDS6501.1																																																																																				0.473	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		T	21239629	C	T	21239629	2	4	61	1	0	0	0	0	0	0	0	1	7555	912	32	3		3	IFNA14	9	21239629	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32594	21239629	119973802	6221	14206										
KLHL9	55958	broad.mit.edu	37	chr9	21333736	21333736	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcatccatttattataccGaggatcaaatctgaaaactg	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:21333736G>A	ENST00000359039.4	-	1	1643	c.1123C>T	c.(1123-1125)Cgg>Tgg	p.R375W	KLHL9_ENST00000537938.1_Missense_Mutation_p.R307W			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	375					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)		p.R375W(1)		endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		TTATTATACCGAGGATCAAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	9											80	80	80					9																	21333736		2203	4300	6503	21323736	SO:0001583	missense	55958			AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.1123C>T	9.37:g.21333736G>A	ENSP00000351933:p.Arg375Trp		21323736	Q8TCQ2	Missense_Mutation	SNP	ENST00000359039.4	37	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478664	0.63849	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	T;T	0.79141	-1.24;-1.24	4.67	4.67	0.58626	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	U	0.000000	D	0.89157	0.6635	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91079	0.4898	10	0.72032	D	0.01	.	15.4698	0.75432	0.0:0.0:1.0:0.0	.	375	Q9P2J3	KLHL9_HUMAN	W	375;307	ENSP00000351933:R375W;ENSP00000437733:R307W	ENSP00000351933:R375W	R	-	1	2	KLHL9	21323736	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.512000	0.73737	2.319000	0.78375	0.650000	0.86243	CGG		0.383	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		A	21333736	G	A	21333736	3	1	61	1	0	0	0	0	1	0	0	0	8417	1057	37	1	734	1	KLHL9	9	21333736	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94107	21333736	119879695	6222	14207										
IFNA2	3440	broad.mit.edu	37	chr9	21384886	21384886	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagatagagagtgattCtttggaagtatttcctcaca	8	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:21384886C>A	ENST00000380206.2	-	1	510	c.443G>T	c.(442-444)aGa>aTa	p.R148I		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	148					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)	p.R148I(1)		breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		GAGAGTGATTCTTTGGAAGTA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											205	205	205					9																	21384886		2203	4300	6503	21374886	SO:0001583	missense	3440				CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.443G>T	9.37:g.21384886C>A	ENSP00000369554:p.Arg148Ile		21374886	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	37	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498628	0.64298	.	.	ENSG00000188379	ENST00000380206	T	0.51574	0.7	3.24	3.24	0.37175	.	0.318425	0.33631	N	0.004718	T	0.72875	0.3515	H	0.94542	3.55	0.20873	N	0.99984	D	0.60160	0.987	D	0.64687	0.928	T	0.67360	-0.5690	10	0.87932	D	0	.	11.4477	0.50134	0.0:1.0:0.0:0.0	.	148	Q6DJX8	.	I	148	ENSP00000369554:R148I	ENSP00000369554:R148I	R	-	2	0	IFNA2	21374886	0.001000	0.12720	0.048000	0.18961	0.509000	0.34042	1.217000	0.32455	1.648000	0.50643	0.484000	0.47621	AGA		0.468	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		A	21384886	C	A	21384886	3	1	61	1	0	0	0	0	1	0	0	0	7558	913	32	2	127	2	IFNA2	9	21384886	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51150	21384886	119828545	6223	14208										
IFNE	338376	broad.mit.edu	37	chr9	21481453	21481453	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgaagcatctcatggaGaatggccagagtgtgtcctt	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:21481453G>T	ENST00000448696.3	-	1	859	c.241C>A	c.(241-243)Ctc>Atc	p.L81I	MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon	81					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.L81I(1)		large_intestine(2)|lung(1)|skin(1)	4						ATCTCATGGAGAATGGCCAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											93	86	89					9																	21481453		2203	4300	6503	21471453	SO:0001583	missense	338376			AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.241C>A	9.37:g.21481453G>T	ENSP00000418018:p.Leu81Ile		21471453		Missense_Mutation	SNP	ENST00000448696.3	37	CCDS34997.1	.	.	.	.	.	.	.	.	.	.	G	6.272	0.418298	0.11870	.	.	ENSG00000184995	ENST00000448696	T	0.03717	3.83	4.71	0.124	0.14714	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.894418	0.09332	U	0.816669	T	0.04543	0.0124	L	0.43701	1.375	0.09310	N	1	B	0.23185	0.081	B	0.26094	0.066	T	0.41288	-0.9517	10	0.66056	D	0.02	.	7.6471	0.28327	0.0:0.2671:0.3253:0.4075	.	81	Q86WN2	IFNE_HUMAN	I	81	ENSP00000418018:L81I	ENSP00000418018:L81I	L	-	1	0	IFNE	21471453	0.068000	0.21057	0.481000	0.27354	0.040000	0.13550	0.166000	0.16583	0.217000	0.20800	0.655000	0.94253	CTC		0.453	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891		T	21481453	G	T	21481453	3	4	61	1	0	0	0	0	1	0	0	0	7568	942	33	2	389	2	IFNE	9	21481453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96567	21481453	119731978	6224	14209										
ELAVL2	1993	broad.mit.edu	37	chr9	23762156	23762156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagagtcaactggtgacGaacagttgttgtttatggtg	12	7	1	2	rs146832864	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:23762156G>A	ENST00000397312.2	-	2	351	c.77C>T	c.(76-78)tCg>tTg	p.S26L	ELAVL2_ENST00000223951.6_Missense_Mutation_p.S26L|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000380117.1_Missense_Mutation_p.S26L|ELAVL2_ENST00000544538.1_Missense_Mutation_p.S26L|ELAVL2_ENST00000380110.4_Missense_Mutation_p.S55L	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	26					regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S26L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		AACTGGTGACGAACAGTTGTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	LEU/SER,LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	333	305	315		77,77,77	5.9	1	9	dbSNP_134	315	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ELAVL2	NM_001171195.1,NM_001171197.1,NM_004432.3	145,145,145	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign,benign	26/347,26/347,26/360	23762156	2,13004	2203	4300	6503	23752156	SO:0001583	missense	1993			BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"RNA binding motif (RRM) containing"	3313	protein-coding gene	gene with protein product	"Hu antigen B"	601673	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.77C>T	9.37:g.23762156G>A	ENSP00000380479:p.Ser26Leu		23752156	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	37	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469605	0.63625	2.27E-4	1.16E-4	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	T;T;T;T;T	0.15372	2.43;2.84;2.84;2.84;2.78	5.92	5.92	0.95590	.	0.067483	0.64402	D	0.000008	T	0.12603	0.0306	N	0.14661	0.345	0.80722	D	1	B;B	0.31100	0.308;0.24	B;B	0.25759	0.018;0.063	T	0.11891	-1.0569	10	0.33940	T	0.23	.	20.33	0.98713	0.0:0.0:1.0:0.0	.	26;26	Q12926;Q12926-2	ELAV2_HUMAN;.	L	26;26;26;26;26;54;26	ENSP00000223951:S26L;ENSP00000380479:S26L;ENSP00000440998:S26L;ENSP00000369460:S26L;ENSP00000412602:S26L	ENSP00000223951:S26L	S	-	2	0	ELAVL2	23752156	1.000000	0.71417	0.966000	0.40874	0.969000	0.65631	9.714000	0.98744	2.810000	0.96702	0.585000	0.79938	TCG		0.433	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		A	23762156	G	A	23762156	3	1	61	1	0	0	0	0	1	0	0	0	5063	1059	37	1	1026	1	ELAVL2	9	23762156	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2280703	23762156	117451275	6225	14210										
IFNK	56832	broad.mit.edu	37	chr9	27524857	27524857	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatagacaatttcctgaaaGaaaagaaatacagtgactgt	9	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:27524857G>T	ENST00000276943.2	+	1	546	c.523G>T	c.(523-525)Gaa>Taa	p.E175*	MOB3B_ENST00000262244.5_Intron	NM_020124.2	NP_064509.2	Q9P0W0	IFNK_HUMAN	interferon, kappa	175					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of cell proliferation (GO:0008285)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of transcription, DNA-templated (GO:0006355)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.E175*(1)		large_intestine(1)	1		all_neural(11;7.9e-11)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.000158)		TTTCCTGAAAGAAAAGAAATA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											50	53	52					9																	27524857		2203	4300	6503	27514857	SO:0001587	stop_gained	56832			AF384048	CCDS6521.1	9p21.2	2008-02-05			ENSG00000147896	ENSG00000147896		"Interferons"	21714	protein-coding gene	gene with protein product		615326				12391192, 11514542	Standard	NM_020124		Approved		uc003zqp.3	Q9P0W0	OTTHUMG00000019715	ENST00000276943.2:c.523G>T	9.37:g.27524857G>T	ENSP00000276943:p.Glu175*		27514857	Q5T166	Nonsense_Mutation	SNP	ENST00000276943.2	37	CCDS6521.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624814	0.96660	.	.	ENSG00000147896	ENST00000276943	.	.	.	6.07	4.96	0.65561	.	0.532630	0.19438	N	0.114268	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.6435	8.8802	0.35370	0.1327:0.0:0.8673:0.0	.	.	.	.	X	175	.	ENSP00000276943:E175X	E	+	1	0	IFNK	27514857	0.599000	0.26891	0.870000	0.34147	0.968000	0.65278	1.855000	0.39378	1.234000	0.43709	0.650000	0.86243	GAA		0.418	IFNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051968.1	NM_020124		T	27524857	G	T	27524857	4	4	61	1	0	0	0	0	0	1	0	0	7572	943	33	2	525	2	IFNK	9	27524857	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3762701	27524857	113688574	6226	14211										
LINGO2	158038	broad.mit.edu	37	chr9	27950633	27950633	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacaccacagccagacccaGgaatggctgccagcatgata	9	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:27950633G>T	ENST00000379992.2	-	6	486	c.37C>A	c.(37-39)Ctg>Atg	p.L13M	LINGO2_ENST00000308675.3_Missense_Mutation_p.L13M	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	13						integral component of membrane (GO:0016021)		p.L13M(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		GCCAGACCCAGGAATGGCTGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	9											67	54	58					9																	27950633		2203	4300	6503	27940633	SO:0001583	missense	158038			AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.37C>A	9.37:g.27950633G>T	ENSP00000369328:p.Leu13Met		27940633	A8K4K7|B2RPM5|Q6ZMD0	Missense_Mutation	SNP	ENST00000379992.2	37	CCDS6524.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.634449	0.87660	.	.	ENSG00000174482	ENST00000379992;ENST00000308675	T;T	0.60920	0.15;0.15	5.74	5.74	0.90152	.	0.154753	0.44483	D	0.000446	T	0.72985	0.3529	M	0.76574	2.34	0.80722	D	1	P	0.49090	0.919	P	0.55161	0.77	T	0.71206	-0.4661	9	.	.	.	.	20.2825	0.98528	0.0:0.0:1.0:0.0	.	13	Q7L985	LIGO2_HUMAN	M	13	ENSP00000369328:L13M;ENSP00000310126:L13M	.	L	-	1	2	LINGO2	27940633	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.717000	0.74707	2.873000	0.98535	0.561000	0.74099	CTG		0.537	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		T	27950633	G	T	27950633	3	4	61	1	0	0	0	0	1	0	0	0	8839	991	35	2	1787	2	LINGO2	9	27950633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	425776	27950633	113262798	6227	14212										
DDX58	23586	broad.mit.edu	37	chr9	32466353	32466353	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtcattcatcattttttCtttgtacatgtttatttgtt	5	5	4	1	rs553716308	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32466353C>A	ENST00000379883.2	-	16	2429	c.2272G>T	c.(2272-2274)Gaa>Taa	p.E758*	DDX58_ENST00000379868.1_Nonsense_Mutation_p.E555*|DDX58_ENST00000379882.1_Nonsense_Mutation_p.E713*|DDX58_ENST00000542096.1_Nonsense_Mutation_p.E687*	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	758	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.E758*(1)|p.E758K(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		ATCATTTTTTCTTTGTACATG	0.368													C|||	4	0.000798722	0	0	5008	,	,		18582	0		0	False		,,,				2504	0.0041															2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	9											208	194	199					9																	32466353		2203	4300	6503	32456353	SO:0001587	stop_gained	23586			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2272G>T	9.37:g.32466353C>A	ENSP00000369213:p.Glu758*		32456353	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Nonsense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	C	43	9.933314	0.99299	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	.	.	.	5.45	5.45	0.79879	.	0.150289	0.44688	D	0.000425	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-24.3592	18.4259	0.90608	0.0:1.0:0.0:0.0	.	.	.	.	X	713;758;555;687	.	ENSP00000369197:E555X	E	-	1	0	DDX58	32456353	1.000000	0.71417	0.991000	0.47740	0.951000	0.60555	3.942000	0.56614	2.725000	0.93324	0.655000	0.94253	GAA		0.368	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		A	32466353	C	A	32466353	4	1	61	1	0	0	0	0	0	1	0	0	4381	922	32	2	517	2	DDX58	9	32466353	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4515720	32466353	108747078	6228	14213										
DDX58	23586	broad.mit.edu	37	chr9	32493818	32493818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacagatcagaaatgatatCggttgggataattctggttt	11	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32493818C>T	ENST00000379883.2	-	3	521	c.364G>A	c.(364-366)Gat>Aat	p.D122N	DDX58_ENST00000379868.1_5'UTR|DDX58_ENST00000379882.1_Missense_Mutation_p.D77N|DDX58_ENST00000545044.1_5'UTR|DDX58_ENST00000542096.1_Missense_Mutation_p.D51N	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	122	CARD 2.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.D122N(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GAAATGATATCGGTTGGGATA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	60	58					9																	32493818		2200	4295	6495	32483818	SO:0001583	missense	23586			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.364G>A	9.37:g.32493818C>T	ENSP00000369213:p.Asp122Asn		32483818	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	C	9.137	1.012784	0.19277	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542096;ENST00000542960	T;T;T	0.05925	3.5;3.51;3.37	4.33	3.41	0.39046	.	0.297626	0.25830	N	0.028030	T	0.10809	0.0264	M	0.70595	2.14	0.21579	N	0.999631	D;P;P	0.53312	0.959;0.931;0.931	P;B;B	0.45406	0.479;0.286;0.227	T	0.11131	-1.0600	10	0.62326	D	0.03	-2.1414	9.435	0.38632	0.1609:0.6827:0.1563:0.0	.	77;51;122	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	N	77;122;51;122	ENSP00000369212:D77N;ENSP00000369213:D122N;ENSP00000442160:D51N	ENSP00000369212:D77N	D	-	1	0	DDX58	32483818	0.034000	0.19679	0.173000	0.22940	0.084000	0.17831	1.658000	0.37376	1.386000	0.46466	0.650000	0.86243	GAT		0.279	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		T	32493818	C	T	32493818	3	4	61	1	0	0	0	0	1	0	0	0	4381	884	31	1	2477	1	DDX58	9	32493818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27465	32493818	108719613	6229	14214										
TOPORS	10210	broad.mit.edu	37	chr9	32542594	32542594	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctagttcttgatctcttTttgtctcttctccctctagg	5	12	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32542594T>G	ENST00000360538.2	-	3	2045	c.1929A>C	c.(1927-1929)aaA>aaC	p.K643N	TOPORS_ENST00000379858.1_Missense_Mutation_p.K578N	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	643	Arg-rich.|Interaction with SUMO1.|Interaction with TOP1.|Interaction with p53/TP53.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K643N(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TTGATCTCTTTTTGTCTCTTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											384	358	367					9																	32542594		2203	4300	6503	32532594	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1929A>C	9.37:g.32542594T>G	ENSP00000353735:p.Lys643Asn		32532594	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672682	0.29693	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18338	2.22;2.28	6.16	0.801	0.18679	.	0.000000	0.53938	D	0.000051	T	0.11324	0.0276	N	0.19112	0.55	0.35127	D	0.767551	P	0.50272	0.933	P	0.44860	0.462	T	0.27191	-1.0081	10	0.32370	T	0.25	-12.627	10.0577	0.42255	0.0:0.3728:0.0:0.6272	.	643	Q9NS56	TOPRS_HUMAN	N	643;578	ENSP00000353735:K643N;ENSP00000369187:K578N	ENSP00000353735:K643N	K	-	3	2	TOPORS	32532594	0.963000	0.33076	1.000000	0.80357	0.874000	0.50279	0.172000	0.16704	0.201000	0.20466	0.528000	0.53228	AAA		0.418	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		G	32542594	T	G	32542594	3	3	61	1	0	0	0	0	1	0	0	0	16410	1838	64	4	1212	4	TOPORS	9	32542594	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	48776	32542594	108670837	6230	14215										
TAF1L	138474	broad.mit.edu	37	chr9	32631214	32631214	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgagatgggtagaggcatTtacgcacattttcacggagt	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32631214T>G	ENST00000242310.4	-	1	4453	c.4364A>C	c.(4363-4365)aAa>aCa	p.K1455T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1455	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.K1455T(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GTAGAGGCATTTACGCACATT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											249	210	223					9																	32631214		2203	4300	6503	32621214	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4364A>C	9.37:g.32631214T>G	ENSP00000418379:p.Lys1455Thr		32621214	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.046558	0.75846	.	.	ENSG00000122728	ENST00000242310	T	0.29655	1.56	1.17	1.17	0.20885	Bromodomain (5);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.23532	0.0569	L	0.48642	1.525	0.48696	D	0.99969	B	0.23591	0.088	B	0.26094	0.066	T	0.05146	-1.0903	10	0.44086	T	0.13	.	6.3927	0.21595	0.0:0.0:0.0:1.0	.	1455	Q8IZX4	TAF1L_HUMAN	T	1455	ENSP00000418379:K1455T	ENSP00000418379:K1455T	K	-	2	0	TAF1L	32621214	1.000000	0.71417	0.986000	0.45419	0.936000	0.57629	3.651000	0.54431	0.431000	0.26258	0.172000	0.16884	AAA		0.453	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32631214	T	G	32631214	3	3	61	1	0	0	0	0	1	0	0	0	15562	1841	64	4	1120	4	TAF1L	9	32631214	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	88620	32631214	108582217	6231	14216										
TAF1L	138474	broad.mit.edu	37	chr9	32632006	32632006	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctttcccctcttcatctCgaaatgtgcgataaatcttg	5	12	5	0	rs199906668		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32632006C>T	ENST00000242310.4	-	1	3661	c.3572G>A	c.(3571-3573)cGa>cAa	p.R1191Q	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1191					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.R1191Q(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTCTTCATCTCGAAATGTGCG	0.453													C|||	1	0.000199681	0	0	5008	,	,		24069	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						C	GLN/ARG	0,4406		0,0,2203	204	166	179		3572	0.5	1	9		179	1,8599	1.2+/-3.3	0,1,4299	no	missense	TAF1L	NM_153809.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1191/1827	32632006	1,13005	2203	4300	6503	32622006	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3572G>A	9.37:g.32632006C>T	ENSP00000418379:p.Arg1191Gln		32622006	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756229	0.49362	0.0	1.16E-4	ENSG00000122728	ENST00000242310	T	0.17213	2.29	0.479	0.479	0.16796	.	0.200519	0.46442	D	0.000285	T	0.11239	0.0274	L	0.38175	1.15	0.38657	D	0.951982	B	0.22746	0.074	B	0.23150	0.044	T	0.12811	-1.0533	10	0.33940	T	0.23	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1191	Q8IZX4	TAF1L_HUMAN	Q	1191	ENSP00000418379:R1191Q	ENSP00000418379:R1191Q	R	-	2	0	TAF1L	32622006	0.998000	0.40836	0.997000	0.53966	0.826000	0.46750	1.734000	0.38166	0.507000	0.28148	0.195000	0.17529	CGA		0.453	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			T	32632006	C	T	32632006	3	4	61	1	0	0	0	0	1	0	0	0	15562	884	31	1	1912	1	TAF1L	9	32632006	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	792	32632006	108581425	6232	14217										
TAF1L	138474	broad.mit.edu	37	chr9	32634895	32634895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcccagccaatggaaggGtcagctttccatcctcagat	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32634895G>A	ENST00000242310.4	-	1	772	c.683C>T	c.(682-684)aCc>aTc	p.T228I	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	228					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.T228I(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CAATGGAAGGGTCAGCTTTCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											143	131	135					9																	32634895		2203	4300	6503	32624895	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.683C>T	9.37:g.32634895G>A	ENSP00000418379:p.Thr228Ile		32624895	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	8.357	0.832243	0.16820	.	.	ENSG00000122728	ENST00000242310	T	0.08282	3.11	1.04	1.04	0.20106	.	0.101306	0.64402	D	0.000002	T	0.08582	0.0213	L	0.57536	1.79	0.33675	D	0.611367	B	0.20887	0.049	B	0.19946	0.027	T	0.06789	-1.0807	10	0.41790	T	0.15	.	7.4859	0.27432	0.0:0.0:1.0:0.0	.	228	Q8IZX4	TAF1L_HUMAN	I	228	ENSP00000418379:T228I	ENSP00000418379:T228I	T	-	2	0	TAF1L	32624895	1.000000	0.71417	0.732000	0.30844	0.279000	0.26890	3.452000	0.52971	0.507000	0.28148	0.195000	0.17529	ACC		0.473	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32634895	G	A	32634895	3	1	61	1	0	0	0	0	1	0	0	0	15562	1261	44	3	4801	3	TAF1L	9	32634895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2889	32634895	108578536	6233	14218										
TAF1L	138474	broad.mit.edu	37	chr9	32634963	32634963	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcagattctgaatcagaGtaactactgaaatccacttt	5	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:32634963G>T	ENST00000242310.4	-	1	704	c.615C>A	c.(613-615)taC>taA	p.Y205*	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	205					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.Y205*(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTGAATCAGAGTAACTACTGA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											135	122	126					9																	32634963		2203	4300	6503	32624963	SO:0001587	stop_gained	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.615C>A	9.37:g.32634963G>T	ENSP00000418379:p.Tyr205*		32624963	Q0VG57	Nonsense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505154	0.44558	.	.	ENSG00000122728	ENST00000242310	.	.	.	1.04	-0.053	0.13820	.	0.174579	0.52532	D	0.000077	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.9434	0.13976	0.2731:0.0:0.7269:0.0	.	.	.	.	X	205	.	ENSP00000418379:Y205X	Y	-	3	2	TAF1L	32624963	1.000000	0.71417	0.790000	0.31976	0.284000	0.27059	0.412000	0.21131	0.507000	0.28148	0.195000	0.17529	TAC		0.468	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			T	32634963	G	T	32634963	4	4	61	1	0	0	0	0	0	1	0	0	15562	1024	36	2	4869	2	TAF1L	9	32634963	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68	32634963	108578468	6234	14219										
DNAJA1	3301	broad.mit.edu	37	chr9	33026823	33026823	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaacagtttaaacagattTctcaagcttacgaagttctc	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33026823T>G	ENST00000330899.4	+	3	328	c.145T>G	c.(145-147)Tct>Gct	p.S49A	DNAJA1_ENST00000495015.1_Intron|DNAJA1_ENST00000544625.1_Intron|APTX_ENST00000473270.1_5'Flank	NM_001539.2	NP_001530.1	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1	49	J.				androgen receptor signaling pathway (GO:0030521)|DNA damage response, detection of DNA damage (GO:0042769)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of apoptotic process (GO:0043065)|protein folding (GO:0006457)|protein localization to mitochondrion (GO:0070585)|regulation of protein transport (GO:0051223)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasmic side of endoplasmic reticulum membrane (GO:0098554)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|G-protein coupled receptor binding (GO:0001664)|Hsp70 protein binding (GO:0030544)|low-density lipoprotein particle receptor binding (GO:0050750)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.S49A(1)		large_intestine(2)|ovary(1)|skin(3)	6			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		TAAACAGATTTCTCAAGCTTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											59	65	63					9																	33026823		2203	4300	6503	33016823	SO:0001583	missense	3301			L08069	CCDS6533.1	9p13.3	2011-09-02			ENSG00000086061	ENSG00000086061		"Heat shock proteins / DNAJ (HSP40)"	5229	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 7"	602837		HSJ2		8334160, 11147971	Standard	NM_001539		Approved	HSPF4, hdj-2, dj-2, NEDD7	uc003zsd.1	P31689	OTTHUMG00000019760	ENST00000330899.4:c.145T>G	9.37:g.33026823T>G	ENSP00000369127:p.Ser49Ala		33016823	Q5T7Q0|Q86TL9	Missense_Mutation	SNP	ENST00000330899.4	37	CCDS6533.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.748187	0.69533	.	.	ENSG00000086061	ENST00000330899	T	0.30981	1.51	4.67	4.67	0.58626	Heat shock protein DnaJ, N-terminal (5);Heat shock protein DnaJ, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	L	0.34521	1.04	0.80722	D	1	P;P	0.49783	0.928;0.928	P;P	0.51999	0.687;0.687	T	0.03278	-1.1053	10	0.34782	T	0.22	-11.1688	12.3554	0.55171	0.0:0.0:0.0:1.0	.	49;49	Q86TL9;P31689	.;DNJA1_HUMAN	A	49	ENSP00000369127:S49A	ENSP00000369127:S49A	S	+	1	0	DNAJA1	33016823	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.947000	0.87758	1.874000	0.54306	0.379000	0.24179	TCT		0.378	DNAJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052031.1			G	33026823	T	G	33026823	3	3	61	1	0	0	0	0	1	0	0	0	4622	1783	62	4	151	4	DNAJA1	9	33026823	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	391860	33026823	108186608	6235	14220										
CHMP5	51510	broad.mit.edu	37	chr9	33266076	33266076	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgagctagtgaagtataaGgatcagatcaagaagatgag	13	4	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33266076G>T	ENST00000223500.8	+	2	275	c.138G>T	c.(136-138)aaG>aaT	p.K46N	BAG1_ENST00000472232.3_5'Flank|CHMP5_ENST00000419016.2_Missense_Mutation_p.K46N|BAG1_ENST00000379704.2_5'Flank	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	46					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.K46N(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			TGAAGTATAAGGATCAGATCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	76	79					9																	33266076		2203	4300	6503	33256076	SO:0001583	missense	51510			AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"Charged multivesicular body proteins"	26942	protein-coding gene	gene with protein product		610900	"chromosome 9 open reading frame 83", "chromatin modifying protein 5"	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765	ENST00000223500.8:c.138G>T	9.37:g.33266076G>T	ENSP00000223500:p.Lys46Asn		33256076	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	37	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.030850	0.75504	.	.	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.72505	-0.66;-0.66	5.56	2.29	0.28610	.	0.000000	0.85682	D	0.000000	D	0.83413	0.5249	M	0.88512	2.96	0.47994	D	0.999568	D;B	0.67145	0.996;0.45	D;P	0.68353	0.957;0.547	D	0.84433	0.0578	10	0.87932	D	0	-2.8598	9.9384	0.41565	0.2671:0.0:0.7329:0.0	.	46;46	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	N	46	ENSP00000223500:K46N;ENSP00000442725:K46N	ENSP00000223500:K46N	K	+	3	2	CHMP5	33256076	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.165000	0.31822	0.719000	0.32188	0.462000	0.41574	AAG		0.448	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410		T	33266076	G	T	33266076	3	4	61	1	0	0	0	0	1	0	0	0	3365	991	35	2	144	2	CHMP5	9	33266076	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239253	33266076	107947355	6236	14221										
NFX1	4799	broad.mit.edu	37	chr9	33294529	33294529	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctaataggattggtagaaGaaattacagttcaccacctc	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33294529G>T	ENST00000379540.3	+	2	199	c.137G>T	c.(136-138)aGa>aTa	p.R46I	NFX1_ENST00000318524.6_Missense_Mutation_p.R46I|NFX1_ENST00000379521.4_Missense_Mutation_p.R46I	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	46					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R46I(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATTGGTAGAAGAAATTACAGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											138	144	142					9																	33294529		2203	4300	6503	33284529	SO:0001583	missense	4799			U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.137G>T	9.37:g.33294529G>T	ENSP00000368856:p.Arg46Ile		33284529	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	37	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.089515	0.76756	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.30448	1.9;1.58;1.53	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.46444	0.1393	L	0.34521	1.04	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.91635	0.999;0.994;0.962;0.999	T	0.44682	-0.9312	10	0.87932	D	0	.	16.7231	0.85415	0.0:0.0:1.0:0.0	.	46;46;46;46	F5GXD0;Q12986;Q12986-2;Q12986-3	.;NFX1_HUMAN;.;.	I	46	ENSP00000368856:R46I;ENSP00000368836:R46I;ENSP00000317695:R46I	ENSP00000317695:R46I	R	+	2	0	NFX1	33284529	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.698000	0.74608	2.528000	0.85240	0.544000	0.68410	AGA		0.413	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33294529	G	T	33294529	3	4	61	1	0	0	0	0	1	0	0	0	10418	942	33	2	143	2	NFX1	9	33294529	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28453	33294529	107918902	6237	14222										
NFX1	4799	broad.mit.edu	37	chr9	33295406	33295406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagaaccatgtgctaaaGaatgtggaaacgcacacagg	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33295406G>T	ENST00000379540.3	+	2	1076	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N	NFX1_ENST00000318524.6_Missense_Mutation_p.K338N|NFX1_ENST00000379521.4_Missense_Mutation_p.K338N	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	338					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K338N(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATGTGCTAAAGAATGTGGAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											64	62	63					9																	33295406		2203	4300	6503	33285406	SO:0001583	missense	4799			U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1014G>T	9.37:g.33295406G>T	ENSP00000368856:p.Lys338Asn		33285406	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	37	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657214	0.47467	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.51574	0.7;0.7;0.7	5.91	3.66	0.41972	.	0.106915	0.64402	D	0.000010	T	0.62392	0.2424	M	0.72118	2.19	0.45284	D	0.998284	D;D;P;D;P	0.71674	0.998;0.99;0.572;0.998;0.858	D;P;B;D;P	0.68621	0.959;0.697;0.122;0.959;0.491	T	0.62158	-0.6913	10	0.40728	T	0.16	.	10.1027	0.42515	0.1953:0.0:0.8047:0.0	.	338;222;338;338;338	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	N	338	ENSP00000368856:K338N;ENSP00000368836:K338N;ENSP00000317695:K338N	ENSP00000317695:K338N	K	+	3	2	NFX1	33285406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.374000	0.44274	1.413000	0.46997	0.643000	0.83706	AAG		0.373	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33295406	G	T	33295406	3	4	61	1	0	0	0	0	1	0	0	0	10418	933	33	2	1020	2	NFX1	9	33295406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	877	33295406	107918025	6238	14223										
AQP3	360	broad.mit.edu	37	chr9	33443768	33443768	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttaaggccttaccagaGacctggccagcgatgaggat	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33443768G>T	ENST00000297991.4	-	2	311	c.231C>A	c.(229-231)gtC>gtA	p.V77V	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	77					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)	p.V77V(1)		endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CCTTACCAGAGACCTGGCCAG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	9											55	48	50					9																	33443768		2203	4300	6503	33433768	SO:0001819	synonymous_variant	360				CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.231C>A	9.37:g.33443768G>T			33433768	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	37	CCDS6542.1																																																																																				0.607	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		T	33443768	G	T	33443768	2	4	61	1	0	0	0	0	0	0	0	1	827	929	33	2		2	AQP3	9	33443768	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148362	33443768	107769663	6239	14224										
UBAP2	54926	broad.mit.edu	37	chr9	33922582	33922582	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggagctgggctggctgcGctgacccgagccactctgag	16	13	1	2	rs138140692		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33922582G>A	ENST00000263228.3	+	0	4075				UBAP2_ENST00000449054.1_Missense_Mutation_p.R1094C|UBAP2_ENST00000379239.4_Missense_Mutation_p.R827C|UBAP2_ENST00000379235.1_Missense_Mutation_p.R333C|UBAP2_ENST00000360802.1_Missense_Mutation_p.R1094C|UBAP2_ENST00000539807.1_Missense_Mutation_p.R849C|UBAP2_ENST00000379238.1_Missense_Mutation_p.R1094C	NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2						protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)	p.R1094C(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		GGCTGGCTGCGCTGACCCGAG	0.602											OREG0019144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	9						G	CYS/ARG	0,4406		0,0,2203	39	40	40		3280	6.2	1	9	dbSNP_134	40	2,8598	2.2+/-6.3	0,2,4298	yes	missense	UBAP2	NM_018449.2	180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	1094/1120	33922582	2,13004	2203	4300	6503	33912582	SO:0001628	intergenic_variant	55833			AK000426	CCDS6546.1	9p11.2	2008-02-05			ENSG00000107341	ENSG00000107341		"Ubiquitin-conjugating enzymes E2"	19907	protein-coding gene	gene with protein product		612506				12037680	Standard	XM_005251496		Approved	UBC3B, CDC34B, FLJ20419, MGC10481	uc003ztm.3	Q712K3	OTTHUMG00000019797		9.37:g.33922582G>A		843	33912582	D3DRL5|Q9NX64	Missense_Mutation	SNP	ENST00000263228.3	37	CCDS6546.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.412542	0.62511	0.0	2.33E-4	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62	6.17	6.17	0.99709	.	0.091243	0.85682	D	0.000000	T	0.71542	0.3352	M	0.80982	2.52	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;P	0.66196	0.917;0.917;0.942;0.877	T	0.72959	-0.4133	10	0.87932	D	0	-9.9635	19.8676	0.96824	0.0:0.0:1.0:0.0	.	849;827;1003;1094	F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;UBAP2_HUMAN	C	1094;1094;1094;1003;333;827;849;528	ENSP00000368540:R1094C;ENSP00000416932:R1094C;ENSP00000354039:R1094C;ENSP00000368537:R333C;ENSP00000368541:R827C;ENSP00000439329:R849C	ENSP00000259602:R528C	R	-	1	0	UBAP2	33912582	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.126000	0.71635	2.941000	0.99782	0.655000	0.94253	CGC		0.602	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052118.1	NM_017811		A	33922582	G	A	33922582	1	1	61	0	1	0	0	0	0	0	0	0	16877	1087	38	1		1	UBAP2	9	33922582	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	478814	33922582	107290849	6240	14225										
UBAP2	55833	broad.mit.edu	37	chr9	33956100	33956100	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccaggtaagatgtgattCtctgctggagcagatgaggc	14	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:33956100C>A	ENST00000379238.1	-	11	960	c.843G>T	c.(841-843)gaG>gaT	p.E281D	UBAP2_ENST00000418786.2_Missense_Mutation_p.E228D|UBAP2_ENST00000449054.1_Missense_Mutation_p.E281D|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000360802.1_Missense_Mutation_p.E281D|UBAP2_ENST00000539807.1_Missense_Mutation_p.E36D					ubiquitin associated protein 2									p.E281D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AGATGTGATTCTCTGCTGGAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	9											117	127	123					9																	33956100		2203	4300	6503	33946100	SO:0001583	missense	55833			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.843G>T	9.37:g.33956100C>A	ENSP00000368540:p.Glu281Asp		33946100		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563663	0.45694	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379260;ENST00000539807;ENST00000418786;ENST00000412543;ENST00000421278	T;T;T;T;T;T	0.39229	2.45;2.45;2.45;1.95;1.75;1.09	5.2	2.96	0.34315	.	0.147219	0.64402	N	0.000013	T	0.42743	0.1216	M	0.78801	2.425	0.46798	D	0.9992	B;P;B;B;B;B	0.34587	0.004;0.458;0.022;0.022;0.328;0.357	B;B;B;B;B;B	0.36134	0.006;0.129;0.018;0.018;0.061;0.218	T	0.42292	-0.9460	10	0.49607	T	0.09	-6.2135	8.2279	0.31579	0.0:0.6742:0.1365:0.1893	.	228;206;36;190;206;281	E7EWG4;F5H4D5;F5H2U4;F5H2C8;B4DH66;Q5T6F2	.;.;.;.;.;UBAP2_HUMAN	D	281;281;281;190;199;36;228;228;135	ENSP00000368540:E281D;ENSP00000416932:E281D;ENSP00000354039:E281D;ENSP00000439329:E36D;ENSP00000404436:E228D;ENSP00000414800:E228D	ENSP00000354039:E281D	E	-	3	2	UBAP2	33946100	1.000000	0.71417	0.990000	0.47175	0.911000	0.54048	0.524000	0.22940	1.157000	0.42530	0.491000	0.48974	GAG		0.338	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		A	33956100	C	A	33956100	3	1	61	1	0	0	0	0	1	0	0	0	16877	912	32	2	2592	2	UBAP2	9	33956100	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33518	33956100	107257331	6241	14226										
UBAP2	55833	broad.mit.edu	37	chr9	34017093	34017093	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgattgtgctgctgaaatCtgtggtttttcccgagcacc	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34017093C>A	ENST00000379238.1	-	2	171	c.54G>T	c.(52-54)caG>caT	p.Q18H	UBAP2_ENST00000418786.2_Missense_Mutation_p.Q18H|RNU7-36P_ENST00000516597.1_RNA|UBAP2_ENST00000449054.1_Missense_Mutation_p.Q18H|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000360802.1_Missense_Mutation_p.Q18H|UBAP2_ENST00000539807.1_5'UTR|UBAP2_ENST00000480885.1_5'UTR					ubiquitin associated protein 2									p.Q18H(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CTGCTGAAATCTGTGGTTTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	9											138	119	125					9																	34017093		2203	4300	6503	34007093	SO:0001583	missense	55833			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.54G>T	9.37:g.34017093C>A	ENSP00000368540:p.Gln18His		34007093		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.157514	0.38119	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000351580;ENST00000418786;ENST00000412543	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.82	3.94	0.45596	.	0.240274	0.43747	N	0.000521	T	0.42854	0.1221	L	0.55990	1.75	0.33921	D	0.640939	B;D	0.69078	0.023;0.997	B;D	0.64144	0.01;0.922	T	0.55108	-0.8192	10	0.48119	T	0.1	-0.4254	6.9595	0.24590	0.2991:0.6047:0.0:0.0962	.	18;18	E7EWG4;Q5T6F2	.;UBAP2_HUMAN	H	18	ENSP00000368540:Q18H;ENSP00000416932:Q18H;ENSP00000354039:Q18H;ENSP00000404436:Q18H;ENSP00000414800:Q18H	ENSP00000259602:Q18H	Q	-	3	2	UBAP2	34007093	0.999000	0.42202	1.000000	0.80357	0.195000	0.23768	0.580000	0.23803	0.767000	0.33267	-0.182000	0.12963	CAG		0.333	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		A	34017093	C	A	34017093	3	1	61	1	0	0	0	0	1	0	0	0	16877	912	32	2	3417	2	UBAP2	9	34017093	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60993	34017093	107196338	6242	14227										
DCAF12	25853	broad.mit.edu	37	chr9	34125241	34125241	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcttcacaggaggaagtCttttccttttgtgaagcgag	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34125241C>A	ENST00000361264.4	-	2	454	c.113G>T	c.(112-114)aGa>aTa	p.R38I	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	38					protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)		p.R38I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						AGGAGGAAGTCTTTTCCTTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											81	77	78					9																	34125241		2203	4300	6503	34115241	SO:0001583	missense	25853			AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	19911	protein-coding gene	gene with protein product	"cancer/testis antigen 102"		"KIAA1892", "WD repeat domain 40A"	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.113G>T	9.37:g.34125241C>A	ENSP00000355114:p.Arg38Ile		34115241	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Missense_Mutation	SNP	ENST00000361264.4	37	CCDS6549.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386822	0.82902	.	.	ENSG00000198876	ENST00000361264;ENST00000396990;ENST00000450964	T;T;T	0.65178	1.78;-0.14;1.09	4.76	3.87	0.44632	.	0.058486	0.64402	D	0.000002	T	0.73753	0.3627	M	0.63843	1.955	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	T	0.76446	-0.2956	10	0.66056	D	0.02	-2.8774	13.0027	0.58685	0.0:0.9222:0.0:0.0778	.	38	Q5T6F0	DCA12_HUMAN	I	38;20;17	ENSP00000355114:R38I;ENSP00000380187:R20I;ENSP00000415833:R17I	ENSP00000355114:R38I	R	-	2	0	DCAF12	34115241	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.965000	0.63708	1.240000	0.43803	0.655000	0.94253	AGA		0.433	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397		A	34125241	C	A	34125241	3	1	61	1	0	0	0	0	1	0	0	0	4269	913	32	2	1280	2	DCAF12	9	34125241	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108148	34125241	107088190	6243	14228										
KIF24	347240	broad.mit.edu	37	chr9	34290240	34290240	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaagctgatccacacaaaGaggtgctttcttggctggga	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34290240G>A	ENST00000402558.2	-	4	1083	c.1059C>T	c.(1057-1059)ctC>ctT	p.L353L	KIF24_ENST00000345050.2_Intron|KIF24_ENST00000379174.3_Intron|KIF24_ENST00000379166.2_Silent_p.L353L			Q5T7B8	KIF24_HUMAN	kinesin family member 24	353	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L353L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TCCACACAAAGAGGTGCTTTC	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	9											131	122	125					9																	34290240		1873	4105	5978	34280240	SO:0001819	synonymous_variant	347240			AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.1059C>T	9.37:g.34290240G>A			34280240	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Silent	SNP	ENST00000402558.2	37	CCDS6551.2																																																																																				0.423	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			A	34290240	G	A	34290240	2	1	61	1	0	0	0	0	0	0	0	1	8313	929	33	3		3	KIF24	9	34290240	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164999	34290240	106923191	6244	14229										
C9orf25	203259	broad.mit.edu	37	chr9	34405953	34405953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgtcagagatggaggcggCggctgggtcctgtggggaga	20	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34405953C>T	ENST00000445726.1	-	2	376	c.70G>A	c.(70-72)Gcc>Acc	p.A24T	FAM219A_ENST00000379080.1_Missense_Mutation_p.A12T|FAM219A_ENST00000379089.1_Missense_Mutation_p.A23T|FAM219A_ENST00000379084.1_Missense_Mutation_p.A23T|FAM219A_ENST00000379087.1_Missense_Mutation_p.A23T|FAM219A_ENST00000297620.4_Missense_Mutation_p.A24T|FAM219A_ENST00000379081.1_Missense_Mutation_p.A12T|FAM219A_ENST00000379078.1_Missense_Mutation_p.A23T	NM_001184940.1|NM_001184941.1	NP_001171869.1|NP_001171870.1	Q8IW50	F219A_HUMAN	family with sequence similarity 219, member A	24								p.A24T(1)									ATGGAGGCGGCGGCTGGGTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	9											61	64	63					9																	34405953		2203	4300	6503	34395953	SO:0001583	missense	203259			AK096350	CCDS6556.1, CCDS55304.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164970	ENSG00000164970			19920	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 25"	C9orf25		9110174, 8619474	Standard	NM_147202		Approved	bA573M23.5, FLJ39031	uc011lok.2	Q8IW50	OTTHUMG00000019822	ENST00000445726.1:c.70G>A	9.37:g.34405953C>T	ENSP00000392452:p.Ala24Thr		34395953	A2A364|B4DFE1|B4DSR8|Q5T590|Q5T591|Q5T592|Q5T594|Q5T595|Q8TAZ8	Missense_Mutation	SNP	ENST00000445726.1	37	CCDS55304.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090515	0.76756	.	.	ENSG00000164970	ENST00000379089;ENST00000379087;ENST00000379084;ENST00000379081;ENST00000379080;ENST00000445726;ENST00000297620;ENST00000422409;ENST00000379078	.	.	.	5.2	4.3	0.51218	.	0.121131	0.56097	D	0.000037	T	0.69223	0.3087	L	0.56769	1.78	0.42430	D	0.992678	P;D;B;B;D	0.89917	0.579;1.0;0.296;0.296;0.999	B;D;B;B;D	0.83275	0.162;0.996;0.049;0.049;0.99	T	0.68985	-0.5265	9	0.45353	T	0.12	-14.3375	10.0239	0.42059	0.0:0.9063:0.0:0.0937	.	13;24;13;13;24	Q8IW50-4;Q8IW50;Q8IW50-3;Q8IW50-2;Q8IW50-6	.;CI025_HUMAN;.;.;.	T	23;23;23;12;12;24;24;23;23	.	ENSP00000297620:A24T	A	-	1	0	C9orf25	34395953	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	3.068000	0.50018	1.212000	0.43366	-0.221000	0.12465	GCC		0.582	FAM219A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001184940		T	34405953	C	T	34405953	3	4	61	1	0	0	0	0	1	0	0	0	2482	768	27	1	507	1	C9orf25	9	34405953	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115713	34405953	106807478	6245	14230										
DNAI1	27019	broad.mit.edu	37	chr9	34490025	34490025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaggttctcaggagtctgTcaaggtgatttcagaaacag	11	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34490025T>C	ENST00000242317.4	+	6	575	c.404T>C	c.(403-405)gTc>gCc	p.V135A	DNAI1_ENST00000488369.1_3'UTR	NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	135					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)	p.V135A(1)		autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		CAGGAGTCTGTCAAGGTGATT	0.507									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	9											56	59	58					9																	34490025		2203	4300	6503	34480025	SO:0001583	missense	27019	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.404T>C	9.37:g.34490025T>C	ENSP00000242317:p.Val135Ala		34480025	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	T	0.368	-0.935821	0.02340	.	.	ENSG00000122735	ENST00000396929;ENST00000242317;ENST00000437363	T;T	0.74106	-0.81;-0.66	4.69	0.548	0.17208	.	48.621200	0.01020	N	0.003977	T	0.42223	0.1193	N	0.01109	-1.01	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.54662	-0.8260	10	0.05351	T	0.99	.	6.347	0.21355	0.0:0.4488:0.0:0.5512	.	135	Q9UI46	DNAI1_HUMAN	A	124;135;124	ENSP00000242317:V135A;ENSP00000395396:V124A	ENSP00000242317:V135A	V	+	2	0	DNAI1	34480025	0.001000	0.12720	0.033000	0.17914	0.986000	0.74619	-0.659000	0.05323	0.093000	0.17368	-0.146000	0.13790	GTC		0.507	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			C	34490025	T	C	34490025	3	2	61	1	0	0	0	0	1	0	0	0	4620	1667	58	4	426	4	DNAI1	9	34490025	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	84072	34490025	106723406	6246	14231										
CNTFR	1271	broad.mit.edu	37	chr9	34552808	34552808	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatgtactccttcccggcGtaggcatctgtgatggtgtg	12	9	1	1	rs202050719		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34552808G>A	ENST00000378980.3	-	8	1106	c.813C>T	c.(811-813)taC>taT	p.Y271Y	CNTFR_ENST00000351266.4_Silent_p.Y271Y	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	271	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)	p.Y271Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		CCTTCCCGGCGTAGGCATCTG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	9											186	138	154					9																	34552808		2203	4300	6503	34542808	SO:0001819	synonymous_variant	1271			M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.813C>T	9.37:g.34552808G>A			34542808	Q5U050	Silent	SNP	ENST00000378980.3	37	CCDS6558.1																																																																																				0.622	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1			A	34552808	G	A	34552808	2	1	61	1	0	0	0	0	0	0	0	1	3644	1140	40	1		1	CNTFR	9	34552808	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62783	34552808	106660623	6247	14232										
ARID3C	138715	broad.mit.edu	37	chr9	34622066	34622066	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatgttgatactgctgatGccactgcctgccagattaag	10	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34622066G>A	ENST00000378909.2	-	6	1181	c.1089C>T	c.(1087-1089)ggC>ggT	p.G363G	DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000378916.4_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	363	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.G363G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		TACTGCTGATGCCACTGCCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	9											135	115	122					9																	34622066		2203	4300	6503	34612066	SO:0001819	synonymous_variant	138715				CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.1089C>T	9.37:g.34622066G>A			34612066		Silent	SNP	ENST00000378909.2	37	CCDS35006.1																																																																																				0.517	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		A	34622066	G	A	34622066	2	1	61	1	0	0	0	0	0	0	0	1	918	1306	46	3		3	ARID3C	9	34622066	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69258	34622066	106591365	6248	14233										
KIAA1045	23349	broad.mit.edu	37	chr9	34971626	34971626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatccgccccacccggaagCtggatgatgacaaacctcca	8	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:34971626C>A	ENST00000242315.3	+	2	413	c.331C>A	c.(331-333)Ctg>Atg	p.L111M	KIAA1045_ENST00000476115.2_Intron|KIAA1045_ENST00000544237.1_Missense_Mutation_p.L111M	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	111							metal ion binding (GO:0046872)	p.L111M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			CACCCGGAAGCTGGATGATGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											123	132	130					9																	34971626		1928	4145	6073	34961626	SO:0001583	missense	23349			AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.331C>A	9.37:g.34971626C>A	ENSP00000242315:p.Leu111Met		34961626	B7Z253|Q58FE9|Q5T662	Missense_Mutation	SNP	ENST00000242315.3	37	CCDS43796.1	.	.	.	.	.	.	.	.	.	.	c	21.5	4.153888	0.78114	.	.	ENSG00000122733	ENST00000544237;ENST00000242315	.	.	.	6.03	5.12	0.69794	.	0.161033	0.43416	D	0.000562	T	0.70439	0.3224	L	0.57536	1.79	0.37937	D	0.932203	D	0.76494	0.999	D	0.69142	0.962	T	0.71283	-0.4639	8	.	.	.	-0.0737	14.7006	0.69154	0.0:0.93:0.0:0.07	.	111	Q9UPV7	K1045_HUMAN	M	111	.	.	L	+	1	2	KIAA1045	34961626	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	0.699000	0.25586	2.861000	0.98227	0.655000	0.94253	CTG		0.592	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592		A	34971626	C	A	34971626	3	1	61	1	0	0	0	0	1	0	0	0	8228	796	28	2	333	2	KIAA1045	9	34971626	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	349560	34971626	106241805	6249	14234										
VCP	7415	broad.mit.edu	37	chr9	35066724	35066724	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacggcttaaggtatacctcGaagagattaccagtaatgcc	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35066724G>A	ENST00000358901.6	-	4	1288	c.393C>T	c.(391-393)ttC>ttT	p.F131F		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	131					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)	p.F131F(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGTATACCTCGAAGAGATTAC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9											144	119	127					9																	35066724		2203	4300	6503	35056724	SO:0001819	synonymous_variant	7415			AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.393C>T	9.37:g.35066724G>A			35056724	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Silent	SNP	ENST00000358901.6	37	CCDS6573.1																																																																																				0.473	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		A	35066724	G	A	35066724	2	1	61	1	0	0	0	0	0	0	0	1	17180	1049	37	1		1	VCP	9	35066724	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95098	35066724	106146707	6250	14235										
FANCG	2189	broad.mit.edu	37	chr9	35074137	35074137	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactttggcagagatgtccGaaattcttcaaggaaggcgt	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35074137G>A	ENST00000378643.3	-	14	2328	c.1837C>T	c.(1837-1839)Cgg>Tgg	p.R613W	VCP_ENST00000358901.6_5'Flank|FANCG_ENST00000476212.1_5'UTR	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	613					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)	p.R613W(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AGAGATGTCCGAAATTCTTCA	0.537			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	1	Substitution - Missense(1)	large_intestine(1)	9											72	70	71					9																	35074137		2203	4300	6503	35064137	SO:0001583	missense	2189			AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"Fanconi anemia, complementation groups"	3588	protein-coding gene	gene with protein product	"DNA repair protein XRCC9", "X-ray repair, complementing defective, in Chinese hamster, 9", "X-ray repair complementing defective repair in Chinese hamster cells 9"	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.1837C>T	9.37:g.35074137G>A	ENSP00000367910:p.Arg613Trp		35064137		Missense_Mutation	SNP	ENST00000378643.3	37	CCDS6574.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636433	0.29068	.	.	ENSG00000221829	ENST00000378643	T	0.57107	0.42	5.49	4.58	0.56647	.	.	.	.	.	T	0.42630	0.1211	L	0.36672	1.1	0.25637	N	0.986247	D	0.56287	0.975	B	0.39876	0.312	T	0.32666	-0.9898	9	0.66056	D	0.02	-2.9242	11.9676	0.53044	0.0:0.1827:0.8173:0.0	.	613	O15287	FANCG_HUMAN	W	613	ENSP00000367910:R613W	ENSP00000367910:R613W	R	-	1	2	FANCG	35064137	0.978000	0.34361	0.782000	0.31804	0.065000	0.16274	2.055000	0.41345	1.287000	0.44583	0.455000	0.32223	CGG		0.537	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		A	35074137	G	A	35074137	3	1	61	1	0	0	0	0	1	0	0	0	5687	1057	37	1	35	1	FANCG	9	35074137	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7413	35074137	106139294	6251	14236										
FANCG	2189	broad.mit.edu	37	chr9	35075282	35075282	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtttagatcaccttgttCtttttcctcaggtgtggccc	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35075282C>A	ENST00000378643.3	-	11	1965	c.1474G>T	c.(1474-1476)Gaa>Taa	p.E492*	VCP_ENST00000358901.6_5'Flank|FANCG_ENST00000476212.1_Intron	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	492					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)	p.E492*(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCACCTTGTTCTTTTTCCTCA	0.488			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	1	Substitution - Nonsense(1)	large_intestine(1)	9											101	103	102					9																	35075282		2203	4300	6503	35065282	SO:0001587	stop_gained	2189			AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"Fanconi anemia, complementation groups"	3588	protein-coding gene	gene with protein product	"DNA repair protein XRCC9", "X-ray repair, complementing defective, in Chinese hamster, 9", "X-ray repair complementing defective repair in Chinese hamster cells 9"	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.1474G>T	9.37:g.35075282C>A	ENSP00000367910:p.Glu492*		35065282		Nonsense_Mutation	SNP	ENST00000378643.3	37	CCDS6574.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.337422|8.337422	0.98767|0.98767	.|.	.|.	ENSG00000221829|ENSG00000221829	ENST00000378643|ENST00000543657	.|.	.|.	.|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68924	.|0.3054	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.75662	.|-0.3240	.|4	0.40728|0.52906	T|T	0.16|0.07	-0.7616|-0.7616	14.4196|14.4196	0.67175|0.67175	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	492|441	.|.	ENSP00000367910:E492X|ENSP00000440458:R441I	E|R	-|-	1|2	0|0	FANCG|FANCG	35065282|35065282	0.892000|0.892000	0.30473|0.30473	0.973000|0.973000	0.42090|0.42090	0.234000|0.234000	0.25298|0.25298	3.462000|3.462000	0.53042|0.53042	2.471000|2.471000	0.83476|0.83476	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.488	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		A	35075282	C	A	35075282	4	1	61	1	0	0	0	0	0	1	0	0	5687	922	32	2	410	2	FANCG	9	35075282	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1145	35075282	106138149	6252	14237										
PIGO	84720	broad.mit.edu	37	chr9	35093113	35093113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccctgagaatagctcagCcatcacttccccgatattcc	5	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35093113C>T	ENST00000378617.3	-	6	1427	c.1033G>A	c.(1033-1035)Gct>Act	p.A345T	PIGO_ENST00000492770.1_5'Flank|PIGO_ENST00000298004.5_Missense_Mutation_p.A345T|PIGO_ENST00000361778.2_Missense_Mutation_p.A345T|PIGO_ENST00000341666.3_Missense_Mutation_p.A345T	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	345					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.A345T(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AATAGCTCAGCCATCACTTCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	9											60	53	56					9																	35093113		2203	4300	6503	35083113	SO:0001583	missense	84720			AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"Phosphatidylinositol glycan anchor biosynthesis"	23215	protein-coding gene	gene with protein product		614730	"phosphatidylinositol glycan, class O"			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.1033G>A	9.37:g.35093113C>T	ENSP00000367880:p.Ala345Thr		35083113	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Missense_Mutation	SNP	ENST00000378617.3	37	CCDS6575.1	.	.	.	.	.	.	.	.	.	.	C	3.203	-0.163339	0.06502	.	.	ENSG00000165282	ENST00000298004;ENST00000378617;ENST00000341666;ENST00000361778	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.55	2.65	0.31530	Alkaline-phosphatase-like, core domain (1);	0.495069	0.22847	N	0.054920	T	0.36248	0.0960	L	0.36672	1.1	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.17379	-1.0371	10	0.26408	T	0.33	-9.2241	5.6384	0.17550	0.0:0.6202:0.1395:0.2403	.	345;345	Q8TEQ8-2;Q8TEQ8	.;PIGO_HUMAN	T	345	ENSP00000298004:A345T;ENSP00000367880:A345T;ENSP00000339382:A345T;ENSP00000354678:A345T	ENSP00000298004:A345T	A	-	1	0	PIGO	35083113	0.016000	0.18221	0.127000	0.21898	0.537000	0.34900	0.288000	0.18939	0.402000	0.25451	-0.137000	0.14449	GCT		0.587	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634		T	35093113	C	T	35093113	3	4	61	1	0	0	0	0	1	0	0	0	11925	739	26	3	2260	3	PIGO	9	35093113	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17831	35093113	106120318	6253	14238										
STOML2	30968	broad.mit.edu	37	chr9	35100048	35100048	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccactaactcatcttgactCgatcaagttcctcatcaaga	4	13	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35100048C>T	ENST00000356493.5	-	10	1117	c.1055G>A	c.(1054-1056)cGa>cAa	p.R352Q	RP11-182N22.8_ENST00000431804.1_RNA|STOML2_ENST00000452248.2_Missense_Mutation_p.R307Q|STOML2_ENST00000487490.1_5'Flank	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	352					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)	p.R352Q(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CATCTTGACTCGATCAAGTTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	9											177	144	155					9																	35100048		2203	4300	6503	35090048	SO:0001583	missense	30968			AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.1055G>A	9.37:g.35100048C>T	ENSP00000348886:p.Arg352Gln		35090048	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	C	9.039	0.989117	0.18966	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.98296	-3.57;-4.85	5.07	4.17	0.49024	.	0.262839	0.27284	N	0.020063	D	0.95023	0.8389	L	0.36672	1.1	0.28680	N	0.905168	B;B	0.14438	0.003;0.01	B;B	0.01281	0.0;0.0	D	0.90669	0.4596	10	0.51188	T	0.08	-0.8362	7.268	0.26239	0.0:0.7398:0.1696:0.0905	.	307;352	B4E1K7;Q9UJZ1	.;STML2_HUMAN	Q	352;307	ENSP00000348886:R352Q;ENSP00000395743:R307Q	ENSP00000348886:R352Q	R	-	2	0	STOML2	35090048	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.631000	0.37092	1.362000	0.46000	0.655000	0.94253	CGA		0.532	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		T	35100048	C	T	35100048	3	4	61	1	0	0	0	0	1	0	0	0	15353	884	31	1	19	1	STOML2	9	35100048	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6935	35100048	106113383	6254	14239										
STOML2	30968	broad.mit.edu	37	chr9	35101799	35101799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactcagggtcctccacacCgtagcttgcctgagatggac	10	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35101799C>T	ENST00000356493.5	-	5	414	c.352G>A	c.(352-354)Ggt>Agt	p.G118S	STOML2_ENST00000452248.2_Missense_Mutation_p.G118S|STOML2_ENST00000487490.1_5'UTR	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	118					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)	p.G118S(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCCTCCACACCGTAGCTTGCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	9											134	132	133					9																	35101799		2203	4300	6503	35091799	SO:0001583	missense	30968			AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.352G>A	9.37:g.35101799C>T	ENSP00000348886:p.Gly118Ser		35091799	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	C	34	5.333184	0.95758	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.93247	-3.19;-3.19	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.96741	0.8936	M	0.79926	2.475	0.80722	D	1	D;D	0.76494	0.974;0.999	P;D	0.79784	0.821;0.993	D	0.97177	0.9848	10	0.87932	D	0	-9.7615	18.2135	0.89878	0.0:1.0:0.0:0.0	.	118;118	B4E1K7;Q9UJZ1	.;STML2_HUMAN	S	118	ENSP00000348886:G118S;ENSP00000395743:G118S	ENSP00000348886:G118S	G	-	1	0	STOML2	35091799	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.616000	0.83018	2.634000	0.89283	0.655000	0.94253	GGT		0.507	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		T	35101799	C	T	35101799	3	4	61	1	0	0	0	0	1	0	0	0	15353	652	23	1	742	1	STOML2	9	35101799	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1751	35101799	106111632	6255	14240										
KIAA1539	80256	broad.mit.edu	37	chr9	35105274	35105274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcggtcacagcctgcagttCgtaggggagccctgtgtcca	13	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35105274C>T	ENST00000378561.1	-	8	4616	c.1561G>A	c.(1561-1563)Gaa>Aaa	p.E521K	FAM214B_ENST00000322813.5_Missense_Mutation_p.E521K|FAM214B_ENST00000378566.1_Missense_Mutation_p.E216K|FAM214B_ENST00000603301.1_Missense_Mutation_p.E521K|FAM214B_ENST00000605244.1_Missense_Mutation_p.E521K|STOML2_ENST00000356493.5_5'Flank|STOML2_ENST00000452248.2_5'Flank|STOML2_ENST00000487490.1_5'Flank|FAM214B_ENST00000378554.2_Intron|FAM214B_ENST00000488109.2_Missense_Mutation_p.E521K|FAM214B_ENST00000378557.1_Missense_Mutation_p.E521K			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	521						nucleus (GO:0005634)		p.E521K(1)									GCCTGCAGTTCGTAGGGGAGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	52	53					9																	35105274		2203	4300	6503	35095274	SO:0001583	missense	80256			AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"KIAA1539"	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.1561G>A	9.37:g.35105274C>T	ENSP00000367823:p.Glu521Lys		35095274	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063812	0.93898	.	.	ENSG00000005238	ENST00000378566;ENST00000322813;ENST00000378561;ENST00000378557	.	.	.	5.31	5.31	0.75309	.	0.165073	0.52532	D	0.000074	T	0.67069	0.2854	L	0.33485	1.01	0.80722	D	1	D	0.76494	0.999	D	0.65573	0.936	T	0.68708	-0.5337	9	0.62326	D	0.03	-5.0481	18.7663	0.91874	0.0:1.0:0.0:0.0	.	521	Q7L5A3	K1539_HUMAN	K	216;521;521;521	.	ENSP00000319897:E521K	E	-	1	0	KIAA1539	35095274	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	7.243000	0.78219	2.759000	0.94783	0.561000	0.74099	GAA		0.602	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182		T	35105274	C	T	35105274	3	4	61	1	0	0	0	0	1	0	0	0	8263	893	31	1	59	1	KIAA1539	9	35105274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3475	35105274	106108157	6256	14241										
UNC13B	10497	broad.mit.edu	37	chr9	35236517	35236517	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggtatggaacaaaggActgatctgggacaccatggt	15	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35236517A>G	ENST00000378495.3	+	4	426	c.204A>G	c.(202-204)ggA>ggG	p.G68G	UNC13B_ENST00000396787.1_Silent_p.G68G|UNC13B_ENST00000378496.4_Silent_p.G68G	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	68	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.G68G(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GGAACAAAGGACTGATCTGGG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9											261	221	234					9																	35236517		2203	4300	6503	35226517	SO:0001819	synonymous_variant	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.204A>G	9.37:g.35236517A>G			35226517	Q5VYM8	Silent	SNP	ENST00000378495.3	37	CCDS6579.1																																																																																				0.473	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35236517	A	G	35236517	2	3	61	1	0	0	0	0	0	0	0	1	17025	262	10	4		4	UNC13B	9	35236517	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	131243	35236517	105976914	6257	14242										
UNC13B	10497	broad.mit.edu	37	chr9	35295718	35295718	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaccctgatagtgccgtCgatgaccgagatagtgacta	12	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35295718C>T	ENST00000378495.3	+	8	774	c.552C>T	c.(550-552)gtC>gtT	p.V184V	UNC13B_ENST00000396787.1_Silent_p.V196V|UNC13B_ENST00000378496.4_Silent_p.V184V	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	184					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.V184V(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			ATAGTGCCGTCGATGACCGAG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	9											132	115	121					9																	35295718		2203	4300	6503	35285718	SO:0001819	synonymous_variant	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.552C>T	9.37:g.35295718C>T			35285718	Q5VYM8	Silent	SNP	ENST00000378495.3	37	CCDS6579.1																																																																																				0.463	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35295718	C	T	35295718	2	4	61	1	0	0	0	0	0	0	0	1	17025	871	31	1		1	UNC13B	9	35295718	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59201	35295718	105917713	6258	14243										
UNC13B	10497	broad.mit.edu	37	chr9	35403824	35403824	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgctttgcccgggaagatCgcgtgctagggctggctgtg	16	10	0	1	rs199514152		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35403824C>T	ENST00000378495.3	+	39	4792	c.4570C>T	c.(4570-4572)Cgc>Tgc	p.R1524C	UNC13B_ENST00000396787.1_Missense_Mutation_p.R1555C|UNC13B_ENST00000378496.4_Missense_Mutation_p.R1543C|ATP8B5P_ENST00000430846.1_RNA	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1524	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.R1524C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CCGGGAAGATCGCGTGCTAGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	9											90	85	86					9																	35403824		2203	4300	6503	35393824	SO:0001583	missense	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4570C>T	9.37:g.35403824C>T	ENSP00000367756:p.Arg1524Cys		35393824	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731041	0.89390	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.69806	-0.43;-0.43;-0.43	6.17	6.17	0.99709	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.111469	0.64402	D	0.000007	D	0.86058	0.5842	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.86857	0.2027	10	0.87932	D	0	-5.4691	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1543;1524	F8W8M9;O14795	.;UN13B_HUMAN	C	1555;1524;1543;1130	ENSP00000380006:R1555C;ENSP00000367756:R1524C;ENSP00000367757:R1543C	ENSP00000367756:R1524C	R	+	1	0	UNC13B	35393824	1.000000	0.71417	0.992000	0.48379	0.983000	0.72400	4.854000	0.62918	2.941000	0.99782	0.655000	0.94253	CGC		0.572	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35403824	C	T	35403824	3	4	61	1	0	0	0	0	1	0	0	0	17025	884	31	1	4724	1	UNC13B	9	35403824	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108106	35403824	105809607	6259	14244										
RUSC2	9853	broad.mit.edu	37	chr9	35560483	35560483	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagctcccaggtctacatCgatggctccattgagggttc	11	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35560483C>T	ENST00000455600.1	+	10	4415	c.3846C>T	c.(3844-3846)atC>atT	p.I1282I	FAM166B_ENST00000492890.1_5'Flank	NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1282						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)	p.I1282I(1)		NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			AGGTCTACATCGATGGCTCCA	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	9											50	59	56					9																	35560483		2203	4299	6502	35550483	SO:0001819	synonymous_variant	9853			AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3846C>T	9.37:g.35560483C>T			35550483	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	37	CCDS35008.1																																																																																				0.657	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		T	35560483	C	T	35560483	2	4	61	1	0	0	0	0	0	0	0	1	13788	874	31	1		1	RUSC2	9	35560483	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156659	35560483	105652948	6260	14245										
CD72	971	broad.mit.edu	37	chr9	35616244	35616244	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacttccagaaccctgttCgtctgctggagctgctgaga	12	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35616244C>T	ENST00000396757.1	-	6	548	c.384G>A	c.(382-384)acG>acA	p.T128T	CD72_ENST00000490239.1_5'UTR|CD72_ENST00000259633.4_Silent_p.T128T|CD72_ENST00000378431.1_3'UTR			P21854	CD72_HUMAN	CD72 molecule	128					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor binding (GO:0005102)|transmembrane signaling receptor activity (GO:0004888)	p.T128T(1)		large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GAACCCTGTTCGTCTGCTGGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	9											29	27	27					9																	35616244		2203	4300	6503	35606244	SO:0001819	synonymous_variant	971				CCDS6581.1	9p	2008-07-21	2006-03-28		ENSG00000137101	ENSG00000137101		"CD molecules"	1696	protein-coding gene	gene with protein product		107272	"CD72 antigen"			2044654, 1711157	Standard	NM_001782		Approved	LYB2, CD72b	uc003zxb.2	P21854	OTTHUMG00000019870	ENST00000396757.1:c.384G>A	9.37:g.35616244C>T			35606244		Silent	SNP	ENST00000396757.1	37	CCDS6581.1																																																																																				0.577	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	NM_001782		T	35616244	C	T	35616244	2	4	61	1	0	0	0	0	0	0	0	1	3040	871	31	1		1	CD72	9	35616244	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55761	35616244	105597187	6261	14246										
TLN1	7094	broad.mit.edu	37	chr9	35717171	35717171	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatggagctaaagatgttCtcagtgacggttaggatggt	13	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35717171C>A	ENST00000314888.9	-	19	2783	c.2430G>T	c.(2428-2430)gaG>gaT	p.E810D	TLN1_ENST00000540444.1_Missense_Mutation_p.E810D	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	810					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.E810D(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TAAAGATGTTCTCAGTGACGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	9											90	88	88					9																	35717171		2203	4300	6503	35707171	SO:0001583	missense	7094			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.2430G>T	9.37:g.35717171C>A	ENSP00000316029:p.Glu810Asp		35707171	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.411637	0.25465	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.67171	-0.25;-0.24	5.6	1.14	0.20703	.	0.103719	0.64402	D	0.000004	T	0.41789	0.1174	N	0.13371	0.34	0.50632	D	0.999887	B	0.02656	0.0	B	0.04013	0.001	T	0.18209	-1.0344	10	0.07990	T	0.79	-24.2094	10.3745	0.44075	0.0:0.7511:0.0:0.2489	.	810	Q9Y490	TLN1_HUMAN	D	810	ENSP00000316029:E810D;ENSP00000442981:E810D	ENSP00000316029:E810D	E	-	3	2	TLN1	35707171	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	0.956000	0.29202	0.159000	0.19401	0.561000	0.74099	GAG		0.547	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35717171	C	A	35717171	3	1	61	1	0	0	0	0	1	0	0	0	15986	912	32	2	5351	2	TLN1	9	35717171	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100927	35717171	105496260	6262	14247										
RGP1	57704	broad.mit.edu	37	chr9	35750881	35750881	+	5'Flank	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagggaccaccctcctttCggggtcagtcagtcaagtac	11	12	3	1	rs373690510		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35750881C>T	ENST00000378103.3	-	0	0				GBA2_ENST00000545786.1_5'Flank|RGP1_ENST00000456972.2_Missense_Mutation_p.R168W|RGP1_ENST00000378078.4_Missense_Mutation_p.R128W|MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000378094.4_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)	p.R128W(1)|p.R168W(1)		NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACCCTCCTTTCGGGGTCAGTC	0.547													C|||	1	0.000199681	0	0	5008	,	,		20493	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	9						C	TRP/ARG	1,3969		0,1,1984	84	84	84		382	3.5	1	9		84	0,8326		0,0,4163	no	missense	RGP1	NM_001080496.2	101	0,1,6147	TT,TC,CC		0.0,0.0252,0.0081	benign	128/392	35750881	1,12295	1985	4163	6148	35740881	SO:0001631	upstream_gene_variant	9827			AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35750881C>T	Exception_encountered		35740881	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	37	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923868	0.73213	2.52E-4	0.0	ENSG00000107185	ENST00000456972;ENST00000378078	.	.	.	5.33	3.45	0.39498	.	0.052553	0.85682	D	0.000000	T	0.78168	0.4241	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79125	-0.1932	9	0.87932	D	0	-8.1769	10.2481	0.43354	0.0:0.7898:0.1362:0.074	.	128;128	Q92546;A8K0K1	RGP1_HUMAN;.	W	168;128	.	ENSP00000367318:R128W	R	+	1	2	RGP1	35740881	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.033000	0.64146	0.703000	0.31848	0.655000	0.94253	CGG		0.547	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		T	35750881	C	T	35750881	1	4	61	0	1	0	0	0	0	0	0	0	13321	875	31	1		1	RGP1	9	35750881	5'Flank	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33710	35750881	105462550	6263	14248										
NPR2	4882	broad.mit.edu	37	chr9	35793932	35793932	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctggagatgctgcatgaGatcctgcttcaggcccagag	12	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35793932G>T	ENST00000342694.2	+	2	960	c.705G>T	c.(703-705)gaG>gaT	p.E235D		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	235					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.E235D(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TGCTGCATGAGATCCTGCTTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											98	95	96					9																	35793932		2203	4300	6503	35783932	SO:0001583	missense	4882			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.705G>T	9.37:g.35793932G>T	ENSP00000341083:p.Glu235Asp		35783932	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.791008	0.31685	.	.	ENSG00000159899	ENST00000342694	D	0.82984	-1.67	4.23	2.38	0.29361	Extracellular ligand-binding receptor (1);	0.000000	0.43747	D	0.000536	T	0.62270	0.2414	N	0.16602	0.42	0.28200	N	0.927374	B;B	0.14012	0.007;0.009	B;B	0.20384	0.007;0.029	T	0.41963	-0.9479	10	0.10902	T	0.67	.	2.5165	0.04669	0.1729:0.1456:0.5321:0.1494	.	235;235	P20594-2;P20594	.;ANPRB_HUMAN	D	235	ENSP00000341083:E235D	ENSP00000341083:E235D	E	+	3	2	NPR2	35783932	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.432000	0.21461	0.531000	0.28639	0.655000	0.94253	GAG		0.562	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35793932	G	T	35793932	3	4	61	1	0	0	0	0	1	0	0	0	10626	933	33	2	711	2	NPR2	9	35793932	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43051	35793932	105419499	6264	14249										
C9orf128	392307	broad.mit.edu	37	chr9	35825819	35825819	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagacagacagacatagtCtcgtgattggggaggaagag	15	5	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35825819C>A	ENST00000423537.2	-	2	609	c.340G>T	c.(340-342)Gac>Tac	p.D114Y	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	114								p.D114Y(1)		endometrium(2)|kidney(1)|lung(4)	7						CAGACATAGTCTCGTGATTGG	0.498											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	9											153	152	153					9																	35825819		1917	4127	6044	35815819	SO:0001583	missense	392307			BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 128"	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.340G>T	9.37:g.35825819C>A	ENSP00000415299:p.Asp114Tyr	858	35815819	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	.	.	.	.	.	.	.	.	.	.	c	7.588	0.670147	0.14776	.	.	ENSG00000204930	ENST00000423537;ENST00000377984	T;T	0.20881	2.32;2.04	3.77	-4.31	0.03698	.	2.108010	0.02113	N	0.055009	T	0.12817	0.0311	N	0.08118	0	0.09310	N	1	B	0.27765	0.188	B	0.27380	0.079	T	0.31081	-0.9956	10	0.59425	D	0.04	1.034	11.8029	0.52137	0.0:0.4391:0.0:0.5609	.	114	A6H8Z2	CI128_HUMAN	Y	114	ENSP00000415299:D114Y;ENSP00000367222:D114Y	ENSP00000367222:D114Y	D	-	1	0	C9orf128	35815819	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.180000	0.03088	-1.452000	0.01931	-1.966000	0.00469	GAC		0.498	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446		A	35825819	C	A	35825819	3	1	61	1	0	0	0	0	1	0	0	0	2461	913	32	2	892	2	C9orf128	9	35825819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31887	35825819	105387612	6265	14250										
OR2S2	56656	broad.mit.edu	37	chr9	35957487	35957487	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcctaggaagatcacattCgtcacctccatgctgatcac	6	14	3	2	rs377240592	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:35957487C>T	ENST00000341959.2	-	1	664	c.609G>A	c.(607-609)acG>acA	p.T203T		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	203					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T193T(1)		central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			AGATCACATTCGTCACCTCCA	0.483													C|||	2	0.000399361	0	0.0029	5008	,	,		24649	0		0	False		,,,				2504	0				Pancreas(172;293 2036 17878 24427 30946)											1	Substitution - coding silent(1)	large_intestine(1)	9						C		1,4405	2.1+/-5.4	0,1,2202	112	109	110		609	-7.9	0	9		110	0,8600		0,0,4300	no	coding-synonymous	OR2S2	NM_019897.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		203/320	35957487	1,13005	2203	4300	6503	35947487	SO:0001819	synonymous_variant	56656			AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"GPCR / Class A : Olfactory receptors"	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.609G>A	9.37:g.35957487C>T			35947487	Q2M3L0|Q6IF19|Q96R42	Silent	SNP	ENST00000341959.2	37	CCDS6596.2																																																																																				0.483	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897		T	35957487	C	T	35957487	2	4	61	1	0	0	0	0	0	0	0	1	11046	871	31	1		1	OR2S2	9	35957487	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131668	35957487	105255944	6266	14251										
RECK	8434	broad.mit.edu	37	chr9	36100335	36100335	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttctctttaggccaacaGaacttttcaggagttgtaat	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:36100335G>T	ENST00000377966.3	+	11	1659	c.1093G>T	c.(1093-1095)Gaa>Taa	p.E365*		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	365					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E365*(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			TAGGCCAACAGAACTTTTCAG	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											51	46	47					9																	36100335		2203	4300	6503	36090335	SO:0001587	stop_gained	8434			E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1093G>T	9.37:g.36100335G>T	ENSP00000367202:p.Glu365*		36090335	B2RNS1|Q5W0K6|Q8WX37	Nonsense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	G	43	10.228864	0.99364	.	.	ENSG00000122707	ENST00000377966	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.043	16.5337	0.84367	0.0:0.0:1.0:0.0	.	.	.	.	X	365	.	ENSP00000367202:E365X	E	+	1	0	RECK	36090335	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.534000	0.98061	2.498000	0.84270	0.655000	0.94253	GAA		0.373	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			T	36100335	G	T	36100335	4	4	61	1	0	0	0	0	0	1	0	0	13237	943	33	2	1135	2	RECK	9	36100335	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142848	36100335	105113096	6267	14252										
CLTA	1211	broad.mit.edu	37	chr9	36204074	36204074	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccttcaaagatgccaattCtcggaagcaagaagcagagt	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:36204074C>A	ENST00000242285.6	+	4	503	c.383C>A	c.(382-384)tCt>tAt	p.S128Y	CLTA_ENST00000470744.1_Missense_Mutation_p.S128Y|CLTA_ENST00000433436.2_Missense_Mutation_p.S128Y|CLTA_ENST00000538225.1_Missense_Mutation_p.S128Y|CLTA_ENST00000540080.1_Missense_Mutation_p.S76Y|CLTA_ENST00000345519.5_Missense_Mutation_p.S128Y|CLTA_ENST00000396603.2_Missense_Mutation_p.S128Y|CLTA_ENST00000466396.1_Missense_Mutation_p.S76Y			P09496	CLCA_HUMAN	clathrin, light chain A	128	Involved in binding clathrin heavy chain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)	p.S128Y(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			GATGCCAATTCTCGGAAGCAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											100	86	91					9																	36204074		2203	4300	6503	36194074	SO:0001583	missense	1211				CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"clathrin, light polypeptide (Lca)"			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.383C>A	9.37:g.36204074C>A	ENSP00000242285:p.Ser128Tyr		36194074	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Missense_Mutation	SNP	ENST00000242285.6	37	CCDS6601.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.734973	0.69189	.	.	ENSG00000122705	ENST00000433436;ENST00000538225;ENST00000540080;ENST00000345519;ENST00000470744;ENST00000242285;ENST00000466396;ENST00000396603	T	0.40756	1.02	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.72045	0.3412	M	0.90369	3.11	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.998	D;D;D;D	0.79784	0.979;0.993;0.987;0.986	T	0.77101	-0.2712	10	0.87932	D	0	-17.1823	17.8186	0.88643	0.0:1.0:0.0:0.0	.	128;128;128;128	B4DIN1;P09496-2;P09496-3;P09496	.;.;.;CLCA_HUMAN	Y	128;128;76;128;128;128;76;128	ENSP00000242284:S128Y	ENSP00000242285:S128Y	S	+	2	0	CLTA	36194074	1.000000	0.71417	1.000000	0.80357	0.294000	0.27393	6.951000	0.75983	2.818000	0.97014	0.655000	0.94253	TCT		0.408	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		A	36204074	C	A	36204074	3	1	61	1	0	0	0	0	1	0	0	0	3570	913	32	2	397	2	CLTA	9	36204074	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103739	36204074	105009357	6268	14253										
MELK	9833	broad.mit.edu	37	chr9	36633110	36633110	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccactaggtggacccaaaGaaacggatttctatgaaaaa	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:36633110G>T	ENST00000298048.2	+	10	931	c.747G>T	c.(745-747)aaG>aaT	p.K249N	MELK_ENST00000541717.1_Missense_Mutation_p.K249N|MELK_ENST00000538311.1_Missense_Mutation_p.K55N|MELK_ENST00000545008.1_Missense_Mutation_p.K178N|MELK_ENST00000536987.1_Missense_Mutation_p.K118N|MELK_ENST00000543751.1_Missense_Mutation_p.K217N|MELK_ENST00000536329.1_Missense_Mutation_p.K178N|MELK_ENST00000536860.1_Missense_Mutation_p.K201N	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.K249N(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TGGACCCAAAGAAACGGATTT	0.363																																					Ovarian(82;980 1317 7225 14391 18624)											1	Substitution - Missense(1)	large_intestine(1)	9											85	85	85					9																	36633110		2203	4300	6503	36623110	SO:0001583	missense	9833			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.747G>T	9.37:g.36633110G>T	ENSP00000298048:p.Lys249Asn		36623110	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096921	0.56075	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	6.04	6.04	0.98038	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	N	0.11154	0.105	0.80722	D	1	D;P;P;P;D;P;P	0.89917	1.0;0.86;0.721;0.516;0.999;0.74;0.571	D;P;B;B;D;P;B	0.79108	0.992;0.561;0.26;0.187;0.986;0.457;0.378	T	0.62167	-0.6911	10	0.21540	T	0.41	-16.0674	19.3663	0.94464	0.0:0.0:1.0:0.0	.	169;178;201;249;178;217;249	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	N	249;55;118;178;201;178;249;217	ENSP00000298048:K249N;ENSP00000438226:K55N;ENSP00000439184:K118N;ENSP00000445452:K178N;ENSP00000439792:K201N;ENSP00000443550:K178N;ENSP00000437804:K249N;ENSP00000441596:K217N	ENSP00000298048:K249N	K	+	3	2	MELK	36623110	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.481000	0.81124	2.873000	0.98535	0.563000	0.77884	AAG		0.363	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		T	36633110	G	T	36633110	3	4	61	1	0	0	0	0	1	0	0	0	9500	933	33	2	781	2	MELK	9	36633110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	429036	36633110	104580321	6269	14254										
MELK	9833	broad.mit.edu	37	chr9	36665465	36665465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatatactcctaagtctgCtgtaaagaatgaagagtact	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:36665465C>T	ENST00000298048.2	+	14	1479	c.1295C>T	c.(1294-1296)gCt>gTt	p.A432V	MELK_ENST00000541717.1_Missense_Mutation_p.A391V|MELK_ENST00000538311.1_Missense_Mutation_p.A238V|MELK_ENST00000545008.1_Missense_Mutation_p.A361V|MELK_ENST00000536987.1_Missense_Mutation_p.A301V|MELK_ENST00000543751.1_Missense_Mutation_p.A400V|MELK_ENST00000536329.1_Missense_Mutation_p.A361V|MELK_ENST00000536860.1_Missense_Mutation_p.A384V	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	432	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.A432V(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			CCTAAGTCTGCTGTAAAGAAT	0.358																																					Ovarian(82;980 1317 7225 14391 18624)											1	Substitution - Missense(1)	large_intestine(1)	9											84	86	85					9																	36665465		2203	4299	6502	36655465	SO:0001583	missense	9833			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1295C>T	9.37:g.36665465C>T	ENSP00000298048:p.Ala432Val		36655465	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	C	7.790	0.711298	0.15239	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.72051	-0.43;0.56;0.35;0.88;0.25;-0.62;-0.43;-0.43	5.65	4.75	0.60458	.	0.481828	0.23712	N	0.045306	T	0.65688	0.2715	L	0.55481	1.735	0.31082	N	0.711866	B;B;B;B;B;B;B	0.22003	0.012;0.063;0.052;0.0;0.025;0.003;0.001	B;B;B;B;B;B;B	0.29077	0.009;0.098;0.075;0.003;0.015;0.004;0.004	T	0.64676	-0.6351	10	0.30854	T	0.27	-1.8548	10.5211	0.44920	0.0:0.9113:0.0:0.0887	.	352;361;384;391;361;400;432	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	V	432;238;301;361;384;361;391;400	ENSP00000298048:A432V;ENSP00000438226:A238V;ENSP00000439184:A301V;ENSP00000445452:A361V;ENSP00000439792:A384V;ENSP00000443550:A361V;ENSP00000437804:A391V;ENSP00000441596:A400V	ENSP00000298048:A432V	A	+	2	0	MELK	36655465	1.000000	0.71417	0.985000	0.45067	0.197000	0.23852	2.139000	0.42149	1.392000	0.46585	-0.142000	0.14014	GCT		0.358	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		T	36665465	C	T	36665465	3	4	61	1	0	0	0	0	1	0	0	0	9500	797	28	3	1345	3	MELK	9	36665465	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32355	36665465	104547966	6270	14255										
FRMPD1	22844	broad.mit.edu	37	chr9	37732310	37732310	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcttctagagctgcagcGatgtgctccaggagcgcttt	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37732310G>A	ENST00000539465.1	+	10	1461	c.868G>A	c.(868-870)Gat>Aat	p.D290N	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.D290N|FRMPD1_ENST00000541302.1_Missense_Mutation_p.D159N|FRMPD1_ENST00000536622.1_Missense_Mutation_p.D112N			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	290	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.D290N(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GAGCTGCAGCGATGTGCTCCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											60	61	61					9																	37732310		2203	4300	6503	37722310	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.868G>A	9.37:g.37732310G>A	ENSP00000444411:p.Asp290Asn		37722310	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	33	5.239046	0.95240	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29	5.34	5.34	0.76211	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.89350	0.6690	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.986;1.0	D	0.90318	0.4342	10	0.72032	D	0.01	-18.6998	16.5411	0.84385	0.0:0.0:1.0:0.0	.	159;290	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	N	290;290;112;159	ENSP00000366995:D290N;ENSP00000444411:D290N;ENSP00000437762:D112N;ENSP00000444804:D159N	ENSP00000366995:D290N	D	+	1	0	FRMPD1	37722310	1.000000	0.71417	0.984000	0.44739	0.991000	0.79684	9.444000	0.97578	2.504000	0.84457	0.655000	0.94253	GAT		0.542	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37732310	G	A	37732310	3	1	61	1	0	0	0	0	1	0	0	0	6076	1058	37	1	902	1	FRMPD1	9	37732310	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1066845	37732310	103481121	6271	14256										
FRMPD1	22844	broad.mit.edu	37	chr9	37735605	37735605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagccaagtatgggattagCcaggttatcaatagcaaact	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37735605C>T	ENST00000539465.1	+	13	1868	c.1275C>T	c.(1273-1275)agC>agT	p.S425S	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Silent_p.S425S|FRMPD1_ENST00000541302.1_Silent_p.S294S|FRMPD1_ENST00000536622.1_Silent_p.S247S			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	425	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.S425S(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		ATGGGATTAGCCAGGTTATCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9											166	150	155					9																	37735605		2203	4300	6503	37725605	SO:0001819	synonymous_variant	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1275C>T	9.37:g.37735605C>T			37725605	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																				0.473	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37735605	C	T	37735605	2	4	61	1	0	0	0	0	0	0	0	1	6076	738	26	3		3	FRMPD1	9	37735605	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3295	37735605	103477826	6272	14257										
FRMPD1	22844	broad.mit.edu	37	chr9	37740134	37740134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggtggactgcgtactcGaacctctctctgacaggcgc	12	13	2	2	rs201548139		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37740134G>A	ENST00000539465.1	+	15	2202	c.1609G>A	c.(1609-1611)Gaa>Aaa	p.E537K	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.E537K|FRMPD1_ENST00000541302.1_Missense_Mutation_p.E406K|FRMPD1_ENST00000536622.1_Missense_Mutation_p.E359K			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	537						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.E537K(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTGCGTACTCGAACCTCTCTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	LYS/GLU	0,4406		0,0,2203	79	85	83		1609	4.7	0.2	9		83	3,8597	3.0+/-9.4	0,3,4297	yes	missense	FRMPD1	NM_014907.2	56	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	537/1579	37740134	3,13003	2203	4300	6503	37730134	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1609G>A	9.37:g.37740134G>A	ENSP00000444411:p.Glu537Lys		37730134	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.599616	0.66332	0.0	3.49E-4	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.25414	2.69;2.69;1.8;1.83	5.65	4.74	0.60224	.	0.413896	0.26407	N	0.024543	T	0.44329	0.1288	M	0.61703	1.905	0.50467	D	0.99987	D;D	0.89917	0.991;1.0	P;D	0.65874	0.646;0.939	T	0.24728	-1.0152	10	0.26408	T	0.33	-11.166	13.6882	0.62529	0.0:0.0:0.8442:0.1558	.	406;537	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	K	537;537;359;406	ENSP00000366995:E537K;ENSP00000444411:E537K;ENSP00000437762:E359K;ENSP00000444804:E406K	ENSP00000366995:E537K	E	+	1	0	FRMPD1	37730134	1.000000	0.71417	0.211000	0.23655	0.356000	0.29392	4.998000	0.63927	1.368000	0.46115	-0.181000	0.13052	GAA		0.557	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37740134	G	A	37740134	3	1	61	1	0	0	0	0	1	0	0	0	6076	1059	37	1	1663	1	FRMPD1	9	37740134	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4529	37740134	103473297	6273	14258										
FRMPD1	22844	broad.mit.edu	37	chr9	37740686	37740686	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccggccagctacctgagtGacagttccgagagtacagct	11	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37740686G>T	ENST00000539465.1	+	15	2754	c.2161G>T	c.(2161-2163)Gac>Tac	p.D721Y	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.D721Y|FRMPD1_ENST00000541302.1_Missense_Mutation_p.D590Y|FRMPD1_ENST00000536622.1_Missense_Mutation_p.D543Y			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	721						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.D721Y(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTACCTGAGTGACAGTTCCGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	9											46	36	39					9																	37740686		2203	4300	6503	37730686	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.2161G>T	9.37:g.37740686G>T	ENSP00000444411:p.Asp721Tyr		37730686	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040691	0.35989	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.18960	3.15;3.15;2.18;2.18	5.75	2.55	0.30701	.	0.454406	0.25720	N	0.028744	T	0.16171	0.0389	L	0.44542	1.39	0.39403	D	0.966624	P;P	0.34780	0.468;0.468	B;B	0.36030	0.075;0.216	T	0.07520	-1.0768	10	0.72032	D	0.01	-19.0798	4.4681	0.11700	0.2018:0.1857:0.6125:0.0	.	590;721	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	Y	721;721;543;590	ENSP00000366995:D721Y;ENSP00000444411:D721Y;ENSP00000437762:D543Y;ENSP00000444804:D590Y	ENSP00000366995:D721Y	D	+	1	0	FRMPD1	37730686	0.000000	0.05858	0.929000	0.37066	0.745000	0.42441	0.323000	0.19593	1.434000	0.47414	0.655000	0.94253	GAC		0.632	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37740686	G	T	37740686	3	4	61	1	0	0	0	0	1	0	0	0	6076	1290	45	2	2215	2	FRMPD1	9	37740686	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	552	37740686	103472745	6274	14259										
FRMPD1	22844	broad.mit.edu	37	chr9	37745265	37745265	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcctttgttgtctcctaGagatgagcctagaagtgatg	12	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37745265G>T	ENST00000539465.1	+	16	3829	c.3236G>T	c.(3235-3237)aGa>aTa	p.R1079I	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.R1079I			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1079						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.R1079I(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TTGTCTCCTAGAGATGAGCCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	89	87					9																	37745265		2203	4300	6503	37735265	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3236G>T	9.37:g.37745265G>T	ENSP00000444411:p.Arg1079Ile		37735265	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853514	0.32791	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07021	3.23;3.23	5.11	0.0504	0.14293	.	5.660440	0.00447	N	0.000089	T	0.05914	0.0154	N	0.14661	0.345	0.09310	N	1	B	0.20368	0.044	B	0.16722	0.016	T	0.34378	-0.9831	10	0.37606	T	0.19	4.0369	4.8944	0.13742	0.3237:0.1573:0.519:0.0	.	1079	Q5SYB0	FRPD1_HUMAN	I	1079	ENSP00000366995:R1079I;ENSP00000444411:R1079I	ENSP00000366995:R1079I	R	+	2	0	FRMPD1	37735265	0.000000	0.05858	0.000000	0.03702	0.854000	0.48673	-0.195000	0.09546	-0.290000	0.09025	0.462000	0.41574	AGA		0.423	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37745265	G	T	37745265	3	4	61	1	0	0	0	0	1	0	0	0	6076	942	33	2	3294	2	FRMPD1	9	37745265	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4579	37745265	103468166	6275	14260										
FRMPD1	22844	broad.mit.edu	37	chr9	37746027	37746027	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccaggatagggatggaccAgtgcagctgtcagttctcct	12	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:37746027A>C	ENST00000539465.1	+	16	4591	c.3998A>C	c.(3997-3999)cAg>cCg	p.Q1333P	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.Q1333P			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1333						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.Q1333P(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GGGATGGACCAGTGCAGCTGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											139	141	140					9																	37746027		2203	4300	6503	37736027	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3998A>C	9.37:g.37746027A>C	ENSP00000444411:p.Gln1333Pro		37736027	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.626772	0.28978	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07021	3.23;3.23	5.38	4.19	0.49359	.	0.393903	0.28883	N	0.013832	T	0.05823	0.0152	N	0.24115	0.695	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35475	-0.9787	10	0.27082	T	0.32	-8.3254	9.4365	0.38641	0.8222:0.1778:0.0:0.0	.	1333	Q5SYB0	FRPD1_HUMAN	P	1333	ENSP00000366995:Q1333P;ENSP00000444411:Q1333P	ENSP00000366995:Q1333P	Q	+	2	0	FRMPD1	37736027	0.998000	0.40836	1.000000	0.80357	0.965000	0.64279	1.191000	0.32138	2.049000	0.60858	0.459000	0.35465	CAG		0.577	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		C	37746027	A	C	37746027	3	2	61	1	0	0	0	0	1	0	0	0	6076	188	7	4	4056	4	FRMPD1	9	37746027	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	762	37746027	103467404	6276	14261										
ALDH1B1	219	broad.mit.edu	37	chr9	38396266	38396266	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgcttcacccggcatgAgcccgttggtgtctgtggcc	12	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:38396266A>C	ENST00000377698.3	+	2	674	c.521A>C	c.(520-522)gAg>gCg	p.E174A		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	174					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)	p.E174A(1)		NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		ACCCGGCATGAGCCCGTTGGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	86	87					9																	38396266		2203	4300	6503	38386266	SO:0001583	missense	219			M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.521A>C	9.37:g.38396266A>C	ENSP00000366927:p.Glu174Ala		38386266	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622878	0.66901	.	.	ENSG00000137124	ENST00000377698	T	0.78707	-1.2	5.61	5.61	0.85477	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000008	D	0.89959	0.6866	M	0.91663	3.23	0.51482	D	0.999928	D	0.69078	0.997	D	0.76071	0.987	D	0.92017	0.5623	10	0.87932	D	0	.	13.7615	0.62968	1.0:0.0:0.0:0.0	.	174	P30837	AL1B1_HUMAN	A	174	ENSP00000366927:E174A	ENSP00000366927:E174A	E	+	2	0	ALDH1B1	38386266	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.967000	0.76079	2.141000	0.66446	0.533000	0.62120	GAG		0.577	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			C	38396266	A	C	38396266	3	2	61	1	0	0	0	0	1	0	0	0	493	304	11	4	523	4	ALDH1B1	9	38396266	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	650239	38396266	102817165	6277	14262										
CNTNAP3	79937	broad.mit.edu	37	chr9	39177400	39177400	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtgaagttgacctgcgtgTcgaggagctcgatgaggacg	17	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:39177400T>C	ENST00000297668.6	-	6	915	c.842A>G	c.(841-843)gAc>gGc	p.D281G	CNTNAP3_ENST00000377659.1_Missense_Mutation_p.D281G|CNTNAP3_ENST00000377653.2_5'UTR|CNTNAP3_ENST00000358144.2_Missense_Mutation_p.D193G|CNTNAP3_ENST00000377656.2_Missense_Mutation_p.D281G|CNTNAP3_ENST00000323947.7_Missense_Mutation_p.D281G	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	281	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D281G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GACCTGCGTGTCGAGGAGCTC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	9											60	58	59					9																	39177400		2203	4300	6503	39167400	SO:0001583	missense	79937			AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.842A>G	9.37:g.39177400T>C	ENSP00000297668:p.Asp281Gly		39167400	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	T	1.286	-0.609000	0.03690	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000323947;ENST00000377659;ENST00000377653	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	3.02	-4.85	0.03142	Concanavalin A-like lectin/glucanase (2);Concanavalin A-like lectin/glucanase, subgroup (2);Laminin G domain (4);Laminin G, subdomain 2 (2);	.	.	.	.	T	0.30448	0.0765	N	0.00210	-1.845	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.004;0.002;0.0;0.004;0.002	T	0.46317	-0.9200	9	0.06625	T	0.88	.	11.14	0.48398	0.0:0.588:0.0:0.412	.	281;281;281;281;281	E2QRH2;Q96NU0;Q9BZ76-2;A6NC89;Q9BZ76	.;CNT3B_HUMAN;.;.;CNTP3_HUMAN	G	281;281;193;281;281;193	ENSP00000297668:D281G;ENSP00000366884:D281G;ENSP00000350863:D193G;ENSP00000320728:D281G;ENSP00000366887:D281G	ENSP00000297668:D281G	D	-	2	0	CNTNAP3	39167400	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-0.094000	0.11094	-1.261000	0.02462	0.456000	0.33151	GAC		0.498	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		C	39177400	T	C	39177400	3	2	61	1	0	0	0	0	1	0	0	0	3654	1667	58	4	3100	4	CNTNAP3	9	39177400	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	781134	39177400	102036031	6278	14263										
ZNF658	26149	broad.mit.edu	37	chr9	40772822	40772822	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctcccctgtgtgaattCtttgatgcactatgagggct	10	9	2	3	rs566711883		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:40772822C>A	ENST00000602553.1	-	5	2747	c.2453G>T	c.(2452-2454)aGa>aTa	p.R818I	ZNF658_ENST00000377626.3_Missense_Mutation_p.R818I|ZNF658_ENST00000441795.1_Intron			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	818					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R818I(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGTGTGAATTCTTTGATGCAC	0.428													C|||	1	0.000199681	0	0	5008	,	,		19345	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											58	58	58					9																	40772822		2200	4295	6495	40762822	SO:0001583	missense	26149			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.2453G>T	9.37:g.40772822C>A	ENSP00000473484:p.Arg818Ile		40762822	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	c	15.39	2.819687	0.50633	.	.	ENSG00000196409	ENST00000377626	T	0.02446	4.29	1.83	1.83	0.25207	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10165	0.0249	L	0.61387	1.9	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	T	0.05338	-1.0891	9	0.56958	D	0.05	.	9.7235	0.40317	0.0:1.0:0.0:0.0	.	818	Q5TYW1	ZN658_HUMAN	I	818	ENSP00000366853:R818I	ENSP00000366853:R818I	R	-	2	0	ZNF658	40762822	0.000000	0.05858	0.997000	0.53966	0.996000	0.88848	0.517000	0.22832	1.359000	0.45940	0.518000	0.50308	AGA		0.428	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		A	40772822	C	A	40772822	3	1	61	1	0	0	0	0	1	0	0	0	18108	913	32	2	730	2	ZNF658	9	40772822	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1595422	40772822	100440609	6279	14264										
ANKRD20A1	84210	broad.mit.edu	37	chr9	67938636	67938636	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttggaacataaaaagaaGatacttaaaaaggagaaatc	7	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:67938636G>T	ENST00000377477.2	+	6	883	c.771G>T	c.(769-771)aaG>aaT	p.K257N	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	257						plasma membrane (GO:0005886)		p.K257N(1)		kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						ATAAAAAGAAGATACTTAAAA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	9											9	11	10					9																	67938636		1502	3107	4609	67528456	SO:0001583	missense	441425			AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"Ankyrin repeat domain containing"	23665	protein-coding gene	gene with protein product			"ankyrin repeat domain 20A"	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.771G>T	9.37:g.67938636G>T	ENSP00000366697:p.Lys257Asn		67528456	Q9H0H6	Missense_Mutation	SNP	ENST00000377477.2	37	CCDS6620.1	.	.	.	.	.	.	.	.	.	.	.	6.504	0.461222	0.12342	.	.	ENSG00000196774	ENST00000377477	T	0.37584	1.19	1.4	0.448	0.16614	Ankyrin repeat-containing domain (2);	.	.	.	.	T	0.18676	0.0448	L	0.38175	1.15	0.09310	N	1	P	0.45594	0.862	B	0.39379	0.298	T	0.13202	-1.0518	9	0.02654	T	1	.	3.5804	0.07950	0.2647:0.0:0.7353:0.0	.	257	Q5TYW2	A20A1_HUMAN	N	257	ENSP00000366697:K257N	ENSP00000366697:K257N	K	+	3	2	ANKRD20A1	67528456	0.042000	0.20092	0.004000	0.12327	0.066000	0.16364	0.569000	0.23638	0.151000	0.19162	0.184000	0.17185	AAG		0.254	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1			T	67938636	G	T	67938636	3	4	61	1	0	0	0	0	1	0	0	0	648	933	33	2	793	2	ANKRD20A1	9	67938636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27165814	67938636	73274795	6280	14265										
PIP5K1B	8395	broad.mit.edu	37	chr9	71509318	71509318	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgtattgtatgcaatcaGgaggcattaatatcaggatt	10	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:71509318G>T	ENST00000265382.3	+	8	840	c.535G>T	c.(535-537)Gga>Tga	p.G179*	PIP5K1B_ENST00000541509.1_Nonsense_Mutation_p.G179*	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	179	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)	p.G179*(1)		breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		TATGCAATCAGGAGGCATTAA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											84	80	81					9																	71509318		2203	4300	6503	70699138	SO:0001587	stop_gained	8395			U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.535G>T	9.37:g.71509318G>T	ENSP00000265382:p.Gly179*		70699138	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Nonsense_Mutation	SNP	ENST00000265382.3	37	CCDS6624.1	.	.	.	.	.	.	.	.	.	.	G	38	6.981810	0.97979	.	.	ENSG00000107242	ENST00000541509;ENST00000377290;ENST00000265382;ENST00000419747	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-17.8222	20.1142	0.97922	0.0:0.0:1.0:0.0	.	.	.	.	X	179;179;179;126	.	ENSP00000265382:G179X	G	+	1	0	PIP5K1B	70699138	1.000000	0.71417	0.959000	0.39883	0.995000	0.86356	7.748000	0.85085	2.765000	0.95021	0.650000	0.86243	GGA		0.353	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558		T	71509318	G	T	71509318	4	4	61	1	0	0	0	0	0	1	0	0	11971	1001	35	2	553	2	PIP5K1B	9	71509318	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3570682	71509318	69704113	6281	14266										
PRKACG	5568	broad.mit.edu	37	chr9	71628877	71628877	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagcgtcctgagccgttcGaactgatccgagctggcggt	13	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:71628877G>A	ENST00000377276.2	-	1	162	c.132C>T	c.(130-132)ttC>ttT	p.F44F		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	44	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.F44F(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TGAGCCGTTCGAACTGATCCG	0.602																																					Esophageal Squamous(110;2236 2623 32146)											1	Substitution - coding silent(1)	large_intestine(1)	9											91	89	90					9																	71628877		2203	4300	6503	70818697	SO:0001819	synonymous_variant	5568			M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.132C>T	9.37:g.71628877G>A			70818697	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	37	CCDS6625.1																																																																																				0.602	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628877	G	A	71628877	2	1	61	1	0	0	0	0	0	0	0	1	12533	1049	37	1		1	PRKACG	9	71628877	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119559	71628877	69584554	6282	14267										
APBA1	320	broad.mit.edu	37	chr9	72056023	72056023	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttgactcgggactgattCtttaagcccttaaacatgaa	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:72056023C>A	ENST00000265381.4	-	11	2412	c.2190G>T	c.(2188-2190)aaG>aaT	p.K730N		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	730	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.			K -> E (in Ref. 1; AAC05304 and 4; AAA61307). {ECO:0000305}.	axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.K730N(2)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						GGGACTGATTCTTTAAGCCCT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	9											122	106	112					9																	72056023		2203	4300	6503	71245843	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.2190G>T	9.37:g.72056023C>A	ENSP00000265381:p.Lys730Asn		71245843	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062073	0.76187	.	.	ENSG00000107282	ENST00000265381	T	0.29142	1.58	5.91	5.91	0.95273	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.59636	0.2208	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65623	-0.6123	10	0.87932	D	0	-28.4966	10.3018	0.43656	0.0:0.8509:0.0:0.1491	.	730	Q02410	APBA1_HUMAN	N	730	ENSP00000265381:K730N	ENSP00000265381:K730N	K	-	3	2	APBA1	71245843	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.994000	0.49433	2.793000	0.96121	0.655000	0.94253	AAG		0.483	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72056023	C	A	72056023	3	1	61	1	0	0	0	0	1	0	0	0	756	912	32	2	335	2	APBA1	9	72056023	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	427146	72056023	69157408	6283	14268										
APBA1	320	broad.mit.edu	37	chr9	72067136	72067136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttctggctgagatcttCggggttaatcccattggccc	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:72067136C>T	ENST00000265381.4	-	9	2092	c.1870G>A	c.(1870-1872)Gaa>Aaa	p.E624K		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	624	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.E624K(2)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CTGAGATCTTCGGGGTTAATC	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	9											205	172	183					9																	72067136		2203	4300	6503	71256956	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1870G>A	9.37:g.72067136C>T	ENSP00000265381:p.Glu624Lys		71256956	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.823790	0.90873	.	.	ENSG00000107282	ENST00000265381	T	0.04502	3.61	5.54	5.54	0.83059	Phosphotyrosine interaction domain (1);	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.00098	-1.2070	10	0.45353	T	0.12	-11.9676	19.4843	0.95024	0.0:1.0:0.0:0.0	.	624	Q02410	APBA1_HUMAN	K	624	ENSP00000265381:E624K	ENSP00000265381:E624K	E	-	1	0	APBA1	71256956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.884000	0.63135	2.610000	0.88304	0.655000	0.94253	GAA		0.502	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72067136	C	T	72067136	3	4	61	1	0	0	0	0	1	0	0	0	756	893	31	1	663	1	APBA1	9	72067136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11113	72067136	69146295	6284	14269										
APBA1	320	broad.mit.edu	37	chr9	72131362	72131362	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatgcgcgggtagggcgcGaactcggcctccttctcggg	15	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:72131362G>A	ENST00000265381.4	-	2	987	c.765C>T	c.(763-765)ttC>ttT	p.F255F		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	255	Munc-18-1 binding.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.F255F(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						GGTAGGGCGCGAACTCGGCCT	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	9											37	29	32					9																	72131362		2202	4300	6502	71321182	SO:0001819	synonymous_variant	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.765C>T	9.37:g.72131362G>A			71321182	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	37	CCDS6630.1																																																																																				0.682	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72131362	G	A	72131362	2	1	61	1	0	0	0	0	0	0	0	1	756	1049	37	1		1	APBA1	9	72131362	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64226	72131362	69082069	6285	14270										
SMC5	23137	broad.mit.edu	37	chr9	72893538	72893538	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggagaaagaaaaacagctCgaggtactttaaatagacaa	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:72893538C>T	ENST00000361138.5	+	5	733	c.675C>T	c.(673-675)ctC>ctT	p.L225L		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	225					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.L225L(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						AAAAACAGCTCGAGGTACTTT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	9											77	74	75					9																	72893538		2203	4300	6503	72083358	SO:0001819	synonymous_variant	23137			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.675C>T	9.37:g.72893538C>T			72083358	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	37	CCDS6632.1																																																																																				0.358	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		T	72893538	C	T	72893538	2	4	61	1	0	0	0	0	0	0	0	1	14823	871	31	1		1	SMC5	9	72893538	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	762176	72893538	68319893	6286	14271										
SMC5	23137	broad.mit.edu	37	chr9	72962064	72962064	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagcttcctgcttcacggGactgaatcctacagtatgcc	9	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:72962064G>A	ENST00000361138.5	+	20	2709	c.2651G>A	c.(2650-2652)gGa>gAa	p.G884E	SMC5_ENST00000471372.1_3'UTR	NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	884					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.G884E(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TGCTTCACGGGACTGAATCCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											85	73	77					9																	72962064		2203	4300	6503	72151884	SO:0001583	missense	23137			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.2651G>A	9.37:g.72962064G>A	ENSP00000354957:p.Gly884Glu		72151884	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357737	0.82243	.	.	ENSG00000198887	ENST00000361138	T	0.17370	2.28	5.91	5.91	0.95273	RecF/RecN/SMC (1);	0.102003	0.64402	D	0.000002	T	0.35711	0.0941	L	0.46614	1.455	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.00978	-1.1493	10	0.17369	T	0.5	-30.3372	20.2963	0.98556	0.0:0.0:1.0:0.0	.	884	Q8IY18	SMC5_HUMAN	E	884	ENSP00000354957:G884E	ENSP00000354957:G884E	G	+	2	0	SMC5	72151884	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.112000	0.94314	2.813000	0.96785	0.655000	0.94253	GGA		0.443	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		A	72962064	G	A	72962064	3	1	61	1	0	0	0	0	1	0	0	0	14823	1174	41	3	2729	3	SMC5	9	72962064	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68526	72962064	68251367	6287	14272										
TRPM3	80036	broad.mit.edu	37	chr9	73151980	73151980	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatattgaccgaatagaaaGaatggcttcgcatacggggc	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:73151980G>T	ENST00000377110.3	-	25	4256	c.4013C>A	c.(4012-4014)tCt>tAt	p.S1338Y	TRPM3_ENST00000408909.2_Missense_Mutation_p.S1197Y|TRPM3_ENST00000360823.2_Missense_Mutation_p.S1200Y|TRPM3_ENST00000377106.1_Missense_Mutation_p.S1210Y|TRPM3_ENST00000423814.3_Missense_Mutation_p.S1365Y|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000357533.2_Missense_Mutation_p.S1342Y|TRPM3_ENST00000358082.3_Missense_Mutation_p.S1200Y|TRPM3_ENST00000377105.1_Missense_Mutation_p.S1197Y|TRPM3_ENST00000396280.5_Missense_Mutation_p.S1187Y|TRPM3_ENST00000396292.4_Missense_Mutation_p.S1210Y|TRPM3_ENST00000396285.1_Missense_Mutation_p.S1197Y			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1363					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.S1210Y(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CGAATAGAAAGAATGGCTTCG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	100	99					9																	73151980		2203	4300	6503	72341800	SO:0001583	missense	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4013C>A	9.37:g.73151980G>T	ENSP00000366314:p.Ser1338Tyr		72341800	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.21|19.21	3.783613|3.783613	0.70222|0.70222	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T	.|0.65178	.|-0.02;-0.13;-0.14;-0.14;-0.03;-0.14;-0.14;-0.13;-0.14;-0.03	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72692|0.72692	0.3492|0.3492	L|L	0.29908|0.29908	0.895|0.895	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D;P;D	.|0.89917	.|0.967;0.999;0.963;0.995;1.0;0.708;0.978	.|P;D;P;D;D;B;P	.|0.75484	.|0.596;0.977;0.677;0.986;0.977;0.281;0.598	T|T	0.73222|0.73222	-0.4051|-0.4051	5|10	.|0.72032	.|D	.|0.01	-16.3402|-16.3402	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1338;1328;1342;1200;1197;1310;1197	.|Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|.;.;.;.;.;.;.	L|Y	1186|1338;1210;1200;1197;1342;1197;1197;1210;1200;1365	.|ENSP00000366314:S1338Y;ENSP00000366310:S1210Y;ENSP00000354066:S1200Y;ENSP00000366309:S1197Y;ENSP00000350140:S1342Y;ENSP00000386127:S1197Y;ENSP00000379581:S1197Y;ENSP00000379587:S1210Y;ENSP00000350791:S1200Y;ENSP00000389542:S1365Y	.|ENSP00000350140:S1342Y	F|S	-|-	3|2	2|0	TRPM3|TRPM3	72341800|72341800	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.230000|9.230000	0.95299|0.95299	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	TTC|TCT		0.463	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		T	73151980	G	T	73151980	3	4	61	1	0	0	0	0	1	0	0	0	16627	942	33	2	1114	2	TRPM3	9	73151980	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189916	73151980	68061451	6288	14273										
TRPM3	80036	broad.mit.edu	37	chr9	73240194	73240194	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccgcccatcaggtactcGatcaccaggccgatgtcaat	9	16	3	0	rs138856820		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:73240194G>A	ENST00000377111.2	-	13	1929	c.1686C>T	c.(1684-1686)atC>atT	p.I562I	TRPM3_ENST00000408909.2_Silent_p.I421I|TRPM3_ENST00000360823.2_Silent_p.I434I|TRPM3_ENST00000377106.1_Silent_p.I434I|TRPM3_ENST00000423814.3_Silent_p.I589I|TRPM3_ENST00000377110.3_Silent_p.I562I|TRPM3_ENST00000357533.2_Silent_p.I576I|TRPM3_ENST00000358082.3_Silent_p.I434I|TRPM3_ENST00000377105.1_Silent_p.I421I|TRPM3_ENST00000396280.5_Silent_p.I421I|TRPM3_ENST00000396292.4_Silent_p.I434I|TRPM3_ENST00000396285.1_Silent_p.I409I	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	587					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.I434I(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TCAGGTACTCGATCACCAGGC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	9						G	,,,,,,	1,4405	2.1+/-5.4	0,1,2202	48	49	49		1686,1227,1263,1227,1263,1302,1302	-1.1	1	9	dbSNP_134	49	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,	562/1708,409/1555,421/1567,409/1545,421/1557,434/1580,434/1570	73240194	1,13005	2203	4300	6503	72430014	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.1686C>T	9.37:g.73240194G>A			72430014	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	G	10.36	1.328659	0.24167	2.27E-4	0.0	ENSG00000083067	ENST00000396280	.	.	.	6.03	-1.15	0.09709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.5998	4.4624	0.11673	0.3525:0.0:0.28:0.3675	.	.	.	.	X	421	.	.	R	-	1	2	TRPM3	72430014	0.978000	0.34361	0.996000	0.52242	0.998000	0.95712	0.223000	0.17719	-0.091000	0.12440	0.555000	0.69702	CGA		0.557	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73240194	G	A	73240194	2	1	61	1	0	0	0	0	0	0	0	1	16627	1048	37	1		1	TRPM3	9	73240194	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88214	73240194	67973237	6289	14274										
TRPM3	80036	broad.mit.edu	37	chr9	73240407	73240407	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattaattcaccttaaaataGatccaaccgaaacctggata	4	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:73240407G>T	ENST00000357533.2	-	13	1664	c.1665C>A	c.(1663-1665)atC>atA	p.I555I	TRPM3_ENST00000408909.2_Silent_p.I400I|TRPM3_ENST00000360823.2_Intron|TRPM3_ENST00000377106.1_Intron|TRPM3_ENST00000423814.3_Intron|TRPM3_ENST00000377110.3_Intron|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000358082.3_Intron|TRPM3_ENST00000377105.1_Silent_p.I400I|TRPM3_ENST00000396280.5_Silent_p.I400I|TRPM3_ENST00000396292.4_Intron|TRPM3_ENST00000396285.1_Intron			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	569					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.I555I(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CCTTAAAATAGATCCAACCGA	0.279																																																1	Substitution - coding silent(1)	large_intestine(1)	9											59	63	62					9																	73240407		2203	4300	6503	72430227	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000357533.2:c.1665C>A	9.37:g.73240407G>T			72430227	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000357533.2	37		.	.	.	.	.	.	.	.	.	.	G	8.806	0.933992	0.18206	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	T	0.77046	0.4073	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73930	-0.3827	4	.	.	.	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	.	.	.	I	400	.	.	L	-	1	2	TRPM3	72430227	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.385000	0.79763	2.835000	0.97688	0.650000	0.86243	CTA		0.279	TRPM3-014	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000214163.1	NM_206945		T	73240407	G	T	73240407	2	4	61	1	0	0	0	0	0	0	0	1	16627	932	33	2		2	TRPM3	9	73240407	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213	73240407	67973024	6290	14275										
TMEM2	23670	broad.mit.edu	37	chr9	74315727	74315727	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatagcaaaggccaactcGaatccagtcattcctttaaa	7	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:74315727G>A	ENST00000377044.4	-	19	3747	c.3208C>T	c.(3208-3210)Cga>Tga	p.R1070*	TMEM2_ENST00000377066.5_Nonsense_Mutation_p.R1007*|TMEM2_ENST00000396272.3_Nonsense_Mutation_p.R63*	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1070					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R1070*(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		AGGCCAACTCGAATCCAGTCA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											82	78	80					9																	74315727		2203	4300	6503	73505547	SO:0001587	stop_gained	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3208C>T	9.37:g.74315727G>A	ENSP00000366243:p.Arg1070*		73505547	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Nonsense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	38	6.772001	0.97825	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272;ENST00000377055	.	.	.	6.17	6.17	0.99709	.	0.190501	0.47093	D	0.000243	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	15.581	0.76439	0.0:0.0:0.8623:0.1377	.	.	.	.	X	1070;1007;63;99	.	ENSP00000366243:R1070X	R	-	1	2	TMEM2	73505547	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.704000	0.74639	2.941000	0.99782	0.655000	0.94253	CGA		0.373	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		A	74315727	G	A	74315727	4	1	61	1	0	0	0	0	0	1	0	0	16160	1066	37	1	967	1	TMEM2	9	74315727	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1075320	74315727	66897704	6291	14276										
TMEM2	23670	broad.mit.edu	37	chr9	74355016	74355016	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagctgtcacagagaacttCtggccatccacagtataaaa	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:74355016C>A	ENST00000377044.4	-	5	1706	c.1167G>T	c.(1165-1167)caG>caT	p.Q389H	TMEM2_ENST00000377066.5_Missense_Mutation_p.Q389H	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	389					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q389H(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		CAGAGAACTTCTGGCCATCCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	9											118	114	115					9																	74355016		2203	4300	6503	73544836	SO:0001583	missense	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1167G>T	9.37:g.74355016C>A	ENSP00000366243:p.Gln389His		73544836	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143226	0.57044	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.73469	-0.75;-0.71	5.65	5.65	0.86999	.	0.179734	0.48767	D	0.000180	T	0.79930	0.4531	L	0.57536	1.79	0.80722	D	1	D;D	0.63880	0.979;0.993	P;P	0.57244	0.659;0.816	T	0.77368	-0.2614	10	0.32370	T	0.25	.	13.9457	0.64082	0.0:0.9273:0.0:0.0727	.	389;389	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	H	389	ENSP00000366243:Q389H;ENSP00000366266:Q389H	ENSP00000366243:Q389H	Q	-	3	2	TMEM2	73544836	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.199000	0.32235	2.673000	0.90976	0.491000	0.48974	CAG		0.388	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		A	74355016	C	A	74355016	3	1	61	1	0	0	0	0	1	0	0	0	16160	912	32	2	3064	2	TMEM2	9	74355016	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39289	74355016	66858415	6292	14277										
TMEM2	23670	broad.mit.edu	37	chr9	74360185	74360185	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaggccccgggaaaagtcCttttcaaaggtataggaccc	11	10	1	1	rs201684156		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:74360185C>A	ENST00000377044.4	-	4	1322	c.783G>T	c.(781-783)aaG>aaT	p.K261N	TMEM2_ENST00000377066.5_Missense_Mutation_p.K261N	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	261					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K261N(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		GGGAAAAGTCCTTTTCAAAGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	9											64	63	63					9																	74360185		2203	4300	6503	73550005	SO:0001583	missense	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.783G>T	9.37:g.74360185C>A	ENSP00000366243:p.Lys261Asn		73550005	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521575	0.64747	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.74737	-0.87;-0.81	6.03	3.23	0.37069	.	0.049385	0.85682	D	0.000000	T	0.78470	0.4288	M	0.72894	2.215	0.80722	D	1	B;P	0.51537	0.209;0.946	B;P	0.56916	0.107;0.809	T	0.73636	-0.3920	10	0.33141	T	0.24	.	6.6524	0.22969	0.1262:0.6857:0.0:0.1881	.	261;261	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	N	261	ENSP00000366243:K261N;ENSP00000366266:K261N	ENSP00000366243:K261N	K	-	3	2	TMEM2	73550005	0.981000	0.34729	0.941000	0.38009	0.953000	0.61014	0.652000	0.24888	0.446000	0.26666	0.655000	0.94253	AAG		0.502	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		A	74360185	C	A	74360185	3	1	61	1	0	0	0	0	1	0	0	0	16160	680	24	2	3452	2	TMEM2	9	74360185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5169	74360185	66853246	6293	14278										
TMEM2	23670	broad.mit.edu	37	chr9	74360390	74360390	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttggatttatagcggcatTtttctgctccaatatgaagc	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:74360390T>G	ENST00000377044.4	-	4	1117	c.578A>C	c.(577-579)aAa>aCa	p.K193T	TMEM2_ENST00000377066.5_Missense_Mutation_p.K193T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	193	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K193T(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		ATAGCGGCATTTTTCTGCTCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	105	105					9																	74360390		2203	4300	6503	73550210	SO:0001583	missense	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.578A>C	9.37:g.74360390T>G	ENSP00000366243:p.Lys193Thr		73550210	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571299	0.45798	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	D;D	0.89415	-2.51;-2.51	6.17	3.86	0.44501	G8 domain (2);	0.040745	0.85682	D	0.000000	T	0.81791	0.4897	L	0.28740	0.885	0.80722	D	1	B;B	0.27316	0.127;0.175	B;B	0.33960	0.173;0.084	T	0.70425	-0.4875	10	0.11794	T	0.64	.	10.5433	0.45045	0.0:0.1292:0.0:0.8708	.	193;193	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	T	193	ENSP00000366243:K193T;ENSP00000366266:K193T	ENSP00000366243:K193T	K	-	2	0	TMEM2	73550210	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.800000	0.62524	0.572000	0.29383	0.533000	0.62120	AAA		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		G	74360390	T	G	74360390	3	3	61	1	0	0	0	0	1	0	0	0	16160	1841	64	4	3657	4	TMEM2	9	74360390	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	205	74360390	66853041	6294	14279										
GDA	9615	broad.mit.edu	37	chr9	74842909	74842909	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaagaactgaacgtattCcatgaacgaggagcatccat	10	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:74842909C>T	ENST00000358399.3	+	9	966	c.873C>T	c.(871-873)ttC>ttT	p.F291F	GDA_ENST00000238018.4_Silent_p.F291F|GDA_ENST00000376989.3_Silent_p.F230F|GDA_ENST00000477618.1_3'UTR|GDA_ENST00000545168.1_Silent_p.F217F|GDA_ENST00000376986.1_Silent_p.F213F	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	291					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)	p.F291F(1)		central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		TGAACGTATTCCATGAACGAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	9											139	107	118					9																	74842909		2203	4300	6503	74032729	SO:0001819	synonymous_variant	9615			AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.873C>T	9.37:g.74842909C>T			74032729	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Silent	SNP	ENST00000358399.3	37	CCDS6641.1																																																																																				0.448	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			T	74842909	C	T	74842909	2	4	61	1	0	0	0	0	0	0	0	1	6326	854	30	3		3	GDA	9	74842909	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	482519	74842909	66370522	6295	14280										
ALDH1A1	216	broad.mit.edu	37	chr9	75524601	75524601	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcctgctgataagccataGaaagtattgtttgctctttt	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:75524601G>T	ENST00000297785.3	-	11	1329	c.1275C>A	c.(1273-1275)ttC>ttA	p.F425L		NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	425					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)	p.F425L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	ATAAGCCATAGAAAGTATTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											182	163	170					9																	75524601		2203	4300	6503	74714421	SO:0001583	missense	216			K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"Aldehyde dehydrogenases"	402	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 1"	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.1275C>A	9.37:g.75524601G>T	ENSP00000297785:p.Phe425Leu		74714421	O00768|Q5SYR1	Missense_Mutation	SNP	ENST00000297785.3	37	CCDS6644.1	.	.	.	.	.	.	.	.	.	.	G	9.952	1.220423	0.22457	.	.	ENSG00000165092	ENST00000297785	T	0.15372	2.43	5.82	0.6	0.17524	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	3.898550	0.00357	N	0.000026	T	0.06962	0.0177	N	0.01874	-0.695	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26395	-1.0104	10	0.30078	T	0.28	.	3.572	0.07921	0.129:0.1105:0.5075:0.2531	.	346;425	B4DDF8;P00352	.;AL1A1_HUMAN	L	425	ENSP00000297785:F425L	ENSP00000297785:F425L	F	-	3	2	ALDH1A1	74714421	0.000000	0.05858	0.041000	0.18516	0.824000	0.46624	-0.828000	0.04419	-0.153000	0.11137	0.655000	0.94253	TTC		0.378	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1			T	75524601	G	T	75524601	3	4	61	1	0	0	0	0	1	0	0	0	490	933	33	2	242	2	ALDH1A1	9	75524601	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681692	75524601	65688830	6296	14281										
RORB	6096	broad.mit.edu	37	chr9	77257577	77257577	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattacaacgtcgattccggTcagccgtcccctgatcagtc	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:77257577T>C	ENST00000396204.2	+	4	516	c.516T>C	c.(514-516)ggT>ggC	p.G172G	RORB_ENST00000376896.3_Silent_p.G161G			Q92753	RORB_HUMAN	RAR-related orphan receptor B	172	Hinge. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.G161G(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	TCGATTCCGGTCAGCCGTCCC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	9											93	79	84					9																	77257577		2203	4300	6503	76447397	SO:0001819	synonymous_variant	6096			Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.516T>C	9.37:g.77257577T>C			76447397	Q8WX73	Silent	SNP	ENST00000396204.2	37																																																																																					0.507	RORB-201	KNOWN	basic	protein_coding	protein_coding				C	77257577	T	C	77257577	2	2	61	1	0	0	0	0	0	0	0	1	13566	1654	58	4		4	RORB	9	77257577	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1732976	77257577	63955854	6297	14282										
TRPM6	140803	broad.mit.edu	37	chr9	77339653	77339653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaggggaatagtcatttCtttttaaatctgcaaggagg	10	5	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:77339653C>A	ENST00000360774.1	-	39	6182	c.5945G>T	c.(5944-5946)aGa>aTa	p.R1982I	TRPM6_ENST00000376872.3_Missense_Mutation_p.R937I|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1977I|TRPM6_ENST00000376871.3_Missense_Mutation_p.R819I|TRPM6_ENST00000451710.3_Missense_Mutation_p.R1986I|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1977I	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1982					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R1982I(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						ATAGTCATTTCTTTTTAAATC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	94	92					9																	77339653		2203	4300	6503	76529473	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.5945G>T	9.37:g.77339653C>A	ENSP00000354006:p.Arg1982Ile		76529473	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095186	0.76870	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870	T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32	5.69	3.86	0.44501	Protein kinase-like domain (1);	0.050014	0.85682	D	0.000000	T	0.23171	0.0560	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.999;0.999	D;D;D;D;D;D	0.76071	0.91;0.957;0.968;0.97;0.972;0.987	T	0.00473	-1.1718	10	0.87932	D	0	.	12.3371	0.55073	0.0:0.8616:0.0:0.1384	.	529;815;933;1982;1977;1977	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3;Q9BX84-2	.;.;.;TRPM6_HUMAN;.;.	I	1982;1986;937;819;1977;1977;528	ENSP00000354006:R1982I;ENSP00000407341:R1986I;ENSP00000366068:R937I;ENSP00000366067:R819I;ENSP00000396672:R1977I;ENSP00000354962:R1977I	ENSP00000354006:R1982I	R	-	2	0	TRPM6	76529473	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	2.866000	0.48420	0.767000	0.33267	0.655000	0.94253	AGA		0.413	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77339653	C	A	77339653	3	1	61	1	0	0	0	0	1	0	0	0	16630	913	32	2	127	2	TRPM6	9	77339653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82076	77339653	63873778	6298	14283										
TRPM6	140803	broad.mit.edu	37	chr9	77397655	77397655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatggctcaaatacaatatCtcgagctagactccaagatg	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:77397655C>A	ENST00000360774.1	-	22	3271	c.3034G>T	c.(3034-3036)Gat>Tat	p.D1012Y	TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.D1007Y|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000451710.3_Missense_Mutation_p.D1012Y|TRPM6_ENST00000361255.3_Missense_Mutation_p.D1007Y|TRPM6_ENST00000376864.4_Missense_Mutation_p.D1012Y	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1012					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.D1012Y(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AATACAATATCTCGAGCTAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											142	119	127					9																	77397655		2203	4300	6503	76587475	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3034G>T	9.37:g.77397655C>A	ENSP00000354006:p.Asp1012Tyr		76587475	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.137285	0.77775	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.57107	0.51;0.51;0.51;0.51;0.42	5.92	5.92	0.95590	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.74913	0.3779	M	0.73430	2.235	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.969	D;D;P	0.87578	0.997;0.998;0.614	T	0.75863	-0.3167	10	0.87932	D	0	.	20.3207	0.98668	0.0:1.0:0.0:0.0	.	675;1012;1007	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	Y	1012;1012;1007;1007;1012;675;675	ENSP00000354006:D1012Y;ENSP00000407341:D1012Y;ENSP00000396672:D1007Y;ENSP00000354962:D1007Y;ENSP00000366060:D1012Y	ENSP00000309693:D675Y	D	-	1	0	TRPM6	76587475	1.000000	0.71417	0.998000	0.56505	0.493000	0.33554	3.248000	0.51430	2.813000	0.96785	0.561000	0.74099	GAT		0.453	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77397655	C	A	77397655	3	1	61	1	0	0	0	0	1	0	0	0	16630	913	32	2	3106	2	TRPM6	9	77397655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58002	77397655	63815776	6299	14284										
GCNT1	2650	broad.mit.edu	37	chr9	79117542	79117542	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatcctaacagtgaaatTtaaaaagcgccctcggtgga	10	8	0	2	rs138234792		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79117542T>G	ENST00000376730.4	+	4	728	c.245T>G	c.(244-246)tTt>tGt	p.F82C	GCNT1_ENST00000444201.2_Missense_Mutation_p.F82C|GCNT1_ENST00000442371.1_Missense_Mutation_p.F82C|GCNT1_ENST00000536223.1_Missense_Mutation_p.F82C	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	82	Stem region. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)	p.F82C(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						ACAGTGAAATTTAAAAAGCGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	9											103	107	105					9																	79117542		2203	4300	6503	78307362	SO:0001583	missense	2650			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4203	protein-coding gene	gene with protein product	"core 2 beta1,6 N-acetylglucosaminyltransferase-I", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"	600391	"glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.245T>G	9.37:g.79117542T>G	ENSP00000365920:p.Phe82Cys		78307362	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	t	11.14	1.551674	0.27739	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.84	5.84	0.93424	.	0.500761	0.22078	N	0.064931	T	0.68284	0.2984	M	0.70595	2.14	0.41466	D	0.988071	D	0.71674	0.998	P	0.56343	0.796	T	0.70385	-0.4886	9	.	.	.	.	11.3276	0.49458	0.1356:0.0:0.0:0.8644	.	82	Q02742	GCNT1_HUMAN	C	82	ENSP00000440883:F82C;ENSP00000415454:F82C;ENSP00000390703:F82C;ENSP00000365920:F82C	.	F	+	2	0	GCNT1	78307362	1.000000	0.71417	0.077000	0.20336	0.236000	0.25371	3.141000	0.50593	2.230000	0.72887	0.528000	0.53228	TTT		0.393	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634		G	79117542	T	G	79117542	3	3	61	1	0	0	0	0	1	0	0	0	6320	1841	64	4	247	4	GCNT1	9	79117542	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1719887	79117542	62095889	6300	14285										
PRUNE2	158471	broad.mit.edu	37	chr9	79321271	79321271	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcctctgcgtgagtaaaGgctgtgtccggatgatcaca	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79321271G>T	ENST00000376718.3	-	8	6042	c.5919C>A	c.(5917-5919)gcC>gcA	p.A1973A	PRUNE2_ENST00000428286.1_Silent_p.A1614A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1973					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.A1973A(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CGTGAGTAAAGGCTGTGTCCG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	9											138	120	126					9																	79321271		1568	3582	5150	78511091	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5919C>A	9.37:g.79321271G>T			78511091	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.563636	0.00903	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.51	-7.47	0.01365	.	.	.	.	.	T	0.15046	0.0363	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21518	-1.0243	4	.	.	.	0.3673	1.0245	0.01525	0.1882:0.1731:0.3076:0.3311	.	.	.	.	I	1295	.	.	L	-	1	0	PRUNE2	78511091	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.147000	0.10234	-1.649000	0.01508	-0.397000	0.06425	CTT		0.453	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79321271	G	T	79321271	2	4	61	1	0	0	0	0	0	0	0	1	12675	987	35	2		2	PRUNE2	9	79321271	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203729	79321271	61892160	6301	14286										
PRUNE2	158471	broad.mit.edu	37	chr9	79322012	79322012	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggatcagctgtgaccaaGaacttattagattcattcaa	7	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79322012G>T	ENST00000376718.3	-	8	5301	c.5178C>A	c.(5176-5178)ttC>ttA	p.F1726L	PRUNE2_ENST00000428286.1_Missense_Mutation_p.F1367L	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1726					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.F1726L(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTGTGACCAAGAACTTATTAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											138	115	122					9																	79322012		1568	3582	5150	78511832	SO:0001583	missense	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5178C>A	9.37:g.79322012G>T	ENSP00000365908:p.Phe1726Leu		78511832	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.552|3.552	-0.091391|-0.091391	0.07053|0.07053	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.44881|.	0.91;0.92|.	5.89|5.89	3.75|3.75	0.43078|0.43078	.|.	0.659654|.	0.14115|.	N|.	0.340454|.	T|T	0.43942|0.43942	0.1270|0.1270	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	N|N	1|1	P|.	0.38922|.	0.651|.	B|.	0.30401|.	0.115|.	T|T	0.28106|0.28106	-1.0054|-1.0054	10|5	0.20046|.	T|.	0.44|.	-0.4038|-0.4038	10.3031|10.3031	0.43663|0.43663	0.2272:0.0:0.7728:0.0|0.2272:0.0:0.7728:0.0	.|.	1726|.	Q8WUY3|.	PRUN2_HUMAN|.	L|I	1726;1367;1725|1048	ENSP00000365908:F1726L;ENSP00000397425:F1367L|.	ENSP00000365908:F1726L|.	F|L	-|-	3|1	2|0	PRUNE2|PRUNE2	78511832|78511832	0.266000|0.266000	0.24112|0.24112	0.671000|0.671000	0.29857|0.29857	0.686000|0.686000	0.39977|0.39977	1.816000|1.816000	0.38992|0.38992	1.506000|1.506000	0.48736|0.48736	0.643000|0.643000	0.83706|0.83706	TTC|CTT		0.433	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79322012	G	T	79322012	3	4	61	1	0	0	0	0	1	0	0	0	12675	933	33	2	4136	2	PRUNE2	9	79322012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	741	79322012	61891419	6302	14287										
PRUNE2	158471	broad.mit.edu	37	chr9	79322192	79322192	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagttgcagaaatgtcatgTtcatttttctcctggtagct	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79322192T>C	ENST00000376718.3	-	8	5121	c.4998A>G	c.(4996-4998)gaA>gaG	p.E1666E	PRUNE2_ENST00000428286.1_Silent_p.E1307E	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1666					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.E1666E(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AAATGTCATGTTCATTTTTCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	9											75	62	66					9																	79322192		1568	3582	5150	78512012	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4998A>G	9.37:g.79322192T>C			78512012	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	T	2.472	-0.321767	0.05386	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.83	-4.02	0.04034	.	.	.	.	.	T	0.29288	0.0729	.	.	.	0.20074	N	0.999931	.	.	.	.	.	.	T	0.36163	-0.9759	4	.	.	.	-2.6821	8.6439	0.33994	0.0:0.5274:0.1237:0.3489	.	.	.	.	A	988	.	.	T	-	1	0	PRUNE2	78512012	0.000000	0.05858	0.003000	0.11579	0.683000	0.39861	-0.359000	0.07632	-0.660000	0.05352	0.533000	0.62120	ACA		0.443	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79322192	T	C	79322192	2	2	61	1	0	0	0	0	0	0	0	1	12675	1722	60	4		4	PRUNE2	9	79322192	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	180	79322192	61891239	6303	14288										
VPS13A	23230	broad.mit.edu	37	chr9	79820894	79820894	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttttaatcttcctatagGaataaaatatgatcctttaa	3	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79820894G>T	ENST00000360280.3	+	5	544	c.284G>T	c.(283-285)aGa>aTa	p.R95I	VPS13A_ENST00000376634.4_Splice_Site_p.R95I|VPS13A_ENST00000357409.5_Splice_Site_p.R95I|VPS13A_ENST00000376636.3_Splice_Site_p.R95I	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	95					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.R95I(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CTTCCTATAGGAATAAAATAT	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	9											43	44	44					9																	79820894		2195	4280	6475	79010714	SO:0001630	splice_region_variant	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.284-1G>T	9.37:g.79820894G>T			79010714	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.95|12.95	2.092846|2.092846	0.36952|0.36952	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000545365	D;D;D;D|.	0.82433|.	-1.61;-1.61;-1.61;-1.61|.	5.34|5.34	-0.134|-0.134	0.13481|0.13481	.|.	0.342132|0.342132	0.29119|0.29119	N|N	0.013093|0.013093	T|T	0.34077|0.34077	0.0885|0.0885	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.06786|.	0.0;0.001;0.001;0.0|.	B;B;B;B|.	0.09377|.	0.002;0.004;0.002;0.002|.	T|T	0.04413|0.04413	-1.0953|-1.0953	9|6	.|.	.|.	.|.	.|.	11.1194|11.1194	0.48279|0.48279	0.1061:0.0:0.7256:0.1683|0.1061:0.0:0.7256:0.1683	.|.	95;95;95;95|.	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;VP13A_HUMAN;.;.|.	I|S	95|48	ENSP00000365821:R95I;ENSP00000365823:R95I;ENSP00000353422:R95I;ENSP00000349985:R95I|.	.|.	R|R	+|+	2|3	0|2	VPS13A|VPS13A	79010714|79010714	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.951000|0.951000	0.60555|0.60555	1.287000|1.287000	0.33284|0.33284	0.066000|0.066000	0.16515|0.16515	0.650000|0.650000	0.86243|0.86243	AGA|AGG		0.308	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Missense_Mutation	T	79820894	G	T	79820894	5	4	61	1	0	0	0	0	0	0	1	0	17229	1188	41	2	302	2	VPS13A	9	79820894	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	498702	79820894	61392537	6304	14289										
VPS13A	23230	broad.mit.edu	37	chr9	79824399	79824399	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attagttacacagatcataaAaaatcttcaggtgaaaattt	5	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79824399A>C	ENST00000360280.3	+	6	706	c.446A>C	c.(445-447)aAa>aCa	p.K149T	VPS13A_ENST00000376634.4_Missense_Mutation_p.K149T|VPS13A_ENST00000357409.5_Missense_Mutation_p.K149T|VPS13A_ENST00000376636.3_Missense_Mutation_p.K149T	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	149					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.K149T(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAGATCATAAAAAATCTTCAG	0.254																																																2	Substitution - Missense(2)	large_intestine(2)	9											36	38	37					9																	79824399		2203	4289	6492	79014219	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.446A>C	9.37:g.79824399A>C	ENSP00000353422:p.Lys149Thr		79014219	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303527	0.81136	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.49139	0.95;0.79;0.87;0.95	5.71	5.71	0.89125	.	0.106862	0.64402	D	0.000007	T	0.65933	0.2739	M	0.87180	2.865	0.80722	D	1	P;D;D;D	0.59357	0.953;0.983;0.985;0.973	P;P;P;P	0.56434	0.798;0.632;0.798;0.798	T	0.72014	-0.4418	10	0.62326	D	0.03	.	10.8152	0.46571	0.9255:0.0:0.0745:0.0	.	149;149;149;149	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	T	149	ENSP00000365821:K149T;ENSP00000365823:K149T;ENSP00000353422:K149T;ENSP00000349985:K149T	ENSP00000349985:K149T	K	+	2	0	VPS13A	79014219	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.666000	0.68059	2.183000	0.69458	0.533000	0.62120	AAA		0.254	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		C	79824399	A	C	79824399	3	2	61	1	0	0	0	0	1	0	0	0	17229	14	1	4	468	4	VPS13A	9	79824399	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3505	79824399	61389032	6305	14290										
VPS13A	23230	broad.mit.edu	37	chr9	79834915	79834915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacttgtgatgaatcgccGatctgattttgacttttctg	8	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79834915G>A	ENST00000360280.3	+	11	1060	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	VPS13A_ENST00000376634.4_Missense_Mutation_p.R267Q|VPS13A_ENST00000357409.5_Missense_Mutation_p.R267Q|VPS13A_ENST00000376636.3_Missense_Mutation_p.R267Q	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	267					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.R267Q(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATGAATCGCCGATCTGATTTT	0.308																																																2	Substitution - Missense(2)	large_intestine(2)	9											81	82	82					9																	79834915		2203	4299	6502	79024735	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.800G>A	9.37:g.79834915G>A	ENSP00000353422:p.Arg267Gln		79024735	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028368	0.93518	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.46819	1.03;0.86;0.94;1.03	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.69468	0.3114	M	0.77616	2.38	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	P;D;D;D	0.83275	0.906;0.996;0.984;0.984	T	0.64563	-0.6378	10	0.19590	T	0.45	.	19.3762	0.94510	0.0:0.0:1.0:0.0	.	267;267;267;267	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	Q	267	ENSP00000365821:R267Q;ENSP00000365823:R267Q;ENSP00000353422:R267Q;ENSP00000349985:R267Q	ENSP00000349985:R267Q	R	+	2	0	VPS13A	79024735	1.000000	0.71417	0.995000	0.50966	0.655000	0.38815	9.091000	0.94151	2.591000	0.87537	0.561000	0.74099	CGA		0.308	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79834915	G	A	79834915	3	1	61	1	0	0	0	0	1	0	0	0	17229	1058	37	1	842	1	VPS13A	9	79834915	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10516	79834915	61378516	6306	14291										
VPS13A	23230	broad.mit.edu	37	chr9	79897094	79897094	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcacttctgaatacaataAattatcttcataatatcctt	2	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79897094A>C	ENST00000360280.3	+	29	3282	c.3022A>C	c.(3022-3024)Aat>Cat	p.N1008H	VPS13A_ENST00000376634.4_Missense_Mutation_p.N1008H|VPS13A_ENST00000357409.5_Missense_Mutation_p.N1008H|VPS13A_ENST00000376636.3_Missense_Mutation_p.N1008H|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1008					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.N1008H(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAATACAATAAATTATCTTCA	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	9											70	75	73					9																	79897094		2202	4295	6497	79086914	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3022A>C	9.37:g.79897094A>C	ENSP00000353422:p.Asn1008His		79086914	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.117240	0.56505	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	5.18	4.02	0.46733	.	0.053759	0.64402	D	0.000001	T	0.38904	0.1058	M	0.69823	2.125	0.80722	D	1	P;P;D;P	0.56521	0.659;0.811;0.976;0.881	P;P;P;P	0.57960	0.694;0.602;0.83;0.776	T	0.20840	-1.0263	10	0.66056	D	0.02	.	11.836	0.52323	0.853:0.147:0.0:0.0	.	1008;1008;1008;1008	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	H	1008	ENSP00000365821:N1008H;ENSP00000365823:N1008H;ENSP00000353422:N1008H;ENSP00000349985:N1008H	ENSP00000349985:N1008H	N	+	1	0	VPS13A	79086914	1.000000	0.71417	0.987000	0.45799	0.694000	0.40290	7.449000	0.80643	0.791000	0.33826	-0.460000	0.05396	AAT		0.323	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		C	79897094	A	C	79897094	3	2	61	1	0	0	0	0	1	0	0	0	17229	14	1	4	3136	4	VPS13A	9	79897094	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	62179	79897094	61316337	6307	14292										
VPS13A	23230	broad.mit.edu	37	chr9	79908403	79908403	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaagtagtttttgtcacGaaatttctatattctatatt	5	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:79908403G>A	ENST00000360280.3	+	32	3746	c.3486G>A	c.(3484-3486)acG>acA	p.T1162T	VPS13A_ENST00000376634.4_Silent_p.T1162T|VPS13A_ENST00000357409.5_Silent_p.T1162T|VPS13A_ENST00000376636.3_Silent_p.T1123T|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1162					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.T1162T(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TTTTTGTCACGAAATTTCTAT	0.279																																																2	Substitution - coding silent(2)	large_intestine(2)	9											73	71	72					9																	79908403		2203	4299	6502	79098223	SO:0001819	synonymous_variant	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3486G>A	9.37:g.79908403G>A			79098223	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																				0.279	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79908403	G	A	79908403	2	1	61	1	0	0	0	0	0	0	0	1	17229	1045	37	1		1	VPS13A	9	79908403	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11309	79908403	61305028	6308	14293										
VPS13A	23230	broad.mit.edu	37	chr9	80018180	80018180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatggaagatttgcaaaatAcaaatattttacccatgtca	5	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:80018180A>G	ENST00000360280.3	+	69	9478	c.9218A>G	c.(9217-9219)tAc>tGc	p.Y3073C	VPS13A_ENST00000376636.3_Missense_Mutation_p.Y3034C|VPS13A_ENST00000376646.3_Missense_Mutation_p.Y9C|VPS13A_ENST00000484581.2_Missense_Mutation_p.Y9C	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	3073					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.Y3073C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TTTGCAAAATACAAATATTTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	9											88	87	87					9																	80018180		2202	4298	6500	79208000	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.9218A>G	9.37:g.80018180A>G	ENSP00000353422:p.Tyr3073Cys		79208000	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.207394	0.58343	.	.	ENSG00000197969	ENST00000376636;ENST00000360280;ENST00000484581;ENST00000376646	T;T;T;T	0.66460	0.83;0.91;-0.21;-0.21	5.77	1.9	0.25705	.	0.396585	0.28736	N	0.014317	T	0.68054	0.2959	L	0.48642	1.525	0.39478	D	0.967834	D;P	0.62365	0.991;0.911	D;B	0.64237	0.923;0.39	T	0.66073	-0.6014	9	.	.	.	.	5.026	0.14385	0.6497:0.0:0.1569:0.1933	.	3034;3073	Q96RL7-3;Q96RL7	.;VP13A_HUMAN	C	3034;3073;9;9	ENSP00000365823:Y3034C;ENSP00000353422:Y3073C;ENSP00000446020:Y9C;ENSP00000365834:Y9C	.	Y	+	2	0	VPS13A	79208000	0.999000	0.42202	0.998000	0.56505	0.993000	0.82548	2.042000	0.41222	1.018000	0.39521	0.528000	0.53228	TAC		0.308	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	80018180	A	G	80018180	3	3	61	1	0	0	0	0	1	0	0	0	17229	391	14	4	9620	4	VPS13A	9	80018180	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	109777	80018180	61195251	6309	14294										
GNA14	9630	broad.mit.edu	37	chr9	80144098	80144098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgaacccctttctgtcttCgtcgctgtaaccagacccat	7	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:80144098C>T	ENST00000341700.6	-	2	709	c.196G>A	c.(196-198)Gaa>Aaa	p.E66K	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	66					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.E66K(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TTTCTGTCTTCGTCGCTGTAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	9											345	321	329					9																	80144098		2203	4300	6503	79333918	SO:0001583	missense	9630			AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.196G>A	9.37:g.80144098C>T	ENSP00000365807:p.Glu66Lys		79333918	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417410	0.83449	.	.	ENSG00000156049	ENST00000341700	D	0.89681	-2.55	5.92	5.92	0.95590	G protein alpha subunit, helical insertion (2);	0.098075	0.64402	D	0.000001	D	0.89563	0.6751	M	0.73372	2.23	0.80722	D	1	B	0.28208	0.203	B	0.26770	0.073	D	0.87018	0.2127	10	0.87932	D	0	.	20.4025	0.99000	0.0:1.0:0.0:0.0	.	66	O95837	GNA14_HUMAN	K	66	ENSP00000365807:E66K	ENSP00000365807:E66K	E	-	1	0	GNA14	79333918	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.815000	0.86186	2.828000	0.97474	0.650000	0.86243	GAA		0.453	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			T	80144098	C	T	80144098	3	4	61	1	0	0	0	0	1	0	0	0	6522	893	31	1	895	1	GNA14	9	80144098	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125918	80144098	61069333	6310	14295										
GNAQ	2776	broad.mit.edu	37	chr9	80336400	80336400	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacatcttcagaatgaattCtcgggctgcctgggcatctc	10	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:80336400C>A	ENST00000286548.4	-	7	1141	c.919G>T	c.(919-921)Gaa>Taa	p.E307*	GNAQ_ENST00000397476.3_Nonsense_Mutation_p.E105*	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	307					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.E307*(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						AGAATGAATTCTCGGGCTGCC	0.473			Mis		uveal melanoma																																		Dom	yes		9	9q21	2776	"guanine nucleotide binding protein (G protein), q polypeptide"		E	1	Substitution - Nonsense(1)	large_intestine(1)	9											104	96	98					9																	80336400		2203	4300	6503	79526220	SO:0001587	stop_gained	2776				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.919G>T	9.37:g.80336400C>A	ENSP00000286548:p.Glu307*		79526220	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Nonsense_Mutation	SNP	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	C	37	6.285393	0.97444	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	.	.	.	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	.	.	.	X	307;105	.	ENSP00000286548:E307X	E	-	1	0	GNAQ	79526220	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.771000	0.85420	2.857000	0.98124	0.650000	0.86243	GAA		0.473	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072		A	80336400	C	A	80336400	4	1	61	1	0	0	0	0	0	1	0	0	6529	922	32	2	164	2	GNAQ	9	80336400	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192302	80336400	60877031	6311	14296										
CEP78	84131	broad.mit.edu	37	chr9	80863213	80863213	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattttactttagatcattCtatgatgaaagcagttatca	5	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:80863213C>A	ENST00000424347.2	+	7	1188	c.899C>A	c.(898-900)tCt>tAt	p.S300Y	CEP78_ENST00000277082.5_Missense_Mutation_p.S300Y|CEP78_ENST00000376597.4_Missense_Mutation_p.S300Y|CEP78_ENST00000415759.2_Missense_Mutation_p.S300Y|CEP78_ENST00000376598.2_Missense_Mutation_p.S300Y			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	300					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)		p.S300Y(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						TTAGATCATTCTATGATGAAA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	54	54					9																	80863213		1782	4065	5847	80053033	SO:0001583	missense	84131			BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 81"	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.899C>A	9.37:g.80863213C>A	ENSP00000411284:p.Ser300Tyr		80053033	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Missense_Mutation	SNP	ENST00000424347.2	37		.	.	.	.	.	.	.	.	.	.	C	17.79	3.476519	0.63737	.	.	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53	6.03	4.11	0.48088	.	0.438594	0.24249	N	0.040196	T	0.61664	0.2365	L	0.53249	1.67	0.31513	N	0.663349	D;D;D;D	0.71674	0.993;0.991;0.998;0.993	P;P;D;P	0.65443	0.641;0.77;0.935;0.758	T	0.64495	-0.6394	10	0.62326	D	0.03	-6.0991	8.0263	0.30438	0.0:0.7261:0.1496:0.1243	.	213;300;300;300	B7Z8H9;E9PHX5;Q5JTW2-2;Q5JTW2	.;.;.;CEP78_HUMAN	Y	300	ENSP00000411284:S300Y;ENSP00000399286:S300Y;ENSP00000365782:S300Y;ENSP00000277082:S300Y;ENSP00000365783:S300Y	ENSP00000277082:S300Y	S	+	2	0	CEP78	80053033	0.083000	0.21467	1.000000	0.80357	0.992000	0.81027	0.353000	0.20130	2.861000	0.98227	0.655000	0.94253	TCT		0.289	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991		A	80863213	C	A	80863213	3	1	61	1	0	0	0	0	1	0	0	0	3268	913	32	2	925	2	CEP78	9	80863213	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	526813	80863213	60350218	6312	14297										
PSAT1	29968	broad.mit.edu	37	chr9	80916919	80916919	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagattattaacaatacagaGaatcttgtgcgggaattgct	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:80916919G>T	ENST00000376588.3	+	3	239	c.171G>T	c.(169-171)gaG>gaT	p.E57D	PSAT1_ENST00000347159.2_Missense_Mutation_p.E57D	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	57					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)	p.E57D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						ACAATACAGAGAATCTTGTGC	0.328																																					Colon(34;187 791 10662 18313 37609)											1	Substitution - Missense(1)	large_intestine(1)	9											120	119	119					9																	80916919		2203	4300	6503	80106739	SO:0001583	missense	29968			BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.171G>T	9.37:g.80916919G>T	ENSP00000365773:p.Glu57Asp		80106739	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	37	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.880953	0.51801	.	.	ENSG00000135069	ENST00000347159;ENST00000376588	D;D	0.87491	-2.26;-2.26	5.42	5.42	0.78866	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.89667	0.6781	M	0.88640	2.97	0.49687	D	0.999818	P;B	0.48503	0.911;0.172	P;B	0.47430	0.547;0.233	D	0.90587	0.4534	10	0.87932	D	0	-18.3788	7.0518	0.25077	0.2072:0.0:0.7928:0.0	.	57;57	Q9Y617-2;Q9Y617	.;SERC_HUMAN	D	57	ENSP00000317606:E57D;ENSP00000365773:E57D	ENSP00000317606:E57D	E	+	3	2	PSAT1	80106739	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	4.957000	0.63652	2.542000	0.85734	0.655000	0.94253	GAG		0.328	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		T	80916919	G	T	80916919	3	4	61	1	0	0	0	0	1	0	0	0	12678	933	33	2	181	2	PSAT1	9	80916919	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53706	80916919	60296512	6313	14298										
TLE4	7091	broad.mit.edu	37	chr9	82336719	82336719	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaatgatggcaccaagctCtggacaggtggtttggacaa	12	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:82336719C>A	ENST00000376552.2	+	17	2920	c.1902C>A	c.(1900-1902)ctC>ctA	p.L634L	TLE4_ENST00000265284.6_Silent_p.L609L|TLE4_ENST00000376534.4_Silent_p.L271L|TLE4_ENST00000376520.4_Silent_p.L666L|TLE4_ENST00000376544.3_Silent_p.L565L|TLE4_ENST00000376537.4_Silent_p.L666L	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	634					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)	p.L634L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						GCACCAAGCTCTGGACAGGTG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	9											77	77	77					9																	82336719		2203	4300	6503	81526539	SO:0001819	synonymous_variant	7091			M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.1902C>A	9.37:g.82336719C>A			81526539	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Silent	SNP	ENST00000376552.2	37	CCDS43837.1																																																																																				0.552	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		A	82336719	C	A	82336719	2	1	61	1	0	0	0	0	0	0	0	1	15980	900	32	2		2	TLE4	9	82336719	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1419800	82336719	58876712	6314	14299										
FLJ46321	389763	broad.mit.edu	37	chr9	84608635	84608635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtgtccggacaacagagGatggcagacagacttttctg	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:84608635G>A	ENST00000344803.2	+	4	3297	c.3250G>A	c.(3250-3252)Gat>Aat	p.D1084N		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1084					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.D1084N(2)									GACAACAGAGGATGGCAGACA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	9											45	47	47					9																	84608635		1917	4125	6042	83798455	SO:0001583	missense	389763				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3250G>A	9.37:g.84608635G>A	ENSP00000341988:p.Asp1084Asn		83798455		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944142	0.34283	.	.	ENSG00000214929	ENST00000344803	T	0.05925	3.37	2.67	-3.64	0.04515	.	.	.	.	.	T	0.02418	0.0074	N	0.14661	0.345	0.09310	N	1	B	0.33044	0.395	B	0.29267	0.1	T	0.43893	-0.9363	9	0.17369	T	0.5	-0.0136	1.4844	0.02444	0.1214:0.3256:0.224:0.329	.	1084	Q6ZQQ2	F75D1_HUMAN	N	1084	ENSP00000341988:D1084N	ENSP00000341988:D1084N	D	+	1	0	FAM75D1	83798455	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.880000	0.04183	-0.888000	0.03956	0.603000	0.83216	GAT		0.507	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84608635	G	A	84608635	3	1	61	1	0	0	0	0	1	0	0	0	5951	1174	41	3	3264	3	FLJ46321	9	84608635	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2271916	84608635	56604796	6315	14300										
FLJ46321	389763	broad.mit.edu	37	chr9	84609655	84609655	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggcataggcatgggataGatatcacctgtccccaagag	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:84609655G>T	ENST00000344803.2	+	4	4317	c.4270G>T	c.(4270-4272)Gat>Tat	p.D1424Y		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1424					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.D1424Y(2)									GCATGGGATAGATATCACCTG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	9											38	38	38					9																	84609655		1893	4119	6012	83799475	SO:0001583	missense	389763				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4270G>T	9.37:g.84609655G>T	ENSP00000341988:p.Asp1424Tyr		83799475		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.341862	0.24339	.	.	ENSG00000214929	ENST00000344803	T	0.05513	3.43	3.13	0.451	0.16629	.	.	.	.	.	T	0.03564	0.0102	L	0.27053	0.805	0.09310	N	1	B	0.33807	0.426	B	0.25405	0.06	T	0.40720	-0.9548	9	0.54805	T	0.06	0.2306	2.1376	0.03766	0.2682:0.0:0.4634:0.2684	.	1424	Q6ZQQ2	F75D1_HUMAN	Y	1424	ENSP00000341988:D1424Y	ENSP00000341988:D1424Y	D	+	1	0	FAM75D1	83799475	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.302000	0.19192	0.070000	0.16634	0.655000	0.94253	GAT		0.517	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84609655	G	T	84609655	3	4	61	1	0	0	0	0	1	0	0	0	5951	942	33	2	4284	2	FLJ46321	9	84609655	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1020	84609655	56603776	6316	14301										
RASEF	158158	broad.mit.edu	37	chr9	85615939	85615939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggtagacaagccgctgtCgaagcagctttcaggcaggc	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:85615939C>T	ENST00000376447.3	-	10	1569	c.1309G>A	c.(1309-1311)Gac>Aac	p.D437N		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	437					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.D437N(1)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						AAGCCGCTGTCGAAGCAGCTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	9											75	71	73					9																	85615939		2203	4300	6503	84805759	SO:0001583	missense	158158			AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.1309G>A	9.37:g.85615939C>T	ENSP00000365630:p.Asp437Asn		84805759	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	C	34	5.368646	0.95900	.	.	ENSG00000165105	ENST00000376447	T	0.69175	-0.38	5.92	5.92	0.95590	.	0.106311	0.64402	D	0.000008	T	0.81138	0.4760	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.81409	-0.0946	10	0.87932	D	0	.	19.9242	0.97098	0.0:1.0:0.0:0.0	.	437	Q8IZ41	RASEF_HUMAN	N	437	ENSP00000365630:D437N	ENSP00000365630:D437N	D	-	1	0	RASEF	84805759	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	5.224000	0.65288	2.814000	0.96858	0.585000	0.79938	GAC		0.532	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		T	85615939	C	T	85615939	3	4	61	1	0	0	0	0	1	0	0	0	13105	884	31	1	945	1	RASEF	9	85615939	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1006284	85615939	55597492	6317	14302										
FRMD3	257019	broad.mit.edu	37	chr9	85950442	85950442	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaattacctgagttcattTttatgaatttccactatttt	4	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:85950442T>C	ENST00000304195.3	-	6	791	c.585A>G	c.(583-585)aaA>aaG	p.K195K	FRMD3_ENST00000376438.1_Silent_p.K195K	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	195	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)		p.K91K(1)|p.K195K(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						TGAGTTCATTTTTATGAATTT	0.373																																																2	Substitution - coding silent(2)	large_intestine(2)	9											109	96	100					9																	85950442		1834	4076	5910	85140262	SO:0001819	synonymous_variant	257019			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.585A>G	9.37:g.85950442T>C			85140262	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Silent	SNP	ENST00000304195.3	37	CCDS43840.1																																																																																				0.373	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938		C	85950442	T	C	85950442	2	2	61	1	0	0	0	0	0	0	0	1	6069	1838	64	4		4	FRMD3	9	85950442	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	334503	85950442	55262989	6318	14303										
FRMD3	257019	broad.mit.edu	37	chr9	85958182	85958182	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaaaaatgtcccttttaAtctgaaggtataaaaggtat	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:85958182A>C	ENST00000304195.3	-	5	601	c.395T>G	c.(394-396)aTt>aGt	p.I132S	FRMD3_ENST00000376438.1_Missense_Mutation_p.I132S	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	132	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)		p.I132S(1)|p.I28S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						GTCCCTTTTAATCTGAAGGTA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	9											83	87	86					9																	85958182		1976	4164	6140	85148002	SO:0001583	missense	257019			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.395T>G	9.37:g.85958182A>C	ENSP00000303508:p.Ile132Ser		85148002	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Missense_Mutation	SNP	ENST00000304195.3	37	CCDS43840.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.725269	0.89298	.	.	ENSG00000172159	ENST00000376438;ENST00000304195;ENST00000376422	T;T	0.77750	-1.12;-1.12	6.17	6.17	0.99709	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.111982	0.64402	D	0.000009	D	0.87014	0.6072	M	0.71581	2.175	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.66497	0.944;0.935	D	0.88114	0.2827	10	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	132;132	A2A2Y4;A2A2Y4-2	FRMD3_HUMAN;.	S	132;132;28	ENSP00000365621:I132S;ENSP00000303508:I132S	ENSP00000303508:I132S	I	-	2	0	FRMD3	85148002	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.184000	0.94893	2.371000	0.80710	0.533000	0.62120	ATT		0.458	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938		C	85958182	A	C	85958182	3	2	61	1	0	0	0	0	1	0	0	0	6069	101	4	4	1438	4	FRMD3	9	85958182	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7740	85958182	55255249	6319	14304										
KIF27	55582	broad.mit.edu	37	chr9	86452199	86452199	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccactggggggtgctaaaGaactatgaattggaggtaat	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:86452199G>T	ENST00000297814.2	-	18	4066	c.3923C>A	c.(3922-3924)tCt>tAt	p.S1308Y	RP11-575L7.2_ENST00000412069.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.2_ENST00000439378.3_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.S1211Y|RP11-575L7.2_ENST00000417672.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.S1242Y|RP11-575L7.2_ENST00000458016.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1308					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S1308Y(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						GGGTGCTAAAGAACTATGAAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											29	32	31					9																	86452199		2201	4279	6480	85642019	SO:0001583	missense	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3923C>A	9.37:g.86452199G>T	ENSP00000297814:p.Ser1308Tyr		85642019	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839999	0.32513	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.72725	-0.64;-0.68;-0.57	3.8	3.8	0.43715	.	0.256528	0.26951	N	0.021666	T	0.73094	0.3543	L	0.27053	0.805	0.30154	N	0.802832	D;P;P	0.69078	0.997;0.942;0.904	D;P;B	0.78314	0.991;0.458;0.269	T	0.71002	-0.4718	10	0.72032	D	0.01	.	11.4246	0.50003	0.0:0.0:1.0:0.0	.	1211;1242;1308	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	Y	1308;1242;1211	ENSP00000297814:S1308Y;ENSP00000401688:S1242Y;ENSP00000333928:S1211Y	ENSP00000297814:S1308Y	S	-	2	0	KIF27	85642019	1.000000	0.71417	0.970000	0.41538	0.778000	0.44026	2.943000	0.49026	2.120000	0.65058	0.580000	0.79431	TCT		0.398	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		T	86452199	G	T	86452199	3	4	61	1	0	0	0	0	1	0	0	0	8317	942	33	2	286	2	KIF27	9	86452199	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	494017	86452199	54761232	6320	14305										
KIF27	55582	broad.mit.edu	37	chr9	86457176	86457176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggtgctagttgccgccGaattgcttcccctaccagtt	10	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:86457176G>A	ENST00000297814.2	-	17	3840	c.3697C>T	c.(3697-3699)Cgg>Tgg	p.R1233W	RP11-575L7.4_ENST00000591217.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.R1136W|KIF27_ENST00000413982.1_Missense_Mutation_p.R1167W	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1233					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1233W(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						AGTTGCCGCCGAATTGCTTCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											74	66	69					9																	86457176		2203	4300	6503	85646996	SO:0001583	missense	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3697C>T	9.37:g.86457176G>A	ENSP00000297814:p.Arg1233Trp		85646996	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.729134	0.48833	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.70749	-0.51;-0.51;-0.37	4.24	4.24	0.50183	.	0.703319	0.12462	N	0.466797	T	0.71787	0.3381	L	0.47716	1.5	0.09310	N	1	D;B;B	0.67145	0.996;0.008;0.005	P;B;B	0.50896	0.653;0.002;0.001	T	0.63915	-0.6529	10	0.62326	D	0.03	.	12.6021	0.56503	0.0:0.166:0.834:0.0	.	1136;1167;1233	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	W	1233;1167;1136	ENSP00000297814:R1233W;ENSP00000401688:R1167W;ENSP00000333928:R1136W	ENSP00000297814:R1233W	R	-	1	2	KIF27	85646996	0.019000	0.18553	0.041000	0.18516	0.833000	0.47200	1.295000	0.33377	2.201000	0.70794	0.465000	0.42564	CGG		0.403	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86457176	G	A	86457176	3	1	61	1	0	0	0	0	1	0	0	0	8317	1057	37	1	516	1	KIF27	9	86457176	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4977	86457176	54756255	6321	14306										
KIF27	55582	broad.mit.edu	37	chr9	86514698	86514698	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttctgattaaatactaCttcatcagcagcaagcacac	4	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:86514698C>A	ENST00000297814.2	-	5	1623	c.1480G>T	c.(1480-1482)Gta>Tta	p.V494L	KIF27_ENST00000334204.2_Missense_Mutation_p.V494L|KIF27_ENST00000413982.1_Missense_Mutation_p.V494L	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	494					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V494L(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TTAAATACTACTTCATCAGCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											131	93	106					9																	86514698		2203	4300	6503	85704518	SO:0001583	missense	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1480G>T	9.37:g.86514698C>A	ENSP00000297814:p.Val494Leu		85704518	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193638	0.38707	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.55588	0.51;0.51;0.51	3.85	3.85	0.44370	.	0.128538	0.31797	N	0.007043	T	0.51312	0.1667	L	0.51422	1.61	0.29686	N	0.84128	P;B;B	0.45715	0.865;0.136;0.067	P;B;B	0.45406	0.479;0.071;0.048	T	0.52771	-0.8531	10	0.27785	T	0.31	.	15.551	0.76152	0.0:1.0:0.0:0.0	.	494;494;494	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	L	494	ENSP00000297814:V494L;ENSP00000401688:V494L;ENSP00000333928:V494L	ENSP00000297814:V494L	V	-	1	0	KIF27	85704518	0.997000	0.39634	0.998000	0.56505	0.837000	0.47467	1.463000	0.35277	1.982000	0.57802	0.585000	0.79938	GTA		0.403	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86514698	C	A	86514698	3	1	61	1	0	0	0	0	1	0	0	0	8317	565	20	2	2781	2	KIF27	9	86514698	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57522	86514698	54698733	6322	14307										
RMI1	80010	broad.mit.edu	37	chr9	86616676	86616676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaaaatgatgagcttacaGcaaataatgacacttcctca	6	8	1	4	rs138543013		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:86616676G>A	ENST00000325875.3	+	3	1107	c.775G>A	c.(775-777)Gca>Aca	p.A259T		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	259				A -> T (in Ref. 1; BAB14325). {ECO:0000305}.	DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)		p.A259T(1)		biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						TGAGCTTACAGCAAATAATGA	0.393													G|||	1	0.000199681	8e-04	0	5008	,	,		20669	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	142	132	136		775	3.6	0.8	9	dbSNP_134	136	0,8600		0,0,4300	no	missense	RMI1	NM_024945.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	259/626	86616676	1,13005	2203	4300	6503	85806496	SO:0001583	missense	80010			AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.775G>A	9.37:g.86616676G>A	ENSP00000317039:p.Ala259Thr		85806496	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	37	CCDS6669.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	3.842	-0.033622	0.07543	2.27E-4	0.0	ENSG00000178966	ENST00000445877;ENST00000325875	T;T	0.46819	0.86;1.47	5.41	3.56	0.40772	.	1.021290	0.07813	N	0.958501	T	0.38799	0.1054	M	0.64997	1.995	0.09310	N	1	P	0.35433	0.501	B	0.27608	0.081	T	0.25779	-1.0122	10	0.15499	T	0.54	-4.685	5.935	0.19161	0.0715:0.2332:0.5611:0.1342	.	259	Q9H9A7	RMI1_HUMAN	T	259	ENSP00000402433:A259T;ENSP00000317039:A259T	ENSP00000317039:A259T	A	+	1	0	RMI1	85806496	0.945000	0.32115	0.807000	0.32361	0.451000	0.32288	1.146000	0.31589	0.758000	0.33059	0.655000	0.94253	GCA		0.393	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		A	86616676	G	A	86616676	3	1	61	1	0	0	0	0	1	0	0	0	13432	971	34	3	777	3	RMI1	9	86616676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101978	86616676	54596755	6323	14308										
RMI1	80010	broad.mit.edu	37	chr9	86617158	86617158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattttacaaataaagaaaaGaacttagagacagataataa	6	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:86617158G>T	ENST00000325875.3	+	3	1589	c.1257G>T	c.(1255-1257)aaG>aaT	p.K419N		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	419					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)		p.K419N(1)		biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						ATAAAGAAAAGAACTTAGAGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	9											50	60	56					9																	86617158		2191	4271	6462	85806978	SO:0001583	missense	80010			AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.1257G>T	9.37:g.86617158G>T	ENSP00000317039:p.Lys419Asn		85806978	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	37	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	G	0.064	-1.218160	0.01542	.	.	ENSG00000178966	ENST00000325875	T	0.32988	1.43	5.16	1.25	0.21368	.	0.854095	0.10308	N	0.690394	T	0.19644	0.0472	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30119	-0.9989	9	.	.	.	-2.0E-4	4.7523	0.13066	0.3789:0.1516:0.4695:0.0	.	419	Q9H9A7	RMI1_HUMAN	N	419	ENSP00000317039:K419N	.	K	+	3	2	RMI1	85806978	0.006000	0.16342	0.207000	0.23584	0.516000	0.34256	0.470000	0.22084	0.026000	0.15269	0.655000	0.94253	AAG		0.308	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		T	86617158	G	T	86617158	3	4	61	1	0	0	0	0	1	0	0	0	13432	933	33	2	1259	2	RMI1	9	86617158	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	482	86617158	54596273	6324	14309										
AGTPBP1	23287	broad.mit.edu	37	chr9	88162071	88162071	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtcagaaagtacttcttCttgagcagaaggttcataat	9	6	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88162071C>A	ENST00000357081.3	-	26	3778	c.3634G>T	c.(3634-3636)Gaa>Taa	p.E1212*	AGTPBP1_ENST00000432218.1_3'UTR|AGTPBP1_ENST00000376083.3_Nonsense_Mutation_p.E1172*|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376109.3_Nonsense_Mutation_p.E1224*			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1212					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.E1172*(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGTACTTCTTCTTGAGCAGAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											146	136	140					9																	88162071		2203	4300	6503	87351891	SO:0001587	stop_gained	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.3634G>T	9.37:g.88162071C>A	ENSP00000349592:p.Glu1212*		87351891	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Nonsense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	C	41	8.652833	0.98901	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109	.	.	.	6.03	5.12	0.69794	.	0.305617	0.37715	N	0.001976	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-22.0984	15.7129	0.77644	0.0:0.9337:0.0:0.0663	.	.	.	.	X	1212;1172;1224	.	ENSP00000349592:E1212X	E	-	1	0	AGTPBP1	87351891	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.056000	0.57448	2.861000	0.98227	0.655000	0.94253	GAA		0.368	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88162071	C	A	88162071	4	1	61	1	0	0	0	0	0	1	0	0	400	922	32	2	50	2	AGTPBP1	9	88162071	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1544913	88162071	53051360	6325	14310										
AGTPBP1	23287	broad.mit.edu	37	chr9	88261274	88261274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatcttcattctcagtttCgttttcagcttctacatcaa	4	11	7	0	rs538837935		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88261274C>T	ENST00000357081.3	-	12	1291	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	AGTPBP1_ENST00000432218.1_Missense_Mutation_p.E221K|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.E343K|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.E395K			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	383					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.E343K(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TTCTCAGTTTCGTTTTCAGCT	0.308													C|||	1	0.000199681	0	0	5008	,	,		17343	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9											201	181	188					9																	88261274		2202	4300	6502	87451094	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1147G>A	9.37:g.88261274C>T	ENSP00000349592:p.Glu383Lys		87451094	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.090658	0.76756	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.57	5.57	0.84162	.	0.045223	0.85682	D	0.000000	T	0.47229	0.1434	M	0.62723	1.935	0.80722	D	1	P;P;D;P	0.54772	0.951;0.455;0.968;0.884	B;B;B;B	0.42827	0.191;0.037;0.399;0.112	T	0.54275	-0.8318	10	0.66056	D	0.02	-27.1518	19.5476	0.95305	0.0:1.0:0.0:0.0	.	395;383;221;343	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	K	383;343;395;221	ENSP00000349592:E383K;ENSP00000365251:E343K;ENSP00000365277:E395K;ENSP00000402804:E221K	ENSP00000349592:E383K	E	-	1	0	AGTPBP1	87451094	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	6.886000	0.75611	2.616000	0.88540	0.563000	0.77884	GAA		0.308	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		T	88261274	C	T	88261274	3	4	61	1	0	0	0	0	1	0	0	0	400	893	31	1	2593	1	AGTPBP1	9	88261274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99203	88261274	52952157	6326	14311										
AGTPBP1	23287	broad.mit.edu	37	chr9	88292362	88292362	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccttaccttttggtccaAtctttgcaagaatagaatga	6	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88292362A>T	ENST00000357081.3	-	6	569	c.425T>A	c.(424-426)aTt>aAt	p.I142N	AGTPBP1_ENST00000376080.1_Missense_Mutation_p.I84N|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.I24N|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.I142N|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000337006.4_Missense_Mutation_p.I84N|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.I194N|AGTPBP1_ENST00000376081.4_Missense_Mutation_p.I142N			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	142					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.I142N(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TTTTGGTCCAATCTTTGCAAG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	119	120					9																	88292362		2203	4300	6503	87482182	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.425T>A	9.37:g.88292362A>T	ENSP00000349592:p.Ile142Asn		87482182	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	A	16.95	3.263529	0.59431	.	.	ENSG00000135049	ENST00000337006;ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218;ENST00000376081;ENST00000376080	T;T;T;T;T;T;T	0.56275	0.53;0.53;0.47;0.47;0.47;0.53;0.53	5.54	4.38	0.52667	Armadillo-like helical (1);Armadillo-type fold (1);	0.168665	0.56097	D	0.000037	T	0.52693	0.1750	L	0.46157	1.445	0.43959	D	0.99663	P;P;P;P	0.51537	0.865;0.71;0.946;0.565	B;B;P;B	0.48921	0.298;0.223;0.595;0.397	T	0.58418	-0.7640	10	0.87932	D	0	-22.8554	12.0561	0.53536	0.9292:0.0:0.0708:0.0	.	194;142;24;142	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	N	84;142;142;194;24;142;84	ENSP00000338512:I84N;ENSP00000349592:I142N;ENSP00000365251:I142N;ENSP00000365277:I194N;ENSP00000402804:I24N;ENSP00000365249:I142N;ENSP00000365248:I84N	ENSP00000338512:I84N	I	-	2	0	AGTPBP1	87482182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.602000	0.74141	2.220000	0.72140	0.533000	0.62120	ATT		0.343	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		T	88292362	A	T	88292362	3	4	61	1	0	0	0	0	1	0	0	0	400	101	4	5	3219	5	AGTPBP1	9	88292362	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	31088	88292362	52921069	6327	14312										
AGTPBP1	23287	broad.mit.edu	37	chr9	88307629	88307629	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgagccagatgaagaatTtttgatgtaacatatcgggc	10	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88307629T>G	ENST00000357081.3	-	3	276	c.132A>C	c.(130-132)aaA>aaC	p.K44N	AGTPBP1_ENST00000376080.1_5'UTR|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.K44N|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000337006.4_5'UTR|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.K96N|AGTPBP1_ENST00000376081.4_Missense_Mutation_p.K44N			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	44					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.K44N(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						GATGAAGAATTTTTGATGTAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											110	95	100					9																	88307629		2203	4300	6503	87497449	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.132A>C	9.37:g.88307629T>G	ENSP00000349592:p.Lys44Asn		87497449	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	T	18.84	3.708282	0.68615	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000376081	T;T;T;T	0.48522	0.81;0.83;0.83;0.81	4.75	2.33	0.28932	Armadillo-like helical (1);Armadillo-type fold (1);	0.054454	0.64402	D	0.000001	T	0.59959	0.2232	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.995;0.997	T	0.59059	-0.7525	10	0.87932	D	0	-21.9665	5.3145	0.15849	0.0:0.5648:0.0:0.4352	.	96;44;44	Q9UPW5-3;Q9UPW5;Q9UPW5-2	.;CBPC1_HUMAN;.	N	44;44;96;44	ENSP00000349592:K44N;ENSP00000365251:K44N;ENSP00000365277:K96N;ENSP00000365249:K44N	ENSP00000349592:K44N	K	-	3	2	AGTPBP1	87497449	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.709000	0.37909	0.655000	0.30866	0.454000	0.30748	AAA		0.373	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88307629	T	G	88307629	3	3	61	1	0	0	0	0	1	0	0	0	400	1838	64	4	3524	4	AGTPBP1	9	88307629	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	15267	88307629	52905802	6328	14313										
NAA35	60560	broad.mit.edu	37	chr9	88557186	88557186	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattacccaagattttgaaGaagcttgtcgaggtgagtct	10	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88557186G>T	ENST00000361671.5	+	2	245	c.112G>T	c.(112-114)Gaa>Taa	p.E38*	NAA35_ENST00000376040.1_Nonsense_Mutation_p.E38*	NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	38					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)		p.E38*(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						AGATTTTGAAGAAGCTTGTCG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											159	151	154					9																	88557186		2203	4300	6503	87747006	SO:0001587	stop_gained	60560			AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"N(alpha)-acetyltransferase subunits"	24340	protein-coding gene	gene with protein product			"MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.112G>T	9.37:g.88557186G>T	ENSP00000354972:p.Glu38*		87747006	Q5VZE6|Q9H631|Q9H703	Nonsense_Mutation	SNP	ENST00000361671.5	37	CCDS6673.1	.	.	.	.	.	.	.	.	.	.	G	37	6.507588	0.97624	.	.	ENSG00000135040	ENST00000361671;ENST00000416045;ENST00000376040	.	.	.	5.11	4.2	0.49525	.	0.434739	0.26407	N	0.024551	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4337	14.6266	0.68626	0.0:0.0:0.8531:0.1469	.	.	.	.	X	38	.	ENSP00000354972:E38X	E	+	1	0	NAA35	87747006	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.918000	0.69996	1.355000	0.45865	0.558000	0.71614	GAA		0.403	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635		T	88557186	G	T	88557186	4	4	61	1	0	0	0	0	0	1	0	0	10153	943	33	2	114	2	NAA35	9	88557186	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	249557	88557186	52656245	6329	14314										
NAA35	60560	broad.mit.edu	37	chr9	88593190	88593190	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatttgctagaccagtgcTgttgcagaagctcaaaaatt	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88593190T>C	ENST00000361671.5	+	11	904	c.771T>C	c.(769-771)gcT>gcC	p.A257A	NAA35_ENST00000376040.1_Silent_p.A257A	NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	257					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)		p.A257A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						AGACCAGTGCTGTTGCAGAAG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	9											118	116	117					9																	88593190		2203	4300	6503	87783010	SO:0001819	synonymous_variant	60560			AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"N(alpha)-acetyltransferase subunits"	24340	protein-coding gene	gene with protein product			"MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.771T>C	9.37:g.88593190T>C			87783010	Q5VZE6|Q9H631|Q9H703	Silent	SNP	ENST00000361671.5	37	CCDS6673.1																																																																																				0.333	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635		C	88593190	T	C	88593190	2	2	61	1	0	0	0	0	0	0	0	1	10153	1567	55	4		4	NAA35	9	88593190	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	36004	88593190	52620241	6330	14315										
GOLM1	51280	broad.mit.edu	37	chr9	88648284	88648286	+	In_Frame_Del	DEL	CTC	CTC	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccatgttgtagtcatcttCtcctctcagtttctgctggt							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CTC	CTC	CTC	-	CTC	CTC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88648284_88648286delCTC	ENST00000388712.3	-	9	1208_1210	c.1040_1042delGAG	c.(1039-1044)ggagaa>gaa	p.G347del	GOLM1_ENST00000257504.6_5'Flank|GOLM1_ENST00000388711.3_In_Frame_Del_p.G347del	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	347					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)		p.G347delG(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						TAGTCATCTTCTCCTCTCAGTTT	0.429																																																1	Deletion - In frame(1)	large_intestine(1)	9																																								87838106	SO:0001651	inframe_deletion	51280			AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"golgi phosphoprotein 2", "chromosome 9 open reading frame 155"	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.1040_1042delGAG	9.37:g.88648287_88648289delCTC	ENSP00000373364:p.Gly347del		87838104	Q6IAF4|Q9NRB9	In_Frame_Del	DEL	ENST00000388712.3	37	CCDS35054.1																																																																																				0.429	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		-	88648286	CTC	-	88648284	7	5	61	1	0	1	0	1	0	0	0	0	6587	922	32	0	171	0	GOLM1	9	88648284	In_Frame_Del	DEL	CTC	TCGA-AG-A002-01A-01W-A00K-09	55094	88648284	52565147	6331	14316										
GOLM1	51280	broad.mit.edu	37	chr9	88651279	88651279	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctttctcaacttgtctCtttgaatccaaaaccacttc	2	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88651279C>A	ENST00000388712.3	-	7	909	c.741G>T	c.(739-741)aaG>aaT	p.K247N	GOLM1_ENST00000257504.6_5'UTR|GOLM1_ENST00000388711.3_Missense_Mutation_p.K247N	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	247					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)		p.K247N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						CAACTTGTCTCTTTGAATCCA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	9											162	145	151					9																	88651279		2203	4300	6503	87841099	SO:0001583	missense	51280			AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"golgi phosphoprotein 2", "chromosome 9 open reading frame 155"	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.741G>T	9.37:g.88651279C>A	ENSP00000373364:p.Lys247Asn		87841099	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437689	0.43224	.	.	ENSG00000135052	ENST00000388712;ENST00000388711	T;T	0.45276	0.9;0.9	4.19	3.3	0.37823	.	0.482216	0.23157	N	0.051288	T	0.49813	0.1579	L	0.56769	1.78	0.09310	N	1	D	0.57257	0.979	P	0.56563	0.801	T	0.35450	-0.9788	10	0.59425	D	0.04	-6.0415	8.1793	0.31300	0.0:0.8922:0.0:0.1078	.	247	Q8NBJ4	GOLM1_HUMAN	N	247	ENSP00000373364:K247N;ENSP00000373363:K247N	ENSP00000373363:K247N	K	-	3	2	GOLM1	87841099	0.204000	0.23447	0.172000	0.22920	0.010000	0.07245	0.149000	0.16243	1.363000	0.46019	0.561000	0.74099	AAG		0.567	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		A	88651279	C	A	88651279	3	1	61	1	0	0	0	0	1	0	0	0	6587	912	32	2	480	2	GOLM1	9	88651279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2995	88651279	52562152	6332	14317										
ZCCHC6	79670	broad.mit.edu	37	chr9	88923455	88923455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcctctgtgtagaaacGaagaaggcccaaccataact	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88923455G>A	ENST00000375963.3	-	22	3899	c.3727C>T	c.(3727-3729)Cgt>Tgt	p.R1243C	ZCCHC6_ENST00000277141.6_Missense_Mutation_p.R532C|ZCCHC6_ENST00000375957.1_Missense_Mutation_p.R143C|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R1007C|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R1205C	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	1243	PAP-associated 2.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.R1243C(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						GTGTAGAAACGAAGAAGGCCC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											132	136	134					9																	88923455		2203	4300	6503	88113275	SO:0001583	missense	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.3727C>T	9.37:g.88923455G>A	ENSP00000365130:p.Arg1243Cys		88113275	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208487	0.79240	.	.	ENSG00000083223	ENST00000277141;ENST00000375960;ENST00000375961;ENST00000375957;ENST00000375963	T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14	5.65	4.75	0.60458	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.88768	0.6526	M	0.84846	2.72	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.995	D	0.90713	0.4629	10	0.87932	D	0	-0.0863	14.5945	0.68395	0.0694:0.0:0.9306:0.0	.	1205;1007;1243	Q5VYS8-6;Q5VYS8-4;Q5VYS8	.;.;TUT7_HUMAN	C	532;1007;1205;143;1243	ENSP00000277141:R532C;ENSP00000365127:R1007C;ENSP00000365128:R1205C;ENSP00000365124:R143C;ENSP00000365130:R1243C	ENSP00000277141:R532C	R	-	1	0	ZCCHC6	88113275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.454000	0.80714	1.616000	0.50265	0.655000	0.94253	CGT		0.378	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88923455	G	A	88923455	3	1	61	1	0	0	0	0	1	0	0	0	17631	1058	37	1	784	1	ZCCHC6	9	88923455	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272176	88923455	52289976	6333	14318										
ZCCHC6	79670	broad.mit.edu	37	chr9	88960627	88960627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccttgatatgcttatggGcaaatgcaatggattcaatt	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:88960627G>A	ENST00000375963.3	-	4	948	c.776C>T	c.(775-777)gCc>gTc	p.A259V	ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375947.1_Missense_Mutation_p.A92V|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.A259V|ZCCHC6_ENST00000375948.1_5'Flank|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.A259V	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	259					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.A259V(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						ATGCTTATGGGCAAATGCAAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	9											208	182	191					9																	88960627		2203	4300	6503	88150447	SO:0001583	missense	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.776C>T	9.37:g.88960627G>A	ENSP00000365130:p.Ala259Val		88150447	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	G	33	5.250925	0.95305	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963;ENST00000427388;ENST00000375947	D;D;D;T	0.84070	-1.8;-1.8;-1.8;1.13	5.49	5.49	0.81192	.	0.121291	0.56097	D	0.000033	D	0.90473	0.7016	M	0.67397	2.05	0.58432	D	0.999997	D;D;D;D	0.89917	0.998;0.999;1.0;1.0	D;D;D;D	0.87578	0.958;0.981;0.998;0.996	D	0.89579	0.3819	10	0.44086	T	0.13	-11.9438	19.3708	0.94484	0.0:0.0:1.0:0.0	.	259;259;259;259	Q5VYS8-5;Q5VYS8-2;Q5VYS8-4;Q5VYS8	.;.;.;TUT7_HUMAN	V	259;259;259;92;92	ENSP00000365127:A259V;ENSP00000365128:A259V;ENSP00000365130:A259V;ENSP00000365114:A92V	ENSP00000365114:A92V	A	-	2	0	ZCCHC6	88150447	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.907000	0.92634	2.571000	0.86741	0.467000	0.42956	GCC		0.353	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88960627	G	A	88960627	3	1	61	1	0	0	0	0	1	0	0	0	17631	1203	42	3	3807	3	ZCCHC6	9	88960627	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37172	88960627	52252804	6334	14319										
C9orf170	401535	broad.mit.edu	37	chr9	89763753	89763753	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaggaaaggggcctcgctCgcaaggcccgggcggggagg	20	11	0	1	rs199831048		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:89763753C>T	ENST00000375941.2	+	1	195	c.108C>T	c.(106-108)ctC>ctT	p.L36L		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	36								p.L36L(1)		large_intestine(3)|lung(2)|prostate(1)	6						GGGCCTCGCTCGCAAGGCCCG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	9						C		1,4401		0,1,2200	27	30	29		108	-7.5	0	9		29	0,8594		0,0,4297	no	coding-synonymous	C9orf170	NM_001001709.2		0,1,6497	TT,TC,CC		0.0,0.0227,0.0077		36/122	89763753	1,12995	2201	4297	6498	88953573	SO:0001819	synonymous_variant	401535			AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.108C>T	9.37:g.89763753C>T			88953573		Silent	SNP	ENST00000375941.2	37	CCDS35058.1																																																																																				0.667	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709		T	89763753	C	T	89763753	2	4	61	1	0	0	0	0	0	0	0	1	2475	871	31	1		1	C9orf170	9	89763753	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	803126	89763753	51449678	6335	14320										
C9orf170	401535	broad.mit.edu	37	chr9	89771577	89771577	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgatttaggagtcggaagCccagattggaaaaacctctt	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:89771577C>T	ENST00000375941.2	+	2	345	c.258C>T	c.(256-258)agC>agT	p.S86S		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	86								p.S86S(1)		large_intestine(3)|lung(2)|prostate(1)	6						gagtcggaagcccagattgga	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	9											64	63	63					9																	89771577		2203	4300	6503	88961397	SO:0001819	synonymous_variant	401535			AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.258C>T	9.37:g.89771577C>T			88961397		Silent	SNP	ENST00000375941.2	37	CCDS35058.1																																																																																				0.413	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709		T	89771577	C	T	89771577	2	4	61	1	0	0	0	0	0	0	0	1	2475	738	26	3		3	C9orf170	9	89771577	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7824	89771577	51441854	6336	14321										
DAPK1	1612	broad.mit.edu	37	chr9	90315114	90315114	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggacatgaaggtacttCgaaatcatctgcaagaaata	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:90315114C>T	ENST00000408954.3	+	24	3168	c.2833C>T	c.(2833-2835)Cga>Tga	p.R945*	DAPK1_ENST00000491893.1_Nonsense_Mutation_p.R879*|DAPK1_ENST00000469640.2_Nonsense_Mutation_p.R945*|DAPK1_ENST00000472284.1_Nonsense_Mutation_p.R945*|DAPK1_ENST00000358077.5_Nonsense_Mutation_p.R945*	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	945					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R946>?(1)|p.R946*(1)|p.R945*(1)|p.R945>?(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GAAGGTACTTCGAAATCATCT	0.453									Chronic Lymphocytic Leukemia, Familial Clustering of																																							4	Substitution - Nonsense(2)|Complex(2)	large_intestine(4)	9											142	139	140					9																	90315114		1942	4129	6071	89504934	SO:0001587	stop_gained	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2833C>T	9.37:g.90315114C>T	ENSP00000386135:p.Arg945*		89504934	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Nonsense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	C	43	10.522740	0.99421	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	.	.	.	5.95	5.95	0.96441	.	0.000000	0.44285	D	0.000470	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1469	0.72662	0.1412:0.8588:0.0:0.0	.	.	.	.	X	945;945;945;945;879	.	ENSP00000350785:R945X	R	+	1	2	DAPK1	89504934	1.000000	0.71417	0.999000	0.59377	0.897000	0.52465	4.784000	0.62411	2.824000	0.97209	0.655000	0.94253	CGA		0.453	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		T	90315114	C	T	90315114	4	4	61	1	0	0	0	0	0	1	0	0	4241	876	31	1	2923	1	DAPK1	9	90315114	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	543537	90315114	50898317	6337	14322										
CTSL1	1514	broad.mit.edu	37	chr9	90344640	90344640	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcatgagtccttcctgttCtataaagaaggtaagcatat	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:90344640C>A	ENST00000343150.5	+	6	1664	c.774C>A	c.(772-774)ttC>ttA	p.F258L	CTSL_ENST00000495822.1_3'UTR|CTSL_ENST00000340342.6_Missense_Mutation_p.F258L			P07711	CATL1_HUMAN	cathepsin L	258					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)	p.F258L(1)									CCTTCCTGTTCTATAAAGAAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											128	122	124					9																	90344640		2203	4300	6503	89534460	SO:0001583	missense	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.774C>A	9.37:g.90344640C>A	ENSP00000345344:p.Phe258Leu		89534460	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	37	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	C	9.982	1.228292	0.22542	.	.	ENSG00000135047	ENST00000343150;ENST00000340342	T;T	0.21361	2.01;2.01	4.19	2.35	0.29111	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.15782	0.0380	N	0.11427	0.14	0.80722	D	1	P	0.47604	0.898	P	0.53988	0.739	T	0.09185	-1.0686	10	0.18710	T	0.47	.	8.048	0.30562	0.0:0.665:0.0:0.335	.	258	P07711	CATL1_HUMAN	L	258	ENSP00000345344:F258L;ENSP00000365061:F258L	ENSP00000365061:F258L	F	+	3	2	CTSL1	89534460	0.505000	0.26131	0.389000	0.26208	0.065000	0.16274	-0.268000	0.08607	0.408000	0.25621	-0.137000	0.14449	TTC		0.418	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		A	90344640	C	A	90344640	3	1	61	1	0	0	0	0	1	0	0	0	4044	912	32	2	792	2	CTSL1	9	90344640	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29526	90344640	50868791	6338	14323										
C9orf79	286234	broad.mit.edu	37	chr9	90501101	90501101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccactggaaaggagtatCttgaatggcccttgaagaag	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:90501101C>A	ENST00000325643.5	+	4	1765	c.1699C>A	c.(1699-1701)Ctt>Att	p.L567I		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	567					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.L567I(1)									AAAGGAGTATCTTGAATGGCC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											111	119	116					9																	90501101		2203	4300	6503	89690921	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1699C>A	9.37:g.90501101C>A	ENSP00000322640:p.Leu567Ile		89690921	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	c	9.542	1.113642	0.20795	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.11821	2.74	2.51	-2.47	0.06442	.	0.761780	0.10731	N	0.640642	T	0.19087	0.0458	M	0.62723	1.935	0.09310	N	1	D;P	0.56521	0.976;0.873	P;B	0.56398	0.797;0.328	T	0.12192	-1.0557	10	0.29301	T	0.29	.	2.44	0.04492	0.4008:0.3223:0.0:0.277	.	567;219	Q6ZUB1;Q8NA33	CI079_HUMAN;.	I	567;219	ENSP00000322640:L567I	ENSP00000322640:L567I	L	+	1	0	C9orf79	89690921	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.684000	0.05173	-0.601000	0.05783	0.508000	0.49915	CTT		0.557	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		A	90501101	C	A	90501101	3	1	61	1	0	0	0	0	1	0	0	0	2503	913	32	2	1713	2	C9orf79	9	90501101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156461	90501101	50712330	6339	14324										
S1PR3	1903	broad.mit.edu	37	chr9	91616622	91616622	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattgccttcacgctgggCgccctgcccattctgggctg	11	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:91616622C>T	ENST00000375846.3	+	1	5202	c.507C>T	c.(505-507)ggC>ggT	p.G169G	S1PR3_ENST00000358157.2_Silent_p.G169G			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	169					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.G169G(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						TCACGCTGGGCGCCCTGCCCA	0.562											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	9											164	117	133					9																	91616622		2203	4300	6503	90806442	SO:0001819	synonymous_variant	1903			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.507C>T	9.37:g.91616622C>T		1283	90806442	Q5SQD8|Q7Z5I2	Silent	SNP	ENST00000375846.3	37	CCDS6680.1																																																																																				0.562	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		T	91616622	C	T	91616622	2	4	61	1	0	0	0	0	0	0	0	1	13832	755	27	1		1	S1PR3	9	91616622	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1115521	91616622	49596809	6340	14325										
S1PR3	1903	broad.mit.edu	37	chr9	91616964	91616964	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcaaggctcagtggttCatcgtgttggctgtgctcaa	11	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:91616964C>A	ENST00000375846.3	+	1	5544	c.849C>A	c.(847-849)ttC>ttA	p.F283L	S1PR3_ENST00000358157.2_Missense_Mutation_p.F283L			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	283					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.F283L(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						CTCAGTGGTTCATCGTGTTGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	9											125	76	92					9																	91616964		2203	4300	6503	90806784	SO:0001583	missense	1903			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.849C>A	9.37:g.91616964C>A	ENSP00000365006:p.Phe283Leu		90806784	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	37	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521818	0.64747	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.72615	-0.67;-0.67	4.85	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78496	0.4292	L	0.59436	1.845	0.53005	D	0.999964	D	0.76494	0.999	D	0.83275	0.996	T	0.78863	-0.2036	10	0.72032	D	0.01	.	7.85	0.29448	0.0:0.7368:0.0:0.2632	.	283	Q99500	S1PR3_HUMAN	L	283	ENSP00000350878:F283L;ENSP00000365006:F283L	ENSP00000350878:F283L	F	+	3	2	S1PR3	90806784	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	1.815000	0.38981	1.399000	0.46721	0.313000	0.20887	TTC		0.602	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		A	91616964	C	A	91616964	3	1	61	1	0	0	0	0	1	0	0	0	13832	825	29	2	851	2	S1PR3	9	91616964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	342	91616964	49596467	6341	14326										
SEMA4D	10507	broad.mit.edu	37	chr9	92002479	92002479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgtcttgtctggcaaattCaaggagctggtgtagttggc	14	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:92002479C>A	ENST00000450295.1	-	12	1928	c.1152G>T	c.(1150-1152)ttG>ttT	p.L384F	SEMA4D_ENST00000455551.2_Missense_Mutation_p.L384F|SEMA4D_ENST00000343780.4_Missense_Mutation_p.L384F|SEMA4D_ENST00000422704.2_Missense_Mutation_p.L384F|SEMA4D_ENST00000438547.2_Missense_Mutation_p.L384F|SEMA4D_ENST00000339861.4_Missense_Mutation_p.L384F|SEMA4D_ENST00000420987.1_Missense_Mutation_p.L384F|SEMA4D_ENST00000356444.2_Missense_Mutation_p.L384F			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	384	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.L384F(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						CTGGCAAATTCAAGGAGCTGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											141	144	143					9																	92002479		2203	4300	6503	91192299	SO:0001583	missense	10507			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.1152G>T	9.37:g.92002479C>A	ENSP00000416523:p.Leu384Phe		91192299	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787701	0.49997	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.36	2.46	0.29980	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	M	0.86178	2.8	0.35973	D	0.835497	D;D	0.76494	0.997;0.999	D;D	0.72338	0.935;0.977	T	0.69749	-0.5061	10	0.72032	D	0.01	.	13.1128	0.59283	0.0989:0.6123:0.2888:0.0	.	384;384	Q92854-2;Q92854	.;SEM4D_HUMAN	F	384	ENSP00000344923:L384F;ENSP00000391733:L384F;ENSP00000411981:L384F;ENSP00000343418:L384F;ENSP00000416523:L384F;ENSP00000405102:L384F;ENSP00000348822:L384F;ENSP00000388768:L384F	ENSP00000344923:L384F	L	-	3	2	SEMA4D	91192299	0.396000	0.25262	0.008000	0.14137	0.637000	0.38172	-0.406000	0.07187	0.364000	0.24374	0.655000	0.94253	TTG		0.542	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		A	92002479	C	A	92002479	3	1	61	1	0	0	0	0	1	0	0	0	14071	825	29	2	2026	2	SEMA4D	9	92002479	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385515	92002479	49210952	6342	14327										
DIRAS2	54769	broad.mit.edu	37	chr9	93375806	93375806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatctcgcagatttgttCgtagatgggcttgagctcct	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:93375806C>T	ENST00000375765.3	-	2	692	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K		NM_017594.3	NP_060064.2	Q96HU8	DIRA2_HUMAN	DIRAS family, GTP-binding RAS-like 2	102					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.E102K(3)		kidney(1)|large_intestine(6)|lung(3)|skin(2)	12						CAGATTTGTTCGTAGATGGGC	0.592																																																3	Substitution - Missense(3)	large_intestine(1)|kidney(1)|skin(1)	9											109	93	99					9																	93375806		2203	4300	6503	92415626	SO:0001583	missense	54769			AB076889	CCDS6687.1	9q22.32	2014-05-09			ENSG00000165023	ENSG00000165023			19323	protein-coding gene	gene with protein product		607863				12194967	Standard	NM_017594		Approved	Di-Ras2, DKFZp761C07121	uc004aqx.1	Q96HU8	OTTHUMG00000020196	ENST00000375765.3:c.304G>A	9.37:g.93375806C>T	ENSP00000364919:p.Glu102Lys		92415626	B3KVM2	Missense_Mutation	SNP	ENST00000375765.3	37	CCDS6687.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.707688	0.48412	.	.	ENSG00000165023	ENST00000375765	T	0.76709	-1.04	5.21	3.33	0.38152	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.66848	0.2831	N	0.21194	0.64	0.58432	D	0.999998	B	0.20988	0.05	B	0.23018	0.043	T	0.63800	-0.6555	10	0.56958	D	0.05	.	15.0417	0.71796	0.0:0.7297:0.2703:0.0	.	102	Q96HU8	DIRA2_HUMAN	K	102	ENSP00000364919:E102K	ENSP00000364919:E102K	E	-	1	0	DIRAS2	92415626	0.998000	0.40836	0.942000	0.38095	0.755000	0.42902	3.797000	0.55514	0.868000	0.35678	-0.175000	0.13238	GAA		0.592	DIRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053012.1			T	93375806	C	T	93375806	3	4	61	1	0	0	0	0	1	0	0	0	4542	893	31	1	299	1	DIRAS2	9	93375806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1373327	93375806	47837625	6343	14328										
SYK	6850	broad.mit.edu	37	chr9	93650169	93650169	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatgggcagaagccatatCgagtgagccagtcctgcttc	11	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:93650169C>T	ENST00000375754.4	+	12	1868	c.1720C>T	c.(1720-1722)Cga>Tga	p.R574*	SYK_ENST00000375746.1_Nonsense_Mutation_p.R574*|SYK_ENST00000375747.1_Nonsense_Mutation_p.R551*|SYK_ENST00000375751.4_Nonsense_Mutation_p.R551*	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	574	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.R551*(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						GAAGCCATATCGAGTGAGCCA	0.458			T	"ETV6, ITK"	"MDS, peripheral T-cell lymphoma"																																		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	1	Substitution - Nonsense(1)	large_intestine(1)	9											121	117	118					9																	93650169		2203	4300	6503	92689990	SO:0001587	stop_gained	6850			L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"SH2 domain containing"	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1720C>T	9.37:g.93650169C>T	ENSP00000364907:p.Arg574*		92689990		Nonsense_Mutation	SNP	ENST00000375754.4	37	CCDS6688.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731989	0.89390	.	.	ENSG00000165025	ENST00000375754;ENST00000375751;ENST00000375747;ENST00000375746	.	.	.	4.43	0.986	0.19784	.	0.204989	0.40302	N	0.001131	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	12.3835	0.55320	0.5528:0.4471:0.0:0.0	.	.	.	.	X	574;551;551;574	.	ENSP00000364898:R574X	R	+	1	2	SYK	92689990	0.870000	0.30015	0.241000	0.24154	0.119000	0.20118	2.381000	0.44336	0.407000	0.25591	0.455000	0.32223	CGA		0.458	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			T	93650169	C	T	93650169	4	4	61	1	0	0	0	0	0	1	0	0	15477	876	31	1	1762	1	SYK	9	93650169	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274363	93650169	47563262	6344	14329										
NFIL3	4783	broad.mit.edu	37	chr9	94171813	94171813	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagttttgccactcagttCtttttgatgccagtgctccg	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:94171813C>A	ENST00000297689.3	-	2	1598	c.1204G>T	c.(1204-1206)Gaa>Taa	p.E402*		NM_005384.2	NP_005375.2	Q16649	NFIL3_HUMAN	nuclear factor, interleukin 3 regulated	402					cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E402*(1)		endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	16						CCACTCAGTTCTTTTTGATGC	0.403																																					Esophageal Squamous(152;732 1832 10053 26981 51762)											1	Substitution - Nonsense(1)	large_intestine(1)	9											141	139	140					9																	94171813		2203	4300	6503	93211634	SO:0001587	stop_gained	4783			X64318	CCDS6690.1	9q22	2013-01-10			ENSG00000165030	ENSG00000165030		"basic leucine zipper proteins"	7787	protein-coding gene	gene with protein product		605327		IL3BP1		7565758, 1620116	Standard	NM_005384		Approved	E4BP4, NFIL3A, NF-IL3A	uc004arh.3	Q16649	OTTHUMG00000020209	ENST00000297689.3:c.1204G>T	9.37:g.94171813C>A	ENSP00000297689:p.Glu402*		93211634	B2R9Y8|Q14211|Q6FGQ8|Q96HS0	Nonsense_Mutation	SNP	ENST00000297689.3	37	CCDS6690.1	.	.	.	.	.	.	.	.	.	.	C	40	8.374724	0.98784	.	.	ENSG00000165030	ENST00000375724;ENST00000297689	.	.	.	5.34	5.34	0.76211	.	0.153970	0.43416	D	0.000580	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-17.1411	19.2381	0.93869	0.0:1.0:0.0:0.0	.	.	.	.	X	402	.	ENSP00000297689:E402X	E	-	1	0	NFIL3	93211634	1.000000	0.71417	0.991000	0.47740	0.646000	0.38490	4.066000	0.57520	2.779000	0.95612	0.655000	0.94253	GAA		0.403	NFIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053038.2	NM_005384		A	94171813	C	A	94171813	4	1	61	1	0	0	0	0	0	1	0	0	10404	922	32	2	188	2	NFIL3	9	94171813	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	521644	94171813	47041618	6345	14330										
ROR2	4920	broad.mit.edu	37	chr9	94486762	94486762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggaccagatgtctgagtCgatggagaacttgccgtaca	13	8	1	3	rs55651110		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:94486762C>T	ENST00000375708.3	-	9	2212	c.2014G>A	c.(2014-2016)Gac>Aac	p.D672N	ROR2_ENST00000375715.1_Missense_Mutation_p.D532N|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	672	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs55651110). {ECO:0000269|PubMed:17344846}.		cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.D672N(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ATGTCTGAGTCGATGGAGAAC	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	9						C	ASN/ASP	0,4406		0,0,2203	71	60	64		2014	4.9	0.9	9	dbSNP_129	64	1,8599	1.2+/-3.3	0,1,4299	no	missense	ROR2	NM_004560.3	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	672/944	94486762	1,13005	2203	4300	6503	93526583	SO:0001583	missense	4920			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2014G>A	9.37:g.94486762C>T	ENSP00000364860:p.Asp672Asn		93526583	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.459951	0.63401	0.0	1.16E-4	ENSG00000169071	ENST00000375715;ENST00000375708	D;D	0.88975	-2.45;-2.45	4.86	4.86	0.63082	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43747	D	0.000521	D	0.88768	0.6526	N	0.05487	-0.04	0.80722	D	1	D;D	0.89917	1.0;0.982	D;P	0.76575	0.988;0.592	D	0.91798	0.5449	10	0.87932	D	0	.	18.2087	0.89863	0.0:1.0:0.0:0.0	rs55651110	672;532	Q01974;B1APY4	ROR2_HUMAN;.	N	532;672	ENSP00000364867:D532N;ENSP00000364860:D672N	ENSP00000364860:D672N	D	-	1	0	ROR2	93526583	1.000000	0.71417	0.944000	0.38274	0.106000	0.19336	7.567000	0.82357	2.526000	0.85167	0.561000	0.74099	GAC		0.582	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94486762	C	T	94486762	3	4	61	1	0	0	0	0	1	0	0	0	13564	884	31	1	821	1	ROR2	9	94486762	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314949	94486762	46726669	6346	14331										
ROR2	4920	broad.mit.edu	37	chr9	94518359	94518359	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagatacttactgaaagTtatgatttgggctgtgcgtt	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:94518359T>G	ENST00000375708.3	-	4	686	c.488A>C	c.(487-489)aAc>aCc	p.N163T	ROR2_ENST00000375715.1_Missense_Mutation_p.N23T|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	163					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.N163T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TTACTGAAAGTTATGATTTGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	99	101					9																	94518359		2203	4300	6503	93558180	SO:0001583	missense	4920			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.488A>C	9.37:g.94518359T>G	ENSP00000364860:p.Asn163Thr		93558180	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.623622	0.46840	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.76839	-1.05;-1.04	5.18	5.18	0.71444	.	0.000000	0.45126	D	0.000383	T	0.75989	0.3925	N	0.08118	0	0.50467	D	0.999871	B;D;B	0.63880	0.007;0.993;0.002	B;D;B	0.70935	0.01;0.971;0.003	T	0.79042	-0.1965	10	0.39692	T	0.17	.	15.2016	0.73142	0.0:0.0:0.0:1.0	.	163;163;23	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	T	23;163	ENSP00000364867:N23T;ENSP00000364860:N163T	ENSP00000364860:N163T	N	-	2	0	ROR2	93558180	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.979000	0.63806	2.171000	0.68590	0.482000	0.46254	AAC		0.408	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			G	94518359	T	G	94518359	3	3	61	1	0	0	0	0	1	0	0	0	13564	1725	60	4	2367	4	ROR2	9	94518359	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31597	94518359	46695072	6347	14332										
NOL8	55035	broad.mit.edu	37	chr9	95060162	95060162	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgtctttatgtttctttcGacaatcctaggaaaaaaaaa	6	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:95060162G>A	ENST00000535387.1	-	15	3345	c.3346C>T	c.(3346-3348)Cga>Tga	p.R1116*	NOL8_ENST00000542053.1_Nonsense_Mutation_p.R1086*|NOL8_ENST00000545558.1_Nonsense_Mutation_p.R1154*|NOL8_ENST00000358855.4_Nonsense_Mutation_p.R1086*|NOL8_ENST00000442668.2_Nonsense_Mutation_p.R1154*					nucleolar protein 8									p.R1154*(1)|p.R1156*(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TGTTTCTTTCGACAATCCTAG	0.333																																																2	Substitution - Nonsense(2)	large_intestine(2)	9											92	75	80					9																	95060162		1723	3925	5648	94099983	SO:0001587	stop_gained	55035			AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.3346C>T	9.37:g.95060162G>A	ENSP00000441300:p.Arg1116*		94099983		Nonsense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	G	44	10.666969	0.99446	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053	.	.	.	5.36	5.36	0.76844	.	0.059242	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8414	13.617	0.62115	0.0:0.0:0.8447:0.1553	.	.	.	.	X	1154;1118;1086;1154;1116;1086	.	ENSP00000351723:R1086X	R	-	1	2	NOL8	94099983	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	4.622000	0.61240	2.507000	0.84556	0.484000	0.47621	CGA		0.333	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		A	95060162	G	A	95060162	4	1	61	1	0	0	0	0	0	1	0	0	10558	1066	37	1	47	1	NOL8	9	95060162	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	541803	95060162	46153269	6348	14333										
OGN	4969	broad.mit.edu	37	chr9	95152321	95152321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcaaatttcctgtaaaatCgagtcttcttaagttagcta	5	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:95152321C>T	ENST00000262551.4	-	5	865	c.445G>A	c.(445-447)Gat>Aat	p.D149N	OGN_ENST00000375561.5_Missense_Mutation_p.D149N|OGN_ENST00000468743.1_5'UTR|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	149					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)		p.D149N(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						CCTGTAAAATCGAGTCTTCTT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	58	56					9																	95152321		2203	4298	6501	94192142	SO:0001583	missense	4969			AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.445G>A	9.37:g.95152321C>T	ENSP00000262551:p.Asp149Asn		94192142	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	37	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843089	0.91197	.	.	ENSG00000106809	ENST00000262551;ENST00000375561;ENST00000447356	T;T;T	0.57907	0.37;0.37;0.37	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.58609	0.2134	N	0.16130	0.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.61277	-0.7095	10	0.39692	T	0.17	.	19.263	0.93975	0.0:1.0:0.0:0.0	.	207;149	B4DI63;P20774	.;MIME_HUMAN	N	149;149;207	ENSP00000262551:D149N;ENSP00000364711:D149N;ENSP00000396709:D207N	ENSP00000262551:D149N	D	-	1	0	OGN	94192142	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	5.778000	0.68940	2.643000	0.89663	0.655000	0.94253	GAT		0.284	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		T	95152321	C	T	95152321	3	4	61	1	0	0	0	0	1	0	0	0	10877	884	31	1	463	1	OGN	9	95152321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92159	95152321	46061110	6349	14334										
OMD	4958	broad.mit.edu	37	chr9	95177694	95177694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtttattttggtccacacGaatgtatgttaaatggtggt	10	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:95177694G>A	ENST00000375550.4	-	3	1281	c.1006C>T	c.(1006-1008)Cgt>Tgt	p.R336C	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	336					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.R336C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TGGTCCACACGAATGTATGTT	0.318			T	USP6	aneurysmal bone cysts																																		Dom	yes		9	9q22.31	4958	osteomodulin		M	1	Substitution - Missense(1)	large_intestine(1)	9											149	145	147					9																	95177694		2203	4300	6503	94217515	SO:0001583	missense	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.1006C>T	9.37:g.95177694G>A	ENSP00000364700:p.Arg336Cys		94217515	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	37	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776980	0.90195	.	.	ENSG00000127083	ENST00000375550	T	0.04603	3.59	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000001	T	0.28797	0.0714	M	0.86864	2.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02417	-1.1162	10	0.87932	D	0	-19.0612	19.9762	0.97309	0.0:0.0:1.0:0.0	.	336	Q99983	OMD_HUMAN	C	336	ENSP00000364700:R336C	ENSP00000364700:R336C	R	-	1	0	OMD	94217515	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.079000	0.71291	2.797000	0.96272	0.555000	0.69702	CGT		0.318	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		A	95177694	G	A	95177694	3	1	61	1	0	0	0	0	1	0	0	0	10896	1058	37	1	263	1	OMD	9	95177694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25373	95177694	46035737	6350	14335										
ZNF484	83744	broad.mit.edu	37	chr9	95609717	95609717	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacatggagttgtgattttTtaataaaggatttcccacag	9	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:95609717T>G	ENST00000375495.3	-	5	1500	c.1352A>C	c.(1351-1353)aAa>aCa	p.K451T	ANKRD19P_ENST00000473204.1_RNA|ZNF484_ENST00000395506.3_Missense_Mutation_p.K453T|ZNF484_ENST00000332591.6_Missense_Mutation_p.K415T|ZNF484_ENST00000395505.2_Missense_Mutation_p.K415T	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K451T(1)		NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						TTGTGATTTTTTAATAAAGGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	9											75	75	75					9																	95609717		2203	4300	6503	94649538	SO:0001583	missense	83744			AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"Zinc fingers, C2H2-type", "-"	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.1352A>C	9.37:g.95609717T>G	ENSP00000364645:p.Lys451Thr		94649538	B1AL89|B4DRI2	Missense_Mutation	SNP	ENST00000375495.3	37	CCDS35066.1	.	.	.	.	.	.	.	.	.	.	.	12.74	2.028406	0.35797	.	.	ENSG00000127081	ENST00000395505;ENST00000395506;ENST00000375495;ENST00000332591	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	2.32	2.32	0.28847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07954	0.0199	N	0.01789	-0.72	0.27484	N	0.952482	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.40608	-0.9554	9	0.25751	T	0.34	.	8.5787	0.33614	0.0:0.0:0.0:1.0	.	453;451	B4DRI2;Q5JVG2	.;ZN484_HUMAN	T	415;453;451;415	ENSP00000378881:K415T;ENSP00000378882:K453T;ENSP00000364645:K451T;ENSP00000364646:K415T	ENSP00000364646:K415T	K	-	2	0	ZNF484	94649538	0.000000	0.05858	0.998000	0.56505	0.993000	0.82548	-0.103000	0.10940	1.324000	0.45282	0.446000	0.29264	AAA		0.393	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861		G	95609717	T	G	95609717	3	3	61	1	0	0	0	0	1	0	0	0	17976	1841	64	4	1210	4	ZNF484	9	95609717	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	432023	95609717	45603714	6351	14336										
ZNF484	83744	broad.mit.edu	37	chr9	95610782	95610782	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattaatctcagactggaaaGaaacttcttcagacatcctc	5	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:95610782G>T	ENST00000375495.3	-	5	435	c.287C>A	c.(286-288)tCt>tAt	p.S96Y	ANKRD19P_ENST00000473204.1_RNA|ZNF484_ENST00000395506.3_Missense_Mutation_p.S98Y|ZNF484_ENST00000332591.6_Missense_Mutation_p.S60Y|ZNF484_ENST00000395505.2_Missense_Mutation_p.S60Y	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	96					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S96Y(1)		NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						AGACTGGAAAGAAACTTCTTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	9											62	62	62					9																	95610782		2203	4300	6503	94650603	SO:0001583	missense	83744			AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"Zinc fingers, C2H2-type", "-"	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.287C>A	9.37:g.95610782G>T	ENSP00000364645:p.Ser96Tyr		94650603	B1AL89|B4DRI2	Missense_Mutation	SNP	ENST00000375495.3	37	CCDS35066.1	.	.	.	.	.	.	.	.	.	.	.	4.982	0.182372	0.09495	.	.	ENSG00000127081	ENST00000395505;ENST00000395506;ENST00000375495;ENST00000332591	T;T;T;T	0.09350	2.99;3.12;3.12;2.99	3.47	1.46	0.22682	.	.	.	.	.	T	0.06280	0.0162	L	0.38175	1.15	0.09310	N	1	B;B	0.31680	0.335;0.335	B;B	0.27500	0.08;0.08	T	0.38564	-0.9655	9	0.07482	T	0.82	.	5.0834	0.14668	0.1246:0.0:0.673:0.2024	.	98;96	B4DRI2;Q5JVG2	.;ZN484_HUMAN	Y	60;98;96;60	ENSP00000378881:S60Y;ENSP00000378882:S98Y;ENSP00000364645:S96Y;ENSP00000364646:S60Y	ENSP00000364646:S60Y	S	-	2	0	ZNF484	94650603	0.038000	0.19896	0.052000	0.19188	0.507000	0.33981	0.799000	0.27028	0.235000	0.21160	-0.195000	0.12781	TCT		0.338	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861		T	95610782	G	T	95610782	3	4	61	1	0	0	0	0	1	0	0	0	17976	942	33	2	2275	2	ZNF484	9	95610782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1065	95610782	45602649	6352	14337										
FAM120A	23196	broad.mit.edu	37	chr9	96261106	96261106	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagttattcgatttaagaGagcaattggatattattcag	8	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:96261106G>T	ENST00000277165.6	+	5	1162	c.968G>T	c.(967-969)aGa>aTa	p.R323I	FAM120A_ENST00000375389.3_Missense_Mutation_p.R323I|FAM120A_ENST00000333936.5_Missense_Mutation_p.R323I|FAM120A_ENST00000340893.4_Missense_Mutation_p.R323I	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	323						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.R323I(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CGATTTAAGAGAGCAATTGGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											161	166	164					9																	96261106		2203	4300	6503	95300927	SO:0001583	missense	23196			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.968G>T	9.37:g.96261106G>T	ENSP00000277165:p.Arg323Ile		95300927	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.114939|4.114939	0.77210|0.77210	.|.	.|.	ENSG00000048828|ENSG00000048828	ENST00000446420|ENST00000375389;ENST00000277165;ENST00000333936;ENST00000340893	.|T;T;T;T	.|0.50277	.|0.75;0.75;0.75;0.75	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.068584	.|0.64402	.|D	.|0.000009	.|T	.|0.34395	.|0.0896	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.999999|0.999999	.|P;P;D;P	.|0.53151	.|0.911;0.899;0.958;0.787	.|P;P;P;B	.|0.47981	.|0.461;0.466;0.563;0.242	.|T	.|0.33111	.|-0.9881	.|10	.|0.72032	.|D	.|0.01	-14.2449|-14.2449	12.0202|12.0202	0.53340|0.53340	0.0784:0.0:0.9216:0.0|0.0784:0.0:0.9216:0.0	.|.	.|323;323;323;323	.|Q9NZB2-6;Q9NZB2-5;Q9NZB2;Q9NZB2-2	.|.;.;F120A_HUMAN;.	X|I	166|323	.|ENSP00000364538:R323I;ENSP00000277165:R323I;ENSP00000334918:R323I;ENSP00000344698:R323I	.|ENSP00000277165:R323I	E|R	+|+	1|2	0|0	FAM120A|FAM120A	95300927|95300927	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.750000|6.750000	0.74888|0.74888	2.631000|2.631000	0.89168|0.89168	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.343	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		T	96261106	G	T	96261106	3	4	61	1	0	0	0	0	1	0	0	0	5431	942	33	2	986	2	FAM120A	9	96261106	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	650324	96261106	44952325	6353	14338										
FAM120A	23196	broad.mit.edu	37	chr9	96291859	96291859	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatcttccatgtcctgacGaaggtattatcaaaggggcc	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:96291859G>A	ENST00000277165.6	+	9	1925	c.1731G>A	c.(1729-1731)acG>acA	p.T577T	FAM120A_ENST00000375389.3_Silent_p.T577T|FAM120A_ENST00000333936.5_Silent_p.T605T|FAM120A_ENST00000340893.4_Silent_p.T577T|FAM120A_ENST00000475933.1_3'UTR	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	577						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.T577T(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ATGTCCTGACGAAGGTATTAT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	9											54	50	51					9																	96291859		2203	4300	6503	95331680	SO:0001819	synonymous_variant	23196			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.1731G>A	9.37:g.96291859G>A			95331680	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Silent	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	G	9.584	1.124288	0.20959	.	.	ENSG00000048828	ENST00000446420	.	.	.	5.51	-10.8	0.00216	.	.	.	.	.	T	0.39989	0.1099	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47222	-0.9134	4	.	.	.	-13.3429	4.6827	0.12743	0.3636:0.4133:0.0848:0.1383	.	.	.	.	Q	420	.	.	R	+	2	0	FAM120A	95331680	0.023000	0.18921	0.722000	0.30670	0.998000	0.95712	-0.897000	0.04110	-1.766000	0.01302	0.655000	0.94253	CGA		0.522	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		A	96291859	G	A	96291859	2	1	61	1	0	0	0	0	0	0	0	1	5431	1045	37	1		1	FAM120A	9	96291859	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30753	96291859	44921572	6354	14339										
PTPDC1	138639	broad.mit.edu	37	chr9	96859681	96859681	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatttgtgcgggcaaagcGacccaattccatacaaacca	7	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:96859681G>A	ENST00000375360.3	+	7	1011	c.671G>A	c.(670-672)cGa>cAa	p.R224Q	PTPDC1_ENST00000288976.3_Missense_Mutation_p.R276Q	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	224	Tyrosine-protein phosphatase.				cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R276Q(1)|p.R224L(1)|p.R276L(1)|p.R224Q(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						CGGGCAAAGCGACCCAATTCC	0.413																																																4	Substitution - Missense(4)	large_intestine(4)	9											79	77	77					9																	96859681		2203	4300	6503	95899502	SO:0001583	missense	138639			BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	30184	protein-coding gene	gene with protein product	"protein tyrosine phosphatase PTP9Q22"					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.671G>A	9.37:g.96859681G>A	ENSP00000364509:p.Arg224Gln		95899502	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	.	33	5.197879	0.94997	.	.	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.50548	0.74;0.74	5.55	5.55	0.83447	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.80407	0.4617	H	0.96720	3.87	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	D	0.86933	0.2074	10	0.87932	D	0	-10.6174	18.4793	0.90806	0.0:0.0:1.0:0.0	.	278;276;278;224	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	Q	224;276	ENSP00000364509:R224Q;ENSP00000288976:R276Q	ENSP00000288976:R276Q	R	+	2	0	PTPDC1	95899502	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.269000	0.95684	2.610000	0.88304	0.591000	0.81541	CGA		0.413	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		A	96859681	G	A	96859681	3	1	61	1	0	0	0	0	1	0	0	0	12808	1058	37	1	935	1	PTPDC1	9	96859681	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	567822	96859681	44353750	6355	14340										
PTPDC1	138639	broad.mit.edu	37	chr9	96860136	96860136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaccctctttggaaaaggCggaatgttgagtgccttcaa	11	8	2	2	rs142408898		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:96860136C>T	ENST00000375360.3	+	7	1466	c.1126C>T	c.(1126-1128)Cgg>Tgg	p.R376W	PTPDC1_ENST00000288976.3_Missense_Mutation_p.R428W	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	376					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R376W(2)|p.R428W(2)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						TTGGAAAAGGCGGAATGTTGA	0.512													.|||	1	0.000199681	0	0	5008	,	,		21270	0		0.001	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	9						C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	62	65	64		1282,1126	1.8	1	9	dbSNP_134	64	3,8597		0,3,4297	yes	missense,missense	PTPDC1	NM_152422.3,NM_177995.1	101,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	428/807,376/755	96860136	3,13003	2203	4300	6503	95899957	SO:0001583	missense	138639			BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	30184	protein-coding gene	gene with protein product	"protein tyrosine phosphatase PTP9Q22"					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.1126C>T	9.37:g.96860136C>T	ENSP00000364509:p.Arg376Trp		95899957	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	CCDS6707.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	18.52	3.642154	0.67244	0.0	3.49E-4	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.16073	2.38;2.37	5.93	1.79	0.24919	.	0.250728	0.39615	N	0.001318	T	0.39809	0.1092	M	0.78916	2.43	0.42954	D	0.994387	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.991;0.996;0.991;0.991	T	0.20773	-1.0265	10	0.87932	D	0	-17.659	11.3461	0.49561	0.5178:0.3784:0.1038:0.0	.	430;428;430;376	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	W	376;428	ENSP00000364509:R376W;ENSP00000288976:R428W	ENSP00000288976:R428W	R	+	1	2	PTPDC1	95899957	0.997000	0.39634	0.998000	0.56505	0.987000	0.75469	1.021000	0.30040	0.055000	0.16094	0.655000	0.94253	CGG		0.512	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		T	96860136	C	T	96860136	3	4	61	1	0	0	0	0	1	0	0	0	12808	759	27	1	1390	1	PTPDC1	9	96860136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455	96860136	44353295	6356	14341										
FAM22F	54754	broad.mit.edu	37	chr9	97081935	97081935	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctgctccagctcctggCttagggccaagaaatccatc	8	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:97081935C>A	ENST00000253262.4	-	6	1465	c.1445G>T	c.(1444-1446)aGc>aTc	p.S482I	NUTM2F_ENST00000341207.4_Missense_Mutation_p.S467I|NUTM2F_ENST00000335456.7_Missense_Mutation_p.S467I	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	482								p.S348I(1)									CAGCTCCTGGCTTAGGGCCAA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											67	72	70					9																	97081935		1870	4088	5958	96121756	SO:0001583	missense	54754				CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1445G>T	9.37:g.97081935C>A	ENSP00000253262:p.Ser482Ile		96121756	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	C	5.561	0.288339	0.10513	.	.	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207;ENST00000375347	T;T;T	0.21191	2.02;2.79;2.8	1.21	-0.963	0.10330	Nuclear Testis protein, C-terminal (1);	1.040500	0.07631	N	0.928680	T	0.12390	0.0301	L	0.31664	0.95	0.09310	N	1	B	0.28400	0.21	B	0.31869	0.137	T	0.38023	-0.9680	10	0.12103	T	0.63	.	2.6437	0.04978	0.2488:0.3449:0.4063:0.0	.	482	A1L443	FA22F_HUMAN	I	467;482;467;316	ENSP00000335067:S467I;ENSP00000253262:S482I;ENSP00000343865:S467I	ENSP00000253262:S482I	S	-	2	0	FAM22F	96121756	0.000000	0.05858	0.007000	0.13788	0.327000	0.28475	-0.663000	0.05299	-0.329000	0.08527	-0.518000	0.04402	AGC		0.592	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		A	97081935	C	A	97081935	3	1	61	1	0	0	0	0	1	0	0	0	5561	797	28	2	833	2	FAM22F	9	97081935	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	221799	97081935	44131496	6357	14342										
FBP2	8789	broad.mit.edu	37	chr9	97333838	97333838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctgcggccacaatattgCggccacactgcagggcatcc	10	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:97333838C>T	ENST00000375337.3	-	4	539	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	158					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)	p.R158H(1)		endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				CACAATATTGCGGCCACACTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											112	92	99					9																	97333838		2203	4300	6503	96373659	SO:0001583	missense	8789			Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.473G>A	9.37:g.97333838C>T	ENSP00000364486:p.Arg158His		96373659	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	37	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.542475	0.45280	.	.	ENSG00000130957	ENST00000375337	T	0.73897	-0.79	5.26	4.36	0.52297	.	0.360466	0.34932	N	0.003573	T	0.78477	0.4289	M	0.82132	2.575	0.23673	N	0.997143	D	0.61080	0.989	P	0.48114	0.567	T	0.71567	-0.4554	10	0.33940	T	0.23	-10.4679	13.3962	0.60853	0.0:0.9244:0.0:0.0756	.	158	O00757	F16P2_HUMAN	H	158	ENSP00000364486:R158H	ENSP00000364486:R158H	R	-	2	0	FBP2	96373659	1.000000	0.71417	0.597000	0.28824	0.139000	0.21198	2.154000	0.42291	1.211000	0.43351	0.557000	0.71058	CGC		0.542	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		T	97333838	C	T	97333838	3	4	61	1	0	0	0	0	1	0	0	0	5725	768	27	1	562	1	FBP2	9	97333838	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	251903	97333838	43879593	6358	14343										
PTCH1	5727	broad.mit.edu	37	chr9	98238333	98238333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctggagggagaacgcccGcagagcgggaattgggatta	16	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:98238333G>A	ENST00000331920.6	-	12	2010	c.1711C>T	c.(1711-1713)Cgg>Tgg	p.R571W	PTCH1_ENST00000421141.1_Missense_Mutation_p.R420W|PTCH1_ENST00000437951.1_Missense_Mutation_p.R505W|PTCH1_ENST00000418258.1_Missense_Mutation_p.R420W|PTCH1_ENST00000430669.2_Missense_Mutation_p.R505W|PTCH1_ENST00000429896.2_Missense_Mutation_p.R420W|PTCH1_ENST00000375274.2_Missense_Mutation_p.R570W	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	571	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.R571W(2)|p.R570W(1)|p.P568_L570del(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GAGAACGCCCGCAGAGCGGGA	0.602																																																4	Substitution - Missense(3)|Deletion - In frame(1)	large_intestine(3)|skin(1)	9											63	50	54					9																	98238333		2203	4300	6503	97278154	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1711C>T	9.37:g.98238333G>A	ENSP00000332353:p.Arg571Trp		97278154	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150601	0.78001	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.96104	-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91	5.63	4.72	0.59763	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.97926	0.9318	M	0.89353	3.025	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.98860	1.0762	10	0.87932	D	0	-23.3623	15.201	0.73136	0.0:0.0:0.7442:0.2558	.	420;505;570;571	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	W	571;505;420;420;505;420;570;236	ENSP00000332353:R571W;ENSP00000389744:R505W;ENSP00000399981:R420W;ENSP00000396135:R420W;ENSP00000410287:R505W;ENSP00000414823:R420W;ENSP00000364423:R570W;ENSP00000364420:R236W	ENSP00000332353:R571W	R	-	1	2	PTCH1	97278154	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.317000	0.43770	1.478000	0.48253	0.655000	0.94253	CGG		0.602	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98238333	G	A	98238333	3	1	61	1	0	0	0	0	1	0	0	0	12764	1086	38	1	2680	1	PTCH1	9	98238333	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	904495	98238333	42975098	6359	14344										
C9orf102	375748	broad.mit.edu	37	chr9	98683478	98683478	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgtattgttctttgacaGatttccagaaagctgtctat	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:98683478G>T	ENST00000288985.7	+	7	1518	c.1213G>T	c.(1213-1215)Gat>Tat	p.D405Y	ERCC6L2_ENST00000437817.1_Missense_Mutation_p.D216Y|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	405					DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)	p.D405Y(1)									TTCTTTGACAGATTTCCAGAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	88	89					9																	98683478		2203	4300	6503	97723299	SO:0001583	missense	375748			BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"chromosome 9 open reading frame 102", "excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1213G>T	9.37:g.98683478G>T	ENSP00000288985:p.Asp405Tyr		97723299	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798645	0.90538	.	.	ENSG00000182150	ENST00000405401;ENST00000288985;ENST00000437817	T;T	0.76839	-1.05;-1.05	5.51	5.51	0.81932	SNF2-related (1);	0.224693	0.29493	N	0.011996	D	0.85146	0.5630	L	0.61036	1.89	0.80722	D	1	P;D;P	0.62365	0.786;0.991;0.928	B;P;P	0.57620	0.439;0.824;0.815	D	0.85997	0.1492	10	0.72032	D	0.01	-10.2114	19.7723	0.96370	0.0:0.0:1.0:0.0	.	216;87;405	Q5T890-2;F2Z2R4;Q5T890	.;.;RAD26_HUMAN	Y	87;405;216	ENSP00000288985:D405Y;ENSP00000416286:D216Y	ENSP00000288985:D405Y	D	+	1	0	C9orf102	97723299	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.046000	0.93817	2.742000	0.94016	0.585000	0.79938	GAT		0.333	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895		T	98683478	G	T	98683478	3	4	61	1	0	0	0	0	1	0	0	0	2451	942	33	2	1239	2	C9orf102	9	98683478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	445145	98683478	42529953	6360	14345										
SLC35D2	11046	broad.mit.edu	37	chr9	99106263	99106263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattgtagaaaagtactcCgtatttccctagctcctgca	8	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99106263C>T	ENST00000253270.7	-	8	669	c.607G>A	c.(607-609)Gga>Aga	p.G203R	SLC35D2_ENST00000375259.4_Intron	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	203					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)	p.G203R(1)		endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				AAAAGTACTCCGTATTTCCCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	128	126					9																	99106263		2203	4300	6503	98146084	SO:0001583	missense	11046			AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.607G>A	9.37:g.99106263C>T	ENSP00000253270:p.Gly203Arg		98146084	O95454|Q498C1|Q75W21|Q7Z5X5	Missense_Mutation	SNP	ENST00000253270.7	37	CCDS6717.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.438874	0.83885	.	.	ENSG00000130958	ENST00000253270	T	0.61980	0.06	4.94	4.94	0.65067	Domain of unknown function DUF250 (1);	0.055372	0.64402	D	0.000001	T	0.79185	0.4403	M	0.87547	2.89	0.80722	D	1	D	0.55385	0.971	P	0.59487	0.858	T	0.79095	-0.1944	10	0.33940	T	0.23	.	17.4527	0.87596	0.0:1.0:0.0:0.0	.	203	Q76EJ3	S35D2_HUMAN	R	203	ENSP00000253270:G203R	ENSP00000253270:G203R	G	-	1	0	SLC35D2	98146084	1.000000	0.71417	0.954000	0.39281	0.868000	0.49771	6.190000	0.72057	2.734000	0.93682	0.650000	0.86243	GGA		0.403	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			T	99106263	C	T	99106263	3	4	61	1	0	0	0	0	1	0	0	0	14619	661	23	1	426	1	SLC35D2	9	99106263	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	422785	99106263	42107168	6361	14346										
HABP4	22927	broad.mit.edu	37	chr9	99227692	99227692	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggggtatgcgcggcagaGgcagaggtggccctgggaac	21	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99227692G>T	ENST00000375249.4	+	3	661	c.586G>T	c.(586-588)Ggc>Tgc	p.G196C	HABP4_ENST00000375251.3_Intron	NM_014282.2	NP_055097.2			hyaluronan binding protein 4									p.G196C(1)		NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				GCGCGGCAGAGGCAGAGGTGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	9											106	118	114					9																	99227692		2203	4300	6503	98267513	SO:0001583	missense	22927			AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.586G>T	9.37:g.99227692G>T	ENSP00000364398:p.Gly196Cys		98267513		Missense_Mutation	SNP	ENST00000375249.4	37	CCDS6719.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663249	0.67700	.	.	ENSG00000130956	ENST00000375249	T	0.44881	0.91	4.86	4.86	0.63082	.	0.050015	0.85682	D	0.000000	T	0.62171	0.2406	L	0.58510	1.815	0.58432	D	0.999999	D	0.89917	1.0	D	0.72625	0.978	T	0.64546	-0.6382	10	0.72032	D	0.01	-15.9732	18.5864	0.91191	0.0:0.0:1.0:0.0	.	196	Q5JVS0	HABP4_HUMAN	C	196	ENSP00000364398:G196C	ENSP00000364398:G196C	G	+	1	0	HABP4	98267513	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	3.981000	0.56902	2.686000	0.91538	0.644000	0.83932	GGC		0.483	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	NM_014282		T	99227692	G	T	99227692	3	4	61	1	0	0	0	0	1	0	0	0	6960	1000	35	2	596	2	HABP4	9	99227692	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121429	99227692	41985739	6362	14347										
CDC14B	8555	broad.mit.edu	37	chr9	99285665	99285665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccctttaacttctgacGaaaatagtccccttccagcc	5	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99285665G>A	ENST00000375241.1	-	11	1574	c.1123C>T	c.(1123-1125)Cgt>Tgt	p.R375C	CDC14B_ENST00000463569.1_Missense_Mutation_p.R375C|CDC14B_ENST00000265659.2_Missense_Mutation_p.R375C|CDC14B_ENST00000375236.1_Missense_Mutation_p.R375C|CDC14B_ENST00000481149.1_5'Flank|CDC14B_ENST00000375242.3_Missense_Mutation_p.R338C|CDC14B_ENST00000375240.3_Missense_Mutation_p.R375C	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B	375	B.				activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R375C(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				AACTTCTGACGAAAATAGTCC	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	9											99	106	104					9																	99285665		2203	4300	6503	98325486	SO:0001583	missense	8555			AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1719	protein-coding gene	gene with protein product		603505	"CDC14 (cell division cycle 14, S. cerevisiae) homolog B", "CDC14 cell division cycle 14 homolog B (S. cerevisiae)"			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.1123C>T	9.37:g.99285665G>A	ENSP00000364389:p.Arg375Cys		98325486	A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Missense_Mutation	SNP	ENST00000375241.1	37	CCDS6722.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.606194	0.66445	.	.	ENSG00000081377	ENST00000265659;ENST00000375241;ENST00000375240;ENST00000375242;ENST00000463569;ENST00000375236	T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88	5.29	5.29	0.74685	.	0.152605	0.64402	D	0.000015	T	0.52645	0.1747	M	0.77486	2.375	0.80722	D	1	B;D;P	0.89917	0.112;1.0;0.86	B;D;B	0.63488	0.022;0.915;0.199	T	0.55724	-0.8096	10	0.72032	D	0.01	-4.3923	19.137	0.93431	0.0:0.0:1.0:0.0	.	375;375;338	O60729-2;O60729;A8MQ20	.;CC14B_HUMAN;.	C	375;375;375;338;375;375	ENSP00000265659:R375C;ENSP00000364389:R375C;ENSP00000364388:R375C;ENSP00000364390:R338C;ENSP00000420572:R375C;ENSP00000364384:R375C	ENSP00000265659:R375C	R	-	1	0	CDC14B	98325486	1.000000	0.71417	0.995000	0.50966	0.785000	0.44390	5.389000	0.66255	2.759000	0.94783	0.555000	0.69702	CGT		0.428	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331		A	99285665	G	A	99285665	3	1	61	1	0	0	0	0	1	0	0	0	3063	1058	37	1	389	1	CDC14B	9	99285665	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57973	99285665	41927766	6363	14348										
ZNF510	22869	broad.mit.edu	37	chr9	99521321	99521321	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattacatttaaatggtttCtccccagtgtgaattctttg	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99521321C>A	ENST00000375231.1	-	6	2441	c.1791G>T	c.(1789-1791)gaG>gaT	p.E597D	ZNF510_ENST00000223428.4_Missense_Mutation_p.E597D			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	597					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E597D(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TAAATGGTTTCTCCCCAGTGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											61	63	63					9																	99521321		2203	4299	6502	98561142	SO:0001583	missense	22869			AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1791G>T	9.37:g.99521321C>A	ENSP00000364379:p.Glu597Asp		98561142	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	37	CCDS35074.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.466574	0.43839	.	.	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.26810	1.71;1.71	3.02	0.00692	0.14068	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34279	0.0892	M	0.64170	1.965	0.22366	N	0.999163	P	0.52170	0.951	P	0.55749	0.783	T	0.16837	-1.0389	9	0.66056	D	0.02	.	3.951	0.09369	0.189:0.5813:0.0:0.2297	.	597	Q9Y2H8	ZN510_HUMAN	D	597	ENSP00000364379:E597D;ENSP00000223428:E597D	ENSP00000223428:E597D	E	-	3	2	ZNF510	98561142	0.942000	0.31987	0.996000	0.52242	0.999000	0.98932	-0.001000	0.12947	-0.009000	0.14296	0.655000	0.94253	GAG		0.418	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		A	99521321	C	A	99521321	3	1	61	1	0	0	0	0	1	0	0	0	17993	912	32	2	264	2	ZNF510	9	99521321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235656	99521321	41692110	6364	14349										
ZNF782	158431	broad.mit.edu	37	chr9	99581386	99581386	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagggtttcacccctatatGaactctatgatgttctctaa	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99581386G>T	ENST00000481138.1	-	6	1580	c.919C>A	c.(919-921)Cat>Aat	p.H307N	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.H175N	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H307N(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				ACCCCTATATGAACTCTATGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	97	97					9																	99581386		2203	4299	6502	98621207	SO:0001583	missense	158431			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.919C>A	9.37:g.99581386G>T	ENSP00000419397:p.His307Asn		98621207	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.98|11.98	1.801487|1.801487	0.31869|0.31869	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000481138;ENST00000535338|ENST00000289032	T;T|.	0.26660|.	1.72;1.72|.	3.52|3.52	0.627|0.627	0.17675|0.17675	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.801903|.	0.10174|.	N|.	0.706718|.	T|.	0.57431|.	0.2053|.	M|M	0.87682|0.87682	2.9|2.9	0.19300|0.19300	N|N	0.999974|0.999974	B|.	0.18610|.	0.029|.	B|.	0.16722|.	0.016|.	T|.	0.52586|.	-0.8556|.	10|.	0.87932|.	D|.	0|.	.|.	4.455|4.455	0.11639|0.11639	0.2075:0.0:0.6132:0.1792|0.2075:0.0:0.6132:0.1792	.|.	307|.	Q6ZMW2|.	ZN782_HUMAN|.	N|X	307;175|295	ENSP00000419397:H307N;ENSP00000440624:H175N|.	ENSP00000419397:H307N|.	H|S	-|-	1|2	0|0	ZNF782|ZNF782	98621207|98621207	0.763000|0.763000	0.28462|0.28462	0.002000|0.002000	0.10522|0.10522	0.194000|0.194000	0.23727|0.23727	1.647000|1.647000	0.37260|0.37260	0.133000|0.133000	0.18654|0.18654	0.644000|0.644000	0.83932|0.83932	CAT|TCA		0.378	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		T	99581386	G	T	99581386	3	4	61	1	0	0	0	0	1	0	0	0	18194	1290	45	2	1184	2	ZNF782	9	99581386	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60065	99581386	41632045	6365	14350										
ZNF782	158431	broad.mit.edu	37	chr9	99581565	99581565	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatttgttttccccaaatTtattgaaattgtaagatttt	4	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99581565T>G	ENST00000481138.1	-	6	1401	c.740A>C	c.(739-741)aAa>aCa	p.K247T	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.K115T	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	247					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K247T(2)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				TTCCCCAAATTTATTGAAATT	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	9											71	77	75					9																	99581565		2203	4299	6502	98621386	SO:0001583	missense	158431			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.740A>C	9.37:g.99581565T>G	ENSP00000419397:p.Lys247Thr		98621386	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.55|11.55	1.672338|1.672338	0.29693|0.29693	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000481138;ENST00000535338|ENST00000289032	T;T|.	0.07327|.	3.35;3.2|.	3.33|3.33	-1.92|-1.92	0.07618|0.07618	.|.	0.703630|.	0.11680|.	N|.	0.539899|.	T|.	0.20414|.	0.0491|.	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B|.	0.11235|.	0.004|.	B|.	0.09377|.	0.004|.	T|.	0.25572|.	-1.0128|.	10|.	0.72032|.	D|.	0.01|.	.|.	0.7445|0.7445	0.00979|0.00979	0.1631:0.2091:0.1678:0.4601|0.1631:0.2091:0.1678:0.4601	.|.	247|.	Q6ZMW2|.	ZN782_HUMAN|.	T|Y	247;115|235	ENSP00000419397:K247T;ENSP00000440624:K115T|.	ENSP00000419397:K247T|.	K|X	-|-	2|3	0|2	ZNF782|ZNF782	98621386|98621386	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.448000|0.448000	0.32197|0.32197	0.120000|0.120000	0.15647|0.15647	-0.389000|-0.389000	0.07786|0.07786	0.529000|0.529000	0.55759|0.55759	AAA|TAA		0.313	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		G	99581565	T	G	99581565	3	3	61	1	0	0	0	0	1	0	0	0	18194	1841	64	4	1363	4	ZNF782	9	99581565	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	179	99581565	41631866	6366	14351										
CTSL2	1515	broad.mit.edu	37	chr9	99797949	99797949	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtcattagcaacagaattCtcaggtctgtacttacagat	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:99797949C>A	ENST00000259470.5	-	6	897	c.648G>T	c.(646-648)gaG>gaT	p.E216D	CTSV_ENST00000538255.1_Missense_Mutation_p.E216D|CTSV_ENST00000479932.1_5'Flank	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V	216					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)	p.E216D(1)									CAACAGAATTCTCAGGTCTGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											69	62	64					9																	99797949		2203	4300	6503	98837770	SO:0001583	missense	1515			Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"Cathepsins"	2538	protein-coding gene	gene with protein product		603308	"cathepsin L2"	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.648G>T	9.37:g.99797949C>A	ENSP00000259470:p.Glu216Asp		98837770	O60233|Q2TB86|Q5T1U0	Missense_Mutation	SNP	ENST00000259470.5	37	CCDS6723.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847411	0.32606	.	.	ENSG00000136943	ENST00000259470;ENST00000538255	T;T	0.21932	1.98;1.98	3.65	-0.48	0.12085	Peptidase C1A, papain C-terminal (2);	0.447688	0.24325	N	0.039512	T	0.08980	0.0222	N	0.12569	0.235	0.23693	N	0.99709	B;B	0.21753	0.06;0.06	B;B	0.28305	0.088;0.088	T	0.30446	-0.9978	9	.	.	.	.	4.1599	0.10278	0.0:0.3458:0.1815:0.4727	.	216;216	B2R717;O60911	.;CATL2_HUMAN	D	216	ENSP00000259470:E216D;ENSP00000445052:E216D	.	E	-	3	2	CTSL2	98837770	0.001000	0.12720	0.013000	0.15412	0.534000	0.34807	-0.225000	0.09151	-0.078000	0.12730	0.561000	0.74099	GAG		0.473	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053301.2	NM_001333		A	99797949	C	A	99797949	3	1	61	1	0	0	0	0	1	0	0	0	4045	912	32	2	368	2	CTSL2	9	99797949	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	216384	99797949	41415482	6367	14352										
KIAA1529	100499483	broad.mit.edu	37	chr9	100092619	100092619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagaagcacatgaaaaacCctcccagaagagagtgaaaa	8	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100092619C>A	ENST00000357054.1	+	32	3328	c.2393C>A	c.(2392-2394)cCc>cAc	p.P798H	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.P659H|CCDC180_ENST00000411667.2_Missense_Mutation_p.P656H|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.P659H			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	798						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.P798H(1)									CATGAAAAACCCTCCCAGAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											64	66	65					9																	100092619		2203	4300	6503	99132440	SO:0001583	missense	57653			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2393C>A	9.37:g.100092619C>A	ENSP00000349562:p.Pro798His		99132440	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	C	0.997	-0.692193	0.03303	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.11712	3.11;3.12;2.75;3.12	4.78	-9.56	0.00566	.	4.086120	0.00481	N	0.000126	T	0.02610	0.0079	N	0.01048	-1.04	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42189	-0.9466	10	0.39692	T	0.17	11.3151	0.9215	0.01316	0.1786:0.177:0.2657:0.3787	.	656;798;659;798	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	H	798;659;656;682;659	ENSP00000349562:P798H;ENSP00000364348:P659H;ENSP00000414000:P656H;ENSP00000434727:P659H	ENSP00000349562:P798H	P	+	2	0	C9orf174	99132440	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.697000	0.01910	-3.758000	0.00110	-1.497000	0.00963	CCC		0.468	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		A	100092619	C	A	100092619	3	1	61	1	0	0	0	0	1	0	0	0	8261	623	22	2	2475	2	KIAA1529	9	100092619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294670	100092619	41120812	6368	14353										
KIAA1529	100499483	broad.mit.edu	37	chr9	100093035	100093035	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggaagagcaagagagtTtatctgtgggtgaggtaagc	15	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100093035T>G	ENST00000357054.1	+	32	3744	c.2809T>G	c.(2809-2811)Tta>Gta	p.L937V	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.L798V|CCDC180_ENST00000411667.2_Missense_Mutation_p.L795V|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.L798V			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	937	Glu-rich.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L937V(1)									GCAAGAGAGTTTATCTGTGGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	9											97	114	108					9																	100093035		2200	4300	6500	99132856	SO:0001583	missense	57653			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2809T>G	9.37:g.100093035T>G	ENSP00000349562:p.Leu937Val		99132856	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	T	3.254	-0.152623	0.06585	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.09073	3.35;3.02;3.35;3.02	3.57	-1.86	0.07760	.	3.258890	0.00864	N	0.001945	T	0.06917	0.0176	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B	0.31817	0.206;0.341;0.206;0.341;0.206	B;B;B;B;B	0.25140	0.058;0.058;0.058;0.058;0.058	T	0.25257	-1.0137	10	0.25106	T	0.35	5.7306	1.3402	0.02153	0.1777:0.1122:0.3648:0.3452	.	821;795;937;798;937	Q86Y65;F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;.;CI174_HUMAN	V	937;798;795;821;798	ENSP00000349562:L937V;ENSP00000364348:L798V;ENSP00000414000:L795V;ENSP00000434727:L798V	ENSP00000349562:L937V	L	+	1	2	C9orf174	99132856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.254000	0.02874	-0.350000	0.08262	-0.379000	0.06801	TTA		0.488	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		G	100093035	T	G	100093035	3	3	61	1	0	0	0	0	1	0	0	0	8261	1838	64	4	2891	4	KIAA1529	9	100093035	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	416	100093035	41120396	6369	14354										
KIAA1529	100499483	broad.mit.edu	37	chr9	100137761	100137761	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccagggatcaaacccaccGaagtcaccatccaaaacaag	8	14	2	0	rs147950391	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100137761G>A	ENST00000357054.1	+	48	5634	c.4699G>A	c.(4699-4701)Gaa>Aaa	p.E1567K	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.E1622K|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.E1622K			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1567						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.E1567K(1)									CAAACCCACCGAAGTCACCAT	0.502													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		17869	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						G	LYS/GLU	36,4370	42.3+/-75.8	0,36,2167	162	132	142		4864	-1.1	0	9	dbSNP_134	142	0,8600		0,0,4300	yes	missense	C9orf174	NM_020893.2	56	0,36,6467	AA,AG,GG		0.0,0.8171,0.2768	possibly-damaging	1622/1702	100137761	36,12970	2203	4300	6503	99177582	SO:0001583	missense	57653			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.4699G>A	9.37:g.100137761G>A	ENSP00000349562:p.Glu1567Lys		99177582	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	3.272	-0.148838	0.06627	0.008171	0.0	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.08458	3.12;3.09;3.09	5.58	-1.09	0.09904	.	0.846199	0.10782	N	0.634799	T	0.02047	0.0064	L	0.31294	0.92	0.09310	N	1	B;P	0.38745	0.309;0.645	B;B	0.29524	0.012;0.103	T	0.37979	-0.9682	10	0.41790	T	0.15	-4.9624	6.3114	0.21166	0.2297:0.3731:0.3972:0.0	.	1761;1567	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	K	1567;1622;1622	ENSP00000349562:E1567K;ENSP00000364348:E1622K;ENSP00000434727:E1622K	ENSP00000349562:E1567K	E	+	1	0	C9orf174	99177582	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.043000	0.12043	-0.089000	0.12484	-0.136000	0.14681	GAA		0.502	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		A	100137761	G	A	100137761	3	1	61	1	0	0	0	0	1	0	0	0	8261	1059	37	1	4845	1	KIAA1529	9	100137761	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44726	100137761	41075670	6370	14355										
TDRD7	23424	broad.mit.edu	37	chr9	100235796	100235796	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacgccatgtacacaaatgTcaaagtaactaatatttgct	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100235796T>G	ENST00000355295.4	+	11	2262	c.1967T>G	c.(1966-1968)gTc>gGc	p.V656G	TDRD7_ENST00000422139.2_Missense_Mutation_p.V582G|TDRD7_ENST00000540902.1_Missense_Mutation_p.V5G	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	656					germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)	p.V656G(1)		endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				TACACAAATGTCAAAGTAACT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											193	176	182					9																	100235796		2203	4300	6503	99275617	SO:0001583	missense	23424			AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.1967T>G	9.37:g.100235796T>G	ENSP00000347444:p.Val656Gly		99275617	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Missense_Mutation	SNP	ENST00000355295.4	37	CCDS6725.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310467	0.81358	.	.	ENSG00000196116	ENST00000355295;ENST00000422139;ENST00000540902	T;T;T	0.49139	2.4;2.4;0.79	4.23	4.23	0.50019	Maternal tudor protein (1);	0.000000	0.85682	D	0.000000	T	0.70290	0.3207	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76200	-0.3046	10	0.87932	D	0	-19.29	13.1363	0.59411	0.0:0.0:0.0:1.0	.	5;656	Q8NHU6-3;Q8NHU6	.;TDRD7_HUMAN	G	656;582;5	ENSP00000347444:V656G;ENSP00000413608:V582G;ENSP00000440717:V5G	ENSP00000347444:V656G	V	+	2	0	TDRD7	99275617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.482000	0.81143	2.143000	0.66587	0.477000	0.44152	GTC		0.438	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		G	100235796	T	G	100235796	3	3	61	1	0	0	0	0	1	0	0	0	15774	1667	58	4	2005	4	TDRD7	9	100235796	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	98035	100235796	40977635	6371	14356										
TDRD7	23424	broad.mit.edu	37	chr9	100245609	100245609	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtggagaaagaccaagTgtatgctgcaaaagtggaaa	13	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100245609T>C	ENST00000355295.4	+	15	3186	c.2891T>C	c.(2890-2892)gTg>gCg	p.V964A	TDRD7_ENST00000422139.2_Missense_Mutation_p.V890A|TDRD7_ENST00000540902.1_Missense_Mutation_p.V284A	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	964	Interacts with CABLES1. {ECO:0000250}.|Interacts with CDK17. {ECO:0000250}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)	p.V964A(1)		endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				AAAGACCAAGTGTATGCTGCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											64	59	61					9																	100245609		2203	4300	6503	99285430	SO:0001583	missense	23424			AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.2891T>C	9.37:g.100245609T>C	ENSP00000347444:p.Val964Ala		99285430	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Missense_Mutation	SNP	ENST00000355295.4	37	CCDS6725.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.206948	0.79127	.	.	ENSG00000196116	ENST00000355295;ENST00000422139;ENST00000540902	T;T;T	0.10763	2.84;2.84;2.84	5.36	4.22	0.49857	Maternal tudor protein (1);	0.184795	0.47852	D	0.000210	T	0.12860	0.0312	L	0.39020	1.185	0.39239	D	0.963814	D;D;P	0.54772	0.968;0.968;0.906	P;P;B	0.50708	0.648;0.57;0.446	T	0.16070	-1.0415	10	0.23302	T	0.38	-16.4307	10.1561	0.42823	0.0:0.0793:0.0:0.9207	.	284;890;964	Q8NHU6-3;Q8NHU6-2;Q8NHU6	.;.;TDRD7_HUMAN	A	964;890;284	ENSP00000347444:V964A;ENSP00000413608:V890A;ENSP00000440717:V284A	ENSP00000347444:V964A	V	+	2	0	TDRD7	99285430	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.671000	0.83941	0.987000	0.38709	0.528000	0.53228	GTG		0.403	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		C	100245609	T	C	100245609	3	2	61	1	0	0	0	0	1	0	0	0	15774	1696	59	4	2945	4	TDRD7	9	100245609	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9813	100245609	40967822	6372	14357										
TMOD1	7111	broad.mit.edu	37	chr9	100328233	100328233	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggagtaatgaccccgtggCgtatgtatgtacctttctgt	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100328233C>T	ENST00000259365.4	+	7	935	c.722C>T	c.(721-723)gCg>gTg	p.A241V	TMOD1_ENST00000395211.2_Missense_Mutation_p.A241V|TMOD1_ENST00000375175.1_Missense_Mutation_p.A114V	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	241					adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)		p.A241V(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		GACCCCGTGGCGTATGTATGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											191	195	194					9																	100328233		2203	4300	6503	99368054	SO:0001583	missense	7111				CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD		1370827, 8661028	Standard	NM_003275		Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.722C>T	9.37:g.100328233C>T	ENSP00000259365:p.Ala241Val		99368054	B2RB77|Q5T7W3|Q9BUF1	Missense_Mutation	SNP	ENST00000259365.4	37	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723705	0.68959	.	.	ENSG00000136842	ENST00000395211;ENST00000259365;ENST00000375175	D;D;D	0.93019	-3.15;-3.15;-3.15	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	D	0.97034	0.9752	10	0.59425	D	0.04	-15.5718	17.6093	0.88048	0.0:1.0:0.0:0.0	.	241	P28289	TMOD1_HUMAN	V	241;241;114	ENSP00000378637:A241V;ENSP00000259365:A241V;ENSP00000364318:A114V	ENSP00000259365:A241V	A	+	2	0	TMOD1	99368054	1.000000	0.71417	0.938000	0.37757	0.053000	0.15095	7.407000	0.80029	2.550000	0.86006	0.561000	0.74099	GCG		0.493	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275		T	100328233	C	T	100328233	3	4	61	1	0	0	0	0	1	0	0	0	16272	768	27	1	744	1	TMOD1	9	100328233	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82624	100328233	40885198	6373	14358										
TSTD2	158427	broad.mit.edu	37	chr9	100373978	100373978	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattccttctgcagcaattcGaatctgagacacaagacggt	9	10	2	2	rs200562502		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100373978G>A	ENST00000341170.4	-	5	989	c.607C>T	c.(607-609)Cga>Tga	p.R203*	TSTD2_ENST00000354801.2_Intron|TSTD2_ENST00000484708.1_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	203								p.R203*(1)		large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						GCAGCAATTCGAATCTGAGAC	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	9						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	140	128	132		607	4	1	9		132	0,8600		0,0,4300	yes	stop-gained	TSTD2	NM_139246.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		203/517	100373978	1,13005	2203	4300	6503	99413799	SO:0001587	stop_gained	158427			AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 97"	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.607C>T	9.37:g.100373978G>A	ENSP00000342499:p.Arg203*		99413799	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Nonsense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	G	38	7.225400	0.98146	2.27E-4	0.0	ENSG00000136925	ENST00000341170	.	.	.	4.94	4.02	0.46733	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-9.7982	14.9831	0.71327	0.0:0.0:0.8557:0.1443	.	.	.	.	X	203	.	ENSP00000342499:R203X	R	-	1	2	TSTD2	99413799	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	5.735000	0.68587	1.359000	0.45940	0.563000	0.77884	CGA		0.413	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		A	100373978	G	A	100373978	4	1	61	1	0	0	0	0	0	1	0	0	16715	1066	37	1	967	1	TSTD2	9	100373978	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45745	100373978	40839453	6374	14359										
NCBP1	4686	broad.mit.edu	37	chr9	100431192	100431192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgaggaacaaatagaacGacttcaggaaaaagtggaat	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100431192G>A	ENST00000375147.3	+	21	2337	c.2081G>A	c.(2080-2082)cGa>cAa	p.R694Q		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	694					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)	p.R694Q(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				CAAATAGAACGACTTCAGGAA	0.383																																					Ovarian(36;879 898 2893 44212 50307)											1	Substitution - Missense(1)	large_intestine(1)	9											108	109	109					9																	100431192		2203	4300	6503	99471013	SO:0001583	missense	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.2081G>A	9.37:g.100431192G>A	ENSP00000364289:p.Arg694Gln		99471013	B2R718|Q59G76|Q5T1V0|Q5T7X2	Missense_Mutation	SNP	ENST00000375147.3	37	CCDS6728.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544578	0.86022	.	.	ENSG00000136937	ENST00000375147;ENST00000375130	.	.	.	5.71	5.71	0.89125	MIF4G-like, type 2 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59404	0.2191	M	0.64404	1.975	0.80722	D	1	P	0.47253	0.892	B	0.42555	0.391	T	0.58081	-0.7699	9	0.31617	T	0.26	-18.4134	19.0048	0.92846	0.0:0.0:1.0:0.0	.	694	Q09161	NCBP1_HUMAN	Q	694;47	.	ENSP00000364272:R47Q	R	+	2	0	NCBP1	99471013	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	7.326000	0.79133	2.854000	0.98071	0.655000	0.94253	CGA		0.383	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		A	100431192	G	A	100431192	3	1	61	1	0	0	0	0	1	0	0	0	10242	1058	37	1	2163	1	NCBP1	9	100431192	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57214	100431192	40782239	6375	14360										
C9orf156	51531	broad.mit.edu	37	chr9	100672462	100672462	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcttgtctgtacctttCtctgaaaagctcttctctgg	7	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100672462C>A	ENST00000375119.3	-	4	922	c.846G>T	c.(844-846)gaG>gaT	p.E282D	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	282					viral process (GO:0016032)		hydrolase activity (GO:0016787)	p.E282D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				CTGTACCTTTCTCTGAAAAGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	9											139	130	133					9																	100672462		2203	4300	6503	99712283	SO:0001583	missense	51531			AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.846G>T	9.37:g.100672462C>A	ENSP00000364260:p.Glu282Asp		99712283	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738880	0.30774	.	.	ENSG00000136932	ENST00000375119;ENST00000375118;ENST00000325350	T;T	0.34275	1.8;1.37	5.03	-0.441	0.12257	Uncharacterised domain UPF0066, YaeB-like domain (1);	0.414623	0.27031	N	0.021278	T	0.38188	0.1031	L	0.52573	1.65	0.09310	N	0.999991	D;B;B	0.56968	0.978;0.041;0.005	P;B;B	0.57776	0.827;0.046;0.004	T	0.18555	-1.0333	10	0.87932	D	0	-27.2378	2.2879	0.04131	0.134:0.482:0.132:0.252	.	179;136;282	Q6Y2L2;Q5T114;Q9BU70	.;.;NAP1_HUMAN	D	282;136;179	ENSP00000364260:E282D;ENSP00000364259:E136D	ENSP00000324426:E179D	E	-	3	2	C9orf156	99712283	0.000000	0.05858	0.077000	0.20336	0.071000	0.16799	-0.430000	0.06973	0.236000	0.21180	0.563000	0.77884	GAG		0.502	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		A	100672462	C	A	100672462	3	1	61	1	0	0	0	0	1	0	0	0	2471	912	32	2	487	2	C9orf156	9	100672462	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241270	100672462	40540969	6376	14361										
C9orf156	51531	broad.mit.edu	37	chr9	100672785	100672785	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttattctgtaaattaaagtCtgctaaaggctccatcacat	6	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100672785C>A	ENST00000375119.3	-	4	599	c.523G>T	c.(523-525)Gac>Tac	p.D175Y	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	175					viral process (GO:0016032)		hydrolase activity (GO:0016787)	p.D175Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				AAATTAAAGTCTGCTAAAGGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											146	139	141					9																	100672785		2203	4300	6503	99712606	SO:0001583	missense	51531			AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.523G>T	9.37:g.100672785C>A	ENSP00000364260:p.Asp175Tyr		99712606	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082000	0.55861	.	.	ENSG00000136932	ENST00000375119;ENST00000375118;ENST00000325350	T;T	0.42513	0.97;0.97	5.09	3.22	0.36961	Uncharacterised domain UPF0066, YaeB-like domain (2);	0.586022	0.16274	N	0.221630	T	0.41534	0.1163	N	0.14661	0.345	0.09310	N	1	D;D;P	0.71674	0.998;0.997;0.761	P;D;B	0.63192	0.888;0.912;0.202	T	0.20306	-1.0279	10	0.87932	D	0	-6.5324	8.8748	0.35339	0.0:0.8115:0.0:0.1885	.	72;29;175	Q6Y2L2;Q5T114;Q9BU70	.;.;NAP1_HUMAN	Y	175;29;72	ENSP00000364260:D175Y;ENSP00000364259:D29Y	ENSP00000324426:D72Y	D	-	1	0	C9orf156	99712606	0.038000	0.19896	0.001000	0.08648	0.208000	0.24298	1.132000	0.31418	0.633000	0.30452	0.563000	0.77884	GAC		0.463	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		A	100672785	C	A	100672785	3	1	61	1	0	0	0	0	1	0	0	0	2471	913	32	2	810	2	C9orf156	9	100672785	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323	100672785	40540646	6377	14362										
HEMGN	55363	broad.mit.edu	37	chr9	100689698	100689698	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataactatagacatcattttCtggatgactctcattcagaa	5	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100689698C>A	ENST00000259456.3	-	5	1566	c.1423G>T	c.(1423-1425)Gaa>Taa	p.E475*		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	475					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.E475*(1)		NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				ACATCATTTTCTGGATGACTC	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											164	164	164					9																	100689698		2203	4299	6502	99729519	SO:0001587	stop_gained	55363			AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.1423G>T	9.37:g.100689698C>A	ENSP00000259456:p.Glu475*		99729519	Q6XAR3|Q86XY5|Q9NPC0	Nonsense_Mutation	SNP	ENST00000259456.3	37	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	C	35	5.460987	0.96240	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.0	3.1	0.35709	.	0.434126	0.21699	N	0.070460	.	.	.	.	.	.	0.40506	D	0.980693	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-21.7707	7.5122	0.27579	0.0:0.8845:0.0:0.1155	.	.	.	.	X	475	.	ENSP00000259456:E475X	E	-	1	0	HEMGN	99729519	0.976000	0.34144	0.779000	0.31741	0.644000	0.38419	1.801000	0.38843	1.263000	0.44181	0.491000	0.48974	GAA		0.303	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		A	100689698	C	A	100689698	4	1	61	1	0	0	0	0	0	1	0	0	7071	922	32	2	35	2	HEMGN	9	100689698	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16913	100689698	40523733	6378	14363										
HEMGN	55363	broad.mit.edu	37	chr9	100693459	100693459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtctctttctgcctcttCgatttccttttcctgttctc	5	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100693459C>T	ENST00000259456.3	-	4	361	c.218G>A	c.(217-219)cGa>cAa	p.R73Q		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	73	Necessary for nuclear localization.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.R73Q(1)		NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TCTGCCTCTTCGATTTCCTTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											148	147	147					9																	100693459		2203	4300	6503	99733280	SO:0001583	missense	55363			AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.218G>A	9.37:g.100693459C>T	ENSP00000259456:p.Arg73Gln		99733280	Q6XAR3|Q86XY5|Q9NPC0	Missense_Mutation	SNP	ENST00000259456.3	37	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	C	9.245	1.039257	0.19669	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.3	0.438	0.16560	.	1.722310	0.02872	N	0.131675	T	0.10294	0.0252	N	0.01352	-0.895	0.21290	N	0.999736	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.10902	T	0.67	0.1231	4.0164	0.09646	0.0:0.1953:0.1787:0.6259	.	73	Q9BXL5	HEMGN_HUMAN	Q	73	.	ENSP00000259456:R73Q	R	-	2	0	HEMGN	99733280	0.033000	0.19621	0.976000	0.42696	0.969000	0.65631	-0.212000	0.09319	0.062000	0.16340	-0.383000	0.06682	CGA		0.413	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		T	100693459	C	T	100693459	3	4	61	1	0	0	0	0	1	0	0	0	7071	884	31	1	1244	1	HEMGN	9	100693459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3761	100693459	40519972	6379	14364										
NANS	54187	broad.mit.edu	37	chr9	100845323	100845323	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtagataatcatggcaaaAaaatcaagtcttaaaaataa	6	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100845323A>C	ENST00000210444.5	+	6	1136	c.1066A>C	c.(1066-1068)Aaa>Caa	p.K356Q	TRIM14_ENST00000478530.1_Intron|NANS_ENST00000461452.1_3'UTR|TRIM14_ENST00000375098.3_Intron	NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	356					lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)	p.K356Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				TCATGGCAAAAAAATCAAGTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											66	65	65					9																	100845323		2203	4300	6503	99885144	SO:0001583	missense	54187			AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"sialic acid synthase"	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.1066A>C	9.37:g.100845323A>C	ENSP00000210444:p.Lys356Gln		99885144	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	37	CCDS6733.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.400184	0.62177	.	.	ENSG00000095380	ENST00000210444	T	0.49139	0.79	5.46	5.46	0.80206	Antifreeze-like/N-acetylneuraminic acid synthase C-terminal (2);	0.130231	0.64402	D	0.000001	T	0.33235	0.0856	N	0.19112	0.55	0.80722	D	1	B	0.29988	0.264	B	0.23150	0.044	T	0.22730	-1.0208	10	0.66056	D	0.02	-20.0984	13.8044	0.63220	1.0:0.0:0.0:0.0	.	356	Q9NR45	SIAS_HUMAN	Q	356	ENSP00000210444:K356Q	ENSP00000210444:K356Q	K	+	1	0	NANS	99885144	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.778000	0.75043	2.223000	0.72356	0.454000	0.30748	AAA		0.443	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946		C	100845323	A	C	100845323	3	2	61	1	0	0	0	0	1	0	0	0	10185	15	1	4	1088	4	NANS	9	100845323	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	151864	100845323	40368108	6380	14365										
CORO2A	7464	broad.mit.edu	37	chr9	100890958	100890958	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcttgtagaagcggaaGatctcgcaggaggacacgtc	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100890958G>T	ENST00000343933.5	-	9	1268	c.1011C>A	c.(1009-1011)atC>atA	p.I337I	CORO2A_ENST00000375077.4_Silent_p.I337I	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	337					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)	p.I337I(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AGAAGCGGAAGATCTCGCAGG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	9											121	107	112					9																	100890958		2203	4300	6503	99930779	SO:0001819	synonymous_variant	7464			U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"Coronins", "WD repeat domain containing"	2255	protein-coding gene	gene with protein product	"coronin 2A", "coronin-like protein B", "WD protein IR10", "WD-repeat protein 2"	602159	"coronin, actin-binding protein, 2A"			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.1011C>A	9.37:g.100890958G>T			99930779	Q5TBR5|Q92829|Q9BWS5	Silent	SNP	ENST00000343933.5	37	CCDS6735.1																																																																																				0.592	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389		T	100890958	G	T	100890958	2	4	61	1	0	0	0	0	0	0	0	1	3762	932	33	2		2	CORO2A	9	100890958	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45635	100890958	40322473	6381	14366										
TBC1D2	55357	broad.mit.edu	37	chr9	100961815	100961815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaccatgcgcagctgccGcagctgtttcatgcggaagg	15	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100961815G>A	ENST00000375066.5	-	13	2693	c.2602C>T	c.(2602-2604)Cgg>Tgg	p.R868W	TBC1D2_ENST00000342112.5_Missense_Mutation_p.R661W|TBC1D2_ENST00000375064.1_3'UTR|TBC1D2_ENST00000375063.1_Missense_Mutation_p.R419W	NM_018421.3	NP_060891.3	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	879					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)	p.R868W(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CGCAGCTGCCGCAGCTGTTTC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											134	139	137					9																	100961815		2203	4299	6502	100001636	SO:0001583	missense	55357			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375066.5:c.2602C>T	9.37:g.100961815G>A	ENSP00000364207:p.Arg868Trp		100001636	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375066.5	37	CCDS35080.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300297	0.60195	.	.	ENSG00000095383	ENST00000375066;ENST00000342112;ENST00000375063	T;T;T	0.09911	2.93;3.38;3.01	5.51	3.51	0.40186	.	0.272292	0.34603	N	0.003838	T	0.13372	0.0324	M	0.76328	2.33	0.30554	N	0.765152	B;P	0.35982	0.396;0.531	B;B	0.31495	0.062;0.131	T	0.09335	-1.0679	10	0.87932	D	0	.	10.2646	0.43447	0.0824:0.0:0.757:0.1607	.	879;868	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	W	868;661;419	ENSP00000364207:R868W;ENSP00000341567:R661W;ENSP00000364203:R419W	ENSP00000341567:R661W	R	-	1	2	TBC1D2	100001636	0.025000	0.19082	0.986000	0.45419	0.658000	0.38924	0.841000	0.27613	1.330000	0.45394	0.511000	0.50034	CGG		0.637	TBC1D2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053367.1	NM_018421		A	100961815	G	A	100961815	3	1	61	1	0	0	0	0	1	0	0	0	15647	1086	38	1	155	1	TBC1D2	9	100961815	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70857	100961815	40251616	6382	14367										
TBC1D2	55357	broad.mit.edu	37	chr9	100965685	100965685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccagcagggcaatggccGccagcctggagtagtaggga	17	10	0	0	rs201501022		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:100965685G>A	ENST00000375064.1	-	10	2194	c.2156C>T	c.(2155-2157)gCg>gTg	p.A719V	TBC1D2_ENST00000375066.5_Missense_Mutation_p.A719V|TBC1D2_ENST00000342112.5_Missense_Mutation_p.A501V|TBC1D2_ENST00000375063.1_Missense_Mutation_p.A259V	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	719	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)	p.A719V(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GGCAATGGCCGCCAGCCTGGA	0.612													G|||	1	0.000199681	0	0.0014	5008	,	,		18445	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											89	83	85					9																	100965685		2203	4300	6503	100005506	SO:0001583	missense	55357			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.2156C>T	9.37:g.100965685G>A	ENSP00000364205:p.Ala719Val		100005506	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.25	3.583376	0.65992	.	.	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112;ENST00000375063	T;T;T;T	0.04406	3.63;3.63;3.63;3.63	5.35	5.35	0.76521	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.14442	0.0349	L	0.41492	1.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.17410	-1.0370	10	0.21014	T	0.42	.	17.8634	0.88789	0.0:0.0:1.0:0.0	.	719;719	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	V	719;719;501;259	ENSP00000364205:A719V;ENSP00000364207:A719V;ENSP00000341567:A501V;ENSP00000364203:A259V	ENSP00000341567:A501V	A	-	2	0	TBC1D2	100005506	1.000000	0.71417	0.996000	0.52242	0.540000	0.34992	4.777000	0.62361	2.503000	0.84419	0.655000	0.94253	GCG		0.612	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421		A	100965685	G	A	100965685	3	1	61	1	0	0	0	0	1	0	0	0	15647	1087	38	1	613	1	TBC1D2	9	100965685	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3870	100965685	40247746	6383	14368										
TBC1D2	55357	broad.mit.edu	37	chr9	101006343	101006343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagggctgcaaggcagctgCcacgcccactagcccagggg	15	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101006343C>T	ENST00000375064.1	-	3	618	c.580G>A	c.(580-582)Gca>Aca	p.A194T	TBC1D2_ENST00000375066.5_Missense_Mutation_p.A194T|TBC1D2_ENST00000342112.5_5'UTR	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	194				Missing (in Ref. 4; BAG60767). {ECO:0000305}.	positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)	p.A194T(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		AAGGCAGCTGCCACGCCCACT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											31	30	30					9																	101006343		2203	4300	6503	100046164	SO:0001583	missense	55357			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.580G>A	9.37:g.101006343C>T	ENSP00000364205:p.Ala194Thr		100046164	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		.	.	.	.	.	.	.	.	.	.	C	5.826	0.336685	0.11013	.	.	ENSG00000095383	ENST00000375064;ENST00000375066	T;T	0.08282	3.4;3.11	5.08	4.18	0.49190	.	0.634145	0.14937	N	0.289764	T	0.11153	0.0272	M	0.65975	2.015	0.35207	D	0.774756	B;B	0.18863	0.031;0.029	B;B	0.15484	0.006;0.013	T	0.04255	-1.0965	10	0.34782	T	0.22	.	9.789	0.40695	0.0:0.9048:0.0:0.0952	.	194;194	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	T	194	ENSP00000364205:A194T;ENSP00000364207:A194T	ENSP00000364205:A194T	A	-	1	0	TBC1D2	100046164	0.001000	0.12720	0.074000	0.20217	0.126000	0.20510	0.703000	0.25646	1.150000	0.42419	-0.126000	0.14955	GCA		0.562	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421		T	101006343	C	T	101006343	3	4	61	1	0	0	0	0	1	0	0	0	15647	739	26	3	2217	3	TBC1D2	9	101006343	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40658	101006343	40207088	6384	14369										
GABBR2	9568	broad.mit.edu	37	chr9	101056076	101056076	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtacttactgttctggaGagtttatatcttctatagga	9	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101056076G>T	ENST00000259455.2	-	18	3110	c.2651C>A	c.(2650-2652)tCt>tAt	p.S884Y		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	884					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.S884Y(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CTGTTCTGGAGAGTTTATATC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											206	200	202					9																	101056076		2203	4300	6503	100095897	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2651C>A	9.37:g.101056076G>T	ENSP00000259455:p.Ser884Tyr		100095897	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465232	0.84425	.	.	ENSG00000136928	ENST00000259455	D	0.83914	-1.78	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.83658	0.5302	N	0.14661	0.345	0.80722	D	1	D	0.61697	0.99	D	0.71656	0.974	D	0.86574	0.1849	10	0.87932	D	0	-27.576	16.0535	0.80777	0.0:0.0:1.0:0.0	.	884	O75899	GABR2_HUMAN	Y	884	ENSP00000259455:S884Y	ENSP00000259455:S884Y	S	-	2	0	GABBR2	100095897	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.048000	0.93830	2.641000	0.89580	0.650000	0.86243	TCT		0.398	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			T	101056076	G	T	101056076	3	4	61	1	0	0	0	0	1	0	0	0	6175	942	33	2	182	2	GABBR2	9	101056076	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49733	101056076	40157355	6385	14370										
GABBR2	9568	broad.mit.edu	37	chr9	101068622	101068622	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccaagctaagaaacaaccGaacaactgaaatggtgaaca	7	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101068622G>A	ENST00000259455.2	-	15	2469	c.2010C>T	c.(2008-2010)ttC>ttT	p.F670F		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	670					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.F670F(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	AGAAACAACCGAACAACTGAA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	9											66	48	54					9																	101068622		2203	4300	6503	100108443	SO:0001819	synonymous_variant	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2010C>T	9.37:g.101068622G>A			100108443	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																				0.532	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101068622	G	A	101068622	2	1	61	1	0	0	0	0	0	0	0	1	6175	1049	37	1		1	GABBR2	9	101068622	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12546	101068622	40144809	6386	14371										
GABBR2	9568	broad.mit.edu	37	chr9	101147978	101147978	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatccatcaaggccaaagaGaaatatggaagcataggaga	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101147978G>T	ENST00000259455.2	-	11	2065	c.1606C>A	c.(1606-1608)Ctc>Atc	p.L536I		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	536					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.L536I(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	AGGCCAAAGAGAAATATGGAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											158	143	148					9																	101147978		2203	4300	6503	100187799	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1606C>A	9.37:g.101147978G>T	ENSP00000259455:p.Leu536Ile		100187799	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516044	0.85495	.	.	ENSG00000136928	ENST00000259455	D	0.88975	-2.45	5.74	5.74	0.90152	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.94656	0.8277	M	0.83012	2.62	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.93942	0.7224	10	0.42905	T	0.14	-29.4607	17.4111	0.87486	0.0:0.0:1.0:0.0	.	536	O75899	GABR2_HUMAN	I	536	ENSP00000259455:L536I	ENSP00000259455:L536I	L	-	1	0	GABBR2	100187799	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	7.972000	0.88022	2.707000	0.92482	0.563000	0.77884	CTC		0.408	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			T	101147978	G	T	101147978	3	4	61	1	0	0	0	0	1	0	0	0	6175	942	33	2	1255	2	GABBR2	9	101147978	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79356	101147978	40065453	6387	14372										
ANKS6	203286	broad.mit.edu	37	chr9	101498866	101498866	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctcaaaggaagagtgaaAgttgtgaatggtttcctgta	12	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101498866A>C	ENST00000353234.4	-	15	2598	c.2551T>G	c.(2551-2553)Ttt>Gtt	p.F851V	ANKS6_ENST00000540940.1_Missense_Mutation_p.F656V|ANKS6_ENST00000375018.1_Missense_Mutation_p.F852V|ANKS6_ENST00000375019.2_Missense_Mutation_p.F550V			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	851						cilium (GO:0005929)|cytoplasm (GO:0005737)		p.F851V(1)		endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				GAAGAGTGAAAGTTGTGAATG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	9											85	88	87					9																	101498866		1935	4131	6066	100538687	SO:0001583	missense	203286			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.2551T>G	9.37:g.101498866A>C	ENSP00000297837:p.Phe851Val		100538687	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	37	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.7|24.7	4.563525|4.563525	0.86335|0.86335	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.71341|.	1.67;-0.56;-0.56;1.85|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.52386|0.52386	0.1731|0.1731	L|L	0.27053|0.27053	0.805|0.805	0.43263|0.43263	D|D	0.995207|0.995207	D;D|.	0.69078|.	0.997;0.995|.	D;D|.	0.77557|.	0.99;0.966|.	T|T	0.49495|0.49495	-0.8934|-0.8934	10|5	0.87932|.	D|.	0|.	-24.8418|-24.8418	13.5089|13.5089	0.61499|0.61499	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	852;851|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	V|R	550;852;851;656|320	ENSP00000364159:F550V;ENSP00000364158:F852V;ENSP00000297837:F851V;ENSP00000442189:F656V|.	ENSP00000297837:F851V|.	F|L	-|-	1|2	0|0	ANKS6|ANKS6	100538687|100538687	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.225000|8.225000	0.89784|0.89784	2.134000|2.134000	0.65973|0.65973	0.533000|0.533000	0.62120|0.62120	TTT|CTT		0.488	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		C	101498866	A	C	101498866	3	2	61	1	0	0	0	0	1	0	0	0	692	72	3	4	68	4	ANKS6	9	101498866	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	350888	101498866	39714565	6388	14373										
ANKS6	203286	broad.mit.edu	37	chr9	101536358	101536358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgaggggagctccgtttCgaagctgaaaaagacaggct	15	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101536358C>T	ENST00000353234.4	-	9	1669	c.1622G>A	c.(1621-1623)cGa>cAa	p.R541Q	ANKS6_ENST00000540940.1_Missense_Mutation_p.R346Q|ANKS6_ENST00000375018.1_Missense_Mutation_p.R541Q|ANKS6_ENST00000375019.2_Missense_Mutation_p.R240Q			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	541						cilium (GO:0005929)|cytoplasm (GO:0005737)		p.R541Q(1)		endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				AGCTCCGTTTCGAAGCTGAAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											32	36	35					9																	101536358		1903	4122	6025	100576179	SO:0001583	missense	203286			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.1622G>A	9.37:g.101536358C>T	ENSP00000297837:p.Arg541Gln		100576179	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	37	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717000	0.89205	.	.	ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	T;T;T;T	0.69561	1.75;-0.41;-0.41;2.02	5.48	5.48	0.80851	.	0.107337	0.64402	D	0.000008	T	0.73621	0.3610	M	0.61703	1.905	0.37218	D	0.905118	D;D	0.71674	0.998;0.996	P;P	0.59115	0.852;0.715	T	0.76146	-0.3066	10	0.38643	T	0.18	-11.1796	10.3084	0.43693	0.0:0.9104:0.0:0.0896	.	541;541	Q68DC2-4;Q68DC2	.;ANKS6_HUMAN	Q	240;541;541;346	ENSP00000364159:R240Q;ENSP00000364158:R541Q;ENSP00000297837:R541Q;ENSP00000442189:R346Q	ENSP00000297837:R541Q	R	-	2	0	ANKS6	100576179	1.000000	0.71417	0.954000	0.39281	0.946000	0.59487	5.237000	0.65360	2.580000	0.87095	0.561000	0.74099	CGA		0.557	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		T	101536358	C	T	101536358	3	4	61	1	0	0	0	0	1	0	0	0	692	884	31	1	1021	1	ANKS6	9	101536358	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37492	101536358	39677073	6389	14374										
GALNT12	79695	broad.mit.edu	37	chr9	101608371	101608371	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcatctctgcgaagaaaCtgccccagagaatcagaagt	9	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101608371C>A	ENST00000375011.3	+	9	1571	c.1571C>A	c.(1570-1572)aCt>aAt	p.T524N	RP11-92C4.3_ENST00000589257.1_RNA|RP11-92C4.3_ENST00000433997.1_RNA	NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	524	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.T524N(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				TGCGAAGAAACTGCCCCAGAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	9											141	128	132					9																	101608371		2203	4300	6503	100648192	SO:0001583	missense	79695			AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.1571C>A	9.37:g.101608371C>A	ENSP00000364150:p.Thr524Asn		100648192	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	37	CCDS6737.1	.	.	.	.	.	.	.	.	.	.	C	6.051	0.377772	0.11466	.	.	ENSG00000119514	ENST00000375011	T	0.27890	1.64	5.93	0.364	0.16124	Ricin B-related lectin (1);Ricin B lectin (3);	0.979266	0.08341	N	0.960936	T	0.14141	0.0342	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32481	-0.9905	10	0.16896	T	0.51	.	0.9416	0.01356	0.2403:0.3985:0.1143:0.2469	.	524	Q8IXK2	GLT12_HUMAN	N	524	ENSP00000364150:T524N	ENSP00000364150:T524N	T	+	2	0	GALNT12	100648192	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.188000	0.17018	0.127000	0.18452	-0.140000	0.14226	ACT		0.507	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		A	101608371	C	A	101608371	3	1	61	1	0	0	0	0	1	0	0	0	6230	565	20	2	1605	2	GALNT12	9	101608371	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72013	101608371	39605060	6390	14375										
COL15A1	1306	broad.mit.edu	37	chr9	101748145	101748145	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggacggccaccagcgGatcatcctctactacacgga	12	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101748145G>A	ENST00000375001.3	+	3	822	c.399G>A	c.(397-399)cgG>cgA	p.R133R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	133	Laminin G-like.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.R133R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				GCCACCAGCGGATCATCCTCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	9											90	84	86					9																	101748145		2203	4300	6503	100787966	SO:0001819	synonymous_variant	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.399G>A	9.37:g.101748145G>A			100787966	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.627	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		A	101748145	G	A	101748145	2	1	61	1	0	0	0	0	0	0	0	1	3678	1161	41	3		3	COL15A1	9	101748145	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139774	101748145	39465286	6391	14376										
COL15A1	1306	broad.mit.edu	37	chr9	101759254	101759254	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacccataaacacacctccAactccatcctccccctttga	2	19	0	1	rs143370845	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101759254A>G	ENST00000375001.3	+	6	1266	c.843A>G	c.(841-843)ccA>ccG	p.P281P		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	281	Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.P281P(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACACACCTCCAACTCCATCCT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9						A		5,4401	9.9+/-24.2	0,5,2198	196	184	188		843	-3.4	0	9	dbSNP_134	188	0,8600		0,0,4300	no	coding-synonymous	COL15A1	NM_001855.3		0,5,6498	GG,GA,AA		0.0,0.1135,0.0384		281/1389	101759254	5,13001	2203	4300	6503	100799075	SO:0001819	synonymous_variant	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.843A>G	9.37:g.101759254A>G			100799075	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.473	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		G	101759254	A	G	101759254	2	3	61	1	0	0	0	0	0	0	0	1	3678	117	5	4		4	COL15A1	9	101759254	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11109	101759254	39454177	6392	14377										
COL15A1	1306	broad.mit.edu	37	chr9	101802809	101802809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtgtgtcacaggggccgGacgggttgcctgggctgcca	18	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101802809G>A	ENST00000375001.3	+	23	2905	c.2482G>A	c.(2482-2484)Gac>Aac	p.D828N		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	828	Collagen-like 3.|Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.D828N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACAGGGGCCGGACGGGTTGCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	9											178	155	163					9																	101802809		2203	4300	6503	100842630	SO:0001583	missense	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2482G>A	9.37:g.101802809G>A	ENSP00000364140:p.Asp828Asn		100842630	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.468569	0.26335	.	.	ENSG00000204291	ENST00000375001	D	0.93488	-3.23	5.51	5.51	0.81932	.	0.564773	0.19101	N	0.122687	D	0.91845	0.7419	L	0.39514	1.22	0.32822	D	0.502872	P	0.41784	0.762	P	0.48063	0.565	D	0.91169	0.4967	10	0.18276	T	0.48	-9.3415	14.9066	0.70724	0.0:0.0:1.0:0.0	.	828	P39059	COFA1_HUMAN	N	828	ENSP00000364140:D828N	ENSP00000364140:D828N	D	+	1	0	COL15A1	100842630	0.975000	0.34042	0.066000	0.19879	0.388000	0.30384	3.797000	0.55514	2.582000	0.87167	0.655000	0.94253	GAC		0.582	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		A	101802809	G	A	101802809	3	1	61	1	0	0	0	0	1	0	0	0	3678	1174	41	3	2572	3	COL15A1	9	101802809	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43555	101802809	39410622	6393	14378										
COL15A1	1306	broad.mit.edu	37	chr9	101804386	101804386	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaggactaaaaggagaAcaggtaagaggggcccaggt	14	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101804386A>G	ENST00000375001.3	+	24	2994	c.2571A>G	c.(2569-2571)gaA>gaG	p.E857E		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	857	Collagen-like 3.|Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.E857E(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TAAAAGGAGAACAGGTAAGAG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	9											85	94	91					9																	101804386		2203	4300	6503	100844207	SO:0001819	synonymous_variant	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2571A>G	9.37:g.101804386A>G			100844207	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		G	101804386	A	G	101804386	2	3	61	1	0	0	0	0	0	0	0	1	3678	40	2	4		4	COL15A1	9	101804386	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1577	101804386	39409045	6394	14379										
COL15A1	1306	broad.mit.edu	37	chr9	101831961	101831961	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattactttataggccccaGaaagtcatttggcatggctc	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101831961G>T	ENST00000375001.3	+	42	4383	c.3960G>T	c.(3958-3960)caG>caT	p.Q1320H		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1320	Nonhelical region 10 (NC10).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.Q1320H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ATAGGCCCCAGAAAGTCATTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	111	108					9																	101831961		2203	4300	6503	100871782	SO:0001583	missense	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.3960G>T	9.37:g.101831961G>T	ENSP00000364140:p.Gln1320His		100871782	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.958017	0.34565	.	.	ENSG00000204291	ENST00000375001	T	0.48522	0.81	6.17	3.35	0.38373	Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1);	0.165028	0.56097	D	0.000040	T	0.48314	0.1493	L	0.58810	1.83	0.51233	D	0.999918	P	0.49253	0.921	P	0.49829	0.623	T	0.48570	-0.9024	10	0.72032	D	0.01	-5.78	5.7736	0.18267	0.206:0.0:0.6475:0.1465	.	1320	P39059	COFA1_HUMAN	H	1320	ENSP00000364140:Q1320H	ENSP00000364140:Q1320H	Q	+	3	2	COL15A1	100871782	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	1.394000	0.34509	0.926000	0.37118	0.655000	0.94253	CAG		0.448	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101831961	G	T	101831961	3	4	61	1	0	0	0	0	1	0	0	0	3678	933	33	2	4126	2	COL15A1	9	101831961	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27575	101831961	39381470	6395	14380										
COL15A1	1306	broad.mit.edu	37	chr9	101832136	101832136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctaattgtcctatgtatcGaaaacagtttcatgacagac	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:101832136G>A	ENST00000375001.3	+	42	4558	c.4135G>A	c.(4135-4137)Gaa>Aaa	p.E1379K		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1379	Nonhelical region 10 (NC10).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.E1379K(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCTATGTATCGAAAACAGTTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											88	79	82					9																	101832136		2203	4300	6503	100871957	SO:0001583	missense	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.4135G>A	9.37:g.101832136G>A	ENSP00000364140:p.Glu1379Lys		100871957	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.726379	0.69074	.	.	ENSG00000204291	ENST00000375001	T	0.61859	0.07	6.17	5.28	0.74379	Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1);	0.046338	0.85682	N	0.000000	T	0.69557	0.3124	M	0.86178	2.8	0.80722	D	1	D	0.61697	0.99	P	0.49561	0.615	T	0.76857	-0.2804	10	0.87932	D	0	-30.6522	14.5279	0.67902	0.0708:0.0:0.9292:0.0	.	1379	P39059	COFA1_HUMAN	K	1379	ENSP00000364140:E1379K	ENSP00000364140:E1379K	E	+	1	0	COL15A1	100871957	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	9.837000	0.99465	1.627000	0.50400	0.655000	0.94253	GAA		0.443	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		A	101832136	G	A	101832136	3	1	61	1	0	0	0	0	1	0	0	0	3678	1059	37	1	4301	1	COL15A1	9	101832136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	175	101832136	39381295	6396	14381										
NR4A3	8013	broad.mit.edu	37	chr9	102595062	102595062	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccgatgtcagtactgtcGatttcagaagtgtctcagtg	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:102595062G>A	ENST00000395097.2	+	4	1772	c.1043G>A	c.(1042-1044)cGa>cAa	p.R348Q	NR4A3_ENST00000338488.4_Missense_Mutation_p.R348Q|NR4A3_ENST00000330847.1_Missense_Mutation_p.R359Q	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	348					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)	p.R359Q(1)	TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				CAGTACTGTCGATTTCAGAAG	0.363			T	EWSR1	extraskeletal myxoid chondrosarcoma																																		Dom	yes		9	9q22	8013	"nuclear receptor subfamily 4, group A, member 3 (NOR1)"		M	1	Substitution - Missense(1)	large_intestine(1)	9											136	131	133					9																	102595062		2203	4300	6503	101634883	SO:0001583	missense	8013			U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"Nuclear hormone receptors"	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1043G>A	9.37:g.102595062G>A	ENSP00000378531:p.Arg348Gln		101634883	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Missense_Mutation	SNP	ENST00000395097.2	37	CCDS6743.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874634	0.91664	.	.	ENSG00000119508	ENST00000395097;ENST00000338488;ENST00000395096;ENST00000330847	D;D;D	0.98550	-4.99;-4.99;-4.99	5.6	5.6	0.85130	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	H	0.98786	4.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.997	D	0.97999	1.0359	10	0.87932	D	0	.	19.9823	0.97331	0.0:0.0:1.0:0.0	.	359;348;348	Q92570-3;Q92570;Q92570-2	.;NR4A3_HUMAN;.	Q	348;348;172;359	ENSP00000378531:R348Q;ENSP00000340301:R348Q;ENSP00000333122:R359Q	ENSP00000333122:R359Q	R	+	2	0	NR4A3	101634883	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.788000	0.95919	0.650000	0.86243	CGA		0.363	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1			A	102595062	G	A	102595062	3	1	61	1	0	0	0	0	1	0	0	0	10665	1058	37	1	1086	1	NR4A3	9	102595062	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	762926	102595062	38618369	6397	14382										
NR4A3	8013	broad.mit.edu	37	chr9	102595662	102595662	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagccctctccaccttctCctccaatctgcatgatgaat	4	17	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:102595662C>A	ENST00000395097.2	+	5	1909	c.1180C>A	c.(1180-1182)Cct>Act	p.P394T	NR4A3_ENST00000338488.4_Missense_Mutation_p.P394T|NR4A3_ENST00000330847.1_Missense_Mutation_p.P405T	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	394					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)	p.P405T(1)	TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TCCACCTTCTCCTCCAATCTG	0.463			T	EWSR1	extraskeletal myxoid chondrosarcoma																																		Dom	yes		9	9q22	8013	"nuclear receptor subfamily 4, group A, member 3 (NOR1)"		M	1	Substitution - Missense(1)	large_intestine(1)	9											199	178	185					9																	102595662		2203	4300	6503	101635483	SO:0001583	missense	8013			U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"Nuclear hormone receptors"	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1180C>A	9.37:g.102595662C>A	ENSP00000378531:p.Pro394Thr		101635483	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Missense_Mutation	SNP	ENST00000395097.2	37	CCDS6743.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.501974	0.64298	.	.	ENSG00000119508	ENST00000395097;ENST00000338488;ENST00000395096;ENST00000330847	T;D;T	0.89552	0.57;-2.53;0.57	5.71	5.71	0.89125	Nuclear hormone receptor, ligand-binding (2);	0.238952	0.43110	D	0.000616	D	0.91965	0.7455	L	0.45137	1.4	0.80722	D	1	D;P;P	0.89917	1.0;0.855;0.537	D;B;B	0.91635	0.999;0.443;0.316	D	0.87443	0.2396	10	0.13470	T	0.59	.	20.2245	0.98337	0.0:1.0:0.0:0.0	.	405;394;394	Q92570-3;Q92570;Q92570-2	.;NR4A3_HUMAN;.	T	394;394;218;405	ENSP00000378531:P394T;ENSP00000340301:P394T;ENSP00000333122:P405T	ENSP00000333122:P405T	P	+	1	0	NR4A3	101635483	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.621000	0.67743	2.861000	0.98227	0.650000	0.86243	CCT		0.463	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1			A	102595662	C	A	102595662	3	1	61	1	0	0	0	0	1	0	0	0	10665	855	30	2	1227	2	NR4A3	9	102595662	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	600	102595662	38617769	6398	14383										
STX17	55014	broad.mit.edu	37	chr9	102730806	102730806	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcctccttgcaggcttcAaagtggcaggaattgcagct	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:102730806A>G	ENST00000259400.6	+	8	896	c.760A>G	c.(760-762)Aaa>Gaa	p.K254E	STX17_ENST00000534052.1_Missense_Mutation_p.K254E|STX17_ENST00000525640.1_Missense_Mutation_p.K254E|STX17_ENST00000525847.1_3'UTR	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	254	Necessary and sufficient for localization to autophagosome.				autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.K254E(1)		endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TGCAGGCTTCAAAGTGGCAGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	9											47	54	52					9																	102730806		2203	4300	6503	101770627	SO:0001583	missense	55014			AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.760A>G	9.37:g.102730806A>G	ENSP00000259400:p.Lys254Glu		101770627	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	37	CCDS6745.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133063	0.77662	.	.	ENSG00000136874	ENST00000259400;ENST00000525640;ENST00000534052	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.78214	0.4248	M	0.76170	2.325	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.80975	-0.1142	9	0.72032	D	0.01	-15.3343	13.8021	0.63206	1.0:0.0:0.0:0.0	.	254	P56962	STX17_HUMAN	E	254	.	ENSP00000259400:K254E	K	+	1	0	STX17	101770627	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.047000	0.89440	1.999000	0.58509	0.533000	0.62120	AAA		0.502	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919		G	102730806	A	G	102730806	3	3	61	1	0	0	0	0	1	0	0	0	15379	131	5	4	786	4	STX17	9	102730806	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	135144	102730806	38482625	6399	14384										
ERP44	23071	broad.mit.edu	37	chr9	102861078	102861078	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactcaccaggagcagaagGgagcatctgaggtcgggtaa	14	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:102861078G>T	ENST00000262455.6	-	1	244	c.45C>A	c.(43-45)tcC>tcA	p.S15S	INVS_ENST00000374921.3_5'Flank|INVS_ENST00000541287.1_5'Flank|INVS_ENST00000262456.2_5'Flank|INVS_ENST00000262457.2_5'Flank	NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	15					cell redox homeostasis (GO:0045454)|glycoprotein metabolic process (GO:0009100)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	protein disulfide isomerase activity (GO:0003756)	p.S15S(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)	19						GGAGCAGAAGGGAGCATCTGA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	9											159	127	138					9																	102861078		2203	4300	6503	101900899	SO:0001819	synonymous_variant	23071			AB011145	CCDS35082.1	9q22.33	2011-10-19	2009-02-23	2009-02-23	ENSG00000023318	ENSG00000023318		"Protein disulfide isomerases"	18311	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 10"	609170	"thioredoxin domain containing 4 (endoplasmic reticulum)"	TXNDC4		11847130	Standard	NM_015051		Approved	KIAA0573, PDIA10	uc004bam.3	Q9BS26	OTTHUMG00000020363	ENST00000262455.6:c.45C>A	9.37:g.102861078G>T			101900899	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Silent	SNP	ENST00000262455.6	37	CCDS35082.1																																																																																				0.637	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1	XM_088476		T	102861078	G	T	102861078	2	4	61	1	0	0	0	0	0	0	0	1	5256	1219	43	2		2	ERP44	9	102861078	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130272	102861078	38352353	6400	14385										
TEX10	54881	broad.mit.edu	37	chr9	103111552	103111552	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatagtctttgttttaaagtTtgtaggagtagcattttgta	9	2	1	0	rs574362745		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:103111552T>G	ENST00000374902.4	-	2	270	c.94A>C	c.(94-96)Aac>Cac	p.N32H	TEX10_ENST00000535814.1_Missense_Mutation_p.N35H|TEX10_ENST00000537512.1_Intron	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	32						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)		p.N32H(1)		NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GTTTTAAAGTTTGTAGGAGTA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	9											156	146	149					9																	103111552		2203	4300	6503	102151373	SO:0001583	missense	54881			AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.94A>C	9.37:g.103111552T>G	ENSP00000364037:p.Asn32His		102151373	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	37	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.732049	0.48939	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730	.	.	.	5.51	4.35	0.52113	.	0.131884	0.64402	D	0.000002	T	0.67059	0.2853	M	0.66939	2.045	0.80722	D	1	D;P;D	0.62365	0.989;0.879;0.991	P;B;P	0.55667	0.781;0.387;0.73	T	0.69331	-0.5173	9	0.66056	D	0.02	-9.575	11.8452	0.52381	0.1312:0.0:0.0:0.8688	.	35;32;32	B4DYV2;B4DQR0;Q9NXF1	.;.;TEX10_HUMAN	H	35;32;32	.	ENSP00000364037:N32H	N	-	1	0	TEX10	102151373	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	8.040000	0.89188	0.897000	0.36392	-0.336000	0.08194	AAC		0.318	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		G	103111552	T	G	103111552	3	3	61	1	0	0	0	0	1	0	0	0	15811	1841	64	4	2751	4	TEX10	9	103111552	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	250474	103111552	38101879	6401	14386										
TMEFF1	8577	broad.mit.edu	37	chr9	103271370	103271370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagaagggctgcttgtaaGcaccagaaagagataacagt	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:103271370G>T	ENST00000374879.4	+	3	822	c.390G>T	c.(388-390)aaG>aaT	p.K130N	TMEFF1_ENST00000334943.6_Missense_Mutation_p.K91N|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.A94S	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	130	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K130N(1)		NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				CTGCTTGTAAGCACCAGAAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	9											105	105	105					9																	103271370		2203	4300	6503	102311191	SO:0001583	missense	8577			U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.390G>T	9.37:g.103271370G>T	ENSP00000364013:p.Lys130Asn		102311191	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	37	CCDS6750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.90|12.90	2.077344|2.077344	0.36662|0.36662	.|.	.|.	ENSG00000251349|ENSG00000241697	ENST00000502978|ENST00000334943;ENST00000374879	.|T;T	.|0.04502	.|3.61;3.61	5.58|5.58	3.51|3.51	0.40186|0.40186	.|Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	.|0.051729	.|0.85682	.|D	.|0.000000	T|T	0.06917|0.06917	0.0176|0.0176	L|L	0.43646|0.43646	1.37|1.37	0.47698|0.47698	D|D	0.999499|0.999499	.|P;B	.|0.35050	.|0.482;0.009	.|P;B	.|0.44811	.|0.461;0.005	T|T	0.32295|0.32295	-0.9912|-0.9912	5|10	.|0.42905	.|T	.|0.14	-32.3874|-32.3874	5.0111|5.0111	0.14313|0.14313	0.3551:0.0:0.6449:0.0|0.3551:0.0:0.6449:0.0	.|.	.|130;91	.|Q8IYR6;Q8IYR6-2	.|TEFF1_HUMAN;.	S|N	94|91;130	.|ENSP00000334447:K91N;ENSP00000364013:K130N	.|ENSP00000334447:K91N	A|K	+|+	1|3	0|2	C9orf30-TMEFF1|TMEFF1	102311191|102311191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.091000|1.091000	0.30915|0.30915	1.353000|1.353000	0.45828|0.45828	0.650000|0.650000	0.86243|0.86243	GCA|AAG		0.363	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		T	103271370	G	T	103271370	3	4	61	1	0	0	0	0	1	0	0	0	16052	962	34	2	400	2	TMEFF1	9	103271370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159818	103271370	37942061	6402	14387										
TMEFF1	8577	broad.mit.edu	37	chr9	103334840	103334840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagcactgtgaaaagacaGactttagtattctctatgta	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:103334840G>T	ENST00000374879.4	+	9	1372	c.940G>T	c.(940-942)Gac>Tac	p.D314Y	TMEFF1_ENST00000334943.6_Missense_Mutation_p.D275Y|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.R277I	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	314					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D314Y(1)		NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				TGAAAAGACAGACTTTAGTAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	9											143	134	137					9																	103334840		2203	4300	6503	102374661	SO:0001583	missense	8577			U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.940G>T	9.37:g.103334840G>T	ENSP00000364013:p.Asp314Tyr		102374661	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	37	CCDS6750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.9|21.9	4.216112|4.216112	0.79352|0.79352	.|.	.|.	ENSG00000241697|ENSG00000251349	ENST00000334943;ENST00000374879|ENST00000502978	T;T|.	0.14022|.	2.54;2.54|.	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.045347|.	0.85682|.	D|.	0.000000|.	T|T	0.55752|0.55752	0.1940|0.1940	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.79784|.	0.993;0.982|.	T|T	0.52117|0.52117	-0.8618|-0.8618	10|5	0.87932|.	D|.	0|.	-41.1487|-41.1487	15.8911|15.8911	0.79299|0.79299	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	314;275|.	Q8IYR6;Q8IYR6-2|.	TEFF1_HUMAN;.|.	Y|I	275;314|277	ENSP00000334447:D275Y;ENSP00000364013:D314Y|.	ENSP00000334447:D275Y|.	D|R	+|+	1|2	0|0	TMEFF1|C9orf30-TMEFF1	102374661|102374661	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.994000|0.994000	0.84299|0.84299	9.471000|9.471000	0.97696|0.97696	2.305000|2.305000	0.77605|0.77605	0.650000|0.650000	0.86243|0.86243	GAC|AGA		0.358	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		T	103334840	G	T	103334840	3	4	61	1	0	0	0	0	1	0	0	0	16052	942	33	2	974	2	TMEFF1	9	103334840	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63470	103334840	37878591	6403	14388										
MURC	347273	broad.mit.edu	37	chr9	103348134	103348134	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatgatgatgatatctttGatcccccagtagatctgtct	9	8	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:103348134G>A	ENST00000307584.5	+	2	561	c.496G>A	c.(496-498)Gat>Aat	p.D166N		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	166					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)		p.D166N(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				TGATATCTTTGATCCCCCAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											68	66	67					9																	103348134		2203	4300	6503	102387955	SO:0001583	missense	347273			BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"muscle-restricted coiled-coil protein"					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.496G>A	9.37:g.103348134G>A	ENSP00000418668:p.Asp166Asn		102387955	B1PRL3|B4DT88	Missense_Mutation	SNP	ENST00000307584.5	37	CCDS35083.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.832152	0.32421	.	.	ENSG00000170681	ENST00000307584	T	0.59083	0.29	5.16	4.13	0.48395	.	0.555553	0.20886	N	0.083902	T	0.47469	0.1447	L	0.34521	1.04	0.09310	N	1	P	0.43701	0.815	P	0.45681	0.49	T	0.28808	-1.0032	10	0.17369	T	0.5	-13.3474	9.9907	0.41870	0.0:0.0:0.669:0.331	.	166	Q5BKX8	MURC_HUMAN	N	166	ENSP00000418668:D166N	ENSP00000418668:D166N	D	+	1	0	MURC	102387955	0.996000	0.38824	0.849000	0.33467	0.074000	0.17049	2.068000	0.41471	2.566000	0.86566	0.561000	0.74099	GAT		0.423	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116		A	103348134	G	A	103348134	3	1	61	1	0	0	0	0	1	0	0	0	10017	1290	45	3	502	3	MURC	9	103348134	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13294	103348134	37865297	6404	14389										
ZNF189	7743	broad.mit.edu	37	chr9	104171635	104171635	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagctttgtaatcttattCgacatcagggtgttcacaca	8	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:104171635C>T	ENST00000339664.2	+	3	1714	c.1585C>T	c.(1585-1587)Cga>Tga	p.R529*	ZNF189_ENST00000259395.4_Nonsense_Mutation_p.R487*|ZNF189_ENST00000374861.3_Nonsense_Mutation_p.R515*	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	529					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R529*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TAATCTTATTCGACATCAGGG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											97	96	96					9																	104171635		2203	4300	6503	103211456	SO:0001587	stop_gained	7743			AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1585C>T	9.37:g.104171635C>T	ENSP00000342019:p.Arg529*		103211456	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Nonsense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.419055	0.83559	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	.	.	.	4.35	3.44	0.39384	.	0.218087	0.23579	N	0.046668	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	9.6954	0.40154	0.3787:0.6213:0.0:0.0	.	.	.	.	X	515;529;487	.	ENSP00000259395:R487X	R	+	1	2	ZNF189	103211456	0.000000	0.05858	1.000000	0.80357	0.842000	0.47809	-1.843000	0.01680	1.400000	0.46741	-0.188000	0.12872	CGA		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		T	104171635	C	T	104171635	4	4	61	1	0	0	0	0	0	1	0	0	17793	876	31	1	1595	1	ZNF189	9	104171635	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	823501	104171635	37041796	6405	14390										
RNF20	56254	broad.mit.edu	37	chr9	104323505	104323505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacatgttcaatttcaaacGagcccaggtaaaagcagttg	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:104323505G>A	ENST00000389120.3	+	18	2732	c.2642G>A	c.(2641-2643)cGa>cAa	p.R881Q		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	881					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R881P(1)|p.R881Q(1)		breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		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)		AATTTCAAACGAGCCCAGGTA	0.403																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	9											139	136	137					9																	104323505		2203	4300	6503	103363326	SO:0001583	missense	56254			AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.2642G>A	9.37:g.104323505G>A	ENSP00000373772:p.Arg881Gln		103363326	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	36	5.635663	0.96682	.	.	ENSG00000155827	ENST00000389120	T	0.37058	1.22	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.65026	0.2652	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.65166	-0.6234	10	0.52906	T	0.07	-7.4183	19.7564	0.96294	0.0:0.0:1.0:0.0	.	881	Q5VTR2	BRE1A_HUMAN	Q	881	ENSP00000373772:R881Q	ENSP00000373772:R881Q	R	+	2	0	RNF20	103363326	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	9.229000	0.95273	2.835000	0.97688	0.650000	0.86243	CGA		0.403	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		A	104323505	G	A	104323505	3	1	61	1	0	0	0	0	1	0	0	0	13510	1058	37	1	2708	1	RNF20	9	104323505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151870	104323505	36889926	6406	14391										
GRIN3A	116443	broad.mit.edu	37	chr9	104341616	104341616	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagcacaaagagcccagaGaagtgtttgatgcccatttg	11	9	0	3	rs138075207		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:104341616G>T	ENST00000361820.3	-	7	3393	c.2793C>A	c.(2791-2793)ttC>ttA	p.F931L		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	931					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)	p.F931L(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	AGAGCCCAGAGAAGTGTTTGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											152	131	138					9																	104341616		2203	4300	6503	103381437	SO:0001583	missense	116443				CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2793C>A	9.37:g.104341616G>T	ENSP00000355155:p.Phe931Leu		103381437	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812149	0.70797	.	.	ENSG00000198785	ENST00000361820	T	0.51325	0.71	5.37	4.24	0.50183	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.45216	0.1331	L	0.34521	1.04	0.58432	D	0.999999	P	0.43701	0.815	P	0.50109	0.631	T	0.35871	-0.9771	10	0.52906	T	0.07	.	9.9458	0.41609	0.1799:0.0:0.8201:0.0	.	931	Q8TCU5	NMD3A_HUMAN	L	931	ENSP00000355155:F931L	ENSP00000355155:F931L	F	-	3	2	GRIN3A	103381437	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.069000	0.30641	2.676000	0.91093	0.655000	0.94253	TTC		0.438	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104341616	G	T	104341616	3	4	61	1	0	0	0	0	1	0	0	0	6804	933	33	2	566	2	GRIN3A	9	104341616	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18111	104341616	36871815	6407	14392										
GRIN3A	116443	broad.mit.edu	37	chr9	104432544	104432544	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagatgttcaaggctgaaGaaaaggagaagactttactt	10	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:104432544G>T	ENST00000361820.3	-	3	2750	c.2150C>A	c.(2149-2151)tCt>tAt	p.S717Y		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	717					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)	p.S717Y(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CAAGGCTGAAGAAAAGGAGAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											125	126	126					9																	104432544		2203	4300	6503	103472365	SO:0001583	missense	116443				CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2150C>A	9.37:g.104432544G>T	ENSP00000355155:p.Ser717Tyr		103472365	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025588	0.75390	.	.	ENSG00000198785	ENST00000361820	T	0.55413	0.52	5.39	5.39	0.77823	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.75474	0.3854	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76550	-0.2918	10	0.52906	T	0.07	.	19.5908	0.95509	0.0:0.0:1.0:0.0	.	717	Q8TCU5	NMD3A_HUMAN	Y	717	ENSP00000355155:S717Y	ENSP00000355155:S717Y	S	-	2	0	GRIN3A	103472365	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.810000	0.99221	2.714000	0.92807	0.580000	0.79431	TCT		0.463	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104432544	G	T	104432544	3	4	61	1	0	0	0	0	1	0	0	0	6804	942	33	2	1225	2	GRIN3A	9	104432544	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90928	104432544	36780887	6408	14393										
SMC2	10592	broad.mit.edu	37	chr9	106882387	106882387	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaactgagaatcaaagaGaatgagctgcgggctctaga	13	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:106882387G>T	ENST00000286398.7	+	16	2364	c.2076G>T	c.(2074-2076)gaG>gaT	p.E692D	SMC2_ENST00000374787.3_Missense_Mutation_p.E692D|SMC2_ENST00000303219.8_Missense_Mutation_p.E692D|SMC2_ENST00000374793.3_Missense_Mutation_p.E692D	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	692					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.E692D(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						GAATCAAAGAGAATGAGCTGC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											108	118	114					9																	106882387		2203	4299	6502	105922208	SO:0001583	missense	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2076G>T	9.37:g.106882387G>T	ENSP00000286398:p.Glu692Asp		105922208	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.506435	0.44558	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	T;T;T;T	0.81078	-1.45;-1.45;3.34;-1.45	5.43	4.52	0.55395	.	0.099686	0.64402	D	0.000002	T	0.62514	0.2434	N	0.08118	0	0.40296	D	0.978559	B;B	0.20261	0.009;0.043	B;B	0.24155	0.022;0.051	T	0.59632	-0.7418	10	0.27785	T	0.31	-15.9244	11.0973	0.48152	0.1443:0.0:0.8557:0.0	.	692;692	O95347;Q2KQ72	SMC2_HUMAN;.	D	692	ENSP00000286398:E692D;ENSP00000363925:E692D;ENSP00000306152:E692D;ENSP00000363919:E692D	ENSP00000286398:E692D	E	+	3	2	SMC2	105922208	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	1.838000	0.39211	2.542000	0.85734	0.585000	0.79938	GAG		0.378	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106882387	G	T	106882387	3	4	61	1	0	0	0	0	1	0	0	0	14820	933	33	2	2134	2	SMC2	9	106882387	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2449843	106882387	34331044	6409	14394										
SMC2	10592	broad.mit.edu	37	chr9	106885486	106885486	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatcacaagcaacaagaaGaattagatgcccttaaaaaa	5	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:106885486G>T	ENST00000286398.7	+	17	2518	c.2230G>T	c.(2230-2232)Gaa>Taa	p.E744*	SMC2_ENST00000374787.3_Nonsense_Mutation_p.E744*|SMC2_ENST00000303219.8_Nonsense_Mutation_p.E744*|SMC2_ENST00000374793.3_Nonsense_Mutation_p.E744*	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	744					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.E744*(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						GCAACAAGAAGAATTAGATGC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											97	90	93					9																	106885486		2203	4300	6503	105925307	SO:0001587	stop_gained	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2230G>T	9.37:g.106885486G>T	ENSP00000286398:p.Glu744*		105925307	Q6IEE0|Q9P1P2	Nonsense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	G	43	9.948459	0.99302	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	.	.	.	5.1	5.1	0.69264	.	0.051849	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-19.8468	17.0807	0.86598	0.0:0.0:1.0:0.0	.	.	.	.	X	744	.	ENSP00000286398:E744X	E	+	1	0	SMC2	105925307	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.087000	0.89521	2.364000	0.80123	0.555000	0.69702	GAA		0.373	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106885486	G	T	106885486	4	4	61	1	0	0	0	0	0	1	0	0	14820	943	33	2	2292	2	SMC2	9	106885486	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3099	106885486	34327945	6410	14395										
SMC2	10592	broad.mit.edu	37	chr9	106900420	106900420	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaaaacattggacagatgCtgcgtactcatttcacacat	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:106900420C>T	ENST00000286398.7	+	24	3679	c.3391C>T	c.(3391-3393)Ctg>Ttg	p.L1131L	SMC2_ENST00000374787.3_Silent_p.L1131L|SMC2_ENST00000374793.3_Silent_p.L1131L	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1131					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.L1131L(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TGGACAGATGCTGCGTACTCA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	9											115	105	109					9																	106900420		2203	4300	6503	105940241	SO:0001819	synonymous_variant	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3391C>T	9.37:g.106900420C>T			105940241	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																				0.363	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106900420	C	T	106900420	2	4	61	1	0	0	0	0	0	0	0	1	14820	796	28	3		3	SMC2	9	106900420	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14934	106900420	34313011	6411	14396										
OR13C4	138804	broad.mit.edu	37	chr9	107289073	107289073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtcagcagtacatacaCcaccttgttcatgatgatgg	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107289073C>T	ENST00000277216.3	-	1	417	c.418G>A	c.(418-420)Gtg>Atg	p.V140M		NM_001001919.1	NP_001001919.1	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C, member 4	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V140M(1)		breast(1)|large_intestine(2)|lung(14)|skin(1)	18						AGTACATACACCACCTTGTTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											146	125	132					9																	107289073		2203	4300	6503	106328894	SO:0001583	missense	138804				CCDS35088.1	9q31.1	2013-09-24			ENSG00000148136	ENSG00000148136		"GPCR / Class A : Olfactory receptors"	14722	protein-coding gene	gene with protein product							Standard	NM_001001919		Approved		uc011lvn.2	Q8NGS5	OTTHUMG00000020407	ENST00000277216.3:c.418G>A	9.37:g.107289073C>T	ENSP00000277216:p.Val140Met		106328894	Q6IF51|Q96R41	Missense_Mutation	SNP	ENST00000277216.3	37	CCDS35088.1	.	.	.	.	.	.	.	.	.	.	C	3.739	-0.054031	0.07362	.	.	ENSG00000148136	ENST00000277216;ENST00000545903	T	0.38887	1.11	4.02	3.04	0.35103	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42053	U	0.000761	T	0.47229	0.1434	M	0.66560	2.04	0.09310	N	1	B	0.31548	0.328	P	0.45310	0.476	T	0.46442	-0.9191	10	0.72032	D	0.01	.	5.1627	0.15070	0.0:0.6721:0.2127:0.1152	.	140	Q8NGS5	O13C4_HUMAN	M	140;169	ENSP00000277216:V140M	ENSP00000277216:V140M	V	-	1	0	OR13C4	106328894	0.000000	0.05858	0.048000	0.18961	0.038000	0.13279	-0.599000	0.05700	2.216000	0.71823	0.585000	0.79938	GTG		0.448	OR13C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053478.1			T	107289073	C	T	107289073	3	4	61	1	0	0	0	0	1	0	0	0	10967	507	18	3	540	3	OR13C4	9	107289073	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	388653	107289073	33924358	6412	14397										
OR13C8	138802	broad.mit.edu	37	chr9	107331606	107331606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagttatcatctttgattCtcacctgcacacccccatgt	4	15	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107331606C>A	ENST00000335040.1	+	1	158	c.158C>A	c.(157-159)tCt>tAt	p.S53Y		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S53Y(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						ATCTTTGATTCTCACCTGCAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											336	311	320					9																	107331606		2203	4300	6503	106371427	SO:0001583	missense	138802				CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"GPCR / Class A : Olfactory receptors"	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.158C>A	9.37:g.107331606C>A	ENSP00000334068:p.Ser53Tyr		106371427	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	.	.	.	.	.	.	.	.	.	.	C	8.960	0.970264	0.18659	.	.	ENSG00000186943	ENST00000335040	T	0.00441	7.41	4.97	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	0.256245	0.28778	N	0.014164	T	0.00496	0.0016	M	0.87456	2.885	0.09310	N	1	B	0.19200	0.034	B	0.17722	0.019	T	0.42882	-0.9425	10	0.51188	T	0.08	.	5.059	0.14548	0.0:0.5908:0.0:0.4092	.	53	Q8NGS7	O13C8_HUMAN	Y	53	ENSP00000334068:S53Y	ENSP00000334068:S53Y	S	+	2	0	OR13C8	106371427	0.000000	0.05858	0.736000	0.30914	0.824000	0.46624	-1.066000	0.03454	1.296000	0.44742	0.655000	0.94253	TCT		0.438	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1			A	107331606	C	A	107331606	3	1	61	1	0	0	0	0	1	0	0	0	10969	913	32	2	160	2	OR13C8	9	107331606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42533	107331606	33881825	6413	14398										
OR13C5	138799	broad.mit.edu	37	chr9	107360864	107360864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaatatgaatataagtttGtcagtggcatccaagtcatc	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107360864G>C	ENST00000374779.2	-	1	924	c.831C>G	c.(829-831)gaC>gaG	p.D277E		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D277E(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						ATATAAGTTTGTCAGTGGCAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											129	121	124					9																	107360864		2203	4300	6503	106400685	SO:0001583	missense	138799				CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"GPCR / Class A : Olfactory receptors"	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.831C>G	9.37:g.107360864G>C	ENSP00000363911:p.Asp277Glu		106400685	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.385225	0.25031	.	.	ENSG00000255800	ENST00000374779	T	0.00227	8.5	3.76	-3.73	0.04398	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37437	U	0.002082	T	0.00210	0.0006	M	0.76574	2.34	0.09310	N	1	B	0.25486	0.127	B	0.34779	0.189	T	0.42396	-0.9454	10	0.33940	T	0.23	.	6.2029	0.20585	0.5195:0.1424:0.3381:0.0	.	277	Q8NGS8	O13C5_HUMAN	E	277	ENSP00000363911:D277E	ENSP00000363911:D277E	D	-	3	2	OR13C5	106400685	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	-1.630000	0.02028	-0.672000	0.05266	0.423000	0.28283	GAC		0.413	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		C	107360864	G	C	107360864	3	2	61	1	0	0	0	0	1	0	0	0	10968	1368	48	5	127	5	OR13C5	9	107360864	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29258	107360864	33852567	6414	14399										
OR13C2	392376	broad.mit.edu	37	chr9	107366971	107366971	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacttgctaaagaaccttCtgttcagtaggtgttttact	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107366971C>A	ENST00000542196.1	-	1	980	c.938G>T	c.(937-939)aGa>aTa	p.R313I		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R313I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AAAGAACCTTCTGTTCAGTAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	9											170	170	170					9																	107366971		2201	4300	6501	106406792	SO:0001583	missense	392376				CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"GPCR / Class A : Olfactory receptors"	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.938G>T	9.37:g.107366971C>A	ENSP00000438815:p.Arg313Ile		106406792	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.419516	0.25552	.	.	ENSG00000257019	ENST00000542196	T	0.39229	1.09	3.65	-3.01	0.05463	.	0.000000	0.37669	U	0.001985	T	0.44850	0.1313	M	0.78456	2.415	0.09310	N	1	B	0.31968	0.349	B	0.40199	0.322	T	0.51865	-0.8651	10	0.66056	D	0.02	.	10.4498	0.44516	0.0:0.301:0.0:0.699	.	313	Q8NGS9	O13C2_HUMAN	I	313	ENSP00000438815:R313I	ENSP00000438815:R313I	R	-	2	0	OR13C2	106406792	0.004000	0.15560	0.000000	0.03702	0.015000	0.08874	-0.126000	0.10563	-0.656000	0.05380	0.407000	0.27541	AGA		0.353	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481		A	107366971	C	A	107366971	3	1	61	1	0	0	0	0	1	0	0	0	10965	913	32	2	21	2	OR13C2	9	107366971	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6107	107366971	33846460	6415	14400										
OR13C2	392376	broad.mit.edu	37	chr9	107367639	107367639	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccagaaagggaaatggtCtttctttctgaaaggaagct	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107367639C>A	ENST00000542196.1	-	1	312	c.270G>T	c.(268-270)aaG>aaT	p.K90N		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K90N(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GGGAAATGGTCTTTCTTTCTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											73	73	73					9																	107367639		2203	4299	6502	106407460	SO:0001583	missense	392376				CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"GPCR / Class A : Olfactory receptors"	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.270G>T	9.37:g.107367639C>A	ENSP00000438815:p.Lys90Asn		106407460	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	C	6.411	0.443866	0.12164	.	.	ENSG00000257019	ENST00000542196	T	0.38240	1.15	3.39	-0.0597	0.13792	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38605	U	0.001630	T	0.36220	0.0959	L	0.52126	1.63	0.09310	N	1	P	0.52842	0.956	P	0.55871	0.786	T	0.25187	-1.0139	10	0.87932	D	0	.	0.3725	0.00382	0.2363:0.3087:0.2339:0.2212	.	90	Q8NGS9	O13C2_HUMAN	N	90	ENSP00000438815:K90N	ENSP00000438815:K90N	K	-	3	2	OR13C2	106407460	0.000000	0.05858	0.482000	0.27366	0.549000	0.35272	-3.021000	0.00642	0.122000	0.18314	0.462000	0.41574	AAG		0.522	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481		A	107367639	C	A	107367639	3	1	61	1	0	0	0	0	1	0	0	0	10965	912	32	2	689	2	OR13C2	9	107367639	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	668	107367639	33845792	6416	14401										
OR13C2	392376	broad.mit.edu	37	chr9	107367844	107367844	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaaagagtaactcaagtCttgggtgaccagaaagtccc	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107367844C>A	ENST00000542196.1	-	1	107	c.65G>T	c.(64-66)aGa>aTa	p.R22I		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	22						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R22I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TAACTCAAGTCTTGGGTGACC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											33	36	35					9																	107367844		2185	4293	6478	106407665	SO:0001583	missense	392376				CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"GPCR / Class A : Olfactory receptors"	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.65G>T	9.37:g.107367844C>A	ENSP00000438815:p.Arg22Ile		106407665	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	C	3.962	-0.010144	0.07727	.	.	ENSG00000257019	ENST00000542196	T	0.00438	7.42	3.39	-3.01	0.05463	.	0.476386	0.15819	U	0.243105	T	0.00210	0.0006	L	0.29908	0.895	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.41448	-0.9508	10	0.49607	T	0.09	.	3.7938	0.08732	0.2781:0.2076:0.0:0.5143	.	22	Q8NGS9	O13C2_HUMAN	I	22	ENSP00000438815:R22I	ENSP00000438815:R22I	R	-	2	0	OR13C2	106407665	0.000000	0.05858	0.012000	0.15200	0.173000	0.22820	-1.718000	0.01875	-0.215000	0.10063	0.462000	0.41574	AGA		0.403	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481		A	107367844	C	A	107367844	3	1	61	1	0	0	0	0	1	0	0	0	10965	913	32	2	894	2	OR13C2	9	107367844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205	107367844	33845587	6417	14402										
OR13C9	286362	broad.mit.edu	37	chr9	107379657	107379657	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacatggatataattttgtCggtagcatccaagtcatctg	9	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107379657C>A	ENST00000259362.1	-	1	828	c.829G>T	c.(829-831)Gac>Tac	p.D277Y		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D277Y(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						ATAATTTTGTCGGTAGCATCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	9											161	149	153					9																	107379657		2203	4300	6503	106419478	SO:0001583	missense	286362				CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"GPCR / Class A : Olfactory receptors"	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.829G>T	9.37:g.107379657C>A	ENSP00000259362:p.Asp277Tyr		106419478	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352322	0.24512	.	.	ENSG00000136839	ENST00000259362	T	0.00256	8.42	4.46	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.125619	0.35040	N	0.003486	T	0.00784	0.0026	H	0.95816	3.725	0.23459	N	0.997638	D	0.89917	1.0	D	0.85130	0.997	T	0.15378	-1.0439	10	0.72032	D	0.01	.	10.4815	0.44695	0.0:0.9044:0.0:0.0956	.	277	Q8NGT0	O13C9_HUMAN	Y	277	ENSP00000259362:D277Y	ENSP00000259362:D277Y	D	-	1	0	OR13C9	106419478	0.000000	0.05858	0.871000	0.34182	0.237000	0.25408	-0.400000	0.07241	1.077000	0.40990	-0.135000	0.14842	GAC		0.393	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1			A	107379657	C	A	107379657	3	1	61	1	0	0	0	0	1	0	0	0	10970	884	31	2	130	2	OR13C9	9	107379657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11813	107379657	33833774	6418	14403										
NIPSNAP3A	25934	broad.mit.edu	37	chr9	107516924	107516924	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttcatgctcatgtcaatCtaggctacacaaaactagtt	6	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107516924C>A	ENST00000374767.4	+	4	628	c.523C>A	c.(523-525)Cta>Ata	p.L175I	NIPSNAP3A_ENST00000471001.1_3'UTR	NM_015469.1	NP_056284.1	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A (C. elegans)	175						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L175I(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	8						TCATGTCAATCTAGGCTACAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	100	107					9																	107516924		2203	4300	6503	106556745	SO:0001583	missense	25934			BC005935	CCDS6760.1	9q31.3	2003-11-27			ENSG00000136783	ENSG00000136783			23619	protein-coding gene	gene with protein product		608871				12477932	Standard	NM_015469		Approved	DKFZp564D177, FLJ13953, HSPC299, MGC14553		Q9UFN0	OTTHUMG00000020413	ENST00000374767.4:c.523C>A	9.37:g.107516924C>A	ENSP00000363899:p.Leu175Ile		106556745	A6NM55|Q5VX32|Q9BRV7|Q9H843|Q9P083	Missense_Mutation	SNP	ENST00000374767.4	37	CCDS6760.1	.	.	.	.	.	.	.	.	.	.	C	6.409	0.443554	0.12164	.	.	ENSG00000136783	ENST00000374767	T	0.54675	0.56	4.99	-0.535	0.11879	Dimeric alpha-beta barrel (1);	0.689827	0.14191	N	0.335351	T	0.27967	0.0689	N	0.19112	0.55	0.09310	N	1	B;B	0.21452	0.056;0.032	B;B	0.21151	0.033;0.033	T	0.10636	-1.0621	10	0.33141	T	0.24	.	0.7969	0.01067	0.3128:0.2974:0.2136:0.1762	.	175;175	B4DW81;Q9UFN0	.;NPS3A_HUMAN	I	175	ENSP00000363899:L175I	ENSP00000363899:L175I	L	+	1	2	NIPSNAP3A	106556745	0.001000	0.12720	0.001000	0.08648	0.875000	0.50365	0.706000	0.25690	0.221000	0.20879	-0.882000	0.02950	CTA		0.418	NIPSNAP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053484.1	NM_015469		A	107516924	C	A	107516924	3	1	61	1	0	0	0	0	1	0	0	0	10461	912	32	2	537	2	NIPSNAP3A	9	107516924	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137267	107516924	33696507	6419	14404										
NIPSNAP3A	25934	broad.mit.edu	37	chr9	107521545	107521545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaaatgtttttccagttCgggaaagtgtcaactaccta	8	7	1	1	rs145918659		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107521545C>T	ENST00000374767.4	+	6	775	c.670C>T	c.(670-672)Cgg>Tgg	p.R224W		NM_015469.1	NP_056284.1	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A (C. elegans)	224						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R224W(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	8						TTTTCCAGTTCGGGAAAGTGT	0.358													.|||	1	0.000199681	0	0	5008	,	,		18980	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9						C	TRP/ARG	0,4406		0,0,2203	137	129	131		670	4	1	9	dbSNP_134	131	1,8599	1.2+/-3.3	0,1,4299	no	missense	NIPSNAP3A	NM_015469.1	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		224/248	107521545	1,13005	2203	4300	6503	106561366	SO:0001583	missense	25934			BC005935	CCDS6760.1	9q31.3	2003-11-27			ENSG00000136783	ENSG00000136783			23619	protein-coding gene	gene with protein product		608871				12477932	Standard	NM_015469		Approved	DKFZp564D177, FLJ13953, HSPC299, MGC14553		Q9UFN0	OTTHUMG00000020413	ENST00000374767.4:c.670C>T	9.37:g.107521545C>T	ENSP00000363899:p.Arg224Trp		106561366	A6NM55|Q5VX32|Q9BRV7|Q9H843|Q9P083	Missense_Mutation	SNP	ENST00000374767.4	37	CCDS6760.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385550	0.61956	0.0	1.16E-4	ENSG00000136783	ENST00000374767	T	0.70986	-0.53	3.97	3.97	0.46021	Dimeric alpha-beta barrel (1);	0.111229	0.56097	D	0.000022	D	0.85660	0.5748	M	0.88031	2.925	0.48901	D	0.999723	D	0.89917	1.0	D	0.97110	1.0	D	0.88566	0.3126	10	0.66056	D	0.02	.	14.7197	0.69297	0.0:1.0:0.0:0.0	.	224	Q9UFN0	NPS3A_HUMAN	W	224	ENSP00000363899:R224W	ENSP00000363899:R224W	R	+	1	2	NIPSNAP3A	106561366	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.730000	0.55006	2.215000	0.71742	0.591000	0.81541	CGG		0.358	NIPSNAP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053484.1	NM_015469		T	107521545	C	T	107521545	3	4	61	1	0	0	0	0	1	0	0	0	10461	875	31	1	692	1	NIPSNAP3A	9	107521545	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4621	107521545	33691886	6420	14405										
ABCA1	19	broad.mit.edu	37	chr9	107553307	107553307	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaactcccaggagcccaaaGcactgaaaaggaaagattaa	8	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107553307G>A	ENST00000374736.3	-	44	6217	c.5823C>T	c.(5821-5823)tgC>tgT	p.C1941C		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1941	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.C1941C(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GGAGCCCAAAGCACTGAAAAG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	9											88	92	91					9																	107553307		2203	4300	6503	106593128	SO:0001819	synonymous_variant	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.5823C>T	9.37:g.107553307G>A			106593128	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																				0.368	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		A	107553307	G	A	107553307	2	1	61	1	0	0	0	0	0	0	0	1	28	963	34	3		3	ABCA1	9	107553307	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31762	107553307	33660124	6421	14406										
ABCA1	19	broad.mit.edu	37	chr9	107583669	107583669	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactcacatgtcaaacagcaCgttatgctggggacagaccc	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107583669C>T	ENST00000374736.3	-	20	3341	c.2947G>A	c.(2947-2949)Gtg>Atg	p.V983M		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	983	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.V983M(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TCAAACAGCACGTTATGCTGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	9											72	57	62					9																	107583669		2203	4300	6503	106623490	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2947G>A	9.37:g.107583669C>T	ENSP00000363868:p.Val983Met		106623490	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737437	0.89482	.	.	ENSG00000165029	ENST00000374736	D	0.93953	-3.32	5.7	5.7	0.88788	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.95987	0.8693	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.96091	0.9061	10	0.87932	D	0	.	19.8306	0.96634	0.0:1.0:0.0:0.0	.	983	O95477	ABCA1_HUMAN	M	983	ENSP00000363868:V983M	ENSP00000363868:V983M	V	-	1	0	ABCA1	106623490	1.000000	0.71417	0.986000	0.45419	0.849000	0.48306	7.731000	0.84895	2.682000	0.91365	0.563000	0.77884	GTG		0.537	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107583669	C	T	107583669	3	4	61	1	0	0	0	0	1	0	0	0	28	536	19	1	3962	1	ABCA1	9	107583669	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30362	107583669	33629762	6422	14407										
ABCA1	19	broad.mit.edu	37	chr9	107584879	107584879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccaccttcatcccatctCggtagacttttaccaggttc	6	15	2	1	rs574919140	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107584879C>T	ENST00000374736.3	-	19	3120	c.2726G>A	c.(2725-2727)cGa>cAa	p.R909Q	ABCA1_ENST00000494467.1_5'Flank	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	909	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R909Q(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CATCCCATCTCGGTAGACTTT	0.547													C|||	3	0.000599042	0	0	5008	,	,		19393	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	9											136	129	131					9																	107584879		2203	4300	6503	106624700	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2726G>A	9.37:g.107584879C>T	ENSP00000363868:p.Arg909Gln		106624700	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188931	0.57909	.	.	ENSG00000165029	ENST00000374736	T	0.80123	-1.34	5.79	3.95	0.45737	ABC transporter-like (1);	0.155416	0.64402	N	0.000016	T	0.63745	0.2537	N	0.20483	0.58	0.80722	D	1	P	0.42518	0.782	B	0.31946	0.138	T	0.63642	-0.6591	10	0.44086	T	0.13	.	12.3583	0.55188	0.0:0.8634:0.0:0.1366	.	909	O95477	ABCA1_HUMAN	Q	909	ENSP00000363868:R909Q	ENSP00000363868:R909Q	R	-	2	0	ABCA1	106624700	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	2.686000	0.46968	0.793000	0.33875	-0.140000	0.14226	CGA		0.547	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107584879	C	T	107584879	3	4	61	1	0	0	0	0	1	0	0	0	28	884	31	1	4187	1	ABCA1	9	107584879	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1210	107584879	33628552	6423	14408										
ABCA1	19	broad.mit.edu	37	chr9	107665905	107665905	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagcttactgtttgtcttCttctgaaagtgaggttcttc	8	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:107665905C>A	ENST00000374736.3	-	2	450	c.56G>T	c.(55-57)aGa>aTa	p.R19I	ABCA1_ENST00000374733.1_Intron|ABCA1_ENST00000423487.2_Missense_Mutation_p.R19I	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	19					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R19I(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TGTTTGTCTTCTTCTGAAAGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	78	82					9																	107665905		2203	4300	6503	106705726	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.56G>T	9.37:g.107665905C>A	ENSP00000363868:p.Arg19Ile		106705726	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177643	0.78564	.	.	ENSG00000165029	ENST00000374736;ENST00000423487	D;D	0.90069	-2.61;-2.61	6.08	5.18	0.71444	.	0.048493	0.85682	D	0.000000	D	0.87525	0.6199	L	0.50333	1.59	0.80722	D	1	P	0.40660	0.726	B	0.44044	0.439	D	0.88000	0.2755	10	0.87932	D	0	.	11.9535	0.52968	0.0:0.9197:0.0:0.0803	.	19	O95477	ABCA1_HUMAN	I	19	ENSP00000363868:R19I;ENSP00000416623:R19I	ENSP00000363868:R19I	R	-	2	0	ABCA1	106705726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.139000	0.50577	2.894000	0.99253	0.655000	0.94253	AGA		0.542	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		A	107665905	C	A	107665905	3	1	61	1	0	0	0	0	1	0	0	0	28	913	32	2	6925	2	ABCA1	9	107665905	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81026	107665905	33547526	6424	14409										
SLC44A1	23446	broad.mit.edu	37	chr9	108072048	108072048	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaacaggtgcagcagcaaGactagtgtcaggatacgaca	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:108072048G>T	ENST00000374720.3	+	3	417	c.170G>T	c.(169-171)aGa>aTa	p.R57I	SLC44A1_ENST00000607692.1_3'UTR|SLC44A1_ENST00000374724.1_Missense_Mutation_p.R57I|SLC44A1_ENST00000374723.1_Missense_Mutation_p.R57I	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	57					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)	p.R57I(1)		breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	GCAGCAGCAAGACTAGTGTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	9											114	108	110					9																	108072048		2203	4300	6503	107111869	SO:0001583	missense	23446			AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214		"CD molecules", "Solute carriers"	18798	protein-coding gene	gene with protein product		606105	"CDW92 antigen"	CDW92		11698453, 10677542	Standard	NM_080546		Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.170G>T	9.37:g.108072048G>T	ENSP00000363852:p.Arg57Ile		107111869	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	Missense_Mutation	SNP	ENST00000374720.3	37	CCDS6763.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.947530	0.92593	.	.	ENSG00000070214	ENST00000374723;ENST00000374720;ENST00000374724	D;D;D	0.81739	-1.53;-1.53;-1.53	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.90906	0.7142	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.991	D	0.90929	0.4789	10	0.56958	D	0.05	-0.1415	19.8545	0.96752	0.0:0.0:1.0:0.0	.	57;57	Q8WWI5-3;Q8WWI5	.;CTL1_HUMAN	I	57	ENSP00000363855:R57I;ENSP00000363852:R57I;ENSP00000363856:R57I	ENSP00000363852:R57I	R	+	2	0	SLC44A1	107111869	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.881000	0.92415	2.695000	0.91970	0.563000	0.77884	AGA		0.413	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053500.1	NM_080546		T	108072048	G	T	108072048	3	4	61	1	0	0	0	0	1	0	0	0	14672	942	33	2	180	2	SLC44A1	9	108072048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	406143	108072048	33141383	6425	14410										
FKTN	2218	broad.mit.edu	37	chr9	108363442	108363442	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcgtgcagttaaaaaatTtattatgttaacatccaacc	5	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:108363442T>G	ENST00000223528.2	+	4	306	c.182T>G	c.(181-183)tTt>tGt	p.F61C	FKTN_ENST00000357998.5_Missense_Mutation_p.F61C|FKTN_ENST00000540160.1_Missense_Mutation_p.F61C|FKTN_ENST00000602661.1_Missense_Mutation_p.F61C|FKTN_ENST00000448551.2_Missense_Mutation_p.F61C	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	61					muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)	p.F61C(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						GTTAAAAAATTTATTATGTTA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	9											48	50	49					9																	108363442		2202	4297	6499	107403263	SO:0001583	missense	2218				CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"Fukuyama type congenital muscular dystrophy (fukutin)"	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.182T>G	9.37:g.108363442T>G	ENSP00000223528:p.Phe61Cys		107403263	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	37	CCDS6766.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812145	0.70797	.	.	ENSG00000106692	ENST00000223528;ENST00000448551;ENST00000540160;ENST00000357998;ENST00000374705	D;D;D;D;D	0.94000	-2.97;-3.33;-2.34;-3.33;-2.8	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.95912	0.8669	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	D	0.96355	0.9261	10	0.87932	D	0	-9.0664	15.0542	0.71901	0.0:0.0:0.0:1.0	.	61;61;61	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	C	61;61;61;61;38	ENSP00000223528:F61C;ENSP00000399140:F61C;ENSP00000439423:F61C;ENSP00000350687:F61C;ENSP00000363837:F38C	ENSP00000223528:F61C	F	+	2	0	FKTN	107403263	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.126000	0.71635	2.155000	0.67459	0.383000	0.25322	TTT		0.279	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731		G	108363442	T	G	108363442	3	3	61	1	0	0	0	0	1	0	0	0	5938	1841	64	4	192	4	FKTN	9	108363442	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	291394	108363442	32849989	6426	14411										
TMEM38B	55151	broad.mit.edu	37	chr9	108510453	108510453	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttatgttcctttataccatCtttattgtggccacaaaggt	6	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:108510453C>A	ENST00000374692.3	+	5	759	c.642C>A	c.(640-642)atC>atA	p.I214I	TMEM38B_ENST00000374688.1_Silent_p.I160I	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	214						integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)	p.I214I(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						TTTATACCATCTTTATTGTGG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	9											77	72	74					9																	108510453		2203	4300	6503	107550274	SO:0001819	synonymous_variant	55151			BC031938	CCDS6768.1	9q31.3	2013-05-23	2004-12-21	2004-12-22	ENSG00000095209	ENSG00000095209			25535	protein-coding gene	gene with protein product		611236	"chromosome 9 open reading frame 87"	C9orf87		17611541, 23316006	Standard	NM_018112		Approved	FLJ10493, bA219P18.1, D4Ertd89e, TRIC-B	uc004bcu.2	Q9NVV0	OTTHUMG00000020429	ENST00000374692.3:c.642C>A	9.37:g.108510453C>A			107550274	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Silent	SNP	ENST00000374692.3	37	CCDS6768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.324|8.324	0.824930|0.824930	0.16678|0.16678	.|.	.|.	ENSG00000095209|ENSG00000095209	ENST00000451560|ENST00000435034	.|.	.|.	.|.	5.47|5.47	1.06|1.06	0.20224|0.20224	.|.	.|.	.|.	.|.	.|.	T|T	0.43853|0.43853	0.1266|0.1266	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.23226|0.23226	-1.0194|-1.0194	4|4	.|.	.|.	.|.	-0.7201|-0.7201	2.9137|2.9137	0.05745|0.05745	0.1127:0.393:0.3173:0.177|0.1127:0.393:0.3173:0.177	.|.	.|.	.|.	.|.	I|Y	75|151	.|.	.|.	L|S	+|+	1|2	0|0	TMEM38B|TMEM38B	107550274|107550274	0.924000|0.924000	0.31332|0.31332	0.990000|0.990000	0.47175|0.47175	0.998000|0.998000	0.95712|0.95712	0.137000|0.137000	0.15995|0.15995	0.297000|0.297000	0.22615|0.22615	0.591000|0.591000	0.81541|0.81541	CTT|TCT		0.398	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112		A	108510453	C	A	108510453	2	1	61	1	0	0	0	0	0	0	0	1	16199	903	32	2		2	TMEM38B	9	108510453	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147011	108510453	32702978	6427	14412										
ZNF462	58499	broad.mit.edu	37	chr9	109689300	109689300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgattgtgatgtttgttCgtttgcaagccccaacatgc	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:109689300C>T	ENST00000277225.5	+	3	3396	c.3107C>T	c.(3106-3108)tCg>tTg	p.S1036L	ZNF462_ENST00000457913.1_Missense_Mutation_p.S1036L|ZNF462_ENST00000441147.2_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1036					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S1036L(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GATGTTTGTTCGTTTGCAAGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											210	203	206					9																	109689300		2203	4300	6503	108729121	SO:0001583	missense	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3107C>T	9.37:g.109689300C>T	ENSP00000277225:p.Ser1036Leu		108729121	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.327520	0.60743	.	.	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.08634	3.07;3.51	5.8	5.8	0.92144	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.22627	0.0546	L	0.59436	1.845	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.60609	0.877;0.773	T	0.00027	-1.2306	10	0.72032	D	0.01	.	14.8523	0.70306	0.1436:0.8564:0.0:0.0	.	1036;1036	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	L	1036	ENSP00000277225:S1036L;ENSP00000414570:S1036L	ENSP00000277225:S1036L	S	+	2	0	ZNF462	108729121	1.000000	0.71417	0.978000	0.43139	0.951000	0.60555	5.831000	0.69330	2.735000	0.93741	0.655000	0.94253	TCG		0.403	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109689300	C	T	109689300	3	4	61	1	0	0	0	0	1	0	0	0	17965	893	31	1	3113	1	ZNF462	9	109689300	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1178847	109689300	31524131	6428	14413										
ZNF462	58499	broad.mit.edu	37	chr9	109690981	109690981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaactaaaaatccactaCgagaagtatcacaatcagcc	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:109690981C>T	ENST00000277225.5	+	3	5077	c.4788C>T	c.(4786-4788)taC>taT	p.Y1596Y	ZNF462_ENST00000457913.1_Silent_p.Y1596Y|ZNF462_ENST00000441147.2_Silent_p.Y441Y			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1596					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Y1596Y(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						AAATCCACTACGAGAAGTATC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	9											89	85	86					9																	109690981		2203	4300	6503	108730802	SO:0001819	synonymous_variant	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.4788C>T	9.37:g.109690981C>T			108730802	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																				0.532	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109690981	C	T	109690981	2	4	61	1	0	0	0	0	0	0	0	1	17965	547	19	1		1	ZNF462	9	109690981	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1681	109690981	31522450	6429	14414										
ZNF462	58499	broad.mit.edu	37	chr9	109691354	109691354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccactaccagaagcgccacGacattgatgcgtattacact	7	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:109691354G>A	ENST00000277225.5	+	3	5450	c.5161G>A	c.(5161-5163)Gac>Aac	p.D1721N	ZNF462_ENST00000457913.1_Missense_Mutation_p.D1721N|ZNF462_ENST00000441147.2_Missense_Mutation_p.D566N			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1721					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D1721N(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAAGCGCCACGACATTGATGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											104	85	91					9																	109691354		2203	4300	6503	108731175	SO:0001583	missense	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5161G>A	9.37:g.109691354G>A	ENSP00000277225:p.Asp1721Asn		108731175	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252868	0.80135	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.08102	3.13;3.52;3.83;3.84	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.20251	0.0487	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.985;0.996	T	0.00839	-1.1545	10	0.49607	T	0.09	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1721;1721	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	N	1721;1721;604;566	ENSP00000277225:D1721N;ENSP00000414570:D1721N;ENSP00000363818:D604N;ENSP00000397306:D566N	ENSP00000277225:D1721N	D	+	1	0	ZNF462	108731175	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.434000	0.97515	2.941000	0.99782	0.655000	0.94253	GAC		0.577	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109691354	G	A	109691354	3	1	61	1	0	0	0	0	1	0	0	0	17965	1058	37	1	5167	1	ZNF462	9	109691354	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	373	109691354	31522077	6430	14415										
ZNF462	58499	broad.mit.edu	37	chr9	109746472	109746472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgtttccacagaagagCgtgttgtccccattgaagtt	9	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:109746472C>T	ENST00000277225.5	+	10	7127	c.6838C>T	c.(6838-6840)Cgt>Tgt	p.R2280C	ZNF462_ENST00000457913.1_Missense_Mutation_p.R2340C|ZNF462_ENST00000441147.2_Missense_Mutation_p.R1186C|ZNF462_ENST00000542028.1_Missense_Mutation_p.R237C|RP11-508N12.2_ENST00000439901.1_RNA			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2280					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R2280C(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CACAGAAGAGCGTGTTGTCCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	81	82					9																	109746472		2203	4300	6503	108786293	SO:0001583	missense	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.6838C>T	9.37:g.109746472C>T	ENSP00000277225:p.Arg2280Cys		108786293	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.712064	0.68730	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	T;T;T;T;T	0.17054	3.29;3.78;3.87;3.85;2.3	5.67	3.69	0.42338	.	0.000000	0.85682	D	0.000000	T	0.43010	0.1228	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.50127	-0.8864	10	0.87932	D	0	.	14.8015	0.69919	0.5116:0.4884:0.0:0.0	.	2340;2280	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	C	2280;2340;1223;1186;237	ENSP00000277225:R2280C;ENSP00000414570:R2340C;ENSP00000363818:R1223C;ENSP00000397306:R1186C;ENSP00000439771:R237C	ENSP00000277225:R2280C	R	+	1	0	ZNF462	108786293	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	1.379000	0.34340	1.293000	0.44690	0.655000	0.94253	CGT		0.418	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109746472	C	T	109746472	3	4	61	1	0	0	0	0	1	0	0	0	17965	768	27	1	6872	1	ZNF462	9	109746472	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55118	109746472	31466959	6431	14416										
ACTL7B	10880	broad.mit.edu	37	chr9	111618067	111618067	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgatgatgaccgccttgatCttgtgcaccttcctgggctt	10	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:111618067C>A	ENST00000374667.3	-	1	1172	c.144G>T	c.(142-144)aaG>aaT	p.K48N		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	48						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)	p.K48N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCGCCTTGATCTTGTGCACCT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	9											123	118	120					9																	111618067		2203	4300	6503	110657888	SO:0001583	missense	10880			BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.144G>T	9.37:g.111618067C>A	ENSP00000363799:p.Lys48Asn		110657888	B2R9Q2|Q5JSV1	Missense_Mutation	SNP	ENST00000374667.3	37	CCDS6771.1	.	.	.	.	.	.	.	.	.	.	C	3.599	-0.081926	0.07141	.	.	ENSG00000148156	ENST00000374667	D	0.94497	-3.44	4.37	2.48	0.30137	.	0.477168	0.15402	U	0.264238	D	0.90246	0.6950	L	0.44542	1.39	0.09310	N	0.999998	B	0.10296	0.003	B	0.09377	0.004	T	0.82952	-0.0202	10	0.87932	D	0	.	7.5215	0.27631	0.0:0.7374:0.1678:0.0949	.	48	Q9Y614	ACL7B_HUMAN	N	48	ENSP00000363799:K48N	ENSP00000363799:K48N	K	-	3	2	ACTL7B	110657888	0.019000	0.18553	0.104000	0.21259	0.033000	0.12548	-0.263000	0.08670	0.455000	0.26910	-0.137000	0.14449	AAG		0.642	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686		A	111618067	C	A	111618067	3	1	61	1	0	0	0	0	1	0	0	0	201	912	32	2	1107	2	ACTL7B	9	111618067	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1871595	111618067	29595364	6432	14417										
CTNNAL1	8727	broad.mit.edu	37	chr9	111705056	111705056	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaaaagcttctcaagttTtactatccatagtgtcctta	4	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:111705056T>G	ENST00000325551.4	-	19	2284	c.2198A>C	c.(2197-2199)aAa>aCa	p.K733T	CTNNAL1_ENST00000374594.1_Missense_Mutation_p.K134T|CTNNAL1_ENST00000374595.4_3'UTR|FAM206A_ENST00000374624.3_Intron|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.K649T	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	733					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.K733T(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TTCTCAAGTTTTACTATCCAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	94	95					9																	111705056		2203	4300	6503	110744877	SO:0001583	missense	8727			AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.2198A>C	9.37:g.111705056T>G	ENSP00000320434:p.Lys733Thr		110744877	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	T	14.09	2.430310	0.43122	.	.	ENSG00000119326	ENST00000325551;ENST00000325580;ENST00000374594	T;T;T	0.51817	1.63;1.42;0.69	5.92	5.92	0.95590	.	0.442238	0.27122	N	0.020834	T	0.37679	0.1012	L	0.27053	0.805	0.21967	N	0.999446	P;P;P;P	0.39480	0.546;0.675;0.546;0.546	B;B;B;B	0.41988	0.136;0.372;0.136;0.136	T	0.41360	-0.9513	10	0.66056	D	0.02	-12.1829	8.7854	0.34818	0.0:0.083:0.0:0.917	.	733;649;733;733	B2RBI4;Q9UBT7-3;B3KMX6;Q9UBT7	.;.;.;CTNL1_HUMAN	T	733;649;134	ENSP00000320434:K733T;ENSP00000323351:K649T;ENSP00000363722:K134T	ENSP00000320434:K733T	K	-	2	0	CTNNAL1	110744877	1.000000	0.71417	0.948000	0.38648	0.070000	0.16714	2.869000	0.48444	2.263000	0.75096	0.533000	0.62120	AAA		0.348	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		G	111705056	T	G	111705056	3	3	61	1	0	0	0	0	1	0	0	0	4021	1841	64	4	10	4	CTNNAL1	9	111705056	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	86989	111705056	29508375	6433	14418										
CTNNAL1	8727	broad.mit.edu	37	chr9	111741743	111741743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaaataaagattctcccGaagagcttcaatattcatct	5	9	4	3	rs200532159		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:111741743G>A	ENST00000325551.4	-	7	1005	c.919C>T	c.(919-921)Cgg>Tgg	p.R307W	CTNNAL1_ENST00000374595.4_Missense_Mutation_p.R307W|CTNNAL1_ENST00000488130.1_5'Flank|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.R307W	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	307					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.R307W(2)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		AGATTCTCCCGAAGAGCTTCA	0.418													G|||	1	0.000199681	0	0	5008	,	,		19322	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	9											73	69	70					9																	111741743		2203	4300	6503	110781564	SO:0001583	missense	8727			AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.919C>T	9.37:g.111741743G>A	ENSP00000320434:p.Arg307Trp		110781564	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.14	3.313101	0.60414	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580	T;T;T	0.32515	1.48;1.61;1.45	5.91	5.0	0.66597	.	0.366625	0.31051	N	0.008355	T	0.33527	0.0866	M	0.80183	2.485	0.80722	D	1	B;P;B;B	0.38110	0.096;0.618;0.287;0.096	B;B;B;B	0.29440	0.024;0.102;0.099;0.024	T	0.36261	-0.9755	10	0.59425	D	0.04	-0.7036	13.3461	0.60573	0.0779:0.0:0.9221:0.0	.	307;307;307;307	B2RBI4;Q9UBT7-3;Q9UBT7-2;Q9UBT7	.;.;.;CTNL1_HUMAN	W	307	ENSP00000363723:R307W;ENSP00000320434:R307W;ENSP00000323351:R307W	ENSP00000320434:R307W	R	-	1	2	CTNNAL1	110781564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.984000	0.56923	2.793000	0.96121	0.655000	0.94253	CGG		0.418	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		A	111741743	G	A	111741743	3	1	61	1	0	0	0	0	1	0	0	0	4021	1057	37	1	1337	1	CTNNAL1	9	111741743	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36687	111741743	29471688	6434	14419										
CTNNAL1	8727	broad.mit.edu	37	chr9	111761512	111761512	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagactttttggtattatCtttatgattaataagcgtgg	8	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:111761512C>A	ENST00000325551.4	-	2	252	c.166G>T	c.(166-168)Gat>Tat	p.D56Y	CTNNAL1_ENST00000374595.4_Missense_Mutation_p.D56Y|CTNNAL1_ENST00000374593.4_Missense_Mutation_p.D56Y|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.D56Y	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	56					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.D56Y(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TTGGTATTATCTTTATGATTA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	9											112	120	117					9																	111761512		2203	4300	6503	110801333	SO:0001583	missense	8727			AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.166G>T	9.37:g.111761512C>A	ENSP00000320434:p.Asp56Tyr		110801333	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.213399	0.79352	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580;ENST00000374593	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	5.93	5.03	0.67393	.	0.043741	0.85682	D	0.000000	T	0.59115	0.2170	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.72338	0.977;0.946;0.977	T	0.63812	-0.6552	10	0.72032	D	0.01	-12.1419	14.8821	0.70542	0.0:0.8556:0.1444:0.0	.	56;56;56	B2RBI4;Q9UBT7-2;Q9UBT7	.;.;CTNL1_HUMAN	Y	56	ENSP00000363723:D56Y;ENSP00000320434:D56Y;ENSP00000323351:D56Y;ENSP00000363721:D56Y	ENSP00000320434:D56Y	D	-	1	0	CTNNAL1	110801333	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.967000	0.70403	1.475000	0.48197	0.655000	0.94253	GAT		0.318	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		A	111761512	C	A	111761512	3	1	61	1	0	0	0	0	1	0	0	0	4021	913	32	2	2110	2	CTNNAL1	9	111761512	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19769	111761512	29451919	6435	14420										
SVEP1	79987	broad.mit.edu	37	chr9	113170353	113170353	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtgtaggtccgtgtaagaGaatttgccattcaaaatctc	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113170353G>T	ENST00000401783.2	-	38	7863	c.7527C>A	c.(7525-7527)ttC>ttA	p.F2509L	SVEP1_ENST00000374469.1_Missense_Mutation_p.F2486L|SVEP1_ENST00000297826.5_Missense_Mutation_p.F435L	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2509	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.F2512L(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGTGTAAGAGAATTTGCCAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	9											50	49	49					9																	113170353		1911	4125	6036	112210174	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7527C>A	9.37:g.113170353G>T	ENSP00000384917:p.Phe2509Leu		112210174	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	1.514	-0.548789	0.04024	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.61274	0.12;0.12;0.12	5.85	0.191	0.15130	Complement control module (2);Sushi/SCR/CCP (3);	0.458800	0.25906	N	0.027539	T	0.23133	0.0559	N	0.05199	-0.095	0.58432	D	0.999996	B	0.06786	0.001	B	0.08055	0.003	T	0.21177	-1.0253	10	0.05620	T	0.96	.	2.9831	0.05960	0.3102:0.1133:0.4613:0.1152	.	2509	Q4LDE5	SVEP1_HUMAN	L	2509;2486;435;181	ENSP00000384917:F2509L;ENSP00000363593:F2486L;ENSP00000297826:F435L	ENSP00000297826:F435L	F	-	3	2	SVEP1	112210174	0.783000	0.28701	0.913000	0.36048	0.349000	0.29174	-0.015000	0.12634	0.103000	0.17682	-0.136000	0.14681	TTC		0.488	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113170353	G	T	113170353	3	4	61	1	0	0	0	0	1	0	0	0	15459	933	33	2	3232	2	SVEP1	9	113170353	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1408841	113170353	28043078	6436	14421										
SVEP1	79987	broad.mit.edu	37	chr9	113170491	113170491	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctggcttgcaggtataGagagctgtgctgagataggc	15	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113170491G>T	ENST00000401783.2	-	38	7725	c.7389C>A	c.(7387-7389)ctC>ctA	p.L2463L	SVEP1_ENST00000374469.1_Silent_p.L2440L|SVEP1_ENST00000297826.5_Silent_p.L389L	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2463	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.L2466L(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGCAGGTATAGAGAGCTGTGC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	9											66	64	64					9																	113170491		1932	4143	6075	112210312	SO:0001819	synonymous_variant	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7389C>A	9.37:g.113170491G>T			112210312	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																				0.478	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113170491	G	T	113170491	2	4	61	1	0	0	0	0	0	0	0	1	15459	929	33	2		2	SVEP1	9	113170491	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138	113170491	28042940	6437	14422										
SVEP1	79987	broad.mit.edu	37	chr9	113170761	113170761	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaacaatcttacaaacaggGaaagagtcattccattgctg	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113170761G>A	ENST00000401783.2	-	38	7455	c.7119C>T	c.(7117-7119)ttC>ttT	p.F2373F	SVEP1_ENST00000374469.1_Silent_p.F2350F|SVEP1_ENST00000297826.5_Silent_p.F299F	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2373	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.F2376F(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TACAAACAGGGAAAGAGTCAT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	9											62	60	61					9																	113170761		1914	4128	6042	112210582	SO:0001819	synonymous_variant	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7119C>T	9.37:g.113170761G>A			112210582	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																				0.463	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113170761	G	A	113170761	2	1	61	1	0	0	0	0	0	0	0	1	15459	1165	41	3		3	SVEP1	9	113170761	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	270	113170761	28042670	6438	14423										
SVEP1	79987	broad.mit.edu	37	chr9	113174010	113174010	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgtcaagaccagcaagaGtatagctgtgaggttgggaa	15	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113174010G>T	ENST00000401783.2	-	37	6317	c.5981C>A	c.(5980-5982)aCt>aAt	p.T1994N	SVEP1_ENST00000374469.1_Missense_Mutation_p.T1971N|SVEP1_ENST00000297826.5_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1994	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.T1997N(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACCAGCAAGAGTATAGCTGTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											23	25	24					9																	113174010		1917	4117	6034	112213831	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5981C>A	9.37:g.113174010G>T	ENSP00000384917:p.Thr1994Asn		112213831	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034599	0.35893	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.64803	-0.12;-0.12	5.58	4.68	0.58851	Complement control module (2);Sushi/SCR/CCP (3);	0.045591	0.85682	D	0.000000	T	0.72882	0.3516	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69327	-0.5174	10	0.22109	T	0.4	.	14.1846	0.65598	0.0718:0.0:0.9282:0.0	.	1994	Q4LDE5	SVEP1_HUMAN	N	1994;1971	ENSP00000384917:T1994N;ENSP00000363593:T1971N	ENSP00000363593:T1971N	T	-	2	0	SVEP1	112213831	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	6.388000	0.73195	1.366000	0.46076	0.591000	0.81541	ACT		0.433	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113174010	G	T	113174010	3	4	61	1	0	0	0	0	1	0	0	0	15459	1029	36	2	4782	2	SVEP1	9	113174010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3249	113174010	28039421	6439	14424										
SVEP1	79987	broad.mit.edu	37	chr9	113197541	113197541	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaacaaaatatgctcttaGaatcgatcttcactttcccc	4	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113197541G>T	ENST00000401783.2	-	29	5204	c.4868C>A	c.(4867-4869)tCt>tAt	p.S1623Y	SVEP1_ENST00000374469.1_Missense_Mutation_p.S1600Y	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1623	Pentaxin.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.S1626Y(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TATGCTCTTAGAATCGATCTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											107	101	103					9																	113197541		1881	4098	5979	112237362	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4868C>A	9.37:g.113197541G>T	ENSP00000384917:p.Ser1623Tyr		112237362	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.390768	0.01185	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.58940	0.3;0.3	5.41	3.53	0.40419	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.656803	0.16649	N	0.205320	T	0.45316	0.1336	L	0.33485	1.01	0.22317	N	0.999202	B	0.14012	0.009	B	0.12156	0.007	T	0.20706	-1.0267	10	0.16420	T	0.52	.	14.0188	0.64541	0.0:0.0:0.4748:0.5252	.	1623	Q4LDE5	SVEP1_HUMAN	Y	1623;1600	ENSP00000384917:S1623Y;ENSP00000363593:S1600Y	ENSP00000363593:S1600Y	S	-	2	0	SVEP1	112237362	1.000000	0.71417	0.300000	0.25030	0.695000	0.40330	1.994000	0.40757	0.620000	0.30215	0.563000	0.77884	TCT		0.438	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113197541	G	T	113197541	3	4	61	1	0	0	0	0	1	0	0	0	15459	942	33	2	5927	2	SVEP1	9	113197541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23531	113197541	28015890	6440	14425										
SVEP1	79987	broad.mit.edu	37	chr9	113212479	113212479	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccccaacctggtcttcacaGactgcattatttaagcatgg	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113212479G>T	ENST00000401783.2	-	24	4299	c.3963C>A	c.(3961-3963)gtC>gtA	p.V1321V	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Silent_p.V1321V|SVEP1_ENST00000374469.1_Silent_p.V1298V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1321	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.V1321V(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGTCTTCACAGACTGCATTAT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	9											155	146	149					9																	113212479		1874	4107	5981	112252300	SO:0001819	synonymous_variant	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.3963C>A	9.37:g.113212479G>T			112252300	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																				0.468	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113212479	G	T	113212479	2	4	61	1	0	0	0	0	0	0	0	1	15459	929	33	2		2	SVEP1	9	113212479	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14938	113212479	28000952	6441	14426										
MUSK	4593	broad.mit.edu	37	chr9	113538923	113538923	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccttcagattataacaaaGaaaacctaaaaagtaagtaa	4	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113538923G>T	ENST00000374448.4	+	11	1506	c.1372G>T	c.(1372-1374)Gaa>Taa	p.E458*	MUSK_ENST00000189978.5_Nonsense_Mutation_p.E458*|MUSK_ENST00000416899.2_Intron|MUSK_ENST00000374438.1_Intron	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	458					cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E458*(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TTATAACAAAGAAAACCTAAA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											121	127	125					9																	113538923		1830	4084	5914	112578744	SO:0001587	stop_gained	4593			AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1372G>T	9.37:g.113538923G>T	ENSP00000363571:p.Glu458*		112578744	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Nonsense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	39	7.730559	0.98459	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335	.	.	.	5.92	5.03	0.67393	.	0.265899	0.42964	D	0.000639	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	11.3307	0.49475	0.0836:0.0:0.9164:0.0	.	.	.	.	X	464;458;458	.	ENSP00000189978:E464X	E	+	1	0	MUSK	112578744	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.240000	0.65378	1.517000	0.48917	0.655000	0.94253	GAA		0.343	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	113538923	G	T	113538923	4	4	61	1	0	0	0	0	0	1	0	0	10019	943	33	2	1446	2	MUSK	9	113538923	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	326444	113538923	27674508	6442	14427										
LPAR1	1902	broad.mit.edu	37	chr9	113637917	113637917	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaggagaaggaagaatttCtcataggccagcacgtcgca	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113637917C>A	ENST00000374431.3	-	5	1262	c.879G>T	c.(877-879)gaG>gaT	p.E293D	LPAR1_ENST00000541779.1_Missense_Mutation_p.E294D|LPAR1_ENST00000374430.2_Missense_Mutation_p.E293D|LPAR1_ENST00000538760.1_Missense_Mutation_p.E294D|LPAR1_ENST00000358883.4_Missense_Mutation_p.E293D	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	293					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.E293D(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						GGAAGAATTTCTCATAGGCCA	0.488																																					NSCLC(115;661 2323 9836 34256)											1	Substitution - Missense(1)	large_intestine(1)	9											112	111	112					9																	113637917		2203	4300	6503	112677738	SO:0001583	missense	1902			U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3166	protein-coding gene	gene with protein product		602282	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.879G>T	9.37:g.113637917C>A	ENSP00000363553:p.Glu293Asp		112677738	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	37	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992196	0.54041	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	6.06	2.82	0.32997	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78991	0.4371	M	0.62723	1.935	0.52501	D	0.999959	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.74348	0.983;0.983;0.983	T	0.76424	-0.2964	10	0.33940	T	0.23	.	11.6587	0.51334	0.0:0.7211:0.0:0.2789	.	294;294;293	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	D	293;294;293;293;275;294	ENSP00000363553:E293D;ENSP00000445697:E294D;ENSP00000363552:E293D;ENSP00000351755:E293D;ENSP00000440201:E294D	ENSP00000351755:E293D	E	-	3	2	LPAR1	112677738	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.788000	0.26872	0.896000	0.36366	0.655000	0.94253	GAG		0.488	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159		A	113637917	C	A	113637917	3	1	61	1	0	0	0	0	1	0	0	0	8933	912	32	2	219	2	LPAR1	9	113637917	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98994	113637917	27575514	6443	14428										
LPAR1	1902	broad.mit.edu	37	chr9	113704061	113704061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaccgtaatgtgcctctCgattgcaatagccagtaagt	9	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:113704061C>T	ENST00000374431.3	-	4	816	c.433G>A	c.(433-435)Gag>Aag	p.E145K	LPAR1_ENST00000541779.1_Missense_Mutation_p.E146K|LPAR1_ENST00000374430.2_Missense_Mutation_p.E145K|LPAR1_ENST00000538760.1_Missense_Mutation_p.E146K|LPAR1_ENST00000358883.4_Missense_Mutation_p.E145K	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	145					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.E145K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						ATGTGCCTCTCGATTGCAATA	0.537																																					NSCLC(115;661 2323 9836 34256)											1	Substitution - Missense(1)	large_intestine(1)	9											119	107	111					9																	113704061		2203	4300	6503	112743882	SO:0001583	missense	1902			U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3166	protein-coding gene	gene with protein product		602282	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.433G>A	9.37:g.113704061C>T	ENSP00000363553:p.Glu145Lys		112743882	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	37	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.920523	0.92249	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760;ENST00000441240	T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	5.53	4.64	0.57946	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88347	0.6412	M	0.91510	3.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90614	0.4554	10	0.87932	D	0	.	13.4093	0.60933	0.0:0.9247:0.0:0.0753	.	146;146;145	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	K	145;146;145;145;127;146;145	ENSP00000363553:E145K;ENSP00000445697:E146K;ENSP00000363552:E145K;ENSP00000351755:E145K;ENSP00000440201:E146K;ENSP00000401810:E145K	ENSP00000351755:E145K	E	-	1	0	LPAR1	112743882	1.000000	0.71417	0.973000	0.42090	0.998000	0.95712	7.818000	0.86416	1.357000	0.45904	0.655000	0.94253	GAG		0.537	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159		T	113704061	C	T	113704061	3	4	61	1	0	0	0	0	1	0	0	0	8933	893	31	1	669	1	LPAR1	9	113704061	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66144	113704061	27509370	6444	14429										
OR2K2	26248	broad.mit.edu	37	chr9	114089768	114089768	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatagggacccaatcagaGatgttcgtgtgtttgatgca	11	8	1	2	rs545492183		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114089768G>A	ENST00000374428.1	-	1	1032	c.1033C>T	c.(1033-1035)Ctc>Ttc	p.L345F	OR2K2_ENST00000302681.1_Missense_Mutation_p.L316F			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	345						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L316F(1)|p.L345I(1)|p.L316I(1)|p.L345F(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						CCCAATCAGAGATGTTCGTGT	0.408													G|||	1	0.000199681	0	0	5008	,	,		20124	0		0	False		,,,				2504	0.001															4	Substitution - Missense(4)	large_intestine(4)	9											102	87	92					9																	114089768		2203	4300	6503	113129589	SO:0001583	missense	26248			X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"GPCR / Class A : Olfactory receptors"	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.1033C>T	9.37:g.114089768G>A	ENSP00000363550:p.Leu345Phe		113129589	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		.	.	.	.	.	.	.	.	.	.	G	10.62	1.401500	0.25291	.	.	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.10860	2.83;2.86	4.84	-2.75	0.05914	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39603	-0.9606	9	0.66056	D	0.02	.	0.993	0.01461	0.3298:0.2714:0.2604:0.1385	.	345	Q8NGT1	OR2K2_HUMAN	F	316;345	ENSP00000305055:L316F;ENSP00000363550:L345F	ENSP00000305055:L316F	L	-	1	0	OR2K2	113129589	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.654000	0.05354	-0.410000	0.07542	-0.176000	0.13171	CTC		0.408	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		A	114089768	G	A	114089768	3	1	61	1	0	0	0	0	1	0	0	0	11036	942	33	3	7	3	OR2K2	9	114089768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	385707	114089768	27123663	6445	14430										
KIAA0368	23392	broad.mit.edu	37	chr9	114151924	114151924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaactggtaacgataaagtCgaggaactagctgaggcaga	12	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114151924C>T	ENST00000338205.5	-	30	3578	c.3359G>A	c.(3358-3360)cGa>cAa	p.R1120Q	KIAA0368_ENST00000259335.4_Missense_Mutation_p.R1298Q|KIAA0368_ENST00000374378.3_5'UTR			Q5VYK3	ECM29_HUMAN	KIAA0368	1126					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.R1298Q(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						ACGATAAAGTCGAGGAACTAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											75	75	75					9																	114151924		1940	4141	6081	113191745	SO:0001583	missense	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.3359G>A	9.37:g.114151924C>T	ENSP00000339889:p.Arg1120Gln		113191745	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	C	37	6.117776	0.97300	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.32515	1.45	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.64740	-0.6336	10	0.72032	D	0.01	.	19.4063	0.94648	0.0:1.0:0.0:0.0	.	595	B3KXF2	.	Q	1120;1298;595	ENSP00000259335:R1298Q	ENSP00000259335:R1298Q	R	-	2	0	KIAA0368	113191745	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.569000	0.86673	0.655000	0.94253	CGA		0.448	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		T	114151924	C	T	114151924	3	4	61	1	0	0	0	0	1	0	0	0	8192	884	31	1	2240	1	KIAA0368	9	114151924	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62156	114151924	27061507	6446	14431										
ZNF483	158399	broad.mit.edu	37	chr9	114304327	114304327	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaaagtcctgagtcactCttcagctcttactgaacatc	8	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114304327C>A	ENST00000309235.5	+	6	1270	c.1112C>A	c.(1111-1113)tCt>tAt	p.S371Y	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S371Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						CTGAGTCACTCTTCAGCTCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											86	95	92					9																	114304327		2203	4300	6503	113344148	SO:0001583	missense	158399			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1112C>A	9.37:g.114304327C>A	ENSP00000311679:p.Ser371Tyr		113344148	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	C	3.252	-0.153001	0.06585	.	.	ENSG00000173258	ENST00000309235	T	0.29397	1.57	4.55	2.69	0.31865	.	0.713203	0.12362	N	0.475512	T	0.21801	0.0525	L	0.56280	1.765	0.09310	N	0.999999	P	0.37398	0.593	B	0.34038	0.174	T	0.13045	-1.0524	10	0.17369	T	0.5	-1.6775	3.4376	0.07452	0.1758:0.5616:0.1703:0.0924	.	371	Q8TF39	ZN483_HUMAN	Y	371	ENSP00000311679:S371Y	ENSP00000311679:S371Y	S	+	2	0	ZNF483	113344148	0.000000	0.05858	0.004000	0.12327	0.150000	0.21749	-0.645000	0.05409	0.834000	0.34852	0.655000	0.94253	TCT		0.428	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		A	114304327	C	A	114304327	3	1	61	1	0	0	0	0	1	0	0	0	17975	913	32	2	1130	2	ZNF483	9	114304327	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152403	114304327	26909104	6447	14432										
PTGR1	22949	broad.mit.edu	37	chr9	114332476	114332476	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcctgatagataacaatCtctgggggtgggcctgtgaa	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114332476C>A	ENST00000407693.2	-	9	1036	c.774G>T	c.(772-774)gaG>gaT	p.E258D	PTGR1_ENST00000309195.5_Missense_Mutation_p.E258D|PTGR1_ENST00000238248.3_Missense_Mutation_p.E135D|ZNF483_ENST00000358151.4_Intron|PTGR1_ENST00000538962.1_Missense_Mutation_p.E258D	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	258					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)	p.E258D(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						AGATAACAATCTCTGGGGGTG	0.532																																					Ovarian(200;132 2151 7551 19220 46064)											1	Substitution - Missense(1)	large_intestine(1)	9											39	40	39					9																	114332476		2203	4300	6503	113372297	SO:0001583	missense	22949			D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.774G>T	9.37:g.114332476C>A	ENSP00000385763:p.Glu258Asp		113372297	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	37	CCDS6779.1	.	.	.	.	.	.	.	.	.	.	C	9.708	1.156282	0.21454	.	.	ENSG00000106853	ENST00000538962;ENST00000309195;ENST00000407693;ENST00000374324;ENST00000238248	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	3.9	0.00518	0.14061	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.635660	0.16374	N	0.217212	T	0.21186	0.0510	L	0.46947	1.48	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.002;0.001;0.001	T	0.30937	-0.9961	10	0.13853	T	0.58	-0.0547	7.9955	0.30265	0.0:0.6468:0.0:0.3532	.	258;258;135;258	F5GY50;B4DPK3;Q5JVP3;Q14914	.;.;.;PTGR1_HUMAN	D	258;258;258;135;135	ENSP00000440281:E258D;ENSP00000311572:E258D;ENSP00000385763:E258D;ENSP00000238248:E135D	ENSP00000238248:E135D	E	-	3	2	PTGR1	113372297	0.000000	0.05858	0.006000	0.13384	0.288000	0.27193	-0.321000	0.08018	0.007000	0.14760	0.460000	0.39030	GAG		0.532	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			A	114332476	C	A	114332476	3	1	61	1	0	0	0	0	1	0	0	0	12788	912	32	2	254	2	PTGR1	9	114332476	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28149	114332476	26880955	6448	14433										
DNAJC25	548645	broad.mit.edu	37	chr9	114411796	114411796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagccacagtgcccaagtacCgtatccaagctacagagatt	8	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114411796C>T	ENST00000313525.3	+	3	609	c.553C>T	c.(553-555)Cgt>Tgt	p.R185C	DNAJC25-GNG10_ENST00000374294.3_Intron|DNAJC25_ENST00000556107.1_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	185						integral component of membrane (GO:0016021)		p.R185C(1)		kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						GCCCAAGTACCGTATCCAAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	9											45	43	44					9																	114411796		1862	4103	5965	113451617	SO:0001583	missense	548645				CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.553C>T	9.37:g.114411796C>T	ENSP00000320650:p.Arg185Cys		113451617	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	37	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430744	0.83776	.	.	ENSG00000059769	ENST00000313525	T	0.56103	0.48	6.17	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.58163	0.2103	M	0.87758	2.905	0.80722	D	1	B	0.28850	0.225	B	0.20184	0.028	T	0.63180	-0.6695	10	0.87932	D	0	-9.6171	13.9053	0.63831	0.0:0.9302:0.0:0.0698	.	185	Q9H1X3	DJC25_HUMAN	C	185	ENSP00000320650:R185C	ENSP00000320650:R185C	R	+	1	0	DNAJC25	113451617	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.565000	0.67365	1.627000	0.50400	0.655000	0.94253	CGT		0.408	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		T	114411796	C	T	114411796	3	4	61	1	0	0	0	0	1	0	0	0	4654	652	23	1	563	1	DNAJC25	9	114411796	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79320	114411796	26801635	6449	14434										
C9orf84	158401	broad.mit.edu	37	chr9	114454043	114454043	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcacatgtgaggccttcaGactcatctgatagacatttt	7	9	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114454043G>A	ENST00000318737.4	-	25	4150	c.4022C>T	c.(4021-4023)tCt>tTt	p.S1341F	C9orf84_ENST00000394777.4_Missense_Mutation_p.S1267F|C9orf84_ENST00000394779.3_Missense_Mutation_p.S1302F|C9orf84_ENST00000374287.3_Missense_Mutation_p.S1341F	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1341								p.S1302F(1)		breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GAGGCCTTCAGACTCATCTGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											75	77	76					9																	114454043		2203	4299	6502	113493864	SO:0001583	missense	158401			AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.4022C>T	9.37:g.114454043G>A	ENSP00000322108:p.Ser1341Phe		113493864	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	G	0.079	-1.187317	0.01620	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04317	3.65;3.65;3.66;3.66	5.29	1.67	0.24075	.	1.353740	0.05203	N	0.505378	T	0.02571	0.0078	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45145	-0.9281	10	0.34782	T	0.22	3.9055	7.5884	0.28006	0.7501:0.0:0.2499:0.0	.	1267;1341;1302	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	F	1302;1267;955;1341;1341	ENSP00000378259:S1302F;ENSP00000378257:S1267F;ENSP00000363405:S1341F;ENSP00000322108:S1341F	ENSP00000322108:S1341F	S	-	2	0	C9orf84	113493864	0.016000	0.18221	0.000000	0.03702	0.015000	0.08874	1.870000	0.39529	0.132000	0.18615	-0.483000	0.04790	TCT		0.378	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		A	114454043	G	A	114454043	3	1	61	1	0	0	0	0	1	0	0	0	2506	942	33	3	320	3	C9orf84	9	114454043	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42247	114454043	26759388	6450	14435										
C9orf84	158401	broad.mit.edu	37	chr9	114462234	114462234	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacataggaaaagaatacCtttacatccagttcttcaga	5	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114462234C>A	ENST00000318737.4	-	22	3119	c.2991G>T	c.(2989-2991)aaG>aaT	p.K997N	C9orf84_ENST00000394777.4_Splice_Site_p.K923N|C9orf84_ENST00000394779.3_Splice_Site_p.K958N|C9orf84_ENST00000374287.3_Splice_Site_p.K997N	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	997								p.K958N(1)		breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						AAAAGAATACCTTTACATCCA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	9											96	100	99					9																	114462234		2203	4300	6503	113502055	SO:0001630	splice_region_variant	158401			AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2991+1G>T	9.37:g.114462234C>A			113502055	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785881	0.90282	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.05649	3.41;3.45;3.42;3.42	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000017	T	0.15869	0.0382	N	0.24115	0.695	0.54753	D	0.999983	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.07927	-1.0747	9	.	.	.	-12.5564	20.2585	0.98435	0.0:1.0:0.0:0.0	.	923;997;958	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	N	958;923;611;997;997	ENSP00000378259:K958N;ENSP00000378257:K923N;ENSP00000363405:K997N;ENSP00000322108:K997N	.	K	-	3	2	C9orf84	113502055	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.260000	0.72502	2.894000	0.99253	0.655000	0.94253	AAG		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	Missense_Mutation	A	114462234	C	A	114462234	5	1	61	1	0	0	0	0	0	0	1	0	2506	695	24	2	1363	2	C9orf84	9	114462234	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8191	114462234	26751197	6451	14436										
UGCG	7357	broad.mit.edu	37	chr9	114691815	114691815	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacatccaagatactatatCtctgccaatgtaactggttt	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114691815C>A	ENST00000374279.3	+	6	1044	c.594C>A	c.(592-594)atC>atA	p.I198I	MIR4668_ENST00000582284.1_RNA|UGCG_ENST00000495085.1_3'UTR	NM_003358.1	NP_003349.1	Q16739	CEGT_HUMAN	UDP-glucose ceramide glucosyltransferase	198					epidermis development (GO:0008544)|glucosylceramide biosynthetic process (GO:0006679)|glycosphingolipid biosynthetic process (GO:0006688)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ceramide glucosyltransferase activity (GO:0008120)	p.I198I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	12				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	GATACTATATCTCTGCCAATG	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	9											117	111	113					9																	114691815		2203	4300	6503	113731636	SO:0001819	synonymous_variant	7357			D50840	CCDS6782.1	9q31	2014-03-13			ENSG00000148154	ENSG00000148154	2.4.1.80	"Glycosyltransferase family 2 domain containing"	12524	protein-coding gene	gene with protein product	"glucosylceramide synthase", "ceramide glucosyltransferase"	602874				8643456, 9605861	Standard	NM_003358		Approved	GCS	uc004bft.3	Q16739	OTTHUMG00000020498	ENST00000374279.3:c.594C>A	9.37:g.114691815C>A			113731636	Q5T258	Silent	SNP	ENST00000374279.3	37	CCDS6782.1																																																																																				0.368	UGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053661.1	NM_003358		A	114691815	C	A	114691815	2	1	61	1	0	0	0	0	0	0	0	1	16979	903	32	2		2	UGCG	9	114691815	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	229581	114691815	26521616	6452	14437										
SUSD1	64420	broad.mit.edu	37	chr9	114804237	114804237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcagcagcatgagtgacGaatctgtgggacaaaaccac	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114804237G>A	ENST00000374270.3	-	16	2325	c.2153C>T	c.(2152-2154)tCg>tTg	p.S718L	SUSD1_ENST00000374264.2_Missense_Mutation_p.R740C|SUSD1_ENST00000374263.3_Missense_Mutation_p.R705C	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	718						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.S718L(1)	SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CATGAGTGACGAATCTGTGGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	9											129	115	120					9																	114804237		2203	4300	6503	113844058	SO:0001583	missense	64420			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.2153C>T	9.37:g.114804237G>A	ENSP00000363388:p.Ser718Leu		113844058	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Missense_Mutation	SNP	ENST00000374270.3	37	CCDS6783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.33|16.33	3.094074|3.094074	0.56075|0.56075	.|.	.|.	ENSG00000106868|ENSG00000106868	ENST00000374263;ENST00000374264|ENST00000355396;ENST00000374270	T;T|T	0.75477|0.38077	0.79;-0.94|1.16	5.08|5.08	4.17|4.17	0.49024|0.49024	.|.	1.144410|.	0.06667|.	N|.	0.765560|.	T|T	0.30510|0.30510	0.0767|0.0767	L|L	0.45581|0.45581	1.43|1.43	0.28303|0.28303	N|N	0.923025|0.923025	D;B|B	0.76494|0.10296	0.999;0.012|0.003	P;B|B	0.62014|0.04013	0.897;0.003|0.001	T|T	0.17745|0.17745	-1.0359|-1.0359	10|8	0.87932|.	D|.	0|.	-0.4096|-0.4096	9.8051|9.8051	0.40789|0.40789	0.0966:0.0:0.9034:0.0|0.0966:0.0:0.9034:0.0	.|.	705;740|718	F8WAQ1;Q6UWL2-2|Q6UWL2	.;.|SUSD1_HUMAN	C|L	705;740|688;718	ENSP00000363381:R705C;ENSP00000363382:R740C|ENSP00000363388:S718L	ENSP00000363381:R705C|.	R|S	-|-	1|2	0|0	SUSD1|SUSD1	113844058|113844058	0.888000|0.888000	0.30383|0.30383	0.022000|0.022000	0.16811|0.16811	0.927000|0.927000	0.56198|0.56198	2.771000|2.771000	0.47670|0.47670	1.112000|1.112000	0.41740|0.41740	0.561000|0.561000	0.74099|0.74099	CGT|TCG		0.552	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		A	114804237	G	A	114804237	3	1	61	1	0	0	0	0	1	0	0	0	15446	1059	37	1	98	1	SUSD1	9	114804237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112422	114804237	26409194	6453	14438										
SUSD1	64420	broad.mit.edu	37	chr9	114864551	114864551	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaaacttccatcatcttCtaagagatcaacttctaaaa	3	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114864551C>A	ENST00000374270.3	-	9	1358	c.1186G>T	c.(1186-1188)Gaa>Taa	p.E396*	SUSD1_ENST00000374264.2_Nonsense_Mutation_p.E396*|SUSD1_ENST00000374263.3_Nonsense_Mutation_p.E396*	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	396						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.E396*(1)	SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CCATCATCTTCTAAGAGATCA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											46	47	47					9																	114864551		2202	4296	6498	113904372	SO:0001587	stop_gained	64420			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1186G>T	9.37:g.114864551C>A	ENSP00000363388:p.Glu396*		113904372	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Nonsense_Mutation	SNP	ENST00000374270.3	37	CCDS6783.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.26|17.26|17.26	3.343856|3.343856|3.343856	0.61073|0.61073|0.61073	.|.|.	.|.|.	ENSG00000106868|ENSG00000106868|ENSG00000106868	ENST00000374270;ENST00000374263;ENST00000374264|ENST00000355396|ENST00000415074	.|.|.	.|.|.	.|.|.	4.41|4.41|4.41	4.41|4.41|4.41	0.53225|0.53225|0.53225	.|.|.	0.348019|.|.	0.20765|.|.	N|.|.	0.086085|.|.	.|T|.	.|0.62368|.	.|0.2422|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|.	.|0.70066|.	.|-0.4974|.	.|3|.	0.40728|.|.	T|.|.	0.16|.|.	-14.079|-14.079|-14.079	12.8623|12.8623|12.8623	0.57920|0.57920|0.57920	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|I|Y	396|379|222	.|.|.	ENSP00000363381:E396X|.|.	E|R|X	-|-|-	1|2|3	0|0|2	SUSD1|SUSD1|SUSD1	113904372|113904372|113904372	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.617000|0.617000|0.617000	0.37484|0.37484|0.37484	0.962000|0.962000|0.962000	0.29280|0.29280|0.29280	2.161000|2.161000|2.161000	0.67846|0.67846|0.67846	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAA|AGA|TAG		0.363	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		A	114864551	C	A	114864551	4	1	61	1	0	0	0	0	0	1	0	0	15446	922	32	2	1093	2	SUSD1	9	114864551	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60314	114864551	26348880	6454	14439										
SUSD1	64420	broad.mit.edu	37	chr9	114911559	114911561	+	In_Frame_Del	DEL	TTG	TTG	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcgttgggaatgaatgtcTtgttgttgtttgtggctcga							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	TTG	TTG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:114911559_114911561delTTG	ENST00000374270.3	-	3	508_510	c.336_338delCAA	c.(334-339)aacaag>aag	p.N112del	SUSD1_ENST00000374264.2_In_Frame_Del_p.N112del|SUSD1_ENST00000374263.3_In_Frame_Del_p.N112del	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	112	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.N112delN(1)	SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AATGAATGTCTTGTTGTTGTTTG	0.507																																																1	Deletion - In frame(1)	large_intestine(1)	9																																								113951382	SO:0001651	inframe_deletion	64420			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.336_338delCAA	9.37:g.114911565_114911567delTTG	ENSP00000363388:p.Asn112del		113951380	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	In_Frame_Del	DEL	ENST00000374270.3	37	CCDS6783.1																																																																																				0.507	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		-	114911561	TTG	-	114911559	7	5	61	1	0	1	0	1	0	0	0	0	15446	1609	56	0	1965	0	SUSD1	9	114911559	In_Frame_Del	DEL	TTG	TCGA-AG-A002-01A-01W-A00K-09	47008	114911559	26301872	6455	14440										
C9orf80	58493	broad.mit.edu	37	chr9	115449849	115449849	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggcgaggtaaaacaggaAgaataaggttcccaaatgca	11	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115449849A>C	ENST00000374242.4	-	5	589	c.284T>G	c.(283-285)cTt>cGt	p.L95R	INIP_ENST00000497712.2_5'UTR|INIP_ENST00000374236.1_Missense_Mutation_p.L65R|INIP_ENST00000374238.1_Missense_Mutation_p.F35V|INIP_ENST00000374234.1_Missense_Mutation_p.F35V	NM_021218.1	NP_067041.1	Q9NRY2	SOSSC_HUMAN	INTS3 and NABP interacting protein	95					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)		p.L95R(1)									TAAAACAGGAAGAATAAGGTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	9											128	124	125					9																	115449849		2203	4300	6503	114489670	SO:0001583	missense	58493			AF161411	CCDS6785.1	9q32	2012-06-19	2012-06-19	2012-06-19	ENSG00000148153	ENSG00000148153			24994	protein-coding gene	gene with protein product	"hSSB-interacting protein 1", "sensor of single-strand DNA complex subunit C", "minute INTS3/hSSB-associated element"	613273	"chromosome 9 open reading frame 80"	C9orf80		11042152	Standard	NM_021218		Approved	HSPC043, hSSBIP1, SOSS-C, MISE	uc004bgg.3	Q9NRY2	OTTHUMG00000020509	ENST00000374242.4:c.284T>G	9.37:g.115449849A>C	ENSP00000363360:p.Leu95Arg		114489670	Q5VWJ7|Q96E04|Q9P090	Missense_Mutation	SNP	ENST00000374242.4	37	CCDS6785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.6|23.6	4.434769|4.434769	0.83885|0.83885	.|.	.|.	ENSG00000148153|ENSG00000148153	ENST00000374238;ENST00000374234|ENST00000374242;ENST00000374236	.|.	.|.	.|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65554|0.65554	0.2702|0.2702	M|M	0.72894|0.72894	2.215|2.215	0.36737|0.36737	D|D	0.882042|0.882042	.|P	.|0.44429	.|0.835	.|P	.|0.47645	.|0.553	T|T	0.76035|0.76035	-0.3106|-0.3106	6|9	0.87932|0.87932	D|D	0|0	-19.5197|-19.5197	15.2564|15.2564	0.73588|0.73588	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|95	.|Q9NRY2	.|SOSSC_HUMAN	V|R	35|95;65	.|.	ENSP00000363351:F35V|ENSP00000363353:L65R	F|L	-|-	1|2	0|0	C9orf80|C9orf80	114489670|114489670	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.904000|7.904000	0.87408|0.87408	2.326000|2.326000	0.78906|0.78906	0.472000|0.472000	0.43445|0.43445	TTC|CTT		0.383	INIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053692.2	NM_021218		C	115449849	A	C	115449849	3	2	61	1	0	0	0	0	1	0	0	0	2504	72	3	4	34	4	C9orf80	9	115449849	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	538290	115449849	25763582	6456	14441										
C9orf80	58493	broad.mit.edu	37	chr9	115451893	115451893	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagagggtctcgagagtgCaatgctaaaatgggaatctt	13	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115451893C>T	ENST00000374242.4	-	4	438	c.133G>A	c.(133-135)Gca>Aca	p.A45T	INIP_ENST00000497712.2_5'UTR|INIP_ENST00000374236.1_Missense_Mutation_p.A15T|INIP_ENST00000374238.1_Intron|INIP_ENST00000374234.1_Intron	NM_021218.1	NP_067041.1	Q9NRY2	SOSSC_HUMAN	INTS3 and NABP interacting protein	45					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)		p.A45T(1)									CTCGAGAGTGCAATGCTAAAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											111	101	104					9																	115451893		2203	4300	6503	114491714	SO:0001583	missense	58493			AF161411	CCDS6785.1	9q32	2012-06-19	2012-06-19	2012-06-19	ENSG00000148153	ENSG00000148153			24994	protein-coding gene	gene with protein product	"hSSB-interacting protein 1", "sensor of single-strand DNA complex subunit C", "minute INTS3/hSSB-associated element"	613273	"chromosome 9 open reading frame 80"	C9orf80		11042152	Standard	NM_021218		Approved	HSPC043, hSSBIP1, SOSS-C, MISE	uc004bgg.3	Q9NRY2	OTTHUMG00000020509	ENST00000374242.4:c.133G>A	9.37:g.115451893C>T	ENSP00000363360:p.Ala45Thr		114491714	Q5VWJ7|Q96E04|Q9P090	Missense_Mutation	SNP	ENST00000374242.4	37	CCDS6785.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.421151	0.42918	.	.	ENSG00000148153	ENST00000374242;ENST00000374236	.	.	.	5.74	3.73	0.42828	.	0.320592	0.38058	N	0.001836	T	0.40932	0.1137	L	0.29908	0.895	0.50171	D	0.999859	B	0.13594	0.008	B	0.12837	0.008	T	0.29427	-1.0012	9	0.02654	T	1	-0.6776	14.1458	0.65349	0.4601:0.5399:0.0:0.0	.	45	Q9NRY2	SOSSC_HUMAN	T	45;15	.	ENSP00000363353:A15T	A	-	1	0	C9orf80	114491714	0.807000	0.29009	0.026000	0.17262	0.185000	0.23345	0.852000	0.27764	0.703000	0.31848	0.579000	0.79373	GCA		0.423	INIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053692.2	NM_021218		T	115451893	C	T	115451893	3	4	61	1	0	0	0	0	1	0	0	0	2504	710	25	3	189	3	C9orf80	9	115451893	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2044	115451893	25761538	6457	14442										
ZFP37	7539	broad.mit.edu	37	chr9	115805204	115805204	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctccccagtatgagttCtctgatgtacaatgaggtga	10	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115805204C>A	ENST00000374227.3	-	4	1721	c.1694G>T	c.(1693-1695)aGa>aTa	p.R565I	ZFP37_ENST00000553380.1_Missense_Mutation_p.R580I|ZFP37_ENST00000555206.1_Missense_Mutation_p.R566I	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	565					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R565I(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						AGTATGAGTTCTCTGATGTAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											124	117	120					9																	115805204		2203	4300	6503	114845025	SO:0001583	missense	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.1694G>T	9.37:g.115805204C>A	ENSP00000363344:p.Arg565Ile		114845025	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	37	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.153043	0.57259	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.24908	1.83;1.83;1.83	4.43	4.43	0.53597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000187	T	0.50718	0.1632	M	0.73598	2.24	0.53005	D	0.999964	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.79784	0.993;0.993;0.942	T	0.53012	-0.8498	10	0.66056	D	0.02	-23.9685	15.373	0.74581	0.0:1.0:0.0:0.0	.	566;580;565	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	I	565;566;580	ENSP00000363344:R565I;ENSP00000451310:R566I;ENSP00000452552:R580I	ENSP00000363344:R565I	R	-	2	0	ZFP37	114845025	0.000000	0.05858	1.000000	0.80357	0.976000	0.68499	0.597000	0.24059	2.752000	0.94435	0.655000	0.94253	AGA		0.403	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		A	115805204	C	A	115805204	3	1	61	1	0	0	0	0	1	0	0	0	17687	913	32	2	202	2	ZFP37	9	115805204	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	353311	115805204	25408227	6458	14443										
ZFP37	7539	broad.mit.edu	37	chr9	115805941	115805941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcattacattcatatggTttctccccagtatgaactct	4	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115805941T>C	ENST00000374227.3	-	4	984	c.957A>G	c.(955-957)aaA>aaG	p.K319K	ZFP37_ENST00000553380.1_Silent_p.K334K|ZFP37_ENST00000555206.1_Silent_p.K320K	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K319K(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						ATTCATATGGTTTCTCCCCAG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	9											145	136	139					9																	115805941		2203	4300	6503	114845762	SO:0001819	synonymous_variant	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.957A>G	9.37:g.115805941T>C			114845762	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	37	CCDS6787.1																																																																																				0.403	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		C	115805941	T	C	115805941	2	2	61	1	0	0	0	0	0	0	0	1	17687	1722	60	4		4	ZFP37	9	115805941	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	737	115805941	25407490	6459	14444										
ZFP37	7539	broad.mit.edu	37	chr9	115806154	115806154	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacagcataatttgtcatgTtttttgccagttttgttaca	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115806154T>C	ENST00000374227.3	-	4	771	c.744A>G	c.(742-744)aaA>aaG	p.K248K	ZFP37_ENST00000553380.1_Silent_p.K263K|ZFP37_ENST00000555206.1_Silent_p.K249K	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K248K(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						ATTTGTCATGTTTTTTGCCAG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	9											236	228	231					9																	115806154		2203	4300	6503	114845975	SO:0001819	synonymous_variant	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.744A>G	9.37:g.115806154T>C			114845975	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	37	CCDS6787.1																																																																																				0.363	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		C	115806154	T	C	115806154	2	2	61	1	0	0	0	0	0	0	0	1	17687	1722	60	4		4	ZFP37	9	115806154	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	213	115806154	25407277	6460	14445										
ZFP37	7539	broad.mit.edu	37	chr9	115818941	115818941	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacggtctctggctttgtcaGaatctggacgccgctggaga	13	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:115818941G>T	ENST00000374227.3	-	1	55	c.28C>A	c.(28-30)Ctg>Atg	p.L10M	ZFP37_ENST00000553380.1_Missense_Mutation_p.L10M|ZFP37_ENST00000555206.1_Missense_Mutation_p.L10M	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	10					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.L10M(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GGCTTTGTCAGAATCTGGACG	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	9											81	80	80					9																	115818941		2203	4300	6503	114858762	SO:0001583	missense	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.28C>A	9.37:g.115818941G>T	ENSP00000363344:p.Leu10Met		114858762	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	37	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	g	16.43	3.121628	0.56613	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.06449	3.41;3.36;3.3	3.19	2.28	0.28536	.	.	.	.	.	T	0.05135	0.0137	N	0.08118	0	0.09310	N	1	D;D;P	0.54964	0.969;0.969;0.948	P;P;B	0.50708	0.648;0.648;0.446	T	0.40924	-0.9537	9	0.36615	T	0.2	.	6.288	0.21043	0.1374:0.0:0.8626:0.0	.	10;10;10	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	M	10	ENSP00000363344:L10M;ENSP00000451310:L10M;ENSP00000452552:L10M	ENSP00000363344:L10M	L	-	1	2	ZFP37	114858762	0.031000	0.19500	0.238000	0.24106	0.062000	0.15995	0.676000	0.25247	0.896000	0.36366	0.558000	0.71614	CTG		0.682	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		T	115818941	G	T	115818941	3	4	61	1	0	0	0	0	1	0	0	0	17687	933	33	2	1880	2	ZFP37	9	115818941	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12787	115818941	25394490	6461	14446										
SLC31A1	1317	broad.mit.edu	37	chr9	116021075	116021075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaagtcacaagtcagcattCgctacaattccatgcctgtc	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116021075C>T	ENST00000374212.4	+	4	456	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Missense_Mutation_p.R102C	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	102					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)	p.R102C(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGTCAGCATTCGCTACAATTC	0.458																																					Ovarian(135;1049 1799 4519 17564 28677)											1	Substitution - Missense(1)	large_intestine(1)	9											151	130	137					9																	116021075		2203	4300	6503	115060896	SO:0001583	missense	1317			U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"Solute carriers"	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.304C>T	9.37:g.116021075C>T	ENSP00000363329:p.Arg102Cys		115060896	A8K8Z6|Q53GR5|Q5T1M4	Missense_Mutation	SNP	ENST00000374212.4	37	CCDS6789.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.840027	0.91117	.	.	ENSG00000136868	ENST00000374212;ENST00000374210	T;T	0.78246	-1.16;-1.16	5.82	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.86904	0.6045	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.939	D	0.87509	0.2438	10	0.62326	D	0.03	-10.4524	14.4332	0.67264	0.0:0.9282:0.0:0.0718	.	102;102	Q5T1M3;O15431	.;COPT1_HUMAN	C	102	ENSP00000363329:R102C;ENSP00000363327:R102C	ENSP00000363327:R102C	R	+	1	0	SLC31A1	115060896	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.175000	0.77632	2.745000	0.94114	0.650000	0.86243	CGC		0.458	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859		T	116021075	C	T	116021075	3	4	61	1	0	0	0	0	1	0	0	0	14600	884	31	1	314	1	SLC31A1	9	116021075	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	202134	116021075	25192356	6462	14447										
C9orf43	257169	broad.mit.edu	37	chr9	116190496	116190496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggaaaaaggaaccacttCgaaacaggtgagagtgtacc	12	7	0	1	rs538217577		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116190496C>T	ENST00000288462.4	+	12	1546	c.1100C>T	c.(1099-1101)tCg>tTg	p.S367L	C9orf43_ENST00000374165.1_Missense_Mutation_p.S367L	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	367								p.S367L(1)		breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						GGAACCACTTCGAAACAGGTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	9											164	156	159					9																	116190496		2203	4300	6503	115230317	SO:0001583	missense	257169			BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.1100C>T	9.37:g.116190496C>T	ENSP00000288462:p.Ser367Leu		115230317		Missense_Mutation	SNP	ENST00000288462.4	37	CCDS6796.1	.	.	.	.	.	.	.	.	.	.	C	5.170	0.216994	0.09810	.	.	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.47177	0.85;0.85	4.22	-5.8	0.02347	.	2.491310	0.01579	N	0.020996	T	0.21103	0.0508	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35525	-0.9785	10	0.05525	T	0.97	17.7815	6.5507	0.22431	0.1312:0.436:0.0:0.4328	.	367	Q8TAL5	CI043_HUMAN	L	367	ENSP00000363280:S367L;ENSP00000288462:S367L	ENSP00000288462:S367L	S	+	2	0	C9orf43	115230317	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.116000	0.03286	-1.214000	0.02614	-1.162000	0.01777	TCG		0.433	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786		T	116190496	C	T	116190496	3	4	61	1	0	0	0	0	1	0	0	0	2489	893	31	1	1142	1	C9orf43	9	116190496	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	169421	116190496	25022935	6463	14448										
RGS3	5998	broad.mit.edu	37	chr9	116358042	116358042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgcgatccaggcatgcaaGgaggtaggacctcagggcag	15	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116358042G>T	ENST00000374140.2	+	25	3617	c.3408G>T	c.(3406-3408)aaG>aaT	p.K1136N	RGS3_ENST00000343817.5_Missense_Mutation_p.K855N|RGS3_ENST00000350696.5_Missense_Mutation_p.K1136N|RGS3_ENST00000394646.3_Missense_Mutation_p.K529N|RGS3_ENST00000462143.1_Missense_Mutation_p.K457N|RGS3_ENST00000374134.3_Missense_Mutation_p.K457N|RGS3_ENST00000462403.1_Missense_Mutation_p.K249N|RGS3_ENST00000342620.5_Missense_Mutation_p.K106N	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1136	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.K1136N(1)|p.K1032N(1)|p.K249N(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						AGGCATGCAAGGAGGTAGGAC	0.582																																																3	Substitution - Missense(3)	large_intestine(3)	9											147	119	129					9																	116358042		2203	4300	6503	115397863	SO:0001583	missense	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3408G>T	9.37:g.116358042G>T	ENSP00000363255:p.Lys1136Asn		115397863	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.843881	0.51164	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000394646;ENST00000474719;ENST00000462143;ENST00000342620;ENST00000374134;ENST00000462403	T;T;T;T;T;T;T;T	0.01963	4.53;4.53;4.53;4.53;4.53;4.53;4.53;4.53	5.46	-0.374	0.12512	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.64402	D	0.000001	T	0.09598	0.0236	M	0.78637	2.42	0.53005	D	0.99996	P;P;D;D;D;D	0.89917	0.698;0.932;1.0;1.0;1.0;1.0	B;P;D;D;D;D	0.91635	0.329;0.859;0.997;0.999;0.999;0.998	T	0.00945	-1.1505	10	0.87932	D	0	.	9.544	0.39268	0.5353:0.0:0.4647:0.0	.	529;249;1032;855;1026;1136	B3KUB2;Q5VZ06;P49796-6;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	N	1136;1136;855;529;304;457;106;457;249	ENSP00000363255:K1136N;ENSP00000259406:K1136N;ENSP00000340284:K855N;ENSP00000378141:K529N;ENSP00000420356:K457N;ENSP00000343359:K106N;ENSP00000363249:K457N;ENSP00000436168:K249N	ENSP00000343359:K106N	K	+	3	2	RGS3	115397863	1.000000	0.71417	0.998000	0.56505	0.649000	0.38597	2.403000	0.44530	0.019000	0.15079	0.456000	0.33151	AAG		0.582	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116358042	G	T	116358042	3	4	61	1	0	0	0	0	1	0	0	0	13343	991	35	2	4178	2	RGS3	9	116358042	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167546	116358042	24855389	6464	14449										
ZNF618	114991	broad.mit.edu	37	chr9	116794994	116794994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagagacgaacagcagttCgcagaactccagcggtgagt	13	9	0	4	rs552764833		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116794994C>T	ENST00000374126.5	+	12	1253	c.1154C>T	c.(1153-1155)tCg>tTg	p.S385L	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Missense_Mutation_p.S292L			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S385L(1)|p.S292L(1)		breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						AACAGCAGTTCGCAGAACTCC	0.592													C|||	1	0.000199681	0	0	5008	,	,		19192	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	9											106	116	113					9																	116794994		2053	4178	6231	115834815	SO:0001583	missense	114991			BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1154C>T	9.37:g.116794994C>T	ENSP00000363241:p.Ser385Leu		115834815	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	37		.	.	.	.	.	.	.	.	.	.	C	28.1	4.893462	0.91889	.	.	ENSG00000157657	ENST00000374126;ENST00000288466;ENST00000452710;ENST00000374124	T;T;T	0.21932	4.42;2.41;1.98	5.57	5.57	0.84162	.	0.430127	0.25636	N	0.029313	T	0.47340	0.1440	.	.	.	0.54753	D	0.999989	D;D;D;D	0.89917	0.994;0.998;1.0;0.999	D;D;D;P	0.83275	0.921;0.945;0.996;0.889	T	0.20907	-1.0261	9	0.33141	T	0.24	-18.1385	18.5351	0.91008	0.0:1.0:0.0:0.0	.	372;352;385;292	B5MDS3;B9EG82;Q5T7W0;Q5T7W0-2	.;.;ZN618_HUMAN;.	L	385;292;301;372	ENSP00000288466:S292L;ENSP00000395400:S301L;ENSP00000363239:S372L	ENSP00000288466:S292L	S	+	2	0	ZNF618	115834815	1.000000	0.71417	0.974000	0.42286	0.741000	0.42261	6.905000	0.75714	2.619000	0.88677	0.561000	0.74099	TCG		0.592	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116794994	C	T	116794994	3	4	61	1	0	0	0	0	1	0	0	0	18081	893	31	1	917	1	ZNF618	9	116794994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	436952	116794994	24418437	6465	14450										
ZNF618	114991	broad.mit.edu	37	chr9	116811400	116811400	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaacgtgctgtcggagttCgtgatgtcggagatcaggac	15	8	1	3	rs369421645		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116811400C>T	ENST00000374126.5	+	15	1917	c.1818C>T	c.(1816-1818)ttC>ttT	p.F606F	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Silent_p.F513F			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	606					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F606F(1)|p.F513F(1)		breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						TGTCGGAGTTCGTGATGTCGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	9						T		1,4381	2.1+/-5.4	0,1,2190	104	104	104		1539	-4.1	0.9	9		104	0,8556		0,0,4278	no	coding-synonymous	ZNF618	NM_133374.2		0,1,6468	TT,TC,CC		0.0,0.0228,0.0077		513/862	116811400	1,12937	2191	4278	6469	115851221	SO:0001819	synonymous_variant	114991			BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1818C>T	9.37:g.116811400C>T			115851221	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																					0.597	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116811400	C	T	116811400	2	4	61	1	0	0	0	0	0	0	0	1	18081	883	31	1		1	ZNF618	9	116811400	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16406	116811400	24402031	6466	14451										
COL27A1	85301	broad.mit.edu	37	chr9	116956726	116956726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcaccaggaaaggcccacGatggggcaaaggtaggtttc	13	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:116956726G>A	ENST00000356083.3	+	6	2450	c.2059G>A	c.(2059-2061)Gat>Aat	p.D687N		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	687	Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.D687N(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						AAAGGCCCACGATGGGGCAAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											137	144	142					9																	116956726		2203	4300	6503	115996547	SO:0001583	missense	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2059G>A	9.37:g.116956726G>A	ENSP00000348385:p.Asp687Asn		115996547	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.378728	0.42207	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.94232	-3.38	5.29	4.39	0.52855	.	.	.	.	.	D	0.84406	0.5465	N	0.25957	0.775	0.26704	N	0.971113	P	0.46457	0.878	B	0.32533	0.147	T	0.76149	-0.3065	9	0.23891	T	0.37	.	8.8674	0.35294	0.0998:0.0:0.9002:0.0	.	687	Q8IZC6	CORA1_HUMAN	N	687	ENSP00000348385:D687N	ENSP00000348385:D687N	D	+	1	0	COL27A1	115996547	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	2.862000	0.48388	2.457000	0.83068	0.655000	0.94253	GAT		0.522	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	116956726	G	A	116956726	3	1	61	1	0	0	0	0	1	0	0	0	3691	1058	37	1	2081	1	COL27A1	9	116956726	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	145326	116956726	24256705	6467	14452										
COL27A1	85301	broad.mit.edu	37	chr9	117012943	117012943	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagccaggaatcgtgggaGaaaaggtaagtggtgttgag	19	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117012943G>T	ENST00000356083.3	+	25	3419	c.3028G>T	c.(3028-3030)Gaa>Taa	p.E1010*		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1010	Collagen-like 7.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.E1010*(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						AATCGTGGGAGAAAAGGTAAG	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											299	323	315					9																	117012943		2203	4300	6503	116052764	SO:0001587	stop_gained	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3028G>T	9.37:g.117012943G>T	ENSP00000348385:p.Glu1010*		116052764	Q66K43|Q96JF7	Nonsense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	45	11.879127	0.99613	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	14.4801	0.67576	0.0:0.0:1.0:0.0	.	.	.	.	X	1010	.	ENSP00000348385:E1010X	E	+	1	0	COL27A1	116052764	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.866000	0.69590	2.495000	0.84180	0.655000	0.94253	GAA		0.453	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		T	117012943	G	T	117012943	4	4	61	1	0	0	0	0	0	1	0	0	3691	943	33	2	3126	2	COL27A1	9	117012943	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56217	117012943	24200488	6468	14453										
COL27A1	85301	broad.mit.edu	37	chr9	117027362	117027362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagggtgtggctggtgagcGaggccacttgggctcgagag	19	9	0	2	rs146653470		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117027362G>A	ENST00000356083.3	+	31	3702	c.3311G>A	c.(3310-3312)cGa>cAa	p.R1104Q		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1104	Collagen-like 8.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.R1104Q(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GCTGGTGAGCGAGGCCACTTG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	86	92	90		3311	3	1	9	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL27A1	NM_032888.2	43	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	1104/1861	117027362	3,13003	2203	4300	6503	116067183	SO:0001583	missense	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3311G>A	9.37:g.117027362G>A	ENSP00000348385:p.Arg1104Gln		116067183	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.903557	0.33628	4.54E-4	1.16E-4	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.94092	-3.35	4.91	3.02	0.34903	.	.	.	.	.	D	0.91229	0.7236	L	0.45352	1.415	0.27310	N	0.957343	D	0.63046	0.992	P	0.55260	0.772	T	0.81707	-0.0810	9	0.10111	T	0.7	.	6.4553	0.21926	0.0939:0.0:0.7277:0.1784	.	1104	Q8IZC6	CORA1_HUMAN	Q	1104	ENSP00000348385:R1104Q	ENSP00000348385:R1104Q	R	+	2	0	COL27A1	116067183	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	1.125000	0.31332	0.574000	0.29417	-0.219000	0.12488	CGA		0.602	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117027362	G	A	117027362	3	1	61	1	0	0	0	0	1	0	0	0	3691	1058	37	1	3433	1	COL27A1	9	117027362	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14419	117027362	24186069	6469	14454										
ORM1	5004	broad.mit.edu	37	chr9	117087090	117087090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaggccaagagcatttcGctcacttgctgatcctcagg	12	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117087090G>A	ENST00000259396.8	+	4	427	c.349G>A	c.(349-351)Gct>Act	p.A117T	ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	117					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.A117T(1)		endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	AGAGCATTTCGCTCACTTGCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											136	136	136					9																	117087090		2203	4300	6503	116126911	SO:0001583	missense	5004				CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"Lipocalins"	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.349G>A	9.37:g.117087090G>A	ENSP00000259396:p.Ala117Thr		116126911	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.933886	0.52866	.	.	ENSG00000229314	ENST00000259396	T	0.09630	2.96	4.24	2.27	0.28462	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.575378	0.18350	N	0.143911	T	0.18002	0.0432	M	0.66939	2.045	0.09310	N	1	D	0.65815	0.995	P	0.52672	0.706	T	0.07366	-1.0776	10	0.66056	D	0.02	-0.5157	5.5457	0.17063	0.1086:0.0:0.6963:0.195	.	117	P02763	A1AG1_HUMAN	T	117	ENSP00000259396:A117T	ENSP00000259396:A117T	A	+	1	0	ORM1	116126911	0.023000	0.18921	0.000000	0.03702	0.012000	0.07955	2.554000	0.45845	0.436000	0.26393	0.205000	0.17691	GCT		0.522	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1			A	117087090	G	A	117087090	3	1	61	1	0	0	0	0	1	0	0	0	11298	1087	38	1	363	1	ORM1	9	117087090	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59728	117087090	24126341	6470	14455										
AKNA	80709	broad.mit.edu	37	chr9	117138749	117138749	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgagtcccactaacctgGagctgatggaccagctcagt	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117138749G>A	ENST00000307564.4	-	3	1499	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	AKNA_ENST00000374088.3_Silent_p.L446L|AKNA_ENST00000374075.5_Silent_p.L365L|AKNA_ENST00000312033.3_Silent_p.L446L|AKNA_ENST00000223791.3_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	446					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L446L(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CACTAACCTGGAGCTGATGGA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	9											50	51	51					9																	117138749		2203	4300	6503	116178570	SO:0001819	synonymous_variant	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1338C>T	9.37:g.117138749G>A			116178570	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1																																																																																				0.602	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117138749	G	A	117138749	2	1	61	1	0	0	0	0	0	0	0	1	463	1161	41	3		3	AKNA	9	117138749	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51659	117138749	24074682	6471	14456										
AKNA	80709	broad.mit.edu	37	chr9	117139240	117139240	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaagaatctggtcgtttCtctcctccatctatctgtgg	9	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117139240C>A	ENST00000307564.4	-	3	1008	c.847G>T	c.(847-849)Gaa>Taa	p.E283*	AKNA_ENST00000374088.3_Nonsense_Mutation_p.E283*|AKNA_ENST00000374075.5_Nonsense_Mutation_p.E202*|AKNA_ENST00000312033.3_Nonsense_Mutation_p.E283*|AKNA_ENST00000223791.3_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	283					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E283*(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTGGTCGTTTCTCTCCTCCAT	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											112	100	104					9																	117139240		2203	4300	6503	116179061	SO:0001587	stop_gained	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.847G>T	9.37:g.117139240C>A	ENSP00000303769:p.Glu283*		116179061	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Nonsense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	35	5.420130	0.96111	.	.	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	.	.	.	4.4	3.48	0.39840	.	1.645760	0.03790	N	0.262756	.	.	.	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	0.0175	10.0974	0.42484	0.0:0.796:0.204:0.0	.	.	.	.	X	283;124;283;202;283;283	.	ENSP00000303769:E283X	E	-	1	0	AKNA	116179061	0.000000	0.05858	0.002000	0.10522	0.085000	0.17905	0.606000	0.24194	1.029000	0.39812	0.561000	0.74099	GAA		0.562	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117139240	C	A	117139240	4	1	61	1	0	0	0	0	0	1	0	0	463	922	32	2	3552	2	AKNA	9	117139240	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	491	117139240	24074191	6472	14457										
DFNB31	25861	broad.mit.edu	37	chr9	117188639	117188639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagcctgacagcctcgtCgtgtaggatgttgagaaagc	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117188639C>T	ENST00000362057.3	-	4	1186	c.1018G>A	c.(1018-1020)Gac>Aac	p.D340N	DFNB31_ENST00000374059.3_5'Flank|DFNB31_ENST00000265134.6_5'UTR	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	340	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)		p.D340Y(1)|p.D340N(1)		central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACAGCCTCGTCGTGTAGGATG	0.567																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	9											106	92	97					9																	117188639		2203	4300	6503	116228460	SO:0001583	missense	25861			AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"whirlin"	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1018G>A	9.37:g.117188639C>T	ENSP00000354623:p.Asp340Asn		116228460	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011083	0.93346	.	.	ENSG00000095397	ENST00000362057	T	0.33216	1.42	5.05	5.05	0.67936	PDZ/DHR/GLGF (4);	0.149852	0.56097	D	0.000021	T	0.45915	0.1366	L	0.28740	0.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.981	T	0.44787	-0.9305	10	0.54805	T	0.06	-28.4029	18.3926	0.90489	0.0:1.0:0.0:0.0	.	340;340	B9EGE6;Q9P202	.;WHRN_HUMAN	N	340	ENSP00000354623:D340N	ENSP00000354623:D340N	D	-	1	0	DFNB31	116228460	1.000000	0.71417	0.990000	0.47175	0.921000	0.55340	7.376000	0.79658	2.361000	0.80049	0.561000	0.74099	GAC		0.567	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		T	117188639	C	T	117188639	3	4	61	1	0	0	0	0	1	0	0	0	4466	884	31	1	1741	1	DFNB31	9	117188639	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49399	117188639	24024792	6473	14458										
TNFSF8	944	broad.mit.edu	37	chr9	117666367	117666367	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattctggtatacgtgtttCgtttgcattccagactcaca	8	9	2	2	rs373154083		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117666367C>T	ENST00000223795.2	-	4	662	c.549G>A	c.(547-549)acG>acA	p.T183T	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	183					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)	p.T183T(2)		endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						ATACGTGTTTCGTTTGCATTC	0.418																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	9						C		1,4405	2.1+/-5.4	0,1,2202	260	225	237		549	-0.9	0	9		237	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TNFSF8	NM_001244.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		183/235	117666367	2,13004	2203	4300	6503	116706188	SO:0001819	synonymous_variant	944			L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.549G>A	9.37:g.117666367C>T			116706188	O43404	Silent	SNP	ENST00000223795.2	37	CCDS6810.1																																																																																				0.418	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			T	117666367	C	T	117666367	2	4	61	1	0	0	0	0	0	0	0	1	16350	871	31	1		1	TNFSF8	9	117666367	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	477728	117666367	23547064	6474	14459										
TNC	3371	broad.mit.edu	37	chr9	117793863	117793863	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtctggatcatattgctCctcaggggcccattgagtgc	12	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117793863C>T	ENST00000350763.4	-	23	6300	c.5889G>A	c.(5887-5889)agG>agA	p.R1963R	TNC_ENST00000340094.3_Silent_p.R1599R|TNC_ENST00000542877.1_Silent_p.R1600R|TNC_ENST00000535648.1_Silent_p.R1508R|TNC_ENST00000537320.1_Silent_p.R1326R|TNC_ENST00000345230.3_Silent_p.R1326R|TNC_ENST00000341037.4_Silent_p.R1781R|TNC_ENST00000423613.2_Silent_p.R1690R|TNC_ENST00000346706.3_Silent_p.R1417R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1963	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.R1963R(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCATATTGCTCCTCAGGGGCC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	9											200	171	181					9																	117793863		2203	4300	6503	116833684	SO:0001819	synonymous_variant	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5889G>A	9.37:g.117793863C>T			116833684	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	8.691	0.907411	0.17833	.	.	ENSG00000041982	ENST00000544972	.	.	.	6.08	4.26	0.50523	.	.	.	.	.	T	0.59307	0.2184	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55379	-0.8150	4	.	.	.	.	9.0379	0.36300	0.0:0.7263:0.0:0.2737	.	.	.	.	K	526	.	.	E	-	1	0	TNC	116833684	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	1.163000	0.31798	0.912000	0.36772	0.655000	0.94253	GAG		0.537	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117793863	C	T	117793863	2	4	61	1	0	0	0	0	0	0	0	1	16309	854	30	3		3	TNC	9	117793863	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127496	117793863	23419568	6475	14460										
TNC	3371	broad.mit.edu	37	chr9	117846615	117846615	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctggtccccaggcacacgGaactgcatttccagaccacc	9	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:117846615G>A	ENST00000350763.4	-	4	2415	c.2004C>T	c.(2002-2004)ttC>ttT	p.F668F	TNC_ENST00000340094.3_Silent_p.F668F|TNC_ENST00000542877.1_Silent_p.F668F|TNC_ENST00000535648.1_Silent_p.F668F|TNC_ENST00000537320.1_Silent_p.F668F|TNC_ENST00000345230.3_Silent_p.F668F|TNC_ENST00000341037.4_Silent_p.F668F|TNC_ENST00000423613.2_Silent_p.F668F|TNC_ENST00000346706.3_Silent_p.F668F	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	668	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.F668F(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CAGGCACACGGAACTGCATTT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	9											125	115	118					9																	117846615		2203	4300	6503	116886436	SO:0001819	synonymous_variant	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2004C>T	9.37:g.117846615G>A			116886436	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		A	117846615	G	A	117846615	2	1	61	1	0	0	0	0	0	0	0	1	16309	1165	41	3		3	TNC	9	117846615	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52752	117846615	23366816	6476	14461										
PAPPA	5069	broad.mit.edu	37	chr9	118989817	118989817	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatcaggacactggagccCtcgtgaagcagaaggtaagc	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:118989817C>A	ENST00000328252.3	+	6	2588	c.2219C>A	c.(2218-2220)cCt>cAt	p.P740H	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	740					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P740H(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CACTGGAGCCCTCGTGAAGCA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											87	73	77					9																	118989817		2203	4300	6503	118029638	SO:0001583	missense	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2219C>A	9.37:g.118989817C>A	ENSP00000330658:p.Pro740His		118029638	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.478709	0.84747	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.03358	3.96	5.85	4.96	0.65561	.	0.092037	0.85682	D	0.000000	T	0.20210	0.0486	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00945	-1.1505	10	0.87932	D	0	-8.8241	14.7148	0.69259	0.0:0.9307:0.0:0.0693	.	184;740	E7EMD3;Q13219	.;PAPP1_HUMAN	H	740;184	ENSP00000330658:P740H	ENSP00000330658:P740H	P	+	2	0	PAPPA	118029638	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.783000	0.85696	1.478000	0.48253	0.591000	0.81541	CCT		0.493	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	118989817	C	A	118989817	3	1	61	1	0	0	0	0	1	0	0	0	11463	681	24	2	2241	2	PAPPA	9	118989817	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1143202	118989817	22223614	6477	14462										
PAPPA	5069	broad.mit.edu	37	chr9	119093634	119093634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagaccactttttggctcCgggtaagctgaagctctgag	11	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:119093634C>T	ENST00000328252.3	+	11	3628	c.3259C>T	c.(3259-3261)Cgg>Tgg	p.R1087W	PAPPA_ENST00000534838.1_Missense_Mutation_p.R125W	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1087					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1087W(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TTTTTGGCTCCGGGTAAGCTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	76	81					9																	119093634		2203	4300	6503	118133455	SO:0001583	missense	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.3259C>T	9.37:g.119093634C>T	ENSP00000330658:p.Arg1087Trp		118133455	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.967267|3.967267	0.74131|0.74131	.|.	.|.	ENSG00000182752|ENSG00000182752	ENST00000443904|ENST00000328252;ENST00000534838	.|T;T	.|0.03982	.|4.53;3.74	6.06|6.06	4.09|4.09	0.47781|0.47781	.|.	.|0.144296	.|0.64402	.|D	.|0.000009	T|T	0.02888|0.02888	0.0086|0.0086	N|N	0.08118|0.08118	0|0	0.32185|0.32185	N|N	0.579826|0.579826	.|P;B	.|0.52842	.|0.956;0.002	.|B;B	.|0.42882	.|0.401;0.001	T|T	0.25813|0.25813	-1.0121|-1.0121	6|10	0.66056|0.66056	D|D	0.02|0.02	-9.4169|-9.4169	6.9022|6.9022	0.24288|0.24288	0.2795:0.6314:0.0:0.0891|0.2795:0.6314:0.0:0.0891	.|.	.|125;1087	.|F5GZ19;Q13219	.|.;PAPP1_HUMAN	L|W	530|1087;125	.|ENSP00000330658:R1087W;ENSP00000441461:R125W	ENSP00000400477:P530L|ENSP00000330658:R1087W	P|R	+|+	2|1	0|2	PAPPA|PAPPA	118133455|118133455	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.840000|0.840000	0.47671|0.47671	3.006000|3.006000	0.49529|0.49529	1.586000|1.586000	0.49944|0.49944	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.522	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	119093634	C	T	119093634	3	4	61	1	0	0	0	0	1	0	0	0	11463	643	23	1	3301	1	PAPPA	9	119093634	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103817	119093634	22119797	6478	14463										
ASTN2	23245	broad.mit.edu	37	chr9	119625945	119625945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgttccgagagcagtcacGaactggcccgaaggaagaca	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:119625945G>A	ENST00000313400.4	-	11	2057	c.1957C>T	c.(1957-1959)Cgt>Tgt	p.R653C	ASTN2_ENST00000361209.2_Missense_Mutation_p.R602C|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.R649C			O75129	ASTN2_HUMAN	astrotactin 2	653	EGF-like 2.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R602C(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GAGCAGTCACGAACTGGCCCG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											118	95	103					9																	119625945		2203	4300	6503	118665766	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1957C>T	9.37:g.119625945G>A	ENSP00000314038:p.Arg653Cys		118665766	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	19.30	3.801028	0.70567	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.15603	2.58;2.58;2.41;2.62	5.71	5.71	0.89125	.	0.131355	0.51477	D	0.000081	T	0.33469	0.0864	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.993;0.998	T	0.01081	-1.1458	9	.	.	.	-11.0318	19.8381	0.96666	0.0:0.0:1.0:0.0	.	602;653;649	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	C	653;649;376;602	ENSP00000314038:R653C;ENSP00000363108:R649C;ENSP00000363098:R376C;ENSP00000354504:R602C	.	R	-	1	0	ASTN2	118665766	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	5.008000	0.63991	2.690000	0.91761	0.655000	0.94253	CGT		0.542	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119625945	G	A	119625945	3	1	61	1	0	0	0	0	1	0	0	0	1066	1058	37	1	2346	1	ASTN2	9	119625945	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	532311	119625945	21587486	6479	14464										
ASTN2	23245	broad.mit.edu	37	chr9	119770383	119770383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctcaccggtttctgggtCgcagagctgctcacaggcat	13	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:119770383C>T	ENST00000313400.4	-	7	1679	c.1579G>A	c.(1579-1581)Gac>Aac	p.D527N	ASTN2_ENST00000361209.2_Missense_Mutation_p.D476N|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.D527N			O75129	ASTN2_HUMAN	astrotactin 2	527	EGF-like 1.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.D476N(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GTTTCTGGGTCGCAGAGCTGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											65	62	63					9																	119770383		2203	4300	6503	118810204	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1579G>A	9.37:g.119770383C>T	ENSP00000314038:p.Asp527Asn		118810204	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	23.6	4.434533	0.83776	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.16897	2.53;2.53;2.31;2.57	5.67	5.67	0.87782	.	0.059892	0.64402	D	0.000003	T	0.33118	0.0852	L	0.32530	0.975	0.54753	D	0.999985	D;D;D	0.89917	0.996;0.976;1.0	P;P;D	0.79784	0.842;0.51;0.993	T	0.01074	-1.1460	9	.	.	.	-31.0695	19.7848	0.96432	0.0:1.0:0.0:0.0	.	476;527;527	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	N	527;527;254;476	ENSP00000314038:D527N;ENSP00000363108:D527N;ENSP00000363098:D254N;ENSP00000354504:D476N	.	D	-	1	0	ASTN2	118810204	1.000000	0.71417	0.997000	0.53966	0.866000	0.49608	7.684000	0.84104	2.673000	0.90976	0.655000	0.94253	GAC		0.577	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119770383	C	T	119770383	3	4	61	1	0	0	0	0	1	0	0	0	1066	884	31	1	2740	1	ASTN2	9	119770383	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	144438	119770383	21443048	6480	14465										
ASTN2	23245	broad.mit.edu	37	chr9	119976846	119976846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttgcagccgggatgaaCggaagctctcccgcgcctgg	16	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:119976846C>T	ENST00000313400.4	-	3	906	c.806G>A	c.(805-807)cGt>cAt	p.R269H	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.R269H|ASTN2_ENST00000361209.2_Missense_Mutation_p.R269H			O75129	ASTN2_HUMAN	astrotactin 2	269					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R269H(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						CCGGGATGAACGGAAGCTCTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	9											93	81	85					9																	119976846		2203	4300	6503	119016667	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.806G>A	9.37:g.119976846C>T	ENSP00000314038:p.Arg269His		119016667	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.088561	0.76756	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.24723	2.0;1.99;1.84	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000003	T	0.38374	0.1038	N	0.24115	0.695	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.991;0.999	T	0.11397	-1.0589	9	.	.	.	-18.1473	18.6589	0.91465	0.0:1.0:0.0:0.0	.	269;269;269	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	H	269	ENSP00000314038:R269H;ENSP00000363108:R269H;ENSP00000354504:R269H	.	R	-	2	0	ASTN2	119016667	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.054000	0.71096	2.491000	0.84063	0.655000	0.94253	CGT		0.602	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119976846	C	T	119976846	3	4	61	1	0	0	0	0	1	0	0	0	1066	536	19	1	3372	1	ASTN2	9	119976846	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	206463	119976846	21236585	6481	14466										
TLR4	7099	broad.mit.edu	37	chr9	120475748	120475748	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtattcctatcactcagaAacctcatttaccttgacatt	3	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:120475748A>C	ENST00000355622.6	+	3	1443	c.1342A>C	c.(1342-1344)Aac>Cac	p.N448H	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.N408H	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	448					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.N448H(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	ATCACTCAGAAACCTCATTTA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											95	94	94					9																	120475748		2203	4300	6503	119515569	SO:0001583	missense	7099			U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1342A>C	9.37:g.120475748A>C	ENSP00000363089:p.Asn448His		119515569	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.176983	0.57692	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.59906	0.23;0.23	5.92	4.76	0.60689	.	0.546700	0.19347	N	0.116520	T	0.64864	0.2637	L	0.38953	1.18	0.09310	N	1	D	0.62365	0.991	D	0.64144	0.922	T	0.58284	-0.7663	10	0.52906	T	0.07	.	13.1913	0.59713	0.8669:0.1331:0.0:0.0	.	448	O00206	TLR4_HUMAN	H	408;448	ENSP00000377997:N408H;ENSP00000363089:N448H	ENSP00000363089:N448H	N	+	1	0	TLR4	119515569	0.974000	0.33945	0.004000	0.12327	0.815000	0.46073	7.667000	0.83888	1.032000	0.39892	0.528000	0.53228	AAC		0.398	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		C	120475748	A	C	120475748	3	2	61	1	0	0	0	0	1	0	0	0	15992	14	1	4	1352	4	TLR4	9	120475748	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	498902	120475748	20737683	6482	14467										
TLR4	7099	broad.mit.edu	37	chr9	120476223	120476223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcttggtggaagttgaacGaatggaatgtgcaacacctt	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:120476223G>A	ENST00000355622.6	+	3	1918	c.1817G>A	c.(1816-1818)cGa>cAa	p.R606Q	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.R566Q	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	606	LRRCT.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R606Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	GAAGTTGAACGAATGGAATGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											134	116	122					9																	120476223		2203	4300	6503	119516044	SO:0001583	missense	7099			U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1817G>A	9.37:g.120476223G>A	ENSP00000363089:p.Arg606Gln		119516044	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.568372	0.00895	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.37584	1.48;1.19	6.02	2.17	0.27698	Cysteine-rich flanking region, C-terminal (1);	1.192230	0.05693	N	0.592566	T	0.12347	0.0300	N	0.02665	-0.54	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.35724	-0.9777	10	0.02654	T	1	.	3.4256	0.07409	0.5961:0.1668:0.1393:0.0978	.	606	O00206	TLR4_HUMAN	Q	566;606	ENSP00000377997:R566Q;ENSP00000363089:R606Q	ENSP00000363089:R606Q	R	+	2	0	TLR4	119516044	0.000000	0.05858	0.645000	0.29479	0.011000	0.07611	0.651000	0.24873	1.090000	0.41315	-0.300000	0.09419	CGA		0.448	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		A	120476223	G	A	120476223	3	1	61	1	0	0	0	0	1	0	0	0	15992	1058	37	1	1827	1	TLR4	9	120476223	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	475	120476223	20737208	6483	14468										
TLR4	7099	broad.mit.edu	37	chr9	120476537	120476537	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctctgccttcactacagaGactttattcccggtgtggcc	9	13	2	1	rs56225594		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:120476537G>T	ENST00000355622.6	+	3	2232	c.2131G>T	c.(2131-2133)Gac>Tac	p.D711Y	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.D671Y	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	711	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.D711Y(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TCACTACAGAGACTTTATTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											100	98	99					9																	120476537		2203	4300	6503	119516358	SO:0001583	missense	7099			U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.2131G>T	9.37:g.120476537G>T	ENSP00000363089:p.Asp711Tyr		119516358	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.854142	0.91355	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.21031	2.03;2.03	6.03	6.03	0.97812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.85682	D	0.000000	T	0.56156	0.1966	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60084	-0.7332	10	0.87932	D	0	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	711	O00206	TLR4_HUMAN	Y	671;711	ENSP00000377997:D671Y;ENSP00000363089:D711Y	ENSP00000363089:D711Y	D	+	1	0	TLR4	119516358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.529000	0.98049	2.861000	0.98227	0.655000	0.94253	GAC		0.468	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		T	120476537	G	T	120476537	3	4	61	1	0	0	0	0	1	0	0	0	15992	942	33	2	2141	2	TLR4	9	120476537	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	314	120476537	20736894	6484	14469										
DBC1	1620	broad.mit.edu	37	chr9	121930276	121930276	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggttcacagcggcctcGatacagcttgtagcccttgt	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:121930276G>A	ENST00000265922.3	-	8	1833	c.1372C>T	c.(1372-1374)Cga>Tga	p.R458*	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	458					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.R458*(2)									CAGCGGCCTCGATACAGCTTG	0.597																																																2	Substitution - Nonsense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	9											81	74	77					9																	121930276		2203	4300	6503	120970097	SO:0001587	stop_gained	1620			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1372C>T	9.37:g.121930276G>A	ENSP00000265922:p.Arg458*		120970097	Q6IPV6|Q6P1A0|Q8WU22	Nonsense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	40	8.202170	0.98704	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	.	.	.	5.55	3.45	0.39498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-6.7066	15.6962	0.77502	0.0:0.0:0.7324:0.2676	.	.	.	.	X	458	.	ENSP00000265922:R458X	R	-	1	2	DBC1	120970097	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.329000	0.52060	1.273000	0.44346	0.655000	0.94253	CGA		0.597	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	121930276	G	A	121930276	4	1	61	1	0	0	0	0	0	1	0	0	4253	1066	37	1	917	1	DBC1	9	121930276	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1453739	121930276	19283155	6485	14470										
CDK5RAP2	55755	broad.mit.edu	37	chr9	123165285	123165285	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacacggagtgctagttgcCgaactgccactgtcgcagga	12	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123165285C>T	ENST00000349780.4	-	34	5285	c.5106G>A	c.(5104-5106)tcG>tcA	p.S1702S	CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000359309.3_Silent_p.S1661S|CDK5RAP2_ENST00000360190.4_Silent_p.S1623S|CDK5RAP2_ENST00000360822.3_Silent_p.S1670S	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1702					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.S1702S(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TGCTAGTTGCCGAACTGCCAC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	81	81					9																	123165285		2203	4300	6503	122205106	SO:0001819	synonymous_variant	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5106G>A	9.37:g.123165285C>T			122205106	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																				0.547	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123165285	C	T	123165285	2	4	61	1	0	0	0	0	0	0	0	1	3152	639	23	1		1	CDK5RAP2	9	123165285	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1235009	123165285	18048146	6486	14471										
CDK5RAP2	55755	broad.mit.edu	37	chr9	123169448	123169448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcctttctagttgcaagCgcagagcctggatctccatc	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123169448C>T	ENST00000349780.4	-	32	4984	c.4805G>A	c.(4804-4806)cGc>cAc	p.R1602H	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.R1561H|CDK5RAP2_ENST00000360190.4_Intron|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.R1570H	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1602					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.R1602H(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TAGTTGCAAGCGCAGAGCCTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	9											93	80	85					9																	123169448		2203	4300	6503	122209269	SO:0001583	missense	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.4805G>A	9.37:g.123169448C>T	ENSP00000343818:p.Arg1602His		122209269	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.011446	0.54468	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T	0.63913	1.67;1.7;1.63;1.04;-0.07	5.36	3.49	0.39957	.	0.146453	0.32015	N	0.006710	T	0.72748	0.3499	M	0.75777	2.31	0.26369	N	0.976912	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	P;P;P;P	0.61003	0.882;0.882;0.765;0.882	T	0.65471	-0.6160	10	0.87932	D	0	.	9.0014	0.36083	0.0:0.7719:0.1484:0.0797	.	612;1570;1602;996	Q5JTU8;Q96SN8-2;Q96SN8;B1AMJ5	.;.;CK5P2_HUMAN;.	H	1570;1561;1602;996;612;1374	ENSP00000354065:R1570H;ENSP00000352258:R1561H;ENSP00000343818:R1602H;ENSP00000400395:R996H;ENSP00000409941:R612H	ENSP00000341695:R1374H	R	-	2	0	CDK5RAP2	122209269	0.997000	0.39634	0.589000	0.28718	0.061000	0.15899	4.354000	0.59417	0.619000	0.30197	0.655000	0.94253	CGC		0.587	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123169448	C	T	123169448	3	4	61	1	0	0	0	0	1	0	0	0	3152	768	27	1	904	1	CDK5RAP2	9	123169448	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4163	123169448	18043983	6487	14472										
PSMD5	5711	broad.mit.edu	37	chr9	123589112	123589112	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attagaaatttggtcaattaCtccttcttgagcaagatatt	6	6	2	3	rs140063358		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123589112C>A	ENST00000210313.3	-	6	819	c.745G>T	c.(745-747)Gta>Tta	p.V249L	PSMD5_ENST00000373904.5_Missense_Mutation_p.V206L|PSMD5-AS1_ENST00000589026.1_RNA	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	249					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)		p.V249L(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						TGGTCAATTACTCCTTCTTGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	101	101					9																	123589112		2203	4300	6503	122628933	SO:0001583	missense	5711			AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"Proteasome (prosome, macropain) subunits"	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.745G>T	9.37:g.123589112C>A	ENSP00000210313:p.Val249Leu		122628933	B4DZM8|Q15045|Q4VXG8	Missense_Mutation	SNP	ENST00000210313.3	37	CCDS6824.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324930	0.60634	.	.	ENSG00000095261	ENST00000210313;ENST00000373904;ENST00000373903	T;T	0.36699	1.24;1.24	6.03	2.88	0.33553	Armadillo-type fold (1);	0.044717	0.85682	D	0.000000	T	0.31104	0.0786	L	0.54323	1.7	0.38824	D	0.955693	P;P	0.40431	0.537;0.717	B;B	0.44133	0.36;0.442	T	0.16305	-1.0407	10	0.07644	T	0.81	.	7.5763	0.27937	0.0:0.5823:0.0:0.4177	.	206;249	B4DZM8;Q16401	.;PSMD5_HUMAN	L	249;206;20	ENSP00000210313:V249L;ENSP00000363011:V206L	ENSP00000210313:V249L	V	-	1	0	PSMD5	122628933	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.066000	0.30604	0.888000	0.36160	0.655000	0.94253	GTA		0.403	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047		A	123589112	C	A	123589112	3	1	61	1	0	0	0	0	1	0	0	0	12735	565	20	2	789	2	PSMD5	9	123589112	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	419664	123589112	17624319	6488	14473										
TRAF1	7185	broad.mit.edu	37	chr9	123685996	123685996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtaccttctcctgagttCgaagacggcttcctgggctt	10	12	1	2	rs200495625		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123685996C>T	ENST00000373887.3	-	3	2660	c.215G>A	c.(214-216)cGa>cAa	p.R72Q	TRAF1_ENST00000540010.1_Missense_Mutation_p.R72Q	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	72					apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R72Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						CTCCTGAGTTCGAAGACGGCT	0.527													C|||	1	0.000199681	0	0	5008	,	,		22334	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											188	161	170					9																	123685996		2203	4300	6503	122725817	SO:0001583	missense	7185			AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.215G>A	9.37:g.123685996C>T	ENSP00000362994:p.Arg72Gln		122725817	B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	37	CCDS6825.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	4.154	0.026924	0.08054	.	.	ENSG00000056558	ENST00000373887;ENST00000540010	T;T	0.31769	1.48;1.48	4.53	0.599	0.17519	.	1.312490	0.05308	N	0.524171	T	0.15176	0.0366	N	0.08118	0	0.09310	N	0.999998	B	0.21688	0.059	B	0.15052	0.012	T	0.25293	-1.0136	10	0.22706	T	0.39	-0.0128	5.9452	0.19215	0.415:0.4392:0.0:0.1457	.	72	Q13077	TRAF1_HUMAN	Q	72	ENSP00000362994:R72Q;ENSP00000443183:R72Q	ENSP00000362994:R72Q	R	-	2	0	TRAF1	122725817	0.072000	0.21174	0.268000	0.24571	0.092000	0.18411	0.512000	0.22755	-0.007000	0.14345	-0.274000	0.10170	CGA		0.527	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658		T	123685996	C	T	123685996	3	4	61	1	0	0	0	0	1	0	0	0	16477	884	31	1	1059	1	TRAF1	9	123685996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96884	123685996	17527435	6489	14474										
C5	727	broad.mit.edu	37	chr9	123753543	123753543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgtatgggaactcctttCgtctgctaatggtacctgta	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123753543C>T	ENST00000223642.1	-	23	2896	c.2867G>A	c.(2866-2868)cGa>cAa	p.R956Q		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	956					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.R956Q(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	GAACTCCTTTCGTCTGCTAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	9											122	124	124					9																	123753543		2203	4300	6503	122793364	SO:0001583	missense	727			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.2867G>A	9.37:g.123753543C>T	ENSP00000223642:p.Arg956Gln		122793364	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.736862	0.49045	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.31510	1.49	5.7	2.68	0.31781	.	3.841640	0.00748	N	0.001054	T	0.26195	0.0639	L	0.49126	1.545	0.26348	N	0.977259	P	0.36438	0.553	B	0.16289	0.015	T	0.25847	-1.0120	10	0.31617	T	0.26	.	8.1511	0.31141	0.0:0.7267:0.0:0.2733	.	956	P01031	CO5_HUMAN	Q	956;1027	ENSP00000223642:R956Q	ENSP00000223642:R956Q	R	-	2	0	C5	122793364	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.779000	0.26746	0.662000	0.31006	0.655000	0.94253	CGA		0.333	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123753543	C	T	123753543	3	4	61	1	0	0	0	0	1	0	0	0	2286	884	31	1	2239	1	C5	9	123753543	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67547	123753543	17459888	6490	14475										
C5	727	broad.mit.edu	37	chr9	123792687	123792687	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcttaccttgcttttataGtaatttcaaaattcttaaag	4	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123792687G>T	ENST00000223642.1	-	7	775	c.746C>A	c.(745-747)aCt>aAt	p.T249N		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	249					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.T249N(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TGCTTTTATAGTAATTTCAAA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	9											14	15	15					9																	123792687		2104	4072	6176	122832508	SO:0001583	missense	727			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.746C>A	9.37:g.123792687G>T	ENSP00000223642:p.Thr249Asn		122832508	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799162	0.50208	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.35048	1.33	5.75	5.75	0.90469	.	0.225469	0.43919	D	0.000519	T	0.46889	0.1416	L	0.41124	1.26	0.48452	D	0.999653	D;P	0.69078	0.997;0.481	P;B	0.59424	0.857;0.284	T	0.10636	-1.0621	10	0.16896	T	0.51	.	18.516	0.90936	0.0:0.0:1.0:0.0	.	320;249	Q59GS8;P01031	.;CO5_HUMAN	N	249;320	ENSP00000223642:T249N	ENSP00000223642:T249N	T	-	2	0	C5	122832508	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.489000	0.60309	2.725000	0.93324	0.655000	0.94253	ACT		0.284	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123792687	G	T	123792687	3	4	61	1	0	0	0	0	1	0	0	0	2286	1029	36	2	4424	2	C5	9	123792687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39144	123792687	17420744	6491	14476										
CEP110	11064	broad.mit.edu	37	chr9	123920109	123920109	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaattgtagcagcaaaaGactcagacttccaatgttta	6	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123920109G>T	ENST00000373855.1	+	29	4848	c.4588G>T	c.(4588-4590)Gac>Tac	p.D1530Y	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.D1530Y|CNTRL_ENST00000373847.1_Missense_Mutation_p.D978Y|CNTRL_ENST00000373850.1_Missense_Mutation_p.D978Y|CNTRL_ENST00000373844.1_5'Flank			Q7Z7A1	CNTRL_HUMAN	centriolin	1530					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)		p.D1530Y(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AGCAGCAAAAGACTCAGACTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	106	104					9																	123920109		2203	4300	6503	122959930	SO:0001583	missense	11064			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.4588G>T	9.37:g.123920109G>T	ENSP00000362962:p.Asp1530Tyr		122959930	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870465	0.72065	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373847;ENST00000431571;ENST00000373845	T;T;T;T;T	0.78246	0.75;0.75;0.75;0.75;-1.16	5.81	4.91	0.64330	.	.	.	.	.	D	0.85957	0.5818	M	0.63843	1.955	0.48395	D	0.999643	D	0.89917	1.0	D	0.87578	0.998	D	0.87347	0.2335	9	0.87932	D	0	.	14.0836	0.64942	0.0719:0.0:0.9281:0.0	.	1530	Q7Z7A1	CNTRL_HUMAN	Y	1530;1530;1530;286;978;978;199;212	ENSP00000362962:D1530Y;ENSP00000238341:D1530Y;ENSP00000362956:D978Y;ENSP00000362953:D978Y;ENSP00000413014:D199Y	ENSP00000238341:D1530Y	D	+	1	0	CNTRL	122959930	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.825000	0.55730	1.450000	0.47717	0.655000	0.94253	GAC		0.418	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		T	123920109	G	T	123920109	3	4	61	1	0	0	0	0	1	0	0	0	3251	942	33	2	4694	2	CEP110	9	123920109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127422	123920109	17293322	6492	14477										
CEP110	11064	broad.mit.edu	37	chr9	123924423	123924423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccttgagagggataaacGagaaatagaacgaatgactg	12	6	0	4	rs536241829		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123924423G>A	ENST00000373855.1	+	34	5557	c.5297G>A	c.(5296-5298)cGa>cAa	p.R1766Q	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.R1766Q|CNTRL_ENST00000373850.1_Missense_Mutation_p.R1214Q			Q7Z7A1	CNTRL_HUMAN	centriolin	1766					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)		p.R1766Q(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AGGGATAAACGAGAAATAGAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											91	90	90					9																	123924423		2203	4300	6503	122964244	SO:0001583	missense	11064			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5297G>A	9.37:g.123924423G>A	ENSP00000362962:p.Arg1766Gln		122964244	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.647933	0.29336	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373845	T;T;T	0.29397	1.57;1.57;1.57	5.89	1.8	0.24995	.	.	.	.	.	T	0.17365	0.0417	N	0.25380	0.74	0.09310	N	1	B	0.16603	0.018	B	0.08055	0.003	T	0.28299	-1.0048	9	0.14252	T	0.57	.	6.4503	0.21900	0.2741:0.0:0.5971:0.1288	.	1766	Q7Z7A1	CNTRL_HUMAN	Q	1766;1766;1766;522;1214;448	ENSP00000362962:R1766Q;ENSP00000238341:R1766Q;ENSP00000362956:R1214Q	ENSP00000238341:R1766Q	R	+	2	0	CNTRL	122964244	0.085000	0.21516	0.983000	0.44433	0.755000	0.42902	0.568000	0.23623	0.820000	0.34516	0.563000	0.77884	CGA		0.438	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		A	123924423	G	A	123924423	3	1	61	1	0	0	0	0	1	0	0	0	3251	1058	37	1	5423	1	CEP110	9	123924423	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4314	123924423	17289008	6493	14478										
CEP110	11064	broad.mit.edu	37	chr9	123930425	123930425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaagaaagcaaattagaaAccagtaaagtgacactgaag	10	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:123930425A>G	ENST00000373855.1	+	38	6156	c.5896A>G	c.(5896-5898)Acc>Gcc	p.T1966A	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.T1966A|CNTRL_ENST00000373850.1_Missense_Mutation_p.T1414A			Q7Z7A1	CNTRL_HUMAN	centriolin	1966	Required for centrosome localization.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)		p.T1966A(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CAAATTAGAAACCAGTAAAGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											74	74	74					9																	123930425		2203	4300	6503	122970246	SO:0001583	missense	11064			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5896A>G	9.37:g.123930425A>G	ENSP00000362962:p.Thr1966Ala		122970246	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	4.007	-0.001405	0.07819	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373845	T;T;T	0.27256	1.99;1.99;1.68	6.07	5.14	0.70334	.	.	.	.	.	T	0.06962	0.0177	N	0.00268	-1.735	0.24219	N	0.995449	B	0.02656	0.0	B	0.01281	0.0	T	0.15896	-1.0421	9	0.08599	T	0.76	.	14.0206	0.64553	0.0734:0.0:0.9266:0.0	.	1966	Q7Z7A1	CNTRL_HUMAN	A	1966;1966;1966;722;1414;648	ENSP00000362962:T1966A;ENSP00000238341:T1966A;ENSP00000362956:T1414A	ENSP00000238341:T1966A	T	+	1	0	CNTRL	122970246	0.982000	0.34865	0.829000	0.32907	0.615000	0.37417	1.539000	0.36104	1.564000	0.49628	-0.177000	0.13119	ACC		0.398	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123930425	A	G	123930425	3	3	61	1	0	0	0	0	1	0	0	0	3251	43	2	4	6038	4	CEP110	9	123930425	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6002	123930425	17283006	6494	14479										
STOM	2040	broad.mit.edu	37	chr9	124103674	124103674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgcattcatttctccttCggctgcaataacctatggac	8	11	2	0	rs201671242		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:124103674C>T	ENST00000286713.2	-	7	690	c.673G>A	c.(673-675)Gaa>Aaa	p.E225K	STOM_ENST00000347359.2_Missense_Mutation_p.E60K|STOM_ENST00000538954.1_Missense_Mutation_p.E174K|AL161784.1_ENST00000594963.1_Missense_Mutation_p.S17L	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	225					protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)		p.E225K(1)		endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		ATTTCTCCTTCGGCTGCAATA	0.522													C|||	1	0.000199681	0	0	5008	,	,		19246	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											86	84	85					9																	124103674		2203	4300	6503	123143495	SO:0001583	missense	2040				CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"erythrocyte membrane protein band 7.2 (stomatin)"	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.673G>A	9.37:g.124103674C>T	ENSP00000286713:p.Glu225Lys		123143495	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Missense_Mutation	SNP	ENST00000286713.2	37	CCDS6830.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	33	5.232370	0.95207	.	.	ENSG00000148175	ENST00000286713;ENST00000538954;ENST00000347359	D;D;D	0.98192	-3.57;-3.57;-4.78	4.89	4.89	0.63831	.	0.108089	0.64402	D	0.000008	D	0.98991	0.9656	H	0.96748	3.875	0.80722	D	1	P;D	0.67145	0.535;0.996	P;P	0.51657	0.54;0.676	D	0.99734	1.1013	10	0.72032	D	0.01	.	17.2181	0.86950	0.0:1.0:0.0:0.0	.	60;225	B1AM77;P27105	.;STOM_HUMAN	K	225;174;60	ENSP00000286713:E225K;ENSP00000445764:E174K;ENSP00000339607:E60K	ENSP00000286713:E225K	E	-	1	0	STOM	123143495	1.000000	0.71417	0.982000	0.44146	0.959000	0.62525	7.414000	0.80117	2.540000	0.85666	0.555000	0.69702	GAA		0.522	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099		T	124103674	C	T	124103674	3	4	61	1	0	0	0	0	1	0	0	0	15351	893	31	1	197	1	STOM	9	124103674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173249	124103674	17109757	6495	14480										
OR1J2	26740	broad.mit.edu	37	chr9	125273092	125273092	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggagtatgagccctgaGaaccagagcagcgtgtccga	13	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125273092G>T	ENST00000335302.5	+	1	12	c.12G>T	c.(10-12)gaG>gaT	p.E4D		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E4D(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TGAGCCCTGAGAACCAGAGCA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											133	125	128					9																	125273092		2203	4300	6503	124312913	SO:0001583	missense	26740				CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.12G>T	9.37:g.125273092G>T	ENSP00000335575:p.Glu4Asp		124312913	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	.	.	.	.	.	.	.	.	.	.	G	6.952	0.545558	0.13312	.	.	ENSG00000197233	ENST00000335302;ENST00000444856	T	0.00466	7.23	4.69	1.56	0.23342	.	0.845163	0.09584	U	0.782447	T	0.00300	0.0009	L	0.28192	0.835	0.22142	N	0.999332	B	0.09022	0.002	B	0.06405	0.002	T	0.35919	-0.9769	10	0.32370	T	0.25	.	4.5823	0.12264	0.0844:0.2797:0.4926:0.1433	.	4	Q8NGS2	OR1J2_HUMAN	D	4	ENSP00000335575:E4D	ENSP00000335575:E4D	E	+	3	2	OR1J2	124312913	0.000000	0.05858	0.891000	0.34965	0.485000	0.33311	-0.751000	0.04803	0.684000	0.31448	0.650000	0.86243	GAG		0.493	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			T	125273092	G	T	125273092	3	4	61	1	0	0	0	0	1	0	0	0	10991	933	33	2	14	2	OR1J2	9	125273092	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1169418	125273092	15940339	6496	14481										
OR1J2	26740	broad.mit.edu	37	chr9	125273356	125273356	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggactaagtacaaatcgatCctctatgaggaatgcatttc	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125273356C>A	ENST00000335302.5	+	1	276	c.276C>A	c.(274-276)atC>atA	p.I92I		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I92I(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						ACAAATCGATCCTCTATGAGG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	9											159	135	143					9																	125273356		2203	4300	6503	124313177	SO:0001819	synonymous_variant	26740				CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.276C>A	9.37:g.125273356C>A			124313177	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Silent	SNP	ENST00000335302.5	37	CCDS35121.1																																																																																				0.408	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			A	125273356	C	A	125273356	2	1	61	1	0	0	0	0	0	0	0	1	10991	845	30	2		2	OR1J2	9	125273356	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	264	125273356	15940075	6497	14482										
OR1N2	138882	broad.mit.edu	37	chr9	125316260	125316260	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttctgctcttctatgggtCtcttatgggtgtgtatttac	11	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125316260C>T	ENST00000373688.2	+	1	870	c.812C>T	c.(811-813)tCt>tTt	p.S271F		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S271F(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						TTCTATGGGTCTCTTATGGGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											220	224	223					9																	125316260		2203	4300	6503	124356081	SO:0001583	missense	138882				CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.812C>T	9.37:g.125316260C>T	ENSP00000362792:p.Ser271Phe		124356081	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.422653	0.43020	.	.	ENSG00000171501	ENST00000373688	T	0.00179	8.61	4.56	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.922528	0.08982	N	0.865691	T	0.00384	0.0012	L	0.42744	1.35	0.09310	N	1	D	0.58268	0.982	P	0.62382	0.901	T	0.67991	-0.5527	10	0.87932	D	0	.	12.8615	0.57915	0.0:0.8347:0.1653:0.0	.	271	Q8NGR9	OR1N2_HUMAN	F	271	ENSP00000362792:S271F	ENSP00000362792:S271F	S	+	2	0	OR1N2	124356081	0.003000	0.15002	0.010000	0.14722	0.808000	0.45660	1.889000	0.39718	2.386000	0.81285	0.644000	0.83932	TCT		0.468	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			T	125316260	C	T	125316260	3	4	61	1	0	0	0	0	1	0	0	0	11001	913	32	3	814	3	OR1N2	9	125316260	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42904	125316260	15897171	6498	14483										
OR1B1	347169	broad.mit.edu	37	chr9	125391094	125391094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggtggagactgctcggcGgcgaccagcagctgaaggca	16	11	0	2	rs140862378		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125391094G>A	ENST00000304833.3	-	1	758	c.721C>T	c.(721-723)Cgc>Tgc	p.R241C	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R241C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						ACTGCTCGGCGGCGACCAGCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9							CYS/ARG	0,4406		0,0,2203	76	72	74		721	0.5	0.1	9	dbSNP_134	74	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR1B1	NM_001004450.1	180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	241/319	125391094	2,13004	2203	4300	6503	124430915	SO:0001583	missense	347169			AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.721C>T	9.37:g.125391094G>A	ENSP00000303151:p.Arg241Cys		124430915	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	.	.	.	.	.	.	.	.	.	.	g	0.622	-0.820820	0.02755	0.0	2.33E-4	ENSG00000171484	ENST00000304833	T	0.00164	8.64	4.72	0.541	0.17168	GPCR, rhodopsin-like superfamily (1);	1.057800	0.07483	N	0.904295	T	0.00144	0.0004	L	0.33668	1.02	0.09310	N	1	B	0.19935	0.04	B	0.27170	0.077	T	0.05419	-1.0886	10	0.33141	T	0.24	-0.9076	5.6116	0.17408	0.1635:0.0:0.5085:0.328	.	241	Q8NGR6	OR1B1_HUMAN	C	241	ENSP00000303151:R241C	ENSP00000303151:R241C	R	-	1	0	OR1B1	124430915	0.000000	0.05858	0.127000	0.21898	0.092000	0.18411	-0.971000	0.03806	0.298000	0.22638	-0.148000	0.13756	CGC		0.557	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		A	125391094	G	A	125391094	3	1	61	1	0	0	0	0	1	0	0	0	10982	1116	39	1	238	1	OR1B1	9	125391094	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74834	125391094	15822337	6499	14484										
OR1L6	392390	broad.mit.edu	37	chr9	125512542	125512542	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgatgtggttatgaaacCacggcattgcctgctcatgc	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125512542C>A	ENST00000373684.1	+	1	524	c.524C>A	c.(523-525)cCa>cAa	p.P175Q	OR1L6_ENST00000304720.2_Missense_Mutation_p.P139Q			Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L, member 6	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P175Q(1)		breast(1)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	12						GTTATGAAACCACGGCATTGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	9											205	160	175					9																	125512542		2203	4300	6503	124552363	SO:0001583	missense	392390				CCDS35130.1, CCDS35130.2	9q33.2	2013-09-20			ENSG00000171459	ENSG00000171459		"GPCR / Class A : Olfactory receptors"	8218	protein-coding gene	gene with protein product				OR1L7			Standard	NM_001004453		Approved		uc022bna.1	Q8NGR2	OTTHUMG00000020621	ENST00000373684.1:c.524C>A	9.37:g.125512542C>A	ENSP00000362788:p.Pro175Gln		124552363	Q6IFM8|Q96R80	Missense_Mutation	SNP	ENST00000373684.1	37		.	.	.	.	.	.	.	.	.	.	.	8.196	0.797182	0.16327	.	.	ENSG00000171459	ENST00000373684;ENST00000304720	T;T	0.01388	4.95;6.81	4.62	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.395673	0.21267	N	0.077392	T	0.01592	0.0051	N	0.25890	0.77	0.09310	N	1	P	0.48230	0.907	P	0.45276	0.475	T	0.51419	-0.8708	10	0.62326	D	0.03	-4.3392	7.1742	0.25734	0.0:0.6256:0.2808:0.0936	.	175	Q8NGR2	OR1L6_HUMAN	Q	175;139	ENSP00000362788:P175Q;ENSP00000304235:P139Q	ENSP00000304235:P139Q	P	+	2	0	OR1L6	124552363	0.000000	0.05858	0.183000	0.23137	0.142000	0.21351	-0.459000	0.06728	1.298000	0.44778	0.655000	0.94253	CCA		0.527	OR1L6-201	KNOWN	basic	protein_coding	protein_coding				A	125512542	C	A	125512542	3	1	61	1	0	0	0	0	1	0	0	0	10997	594	21	2	418	2	OR1L6	9	125512542	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121448	125512542	15700889	6500	14485										
OR1L6	392390	broad.mit.edu	37	chr9	125512903	125512903	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgggagtattatttatgtCtattttaggcccctgtccat	8	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125512903C>T	ENST00000373684.1	+	1	885	c.885C>T	c.(883-885)gtC>gtT	p.V295V	OR1L6_ENST00000304720.2_Silent_p.V259V			Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L, member 6	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V295V(1)		breast(1)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	12						TTATTTATGTCTATTTTAGGC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	9											109	93	98					9																	125512903		2203	4300	6503	124552724	SO:0001819	synonymous_variant	392390				CCDS35130.1, CCDS35130.2	9q33.2	2013-09-20			ENSG00000171459	ENSG00000171459		"GPCR / Class A : Olfactory receptors"	8218	protein-coding gene	gene with protein product				OR1L7			Standard	NM_001004453		Approved		uc022bna.1	Q8NGR2	OTTHUMG00000020621	ENST00000373684.1:c.885C>T	9.37:g.125512903C>T			124552724	Q6IFM8|Q96R80	Silent	SNP	ENST00000373684.1	37																																																																																					0.512	OR1L6-201	KNOWN	basic	protein_coding	protein_coding				T	125512903	C	T	125512903	2	4	61	1	0	0	0	0	0	0	0	1	10997	900	32	3		3	OR1L6	9	125512903	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	361	125512903	15700528	6501	14486										
OR1K1	392392	broad.mit.edu	37	chr9	125562716	125562716	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacccaaatgtacttcttCtttgccctgggggtaactga	9	11	2	2	rs150655492		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125562716C>A	ENST00000277309.2	+	1	347	c.315C>A	c.(313-315)ttC>ttA	p.F105L		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F105L(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						TGTACTTCTTCTTTGCCCTGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											117	98	104					9																	125562716		2203	4300	6503	124602537	SO:0001583	missense	392392			AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.315C>A	9.37:g.125562716C>A	ENSP00000277309:p.Phe105Leu		124602537	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	37	CCDS35132.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.207823	0.58343	.	.	ENSG00000165204	ENST00000277309	T	0.00309	8.16	4.37	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.185884	0.26163	U	0.025979	T	0.00210	0.0006	L	0.46741	1.465	0.23180	N	0.998169	P	0.40794	0.729	B	0.43194	0.411	T	0.42172	-0.9467	10	0.40728	T	0.16	.	5.928	0.19122	0.0:0.7011:0.0:0.2989	.	105	Q8NGR3	OR1K1_HUMAN	L	105	ENSP00000277309:F105L	ENSP00000277309:F105L	F	+	3	2	OR1K1	124602537	0.000000	0.05858	0.962000	0.40283	0.944000	0.59088	-0.073000	0.11468	1.065000	0.40693	0.655000	0.94253	TTC		0.592	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			A	125562716	C	A	125562716	3	1	61	1	0	0	0	0	1	0	0	0	10993	912	32	2	317	2	OR1K1	9	125562716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49813	125562716	15650715	6502	14487										
OR1K1	392392	broad.mit.edu	37	chr9	125563049	125563049	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcccttcctgctcatcctCgcctcctatggggccatcgc	7	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125563049C>T	ENST00000277309.2	+	1	680	c.648C>T	c.(646-648)ctC>ctT	p.L216L		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L216L(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						TGCTCATCCTCGCCTCCTATG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	9											64	55	58					9																	125563049		2203	4300	6503	124602870	SO:0001819	synonymous_variant	392392			AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.648C>T	9.37:g.125563049C>T			124602870	B9EH41|Q4VXB7|Q96R23	Silent	SNP	ENST00000277309.2	37	CCDS35132.1																																																																																				0.647	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			T	125563049	C	T	125563049	2	4	61	1	0	0	0	0	0	0	0	1	10993	871	31	1		1	OR1K1	9	125563049	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	333	125563049	15650382	6503	14488										
RC3H2	54542	broad.mit.edu	37	chr9	125655189	125655189	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcattttatgaacttaccTttacctccacttagtggttt	5	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125655189T>G	ENST00000373670.1	-	2	948	c.348A>C	c.(346-348)aaA>aaC	p.K116N	RC3H2_ENST00000478216.1_Intron|RC3H2_ENST00000423239.2_Splice_Site_p.K116N|RC3H2_ENST00000373665.2_Splice_Site_p.K116N|RC3H2_ENST00000357244.2_Splice_Site_p.K116N|RC3H2_ENST00000335387.5_Splice_Site_p.K116N|RC3H2_ENST00000471874.2_Splice_Site_p.K116N			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	116					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K116N(2)		breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						TGAACTTACCTTTACCTCCAC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	9											136	126	129					9																	125655189		1873	4099	5972	124695010	SO:0001630	splice_region_variant	54542			AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.349+1A>C	9.37:g.125655189T>G			124695010	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.007754	0.75046	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000423239;ENST00000373665;ENST00000335387	D;D;D;T;T	0.92911	-3.13;-3.13;-3.13;7.22;7.22	5.72	4.59	0.56863	.	0.000000	0.85682	D	0.000000	D	0.89787	0.6816	L	0.40543	1.245	0.53005	D	0.999966	B;D;B;D	0.58268	0.0;0.982;0.001;0.969	B;P;B;P	0.52758	0.001;0.514;0.006;0.708	D	0.86120	0.1568	10	0.17369	T	0.5	-1.2415	9.3819	0.38318	0.0:0.1129:0.0:0.8871	.	116;116;116;116	A6NHN2;Q9HBD1;Q9HBD1-5;Q9HBD1-4	.;RC3H2_HUMAN;.;.	N	116	ENSP00000362774:K116N;ENSP00000349783:K116N;ENSP00000411767:K116N;ENSP00000362769:K116N;ENSP00000335150:K116N	ENSP00000335150:K116N	K	-	3	2	RC3H2	124695010	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.964000	0.49192	2.179000	0.69175	0.482000	0.46254	AAA		0.338	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	Missense_Mutation	G	125655189	T	G	125655189	5	3	61	1	0	0	0	0	0	0	1	0	13204	1623	56	4	3381	4	RC3H2	9	125655189	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	92140	125655189	15558242	6504	14489										
RC3H2	54542	broad.mit.edu	37	chr9	125659649	125659649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcaaaaggacaagcttttCgatgaagtttattcaagcag	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125659649C>T	ENST00000373670.1	-	1	740	c.140G>A	c.(139-141)cGa>cAa	p.R47Q	RC3H2_ENST00000478216.1_Intron|RC3H2_ENST00000423239.2_Missense_Mutation_p.R47Q|RC3H2_ENST00000373665.2_Missense_Mutation_p.R47Q|RC3H2_ENST00000357244.2_Missense_Mutation_p.R47Q|RC3H2_ENST00000335387.5_Missense_Mutation_p.R47Q|RC3H2_ENST00000471874.2_Missense_Mutation_p.R47Q			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	47					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R47Q(2)		breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						ACAAGCTTTTCGATGAAGTTT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	9											105	101	102					9																	125659649		1918	4128	6046	124699470	SO:0001583	missense	54542			AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.140G>A	9.37:g.125659649C>T	ENSP00000362774:p.Arg47Gln		124699470	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	C	35	5.566327	0.96540	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000423239;ENST00000373665;ENST00000335387	D;D;D;D;D	0.94046	-3.34;-3.34;-3.34;-3.34;-3.34	6.13	6.13	0.99165	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.95124	0.8420	L	0.39326	1.205	0.54753	D	0.999981	D;D;D;D	0.69078	0.979;0.994;0.997;0.997	P;D;P;D	0.69479	0.791;0.921;0.832;0.964	D	0.94328	0.7559	10	0.48119	T	0.1	-21.6384	19.8481	0.96728	0.0:1.0:0.0:0.0	.	47;47;47;47	A6NHN2;Q9HBD1;Q9HBD1-5;Q9HBD1-4	.;RC3H2_HUMAN;.;.	Q	47	ENSP00000362774:R47Q;ENSP00000349783:R47Q;ENSP00000411767:R47Q;ENSP00000362769:R47Q;ENSP00000335150:R47Q	ENSP00000335150:R47Q	R	-	2	0	RC3H2	124699470	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.484000	0.81180	2.937000	0.99478	0.650000	0.86243	CGA		0.413	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		T	125659649	C	T	125659649	3	4	61	1	0	0	0	0	1	0	0	0	13204	884	31	1	3593	1	RC3H2	9	125659649	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4460	125659649	15553782	6505	14490										
ZBTB6	10773	broad.mit.edu	37	chr9	125674110	125674110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacagtaacaattttctgCcaacttctgcactctgtaag	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125674110C>T	ENST00000373659.3	-	2	330	c.242G>A	c.(241-243)gGc>gAc	p.G81D		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	81	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G81D(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						CAATTTTCTGCCAACTTCTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	9											103	106	105					9																	125674110		2203	4300	6503	124713931	SO:0001583	missense	10773			X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.242G>A	9.37:g.125674110C>T	ENSP00000362763:p.Gly81Asp		124713931	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	37	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022823	0.75275	.	.	ENSG00000186130	ENST00000373659	T	0.67345	-0.26	6.17	6.17	0.99709	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.83640	0.5298	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.83255	-0.0051	10	0.56958	D	0.05	.	19.8676	0.96824	0.0:1.0:0.0:0.0	.	81	Q15916	ZBTB6_HUMAN	D	81	ENSP00000362763:G81D	ENSP00000362763:G81D	G	-	2	0	ZBTB6	124713931	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.573000	0.60893	2.941000	0.99782	0.655000	0.94253	GGC		0.398	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		T	125674110	C	T	125674110	3	4	61	1	0	0	0	0	1	0	0	0	17591	739	26	3	1036	3	ZBTB6	9	125674110	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14461	125674110	15539321	6506	14491										
GPR21	2844	broad.mit.edu	37	chr9	125796995	125796995	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggcaacatcattgtgatTtttgtatttcactgtgcacc	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125796995T>G	ENST00000373642.1	+	1	190	c.150T>G	c.(148-150)atT>atG	p.I50M	RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373643.5_Intron|RABGAP1_ENST00000373647.4_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	50					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.I50M(1)		endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						TCATTGTGATTTTTGTATTTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	9											208	180	190					9																	125796995		2203	4300	6503	124836816	SO:0001583	missense	2844			BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"GPCR / Class A : Orphans"	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.150T>G	9.37:g.125796995T>G	ENSP00000362746:p.Ile50Met		124836816	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	37	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.210802	0.39102	.	.	ENSG00000188394	ENST00000373642;ENST00000412269	T	0.76316	-1.01	5.54	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000001	T	0.80696	0.4672	L	0.48986	1.54	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.76806	-0.2823	10	0.49607	T	0.09	-11.938	4.1625	0.10291	0.1561:0.3118:0.0:0.5321	.	50	Q99679	GPR21_HUMAN	M	50	ENSP00000362746:I50M	ENSP00000362746:I50M	I	+	3	3	GPR21	124836816	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.511000	0.22739	0.398000	0.25338	0.460000	0.39030	ATT		0.368	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294		G	125796995	T	G	125796995	3	3	61	1	0	0	0	0	1	0	0	0	6701	1829	64	4	152	4	GPR21	9	125796995	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	122885	125796995	15416436	6507	14492										
GPR21	2844	broad.mit.edu	37	chr9	125797263	125797263	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctttaacctataatactCtggttacaccctggagacta	5	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125797263C>A	ENST00000373642.1	+	1	458	c.418C>A	c.(418-420)Ctg>Atg	p.L140M	RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373643.5_Intron|RABGAP1_ENST00000373647.4_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	140					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.L140M(1)		endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						CTATAATACTCTGGTTACACC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											118	113	114					9																	125797263		2203	4300	6503	124837084	SO:0001583	missense	2844			BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"GPCR / Class A : Orphans"	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.418C>A	9.37:g.125797263C>A	ENSP00000362746:p.Leu140Met		124837084	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	37	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446886	0.43429	.	.	ENSG00000188394	ENST00000373642;ENST00000412269	T	0.32272	1.46	5.25	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	U	0.000084	T	0.56077	0.1961	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.61312	-0.7088	10	0.51188	T	0.08	-3.8286	11.6655	0.51370	0.0:0.7941:0.1277:0.0782	.	140	Q99679	GPR21_HUMAN	M	140	ENSP00000362746:L140M	ENSP00000362746:L140M	L	+	1	2	GPR21	124837084	1.000000	0.71417	0.977000	0.42913	0.938000	0.57974	4.666000	0.61554	1.204000	0.43247	0.563000	0.77884	CTG		0.443	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294		A	125797263	C	A	125797263	3	1	61	1	0	0	0	0	1	0	0	0	6701	912	32	2	420	2	GPR21	9	125797263	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	268	125797263	15416168	6508	14493										
STRBP	55342	broad.mit.edu	37	chr9	125898673	125898673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacacacctccattacaaagCgcttgtcatggcttccacca	5	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125898673C>T	ENST00000348403.5	-	15	2048	c.1619G>A	c.(1618-1620)cGc>cAc	p.R540H	STRBP_ENST00000447404.2_Missense_Mutation_p.R540H|STRBP_ENST00000360998.3_Missense_Mutation_p.R526H	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	540	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R540H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CATTACAAAGCGCTTGTCATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											122	117	118					9																	125898673		2203	4300	6503	124938494	SO:0001583	missense	55342			AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1619G>A	9.37:g.125898673C>T	ENSP00000321347:p.Arg540His		124938494	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Missense_Mutation	SNP	ENST00000348403.5	37	CCDS6851.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.526855	0.85706	.	.	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998	T;T;T	0.77229	-1.08;-1.08;-1.08	5.55	4.65	0.58169	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.79545	0.4464	L	0.46567	1.45	0.80722	D	1	D;D	0.56746	0.977;0.972	P;P	0.52514	0.701;0.674	T	0.81846	-0.0745	10	0.87932	D	0	-4.7944	14.2349	0.65919	0.0:0.9283:0.0:0.0716	.	540;526	Q96SI9;Q96SI9-2	STRBP_HUMAN;.	H	540;540;526	ENSP00000415968:R540H;ENSP00000321347:R540H;ENSP00000354271:R526H	ENSP00000321347:R540H	R	-	2	0	STRBP	124938494	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.089000	0.71384	1.348000	0.45733	0.655000	0.94253	CGC		0.423	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			T	125898673	C	T	125898673	3	4	61	1	0	0	0	0	1	0	0	0	15366	768	27	1	419	1	STRBP	9	125898673	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101410	125898673	15314758	6509	14494										
STRBP	55342	broad.mit.edu	37	chr9	125941323	125941323	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctcatctttcttcacttCtgtctcaccctctgtttttg	5	14	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:125941323C>A	ENST00000348403.5	-	4	616	c.187G>T	c.(187-189)Gaa>Taa	p.E63*	STRBP_ENST00000447404.2_Nonsense_Mutation_p.E63*|STRBP_ENST00000360998.3_Nonsense_Mutation_p.E49*	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	63	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.E63*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						TTCTTCACTTCTGTCTCACCC	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											241	218	226					9																	125941323		2203	4300	6503	124981144	SO:0001587	stop_gained	55342			AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.187G>T	9.37:g.125941323C>A	ENSP00000321347:p.Glu63*		124981144	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Nonsense_Mutation	SNP	ENST00000348403.5	37	CCDS6851.1	.	.	.	.	.	.	.	.	.	.	C	35	5.569183	0.96540	.	.	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998;ENST00000479114	.	.	.	5.77	5.77	0.91146	.	0.470183	0.24678	N	0.036497	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-11.4446	15.4722	0.75449	0.0:0.8621:0.1379:0.0	.	.	.	.	X	63;63;49;63	.	ENSP00000321347:E63X	E	-	1	0	STRBP	124981144	0.996000	0.38824	1.000000	0.80357	0.972000	0.66771	3.103000	0.50298	2.720000	0.93068	0.557000	0.71058	GAA		0.443	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			A	125941323	C	A	125941323	4	1	61	1	0	0	0	0	0	1	0	0	15366	922	32	2	1895	2	STRBP	9	125941323	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42650	125941323	15272108	6510	14495										
DENND1A	57706	broad.mit.edu	37	chr9	126219675	126219675	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaaaacatcactgaaacCttcgccggaattgagaagat	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:126219675C>A	ENST00000373624.2	-	15	1339	c.1138G>T	c.(1138-1140)Ggt>Tgt	p.G380C	DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000394219.3_Missense_Mutation_p.G348C|DENND1A_ENST00000394215.2_Missense_Mutation_p.G350C|DENND1A_ENST00000542603.1_Missense_Mutation_p.G122C|DENND1A_ENST00000373620.3_Missense_Mutation_p.G380C|DENND1A_ENST00000373618.1_Missense_Mutation_p.G348C	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	380					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.G380C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						TCACTGAAACCTTCGCCGGAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											138	132	134					9																	126219675		2203	4300	6503	125259496	SO:0001583	missense	57706			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1138G>T	9.37:g.126219675C>A	ENSP00000362727:p.Gly380Cys		125259496	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.833921	0.91036	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T;T	0.33216	3.1;1.42;3.03;3.13;2.99;3.02	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.64271	0.2583	M	0.88105	2.93	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;0.998;0.999;1.0;0.999;0.995	T	0.70745	-0.4788	10	0.87932	D	0	-14.535	18.6769	0.91531	0.0:1.0:0.0:0.0	.	348;338;348;350;380;380	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3	.;.;.;.;.;DEN1A_HUMAN	C	380;122;348;380;350;348	ENSP00000362727:G380C;ENSP00000437457:G122C;ENSP00000377766:G348C;ENSP00000362722:G380C;ENSP00000377763:G350C;ENSP00000362720:G348C	ENSP00000362720:G348C	G	-	1	0	DENND1A	125259496	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.252000	0.78309	2.706000	0.92434	0.655000	0.94253	GGT		0.438	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126219675	C	A	126219675	3	1	61	1	0	0	0	0	1	0	0	0	4437	681	24	2	2030	2	DENND1A	9	126219675	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	278352	126219675	14993756	6511	14496										
DENND1A	57706	broad.mit.edu	37	chr9	126220144	126220144	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggagcggtagtgggacacGaaggcttcctcacagaaagt	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:126220144G>A	ENST00000373624.2	-	14	1227	c.1026C>T	c.(1024-1026)ttC>ttT	p.F342F	DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000394219.3_Silent_p.F310F|DENND1A_ENST00000394215.2_Silent_p.F312F|DENND1A_ENST00000542603.1_Silent_p.F84F|DENND1A_ENST00000373620.3_Silent_p.F342F|DENND1A_ENST00000373618.1_Silent_p.F310F	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	342	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.F342F(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						AGTGGGACACGAAGGCTTCCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	9											52	44	47					9																	126220144		2203	4300	6503	125259965	SO:0001819	synonymous_variant	57706			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1026C>T	9.37:g.126220144G>A			125259965	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																				0.592	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126220144	G	A	126220144	2	1	61	1	0	0	0	0	0	0	0	1	4437	1049	37	1		1	DENND1A	9	126220144	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	469	126220144	14993287	6512	14497										
NR6A1	2649	broad.mit.edu	37	chr9	127302449	127302449	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccagacatgatcctttcGatttcttcttccgatatctt	5	12	3	2	rs538806855		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:127302449G>A	ENST00000487099.2	-	5	616	c.459C>T	c.(457-459)atC>atT	p.I153I	NR6A1_ENST00000416460.2_Silent_p.I149I|NR6A1_ENST00000373584.3_Silent_p.I149I|NR6A1_ENST00000344523.4_Silent_p.I153I	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	153					cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.I153I(1)		NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						TGATCCTTTCGATTTCTTCTT	0.468													G|||	1	0.000199681	0	0	5008	,	,		22807	0.001		0	False		,,,				2504	0				Esophageal Squamous(192;272 2884 6208 20560)											1	Substitution - coding silent(1)	large_intestine(1)	9											224	187	199					9																	127302449		2203	4300	6503	126342270	SO:0001819	synonymous_variant	2649			U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"Nuclear hormone receptors"	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.459C>T	9.37:g.127302449G>A			126342270	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Silent	SNP	ENST00000487099.2	37	CCDS35137.1																																																																																				0.468	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4			A	127302449	G	A	127302449	2	1	61	1	0	0	0	0	0	0	0	1	10668	1048	37	1		1	NR6A1	9	127302449	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1082305	127302449	13910982	6513	14498										
ARPC5L	81873	broad.mit.edu	37	chr9	127639217	127639218	+	Stop_Codon_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagcaagaaagactgtttINSaaaaaaaataaaaagactca							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:127639217_127639218insA	ENST00000353214.2	+	0	1712_1713				ARPC5L_ENST00000465124.1_3'UTR|ARPC5L_ENST00000259477.6_Stop_Codon_Ins			Q9BPX5	ARP5L_HUMAN	actin related protein 2/3 complex, subunit 5-like						regulation of actin filament polymerization (GO:0030833)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)		p.?(1)		large_intestine(2)|lung(1)	3						AAAGACTGTTTAAAAAAAATAA	0.441																																																1	Unknown(1)	large_intestine(1)	9																																								126679039	SO:0001567	stop_retained_variant	81873			AF087842	CCDS6859.1	9q34.11	2011-07-06			ENSG00000136950	ENSG00000136950		"Actin related protein 2/3 complex subunits"	23366	protein-coding gene	gene with protein product							Standard	NM_030978		Approved	MGC3038, ARC16-2	uc004bpa.4	Q9BPX5	OTTHUMG00000020660	ENST00000353214.2:c.467dupA	9.37:g.127639225_127639225dupA			126679038	Q7Z523	Frame_Shift_Ins	INS	ENST00000353214.2	37	CCDS6859.1																																																																																				0.441	ARPC5L-002	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054041.1	NM_030978		A	127639218	-	A	127639217	7	5	61	1	0	1	1	0	0	0	0	0	976	1767	61	0	474	0	ARPC5L	9	127639217	Stop_Codon_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	336768	127639217	13574214	6514	14499										
SCAI	286205	broad.mit.edu	37	chr9	127757235	127757235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatacgcaacactattagacGaatccacaatgatgaacagt	6	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:127757235G>A	ENST00000336505.6	-	14	1362	c.1304C>T	c.(1303-1305)tCg>tTg	p.S435L	SCAI_ENST00000373549.4_Missense_Mutation_p.S458L	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	435					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.S458L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						ACTATTAGACGAATCCACAAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											97	94	95					9																	127757235		1985	4159	6144	126797056	SO:0001583	missense	286205			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1304C>T	9.37:g.127757235G>A	ENSP00000336756:p.Ser435Leu		126797056	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	37	CCDS48017.1	.	.	.	.	.	.	.	.	.	.	G	31	5.073949	0.94000	.	.	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.63744	-0.06;-0.05	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.82421	0.5033	M	0.87971	2.92	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72982	0.979;0.975	D	0.84932	0.0860	10	0.87932	D	0	-7.367	18.8499	0.92224	0.0:0.0:1.0:0.0	.	435;458	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	L	435;458	ENSP00000336756:S435L;ENSP00000362650:S458L	ENSP00000336756:S435L	S	-	2	0	SCAI	126797056	1.000000	0.71417	0.860000	0.33809	0.702000	0.40608	9.173000	0.94815	2.770000	0.95276	0.563000	0.77884	TCG		0.468	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		A	127757235	G	A	127757235	3	1	61	1	0	0	0	0	1	0	0	0	13906	1059	37	1	536	1	SCAI	9	127757235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118018	127757235	13456196	6515	14500										
PPP6C	5537	broad.mit.edu	37	chr9	127915943	127915943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaatttcctgattccgttCgatggttcgaatttgatcca	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:127915943C>T	ENST00000373547.4	-	6	637	c.538G>A	c.(538-540)Gaa>Aaa	p.E180K	PPP6C_ENST00000373546.3_Missense_Mutation_p.E33K|PPP6C_ENST00000451402.1_Missense_Mutation_p.E217K|PPP6C_ENST00000415905.1_Missense_Mutation_p.E158K	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit	180					G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.E180K(1)		NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						TGATTCCGTTCGATGGTTCGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											89	79	82					9																	127915943		2203	4300	6503	126955764	SO:0001583	missense	5537			AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.538G>A	9.37:g.127915943C>T	ENSP00000362648:p.Glu180Lys		126955764	B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Missense_Mutation	SNP	ENST00000373547.4	37	CCDS6861.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315143	0.81358	.	.	ENSG00000119414	ENST00000373547;ENST00000451402;ENST00000415905;ENST00000373546	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.76	5.76	0.90799	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.34193	0.0889	N	0.20610	0.595	0.80722	D	1	B;B;B	0.20550	0.006;0.046;0.015	B;B;B	0.20767	0.008;0.031;0.021	T	0.11690	-1.0577	10	0.72032	D	0.01	-19.3737	18.9632	0.92684	0.0:1.0:0.0:0.0	.	158;217;180	O00743-2;O00743-3;O00743	.;.;PPP6_HUMAN	K	180;217;158;33	ENSP00000362648:E180K;ENSP00000392147:E217K;ENSP00000411744:E158K;ENSP00000362647:E33K	ENSP00000362647:E33K	E	-	1	0	PPP6C	126955764	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.445000	0.80570	2.724000	0.93272	0.585000	0.79938	GAA		0.423	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294		T	127915943	C	T	127915943	3	4	61	1	0	0	0	0	1	0	0	0	12441	893	31	1	387	1	PPP6C	9	127915943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158708	127915943	13297488	6516	14501										
HSPA5	3309	broad.mit.edu	37	chr9	128001387	128001387	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctattgtctttcctgacatCtttgcccgtcttctttttgt	5	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:128001387C>A	ENST00000324460.6	-	5	1032	c.829G>T	c.(829-831)Gat>Tat	p.D277Y	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	277					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.D277Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	TTCCTGACATCTTTGCCCGTC	0.468										Prostate(1;0.17)																																						1	Substitution - Missense(1)	large_intestine(1)	9											79	78	78					9																	128001387		2203	4300	6503	127041208	SO:0001583	missense	3309				CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"Heat shock proteins / HSP70"	5238	protein-coding gene	gene with protein product		138120	"heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.829G>T	9.37:g.128001387C>A	ENSP00000324173:p.Asp277Tyr		127041208	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Missense_Mutation	SNP	ENST00000324460.6	37	CCDS6863.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697494	0.68386	.	.	ENSG00000044574	ENST00000324460	T	0.01705	4.68	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	H	0.99475	4.585	0.80722	D	1	P	0.44044	0.825	B	0.43728	0.429	T	0.37009	-0.9724	10	0.87932	D	0	-12.4	15.4514	0.75277	0.0:1.0:0.0:0.0	.	277	P11021	GRP78_HUMAN	Y	277	ENSP00000324173:D277Y	ENSP00000324173:D277Y	D	-	1	0	HSPA5	127041208	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	7.795000	0.85887	1.864000	0.54056	0.462000	0.41574	GAT		0.468	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			A	128001387	C	A	128001387	3	1	61	1	0	0	0	0	1	0	0	0	7435	913	32	2	1151	2	HSPA5	9	128001387	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85444	128001387	13212044	6517	14502										
GAPVD1	26130	broad.mit.edu	37	chr9	128064674	128064674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttttcctcacagccactTtacatgagccaattatgcaa	4	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:128064674T>C	ENST00000495955.1	+	5	888	c.598T>C	c.(598-600)Tta>Cta	p.L200L	RNU6-1020P_ENST00000363684.1_RNA|GAPVD1_ENST00000297933.6_Silent_p.L200L|GAPVD1_ENST00000394104.2_Silent_p.L200L|GAPVD1_ENST00000394083.2_Silent_p.L200L|GAPVD1_ENST00000394105.2_Silent_p.L200L|GAPVD1_ENST00000470056.1_Silent_p.L200L|GAPVD1_ENST00000312123.9_Silent_p.L200L|GAPVD1_ENST00000265956.4_Silent_p.L200L|GAPVD1_ENST00000394084.1_Silent_p.L200L			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	200	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.L200L(1)		central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CACAGCCACTTTACATGAGCC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	9											63	60	61					9																	128064674		2203	4300	6503	127104495	SO:0001819	synonymous_variant	26130				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.598T>C	9.37:g.128064674T>C			127104495	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	T	6.967	0.548457	0.13312	.	.	ENSG00000165219	ENST00000436712	.	.	.	6.03	2.52	0.30459	.	.	.	.	.	T	0.55940	0.1952	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48328	-0.9045	4	.	.	.	.	8.0672	0.30667	0.0:0.2913:0.0:0.7087	.	.	.	.	S	30	.	.	F	+	2	0	GAPVD1	127104495	0.990000	0.36364	1.000000	0.80357	0.985000	0.73830	1.745000	0.38278	0.532000	0.28657	-0.274000	0.10170	TTT		0.418	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			C	128064674	T	C	128064674	2	2	61	1	0	0	0	0	0	0	0	1	6259	1838	64	4		4	GAPVD1	9	128064674	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	63287	128064674	13148757	6518	14503										
GAPVD1	26130	broad.mit.edu	37	chr9	128088850	128088850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctaatattgatgaagatCgcttgcaagaaattgcaggt	9	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:128088850C>T	ENST00000495955.1	+	12	2304	c.2014C>T	c.(2014-2016)Cgc>Tgc	p.R672C	GAPVD1_ENST00000297933.6_Missense_Mutation_p.R672C|GAPVD1_ENST00000394104.2_Missense_Mutation_p.R672C|GAPVD1_ENST00000394083.2_Missense_Mutation_p.R651C|GAPVD1_ENST00000394105.2_Missense_Mutation_p.R672C|GAPVD1_ENST00000470056.1_Missense_Mutation_p.R672C|GAPVD1_ENST00000312123.9_Missense_Mutation_p.R651C|GAPVD1_ENST00000265956.4_Missense_Mutation_p.R672C			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	672					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.R672C(1)		central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TGATGAAGATCGCTTGCAAGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											186	171	176					9																	128088850		2203	4300	6503	127128671	SO:0001583	missense	26130				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2014C>T	9.37:g.128088850C>T	ENSP00000419063:p.Arg672Cys		127128671	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.6|27.6	4.846935|4.846935	0.91277|0.91277	.|.	.|.	ENSG00000165219|ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000436712	T;T;T;T;T;T;T;T;T|.	0.14893|.	2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61527|0.61527	0.2354|0.2354	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.81914|.	0.992;0.982;0.988;0.988;0.988;0.995|.	T|T	0.57447|0.57447	-0.7810|-0.7810	10|5	0.72032|.	D|.	0.01|.	.|.	17.568|17.568	0.87926|0.87926	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	672;672;672;651;672;672|.	Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6|.	.;GAPD1_HUMAN;.;.;.;.|.	C|L	672;672;672;672;651;672;672;672;651|508	ENSP00000419767:R672C;ENSP00000377665:R672C;ENSP00000377664:R672C;ENSP00000265956:R672C;ENSP00000377645:R651C;ENSP00000419063:R672C;ENSP00000418747:R672C;ENSP00000297933:R672C;ENSP00000309582:R651C|.	ENSP00000265956:R672C|.	R|S	+|+	1|2	0|0	GAPVD1|GAPVD1	127128671|127128671	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.469000|3.469000	0.53093|0.53093	2.402000|2.402000	0.81655|0.81655	0.491000|0.491000	0.48974|0.48974	CGC|TCG		0.428	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128088850	C	T	128088850	3	4	61	1	0	0	0	0	1	0	0	0	6259	884	31	1	2048	1	GAPVD1	9	128088850	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24176	128088850	13124581	6519	14504										
GAPVD1	26130	broad.mit.edu	37	chr9	128097501	128097501	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttcaacacattgaagcaGaagcagacatgagaatccag	8	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:128097501G>T	ENST00000495955.1	+	16	2718				GAPVD1_ENST00000297933.6_Intron|GAPVD1_ENST00000394104.2_Intron|GAPVD1_ENST00000394083.2_Intron|GAPVD1_ENST00000394105.2_Nonsense_Mutation_p.E827*|GAPVD1_ENST00000470056.1_Intron|GAPVD1_ENST00000312123.9_Intron|GAPVD1_ENST00000265956.4_Intron			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.E827*(1)		central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						cattgaagcagaagcagacat	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											57	56	56					9																	128097501		2203	4300	6503	127137322	SO:0001627	intron_variant	26130				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2429-1796G>T	9.37:g.128097501G>T			127137322	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Nonsense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	G	37	6.184120	0.97357	.	.	ENSG00000165219	ENST00000394105	.	.	.	0.564	0.564	0.17302	.	.	.	.	.	.	.	.	.	.	.	0.27742	N	0.944446	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	827	.	ENSP00000377665:E827X	E	+	1	0	GAPVD1	127137322	0.381000	0.25140	0.421000	0.26609	0.699000	0.40488	-0.047000	0.11963	0.556000	0.29098	0.195000	0.17529	GAA		0.333	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128097501	G	T	128097501	1	4	61	0	1	0	0	0	0	0	0	0	6259	943	33	2		2	GAPVD1	9	128097501	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8651	128097501	13115930	6520	14505										
FAM125B	89853	broad.mit.edu	37	chr9	129157901	129157901	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgaatgggcagagtaccaaGaaatcatgactcatctcaac	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:129157901G>T	ENST00000361171.3	+	6	668	c.587G>T	c.(586-588)aGa>aTa	p.R196I	MVB12B_ENST00000535766.1_Missense_Mutation_p.R189I|MVB12B_ENST00000436593.3_Missense_Mutation_p.R181I|MVB12B_ENST00000545391.1_Missense_Mutation_p.R196I	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	196					protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)	p.R196I(1)									AGAGTACCAAGAAATCATGAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											200	173	182					9																	129157901		2203	4300	6503	128197722	SO:0001583	missense	89853			AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 28", "family with sequence similarity 125, member B"	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.587G>T	9.37:g.129157901G>T	ENSP00000354772:p.Arg196Ile		128197722	Q8N6S7	Missense_Mutation	SNP	ENST00000361171.3	37	CCDS35142.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910183	0.72983	.	.	ENSG00000196814	ENST00000361171;ENST00000545391;ENST00000402437;ENST00000436593;ENST00000535766	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.69	5.69	0.88448	.	0.052934	0.85682	D	0.000000	T	0.63920	0.2552	M	0.62723	1.935	0.80722	D	1	D;B;D;D	0.76494	0.999;0.288;0.999;0.996	D;B;D;P	0.75020	0.985;0.241;0.985;0.898	T	0.61564	-0.7037	10	0.48119	T	0.1	-1.7583	19.8045	0.96525	0.0:0.0:1.0:0.0	.	189;181;65;196	B7Z4X0;B7Z1P9;Q9H7N7;Q9H7P6	.;.;.;F125B_HUMAN	I	196;196;181;181;189	ENSP00000354772:R196I;ENSP00000441988:R196I;ENSP00000384751:R181I;ENSP00000401379:R181I;ENSP00000442846:R189I	ENSP00000354772:R196I	R	+	2	0	FAM125B	128197722	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.153000	0.77428	2.676000	0.91093	0.655000	0.94253	AGA		0.517	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525		T	129157901	G	T	129157901	3	4	61	1	0	0	0	0	1	0	0	0	5444	942	33	2	609	2	FAM125B	9	129157901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1060400	129157901	12055530	6521	14506										
ZBTB43	23099	broad.mit.edu	37	chr9	129595886	129595886	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcttcccacttaggattCtcagccactgacaagctgta	8	12	1	1	rs376108916		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:129595886C>A	ENST00000373464.4	+	3	1362	c.1098C>A	c.(1096-1098)ttC>ttA	p.F366L	ZBTB43_ENST00000449886.1_Missense_Mutation_p.F366L|ZBTB43_ENST00000373457.1_Missense_Mutation_p.F366L	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F366L(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						ACTTAGGATTCTCAGCCACTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	9											73	73	73					9																	129595886		2203	4300	6503	128635707	SO:0001583	missense	23099			AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	17908	protein-coding gene	gene with protein product			"zinc finger protein 297B"	ZNF297B			Standard	NM_014007		Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.1098C>A	9.37:g.129595886C>A	ENSP00000362563:p.Phe366Leu		128635707	Q5JU96	Missense_Mutation	SNP	ENST00000373464.4	37	CCDS6867.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518674	0.44763	.	.	ENSG00000169155	ENST00000449886;ENST00000373464;ENST00000373457	T;T;T	0.13901	2.55;2.55;2.55	5.64	0.604	0.17547	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.09598	0.0236	L	0.29908	0.895	0.34401	D	0.695319	B	0.32409	0.37	B	0.35607	0.206	T	0.33033	-0.9884	10	0.15952	T	0.53	.	11.05	0.47880	0.0:0.6154:0.0:0.3846	.	366	O43298	ZBT43_HUMAN	L	366	ENSP00000390344:F366L;ENSP00000362563:F366L;ENSP00000362556:F366L	ENSP00000362556:F366L	F	+	3	2	ZBTB43	128635707	0.969000	0.33509	0.996000	0.52242	0.971000	0.66376	0.057000	0.14279	0.134000	0.18681	-0.258000	0.10820	TTC		0.483	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054124.1	NM_001135776		A	129595886	C	A	129595886	3	1	61	1	0	0	0	0	1	0	0	0	17583	912	32	2	1100	2	ZBTB43	9	129595886	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	437985	129595886	11617545	6522	14507										
ZBTB34	403341	broad.mit.edu	37	chr9	129642585	129642585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccaatgtatcagaagctTttggaagtttgagtaattcc	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:129642585T>G	ENST00000373452.2	+	1	959	c.895T>G	c.(895-897)Ttt>Gtt	p.F299V	ZBTB34_ENST00000319119.4_Missense_Mutation_p.F303V			Q8NCN2	ZBT34_HUMAN	zinc finger and BTB domain containing 34	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F303V(1)		endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12						ATCAGAAGCTTTTGGAAGTTT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											56	59	58					9																	129642585		2008	4207	6215	128682406	SO:0001583	missense	403341			DQ227306	CCDS48023.1	9q33.3	2013-01-08			ENSG00000177125	ENSG00000177125		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31446	protein-coding gene	gene with protein product		611692				16718364	Standard	NM_001099270		Approved	KIAA1993, MGC24652, ZNF918	uc004bqm.4	Q8NCN2	OTTHUMG00000020694	ENST00000373452.2:c.895T>G	9.37:g.129642585T>G	ENSP00000362551:p.Phe299Val		128682406	Q38IA7|Q5VYE9	Missense_Mutation	SNP	ENST00000373452.2	37	CCDS48023.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.592683	0.66219	.	.	ENSG00000177125	ENST00000319119;ENST00000373452	T;T	0.08546	3.08;3.09	5.78	5.78	0.91487	.	0.159187	0.44902	D	0.000420	T	0.06872	0.0175	L	0.29908	0.895	0.58432	D	0.999992	B	0.30068	0.267	B	0.22386	0.039	T	0.35101	-0.9802	10	0.11485	T	0.65	.	16.1095	0.81250	0.0:0.0:0.0:1.0	.	299	Q8NCN2	ZBT34_HUMAN	V	303;299	ENSP00000317534:F303V;ENSP00000362551:F299V	ENSP00000317534:F303V	F	+	1	0	ZBTB34	128682406	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.430000	0.80321	2.205000	0.71048	0.533000	0.62120	TTT		0.542	ZBTB34-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001099270		G	129642585	T	G	129642585	3	3	61	1	0	0	0	0	1	0	0	0	17576	1841	64	4	897	4	ZBTB34	9	129642585	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	46699	129642585	11570846	6523	14508										
RALGPS1	9649	broad.mit.edu	37	chr9	129831541	129831541	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacaagactacctttgaGaaattggactacctgatgtc	8	8	0	4	rs375120770		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:129831541G>T	ENST00000259351.5	+	8	783	c.516G>T	c.(514-516)gaG>gaT	p.E172D	RALGPS1_ENST00000394022.3_Missense_Mutation_p.E172D|RALGPS1_ENST00000373434.1_Missense_Mutation_p.E172D|RALGPS1_ENST00000373436.1_Missense_Mutation_p.E172D|RALGPS1_ENST00000424082.2_Missense_Mutation_p.E172D	NM_014636.2	NP_055451.1	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	172	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ral GTPase activity (GO:0032852)|regulation of Ral protein signal transduction (GO:0032485)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.E172D(2)		kidney(2)|large_intestine(6)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						CTACCTTTGAGAAATTGGACT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	9											91	91	91					9																	129831541		2203	4300	6503	128871362	SO:0001583	missense	9649			AB002349	CCDS35143.1, CCDS55344.1, CCDS55345.1, CCDS55346.1	9q33.3	2013-01-10			ENSG00000136828	ENSG00000136828		"Pleckstrin homology (PH) domain containing"	16851	protein-coding gene	gene with protein product		614444				9205841, 10747847	Standard	NM_001190728		Approved	RALGPS1A, RALGEF2, KIAA0351	uc004bqo.2	Q5JS13	OTTHUMG00000020696	ENST00000259351.5:c.516G>T	9.37:g.129831541G>T	ENSP00000259351:p.Glu172Asp		128871362	B4DR86|E9PBQ5|O15059|Q5JT60|Q5JT65|Q5JUG5|Q8N4S6|Q8N5H4|Q8WUV7|Q9NZ16	Missense_Mutation	SNP	ENST00000259351.5	37	CCDS35143.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.445877	0.25987	.	.	ENSG00000136828	ENST00000259351;ENST00000424082;ENST00000394022;ENST00000373439;ENST00000319107;ENST00000373436;ENST00000373434	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.34	4.43	0.53597	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	L	0.33093	0.98	0.58432	D	0.999991	B;B;B;B	0.27951	0.006;0.009;0.195;0.034	B;B;B;B	0.22880	0.024;0.021;0.035;0.042	T	0.03750	-1.1007	10	0.18276	T	0.48	.	12.2273	0.54468	0.1364:0.0:0.8636:0.0	.	172;172;172;172	E9PBQ5;Q5JS13-3;Q5JS13-2;Q5JS13	.;.;.;RGPS1_HUMAN	D	172;172;172;172;142;172;172	ENSP00000259351:E172D;ENSP00000415630:E172D;ENSP00000377590:E172D;ENSP00000317149:E142D;ENSP00000362535:E172D;ENSP00000362533:E172D	ENSP00000259351:E172D	E	+	3	2	RALGPS1	128871362	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	3.276000	0.51646	2.684000	0.91462	0.637000	0.83480	GAG		0.373	RALGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054133.1	NM_014636		T	129831541	G	T	129831541	3	4	61	1	0	0	0	0	1	0	0	0	13054	933	33	2	542	2	RALGPS1	9	129831541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188956	129831541	11381890	6524	14509										
ZNF79	7633	broad.mit.edu	37	chr9	130206519	130206519	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacacaccgagagcttcaaGaactcggaaatcctgaaacc	7	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:130206519G>T	ENST00000342483.5	+	5	946	c.540G>T	c.(538-540)aaG>aaT	p.K180N	ZNF79_ENST00000543471.1_Missense_Mutation_p.K156N	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K180N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						AGAGCTTCAAGAACTCGGAAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	9											107	102	104					9																	130206519		2203	4300	6503	129246340	SO:0001583	missense	7633			X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"Zinc fingers, C2H2-type"	13153	protein-coding gene	gene with protein product		194552	"zinc finger protein 79 (pT7)"			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.540G>T	9.37:g.130206519G>T	ENSP00000362446:p.Lys180Asn		129246340	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	37	CCDS6871.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817780	0.32145	.	.	ENSG00000196152	ENST00000342483;ENST00000543471	T;T	0.06528	3.29;3.29	4.01	0.00856	0.14075	.	.	.	.	.	T	0.02807	0.0084	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46610	-0.9179	9	0.25106	T	0.35	.	0.7442	0.00979	0.2968:0.1643:0.3707:0.1682	.	180	Q15937	ZNF79_HUMAN	N	180;156	ENSP00000362446:K180N;ENSP00000438418:K156N	ENSP00000362446:K180N	K	+	3	2	ZNF79	129246340	0.016000	0.18221	0.000000	0.03702	0.584000	0.36387	0.724000	0.25954	-0.189000	0.10482	0.655000	0.94253	AAG		0.478	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135		T	130206519	G	T	130206519	3	4	61	1	0	0	0	0	1	0	0	0	18200	933	33	2	558	2	ZNF79	9	130206519	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	374978	130206519	11006912	6525	14510										
SH2D3C	10044	broad.mit.edu	37	chr9	130509431	130509431	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgctggccataccagtgCtgtaggcaggggagctaggg	16	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:130509431C>A	ENST00000314830.8	-	6	1372	c.1259G>T	c.(1258-1260)aGc>aTc	p.S420I	SH2D3C_ENST00000429553.1_Missense_Mutation_p.S66I|SH2D3C_ENST00000373277.4_Missense_Mutation_p.S263I|SH2D3C_ENST00000420366.1_Missense_Mutation_p.S262I|SH2D3C_ENST00000373274.3_Missense_Mutation_p.S260I|SH2D3C_ENST00000373276.3_Missense_Mutation_p.S352I|SH2D3C_ENST00000471939.1_Intron	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	420					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)	p.S420I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CATACCAGTGCTGTAGGCAGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											95	93	94					9																	130509431		2203	4300	6503	129549252	SO:0001583	missense	10044			AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.1259G>T	9.37:g.130509431C>A	ENSP00000317817:p.Ser420Ile		129549252	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	37	CCDS6877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.8|26.8	4.775011|4.775011	0.90108|0.90108	.|.	.|.	ENSG00000095370|ENSG00000095370	ENST00000440630|ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830	.|T;T;T;T;T;T	.|0.53423	.|0.62;0.62;0.62;0.62;0.62;0.62	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.152755	.|0.64402	.|D	.|0.000001	T|T	0.67401|0.67401	0.2889|0.2889	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	.|P;P;D;D;D	.|0.89917	.|0.92;0.954;0.999;1.0;0.996	.|P;P;D;D;P	.|0.85130	.|0.468;0.622;0.994;0.997;0.865	T|T	0.66544|0.66544	-0.5897|-0.5897	5|10	.|0.48119	.|T	.|0.1	-22.8567|-22.8567	18.3472|18.3472	0.90326|0.90326	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|260;420;352;263;262	.|E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.|.;SH2D3_HUMAN;.;.;.	S|I	257|263;262;352;260;66;420	.|ENSP00000362374:S263I;ENSP00000388536:S262I;ENSP00000362373:S352I;ENSP00000362371:S260I;ENSP00000394632:S66I;ENSP00000317817:S420I	.|ENSP00000317817:S420I	A|S	-|-	1|2	0|0	SH2D3C|SH2D3C	129549252|129549252	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.872000|0.872000	0.50106|0.50106	7.372000|7.372000	0.79612|0.79612	2.584000|2.584000	0.87258|0.87258	0.561000|0.561000	0.74099|0.74099	GCA|AGC		0.577	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		A	130509431	C	A	130509431	3	1	61	1	0	0	0	0	1	0	0	0	14271	797	28	2	1351	2	SH2D3C	9	130509431	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	302912	130509431	10704000	6526	14511										
ST6GALNAC4	27090	broad.mit.edu	37	chr9	130674552	130674552	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccccaggctcaccggttCttgcccgtctcgtcctggaa	11	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:130674552C>A	ENST00000335791.5	-	4	881	c.606G>T	c.(604-606)aaG>aaT	p.K202N	ST6GALNAC4_ENST00000343609.2_Missense_Mutation_p.K118N|ST6GALNAC4_ENST00000495983.1_5'UTR	NM_175039.3	NP_778204.1	Q9H4F1	SIA7D_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	202					cellular protein metabolic process (GO:0044267)|glycolipid metabolic process (GO:0006664)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity (GO:0047290)|sialyltransferase activity (GO:0008373)	p.K202N(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7						CTCACCGGTTCTTGCCCGTCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											38	36	36					9																	130674552		2203	4299	6502	129714373	SO:0001583	missense	27090			AB035172	CCDS6883.1	9q34	2013-03-01	2005-02-07	2005-02-07	ENSG00000136840	ENSG00000136840	2.4.99.7	"Sialyltransferases"	17846	protein-coding gene	gene with protein product		606378	"sialyltransferase 7D ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"	SIAT7D		10207017, 11062056	Standard	XM_005251922		Approved	ST6GALNACIV, SIAT3C	uc004bss.3	Q9H4F1	OTTHUMG00000020724	ENST00000335791.5:c.606G>T	9.37:g.130674552C>A	ENSP00000336733:p.Lys202Asn		129714373	Q5T9D0|Q9NWU6|Q9UKU1|Q9ULB9|Q9Y3G3|Q9Y3G4	Missense_Mutation	SNP	ENST00000335791.5	37	CCDS6883.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736010	0.69189	.	.	ENSG00000136840	ENST00000541933;ENST00000335791;ENST00000343609;ENST00000361444	T;T;T	0.35789	1.29;1.37;1.37	5.05	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.63248	0.2495	M	0.86651	2.83	0.53005	D	0.999966	D	0.89917	1.0	D	0.97110	1.0	T	0.68743	-0.5328	10	0.52906	T	0.07	-35.2396	12.7783	0.57461	0.0:0.9207:0.0:0.0793	.	202	Q9H4F1	SIA7D_HUMAN	N	118;202;118;118	ENSP00000336733:K202N;ENSP00000340382:K118N;ENSP00000355130:K118N	ENSP00000336733:K202N	K	-	3	2	ST6GALNAC4	129714373	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.889000	0.39718	1.360000	0.45960	0.462000	0.41574	AAG		0.637	ST6GALNAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054317.2	NM_175040		A	130674552	C	A	130674552	3	1	61	1	0	0	0	0	1	0	0	0	15265	912	32	2	314	2	ST6GALNAC4	9	130674552	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165121	130674552	10538879	6527	14512										
CIZ1	25792	broad.mit.edu	37	chr9	130931780	130931780	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaacggtgcagaagggtcGcaaggattgtttggcaatct	14	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:130931780G>A	ENST00000393608.1	-	13	2252	c.2050C>T	c.(2050-2052)Cga>Tga	p.R684*	CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000372948.3_Nonsense_Mutation_p.R628*|CIZ1_ENST00000325721.8_Nonsense_Mutation_p.R655*|CIZ1_ENST00000372938.5_Nonsense_Mutation_p.R684*|CIZ1_ENST00000357558.5_Nonsense_Mutation_p.R656*|CIZ1_ENST00000277465.4_Nonsense_Mutation_p.R656*|CIZ1_ENST00000372954.1_Nonsense_Mutation_p.R604*|CIZ1_ENST00000541172.1_Nonsense_Mutation_p.R583*|CIZ1_ENST00000538431.1_Nonsense_Mutation_p.R710*	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	684					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R684*(2)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CAGAAGGGTCGCAAGGATTGT	0.567																																																2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	9											106	96	100					9																	130931780		2203	4300	6503	129971601	SO:0001587	stop_gained	25792			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.2050C>T	9.37:g.130931780G>A	ENSP00000377232:p.Arg684*		129971601	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Nonsense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	G	40	8.351770	0.98772	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	.	.	.	5.34	2.01	0.26516	.	0.000000	0.38548	N	0.001650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.3476	14.4788	0.67564	0.0:0.0:0.4026:0.5974	.	.	.	.	X	604;684;710;656;655;623;583;656;628;684;606	.	.	R	-	1	2	CIZ1	129971601	1.000000	0.71417	0.997000	0.53966	0.866000	0.49608	1.560000	0.36331	0.148000	0.19059	0.462000	0.41574	CGA		0.567	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		A	130931780	G	A	130931780	4	1	61	1	0	0	0	0	0	1	0	0	3447	1095	38	1	666	1	CIZ1	9	130931780	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	257228	130931780	10281651	6528	14513										
DNM1	1759	broad.mit.edu	37	chr9	131001759	131001759	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatatcgagctggcttacatGaacaccaaccatgaggactt	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131001759G>T	ENST00000372923.3	+	12	1550	c.1458G>T	c.(1456-1458)atG>atT	p.M486I	DNM1_ENST00000393594.3_Missense_Mutation_p.M486I|DNM1_ENST00000486160.1_Missense_Mutation_p.M486I|DNM1_ENST00000341179.7_Missense_Mutation_p.M486I|DNM1_ENST00000475805.1_Missense_Mutation_p.M486I	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	486					endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.M486I(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						TGGCTTACATGAACACCAACC	0.493																																					GBM(113;146 1575 2722 28670 29921)											2	Substitution - Missense(2)	large_intestine(2)	9											352	344	347					9																	131001759		2203	4300	6503	130041580	SO:0001583	missense	1759			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1458G>T	9.37:g.131001759G>T	ENSP00000362014:p.Met486Ile		130041580	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243424	0.22796	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160;ENST00000543158	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	4.8	4.8	0.61643	Dynamin central domain (1);Pleckstrin homology-type (1);	0.043207	0.85682	D	0.000000	T	0.32734	0.0839	N	0.01493	-0.835	0.80722	D	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.08055	0.003;0.001;0.003	T	0.42015	-0.9476	10	0.02654	T	1	-0.327	18.4066	0.90538	0.0:0.0:1.0:0.0	.	486;486;486	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	I	486;486;486;481;486;486;31	ENSP00000419225:M486I;ENSP00000345680:M486I;ENSP00000362014:M486I;ENSP00000377219:M486I;ENSP00000420045:M486I	ENSP00000345680:M486I	M	+	3	0	DNM1	130041580	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.062000	0.64326	2.653000	0.90120	0.563000	0.77884	ATG		0.493	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		T	131001759	G	T	131001759	3	4	61	1	0	0	0	0	1	0	0	0	4681	1290	45	2	1504	2	DNM1	9	131001759	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69979	131001759	10211672	6529	14514										
ODF2	4957	broad.mit.edu	37	chr9	131233697	131233697	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagactgagcacgagaacacGgtgttgaggcacaacatcga	13	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131233697G>A	ENST00000434106.3	+	6	894	c.531G>A	c.(529-531)acG>acA	p.T177T	ODF2_ENST00000393527.3_Silent_p.T153T|ODF2_ENST00000372807.5_Silent_p.T172T|ODF2_ENST00000604420.1_Silent_p.T177T|ODF2_ENST00000546203.1_Silent_p.T158T|ODF2_ENST00000535026.1_Intron|ODF2_ENST00000444119.2_Silent_p.T153T|ODF2_ENST00000393533.2_Silent_p.T177T|ODF2_ENST00000372791.3_Silent_p.T158T|ODF2_ENST00000351030.3_Silent_p.T172T|RP11-339B21.9_ENST00000420801.1_RNA|ODF2_ENST00000372814.3_Silent_p.T221T|ODF2_ENST00000448249.3_Silent_p.T96T	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	177					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.T153T(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						ACGAGAACACGGTGTTGAGGC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	9											189	162	171					9																	131233697		2203	4300	6503	130273518	SO:0001819	synonymous_variant	4957			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.531G>A	9.37:g.131233697G>A			130273518	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																				0.567	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			A	131233697	G	A	131233697	2	1	61	1	0	0	0	0	0	0	0	1	10858	1103	39	1		1	ODF2	9	131233697	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231938	131233697	9979734	6530	14515										
SPTAN1	6709	broad.mit.edu	37	chr9	131329190	131329190	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatgctgaagagctggaGaaatggatacaggaaaaact	13	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131329190G>T	ENST00000372731.4	+	2	281	c.171G>T	c.(169-171)gaG>gaT	p.E57D	SPTAN1_ENST00000358161.5_Missense_Mutation_p.E57D|SPTAN1_ENST00000372739.3_Missense_Mutation_p.E57D	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	57					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.E57D(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AAGAGCTGGAGAAATGGATAC	0.443																																					NSCLC(120;833 1744 2558 35612 37579)											1	Substitution - Missense(1)	large_intestine(1)	9											68	69	68					9																	131329190		2203	4300	6503	130369011	SO:0001583	missense	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.171G>T	9.37:g.131329190G>T	ENSP00000361816:p.Glu57Asp		130369011	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162363	0.57368	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.54866	0.55;0.55;0.55	5.51	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.67401	0.2889	M	0.79614	2.46	0.51482	D	0.999924	P;P;P;B;D	0.54772	0.916;0.945;0.616;0.06;0.968	P;D;B;B;D	0.63793	0.892;0.918;0.341;0.122;0.91	T	0.64219	-0.6459	10	0.29301	T	0.29	.	11.1296	0.48339	0.1319:0.0:0.8681:0.0	.	57;57;57;57;57	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	D	57	ENSP00000350882:E57D;ENSP00000361816:E57D;ENSP00000361824:E57D	ENSP00000350882:E57D	E	+	3	2	SPTAN1	130369011	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.476000	0.45171	2.742000	0.94016	0.655000	0.94253	GAG		0.443	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131329190	G	T	131329190	3	4	61	1	0	0	0	0	1	0	0	0	15156	933	33	2	173	2	SPTAN1	9	131329190	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95493	131329190	9884241	6531	14516										
SPTAN1	6709	broad.mit.edu	37	chr9	131374463	131374463	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagagccagaaactgaaaGaagccaacaagcagcagaac	9	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131374463G>T	ENST00000372731.4	+	38	5076	c.4966G>T	c.(4966-4968)Gaa>Taa	p.E1656*	SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.E1661*|SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.E1661*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1656					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.E1656*(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GAAACTGAAAGAAGCCAACAA	0.522																																					NSCLC(120;833 1744 2558 35612 37579)											1	Substitution - Nonsense(1)	large_intestine(1)	9											130	128	129					9																	131374463		2203	4300	6503	130414284	SO:0001587	stop_gained	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4966G>T	9.37:g.131374463G>T	ENSP00000361816:p.Glu1656*		130414284	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	47	12.990343	0.99711	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.756	0.96291	0.0:0.0:1.0:0.0	.	.	.	.	X	1661;1656;1661;1636	.	ENSP00000350882:E1661X	E	+	1	0	SPTAN1	130414284	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	9.420000	0.97426	2.665000	0.90641	0.655000	0.94253	GAA		0.522	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131374463	G	T	131374463	4	4	61	1	0	0	0	0	0	1	0	0	15156	943	33	2	5131	2	SPTAN1	9	131374463	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45273	131374463	9838968	6532	14517										
SPTAN1	6709	broad.mit.edu	37	chr9	131379971	131379971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggccgggacctaaccggcGtgcagaacctgaggaagaag	15	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131379971G>A	ENST00000372731.4	+	41	5505	c.5395G>A	c.(5395-5397)Gtg>Atg	p.V1799M	SPTAN1_ENST00000358161.5_Missense_Mutation_p.V1804M|SPTAN1_ENST00000372739.3_Missense_Mutation_p.V1804M	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1799					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.V1799M(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						CCTAACCGGCGTGCAGAACCT	0.602																																					NSCLC(120;833 1744 2558 35612 37579)											1	Substitution - Missense(1)	large_intestine(1)	9											58	61	60					9																	131379971		2203	4300	6503	130419792	SO:0001583	missense	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5395G>A	9.37:g.131379971G>A	ENSP00000361816:p.Val1799Met		130419792	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468867	0.63625	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719;ENST00000372721	T;T;T	0.57436	0.4;0.4;0.4	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.83022	0.5164	H	0.96662	3.86	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.989;0.988;0.993	D	0.88194	0.2879	10	0.87932	D	0	.	19.9559	0.97218	0.0:0.0:1.0:0.0	.	1779;1804;1799	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	M	1804;1799;1804;1779;48	ENSP00000350882:V1804M;ENSP00000361816:V1799M;ENSP00000361824:V1804M	ENSP00000350882:V1804M	V	+	1	0	SPTAN1	130419792	1.000000	0.71417	0.231000	0.23993	0.094000	0.18550	9.385000	0.97223	2.728000	0.93425	0.462000	0.41574	GTG		0.602	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131379971	G	A	131379971	3	1	61	1	0	0	0	0	1	0	0	0	15156	1145	40	1	5572	1	SPTAN1	9	131379971	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5508	131379971	9833460	6533	14518										
NUP188	23511	broad.mit.edu	37	chr9	131767474	131767474	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacctctctcctgcacagtCgaaagatgctgcagcattac	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:131767474C>T	ENST00000372577.2	+	39	4504	c.4483C>T	c.(4483-4485)Cga>Tga	p.R1495*	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1495					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.R1495*(1)		breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CCTGCACAGTCGAAAGATGCT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											168	138	148					9																	131767474		2203	4300	6503	130807295	SO:0001587	stop_gained	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4483C>T	9.37:g.131767474C>T	ENSP00000361658:p.Arg1495*		130807295	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Nonsense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	C	42	9.756793	0.99256	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	.	.	.	5.23	5.23	0.72850	.	0.186621	0.47093	D	0.000260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-22.8091	17.8008	0.88586	0.0:1.0:0.0:0.0	.	.	.	.	X	1384;1495	.	ENSP00000349125:R1384X	R	+	1	2	NUP188	130807295	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.764000	0.68826	2.446000	0.82766	0.561000	0.74099	CGA		0.522	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131767474	C	T	131767474	4	4	61	1	0	0	0	0	0	1	0	0	10789	876	31	1	4637	1	NUP188	9	131767474	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	387503	131767474	9445957	6534	14519										
ASB6	140459	broad.mit.edu	37	chr9	132400297	132400297	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccacagggtggatatcGaagttttcgggcagctggag	15	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:132400297G>A	ENST00000277458.4	-	6	1203	c.1038C>T	c.(1036-1038)ttC>ttT	p.F346F	RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000450050.2_Silent_p.F267F|ASB6_ENST00000277459.4_3'UTR	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	346					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.F346F(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				GGTGGATATCGAAGTTTTCGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	9											79	75	76					9																	132400297		2203	4300	6503	131440118	SO:0001819	synonymous_variant	140459				CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"Ankyrin repeat domain containing"	17181	protein-coding gene	gene with protein product		615051	"ankyrin repeat and SOCS box-containing 6"				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.1038C>T	9.37:g.132400297G>A			131440118	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																				0.597	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873		A	132400297	G	A	132400297	2	1	61	1	0	0	0	0	0	0	0	1	1028	1049	37	1		1	ASB6	9	132400297	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	632823	132400297	8813134	6535	14520										
TOR1A	1861	broad.mit.edu	37	chr9	132581178	132581178	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggcactcacgttgcctcGaatccacaactgtaactgat	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:132581178G>A	ENST00000351698.4	-	3	514	c.466C>T	c.(466-468)Cga>Tga	p.R156*	TOR1A_ENST00000473084.1_5'Flank	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	156	Interaction with SNAPIN.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.R156*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				ACGTTGCCTCGAATCCACAAC	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											72	63	66					9																	132581178		2203	4300	6503	131620999	SO:0001587	stop_gained	1861			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"dystonia 1, torsion (autosomal dominant; torsin A)"	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.466C>T	9.37:g.132581178G>A	ENSP00000345719:p.Arg156*		131620999	B2RB58|Q53Y64|Q96CA0	Nonsense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	G	37	6.143447	0.97320	.	.	ENSG00000136827	ENST00000427355;ENST00000351698	.	.	.	5.91	5.91	0.95273	.	0.197627	0.49916	D	0.000132	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.9644	14.1594	0.65436	0.0:0.0:0.8505:0.1495	.	.	.	.	X	125;156	.	ENSP00000345719:R156X	R	-	1	2	TOR1A	131620999	0.991000	0.36638	1.000000	0.80357	0.994000	0.84299	3.164000	0.50770	2.793000	0.96121	0.655000	0.94253	CGA		0.468	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113		A	132581178	G	A	132581178	4	1	61	1	0	0	0	0	0	1	0	0	16411	1066	37	1	544	1	TOR1A	9	132581178	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180881	132581178	8632253	6536	14521										
USP20	10868	broad.mit.edu	37	chr9	132620356	132620356	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctatgttggctgcggaGaatcctttgctgaccacagc	11	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:132620356G>T	ENST00000315480.4	+	5	321	c.163G>T	c.(163-165)Gaa>Taa	p.E55*	USP20_ENST00000358355.1_Nonsense_Mutation_p.E55*|USP20_ENST00000372429.3_Nonsense_Mutation_p.E55*			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	55					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.E55*(3)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TGGCTGCGGAGAATCCTTTGC	0.562																																																3	Substitution - Nonsense(3)	large_intestine(3)	9											163	167	166					9																	132620356		2093	4214	6307	131660177	SO:0001587	stop_gained	10868			AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.163G>T	9.37:g.132620356G>T	ENSP00000313811:p.Glu55*		131660177	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Nonsense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792594	0.90453	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.561	0.87908	0.0:0.0:1.0:0.0	.	.	.	.	X	55	.	ENSP00000313811:E55X	E	+	1	0	USP20	131660177	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	9.544000	0.98092	2.374000	0.81015	0.561000	0.74099	GAA		0.562	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132620356	G	T	132620356	4	4	61	1	0	0	0	0	0	1	0	0	17092	943	33	2	173	2	USP20	9	132620356	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39178	132620356	8593075	6537	14522										
USP20	10868	broad.mit.edu	37	chr9	132630302	132630302	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacacccaagagttccttCgctgcctgatggaccagctg	11	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:132630302C>T	ENST00000315480.4	+	11	867	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	USP20_ENST00000358355.1_Missense_Mutation_p.R237C|USP20_ENST00000372429.3_Missense_Mutation_p.R237C			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	237	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R237C(3)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AGAGTTCCTTCGCTGCCTGAT	0.637																																																3	Substitution - Missense(3)	large_intestine(3)	9											40	45	44					9																	132630302		2107	4233	6340	131670123	SO:0001583	missense	10868			AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.709C>T	9.37:g.132630302C>T	ENSP00000313811:p.Arg237Cys		131670123	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.108004	0.77096	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.32272	1.46;1.46;1.46	5.18	4.28	0.50868	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.046636	0.85682	N	0.000000	T	0.51346	0.1669	M	0.73319	2.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.52902	-0.8513	10	0.72032	D	0.01	.	9.4508	0.38725	0.142:0.7813:0.0:0.0767	.	237	Q9Y2K6	UBP20_HUMAN	C	237	ENSP00000361506:R237C;ENSP00000313811:R237C;ENSP00000351122:R237C	ENSP00000313811:R237C	R	+	1	0	USP20	131670123	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.879000	0.63100	1.173000	0.42796	0.561000	0.74099	CGC		0.637	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132630302	C	T	132630302	3	4	61	1	0	0	0	0	1	0	0	0	17092	884	31	1	743	1	USP20	9	132630302	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9946	132630302	8583129	6538	14523										
FNBP1	23048	broad.mit.edu	37	chr9	132720794	132720794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagctgcttccagcaagtCtcgatgtgctgctgtgcttt	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:132720794C>A	ENST00000446176.2	-	5	570	c.384G>T	c.(382-384)gaG>gaT	p.E128D	FNBP1_ENST00000355681.3_Missense_Mutation_p.E128D|FNBP1_ENST00000420781.1_Missense_Mutation_p.E128D	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	128	F-BAR domain.|Interaction with microtubules. {ECO:0000250}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.E128D(1)					Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TCCAGCAAGTCTCGATGTGCT	0.443			T	MLL	AML																																		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	1	Substitution - Missense(1)	large_intestine(1)	9											70	68	69					9																	132720794		1913	4136	6049	131760615	SO:0001583	missense	23048			AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.384G>T	9.37:g.132720794C>A	ENSP00000413625:p.Glu128Asp		131760615	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	37	CCDS48040.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.06|10.06	1.246955|1.246955	0.22796|0.22796	.|.	.|.	ENSG00000187239|ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000355681|ENST00000449089	T;T;T|.	0.17213|.	2.29;2.29;2.29|.	5.58|5.58	2.31|2.31	0.28768|0.28768	.|.	0.103647|.	0.64402|.	D|.	0.000002|.	T|T	0.49779|0.49779	0.1577|0.1577	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	B;P;B;B;D;B;B|.	0.61697|.	0.023;0.954;0.0;0.015;0.99;0.038;0.029|.	B;D;B;B;D;B;B|.	0.70227|.	0.018;0.921;0.001;0.023;0.968;0.028;0.029|.	T|T	0.33292|0.33292	-0.9874|-0.9874	10|5	0.24483|.	T|.	0.36|.	-37.9734|-37.9734	7.5571|7.5571	0.27831|0.27831	0.0:0.6324:0.0:0.3675|0.0:0.6324:0.0:0.3675	.|.	128;128;128;128;89;128;128|.	B7ZL12;B7ZL13;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3|.	.;.;.;.;.;.;FNBP1_HUMAN|.	D|I	128|90	ENSP00000413625:E128D;ENSP00000407548:E128D;ENSP00000347907:E128D|.	ENSP00000347907:E128D|.	E|R	-|-	3|2	2|0	FNBP1|FNBP1	131760615|131760615	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.819000|0.819000	0.46315|0.46315	0.742000|0.742000	0.26216|0.26216	0.699000|0.699000	0.31761|0.31761	0.491000|0.491000	0.48974|0.48974	GAG|AGA		0.443	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2			A	132720794	C	A	132720794	3	1	61	1	0	0	0	0	1	0	0	0	5984	912	32	2	1521	2	FNBP1	9	132720794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90492	132720794	8492637	6539	14524										
ASS1	445	broad.mit.edu	37	chr9	133355131	133355131	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaggtgaccaacgtcaaGgatggcaccacccaccagac	11	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133355131G>T	ENST00000372394.1	+	11	1198	c.717G>T	c.(715-717)aaG>aaT	p.K239N	ASS1_ENST00000352480.5_Missense_Mutation_p.K239N|ASS1_ENST00000372393.3_Missense_Mutation_p.K239N|ASS1_ENST00000493984.2_Intron			P00966	ASSY_HUMAN	argininosuccinate synthase 1	239					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)	p.K239N(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	CCAACGTCAAGGATGGCACCA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	9											78	70	73					9																	133355131		2203	4300	6503	132344952	SO:0001583	missense	445			X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.717G>T	9.37:g.133355131G>T	ENSP00000361471:p.Lys239Asn		132344952	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	37	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	G	8.960	0.970365	0.18659	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393	D;D;D	0.99136	-5.47;-5.47;-5.47	4.91	1.47	0.22746	Argininosuccinate synthetase, catalytic/multimerisation domain body (1);	0.316553	0.32386	U	0.006170	D	0.97018	0.9026	L	0.51422	1.61	0.32211	N	0.57656	B;B;B;B;B	0.11235	0.001;0.004;0.004;0.001;0.001	B;B;B;B;B	0.15870	0.003;0.014;0.014;0.003;0.003	D	0.96402	0.9297	10	0.62326	D	0.03	.	10.1936	0.43041	0.2743:0.0:0.7257:0.0	.	239;122;122;239;239	A8KAP9;B4E395;E9PDT0;Q5T6L4;P00966	.;.;.;.;ASSY_HUMAN	N	239	ENSP00000253004:K239N;ENSP00000361471:K239N;ENSP00000361469:K239N	ENSP00000361470:K239N	K	+	3	2	ASS1	132344952	0.992000	0.36948	0.998000	0.56505	0.903000	0.53119	0.382000	0.20635	0.461000	0.27071	0.467000	0.42956	AAG		0.647	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050		T	133355131	G	T	133355131	3	4	61	1	0	0	0	0	1	0	0	0	1062	991	35	2	751	2	ASS1	9	133355131	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	634337	133355131	7858300	6540	14525										
PRDM12	59335	broad.mit.edu	37	chr9	133543638	133543638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcaagtgtgcacgtaacGaacaggagcagaacctggag	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133543638G>A	ENST00000253008.2	+	3	568	c.508G>A	c.(508-510)Gaa>Aaa	p.E170K		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	170	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				neurogenesis (GO:0022008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.E170K(1)		kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		TGCACGTAACGAACAGGAGCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											218	160	180					9																	133543638		2203	4300	6503	132533459	SO:0001583	missense	59335			AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"Zinc fingers, C2H2-type"	13997	protein-coding gene	gene with protein product	"PR-domain containing protein 12", "PR-domain zinc finger protein 12"					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.508G>A	9.37:g.133543638G>A	ENSP00000253008:p.Glu170Lys		132533459	A3KFK9	Missense_Mutation	SNP	ENST00000253008.2	37	CCDS6934.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560151	0.65538	.	.	ENSG00000130711	ENST00000253008	T	0.40476	1.03	5.21	5.21	0.72293	SET domain (2);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	L	0.31371	0.925	0.58432	D	0.999999	D	0.69078	0.997	D	0.65233	0.933	T	0.25152	-1.0140	10	0.08599	T	0.76	-28.7162	17.7439	0.88414	0.0:0.0:1.0:0.0	.	170	Q9H4Q4	PRD12_HUMAN	K	170	ENSP00000253008:E170K	ENSP00000253008:E170K	E	+	1	0	PRDM12	132533459	1.000000	0.71417	0.646000	0.29493	0.803000	0.45373	9.238000	0.95380	2.423000	0.82170	0.655000	0.94253	GAA		0.562	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619		A	133543638	G	A	133543638	3	1	61	1	0	0	0	0	1	0	0	0	12487	1059	37	1	518	1	PRDM12	9	133543638	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188507	133543638	7669793	6541	14526										
EXOSC2	23404	broad.mit.edu	37	chr9	133578479	133578479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaggtgatatcccggcttCggaactgcatcatctcgctg	12	11	2	2	rs561877923		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133578479C>T	ENST00000372358.5	+	8	783	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	EXOSC2_ENST00000467138.1_3'UTR|EXOSC2_ENST00000372352.3_Missense_Mutation_p.R230W|EXOSC2_ENST00000372351.3_Missense_Mutation_p.R208W|EXOSC2_ENST00000546165.1_Missense_Mutation_p.R212W			Q13868	EXOS2_HUMAN	exosome component 2	238					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)	p.R238W(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		ATCCCGGCTTCGGAACTGCAT	0.502																																					Pancreas(134;1683 1824 10118 27928 31640)											1	Substitution - Missense(1)	large_intestine(1)	9											152	136	142					9																	133578479		2203	4300	6503	132568300	SO:0001583	missense	23404			AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.712C>T	9.37:g.133578479C>T	ENSP00000361433:p.Arg238Trp		132568300	A3KFL3|B4DKK6|Q9NUY4	Missense_Mutation	SNP	ENST00000372358.5	37	CCDS6935.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736711	0.69304	.	.	ENSG00000130713	ENST00000372358;ENST00000546165;ENST00000372352;ENST00000372351;ENST00000495699	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.84602	0.5508	M	0.91561	3.22	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.87469	0.2413	9	0.87932	D	0	-25.8006	13.3613	0.60657	0.1573:0.8427:0.0:0.0	.	212;238	B4DKK6;Q13868	.;EXOS2_HUMAN	W	238;212;230;208;215	.	ENSP00000361426:R208W	R	+	1	2	EXOSC2	132568300	0.999000	0.42202	1.000000	0.80357	0.598000	0.36846	3.960000	0.56752	2.648000	0.89879	0.650000	0.86243	CGG		0.502	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285		T	133578479	C	T	133578479	3	4	61	1	0	0	0	0	1	0	0	0	5328	875	31	1	742	1	EXOSC2	9	133578479	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34841	133578479	7634952	6542	14527										
ABL1	25	broad.mit.edu	37	chr9	133729569	133729569	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaatgaccccaaccttttCgttgcactgtatgattttgt	7	9	0	2	rs372724991		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133729569C>T	ENST00000318560.5	+	2	579	c.198C>T	c.(196-198)ttC>ttT	p.F66F		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	66	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)	p.F66F(2)		breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCAACCTTTTCGTTGCACTGT	0.478			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	2	Substitution - coding silent(2)	large_intestine(2)	9						C	,	0,4406		0,0,2203	133	131	132		198,255	-11.2	0.1	9		132	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	66/1131,85/1150	133729569	1,13005	2203	4300	6503	132719390	SO:0001819	synonymous_variant	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.198C>T	9.37:g.133729569C>T			132719390	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																				0.478	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133729569	C	T	133729569	2	4	61	1	0	0	0	0	0	0	0	1	92	883	31	1		1	ABL1	9	133729569	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151090	133729569	7483862	6543	14528										
LAMC3	10319	broad.mit.edu	37	chr9	133921035	133921035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgcatcacatcctcagcGatttccaccagggtaagaga	10	11	2	1	rs200393760		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133921035G>A	ENST00000361069.4	+	8	1640	c.1507G>A	c.(1507-1509)Gat>Aat	p.D503N	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	503	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.D503N(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CATCCTCAGCGATTTCCACCA	0.597													G|||	1	0.000199681	0	0	5008	,	,		18699	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											83	72	76					9																	133921035		2203	4300	6503	132910856	SO:0001583	missense	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1507G>A	9.37:g.133921035G>A	ENSP00000354360:p.Asp503Asn		132910856	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	9.692	1.152172	0.21371	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.28895	1.59	4.53	2.69	0.31865	.	0.207319	0.49305	D	0.000144	T	0.26702	0.0653	M	0.65975	2.015	0.29291	N	0.869379	B	0.25272	0.122	B	0.17098	0.017	T	0.15521	-1.0434	10	0.32370	T	0.25	.	6.3777	0.21517	0.3019:0.0:0.6981:0.0	.	503	Q9Y6N6	LAMC3_HUMAN	N	503	ENSP00000354360:D503N	ENSP00000347156:D503N	D	+	1	0	LAMC3	132910856	0.126000	0.22350	0.178000	0.23040	0.027000	0.11550	0.453000	0.21811	0.541000	0.28827	0.555000	0.69702	GAT		0.597	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133921035	G	A	133921035	3	1	61	1	0	0	0	0	1	0	0	0	8638	1058	37	1	1537	1	LAMC3	9	133921035	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191466	133921035	7292396	6544	14529										
LAMC3	10319	broad.mit.edu	37	chr9	133946984	133946984	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaggccccaaggggggaCgtctaccagggccatcacct	15	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:133946984C>T	ENST00000361069.4	+	18	3316	c.3183C>T	c.(3181-3183)gaC>gaT	p.D1061D	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1061	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.D1061D(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CAAGGGGGGACGTCTACCAGG	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	9											45	45	45					9																	133946984		2203	4300	6503	132936805	SO:0001819	synonymous_variant	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3183C>T	9.37:g.133946984C>T			132936805	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																				0.657	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		T	133946984	C	T	133946984	2	4	61	1	0	0	0	0	0	0	0	1	8638	535	19	1		1	LAMC3	9	133946984	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25949	133946984	7266447	6545	14530										
NUP214	8021	broad.mit.edu	37	chr9	134025762	134025762	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagggacatcagtggaaaGattcagatcctgtaatggct	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134025762G>T	ENST00000359428.5	+	15	2236	c.2092G>T	c.(2092-2094)Gat>Tat	p.D698Y	RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.D688Y|RP11-544A12.4_ENST00000590461.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.D699Y			P35658	NU214_HUMAN	nucleoporin 214kDa	698	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.D698Y(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TCAGTGGAAAGATTCAGATCC	0.443			T	"DEK, SET, ABL1"	"AML, T-ALL"																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	1	Substitution - Missense(1)	large_intestine(1)	9											108	104	105					9																	134025762		2203	4300	6503	133015583	SO:0001583	missense	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.2092G>T	9.37:g.134025762G>T	ENSP00000352400:p.Asp698Tyr		133015583	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068722	0.93950	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.48201	0.97;0.97;0.82	6.16	6.16	0.99307	.	0.489601	0.17090	N	0.187424	T	0.50786	0.1636	N	0.08118	0	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.66497	0.944;0.912;0.912	T	0.59461	-0.7450	10	0.87932	D	0	-7.7808	18.0158	0.89239	0.0:0.0:1.0:0.0	.	292;688;698	Q5JUP9;P35658-4;P35658	.;.;NU214_HUMAN	Y	698;688;699;687;292;127	ENSP00000352400:D698Y;ENSP00000396576:D688Y;ENSP00000405014:D699Y	ENSP00000352400:D698Y	D	+	1	0	NUP214	133015583	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.714000	0.91412	2.937000	0.99478	0.650000	0.86243	GAT		0.443	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134025762	G	T	134025762	3	4	61	1	0	0	0	0	1	0	0	0	10793	942	33	2	2150	2	NUP214	9	134025762	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78778	134025762	7187669	6546	14531										
NUP214	8021	broad.mit.edu	37	chr9	134077036	134077036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctttgtattttacaggtTttgggtctagtaatactggt	9	4	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134077036T>A	ENST00000359428.5	+	30	5668	c.5524T>A	c.(5524-5526)Ttt>Att	p.F1842I	NUP214_ENST00000483497.2_Missense_Mutation_p.F668I|NUP214_ENST00000411637.2_Missense_Mutation_p.F1832I|NUP214_ENST00000451030.1_Missense_Mutation_p.F1843I			P35658	NU214_HUMAN	nucleoporin 214kDa	1842	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.F1842I(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTTTACAGGTTTTGGGTCTAG	0.358			T	"DEK, SET, ABL1"	"AML, T-ALL"																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	1	Substitution - Missense(1)	large_intestine(1)	9											178	163	168					9																	134077036		2203	4300	6503	133066857	SO:0001583	missense	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5524T>A	9.37:g.134077036T>A	ENSP00000352400:p.Phe1842Ile		133066857	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.805310	0.90623	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497	T;T;T;T	0.57273	1.16;1.17;1.17;0.41	5.81	5.81	0.92471	.	0.163922	0.29165	N	0.012950	T	0.51244	0.1663	N	0.08118	0	0.53005	D	0.999961	D;D;D;D	0.67145	0.996;0.996;0.996;0.996	D;D;D;D	0.77557	0.99;0.99;0.99;0.99	T	0.51284	-0.8725	10	0.15499	T	0.54	-16.7512	15.3601	0.74464	0.0:0.0:0.0:1.0	.	668;1436;1832;1842	B7ZAV2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	I	1842;1832;1843;1821;1436;1271;668	ENSP00000352400:F1842I;ENSP00000396576:F1832I;ENSP00000405014:F1843I;ENSP00000436793:F668I	ENSP00000352400:F1842I	F	+	1	0	NUP214	133066857	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.454000	0.66651	2.225000	0.72522	0.455000	0.32223	TTT		0.358	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134077036	T	A	134077036	3	1	61	1	0	0	0	0	1	0	0	0	10793	1841	64	5	5642	5	NUP214	9	134077036	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	51274	134077036	7136395	6547	14532										
FAM78A	286336	broad.mit.edu	37	chr9	134136326	134136326	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcgggatgggctcattCttgctcaggattttgggctg	16	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134136326C>A	ENST00000372271.3	-	2	1102	c.735G>T	c.(733-735)aaG>aaT	p.K245N	FAM78A_ENST00000372269.3_Missense_Mutation_p.K242N|FAM78A_ENST00000247295.4_5'UTR	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	245								p.K245N(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		TGGGCTCATTCTTGCTCAGGA	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	9											86	91	89					9																	134136326		2203	4300	6503	133126147	SO:0001583	missense	286336			AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 59"	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.735G>T	9.37:g.134136326C>A	ENSP00000361345:p.Lys245Asn		133126147	Q86VQ9|Q9H7P4	Missense_Mutation	SNP	ENST00000372271.3	37	CCDS6941.2	.	.	.	.	.	.	.	.	.	.	C	14.12	2.440643	0.43326	.	.	ENSG00000126882	ENST00000372269;ENST00000372271;ENST00000464831	D;D;D	0.94497	-3.44;-3.44;-3.44	4.75	2.87	0.33458	.	0.088221	0.85682	D	0.000000	D	0.87589	0.6215	L	0.27053	0.805	0.58432	D	0.999994	B;B	0.25441	0.002;0.126	B;B	0.19946	0.002;0.027	T	0.82139	-0.0605	10	0.34782	T	0.22	-35.0377	7.518	0.27612	0.0:0.7362:0.0:0.2638	.	245;242	Q5JUQ0;Q5JUQ2	FA78A_HUMAN;.	N	242;245;214	ENSP00000361343:K242N;ENSP00000361345:K245N;ENSP00000419959:K214N	ENSP00000361343:K242N	K	-	3	2	FAM78A	133126147	0.993000	0.37304	1.000000	0.80357	0.732000	0.41865	0.468000	0.22051	1.110000	0.41699	0.462000	0.41574	AAG		0.677	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387		A	134136326	C	A	134136326	3	1	61	1	0	0	0	0	1	0	0	0	5645	912	32	2	120	2	FAM78A	9	134136326	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59290	134136326	7077105	6548	14533										
BAT2L1	84726	broad.mit.edu	37	chr9	134321983	134321983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggcttcacagttcatggGaaatgtataccacccaccta	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134321983G>A	ENST00000357304.4	+	6	864	c.809G>A	c.(808-810)gGa>gAa	p.G270E	PRRC2B_ENST00000372249.1_5'Flank|PRRC2B_ENST00000458550.1_Missense_Mutation_p.G270E|PRRC2B_ENST00000405995.1_Missense_Mutation_p.G270E	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	270							poly(A) RNA binding (GO:0044822)	p.G270E(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CAGTTCATGGGAAATGTATAC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	9											100	95	96					9																	134321983		1926	4130	6056	133311804	SO:0001583	missense	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.809G>A	9.37:g.134321983G>A	ENSP00000349856:p.Gly270Glu		133311804	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280987	0.80692	.	.	ENSG00000130723	ENST00000405995;ENST00000541684;ENST00000357304;ENST00000458550	T;T;T	0.02421	4.3;4.62;4.3	5.09	5.09	0.68999	.	0.426067	0.16545	U	0.209732	T	0.12220	0.0297	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.04991	-1.0913	10	0.33141	T	0.24	-8.0917	18.0312	0.89285	0.0:0.0:1.0:0.0	.	270	Q5JSZ5	PRC2B_HUMAN	E	270	ENSP00000384606:G270E;ENSP00000349856:G270E;ENSP00000398853:G270E	ENSP00000349856:G270E	G	+	2	0	PRRC2B	133311804	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	6.348000	0.73009	2.804000	0.96469	0.655000	0.94253	GGA		0.527	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134321983	G	A	134321983	3	1	61	1	0	0	0	0	1	0	0	0	1321	1174	41	3	831	3	BAT2L1	9	134321983	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185657	134321983	6891448	6549	14534										
BAT2L1	84726	broad.mit.edu	37	chr9	134350976	134350976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgccggcagaggggctccGagaacgggaatgaaggctcg	18	11	0	3	rs200008435	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134350976G>A	ENST00000357304.4	+	15	3515	c.3460G>A	c.(3460-3462)Gag>Aag	p.E1154K	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1154							poly(A) RNA binding (GO:0044822)	p.E1154K(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GAGGGGCTCCGAGAACGGGAA	0.617													G|||	5	0.000998403	0.0038	0	5008	,	,		15115	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	9						G	LYS/GLU	16,3844		0,16,1914	17	20	19		3460	5.7	0.1	9		19	0,8282		0,0,4141	yes	missense	PRRC2B	NM_013318.3	56	0,16,6055	AA,AG,GG		0.0,0.4145,0.1318	benign	1154/2230	134350976	16,12126	1930	4141	6071	133340797	SO:0001583	missense	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3460G>A	9.37:g.134350976G>A	ENSP00000349856:p.Glu1154Lys		133340797	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	19.13	3.767668	0.69878	0.004145	0.0	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.27104	1.69	5.69	5.69	0.88448	.	.	.	.	.	T	0.36771	0.0979	M	0.69823	2.125	0.80722	D	1	D;P	0.65815	0.995;0.826	P;B	0.54431	0.752;0.137	T	0.14587	-1.0467	8	.	.	.	.	18.7888	0.91965	0.0:0.0:1.0:0.0	.	450;1154	Q5H9R5;Q5JSZ5	.;PRC2B_HUMAN	K	1154;450	ENSP00000349856:E1154K	.	E	+	1	0	PRRC2B	133340797	1.000000	0.71417	0.081000	0.20488	0.917000	0.54804	9.451000	0.97610	2.687000	0.91594	0.462000	0.41574	GAG		0.617	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134350976	G	A	134350976	3	1	61	1	0	0	0	0	1	0	0	0	1321	1059	37	1	3518	1	BAT2L1	9	134350976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28993	134350976	6862455	6550	14535										
BAT2L1	84726	broad.mit.edu	37	chr9	134353960	134353960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcctgaccaagaagcagcGccgcctgctggaggaagaga	14	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134353960G>A	ENST00000357304.4	+	17	4767	c.4712G>A	c.(4711-4713)cGc>cAc	p.R1571H	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.R877H|PRRC2B_ENST00000405995.1_Missense_Mutation_p.R877H	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1571							poly(A) RNA binding (GO:0044822)	p.R1571H(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AAGAAGCAGCGCCGCCTGCTG	0.637											OREG0019562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	9											67	74	72					9																	134353960		1880	4109	5989	133343781	SO:0001583	missense	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4712G>A	9.37:g.134353960G>A	ENSP00000349856:p.Arg1571His	1610	133343781	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.908653	0.92107	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.03124	4.04;4.3;4.04	5.42	5.42	0.78866	.	0.000000	0.42682	U	0.000676	T	0.15219	0.0367	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.00134	-1.2009	10	0.72032	D	0.01	-44.0546	18.2062	0.89855	0.0:0.0:1.0:0.0	.	304;1571	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	H	877;1571;877	ENSP00000384606:R877H;ENSP00000349856:R1571H;ENSP00000398853:R877H	ENSP00000349856:R1571H	R	+	2	0	PRRC2B	133343781	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.655000	0.67981	2.549000	0.85964	0.561000	0.74099	CGC		0.637	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134353960	G	A	134353960	3	1	61	1	0	0	0	0	1	0	0	0	1321	1087	38	1	4778	1	BAT2L1	9	134353960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2984	134353960	6859471	6551	14536										
UCK1	83549	broad.mit.edu	37	chr9	134404928	134404928	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccgttttgccctccacGatgttcttcagagtcctgtg	8	14	2	1	rs370115943		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134404928G>A	ENST00000372215.4	-	3	405	c.312C>T	c.(310-312)atC>atT	p.I104I	UCK1_ENST00000372208.3_Silent_p.I104I|UCK1_ENST00000372210.3_Silent_p.I95I|UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372211.3_Silent_p.I109I	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	104					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)	p.I104I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		TGCCCTCCACGATGTTCTTCA	0.547																																					Melanoma(42;523 1129 28385 43975 48113)											1	Substitution - coding silent(1)	large_intestine(1)	9						G	,	2,4404	4.2+/-10.8	0,2,2201	283	234	250		312,312	-8.5	0.1	9		250	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UCK1	NM_001135954.1,NM_031432.2	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	104/202,104/278	134404928	2,13004	2203	4300	6503	133394749	SO:0001819	synonymous_variant	83549			AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.312C>T	9.37:g.134404928G>A			133394749	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Silent	SNP	ENST00000372215.4	37	CCDS6944.1																																																																																				0.547	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432		A	134404928	G	A	134404928	2	1	61	1	0	0	0	0	0	0	0	1	16963	1048	37	1		1	UCK1	9	134404928	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50968	134404928	6808503	6552	14537										
RAPGEF1	2889	broad.mit.edu	37	chr9	134465302	134465302	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccacccgtaccagcacGaagaacgtgttcttgctgac	8	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134465302G>A	ENST00000372189.3	-	16	2403	c.2280C>T	c.(2278-2280)ttC>ttT	p.F760F	RAPGEF1_ENST00000372190.3_Silent_p.F778F|RAPGEF1_ENST00000372195.1_Silent_p.F777F	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	760	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.F778F(1)		NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GTACCAGCACGAAGAACGTGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	9											115	124	121					9																	134465302		2059	4187	6246	133455123	SO:0001819	synonymous_variant	2889			BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.2280C>T	9.37:g.134465302G>A			133455123	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	G	7.854	0.724584	0.15439	.	.	ENSG00000107263	ENST00000414781	.	.	.	5.57	-0.49	0.12049	.	.	.	.	.	T	0.55561	0.1928	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	.	9.479	0.38889	0.5325:0.0:0.4675:0.0	.	.	.	.	C	188	.	.	R	-	1	0	RAPGEF1	133455123	0.158000	0.22850	0.995000	0.50966	0.664000	0.39144	-0.322000	0.08007	-0.148000	0.11234	-0.258000	0.10820	CGT		0.557	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		A	134465302	G	A	134465302	2	1	61	1	0	0	0	0	0	0	0	1	13080	1049	37	1		1	RAPGEF1	9	134465302	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60374	134465302	6748129	6553	14538										
RAPGEF1	2889	broad.mit.edu	37	chr9	134501371	134501371	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcaccggttgactcaggaGcagtaaaatcacccacaaat	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134501371G>A	ENST00000372189.3	-	10	1712	c.1589C>T	c.(1588-1590)gCt>gTt	p.A530V	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.A548V|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.A547V|RAPGEF1_ENST00000481260.1_5'Flank	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	530					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.A548V(1)|p.A225V(1)		NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		TGACTCAGGAGCAGTAAAATC	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	9											99	99	99					9																	134501371		1957	4134	6091	133491192	SO:0001583	missense	2889			BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1589C>T	9.37:g.134501371G>A	ENSP00000361263:p.Ala530Val		133491192	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126075	0.37533	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000372191;ENST00000357686	T;T;T	0.28666	1.61;1.6;1.6	5.17	0.56	0.17279	.	0.364959	0.30959	N	0.008524	T	0.18257	0.0438	L	0.27053	0.805	0.36514	D	0.869749	B;B;B	0.11235	0.004;0.001;0.002	B;B;B	0.15484	0.006;0.006;0.013	T	0.16988	-1.0384	10	0.19147	T	0.46	.	10.5419	0.45037	0.2362:0.0:0.7638:0.0	.	547;530;548	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	V	530;547;424;530;548;510;456;225;547	ENSP00000361269:A547V;ENSP00000361263:A530V;ENSP00000361264:A548V	ENSP00000266110:A530V	A	-	2	0	RAPGEF1	133491192	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	2.388000	0.44398	0.118000	0.18165	0.655000	0.94253	GCT		0.512	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		A	134501371	G	A	134501371	3	1	61	1	0	0	0	0	1	0	0	0	13080	971	34	3	1704	3	RAPGEF1	9	134501371	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36069	134501371	6712060	6554	14539										
RAPGEF1	2889	broad.mit.edu	37	chr9	134526251	134526251	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcagctggttttcccttCtttgatggcgttctcttgat	8	11	3	2	rs374143304		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134526251C>A	ENST00000372189.3	-	2	219	c.96G>T	c.(94-96)aaG>aaT	p.K32N	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.K50N|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.K49N	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	32					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.K50N(1)		NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GTTTTCCCTTCTTTGATGGCG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	ASN/LYS,ASN/LYS	0,3872		0,0,1936	268	249	255		96,150	4.7	1	9		255	1,8281		0,1,4140	no	missense,missense	RAPGEF1	NM_005312.2,NM_198679.1	94,94	0,1,6076	AA,AC,CC		0.0121,0.0,0.0082	possibly-damaging,possibly-damaging	32/1078,50/1096	134526251	1,12153	1936	4141	6077	133516072	SO:0001583	missense	2889			BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.96G>T	9.37:g.134526251C>A	ENSP00000361263:p.Lys32Asn		133516072	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.435012	0.43224	0.0	1.21E-4	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000357686;ENST00000438647;ENST00000427994	T;T;T;T	0.51071	0.81;0.88;0.72;1.16	5.61	4.71	0.59529	.	1.310530	0.04485	N	0.378517	T	0.66597	0.2805	L	0.50333	1.59	0.52501	D	0.999957	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71414	0.939;0.939;0.973	T	0.37244	-0.9714	10	0.45353	T	0.12	.	13.3816	0.60770	0.0:0.925:0.0:0.075	.	49;32;50	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	N	32;49;32;50;50;49;49;50	ENSP00000361269:K49N;ENSP00000361263:K32N;ENSP00000361264:K50N;ENSP00000410640:K49N	ENSP00000266110:K32N	K	-	3	2	RAPGEF1	133516072	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.029000	0.49712	1.367000	0.46095	0.655000	0.94253	AAG		0.473	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		A	134526251	C	A	134526251	3	1	61	1	0	0	0	0	1	0	0	0	13080	912	32	2	3229	2	RAPGEF1	9	134526251	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24880	134526251	6687180	6555	14540										
MED27	9442	broad.mit.edu	37	chr9	134955096	134955096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggccttctcccggccctCcagcgtctccttgttccgca	8	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:134955096C>T	ENST00000292035.5	-	1	199	c.136G>A	c.(136-138)Gag>Aag	p.E46K	MED27_ENST00000357028.2_Missense_Mutation_p.E46K|RP11-32B11.2_ENST00000444872.2_RNA|MED27_ENST00000474263.1_Missense_Mutation_p.E46K	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	46					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.E46K(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		TCCCGGCCCTCCAGCGTCTCC	0.617																																					Colon(41;784 923 6932 42329 52483)											1	Substitution - Missense(1)	large_intestine(1)	9											72	74	74					9																	134955096		2203	4300	6503	133944917	SO:0001583	missense	9442			AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.136G>A	9.37:g.134955096C>T	ENSP00000292035:p.Glu46Lys		133944917	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Missense_Mutation	SNP	ENST00000292035.5	37	CCDS6945.1	.	.	.	.	.	.	.	.	.	.	C	33	5.214502	0.95104	.	.	ENSG00000160563	ENST00000292035;ENST00000357028;ENST00000372184	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.78007	0.4216	M	0.67397	2.05	0.80722	D	1	D;D;D	0.56035	0.969;0.974;0.97	P;D;P	0.67725	0.723;0.953;0.665	T	0.78816	-0.2055	9	0.62326	D	0.03	-15.6889	18.591	0.91212	0.0:1.0:0.0:0.0	.	46;46;46	B4DPP5;Q6P2C8-2;Q6P2C8	.;.;MED27_HUMAN	K	46;8;46	.	ENSP00000292035:E46K	E	-	1	0	MED27	133944917	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.538000	0.82048	2.625000	0.88918	0.650000	0.86243	GAG		0.617	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		T	134955096	C	T	134955096	3	4	61	1	0	0	0	0	1	0	0	0	9475	864	30	3	831	3	MED27	9	134955096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	428845	134955096	6258335	6556	14541										
SETX	23064	broad.mit.edu	37	chr9	135172396	135172396	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccatagcatatgcagtttCtattgctttcttttgatctt	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135172396C>A	ENST00000224140.5	-	14	6009	c.5827G>T	c.(5827-5829)Gaa>Taa	p.E1943*	SETX_ENST00000393220.1_Nonsense_Mutation_p.E1943*|SETX_ENST00000372169.2_Nonsense_Mutation_p.E1943*	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1943					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.E1943*(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TATGCAGTTTCTATTGCTTTC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											151	123	132					9																	135172396		2203	4300	6503	134162217	SO:0001587	stop_gained	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5827G>T	9.37:g.135172396C>A	ENSP00000224140:p.Glu1943*		134162217	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Nonsense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	48	14.291482	0.99788	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	.	.	.	5.53	5.53	0.82687	.	0.059603	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	18.0171	0.89245	0.0:1.0:0.0:0.0	.	.	.	.	X	1943;185;1943;1943	.	ENSP00000224140:E1943X	E	-	1	0	SETX	134162217	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.237000	0.51344	2.601000	0.87937	0.563000	0.77884	GAA		0.353	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		A	135172396	C	A	135172396	4	1	61	1	0	0	0	0	0	1	0	0	14178	922	32	2	2258	2	SETX	9	135172396	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	217300	135172396	6041035	6557	14542										
SETX	23064	broad.mit.edu	37	chr9	135203235	135203235	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacttctattctgtcctttTttggcatctgaatgagtttt	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135203235T>G	ENST00000224140.5	-	10	3932	c.3750A>C	c.(3748-3750)aaA>aaC	p.K1250N	SETX_ENST00000393220.1_Missense_Mutation_p.K1250N|SETX_ENST00000372169.2_Missense_Mutation_p.K1250N	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1250					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.K1250N(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TCTGTCCTTTTTTGGCATCTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											117	111	113					9																	135203235		2203	4300	6503	134193056	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.3750A>C	9.37:g.135203235T>G	ENSP00000224140:p.Lys1250Asn		134193056	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.049528	0.36181	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87029	-2.11;-2.2;-1.82	5.8	2.01	0.26516	.	0.751984	0.12234	N	0.487183	T	0.81088	0.4750	L	0.57536	1.79	0.09310	N	1	B;B;B	0.20052	0.041;0.024;0.041	B;B;B	0.20955	0.032;0.008;0.032	T	0.68021	-0.5519	10	0.39692	T	0.17	.	1.9031	0.03272	0.1317:0.1509:0.1364:0.581	.	1250;1250;1250	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	N	1250	ENSP00000224140:K1250N;ENSP00000361242:K1250N;ENSP00000376913:K1250N	ENSP00000224140:K1250N	K	-	3	2	SETX	134193056	0.000000	0.05858	0.781000	0.31783	0.358000	0.29455	-0.021000	0.12504	0.466000	0.27193	0.528000	0.53228	AAA		0.403	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135203235	T	G	135203235	3	3	61	1	0	0	0	0	1	0	0	0	14178	1838	64	4	4351	4	SETX	9	135203235	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	30839	135203235	6010196	6558	14543										
SETX	23064	broad.mit.edu	37	chr9	135204031	135204031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactttcctttgcagctgcGatgagttctgaggtgaatcg	11	8	1	3	rs557074957	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135204031G>A	ENST00000224140.5	-	10	3136	c.2954C>T	c.(2953-2955)tCg>tTg	p.S985L	SETX_ENST00000393220.1_Missense_Mutation_p.S985L|SETX_ENST00000372169.2_Missense_Mutation_p.S985L	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	985					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.S985L(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTGCAGCTGCGATGAGTTCTG	0.388													G|||	4	0.000798722	0	0	5008	,	,		21550	0.001		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	9											132	130	131					9																	135204031		2203	4300	6503	134193852	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2954C>T	9.37:g.135204031G>A	ENSP00000224140:p.Ser985Leu		134193852	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	G	8.155	0.788218	0.16258	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87103	-2.12;-2.21;-1.83	5.63	-1.29	0.09288	.	108.267000	0.00166	N	0.000000	T	0.74921	0.3780	L	0.29908	0.895	0.09310	N	1	P;B;P	0.38280	0.625;0.342;0.625	B;B;B	0.28305	0.088;0.028;0.088	T	0.64984	-0.6278	10	0.30078	T	0.28	.	2.7683	0.05327	0.3619:0.1096:0.4171:0.1114	.	985;985;985	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	L	985	ENSP00000224140:S985L;ENSP00000361242:S985L;ENSP00000376913:S985L	ENSP00000224140:S985L	S	-	2	0	SETX	134193852	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	-0.256000	0.08757	-0.111000	0.12001	0.655000	0.94253	TCG		0.388	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		A	135204031	G	A	135204031	3	1	61	1	0	0	0	0	1	0	0	0	14178	1059	37	1	5147	1	SETX	9	135204031	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	796	135204031	6009400	6559	14544										
TTF1	7270	broad.mit.edu	37	chr9	135271843	135271843	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgtaattgttgacatcGaacatcttctttgctcgata	6	9	2	1	rs371348195		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135271843G>A	ENST00000334270.2	-	5	1872	c.1833C>T	c.(1831-1833)ttC>ttT	p.F611F		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	611					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.F611F(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		TGTTGACATCGAACATCTTCT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	9						G	,	0,4406		0,0,2203	129	115	120		288,1833	-4.1	1	9		120	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TTF1	NM_001205296.1,NM_007344.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	96/391,611/906	135271843	2,13004	2203	4300	6503	134261664	SO:0001819	synonymous_variant	7270			BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1833C>T	9.37:g.135271843G>A			134261664	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Silent	SNP	ENST00000334270.2	37	CCDS6948.1																																																																																				0.388	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		A	135271843	G	A	135271843	2	1	61	1	0	0	0	0	0	0	0	1	16758	1049	37	1		1	TTF1	9	135271843	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67812	135271843	5941588	6560	14545										
TTF1	7270	broad.mit.edu	37	chr9	135277656	135277656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgactgaggcagggtgtCccttgcccgctggctctccc	12	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135277656C>T	ENST00000334270.2	-	2	592	c.553G>A	c.(553-555)Gac>Aac	p.D185N		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	185	N-terminal region (NRD). {ECO:0000250}.				chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D185N(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		GGCAGGGTGTCCCTTGCCCGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											52	49	50					9																	135277656		2203	4299	6502	134267477	SO:0001583	missense	7270			BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.553G>A	9.37:g.135277656C>T	ENSP00000333920:p.Asp185Asn		134267477	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.097377	0.56075	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.10382	2.88	4.43	-8.25	0.01025	.	3.513710	0.00987	N	0.003474	T	0.06690	0.0171	L	0.36672	1.1	0.09310	N	1	B	0.27316	0.175	B	0.24394	0.053	T	0.26018	-1.0115	10	0.28530	T	0.3	.	2.2973	0.04153	0.1051:0.2357:0.3762:0.283	.	185	Q15361	TTF1_HUMAN	N	185	ENSP00000333920:D185N	ENSP00000245588:D185N	D	-	1	0	TTF1	134267477	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.519000	0.02243	-1.113000	0.02981	-0.136000	0.14681	GAC		0.493	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135277656	C	T	135277656	3	4	61	1	0	0	0	0	1	0	0	0	16758	855	30	3	2204	3	TTF1	9	135277656	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5813	135277656	5935775	6561	14546										
DDX31	64794	broad.mit.edu	37	chr9	135521323	135521323	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccgtaggaattttaatcGcatggaggcagatggcaact	12	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135521323G>A	ENST00000372159.3	-	13	1805	c.1654C>T	c.(1654-1656)Cga>Tga	p.R552*	DDX31_ENST00000438527.3_Nonsense_Mutation_p.R423*|DDX31_ENST00000372153.1_Nonsense_Mutation_p.R552*|DDX31_ENST00000310532.2_Nonsense_Mutation_p.R552*	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	552	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.R552*(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		AATTTTAATCGCATGGAGGCA	0.612																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											36	36	36					9																	135521323		2203	4300	6503	134511144	SO:0001587	stop_gained	64794			AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"DEAD-boxes", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16715	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 25"		"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1654C>T	9.37:g.135521323G>A	ENSP00000361232:p.Arg552*		134511144	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Nonsense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	G	36	5.777643	0.96929	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000438527;ENST00000310532	.	.	.	5.58	-0.00354	0.14025	.	1.130320	0.06352	N	0.710006	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	1.8196	10.4076	0.44274	0.0:0.2173:0.3364:0.4463	.	.	.	.	X	552;552;552;423;552	.	ENSP00000310539:R552X	R	-	1	2	DDX31	134511144	0.000000	0.05858	0.000000	0.03702	0.654000	0.38779	-0.134000	0.10436	-0.274000	0.09232	0.563000	0.77884	CGA		0.612	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		A	135521323	G	A	135521323	4	1	61	1	0	0	0	0	0	1	0	0	4362	1095	38	1	940	1	DDX31	9	135521323	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	243667	135521323	5692108	6562	14547										
GTF3C4	9329	broad.mit.edu	37	chr9	135553405	135553405	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgagtgcaaggagaaattCgccgcctccaaggaccccac	11	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135553405C>T	ENST00000372146.4	+	2	963	c.399C>T	c.(397-399)ttC>ttT	p.F133F	GTF3C4_ENST00000483873.2_Silent_p.F133F	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	133					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)	p.F133F(2)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		AGGAGAAATTCGCCGCCTCCA	0.443																																					Pancreas(142;417 1875 11086 31973 47667)											2	Substitution - coding silent(2)	large_intestine(2)	9											63	64	64					9																	135553405		2203	4300	6503	134543226	SO:0001819	synonymous_variant	9329			AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.399C>T	9.37:g.135553405C>T			134543226	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																				0.443	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			T	135553405	C	T	135553405	2	4	61	1	0	0	0	0	0	0	0	1	6896	883	31	1		1	GTF3C4	9	135553405	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32082	135553405	5660026	6563	14548										
GTF3C4	9329	broad.mit.edu	37	chr9	135559041	135559041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcttgccattcacagatcGcaaacaggcagtctgttcca	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135559041G>A	ENST00000372146.4	+	3	2840	c.2276G>A	c.(2275-2277)cGc>cAc	p.R759H		NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	759					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)	p.R759H(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TTCACAGATCGCAAACAGGCA	0.408																																					Pancreas(142;417 1875 11086 31973 47667)											1	Substitution - Missense(1)	large_intestine(1)	9											135	122	126					9																	135559041		2203	4300	6503	134548862	SO:0001583	missense	9329			AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.2276G>A	9.37:g.135559041G>A	ENSP00000361219:p.Arg759His		134548862	Q5VZJ7	Missense_Mutation	SNP	ENST00000372146.4	37	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.071345	0.55646	.	.	ENSG00000125484	ENST00000372146	T	0.44482	0.92	5.88	4.97	0.65823	Transcription factor IIIC, putative zinc-finger (1);	0.172968	0.53938	D	0.000060	T	0.18257	0.0438	N	0.03608	-0.345	0.34073	D	0.658738	B	0.11235	0.004	B	0.08055	0.003	T	0.24225	-1.0166	10	0.15066	T	0.55	-25.5076	9.8528	0.41068	0.0752:0.138:0.7867:0.0	.	759	Q9UKN8	TF3C4_HUMAN	H	759	ENSP00000361219:R759H	ENSP00000361219:R759H	R	+	2	0	GTF3C4	134548862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.784000	0.47774	2.789000	0.95967	0.655000	0.94253	CGC		0.408	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			A	135559041	G	A	135559041	3	1	61	1	0	0	0	0	1	0	0	0	6896	1087	38	1	2286	1	GTF3C4	9	135559041	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5636	135559041	5654390	6564	14549										
TSC1	7248	broad.mit.edu	37	chr9	135771933	135771933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccatagtcgtctcccaccGactgctgaatgggcctgccc	9	17	1	1	rs118203745		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135771933G>A	ENST00000298552.3	-	23	3405	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	TSC1_ENST00000440111.2_Missense_Mutation_p.R1062W|TSC1_ENST00000545250.1_Missense_Mutation_p.R1011W	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1062					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.R1062W(1)|p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GTCTCCCACCGACTGCTGAAT	0.587			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																													yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|bone(1)	9											49	50	50					9																	135771933		2203	4300	6503	134761754	SO:0001583	missense	7248	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3184C>T	9.37:g.135771933G>A	ENSP00000298552:p.Arg1062Trp		134761754	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	37	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531359	0.64972	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;T	0.82433	-1.61;-1.61;-1.42	5.31	3.45	0.39498	.	0.133956	0.51477	D	0.000091	D	0.87083	0.6089	M	0.64997	1.995	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.61722	0.893;0.857	D	0.87593	0.2492	10	0.72032	D	0.01	-10.2471	11.1565	0.48491	0.153:0.0:0.847:0.0	.	1011;1062	B7Z897;Q92574	.;TSC1_HUMAN	W	1062;1062;1011	ENSP00000298552:R1062W;ENSP00000394524:R1062W;ENSP00000444017:R1011W	ENSP00000298552:R1062W	R	-	1	2	TSC1	134761754	1.000000	0.71417	0.996000	0.52242	0.691000	0.40173	5.305000	0.65750	1.231000	0.43661	0.563000	0.77884	CGG		0.587	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135771933	G	A	135771933	3	1	61	1	0	0	0	0	1	0	0	0	16645	1057	37	1	314	1	TSC1	9	135771933	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	212892	135771933	5441498	6565	14550										
GFI1B	8328	broad.mit.edu	37	chr9	135864453	135864453	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccctgctcccaggtcttCtccacccctcacgggctcga	8	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135864453C>A	ENST00000339463.3	+	9	1335	c.516C>A	c.(514-516)ttC>ttA	p.F172L	GFI1B_ENST00000450530.1_Missense_Mutation_p.F172L|GFI1B_ENST00000372122.1_Missense_Mutation_p.F172L|GFI1B_ENST00000534944.1_Intron|GFI1B_ENST00000372124.1_Intron|GFI1B_ENST00000372123.1_Intron			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	172	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)	p.F172L(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		CCCAGGTCTTCTCCACCCCTC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	9											55	44	48					9																	135864453		2203	4300	6503	134854274	SO:0001583	missense	8328			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"Zinc fingers, C2H2-type"	4238	protein-coding gene	gene with protein product		604383	"growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.516C>A	9.37:g.135864453C>A	ENSP00000344782:p.Phe172Leu		134854274	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.757500	0.69648	.	.	ENSG00000165702	ENST00000339463;ENST00000450530;ENST00000372122	T;T;T	0.28069	1.63;1.63;1.63	5.42	4.32	0.51571	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.48409	0.1498	M	0.71581	2.175	0.80722	D	1	D	0.56035	0.974	P	0.56960	0.81	T	0.52064	-0.8625	10	0.66056	D	0.02	-40.9221	14.1357	0.65287	0.0:0.9147:0.0:0.0853	.	172	Q5VTD9	GFI1B_HUMAN	L	172	ENSP00000344782:F172L;ENSP00000409546:F172L;ENSP00000361195:F172L	ENSP00000344782:F172L	F	+	3	2	GFI1B	134854274	1.000000	0.71417	1.000000	0.80357	0.360000	0.29518	4.040000	0.57333	2.519000	0.84933	0.655000	0.94253	TTC		0.652	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		A	135864453	C	A	135864453	3	1	61	1	0	0	0	0	1	0	0	0	6360	912	32	2	530	2	GFI1B	9	135864453	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92520	135864453	5348978	6566	14551										
GFI1B	8328	broad.mit.edu	37	chr9	135866422	135866422	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcggcaccgcgagagccaGcacaatctcaagtgaggctg	14	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135866422G>T	ENST00000339463.3	+	11	1797	c.978G>T	c.(976-978)caG>caT	p.Q326H	GFI1B_ENST00000450530.1_Missense_Mutation_p.Q326H|GFI1B_ENST00000372122.1_Missense_Mutation_p.Q326H|GFI1B_ENST00000534944.1_Missense_Mutation_p.Q280H|GFI1B_ENST00000372124.1_Missense_Mutation_p.Q280H|GFI1B_ENST00000372123.1_Missense_Mutation_p.Q280H			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	326	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)	p.Q326H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		GCGAGAGCCAGCACAATCTCA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	9											55	50	52					9																	135866422		2203	4300	6503	134856243	SO:0001583	missense	8328			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"Zinc fingers, C2H2-type"	4238	protein-coding gene	gene with protein product		604383	"growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.978G>T	9.37:g.135866422G>T	ENSP00000344782:p.Gln326His		134856243	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.958631	0.74016	.	.	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.48836	0.8;2.99;2.99;0.8;0.8;2.99	5.0	3.09	0.35607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.12475	0.0303	N	0.00007	-3.15	0.58432	D	0.999999	P;P	0.48998	0.918;0.828	P;P	0.58391	0.749;0.838	T	0.50021	-0.8876	10	0.02654	T	1	-32.1443	8.37	0.32410	0.2608:0.0:0.7392:0.0	.	280;326	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	H	280;326;326;280;280;326	ENSP00000361197:Q280H;ENSP00000344782:Q326H;ENSP00000409546:Q326H;ENSP00000446134:Q280H;ENSP00000361196:Q280H;ENSP00000361195:Q326H	ENSP00000344782:Q326H	Q	+	3	2	GFI1B	134856243	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.284000	0.33249	1.208000	0.43306	0.462000	0.41574	CAG		0.652	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		T	135866422	G	T	135866422	3	4	61	1	0	0	0	0	1	0	0	0	6360	962	34	2	1000	2	GFI1B	9	135866422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1969	135866422	5347009	6567	14552										
GTF3C5	9328	broad.mit.edu	37	chr9	135926232	135926232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcctgagcagagcccggcGcccccacaatgccatctttg	11	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:135926232G>A	ENST00000372097.5	+	4	958	c.635G>A	c.(634-636)cGc>cAc	p.R212H	GTF3C5_ENST00000342018.8_Missense_Mutation_p.R212H|GTF3C5_ENST00000372108.5_Missense_Mutation_p.R212H|GTF3C5_ENST00000372099.6_Missense_Mutation_p.R203H|GTF3C5_ENST00000372095.5_Missense_Mutation_p.R87H	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	212					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.R212H(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		AGAGCCCGGCGCCCCCACAAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	9											59	58	58					9																	135926232		2203	4300	6503	134916053	SO:0001583	missense	9328			AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.635G>A	9.37:g.135926232G>A	ENSP00000361169:p.Arg212His		134916053	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	SNP	ENST00000372097.5	37	CCDS6958.1	.	.	.	.	.	.	.	.	.	.	G	34	5.374599	0.95923	.	.	ENSG00000148308	ENST00000372097;ENST00000440319;ENST00000372099;ENST00000372095;ENST00000372089;ENST00000372108;ENST00000342018;ENST00000439697	T;T;T;T	0.55234	0.73;0.71;0.73;0.53	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.73923	0.3649	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72527	-0.4266	10	0.31617	T	0.26	-4.7154	18.0209	0.89254	0.0:0.0:1.0:0.0	.	212;212	Q9Y5Q8-3;Q9Y5Q8	.;TF3C5_HUMAN	H	212;165;203;87;62;212;212;87	ENSP00000361169:R212H;ENSP00000361171:R203H;ENSP00000361180:R212H;ENSP00000339530:R212H	ENSP00000339530:R212H	R	+	2	0	GTF3C5	134916053	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.197000	0.94985	2.490000	0.84030	0.561000	0.74099	CGC		0.587	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		A	135926232	G	A	135926232	3	1	61	1	0	0	0	0	1	0	0	0	6897	1087	38	1	649	1	GTF3C5	9	135926232	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59810	135926232	5287199	6568	14553										
SARDH	1757	broad.mit.edu	37	chr9	136582546	136582546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacacctcccagtccaggTcaaagaggccgaaggcaaac	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:136582546T>C	ENST00000371872.4	-	8	1309	c.1052A>G	c.(1051-1053)gAc>gGc	p.D351G	SARDH_ENST00000422262.2_Missense_Mutation_p.D183G|SARDH_ENST00000439388.1_Missense_Mutation_p.D351G	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	351					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.D351G(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CCAGTCCAGGTCAAAGAGGCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											90	78	82					9																	136582546		2203	4300	6503	135572367	SO:0001583	missense	1757				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1052A>G	9.37:g.136582546T>C	ENSP00000360938:p.Asp351Gly		135572367	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901695	0.72754	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227;ENST00000535281	D;D;D	0.83755	-1.76;-1.76;-1.76	3.95	3.95	0.45737	FAD dependent oxidoreductase (1);	0.061176	0.64402	D	0.000006	D	0.85301	0.5665	M	0.67569	2.06	0.80722	D	1	B	0.32573	0.376	B	0.44163	0.443	D	0.86259	0.1654	10	0.72032	D	0.01	-38.7506	12.8491	0.57848	0.0:0.0:0.0:1.0	.	351	Q9UL12	SARDH_HUMAN	G	351;351;183;351;351;351	ENSP00000360938:D351G;ENSP00000403084:D351G;ENSP00000415537:D183G	ENSP00000360938:D351G	D	-	2	0	SARDH	135572367	1.000000	0.71417	0.999000	0.59377	0.867000	0.49689	7.923000	0.87546	1.438000	0.47492	0.379000	0.24179	GAC		0.592	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			C	136582546	T	C	136582546	3	2	61	1	0	0	0	0	1	0	0	0	13878	1667	58	4	1760	4	SARDH	9	136582546	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	656314	136582546	4630885	6569	14554										
VAV2	7410	broad.mit.edu	37	chr9	136633646	136633646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacgtcaccctcccgcagcGaaagctccctcatatctcgg	7	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:136633646G>A	ENST00000371850.3	-	29	2538	c.2507C>T	c.(2506-2508)tCg>tTg	p.S836L	VAV2_ENST00000371851.1_Missense_Mutation_p.S826L|VAV2_ENST00000406606.3_Missense_Mutation_p.S797L	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	836	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S797L(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		CTCCCGCAGCGAAAGCTCCCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											90	80	83					9																	136633646		2203	4300	6503	135623467	SO:0001583	missense	7410				CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12658	protein-coding gene	gene with protein product		600428	"vav 2 oncogene"			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2507C>T	9.37:g.136633646G>A	ENSP00000360916:p.Ser836Leu		135623467	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470823	0.84533	.	.	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;T	0.23754	1.89;1.89;2.93	4.98	4.98	0.66077	Src homology-3 domain (4);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.61211	0.2329	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.955;0.994	T	0.72312	-0.4331	10	0.87932	D	0	.	18.227	0.89921	0.0:0.0:1.0:0.0	.	836;797	P52735;P52735-3	VAV2_HUMAN;.	L	836;826;797;826	ENSP00000360916:S836L;ENSP00000360917:S826L;ENSP00000385362:S797L	ENSP00000317258:S826L	S	-	2	0	VAV2	135623467	1.000000	0.71417	0.994000	0.49952	0.342000	0.28953	9.686000	0.98664	2.297000	0.77311	0.563000	0.77884	TCG		0.637	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1			A	136633646	G	A	136633646	3	1	61	1	0	0	0	0	1	0	0	0	17172	1059	37	1	137	1	VAV2	9	136633646	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51100	136633646	4579785	6570	14555										
COL5A1	1289	broad.mit.edu	37	chr9	137623485	137623485	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgggccgggaatgccggcGaaccaggataccatctatga	13	11	1	1	rs200959477		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:137623485G>A	ENST00000371817.3	+	8	1722	c.1308G>A	c.(1306-1308)gcG>gcA	p.A436A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	436	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.A436A(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GAATGCCGGCGAACCAGGATA	0.637													G|||	1	0.000199681	0	0	5008	,	,		11666	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9						G		0,4406		0,0,2203	81	83	82		1308	-6.6	0.5	9		82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL5A1	NM_000093.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		436/1839	137623485	1,13005	2203	4300	6503	136763306	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1308G>A	9.37:g.137623485G>A			136763306	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137623485	G	A	137623485	2	1	61	1	0	0	0	0	0	0	0	1	3702	1045	37	1		1	COL5A1	9	137623485	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	989839	137623485	3589946	6571	14556										
FCN2	2220	broad.mit.edu	37	chr9	137778296	137778296	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccagcgagctccgtgtaGacctggtggactttgaggac	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:137778296G>T	ENST00000291744.6	+	7	590	c.580G>T	c.(580-582)Gac>Tac	p.D194Y	FCN2_ENST00000350339.2_Missense_Mutation_p.D156Y	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	194	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)	p.D194Y(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		GCTCCGTGTAGACCTGGTGGA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											171	156	161					9																	137778296		2203	4300	6503	136918117	SO:0001583	missense	2220			D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"Fibrinogen C domain containing"	3624	protein-coding gene	gene with protein product	"hucolin", "collagen/fibrinogen domain-containing protein 2", "ficolin B", "serum lectin p35", "L-ficolin"	601624	"ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.580G>T	9.37:g.137778296G>T	ENSP00000291744:p.Asp194Tyr		136918117	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201882	0.58234	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79845	-1.31;-1.31	3.97	3.97	0.46021	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.42172	U	0.000758	D	0.88537	0.6463	M	0.83852	2.665	0.48511	D	0.999667	D;P	0.55172	0.97;0.943	P;P	0.61940	0.768;0.896	D	0.90212	0.4265	10	0.66056	D	0.02	.	13.5334	0.61635	0.0:0.0:1.0:0.0	.	156;194	Q15485-2;Q15485	.;FCN2_HUMAN	Y	156;194	ENSP00000291741:D156Y;ENSP00000291744:D194Y	ENSP00000291744:D194Y	D	+	1	0	FCN2	136918117	1.000000	0.71417	0.326000	0.25389	0.626000	0.37791	7.616000	0.83018	1.749000	0.51849	0.563000	0.77884	GAC		0.557	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108		T	137778296	G	T	137778296	3	4	61	1	0	0	0	0	1	0	0	0	5811	942	33	2	606	2	FCN2	9	137778296	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154811	137778296	3435135	6572	14557										
FCN1	2219	broad.mit.edu	37	chr9	137804955	137804955	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccagccgctcaggaaataCccccggtctagcaggtcctt	10	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:137804955C>A	ENST00000371806.3	-	6	466	c.375G>T	c.(373-375)ggG>ggT	p.G125G		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	125	A domain; contributes to trimerization.|Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)	p.G125G(1)		endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		TCAGGAAATACCCCCGGTCTA	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	9											47	45	45					9																	137804955		2203	4300	6503	136944776	SO:0001819	synonymous_variant	2219			D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.375G>T	9.37:g.137804955C>A			136944776	Q5VYV5|Q92596	Silent	SNP	ENST00000371806.3	37	CCDS6985.1																																																																																				0.677	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		A	137804955	C	A	137804955	2	1	61	1	0	0	0	0	0	0	0	1	5810	494	18	2		2	FCN1	9	137804955	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26659	137804955	3408476	6573	14558										
FCN1	2219	broad.mit.edu	37	chr9	137806239	137806239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggtggctcacctttctctCcacgcatccccttctctcct	6	19	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:137806239C>T	ENST00000371806.3	-	4	390	c.299G>A	c.(298-300)gGa>gAa	p.G100E		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	100					cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)	p.G100E(1)		endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		ACCTTTCTCTCCACGCATCCC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	9											141	131	134					9																	137806239		2203	4300	6503	136946060	SO:0001583	missense	2219			D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.299G>A	9.37:g.137806239C>T	ENSP00000360871:p.Gly100Glu		136946060	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	37	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	C	9.886	1.203022	0.22121	.	.	ENSG00000085265	ENST00000371807;ENST00000371806	D	0.99619	-6.28	2.86	2.86	0.33363	.	.	.	.	.	D	0.99539	0.9835	M	0.91140	3.18	0.39423	D	0.966941	D	0.56746	0.977	D	0.65323	0.934	D	0.98660	1.0683	9	0.49607	T	0.09	.	9.395	0.38397	0.0:1.0:0.0:0.0	.	100	O00602	FCN1_HUMAN	E	100	ENSP00000360871:G100E	ENSP00000360871:G100E	G	-	2	0	FCN1	136946060	0.995000	0.38212	0.862000	0.33874	0.111000	0.19643	3.190000	0.50973	1.909000	0.55274	0.549000	0.68633	GGA		0.632	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		T	137806239	C	T	137806239	3	4	61	1	0	0	0	0	1	0	0	0	5810	855	30	3	705	3	FCN1	9	137806239	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1284	137806239	3407192	6574	14559										
OLFM1	10439	broad.mit.edu	37	chr9	137990137	137990137	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttaaccttgcaggcgatAaaagcgaaaatggatgaact	9	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:137990137A>G	ENST00000371793.3	+	4	713	c.462A>G	c.(460-462)atA>atG	p.I154M	OLFM1_ENST00000252854.4_Missense_Mutation_p.I136M|OLFM1_ENST00000371796.3_Missense_Mutation_p.I127M	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	154					negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)	p.I136M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		TGCAGGCGATAAAAGCGAAAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											87	83	85					9																	137990137		2203	4300	6503	137129958	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.462A>G	9.37:g.137990137A>G	ENSP00000360858:p.Ile154Met		137129958	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.70|15.70	2.910306|2.910306	0.52439|0.52439	.|.	.|.	ENSG00000130558|ENSG00000130558	ENST00000252854;ENST00000339720;ENST00000371796;ENST00000539529;ENST00000371793;ENST00000539877|ENST00000545657	D;T;D;T;D;D|.	0.88664|.	-2.39;1.23;-2.41;0.29;-2.4;-2.03|.	5.12|5.12	2.63|2.63	0.31362|0.31362	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53110|0.53110	0.1776|0.1776	L|L	0.40543|0.40543	1.245|1.245	0.53688|0.53688	D|D	0.999979|0.999979	D;D|.	0.71674|.	0.998;0.968|.	D;P|.	0.78314|.	0.991;0.67|.	T|T	0.39333|0.39333	-0.9619|-0.9619	10|5	0.48119|.	T|.	0.1|.	.|.	10.1309|10.1309	0.42678|0.42678	0.7143:0.0:0.0:0.2857|0.7143:0.0:0.0:0.2857	.|.	154;136|.	Q99784;Q6IMJ8|.	NOE1_HUMAN;.|.	M|E	136;143;127;71;154;51|14	ENSP00000252854:I136M;ENSP00000340318:I143M;ENSP00000360861:I127M;ENSP00000444296:I71M;ENSP00000360858:I154M;ENSP00000443806:I51M|.	ENSP00000252854:I136M|.	I|K	+|+	3|1	3|0	OLFM1|OLFM1	137129958|137129958	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.504000|3.504000	0.53347|0.53347	0.303000|0.303000	0.22785|0.22785	0.519000|0.519000	0.50382|0.50382	ATA|AAA		0.473	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		G	137990137	A	G	137990137	3	3	61	1	0	0	0	0	1	0	0	0	10883	352	13	4	432	4	OLFM1	9	137990137	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	183898	137990137	3223294	6575	14560										
OBP2A	29991	broad.mit.edu	37	chr9	138438725	138438725	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaggtgacagccctgggCggtgggaacttggaagccac	17	9	0	2	rs561640530		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:138438725C>T	ENST00000539850.1	+	2	200	c.174C>T	c.(172-174)ggC>ggT	p.G58G	OBP2A_ENST00000340780.3_Silent_p.G58G|OBP2A_ENST00000342114.4_Intron|OBP2A_ENST00000371776.1_Silent_p.G58G			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	58					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)	p.G58G(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		CAGCCCTGGGCGGTGGGAACT	0.632													.|||	1	0.000199681	0	0	5008	,	,		15941	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	9											96	88	91					9																	138438725		2203	4300	6503	137578546	SO:0001819	synonymous_variant	29991			AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"Lipocalins"	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.174C>T	9.37:g.138438725C>T			137578546	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Silent	SNP	ENST00000539850.1	37	CCDS6992.1																																																																																				0.632	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582		T	138438725	C	T	138438725	2	4	61	1	0	0	0	0	0	0	0	1	10841	755	27	1		1	OBP2A	9	138438725	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	448588	138438725	2774706	6576	14561										
GLT6D1	360203	broad.mit.edu	37	chr9	138516053	138516053	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatattctttgatgaagtCtaaaatattatggggtgtgc	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:138516053C>A	ENST00000371763.1	-	5	974	c.721G>T	c.(721-723)Gac>Tac	p.D241Y		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	241					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)	p.D241Y(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TTGATGAAGTCTAAAATATTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	9											124	123	123					9																	138516053		1855	4099	5954	137655874	SO:0001583	missense	360203			AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"Glycosyltransferase family 6 domain containing"	23671	protein-coding gene	gene with protein product		613699	"galactosyltransferase family 6 domain containing 1"	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.721G>T	9.37:g.138516053C>A	ENSP00000360829:p.Asp241Tyr		137655874		Missense_Mutation	SNP	ENST00000371763.1	37	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.155499	0.38021	.	.	ENSG00000204007	ENST00000371763	T	0.01252	5.1	3.49	-6.99	0.01605	.	1.758260	0.02457	N	0.086179	T	0.05090	0.0136	L	0.59436	1.845	0.09310	N	1	D	0.62365	0.991	P	0.62014	0.897	T	0.31558	-0.9939	10	0.72032	D	0.01	-1.361	10.6512	0.45649	0.0:0.6133:0.1204:0.2663	.	241	Q7Z4J2	GL6D1_HUMAN	Y	241	ENSP00000360829:D241Y	ENSP00000360829:D241Y	D	-	1	0	GLT6D1	137655874	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.440000	0.06888	-1.807000	0.01236	-0.302000	0.09304	GAC		0.388	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		A	138516053	C	A	138516053	3	1	61	1	0	0	0	0	1	0	0	0	6488	913	32	2	113	2	GLT6D1	9	138516053	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77328	138516053	2697378	6577	14562										
CAMSAP1	157922	broad.mit.edu	37	chr9	138703317	138703317	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagtttgtcgatcattttCttggtgatgttctttggccc	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:138703317C>A	ENST00000389532.4	-	17	4711	c.4647G>T	c.(4645-4647)aaG>aaT	p.K1549N	CAMSAP1_ENST00000312405.6_Missense_Mutation_p.K1271N|CAMSAP1_ENST00000409386.3_Missense_Mutation_p.K1560N|CAMSAP1_ENST00000483991.1_5'UTR	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	1549	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)	p.K1549N(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CGATCATTTTCTTGGTGATGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											219	175	190					9																	138703317		2203	4300	6503	137843138	SO:0001583	missense	157922			AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.4647G>T	9.37:g.138703317C>A	ENSP00000374183:p.Lys1549Asn		137843138	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	37	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185840	0.78789	.	.	ENSG00000130559	ENST00000389532;ENST00000312405;ENST00000409386	T;T;T	0.15718	2.4;2.4;2.4	5.2	4.3	0.51218	PRC-barrel-like (1);Microtubule-binding calmodulin-regulated spectrin-associated, C-terminal (2);	0.048847	0.85682	D	0.000000	T	0.32406	0.0828	L	0.41236	1.265	0.58432	D	0.999999	D;P	0.71674	0.998;0.928	D;P	0.81914	0.995;0.777	T	0.06058	-1.0848	10	0.87932	D	0	.	13.8964	0.63775	0.0:0.9261:0.0:0.0739	.	1549;1560	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	N	1549;1271;1560	ENSP00000374183:K1549N;ENSP00000312463:K1271N;ENSP00000386420:K1560N	ENSP00000312463:K1271N	K	-	3	2	CAMSAP1	137843138	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.720000	0.61944	1.321000	0.45227	0.561000	0.74099	AAG		0.463	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		A	138703317	C	A	138703317	3	1	61	1	0	0	0	0	1	0	0	0	2617	912	32	2	165	2	CAMSAP1	9	138703317	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187264	138703317	2510114	6578	14563										
CAMSAP1	157922	broad.mit.edu	37	chr9	138713151	138713151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcgttggggttttacttCgggaggagccctgtggcctg	18	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:138713151C>T	ENST00000389532.4	-	11	3420	c.3356G>A	c.(3355-3357)cGa>cAa	p.R1119Q	CAMSAP1_ENST00000312405.6_Missense_Mutation_p.R841Q|CAMSAP1_ENST00000409386.3_Missense_Mutation_p.R1130Q|CAMSAP1_ENST00000483991.1_5'UTR	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	1119					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)	p.R1119Q(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		GGTTTTACTTCGGGAGGAGCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	9											37	48	44					9																	138713151		2197	4296	6493	137852972	SO:0001583	missense	157922			AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.3356G>A	9.37:g.138713151C>T	ENSP00000374183:p.Arg1119Gln		137852972	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	37	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506612	0.85282	.	.	ENSG00000130559	ENST00000389532;ENST00000312405;ENST00000409386	T;T;T	0.26223	1.76;1.75;1.75	5.11	5.11	0.69529	.	0.309667	0.31347	N	0.007804	T	0.55353	0.1915	M	0.80616	2.505	0.38773	D	0.954593	D;D	0.76494	0.999;0.999	P;D	0.72075	0.895;0.976	T	0.64058	-0.6496	10	0.87932	D	0	-2.3555	18.8693	0.92306	0.0:1.0:0.0:0.0	.	1119;1130	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	Q	1119;841;1130	ENSP00000374183:R1119Q;ENSP00000312463:R841Q;ENSP00000386420:R1130Q	ENSP00000312463:R841Q	R	-	2	0	CAMSAP1	137852972	1.000000	0.71417	0.322000	0.25334	0.884000	0.51177	4.381000	0.59587	2.518000	0.84900	0.561000	0.74099	CGA		0.667	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		T	138713151	C	T	138713151	3	4	61	1	0	0	0	0	1	0	0	0	2617	884	31	1	1480	1	CAMSAP1	9	138713151	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9834	138713151	2500280	6579	14564										
UBAC1	10422	broad.mit.edu	37	chr9	138838167	138838167	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggttcagcgctaacagcttCtgcgccacctcgatgagaga	12	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:138838167C>A	ENST00000371756.3	-	5	709	c.492G>T	c.(490-492)caG>caT	p.Q164H	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	164					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.Q164H(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTAACAGCTTCTGCGCCACCT	0.502																																					NSCLC(78;973 1398 27381 29552 42415)											1	Substitution - Missense(1)	large_intestine(1)	9											111	102	105					9																	138838167		2203	4300	6503	137977988	SO:0001583	missense	10422			AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.492G>T	9.37:g.138838167C>A	ENSP00000360821:p.Gln164His		137977988	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	37	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.704923	0.30232	.	.	ENSG00000130560	ENST00000371756	T	0.24538	1.85	5.11	3.21	0.36854	.	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	M	0.74881	2.28	0.80722	D	1	B	0.30889	0.299	B	0.21546	0.035	T	0.03545	-1.1026	10	0.39692	T	0.17	-34.4804	9.9546	0.41660	0.0:0.8293:0.0:0.1707	.	164	Q9BSL1	UBAC1_HUMAN	H	164	ENSP00000360821:Q164H	ENSP00000360821:Q164H	Q	-	3	2	UBAC1	137977988	1.000000	0.71417	0.878000	0.34440	0.247000	0.25773	1.720000	0.38022	0.509000	0.28195	0.561000	0.74099	CAG		0.502	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		A	138838167	C	A	138838167	3	1	61	1	0	0	0	0	1	0	0	0	16874	912	32	2	749	2	UBAC1	9	138838167	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125016	138838167	2375264	6580	14565										
LCN10	414332	broad.mit.edu	37	chr9	139635783	139635783	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcccgtctttcctcagGatcacctcctgggactggca	8	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:139635783G>T	ENST00000474369.1	-	3	257				LCN10_ENST00000497771.1_Silent_p.I96I|LCN6_ENST00000471509.1_5'Flank|LCN6_ENST00000435202.1_Intron|LCN10_ENST00000527229.1_Silent_p.I96I|LCN6_ENST00000480584.1_5'Flank			Q6JVE6	LCN10_HUMAN	lipocalin 10						transport (GO:0006810)	extracellular region (GO:0005576)		p.I96I(1)		breast(2)|cervix(1)|large_intestine(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		CTTTCCTCAGGATCACCTCCT	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	9											59	65	63					9																	139635783		1999	4147	6146	138755604	SO:0001627	intron_variant	414332			AY301271	CCDS35182.2	9q34.3	2011-10-24			ENSG00000187922	ENSG00000187922		"Lipocalins"	20892	protein-coding gene	gene with protein product		612904				15363845	Standard	NM_001001712		Approved		uc004civ.3	Q6JVE6	OTTHUMG00000150428	ENST00000474369.1:c.258-317C>A	9.37:g.139635783G>T			138755604	A2RUU3|B0QZ79	Silent	SNP	ENST00000474369.1	37	CCDS35182.2																																																																																				0.687	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712		T	139635783	G	T	139635783	1	4	61	0	1	0	0	0	0	0	0	0	8703	1164	41	2		2	LCN10	9	139635783	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	797616	139635783	1577648	6581	14566										
LCN8	138307	broad.mit.edu	37	chr9	139651020	139651020	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatttctgagcccacgatCttctctatctcacagcttcc	4	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:139651020C>A	ENST00000371688.3	-	3	475	c.180G>T	c.(178-180)aaG>aaT	p.K60N	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	83					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)		p.K60N(1)		endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		AGCCCACGATCTTCTCTATCT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	9											199	180	187					9																	139651020		2203	4300	6503	138770841	SO:0001583	missense	138307			AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"Lipocalins"	27038	protein-coding gene	gene with protein product		612902	"chromosome 9 open reading frame 137", "lipocalin 5"	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.180G>T	9.37:g.139651020C>A	ENSP00000360753:p.Lys60Asn		138770841	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	.	.	.	.	.	.	.	.	.	.	C	0.118	-1.129597	0.01756	.	.	ENSG00000204001	ENST00000371688	T	0.08984	3.03	3.55	-7.1	0.01547	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.03136	0.0092	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44513	-0.9323	9	0.20046	T	0.44	.	6.9695	0.24640	0.1099:0.0913:0.6355:0.1633	.	83;60	Q6JVE9;Q6JVE9-2	LCN8_HUMAN;.	N	60	ENSP00000360753:K60N	ENSP00000360753:K60N	K	-	3	2	LCN8	138770841	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.528000	0.02225	-2.229000	0.00720	-0.339000	0.08088	AAG		0.557	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469		A	139651020	C	A	139651020	3	1	61	1	0	0	0	0	1	0	0	0	8708	912	32	2	298	2	LCN8	9	139651020	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15237	139651020	1562411	6582	14567										
CACNA1B	774	broad.mit.edu	37	chr9	140777256	140777256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagggatcaaaatcatcGctctgggctttgtcttccac	10	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:140777256G>A	ENST00000371372.1	+	3	596	c.451G>A	c.(451-453)Gct>Act	p.A151T	CACNA1B_ENST00000277549.5_5'UTR|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A151T|CACNA1B_ENST00000277551.2_Missense_Mutation_p.A151T|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A151T|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A151T	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	151					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.A151T(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CAAAATCATCGCTCTGGGCTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	9											185	197	193					9																	140777256		2098	4211	6309	139897077	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.451G>A	9.37:g.140777256G>A	ENSP00000360423:p.Ala151Thr		139897077	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070415	0.76301	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.99023	-5.34;-5.34;-5.34;-5.34;-5.34	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98421	1.0577	10	0.66056	D	0.02	.	17.6755	0.88229	0.0:0.0:1.0:0.0	.	151	B1AQK6	.	T	151	ENSP00000360423:A151T;ENSP00000277551:A151T;ENSP00000360414:A151T;ENSP00000360408:A151T;ENSP00000360406:A151T	ENSP00000277551:A151T	A	+	1	0	CACNA1B	139897077	1.000000	0.71417	0.087000	0.20705	0.719000	0.41307	9.637000	0.98443	2.164000	0.68074	0.467000	0.42956	GCT		0.572	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140777256	G	A	140777256	3	1	61	1	0	0	0	0	1	0	0	0	2545	1087	38	1	461	1	CACNA1B	9	140777256	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1126236	140777256	436175	6583	14568										
CACNA1B	774	broad.mit.edu	37	chr9	140811755	140811755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcccggctgtgcgagggcGacactgagtgccgggagtac	17	12	0	1	rs200775337		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr9:140811755G>A	ENST00000371372.1	+	6	983	c.838G>A	c.(838-840)Gac>Aac	p.D280N	CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371363.1_Missense_Mutation_p.D280N|CACNA1B_ENST00000277551.2_Missense_Mutation_p.D280N|CACNA1B_ENST00000371355.4_Missense_Mutation_p.D280N|CACNA1B_ENST00000371357.1_Missense_Mutation_p.D280N	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	280					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.D280N(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGCGAGGGCGACACTGAGTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	9											104	119	114					9																	140811755		2131	4261	6392	139931576	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.838G>A	9.37:g.140811755G>A	ENSP00000360423:p.Asp280Asn		139931576	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171316	0.38315	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.83;-3.83	4.86	3.96	0.45880	.	0.111133	0.64402	N	0.000010	D	0.83631	0.5296	N	0.00754	-1.215	0.80722	D	1	B	0.16166	0.016	B	0.12837	0.008	T	0.79017	-0.1975	10	0.52906	T	0.07	.	9.4409	0.38668	0.1623:0.0:0.8377:0.0	.	280	B1AQK6	.	N	280	ENSP00000360423:D280N;ENSP00000277551:D280N;ENSP00000360414:D280N;ENSP00000360408:D280N;ENSP00000360406:D280N	ENSP00000277551:D280N	D	+	1	0	CACNA1B	139931576	1.000000	0.71417	0.678000	0.29963	0.411000	0.31082	7.716000	0.84723	1.161000	0.42604	0.655000	0.94253	GAC		0.577	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140811755	G	A	140811755	3	1	61	1	0	0	0	0	1	0	0	0	2545	1058	37	1	860	1	CACNA1B	9	140811755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34499	140811755	401676	6584	14569										
TUBB8	347688	broad.mit.edu	37	chr10	94559	94559	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcccgcagctcaccgaaGatgaagttgtctggcctgaa	11	13	2	3	rs201828096		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94559G>T	ENST00000309812.4	-	3	335	c.273C>A	c.(271-273)atC>atA	p.I91I	TUBB8_ENST00000447903.2_Silent_p.I19I|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_Missense_Mutation_p.S55Y	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	91					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.I91I(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GCTCACCGAAGATGAAGTTGT	0.632																																					Pancreas(192;2041 3010 9013 18103)											1	Substitution - coding silent(1)	large_intestine(1)	10											42	52	48					10																	94559		2201	4297	6498	84559	SO:0001819	synonymous_variant	347688			AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"Tubulins"	20773	protein-coding gene	gene with protein product	"class VIII beta-tubulin"						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.273C>A	10.37:g.94559G>T			84559	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	G	1.772	-0.484200	0.04383	.	.	ENSG00000173876	ENST00000332708	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.56352	0.1979	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56086	-0.8037	5	0.87932	D	0	.	3.7025	0.08387	1.0E-4:0.4891:0.5106:2.0E-4	.	.	.	.	Y	55	.	ENSP00000371071:S55Y	S	-	2	0	RP11-631M21.2	84559	0.969000	0.33509	0.043000	0.18650	0.046000	0.14306	-0.238000	0.08977	0.181000	0.19994	0.184000	0.17185	TCT		0.632	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		T	94559	G	T	94559	2	4	61	1	0	0	0	0	0	0	0	1	16801	932	33	2		2	TUBB8	10	94559	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		94559	135440188	6585	14570										
ZMYND11	10771	broad.mit.edu	37	chr10	286020	286020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgagcaagctgacattgCgaggatgctatataaagaca	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:286020C>T	ENST00000397962.3	+	8	1150	c.722C>T	c.(721-723)gCg>gTg	p.A241V	ZMYND11_ENST00000381604.4_Missense_Mutation_p.A201V|ZMYND11_ENST00000402736.1_Missense_Mutation_p.A210V|ZMYND11_ENST00000558098.2_Missense_Mutation_p.A241V|ZMYND11_ENST00000397959.3_Missense_Mutation_p.A156V|ZMYND11_ENST00000381584.1_Missense_Mutation_p.A224V|ZMYND11_ENST00000381591.1_Missense_Mutation_p.A241V|ZMYND11_ENST00000309776.4_Missense_Mutation_p.A201V|ZMYND11_ENST00000381607.4_Missense_Mutation_p.A147V|ZMYND11_ENST00000535374.1_Intron|ZMYND11_ENST00000545619.1_Missense_Mutation_p.A147V|ZMYND11_ENST00000509513.2_Missense_Mutation_p.A240V|ZMYND11_ENST00000381602.4_Missense_Mutation_p.A201V|ZMYND11_ENST00000602682.1_Missense_Mutation_p.A156V|ZMYND11_ENST00000403354.1_Missense_Mutation_p.A187V			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	241					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A201V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GCTGACATTGCGAGGATGCTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											110	117	115					10																	286020		2203	4300	6503	276020	SO:0001583	missense	10771			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"Zinc fingers, MYND-type"	16966	protein-coding gene	gene with protein product		608668	"zinc finger, MYND domain containing 11"			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.722C>T	10.37:g.286020C>T	ENSP00000381053:p.Ala241Val		276020	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Missense_Mutation	SNP	ENST00000397962.3	37	CCDS7052.2	.	.	.	.	.	.	.	.	.	.	C	31	5.093592	0.94149	.	.	ENSG00000015171	ENST00000397962;ENST00000309776;ENST00000381602;ENST00000509513;ENST00000397959;ENST00000381591;ENST00000403354;ENST00000381607;ENST00000402736;ENST00000381604;ENST00000381584;ENST00000545619	T;T;T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.65974	0.2743	M	0.73962	2.25	0.43342	D	0.995399	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;0.999;0.999;0.999;1.0	D;D;D;D;D;D;P;P;D	0.79784	0.987;0.993;0.984;0.954;0.989;0.936;0.906;0.906;0.954	T	0.67616	-0.5625	9	0.59425	D	0.04	-19.1681	17.7538	0.88442	0.0:1.0:0.0:0.0	.	241;156;186;241;187;170;187;187;210	Q2LD45;B7Z293;B7Z2J6;Q2LD48;B0QZE2;B0QZE3;Q2LD46;Q2LD47;E7ENI9	.;.;.;.;.;.;.;.;.	V	241;201;201;241;156;241;187;147;210;201;224;147	ENSP00000381053:A241V;ENSP00000309992:A201V;ENSP00000371015:A201V;ENSP00000381050:A156V;ENSP00000371003:A241V;ENSP00000385484:A187V;ENSP00000371020:A147V;ENSP00000386010:A210V;ENSP00000371017:A201V;ENSP00000370996:A224V;ENSP00000438461:A147V	ENSP00000309992:A201V	A	+	2	0	ZMYND11	276020	1.000000	0.71417	0.804000	0.32291	0.863000	0.49368	5.556000	0.67307	2.618000	0.88619	0.563000	0.77884	GCG		0.328	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624		T	286020	C	T	286020	3	4	61	1	0	0	0	0	1	0	0	0	17745	768	27	1	748	1	ZMYND11	10	286020	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191461	286020	135248727	6586	14571										
LARP4B	23185	broad.mit.edu	37	chr10	860951	860951	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcacaagaagccggcacCgagggctctctggagaccac	12	14	1	2	rs140726859	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:860951C>T	ENST00000316157.3	-	15	1795	c.1755G>A	c.(1753-1755)tcG>tcA	p.S585S	LARP4B_ENST00000469487.1_5'UTR	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	585					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.S585S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						AAGCCGGCACCGAGGGCTCTC	0.567													C|||	11	0.00219649	0.0083	0	5008	,	,		19066	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10						C		29,4377	34.3+/-65.2	0,29,2174	85	80	81		1755	-11.7	0	10	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LARP4B	NM_015155.1		0,30,6473	TT,TC,CC		0.0116,0.6582,0.2307		585/739	860951	30,12976	2203	4300	6503	850951	SO:0001819	synonymous_variant	23185			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1755G>A	10.37:g.860951C>T			850951	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	37	CCDS31131.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	0.373|0.373	-0.932706|-0.932706	0.02359|0.02359	0.006582|0.006582	1.16E-4|1.16E-4	ENSG00000107929|ENSG00000107929	ENST00000448368|ENST00000440895	.|.	.|.	.|.	5.85|5.85	-11.7|-11.7	0.00046|0.00046	.|.	.|.	.|.	.|.	.|.	T|T	0.18257|0.18257	0.0438|0.0438	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.20739|0.20739	-1.0266|-1.0266	4|4	.|.	.|.	.|.	-0.224|-0.224	9.369|9.369	0.38241|0.38241	0.2599:0.544:0.0924:0.1036|0.2599:0.544:0.0924:0.1036	.|.	.|.	.|.	.|.	S|Q	151|61	.|.	.|.	G|R	-|-	1|2	0|0	LARP4B|LARP4B	850951|850951	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-2.313000|-2.313000	0.01126|0.01126	-3.740000|-3.740000	0.00113|0.00113	-0.921000|-0.921000	0.02739|0.02739	GGT|CGG		0.567	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		T	860951	C	T	860951	2	4	61	1	0	0	0	0	0	0	0	1	8653	639	23	1		1	LARP4B	10	860951	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	574931	860951	134673796	6587	14572										
LARP4B	23185	broad.mit.edu	37	chr10	863670	863670	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatatatcccttaccctttCtttggatggtcctattatca	4	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:863670C>A	ENST00000316157.3	-	14	1730	c.1690G>T	c.(1690-1692)Gaa>Taa	p.E564*	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	564					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.E564*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						CTTACCCTTTCTTTGGATGGT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											227	243	238					10																	863670		2203	4300	6503	853670	SO:0001587	stop_gained	23185			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1690G>T	10.37:g.863670C>A	ENSP00000326128:p.Glu564*		853670	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Nonsense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	22.0|22.0|22.0	4.231156|4.231156|4.231156	0.79688|0.79688|0.79688	.|.|.	.|.|.	ENSG00000107929|ENSG00000107929|ENSG00000107929	ENST00000316157|ENST00000440895|ENST00000448368	.|.|.	.|.|.	.|.|.	6.11|6.11|6.11	5.21|5.21|5.21	0.72293|0.72293|0.72293	.|.|.	0.132236|.|.	0.64402|.|.	D|.|.	0.000002|.|.	.|T|T	.|0.71117|0.71117	.|0.3302|0.3302	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.74768|0.74768	.|-0.3553|-0.3553	.|4|3	0.62326|0.87932|.	D|D|.	0.03|0|.	-12.3297|-12.3297|-12.3297	15.4396|15.4396|15.4396	0.75173|0.75173|0.75173	0.0:0.9339:0.0:0.0661|0.0:0.9339:0.0:0.0661|0.0:0.9339:0.0:0.0661	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	564|39|129	.|.|.	ENSP00000326128:E564X|ENSP00000403018:K39N|.	E|K|R	-|-|-	1|3|2	0|2|0	LARP4B|LARP4B|LARP4B	853670|853670|853670	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.298000|0.298000|0.298000	0.27526|0.27526|0.27526	7.208000|7.208000|7.208000	0.77907|0.77907|0.77907	1.605000|1.605000|1.605000	0.50152|0.50152|0.50152	-0.136000|-0.136000|-0.136000	0.14681|0.14681|0.14681	GAA|AAG|AGA		0.453	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		A	863670	C	A	863670	4	1	61	1	0	0	0	0	0	1	0	0	8653	922	32	2	542	2	LARP4B	10	863670	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2719	863670	134671077	6588	14573										
LARP4B	23185	broad.mit.edu	37	chr10	875487	875487	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggggtctaaatccattCtttggcaaaaatgtgtttat	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:875487C>A	ENST00000316157.3	-	10	1003	c.963G>T	c.(961-963)aaG>aaT	p.K321N		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	321					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.K321N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						TAAATCCATTCTTTGGCAAAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											117	91	100					10																	875487		2203	4300	6503	865487	SO:0001583	missense	23185			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.963G>T	10.37:g.875487C>A	ENSP00000326128:p.Lys321Asn		865487	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Missense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669197	0.88348	.	.	ENSG00000107929	ENST00000316157	T	0.42131	0.98	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.61937	0.2387	L	0.58510	1.815	0.80722	D	1	D	0.55800	0.973	D	0.63597	0.916	T	0.62348	-0.6873	10	0.72032	D	0.01	-2.4322	19.7859	0.96437	0.0:1.0:0.0:0.0	.	321	Q92615	LAR4B_HUMAN	N	321	ENSP00000326128:K321N	ENSP00000326128:K321N	K	-	3	2	LARP4B	865487	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.912000	0.69948	2.746000	0.94184	0.655000	0.94253	AAG		0.453	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		A	875487	C	A	875487	3	1	61	1	0	0	0	0	1	0	0	0	8653	912	32	2	1285	2	LARP4B	10	875487	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11817	875487	134659260	6589	14574										
ADARB2	105	broad.mit.edu	37	chr10	1313259	1313259	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgggatatggagtctgcGaattcctgaaagacacaagc	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:1313259G>A	ENST00000381312.1	-	4	1408	c.1083C>T	c.(1081-1083)ttC>ttT	p.F361F		NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	361					mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.F361F(2)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		TGGAGTCTGCGAATTCCTGAA	0.612																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	10											91	65	74					10																	1313259		2203	4300	6503	1303259	SO:0001819	synonymous_variant	105			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1083C>T	10.37:g.1313259G>A			1303259	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																				0.612	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1313259	G	A	1313259	2	1	61	1	0	0	0	0	0	0	0	1	283	1049	37	1		1	ADARB2	10	1313259	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	437772	1313259	134221488	6590	14575										
AKR1C3	8644	broad.mit.edu	37	chr10	5136668	5136668	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccagtgtgtaaagctaaAtgatggccacttcatgcctg	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5136668A>C	ENST00000380554.3	+	1	684	c.32A>C	c.(31-33)aAt>aCt	p.N11T	AKR1C3_ENST00000439082.2_Intron|AKR1C3_ENST00000470862.2_Intron|AKR1C3_ENST00000605149.1_Intron|U8_ENST00000459536.1_RNA	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	11					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.N11T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	GTAAAGCTAAATGATGGCCAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											243	210	221					10																	5136668		2203	4299	6502	5126668	SO:0001583	missense	8644			L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.32A>C	10.37:g.5136668A>C	ENSP00000369927:p.Asn11Thr		5126668	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.435892	0.43224	.	.	ENSG00000196139	ENST00000380554	T	0.55052	0.54	2.18	0.979	0.19745	NADP-dependent oxidoreductase domain (2);	0.189949	0.34245	N	0.004126	T	0.57651	0.2068	M	0.83384	2.64	0.80722	D	1	P;P	0.40180	0.614;0.705	P;B	0.46110	0.504;0.214	T	0.58059	-0.7703	10	0.87932	D	0	.	6.6165	0.22780	0.756:0.244:0.0:0.0	.	11;11	B4DKT3;P42330	.;AK1C3_HUMAN	T	11	ENSP00000369927:N11T	ENSP00000369927:N11T	N	+	2	0	AKR1C3	5126668	0.988000	0.35896	0.020000	0.16555	0.656000	0.38851	1.758000	0.38410	0.254000	0.21573	0.260000	0.18958	AAT		0.413	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		C	5136668	A	C	5136668	3	2	61	1	0	0	0	0	1	0	0	0	471	101	4	4	34	4	AKR1C3	10	5136668	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3823409	5136668	130398079	6591	14576										
TUBAL3	79861	broad.mit.edu	37	chr10	5436009	5436009	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcatggggaaatgtattCtcggataaggtaccaggttg	13	6	2	0	rs200240096		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5436009C>A	ENST00000380419.3	-	4	849	c.812G>T	c.(811-813)aGa>aTa	p.R271I	TUBAL3_ENST00000479328.1_Missense_Mutation_p.R231I	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	271					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R271I(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						GAAATGTATTCTCGGATAAGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	ILE/ARG,ILE/ARG	0,4406		0,0,2203	173	172	172		692,812	2.3	0.1	10		172	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TUBAL3	NM_001171864.1,NM_024803.2	97,97	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	231/407,271/447	5436009	1,13005	2203	4300	6503	5426009	SO:0001583	missense	79861			AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"Tubulins"	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.812G>T	10.37:g.5436009C>A	ENSP00000369784:p.Arg271Ile		5426009	B4DKL2|Q4QQJ5|Q9H6Z0	Missense_Mutation	SNP	ENST00000380419.3	37	CCDS7066.2	.	.	.	.	.	.	.	.	.	.	C	12.38	1.919390	0.33908	0.0	1.16E-4	ENSG00000178462	ENST00000380419;ENST00000479328	D;D	0.84660	-1.88;-1.88	4.2	2.32	0.28847	Tubulin/FtsZ, 2-layer sandwich domain (2);Tubulin/FtsZ, GTPase domain (1);Tubulin/FtsZ, C-terminal (1);	0.114391	0.39407	N	0.001378	D	0.95974	0.8689	H	0.99976	5.16	0.50632	D	0.999885	D;D	0.89917	1.0;0.995	D;P	0.87578	0.998;0.867	D	0.94186	0.7436	10	0.87932	D	0	.	9.709	0.40233	0.0:0.8226:0.0:0.1774	.	231;271	A6NHL2-2;A6NHL2	.;TBAL3_HUMAN	I	271;231	ENSP00000369784:R271I;ENSP00000418799:R231I	ENSP00000369784:R271I	R	-	2	0	TUBAL3	5426009	0.994000	0.37717	0.052000	0.19188	0.001000	0.01503	4.805000	0.62561	0.504000	0.28082	-0.145000	0.13849	AGA		0.512	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803		A	5436009	C	A	5436009	3	1	61	1	0	0	0	0	1	0	0	0	16791	913	32	2	532	2	TUBAL3	10	5436009	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	299341	5436009	130098738	6592	14577										
NET1	10276	broad.mit.edu	37	chr10	5496339	5496339	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacttcctccagcgatgtCtcgagtctcccttcagtcga	8	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5496339C>A	ENST00000355029.4	+	9	1022	c.880C>A	c.(880-882)Ctc>Atc	p.L294I	NET1_ENST00000542715.1_Missense_Mutation_p.L113I|NET1_ENST00000380359.3_Missense_Mutation_p.L240I	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	294	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L240I(1)|p.L294I(1)		breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CCAGCGATGTCTCGAGTCTCC	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	10											74	70	72					10																	5496339		2203	4300	6503	5486339	SO:0001583	missense	10276			AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.880C>A	10.37:g.5496339C>A	ENSP00000347134:p.Leu294Ile		5486339	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	37	CCDS41483.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343694	0.61073	.	.	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000449083;ENST00000380359;ENST00000380337	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.97	5.97	0.96955	Dbl homology (DH) domain (5);	0.000000	0.36972	N	0.002302	T	0.67534	0.2903	M	0.73962	2.25	0.58432	D	0.999995	B;B	0.13145	0.002;0.007	B;B	0.26094	0.066;0.066	T	0.62760	-0.6786	10	0.45353	T	0.12	-18.0352	18.9877	0.92779	0.0:1.0:0.0:0.0	.	240;294	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	I	294;113;112;240;112	ENSP00000347134:L294I;ENSP00000446452:L113I;ENSP00000403101:L112I;ENSP00000369717:L240I	ENSP00000347134:L294I	L	+	1	0	NET1	5486339	1.000000	0.71417	0.977000	0.42913	0.907000	0.53573	5.954000	0.70298	2.828000	0.97474	0.655000	0.94253	CTC		0.433	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		A	5496339	C	A	5496339	3	1	61	1	0	0	0	0	1	0	0	0	10369	913	32	2	1011	2	NET1	10	5496339	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60330	5496339	130038408	6593	14578										
NET1	10276	broad.mit.edu	37	chr10	5498571	5498571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaaaatatctttagaattCgcttccatgacccctctcca	3	13	2	2	rs150542987	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5498571C>T	ENST00000355029.4	+	12	1547	c.1405C>T	c.(1405-1407)Cgc>Tgc	p.R469C	NET1_ENST00000542715.1_Missense_Mutation_p.R288C|NET1_ENST00000380359.3_Missense_Mutation_p.R415C	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	469	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R469C(1)|p.R415C(1)		breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CTTTAGAATTCGCTTCCATGA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	10						C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	49	54	52		1405,1243	4.3	1	10	dbSNP_134	52	1,8599		0,1,4299	no	missense,missense	NET1	NM_001047160.1,NM_005863.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	469/597,415/543	5498571	1,13005	2203	4300	6503	5488571	SO:0001583	missense	10276			AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.1405C>T	10.37:g.5498571C>T	ENSP00000347134:p.Arg469Cys		5488571	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	37	CCDS41483.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060270	0.36373	0.0	1.16E-4	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000380359	T;T;T	0.30714	1.52;1.52;1.52	5.23	4.33	0.51752	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.162786	0.28688	N	0.014461	T	0.50360	0.1611	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.959	T	0.52275	-0.8597	10	0.59425	D	0.04	-6.7999	14.7327	0.69393	0.0:0.8542:0.1458:0.0	.	415;469	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	C	469;288;415	ENSP00000347134:R469C;ENSP00000446452:R288C;ENSP00000369717:R415C	ENSP00000347134:R469C	R	+	1	0	NET1	5488571	0.978000	0.34361	1.000000	0.80357	0.236000	0.25371	1.880000	0.39628	1.198000	0.43158	-0.223000	0.12442	CGC		0.403	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		T	5498571	C	T	5498571	3	4	61	1	0	0	0	0	1	0	0	0	10369	884	31	1	1548	1	NET1	10	5498571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2232	5498571	130036176	6594	14579										
C10orf18	54906	broad.mit.edu	37	chr10	5772558	5772558	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatcacttcctgaagaaaGaatccatccaaacacattag	5	10	1	3	rs370325689		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5772558G>T	ENST00000328090.5	+	11	1221	c.596G>T	c.(595-597)aGa>aTa	p.R199I	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	199								p.R199I(1)									CCTGAAGAAAGAATCCATCCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											124	114	117					10																	5772558		1856	4103	5959	5812564	SO:0001583	missense	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.596G>T	10.37:g.5772558G>T	ENSP00000328426:p.Arg199Ile		5812564	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	G	7.709	0.694802	0.15039	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.04406	3.63	5.95	1.44	0.22558	.	0.532850	0.18566	N	0.137469	T	0.02267	0.0070	N	0.08118	0	0.25366	N	0.988743	P	0.35363	0.497	B	0.26202	0.067	T	0.45716	-0.9242	10	0.52906	T	0.07	.	8.7843	0.34811	0.1462:0.3413:0.5125:0.0	.	199	Q5VWN6	F208B_HUMAN	I	199	ENSP00000328426:R199I	ENSP00000328426:R199I	R	+	2	0	C10orf18	5812564	0.474000	0.25886	0.615000	0.29064	0.184000	0.23303	0.869000	0.27996	0.401000	0.25424	-0.300000	0.09419	AGA		0.388	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5772558	G	T	5772558	3	4	61	1	0	0	0	0	1	0	0	0	1600	942	33	2	626	2	C10orf18	10	5772558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273987	5772558	129762189	6595	14580										
C10orf18	54906	broad.mit.edu	37	chr10	5772886	5772886	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatgactccagatcctgaAtttcttgtctcagaggcaga	9	9	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5772886A>C	ENST00000328090.5	+	11	1549	c.924A>C	c.(922-924)gaA>gaC	p.E308D	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	308								p.E308D(1)									CAGATCCTGAATTTCTTGTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											141	128	132					10																	5772886		1855	4107	5962	5812892	SO:0001583	missense	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.924A>C	10.37:g.5772886A>C	ENSP00000328426:p.Glu308Asp		5812892	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.013|9.013	0.983090|0.983090	0.18889|0.18889	.|.	.|.	ENSG00000108021|ENSG00000108021	ENST00000328090;ENST00000442808|ENST00000380270	T|.	0.07021|.	3.23|.	5.92|5.92	0.933|0.933	0.19471|0.19471	.|.	0.201967|.	0.35378|.	N|.	0.003244|.	T|T	0.42291|0.42291	0.1196|0.1196	M|M	0.72894|0.72894	2.215|2.215	0.20563|0.20563	N|N	0.999884|0.999884	B|.	0.12630|.	0.006|.	B|.	0.12156|.	0.007|.	T|T	0.39820|0.39820	-0.9595|-0.9595	10|5	0.46703|.	T|.	0.11|.	.|.	1.9215|1.9215	0.03308|0.03308	0.5384:0.111:0.1322:0.2184|0.5384:0.111:0.1322:0.2184	.|.	308|.	Q5VWN6|.	F208B_HUMAN|.	D|L	308|88	ENSP00000328426:E308D|.	ENSP00000328426:E308D|.	E|I	+|+	3|1	2|0	C10orf18|C10orf18	5812892|5812892	0.881000|0.881000	0.30235|0.30235	0.984000|0.984000	0.44739|0.44739	0.105000|0.105000	0.19272|0.19272	-0.086000|-0.086000	0.11233|0.11233	-0.099000|-0.099000	0.12263|0.12263	-1.533000|-1.533000	0.00918|0.00918	GAA|ATT		0.403	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5772886	A	C	5772886	3	2	61	1	0	0	0	0	1	0	0	0	1600	98	4	4	954	4	C10orf18	10	5772886	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	328	5772886	129761861	6596	14581										
C10orf18	54906	broad.mit.edu	37	chr10	5789270	5789270	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccacctacaagtcccagaGaagaaatgccagctggtgaa	9	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5789270G>T	ENST00000328090.5	+	15	4511	c.3886G>T	c.(3886-3888)Gaa>Taa	p.E1296*		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1296								p.E1296*(1)									AAGTCCCAGAGAAGAAATGCC	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											124	127	126					10																	5789270		1844	4102	5946	5829276	SO:0001587	stop_gained	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.3886G>T	10.37:g.5789270G>T	ENSP00000328426:p.Glu1296*		5829276	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Nonsense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	G	46	12.883542	0.99703	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	.	.	.	5.02	4.11	0.48088	.	0.224834	0.31415	N	0.007692	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	9.5164	0.39109	0.0976:0.0:0.9024:0.0	.	.	.	.	X	1296;491	.	ENSP00000328426:E1296X	E	+	1	0	C10orf18	5829276	0.033000	0.19621	0.664000	0.29753	0.829000	0.46940	1.401000	0.34589	1.312000	0.45043	0.491000	0.48974	GAA		0.443	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5789270	G	T	5789270	4	4	61	1	0	0	0	0	0	1	0	0	1600	943	33	2	3932	2	C10orf18	10	5789270	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16384	5789270	129745477	6597	14582										
C10orf18	54906	broad.mit.edu	37	chr10	5798644	5798644	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcaagctttccacagagaGaatgatacactaatcatcat	6	9	3	3	rs377533232		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5798644G>T	ENST00000328090.5	+	16	7300	c.6675G>T	c.(6673-6675)gaG>gaT	p.E2225D		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2225								p.E2225D(1)									TCCACAGAGAGAATGATACAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	102	106					10																	5798644		1875	4103	5978	5838650	SO:0001583	missense	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.6675G>T	10.37:g.5798644G>T	ENSP00000328426:p.Glu2225Asp		5838650	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	G	9.227	1.034860	0.19590	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.43294	0.95	5.82	1.43	0.22495	.	0.376189	0.25863	N	0.027803	T	0.19725	0.0474	N	0.17379	0.485	0.20764	N	0.999851	B	0.21753	0.06	B	0.20577	0.03	T	0.07009	-1.0795	10	0.25106	T	0.35	.	2.6206	0.04915	0.2207:0.1906:0.4754:0.1133	.	2225	Q5VWN6	F208B_HUMAN	D	2225;1420	ENSP00000328426:E2225D	ENSP00000328426:E2225D	E	+	3	2	C10orf18	5838650	0.660000	0.27420	0.142000	0.22268	0.015000	0.08874	0.798000	0.27014	0.789000	0.33779	0.561000	0.74099	GAG		0.368	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5798644	G	T	5798644	3	4	61	1	0	0	0	0	1	0	0	0	1600	933	33	2	6725	2	C10orf18	10	5798644	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9374	5798644	129736103	6598	14583										
ANKRD16	54522	broad.mit.edu	37	chr10	5922267	5922267	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattaaacggtacctgatcGatttttttcatctttagaat	5	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:5922267G>A	ENST00000380094.5	-	6	1465	c.922C>T	c.(922-924)Cga>Tga	p.R308*	ANKRD16_ENST00000191063.8_Intron|ANKRD16_ENST00000380092.4_Nonsense_Mutation_p.R308*	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	308								p.R308*(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						GTACCTGATCGATTTTTTTCA	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											77	75	76					10																	5922267		2203	4300	6503	5962273	SO:0001587	stop_gained	54522			AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"Ankyrin repeat domain containing"	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.922C>T	10.37:g.5922267G>A	ENSP00000369436:p.Arg308*		5962273	A6NEF0|F8WEI4|Q9NT01	Nonsense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	.	.	.	.	.	.	.	.	.	.	G	40	8.179958	0.98693	.	.	ENSG00000134461	ENST00000380094;ENST00000380092	.	.	.	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-5.1798	10.9767	0.47469	0.0:0.0:0.813:0.187	.	.	.	.	X	308	.	ENSP00000369434:R308X	R	-	1	2	ANKRD16	5962273	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	3.339000	0.52135	2.023000	0.59567	0.478000	0.44815	CGA		0.294	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138		A	5922267	G	A	5922267	4	1	61	1	0	0	0	0	0	1	0	0	645	1066	37	1	171	1	ANKRD16	10	5922267	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123623	5922267	129612480	6599	14584										
IL2RA	3559	broad.mit.edu	37	chr10	6063598	6063598	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaccatctgccccaccacGaaatgataaattctctctgt	4	13	3	1	rs373429536		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:6063598G>A	ENST00000379959.3	-	4	599	c.426C>T	c.(424-426)ttC>ttT	p.F142F	IL2RA_ENST00000256876.6_Silent_p.F142F|IL2RA_ENST00000379954.1_Intron	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	142	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)	p.F142F(2)		endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GCCCCACCACGAAATGATAAA	0.512																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	10											153	134	140					10																	6063598		2203	4300	6503	6103604	SO:0001819	synonymous_variant	3559			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.426C>T	10.37:g.6063598G>A			6103604	Q5W007	Silent	SNP	ENST00000379959.3	37	CCDS7076.1																																																																																				0.512	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		A	6063598	G	A	6063598	2	1	61	1	0	0	0	0	0	0	0	1	7707	1049	37	1		1	IL2RA	10	6063598	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141331	6063598	129471149	6600	14585										
SFMBT2	57713	broad.mit.edu	37	chr10	7423837	7423837	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaagggtcttgcatattGgaagctgacaaagtgctctc	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7423837G>T	ENST00000361972.4	-	2	114	c.24C>A	c.(22-24)tcC>tcA	p.S8S	SFMBT2_ENST00000379713.3_Silent_p.S8S|SFMBT2_ENST00000379711.2_Silent_p.S8S|SFMBT2_ENST00000397160.3_Silent_p.S8S|SFMBT2_ENST00000397167.1_Silent_p.S8S	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	8					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.S8S(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CTTGCATATTGGAAGCTGACA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	10											121	114	116					10																	7423837		2203	4300	6503	7463843	SO:0001819	synonymous_variant	57713			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.24C>A	10.37:g.7423837G>T			7463843	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																				0.393	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		T	7423837	G	T	7423837	2	4	61	1	0	0	0	0	0	0	0	1	14195	1335	47	2		2	SFMBT2	10	7423837	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1360239	7423837	128110910	6601	14586										
ITIH5	80760	broad.mit.edu	37	chr10	7611708	7611708	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcacacggtgagtctgCtcagggggaaatccacaaca	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7611708C>A	ENST00000256861.6	-	12	2150	c.2072G>T	c.(2071-2073)aGc>aTc	p.S691I	ITIH5_ENST00000434980.1_5'Flank|ITIH5_ENST00000298441.6_Missense_Mutation_p.S477I|ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000446830.2_Missense_Mutation_p.S473I	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	691					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S691I(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GGTGAGTCTGCTCAGGGGGAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	10											61	52	55					10																	7611708		2203	4300	6503	7651714	SO:0001583	missense	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2072G>T	10.37:g.7611708C>A	ENSP00000256861:p.Ser691Ile		7651714	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	15.95	2.983242	0.53827	.	.	ENSG00000123243	ENST00000256861;ENST00000298441;ENST00000446830	T;T;T	0.02345	4.53;4.33;4.33	5.52	4.61	0.57282	.	0.035436	0.85682	D	0.000000	T	0.11750	0.0286	.	.	.	0.80722	D	1	D;D	0.69078	0.995;0.997	P;D	0.66979	0.888;0.948	T	0.00431	-1.1743	9	0.62326	D	0.03	-33.6691	10.3942	0.44190	0.0:0.8503:0.0:0.1497	.	691;477	Q86UX2;Q86UX2-3	ITIH5_HUMAN;.	I	691;477;473	ENSP00000256861:S691I;ENSP00000298441:S477I;ENSP00000387969:S473I	ENSP00000256861:S691I	S	-	2	0	ITIH5	7651714	1.000000	0.71417	0.904000	0.35570	0.031000	0.12232	3.616000	0.54174	1.321000	0.45227	0.557000	0.71058	AGC		0.517	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		A	7611708	C	A	7611708	3	1	61	1	0	0	0	0	1	0	0	0	7928	797	28	2	810	2	ITIH5	10	7611708	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187871	7611708	127923039	6602	14587										
ITIH5	80760	broad.mit.edu	37	chr10	7657989	7657989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagcactgctgtcaagcaCgaataccacattcttgggta	9	10	2	1	rs199952014		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7657989C>T	ENST00000256861.6	-	7	973	c.895G>A	c.(895-897)Gtg>Atg	p.V299M	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000298441.6_Missense_Mutation_p.V85M|ITIH5_ENST00000397146.2_Missense_Mutation_p.V299M|ITIH5_ENST00000446830.2_Missense_Mutation_p.V81M|ITIH5_ENST00000397145.2_Missense_Mutation_p.V299M	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	299	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V299M(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTGTCAAGCACGAATACCACA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											134	126	128					10																	7657989		2203	4300	6503	7697995	SO:0001583	missense	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.895G>A	10.37:g.7657989C>T	ENSP00000256861:p.Val299Met		7697995	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	24.2	4.506697	0.85282	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29	6.08	5.18	0.71444	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	.	.	.	0.53005	D	0.999968	D;D;D	0.89917	1.0;0.999;0.998	D;D;P	0.83275	0.996;0.944;0.906	D	0.94728	0.7907	9	0.87932	D	0	-31.5257	16.5965	0.84797	0.1313:0.8687:0.0:0.0	.	299;299;85	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	M	299;299;85;81;299	ENSP00000256861:V299M;ENSP00000380333:V299M;ENSP00000298441:V85M;ENSP00000387969:V81M;ENSP00000380332:V299M	ENSP00000256861:V299M	V	-	1	0	ITIH5	7697995	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.563000	0.67352	1.573000	0.49748	0.655000	0.94253	GTG		0.473	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7657989	C	T	7657989	3	4	61	1	0	0	0	0	1	0	0	0	7928	536	19	1	2088	1	ITIH5	10	7657989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46281	7657989	127876758	6603	14588										
ITIH2	3698	broad.mit.edu	37	chr10	7762890	7762890	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacatttgaaggccatttCgatggtgttccggtcatttc	10	9	1	1	rs148694864	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7762890C>T	ENST00000358415.4	+	7	868	c.702C>T	c.(700-702)ttC>ttT	p.F234F	ITIH2_ENST00000379587.4_Silent_p.F223F	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	234					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F234F(2)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						AAGGCCATTTCGATGGTGTTC	0.483																																																2	Substitution - coding silent(2)	large_intestine(2)	10						C		3,4403	6.2+/-15.9	0,3,2200	162	136	145		702	0.4	1	10	dbSNP_134	145	0,8600		0,0,4300	no	coding-synonymous	ITIH2	NM_002216.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		234/947	7762890	3,13003	2203	4300	6503	7802896	SO:0001819	synonymous_variant	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.702C>T	10.37:g.7762890C>T			7802896	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.483	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7762890	C	T	7762890	2	4	61	1	0	0	0	0	0	0	0	1	7925	883	31	1		1	ITIH2	10	7762890	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104901	7762890	127771857	6604	14589										
ITIH2	3698	broad.mit.edu	37	chr10	7773900	7773900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggctcagagattgtggtgGcaggaaaatttgaccctgct	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7773900G>A	ENST00000358415.4	+	13	1754	c.1588G>A	c.(1588-1590)Gca>Aca	p.A530T	ITIH2_ENST00000379587.4_Missense_Mutation_p.A519T	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	530					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A530T(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GATTGTGGTGGCAGGAAAATT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											139	135	136					10																	7773900		2203	4300	6503	7813906	SO:0001583	missense	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1588G>A	10.37:g.7773900G>A	ENSP00000351190:p.Ala530Thr		7813906	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	G	33	5.232251	0.95207	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.16073	2.37;2.37	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53408	-0.8443	10	0.87932	D	0	-22.7298	19.2749	0.94027	0.0:0.0:1.0:0.0	.	530	P19823	ITIH2_HUMAN	T	530;519	ENSP00000351190:A530T;ENSP00000368906:A519T	ENSP00000351190:A530T	A	+	1	0	ITIH2	7813906	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	7.266000	0.78452	2.558000	0.86282	0.643000	0.83706	GCA		0.428	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		A	7773900	G	A	7773900	3	1	61	1	0	0	0	0	1	0	0	0	7925	1203	42	3	1638	3	ITIH2	10	7773900	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11010	7773900	127760847	6605	14590										
ITIH2	3698	broad.mit.edu	37	chr10	7776914	7776914	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctacagctgccgccaagaGaagaattacaagatcgatcc	8	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7776914G>T	ENST00000358415.4	+	15	1983	c.1817G>T	c.(1816-1818)aGa>aTa	p.R606I	ITIH2_ENST00000379587.4_Missense_Mutation_p.R595I	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	606					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R606I(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GCCGCCAAGAGAAGAATTACA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	10											111	109	110					10																	7776914		2203	4300	6503	7816920	SO:0001583	missense	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1817G>T	10.37:g.7776914G>T	ENSP00000351190:p.Arg606Ile		7816920	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.485040	0.44147	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.29917	1.55;1.55	5.45	-0.204	0.13200	.	0.152275	0.56097	D	0.000031	T	0.51193	0.1660	M	0.80183	2.485	0.80722	D	1	D	0.59357	0.985	D	0.63381	0.914	T	0.58640	-0.7601	10	0.66056	D	0.02	-13.4492	13.3635	0.60669	0.2192:0.0:0.7808:0.0	.	606	P19823	ITIH2_HUMAN	I	606;595	ENSP00000351190:R606I;ENSP00000368906:R595I	ENSP00000351190:R606I	R	+	2	0	ITIH2	7816920	1.000000	0.71417	0.011000	0.14972	0.043000	0.13939	4.297000	0.59061	0.025000	0.15241	0.543000	0.68304	AGA		0.547	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7776914	G	T	7776914	3	4	61	1	0	0	0	0	1	0	0	0	7925	942	33	2	1875	2	ITIH2	10	7776914	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3014	7776914	127757833	6606	14591										
ATP5C1	509	broad.mit.edu	37	chr10	7838103	7838103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggattcaagttcgaaatatgGcaactttgaaagatagtaag	10	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7838103G>A	ENST00000356708.7	+	2	155	c.76G>A	c.(76-78)Gca>Aca	p.A26T	ATP5C1_ENST00000541227.1_Intron|ATP5C1_ENST00000493053.1_Intron|ATP5C1_ENST00000335698.4_Missense_Mutation_p.A26T	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	26					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.A26T(1)		breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						TCGAAATATGGCAACTTTGAA	0.239																																					Melanoma(143;1012 1820 16249 30920 33158)											1	Substitution - Missense(1)	large_intestine(1)	10											35	38	37					10																	7838103		2198	4290	6488	7878109	SO:0001583	missense	509			D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.76G>A	10.37:g.7838103G>A	ENSP00000349142:p.Ala26Thr		7878109	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	37	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	G	34	5.309351	0.95629	.	.	ENSG00000165629	ENST00000356708;ENST00000335698	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.86863	0.6035	M	0.93197	3.39	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.90331	0.4352	9	0.87932	D	0	-6.0805	18.8351	0.92159	0.0:0.0:1.0:0.0	.	26	P36542	ATPG_HUMAN	T	26	.	ENSP00000338568:A26T	A	+	1	0	ATP5C1	7878109	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.331000	0.96430	2.460000	0.83146	0.561000	0.74099	GCA		0.239	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		A	7838103	G	A	7838103	3	1	61	1	0	0	0	0	1	0	0	0	1150	1203	42	3	82	3	ATP5C1	10	7838103	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61189	7838103	127696644	6607	14592										
ATP5C1	509	broad.mit.edu	37	chr10	7841769	7841769	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttctggtggcattcaaaGaagtgggaagaaagcccccc	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:7841769G>T	ENST00000356708.7	+	5	542	c.463G>T	c.(463-465)Gaa>Taa	p.E155*	ATP5C1_ENST00000541227.1_Nonsense_Mutation_p.E108*|ATP5C1_ENST00000493053.1_3'UTR|ATP5C1_ENST00000335698.4_Nonsense_Mutation_p.E155*	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	155					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.E155*(1)		breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						GGCATTCAAAGAAGTGGGAAG	0.413																																					Melanoma(143;1012 1820 16249 30920 33158)											1	Substitution - Nonsense(1)	large_intestine(1)	10											63	64	64					10																	7841769		2203	4300	6503	7881775	SO:0001587	stop_gained	509			D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.463G>T	10.37:g.7841769G>T	ENSP00000349142:p.Glu155*		7881775	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Nonsense_Mutation	SNP	ENST00000356708.7	37	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	G	36	5.907495	0.97093	.	.	ENSG00000165629	ENST00000356708;ENST00000335698;ENST00000541227	.	.	.	5.73	5.73	0.89815	.	0.050091	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-12.0384	20.2602	0.98440	0.0:0.0:1.0:0.0	.	.	.	.	X	155;155;108	.	ENSP00000338568:E155X	E	+	1	0	ATP5C1	7881775	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.686000	0.98664	2.861000	0.98227	0.655000	0.94253	GAA		0.413	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		T	7841769	G	T	7841769	4	4	61	1	0	0	0	0	0	1	0	0	1150	943	33	2	481	2	ATP5C1	10	7841769	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3666	7841769	127692978	6608	14593										
TAF3	83860	broad.mit.edu	37	chr10	8006604	8006604	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaacagtgagaatcagccGaaaaaggctgtggtagcaga	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:8006604G>A	ENST00000344293.5	+	3	1337	c.1131G>A	c.(1129-1131)ccG>ccA	p.P377P		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	377					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)	p.P377P(1)		NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						AGAATCAGCCGAAAAAGGCTG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	10											62	59	60					10																	8006604		1897	4125	6022	8046610	SO:0001819	synonymous_variant	83860			AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1131G>A	10.37:g.8006604G>A			8046610	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Silent	SNP	ENST00000344293.5	37	CCDS41487.1																																																																																				0.453	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		A	8006604	G	A	8006604	2	1	61	1	0	0	0	0	0	0	0	1	15564	1045	37	1		1	TAF3	10	8006604	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164835	8006604	127528143	6609	14594										
GATA3	2625	broad.mit.edu	37	chr10	8115902	8115902	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccactccagccacatgctGaccacgcccacgccgatgca	8	19	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:8115902G>A	ENST00000346208.3	+	6	1703	c.1248G>A	c.(1246-1248)ctG>ctA	p.L416L	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.L417L			P23771	GATA3_HUMAN	GATA binding protein 3	416					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.L417L(1)		NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						GCCACATGCTGACCACGCCCA	0.627			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																																Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	1	Substitution - coding silent(1)	large_intestine(1)	10											98	86	90					10																	8115902		2203	4300	6503	8155908	SO:0001819	synonymous_variant	2625			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.1248G>A	10.37:g.8115902G>A			8155908	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																				0.627	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8115902	G	A	8115902	2	1	61	1	0	0	0	0	0	0	0	1	6275	1277	45	3		3	GATA3	10	8115902	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109298	8115902	127418845	6610	14595										
UPF2	26019	broad.mit.edu	37	chr10	11971886	11971886	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaccagtcttaaagattaGatctgcattaggtgctccct	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:11971886G>T	ENST00000356352.2	-	20	4260	c.3787C>A	c.(3787-3789)Cta>Ata	p.L1263I	UPF2_ENST00000397053.2_Missense_Mutation_p.L1263I|UPF2_ENST00000357604.5_Missense_Mutation_p.L1263I			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	1263	Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF1 C- terminus.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.L1263I(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				TTAAAGATTAGATCTGCATTA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											167	150	156					10																	11971886		2203	4300	6503	12011892	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.3787C>A	10.37:g.11971886G>T	ENSP00000348708:p.Leu1263Ile		12011892	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.934381	0.92458	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.49720	0.77;0.77;0.77	5.23	5.23	0.72850	.	0.183519	0.36591	N	0.002513	T	0.66406	0.2786	M	0.65975	2.015	0.58432	D	0.99999	P	0.52842	0.956	P	0.62184	0.899	T	0.67868	-0.5559	10	0.54805	T	0.06	.	18.7827	0.91941	0.0:0.0:1.0:0.0	.	1263	Q9HAU5	RENT2_HUMAN	I	1263	ENSP00000348708:L1263I;ENSP00000350221:L1263I;ENSP00000380244:L1263I	ENSP00000348708:L1263I	L	-	1	2	UPF2	12011892	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.199000	0.95003	2.439000	0.82584	0.462000	0.41574	CTA		0.458	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			T	11971886	G	T	11971886	3	4	61	1	0	0	0	0	1	0	0	0	17044	933	33	2	39	2	UPF2	10	11971886	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3855984	11971886	123562861	6611	14596										
UPF2	26019	broad.mit.edu	37	chr10	11998332	11998332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttacctccattcctaatCgaatatcttctaacactcca	2	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:11998332C>T	ENST00000356352.2	-	12	3034	c.2561G>A	c.(2560-2562)cGa>cAa	p.R854Q	UPF2_ENST00000397053.2_Missense_Mutation_p.R854Q|UPF2_ENST00000357604.5_Missense_Mutation_p.R854Q			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	854	Binds to UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF3A and UPF3B.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.R854Q(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				CATTCCTAATCGAATATCTTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											123	113	116					10																	11998332		2203	4300	6503	12038338	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.2561G>A	10.37:g.11998332C>T	ENSP00000348708:p.Arg854Gln		12038338	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	C	34	5.385895	0.95967	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.20069	2.1;2.1;2.1	5.53	5.53	0.82687	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.075912	0.53938	D	0.000045	T	0.50786	0.1636	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.49234	-0.8961	10	0.45353	T	0.12	.	19.4313	0.94768	0.0:1.0:0.0:0.0	.	854	Q9HAU5	RENT2_HUMAN	Q	854	ENSP00000348708:R854Q;ENSP00000350221:R854Q;ENSP00000380244:R854Q	ENSP00000348708:R854Q	R	-	2	0	UPF2	12038338	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.277000	0.78572	2.596000	0.87737	0.484000	0.47621	CGA		0.383	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			T	11998332	C	T	11998332	3	4	61	1	0	0	0	0	1	0	0	0	17044	884	31	1	1297	1	UPF2	10	11998332	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26446	11998332	123536415	6612	14597										
UPF2	26019	broad.mit.edu	37	chr10	12043687	12043687	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttaccttgttcatcaaGaagtttctttgtaagatctt	5	7	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12043687G>T	ENST00000356352.2	-	5	2115	c.1642C>A	c.(1642-1644)Ctt>Att	p.L548I	UPF2_ENST00000397053.2_Missense_Mutation_p.L548I|UPF2_ENST00000357604.5_Missense_Mutation_p.L548I			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	548					gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.L548I(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				TGTTCATCAAGAAGTTTCTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	108	110					10																	12043687		2202	4300	6502	12083693	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1642C>A	10.37:g.12043687G>T	ENSP00000348708:p.Leu548Ile		12083693	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615494	0.46631	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000379172;ENST00000397053;ENST00000313977	T;T;T	0.45668	0.89;0.89;0.89	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	L	0.44542	1.39	0.58432	D	0.999998	D;B	0.56035	0.974;0.068	D;B	0.67725	0.953;0.031	T	0.44143	-0.9347	10	0.37606	T	0.19	.	12.7855	0.57502	0.0759:0.0:0.9241:0.0	.	518;548	Q9HAU5-2;Q9HAU5	.;RENT2_HUMAN	I	548;548;518;548;518	ENSP00000348708:L548I;ENSP00000350221:L548I;ENSP00000380244:L548I	ENSP00000313617:L518I	L	-	1	0	UPF2	12083693	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.861000	0.69553	2.775000	0.95449	0.655000	0.94253	CTT		0.333	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			T	12043687	G	T	12043687	3	4	61	1	0	0	0	0	1	0	0	0	17044	942	33	2	2244	2	UPF2	10	12043687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45355	12043687	123491060	6613	14598										
UPF2	26019	broad.mit.edu	37	chr10	12077380	12077380	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgttgtttggtaaagagtCtttttcttccatacttgctg	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12077380C>A	ENST00000356352.2	-	1	516	c.43G>T	c.(43-45)Gac>Tac	p.D15Y	UPF2_ENST00000460569.1_5'UTR|UPF2_ENST00000397053.2_Missense_Mutation_p.D15Y|UPF2_ENST00000357604.5_Missense_Mutation_p.D15Y			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	15	Glu/Lys-rich.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.D15Y(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				GGTAAAGAGTCTTTTTCTTCC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											163	150	154					10																	12077380		2203	4300	6503	12117386	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.43G>T	10.37:g.12077380C>A	ENSP00000348708:p.Asp15Tyr		12117386	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698286	0.68386	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000379172;ENST00000397053;ENST00000313977	T;T;T	0.13657	2.57;2.57;2.57	5.78	5.78	0.91487	.	0.296342	0.36778	N	0.002404	T	0.14874	0.0359	N	0.19112	0.55	0.43476	D	0.995691	B	0.31790	0.34	B	0.37091	0.241	T	0.07829	-1.0752	10	0.87932	D	0	.	20.3754	0.98918	0.0:1.0:0.0:0.0	.	15	Q9HAU5	RENT2_HUMAN	Y	15	ENSP00000348708:D15Y;ENSP00000350221:D15Y;ENSP00000380244:D15Y	ENSP00000313617:D15Y	D	-	1	0	UPF2	12117386	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.305000	0.65750	2.894000	0.99253	0.591000	0.81541	GAC		0.453	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			A	12077380	C	A	12077380	3	1	61	1	0	0	0	0	1	0	0	0	17044	913	32	2	3859	2	UPF2	10	12077380	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33693	12077380	123457367	6614	14599										
DHTKD1	55526	broad.mit.edu	37	chr10	12136141	12136141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagtggtccgtgccacacGactggcttttgaataccaac	11	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12136141G>A	ENST00000263035.4	+	7	1291	c.1229G>A	c.(1228-1230)cGa>cAa	p.R410Q	DHTKD1_ENST00000465617.1_3'UTR	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	410					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R410Q(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CGTGCCACACGACTGGCTTTT	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	10											179	144	155					10																	12136141		2203	4300	6503	12176147	SO:0001583	missense	55526			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.1229G>A	10.37:g.12136141G>A	ENSP00000263035:p.Arg410Gln		12176147	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.359676	0.41801	.	.	ENSG00000181192	ENST00000263035;ENST00000415935	D;D	0.95885	-3.84;-3.84	4.59	1.22	0.21188	Dehydrogenase, E1 component (1);	0.190701	0.47455	N	0.000236	D	0.90854	0.7127	L	0.31120	0.905	0.58432	D	0.999998	B	0.18741	0.03	B	0.29942	0.109	T	0.82212	-0.0569	10	0.42905	T	0.14	-2.108	9.2773	0.37707	0.2649:0.0:0.7351:0.0	.	410	Q96HY7	DHTK1_HUMAN	Q	410;108	ENSP00000263035:R410Q;ENSP00000400625:R108Q	ENSP00000263035:R410Q	R	+	2	0	DHTKD1	12176147	1.000000	0.71417	0.255000	0.24374	0.969000	0.65631	4.244000	0.58728	-0.054000	0.13266	0.491000	0.48974	CGA		0.527	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		A	12136141	G	A	12136141	3	1	61	1	0	0	0	0	1	0	0	0	4511	1058	37	1	1255	1	DHTKD1	10	12136141	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58761	12136141	123398606	6615	14600										
DHTKD1	55526	broad.mit.edu	37	chr10	12149995	12149995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagaccactcatcctgtcGaatagagcgtttcctgcagg	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12149995G>A	ENST00000263035.4	+	12	2197	c.2135G>A	c.(2134-2136)cGa>cAa	p.R712Q		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	712					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R712Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TCATCCTGTCGAATAGAGCGT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	10											138	111	120					10																	12149995		2203	4300	6503	12190001	SO:0001583	missense	55526			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2135G>A	10.37:g.12149995G>A	ENSP00000263035:p.Arg712Gln		12190001	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707953	0.68615	.	.	ENSG00000181192	ENST00000263035;ENST00000448829	D	0.92397	-3.03	5.61	4.71	0.59529	Transketolase-like, pyrimidine-binding domain (2);	0.256366	0.39210	N	0.001421	D	0.97399	0.9149	H	0.98370	4.215	0.46167	D	0.998903	D	0.62365	0.991	D	0.66351	0.943	D	0.98041	1.0382	10	0.87932	D	0	-6.7202	12.6193	0.56594	0.0765:0.0:0.9235:0.0	.	712	Q96HY7	DHTK1_HUMAN	Q	712;213	ENSP00000263035:R712Q	ENSP00000263035:R712Q	R	+	2	0	DHTKD1	12190001	1.000000	0.71417	0.597000	0.28824	0.465000	0.32709	7.010000	0.76353	1.384000	0.46424	0.456000	0.33151	CGA		0.527	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		A	12149995	G	A	12149995	3	1	61	1	0	0	0	0	1	0	0	0	4511	1058	37	1	2181	1	DHTKD1	10	12149995	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13854	12149995	123384752	6616	14601										
CDC123	8872	broad.mit.edu	37	chr10	12292314	12292314	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttttctttgacagaagaGaaatcagcaggaggacgact	12	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12292314G>T	ENST00000281141.4	+	13	1269	c.989G>T	c.(988-990)aGa>aTa	p.R330I	RP11-186N15.3_ENST00000421657.1_RNA|CDC123_ENST00000378900.2_Missense_Mutation_p.R289I	NM_006023.2	NP_006014.2	O75794	CD123_HUMAN	cell division cycle 123	330					cell cycle arrest (GO:0007050)|cell division (GO:0051301)|positive regulation of cell proliferation (GO:0008284)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)		p.R330I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12						TGACAGAAGAGAAATCAGCAG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	10											71	72	72					10																	12292314		2203	4300	6503	12332320	SO:0001583	missense	8872			BC001600	CCDS7090.1	10p13	2013-01-17	2013-01-17	2006-11-06	ENSG00000151465	ENSG00000151465			16827	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 7", "cell division cycle 123 homolog (S. cerevisiae)"	C10orf7		15319434	Standard	NM_006023		Approved	D123	uc001ill.3	O75794	OTTHUMG00000017680	ENST00000281141.4:c.989G>T	10.37:g.12292314G>T	ENSP00000281141:p.Arg330Ile		12332320	A8JZZ7|Q14107|Q5T0L4|Q5T0L5|Q5T0L7|Q5T0L8|Q5T0L9	Missense_Mutation	SNP	ENST00000281141.4	37	CCDS7090.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.13|16.13|16.13	3.036132|3.036132|3.036132	0.54896|0.54896|0.54896	.|.|.	.|.|.	ENSG00000151465|ENSG00000151465|ENSG00000151465	ENST00000455773|ENST00000440613|ENST00000281141;ENST00000378900	.|.|.	.|.|.	.|.|.	5.91|5.91|5.91	5.91|5.91|5.91	0.95273|0.95273|0.95273	.|.|.	.|.|0.548830	.|.|0.18272	.|.|N	.|.|0.146282	.|T|T	.|0.44912|0.44912	.|0.1316|0.1316	N|N|N	0.16478|0.16478|0.16478	0.41|0.41|0.41	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|B	.|.|0.30763	.|.|0.294	.|.|B	.|.|0.30251	.|.|0.113	.|T|T	.|0.36261|0.36261	.|-0.9755|-0.9755	.|5|9	.|.|0.36615	.|.|T	.|.|0.2	.|-4.1354|-4.1354	17.2153|17.2153|17.2153	0.86941|0.86941|0.86941	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|330	.|.|O75794	.|.|CD123_HUMAN	.|D|I	-1|137|330;289	.|.|.	.|.|ENSP00000281141:R330I	.|E|R	+|+|+	.|3|2	.|2|0	CDC123|CDC123|CDC123	12332320|12332320|12332320	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.559000|0.559000|0.559000	0.35586|0.35586|0.35586	5.328000|5.328000|5.328000	0.65887|0.65887|0.65887	2.793000|2.793000|2.793000	0.96121|0.96121|0.96121	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	.|GAG|AGA		0.527	CDC123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046801.1	NM_006023		T	12292314	G	T	12292314	3	4	61	1	0	0	0	0	1	0	0	0	3061	942	33	2	1039	2	CDC123	10	12292314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142319	12292314	123242433	6617	14602										
CAMK1D	57118	broad.mit.edu	37	chr10	12595255	12595255	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgaagtggttttagctgaaGagaaggcaactggcaagctc	13	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:12595255G>T	ENST00000378847.3	+	2	461	c.124G>T	c.(124-126)Gag>Tag	p.E42*	CAMK1D_ENST00000487696.1_Intron|CAMK1D_ENST00000378845.1_Nonsense_Mutation_p.E42*	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	42	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.E42*(2)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		TTTAGCTGAAGAGAAGGCAAC	0.473																																																2	Substitution - Nonsense(2)	large_intestine(2)	10											162	152	156					10																	12595255		2203	4300	6503	12635261	SO:0001587	stop_gained	57118			AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.124G>T	10.37:g.12595255G>T	ENSP00000368124:p.Glu42*		12635261	B0YIY0|Q9HD31	Nonsense_Mutation	SNP	ENST00000378847.3	37	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	37	6.414785	0.97546	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	.	.	.	5.14	5.14	0.70334	.	0.055898	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	-25.4575	17.1858	0.86866	0.0:0.0:1.0:0.0	.	.	.	.	X	42	.	ENSP00000368122:E42X	E	+	1	0	CAMK1D	12635261	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	9.392000	0.97252	2.370000	0.80446	0.561000	0.74099	GAG		0.473	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		T	12595255	G	T	12595255	4	4	61	1	0	0	0	0	0	1	0	0	2603	943	33	2	130	2	CAMK1D	10	12595255	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	302941	12595255	122939492	6618	14603										
CCDC3	83643	broad.mit.edu	37	chr10	13040440	13040440	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagaaaacatccttctgttCtcttgagtgtctgggaagat	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:13040440C>A	ENST00000378825.3	-	2	573	c.447G>T	c.(445-447)gaG>gaT	p.E149D	CCDC3_ENST00000378839.1_Missense_Mutation_p.E24D	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	149						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.E149D(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			TCCTTCTGTTCTCTTGAGTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											130	116	121					10																	13040440		2203	4300	6503	13080446	SO:0001583	missense	83643			BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.447G>T	10.37:g.13040440C>A	ENSP00000368102:p.Glu149Asp		13080446	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.243296	0.58995	.	.	ENSG00000151468	ENST00000378839;ENST00000378825	.	.	.	4.92	1.03	0.20045	.	0.047523	0.85682	D	0.000000	T	0.65903	0.2736	L	0.56769	1.78	0.40642	D	0.981958	D	0.67145	0.996	D	0.76071	0.987	T	0.60535	-0.7244	9	0.29301	T	0.29	-0.639	8.9823	0.35972	0.0:0.7009:0.0:0.2991	.	149	Q9BQI4	CCDC3_HUMAN	D	24;149	.	ENSP00000368102:E149D	E	-	3	2	CCDC3	13080446	0.972000	0.33761	0.998000	0.56505	0.966000	0.64601	0.196000	0.17176	-0.002000	0.14469	-0.379000	0.06801	GAG		0.448	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		A	13040440	C	A	13040440	3	1	61	1	0	0	0	0	1	0	0	0	2810	912	32	2	373	2	CCDC3	10	13040440	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	445185	13040440	122494307	6619	14604										
OPTN	10133	broad.mit.edu	37	chr10	13160940	13160940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggggccaagaattacttcGaacatgaggagttaactgtg	12	6	0	2	rs368244180	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:13160940G>A	ENST00000378748.3	+	8	1041	c.679G>A	c.(679-681)Gaa>Aaa	p.E227K	OPTN_ENST00000378747.3_Missense_Mutation_p.E227K|OPTN_ENST00000378764.2_Missense_Mutation_p.E221K|OPTN_ENST00000378752.3_Missense_Mutation_p.E221K|OPTN_ENST00000482140.1_3'UTR|OPTN_ENST00000378757.2_Missense_Mutation_p.E227K|OPTN_ENST00000263036.5_Missense_Mutation_p.E227K	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	227					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)	p.E227K(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GAATTACTTCGAACATGAGGA	0.438													G|||	3	0.000599042	0	0	5008	,	,		18848	0.003		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	98	97	97		679,679,679,679	5.3	0.7	10		97	0,8600		0,0,4300	no	missense,missense,missense,missense	OPTN	NM_001008211.1,NM_001008212.1,NM_001008213.1,NM_021980.4	56,56,56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	227/578,227/578,227/578,227/578	13160940	1,13005	2203	4300	6503	13200946	SO:0001583	missense	10133			AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"glaucoma 1, open angle, E (adult-onset)"	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.679G>A	10.37:g.13160940G>A	ENSP00000368022:p.Glu227Lys		13200946	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.384156	0.61845	2.27E-4	0.0	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.88354	-2.37;-2.36;-2.37;-2.36;-2.37;-2.37	6.16	5.26	0.73747	.	0.220376	0.53938	N	0.000055	D	0.93174	0.7826	M	0.77103	2.36	0.53005	D	0.999963	D;D	0.89917	1.0;0.999	D;D	0.70487	0.969;0.932	D	0.92541	0.6042	10	0.41790	T	0.15	-16.5552	10.6197	0.45472	0.0721:0.1335:0.7944:0.0	.	221;227	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	K	227;221;227;221;227;227	ENSP00000263036:E227K;ENSP00000368040:E221K;ENSP00000368032:E227K;ENSP00000368027:E221K;ENSP00000368022:E227K;ENSP00000368021:E227K	ENSP00000263036:E227K	E	+	1	0	OPTN	13200946	1.000000	0.71417	0.745000	0.31077	0.164000	0.22412	4.263000	0.58853	1.617000	0.50277	0.650000	0.86243	GAA		0.438	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		A	13160940	G	A	13160940	3	1	61	1	0	0	0	0	1	0	0	0	10920	1059	37	1	697	1	OPTN	10	13160940	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120500	13160940	122373807	6620	14605										
PRPF18	8559	broad.mit.edu	37	chr10	13642285	13642285	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaccattaacttcatcGaatccagtgttagaacttga	6	9	1	3	rs11540073		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:13642285G>A	ENST00000378572.3	+	3	346	c.186G>A	c.(184-186)tcG>tcA	p.S62S		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	62					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)	p.S62S(2)		central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						TAACTTCATCGAATCCAGTGT	0.333																																																2	Substitution - coding silent(2)	large_intestine(2)	10											108	105	106					10																	13642285		2203	4300	6503	13682291	SO:0001819	synonymous_variant	8559			U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.186G>A	10.37:g.13642285G>A			13682291	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																				0.333	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			A	13642285	G	A	13642285	2	1	61	1	0	0	0	0	0	0	0	1	12597	1045	37	1		1	PRPF18	10	13642285	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	481345	13642285	121892462	6621	14606										
FRMD4A	55691	broad.mit.edu	37	chr10	13702491	13702491	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgttgtgcgacggtggccGaggagggagtcccttgtgag	18	9	0	1	rs376696301		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:13702491G>A	ENST00000357447.2	-	20	2091	c.1723C>T	c.(1723-1725)Cgg>Tgg	p.R575W	FRMD4A_ENST00000378503.1_Missense_Mutation_p.R575W|FRMD4A_ENST00000358621.4_Missense_Mutation_p.R560W	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	575					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)		p.R575R(1)|p.R575W(1)		breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						GACGGTGGCCGAGGAGGGAGT	0.577											OREG0020030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	10						G	TRP/ARG	0,4406		0,0,2203	111	106	108		1723	4.9	1	10		108	1,8599	1.2+/-3.3	0,1,4299	no	missense	FRMD4A	NM_018027.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	575/1040	13702491	1,13005	2203	4300	6503	13742497	SO:0001583	missense	55691			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"FERM domain containing 4"	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.1723C>T	10.37:g.13702491G>A	ENSP00000350032:p.Arg575Trp	689	13742497	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	37	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714339	0.89112	0.0	1.16E-4	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503	D;D;D	0.84442	-1.85;-1.85;-1.85	5.81	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.83686	0.5308	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	P	0.52554	0.702	D	0.85369	0.1112	10	0.62326	D	0.03	-12.3121	14.0568	0.64774	0.0:0.0:0.7259:0.274	.	575	Q9P2Q2	FRM4A_HUMAN	W	560;575;575	ENSP00000351438:R560W;ENSP00000350032:R575W;ENSP00000367764:R575W	ENSP00000350032:R575W	R	-	1	2	FRMD4A	13742497	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.609000	0.61148	1.460000	0.47911	0.462000	0.41574	CGG		0.577	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		A	13702491	G	A	13702491	3	1	61	1	0	0	0	0	1	0	0	0	6070	1057	37	1	1416	1	FRMD4A	10	13702491	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60206	13702491	121832256	6622	14607										
FRMD4A	55691	broad.mit.edu	37	chr10	13782232	13782232	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccccgtaggttgggagagActccacgatgctcatgtagc	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:13782232A>T	ENST00000357447.2	-	11	1002	c.634T>A	c.(634-636)Tct>Act	p.S212T	RP11-353M9.1_ENST00000449462.1_RNA|FRMD4A_ENST00000378503.1_Missense_Mutation_p.S212T|FRMD4A_ENST00000358621.4_Missense_Mutation_p.S197T|FRMD4A_ENST00000342409.2_Missense_Mutation_p.S228T	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	212	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)		p.S212T(1)		breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						GTTGGGAGAGACTCCACGATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											117	111	113					10																	13782232		2203	4300	6503	13822238	SO:0001583	missense	55691			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"FERM domain containing 4"	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.634T>A	10.37:g.13782232A>T	ENSP00000350032:p.Ser212Thr		13822238	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	37	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313835	0.81358	.	.	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503;ENST00000264546;ENST00000342409	T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25	5.9	5.9	0.94986	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	T	0.81875	0.4915	L	0.58302	1.8	0.80722	D	1	B;B;P	0.35844	0.139;0.211;0.524	B;B;P	0.48795	0.224;0.224;0.59	T	0.77643	-0.2511	10	0.20519	T	0.43	-10.8278	16.3322	0.83039	1.0:0.0:0.0:0.0	.	228;245;212	Q5T378;Q5T376;Q9P2Q2	.;.;FRM4A_HUMAN	T	197;212;212;245;228	ENSP00000351438:S197T;ENSP00000350032:S212T;ENSP00000367764:S212T;ENSP00000264546:S245T;ENSP00000344237:S228T	ENSP00000264546:S245T	S	-	1	0	FRMD4A	13822238	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.056000	0.76662	2.251000	0.74343	0.528000	0.53228	TCT		0.428	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		T	13782232	A	T	13782232	3	4	61	1	0	0	0	0	1	0	0	0	6070	275	10	5	2541	5	FRMD4A	10	13782232	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	79741	13782232	121752515	6623	14608										
FAM107B	83641	broad.mit.edu	37	chr10	14563226	14563226	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcgacttcttggcctgttCtcctgagattgcctttcacc	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:14563226C>A	ENST00000378470.1	-	4	645	c.359G>T	c.(358-360)aGa>aTa	p.R120I	FAM107B_ENST00000181796.2_Missense_Mutation_p.R295I|FAM107B_ENST00000378465.3_Missense_Mutation_p.R120I|FAM107B_ENST00000479731.1_Missense_Mutation_p.R120I|FAM107B_ENST00000378458.2_Missense_Mutation_p.R120I|FAM107B_ENST00000496330.1_Missense_Mutation_p.R120I|FAM107B_ENST00000378462.1_Missense_Mutation_p.R120I|FAM107B_ENST00000468747.1_Missense_Mutation_p.R120I|FAM107B_ENST00000378467.4_Missense_Mutation_p.R120I|FAM107B_ENST00000478076.1_Missense_Mutation_p.R120I	NM_001282695.1|NM_001282696.1|NM_001282697.1|NM_001282698.1|NM_001282700.1|NM_001282701.1|NM_001282702.1|NM_001282703.1	NP_001269624.1|NP_001269625.1|NP_001269626.1|NP_001269627.1|NP_001269629.1|NP_001269630.1|NP_001269631.1|NP_001269632.1	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	120					sensory perception of sound (GO:0007605)			p.R295I(1)		breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTGGCCTGTTCTCCTGAGATT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											172	153	159					10																	14563226		2203	4300	6503	14603232	SO:0001583	missense	83641			AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 45"	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000378470.1:c.359G>T	10.37:g.14563226C>A	ENSP00000367731:p.Arg120Ile		14603232	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Missense_Mutation	SNP	ENST00000378470.1	37		.	.	.	.	.	.	.	.	.	.	C	27.8	4.865721	0.91511	.	.	ENSG00000065809	ENST00000378470;ENST00000181796;ENST00000468747;ENST00000378467;ENST00000378465;ENST00000378458;ENST00000478076;ENST00000378462;ENST00000378461;ENST00000496330;ENST00000479731;ENST00000468492;ENST00000452706;ENST00000489100;ENST00000494865	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.62	5.62	0.85841	.	0.081241	0.85682	D	0.000000	T	0.64516	0.2605	M	0.67397	2.05	0.80722	D	1	D;P	0.76494	0.999;0.918	D;P	0.71656	0.974;0.604	T	0.66991	-0.5783	10	0.87932	D	0	.	11.6661	0.51374	0.0:0.9184:0.0:0.0816	.	295;120	Q9H098-2;Q9H098	.;F107B_HUMAN	I	120;295;120;120;120;120;120;120;120;120;120;120;120;120;120	ENSP00000367731:R120I;ENSP00000181796:R295I;ENSP00000418120:R120I;ENSP00000367728:R120I;ENSP00000367726:R120I;ENSP00000367719:R120I;ENSP00000417782:R120I;ENSP00000367723:R120I;ENSP00000418330:R120I;ENSP00000419603:R120I;ENSP00000420444:R120I;ENSP00000413676:R120I;ENSP00000420249:R120I;ENSP00000418395:R120I	ENSP00000181796:R295I	R	-	2	0	FAM107B	14603232	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.590000	0.67530	2.642000	0.89623	0.563000	0.77884	AGA		0.507	FAM107B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046899.1	NM_031453		A	14563226	C	A	14563226	3	1	61	1	0	0	0	0	1	0	0	0	5406	913	32	2	40	2	FAM107B	10	14563226	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	780994	14563226	120971521	6624	14609										
HSPA14	51182	broad.mit.edu	37	chr10	14894396	14894396	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtgtttaagcttggaggAacatccttatctctcagcgt	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:14894396A>G	ENST00000378372.3	+	8	839	c.600A>G	c.(598-600)ggA>ggG	p.G200G		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	200					'de novo' cotranslational protein folding (GO:0051083)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.G200G(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	17						AGCTTGGAGGAACATCCTTAT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	10											155	146	149					10																	14894396		2203	4300	6503	14934402	SO:0001819	synonymous_variant	51182			AF112210	CCDS7103.1, CCDS60487.1	10p13	2011-09-02			ENSG00000187522	ENSG00000187522		"Heat shock proteins / HSP70"	29526	protein-coding gene	gene with protein product		610369				12477932	Standard	NM_016299		Approved	HSP70-4, HSP70L1	uc001ind.4	Q0VDF9	OTTHUMG00000017712	ENST00000378372.3:c.600A>G	10.37:g.14894396A>G			14934402	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Silent	SNP	ENST00000378372.3	37	CCDS7103.1																																																																																				0.353	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		G	14894396	A	G	14894396	2	3	61	1	0	0	0	0	0	0	0	1	7428	233	9	4		4	HSPA14	10	14894396	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	331170	14894396	120640351	6625	14610										
ITGA8	8516	broad.mit.edu	37	chr10	15646222	15646222	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaccttgttgttgcgttcGattccaacataatctgcctc	6	11	1	0	rs45604340		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:15646222G>A	ENST00000378076.3	-	20	2456	c.2103C>T	c.(2101-2103)atC>atT	p.I701I	ITGA8_ENST00000477064.1_5'UTR	NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	701					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.I701I(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						TGTTGCGTTCGATTCCAACAT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	10											229	187	201					10																	15646222		2203	4300	6503	15686228	SO:0001819	synonymous_variant	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.2103C>T	10.37:g.15646222G>A			15686228	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	37	CCDS31155.1																																																																																				0.378	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15646222	G	A	15646222	2	1	61	1	0	0	0	0	0	0	0	1	7903	1048	37	1		1	ITGA8	10	15646222	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	751826	15646222	119888525	6626	14611										
ITGA8	8516	broad.mit.edu	37	chr10	15649776	15649776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttatcaaggaagagcgtcCgtttaatagctcctttctgt	10	8	2	1	rs140395954		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:15649776C>T	ENST00000378076.3	-	17	2017	c.1664G>A	c.(1663-1665)cGg>cAg	p.R555Q		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	555					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.R555Q(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GAAGAGCGTCCGTTTAATAGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	GLN/ARG	0,4406		0,0,2203	141	135	137		1664	5.8	0.3	10	dbSNP_134	137	1,8599		0,1,4299	no	missense	ITGA8	NM_003638.1	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	555/1064	15649776	1,13005	2203	4300	6503	15689782	SO:0001583	missense	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1664G>A	10.37:g.15649776C>T	ENSP00000367316:p.Arg555Gln		15689782	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.978062	0.74360	0.0	1.16E-4	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.79940	-1.32	5.84	5.84	0.93424	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	D	0.91905	0.7437	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92533	0.6035	10	0.87932	D	0	.	20.1336	0.98010	0.0:1.0:0.0:0.0	.	540;555	F5H818;P53708	.;ITA8_HUMAN	Q	555;540	ENSP00000367316:R555Q	ENSP00000367316:R555Q	R	-	2	0	ITGA8	15689782	1.000000	0.71417	0.257000	0.24404	0.121000	0.20230	6.043000	0.71004	2.767000	0.95098	0.591000	0.81541	CGG		0.433	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		T	15649776	C	T	15649776	3	4	61	1	0	0	0	0	1	0	0	0	7903	652	23	1	1583	1	ITGA8	10	15649776	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3554	15649776	119884971	6627	14612										
FAM188A	80013	broad.mit.edu	37	chr10	15838104	15838104	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaaaatcttttaccttctGggtcgtaggtttgaaaaact	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:15838104G>A	ENST00000277632.3	-	11	1170	c.950C>T	c.(949-951)cCa>cTa	p.P317L	FAM188A_ENST00000378036.1_Missense_Mutation_p.P22L|FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	317					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.P317L(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						TTTACCTTCTGGGTCGTAGGT	0.358																																					Pancreas(159;946 1953 2111 4475 22008)											1	Substitution - Missense(1)	large_intestine(1)	10											135	145	141					10																	15838104		2203	4300	6503	15878110	SO:0001583	missense	80013			AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.950C>T	10.37:g.15838104G>A	ENSP00000277632:p.Pro317Leu		15878110	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Missense_Mutation	SNP	ENST00000277632.3	37	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	G	33	5.280962	0.95489	.	.	ENSG00000148481	ENST00000277632;ENST00000378036;ENST00000378033;ENST00000418767	T;T	0.43294	1.47;0.95	6.08	6.08	0.98989	EF-hand-like domain (1);	0.096119	0.85682	D	0.000000	T	0.50837	0.1639	M	0.65975	2.015	0.80722	D	1	P	0.50066	0.931	P	0.45310	0.476	T	0.53781	-0.8390	10	0.66056	D	0.02	-4.9955	18.8526	0.92238	0.0:0.0:1.0:0.0	.	317	Q9H8M7	F188A_HUMAN	L	317;22;22;157	ENSP00000277632:P317L;ENSP00000388661:P157L	ENSP00000277632:P317L	P	-	2	0	FAM188A	15878110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.801000	0.91905	2.894000	0.99253	0.591000	0.81541	CCA		0.358	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		A	15838104	G	A	15838104	3	1	61	1	0	0	0	0	1	0	0	0	5530	1348	47	3	407	3	FAM188A	10	15838104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188328	15838104	119696643	6628	14613										
PTER	9317	broad.mit.edu	37	chr10	16526737	16526738	+	Missense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttgcagaagagactggCgtccatatcatatctggagc					rs561887103		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:16526737_16526738CG>TA	ENST00000378000.1	+	3	600_601	c.354_355CG>TA	c.(352-357)ggCGtc>ggTAtc	p.V119I	PTER_ENST00000535784.2_Missense_Mutation_p.V119I|PTER_ENST00000485788.1_3'UTR|PTER_ENST00000423462.2_Missense_Mutation_p.V119I|PTER_ENST00000298942.3_Missense_Mutation_p.V119I	NM_001001484.2|NM_001261838.1|NM_030664.4	NP_001001484.1|NP_001248767.1|NP_109589.2	Q96BW5	PTER_HUMAN	phosphotriesterase related	119					catabolic process (GO:0009056)|epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)	p.G118>?(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						AAGAGACTGGCGTCCATATCAT	0.485																																					Ovarian(2;46 150 15648 38137 47908)											1	Complex(1)	large_intestine(1)	10																																								16566744	SO:0001583	missense	9317			BC015092	CCDS7111.1, CCDS58070.1, CCDS73070.1	10p12	2003-11-05			ENSG00000165983	ENSG00000165983			9590	protein-coding gene	gene with protein product		604446				9925913	Standard	NM_001001484		Approved		uc001ioi.2	Q96BW5	OTTHUMG00000017737	Exception_encountered	10.37:g.16526737_16526738delinsTA	ENSP00000367239:p.Val119Ile		16566743	B0YJ77|B3KTF5|D3DRU0|Q9BY46	Missense_Mutation	DNP	ENST00000378000.1	37	CCDS7111.1																																																																																				0.485	PTER-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047001.2	NM_030664		TA	16526738	CG	TA	16526737	3	4	61	1	0	0	0	0	1	0	0	0	12773	755	27	1	356	1	PTER	10	16526737	Missense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	688633	16526737	119008010	6629	14614										
CUBN	8029	broad.mit.edu	37	chr10	16911739	16911739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttcacatttggtgggCgcttggaaccgcagaatttg	12	9	2	1	rs184750323	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:16911739C>T	ENST00000377833.4	-	59	9415	c.9350G>A	c.(9349-9351)cGc>cAc	p.R3117H		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3117	CUB 23. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.R3117H(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTTGGTGGGCGCTTGGAACC	0.498													C|||	2	0.000399361	0	0.0014	5008	,	,		14859	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											144	149	147					10																	16911739		2203	4300	6503	16951745	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9350G>A	10.37:g.16911739C>T	ENSP00000367064:p.Arg3117His		16951745	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	5.412	0.261103	0.10239	.	.	ENSG00000107611	ENST00000377833	T	0.18338	2.22	5.69	-1.14	0.09741	CUB (5);	1.516350	0.04274	N	0.342609	T	0.11067	0.0270	L	0.39633	1.23	0.09310	N	1	P	0.41393	0.748	B	0.37422	0.249	T	0.16571	-1.0398	10	0.14252	T	0.57	.	1.3971	0.02263	0.4125:0.2571:0.2107:0.1197	.	3117	O60494	CUBN_HUMAN	H	3117	ENSP00000367064:R3117H	ENSP00000367064:R3117H	R	-	2	0	CUBN	16951745	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.975000	0.29449	-0.461000	0.06993	-0.355000	0.07637	CGC		0.498	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16911739	C	T	16911739	3	4	61	1	0	0	0	0	1	0	0	0	4057	768	27	1	1557	1	CUBN	10	16911739	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385002	16911739	118623008	6630	14615										
CUBN	8029	broad.mit.edu	37	chr10	16946039	16946039	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagtgaatccatacctgaGaataaggtataaccaatggc	8	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:16946039G>T	ENST00000377833.4	-	51	8053	c.7988C>A	c.(7987-7989)tCt>tAt	p.S2663Y		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2663	CUB 19. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.S2663Y(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCATACCTGAGAATAAGGTAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											84	77	79					10																	16946039		2203	4300	6503	16986045	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7988C>A	10.37:g.16946039G>T	ENSP00000367064:p.Ser2663Tyr		16986045	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.550761	0.27739	.	.	ENSG00000107611	ENST00000377833	T	0.32515	1.45	5.39	3.49	0.39957	CUB (5);	1.209910	0.06149	N	0.673837	T	0.44623	0.1302	M	0.68317	2.08	0.42961	D	0.994402	P	0.43607	0.812	B	0.44315	0.446	T	0.37454	-0.9705	10	0.62326	D	0.03	.	15.9379	0.79729	0.0:0.2562:0.7438:0.0	.	2663	O60494	CUBN_HUMAN	Y	2663	ENSP00000367064:S2663Y	ENSP00000367064:S2663Y	S	-	2	0	CUBN	16986045	0.999000	0.42202	0.089000	0.20774	0.416000	0.31233	3.660000	0.54496	0.718000	0.32166	-0.282000	0.10007	TCT		0.393	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16946039	G	T	16946039	3	4	61	1	0	0	0	0	1	0	0	0	4057	942	33	2	2951	2	CUBN	10	16946039	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34300	16946039	118588708	6631	14616										
CUBN	8029	broad.mit.edu	37	chr10	16990518	16990518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgtggaaacccccagcaCtgatgctagaatcagagacg	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:16990518C>T	ENST00000377833.4	-	35	5233	c.5168G>A	c.(5167-5169)aGt>aAt	p.S1723N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1723	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.S1723N(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACCCCCAGCACTGATGCTAGA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	73	77					10																	16990518		2203	4300	6503	17030524	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5168G>A	10.37:g.16990518C>T	ENSP00000367064:p.Ser1723Asn		17030524	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	7.036	0.561634	0.13498	.	.	ENSG00000107611	ENST00000377833	T	0.18810	2.19	5.55	-11.1	0.00147	CUB (5);	1.553420	0.04035	N	0.302213	T	0.10337	0.0253	N	0.11364	0.135	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.29427	-1.0012	10	0.13470	T	0.59	.	16.3787	0.83431	0.0:0.293:0.605:0.102	.	1723	O60494	CUBN_HUMAN	N	1723	ENSP00000367064:S1723N	ENSP00000367064:S1723N	S	-	2	0	CUBN	17030524	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.692000	0.05127	-2.861000	0.00327	-0.793000	0.03317	AGT		0.517	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16990518	C	T	16990518	3	4	61	1	0	0	0	0	1	0	0	0	4057	565	20	3	5835	3	CUBN	10	16990518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44479	16990518	118544229	6632	14617										
CUBN	8029	broad.mit.edu	37	chr10	17152965	17152965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccaggtgtattcacacacTcaacgggtggagccacagaa	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:17152965T>C	ENST00000377833.4	-	9	1033	c.968A>G	c.(967-969)gAg>gGg	p.E323G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	323	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.E323G(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCACACACTCAACGGGTGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											87	82	84					10																	17152965		2203	4300	6503	17192971	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.968A>G	10.37:g.17152965T>C	ENSP00000367064:p.Glu323Gly		17192971	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	8.631	0.893766	0.17613	.	.	ENSG00000107611	ENST00000377833	D	0.92348	-3.02	5.83	-7.64	0.01286	Growth factor, receptor (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);	1.985910	0.02384	N	0.079030	T	0.81531	0.4842	N	0.16862	0.45	0.09310	N	1	B	0.27791	0.189	B	0.25614	0.062	T	0.73455	-0.3977	10	0.24483	T	0.36	.	5.9023	0.18974	0.0896:0.1069:0.4749:0.3287	.	323	O60494	CUBN_HUMAN	G	323	ENSP00000367064:E323G	ENSP00000367064:E323G	E	-	2	0	CUBN	17192971	0.001000	0.12720	0.000000	0.03702	0.094000	0.18550	0.449000	0.21744	-1.773000	0.01290	0.528000	0.53228	GAG		0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17152965	T	C	17152965	3	2	61	1	0	0	0	0	1	0	0	0	4057	1551	54	4	10139	4	CUBN	10	17152965	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162447	17152965	118381782	6633	14618										
TRDMT1	1787	broad.mit.edu	37	chr10	17210880	17210880	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggctcattaaaatcatatCaaaagataatctgtcaaact	5	7	5	1	rs371526424		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:17210880C>T	ENST00000377799.3	-	3	258	c.211G>A	c.(211-213)Gat>Aat	p.D71N	TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000351358.4_Missense_Mutation_p.D71N|TRDMT1_ENST00000358282.7_Intron|TRDMT1_ENST00000412821.3_Missense_Mutation_p.D71N|TRDMT1_ENST00000457442.2_Intron|TRDMT1_ENST00000377766.5_Intron|TRDMT1_ENST00000488990.1_Intron	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	71	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)	p.D71N(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	AAAATCATATCAAAAGATAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	73	72	72		211	-6.4	0.3	10		72	0,8600		0,0,4300	no	missense	TRDMT1	NM_004412.5	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	71/392	17210880	1,13005	2203	4300	6503	17250886	SO:0001583	missense	1787			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"DNA (cytosine-5-)-methyltransferase 2"	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.211G>A	10.37:g.17210880C>T	ENSP00000367030:p.Asp71Asn		17250886	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Missense_Mutation	SNP	ENST00000377799.3	37	CCDS7114.1	.	.	.	.	.	.	.	.	.	.	C	5.777	0.327737	0.10956	2.27E-4	0.0	ENSG00000107614	ENST00000377799;ENST00000412821;ENST00000351358;ENST00000525762	D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1	5.95	-6.41	0.01938	.	0.358563	0.35525	N	0.003153	D	0.83585	0.5286	L	0.28556	0.865	0.80722	D	1	B;B;B	0.18166	0.008;0.026;0.007	B;B;B	0.20577	0.006;0.022;0.03	T	0.59354	-0.7470	10	0.15066	T	0.55	-5.9574	17.1956	0.86891	0.0:0.6809:0.0:0.3191	.	71;71;71	O14717-3;O14717-2;O14717	.;.;TRDMT_HUMAN	N	71;71;71;53	ENSP00000367030:D71N;ENSP00000409354:D71N;ENSP00000324328:D71N;ENSP00000431476:D53N	ENSP00000324328:D71N	D	-	1	0	TRDMT1	17250886	0.999000	0.42202	0.348000	0.25681	0.479000	0.33129	0.515000	0.22801	-1.174000	0.02754	-0.802000	0.03209	GAT		0.383	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412		T	17210880	C	T	17210880	3	4	61	1	0	0	0	0	1	0	0	0	16507	826	29	3	1000	3	TRDMT1	10	17210880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57915	17210880	118323867	6634	14619										
ST8SIA6	338596	broad.mit.edu	37	chr10	17362951	17362951	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaggatctggctgtattCtttgggcatctgatggaaac	13	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:17362951C>A	ENST00000377602.4	-	8	1197	c.1123G>T	c.(1123-1125)Gaa>Taa	p.E375*		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	375					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)	p.E375*(1)		endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TGGCTGTATTCTTTGGGCATC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											253	239	243					10																	17362951		2203	4300	6503	17402957	SO:0001587	stop_gained	338596				CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.1123G>T	10.37:g.17362951C>A	ENSP00000366827:p.Glu375*		17402957	B0YJ97|B9EH72|Q5VZH4	Nonsense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	C	38	6.762160	0.97821	.	.	ENSG00000148488	ENST00000377602	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.3582	19.5818	0.95469	0.0:1.0:0.0:0.0	.	.	.	.	X	375	.	ENSP00000366827:E375X	E	-	1	0	ST8SIA6	17402957	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.651000	0.83577	2.850000	0.98022	0.650000	0.86243	GAA		0.393	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		A	17362951	C	A	17362951	4	1	61	1	0	0	0	0	0	1	0	0	15275	922	32	2	77	2	ST8SIA6	10	17362951	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	152071	17362951	118171796	6635	14620										
STAM	8027	broad.mit.edu	37	chr10	17742200	17742200	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcttacagttaaaacagaGaagaagacggtacaatttag	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:17742200G>T	ENST00000377524.3	+	9	1049	c.834G>T	c.(832-834)gaG>gaT	p.E278D	STAM_ENST00000540523.1_Missense_Mutation_p.E167D|RP11-390B4.3_ENST00000445235.1_RNA	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	278					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)	p.E278D(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TTAAAACAGAGAAGAAGACGG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											110	101	104					10																	17742200		2203	4300	6503	17782206	SO:0001583	missense	8027			U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.834G>T	10.37:g.17742200G>T	ENSP00000366746:p.Glu278Asp		17782206	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	37	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.943659	0.53079	.	.	ENSG00000136738	ENST00000377524;ENST00000377500;ENST00000540523	T;T	0.46451	1.17;0.87	5.47	4.57	0.56435	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.50990	0.1648	L	0.37697	1.125	0.58432	D	0.999999	D	0.64830	0.994	D	0.70716	0.97	T	0.40079	-0.9582	10	0.18710	T	0.47	-25.9188	14.5197	0.67842	0.0706:0.0:0.9294:0.0	.	278	Q92783	STAM1_HUMAN	D	278;181;167	ENSP00000366746:E278D;ENSP00000438073:E167D	ENSP00000366721:E181D	E	+	3	2	STAM	17782206	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.593000	0.61034	1.458000	0.47871	0.655000	0.94253	GAG		0.328	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		T	17742200	G	T	17742200	3	4	61	1	0	0	0	0	1	0	0	0	15287	933	33	2	868	2	STAM	10	17742200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	379249	17742200	117792547	6636	14621										
NSUN6	221078	broad.mit.edu	37	chr10	18940104	18940104	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatagttttcaacctcaggtCtcaaagatatcttagggaaa	8	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:18940104C>T	ENST00000377304.4	-	1	447	c.29G>A	c.(28-30)aGa>aAa	p.R10K	RP11-139J15.7_ENST00000606425.1_Intron	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	10							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.R10K(1)		endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						AACCTCAGGTCTCAAAGATAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	99	99					10																	18940104		2202	4300	6502	18980110	SO:0001583	missense	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.29G>A	10.37:g.18940104C>T	ENSP00000366519:p.Arg10Lys		18980110	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	37	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.498451	0.44455	.	.	ENSG00000241058	ENST00000377304	T	0.27890	1.64	5.32	5.32	0.75619	.	0.142745	0.64402	D	0.000007	T	0.24431	0.0592	L	0.37561	1.115	0.33726	D	0.617586	B	0.14438	0.01	B	0.10450	0.005	T	0.19811	-1.0294	10	0.27082	T	0.32	.	12.3879	0.55343	0.0:0.9175:0.0:0.0824	.	10	Q8TEA1	NSUN6_HUMAN	K	10	ENSP00000366519:R10K	ENSP00000366519:R10K	R	-	2	0	NSUN6	18980110	0.184000	0.23200	1.000000	0.80357	0.959000	0.62525	0.420000	0.21263	2.653000	0.90120	0.655000	0.94253	AGA		0.338	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		T	18940104	C	T	18940104	3	4	61	1	0	0	0	0	1	0	0	0	10713	913	32	3	1424	3	NSUN6	10	18940104	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1197904	18940104	116594643	6637	14622										
PLXDC2	84898	broad.mit.edu	37	chr10	20432300	20432300	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacctttaatggcaaatttCgatcccagtgtatccagaaa	7	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:20432300C>T	ENST00000377252.4	+	5	1459	c.618C>T	c.(616-618)ttC>ttT	p.F206F	PLXDC2_ENST00000377242.3_Silent_p.F157F|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	206					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.F206F(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						TGGCAAATTTCGATCCCAGTG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	10											155	148	150					10																	20432300		2203	4300	6503	20472306	SO:0001819	synonymous_variant	84898			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.618C>T	10.37:g.20432300C>T			20472306	Q96E59|Q96PD9|Q96SU9	Silent	SNP	ENST00000377252.4	37	CCDS7132.1																																																																																				0.353	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20432300	C	T	20432300	2	4	61	1	0	0	0	0	0	0	0	1	12149	883	31	1		1	PLXDC2	10	20432300	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1492196	20432300	115102447	6638	14623										
NEBL	10529	broad.mit.edu	37	chr10	21098789	21098789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttccaggggatcaaggtCgaagatggagccaggatctg	15	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:21098789C>T	ENST00000377122.4	-	25	2953	c.2557G>A	c.(2557-2559)Gac>Aac	p.D853N	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	853	Linker.				cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.D853N(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GGATCAAGGTCGAAGATGGAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											97	96	96					10																	21098789		2203	4300	6503	21138795	SO:0001583	missense	10529			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.2557G>A	10.37:g.21098789C>T	ENSP00000366326:p.Asp853Asn		21138795	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198155	0.94997	.	.	ENSG00000078114	ENST00000377122	T	0.14266	2.52	5.81	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.16685	0.0401	L	0.57536	1.79	0.80722	D	1	P	0.38335	0.627	B	0.34180	0.177	T	0.01670	-1.1299	10	0.54805	T	0.06	.	16.1681	0.81785	0.1343:0.8657:0.0:0.0	.	853	O76041	NEBL_HUMAN	N	853	ENSP00000366326:D853N	ENSP00000366326:D853N	D	-	1	0	NEBL	21138795	1.000000	0.71417	0.999000	0.59377	0.798000	0.45092	7.590000	0.82653	1.420000	0.47138	0.650000	0.86243	GAC		0.388	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		T	21098789	C	T	21098789	3	4	61	1	0	0	0	0	1	0	0	0	10334	884	31	1	503	1	NEBL	10	21098789	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	666489	21098789	114435958	6639	14624										
NEBL	10529	broad.mit.edu	37	chr10	21139426	21139426	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcatattcttctttataTttcaccttcattggaaaaag	3	8	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:21139426T>G	ENST00000377122.4	-	11	1410	c.1014A>C	c.(1012-1014)aaA>aaC	p.K338N	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	338					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.K338N(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CTTCTTTATATTTCACCTTCA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	10											103	101	101					10																	21139426		2203	4300	6503	21179432	SO:0001583	missense	10529			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1014A>C	10.37:g.21139426T>G	ENSP00000366326:p.Lys338Asn		21179432	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	T	18.92	3.725394	0.68959	.	.	ENSG00000078114	ENST00000377122	T	0.58506	0.33	5.63	1.71	0.24356	.	0.050318	0.85682	D	0.000000	T	0.75049	0.3797	M	0.89715	3.055	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.74225	-0.3734	10	0.54805	T	0.06	.	7.5551	0.27819	0.0:0.3288:0.0:0.6712	.	338	O76041	NEBL_HUMAN	N	338	ENSP00000366326:K338N	ENSP00000366326:K338N	K	-	3	2	NEBL	21179432	0.933000	0.31639	1.000000	0.80357	0.946000	0.59487	-0.112000	0.10791	0.530000	0.28619	0.533000	0.62120	AAA		0.318	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		G	21139426	T	G	21139426	3	3	61	1	0	0	0	0	1	0	0	0	10334	1490	52	4	2102	4	NEBL	10	21139426	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	40637	21139426	114395321	6640	14625										
NEBL	10529	broad.mit.edu	37	chr10	21177028	21177028	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttagaaaaaccctacctCactctggagctgtgtaactt	6	11	2	1	rs189440246	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:21177028C>A	ENST00000377122.4	-	4	763	c.367G>T	c.(367-369)Gag>Tag	p.E123*	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377119.1_Nonsense_Mutation_p.E123*|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	123					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.E123*(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AACCCTACCTCACTCTGGAGC	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											88	89	89					10																	21177028		2203	4300	6503	21217034	SO:0001587	stop_gained	10529			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.367G>T	10.37:g.21177028C>A	ENSP00000366326:p.Glu123*		21217034	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Nonsense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	39	7.436801	0.98282	.	.	ENSG00000078114	ENST00000377122;ENST00000377119;ENST00000434381	.	.	.	5.94	4.08	0.47627	.	0.230179	0.44483	D	0.000448	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	10.0247	0.42063	0.0:0.7562:0.0:0.2438	.	.	.	.	X	123;123;107	.	ENSP00000366323:E123X	E	-	1	0	NEBL	21217034	0.998000	0.40836	1.000000	0.80357	0.776000	0.43924	0.547000	0.23299	1.516000	0.48900	0.557000	0.71058	GAG		0.368	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		A	21177028	C	A	21177028	4	1	61	1	0	0	0	0	0	1	0	0	10334	835	29	2	2777	2	NEBL	10	21177028	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37602	21177028	114357719	6641	14626										
C10orf140	387640	broad.mit.edu	37	chr10	21804489	21804489	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagtgcatgaaaggccctGactttgagccagtggattta	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:21804489G>T	ENST00000449193.2	-	4	4515	c.2263C>A	c.(2263-2265)Cag>Aag	p.Q755K	SKIDA1_ENST00000444772.3_Missense_Mutation_p.Q676K	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	674						nucleus (GO:0005634)		p.Q755K(2)									GAAAGGCCCTGACTTTGAGCC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	10											158	151	153					10																	21804489		1856	4092	5948	21844495	SO:0001583	missense	387640			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2263C>A	10.37:g.21804489G>T	ENSP00000410041:p.Gln755Lys		21844495	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	37	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.472728	0.43942	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	.	.	.	5.87	4.97	0.65823	.	0.514051	0.20016	N	0.101013	T	0.36138	0.0956	L	0.27053	0.805	0.28605	N	0.908978	B	0.27229	0.172	B	0.18871	0.023	T	0.35025	-0.9805	9	0.59425	D	0.04	-12.5016	14.4654	0.67480	0.0702:0.0:0.9297:0.0	.	755	E9PAX1	.	K	755;676	.	ENSP00000442432:Q676K	Q	-	1	0	C10orf140	21844495	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.997000	0.57016	1.634000	0.50500	0.655000	0.94253	CAG		0.453	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		T	21804489	G	T	21804489	3	4	61	1	0	0	0	0	1	0	0	0	1599	1299	45	2	467	2	C10orf140	10	21804489	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	627461	21804489	113730258	6642	14627										
SPAG6	9576	broad.mit.edu	37	chr10	22676871	22676871	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaggacaaggatgaataCgtgaagaaaaatgcttctac	10	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:22676871C>A	ENST00000376624.3	+	6	940	c.798C>A	c.(796-798)taC>taA	p.Y266*	SPAG6_ENST00000376601.1_Intron|SPAG6_ENST00000376603.2_Nonsense_Mutation_p.Y342*|SPAG6_ENST00000313311.6_Nonsense_Mutation_p.Y266*|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Nonsense_Mutation_p.Y241*	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	266					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.Y266*(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						AGGATGAATACGTGAAGAAAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											77	77	77					10																	22676871		2203	4300	6503	22716877	SO:0001587	stop_gained	9576			AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.798C>A	10.37:g.22676871C>A	ENSP00000365811:p.Tyr266*		22716877	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Nonsense_Mutation	SNP	ENST00000376624.3	37	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	C	34	5.330026	0.95733	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311	.	.	.	5.64	-6.05	0.02172	.	0.282033	0.41500	D	0.000870	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8741	18.0914	0.89476	0.0:0.1565:0.0:0.8435	.	.	.	.	X	266;342;241;266	.	ENSP00000323599:Y266X	Y	+	3	2	SPAG6	22716877	0.013000	0.17824	0.026000	0.17262	0.995000	0.86356	-1.111000	0.03303	-1.045000	0.03250	-0.136000	0.14681	TAC		0.368	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			A	22676871	C	A	22676871	4	1	61	1	0	0	0	0	0	1	0	0	15021	547	19	2	820	2	SPAG6	10	22676871	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	872382	22676871	112857876	6643	14628										
ARMC3	219681	broad.mit.edu	37	chr10	23250825	23250825	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggcaggattttcagtgtCgagctaaacttcaagaacta	10	7	2	1	rs201134940		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:23250825C>T	ENST00000298032.5	+	7	634	c.550C>T	c.(550-552)Cga>Tga	p.R184*	ARMC3_ENST00000409983.3_Nonsense_Mutation_p.R184*|ARMC3_ENST00000409049.3_Nonsense_Mutation_p.R184*|ARMC3_ENST00000376528.4_Intron	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	184						extracellular vesicular exosome (GO:0070062)		p.R184*(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TTTTCAGTGTCGAGCTAAACT	0.343													C|||	1	0.000199681	0	0	5008	,	,		16235	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	10											71	70	70					10																	23250825		2203	4299	6502	23290831	SO:0001587	stop_gained	219681			AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.550C>T	10.37:g.23250825C>T	ENSP00000298032:p.Arg184*		23290831	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Nonsense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	16.98	3.271497	0.59649	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000409049;ENST00000447081	.	.	.	5.73	4.83	0.62350	.	0.122763	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5531	16.2556	0.82516	0.1338:0.8661:0.0:0.0	.	.	.	.	X	184;184;184;96	.	ENSP00000298032:R184X	R	+	1	2	ARMC3	23290831	1.000000	0.71417	0.995000	0.50966	0.164000	0.22412	2.230000	0.42999	1.423000	0.47198	-0.158000	0.13435	CGA		0.343	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23250825	C	T	23250825	4	4	61	1	0	0	0	0	0	1	0	0	953	876	31	1	572	1	ARMC3	10	23250825	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	573954	23250825	112283922	6644	14629										
ARMC3	219681	broad.mit.edu	37	chr10	23292194	23292194	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctttagatatccttgaaGaagttaacgtatcaggaact	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:23292194G>T	ENST00000298032.5	+	13	1666	c.1582G>T	c.(1582-1584)Gaa>Taa	p.E528*	ARMC3_ENST00000409983.3_Nonsense_Mutation_p.E528*|ARMC3_ENST00000409049.3_Nonsense_Mutation_p.E528*|ARMC3_ENST00000376528.4_Nonsense_Mutation_p.E265*	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	528						extracellular vesicular exosome (GO:0070062)		p.E528*(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TATCCTTGAAGAAGTTAACGT	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											79	79	79					10																	23292194		2203	4300	6503	23332200	SO:0001587	stop_gained	219681			AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1582G>T	10.37:g.23292194G>T	ENSP00000298032:p.Glu528*		23332200	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Nonsense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	G	38	6.927127	0.97940	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000376528	.	.	.	5.53	5.53	0.82687	.	0.117086	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-7.811	19.4481	0.94855	0.0:0.0:1.0:0.0	.	.	.	.	X	528;528;464;528;265	.	ENSP00000298032:E528X	E	+	1	0	ARMC3	23332200	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.155000	0.64900	2.590000	0.87494	0.563000	0.77884	GAA		0.363	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23292194	G	T	23292194	4	4	61	1	0	0	0	0	0	1	0	0	953	943	33	2	1628	2	ARMC3	10	23292194	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41369	23292194	112242553	6645	14630										
MSRB2	22921	broad.mit.edu	37	chr10	23393122	23393122	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaagagtgagtggcaaaaGaaactaaccccggagcagtt	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:23393122G>T	ENST00000376510.3	+	2	271	c.168G>T	c.(166-168)aaG>aaT	p.K56N		NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	56					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K56N(1)		endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	AGTGGCAAAAGAAACTAACCC	0.433																																					Esophageal Squamous(89;1240 1363 4973 30188 42299)											1	Substitution - Missense(1)	large_intestine(1)	10											83	81	81					10																	23393122		1902	4126	6028	23433128	SO:0001583	missense	22921			AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"methionine sulfoxide reductase B"	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.168G>T	10.37:g.23393122G>T	ENSP00000365693:p.Lys56Asn		23433128	Q17R44|Q4G1C7|Q9Y5W6	Missense_Mutation	SNP	ENST00000376510.3	37	CCDS41495.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909044	0.72868	.	.	ENSG00000148450	ENST00000376510	T	0.77358	-1.09	4.69	3.78	0.43462	Mss4-like (1);Methionine sulphoxide reductase B (3);	0.215316	0.46442	D	0.000299	T	0.78470	0.4288	L	0.49256	1.55	0.41931	D	0.990565	P	0.40638	0.725	P	0.50270	0.636	T	0.79242	-0.1884	10	0.66056	D	0.02	-13.2929	9.2481	0.37539	0.1041:0.0:0.8959:0.0	.	56	Q9Y3D2	MSRB2_HUMAN	N	56	ENSP00000365693:K56N	ENSP00000365693:K56N	K	+	3	2	MSRB2	23433128	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	1.784000	0.38674	1.280000	0.44463	0.557000	0.71058	AAG		0.433	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228		T	23393122	G	T	23393122	3	4	61	1	0	0	0	0	1	0	0	0	9918	933	33	2	174	2	MSRB2	10	23393122	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100928	23393122	112141625	6646	14631										
KIAA1217	56243	broad.mit.edu	37	chr10	24762473	24762473	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaacattgcaatgtacaGaaatgagggtttctatgctg	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:24762473G>T	ENST00000376454.3	+	6	1193	c.1163G>T	c.(1162-1164)aGa>aTa	p.R388I	KIAA1217_ENST00000458595.1_Missense_Mutation_p.R388I|KIAA1217_ENST00000396446.1_Missense_Mutation_p.R106I|KIAA1217_ENST00000307544.6_Missense_Mutation_p.R106I|KIAA1217_ENST00000376452.3_Missense_Mutation_p.R388I|KIAA1217_ENST00000430453.2_Missense_Mutation_p.R309I|KIAA1217_ENST00000376462.1_Missense_Mutation_p.R308I|KIAA1217_ENST00000376451.2_Missense_Mutation_p.R106I|KIAA1217_ENST00000396445.1_Missense_Mutation_p.R106I	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	388					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.R388I(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GCAATGTACAGAAATGAGGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10											119	113	115					10																	24762473		2203	4300	6503	24802479	SO:0001583	missense	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.1163G>T	10.37:g.24762473G>T	ENSP00000365637:p.Arg388Ile		24802479	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.505996	0.85282	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000430453;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D	0.91635	0.999;0.981;0.998;0.988;0.999;0.999;0.998;0.952	T	0.78677	-0.2111	10	0.87932	D	0	.	19.4826	0.95016	0.0:0.0:1.0:0.0	.	388;388;106;106;106;106;388;388	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	I	308;388;388;106;388;388;238;309;106;106;106;106;106	ENSP00000365645:R308I;ENSP00000365639:R388I;ENSP00000392625:R388I;ENSP00000365637:R388I;ENSP00000365635:R388I;ENSP00000404798:R238I;ENSP00000389680:R309I;ENSP00000302343:R106I;ENSP00000379722:R106I;ENSP00000365634:R106I;ENSP00000379723:R106I	ENSP00000302343:R106I	R	+	2	0	KIAA1217	24802479	0.997000	0.39634	0.926000	0.36857	0.914000	0.54420	6.851000	0.75425	2.622000	0.88805	0.655000	0.94253	AGA		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24762473	G	T	24762473	3	4	61	1	0	0	0	0	1	0	0	0	8237	942	33	2	1185	2	KIAA1217	10	24762473	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1369351	24762473	110772274	6647	14632										
ARHGAP21	57584	broad.mit.edu	37	chr10	24886893	24886893	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcatcagattgttgtattCttttattcttcgactaatta	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:24886893C>A	ENST00000396432.2	-	15	3664	c.3178G>T	c.(3178-3180)Gaa>Taa	p.E1060*	ARHGAP21_ENST00000493154.1_5'UTR|ARHGAP21_ENST00000320481.6_Nonsense_Mutation_p.E847*	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1059	Interaction with ARF1 and ARF6.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.E1059*(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TTGTTGTATTCTTTTATTCTT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											194	183	187					10																	24886893		2203	4300	6503	24926899	SO:0001587	stop_gained	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.3178G>T	10.37:g.24886893C>A	ENSP00000379709:p.Glu1060*		24926899	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Nonsense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	46	12.125345	0.99638	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	1060;847;1050;1060;895	.	ENSP00000365604:E847X	E	-	1	0	ARHGAP21	24926899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.695000	0.84257	2.941000	0.99782	0.655000	0.94253	GAA		0.343	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		A	24886893	C	A	24886893	4	1	61	1	0	0	0	0	0	1	0	0	871	922	32	2	2746	2	ARHGAP21	10	24886893	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124420	24886893	110647854	6648	14633										
ARHGAP21	57584	broad.mit.edu	37	chr10	24889580	24889580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgaacacccacctcttCgtttaggttgctgctctcct	6	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:24889580C>T	ENST00000396432.2	-	14	3613	c.3127G>A	c.(3127-3129)Gaa>Aaa	p.E1043K	ARHGAP21_ENST00000493154.1_5'UTR|ARHGAP21_ENST00000320481.6_Missense_Mutation_p.E830K	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1042	Interaction with ARF1 and ARF6.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.E1042K(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CCCACCTCTTCGTTTAGGTTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											118	114	115					10																	24889580		2203	4300	6503	24929586	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.3127G>A	10.37:g.24889580C>T	ENSP00000379709:p.Glu1043Lys		24929586	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340372	0.60963	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22	6.17	6.17	0.99709	Pleckstrin homology-type (1);	0.091745	0.64402	D	0.000001	T	0.69762	0.3147	L	0.39898	1.24	0.53688	D	0.99997	P;P	0.51537	0.889;0.946	B;B	0.42625	0.291;0.393	T	0.66106	-0.6006	10	0.15066	T	0.55	.	14.9567	0.71120	0.0:0.9326:0.0:0.0674	.	1033;1042	F8W9U9;Q5T5U3	.;RHG21_HUMAN	K	1043;830;1033;1043;878	ENSP00000379709:E1043K;ENSP00000365604:E830K;ENSP00000365592:E1033K;ENSP00000405018:E1043K	ENSP00000365604:E830K	E	-	1	0	ARHGAP21	24929586	0.995000	0.38212	0.360000	0.25837	0.601000	0.36947	3.989000	0.56958	2.941000	0.99782	0.655000	0.94253	GAA		0.413	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24889580	C	T	24889580	3	4	61	1	0	0	0	0	1	0	0	0	871	893	31	1	2801	1	ARHGAP21	10	24889580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2687	24889580	110645167	6649	14634										
ARHGAP21	57584	broad.mit.edu	37	chr10	24908904	24908904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatagaaacaaatgatttCtggctaaatgatggttttgt	9	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:24908904C>A	ENST00000396432.2	-	9	2406	c.1920G>T	c.(1918-1920)caG>caT	p.Q640H	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.Q427H	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	639					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.Q639H(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CAAATGATTTCTGGCTAAATG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											130	122	124					10																	24908904		2203	4300	6503	24948910	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.1920G>T	10.37:g.24908904C>A	ENSP00000379709:p.Gln640His		24948910	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745145	0.49151	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.46063	2.83;2.93;0.88;0.89	5.36	4.43	0.53597	.	0.741088	0.13134	N	0.411228	T	0.57961	0.2089	M	0.63428	1.95	0.27605	N	0.948844	D;D	0.56287	0.975;0.958	P;P	0.57152	0.814;0.656	T	0.53704	-0.8401	10	0.44086	T	0.13	.	16.1486	0.81594	0.0:0.8662:0.1338:0.0	.	630;639	F8W9U9;Q5T5U3	.;RHG21_HUMAN	H	640;427;630;640;475	ENSP00000379709:Q640H;ENSP00000365604:Q427H;ENSP00000365592:Q630H;ENSP00000405018:Q640H	ENSP00000365604:Q427H	Q	-	3	2	ARHGAP21	24948910	1.000000	0.71417	0.976000	0.42696	0.943000	0.58893	1.884000	0.39668	1.342000	0.45619	0.655000	0.94253	CAG		0.448	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		A	24908904	C	A	24908904	3	1	61	1	0	0	0	0	1	0	0	0	871	912	32	2	4028	2	ARHGAP21	10	24908904	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19324	24908904	110625843	6650	14635										
ARHGAP21	57584	broad.mit.edu	37	chr10	24909349	24909349	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataatcccatgaacgagttCtatgattactaaaactaaca	4	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:24909349C>A	ENST00000396432.2	-	9	1961	c.1475G>T	c.(1474-1476)aGa>aTa	p.R492I	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.R279I	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	491					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.R491I(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TGAACGAGTTCTATGATTACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											26	27	27					10																	24909349		2124	4238	6362	24949355	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.1475G>T	10.37:g.24909349C>A	ENSP00000379709:p.Arg492Ile		24949355	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	23.8	4.462658	0.84425	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.72394	1.38;1.15;-0.65;-0.65	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.85548	0.5722	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.991	D	0.85983	0.1484	10	0.87932	D	0	.	20.3431	0.98773	0.0:1.0:0.0:0.0	.	482;491	F8W9U9;Q5T5U3	.;RHG21_HUMAN	I	492;481;279;482;492;327	ENSP00000379709:R492I;ENSP00000365604:R279I;ENSP00000365592:R482I;ENSP00000405018:R492I	ENSP00000365604:R279I	R	-	2	0	ARHGAP21	24949355	0.985000	0.35326	0.111000	0.21465	0.991000	0.79684	5.070000	0.64376	2.880000	0.98712	0.650000	0.86243	AGA		0.393	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		A	24909349	C	A	24909349	3	1	61	1	0	0	0	0	1	0	0	0	871	913	32	2	4473	2	ARHGAP21	10	24909349	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	445	24909349	110625398	6651	14636										
PRTFDC1	56952	broad.mit.edu	37	chr10	25226159	25226159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccttcattgagacaaatCgatctgaatttcggctgatg	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25226159C>T	ENST00000320152.6	-	3	321	c.293G>A	c.(292-294)cGa>cAa	p.R98Q	PRTFDC1_ENST00000376378.1_Missense_Mutation_p.R98Q|PRTFDC1_ENST00000376376.3_Missense_Mutation_p.R98Q	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	98					nucleoside metabolic process (GO:0009116)	cytosol (GO:0005829)	magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)	p.R98Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9						TGAGACAAATCGATCTGAATT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											113	107	109					10																	25226159		2203	4300	6503	25266165	SO:0001583	missense	56952			AF226056	CCDS7145.1, CCDS60506.1	10p12.31	2003-11-10			ENSG00000099256	ENSG00000099256			23333	protein-coding gene	gene with protein product		610751					Standard	XM_005252537		Approved	HHGP	uc001ise.1	Q9NRG1	OTTHUMG00000017829	ENST00000320152.6:c.293G>A	10.37:g.25226159C>T	ENSP00000318602:p.Arg98Gln		25266165	B7Z1Z3|Q53HA7|Q59EL9|Q5VV18|Q5VV20	Missense_Mutation	SNP	ENST00000320152.6	37	CCDS7145.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008082	0.35415	.	.	ENSG00000099256	ENST00000320152;ENST00000358336;ENST00000376378;ENST00000376376	D;D;D	0.99683	-5.75;-5.75;-6.39	5.63	-0.153	0.13403	Phosphoribosyltransferase (1);	0.436518	0.22644	N	0.057404	D	0.97371	0.9140	N	0.16903	0.455	0.09310	N	1	B;B	0.20164	0.042;0.012	B;B	0.08055	0.003;0.001	D	0.95943	0.8948	10	0.22109	T	0.4	.	9.0019	0.36088	0.0:0.5996:0.2121:0.1883	.	98;98	Q9NRG1-2;Q9NRG1	.;PRDC1_HUMAN	Q	98	ENSP00000318602:R98Q;ENSP00000365558:R98Q;ENSP00000365556:R98Q	ENSP00000318602:R98Q	R	-	2	0	PRTFDC1	25266165	0.006000	0.16342	0.087000	0.20705	0.982000	0.71751	0.078000	0.14761	0.039000	0.15632	0.655000	0.94253	CGA		0.368	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047243.2	NM_020200		T	25226159	C	T	25226159	3	4	61	1	0	0	0	0	1	0	0	0	12671	884	31	1	412	1	PRTFDC1	10	25226159	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	316810	25226159	110308588	6652	14637										
ENKUR	219670	broad.mit.edu	37	chr10	25279466	25279466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggttttcctggatataacGatcatagtcttcttgggctt	9	7	3	0	rs372214436		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25279466G>T	ENST00000331161.4	-	4	739	c.520C>A	c.(520-522)Cgt>Agt	p.R174S	ENKUR_ENST00000376363.1_Missense_Mutation_p.R174S	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	174	Enkurin. {ECO:0000255|PROSITE- ProRule:PRU01000}.					motile cilium (GO:0031514)		p.R174S(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						TGGATATAACGATCATAGTCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											189	167	174					10																	25279466		2203	4300	6503	25319472	SO:0001583	missense	219670			AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"chromosome 10 open reading frame 63"	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.520C>A	10.37:g.25279466G>T	ENSP00000331044:p.Arg174Ser		25319472	A8K8Y0|D3DRV2	Missense_Mutation	SNP	ENST00000331161.4	37	CCDS7146.1	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.377334	0.01204	.	.	ENSG00000151023	ENST00000331161;ENST00000376363	.	.	.	5.64	-0.737	0.11129	.	0.879386	0.10389	N	0.680669	T	0.08447	0.0210	N	0.01874	-0.695	0.09310	N	1	B;B	0.15141	0.012;0.001	B;B	0.14023	0.01;0.006	T	0.34925	-0.9809	9	0.09590	T	0.72	-14.9871	2.6171	0.04907	0.095:0.1847:0.1896:0.5307	.	174;174	Q5VV23;Q8TC29	.;ENKUR_HUMAN	S	174	.	ENSP00000331044:R174S	R	-	1	0	ENKUR	25319472	0.002000	0.14202	0.010000	0.14722	0.109000	0.19521	0.208000	0.17415	-0.127000	0.11661	-0.261000	0.10672	CGT		0.378	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010		T	25279466	G	T	25279466	3	4	61	1	0	0	0	0	1	0	0	0	5133	1058	37	2	262	2	ENKUR	10	25279466	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53307	25279466	110255281	6653	14638										
THNSL1	79896	broad.mit.edu	37	chr10	25313614	25313614	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatcatgcttccgcatatCttgatcttgttagtcaagga	7	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25313614C>A	ENST00000524413.1	+	3	1809	c.1462C>A	c.(1462-1464)Ctt>Att	p.L488I	THNSL1_ENST00000376356.4_Missense_Mutation_p.L488I			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	488						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.L488I(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TTCCGCATATCTTGATCTTGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											83	83	83					10																	25313614		2203	4300	6503	25353620	SO:0001583	missense	79896			AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1462C>A	10.37:g.25313614C>A	ENSP00000434887:p.Leu488Ile		25353620	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001898	0.54254	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	D;D	0.97114	-4.25;-4.25	5.58	5.58	0.84498	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.98191	0.9402	M	0.67517	2.055	0.47994	D	0.99956	D	0.89917	1.0	D	0.79784	0.993	D	0.98725	1.0710	10	0.59425	D	0.04	-28.956	19.5829	0.95475	0.0:1.0:0.0:0.0	.	488	Q8IYQ7	THNS1_HUMAN	I	488	ENSP00000434887:L488I;ENSP00000365534:L488I	ENSP00000365534:L488I	L	+	1	0	THNSL1	25353620	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.280000	0.58959	2.636000	0.89361	0.561000	0.74099	CTT		0.418	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		A	25313614	C	A	25313614	3	1	61	1	0	0	0	0	1	0	0	0	15901	913	32	2	1464	2	THNSL1	10	25313614	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34148	25313614	110221133	6654	14639										
GPR158	57512	broad.mit.edu	37	chr10	25861759	25861759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggccaggggaaaacatccGatcacctcatcttcaatatg	8	11	4	0	rs144380617		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25861759G>A	ENST00000376351.3	+	7	2055	c.1696G>A	c.(1696-1698)Gat>Aat	p.D566N		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	566					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D566N(2)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GAAAACATCCGATCACCTCAT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	10						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	182	137	152		1696	5.7	1	10	dbSNP_134	152	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR158	NM_020752.2	23	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	566/1216	25861759	2,13004	2203	4300	6503	25901765	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1696G>A	10.37:g.25861759G>A	ENSP00000365529:p.Asp566Asn		25901765	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.496089	0.85069	2.27E-4	1.16E-4	ENSG00000151025	ENST00000376351	D	0.87334	-2.24	5.67	5.67	0.87782	GPCR, family 3, C-terminal (2);	0.307372	0.31760	N	0.007115	D	0.84179	0.5415	L	0.34521	1.04	0.80722	D	1	P	0.37731	0.607	B	0.39971	0.315	T	0.82589	-0.0382	10	0.35671	T	0.21	.	19.7579	0.96301	0.0:0.0:1.0:0.0	.	566	Q5T848	GP158_HUMAN	N	566	ENSP00000365529:D566N	ENSP00000365529:D566N	D	+	1	0	GPR158	25901765	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.972000	0.88022	2.677000	0.91161	0.557000	0.71058	GAT		0.428	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25861759	G	A	25861759	3	1	61	1	0	0	0	0	1	0	0	0	6683	1058	37	1	1722	1	GPR158	10	25861759	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	548145	25861759	109672988	6655	14640										
GPR158	57512	broad.mit.edu	37	chr10	25885617	25885617	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatgatattgctacagaaGcatatgaggatgagctagac	12	5	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25885617G>T	ENST00000376351.3	+	10	2403	c.2044G>T	c.(2044-2046)Gca>Tca	p.A682S	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	682					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A682S(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						TGCTACAGAAGCATATGAGGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											142	112	122					10																	25885617		2203	4300	6503	25925623	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2044G>T	10.37:g.25885617G>T	ENSP00000365529:p.Ala682Ser		25925623	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	34	5.390719	0.95988	.	.	ENSG00000151025	ENST00000376351	T	0.62232	0.04	6.16	6.16	0.99307	.	0.000000	0.64402	D	0.000001	T	0.77294	0.4109	L	0.58101	1.795	0.80722	D	1	D	0.65815	0.995	D	0.67103	0.949	T	0.73588	-0.3935	10	0.45353	T	0.12	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	682	Q5T848	GP158_HUMAN	S	682	ENSP00000365529:A682S	ENSP00000365529:A682S	A	+	1	0	GPR158	25925623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	GCA		0.443	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25885617	G	T	25885617	3	4	61	1	0	0	0	0	1	0	0	0	6683	971	34	2	2082	2	GPR158	10	25885617	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23858	25885617	109649130	6656	14641										
GPR158	57512	broad.mit.edu	37	chr10	25886744	25886744	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaactggaaatatataaaaGaaagaagatgatcacaaaca	6	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:25886744G>T	ENST00000376351.3	+	11	2548	c.2189G>T	c.(2188-2190)aGa>aTa	p.R730I	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	730					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R730I(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						ATATATAAAAGAAAGAAGATG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	99	95					10																	25886744		2203	4300	6503	25926750	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2189G>T	10.37:g.25886744G>T	ENSP00000365529:p.Arg730Ile		25926750	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626606	0.66901	.	.	ENSG00000151025	ENST00000376351	T	0.61274	0.12	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000006	T	0.69233	0.3088	L	0.55481	1.735	0.80722	D	1	D	0.59357	0.985	P	0.58520	0.84	T	0.66716	-0.5853	10	0.37606	T	0.19	.	19.1925	0.93672	0.0:0.0:1.0:0.0	.	730	Q5T848	GP158_HUMAN	I	730	ENSP00000365529:R730I	ENSP00000365529:R730I	R	+	2	0	GPR158	25926750	1.000000	0.71417	0.999000	0.59377	0.005000	0.04900	9.476000	0.97823	2.537000	0.85549	0.557000	0.71058	AGA		0.433	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25886744	G	T	25886744	3	4	61	1	0	0	0	0	1	0	0	0	6683	942	33	2	2231	2	GPR158	10	25886744	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1127	25886744	109648003	6657	14642										
MYO3A	53904	broad.mit.edu	37	chr10	26315388	26315388	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactcaaattgagggcaaaGatgtgatgctacaaaaacaa	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26315388G>T	ENST00000265944.5	+	10	1046	c.880G>T	c.(880-882)Gat>Tat	p.D294Y	MYO3A_ENST00000543632.1_Missense_Mutation_p.D294Y	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	294					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D294Y(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TGAGGGCAAAGATGTGATGCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											91	85	87					10																	26315388		2203	4300	6503	26355394	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.880G>T	10.37:g.26315388G>T	ENSP00000265944:p.Asp294Tyr		26355394	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049193	0.75846	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;T	0.13778	2.56;2.56	5.76	4.85	0.62838	Protein kinase-like domain (1);	0.133664	0.64402	D	0.000002	T	0.30854	0.0778	M	0.66939	2.045	0.51012	D	0.999905	D;D;D	0.61080	0.989;0.981;0.966	P;P;P	0.59546	0.859;0.726;0.702	T	0.03514	-1.1029	10	0.62326	D	0.03	.	13.1666	0.59575	0.0737:0.0:0.9263:0.0	.	294;294;294	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	Y	294	ENSP00000265944:D294Y;ENSP00000445909:D294Y	ENSP00000265944:D294Y	D	+	1	0	MYO3A	26355394	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.116000	0.77119	1.569000	0.49696	0.655000	0.94253	GAT		0.378	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26315388	G	T	26315388	3	4	61	1	0	0	0	0	1	0	0	0	10106	942	33	2	910	2	MYO3A	10	26315388	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	428644	26315388	109219359	6658	14643										
MYO3A	53904	broad.mit.edu	37	chr10	26357736	26357736	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagaagtgttattccagaGatcagatctacgtctatgtg	10	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26357736G>T	ENST00000265944.5	+	12	1259	c.1093G>T	c.(1093-1095)Gat>Tat	p.D365Y	MYO3A_ENST00000543632.1_Missense_Mutation_p.D365Y	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	365	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D365Y(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TTATTCCAGAGATCAGATCTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											143	124	131					10																	26357736		2203	4300	6503	26397742	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1093G>T	10.37:g.26357736G>T	ENSP00000265944:p.Asp365Tyr		26397742	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497815	0.64186	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;D	0.88277	-0.76;-2.36	5.55	5.55	0.83447	Myosin head, motor domain (2);	0.045895	0.85682	D	0.000000	D	0.95535	0.8549	M	0.90019	3.08	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.74348	0.974;0.983;0.942	D	0.94926	0.8078	10	0.41790	T	0.15	.	19.4992	0.95086	0.0:0.0:1.0:0.0	.	365;365;365	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	Y	365	ENSP00000265944:D365Y;ENSP00000445909:D365Y	ENSP00000265944:D365Y	D	+	1	0	MYO3A	26397742	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	2.390000	0.44416	2.598000	0.87819	0.655000	0.94253	GAT		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26357736	G	T	26357736	3	4	61	1	0	0	0	0	1	0	0	0	10106	942	33	2	1131	2	MYO3A	10	26357736	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42348	26357736	109177011	6659	14644										
MYO3A	53904	broad.mit.edu	37	chr10	26377271	26377271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattcacctcttctggagCggtagtgggagcacagattt	12	8	3	1	rs138526349	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26377271C>T	ENST00000265944.5	+	15	1665	c.1499C>T	c.(1498-1500)gCg>gTg	p.A500V	MYO3A_ENST00000543632.1_Missense_Mutation_p.A500V	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	500	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A500V(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCTTCTGGAGCGGTAGTGGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	68	70	69		1499	4.4	1	10	dbSNP_134	69	0,8600		0,0,4300	no	missense	MYO3A	NM_017433.4	64	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	500/1617	26377271	3,13003	2203	4300	6503	26417277	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1499C>T	10.37:g.26377271C>T	ENSP00000265944:p.Ala500Val		26417277	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287156	0.40494	6.81E-4	0.0	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.87491	-2.26;-2.26	5.54	4.41	0.53225	Myosin head, motor domain (2);	0.198431	0.52532	D	0.000062	T	0.75228	0.3821	N	0.17594	0.5	0.35804	D	0.82337	B;B;B	0.31519	0.067;0.083;0.327	B;B;B	0.24394	0.015;0.023;0.053	T	0.78026	-0.2365	10	0.33141	T	0.24	.	13.0709	0.59061	0.0:0.8908:0.0:0.1092	.	500;500;500	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	V	500	ENSP00000265944:A500V;ENSP00000445909:A500V	ENSP00000265944:A500V	A	+	2	0	MYO3A	26417277	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.910000	0.63321	2.779000	0.95612	0.655000	0.94253	GCG		0.378	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26377271	C	T	26377271	3	4	61	1	0	0	0	0	1	0	0	0	10106	768	27	1	1549	1	MYO3A	10	26377271	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19535	26377271	109157476	6660	14645										
MYO3A	53904	broad.mit.edu	37	chr10	26414413	26414413	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagaggagaaacaattataCgacccaatactgtagaaaaa	7	7	0	3	rs370314254		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26414413C>T	ENST00000265944.5	+	19	2156	c.1990C>T	c.(1990-1992)Cga>Tga	p.R664*	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	664	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R664*(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AACAATTATACGACCCAATAC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											116	112	113					10																	26414413		2203	4300	6503	26454419	SO:0001587	stop_gained	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1990C>T	10.37:g.26414413C>T	ENSP00000265944:p.Arg664*		26454419	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Nonsense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	41	8.593374	0.98877	.	.	ENSG00000095777	ENST00000265944	.	.	.	5.91	4.99	0.66335	.	0.051882	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3079	0.82855	0.1334:0.8666:0.0:0.0	.	.	.	.	X	664	.	ENSP00000265944:R664X	R	+	1	2	MYO3A	26454419	0.998000	0.40836	0.995000	0.50966	0.991000	0.79684	2.896000	0.48656	1.461000	0.47929	0.585000	0.79938	CGA		0.418	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26414413	C	T	26414413	4	4	61	1	0	0	0	0	0	1	0	0	10106	528	19	1	2056	1	MYO3A	10	26414413	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37142	26414413	109120334	6661	14646										
MYO3A	53904	broad.mit.edu	37	chr10	26446395	26446395	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggaaacagcaagaattCgaagactaggattctcccat	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26446395C>T	ENST00000265944.5	+	26	3116	c.2950C>T	c.(2950-2952)Cga>Tga	p.R984*	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	984	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R984*(3)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AGCAAGAATTCGAAGACTAGG	0.363																																																3	Substitution - Nonsense(3)	large_intestine(3)	10											113	110	111					10																	26446395		2203	4300	6503	26486401	SO:0001587	stop_gained	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2950C>T	10.37:g.26446395C>T	ENSP00000265944:p.Arg984*		26486401	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Nonsense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	42	9.671764	0.99234	.	.	ENSG00000095777	ENST00000265944	.	.	.	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8211	0.92097	0.0:1.0:0.0:0.0	.	.	.	.	X	984	.	ENSP00000265944:R984X	R	+	1	2	MYO3A	26486401	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.217000	0.51184	2.524000	0.85096	0.655000	0.94253	CGA		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26446395	C	T	26446395	4	4	61	1	0	0	0	0	0	1	0	0	10106	876	31	1	3044	1	MYO3A	10	26446395	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31982	26446395	109088352	6662	14647										
MYO3A	53904	broad.mit.edu	37	chr10	26457736	26457736	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcttgtgtcagagcattCttgtgttcaagaagatacca	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26457736C>A	ENST00000265944.5	+	28	3373	c.3207C>A	c.(3205-3207)ttC>ttA	p.F1069L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1069	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F1069L(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCAGAGCATTCTTGTGTTCAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	10											122	124	124					10																	26457736		2203	4300	6503	26497742	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3207C>A	10.37:g.26457736C>A	ENSP00000265944:p.Phe1069Leu		26497742	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468878	0.63625	.	.	ENSG00000095777	ENST00000265944	T	0.71817	-0.6	5.63	4.73	0.59995	.	0.109911	0.64402	D	0.000003	T	0.61899	0.2384	L	0.47716	1.5	0.80722	D	1	B	0.32051	0.354	B	0.32465	0.146	T	0.60110	-0.7327	10	0.35671	T	0.21	.	9.6809	0.40070	0.0:0.6751:0.2453:0.0795	.	1069	Q8NEV4	MYO3A_HUMAN	L	1069	ENSP00000265944:F1069L	ENSP00000265944:F1069L	F	+	3	2	MYO3A	26497742	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.808000	0.55598	1.509000	0.48786	0.655000	0.94253	TTC		0.343	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26457736	C	A	26457736	3	1	61	1	0	0	0	0	1	0	0	0	10106	912	32	2	3309	2	MYO3A	10	26457736	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11341	26457736	109077011	6663	14648										
MYO3A	53904	broad.mit.edu	37	chr10	26465714	26465714	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaactgaagtcactttatCtgggtgtctcgcaccataag	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26465714C>A	ENST00000265944.5	+	31	4544	c.4378C>A	c.(4378-4380)Ctg>Atg	p.L1460M	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1460					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1460M(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GTCACTTTATCTGGGTGTCTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											89	84	86					10																	26465714		2203	4300	6503	26505720	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4378C>A	10.37:g.26465714C>A	ENSP00000265944:p.Leu1460Met		26505720	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	9.098	1.003476	0.19121	.	.	ENSG00000095777	ENST00000265944	T	0.77620	-1.11	5.91	4.06	0.47325	.	0.597412	0.17528	N	0.170966	T	0.67392	0.2888	L	0.39898	1.24	0.09310	N	0.999992	B	0.20780	0.048	B	0.15870	0.014	T	0.54470	-0.8289	10	0.31617	T	0.26	.	9.6582	0.39939	0.0:0.59:0.3345:0.0755	.	1460	Q8NEV4	MYO3A_HUMAN	M	1460	ENSP00000265944:L1460M	ENSP00000265944:L1460M	L	+	1	2	MYO3A	26505720	0.336000	0.24757	0.510000	0.27712	0.921000	0.55340	1.047000	0.30367	0.837000	0.34925	-0.172000	0.13284	CTG		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26465714	C	A	26465714	3	1	61	1	0	0	0	0	1	0	0	0	10106	912	32	2	4492	2	MYO3A	10	26465714	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7978	26465714	109069033	6664	14649										
GAD2	2572	broad.mit.edu	37	chr10	26569984	26569984	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagatgatgggagtccctTtgcagtgctctgctctcctg	11	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26569984T>C	ENST00000376261.3	+	12	1707	c.1204T>C	c.(1204-1206)Ttg>Ctg	p.L402L	GAD2_ENST00000259271.3_Silent_p.L402L	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	402					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.L402L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGGAGTCCCTTTGCAGTGCTC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	10											197	174	182					10																	26569984		2203	4300	6503	26609990	SO:0001819	synonymous_variant	2572			AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.1204T>C	10.37:g.26569984T>C			26609990	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																				0.512	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		C	26569984	T	C	26569984	2	2	61	1	0	0	0	0	0	0	0	1	6199	1838	64	4		4	GAD2	10	26569984	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	104270	26569984	108964763	6665	14650										
APBB1IP	54518	broad.mit.edu	37	chr10	26789770	26789770	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttaaatgcactggaagaCcaagatttagatgctctcat	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:26789770C>T	ENST00000376236.4	+	5	638	c.183C>T	c.(181-183)gaC>gaT	p.D61D	APBB1IP_ENST00000356785.4_Silent_p.D61D	NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	61					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.D61D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						CACTGGAAGACCAAGATTTAG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	10											90	87	88					10																	26789770		2203	4300	6503	26829776	SO:0001819	synonymous_variant	54518			AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"Pleckstrin homology (PH) domain containing"	17379	protein-coding gene	gene with protein product	"Rap1-GTP-interacting adaptor molecule"	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.183C>T	10.37:g.26789770C>T			26829776	Q8IWS8|Q8IYL7|Q8IZZ7	Silent	SNP	ENST00000376236.4	37	CCDS31167.1																																																																																				0.393	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043		T	26789770	C	T	26789770	2	4	61	1	0	0	0	0	0	0	0	1	760	506	18	3		3	APBB1IP	10	26789770	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219786	26789770	108744977	6666	14651										
PDSS1	23590	broad.mit.edu	37	chr10	27009245	27009245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgacgatgcaagttctcGaagaggaaaacacacagtta	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27009245G>A	ENST00000376215.5	+	6	619	c.566G>A	c.(565-567)cGa>cAa	p.R189Q	PDSS1_ENST00000376203.5_Missense_Mutation_p.R189Q|RP13-16H11.5_ENST00000458171.1_RNA	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	189					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.R189Q(1)		autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						GCAAGTTCTCGAAGAGGAAAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											115	110	111					10																	27009245		2203	4300	6503	27049251	SO:0001583	missense	23590			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"coenzyme Q1 homolog (yeast)"	607429	"trans-prenyltransferase"	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.566G>A	10.37:g.27009245G>A	ENSP00000365388:p.Arg189Gln		27049251	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	G	35	5.489682	0.96323	.	.	ENSG00000148459	ENST00000376215;ENST00000376203;ENST00000396343	D;D	0.89050	-2.46;-2.46	5.65	5.65	0.86999	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	D	0.97636	0.9225	H	0.99789	4.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99257	1.0889	10	0.87932	D	0	-7.3225	19.716	0.96121	0.0:0.0:1.0:0.0	.	189;189	Q5T2R2-2;Q5T2R2	.;DPS1_HUMAN	Q	189;189;150	ENSP00000365388:R189Q;ENSP00000365376:R189Q	ENSP00000365376:R189Q	R	+	2	0	PDSS1	27049251	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.624000	0.98398	2.681000	0.91329	0.591000	0.81541	CGA		0.423	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1			A	27009245	G	A	27009245	3	1	61	1	0	0	0	0	1	0	0	0	11724	1058	37	1	588	1	PDSS1	10	27009245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219475	27009245	108525502	6667	14652										
ABI1	10006	broad.mit.edu	37	chr10	27048111	27048111	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtagtagagttgtgtcGagatatctgcctggtcattg	13	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27048111G>A	ENST00000376142.2	-	9	1029	c.958C>T	c.(958-960)Cga>Tga	p.R320*	ABI1_ENST00000355394.4_Nonsense_Mutation_p.R321*|ABI1_ENST00000376166.1_Nonsense_Mutation_p.R287*|ABI1_ENST00000376160.1_Nonsense_Mutation_p.R287*|ABI1_ENST00000376170.4_Nonsense_Mutation_p.R292*|ABI1_ENST00000376138.3_Nonsense_Mutation_p.R293*|ABI1_ENST00000376139.2_Nonsense_Mutation_p.R288*|ABI1_ENST00000490841.2_Intron|ABI1_ENST00000359188.4_Nonsense_Mutation_p.R292*|ABI1_ENST00000376137.4_Intron|ABI1_ENST00000376134.3_Nonsense_Mutation_p.R294*|ABI1_ENST00000376140.3_Nonsense_Mutation_p.R293*|ABI1_ENST00000536334.1_Intron|ABI1_ENST00000346832.5_Nonsense_Mutation_p.R337*	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	320	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)	p.R320*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAGTTGTGTCGAGATATCTGC	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											154	138	144					10																	27048111		2203	4300	6503	27088117	SO:0001587	stop_gained	10006			U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"spectrin SH3 domain binding protein 1"	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.958C>T	10.37:g.27048111G>A	ENSP00000365312:p.Arg320*		27088117	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Nonsense_Mutation	SNP	ENST00000376142.2	37	CCDS7150.1	.	.	.	.	.	.	.	.	.	.	G	38	6.978923	0.97979	.	.	ENSG00000136754	ENST00000376138;ENST00000376170;ENST00000376166;ENST00000376160;ENST00000376142;ENST00000359188;ENST00000376139;ENST00000355394;ENST00000346832;ENST00000376134;ENST00000376140	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.5914	19.4511	0.94867	0.0:0.0:1.0:0.0	.	.	.	.	X	293;292;287;287;320;292;288;321;337;294;293	.	ENSP00000279599:R337X	R	-	1	2	ABI1	27088117	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.849000	0.86908	2.599000	0.87857	0.591000	0.81541	CGA		0.493	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1	NM_005470		A	27048111	G	A	27048111	4	1	61	1	0	0	0	0	0	1	0	0	88	1066	37	1	584	1	ABI1	10	27048111	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38866	27048111	108486636	6668	14653										
ANKRD26	22852	broad.mit.edu	37	chr10	27326130	27326130	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacctcagaattcattttCttttgagccatttcaatctc	3	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27326130C>A	ENST00000376087.4	-	23	2847	c.2682G>T	c.(2680-2682)aaG>aaT	p.K894N	ANKRD26_ENST00000376070.3_Missense_Mutation_p.K451N|ANKRD26_ENST00000436985.2_Missense_Mutation_p.K910N	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	893					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)		p.K894N(1)		breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						AATTCATTTTCTTTTGAGCCA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											110	98	102					10																	27326130		1824	4071	5895	27366136	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.2682G>T	10.37:g.27326130C>A	ENSP00000365255:p.Lys894Asn		27366136	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.424411	0.25639	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.35421	3.82;1.31;1.33	5.34	-0.496	0.12027	.	0.762215	0.10577	U	0.658366	T	0.39279	0.1072	M	0.63843	1.955	0.09310	N	1	P;P;B	0.50272	0.933;0.89;0.079	P;P;B	0.51324	0.666;0.466;0.044	T	0.24368	-1.0162	10	0.41790	T	0.15	.	3.4021	0.07327	0.1824:0.3675:0.0:0.4501	.	894;893;910	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	N	451;894;910	ENSP00000365238:K451N;ENSP00000365255:K894N;ENSP00000405112:K910N	ENSP00000365238:K451N	K	-	3	2	ANKRD26	27366136	0.045000	0.20229	0.000000	0.03702	0.299000	0.27559	-0.122000	0.10627	0.013000	0.14918	-0.991000	0.02546	AAG		0.313	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27326130	C	A	27326130	3	1	61	1	0	0	0	0	1	0	0	0	654	912	32	2	2498	2	ANKRD26	10	27326130	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	278019	27326130	108208617	6669	14654										
ANKRD26	22852	broad.mit.edu	37	chr10	27326956	27326956	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtatcagcatttcttctCttctcttcttcttggtttaa	4	10	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27326956C>A	ENST00000376087.4	-	22	2568	c.2403G>T	c.(2401-2403)aaG>aaT	p.K801N	ANKRD26_ENST00000376070.3_Missense_Mutation_p.K358N|ANKRD26_ENST00000436985.2_Missense_Mutation_p.K817N	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	800					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)		p.K801N(1)		breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CATTTCTTCTCTTCTCTTCTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											117	101	106					10																	27326956		1819	4072	5891	27366962	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.2403G>T	10.37:g.27326956C>A	ENSP00000365255:p.Lys801Asn		27366962	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220605	0.58560	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.18657	2.2;2.2;2.2	5.15	0.678	0.17969	.	0.102807	0.39544	N	0.001330	T	0.30479	0.0766	L	0.48642	1.525	0.41360	D	0.987421	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.976;0.946;0.994	T	0.07868	-1.0750	10	0.87932	D	0	.	3.9144	0.09216	0.1582:0.4435:0.0:0.3984	.	801;800;817	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	N	358;801;817	ENSP00000365238:K358N;ENSP00000365255:K801N;ENSP00000405112:K817N	ENSP00000365238:K358N	K	-	3	2	ANKRD26	27366962	0.984000	0.35163	0.973000	0.42090	0.988000	0.76386	0.126000	0.15769	-0.077000	0.12752	0.585000	0.79938	AAG		0.308	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27326956	C	A	27326956	3	1	61	1	0	0	0	0	1	0	0	0	654	912	32	2	2781	2	ANKRD26	10	27326956	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	826	27326956	108207791	6670	14655										
ANKRD26	22852	broad.mit.edu	37	chr10	27328955	27328955	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctaactgtgattttatttCttttgtttcagatagctccc	5	9	3	2	rs568696333	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27328955C>A	ENST00000376087.4	-	21	2479	c.2314G>T	c.(2314-2316)Gaa>Taa	p.E772*	ANKRD26_ENST00000376070.3_Nonsense_Mutation_p.E329*|ANKRD26_ENST00000436985.2_Nonsense_Mutation_p.E788*	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	771					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)		p.E772*(1)		breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						GATTTTATTTCTTTTGTTTCA	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											195	175	181					10																	27328955		1834	4073	5907	27368961	SO:0001587	stop_gained	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.2314G>T	10.37:g.27328955C>A	ENSP00000365255:p.Glu772*		27368961	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Nonsense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	40	8.357240	0.98774	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	.	.	.	5.03	5.03	0.67393	.	0.000000	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	16.2166	0.82231	0.0:1.0:0.0:0.0	.	.	.	.	X	329;772;788	.	ENSP00000365238:E329X	E	-	1	0	ANKRD26	27368961	1.000000	0.71417	0.103000	0.21229	0.989000	0.77384	2.265000	0.43311	2.474000	0.83562	0.585000	0.79938	GAA		0.299	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27328955	C	A	27328955	4	1	61	1	0	0	0	0	0	1	0	0	654	922	32	2	2874	2	ANKRD26	10	27328955	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1999	27328955	108205792	6671	14656										
YME1L1	10730	broad.mit.edu	37	chr10	27406549	27406549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgattgtagctttgttgaTaggcattgcatcttttgtgt	10	5	1	2	rs200047558		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27406549T>C	ENST00000326799.3	-	16	1994	c.1846A>G	c.(1846-1848)Atc>Gtc	p.I616V	YME1L1_ENST00000376016.3_Missense_Mutation_p.I559V|YME1L1_ENST00000375972.3_Missense_Mutation_p.I526V	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	616					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.I616V(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						GCTTTGTTGATAGGCATTGCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											325	274	292					10																	27406549		2203	4300	6503	27446555	SO:0001583	missense	10730			AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1846A>G	10.37:g.27406549T>C	ENSP00000318480:p.Ile616Val		27446555	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	37	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889169	0.52014	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000546122	T;T;T	0.79749	-1.3;-1.3;-1.3	5.49	5.49	0.81192	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.044743	0.85682	D	0.000000	T	0.68595	0.3018	N	0.00855	-1.145	0.80722	D	1	D;B;B	0.53151	0.958;0.257;0.379	D;B;B	0.70716	0.97;0.147;0.401	T	0.70103	-0.4964	10	0.02654	T	1	-6.379	15.8844	0.79232	0.0:0.0:0.0:1.0	.	526;559;616	B4DNM1;Q96TA2-2;Q96TA2	.;.;YMEL1_HUMAN	V	559;616;616;526;362	ENSP00000365184:I559V;ENSP00000318480:I616V;ENSP00000365139:I526V	ENSP00000318480:I616V	I	-	1	0	YME1L1	27446555	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	7.954000	0.87848	2.218000	0.71995	0.533000	0.62120	ATC		0.428	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		C	27406549	T	C	27406549	3	2	61	1	0	0	0	0	1	0	0	0	17527	1406	49	4	495	4	YME1L1	10	27406549	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	77594	27406549	108128198	6672	14657										
MASTL	84930	broad.mit.edu	37	chr10	27459067	27459067	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccttgctaaaaaatgcttCtctggggaagtttcttggga	10	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27459067C>A	ENST00000375940.4	+	8	1236	c.1179C>A	c.(1177-1179)ttC>ttA	p.F393L	MASTL_ENST00000342386.6_Missense_Mutation_p.F393L|MASTL_ENST00000375946.4_Missense_Mutation_p.F393L|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	393	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)	p.F393L(1)		breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAAAATGCTTCTCTGGGGAAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											96	97	97					10																	27459067		2203	4300	6503	27499073	SO:0001583	missense	84930			BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.1179C>A	10.37:g.27459067C>A	ENSP00000365107:p.Phe393Leu		27499073	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.522353	0.00149	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.75938	-0.98;-0.98;-0.98	5.78	1.35	0.21983	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.108720	0.06554	N	0.745474	T	0.56731	0.2005	N	0.25144	0.715	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34129	-0.9841	10	0.02654	T	1	5.1789	9.4213	0.38553	0.1038:0.6451:0.0:0.2512	.	393;393;393	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	L	393	ENSP00000365113:F393L;ENSP00000343446:F393L;ENSP00000365107:F393L	ENSP00000343446:F393L	F	+	3	2	MASTL	27499073	0.219000	0.23619	0.001000	0.08648	0.004000	0.04260	-0.052000	0.11865	0.093000	0.17368	-0.824000	0.03097	TTC		0.418	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		A	27459067	C	A	27459067	3	1	61	1	0	0	0	0	1	0	0	0	9358	912	32	2	1209	2	MASTL	10	27459067	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52518	27459067	108075680	6673	14658										
MASTL	84930	broad.mit.edu	37	chr10	27459707	27459707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatcaaatattgaagatCcacttattgtaacaccagat	5	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:27459707C>T	ENST00000375940.4	+	8	1876	c.1819C>T	c.(1819-1821)Cca>Tca	p.P607S	MASTL_ENST00000342386.6_Missense_Mutation_p.P607S|MASTL_ENST00000375946.4_Missense_Mutation_p.P607S|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	607	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)	p.P607S(1)		breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TATTGAAGATCCACTTATTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											39	39	39					10																	27459707		2203	4300	6503	27499713	SO:0001583	missense	84930			BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.1819C>T	10.37:g.27459707C>T	ENSP00000365107:p.Pro607Ser		27499713	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.644967	0.00792	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.22743	1.94;1.94;1.94	5.14	0.741	0.18336	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.196920	0.05691	N	0.592129	T	0.07954	0.0199	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.17465	0.001;0.0;0.022	B;B;B	0.15870	0.001;0.001;0.014	T	0.34725	-0.9817	10	0.16896	T	0.51	-0.2648	2.0454	0.03559	0.2187:0.272:0.357:0.1522	.	607;607;607	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	S	607	ENSP00000365113:P607S;ENSP00000343446:P607S;ENSP00000365107:P607S	ENSP00000343446:P607S	P	+	1	0	MASTL	27499713	0.000000	0.05858	0.318000	0.25279	0.387000	0.30353	-0.959000	0.03853	0.228000	0.21019	0.591000	0.81541	CCA		0.378	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		T	27459707	C	T	27459707	3	4	61	1	0	0	0	0	1	0	0	0	9358	855	30	3	1849	3	MASTL	10	27459707	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	640	27459707	108075040	6674	14659										
ARMC4	55130	broad.mit.edu	37	chr10	28151422	28151422	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgtgataacagctaaatTttcttgatcttttgctatgt	6	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:28151422T>G	ENST00000305242.5	-	18	2832	c.2740A>C	c.(2740-2742)Aat>Cat	p.N914H	ARMC4_ENST00000545014.1_Missense_Mutation_p.N439H|ARMC4_ENST00000537576.1_Missense_Mutation_p.N606H	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	914					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.N914H(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						ACAGCTAAATTTTCTTGATCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											174	154	161					10																	28151422		2203	4300	6503	28191428	SO:0001583	missense	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2740A>C	10.37:g.28151422T>G	ENSP00000306410:p.Asn914His		28191428	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.486434	0.84854	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	D;D;T	0.92397	-3.03;-3.03;-0.24	5.9	5.9	0.94986	Armadillo-like helical (1);Armadillo-type fold (1);	0.084158	0.85682	D	0.000000	D	0.96027	0.8706	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.73380	0.963;0.98	D	0.96332	0.9244	10	0.66056	D	0.02	-40.3693	16.3322	0.83039	0.0:0.0:0.0:1.0	.	439;914	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	H	606;914;439	ENSP00000443208:N606H;ENSP00000306410:N914H;ENSP00000441076:N439H	ENSP00000306410:N914H	N	-	1	0	ARMC4	28191428	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.218000	0.72224	2.251000	0.74343	0.528000	0.53228	AAT		0.348	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		G	28151422	T	G	28151422	3	3	61	1	0	0	0	0	1	0	0	0	954	1841	64	4	406	4	ARMC4	10	28151422	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	691715	28151422	107383325	6675	14660										
MPP7	143098	broad.mit.edu	37	chr10	28348654	28348654	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccatcactctcctggcttCttcttgctctggtggtatct	7	14	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:28348654C>A	ENST00000375732.1	-	14	1482	c.1223G>T	c.(1222-1224)aGa>aTa	p.R408I	MPP7_ENST00000375719.3_Missense_Mutation_p.R408I|MPP7_ENST00000445954.2_Missense_Mutation_p.R283I|MPP7_ENST00000540098.1_Missense_Mutation_p.R408I|MPP7_ENST00000337532.5_Missense_Mutation_p.R408I			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	408	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)	p.R408I(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						CTCCTGGCTTCTTCTTGCTCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											107	102	104					10																	28348654		2203	4299	6502	28388660	SO:0001583	missense	143098			BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.1223G>T	10.37:g.28348654C>A	ENSP00000364884:p.Arg408Ile		28388660	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368024	0.82463	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000441595;ENST00000445954	T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08	5.51	5.51	0.81932	Guanylate kinase/L-type calcium channel (1);Guanylate kinase, conserved site (1);Guanylate kinase (2);	0.044816	0.85682	D	0.000000	T	0.78046	0.4222	H	0.97415	4	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.86142	0.1582	10	0.87932	D	0	.	19.4309	0.94765	0.0:1.0:0.0:0.0	.	408	Q5T2T1	MPP7_HUMAN	I	408;408;408;408;169;283	ENSP00000364884:R408I;ENSP00000337907:R408I;ENSP00000438693:R408I;ENSP00000364871:R408I;ENSP00000398319:R169I;ENSP00000405397:R283I	ENSP00000337907:R408I	R	-	2	0	MPP7	28388660	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.659000	0.54489	2.592000	0.87571	0.650000	0.86243	AGA		0.338	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		A	28348654	C	A	28348654	3	1	61	1	0	0	0	0	1	0	0	0	9769	913	32	2	523	2	MPP7	10	28348654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	197232	28348654	107186093	6676	14661										
BAMBI	25805	broad.mit.edu	37	chr10	28970244	28970244	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccactggttatatgtgtaAatctgagctcagcgcctgct	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:28970244A>C	ENST00000375533.3	+	2	690	c.134A>C	c.(133-135)aAa>aCa	p.K45T		NM_012342.2	NP_036474.1	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor	45					cell migration (GO:0016477)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell shape (GO:0008360)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|type II transforming growth factor beta receptor binding (GO:0005114)	p.K45T(1)		central_nervous_system(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	17						TATATGTGTAAATCTGAGCTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	106	109					10																	28970244		2203	4300	6503	29010250	SO:0001583	missense	25805			U23070	CCDS7162.1	10p12.3-p11.2	2013-07-23	2013-07-23		ENSG00000095739	ENSG00000095739			30251	protein-coding gene	gene with protein product		604444	"BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)"			8621228, 19758997	Standard	NM_012342		Approved	NMA	uc001iuj.1	Q13145	OTTHUMG00000017874	ENST00000375533.3:c.134A>C	10.37:g.28970244A>C	ENSP00000364683:p.Lys45Thr		29010250		Missense_Mutation	SNP	ENST00000375533.3	37	CCDS7162.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.224149	0.79576	.	.	ENSG00000095739	ENST00000375533;ENST00000542444	D	0.89875	-2.58	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.93367	0.7885	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.93817	0.7115	10	0.62326	D	0.03	.	15.6899	0.77442	1.0:0.0:0.0:0.0	.	45;45	Q13145;Q53G66	BAMBI_HUMAN;.	T	45	ENSP00000364683:K45T	ENSP00000364683:K45T	K	+	2	0	BAMBI	29010250	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	9.279000	0.95777	2.110000	0.64415	0.533000	0.62120	AAA		0.493	BAMBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047374.1	NM_012342		C	28970244	A	C	28970244	3	2	61	1	0	0	0	0	1	0	0	0	1307	14	1	4	140	4	BAMBI	10	28970244	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	621590	28970244	106564503	6677	14662										
BAMBI	25805	broad.mit.edu	37	chr10	28971076	28971076	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttggccctgaggatgcttCgaagtgaaaataagaggctg	14	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:28971076C>T	ENST00000375533.3	+	3	1085	c.529C>T	c.(529-531)Cga>Tga	p.R177*		NM_012342.2	NP_036474.1	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor	177					cell migration (GO:0016477)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell shape (GO:0008360)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R177*(1)		central_nervous_system(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	17						GAGGATGCTTCGAAGTGAAAA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											116	103	107					10																	28971076		2203	4300	6503	29011082	SO:0001587	stop_gained	25805			U23070	CCDS7162.1	10p12.3-p11.2	2013-07-23	2013-07-23		ENSG00000095739	ENSG00000095739			30251	protein-coding gene	gene with protein product		604444	"BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)"			8621228, 19758997	Standard	NM_012342		Approved	NMA	uc001iuj.1	Q13145	OTTHUMG00000017874	ENST00000375533.3:c.529C>T	10.37:g.28971076C>T	ENSP00000364683:p.Arg177*		29011082		Nonsense_Mutation	SNP	ENST00000375533.3	37	CCDS7162.1	.	.	.	.	.	.	.	.	.	.	C	40	8.302631	0.98750	.	.	ENSG00000095739	ENST00000375533;ENST00000542444	.	.	.	5.86	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7785	0.85558	0.274:0.726:0.0:0.0	.	.	.	.	X	177;164	.	ENSP00000364683:R177X	R	+	1	2	BAMBI	29011082	1.000000	0.71417	0.101000	0.21167	0.958000	0.62258	5.063000	0.64332	0.831000	0.34780	-0.808000	0.03180	CGA		0.507	BAMBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047374.1	NM_012342		T	28971076	C	T	28971076	4	4	61	1	0	0	0	0	0	1	0	0	1307	876	31	1	539	1	BAMBI	10	28971076	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	832	28971076	106563671	6678	14663										
LYZL1	84569	broad.mit.edu	37	chr10	29581548	29581548	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttccagatcaacagcttCgcgtggtgcagacgcggaaa	11	11	2	2	rs142250687	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29581548C>T	ENST00000375500.3	+	3	435	c.378C>T	c.(376-378)ttC>ttT	p.F126F		NM_032517.4	NP_115906.3	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	80					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.F126F(1)		central_nervous_system(1)|cervix(2)|large_intestine(2)|lung(5)|skin(1)	11		Breast(68;0.203)				TCAACAGCTTCGCGTGGTGCA	0.557													c|||	2	0.000399361	0	0	5008	,	,		18777	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10						T		2,4404	4.2+/-10.8	0,2,2201	168	136	147		378	0.1	0.1	10	dbSNP_134	147	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	LYZL1	NM_032517.4		0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538		126/195	29581548	7,12999	2203	4300	6503	29621554	SO:0001819	synonymous_variant	84569				CCDS31174.1	10p12.1	2004-08-02			ENSG00000120563	ENSG00000120563	3.2.1.1		30502	protein-coding gene	gene with protein product						12477932	Standard	XM_005252627		Approved	MGC33408, LYC2	uc001iul.3	Q6UWQ5	OTTHUMG00000017880	ENST00000375500.3:c.378C>T	10.37:g.29581548C>T			29621554	Q5T921|Q8WW16	Silent	SNP	ENST00000375500.3	37	CCDS31174.1																																																																																				0.557	LYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047381.1	NM_032517		T	29581548	C	T	29581548	2	4	61	1	0	0	0	0	0	0	0	1	9161	883	31	1		1	LYZL1	10	29581548	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	610472	29581548	105953199	6679	14664										
SVIL	6840	broad.mit.edu	37	chr10	29747377	29747377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttacctcgaagtcttcgtCggtgagatagatctcaagct	10	10	2	2	rs147020336		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29747377C>T	ENST00000355867.4	-	37	7296	c.6544G>A	c.(6544-6546)Gac>Aac	p.D2182N	PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.D2182N|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.D1756N|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.D1096N|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000455774.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2182	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.				cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.D2182N(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AAGTCTTCGTCGGTGAGATAG	0.597													C|||	1	0.000199681	8e-04	0	5008	,	,		16467	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						C	ASN/ASP,ASN/ASP	3,4403	6.2+/-15.9	0,3,2200	44	44	44		5266,6544	4.4	0.5	10	dbSNP_134	44	0,8600		0,0,4300	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	23,23	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging,probably-damaging	1756/1789,2182/2215	29747377	3,13003	2203	4300	6503	29787383	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6544G>A	10.37:g.29747377C>T	ENSP00000348128:p.Asp2182Asn		29787383	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847656	0.71603	6.81E-4	0.0	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.16324	2.46;2.47;2.47;2.35	4.39	4.39	0.52855	Villin headpiece (5);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.86343	2.81	0.80722	D	1	D;P;D	0.56746	0.971;0.943;0.977	P;P;P	0.52514	0.611;0.576;0.701	T	0.53947	-0.8366	10	0.72032	D	0.01	-13.2492	17.1971	0.86895	0.0:1.0:0.0:0.0	.	1096;1756;2182	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	N	1756;2182;2182;1096	ENSP00000364549:D1756N;ENSP00000364547:D2182N;ENSP00000348128:D2182N;ENSP00000445472:D1096N	ENSP00000348128:D2182N	D	-	1	0	SVIL	29787383	1.000000	0.71417	0.497000	0.27552	0.043000	0.13939	7.480000	0.81109	2.264000	0.75181	0.644000	0.83932	GAC		0.597	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29747377	C	T	29747377	3	4	61	1	0	0	0	0	1	0	0	0	15460	884	31	1	108	1	SVIL	10	29747377	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165829	29747377	105787370	6680	14665										
SVIL	6840	broad.mit.edu	37	chr10	29762810	29762810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccaccgtcatcagcgccGacgtgcccttctcactcacg	8	19	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29762810G>A	ENST00000355867.4	-	30	6238	c.5486C>T	c.(5485-5487)tCg>tTg	p.S1829L	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.S1829L|SVIL_ENST00000460007.1_5'UTR|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.S1403L|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.S743L	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1829					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.S1829L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CATCAGCGCCGACGTGCCCTT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	10											60	51	54					10																	29762810		2203	4300	6503	29802816	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5486C>T	10.37:g.29762810G>A	ENSP00000348128:p.Ser1829Leu		29802816	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	36	5.621673	0.96660	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.57436	0.4;2.27;2.27;0.4	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.74199	0.3685	M	0.85041	2.73	0.80722	D	1	D;P;D	0.71674	0.998;0.935;0.968	P;P;P	0.61070	0.883;0.463;0.506	T	0.79629	-0.1724	10	0.87932	D	0	-9.3097	18.8101	0.92054	0.0:0.0:1.0:0.0	.	743;1403;1829	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	L	1403;1829;1829;743	ENSP00000364549:S1403L;ENSP00000364547:S1829L;ENSP00000348128:S1829L;ENSP00000445472:S743L	ENSP00000348128:S1829L	S	-	2	0	SVIL	29802816	1.000000	0.71417	0.969000	0.41365	0.991000	0.79684	9.751000	0.98889	2.418000	0.82041	0.655000	0.94253	TCG		0.652	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29762810	G	A	29762810	3	1	61	1	0	0	0	0	1	0	0	0	15460	1059	37	1	1194	1	SVIL	10	29762810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15433	29762810	105771937	6681	14666										
SVIL	6840	broad.mit.edu	37	chr10	29782172	29782172	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggatcgaaaatgacatcGaagtcctcatccatctccac	6	12	2	1	rs376322653		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29782172G>A	ENST00000355867.4	-	21	4742	c.3990C>T	c.(3988-3990)ttC>ttT	p.F1330F	SVIL_ENST00000375398.2_Silent_p.F1330F|SVIL_ENST00000375400.3_Silent_p.F904F|SVIL_ENST00000538146.1_Silent_p.F122F|SVIL_ENST00000535393.1_Silent_p.F244F	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1330					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.F1330F(2)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AAATGACATCGAAGTCCTCAT	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	10											111	95	100					10																	29782172		2203	4300	6503	29822178	SO:0001819	synonymous_variant	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3990C>T	10.37:g.29782172G>A			29822178	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.478	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29782172	G	A	29782172	2	1	61	1	0	0	0	0	0	0	0	1	15460	1049	37	1		1	SVIL	10	29782172	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19362	29782172	105752575	6682	14667										
SVIL	6840	broad.mit.edu	37	chr10	29812595	29812595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttatggctgtctccttccCtggctcggttcaggatgggg	13	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29812595C>T	ENST00000355867.4	-	15	3700	c.2948G>A	c.(2947-2949)aGg>aAg	p.R983K	SVIL_ENST00000375398.2_Missense_Mutation_p.R983K|SVIL_ENST00000375400.3_Missense_Mutation_p.R557K|SVIL_ENST00000535393.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	983					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.R983K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GTCTCCTTCCCTGGCTCGGTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	10											139	123	128					10																	29812595		2203	4300	6503	29852601	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2948G>A	10.37:g.29812595C>T	ENSP00000348128:p.Arg983Lys		29852601	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	2.216	-0.379605	0.05000	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.11169	2.8;2.85;2.85	5.14	5.14	0.70334	.	0.534626	0.20892	N	0.083809	T	0.09598	0.0236	L	0.42245	1.32	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.08055	0.001;0.003	T	0.15321	-1.0441	9	.	.	.	-2.2724	8.9702	0.35901	0.0:0.7694:0.1501:0.0805	.	557;983	O95425-2;O95425	.;SVIL_HUMAN	K	557;983;983	ENSP00000364549:R557K;ENSP00000364547:R983K;ENSP00000348128:R983K	.	R	-	2	0	SVIL	29852601	0.021000	0.18746	0.958000	0.39756	0.098000	0.18820	0.687000	0.25407	2.553000	0.86117	0.563000	0.77884	AGG		0.537	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29812595	C	T	29812595	3	4	61	1	0	0	0	0	1	0	0	0	15460	681	24	3	3792	3	SVIL	10	29812595	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30423	29812595	105722152	6683	14668										
SVIL	6840	broad.mit.edu	37	chr10	29812760	29812760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaaggctgccaagcttgcGatttcagaatgcttctaact	8	11	2	1	rs148261163		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29812760G>A	ENST00000355867.4	-	15	3535	c.2783C>T	c.(2782-2784)tCg>tTg	p.S928L	SVIL_ENST00000375398.2_Missense_Mutation_p.S928L|SVIL_ENST00000375400.3_Missense_Mutation_p.S502L|SVIL_ENST00000535393.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	928					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.S928L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CCAAGCTTGCGATTTCAGAAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	157	143	148		1505,2783	5.6	0	10	dbSNP_134	148	0,8600		0,0,4300	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	145,145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	502/1789,928/2215	29812760	1,13005	2203	4300	6503	29852766	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2783C>T	10.37:g.29812760G>A	ENSP00000348128:p.Ser928Leu		29852766	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.552904	0.27739	2.27E-4	0.0	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.13307	2.6;2.62;2.62	5.57	5.57	0.84162	.	0.389110	0.26903	N	0.021912	T	0.16685	0.0401	M	0.64997	1.995	0.80722	D	1	P;B	0.34743	0.466;0.448	B;B	0.28011	0.071;0.085	T	0.02301	-1.1180	9	.	.	.	-4.1372	17.7354	0.88391	0.0:0.0:1.0:0.0	.	502;928	O95425-2;O95425	.;SVIL_HUMAN	L	502;928;928	ENSP00000364549:S502L;ENSP00000364547:S928L;ENSP00000348128:S928L	.	S	-	2	0	SVIL	29852766	0.937000	0.31787	0.026000	0.17262	0.059000	0.15707	5.949000	0.70257	2.622000	0.88805	0.655000	0.94253	TCG		0.453	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29812760	G	A	29812760	3	1	61	1	0	0	0	0	1	0	0	0	15460	1059	37	1	3957	1	SVIL	10	29812760	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165	29812760	105721987	6684	14669										
SVIL	6840	broad.mit.edu	37	chr10	29812951	29812951	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggaatgagctttccactCtgcacctggaaggacacagt	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29812951C>A	ENST00000355867.4	-	15	3344	c.2592G>T	c.(2590-2592)caG>caT	p.Q864H	SVIL_ENST00000375398.2_Missense_Mutation_p.Q864H|SVIL_ENST00000375400.3_Missense_Mutation_p.Q438H|SVIL_ENST00000535393.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	864					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.Q864H(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GCTTTCCACTCTGCACCTGGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											33	34	33					10																	29812951		2176	4279	6455	29852957	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2592G>T	10.37:g.29812951C>A	ENSP00000348128:p.Gln864His		29852957	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145943	0.57044	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.52057	0.68;0.68;0.68	5.32	-6.27	0.02026	.	0.158708	0.56097	D	0.000025	T	0.60077	0.2241	M	0.71581	2.175	0.51767	D	0.999937	D;D	0.69078	0.996;0.997	D;P	0.63597	0.916;0.907	T	0.68258	-0.5456	9	.	.	.	-18.5026	18.8742	0.92328	0.0:0.6653:0.0:0.3347	.	438;864	O95425-2;O95425	.;SVIL_HUMAN	H	438;864;864	ENSP00000364549:Q438H;ENSP00000364547:Q864H;ENSP00000348128:Q864H	.	Q	-	3	2	SVIL	29852957	0.310000	0.24527	0.818000	0.32626	0.924000	0.55760	-0.954000	0.03873	-1.224000	0.02581	-0.302000	0.09304	CAG		0.418	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29812951	C	A	29812951	3	1	61	1	0	0	0	0	1	0	0	0	15460	912	32	2	4148	2	SVIL	10	29812951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191	29812951	105721796	6685	14670										
SVIL	6840	broad.mit.edu	37	chr10	29840027	29840027	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtcgccttctttctgctTtgtaccttgcaattctttcg	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:29840027T>G	ENST00000355867.4	-	6	1078	c.326A>C	c.(325-327)aAa>aCa	p.K109T	SVIL_ENST00000375398.2_Missense_Mutation_p.K109T|SVIL_ENST00000375400.3_Missense_Mutation_p.K109T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	109	Interaction with MYLK. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.K109T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TCTTTCTGCTTTGTACCTTGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	10											187	158	168					10																	29840027		2203	4300	6503	29880033	SO:0001583	missense	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.326A>C	10.37:g.29840027T>G	ENSP00000348128:p.Lys109Thr		29880033	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.011020	0.75046	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.54279	0.58;0.58;0.58	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.72087	0.3417	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73946	-0.3822	9	.	.	.	-27.2715	15.4477	0.75243	0.0:0.0:0.0:1.0	.	109;109	O95425-2;O95425	.;SVIL_HUMAN	T	109	ENSP00000364549:K109T;ENSP00000364547:K109T;ENSP00000348128:K109T	.	K	-	2	0	SVIL	29880033	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	7.063000	0.76714	2.050000	0.60909	0.482000	0.46254	AAA		0.542	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29840027	T	G	29840027	3	3	61	1	0	0	0	0	1	0	0	0	15460	1841	64	4	6450	4	SVIL	10	29840027	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27076	29840027	105694720	6686	14671										
KIAA1462	57608	broad.mit.edu	37	chr10	30315051	30315051	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggcaccagaagtcttgAtccatgctcttctccttttg	8	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:30315051A>C	ENST00000375377.1	-	3	4127	c.4026T>G	c.(4024-4026)gaT>gaG	p.D1342E		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	1342					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.D1342E(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AGAAGTCTTGATCCATGCTCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											132	129	130					10																	30315051		2041	4201	6242	30355057	SO:0001583	missense	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.4026T>G	10.37:g.30315051A>C	ENSP00000364526:p.Asp1342Glu		30355057	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.776046	0.31411	.	.	ENSG00000165757	ENST00000375377	T	0.11604	2.76	5.6	-11.2	0.00127	.	1.294630	0.05105	N	0.487804	T	0.08670	0.0215	L	0.46157	1.445	0.09310	N	1	B	0.21606	0.058	B	0.22152	0.038	T	0.25502	-1.0130	10	0.40728	T	0.16	-0.0357	9.555	0.39332	0.1124:0.2575:0.545:0.085	.	1342	Q9P266	K1462_HUMAN	E	1342	ENSP00000364526:D1342E	ENSP00000364526:D1342E	D	-	3	2	KIAA1462	30355057	0.000000	0.05858	0.000000	0.03702	0.286000	0.27126	-1.941000	0.01542	-1.869000	0.01141	-0.250000	0.11733	GAT		0.507	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		C	30315051	A	C	30315051	3	2	61	1	0	0	0	0	1	0	0	0	8255	330	12	4	61	4	KIAA1462	10	30315051	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	475024	30315051	105219696	6687	14672										
KIAA1462	57608	broad.mit.edu	37	chr10	30316882	30316882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtagggaatgctgtgtgcGtctgagcttcggaggcagca	17	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:30316882G>A	ENST00000375377.1	-	3	2296	c.2195C>T	c.(2194-2196)aCg>aTg	p.T732M		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	732					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.T732M(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TGCTGTGTGCGTCTGAGCTTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10											57	60	59					10																	30316882		2118	4243	6361	30356888	SO:0001583	missense	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.2195C>T	10.37:g.30316882G>A	ENSP00000364526:p.Thr732Met		30356888	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	G	9.743	1.165310	0.21538	.	.	ENSG00000165757	ENST00000375377	T	0.11277	2.79	5.52	-11.0	0.00169	.	3.447750	0.00604	N	0.000387	T	0.02807	0.0084	N	0.02011	-0.69	0.09310	N	1	B	0.22604	0.072	B	0.13407	0.009	T	0.38200	-0.9672	10	0.38643	T	0.18	2.1835	1.9526	0.03370	0.1535:0.2773:0.3126:0.2566	.	732	Q9P266	K1462_HUMAN	M	732	ENSP00000364526:T732M	ENSP00000364526:T732M	T	-	2	0	KIAA1462	30356888	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.017000	0.03630	-2.348000	0.00619	-0.339000	0.08088	ACG		0.577	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		A	30316882	G	A	30316882	3	1	61	1	0	0	0	0	1	0	0	0	8255	1145	40	1	1892	1	KIAA1462	10	30316882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1831	30316882	105217865	6688	14673										
KIAA1462	57608	broad.mit.edu	37	chr10	30318503	30318503	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctccctaatttccttgGctggttccagctttccaggc	8	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:30318503G>T	ENST00000375377.1	-	3	675	c.574C>A	c.(574-576)Cca>Aca	p.P192T		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	192					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.P192T(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AATTTCCTTGGCTGGTTCCAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											198	195	196					10																	30318503		2061	4199	6260	30358509	SO:0001583	missense	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.574C>A	10.37:g.30318503G>T	ENSP00000364526:p.Pro192Thr		30358509	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	G	7.978	0.750474	0.15778	.	.	ENSG00000165757	ENST00000375377	T	0.19806	2.12	5.17	2.23	0.28157	.	0.278881	0.34460	N	0.003947	T	0.17450	0.0419	L	0.56769	1.78	0.40150	D	0.976939	P	0.35793	0.521	B	0.33121	0.158	T	0.04140	-1.0974	10	0.62326	D	0.03	-5.5754	4.7766	0.13182	0.0719:0.1326:0.5211:0.2744	.	192	Q9P266	K1462_HUMAN	T	192	ENSP00000364526:P192T	ENSP00000364526:P192T	P	-	1	0	KIAA1462	30358509	1.000000	0.71417	0.009000	0.14445	0.041000	0.13682	4.094000	0.57721	0.171000	0.19730	-0.175000	0.13238	CCA		0.473	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30318503	G	T	30318503	3	4	61	1	0	0	0	0	1	0	0	0	8255	1203	42	2	3513	2	KIAA1462	10	30318503	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1621	30318503	105216244	6689	14674										
MTPAP	55149	broad.mit.edu	37	chr10	30611410	30611410	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcattgtaagggagaaatTtgtaatccatgcaccaggaa	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:30611410T>G	ENST00000263063.4	-	6	1172	c.1129A>C	c.(1129-1131)Aat>Cat	p.N377H	MTPAP_ENST00000488290.1_5'UTR|MTPAP_ENST00000358107.4_Missense_Mutation_p.N507H	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	377					cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)	p.N377H(1)|p.N507H(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						AGGGAGAAATTTGTAATCCAT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	10											126	121	123					10																	30611410		2203	4300	6503	30651416	SO:0001583	missense	55149			AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"TUTase1"	613669	"PAP associated domain containing 1"	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.1129A>C	10.37:g.30611410T>G	ENSP00000263063:p.Asn377His		30651416	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Missense_Mutation	SNP	ENST00000263063.4	37	CCDS7165.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.626390	0.87560	.	.	ENSG00000107951	ENST00000358107;ENST00000263063	T;T	0.55930	0.49;0.49	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.77824	0.4188	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.83105	-0.0126	10	0.87932	D	0	-31.8261	15.7781	0.78240	0.0:0.0:0.0:1.0	.	507;377	Q9NVV4-2;Q9NVV4	.;PAPD1_HUMAN	H	507;377	ENSP00000350820:N507H;ENSP00000263063:N377H	ENSP00000263063:N377H	N	-	1	0	MTPAP	30651416	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	7.632000	0.83247	2.187000	0.69744	0.372000	0.22366	AAT		0.448	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109		G	30611410	T	G	30611410	3	3	61	1	0	0	0	0	1	0	0	0	9986	1841	64	4	635	4	MTPAP	10	30611410	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	292907	30611410	104923337	6690	14675										
ZNF438	220929	broad.mit.edu	37	chr10	31137538	31137538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggctgcagttcactgggcGcaggctcagtgctgatcaca	13	12	3	1	rs147456266		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:31137538G>A	ENST00000361310.3	-	6	2125	c.1796C>T	c.(1795-1797)gCg>gTg	p.A599V	ZNF438_ENST00000538351.2_Missense_Mutation_p.A550V|ZNF438_ENST00000442986.1_Missense_Mutation_p.A599V|ZNF438_ENST00000331737.6_Missense_Mutation_p.A589V|ZNF438_ENST00000413025.1_Missense_Mutation_p.A599V|ZNF438_ENST00000375311.1_Missense_Mutation_p.A163V|ZNF438_ENST00000452305.1_Missense_Mutation_p.A589V|ZNF438_ENST00000444692.2_Missense_Mutation_p.A589V|ZNF438_ENST00000436087.2_Missense_Mutation_p.A599V			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	599					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A599V(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TTCACTGGGCGCAGGCTCAGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	129	116	120		1796,1796,1796,1649,1766,1766,1796	4.3	0	10	dbSNP_134	120	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	ZNF438	NM_001143766.1,NM_001143767.1,NM_001143768.1,NM_001143769.1,NM_001143770.1,NM_001143771.1,NM_182755.2	64,64,64,64,64,64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	599/829,599/829,599/829,550/780,589/819,589/819,599/829	31137538	1,13005	2203	4300	6503	31177544	SO:0001583	missense	220929			AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"Zinc fingers, C2H2-type"	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.1796C>T	10.37:g.31137538G>A	ENSP00000354663:p.Ala599Val		31177544	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	G	8.996	0.978803	0.18812	2.27E-4	0.0	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896;ENST00000375311	T;T;T;T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15	5.24	4.31	0.51392	.	0.279307	0.41938	D	0.000794	T	0.02848	0.0085	N	0.08118	0	0.09310	N	1	P;P	0.42039	0.53;0.769	B;B	0.28305	0.025;0.088	T	0.41395	-0.9511	10	0.33141	T	0.24	-3.1	5.1161	0.14834	0.0795:0.1469:0.6214:0.1522	.	599;589	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	V	589;599;599;599;599;589;589;550;318;163	ENSP00000333571:A589V;ENSP00000354663:A599V;ENSP00000406934:A599V;ENSP00000412363:A599V;ENSP00000387546:A599V;ENSP00000413060:A589V;ENSP00000410898:A589V;ENSP00000445461:A550V;ENSP00000364460:A163V	ENSP00000333571:A589V	A	-	2	0	ZNF438	31177544	0.466000	0.25823	0.008000	0.14137	0.016000	0.09150	3.082000	0.50128	1.162000	0.42619	0.467000	0.42956	GCG		0.493	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		A	31137538	G	A	31137538	3	1	61	1	0	0	0	0	1	0	0	0	17949	1087	38	1	698	1	ZNF438	10	31137538	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	526128	31137538	104397209	6691	14676										
ARHGAP12	94134	broad.mit.edu	37	chr10	32106798	32106798	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaattagcagttctgttCcttgacgagttttcagcttt	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32106798C>A	ENST00000344936.2	-	13	1883	c.1649G>T	c.(1648-1650)gGa>gTa	p.G550V	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.G498V|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.G545V|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.G520V|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.G498V|ARHGAP12_ENST00000492028.1_5'UTR	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	550	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.G550V(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				CAGTTCTGTTCCTTGACGAGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											99	100	99					10																	32106798		2202	4299	6501	32146804	SO:0001583	missense	94134			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1649G>T	10.37:g.32106798C>A	ENSP00000345808:p.Gly550Val		32146804	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491799	0.84962	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39	5.31	5.31	0.75309	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.047451	0.85682	D	0.000000	D	0.90515	0.7028	M	0.81239	2.535	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.91407	0.5148	10	0.87932	D	0	.	19.3322	0.94295	0.0:1.0:0.0:0.0	.	503;520;520;545;550;498	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	V	498;520;550;545;498	ENSP00000310984:G498V;ENSP00000364399:G520V;ENSP00000345808:G550V;ENSP00000379448:G545V;ENSP00000364394:G498V	ENSP00000310984:G498V	G	-	2	0	ARHGAP12	32146804	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.079000	0.76829	2.632000	0.89209	0.655000	0.94253	GGA		0.338	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			A	32106798	C	A	32106798	3	1	61	1	0	0	0	0	1	0	0	0	865	855	30	2	923	2	ARHGAP12	10	32106798	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	969260	32106798	103427949	6692	14677										
ARHGAP12	94134	broad.mit.edu	37	chr10	32109327	32109327	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtattacctcaaatacattCtttttgctggatttatcctt	4	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32109327C>A	ENST00000344936.2	-	12	1854	c.1620G>T	c.(1618-1620)aaG>aaT	p.K540N	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.K488N|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.K535N|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.K510N|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.K488N|ARHGAP12_ENST00000492028.1_5'UTR	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	540	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.K540N(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				CAAATACATTCTTTTTGCTGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											95	87	89					10																	32109327		2203	4300	6503	32149333	SO:0001583	missense	94134			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1620G>T	10.37:g.32109327C>A	ENSP00000345808:p.Lys540Asn		32149333	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985236	0.74474	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	5.74	5.74	0.90152	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.90424	0.7002	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0;0.999	D	0.91420	0.5158	10	0.87932	D	0	.	10.3411	0.43879	0.0:0.8546:0.0:0.1454	.	493;510;510;535;540;488	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	N	488;510;540;535;488	ENSP00000310984:K488N;ENSP00000364399:K510N;ENSP00000345808:K540N;ENSP00000379448:K535N;ENSP00000364394:K488N	ENSP00000310984:K488N	K	-	3	2	ARHGAP12	32149333	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.815000	0.38981	2.709000	0.92574	0.591000	0.81541	AAG		0.348	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			A	32109327	C	A	32109327	3	1	61	1	0	0	0	0	1	0	0	0	865	912	32	2	956	2	ARHGAP12	10	32109327	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2529	32109327	103425420	6693	14678										
ARHGAP12	94134	broad.mit.edu	37	chr10	32132487	32132487	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcctacttttaattatttCtctttgctgctgggatgaag	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32132487C>A	ENST00000344936.2	-	7	1432	c.1198G>T	c.(1198-1200)Gaa>Taa	p.E400*	ARHGAP12_ENST00000375245.4_Nonsense_Mutation_p.E353*|ARHGAP12_ENST00000396144.4_Nonsense_Mutation_p.E400*|ARHGAP12_ENST00000375250.5_Nonsense_Mutation_p.E400*|ARHGAP12_ENST00000311380.4_Nonsense_Mutation_p.E353*	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	400					morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.E400*(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				TTAATTATTTCTCTTTGCTGC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											75	73	74					10																	32132487		2203	4300	6503	32172493	SO:0001587	stop_gained	94134			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1198G>T	10.37:g.32132487C>A	ENSP00000345808:p.Glu400*		32172493	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Nonsense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.591420|9.591420	0.99213|0.99213	.|.	.|.	ENSG00000165322|ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245|ENST00000454919	.|T	.|0.37411	.|1.2	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	0.100457|.	0.64402|.	D|.	0.000003|.	.|T	.|0.47395	.|0.1443	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.17048	.|-1.0382	.|5	0.21540|0.21540	T|T	0.41|0.41	.|.	18.9171|18.9171	0.92510|0.92510	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	353;400;400;400;353|75	.|ENSP00000398050:R75I	ENSP00000310984:E353X|ENSP00000398050:R75I	E|R	-|-	1|2	0|0	ARHGAP12|ARHGAP12	32172493|32172493	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.477000|6.477000	0.73591|0.73591	2.461000|2.461000	0.83175|0.83175	0.563000|0.563000	0.77884|0.77884	GAA|AGA		0.348	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			A	32132487	C	A	32132487	4	1	61	1	0	0	0	0	0	1	0	0	865	922	32	2	1398	2	ARHGAP12	10	32132487	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23160	32132487	103402260	6694	14679										
ARHGAP12	94134	broad.mit.edu	37	chr10	32150552	32150552	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggttagcatagacaggaGaatctggccttccttgattt	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32150552G>T	ENST00000344936.2	-	4	953	c.719C>A	c.(718-720)tCt>tAt	p.S240Y	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.S240Y|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.S240Y|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.S240Y|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.S240Y	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	240					morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.S240Y(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				ATAGACAGGAGAATCTGGCCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											73	76	75					10																	32150552		2203	4300	6503	32190558	SO:0001583	missense	94134			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.719C>A	10.37:g.32150552G>T	ENSP00000345808:p.Ser240Tyr		32190558	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588471	0.86851	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.10960	2.85;2.82;2.9;2.91;2.85	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.26376	0.0644	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999	T	0.00668	-1.1618	10	0.72032	D	0.01	.	19.85	0.96736	0.0:0.0:1.0:0.0	.	240;240;240;240;240;240	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	Y	240	ENSP00000310984:S240Y;ENSP00000364399:S240Y;ENSP00000345808:S240Y;ENSP00000379448:S240Y;ENSP00000364394:S240Y	ENSP00000310984:S240Y	S	-	2	0	ARHGAP12	32190558	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.025000	0.93694	2.697000	0.92050	0.563000	0.77884	TCT		0.388	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			T	32150552	G	T	32150552	3	4	61	1	0	0	0	0	1	0	0	0	865	942	33	2	1889	2	ARHGAP12	10	32150552	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18065	32150552	103384195	6695	14680										
KIF5B	3799	broad.mit.edu	37	chr10	32307309	32307309	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtgtaaagtctgaagttCttttgccttggattaagaac	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32307309C>A	ENST00000302418.4	-	22	2831	c.2374G>T	c.(2374-2376)Gaa>Taa	p.E792*	KIF5B_ENST00000493889.1_Intron	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	792					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E792*(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				GTCTGAAGTTCTTTTGCCTTG	0.373			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Nonsense(1)	large_intestine(1)	10											138	135	136					10																	32307309		2203	4300	6503	32347315	SO:0001587	stop_gained	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2374G>T	10.37:g.32307309C>A	ENSP00000307078:p.Glu792*		32347315	A0AVB2|Q5VZ85	Nonsense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	44	11.134787	0.99521	.	.	ENSG00000170759	ENST00000302418	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	18.8765	0.92338	0.0:1.0:0.0:0.0	.	.	.	.	X	792	.	ENSP00000307078:E792X	E	-	1	0	KIF5B	32347315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.752000	0.85141	2.532000	0.85374	0.591000	0.81541	GAA		0.373	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32307309	C	A	32307309	4	1	61	1	0	0	0	0	0	1	0	0	8327	922	32	2	533	2	KIF5B	10	32307309	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156757	32307309	103227438	6696	14681										
KIF5B	3799	broad.mit.edu	37	chr10	32310026	32310026	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctgtttttgatgagtttCtctatggctctggatctgct	10	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32310026C>T	ENST00000302418.4	-	19	2585	c.2128G>A	c.(2128-2130)Gaa>Aaa	p.E710K	KIF5B_ENST00000493889.1_5'Flank	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	710					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E710K(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TGATGAGTTTCTCTATGGCTC	0.328			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Missense(1)	large_intestine(1)	10											163	160	161					10																	32310026		2202	4299	6501	32350032	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2128G>A	10.37:g.32310026C>T	ENSP00000307078:p.Glu710Lys		32350032	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	35	5.529130	0.96446	.	.	ENSG00000170759	ENST00000302418	T	0.80304	-1.36	5.36	5.36	0.76844	.	0.048141	0.85682	D	0.000000	D	0.88243	0.6384	M	0.86343	2.81	0.80722	D	1	P	0.45176	0.852	P	0.49597	0.616	D	0.90163	0.4229	10	0.72032	D	0.01	.	19.0712	0.93138	0.0:1.0:0.0:0.0	.	710	P33176	KINH_HUMAN	K	710	ENSP00000307078:E710K	ENSP00000307078:E710K	E	-	1	0	KIF5B	32350032	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.503000	0.84419	0.591000	0.81541	GAA		0.328	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		T	32310026	C	T	32310026	3	4	61	1	0	0	0	0	1	0	0	0	8327	922	32	3	791	3	KIF5B	10	32310026	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2717	32310026	103224721	6697	14682										
KIF5B	3799	broad.mit.edu	37	chr10	32311787	32311787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataacatacttgagagatacGaagctgacatgctgctaact	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32311787G>A	ENST00000302418.4	-	16	2360	c.1903C>T	c.(1903-1905)Cgt>Tgt	p.R635C	KIF5B_ENST00000493889.1_5'Flank	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	635					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R635C(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TGAGAGATACGAAGCTGACAT	0.318			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Missense(1)	large_intestine(1)	10											219	188	198					10																	32311787		2201	4298	6499	32351793	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1903C>T	10.37:g.32311787G>A	ENSP00000307078:p.Arg635Cys		32351793	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806249	0.90623	.	.	ENSG00000170759	ENST00000302418	D	0.87809	-2.3	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.87857	0.6283	L	0.54323	1.7	0.80722	D	1	P	0.44776	0.843	P	0.44860	0.462	D	0.88797	0.3282	10	0.66056	D	0.02	.	19.6656	0.95891	0.0:0.0:1.0:0.0	.	635	P33176	KINH_HUMAN	C	635	ENSP00000307078:R635C	ENSP00000307078:R635C	R	-	1	0	KIF5B	32351793	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	9.813000	0.99286	2.713000	0.92767	0.455000	0.32223	CGT		0.318	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32311787	G	A	32311787	3	1	61	1	0	0	0	0	1	0	0	0	8327	1058	37	1	1028	1	KIF5B	10	32311787	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1761	32311787	103222960	6698	14683										
KIF5B	3799	broad.mit.edu	37	chr10	32323684	32323684	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcaggatcttatttttttCtttttctttttcatacttct	3	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32323684C>A	ENST00000302418.4	-	11	1502	c.1045G>T	c.(1045-1047)Gaa>Taa	p.E349*		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	349					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E349*(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TTATTTTTTTCTTTTTCTTTT	0.348			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Nonsense(1)	large_intestine(1)	10											63	61	62					10																	32323684		2203	4300	6503	32363690	SO:0001587	stop_gained	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1045G>T	10.37:g.32323684C>A	ENSP00000307078:p.Glu349*		32363690	A0AVB2|Q5VZ85	Nonsense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	43	9.839737	0.99276	.	.	ENSG00000170759	ENST00000302418	.	.	.	5.26	5.26	0.73747	.	0.050634	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	18.8538	0.92242	0.0:1.0:0.0:0.0	.	.	.	.	X	349	.	ENSP00000307078:E349X	E	-	1	0	KIF5B	32363690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.750000	0.85110	2.435000	0.82474	0.563000	0.77884	GAA		0.348	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32323684	C	A	32323684	4	1	61	1	0	0	0	0	0	1	0	0	8327	922	32	2	1906	2	KIF5B	10	32323684	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11897	32323684	103211063	6699	14684										
KIF5B	3799	broad.mit.edu	37	chr10	32324579	32324579	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgtcattttactatctCgatatggaacatatgtctgc	6	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32324579C>T	ENST00000302418.4	-	10	1290	c.833G>A	c.(832-834)cGa>cAa	p.R278Q		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	278	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R278Q(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TTTACTATCTCGATATGGAAC	0.313			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Missense(1)	large_intestine(1)	10											88	83	85					10																	32324579		2203	4298	6501	32364585	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.833G>A	10.37:g.32324579C>T	ENSP00000307078:p.Arg278Gln		32364585	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	35	5.477991	0.96291	.	.	ENSG00000170759	ENST00000302418	D	0.85339	-1.97	5.67	5.67	0.87782	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	H	0.99104	4.43	0.80722	D	1	D	0.76494	0.999	D	0.65323	0.934	D	0.97604	1.0125	10	0.87932	D	0	.	19.7723	0.96370	0.0:1.0:0.0:0.0	.	278	P33176	KINH_HUMAN	Q	278	ENSP00000307078:R278Q	ENSP00000307078:R278Q	R	-	2	0	KIF5B	32364585	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.750000	0.85110	2.670000	0.90874	0.650000	0.86243	CGA		0.313	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		T	32324579	C	T	32324579	3	4	61	1	0	0	0	0	1	0	0	0	8327	884	31	1	2122	1	KIF5B	10	32324579	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	895	32324579	103210168	6700	14685										
KIF5B	3799	broad.mit.edu	37	chr10	32326502	32326502	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctatggtatccataacttCatctggactacatacaaaac	4	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:32326502C>T	ENST00000302418.4	-	7	989	c.532G>A	c.(532-534)Gaa>Aaa	p.E178K		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	178	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E178K(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TCCATAACTTCATCTGGACTA	0.333			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Missense(1)	large_intestine(1)	10											140	120	127					10																	32326502		2202	4300	6502	32366508	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.532G>A	10.37:g.32326502C>T	ENSP00000307078:p.Glu178Lys		32366508	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	35	5.511103	0.96386	.	.	ENSG00000170759	ENST00000302418	T	0.75260	-0.92	5.38	5.38	0.77491	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.89455	0.6720	M	0.91561	3.22	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.91369	0.5118	10	0.87932	D	0	.	19.4918	0.95052	0.0:1.0:0.0:0.0	.	178	P33176	KINH_HUMAN	K	178	ENSP00000307078:E178K	ENSP00000307078:E178K	E	-	1	0	KIF5B	32366508	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.811000	0.86092	2.666000	0.90696	0.650000	0.86243	GAA		0.333	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		T	32326502	C	T	32326502	3	4	61	1	0	0	0	0	1	0	0	0	8327	835	29	3	2435	3	KIF5B	10	32326502	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1923	32326502	103208245	6701	14686										
C10orf68	79741	broad.mit.edu	37	chr10	33165299	33165299	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgctgctgcccgaaaatCtgtaccacacccatactttt	5	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:33165299C>A	ENST00000375030.2	+	23	2360	c.1742C>A	c.(1741-1743)tCt>tAt	p.S581Y	C10orf68_ENST00000375028.3_Missense_Mutation_p.S626Y|C10orf68_ENST00000375025.4_Missense_Mutation_p.S686Y			Q9H943	CJ068_HUMAN		622								p.S622Y(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						GCCCGAAAATCTGTACCACAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											78	76	77					10																	33165299		2203	4300	6503	33205305	SO:0001583	missense	79741																														ENST00000375030.2:c.1742C>A	10.37:g.33165299C>A	ENSP00000364170:p.Ser581Tyr		33205305	B0QZ71|Q08AN7|Q8N7T7	Missense_Mutation	SNP	ENST00000375030.2	37		.	.	.	.	.	.	.	.	.	.	.	9.703	1.154941	0.21371	.	.	ENSG00000150076	ENST00000302316;ENST00000375030;ENST00000375028;ENST00000375025;ENST00000375037	T;T;T;T	0.31510	1.51;1.5;1.49;1.49	3.62	0.681	0.17986	.	.	.	.	.	T	0.23611	0.0571	L	0.40543	1.245	0.09310	N	1	P;P;P;P	0.49090	0.851;0.919;0.919;0.851	B;B;B;B	0.44224	0.444;0.444;0.444;0.444	T	0.15752	-1.0426	9	0.87932	D	0	.	3.0301	0.06104	0.2138:0.5518:0.0:0.2344	.	603;622;626;581	B4DX58;Q9H943;A2A3B4;A2A3D6	.;CJ068_HUMAN;.;.	Y	622;581;626;686;598	ENSP00000303710:S622Y;ENSP00000364170:S581Y;ENSP00000364168:S626Y;ENSP00000364165:S686Y	ENSP00000303710:S622Y	S	+	2	0	C10orf68	33205305	0.009000	0.17119	0.004000	0.12327	0.035000	0.12851	0.085000	0.14912	0.147000	0.19030	0.655000	0.94253	TCT		0.313	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000313999.2			A	33165299	C	A	33165299	3	1	61	1	0	0	0	0	1	0	0	0	1617	913	32	2	1943	2	C10orf68	10	33165299	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	838797	33165299	102369448	6702	14687										
PARD3	56288	broad.mit.edu	37	chr10	34620159	34620159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattatccgcggccgtggacGatggaaaggaatatccccat	12	10	0	0	rs566752362		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:34620159G>A	ENST00000374789.3	-	19	3053	c.2728C>T	c.(2728-2730)Cgt>Tgt	p.R910C	PARD3_ENST00000346874.4_Missense_Mutation_p.R910C|PARD3_ENST00000374773.1_Missense_Mutation_p.R877C|PARD3_ENST00000544292.1_Missense_Mutation_p.R623C|PARD3_ENST00000374794.3_Missense_Mutation_p.R835C|PARD3_ENST00000545260.1_Missense_Mutation_p.R820C|PARD3_ENST00000466092.1_5'UTR|PARD3_ENST00000374776.1_Missense_Mutation_p.R864C|PARD3_ENST00000340077.5_Missense_Mutation_p.R907C|PARD3_ENST00000350537.4_Missense_Mutation_p.R864C|PARD3_ENST00000545693.1_Missense_Mutation_p.R894C|PARD3_ENST00000374788.3_Missense_Mutation_p.R907C|PARD3_ENST00000374790.3_Missense_Mutation_p.R850C	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	910	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R910C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GGCCGTGGACGATGGAAAGGA	0.517													G|||	1	0.000199681	8e-04	0	5008	,	,		14480	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											115	101	106					10																	34620159		2203	4300	6503	34660165	SO:0001583	missense	56288			AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2728C>T	10.37:g.34620159G>A	ENSP00000363921:p.Arg910Cys		34660165	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	37	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756512	0.89843	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292	T;T;T;T;T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.65544	0.2701	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.998;0.999;0.999;0.999;1.0;0.999;0.995;0.991;0.998;0.999;1.0;0.998;1.0;1.0	T	0.68465	-0.5401	10	0.87932	D	0	.	19.8904	0.96928	0.0:0.0:1.0:0.0	.	835;820;864;864;894;910;907;910;850;894;877;907;864;876;623	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	C	894;820;910;907;910;835;864;850;864;907;877;623	ENSP00000443147:R894C;ENSP00000440857:R820C;ENSP00000363921:R910C;ENSP00000363920:R907C;ENSP00000340591:R910C;ENSP00000363926:R835C;ENSP00000311986:R864C;ENSP00000363922:R850C;ENSP00000363908:R864C;ENSP00000341844:R907C;ENSP00000363905:R877C;ENSP00000444429:R623C	ENSP00000341844:R907C	R	-	1	0	PARD3	34660165	1.000000	0.71417	0.987000	0.45799	0.979000	0.70002	3.633000	0.54295	2.697000	0.92050	0.650000	0.86243	CGT		0.517	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34620159	G	A	34620159	3	1	61	1	0	0	0	0	1	0	0	0	11474	1058	37	1	1405	1	PARD3	10	34620159	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1454860	34620159	100914588	6703	14688										
PARD3	56288	broad.mit.edu	37	chr10	34673118	34673118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaatgcaatcattctcacGaaaaagattttcatgttcag	6	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:34673118G>A	ENST00000374789.3	-	8	1280	c.955C>T	c.(955-957)Cgt>Tgt	p.R319C	PARD3_ENST00000346874.4_Missense_Mutation_p.R319C|PARD3_ENST00000374773.1_Missense_Mutation_p.R319C|PARD3_ENST00000544292.1_Missense_Mutation_p.R49C|PARD3_ENST00000374794.3_Missense_Mutation_p.R275C|PARD3_ENST00000545260.1_Missense_Mutation_p.R275C|PARD3_ENST00000374776.1_Missense_Mutation_p.R319C|PARD3_ENST00000340077.5_Missense_Mutation_p.R319C|PARD3_ENST00000350537.4_Missense_Mutation_p.R319C|PARD3_ENST00000545693.1_Missense_Mutation_p.R319C|PARD3_ENST00000374788.3_Missense_Mutation_p.R319C|PARD3_ENST00000374790.3_Missense_Mutation_p.R275C	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	319	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R319C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				TCATTCTCACGAAAAAGATTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											180	159	166					10																	34673118		2203	4300	6503	34713124	SO:0001583	missense	56288			AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.955C>T	10.37:g.34673118G>A	ENSP00000363921:p.Arg319Cys		34713124	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	37	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905739	0.52333	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292	T;T;T;T;T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.98	5.98	0.97165	PDZ/DHR/GLGF (3);	0.301676	0.41500	D	0.000872	T	0.24275	0.0588	N	0.24115	0.695	0.38215	D	0.940595	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.10296	0.0;0.0;0.0;0.001;0.0;0.001;0.001;0.0;0.0;0.001;0.003;0.003;0.0;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.12837	0.001;0.0;0.001;0.002;0.001;0.001;0.002;0.001;0.0;0.0;0.002;0.008;0.003;0.002	T	0.04635	-1.0937	10	0.46703	T	0.11	.	15.5733	0.76356	0.0673:0.0:0.9327:0.0	.	275;275;319;319;319;319;319;319;275;319;319;319;319;49	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.	C	319;275;319;319;319;275;319;275;319;319;319;49	ENSP00000443147:R319C;ENSP00000440857:R275C;ENSP00000363921:R319C;ENSP00000363920:R319C;ENSP00000340591:R319C;ENSP00000363926:R275C;ENSP00000311986:R319C;ENSP00000363922:R275C;ENSP00000363908:R319C;ENSP00000341844:R319C;ENSP00000363905:R319C;ENSP00000444429:R49C	ENSP00000341844:R319C	R	-	1	0	PARD3	34713124	1.000000	0.71417	0.958000	0.39756	0.725000	0.41563	6.186000	0.72026	2.835000	0.97688	0.650000	0.86243	CGT		0.378	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34673118	G	A	34673118	3	1	61	1	0	0	0	0	1	0	0	0	11474	1058	37	1	3222	1	PARD3	10	34673118	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52959	34673118	100861629	6704	14689										
CUL2	8453	broad.mit.edu	37	chr10	35327979	35327979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtaggtattttcgacatCgaatttcttcatcttttaat	6	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:35327979C>T	ENST00000374748.1	-	10	1059	c.746G>A	c.(745-747)cGa>cAa	p.R249Q	CUL2_ENST00000374746.1_Missense_Mutation_p.R249Q|CUL2_ENST00000374742.1_Missense_Mutation_p.R249Q|CUL2_ENST00000602371.1_Missense_Mutation_p.R192Q|CUL2_ENST00000374749.3_Missense_Mutation_p.R249Q|CUL2_ENST00000374751.3_Missense_Mutation_p.R249Q|CUL2_ENST00000537177.1_Missense_Mutation_p.R268Q			Q13617	CUL2_HUMAN	cullin 2	249					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)	p.R249Q(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TTTTCGACATCGAATTTCTTC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	10											116	106	109					10																	35327979		2203	4296	6499	35367985	SO:0001583	missense	8453			U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.746G>A	10.37:g.35327979C>T	ENSP00000363880:p.Arg249Gln		35367985	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	37	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	C	36	5.889487	0.97068	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	6.16	6.16	0.99307	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73063	0.3539	M	0.89095	3.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.75900	-0.3154	10	0.87932	D	0	-8.0139	20.8598	0.99761	0.0:1.0:0.0:0.0	.	249;268;249	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	Q	249;249;249;249;192;249;268	ENSP00000363883:R249Q;ENSP00000363880:R249Q;ENSP00000363878:R249Q;ENSP00000363881:R249Q;ENSP00000363874:R249Q;ENSP00000444856:R268Q	ENSP00000363874:R249Q	R	-	2	0	CUL2	35367985	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CGA		0.318	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		T	35327979	C	T	35327979	3	4	61	1	0	0	0	0	1	0	0	0	4061	884	31	1	1543	1	CUL2	10	35327979	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	654861	35327979	100206768	6705	14690										
ANKRD30A	91074	broad.mit.edu	37	chr10	37419198	37419198	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggtgccgatataaatctCgtagatgtgtatggcaacac	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:37419198C>T	ENST00000602533.1	+	3	333	c.234C>T	c.(232-234)ctC>ctT	p.L78L	ANKRD30A_ENST00000374660.1_Silent_p.L78L|ANKRD30A_ENST00000361713.1_Silent_p.L78L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	134					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L78L(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						ATATAAATCTCGTAGATGTGT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	10											89	79	82					10																	37419198		1874	4119	5993	37459204	SO:0001819	synonymous_variant	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.234C>T	10.37:g.37419198C>T			37459204	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																					0.423	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37419198	C	T	37419198	2	4	61	1	0	0	0	0	0	0	0	1	658	871	31	1		1	ANKRD30A	10	37419198	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2091219	37419198	98115549	6706	14691										
ANKRD30A	91074	broad.mit.edu	37	chr10	37430688	37430688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgaggctgcacccttggCggaaagaacacctgacacag	12	11	0	4	rs529585679		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:37430688C>T	ENST00000602533.1	+	7	794	c.695C>T	c.(694-696)gCg>gTg	p.A232V	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.A232V|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A232V			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	288					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A232V(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						GCACCCTTGGCGGAAAGAACA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10											34	35	35					10																	37430688		1876	4105	5981	37470694	SO:0001583	missense	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.695C>T	10.37:g.37430688C>T	ENSP00000473551:p.Ala232Val		37470694	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	5.177	0.218204	0.09810	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.06294	3.32;3.32	0.566	-1.13	0.09775	.	.	.	.	.	T	0.04497	0.0123	L	0.43152	1.355	0.09310	N	1	P	0.42993	0.797	B	0.37692	0.256	T	0.33599	-0.9862	8	0.23302	T	0.38	.	.	.	.	.	288	Q9BXX3	AN30A_HUMAN	V	232	ENSP00000354432:A232V;ENSP00000363792:A232V	ENSP00000354432:A232V	A	+	2	0	ANKRD30A	37470694	0.749000	0.28305	0.037000	0.18230	0.177000	0.22998	-1.289000	0.02780	-1.015000	0.03375	-0.749000	0.03505	GCG		0.483	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37430688	C	T	37430688	3	4	61	1	0	0	0	0	1	0	0	0	658	768	27	1	721	1	ANKRD30A	10	37430688	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11490	37430688	98104059	6707	14692										
ANKRD30A	91074	broad.mit.edu	37	chr10	37431191	37431191	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattgcatgtcctacaaaaGaatcatctacaaaagcaagt	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:37431191G>T	ENST00000602533.1	+	7	1297	c.1198G>T	c.(1198-1200)Gaa>Taa	p.E400*	ANKRD30A_ENST00000374660.1_Nonsense_Mutation_p.E400*|ANKRD30A_ENST00000361713.1_Nonsense_Mutation_p.E400*			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	456					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E400*(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TCCTACAAAAGAATCATCTAC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											53	50	51					10																	37431191		1876	4118	5994	37471197	SO:0001587	stop_gained	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1198G>T	10.37:g.37431191G>T	ENSP00000473551:p.Glu400*		37471197	Q5W025	Nonsense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	16.17	3.047849	0.55110	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	.	.	.	0.509	-0.802	0.10889	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	.	.	.	.	.	.	.	X	400	.	ENSP00000354432:E400X	E	+	1	0	ANKRD30A	37471197	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-2.425000	0.01028	-0.293000	0.08986	-1.368000	0.01194	GAA		0.378	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37431191	G	T	37431191	4	4	61	1	0	0	0	0	0	1	0	0	658	943	33	2	1224	2	ANKRD30A	10	37431191	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	503	37431191	98103556	6708	14693										
ZNF248	57209	broad.mit.edu	37	chr10	38120580	38120580	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcacccttgtgtgaattCtctgatgtttggtgagcact	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38120580C>A	ENST00000395867.3	-	6	2253	c.1703G>T	c.(1702-1704)aGa>aTa	p.R568I	AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000357328.4_Missense_Mutation_p.R568I	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	568					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R568I(2)		NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TGTGTGAATTCTCTGATGTTT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	10											96	91	93					10																	38120580		2203	4300	6503	38160586	SO:0001583	missense	57209			AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1703G>T	10.37:g.38120580C>A	ENSP00000379208:p.Arg568Ile		38160586	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098529	0.56183	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.10005	2.92;2.92	4.52	4.52	0.55395	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000048	T	0.26484	0.0647	L	0.61387	1.9	0.54753	D	0.999987	D	0.64830	0.994	P	0.59546	0.859	T	0.00899	-1.1522	10	0.87932	D	0	.	15.1139	0.72384	0.0:1.0:0.0:0.0	.	568	Q8NDW4	ZN248_HUMAN	I	568	ENSP00000379208:R568I;ENSP00000349882:R568I	ENSP00000349882:R568I	R	-	2	0	ZNF248	38160586	0.009000	0.17119	1.000000	0.80357	0.945000	0.59286	0.968000	0.29357	2.509000	0.84616	0.650000	0.86243	AGA		0.423	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		A	38120580	C	A	38120580	3	1	61	1	0	0	0	0	1	0	0	0	17832	913	32	2	40	2	ZNF248	10	38120580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	689389	38120580	97414167	6709	14694										
ZNF248	57209	broad.mit.edu	37	chr10	38121941	38121941	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcttcctctatctccattTtctacacttactgttttgtt	3	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38121941T>G	ENST00000395867.3	-	6	892	c.342A>C	c.(340-342)gaA>gaC	p.E114D	AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000357328.4_Missense_Mutation_p.E114D	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E114D(1)		NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TATCTCCATTTTCTACACTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											78	73	74					10																	38121941		2202	4300	6502	38161947	SO:0001583	missense	57209			AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.342A>C	10.37:g.38121941T>G	ENSP00000379208:p.Glu114Asp		38161947	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	T	4.113	0.019158	0.08006	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.06218	3.33;3.33	4.86	-2.13	0.07144	.	0.689437	0.12778	N	0.439875	T	0.04003	0.0112	L	0.28400	0.85	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37526	-0.9702	10	0.48119	T	0.1	.	3.6565	0.08222	0.4037:0.2661:0.0:0.3301	.	114	Q8NDW4	ZN248_HUMAN	D	114	ENSP00000379208:E114D;ENSP00000349882:E114D	ENSP00000349882:E114D	E	-	3	2	ZNF248	38161947	0.000000	0.05858	0.003000	0.11579	0.073000	0.16967	-0.581000	0.05820	-0.143000	0.11334	0.460000	0.39030	GAA		0.363	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		G	38121941	T	G	38121941	3	3	61	1	0	0	0	0	1	0	0	0	17832	1838	64	4	1401	4	ZNF248	10	38121941	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1361	38121941	97412806	6710	14695										
ZNF25	219749	broad.mit.edu	37	chr10	38241173	38241173	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctcccctgtgtgttttCtctgatgtataataaaatgt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38241173C>T	ENST00000302609.7	-	6	1465	c.1253G>A	c.(1252-1254)aGa>aAa	p.R418K	ZNF25_ENST00000374633.1_5'UTR|AL117337.1_ENST00000582458.1_RNA	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	418					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R418K(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				TGTGTGTTTTCTCTGATGTAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	105	105					10																	38241173		2203	4300	6503	38281179	SO:0001583	missense	219749			AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"Zinc fingers, C2H2-type", "-"	13043	protein-coding gene	gene with protein product		194528	"zinc finger protein 25 (KOX 19)"			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1253G>A	10.37:g.38241173C>T	ENSP00000302222:p.Arg418Lys		38281179	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	37	CCDS7195.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.839396	0.71488	.	.	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.18338	2.22	4.76	3.86	0.44501	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000288	T	0.12050	0.0293	N	0.20574	0.59	0.31069	N	0.713264	P	0.38250	0.624	B	0.38985	0.287	T	0.06006	-1.0851	10	0.44086	T	0.13	-44.6275	10.7965	0.46464	0.0:0.9072:0.0:0.0928	.	418	P17030	ZNF25_HUMAN	K	418;382	ENSP00000302222:R418K	ENSP00000302222:R418K	R	-	2	0	ZNF25	38281179	0.006000	0.16342	0.998000	0.56505	0.997000	0.91878	1.737000	0.38197	1.360000	0.45960	0.561000	0.74099	AGA		0.443	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966		T	38241173	C	T	38241173	3	4	61	1	0	0	0	0	1	0	0	0	17833	913	32	3	121	3	ZNF25	10	38241173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119232	38241173	97293574	6711	14696										
ZNF25	219749	broad.mit.edu	37	chr10	38241884	38241884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgataggtggtaaaatattTtcttacattctttacactca	5	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38241884T>G	ENST00000302609.7	-	6	754	c.542A>C	c.(541-543)aAa>aCa	p.K181T	ZNF25_ENST00000374633.1_5'UTR|AL117337.1_ENST00000582458.1_RNA	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	181					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K181T(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				GTAAAATATTTTCTTACATTC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											147	151	150					10																	38241884		2203	4300	6503	38281890	SO:0001583	missense	219749			AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"Zinc fingers, C2H2-type", "-"	13043	protein-coding gene	gene with protein product		194528	"zinc finger protein 25 (KOX 19)"			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.542A>C	10.37:g.38241884T>G	ENSP00000302222:p.Lys181Thr		38281890	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	37	CCDS7195.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.318392	0.60524	.	.	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.24723	1.84	4.84	3.71	0.42584	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47455	D	0.000221	T	0.37073	0.0990	M	0.90922	3.16	0.36252	D	0.853949	B	0.32731	0.382	B	0.33750	0.169	T	0.51553	-0.8691	10	0.87932	D	0	-13.2927	8.7574	0.34654	0.0:0.0906:0.0:0.9094	.	181	P17030	ZNF25_HUMAN	T	181;145	ENSP00000302222:K181T	ENSP00000302222:K181T	K	-	2	0	ZNF25	38281890	1.000000	0.71417	0.974000	0.42286	0.961000	0.63080	7.394000	0.79862	0.995000	0.38917	0.524000	0.50904	AAA		0.348	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966		G	38241884	T	G	38241884	3	3	61	1	0	0	0	0	1	0	0	0	17833	1841	64	4	832	4	ZNF25	10	38241884	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	711	38241884	97292863	6712	14697										
ZNF37A	7587	broad.mit.edu	37	chr10	38407287	38407287	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacctcattaaacatcaaaGaatacacacaggtgaaaaac	5	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38407287G>T	ENST00000361085.5	+	7	1553	c.1208G>T	c.(1207-1209)aGa>aTa	p.R403I	ZNF37A_ENST00000351773.3_Missense_Mutation_p.R403I	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	403					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R403I(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						AAACATCAAAGAATACACACA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											51	52	52					10																	38407287		2203	4299	6502	38447293	SO:0001583	missense	7587			X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"Zinc fingers, C2H2-type", "-"	13102	protein-coding gene	gene with protein product			"zinc finger protein 37a (KOX 21)"			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1208G>T	10.37:g.38407287G>T	ENSP00000354377:p.Arg403Ile		38447293	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	CCDS31183.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.076920	0.55753	.	.	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.02446	4.29;4.29	2.34	2.34	0.29019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11367	0.0277	M	0.73372	2.23	0.45607	D	0.998541	D	0.76494	0.999	D	0.71870	0.975	T	0.01596	-1.1316	9	0.72032	D	0.01	.	10.3666	0.44028	0.0:0.0:1.0:0.0	.	403	P17032	ZN37A_HUMAN	I	403	ENSP00000329141:R403I;ENSP00000354377:R403I	ENSP00000329141:R403I	R	+	2	0	ZNF37A	38447293	0.001000	0.12720	0.983000	0.44433	0.793000	0.44817	0.103000	0.15292	1.313000	0.45069	0.591000	0.81541	AGA		0.403	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		T	38407287	G	T	38407287	3	4	61	1	0	0	0	0	1	0	0	0	17911	942	33	2	1222	2	ZNF37A	10	38407287	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165403	38407287	97127460	6713	14698										
ZNF37A	7587	broad.mit.edu	37	chr10	38407471	38407471	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaagacacacaggggaGaaaccttttggatgtaatga	12	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:38407471G>T	ENST00000361085.5	+	7	1737	c.1392G>T	c.(1390-1392)gaG>gaT	p.E464D	ZNF37A_ENST00000351773.3_Missense_Mutation_p.E464D	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E464D(2)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						ACACAGGGGAGAAACCTTTTG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	10											52	54	54					10																	38407471		2203	4299	6502	38447477	SO:0001583	missense	7587			X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"Zinc fingers, C2H2-type", "-"	13102	protein-coding gene	gene with protein product			"zinc finger protein 37a (KOX 21)"			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1392G>T	10.37:g.38407471G>T	ENSP00000354377:p.Glu464Asp		38447477	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	CCDS31183.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.122524	0.56613	.	.	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.26810	1.71;1.71	2.05	0.927	0.19437	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20901	0.0503	L	0.49256	1.55	0.30466	N	0.773817	P	0.45672	0.864	B	0.38954	0.286	T	0.26950	-1.0088	9	0.72032	D	0.01	.	7.2348	0.26064	0.0:0.0:0.7394:0.2606	.	464	P17032	ZN37A_HUMAN	D	464	ENSP00000329141:E464D;ENSP00000354377:E464D	ENSP00000329141:E464D	E	+	3	2	ZNF37A	38447477	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.205000	0.42770	1.151000	0.42436	0.467000	0.42956	GAG		0.413	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		T	38407471	G	T	38407471	3	4	61	1	0	0	0	0	1	0	0	0	17911	933	33	2	1406	2	ZNF37A	10	38407471	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184	38407471	97127276	6714	14699										
ZNF33B	7582	broad.mit.edu	37	chr10	43088072	43088072	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatccaattcattcataagGtttttctcctatgtgtgttc	5	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43088072G>T	ENST00000359467.3	-	5	2440	c.2326C>A	c.(2326-2328)Cct>Act	p.P776T	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	776					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P776T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CATTCATAAGGTTTTTCTCCT	0.413																																					Melanoma(137;1247 1767 16772 25727 43810)											1	Substitution - Missense(1)	large_intestine(1)	10											110	106	107					10																	43088072		2203	4300	6503	42408078	SO:0001583	missense	7582			X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.2326C>A	10.37:g.43088072G>T	ENSP00000352444:p.Pro776Thr		42408078	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065154	0.36470	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.20332	2.08	2.5	-4.99	0.03010	Zinc finger, C2H2 (1);	2.749770	0.01634	N	0.023712	T	0.21801	0.0525	L	0.49640	1.575	0.09310	N	0.999995	B	0.30634	0.288	B	0.26969	0.075	T	0.35525	-0.9785	10	0.56958	D	0.05	.	13.2496	0.60043	0.2162:0.0:0.7838:0.0	.	776	Q06732	ZN33B_HUMAN	T	776;742	ENSP00000352444:P776T	ENSP00000352444:P776T	P	-	1	0	ZNF33B	42408078	0.061000	0.20836	0.012000	0.15200	0.657000	0.38888	0.514000	0.22786	-1.293000	0.02362	-0.499000	0.04595	CCT		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		T	43088072	G	T	43088072	3	4	61	1	0	0	0	0	1	0	0	0	17894	1261	44	2	14	2	ZNF33B	10	43088072	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4680601	43088072	92446675	6715	14700										
ZNF33B	7582	broad.mit.edu	37	chr10	43089168	43089168	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattacactgatagggtttCtcccctgtatgtgttctctg	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43089168C>A	ENST00000359467.3	-	5	1344	c.1230G>T	c.(1228-1230)gaG>gaT	p.E410D	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E410D(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						GATAGGGTTTCTCCCCTGTAT	0.433																																					Melanoma(137;1247 1767 16772 25727 43810)											1	Substitution - Missense(1)	large_intestine(1)	10											97	104	102					10																	43089168		2203	4300	6503	42409174	SO:0001583	missense	7582			X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1230G>T	10.37:g.43089168C>A	ENSP00000352444:p.Glu410Asp		42409174	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912548	0.33721	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.26810	1.71	2.09	2.09	0.27110	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.436144	0.16925	N	0.193912	T	0.24851	0.0603	L	0.33137	0.985	0.24613	N	0.993716	P	0.48694	0.914	P	0.48114	0.567	T	0.07462	-1.0771	10	0.87932	D	0	.	10.3212	0.43767	0.0:1.0:0.0:0.0	.	410	Q06732	ZN33B_HUMAN	D	410;376	ENSP00000352444:E410D	ENSP00000352444:E410D	E	-	3	2	ZNF33B	42409174	0.974000	0.33945	1.000000	0.80357	0.845000	0.48019	0.231000	0.17872	1.514000	0.48869	0.416000	0.27883	GAG		0.433	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		A	43089168	C	A	43089168	3	1	61	1	0	0	0	0	1	0	0	0	17894	912	32	2	1110	2	ZNF33B	10	43089168	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1096	43089168	92445579	6716	14701										
BMS1	9790	broad.mit.edu	37	chr10	43279900	43279900	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtggacccaaagctgcaAagaaaaagaagcggcttctg	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43279900A>C	ENST00000374518.5	+	2	121	c.58A>C	c.(58-60)Aag>Cag	p.K20Q		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	20					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.K20Q(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CAAAGCTGCAAAGAAAAAGAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											58	66	63					10																	43279900		2203	4300	6503	42599906	SO:0001583	missense	9790			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.58A>C	10.37:g.43279900A>C	ENSP00000363642:p.Lys20Gln		42599906	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035458	0.75617	.	.	ENSG00000165733	ENST00000374518	T	0.14144	2.53	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.47581	0.1453	H	0.94808	3.585	0.51767	D	0.999935	D	0.89917	1.0	D	0.74023	0.982	T	0.62388	-0.6865	10	0.56958	D	0.05	.	13.9576	0.64160	1.0:0.0:0.0:0.0	.	20	Q14692	BMS1_HUMAN	Q	20	ENSP00000363642:K20Q	ENSP00000363642:K20Q	K	+	1	0	BMS1	42599906	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	8.947000	0.93000	1.703000	0.51240	0.411000	0.27672	AAG		0.453	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		C	43279900	A	C	43279900	3	2	61	1	0	0	0	0	1	0	0	0	1473	15	1	4	60	4	BMS1	10	43279900	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	190732	43279900	92254847	6717	14702										
BMS1	9790	broad.mit.edu	37	chr10	43292146	43292146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgttaagggcatcaaacGacggaaacttgagttggaag	14	6	1	1	rs147587227		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43292146G>A	ENST00000374518.5	+	10	1517	c.1454G>A	c.(1453-1455)cGa>cAa	p.R485Q		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	485					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.R485Q(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GGCATCAAACGACGGAAACTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10											169	154	159					10																	43292146		2203	4300	6503	42612152	SO:0001583	missense	9790			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.1454G>A	10.37:g.43292146G>A	ENSP00000363642:p.Arg485Gln		42612152	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	g	5.211	0.224469	0.09863	.	.	ENSG00000165733	ENST00000374518	T	0.24723	1.84	5.0	4.09	0.47781	.	0.510391	0.21139	N	0.079501	T	0.20414	0.0491	L	0.44542	1.39	0.09310	N	1	B	0.24768	0.111	B	0.12837	0.008	T	0.12837	-1.0532	10	0.25106	T	0.35	.	11.2055	0.48767	0.1509:0.0:0.8491:0.0	.	485	Q14692	BMS1_HUMAN	Q	485	ENSP00000363642:R485Q	ENSP00000363642:R485Q	R	+	2	0	BMS1	42612152	0.926000	0.31397	0.010000	0.14722	0.021000	0.10359	3.009000	0.49552	1.229000	0.43630	0.580000	0.79431	CGA		0.483	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		A	43292146	G	A	43292146	3	1	61	1	0	0	0	0	1	0	0	0	1473	1058	37	1	1488	1	BMS1	10	43292146	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12246	43292146	92242601	6718	14703										
RET	5979	broad.mit.edu	37	chr10	43610160	43610160	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactccatggagaaccaggtCtccgtggatgccttcaagat	11	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43610160C>A	ENST00000355710.3	+	11	2344	c.2112C>A	c.(2110-2112)gtC>gtA	p.V704V	RET_ENST00000340058.5_Silent_p.V704V	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	704					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V704V(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGAACCAGGTCTCCGTGGATG	0.682		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	1	Substitution - coding silent(1)	large_intestine(1)	10											30	30	30					10																	43610160		2203	4300	6503	42930166	SO:0001819	synonymous_variant	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2112C>A	10.37:g.43610160C>A			42930166	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																				0.682	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43610160	C	A	43610160	2	1	61	1	0	0	0	0	0	0	0	1	13272	900	32	2		2	RET	10	43610160	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	318014	43610160	91924587	6719	14704										
CSGALNACT2	55454	broad.mit.edu	37	chr10	43651251	43651251	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttaatgaaaatgacttCgtagaaggtaatgtgaaaaa	8	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43651251C>T	ENST00000374466.3	+	2	989	c.654C>T	c.(652-654)ttC>ttT	p.F218F	CSGALNACT2_ENST00000374464.1_Silent_p.F218F	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	218					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.F218F(1)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AAAATGACTTCGTAGAAGGTA	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	10											35	36	36					10																	43651251		2203	4297	6500	42971257	SO:0001819	synonymous_variant	55454			AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.654C>T	10.37:g.43651251C>T			42971257	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	37	CCDS7201.1																																																																																				0.353	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43651251	C	T	43651251	2	4	61	1	0	0	0	0	0	0	0	1	3945	883	31	1		1	CSGALNACT2	10	43651251	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41091	43651251	91883496	6720	14705										
RASGEF1A	221002	broad.mit.edu	37	chr10	43691985	43691985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctcactttcaaaggaggCgacgaagagagctgagagat	12	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43691985C>T	ENST00000395809.1	-	12	3866	c.1360G>A	c.(1360-1362)Gcc>Acc	p.A454T	RASGEF1A_ENST00000395810.1_Missense_Mutation_p.A454T|RASGEF1A_ENST00000374459.1_Missense_Mutation_p.A462T			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	454	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.A401T(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						TCAAAGGAGGCGACGAAGAGA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	121	125					10																	43691985		2203	4300	6503	43011991	SO:0001583	missense	221002			AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.1360G>A	10.37:g.43691985C>T	ENSP00000379154:p.Ala454Thr		43011991	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	37	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	C	32	5.162848	0.94727	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.30981	1.51;1.51;1.51	5.14	5.14	0.70334	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000001	T	0.45175	0.1329	M	0.61703	1.905	0.80722	D	1	P;P	0.50819	0.807;0.939	B;P	0.50314	0.356;0.637	T	0.44283	-0.9338	10	0.59425	D	0.04	.	18.9656	0.92695	0.0:1.0:0.0:0.0	.	454;462	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	T	462;454;454	ENSP00000363583:A462T;ENSP00000379155:A454T;ENSP00000379154:A454T	ENSP00000363583:A462T	A	-	1	0	RASGEF1A	43011991	1.000000	0.71417	0.958000	0.39756	0.922000	0.55478	7.403000	0.79983	2.550000	0.86006	0.462000	0.41574	GCC		0.557	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313		T	43691985	C	T	43691985	3	4	61	1	0	0	0	0	1	0	0	0	13106	768	27	1	93	1	RASGEF1A	10	43691985	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40734	43691985	91842762	6721	14706										
HNRNPF	3185	broad.mit.edu	37	chr10	43882987	43882987	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatccaaatgggagtcctcGaagccgcacgaagccatcgt	11	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:43882987G>A	ENST00000544000.1	-	4	753	c.346C>T	c.(346-348)Cga>Tga	p.R116*	HNRNPF_ENST00000356053.3_Nonsense_Mutation_p.R116*|HNRNPF_ENST00000498176.1_5'Flank|HNRNPF_ENST00000357065.4_Nonsense_Mutation_p.R116*|HNRNPF_ENST00000443950.2_Nonsense_Mutation_p.R116*|HNRNPF_ENST00000337970.3_Nonsense_Mutation_p.R116*	NM_001098207.1	NP_001091677.1	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F	116	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.	Interaction with RNA.			gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.R116*(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|urinary_tract(1)	19						GGGAGTCCTCGAAGCCGCACG	0.527																																																2	Substitution - Nonsense(2)	large_intestine(2)	10											129	109	115					10																	43882987		2203	4300	6503	43202993	SO:0001587	stop_gained	3185				CCDS7204.1	10q11.21	2013-02-12		2008-04-18	ENSG00000169813	ENSG00000169813		"RNA binding motif (RRM) containing"	5039	protein-coding gene	gene with protein product		601037		HNRPF		7499401	Standard	NM_001098208		Approved		uc001jas.2	P52597	OTTHUMG00000018029	ENST00000544000.1:c.346C>T	10.37:g.43882987G>A	ENSP00000438061:p.Arg116*		43202993	B3KM84|Q5T0N2|Q96AU2	Nonsense_Mutation	SNP	ENST00000544000.1	37	CCDS7204.1	.	.	.	.	.	.	.	.	.	.	G	34	5.365569	0.95900	.	.	ENSG00000169813	ENST00000544000;ENST00000443950;ENST00000356053;ENST00000357065;ENST00000337970;ENST00000540544	.	.	.	4.04	4.04	0.47022	.	0.122716	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.2152	14.4937	0.67670	0.0:0.0:1.0:0.0	.	.	.	.	X	116;116;116;116;116;39	.	ENSP00000338477:R116X	R	-	1	2	HNRNPF	43202993	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	4.140000	0.58031	2.539000	0.85634	0.655000	0.94253	CGA		0.527	HNRNPF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047705.2			A	43882987	G	A	43882987	4	1	61	1	0	0	0	0	0	1	0	0	7286	1066	37	1	905	1	HNRNPF	10	43882987	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191002	43882987	91651760	6722	14707										
ZNF239	8187	broad.mit.edu	37	chr10	44052379	44052379	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatccgagctctggctgaaAcccttcccacactcatagca	7	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:44052379A>C	ENST00000306006.6	-	2	1801	c.1149T>G	c.(1147-1149)ggT>ggG	p.G383G	ZNF239_ENST00000491188.1_5'Flank|ZNF239_ENST00000374446.2_Silent_p.G383G|ZNF239_ENST00000426961.1_Silent_p.G383G|ZNF239_ENST00000535642.1_Silent_p.G383G	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	383					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G383G(1)		endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TCTGGCTGAAACCCTTCCCAC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	10											102	111	108					10																	44052379		2197	4300	6497	43372385	SO:0001819	synonymous_variant	8187			X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"Zinc fingers, C2H2-type"	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.1149T>G	10.37:g.44052379A>C			43372385	Q5T1G9|Q8TAS5	Silent	SNP	ENST00000306006.6	37	CCDS41502.1																																																																																				0.532	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1			C	44052379	A	C	44052379	2	2	61	1	0	0	0	0	0	0	0	1	17830	30	2	4		4	ZNF239	10	44052379	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	169392	44052379	91482368	6723	14708										
ZNF239	8187	broad.mit.edu	37	chr10	44053363	44053363	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcactttcaatgttttcGaaacaaccactttgaagagt	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:44053363G>A	ENST00000306006.6	-	2	817	c.165C>T	c.(163-165)ttC>ttT	p.F55F	ZNF239_ENST00000491188.1_5'UTR|ZNF239_ENST00000374446.2_Silent_p.F55F|ZNF239_ENST00000426961.1_Silent_p.F55F|ZNF239_ENST00000535642.1_Silent_p.F55F	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	55					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F55F(1)		endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CAATGTTTTCGAAACAACCAC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											136	122	127					10																	44053363		1896	4121	6017	43373369	SO:0001819	synonymous_variant	8187			X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"Zinc fingers, C2H2-type"	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.165C>T	10.37:g.44053363G>A			43373369	Q5T1G9|Q8TAS5	Silent	SNP	ENST00000306006.6	37	CCDS41502.1																																																																																				0.413	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1			A	44053363	G	A	44053363	2	1	61	1	0	0	0	0	0	0	0	1	17830	1049	37	1		1	ZNF239	10	44053363	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	984	44053363	91481384	6724	14709										
ZNF32	7580	broad.mit.edu	37	chr10	44140135	44140135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcttcctgtagtgtcttcGaatctggggatttttgttcc	9	8	3	0	rs144676378	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:44140135G>A	ENST00000395797.1	-	3	373	c.185C>T	c.(184-186)tCg>tTg	p.S62L	ZNF32_ENST00000485351.1_5'UTR|ZNF32-AS3_ENST00000458063.1_RNA|ZNF32_ENST00000374433.2_Missense_Mutation_p.S62L|ZNF32-AS1_ENST00000453284.1_RNA|ZNF32-AS2_ENST00000418966.1_RNA	NM_001005368.1	NP_001005368.1	P17041	ZNF32_HUMAN	zinc finger protein 32	62					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S62L(3)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	14		all_neural(218;0.0182)|Ovarian(717;0.0443)|Renal(717;0.157)		Lung(62;0.179)		TAGTGTCTTCGAATCTGGGGA	0.458													G|||	4	0.000798722	0	0	5008	,	,		19945	0		0	False		,,,				2504	0.0041															3	Substitution - Missense(3)	large_intestine(2)|NS(1)	10											117	121	119					10																	44140135		2203	4300	6503	43460141	SO:0001583	missense	7580			U69645	CCDS7206.1	10q22-q25	2013-01-08	2006-05-11		ENSG00000169740	ENSG00000169740		"Zinc fingers, C2H2-type"	13095	protein-coding gene	gene with protein product		194539	"zinc finger protein 32 (KOX 30)"				Standard	XM_005271822		Approved	KOX30	uc001jbc.3	P17041	OTTHUMG00000018043	ENST00000395797.1:c.185C>T	10.37:g.44140135G>A	ENSP00000379143:p.Ser62Leu		43460141	Q92951	Missense_Mutation	SNP	ENST00000395797.1	37	CCDS7206.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.791948	0.31685	.	.	ENSG00000169740	ENST00000374433;ENST00000395797	T;T	0.11930	2.73;2.73	4.64	2.75	0.32379	.	0.725568	0.11965	N	0.512321	T	0.06826	0.0174	N	0.08118	0	0.30656	N	0.754935	B	0.19073	0.033	B	0.04013	0.001	T	0.13764	-1.0497	10	0.62326	D	0.03	-0.0423	5.7493	0.18138	0.0975:0.0:0.7112:0.1913	.	62	P17041	ZNF32_HUMAN	L	62	ENSP00000363556:S62L;ENSP00000379143:S62L	ENSP00000363556:S62L	S	-	2	0	ZNF32	43460141	0.026000	0.19158	0.998000	0.56505	0.768000	0.43524	0.696000	0.25541	0.844000	0.35094	0.655000	0.94253	TCG		0.458	ZNF32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047723.1	NM_006973		A	44140135	G	A	44140135	3	1	61	1	0	0	0	0	1	0	0	0	17877	1059	37	1	640	1	ZNF32	10	44140135	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86772	44140135	91394612	6725	14710										
TMEM72	643236	broad.mit.edu	37	chr10	45423376	45423376	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgccccttagtgttgatCggcgtgggcactgagacctt	12	11	1	2	rs532437325	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:45423376C>T	ENST00000544540.1	+	2	267				TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)		p.I26I(2)		breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						TAGTGTTGATCGGCGTGGGCA	0.537													C|||	2	0.000399361	0	0	5008	,	,		18062	0.001		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	10											200	176	184					10																	45423376		1568	3582	5150	44743382	SO:0001627	intron_variant	643236			AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-217-4070C>T	10.37:g.45423376C>T			44743382	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	37																																																																																					0.537	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		T	45423376	C	T	45423376	1	4	61	0	1	0	0	0	0	0	0	0	16240	874	31	1		1	TMEM72	10	45423376	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1283241	45423376	90111371	6726	14711										
MARCH8	220972	broad.mit.edu	37	chr10	45953749	45953749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaacaagaagagtttgtgtCggaatgacagattccatatc	10	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:45953749C>T	ENST00000319836.3	-	7	1563	c.814G>A	c.(814-816)Gac>Aac	p.D272N	MARCH8_ENST00000395771.3_Missense_Mutation_p.D272N|MARCH8_ENST00000453424.2_Missense_Mutation_p.D554N|MARCH8_ENST00000395769.2_Missense_Mutation_p.D272N|MARCH8_ENST00000476962.1_5'UTR	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	272					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D272N(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						GAGTTTGTGTCGGAATGACAG	0.398																																					NSCLC(102;658 1594 2173 16344 34808)											1	Substitution - Missense(1)	large_intestine(1)	10											103	102	102					10																	45953749		2203	4300	6503	45273755	SO:0001583	missense	220972			AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	23356	protein-coding gene	gene with protein product		613335	"c-mir, cellular modulator of immune recognition", "membrane-associated ring finger (C3HC4) 8"	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.814G>A	10.37:g.45953749C>T	ENSP00000317087:p.Asp272Asn		45273755	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.47|17.47	3.396502|3.396502	0.62177|0.62177	.|.	.|.	ENSG00000165406|ENSG00000165406	ENST00000395771;ENST00000319836;ENST00000395769|ENST00000453424	T;T;T|.	0.13307|.	2.6;2.6;2.6|.	5.67|5.67	2.79|2.79	0.32731|0.32731	.|.	0.183568|.	0.45867|.	D|.	0.000324|.	T|T	0.53642|0.53642	0.1809|0.1809	L|L	0.44542|0.44542	1.39|1.39	0.47094|0.47094	D|D	0.999312|0.999312	B;D|.	0.57899|.	0.322;0.981|.	B;P|.	0.48738|.	0.102;0.588|.	T|T	0.40942|0.40942	-0.9536|-0.9536	10|5	0.27082|.	T|.	0.32|.	-22.4651|-22.4651	8.8785|8.8785	0.35360|0.35360	0.0:0.7495:0.0:0.2505|0.0:0.7495:0.0:0.2505	.|.	272;436|.	Q5T0T0;Q5JQ16|.	MARH8_HUMAN;.|.	N|Q	272|436	ENSP00000379118:D272N;ENSP00000317087:D272N;ENSP00000379116:D272N|.	ENSP00000317087:D272N|.	D|R	-|-	1|2	0|0	MARCH8|MARCH8	45273755|45273755	0.999000|0.999000	0.42202|0.42202	0.414000|0.414000	0.26521|0.26521	0.913000|0.913000	0.54294|0.54294	4.089000|4.089000	0.57685|0.57685	0.323000|0.323000	0.23307|0.23307	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.398	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021		T	45953749	C	T	45953749	3	4	61	1	0	0	0	0	1	0	0	0	9337	884	31	1	65	1	MARCH8	10	45953749	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	530373	45953749	89580998	6727	14712										
ANUBL1	93550	broad.mit.edu	37	chr10	46121867	46121867	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtgacaagagtctattCttgtgaggacttaattcccg	11	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:46121867C>A	ENST00000344646.5	-	7	1619	c.1404G>T	c.(1402-1404)aaG>aaT	p.K468N	ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374371.2_Intron|ZFAND4_ENST00000374366.3_Missense_Mutation_p.K394N	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	468							zinc ion binding (GO:0008270)	p.K468N(1)									AGAGTCTATTCTTGTGAGGAC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											158	161	160					10																	46121867		2203	4300	6503	45441873	SO:0001583	missense	93550			AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.1404G>T	10.37:g.46121867C>A	ENSP00000339484:p.Lys468Asn		45441873	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.199719	0.38905	.	.	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.29917	1.55;1.56	5.48	4.57	0.56435	.	1.849610	0.05172	U	0.499753	T	0.36880	0.0983	M	0.67953	2.075	0.32402	N	0.551824	P	0.46706	0.883	B	0.41135	0.348	T	0.40664	-0.9551	10	0.56958	D	0.05	-36.3126	8.2057	0.31454	0.0:0.8216:0.0:0.1784	.	468	Q86XD8	ANUB1_HUMAN	N	468;394;350	ENSP00000339484:K468N;ENSP00000363486:K394N	ENSP00000339484:K468N	K	-	3	2	ANUBL1	45441873	0.998000	0.40836	0.988000	0.46212	0.990000	0.78478	0.372000	0.20467	1.319000	0.45190	0.561000	0.74099	AAG		0.453	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		A	46121867	C	A	46121867	3	1	61	1	0	0	0	0	1	0	0	0	713	912	32	2	795	2	ANUBL1	10	46121867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168118	46121867	89412880	6728	14713										
ANUBL1	93550	broad.mit.edu	37	chr10	46122403	46122403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattccattcctggagatttCgggcggatatgcattcccaa	9	10	0	1	rs114572261	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:46122403C>T	ENST00000344646.5	-	7	1083	c.868G>A	c.(868-870)Gaa>Aaa	p.E290K	ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374371.2_Intron|ZFAND4_ENST00000374366.3_Missense_Mutation_p.E216K	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	290							zinc ion binding (GO:0008270)	p.E290K(1)									CTGGAGATTTCGGGCGGATAT	0.443													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		19399	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						C	LYS/GLU,LYS/GLU	70,4336	63.5+/-100.7	0,70,2133	111	105	107		868,868	5.6	0.5	10	dbSNP_132	107	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ANUBL1	NM_001128324.1,NM_174890.2	56,56	0,71,6432	TT,TC,CC		0.0116,1.5887,0.5459	benign,benign	290/728,290/728	46122403	71,12935	2203	4300	6503	45442409	SO:0001583	missense	93550			AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.868G>A	10.37:g.46122403C>T	ENSP00000339484:p.Glu290Lys		45442409	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	13.33	2.206158	0.39003	0.015887	1.16E-4	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.25085	1.82;1.83	5.62	5.62	0.85841	.	1.225110	0.05778	N	0.608038	T	0.13200	0.0320	L	0.59436	1.845	0.43803	D	0.996356	P	0.49358	0.923	B	0.37692	0.256	T	0.41538	-0.9503	10	0.72032	D	0.01	-31.708	17.1646	0.86812	0.0:1.0:0.0:0.0	.	290	Q86XD8	ANUB1_HUMAN	K	290;216;172	ENSP00000339484:E290K;ENSP00000363486:E216K	ENSP00000339484:E290K	E	-	1	0	ANUBL1	45442409	0.976000	0.34144	0.540000	0.28089	0.018000	0.09664	5.549000	0.67261	2.651000	0.90000	0.650000	0.86243	GAA		0.443	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		T	46122403	C	T	46122403	3	4	61	1	0	0	0	0	1	0	0	0	713	893	31	1	1331	1	ANUBL1	10	46122403	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	536	46122403	89412344	6729	14714										
PPYR1	5540	broad.mit.edu	37	chr10	47086868	47086868	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacccctgggcaccccatacAacttctctgaacattgccag	6	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:47086868A>G	ENST00000395716.1	+	2	170	c.85A>G	c.(85-87)Aac>Gac	p.N29D	NPY4R_ENST00000374312.1_Missense_Mutation_p.N29D			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	29					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)	p.N29D(1)									CACCCCATACAACTTCTCTGA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	10											158	146	150					10																	47086868		2203	4300	6503	46506874	SO:0001583	missense	5540				CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.85A>G	10.37:g.47086868A>G	ENSP00000379066:p.Asn29Asp		46506874	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	A	3.783	-0.045239	0.07452	.	.	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.36520	1.25;1.25	4.78	3.64	0.41730	.	1.362600	0.04808	N	0.434704	T	0.36635	0.0974	M	0.65975	2.015	0.25319	N	0.989134	B	0.15141	0.012	B	0.12156	0.007	T	0.38693	-0.9649	10	0.11794	T	0.64	.	7.4156	0.27042	0.8984:0.0:0.1016:0.0	.	29	P50391	NPY4R_HUMAN	D	29	ENSP00000363431:N29D;ENSP00000379066:N29D	ENSP00000363431:N29D	N	+	1	0	PPYR1	46506874	0.908000	0.30866	0.721000	0.30653	0.223000	0.24884	1.629000	0.37071	0.940000	0.37473	0.533000	0.62120	AAC		0.517	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			G	47086868	A	G	47086868	3	3	61	1	0	0	0	0	1	0	0	0	12450	130	5	4	87	4	PPYR1	10	47086868	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	964465	47086868	88447879	6730	14715										
PPYR1	5540	broad.mit.edu	37	chr10	47087502	47087502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgcacgcatctaccggcGcctgcagaggcaggggcgcg	15	13	1	1	rs139014994		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:47087502G>A	ENST00000395716.1	+	2	804	c.719G>A	c.(718-720)cGc>cAc	p.R240H	NPY4R_ENST00000374312.1_Missense_Mutation_p.R240H			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	240			R -> C (in dbSNP:rs3824733). {ECO:0000269|Ref.6}.		blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)	p.R240H(1)									ATCTACCGGCGCCTGCAGAGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	HIS/ARG	0,4406		0,0,2203	153	129	137		719	4.2	1	10	dbSNP_134	137	3,8597	3.0+/-9.4	0,3,4297	no	missense	PPYR1	NM_005972.4	29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	240/376	47087502	3,13003	2203	4300	6503	46507508	SO:0001583	missense	5540				CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.719G>A	10.37:g.47087502G>A	ENSP00000379066:p.Arg240His		46507508	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.746607	0.49257	0.0	3.49E-4	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.37752	1.18;1.18	5.12	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.116071	0.64402	N	0.000009	T	0.30916	0.0780	L	0.35793	1.09	0.80722	D	1	B	0.30439	0.279	B	0.34931	0.192	T	0.11717	-1.0576	10	0.49607	T	0.09	.	10.9494	0.47321	0.0968:0.0:0.9032:0.0	.	240	P50391	NPY4R_HUMAN	H	240	ENSP00000363431:R240H;ENSP00000379066:R240H	ENSP00000363431:R240H	R	+	2	0	PPYR1	46507508	1.000000	0.71417	0.970000	0.41538	0.618000	0.37518	4.580000	0.60942	1.241000	0.43820	0.609000	0.83330	CGC		0.607	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			A	47087502	G	A	47087502	3	1	61	1	0	0	0	0	1	0	0	0	12450	1087	38	1	721	1	PPYR1	10	47087502	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	634	47087502	88447245	6731	14716										
FAM21B	387680	broad.mit.edu	37	chr10	47922315	47922315	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagaaagcaaaagcctcCgagctctccaaaaagaaagc	9	10	1	2	rs377497548		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:47922315C>T	ENST00000358474.5	+	17	1554	c.1554C>T	c.(1552-1554)tcC>tcT	p.S518S		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		518					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.S518S(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CAAAAGCCTCCGAGCTCTCCA	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	10						C		0,1148		0,0,574	27	31	30		1554	-5.5	0	10		30	2,4840		1,0,2420	no	coding-synonymous	FAM21B	NM_018232.1		1,0,2994	TT,TC,CC		0.0413,0.0,0.0334		518/1254	47922315	2,5988	574	2421	2995	47442321	SO:0001819	synonymous_variant	55747																														ENST00000358474.5:c.1554C>T	10.37:g.47922315C>T			47442321		Silent	SNP	ENST00000358474.5	37	CCDS44379.1																																																																																				0.438	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2			T	47922315	C	T	47922315	2	4	61	1	0	0	0	0	0	0	0	1	5557	639	23	1		1	FAM21B	10	47922315	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	834813	47922315	87612432	6732	14717										
RBP3	5949	broad.mit.edu	37	chr10	48388066	48388066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccgtctgcagcaccgtggGcaccttggcacgcagagcca	14	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:48388066G>A	ENST00000224600.4	-	1	2925	c.2812C>T	c.(2812-2814)Ccc>Tcc	p.P938S	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	938	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)	p.P938S(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	AGCACCGTGGGCACCTTGGCA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	10											53	52	52					10																	48388066		2203	4300	6503	48008072	SO:0001583	missense	5949			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2812C>T	10.37:g.48388066G>A	ENSP00000224600:p.Pro938Ser		48008072	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.388318	0.42308	.	.	ENSG00000107618	ENST00000224600	T	0.71103	-0.54	5.56	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.84862	0.5566	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87077	0.2163	10	0.66056	D	0.02	-43.4495	13.7306	0.62785	0.074:0.0:0.926:0.0	.	938	P10745	RET3_HUMAN	S	938	ENSP00000224600:P938S	ENSP00000224600:P938S	P	-	1	0	RBP3	48008072	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	4.996000	0.63914	1.375000	0.46248	-0.137000	0.14449	CCC		0.637	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		A	48388066	G	A	48388066	3	1	61	1	0	0	0	0	1	0	0	0	13194	1203	42	3	947	3	RBP3	10	48388066	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	465751	48388066	87146681	6733	14718										
GDF2	2658	broad.mit.edu	37	chr10	48413860	48413860	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcccagccgatgtcctcGaagtttacccgcagggaggt	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:48413860G>A	ENST00000249598.1	-	2	1167	c.1008C>T	c.(1006-1008)ttC>ttT	p.F336F		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	336					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.F336F(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						CGATGTCCTCGAAGTTTACCC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	10											72	71	72					10																	48413860		2203	4300	6503	48033866	SO:0001819	synonymous_variant	2658			AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.1008C>T	10.37:g.48413860G>A			48033866	Q5VSQ9|Q9Y571	Silent	SNP	ENST00000249598.1	37	CCDS7219.1																																																																																				0.607	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		A	48413860	G	A	48413860	2	1	61	1	0	0	0	0	0	0	0	1	6334	1049	37	1		1	GDF2	10	48413860	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25794	48413860	87120887	6734	14719										
FRMPD2	143162	broad.mit.edu	37	chr10	49393619	49393619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccacgatgtgggtcacgtTtcagtgtcacacgtacaatt	9	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:49393619T>C	ENST00000374201.3	-	18	2638	c.2336A>G	c.(2335-2337)aAa>aGa	p.K779R	FRMPD2_ENST00000305531.3_Missense_Mutation_p.K754R|FRMPD2_ENST00000407470.4_Missense_Mutation_p.K747R	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	779	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)	p.K779R(1)		NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TGGGTCACGTTTCAGTGTCAC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											186	158	167					10																	49393619		2203	4300	6503	49063625	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2336A>G	10.37:g.49393619T>C	ENSP00000363317:p.Lys779Arg		49063625	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.011570	0.35511	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.28069	1.63;1.63;1.63	5.29	-3.67	0.04476	PDZ/DHR/GLGF (3);	.	.	.	.	T	0.23688	0.0573	L	0.49640	1.575	0.09310	N	1	B;B;B	0.22480	0.002;0.07;0.002	B;B;B	0.23419	0.004;0.046;0.004	T	0.30736	-0.9968	9	0.35671	T	0.21	.	7.3335	0.26596	0.0:0.1367:0.1268:0.7365	.	754;779;747	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	R	779;754;747	ENSP00000363317:K779R;ENSP00000307079:K754R;ENSP00000384339:K747R	ENSP00000307079:K754R	K	-	2	0	FRMPD2	49063625	0.031000	0.19500	0.007000	0.13788	0.036000	0.12997	-0.719000	0.04974	-0.638000	0.05509	0.533000	0.62120	AAA		0.507	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		C	49393619	T	C	49393619	3	2	61	1	0	0	0	0	1	0	0	0	6077	1841	64	4	1641	4	FRMPD2	10	49393619	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	979759	49393619	86141128	6735	14720										
MAPK8	5599	broad.mit.edu	37	chr10	49617976	49617976	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccctagaagaatttcaaGatgtgtaagtgtaataatta	7	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:49617976G>T	ENST00000374189.1	+	4	488	c.307G>T	c.(307-309)Gat>Tat	p.D103Y	MAPK8_ENST00000374182.3_Missense_Mutation_p.D103Y|MAPK8_ENST00000360332.3_Missense_Mutation_p.D103Y|MAPK8_ENST00000374174.1_Missense_Mutation_p.D103Y|MAPK8_ENST00000395611.3_Missense_Mutation_p.D103Y			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	103	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.D103Y(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		AGAATTTCAAGATGTGTAAGT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	10											44	48	46					10																	49617976		2197	4298	6495	49287982	SO:0001583	missense	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.307G>T	10.37:g.49617976G>T	ENSP00000363304:p.Asp103Tyr		49287982	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616816	0.87359	.	.	ENSG00000107643	ENST00000432379;ENST00000429041;ENST00000374189;ENST00000426557;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000374174;ENST00000395611	T;T;T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77301	0.4110	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.99;0.998;0.998;0.99	T	0.78198	-0.2297	10	0.87932	D	0	.	19.767	0.96349	0.0:0.0:1.0:0.0	.	103;103;103;103;103	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	Y	103;20;103;103;103;103;103;103;103;103	ENSP00000387936:D103Y;ENSP00000393223:D20Y;ENSP00000363304:D103Y;ENSP00000397729:D103Y;ENSP00000363297:D103Y;ENSP00000363294:D103Y;ENSP00000353483:D103Y;ENSP00000363291:D103Y;ENSP00000363289:D103Y;ENSP00000378974:D103Y	ENSP00000353483:D103Y	D	+	1	0	MAPK8	49287982	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.812000	0.99227	2.751000	0.94390	0.650000	0.86243	GAT		0.289	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			T	49617976	G	T	49617976	3	4	61	1	0	0	0	0	1	0	0	0	9313	942	33	2	317	2	MAPK8	10	49617976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	224357	49617976	85916771	6736	14721										
MAPK8	5599	broad.mit.edu	37	chr10	49632628	49632628	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttcccaggtacagatCgtatccttatctttggccta	7	10	1	1	rs576809977		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:49632628C>A	ENST00000374189.1	+	7	869				MAPK8_ENST00000374182.3_Intron|MAPK8_ENST00000360332.3_Intron|MAPK8_ENST00000374174.1_Intron|MAPK8_ENST00000395611.3_Intron			P45983	MK08_HUMAN	mitogen-activated protein kinase 8						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.H230N(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		AGGTACAGATCGTATCCTTAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											188	172	178					10																	49632628		2203	4300	6503	49302634	SO:0001627	intron_variant	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.688+426C>A	10.37:g.49632628C>A			49302634	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362131	0.61403	.	.	ENSG00000107643	ENST00000374179;ENST00000374176	T;T	0.63580	-0.05;-0.05	5.68	5.68	0.88126	.	0.423213	0.28459	N	0.015276	T	0.48857	0.1523	N	0.05351	-0.065	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.23150	0.044;0.016	T	0.46707	-0.9172	10	0.87932	D	0	.	20.1412	0.98058	0.0:1.0:0.0:0.0	.	230;230	A1L4K2;P45983-3	.;.	N	230	ENSP00000363294:H230N;ENSP00000363291:H230N	ENSP00000363291:H230N	H	+	1	0	MAPK8	49302634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.740000	0.84986	2.838000	0.97847	0.585000	0.79938	CAT		0.363	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			A	49632628	C	A	49632628	1	1	61	0	1	0	0	0	0	0	0	0	9313	898	31	2		2	MAPK8	10	49632628	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14652	49632628	85902119	6737	14722										
MAPK8	5599	broad.mit.edu	37	chr10	49634510	49634510	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagctctccaacacccgtAcatcaatgtctggtatgatc	7	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:49634510A>G	ENST00000374189.1	+	9	1140	c.959A>G	c.(958-960)tAc>tGc	p.Y320C	MAPK8_ENST00000374182.3_Missense_Mutation_p.Y320C|MAPK8_ENST00000360332.3_Missense_Mutation_p.Y320C|MAPK8_ENST00000395611.3_Missense_Mutation_p.Y244C			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	320	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.Y320C(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		CAACACCCGTACATCAATGTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											118	107	111					10																	49634510		2203	4300	6503	49304516	SO:0001583	missense	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.959A>G	10.37:g.49634510A>G	ENSP00000363304:p.Tyr320Cys		49304516	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535577	0.85812	.	.	ENSG00000107643	ENST00000374189;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000395611	T;T;T;T;T;D	0.83837	-0.34;-0.34;-0.34;-0.34;-0.34;-1.77	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92925	0.7749	M	0.91300	3.195	0.41450	D	0.987971	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.984;0.999;1.0;1.0;0.999	D	0.94536	0.7740	10	0.87932	D	0	.	16.175	0.81844	1.0:0.0:0.0:0.0	.	244;320;320;320;320	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	C	320;320;320;320;320;244	ENSP00000363304:Y320C;ENSP00000363297:Y320C;ENSP00000363294:Y320C;ENSP00000353483:Y320C;ENSP00000363291:Y320C;ENSP00000378974:Y244C	ENSP00000353483:Y320C	Y	+	2	0	MAPK8	49304516	1.000000	0.71417	0.747000	0.31113	0.992000	0.81027	9.283000	0.95860	2.274000	0.75844	0.528000	0.53228	TAC		0.378	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			G	49634510	A	G	49634510	3	3	61	1	0	0	0	0	1	0	0	0	9313	391	14	4	1065	4	MAPK8	10	49634510	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1882	49634510	85900237	6738	14723										
C10orf72	196740	broad.mit.edu	37	chr10	50315817	50315817	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcagcctccgccgtttggcGctgcggctgaaattcccata	11	15	0	1	rs111748147	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50315817G>A	ENST00000332853.4	-	2	302	c.279C>T	c.(277-279)agC>agT	p.S93S	VSTM4_ENST00000298454.3_Silent_p.S93S	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	93	Ig-like.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S93S(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						GCCGTTTGGCGCTGCGGCTGA	0.612													g|||	36	0.0071885	0.0257	0.0029	5008	,	,		17400	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	10						A	,	84,4322	71.4+/-109.4	2,80,2121	63	64	63		279,279	-10.7	0	10	dbSNP_132	63	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	VSTM4	NM_001031746.3,NM_144984.2	,	2,82,6419	AA,AG,GG		0.0233,1.9065,0.6612	,	93/321,93/192	50315817	86,12920	2203	4300	6503	49985823	SO:0001819	synonymous_variant	196740			BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.279C>T	10.37:g.50315817G>A			49985823	B4DNI6|Q96MX7	Silent	SNP	ENST00000332853.4	37	CCDS31198.1																																																																																				0.612	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		A	50315817	G	A	50315817	2	1	61	1	0	0	0	0	0	0	0	1	1619	1078	38	1		1	C10orf72	10	50315817	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681307	50315817	85218930	6739	14724										
ERCC6	2074	broad.mit.edu	37	chr10	50666882	50666882	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcagtattctggcttgagTttccaaattccttcaccacc	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50666882T>C	ENST00000355832.5	-	21	4539	c.4461A>G	c.(4459-4461)aaA>aaG	p.K1487K	ERCC6_ENST00000542458.1_Silent_p.K857K|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1487					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.K1487K(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTGGCTTGAGTTTCCAAATTC	0.353								Direct reversal of damage;Nucleotide excision repair (NER)																																								1	Substitution - coding silent(1)	large_intestine(1)	10											123	126	125					10																	50666882		2203	4300	6503	50336888	SO:0001819	synonymous_variant	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.4461A>G	10.37:g.50666882T>C			50336888	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																				0.353	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50666882	T	C	50666882	2	2	61	1	0	0	0	0	0	0	0	1	5230	1722	60	4		4	ERCC6	10	50666882	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	351065	50666882	84867865	6740	14725										
ERCC6	2074	broad.mit.edu	37	chr10	50667133	50667133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgctttcactttctaaacGctctggcagaatcaggtggt	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50667133G>A	ENST00000355832.5	-	21	4288	c.4210C>T	c.(4210-4212)Cgt>Tgt	p.R1404C	ERCC6_ENST00000542458.1_Missense_Mutation_p.R774C|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1404	Ubiquitin-binding domain (UBD).				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.R1404C(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTTTCTAAACGCTCTGGCAGA	0.522								Direct reversal of damage;Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	10											94	98	97					10																	50667133		2203	4300	6503	50337139	SO:0001583	missense	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.4210C>T	10.37:g.50667133G>A	ENSP00000348089:p.Arg1404Cys		50337139	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.453786	0.43531	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;D	0.83992	-1.79;-1.53	5.73	3.62	0.41486	.	.	.	.	.	T	0.81650	0.4867	M	0.76838	2.35	0.53688	D	0.999974	B;B	0.23490	0.086;0.018	B;B	0.12837	0.008;0.003	T	0.81228	-0.1028	9	0.56958	D	0.05	-10.7434	11.6257	0.51145	0.0745:0.0:0.7556:0.1699	.	1404;781	Q03468;Q59FF6	ERCC6_HUMAN;.	C	1404;781;774	ENSP00000348089:R1404C;ENSP00000445134:R774C	ENSP00000348089:R1404C	R	-	1	0	ERCC6	50337139	0.173000	0.23056	0.955000	0.39395	0.740000	0.42216	0.730000	0.26043	1.558000	0.49541	0.655000	0.94253	CGT		0.522	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		A	50667133	G	A	50667133	3	1	61	1	0	0	0	0	1	0	0	0	5230	1087	38	1	275	1	ERCC6	10	50667133	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	251	50667133	84867614	6741	14726										
PGBD3	267004	broad.mit.edu	37	chr10	50723687	50723687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcattttgtaagaccagttCgaaacagaacaaaagagggc	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50723687C>T	ENST00000374127.3	-	2	1675	c.1474G>A	c.(1474-1476)Gaa>Aaa	p.E492K	ERCC6_ENST00000355832.5_Intron|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.E960K|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.E960K|PGBD3_ENST00000603152.1_Missense_Mutation_p.E960K|PGBD3_ENST00000508005.2_Missense_Mutation_p.E492K	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	492								p.E492K(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						AAGACCAGTTCGAAACAGAAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											125	119	121					10																	50723687		2203	4300	6503	50393693	SO:0001583	missense	267004			AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.1474G>A	10.37:g.50723687C>T	ENSP00000363242:p.Glu492Lys		50393693	B3KQC4|Q5W0M0|Q6PIH0	Missense_Mutation	SNP	ENST00000374127.3	37	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.264456	0.59431	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	0.706	-0.386	0.12466	.	.	.	.	.	T	0.19725	0.0474	N	0.24115	0.695	0.09310	N	1	B;D	0.58970	0.046;0.984	B;P	0.55087	0.001;0.768	T	0.15752	-1.0426	8	0.40728	T	0.16	-14.0221	.	.	.	.	960;492	E7EV46;Q8N328	.;PGBD3_HUMAN	K	492;492;960;960	ENSP00000363242:E492K;ENSP00000426963:E492K;ENSP00000423550:E960K;ENSP00000387966:E960K	ENSP00000387966:E960K	E	-	1	0	PGBD3;RP11-123B3.6	50393693	0.930000	0.31532	0.003000	0.11579	0.874000	0.50279	1.663000	0.37429	-0.183000	0.10585	-0.339000	0.08088	GAA		0.418	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1			T	50723687	C	T	50723687	3	4	61	1	0	0	0	0	1	0	0	0	11813	893	31	1	311	1	PGBD3	10	50723687	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56554	50723687	84811060	6742	14727										
PGBD3	267004	broad.mit.edu	37	chr10	50724310	50724310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggctttccccgaataaatTgtttgcacccgtgacgacca	9	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50724310T>G	ENST00000374127.3	-	2	1052	c.851A>C	c.(850-852)cAa>cCa	p.Q284P	ERCC6_ENST00000355832.5_Intron|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.Q752P|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.Q752P|PGBD3_ENST00000603152.1_Missense_Mutation_p.Q752P|PGBD3_ENST00000508005.2_Missense_Mutation_p.Q284P	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	284								p.Q284P(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						CCGAATAAATTGTTTGCACCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											42	39	40					10																	50724310		2203	4300	6503	50394316	SO:0001583	missense	267004			AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.851A>C	10.37:g.50724310T>G	ENSP00000363242:p.Gln284Pro		50394316	B3KQC4|Q5W0M0|Q6PIH0	Missense_Mutation	SNP	ENST00000374127.3	37	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.532285	0.27387	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	0.468	0.468	0.16732	.	.	.	.	.	T	0.42630	0.1211	M	0.79123	2.44	0.09310	N	1	B;D	0.76494	0.274;0.999	B;D	0.87578	0.098;0.998	T	0.13469	-1.0508	8	0.72032	D	0.01	-5.3336	.	.	.	.	752;284	E7EV46;Q8N328	.;PGBD3_HUMAN	P	284;284;752;752	ENSP00000363242:Q284P;ENSP00000426963:Q284P;ENSP00000423550:Q752P;ENSP00000387966:Q752P	ENSP00000387966:Q752P	Q	-	2	0	PGBD3;RP11-123B3.6	50394316	0.990000	0.36364	0.003000	0.11579	0.003000	0.03518	2.665000	0.46791	0.413000	0.25759	0.402000	0.26972	CAA		0.413	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1			G	50724310	T	G	50724310	3	3	61	1	0	0	0	0	1	0	0	0	11813	1812	63	4	934	4	PGBD3	10	50724310	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	623	50724310	84810437	6743	14728										
ERCC6	2074	broad.mit.edu	37	chr10	50736558	50736558	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgttttgcagtgatctttTttagctgttgttccttgaat	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50736558T>C	ENST00000355832.5	-	4	635	c.557A>G	c.(556-558)aAa>aGa	p.K186R	ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.K186R|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.K186R|PGBD3_ENST00000603152.1_Missense_Mutation_p.K186R	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	186					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.K186R(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AGTGATCTTTTTTAGCTGTTG	0.373								Direct reversal of damage;Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	10											143	129	134					10																	50736558		2203	4300	6503	50406564	SO:0001583	missense	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.557A>G	10.37:g.50736558T>C	ENSP00000348089:p.Lys186Arg		50406564	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.389022	0.82902	.	.	ENSG00000225830;ENSG00000258838;ENSG00000258838	ENST00000355832;ENST00000515869;ENST00000447839	D;T;T	0.86769	-2.17;2.55;2.55	5.51	4.39	0.52855	.	.	.	.	.	D	0.86548	0.5959	M	0.74258	2.255	0.80722	D	1	P;B	0.48503	0.911;0.125	B;B	0.43809	0.432;0.056	D	0.86913	0.2062	9	0.49607	T	0.09	-35.4757	10.5635	0.45159	0.0:0.0763:0.0:0.9237	.	186;186	E7EV46;Q03468	.;ERCC6_HUMAN	R	186	ENSP00000348089:K186R;ENSP00000423550:K186R;ENSP00000387966:K186R	ENSP00000348089:K186R	K	-	2	0	ERCC6;RP11-123B3.6	50406564	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.893000	0.48633	2.081000	0.62600	0.533000	0.62120	AAA		0.373	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50736558	T	C	50736558	3	2	61	1	0	0	0	0	1	0	0	0	5230	1841	64	4	3996	4	ERCC6	10	50736558	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12248	50736558	84798189	6744	14729										
CHAT	1103	broad.mit.edu	37	chr10	50873015	50873015	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgagagacctctgcagtCtgctgccgcctactgagagc	11	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50873015C>T	ENST00000337653.2	+	15	2323	c.2170C>T	c.(2170-2172)Ctg>Ttg	p.L724L	CHAT_ENST00000351556.3_Silent_p.L606L|CHAT_ENST00000395559.2_Silent_p.L606L|CHAT_ENST00000395562.2_Silent_p.L642L|CHAT_ENST00000455728.2_Intron|CHAT_ENST00000339797.1_Silent_p.L606L	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	724					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.L724L(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CCTCTGCAGTCTGCTGCCGCC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	10											97	95	96					10																	50873015		2203	4300	6503	50543021	SO:0001819	synonymous_variant	1103			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.2170C>T	10.37:g.50873015C>T			50543021	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	37	CCDS7232.1																																																																																				0.507	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		T	50873015	C	T	50873015	2	4	61	1	0	0	0	0	0	0	0	1	3319	912	32	3		3	CHAT	10	50873015	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136457	50873015	84661732	6745	14730										
OGDHL	55753	broad.mit.edu	37	chr10	50952740	50952740	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttatatgcagaatctttTtatccttggacctgccataa	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50952740T>G	ENST00000374103.4	-	13	1773	c.1688A>C	c.(1687-1689)aAa>aCa	p.K563T	OGDHL_ENST00000432695.1_Missense_Mutation_p.K354T|OGDHL_ENST00000419399.1_Missense_Mutation_p.K506T	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	563					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.K563T(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CAGAATCTTTTTATCCTTGGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											135	129	131					10																	50952740		2203	4300	6503	50622746	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1688A>C	10.37:g.50952740T>G	ENSP00000363216:p.Lys563Thr		50622746	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.014774	0.54468	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.95949	-3.86;-3.86;-3.86	5.6	5.6	0.85130	Dehydrogenase, E1 component (1);	0.150331	0.64402	D	0.000018	D	0.88887	0.6559	N	0.02854	-0.475	0.51482	D	0.999924	B;B;B	0.17038	0.006;0.003;0.02	B;B;B	0.25987	0.039;0.039;0.065	D	0.85088	0.0950	10	0.45353	T	0.12	.	16.0816	0.81007	0.0:0.0:0.0:1.0	.	506;354;563	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	T	563;506;354	ENSP00000363216:K563T;ENSP00000401356:K506T;ENSP00000390240:K354T	ENSP00000363216:K563T	K	-	2	0	OGDHL	50622746	1.000000	0.71417	0.290000	0.24890	0.949000	0.60115	7.997000	0.88414	2.266000	0.75297	0.528000	0.53228	AAA		0.532	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		G	50952740	T	G	50952740	3	3	61	1	0	0	0	0	1	0	0	0	10871	1841	64	4	1388	4	OGDHL	10	50952740	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	79725	50952740	84582007	6746	14731										
OGDHL	55753	broad.mit.edu	37	chr10	50954894	50954894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgccctggccagcaaaggCggcgtccccatgaaccagga	12	16	0	1	rs199864072		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:50954894C>T	ENST00000374103.4	-	10	1283	c.1198G>A	c.(1198-1200)Gcc>Acc	p.A400T	OGDHL_ENST00000432695.1_Missense_Mutation_p.A191T|OGDHL_ENST00000419399.1_Missense_Mutation_p.A343T	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	400					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.A400T(3)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CCAGCAAAGGCGGCGTCCCCA	0.632																																																3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	10						C	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	114	84	94		1027,571,1198	5.8	1	10		94	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	58,58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	343/954,191/802,400/1011	50954894	2,13004	2203	4300	6503	50624900	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1198G>A	10.37:g.50954894C>T	ENSP00000363216:p.Ala400Thr		50624900	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	35	5.554669	0.96501	0.0	2.33E-4	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.97831	-4.56;-4.56;-4.56	5.76	5.76	0.90799	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99330	0.9765	H	0.97918	4.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.986;0.975;0.995	D	0.98581	1.0650	10	0.87932	D	0	.	19.9576	0.97228	0.0:1.0:0.0:0.0	.	343;191;400	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	T	400;343;191	ENSP00000363216:A400T;ENSP00000401356:A343T;ENSP00000390240:A191T	ENSP00000363216:A400T	A	-	1	0	OGDHL	50624900	1.000000	0.71417	0.969000	0.41365	0.734000	0.41952	7.776000	0.85560	2.736000	0.93811	0.655000	0.94253	GCC		0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		T	50954894	C	T	50954894	3	4	61	1	0	0	0	0	1	0	0	0	10871	768	27	1	1890	1	OGDHL	10	50954894	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2154	50954894	84579853	6747	14732										
NCOA4	8031	broad.mit.edu	37	chr10	51585586	51585586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagacaagtggctgcttcGaaagaaggcccaggtgagca	14	8	0	4	rs139624796	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:51585586G>A	ENST00000443446.1	+	8	1914	c.1685G>A	c.(1684-1686)cGa>cAa	p.R562Q	NCOA4_ENST00000414907.2_Missense_Mutation_p.R396Q|NCOA4_ENST00000374082.1_Intron|NCOA4_ENST00000430396.2_Missense_Mutation_p.R462Q|NCOA4_ENST00000438493.1_Missense_Mutation_p.R578Q|NCOA4_ENST00000374087.4_Missense_Mutation_p.R562Q|NCOA4_ENST00000344348.6_Missense_Mutation_p.R562Q|NCOA4_ENST00000452682.1_Missense_Mutation_p.R578Q	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	562					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)	p.R578Q(2)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TGGCTGCTTCGAAAGAAGGCC	0.448			T	RET	papillary thyroid								.|||	4	0.000798722	0.0023	0.0014	5008	,	,		19218	0		0	False		,,,				2504	0						Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	2	Substitution - Missense(2)	large_intestine(2)	10						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	5,4391		0,5,2193	47	51	49		1733,1733,1685,1685,1685	5.9	1	10	dbSNP_134	49	0,8554		0,0,4277	yes	missense,missense,missense,missense,missense	NCOA4	NM_001145260.1,NM_001145261.1,NM_001145262.1,NM_001145263.1,NM_005437.3	43,43,43,43,43	0,5,6470	AA,AG,GG		0.0,0.1137,0.0386	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	578/651,578/631,562/615,562/615,562/615	51585586	5,12945	2198	4277	6475	51255592	SO:0001583	missense	8031			L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1685G>A	10.37:g.51585586G>A	ENSP00000390713:p.Arg562Gln		51255592	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	37	CCDS7237.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	18.89	3.720117	0.68844	0.001137	0.0	ENSG00000138293	ENST00000438493;ENST00000452682;ENST00000430396;ENST00000374087;ENST00000414907;ENST00000344348;ENST00000443446	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.93	5.93	0.95920	.	0.267719	0.33959	N	0.004394	T	0.46658	0.1404	L	0.51422	1.61	0.32488	N	0.540631	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	P;P;P;P	0.61275	0.886;0.838;0.838;0.735	T	0.52351	-0.8587	9	.	.	.	-10.8638	15.478	0.75501	0.0679:0.0:0.9321:0.0	.	462;578;578;562	B4DF87;B4E260;E9PAV7;Q13772	.;.;.;NCOA4_HUMAN	Q	578;578;462;562;396;562;562	ENSP00000405146:R578Q;ENSP00000395465:R578Q;ENSP00000393053:R462Q;ENSP00000363200:R562Q;ENSP00000411018:R396Q;ENSP00000344552:R562Q;ENSP00000390713:R562Q	.	R	+	2	0	NCOA4	51255592	1.000000	0.71417	0.992000	0.48379	0.977000	0.68977	4.827000	0.62723	2.821000	0.97095	0.555000	0.69702	CGA		0.448	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		A	51585586	G	A	51585586	3	1	61	1	0	0	0	0	1	0	0	0	10262	1058	37	1	1763	1	NCOA4	10	51585586	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	630692	51585586	83949161	6748	14733										
A1CF	29974	broad.mit.edu	37	chr10	52610439	52610439	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttaccttttccagcaaagTttgcaaaatgatggactgca	8	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:52610439T>G	ENST00000373993.1	-	2	144				A1CF_ENST00000395495.1_Intron|A1CF_ENST00000282641.2_Intron|A1CF_ENST00000395489.2_Missense_Mutation_p.T22P|A1CF_ENST00000373997.3_Intron|A1CF_ENST00000373995.3_Missense_Mutation_p.T37P|A1CF_ENST00000374001.2_Intron			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor						cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.T37P(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						TCCAGCAAAGTTTGCAAAATG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											144	142	143					10																	52610439		2203	4300	6503	52280445	SO:0001627	intron_variant	29974			AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.100-6557A>C	10.37:g.52610439T>G			52280445	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	37	CCDS7242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.02|13.02	2.111423|2.111423	0.37242|0.37242	.|.	.|.	ENSG00000148584|ENSG00000148584	ENST00000395488|ENST00000373995;ENST00000395489	.|T;T	.|0.12039	.|2.73;2.72	4.03|4.03	2.88|2.88	0.33553|0.33553	.|.	.|.	.|.	.|.	.|.	T|T	0.40719|0.40719	0.1128|0.1128	M|M	0.92923|0.92923	3.36|3.36	0.09310|0.09310	N|N	1|1	.|D;P	.|0.71674	.|0.998;0.513	.|D;B	.|0.65010	.|0.931;0.346	T|T	0.22034|0.22034	-1.0228|-1.0228	6|9	0.87932|0.87932	D|D	0|0	-0.9941|-0.9941	7.66|7.66	0.28398|0.28398	0.0:0.0:0.2159:0.7841|0.0:0.0:0.2159:0.7841	.|.	.|22;37	.|F8W9F8;Q9NQ94-4	.|.;.	N|P	9|37;22	.|ENSP00000363107:T37P;ENSP00000378868:T22P	ENSP00000378867:K9N|ENSP00000363107:T37P	K|T	-|-	3|1	2|0	A1CF|A1CF	52280445|52280445	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.020000|0.020000	0.10135|0.10135	0.691000|0.691000	0.25467|0.25467	0.868000|0.868000	0.35678|0.35678	0.528000|0.528000	0.53228|0.53228	AAA|ACT		0.433	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		G	52610439	T	G	52610439	1	3	61	0	1	0	0	0	0	0	0	0	2	1725	60	4		4	A1CF	10	52610439	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1024853	52610439	82924308	6749	14734										
PRKG1	5592	broad.mit.edu	37	chr10	53227595	53227595	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccggacagcgaccgtcaaGagtaagactattttcatatt	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:53227595G>T	ENST00000401604.2	+	3	740	c.546G>T	c.(544-546)aaG>aaT	p.K182N	PRKG1_ENST00000373985.1_Splice_Site_p.K170N|PRKG1_ENST00000373980.4_Splice_Site_p.K197N			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	182	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.K197N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CGACCGTCAAGAGTAAGACTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											99	93	95					10																	53227595		2203	4300	6503	52897601	SO:0001630	splice_region_variant	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.547+1G>T	10.37:g.53227595G>T			52897601	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.583879	0.46110	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.97066	-4.23;-4.23;-3.15;-3.15	5.79	-2.5	0.06384	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.96617	0.8896	M	0.93720	3.45	0.46542	D	0.999092	P;P;P	0.40180	0.556;0.656;0.705	B;B;B	0.39660	0.247;0.216;0.306	D	0.93290	0.6667	10	0.49607	T	0.09	-6.517	11.1255	0.48315	0.7177:0.0:0.2823:0.0	.	182;197;182	B4DT93;Q13976-2;Q13976	.;.;KGP1_HUMAN	N	182;170;197;55	ENSP00000384200:K182N;ENSP00000363097:K170N;ENSP00000363092:K197N;ENSP00000363087:K55N	ENSP00000363087:K55N	K	+	3	2	PRKG1	52897601	1.000000	0.71417	0.986000	0.45419	0.908000	0.53690	1.531000	0.36018	-0.323000	0.08602	-0.253000	0.11424	AAG		0.353	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	T	53227595	G	T	53227595	5	4	61	1	0	0	0	0	0	0	1	0	12556	956	33	2	871	2	PRKG1	10	53227595	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	617156	53227595	82307152	6750	14735										
CSTF2T	23283	broad.mit.edu	37	chr10	53458685	53458685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccagggccagagacagAcacagactgagatttgcctg	14	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:53458685A>G	ENST00000331173.4	-	1	670	c.625T>C	c.(625-627)Tct>Cct	p.S209P	PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	209					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S209P(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				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)		ccagAGACAGACACAGACTGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	10											85	75	78					10																	53458685		2203	4300	6503	53128691	SO:0001583	missense	23283			AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.625T>C	10.37:g.53458685A>G	ENSP00000332444:p.Ser209Pro		53128691	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	37	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.437205	0.01098	.	.	ENSG00000177613	ENST00000331173	T	0.20332	2.08	0.893	-0.324	0.12706	.	0.567450	0.18057	N	0.153079	T	0.07413	0.0187	N	0.08118	0	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.30475	-0.9977	10	0.20519	T	0.43	-11.6809	3.0044	0.06024	0.6994:0.0:0.3006:0.0	.	209	Q9H0L4	CSTFT_HUMAN	P	209	ENSP00000332444:S209P	ENSP00000332444:S209P	S	-	1	0	CSTF2T	53128691	0.040000	0.19996	0.278000	0.24718	0.878000	0.50629	0.102000	0.15272	-0.133000	0.11537	-0.264000	0.10439	TCT		0.527	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		G	53458685	A	G	53458685	3	3	61	1	0	0	0	0	1	0	0	0	3991	275	10	4	1229	4	CSTF2T	10	53458685	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	231090	53458685	82076062	6751	14736										
PRKG1	5592	broad.mit.edu	37	chr10	53893621	53893621	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatgtgagaacagcaaaCgtaattgctgcagaagctgt	12	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:53893621C>T	ENST00000401604.2	+	8	1106	c.912C>T	c.(910-912)aaC>aaT	p.N304N	PRKG1_ENST00000373975.2_Silent_p.N22N|PRKG1_ENST00000373985.1_Silent_p.N292N|PRKG1_ENST00000373980.4_Silent_p.N319N			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	304	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.N319N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		GAACAGCAAACGTAATTGCTG	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	10											169	168	168					10																	53893621		2203	4300	6503	53563627	SO:0001819	synonymous_variant	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.912C>T	10.37:g.53893621C>T			53563627	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	37	CCDS44399.1																																																																																				0.348	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	53893621	C	T	53893621	2	4	61	1	0	0	0	0	0	0	0	1	12556	535	19	1		1	PRKG1	10	53893621	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	434936	53893621	81641126	6752	14737										
PRKG1	5592	broad.mit.edu	37	chr10	54032231	54032231	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggagagctctggaccattCtcagggataggtaggagatt	15	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:54032231C>A	ENST00000401604.2	+	12	1542	c.1348C>A	c.(1348-1350)Ctc>Atc	p.L450I	PRKG1_ENST00000373975.2_Missense_Mutation_p.L168I|PRKG1_ENST00000373985.1_Missense_Mutation_p.L438I|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.L465I|PRKG1-AS1_ENST00000426785.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	450	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.L465I(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CTGGACCATTCTCAGGGATAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10											120	117	118					10																	54032231		2203	4300	6503	53702237	SO:0001583	missense	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1348C>A	10.37:g.54032231C>A	ENSP00000384200:p.Leu450Ile		53702237	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220082	0.95139	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.67345	-0.26;-0.26;-0.26	5.88	5.88	0.94601	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71134	0.3304	N	0.12443	0.215	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.951;0.997;0.998	T	0.76512	-0.2932	10	0.87932	D	0	-13.2384	19.8265	0.96619	0.0:1.0:0.0:0.0	.	168;465;450	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	I	450;438;465;168;62	ENSP00000384200:L450I;ENSP00000363097:L438I;ENSP00000363092:L465I	ENSP00000327642:L168I	L	+	1	0	PRKG1	53702237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.481000	0.81124	2.789000	0.95967	0.591000	0.81541	CTC		0.333	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	54032231	C	A	54032231	3	1	61	1	0	0	0	0	1	0	0	0	12556	913	32	2	1709	2	PRKG1	10	54032231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138610	54032231	81502516	6753	14738										
PRKG1	5592	broad.mit.edu	37	chr10	54048734	54048734	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatttgaaaaatggagtaAaagacattcaaaagcacaag	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:54048734A>C	ENST00000401604.2	+	16	2025	c.1831A>C	c.(1831-1833)Aaa>Caa	p.K611Q	PRKG1_ENST00000373975.2_Missense_Mutation_p.K329Q|PRKG1_ENST00000373985.1_Missense_Mutation_p.K599Q|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.K626Q|PRKG1-AS1_ENST00000426785.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	611	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.K626Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AAATGGAGTAAAAGACATTCA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											101	112	108					10																	54048734		2200	4295	6495	53718740	SO:0001583	missense	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1831A>C	10.37:g.54048734A>C	ENSP00000384200:p.Lys611Gln		53718740	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	9.272	1.045809	0.19748	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.66460	-0.21;-0.21;-0.21	5.59	5.59	0.84812	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.44808	0.1311	N	0.08118	0	0.51233	D	0.999912	B;B;B	0.29341	0.008;0.203;0.242	B;B;B	0.25987	0.026;0.039;0.065	T	0.44982	-0.9292	10	0.11182	T	0.66	-19.9499	15.465	0.75394	1.0:0.0:0.0:0.0	.	329;626;611	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	Q	611;599;626;329;223	ENSP00000384200:K611Q;ENSP00000363097:K599Q;ENSP00000363092:K626Q	ENSP00000327642:K329Q	K	+	1	0	PRKG1	53718740	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	7.572000	0.82409	2.131000	0.65755	0.524000	0.50904	AAA		0.308	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	54048734	A	C	54048734	3	2	61	1	0	0	0	0	1	0	0	0	12556	15	1	4	2208	4	PRKG1	10	54048734	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16503	54048734	81486013	6754	14739										
PCDH15	65217	broad.mit.edu	37	chr10	55582852	55582852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggtctacaaaatctgttCtctgtgaaatgtctgaattt	8	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55582852C>A	ENST00000320301.6	-	33	5028	c.4634G>T	c.(4633-4635)aGa>aTa	p.R1545I	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.R1505I|PCDH15_ENST00000361849.3_Missense_Mutation_p.R1547I|PCDH15_ENST00000437009.1_Missense_Mutation_p.R1476I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.R1542I|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.R1522I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1545					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.R1552I(2)|p.R1545I(2)|p.R1552K(1)|p.R1545K(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAAATCTGTTCTCTGTGAAAT	0.393										HNSCC(58;0.16)																																						6	Substitution - Missense(6)	large_intestine(4)|upper_aerodigestive_tract(2)	10											86	93	90					10																	55582852		2203	4297	6500	55252858	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4634G>T	10.37:g.55582852C>A	ENSP00000322604:p.Arg1545Ile		55252858	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	5.722	0.317719	0.10845	.	.	ENSG00000150275	ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T	0.59906	0.28;0.26;0.3;0.27;0.26;0.23	5.91	0.533	0.17121	.	.	.	.	.	T	0.60534	0.2276	M	0.65498	2.005	0.39324	D	0.965307	P;B;B;B;B;P;P;B	0.49090	0.919;0.04;0.047;0.04;0.399;0.7;0.859;0.022	P;B;B;B;B;B;P;B	0.49708	0.62;0.018;0.04;0.018;0.071;0.288;0.62;0.018	T	0.60850	-0.7181	9	0.48119	T	0.1	.	10.663	0.45712	0.0:0.5206:0.0:0.4794	.	1522;1545;1547;1552;1476;1505;1542;1545	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;Q96QU1	.;.;.;.;.;.;.;PCD15_HUMAN	I	1505;1547;1522;1545;1542;1552;1476	ENSP00000378820:R1505I;ENSP00000354950:R1547I;ENSP00000378821:R1522I;ENSP00000322604:R1545I;ENSP00000378818:R1542I;ENSP00000412628:R1476I	ENSP00000322604:R1545I	R	-	2	0	PCDH15	55252858	0.939000	0.31865	0.008000	0.14137	0.030000	0.12068	1.257000	0.32932	-0.147000	0.11254	-0.157000	0.13467	AGA		0.393	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55582852	C	A	55582852	3	1	61	1	0	0	0	0	1	0	0	0	11542	913	32	2	2843	2	PCDH15	10	55582852	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1534118	55582852	79951895	6755	14740										
PCDH15	65217	broad.mit.edu	37	chr10	55583189	55583189	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcatgagaaagatgtttTtatggctctcattactatta	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55583189T>C	ENST00000320301.6	-	33	4762				PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395432.2_Intron|PCDH15_ENST00000361849.3_Intron|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000463095.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395430.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15						equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAAGATGTTTTTATGGCTCTC	0.318										HNSCC(58;0.16)																																						0			10											77	70	72					10																	55583189		1568	3582	5150	55253195	SO:0001627	intron_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4368-71A>G	10.37:g.55583189T>C			55253195	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.318	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55583189	T	C	55583189	1	2	61	0	1	0	0	0	0	0	0	0	11542	1855	64	4		4	PCDH15	10	55583189	Intron	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	337	55583189	79951558	6756	14741										
PCDH15	65217	broad.mit.edu	37	chr10	55591101	55591101	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgaccaaaaccaccaaGatggcaggaatgcagcagag	11	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55591101G>T	ENST00000320301.6	-	30	4570	c.4176C>A	c.(4174-4176)atC>atA	p.I1392I	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Silent_p.I1003I|PCDH15_ENST00000395432.2_Silent_p.I1355I|PCDH15_ENST00000361849.3_Silent_p.I1392I|PCDH15_ENST00000437009.1_Silent_p.I1321I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Silent_p.I1397I|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373965.2_Silent_p.I1399I|PCDH15_ENST00000395445.1_Silent_p.I1399I|PCDH15_ENST00000395438.1_Silent_p.I1392I|PCDH15_ENST00000395430.1_Silent_p.I1392I|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.I1370I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1392					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.I1397I(1)|p.I1392I(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAACCACCAAGATGGCAGGAA	0.463										HNSCC(58;0.16)																																						2	Substitution - coding silent(2)	large_intestine(2)	10											237	207	217					10																	55591101		2203	4300	6503	55261107	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4176C>A	10.37:g.55591101G>T			55261107	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.463	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55591101	G	T	55591101	2	4	61	1	0	0	0	0	0	0	0	1	11542	932	33	2		2	PCDH15	10	55591101	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7912	55591101	79943646	6757	14742										
PCDH15	65217	broad.mit.edu	37	chr10	55600099	55600099	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaaaaagctcatttctatCgatggctctgttggtttggg	10	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55600099C>A	ENST00000320301.6	-	29	4358	c.3964G>T	c.(3964-3966)Gat>Tat	p.D1322Y	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.D933Y|PCDH15_ENST00000395432.2_Missense_Mutation_p.D1285Y|PCDH15_ENST00000361849.3_Missense_Mutation_p.D1322Y|PCDH15_ENST00000437009.1_Missense_Mutation_p.D1251Y|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.D1327Y|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373965.2_Missense_Mutation_p.D1329Y|PCDH15_ENST00000395445.1_Missense_Mutation_p.D1329Y|PCDH15_ENST00000395438.1_Missense_Mutation_p.D1322Y|PCDH15_ENST00000395430.1_Missense_Mutation_p.D1322Y|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.D1300Y	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1322					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.D1322N(2)|p.D1327N(2)|p.D1327Y(1)|p.D1322Y(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCATTTCTATCGATGGCTCTG	0.413										HNSCC(58;0.16)																																						6	Substitution - Missense(6)	lung(4)|large_intestine(2)	10											145	139	141					10																	55600099		2203	4300	6503	55270105	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3964G>T	10.37:g.55600099C>A	ENSP00000322604:p.Asp1322Tyr		55270105	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865643	0.51588	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.59772	0.32;0.37;0.29;0.29;0.28;0.27;0.24;0.29;0.26;0.24;0.27	5.43	4.3	0.51218	.	.	.	.	.	T	0.50531	0.1621	N	0.08118	0	0.20074	N	0.999933	D;D;D;D;D;D;D;P;D;D;D;D;D	0.71674	0.989;0.986;0.986;0.986;0.998;0.986;0.989;0.795;0.975;0.975;0.975;0.96;0.986	P;P;P;P;D;P;P;P;P;P;P;P;P	0.68192	0.869;0.869;0.869;0.744;0.956;0.869;0.869;0.572;0.744;0.643;0.663;0.818;0.869	T	0.43572	-0.9383	9	0.87932	D	0	.	2.972	0.05926	0.2703:0.5523:0.0:0.1774	.	1300;1322;1322;1327;1251;1285;1322;1322;1329;1329;1322;1327;1322	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	Y	1329;1327;1322;1322;933;1329;1285;1322;1300;1322;1322;1327;1251	ENSP00000363076:D1329Y;ENSP00000410304:D1327Y;ENSP00000378826:D1322Y;ENSP00000386693:D933Y;ENSP00000378832:D1329Y;ENSP00000378820:D1285Y;ENSP00000354950:D1322Y;ENSP00000378821:D1300Y;ENSP00000322604:D1322Y;ENSP00000378818:D1322Y;ENSP00000412628:D1251Y	ENSP00000322604:D1322Y	D	-	1	0	PCDH15	55270105	0.998000	0.40836	0.920000	0.36463	0.937000	0.57800	3.464000	0.53057	2.703000	0.92315	0.579000	0.79373	GAT		0.413	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55600099	C	A	55600099	3	1	61	1	0	0	0	0	1	0	0	0	11542	884	31	2	3542	2	PCDH15	10	55600099	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8998	55600099	79934648	6758	14743										
PCDH15	65217	broad.mit.edu	37	chr10	55698593	55698593	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttttgaaggaactcggaGattggcaaggaccacttcca	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55698593G>T	ENST00000320301.6	-	25	3749	c.3355C>A	c.(3355-3357)Ctc>Atc	p.L1119I	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.L730I|PCDH15_ENST00000395432.2_Missense_Mutation_p.L1082I|PCDH15_ENST00000361849.3_Missense_Mutation_p.L1119I|PCDH15_ENST00000437009.1_Missense_Mutation_p.L1048I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.L1124I|PCDH15_ENST00000373965.2_Missense_Mutation_p.L1126I|PCDH15_ENST00000395445.1_Missense_Mutation_p.L1126I|PCDH15_ENST00000395438.1_Missense_Mutation_p.L1119I|PCDH15_ENST00000395430.1_Missense_Mutation_p.L1119I|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.L1097I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1119	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.L1124I(1)|p.L1119I(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GGAACTCGGAGATTGGCAAGG	0.383										HNSCC(58;0.16)																																						2	Substitution - Missense(2)	large_intestine(2)	10											113	104	107					10																	55698593		2203	4300	6503	55368599	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3355C>A	10.37:g.55698593G>T	ENSP00000322604:p.Leu1119Ile		55368599	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498164	0.64186	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.77	2.9	0.33743	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.59252	0.2180	L	0.61036	1.89	0.52501	D	0.999958	D;D;D;D;D;D;D;P;D;D;D;D;D	0.69078	0.994;0.997;0.988;0.974;0.997;0.997;0.994;0.955;0.988;0.977;0.977;0.997;0.997	D;D;D;P;D;D;D;P;D;D;D;D;D	0.74348	0.981;0.968;0.933;0.879;0.983;0.983;0.981;0.826;0.926;0.926;0.926;0.968;0.977	T	0.57688	-0.7768	9	0.44086	T	0.13	.	7.2596	0.26195	0.1584:0.1531:0.6884:0.0	.	1097;1119;1119;1124;1048;1082;1119;1119;1126;1126;1119;1124;1119	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	I	1126;1124;1119;1119;730;1126;1082;1119;1097;1119;1119;1124;1048	ENSP00000363076:L1126I;ENSP00000410304:L1124I;ENSP00000378826:L1119I;ENSP00000386693:L730I;ENSP00000378832:L1126I;ENSP00000378820:L1082I;ENSP00000354950:L1119I;ENSP00000378821:L1097I;ENSP00000322604:L1119I;ENSP00000378818:L1119I;ENSP00000412628:L1048I	ENSP00000322604:L1119I	L	-	1	0	PCDH15	55368599	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	2.848000	0.48278	1.441000	0.47550	0.655000	0.94253	CTC		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55698593	G	T	55698593	3	4	61	1	0	0	0	0	1	0	0	0	11542	942	33	2	4167	2	PCDH15	10	55698593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98494	55698593	79836154	6759	14744										
PCDH15	65217	broad.mit.edu	37	chr10	55719536	55719536	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatctcaccaggatgtaaGacaagaatcttcactgtggc	11	9	3	2	rs535499066		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55719536G>T	ENST00000320301.6	-	23	3472	c.3078C>A	c.(3076-3078)gtC>gtA	p.V1026V	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Silent_p.V637V|PCDH15_ENST00000395432.2_Silent_p.V989V|PCDH15_ENST00000361849.3_Silent_p.V1026V|PCDH15_ENST00000437009.1_Silent_p.V955V|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Silent_p.V1031V|PCDH15_ENST00000373965.2_Silent_p.V1033V|PCDH15_ENST00000395445.1_Silent_p.V1033V|PCDH15_ENST00000395438.1_Silent_p.V1026V|PCDH15_ENST00000395430.1_Silent_p.V1026V|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.V1004V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1026	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.V1031V(1)|p.V1026V(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CAGGATGTAAGACAAGAATCT	0.398										HNSCC(58;0.16)																																						2	Substitution - coding silent(2)	large_intestine(2)	10											88	79	82					10																	55719536		2203	4300	6503	55389542	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3078C>A	10.37:g.55719536G>T			55389542	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.398	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55719536	G	T	55719536	2	4	61	1	0	0	0	0	0	0	0	1	11542	929	33	2		2	PCDH15	10	55719536	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20943	55719536	79815211	6760	14745										
PCDH15	65217	broad.mit.edu	37	chr10	55913042	55913042	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgacccttcgtctgcgtcGactgcagtgagctggaattg	12	10	1	2	rs201215741		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55913042G>A	ENST00000320301.6	-	14	1996	c.1602C>T	c.(1600-1602)gtC>gtT	p.V534V	PCDH15_ENST00000373957.3_Silent_p.V512V|PCDH15_ENST00000373955.1_Silent_p.V534V|PCDH15_ENST00000409834.1_Silent_p.V145V|PCDH15_ENST00000395432.2_Silent_p.V497V|PCDH15_ENST00000361849.3_Silent_p.V534V|PCDH15_ENST00000437009.1_Silent_p.V534V|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Silent_p.V539V|PCDH15_ENST00000373965.2_Silent_p.V541V|PCDH15_ENST00000395445.1_Silent_p.V541V|PCDH15_ENST00000395438.1_Silent_p.V534V|PCDH15_ENST00000395430.1_Silent_p.V534V|PCDH15_ENST00000395446.1_Silent_p.V534V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.V512V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	534	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.V539V(1)|p.V534V(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CGTCTGCGTCGACTGCAGTGA	0.443										HNSCC(58;0.16)																																						2	Substitution - coding silent(2)	large_intestine(2)	10											102	96	98					10																	55913042		2203	4300	6503	55583048	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1602C>T	10.37:g.55913042G>A			55583048	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.443	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55913042	G	A	55913042	2	1	61	1	0	0	0	0	0	0	0	1	11542	1045	37	1		1	PCDH15	10	55913042	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	193506	55913042	79621705	6761	14746										
PCDH15	65217	broad.mit.edu	37	chr10	55944895	55944895	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacacaaaagctctttaccGaaaaggtgtaagtttgctgt	8	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:55944895G>A	ENST00000320301.6	-	12	1833	c.1439C>T	c.(1438-1440)tCg>tTg	p.S480L	PCDH15_ENST00000373957.3_Splice_Site_p.S458L|PCDH15_ENST00000373955.1_Splice_Site_p.S480L|PCDH15_ENST00000409834.1_Splice_Site_p.S91L|PCDH15_ENST00000395432.2_Splice_Site_p.S443L|PCDH15_ENST00000361849.3_Splice_Site_p.S480L|PCDH15_ENST00000437009.1_Splice_Site_p.S480L|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Splice_Site_p.S485L|PCDH15_ENST00000373965.2_Splice_Site_p.S487L|PCDH15_ENST00000395445.1_Splice_Site_p.S487L|PCDH15_ENST00000395438.1_Splice_Site_p.S480L|PCDH15_ENST00000395430.1_Splice_Site_p.S480L|PCDH15_ENST00000395446.1_Splice_Site_p.S480L|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Splice_Site_p.S458L	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	480	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.S485L(1)|p.S480L(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCTCTTTACCGAAAAGGTGTA	0.383										HNSCC(58;0.16)																																						2	Substitution - Missense(2)	large_intestine(2)	10											144	120	128					10																	55944895		2203	4300	6503	55614901	SO:0001630	splice_region_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1440+1C>T	10.37:g.55944895G>A			55614901	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691913	0.48097	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59906	0.23;0.64;0.64;0.36;0.23;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64	5.1	4.18	0.49190	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.48205	0.1487	L	0.51422	1.61	0.38393	D	0.945465	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.29188	0.102;0.048;0.021;0.048;0.236;0.102;0.102;0.003;0.01;0.01;0.013;0.003;0.001;0.006;0.102	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.20955	0.032;0.021;0.006;0.014;0.021;0.021;0.032;0.005;0.005;0.005;0.008;0.005;0.003;0.014;0.021	T	0.48422	-0.9037	9	0.30078	T	0.28	.	12.0153	0.53311	0.0879:0.0:0.9121:0.0	.	458;480;480;485;480;443;480;480;487;487;480;485;480;458;480	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	L	487;485;480;480;91;487;480;443;480;458;458;480;480;485;480;480	ENSP00000363076:S487L;ENSP00000410304:S485L;ENSP00000378826:S480L;ENSP00000386693:S91L;ENSP00000378832:S487L;ENSP00000378833:S480L;ENSP00000378820:S443L;ENSP00000354950:S480L;ENSP00000378821:S458L;ENSP00000363068:S458L;ENSP00000322604:S480L;ENSP00000378818:S480L;ENSP00000412628:S480L;ENSP00000363066:S480L	ENSP00000322604:S480L	S	-	2	0	PCDH15	55614901	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	4.228000	0.58619	1.275000	0.44379	0.586000	0.80456	TCG		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	Missense_Mutation	A	55944895	G	A	55944895	5	1	61	1	0	0	0	0	0	0	1	0	11542	1072	37	1	6135	1	PCDH15	10	55944895	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31853	55944895	79589852	6762	14747										
PCDH15	65217	broad.mit.edu	37	chr10	56077174	56077174	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagtggtggtggtggttcGcctctcattcagattttggg	16	6	2	2	rs111033260	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:56077174G>A	ENST00000320301.6	-	8	1127	c.733C>T	c.(733-735)Cga>Tga	p.R245*	PCDH15_ENST00000373957.3_Nonsense_Mutation_p.R223*|PCDH15_ENST00000373955.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.R208*|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.R245*|PCDH15_ENST00000437009.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395440.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.R250*|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395446.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395442.1_Nonsense_Mutation_p.R245*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.R223*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	245	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.R245*(1)|p.R250*(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTGGTGGTTCGCCTCTCATTC	0.483										HNSCC(58;0.16)																																						2	Substitution - Nonsense(2)	large_intestine(2)	10	GRCh37	CM030933	PCDH15	M	rs111033260		stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	167	127	141	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	748,733,733,733,622,667,748,733,748,733,667,733	2.5	1	10	dbSNP_132	141	4,8596	3.7+/-12.6	0,4,4296	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	,,,,,,,,,,,	250/1963,245/1958,245/1887,245/1953,208/1916,223/1936,250/1791,245/1540,250/1683,245/1678,223/1933,245/1956	56077174	5,13001	2203	4300	6503	55747180	SO:0001587	stop_gained	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.733C>T	10.37:g.56077174G>A	ENSP00000322604:p.Arg245*		55747180	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	37	6.189662	0.97362	2.27E-4	4.65E-4	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	.	.	.	4.77	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0829	0.53682	0.0:0.0:0.5788:0.4212	.	.	.	.	X	245;250;245;245;245;245;245;245;208;245;223;223;245;245;250;245;245	.	ENSP00000322604:R245X	R	-	1	2	PCDH15	55747180	0.967000	0.33354	0.987000	0.45799	0.115000	0.19883	3.304000	0.51866	1.103000	0.41568	-0.321000	0.08615	CGA		0.483	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	56077174	G	A	56077174	4	1	61	1	0	0	0	0	0	1	0	0	11542	1095	38	1	6882	1	PCDH15	10	56077174	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132279	56077174	79457573	6763	14748										
PCDH15	65217	broad.mit.edu	37	chr10	56106210	56106210	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctccattgtctcctgaaAatcctgtgaatattgtggta	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:56106210A>T	ENST00000320301.6	-	6	903	c.509T>A	c.(508-510)tTt>tAt	p.F170Y	PCDH15_ENST00000373957.3_Missense_Mutation_p.F148Y|PCDH15_ENST00000373955.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.F170Y|PCDH15_ENST00000361849.3_Missense_Mutation_p.F170Y|PCDH15_ENST00000437009.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395440.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000414778.1_Missense_Mutation_p.F175Y|PCDH15_ENST00000373965.2_Missense_Mutation_p.F170Y|AC013737.1_ENST00000583830.1_RNA|PCDH15_ENST00000395445.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395438.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395430.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395446.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395442.1_Missense_Mutation_p.F170Y|PCDH15_ENST00000395433.1_Missense_Mutation_p.F148Y	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	170	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.F175Y(1)|p.F170Y(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTCTCCTGAAAATCCTGTGAA	0.348										HNSCC(58;0.16)																																						2	Substitution - Missense(2)	large_intestine(2)	10											150	152	151					10																	56106210		2203	4300	6503	55776216	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.509T>A	10.37:g.56106210A>T	ENSP00000322604:p.Phe170Tyr		55776216	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790753	0.90367	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59083	0.46;0.51;0.44;0.43;0.43;0.68;0.57;0.36;0.35;0.4;0.29;0.35;0.35;0.44;0.49	5.35	5.35	0.76521	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.71913	0.3396	L	0.60455	1.87	0.43179	D	0.994998	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.998;0.999;0.999;1.0;0.998;0.998;0.998;0.999;0.999;0.999;1.0;0.999;0.999;0.999;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.996;0.999;0.999;0.999;0.998;0.996;0.996;0.998;0.998;0.998;0.997;0.999;0.998;0.999;0.999	T	0.73490	-0.3966	9	0.49607	T	0.09	.	14.3239	0.66505	1.0:0.0:0.0:0.0	.	148;170;170;175;170;170;170;170;170;170;170;175;170;148;170	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	Y	170;175;170;170;170;170;170;170;170;170;148;148;170;170;175;170;170	ENSP00000363076:F170Y;ENSP00000410304:F175Y;ENSP00000378826:F170Y;ENSP00000378832:F170Y;ENSP00000378833:F170Y;ENSP00000378829:F170Y;ENSP00000378827:F170Y;ENSP00000378820:F170Y;ENSP00000354950:F170Y;ENSP00000378821:F148Y;ENSP00000363068:F148Y;ENSP00000322604:F170Y;ENSP00000378818:F170Y;ENSP00000412628:F170Y;ENSP00000363066:F170Y	ENSP00000322604:F170Y	F	-	2	0	PCDH15	55776216	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.526000	0.90588	2.034000	0.60081	0.528000	0.53228	TTT		0.348	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	56106210	A	T	56106210	3	4	61	1	0	0	0	0	1	0	0	0	11542	14	1	5	7114	5	PCDH15	10	56106210	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29036	56106210	79428537	6764	14749										
ZWINT	11130	broad.mit.edu	37	chr10	58119488	58119488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttcccggagttgtgtcCgtttcctctgggcttcctcc	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:58119488C>T	ENST00000373944.3	-	4	421	c.383G>A	c.(382-384)cGg>cAg	p.R128Q	ZWINT_ENST00000395405.1_Missense_Mutation_p.R128Q|ZWINT_ENST00000460654.1_5'UTR|ZWINT_ENST00000318387.2_Missense_Mutation_p.R8Q|ZWINT_ENST00000361148.6_Missense_Mutation_p.R128Q			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	128	Interaction with NDC80 and ZW10.				establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)	p.R128Q(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						GAGTTGTGTCCGTTTCCTCTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	10											136	131	132					10																	58119488		2203	4300	6503	57789494	SO:0001583	missense	11130			AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"ZW10 interactor"				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.383G>A	10.37:g.58119488C>T	ENSP00000363055:p.Arg128Gln		57789494	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	C	1.345	-0.592902	0.03771	.	.	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387;ENST00000361148	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.8	-6.35	0.01975	.	1.202850	0.06140	N	0.672178	T	0.29914	0.0748	N	0.16307	0.4	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.06405	0.002;0.002	T	0.23404	-1.0189	10	0.23891	T	0.37	-0.7288	15.0023	0.71483	0.0:0.185:0.0:0.815	.	128;128	A6NNV6;O95229	.;ZWINT_HUMAN	Q	128;128;8;128	ENSP00000363055:R128Q;ENSP00000378801:R128Q;ENSP00000322850:R8Q;ENSP00000354921:R128Q	ENSP00000322850:R8Q	R	-	2	0	ZWINT	57789494	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.564000	0.02152	-1.274000	0.02421	-1.121000	0.02013	CGG		0.557	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1			T	58119488	C	T	58119488	3	4	61	1	0	0	0	0	1	0	0	0	18288	652	23	1	470	1	ZWINT	10	58119488	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2013278	58119488	77415259	6765	14750										
BICC1	80114	broad.mit.edu	37	chr10	60546739	60546739	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaacattcacatgtaatCggcaaaggtggcaacaatat	8	8	1	1	rs144991685	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:60546739C>T	ENST00000373886.3	+	5	448	c.444C>T	c.(442-444)atC>atT	p.I148I		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	148	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I148I(2)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CACATGTAATCGGCAAAGGTG	0.368													C|||	3	0.000599042	0	0	5008	,	,		16926	0		0	False		,,,				2504	0.0031															2	Substitution - coding silent(2)	large_intestine(1)|skin(1)	10											114	106	109					10																	60546739		2203	4300	6503	60216745	SO:0001819	synonymous_variant	80114			AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.444C>T	10.37:g.60546739C>T			60216745		Silent	SNP	ENST00000373886.3	37	CCDS31206.1																																																																																				0.368	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		T	60546739	C	T	60546739	2	4	61	1	0	0	0	0	0	0	0	1	1428	874	31	1		1	BICC1	10	60546739	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2427251	60546739	74988008	6766	14751										
BICC1	80114	broad.mit.edu	37	chr10	60549593	60549593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcatgcagagaacaggtgCtcagatccactttcctgatc	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:60549593C>T	ENST00000373886.3	+	8	951	c.947C>T	c.(946-948)gCt>gTt	p.A316V		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	316	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.A316V(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						AGAACAGGTGCTCAGATCCAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											178	160	166					10																	60549593		2203	4300	6503	60219599	SO:0001583	missense	80114			AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.947C>T	10.37:g.60549593C>T	ENSP00000362993:p.Ala316Val		60219599		Missense_Mutation	SNP	ENST00000373886.3	37	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	C	35	5.489896	0.96339	.	.	ENSG00000122870	ENST00000373886	T	0.30714	1.52	5.67	5.67	0.87782	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	M	0.72576	2.205	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.43940	-0.9360	10	0.16420	T	0.52	-13.2676	19.7848	0.96432	0.0:1.0:0.0:0.0	.	316	Q9H694	BICC1_HUMAN	V	316	ENSP00000362993:A316V	ENSP00000362993:A316V	A	+	2	0	BICC1	60219599	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.711000	0.84669	2.673000	0.90976	0.655000	0.94253	GCT		0.443	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		T	60549593	C	T	60549593	3	4	61	1	0	0	0	0	1	0	0	0	1428	797	28	3	977	3	BICC1	10	60549593	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2854	60549593	74985154	6767	14752										
FAM13C	220965	broad.mit.edu	37	chr10	61012575	61012575	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacatggtagcctcatgtaAattagacatggagagagctg	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:61012575A>C	ENST00000373868.2	-	12	1603	c.1516T>G	c.(1516-1518)Tta>Gta	p.L506V	FAM13C_ENST00000435852.2_Missense_Mutation_p.L506V|FAM13C_ENST00000442566.3_Missense_Mutation_p.L527V|FAM13C_ENST00000373867.3_Missense_Mutation_p.L422V|FAM13C_ENST00000419214.2_Missense_Mutation_p.L408V|FAM13C_ENST00000277705.6_Missense_Mutation_p.L526V|FAM13C_ENST00000468840.2_Missense_Mutation_p.L423V	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	506								p.L506V(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCCTCATGTAAATTAGACATG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											154	133	140					10																	61012575		2203	4300	6503	60682581	SO:0001583	missense	220965			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.1516T>G	10.37:g.61012575A>C	ENSP00000362975:p.Leu506Val		60682581	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650190	0.67472	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852	T;T;T;T;T	0.58506	0.4;0.33;0.35;0.52;0.36	5.72	3.32	0.38043	.	0.106123	0.41500	D	0.000874	T	0.72095	0.3418	M	0.74258	2.255	0.34606	D	0.717029	D;D;D;D	0.76494	0.999;0.996;0.967;0.991	D;P;P;P	0.87578	0.998;0.894;0.758;0.861	T	0.79600	-0.1736	10	0.59425	D	0.04	-8.15	9.7534	0.40490	0.8559:0.0:0.1441:0.0	.	506;422;408;506	B7Z2K3;B7ZB77;Q8NE31-3;Q8NE31	.;.;.;FA13C_HUMAN	V	422;506;527;526;408;423;506	ENSP00000362975:L506V;ENSP00000395661:L527V;ENSP00000277705:L526V;ENSP00000391993:L408V;ENSP00000392302:L506V	ENSP00000277705:L526V	L	-	1	2	FAM13C	60682581	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.666000	0.37460	1.069000	0.40788	0.533000	0.62120	TTA		0.438	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			C	61012575	A	C	61012575	3	2	61	1	0	0	0	0	1	0	0	0	5470	11	1	4	253	4	FAM13C	10	61012575	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	462982	61012575	74522172	6768	14753										
FAM13C	220965	broad.mit.edu	37	chr10	61112038	61112038	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagctgctacctgactttCtccgtggctcctcccgctct	9	16	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:61112038C>T	ENST00000373868.2	-	3	403	c.316G>A	c.(316-318)Gaa>Aaa	p.E106K	FAM13C_ENST00000435852.2_Missense_Mutation_p.E106K|FAM13C_ENST00000442566.3_Missense_Mutation_p.E106K|FAM13C_ENST00000422313.2_Missense_Mutation_p.E106K|FAM13C_ENST00000373867.3_Missense_Mutation_p.E23K|FAM13C_ENST00000419214.2_Missense_Mutation_p.E106K|FAM13C_ENST00000277705.6_Missense_Mutation_p.E106K|FAM13C_ENST00000468840.2_Missense_Mutation_p.E23K	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	106								p.E106K(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCTGACTTTCTCCGTGGCTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	10											76	74	74					10																	61112038		2203	4300	6503	60782044	SO:0001583	missense	220965			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.316G>A	10.37:g.61112038C>T	ENSP00000362975:p.Glu106Lys		60782044	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650696	0.67472	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000512919	T;T;T;T;T;T	0.58797	0.37;0.55;0.53;0.31;0.38;0.4	5.93	5.03	0.67393	.	0.070763	0.64402	D	0.000016	T	0.53367	0.1792	L	0.56769	1.78	0.27534	N	0.951018	P;B;P;P;P	0.38827	0.649;0.184;0.649;0.51;0.51	B;B;B;B;B	0.36666	0.23;0.133;0.23;0.181;0.154	T	0.57039	-0.7879	10	0.66056	D	0.02	.	12.2425	0.54551	0.0:0.9214:0.0:0.0786	.	106;23;106;106;106	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	K	23;106;106;106;106;23;106;106;23	ENSP00000362975:E106K;ENSP00000395661:E106K;ENSP00000277705:E106K;ENSP00000391993:E106K;ENSP00000392302:E106K;ENSP00000400241:E106K	ENSP00000277705:E106K	E	-	1	0	FAM13C	60782044	0.998000	0.40836	0.995000	0.50966	0.224000	0.24922	4.150000	0.58098	1.534000	0.49203	-0.145000	0.13849	GAA		0.557	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			T	61112038	C	T	61112038	3	4	61	1	0	0	0	0	1	0	0	0	5470	922	32	3	1489	3	FAM13C	10	61112038	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99463	61112038	74422709	6769	14754										
SLC16A9	220963	broad.mit.edu	37	chr10	61414085	61414085	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctgcatttttcctcactActgtagctcttgtcaagaat	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:61414085A>T	ENST00000395348.3	-	5	1335	c.699T>A	c.(697-699)agT>agA	p.S233R	SLC16A9_ENST00000395347.1_Missense_Mutation_p.S233R	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	233					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.S233R(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						TTTCCTCACTACTGTAGCTCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											247	235	239					10																	61414085		2203	4300	6503	61084091	SO:0001583	missense	220963			AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.699T>A	10.37:g.61414085A>T	ENSP00000378757:p.Ser233Arg		61084091	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	1.223	-0.626392	0.03610	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.04406	3.63;3.63	5.02	1.24	0.21308	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.205460	0.05428	N	0.545372	T	0.02888	0.0086	N	0.14661	0.345	0.09310	N	1	B	0.27316	0.175	B	0.23716	0.048	T	0.46624	-0.9178	10	0.16420	T	0.52	.	2.9363	0.05816	0.6294:0.1497:0.0779:0.143	.	233	Q7RTY1	MOT9_HUMAN	R	233	ENSP00000378757:S233R;ENSP00000378756:S233R	ENSP00000378756:S233R	S	-	3	2	SLC16A9	61084091	0.000000	0.05858	0.000000	0.03702	0.616000	0.37450	0.445000	0.21677	-0.044000	0.13491	0.482000	0.46254	AGT		0.378	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		T	61414085	A	T	61414085	3	4	61	1	0	0	0	0	1	0	0	0	14452	388	14	5	838	5	SLC16A9	10	61414085	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	302047	61414085	74120662	6770	14755										
SLC16A9	220963	broad.mit.edu	37	chr10	61444038	61444038	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccaccgtcaggcgacttTttaagttccattgtaagaca	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:61444038T>G	ENST00000395348.3	-	2	648	c.12A>C	c.(10-12)aaA>aaC	p.K4N	SLC16A9_ENST00000395347.1_Missense_Mutation_p.K4N|SLC16A9_ENST00000490066.1_5'UTR	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	4					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.K4N(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						CAGGCGACTTTTTAAGTTCCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											110	103	105					10																	61444038		2203	4300	6503	61114044	SO:0001583	missense	220963			AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.12A>C	10.37:g.61444038T>G	ENSP00000378757:p.Lys4Asn		61114044	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.495934	0.44352	.	.	ENSG00000165449	ENST00000395348;ENST00000395347;ENST00000490066	T;T	0.04758	3.56;3.56	5.33	-1.3	0.09259	Major facilitator superfamily domain, general substrate transporter (1);	0.624103	0.15416	N	0.263502	T	0.04003	0.0112	L	0.38838	1.175	0.23089	N	0.998315	B	0.32245	0.361	B	0.26864	0.074	T	0.34004	-0.9846	10	0.28530	T	0.3	.	12.633	0.56667	0.0:0.6006:0.0:0.3994	.	4	Q7RTY1	MOT9_HUMAN	N	4	ENSP00000378757:K4N;ENSP00000378756:K4N	ENSP00000378756:K4N	K	-	3	2	SLC16A9	61114044	0.432000	0.25554	0.224000	0.23877	0.861000	0.49209	0.258000	0.18387	-0.512000	0.06505	0.533000	0.62120	AAA		0.443	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61444038	T	G	61444038	3	3	61	1	0	0	0	0	1	0	0	0	14452	1838	64	4	1537	4	SLC16A9	10	61444038	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	29953	61444038	74090709	6771	14756										
ANK3	288	broad.mit.edu	37	chr10	61830428	61830428	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggcatccgtgtcatgaGaaaactctgctgtggtggca	13	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:61830428G>T	ENST00000280772.2	-	37	10402	c.10211C>A	c.(10210-10212)tCt>tAt	p.S3404Y	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3404					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.S3404Y(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CGTGTCATGAGAAAACTCTGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											142	131	135					10																	61830428		2203	4300	6503	61500434	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.10211C>A	10.37:g.61830428G>T	ENSP00000280772:p.Ser3404Tyr		61500434	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741907	0.69418	.	.	ENSG00000151150	ENST00000280772	T	0.74947	-0.89	5.48	5.48	0.80851	.	0.000000	0.41823	D	0.000812	D	0.84037	0.5384	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.85147	0.0984	10	0.87932	D	0	.	19.359	0.94428	0.0:0.0:1.0:0.0	.	3404	Q12955	ANK3_HUMAN	Y	3404	ENSP00000280772:S3404Y	ENSP00000280772:S3404Y	S	-	2	0	ANK3	61500434	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	8.062000	0.89475	2.584000	0.87258	0.561000	0.74099	TCT		0.473	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61830428	G	T	61830428	3	4	61	1	0	0	0	0	1	0	0	0	622	942	33	2	3263	2	ANK3	10	61830428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	386390	61830428	73704319	6772	14757										
ANK3	288	broad.mit.edu	37	chr10	62149261	62149261	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcattgatttctaaatcCctgtttttctttaattgtga	5	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:62149261C>A	ENST00000280772.2	-	1	227	c.36G>T	c.(34-36)agG>agT	p.R12S	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	12					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R12S(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTTCTAAATCCCTGTTTTTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											152	149	150					10																	62149261		2203	4300	6503	61819267	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.36G>T	10.37:g.62149261C>A	ENSP00000280772:p.Arg12Ser		61819267	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.713640	0.48517	.	.	ENSG00000151150	ENST00000280772	T	0.63096	-0.02	5.96	5.96	0.96718	.	0.000000	0.36409	U	0.002609	T	0.45236	0.1332	N	0.08118	0	0.80722	D	1	P	0.39809	0.689	B	0.34590	0.186	T	0.55457	-0.8138	10	0.87932	D	0	.	19.4101	0.94667	0.0:1.0:0.0:0.0	.	12	Q12955	ANK3_HUMAN	S	12	ENSP00000280772:R12S	ENSP00000280772:R12S	R	-	3	2	ANK3	61819267	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.288000	0.51739	2.832000	0.97577	0.655000	0.94253	AGG		0.423	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	62149261	C	A	62149261	3	1	61	1	0	0	0	0	1	0	0	0	622	622	22	2	13602	2	ANK3	10	62149261	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	318833	62149261	73385486	6773	14758										
CDK1	983	broad.mit.edu	37	chr10	62553663	62553663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatctatgatccagccaaacGaatttctggcaaaatggcac	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:62553663G>A	ENST00000395284.3	+	8	966	c.824G>A	c.(823-825)cGa>cAa	p.R275Q	CDK1_ENST00000448257.2_Missense_Mutation_p.R275Q|CDK1_ENST00000316629.4_Missense_Mutation_p.R218Q|CDK1_ENST00000373809.2_Missense_Mutation_p.R218Q	NM_001786.4	NP_001777.1	P06493	CDK1_HUMAN	cyclin-dependent kinase 1	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell aging (GO:0007569)|cell migration (GO:0016477)|cellular response to hydrogen peroxide (GO:0070301)|centrosome cycle (GO:0007098)|chromosome condensation (GO:0030261)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|pronuclear fusion (GO:0007344)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|Ras protein signal transduction (GO:0007265)|regulation of embryonic development (GO:0045995)|regulation of Schwann cell differentiation (GO:0014038)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to activity (GO:0014823)|response to amine (GO:0014075)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organic cyclic compound (GO:0014070)|response to toxic substance (GO:0009636)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|histone kinase activity (GO:0035173)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.R275Q(1)		ovary(1)	1						CCAGCCAAACGAATTTCTGGC	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	10											69	71	70					10																	62553663		2202	4293	6495	62223669	SO:0001583	missense	983			BC014563	CCDS7260.1, CCDS44408.1	10q21.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000170312	ENSG00000170312		"Cyclin-dependent kinases"	1722	protein-coding gene	gene with protein product		116940	"cell division cycle 2, G1 to S and G2 to M"	CDC2		3553962, 19884882	Standard	NM_001786		Approved	CDC28A	uc001jld.3	P06493	OTTHUMG00000018290	ENST00000395284.3:c.824G>A	10.37:g.62553663G>A	ENSP00000378699:p.Arg275Gln		62223669	A8K7C4|C9J497|O60764	Missense_Mutation	SNP	ENST00000395284.3	37	CCDS44408.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631986	0.87660	.	.	ENSG00000170312	ENST00000395284;ENST00000316629;ENST00000448257;ENST00000373809	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	6.02	4.18	0.49190	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055200	0.64402	D	0.000001	D	0.89529	0.6741	H	0.98542	4.26	0.80722	D	1	D;D;D	0.76494	0.991;0.999;0.999	P;P;P	0.58210	0.575;0.835;0.835	D	0.92334	0.5876	10	0.87932	D	0	-10.2378	13.0901	0.59162	0.1293:0.0:0.8707:0.0	.	218;281;275	P06493-2;Q5H9N4;P06493	.;.;CDK1_HUMAN	Q	275;218;275;218	ENSP00000378699:R275Q;ENSP00000325970:R218Q;ENSP00000397973:R275Q;ENSP00000362915:R218Q	ENSP00000325970:R218Q	R	+	2	0	CDK1	62223669	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	7.699000	0.84547	0.886000	0.36113	0.655000	0.94253	CGA		0.289	CDK1-007	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048211.2	NM_001786		A	62553663	G	A	62553663	3	1	61	1	0	0	0	0	1	0	0	0	3130	1058	37	1	862	1	CDK1	10	62553663	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	404402	62553663	72981084	6774	14759										
RTKN2	219790	broad.mit.edu	37	chr10	63964728	63964728	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacaggattgatgacagaGaaattatggattcttttctt	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:63964728G>A	ENST00000373789.3	-	10	1170	c.1074C>T	c.(1072-1074)ttC>ttT	p.F358F	RTKN2_ENST00000315289.2_Silent_p.F160F|RTKN2_ENST00000395265.1_Silent_p.F379F	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	358	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)		p.F358F(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					TGATGACAGAGAAATTATGGA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	10											99	101	100					10																	63964728		2203	4300	6503	63634734	SO:0001819	synonymous_variant	219790			BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"Pleckstrin homology (PH) domain containing"	19364	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family K member 1"	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1074C>T	10.37:g.63964728G>A			63634734	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Silent	SNP	ENST00000373789.3	37	CCDS7263.1																																																																																				0.378	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307		A	63964728	G	A	63964728	2	1	61	1	0	0	0	0	0	0	0	1	13760	933	33	3		3	RTKN2	10	63964728	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1411065	63964728	71570019	6775	14760										
ZNF365	22891	broad.mit.edu	37	chr10	64136406	64136406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctggactgcccacctcaGacaccaaagcttctttcgag	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64136406G>T	ENST00000395254.3	+	2	734	c.454G>T	c.(454-456)Gac>Tac	p.D152Y	ZNF365_ENST00000410046.3_Missense_Mutation_p.D152Y|ZNF365_ENST00000466727.1_Intron|ZNF365_ENST00000395255.3_Missense_Mutation_p.D152Y	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0								p.D152Y(2)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GCCCACCTCAGACACCAAAGC	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	10											70	69	69					10																	64136406		2203	4300	6503	63806412	SO:0001583	missense	22891			AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.454G>T	10.37:g.64136406G>T	ENSP00000378674:p.Asp152Tyr		63806412		Missense_Mutation	SNP	ENST00000395254.3	37	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214371	0.58452	.	.	ENSG00000138311	ENST00000395254;ENST00000395255;ENST00000410046	T;T;T	0.39056	1.1;1.1;1.1	5.51	4.61	0.57282	.	0.342457	0.28279	N	0.015923	T	0.59542	0.2201	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76575	0.98;0.988;0.988;0.988	T	0.61652	-0.7019	10	0.66056	D	0.02	.	9.9156	0.41432	0.073:0.1384:0.7885:0.0	.	152;152;152;167	Q70YC5-3;Q70YC5-2;Q70YC5;Q70YC5-4	.;.;ZN365_HUMAN;.	Y	152	ENSP00000378674:D152Y;ENSP00000378675:D152Y;ENSP00000387091:D152Y	ENSP00000378674:D152Y	D	+	1	0	ZNF365	63806412	1.000000	0.71417	0.927000	0.36925	0.877000	0.50540	4.512000	0.60469	1.331000	0.45412	0.555000	0.69702	GAC		0.517	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		T	64136406	G	T	64136406	3	4	61	1	0	0	0	0	1	0	0	0	17908	942	33	2	456	2	ZNF365	10	64136406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171678	64136406	71398341	6776	14761										
ZNF365	22891	broad.mit.edu	37	chr10	64148203	64148203	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcggcagctgagaaggaGgttcaagggaaagcccggct	17	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64148203G>A	ENST00000395254.3	+	3	1072	c.792G>A	c.(790-792)gaG>gaA	p.E264E	ZNF365_ENST00000410046.3_Silent_p.E264E|ZNF365_ENST00000466727.1_3'UTR|ZNF365_ENST00000395255.3_Silent_p.E264E	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0								p.E264E(2)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					CTGAGAAGGAGGTTCAAGGGA	0.483																																																2	Substitution - coding silent(2)	large_intestine(2)	10											67	67	67					10																	64148203		2203	4300	6503	63818209	SO:0001819	synonymous_variant	22891			AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.792G>A	10.37:g.64148203G>A			63818209		Silent	SNP	ENST00000395254.3	37	CCDS31209.1																																																																																				0.483	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		A	64148203	G	A	64148203	2	1	61	1	0	0	0	0	0	0	0	1	17908	991	35	3		3	ZNF365	10	64148203	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11797	64148203	71386544	6777	14762										
ZNF365	22891	broad.mit.edu	37	chr10	64159458	64159458	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctctgcagacctccaaaGaaaggggagctcctggggtt	13	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64159458G>T	ENST00000395254.3	+	5	1414	c.1134G>T	c.(1132-1134)aaG>aaT	p.K378N	ZNF365_ENST00000410046.3_Intron|ZNF365_ENST00000466727.1_3'UTR|ZNF365_ENST00000395255.3_Intron	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0								p.K378N(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GACCTCCAAAGAAAGGGGAGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											72	73	73					10																	64159458		2203	4300	6503	63829464	SO:0001583	missense	22891			AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.1134G>T	10.37:g.64159458G>T	ENSP00000378674:p.Lys378Asn		63829464		Missense_Mutation	SNP	ENST00000395254.3	37	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398894	0.62177	.	.	ENSG00000138311	ENST00000395254	T	0.54675	0.56	5.76	4.85	0.62838	.	.	.	.	.	T	0.55970	0.1954	M	0.62723	1.935	0.80722	D	1	P;P	0.44946	0.603;0.846	B;P	0.47470	0.42;0.548	T	0.60424	-0.7266	9	0.87932	D	0	.	9.8197	0.40874	0.1579:0.0:0.8421:0.0	.	378;393	Q70YC5;Q70YC5-4	ZN365_HUMAN;.	N	378	ENSP00000378674:K378N	ENSP00000378674:K378N	K	+	3	2	ZNF365	63829464	1.000000	0.71417	0.998000	0.56505	0.757000	0.42996	1.070000	0.30653	1.441000	0.47550	0.650000	0.86243	AAG		0.522	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		T	64159458	G	T	64159458	3	4	61	1	0	0	0	0	1	0	0	0	17908	933	33	2	1148	2	ZNF365	10	64159458	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11255	64159458	71375289	6778	14763										
ZNF365	22891	broad.mit.edu	37	chr10	64414616	64414616	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctaggtgctggaatacaGagaggaaccaaacagataaa	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64414616G>A	ENST00000395251.1	+	3	386	c.52G>A	c.(52-54)Gag>Aag	p.E18K	ZNF365_ENST00000395249.1_Intron|ZNF365_ENST00000410046.3_Intron	NM_199452.3	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365	18								p.E18K(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					ctggaatacagagaggaacca	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											149	150	150					10																	64414616		2203	4300	6503	64084622	SO:0001583	missense	22891			AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395251.1:c.52G>A	10.37:g.64414616G>A	ENSP00000378672:p.Glu18Lys		64084622		Missense_Mutation	SNP	ENST00000395251.1	37	CCDS7265.1	.	.	.	.	.	.	.	.	.	.	G	3.433	-0.115640	0.06881	.	.	ENSG00000138311	ENST00000395251	T	0.54479	0.57	1.7	-1.13	0.09775	.	.	.	.	.	T	0.27663	0.0680	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17592	-1.0364	9	0.87932	D	0	.	4.6276	0.12486	0.5537:0.0:0.4463:0.0	.	18	Q70YC4	TALAN_HUMAN	K	18	ENSP00000378672:E18K	ENSP00000345300:E18K	E	+	1	0	ZNF365	64084622	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.068000	0.11561	-0.345000	0.08325	-0.379000	0.06801	GAG		0.453	ZNF365-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277036.1	NM_014951		A	64414616	G	A	64414616	3	1	61	1	0	0	0	0	1	0	0	0	17908	943	33	3	1536	3	ZNF365	10	64414616	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	255158	64414616	71120131	6779	14764										
EGR2	1959	broad.mit.edu	37	chr10	64573884	64573884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcacagccagaataaggagGaggaggcggtggcggagagt	19	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64573884G>A	ENST00000242480.3	-	2	839	c.514C>T	c.(514-516)Cct>Tct	p.P172S	EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000411732.1_Missense_Mutation_p.P122S|EGR2_ENST00000439032.1_Missense_Mutation_p.P172S	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	172					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.P172S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					GAATAAGGAGGAGGAGGCGGT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	10											81	85	83					10																	64573884		2203	4300	6503	64243890	SO:0001583	missense	1959			BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"Zinc fingers, C2H2-type"	3239	protein-coding gene	gene with protein product	"Krox-20 homolog, Drosophila"	129010	"early growth response 2 (Krox-20 homolog, Drosophila)"	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.514C>T	10.37:g.64573884G>A	ENSP00000242480:p.Pro172Ser		64243890	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944307	0.73672	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000411732;ENST00000432380	T;T;T	0.68624	-0.34;-0.34;-0.34	5.14	5.14	0.70334	.	0.141445	0.48767	D	0.000171	T	0.64583	0.2611	L	0.50333	1.59	0.37347	D	0.910649	B;B	0.28713	0.22;0.149	B;B	0.31751	0.135;0.088	T	0.70421	-0.4876	10	0.87932	D	0	-11.0981	16.1402	0.81517	0.0:0.0:1.0:0.0	.	122;172	P11161-2;P11161	.;EGR2_HUMAN	S	172;172;122;185	ENSP00000242480:P172S;ENSP00000402040:P172S;ENSP00000387634:P122S	ENSP00000242480:P172S	P	-	1	0	EGR2	64243890	1.000000	0.71417	0.974000	0.42286	0.986000	0.74619	7.881000	0.87252	2.656000	0.90262	0.650000	0.86243	CCT		0.637	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		A	64573884	G	A	64573884	3	1	61	1	0	0	0	0	1	0	0	0	4983	1174	41	3	920	3	EGR2	10	64573884	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159268	64573884	70960863	6780	14765										
NRBF2	29982	broad.mit.edu	37	chr10	64893234	64893234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttaccccggggtctatgGaagtaatggaaggacccctc	12	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:64893234G>A	ENST00000277746.6	+	1	185	c.4G>A	c.(4-6)Gaa>Aaa	p.E2K	NRBF2_ENST00000435510.2_Missense_Mutation_p.G20E	NM_030759.3	NP_110386.2	Q96F24	NRBF2_HUMAN	nuclear receptor binding factor 2	2					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)		p.E2K(1)		large_intestine(2)|lung(3)|skin(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					GGGGTCTATGGAAGTAATGGA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	10											48	42	44					10																	64893234		2203	4300	6503	64563240	SO:0001583	missense	29982			D82519	CCDS7268.1, CCDS60537.1	10q22.1	2012-11-01			ENSG00000148572	ENSG00000148572			19692	protein-coding gene	gene with protein product	"comodulator of PPAR and RXR 1", "comodulator of PPAR and RXR 2"					10786636	Standard	NM_001282405		Approved	DKFZp564C1664, FLJ30395, COPR1, COPR2	uc001jmj.4	Q96F24	OTTHUMG00000018309	ENST00000277746.6:c.4G>A	10.37:g.64893234G>A	ENSP00000277746:p.Glu2Lys		64563240	A6PW36|B4DWS0|Q86UR2|Q96NP6|Q9H0S9|Q9H2I2	Missense_Mutation	SNP	ENST00000277746.6	37	CCDS7268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.606401|4.606401	0.87157|0.87157	.|.	.|.	ENSG00000148572|ENSG00000148572	ENST00000277746;ENST00000395241|ENST00000435510	.|.	.|.	.|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	0.221310|.	0.45606|.	D|.	0.000344|.	T|T	0.61899|0.61899	0.2384|0.2384	L|L	0.47716|0.47716	1.5|1.5	0.28343|0.28343	N|N	0.921237|0.921237	P|D	0.34562|0.89917	0.457|1.0	B|D	0.33890|0.87578	0.172|0.998	T|T	0.55566|0.55566	-0.8121|-0.8121	9|8	0.87932|0.87932	D|D	0|0	-1.6876|-1.6876	13.1767|13.1767	0.59630|0.59630	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2|20	Q96F24|B4DWS0	NRBF2_HUMAN|.	K|E	2|20	.|.	ENSP00000277746:E2K|ENSP00000397502:G20E	E|G	+|+	1|2	0|0	NRBF2|NRBF2	64563240|64563240	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.885000|3.885000	0.56182|0.56182	2.556000|2.556000	0.86216|0.86216	0.561000|0.561000	0.74099|0.74099	GAA|GGA		0.647	NRBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048247.1	NM_030759		A	64893234	G	A	64893234	3	1	61	1	0	0	0	0	1	0	0	0	10672	1175	41	3	6	3	NRBF2	10	64893234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	319350	64893234	70641513	6781	14766										
CTNNA3	29119	broad.mit.edu	37	chr10	67748510	67748510	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgattctgatatcattttCgctgcatagatcacatcagt	6	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:67748510C>A	ENST00000433211.2	-	16	2379	c.2205G>T	c.(2203-2205)gcG>gcT	p.A735A	CTNNA3_ENST00000373735.1_5'UTR|CTNNA3_ENST00000373744.4_Silent_p.A735A	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3									p.A735A(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						ATATCATTTTCGCTGCATAGA	0.378																																																2	Substitution - coding silent(2)	large_intestine(2)	10											193	161	172					10																	67748510		2203	4300	6503	67418516	SO:0001819	synonymous_variant	29119			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.2205G>T	10.37:g.67748510C>A			67418516		Silent	SNP	ENST00000433211.2	37	CCDS7269.1																																																																																				0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		A	67748510	C	A	67748510	2	1	61	1	0	0	0	0	0	0	0	1	4020	871	31	2		2	CTNNA3	10	67748510	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2855276	67748510	67786237	6782	14767										
LRRTM3	347731	broad.mit.edu	37	chr10	68687508	68687508	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgttttccagtgtgtcccGaatctgcagcgcctcaacct	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:68687508G>A	ENST00000361320.4	+	2	1412	c.834G>A	c.(832-834)ccG>ccA	p.P278P	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	278					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.P278P(2)		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						AGTGTGTCCCGAATCTGCAGC	0.473																																																2	Substitution - coding silent(2)	large_intestine(2)	10											117	124	121					10																	68687508		2203	4300	6503	68357514	SO:0001819	synonymous_variant	347731			BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.834G>A	10.37:g.68687508G>A			68357514	A8K2A3|Q2NKX7|Q6N0A3	Silent	SNP	ENST00000361320.4	37	CCDS7270.1																																																																																				0.473	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		A	68687508	G	A	68687508	2	1	61	1	0	0	0	0	0	0	0	1	9070	1045	37	1		1	LRRTM3	10	68687508	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	938998	68687508	66847239	6783	14768										
SIRT1	23411	broad.mit.edu	37	chr10	69647188	69647188	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcagataaccttctgttCggtgatgaaattatcactaa	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:69647188C>T	ENST00000212015.6	+	2	497	c.444C>T	c.(442-444)ttC>ttT	p.F148F	SIRT1_ENST00000497639.1_3'UTR|SIRT1_ENST00000432464.1_5'UTR	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	148	Interaction with CCAR2.|Interaction with HIST1H1E.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.F148F(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ACCTTCTGTTCGGTGATGAAA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											176	165	169					10																	69647188		2203	4300	6503	69317194	SO:0001819	synonymous_variant	23411			AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1", "sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.444C>T	10.37:g.69647188C>T			69317194	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Silent	SNP	ENST00000212015.6	37	CCDS7273.1																																																																																				0.413	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			T	69647188	C	T	69647188	2	4	61	1	0	0	0	0	0	0	0	1	14374	883	31	1		1	SIRT1	10	69647188	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	959680	69647188	65887559	6784	14769										
SIRT1	23411	broad.mit.edu	37	chr10	69666547	69666547	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaccatttgcttgatacagGaaatatatcctggacaattc	6	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:69666547G>T	ENST00000212015.6	+	5	996	c.943G>T	c.(943-945)Gaa>Taa	p.E315*	SIRT1_ENST00000403579.1_Splice_Site_p.E12*|SIRT1_ENST00000406900.1_Splice_Site_p.E12*|SIRT1_ENST00000432464.1_Splice_Site_p.E20*	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	315	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.E315*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						CTTGATACAGGAAATATATCC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											61	63	62					10																	69666547		2203	4300	6503	69336553	SO:0001630	splice_region_variant	23411			AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1", "sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.943-1G>T	10.37:g.69666547G>T			69336553	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Nonsense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1	.	.	.	.	.	.	.	.	.	.	G	37	6.550840	0.97658	.	.	ENSG00000096717	ENST00000212015;ENST00000432464;ENST00000406900;ENST00000403579	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.377	18.5847	0.91185	0.0:0.0:1.0:0.0	.	.	.	.	X	315;20;12;12	.	.	E	+	1	0	SIRT1	69336553	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	9.402000	0.97298	2.480000	0.83734	0.585000	0.79938	GAA		0.328	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		Nonsense_Mutation	T	69666547	G	T	69666547	5	4	61	1	0	0	0	0	0	0	1	0	14374	1188	41	2	961	2	SIRT1	10	69666547	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19359	69666547	65868200	6785	14770										
HERC4	26091	broad.mit.edu	37	chr10	69695911	69695911	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctaaaattcacttaccGattttgtttgttaacagctg	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:69695911G>A	ENST00000395198.3	-	23	2924	c.2677C>T	c.(2677-2679)Cgg>Tgg	p.R893W	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000412272.2_Splice_Site_p.R815W|HERC4_ENST00000277817.6_Splice_Site_p.R783W|HERC4_ENST00000373700.4_Splice_Site_p.R885W	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	893	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R893W(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TTCACTTACCGATTTTGTTTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											174	160	164					10																	69695911		2203	4300	6503	69365917	SO:0001630	splice_region_variant	26091			AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2678+1C>T	10.37:g.69695911G>A			69365917	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075631	0.76415	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.1	5.1	0.69264	HECT (4);	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	H	0.97315	3.98	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.994;0.998;0.999;0.999;0.999	D	0.84958	0.0875	10	0.87932	D	0	.	12.1499	0.54044	0.0:0.0:0.7117:0.2883	.	815;783;743;885;893	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	W	783;815;893;885	ENSP00000277817:R783W;ENSP00000416504:R815W;ENSP00000378624:R893W;ENSP00000362804:R885W	ENSP00000277817:R783W	R	-	1	2	HERC4	69365917	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.535000	0.53575	2.512000	0.84698	0.460000	0.39030	CGG		0.353	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	Missense_Mutation	A	69695911	G	A	69695911	5	1	61	1	0	0	0	0	0	0	1	0	7081	1072	37	1	512	1	HERC4	10	69695911	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29364	69695911	65838836	6786	14771										
MYPN	84665	broad.mit.edu	37	chr10	69921491	69921491	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttttcttttagaacctCgatccatggcagagccaggt	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:69921491C>T	ENST00000358913.5	+	8	1953	c.1465C>T	c.(1465-1467)Cga>Tga	p.R489*	MYPN_ENST00000540630.1_Intron|MYPN_ENST00000373675.3_Nonsense_Mutation_p.R489*|MYPN_ENST00000354393.2_Nonsense_Mutation_p.R214*	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	489	Ig-like 2.|Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.R489*(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TTTAGAACCTCGATCCATGGC	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											51	54	53					10																	69921491		2203	4299	6502	69591497	SO:0001587	stop_gained	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1465C>T	10.37:g.69921491C>T	ENSP00000351790:p.Arg489*		69591497	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Nonsense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	C	42	9.308102	0.99132	.	.	ENSG00000138347	ENST00000354393;ENST00000358913;ENST00000373675	.	.	.	5.63	4.68	0.58851	.	0.070658	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6337	0.76933	0.1372:0.8628:0.0:0.0	.	.	.	.	X	214;489;489	.	.	R	+	1	2	MYPN	69591497	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.321000	0.43805	2.798000	0.96311	0.655000	0.94253	CGA		0.308	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69921491	C	T	69921491	4	4	61	1	0	0	0	0	0	1	0	0	10128	876	31	1	1491	1	MYPN	10	69921491	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	225580	69921491	65613256	6787	14772										
MYPN	84665	broad.mit.edu	37	chr10	69934130	69934130	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagaggacagtgagcaaaGaaagcctcttagtgtctcac	10	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:69934130G>T	ENST00000358913.5	+	11	2769	c.2281G>T	c.(2281-2283)Gaa>Taa	p.E761*	MYPN_ENST00000540630.1_Nonsense_Mutation_p.E761*|MYPN_ENST00000354393.2_Nonsense_Mutation_p.E486*	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	761					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.E761*(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						AGTGAGCAAAGAAAGCCTCTT	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											101	96	98					10																	69934130		2203	4300	6503	69604136	SO:0001587	stop_gained	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2281G>T	10.37:g.69934130G>T	ENSP00000351790:p.Glu761*		69604136	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Nonsense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	44	11.080027	0.99513	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	.	.	.	5.76	4.85	0.62838	.	0.272209	0.42548	D	0.000688	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1725	0.72884	0.0682:0.0:0.9318:0.0	.	.	.	.	X	486;486;761;761	.	.	E	+	1	0	MYPN	69604136	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.736000	0.84948	1.427000	0.47276	0.655000	0.94253	GAA		0.547	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69934130	G	T	69934130	4	4	61	1	0	0	0	0	0	1	0	0	10128	943	33	2	2319	2	MYPN	10	69934130	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12639	69934130	65600617	6788	14773										
DNA2	1763	broad.mit.edu	37	chr10	70231657	70231657	+	5'UTR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaaactgtagacagaaaaGacagcggaaccgggggtaac	13	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70231657G>T	ENST00000358410.3	-	0	15				DNA2_ENST00000399179.2_5'UTR|DNA2_ENST00000399180.2_Missense_Mutation_p.L75I	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2						ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)	p.L75I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						AGACAGAAAAGACAGCGGAAC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10											35	40	38					10																	70231657		1877	4107	5984	69901663	SO:0001623	5_prime_UTR_variant	1763			D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.-36C>A	10.37:g.70231657G>T			69901663	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	G	8.260	0.810951	0.16537	.	.	ENSG00000138346	ENST00000399180	D	0.91894	-2.93	4.19	-8.38	0.00973	.	.	.	.	.	D	0.83862	0.5346	.	.	.	0.20196	N	0.999926	.	.	.	.	.	.	T	0.72374	-0.4313	5	.	.	.	.	6.6256	0.22828	0.1296:0.1055:0.5564:0.2085	.	.	.	.	I	75	ENSP00000382133:L75I	.	L	-	1	0	DNA2	69901663	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.065000	0.00302	-2.790000	0.00356	-1.076000	0.02234	CTT		0.577	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			T	70231657	G	T	70231657	1	4	61	0	1	0	0	0	0	0	0	0	4607	942	33	2		2	DNA2	10	70231657	5'UTR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297527	70231657	65303090	6789	14774										
SLC25A16	8034	broad.mit.edu	37	chr10	70243299	70243299	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacgatagagtccttttcGaattccatggtgtccataga	8	10	0	2	rs139107749		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70243299G>A	ENST00000609923.1	-	9	987	c.889C>T	c.(889-891)Cga>Tga	p.R297*	SLC25A16_ENST00000265870.3_5'UTR|SLC25A16_ENST00000539557.1_Nonsense_Mutation_p.R199*	NM_152707.3	NP_689920.1	P16260	GDC_HUMAN	solute carrier family 25 (mitochondrial carrier), member 16	297					coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	antiporter activity (GO:0015297)	p.R297*(1)		endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	7						AGTCCTTTTCGAATTCCATGG	0.378													G|||	1	0.000199681	0	0	5008	,	,		18292	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	10											156	153	154					10																	70243299		2203	4300	6503	69913305	SO:0001587	stop_gained	8034			M31659	CCDS7280.1	10q21.3-q22.1	2014-06-17	2014-06-17		ENSG00000122912	ENSG00000122912		"Solute carriers"	10986	protein-coding gene	gene with protein product	"Graves disease autoantigen"	139080				8444471, 2575220	Standard	NM_152707		Approved	GDA, D10S105E, HGT.1, ML7	uc001joi.3	P16260	OTTHUMG00000018354	ENST00000609923.1:c.889C>T	10.37:g.70243299G>A	ENSP00000476815:p.Arg297*		69913305	Q8N2U1	Nonsense_Mutation	SNP	ENST00000609923.1	37	CCDS7280.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.9	4.577125	0.86645	.	.	ENSG00000122912	ENST00000265870;ENST00000539557	.	.	.	5.67	4.71	0.59529	.	0.060409	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3668	13.2988	0.60313	0.0:0.0:0.7229:0.2771	.	.	.	.	X	297;199	.	ENSP00000265870:R297X	R	-	1	2	SLC25A16	69913305	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.935000	0.56560	2.682000	0.91365	0.555000	0.69702	CGA		0.378	SLC25A16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048347.2			A	70243299	G	A	70243299	4	1	61	1	0	0	0	0	0	1	0	0	14515	1066	37	1	113	1	SLC25A16	10	70243299	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11642	70243299	65291448	6790	14775										
TET1	80312	broad.mit.edu	37	chr10	70332931	70332931	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgggttcacgagtagaatCtcttaagttatctgattctt	9	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70332931C>A	ENST00000373644.4	+	2	1045	c.836C>A	c.(835-837)tCt>tAt	p.S279Y		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	279					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.S279Y(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CGAGTAGAATCTCTTAAGTTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											70	75	73					10																	70332931		2203	4300	6503	70002937	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.836C>A	10.37:g.70332931C>A	ENSP00000362748:p.Ser279Tyr		70002937	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036498	0.54896	.	.	ENSG00000138336	ENST00000373644	T	0.12361	2.69	5.53	4.62	0.57501	.	0.000000	0.43919	D	0.000511	T	0.10680	0.0261	L	0.32530	0.975	0.32209	N	0.576835	P	0.47841	0.901	B	0.40565	0.333	T	0.05903	-1.0857	10	0.87932	D	0	.	8.8351	0.35107	0.146:0.7749:0.0:0.0791	.	279	Q8NFU7	TET1_HUMAN	Y	279	ENSP00000362748:S279Y	ENSP00000362748:S279Y	S	+	2	0	TET1	70002937	0.968000	0.33430	1.000000	0.80357	0.969000	0.65631	0.838000	0.27572	2.589000	0.87451	0.563000	0.77884	TCT		0.433	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70332931	C	A	70332931	3	1	61	1	0	0	0	0	1	0	0	0	15808	913	32	2	838	2	TET1	10	70332931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89632	70332931	65201816	6791	14776										
TET1	80312	broad.mit.edu	37	chr10	70333384	70333384	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgttgtcccagacttgcCtgtcttccttcctgttcctc	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70333384C>A	ENST00000373644.4	+	2	1498	c.1289C>A	c.(1288-1290)cCt>cAt	p.P430H		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	430					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.P430H(1)|p.P430T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCAGACTTGCCTGTCTTCCTT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	10											138	124	129					10																	70333384		2203	4300	6503	70003390	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1289C>A	10.37:g.70333384C>A	ENSP00000362748:p.Pro430His		70003390	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.729546	0.30684	.	.	ENSG00000138336	ENST00000373644	T	0.08896	3.04	4.59	2.66	0.31614	.	0.964311	0.08526	N	0.932805	T	0.11623	0.0283	L	0.27053	0.805	0.09310	N	1	D	0.63046	0.992	P	0.52710	0.707	T	0.34004	-0.9846	10	0.87932	D	0	.	8.1033	0.30870	0.1803:0.6457:0.174:0.0	.	430	Q8NFU7	TET1_HUMAN	H	430	ENSP00000362748:P430H	ENSP00000362748:P430H	P	+	2	0	TET1	70003390	0.001000	0.12720	0.012000	0.15200	0.771000	0.43674	0.767000	0.26575	0.590000	0.29694	0.313000	0.20887	CCT		0.473	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70333384	C	A	70333384	3	1	61	1	0	0	0	0	1	0	0	0	15808	681	24	2	1291	2	TET1	10	70333384	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	453	70333384	65201363	6792	14777										
TET1	80312	broad.mit.edu	37	chr10	70406721	70406721	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctacaaaaaacctagtgtCtataactaaagattctgaac	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70406721C>A	ENST00000373644.4	+	4	4444	c.4235C>A	c.(4234-4236)tCt>tAt	p.S1412Y		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1412					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.S1412Y(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AACCTAGTGTCTATAACTAAA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	10											65	64	64					10																	70406721		2203	4300	6503	70076727	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4235C>A	10.37:g.70406721C>A	ENSP00000362748:p.Ser1412Tyr		70076727	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721375	0.68959	.	.	ENSG00000138336	ENST00000373644	T	0.07327	3.2	5.22	5.22	0.72569	.	0.900349	0.09370	N	0.811381	T	0.14527	0.0351	L	0.29908	0.895	0.30264	N	0.792915	D	0.57571	0.98	P	0.50440	0.641	T	0.14783	-1.0460	10	0.72032	D	0.01	.	16.976	0.86313	0.0:1.0:0.0:0.0	.	1412	Q8NFU7	TET1_HUMAN	Y	1412	ENSP00000362748:S1412Y	ENSP00000362748:S1412Y	S	+	2	0	TET1	70076727	0.939000	0.31865	0.829000	0.32907	0.880000	0.50808	3.247000	0.51422	2.446000	0.82766	0.557000	0.71058	TCT		0.378	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70406721	C	A	70406721	3	1	61	1	0	0	0	0	1	0	0	0	15808	913	32	2	4245	2	TET1	10	70406721	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73337	70406721	65128026	6793	14778										
CCAR1	55749	broad.mit.edu	37	chr10	70509019	70509019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctaacagaaaagatgatcGaaggtatattttctaaagtg	9	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70509019G>A	ENST00000265872.6	+	9	1072	c.953G>A	c.(952-954)cGa>cAa	p.R318Q	CCAR1_ENST00000535016.1_Missense_Mutation_p.R303Q|CCAR1_ENST00000543719.1_Missense_Mutation_p.R303Q	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	318	Arg-rich.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)	p.R318Q(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						AAAGATGATCGAAGGTATATT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											46	47	47					10																	70509019		2203	4300	6503	70179025	SO:0001583	missense	55749			AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.953G>A	10.37:g.70509019G>A	ENSP00000265872:p.Arg318Gln		70179025	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	37	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686335	0.88639	.	.	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.30182	1.6;2.68;2.68;2.68;2.68;1.54	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.52661	0.1748	L	0.50333	1.59	0.58432	D	0.999992	D;D;D	0.71674	0.997;0.997;0.998	D;D;D	0.75484	0.947;0.968;0.986	T	0.49790	-0.8902	10	0.59425	D	0.04	-9.1525	19.6341	0.95722	0.0:0.0:1.0:0.0	.	303;318;292	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	Q	318;303;303;303;292;123	ENSP00000265872:R318Q;ENSP00000441820:R303Q;ENSP00000445254:R303Q;ENSP00000439252:R303Q;ENSP00000438610:R292Q;ENSP00000439642:R123Q	ENSP00000265872:R318Q	R	+	2	0	CCAR1	70179025	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.751000	0.91628	2.626000	0.88956	0.650000	0.86243	CGA		0.393	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		A	70509019	G	A	70509019	3	1	61	1	0	0	0	0	1	0	0	0	2736	1058	37	1	983	1	CCAR1	10	70509019	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102298	70509019	65025728	6794	14779										
STOX1	219736	broad.mit.edu	37	chr10	70644366	70644366	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggaagagtcacagaggtCttggggaatccgtatcttgg	14	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70644366C>A	ENST00000298596.6	+	3	897	c.814C>A	c.(814-816)Ctt>Att	p.L272I	STOX1_ENST00000399169.4_Missense_Mutation_p.L272I|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Missense_Mutation_p.L162I	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	272						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L272I(1)		breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						TCACAGAGGTCTTGGGGAATC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	10											125	125	125					10																	70644366		1958	4147	6105	70314372	SO:0001583	missense	219736			AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.814C>A	10.37:g.70644366C>A	ENSP00000298596:p.Leu272Ile		70314372	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	C	0.061	-1.224795	0.01530	.	.	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.74315	-0.83;-0.83;-0.5	5.57	2.5	0.30297	.	1.196050	0.06476	U	0.732075	T	0.61489	0.2351	L	0.45581	1.43	0.09310	N	1	B	0.26195	0.144	B	0.20955	0.032	T	0.47724	-0.9095	10	0.18710	T	0.47	.	1.2879	0.02054	0.1596:0.4316:0.1554:0.2534	.	272	Q6ZVD7	STOX1_HUMAN	I	272;272;162	ENSP00000382121:L272I;ENSP00000298596:L272I;ENSP00000394509:L162I	ENSP00000298596:L272I	L	+	1	0	STOX1	70314372	0.116000	0.22171	0.003000	0.11579	0.006000	0.05464	0.930000	0.28858	1.371000	0.46172	0.591000	0.81541	CTT		0.498	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		A	70644366	C	A	70644366	3	1	61	1	0	0	0	0	1	0	0	0	15358	913	32	2	824	2	STOX1	10	70644366	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135347	70644366	64890381	6795	14780										
DDX21	9188	broad.mit.edu	37	chr10	70719767	70719767	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccaaaagtttgagaaagaAaaaggagcccattgaaaaga	9	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70719767A>C	ENST00000354185.4	+	2	391	c.293A>C	c.(292-294)aAa>aCa	p.K98T		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	98					ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.K98T(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TTGAGAAAGAAAAAGGAGCCC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											40	43	42					10																	70719767		2202	4299	6501	70389773	SO:0001583	missense	9188			U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.293A>C	10.37:g.70719767A>C	ENSP00000346120:p.Lys98Thr		70389773	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	37	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.010682	0.35511	.	.	ENSG00000165732	ENST00000354185	T	0.26810	1.71	5.76	3.5	0.40072	.	0.593582	0.17743	N	0.163499	T	0.11110	0.0271	N	0.08118	0	0.38041	D	0.935456	B	0.02656	0.0	B	0.04013	0.001	T	0.14117	-1.0484	10	0.15499	T	0.54	-12.7926	7.3447	0.26656	0.7419:0.175:0.0831:0.0	.	98	Q9NR30	DDX21_HUMAN	T	98	ENSP00000346120:K98T	ENSP00000346120:K98T	K	+	2	0	DDX21	70389773	0.962000	0.33011	1.000000	0.80357	0.835000	0.47333	0.803000	0.27083	1.197000	0.43143	0.528000	0.53228	AAA		0.363	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		C	70719767	A	C	70719767	3	2	61	1	0	0	0	0	1	0	0	0	4355	14	1	4	299	4	DDX21	10	70719767	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	75401	70719767	64814980	6796	14781										
DDX21	9188	broad.mit.edu	37	chr10	70738712	70738712	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccaaagtgaagggaatgGtttttctcaaaggaaagctg	11	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70738712G>T	ENST00000354185.4	+	13	2115	c.2017G>T	c.(2017-2019)Gtt>Ttt	p.V673F		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	673					ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.V673F(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GAAGGGAATGGTTTTTCTCAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10											136	141	139					10																	70738712		2203	4300	6503	70408718	SO:0001583	missense	9188			U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.2017G>T	10.37:g.70738712G>T	ENSP00000346120:p.Val673Phe		70408718	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	37	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926301	0.52759	.	.	ENSG00000165732	ENST00000354185	T	0.17213	2.29	5.26	2.21	0.28008	GUCT (1);	0.713084	0.14435	N	0.319765	T	0.18341	0.0440	L	0.36672	1.1	0.41194	D	0.986324	D	0.61697	0.99	P	0.60236	0.871	T	0.42155	-0.9468	10	0.13470	T	0.59	-36.4238	1.5828	0.02638	0.1639:0.1726:0.4378:0.2257	.	673	Q9NR30	DDX21_HUMAN	F	673	ENSP00000346120:V673F	ENSP00000346120:V673F	V	+	1	0	DDX21	70408718	0.994000	0.37717	1.000000	0.80357	0.762000	0.43233	0.811000	0.27198	0.885000	0.36088	-0.119000	0.15052	GTT		0.448	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		T	70738712	G	T	70738712	3	4	61	1	0	0	0	0	1	0	0	0	4355	1261	44	2	2067	2	DDX21	10	70738712	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18945	70738712	64796035	6797	14782										
VPS26A	9559	broad.mit.edu	37	chr10	70892660	70892660	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattttatttcagagttttCttggaggcttttttggtcca	8	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70892660C>A	ENST00000373382.1	+	3	663	c.10C>A	c.(10-12)Ctt>Att	p.L4I	VPS26A_ENST00000541711.1_De_novo_Start_OutOfFrame|VPS26A_ENST00000490696.1_3'UTR|VPS26A_ENST00000263559.6_Missense_Mutation_p.L4I|VPS26A_ENST00000489794.1_De_novo_Start_OutOfFrame|VPS26A_ENST00000546041.1_De_novo_Start_InFrame|VPS26A_ENST00000395098.1_Missense_Mutation_p.L4I			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	4					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)	p.L4I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						TCAGAGTTTTCTTGGAGGCTT	0.308																																					Colon(90;545 1358 4729 6702 16773)											1	Substitution - Missense(1)	large_intestine(1)	10											57	63	61					10																	70892660		2200	4300	6500	70562666	SO:0001583	missense	9559			AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"vacuolar protein sorting 26 (yeast homolog)", "vacuolar protein sorting 26 (yeast)", "vacuolar protein sorting 26 homolog A (yeast)"	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.10C>A	10.37:g.70892660C>A	ENSP00000362480:p.Leu4Ile		70562666	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Missense_Mutation	SNP	ENST00000373382.1	37	CCDS7286.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927128	0.92389	.	.	ENSG00000122958	ENST00000373382;ENST00000263559;ENST00000395098	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.76314	0.3970	L	0.61218	1.895	0.80722	D	1	P;B	0.52842	0.956;0.019	P;B	0.62184	0.899;0.024	T	0.75175	-0.3410	9	0.46703	T	0.11	0.0264	19.5924	0.95520	0.0:1.0:0.0:0.0	.	4;4	A8MZ56;O75436	.;VP26A_HUMAN	I	4	.	ENSP00000263559:L4I	L	+	1	0	VPS26A	70562666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.737000	0.84957	2.689000	0.91719	0.655000	0.94253	CTT		0.308	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896		A	70892660	C	A	70892660	3	1	61	1	0	0	0	0	1	0	0	0	17237	913	32	2	16	2	VPS26A	10	70892660	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153948	70892660	64642087	6798	14783										
VPS26A	9559	broad.mit.edu	37	chr10	70916899	70916899	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccatatgaatcttacatCggtgccaatgtccgcttgag	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70916899C>T	ENST00000373382.1	+	5	1019	c.366C>T	c.(364-366)atC>atT	p.I122I	VPS26A_ENST00000490696.1_3'UTR|VPS26A_ENST00000395098.1_Silent_p.I122I|VPS26A_ENST00000489794.1_Silent_p.I97I|VPS26A_ENST00000263559.6_Silent_p.I122I|VPS26A_ENST00000546041.1_Silent_p.I105I|VPS26A_ENST00000541711.1_Silent_p.I11I			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	122					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)	p.I122I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						AATCTTACATCGGTGCCAATG	0.353																																					Colon(90;545 1358 4729 6702 16773)											1	Substitution - coding silent(1)	large_intestine(1)	10											103	100	101					10																	70916899		2203	4300	6503	70586905	SO:0001819	synonymous_variant	9559			AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"vacuolar protein sorting 26 (yeast homolog)", "vacuolar protein sorting 26 (yeast)", "vacuolar protein sorting 26 homolog A (yeast)"	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.366C>T	10.37:g.70916899C>T			70586905	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Silent	SNP	ENST00000373382.1	37	CCDS7286.1																																																																																				0.353	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896		T	70916899	C	T	70916899	2	4	61	1	0	0	0	0	0	0	0	1	17237	874	31	1		1	VPS26A	10	70916899	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24239	70916899	64617848	6799	14784										
SUPV3L1	6832	broad.mit.edu	37	chr10	70962270	70962270	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatgcaacactgtccaatCtcattgtaagtggaaactcc	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:70962270C>T	ENST00000359655.4	+	12	1654	c.1594C>T	c.(1594-1596)Ctc>Ttc	p.L532F		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	532					ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.L532F(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACTGTCCAATCTCATTGTAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											149	131	137					10																	70962270		2203	4300	6503	70632276	SO:0001583	missense	6832			AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.1594C>T	10.37:g.70962270C>T	ENSP00000352678:p.Leu532Phe		70632276	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	37	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.661320	0.67700	.	.	ENSG00000156502	ENST00000359655	T	0.43294	0.95	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.70245	0.3202	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.77534	-0.2552	10	0.72032	D	0.01	-23.274	13.5657	0.61817	0.0:0.9223:0.0:0.0777	.	532	Q8IYB8	SUV3_HUMAN	F	532	ENSP00000352678:L532F	ENSP00000352678:L532F	L	+	1	0	SUPV3L1	70632276	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	3.831000	0.55776	2.292000	0.77174	0.462000	0.41574	CTC		0.408	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		T	70962270	C	T	70962270	3	4	61	1	0	0	0	0	1	0	0	0	15441	913	32	3	1640	3	SUPV3L1	10	70962270	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45371	70962270	64572477	6800	14785										
HKDC1	80201	broad.mit.edu	37	chr10	71017155	71017155	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacctgtggctatgaagatCctaattgtgagattggcctg	12	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:71017155C>T	ENST00000354624.5	+	14	2138	c.2005C>T	c.(2005-2007)Cct>Tct	p.P669S	HKDC1_ENST00000395086.2_Missense_Mutation_p.P669S	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	669					carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)	p.P669S(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CTATGAAGATCCTAATTGTGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											238	199	213					10																	71017155		2203	4300	6503	70687161	SO:0001583	missense	80201				CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2005C>T	10.37:g.71017155C>T	ENSP00000346643:p.Pro669Ser		70687161	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	.	16.95	3.262499	0.59431	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.97731	-4.41;-4.51	4.82	3.91	0.45181	.	0.110266	0.64402	N	0.000006	D	0.96917	0.8993	M	0.81239	2.535	0.46499	D	0.999076	B	0.09022	0.002	B	0.18263	0.021	D	0.95637	0.8695	10	0.56958	D	0.05	-1.8582	14.4955	0.67683	0.1481:0.8519:0.0:0.0	.	669	Q2TB90	HKDC1_HUMAN	S	669	ENSP00000346643:P669S;ENSP00000378521:P669S	ENSP00000346643:P669S	P	+	1	0	HKDC1	70687161	1.000000	0.71417	0.954000	0.39281	0.893000	0.52053	5.881000	0.69706	1.227000	0.43598	0.556000	0.70494	CCT		0.423	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		T	71017155	C	T	71017155	3	4	61	1	0	0	0	0	1	0	0	0	7214	855	30	3	2059	3	HKDC1	10	71017155	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54885	71017155	64517592	6801	14786										
HKDC1	80201	broad.mit.edu	37	chr10	71021022	71021022	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccggaccaggggcatcttcGaaaccaagttcctgtcccag	10	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:71021022G>A	ENST00000354624.5	+	16	2477	c.2344G>A	c.(2344-2346)Gaa>Aaa	p.E782K	HKDC1_ENST00000395086.2_Missense_Mutation_p.E782K	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	782	Hexokinase type-2 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)	p.E782K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GGGCATCTTCGAAACCAAGTT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	10											64	59	61					10																	71021022		2203	4300	6503	70691028	SO:0001583	missense	80201				CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2344G>A	10.37:g.71021022G>A	ENSP00000346643:p.Glu782Lys		70691028	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.635745	0.67130	.	.	ENSG00000156510	ENST00000354624;ENST00000395086	D;D	0.98120	-4.73;-4.73	4.66	4.66	0.58398	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95636	0.8581	L	0.55213	1.73	0.80722	D	1	B	0.29936	0.262	B	0.23275	0.045	D	0.94668	0.7854	10	0.23302	T	0.38	-18.8821	17.7153	0.88335	0.0:0.0:1.0:0.0	.	782	Q2TB90	HKDC1_HUMAN	K	782	ENSP00000346643:E782K;ENSP00000378521:E782K	ENSP00000346643:E782K	E	+	1	0	HKDC1	70691028	1.000000	0.71417	0.997000	0.53966	0.957000	0.61999	7.742000	0.85008	2.407000	0.81776	0.491000	0.48974	GAA		0.562	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		A	71021022	G	A	71021022	3	1	61	1	0	0	0	0	1	0	0	0	7214	1059	37	1	2406	1	HKDC1	10	71021022	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3867	71021022	64513725	6802	14787										
SAR1A	56681	broad.mit.edu	37	chr10	71912263	71912263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgggagagccagcggaaaCcctcgccgtaaccttgcctc	11	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:71912263C>T	ENST00000373242.2	-	8	762	c.566G>A	c.(565-567)gGt>gAt	p.G189D	SAR1A_ENST00000373241.4_Missense_Mutation_p.G189D|SAR1A_ENST00000431664.2_Missense_Mutation_p.G189D|SAR1A_ENST00000458634.2_Missense_Mutation_p.G146D|SAR1A_ENST00000373238.1_Missense_Mutation_p.G189D	NM_001142648.1	NP_001136120.1	Q9NR31	SAR1A_HUMAN	secretion associated, Ras related GTPase 1A	189					intracellular protein transport (GO:0006886)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)	p.G189D(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(3)	6						CCAGCGGAAACCCTCGCCGTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	76	79					10																	71912263		2203	4300	6503	71582269	SO:0001583	missense	56681				CCDS7298.1	10q22.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000079332	ENSG00000079332			10534	protein-coding gene	gene with protein product		607691	"SAR1a gene homolog (S. cerevisiae) 1", "SAR1a gene homolog 1 (S. cerevisiae)", "SAR1 homolog A (S. cerevisiae)"	SARA1		10871277	Standard	NM_020150		Approved	SAR1, Sara	uc010qji.2	Q9NR31	OTTHUMG00000018400	ENST00000373242.2:c.566G>A	10.37:g.71912263C>T	ENSP00000362339:p.Gly189Asp		71582269	B4DQ19	Missense_Mutation	SNP	ENST00000373242.2	37	CCDS7298.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972915	0.92919	.	.	ENSG00000079332	ENST00000373241;ENST00000373239;ENST00000373238;ENST00000373242;ENST00000431664;ENST00000458634;ENST00000395026	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.95265	0.8464	H	0.99143	4.445	0.80722	D	1	D	0.71674	0.998	D	0.71414	0.973	D	0.97201	0.9864	10	0.87932	D	0	.	18.2046	0.89851	0.0:1.0:0.0:0.0	.	189	Q9NR31	SAR1A_HUMAN	D	189;189;189;189;189;146;108	ENSP00000362338:G189D;ENSP00000362335:G189D;ENSP00000362339:G189D;ENSP00000399698:G189D;ENSP00000437979:G146D	ENSP00000362335:G189D	G	-	2	0	SAR1A	71582269	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.658000	0.90341	0.585000	0.79938	GGT		0.483	SAR1A-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048500.2			T	71912263	C	T	71912263	3	4	61	1	0	0	0	0	1	0	0	0	13876	507	18	3	34	3	SAR1A	10	71912263	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	891241	71912263	63622484	6803	14788										
EIF4EBP2	1979	broad.mit.edu	37	chr10	72179801	72179801	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaattgaagactccaaaGtagaagtaaacaatttgaac	6	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:72179801G>T	ENST00000373218.4	+	2	300	c.277G>T	c.(277-279)Gta>Tta	p.V93L		NM_004096.4	NP_004087.1	Q13542	4EBP2_HUMAN	eukaryotic translation initiation factor 4E binding protein 2	93					cAMP-mediated signaling (GO:0019933)|insulin receptor signaling pathway (GO:0008286)|negative regulation of translational initiation (GO:0045947)|translation (GO:0006412)			p.V93L(1)		large_intestine(1)	1						AGACTCCAAAGTAGAAGTAAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	10											79	77	77					10																	72179801		2203	4300	6503	71849807	SO:0001583	missense	1979				CCDS7303.1	10q21-q22	2008-08-01			ENSG00000148730	ENSG00000148730			3289	protein-coding gene	gene with protein product		602224				7935836, 8975712	Standard	NM_004096		Approved		uc001jrb.3	Q13542	OTTHUMG00000018409	ENST00000373218.4:c.277G>T	10.37:g.72179801G>T	ENSP00000362314:p.Val93Leu		71849807		Missense_Mutation	SNP	ENST00000373218.4	37	CCDS7303.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.822138	0.32237	.	.	ENSG00000148730	ENST00000373218	.	.	.	5.32	3.44	0.39384	.	0.283462	0.39759	N	0.001274	T	0.40171	0.1106	L	0.29908	0.895	0.34945	D	0.750665	B	0.28820	0.224	B	0.33846	0.171	T	0.46048	-0.9219	9	0.27785	T	0.31	-2.7505	9.9724	0.41763	0.074:0.0:0.7882:0.1378	.	93	Q13542	4EBP2_HUMAN	L	93	.	ENSP00000362314:V93L	V	+	1	0	EIF4EBP2	71849807	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.785000	0.55424	0.730000	0.32425	0.650000	0.86243	GTA		0.488	EIF4EBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048513.1	NM_004096		T	72179801	G	T	72179801	3	4	61	1	0	0	0	0	1	0	0	0	5046	1029	36	2	283	2	EIF4EBP2	10	72179801	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	267538	72179801	63354946	6804	14789										
ADAMTS14	140766	broad.mit.edu	37	chr10	72495045	72495045	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactttggcagtggctaccaGacctgcttggcagtaagtag	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:72495045G>T	ENST00000373207.1	+	9	1473	c.1473G>T	c.(1471-1473)caG>caT	p.Q491H	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.Q494H	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	491	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Q494H(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GTGGCTACCAGACCTGCTTGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											52	52	52					10																	72495045		2203	4300	6503	72165051	SO:0001583	missense	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1473G>T	10.37:g.72495045G>T	ENSP00000362303:p.Gln491His		72165051	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	9.348	1.064784	0.20067	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.63417	-0.04;-0.04	4.51	1.41	0.22369	.	0.263396	0.35235	N	0.003354	T	0.48502	0.1503	L	0.50333	1.59	0.29291	N	0.86938	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.002	T	0.37686	-0.9695	10	0.37606	T	0.19	.	4.7186	0.12906	0.0914:0.4201:0.3676:0.1209	.	424;491;494	Q8WXS8-2;Q8WXS8;Q5T4G1	.;ATS14_HUMAN;.	H	494;491	ENSP00000362304:Q494H;ENSP00000362303:Q491H	ENSP00000362303:Q491H	Q	+	3	2	ADAMTS14	72165051	0.997000	0.39634	0.999000	0.59377	0.969000	0.65631	0.378000	0.20569	0.174000	0.19809	0.655000	0.94253	CAG		0.592	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72495045	G	T	72495045	3	4	61	1	0	0	0	0	1	0	0	0	259	933	33	2	1516	2	ADAMTS14	10	72495045	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315244	72495045	63039702	6805	14790										
SGPL1	8879	broad.mit.edu	37	chr10	72617372	72617372	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttacctttctctgcagaCgccttctggcaagaggggag	11	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:72617372C>T	ENST00000373202.3	+	6	611	c.411C>T	c.(409-411)gaC>gaT	p.D137D		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	137					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)	p.D137D(1)		large_intestine(4)	4						TCTCTGCAGACGCCTTCTGGC	0.493																																					Colon(151;1054 2458 6676 40971)											1	Substitution - coding silent(1)	large_intestine(1)	10											114	104	107					10																	72617372		2203	4300	6503	72287378	SO:0001630	splice_region_variant	8879			AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.410-1C>T	10.37:g.72617372C>T			72287378	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Silent	SNP	ENST00000373202.3	37	CCDS31216.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284062	0.23392	.	.	ENSG00000166224	ENST00000409118	.	.	.	5.86	2.07	0.26955	.	.	.	.	.	T	0.57577	0.2063	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49041	-0.8980	4	.	.	.	.	8.931	0.35670	0.0:0.2938:0.0:0.7062	.	.	.	.	M	51	.	.	T	+	2	0	SGPL1	72287378	0.732000	0.28121	0.289000	0.24876	0.726000	0.41606	0.470000	0.22084	0.135000	0.18707	-0.300000	0.09419	ACG		0.493	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901	Silent	T	72617372	C	T	72617372	5	4	61	1	0	0	0	0	0	0	1	0	14255	550	19	1	429	1	SGPL1	10	72617372	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122327	72617372	62917375	6806	14791										
CDH23	64072	broad.mit.edu	37	chr10	73206112	73206112	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttcttcaccaaccacttCtttgatacatacctgctgat	3	15	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:73206112C>A	ENST00000224721.6	+	2	110	c.105C>A	c.(103-105)ttC>ttA	p.F35L	CDH23_ENST00000461841.3_Missense_Mutation_p.F80L|CDH23_ENST00000299366.7_Missense_Mutation_p.F80L|CDH23_ENST00000398842.3_Missense_Mutation_p.F35L|CDH23_ENST00000398809.4_Missense_Mutation_p.F35L	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	35	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.F35L(2)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCAACCACTTCTTTGATACAT	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	10											92	94	93					10																	73206112		2088	4195	6283	72876118	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.105C>A	10.37:g.73206112C>A	ENSP00000224721:p.Phe35Leu		72876118	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	19.18	3.777316	0.70107	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721	T;T	0.59772	0.24;0.24	5.27	5.27	0.74061	Cadherin-like (1);	0.000000	0.64402	D	0.000016	T	0.62600	0.2441	N	0.24115	0.695	0.80722	D	1	D;D;D	0.69078	0.995;0.995;0.997	D;D;D	0.77004	0.976;0.976;0.989	T	0.53899	-0.8373	10	0.11485	T	0.65	.	19.0885	0.93215	0.0:1.0:0.0:0.0	.	35;35;35	A5D6V9;Q9H251;Q9H251-5	.;CAD23_HUMAN;.	L	35	ENSP00000381789:F35L;ENSP00000381822:F35L	ENSP00000224721:F35L	F	+	3	2	CDH23	72876118	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.909000	0.63314	2.758000	0.94735	0.561000	0.74099	TTC		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73206112	C	A	73206112	3	1	61	1	0	0	0	0	1	0	0	0	3114	912	32	2	111	2	CDH23	10	73206112	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	588740	73206112	62328635	6807	14792										
CDH23	64072	broad.mit.edu	37	chr10	73326600	73326600	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagcccccctcccaattCttcgccattgacagcgcccg	6	20	1	1	rs371933124		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:73326600C>A	ENST00000224721.6	+	6	551	c.546C>A	c.(544-546)ttC>ttA	p.F182L	CDH23_ENST00000461841.3_Missense_Mutation_p.F222L|CDH23_ENST00000299366.7_Missense_Mutation_p.F222L|CDH23_ENST00000398842.3_Missense_Mutation_p.F177L|CDH23_ENST00000398809.4_Missense_Mutation_p.F177L	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	177	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.F177L(2)|p.F182L(2)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCTCCCAATTCTTCGCCATTG	0.617																																																4	Substitution - Missense(4)	large_intestine(4)	10											48	51	50					10																	73326600		2031	4183	6214	72996606	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.546C>A	10.37:g.73326600C>A	ENSP00000224721:p.Phe182Leu		72996606	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	13.13	2.144130	0.37825	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.01665	4.7;4.7	5.43	3.2	0.36748	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.02156	0.0067	N	0.04090	-0.28	0.80722	D	1	B;D;B;D	0.69078	0.419;0.997;0.029;0.997	B;D;B;D	0.78314	0.168;0.91;0.01;0.991	T	0.68735	-0.5330	10	0.11485	T	0.65	.	7.956	0.30042	0.1397:0.716:0.0:0.1443	.	177;177;177;177	A5D6V9;Q9H251;Q9H251-5;E7ESV7	.;CAD23_HUMAN;.;.	L	182;177;177;177;177;182;182;118	ENSP00000381789:F177L;ENSP00000381822:F177L	ENSP00000224721:F182L	F	+	3	2	CDH23	72996606	1.000000	0.71417	0.998000	0.56505	0.944000	0.59088	1.909000	0.39917	1.277000	0.44412	0.561000	0.74099	TTC		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73326600	C	A	73326600	3	1	61	1	0	0	0	0	1	0	0	0	3114	912	32	2	553	2	CDH23	10	73326600	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120488	73326600	62208147	6808	14793										
CDH23	64072	broad.mit.edu	37	chr10	73558958	73558958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacaacgggtccccgccccGggcagctgagatccctgtct	12	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:73558958G>A	ENST00000224721.6	+	50	7165	c.7160G>A	c.(7159-7161)cGg>cAg	p.R2387Q	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.R142Q	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2382	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.R2387Q(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TCCCCGCCCCGGGCAGCTGAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											65	76	72					10																	73558958		2015	4149	6164	73228964	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7160G>A	10.37:g.73558958G>A	ENSP00000224721:p.Arg2387Gln		73228964	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	21.8	4.195406	0.78902	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.01725	4.67	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.06462	0.0166	L	0.46741	1.465	0.80722	D	1	D;D	0.89917	1.0;0.972	D;P	0.79108	0.992;0.854	T	0.53592	-0.8417	10	0.25751	T	0.34	.	13.7674	0.63004	0.0734:0.0:0.9266:0.0	.	2382;2382	E9PEX1;Q9H251	.;CAD23_HUMAN	Q	2387;2382;2385;142	ENSP00000381768:R142Q	ENSP00000224721:R2387Q	R	+	2	0	CDH23	73228964	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	5.654000	0.67974	2.623000	0.88846	0.655000	0.94253	CGG		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73558958	G	A	73558958	3	1	61	1	0	0	0	0	1	0	0	0	3114	1116	39	1	7688	1	CDH23	10	73558958	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232358	73558958	61975789	6809	14794										
PSAP	5660	broad.mit.edu	37	chr10	73587796	73587796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggccatgccagggcccaggCggtcacactcctccttgaca	11	17	1	1	rs147265566	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:73587796C>T	ENST00000394936.3	-	6	842	c.695G>A	c.(694-696)cGc>cAc	p.R232H	PSAP_ENST00000394934.1_Missense_Mutation_p.R232H			P07602	SAP_HUMAN	prosaposin	232	Saposin B-type 2. {ECO:0000255|PROSITE- ProRule:PRU00415}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)	p.R232H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						AGGGCCCAGGCGGTCACACTC	0.582													C|||	2	0.000399361	0	0.0029	5008	,	,		17455	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											127	92	104					10																	73587796		2203	4300	6503	73257802	SO:0001583	missense	5660			BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.695G>A	10.37:g.73587796C>T	ENSP00000378394:p.Arg232His		73257802	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	37	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	c	11.99	1.802394	0.31869	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000404083;ENST00000394940	D;D	0.84730	-1.89;-1.89	5.6	1.39	0.22231	Saposin-like (2);Saposin-like type B, 1 (1);Saposin B (2);	0.376195	0.30036	N	0.010571	T	0.75627	0.3875	L	0.44542	1.39	0.38709	D	0.953172	B	0.22800	0.075	B	0.21546	0.035	T	0.65573	-0.6135	10	0.15499	T	0.54	0.0183	9.1903	0.37195	0.4943:0.4368:0.0:0.0689	.	232	P07602	SAP_HUMAN	H	232;232;232;232;235;157	ENSP00000378394:R232H;ENSP00000378392:R232H	ENSP00000350063:R232H	R	-	2	0	PSAP	73257802	0.990000	0.36364	0.987000	0.45799	0.994000	0.84299	0.305000	0.19254	0.780000	0.33566	0.542000	0.68232	CGC		0.582	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		T	73587796	C	T	73587796	3	4	61	1	0	0	0	0	1	0	0	0	12677	768	27	1	931	1	PSAP	10	73587796	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28838	73587796	61946951	6810	14795										
DNAJB12	54788	broad.mit.edu	37	chr10	74100765	74100765	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagggaagccgccgccaaaGaacatgttgaagaggtcttc	13	9	1	3	rs536864860	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:74100765G>T	ENST00000444643.2	-	4	953	c.621C>A	c.(619-621)ttC>ttA	p.F207L	DNAJB12_ENST00000461919.1_Missense_Mutation_p.F2L|DNAJB12_ENST00000394903.2_Missense_Mutation_p.F241L|DNAJB12_ENST00000338820.3_Missense_Mutation_p.F241L			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	207						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.F207L(1)		endometrium(1)|large_intestine(2)|skin(1)	4						CGCCGCCAAAGAACATGTTGA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	10											50	48	49					10																	74100765		2203	4300	6503	73770771	SO:0001583	missense	54788			AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.621C>A	10.37:g.74100765G>T	ENSP00000403313:p.Phe207Leu		73770771	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	37		.	.	.	.	.	.	.	.	.	.	G	24.1	4.496217	0.85069	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.72835	-0.69;-0.69;-0.69	5.66	1.44	0.22558	Heat shock protein DnaJ, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84696	0.5529	M	0.90977	3.165	0.58432	D	0.99999	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.99	D	0.83885	0.0281	10	0.87932	D	0	-8.4491	9.6905	0.40125	0.3628:0.0:0.6372:0.0	.	207;207	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	L	241;241;207	ENSP00000345575:F241L;ENSP00000378363:F241L;ENSP00000403313:F207L	ENSP00000345575:F241L	F	-	3	2	DNAJB12	73770771	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.723000	0.38053	0.014000	0.14944	0.650000	0.86243	TTC		0.612	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			T	74100765	G	T	74100765	3	4	61	1	0	0	0	0	1	0	0	0	4628	933	33	2	526	2	DNAJB12	10	74100765	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	512969	74100765	61433982	6811	14796										
CCDC109A	90550	broad.mit.edu	37	chr10	74631334	74631334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatattttgtaatgacacGccaggtaagaattctcttca	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:74631334G>A	ENST00000373053.3	+	6	878	c.857G>A	c.(856-858)cGc>cAc	p.R286H	MCU_ENST00000605416.1_3'UTR|MCU_ENST00000357157.6_Missense_Mutation_p.R265H|MCU_ENST00000536019.1_Missense_Mutation_p.R237H	NM_138357.2	NP_612366.1	Q8NE86	MCU_HUMAN	mitochondrial calcium uniporter	286					calcium ion transmembrane import into mitochondrion (GO:0036444)|calcium-mediated signaling (GO:0019722)|glucose homeostasis (GO:0042593)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein complex oligomerization (GO:0035786)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|uniplex complex (GO:1990246)	calcium channel activity (GO:0005262)|uniporter activity (GO:0015292)	p.R286H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	14						GTAATGACACGCCAGGTAAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	10											82	79	80					10																	74631334		2203	4300	6503	74301340	SO:0001583	missense	90550			BC034235	CCDS7317.1, CCDS59218.1, CCDS59219.1	10q22.2	2011-06-23	2011-06-23	2011-06-23	ENSG00000156026	ENSG00000156026			23526	protein-coding gene	gene with protein product		614197	"coiled-coil domain containing 109A"	C10orf42, CCDC109A		21685886, 21685888	Standard	NM_138357		Approved	FLJ46135	uc001jtc.3	Q8NE86	OTTHUMG00000018443	ENST00000373053.3:c.857G>A	10.37:g.74631334G>A	ENSP00000362144:p.Arg286His		74301340	B2RDF3|B3KXV7|Q96FL3	Missense_Mutation	SNP	ENST00000373053.3	37	CCDS7317.1	.	.	.	.	.	.	.	.	.	.	G	35	5.447812	0.96205	.	.	ENSG00000156026	ENST00000373053;ENST00000357157;ENST00000536019	T;T;T	0.32753	1.44;1.44;1.44	5.92	5.92	0.95590	Coiled-coil domain containing protein 109, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	M	0.68593	2.085	0.80722	D	1	D;D;D	0.67145	0.994;0.989;0.996	P;P;P	0.61070	0.814;0.746;0.883	T	0.53606	-0.8415	10	0.87932	D	0	-9.9603	20.327	0.98704	0.0:0.0:1.0:0.0	.	265;237;286	Q8NE86-2;Q8NE86-3;Q8NE86	.;.;MCU_HUMAN	H	286;265;237	ENSP00000362144:R286H;ENSP00000349680:R265H;ENSP00000440913:R237H	ENSP00000349680:R265H	R	+	2	0	MCU	74301340	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.794000	0.96219	0.650000	0.86243	CGC		0.358	MCU-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048594.1	NM_138357		A	74631334	G	A	74631334	3	1	61	1	0	0	0	0	1	0	0	0	2750	1087	38	1	879	1	CCDC109A	10	74631334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	530569	74631334	60903413	6812	14797										
OIT3	170392	broad.mit.edu	37	chr10	74658796	74658796	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttccacgtctactgtggtCgtgagtaccttccctgtgct	10	13	1	1	rs535158135		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:74658796C>T	ENST00000334011.5	+	2	654	c.436C>T	c.(436-438)Cat>Tat	p.H146Y		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	146						nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.H146Y(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					CTACTGTGGTCGTGAGTACCT	0.512																																					Colon(7;19 345 13446 17537)											1	Substitution - Missense(1)	large_intestine(1)	10											80	63	68					10																	74658796		2200	4297	6497	74328802	SO:0001630	splice_region_variant	170392				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.436+1C>T	10.37:g.74658796C>T			74328802	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378866	0.82682	.	.	ENSG00000138315	ENST00000334011;ENST00000415725	T	0.49720	0.77	5.48	4.57	0.56435	.	0.000000	0.64402	D	0.000015	T	0.60766	0.2294	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.56866	-0.7908	10	0.26408	T	0.33	-9.6658	14.3602	0.66766	0.0:0.929:0.0:0.071	.	146	Q8WWZ8	OIT3_HUMAN	Y	146	ENSP00000333900:H146Y	ENSP00000333900:H146Y	H	+	1	0	OIT3	74328802	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	6.003000	0.70701	1.315000	0.45114	0.655000	0.94253	CAT		0.512	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635	Missense_Mutation	T	74658796	C	T	74658796	5	4	61	1	0	0	0	0	0	0	1	0	10880	898	31	1	442	1	OIT3	10	74658796	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27462	74658796	60875951	6813	14798										
OIT3	170392	broad.mit.edu	37	chr10	74684104	74684104	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgatcccggtgacctgcGagtttccacgcctgtacacc	10	15	0	2	rs367570425		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:74684104G>A	ENST00000334011.5	+	7	1287	c.1069G>A	c.(1069-1071)Gag>Aag	p.E357K		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	357	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.E357K(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					GGTGACCTGCGAGTTTCCACG	0.557																																					Colon(7;19 345 13446 17537)											1	Substitution - Missense(1)	large_intestine(1)	10						G	LYS/GLU	0,4406		0,0,2203	74	72	73		1069	4.8	1	10		73	1,8599	2.2+/-6.3	0,1,4299	no	missense	OIT3	NM_152635.1	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	357/546	74684104	1,13005	2203	4300	6503	74354110	SO:0001583	missense	170392				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1069G>A	10.37:g.74684104G>A	ENSP00000333900:p.Glu357Lys		74354110	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.705705	0.89018	0.0	1.16E-4	ENSG00000138315	ENST00000334011	D	0.81996	-1.56	5.72	4.79	0.61399	Zona pellucida sperm-binding protein (3);	0.000000	0.64402	D	0.000018	D	0.87354	0.6156	L	0.52905	1.665	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.83881	0.0279	10	0.08381	T	0.77	-26.7667	15.8633	0.79043	0.0:0.0:0.8633:0.1367	.	357	Q8WWZ8	OIT3_HUMAN	K	357	ENSP00000333900:E357K	ENSP00000333900:E357K	E	+	1	0	OIT3	74354110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.490000	0.97952	1.372000	0.46190	0.655000	0.94253	GAG		0.557	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		A	74684104	G	A	74684104	3	1	61	1	0	0	0	0	1	0	0	0	10880	1059	37	1	1095	1	OIT3	10	74684104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25308	74684104	60850643	6814	14799										
DNAJC9	23234	broad.mit.edu	37	chr10	75003266	75003266	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatttccttttgccgatcCttttgtctgctctgtttgag	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75003266C>A	ENST00000372950.4	-	5	2347	c.675G>T	c.(673-675)aaG>aaT	p.K225N	DNAJC9_ENST00000453189.2_5'Flank|FAM149B1_ENST00000242505.6_3'UTR	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	225					social behavior (GO:0035176)	nucleus (GO:0005634)		p.K225N(1)		endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					TTTGCCGATCCTTTTGTCTGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											108	105	106					10																	75003266		2203	4299	6502	74673272	SO:0001583	missense	23234			AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"Heat shock proteins / DNAJ (HSP40)"	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.675G>T	10.37:g.75003266C>A	ENSP00000362041:p.Lys225Asn		74673272	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467188	0.43839	.	.	ENSG00000213551	ENST00000372950	T	0.19394	2.15	5.88	4.92	0.64577	.	0.139965	0.64402	D	0.000004	T	0.14960	0.0361	L	0.33624	1.015	0.50467	D	0.999877	B	0.16396	0.017	B	0.15052	0.012	T	0.06023	-1.0850	10	0.27785	T	0.31	.	9.1397	0.36897	0.1635:0.6788:0.1577:0.0	.	225	Q8WXX5	DNJC9_HUMAN	N	225	ENSP00000362041:K225N	ENSP00000362041:K225N	K	-	3	2	DNAJC9	74673272	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.387000	0.20718	2.790000	0.95986	0.591000	0.81541	AAG		0.408	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190		A	75003266	C	A	75003266	3	1	61	1	0	0	0	0	1	0	0	0	4667	680	24	2	111	2	DNAJC9	10	75003266	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	319162	75003266	60531481	6815	14800										
TTC18	118491	broad.mit.edu	37	chr10	75037110	75037110	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctgatgaatcttgacatTttgatgcttctgaaaatatt	8	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75037110T>G	ENST00000310715.3	-	22	2738	c.2618A>C	c.(2617-2619)aAa>aCa	p.K873T	TTC18_ENST00000493787.1_Intron|TTC18_ENST00000355577.3_Missense_Mutation_p.K342T|TTC18_ENST00000394865.1_Missense_Mutation_p.K873T|TTC18_ENST00000340329.3_Intron|DNAJC9-AS1_ENST00000440197.2_RNA|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000401621.2_Missense_Mutation_p.K873T	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		873						extracellular vesicular exosome (GO:0070062)		p.K873T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ATCTTGACATTTTGATGCTTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											92	92	92					10																	75037110		2203	4300	6503	74707116	SO:0001583	missense	118491																														ENST00000310715.3:c.2618A>C	10.37:g.75037110T>G	ENSP00000310829:p.Lys873Thr		74707116	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	T	15.89	2.965489	0.53507	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.33865	1.85;1.85;1.39;1.44	5.62	4.5	0.54988	.	0.286983	0.33854	N	0.004499	T	0.45915	0.1366	M	0.62723	1.935	0.35373	D	0.789208	D	0.59357	0.985	P	0.55871	0.786	T	0.58457	-0.7633	10	0.49607	T	0.09	-13.6376	7.5121	0.27579	0.0:0.0936:0.0:0.9064	.	873	Q5T0N1	TTC18_HUMAN	T	873;873;873;280;873	ENSP00000310829:K873T;ENSP00000384479:K873T;ENSP00000409527:K280T;ENSP00000378334:K873T	ENSP00000310829:K873T	K	-	2	0	TTC18	74707116	0.998000	0.40836	1.000000	0.80357	0.623000	0.37688	1.595000	0.36708	2.136000	0.66102	0.533000	0.62120	AAA		0.398	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	75037110	T	G	75037110	3	3	61	1	0	0	0	0	1	0	0	0	16725	1841	64	4	775	4	TTC18	10	75037110	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33844	75037110	60497637	6816	14801										
TTC18	118491	broad.mit.edu	37	chr10	75082771	75082771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaacatgaaaagctccccGaattctcttcacacctggat	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75082771G>A	ENST00000310715.3	-	10	1192	c.1072C>T	c.(1072-1074)Cgg>Tgg	p.R358W	TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000355577.3_5'UTR|TTC18_ENST00000394865.1_Missense_Mutation_p.R358W|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000401621.2_Missense_Mutation_p.R358W	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		358						extracellular vesicular exosome (GO:0070062)		p.R358W(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					AAAGCTCCCCGAATTCTCTTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	10											117	112	113					10																	75082771		2203	4300	6503	74752777	SO:0001583	missense	118491																														ENST00000310715.3:c.1072C>T	10.37:g.75082771G>A	ENSP00000310829:p.Arg358Trp		74752777	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007189	0.75046	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000372928;ENST00000394865	T;T;T	0.37584	1.6;1.6;1.19	5.81	3.88	0.44766	.	0.000000	0.64402	D	0.000001	T	0.58032	0.2094	M	0.71581	2.175	0.45791	D	0.998672	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.63651	-0.6589	10	0.87932	D	0	-22.0931	13.491	0.61395	0.0:0.0:0.719:0.281	.	358;358	Q5T0N1-2;Q5T0N1	.;TTC18_HUMAN	W	358	ENSP00000310829:R358W;ENSP00000384479:R358W;ENSP00000378334:R358W	ENSP00000310829:R358W	R	-	1	2	TTC18	74752777	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	1.181000	0.32017	1.425000	0.47237	0.655000	0.94253	CGG		0.358	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	75082771	G	A	75082771	3	1	61	1	0	0	0	0	1	0	0	0	16725	1057	37	1	2369	1	TTC18	10	75082771	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45661	75082771	60451976	6817	14802										
ZMYND17	118490	broad.mit.edu	37	chr10	75184448	75184448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctgttcaggtttgagggAcatgaaaggattagacccaa	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75184448A>G	ENST00000372912.1	-	6	1248	c.1246T>C	c.(1246-1248)Tcc>Ccc	p.S416P	MSS51_ENST00000299432.2_Missense_Mutation_p.S416P			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	416					social behavior (GO:0035176)		metal ion binding (GO:0046872)	p.S416P(1)									GGTTTGAGGGACATGAAAGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											137	127	130					10																	75184448		2203	4300	6503	74854454	SO:0001583	missense	118490			AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.1246T>C	10.37:g.75184448A>G	ENSP00000362003:p.Ser416Pro		74854454	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.910104	0.72983	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.68765	-0.35;-0.35	5.62	4.49	0.54785	.	0.180261	0.49916	D	0.000122	T	0.77618	0.4157	M	0.66939	2.045	0.39855	D	0.973297	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.963	T	0.79366	-0.1833	10	0.87932	D	0	-3.6614	9.6512	0.39899	0.9173:0.0:0.0826:0.0	.	195;416	Q4VC12-2;Q4VC12	.;ZMY17_HUMAN	P	416	ENSP00000299432:S416P;ENSP00000362003:S416P	ENSP00000299432:S416P	S	-	1	0	ZMYND17	74854454	1.000000	0.71417	0.499000	0.27577	0.982000	0.71751	6.391000	0.73208	0.970000	0.38263	0.455000	0.32223	TCC		0.458	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		G	75184448	A	G	75184448	3	3	61	1	0	0	0	0	1	0	0	0	17748	275	10	4	140	4	ZMYND17	10	75184448	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	101677	75184448	60350299	6818	14803										
PPP3CB	5532	broad.mit.edu	37	chr10	75206289	75206289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccatcttgccaattgctCgaattttgtttcttatgatt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75206289C>T	ENST00000360663.5	-	11	1340	c.1229G>A	c.(1228-1230)cGa>cAa	p.R410Q	PPP3CB_ENST00000545874.1_Missense_Mutation_p.R325Q|PPP3CB_ENST00000544628.1_Missense_Mutation_p.R38Q|PPP3CB_ENST00000394829.2_Missense_Mutation_p.R411Q|PPP3CB_ENST00000342558.3_Missense_Mutation_p.R410Q|PPP3CB_ENST00000394822.2_Missense_Mutation_p.R428Q|PPP3CB_ENST00000394828.2_Missense_Mutation_p.R411Q			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	410	Calmodulin-binding. {ECO:0000255}.				axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)	p.R82Q(1)|p.R410Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					GCCAATTGCTCGAATTTTGTT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	10											191	174	180					10																	75206289		2203	4300	6503	74876295	SO:0001583	missense	5532			M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9315	protein-coding gene	gene with protein product	"calcineurin A beta", "protein phosphatase 2B, catalytic subunit, beta isoform"	114106	"protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)", "protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.1229G>A	10.37:g.75206289C>T	ENSP00000353881:p.Arg410Gln		74876295	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Missense_Mutation	SNP	ENST00000360663.5	37	CCDS7328.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104709	0.94245	.	.	ENSG00000107758	ENST00000360663;ENST00000394829;ENST00000394828;ENST00000394823;ENST00000544628;ENST00000430762;ENST00000342558;ENST00000545874;ENST00000394822	T;T;T;T;T;T;T	0.05447	3.44;3.44;3.44;3.44;3.44;3.44;3.44	5.12	5.12	0.69794	.	0.149195	0.34802	N	0.003675	T	0.20373	0.0490	L	0.49455	1.56	0.80722	D	1	D;D;P;D;P	0.89917	1.0;0.98;0.882;0.999;0.905	D;P;B;D;P	0.91635	0.999;0.759;0.325;0.99;0.484	T	0.01416	-1.1360	10	0.27785	T	0.31	.	18.5681	0.91124	0.0:1.0:0.0:0.0	.	428;325;410;411;410	P16298-2;F5H0F8;P16298-3;Q8N1F0;P16298	.;.;.;.;PP2BB_HUMAN	Q	410;411;411;82;38;72;410;325;428	ENSP00000353881:R410Q;ENSP00000378306:R411Q;ENSP00000378305:R411Q;ENSP00000437596:R38Q;ENSP00000343147:R410Q;ENSP00000439876:R325Q;ENSP00000378299:R428Q	ENSP00000343147:R410Q	R	-	2	0	PPP3CB	74876295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.625000	0.83145	2.375000	0.81037	0.585000	0.79938	CGA		0.363	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132		T	75206289	C	T	75206289	3	4	61	1	0	0	0	0	1	0	0	0	12432	884	31	1	361	1	PPP3CB	10	75206289	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21841	75206289	60328458	6819	14804										
USP54	159195	broad.mit.edu	37	chr10	75277235	75277235	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccaactatgatgagaattCttctcagtccaccctggtgc	7	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75277235C>A	ENST00000339859.4	-	19	3049	c.2949G>T	c.(2947-2949)aaG>aaT	p.K983N	RP11-137L10.6_ENST00000593790.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000422491.2_Missense_Mutation_p.K165N|USP54_ENST00000394811.2_Missense_Mutation_p.K71N|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000428547.1_Missense_Mutation_p.K833N|USP54_ENST00000408019.1_Missense_Mutation_p.K983N|RP11-137L10.6_ENST00000597958.1_RNA			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	983					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.K983N(1)|p.K71N(1)		breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					GATGAGAATTCTTCTCAGTCC	0.502																																					Colon(195;880 2046 8854 25025 38456)											2	Substitution - Missense(2)	large_intestine(2)	10											102	96	98					10																	75277235		2203	4300	6503	74947241	SO:0001583	missense	159195			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.2949G>T	10.37:g.75277235C>A	ENSP00000345216:p.Lys983Asn		74947241	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	37	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730145	0.48939	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000394811;ENST00000422491	T;T;T;T;T	0.23348	1.92;1.92;1.92;1.91;1.92	5.67	3.78	0.43462	.	.	.	.	.	T	0.13030	0.0316	N	0.14661	0.345	0.80722	D	1	B;B	0.19583	0.037;0.002	B;B	0.19148	0.024;0.004	T	0.10177	-1.0641	9	0.23891	T	0.37	-0.3139	6.61	0.22747	0.1606:0.6586:0.1086:0.0722	.	165;983	E7EW90;Q70EL1	.;UBP54_HUMAN	N	983;983;833;71;165	ENSP00000345216:K983N;ENSP00000386080:K983N;ENSP00000408714:K833N;ENSP00000378290:K71N;ENSP00000407368:K165N	ENSP00000345216:K983N	K	-	3	2	USP54	74947241	0.708000	0.27876	0.974000	0.42286	0.992000	0.81027	-0.029000	0.12329	1.380000	0.46344	0.561000	0.74099	AAG		0.502	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		A	75277235	C	A	75277235	3	1	61	1	0	0	0	0	1	0	0	0	17125	912	32	2	2125	2	USP54	10	75277235	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70946	75277235	60257512	6820	14805										
USP54	159195	broad.mit.edu	37	chr10	75289664	75289664	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttcatctggtataaattCtttagctatcccaatcaaaa	5	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75289664C>A	ENST00000339859.4	-	14	1934	c.1834G>T	c.(1834-1836)Gaa>Taa	p.E612*	USP54_ENST00000319786.7_Nonsense_Mutation_p.E612*|USP54_ENST00000394811.2_5'UTR|RNU6-883P_ENST00000384597.1_RNA|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000428547.1_Nonsense_Mutation_p.E462*|USP54_ENST00000408019.1_Nonsense_Mutation_p.E612*			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	612					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.E612*(1)		breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					GGTATAAATTCTTTAGCTATC	0.458											OREG0020266	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(195;880 2046 8854 25025 38456)											1	Substitution - Nonsense(1)	large_intestine(1)	10											38	40	39					10																	75289664		1879	4122	6001	74959670	SO:0001587	stop_gained	159195			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.1834G>T	10.37:g.75289664C>A	ENSP00000345216:p.Glu612*	1159	74959670	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Nonsense_Mutation	SNP	ENST00000339859.4	37	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	C	36	5.620579	0.96660	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000319786	.	.	.	5.66	5.66	0.87406	.	0.075067	0.52532	U	0.000080	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-9.3048	18.3055	0.90179	0.0:1.0:0.0:0.0	.	.	.	.	X	612;612;462;612	.	ENSP00000326547:E612X	E	-	1	0	USP54	74959670	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.699000	0.61796	2.832000	0.97577	0.655000	0.94253	GAA		0.458	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		A	75289664	C	A	75289664	4	1	61	1	0	0	0	0	0	1	0	0	17125	922	32	2	3260	2	USP54	10	75289664	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12429	75289664	60245083	6821	14806										
SEC24C	9632	broad.mit.edu	37	chr10	75529199	75529199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctggctgatctatatcGaaactgtgagactgacacgc	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75529199G>A	ENST00000339365.2	+	19	2681	c.2519G>A	c.(2518-2520)cGa>cAa	p.R840Q	SEC24C_ENST00000535742.1_Missense_Mutation_p.R88Q|SEC24C_ENST00000540668.1_Missense_Mutation_p.R88Q|SEC24C_ENST00000496827.1_3'UTR|SEC24C_ENST00000411652.2_Missense_Mutation_p.R721Q|FUT11_ENST00000394790.1_5'Flank|SEC24C_ENST00000345254.4_Missense_Mutation_p.R840Q|FUT11_ENST00000372841.3_5'Flank	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	840					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.R840Q(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					GATCTATATCGAAACTGTGAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	10											59	53	55					10																	75529199		2203	4300	6503	75199205	SO:0001583	missense	9632			D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2519G>A	10.37:g.75529199G>A	ENSP00000343405:p.Arg840Gln		75199205	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	G	36	5.753938	0.96890	.	.	ENSG00000176986	ENST00000535742;ENST00000345254;ENST00000540668;ENST00000339365;ENST00000411652	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.50188	0.1601	M	0.74467	2.265	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60012	0.867;0.867	T	0.47661	-0.9100	10	0.49607	T	0.09	-7.8026	19.5319	0.95232	0.0:0.0:1.0:0.0	.	721;840	E7EP00;P53992	.;SC24C_HUMAN	Q	88;840;88;840;721	ENSP00000446174:R88Q;ENSP00000321845:R840Q;ENSP00000445023:R88Q;ENSP00000343405:R840Q;ENSP00000402913:R721Q	ENSP00000343405:R840Q	R	+	2	0	SEC24C	75199205	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	7.948000	0.87774	2.628000	0.89032	0.313000	0.20887	CGA		0.572	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			A	75529199	G	A	75529199	3	1	61	1	0	0	0	0	1	0	0	0	14033	1058	37	1	2585	1	SEC24C	10	75529199	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239535	75529199	60005548	6822	14807										
FUT11	170384	broad.mit.edu	37	chr10	75533257	75533257	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcagagtttattgactttCtggacaagaatgatgaggag	13	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75533257C>A	ENST00000372841.3	+	2	1061	c.1018C>A	c.(1018-1020)Ctg>Atg	p.L340M	RMRPP1_ENST00000517236.1_RNA|AC022400.2_ENST00000595757.1_5'Flank|FUT11_ENST00000465695.1_3'UTR|FUT11_ENST00000394790.1_Missense_Mutation_p.L340M	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	340					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.L340M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					TATTGACTTTCTGGACAAGAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	83	84					10																	75533257		2203	4300	6503	75203263	SO:0001583	missense	170384			BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.1018C>A	10.37:g.75533257C>A	ENSP00000361932:p.Leu340Met		75203263	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	37	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696223	0.68386	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.53857	0.6;0.6	5.68	1.83	0.25207	.	0.000000	0.85682	D	0.000000	T	0.70020	0.3176	M	0.82517	2.595	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.68934	-0.5278	10	0.87932	D	0	-16.4848	8.7438	0.34573	0.0:0.6499:0.0:0.3501	.	340;340	Q495W5;Q495W5-2	FUT11_HUMAN;.	M	340	ENSP00000361932:L340M;ENSP00000378270:L340M	ENSP00000361932:L340M	L	+	1	2	FUT11	75203263	0.997000	0.39634	0.955000	0.39395	0.964000	0.63967	1.591000	0.36665	0.083000	0.17047	0.563000	0.77884	CTG		0.473	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		A	75533257	C	A	75533257	3	1	61	1	0	0	0	0	1	0	0	0	6122	912	32	2	1024	2	FUT11	10	75533257	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4058	75533257	60001490	6823	14808										
KIAA0913	23053	broad.mit.edu	37	chr10	75550024	75550024	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagacactgcacaagttCtgtggcccctcccctgtggt	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75550024C>A	ENST00000605216.1	+	7	1132	c.915C>A	c.(913-915)ttC>ttA	p.F305L	ZSWIM8_ENST00000604524.1_Missense_Mutation_p.F305L|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.F305L|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.F305L|ZSWIM8_ENST00000603114.1_Missense_Mutation_p.F305L	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	305							zinc ion binding (GO:0008270)	p.F305L(2)									TGCACAAGTTCTGTGGCCCCT	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	10											160	161	160					10																	75550024		2008	4182	6190	75220030	SO:0001583	missense	23053			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.915C>A	10.37:g.75550024C>A	ENSP00000474748:p.Phe305Leu		75220030	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.07|15.07|15.07	2.725500|2.725500|2.725500	0.48833|0.48833|0.48833	.|.|.	.|.|.	ENSG00000214655|ENSG00000214655|ENSG00000214655	ENST00000398706|ENST00000433366|ENST00000451629	T|.|.	0.61742|.|.	0.08|.|.	5.34|5.34|5.34	5.34|5.34|5.34	0.76211|0.76211|0.76211	.|.|.	0.876351|.|.	0.09296|.|.	U|.|.	0.821670|.|.	T|T|T	0.55257|0.55257|0.55257	0.1909|0.1909|0.1909	L|L|L	0.40543|0.40543|0.40543	1.245|1.245|1.245	0.51012|0.51012|0.51012	D|D|D	0.999902|0.999902|0.999902	D;D;D|.|.	0.56035|.|.	0.974;0.974;0.974|.|.	D;D;D|.|.	0.67725|.|.	0.953;0.953;0.953|.|.	T|T|T	0.50030|0.50030|0.50030	-0.8875|-0.8875|-0.8875	10|5|5	0.48119|.|.	T|.|.	0.1|.|.	-6.5505|-6.5505|-6.5505	9.7673|9.7673|9.7673	0.40567|0.40567|0.40567	0.0:0.8491:0.0:0.1509|0.0:0.8491:0.0:0.1509|0.0:0.8491:0.0:0.1509	.|.|.	305;305;305|.|.	A7E2V4;A7E2V4-5;A7E2V4-4|.|.	K0913_HUMAN;.;.|.|.	L|M|Y	305|28|108	ENSP00000381693:F305L|.|.	ENSP00000381693:F305L|.|.	F|L|S	+|+|+	3|1|2	2|2|0	KIAA0913|KIAA0913|KIAA0913	75220030|75220030|75220030	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	2.911000|2.911000|2.911000	0.48774|0.48774|0.48774	2.780000|2.780000|2.780000	0.95670|0.95670|0.95670	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTG|TCT		0.542	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		A	75550024	C	A	75550024	3	1	61	1	0	0	0	0	1	0	0	0	8221	912	32	2	941	2	KIAA0913	10	75550024	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16767	75550024	59984723	6824	14809										
PLAU	414236	broad.mit.edu	37	chr10	75673383	75673383	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttaagattattgggggaGaattcaccaccatcgagaac	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75673383G>T	ENST00000409178.1	-	3	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000446342.1_Nonsense_Mutation_p.E166*|PLAU_ENST00000372762.4_Nonsense_Mutation_p.E147*|PLAU_ENST00000372764.3_Nonsense_Mutation_p.E183*	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55									p.E183*(1)		endometrium(1)	1	Prostate(51;0.0112)					TATTGGGGGAGAATTCACCAC	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											112	133	126					10																	75673383		2203	4300	6503	75343389	SO:0001627	intron_variant	5328				CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-550C>A	10.37:g.75673383G>T			75343389	Q3KRG4|Q8NAK4	Nonsense_Mutation	SNP	ENST00000409178.1	37	CCDS53541.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748048	0.69533	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	.	.	.	5.25	1.13	0.20643	.	0.796636	0.12823	N	0.436247	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	2.5138	0.04663	0.1739:0.1496:0.5227:0.1538	.	.	.	.	X	166;183;147;147	.	ENSP00000361847:E147X	E	+	1	0	PLAU	75343389	0.175000	0.23083	0.102000	0.21198	0.679000	0.39708	0.641000	0.24720	0.268000	0.21939	0.650000	0.86243	GAA		0.542	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		T	75673383	G	T	75673383	1	4	61	0	1	0	0	0	0	0	0	0	12053	943	33	2		2	PLAU	10	75673383	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123359	75673383	59861364	6825	14810										
VCL	7414	broad.mit.edu	37	chr10	75877872	75877872	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgcttcaatcaaaattcGaacagatgctggatttacac	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:75877872G>A	ENST00000211998.4	+	22	3444	c.3350G>A	c.(3349-3351)cGa>cAa	p.R1117Q	VCL_ENST00000372755.3_Missense_Mutation_p.R1049Q|RP11-178G16.5_ENST00000599110.1_lincRNA|VCL_ENST00000417648.2_Missense_Mutation_p.R310Q|RP11-178G16.4_ENST00000598318.1_lincRNA	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	1117	C-terminal tail.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.R1117Q(1)	VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					ATCAAAATTCGAACAGATGCT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	10											118	104	109					10																	75877872		2203	4300	6503	75547878	SO:0001583	missense	7414			M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"metavinculin"	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.3350G>A	10.37:g.75877872G>A	ENSP00000211998:p.Arg1117Gln		75547878	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Missense_Mutation	SNP	ENST00000211998.4	37	CCDS7341.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.685998|5.685998	0.96784|0.96784	.|.	.|.	ENSG00000035403|ENSG00000035403	ENST00000537043|ENST00000372755;ENST00000211998;ENST00000417648;ENST00000436396	.|T;T;T;T	.|0.47869	.|0.83;0.83;0.83;0.83	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.146314	.|0.45867	.|D	.|0.000334	T|T	0.57607|0.57607	0.2065|0.2065	L|L	0.31804|0.31804	0.96|0.96	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.986;0.996	.|D;P;D	.|0.69479	.|0.964;0.727;0.926	T|T	0.52518|0.52518	-0.8565|-0.8565	6|10	0.59425|0.30854	D|T	0.04|0.27	.|.	19.4027|19.4027	0.94637|0.94637	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|310;1049;1117	.|B4DTM7;P18206-2;P18206	.|.;.;VINC_HUMAN	K|Q	976|1049;1117;310;789	.|ENSP00000361841:R1049Q;ENSP00000211998:R1117Q;ENSP00000411887:R310Q;ENSP00000415489:R789Q	ENSP00000442299:E976K|ENSP00000211998:R1117Q	E|R	+|+	1|2	0|0	VCL|VCL	75547878|75547878	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.476000|9.476000	0.97823|0.97823	2.576000|2.576000	0.86940|0.86940	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.512	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000		A	75877872	G	A	75877872	3	1	61	1	0	0	0	0	1	0	0	0	17179	1058	37	1	3436	1	VCL	10	75877872	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	204489	75877872	59656875	6826	14811										
ADK	132	broad.mit.edu	37	chr10	76074455	76074455	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtgaaaaaattcaaagtCgaatatcatgctggtggctc	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:76074455C>T	ENST00000286621.2	+	4	275	c.225C>T	c.(223-225)gtC>gtT	p.V75V	ADK_ENST00000372734.3_Silent_p.V58V|ADK_ENST00000541550.1_Silent_p.V40V|ADK_ENST00000539909.1_Silent_p.V75V	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	75					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)	p.V75V(1)		breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	AATTCAAAGTCGAATATCATG	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	10											54	55	55					10																	76074455		2203	4298	6501	75744461	SO:0001819	synonymous_variant	132			U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"adenosine 5'-phosphotransferase"	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.225C>T	10.37:g.76074455C>T			75744461	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Silent	SNP	ENST00000286621.2	37	CCDS7343.1																																																																																				0.328	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		T	76074455	C	T	76074455	2	4	61	1	0	0	0	0	0	0	0	1	320	871	31	1		1	ADK	10	76074455	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	196583	76074455	59460292	6827	14812										
MYST4	23522	broad.mit.edu	37	chr10	76732382	76732382	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacgaccgaaaaataaatTaaagcaacgattgttgtagg	10	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:76732382T>G	ENST00000287239.4	+	7	1535	c.1046T>G	c.(1045-1047)tTa>tGa	p.L349*	KAT6B_ENST00000372714.1_Nonsense_Mutation_p.L349*|KAT6B_ENST00000372725.1_Nonsense_Mutation_p.L349*|KAT6B_ENST00000372711.1_Nonsense_Mutation_p.L349*|KAT6B_ENST00000372724.1_Nonsense_Mutation_p.L349*	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	349					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.L349*(1)									AAAAATAAATTAAAGCAACGA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											131	138	136					10																	76732382		2203	4300	6503	76402388	SO:0001587	stop_gained	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.1046T>G	10.37:g.76732382T>G	ENSP00000287239:p.Leu349*		76402388	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Nonsense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	T	40	8.424321	0.98806	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	.	.	.	5.7	5.7	0.88788	.	0.000000	0.36628	N	0.002497	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.216	15.955	0.79880	0.0:0.0:0.0:1.0	.	.	.	.	X	349	.	ENSP00000287239:L349X	L	+	2	0	KAT6B	76402388	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.475000	0.60210	2.168000	0.68352	0.533000	0.62120	TTA		0.343	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76732382	T	G	76732382	4	3	61	1	0	0	0	0	0	1	0	0	10135	1764	61	4	1064	4	MYST4	10	76732382	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	657927	76732382	58802365	6828	14813										
MYST4	23522	broad.mit.edu	37	chr10	76744867	76744867	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatgagcaaaatttattgCcaaaacctttgcttgttagc	6	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:76744867C>G	ENST00000287239.4	+	12	2892	c.2403C>G	c.(2401-2403)tgC>tgG	p.C801W	KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372714.1_Missense_Mutation_p.C509W|KAT6B_ENST00000372725.1_Missense_Mutation_p.C509W|KAT6B_ENST00000372711.1_Missense_Mutation_p.C618W|KAT6B_ENST00000372724.1_Missense_Mutation_p.C509W	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	801	Catalytic.|Interaction with BRPF1.|MYST-type HAT.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.C801W(1)									AAATTTATTGCCAAAACCTTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	10											116	112	113					10																	76744867		2203	4300	6503	76414873	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2403C>G	10.37:g.76744867C>G	ENSP00000287239:p.Cys801Trp		76414873	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387936	0.42308	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.89415	-2.42;-2.42;-2.51;-2.42;-2.47	6.07	6.07	0.98685	.	0.000000	0.56097	D	0.000038	D	0.96753	0.8940	H	0.98276	4.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.97567	1.0102	10	0.87932	D	0	-7.8647	14.2124	0.65773	0.0:0.9237:0.0:0.0763	.	618;509;801	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	W	509;509;801;509;618	ENSP00000361810:C509W;ENSP00000361809:C509W;ENSP00000287239:C801W;ENSP00000361799:C509W;ENSP00000361796:C618W	ENSP00000287239:C801W	C	+	3	2	KAT6B	76414873	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.097000	0.57741	2.885000	0.99019	0.650000	0.86243	TGC		0.318	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76744867	C	G	76744867	3	3	61	1	0	0	0	0	1	0	0	0	10135	747	26	5	2441	5	MYST4	10	76744867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12485	76744867	58789880	6829	14814										
DUSP13	51207	broad.mit.edu	37	chr10	76854632	76854632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcacagtgtaccagcacGcggcctgtagggagaaccaa	13	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:76854632G>A	ENST00000472493.2	-	4	477	c.399C>T	c.(397-399)cgC>cgT	p.R133R	DUSP13_ENST00000464872.1_Silent_p.R82R|DUSP13_ENST00000605915.1_Silent_p.R155R|DUSP13_ENST00000607009.1_5'Flank|DUSP13_ENST00000478873.2_Silent_p.R269R|DUSP13_ENST00000491677.2_Silent_p.R262R|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000607131.1_Silent_p.R226R|DUSP13_ENST00000372700.3_Silent_p.R183R	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	133	Tyrosine-protein phosphatase.				meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R262R(1)|p.R133R(1)		large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GTACCAGCACGCGGCCTGTAG	0.562																																					NSCLC(174;1655 2059 12324 40663 42963)											2	Substitution - coding silent(2)	large_intestine(2)	10											86	65	72					10																	76854632		2203	4300	6503	76524638	SO:0001819	synonymous_variant	51207			AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000472493.2:c.399C>T	10.37:g.76854632G>A			76524638	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Silent	SNP	ENST00000472493.2	37	CCDS7346.1																																																																																				0.562	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3			A	76854632	G	A	76854632	2	1	61	1	0	0	0	0	0	0	0	1	4824	1074	38	1		1	DUSP13	10	76854632	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109765	76854632	58680115	6830	14815										
C10orf11	83938	broad.mit.edu	37	chr10	77806943	77806943	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactgatttggagaacctgCtggatcacttggcagaagtg	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:77806943C>A	ENST00000372499.1	+	3	411	c.196C>A	c.(196-198)Ctg>Atg	p.L66M	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	66					melanocyte differentiation (GO:0030318)			p.L66M(1)		endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GGAGAACCTGCTGGATCACTT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	121	125					10																	77806943		2203	4300	6503	77476949	SO:0001583	missense	83938			AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"oculocutaneous albinism 7, autosomal recessive"	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.196C>A	10.37:g.77806943C>A	ENSP00000361577:p.Leu66Met		77476949	B1AVW6	Missense_Mutation	SNP	ENST00000372499.1	37	CCDS7351.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.132890	0.56828	.	.	ENSG00000148655	ENST00000354343;ENST00000372499	T	0.38722	1.12	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.67221	0.2870	M	0.88704	2.975	0.43095	D	0.99477	D	0.64830	0.994	D	0.68943	0.961	T	0.70806	-0.4772	10	0.49607	T	0.09	-5.6112	11.8159	0.52211	0.0:0.8656:0.0:0.1344	.	66	Q9H2I8	CJ011_HUMAN	M	94;66	ENSP00000361577:L66M	ENSP00000346310:L94M	L	+	1	2	C10orf11	77476949	1.000000	0.71417	1.000000	0.80357	0.439000	0.31926	3.598000	0.54038	2.885000	0.99019	0.655000	0.94253	CTG		0.507	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024		A	77806943	C	A	77806943	3	1	61	1	0	0	0	0	1	0	0	0	1586	796	28	2	206	2	C10orf11	10	77806943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	952311	77806943	57727804	6831	14816										
KCNMA1	3778	broad.mit.edu	37	chr10	78944625	78944625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacacgttgaaagccatgtCgatctgtaatgtgaaatctt	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:78944625C>T	ENST00000286628.8	-	4	651	c.652G>A	c.(652-654)Gac>Aac	p.D218N	KCNMA1_ENST00000404857.1_Missense_Mutation_p.D218N|KCNMA1_ENST00000372440.1_Missense_Mutation_p.D218N|KCNMA1_ENST00000354353.5_Missense_Mutation_p.D218N|KCNMA1_ENST00000372443.1_Missense_Mutation_p.D218N|KCNMA1_ENST00000404771.3_Missense_Mutation_p.D218N|KCNMA1_ENST00000286627.5_Missense_Mutation_p.D218N|KCNMA1_ENST00000406533.3_Missense_Mutation_p.D218N	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	218					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.D218N(1)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	AAAGCCATGTCGATCTGTAAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											185	166	172					10																	78944625		2203	4300	6503	78614631	SO:0001583	missense	3778			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.652G>A	10.37:g.78944625C>T	ENSP00000286628:p.Asp218Asn		78614631	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.9|20.9	4.059607|4.059607	0.76074|0.76074	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857|ENST00000372421	T;T;T;T;T;T;T;T;T|.	0.50001|.	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Ion transport (1);|.	0.100042|.	0.64402|.	D|.	0.000003|.	T|T	0.73233|0.73233	0.3561|0.3561	L|L	0.58510|0.58510	1.815|1.815	0.80722|0.80722	D|D	1|1	B;P;B;P;P;P|.	0.42735|.	0.027;0.478;0.423;0.478;0.788;0.478|.	B;B;B;B;B;B|.	0.41723|.	0.012;0.258;0.168;0.365;0.216;0.258|.	T|T	0.69335|0.69335	-0.5172|-0.5172	10|5	0.72032|.	D|.	0.01|.	-20.5725|-20.5725	19.8617|19.8617	0.96787|0.96787	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	218;218;218;218;218;218|.	Q12791-4;B7ZMF5;Q12791-2;Q12791;Q12791-5;Q5SVJ7|.	.;.;.;KCMA1_HUMAN;.;.|.	N|Q	218;155;153;192;155;218;218;192;218;218;218|206	ENSP00000361517:D218N;ENSP00000361485:D155N;ENSP00000361514:D153N;ENSP00000396608:D192N;ENSP00000361520:D218N;ENSP00000286627:D218N;ENSP00000385552:D218N;ENSP00000346321:D218N;ENSP00000385806:D218N|.	ENSP00000286627:D218N|.	D|R	-|-	1|2	0|0	KCNMA1|KCNMA1	78614631|78614631	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.720000|7.720000	0.84759|0.84759	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.418	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		T	78944625	C	T	78944625	3	4	61	1	0	0	0	0	1	0	0	0	8094	884	31	1	3330	1	KCNMA1	10	78944625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1137682	78944625	56590122	6832	14817										
DLG5	9231	broad.mit.edu	37	chr10	79571797	79571797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgctccgtggcgctccGcaggtttatgccgttgaact	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:79571797G>A	ENST00000372391.2	-	22	4212	c.4207C>T	c.(4207-4209)Cgg>Tgg	p.R1403W	DLG5_ENST00000372388.2_Missense_Mutation_p.R1063W|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1403	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)	p.R1403W(1)		breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GTGGCGCTCCGCAGGTTTATG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	10											75	65	68					10																	79571797		2203	4300	6503	79241803	SO:0001583	missense	9231			U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.4207C>T	10.37:g.79571797G>A	ENSP00000361467:p.Arg1403Trp		79241803	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971636	0.74246	.	.	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.29917	1.55;1.55;1.55	5.5	2.06	0.26882	PDZ/DHR/GLGF (4);	0.216466	0.23275	N	0.049980	T	0.64349	0.2590	H	0.96576	3.845	0.38081	D	0.936662	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.72225	-0.4355	10	0.87932	D	0	.	8.7332	0.34512	0.0798:0.0:0.5112:0.409	.	1403;1063	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	W	1403;364;1063	ENSP00000361467:R1403W;ENSP00000394797:R364W;ENSP00000361464:R1063W	ENSP00000361464:R1063W	R	-	1	2	DLG5	79241803	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.258000	0.43249	0.746000	0.32786	0.655000	0.94253	CGG		0.647	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			A	79571797	G	A	79571797	3	1	61	1	0	0	0	0	1	0	0	0	4569	1086	38	1	1596	1	DLG5	10	79571797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	627172	79571797	55962950	6833	14818										
POLR3A	11128	broad.mit.edu	37	chr10	79744968	79744968	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatctctttaatccgggGcacgcccagggtgatgttca	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:79744968G>T	ENST00000372371.3	-	24	3339	c.3202C>A	c.(3202-3204)Ccc>Acc	p.P1068T		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1068					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)	p.P1068T(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TTAATCCGGGGCACGCCCAGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	10											136	131	133					10																	79744968		2203	4300	6503	79414974	SO:0001583	missense	11128			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3202C>A	10.37:g.79744968G>T	ENSP00000361446:p.Pro1068Thr		79414974	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.921795	0.92319	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.79554	-1.28	5.95	5.95	0.96441	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.94709	0.8293	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96179	0.9129	9	.	.	.	-25.1454	20.3802	0.98930	0.0:0.0:1.0:0.0	.	1068	O14802	RPC1_HUMAN	T	1068;1047	ENSP00000361446:P1068T	.	P	-	1	0	POLR3A	79414974	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.275000	0.95738	2.822000	0.97130	0.563000	0.77884	CCC		0.527	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		T	79744968	G	T	79744968	3	4	61	1	0	0	0	0	1	0	0	0	12259	1203	42	2	1002	2	POLR3A	10	79744968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173171	79744968	55789779	6834	14819										
POLR3A	11128	broad.mit.edu	37	chr10	79745917	79745917	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaatgaatttttttatttCctgaaagattacacagcaaa	4	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:79745917C>T	ENST00000372371.3	-	22	3039	c.2902G>A	c.(2902-2904)Gaa>Aaa	p.E968K		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	968					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)	p.E968K(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TTTTTTATTTCCTGAAAGATT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											108	110	109					10																	79745917		2203	4300	6503	79415923	SO:0001630	splice_region_variant	11128			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.2902-1G>A	10.37:g.79745917C>T			79415923	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457618	0.63401	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.67698	-0.28	5.55	4.64	0.57946	RNA polymerase Rpb1, domain 5 (1);	0.109128	0.64402	D	0.000010	T	0.57917	0.2086	L	0.38649	1.16	0.80722	D	1	B	0.29835	0.258	B	0.31614	0.133	T	0.53265	-0.8463	9	.	.	.	-28.0398	15.9665	0.79974	0.1355:0.8645:0.0:0.0	.	968	O14802	RPC1_HUMAN	K	968	ENSP00000361446:E968K	.	E	-	1	0	POLR3A	79415923	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.738000	0.68613	1.323000	0.45263	0.557000	0.71058	GAA		0.348	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	Missense_Mutation	T	79745917	C	T	79745917	5	4	61	1	0	0	0	0	0	0	1	0	12259	869	30	3	1310	3	POLR3A	10	79745917	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	949	79745917	55788830	6835	14820										
POLR3A	11128	broad.mit.edu	37	chr10	79764633	79764633	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcaccgatcccaattgaGaaaccacggttagctgttga	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:79764633G>T	ENST00000372371.3	-	16	2225	c.2088C>A	c.(2086-2088)ttC>ttA	p.F696L		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	696					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)	p.F696L(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TCCCAATTGAGAAACCACGGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	92	96					10																	79764633		2203	4300	6503	79434639	SO:0001583	missense	11128			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.2088C>A	10.37:g.79764633G>T	ENSP00000361446:p.Phe696Leu		79434639	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228660	0.58777	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.80123	-1.34	5.79	3.95	0.45737	RNA polymerase Rpb1, domain 3 (1);	0.049038	0.85682	D	0.000000	T	0.81517	0.4839	M	0.85859	2.78	0.80722	D	1	P	0.34639	0.461	B	0.37650	0.255	T	0.78201	-0.2296	9	.	.	.	-26.3868	9.0197	0.36193	0.2771:0.0:0.7229:0.0	.	696	O14802	RPC1_HUMAN	L	696	ENSP00000361446:F696L	.	F	-	3	2	POLR3A	79434639	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	2.662000	0.46766	0.794000	0.33899	0.650000	0.86243	TTC		0.453	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		T	79764633	G	T	79764633	3	4	61	1	0	0	0	0	1	0	0	0	12259	933	33	2	2148	2	POLR3A	10	79764633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18716	79764633	55770114	6836	14821										
POLR3A	11128	broad.mit.edu	37	chr10	79785513	79785513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggacgatccttctcactcGtaccctttgaaaaaaagcac	6	12	1	1	rs185508362		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:79785513G>A	ENST00000372371.3	-	3	322	c.185C>T	c.(184-186)aCg>aTg	p.T62M		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	62					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)	p.T62M(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CTTCTCACTCGTACCCTTTGA	0.483													G|||	1	0.000199681	0	0	5008	,	,		17867	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											117	108	111					10																	79785513		2203	4300	6503	79455519	SO:0001583	missense	11128			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.185C>T	10.37:g.79785513G>A	ENSP00000361446:p.Thr62Met		79455519	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.36	3.370937	0.61624	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.26660	1.72	5.18	5.18	0.71444	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.37100	0.0991	M	0.80982	2.52	0.80722	D	1	D	0.60575	0.988	B	0.42995	0.404	T	0.45818	-0.9235	9	.	.	.	-17.7882	18.6999	0.91617	0.0:0.0:1.0:0.0	.	62	O14802	RPC1_HUMAN	M	62	ENSP00000361446:T62M	.	T	-	2	0	POLR3A	79455519	1.000000	0.71417	0.238000	0.24106	0.695000	0.40330	9.102000	0.94226	2.412000	0.81896	0.555000	0.69702	ACG		0.483	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		A	79785513	G	A	79785513	3	1	61	1	0	0	0	0	1	0	0	0	12259	1145	40	1	4103	1	POLR3A	10	79785513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20880	79785513	55749234	6837	14822										
ZMIZ1	57178	broad.mit.edu	37	chr10	81050780	81050780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcggcaaccccatggcgtCgggcatgaccaccagcaacc	12	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:81050780C>T	ENST00000334512.5	+	10	1177	c.605C>T	c.(604-606)tCg>tTg	p.S202L	ZMIZ1_ENST00000478357.1_3'UTR	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	202					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.S202L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CCCATGGCGTCGGGCATGACC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	10											116	98	104					10																	81050780		2203	4300	6503	80720786	SO:0001583	missense	57178			AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.605C>T	10.37:g.81050780C>T	ENSP00000334474:p.Ser202Leu		80720786	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	37	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	C	36	5.717754	0.96839	.	.	ENSG00000108175	ENST00000334512;ENST00000360331	T	0.32515	1.45	5.67	5.67	0.87782	.	0.000000	0.37095	N	0.002246	T	0.52597	0.1744	L	0.51422	1.61	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.77557	0.99;0.787	T	0.46693	-0.9173	10	0.52906	T	0.07	-6.3626	19.7667	0.96346	0.0:1.0:0.0:0.0	.	112;202	Q9H7J0;Q9ULJ6	.;ZMIZ1_HUMAN	L	202;132	ENSP00000334474:S202L	ENSP00000334474:S202L	S	+	2	0	ZMIZ1	80720786	1.000000	0.71417	0.870000	0.34147	0.998000	0.95712	7.487000	0.81328	2.681000	0.91329	0.655000	0.94253	TCG		0.612	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		T	81050780	C	T	81050780	3	4	61	1	0	0	0	0	1	0	0	0	17735	893	31	1	627	1	ZMIZ1	10	81050780	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1265267	81050780	54483967	6838	14823										
C10orf58	84293	broad.mit.edu	37	chr10	82191769	82191769	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgagcaccgagaaaaaGaatttggagacaaagtaaac	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:82191769G>T	ENST00000372181.1	+	5	1074	c.604G>T	c.(604-606)Gaa>Taa	p.E202*	FAM213A_ENST00000372188.1_Nonsense_Mutation_p.E202*|FAM213A_ENST00000372185.1_Nonsense_Mutation_p.E191*|RP11-137H2.6_ENST00000606162.1_lincRNA|FAM213A_ENST00000372187.5_Nonsense_Mutation_p.E202*	NM_001243778.1|NM_001243782.1	NP_001230707.1|NP_001230711.1	Q9BRX8	F213A_HUMAN	family with sequence similarity 213, member A	202					oxidation-reduction process (GO:0055114)|regulation of osteoclast differentiation (GO:0045670)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)	p.E202*(1)									CCGAGAAAAAGAATTTGGAGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											94	93	94					10																	82191769		2203	4300	6503	82181749	SO:0001587	stop_gained	84293			AF086462	CCDS7368.1, CCDS58089.1	10q23.1	2011-12-08	2011-12-08	2011-12-08	ENSG00000122378	ENSG00000122378			28651	protein-coding gene	gene with protein product	"peroxiredoxin-like 2 activated in M-CSF stimulated monocytes"		"chromosome 10 open reading frame 58"	C10orf58		11483580, 19951071	Standard	NM_032333		Approved	MGC4248, PAMM	uc001kce.4	Q9BRX8	OTTHUMG00000018614	ENST00000372181.1:c.604G>T	10.37:g.82191769G>T	ENSP00000361254:p.Glu202*		82181749	B2RD81|Q6UW08|Q8N2K3|Q8NBK9|Q96JR0	Nonsense_Mutation	SNP	ENST00000372181.1	37	CCDS7368.1	.	.	.	.	.	.	.	.	.	.	G	39	7.903141	0.98551	.	.	ENSG00000122378	ENST00000372188;ENST00000372187;ENST00000372185;ENST00000372181	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-19.0916	16.8213	0.85747	0.0:0.0:1.0:0.0	.	.	.	.	X	202;202;191;202	.	ENSP00000361254:E202X	E	+	1	0	C10orf58	82181749	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.455000	0.73497	2.561000	0.86390	0.650000	0.86243	GAA		0.418	FAM213A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049077.2			T	82191769	G	T	82191769	4	4	61	1	0	0	0	0	0	1	0	0	1614	943	33	2	622	2	C10orf58	10	82191769	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1140989	82191769	53342978	6839	14824										
SH2D4B	387694	broad.mit.edu	37	chr10	82363342	82363342	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctctttccagtgcgccgGtccaaggcggctgatgagga	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:82363342G>A	ENST00000470604.2	+	5	648	c.648G>A	c.(646-648)cgG>cgA	p.R216R	SH2D4B_ENST00000313455.4_Silent_p.R168R|SH2D4B_ENST00000339284.2_Silent_p.R217R			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	216	Glu-rich.							p.R217R(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			CAGTGCGCCGGTCCAAGGCGG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	10											13	14	14					10																	82363342		2167	4257	6424	82353322	SO:0001819	synonymous_variant	387694				CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"SH2 domain containing"	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.648G>A	10.37:g.82363342G>A			82353322	Q5SQS5|Q6ZVW9|Q6ZVZ3	Silent	SNP	ENST00000470604.2	37																																																																																					0.647	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984		A	82363342	G	A	82363342	2	1	61	1	0	0	0	0	0	0	0	1	14273	1248	44	3		3	SH2D4B	10	82363342	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171573	82363342	53171405	6840	14825										
SH2D4B	387694	broad.mit.edu	37	chr10	82403754	82403754	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttctgttttaggaggaAattatcactgtttcaggagg	10	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:82403754A>C	ENST00000470604.2	+	8	1209	c.1209A>C	c.(1207-1209)gaA>gaC	p.E403D	SH2D4B_ENST00000313455.4_Missense_Mutation_p.N283H|SH2D4B_ENST00000339284.2_Missense_Mutation_p.N331H|SH2D4B_ENST00000372150.3_3'UTR			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	403	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.							p.N331H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			TTTAGGAGGAAATTATCACTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											78	78	78					10																	82403754		2203	4300	6503	82393734	SO:0001583	missense	387694				CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"SH2 domain containing"	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.1209A>C	10.37:g.82403754A>C	ENSP00000417953:p.Glu403Asp		82393734	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.31|19.31	3.803534|3.803534	0.70682|0.70682	.|.	.|.	ENSG00000178217|ENSG00000178217	ENST00000470604|ENST00000339284;ENST00000313455	T|T;T	0.38240|0.13420	1.15|2.65;2.59	5.05|5.05	1.16|1.16	0.20824|0.20824	SH2 motif (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.14485|0.14485	0.0350|0.0350	.|.	.|.	.|.	0.22096|0.22096	N|N	0.999368|0.999368	D|P;P	0.76494|0.47191	0.999|0.891;0.514	D|B;B	0.77004|0.44224	0.989|0.444;0.351	T|T	0.12426|0.12426	-1.0548|-1.0548	9|8	0.51188|0.72032	T|D	0.08|0.01	-10.9231|-10.9231	8.3932|8.3932	0.32542|0.32542	0.7543:0.0:0.2457:0.0|0.7543:0.0:0.2457:0.0	.|.	403|283;331	Q5SQS7|Q5SQS7-3;Q5SQS7-2	SH24B_HUMAN|.;.	D|H	403|331;283	ENSP00000417953:E403D|ENSP00000345295:N331H;ENSP00000314242:N283H	ENSP00000417953:E403D|ENSP00000314242:N283H	E|N	+|+	3|1	2|0	SH2D4B|SH2D4B	82393734|82393734	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.997000|0.997000	0.91878|0.91878	2.676000|2.676000	0.46883|0.46883	0.008000|0.008000	0.14787|0.14787	0.482000|0.482000	0.46254|0.46254	GAA|AAT		0.393	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984		C	82403754	A	C	82403754	3	2	61	1	0	0	0	0	1	0	0	0	14273	14	1	4	1061	4	SH2D4B	10	82403754	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40412	82403754	53130993	6841	14826										
NRG3	10718	broad.mit.edu	37	chr10	83635919	83635919	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagcaccagccccaaatttCgtaagtaaacactgtgtctc	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:83635919C>T	ENST00000404547.1	+	1	823	c.823C>T	c.(823-825)Cat>Tat	p.H275Y	NRG3_ENST00000404576.2_5'Flank|NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank|NRG3_ENST00000372141.2_Splice_Site_p.H275Y			P56975	NRG3_HUMAN	neuregulin 3	275	Ser/Thr-rich.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.H275Y(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CCCCAAATTTCGTAAGTAAAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	10											23	16	19					10																	83635919		2202	4298	6500	83625899	SO:0001630	splice_region_variant	10718			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.823+1C>T	10.37:g.83635919C>T			83625899	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	C	5.213	0.224776	0.09916	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.35973	1.28;1.28	4.14	4.14	0.48551	.	0.129391	0.34314	N	0.004070	T	0.21387	0.0515	N	0.14661	0.345	0.80722	D	1	D;D	0.65815	0.995;0.992	P;B	0.45071	0.468;0.41	T	0.06285	-1.0835	10	0.02654	T	1	-4.5388	14.3436	0.66643	0.0:1.0:0.0:0.0	.	275;275	B9EGV5;P56975-4	.;.	Y	275	ENSP00000361214:H275Y;ENSP00000384796:H275Y	ENSP00000361214:H275Y	H	+	1	0	NRG3	83625899	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.669000	0.61575	2.318000	0.78349	0.650000	0.86243	CAT		0.517	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	Missense_Mutation	T	83635919	C	T	83635919	5	4	61	1	0	0	0	0	0	0	1	0	10680	898	31	1	825	1	NRG3	10	83635919	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1232165	83635919	51898828	6842	14827										
NRG3	10718	broad.mit.edu	37	chr10	84745121	84745121	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgagtattccagtcagCgattgtcttatagcagaaca	9	7	2	2	rs148300013		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:84745121C>A	ENST00000404547.1	+	10	1923	c.1923C>A	c.(1921-1923)agC>agA	p.S641R	NRG3_ENST00000404576.2_Missense_Mutation_p.S421R|NRG3_ENST00000545131.1_Missense_Mutation_p.S267R|NRG3_ENST00000372142.2_Missense_Mutation_p.S420R|NRG3_ENST00000556918.1_Missense_Mutation_p.S447R|NRG3_ENST00000537893.1_Missense_Mutation_p.S267R|NRG3_ENST00000372141.2_Missense_Mutation_p.S617R			P56975	NRG3_HUMAN	neuregulin 3	641					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.S617R(1)|p.S420R(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TTCCAGTCAGCGATTGTCTTA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	10											82	80	81					10																	84745121		2203	4300	6503	84735101	SO:0001583	missense	10718			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1923C>A	10.37:g.84745121C>A	ENSP00000384796:p.Ser641Arg		84735101	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.655586	0.47467	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.56611	1.08;1.11;1.12;0.45;1.02;0.56;0.56	5.96	2.98	0.34508	.	0.209202	0.48286	D	0.000184	T	0.52821	0.1758	L	0.43152	1.355	0.35648	D	0.811556	P;P;P;D	0.53312	0.667;0.949;0.773;0.959	P;P;B;P	0.52909	0.473;0.713;0.36;0.648	T	0.61983	-0.6950	10	0.87932	D	0	-27.4467	8.8117	0.34971	0.0:0.7339:0.0:0.2661	.	616;641;420;617	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	R	617;641;616;420;421;447;267;267	ENSP00000361214:S617R;ENSP00000384796:S641R;ENSP00000361215:S420R;ENSP00000385804:S421R;ENSP00000451376:S447R;ENSP00000441201:S267R;ENSP00000440377:S267R	ENSP00000361214:S617R	S	+	3	2	NRG3	84735101	0.996000	0.38824	1.000000	0.80357	0.999000	0.98932	0.247000	0.18179	0.340000	0.23745	0.655000	0.94253	AGC		0.433	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		A	84745121	C	A	84745121	3	1	61	1	0	0	0	0	1	0	0	0	10680	767	27	2	2129	2	NRG3	10	84745121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1109202	84745121	50789626	6843	14828										
GHITM	27069	broad.mit.edu	37	chr10	85903852	85903852	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatgagattggagctattGaaaaggctgtgtaagtaaat	11	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:85903852G>T	ENST00000372134.3	+	4	524	c.331G>T	c.(331-333)Gaa>Taa	p.E111*		NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	111					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.E111*(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						TGGAGCTATTGAAAAGGCTGT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											205	205	205					10																	85903852		1955	4128	6083	85893832	SO:0001587	stop_gained	27069			AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 5"					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.331G>T	10.37:g.85903852G>T	ENSP00000361207:p.Glu111*		85893832	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Nonsense_Mutation	SNP	ENST00000372134.3	37	CCDS41542.1	.	.	.	.	.	.	.	.	.	.	G	39	7.783360	0.98486	.	.	ENSG00000165678	ENST00000372134;ENST00000538477;ENST00000436406;ENST00000339736	.	.	.	6.16	6.16	0.99307	.	0.085209	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-23.1364	19.6313	0.95704	0.0:0.0:1.0:0.0	.	.	.	.	X	111;98;111;91	.	ENSP00000342214:E91X	E	+	1	0	GHITM	85893832	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.306000	0.96204	2.937000	0.99478	0.650000	0.86243	GAA		0.388	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394		T	85903852	G	T	85903852	4	4	61	1	0	0	0	0	0	1	0	0	6390	1291	45	2	341	2	GHITM	10	85903852	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1158731	85903852	49630895	6844	14829										
LRIT2	340745	broad.mit.edu	37	chr10	85984209	85984209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggtgatattggcactggGggttgagatctgtggcttca	16	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:85984209G>A	ENST00000372113.4	-	2	777	c.772C>T	c.(772-774)Ccc>Tcc	p.P258S	LRIT2_ENST00000538192.1_Missense_Mutation_p.P258S	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	258	Ig-like.					integral component of membrane (GO:0016021)		p.P258S(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						TTGGCACTGGGGGTTGAGATC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	10											112	102	106					10																	85984209		2203	4300	6503	85974189	SO:0001583	missense	340745				CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"Immunoglobulin superfamily / I-set domain containing"	23443	protein-coding gene	gene with protein product			"leucine rich repeat containing 22"	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.772C>T	10.37:g.85984209G>A	ENSP00000361185:p.Pro258Ser		85974189	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959852	0.34565	.	.	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.66995	-0.24;-0.24	5.76	3.85	0.44370	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.212817	0.49305	N	0.000143	T	0.54919	0.1888	L	0.41961	1.31	0.36871	D	0.888911	P;P	0.37083	0.581;0.521	B;B	0.39258	0.295;0.169	T	0.53114	-0.8484	10	0.08599	T	0.76	.	10.5465	0.45062	0.1673:0.0:0.8327:0.0	.	258;258	B7ZME6;A6NDA9	.;LRIT2_HUMAN	S	258	ENSP00000361185:P258S;ENSP00000438264:P258S	ENSP00000361185:P258S	P	-	1	0	LRIT2	85974189	0.983000	0.35010	0.991000	0.47740	0.999000	0.98932	2.541000	0.45735	0.724000	0.32296	0.655000	0.94253	CCC		0.542	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		A	85984209	G	A	85984209	3	1	61	1	0	0	0	0	1	0	0	0	8977	1232	43	3	888	3	LRIT2	10	85984209	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80357	85984209	49550538	6845	14830										
LRIT1	26103	broad.mit.edu	37	chr10	85992306	85992306	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccgcccatcagagagctCtcccagggcatccatctgga	10	16	3	1	rs144402289		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:85992306C>A	ENST00000372105.3	-	4	1270	c.1249G>T	c.(1249-1251)Gag>Tag	p.E417*		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	417						integral component of endoplasmic reticulum membrane (GO:0030176)		p.E417*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						TCAGAGAGCTCTCCCAGGGCA	0.617																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											82	72	75					10																	85992306		2203	4300	6503	85982286	SO:0001587	stop_gained	26103			AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1249G>T	10.37:g.85992306C>A	ENSP00000361177:p.Glu417*		85982286	Q0QD41|Q9Y4N7	Nonsense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.528200	0.44969	.	.	ENSG00000148602	ENST00000372105	.	.	.	5.23	4.27	0.50696	.	0.619591	0.16854	N	0.196819	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	13.5716	0.61849	0.0:0.7535:0.2465:0.0	.	.	.	.	X	417	.	ENSP00000361177:E417X	E	-	1	0	LRIT1	85982286	0.757000	0.28394	0.054000	0.19295	0.133000	0.20885	2.380000	0.44327	2.435000	0.82474	0.655000	0.94253	GAG		0.617	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		A	85992306	C	A	85992306	4	1	61	1	0	0	0	0	0	1	0	0	8976	922	32	2	626	2	LRIT1	10	85992306	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8097	85992306	49542441	6846	14831										
FAM190B	54462	broad.mit.edu	37	chr10	86131788	86131788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctactgaaatctagccGatctccattttctgggacta	6	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:86131788G>A	ENST00000224756.8	+	2	1165	c.980G>A	c.(979-981)cGa>cAa	p.R327Q	CCSER2_ENST00000359979.4_Missense_Mutation_p.R327Q|CCSER2_ENST00000372088.2_Missense_Mutation_p.R327Q	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	327					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)		p.R327Q(1)									AAATCTAGCCGATCTCCATTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											107	107	107					10																	86131788		2203	4300	6503	86121768	SO:0001583	missense	54462				CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.980G>A	10.37:g.86131788G>A	ENSP00000224756:p.Arg327Gln		86121768	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	37	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113716	0.56398	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.50548	0.74;2.09;2.08	5.73	3.88	0.44766	.	0.203885	0.31721	N	0.007175	T	0.57242	0.2040	L	0.52364	1.645	0.80722	D	1	P;P;D	0.89917	0.944;0.944;1.0	B;B;D	0.83275	0.372;0.252;0.996	T	0.51364	-0.8715	10	0.16896	T	0.51	-4.8321	10.4304	0.44405	0.1587:0.0:0.8413:0.0	.	327;327;327	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	Q	327	ENSP00000353068:R327Q;ENSP00000224756:R327Q;ENSP00000361160:R327Q	ENSP00000224756:R327Q	R	+	2	0	FAM190B	86121768	0.991000	0.36638	0.998000	0.56505	0.995000	0.86356	2.452000	0.44961	0.778000	0.33520	0.655000	0.94253	CGA		0.423	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		A	86131788	G	A	86131788	3	1	61	1	0	0	0	0	1	0	0	0	5538	1058	37	1	982	1	FAM190B	10	86131788	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139482	86131788	49402959	6847	14832										
GRID1	2894	broad.mit.edu	37	chr10	87379701	87379701	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctgctgatgctgttgccGatgacagtcaccgagcagtc	12	11	1	2	rs112935027		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:87379701G>A	ENST00000327946.7	-	14	2368	c.2283C>T	c.(2281-2283)atC>atT	p.I761I	GRID1_ENST00000536331.1_Silent_p.I332I	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	761					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.I761I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						TGCTGTTGCCGATGACAGTCA	0.582										Multiple Myeloma(13;0.14)																																						1	Substitution - coding silent(1)	large_intestine(1)	10											134	98	110					10																	87379701		2203	4300	6503	87369681	SO:0001819	synonymous_variant	2894			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2283C>T	10.37:g.87379701G>A			87369681	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																				0.582	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		A	87379701	G	A	87379701	2	1	61	1	0	0	0	0	0	0	0	1	6792	1048	37	1		1	GRID1	10	87379701	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1247913	87379701	48155046	6848	14833										
GRID1	2894	broad.mit.edu	37	chr10	87482865	87482865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagctgcccatcacgatgCgcatggccatggagttcacg	11	14	2	0	rs191266908	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:87482865C>T	ENST00000327946.7	-	12	1977	c.1892G>A	c.(1891-1893)cGc>cAc	p.R631H	GRID1_ENST00000536331.1_Missense_Mutation_p.R202H	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	631					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R631H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CATCACGATGCGCATGGCCAT	0.592										Multiple Myeloma(13;0.14)			C|||	3	0.000599042	0	0.0014	5008	,	,		19208	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	10											121	88	99					10																	87482865		2203	4300	6503	87472845	SO:0001583	missense	2894			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1892G>A	10.37:g.87482865C>T	ENSP00000330148:p.Arg631His		87472845	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	35	5.563782	0.96527	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.74526	-0.85;-0.85	5.95	5.95	0.96441	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.047867	0.85682	D	0.000000	D	0.91257	0.7244	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93199	0.6590	10	0.87932	D	0	.	19.3527	0.94395	0.0:1.0:0.0:0.0	.	631	Q9ULK0	GRID1_HUMAN	H	631;202	ENSP00000330148:R631H;ENSP00000444455:R202H	ENSP00000330148:R631H	R	-	2	0	GRID1	87472845	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.743000	0.85020	2.821000	0.97095	0.561000	0.74099	CGC		0.592	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		T	87482865	C	T	87482865	3	4	61	1	0	0	0	0	1	0	0	0	6792	768	27	1	1157	1	GRID1	10	87482865	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103164	87482865	48051882	6849	14834										
WAPAL	23063	broad.mit.edu	37	chr10	88227215	88227215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaagatccatgttcaaacGatctctactcagtatataca	4	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88227215G>A	ENST00000298767.5	-	9	2663	c.2191C>T	c.(2191-2193)Cgt>Tgt	p.R731C	WAPAL_ENST00000263070.7_5'UTR|WAPAL_ENST00000372075.1_5'UTR	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	731	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)		p.R731C(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						ATGTTCAAACGATCTCTACTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											80	70	73					10																	88227215		2203	4300	6503	88217195	SO:0001583	missense	23063			AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2191C>T	10.37:g.88227215G>A	ENSP00000298767:p.Arg731Cys		88217195	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	G	34	5.315377	0.95655	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.49720	0.77	5.99	5.99	0.97316	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	0.92;1.0;0.92;0.917	T	0.73225	-0.4050	10	0.72032	D	0.01	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	725;769;731;768	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	C	816;731;816	ENSP00000298767:R731C	ENSP00000298767:R731C	R	-	1	0	WAPAL	88217195	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	CGT		0.383	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		A	88227215	G	A	88227215	3	1	61	1	0	0	0	0	1	0	0	0	17288	1058	37	1	1425	1	WAPAL	10	88227215	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	744350	88227215	47307532	6850	14835										
WAPAL	23063	broad.mit.edu	37	chr10	88260098	88260098	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttgggaggatttcgttTtattggccctacagtacgtc	10	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88260098T>G	ENST00000298767.5	-	3	1374	c.902A>C	c.(901-903)aAa>aCa	p.K301T		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	301	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)		p.K301T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						GGATTTCGTTTTATTGGCCCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											139	128	132					10																	88260098		2203	4300	6503	88250078	SO:0001583	missense	23063			AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.902A>C	10.37:g.88260098T>G	ENSP00000298767:p.Lys301Thr		88250078	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.714231	0.68730	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.29397	1.57	5.77	5.77	0.91146	.	0.062141	0.64402	D	0.000007	T	0.51669	0.1688	L	0.58101	1.795	0.80722	D	1	D;D;D	0.76494	0.997;0.997;0.999	P;P;D	0.69479	0.888;0.888;0.964	T	0.50482	-0.8823	10	0.52906	T	0.07	.	16.0902	0.81086	0.0:0.0:0.0:1.0	.	301;301;344	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	T	386;301;386	ENSP00000298767:K301T	ENSP00000298767:K301T	K	-	2	0	WAPAL	88250078	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.019000	0.76412	2.194000	0.70268	0.528000	0.53228	AAA		0.423	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88260098	T	G	88260098	3	3	61	1	0	0	0	0	1	0	0	0	17288	1841	64	4	2738	4	WAPAL	10	88260098	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32883	88260098	47274649	6851	14836										
OPN4	94233	broad.mit.edu	37	chr10	88419161	88419161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctgcttcgtgttcttcCtccctctgcttatcatcatc	5	15	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88419161C>T	ENST00000241891.5	+	5	903	c.736C>T	c.(736-738)Ctc>Ttc	p.L246F	OPN4_ENST00000372071.2_Missense_Mutation_p.L257F	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	246					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)	p.L257F(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CGTGTTCTTCCTCCCTCTGCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											260	190	214					10																	88419161		2203	4300	6503	88409141	SO:0001583	missense	94233			AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.736C>T	10.37:g.88419161C>T	ENSP00000241891:p.Leu246Phe		88409141	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.693067	0.68271	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.42900	0.96;0.96;0.96	5.15	1.98	0.26296	GPCR, rhodopsin-like superfamily (1);	0.156406	0.39083	N	0.001476	T	0.47948	0.1473	L	0.45744	1.44	0.40839	D	0.983653	D;D;D	0.67145	0.996;0.992;0.99	D;P;P	0.65684	0.937;0.889;0.843	T	0.46442	-0.9191	10	0.66056	D	0.02	.	4.6123	0.12408	0.3818:0.4202:0.0:0.198	.	257;246;257	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	F	257;246;257	ENSP00000361141:L257F;ENSP00000241891:L246F;ENSP00000393132:L257F	ENSP00000241891:L246F	L	+	1	0	OPN4	88409141	1.000000	0.71417	0.910000	0.35882	0.941000	0.58515	2.970000	0.49240	0.570000	0.29347	0.655000	0.94253	CTC		0.592	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		T	88419161	C	T	88419161	3	4	61	1	0	0	0	0	1	0	0	0	10913	681	24	3	791	3	OPN4	10	88419161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159063	88419161	47115586	6852	14837										
AGAP11	119385	broad.mit.edu	37	chr10	88768132	88768132	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttccaccgtgcacattacGaagaaaagaaatggaggtgg	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88768132G>A	ENST00000444431.1	+	0	2732				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										TGCACATTACGAAGAAAAGAA	0.448																																																0			10											119	112	114					10																	88768132		2019	4226	6245	88758112			119385					10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88768132G>A			88758112	B9EIP7|D3DWE4	Silent	SNP	ENST00000444431.1	37																																																																																					0.448	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		A	88768132	G	A	88768132	1	1	61	0	1	0	0	0	0	0	0	0	367	1045	37	1		1	AGAP11	10	88768132	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	348971	88768132	46766615	6853	14838										
AGAP11	119385	broad.mit.edu	37	chr10	88768686	88768686	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgactccatatgcttcaGccccagtatctccagcacca	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88768686G>T	ENST00000444431.1	+	0	3286				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										ATATGCTTCAGCCCCAGTATC	0.507																																																0			10											71	82	78					10																	88768686		2203	4300	6503	88758666			119385					10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88768686G>T			88758666	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	37																																																																																					0.507	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		T	88768686	G	T	88768686	1	4	61	0	1	0	0	0	0	0	0	0	367	971	34	2		2	AGAP11	10	88768686	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	554	88768686	46766061	6854	14839										
AGAP11	119385	broad.mit.edu	37	chr10	88768826	88768826	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactgctgaggaagaagaaGaaaagtttatgattgtgtcc	12	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88768826G>T	ENST00000444431.1	+	0	3426				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										GGAAGAAGAAGAAAAGTTTAT	0.493																																																0			10											78	88	85					10																	88768826		2202	4299	6501	88758806			119385					10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88768826G>T			88758806	B9EIP7|D3DWE4	Nonsense_Mutation	SNP	ENST00000444431.1	37																																																																																					0.493	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		T	88768826	G	T	88768826	1	4	61	0	1	0	0	0	0	0	0	0	367	943	33	2		2	AGAP11	10	88768826	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140	88768826	46765921	6855	14840										
AGAP11	119385	broad.mit.edu	37	chr10	88768972	88768972	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtaaaagcaagtcccaGctgaccagccagagtgaggc	12	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88768972G>T	ENST00000444431.1	+	0	3572				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										GCAAGTCCCAGCTGACCAGCC	0.592																																																0			10											96	104	101					10																	88768972		2203	4297	6500	88758952			119385					10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88768972G>T			88758952	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	37																																																																																					0.592	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		T	88768972	G	T	88768972	1	4	61	0	1	0	0	0	0	0	0	0	367	962	34	2		2	AGAP11	10	88768972	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146	88768972	46765775	6856	14841										
FAM35A	54537	broad.mit.edu	37	chr10	88911886	88911886	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttttagctcaaaagaaaGataaaaggcggagtcctgta	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:88911886G>T	ENST00000298784.1	+	3	889	c.775G>T	c.(775-777)Gat>Tat	p.D259Y	FAM35A_ENST00000298786.4_Missense_Mutation_p.D259Y|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	259								p.D259Y(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						TCAAAAGAAAGATAAAAGGCG	0.388																																					Ovarian(175;703 2004 25460 32514 43441)											1	Substitution - Missense(1)	large_intestine(1)	10											28	29	28					10																	88911886		2196	4296	6492	88901866	SO:0001583	missense	54537			BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.775G>T	10.37:g.88911886G>T	ENSP00000298784:p.Asp259Tyr		88901866	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	g	0.890	-0.725883	0.03158	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.23754	1.89;1.89;1.89	3.79	-3.13	0.05266	.	1.863010	0.02989	N	0.146670	T	0.11879	0.0289	N	0.16656	0.425	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21621	-1.0240	10	0.02654	T	1	2.7682	4.7606	0.13106	0.0862:0.0927:0.4231:0.398	.	259	Q86V20	FA35A_HUMAN	Y	259	ENSP00000298786:D259Y;ENSP00000298784:D259Y;ENSP00000351064:D259Y	ENSP00000298784:D259Y	D	+	1	0	FAM35A	88901866	0.000000	0.05858	0.000000	0.03702	0.672000	0.39443	-0.616000	0.05591	-0.317000	0.08677	0.537000	0.68136	GAT		0.388	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		T	88911886	G	T	88911886	3	4	61	1	0	0	0	0	1	0	0	0	5572	942	33	2	777	2	FAM35A	10	88911886	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142914	88911886	46622861	6857	14842										
MINPP1	9562	broad.mit.edu	37	chr10	89312018	89312018	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttatgcctcgaacctgaTatttgtgctttaccactgtg	7	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89312018T>G	ENST00000371996.4	+	5	1288	c.1247T>G	c.(1246-1248)aTa>aGa	p.I416R	MINPP1_ENST00000371994.4_3'UTR|MINPP1_ENST00000472891.1_3'UTR|MINPP1_ENST00000536010.1_Missense_Mutation_p.I215R	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	416					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)	p.I416R(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		TCGAACCTGATATTTGTGCTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											139	132	134					10																	89312018		2203	4300	6503	89301998	SO:0001583	missense	9562			AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"multiple inositol polyphosphate histidine phosphatase, 1"			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1247T>G	10.37:g.89312018T>G	ENSP00000361064:p.Ile416Arg		89301998	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	37	CCDS7384.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743691	0.69418	.	.	ENSG00000107789	ENST00000371996;ENST00000546140;ENST00000536010	T;T	0.32272	1.46;1.46	6.08	6.08	0.98989	.	0.283491	0.39020	N	0.001499	T	0.35885	0.0947	L	0.58101	1.795	0.46149	D	0.998896	P	0.51057	0.941	P	0.49047	0.599	T	0.12243	-1.0555	10	0.30854	T	0.27	-6.8826	8.8892	0.35423	0.0:0.1413:0.0:0.8587	.	416	Q9UNW1	MINP1_HUMAN	R	416;275;215	ENSP00000361064:I416R;ENSP00000437823:I215R	ENSP00000361064:I416R	I	+	2	0	MINPP1	89301998	0.923000	0.31300	0.709000	0.30452	0.912000	0.54170	3.889000	0.56212	2.333000	0.79357	0.482000	0.46254	ATA		0.388	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			G	89312018	T	G	89312018	3	3	61	1	0	0	0	0	1	0	0	0	9618	1406	49	4	1303	4	MINPP1	10	89312018	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	400132	89312018	46222729	6858	14843										
PAPSS2	9060	broad.mit.edu	37	chr10	89472834	89472834	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatctgttctgaacaggtCtctctggtgctggaaaaaca	9	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89472834C>A	ENST00000361175.4	+	3	517	c.148C>A	c.(148-150)Ctc>Atc	p.L50I	PAPSS2_ENST00000482258.1_3'UTR|PAPSS2_ENST00000427144.2_Missense_Mutation_p.L54I|PAPSS2_ENST00000456849.1_Missense_Mutation_p.L50I	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	50					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)	p.L50I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		CTGAACAGGTCTCTCTGGTGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											130	133	132					10																	89472834		2203	4300	6503	89462814	SO:0001583	missense	9060			AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.148C>A	10.37:g.89472834C>A	ENSP00000354436:p.Leu50Ile		89462814	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341611	0.81911	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.78816	-1.21;-1.21;-1.21	5.87	5.87	0.94306	Adenylylsulphate kinase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.92818	0.7716	H	0.96970	3.915	0.80722	D	1	D;D	0.71674	0.99;0.998	D;D	0.83275	0.994;0.996	D	0.94436	0.7654	10	0.87932	D	0	-24.579	20.2245	0.98337	0.0:1.0:0.0:0.0	.	50;50	O95340;O95340-2	PAPS2_HUMAN;.	I	50;50;54;49	ENSP00000354436:L50I;ENSP00000406157:L50I;ENSP00000397123:L54I	ENSP00000354436:L50I	L	+	1	0	PAPSS2	89462814	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.566000	0.67372	2.770000	0.95276	0.650000	0.86243	CTC		0.408	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			A	89472834	C	A	89472834	3	1	61	1	0	0	0	0	1	0	0	0	11466	913	32	2	158	2	PAPSS2	10	89472834	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	160816	89472834	46061913	6859	14844										
PAPSS2	9060	broad.mit.edu	37	chr10	89501105	89501105	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacctctggagctcaaacaGaaatgtaaagaaatgaatgc	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89501105G>T	ENST00000361175.4	+	9	1554	c.1185G>T	c.(1183-1185)caG>caT	p.Q395H	PAPSS2_ENST00000427144.2_Missense_Mutation_p.Q399H|PAPSS2_ENST00000456849.1_Missense_Mutation_p.Q400H	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	395					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)	p.Q395H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		AGCTCAAACAGAAATGTAAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											132	122	126					10																	89501105		2203	4300	6503	89491085	SO:0001583	missense	9060			AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.1185G>T	10.37:g.89501105G>T	ENSP00000354436:p.Gln395His		89491085	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745506	0.69418	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.33216	1.42;1.42;1.42	5.15	5.15	0.70609	Sulphate adenylyltransferase (2);	0.051139	0.85682	D	0.000000	T	0.49898	0.1584	M	0.75777	2.31	0.58432	D	0.999991	B;P	0.36616	0.001;0.561	B;P	0.48063	0.031;0.565	T	0.51631	-0.8681	10	0.62326	D	0.03	-18.5656	18.8112	0.92058	0.0:0.0:1.0:0.0	.	395;400	O95340;O95340-2	PAPS2_HUMAN;.	H	395;400;399;399	ENSP00000354436:Q395H;ENSP00000406157:Q400H;ENSP00000397123:Q399H	ENSP00000354436:Q395H	Q	+	3	2	PAPSS2	89491085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.973000	0.49264	2.676000	0.91093	0.591000	0.81541	CAG		0.438	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89501105	G	T	89501105	3	4	61	1	0	0	0	0	1	0	0	0	11466	933	33	2	1238	2	PAPSS2	10	89501105	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28271	89501105	46033642	6860	14845										
ATAD1	84896	broad.mit.edu	37	chr10	89514504	89514504	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcctttgatttcttcatCttttcaattgcccgatgcag	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89514504C>A	ENST00000308448.7	-	10	1404	c.1026G>T	c.(1024-1026)aaG>aaT	p.K342N	ATAD1_ENST00000400215.3_Missense_Mutation_p.K254N|ATAD1_ENST00000328142.3_Missense_Mutation_p.K342N	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	342					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.K342N(1)		kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		ATTTCTTCATCTTTTCAATTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	86	90					10																	89514504		2203	4300	6503	89504484	SO:0001583	missense	84896			AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.1026G>T	10.37:g.89514504C>A	ENSP00000339017:p.Lys342Asn		89504484	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	37	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273423	0.40194	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215	D;D;D	0.99060	-5.38;-5.38;-5.38	5.36	3.52	0.40303	.	0.000000	0.85682	D	0.000000	D	0.97517	0.9187	M	0.73598	2.24	0.80722	D	1	B;B	0.26876	0.162;0.162	B;B	0.24155	0.051;0.051	D	0.95554	0.8623	10	0.34782	T	0.22	-17.9175	8.4807	0.33040	0.0:0.7053:0.0:0.2947	.	254;342	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	N	342;342;254	ENSP00000339017:K342N;ENSP00000339016:K342N;ENSP00000412968:K254N	ENSP00000339017:K342N	K	-	3	2	ATAD1	89504484	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.838000	0.27572	0.754000	0.32968	0.563000	0.77884	AAG		0.353	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		A	89514504	C	A	89514504	3	1	61	1	0	0	0	0	1	0	0	0	1071	912	32	2	63	2	ATAD1	10	89514504	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13399	89514504	46020243	6861	14846										
ATAD1	84896	broad.mit.edu	37	chr10	89550136	89550136	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataggtaagatgactgtgtCtttcagatccgtaatgacat	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89550136C>A	ENST00000308448.7	-	4	691	c.313G>T	c.(313-315)Gac>Tac	p.D105Y	ATAD1_ENST00000400215.3_Missense_Mutation_p.D47Y|ATAD1_ENST00000495903.1_5'UTR|ATAD1_ENST00000328142.3_Missense_Mutation_p.D105Y|ATAD1_ENST00000541004.1_Missense_Mutation_p.D105Y	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	105					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.D105Y(1)		kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		ATGACTGTGTCTTTCAGATCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											121	114	117					10																	89550136		2203	4300	6503	89540116	SO:0001583	missense	84896			AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.313G>T	10.37:g.89550136C>A	ENSP00000339017:p.Asp105Tyr		89540116	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	37	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354320	0.82243	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215;ENST00000541004	D;D;D;D	0.96802	-3.47;-3.47;-4.13;-3.77	5.4	4.5	0.54988	.	0.142073	0.64402	D	0.000005	D	0.97439	0.9162	M	0.82433	2.59	0.80722	D	1	P;P	0.45474	0.848;0.859	P;P	0.55161	0.77;0.77	D	0.97277	0.9915	9	.	.	.	-7.9456	14.1714	0.65512	0.0:0.9275:0.0:0.0725	.	47;105	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	Y	105;105;47;105	ENSP00000339017:D105Y;ENSP00000339016:D105Y;ENSP00000412968:D47Y;ENSP00000445500:D105Y	.	D	-	1	0	ATAD1	89540116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	1.404000	0.46819	0.563000	0.77884	GAC		0.373	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		A	89550136	C	A	89550136	3	1	61	1	0	0	0	0	1	0	0	0	1071	913	32	2	800	2	ATAD1	10	89550136	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35632	89550136	45984611	6862	14847										
PTEN	5728	broad.mit.edu	37	chr10	89692905	89692905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaaagctggaaagggacGaactggtgtaatgatatgtg	14	4	0	1	rs121913292|rs121909229		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89692905G>A	ENST00000371953.3	+	5	1746	c.389G>A	c.(388-390)cGa>cAa	p.R130Q		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	130	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3).|R -> L (in CWS1 and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9635567}.|R -> Q (in CWS1; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9915974}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R130Q(62)|p.0?(37)|p.R130fs*4(13)|p.R130L(12)|p.R130P(7)|p.?(5)|p.R55fs*1(5)|p.K128_R130del(3)|p.Y27fs*1(2)|p.A121_F145del(1)|p.R130fs*2(1)|p.T131fs*50(1)|p.F56fs*2(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGAAAGGGACGAACTGGTGTA	0.403	R130Q(JHUEM1_ENDOMETRIUM)|R130Q(MDAPCA2B_PROSTATE)|R130Q(MFE296_ENDOMETRIUM)|R130fs*4(AN3CA_ENDOMETRIUM)	31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	151	Substitution - Missense(81)|Whole gene deletion(37)|Deletion - Frameshift(23)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(1)	endometrium(77)|prostate(18)|central_nervous_system(16)|lung(7)|breast(7)|ovary(7)|skin(6)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|thyroid(2)|soft_tissue(2)|urinary_tract(1)	10	GRCh37	CM981670|CM991081	PTEN	M	rs121909229						139	129	133					10																	89692905		2203	4300	6503	89682885	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.389G>A	10.37:g.89692905G>A	ENSP00000361021:p.Arg130Gln		89682885	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	36	5.637233	0.96693	.	.	ENSG00000171862	ENST00000371953	D	0.98345	-4.88	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99378	0.9781	H	0.96889	3.9	0.80722	A	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98503	1.0615	8	.	.	.	-1.7685	18.7776	0.91918	0.0:0.0:1.0:0.0	.	130	P60484	PTEN_HUMAN	Q	130	ENSP00000361021:R130Q	.	R	+	2	0	PTEN	89682885	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.429000	0.97481	2.411000	0.81874	0.655000	0.94253	CGA		0.403	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89692905	G	A	89692905	3	1	61	1	0	0	0	0	1	0	0	0	12772	1058	37	1	407	1	PTEN	10	89692905	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142769	89692905	45841842	6863	14848										
PTEN	5728	broad.mit.edu	37	chr10	89711876	89711876	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttttctgtccaccaggGagtaactattcccagtcaga	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:89711876G>A	ENST00000371953.3	+	6	1851	c.494G>A	c.(493-495)gGa>gAa	p.G165E		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	165	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		G -> E (in CWS1). {ECO:0000269|PubMed:10234502}.|G -> R (in glioblastoma; severely reduced protein phosphatase activity; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9331071}.|G -> V (in CWS1).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.G165E(6)|p.R55fs*1(5)|p.?(4)|p.G165fs*9(3)|p.Y27fs*1(2)|p.G165_*404del(1)|p.K163_V166>NKGE(1)|p.G165V(1)|p.G165del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GTCCACCAGGGAGTAACTATT	0.368		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	61	Whole gene deletion(37)|Deletion - Frameshift(10)|Substitution - Missense(7)|Unknown(4)|Deletion - In frame(2)|Complex - compound substitution(1)	central_nervous_system(17)|prostate(16)|skin(8)|lung(5)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|thyroid(1)|large_intestine(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)|pancreas(1)	10	GRCh37	CM981671|CM993670	PTEN	M							107	111	109					10																	89711876		2203	4300	6503	89701856	SO:0001630	splice_region_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.493-1G>A	10.37:g.89711876G>A			89701856	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	30	5.058096	0.93846	.	.	ENSG00000171862	ENST00000371953	D	0.98747	-5.11	5.74	5.74	0.90152	Phosphatase tensin type (1);	0.049404	0.85682	D	0.000000	D	0.99417	0.9794	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98737	1.0715	9	.	.	.	-2.7522	19.9308	0.97118	0.0:0.0:1.0:0.0	.	165	P60484	PTEN_HUMAN	E	165	ENSP00000361021:G165E	.	G	+	2	0	PTEN	89701856	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.370000	0.97159	2.722000	0.93159	0.591000	0.81541	GGA		0.368	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Missense_Mutation	A	89711876	G	A	89711876	5	1	61	1	0	0	0	0	0	0	1	0	12772	1188	41	3	516	3	PTEN	10	89711876	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18971	89711876	45822871	6864	14849										
LIPJ	142910	broad.mit.edu	37	chr10	90365400	90365400	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctttcagcttttaaattCtactcatttgaaagcttatg	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90365400C>A	ENST00000371939.3	+	10	1120	c.806C>A	c.(805-807)tCt>tAt	p.S269Y		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	269					lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)	p.S269Y(1)		large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		CTTTTAAATTCTACTCATTTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											91	92	91					10																	90365400		2203	4300	6503	90355380	SO:0001583	missense	142910			BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"lipase-like, ab-hydrolase domain containing 1", "lipase, family member J"	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.806C>A	10.37:g.90365400C>A	ENSP00000361007:p.Ser269Tyr		90355380	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	37	CCDS31240.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746262	0.30955	.	.	ENSG00000204022	ENST00000371939;ENST00000531458	T;T	0.72725	-0.68;-0.68	3.69	2.74	0.32292	Alpha/beta hydrolase fold-1 (1);	0.508491	0.16724	N	0.202147	T	0.75324	0.3834	M	0.79693	2.465	0.09310	N	1	P	0.35628	0.513	B	0.43838	0.433	T	0.67933	-0.5542	10	0.56958	D	0.05	-12.348	10.1134	0.42576	0.2021:0.7979:0.0:0.0	.	269	Q5W064	LIPJ_HUMAN	Y	269;84	ENSP00000361007:S269Y;ENSP00000434211:S84Y	ENSP00000361007:S269Y	S	+	2	0	LIPJ	90355380	0.377000	0.25106	0.052000	0.19188	0.011000	0.07611	2.640000	0.46579	0.830000	0.34757	0.643000	0.83706	TCT		0.353	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377		A	90365400	C	A	90365400	3	1	61	1	0	0	0	0	1	0	0	0	8850	913	32	2	836	2	LIPJ	10	90365400	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	653524	90365400	45169347	6865	14850										
LIPJ	142910	broad.mit.edu	37	chr10	90366571	90366571	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacatttattataaaactatTtcttactacaatcatataga	1	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90366571T>G	ENST00000371939.3	+	11	1322	c.1008T>G	c.(1006-1008)atT>atG	p.I336M		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	336					lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)	p.I336M(1)		large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		ATAAAACTATTTCTTACTACA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											50	52	51					10																	90366571		2203	4299	6502	90356551	SO:0001583	missense	142910			BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"lipase-like, ab-hydrolase domain containing 1", "lipase, family member J"	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.1008T>G	10.37:g.90366571T>G	ENSP00000361007:p.Ile336Met		90356551	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	37	CCDS31240.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.666754	0.47677	.	.	ENSG00000204022	ENST00000371939;ENST00000531458	T;T	0.73469	-0.75;-0.75	5.42	3.0	0.34707	Alpha/beta hydrolase fold-1 (1);	0.000000	0.44097	D	0.000490	T	0.81578	0.4852	M	0.71296	2.17	0.24793	N	0.992747	P	0.49635	0.926	D	0.72338	0.977	T	0.70641	-0.4816	10	0.56958	D	0.05	-27.7535	5.2011	0.15264	0.0:0.1581:0.1522:0.6898	.	336	Q5W064	LIPJ_HUMAN	M	336;151	ENSP00000361007:I336M;ENSP00000434211:I151M	ENSP00000361007:I336M	I	+	3	3	LIPJ	90356551	0.943000	0.32029	0.142000	0.22268	0.649000	0.38597	0.864000	0.27926	0.330000	0.23485	0.460000	0.39030	ATT		0.308	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377		G	90366571	T	G	90366571	3	3	61	1	0	0	0	0	1	0	0	0	8850	1829	64	4	1042	4	LIPJ	10	90366571	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1171	90366571	45168176	6866	14851										
LIPF	8513	broad.mit.edu	37	chr10	90428417	90428417	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccttcattctggcagatgCtggttatgatgtgtggctgg	14	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90428417C>T	ENST00000238983.4	+	4	372	c.326C>T	c.(325-327)gCt>gTt	p.A109V	LIPF_ENST00000394375.3_Missense_Mutation_p.A119V|LIPF_ENST00000608620.1_Missense_Mutation_p.A76V|LIPF_ENST00000355843.2_Missense_Mutation_p.A86V	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	109					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)	p.A109V(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	CTGGCAGATGCTGGTTATGAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	10											91	83	86					10																	90428417		2203	4300	6503	90418397	SO:0001583	missense	8513			X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.326C>T	10.37:g.90428417C>T	ENSP00000238983:p.Ala109Val		90418397	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Missense_Mutation	SNP	ENST00000238983.4	37	CCDS7389.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632525	0.67015	.	.	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	T;T;T	0.72505	-0.66;-0.66;-0.66	4.71	4.71	0.59529	.	0.000000	0.44097	D	0.000490	D	0.85053	0.5609	M	0.93939	3.475	0.48975	D	0.999738	P;P;D;P;P	0.56746	0.922;0.917;0.977;0.922;0.865	P;B;B;P;B	0.54856	0.762;0.378;0.361;0.762;0.21	D	0.89504	0.3766	10	0.72032	D	0.01	-20.7781	16.5945	0.84792	0.0:1.0:0.0:0.0	.	76;119;119;86;109	Q5VXI8;F5H1P4;B7Z723;Q658L8;P07098	.;.;.;.;LIPG_HUMAN	V	119;109;76	ENSP00000377900:A119V;ENSP00000238983:A109V;ENSP00000348101:A76V	ENSP00000238983:A109V	A	+	2	0	LIPF	90418397	0.999000	0.42202	0.864000	0.33941	0.980000	0.70556	3.772000	0.55325	2.448000	0.82819	0.557000	0.71058	GCT		0.478	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			T	90428417	C	T	90428417	3	4	61	1	0	0	0	0	1	0	0	0	8846	797	28	3	336	3	LIPF	10	90428417	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61846	90428417	45106330	6867	14852										
LIPK	643414	broad.mit.edu	37	chr10	90490804	90490804	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagtaactggatttgcaaCctgcccaacaacagtttggc	9	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90490804C>T	ENST00000404190.1	+	3	288	c.288C>T	c.(286-288)aaC>aaT	p.N96N		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	96					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)	p.N96N(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		GGATTTGCAACCTGCCCAACA	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	10											76	77	77					10																	90490804		2046	4239	6285	90480784	SO:0001819	synonymous_variant	643414				CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"lipase-like, ab-hydrolase domain containing 2"	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.288C>T	10.37:g.90490804C>T			90480784	A7KIH8	Silent	SNP	ENST00000404190.1	37	CCDS44455.1																																																																																				0.448	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222		T	90490804	C	T	90490804	2	4	61	1	0	0	0	0	0	0	0	1	8851	506	18	3		3	LIPK	10	90490804	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62387	90490804	45043943	6868	14853										
STAMBPL1	57559	broad.mit.edu	37	chr10	90676446	90676446	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttttttagacacataatGaatttactattacccatgta	4	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90676446G>T	ENST00000371926.3	+	8	1871	c.913G>T	c.(913-915)Gaa>Taa	p.E305*	STAMBPL1_ENST00000371922.1_Nonsense_Mutation_p.E139*|STAMBPL1_ENST00000371927.3_Nonsense_Mutation_p.E305*|STAMBPL1_ENST00000371924.1_Nonsense_Mutation_p.E305*	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	305	MPN.					membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.E305*(1)		breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		GACACATAATGAATTTACTAT	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											121	115	117					10																	90676446		2203	4300	6503	90666426	SO:0001587	stop_gained	57559			AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"associated molecule with the SH3 domain of STAM (AMSH) like protein", "associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.913G>T	10.37:g.90676446G>T	ENSP00000360994:p.Glu305*		90666426	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Nonsense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	.	.	.	.	.	.	.	.	.	.	G	47	13.655154	0.99755	.	.	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924;ENST00000371922	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-5.3522	19.209	0.93747	0.0:0.0:1.0:0.0	.	.	.	.	X	305;305;305;139	.	ENSP00000360990:E139X	E	+	1	0	STAMBPL1	90666426	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.832000	0.99423	2.885000	0.99019	0.650000	0.86243	GAA		0.338	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799		T	90676446	G	T	90676446	4	4	61	1	0	0	0	0	0	1	0	0	15290	1291	45	2	939	2	STAMBPL1	10	90676446	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185642	90676446	44858301	6869	14854										
ACTA2	59	broad.mit.edu	37	chr10	90700996	90700996	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcctcaccagtagtaacGaaggaatagccacgctcagt	10	12	2	0	rs143771352		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:90700996G>A	ENST00000458208.1	-	6	1080	c.606C>T	c.(604-606)ttC>ttT	p.F202F	ACTA2_ENST00000224784.6_Silent_p.F202F|STAMBPL1_ENST00000371927.3_Intron|ACTA2-AS1_ENST00000596007.1_RNA|ACTA2-AS1_ENST00000437930.4_RNA|ACTA2_ENST00000480297.1_5'UTR	NM_001141945.1	NP_001135417.1	P62736	ACTA_HUMAN	actin, alpha 2, smooth muscle, aorta	202					glomerular mesangial cell development (GO:0072144)|muscle contraction (GO:0006936)|regulation of blood pressure (GO:0008217)|response to virus (GO:0009615)|vascular smooth muscle contraction (GO:0014829)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|smooth muscle contractile fiber (GO:0030485)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)	p.F202F(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(2)	17		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)		CAGTAGTAACGAAGGAATAGC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	10						G	,	0,4406		0,0,2203	114	87	96		606,606	-5.9	0.8	10	dbSNP_134	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ACTA2	NM_001141945.1,NM_001613.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	202/378,202/378	90700996	2,13004	2203	4300	6503	90690976	SO:0001819	synonymous_variant	59			X13839	CCDS7392.1	10q23.31	2014-09-17			ENSG00000107796	ENSG00000107796			130	protein-coding gene	gene with protein product		102620				2398629	Standard	NM_001141945		Approved	ACTSA	uc001kfp.3	P62736	OTTHUMG00000018700	ENST00000458208.1:c.606C>T	10.37:g.90700996G>A			90690976	B2R8A4|P03996|P04108|Q6FI19	Silent	SNP	ENST00000458208.1	37	CCDS7392.1																																																																																				0.547	ACTA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049264.1	NM_001613		A	90700996	G	A	90700996	2	1	61	1	0	0	0	0	0	0	0	1	192	1049	37	1		1	ACTA2	10	90700996	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24550	90700996	44833751	6870	14855										
IFIT2	3433	broad.mit.edu	37	chr10	91066223	91066223	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctggaaaagaagccaaaGaacccagaattcacctctgg	9	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91066223G>T	ENST00000371826.3	+	2	679	c.510G>T	c.(508-510)aaG>aaT	p.K170N	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	170					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)	p.K170N(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				AGAAGCCAAAGAACCCAGAAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	10											51	53	52					10																	91066223		2011	4207	6218	91056203	SO:0001583	missense	3433			M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.510G>T	10.37:g.91066223G>T	ENSP00000360891:p.Lys170Asn		91056203	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	37	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	G	8.460	0.855013	0.17106	.	.	ENSG00000119922	ENST00000371826	T	0.72394	-0.65	4.47	-0.914	0.10497	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.307723	0.31071	U	0.008312	T	0.43010	0.1228	N	0.12443	0.215	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.19484	-1.0304	10	0.17369	T	0.5	-2.5362	6.4624	0.21964	0.0758:0.531:0.1756:0.2175	.	170	P09913	IFIT2_HUMAN	N	170	ENSP00000360891:K170N	ENSP00000360891:K170N	K	+	3	2	IFIT2	91056203	0.000000	0.05858	0.001000	0.08648	0.997000	0.91878	-0.960000	0.03849	-0.151000	0.11176	0.655000	0.94253	AAG		0.512	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		T	91066223	G	T	91066223	3	4	61	1	0	0	0	0	1	0	0	0	7544	933	33	2	516	2	IFIT2	10	91066223	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	365227	91066223	44468524	6871	14856										
IFIT2	3433	broad.mit.edu	37	chr10	91066537	91066537	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcttaaaaaggctttagAatacataccaaacaatgcct	5	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91066537A>G	ENST00000371826.3	+	2	993	c.824A>G	c.(823-825)gAa>gGa	p.E275G	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	275					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)	p.E275G(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				AAGGCTTTAGAATACATACCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											126	121	122					10																	91066537		1910	4148	6058	91056517	SO:0001583	missense	3433			M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.824A>G	10.37:g.91066537A>G	ENSP00000360891:p.Glu275Gly		91056517	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	37	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.902929	0.33628	.	.	ENSG00000119922	ENST00000371826	T	0.62232	0.04	4.58	2.26	0.28386	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.273885	0.34435	U	0.003972	T	0.59266	0.2181	M	0.81802	2.56	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.57670	-0.7771	10	0.72032	D	0.01	-0.4896	6.177	0.20449	0.7108:0.1362:0.153:0.0	.	275	P09913	IFIT2_HUMAN	G	275	ENSP00000360891:E275G	ENSP00000360891:E275G	E	+	2	0	IFIT2	91056517	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.457000	0.21875	0.509000	0.28195	-0.250000	0.11733	GAA		0.418	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		G	91066537	A	G	91066537	3	3	61	1	0	0	0	0	1	0	0	0	7544	246	9	4	830	4	IFIT2	10	91066537	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	314	91066537	44468210	6872	14857										
IFIT2	3433	broad.mit.edu	37	chr10	91066642	91066642	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatggaatgtatgggaaaaGaaagttactggaactaatag	12	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91066642G>T	ENST00000371826.3	+	2	1098	c.929G>T	c.(928-930)aGa>aTa	p.R310I	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	310					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)	p.R310I(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TATGGGAAAAGAAAGTTACTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											92	88	89					10																	91066642		1879	4106	5985	91056622	SO:0001583	missense	3433			M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.929G>T	10.37:g.91066642G>T	ENSP00000360891:p.Arg310Ile		91056622	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	37	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758729	0.69763	.	.	ENSG00000119922	ENST00000371826	T	0.16897	2.31	4.48	-0.251	0.13003	Tetratricopeptide-like helical (1);	1.664840	0.04255	U	0.339363	T	0.24967	0.0606	M	0.74258	2.255	0.24698	N	0.993271	P	0.48162	0.906	P	0.44732	0.459	T	0.30031	-0.9992	10	0.66056	D	0.02	-2.4992	5.6444	0.17582	0.2446:0.2576:0.4978:0.0	.	310	P09913	IFIT2_HUMAN	I	310	ENSP00000360891:R310I	ENSP00000360891:R310I	R	+	2	0	IFIT2	91056622	0.002000	0.14202	0.001000	0.08648	0.595000	0.36748	-0.096000	0.11059	-0.034000	0.13713	0.655000	0.94253	AGA		0.433	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		T	91066642	G	T	91066642	3	4	61	1	0	0	0	0	1	0	0	0	7544	942	33	2	935	2	IFIT2	10	91066642	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105	91066642	44468105	6873	14858										
IFIT3	3437	broad.mit.edu	37	chr10	91099046	91099046	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaccaatacgtcaaggttCtcttgggcctgaaactgcag	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91099046C>A	ENST00000371818.4	+	2	814	c.634C>A	c.(634-636)Ctc>Atc	p.L212I	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron|IFIT3_ENST00000371811.4_Missense_Mutation_p.L212I	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	212					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)	p.L212I(1)		breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						CGTCAAGGTTCTCTTGGGCCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											60	67	64					10																	91099046		2203	4300	6503	91089026	SO:0001583	missense	3437			U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"Tetratricopeptide (TTC) repeat domain containing"	5411	protein-coding gene	gene with protein product		604650	"interferon-induced protein with tetratricopeptide repeats 4"	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.634C>A	10.37:g.91099046C>A	ENSP00000360883:p.Leu212Ile		91089026	Q99634|Q9BSK7	Missense_Mutation	SNP	ENST00000371818.4	37	CCDS7402.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747762	0.49257	.	.	ENSG00000119917	ENST00000371818;ENST00000371811;ENST00000543062	T;T	0.38722	1.12;1.12	4.48	3.56	0.40772	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.214170	0.37669	N	0.001982	T	0.63236	0.2494	M	0.86953	2.85	0.45822	D	0.998699	D	0.89917	1.0	D	0.74348	0.983	T	0.65899	-0.6056	10	0.59425	D	0.04	-8.4318	7.0964	0.25311	0.1768:0.7281:0.0:0.0951	.	212	O14879	IFIT3_HUMAN	I	212;212;33	ENSP00000360883:L212I;ENSP00000360876:L212I	ENSP00000360876:L212I	L	+	1	0	IFIT3	91089026	0.948000	0.32251	0.998000	0.56505	0.444000	0.32077	0.680000	0.25306	1.455000	0.47813	0.655000	0.94253	CTC		0.453	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549		A	91099046	C	A	91099046	3	1	61	1	0	0	0	0	1	0	0	0	7545	913	32	2	649	2	IFIT3	10	91099046	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32404	91099046	44435701	6874	14859										
IFIT1B	439996	broad.mit.edu	37	chr10	91143308	91143308	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcttgaaaaaggctgaaGacttaattcagaaagaacat	8	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91143308G>A	ENST00000371809.3	+	2	318	c.238G>A	c.(238-240)Gac>Aac	p.D80N	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	80								p.D80N(1)		endometrium(2)|large_intestine(3)|lung(8)	13						AAAGGCTGAAGACTTAATTCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	10											84	83	83					10																	91143308		2203	4300	6503	91133288	SO:0001583	missense	439996				CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"Tetratricopeptide (TTC) repeat domain containing"	23442	protein-coding gene	gene with protein product			"interferon-induced protein with tetratricopeptide repeats 1-like"	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.238G>A	10.37:g.91143308G>A	ENSP00000360874:p.Asp80Asn		91133288	A7E245	Missense_Mutation	SNP	ENST00000371809.3	37	CCDS31242.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.642146	0.47153	.	.	ENSG00000204010	ENST00000371809	D	0.94092	-3.35	4.61	2.71	0.32032	Tetratricopeptide-like helical (1);	0.537542	0.19876	N	0.104090	D	0.88633	0.6489	L	0.41824	1.3	0.20764	N	0.99985	B	0.06786	0.001	B	0.17433	0.018	T	0.80478	-0.1365	10	0.44086	T	0.13	.	10.3267	0.43798	0.1498:0.0:0.8502:0.0	.	80	Q5T764	IFT1B_HUMAN	N	80	ENSP00000360874:D80N	ENSP00000360874:D80N	D	+	1	0	IFIT1B	91133288	1.000000	0.71417	0.427000	0.26684	0.132000	0.20833	2.992000	0.49417	2.098000	0.63641	0.557000	0.71058	GAC		0.463	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987		A	91143308	G	A	91143308	3	1	61	1	0	0	0	0	1	0	0	0	7543	942	33	3	244	3	IFIT1B	10	91143308	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44262	91143308	44391439	6875	14860										
IFIT1	3434	broad.mit.edu	37	chr10	91163115	91163115	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcacagaaaagctgaagaGaattttcaaaaattgttatg	7	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91163115G>T	ENST00000371804.3	+	2	1250	c.1083G>T	c.(1081-1083)gaG>gaT	p.E361D	IFIT1_ENST00000546318.1_Missense_Mutation_p.E330D|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	361					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)	p.E361D(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						AAGCTGAAGAGAATTTTCAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											39	41	40					10																	91163115		2202	4300	6502	91153095	SO:0001583	missense	3434			M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"Tetratricopeptide (TTC) repeat domain containing"	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.1083G>T	10.37:g.91163115G>T	ENSP00000360869:p.Glu361Asp		91153095	B3KS50|D3DR31|Q5T7J1|Q96QM5	Missense_Mutation	SNP	ENST00000371804.3	37	CCDS31243.1	.	.	.	.	.	.	.	.	.	.	G	0.305	-0.971553	0.02215	.	.	ENSG00000185745	ENST00000371804;ENST00000546318	T;T	0.76448	-1.02;-1.02	5.62	-11.2	0.00127	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.847041	0.10625	N	0.652836	T	0.35335	0.0928	N	0.01493	-0.835	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.34601	-0.9822	10	0.10377	T	0.69	.	3.5123	0.07713	0.2671:0.0929:0.4144:0.2256	.	361;361	Q5T7J1;P09914	.;IFIT1_HUMAN	D	361;330	ENSP00000360869:E361D;ENSP00000441968:E330D	ENSP00000360869:E361D	E	+	3	2	IFIT1	91153095	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.907000	0.00337	-3.120000	0.00239	-2.085000	0.00377	GAG		0.373	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548		T	91163115	G	T	91163115	3	4	61	1	0	0	0	0	1	0	0	0	7542	933	33	2	1089	2	IFIT1	10	91163115	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19807	91163115	44371632	6876	14861										
IFIT5	24138	broad.mit.edu	37	chr10	91177038	91177038	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggaatttacttaaggaaGacattgatctgtttgaggta	10	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91177038G>T	ENST00000371795.4	+	2	295	c.82G>T	c.(82-84)Gac>Tac	p.D28Y	IFIT5_ENST00000416601.1_Missense_Mutation_p.D28Y|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	28					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)	p.D28Y(1)		endometrium(1)|large_intestine(4)|lung(4)	9						ACTTAAGGAAGACATTGATCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	10											79	82	81					10																	91177038		2203	4300	6503	91167018	SO:0001583	missense	24138			U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.82G>T	10.37:g.91177038G>T	ENSP00000360860:p.Asp28Tyr		91167018	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Missense_Mutation	SNP	ENST00000371795.4	37	CCDS7403.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013475	0.54468	.	.	ENSG00000152778	ENST00000371795;ENST00000416601	T;T	0.55588	0.51;0.51	6.03	5.11	0.69529	.	0.515918	0.22326	N	0.061537	T	0.66086	0.2754	L	0.60957	1.885	0.41032	D	0.985166	D;D	0.76494	0.999;0.999	D;D	0.66602	0.945;0.945	T	0.68743	-0.5328	10	0.66056	D	0.02	-19.6885	11.8208	0.52237	0.0679:0.1228:0.8093:0.0	.	28;28	Q13325;B4DDV1	IFIT5_HUMAN;.	Y	28	ENSP00000360860:D28Y;ENSP00000414042:D28Y	ENSP00000360860:D28Y	D	+	1	0	IFIT5	91167018	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.901000	0.39838	1.527000	0.49086	0.655000	0.94253	GAC		0.343	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		T	91177038	G	T	91177038	3	4	61	1	0	0	0	0	1	0	0	0	7546	942	33	2	88	2	IFIT5	10	91177038	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13923	91177038	44357709	6877	14862										
SLC16A12	387700	broad.mit.edu	37	chr10	91192894	91192894	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctaattctcttgccacaGaataagccactgatccattg	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91192894G>T	ENST00000341233.4	-	8	1778	c.1388C>A	c.(1387-1389)tCt>tAt	p.S463Y	SLC16A12_ENST00000371790.4_Missense_Mutation_p.S493Y	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	463						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.S463Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						TCTTGCCACAGAATAAGCCAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	117	121					10																	91192894		2203	4300	6503	91182874	SO:0001583	missense	387700				CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"Solute carriers"	23094	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 12"	611910	"solute carrier family 16 (monocarboxylic acid transporters), member 12", "solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.1388C>A	10.37:g.91192894G>T	ENSP00000343022:p.Ser463Tyr		91182874	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.983398	0.74474	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.25749	1.83;1.78	5.78	5.78	0.91487	.	0.176614	0.40222	N	0.001141	T	0.40645	0.1125	L	0.31294	0.92	0.46061	D	0.998843	D	0.71674	0.998	D	0.66979	0.948	T	0.10965	-1.0607	10	0.52906	T	0.07	.	19.0025	0.92839	0.0:0.0:1.0:0.0	.	463	Q6ZSM3	MOT12_HUMAN	Y	463;493	ENSP00000343022:S463Y;ENSP00000360855:S493Y	ENSP00000343022:S463Y	S	-	2	0	SLC16A12	91182874	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	6.394000	0.73223	2.740000	0.93945	0.313000	0.20887	TCT		0.473	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		T	91192894	G	T	91192894	3	4	61	1	0	0	0	0	1	0	0	0	14442	942	33	2	76	2	SLC16A12	10	91192894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15856	91192894	44341853	6878	14863										
SLC16A12	387700	broad.mit.edu	37	chr10	91193027	91193027	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagaactaaatatcattgAaaatccacagaggaggaatg	8	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91193027A>G	ENST00000341233.4	-	8	1645	c.1255T>C	c.(1255-1257)Tca>Cca	p.S419P	SLC16A12_ENST00000371790.4_Missense_Mutation_p.S449P	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	419						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.S419P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						AATATCATTGAAAATCCACAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	68	68					10																	91193027		2203	4300	6503	91183007	SO:0001583	missense	387700				CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"Solute carriers"	23094	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 12"	611910	"solute carrier family 16 (monocarboxylic acid transporters), member 12", "solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.1255T>C	10.37:g.91193027A>G	ENSP00000343022:p.Ser419Pro		91183007	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	37		.	.	.	.	.	.	.	.	.	.	A	18.12	3.552957	0.65425	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.80909	-1.43;-1.43	5.77	3.35	0.38373	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.284524	0.34932	N	0.003573	T	0.80523	0.4639	L	0.37897	1.145	0.37840	D	0.929039	P	0.49783	0.928	P	0.56434	0.798	T	0.78623	-0.2132	10	0.34782	T	0.22	.	11.9422	0.52907	0.7146:0.2854:0.0:0.0	.	419	Q6ZSM3	MOT12_HUMAN	P	419;449	ENSP00000343022:S419P;ENSP00000360855:S449P	ENSP00000343022:S419P	S	-	1	0	SLC16A12	91183007	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	2.951000	0.49089	0.412000	0.25729	0.383000	0.25322	TCA		0.393	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		G	91193027	A	G	91193027	3	3	61	1	0	0	0	0	1	0	0	0	14442	246	9	4	209	4	SLC16A12	10	91193027	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	133	91193027	44341720	6879	14864										
KIF20B	9585	broad.mit.edu	37	chr10	91468936	91468936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttaaggcaaacagtttcGaatctaaagattatctccag	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91468936G>A	ENST00000371728.3	+	3	225	c.160G>A	c.(160-162)Gaa>Aaa	p.E54K	KIF20B_ENST00000260753.4_Missense_Mutation_p.E54K|KIF20B_ENST00000416354.1_Missense_Mutation_p.E54K|KIF20B_ENST00000394289.2_Missense_Mutation_p.E54K	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	54					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.E54K(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AAACAGTTTCGAATCTAAAGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											45	50	48					10																	91468936		2203	4296	6499	91458916	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.160G>A	10.37:g.91468936G>A	ENSP00000360793:p.Glu54Lys		91458916	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	G	21.8	4.197510	0.79015	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728;ENST00000439656;ENST00000447580	T;T;T;T;T	0.69040	-0.26;-0.28;-0.37;-0.3;2.24	5.58	3.6	0.41247	Kinesin, motor domain (1);	0.384350	0.22197	N	0.063281	T	0.64713	0.2623	L	0.43152	1.355	0.26329	N	0.977553	D;P	0.55605	0.972;0.873	P;B	0.50440	0.641;0.35	T	0.58674	-0.7595	10	0.10377	T	0.69	-7.778	16.697	0.85338	0.0:0.2422:0.7578:0.0	.	54;54	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	K	54	ENSP00000260753:E54K;ENSP00000411545:E54K;ENSP00000377830:E54K;ENSP00000360793:E54K;ENSP00000390946:E54K	ENSP00000260753:E54K	E	+	1	0	KIF20B	91458916	1.000000	0.71417	0.996000	0.52242	0.960000	0.62799	3.074000	0.50065	1.464000	0.47987	0.655000	0.94253	GAA		0.313	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		A	91468936	G	A	91468936	3	1	61	1	0	0	0	0	1	0	0	0	8308	1059	37	1	166	1	KIF20B	10	91468936	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	275909	91468936	44065811	6880	14865										
KIF20B	9585	broad.mit.edu	37	chr10	91497569	91497569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgcacacgaaaatagacGaactacgtactcttgattca	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91497569G>A	ENST00000371728.3	+	20	3036	c.2971G>A	c.(2971-2973)Gaa>Aaa	p.E991K	KIF20B_ENST00000260753.4_Missense_Mutation_p.E951K|KIF20B_ENST00000416354.1_Missense_Mutation_p.E1021K|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Missense_Mutation_p.E991K	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	991					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.E951K(3)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GAAAATAGACGAACTACGTAC	0.338																																																3	Substitution - Missense(3)	large_intestine(3)	10											60	64	63					10																	91497569		2203	4299	6502	91487549	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.2971G>A	10.37:g.91497569G>A	ENSP00000360793:p.Glu991Lys		91487549	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	G	13.37	2.216206	0.39201	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.70164	-0.37;-0.38;-0.46;-0.39	5.69	2.47	0.30058	.	0.231808	0.30455	N	0.009582	T	0.48295	0.1492	L	0.40543	1.245	0.32394	N	0.552863	P;P	0.40638	0.462;0.725	B;B	0.30646	0.023;0.118	T	0.59306	-0.7479	10	0.33940	T	0.23	-9.2566	9.3056	0.37874	0.1501:0.1249:0.725:0.0	.	991;951	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	K	951;1021;991;991	ENSP00000260753:E951K;ENSP00000411545:E1021K;ENSP00000377830:E991K;ENSP00000360793:E991K	ENSP00000260753:E951K	E	+	1	0	KIF20B	91487549	1.000000	0.71417	1.000000	0.80357	0.327000	0.28475	1.275000	0.33144	1.398000	0.46701	0.591000	0.81541	GAA		0.338	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		A	91497569	G	A	91497569	3	1	61	1	0	0	0	0	1	0	0	0	8308	1059	37	1	2925	1	KIF20B	10	91497569	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28633	91497569	44037178	6881	14866										
KIF20B	9585	broad.mit.edu	37	chr10	91497974	91497974	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttatacagcagctgaaaGaagaattgcaagaaaaaaat	7	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91497974G>T	ENST00000371728.3	+	20	3441	c.3376G>T	c.(3376-3378)Gaa>Taa	p.E1126*	KIF20B_ENST00000260753.4_Nonsense_Mutation_p.E1086*|KIF20B_ENST00000416354.1_Nonsense_Mutation_p.E1156*|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Nonsense_Mutation_p.E1126*	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1126					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.E1086*(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GCAGCTGAAAGAAGAATTGCA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											59	67	64					10																	91497974		2201	4296	6497	91487954	SO:0001587	stop_gained	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3376G>T	10.37:g.91497974G>T	ENSP00000360793:p.Glu1126*		91487954	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Nonsense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	G	38	7.092099	0.98059	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	.	.	.	5.87	4.0	0.46444	.	0.670490	0.13671	N	0.370874	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-1.8222	6.3143	0.21182	0.2082:0.1355:0.6563:0.0	.	.	.	.	X	1086;1156;1126;1126	.	ENSP00000260753:E1086X	E	+	1	0	KIF20B	91487954	0.920000	0.31207	0.508000	0.27688	0.511000	0.34104	1.335000	0.33839	0.801000	0.34066	0.591000	0.81541	GAA		0.343	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		T	91497974	G	T	91497974	4	4	61	1	0	0	0	0	0	1	0	0	8308	943	33	2	3330	2	KIF20B	10	91497974	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	405	91497974	44036773	6882	14867										
KIF20B	9585	broad.mit.edu	37	chr10	91498277	91498277	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaggaactcaagctgaaaGaagaaatcacacagttaaca	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:91498277G>T	ENST00000371728.3	+	20	3744	c.3679G>T	c.(3679-3681)Gaa>Taa	p.E1227*	KIF20B_ENST00000260753.4_Nonsense_Mutation_p.E1187*|KIF20B_ENST00000416354.1_Nonsense_Mutation_p.E1257*|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Nonsense_Mutation_p.E1227*	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1227					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.E1187*(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						CAAGCTGAAAGAAGAAATCAC	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											50	54	53					10																	91498277		2133	4267	6400	91488257	SO:0001587	stop_gained	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3679G>T	10.37:g.91498277G>T	ENSP00000360793:p.Glu1227*		91488257	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Nonsense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	G	39	7.614788	0.98390	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	.	.	.	5.82	3.92	0.45320	.	0.262618	0.27008	N	0.021394	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-8.3286	7.8954	0.29704	0.1392:0.1331:0.7278:0.0	.	.	.	.	X	1187;1257;1227;1227	.	ENSP00000260753:E1187X	E	+	1	0	KIF20B	91488257	1.000000	0.71417	0.997000	0.53966	0.395000	0.30598	2.818000	0.48041	0.762000	0.33152	0.467000	0.42956	GAA		0.299	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		T	91498277	G	T	91498277	4	4	61	1	0	0	0	0	0	1	0	0	8308	943	33	2	3633	2	KIF20B	10	91498277	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	303	91498277	44036470	6883	14868										
HTR7	3363	broad.mit.edu	37	chr10	92503443	92503443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaccctccttgtgcaggCcctcctgcaatttatggcaa	8	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:92503443C>T	ENST00000336152.3	-	3	1326	c.1300G>A	c.(1300-1302)Gcc>Acc	p.A434T	HTR7_ENST00000277874.6_Intron|HTR7_ENST00000371721.3_Intron|HTR7_ENST00000371719.2_Intron	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	434					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.A434T(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CTTGTGCAGGCCCTCCTGCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											132	113	120					10																	92503443		2203	4300	6503	92493423	SO:0001583	missense	3363			BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.1300G>A	10.37:g.92503443C>T	ENSP00000337949:p.Ala434Thr		92493423	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	37	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	C	0.572	-0.840826	0.02692	.	.	ENSG00000148680	ENST00000336152	T	0.64803	-0.12	2.53	-0.642	0.11486	.	1.749270	0.03082	N	0.158664	T	0.37652	0.1011	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.16630	-1.0396	10	0.11794	T	0.64	.	5.2693	0.15617	0.0:0.5292:0.0:0.4708	.	434	P34969	5HT7R_HUMAN	T	434	ENSP00000337949:A434T	ENSP00000337949:A434T	A	-	1	0	HTR7	92493423	0.000000	0.05858	0.012000	0.15200	0.090000	0.18270	-0.058000	0.11750	-0.145000	0.11294	0.461000	0.40582	GCC		0.393	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		T	92503443	C	T	92503443	3	4	61	1	0	0	0	0	1	0	0	0	7473	739	26	3	147	3	HTR7	10	92503443	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1005166	92503443	43031304	6884	14869										
HTR7	3363	broad.mit.edu	37	chr10	92508832	92508832	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgcaggaagtgccacaGatgaagggtctggctgtcga	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:92508832G>T	ENST00000336152.3	-	2	1085	c.1059C>A	c.(1057-1059)atC>atA	p.I353I	HTR7_ENST00000277874.6_Silent_p.I353I|HTR7_ENST00000371721.3_Silent_p.I353I|HTR7_ENST00000371719.2_Silent_p.I353I	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	353					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.I353I(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	AAGTGCCACAGATGAAGGGTC	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	10											92	89	90					10																	92508832		2203	4300	6503	92498812	SO:0001819	synonymous_variant	3363			BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.1059C>A	10.37:g.92508832G>T			92498812	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Silent	SNP	ENST00000336152.3	37	CCDS7408.1																																																																																				0.532	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		T	92508832	G	T	92508832	2	4	61	1	0	0	0	0	0	0	0	1	7473	932	33	2		2	HTR7	10	92508832	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5389	92508832	43025915	6885	14870										
ANKRD1	27063	broad.mit.edu	37	chr10	92677531	92677531	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccagcttccattaacttCtccacaattgccaaatgtcc	4	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:92677531C>A	ENST00000371697.3	-	5	758	c.510G>T	c.(508-510)gaG>gaT	p.E170D		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	170					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)	p.E170D(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				CCATTAACTTCTCCACAATTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	90	93					10																	92677531		2203	4300	6503	92667511	SO:0001583	missense	27063			X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.510G>T	10.37:g.92677531C>A	ENSP00000360762:p.Glu170Asp		92667511	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	37	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400130	0.62177	.	.	ENSG00000148677	ENST00000371697	T	0.66280	-0.2	5.51	3.64	0.41730	Ankyrin repeat-containing domain (4);	0.143237	0.48286	D	0.000191	T	0.61350	0.2340	L	0.37897	1.145	0.37262	D	0.907042	P	0.42296	0.775	P	0.51297	0.665	T	0.68322	-0.5439	10	0.66056	D	0.02	.	10.0427	0.42169	0.0:0.7449:0.0:0.2551	.	170	Q15327	ANKR1_HUMAN	D	170	ENSP00000360762:E170D	ENSP00000360762:E170D	E	-	3	2	ANKRD1	92667511	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.555000	0.23422	1.456000	0.47831	0.585000	0.79938	GAG		0.378	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		A	92677531	C	A	92677531	3	1	61	1	0	0	0	0	1	0	0	0	637	912	32	2	469	2	ANKRD1	10	92677531	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168699	92677531	42857216	6886	14871										
PCGF5	84333	broad.mit.edu	37	chr10	93021137	93021137	+	Frame_Shift_Del	DEL	A	A	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtaactgtgggaactattAaaaaatttctaagtttaaaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93021137delA	ENST00000336126.5	+	7	761	c.529delA	c.(529-531)aaafs	p.K178fs	PCGF5_ENST00000543648.1_Frame_Shift_Del_p.K178fs	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)	p.K178fs*3(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						GGGAACTATTAAAAAATTTCT	0.264																																					Colon(178;732 2696 46441 50370)											1	Deletion - Frameshift(1)	large_intestine(1)	10											24	28	27					10																	93021137		2180	4255	6435	93011117	SO:0001589	frameshift_variant	84333			AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	28264	protein-coding gene	gene with protein product			"ring finger protein (C3HC4 type) 159"	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.529delA	10.37:g.93021137delA	ENSP00000337500:p.Lys178fs		93011117	B7Z892|D3DR33|Q6PK47|Q86TD0	Frame_Shift_Del	DEL	ENST00000336126.5	37	CCDS7413.1																																																																																				0.264	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373		-	93021137	A	-	93021137	7	5	61	1	0	1	0	1	0	0	0	0	11608	363	13	0	551	0	PCGF5	10	93021137	Frame_Shift_Del	DEL	A	TCGA-AG-A002-01A-01W-A00K-09	343606	93021137	42513610	6887	14872										
HECTD2	143279	broad.mit.edu	37	chr10	93244317	93244317	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagattgctgcaatttatttCtttacgcctgtttcctgcaa	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93244317C>T	ENST00000298068.5	+	9	969	c.875C>T	c.(874-876)tCt>tTt	p.S292F	HECTD2_ENST00000371667.1_5'UTR|HECTD2_ENST00000446394.1_Missense_Mutation_p.S296F|HECTD2_ENST00000536715.1_5'UTR|HECTD2_ENST00000498446.1_3'UTR	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	292					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S292F(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CAATTTATTTCTTTACGCCTG	0.373																																					NSCLC(12;376 469 1699 39910 41417)											1	Substitution - Missense(1)	large_intestine(1)	10											96	97	97					10																	93244317		2203	4300	6503	93234297	SO:0001583	missense	143279			AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"HECT domain containing 2"			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.875C>T	10.37:g.93244317C>T	ENSP00000298068:p.Ser292Phe		93234297	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	37	CCDS7414.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.784175	0.90282	.	.	ENSG00000165338	ENST00000446394;ENST00000371668;ENST00000298068	T;T	0.38722	1.12;1.13	5.97	5.97	0.96955	.	0.056069	0.64402	D	0.000001	T	0.63248	0.2495	M	0.75264	2.295	0.80722	D	1	P;D	0.57899	0.943;0.981	B;P	0.57371	0.445;0.819	T	0.63440	-0.6637	10	0.59425	D	0.04	.	20.4209	0.99038	0.0:1.0:0.0:0.0	.	296;292	E7ERR3;Q5U5R9	.;HECD2_HUMAN	F	296;18;292	ENSP00000401023:S296F;ENSP00000298068:S292F	ENSP00000298068:S292F	S	+	2	0	HECTD2	93234297	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.175000	0.77632	2.823000	0.97156	0.591000	0.81541	TCT		0.373	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			T	93244317	C	T	93244317	3	4	61	1	0	0	0	0	1	0	0	0	7061	913	32	3	933	3	HECTD2	10	93244317	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	223180	93244317	42290430	6888	14873										
PPP1R3C	5507	broad.mit.edu	37	chr10	93390258	93390258	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttttctcctcgtggtgtTttaaggcagaggagatatca	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93390258T>A	ENST00000238994.5	-	2	464	c.380A>T	c.(379-381)aAa>aTa	p.K127I		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C									p.K127I(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				CTCGTGGTGTTTTAAGGCAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											80	81	81					10																	93390258		2203	4300	6503	93380238	SO:0001583	missense	5507			Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9293	protein-coding gene	gene with protein product	"Phosphatase 1, regulatory inhibitor subunit 5", "protein targeting to glycogen"	602999	"protein phosphatase 1, regulatory (inhibitor) subunit 3C"	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.380A>T	10.37:g.93390258T>A	ENSP00000238994:p.Lys127Ile		93380238		Missense_Mutation	SNP	ENST00000238994.5	37	CCDS7416.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.632243	0.67015	.	.	ENSG00000119938	ENST00000238994;ENST00000500094	T	0.48836	0.8	5.79	4.66	0.58398	.	0.208451	0.49305	D	0.000151	T	0.57755	0.2075	L	0.49640	1.575	0.39541	D	0.968824	D	0.71674	0.998	D	0.65773	0.938	T	0.55192	-0.8179	10	0.25751	T	0.34	-24.2206	11.7107	0.51623	0.0:0.0687:0.0:0.9312	.	127	Q9UQK1	PPR3C_HUMAN	I	127;9	ENSP00000238994:K127I	ENSP00000238994:K127I	K	-	2	0	PPP1R3C	93380238	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	5.913000	0.69957	1.023000	0.39654	0.533000	0.62120	AAA		0.458	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398		A	93390258	T	A	93390258	3	1	61	1	0	0	0	0	1	0	0	0	12407	1841	64	5	577	5	PPP1R3C	10	93390258	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	145941	93390258	42144489	6889	14874										
TNKS2	80351	broad.mit.edu	37	chr10	93588096	93588096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgagaagctgatgttactcGaatcaaaaaacatctctctc	6	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93588096G>A	ENST00000371627.4	+	9	1416	c.1037G>A	c.(1036-1038)cGa>cAa	p.R346Q		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	346					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R346Q(1)		biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GATGTTACTCGAATCAAAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	10											66	66	66					10																	93588096		2203	4300	6503	93578076	SO:0001583	missense	80351			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1037G>A	10.37:g.93588096G>A	ENSP00000360689:p.Arg346Gln		93578076	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	37	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857368	0.71834	.	.	ENSG00000107854	ENST00000371627	T	0.63913	-0.07	5.5	5.5	0.81552	Ankyrin repeat-containing domain (4);	0.000000	0.50627	D	0.000107	T	0.50411	0.1614	N	0.25245	0.725	0.46096	D	0.998866	B	0.25351	0.124	B	0.23150	0.044	T	0.41574	-0.9501	10	0.22109	T	0.4	.	19.4011	0.94630	0.0:0.0:1.0:0.0	.	346	Q9H2K2	TNKS2_HUMAN	Q	346	ENSP00000360689:R346Q	ENSP00000360689:R346Q	R	+	2	0	TNKS2	93578076	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.480000	0.66820	2.591000	0.87537	0.462000	0.41574	CGA		0.343	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		A	93588096	G	A	93588096	3	1	61	1	0	0	0	0	1	0	0	0	16360	1058	37	1	1071	1	TNKS2	10	93588096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197838	93588096	41946651	6890	14875										
BTAF1	9044	broad.mit.edu	37	chr10	93719836	93719836	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtggatgtgctgctaaaAttacttacacaagaacaatg	8	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93719836A>C	ENST00000265990.6	+	11	1496	c.1188A>C	c.(1186-1188)aaA>aaC	p.K396N	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	396					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K396N(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TGCTGCTAAAATTACTTACAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											170	167	168					10																	93719836		2203	4300	6503	93709816	SO:0001583	missense	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.1188A>C	10.37:g.93719836A>C	ENSP00000265990:p.Lys396Asn		93709816	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777499	0.49786	.	.	ENSG00000095564	ENST00000265990	T	0.65732	-0.17	5.26	1.7	0.24286	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57286	0.2043	M	0.63843	1.955	0.80722	D	1	P	0.50710	0.938	P	0.44477	0.451	T	0.54846	-0.8232	10	0.42905	T	0.14	-38.2789	8.7225	0.34449	0.6905:0.0:0.3095:0.0	.	396	O14981	BTAF1_HUMAN	N	396	ENSP00000265990:K396N	ENSP00000265990:K396N	K	+	3	2	BTAF1	93709816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.646000	0.37249	0.329000	0.23460	0.477000	0.44152	AAA		0.393	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		C	93719836	A	C	93719836	3	2	61	1	0	0	0	0	1	0	0	0	1539	98	4	4	1230	4	BTAF1	10	93719836	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	131740	93719836	41814911	6891	14876										
BTAF1	9044	broad.mit.edu	37	chr10	93743960	93743960	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctgttgtattttaggaGtgtaaagctgttaccttagc	9	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93743960G>T	ENST00000265990.6	+	19	2534	c.2226G>T	c.(2224-2226)gaG>gaT	p.E742D	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	742					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E742D(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TATTTTAGGAGTGTAAAGCTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											93	89	90					10																	93743960		2203	4299	6502	93733940	SO:0001583	missense	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.2226G>T	10.37:g.93743960G>T	ENSP00000265990:p.Glu742Asp		93733940	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	G	5.023	0.189854	0.09547	.	.	ENSG00000095564	ENST00000265990	T	0.65916	-0.18	5.82	-1.07	0.09968	Domain of unknown function DUF3535 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.105164	0.64402	D	0.000005	T	0.46658	0.1404	L	0.43152	1.355	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.29488	-1.0010	10	0.13470	T	0.59	-13.413	11.0825	0.48068	0.5996:0.0:0.4004:0.0	.	742;742	Q2M1V9;O14981	.;BTAF1_HUMAN	D	742	ENSP00000265990:E742D	ENSP00000265990:E742D	E	+	3	2	BTAF1	93733940	0.750000	0.28316	0.996000	0.52242	0.940000	0.58332	-0.068000	0.11561	-0.084000	0.12595	-0.827000	0.03088	GAG		0.348	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93743960	G	T	93743960	3	4	61	1	0	0	0	0	1	0	0	0	1539	1020	36	2	2300	2	BTAF1	10	93743960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24124	93743960	41790787	6892	14877										
BTAF1	9044	broad.mit.edu	37	chr10	93753589	93753589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccattgaggaatacaatcGacataaataattttggtata	7	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93753589G>A	ENST00000265990.6	+	22	3492	c.3184G>A	c.(3184-3186)Gac>Aac	p.D1062N	BTAF1_ENST00000544642.1_5'Flank	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1062					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1062N(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				GAATACAATCGACATAAATAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											77	73	75					10																	93753589		2203	4300	6503	93743569	SO:0001583	missense	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.3184G>A	10.37:g.93753589G>A	ENSP00000265990:p.Asp1062Asn		93743569	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731806	0.30684	.	.	ENSG00000095564	ENST00000265990	D	0.89875	-2.58	5.27	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (1);	0.362006	0.31636	N	0.007315	T	0.73598	0.3607	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.67317	-0.5701	10	0.30078	T	0.28	-7.5088	5.5152	0.16902	0.1917:0.2073:0.6009:0.0	.	1062;1062	Q2M1V9;O14981	.;BTAF1_HUMAN	N	1062	ENSP00000265990:D1062N	ENSP00000265990:D1062N	D	+	1	0	BTAF1	93743569	0.993000	0.37304	1.000000	0.80357	0.977000	0.68977	1.647000	0.37260	2.468000	0.83385	0.650000	0.86243	GAC		0.313	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		A	93753589	G	A	93753589	3	1	61	1	0	0	0	0	1	0	0	0	1539	1058	37	1	3270	1	BTAF1	10	93753589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9629	93753589	41781158	6893	14878										
BTAF1	9044	broad.mit.edu	37	chr10	93786934	93786934	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaccagaggaacattggaAgaaaaaataatggggttgca	11	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:93786934A>G	ENST00000265990.6	+	37	5591	c.5283A>G	c.(5281-5283)gaA>gaG	p.E1761E	BTAF1_ENST00000544642.1_Silent_p.E589E	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1761	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E1761E(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				GAACATTGGAAGAAAAAATAA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	10											127	127	127					10																	93786934		2203	4300	6503	93776914	SO:0001819	synonymous_variant	9044			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.5283A>G	10.37:g.93786934A>G			93776914	B4E0W6|O43578	Silent	SNP	ENST00000265990.6	37	CCDS7419.1																																																																																				0.383	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		G	93786934	A	G	93786934	2	3	61	1	0	0	0	0	0	0	0	1	1539	69	3	4		4	BTAF1	10	93786934	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33345	93786934	41747813	6894	14879										
IDE	3416	broad.mit.edu	37	chr10	94294469	94294469	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattttctttagggtatttCtttgttcccaaaaaaagcat	5	7	3	0	rs61078556		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94294469C>A	ENST00000265986.6	-	3	413	c.357G>T	c.(355-357)aaG>aaT	p.K119N		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	119					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.K119N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TAGGGTATTTCTTTGTTCCCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											101	99	100					10																	94294469		2203	4300	6503	94284449	SO:0001583	missense	3416			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.357G>T	10.37:g.94294469C>A	ENSP00000265986:p.Lys119Asn		94284449	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236051	0.58886	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	T;T	0.20332	2.08;2.08	5.93	4.9	0.64082	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.104023	0.64402	D	0.000004	T	0.29093	0.0723	M	0.73430	2.235	0.80722	D	1	B	0.26635	0.155	B	0.33521	0.165	T	0.07309	-1.0779	10	0.62326	D	0.03	-9.0523	10.3723	0.44062	0.0:0.8218:0.0:0.1782	.	119	P14735	IDE_HUMAN	N	119;105	ENSP00000265986:K119N;ENSP00000408850:K105N	ENSP00000265986:K119N	K	-	3	2	IDE	94284449	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.058000	0.57463	1.253000	0.44018	0.655000	0.94253	AAG		0.353	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		A	94294469	C	A	94294469	3	1	61	1	0	0	0	0	1	0	0	0	7514	912	32	2	2794	2	IDE	10	94294469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	507535	94294469	41240278	6895	14880										
IDE	3416	broad.mit.edu	37	chr10	94297213	94297213	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggccagctctagccctcGatattctcgcttgtcttcag	8	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94297213G>A	ENST00000265986.6	-	2	249	c.193C>T	c.(193-195)Cga>Tga	p.R65*		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	65					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.R65*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TCTAGCCCTCGATATTCTCGC	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											219	194	202					10																	94297213		2203	4300	6503	94287193	SO:0001587	stop_gained	3416			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.193C>T	10.37:g.94297213G>A	ENSP00000265986:p.Arg65*		94287193	B2R721|B7ZAU2|D3DR35|Q5T5N2	Nonsense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893588	0.91889	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	.	.	.	5.58	3.66	0.41972	.	0.121362	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0843	8.6772	0.34187	0.0695:0.0:0.6652:0.2653	.	.	.	.	X	65;51	.	ENSP00000265986:R65X	R	-	1	2	IDE	94287193	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.534000	0.45676	1.355000	0.45865	0.655000	0.94253	CGA		0.408	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		A	94297213	G	A	94297213	4	1	61	1	0	0	0	0	0	1	0	0	7514	1066	37	1	2962	1	IDE	10	94297213	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2744	94297213	41237534	6896	14881										
KIF11	3832	broad.mit.edu	37	chr10	94368819	94368819	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgtacccttcatcaaattTttgagaaacttactgataat	4	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94368819T>A	ENST00000260731.3	+	5	520	c.430T>A	c.(430-432)Ttt>Att	p.F144I		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	144	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		F -> L (in MCLMR). {ECO:0000269|PubMed:22284827}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)	p.F144I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCATCAAATTTTTGAGAAACT	0.338																																					Colon(47;212 1003 2764 4062 8431)											1	Substitution - Missense(1)	large_intestine(1)	10											65	68	67					10																	94368819		2202	4298	6500	94358799	SO:0001583	missense	3832			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.430T>A	10.37:g.94368819T>A	ENSP00000260731:p.Phe144Ile		94358799	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	37	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	T	32	5.182154	0.94885	.	.	ENSG00000138160	ENST00000260731	D	0.84370	-1.84	5.54	5.54	0.83059	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.94288	0.8165	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95510	0.8585	10	0.72032	D	0.01	.	15.8422	0.78857	0.0:0.0:0.0:1.0	.	144	P52732	KIF11_HUMAN	I	144	ENSP00000260731:F144I	ENSP00000260731:F144I	F	+	1	0	KIF11	94358799	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.820000	0.86633	2.323000	0.78572	0.528000	0.53228	TTT		0.338	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		A	94368819	T	A	94368819	3	1	61	1	0	0	0	0	1	0	0	0	8293	1841	64	5	448	5	KIF11	10	94368819	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	71606	94368819	41165928	6897	14882										
HHEX	3087	broad.mit.edu	37	chr10	94454504	94454504	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggacattgagggcgataaAagctattttaatgctggatg	13	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94454504A>C	ENST00000282728.5	+	4	2591	c.792A>C	c.(790-792)aaA>aaC	p.K264N	HHEX_ENST00000472590.2_Missense_Mutation_p.K92N|HHEX_ENST00000492654.2_Missense_Mutation_p.K92N	NM_002729.4	NP_002720.1	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	264					anterior/posterior pattern specification (GO:0009952)|B cell differentiation (GO:0030183)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|DNA conformation change (GO:0071103)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|forebrain morphogenesis (GO:0048853)|gall bladder development (GO:0061010)|hepatic duct development (GO:0061011)|hepatoblast differentiation (GO:0061017)|hepatocyte differentiation (GO:0070365)|in utero embryonic development (GO:0001701)|interkinetic nuclear migration (GO:0022027)|mRNA export from nucleus (GO:0006406)|multicellular organism growth (GO:0035264)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|pancreas development (GO:0031016)|poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|primary lung bud formation (GO:0060431)|primitive streak formation (GO:0090009)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|eukaryotic initiation factor 4E binding (GO:0008190)|protein homodimerization activity (GO:0042803)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K264N(1)		kidney(2)|large_intestine(2)|lung(5)|ovary(1)	10						AGGGCGATAAAAGCTATTTTA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	67	67					10																	94454504		2203	4300	6503	94444484	SO:0001583	missense	3087			Z21533	CCDS7423.1	10q23.33	2011-06-20	2007-02-15		ENSG00000152804	ENSG00000152804		"Homeoboxes / ANTP class : NKL subclass"	4901	protein-coding gene	gene with protein product		604420		PRHX		8096636, 8103988	Standard	NM_002729		Approved	HEX, HOX11L-PEN	uc001kid.3	Q03014	OTTHUMG00000018762	ENST00000282728.5:c.792A>C	10.37:g.94454504A>C	ENSP00000282728:p.Lys264Asn		94444484	B1AQ17|Q96CE9	Missense_Mutation	SNP	ENST00000282728.5	37	CCDS7423.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914337	0.72983	.	.	ENSG00000152804	ENST00000282728;ENST00000472590;ENST00000492654	D;D;D	0.91521	-2.86;-1.82;-1.82	5.44	4.3	0.51218	.	0.055330	0.64402	D	0.000001	D	0.87884	0.6290	L	0.27053	0.805	0.39681	D	0.970906	D	0.58620	0.983	P	0.53401	0.725	D	0.87378	0.2355	10	0.51188	T	0.08	-6.3975	9.2257	0.37405	0.8552:0.0:0.1448:0.0	.	264	Q03014	HHEX_HUMAN	N	264;92;92	ENSP00000282728:K264N;ENSP00000450017:K92N;ENSP00000447953:K92N	ENSP00000282728:K264N	K	+	3	2	HHEX	94444484	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.231000	0.43009	1.080000	0.41073	0.533000	0.62120	AAA		0.428	HHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049402.2			C	94454504	A	C	94454504	3	2	61	1	0	0	0	0	1	0	0	0	7112	11	1	4	806	4	HHEX	10	94454504	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	85685	94454504	41080243	6898	14883										
CYP26A1	1592	broad.mit.edu	37	chr10	94837058	94837058	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccatttccatggggaaatCtgatgagcttgaatgttcaa	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:94837058C>A	ENST00000224356.4	+	7	1536	c.1491C>A	c.(1489-1491)atC>atA	p.I497I	CYP26A1_ENST00000371531.1_Silent_p.I428I|CYP26A1_ENST00000394139.1_Silent_p.I428I	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	497					anterior/posterior pattern specification (GO:0009952)|cellular response to retinoic acid (GO:0071300)|central nervous system development (GO:0007417)|metabolic process (GO:0008152)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)	p.I428I(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Colorectal(252;0.122)			Acitretin(DB00459)|Ketoconazole(DB01026)|Vitamin A(DB00162)	ATGGGGAAATCTGATGAGCTT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	10											33	35	34					10																	94837058		2173	4289	6462	94827048	SO:0001819	synonymous_variant	1592			AF005418	CCDS7426.1, CCDS7427.1	10q23-q24	2003-10-06	2003-01-14		ENSG00000095596	ENSG00000095596		"Cytochrome P450s"	2603	protein-coding gene	gene with protein product		602239	"cytochrome P450, subfamily XXVIA, polypeptide 1"			9228017, 9521883	Standard	NM_000783		Approved	P450RAI, CP26, CYP26, P450RAI1	uc001kil.2	O43174	OTTHUMG00000018765	ENST00000224356.4:c.1491C>A	10.37:g.94837058C>A			94827048	B3KNI4|Q5VXH9|Q5VXI0	Silent	SNP	ENST00000224356.4	37	CCDS7426.1																																																																																				0.388	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3			A	94837058	C	A	94837058	2	1	61	1	0	0	0	0	0	0	0	1	4161	903	32	2		2	CYP26A1	10	94837058	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382554	94837058	40697689	6899	14884										
MYOF	26509	broad.mit.edu	37	chr10	95095718	95095718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatcttcattttcatccGacttgcctcggtacaacttg	7	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95095718G>A	ENST00000359263.4	-	41	4522	c.4523C>T	c.(4522-4524)tCg>tTg	p.S1508L	MYOF_ENST00000371502.4_Missense_Mutation_p.S1527L|MYOF_ENST00000371501.4_Missense_Mutation_p.S1508L|MYOF_ENST00000358334.5_Missense_Mutation_p.S1495L	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1508					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)	p.S1508L(1)		NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATTTTCATCCGACTTGCCTCG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											214	196	202					10																	95095718		1894	4112	6006	95085708	SO:0001583	missense	26509			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4523C>T	10.37:g.95095718G>A	ENSP00000352208:p.Ser1508Leu		95085708	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.181987	0.38511	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.91	5.91	0.95273	.	0.349620	0.31673	N	0.007259	T	0.76586	0.4008	L	0.38953	1.18	0.39632	D	0.970183	B;P	0.37612	0.056;0.602	B;B	0.27796	0.04;0.083	T	0.79257	-0.1878	10	0.66056	D	0.02	-7.7564	20.2946	0.98546	0.0:0.0:1.0:0.0	.	1495;1508	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	L	1495;1508;1508;1527	ENSP00000351094:S1495L;ENSP00000352208:S1508L;ENSP00000360556:S1508L;ENSP00000360557:S1527L	ENSP00000351094:S1495L	S	-	2	0	MYOF	95085708	0.993000	0.37304	0.991000	0.47740	0.082000	0.17680	2.826000	0.48104	2.804000	0.96469	0.462000	0.41574	TCG		0.403	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95095718	G	A	95095718	3	1	61	1	0	0	0	0	1	0	0	0	10119	1059	37	1	1718	1	MYOF	10	95095718	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	258660	95095718	40439029	6900	14885										
MYOF	26509	broad.mit.edu	37	chr10	95119674	95119674	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatgagtgtggtacattttCtctgctgcaacccaggattt	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95119674C>A	ENST00000359263.4	-	29	3035	c.3036G>T	c.(3034-3036)gaG>gaT	p.E1012D	MYOF_ENST00000371502.4_Missense_Mutation_p.E1012D|MYOF_ENST00000371501.4_Missense_Mutation_p.E1012D|MYOF_ENST00000358334.5_Missense_Mutation_p.E999D	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1012					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)	p.E1012D(1)		NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GGTACATTTTCTCTGCTGCAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	10											198	188	191					10																	95119674		1948	4153	6101	95109664	SO:0001583	missense	26509			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3036G>T	10.37:g.95119674C>A	ENSP00000352208:p.Glu1012Asp		95109664	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334365	0.81801	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.85258	-1.96;-1.95;-1.95;-1.96	5.36	3.38	0.38709	Ferlin/Peroxisome membrane (1);	0.000000	0.85682	D	0.000000	D	0.91616	0.7351	M	0.86268	2.805	0.80722	D	1	D;D	0.62365	0.991;0.987	D;D	0.77004	0.989;0.979	D	0.91061	0.4885	10	0.87932	D	0	-26.9108	9.405	0.38455	0.0:0.7698:0.0:0.2302	.	999;1012	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	D	999;1012;1012;1012	ENSP00000351094:E999D;ENSP00000352208:E1012D;ENSP00000360556:E1012D;ENSP00000360557:E1012D	ENSP00000351094:E999D	E	-	3	2	MYOF	95109664	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.613000	0.36900	0.726000	0.32339	0.561000	0.74099	GAG		0.483	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95119674	C	A	95119674	3	1	61	1	0	0	0	0	1	0	0	0	10119	912	32	2	3253	2	MYOF	10	95119674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23956	95119674	40415073	6901	14886										
CEP55	55165	broad.mit.edu	37	chr10	95262902	95262902	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaggctgagaaggagaaGaatgcttatcaactcacaga	11	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95262902G>T	ENST00000371485.3	+	3	520	c.216G>T	c.(214-216)aaG>aaT	p.K72N		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	72					establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)		p.K72N(1)		kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				AGAAGGAGAAGAATGCTTATC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	10											90	84	86					10																	95262902		2203	4300	6503	95252892	SO:0001583	missense	55165			AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.216G>T	10.37:g.95262902G>T	ENSP00000360540:p.Lys72Asn		95252892	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.277867	0.59758	.	.	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.21191	2.02	5.28	2.43	0.29744	.	0.050963	0.85682	D	0.000000	T	0.37865	0.1019	M	0.64997	1.995	0.39687	D	0.970994	D	0.89917	1.0	D	0.83275	0.996	T	0.10291	-1.0636	10	0.56958	D	0.05	-21.9216	7.5283	0.27668	0.3901:0.0:0.6099:0.0	.	72	Q53EZ4	CEP55_HUMAN	N	72	ENSP00000360540:K72N	ENSP00000351102:K72N	K	+	3	2	CEP55	95252892	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	0.931000	0.28871	0.316000	0.23135	0.591000	0.81541	AAG		0.393	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		T	95262902	G	T	95262902	3	4	61	1	0	0	0	0	1	0	0	0	3261	933	33	2	222	2	CEP55	10	95262902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143228	95262902	40271845	6902	14887										
CEP55	55165	broad.mit.edu	37	chr10	95279477	95279477	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactttgaaaatgaaaaactCgaccgtcaacatgtgcagca	8	9	1	2	rs370915787		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95279477C>T	ENST00000371485.3	+	8	1408	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	CEP55_ENST00000496302.1_3'UTR	NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	368	Required for localization to the interphase centrosome and to the midbody during cytokinesis.				establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)		p.L368L(1)		kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				ATGAAAAACTCGACCGTCAAC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10						C	,	1,4405	2.1+/-5.4	0,1,2202	115	100	105		1104,1104	2.1	1	10		105	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CEP55	NM_001127182.1,NM_018131.4	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	368/465,368/465	95279477	1,13005	2203	4300	6503	95269467	SO:0001819	synonymous_variant	55165			AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.1104C>T	10.37:g.95279477C>T			95269467	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	37	CCDS7428.1																																																																																				0.413	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		T	95279477	C	T	95279477	2	4	61	1	0	0	0	0	0	0	0	1	3261	871	31	1		1	CEP55	10	95279477	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16575	95279477	40255270	6903	14888										
PDE6C	5146	broad.mit.edu	37	chr10	95399866	95399866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgctcagcagaactgtacGaattccgcttcagtgacttc	8	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95399866G>A	ENST00000371447.3	+	12	1660	c.1522G>A	c.(1522-1524)Gaa>Aaa	p.E508K		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	508					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.E508K(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	AGAACTGTACGAATTCCGCTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											130	113	119					10																	95399866		2203	4300	6503	95389856	SO:0001583	missense	5146			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"Phosphodiesterases"	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1522G>A	10.37:g.95399866G>A	ENSP00000360502:p.Glu508Lys		95389856	A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363956	0.41902	.	.	ENSG00000095464	ENST00000371447	T	0.77620	-1.11	4.99	4.99	0.66335	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.337819	0.33691	N	0.004643	T	0.79598	0.4473	M	0.74389	2.26	0.53688	D	0.999977	D	0.58970	0.984	B	0.44044	0.439	T	0.80226	-0.1470	10	0.33141	T	0.24	.	18.4657	0.90753	0.0:0.0:1.0:0.0	.	508	P51160	PDE6C_HUMAN	K	508	ENSP00000360502:E508K	ENSP00000360502:E508K	E	+	1	0	PDE6C	95389856	1.000000	0.71417	0.990000	0.47175	0.362000	0.29581	3.339000	0.52135	2.595000	0.87683	0.563000	0.77884	GAA		0.423	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		A	95399866	G	A	95399866	3	1	61	1	0	0	0	0	1	0	0	0	11678	1059	37	1	1568	1	PDE6C	10	95399866	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120389	95399866	40134881	6904	14889										
PDE6C	5146	broad.mit.edu	37	chr10	95399952	95399952	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaaataaatgtggtggaGaaattcaaagtacctgtaga	10	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95399952G>T	ENST00000371447.3	+	12	1746	c.1608G>T	c.(1606-1608)gaG>gaT	p.E536D		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	536					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.E536D(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ATGTGGTGGAGAAATTCAAAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											101	103	102					10																	95399952		2203	4300	6503	95389942	SO:0001583	missense	5146			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"Phosphodiesterases"	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1608G>T	10.37:g.95399952G>T	ENSP00000360502:p.Glu536Asp		95389942	A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	G	8.816	0.936419	0.18206	.	.	ENSG00000095464	ENST00000371447	T	0.77098	-1.07	4.99	2.98	0.34508	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.097400	0.64402	D	0.000001	T	0.58878	0.2153	L	0.34521	1.04	0.45704	D	0.998617	B	0.26318	0.146	B	0.21708	0.036	T	0.49051	-0.8979	10	0.18710	T	0.47	.	2.9809	0.05953	0.2982:0.2369:0.4648:0.0	.	536	P51160	PDE6C_HUMAN	D	536	ENSP00000360502:E536D	ENSP00000360502:E536D	E	+	3	2	PDE6C	95389942	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.559000	0.36320	1.325000	0.45301	0.563000	0.77884	GAG		0.398	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		T	95399952	G	T	95399952	3	4	61	1	0	0	0	0	1	0	0	0	11678	933	33	2	1654	2	PDE6C	10	95399952	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86	95399952	40134795	6905	14890										
FRA10AC1	118924	broad.mit.edu	37	chr10	95451832	95451832	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatttatcatagtatttCttagcaagtctcttctccct	3	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95451832C>A	ENST00000359204.4	-	7	596	c.399G>T	c.(397-399)aaG>aaT	p.K133N	FRA10AC1_ENST00000536233.1_Missense_Mutation_p.K133N|FRA10AC1_ENST00000371430.2_Missense_Mutation_p.K133N|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.K133N	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	133	Lys-rich.					nucleus (GO:0005634)		p.K133N(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						CATAGTATTTCTTAGCAAGTC	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	10											39	43	42					10																	95451832		2188	4274	6462	95441822	SO:0001583	missense	118924			AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"chromosome 10 open reading frame 4"	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.399G>T	10.37:g.95451832C>A	ENSP00000360488:p.Lys133Asn		95441822	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.616941	0.66672	.	.	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.28666	1.61;1.64;1.6;1.61	5.49	3.65	0.41850	.	0.088857	0.85682	D	0.000000	T	0.55417	0.1919	M	0.89968	3.075	0.53688	D	0.999977	D;D	0.54207	0.962;0.965	P;P	0.57620	0.558;0.824	T	0.62900	-0.6756	10	0.72032	D	0.01	-25.3316	11.5829	0.50902	0.0:0.8561:0.0:0.1439	.	133;133	Q70Z53-2;Q70Z53	.;F10C1_HUMAN	N	133	ENSP00000360488:K133N;ENSP00000438405:K133N;ENSP00000360484:K133N;ENSP00000377660:K133N	ENSP00000360488:K133N	K	-	3	2	FRA10AC1	95441822	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.386000	0.44380	0.684000	0.31448	0.585000	0.79938	AAG		0.299	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246		A	95451832	C	A	95451832	3	1	61	1	0	0	0	0	1	0	0	0	6060	912	32	2	580	2	FRA10AC1	10	95451832	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51880	95451832	40082915	6906	14891										
FRA10AC1	118924	broad.mit.edu	37	chr10	95452437	95452437	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtcctcctcattccataGgaatctatgattttctcgta	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95452437G>T	ENST00000359204.4	-	6	543	c.346C>A	c.(346-348)Cta>Ata	p.L116I	FRA10AC1_ENST00000536233.1_Missense_Mutation_p.L116I|FRA10AC1_ENST00000371430.2_Missense_Mutation_p.L116I|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.L116I	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	116						nucleus (GO:0005634)		p.L116I(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						TCATTCCATAGGAATCTATGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											170	142	151					10																	95452437		2203	4300	6503	95442427	SO:0001583	missense	118924			AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"chromosome 10 open reading frame 4"	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.346C>A	10.37:g.95452437G>T	ENSP00000360488:p.Leu116Ile		95442427	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.512193	0.64522	.	.	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.28069	1.63;1.79;1.7;1.74	5.26	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	L	0.28192	0.835	0.54753	D	0.999986	D;D;D	0.69078	0.996;0.996;0.997	D;D;D	0.71656	0.933;0.933;0.974	T	0.09773	-1.0659	10	0.27082	T	0.32	-19.0203	13.6926	0.62556	0.0744:0.0:0.9256:0.0	.	116;116;116	F8WCS9;Q70Z53-2;Q70Z53	.;.;F10C1_HUMAN	I	116	ENSP00000360488:L116I;ENSP00000438405:L116I;ENSP00000360484:L116I;ENSP00000377660:L116I	ENSP00000360488:L116I	L	-	1	2	FRA10AC1	95442427	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.402000	0.59722	1.223000	0.43536	0.585000	0.79938	CTA		0.363	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246		T	95452437	G	T	95452437	3	4	61	1	0	0	0	0	1	0	0	0	6060	991	35	2	637	2	FRA10AC1	10	95452437	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	605	95452437	40082310	6907	14892										
LGI1	9211	broad.mit.edu	37	chr10	95557484	95557484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatgtgtccattaataagcGtaattttctttttgcttcca	5	8	1	0	rs543647504		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:95557484G>A	ENST00000371418.4	+	8	1858	c.1598G>A	c.(1597-1599)cGt>cAt	p.R533H	LGI1_ENST00000371413.3_Intron|LGI1_ENST00000542308.1_Missense_Mutation_p.R485H	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	533					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)	p.R533H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ATTAATAAGCGTAATTTTCTT	0.368													G|||	1	0.000199681	8e-04	0	5008	,	,		21476	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											70	72	71					10																	95557484		2203	4298	6501	95547474	SO:0001583	missense	9211			AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"epilepsy, partial"	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.1598G>A	10.37:g.95557484G>A	ENSP00000360472:p.Arg533His		95547474	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Missense_Mutation	SNP	ENST00000371418.4	37	CCDS7431.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060609	0.36373	.	.	ENSG00000108231	ENST00000542308;ENST00000371418	T;T	0.81163	-1.46;-1.46	5.65	4.68	0.58851	.	0.118960	0.64402	D	0.000007	T	0.81640	0.4865	M	0.77820	2.39	0.58432	D	0.999996	B;B	0.20671	0.002;0.047	B;B	0.30495	0.004;0.116	T	0.80299	-0.1441	10	0.66056	D	0.02	-8.3878	12.548	0.56212	0.1258:0.0:0.8742:0.0	.	485;533	O95970-3;O95970	.;LGI1_HUMAN	H	485;533	ENSP00000440763:R485H;ENSP00000360472:R533H	ENSP00000360472:R533H	R	+	2	0	LGI1	95547474	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.141000	0.64814	2.941000	0.99782	0.655000	0.94253	CGT		0.368	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		A	95557484	G	A	95557484	3	1	61	1	0	0	0	0	1	0	0	0	8774	1145	40	1	1628	1	LGI1	10	95557484	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105047	95557484	39977263	6908	14893										
PLCE1	51196	broad.mit.edu	37	chr10	96064313	96064313	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtattgaaacctccagttCtgtgggacaagaactgcccc	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96064313C>A	ENST00000371380.3	+	24	5768	c.5533C>A	c.(5533-5535)Ctg>Atg	p.L1845M	PLCE1_ENST00000371385.3_Missense_Mutation_p.L1537M|PLCE1_ENST00000260766.3_Missense_Mutation_p.L1845M|PLCE1_ENST00000371375.1_Missense_Mutation_p.L1537M			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1845	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)	p.L1845M(1)		liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				ACCTCCAGTTCTGTGGGACAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											201	182	188					10																	96064313		1897	4116	6013	96054303	SO:0001583	missense	51196				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.5533C>A	10.37:g.96064313C>A	ENSP00000360431:p.Leu1845Met		96054303	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.186200	0.57909	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.60040	0.22;0.22;0.22;0.22	5.8	4.9	0.64082	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.64402	D	0.000001	T	0.59756	0.2217	N	0.21194	0.64	0.45822	D	0.998698	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.77004	0.98;0.95;0.989	T	0.55724	-0.8096	10	0.21540	T	0.41	.	11.6634	0.51361	0.0:0.8564:0.0:0.1436	.	1829;1537;1845	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	M	1845;1845;1537;1537	ENSP00000260766:L1845M;ENSP00000360431:L1845M;ENSP00000360438:L1537M;ENSP00000360426:L1537M	ENSP00000260766:L1845M	L	+	1	2	PLCE1	96054303	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.732000	0.38146	1.475000	0.48197	-0.258000	0.10820	CTG		0.413	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		A	96064313	C	A	96064313	3	1	61	1	0	0	0	0	1	0	0	0	12065	912	32	2	5913	2	PLCE1	10	96064313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	506829	96064313	39470434	6909	14894										
PLCE1	51196	broad.mit.edu	37	chr10	96064395	96064395	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggatcctgcagtctattCtttaactgtaagtacggccc	8	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96064395C>A	ENST00000371380.3	+	24	5850	c.5615C>A	c.(5614-5616)tCt>tAt	p.S1872Y	PLCE1_ENST00000371385.3_Missense_Mutation_p.S1564Y|PLCE1_ENST00000260766.3_Missense_Mutation_p.S1872Y|PLCE1_ENST00000371375.1_Missense_Mutation_p.S1564Y			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1872	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)	p.S1872Y(1)		liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GCAGTCTATTCTTTAACTGTA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											89	82	84					10																	96064395		1860	4100	5960	96054385	SO:0001583	missense	51196				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.5615C>A	10.37:g.96064395C>A	ENSP00000360431:p.Ser1872Tyr		96054385	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110082	0.77210	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.28255	1.62;1.62;1.63;1.63	5.39	5.39	0.77823	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.057945	0.64402	D	0.000001	T	0.53449	0.1797	M	0.70108	2.13	0.45822	D	0.998691	D;D;D	0.58970	0.966;0.957;0.984	P;P;P	0.59761	0.848;0.792;0.863	T	0.56565	-0.7958	10	0.72032	D	0.01	.	18.7705	0.91890	0.0:1.0:0.0:0.0	.	1856;1564;1872	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	Y	1872;1872;1564;1564	ENSP00000260766:S1872Y;ENSP00000360431:S1872Y;ENSP00000360438:S1564Y;ENSP00000360426:S1564Y	ENSP00000260766:S1872Y	S	+	2	0	PLCE1	96054385	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	5.839000	0.69395	2.521000	0.84997	0.561000	0.74099	TCT		0.438	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		A	96064395	C	A	96064395	3	1	61	1	0	0	0	0	1	0	0	0	12065	913	32	2	5995	2	PLCE1	10	96064395	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82	96064395	39470352	6910	14895										
NOC3L	64318	broad.mit.edu	37	chr10	96109974	96109974	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacacaagctcttcacagCgacttctgccagtcctttgt	6	15	4	0	rs142493625		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96109974C>T	ENST00000371361.3	-	9	1124	c.1024G>A	c.(1024-1026)Gct>Act	p.A342T	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.A342T|NOC3L_ENST00000543788.1_Missense_Mutation_p.A80T	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	342					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.A342T(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CTCTTCACAGCGACTTCTGCC	0.388													C|||	1	0.000199681	8e-04	0	5008	,	,		18872	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						C	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	282	255	264		1024	5.8	1	10	dbSNP_134	264	0,8600		0,0,4300	no	missense	NOC3L	NM_022451.9	58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	342/801	96109974	3,13003	2203	4300	6503	96099964	SO:0001583	missense	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1024G>A	10.37:g.96109974C>T	ENSP00000360412:p.Ala342Thr		96099964	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	36	5.882502	0.97062	6.81E-4	0.0	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.72942	-0.7;1.29;1.29	5.79	5.79	0.91817	Armadillo-like helical (1);	0.097026	0.64402	D	0.000001	D	0.87489	0.6190	M	0.89095	3.005	0.58432	D	0.999998	D	0.89917	1.0	D	0.77004	0.989	D	0.88841	0.3312	10	0.87932	D	0	-4.3644	20.0987	0.97860	0.0:1.0:0.0:0.0	.	342	Q8WTT2	NOC3L_HUMAN	T	80;342;342	ENSP00000437838:A80T;ENSP00000360412:A342T;ENSP00000360401:A342T	ENSP00000360401:A342T	A	-	1	0	NOC3L	96099964	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.608000	0.61141	2.771000	0.95319	0.644000	0.83932	GCT		0.388	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		T	96109974	C	T	96109974	3	4	61	1	0	0	0	0	1	0	0	0	10545	768	27	1	1430	1	NOC3L	10	96109974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45579	96109974	39424773	6911	14896										
NOC3L	64318	broad.mit.edu	37	chr10	96112665	96112665	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcattaccttagtagatttTtctgcttctgtgaggggccg	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96112665T>G	ENST00000371361.3	-	7	946	c.846A>C	c.(844-846)gaA>gaC	p.E282D	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.E282D|NOC3L_ENST00000543788.1_Missense_Mutation_p.E20D	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	282					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E282D(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				TAGTAGATTTTTCTGCTTCTG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	10											75	78	77					10																	96112665		2203	4300	6503	96102655	SO:0001583	missense	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.846A>C	10.37:g.96112665T>G	ENSP00000360412:p.Glu282Asp		96102655	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.679455	0.68042	.	.	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.21191	2.02;2.18;2.18	4.88	1.25	0.21368	Nucleolar complex-associated (1);	0.000000	0.85682	D	0.000000	T	0.40743	0.1129	M	0.74647	2.275	0.40396	D	0.979592	D	0.89917	1.0	D	0.87578	0.998	T	0.12218	-1.0556	10	0.51188	T	0.08	-3.5886	8.5986	0.33732	0.0:0.2222:0.0:0.7778	.	282	Q8WTT2	NOC3L_HUMAN	D	20;282;282	ENSP00000437838:E20D;ENSP00000360412:E282D;ENSP00000360401:E282D	ENSP00000360401:E282D	E	-	3	2	NOC3L	96102655	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	1.981000	0.40628	-0.034000	0.13713	0.477000	0.44152	GAA		0.323	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		G	96112665	T	G	96112665	3	3	61	1	0	0	0	0	1	0	0	0	10545	1838	64	4	1616	4	NOC3L	10	96112665	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2691	96112665	39422082	6912	14897										
NOC3L	64318	broad.mit.edu	37	chr10	96112799	96112799	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaacatagaacgtaattCtttcaattttttaatctgtt	3	7	4	1	rs150224263		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96112799C>A	ENST00000371361.3	-	7	812	c.712G>T	c.(712-714)Gaa>Taa	p.E238*	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Nonsense_Mutation_p.E238*|NOC3L_ENST00000543788.1_5'Flank	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	238					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E238*(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				GAACGTAATTCTTTCAATTTT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											73	78	76					10																	96112799		2203	4300	6503	96102789	SO:0001587	stop_gained	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.712G>T	10.37:g.96112799C>A	ENSP00000360412:p.Glu238*		96102789	Q9H5M6|Q9H9D8	Nonsense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	C	39	7.432390	0.98279	.	.	ENSG00000173145	ENST00000371361;ENST00000371350	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-7.8002	18.5161	0.90936	0.0:1.0:0.0:0.0	.	.	.	.	X	238	.	ENSP00000360401:E238X	E	-	1	0	NOC3L	96102789	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	2.359000	0.80004	0.591000	0.81541	GAA		0.348	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		A	96112799	C	A	96112799	4	1	61	1	0	0	0	0	0	1	0	0	10545	922	32	2	1750	2	NOC3L	10	96112799	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	134	96112799	39421948	6913	14898										
NOC3L	64318	broad.mit.edu	37	chr10	96114789	96114789	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcttctcctgtaatttCttctttctctcaatcaaatg	2	11	8	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96114789C>A	ENST00000371361.3	-	6	727	c.627G>T	c.(625-627)aaG>aaT	p.K209N	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.K209N|NOC3L_ENST00000543788.1_5'Flank	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	209					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.K209N(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CCTGTAATTTCTTCTTTCTCT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											181	183	182					10																	96114789		2202	4298	6500	96104779	SO:0001583	missense	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.627G>T	10.37:g.96114789C>A	ENSP00000360412:p.Lys209Asn		96104779	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777307	0.31411	.	.	ENSG00000173145	ENST00000371361;ENST00000371350	T;T	0.12147	2.72;2.71	5.86	2.4	0.29515	.	0.753413	0.13205	N	0.405624	T	0.08403	0.0209	N	0.19112	0.55	0.35928	D	0.83229	B	0.22604	0.072	B	0.21546	0.035	T	0.23511	-1.0186	10	0.35671	T	0.21	-6.8069	6.0666	0.19866	0.0:0.5471:0.1213:0.3316	.	209	Q8WTT2	NOC3L_HUMAN	N	209	ENSP00000360412:K209N;ENSP00000360401:K209N	ENSP00000360401:K209N	K	-	3	2	NOC3L	96104779	0.517000	0.26226	0.999000	0.59377	0.939000	0.58152	0.283000	0.18846	0.173000	0.19788	0.650000	0.86243	AAG		0.353	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		A	96114789	C	A	96114789	3	1	61	1	0	0	0	0	1	0	0	0	10545	912	32	2	1839	2	NOC3L	10	96114789	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1990	96114789	39419958	6914	14899										
NOC3L	64318	broad.mit.edu	37	chr10	96117871	96117871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcttgttagaaaagataCtctttgtcctaaatccttca	4	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96117871C>A	ENST00000371361.3	-	3	419	c.319G>T	c.(319-321)Gta>Tta	p.V107L	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.V107L	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	107					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.V107L(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				AGAAAAGATACTCTTTGTCCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											133	128	130					10																	96117871		2203	4300	6503	96107861	SO:0001583	missense	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.319G>T	10.37:g.96117871C>A	ENSP00000360412:p.Val107Leu		96107861	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411045	0.42817	.	.	ENSG00000173145	ENST00000371361;ENST00000371350	T;T	0.10960	2.82;2.82	5.7	2.21	0.28008	.	0.213327	0.47455	D	0.000235	T	0.05090	0.0136	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.08055	0.003	T	0.39099	-0.9630	10	0.27785	T	0.31	-14.1443	9.8624	0.41123	0.0:0.6577:0.2455:0.0968	.	107	Q8WTT2	NOC3L_HUMAN	L	107	ENSP00000360412:V107L;ENSP00000360401:V107L	ENSP00000360401:V107L	V	-	1	0	NOC3L	96107861	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.043000	0.41231	1.404000	0.46819	-0.156000	0.13503	GTA		0.328	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		A	96117871	C	A	96117871	3	1	61	1	0	0	0	0	1	0	0	0	10545	565	20	2	2159	2	NOC3L	10	96117871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3082	96117871	39416876	6915	14900										
HELLS	3070	broad.mit.edu	37	chr10	96336549	96336549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaatagccatgagagaccGaaatgcgttacaggtacaaa	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96336549G>A	ENST00000348459.5	+	10	1124	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q	RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000394045.1_Missense_Mutation_p.R340Q|HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000371332.4_Missense_Mutation_p.R340Q|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000394044.1_Intron	NM_018063.3	NP_060533.2			helicase, lymphoid-specific									p.R340Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		ATGAGAGACCGAAATGCGTTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	10											133	122	126					10																	96336549		2203	4300	6503	96326539	SO:0001583	missense	3070			AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1019G>A	10.37:g.96336549G>A	ENSP00000239027:p.Arg340Gln		96326539		Missense_Mutation	SNP	ENST00000348459.5	37	CCDS7434.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.225940	0.58668	.	.	ENSG00000119969	ENST00000348459;ENST00000394045;ENST00000371332	D;D;D	0.93366	-3.21;-3.21;-3.21	4.91	4.01	0.46588	DEAD-like helicase (2);SNF2-related (1);	0.053592	0.64402	N	0.000001	D	0.86213	0.5879	L	0.33792	1.035	0.80722	D	1	B;B;P;B	0.44429	0.005;0.014;0.835;0.051	B;B;B;B	0.31390	0.02;0.025;0.129;0.058	D	0.84690	0.0722	10	0.42905	T	0.14	-2.3548	11.9753	0.53087	0.0847:0.0:0.9153:0.0	.	324;340;340;340	Q9NRZ9-2;Q6I7N8;Q9NRZ9-5;Q9NRZ9	.;.;.;HELLS_HUMAN	Q	340	ENSP00000239027:R340Q;ENSP00000377609:R340Q;ENSP00000360383:R340Q	ENSP00000239027:R340Q	R	+	2	0	HELLS	96326539	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.303000	0.72794	1.047000	0.40274	0.655000	0.94253	CGA		0.358	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		A	96336549	G	A	96336549	3	1	61	1	0	0	0	0	1	0	0	0	7067	1058	37	1	1057	1	HELLS	10	96336549	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218678	96336549	39198198	6916	14901										
CYP2C18	1562	broad.mit.edu	37	chr10	96466569	96466569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttccctgctctcatcgAttatctcccaggaagtcata	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96466569A>G	ENST00000285979.6	+	5	870	c.671A>G	c.(670-672)gAt>gGt	p.D224G	CYP2C19_ENST00000464755.1_3'UTR|CYP2C18_ENST00000339022.5_Intron	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	224					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.D224G(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	GCTCTCATCGATTATCTCCCA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											40	42	41					10																	96466569		2202	4300	6502	96456559	SO:0001583	missense	1562			M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.671A>G	10.37:g.96466569A>G	ENSP00000285979:p.Asp224Gly		96456559	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Missense_Mutation	SNP	ENST00000285979.6	37	CCDS7435.1	.	.	.	.	.	.	.	.	.	.	a	12.89	2.072985	0.36566	.	.	ENSG00000108242	ENST00000285979	T	0.12255	2.7	3.8	2.65	0.31530	.	0.394239	0.24445	U	0.038463	T	0.12135	0.0295	L	0.48877	1.53	0.09310	N	0.999998	B	0.10296	0.003	B	0.17722	0.019	T	0.19484	-1.0304	10	0.49607	T	0.09	.	7.459	0.27283	0.8923:0.0:0.1077:0.0	.	224	P33260	CP2CI_HUMAN	G	224	ENSP00000285979:D224G	ENSP00000285979:D224G	D	+	2	0	CYP2C18	96456559	0.398000	0.25279	0.002000	0.10522	0.694000	0.40290	6.006000	0.70724	0.626000	0.30322	0.255000	0.18592	GAT		0.308	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		G	96466569	A	G	96466569	3	3	61	1	0	0	0	0	1	0	0	0	4171	333	12	4	689	4	CYP2C18	10	96466569	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	130020	96466569	39068178	6917	14902										
CYP2C9	1559	broad.mit.edu	37	chr10	96707608	96707608	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctccattattttccataAacgttttgattataaagatc	4	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96707608A>C	ENST00000260682.6	+	4	566	c.554A>C	c.(553-555)aAa>aCa	p.K185T		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	185					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)	p.K185T(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	ATTTTCCATAAACGTTTTGAT	0.378																																					Ovarian(54;1266 1406 16072 35076)											1	Substitution - Missense(1)	large_intestine(1)	10											124	123	123					10																	96707608		2203	4300	6503	96697598	SO:0001583	missense	1559			M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.554A>C	10.37:g.96707608A>C	ENSP00000260682:p.Lys185Thr		96697598	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	13.75	2.330283	0.41297	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.69561	-0.41	3.55	3.55	0.40652	.	0.381500	0.22217	U	0.063001	T	0.55878	0.1948	L	0.41356	1.27	0.28349	N	0.920987	B;B	0.15473	0.013;0.013	B;B	0.15484	0.013;0.013	T	0.56238	-0.8012	10	0.62326	D	0.03	.	10.3329	0.43833	1.0:0.0:0.0:0.0	.	185;185	Q5VX92;P11712	.;CP2C9_HUMAN	T	185	ENSP00000260682:K185T	ENSP00000260682:K185T	K	+	2	0	CYP2C9	96697598	0.528000	0.26314	0.747000	0.31113	0.890000	0.51754	5.844000	0.69430	1.590000	0.49995	0.402000	0.26972	AAA		0.378	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		C	96707608	A	C	96707608	3	2	61	1	0	0	0	0	1	0	0	0	4174	14	1	4	568	4	CYP2C9	10	96707608	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	241039	96707608	38827139	6918	14903										
CYP2C9	1559	broad.mit.edu	37	chr10	96748609	96748609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgctattttcaggaaaaCggatttgtgtgggagaagcc	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96748609C>T	ENST00000260682.6	+	9	1309	c.1297C>T	c.(1297-1299)Cgg>Tgg	p.R433W		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	433					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)	p.R433W(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TTCAGGAAAACGGATTTGTGT	0.438																																					Ovarian(54;1266 1406 16072 35076)											1	Substitution - Missense(1)	large_intestine(1)	10											134	123	127					10																	96748609		2203	4300	6503	96738599	SO:0001583	missense	1559			M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.1297C>T	10.37:g.96748609C>T	ENSP00000260682:p.Arg433Trp		96738599	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	13.02	2.111201	0.37242	.	.	ENSG00000138109	ENST00000260682	D	0.84873	-1.91	3.42	1.48	0.22813	Cytochrome P450, conserved site (1);	0.000000	0.64402	U	0.000004	D	0.93354	0.7881	H	0.97103	3.94	0.38906	D	0.957435	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	D	0.91946	0.5567	10	0.87932	D	0	.	7.7174	0.28712	0.0:0.7755:0.0:0.2245	.	433;433	Q5VX92;P11712	.;CP2C9_HUMAN	W	433	ENSP00000260682:R433W	ENSP00000260682:R433W	R	+	1	2	CYP2C9	96738599	1.000000	0.71417	0.783000	0.31826	0.481000	0.33189	1.239000	0.32719	0.254000	0.21573	-0.397000	0.06425	CGG		0.438	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		T	96748609	C	T	96748609	3	4	61	1	0	0	0	0	1	0	0	0	4174	527	19	1	1331	1	CYP2C9	10	96748609	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41001	96748609	38786138	6919	14904										
CYP2C9	1559	broad.mit.edu	37	chr10	96748674	96748674	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgacctccattttacaGaactttaacctgaaatctct	3	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96748674G>T	ENST00000260682.6	+	9	1374	c.1362G>T	c.(1360-1362)caG>caT	p.Q454H		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	454					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)	p.Q454H(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	CCATTTTACAGAACTTTAACC	0.473																																					Ovarian(54;1266 1406 16072 35076)											1	Substitution - Missense(1)	large_intestine(1)	10											153	146	148					10																	96748674		2203	4300	6503	96738664	SO:0001583	missense	1559			M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.1362G>T	10.37:g.96748674G>T	ENSP00000260682:p.Gln454His		96738664	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.895691	0.33442	.	.	ENSG00000138109	ENST00000260682	T	0.72167	-0.63	3.42	1.52	0.23074	.	0.082934	0.49916	U	0.000123	T	0.77922	0.4203	M	0.63843	1.955	0.36837	D	0.887193	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78267	-0.2270	10	0.87932	D	0	.	7.1037	0.25353	0.236:0.0:0.764:0.0	.	454;454	Q5VX92;P11712	.;CP2C9_HUMAN	H	454	ENSP00000260682:Q454H	ENSP00000260682:Q454H	Q	+	3	2	CYP2C9	96738664	1.000000	0.71417	0.917000	0.36280	0.120000	0.20174	2.079000	0.41577	0.273000	0.22049	0.453000	0.30009	CAG		0.473	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		T	96748674	G	T	96748674	3	4	61	1	0	0	0	0	1	0	0	0	4174	933	33	2	1396	2	CYP2C9	10	96748674	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65	96748674	38786073	6920	14905										
CYP2C8	1558	broad.mit.edu	37	chr10	96818118	96818118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttgatcaggaagcaatCgataaagtcccgaggattgt	10	7	1	1	rs551515028		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96818118C>T	ENST00000371270.3	-	5	887	c.793G>A	c.(793-795)Gat>Aat	p.D265N	CYP2C8_ENST00000535898.1_Missense_Mutation_p.D163N|CYP2C8_ENST00000539050.1_Missense_Mutation_p.D179N	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	265					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.D265N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	AGGAAGCAATCGATAAAGTCC	0.358													C|||	1	0.000199681	8e-04	0	5008	,	,		17713	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											175	155	162					10																	96818118		2203	4300	6503	96808108	SO:0001583	missense	1558			M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.793G>A	10.37:g.96818118C>T	ENSP00000360317:p.Asp265Asn		96808108	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.237271	0.58886	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.15834	2.39;2.39;2.39	4.17	4.17	0.49024	.	0.000000	0.85682	U	0.000000	T	0.52613	0.1745	H	0.94183	3.505	0.46336	D	0.998992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.991;0.996;0.995	T	0.68006	-0.5523	10	0.87932	D	0	.	14.2979	0.66327	0.0:1.0:0.0:0.0	.	179;163;233;265	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	N	265;232;163;179	ENSP00000360317:D265N;ENSP00000445062:D163N;ENSP00000442343:D179N	ENSP00000360317:D265N	D	-	1	0	CYP2C8	96808108	1.000000	0.71417	0.631000	0.29282	0.120000	0.20174	6.452000	0.73485	2.021000	0.59480	0.305000	0.20034	GAT		0.358	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		T	96818118	C	T	96818118	3	4	61	1	0	0	0	0	1	0	0	0	4173	884	31	1	699	1	CYP2C8	10	96818118	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69444	96818118	38716629	6921	14906										
CYP2C8	1558	broad.mit.edu	37	chr10	96824642	96824642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgatctttataatcaaatCgtttctggaaaacaacggag	7	7	4	1	rs543793530		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:96824642C>T	ENST00000371270.3	-	4	651	c.557G>A	c.(556-558)cGa>cAa	p.R186Q	CYP2C8_ENST00000535898.1_Missense_Mutation_p.R84Q|CYP2C8_ENST00000539050.1_Missense_Mutation_p.R100Q	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	186					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.R186Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	ATAATCAAATCGTTTCTGGAA	0.388													C|||	1	0.000199681	0	0	5008	,	,		13283	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	10											95	91	93					10																	96824642		2203	4300	6503	96814632	SO:0001583	missense	1558			M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.557G>A	10.37:g.96824642C>T	ENSP00000360317:p.Arg186Gln		96814632	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215885	0.79352	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.13901	2.55;2.55;2.55	4.45	2.54	0.30619	.	0.000000	0.64402	U	0.000001	T	0.40570	0.1122	M	0.92219	3.285	0.38487	D	0.947888	D;D;D;D	0.89917	0.997;0.997;1.0;0.997	P;P;D;P	0.70227	0.772;0.775;0.968;0.712	T	0.52215	-0.8605	10	0.87932	D	0	.	8.6143	0.33822	0.0:0.8202:0.0:0.1798	.	100;84;154;186	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	Q	186;153;84;100	ENSP00000360317:R186Q;ENSP00000445062:R84Q;ENSP00000442343:R100Q	ENSP00000360317:R186Q	R	-	2	0	CYP2C8	96814632	0.938000	0.31826	0.996000	0.52242	0.886000	0.51366	1.906000	0.39887	2.027000	0.59764	0.313000	0.20887	CGA		0.388	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		T	96824642	C	T	96824642	3	4	61	1	0	0	0	0	1	0	0	0	4173	884	31	1	939	1	CYP2C8	10	96824642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6524	96824642	38710105	6922	14907										
PDLIM1	9124	broad.mit.edu	37	chr10	97007027	97007027	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaagacgtggactgtttCgggggctcattcaactcctg	12	9	2	2	rs141682059		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97007027C>T	ENST00000329399.6	-	5	738	c.630G>A	c.(628-630)ccG>ccA	p.P210P	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	210					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.P210P(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TGGACTGTTTCGGGGGCTCAT	0.468													c|||	1	0.000199681	0	0	5008	,	,		20875	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10						T		1,4405	2.1+/-5.4	0,1,2202	119	112	115		630	-11.5	0	10	dbSNP_134	115	0,8600		0,0,4300	no	coding-synonymous	PDLIM1	NM_020992.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		210/330	97007027	1,13005	2203	4300	6503	96997017	SO:0001819	synonymous_variant	9124			U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"carboxyl terminal LIM domain protein 1", "elfin"	605900	"PDZ and LIM domain 1 (elfin)"	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.630G>A	10.37:g.97007027C>T			96997017	B2RBS6|Q5VZH5|Q9BPZ9	Silent	SNP	ENST00000329399.6	37	CCDS7441.1																																																																																				0.468	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1			T	97007027	C	T	97007027	2	4	61	1	0	0	0	0	0	0	0	1	11710	871	31	1		1	PDLIM1	10	97007027	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	182385	97007027	38527720	6923	14908										
SORBS1	10580	broad.mit.edu	37	chr10	97111111	97111111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttgctcgcgtttaagtCgtctctggtccgctaaaagt	9	11	2	0	rs202075782		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97111111C>T	ENST00000361941.3	-	23	2263	c.2237G>A	c.(2236-2238)cGa>cAa	p.R746Q	SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000347291.4_Missense_Mutation_p.R558Q|SORBS1_ENST00000353505.5_Missense_Mutation_p.R597Q|SORBS1_ENST00000277982.5_Missense_Mutation_p.R768Q|SORBS1_ENST00000371239.1_Missense_Mutation_p.R523Q|SORBS1_ENST00000371245.3_Missense_Mutation_p.R597Q|SORBS1_ENST00000354106.3_Missense_Mutation_p.R716Q|SORBS1_ENST00000371227.4_Missense_Mutation_p.R700Q|SORBS1_ENST00000371247.2_Missense_Mutation_p.R746Q|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Missense_Mutation_p.R1006Q|SORBS1_ENST00000393949.1_Missense_Mutation_p.R716Q|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000306402.6_Missense_Mutation_p.R493Q|SORBS1_ENST00000371246.2_Missense_Mutation_p.R768Q	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.R597Q(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCGTTTAAGTCGTCTCTGGTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	97	100					10																	97111111		2203	4300	6503	97101101	SO:0001583	missense	10580			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2237G>A	10.37:g.97111111C>T	ENSP00000355136:p.Arg746Gln		97101101		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	C	35	5.597758	0.96602	.	.	ENSG00000095637	ENST00000371245;ENST00000306402;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000347291;ENST00000361941;ENST00000277982;ENST00000354106;ENST00000371239	T;T;T;T;T;T;T;T;T;T;T;T	0.14766	3.17;2.58;2.68;2.69;3.06;2.64;3.17;2.48;2.68;3.06;2.64;2.51	5.99	5.99	0.97316	.	0.000000	0.32204	N	0.006427	T	0.37598	0.1009	L	0.58101	1.795	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;P;D;D;D;D;D;D;D;D;D	0.91635	0.996;0.711;0.998;0.996;0.993;0.999;0.984;0.996;0.998;0.998;0.927	T	0.00666	-1.1619	10	0.51188	T	0.08	-6.0066	20.4777	0.99188	0.0:1.0:0.0:0.0	.	814;461;700;493;523;597;746;768;558;716;240	B7Z9B7;B4DTX5;Q9BX66-11;Q9BX66-9;Q9BX66-8;Q9BX66-3;Q9BX66;Q9BX66-2;Q9BX66-6;Q9BX66-5;Q6MZY5	.;.;.;.;.;.;SRBS1_HUMAN;.;.;.;.	Q	597;493;746;700;768;716;597;558;746;768;716;523	ENSP00000360291:R597Q;ENSP00000302556:R493Q;ENSP00000360293:R746Q;ENSP00000360271:R700Q;ENSP00000360292:R768Q;ENSP00000377521:R716Q;ENSP00000343998:R597Q;ENSP00000277985:R558Q;ENSP00000355136:R746Q;ENSP00000277982:R768Q;ENSP00000277984:R716Q;ENSP00000360283:R523Q	ENSP00000277982:R768Q	R	-	2	0	SORBS1	97101101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.786000	0.85741	2.840000	0.97914	0.655000	0.94253	CGA		0.453	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			T	97111111	C	T	97111111	3	4	61	1	0	0	0	0	1	0	0	0	14964	884	31	1	1741	1	SORBS1	10	97111111	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104084	97111111	38423636	6924	14909										
SORBS1	10580	broad.mit.edu	37	chr10	97114661	97114661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttatcatcatgacgtcttCgaataaattcttccgtggat	6	9	4	1	rs370866519		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97114661C>T	ENST00000361941.3	-	22	2218	c.2192G>A	c.(2191-2193)cGa>cAa	p.R731Q	SORBS1_ENST00000371249.2_Missense_Mutation_p.R569Q|SORBS1_ENST00000347291.4_Missense_Mutation_p.R543Q|SORBS1_ENST00000353505.5_Missense_Mutation_p.R582Q|SORBS1_ENST00000277982.5_Missense_Mutation_p.R753Q|SORBS1_ENST00000371239.1_Missense_Mutation_p.R508Q|SORBS1_ENST00000371245.3_Missense_Mutation_p.R582Q|SORBS1_ENST00000354106.3_Missense_Mutation_p.R701Q|SORBS1_ENST00000371227.4_Missense_Mutation_p.R685Q|SORBS1_ENST00000371247.2_Missense_Mutation_p.R731Q|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Missense_Mutation_p.R991Q|SORBS1_ENST00000393949.1_Missense_Mutation_p.R701Q|SORBS1_ENST00000371241.1_Missense_Mutation_p.R437Q|SORBS1_ENST00000306402.6_Missense_Mutation_p.R478Q|SORBS1_ENST00000371246.2_Missense_Mutation_p.R753Q	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.R582Q(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		ATGACGTCTTCGAATAAATTC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4402		0,0,2201	113	115	114		2192,2258,1745,1310,1310,1706,1433	6.1	1	10		114	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	43,43,43,43,43,43,43	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	731/1293,753/1152,582/906,437/741,437/685,569/817,478/782	97114661	1,13001	2201	4300	6501	97104651	SO:0001583	missense	10580			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2192G>A	10.37:g.97114661C>T	ENSP00000355136:p.Arg731Gln		97104651		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	C	34	5.308406	0.95629	0.0	1.16E-4	ENSG00000095637	ENST00000371245;ENST00000306402;ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000347291;ENST00000361941;ENST00000277982;ENST00000371241;ENST00000354106;ENST00000371239	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.12039	3.35;2.77;2.87;2.89;2.89;3.27;2.86;3.35;2.72;2.89;3.27;2.79;2.86;2.74	6.06	6.06	0.98353	.	0.000000	0.34652	N	0.003800	T	0.34337	0.0894	L	0.59436	1.845	0.58432	D	0.999999	D;D;D;B;D;D;D;D;D;D;D;D;P	0.89917	1.0;0.999;1.0;0.406;1.0;0.993;1.0;1.0;0.991;0.997;1.0;0.995;0.647	D;D;D;B;D;P;D;D;P;D;D;P;B	0.91635	0.961;0.924;0.999;0.167;0.998;0.694;0.996;0.981;0.837;0.942;0.981;0.898;0.09	T	0.00630	-1.1636	10	0.66056	D	0.02	-6.9223	14.7322	0.69391	0.0:0.9314:0.0:0.0686	.	799;446;685;569;478;437;508;582;731;753;543;701;225	B7Z9B7;B4DTX5;Q9BX66-11;Q9BX66-10;Q9BX66-9;Q9BX66-4;Q9BX66-8;Q9BX66-3;Q9BX66;Q9BX66-2;Q9BX66-6;Q9BX66-5;Q6MZY5	.;.;.;.;.;.;.;.;SRBS1_HUMAN;.;.;.;.	Q	582;478;569;731;685;753;701;582;543;731;753;437;701;508	ENSP00000360291:R582Q;ENSP00000302556:R478Q;ENSP00000360295:R569Q;ENSP00000360293:R731Q;ENSP00000360271:R685Q;ENSP00000360292:R753Q;ENSP00000377521:R701Q;ENSP00000343998:R582Q;ENSP00000277985:R543Q;ENSP00000355136:R731Q;ENSP00000277982:R753Q;ENSP00000360285:R437Q;ENSP00000277984:R701Q;ENSP00000360283:R508Q	ENSP00000277982:R753Q	R	-	2	0	SORBS1	97104651	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	4.446000	0.60014	2.882000	0.98803	0.655000	0.94253	CGA		0.333	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			T	97114661	C	T	97114661	3	4	61	1	0	0	0	0	1	0	0	0	14964	884	31	1	1790	1	SORBS1	10	97114661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3550	97114661	38420086	6925	14910										
SORBS1	10580	broad.mit.edu	37	chr10	97135810	97135810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttctgggcttatatcccGactctataggggttggtgat	11	9	3	1	rs143262691		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97135810G>A	ENST00000361941.3	-	17	1683	c.1657C>T	c.(1657-1659)Cgg>Tgg	p.R553W	SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000347291.4_Missense_Mutation_p.R421W|SORBS1_ENST00000353505.5_Missense_Mutation_p.R438W|SORBS1_ENST00000277982.5_Missense_Mutation_p.R575W|SORBS1_ENST00000371239.1_Missense_Mutation_p.R352W|SORBS1_ENST00000371245.3_Missense_Mutation_p.R438W|SORBS1_ENST00000354106.3_Missense_Mutation_p.R523W|SORBS1_ENST00000371227.4_Missense_Mutation_p.R507W|SORBS1_ENST00000371247.2_Missense_Mutation_p.R553W|SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000607232.1_Missense_Mutation_p.R342W|SORBS1_ENST00000393949.1_Missense_Mutation_p.R523W|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371246.2_Missense_Mutation_p.R575W	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.R438W(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CTTATATCCCGACTCTATAGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	TRP/ARG,TRP/ARG,TRP/ARG,,,,	1,4403	2.1+/-5.4	0,1,2201	65	67	66		1657,1723,1312,,,,	5.8	1	10	dbSNP_134	66	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,intron,intron,intron,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	101,101,101,,,,	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging,,,,	553/1293,575/1152,438/906,,,,	97135810	2,13002	2202	4300	6502	97125800	SO:0001583	missense	10580			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1657C>T	10.37:g.97135810G>A	ENSP00000355136:p.Arg553Trp		97125800		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787090	0.70337	2.27E-4	1.16E-4	ENSG00000095637	ENST00000371245;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000347291;ENST00000361941;ENST00000277982;ENST00000354106;ENST00000371239	T;T;T;T;T;T;T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52	5.77	5.77	0.91146	.	0.000000	0.33199	N	0.005172	T	0.63367	0.2505	L	0.27053	0.805	0.32863	D	0.50823	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.997;0.977;0.999;0.975;0.977;0.995	T	0.67051	-0.5768	10	0.42905	T	0.14	-12.8611	19.9981	0.97395	0.0:0.0:1.0:0.0	.	507;438;553;575;421;523	Q9BX66-11;Q9BX66-3;Q9BX66;Q9BX66-2;Q9BX66-6;Q9BX66-5	.;.;SRBS1_HUMAN;.;.;.	W	438;553;507;575;523;438;421;553;575;523;352	ENSP00000360291:R438W;ENSP00000360293:R553W;ENSP00000360271:R507W;ENSP00000360292:R575W;ENSP00000377521:R523W;ENSP00000343998:R438W;ENSP00000277985:R421W;ENSP00000355136:R553W;ENSP00000277982:R575W;ENSP00000277984:R523W;ENSP00000360283:R352W	ENSP00000277982:R575W	R	-	1	2	SORBS1	97125800	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.558000	0.82253	2.729000	0.93468	0.655000	0.94253	CGG		0.388	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			A	97135810	G	A	97135810	3	1	61	1	0	0	0	0	1	0	0	0	14964	1057	37	1	2345	1	SORBS1	10	97135810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21149	97135810	38398937	6926	14911										
TCTN3	26123	broad.mit.edu	37	chr10	97423938	97423938	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccactttgaagggaaaGaagtcgaatggccatttcca	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97423938G>T	ENST00000371217.5	-	14	1733	c.1710C>A	c.(1708-1710)ttC>ttA	p.F570L	TCTN3_ENST00000430368.2_Missense_Mutation_p.F422L|TCTN3_ENST00000265993.9_Missense_Mutation_p.F588L			Q6NUS6	TECT3_HUMAN	tectonic family member 3	570					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.F392L(1)		breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		TGAAGGGAAAGAAGTCGAATG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	10											271	272	272					10																	97423938		2203	4300	6503	97413928	SO:0001583	missense	26123			AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.1710C>A	10.37:g.97423938G>T	ENSP00000360261:p.Phe570Leu		97413928	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Missense_Mutation	SNP	ENST00000371217.5	37	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796147	0.50208	.	.	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000343162	D	0.90620	-2.7	5.86	1.51	0.23008	.	0.000000	0.64402	D	0.000002	D	0.89691	0.6788	M	0.86178	2.8	0.29684	N	0.841488	B;B;P	0.34800	0.349;0.132;0.469	B;B;B	0.37480	0.175;0.055;0.251	D	0.83578	0.0116	10	0.38643	T	0.18	-12.8909	7.8311	0.29342	0.387:0.0:0.613:0.0	.	422;570;392	B4DR81;Q6NUS6;Q6NUS6-3	.;TECT3_HUMAN;.	L	570;422;588;392	ENSP00000265993:F570L	ENSP00000265993:F570L	F	-	3	2	TCTN3	97413928	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	0.419000	0.21247	0.256000	0.21614	0.563000	0.77884	TTC		0.463	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631		T	97423938	G	T	97423938	3	4	61	1	0	0	0	0	1	0	0	0	15763	933	33	2	117	2	TCTN3	10	97423938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288128	97423938	38110809	6927	14912										
CC2D2B	387707	broad.mit.edu	37	chr10	97791713	97791713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacattcacccatacccaaAcaacatattatctgtgtggg	5	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97791713A>G	ENST00000344386.3	+	9	1081	c.917A>G	c.(916-918)aAc>aGc	p.N306S	CC2D2B_ENST00000371198.2_3'UTR|ENTPD1-AS1_ENST00000451364.1_RNA|RP11-690P14.4_ENST00000475252.2_3'UTR|ENTPD1-AS1_ENST00000458228.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.N385S|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|ENTPD1-AS1_ENST00000452728.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	306								p.N306S(1)		large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		CCATACCCAAACAACATATTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											118	104	108					10																	97791713		1827	4093	5920	97781703	SO:0001583	missense	387707			BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 130"	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.917A>G	10.37:g.97791713A>G	ENSP00000343747:p.Asn306Ser		97781703	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.728299	0.48833	.	.	ENSG00000188649	ENST00000451649;ENST00000344386	T	0.70869	-0.52	6.04	1.17	0.20885	.	.	.	.	.	T	0.51686	0.1689	L	0.35723	1.085	0.27130	N	0.96192	B;P	0.39352	0.081;0.669	B;B	0.34824	0.028;0.19	T	0.41124	-0.9526	9	0.06494	T	0.89	.	9.4701	0.38837	0.7336:0.0:0.2664:0.0	.	385;306	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	S	385;306	ENSP00000343747:N306S	ENSP00000343747:N306S	N	+	2	0	CC2D2B	97781703	1.000000	0.71417	0.997000	0.53966	0.808000	0.45660	4.727000	0.61993	-0.036000	0.13669	-0.468000	0.05107	AAC		0.373	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		G	97791713	A	G	97791713	3	3	61	1	0	0	0	0	1	0	0	0	2735	43	2	4	1192	4	CC2D2B	10	97791713	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	367775	97791713	37743034	6928	14913										
CCNJ	54619	broad.mit.edu	37	chr10	97810174	97810174	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatggaccgctatgacatCtctatccagcagctgcattt	7	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97810174C>T	ENST00000265992.5	+	3	598	c.231C>T	c.(229-231)atC>atT	p.I77I	CCNJ_ENST00000465148.2_Silent_p.I77I|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1-AS1_ENST00000458228.1_RNA|CCNJ_ENST00000403870.3_Silent_p.I77I|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000427846.1_RNA|CCNJ_ENST00000534974.1_Silent_p.I77I|ENTPD1-AS1_ENST00000452728.1_RNA	NM_001134375.1|NM_001134376.1|NM_019084.4	NP_001127847.1|NP_001127848.1|NP_061957.2	Q5T5M9	CCNJ_HUMAN	cyclin J	77	Cyclin N-terminal.					nucleus (GO:0005634)		p.I77I(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	11				Epithelial(162;6.1e-08)|all cancers(201;2.32e-06)		GCTATGACATCTCTATCCAGC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	10											168	151	157					10																	97810174		2203	4300	6503	97800164	SO:0001819	synonymous_variant	54619			AK001757	CCDS7445.1, CCDS44462.1, CCDS44463.1	10q23.33	2008-05-14			ENSG00000107443	ENSG00000107443			23434	protein-coding gene	gene with protein product						12477932	Standard	NM_019084		Approved	FLJ10895, bA690P14.1	uc010qoq.2	Q5T5M9	OTTHUMG00000018823	ENST00000265992.5:c.231C>T	10.37:g.97810174C>T			97800164	B7Z4E7|Q86XL1|Q9NV69	Silent	SNP	ENST00000265992.5	37	CCDS7445.1																																																																																				0.433	CCNJ-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090166.3	NM_019084		T	97810174	C	T	97810174	2	4	61	1	0	0	0	0	0	0	0	1	2934	903	32	3		3	CCNJ	10	97810174	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18461	97810174	37724573	6929	14914										
ZNF518A	9849	broad.mit.edu	37	chr10	97920132	97920132	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccagttgtagttttgaatCatcctgacgcagatgcacca	8	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:97920132C>A	ENST00000534948.1	+	0	4908							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		AGTTTTGAATCATCCTGACGC	0.353																																																0			10											110	107	108					10																	97920132		1840	4095	5935	97910122			9849			AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"Zinc fingers, C2H2-type"	29009	protein-coding gene	gene with protein product			"zinc finger protein 518"	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97920132C>A			97910122	A0PJI5|O15044|Q32MP4	Missense_Mutation	SNP	ENST00000534948.1	37																																																																																					0.353	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		A	97920132	C	A	97920132	1	1	61	0	1	0	0	0	0	0	0	0	18001	816	29	2		2	ZNF518A	10	97920132	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109958	97920132	37614615	6930	14915										
OPALIN	93377	broad.mit.edu	37	chr10	98115020	98115020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtacttactgtgttcgCcggcagggtgaagttcagtg	14	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98115020C>T	ENST00000371172.3	-	2	436	c.31G>A	c.(31-33)Gcg>Acg	p.A11T	OPALIN_ENST00000393871.1_Intron|OPALIN_ENST00000393870.2_Missense_Mutation_p.A11T|OPALIN_ENST00000419479.1_5'UTR|OPALIN_ENST00000536387.1_5'UTR	NM_001284326.1|NM_001284327.1|NM_033207.3	NP_001271255.1|NP_001271256.1|NP_149984.1	Q96PE5	OPALI_HUMAN	oligodendrocytic myelin paranodal and inner loop protein	11						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A11T(1)		breast(1)|large_intestine(1)|lung(5)|prostate(2)	9						ACTGTGTTCGCCGGCAGGGTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	10											135	132	133					10																	98115020		2203	4300	6503	98105010	SO:0001583	missense	93377			AF367761	CCDS7448.1, CCDS41556.1, CCDS44466.1, CCDS60602.1, CCDS73172.1, CCDS73173.1	10q23-q24	2010-11-23	2008-05-01	2008-05-01	ENSG00000197430	ENSG00000197430			20707	protein-coding gene	gene with protein product			"transmembrane protein 10"	TMEM10		11814680, 17442045	Standard	NM_001284324		Approved	TMP10, HTMP10	uc001kmj.3	Q96PE5	OTTHUMG00000018831	ENST00000371172.3:c.31G>A	10.37:g.98115020C>T	ENSP00000360214:p.Ala11Thr		98105010	A8MX69|A8MYG4|B4DK96|B4DKH0|Q5W102	Missense_Mutation	SNP	ENST00000371172.3	37	CCDS7448.1	.	.	.	.	.	.	.	.	.	.	C	7.760	0.705219	0.15172	.	.	ENSG00000197430	ENST00000371172;ENST00000393870	.	.	.	4.59	1.4	0.22301	.	0.724984	0.12414	N	0.471010	T	0.26122	0.0637	L	0.29908	0.895	0.09310	N	0.99999	B	0.02656	0.0	B	0.08055	0.003	T	0.23440	-1.0188	9	0.62326	D	0.03	-5.135	2.4487	0.04512	0.2044:0.5068:0.1826:0.1061	.	11	Q96PE5	OPALI_HUMAN	T	11	.	ENSP00000360214:A11T	A	-	1	0	OPALIN	98105010	0.001000	0.12720	0.041000	0.18516	0.010000	0.07245	-0.088000	0.11198	0.615000	0.30124	0.643000	0.83706	GCG		0.488	OPALIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049606.1	NM_033207		T	98115020	C	T	98115020	3	4	61	1	0	0	0	0	1	0	0	0	10904	739	26	3	427	3	OPALIN	10	98115020	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	194888	98115020	37419727	6931	14916										
TLL2	7093	broad.mit.edu	37	chr10	98133400	98133400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctgcactgaggcatccGaataaaacctgagaaacata	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98133400G>A	ENST00000357947.3	-	19	2840	c.2615C>T	c.(2614-2616)tCg>tTg	p.S872L		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	872	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S872L(2)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TGAGGCATCCGAATAAAACCT	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	10											76	76	76					10																	98133400		2203	4300	6503	98123390	SO:0001583	missense	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2615C>T	10.37:g.98133400G>A	ENSP00000350630:p.Ser872Leu		98123390	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	34	5.362335	0.95877	.	.	ENSG00000095587	ENST00000357947	T	0.47177	0.85	4.85	4.85	0.62838	CUB (5);	0.000000	0.41097	D	0.000957	D	0.82356	0.5019	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89913	0.4053	10	0.87932	D	0	.	17.4922	0.87707	0.0:0.0:1.0:0.0	.	872	Q9Y6L7	TLL2_HUMAN	L	872	ENSP00000350630:S872L	ENSP00000350630:S872L	S	-	2	0	TLL2	98123390	1.000000	0.71417	0.746000	0.31095	0.988000	0.76386	9.601000	0.98297	2.677000	0.91161	0.561000	0.74099	TCG		0.597	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98133400	G	A	98133400	3	1	61	1	0	0	0	0	1	0	0	0	15985	1059	37	1	444	1	TLL2	10	98133400	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18380	98133400	37401347	6932	14917										
TLL2	7093	broad.mit.edu	37	chr10	98136533	98136533	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtcaggccagttggggctCgccagggtcccctccacact	12	15	1	0	rs553436918		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98136533C>T	ENST00000357947.3	-	18	2589	c.2364G>A	c.(2362-2364)gcG>gcA	p.A788A		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	788	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A788A(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AGTTGGGGCTCGCCAGGGTCC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	10											69	69	69					10																	98136533		2203	4300	6503	98126523	SO:0001819	synonymous_variant	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2364G>A	10.37:g.98136533C>T			98126523	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Silent	SNP	ENST00000357947.3	37	CCDS7449.1																																																																																				0.562	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			T	98136533	C	T	98136533	2	4	61	1	0	0	0	0	0	0	0	1	15985	871	31	1		1	TLL2	10	98136533	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3133	98136533	37398214	6933	14918										
PIK3AP1	118788	broad.mit.edu	37	chr10	98416630	98416630	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcggcaggttctgctgcttCgagtaggaaacaaccttctc	11	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98416630C>T	ENST00000339364.5	-	3	611	c.492G>A	c.(490-492)tcG>tcA	p.S164S	PIK3AP1_ENST00000468783.1_5'UTR|PIK3AP1_ENST00000371110.2_5'UTR	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	164					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)	p.S164S(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		TCTGCTGCTTCGAGTAGGAAA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	10											120	93	102					10																	98416630		2203	4300	6503	98406620	SO:0001819	synonymous_variant	118788			AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.492G>A	10.37:g.98416630C>T			98406620	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																				0.577	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		T	98416630	C	T	98416630	2	4	61	1	0	0	0	0	0	0	0	1	11939	871	31	1		1	PIK3AP1	10	98416630	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280097	98416630	37118117	6934	14919										
SLIT1	6585	broad.mit.edu	37	chr10	98790581	98790581	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagatgtcattgccgtggaGagacctgagaagggaagagg	18	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98790581G>T	ENST00000266058.4	-	25	2760	c.2515C>A	c.(2515-2517)Ctc>Atc	p.L839I	SLIT1_ENST00000371070.4_Missense_Mutation_p.L839I|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	839					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.L839I(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TTGCCGTGGAGAGACCTGAGA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	10											136	111	119					10																	98790581		2203	4300	6503	98780571	SO:0001583	missense	6585			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.2515C>A	10.37:g.98790581G>T	ENSP00000266058:p.Leu839Ile		98780571	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.517776	0.64634	.	.	ENSG00000187122	ENST00000266058;ENST00000371070	T;T	0.74421	-0.84;-0.84	5.17	4.26	0.50523	.	0.064498	0.64402	D	0.000009	T	0.77239	0.4101	M	0.82132	2.575	0.80722	D	1	B	0.29552	0.248	B	0.38880	0.284	T	0.78091	-0.2339	10	0.87932	D	0	.	8.757	0.34652	0.0804:0.1513:0.7684:0.0	.	839	O75093	SLIT1_HUMAN	I	839	ENSP00000266058:L839I;ENSP00000360109:L839I	ENSP00000266058:L839I	L	-	1	0	SLIT1	98780571	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.597000	0.61062	1.388000	0.46506	0.561000	0.74099	CTC		0.602	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		T	98790581	G	T	98790581	3	4	61	1	0	0	0	0	1	0	0	0	14776	942	33	2	2141	2	SLIT1	10	98790581	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	373951	98790581	36744166	6935	14920										
SLIT1	6585	broad.mit.edu	37	chr10	98806509	98806509	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacagaggctgcgccctcGaaggccccatcttcaatttc	8	16	3	1	rs565102855		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:98806509G>A	ENST00000266058.4	-	18	2000	c.1755C>T	c.(1753-1755)ttC>ttT	p.F585F	SLIT1_ENST00000371070.4_Silent_p.F585F|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	585					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.F585F(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CTGCGCCCTCGAAGGCCCCAT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	10											61	60	61					10																	98806509		2203	4300	6503	98796499	SO:0001819	synonymous_variant	6585			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1755C>T	10.37:g.98806509G>A			98796499	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																				0.597	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98806509	G	A	98806509	2	1	61	1	0	0	0	0	0	0	0	1	14776	1049	37	1		1	SLIT1	10	98806509	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15928	98806509	36728238	6936	14921										
ARHGAP19	84986	broad.mit.edu	37	chr10	99023341	99023341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcccttaaaatctgctgtCggacactattacccggtact	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:99023341C>T	ENST00000358531.4	-	4	477	c.449G>A	c.(448-450)cGa>cAa	p.R150Q	ARHGAP19-SLIT1_ENST00000316676.8_Missense_Mutation_p.R150Q|ARHGAP19_ENST00000355366.5_Missense_Mutation_p.R141Q|ARHGAP19-SLIT1_ENST00000453547.2_Missense_Mutation_p.R150Q|ARHGAP19_ENST00000371027.1_Missense_Mutation_p.R141Q|ARHGAP19-SLIT1_ENST00000358308.3_Missense_Mutation_p.R150Q	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	150	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.R150Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		AATCTGCTGTCGGACACTATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											128	120	123					10																	99023341		2203	4300	6503	99013331	SO:0001583	missense	84986			AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"Rho GTPase activating proteins"	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.449G>A	10.37:g.99023341C>T	ENSP00000351333:p.Arg150Gln		99013331	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Missense_Mutation	SNP	ENST00000358531.4	37	CCDS7454.2	.	.	.	.	.	.	.	.	.	.	C	36	5.927646	0.97110	.	.	ENSG00000213390	ENST00000453547;ENST00000316676;ENST00000355366;ENST00000358531;ENST00000371027;ENST00000358308	T;T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11;2.11	5.87	5.87	0.94306	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.64402	U	0.000001	T	0.49643	0.1569	M	0.69823	2.125	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	0.999;0.976;1.0	T	0.42310	-0.9459	10	0.62326	D	0.03	-5.7991	20.197	0.98244	0.0:1.0:0.0:0.0	.	150;150;141	Q14CB8-6;Q14CB8;Q14CB8-3	.;RHG19_HUMAN;.	Q	150;150;141;150;141;150	ENSP00000414774:R150Q;ENSP00000324468:R150Q;ENSP00000347526:R141Q;ENSP00000351333:R150Q;ENSP00000360066:R141Q;ENSP00000351058:R150Q	ENSP00000324468:R150Q	R	-	2	0	ARHGAP19	99013331	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.675000	0.84002	2.775000	0.95449	0.655000	0.94253	CGA		0.403	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900		T	99023341	C	T	99023341	3	4	61	1	0	0	0	0	1	0	0	0	869	884	31	1	1071	1	ARHGAP19	10	99023341	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	216832	99023341	36511406	6937	14922										
GOLGA7B	401647	broad.mit.edu	37	chr10	99619240	99619240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatctgcaggagctccggcGaagtgcctcactggccacca	11	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:99619240G>A	ENST00000370602.1	+	2	103	c.38G>A	c.(37-39)cGa>cAa	p.R13Q		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	13						Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.R13Q(1)		endometrium(1)|large_intestine(3)|prostate(1)	5						GAGCTCCGGCGAAGTGCCTCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	10											66	59	62					10																	99619240		2203	4300	6503	99609230	SO:0001583	missense	401647			BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.38G>A	10.37:g.99619240G>A	ENSP00000359634:p.Arg13Gln		99609230	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	37	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.407805	0.42715	.	.	ENSG00000155265	ENST00000370602	.	.	.	4.89	4.89	0.63831	.	0.134085	0.51477	D	0.000099	T	0.12263	0.0298	N	0.01048	-1.04	0.36394	D	0.862708	P	0.43352	0.804	B	0.27262	0.078	T	0.35525	-0.9785	9	0.07325	T	0.83	-12.1217	17.8428	0.88720	0.0:0.0:1.0:0.0	.	13	Q2TAP0	GOG7B_HUMAN	Q	13	.	ENSP00000359634:R13Q	R	+	2	0	GOLGA7B	99609230	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.937000	0.56575	2.566000	0.86566	0.555000	0.69702	CGA		0.582	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917		A	99619240	G	A	99619240	3	1	61	1	0	0	0	0	1	0	0	0	6582	1058	37	1	44	1	GOLGA7B	10	99619240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	595899	99619240	35915507	6938	14923										
CRTAC1	55118	broad.mit.edu	37	chr10	99640059	99640059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccccgactgcacttcttgTtggtccggcacctgtagctt	10	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:99640059T>C	ENST00000370597.3	-	14	2121	c.1766A>G	c.(1765-1767)aAc>aGc	p.N589S	CRTAC1_ENST00000298819.4_Missense_Mutation_p.T575A|CRTAC1_ENST00000468549.1_5'Flank|CRTAC1_ENST00000370591.2_Missense_Mutation_p.N589S	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	589	EGF-like.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.N589S(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GCACTTCTTGTTGGTCCGGCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	10											141	115	124					10																	99640059		2203	4300	6503	99630049	SO:0001583	missense	55118			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1766A>G	10.37:g.99640059T>C	ENSP00000359629:p.Asn589Ser		99630049	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.47|15.47	2.842599|2.842599	0.51057|0.51057	.|.	.|.	ENSG00000095713|ENSG00000095713	ENST00000370597;ENST00000436034;ENST00000309155;ENST00000370591|ENST00000413387;ENST00000298819	T;T;T|T;T	0.73258|0.32988	-0.73;0.11;0.1|1.43;1.46	4.39|4.39	4.39|4.39	0.52855|0.52855	EGF-like calcium-binding (1);|.	0.119478|.	0.56097|.	D|.	0.000031|.	T|T	0.15132|0.15132	0.0365|0.0365	N|N	0.12887|0.12887	0.27|0.27	0.44462|0.44462	D|D	0.997398|0.997398	P;P|B	0.37061|0.12013	0.525;0.58|0.005	B;B|B	0.40256|0.14023	0.156;0.324|0.01	T|T	0.06006|0.06006	-1.0851|-1.0851	10|9	0.59425|0.02654	D|T	0.04|1	-29.615|-29.615	12.7241|12.7241	0.57159|0.57159	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	589;589|471	Q9NQ79-2;Q9NQ79|Q5T4F6	.;CRAC1_HUMAN|.	S|A	589;43;581;589|471;575	ENSP00000359629:N589S;ENSP00000310810:N581S;ENSP00000359623:N589S|ENSP00000408445:T471A;ENSP00000298819:T575A	ENSP00000310810:N581S|ENSP00000298819:T575A	N|T	-|-	2|1	0|0	CRTAC1|CRTAC1	99630049|99630049	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	5.555000|5.555000	0.67301|0.67301	1.852000|1.852000	0.53769|0.53769	0.368000|0.368000	0.22195|0.22195	AAC|ACA		0.572	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		C	99640059	T	C	99640059	3	2	61	1	0	0	0	0	1	0	0	0	3902	1725	60	4	227	4	CRTAC1	10	99640059	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20819	99640059	35894688	6939	14924										
CRTAC1	55118	broad.mit.edu	37	chr10	99640121	99640121	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttgtctcgagggcacacGaatgggaactggatgcattc	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:99640121G>A	ENST00000370597.3	-	14	2059	c.1704C>T	c.(1702-1704)ttC>ttT	p.F568F	CRTAC1_ENST00000298819.4_Missense_Mutation_p.S554L|CRTAC1_ENST00000468549.1_5'UTR|CRTAC1_ENST00000370591.2_Silent_p.F568F	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	568	EGF-like.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.F568F(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GAGGGCACACGAATGGGAACT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	10											138	104	115					10																	99640121		2203	4300	6503	99630111	SO:0001819	synonymous_variant	55118			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1704C>T	10.37:g.99640121G>A			99630111	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424317	0.25639	.	.	ENSG00000095713	ENST00000413387;ENST00000298819	T;T	0.35421	1.31;1.33	4.39	-5.57	0.02521	.	.	.	.	.	T	0.18759	0.0450	.	.	.	0.58432	D	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.32134	-0.9918	8	0.10902	T	0.67	-17.3058	13.8944	0.63761	0.7094:0.0:0.2906:0.0	.	450	Q5T4F6	.	L	450;554	ENSP00000408445:S450L;ENSP00000298819:S554L	ENSP00000298819:S554L	S	-	2	0	CRTAC1	99630111	0.011000	0.17503	0.671000	0.29857	0.967000	0.64934	-0.874000	0.04210	-1.149000	0.02843	-0.480000	0.04831	TCG		0.577	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		A	99640121	G	A	99640121	2	1	61	1	0	0	0	0	0	0	0	1	3902	1049	37	1		1	CRTAC1	10	99640121	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	99640121	35894626	6940	14925										
C10orf28	27291	broad.mit.edu	37	chr10	99967933	99967933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgacatggcactttatgTacctaaagctcgtaggggtg	12	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:99967933T>C	ENST00000298999.3	+	5	365	c.62T>C	c.(61-63)gTa>gCa	p.V21A	R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.V21A	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	21	EJC-binding motif; may mediate interaction with the EJC.						nucleotide binding (GO:0000166)	p.V21A(1)									GCACTTTATGTACCTAAAGCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											48	46	47					10																	99967933		2203	4300	6503	99957923	SO:0001583	missense	27291			AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.62T>C	10.37:g.99967933T>C	ENSP00000298999:p.Val21Ala		99957923	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	T	18.14	3.558331	0.65538	.	.	ENSG00000166024	ENST00000370584;ENST00000538495;ENST00000298999	T;T	0.20200	2.09;2.09	6.11	6.11	0.99139	.	0.481115	0.19214	N	0.119860	T	0.37972	0.1023	M	0.71581	2.175	0.80722	D	1	D;D	0.55385	0.971;0.971	P;P	0.53224	0.721;0.721	T	0.17379	-1.0371	10	0.72032	D	0.01	-3.6085	13.0939	0.59180	0.0:0.0:0.0:1.0	.	21;21	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	A	21	ENSP00000359616:V21A;ENSP00000298999:V21A	ENSP00000298999:V21A	V	+	2	0	C10orf28	99957923	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	4.416000	0.59815	2.343000	0.79666	0.533000	0.62120	GTA		0.433	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		C	99967933	T	C	99967933	3	2	61	1	0	0	0	0	1	0	0	0	1605	1638	57	4	64	4	C10orf28	10	99967933	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	327812	99967933	35566814	6941	14926										
PYROXD2	84795	broad.mit.edu	37	chr10	100144783	100144783	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggggcacggggcgggcGaagtagagctggtccaggga	21	8	0	1	rs369487361		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:100144783G>A	ENST00000370575.4	-	15	1644	c.1596C>T	c.(1594-1596)ttC>ttT	p.F532F	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	532							oxidoreductase activity (GO:0016491)	p.F532F(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CGGGGCGGGCGAAGTAGAGCT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	10						G		0,4406		0,0,2203	82	77	79		1596	-6.9	0.8	10		79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PYROXD2	NM_032709.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		532/582	100144783	1,13005	2203	4300	6503	100134773	SO:0001819	synonymous_variant	84795			AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1596C>T	10.37:g.100144783G>A			100134773	D3DR61|Q5TAA9|Q9BRQ1	Silent	SNP	ENST00000370575.4	37	CCDS7474.1																																																																																				0.612	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		A	100144783	G	A	100144783	2	1	61	1	0	0	0	0	0	0	0	1	12904	1049	37	1		1	PYROXD2	10	100144783	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176850	100144783	35389964	6942	14927										
HPSE2	60495	broad.mit.edu	37	chr10	100904147	100904147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctaaggcaacatcacttCgaacaatgtctacaaaaaga	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:100904147C>T	ENST00000370552.3	-	3	517	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	HPSE2_ENST00000404542.1_Intron|HPSE2_ENST00000370549.1_Missense_Mutation_p.R153Q|HPSE2_ENST00000370546.1_Missense_Mutation_p.R153Q	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	153					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)	p.R153Q(2)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		AACATCACTTCGAACAATGTC	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	10											84	86	85					10																	100904147		2203	4300	6503	100894137	SO:0001583	missense	60495			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.458G>A	10.37:g.100904147C>T	ENSP00000359583:p.Arg153Gln		100894137	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830119	0.91036	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546	T;T;T	0.48522	0.81;1.49;1.37	5.81	5.81	0.92471	Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000001	T	0.65533	0.2700	L	0.51422	1.61	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.75484	0.986;0.986;0.968	T	0.61481	-0.7054	10	0.44086	T	0.13	-3.2947	20.064	0.97700	0.0:1.0:0.0:0.0	.	153;153;153	Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;HPSE2_HUMAN	Q	153	ENSP00000359583:R153Q;ENSP00000359580:R153Q;ENSP00000359577:R153Q	ENSP00000359577:R153Q	R	-	2	0	HPSE2	100894137	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.345000	0.79337	2.746000	0.94184	0.650000	0.86243	CGA		0.403	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100904147	C	T	100904147	3	4	61	1	0	0	0	0	1	0	0	0	7366	884	31	1	1398	1	HPSE2	10	100904147	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	759364	100904147	34630600	6943	14928										
HPSE2	60495	broad.mit.edu	37	chr10	100995386	100995386	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcaagtagaatcagggtCttttccttcaaacctgcagc	7	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:100995386C>A	ENST00000370552.3	-	1	233	c.174G>T	c.(172-174)aaG>aaT	p.K58N	HPSE2_ENST00000404542.1_Missense_Mutation_p.K58N|HPSE2_ENST00000370549.1_Missense_Mutation_p.K58N|HPSE2_ENST00000370546.1_Missense_Mutation_p.K58N	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	58					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)	p.K58N(6)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		GAATCAGGGTCTTTTCCTTCA	0.522																																																6	Substitution - Missense(6)	large_intestine(6)	10											180	178	179					10																	100995386		2203	4300	6503	100985376	SO:0001583	missense	60495			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.174G>T	10.37:g.100995386C>A	ENSP00000359583:p.Lys58Asn		100985376	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869121	0.32977	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.00477	7.14;7.14;7.14;7.14	5.8	5.8	0.92144	.	0.052749	0.64402	D	0.000001	T	0.00328	0.0010	N	0.14661	0.345	0.30882	N	0.731298	P;P;P;P	0.40731	0.557;0.728;0.59;0.455	B;B;B;B	0.38803	0.221;0.282;0.282;0.146	T	0.70619	-0.4822	10	0.35671	T	0.21	-12.1322	15.1633	0.72801	0.0:0.9311:0.0:0.0689	.	58;58;58;58	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	N	58	ENSP00000359583:K58N;ENSP00000359580:K58N;ENSP00000359577:K58N;ENSP00000384384:K58N	ENSP00000359577:K58N	K	-	3	2	HPSE2	100985376	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.374000	0.44274	2.758000	0.94735	0.561000	0.74099	AAG		0.522	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		A	100995386	C	A	100995386	3	1	61	1	0	0	0	0	1	0	0	0	7366	912	32	2	1690	2	HPSE2	10	100995386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91239	100995386	34539361	6944	14929										
CNNM1	26507	broad.mit.edu	37	chr10	101120624	101120624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagcagagggtcccgcaaCgggagcggaagcggcatgac	16	10	0	2	rs370860509		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101120624C>T	ENST00000356713.4	+	3	2039	c.1750C>T	c.(1750-1752)Cgg>Tgg	p.R584W	CNNM1_ENST00000370534.4_Missense_Mutation_p.R219W|CNNM1_ENST00000370528.3_Missense_Mutation_p.R513W|CNNM1_ENST00000446890.1_Missense_Mutation_p.R513W	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	584					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.R219W(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		GGTCCCGCAACGGGAGCGGAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											138	143	141					10																	101120624		2203	4300	6503	101110614	SO:0001583	missense	26507			AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1750C>T	10.37:g.101120624C>T	ENSP00000349147:p.Arg584Trp		101110614	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486145	0.84854	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	D;D;D;T	0.84370	-1.84;-1.79;-1.78;-0.81	5.74	4.82	0.62117	.	0.058743	0.64402	D	0.000001	D	0.92541	0.7631	M	0.83953	2.67	0.51482	D	0.999921	D;D;D;D	0.89917	1.0;0.999;0.998;0.999	D;D;P;D	0.74674	0.984;0.972;0.786;0.937	D	0.93566	0.6899	10	0.72032	D	0.01	-12.3558	16.0677	0.80897	0.142:0.858:0.0:0.0	.	219;584;219;584	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	W	584;513;513;219;37	ENSP00000349147:R584W;ENSP00000406492:R513W;ENSP00000359559:R513W;ENSP00000359565:R219W	ENSP00000349147:R584W	R	+	1	2	CNNM1	101110614	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	3.944000	0.56629	1.376000	0.46267	0.655000	0.94253	CGG		0.522	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		T	101120624	C	T	101120624	3	4	61	1	0	0	0	0	1	0	0	0	3618	527	19	1	1760	1	CNNM1	10	101120624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125238	101120624	34414123	6945	14930										
CNNM1	26507	broad.mit.edu	37	chr10	101122145	101122145	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggactactttgtgctgCttctacaggtgagtaggaaa	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101122145C>A	ENST00000356713.4	+	4	2309	c.2020C>A	c.(2020-2022)Ctt>Att	p.L674I	CNNM1_ENST00000370534.4_Missense_Mutation_p.L309I|CNNM1_ENST00000370528.3_Missense_Mutation_p.L603I|CNNM1_ENST00000446890.1_Missense_Mutation_p.L603I	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	674					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.L309I(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CTTTGTGCTGCTTCTACAGGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	10											51	49	50					10																	101122145		2203	4300	6503	101112135	SO:0001583	missense	26507			AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2020C>A	10.37:g.101122145C>A	ENSP00000349147:p.Leu674Ile		101112135	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	C	2.294	-0.361750	0.05103	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	T;T;T;T	0.76186	-1.0;-0.96;-0.94;-0.06	5.1	4.17	0.49024	.	0.149283	0.46758	D	0.000263	T	0.29158	0.0725	N	0.00079	-2.23	0.80722	D	1	B;B;B;B	0.12013	0.002;0.005;0.0;0.003	B;B;B;B	0.15484	0.006;0.013;0.001;0.007	T	0.49322	-0.8952	10	0.02654	T	1	-17.454	9.711	0.40245	0.268:0.6069:0.125:0.0	.	309;674;309;674	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	I	674;603;603;309;127	ENSP00000349147:L674I;ENSP00000406492:L603I;ENSP00000359559:L603I;ENSP00000359565:L309I	ENSP00000349147:L674I	L	+	1	0	CNNM1	101112135	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	2.292000	0.43549	1.227000	0.43598	0.655000	0.94253	CTT		0.542	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101122145	C	A	101122145	3	1	61	1	0	0	0	0	1	0	0	0	3618	797	28	2	2034	2	CNNM1	10	101122145	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1521	101122145	34412602	6946	14931										
GOT1	2805	broad.mit.edu	37	chr10	101163356	101163356	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcaggatgctctcaggttCttttccaaccacagtcagat	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101163356C>A	ENST00000370508.5	-	7	856	c.829G>T	c.(829-831)Gaa>Taa	p.E277*	GOT1_ENST00000543866.1_Nonsense_Mutation_p.E256*	NM_002079.2	NP_002070.1	P17174	AATC_HUMAN	glutamic-oxaloacetic transaminase 1, soluble	277					2-oxoglutarate metabolic process (GO:0006103)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to insulin stimulus (GO:0032869)|fatty acid homeostasis (GO:0055089)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|glycerol biosynthetic process (GO:0006114)|L-methionine biosynthetic process from methylthioadenosine (GO:0019509)|oxaloacetate metabolic process (GO:0006107)|polyamine metabolic process (GO:0006595)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	carboxylic acid binding (GO:0031406)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-cysteine:2-oxoglutarate aminotransferase activity (GO:0047801)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|phosphatidylserine decarboxylase activity (GO:0004609)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.E277*(2)		endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)	16		Ovarian(717;0.028)|Colorectal(252;0.234)		Epithelial(162;4.76e-10)|all cancers(201;3.84e-08)	L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)	CTCTCAGGTTCTTTTCCAACC	0.557																																					Melanoma(173;770 3544 21601)											2	Substitution - Nonsense(2)	large_intestine(2)	10											96	91	93					10																	101163356		2203	4300	6503	101153346	SO:0001587	stop_gained	2805			M37400	CCDS7479.1	10q24.1-q25.1	2013-05-29	2013-05-29		ENSG00000120053	ENSG00000120053	2.6.1.1		4432	protein-coding gene	gene with protein product	"aspartate aminotransferase 1", "aspartate transaminase 1"	138180	"glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1)"			1974457	Standard	NM_002079		Approved		uc001kpr.3	P17174	OTTHUMG00000018882	ENST00000370508.5:c.829G>T	10.37:g.101163356C>A	ENSP00000359539:p.Glu277*		101153346	B2R6R7|B7Z7E9|Q5VW80	Nonsense_Mutation	SNP	ENST00000370508.5	37	CCDS7479.1	.	.	.	.	.	.	.	.	.	.	C	37	6.300439	0.97453	.	.	ENSG00000120053	ENST00000370508;ENST00000535447;ENST00000543866	.	.	.	5.03	5.03	0.67393	.	0.198027	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-6.3713	18.7783	0.91920	0.0:1.0:0.0:0.0	.	.	.	.	X	277;230;256	.	ENSP00000359539:E277X	E	-	1	0	GOT1	101153346	1.000000	0.71417	0.993000	0.49108	0.335000	0.28730	6.042000	0.70996	2.498000	0.84270	0.558000	0.71614	GAA		0.557	GOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049794.1	NM_002079		A	101163356	C	A	101163356	4	1	61	1	0	0	0	0	0	1	0	0	6599	922	32	2	424	2	GOT1	10	101163356	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41211	101163356	34371391	6947	14932										
COX15	1355	broad.mit.edu	37	chr10	101487299	101487299	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaaatgccaatctaccatCgagaggccagactctgtcaa	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101487299C>T	ENST00000016171.5	-	3	344	c.294G>A	c.(292-294)tcG>tcA	p.S98S	CUTC_ENST00000493385.1_Intron|COX15_ENST00000370483.5_Silent_p.S98S			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	98					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	p.S98S(1)		endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		AATCTACCATCGAGAGGCCAG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											149	150	150					10																	101487299		2203	4300	6503	101477289	SO:0001819	synonymous_variant	1355			AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.294G>A	10.37:g.101487299C>T			101477289	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Silent	SNP	ENST00000016171.5	37	CCDS7482.1																																																																																				0.413	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		T	101487299	C	T	101487299	2	4	61	1	0	0	0	0	0	0	0	1	3770	871	31	1		1	COX15	10	101487299	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323943	101487299	34047448	6948	14933										
COX15	1355	broad.mit.edu	37	chr10	101489326	101489326	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctagttactccaccaaGaataactgctccagccactg	5	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101489326G>T	ENST00000016171.5	-	2	306	c.256C>A	c.(256-258)Ctt>Att	p.L86I	CUTC_ENST00000370476.5_5'Flank|CUTC_ENST00000493385.1_Intron|COX15_ENST00000370483.5_Missense_Mutation_p.L86I			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	86					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	p.L86I(2)		endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		ACTCCACCAAGAATAACTGCT	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	10											105	111	109					10																	101489326		2203	4300	6503	101479316	SO:0001583	missense	1355			AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.256C>A	10.37:g.101489326G>T	ENSP00000016171:p.Leu86Ile		101479316	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	37	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775113	0.70107	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	D;D	0.83673	-1.75;-1.75	4.45	4.45	0.53987	Peptidase cysteine/serine, trypsin-like (1);	0.000000	0.85682	D	0.000000	D	0.83797	0.5332	N	0.25485	0.75	0.80722	D	1	P;P	0.45827	0.867;0.737	P;P	0.57548	0.54;0.823	D	0.84180	0.0439	10	0.42905	T	0.14	-15.0835	17.2268	0.86972	0.0:0.0:1.0:0.0	.	86;86	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	I	86	ENSP00000359514:L86I;ENSP00000016171:L86I	ENSP00000016171:L86I	L	-	1	0	COX15	101479316	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.082000	0.64450	2.484000	0.83849	0.555000	0.69702	CTT		0.488	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		T	101489326	G	T	101489326	3	4	61	1	0	0	0	0	1	0	0	0	3770	942	33	2	1078	2	COX15	10	101489326	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2027	101489326	34045421	6949	14934										
COX15	1355	broad.mit.edu	37	chr10	101489475	101489475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgccctggcctcaaagggCgcctgatgcaatcacactaa	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101489475C>T	ENST00000016171.5	-	2	157	c.107G>A	c.(106-108)cGc>cAc	p.R36H	CUTC_ENST00000370476.5_5'Flank|CUTC_ENST00000493385.1_Intron|COX15_ENST00000370483.5_Missense_Mutation_p.R36H			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	36					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	p.R36H(1)		endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		CCTCAAAGGGCGCCTGATGCA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	10											71	69	70					10																	101489475		2203	4300	6503	101479465	SO:0001583	missense	1355			AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.107G>A	10.37:g.101489475C>T	ENSP00000016171:p.Arg36His		101479465	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	37	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747068	0.30955	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	.	.	.	4.97	-2.28	0.06826	Peptidase cysteine/serine, trypsin-like (1);	0.667620	0.15307	N	0.269263	T	0.20495	0.0493	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.09952	-1.0651	9	0.33940	T	0.23	0.0572	4.2642	0.10756	0.4822:0.2633:0.0:0.2546	.	36;36	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	H	36	.	ENSP00000016171:R36H	R	-	2	0	COX15	101479465	0.003000	0.15002	0.033000	0.17914	0.939000	0.58152	-0.607000	0.05648	-0.202000	0.10268	0.555000	0.69702	CGC		0.507	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		T	101489475	C	T	101489475	3	4	61	1	0	0	0	0	1	0	0	0	3770	768	27	1	1227	1	COX15	10	101489475	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149	101489475	34045272	6950	14935										
ABCC2	1244	broad.mit.edu	37	chr10	101544527	101544527	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctaccaccaaactctatCttgctaagcaggtaaagtta	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101544527C>A	ENST00000370449.4	+	2	309	c.196C>A	c.(196-198)Ctt>Att	p.L66I	ABCC2_ENST00000370434.1_Missense_Mutation_p.L66I	NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	66					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.L66I(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CAAACTCTATCTTGCTAAGCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											93	92	93					10																	101544527		2203	4300	6503	101534517	SO:0001583	missense	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.196C>A	10.37:g.101544527C>A	ENSP00000359478:p.Leu66Ile		101534517	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	C	3.893	-0.023623	0.07634	.	.	ENSG00000023839	ENST00000370449;ENST00000370434	T;T	0.37411	1.2;1.2	5.7	2.71	0.32032	.	0.688503	0.14517	N	0.314722	T	0.25457	0.0619	L	0.37800	1.135	0.31839	N	0.62368	B	0.13594	0.008	B	0.14023	0.01	T	0.32428	-0.9907	10	0.09338	T	0.73	-7.7124	10.7849	0.46398	0.264:0.6088:0.1273:0.0	.	66	Q92887	MRP2_HUMAN	I	66	ENSP00000359478:L66I;ENSP00000359463:L66I	ENSP00000359463:L66I	L	+	1	0	ABCC2	101534517	0.996000	0.38824	0.978000	0.43139	0.002000	0.02628	0.371000	0.20450	0.279000	0.22186	-0.304000	0.09214	CTT		0.473	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101544527	C	A	101544527	3	1	61	1	0	0	0	0	1	0	0	0	53	913	32	2	202	2	ABCC2	10	101544527	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55052	101544527	33990220	6951	14936										
DNMBP	23268	broad.mit.edu	37	chr10	101667793	101667793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcagccaataattgcttcGagaccttaatcaccatctgc	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101667793G>A	ENST00000324109.4	-	6	2604	c.2513C>T	c.(2512-2514)tCg>tTg	p.S838L	DNMBP_ENST00000543621.1_Missense_Mutation_p.S84L|DNMBP_ENST00000342239.3_Missense_Mutation_p.S838L	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	838	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S838L(1)		central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TAATTGCTTCGAGACCTTAAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	102	103					10																	101667793		2203	4300	6503	101657783	SO:0001583	missense	23268			AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2513C>T	10.37:g.101667793G>A	ENSP00000315659:p.Ser838Leu		101657783	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977580	0.92982	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000370423;ENST00000422692	T;T;T;T	0.48522	0.81;2.09;2.09;1.36	5.99	5.99	0.97316	Dbl homology (DH) domain (5);	0.000000	0.40469	N	0.001088	T	0.72407	0.3456	M	0.77712	2.385	0.80722	D	1	D;D;D	0.89917	1.0;0.997;1.0	D;P;D	0.91635	0.999;0.862;0.999	T	0.73566	-0.3942	10	0.87932	D	0	-13.8605	20.4777	0.99188	0.0:0.0:1.0:0.0	.	838;84;838	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	L	838;838;84;84;126;126	ENSP00000344914:S838L;ENSP00000315659:S838L;ENSP00000443657:S84L;ENSP00000409476:S126L	ENSP00000315659:S838L	S	-	2	0	DNMBP	101657783	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.860000	0.86993	2.840000	0.97914	0.655000	0.94253	TCG		0.398	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		A	101667793	G	A	101667793	3	1	61	1	0	0	0	0	1	0	0	0	4685	1059	37	1	2268	1	DNMBP	10	101667793	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123266	101667793	33866954	6952	14937										
CPN1	1369	broad.mit.edu	37	chr10	101802226	101802226	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctcatctccatttctttCtttctggcttggggctgcac	8	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101802226C>T	ENST00000370418.3	-	9	1586	c.1335G>A	c.(1333-1335)aaG>aaA	p.K445K		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	445					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.K445K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CCATTTCTTTCTTTCTGGCTT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	10											97	86	89					10																	101802226		2203	4300	6503	101792216	SO:0001819	synonymous_variant	1369			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1335G>A	10.37:g.101802226C>T			101792216	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																				0.547	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101802226	C	T	101802226	2	4	61	1	0	0	0	0	0	0	0	1	3815	912	32	3		3	CPN1	10	101802226	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	134433	101802226	33732521	6953	14938										
CPN1	1369	broad.mit.edu	37	chr10	101814136	101814136	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggttaatcccactgacaGaaatgacagcattggcgaga	10	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101814136G>T	ENST00000370418.3	-	7	1330	c.1079C>A	c.(1078-1080)tCt>tAt	p.S360Y		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	360					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S360Y(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CCCACTGACAGAAATGACAGC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											217	187	197					10																	101814136		2203	4300	6503	101804126	SO:0001583	missense	1369			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1079C>A	10.37:g.101814136G>T	ENSP00000359446:p.Ser360Tyr		101804126	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.190035	0.78789	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.47869	0.83;0.83	4.23	4.23	0.50019	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.124895	0.56097	D	0.000032	T	0.65512	0.2698	M	0.66939	2.045	0.80722	D	1	D	0.71674	0.998	D	0.70016	0.967	T	0.66732	-0.5849	10	0.41790	T	0.15	-14.7348	16.3866	0.83507	0.0:0.0:1.0:0.0	.	360	P15169	CBPN_HUMAN	Y	360;157	ENSP00000359446:S360Y;ENSP00000410895:S157Y	ENSP00000359446:S360Y	S	-	2	0	CPN1	101804126	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.232000	0.95325	2.189000	0.69895	0.462000	0.41574	TCT		0.428	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101814136	G	T	101814136	3	4	61	1	0	0	0	0	1	0	0	0	3815	942	33	2	309	2	CPN1	10	101814136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11910	101814136	33720611	6954	14939										
CPN1	1369	broad.mit.edu	37	chr10	101835694	101835694	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagccacctcgtagccgtCggggttcatggatggcagga	15	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101835694C>T	ENST00000370418.3	-	2	645	c.394G>A	c.(394-396)Gac>Aac	p.D132N		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	132	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.D132N(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		TCGTAGCCGTCGGGGTTCATG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10											100	87	91					10																	101835694		2203	4300	6503	101825684	SO:0001583	missense	1369			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.394G>A	10.37:g.101835694C>T	ENSP00000359446:p.Asp132Asn		101825684	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	35	5.469642	0.96274	.	.	ENSG00000120054	ENST00000370418	D	0.83673	-1.75	5.74	5.74	0.90152	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	D	0.94912	0.8355	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96165	0.9118	10	0.87932	D	0	-19.2659	19.9353	0.97137	0.0:1.0:0.0:0.0	.	132	P15169	CBPN_HUMAN	N	132	ENSP00000359446:D132N	ENSP00000359446:D132N	D	-	1	0	CPN1	101825684	1.000000	0.71417	0.926000	0.36857	0.665000	0.39181	7.815000	0.86186	2.724000	0.93272	0.655000	0.94253	GAC		0.577	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101835694	C	T	101835694	3	4	61	1	0	0	0	0	1	0	0	0	3815	884	31	1	1014	1	CPN1	10	101835694	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21558	101835694	33699053	6955	14940										
CHUK	1147	broad.mit.edu	37	chr10	101964323	101964323	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgaatgcttttgtgaaAaaactccaatttagctttca	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101964323A>C	ENST00000370397.7	-	13	1533	c.1447T>G	c.(1447-1449)Ttt>Gtt	p.F483V		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	483					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.F483V(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CTTTTGTGAAAAAACTCCAAT	0.363																																					Ovarian(159;52 1904 10536 35305 37148)											1	Substitution - Missense(1)	large_intestine(1)	10											151	136	141					10																	101964323		2203	4300	6503	101954313	SO:0001583	missense	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1447T>G	10.37:g.101964323A>C	ENSP00000359424:p.Phe483Val		101954313	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	37	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.848575	0.91277	.	.	ENSG00000213341	ENST00000370397	D	0.84070	-1.8	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.90380	0.6989	M	0.79123	2.44	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.90096	0.4181	10	0.41790	T	0.15	-7.7482	14.1191	0.65175	1.0:0.0:0.0:0.0	.	483	O15111	IKKA_HUMAN	V	483	ENSP00000359424:F483V	ENSP00000359424:F483V	F	-	1	0	CHUK	101954313	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.224000	0.72417	0.528000	0.53228	TTT		0.363	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101964323	A	C	101964323	3	2	61	1	0	0	0	0	1	0	0	0	3422	14	1	4	826	4	CHUK	10	101964323	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	128629	101964323	33570424	6956	14941										
CHUK	1147	broad.mit.edu	37	chr10	101966987	101966987	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaaatggactggacttacCaatataatttacacaatcag	5	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:101966987C>A	ENST00000370397.7	-	11	1317	c.1231G>T	c.(1231-1233)Gta>Tta	p.V411L		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	411					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.V411L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CTGGACTTACCAATATAATTT	0.328																																					Ovarian(159;52 1904 10536 35305 37148)											1	Substitution - Missense(1)	large_intestine(1)	10											62	62	62					10																	101966987		2203	4297	6500	101956977	SO:0001630	splice_region_variant	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1231+1G>T	10.37:g.101966987C>A			101956977	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	37	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	C	0.455	-0.891990	0.02491	.	.	ENSG00000213341	ENST00000370397	T	0.55234	0.53	5.55	4.65	0.58169	.	0.000000	0.85682	U	0.000000	T	0.57330	0.2046	N	0.26042	0.785	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.55010	-0.8207	9	.	.	.	-11.9075	12.2262	0.54461	0.0:0.9173:0.0:0.0827	.	411	O15111	IKKA_HUMAN	L	411	ENSP00000359424:V411L	.	V	-	1	0	CHUK	101956977	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	7.814000	0.86154	1.348000	0.45733	-0.266000	0.10368	GTA		0.328	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	Missense_Mutation	A	101966987	C	A	101966987	5	1	61	1	0	0	0	0	0	0	1	0	3422	608	21	2	1050	2	CHUK	10	101966987	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2664	101966987	33567760	6957	14942										
BLOC1S2	282991	broad.mit.edu	37	chr10	102035223	102035223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagaaataagtttctcatCgcttctccagcttcttgtac	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102035223C>T	ENST00000370372.2	-	5	477	c.425G>A	c.(424-426)cGa>cAa	p.R142Q	BLOC1S2_ENST00000441611.1_Missense_Mutation_p.R99Q	NM_173809.4	NP_776170.2	Q6QNY1	BL1S2_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 2	142					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|melanosome organization (GO:0032438)|microtubule nucleation (GO:0007020)|mitochondrial outer membrane permeabilization (GO:0097345)|neuron projection development (GO:0031175)|platelet dense granule organization (GO:0060155)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	BLOC-1 complex (GO:0031083)|centrosome (GO:0005813)|gamma-tubulin complex (GO:0000930)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	gamma-tubulin binding (GO:0043015)|protein C-terminus binding (GO:0008022)	p.R142Q(1)		large_intestine(1)|lung(2)|ovary(1)	4		Colorectal(252;0.117)		Epithelial(162;2.44e-10)|all cancers(201;1.97e-08)		AGTTTCTCATCGCTTCTCCAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											144	146	145					10																	102035223		2203	4300	6503	102025213	SO:0001583	missense	282991			AK054697	CCDS7490.1, CCDS73179.1	10q24.31	2012-08-01	2008-08-11		ENSG00000196072	ENSG00000196072		"Biogenesis of lysosomal organelles complex-1 subunits"	20984	protein-coding gene	gene with protein product	"centrosome protein oncogene", "Biogenesis of Lysosome-related Organelles complex-1 Subunit 2", "BLOC-1 subunit 2"	609768				11483580, 15102850	Standard	NM_173809		Approved	MGC10120, FLJ30135, BLOS2	uc001kqw.2	Q6QNY1	OTTHUMG00000018908	ENST00000370372.2:c.425G>A	10.37:g.102035223C>T	ENSP00000359398:p.Arg142Gln		102025213	B4DQV2|Q5W040|Q8WUI8	Missense_Mutation	SNP	ENST00000370372.2	37	CCDS7490.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.250259	0.80024	.	.	ENSG00000196072	ENST00000361832;ENST00000358848;ENST00000441611;ENST00000370372	.	.	.	5.53	5.53	0.82687	.	0.062989	0.64402	D	0.000003	T	0.76463	0.3991	M	0.70595	2.14	0.80722	D	1	D	0.64830	0.994	P	0.61201	0.885	T	0.78790	-0.2066	9	0.72032	D	0.01	.	16.6117	0.84885	0.0:1.0:0.0:0.0	.	142	Q6QNY1	BL1S2_HUMAN	Q	74;142;99;74	.	ENSP00000351716:R142Q	R	-	2	0	BLOC1S2	102025213	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	6.668000	0.74457	2.602000	0.87976	0.555000	0.69702	CGA		0.368	BLOC1S2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049861.2	NM_173809		T	102035223	C	T	102035223	3	4	61	1	0	0	0	0	1	0	0	0	1450	884	31	1	7	1	BLOC1S2	10	102035223	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68236	102035223	33499524	6958	14943										
PKD2L1	9033	broad.mit.edu	37	chr10	102055945	102055945	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtctgccagaaggcgagGaactcaaagtctgcatacgt	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102055945G>A	ENST00000318222.3	-	7	1672	c.1290C>T	c.(1288-1290)ttC>ttT	p.F430F	PKD2L1_ENST00000353274.3_Silent_p.F430F|PKD2L1_ENST00000338519.3_Silent_p.F355F	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	430					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)	p.F430F(1)		NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		AGAAGGCGAGGAACTCAAAGT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	10											170	132	145					10																	102055945		2203	4300	6503	102045935	SO:0001819	synonymous_variant	9033			AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.1290C>T	10.37:g.102055945G>A			102045935	O75972|Q5W039|Q9UP35|Q9UPA2	Silent	SNP	ENST00000318222.3	37	CCDS7492.1																																																																																				0.527	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		A	102055945	G	A	102055945	2	1	61	1	0	0	0	0	0	0	0	1	11998	1165	41	3		3	PKD2L1	10	102055945	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20722	102055945	33478802	6959	14944										
SEC31B	25956	broad.mit.edu	37	chr10	102262142	102262142	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcatcaggaattcagattCtgtggtgacttgactgatga	11	7	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102262142C>A	ENST00000370345.3	-	11	1376	c.1279G>T	c.(1279-1281)Gaa>Taa	p.E427*	SEC31B_ENST00000451524.1_Nonsense_Mutation_p.E427*|SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	427					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)		p.E427*(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		AATTCAGATTCTGTGGTGACT	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											82	78	79					10																	102262142		2203	4300	6503	102252132	SO:0001587	stop_gained	25956			AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1279G>T	10.37:g.102262142C>A	ENSP00000359370:p.Glu427*		102252132	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Nonsense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	c	37	6.134900	0.97315	.	.	ENSG00000075826	ENST00000370345;ENST00000451524	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.0334	18.3476	0.90327	0.0:1.0:0.0:0.0	.	.	.	.	X	427	.	ENSP00000359370:E427X	E	-	1	0	SEC31B	102252132	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.538000	0.82048	2.582000	0.87167	0.556000	0.70494	GAA		0.532	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		A	102262142	C	A	102262142	4	1	61	1	0	0	0	0	0	1	0	0	14036	922	32	2	2324	2	SEC31B	10	102262142	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	206197	102262142	33272605	6960	14945										
HIF1AN	55662	broad.mit.edu	37	chr10	102296271	102296271	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagacttctctgtgtacaGtgccagcacccacaagttct	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102296271G>A	ENST00000299163.6	+	2	381	c.281G>A	c.(280-282)aGt>aAt	p.S94N	HIF1AN_ENST00000528044.1_3'UTR	NM_017902.2	NP_060372.2	Q9NWT6	HIF1N_HUMAN	hypoxia inducible factor 1, alpha subunit inhibitor	94	Interaction with VHL.				cellular response to hypoxia (GO:0071456)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|oxidation-reduction process (GO:0055114)|peptidyl-asparagine hydroxylation (GO:0042265)|peptidyl-aspartic acid hydroxylation (GO:0042264)|peptidyl-histidine hydroxylation (GO:0036138)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of vasculogenesis (GO:2001214)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ankyrin repeat binding (GO:0071532)|carboxylic acid binding (GO:0031406)|cofactor binding (GO:0048037)|iron ion binding (GO:0005506)|NF-kappaB binding (GO:0051059)|Notch binding (GO:0005112)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-asparagine 3-dioxygenase activity (GO:0036140)|peptidyl-histidine dioxygenase activity (GO:0036139)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.S94N(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	10		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)		TCTGTGTACAGTGCCAGCACC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											103	104	104					10																	102296271		2203	4300	6503	102286261	SO:0001583	missense	55662			AK000622	CCDS7498.1	10q24	2008-12-18	2008-12-02		ENSG00000166135	ENSG00000166135	1.14.11.16		17113	protein-coding gene	gene with protein product	"Peptide-aspartate beta-dioxygenase"	606615				11641274	Standard	NM_017902		Approved	FLJ20615, DKFZp762F1811, FLJ22027, FIH1	uc001krj.4	Q9NWT6	OTTHUMG00000018911	ENST00000299163.6:c.281G>A	10.37:g.102296271G>A	ENSP00000299163:p.Ser94Asn		102286261	D3DR69|Q5W147|Q969Q7|Q9NPV5	Missense_Mutation	SNP	ENST00000299163.6	37	CCDS7498.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686500	0.29962	.	.	ENSG00000166135	ENST00000299163;ENST00000442724	T	0.69806	-0.43	5.7	5.7	0.88788	.	0.175795	0.64402	D	0.000008	T	0.51244	0.1663	N	0.12182	0.205	0.43292	D	0.995272	B	0.14438	0.01	B	0.12837	0.008	T	0.43750	-0.9372	10	0.19147	T	0.46	-10.097	19.8212	0.96595	0.0:0.0:1.0:0.0	.	94	Q9NWT6	HIF1N_HUMAN	N	94;127	ENSP00000299163:S94N	ENSP00000299163:S94N	S	+	2	0	HIF1AN	102286261	0.997000	0.39634	1.000000	0.80357	0.957000	0.61999	2.156000	0.42310	2.694000	0.91930	0.650000	0.86243	AGT		0.453	HIF1AN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049865.5	NM_017902		A	102296271	G	A	102296271	3	1	61	1	0	0	0	0	1	0	0	0	7125	1029	36	3	287	3	HIF1AN	10	102296271	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34129	102296271	33238476	6961	14946										
PAX2	5076	broad.mit.edu	37	chr10	102566243	102566243	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtggtgtggacagtttgCggaagcacttgcgagctgac	16	7	0	2	rs142737641		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102566243C>T	ENST00000428433.1	+	7	1292	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	PAX2_ENST00000370296.2_Missense_Mutation_p.R248W|PAX2_ENST00000361791.3_Missense_Mutation_p.R225W|PAX2_ENST00000553492.1_3'UTR|PAX2_ENST00000355243.3_Missense_Mutation_p.R225W|PAX2_ENST00000556085.1_Missense_Mutation_p.R224W	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	248					aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)	p.R225W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		GGACAGTTTGCGGAAGCACTT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	211	191	198		673,742,673,673,742	5.1	1	10	dbSNP_134	198	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	PAX2	NM_000278.3,NM_003987.3,NM_003988.3,NM_003989.3,NM_003990.3	101,101,101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	225/395,248/418,225/397,225/410,248/433	102566243	1,13005	2203	4300	6503	102556233	SO:0001583	missense	5076				CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"Paired boxes", "Homeoboxes / PRD class"	8616	protein-coding gene	gene with protein product		167409	"paired box gene 2"			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.742C>T	10.37:g.102566243C>T	ENSP00000396259:p.Arg248Trp		102556233	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Missense_Mutation	SNP	ENST00000428433.1	37	CCDS53569.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608507	0.87258	2.27E-4	0.0	ENSG00000075891	ENST00000370294;ENST00000370296;ENST00000428433;ENST00000361791;ENST00000355243;ENST00000556085;ENST00000554172	D;D;D;D;D;D	0.98666	-4.9;-5.06;-4.79;-4.79;-4.78;-5.03	5.06	5.06	0.68205	Homeodomain-related (1);	0.054868	0.64402	D	0.000001	D	0.99336	0.9767	M	0.92833	3.35	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.992;0.997;0.987;0.998;0.999;0.999	D	0.98858	1.0761	10	0.87932	D	0	.	17.4294	0.87535	0.0:1.0:0.0:0.0	.	224;248;225;221;248;225;221	G3V5U4;Q02962-2;Q02962-3;Q6YFJ8;Q02962;Q02962-4;G3V5S4	.;.;.;.;PAX2_HUMAN;.;.	W	140;248;248;225;225;224;221	ENSP00000359319:R248W;ENSP00000396259:R248W;ENSP00000355069:R225W;ENSP00000347385:R225W;ENSP00000452527:R224W;ENSP00000452489:R221W	ENSP00000347385:R225W	R	+	1	2	PAX2	102556233	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.679000	0.54634	2.326000	0.78906	0.462000	0.41574	CGG		0.577	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	102566243	C	T	102566243	3	4	61	1	0	0	0	0	1	0	0	0	11510	759	27	1	768	1	PAX2	10	102566243	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	269972	102566243	32968504	6962	14947										
FAM178A	55719	broad.mit.edu	37	chr10	102698458	102698458	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatctttgtttcccctggaGaatcttcagccagactttaa	7	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102698458G>T	ENST00000238961.4	+	11	3161	c.2619G>T	c.(2617-2619)gaG>gaT	p.E873D	FAM178A_ENST00000370269.3_Missense_Mutation_p.E873D	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	873						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.E873D(1)									TTCCCCTGGAGAATCTTCAGC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											177	173	174					10																	102698458		2203	4300	6503	102688448	SO:0001583	missense	55719			AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.2619G>T	10.37:g.102698458G>T	ENSP00000238961:p.Glu873Asp		102688448	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.443152	0.43326	.	.	ENSG00000119906	ENST00000238961;ENST00000370269	T;T	0.31769	1.49;1.48	6.08	6.08	0.98989	.	0.318751	0.29987	N	0.010684	T	0.13970	0.0338	N	0.03608	-0.345	0.27901	N	0.938973	B;B	0.32467	0.372;0.372	B;B	0.33392	0.163;0.163	T	0.13737	-1.0498	10	0.30078	T	0.28	-16.9362	9.0063	0.36113	0.0769:0.1498:0.7733:0.0	.	873;873	Q8IX21;B1AL17	F178A_HUMAN;.	D	873	ENSP00000238961:E873D;ENSP00000359292:E873D	ENSP00000238961:E873D	E	+	3	2	FAM178A	102688448	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.301000	0.19174	2.894000	0.99253	0.591000	0.81541	GAG		0.363	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102698458	G	T	102698458	3	4	61	1	0	0	0	0	1	0	0	0	5519	933	33	2	2661	2	FAM178A	10	102698458	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132215	102698458	32836289	6963	14948										
C10orf2	56652	broad.mit.edu	37	chr10	102748293	102748293	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcattgacaagaccacagGccactttctctgcatgacca	6	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102748293G>A	ENST00000311916.2	+	1	511	c.326G>A	c.(325-327)gGc>gAc	p.G109D	MRPL43_ENST00000318325.2_5'Flank|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000370236.1_5'Flank|MRPL43_ENST00000370234.4_5'Flank|C10orf2_ENST00000473656.1_Intron|MRPL43_ENST00000477279.1_5'Flank|MRPL43_ENST00000299179.5_5'Flank|MRPL43_ENST00000342071.1_5'Flank|MRPL43_ENST00000318364.8_5'Flank|C10orf2_ENST00000370228.1_Missense_Mutation_p.G109D|MRPL43_ENST00000370241.3_5'Flank|MRPL43_ENST00000493646.1_5'Flank|MRPL43_ENST00000370242.4_5'Flank	NM_001163813.1|NM_021830.4	NP_001157285.1|NP_068602.2	Q96RR1	PEO1_HUMAN	chromosome 10 open reading frame 2	109					cell death (GO:0008219)|DNA unwinding involved in DNA replication (GO:0006268)|mitochondrial DNA replication (GO:0006264)|protein hexamerization (GO:0034214)|protein homooligomerization (GO:0051260)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial nucleoid (GO:0042645)	5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.G109D(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|stomach(1)	24		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AAGACCACAGGCCACTTTCTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	123	120					10																	102748293		2203	4300	6503	102738283	SO:0001583	missense	56652			AF292004	CCDS7506.1, CCDS53570.1	10q24	2013-05-13			ENSG00000107815	ENSG00000107815			1160	protein-coding gene	gene with protein product	"twinkle", "T7 helicase-related protein with intramitochondrial nucleoid localization"	606075	"infantile onset spinocerebellar ataxia (autosomal recessive)"	IOSCA		11431692, 10645945, 16135556	Standard	NM_021830		Approved	PEO, PEO1, TWINKLE, FLJ21832, TWINL	uc001ksf.2	Q96RR1	OTTHUMG00000018917	ENST00000311916.2:c.326G>A	10.37:g.102748293G>A	ENSP00000309595:p.Gly109Asp		102738283	B2CQL2|Q6MZX2|Q6PJP5|Q96RR0	Missense_Mutation	SNP	ENST00000311916.2	37	CCDS7506.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.525806	0.85600	.	.	ENSG00000107815	ENST00000311916;ENST00000370228	D;D	0.97924	-4.35;-4.61	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99509	1.0955	10	0.62326	D	0.03	-26.3494	18.0	0.89196	0.0:0.0:1.0:0.0	.	109;109	Q96RR1-2;Q96RR1	.;PEO1_HUMAN	D	109	ENSP00000309595:G109D;ENSP00000359248:G109D	ENSP00000309595:G109D	G	+	2	0	C10orf2	102738283	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.578000	0.98200	2.593000	0.87608	0.455000	0.32223	GGC		0.587	C10orf2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049886.1	NM_021830		A	102748293	G	A	102748293	3	1	61	1	0	0	0	0	1	0	0	0	1601	1203	42	3	328	3	C10orf2	10	102748293	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49835	102748293	32786454	6964	14949										
LBX1	10660	broad.mit.edu	37	chr10	102987347	102987347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcttgagcttagcgcgccGattctggaaccaggtgatga	13	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:102987347G>A	ENST00000370193.2	-	2	1504	c.526C>T	c.(526-528)Cgg>Tgg	p.R176W	LBX1-AS1_ENST00000547077.1_RNA|LBX1-AS1_ENST00000546988.1_RNA	NM_006562.4	NP_006553.2	P52954	LBX1_HUMAN	ladybird homeobox 1	176					anatomical structure morphogenesis (GO:0009653)|heart looping (GO:0001947)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neuron fate determination (GO:0048664)|regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification (GO:0021920)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R176W(2)		large_intestine(2)|lung(4)|ovary(1)	7		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)		TTAGCGCGCCGATTCTGGAAC	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	10											74	75	75					10																	102987347		2203	4300	6503	102977337	SO:0001583	missense	10660			X90828	CCDS31270.1	10q24.32	2011-06-20	2007-02-15		ENSG00000138136	ENSG00000138136		"Homeoboxes / ANTP class : NKL subclass"	16960	protein-coding gene	gene with protein product		604255	"ladybird homeobox homolog 1 (Drosophila)"			8645601	Standard	XM_005269443		Approved	LBX1H, HPX6	uc001ksx.3	P52954	OTTHUMG00000018927	ENST00000370193.2:c.526C>T	10.37:g.102987347G>A	ENSP00000359212:p.Arg176Trp		102977337	B9EGA2|Q05BB2	Missense_Mutation	SNP	ENST00000370193.2	37	CCDS31270.1	.	.	.	.	.	.	.	.	.	.	G	31	5.071438	0.93950	.	.	ENSG00000138136	ENST00000370193	D	0.97831	-4.56	5.61	5.61	0.85477	Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99378	0.9781	H	0.98721	4.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98350	1.0543	10	0.87932	D	0	.	19.2382	0.93871	0.0:0.0:1.0:0.0	.	176	P52954	LBX1_HUMAN	W	176	ENSP00000359212:R176W	ENSP00000359212:R176W	R	-	1	2	LBX1	102977337	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.777000	0.85628	2.646000	0.89796	0.561000	0.74099	CGG		0.627	LBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049928.3	NM_006562		A	102987347	G	A	102987347	3	1	61	1	0	0	0	0	1	0	0	0	8675	1057	37	1	323	1	LBX1	10	102987347	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239054	102987347	32547400	6965	14950										
BTRC	8945	broad.mit.edu	37	chr10	103285772	103285772	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccccctactgaaagctCggggattggatcatattgct	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:103285772C>T	ENST00000370187.3	+	6	677	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	BTRC_ENST00000408038.2_Missense_Mutation_p.R151W|BTRC_ENST00000393441.4_Missense_Mutation_p.R146W	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	187					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R187W(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		ACTGAAAGCTCGGGGATTGGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	10											87	70	76					10																	103285772		2203	4300	6503	103275762	SO:0001583	missense	8945			Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.559C>T	10.37:g.103285772C>T	ENSP00000359206:p.Arg187Trp		103275762	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.704605	0.88924	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038;ENST00000370183	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.53	5.53	0.82687	F-box domain, Skp2-like (1);	0.000000	0.64402	D	0.000002	T	0.41994	0.1183	M	0.71581	2.175	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	P;P;P	0.54544	0.596;0.755;0.713	T	0.34950	-0.9808	10	0.87932	D	0	-11.1644	19.4679	0.94950	0.0:1.0:0.0:0.0	.	161;151;187	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	W	187;146;151;169	ENSP00000359206:R187W;ENSP00000377088:R146W;ENSP00000385339:R151W;ENSP00000359202:R169W	ENSP00000359202:R169W	R	+	1	2	BTRC	103275762	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.818000	0.86416	2.611000	0.88343	0.650000	0.86243	CGG		0.438	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		T	103285772	C	T	103285772	3	4	61	1	0	0	0	0	1	0	0	0	1572	875	31	1	581	1	BTRC	10	103285772	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298425	103285772	32248975	6966	14951										
BTRC	8945	broad.mit.edu	37	chr10	103310477	103310477	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcattccggaagagtttttCgactacagtttgatgaattc	9	7	0	3	rs375317445		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:103310477C>T	ENST00000370187.3	+	14	1796	c.1678C>T	c.(1678-1680)Cga>Tga	p.R560*	BTRC_ENST00000408038.2_Nonsense_Mutation_p.R524*|BTRC_ENST00000393441.4_Nonsense_Mutation_p.R519*|BTRC_ENST00000493877.1_3'UTR	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	560					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R560*(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AAGAGTTTTTCGACTACAGTT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	10						C	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	171	158	162		1570,1678	6.1	1	10		162	0,8600		0,0,4300	no	stop-gained,stop-gained	BTRC	NM_003939.3,NM_033637.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	524/570,560/606	103310477	1,13005	2203	4300	6503	103300467	SO:0001587	stop_gained	8945			Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1678C>T	10.37:g.103310477C>T	ENSP00000359206:p.Arg560*		103300467	B5MD49|Q5W141|Q5W142|Q9Y213	Nonsense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	C	37	6.386582	0.97524	2.27E-4	0.0	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	.	.	.	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-6.067	20.6282	0.99521	0.0:1.0:0.0:0.0	.	.	.	.	X	560;519;524	.	ENSP00000359206:R560X	R	+	1	2	BTRC	103300467	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.024000	0.49674	2.871000	0.98454	0.655000	0.94253	CGA		0.408	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		T	103310477	C	T	103310477	4	4	61	1	0	0	0	0	0	1	0	0	1572	876	31	1	1732	1	BTRC	10	103310477	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24705	103310477	32224270	6967	14952										
KCNIP2	30819	broad.mit.edu	37	chr10	103587117	103587117	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctcctgggggctagatgAcattgtcaaagagctgcatg	12	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:103587117A>G	ENST00000356640.2	-	10	1081	c.806T>C	c.(805-807)gTc>gCc	p.V269A	KCNIP2_ENST00000461105.1_Missense_Mutation_p.V284A|KCNIP2_ENST00000370046.1_Missense_Mutation_p.V183A|KCNIP2_ENST00000343195.4_Missense_Mutation_p.V219A|KCNIP2-AS1_ENST00000412353.1_RNA|KCNIP2_ENST00000353068.3_Missense_Mutation_p.V226A|KCNIP2_ENST00000358038.3_Missense_Mutation_p.V251A|KCNIP2_ENST00000355657.2_5'UTR|KCNIP2_ENST00000348850.5_Missense_Mutation_p.V224A	NM_014591.4|NM_173191.2	NP_055406.2|NP_775283.1	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2	269	Interaction with KCND2. {ECO:0000250}.				clustering of voltage-gated potassium channels (GO:0045163)|detection of calcium ion (GO:0005513)|membrane repolarization (GO:0086009)|muscle contraction (GO:0006936)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|calcium ion binding (GO:0005509)|ER retention sequence binding (GO:0046923)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein N-terminus binding (GO:0047485)	p.V284A(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		GGGCTAGATGACATTGTCAAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											163	146	152					10																	103587117		2203	4300	6503	103577107	SO:0001583	missense	30819				CCDS7521.1, CCDS7522.1, CCDS7523.1, CCDS7524.1, CCDS7525.1, CCDS7526.1, CCDS41562.1	10q24.32	2013-09-20	2001-11-29		ENSG00000120049	ENSG00000120049		"EF-hand domain containing"	15522	protein-coding gene	gene with protein product		604661	"Kv channel-interacting protein 2"			10676964	Standard	NM_173192		Approved	KCHIP2	uc001kuc.3	Q9NS61	OTTHUMG00000018937	ENST00000356640.2:c.806T>C	10.37:g.103587117A>G	ENSP00000349055:p.Val269Ala		103577107	A6NJE5|A8MQ75|Q3YAC6|Q3YAC8|Q3YAC9|Q7Z6F1|Q96K86|Q96T41|Q96T42|Q96T43|Q96T44|Q9H0N4|Q9HD10|Q9HD11|Q9NS60|Q9NY10|Q9NZI1	Missense_Mutation	SNP	ENST00000356640.2	37	CCDS7522.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618351	0.46736	.	.	ENSG00000120049	ENST00000348850;ENST00000358038;ENST00000359877;ENST00000370059;ENST00000356640;ENST00000370046;ENST00000434163;ENST00000353068;ENST00000461105;ENST00000343195	T;T;T;T;T;T;T;T	0.73363	-0.49;-0.73;-0.7;-0.48;-0.57;-0.53;-0.74;-0.46	4.8	4.8	0.61643	.	0.135528	0.47852	D	0.000210	T	0.79621	0.4477	L	0.43923	1.385	0.58432	D	0.999995	B;P;P;P;P;P;P;B;B;B;B	0.49185	0.051;0.661;0.53;0.661;0.885;0.661;0.92;0.291;0.061;0.168;0.004	B;P;B;P;P;P;P;B;B;B;B	0.61201	0.251;0.52;0.321;0.52;0.885;0.52;0.788;0.176;0.227;0.072;0.088	T	0.78780	-0.2070	10	0.39692	T	0.17	.	14.8014	0.69919	1.0:0.0:0.0:0.0	.	213;215;218;219;251;226;284;269;200;224;176	B4DHY9;Q9NS61-5;Q3YAC7;Q9NS61-3;Q9NS61-2;Q9NS61-7;Q9NS61-6;Q9NS61;B3KSZ5;Q3YAC6;Q9NS61-8	.;.;.;.;.;.;.;KCIP2_HUMAN;.;.;.	A	224;251;200;251;269;183;176;226;284;219	ENSP00000239118:V224A;ENSP00000350733:V251A;ENSP00000349055:V269A;ENSP00000359063:V183A;ENSP00000411679:V176A;ENSP00000341624:V226A;ENSP00000420040:V284A;ENSP00000344169:V219A	ENSP00000344169:V219A	V	-	2	0	KCNIP2	103577107	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.087000	0.94110	2.152000	0.67230	0.459000	0.35465	GTC		0.532	KCNIP2-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049973.1			G	103587117	A	G	103587117	3	3	61	1	0	0	0	0	1	0	0	0	8061	275	10	4	10	4	KCNIP2	10	103587117	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	276640	103587117	31947630	6968	14953										
HPS6	79803	broad.mit.edu	37	chr10	103827491	103827491	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggctgtcgggcccagttCtaagcccatatgaggacatc	12	11	1	1	rs202188533		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:103827491C>A	ENST00000299238.5	+	1	2345	c.2260C>A	c.(2260-2262)Cta>Ata	p.L754I		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	754					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)	p.L754I(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		GGGCCCAGTTCTAAGCCCATA	0.612									Hermansky-Pudlak syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	10											34	36	35					10																	103827491		2199	4297	6496	103817481	SO:0001583	missense	79803	Familial Cancer Database	HPS, HPS1-8	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.2260C>A	10.37:g.103827491C>A	ENSP00000299238:p.Leu754Ile		103817481	Q5VV69|Q9H685	Missense_Mutation	SNP	ENST00000299238.5	37	CCDS7527.1	.	.	.	.	.	.	.	.	.	.	C	4.473	0.087629	0.08583	.	.	ENSG00000166189	ENST00000299238	T	0.78924	-1.22	4.12	3.19	0.36642	.	0.643920	0.11938	N	0.514998	T	0.55689	0.1936	N	0.08118	0	0.22982	N	0.998473	B	0.29646	0.253	B	0.27500	0.08	T	0.44221	-0.9342	10	0.27785	T	0.31	-1.2486	7.3204	0.26523	0.0:0.7309:0.1748:0.0943	.	754	Q86YV9	HPS6_HUMAN	I	754	ENSP00000299238:L754I	ENSP00000299238:L754I	L	+	1	2	HPS6	103817481	0.990000	0.36364	1.000000	0.80357	0.103000	0.19146	0.450000	0.21762	1.284000	0.44531	0.655000	0.94253	CTA		0.612	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747		A	103827491	C	A	103827491	3	1	61	1	0	0	0	0	1	0	0	0	7364	912	32	2	2262	2	HPS6	10	103827491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240374	103827491	31707256	6969	14954										
LDB1	8861	broad.mit.edu	37	chr10	103869710	103869710	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctgcgggggatgagctCtcggtgctgccggatgctga	18	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:103869710C>A	ENST00000425280.1	-	7	958	c.616G>T	c.(616-618)Gag>Tag	p.E206*	LDB1_ENST00000490751.1_5'Flank|LDB1_ENST00000361198.5_Nonsense_Mutation_p.E170*	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	206					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)	p.E170*(1)		breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		GGGATGAGCTCTCGGTGCTGC	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											123	104	111					10																	103869710		2203	4300	6503	103859700	SO:0001587	stop_gained	8861			AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.616G>T	10.37:g.103869710C>A	ENSP00000392466:p.Glu206*		103859700	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Nonsense_Mutation	SNP	ENST00000425280.1	37	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	C	39	7.770769	0.98480	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9528	0.92646	0.0:1.0:0.0:0.0	.	.	.	.	X	170;206	.	ENSP00000354616:E170X	E	-	1	0	LDB1	103859700	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.482000	0.83794	0.462000	0.41574	GAG		0.597	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		A	103869710	C	A	103869710	4	1	61	1	0	0	0	0	0	1	0	0	8717	922	32	2	639	2	LDB1	10	103869710	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42219	103869710	31665037	6970	14955										
GBF1	8729	broad.mit.edu	37	chr10	104119978	104119978	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggtcttccctgcatccgCgagctcttccgcttcctcat	7	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104119978C>T	ENST00000369983.3	+	12	1475	c.1215C>T	c.(1213-1215)cgC>cgT	p.R405R	GBF1_ENST00000476019.1_Intron	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	405					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.R405R(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTGCATCCGCGAGCTCTTCC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	10											333	326	328					10																	104119978		2203	4300	6503	104109968	SO:0001819	synonymous_variant	8729			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.1215C>T	10.37:g.104119978C>T			104109968	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																				0.542	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104119978	C	T	104119978	2	4	61	1	0	0	0	0	0	0	0	1	6291	755	27	1		1	GBF1	10	104119978	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	250268	104119978	31414769	6971	14956										
GBF1	8729	broad.mit.edu	37	chr10	104136708	104136708	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggatgcaagtcccaggaGaaacgtggcaagagtcacaa	12	9	2	2	rs371570408		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104136708G>T	ENST00000369983.3	+	33	4562	c.4302G>T	c.(4300-4302)gaG>gaT	p.E1434D		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1434					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.E1434D(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		AGTCCCAGGAGAAACGTGGCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	10											89	85	86					10																	104136708		2203	4300	6503	104126698	SO:0001583	missense	8729			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4302G>T	10.37:g.104136708G>T	ENSP00000359000:p.Glu1434Asp		104126698	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	7.731	0.699212	0.15106	.	.	ENSG00000107862	ENST00000369983	T	0.10099	2.91	5.22	2.08	0.27032	.	0.142233	0.64402	N	0.000005	T	0.09468	0.0233	L	0.54323	1.7	0.39072	D	0.960745	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.15867	-1.0422	10	0.15952	T	0.53	-10.3837	8.3053	0.32038	0.155:0.0:0.7103:0.1347	.	1434;1434;1434	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	D	1434	ENSP00000359000:E1434D	ENSP00000359000:E1434D	E	+	3	2	GBF1	104126698	0.978000	0.34361	1.000000	0.80357	0.983000	0.72400	0.071000	0.14594	0.734000	0.32515	0.561000	0.74099	GAG		0.517	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104136708	G	T	104136708	3	4	61	1	0	0	0	0	1	0	0	0	6291	933	33	2	4428	2	GBF1	10	104136708	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16730	104136708	31398039	6972	14957										
NFKB2	4791	broad.mit.edu	37	chr10	104156492	104156492	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccttcagagaggcttccGatttcgatatggctgtgaag	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104156492G>A	ENST00000369966.3	+	5	405	c.155G>A	c.(154-156)cGa>cAa	p.R52Q	NFKB2_ENST00000428099.1_Missense_Mutation_p.R52Q|NFKB2_ENST00000189444.6_Missense_Mutation_p.R52Q	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	52	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.R52Q(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	AGAGGCTTCCGATTTCGATAT	0.577			T	IGH@	B-NHL																																		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	1	Substitution - Missense(1)	large_intestine(1)	10											75	74	74					10																	104156492		2017	4163	6180	104146482	SO:0001583	missense	4791			X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.155G>A	10.37:g.104156492G>A	ENSP00000358983:p.Arg52Gln		104146482	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262561	0.95399	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.72505	-0.66;-0.66;-0.66	5.15	5.15	0.70609	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.142200	0.44902	D	0.000411	D	0.87229	0.6125	M	0.91406	3.205	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.967;0.991	D	0.90205	0.4260	10	0.87932	D	0	.	16.3809	0.83461	0.0:0.0:1.0:0.0	.	52;52;52	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	Q	52	ENSP00000410256:R52Q;ENSP00000358983:R52Q;ENSP00000189444:R52Q	ENSP00000189444:R52Q	R	+	2	0	NFKB2	104146482	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.833000	0.86765	2.369000	0.80426	0.561000	0.74099	CGA		0.577	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104156492	G	A	104156492	3	1	61	1	0	0	0	0	1	0	0	0	10407	1058	37	1	169	1	NFKB2	10	104156492	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19784	104156492	31378255	6973	14958										
ARL3	403	broad.mit.edu	37	chr10	104436657	104436657	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcgtctagattttatttCttctttgcattgacattttt	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104436657C>A	ENST00000260746.5	-	6	674	c.543G>T	c.(541-543)aaG>aaT	p.K181N		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	181					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)	p.K181N(1)		large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		GATTTTATTTCTTCTTTGCAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											157	163	161					10																	104436657		2203	4300	6503	104426647	SO:0001583	missense	403			U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.543G>T	10.37:g.104436657C>A	ENSP00000260746:p.Lys181Asn		104426647	B2R6C7|Q53X83|Q5JSM2	Missense_Mutation	SNP	ENST00000260746.5	37	CCDS7538.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.397166	0.42512	.	.	ENSG00000138175	ENST00000260746	T	0.72394	-0.65	5.46	4.56	0.56223	.	0.140671	0.64402	D	0.000004	T	0.69070	0.3070	M	0.73598	2.24	0.58432	D	0.99999	P	0.38250	0.624	B	0.34590	0.186	T	0.70498	-0.4855	10	0.41790	T	0.15	-20.9172	14.2274	0.65868	0.0:0.9282:0.0:0.0718	.	181	P36405	ARL3_HUMAN	N	181	ENSP00000260746:K181N	ENSP00000260746:K181N	K	-	3	2	ARL3	104426647	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.409000	0.44583	1.300000	0.44818	0.561000	0.74099	AAG		0.428	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311		A	104436657	C	A	104436657	3	1	61	1	0	0	0	0	1	0	0	0	936	912	32	2	9	2	ARL3	10	104436657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280165	104436657	31098090	6974	14959										
CNNM2	54805	broad.mit.edu	37	chr10	104679492	104679492	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaactgctggagatgctcCgggtcaccgatccctacaac	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104679492C>T	ENST00000369878.4	+	1	1443	c.1255C>T	c.(1255-1257)Cgg>Tgg	p.R419W	CNNM2_ENST00000369875.3_Missense_Mutation_p.R419W|CNNM2_ENST00000433628.2_Missense_Mutation_p.R419W	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	419	DUF21.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)	p.R419W(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGAGATGCTCCGGGTCACCGA	0.607																																																2	Substitution - Missense(2)	large_intestine(2)	10											81	81	81					10																	104679492		2203	4300	6503	104669482	SO:0001583	missense	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1255C>T	10.37:g.104679492C>T	ENSP00000358894:p.Arg419Trp		104669482	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.596869	0.46318	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	D;D;D	0.88896	-2.44;-2.44;-2.44	4.44	4.44	0.53790	Domain of unknown function DUF21 (1);	0.000000	0.85682	D	0.000000	D	0.93874	0.8040	M	0.84326	2.69	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.76575	0.972;0.983;0.988	D	0.94332	0.7563	10	0.87932	D	0	.	11.2054	0.48767	0.3221:0.6779:0.0:0.0	.	419;419;419	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	W	419	ENSP00000392875:R419W;ENSP00000358891:R419W;ENSP00000358894:R419W	ENSP00000286899:R419W	R	+	1	2	CNNM2	104669482	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.813000	0.55636	1.990000	0.58119	0.561000	0.74099	CGG		0.607	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104679492	C	T	104679492	3	4	61	1	0	0	0	0	1	0	0	0	3619	643	23	1	1257	1	CNNM2	10	104679492	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	242835	104679492	30855255	6975	14960										
CNNM2	54805	broad.mit.edu	37	chr10	104687123	104687123	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacacaaacaagaaacccaAatcataccaacactgaaaag	3	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104687123A>C	ENST00000369878.4	+	1	1809				CNNM2_ENST00000369875.3_Missense_Mutation_p.K548T|CNNM2_ENST00000433628.2_Intron	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2						magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)	p.K548T(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AAGAAACCCAAATCATACCAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											162	155	157					10																	104687123		2203	4300	6503	104677113	SO:0001627	intron_variant	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1621+7265A>C	10.37:g.104687123A>C			104677113	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	A	10.62	1.400379	0.25291	.	.	ENSG00000148842	ENST00000369875;ENST00000541201	T	0.75260	-0.92	2.7	2.7	0.31948	.	.	.	.	.	T	0.61274	0.2334	L	0.39898	1.24	0.21861	N	0.999506	B	0.19935	0.04	B	0.12837	0.008	T	0.45293	-0.9271	9	0.22109	T	0.4	.	7.2794	0.26302	1.0:0.0:0.0:0.0	.	548	F5H1I3	.	T	548	ENSP00000358891:K548T	ENSP00000358891:K548T	K	+	2	0	CNNM2	104677113	0.004000	0.15560	0.032000	0.17829	0.877000	0.50540	1.588000	0.36633	1.500000	0.48636	0.459000	0.35465	AAA		0.338	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		C	104687123	A	C	104687123	1	2	61	0	1	0	0	0	0	0	0	0	3619	14	1	4		4	CNNM2	10	104687123	Intron	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7631	104687123	30847624	6976	14961										
CNNM2	54805	broad.mit.edu	37	chr10	104809536	104809536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccattttatgaagttctggGaatcgtcaccttagaagatg	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:104809536G>A	ENST00000369878.4	+	2	1882	c.1694G>A	c.(1693-1695)gGa>gAa	p.G565E	CNNM2_ENST00000433628.2_Missense_Mutation_p.G565E	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	565	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)	p.G565E(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GAAGTTCTGGGAATCGTCACC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											158	155	156					10																	104809536		1880	4141	6021	104799526	SO:0001583	missense	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1694G>A	10.37:g.104809536G>A	ENSP00000358894:p.Gly565Glu		104799526	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	32	5.117431	0.94385	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369878;ENST00000345419	D;D	0.99594	-6.25;-6.25	5.61	5.61	0.85477	Cystathionine beta-synthase, core (1);	0.000000	0.85682	D	0.000000	D	0.99846	0.9929	H	0.98936	4.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96607	0.9449	10	0.87932	D	0	.	19.6562	0.95842	0.0:0.0:1.0:0.0	.	565;565	Q9H8M5-2;Q9H8M5	.;CNNM2_HUMAN	E	565	ENSP00000392875:G565E;ENSP00000358894:G565E	ENSP00000286899:G565E	G	+	2	0	CNNM2	104799526	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.363000	0.97131	2.639000	0.89480	0.555000	0.69702	GGA		0.388	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		A	104809536	G	A	104809536	3	1	61	1	0	0	0	0	1	0	0	0	3619	1174	41	3	1742	3	CNNM2	10	104809536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122413	104809536	30725211	6977	14962										
TAF5	6877	broad.mit.edu	37	chr10	105147386	105147386	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatggtttgatggttggaGaattaaaaggccacactgat	12	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105147386G>T	ENST00000369839.3	+	10	2139	c.2116G>T	c.(2116-2118)Gaa>Taa	p.E706*	TAF5_ENST00000351396.4_Nonsense_Mutation_p.E651*	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	706					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E706*(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GATGGTTGGAGAATTAAAAGG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											185	183	184					10																	105147386		2203	4300	6503	105137376	SO:0001587	stop_gained	6877			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"WD repeat domain containing"	11539	protein-coding gene	gene with protein product		601787	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.2116G>T	10.37:g.105147386G>T	ENSP00000358854:p.Glu706*		105137376	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Nonsense_Mutation	SNP	ENST00000369839.3	37	CCDS7547.1	.	.	.	.	.	.	.	.	.	.	G	34	5.399697	0.96030	.	.	ENSG00000148835	ENST00000369839;ENST00000351396	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-19.2989	19.359	0.94428	0.0:0.0:1.0:0.0	.	.	.	.	X	706;651	.	ENSP00000311024:E651X	E	+	1	0	TAF5	105137376	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.459000	0.97638	2.552000	0.86080	0.557000	0.71058	GAA		0.403	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1			T	105147386	G	T	105147386	4	4	61	1	0	0	0	0	0	1	0	0	15567	943	33	2	2154	2	TAF5	10	105147386	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	337850	105147386	30387361	6978	14963										
SLK	9748	broad.mit.edu	37	chr10	105752806	105752806	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagactttagatgcattGaactacttacatgataataa	6	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105752806G>T	ENST00000369755.3	+	4	974	c.429G>T	c.(427-429)ttG>ttT	p.L143F	SLK_ENST00000335753.4_Missense_Mutation_p.L143F	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.L143F(1)		kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TAGATGCATTGAACTACTTAC	0.338																																					NSCLC(111;540 1651 1927 4474 17706)											1	Substitution - Missense(1)	large_intestine(1)	10											91	94	93					10																	105752806		2202	4298	6500	105742796	SO:0001583	missense	9748				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.429G>T	10.37:g.105752806G>T	ENSP00000358770:p.Leu143Phe		105742796	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.991060	0.54041	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.74632	-0.86;-0.86	5.16	3.28	0.37604	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000008	D	0.87478	0.6187	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.89120	0.3502	10	0.87932	D	0	.	11.2991	0.49295	0.1497:0.0:0.8503:0.0	.	143;143	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	F	143	ENSP00000336824:L143F;ENSP00000358770:L143F	ENSP00000336824:L143F	L	+	3	2	SLK	105742796	1.000000	0.71417	0.992000	0.48379	0.477000	0.33069	1.419000	0.34793	1.165000	0.42670	0.557000	0.71058	TTG		0.338	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		T	105752806	G	T	105752806	3	4	61	1	0	0	0	0	1	0	0	0	14785	1281	45	2	443	2	SLK	10	105752806	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	605420	105752806	29781941	6979	14964										
SLK	9748	broad.mit.edu	37	chr10	105762404	105762404	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagcttataaaatctgaaGaaattaaagatactattttg	5	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105762404G>T	ENST00000369755.3	+	9	2013	c.1468G>T	c.(1468-1470)Gaa>Taa	p.E490*	SLK_ENST00000335753.4_Nonsense_Mutation_p.E490*	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	490	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.E490*(1)		kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AAAATCTGAAGAAATTAAAGA	0.313																																					NSCLC(111;540 1651 1927 4474 17706)											1	Substitution - Nonsense(1)	large_intestine(1)	10											36	39	38					10																	105762404		2178	4294	6472	105752394	SO:0001587	stop_gained	9748				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1468G>T	10.37:g.105762404G>T	ENSP00000358770:p.Glu490*		105752394	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Nonsense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	G	40	8.026921	0.98616	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	.	.	.	6.03	6.03	0.97812	.	0.207935	0.41605	D	0.000842	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	19.1377	0.93435	0.0:0.0:1.0:0.0	.	.	.	.	X	490	.	ENSP00000336824:E490X	E	+	1	0	SLK	105752394	1.000000	0.71417	1.000000	0.80357	0.449000	0.32228	2.161000	0.42358	2.868000	0.98415	0.555000	0.69702	GAA		0.313	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		T	105762404	G	T	105762404	4	4	61	1	0	0	0	0	0	1	0	0	14785	943	33	2	1502	2	SLK	10	105762404	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9598	105762404	29772343	6980	14965										
SLK	9748	broad.mit.edu	37	chr10	105762800	105762800	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaataaggaacaagcaataAacagttcagagaacataatg	7	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105762800A>C	ENST00000369755.3	+	9	2409	c.1864A>C	c.(1864-1866)Aac>Cac	p.N622H	SLK_ENST00000335753.4_Missense_Mutation_p.N622H	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	622	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.N622H(1)		kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ACAAGCAATAAACAGTTCAGA	0.388																																					NSCLC(111;540 1651 1927 4474 17706)											1	Substitution - Missense(1)	large_intestine(1)	10											59	56	57					10																	105762800		2203	4300	6503	105752790	SO:0001583	missense	9748				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1864A>C	10.37:g.105762800A>C	ENSP00000358770:p.Asn622His		105752790	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	7.714	0.695686	0.15106	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69040	-0.36;-0.37	5.61	4.47	0.54385	Protein kinase-like domain (1);	1.297720	0.04522	N	0.384841	T	0.61489	0.2351	N	0.24115	0.695	0.09310	N	1	P;B	0.36315	0.547;0.412	B;B	0.41036	0.346;0.188	T	0.54576	-0.8273	10	0.52906	T	0.07	.	10.0801	0.42384	0.9237:0.0:0.0763:0.0	.	622;622	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	H	622	ENSP00000336824:N622H;ENSP00000358770:N622H	ENSP00000336824:N622H	N	+	1	0	SLK	105752790	0.000000	0.05858	0.013000	0.15412	0.570000	0.35934	0.678000	0.25277	0.959000	0.37980	0.454000	0.30748	AAC		0.388	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		C	105762800	A	C	105762800	3	2	61	1	0	0	0	0	1	0	0	0	14785	14	1	4	1898	4	SLK	10	105762800	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	396	105762800	29771947	6981	14966										
C10orf78	119392	broad.mit.edu	37	chr10	105883568	105883568	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttaaagtagagagtgaaGaaaatgatcagaccttttca	9	5	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105883568G>T	ENST00000369727.3	+	3	251	c.232G>T	c.(232-234)Gaa>Taa	p.E78*	SFR1_ENST00000369729.3_Nonsense_Mutation_p.E65*|SFR1_ENST00000336358.5_Nonsense_Mutation_p.E140*	NM_001002759.1	NP_001002759.1	Q86XK3	SFR1_HUMAN	SWI5-dependent recombination repair 1	78					double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)		p.E65*(1)|p.E65K(1)									AGAGAGTGAAGAAAATGATCA	0.333																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|endometrium(1)	10											64	71	68					10																	105883568		2203	4296	6499	105873558	SO:0001587	stop_gained	119392			BC020892	CCDS31279.1, CCDS31280.1	10q25.1	2013-10-11	2011-08-01	2011-08-01	ENSG00000156384	ENSG00000156384			29574	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 78", "MEI5 recombination repair protein homolog (S. cerevisiae)"	C10orf78, MEIR5		21252223, 21779174, 20976249	Standard	NM_145247		Approved	MEI5, bA373N18.1, FLJ41960	uc001kxu.3	Q86XK3	OTTHUMG00000019000	ENST00000369727.3:c.232G>T	10.37:g.105883568G>T	ENSP00000358742:p.Glu78*		105873558	A8K569|B2RTV8|Q5JT39|Q5JT40|Q8WW47	Nonsense_Mutation	SNP	ENST00000369727.3	37	CCDS31279.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.783476	0.90282	.	.	ENSG00000156384	ENST00000369729;ENST00000369727;ENST00000336358	.	.	.	5.72	5.72	0.89469	.	0.211720	0.48767	D	0.000162	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.7245	20.2764	0.98486	0.0:0.0:1.0:0.0	.	.	.	.	X	65;78;140	.	ENSP00000338089:E140X	E	+	1	0	SFR1	105873558	1.000000	0.71417	0.865000	0.33974	0.966000	0.64601	7.924000	0.87555	2.880000	0.98712	0.655000	0.94253	GAA		0.333	SFR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050191.1	NM_145247		T	105883568	G	T	105883568	4	4	61	1	0	0	0	0	0	1	0	0	1621	943	33	2	242	2	C10orf78	10	105883568	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120768	105883568	29651179	6982	14967										
C10orf79	80217	broad.mit.edu	37	chr10	105985307	105985307	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtaaagtgtagtccaggaGaatgttgcctaaaatataaa	9	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:105985307G>A	ENST00000278064.2	-	3	443	c.118C>T	c.(118-120)Ctc>Ttc	p.L40F	WDR96_ENST00000428666.1_Missense_Mutation_p.L110F|WDR96_ENST00000369719.1_Missense_Mutation_p.L40F|WDR96_ENST00000357060.3_Missense_Mutation_p.L110F|WDR96_ENST00000369720.1_Missense_Mutation_p.L40F														p.L110F(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TAGTCCAGGAGAATGTTGCCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											79	72	74					10																	105985307		2202	4300	6502	105975297	SO:0001583	missense	80217																														ENST00000278064.2:c.118C>T	10.37:g.105985307G>A	ENSP00000278064:p.Leu40Phe		105975297		Missense_Mutation	SNP	ENST00000278064.2	37		.	.	.	.	.	.	.	.	.	.	G	19.34	3.808984	0.70797	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720;ENST00000369719	T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.38381	N	0.001717	T	0.30634	0.0771	L	0.40543	1.245	0.26026	N	0.981809	D;D;D	0.67145	0.982;0.996;0.979	P;P;P	0.62014	0.788;0.897;0.666	T	0.04229	-1.0967	10	0.56958	D	0.05	.	15.361	0.74475	0.0:0.0:0.8599:0.1401	.	110;110;110	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	F	110;110;40;40;40	ENSP00000349568:L110F;ENSP00000400289:L110F;ENSP00000278064:L40F;ENSP00000358734:L40F;ENSP00000358733:L40F	ENSP00000278064:L40F	L	-	1	0	WDR96	105975297	1.000000	0.71417	0.982000	0.44146	0.910000	0.53928	4.130000	0.57964	2.733000	0.93635	0.655000	0.94253	CTC		0.373	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			A	105985307	G	A	105985307	3	1	61	1	0	0	0	0	1	0	0	0	1622	942	33	3	4813	3	C10orf79	10	105985307	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101739	105985307	29549440	6983	14968										
GSTO2	119391	broad.mit.edu	37	chr10	106058959	106058959	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccacagtctgtgctcttCtcatggataagagcattttc	7	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106058959C>A	ENST00000338595.2	+	7	969	c.649C>A	c.(649-651)Ctc>Atc	p.L217I	GSTO2_ENST00000369707.2_Missense_Mutation_p.L189I|GSTO2_ENST00000429569.2_Missense_Mutation_p.S119Y|GSTO2_ENST00000450629.2_Missense_Mutation_p.L183I	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	217	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)	p.L217I(1)		NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	CTGTGCTCTTCTCATGGATAA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	108	110					10																	106058959		2203	4300	6503	106048949	SO:0001583	missense	119391			AY191318	CCDS7556.1, CCDS53574.1, CCDS53575.1	10q25.1	2012-06-21			ENSG00000065621	ENSG00000065621	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	23064	protein-coding gene	gene with protein product		612314				12618591	Standard	NM_001191013		Approved		uc001kyb.3	Q9H4Y5	OTTHUMG00000019006	ENST00000338595.2:c.649C>A	10.37:g.106058959C>A	ENSP00000345023:p.Leu217Ile		106048949	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Missense_Mutation	SNP	ENST00000338595.2	37	CCDS7556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.194|8.194	0.796733|0.796733	0.16327|0.16327	.|.	.|.	ENSG00000065621|ENSG00000065621	ENST00000369708;ENST00000338595;ENST00000450629;ENST00000369707|ENST00000429569	T;T;T|T	0.16457|0.15718	2.34;2.34;2.34|2.4	5.9|5.9	-0.406|-0.406	0.12389|0.12389	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);|.	0.806631|.	0.11993|.	N|.	0.509665|.	T|T	0.10078|0.10078	0.0247|0.0247	N|N	0.26042|0.26042	0.785|0.785	0.09310|0.09310	N|N	1|1	B;B|B	0.10296|0.02656	0.003;0.0|0.0	B;B|B	0.08055|0.01281	0.002;0.003|0.0	T|T	0.31668|0.31668	-0.9935|-0.9935	10|9	0.27785|0.56958	T|D	0.31|0.05	-4.7224|-4.7224	3.2099|3.2099	0.06678|0.06678	0.296:0.381:0.0:0.3229|0.296:0.381:0.0:0.3229	.|.	183;217|119	B4DJW6;Q9H4Y5|B4DML4	.;GSTO2_HUMAN|.	I|Y	217;217;183;189|119	ENSP00000345023:L217I;ENSP00000390986:L183I;ENSP00000358721:L189I|ENSP00000407381:S119Y	ENSP00000345023:L217I|ENSP00000407381:S119Y	L|S	+|+	1|2	0|0	GSTO2|GSTO2	106048949|106048949	0.005000|0.005000	0.15991|0.15991	0.011000|0.011000	0.14972|0.14972	0.097000|0.097000	0.18754|0.18754	-0.238000|-0.238000	0.08977|0.08977	-0.110000|-0.110000	0.12022|0.12022	0.563000|0.563000	0.77884|0.77884	CTC|TCT		0.522	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239		A	106058959	C	A	106058959	3	1	61	1	0	0	0	0	1	0	0	0	6864	913	32	2	671	2	GSTO2	10	106058959	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73652	106058959	29475788	6984	14969										
CCDC147	159686	broad.mit.edu	37	chr10	106130676	106130676	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaggaagaagtccatcaAatgcgccttgacatcgggaa	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106130676A>C	ENST00000369704.3	+	7	1088	c.954A>C	c.(952-954)caA>caC	p.Q318H	CCDC147_ENST00000312902.5_5'UTR	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		318						extracellular space (GO:0005615)		p.Q318H(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AAGTCCATCAAATGCGCCTTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											68	63	65					10																	106130676		2203	4300	6503	106120666	SO:0001583	missense	159686																														ENST00000369704.3:c.954A>C	10.37:g.106130676A>C	ENSP00000358718:p.Gln318His		106120666	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.540471	0.65085	.	.	ENSG00000120051	ENST00000369704	T	0.33438	1.41	5.79	2.89	0.33648	.	0.048650	0.85682	D	0.000000	T	0.40448	0.1117	L	0.61036	1.89	0.80722	D	1	P	0.40638	0.725	P	0.52881	0.712	T	0.12243	-1.0555	10	0.48119	T	0.1	-15.4375	5.9271	0.19118	0.2839:0.1279:0.5882:0.0	.	318	Q5T655	CC147_HUMAN	H	318	ENSP00000358718:Q318H	ENSP00000358718:Q318H	Q	+	3	2	CCDC147	106120666	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.970000	0.40520	0.341000	0.23771	-0.366000	0.07423	CAA		0.408	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			C	106130676	A	C	106130676	3	2	61	1	0	0	0	0	1	0	0	0	2787	11	1	4	980	4	CCDC147	10	106130676	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	71717	106130676	29404071	6985	14970										
CCDC147	159686	broad.mit.edu	37	chr10	106159137	106159137	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgagctgcagaagctgaGacaacaagccctggagacaa	13	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106159137G>T	ENST00000369704.3	+	12	1828	c.1694G>T	c.(1693-1695)aGa>aTa	p.R565I	snoU13_ENST00000458914.1_RNA	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		565						extracellular space (GO:0005615)		p.R565I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CAGAAGCTGAGACAACAAGCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											57	57	57					10																	106159137		2203	4300	6503	106149127	SO:0001583	missense	159686																														ENST00000369704.3:c.1694G>T	10.37:g.106159137G>T	ENSP00000358718:p.Arg565Ile		106149127	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848960	0.51164	.	.	ENSG00000120051	ENST00000369704	T	0.42131	0.98	5.54	4.62	0.57501	.	0.146523	0.64402	D	0.000013	T	0.26991	0.0661	N	0.24115	0.695	0.80722	D	1	B	0.17465	0.022	B	0.23574	0.047	T	0.10660	-1.0620	10	0.44086	T	0.13	-3.6068	6.2525	0.20854	0.1908:0.1544:0.6547:0.0	.	565	Q5T655	CC147_HUMAN	I	565	ENSP00000358718:R565I	ENSP00000358718:R565I	R	+	2	0	CCDC147	106149127	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.177000	0.50871	2.776000	0.95493	0.650000	0.86243	AGA		0.473	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			T	106159137	G	T	106159137	3	4	61	1	0	0	0	0	1	0	0	0	2787	942	33	2	1740	2	CCDC147	10	106159137	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28461	106159137	29375610	6986	14971										
CCDC147	159686	broad.mit.edu	37	chr10	106214193	106214193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacagaaacaaggacacaGcacccatggataacaccttc	6	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106214193G>A	ENST00000369704.3	+	18	2658	c.2524G>A	c.(2524-2526)Gca>Aca	p.A842T		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		842						extracellular space (GO:0005615)		p.A842T(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CAAGGACACAGCACCCATGGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											219	199	206					10																	106214193		2203	4300	6503	106204183	SO:0001583	missense	159686																														ENST00000369704.3:c.2524G>A	10.37:g.106214193G>A	ENSP00000358718:p.Ala842Thr		106204183	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	G	0.169	-1.073423	0.01918	.	.	ENSG00000120051	ENST00000369704	T	0.41758	0.99	5.47	-2.31	0.06765	.	0.941217	0.09056	N	0.854989	T	0.24851	0.0603	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.27673	-1.0067	10	0.14252	T	0.57	-0.1233	2.3752	0.04340	0.261:0.4337:0.1739:0.1314	.	842	Q5T655	CC147_HUMAN	T	842	ENSP00000358718:A842T	ENSP00000358718:A842T	A	+	1	0	CCDC147	106204183	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.554000	0.06006	-0.121000	0.11787	-0.312000	0.09012	GCA		0.428	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			A	106214193	G	A	106214193	3	1	61	1	0	0	0	0	1	0	0	0	2787	971	34	3	2594	3	CCDC147	10	106214193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55056	106214193	29320554	6987	14972										
SORCS3	22986	broad.mit.edu	37	chr10	106602567	106602567	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtcatacttatcctgacGaagctgtatgacttcaacct	7	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106602567G>A	ENST00000369701.3	+	2	872	c.645G>A	c.(643-645)acG>acA	p.T215T		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	215					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.T215T(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TTATCCTGACGAAGCTGTATG	0.463																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - coding silent(1)	large_intestine(1)	10											99	90	93					10																	106602567		2203	4300	6503	106592557	SO:0001819	synonymous_variant	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.645G>A	10.37:g.106602567G>A			106592557	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																				0.463	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	106602567	G	A	106602567	2	1	61	1	0	0	0	0	0	0	0	1	14969	1045	37	1		1	SORCS3	10	106602567	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	388374	106602567	28932180	6988	14973										
SORCS3	22986	broad.mit.edu	37	chr10	106907471	106907471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctctacatctcagacacgCgtgggatttacttcactctg	7	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:106907471C>T	ENST00000369701.3	+	9	1626	c.1399C>T	c.(1399-1401)Cgt>Tgt	p.R467C		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	467					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.R467C(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CTCAGACACGCGTGGGATTTA	0.453																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - Missense(1)	large_intestine(1)	10											251	200	217					10																	106907471		2203	4299	6502	106897461	SO:0001583	missense	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1399C>T	10.37:g.106907471C>T	ENSP00000358715:p.Arg467Cys		106897461	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404219	0.62288	.	.	ENSG00000156395	ENST00000369701	T	0.23552	1.9	5.42	4.51	0.55191	VPS10 (1);	0.270717	0.37393	N	0.002119	T	0.49098	0.1537	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.66351	0.943	T	0.55211	-0.8176	10	0.87932	D	0	.	15.5495	0.76137	0.1487:0.8513:0.0:0.0	.	467	Q9UPU3	SORC3_HUMAN	C	467	ENSP00000358715:R467C	ENSP00000358715:R467C	R	+	1	0	SORCS3	106897461	0.725000	0.28048	0.878000	0.34440	0.859000	0.49053	1.486000	0.35530	1.385000	0.46445	-0.284000	0.09977	CGT		0.453	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106907471	C	T	106907471	3	4	61	1	0	0	0	0	1	0	0	0	14969	768	27	1	1433	1	SORCS3	10	106907471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	304904	106907471	28627276	6989	14974										
SORCS1	114815	broad.mit.edu	37	chr10	108377917	108377917	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcactcaccatatactgcGatggtctttgtgtcttgtag	11	9	3	0	rs138510886		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:108377917G>A	ENST00000263054.6	-	21	2917	c.2910C>T	c.(2908-2910)atC>atT	p.I970I	SORCS1_ENST00000369698.1_Silent_p.I505I|SORCS1_ENST00000344440.6_Silent_p.I970I|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	970					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.I970I(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CATATACTGCGATGGTCTTTG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	10						G	,,,,,	0,4406		0,0,2203	252	195	215		2910,2910,2910,2910,2910,2910	-3.3	0.9	10	dbSNP_134	215	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	970/1199,970/1180,970/1131,970/1160,970/1180,970/1169	108377917	1,13005	2203	4300	6503	108367907	SO:0001819	synonymous_variant	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2910C>T	10.37:g.108377917G>A			108367907	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																				0.493	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108377917	G	A	108377917	2	1	61	1	0	0	0	0	0	0	0	1	14967	1048	37	1		1	SORCS1	10	108377917	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1470446	108377917	27156830	6990	14975										
SORCS1	114815	broad.mit.edu	37	chr10	108412302	108412302	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcaattattggaaaccacCttcctgtacctaaatggaaa	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:108412302C>T	ENST00000263054.6	-	18	2320	c.2313G>A	c.(2311-2313)aaG>aaA	p.K771K	SORCS1_ENST00000369698.1_Silent_p.K306K|SORCS1_ENST00000344440.6_Silent_p.K771K	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	771					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.K771K(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TGGAAACCACCTTCCTGTACC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	10											107	102	104					10																	108412302		2203	4300	6503	108402292	SO:0001819	synonymous_variant	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2313G>A	10.37:g.108412302C>T			108402292	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																				0.478	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108412302	C	T	108412302	2	4	61	1	0	0	0	0	0	0	0	1	14967	680	24	3		3	SORCS1	10	108412302	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34385	108412302	27122445	6991	14976										
XPNPEP1	7511	broad.mit.edu	37	chr10	111629770	111629770	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaattccaaaagccccatCttcatagtacccgggctcta	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:111629770C>A	ENST00000502935.1	-	19	1833	c.1714G>T	c.(1714-1716)Gat>Tat	p.D572Y	XPNPEP1_ENST00000369680.4_Missense_Mutation_p.D529Y|U4_ENST00000607255.1_RNA|XPNPEP1_ENST00000322238.8_Missense_Mutation_p.D548Y|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.D458Y					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble									p.D529Y(1)		endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		AAAGCCCCATCTTCATAGTAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	10											66	62	63					10																	111629770		2203	4300	6503	111619760	SO:0001583	missense	7511				CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"X-prolyl aminopeptidase (aminopeptidase P)-like"	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.1714G>T	10.37:g.111629770C>A	ENSP00000421566:p.Asp572Tyr		111619760		Missense_Mutation	SNP	ENST00000502935.1	37	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	C	28.3	4.910743	0.92107	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000322238;ENST00000369680	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.97	5.97	0.96955	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	D	0.90967	0.7160	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.92126	0.5708	10	0.87932	D	0	-19.6738	18.6193	0.91316	0.0:1.0:0.0:0.0	.	572;529	G5E9Y2;Q9NQW7	.;XPP1_HUMAN	Y	572;458;548;529	ENSP00000421566:D572Y;ENSP00000358697:D458Y;ENSP00000324011:D548Y;ENSP00000358694:D529Y	ENSP00000324011:D548Y	D	-	1	0	XPNPEP1	111619760	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.274000	0.78538	2.836000	0.97738	0.655000	0.94253	GAT		0.403	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2			A	111629770	C	A	111629770	3	1	61	1	0	0	0	0	1	0	0	0	17482	913	32	2	298	2	XPNPEP1	10	111629770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3217468	111629770	23904977	6992	14977										
XPNPEP1	7511	broad.mit.edu	37	chr10	111667493	111667493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtaggcctggatcggttCggtcacatactcagagttcc	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:111667493C>T	ENST00000502935.1	-	3	321	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	XPNPEP1_ENST00000369680.4_Missense_Mutation_p.E25K|XPNPEP1_ENST00000322238.8_Missense_Mutation_p.E68K|XPNPEP1_ENST00000430337.1_5'UTR|XPNPEP1_ENST00000369683.1_5'UTR					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble									p.E25K(1)		endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		TGGATCGGTTCGGTCACATAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											250	210	224					10																	111667493		2203	4300	6503	111657483	SO:0001583	missense	7511				CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"X-prolyl aminopeptidase (aminopeptidase P)-like"	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.202G>A	10.37:g.111667493C>T	ENSP00000421566:p.Glu68Lys		111657483		Missense_Mutation	SNP	ENST00000502935.1	37	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.698235	0.48307	.	.	ENSG00000108039	ENST00000502935;ENST00000322238;ENST00000369680;ENST00000403138;ENST00000423625	.	.	.	5.33	5.33	0.75918	Creatinase (1);	0.000000	0.85682	D	0.000000	T	0.44008	0.1273	L	0.28694	0.88	0.58432	D	0.999997	B;B;B	0.25272	0.087;0.122;0.018	B;B;B	0.17722	0.019;0.017;0.019	T	0.33007	-0.9885	9	0.12766	T	0.61	-15.3116	15.934	0.79688	0.0:1.0:0.0:0.0	.	68;68;25	B4E2P4;G5E9Y2;Q9NQW7	.;.;XPP1_HUMAN	K	68;68;25;25;25	.	ENSP00000324011:E68K	E	-	1	0	XPNPEP1	111657483	1.000000	0.71417	0.994000	0.49952	0.533000	0.34776	5.175000	0.65021	2.504000	0.84457	0.655000	0.94253	GAA		0.522	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2			T	111667493	C	T	111667493	3	4	61	1	0	0	0	0	1	0	0	0	17482	893	31	1	1874	1	XPNPEP1	10	111667493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37723	111667493	23867254	6993	14978										
DUSP5	1847	broad.mit.edu	37	chr10	112266841	112266841	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcgacccacctacactacaAatggatccctgtggaagaca	8	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112266841A>C	ENST00000369583.3	+	3	961	c.677A>C	c.(676-678)aAa>aCa	p.K226T	DUSP5_ENST00000468749.1_3'UTR	NM_004419.3	NP_004410.3	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	226	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.K226T(2)		kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	13		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		CTACACTACAAATGGATCCCT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	10											156	156	156					10																	112266841		2203	4300	6503	112256831	SO:0001583	missense	1847			U16996	CCDS7566.1	10q25	2011-06-09			ENSG00000138166	ENSG00000138166		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3071	protein-coding gene	gene with protein product		603069				7806236	Standard	NM_004419		Approved	HVH3	uc001kzd.3	Q16690	OTTHUMG00000019040	ENST00000369583.3:c.677A>C	10.37:g.112266841A>C	ENSP00000358596:p.Lys226Thr		112256831	Q12997|Q5T603	Missense_Mutation	SNP	ENST00000369583.3	37	CCDS7566.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.033961	0.93575	.	.	ENSG00000138166	ENST00000369583	D	0.85411	-1.98	5.63	5.63	0.86233	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95531	0.8603	10	0.87932	D	0	.	15.0207	0.71630	1.0:0.0:0.0:0.0	.	226	Q16690	DUS5_HUMAN	T	226	ENSP00000358596:K226T	ENSP00000358596:K226T	K	+	2	0	DUSP5	112256831	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.152000	0.67230	0.533000	0.62120	AAA		0.532	DUSP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050333.1	NM_004419		C	112266841	A	C	112266841	3	2	61	1	0	0	0	0	1	0	0	0	4839	14	1	4	687	4	DUSP5	10	112266841	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	599348	112266841	23267906	6994	14979										
SMC3	9126	broad.mit.edu	37	chr10	112337595	112337595	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttacattttttcttagatCgataaagaggaagtttcact	6	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112337595C>T	ENST00000361804.4	+	6	399	c.273C>T	c.(271-273)atC>atT	p.I91I	SMC3_ENST00000462899.1_3'UTR|snoU13_ENST00000458966.1_RNA	NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	91					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)	p.I91I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		TTTCTTAGATCGATAAAGAGG	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	10											64	66	65					10																	112337595		2203	4300	6503	112327585	SO:0001819	synonymous_variant	9126			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.273C>T	10.37:g.112337595C>T			112327585	A8K156|O60464|Q5T482	Silent	SNP	ENST00000361804.4	37	CCDS31285.1																																																																																				0.294	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		T	112337595	C	T	112337595	2	4	61	1	0	0	0	0	0	0	0	1	14821	874	31	1		1	SMC3	10	112337595	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70754	112337595	23197152	6995	14980										
SMC3	9126	broad.mit.edu	37	chr10	112350302	112350302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgaaccagctttctacAcatgcgtggaagtcactgct	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112350302A>G	ENST00000361804.4	+	16	1768	c.1642A>G	c.(1642-1644)Aca>Gca	p.T548A		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	548	Flexible hinge.				DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)	p.T548A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AGCTTTCTACACATGCGTGGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											104	103	103					10																	112350302		2203	4300	6503	112340292	SO:0001583	missense	9126			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1642A>G	10.37:g.112350302A>G	ENSP00000354720:p.Thr548Ala		112340292	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	37	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.519384	0.85495	.	.	ENSG00000108055	ENST00000361804	D	0.86230	-2.09	5.91	5.91	0.95273	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.88295	0.6398	M	0.71871	2.18	0.80722	D	1	P	0.48834	0.916	P	0.45099	0.469	D	0.88410	0.3021	10	0.44086	T	0.13	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	548	Q9UQE7	SMC3_HUMAN	A	548	ENSP00000354720:T548A	ENSP00000354720:T548A	T	+	1	0	SMC3	112340292	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.962000	0.93254	2.254000	0.74563	0.533000	0.62120	ACA		0.363	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		G	112350302	A	G	112350302	3	3	61	1	0	0	0	0	1	0	0	0	14821	159	6	4	1704	4	SMC3	10	112350302	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12707	112350302	23184445	6996	14981										
PDCD4	27250	broad.mit.edu	37	chr10	112655829	112655829	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttccaaacaactcagaGatctttgtccttcaaggtac	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112655829G>T	ENST00000280154.7	+	11	1607	c.1333G>T	c.(1333-1335)Gat>Tat	p.D445Y	PDCD4_ENST00000393104.2_Missense_Mutation_p.D434Y|MIR4680_ENST00000580906.1_RNA	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	445	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.D445Y(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		ACAACTCAGAGATCTTTGTCC	0.363																																					Ovarian(115;1498 1603 9363 40056 40885)											1	Substitution - Missense(1)	large_intestine(1)	10											70	71	71					10																	112655829		2202	4300	6502	112645819	SO:0001583	missense	27250			U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"nuclear antigen H731"	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1333G>T	10.37:g.112655829G>T	ENSP00000280154:p.Asp445Tyr		112645819	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Missense_Mutation	SNP	ENST00000280154.7	37	CCDS7567.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928966	0.92389	.	.	ENSG00000150593	ENST00000280154;ENST00000393104	T;T	0.33216	1.42;1.43	5.97	5.97	0.96955	Initiation factor eIF-4 gamma, MA3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51244	0.1663	M	0.78223	2.4	0.80722	D	1	D;D;D	0.56287	0.975;0.975;0.975	P;P;P	0.52109	0.69;0.69;0.69	T	0.49184	-0.8966	10	0.48119	T	0.1	-23.064	20.4238	0.99064	0.0:0.0:1.0:0.0	.	431;445;434	B4DKX4;Q53EL6;B5ME91	.;PDCD4_HUMAN;.	Y	445;434	ENSP00000280154:D445Y;ENSP00000376816:D434Y	ENSP00000280154:D445Y	D	+	1	0	PDCD4	112645819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.834000	0.97654	0.650000	0.86243	GAT		0.363	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		T	112655829	G	T	112655829	3	4	61	1	0	0	0	0	1	0	0	0	11652	942	33	2	1385	2	PDCD4	10	112655829	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	305527	112655829	22878918	6997	14982										
SHOC2	8036	broad.mit.edu	37	chr10	112724663	112724663	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacggcataataaactgagaGaaattccttcagtggtgtat	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112724663G>T	ENST00000369452.4	+	2	892	c.547G>T	c.(547-549)Gaa>Taa	p.E183*	SHOC2_ENST00000265277.5_Nonsense_Mutation_p.E183*|SHOC2_ENST00000489390.1_Intron	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	183					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)	p.E183*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		TAAACTGAGAGAAATTCCTTC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											88	94	92					10																	112724663		2203	4299	6502	112714653	SO:0001587	stop_gained	8036			AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.547G>T	10.37:g.112724663G>T	ENSP00000358464:p.Glu183*		112714653	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Nonsense_Mutation	SNP	ENST00000369452.4	37	CCDS7568.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747368	0.89663	.	.	ENSG00000108061	ENST00000265277;ENST00000369452;ENST00000451838	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	19.7369	0.96210	0.0:0.0:1.0:0.0	.	.	.	.	X	183;183;19	.	ENSP00000265277:E183X	E	+	1	0	SHOC2	112714653	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.863000	0.87023	2.665000	0.90641	0.561000	0.74099	GAA		0.398	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		T	112724663	G	T	112724663	4	4	61	1	0	0	0	0	0	1	0	0	14324	943	33	2	549	2	SHOC2	10	112724663	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68834	112724663	22810084	6998	14983										
SHOC2	8036	broad.mit.edu	37	chr10	112769479	112769479	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatcttttagaaattagtCttgacaaacaaccagttgac	5	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112769479C>A	ENST00000369452.4	+	8	1776	c.1431C>A	c.(1429-1431)gtC>gtA	p.V477V	SHOC2_ENST00000265277.5_Silent_p.V431V|SHOC2_ENST00000489390.1_3'UTR	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	477					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)	p.V477V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		AGAAATTAGTCTTGACAAACA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	10											51	48	49					10																	112769479		2203	4300	6503	112759469	SO:0001819	synonymous_variant	8036			AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.1431C>A	10.37:g.112769479C>A			112759469	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Silent	SNP	ENST00000369452.4	37	CCDS7568.1																																																																																				0.328	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		A	112769479	C	A	112769479	2	1	61	1	0	0	0	0	0	0	0	1	14324	900	32	2		2	SHOC2	10	112769479	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44816	112769479	22765268	6999	14984										
SHOC2	8036	broad.mit.edu	37	chr10	112771467	112771467	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaagctttcaatcatgaGtattgagaactgtccactca	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:112771467G>T	ENST00000369452.4	+	9	1985	c.1640G>T	c.(1639-1641)aGt>aTt	p.S547I	SHOC2_ENST00000265277.5_Missense_Mutation_p.S501I	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	547					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)	p.S547I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		TCAATCATGAGTATTGAGAAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	10											137	128	131					10																	112771467		2203	4300	6503	112761457	SO:0001583	missense	8036			AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.1640G>T	10.37:g.112771467G>T	ENSP00000358464:p.Ser547Ile		112761457	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Missense_Mutation	SNP	ENST00000369452.4	37	CCDS7568.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432628	0.62844	.	.	ENSG00000108061	ENST00000265277;ENST00000369452;ENST00000451838	T;T;D	0.83591	1.81;1.81;-1.74	5.64	4.74	0.60224	.	0.071451	0.85682	D	0.000000	D	0.89959	0.6866	M	0.78637	2.42	0.80722	D	1	B;D	0.76494	0.207;0.999	B;D	0.67103	0.158;0.949	D	0.88489	0.3074	10	0.24483	T	0.36	.	16.6894	0.85317	0.0:0.1297:0.8703:0.0	.	501;547	Q9UQ13-2;Q9UQ13	.;SHOC2_HUMAN	I	501;547;337	ENSP00000265277:S501I;ENSP00000358464:S547I;ENSP00000408275:S337I	ENSP00000265277:S501I	S	+	2	0	SHOC2	112761457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.803000	0.99136	1.358000	0.45922	0.655000	0.94253	AGT		0.478	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		T	112771467	G	T	112771467	3	4	61	1	0	0	0	0	1	0	0	0	14324	1029	36	2	1670	2	SHOC2	10	112771467	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1988	112771467	22763280	7000	14985										
GPAM	57678	broad.mit.edu	37	chr10	113920419	113920419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgctgtagaagttgagttCgaagactgatgggacagttg	14	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:113920419C>T	ENST00000348367.4	-	16	1899	c.1702G>A	c.(1702-1704)Gaa>Aaa	p.E568K	GPAM_ENST00000369425.1_Missense_Mutation_p.E568K|GPAM_ENST00000423155.1_Missense_Mutation_p.E568K			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	568					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.E568K(1)		breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		AAGTTGAGTTCGAAGACTGAT	0.428																																					Ovarian(161;1017 2606 18293 52943)											1	Substitution - Missense(1)	large_intestine(1)	10											130	113	119					10																	113920419		2203	4300	6503	113910409	SO:0001583	missense	57678			AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1702G>A	10.37:g.113920419C>T	ENSP00000265276:p.Glu568Lys		113910409	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	C	34	5.377209	0.95945	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.71461	-0.57;-0.57;-0.54	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.81197	0.4772	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.73708	0.981;0.972	T	0.75775	-0.3199	10	0.22706	T	0.39	-23.5746	18.3607	0.90374	0.0:1.0:0.0:0.0	.	568;568	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	K	568	ENSP00000265276:E568K;ENSP00000409242:E568K;ENSP00000358433:E568K	ENSP00000265276:E568K	E	-	1	0	GPAM	113910409	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.368000	0.79567	2.777000	0.95525	0.655000	0.94253	GAA		0.428	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		T	113920419	C	T	113920419	3	4	61	1	0	0	0	0	1	0	0	0	6608	893	31	1	812	1	GPAM	10	113920419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1148952	113920419	21614328	7001	14986										
TECTB	6975	broad.mit.edu	37	chr10	114044301	114044301	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctctttccagatgtcattCttgtgttttgctatcccaaa	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:114044301C>A	ENST00000369422.3	+	2	85	c.85C>A	c.(85-87)Ctt>Att	p.L29I		NM_058222.1	NP_478129.1	Q96PL2	TECTB_HUMAN	tectorin beta	29	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.L29I(2)		kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)		AGATGTCATTCTTGTGTTTTG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	10											92	84	87					10																	114044301		2203	4300	6503	114034291	SO:0001583	missense	6975			AF312827	CCDS7571.1	10q25-q26	2005-06-09			ENSG00000119913	ENSG00000119913			11721	protein-coding gene	gene with protein product		602653				9079715	Standard	NM_058222		Approved		uc001kzr.1	Q96PL2	OTTHUMG00000019056	ENST00000369422.3:c.85C>A	10.37:g.114044301C>A	ENSP00000358430:p.Leu29Ile		114034291	Q5VW53	Missense_Mutation	SNP	ENST00000369422.3	37	CCDS7571.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.368426	0.24771	.	.	ENSG00000119913	ENST00000369422	T	0.74209	-0.82	5.52	5.52	0.82312	Zona pellucida sperm-binding protein (1);	0.201648	0.51477	D	0.000091	T	0.50120	0.1597	N	0.03177	-0.4	0.42160	D	0.991596	B	0.14012	0.009	B	0.17722	0.019	T	0.49588	-0.8924	10	0.35671	T	0.21	.	9.0252	0.36224	0.1479:0.7781:0.0:0.0739	.	29	Q96PL2	TECTB_HUMAN	I	29	ENSP00000358430:L29I	ENSP00000358430:L29I	L	+	1	0	TECTB	114034291	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.616000	0.36933	2.760000	0.94817	0.655000	0.94253	CTT		0.458	TECTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050381.1	NM_058222		A	114044301	C	A	114044301	3	1	61	1	0	0	0	0	1	0	0	0	15787	913	32	2	91	2	TECTB	10	114044301	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123882	114044301	21490446	7002	14987										
ZDHHC6	64429	broad.mit.edu	37	chr10	114192019	114192019	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctataaaggaatcatcaaGaattttgtctccatataacc	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:114192019G>T	ENST00000369405.3	-	10	1540	c.1117C>A	c.(1117-1119)Ctt>Att	p.L373I	ZDHHC6_ENST00000482410.1_5'UTR|ZDHHC6_ENST00000369404.3_Missense_Mutation_p.L369I	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	373					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.L373I(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		GAATCATCAAGAATTTTGTCT	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	10											64	66	65					10																	114192019		2202	4297	6499	114182009	SO:0001583	missense	64429			AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"Zinc fingers, DHHC-type"	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.1117C>A	10.37:g.114192019G>T	ENSP00000358413:p.Leu373Ile		114182009	D3DRB6|Q53G45|Q96IV7|Q9H605	Missense_Mutation	SNP	ENST00000369405.3	37	CCDS7574.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.024901	0.35701	.	.	ENSG00000023041	ENST00000369405;ENST00000369404	T;T	0.08546	3.08;3.08	6.17	5.24	0.73138	Src homology-3 domain (1);Variant SH3 (1);	0.219510	0.41712	D	0.000827	T	0.09642	0.0237	L	0.46947	1.48	0.40306	D	0.978661	B;B	0.30763	0.135;0.294	B;B	0.29942	0.022;0.109	T	0.10847	-1.0612	10	0.33940	T	0.23	-0.1718	13.9489	0.64104	0.0:0.0:0.7336:0.2664	.	369;373	Q9H6R6-2;Q9H6R6	.;ZDHC6_HUMAN	I	373;369	ENSP00000358413:L373I;ENSP00000358412:L369I	ENSP00000358412:L369I	L	-	1	0	ZDHHC6	114182009	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.001000	0.40825	2.941000	0.99782	0.655000	0.94253	CTT		0.269	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494		T	114192019	G	T	114192019	3	4	61	1	0	0	0	0	1	0	0	0	17658	942	33	2	132	2	ZDHHC6	10	114192019	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147718	114192019	21342728	7003	14988										
TCF7L2	6934	broad.mit.edu	37	chr10	114912121	114912121	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtccagagaagagcaagcGaaatactacgagctggcccg	12	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:114912121G>A	ENST00000355995.4	+	11	1698	c.1191G>A	c.(1189-1191)gcG>gcA	p.A397A	TCF7L2_ENST00000369389.1_Silent_p.A108A|TCF7L2_ENST00000545257.1_Silent_p.A397A|TCF7L2_ENST00000355717.4_Silent_p.A421A|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000369386.1_Silent_p.A40A|TCF7L2_ENST00000534894.1_Silent_p.A397A|TCF7L2_ENST00000536810.1_Silent_p.A397A|TCF7L2_ENST00000369397.4_Silent_p.A374A|TCF7L2_ENST00000352065.5_Silent_p.A374A|TCF7L2_ENST00000542695.1_Silent_p.A113A|TCF7L2_ENST00000538897.1_Silent_p.A397A|TCF7L2_ENST00000543371.1_Silent_p.A397A			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	397					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A397A(1)|p.A374A(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		AAGAGCAAGCGAAATACTACG	0.502			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	2	Substitution - coding silent(2)	large_intestine(2)	10											186	192	190					10																	114912121		2203	4300	6503	114902111	SO:0001819	synonymous_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1191G>A	10.37:g.114912121G>A			114902111	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	ENST00000355995.4	37																																																																																					0.502	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114912121	G	A	114912121	2	1	61	1	0	0	0	0	0	0	0	1	15737	1045	37	1		1	TCF7L2	10	114912121	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	720102	114912121	20622626	7004	14989										
NRAP	4892	broad.mit.edu	37	chr10	115364613	115364613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtgctggatccgggggtCgtctcttacactctggggcc	15	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115364613C>T	ENST00000359988.3	-	35	4226	c.3982G>A	c.(3982-3984)Gac>Aac	p.D1328N	NRAP_ENST00000369360.3_Missense_Mutation_p.D1301N|NRAP_ENST00000360478.3_Missense_Mutation_p.D1293N|NRAP_ENST00000369358.4_Missense_Mutation_p.D1336N	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.D1328N(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ATCCGGGGGTCGTCTCTTACA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	10											74	78	77					10																	115364613		2203	4300	6503	115354603	SO:0001583	missense	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3982G>A	10.37:g.115364613C>T	ENSP00000353078:p.Asp1328Asn		115354603		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472938	0.84640	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.69913	0.3164	M	0.84156	2.68	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.973;0.999;0.999;0.999	T	0.73180	-0.4064	10	0.72032	D	0.01	.	19.7905	0.96454	0.0:1.0:0.0:0.0	.	486;1328;1293;1328	B1ANW7;A0AVL2;Q86VF7-4;Q86VF7	.;.;.;NRAP_HUMAN	N	1336;1301;1328;1293;486	ENSP00000358365:D1336N;ENSP00000358367:D1301N;ENSP00000353078:D1328N;ENSP00000353666:D1293N	ENSP00000353078:D1328N	D	-	1	0	NRAP	115354603	1.000000	0.71417	0.962000	0.40283	0.380000	0.30137	7.818000	0.86416	2.691000	0.91804	0.650000	0.86243	GAC		0.582	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115364613	C	T	115364613	3	4	61	1	0	0	0	0	1	0	0	0	10669	884	31	1	1242	1	NRAP	10	115364613	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	452492	115364613	20170134	7005	14990										
NRAP	4892	broad.mit.edu	37	chr10	115393892	115393892	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactcagctgctgggcattGattttggcttgaacaatctg	11	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115393892G>T	ENST00000359988.3	-	15	1750	c.1506C>A	c.(1504-1506)atC>atA	p.I502I	NRAP_ENST00000369360.3_Silent_p.I467I|NRAP_ENST00000360478.3_Silent_p.I467I|NRAP_ENST00000369358.4_Silent_p.I502I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.I502I(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GCTGGGCATTGATTTTGGCTT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	10											216	187	197					10																	115393892		2203	4300	6503	115383882	SO:0001819	synonymous_variant	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.1506C>A	10.37:g.115393892G>T			115383882		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																				0.483	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115393892	G	T	115393892	2	4	61	1	0	0	0	0	0	0	0	1	10669	1280	45	2		2	NRAP	10	115393892	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29279	115393892	20140855	7006	14991										
NRAP	4892	broad.mit.edu	37	chr10	115406696	115406696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttacgtcactagcgagttCgtgagctttcttggcgttct	10	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115406696C>T	ENST00000359988.3	-	10	1223	c.979G>A	c.(979-981)Gaa>Aaa	p.E327K	NRAP_ENST00000369360.3_Missense_Mutation_p.E327K|NRAP_ENST00000360478.3_Missense_Mutation_p.E327K|NRAP_ENST00000369358.4_Missense_Mutation_p.E327K	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.E327K(3)|p.E327*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTAGCGAGTTCGTGAGCTTTC	0.527																																																4	Substitution - Missense(3)|Substitution - Nonsense(1)	large_intestine(4)	10											249	194	213					10																	115406696		2203	4300	6503	115396686	SO:0001583	missense	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.979G>A	10.37:g.115406696C>T	ENSP00000353078:p.Glu327Lys		115396686		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413299	0.62511	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.71	3.87	0.44632	.	0.142736	0.64402	D	0.000006	T	0.49779	0.1577	M	0.77313	2.365	0.37841	D	0.929041	P;P;P	0.49862	0.902;0.929;0.812	P;P;B	0.48795	0.544;0.59;0.311	T	0.54925	-0.8220	10	0.19590	T	0.45	.	12.5859	0.56416	0.0:0.8654:0.0:0.1346	.	327;327;327	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	K	327;327;327;327;56;56	ENSP00000358365:E327K;ENSP00000358367:E327K;ENSP00000353078:E327K;ENSP00000353666:E327K	ENSP00000353078:E327K	E	-	1	0	NRAP	115396686	1.000000	0.71417	0.977000	0.42913	0.923000	0.55619	5.461000	0.66699	0.884000	0.36064	0.643000	0.83706	GAA		0.527	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115406696	C	T	115406696	3	4	61	1	0	0	0	0	1	0	0	0	10669	893	31	1	4345	1	NRAP	10	115406696	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12804	115406696	20128051	7007	14992										
NRAP	4892	broad.mit.edu	37	chr10	115411573	115411573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcttacatcactttgaaGctgtgccccagccttgctcc	6	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115411573G>T	ENST00000359988.3	-	7	908	c.664C>A	c.(664-666)Ctt>Att	p.L222I	NRAP_ENST00000369360.3_Missense_Mutation_p.L222I|NRAP_ENST00000360478.3_Missense_Mutation_p.L222I|NRAP_ENST00000369358.4_Missense_Mutation_p.L222I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.L222I(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCACTTTGAAGCTGTGCCCCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	10											92	69	77					10																	115411573		2203	4300	6503	115401563	SO:0001583	missense	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.664C>A	10.37:g.115411573G>T	ENSP00000353078:p.Leu222Ile		115401563		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	G	9.535	1.111899	0.20714	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	6.03	6.03	0.97812	.	0.169461	0.52532	D	0.000073	T	0.39332	0.1074	L	0.31420	0.93	0.34269	D	0.680811	P;B;B	0.35107	0.484;0.286;0.345	B;B;B	0.38225	0.268;0.175;0.196	T	0.44667	-0.9313	10	0.15952	T	0.53	.	16.0597	0.80832	0.0:0.0:1.0:0.0	.	222;222;222	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	I	222	ENSP00000358365:L222I;ENSP00000358367:L222I;ENSP00000353078:L222I;ENSP00000353666:L222I	ENSP00000353078:L222I	L	-	1	0	NRAP	115401563	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	5.202000	0.65169	2.868000	0.98415	0.555000	0.69702	CTT		0.502	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115411573	G	T	115411573	3	4	61	1	0	0	0	0	1	0	0	0	10669	971	34	2	4672	2	NRAP	10	115411573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4877	115411573	20123174	7008	14993										
NRAP	4892	broad.mit.edu	37	chr10	115423147	115423147	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctggtgactcacaaagTtattaacagacagcatcatc	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115423147T>C	ENST00000359988.3	-	2	375	c.131A>G	c.(130-132)aAc>aGc	p.N44S	NRAP_ENST00000369360.3_Missense_Mutation_p.N44S|NRAP_ENST00000360478.3_Missense_Mutation_p.N44S|NRAP_ENST00000369358.4_Missense_Mutation_p.N44S	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.N44S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ACTCACAAAGTTATTAACAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	10											108	102	104					10																	115423147		2203	4300	6503	115413137	SO:0001583	missense	4892				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.131A>G	10.37:g.115423147T>C	ENSP00000353078:p.Asn44Ser		115413137		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683770	0.88639	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.68	5.68	0.88126	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.89245	0.6660	L	0.27053	0.805	0.54753	D	0.999984	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.997;0.983	D	0.89527	0.3782	10	0.44086	T	0.13	.	15.9355	0.79704	0.0:0.0:0.0:1.0	.	44;44;44	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	S	44	ENSP00000358365:N44S;ENSP00000358367:N44S;ENSP00000353078:N44S;ENSP00000353666:N44S	ENSP00000353078:N44S	N	-	2	0	NRAP	115413137	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.441000	0.80485	2.179000	0.69175	0.459000	0.35465	AAC		0.398	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		C	115423147	T	C	115423147	3	2	61	1	0	0	0	0	1	0	0	0	10669	1725	60	4	5225	4	NRAP	10	115423147	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11574	115423147	20111600	7009	14994										
DCLRE1A	9937	broad.mit.edu	37	chr10	115609268	115609268	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaatattttcaaatacttCggagcaggtgtactagacaa	9	7	1	1	rs181214695	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115609268C>T	ENST00000361384.2	-	2	2513	c.1596G>A	c.(1594-1596)ccG>ccA	p.P532P	DCLRE1A_ENST00000369305.1_Silent_p.P532P	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	532	Nuclear focus formation.				mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)		p.P532P(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		TCAAATACTTCGGAGCAGGTG	0.373								Other identified genes with known or suspected DNA repair function					C|||	2	0.000399361	0	0	5008	,	,		19886	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											114	117	116					10																	115609268		2203	4300	6503	115599258	SO:0001819	synonymous_variant	9937				CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.1596G>A	10.37:g.115609268C>T			115599258	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Silent	SNP	ENST00000361384.2	37	CCDS7584.1																																																																																				0.373	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		T	115609268	C	T	115609268	2	4	61	1	0	0	0	0	0	0	0	1	4300	871	31	1		1	DCLRE1A	10	115609268	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	186121	115609268	19925479	7010	14995										
DCLRE1A	9937	broad.mit.edu	37	chr10	115609698	115609698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtactctcattattttgaGaaataggttgagacaaatca	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115609698G>T	ENST00000361384.2	-	2	2083	c.1166C>A	c.(1165-1167)tCt>tAt	p.S389Y	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.S389Y	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	389					mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)		p.S389Y(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		ATTATTTTGAGAAATAGGTTG	0.403								Other identified genes with known or suspected DNA repair function																																								1	Substitution - Missense(1)	large_intestine(1)	10											71	72	72					10																	115609698		2203	4300	6503	115599688	SO:0001583	missense	9937				CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.1166C>A	10.37:g.115609698G>T	ENSP00000355185:p.Ser389Tyr		115599688	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	37	CCDS7584.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864477	0.32977	.	.	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.67523	-0.27;-0.27	5.89	-0.684	0.11331	.	0.541902	0.21231	N	0.077965	T	0.53206	0.1782	L	0.39898	1.24	0.09310	N	1	P	0.41947	0.766	B	0.39706	0.307	T	0.48410	-0.9038	10	0.39692	T	0.17	0.8053	10.8519	0.46775	0.469:0.0:0.531:0.0	.	389	Q6PJP8	DCR1A_HUMAN	Y	389	ENSP00000355185:S389Y;ENSP00000358311:S389Y	ENSP00000355185:S389Y	S	-	2	0	DCLRE1A	115599688	0.940000	0.31905	0.001000	0.08648	0.040000	0.13550	0.967000	0.29344	-0.425000	0.07371	0.557000	0.71058	TCT		0.403	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		T	115609698	G	T	115609698	3	4	61	1	0	0	0	0	1	0	0	0	4300	942	33	2	1988	2	DCLRE1A	10	115609698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	430	115609698	19925049	7011	14996										
TDRD1	56165	broad.mit.edu	37	chr10	115963246	115963246	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactctctgccagcttaaaaGaaacatatgcaaatgtgcat	6	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:115963246G>T	ENST00000369280.1	+	8	1361	c.901G>T	c.(901-903)Gaa>Taa	p.E301*	TDRD1_ENST00000251864.2_Nonsense_Mutation_p.E301*|TDRD1_ENST00000369282.1_Nonsense_Mutation_p.E301*|TDRD1_ENST00000369281.2_Nonsense_Mutation_p.E301*|TDRD1_ENST00000422662.1_Nonsense_Mutation_p.E10*			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	301					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)	p.E301*(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		CAGCTTAAAAGAAACATATGC	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											75	77	76					10																	115963246		2203	4300	6503	115953236	SO:0001587	stop_gained	56165			AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.901G>T	10.37:g.115963246G>T	ENSP00000358286:p.Glu301*		115953236	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Nonsense_Mutation	SNP	ENST00000369280.1	37		.	.	.	.	.	.	.	.	.	.	G	23.9	4.469590	0.84533	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	.	.	.	5.36	5.36	0.76844	.	0.250879	0.41605	D	0.000856	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-27.2656	14.5911	0.68365	0.0:0.0:1.0:0.0	.	.	.	.	X	301;301;301;10;301	.	ENSP00000251864:E301X	E	+	1	0	TDRD1	115953236	1.000000	0.71417	1.000000	0.80357	0.206000	0.24218	3.845000	0.55880	2.533000	0.85409	0.467000	0.42956	GAA		0.388	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115963246	G	T	115963246	4	4	61	1	0	0	0	0	0	1	0	0	15769	943	33	2	927	2	TDRD1	10	115963246	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	353548	115963246	19571501	7012	14997										
ABLIM1	3983	broad.mit.edu	37	chr10	116232816	116232816	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaataagatctggacgttCaatgtcataaattgccttga	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:116232816C>A	ENST00000277895.5	-	10	1292	c.1195G>T	c.(1195-1197)Gaa>Taa	p.E399*	ABLIM1_ENST00000392952.3_Nonsense_Mutation_p.E111*|ABLIM1_ENST00000369253.2_Nonsense_Mutation_p.E57*|ABLIM1_ENST00000369252.4_Nonsense_Mutation_p.E339*|ABLIM1_ENST00000369266.3_Nonsense_Mutation_p.E111*|ABLIM1_ENST00000533213.2_Nonsense_Mutation_p.E339*	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	399					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.E339*(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		TCTGGACGTTCAATGTCATAA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											217	192	200					10																	116232816		2203	4300	6503	116222806	SO:0001587	stop_gained	3983			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1195G>T	10.37:g.116232816C>A	ENSP00000277895:p.Glu399*		116222806	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Nonsense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.378540|7.378540	0.98248|0.98248	.|.	.|.	ENSG00000099204|ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000369260;ENST00000277895;ENST00000369253;ENST00000440467;ENST00000428430|ENST00000392955	.|.	.|.	.|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.66426	.|0.2788	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68693	.|-0.5341	.|3	0.62326|.	D|.	0.03|.	.|.	15.2089|15.2089	0.73202|0.73202	0.0:0.8598:0.1402:0.0|0.0:0.8598:0.1402:0.0	.|.	.|.	.|.	.|.	X|F	399;339;111;57;367;339;427;323;111;323;323;427;111;64;83|307	.|.	ENSP00000277895:E427X|.	E|L	-|-	1|3	0|2	ABLIM1|ABLIM1	116222806|116222806	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.998000|0.998000	0.95712|0.95712	7.750000|7.750000	0.85110|0.85110	2.723000|2.723000	0.93209|0.93209	0.655000|0.655000	0.94253|0.94253	GAA|TTG		0.423	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			A	116232816	C	A	116232816	4	1	61	1	0	0	0	0	0	1	0	0	94	835	29	2	1193	2	ABLIM1	10	116232816	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	269570	116232816	19301931	7013	14998										
ABLIM1	3983	broad.mit.edu	37	chr10	116304803	116304803	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaactggtgacacgcctcAcatttcaccccaaagagtcc	6	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:116304803A>G	ENST00000277895.5	-	6	952	c.855T>C	c.(853-855)tgT>tgC	p.C285C	ABLIM1_ENST00000369252.4_Silent_p.C225C|ABLIM1_ENST00000533213.2_Silent_p.C225C	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	285	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.C225C(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		GACACGCCTCACATTTCACCC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	10											181	163	169					10																	116304803		2203	4300	6503	116294793	SO:0001819	synonymous_variant	3983			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.855T>C	10.37:g.116304803A>G			116294793	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	A	11.19	1.565990	0.27915	.	.	ENSG00000099204	ENST00000392955	.	.	.	5.31	-3.33	0.04958	.	.	.	.	.	T	0.56499	0.1989	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53655	-0.8408	4	.	.	.	.	11.4525	0.50160	0.6112:0.0:0.3888:0.0	.	.	.	.	A	194	.	.	V	-	2	0	ABLIM1	116294793	1.000000	0.71417	0.903000	0.35520	0.960000	0.62799	1.001000	0.29783	-0.974000	0.03550	0.460000	0.39030	GTG		0.557	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			G	116304803	A	G	116304803	2	3	61	1	0	0	0	0	0	0	0	1	94	157	6	4		4	ABLIM1	10	116304803	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	71987	116304803	19229944	7014	14999										
FAM160B1	57700	broad.mit.edu	37	chr10	116602892	116602892	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtccacaagcttggataaCctcagtgtcacctcactgcc	7	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:116602892C>T	ENST00000369248.4	+	6	1058	c.723C>T	c.(721-723)aaC>aaT	p.N241N	FAM160B1_ENST00000369250.3_Silent_p.N241N	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	241								p.N241N(2)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GCTTGGATAACCTCAGTGTCA	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	10											163	133	144					10																	116602892		2203	4300	6503	116592882	SO:0001819	synonymous_variant	57700			AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.723C>T	10.37:g.116602892C>T			116592882	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Silent	SNP	ENST00000369248.4	37	CCDS31290.1																																																																																				0.443	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		T	116602892	C	T	116602892	2	4	61	1	0	0	0	0	0	0	0	1	5486	506	18	3		3	FAM160B1	10	116602892	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298089	116602892	18931855	7015	15000										
FAM160B1	57700	broad.mit.edu	37	chr10	116615010	116615010	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggcctgggtctccaaaaGcattggaaaagtgcaattta	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:116615010G>T	ENST00000369248.4	+	14	2193	c.1858G>T	c.(1858-1860)Gca>Tca	p.A620S	FAM160B1_ENST00000369250.3_Missense_Mutation_p.A620S	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	620								p.A620S(2)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GTCTCCAAAAGCATTGGAAAA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	10											101	101	101					10																	116615010		2203	4300	6503	116605000	SO:0001583	missense	57700			AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1858G>T	10.37:g.116615010G>T	ENSP00000358251:p.Ala620Ser		116605000	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	37	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740141	0.49045	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.13420	2.6;2.59	5.66	4.74	0.60224	.	0.146457	0.64402	D	0.000007	T	0.11196	0.0273	L	0.40543	1.245	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.001	T	0.10245	-1.0638	10	0.13108	T	0.6	-17.6787	11.097	0.48150	0.0:0.2467:0.6183:0.135	.	620;620	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	S	620	ENSP00000358251:A620S;ENSP00000358253:A620S	ENSP00000358251:A620S	A	+	1	0	FAM160B1	116605000	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.265000	0.43311	1.484000	0.48361	0.650000	0.86243	GCA		0.383	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		T	116615010	G	T	116615010	3	4	61	1	0	0	0	0	1	0	0	0	5486	971	34	2	1912	2	FAM160B1	10	116615010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12118	116615010	18919737	7016	15001										
ATRNL1	26033	broad.mit.edu	37	chr10	116930820	116930820	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctttatgtatggaggcaGaattgaaacaaatgatggca	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:116930820G>T	ENST00000355044.3	+	8	1244	c.1118G>T	c.(1117-1119)aGa>aTa	p.R373I	ATRNL1_ENST00000529665.1_3'UTR|ATRNL1_ENST00000527407.1_Nonsense_Mutation_p.E344*	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	373					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R373I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TATGGAGGCAGAATTGAAACA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	108	110					10																	116930820		2203	4300	6503	116920810	SO:0001583	missense	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.1118G>T	10.37:g.116930820G>T	ENSP00000347152:p.Arg373Ile		116920810	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676737	0.47886	.	.	ENSG00000107518	ENST00000355044	T	0.29655	1.56	5.75	2.57	0.30868	Kelch-type beta propeller (1);	0.086330	0.85682	D	0.000000	T	0.19327	0.0464	L	0.48362	1.52	0.80722	D	1	B;P	0.41569	0.301;0.755	B;B	0.35770	0.21;0.203	T	0.04593	-1.0940	10	0.20046	T	0.44	-21.6857	5.261	0.15573	0.5474:0.0:0.4526:0.0	.	373;373	Q5VV63;Q5VV63-2	ATRN1_HUMAN;.	I	373	ENSP00000347152:R373I	ENSP00000347152:R373I	R	+	2	0	ATRNL1	116920810	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	5.754000	0.68743	0.797000	0.33971	-0.142000	0.14014	AGA		0.274	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	116930820	G	T	116930820	3	4	61	1	0	0	0	0	1	0	0	0	1208	942	33	2	1148	2	ATRNL1	10	116930820	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315810	116930820	18603927	7017	15002										
GFRA1	2674	broad.mit.edu	37	chr10	117823923	117823923	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcagctatgatgtttctgTtaaagataatagggtggaca	11	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:117823923T>A	ENST00000355422.6	-	11	1934	c.1384A>T	c.(1384-1386)Aca>Tca	p.T462S	GFRA1_ENST00000439649.3_Missense_Mutation_p.T457S|GFRA1_ENST00000544592.1_Missense_Mutation_p.T341S|GFRA1_ENST00000369236.1_Missense_Mutation_p.T457S	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	462					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.T457S(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		GATGTTTCTGTTAAAGATAAT	0.413																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - Missense(1)	large_intestine(1)	10											104	92	96					10																	117823923		2203	4300	6503	117813913	SO:0001583	missense	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.1384A>T	10.37:g.117823923T>A	ENSP00000347591:p.Thr462Ser		117813913	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	T	8.318	0.823556	0.16678	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T;T;T	0.39056	1.72;1.53;1.1;1.53	6.06	4.22	0.49857	.	0.810362	0.11287	N	0.579655	T	0.21921	0.0528	N	0.08118	0	0.18873	N	0.999984	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.23261	-1.0193	10	0.21540	T	0.41	-1.0108	7.4278	0.27109	0.1425:0.7144:0.0:0.1431	.	462;457	P56159;P56159-2	GFRA1_HUMAN;.	S	462;457;457;341;457	ENSP00000358239:T457S;ENSP00000347591:T457S;ENSP00000442179:T341S;ENSP00000358237:T457S	ENSP00000347591:T457S	T	-	1	0	GFRA1	117813913	1.000000	0.71417	0.969000	0.41365	0.947000	0.59692	1.698000	0.37794	0.910000	0.36722	-0.798000	0.03219	ACA		0.413	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		A	117823923	T	A	117823923	3	1	61	1	0	0	0	0	1	0	0	0	6367	1725	60	5	17	5	GFRA1	10	117823923	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	893103	117823923	17710824	7018	15003										
C10orf96	374355	broad.mit.edu	37	chr10	118100348	118100348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaaaccataggaatatgCttcttcaaacctttgtaagt	5	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118100348C>T	ENST00000333254.3	+	4	519	c.268C>T	c.(268-270)Ctt>Ttt	p.L90F	CCDC172_ENST00000497093.1_3'UTR	NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	90								p.L90F(1)									TAGGAATATGCTTCTTCAAAC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	10											56	59	58					10																	118100348		2203	4287	6490	118090338	SO:0001583	missense	374355			BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.268C>T	10.37:g.118100348C>T	ENSP00000329860:p.Leu90Phe		118090338		Missense_Mutation	SNP	ENST00000333254.3	37	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049716	0.36181	.	.	ENSG00000182645	ENST00000333254;ENST00000423072	.	.	.	5.95	4.12	0.48240	.	0.070231	0.56097	N	0.000034	T	0.56572	0.1994	M	0.76002	2.32	0.40606	D	0.981623	P	0.41041	0.736	B	0.38500	0.275	T	0.61182	-0.7114	9	0.62326	D	0.03	-20.6727	10.7399	0.46147	0.0:0.8547:0.0:0.1453	.	90	P0C7W6	CJ096_HUMAN	F	90	.	ENSP00000329860:L90F	L	+	1	0	C10orf96	118090338	0.960000	0.32886	0.986000	0.45419	0.824000	0.46624	1.444000	0.35068	0.864000	0.35578	0.650000	0.86243	CTT		0.274	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		T	118100348	C	T	118100348	3	4	61	1	0	0	0	0	1	0	0	0	1631	797	28	3	278	3	C10orf96	10	118100348	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	276425	118100348	17434399	7019	15004										
PNLIPRP3	119548	broad.mit.edu	37	chr10	118228827	118228827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtccctttccccatttgCccgtaagtatcatagctaag	8	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118228827C>T	ENST00000369230.3	+	9	1204	c.1058C>T	c.(1057-1059)gCc>gTc	p.A353V		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	353					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.A353V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		TCCCCATTTGCCCGTAAGTAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	10											54	56	55					10																	118228827		2203	4299	6502	118218817	SO:0001583	missense	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1058C>T	10.37:g.118228827C>T	ENSP00000358232:p.Ala353Val		118218817		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735236	0.48939	.	.	ENSG00000203837	ENST00000369230	D	0.92858	-3.12	4.68	2.43	0.29744	.	0.155822	0.28166	N	0.016349	D	0.90177	0.6930	M	0.81802	2.56	0.25670	N	0.985901	P	0.37824	0.609	B	0.34301	0.179	D	0.84560	0.0649	10	0.72032	D	0.01	.	9.8823	0.41240	0.0:0.722:0.2019:0.0761	.	353	Q17RR3	LIPR3_HUMAN	V	353	ENSP00000358232:A353V	ENSP00000358232:A353V	A	+	2	0	PNLIPRP3	118218817	0.997000	0.39634	0.938000	0.37757	0.742000	0.42306	3.359000	0.52292	0.900000	0.36469	0.591000	0.81541	GCC		0.323	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		T	118228827	C	T	118228827	3	4	61	1	0	0	0	0	1	0	0	0	12183	739	26	3	1092	3	PNLIPRP3	10	118228827	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128479	118228827	17305920	7020	15005										
PNLIPRP3	119548	broad.mit.edu	37	chr10	118236203	118236203	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacttacacaaaattaatCgatgcagatgttaacgttgg	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118236203C>T	ENST00000369230.3	+	11	1358	c.1212C>T	c.(1210-1212)atC>atT	p.I404I		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	404	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.I404I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CAAAATTAATCGATGCAGATG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	10											122	118	119					10																	118236203		2203	4300	6503	118226193	SO:0001819	synonymous_variant	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1212C>T	10.37:g.118236203C>T			118226193		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.363	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		T	118236203	C	T	118236203	2	4	61	1	0	0	0	0	0	0	0	1	12183	874	31	1		1	PNLIPRP3	10	118236203	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7376	118236203	17298544	7021	15006										
PNLIPRP2	5408	broad.mit.edu	37	chr10	118404564	118404564	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtataatttttgtagcagcGacactgtggaagaaaacgtc	11	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118404564G>A	ENST00000298771.7	+	0	1391				PNLIPRP2_ENST00000537242.1_RNA|PNLIPRP2_ENST00000433618.4_RNA	NR_103727.1		P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process (GO:0019376)|lipid digestion (GO:0044241)|phospholipid catabolic process (GO:0009395)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	acylglycerol lipase activity (GO:0047372)|calcium ion binding (GO:0005509)|galactolipase activity (GO:0047714)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)	p.D455N(1)		endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		TTGTAGCAGCGACACTGTGGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	10											87	85	86					10																	118404564		1866	4111	5977	118394554			5408			M93284		10q26.12	2014-03-14				ENSG00000266200	3.1.1.3		9157	protein-coding gene	gene with protein product		604423				1379598	Standard	NM_005396		Approved	PLRP2	uc001lcq.3	P54317			10.37:g.118404564G>A			118394554	A8K627|Q6IB55	Missense_Mutation	SNP	ENST00000298771.7	37		.	.	.	.	.	.	.	.	.	.	G	11.30	1.597332	0.28445	.	.	ENSG00000165862	ENST00000537242	T	0.65364	-0.15	5.26	0.951	0.19579	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.540977	0.17220	N	0.182350	T	0.41259	0.1151	.	.	.	0.09310	N	1	B	0.18863	0.031	B	0.13407	0.009	T	0.16100	-1.0414	9	0.27785	T	0.31	.	4.9876	0.14198	0.1626:0.0:0.5477:0.2897	.	456	P54317	LIPR2_HUMAN	N	455	ENSP00000446346:D455N	ENSP00000446346:D455N	D	+	1	0	PNLIPRP2	118394554	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-0.018000	0.12568	0.200000	0.20447	0.650000	0.86243	GAC		0.418	PNLIPRP2-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000050546.6	NM_005396		A	118404564	G	A	118404564	1	1	61	0	1	0	0	0	0	0	0	0	12182	1058	37	1		1	PNLIPRP2	10	118404564	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168361	118404564	17130183	7022	15007										
KIAA1598	57698	broad.mit.edu	37	chr10	118689430	118689430	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaattcctttttatcttcCtctagaagctccagttgctg	5	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118689430C>A	ENST00000355371.4	-	10	1439	c.942G>T	c.(940-942)gaG>gaT	p.E314D	KIAA1598_ENST00000392903.2_Missense_Mutation_p.E314D|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392901.4_Missense_Mutation_p.E254D|KIAA1598_ENST00000260777.10_Missense_Mutation_p.E314D	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	314					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)		p.E314D(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		TTTTATCTTCCTCTAGAAGCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10											183	176	178					10																	118689430		2202	4299	6501	118679420	SO:0001583	missense	57698			BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.942G>T	10.37:g.118689430C>A	ENSP00000347532:p.Glu314Asp		118679420	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	37	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303778	0.60305	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.12255	2.98;2.7;2.98;2.7	5.59	1.78	0.24846	.	0.046788	0.85682	D	0.000000	T	0.27098	0.0664	L	0.55743	1.74	0.40919	D	0.984299	D;D;P	0.61697	0.99;0.974;0.607	D;D;B	0.73380	0.98;0.969;0.12	T	0.00425	-1.1747	10	0.46703	T	0.11	-19.3396	9.1599	0.37016	0.0:0.2825:0.0:0.7175	.	314;314;284	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	D	314;314;314;254	ENSP00000376636:E314D;ENSP00000260777:E314D;ENSP00000347532:E314D;ENSP00000376635:E254D	ENSP00000260777:E314D	E	-	3	2	KIAA1598	118679420	0.998000	0.40836	0.997000	0.53966	0.936000	0.57629	0.161000	0.16481	-0.112000	0.11979	-0.361000	0.07541	GAG		0.333	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		A	118689430	C	A	118689430	3	1	61	1	0	0	0	0	1	0	0	0	8267	680	24	2	985	2	KIAA1598	10	118689430	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	284866	118689430	16845317	7023	15008										
KCNK18	338567	broad.mit.edu	37	chr10	118969148	118969148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttatctacatcttataatCggttccgaaaattccctttc	3	11	3	0	rs115251364	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118969148C>T	ENST00000334549.1	+	3	493	c.493C>T	c.(493-495)Cgg>Tgg	p.R165W		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	165					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)	p.R165W(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		ATCTTATAATCGGTTCCGAAA	0.507													C|||	16	0.00319489	0.0121	0	5008	,	,		17747	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						C	TRP/ARG	44,4362	47.5+/-82.1	0,44,2159	134	133	133		493	2.6	0	10	dbSNP_132	133	0,8600		0,0,4300	yes	missense	KCNK18	NM_181840.1	101	0,44,6459	TT,TC,CC		0.0,0.9986,0.3383	benign	165/385	118969148	44,12962	2203	4300	6503	118959138	SO:0001583	missense	338567			AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.493C>T	10.37:g.118969148C>T	ENSP00000334650:p.Arg165Trp		118959138	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	17.21	3.330987	0.60853	0.009986	0.0	ENSG00000186795	ENST00000334549	T	0.30182	1.54	4.83	2.64	0.31445	.	0.488989	0.20870	N	0.084199	T	0.11281	0.0275	L	0.27053	0.805	0.09310	N	1	P	0.37914	0.611	B	0.20955	0.032	T	0.07673	-1.0760	10	0.42905	T	0.14	.	9.7784	0.40634	0.356:0.5471:0.0969:0.0	.	165	Q7Z418	KCNKI_HUMAN	W	165	ENSP00000334650:R165W	ENSP00000334650:R165W	R	+	1	2	KCNK18	118959138	0.000000	0.05858	0.001000	0.08648	0.515000	0.34225	0.554000	0.23407	0.511000	0.28236	0.655000	0.94253	CGG		0.507	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		T	118969148	C	T	118969148	3	4	61	1	0	0	0	0	1	0	0	0	8086	875	31	1	503	1	KCNK18	10	118969148	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279718	118969148	16565599	7024	15009										
KCNK18	338567	broad.mit.edu	37	chr10	118969404	118969404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacaagccatggagaggaGtaactcgtgtcccgaactgg	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118969404G>A	ENST00000334549.1	+	3	749	c.749G>A	c.(748-750)aGt>aAt	p.S250N		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	250	Interaction with YWHAH. {ECO:0000250}.				cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)	p.S250N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		ATGGAGAGGAGTAACTCGTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	10											143	129	134					10																	118969404		2203	4300	6503	118959394	SO:0001583	missense	338567			AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.749G>A	10.37:g.118969404G>A	ENSP00000334650:p.Ser250Asn		118959394	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.505871	0.64410	.	.	ENSG00000186795	ENST00000334549	T	0.14766	2.48	5.4	5.4	0.78164	.	0.207303	0.49916	D	0.000122	T	0.17066	0.0410	L	0.36672	1.1	0.23916	N	0.996476	D	0.60575	0.988	P	0.52514	0.701	T	0.15350	-1.0440	10	0.15952	T	0.53	.	12.8646	0.57932	0.0748:0.0:0.9252:0.0	.	250	Q7Z418	KCNKI_HUMAN	N	250	ENSP00000334650:S250N	ENSP00000334650:S250N	S	+	2	0	KCNK18	118959394	1.000000	0.71417	0.409000	0.26459	0.142000	0.21351	3.889000	0.56212	2.704000	0.92352	0.655000	0.94253	AGT		0.537	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		A	118969404	G	A	118969404	3	1	61	1	0	0	0	0	1	0	0	0	8086	1029	36	3	759	3	KCNK18	10	118969404	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	256	118969404	16565343	7025	15010										
KCNK18	338567	broad.mit.edu	37	chr10	118969597	118969597	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggatttcgagaatgccttCtatttctgctttgtcacact	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:118969597C>A	ENST00000334549.1	+	3	942	c.942C>A	c.(940-942)ttC>ttA	p.F314L		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	314					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)	p.F314L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		AGAATGCCTTCTATTTCTGCT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											329	277	295					10																	118969597		2203	4300	6503	118959587	SO:0001583	missense	338567			AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.942C>A	10.37:g.118969597C>A	ENSP00000334650:p.Phe314Leu		118959587	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925334	0.73213	.	.	ENSG00000186795	ENST00000334549	T	0.26067	1.76	5.4	2.54	0.30619	Ion transport 2 (1);	0.051603	0.85682	D	0.000000	T	0.27765	0.0683	L	0.35288	1.05	0.58432	D	0.999996	P	0.37500	0.597	P	0.51016	0.656	T	0.03413	-1.1039	10	0.30854	T	0.27	.	7.9993	0.30286	0.0:0.6147:0.0:0.3853	.	314	Q7Z418	KCNKI_HUMAN	L	314	ENSP00000334650:F314L	ENSP00000334650:F314L	F	+	3	2	KCNK18	118959587	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	0.755000	0.26405	0.788000	0.33755	0.655000	0.94253	TTC		0.458	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		A	118969597	C	A	118969597	3	1	61	1	0	0	0	0	1	0	0	0	8086	912	32	2	952	2	KCNK18	10	118969597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	193	118969597	16565150	7026	15011										
SLC18A2	6571	broad.mit.edu	37	chr10	119003750	119003750	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgaatgaaaacgtgcaAgttggtctgttgtttgcctc	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119003750A>G	ENST00000298472.5	+	3	533	c.390A>G	c.(388-390)caA>caG	p.Q130Q	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	130					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.Q130Q(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AAAACGTGCAAGTTGGTCTGT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	10											81	71	75					10																	119003750		2203	4300	6503	118993740	SO:0001819	synonymous_variant	6571			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.390A>G	10.37:g.119003750A>G			118993740	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																				0.512	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		G	119003750	A	G	119003750	2	3	61	1	0	0	0	0	0	0	0	1	14463	69	3	4		4	SLC18A2	10	119003750	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	34153	119003750	16530997	7027	15012										
SLC18A2	6571	broad.mit.edu	37	chr10	119029918	119029918	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattgggataattgatattCtttttgcccctctctgcttt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119029918C>A	ENST00000298472.5	+	15	1527	c.1384C>A	c.(1384-1386)Ctt>Att	p.L462I	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	462					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.L462I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AATTGATATTCTTTTTGCCCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											193	178	183					10																	119029918		2203	4300	6503	119019908	SO:0001583	missense	6571			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.1384C>A	10.37:g.119029918C>A	ENSP00000298472:p.Leu462Ile		119019908	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	37	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.367537	0.24771	.	.	ENSG00000165646	ENST00000298472	D	0.81659	-1.52	5.5	2.24	0.28232	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.636741	0.16399	N	0.216135	T	0.65091	0.2658	L	0.39020	1.185	0.29592	N	0.848334	B	0.06786	0.001	B	0.06405	0.002	T	0.49854	-0.8895	10	0.13108	T	0.6	-3.9379	4.3755	0.11269	0.3589:0.4002:0.1711:0.0699	.	462	Q05940	VMAT2_HUMAN	I	462	ENSP00000298472:L462I	ENSP00000298472:L462I	L	+	1	0	SLC18A2	119019908	0.811000	0.29063	0.998000	0.56505	0.947000	0.59692	0.239000	0.18023	0.525000	0.28522	0.462000	0.41574	CTT		0.373	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		A	119029918	C	A	119029918	3	1	61	1	0	0	0	0	1	0	0	0	14463	913	32	2	1438	2	SLC18A2	10	119029918	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26168	119029918	16504829	7028	15013										
PDZD8	118987	broad.mit.edu	37	chr10	119044226	119044226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatgtttgacggtcgtccGaactgtccttagtagggcag	12	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119044226G>A	ENST00000334464.5	-	5	2257	c.2018C>T	c.(2017-2019)tCg>tTg	p.S673L	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	673					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.S673L(1)		kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		ACGGTCGTCCGAACTGTCCTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	95	96					10																	119044226		2203	4300	6503	119034216	SO:0001583	missense	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.2018C>T	10.37:g.119044226G>A	ENSP00000334642:p.Ser673Leu		119034216	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	0.276	-0.989754	0.02162	.	.	ENSG00000165650	ENST00000334464	D	0.85258	-1.96	5.87	4.96	0.65561	.	0.930568	0.09141	N	0.842913	T	0.75191	0.3816	N	0.24115	0.695	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.62982	-0.6738	10	0.51188	T	0.08	-3.2894	5.301	0.15778	0.0728:0.2675:0.5213:0.1384	.	673	Q8NEN9	PDZD8_HUMAN	L	673	ENSP00000334642:S673L	ENSP00000334642:S673L	S	-	2	0	PDZD8	119034216	0.615000	0.27026	0.143000	0.22291	0.277000	0.26821	4.390000	0.59646	1.472000	0.48140	0.591000	0.81541	TCG		0.433	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119044226	G	A	119044226	3	1	61	1	0	0	0	0	1	0	0	0	11736	1059	37	1	1450	1	PDZD8	10	119044226	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14308	119044226	16490521	7029	15014										
PDZD8	118987	broad.mit.edu	37	chr10	119049715	119049715	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccaatggcgataagtcGatctccccgctgaagatctg	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119049715G>A	ENST00000334464.5	-	4	1482	c.1243C>T	c.(1243-1245)Cga>Tga	p.R415*	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	415	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.R415*(1)		kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		GCGATAAGTCGATCTCCCCGC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											98	87	91					10																	119049715		2203	4300	6503	119039705	SO:0001587	stop_gained	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1243C>T	10.37:g.119049715G>A	ENSP00000334642:p.Arg415*		119039705	Q86WE0|Q86WE5|Q9UFF1	Nonsense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	37	6.440007	0.97568	.	.	ENSG00000165650	ENST00000334464	.	.	.	5.48	3.45	0.39498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-8.4792	11.2069	0.48775	0.0:0.0:0.4813:0.5187	.	.	.	.	X	415	.	ENSP00000334642:R415X	R	-	1	2	PDZD8	119039705	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.815000	0.55651	1.306000	0.44926	0.563000	0.77884	CGA		0.428	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119049715	G	A	119049715	4	1	61	1	0	0	0	0	0	1	0	0	11736	1066	37	1	2229	1	PDZD8	10	119049715	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5489	119049715	16485032	7030	15015										
EMX2	2018	broad.mit.edu	37	chr10	119305162	119305162	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaacgacactagccccgaGagtttccttttgcacaacgc	10	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119305162G>T	ENST00000553456.3	+	2	1250	c.426G>T	c.(424-426)gaG>gaT	p.E142D	EMX2_ENST00000546446.1_3'UTR|EMX2OS_ENST00000551288.1_RNA|EMX2_ENST00000442245.4_Intron	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	142					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.E142D(1)		endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		CTAGCCCCGAGAGTTTCCTTT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	10											63	54	57					10																	119305162		2203	4300	6503	119295152	SO:0001583	missense	2018			AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"Homeoboxes / ANTP class : NKL subclass"	3341	protein-coding gene	gene with protein product		600035	"empty spiracles homolog 2 (Drosophila)"			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.426G>T	10.37:g.119305162G>T	ENSP00000450962:p.Glu142Asp		119295152	G3V305|Q96NN8|Q9BQF4	Missense_Mutation	SNP	ENST00000553456.3	37	CCDS7601.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899247	0.33535	.	.	ENSG00000170370	ENST00000369201	.	.	.	5.9	2.63	0.31362	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	L	0.28344	0.845	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.23404	-1.0189	9	0.33940	T	0.23	-14.8166	11.6179	0.51099	0.2741:0.0:0.7259:0.0	.	142	Q04743	EMX2_HUMAN	D	142	.	ENSP00000358202:E142D	E	+	3	2	EMX2	119295152	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.342000	0.33919	0.835000	0.34877	0.643000	0.83706	GAG		0.637	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050569.4	NM_004098		T	119305162	G	T	119305162	3	4	61	1	0	0	0	0	1	0	0	0	5121	933	33	2	432	2	EMX2	10	119305162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	255447	119305162	16229585	7031	15016										
EMX2	2018	broad.mit.edu	37	chr10	119305283	119305283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcactacgtggtgggcgccGaaaggaagcagctggcacac	14	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:119305283G>A	ENST00000553456.3	+	2	1371	c.547G>A	c.(547-549)Gaa>Aaa	p.E183K	EMX2_ENST00000546446.1_3'UTR|EMX2OS_ENST00000551288.1_RNA|EMX2_ENST00000442245.4_Intron	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	183					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.E183K(1)		endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		GGTGGGCGCCGAAAGGAAGCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	10											46	44	45					10																	119305283		2203	4300	6503	119295273	SO:0001583	missense	2018			AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"Homeoboxes / ANTP class : NKL subclass"	3341	protein-coding gene	gene with protein product		600035	"empty spiracles homolog 2 (Drosophila)"			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.547G>A	10.37:g.119305283G>A	ENSP00000450962:p.Glu183Lys		119295273	G3V305|Q96NN8|Q9BQF4	Missense_Mutation	SNP	ENST00000553456.3	37	CCDS7601.1	.	.	.	.	.	.	.	.	.	.	G	37	6.610881	0.97705	.	.	ENSG00000170370	ENST00000369201	.	.	.	5.9	5.9	0.94986	Homeobox, eukaryotic (1);Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.63604	0.2525	N	0.24115	0.695	0.80722	D	1	D	0.65815	0.995	P	0.62382	0.901	T	0.59888	-0.7369	9	0.33141	T	0.24	-12.3677	20.2806	0.98513	0.0:0.0:1.0:0.0	.	183	Q04743	EMX2_HUMAN	K	183	.	ENSP00000358202:E183K	E	+	1	0	EMX2	119295273	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.795000	0.96236	0.643000	0.83706	GAA		0.642	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050569.4	NM_004098		A	119305283	G	A	119305283	3	1	61	1	0	0	0	0	1	0	0	0	5121	1059	37	1	553	1	EMX2	10	119305283	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121	119305283	16229464	7032	15017										
C10orf84	63877	broad.mit.edu	37	chr10	120070408	120070408	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttggtttcccatctcttCtttgcttcaaacctaaaagg	5	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:120070408C>A	ENST00000369183.4	-	9	922	c.663G>T	c.(661-663)aaG>aaT	p.K221N	FAM204A_ENST00000469758.1_5'UTR|FAM204A_ENST00000369172.4_Missense_Mutation_p.K221N	NM_022063.2	NP_071346.1	Q9H8W3	F204A_HUMAN	family with sequence similarity 204, member A	221								p.K221N(1)		kidney(1)|large_intestine(5)|lung(4)|ovary(1)	11						CCCATCTCTTCTTTGCTTCAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	10											120	109	113					10																	120070408		2203	4300	6503	120060398	SO:0001583	missense	63877			AK023250	CCDS7605.1	10q26.12	2011-06-01	2011-06-01	2011-06-01	ENSG00000165669	ENSG00000165669			25794	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 84"	C10orf84		12477932	Standard	NM_022063		Approved	FLJ13188, bA319I23.1	uc010qss.1	Q9H8W3	OTTHUMG00000019131	ENST00000369183.4:c.663G>T	10.37:g.120070408C>A	ENSP00000358183:p.Lys221Asn		120060398	D3DRC6|Q5T373|Q9H5V5	Missense_Mutation	SNP	ENST00000369183.4	37	CCDS7605.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397874	0.83120	.	.	ENSG00000165669	ENST00000369183;ENST00000369172	.	.	.	6.08	6.08	0.98989	.	0.040549	0.85682	D	0.000000	T	0.73590	0.3606	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74325	-0.3702	9	0.87932	D	0	-21.6781	20.6647	0.99678	0.0:1.0:0.0:0.0	.	221	Q9H8W3	F204A_HUMAN	N	221	.	ENSP00000358170:K221N	K	-	3	2	FAM204A	120060398	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.578000	0.67450	2.890000	0.99128	0.655000	0.94253	AAG		0.328	FAM204A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050596.2	NM_022063		A	120070408	C	A	120070408	3	1	61	1	0	0	0	0	1	0	0	0	1625	912	32	2	42	2	C10orf84	10	120070408	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	765125	120070408	15464339	7033	15018										
EIF3A	340719	broad.mit.edu	37	chr10	120796666	120796666	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgagtggaggtcctcttCggtccctgtcgtctcttaga	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:120796666C>T	ENST00000425699.1	+	0	4627				EIF3A_ENST00000369144.3_Missense_Mutation_p.R1295Q|EIF3A_ENST00000541549.1_Missense_Mutation_p.R1261Q	NM_199461.2	NP_955631.1	Q8WY41	NANO1_HUMAN	nanos homolog 1 (Drosophila)						cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.R1295Q(1)		lung(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0193)		AGGTCCTCTTCGGTCCCTGTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											239	215	223					10																	120796666		2203	4300	6503	120786656	SO:0001628	intergenic_variant	8661			AF275269	CCDS7607.1	10q26.13	2003-12-01			ENSG00000188613	ENSG00000188613			23044	protein-coding gene	gene with protein product		608226				12690449	Standard	NM_199461		Approved	NOS1	uc009xzf.1	Q8WY41	OTTHUMG00000019141		10.37:g.120796666C>T			120786656		Missense_Mutation	SNP	ENST00000425699.1	37	CCDS7607.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.704811	0.48412	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.24538	1.85;1.85	4.81	4.81	0.61882	.	0.000000	0.33670	N	0.004672	T	0.39809	0.1092	L	0.50333	1.59	0.36511	D	0.869614	D	0.64830	0.994	P	0.61201	0.885	T	0.20472	-1.0274	10	0.15066	T	0.55	-10.7596	16.6052	0.84826	0.0:1.0:0.0:0.0	.	1295	Q14152	EIF3A_HUMAN	Q	1295;1261	ENSP00000358140:R1295Q;ENSP00000438178:R1261Q	ENSP00000358140:R1295Q	R	-	2	0	EIF3A	120786656	0.990000	0.36364	0.991000	0.47740	0.695000	0.40330	4.156000	0.58138	2.663000	0.90544	0.650000	0.86243	CGA		0.532	NANOS1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000110794.1			T	120796666	C	T	120796666	1	4	61	0	1	0	0	0	0	0	0	0	5023	884	31	1		1	EIF3A	10	120796666	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726258	120796666	14738081	7034	15019										
EIF3A	8661	broad.mit.edu	37	chr10	120801943	120801943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtcctcatcagctgttCgccagcttcctctgtcctca	6	17	5	0	rs138563024		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:120801943C>T	ENST00000369144.3	-	19	3216	c.3089G>A	c.(3088-3090)cGa>cAa	p.R1030Q	EIF3A_ENST00000541549.1_Missense_Mutation_p.R996Q	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)	p.R1030Q(1)		endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		ATCAGCTGTTCGCCAGCTTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	GLN/ARG	0,4406		0,0,2203	325	238	268		3089	6.2	1	10	dbSNP_134	268	2,8598	2.2+/-6.3	0,2,4298	no	missense	EIF3A	NM_003750.2	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	1030/1383	120801943	2,13004	2203	4300	6503	120791933	SO:0001583	missense	8661			U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.3089G>A	10.37:g.120801943C>T	ENSP00000358140:p.Arg1030Gln		120791933	B7ZBG9|Q6IBN8|Q96TD5	Missense_Mutation	SNP	ENST00000369144.3	37	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	C	37	6.051757	0.97236	0.0	2.33E-4	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.26518	1.73;1.74	6.17	6.17	0.99709	.	0.000000	0.35040	N	0.003496	T	0.54565	0.1866	M	0.74389	2.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.71870	0.975;0.859	T	0.48703	-0.9012	10	0.54805	T	0.06	-11.3457	20.8794	0.99867	0.0:1.0:0.0:0.0	.	996;1030	F5H335;Q14152	.;EIF3A_HUMAN	Q	1030;996	ENSP00000358140:R1030Q;ENSP00000438178:R996Q	ENSP00000358140:R1030Q	R	-	2	0	EIF3A	120791933	0.999000	0.42202	0.980000	0.43619	0.998000	0.95712	4.336000	0.59304	2.941000	0.99782	0.655000	0.94253	CGA		0.582	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		T	120801943	C	T	120801943	3	4	61	1	0	0	0	0	1	0	0	0	5023	884	31	1	1075	1	EIF3A	10	120801943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5277	120801943	14732804	7035	15020										
EIF3A	8661	broad.mit.edu	37	chr10	120810097	120810097	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctctatagtatgttatCctgcgttcttctttacgctg	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:120810097C>T	ENST00000369144.3	-	16	2536	c.2409G>A	c.(2407-2409)agG>agA	p.R803R	EIF3A_ENST00000541549.1_Silent_p.R769R	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)	p.R803R(1)		endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		AGTATGTTATCCTGCGTTCTT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	10											504	439	461					10																	120810097		2203	4300	6503	120800087	SO:0001819	synonymous_variant	8661			U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.2409G>A	10.37:g.120810097C>T			120800087	B7ZBG9|Q6IBN8|Q96TD5	Silent	SNP	ENST00000369144.3	37	CCDS7608.1																																																																																				0.418	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		T	120810097	C	T	120810097	2	4	61	1	0	0	0	0	0	0	0	1	5023	854	30	3		3	EIF3A	10	120810097	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8154	120810097	14724650	7036	15021										
FAM45A	404636	broad.mit.edu	37	chr10	120896004	120896004	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattgctctaaaaacaagaGaaatctttaccaacctagca	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:120896004G>A	ENST00000361432.2	+	9	945	c.919G>A	c.(919-921)Gaa>Aaa	p.E307K	FAM45A_ENST00000535029.1_3'UTR|FAM45A_ENST00000489988.1_3'UTR|FAM45A_ENST00000544016.1_Missense_Mutation_p.E156K	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	307								p.E307K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		AAAAACAAGAGAAATCTTTAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	71	70					10																	120896004		2201	4300	6501	120885994	SO:0001583	missense	404636			AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.919G>A	10.37:g.120896004G>A	ENSP00000354688:p.Glu307Lys		120885994	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Missense_Mutation	SNP	ENST00000361432.2	37	CCDS7609.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077373	0.94000	.	.	ENSG00000119979	ENST00000361432;ENST00000544016	.	.	.	5.4	5.4	0.78164	.	0.099782	0.64402	D	0.000002	T	0.76955	0.4060	M	0.74258	2.255	0.80722	D	1	D;P;D;D	0.63880	0.964;0.883;0.993;0.989	B;B;P;P	0.59487	0.434;0.338;0.858;0.744	T	0.79045	-0.1964	9	0.66056	D	0.02	.	17.8895	0.88867	0.0:0.0:1.0:0.0	.	234;156;299;307	B4DNL9;B4DMU4;Q8TCE6-2;Q8TCE6	.;.;.;FA45A_HUMAN	K	307;156	.	ENSP00000354688:E307K	E	+	1	0	FAM45A	120885994	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	8.626000	0.90969	2.740000	0.93945	0.644000	0.83932	GAA		0.353	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009		A	120896004	G	A	120896004	3	1	61	1	0	0	0	0	1	0	0	0	5583	943	33	3	953	3	FAM45A	10	120896004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85907	120896004	14638743	7037	15022										
GRK5	2869	broad.mit.edu	37	chr10	121140355	121140355	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgcagtttatgtgacaaGcagccaatcgggaggctgct	12	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:121140355G>A	ENST00000392870.2	+	3	506	c.177G>A	c.(175-177)aaG>aaA	p.K59K	GRK5_ENST00000369108.3_5'UTR|MIR4681_ENST00000580598.1_RNA	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	59	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)	p.K59K(1)		endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		TATGTGACAAGCAGCCAATCG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	10											105	106	105					10																	121140355		2203	4300	6503	121130345	SO:0001819	synonymous_variant	2869			L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.177G>A	10.37:g.121140355G>A			121130345	D3DRD0|Q5T059	Silent	SNP	ENST00000392870.2	37	CCDS7612.1																																																																																				0.517	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308		A	121140355	G	A	121140355	2	1	61	1	0	0	0	0	0	0	0	1	6813	962	34	3		3	GRK5	10	121140355	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244351	121140355	14394392	7038	15023										
GRK5	2869	broad.mit.edu	37	chr10	121203196	121203196	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgggaggaggtggaccgcCgggtcctggagacggaggag	22	8	0	1	rs147170538		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:121203196C>T	ENST00000392870.2	+	12	1527	c.1198C>T	c.(1198-1200)Cgg>Tgg	p.R400W	GRK5_ENST00000369108.3_Missense_Mutation_p.R295W	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	400	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)	p.R400W(1)		endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		GGTGGACCGCCGGGTCCTGGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	TRP/ARG	0,4406		0,0,2203	42	44	43		1198	2.9	1	10	dbSNP_134	43	1,8599	1.2+/-3.3	0,1,4299	no	missense	GRK5	NM_005308.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	400/591	121203196	1,13005	2203	4300	6503	121193186	SO:0001583	missense	2869			L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.1198C>T	10.37:g.121203196C>T	ENSP00000376609:p.Arg400Trp		121193186	D3DRD0|Q5T059	Missense_Mutation	SNP	ENST00000392870.2	37	CCDS7612.1	.	.	.	.	.	.	.	.	.	.	c	19.33	3.807762	0.70797	0.0	1.16E-4	ENSG00000198873	ENST00000392870;ENST00000369108	T;T	0.53640	0.61;0.61	5.0	2.89	0.33648	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000026	T	0.65811	0.2727	M	0.76838	2.35	0.58432	D	0.999993	D;D	0.89917	0.999;1.0	D;D	0.68353	0.957;0.947	T	0.70673	-0.4807	10	0.87932	D	0	-2.8538	12.1264	0.53919	0.4389:0.5611:0.0:0.0	.	400;400	B2R7K0;P34947	.;GRK5_HUMAN	W	400;295	ENSP00000376609:R400W;ENSP00000358104:R295W	ENSP00000358104:R295W	R	+	1	2	GRK5	121193186	0.564000	0.26602	1.000000	0.80357	0.997000	0.91878	-0.055000	0.11807	1.057000	0.40506	0.561000	0.74099	CGG		0.627	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308		T	121203196	C	T	121203196	3	4	61	1	0	0	0	0	1	0	0	0	6813	643	23	1	1244	1	GRK5	10	121203196	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62841	121203196	14331551	7039	15024										
INPP5F	22876	broad.mit.edu	37	chr10	121551679	121551679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttttctaggttgatgaccGatttttttggaataaataca	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:121551679G>A	ENST00000361976.2	+	6	789	c.623G>A	c.(622-624)cGa>cAa	p.R208Q	INPP5F_ENST00000369083.3_Missense_Mutation_p.R208Q|INPP5F_ENST00000369081.1_3'UTR	NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0					cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.R208Q(1)		breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		GTTGATGACCGATTTTTTTGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											119	121	120					10																	121551679		2203	4300	6503	121541669	SO:0001583	missense	22876			AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.623G>A	10.37:g.121551679G>A	ENSP00000354519:p.Arg208Gln		121541669	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	37	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153604	0.78114	.	.	ENSG00000198825	ENST00000361976;ENST00000369083	T;T	0.59906	0.23;0.23	5.43	5.43	0.79202	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.75777	2.31	0.80722	D	1	B	0.31351	0.32	B	0.34138	0.176	T	0.65647	-0.6117	10	0.56958	D	0.05	-14.7163	19.5966	0.95541	0.0:0.0:1.0:0.0	.	208	Q9Y2H2	SAC2_HUMAN	Q	208	ENSP00000354519:R208Q;ENSP00000358079:R208Q	ENSP00000354519:R208Q	R	+	2	0	INPP5F	121541669	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.534000	0.90620	2.698000	0.92095	0.655000	0.94253	CGA		0.353	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		A	121551679	G	A	121551679	3	1	61	1	0	0	0	0	1	0	0	0	7779	1058	37	1	645	1	INPP5F	10	121551679	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	348483	121551679	13983068	7040	15025										
INPP5F	22876	broad.mit.edu	37	chr10	121569697	121569697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagatattacctcaaccGatttaaggatgcttataggc	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:121569697G>A	ENST00000361976.2	+	14	1821	c.1655G>A	c.(1654-1656)cGa>cAa	p.R552Q		NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.R552Q(1)		breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		TACCTCAACCGATTTAAGGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	10											132	112	119					10																	121569697		2203	4300	6503	121559687	SO:0001583	missense	22876			AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.1655G>A	10.37:g.121569697G>A	ENSP00000354519:p.Arg552Gln		121559687	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	37	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.520969	0.64747	.	.	ENSG00000198825	ENST00000361976	T	0.28895	1.59	5.04	4.14	0.48551	.	0.064477	0.64402	N	0.000005	T	0.29389	0.0732	L	0.52364	1.645	0.80722	D	1	B	0.11235	0.004	B	0.10450	0.005	T	0.05683	-1.0870	10	0.41790	T	0.15	-6.9188	13.2338	0.59958	0.0762:0.0:0.9238:0.0	.	552	Q9Y2H2	SAC2_HUMAN	Q	552	ENSP00000354519:R552Q	ENSP00000354519:R552Q	R	+	2	0	INPP5F	121559687	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.635000	0.74295	1.136000	0.42199	0.561000	0.74099	CGA		0.368	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		A	121569697	G	A	121569697	3	1	61	1	0	0	0	0	1	0	0	0	7779	1058	37	1	1709	1	INPP5F	10	121569697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18018	121569697	13965050	7041	15026										
SEC23IP	11196	broad.mit.edu	37	chr10	121689932	121689932	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcacaaaggcagaaaaaGacttcatttaggtaaaaagc	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:121689932G>T	ENST00000369075.3	+	15	2633	c.2561G>T	c.(2560-2562)aGa>aTa	p.R854I	SEC23IP_ENST00000475542.1_Intron|SEC23IP_ENST00000543134.1_Missense_Mutation_p.R643I	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	854	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R854I(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GGCAGAAAAAGACTTCATTTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											53	55	55					10																	121689932		2202	4294	6496	121679922	SO:0001583	missense	11196			AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2561G>T	10.37:g.121689932G>T	ENSP00000358071:p.Arg854Ile		121679922	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	37	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926597	0.92319	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.38077	1.16;1.22	5.52	5.52	0.82312	DDHD (2);	0.000000	0.85682	D	0.000000	T	0.69878	0.3160	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.74450	-0.3661	10	0.51188	T	0.08	-25.6438	19.7923	0.96464	0.0:0.0:1.0:0.0	.	643;854	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	I	854;643	ENSP00000358071:R854I;ENSP00000438773:R643I	ENSP00000358071:R854I	R	+	2	0	SEC23IP	121679922	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.468000	0.97676	2.765000	0.95021	0.591000	0.81541	AGA		0.313	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			T	121689932	G	T	121689932	3	4	61	1	0	0	0	0	1	0	0	0	14030	942	33	2	2619	2	SEC23IP	10	121689932	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120235	121689932	13844815	7042	15027										
WDR11	55717	broad.mit.edu	37	chr10	122648616	122648616	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggtagtattacctgcatCgcttggaaaggtgatacatt	11	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:122648616C>T	ENST00000263461.6	+	17	2394	c.2148C>T	c.(2146-2148)atC>atT	p.I716I	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.I716I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TTACCTGCATCGCTTGGAAAG	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	10											138	142	141					10																	122648616		2203	4300	6503	122638606	SO:0001819	synonymous_variant	55717			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2148C>T	10.37:g.122648616C>T			122638606	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																				0.323	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			T	122648616	C	T	122648616	2	4	61	1	0	0	0	0	0	0	0	1	17313	874	31	1		1	WDR11	10	122648616	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	958684	122648616	12886131	7043	15028										
WDR11	55717	broad.mit.edu	37	chr10	122668211	122668211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagtcccccaaggaagaaCccattgaagagtgacagctt	10	10	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:122668211C>T	ENST00000263461.6	+	29	3907	c.3661C>T	c.(3661-3663)Ccc>Tcc	p.P1221S	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.P1221S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CAAGGAAGAACCCATTGAAGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											90	92	91					10																	122668211		2203	4300	6503	122658201	SO:0001583	missense	55717			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3661C>T	10.37:g.122668211C>T	ENSP00000263461:p.Pro1221Ser		122658201	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	C	5.957	0.360633	0.11296	.	.	ENSG00000120008	ENST00000263461	D	0.89485	-2.52	5.4	-7.65	0.01281	.	3.664390	0.00628	N	0.000465	T	0.70098	0.3185	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.67329	-0.5698	10	0.07813	T	0.8	17.7967	3.7361	0.08511	0.3251:0.125:0.4171:0.1329	.	1221	Q9BZH6	WDR11_HUMAN	S	1221	ENSP00000263461:P1221S	ENSP00000263461:P1221S	P	+	1	0	WDR11	122658201	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.047000	0.11963	-1.010000	0.03396	-0.311000	0.09066	CCC		0.522	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			T	122668211	C	T	122668211	3	4	61	1	0	0	0	0	1	0	0	0	17313	507	18	3	3775	3	WDR11	10	122668211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19595	122668211	12866536	7044	15029										
FGFR2	2263	broad.mit.edu	37	chr10	123239508	123239508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaactaggtgaatactgttCgagaggttggctgaggtcca	14	6	0	3	rs374993905		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123239508C>T	ENST00000358487.5	-	18	2601	c.2329G>A	c.(2329-2331)Gaa>Aaa	p.E777K	FGFR2_ENST00000478859.1_Missense_Mutation_p.E549K|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000369060.4_Missense_Mutation_p.E661K|FGFR2_ENST00000457416.2_Missense_Mutation_p.E778K|FGFR2_ENST00000346997.2_Missense_Mutation_p.E775K|FGFR2_ENST00000369061.4_Missense_Mutation_p.E665K|FGFR2_ENST00000356226.4_Missense_Mutation_p.E660K|FGFR2_ENST00000369059.1_Missense_Mutation_p.E663K	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	777					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.E777K(1)|p.E778*(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GAATACTGTTCGAGAGGTTGG	0.453		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	10						C	LYS/GLU,LYS/GLU,,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	174	160	165		2329,1993,,1984,1981,1978,2332	5.8	1	10		165	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,missense,missense,missense,missense	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	56,56,,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging	777/822,665/710,,662/707,661/706,660/705,778/823	123239508	1,13005	2203	4300	6503	123229498	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.2329G>A	10.37:g.123239508C>T	ENSP00000351276:p.Glu777Lys		123229498	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.921835	0.92319	0.0	1.16E-4	ENSG00000066468	ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416	D;D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93009	0.7775	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.992;1.0	P;D;D;P;D	0.91635	0.906;0.988;0.999;0.656;0.999	D	0.92360	0.5896	10	0.51188	T	0.08	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	794;776;660;777;680	D3DRD5;P21802-18;P21802-20;P21802;D3DRD3	.;.;.;FGFR2_HUMAN;.	K	778;665;777;660;661;663;775;778	ENSP00000358057:E665K;ENSP00000351276:E777K;ENSP00000348559:E660K;ENSP00000358056:E661K;ENSP00000358055:E663K;ENSP00000263451:E775K;ENSP00000410294:E778K	ENSP00000263451:E775K	E	-	1	0	FGFR2	123229498	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.624000	0.83124	2.756000	0.94617	0.561000	0.74099	GAA		0.453	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123239508	C	T	123239508	3	4	61	1	0	0	0	0	1	0	0	0	5885	893	31	1	234	1	FGFR2	10	123239508	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	571297	123239508	12295239	7045	15030										
FGFR2	2263	broad.mit.edu	37	chr10	123246935	123246935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccacttgactggaagccGcccctgcaaatgtagaggaa	10	12	0	2	rs113014479		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123246935G>A	ENST00000358487.5	-	15	2262	c.1990C>T	c.(1990-1992)Cgg>Tgg	p.R664W	FGFR2_ENST00000478859.1_Missense_Mutation_p.R436W|FGFR2_ENST00000357555.5_Missense_Mutation_p.R575W|FGFR2_ENST00000360144.3_Missense_Mutation_p.R576W|FGFR2_ENST00000369060.4_Missense_Mutation_p.R548W|FGFR2_ENST00000457416.2_Missense_Mutation_p.R665W|FGFR2_ENST00000351936.6_Missense_Mutation_p.R662W|FGFR2_ENST00000346997.2_Missense_Mutation_p.R662W|FGFR2_ENST00000369061.4_Missense_Mutation_p.R552W|FGFR2_ENST00000356226.4_Missense_Mutation_p.R547W|FGFR2_ENST00000369056.1_Missense_Mutation_p.R665W|FGFR2_ENST00000369059.1_Missense_Mutation_p.R550W	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.R664W(1)|p.R575W(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	ACTGGAAGCCGCCCCTGCAAA	0.408		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	2	Substitution - Missense(2)	large_intestine(2)	10											42	46	44					10																	123246935		2203	4300	6503	123236925	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1990C>T	10.37:g.123246935G>A	ENSP00000351276:p.Arg664Trp		123236925	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007776	0.75046	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96386	0.8821	M	0.82193	2.58	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.982;0.968;0.998;0.986;0.992;0.991;0.986;0.995	D	0.96810	0.9596	10	0.87932	D	0	.	18.6972	0.91605	0.0:0.0:1.0:0.0	.	681;663;575;547;664;576;665;567	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	W	575;665;552;664;547;548;550;256;662;665;662;576;665;665;573	ENSP00000350166:R575W;ENSP00000358057:R552W;ENSP00000351276:R664W;ENSP00000348559:R547W;ENSP00000358056:R548W;ENSP00000358055:R550W;ENSP00000404219:R256W;ENSP00000263451:R662W;ENSP00000410294:R665W;ENSP00000309878:R662W;ENSP00000353262:R576W;ENSP00000358052:R665W;ENSP00000358054:R665W;ENSP00000337665:R573W	ENSP00000337665:R573W	R	-	1	2	FGFR2	123236925	1.000000	0.71417	0.946000	0.38457	0.398000	0.30690	9.540000	0.98080	2.572000	0.86782	0.655000	0.94253	CGG		0.408	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123246935	G	A	123246935	3	1	61	1	0	0	0	0	1	0	0	0	5885	1086	38	1	595	1	FGFR2	10	123246935	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7427	123246935	12287812	7046	15031										
FGFR2	2263	broad.mit.edu	37	chr10	123258030	123258030	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctgtgtgcaggctccaaGaagatttatgatattcttgt	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123258030G>T	ENST00000358487.5	-	12	1923	c.1651C>A	c.(1651-1653)Ctt>Att	p.L551I	FGFR2_ENST00000478859.1_Missense_Mutation_p.L323I|FGFR2_ENST00000357555.5_Missense_Mutation_p.L462I|FGFR2_ENST00000360144.3_Missense_Mutation_p.L463I|FGFR2_ENST00000369060.4_Missense_Mutation_p.L435I|FGFR2_ENST00000457416.2_Missense_Mutation_p.L552I|FGFR2_ENST00000351936.6_Missense_Mutation_p.L549I|FGFR2_ENST00000346997.2_Missense_Mutation_p.L549I|FGFR2_ENST00000369061.4_Missense_Mutation_p.L439I|FGFR2_ENST00000356226.4_Missense_Mutation_p.L434I|FGFR2_ENST00000369056.1_Missense_Mutation_p.L552I|FGFR2_ENST00000369059.1_Missense_Mutation_p.L437I	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	551	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L462I(1)|p.L551I(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	CAGGCTCCAAGAAGATTTATG	0.423		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	2	Substitution - Missense(2)	large_intestine(2)	10											166	148	154					10																	123258030		2203	4300	6503	123248020	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1651C>A	10.37:g.123258030G>T	ENSP00000351276:p.Leu551Ile		123248020	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265035	0.80358	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	5.02	5.02	0.67125	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92554	0.7635	N	0.17474	0.49	0.80722	D	1	B;P;D;D;D;D;D;D	0.59767	0.367;0.842;0.972;0.962;0.969;0.961;0.986;0.97	P;P;D;P;D;D;P;D	0.72075	0.71;0.708;0.976;0.855;0.911;0.935;0.855;0.945	D	0.94078	0.7341	10	0.62326	D	0.03	.	18.3256	0.90252	0.0:0.0:1.0:0.0	.	568;550;462;434;551;463;552;454	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	I	462;552;439;551;434;435;437;143;549;552;549;463;552;552;460	ENSP00000350166:L462I;ENSP00000358057:L439I;ENSP00000351276:L551I;ENSP00000348559:L434I;ENSP00000358056:L435I;ENSP00000358055:L437I;ENSP00000404219:L143I;ENSP00000263451:L549I;ENSP00000410294:L552I;ENSP00000309878:L549I;ENSP00000353262:L463I;ENSP00000358052:L552I;ENSP00000358054:L552I;ENSP00000337665:L460I	ENSP00000337665:L460I	L	-	1	0	FGFR2	123248020	0.998000	0.40836	0.960000	0.40013	0.997000	0.91878	2.698000	0.47068	2.323000	0.78572	0.591000	0.81541	CTT		0.423	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123258030	G	T	123258030	3	4	61	1	0	0	0	0	1	0	0	0	5885	942	33	2	946	2	FGFR2	10	123258030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11095	123258030	12276717	7047	15032										
FGFR2	2263	broad.mit.edu	37	chr10	123298225	123298225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggctccagtgctggtttCgtacctgaaaagatcaaagc	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123298225C>T	ENST00000358487.5	-	6	901	c.629G>A	c.(628-630)cGa>cAa	p.R210Q	FGFR2_ENST00000357555.5_Missense_Mutation_p.R121Q|FGFR2_ENST00000360144.3_Missense_Mutation_p.R121Q|FGFR2_ENST00000359354.2_Missense_Mutation_p.R210Q|FGFR2_ENST00000369060.4_Missense_Mutation_p.R210Q|FGFR2_ENST00000457416.2_Missense_Mutation_p.R210Q|FGFR2_ENST00000351936.6_Missense_Mutation_p.R210Q|FGFR2_ENST00000346997.2_Missense_Mutation_p.R210Q|FGFR2_ENST00000369061.4_Missense_Mutation_p.R210Q|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000356226.4_Missense_Mutation_p.R95Q|FGFR2_ENST00000369056.1_Missense_Mutation_p.R210Q|FGFR2_ENST00000369059.1_Missense_Mutation_p.R95Q	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	210	Ig-like C2-type 2.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.R121Q(1)|p.R210Q(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GTGCTGGTTTCGTACCTGAAA	0.423		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	2	Substitution - Missense(2)	large_intestine(2)	10											140	122	128					10																	123298225		2203	4300	6503	123288215	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.629G>A	10.37:g.123298225C>T	ENSP00000351276:p.Arg210Gln		123288215	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	36	5.866600	0.97043	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23	5.87	5.87	0.94306	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79992	0.4542	L	0.49256	1.55	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.957;0.989;0.978;0.975;0.986;0.994;0.978;1.0;1.0;0.999;0.955;0.999	T	0.79654	-0.1713	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	229;229;95;210;229;210;121;95;210;229;121;210	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	Q	121;210;210;210;95;210;95;210;210;210;121;210;210;121;210	ENSP00000350166:R121Q;ENSP00000358057:R210Q;ENSP00000351276:R210Q;ENSP00000348559:R95Q;ENSP00000358056:R210Q;ENSP00000358055:R95Q;ENSP00000263451:R210Q;ENSP00000410294:R210Q;ENSP00000309878:R210Q;ENSP00000353262:R121Q;ENSP00000358052:R210Q;ENSP00000358054:R210Q;ENSP00000337665:R121Q;ENSP00000352309:R210Q	ENSP00000337665:R121Q	R	-	2	0	FGFR2	123288215	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.730000	0.84881	2.941000	0.99782	0.655000	0.94253	CGA		0.423	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123298225	C	T	123298225	3	4	61	1	0	0	0	0	1	0	0	0	5885	884	31	1	2144	1	FGFR2	10	123298225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40195	123298225	12236522	7048	15033										
ATE1	11101	broad.mit.edu	37	chr10	123596331	123596331	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctagtaaaagcaatttCtctgcgaaaagaaaaagaag	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123596331C>T	ENST00000224652.6	-	10	1244	c.1159G>A	c.(1159-1161)Gaa>Aaa	p.E387K	ATE1_ENST00000369043.3_Splice_Site_p.E387K|ATE1_ENST00000535655.1_Splice_Site_p.E88K|ATE1_ENST00000369040.3_Splice_Site_p.E291K|ATE1_ENST00000543447.1_Splice_Site_p.E272K|ATE1_ENST00000540606.1_Splice_Site_p.E380K	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	387					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)	p.E387K(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				AAAGCAATTTCTCTGCGAAAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	10											40	44	42					10																	123596331		2187	4293	6480	123586321	SO:0001630	splice_region_variant	11101			AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.1158-1G>A	10.37:g.123596331C>T			123586321	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.7|26.7	4.765045|4.765045	0.90020|0.90020	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000369043;ENST00000535655;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447|ENST00000423243	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Acyl-CoA N-acyltransferase (1);Arginine-tRNA-protein transferase, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88455|0.88455	0.6441|0.6441	H|H	0.96301|0.96301	3.8|3.8	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.67145|.	0.996;0.973;0.987;0.996|.	D;P;P;D|.	0.72075|.	0.965;0.85;0.889;0.976|.	D|D	0.91551|0.91551	0.5257|0.5257	9|5	0.72032|.	D|.	0.01|.	-22.4363|-22.4363	19.7537|19.7537	0.96281|0.96281	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	380;291;387;387|.	F5GXE4;B4E107;O95260;O95260-2|.	.;.;ATE1_HUMAN;.|.	K|K	387;88;387;291;380;272|383	.|.	ENSP00000224652:E387K|.	E|R	-|-	1|2	0|0	ATE1|ATE1	123586321|123586321	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.762000|7.762000	0.85270|0.85270	2.676000|2.676000	0.91093|0.91093	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.323	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	Missense_Mutation	T	123596331	C	T	123596331	5	4	61	1	0	0	0	0	0	0	1	0	1079	927	32	3	409	3	ATE1	10	123596331	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298106	123596331	11938416	7049	15034										
TACC2	10579	broad.mit.edu	37	chr10	123844606	123844606	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttctccaagccatccagGttttaaggaccagggagcag	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123844606G>A	ENST00000369005.1	+	4	2931	c.2591G>A	c.(2590-2592)gGt>gAt	p.G864D	TACC2_ENST00000515603.1_Missense_Mutation_p.G864D|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.G864D|TACC2_ENST00000515273.1_Missense_Mutation_p.G864D|TACC2_ENST00000334433.3_Missense_Mutation_p.G864D	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	864					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)	p.G864D(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGCCATCCAGGTTTTAAGGAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											107	110	109					10																	123844606		2203	4300	6503	123834596	SO:0001583	missense	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2591G>A	10.37:g.123844606G>A	ENSP00000358001:p.Gly864Asp		123834596	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.281597	0.23392	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.25414	2.0;1.8;1.83;2.0;1.8	4.99	2.09	0.27110	.	0.000000	0.37623	N	0.002017	T	0.14830	0.0358	N	0.20986	0.625	0.09310	N	1	B;B;B	0.22080	0.064;0.064;0.023	B;B;B	0.21151	0.033;0.019;0.019	T	0.17048	-1.0382	10	0.46703	T	0.11	-2.6565	6.4647	0.21975	0.4101:0.0:0.5899:0.0	.	864;864;864	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	D	864;864;864;864;864;854	ENSP00000358001:G864D;ENSP00000424467:G864D;ENSP00000427618:G864D;ENSP00000334280:G864D;ENSP00000395048:G864D	ENSP00000334280:G864D	G	+	2	0	TACC2	123834596	0.260000	0.24053	0.003000	0.11579	0.002000	0.02628	0.701000	0.25616	0.260000	0.21731	0.549000	0.68633	GGT		0.522	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	123844606	G	A	123844606	3	1	61	1	0	0	0	0	1	0	0	0	15541	1261	44	3	2601	3	TACC2	10	123844606	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248275	123844606	11690141	7050	15035										
TACC2	10579	broad.mit.edu	37	chr10	123892137	123892137	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagttcacctgtggcaGatgatatcatccagcccgct	8	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:123892137G>T	ENST00000369005.1	+	6	5927	c.5587G>T	c.(5587-5589)Gat>Tat	p.D1863Y	TACC2_ENST00000515603.1_Missense_Mutation_p.D1863Y|TACC2_ENST00000358010.1_Missense_Mutation_p.D54Y|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000513429.1_Missense_Mutation_p.D54Y|TACC2_ENST00000453444.2_Missense_Mutation_p.D1912Y|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000515273.1_Missense_Mutation_p.D1912Y|TACC2_ENST00000334433.3_Missense_Mutation_p.D1863Y|TACC2_ENST00000493951.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1863					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)	p.D1863Y(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ACCTGTGGCAGATGATATCAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	10											123	110	114					10																	123892137		2203	4300	6503	123882127	SO:0001583	missense	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5587G>T	10.37:g.123892137G>T	ENSP00000358001:p.Asp1863Tyr		123882127	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.749608	0.30955	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076	T;T;T;T;T;T;T	0.57107	0.42;0.42;3.65;3.88;0.42;0.42;3.65	3.1	1.17	0.20885	.	0.258368	0.20552	N	0.090099	T	0.53594	0.1806	L	0.29908	0.895	0.09310	N	1	D;D;P;D	0.89917	0.999;1.0;0.946;1.0	D;D;P;D	0.79784	0.993;0.96;0.648;0.96	T	0.37888	-0.9686	10	0.72032	D	0.01	-5.6909	5.4255	0.16423	0.2727:0.0:0.7273:0.0	.	1912;1863;54;1863	E9PBC6;E7EMZ9;O95359-5;O95359	.;.;.;TACC2_HUMAN	Y	1863;54;1912;1863;1863;54;1912;1853	ENSP00000358001:D1863Y;ENSP00000425062:D54Y;ENSP00000424467:D1912Y;ENSP00000427618:D1863Y;ENSP00000334280:D1863Y;ENSP00000350701:D54Y;ENSP00000395048:D1912Y	ENSP00000334280:D1863Y	D	+	1	0	TACC2	123882127	0.047000	0.20315	0.034000	0.17996	0.154000	0.21943	1.432000	0.34936	0.313000	0.23062	0.561000	0.74099	GAT		0.498	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123892137	G	T	123892137	3	4	61	1	0	0	0	0	1	0	0	0	15541	942	33	2	5605	2	TACC2	10	123892137	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47531	123892137	11642610	7051	15036										
BTBD16	118663	broad.mit.edu	37	chr10	124049512	124049512	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacccactggtcactaaagtCggtatgtatatacccgtcta	8	11	2	0	rs367755013		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124049512C>T	ENST00000260723.4	+	6	725	c.474C>T	c.(472-474)gtC>gtT	p.V158V	BTBD16_ENST00000368994.2_Splice_Site_p.V159V	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	158	BTB.							p.V158V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TCACTAAAGTCGGTATGTATA	0.388													c|||	1	0.000199681	8e-04	0	5008	,	,		16466	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10						T		1,4405	2.1+/-5.4	0,1,2202	110	113	112		474	-6.7	0	10		112	0,8600		0,0,4300	no	coding-synonymous-near-splice	BTBD16	NM_144587.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		158/507	124049512	1,13005	2203	4300	6503	124039502	SO:0001630	splice_region_variant	118663			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.475+1C>T	10.37:g.124049512C>T			124039502	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																				0.388	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	Silent	T	124049512	C	T	124049512	5	4	61	1	0	0	0	0	0	0	1	0	1544	898	31	1	492	1	BTBD16	10	124049512	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157375	124049512	11485235	7052	15037										
BTBD16	118663	broad.mit.edu	37	chr10	124066776	124066776	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgcaactgaactacaaGattcaggcaattccgactta	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124066776G>T	ENST00000260723.4	+	10	1115	c.864G>T	c.(862-864)aaG>aaT	p.K288N	BTBD16_ENST00000368994.2_Missense_Mutation_p.K289N	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	288								p.K288N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TGAACTACAAGATTCAGGCAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	10											122	123	123					10																	124066776		2202	4300	6502	124056766	SO:0001583	missense	118663			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.864G>T	10.37:g.124066776G>T	ENSP00000260723:p.Lys288Asn		124056766	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	G	9.875	1.199949	0.22121	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.19250	2.16;2.16	5.45	-3.6	0.04570	.	0.677910	0.14402	N	0.321801	T	0.11324	0.0276	L	0.46157	1.445	0.09310	N	1	B;B	0.14438	0.01;0.01	B;B	0.11329	0.006;0.006	T	0.36456	-0.9747	10	0.16420	T	0.52	-3.1924	0.4963	0.00572	0.3047:0.1383:0.288:0.269	.	289;288	Q32M84-2;Q32M84	.;BTBDG_HUMAN	N	288;289	ENSP00000260723:K288N;ENSP00000357990:K289N	ENSP00000260723:K288N	K	+	3	2	BTBD16	124056766	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.495000	0.06443	-0.972000	0.03559	-0.302000	0.09304	AAG		0.323	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		T	124066776	G	T	124066776	3	4	61	1	0	0	0	0	1	0	0	0	1544	933	33	2	898	2	BTBD16	10	124066776	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17264	124066776	11467971	7053	15038										
BTBD16	118663	broad.mit.edu	37	chr10	124094418	124094418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatacaacttattcgaaaaCgattgctctatatggattct	6	7	2	0	rs577596137		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124094418C>T	ENST00000260723.4	+	14	1438	c.1187C>T	c.(1186-1188)aCg>aTg	p.T396M	BTBD16_ENST00000368994.2_Missense_Mutation_p.T397M|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	396								p.T396M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TATTCGAAAACGATTGCTCTA	0.368													C|||	1	0.000199681	8e-04	0	5008	,	,		18797	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10											116	115	115					10																	124094418		2202	4300	6502	124084408	SO:0001583	missense	118663			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1187C>T	10.37:g.124094418C>T	ENSP00000260723:p.Thr396Met		124084408	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	C	8.384	0.838292	0.16891	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.18810	2.19;2.19	5.53	-10.7	0.00240	.	1.354520	0.04802	N	0.433645	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.26916	-1.0089	10	0.30078	T	0.28	-0.0024	11.6397	0.51224	0.0:0.5543:0.2107:0.235	.	397;396	Q32M84-2;Q32M84	.;BTBDG_HUMAN	M	396;397	ENSP00000260723:T396M;ENSP00000357990:T397M	ENSP00000260723:T396M	T	+	2	0	BTBD16	124084408	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.792000	0.01756	-2.218000	0.00730	-1.021000	0.02439	ACG		0.368	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		T	124094418	C	T	124094418	3	4	61	1	0	0	0	0	1	0	0	0	1544	536	19	1	1237	1	BTBD16	10	124094418	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27642	124094418	11440329	7054	15039										
PLEKHA1	59338	broad.mit.edu	37	chr10	124152833	124152833	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataccagagaagatagtttCgtgtggtacatggataatcc	11	6	0	2	rs142005373		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124152833C>T	ENST00000368990.3	+	2	248	c.117C>T	c.(115-117)ttC>ttT	p.F39F	PLEKHA1_ENST00000538022.1_Silent_p.F39F|PLEKHA1_ENST00000494222.1_3'UTR|PLEKHA1_ENST00000368989.2_Silent_p.F39F|PLEKHA1_ENST00000368988.1_Silent_p.F39F|PLEKHA1_ENST00000433307.1_Silent_p.F39F	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	39	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)	p.F39F(2)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AAGATAGTTTCGTGTGGTACA	0.343																																																2	Substitution - coding silent(2)	urinary_tract(1)|large_intestine(1)	10						C	,,	1,4405	2.1+/-5.4	0,1,2202	74	76	76		117,117,117	1.2	1	10	dbSNP_134	76	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PLEKHA1	NM_001001974.2,NM_001195608.1,NM_021622.4	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	39/405,39/335,39/405	124152833	1,13005	2203	4300	6503	124142823	SO:0001819	synonymous_variant	59338			AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.117C>T	10.37:g.124152833C>T			124142823	B3KQ55|D3DRE2|Q9BVK0	Silent	SNP	ENST00000368990.3	37	CCDS7629.1																																																																																				0.343	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		T	124152833	C	T	124152833	2	4	61	1	0	0	0	0	0	0	0	1	12086	883	31	1		1	PLEKHA1	10	124152833	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58415	124152833	11381914	7055	15040										
DMBT1	1755	broad.mit.edu	37	chr10	124384803	124384803	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttgcagccacccaaatAaattctactacgacaggtga	6	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124384803A>C	ENST00000338354.3	+	42	5338	c.5232A>C	c.(5230-5232)atA>atC	p.I1744I	DMBT1_ENST00000330163.4_Silent_p.I1116I|DMBT1_ENST00000359586.6_Silent_p.I464I|DMBT1_ENST00000368909.3_Silent_p.I1744I|DMBT1_ENST00000368956.2_Silent_p.I1116I|DMBT1_ENST00000344338.3_Silent_p.I1734I|DMBT1_ENST00000368955.3_Silent_p.I1734I			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1744					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)	p.I1873I(1)|p.I1744I(1)		breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCACCCAAATAAATTCTACTA	0.483																																					Ovarian(182;93 2026 18125 22222 38972)											2	Substitution - coding silent(2)	large_intestine(2)	10											91	86	87					10																	124384803		1967	4156	6123	124374793	SO:0001819	synonymous_variant	1755				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.5232A>C	10.37:g.124384803A>C			124374793	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																					0.483	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		C	124384803	A	C	124384803	2	2	61	1	0	0	0	0	0	0	0	1	4588	352	13	4		4	DMBT1	10	124384803	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	231970	124384803	11149944	7056	15041										
C10orf120	399814	broad.mit.edu	37	chr10	124458004	124458004	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgtgaatgccacctagacGctgacaatggagaaaggact	13	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124458004G>A	ENST00000329446.4	-	3	284	c.253C>T	c.(253-255)Cgt>Tgt	p.R85C		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	85								p.R85C(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				CCACCTAGACGCTGACAATGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10											164	173	170					10																	124458004		2202	4299	6501	124447994	SO:0001630	splice_region_variant	399814				CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.253-1C>T	10.37:g.124458004G>A			124447994	B2RU17	Missense_Mutation	SNP	ENST00000329446.4	37	CCDS31302.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658356	0.47467	.	.	ENSG00000183559	ENST00000329446	T	0.35048	1.33	4.82	4.82	0.62117	.	0.549745	0.16755	N	0.200860	T	0.48960	0.1529	M	0.64997	1.995	0.80722	D	1	D	0.67145	0.996	P	0.53593	0.73	T	0.51060	-0.8753	10	0.87932	D	0	-2.9125	13.6001	0.62013	0.0:0.0:1.0:0.0	.	85	Q5SQS8	CJ120_HUMAN	C	85	ENSP00000331012:R85C	ENSP00000331012:R85C	R	-	1	0	C10orf120	124447994	1.000000	0.71417	0.985000	0.45067	0.183000	0.23260	2.459000	0.45023	2.652000	0.90054	0.603000	0.83216	CGT		0.493	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	Missense_Mutation	A	124458004	G	A	124458004	5	1	61	1	0	0	0	0	0	0	1	0	1594	1101	38	1	758	1	C10orf120	10	124458004	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73201	124458004	11076743	7057	15042										
CUZD1	50624	broad.mit.edu	37	chr10	124593361	124593361	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacactgcagatacacaGagctcatacttctcaagaat	5	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124593361G>T	ENST00000368904.1	-	10	2427	c.1478C>A	c.(1477-1479)tCt>tAt	p.S493Y	CUZD1_ENST00000545804.1_Missense_Mutation_p.S493Y|CUZD1_ENST00000392790.1_Missense_Mutation_p.S493Y					CUB and zona pellucida-like domains 1									p.S493Y(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		CAGATACACAGAGCTCATACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	105	108					10																	124593361		2203	4300	6503	124583351	SO:0001583	missense	50624			AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.1478C>A	10.37:g.124593361G>T	ENSP00000357900:p.Ser493Tyr		124583351		Missense_Mutation	SNP	ENST00000368904.1	37	CCDS7631.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.209217	0.58343	.	.	ENSG00000138161	ENST00000368904;ENST00000368901;ENST00000368900;ENST00000338948;ENST00000368899;ENST00000545804;ENST00000392790	D;D;D	0.83591	-1.74;-1.74;-1.74	5.1	5.1	0.69264	Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.192751	0.47093	D	0.000248	D	0.90058	0.6895	M	0.64997	1.995	0.45108	D	0.998125	D	0.89917	1.0	D	0.97110	1.0	D	0.90344	0.4361	10	0.56958	D	0.05	-21.1129	18.4878	0.90835	0.0:0.0:1.0:0.0	.	493	Q86UP6	CUZD1_HUMAN	Y	493;212;212;127;212;493;493	ENSP00000357900:S493Y;ENSP00000441590:S493Y;ENSP00000376540:S493Y	ENSP00000340905:S127Y	S	-	2	0	CUZD1	124583351	0.815000	0.29118	0.144000	0.22314	0.688000	0.40055	2.477000	0.45180	2.528000	0.85240	0.655000	0.94253	TCT		0.408	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034		T	124593361	G	T	124593361	3	4	61	1	0	0	0	0	1	0	0	0	4072	942	33	2	353	2	CUZD1	10	124593361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135357	124593361	10941386	7058	15043										
CUZD1	50624	broad.mit.edu	37	chr10	124596945	124596945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttgaagtttagttttaTcttgtaatctttctccactt	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124596945T>C	ENST00000368904.1	-	6	1523	c.574A>G	c.(574-576)Ata>Gta	p.I192V	CUZD1_ENST00000545804.1_Missense_Mutation_p.I192V|CUZD1_ENST00000392790.1_Missense_Mutation_p.I192V					CUB and zona pellucida-like domains 1									p.I192V(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		TTTAGTTTTATCTTGTAATCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	10											114	108	110					10																	124596945		2203	4300	6503	124586935	SO:0001583	missense	50624			AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.574A>G	10.37:g.124596945T>C	ENSP00000357900:p.Ile192Val		124586935		Missense_Mutation	SNP	ENST00000368904.1	37	CCDS7631.1	.	.	.	.	.	.	.	.	.	.	T	14.07	2.424874	0.43020	.	.	ENSG00000138161	ENST00000368904;ENST00000545804;ENST00000392790	T;T;T	0.16743	2.32;2.32;2.32	4.75	4.75	0.60458	CUB (5);	0.053369	0.64402	D	0.000001	T	0.21921	0.0528	L	0.31926	0.97	0.36733	D	0.881811	P	0.46142	0.873	P	0.56960	0.81	T	0.02774	-1.1112	10	0.05833	T	0.94	-18.9164	13.9212	0.63933	0.0:0.0:0.0:1.0	.	192	Q86UP6	CUZD1_HUMAN	V	192	ENSP00000357900:I192V;ENSP00000441590:I192V;ENSP00000376540:I192V	ENSP00000357900:I192V	I	-	1	0	CUZD1	124586935	0.878000	0.30173	0.978000	0.43139	0.993000	0.82548	1.763000	0.38461	1.773000	0.52216	0.460000	0.39030	ATA		0.453	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034		C	124596945	T	C	124596945	3	2	61	1	0	0	0	0	1	0	0	0	4072	1435	50	4	1273	4	CUZD1	10	124596945	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3584	124596945	10937802	7059	15044										
PSTK	118672	broad.mit.edu	37	chr10	124742803	124742803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagattcgttgggcttttGccagctctttttagattgtc	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:124742803G>A	ENST00000368887.3	+	3	964	c.524G>A	c.(523-525)tGc>tAc	p.C175Y	PSTK_ENST00000497219.1_3'UTR|PSTK_ENST00000405485.1_Missense_Mutation_p.C175Y	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	175					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)	p.C175Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		TTGGGCTTTTGCCAGCTCTTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	10											55	54	54					10																	124742803		2203	4300	6503	124732793	SO:0001583	missense	118672			AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"chromosome 10 open reading frame 89"	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.524G>A	10.37:g.124742803G>A	ENSP00000357882:p.Cys175Tyr		124732793	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	37	CCDS7633.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.49|18.49	3.635700|3.635700	0.67130|0.67130	.|.	.|.	ENSG00000179988|ENSG00000179988	ENST00000406217|ENST00000368887;ENST00000405485	.|T;T	.|0.37058	.|1.22;1.22	5.86|5.86	4.96|4.96	0.65561|0.65561	.|.	.|0.094648	.|0.85682	.|D	.|0.000000	T|T	0.63248|0.63248	0.2495|0.2495	M|M	0.85859|0.85859	2.78|2.78	0.46874|0.46874	D|D	0.999238|0.999238	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	T|T	0.69057|0.69057	-0.5246|-0.5246	5|10	.|0.59425	.|D	.|0.04	-16.7884|-16.7884	13.6725|13.6725	0.62434|0.62434	0.0748:0.0:0.9252:0.0|0.0748:0.0:0.9252:0.0	.|.	.|175	.|Q8IV42	.|PSTK_HUMAN	T|Y	176|175	.|ENSP00000357882:C175Y;ENSP00000384764:C175Y	.|ENSP00000357882:C175Y	A|C	+|+	1|2	0|0	PSTK|PSTK	124732793|124732793	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.838000|7.838000	0.86804|0.86804	1.485000|1.485000	0.48380|0.48380	0.563000|0.563000	0.77884|0.77884	GCC|TGC		0.388	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336		A	124742803	G	A	124742803	3	1	61	1	0	0	0	0	1	0	0	0	12754	1319	46	3	534	3	PSTK	10	124742803	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	145858	124742803	10791944	7060	15045										
CPXM2	119587	broad.mit.edu	37	chr10	125506367	125506367	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccaaacttctccatgatCtctcggatcctggccatgtt	6	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:125506367C>A	ENST00000241305.3	-	14	2338	c.2184G>T	c.(2182-2184)gaG>gaT	p.E728D	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	728					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.E728D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TCTCCATGATCTCTCGGATCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	100	102					10																	125506367		2203	4300	6503	125496357	SO:0001583	missense	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.2184G>T	10.37:g.125506367C>A	ENSP00000241305:p.Glu728Asp		125496357	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999039	0.74818	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	T	0.14144	2.53	5.24	1.24	0.21308	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.000000	0.85682	D	0.000000	T	0.25269	0.0614	L	0.56769	1.78	0.80722	D	1	D	0.59767	0.986	P	0.60012	0.867	T	0.01059	-1.1465	10	0.56958	D	0.05	-3.3865	10.1438	0.42751	0.0:0.6497:0.0:0.3503	.	728	Q8N436	CPXM2_HUMAN	D	728;561;703	ENSP00000241305:E728D	ENSP00000241305:E728D	E	-	3	2	CPXM2	125496357	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	0.752000	0.26362	0.346000	0.23899	0.655000	0.94253	GAG		0.582	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125506367	C	A	125506367	3	1	61	1	0	0	0	0	1	0	0	0	3844	912	32	2	90	2	CPXM2	10	125506367	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	763564	125506367	10028380	7061	15046										
CPXM2	119587	broad.mit.edu	37	chr10	125521394	125521394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagggaggcttacttccagCgacggtgtgccaggaggccc	16	11	0	1	rs564623475		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:125521394C>T	ENST00000241305.3	-	11	1925	c.1771G>A	c.(1771-1773)Gct>Act	p.A591T	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	591					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.A591T(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TTACTTCCAGCGACGGTGTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	10											25	25	25					10																	125521394		2203	4300	6503	125511384	SO:0001583	missense	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1771G>A	10.37:g.125521394C>T	ENSP00000241305:p.Ala591Thr		125511384	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432632	0.25813	.	.	ENSG00000121898	ENST00000368854;ENST00000241305;ENST00000540123;ENST00000418782	T	0.11277	2.79	5.36	5.36	0.76844	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.05914	0.0154	N	0.10760	0.04	0.52099	D	0.999948	P	0.39696	0.683	B	0.32805	0.153	T	0.49542	-0.8929	10	0.13853	T	0.58	-21.8858	19.2795	0.94046	0.0:1.0:0.0:0.0	.	591	Q8N436	CPXM2_HUMAN	T	87;591;424;566	ENSP00000241305:A591T	ENSP00000241305:A591T	A	-	1	0	CPXM2	125511384	1.000000	0.71417	0.306000	0.25113	0.082000	0.17680	5.913000	0.69957	2.790000	0.95986	0.609000	0.83330	GCT		0.657	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		T	125521394	C	T	125521394	3	4	61	1	0	0	0	0	1	0	0	0	3844	768	27	1	515	1	CPXM2	10	125521394	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15027	125521394	10013353	7062	15047										
CPXM2	119587	broad.mit.edu	37	chr10	125639805	125639806	+	Frame_Shift_Ins	INS	-	-	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctcttggttctcataacINSttttttgttgctgtgtttac							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:125639805_125639806insT	ENST00000241305.3	-	2	478_479	c.324_325insA	c.(322-327)aaagttfs	p.V109fs	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	109					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.V109fs*8(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GTTCTCATAACTTTTTTGTTGC	0.48																																																1	Insertion - Frameshift(1)	large_intestine(1)	10																																								125629796	SO:0001589	frameshift_variant	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.325dupA	10.37:g.125639811_125639811dupT	ENSP00000241305:p.Val109fs		125629795	B4E3Q2	Frame_Shift_Ins	INS	ENST00000241305.3	37	CCDS7637.1																																																																																				0.48	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		T	125639806	-	T	125639805	7	5	61	1	0	1	1	0	0	0	0	0	3844	565	20	0	1997	0	CPXM2	10	125639805	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	118411	125639805	9894942	7063	15048										
OAT	4942	broad.mit.edu	37	chr10	126089546	126089546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagcaaggttttcttctTctaaaacctacgtttaaaga	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:126089546T>C	ENST00000368845.5	-	9	1114	c.1022A>G	c.(1021-1023)gAa>gGa	p.E341G	OAT_ENST00000467675.1_5'Flank|OAT_ENST00000539214.1_Missense_Mutation_p.E203G	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	341					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)	p.E341G(1)		endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	GTTTTCTTCTTCTAAAACCTA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	10											61	57	58					10																	126089546		2203	4298	6501	126079536	SO:0001583	missense	4942			BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.1022A>G	10.37:g.126089546T>C	ENSP00000357838:p.Glu341Gly		126079536	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Missense_Mutation	SNP	ENST00000368845.5	37	CCDS7639.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.584172	0.46110	.	.	ENSG00000065154	ENST00000539214;ENST00000368845	D;D	0.87179	-2.22;-2.22	4.97	4.97	0.65823	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.044348	0.85682	D	0.000000	D	0.88243	0.6384	M	0.87547	2.89	0.58432	D	0.999996	P	0.36354	0.549	B	0.34301	0.179	D	0.88397	0.3012	10	0.38643	T	0.18	-26.2705	15.3597	0.74460	0.0:0.0:0.0:1.0	.	341	P04181	OAT_HUMAN	G	203;341	ENSP00000439042:E203G;ENSP00000357838:E341G	ENSP00000357838:E341G	E	-	2	0	OAT	126079536	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	7.515000	0.81761	2.167000	0.68274	0.533000	0.62120	GAA		0.348	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		C	126089546	T	C	126089546	3	2	61	1	0	0	0	0	1	0	0	0	10834	1783	62	4	305	4	OAT	10	126089546	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	449741	126089546	9445201	7064	15049										
FAM175B	23172	broad.mit.edu	37	chr10	126495409	126495409	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacttttaggaaggatttTtactgggagaggtaagacaa	11	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:126495409T>G	ENST00000298492.5	+	2	127	c.82T>G	c.(82-84)Tta>Gta	p.L28V		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	28	MPN-like.				cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)	p.L28V(1)		NS(1)	1						GGAAGGATTTTTACTGGGAGA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	10											82	79	80					10																	126495409		1800	4069	5869	126485399	SO:0001583	missense	23172			D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"Abraxas brother"	611144	"KIAA0157"	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.82T>G	10.37:g.126495409T>G	ENSP00000298492:p.Leu28Val		126485399	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	37	CCDS31308.2	.	.	.	.	.	.	.	.	.	.	T	14.41	2.526690	0.44969	.	.	ENSG00000165660	ENST00000298492	T	0.45668	0.89	5.41	1.81	0.25067	.	0.318404	0.26362	N	0.024809	T	0.59865	0.2225	M	0.78456	2.415	0.46356	D	0.999008	D	0.67145	0.996	D	0.80764	0.994	T	0.57952	-0.7722	10	0.87932	D	0	-1.0369	8.14	0.31078	0.0:0.3143:0.0:0.6857	.	28	Q15018	F175B_HUMAN	V	28	ENSP00000298492:L28V	ENSP00000298492:L28V	L	+	1	2	FAM175B	126485399	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	1.707000	0.37888	0.059000	0.16252	0.454000	0.30748	TTA		0.294	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		G	126495409	T	G	126495409	3	3	61	1	0	0	0	0	1	0	0	0	5514	1838	64	4	88	4	FAM175B	10	126495409	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	405863	126495409	9039338	7065	15050										
MMP21	118856	broad.mit.edu	37	chr10	127455418	127455418	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcataggagtaataagcgGaatctatatttctgaaagga	10	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127455418G>A	ENST00000368808.3	-	7	1522	c.1523C>T	c.(1522-1524)tCc>tTc	p.S508F		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	508					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S508F(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	GTAATAAGCGGAATCTATATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											109	111	110					10																	127455418		2203	4300	6503	127445408	SO:0001583	missense	118856			AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1523C>T	10.37:g.127455418G>A	ENSP00000357798:p.Ser508Phe		127445408	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141715	0.77775	.	.	ENSG00000154485	ENST00000368808	T	0.08896	3.04	5.95	5.95	0.96441	Hemopexin/matrixin (2);	0.301944	0.29307	N	0.012524	T	0.14830	0.0358	L	0.47716	1.5	0.42665	D	0.993491	P	0.51351	0.944	P	0.47206	0.541	T	0.00079	-1.2112	10	0.87932	D	0	-20.2644	17.8792	0.88835	0.0:0.0:1.0:0.0	.	508	Q8N119	MMP21_HUMAN	F	508	ENSP00000357798:S508F	ENSP00000357798:S508F	S	-	2	0	MMP21	127445408	0.970000	0.33590	0.008000	0.14137	0.046000	0.14306	6.466000	0.73543	2.825000	0.97269	0.655000	0.94253	TCC		0.353	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			A	127455418	G	A	127455418	3	1	61	1	0	0	0	0	1	0	0	0	9690	1174	41	3	190	3	MMP21	10	127455418	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	960009	127455418	8079329	7066	15051										
MMP21	118856	broad.mit.edu	37	chr10	127459049	127459049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgattttcataaagccagTaccagctgttacggaagaaa	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127459049T>C	ENST00000368808.3	-	5	1090	c.1091A>G	c.(1090-1092)tAc>tGc	p.Y364C		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	364					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y364C(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	ATAAAGCCAGTACCAGCTGTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											249	221	230					10																	127459049		2203	4300	6503	127449039	SO:0001583	missense	118856			AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1091A>G	10.37:g.127459049T>C	ENSP00000357798:p.Tyr364Cys		127449039	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.299596	0.81136	.	.	ENSG00000154485	ENST00000368808	T	0.06768	3.26	5.62	5.62	0.85841	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	L	0.61218	1.895	0.54753	D	0.999987	D	0.89917	1.0	D	0.85130	0.997	T	0.00531	-1.1686	10	0.87932	D	0	-16.5928	13.7643	0.62986	0.0:0.0:0.0:1.0	.	364	Q8N119	MMP21_HUMAN	C	364	ENSP00000357798:Y364C	ENSP00000357798:Y364C	Y	-	2	0	MMP21	127449039	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.837000	0.62796	2.143000	0.66587	0.533000	0.62120	TAC		0.443	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			C	127459049	T	C	127459049	3	2	61	1	0	0	0	0	1	0	0	0	9690	1638	57	4	630	4	MMP21	10	127459049	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3631	127459049	8075698	7067	15052										
DHX32	55760	broad.mit.edu	37	chr10	127529550	127529550	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctccatgtggcacatgtGaaaagcaatttggagcttca	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127529550G>A	ENST00000284690.3	-	8	2049	c.1559C>T	c.(1558-1560)tCa>tTa	p.S520L	BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000368721.1_Missense_Mutation_p.S144L|BCCIP_ENST00000429863.2_Intron|BCCIP_ENST00000299130.3_Intron|AL360176.1_ENST00000401153.1_RNA|DHX32_ENST00000284688.6_Missense_Mutation_p.S439L	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	520						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.S520L(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TGGCACATGTGAAAAGCAATT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	10											85	73	77					10																	127529550		2203	4300	6503	127519540	SO:0001583	missense	55760				CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1559C>T	10.37:g.127529550G>A	ENSP00000284690:p.Ser520Leu		127519540	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation	SNP	ENST00000284690.3	37	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.656380	0.00779	.	.	ENSG00000089876	ENST00000368721;ENST00000284690;ENST00000284688	T;T;T	0.02709	4.19;4.19;4.19	4.43	0.0928	0.14474	Helicase-associated domain (2);	0.896269	0.09603	N	0.779978	T	0.01222	0.0040	N	0.00972	-1.085	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46652	-0.9176	10	0.87932	D	0	-0.257	6.8598	0.24060	0.6305:0.0:0.3695:0.0	.	520	Q7L7V1	DHX32_HUMAN	L	144;520;439	ENSP00000357710:S144L;ENSP00000284690:S520L;ENSP00000284688:S439L	ENSP00000284688:S439L	S	-	2	0	DHX32	127519540	0.000000	0.05858	0.003000	0.11579	0.218000	0.24690	0.424000	0.21330	0.135000	0.18707	0.655000	0.94253	TCA		0.433	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		A	127529550	G	A	127529550	3	1	61	1	0	0	0	0	1	0	0	0	4516	1294	45	3	688	3	DHX32	10	127529550	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70501	127529550	8005197	7068	15053										
DHX32	55760	broad.mit.edu	37	chr10	127540946	127540946	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcttgttaggttggcttCctgcatttctgctggcttca	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127540946C>A	ENST00000284690.3	-	6	1757	c.1267G>T	c.(1267-1269)Gaa>Taa	p.E423*	BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000368721.1_Nonsense_Mutation_p.E47*|DHX32_ENST00000284688.6_Nonsense_Mutation_p.E342*	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	423						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.E423*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AGGTTGGCTTCCTGCATTTCT	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											193	175	181					10																	127540946		2203	4300	6503	127530936	SO:0001587	stop_gained	55760				CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1267G>T	10.37:g.127540946C>A	ENSP00000284690:p.Glu423*		127530936	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Nonsense_Mutation	SNP	ENST00000284690.3	37	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	C	43	9.994470	0.99313	.	.	ENSG00000089876	ENST00000368721;ENST00000284690;ENST00000284688	.	.	.	5.72	5.72	0.89469	.	0.052972	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.2267	18.885	0.92372	0.0:1.0:0.0:0.0	.	.	.	.	X	47;423;342	.	ENSP00000284688:E342X	E	-	1	0	DHX32	127530936	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.740000	0.68629	2.691000	0.91804	0.655000	0.94253	GAA		0.458	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		A	127540946	C	A	127540946	4	1	61	1	0	0	0	0	0	1	0	0	4516	864	30	2	988	2	DHX32	10	127540946	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11396	127540946	7993801	7069	15054										
DHX32	55760	broad.mit.edu	37	chr10	127555591	127555591	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgttggtacagcagttctcGaaagggatcacgtagccaac	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127555591G>A	ENST00000284690.3	-	2	934	c.444C>T	c.(442-444)ttC>ttT	p.F148F	DHX32_ENST00000284688.6_Silent_p.F148F	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	148	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.F148F(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AGCAGTTCTCGAAAGGGATCA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	10											182	146	158					10																	127555591		2203	4300	6503	127545581	SO:0001819	synonymous_variant	55760				CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.444C>T	10.37:g.127555591G>A			127545581	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	37	CCDS7652.1																																																																																				0.517	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		A	127555591	G	A	127555591	2	1	61	1	0	0	0	0	0	0	0	1	4516	1049	37	1		1	DHX32	10	127555591	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14645	127555591	7979156	7070	15055										
FANK1	92565	broad.mit.edu	37	chr10	127677132	127677132	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtctaggggatatgcaacGaagcatgttgttgaaggtct	13	6	2	1	rs146192515		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127677132G>A	ENST00000368693.1	+	3	308	c.204G>A	c.(202-204)acG>acA	p.T68T	FANK1_ENST00000368689.1_Silent_p.T62T|FANK1_ENST00000449042.2_Silent_p.T62T|FANK1_ENST00000368695.1_Silent_p.T62T			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	68	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T68T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GATATGCAACGAAGCATGTTG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	10						G		0,4406		0,0,2203	254	232	239		204	-10.1	0	10	dbSNP_134	239	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FANK1	NM_145235.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		68/346	127677132	1,13005	2203	4300	6503	127667122	SO:0001819	synonymous_variant	92565			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.204G>A	10.37:g.127677132G>A			127667122	Q6UXY9|Q6X7T6	Silent	SNP	ENST00000368693.1	37	CCDS31309.1																																																																																				0.512	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		A	127677132	G	A	127677132	2	1	61	1	0	0	0	0	0	0	0	1	5691	1045	37	1		1	FANK1	10	127677132	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121541	127677132	7857615	7071	15056										
ADAM12	8038	broad.mit.edu	37	chr10	127760098	127760098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccacaaatctgttcccaCacttctggcccccgaaagac	5	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:127760098C>T	ENST00000368679.4	-	12	1589	c.1280G>A	c.(1279-1281)tGt>tAt	p.C427Y	ADAM12_ENST00000467145.1_5'Flank|ADAM12_ENST00000368676.4_Missense_Mutation_p.C427Y	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	427	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.C427Y(3)		biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TCTGTTCCCACACTTCTGGCC	0.532																																																3	Substitution - Missense(3)	large_intestine(3)	10											99	98	99					10																	127760098		2203	4300	6503	127750088	SO:0001583	missense	8038			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1280G>A	10.37:g.127760098C>T	ENSP00000357668:p.Cys427Tyr		127750088	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482384	0.84747	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	T;T	0.43688	3.55;0.94	4.99	4.99	0.66335	Blood coagulation inhibitor, Disintegrin (1);	0.000000	0.85682	D	0.000000	T	0.79885	0.4523	H	0.98738	4.315	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.999;0.999;0.999	D	0.88492	0.3076	10	0.87932	D	0	.	18.4657	0.90753	0.0:1.0:0.0:0.0	.	424;424;427;424;427	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	Y	427	ENSP00000357668:C427Y;ENSP00000357665:C427Y	ENSP00000357665:C427Y	C	-	2	0	ADAM12	127750088	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.521000	0.81832	2.595000	0.87683	0.563000	0.77884	TGT		0.532	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			T	127760098	C	T	127760098	3	4	61	1	0	0	0	0	1	0	0	0	236	478	17	3	1605	3	ADAM12	10	127760098	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82966	127760098	7774649	7072	15057										
C10orf90	118611	broad.mit.edu	37	chr10	128114574	128114574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattacctttttgaagacttCggcacggagtctgttacttt	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128114574C>T	ENST00000284694.7	-	8	2167	c.2047G>A	c.(2047-2049)Gaa>Aaa	p.E683K	C10orf90_ENST00000356858.3_Missense_Mutation_p.E636K|C10orf90_ENST00000480379.1_Missense_Mutation_p.E87K|C10orf90_ENST00000454341.1_Missense_Mutation_p.E586K|C10orf90_ENST00000544758.1_Missense_Mutation_p.E780K	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	683	ALMS motif. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.E683K(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TTGAAGACTTCGGCACGGAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											214	196	202					10																	128114574		2203	4300	6503	128104564	SO:0001583	missense	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.2047G>A	10.37:g.128114574C>T	ENSP00000284694:p.Glu683Lys		128104564	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960696	0.74016	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758	T;T;T	0.19105	2.17;2.23;2.18	5.58	2.71	0.32032	.	0.000000	0.45126	D	0.000382	T	0.25044	0.0608	M	0.61703	1.905	0.58432	D	0.999999	D;D;D	0.65815	0.985;0.995;0.985	B;P;B	0.47603	0.412;0.551;0.412	T	0.02275	-1.1184	10	0.45353	T	0.12	-27.6394	8.489	0.33089	0.0:0.7603:0.0:0.2397	.	780;683;586	F5GZL2;Q96M02;Q96M02-2	.;CJ090_HUMAN;.	K	636;683;586;780	ENSP00000284694:E683K;ENSP00000398786:E586K;ENSP00000444369:E780K	ENSP00000284694:E683K	E	-	1	0	C10orf90	128104564	0.867000	0.29959	0.514000	0.27761	0.995000	0.86356	1.485000	0.35519	0.825000	0.34637	0.655000	0.94253	GAA		0.423	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128114574	C	T	128114574	3	4	61	1	0	0	0	0	1	0	0	0	1627	893	31	1	60	1	C10orf90	10	128114574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	354476	128114574	7420173	7073	15058										
C10orf90	118611	broad.mit.edu	37	chr10	128153272	128153272	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgctccttacctttgggGaacttgctttctatctgaac	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128153272G>A	ENST00000284694.7	-	4	1647	c.1527C>T	c.(1525-1527)ttC>ttT	p.F509F	C10orf90_ENST00000356858.3_Silent_p.F462F|C10orf90_ENST00000480379.1_5'Flank|C10orf90_ENST00000454341.1_Intron|C10orf90_ENST00000544758.1_Silent_p.F606F	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	509					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.F509F(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TACCTTTGGGGAACTTGCTTT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	10											177	191	186					10																	128153272		2203	4300	6503	128143262	SO:0001819	synonymous_variant	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1527C>T	10.37:g.128153272G>A			128143262	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																				0.458	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128153272	G	A	128153272	2	1	61	1	0	0	0	0	0	0	0	1	1627	1165	41	3		3	C10orf90	10	128153272	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38698	128153272	7381475	7074	15059										
C10orf90	118611	broad.mit.edu	37	chr10	128153524	128153524	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacttctccttgttgcctCttgctgcttccagaaaatac	5	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128153524C>A	ENST00000284694.7	-	4	1395	c.1275G>T	c.(1273-1275)aaG>aaT	p.K425N	C10orf90_ENST00000356858.3_Missense_Mutation_p.K378N|C10orf90_ENST00000480379.1_5'Flank|C10orf90_ENST00000454341.1_Intron|C10orf90_ENST00000544758.1_Missense_Mutation_p.K522N	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	425					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.K425N(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CTTGTTGCCTCTTGCTGCTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	10											107	102	104					10																	128153524		2203	4300	6503	128143514	SO:0001583	missense	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1275G>T	10.37:g.128153524C>A	ENSP00000284694:p.Lys425Asn		128143514	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.820263	0.50633	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000544758;ENST00000432642	T;T;T	0.21361	2.02;2.03;2.01	4.34	4.34	0.51931	.	0.593585	0.15124	N	0.279196	T	0.32704	0.0838	L	0.52573	1.65	0.80722	D	1	P;P	0.51351	0.944;0.728	P;B	0.52957	0.714;0.343	T	0.07158	-1.0787	10	0.87932	D	0	-8.5751	13.7114	0.62670	0.0:1.0:0.0:0.0	.	522;425	F5GZL2;Q96M02	.;CJ090_HUMAN	N	378;425;522;425	ENSP00000284694:K425N;ENSP00000444369:K522N;ENSP00000405995:K425N	ENSP00000284694:K425N	K	-	3	2	C10orf90	128143514	0.392000	0.25229	0.101000	0.21167	0.013000	0.08279	4.126000	0.57937	2.251000	0.74343	0.637000	0.83480	AAG		0.428	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128153524	C	A	128153524	3	1	61	1	0	0	0	0	1	0	0	0	1627	912	32	2	848	2	C10orf90	10	128153524	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252	128153524	7381223	7075	15060										
C10orf90	118611	broad.mit.edu	37	chr10	128193589	128193589	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttttctcttgacttattCtcatcaatcatctgggagat	6	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128193589C>A	ENST00000284694.7	-	3	300	c.180G>T	c.(178-180)gaG>gaT	p.E60D	C10orf90_ENST00000356858.3_Missense_Mutation_p.E13D|C10orf90_ENST00000392694.1_Missense_Mutation_p.E13D|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000454341.1_Missense_Mutation_p.E60D|C10orf90_ENST00000544758.1_Missense_Mutation_p.E157D	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	60					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.E60D(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TTGACTTATTCTCATCAATCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											124	113	117					10																	128193589		2203	4300	6503	128183579	SO:0001583	missense	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.180G>T	10.37:g.128193589C>A	ENSP00000284694:p.Glu60Asp		128183579	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.885268	0.33255	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.36340	1.57;1.53;1.64;1.57;1.26	4.76	0.998	0.19857	.	0.000000	0.56097	D	0.000032	T	0.48822	0.1521	M	0.65498	2.005	0.19575	N	0.999968	D;D;D;D;P	0.76494	0.999;0.999;0.999;0.999;0.946	D;D;D;D;P	0.72075	0.972;0.972;0.937;0.976;0.586	T	0.25363	-1.0134	10	0.46703	T	0.11	-24.0068	5.3078	0.15813	0.0:0.4572:0.1399:0.4029	.	157;157;13;60;60	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	D	13;60;60;157;60;13;13	ENSP00000284694:E60D;ENSP00000398786:E60D;ENSP00000444369:E157D;ENSP00000405995:E60D;ENSP00000376459:E13D	ENSP00000284694:E60D	E	-	3	2	C10orf90	128183579	0.029000	0.19370	0.402000	0.26371	0.058000	0.15608	-0.053000	0.11846	0.310000	0.22990	0.561000	0.74099	GAG		0.473	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128193589	C	A	128193589	3	1	61	1	0	0	0	0	1	0	0	0	1627	912	32	2	1947	2	C10orf90	10	128193589	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40065	128193589	7341158	7076	15061										
DOCK1	1793	broad.mit.edu	37	chr10	128836003	128836003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaccttctggggctcttgAaatggcgctccaacaccagc	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128836003A>G	ENST00000280333.6	+	19	1979	c.1870A>G	c.(1870-1872)Aaa>Gaa	p.K624E		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	624					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.K624E(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GGGGCTCTTGAAATGGCGCTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											52	49	50					10																	128836003		1875	4109	5984	128725993	SO:0001583	missense	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1870A>G	10.37:g.128836003A>G	ENSP00000280333:p.Lys624Glu		128725993	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	A	18.79	3.699147	0.68501	.	.	ENSG00000150760	ENST00000280333	T	0.20200	2.09	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.33818	0.0876	M	0.83312	2.635	0.58432	D	0.999997	B;B	0.33883	0.266;0.43	B;B	0.38194	0.267;0.207	T	0.32508	-0.9904	10	0.66056	D	0.02	.	14.4146	0.67139	1.0:0.0:0.0:0.0	.	624;624	B2RUU3;Q14185	.;DOCK1_HUMAN	E	624	ENSP00000280333:K624E	ENSP00000280333:K624E	K	+	1	0	DOCK1	128725993	1.000000	0.71417	0.979000	0.43373	0.908000	0.53690	8.841000	0.92131	1.990000	0.58119	0.379000	0.24179	AAA		0.473	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		G	128836003	A	G	128836003	3	3	61	1	0	0	0	0	1	0	0	0	4695	247	9	4	1944	4	DOCK1	10	128836003	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	642414	128836003	6698744	7077	15062										
DOCK1	1793	broad.mit.edu	37	chr10	128908585	128908585	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaactctactgcttgatcGaaatcgtccacagtgacctc	7	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128908585G>A	ENST00000280333.6	+	25	2636	c.2527G>A	c.(2527-2529)Gaa>Aaa	p.E843K		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	843					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.E843K(2)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CTGCTTGATCGAAATCGTCCA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	10											86	81	82					10																	128908585		1924	4148	6072	128798575	SO:0001583	missense	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2527G>A	10.37:g.128908585G>A	ENSP00000280333:p.Glu843Lys		128798575	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	11.48	1.650665	0.29336	.	.	ENSG00000150760	ENST00000280333	T	0.29655	1.56	4.87	4.87	0.63330	.	0.062753	0.64402	D	0.000008	T	0.12008	0.0292	N	0.01168	-0.975	0.58432	D	0.999991	B;B	0.18461	0.006;0.028	B;B	0.14023	0.01;0.01	T	0.18147	-1.0346	10	0.16420	T	0.52	.	15.9463	0.79796	0.0:0.0:1.0:0.0	.	843;843	B2RUU3;Q14185	.;DOCK1_HUMAN	K	843	ENSP00000280333:E843K	ENSP00000280333:E843K	E	+	1	0	DOCK1	128798575	1.000000	0.71417	0.954000	0.39281	0.512000	0.34134	8.448000	0.90335	2.533000	0.85409	0.655000	0.94253	GAA		0.418	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	128908585	G	A	128908585	3	1	61	1	0	0	0	0	1	0	0	0	4695	1059	37	1	2625	1	DOCK1	10	128908585	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72582	128908585	6626162	7078	15063										
FAM196A	642938	broad.mit.edu	37	chr10	128973613	128973613	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacttccgtatgaggcacGattcgttggcattcttcacc	8	13	2	1	rs184333971	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:128973613G>A	ENST00000522781.1	-	4	1602	c.1047C>T	c.(1045-1047)atC>atT	p.I349I	FAM196A_ENST00000424811.2_Silent_p.I349I|DOCK1_ENST00000280333.6_Intron	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	349								p.I349I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TATGAGGCACGATTCGTTGGC	0.552													G|||	3	0.000599042	8e-04	0	5008	,	,		18634	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											146	152	150					10																	128973613		2203	4300	6503	128863603	SO:0001819	synonymous_variant	642938				CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 141"	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.1047C>T	10.37:g.128973613G>A			128863603	B2RNT4|B7ZME7	Silent	SNP	ENST00000522781.1	37	CCDS31312.1																																																																																				0.552	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762		A	128973613	G	A	128973613	2	1	61	1	0	0	0	0	0	0	0	1	5544	1048	37	1		1	FAM196A	10	128973613	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65028	128973613	6561134	7079	15064										
FOXI2	399823	broad.mit.edu	37	chr10	129537084	129537084	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcctggcgggcgacttttCtttcgggaggcggccaccga	17	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129537084C>A	ENST00000388920.4	+	2	851	c.812C>A	c.(811-813)tCt>tAt	p.S271Y		NM_207426.2	NP_997309.2	Q6ZQN5	FOXI2_HUMAN	forkhead box I2	271					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S87Y(1)		large_intestine(1)|lung(3)	4		all_epithelial(44;0.0021)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)				GGCGACTTTTCTTTCGGGAGG	0.711																																					Esophageal Squamous(54;1038 1280 2528 31583)											1	Substitution - Missense(1)	large_intestine(1)	10											7	10	9					10																	129537084		2160	4272	6432	129427074	SO:0001583	missense	399823			AK128865	CCDS7655.2	10q26.2	2008-04-10			ENSG00000186766	ENSG00000186766		"Forkhead boxes"	32448	protein-coding gene	gene with protein product							Standard	NM_207426		Approved	FLJ46831	uc009yas.2	Q6ZQN5	OTTHUMG00000019250	ENST00000388920.4:c.812C>A	10.37:g.129537084C>A	ENSP00000373572:p.Ser271Tyr		129427074		Missense_Mutation	SNP	ENST00000388920.4	37	CCDS7655.2	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959565	0.53400	.	.	ENSG00000186766	ENST00000388920	D	0.93604	-3.25	4.15	4.15	0.48705	.	0.683607	0.14216	N	0.333743	D	0.90403	0.6996	L	0.36672	1.1	0.32328	N	0.561533	P	0.52842	0.956	P	0.48030	0.564	D	0.90525	0.4491	10	0.72032	D	0.01	.	7.73	0.28781	0.0:0.8874:0.0:0.1126	.	271	Q6ZQN5	FOXI2_HUMAN	Y	271	ENSP00000373572:S271Y	ENSP00000373572:S271Y	S	+	2	0	FOXI2	129427074	0.000000	0.05858	0.196000	0.23383	0.771000	0.43674	0.677000	0.25262	2.138000	0.66242	0.561000	0.74099	TCT		0.711	FOXI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050984.2	NM_207426		A	129537084	C	A	129537084	3	1	61	1	0	0	0	0	1	0	0	0	6029	913	32	2	818	2	FOXI2	10	129537084	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	563471	129537084	5997663	7080	15065										
PTPRE	5791	broad.mit.edu	37	chr10	129869087	129869087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagaaattgacaaatgtcCggatcatgaaggagaacatg	11	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129869087C>T	ENST00000254667.3	+	15	1588	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	PTPRE_ENST00000419012.2_Missense_Mutation_p.R437W|PTPRE_ENST00000306042.5_Missense_Mutation_p.R379W	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	437	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R437W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GACAAATGTCCGGATCATGAA	0.522																																					Colon(52;977 1184 20575 41685)											1	Substitution - Missense(1)	large_intestine(1)	10											79	68	72					10																	129869087		2203	4300	6503	129759077	SO:0001583	missense	5791			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1309C>T	10.37:g.129869087C>T	ENSP00000254667:p.Arg437Trp		129759077	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Missense_Mutation	SNP	ENST00000254667.3	37	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295720	0.81025	.	.	ENSG00000132334	ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042	T;T;T	0.11712	2.75;2.75;2.75	4.51	4.51	0.55191	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.64402	D	0.000001	T	0.32164	0.0820	M	0.66378	2.025	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.74674	0.984;0.952;0.963;0.952	T	0.07947	-1.0746	10	0.87932	D	0	.	17.4459	0.87577	0.0:1.0:0.0:0.0	.	415;437;379;437	F5H0X4;Q5VWH4;P23469-2;P23469	.;.;.;PTPRE_HUMAN	W	437;415;437;379	ENSP00000254667:R437W;ENSP00000402337:R437W;ENSP00000303350:R379W	ENSP00000254667:R437W	R	+	1	2	PTPRE	129759077	0.981000	0.34729	0.996000	0.52242	0.959000	0.62525	2.371000	0.44248	2.337000	0.79520	0.650000	0.86243	CGG		0.522	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			T	129869087	C	T	129869087	3	4	61	1	0	0	0	0	1	0	0	0	12837	643	23	1	1398	1	PTPRE	10	129869087	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	332003	129869087	5665660	7081	15066										
PTPRE	5791	broad.mit.edu	37	chr10	129881110	129881110	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaggaacagtatgaattCtgctacaaagtggtacaaga	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129881110C>T	ENST00000254667.3	+	21	2322	c.2043C>T	c.(2041-2043)ttC>ttT	p.F681F	PTPRE_ENST00000419012.2_Silent_p.F681F|PTPRE_ENST00000306042.5_Silent_p.F623F	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	681	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.F681F(1)|p.F681L(1)|p.F623L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	AGTATGAATTCTGCTACAAAG	0.264																																					Colon(52;977 1184 20575 41685)											3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(3)	10											74	77	76					10																	129881110		2197	4284	6481	129771100	SO:0001819	synonymous_variant	5791			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.2043C>T	10.37:g.129881110C>T			129771100	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	C	8.188	0.795300	0.16327	.	.	ENSG00000132334	ENST00000439034	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	T	0.54398	0.1856	.	.	.	0.80722	D	1	B	0.24768	0.111	B	0.26202	0.067	T	0.45818	-0.9235	6	.	.	.	.	19.6787	0.95950	0.0:1.0:0.0:0.0	.	614	F5H0X4	.	F	614	.	.	S	+	2	0	PTPRE	129771100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.905000	0.56333	2.884000	0.98904	0.655000	0.94253	TCT		0.264	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			T	129881110	C	T	129881110	2	4	61	1	0	0	0	0	0	0	0	1	12837	912	32	3		3	PTPRE	10	129881110	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12023	129881110	5653637	7082	15067										
MKI67	4288	broad.mit.edu	37	chr10	129903086	129903086	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtggagatttgcaggctaTtttggtagttttctcatcag	11	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129903086T>A	ENST00000368654.3	-	13	7393	c.7018A>T	c.(7018-7020)Ata>Tta	p.I2340L	MKI67_ENST00000368653.3_Missense_Mutation_p.I1980L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2340	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I2340L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTGCAGGCTATTTTGGTAGTT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	10											306	321	316					10																	129903086		2203	4300	6503	129793076	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.7018A>T	10.37:g.129903086T>A	ENSP00000357643:p.Ile2340Leu		129793076	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	6.749	0.506939	0.12883	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02974	4.09;4.09	2.91	-0.725	0.11174	.	1.101030	0.07104	N	0.840966	T	0.04092	0.0114	L	0.55481	1.735	0.09310	N	1	B;B;B	0.19445	0.002;0.036;0.023	B;B;B	0.26202	0.002;0.067;0.012	T	0.47315	-0.9127	10	0.28530	T	0.3	.	7.6075	0.28110	0.0:0.5945:0.0:0.4055	.	2339;1980;2340	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	2340;1980;2339	ENSP00000357643:I2340L;ENSP00000357642:I1980L	ENSP00000357642:I1980L	I	-	1	0	MKI67	129793076	.	.	0.000000	0.03702	0.003000	0.03518	.	.	-0.155000	0.11098	0.379000	0.24179	ATA		0.512	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129903086	T	A	129903086	3	1	61	1	0	0	0	0	1	0	0	0	9628	1493	52	5	2764	5	MKI67	10	129903086	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	21976	129903086	5631661	7083	15068										
MKI67	4288	broad.mit.edu	37	chr10	129903377	129903377	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctacgtctgctttcctgaGacttctcttggactgtggct	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129903377G>T	ENST00000368654.3	-	13	7102	c.6727C>A	c.(6727-6729)Ctc>Atc	p.L2243I	MKI67_ENST00000368653.3_Missense_Mutation_p.L1883I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2243	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.L2243I(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GCTTTCCTGAGACTTCTCTTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	10											274	261	265					10																	129903377		2203	4300	6503	129793367	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6727C>A	10.37:g.129903377G>T	ENSP00000357643:p.Leu2243Ile		129793367	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.425304	0.25639	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02916	4.11;4.11	2.51	-0.913	0.10500	.	1.273700	0.05791	N	0.610397	T	0.07324	0.0185	L	0.50333	1.59	0.09310	N	1	P;P;D	0.63880	0.784;0.936;0.993	B;P;P	0.57620	0.235;0.692;0.824	T	0.38394	-0.9663	10	0.37606	T	0.19	.	6.5486	0.22420	0.0:0.4788:0.2701:0.2511	.	2242;1883;2243	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	I	2243;1883;2242	ENSP00000357643:L2243I;ENSP00000357642:L1883I	ENSP00000357642:L1883I	L	-	1	0	MKI67	129793367	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.107000	0.03316	-0.186000	0.10533	0.561000	0.74099	CTC		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129903377	G	T	129903377	3	4	61	1	0	0	0	0	1	0	0	0	9628	942	33	2	3055	2	MKI67	10	129903377	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	291	129903377	5631370	7084	15069										
MKI67	4288	broad.mit.edu	37	chr10	129903471	129903471	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggtagttttctcatgagtCgtgggcttgtcagtgcatat	12	6	2	1	rs377502553		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129903471C>T	ENST00000368654.3	-	13	7008	c.6633G>A	c.(6631-6633)acG>acA	p.T2211T	MKI67_ENST00000368653.3_Silent_p.T1851T	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2211	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.T2211T(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TCTCATGAGTCGTGGGCTTGT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	10						C	,	0,4406		0,0,2203	236	228	230		5553,6633	-0.4	0	10		230	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	1851/2897,2211/3257	129903471	1,13005	2203	4300	6503	129793461	SO:0001819	synonymous_variant	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6633G>A	10.37:g.129903471C>T			129793461	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																				0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129903471	C	T	129903471	2	4	61	1	0	0	0	0	0	0	0	1	9628	871	31	1		1	MKI67	10	129903471	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94	129903471	5631276	7085	15070										
MKI67	4288	broad.mit.edu	37	chr10	129905977	129905977	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctgctgattctggtggaGaagattcgcagggcatttta	13	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129905977G>T	ENST00000368654.3	-	13	4502	c.4127C>A	c.(4126-4128)tCt>tAt	p.S1376Y	MKI67_ENST00000368653.3_Missense_Mutation_p.S1016Y	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1376	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.S1376Y(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCTGGTGGAGAAGATTCGCA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	10											158	149	152					10																	129905977		2203	4300	6503	129795967	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4127C>A	10.37:g.129905977G>T	ENSP00000357643:p.Ser1376Tyr		129795967	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590505	0.46214	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02579	4.24;4.24	4.02	2.06	0.26882	.	.	.	.	.	T	0.05868	0.0153	L	0.34521	1.04	0.09310	N	1	D;D;D	0.67145	0.986;0.986;0.996	P;P;P	0.60609	0.808;0.808;0.877	T	0.40776	-0.9545	9	0.42905	T	0.14	.	6.9906	0.24753	0.2221:0.0:0.7779:0.0	.	1375;1016;1376	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	Y	1376;1016;1375	ENSP00000357643:S1376Y;ENSP00000357642:S1016Y	ENSP00000357642:S1016Y	S	-	2	0	MKI67	129795967	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.133000	0.15912	0.433000	0.26313	0.561000	0.74099	TCT		0.512	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129905977	G	T	129905977	3	4	61	1	0	0	0	0	1	0	0	0	9628	942	33	2	5655	2	MKI67	10	129905977	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2506	129905977	5628770	7086	15071										
MKI67	4288	broad.mit.edu	37	chr10	129906624	129906624	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttagtttcctgagtgctaaGaattcttcctctacatctgc	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:129906624G>T	ENST00000368654.3	-	13	3855	c.3480C>A	c.(3478-3480)ttC>ttA	p.F1160L	MKI67_ENST00000368653.3_Missense_Mutation_p.F800L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1160	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.F1160L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGAGTGCTAAGAATTCTTCCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	10											332	317	322					10																	129906624		2203	4300	6503	129796614	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3480C>A	10.37:g.129906624G>T	ENSP00000357643:p.Phe1160Leu		129796614	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.547379	0.00926	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01804	4.63;4.63	2.87	-0.269	0.12930	.	2.776490	0.01645	N	0.024249	T	0.01092	0.0036	N	0.04355	-0.22	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.44544	-0.9321	10	0.09590	T	0.72	.	5.9388	0.19181	0.226:0.5262:0.2477:0.0	.	1159;800;1160	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	1160;800;1159	ENSP00000357643:F1160L;ENSP00000357642:F800L	ENSP00000357642:F800L	F	-	3	2	MKI67	129796614	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.348000	0.07740	-0.045000	0.13468	-0.304000	0.09214	TTC		0.463	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129906624	G	T	129906624	3	4	61	1	0	0	0	0	1	0	0	0	9628	933	33	2	6302	2	MKI67	10	129906624	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	647	129906624	5628123	7087	15072										
MGMT	4255	broad.mit.edu	37	chr10	131557519	131557519	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggttgtgaaattcggaGaagtgatttcttaccagcaa	11	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:131557519G>T	ENST00000306010.7	+	4	453	c.421G>T	c.(421-423)Gaa>Taa	p.E141*		NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	110					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)	p.E110*(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		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)	L-Cysteine(DB00151)	GAAATTCGGAGAAGTGATTTC	0.498								Direct reversal of damage																																								1	Substitution - Nonsense(1)	large_intestine(1)	10											108	112	111					10																	131557519		2203	4300	6503	131447509	SO:0001587	stop_gained	4255			M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.421G>T	10.37:g.131557519G>T	ENSP00000302111:p.Glu141*		131447509	Q5VY78	Nonsense_Mutation	SNP	ENST00000306010.7	37	CCDS7660.2	.	.	.	.	.	.	.	.	.	.	G	34	5.322163	0.95708	.	.	ENSG00000170430	ENST00000306010	.	.	.	5.53	4.61	0.57282	.	0.112392	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	16.2896	0.82739	0.0:0.1329:0.8671:0.0	.	.	.	.	X	141	.	ENSP00000302111:E141X	E	+	1	0	MGMT	131447509	1.000000	0.71417	0.978000	0.43139	0.977000	0.68977	5.799000	0.69101	1.449000	0.47699	0.650000	0.86243	GAA		0.498	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412		T	131557519	G	T	131557519	4	4	61	1	0	0	0	0	0	1	0	0	9587	943	33	2	435	2	MGMT	10	131557519	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1650895	131557519	3977228	7088	15073										
JAKMIP3	282973	broad.mit.edu	37	chr10	133930957	133930957	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaggcaggtggaggaggCgctgacgctggtgatccaag	17	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:133930957C>T	ENST00000298622.4	+	2	650	c.512C>T	c.(511-513)gCg>gTg	p.A171V		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	171						Golgi apparatus (GO:0005794)		p.A171V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GTGGAGGAGGCGCTGACGCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10																																								133780947	SO:0001583	missense	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.512C>T	10.37:g.133930957C>T	ENSP00000298622:p.Ala171Val		133780947	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685906	0.88639	.	.	ENSG00000188385	ENST00000298622	T	0.07567	3.18	4.66	4.66	0.58398	.	0.057116	0.64402	D	0.000001	T	0.28001	0.0690	M	0.67397	2.05	0.37993	D	0.933973	D	0.89917	1.0	D	0.85130	0.997	T	0.04360	-1.0957	10	0.42905	T	0.14	-29.4412	17.7631	0.88470	0.0:1.0:0.0:0.0	.	171	Q5VZ66	JKIP3_HUMAN	V	171	ENSP00000298622:A171V	ENSP00000298622:A171V	A	+	2	0	JAKMIP3	133780947	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.215000	0.77966	2.419000	0.82065	0.591000	0.81541	GCG		0.607	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		T	133930957	C	T	133930957	3	4	61	1	0	0	0	0	1	0	0	0	7963	768	27	1	518	1	JAKMIP3	10	133930957	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2373438	133930957	1603790	7089	15074										
DPYSL4	10570	broad.mit.edu	37	chr10	134006168	134006168	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctgctttcagacaaatCggagaaaacctcatcgtccc	7	13	3	2	rs148548080		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:134006168C>T	ENST00000338492.4	+	3	299	c.135C>T	c.(133-135)atC>atT	p.I45I	DPYSL4_ENST00000368629.1_5'UTR|DPYSL4_ENST00000493882.1_3'UTR|DPYSL4_ENST00000368627.1_5'Flank	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	45					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.I45I(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		TCAGACAAATCGGAGAAAACC	0.562													C|||	1	0.000199681	0	0.0014	5008	,	,		18277	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											84	79	80					10																	134006168		2203	4300	6503	133856158	SO:0001819	synonymous_variant	10570			AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.135C>T	10.37:g.134006168C>T			133856158	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																				0.562	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			T	134006168	C	T	134006168	2	4	61	1	0	0	0	0	0	0	0	1	4760	874	31	1		1	DPYSL4	10	134006168	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75211	134006168	1528579	7090	15075										
C10orf93	54777	broad.mit.edu	37	chr10	134748292	134748292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggaaagcgctggtggttgTaatgacctaagtgtctgtag	15	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:134748292T>C	ENST00000368586.5	-	8	930	c.830A>G	c.(829-831)tAc>tGc	p.Y277C	TTC40_ENST00000368582.2_Missense_Mutation_p.Y277C|TTC40_ENST00000368585.3_Missense_Mutation_p.Y277C	NM_001200049.2	NP_001186978.2												p.Y277C(1)|p.Y219C(1)		breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGGTGGTTGTAATGACCTAA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	10											105	101	103					10																	134748292		2203	4300	6503	134598282	SO:0001583	missense	255352																														ENST00000368586.5:c.830A>G	10.37:g.134748292T>C	ENSP00000357575:p.Tyr277Cys		134598282		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346273	0.41599	.	.	ENSG00000171811	ENST00000368586;ENST00000368582;ENST00000368585	T;T;T	0.54866	0.55;0.55;0.55	4.08	-0.00985	0.13999	.	0.718318	0.12508	N	0.462742	T	0.56514	0.1990	L	0.58101	1.795	0.09310	N	1	D	0.67145	0.996	P	0.59288	0.855	T	0.45731	-0.9241	10	0.54805	T	0.06	.	3.4084	0.07350	0.349:0.1044:0.0:0.5466	.	277	Q5SR76-1	.	C	277	ENSP00000357575:Y277C;ENSP00000357571:Y277C;ENSP00000357574:Y277C	ENSP00000357571:Y277C	Y	-	2	0	C10orf93	134598282	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.488000	0.06497	-0.105000	0.12132	0.496000	0.49642	TAC		0.378	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3			C	134748292	T	C	134748292	3	2	61	1	0	0	0	0	1	0	0	0	1629	1638	57	4	395	4	C10orf93	10	134748292	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	742124	134748292	786455	7091	15076										
KNDC1	85442	broad.mit.edu	37	chr10	135020445	135020445	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattcctcagcttggtcaaGaagtatctgcaggcaagtgg	11	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:135020445G>T	ENST00000304613.3	+	19	3588	c.3567G>T	c.(3565-3567)aaG>aaT	p.K1189N	KNDC1_ENST00000368572.2_Missense_Mutation_p.K1191N|KNDC1_ENST00000368571.2_Missense_Mutation_p.K1124N			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1189					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.K1189N(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GCTTGGTCAAGAAGTATCTGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	10											78	81	80					10																	135020445		2203	4300	6503	134870435	SO:0001583	missense	85442			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3567G>T	10.37:g.135020445G>T	ENSP00000304437:p.Lys1189Asn		134870435	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770300	0.69992	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.33216	2.02;2.02;1.42	4.45	4.45	0.53987	.	0.000000	0.64402	U	0.000001	T	0.48519	0.1504	M	0.64997	1.995	0.45046	D	0.998068	D;D	0.89917	0.999;1.0	D;D	0.80764	0.964;0.994	T	0.49615	-0.8921	10	0.87932	D	0	-32.1324	8.7668	0.34708	0.1065:0.0:0.8934:0.0	.	1124;1189	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	N	1189;1191;1124	ENSP00000304437:K1189N;ENSP00000357561:K1191N;ENSP00000357560:K1124N	ENSP00000304437:K1189N	K	+	3	2	KNDC1	134870435	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.698000	0.47068	2.192000	0.70111	0.537000	0.68136	AAG		0.567	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135020445	G	T	135020445	3	4	61	1	0	0	0	0	1	0	0	0	8447	933	33	2	3641	2	KNDC1	10	135020445	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272153	135020445	514302	7092	15077										
VENTX	27287	broad.mit.edu	37	chr10	135053457	135053457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaacctggtttcagaatCgccgcatgaaacacaaacgg	8	10	1	2	rs375001040		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:135053457C>T	ENST00000325980.9	+	3	935	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	142					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R142C(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		GTTTCAGAATCGCCGCATGAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	CYS/ARG	0,4406		0,0,2203	47	55	52		424	1.7	0.9	10		52	1,8599	1.2+/-3.3	0,1,4299	no	missense	VENTX	NM_014468.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	142/259	135053457	1,13005	2203	4300	6503	134903447	SO:0001583	missense	27287			AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"Homeoboxes / ANTP class : NKL subclass"	13639	protein-coding gene	gene with protein product		607158	"VENT-like homeobox 2", "VENT homeobox homolog (Xenopus laevis)"	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.424C>T	10.37:g.135053457C>T	ENSP00000357556:p.Arg142Cys		134903447	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.957669	0.34565	0.0	1.16E-4	ENSG00000151650	ENST00000325980	D	0.97598	-4.45	2.59	1.66	0.24008	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.071156	0.56097	U	0.000030	D	0.98779	0.9589	H	0.98883	4.36	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.96702	0.9519	10	0.87932	D	0	.	5.1615	0.15064	0.0:0.8225:0.0:0.1775	.	142	O95231	VENTX_HUMAN	C	142	ENSP00000357556:R142C	ENSP00000357556:R142C	R	+	1	0	VENTX	134903447	0.979000	0.34478	0.924000	0.36721	0.392000	0.30506	0.429000	0.21412	0.419000	0.25927	0.442000	0.29010	CGC		0.577	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468		T	135053457	C	T	135053457	3	4	61	1	0	0	0	0	1	0	0	0	17193	884	31	1	434	1	VENTX	10	135053457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33012	135053457	481290	7093	15078										
PAOX	196743	broad.mit.edu	37	chr10	135197516	135197516	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctcccctgccggctgaGaaggcagaagcaatcaggaa	12	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:135197516G>A	ENST00000278060.5	+	4	1004	c.921G>A	c.(919-921)gaG>gaA	p.E307E	PAOX_ENST00000368535.2_3'UTR|PAOX_ENST00000480071.2_Intron|PAOX_ENST00000368539.4_3'UTR|PAOX_ENST00000357296.3_Silent_p.E307E	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	445					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)	p.E307E(2)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		TGCCGGCTGAGAAGGCAGAAG	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	10											125	136	132					10																	135197516		2203	4300	6503	135047506	SO:0001819	synonymous_variant	196743			BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.921G>A	10.37:g.135197516G>A			135047506	D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Silent	SNP	ENST00000278060.5	37	CCDS7683.1																																																																																				0.502	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911		A	135197516	G	A	135197516	2	1	61	1	0	0	0	0	0	0	0	1	11454	933	33	3		3	PAOX	10	135197516	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144059	135197516	337231	7094	15079										
CYP2E1	1571	broad.mit.edu	37	chr10	135350581	135350581	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcagagaagctccatgaaGaaattgacagggtgattggg	15	5	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:135350581G>T	ENST00000463117.2	+	9	1254	c.982G>T	c.(982-984)Gaa>Taa	p.E328*	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Nonsense_Mutation_p.E328*			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	328					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.E328*(1)		NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	GCTCCATGAAGAAATTGACAG	0.493									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																																							1	Substitution - Nonsense(1)	large_intestine(1)	10											94	84	87					10																	135350581		2203	4300	6503	135200571	SO:0001587	stop_gained	1571	Familial Cancer Database	incl.: Familial Head and Neck Cancer	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"Cytochrome P450s"	2631	protein-coding gene	gene with protein product		124040	"cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.982G>T	10.37:g.135350581G>T	ENSP00000440689:p.Glu328*		135200571	Q5VZD5|Q6NWT9|Q9UK47	Nonsense_Mutation	SNP	ENST00000463117.2	37	CCDS7686.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301888	0.81136	.	.	ENSG00000130649	ENST00000463117;ENST00000252945;ENST00000421586;ENST00000418356	.	.	.	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.1336	0.72545	0.0:0.0:1.0:0.0	.	.	.	.	X	328;328;241;191	.	ENSP00000252945:E328X	E	+	1	0	CYP2E1	135200571	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	8.651000	0.91078	2.510000	0.84645	0.598000	0.82781	GAA		0.493	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773		T	135350581	G	T	135350581	4	4	61	1	0	0	0	0	0	1	0	0	4176	943	33	2	1008	2	CYP2E1	10	135350581	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153065	135350581	184166	7095	15080										
SYCE1	93426	broad.mit.edu	37	chr10	135373634	135373634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttccatcaagtcttcaaTtttctgtgaggacgtgtcct	7	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr10:135373634T>C	ENST00000343131.5	-	2	201	c.97A>G	c.(97-99)Att>Gtt	p.I33V	SYCE1_ENST00000368517.3_5'UTR|SYCE1_ENST00000432597.2_5'UTR|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	33					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.I33V(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAGTCTTCAATTTTCTGTGAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											173	123	140					10																	135373634		2203	4300	6503	135223624	SO:0001583	missense	93426			AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"cancer/testis antigen 76"	611486	"chromosome 10 open reading frame 94"	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.97A>G	10.37:g.135373634T>C	ENSP00000341282:p.Ile33Val		135223624	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	.	.	.	.	.	.	.	.	.	.	.	15.59	2.879419	0.51801	.	.	ENSG00000171772	ENST00000303903;ENST00000343131	T;T	0.30981	1.51;1.9	4.42	2.05	0.26809	.	.	.	.	.	T	0.23054	0.0557	L	0.46157	1.445	0.25923	N	0.983096	B	0.21753	0.06	B	0.20184	0.028	T	0.23084	-1.0198	9	0.29301	T	0.29	-6.5125	4.5335	0.12017	0.0:0.1009:0.198:0.7011	.	33	Q8N0S2	SYCE1_HUMAN	V	33	ENSP00000303978:I33V;ENSP00000341282:I33V	ENSP00000303978:I33V	I	-	1	0	SYCE1	135223624	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.382000	0.44345	0.456000	0.26937	-0.460000	0.05396	ATT		0.532	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564		C	135373634	T	C	135373634	3	2	61	1	0	0	0	0	1	0	0	0	15467	1493	52	4	1049	4	SYCE1	10	135373634	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	23053	135373634	161113	7096	15081										
RIC8A	60626	broad.mit.edu	37	chr11	209294	209294	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagagcttcacgtttgaTgatgcccaacaggaggaccg	11	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:209294T>G	ENST00000526104.1	+	2	1452	c.108T>G	c.(106-108)gaT>gaG	p.D36E	RIC8A_ENST00000527696.1_Start_Codon_SNP_p.M1R|BET1L_ENST00000410108.1_5'Flank|BET1L_ENST00000325147.9_5'Flank|BET1L_ENST00000529614.2_5'Flank|RIC8A_ENST00000325207.5_Missense_Mutation_p.D36E|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000382762.3_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	36					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D36E(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCACGTTTGATGATGCCCAAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											137	148	144					11																	209294		2203	4300	6503	199294	SO:0001583	missense	60626			AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.108T>G	11.37:g.209294T>G	ENSP00000432008:p.Asp36Glu		199294	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.799|4.799	0.148592|0.148592	0.09134|0.09134	.|.	.|.	ENSG00000177963|ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000531209;ENST00000528357;ENST00000530889|ENST00000527696	.|.	.|.	.|.	3.36|3.36	-6.73|-6.73	0.01749|0.01749	.|.	0.408611|.	0.26677|.	N|.	0.023068|.	T|T	0.34745|0.34745	0.0908|0.0908	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.09377|.	0.001;0.004|.	T|T	0.43669|0.43669	-0.9377|-0.9377	9|6	0.10902|0.87932	T|D	0.67|0	-11.6641|-11.6641	4.1008|4.1008	0.10012|0.10012	0.1021:0.4413:0.2068:0.2498|0.1021:0.4413:0.2068:0.2498	.|.	36;36|.	Q9NPQ8;Q9NPQ8-3|.	RIC8A_HUMAN;.|.	E|R	36;36;36;36;40|1	.|.	ENSP00000325941:D36E|ENSP00000434833:M1R	D|M	+|+	3|2	2|0	RIC8A|RIC8A	199294|199294	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.207000|0.207000	0.24258|0.24258	-6.424000|-6.424000	0.00066|0.00066	-2.575000|-2.575000	0.00465|0.00465	-1.426000|-1.426000	0.01102|0.01102	GAT|ATG		0.612	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		G	209294	T	G	209294	3	3	61	1	0	0	0	0	1	0	0	0	13392	1461	51	4	114	4	RIC8A	11	209294	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09		209294	134797222	7097	15082										
IFITM2	10581	broad.mit.edu	37	chr11	308216	308216	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccacattgtgcaaaccttCtctcctgtcaacagcggcca	6	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:308216C>A	ENST00000399817.4	+	1	54	c.24C>A	c.(22-24)ttC>ttA	p.F8L	IFITM2_ENST00000533141.1_Intron|RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000602569.1_5'Flank	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	8					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F8L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		TGCAAACCTTCTCTCCTGTCA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	11											165	192	183					11																	308216		2029	4182	6211	298216	SO:0001583	missense	10581			X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"interferon induced transmembrane protein 2 (1-8D)"			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.24C>A	11.37:g.308216C>A	ENSP00000382714:p.Phe8Leu		298216	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996407	0.54147	.	.	ENSG00000185201	ENST00000399817;ENST00000327366	T	0.80214	-1.35	2.89	0.833	0.18875	.	.	.	.	.	D	0.83041	0.5168	L	0.46741	1.465	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.69544	-0.5117	9	0.59425	D	0.04	.	5.2024	0.15273	0.0:0.6664:0.0:0.3336	.	8	Q01629	IFM2_HUMAN	L	8	ENSP00000382714:F8L	ENSP00000327996:F8L	F	+	3	2	IFITM2	298216	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.609000	0.05635	0.045000	0.15804	0.313000	0.20887	TTC		0.577	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435		A	308216	C	A	308216	3	1	61	1	0	0	0	0	1	0	0	0	7548	912	32	2	26	2	IFITM2	11	308216	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98922	308216	134698300	7098	15083										
CDHR5	53841	broad.mit.edu	37	chr11	621658	621658	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacggtggagttcactttCgtgtcctggggagggagagg	18	6	1	2	rs140067219		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:621658C>T	ENST00000358353.3	-	6	733	c.411G>A	c.(409-411)acG>acA	p.T137T	CDHR5_ENST00000529337.1_5'Flank|CDHR5_ENST00000397542.2_Silent_p.T137T|CDHR5_ENST00000349570.7_Silent_p.T137T			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.T137T(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						AGTTCACTTTCGTGTCCTGGG	0.627													c|||	1	0.000199681	8e-04	0	5008	,	,		15813	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11							,,	1,4405	2.1+/-5.4	0,1,2202	118	97	104		411,411,411	-7.8	0.4	11	dbSNP_134	104	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	137/840,137/846,137/652	621658	1,13005	2203	4300	6503	611658	SO:0001819	synonymous_variant	53841			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.411G>A	11.37:g.621658C>T			611658	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																				0.627	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		T	621658	C	T	621658	2	4	61	1	0	0	0	0	0	0	0	1	3128	871	31	1		1	CDHR5	11	621658	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	313442	621658	134384858	7099	15084										
DEAF1	10522	broad.mit.edu	37	chr11	688019	688019	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttagttccacctttttCttggccgggagccagagggg	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:688019C>A	ENST00000382409.3	-	4	1040	c.556G>T	c.(556-558)Gaa>Taa	p.E186*	DEAF1_ENST00000338675.6_Nonsense_Mutation_p.E186*	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	186			E -> V (in a primary colorectal cancer). {ECO:0000269|PubMed:11705868}.		anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E186*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CCACCTTTTTCTTGGCCGGGA	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											59	67	64					11																	688019		2203	4300	6503	678019	SO:0001587	stop_gained	10522			AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"Zinc fingers, MYND-type"	14677	protein-coding gene	gene with protein product		602635	"deformed epidermal autoregulatory factor 1 (Drosophila)"			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.556G>T	11.37:g.688019C>A	ENSP00000371846:p.Glu186*		678019	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Nonsense_Mutation	SNP	ENST00000382409.3	37	CCDS31327.1	.	.	.	.	.	.	.	.	.	.	C	42	9.338889	0.99142	.	.	ENSG00000177030	ENST00000382409;ENST00000338675;ENST00000359958;ENST00000388804	.	.	.	4.77	4.77	0.60923	.	0.309163	0.29348	N	0.012402	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-14.5834	16.9509	0.86245	0.0:1.0:0.0:0.0	.	.	.	.	X	186;186;172;109	.	ENSP00000341902:E186X	E	-	1	0	DEAF1	678019	1.000000	0.71417	0.395000	0.26283	0.854000	0.48673	7.348000	0.79366	2.349000	0.79799	0.655000	0.94253	GAA		0.552	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008		A	688019	C	A	688019	4	1	61	1	0	0	0	0	0	1	0	0	4386	922	32	2	1177	2	DEAF1	11	688019	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66361	688019	134318497	7100	15085										
AP2A2	161	broad.mit.edu	37	chr11	985550	985550	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaagaatgccgtgctcttCgaggccatcagcttaatcat	10	11	3	1	rs375464272		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:985550C>T	ENST00000448903.2	+	8	1071	c.930C>T	c.(928-930)ttC>ttT	p.F310F	AP2A2_ENST00000332231.5_Silent_p.F311F|AP2A2_ENST00000534328.1_Silent_p.F310F	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	310					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.F311F(1)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCGTGCTCTTCGAGGCCATCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C	,	1,4291		0,1,2145	88	89	89		933,930	-1.7	1	11		89	0,8498		0,0,4249	no	coding-synonymous,coding-synonymous	AP2A2	NM_001242837.1,NM_012305.3	,	0,1,6394	TT,TC,CC		0.0,0.0233,0.0078	,	311/941,310/940	985550	1,12789	2146	4249	6395	975550	SO:0001819	synonymous_variant	161			AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.930C>T	11.37:g.985550C>T			975550	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	37	CCDS44512.1																																																																																				0.577	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	985550	C	T	985550	2	4	61	1	0	0	0	0	0	0	0	1	740	883	31	1		1	AP2A2	11	985550	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	297531	985550	134020966	7101	15086										
MUC6	4588	broad.mit.edu	37	chr11	1018764	1018764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcagttcctgattggtcGattttgctgtgggaattggt	14	6	0	1	rs369767214		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:1018764G>A	ENST00000421673.2	-	31	4087	c.4037C>T	c.(4036-4038)tCg>tTg	p.S1346L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1346	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.S1346L(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGATTGGTCGATTTTGCTGT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	11						G	LEU/SER	0,4350		0,0,2175	182	187	185		4037	1	0	11		185	1,8537		0,1,4268	no	missense	MUC6	NM_005961.2	145	0,1,6443	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	1346/2440	1018764	1,12887	2175	4269	6444	1008764	SO:0001583	missense	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4037C>T	11.37:g.1018764G>A	ENSP00000406861:p.Ser1346Leu		1008764	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.656340	0.29425	0.0	1.17E-4	ENSG00000184956	ENST00000421673	T	0.21543	2.0	1.03	1.03	0.20045	.	.	.	.	.	T	0.10165	0.0249	N	0.19112	0.55	0.09310	N	1	B	0.33694	0.421	B	0.15052	0.012	T	0.21042	-1.0257	9	0.33940	T	0.23	.	7.8974	0.29715	0.0:0.0:1.0:0.0	.	1346	Q6W4X9	MUC6_HUMAN	L	1346	ENSP00000406861:S1346L	ENSP00000406861:S1346L	S	-	2	0	MUC6	1008764	0.000000	0.05858	0.003000	0.11579	0.091000	0.18340	-1.014000	0.03641	0.878000	0.35920	0.305000	0.20034	TCG		0.532	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1018764	G	A	1018764	3	1	61	1	0	0	0	0	1	0	0	0	10010	1059	37	1	3294	1	MUC6	11	1018764	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33214	1018764	133987752	7102	15087										
MUC5B	727897	broad.mit.edu	37	chr11	1265445	1265445	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaccacaacagccactacGactgagtccactggatccac	7	16	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:1265445G>A	ENST00000529681.1	+	31	7393	c.7335G>A	c.(7333-7335)acG>acA	p.T2445T	MUC5B_ENST00000447027.1_Silent_p.T2448T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2445	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.T2448T(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CAGCCACTACGACTGAGTCCA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	11											70	75	73					11																	1265445		1998	4093	6091	1222021	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.7335G>A	11.37:g.1265445G>A			1222021	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1265445	G	A	1265445	2	1	61	1	0	0	0	0	0	0	0	1	10009	1045	37	1		1	MUC5B	11	1265445	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246681	1265445	133741071	7103	15088										
MUC5B	727897	broad.mit.edu	37	chr11	1271837	1271837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccacaaccggggccaccgGctctgtggccaccccctcct	9	21	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:1271837G>A	ENST00000529681.1	+	31	13785	c.13727G>A	c.(13726-13728)gGc>gAc	p.G4576D	MUC5B_ENST00000447027.1_Missense_Mutation_p.G4579D|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4576	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.G4531D(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		GGGGCCACCGGCTCTGTGGCC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	105	94					11																	1271837		2014	4160	6174	1228413	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13727G>A	11.37:g.1271837G>A	ENSP00000436812:p.Gly4576Asp		1228413	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	5.591|5.591	0.293852|0.293852	0.10567|0.10567	.|.	.|.	ENSG00000117983|ENSG00000117983	ENST00000535652|ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	.|T;T	.|0.18657	.|2.2;2.38	2.37|2.37	-4.74|-4.74	0.03249|0.03249	.|.	.|.	.|.	.|.	.|.	T|T	0.15435|0.15435	0.0372|0.0372	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	.|B;B	.|0.13594	.|0.008;0.008	.|B;B	.|0.10450	.|0.005;0.005	T|T	0.30504|0.30504	-0.9976|-0.9976	6|9	0.07325|0.87932	T|D	0.83|0	.|.	5.2764|5.2764	0.15651|0.15651	0.1593:0.3588:0.4818:0.0|0.1593:0.3588:0.4818:0.0	.|.	.|5049;4579	.|A7Y9J9;E9PBJ0	.|.;.	T|D	352|4576;4579;4520;4426	.|ENSP00000436812:G4576D;ENSP00000415793:G4579D	ENSP00000439776:A352T|ENSP00000343037:G4520D	A|G	+|+	1|2	0|0	MUC5B|MUC5B	1228413|1228413	.|.	.|.	0.000000|0.000000	0.03702|0.03702	0.025000|0.025000	0.11179|0.11179	.|.	.|.	-1.509000|-1.509000	0.01798|0.01798	0.184000|0.184000	0.17185|0.17185	GCT|GGC		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1271837	G	A	1271837	3	1	61	1	0	0	0	0	1	0	0	0	10009	1203	42	3	13858	3	MUC5B	11	1271837	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6392	1271837	133734679	7104	15089										
MOB2	81532	broad.mit.edu	37	chr11	1501712	1501712	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgtggtggaaaaacgtCgtggctggaagagaagagaa	16	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:1501712C>T	ENST00000329957.6	-	3	465	c.276G>A	c.(274-276)acG>acA	p.T92T	MOB2_ENST00000526462.1_5'UTR	NM_001172223.1	NP_001165694.1	Q70IA6	MOB2_HUMAN	MOB kinase activator 2	61					actin cytoskeleton organization (GO:0030036)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cytoplasm (GO:0005737)|neuron projection terminus (GO:0044306)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)	4						GGAAAAACGTCGTGGCTGGAA	0.582																																																0			11											109	118	115					11																	1501712		2066	4197	6263	1458288	SO:0001819	synonymous_variant	81532				CCDS53591.1	11p15.5	2011-09-28			ENSG00000182208	ENSG00000182208		"MOB kinase activators"	24904	protein-coding gene	gene with protein product	"MOB2 Mps One Binder homolog (yeast)"	611969				11223154, 15067004	Standard	NM_053005		Approved	HCCA2	uc010qwz.2	Q70IA6	OTTHUMG00000165545	ENST00000329957.6:c.276G>A	11.37:g.1501712C>T			1458288	B4DKP3|Q96M67	Silent	SNP	ENST00000329957.6	37	CCDS53591.1																																																																																				0.582	MOB2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000384770.1	NM_053005		T	1501712	C	T	1501712	2	4	61	1	0	0	0	0	0	0	0	1	9711	871	31	1		1	MOB2	11	1501712	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	229875	1501712	133504804	7105	15090										
NAP1L4	4676	broad.mit.edu	37	chr11	2972545	2972545	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctcgtcaccttctaattCctgtatttaaaaagtgagaa	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:2972545C>A	ENST00000380542.4	-	14	1206	c.1066G>T	c.(1066-1068)Gaa>Taa	p.E356*	NAP1L4_ENST00000469089.1_5'Flank|NAP1L4_ENST00000526115.1_Splice_Site_p.E356*	NM_005969.3	NP_005960.1	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	356	Asp/Glu-rich (acidic).				nucleosome assembly (GO:0006334)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.E356*(1)		endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)	13		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;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		CCTTCTAATTCCTGTATTTAA	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											240	243	242					11																	2972545		1895	4114	6009	2929121	SO:0001630	splice_region_variant	4676			AA573896, BC022090, U77456	CCDS41599.1	11p15.5	2007-12-06			ENSG00000205531	ENSG00000205531			7640	protein-coding gene	gene with protein product		601651				8923002	Standard	NM_005969		Approved	NAP2	uc001lxc.3	Q99733	OTTHUMG00000011009	ENST00000380542.4:c.1066-1G>T	11.37:g.2972545C>A			2929121	B2R6J4|F5HFY4	Nonsense_Mutation	SNP	ENST00000380542.4	37	CCDS41599.1	.	.	.	.	.	.	.	.	.	.	C	37	6.242416	0.97408	.	.	ENSG00000205531	ENST00000399624;ENST00000380542;ENST00000526115	.	.	.	3.63	3.63	0.41609	.	0.146153	0.45126	D	0.000400	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-17.3912	13.6283	0.62181	0.0:1.0:0.0:0.0	.	.	.	.	X	356	.	ENSP00000369915:E356X	E	-	1	0	NAP1L4	2929121	1.000000	0.71417	0.885000	0.34714	0.428000	0.31595	2.070000	0.41491	2.331000	0.79229	0.655000	0.94253	GAA		0.433	NAP1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030273.3	NM_005969	Nonsense_Mutation	A	2972545	C	A	2972545	5	1	61	1	0	0	0	0	0	0	1	0	10189	869	30	2	69	2	NAP1L4	11	2972545	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1470833	2972545	132033971	7106	15091										
CARS	833	broad.mit.edu	37	chr11	3041553	3041553	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggcggtctgcagagatgCtcaggtcacctgcaaacacg	12	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3041553C>A	ENST00000397111.5	-	10	1159	c.914G>T	c.(913-915)aGc>aTc	p.S305I	CARS_ENST00000380525.4_Missense_Mutation_p.S388I|CARS_ENST00000401769.3_Missense_Mutation_p.S318I|CARS_ENST00000278224.9_Missense_Mutation_p.S305I|CARS_ENST00000397114.3_Missense_Mutation_p.S295I			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	305					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.S305I(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TGCAGAGATGCTCAGGTCACC	0.602			T	ALK	ALCL																																Ovarian(61;932 1157 5961 20446 52152)		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	1	Substitution - Missense(1)	large_intestine(1)	11											103	70	81					11																	3041553		2202	4298	6500	2998129	SO:0001583	missense	833			AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	1493	protein-coding gene	gene with protein product	"cysteine tRNA ligase 1, cytoplasmic"	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.914G>T	11.37:g.3041553C>A	ENSP00000380300:p.Ser305Ile		2998129	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Missense_Mutation	SNP	ENST00000397111.5	37	CCDS7742.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145130	0.57044	.	.	ENSG00000110619	ENST00000380525;ENST00000397111;ENST00000278224;ENST00000397114;ENST00000401769	T;T;T;T;T	0.49432	0.78;0.79;0.78;0.79;0.78	4.31	4.31	0.51392	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.72930	0.3522	M	0.87456	2.885	0.80722	D	1	D;D;D;D;P;D	0.89917	0.985;0.996;1.0;0.999;0.507;0.999	D;D;D;D;B;D	0.83275	0.942;0.979;0.996;0.994;0.304;0.995	T	0.79694	-0.1696	10	0.72032	D	0.01	-32.4039	16.9598	0.86269	0.0:1.0:0.0:0.0	.	318;388;305;305;388;295	B4DKY1;B4DPV7;P49589;P49589-2;Q5HYE4;A8MVQ3	.;.;SYCC_HUMAN;.;.;.	I	388;305;305;295;318	ENSP00000369897:S388I;ENSP00000380300:S305I;ENSP00000278224:S305I;ENSP00000380303:S295I;ENSP00000384069:S318I	ENSP00000278224:S305I	S	-	2	0	CARS	2998129	1.000000	0.71417	0.993000	0.49108	0.020000	0.10135	7.170000	0.77587	2.222000	0.72286	0.467000	0.42956	AGC		0.602	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751		A	3041553	C	A	3041553	3	1	61	1	0	0	0	0	1	0	0	0	2663	797	28	2	1392	2	CARS	11	3041553	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69008	3041553	131964963	7107	15092										
NUP98	4928	broad.mit.edu	37	chr11	3704593	3704593	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttctgggtaaggaaagtCtctttagcccaagattcagg	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3704593C>A	ENST00000324932.7	-	30	5175	c.4755G>T	c.(4753-4755)gaG>gaT	p.E1585D	NUP98_ENST00000359171.4_Missense_Mutation_p.E1511D|NUP98_ENST00000355260.3_Missense_Mutation_p.E1511D	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1602					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.E1585D(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TAAGGAAAGTCTCTTTAGCCC	0.527			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	1	Substitution - Missense(1)	large_intestine(1)	11											115	109	111					11																	3704593		2201	4298	6499	3661169	SO:0001583	missense	4928			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4755G>T	11.37:g.3704593C>A	ENSP00000316032:p.Glu1585Asp		3661169	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.525408|4.525408	0.85600|0.85600	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000429801|ENST00000324932;ENST00000359171;ENST00000355260	.|.	.|.	.|.	6.02|6.02	3.18|3.18	0.36537|0.36537	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66066|0.66066	0.2752|0.2752	M|M	0.81497|0.81497	2.545|2.545	0.23731|0.23731	N|N	0.996995|0.996995	.|D;D;D	.|0.89917	.|0.997;0.999;1.0	.|D;D;D	.|0.83275	.|0.99;0.995;0.996	T|T	0.57596|0.57596	-0.7784|-0.7784	5|9	.|0.36615	.|T	.|0.2	-17.253|-17.253	10.3892|10.3892	0.44158|0.44158	0.0:0.7921:0.0:0.2079|0.0:0.7921:0.0:0.2079	.|.	.|1511;1585;1499	.|P52948-2;P52948-5;P52948-6	.|.;.;.	Y|D	538|1585;1511;1511	.|.	.|ENSP00000316032:E1585D	D|E	-|-	1|3	0|2	NUP98|NUP98	3661169|3661169	0.988000|0.988000	0.35896|0.35896	0.982000|0.982000	0.44146|0.44146	0.980000|0.980000	0.70556|0.70556	0.911000|0.911000	0.28584|0.28584	0.460000|0.460000	0.27045|0.27045	0.650000|0.650000	0.86243|0.86243	GAC|GAG		0.527	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3704593	C	A	3704593	3	1	61	1	0	0	0	0	1	0	0	0	10804	912	32	2	663	2	NUP98	11	3704593	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	663040	3704593	131301923	7108	15093										
NUP98	4928	broad.mit.edu	37	chr11	3740705	3740705	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagacaactacttctttcCtccggatatgcacaatatca	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3740705C>A	ENST00000324932.7	-	18	2756	c.2336G>T	c.(2335-2337)aGg>aTg	p.R779M	NUP98_ENST00000359171.4_Missense_Mutation_p.R779M|NUP98_ENST00000397007.4_Missense_Mutation_p.R796M|NUP98_ENST00000355260.3_Missense_Mutation_p.R779M|NUP98_ENST00000397004.4_Missense_Mutation_p.R779M	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	796	Peptidase S59. {ECO:0000255|PROSITE- ProRule:PRU00765}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.R779M(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TACTTCTTTCCTCCGGATATG	0.328			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	1	Substitution - Missense(1)	large_intestine(1)	11											117	115	116					11																	3740705		2201	4295	6496	3697281	SO:0001583	missense	4928			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.2336G>T	11.37:g.3740705C>A	ENSP00000316032:p.Arg779Met		3697281	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.836161	0.91117	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77445	0.4131	M	0.67700	2.07	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.979;0.989;0.997;0.986	T	0.77534	-0.2552	9	0.48119	T	0.1	.	16.2641	0.82565	0.0:1.0:0.0:0.0	.	796;779;779;779	P52948-3;P52948-4;P52948-2;P52948-5	.;.;.;.	M	779;779;779;779;796	.	ENSP00000316032:R779M	R	-	2	0	NUP98	3697281	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.269000	0.78482	2.509000	0.84616	0.563000	0.77884	AGG		0.328	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3740705	C	A	3740705	3	1	61	1	0	0	0	0	1	0	0	0	10804	681	24	2	3151	2	NUP98	11	3740705	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36112	3740705	131265811	7109	15094										
NUP98	4928	broad.mit.edu	37	chr11	3752790	3752790	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagccttctgggctgctgGatttgttggtttcaatctct	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3752790G>T	ENST00000324932.7	-	14	1981	c.1561C>A	c.(1561-1563)Cca>Aca	p.P521T	NUP98_ENST00000359171.4_Missense_Mutation_p.P521T|NUP98_ENST00000397007.4_Missense_Mutation_p.P538T|NUP98_ENST00000355260.3_Missense_Mutation_p.P521T|NUP98_ENST00000397004.4_Missense_Mutation_p.P521T	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	538					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.P521T(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TGGGCTGCTGGATTTGTTGGT	0.428			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	1	Substitution - Missense(1)	large_intestine(1)	11											135	149	145					11																	3752790		2201	4298	6499	3709366	SO:0001583	missense	4928			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1561C>A	11.37:g.3752790G>T	ENSP00000316032:p.Pro521Thr		3709366	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.0|25.0	4.592781|4.592781	0.86953|0.86953	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007|ENST00000527104	.|.	.|.	.|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73916|0.73916	0.3648|0.3648	M|M	0.66439|0.66439	2.03|2.03	0.58432|0.58432	D|D	0.999999|0.999999	D;P;D;D|.	0.89917|.	1.0;0.939;1.0;1.0|.	D;P;D;D|.	0.91635|.	0.999;0.654;0.999;0.999|.	T|T	0.72874|0.72874	-0.4160|-0.4160	9|5	0.52906|.	T|.	0.07|.	.|.	17.8797|17.8797	0.88837|0.88837	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	538;521;521;521|.	P52948-3;P52948-4;P52948-2;P52948-5|.	.;.;.;.|.	T|Y	521;521;521;521;538|140	.|.	ENSP00000316032:P521T|.	P|S	-|-	1|2	0|0	NUP98|NUP98	3709366|3709366	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.476000|9.476000	0.97823|0.97823	2.462000|2.462000	0.83206|0.83206	0.467000|0.467000	0.42956|0.42956	CCA|TCC		0.428	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		T	3752790	G	T	3752790	3	4	61	1	0	0	0	0	1	0	0	0	10804	1174	41	2	3942	2	NUP98	11	3752790	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12085	3752790	131253726	7110	15095										
PGAP2	27315	broad.mit.edu	37	chr11	3838603	3838603	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacgccctgcaggatgttCtctgcggcctcccagccttt	10	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3838603C>A	ENST00000463452.2	+	2	248				PGAP2_ENST00000465307.2_Intron|PGAP2_ENST00000278243.4_Missense_Mutation_p.F62L|PGAP2_ENST00000396991.2_Missense_Mutation_p.F62L|PGAP2_ENST00000493547.2_Intron|PGAP2_ENST00000396993.4_Intron|PGAP2_ENST00000396986.2_Intron|PGAP2_ENST00000300730.6_Intron|PGAP2_ENST00000532017.1_Intron|PGAP2_ENST00000479072.1_Intron|PGAP2_ENST00000496834.2_Intron|AC090587.2_ENST00000507938.1_RNA	NM_001256240.1	NP_001243169.1	Q9UHJ9	PGAP2_HUMAN	post-GPI attachment to proteins 2						GPI anchor biosynthetic process (GO:0006506)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|signal transduction in response to DNA damage (GO:0042770)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.F62L(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11						GCAGGATGTTCTCTGCGGCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11											125	115	118					11																	3838603		2201	4298	6499	3795179	SO:0001627	intron_variant	27315			AF159615	CCDS7747.1, CCDS44523.1, CCDS58112.1, CCDS58113.1, CCDS73244.1, CCDS73245.1	11p15.4	2014-01-31			ENSG00000148985	ENSG00000148985			17893	protein-coding gene	gene with protein product	"FGF receptor activating protein 1", "cell wall biogenesis 43 N-terminal homolog (S. cerevisiae)"	615187	"mental retardation, non-syndromic, autosomal recessive, 21"	MRT21		10585768, 16407401, 23561846	Standard	NM_014489		Approved	FRAG1, CWH43-N	uc010qxw.3	Q9UHJ9	OTTHUMG00000012238	ENST00000463452.2:c.165+5949C>A	11.37:g.3838603C>A			3795179	E9PJG5|H7BXL9|Q6UC77|Q96G66|Q9UF01|Q9Y4N1	Missense_Mutation	SNP	ENST00000463452.2	37	CCDS58112.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.16|15.16	2.749892|2.749892	0.49257|0.49257	.|.	.|.	ENSG00000148985|ENSG00000148985	ENST00000396991;ENST00000278243;ENST00000502872|ENST00000464906	.|.	.|.	.|.	5.53|5.53	2.43|2.43	0.29744|0.29744	.|.	0.277861|.	0.29053|.	N|.	0.013295|.	T|T	0.03564|0.03564	0.0102|0.0102	N|N	0.00034|0.00034	-2.56|-2.56	0.26521|0.26521	N|N	0.974425|0.974425	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.38457|0.38457	-0.9660|-0.9660	9|5	0.07030|.	T|.	0.85|.	-12.5783|-12.5783	5.4408|5.4408	0.16507|0.16507	0.0:0.654:0.1657:0.1802|0.0:0.654:0.1657:0.1802	.|.	62|.	Q9UHJ9|.	PGAP2_HUMAN|.	L|Y	62;62;2|92	.|.	ENSP00000278243:F62L|.	F|S	+|+	3|2	2|0	PGAP2|PGAP2	3795179|3795179	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.081000|0.081000	0.14823|0.14823	1.330000|1.330000	0.45394|0.45394	0.650000|0.650000	0.86243|0.86243	TTC|TCT		0.597	PGAP2-049	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383260.1			A	3838603	C	A	3838603	1	1	61	0	1	0	0	0	0	0	0	0	11809	912	32	2		2	PGAP2	11	3838603	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85813	3838603	131167913	7111	15096										
PGAP2	27315	broad.mit.edu	37	chr11	3838696	3838696	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcacttttcctgtgttCggcttcttcttctgcatcat	6	13	5	0	rs75812077		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:3838696C>T	ENST00000463452.2	+	2	248				PGAP2_ENST00000465307.2_Intron|PGAP2_ENST00000278243.4_Silent_p.F93F|PGAP2_ENST00000396991.2_Silent_p.F93F|PGAP2_ENST00000493547.2_Intron|PGAP2_ENST00000396993.4_Intron|PGAP2_ENST00000396986.2_Intron|PGAP2_ENST00000300730.6_Intron|PGAP2_ENST00000532017.1_Intron|PGAP2_ENST00000479072.1_Intron|PGAP2_ENST00000496834.2_Intron|AC090587.2_ENST00000507938.1_RNA	NM_001256240.1	NP_001243169.1	Q9UHJ9	PGAP2_HUMAN	post-GPI attachment to proteins 2						GPI anchor biosynthetic process (GO:0006506)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|signal transduction in response to DNA damage (GO:0042770)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.F93F(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11						TTCCTGTGTTCGGCTTCTTCT	0.597													C|||	1	0.000199681	0	0	5008	,	,		18775	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11											160	143	149					11																	3838696		2201	4298	6499	3795272	SO:0001627	intron_variant	27315			AF159615	CCDS7747.1, CCDS44523.1, CCDS58112.1, CCDS58113.1, CCDS73244.1, CCDS73245.1	11p15.4	2014-01-31			ENSG00000148985	ENSG00000148985			17893	protein-coding gene	gene with protein product	"FGF receptor activating protein 1", "cell wall biogenesis 43 N-terminal homolog (S. cerevisiae)"	615187	"mental retardation, non-syndromic, autosomal recessive, 21"	MRT21		10585768, 16407401, 23561846	Standard	NM_014489		Approved	FRAG1, CWH43-N	uc010qxw.3	Q9UHJ9	OTTHUMG00000012238	ENST00000463452.2:c.165+6042C>T	11.37:g.3838696C>T			3795272	E9PJG5|H7BXL9|Q6UC77|Q96G66|Q9UF01|Q9Y4N1	Silent	SNP	ENST00000463452.2	37	CCDS58112.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	15.15	2.747595	0.49257	.	.	ENSG00000148985	ENST00000532535;ENST00000464906	.	.	.	5.39	4.47	0.54385	.	.	.	.	.	T	0.61751	0.2372	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59674	-0.7410	4	.	.	.	-17.504	10.4435	0.44479	0.0:0.9089:0.0:0.0911	.	.	.	.	L	106;123	.	.	S	+	2	0	PGAP2	3795272	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.689000	0.25437	1.246000	0.43901	0.650000	0.86243	TCG		0.597	PGAP2-049	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383260.1			T	3838696	C	T	3838696	1	4	61	0	1	0	0	0	0	0	0	0	11809	883	31	1		1	PGAP2	11	3838696	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93	3838696	131167820	7112	15097										
RRM1	6240	broad.mit.edu	37	chr11	4148290	4148290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatcaaataaacgccatcGccccattggaattggggtac	8	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4148290G>A	ENST00000300738.5	+	14	1700	c.1496G>A	c.(1495-1497)cGc>cAc	p.R499H	RRM1_ENST00000534285.1_Missense_Mutation_p.R277H|RRM1_ENST00000423050.2_Missense_Mutation_p.R402H|RRM1_ENST00000537197.1_Missense_Mutation_p.R161H	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	499					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)	p.R499H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	AAACGCCATCGCCCCATTGGA	0.408																																					NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)											1	Substitution - Missense(1)	large_intestine(1)	11											105	108	107					11																	4148290		2201	4298	6499	4104866	SO:0001583	missense	6240			X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1496G>A	11.37:g.4148290G>A	ENSP00000300738:p.Arg499His		4104866	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	37	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	G	33	5.278779	0.95489	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.74	5.74	0.90152	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87985	0.6316	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90014	0.4123	10	0.87932	D	0	-8.2326	18.483	0.90819	0.0:0.0:1.0:0.0	.	499	P23921	RIR1_HUMAN	H	499;402;412;277;277;161	ENSP00000300738:R499H;ENSP00000390539:R402H;ENSP00000431464:R277H;ENSP00000442148:R161H	ENSP00000300738:R499H	R	+	2	0	RRM1	4104866	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.407000	0.97325	2.719000	0.93026	0.655000	0.94253	CGC		0.408	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		A	4148290	G	A	4148290	3	1	61	1	0	0	0	0	1	0	0	0	13718	1087	38	1	1550	1	RRM1	11	4148290	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	309594	4148290	130858226	7113	15098										
OR52B4	143496	broad.mit.edu	37	chr11	4388943	4388943	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccataccaaatgtttattcGaatgtcattacatgcatatt	4	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4388943G>A	ENST00000408920.2	-	1	673	c.583C>T	c.(583-585)Cga>Tga	p.R195*		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	195					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R195*(1)		NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATGTTTATTCGAATGTCATTA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											72	69	70					11																	4388943		1854	4097	5951	4345519	SO:0001587	stop_gained	143496			AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.583C>T	11.37:g.4388943G>A	ENSP00000386160:p.Arg195*		4345519	A6NP68|Q6IFK6	Nonsense_Mutation	SNP	ENST00000408920.2	37	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.863359	0.32884	.	.	ENSG00000221996	ENST00000408920	.	.	.	5.29	-0.0532	0.13819	.	1.058310	0.07455	N	0.899735	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.7048	0.08397	0.2928:0.0:0.3248:0.3824	.	.	.	.	X	195	.	ENSP00000386160:R195X	R	-	1	2	OR52B4	4345519	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.420000	0.07062	0.072000	0.16694	-0.182000	0.12963	CGA		0.338	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		A	4388943	G	A	4388943	4	1	61	1	0	0	0	0	0	1	0	0	11143	1066	37	1	365	1	OR52B4	11	4388943	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	240653	4388943	130617573	7114	15099										
OR52B4	143496	broad.mit.edu	37	chr11	4389010	4389010	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgtggaataatattattCtggcagaaagtcaatctttt	9	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4389010C>T	ENST00000408920.2	-	1	606	c.516G>A	c.(514-516)caG>caA	p.Q172Q		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	172					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q172Q(1)		NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TAATATTATTCTGGCAGAAAG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	11											62	60	61					11																	4389010		1824	4078	5902	4345586	SO:0001819	synonymous_variant	143496			AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.516G>A	11.37:g.4389010C>T			4345586	A6NP68|Q6IFK6	Silent	SNP	ENST00000408920.2	37	CCDS41609.1																																																																																				0.333	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		T	4389010	C	T	4389010	2	4	61	1	0	0	0	0	0	0	0	1	11143	912	32	3		3	OR52B4	11	4389010	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67	4389010	130617506	7115	15100										
OR52K1	390036	broad.mit.edu	37	chr11	4510907	4510907	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctacactccagtagtcatCtcttcagtcatgcaccgtgt	6	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4510907C>A	ENST00000307632.3	+	1	799	c.777C>A	c.(775-777)atC>atA	p.I259I		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I259I(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(18)|skin(2)|stomach(1)	32		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		CAGTAGTCATCTCTTCAGTCA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	11											250	220	230					11																	4510907		2201	4298	6499	4467483	SO:0001819	synonymous_variant	390036			AB065790	CCDS31352.1	11p15.4	2012-08-09			ENSG00000196778	ENSG00000196778		"GPCR / Class A : Olfactory receptors"	15222	protein-coding gene	gene with protein product							Standard	NM_001005171		Approved		uc001lza.2	Q8NGK4	OTTHUMG00000165705	ENST00000307632.3:c.777C>A	11.37:g.4510907C>A			4467483	B9EH54|Q6IFK5	Silent	SNP	ENST00000307632.3	37	CCDS31352.1																																																																																				0.527	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171		A	4510907	C	A	4510907	2	1	61	1	0	0	0	0	0	0	0	1	11154	903	32	2		2	OR52K1	11	4510907	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121897	4510907	130495609	7116	15101										
C11orf40	143501	broad.mit.edu	37	chr11	4594546	4594546	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacacttacagtaccctaaAgcaaggtcttttgtcatctt	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4594546A>C	ENST00000307616.1	-	2	297	c.298T>G	c.(298-300)Ttt>Gtt	p.F100V		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	100			F -> S (in dbSNP:rs12795289).					p.F100V(1)		large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGTACCCTAAAGCAAGGTCTT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											213	174	187					11																	4594546		2201	4298	6499	4551122	SO:0001583	missense	143501				CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.298T>G	11.37:g.4594546A>C	ENSP00000302918:p.Phe100Val		4551122		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	A	5.104	0.204870	0.09704	.	.	ENSG00000171987	ENST00000307616	T	0.54279	0.58	1.45	-1.26	0.09376	.	.	.	.	.	T	0.25680	0.0625	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.16335	-1.0406	9	0.87932	D	0	.	1.5754	0.02624	0.3149:0.2195:0.0:0.4656	.	100	Q8WZ69	CK040_HUMAN	V	100	ENSP00000302918:F100V	ENSP00000302918:F100V	F	-	1	0	C11orf40	4551122	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.711000	0.05019	-0.377000	0.07930	-0.811000	0.03165	TTT		0.488	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		C	4594546	A	C	4594546	3	2	61	1	0	0	0	0	1	0	0	0	1643	72	3	4	366	4	C11orf40	11	4594546	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	83639	4594546	130411970	7117	15102										
C11orf40	143501	broad.mit.edu	37	chr11	4599000	4599000	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctgtccatctgcaaaatGgacagctttggctctctttc	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4599000G>T	ENST00000307616.1	-	1	50	c.51C>A	c.(49-51)tcC>tcA	p.S17S		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	17								p.S17S(1)		large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		tctgcaaaatggacagctttg	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	11											51	44	46					11																	4599000		2201	4297	6498	4555576	SO:0001819	synonymous_variant	143501				CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.51C>A	11.37:g.4599000G>T			4555576		Silent	SNP	ENST00000307616.1	37	CCDS31354.1																																																																																				0.542	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		T	4599000	G	T	4599000	2	4	61	1	0	0	0	0	0	0	0	1	1643	1335	47	2		2	C11orf40	11	4599000	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4454	4599000	130407516	7118	15103										
OR52I2	143502	broad.mit.edu	37	chr11	4608533	4608533	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcctctacactacaagaGaattctcacgcctcaagtga	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4608533G>T	ENST00000312614.4	+	1	513	c.491G>T	c.(490-492)aGa>aTa	p.R164I		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R164I(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CACTACAAGAGAATTCTCACG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	58	58					11																	4608533		2201	4298	6499	4565109	SO:0001583	missense	143502			BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"GPCR / Class A : Olfactory receptors"	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.491G>T	11.37:g.4608533G>T	ENSP00000308764:p.Arg164Ile		4565109	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	.	.	.	.	.	.	.	.	.	.	G	5.779	0.328066	0.10956	.	.	ENSG00000226288	ENST00000312614	T	0.00418	7.49	4.18	0.72	0.18214	GPCR, rhodopsin-like superfamily (1);	0.766887	0.11161	N	0.593031	T	0.00300	0.0009	N	0.17278	0.47	0.28659	N	0.906235	B	0.22003	0.063	B	0.27170	0.077	T	0.38090	-0.9677	10	0.66056	D	0.02	-2.0024	13.9525	0.64126	0.0:0.5153:0.4846:0.0	.	164	Q8NH67	O52I2_HUMAN	I	164	ENSP00000308764:R164I	ENSP00000308764:R164I	R	+	2	0	OR52I2	4565109	0.000000	0.05858	0.986000	0.45419	0.160000	0.22226	-0.743000	0.04845	0.347000	0.23924	0.644000	0.83932	AGA		0.493	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170		T	4608533	G	T	4608533	3	4	61	1	0	0	0	0	1	0	0	0	11152	942	33	2	493	2	OR52I2	11	4608533	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9533	4608533	130397983	7119	15104										
OR52I1	390037	broad.mit.edu	37	chr11	4615426	4615426	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccctcatcgtgactgcaaTctggatggattccactcggc	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4615426T>G	ENST00000530443.2	+	1	158	c.158T>G	c.(157-159)aTc>aGc	p.I53S	OR52I1_ENST00000450052.2_Missense_Mutation_p.I77S	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I78S(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGACTGCAATCTGGATGGAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											175	143	154					11																	4615426		2201	4298	6499	4572002	SO:0001583	missense	390037			BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"GPCR / Class A : Olfactory receptors"	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.158T>G	11.37:g.4615426T>G	ENSP00000436453:p.Ile53Ser		4572002	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.387034	0.42308	.	.	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.08634	3.07;3.07	4.92	4.92	0.64577	GPCR, rhodopsin-like superfamily (1);	0.150415	0.30704	N	0.009051	T	0.29620	0.0739	M	0.82132	2.575	0.36698	D	0.879936	D	0.89917	1.0	D	0.76575	0.988	T	0.40646	-0.9552	9	0.87932	D	0	-8.1494	12.8674	0.57948	0.0:0.0:0.0:1.0	.	53	Q8NGK6	O52I1_HUMAN	S	77;53	ENSP00000409094:I77S;ENSP00000436453:I53S	ENSP00000409094:I77S	I	+	2	0	OR52I1	4572002	0.000000	0.05858	0.918000	0.36340	0.209000	0.24338	0.883000	0.28200	2.208000	0.71279	0.449000	0.29647	ATC		0.512	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169		G	4615426	T	G	4615426	3	3	61	1	0	0	0	0	1	0	0	0	11151	1435	50	4	160	4	OR52I1	11	4615426	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6893	4615426	130391090	7120	15105										
OR52I1	390037	broad.mit.edu	37	chr11	4615635	4615635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggggctgctgctgaccatgGcttttgaccgctatgtagcc	13	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4615635G>A	ENST00000530443.2	+	1	367	c.367G>A	c.(367-369)Gct>Act	p.A123T	OR52I1_ENST00000450052.2_Missense_Mutation_p.A147T	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A148T(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCTGACCATGGCTTTTGACCG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											49	43	45					11																	4615635		2200	4278	6478	4572211	SO:0001583	missense	390037			BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"GPCR / Class A : Olfactory receptors"	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.367G>A	11.37:g.4615635G>A	ENSP00000436453:p.Ala123Thr		4572211	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145117	0.57044	.	.	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.76186	-1.0;-1.0	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000449	D	0.90338	0.6977	H	0.96518	3.835	0.33532	D	0.593752	D	0.89917	1.0	D	0.77004	0.989	D	0.92962	0.6390	9	0.87932	D	0	-10.8267	16.0681	0.80903	0.0:0.0:1.0:0.0	.	123	Q8NGK6	O52I1_HUMAN	T	147;123	ENSP00000409094:A147T;ENSP00000436453:A123T	ENSP00000409094:A147T	A	+	1	0	OR52I1	4572211	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	2.546000	0.45778	2.741000	0.93983	0.555000	0.69702	GCT		0.517	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169		A	4615635	G	A	4615635	3	1	61	1	0	0	0	0	1	0	0	0	11151	1203	42	3	369	3	OR52I1	11	4615635	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	209	4615635	130390881	7121	15106										
OR51E1	143503	broad.mit.edu	37	chr11	4673952	4673952	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagcccatgtatatatttCtttgcatgctttcaggcatt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4673952C>A	ENST00000396952.5	+	2	846	c.196C>A	c.(196-198)Ctt>Att	p.L66I	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L65I(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		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)		GTATATATTTCTTTGCATGCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											163	130	141					11																	4673952		2201	4298	6499	4630528	SO:0001583	missense	143503			AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"GPCR / Class A : Olfactory receptors"	15194	protein-coding gene	gene with protein product		611267	"olfactory receptor, family 51, subfamily E, member 1 pseudogene"	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.196C>A	11.37:g.4673952C>A	ENSP00000380155:p.Leu66Ile		4630528	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	C	16.72	3.200663	0.58126	.	.	ENSG00000180785	ENST00000396952	T	0.13778	2.56	4.87	4.87	0.63330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000166	T	0.40015	0.1100	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.29305	-1.0016	10	0.66056	D	0.02	.	16.7377	0.85451	0.0:1.0:0.0:0.0	.	65	Q8TCB6	O51E1_HUMAN	I	66	ENSP00000380155:L66I	ENSP00000380155:L66I	L	+	1	0	OR51E1	4630528	0.662000	0.27439	1.000000	0.80357	0.996000	0.88848	0.760000	0.26475	2.530000	0.85305	0.655000	0.94253	CTT		0.468	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		A	4673952	C	A	4673952	3	1	61	1	0	0	0	0	1	0	0	0	11125	913	32	2	198	2	OR51E1	11	4673952	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58317	4673952	130332564	7122	15107										
OR51E2	81285	broad.mit.edu	37	chr11	4703157	4703157	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaaggctgtttccaaagCggtgtaccactgagaggcca	13	9	0	2	rs143376710		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4703157C>T	ENST00000396950.3	-	2	1024	c.785G>A	c.(784-786)cGc>cAc	p.R262H		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	262					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)	p.R262H(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GTTTCCAAAGCGGTGTACCAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG	0,4402		0,0,2201	161	119	133		785	5	1	11	dbSNP_134	133	1,8595	1.2+/-3.3	0,1,4297	no	missense	OR51E2	NM_030774.3	29	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	262/321	4703157	1,12997	2201	4298	6499	4659733	SO:0001583	missense	81285			AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.785G>A	11.37:g.4703157C>T	ENSP00000380153:p.Arg262His		4659733	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	37	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303602	0.60305	0.0	1.16E-4	ENSG00000167332	ENST00000396950	T	0.37235	1.21	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000236	T	0.63319	0.2501	M	0.88775	2.98	0.21020	N	0.999805	D	0.89917	1.0	D	0.97110	1.0	T	0.60296	-0.7291	10	0.87932	D	0	.	10.5365	0.45007	0.0:0.9112:0.0:0.0888	.	262	Q9H255	O51E2_HUMAN	H	262	ENSP00000380153:R262H	ENSP00000380153:R262H	R	-	2	0	OR51E2	4659733	0.596000	0.26866	0.994000	0.49952	0.984000	0.73092	1.610000	0.36869	2.589000	0.87451	0.655000	0.94253	CGC		0.522	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		T	4703157	C	T	4703157	3	4	61	1	0	0	0	0	1	0	0	0	11126	768	27	1	181	1	OR51E2	11	4703157	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29205	4703157	130303359	7123	15108										
OR51F1	256892	broad.mit.edu	37	chr11	4790355	4790355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggctgaccgaccatagcGatacaccaaggacaggctca	13	12	1	1	rs369623823		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4790355G>A	ENST00000380383.1	-	1	813	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.R265C|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R265C(1)		kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		CGACCATAGCGATACACCAAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	CYS/ARG	0,4402		0,0,2201	97	87	90		793	3.4	0.7	11		90	1,8595	1.2+/-3.3	0,1,4297	no	missense	OR51F1	NM_001004752.1	180	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	265/313	4790355	1,12997	2201	4298	6499	4746931	SO:0001583	missense	256892			BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"GPCR / Class A : Olfactory receptors"	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.814C>T	11.37:g.4790355G>A	ENSP00000369744:p.Arg272Cys		4746931		Missense_Mutation	SNP	ENST00000380383.1	37		.	.	.	.	.	.	.	.	.	.	G	7.811	0.715763	0.15306	0.0	1.16E-4	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00164	8.64;8.64	5.24	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.106625	0.42294	N	0.000721	T	0.00300	0.0009	M	0.92268	3.29	0.09310	N	0.999997	P	0.45715	0.865	B	0.43194	0.411	T	0.25398	-1.0133	10	0.87932	D	0	.	7.2545	0.26168	0.0788:0.0:0.6216:0.2996	.	272	A6NGY5	O51F1_HUMAN	C	265;272	ENSP00000345163:R265C;ENSP00000369744:R272C	ENSP00000345163:R265C	R	-	1	0	OR51F1	4746931	0.004000	0.15560	0.747000	0.31113	0.050000	0.14768	0.526000	0.22971	0.776000	0.33473	0.655000	0.94253	CGC		0.512	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752		A	4790355	G	A	4790355	3	1	61	1	0	0	0	0	1	0	0	0	11127	1058	37	1	148	1	OR51F1	11	4790355	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87198	4790355	130216161	7124	15109										
OR51S1	119692	broad.mit.edu	37	chr11	4869859	4869859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttctgggcaggccaaacGagccacatctggatgcaagc	12	12	2	0	rs142743963	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4869859G>A	ENST00000322101.2	-	1	655	c.580C>T	c.(580-582)Cgt>Tgt	p.R194C	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R194C(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGCCAAACGAGCCACATCT	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	11						G	CYS/ARG	0,4402		0,0,2201	82	89	87		580	4.3	0	11	dbSNP_134	87	3,8593	3.0+/-9.4	0,3,4295	no	missense	OR51S1	NM_001004758.1	180	0,3,6496	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	194/324	4869859	3,12995	2201	4298	6499	4826435	SO:0001583	missense	119692			AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.580C>T	11.37:g.4869859G>A	ENSP00000322754:p.Arg194Cys		4826435	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409326	0.42715	0.0	3.49E-4	ENSG00000176922	ENST00000322101	T	0.38240	1.15	5.25	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.358179	0.19328	N	0.116980	T	0.59280	0.2182	M	0.89414	3.03	0.09310	N	1	D	0.71674	0.998	P	0.57846	0.828	T	0.57602	-0.7783	10	0.72032	D	0.01	-5.9604	11.4627	0.50219	0.0:0.0:0.5644:0.4356	.	194	Q8NGJ8	O51S1_HUMAN	C	194	ENSP00000322754:R194C	ENSP00000322754:R194C	R	-	1	0	OR51S1	4826435	0.000000	0.05858	0.003000	0.11579	0.714000	0.41099	0.496000	0.22499	1.428000	0.47296	0.655000	0.94253	CGT		0.552	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		A	4869859	G	A	4869859	3	1	61	1	0	0	0	0	1	0	0	0	11136	1058	37	1	394	1	OR51S1	11	4869859	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79504	4869859	130136657	7125	15110										
OR51T1	56547	broad.mit.edu	37	chr11	4903051	4903051	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaaattgtatataaaatGactaataaaatgtatgctat	4	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4903051G>T	ENST00000380390.1	+	2	72				OR51T1_ENST00000380378.1_Start_Codon_SNP_p.M1I|OR51T1_ENST00000322049.1_5'Flank|MMP26_ENST00000477339.1_Intron			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26						collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.M1I(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	TATATAAAATGACTAATAAAA	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	11											9	9	9					11																	4903051		2134	4212	6346	4859627	SO:0001627	intron_variant	401665			AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.-144-106247G>T	11.37:g.4903051G>T			4859627	Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	37	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	G	8.728	0.915992	0.17907	.	.	ENSG00000176900	ENST00000380378	T	0.01059	5.39	3.76	0.584	0.17422	.	.	.	.	.	T	0.01387	0.0045	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.48479	-0.9032	6	0.56958	D	0.05	.	3.7843	0.08694	0.2416:0.2042:0.5541:0.0	.	.	.	.	I	1	ENSP00000369738:M1I	ENSP00000369738:M1I	M	+	3	0	OR51T1	4859627	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.343000	0.07791	0.286000	0.22352	0.650000	0.86243	ATG		0.259	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		T	4903051	G	T	4903051	1	4	61	0	1	0	0	0	0	0	0	0	11137	1290	45	2		2	OR51T1	11	4903051	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33192	4903051	130103465	7126	15111										
OR51T1	401665	broad.mit.edu	37	chr11	4903504	4903504	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatggcctttgaccgcttCgtggctatctgtaacccact	9	14	1	1	rs143185351	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4903504C>T	ENST00000322049.1	+	1	375	c.375C>T	c.(373-375)ttC>ttT	p.F125F	MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Silent_p.F152F|MMP26_ENST00000477339.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F152F(1)|p.F125F(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGACCGCTTCGTGGCTATCT	0.488													C|||	3	0.000599042	0.0023	0	5008	,	,		22774	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	11						C		21,4381	28.1+/-56.4	0,21,2180	147	125	133		456	2.5	1	11	dbSNP_134	133	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	OR51T1	NM_001004759.1		0,23,6476	TT,TC,CC		0.0233,0.4771,0.177		152/355	4903504	23,12975	2201	4298	6499	4860080	SO:0001819	synonymous_variant	401665			BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.375C>T	11.37:g.4903504C>T			4860080	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																					0.488	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		T	4903504	C	T	4903504	2	4	61	1	0	0	0	0	0	0	0	1	11137	883	31	1		1	OR51T1	11	4903504	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	453	4903504	130103012	7127	15112										
OR51G2	81282	broad.mit.edu	37	chr11	4936413	4936413	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataaaaggtaatggaaaaaTgagtgctacactacgaccca	8	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4936413T>G	ENST00000322013.3	-	1	509	c.481A>C	c.(481-483)Att>Ctt	p.I161L	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I161L(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATGGAAAAATGAGTGCTACA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	81	80					11																	4936413		2201	4298	6499	4892989	SO:0001583	missense	81282			AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.481A>C	11.37:g.4936413T>G	ENSP00000322593:p.Ile161Leu		4892989	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	T	3.379	-0.126870	0.06795	.	.	ENSG00000176893	ENST00000322013	T	0.00020	9.05	5.58	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.270733	0.26507	N	0.023985	T	0.00144	0.0004	N	0.16790	0.44	0.09310	N	1	D	0.71674	0.998	D	0.80764	0.994	T	0.47724	-0.9095	10	0.02654	T	1	.	5.542	0.17043	0.0:0.1468:0.1492:0.704	.	161	Q8NGK0	O51G2_HUMAN	L	161	ENSP00000322593:I161L	ENSP00000322593:I161L	I	-	1	0	OR51G2	4892989	0.000000	0.05858	0.922000	0.36590	0.112000	0.19704	-0.302000	0.08221	1.110000	0.41699	0.533000	0.62120	ATT		0.463	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		G	4936413	T	G	4936413	3	3	61	1	0	0	0	0	1	0	0	0	11130	1464	51	4	467	4	OR51G2	11	4936413	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32909	4936413	130070103	7128	15113										
OR51G2	81282	broad.mit.edu	37	chr11	4936570	4936570	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaggagaagcagtgaatGaaaaagagctgagcaaagca	14	4	0	5	rs184375832		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:4936570G>T	ENST00000322013.3	-	1	352	c.324C>A	c.(322-324)ttC>ttA	p.F108L	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F108L(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGCAGTGAATGAAAAAGAGCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											95	87	90					11																	4936570		2201	4298	6499	4893146	SO:0001583	missense	81282			AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.324C>A	11.37:g.4936570G>T	ENSP00000322593:p.Phe108Leu		4893146	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582124	0.65992	.	.	ENSG00000176893	ENST00000322013	T	0.00625	6.14	5.58	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000061	T	0.01940	0.0061	L	0.53617	1.68	0.33606	D	0.602926	D	0.76494	0.999	D	0.75484	0.986	T	0.49661	-0.8916	10	0.52906	T	0.07	.	7.4005	0.26960	0.2998:0.0:0.7002:0.0	.	108	Q8NGK0	O51G2_HUMAN	L	108	ENSP00000322593:F108L	ENSP00000322593:F108L	F	-	3	2	OR51G2	4893146	0.031000	0.19500	1.000000	0.80357	0.990000	0.78478	0.393000	0.20817	1.597000	0.50072	0.655000	0.94253	TTC		0.507	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		T	4936570	G	T	4936570	3	4	61	1	0	0	0	0	1	0	0	0	11130	1281	45	2	624	2	OR51G2	11	4936570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157	4936570	130069946	7129	15114										
MMP26	56547	broad.mit.edu	37	chr11	5011871	5011871	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagccatccgcagtgaaaGacagtatatataatgcagtt	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5011871G>T	ENST00000380390.1	+	4	580	c.364G>T	c.(364-366)Gac>Tac	p.D122Y	MMP26_ENST00000300762.1_Missense_Mutation_p.D122Y			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	122					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D122Y(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	CGCAGTGAAAGACAGTATATA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											112	105	107					11																	5011871		2201	4298	6499	4968447	SO:0001583	missense	56547			AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.364G>T	11.37:g.5011871G>T	ENSP00000369753:p.Asp122Tyr		4968447	Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	37	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.296998	0.23650	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.54279	0.58;0.58	4.12	-3.64	0.04515	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	1.528680	0.04322	N	0.350974	T	0.54838	0.1883	L	0.46157	1.445	0.09310	N	1	D	0.55385	0.971	P	0.55161	0.77	T	0.53920	-0.8370	10	0.39692	T	0.17	1.7436	6.8296	0.23902	0.4586:0.1236:0.4178:0.0	.	122	Q9NRE1	MMP26_HUMAN	Y	122	ENSP00000369753:D122Y;ENSP00000300762:D122Y	ENSP00000300762:D122Y	D	+	1	0	MMP26	4968447	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.041000	0.13927	-0.712000	0.04988	-0.965000	0.02619	GAC		0.408	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		T	5011871	G	T	5011871	3	4	61	1	0	0	0	0	1	0	0	0	9693	942	33	2	374	2	MMP26	11	5011871	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75301	5011871	129994645	7130	15115										
MMP26	56547	broad.mit.edu	37	chr11	5013288	5013288	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccataatgtaccccacttaCtggtatcacgaccctagaac	5	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5013288C>A	ENST00000380390.1	+	6	906	c.690C>A	c.(688-690)taC>taA	p.Y230*	MMP26_ENST00000300762.1_Nonsense_Mutation_p.Y230*			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	230					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y230*(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	ACCCCACTTACTGGTATCACG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											83	76	78					11																	5013288		2201	4298	6499	4969864	SO:0001587	stop_gained	56547			AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.690C>A	11.37:g.5013288C>A	ENSP00000369753:p.Tyr230*		4969864	Q3MJ78|Q9GZS2|Q9NR87	Nonsense_Mutation	SNP	ENST00000380390.1	37	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	C	9.182	1.023809	0.19433	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	.	.	.	3.79	-1.18	0.09617	.	3.647060	0.01066	N	0.004728	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.6542	8.903	0.35505	0.0:0.5752:0.0:0.4248	.	.	.	.	X	230	.	ENSP00000300762:Y230X	Y	+	3	2	MMP26	4969864	0.357000	0.24938	0.002000	0.10522	0.099000	0.18886	0.174000	0.16743	-0.459000	0.07013	-0.291000	0.09656	TAC		0.473	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		A	5013288	C	A	5013288	4	1	61	1	0	0	0	0	0	1	0	0	9693	576	20	2	708	2	MMP26	11	5013288	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1417	5013288	129993228	7131	15116										
OR51L1	119682	broad.mit.edu	37	chr11	5020890	5020890	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgttctgattcttaatacTgtgctggatattgcatctcg	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5020890T>A	ENST00000321543.1	+	1	678	c.678T>A	c.(676-678)acT>acA	p.T226T		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T226T(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCTTAATACTGTGCTGGATA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	11											204	181	189					11																	5020890		2201	4298	6499	4977466	SO:0001819	synonymous_variant	119682			AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.678T>A	11.37:g.5020890T>A			4977466	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																				0.418	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		A	5020890	T	A	5020890	2	1	61	1	0	0	0	0	0	0	0	1	11133	1567	55	5		5	OR51L1	11	5020890	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7602	5020890	129985626	7132	15117										
OR52A5	390054	broad.mit.edu	37	chr11	5153356	5153356	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagagatgactgtagttcGatagtgtttcagacagcatt	12	5	1	4	rs139667116	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5153356G>A	ENST00000307388.1	-	1	516	c.517C>T	c.(517-519)Cga>Tga	p.R173*		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	173					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R173*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		ACTGTAGTTCGATAGTGTTTC	0.448													G|||	2	0.000399361	8e-04	0	5008	,	,		21860	0		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	11						G	stop/ARG	0,4402		0,0,2201	122	117	118		517	-1.4	0	11	dbSNP_134	118	2,8594	2.2+/-6.3	0,2,4296	yes	stop-gained	OR52A5	NM_001005160.2		0,2,6497	AA,AG,GG		0.0233,0.0,0.0154		173/317	5153356	2,12996	2201	4298	6499	5109932	SO:0001587	stop_gained	390054			BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"GPCR / Class A : Olfactory receptors"	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.517C>T	11.37:g.5153356G>A	ENSP00000303469:p.Arg173*		5109932		Nonsense_Mutation	SNP	ENST00000307388.1	37	CCDS31373.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.359996	0.24598	0.0	2.33E-4	ENSG00000171944	ENST00000307388	.	.	.	5.22	-1.4	0.08968	.	1.505630	0.04679	N	0.412078	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.7493	0.18138	0.0703:0.1031:0.2667:0.5599	.	.	.	.	X	173	.	ENSP00000303469:R173X	R	-	1	2	OR52A5	5109932	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.700000	0.01905	-0.310000	0.08766	0.655000	0.94253	CGA		0.448	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160		A	5153356	G	A	5153356	4	1	61	1	0	0	0	0	0	1	0	0	11141	1066	37	1	436	1	OR52A5	11	5153356	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132466	5153356	129853160	7133	15118										
OR51B4	79339	broad.mit.edu	37	chr11	5322877	5322877	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatggccagtgaatgaatGaaggattgggtgaaacaggc	14	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5322877G>T	ENST00000380224.1	-	1	349	c.300C>A	c.(298-300)ttC>ttA	p.F100L	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	100					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F100L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGAATGAATGAAGGATTGGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											152	138	143					11																	5322877		2201	4297	6498	5279453	SO:0001583	missense	79339			BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.300C>A	11.37:g.5322877G>T	ENSP00000369573:p.Phe100Leu		5279453	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	G	0.781	-0.762157	0.02996	.	.	ENSG00000183251	ENST00000380224	T	0.05382	3.45	0.893	-1.32	0.09201	GPCR, rhodopsin-like superfamily (1);	0.241431	0.29335	N	0.012454	T	0.07052	0.0179	M	0.72576	2.205	0.22531	N	0.999016	B	0.14012	0.009	B	0.15052	0.012	T	0.25606	-1.0127	10	0.87932	D	0	.	3.9796	0.09489	0.5228:0.0:0.4772:0.0	.	100	Q9Y5P0	O51B4_HUMAN	L	100	ENSP00000369573:F100L	ENSP00000369573:F100L	F	-	3	2	OR51B4	5279453	0.696000	0.27757	0.183000	0.23137	0.001000	0.01503	-0.048000	0.11944	-0.562000	0.06086	-0.768000	0.03414	TTC		0.493	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		T	5322877	G	T	5322877	3	4	61	1	0	0	0	0	1	0	0	0	11121	1281	45	2	635	2	OR51B4	11	5322877	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	169521	5322877	129683639	7134	15119										
OR51B2	79345	broad.mit.edu	37	chr11	5345022	5345022	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcacgtgtgataacatgaGatttgcaatatgaaaatgaa	9	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5345022G>A	ENST00000328813.2	-	1	560	c.506C>T	c.(505-507)tCt>tTt	p.S169F	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S169F(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GATAACATGAGATTTGCAATA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											98	96	97					11																	5345022		2201	4297	6498	5301598	SO:0001583	missense	79345			AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"GPCR / Class A : Olfactory receptors"	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.506C>T	11.37:g.5345022G>A	ENSP00000327540:p.Ser169Phe		5301598	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.529712	0.27387	.	.	ENSG00000184881	ENST00000328813	T	0.38887	1.11	4.28	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.200626	0.24633	U	0.036871	T	0.63651	0.2529	M	0.90369	3.11	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57219	-0.7849	10	0.87932	D	0	.	3.1132	0.06365	0.0979:0.1734:0.5501:0.1786	.	169	Q9Y5P1	O51B2_HUMAN	F	169	ENSP00000327540:S169F	ENSP00000327540:S169F	S	-	2	0	OR51B2	5301598	0.001000	0.12720	0.202000	0.23494	0.463000	0.32649	1.079000	0.30766	1.051000	0.40369	0.644000	0.83932	TCT		0.388	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180		A	5345022	G	A	5345022	3	1	61	1	0	0	0	0	1	0	0	0	11120	942	33	3	436	3	OR51B2	11	5345022	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22145	5345022	129661494	7135	15120										
OR51B6	390058	broad.mit.edu	37	chr11	5373588	5373588	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacttccttttcccaccttTtatgaacccatttatctata	1	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5373588T>G	ENST00000380219.1	+	1	851	c.851T>G	c.(850-852)tTt>tGt	p.F284C	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	284					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F284C(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCCCACCTTTTATGAACCCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											139	133	135					11																	5373588		2201	4297	6498	5330164	SO:0001583	missense	390058				CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"GPCR / Class A : Olfactory receptors"	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.851T>G	11.37:g.5373588T>G	ENSP00000369568:p.Phe284Cys		5330164		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.861593	0.51482	.	.	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.33438	1.41	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.275080	0.26450	N	0.024315	T	0.41650	0.1168	L	0.38175	1.15	0.09310	N	1	D	0.71674	0.998	P	0.60345	0.873	T	0.28396	-1.0045	10	0.87932	D	0	.	13.8994	0.63794	0.0:0.0:0.0:1.0	.	284	Q9H340	O51B6_HUMAN	C	283;284	ENSP00000369568:F284C	ENSP00000369568:F284C	F	+	2	0	OR51B6	5330164	0.000000	0.05858	0.997000	0.53966	0.897000	0.52465	0.485000	0.22324	2.148000	0.66965	0.528000	0.53228	TTT		0.388	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		G	5373588	T	G	5373588	3	3	61	1	0	0	0	0	1	0	0	0	11123	1841	64	4	853	4	OR51B6	11	5373588	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	28566	5373588	129632928	7136	15121										
OR51M1	390059	broad.mit.edu	37	chr11	5411032	5411032	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgatgtcctttgaccgccTtgtggccatctgccaccctc	8	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5411032T>G	ENST00000328611.3	+	1	426	c.404T>G	c.(403-405)cTt>cGt	p.L135R	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	135			L -> F (in dbSNP:rs1498468). {ECO:0000269|PubMed:11121057, ECO:0000269|PubMed:14983052}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L135R(1)		NS(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTGACCGCCTTGTGGCCATC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											219	209	212					11																	5411032		2060	4241	6301	5367608	SO:0001583	missense	390059			BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"GPCR / Class A : Olfactory receptors"	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.404T>G	11.37:g.5411032T>G	ENSP00000333196:p.Leu135Arg		5367608	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	37	CCDS53596.1	.	.	.	.	.	.	.	.	.	.	T	9.360	1.067808	0.20067	.	.	ENSG00000184698	ENST00000328611	T	0.38401	1.14	5.06	1.1	0.20463	.	0.231155	0.22128	U	0.064226	T	0.57755	0.2075	H	0.94925	3.6	0.20403	N	0.999905	.	.	.	.	.	.	T	0.52859	-0.8519	8	0.87932	D	0	.	6.3473	0.21357	0.2186:0.0:0.2475:0.5339	.	.	.	.	R	135	ENSP00000333196:L135R	ENSP00000333196:L135R	L	+	2	0	OR51M1	5367608	0.008000	0.16893	0.994000	0.49952	0.306000	0.27790	0.096000	0.15147	0.369000	0.24510	0.533000	0.62120	CTT		0.512	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756		G	5411032	T	G	5411032	3	3	61	1	0	0	0	0	1	0	0	0	11134	1609	56	4	406	4	OR51M1	11	5411032	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37444	5411032	129595484	7137	15122										
OR51I1	390063	broad.mit.edu	37	chr11	5461969	5461969	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggtgaatcatggagacaGcaattatgggcacataaaag	12	6	1	2	rs373951420		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5461969G>A	ENST00000380211.1	-	1	775	c.776C>T	c.(775-777)gCt>gTt	p.A259V	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	259					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A259V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGGAGACAGCAATTATGGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	VAL/ALA	0,4402		0,0,2201	132	114	120		776	1.1	0.8	11		120	1,8593	1.2+/-3.3	0,1,4296	no	missense	OR51I1	NM_001005288.2	64	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	259/315	5461969	1,12995	2201	4297	6498	5418545	SO:0001583	missense	390063			BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"GPCR / Class A : Olfactory receptors"	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.776C>T	11.37:g.5461969G>A	ENSP00000369559:p.Ala259Val		5418545	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475858	0.63737	0.0	1.16E-4	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.00039	8.85	5.47	1.13	0.20643	GPCR, rhodopsin-like superfamily (1);	0.365985	0.23487	N	0.047652	T	0.00109	0.0003	N	0.02539	-0.55	0.09310	N	1	P	0.51351	0.944	P	0.55785	0.784	T	0.57808	-0.7747	10	0.66056	D	0.02	.	8.9425	0.35738	0.1158:0.5664:0.3177:0.0	.	259	Q9H343	O51I1_HUMAN	V	256;259	ENSP00000369559:A259V	ENSP00000439622:A256V	A	-	2	0	OR51I1	5418545	0.000000	0.05858	0.807000	0.32361	0.976000	0.68499	-0.947000	0.03901	0.641000	0.30601	0.551000	0.68910	GCT		0.498	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		A	5461969	G	A	5461969	3	1	61	1	0	0	0	0	1	0	0	0	11131	971	34	3	172	3	OR51I1	11	5461969	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50937	5461969	129544547	7138	15123										
OR51I1	390063	broad.mit.edu	37	chr11	5462341	5462341	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgtgagtgagcacagtgAcatagcgtaatggataacaa	13	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5462341A>G	ENST00000380211.1	-	1	403	c.404T>C	c.(403-405)gTc>gCc	p.V135A	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	135					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V135A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGCACAGTGACATAGCGTAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											151	116	128					11																	5462341		2201	4297	6498	5418917	SO:0001583	missense	390063			BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"GPCR / Class A : Olfactory receptors"	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.404T>C	11.37:g.5462341A>G	ENSP00000369559:p.Val135Ala		5418917	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	A	0.092	-1.166186	0.01673	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.18960	2.18	5.74	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.519505	0.17552	N	0.170149	T	0.04227	0.0117	N	0.00098	-2.145	0.21527	N	0.999658	B	0.02656	0.0	B	0.01281	0.0	T	0.24440	-1.0160	10	0.02654	T	1	.	13.6054	0.62044	0.0756:0.0:0.9244:0.0	.	135	Q9H343	O51I1_HUMAN	A	120;132;135	ENSP00000369559:V135A	ENSP00000348350:V120A	V	-	2	0	OR51I1	5418917	0.105000	0.21958	0.995000	0.50966	0.265000	0.26407	2.601000	0.46249	1.454000	0.47793	-0.288000	0.09946	GTC		0.473	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		G	5462341	A	G	5462341	3	3	61	1	0	0	0	0	1	0	0	0	11131	275	10	4	544	4	OR51I1	11	5462341	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	372	5462341	129544175	7139	15124										
OR51I2	390064	broad.mit.edu	37	chr11	5474755	5474755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactcaccctgcattcttcCtcctgactggtatccctggt	6	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5474755C>A	ENST00000341449.2	+	1	118	c.37C>A	c.(37-39)Ctc>Atc	p.L13I	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	13					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L13I(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCATTCTTCCTCCTGACTGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											134	113	120					11																	5474755		2201	4297	6498	5431331	SO:0001583	missense	390064			BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.37C>A	11.37:g.5474755C>A	ENSP00000341987:p.Leu13Ile		5431331	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	C	9.532	1.111197	0.20714	.	.	ENSG00000187918	ENST00000341449	T	0.00540	6.7	5.58	3.71	0.42584	.	0.104093	0.43260	D	0.000589	T	0.00271	0.0008	N	0.02685	-0.53	0.25597	N	0.986639	B	0.10296	0.003	B	0.08055	0.003	T	0.41945	-0.9480	10	0.26408	T	0.33	.	7.4559	0.27266	0.297:0.6267:0.0:0.0763	.	13	Q9H344	O51I2_HUMAN	I	13	ENSP00000341987:L13I	ENSP00000341987:L13I	L	+	1	0	OR51I2	5431331	0.000000	0.05858	1.000000	0.80357	0.920000	0.55202	-0.956000	0.03865	0.900000	0.36469	0.655000	0.94253	CTC		0.498	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		A	5474755	C	A	5474755	3	1	61	1	0	0	0	0	1	0	0	0	11132	681	24	2	39	2	OR51I2	11	5474755	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12414	5474755	129531761	7140	15125										
OR52D1	390066	broad.mit.edu	37	chr11	5510073	5510073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagcactggttggaaatgCtgccctcatcctggtcattg	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5510073C>T	ENST00000322641.5	+	1	159	c.137C>T	c.(136-138)gCt>gTt	p.A46V	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	46					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A46V(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTTGGAAATGCTGCCCTCATC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											284	221	242					11																	5510073		2201	4297	6498	5466649	SO:0001583	missense	390066			BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"GPCR / Class A : Olfactory receptors"	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.137C>T	11.37:g.5510073C>T	ENSP00000326232:p.Ala46Val		5466649	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	C	2.432	-0.330523	0.05314	.	.	ENSG00000181609	ENST00000322641	T	0.00949	5.51	5.37	2.33	0.28932	GPCR, rhodopsin-like superfamily (1);	0.786081	0.11516	N	0.556195	T	0.00496	0.0016	N	0.02539	-0.55	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.46527	-0.9185	10	0.23302	T	0.38	.	3.9807	0.09493	0.0:0.4821:0.1696:0.3483	.	46	Q9H346	O52D1_HUMAN	V	46	ENSP00000326232:A46V	ENSP00000326232:A46V	A	+	2	0	OR52D1	5466649	0.000000	0.05858	0.716000	0.30569	0.467000	0.32768	-0.845000	0.04340	0.848000	0.35191	0.650000	0.86243	GCT		0.522	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		T	5510073	C	T	5510073	3	4	61	1	0	0	0	0	1	0	0	0	11145	797	28	3	139	3	OR52D1	11	5510073	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35318	5510073	129496443	7141	15126										
OR52D1	390066	broad.mit.edu	37	chr11	5510308	5510308	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttgccatggcctttgaTaggtatgtggctatctgtaa	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5510308T>A	ENST00000322641.5	+	1	394	c.372T>A	c.(370-372)gaT>gaA	p.D124E	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	124					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D124E(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGCCTTTGATAGGTATGTGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											182	168	173					11																	5510308		2201	4297	6498	5466884	SO:0001583	missense	390066			BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"GPCR / Class A : Olfactory receptors"	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.372T>A	11.37:g.5510308T>A	ENSP00000326232:p.Asp124Glu		5466884	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629167	0.67015	.	.	ENSG00000181609	ENST00000322641	T	0.51817	0.69	5.58	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.81498	0.4835	H	0.99909	4.93	0.32876	D	0.509845	D	0.89917	1.0	D	0.83275	0.996	D	0.87315	0.2314	10	0.87932	D	0	.	9.3884	0.38359	0.0:0.1497:0.0:0.8503	.	124	Q9H346	O52D1_HUMAN	E	124	ENSP00000326232:D124E	ENSP00000326232:D124E	D	+	3	2	OR52D1	5466884	0.388000	0.25197	0.924000	0.36721	0.883000	0.51084	-0.153000	0.10144	1.143000	0.42306	0.533000	0.62120	GAT		0.458	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		A	5510308	T	A	5510308	3	1	61	1	0	0	0	0	1	0	0	0	11145	1403	49	5	374	5	OR52D1	11	5510308	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	235	5510308	129496208	7142	15127										
UBQLN3	50613	broad.mit.edu	37	chr11	5528988	5528988	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatttgtactaactaaatCttgcagcatatggagaaagg	11	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5528988C>A	ENST00000311659.4	-	2	1948	c.1801G>T	c.(1801-1803)Gat>Tat	p.D601Y	HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380252.1_5'Flank|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	601								p.D601Y(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTAACTAAATCTTGCAGCATA	0.542																																					Ovarian(72;684 1260 12332 41642 52180)											1	Substitution - Missense(1)	large_intestine(1)	11											60	65	64					11																	5528988		2201	4297	6498	5485564	SO:0001583	missense	50613			AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1801G>T	11.37:g.5528988C>A	ENSP00000347997:p.Asp601Tyr		5485564	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	0.679	-0.798958	0.02841	.	.	ENSG00000175520	ENST00000311659	T	0.41758	0.99	5.02	0.997	0.19851	UBA-like (1);	0.635267	0.13901	N	0.354881	T	0.19604	0.0471	N	0.22421	0.69	0.09310	N	1	P	0.42785	0.79	B	0.28916	0.096	T	0.13469	-1.0508	10	0.62326	D	0.03	-0.3937	4.1391	0.10184	0.323:0.5032:0.0:0.1738	.	601	Q9H347	UBQL3_HUMAN	Y	601	ENSP00000347997:D601Y	ENSP00000347997:D601Y	D	-	1	0	UBQLN3	5485564	0.396000	0.25262	0.001000	0.08648	0.141000	0.21300	1.527000	0.35975	0.096000	0.17463	0.655000	0.94253	GAT		0.542	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		A	5528988	C	A	5528988	3	1	61	1	0	0	0	0	1	0	0	0	16938	913	32	2	170	2	UBQLN3	11	5528988	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18680	5528988	129477528	7143	15128										
UBQLN3	50613	broad.mit.edu	37	chr11	5529738	5529738	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctagggactgggggttctCgtgtaattgctggagatagt	15	6	1	1	rs201503283		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5529738C>T	ENST00000311659.4	-	2	1198	c.1051G>A	c.(1051-1053)Gag>Aag	p.E351K	HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380252.1_5'Flank|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	351								p.E351K(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGGGGTTCTCGTGTAATTGC	0.493													C|||	1	0.000199681	0	0	5008	,	,		20438	0		0.001	False		,,,				2504	0				Ovarian(72;684 1260 12332 41642 52180)											1	Substitution - Missense(1)	large_intestine(1)	11											113	114	113					11																	5529738		2201	4297	6498	5486314	SO:0001583	missense	50613			AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1051G>A	11.37:g.5529738C>T	ENSP00000347997:p.Glu351Lys		5486314	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.284	0.420577	0.11928	.	.	ENSG00000175520	ENST00000311659	T	0.41400	1.0	5.39	4.47	0.54385	.	0.358239	0.20243	N	0.096253	T	0.38639	0.1048	M	0.80982	2.52	0.09310	N	1	P	0.41710	0.76	B	0.19666	0.026	T	0.50608	-0.8808	10	0.87932	D	0	-7.9073	12.0289	0.53386	0.0:0.8268:0.1732:0.0	.	351	Q9H347	UBQL3_HUMAN	K	351	ENSP00000347997:E351K	ENSP00000347997:E351K	E	-	1	0	UBQLN3	5486314	0.008000	0.16893	0.010000	0.14722	0.002000	0.02628	2.228000	0.42981	1.489000	0.48450	0.655000	0.94253	GAG		0.493	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		T	5529738	C	T	5529738	3	4	61	1	0	0	0	0	1	0	0	0	16938	893	31	1	920	1	UBQLN3	11	5529738	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	750	5529738	129476778	7144	15129										
OR52H1	390067	broad.mit.edu	37	chr11	5566564	5566564	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaagaacatgggttcatGaagactatgctccaccacaa	8	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5566564G>T	ENST00000322653.4	-	1	215	c.190C>A	c.(190-192)Cat>Aat	p.H64N	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H64N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGGGTTCATGAAGACTATGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											90	75	80					11																	5566564		2201	4297	6498	5523140	SO:0001583	missense	390067			AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"GPCR / Class A : Olfactory receptors"	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.190C>A	11.37:g.5566564G>T	ENSP00000326259:p.His64Asn		5523140	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765579	0.69878	.	.	ENSG00000181616	ENST00000322653	T	0.15952	2.38	5.4	5.4	0.78164	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	T	0.46014	0.1371	H	0.94345	3.525	0.38717	D	0.953359	D	0.56287	0.975	P	0.51453	0.67	T	0.66085	-0.6011	10	0.87932	D	0	.	17.7507	0.88432	0.0:0.0:1.0:0.0	.	64	Q8NGJ2	O52H1_HUMAN	N	64	ENSP00000326259:H64N	ENSP00000326259:H64N	H	-	1	0	OR52H1	5523140	1.000000	0.71417	0.992000	0.48379	0.796000	0.44982	6.421000	0.73353	2.539000	0.85634	0.650000	0.86243	CAT		0.468	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		T	5566564	G	T	5566564	3	4	61	1	0	0	0	0	1	0	0	0	11150	1290	45	2	775	2	OR52H1	11	5566564	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36826	5566564	129439952	7145	15130										
TRIM6	117854	broad.mit.edu	37	chr11	5632525	5632525	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttgtccatattttaatCcttgcaactgtgtaattcct	4	10	1	0	rs143334533		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5632525C>A	ENST00000278302.5	+	8	1560	c.1420C>A	c.(1420-1422)Cct>Act	p.P474T	TRIM6_ENST00000380107.1_Missense_Mutation_p.P448T|TRIM6_ENST00000481603.1_3'UTR|TRIM6_ENST00000507320.1_Missense_Mutation_p.P299T|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000515022.1_Missense_Mutation_p.P299T|TRIM6-TRIM34_ENST00000354852.5_Intron|HBG2_ENST00000380259.2_Intron|TRIM6_ENST00000380097.3_Missense_Mutation_p.P502T|TRIM6_ENST00000445329.1_Missense_Mutation_p.P299T|TRIM6_ENST00000506134.1_Missense_Mutation_p.P299T	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	474	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.P502T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|prostate(2)|stomach(1)	22		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)		ATATTTTAATCCTTGCAACTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	THR/PRO,,THR/PRO,THR/PRO,THR/PRO	1,4401	2.1+/-5.4	0,1,2200	123	123	123		1504,,895,895,1420	4.1	1	11	dbSNP_134	123	0,8594		0,0,4297	yes	missense,intron,missense,missense,missense	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	38,,38,38,38	0,1,6497	AA,AC,CC		0.0,0.0227,0.0077	,,,,	502/517,,299/314,299/314,474/489	5632525	1,12995	2201	4297	6498	5589101	SO:0001583	missense	117854			AF220030	CCDS31389.1, CCDS31390.1, CCDS55738.1	11p15	2013-01-09	2011-01-25		ENSG00000121236	ENSG00000121236		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16277	protein-coding gene	gene with protein product		607564	"tripartite motif-containing 6"			11331580	Standard	NM_058166		Approved	RNF89		Q9C030	OTTHUMG00000150029	ENST00000278302.5:c.1420C>A	11.37:g.5632525C>A	ENSP00000278302:p.Pro474Thr		5589101	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Missense_Mutation	SNP	ENST00000278302.5	37	CCDS31390.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.519927	0.64634	2.27E-4	0.0	ENSG00000121236	ENST00000278302;ENST00000507320;ENST00000380107;ENST00000380097;ENST00000445329;ENST00000396867;ENST00000515022;ENST00000506134	T;T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	4.07	4.07	0.47477	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.81221	0.4777	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.81531	-0.0890	9	0.42905	T	0.14	.	14.5622	0.68148	0.0:1.0:0.0:0.0	.	448;502;474	E9PFM0;Q9C030-2;Q9C030	.;.;TRIM6_HUMAN	T	474;299;448;502;299;381;299;299	ENSP00000278302:P474T;ENSP00000427704:P299T;ENSP00000369450:P448T;ENSP00000369440:P502T;ENSP00000399215:P299T;ENSP00000421802:P299T;ENSP00000421079:P299T	ENSP00000278302:P474T	P	+	1	0	TRIM6	5589101	0.968000	0.33430	1.000000	0.80357	0.880000	0.50808	1.241000	0.32743	2.573000	0.86826	0.491000	0.48974	CCT		0.418	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818		A	5632525	C	A	5632525	3	1	61	1	0	0	0	0	1	0	0	0	16573	855	30	2	1534	2	TRIM6	11	5632525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65961	5632525	129373991	7146	15131										
TRIM22	10346	broad.mit.edu	37	chr11	5717856	5717856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaggtcaccaaacattcCgcataaacgaggtggtcaag	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5717856C>T	ENST00000379965.3	+	2	671	c.394C>T	c.(394-396)Cgc>Tgc	p.R132C	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	132					defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R132C(1)		kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		CCAAACATTCCGCATAAACGA	0.448																																					GBM(104;491 2336 5222)											1	Substitution - Missense(1)	large_intestine(1)	11											71	74	73					11																	5717856		2033	4223	6256	5674432	SO:0001583	missense	10346			X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16379	protein-coding gene	gene with protein product		606559	"tripartite motif-containing 22"			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.394C>T	11.37:g.5717856C>T	ENSP00000369299:p.Arg132Cys		5674432	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.247016	0.39697	.	.	ENSG00000132274	ENST00000379965;ENST00000425490;ENST00000454828;ENST00000414641	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	4.67	1.7	0.24286	Zinc finger, B-box (2);	.	.	.	.	T	0.33411	0.0862	N	0.03608	-0.345	0.09310	N	1	B;P;P	0.52170	0.017;0.951;0.917	B;P;P	0.48901	0.017;0.594;0.56	T	0.15607	-1.0431	9	0.87932	D	0	.	6.1154	0.20124	0.1516:0.6902:0.0:0.1582	.	132;132;132	C9JWC5;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	C	132	ENSP00000369299:R132C;ENSP00000400417:R132C;ENSP00000393250:R132C;ENSP00000396849:R132C	ENSP00000369299:R132C	R	+	1	0	TRIM22	5674432	0.000000	0.05858	0.001000	0.08648	0.196000	0.23810	1.027000	0.30115	0.157000	0.19338	0.461000	0.40582	CGC		0.448	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		T	5717856	C	T	5717856	3	4	61	1	0	0	0	0	1	0	0	0	16536	652	23	1	396	1	TRIM22	11	5717856	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85331	5717856	129288660	7147	15132										
OR52E8	390079	broad.mit.edu	37	chr11	5878108	5878108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaatataatatgtatataCtgtgggatattatggccaaa	8	4	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5878108C>A	ENST00000537935.1	-	1	856	c.825G>T	c.(823-825)caG>caT	p.Q275H	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q275H(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TATGTATATACTGTGGGATAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	115	110					11																	5878108		2145	4296	6441	5834684	SO:0001583	missense	390079			BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"GPCR / Class A : Olfactory receptors"	15217	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily E, member 8 pseudogene"				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.825G>T	11.37:g.5878108C>A	ENSP00000444054:p.Gln275His		5834684	B9EH38	Missense_Mutation	SNP	ENST00000537935.1	37	CCDS31400.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.908860	0.00508	.	.	ENSG00000183269	ENST00000537935	T	0.00123	8.7	4.12	-7.15	0.01521	GPCR, rhodopsin-like superfamily (1);	1.115960	0.06930	N	0.810906	T	0.00039	0.0001	N	0.01473	-0.845	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.06232	-1.0838	10	0.11182	T	0.66	.	5.1731	0.15120	0.1042:0.4617:0.1056:0.3285	.	275	Q6IFG1	O52E8_HUMAN	H	275	ENSP00000444054:Q275H	ENSP00000444054:Q275H	Q	-	3	2	OR52E8	5834684	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-7.197000	0.00042	-1.112000	0.02984	-1.328000	0.01277	CAG		0.408	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168		A	5878108	C	A	5878108	3	1	61	1	0	0	0	0	1	0	0	0	11149	564	20	2	130	2	OR52E8	11	5878108	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	160252	5878108	129128408	7148	15133										
OR52E4	390081	broad.mit.edu	37	chr11	5905728	5905728	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttcctggccatgttgtCtatgattgatctgggtctgt	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5905728C>A	ENST00000316987.2	+	1	228	c.206C>A	c.(205-207)tCt>tAt	p.S69Y		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S69Y(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCCATGTTGTCTATGATTGAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											186	158	168					11																	5905728		2201	4296	6497	5862304	SO:0001583	missense	390081			AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.206C>A	11.37:g.5905728C>A	ENSP00000321426:p.Ser69Tyr		5862304	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223604	0.58668	.	.	ENSG00000180974	ENST00000316987	T	0.12361	2.69	5.04	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.145220	0.32028	N	0.006694	T	0.44456	0.1294	H	0.96269	3.795	0.32262	N	0.570061	D	0.59357	0.985	D	0.63033	0.91	T	0.64884	-0.6302	10	0.87932	D	0	.	8.5746	0.33590	0.0:0.8248:0.0:0.1752	.	69	Q8NGH9	O52E4_HUMAN	Y	69	ENSP00000321426:S69Y	ENSP00000321426:S69Y	S	+	2	0	OR52E4	5862304	0.002000	0.14202	0.957000	0.39632	0.994000	0.84299	1.226000	0.32563	1.345000	0.45676	0.643000	0.83706	TCT		0.458	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		A	5905728	C	A	5905728	3	1	61	1	0	0	0	0	1	0	0	0	11147	913	32	2	208	2	OR52E4	11	5905728	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27620	5905728	129100788	7149	15134										
OR52E4	390081	broad.mit.edu	37	chr11	5906119	5906119	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccattaagatcaacataatCtatgggctcatggtgatttc	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5906119C>A	ENST00000316987.2	+	1	619	c.597C>A	c.(595-597)atC>atA	p.I199I		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I199I(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCAACATAATCTATGGGCTCA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	11											259	227	237					11																	5906119		2201	4296	6497	5862695	SO:0001819	synonymous_variant	390081			AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.597C>A	11.37:g.5906119C>A			5862695	Q6IFG0	Silent	SNP	ENST00000316987.2	37	CCDS31401.1																																																																																				0.463	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		A	5906119	C	A	5906119	2	1	61	1	0	0	0	0	0	0	0	1	11147	903	32	2		2	OR52E4	11	5906119	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	391	5906119	129100397	7150	15135										
OR52E4	390081	broad.mit.edu	37	chr11	5906298	5906298	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacacaccagcatttttttCttttatgacacatcgttttg	4	9	1	1	rs201423767		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5906298C>A	ENST00000316987.2	+	1	798	c.776C>A	c.(775-777)tCt>tAt	p.S259Y		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S259Y(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCATTTTTTTCTTTTATGACA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											207	189	195					11																	5906298		2201	4296	6497	5862874	SO:0001583	missense	390081			AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.776C>A	11.37:g.5906298C>A	ENSP00000321426:p.Ser259Tyr		5862874	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279990	0.59758	.	.	ENSG00000180974	ENST00000316987	T	0.00115	8.71	5.1	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.142319	0.32655	N	0.005815	T	0.00784	0.0026	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.54833	-0.8234	10	0.87932	D	0	.	16.0581	0.80820	0.0:1.0:0.0:0.0	.	259	Q8NGH9	O52E4_HUMAN	Y	259	ENSP00000321426:S259Y	ENSP00000321426:S259Y	S	+	2	0	OR52E4	5862874	0.001000	0.12720	1.000000	0.80357	0.958000	0.62258	1.414000	0.34736	2.660000	0.90430	0.643000	0.83706	TCT		0.428	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		A	5906298	C	A	5906298	3	1	61	1	0	0	0	0	1	0	0	0	11147	913	32	2	778	2	OR52E4	11	5906298	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179	5906298	129100218	7151	15136										
OR56A3	390083	broad.mit.edu	37	chr11	5968959	5968959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcctatgatcgttatgTagccatctgccacccactga	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:5968959T>C	ENST00000329564.6	+	1	390	c.383T>C	c.(382-384)gTa>gCa	p.V128A	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V128A(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GATCGTTATGTAGCCATCTGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											178	169	172					11																	5968959		2201	4296	6497	5925535	SO:0001583	missense	390083				CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478		"GPCR / Class A : Olfactory receptors"	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P			Standard	NM_001003443		Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.383T>C	11.37:g.5968959T>C	ENSP00000331572:p.Val128Ala		5925535	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	37	CCDS41614.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652758	0.29336	.	.	ENSG00000184478	ENST00000329564	T	0.20738	2.05	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.363846	0.14725	U	0.302113	T	0.36276	0.0961	M	0.82193	2.58	0.09310	N	0.999993	P	0.39903	0.694	B	0.43018	0.405	T	0.34925	-0.9809	10	0.87932	D	0	-4.8374	13.9713	0.64242	0.0:0.0:0.0:1.0	.	128	Q8NH54	O56A3_HUMAN	A	128	ENSP00000331572:V128A	ENSP00000331572:V128A	V	+	2	0	OR56A3	5925535	0.542000	0.26426	0.048000	0.18961	0.033000	0.12548	4.395000	0.59678	2.170000	0.68504	0.529000	0.55759	GTA		0.453	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443		C	5968959	T	C	5968959	3	2	61	1	0	0	0	0	1	0	0	0	11165	1638	57	4	385	4	OR56A3	11	5968959	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	62661	5968959	129037557	7152	15137										
OR52L1	338751	broad.mit.edu	37	chr11	6008035	6008035	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggcagtgcaatccagtgCtggctttcctctaaacctgg	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6008035C>T	ENST00000332249.4	-	1	180	c.126G>A	c.(124-126)caG>caA	p.Q42Q		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q27Q(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAATCCAGTGCTGGCTTTCCT	0.493																																					Melanoma(121;653 1666 10547 22796 51255)											2	Substitution - coding silent(2)	large_intestine(2)	11											57	57	57					11																	6008035		1921	4140	6061	5964611	SO:0001819	synonymous_variant	338751			AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.126G>A	11.37:g.6008035C>T			5964611	B2RPA6|Q6IFK9	Silent	SNP	ENST00000332249.4	37	CCDS44529.1																																																																																				0.493	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		T	6008035	C	T	6008035	2	4	61	1	0	0	0	0	0	0	0	1	11156	796	28	3		3	OR52L1	11	6008035	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39076	6008035	128998481	7153	15138										
OR56A4	120793	broad.mit.edu	37	chr11	6023558	6023558	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacaactttcaatataaaaGaataggagataacaataagg	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6023558G>T	ENST00000330728.4	-	1	866	c.821C>A	c.(820-822)tCt>tAt	p.S274Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S274Y(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAATATAAAAGAATAGGAGAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											36	36	36					11																	6023558		2201	4296	6497	5980134	SO:0001583	missense	120793			BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"GPCR / Class A : Olfactory receptors"	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.821C>A	11.37:g.6023558G>T	ENSP00000328215:p.Ser274Tyr		5980134	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.553596	0.00918	.	.	ENSG00000183389	ENST00000330728	T	0.00152	8.66	3.72	1.76	0.24704	GPCR, rhodopsin-like superfamily (1);	0.518300	0.13961	U	0.350853	T	0.00210	0.0006	M	0.81497	2.545	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.32955	-0.9887	10	0.62326	D	0.03	.	8.8874	0.35411	0.0:0.1637:0.6667:0.1696	.	222	Q8NGH8	O56A4_HUMAN	Y	274	ENSP00000328215:S274Y	ENSP00000328215:S274Y	S	-	2	0	OR56A4	5980134	0.000000	0.05858	0.076000	0.20297	0.082000	0.17680	-0.143000	0.10296	0.327000	0.23409	-0.127000	0.14921	TCT		0.463	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179		T	6023558	G	T	6023558	3	4	61	1	0	0	0	0	1	0	0	0	11166	942	33	2	278	2	OR56A4	11	6023558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15523	6023558	128982958	7154	15139										
OR56A1	120796	broad.mit.edu	37	chr11	6048164	6048164	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagcagtatggtgctgaaGaaaagaatgaggatgaagtg	14	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6048164G>T	ENST00000316650.5	-	1	807	c.771C>A	c.(769-771)ttC>ttA	p.F257L		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F257L(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGTGCTGAAGAAAAGAATGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											77	75	76					11																	6048164		2201	4296	6497	6004740	SO:0001583	missense	120796			AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"GPCR / Class A : Olfactory receptors"	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.771C>A	11.37:g.6048164G>T	ENSP00000321246:p.Phe257Leu		6004740	B2RNI2|Q6IFL0	Missense_Mutation	SNP	ENST00000316650.5	37	CCDS31405.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890836	0.52014	.	.	ENSG00000180934	ENST00000316650	T	0.00013	9.23	4.27	1.33	0.21861	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000417	T	0.00144	0.0004	N	0.25144	0.715	0.26246	N	0.978793	D	0.89917	1.0	D	0.91635	0.999	T	0.50775	-0.8788	10	0.22706	T	0.39	.	4.774	0.13169	0.2763:0.2438:0.4799:0.0	.	257	Q8NGH5	O56A1_HUMAN	L	257	ENSP00000321246:F257L	ENSP00000321246:F257L	F	-	3	2	OR56A1	6004740	0.237000	0.23815	0.987000	0.45799	0.807000	0.45602	0.465000	0.22004	0.184000	0.20083	-0.150000	0.13652	TTC		0.502	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		T	6048164	G	T	6048164	3	4	61	1	0	0	0	0	1	0	0	0	11164	933	33	2	189	2	OR56A1	11	6048164	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24606	6048164	128958352	7155	15140										
CNGA4	1262	broad.mit.edu	37	chr11	6261486	6261486	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccgcctcttcgaggccttCgaccgcacagagacccgcac	9	20	1	1	rs201074130	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6261486C>T	ENST00000379936.2	+	4	577	c.462C>T	c.(460-462)ttC>ttT	p.F154F	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	154					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.F154F(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCGAGGCCTTCGACCGCACAG	0.587													C|||	2	0.000399361	0	0.0014	5008	,	,		18214	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		0,4402		0,0,2201	74	81	79		462	-6.3	0.9	11		79	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous	CNGA4	NM_001037329.3		0,3,6494	TT,TC,CC		0.0349,0.0,0.0231		154/576	6261486	3,12991	2201	4296	6497	6218062	SO:0001819	synonymous_variant	1262			AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.462C>T	11.37:g.6261486C>T			6218062		Silent	SNP	ENST00000379936.2	37	CCDS31408.1																																																																																				0.587	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		T	6261486	C	T	6261486	2	4	61	1	0	0	0	0	0	0	0	1	3605	883	31	1		1	CNGA4	11	6261486	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213322	6261486	128745030	7156	15141										
APBB1	322	broad.mit.edu	37	chr11	6422619	6422619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagtggtccagggagagtCcatttaccaagcagcgggca	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6422619C>A	ENST00000609360.1	-	11	1643	c.1544G>T	c.(1543-1545)gGa>gTa	p.G515V	APBB1_ENST00000389906.2_Missense_Mutation_p.G515V|APBB1_ENST00000299402.6_Missense_Mutation_p.G513V|APBB1_ENST00000608645.1_Missense_Mutation_p.G256V|APBB1_ENST00000530885.1_Missense_Mutation_p.G293V|APBB1_ENST00000529519.1_Missense_Mutation_p.G40V|APBB1_ENST00000608394.1_Missense_Mutation_p.G256V|APBB1_ENST00000609331.1_Missense_Mutation_p.G280V|APBB1_ENST00000608655.1_Missense_Mutation_p.G295V|APBB1_ENST00000311051.3_Missense_Mutation_p.G513V|APBB1_ENST00000608704.1_Missense_Mutation_p.G256V	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	515					apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.G513V(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		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)		CAGGGAGAGTCCATTTACCAA	0.552																																					GBM(147;1810 2556 5672 39622)											1	Substitution - Missense(1)	large_intestine(1)	11											75	68	71					11																	6422619		2201	4296	6497	6379195	SO:0001583	missense	322			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1544G>T	11.37:g.6422619C>A	ENSP00000477213:p.Gly515Val		6379195	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	C	19.80	3.895497	0.72639	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906;ENST00000539758;ENST00000536523;ENST00000544288;ENST00000530885	T;T;T;T	0.18016	2.49;2.49;2.5;2.24	4.94	4.94	0.65067	.	0.244366	0.33875	N	0.004472	T	0.32133	0.0819	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.994;0.968	D;P;P;P	0.91635	0.999;0.879;0.865;0.79	T	0.01626	-1.1309	10	0.28530	T	0.3	-7.7601	15.6382	0.76973	0.0:1.0:0.0:0.0	.	118;515;293;513	B7Z4M4;O00213;B7Z2Y0;O00213-2	.;APBB1_HUMAN;.;.	V	513;513;515;364;256;280;293	ENSP00000299402:G513V;ENSP00000311912:G513V;ENSP00000374556:G515V;ENSP00000433338:G293V	ENSP00000299402:G513V	G	-	2	0	APBB1	6379195	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.054000	0.57434	2.269000	0.75478	0.655000	0.94253	GGA		0.552	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		A	6422619	C	A	6422619	3	1	61	1	0	0	0	0	1	0	0	0	759	855	30	2	608	2	APBB1	11	6422619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161133	6422619	128583897	7157	15142										
TRIM3	10612	broad.mit.edu	37	chr11	6470405	6470405	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaggagccagagctgtcGaatacctggggaaggagtgc	17	7	0	1	rs370951694		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6470405G>T	ENST00000525074.1	-	12	2482	c.2088C>A	c.(2086-2088)ttC>ttA	p.F696L	TRIM3_ENST00000536344.1_Missense_Mutation_p.F577L|TRIM3_ENST00000359518.3_Missense_Mutation_p.F696L|TRIM3_ENST00000345851.3_Missense_Mutation_p.F696L|TRIM3_ENST00000537602.1_Missense_Mutation_p.F618L	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	696					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F696L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAGAGCTGTCGAATACCTGGG	0.562																																					Melanoma(6;5 510 1540 25169 29084)											1	Substitution - Missense(1)	large_intestine(1)	11											91	79	83					11																	6470405		2201	4296	6497	6426981	SO:0001583	missense	10612			AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.2088C>A	11.37:g.6470405G>T	ENSP00000433102:p.Phe696Leu		6426981	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	37	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.645872	0.47258	.	.	ENSG00000110171	ENST00000525074;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19	4.8	1.21	0.21127	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.81014	0.4735	M	0.72118	2.19	0.48452	D	0.999655	B;B	0.31256	0.139;0.316	B;P	0.48454	0.177;0.578	T	0.75593	-0.3264	10	0.46703	T	0.11	-16.8289	6.992	0.24761	0.725:0.0:0.275:0.0	.	577;696	F5H2Q8;O75382	.;TRIM3_HUMAN	L	696;696;685;618;696;577	ENSP00000433102:F696L;ENSP00000340797:F696L;ENSP00000441091:F618L;ENSP00000352508:F696L;ENSP00000445460:F577L	ENSP00000337094:F685L	F	-	3	2	TRIM3	6426981	0.980000	0.34600	0.999000	0.59377	0.997000	0.91878	0.320000	0.19540	0.160000	0.19432	0.563000	0.77884	TTC		0.562	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6470405	G	T	6470405	3	4	61	1	0	0	0	0	1	0	0	0	16544	1049	37	2	150	2	TRIM3	11	6470405	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47786	6470405	128536111	7158	15143										
DNHD1	144132	broad.mit.edu	37	chr11	6524034	6524034	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggccttccaaaagagcagCaccggcttttcacctgagac	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6524034C>A	ENST00000527990.2	+	2	798	c.798C>A	c.(796-798)agC>agA	p.S266R	DNHD1_ENST00000354685.3_Missense_Mutation_p.S266R|DNHD1_ENST00000254579.6_Missense_Mutation_p.S266R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	266					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.S266R(2)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AAAAGAGCAGCACCGGCTTTT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	11											104	87	92					11																	6524034		2201	4296	6497	6480610	SO:0001583	missense	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.798C>A	11.37:g.6524034C>A	ENSP00000436180:p.Ser266Arg		6480610	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.821254	0.32237	.	.	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.28069	1.63;2.6;1.63	5.64	-0.238	0.13055	.	0.496507	0.21739	N	0.069857	T	0.32496	0.0831	L	0.42245	1.32	0.09310	N	1	B;D	0.59357	0.139;0.985	B;P	0.55391	0.058;0.775	T	0.15809	-1.0424	10	0.62326	D	0.03	.	5.4677	0.16652	0.0:0.5381:0.1424:0.3195	.	266;266	Q96M86;Q96M86-4	DNHD1_HUMAN;.	R	266	ENSP00000254579:S266R;ENSP00000346716:S266R;ENSP00000436180:S266R	ENSP00000254579:S266R	S	+	3	2	DNHD1	6480610	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.206000	0.09398	-0.321000	0.08627	0.563000	0.77884	AGC		0.468	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6524034	C	A	6524034	3	1	61	1	0	0	0	0	1	0	0	0	4679	709	25	2	804	2	DNHD1	11	6524034	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53629	6524034	128482482	7159	15144										
DNHD1	144132	broad.mit.edu	37	chr11	6587953	6587953	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccgctggcaggacctaaaGatcagagccctagatacctg	10	13	1	3	rs372317431		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6587953G>T	ENST00000527990.2	+	33	11343	c.11343G>T	c.(11341-11343)aaG>aaT	p.K3781N	DNHD1_ENST00000254579.6_Missense_Mutation_p.K3781N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3781					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.K3781N(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGGACCTAAAGATCAGAGCCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											53	56	55					11																	6587953		2012	4188	6200	6544529	SO:0001583	missense	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.11343G>T	11.37:g.6587953G>T	ENSP00000436180:p.Lys3781Asn		6544529	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657456	0.29425	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.26223	1.75;1.75	4.52	-3.64	0.04515	.	0.694941	0.12509	N	0.462610	T	0.11836	0.0288	N	0.24115	0.695	0.09310	N	1	B;B;B	0.33694	0.421;0.421;0.421	B;B;B	0.27500	0.08;0.08;0.08	T	0.15292	-1.0442	10	0.37606	T	0.19	-3.3849	6.6029	0.22710	0.5544:0.2557:0.1899:0.0	.	2869;49;3781	B0I1S4;D3DQT9;Q96M86	.;.;DNHD1_HUMAN	N	3781;3781;49;49	ENSP00000254579:K3781N;ENSP00000436180:K3781N	ENSP00000254579:K3781N	K	+	3	2	DNHD1	6544529	0.000000	0.05858	0.000000	0.03702	0.489000	0.33432	-0.352000	0.07701	-0.604000	0.05760	0.655000	0.94253	AAG		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6587953	G	T	6587953	3	4	61	1	0	0	0	0	1	0	0	0	4679	933	33	2	11482	2	DNHD1	11	6587953	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63919	6587953	128418563	7160	15145										
DNHD1	144132	broad.mit.edu	37	chr11	6588357	6588357	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcagaacctgctgccacTtttctgtatgagcccagaga	9	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6588357T>G	ENST00000527990.2	+	34	11618	c.11618T>G	c.(11617-11619)cTt>cGt	p.L3873R	DNHD1_ENST00000254579.6_Missense_Mutation_p.L3873R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3873					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.L3873R(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTGCTGCCACTTTTCTGTATG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											92	93	92					11																	6588357		1964	4155	6119	6544933	SO:0001583	missense	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.11618T>G	11.37:g.6588357T>G	ENSP00000436180:p.Leu3873Arg		6544933	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	8.813	0.935635	0.18206	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.27402	1.67;1.67	4.78	-0.618	0.11576	.	0.915968	0.09099	N	0.848815	T	0.23014	0.0556	N	0.24115	0.695	0.09310	N	0.999991	P;P;P	0.40476	0.718;0.718;0.718	B;B;B	0.42422	0.387;0.293;0.293	T	0.25467	-1.0131	10	0.87932	D	0	0.1716	8.2719	0.31849	0.0:0.3746:0.0:0.6254	.	2961;141;3873	B0I1S4;D3DQT9;Q96M86	.;.;DNHD1_HUMAN	R	3873;3873;141;141	ENSP00000254579:L3873R;ENSP00000436180:L3873R	ENSP00000254579:L3873R	L	+	2	0	DNHD1	6544933	0.374000	0.25081	0.545000	0.28153	0.479000	0.33129	0.314000	0.19432	-0.273000	0.09246	0.459000	0.35465	CTT		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		G	6588357	T	G	6588357	3	3	61	1	0	0	0	0	1	0	0	0	4679	1609	56	4	11761	4	DNHD1	11	6588357	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	404	6588357	128418159	7161	15146										
DCHS1	8642	broad.mit.edu	37	chr11	6655082	6655082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggatatggtaggagagtCgcccatgggatccctggtca	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6655082C>T	ENST00000299441.3	-	4	2567	c.2156G>A	c.(2155-2157)cGa>cAa	p.R719Q	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	719	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R719Q(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTAGGAGAGTCGCCCATGGGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11											66	71	69					11																	6655082		2201	4296	6497	6611658	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2156G>A	11.37:g.6655082C>T	ENSP00000299441:p.Arg719Gln		6611658	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.009104	0.35415	.	.	ENSG00000166341	ENST00000299441	T	0.52526	0.66	4.64	3.68	0.42216	Cadherin (4);Cadherin-like (1);	0.398969	0.16571	N	0.208638	T	0.32255	0.0823	L	0.38649	1.16	0.38092	D	0.936996	B	0.16396	0.017	B	0.11329	0.006	T	0.12218	-1.0556	10	0.11794	T	0.64	.	8.2209	0.31541	0.0:0.7311:0.1737:0.0952	.	719	Q96JQ0	PCD16_HUMAN	Q	719	ENSP00000299441:R719Q	ENSP00000299441:R719Q	R	-	2	0	DCHS1	6611658	0.061000	0.20836	1.000000	0.80357	0.997000	0.91878	0.665000	0.25083	2.410000	0.81850	0.561000	0.74099	CGA		0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6655082	C	T	6655082	3	4	61	1	0	0	0	0	1	0	0	0	4293	884	31	1	7812	1	DCHS1	11	6655082	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66725	6655082	128351434	7162	15147										
OR6A2	8590	broad.mit.edu	37	chr11	6816052	6816052	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacctcttgattgcgcagGcagtaaatgatgggattgag	13	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6816052G>A	ENST00000332601.3	-	1	1076	c.888C>T	c.(886-888)tgC>tgT	p.C296C		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	296					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C296C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GATTGCGCAGGCAGTAAATGA	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	11											140	132	135					11																	6816052		2201	4296	6497	6772628	SO:0001819	synonymous_variant	8590			AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"GPCR / Class A : Olfactory receptors"	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.888C>T	11.37:g.6816052G>A			6772628	Q3MJC7|Q6IF35|Q9H206	Silent	SNP	ENST00000332601.3	37	CCDS7772.1																																																																																				0.483	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		A	6816052	G	A	6816052	2	1	61	1	0	0	0	0	0	0	0	1	11217	1195	42	3		3	OR6A2	11	6816052	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160970	6816052	128190464	7163	15148										
OR10A2	341276	broad.mit.edu	37	chr11	6891362	6891362	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagtcatcatgaaccaaaGgactcgtgccaaactggctg	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6891362G>T	ENST00000307322.4	+	1	439	c.377G>T	c.(376-378)aGg>aTg	p.R126M		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R126M(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ATGAACCAAAGGACTCGTGCC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											159	150	153					11																	6891362		2201	4296	6497	6847938	SO:0001583	missense	341276			BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.377G>T	11.37:g.6891362G>T	ENSP00000303862:p.Arg126Met		6847938	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	g	7.958	0.746335	0.15710	.	.	ENSG00000170790	ENST00000307322	T	0.01599	4.74	3.99	3.07	0.35406	GPCR, rhodopsin-like superfamily (1);	0.509728	0.19729	N	0.107382	T	0.04497	0.0123	M	0.72479	2.2	0.09310	N	1	P	0.36222	0.544	P	0.44477	0.451	T	0.08249	-1.0731	10	0.72032	D	0.01	.	9.4715	0.38844	0.1094:0.0:0.8906:0.0	.	126	Q9H208	O10A2_HUMAN	M	126	ENSP00000303862:R126M	ENSP00000303862:R126M	R	+	2	0	OR10A2	6847938	0.000000	0.05858	0.998000	0.56505	0.079000	0.17450	-0.847000	0.04331	2.222000	0.72286	0.650000	0.86243	AGG		0.532	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891362	G	T	6891362	3	4	61	1	0	0	0	0	1	0	0	0	10921	1000	35	2	379	2	OR10A2	11	6891362	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75310	6891362	128115154	7164	15149										
OR10A2	341276	broad.mit.edu	37	chr11	6891840	6891840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaaataacgaggtgaaGaatgccctcagcaggacggt	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6891840G>T	ENST00000307322.4	+	1	917	c.855G>T	c.(853-855)aaG>aaT	p.K285N		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K285N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACGAGGTGAAGAATGCCCTCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	100	101					11																	6891840		2201	4296	6497	6848416	SO:0001583	missense	341276			BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.855G>T	11.37:g.6891840G>T	ENSP00000303862:p.Lys285Asn		6848416	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	g	12.29	1.893894	0.33442	.	.	ENSG00000170790	ENST00000307322	T	0.40756	1.02	4.18	-1.12	0.09808	.	0.000000	0.64402	D	0.000008	T	0.55257	0.1909	M	0.70787	2.145	0.30214	N	0.797439	D	0.89917	1.0	D	0.77557	0.99	T	0.54860	-0.8230	10	0.62326	D	0.03	.	8.0966	0.30833	0.5882:0.0:0.4118:0.0	.	285	Q9H208	O10A2_HUMAN	N	285	ENSP00000303862:K285N	ENSP00000303862:K285N	K	+	3	2	OR10A2	6848416	0.001000	0.12720	0.997000	0.53966	0.347000	0.29111	0.159000	0.16442	-0.063000	0.13065	-0.141000	0.14075	AAG		0.453	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891840	G	T	6891840	3	4	61	1	0	0	0	0	1	0	0	0	10921	933	33	2	857	2	OR10A2	11	6891840	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	478	6891840	128114676	7165	15150										
OR10A4	283297	broad.mit.edu	37	chr11	6898764	6898764	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatctacagctcaaggaatAaagaagtgaaggctgcactg	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6898764A>G	ENST00000379829.2	+	1	909	c.886A>G	c.(886-888)Aaa>Gaa	p.K296E		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	296					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K296E(1)		kidney(1)|large_intestine(2)|liver(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTCAAGGAATAAAGAAGTGAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											105	104	105					11																	6898764		2201	4296	6497	6855340	SO:0001583	missense	283297			AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"GPCR / Class A : Olfactory receptors"	15130	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily A, member 4 pseudogene"	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.886A>G	11.37:g.6898764A>G	ENSP00000369157:p.Lys296Glu		6855340	B2RNP5|B9EH36|Q96R20	Missense_Mutation	SNP	ENST00000379829.2	37	CCDS7774.1	.	.	.	.	.	.	.	.	.	.	a	11.62	1.691562	0.30052	.	.	ENSG00000170782	ENST00000379829	T	0.44083	0.93	3.9	3.9	0.45041	.	0.292228	0.24742	N	0.035977	T	0.39886	0.1095	M	0.70787	2.145	0.09310	N	0.999998	B	0.06786	0.001	B	0.09377	0.004	T	0.40590	-0.9555	10	0.72032	D	0.01	.	7.5996	0.28069	0.7827:0.2173:0.0:0.0	.	296	Q9H209	O10A4_HUMAN	E	296	ENSP00000369157:K296E	ENSP00000369157:K296E	K	+	1	0	OR10A4	6855340	0.012000	0.17670	0.813000	0.32504	0.841000	0.47740	2.729000	0.47327	1.999000	0.58509	0.529000	0.55759	AAA		0.483	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186		G	6898764	A	G	6898764	3	3	61	1	0	0	0	0	1	0	0	0	10923	363	13	4	888	4	OR10A4	11	6898764	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6924	6898764	128107752	7166	15151										
OR2D3	120775	broad.mit.edu	37	chr11	6942290	6942290	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaatatcaatgggagaaGaaaaccaaacctttgtgtcc	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6942290G>T	ENST00000317834.3	+	1	86	c.58G>T	c.(58-60)Gaa>Taa	p.E20*		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E20*(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AATGGGAGAAGAAAACCAAAC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											86	88	87					11																	6942290		2201	4296	6497	6898866	SO:0001587	stop_gained	120775			BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"GPCR / Class A : Olfactory receptors"	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.58G>T	11.37:g.6942290G>T	ENSP00000320560:p.Glu20*		6898866	B2RP06|Q6IFG8|Q96R51	Nonsense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.459988	0.43736	.	.	ENSG00000178358	ENST00000317834	.	.	.	5.12	2.09	0.27110	.	1.278540	0.05581	N	0.572808	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	0.5306	7.0213	0.24916	0.3859:0.0:0.6141:0.0	.	.	.	.	X	20	.	ENSP00000320560:E20X	E	+	1	0	OR2D3	6898866	0.061000	0.20836	0.603000	0.28903	0.083000	0.17756	0.981000	0.29526	0.371000	0.24564	-0.141000	0.14075	GAA		0.398	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684		T	6942290	G	T	6942290	4	4	61	1	0	0	0	0	0	1	0	0	11026	943	33	2	60	2	OR2D3	11	6942290	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43526	6942290	128064226	7167	15152										
OR2D3	120775	broad.mit.edu	37	chr11	6942352	6942352	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaggacttgcagacccaGatcctgctatttatcctttt	6	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:6942352G>A	ENST00000317834.3	+	1	148	c.120G>A	c.(118-120)caG>caA	p.Q40Q		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q40Q(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGCAGACCCAGATCCTGCTAT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	11											105	105	105					11																	6942352		2201	4296	6497	6898928	SO:0001819	synonymous_variant	120775			BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"GPCR / Class A : Olfactory receptors"	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.120G>A	11.37:g.6942352G>A			6898928	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																				0.438	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684		A	6942352	G	A	6942352	2	1	61	1	0	0	0	0	0	0	0	1	11026	933	33	3		3	OR2D3	11	6942352	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	6942352	128064164	7168	15153										
NLRP14	338323	broad.mit.edu	37	chr11	7063733	7063733	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaattgcagagaaagataGaaaactgttggaacacttgt	11	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7063733G>T	ENST00000299481.4	+	4	822	c.476G>T	c.(475-477)aGa>aTa	p.R159I		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	159					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.R159I(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GAGAAAGATAGAAAACTGTTG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	11											83	89	87					11																	7063733		2201	4296	6497	7020309	SO:0001583	missense	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.476G>T	11.37:g.7063733G>T	ENSP00000299481:p.Arg159Ile		7020309	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.837926	0.32513	.	.	ENSG00000158077	ENST00000299481	D	0.81739	-1.53	4.25	-4.07	0.03975	.	2.193420	0.02245	N	0.066158	T	0.72415	0.3457	L	0.34521	1.04	0.09310	N	1	P	0.36438	0.553	B	0.38712	0.28	T	0.60642	-0.7223	10	0.23302	T	0.38	.	10.9995	0.47596	0.7339:0.0:0.2661:0.0	.	159	Q86W24	NAL14_HUMAN	I	159	ENSP00000299481:R159I	ENSP00000299481:R159I	R	+	2	0	NLRP14	7020309	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.925000	0.03992	-1.061000	0.03185	-0.145000	0.13849	AGA		0.433	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7063733	G	T	7063733	3	4	61	1	0	0	0	0	1	0	0	0	10507	942	33	2	486	2	NLRP14	11	7063733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121381	7063733	127942783	7169	15154										
NLRP14	338323	broad.mit.edu	37	chr11	7064821	7064821	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaagcacaagttataaaGacccccatttgacacagatg	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7064821G>T	ENST00000299481.4	+	4	1910	c.1564G>T	c.(1564-1566)Gac>Tac	p.D522Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	522			D -> Q (associated with spermatogenic failure; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.D522Y(1)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AAGTTATAAAGACCCCCATTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											75	78	77					11																	7064821		2201	4296	6497	7021397	SO:0001583	missense	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1564G>T	11.37:g.7064821G>T	ENSP00000299481:p.Asp522Tyr		7021397	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	6.531	0.466193	0.12402	.	.	ENSG00000158077	ENST00000299481	D	0.84442	-1.85	4.55	1.56	0.23342	.	0.380726	0.22703	N	0.056676	T	0.72708	0.3494	L	0.39245	1.2	0.09310	N	1	B	0.18310	0.027	B	0.13407	0.009	T	0.53429	-0.8440	10	0.18710	T	0.47	.	3.9529	0.09377	0.2016:0.0:0.6106:0.1878	.	522	Q86W24	NAL14_HUMAN	Y	522	ENSP00000299481:D522Y	ENSP00000299481:D522Y	D	+	1	0	NLRP14	7021397	0.001000	0.12720	0.002000	0.10522	0.029000	0.11900	0.805000	0.27112	0.240000	0.21263	-0.136000	0.14681	GAC		0.393	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7064821	G	T	7064821	3	4	61	1	0	0	0	0	1	0	0	0	10507	942	33	2	1574	2	NLRP14	11	7064821	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1088	7064821	127941695	7170	15155										
NLRP14	338323	broad.mit.edu	37	chr11	7067969	7067969	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaaatgaacacttgagaGaattggacctgtaccatagc	8	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7067969G>T	ENST00000299481.4	+	5	2375	c.2029G>T	c.(2029-2031)Gaa>Taa	p.E677*		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	677					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.E677*(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		ACACTTGAGAGAATTGGACCT	0.378																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											225	193	204					11																	7067969		2201	4296	6497	7024545	SO:0001587	stop_gained	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2029G>T	11.37:g.7067969G>T	ENSP00000299481:p.Glu677*		7024545	Q7RTR6	Nonsense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	39	7.574328	0.98368	.	.	ENSG00000158077	ENST00000299481	.	.	.	4.52	3.61	0.41365	.	0.149577	0.31323	N	0.007842	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	10.8792	0.46929	0.0:0.1903:0.8097:0.0	.	.	.	.	X	677	.	ENSP00000299481:E677X	E	+	1	0	NLRP14	7024545	1.000000	0.71417	0.391000	0.26233	0.307000	0.27823	1.718000	0.38001	1.275000	0.44379	-0.203000	0.12734	GAA		0.378	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7067969	G	T	7067969	4	4	61	1	0	0	0	0	0	1	0	0	10507	943	33	2	2043	2	NLRP14	11	7067969	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3148	7067969	127938547	7171	15156										
NLRP14	338323	broad.mit.edu	37	chr11	7079056	7079056	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaggccttaagacatccaAagtgttatctagagagactg	11	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7079056A>C	ENST00000299481.4	+	7	2786	c.2440A>C	c.(2440-2442)Aag>Cag	p.K814Q		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	814					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.K814Q(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AAGACATCCAAAGTGTTATCT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	11											223	198	207					11																	7079056		2201	4296	6497	7035632	SO:0001583	missense	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2440A>C	11.37:g.7079056A>C	ENSP00000299481:p.Lys814Gln		7035632	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	A	6.095	0.385818	0.11524	.	.	ENSG00000158077	ENST00000299481	T	0.52057	0.68	4.89	-3.38	0.04883	.	0.638092	0.13890	N	0.355641	T	0.17109	0.0411	N	0.12637	0.245	0.09310	N	1	B	0.23854	0.092	B	0.21360	0.034	T	0.26224	-1.0109	10	0.06625	T	0.88	.	1.9245	0.03314	0.3183:0.1532:0.3794:0.1491	.	814	Q86W24	NAL14_HUMAN	Q	814	ENSP00000299481:K814Q	ENSP00000299481:K814Q	K	+	1	0	NLRP14	7035632	0.001000	0.12720	0.056000	0.19401	0.905000	0.53344	-0.049000	0.11924	-0.204000	0.10235	-0.386000	0.06593	AAG		0.408	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		C	7079056	A	C	7079056	3	2	61	1	0	0	0	0	1	0	0	0	10507	15	1	4	2462	4	NLRP14	11	7079056	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11087	7079056	127927460	7172	15157										
NLRP14	338323	broad.mit.edu	37	chr11	7079555	7079555	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctggctgtgagtatctttCtttggctctcatcagcaata	10	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7079555C>A	ENST00000299481.4	+	8	2853	c.2507C>A	c.(2506-2508)tCt>tAt	p.S836Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	836					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.S836Y(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GAGTATCTTTCTTTGGCTCTC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	11											187	168	175					11																	7079555		2201	4296	6497	7036131	SO:0001583	missense	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2507C>A	11.37:g.7079555C>A	ENSP00000299481:p.Ser836Tyr		7036131	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514427	0.64522	.	.	ENSG00000158077	ENST00000299481	T	0.43294	0.95	3.85	3.85	0.44370	.	0.000000	0.38897	N	0.001538	T	0.64091	0.2567	M	0.82193	2.58	0.40303	D	0.978636	D	0.89917	1.0	D	0.81914	0.995	T	0.69355	-0.5167	10	0.56958	D	0.05	.	11.4723	0.50278	0.0:1.0:0.0:0.0	.	836	Q86W24	NAL14_HUMAN	Y	836	ENSP00000299481:S836Y	ENSP00000299481:S836Y	S	+	2	0	NLRP14	7036131	0.583000	0.26757	0.448000	0.26945	0.985000	0.73830	2.394000	0.44450	2.158000	0.67659	0.650000	0.86243	TCT		0.448	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		A	7079555	C	A	7079555	3	1	61	1	0	0	0	0	1	0	0	0	10507	913	32	2	2533	2	NLRP14	11	7079555	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	499	7079555	127926961	7173	15158										
NLRP14	338323	broad.mit.edu	37	chr11	7081260	7081260	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaagcttctgtgtgatgtCtttcggcatccaagctgtaa	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7081260C>A	ENST00000299481.4	+	9	3115	c.2769C>A	c.(2767-2769)gtC>gtA	p.V923V		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	923					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.V923V(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TGTGTGATGTCTTTCGGCATC	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	11											225	214	218					11																	7081260		2201	4295	6496	7037836	SO:0001819	synonymous_variant	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2769C>A	11.37:g.7081260C>A			7037836	Q7RTR6	Silent	SNP	ENST00000299481.4	37	CCDS7776.1																																																																																				0.423	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		A	7081260	C	A	7081260	2	1	61	1	0	0	0	0	0	0	0	1	10507	900	32	2		2	NLRP14	11	7081260	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1705	7081260	127925256	7174	15159										
RBMXL2	27288	broad.mit.edu	37	chr11	7110403	7110403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattgggggcctcaacctcGaaaccgacgagaaagccctc	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7110403G>A	ENST00000306904.5	+	1	239	c.52G>A	c.(52-54)Gaa>Aaa	p.E18K		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	18	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.E18K(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCTCAACCTCGAAACCGACGA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	11											40	43	42					11																	7110403		2201	4296	6497	7066979	SO:0001583	missense	27288			AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"RNA binding motif (RRM) containing"	17886	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G T"	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.52G>A	11.37:g.7110403G>A	ENSP00000304139:p.Glu18Lys		7066979	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.351853	0.41700	.	.	ENSG00000170748	ENST00000306904	D	0.93859	-3.3	2.39	2.39	0.29439	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	D	0.84848	0.5563	N	0.05510	-0.035	0.58432	D	0.999993	B	0.26672	0.156	B	0.33750	0.169	T	0.80346	-0.1421	10	0.30078	T	0.28	.	10.8937	0.47010	0.0:0.0:1.0:0.0	.	18	O75526	HNRGT_HUMAN	K	18	ENSP00000304139:E18K	ENSP00000304139:E18K	E	+	1	0	RBMXL2	7066979	1.000000	0.71417	0.843000	0.33291	0.877000	0.50540	8.872000	0.92352	1.624000	0.50355	0.455000	0.32223	GAA		0.607	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		A	7110403	G	A	7110403	3	1	61	1	0	0	0	0	1	0	0	0	13191	1059	37	1	54	1	RBMXL2	11	7110403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29143	7110403	127896113	7175	15160										
SYT9	143425	broad.mit.edu	37	chr11	7334765	7334765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcattggataatgatgacGggagacggagtaacagcaag	15	5	1	3	rs568579361		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7334765G>A	ENST00000318881.6	+	3	874	c.637G>A	c.(637-639)Ggg>Agg	p.G213R	SYT9_ENST00000396716.2_Missense_Mutation_p.G181R	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	213					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.G213R(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TAATGATGACGGGAGACGGAG	0.398													G|||	1	0.000199681	0	0	5008	,	,		19759	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											128	131	130					11																	7334765		2201	4296	6497	7291341	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.637G>A	11.37:g.7334765G>A	ENSP00000324419:p.Gly213Arg		7291341		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249359	0.80024	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.57107	0.42;0.47	5.85	5.85	0.93711	.	0.076993	0.56097	D	0.000031	T	0.62877	0.2464	M	0.67953	2.075	0.51482	D	0.999929	D	0.54397	0.966	P	0.50791	0.65	T	0.61053	-0.7140	10	0.41790	T	0.15	.	18.0311	0.89285	0.0:0.0:1.0:0.0	.	213	Q86SS6	SYT9_HUMAN	R	181;213	ENSP00000379944:G181R;ENSP00000324419:G213R	ENSP00000324419:G213R	G	+	1	0	SYT9	7291341	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.892000	0.87324	2.932000	0.99384	0.643000	0.83706	GGG		0.398	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		A	7334765	G	A	7334765	3	1	61	1	0	0	0	0	1	0	0	0	15520	1116	39	1	647	1	SYT9	11	7334765	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	224362	7334765	127671751	7176	15161										
SYT9	143425	broad.mit.edu	37	chr11	7334914	7334914	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagatccttatgtcaagatCtatttgcttcctgatcggaa	7	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7334914C>A	ENST00000318881.6	+	3	1023	c.786C>A	c.(784-786)atC>atA	p.I262I	SYT9_ENST00000396716.2_Silent_p.I230I	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	262	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.I262I(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ATGTCAAGATCTATTTGCTTC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	11											136	135	136					11																	7334914		2201	4296	6497	7291490	SO:0001819	synonymous_variant	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.786C>A	11.37:g.7334914C>A			7291490		Silent	SNP	ENST00000318881.6	37	CCDS7778.1																																																																																				0.413	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		A	7334914	C	A	7334914	2	1	61	1	0	0	0	0	0	0	0	1	15520	903	32	2		2	SYT9	11	7334914	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149	7334914	127671602	7177	15162										
SYT9	143425	broad.mit.edu	37	chr11	7334975	7334975	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacagaaagaccctgaacCctgtgtttgatgaagtgttt	9	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7334975C>A	ENST00000318881.6	+	3	1084	c.847C>A	c.(847-849)Cct>Act	p.P283T	SYT9_ENST00000396716.2_Missense_Mutation_p.P251T	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	283	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.P283T(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		GACCCTGAACCCTGTGTTTGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											205	204	205					11																	7334975		2201	4296	6497	7291551	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.847C>A	11.37:g.7334975C>A	ENSP00000324419:p.Pro283Thr		7291551		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559913	0.86335	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	D;D	0.91295	-2.82;-2.82	6.17	6.17	0.99709	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000002	D	0.97433	0.9160	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98198	1.0466	9	.	.	.	.	18.3732	0.90420	0.0:1.0:0.0:0.0	.	283	Q86SS6	SYT9_HUMAN	T	251;283	ENSP00000379944:P251T;ENSP00000324419:P283T	.	P	+	1	0	SYT9	7291551	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CCT		0.428	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		A	7334975	C	A	7334975	3	1	61	1	0	0	0	0	1	0	0	0	15520	623	22	2	857	2	SYT9	11	7334975	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61	7334975	127671541	7178	15163										
SYT9	143425	broad.mit.edu	37	chr11	7439352	7439352	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccatagcagtcatggacTatgaccggtgagatacctgg	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7439352T>G	ENST00000318881.6	+	5	1567	c.1330T>G	c.(1330-1332)Tat>Gat	p.Y444D		NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	444	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.Y444H(1)|p.Y444D(1)		NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		AGTCATGGACTATGACCGGTG	0.502																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	11											141	122	129					11																	7439352		2201	4296	6497	7395928	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1330T>G	11.37:g.7439352T>G	ENSP00000324419:p.Tyr444Asp		7395928		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.552989	0.86127	.	.	ENSG00000170743	ENST00000318881	T	0.68025	-0.3	5.85	5.85	0.93711	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.53938	D	0.000060	T	0.76884	0.4050	L	0.46741	1.465	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78783	-0.2069	10	0.72032	D	0.01	.	14.1896	0.65630	0.0:0.0:0.0:1.0	.	444	Q86SS6	SYT9_HUMAN	D	444	ENSP00000324419:Y444D	ENSP00000324419:Y444D	Y	+	1	0	SYT9	7395928	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.698000	0.84413	2.222000	0.72286	0.533000	0.62120	TAT		0.502	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		G	7439352	T	G	7439352	3	3	61	1	0	0	0	0	1	0	0	0	15520	1522	53	4	1348	4	SYT9	11	7439352	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	104377	7439352	127567164	7179	15164										
PPFIBP2	8495	broad.mit.edu	37	chr11	7631633	7631633	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagcagagagagcaggagGagaagcagagaaaagcagag	18	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7631633G>T	ENST00000299492.4	+	6	986	c.598G>T	c.(598-600)Gag>Tag	p.E200*	PPFIBP2_ENST00000530181.1_Nonsense_Mutation_p.E57*|PPFIBP2_ENST00000533792.1_Nonsense_Mutation_p.E42*|PPFIBP2_ENST00000528883.1_Nonsense_Mutation_p.E88*	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	200					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.E200*(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGAGCAGGAGGAGAAGCAGAG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											258	250	252					11																	7631633		2201	4296	6497	7588209	SO:0001587	stop_gained	8495			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.598G>T	11.37:g.7631633G>T	ENSP00000299492:p.Glu200*		7588209	B7Z433|E9PK77|O75337|Q8WW26	Nonsense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	G	37	6.288627	0.97444	.	.	ENSG00000166387	ENST00000299492;ENST00000529575;ENST00000533792;ENST00000525597;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181	.	.	.	5.79	5.79	0.91817	.	0.071509	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-24.1382	17.5252	0.87798	0.0:0.0:1.0:0.0	.	.	.	.	X	200;42;42;42;42;123;88;57	.	ENSP00000299492:E200X	E	+	1	0	PPFIBP2	7588209	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	6.187000	0.72039	2.746000	0.94184	0.655000	0.94253	GAG		0.512	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		T	7631633	G	T	7631633	4	4	61	1	0	0	0	0	0	1	0	0	12345	1175	41	2	616	2	PPFIBP2	11	7631633	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192281	7631633	127374883	7180	15165										
PPFIBP2	8495	broad.mit.edu	37	chr11	7672896	7672896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccttcttagatcctggagCcacgcttcactggggacacc	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7672896C>T	ENST00000299492.4	+	23	2645	c.2257C>T	c.(2257-2259)Cca>Tca	p.P753S	PPFIBP2_ENST00000530181.1_Missense_Mutation_p.P610S|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.P595S|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.P641S	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	753	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.P753S(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GATCCTGGAGCCACGCTTCAC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	90	93					11																	7672896		2201	4296	6497	7629472	SO:0001583	missense	8495			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2257C>T	11.37:g.7672896C>T	ENSP00000299492:p.Pro753Ser		7629472	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	18.49	3.634829	0.67130	.	.	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98	5.77	3.9	0.45041	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (1);Sterile alpha motif, type 2 (1);	0.078575	0.53938	N	0.000046	D	0.89539	0.6744	L	0.60067	1.865	0.80722	D	1	D;P;D;D;D;D	0.89917	1.0;0.921;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.97110	1.0;0.701;1.0;0.999;0.999;1.0	D	0.88841	0.3312	10	0.59425	D	0.04	-4.9389	10.655	0.45669	0.0:0.8438:0.0:0.1562	.	641;641;676;595;610;753	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	S	753;94;595;676;641;610	ENSP00000299492:P753S;ENSP00000436498:P595S;ENSP00000435469:P641S;ENSP00000437321:P610S	ENSP00000299492:P753S	P	+	1	0	PPFIBP2	7629472	1.000000	0.71417	0.998000	0.56505	0.588000	0.36517	4.041000	0.57339	0.895000	0.36342	0.655000	0.94253	CCA		0.577	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		T	7672896	C	T	7672896	3	4	61	1	0	0	0	0	1	0	0	0	12345	739	26	3	2343	3	PPFIBP2	11	7672896	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41263	7672896	127333620	7181	15166										
CYB5R2	51700	broad.mit.edu	37	chr11	7690472	7690472	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcgtccccttggccctcGaaaaaagatggtctccccga	9	15	1	1	rs141969366		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7690472G>A	ENST00000533558.1	-	5	908	c.352C>T	c.(352-354)Cga>Tga	p.R118*	CYB5R2_ENST00000524790.1_Nonsense_Mutation_p.R118*|CYB5R2_ENST00000528585.1_5'UTR|CYB5R2_ENST00000299498.6_Nonsense_Mutation_p.R118*|CYB5R2_ENST00000299497.9_Nonsense_Mutation_p.R118*			Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase 2	118	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				oxidation-reduction process (GO:0055114)|sterol biosynthetic process (GO:0016126)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)	p.R118*(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTTGGCCCTCGAAAAAAGATG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	11						G	stop/ARG	1,4401	2.1+/-5.4	0,1,2200	147	140	142		352	5.4	1	11	dbSNP_134	142	0,8592		0,0,4296	no	stop-gained	CYB5R2	NM_016229.3		0,1,6496	AA,AG,GG		0.0,0.0227,0.0077		118/277	7690472	1,12993	2201	4296	6497	7647048	SO:0001587	stop_gained	51700			AF169802	CCDS7780.1	11p15.4	2014-08-12			ENSG00000166394	ENSG00000166394	1.6.2.2		24376	protein-coding gene	gene with protein product		608342				10611283	Standard	XM_005252973		Approved		uc001mfm.3	Q6BCY4	OTTHUMG00000165665	ENST00000533558.1:c.352C>T	11.37:g.7690472G>A	ENSP00000437041:p.Arg118*		7647048	Q9BVA3|Q9UF68|Q9UHJ0	Nonsense_Mutation	SNP	ENST00000533558.1	37	CCDS7780.1	.	.	.	.	.	.	.	.	.	.	G	34	5.312807	0.95655	2.27E-4	0.0	ENSG00000166394	ENST00000524790;ENST00000299498;ENST00000533558;ENST00000299497;ENST00000531096;ENST00000527542;ENST00000524608	.	.	.	5.37	5.37	0.77165	.	0.055448	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.8108	16.6555	0.85227	0.0:0.0:1.0:0.0	.	.	.	.	X	118;118;118;118;118;118;178	.	ENSP00000299497:R118X	R	-	1	2	CYB5R2	7647048	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.810000	0.38932	2.793000	0.96121	0.563000	0.77884	CGA		0.473	CYB5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385679.1	NM_016229		A	7690472	G	A	7690472	4	1	61	1	0	0	0	0	0	1	0	0	4133	1066	37	1	498	1	CYB5R2	11	7690472	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17576	7690472	127316044	7182	15167										
OVCH2	341277	broad.mit.edu	37	chr11	7716871	7716871	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattatctgtggcatcagaGacgaatttcagccttagaga	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7716871G>T	ENST00000533663.1	-	0	0				OVCH2_ENST00000454689.1_RNA|OVCH2_ENST00000534193.2_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V404V(1)		cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		TGGCATCAGAGACGAATTTCA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	11											62	57	58					11																	7716871		1821	4068	5889	7673447			341277			BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"ovochymase 2"			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7716871G>T			7673447		Silent	SNP	ENST00000533663.1	37																																																																																					0.458	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185		T	7716871	G	T	7716871	1	4	61	0	1	0	0	0	0	0	0	0	11355	929	33	2		2	OVCH2	11	7716871	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26399	7716871	127289645	7183	15168										
OR10A6	390093	broad.mit.edu	37	chr11	7949470	7949470	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccatagaatagggtcacaGatgtgaggtgagcggcacag	15	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7949470G>T	ENST00000309838.2	-	1	739	c.740C>A	c.(739-741)tCt>tAt	p.S247Y		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S247Y(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TAGGGTCACAGATGTGAGGTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											128	115	119					11																	7949470		2201	4296	6497	7906046	SO:0001583	missense	390093			AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"GPCR / Class A : Olfactory receptors"	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.740C>A	11.37:g.7949470G>T	ENSP00000312470:p.Ser247Tyr		7906046	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.050582	0.55218	.	.	ENSG00000175393	ENST00000309838	T	0.00123	8.7	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.378221	0.19507	N	0.112613	T	0.00384	0.0012	L	0.61036	1.89	0.24646	N	0.993542	D	0.89917	1.0	D	0.91635	0.999	T	0.54443	-0.8293	10	0.87932	D	0	.	10.7212	0.46042	0.0:0.1935:0.8065:0.0	.	247	Q8NH74	O10A6_HUMAN	Y	247	ENSP00000312470:S247Y	ENSP00000312470:S247Y	S	-	2	0	OR10A6	7906046	0.015000	0.18098	0.999000	0.59377	0.982000	0.71751	1.928000	0.40104	2.452000	0.82932	0.655000	0.94253	TCT		0.453	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		T	7949470	G	T	7949470	3	4	61	1	0	0	0	0	1	0	0	0	10925	942	33	2	207	2	OR10A6	11	7949470	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232599	7949470	127057046	7184	15169										
OR10A6	390093	broad.mit.edu	37	chr11	7949552	7949552	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggatggcaaacagaactcGaatgtaagacaagagtatca	10	7	1	3	rs267603211		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7949552G>A	ENST00000309838.2	-	1	657	c.658C>T	c.(658-660)Cga>Tga	p.R220*		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R220*(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AACAGAACTCGAATGTAAGAC	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											89	78	81					11																	7949552		2201	4296	6497	7906128	SO:0001587	stop_gained	390093			AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"GPCR / Class A : Olfactory receptors"	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.658C>T	11.37:g.7949552G>A	ENSP00000312470:p.Arg220*		7906128	Q6IF59	Nonsense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	.	.	.	.	.	.	.	.	.	.	G	8.394	0.840452	0.16891	.	.	ENSG00000175393	ENST00000309838	.	.	.	4.43	0.33	0.15929	.	0.503989	0.14983	N	0.287139	.	.	.	.	.	.	0.53688	D	0.999978	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	2.6865	0.05109	0.2689:0.0:0.3631:0.368	.	.	.	.	X	220	.	ENSP00000312470:R220X	R	-	1	2	OR10A6	7906128	0.000000	0.05858	0.023000	0.16930	0.034000	0.12701	-0.226000	0.09139	0.203000	0.20529	-0.182000	0.12963	CGA		0.433	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		A	7949552	G	A	7949552	4	1	61	1	0	0	0	0	0	1	0	0	10925	1066	37	1	289	1	OR10A6	11	7949552	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82	7949552	127056964	7185	15170										
OR10A6	390093	broad.mit.edu	37	chr11	7949878	7949878	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctcccagaagaaaacatTcagccccaccaaaaagaagg	7	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7949878T>G	ENST00000309838.2	-	1	331	c.332A>C	c.(331-333)gAa>gCa	p.E111A		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E111A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGAAAACATTCAGCCCCACC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											79	82	81					11																	7949878		2201	4296	6497	7906454	SO:0001583	missense	390093			AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"GPCR / Class A : Olfactory receptors"	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.332A>C	11.37:g.7949878T>G	ENSP00000312470:p.Glu111Ala		7906454	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.095570	0.56075	.	.	ENSG00000175393	ENST00000309838	T	0.02177	4.41	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000439	T	0.18173	0.0436	H	0.95539	3.685	0.25634	N	0.986274	D	0.76494	0.999	D	0.81914	0.995	T	0.16188	-1.0411	10	0.87932	D	0	.	11.9092	0.52729	0.0:0.0:0.0:1.0	.	111	Q8NH74	O10A6_HUMAN	A	111	ENSP00000312470:E111A	ENSP00000312470:E111A	E	-	2	0	OR10A6	7906454	0.983000	0.35010	0.998000	0.56505	0.937000	0.57800	3.041000	0.49807	1.983000	0.57843	0.533000	0.62120	GAA		0.388	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		G	7949878	T	G	7949878	3	3	61	1	0	0	0	0	1	0	0	0	10925	1783	62	4	615	4	OR10A6	11	7949878	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	326	7949878	127056638	7186	15171										
OR10A3	26496	broad.mit.edu	37	chr11	7960755	7960755	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtcccaccaaaaagaaGgatgaaatacatctgtgcaa	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7960755G>T	ENST00000360759.3	-	1	386	c.313C>A	c.(313-315)Ctt>Att	p.L105I		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	105					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L105I(1)		endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCAAAAAGAAGGATGAAATAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											100	92	94					11																	7960755		2201	4296	6497	7917331	SO:0001583	missense	26496			BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.313C>A	11.37:g.7960755G>T	ENSP00000353988:p.Leu105Ile		7917331	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	37	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.583540	0.46006	.	.	ENSG00000170683	ENST00000360759	T	0.01347	4.99	4.95	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.207048	0.23551	N	0.046980	T	0.01730	0.0055	L	0.37630	1.12	0.09310	N	1	P	0.43973	0.823	P	0.44732	0.459	T	0.52396	-0.8581	10	0.33940	T	0.23	.	6.4332	0.21809	0.0958:0.1861:0.718:0.0	.	105	P58181	O10A3_HUMAN	I	105	ENSP00000353988:L105I	ENSP00000353988:L105I	L	-	1	0	OR10A3	7917331	0.000000	0.05858	1.000000	0.80357	0.964000	0.63967	-0.211000	0.09332	2.742000	0.94016	0.650000	0.86243	CTT		0.438	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		T	7960755	G	T	7960755	3	4	61	1	0	0	0	0	1	0	0	0	10922	1000	35	2	634	2	OR10A3	11	7960755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10877	7960755	127045761	7187	15172										
NLRP10	338322	broad.mit.edu	37	chr11	7981498	7981498	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtcctgttgtgcttcataGattccatctgttctttaaaa	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7981498G>T	ENST00000328600.2	-	2	1822	c.1661C>A	c.(1660-1662)tCt>tAt	p.S554Y		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	554					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)	p.S554Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GTGCTTCATAGATTCCATCTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	64	64					11																	7981498		2201	4296	6497	7938074	SO:0001583	missense	338322			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1661C>A	11.37:g.7981498G>T	ENSP00000327763:p.Ser554Tyr		7938074	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.252084	0.39797	.	.	ENSG00000182261	ENST00000328600	D	0.88818	-2.43	3.91	2.96	0.34315	.	0.497976	0.15194	N	0.275384	D	0.87601	0.6218	N	0.24115	0.695	0.09310	N	1	D	0.61697	0.99	P	0.59703	0.862	T	0.78542	-0.2164	10	0.56958	D	0.05	.	9.8762	0.41205	0.0:0.2099:0.7901:0.0	.	554	Q86W26	NAL10_HUMAN	Y	554	ENSP00000327763:S554Y	ENSP00000327763:S554Y	S	-	2	0	NLRP10	7938074	0.001000	0.12720	0.001000	0.08648	0.116000	0.19942	0.581000	0.23819	0.914000	0.36822	0.563000	0.77884	TCT		0.388	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		T	7981498	G	T	7981498	3	4	61	1	0	0	0	0	1	0	0	0	10503	942	33	2	310	2	NLRP10	11	7981498	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20743	7981498	127025018	7188	15173										
NLRP10	338322	broad.mit.edu	37	chr11	7981569	7981569	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctgaagcagaacttgagCtccaagttcgagaagctgtc	10	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7981569C>T	ENST00000328600.2	-	2	1751	c.1590G>A	c.(1588-1590)gaG>gaA	p.E530E		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	530					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)	p.E530E(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGAACTTGAGCTCCAAGTTCG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	11											73	70	71					11																	7981569		2201	4296	6497	7938145	SO:0001819	synonymous_variant	338322			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1590G>A	11.37:g.7981569C>T			7938145	Q2M3C4|Q6JGT0	Silent	SNP	ENST00000328600.2	37	CCDS7784.1																																																																																				0.453	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		T	7981569	C	T	7981569	2	4	61	1	0	0	0	0	0	0	0	1	10503	796	28	3		3	NLRP10	11	7981569	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71	7981569	127024947	7189	15174										
NLRP10	338322	broad.mit.edu	37	chr11	7982546	7982546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttctttgcagcttacatAaaagacataatcaaaccggc	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:7982546A>G	ENST00000328600.2	-	2	774	c.613T>C	c.(613-615)Tat>Cat	p.Y205H		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	205	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)	p.Y205H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGCTTACATAAAAGACATAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											46	48	47					11																	7982546		2201	4296	6497	7939122	SO:0001583	missense	338322			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.613T>C	11.37:g.7982546A>G	ENSP00000327763:p.Tyr205His		7939122	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109283	0.37242	.	.	ENSG00000182261	ENST00000328600	D	0.81739	-1.53	5.25	4.13	0.48395	NACHT nucleoside triphosphatase (1);	0.211078	0.24115	N	0.041414	D	0.86502	0.5948	M	0.67953	2.075	0.24587	N	0.993849	D	0.89917	1.0	D	0.87578	0.998	T	0.77627	-0.2517	10	0.87932	D	0	.	7.9345	0.29923	0.9063:0.0:0.0937:0.0	.	205	Q86W26	NAL10_HUMAN	H	205	ENSP00000327763:Y205H	ENSP00000327763:Y205H	Y	-	1	0	NLRP10	7939122	0.996000	0.38824	0.993000	0.49108	0.024000	0.10985	2.407000	0.44565	0.967000	0.38186	0.533000	0.62120	TAT		0.532	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		G	7982546	A	G	7982546	3	3	61	1	0	0	0	0	1	0	0	0	10503	362	13	4	1358	4	NLRP10	11	7982546	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	977	7982546	127023970	7190	15175										
EIF3F	8665	broad.mit.edu	37	chr11	8009135	8009135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagcgcccgctctgcctgGtcctgctcttccagggccct	10	20	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8009135G>A	ENST00000533626.1	+	3	862	c.236G>A	c.(235-237)gGt>gAt	p.G79D	EIF3F_ENST00000309828.4_Missense_Mutation_p.G79D|EIF3F_ENST00000449102.2_5'UTR|EIF3F_ENST00000537635.1_Missense_Mutation_p.G94D					eukaryotic translation initiation factor 3, subunit F									p.G79D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCTCTGCCTGGTCCTGCTCTT	0.687											OREG0020726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											7	8	7					11																	8009135		2017	4087	6104	7965711	SO:0001583	missense	8665			U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.236G>A	11.37:g.8009135G>A	ENSP00000431800:p.Gly79Asp	646	7965711		Missense_Mutation	SNP	ENST00000533626.1	37	CCDS7785.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476887	0.44044	.	.	ENSG00000175390	ENST00000533626;ENST00000537635;ENST00000309828;ENST00000538607	T;T;T	0.46819	0.86;1.42;0.86	2.97	0.982	0.19762	.	0.685074	0.13328	N	0.396159	T	0.33498	0.0865	L	0.32530	0.975	0.20489	N	0.999899	B	0.20671	0.047	B	0.19946	0.027	T	0.29701	-1.0003	10	0.72032	D	0.01	-17.4027	6.3061	0.21139	0.0:0.3928:0.4063:0.2009	.	79	O00303	EIF3F_HUMAN	D	79;94;79;29	ENSP00000431800:G79D;ENSP00000442283:G94D;ENSP00000310040:G79D	ENSP00000310040:G79D	G	+	2	0	EIF3F	7965711	0.037000	0.19845	0.000000	0.03702	0.610000	0.37248	0.391000	0.20784	0.281000	0.22233	0.549000	0.68633	GGT		0.687	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754		A	8009135	G	A	8009135	3	1	61	1	0	0	0	0	1	0	0	0	5029	1261	44	3	238	3	EIF3F	11	8009135	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26589	8009135	126997381	7191	15176										
EIF3F	8665	broad.mit.edu	37	chr11	8013365	8013365	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtggaggtcaccaattgCttttcagtgccgcacaatga	10	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8013365C>A	ENST00000533626.1	+	4	1028	c.402C>A	c.(400-402)tgC>tgA	p.C134*	EIF3F_ENST00000309828.4_Nonsense_Mutation_p.C134*|EIF3F_ENST00000449102.2_Intron|EIF3F_ENST00000537635.1_Nonsense_Mutation_p.C149*					eukaryotic translation initiation factor 3, subunit F									p.C134*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCACCAATTGCTTTTCAGTGC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											182	170	174					11																	8013365		2201	4296	6497	7969941	SO:0001587	stop_gained	8665			U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.402C>A	11.37:g.8013365C>A	ENSP00000431800:p.Cys134*		7969941		Nonsense_Mutation	SNP	ENST00000533626.1	37	CCDS7785.1	.	.	.	.	.	.	.	.	.	.	C	37	6.237258	0.97403	.	.	ENSG00000175390	ENST00000533626;ENST00000537635;ENST00000309828;ENST00000538607	.	.	.	4.39	2.41	0.29592	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.2919	8.1104	0.30911	0.0:0.7842:0.0:0.2158	.	.	.	.	X	134;149;134;84	.	ENSP00000310040:C134X	C	+	3	2	EIF3F	7969941	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.361000	0.44160	0.494000	0.27859	0.655000	0.94253	TGC		0.483	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754		A	8013365	C	A	8013365	4	1	61	1	0	0	0	0	0	1	0	0	5029	805	28	2	408	2	EIF3F	11	8013365	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4230	8013365	126993151	7192	15177										
TUB	7275	broad.mit.edu	37	chr11	8060574	8060574	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacggggccaccgaagagatCggtaagctttcaacatcctg	11	11	1	1	rs150936269		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8060574C>T	ENST00000305253.4	+	1	395	c.154C>T	c.(154-156)Cgg>Tgg	p.R52W	RP11-236J17.6_ENST00000526646.1_RNA|RP11-236J17.6_ENST00000528151.1_RNA|TUB_ENST00000534099.1_Intron	NM_003320.4	NP_003311.2	P50607	TUB_HUMAN	tubby bipartite transcription factor	0					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)	p.R52W(1)		breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		CCGAAGAGATCGGTAAGCTTT	0.577													C|||	1	0.000199681	0	0.0014	5008	,	,		16519	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						C	TRP/ARG	0,4402		0,0,2201	60	56	58		154	-1.1	1	11	dbSNP_134	58	2,8590	2.2+/-6.3	0,2,4294	yes	missense-near-splice	TUB	NM_003320.4	101	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	52/562	8060574	2,12992	2201	4296	6497	8017150	SO:0001630	splice_region_variant	7275			U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"tubby (mouse) homolog", "tubby homolog (mouse)"			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000305253.4:c.155+1C>T	11.37:g.8060574C>T			8017150	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000305253.4	37	CCDS7786.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	13.49	2.251971	0.39797	0.0	2.33E-4	ENSG00000166402	ENST00000305253	D	0.86030	-2.06	4.79	-1.11	0.09840	.	1.310990	0.05836	N	0.618474	T	0.75004	0.3791	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64820	-0.6317	9	0.49607	T	0.09	-12.5866	1.5424	0.02558	0.1607:0.3622:0.2932:0.1838	.	52	P50607-2	.	W	52	ENSP00000305426:R52W	ENSP00000305426:R52W	R	+	1	2	TUB	8017150	0.195000	0.23338	0.998000	0.56505	0.827000	0.46813	-1.547000	0.02186	0.012000	0.14892	-0.222000	0.12452	CGG		0.577	TUB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385822.1	NM_003320	Missense_Mutation	T	8060574	C	T	8060574	5	4	61	1	0	0	0	0	0	0	1	0	16782	898	31	1	156	1	TUB	11	8060574	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47209	8060574	126945942	7193	15178										
C11orf17	56672	broad.mit.edu	37	chr11	8936409	8936409	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccagaggaaggaggggcaAcccatgtctatcgttatcac	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8936409A>G	ENST00000309377.4	+	4	430	c.340A>G	c.(340-342)Acc>Gcc	p.T114A	AKIP1_ENST00000534147.1_Missense_Mutation_p.T114A|AKIP1_ENST00000529876.1_Missense_Mutation_p.T87A|AKIP1_ENST00000525005.1_Missense_Mutation_p.T114A|AKIP1_ENST00000396648.2_Missense_Mutation_p.T87A|AKIP1_ENST00000309357.4_Missense_Mutation_p.T114A|AKIP1_ENST00000299576.5_Missense_Mutation_p.T87A|AKIP1_ENST00000534506.1_Missense_Mutation_p.T87A	NM_020642.3	NP_065693.2	Q9NQ31	AKIP1_HUMAN	A kinase (PRKA) interacting protein 1	114					substrate adhesion-dependent cell spreading (GO:0034446)	nucleus (GO:0005634)		p.T114A(1)		kidney(1)|large_intestine(2)|lung(2)	5						AGGAGGGGCAACCCATGTCTA	0.438											OREG0020740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											196	169	178					11																	8936409		2201	4296	6497	8892985	SO:0001583	missense	56672			AF512007	CCDS7793.1, CCDS55743.1, CCDS55744.1	11p15.3	2011-04-18	2011-04-18	2011-04-18	ENSG00000166452	ENSG00000166452			1170	protein-coding gene	gene with protein product		609191	"chromosome 11 open reading frame 17"	C11orf17		20562110, 18178962, 15630084	Standard	NM_020642		Approved	BCA3	uc001mgx.3	Q9NQ31	OTTHUMG00000165653	ENST00000309377.4:c.340A>G	11.37:g.8936409A>G	ENSP00000310459:p.Thr114Ala	653	8892985	Q8NBS2|Q8TAC6|Q8TAD3|Q8TAE0	Missense_Mutation	SNP	ENST00000309377.4	37	CCDS7793.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.261337	0.23051	.	.	ENSG00000166452	ENST00000299576;ENST00000309377;ENST00000309357;ENST00000529876;ENST00000525005;ENST00000524577;ENST00000534506;ENST00000530281;ENST00000396648;ENST00000534147;ENST00000529942	T;T;T;T;T;T;T;T;T;T;T	0.44881	1.57;1.49;1.51;1.4;1.44;1.47;1.4;0.91;1.57;1.49;1.51	5.47	-0.875	0.10628	.	0.600495	0.16469	N	0.213071	T	0.22282	0.0537	N	0.17379	0.485	0.09310	N	1	B;B;B;B;B	0.20671	0.001;0.047;0.002;0.002;0.002	B;B;B;B;B	0.20767	0.004;0.031;0.003;0.003;0.004	T	0.20405	-1.0276	10	0.22706	T	0.39	-0.0041	8.8858	0.35402	0.526:0.0:0.474:0.0	.	87;114;114;87;114	E9PN38;B4DGE2;Q9NQ31-2;Q9NQ31-3;Q9NQ31	.;.;.;.;AKIP1_HUMAN	A	87;114;114;87;114;114;87;26;87;114;82	ENSP00000299576:T87A;ENSP00000310459:T114A;ENSP00000310644:T114A;ENSP00000434726:T87A;ENSP00000433510:T114A;ENSP00000434785:T114A;ENSP00000434820:T87A;ENSP00000436989:T26A;ENSP00000379885:T87A;ENSP00000431331:T114A;ENSP00000431602:T82A	ENSP00000299576:T87A	T	+	1	0	AKIP1	8892985	0.010000	0.17322	0.579000	0.28588	0.788000	0.44548	0.808000	0.27154	-0.100000	0.12241	-0.379000	0.06801	ACC		0.438	AKIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385615.1	NM_020642		G	8936409	A	G	8936409	3	3	61	1	0	0	0	0	1	0	0	0	1636	43	2	4	350	4	C11orf17	11	8936409	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	875835	8936409	126070107	7194	15179										
C11orf16	56673	broad.mit.edu	37	chr11	8942863	8942863	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcctcagggctcttagtCtaacgggaattcttgttcca	9	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8942863C>A	ENST00000326053.5	-	6	1510	c.1404G>T	c.(1402-1404)taG>taT	p.*468Y	C11orf16_ENST00000525780.1_Intron	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	0								p.*468Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		GGCTCTTAGTCTAACGGGAAT	0.527																																																1	Nonstop extension(1)	large_intestine(1)	11											109	108	109					11																	8942863		2201	4296	6497	8899439	SO:0001578	stop_lost	56673			AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.1404G>T	11.37:g.8942863C>A			8899439	Q53FB2|Q8N6Y9	Nonstop_Mutation	SNP	ENST00000326053.5	37	CCDS7794.1	.	.	.	.	.	.	.	.	.	.	C	1.131	-0.652368	0.03480	.	.	ENSG00000176029	ENST00000326053	.	.	.	4.21	-2.84	0.05751	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.5231	0.11969	0.0:0.2251:0.3213:0.4536	.	.	.	.	Y	468	.	.	X	-	3	2	C11orf16	8899439	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.165000	0.03132	-0.499000	0.06623	0.585000	0.79938	TAG		0.527	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643		A	8942863	C	A	8942863	4	1	61	1	0	0	0	0	0	0	0	0	1635	924	32	2	3	2	C11orf16	11	8942863	Nonstop_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6454	8942863	126063653	7195	15180										
ASCL3	56676	broad.mit.edu	37	chr11	8959396	8959396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattgacacatttcacccGctgcctttcccgctcattcc	4	17	3	1	rs560348439		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:8959396G>A	ENST00000531618.1	-	1	362	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	ASCL3_ENST00000325884.1_Missense_Mutation_p.R105W			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	104	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)	p.R105W(1)		breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		CATTTCACCCGCTGCCTTTCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	72	72					11																	8959396		2201	4295	6496	8915972	SO:0001583	missense	56676			AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"Basic helix-loop-helix proteins"	740	protein-coding gene	gene with protein product		609154	"achaete-scute complex (Drosophila) homolog-like 3", "achaete-scute complex homolog 3 (Drosophila)"			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.313C>T	11.37:g.8959396G>A	ENSP00000435770:p.Arg105Trp		8915972	Q8WYQ6	Missense_Mutation	SNP	ENST00000531618.1	37	CCDS7795.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.661760	0.67700	.	.	ENSG00000176009	ENST00000325884;ENST00000531618	D;D	0.99722	-6.53;-6.53	5.72	2.51	0.30379	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.98833	4.345	0.44337	D	0.997225	D	0.89917	1.0	D	0.97110	1.0	D	0.96197	0.9142	10	0.87932	D	0	-13.9271	16.5442	0.84410	0.0:0.0:0.667:0.333	.	104	Q9NQ33	ASCL3_HUMAN	W	105	ENSP00000318846:R105W;ENSP00000435770:R105W	ENSP00000318846:R105W	R	-	1	2	ASCL3	8915972	0.998000	0.40836	1.000000	0.80357	0.877000	0.50540	0.334000	0.19787	1.409000	0.46915	0.650000	0.86243	CGG		0.552	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1			A	8959396	G	A	8959396	3	1	61	1	0	0	0	0	1	0	0	0	1036	1086	38	1	236	1	ASCL3	11	8959396	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16533	8959396	126047120	7196	15181										
SCUBE2	57758	broad.mit.edu	37	chr11	9048966	9048966	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctatgggcaggaagatCtcagggaccacgatcaggat	12	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9048966C>A	ENST00000309263.3	-	19	2631	c.2559G>T	c.(2557-2559)gaG>gaT	p.E853D	SCUBE2_ENST00000520467.1_Missense_Mutation_p.E825D|RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000457346.2_Missense_Mutation_p.E882D|SCUBE2_ENST00000450649.2_Intron			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	853	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.E853D(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GCAGGAAGATCTCAGGGACCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	11											136	113	121					11																	9048966		2201	4296	6497	9005542	SO:0001583	missense	57758			AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.2559G>T	11.37:g.9048966C>A	ENSP00000310658:p.Glu853Asp		9005542	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	23.5|23.5|23.5	4.418855|4.418855|4.418855	0.83559|0.83559|0.83559	.|.|.	.|.|.	ENSG00000175356|ENSG00000175356|ENSG00000175356	ENST00000528651|ENST00000457346;ENST00000309263;ENST00000520467|ENST00000519202	.|T;T;T|.	.|0.17528|.	.|2.27;2.27;2.27|.	5.34|5.34|5.34	5.34|5.34|5.34	0.76211|0.76211|0.76211	.|CUB (5);|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.42471|0.42471|0.42471	0.1204|0.1204|0.1204	N|N|N	0.17764|0.17764|0.17764	0.52|0.52|0.52	0.58432|0.58432|0.58432	D|D|D	0.999998|0.999998|0.999998	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.91635|.	.|0.999;0.999|.	T|T|T	0.27020|0.27020|0.27020	-1.0086|-1.0086|-1.0086	5|10|5	.|0.72032|.	.|D|.	.|0.01|.	.|.|.	10.2465|10.2465|10.2465	0.43343|0.43343|0.43343	0.0:0.878:0.0:0.122|0.0:0.878:0.0:0.122|0.0:0.878:0.0:0.122	.|.|.	.|825;853|.	.|Q9NQ36-2;Q9NQ36|.	.|.;SCUB2_HUMAN|.	Y|D|I	41|882;853;825|36	.|ENSP00000390481:E882D;ENSP00000310658:E853D;ENSP00000429969:E825D|.	.|ENSP00000310658:E853D|.	D|E|R	-|-|-	1|3|2	0|2|0	SCUBE2|SCUBE2|SCUBE2	9005542|9005542|9005542	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	1.449000|1.449000|1.449000	0.35123|0.35123|0.35123	2.506000|2.506000|2.506000	0.84524|0.84524|0.84524	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	GAT|GAG|AGA		0.582	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		A	9048966	C	A	9048966	3	1	61	1	0	0	0	0	1	0	0	0	13982	912	32	2	456	2	SCUBE2	11	9048966	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89570	9048966	125957550	7197	15182										
SCUBE2	57758	broad.mit.edu	37	chr11	9100984	9100984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccatcaaaacaagtgcaaCgataattgcctggaatattc	7	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9100984C>T	ENST00000309263.3	-	3	401	c.329G>A	c.(328-330)cGt>cAt	p.R110H	SCUBE2_ENST00000520467.1_Missense_Mutation_p.R110H|SCUBE2_ENST00000534295.1_5'Flank|SCUBE2_ENST00000457346.2_Missense_Mutation_p.R110H|SCUBE2_ENST00000450649.2_Missense_Mutation_p.R110H			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	110	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R110H(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		ACAAGTGCAACGATAATTGCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											229	184	199					11																	9100984		2201	4296	6497	9057560	SO:0001583	missense	57758			AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.329G>A	11.37:g.9100984C>T	ENSP00000310658:p.Arg110His		9057560	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		.	.	.	.	.	.	.	.	.	.	C	19.85	3.903110	0.72754	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	5.37	5.37	0.77165	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.92896	0.7740	L	0.34521	1.04	0.80722	D	1	P;P;P	0.49447	0.924;0.467;0.523	P;B;B	0.50049	0.629;0.233;0.344	D	0.93157	0.6554	10	0.62326	D	0.03	.	13.7543	0.62926	0.0:0.9261:0.0:0.0739	.	110;110;110	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	H	110	ENSP00000390481:R110H;ENSP00000310658:R110H;ENSP00000415187:R110H;ENSP00000429969:R110H	ENSP00000310658:R110H	R	-	2	0	SCUBE2	9057560	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.779000	0.62375	2.676000	0.91093	0.655000	0.94253	CGT		0.428	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		T	9100984	C	T	9100984	3	4	61	1	0	0	0	0	1	0	0	0	13982	536	19	1	2841	1	SCUBE2	11	9100984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52018	9100984	125905532	7198	15183										
TMEM41B	440026	broad.mit.edu	37	chr11	9308005	9308005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaccagagggcttacctaGaaaagtaccaataaaaaaaa	7	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9308005G>T	ENST00000528080.1	-	6	1041	c.703C>A	c.(703-705)Cta>Ata	p.L235I	TMEM41B_ENST00000527813.1_Intron	NM_015012.3	NP_055827.1	Q5BJD5	TM41B_HUMAN	transmembrane protein 41B	235					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)		p.L235I(1)		kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(2)	7				all cancers(16;9.96e-08)|Epithelial(150;4.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0972)		GGCTTACCTAGAAAAGTACCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											104	102	103					11																	9308005		2201	4296	6497	9264581	SO:0001583	missense	440026			D26067	CCDS31424.1, CCDS53600.1	11p15.3	2008-02-05			ENSG00000166471	ENSG00000166471			28948	protein-coding gene	gene with protein product						7584026, 7584028	Standard	NM_015012		Approved	KIAA0033	uc001mhn.2	Q5BJD5	OTTHUMG00000165719	ENST00000528080.1:c.703C>A	11.37:g.9308005G>T	ENSP00000433126:p.Leu235Ile		9264581	D3DQU9|E9PP29|Q15055|Q4G0P0	Missense_Mutation	SNP	ENST00000528080.1	37	CCDS31424.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.248685	0.22880	.	.	ENSG00000166471	ENST00000299596;ENST00000528080	T;T	0.58940	0.3;0.3	5.45	4.53	0.55603	.	0.066647	0.64402	D	0.000009	T	0.36771	0.0979	N	0.11284	0.12	0.80722	D	1	B	0.09022	0.002	B	0.20577	0.03	T	0.15178	-1.0446	10	0.12430	T	0.62	.	13.6437	0.62267	0.0:0.0:0.7181:0.2819	.	235	Q5BJD5	TM41B_HUMAN	I	235	ENSP00000299596:L235I;ENSP00000433126:L235I	ENSP00000299596:L235I	L	-	1	2	TMEM41B	9264581	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.763000	0.55257	1.435000	0.47434	0.585000	0.79938	CTA		0.373	TMEM41B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385940.2			T	9308005	G	T	9308005	3	4	61	1	0	0	0	0	1	0	0	0	16204	933	33	2	180	2	TMEM41B	11	9308005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207021	9308005	125698511	7199	15184										
IPO7	10527	broad.mit.edu	37	chr11	9459657	9459657	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagatgtgtgttctcggActctgtgctcttattgatat	10	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9459657A>G	ENST00000379719.3	+	22	2662	c.2520A>G	c.(2518-2520)ggA>ggG	p.G840G		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	840					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)	p.G840G(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		GTGTTCTCGGACTCTGTGCTC	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	11											134	145	141					11																	9459657		2201	4294	6495	9416233	SO:0001819	synonymous_variant	10527			AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2520A>G	11.37:g.9459657A>G			9416233	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	37	CCDS31425.1																																																																																				0.318	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		G	9459657	A	G	9459657	2	3	61	1	0	0	0	0	0	0	0	1	7818	262	10	4		4	IPO7	11	9459657	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	151652	9459657	125546859	7200	15185										
ZNF143	7702	broad.mit.edu	37	chr11	9537756	9537756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtattgcaggtcaacatAtctcaagctgacatgcaggc	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9537756A>G	ENST00000396602.2	+	14	1652	c.1533A>G	c.(1531-1533)atA>atG	p.I511M	ZNF143_ENST00000299606.2_Missense_Mutation_p.I483M|ZNF143_ENST00000396604.1_Missense_Mutation_p.I510M|ZNF143_ENST00000530463.1_Missense_Mutation_p.I510M|ZNF143_ENST00000396597.3_Missense_Mutation_p.I480M	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	511					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I511M(1)		endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		AGGTCAACATATCTCAAGCTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											109	81	90					11																	9537756		2201	4294	6495	9494332	SO:0001583	missense	7702			U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1533A>G	11.37:g.9537756A>G	ENSP00000379847:p.Ile511Met		9494332	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Missense_Mutation	SNP	ENST00000396602.2	37	CCDS7799.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.37|17.37	3.373511|3.373511	0.61624|0.61624	.|.	.|.	ENSG00000166478|ENSG00000166478	ENST00000396604;ENST00000396602;ENST00000530463;ENST00000396597;ENST00000299606|ENST00000447186	T;T;T;T;T|T	0.10573|0.51071	2.86;2.87;2.86;2.91;2.92|0.72	5.92|5.92	3.43|3.43	0.39272|0.39272	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000002|0.000002	T|T	0.38558|0.38558	0.1045|0.1045	N|N	0.24115|0.24115	0.695|0.695	0.44871|0.44871	D|D	0.997889|0.997889	P;P;P|.	0.49635|.	0.926;0.879;0.879|.	P;B;B|.	0.49999|.	0.628;0.328;0.328|.	T|T	0.27706|0.27706	-1.0066|-1.0066	10|8	0.35671|0.59425	T|D	0.21|0.04	.|.	7.4227|7.4227	0.27081|0.27081	0.6078:0.2605:0.0:0.1316|0.6078:0.2605:0.0:0.1316	.|.	480;510;511|.	P52747-2;E7ER34;P52747|.	.;.;ZN143_HUMAN|.	M|V	510;511;510;480;483|37	ENSP00000379849:I510M;ENSP00000379847:I511M;ENSP00000432154:I510M;ENSP00000379843:I480M;ENSP00000299606:I483M|ENSP00000401493:I37V	ENSP00000299606:I483M|ENSP00000401493:I37V	I|I	+|+	3|1	3|0	ZNF143|ZNF143	9494332|9494332	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	0.479000|0.479000	0.22228|0.22228	1.024000|1.024000	0.39682|0.39682	0.533000|0.533000	0.62120|0.62120	ATA|ATC		0.453	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		G	9537756	A	G	9537756	3	3	61	1	0	0	0	0	1	0	0	0	17771	439	16	4	1583	4	ZNF143	11	9537756	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	78099	9537756	125468760	7201	15186										
SBF2	81846	broad.mit.edu	37	chr11	9806724	9806724	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagcgtggctgctcttcGctccactccattggatgggg	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9806724G>A	ENST00000256190.8	-	37	5316	c.5179C>T	c.(5179-5181)Cga>Tga	p.R1727*	SBF2-AS1_ENST00000526617.1_RNA|SBF2-AS1_ENST00000534671.1_RNA|SBF2-AS1_ENST00000499953.2_RNA|SBF2-AS1_ENST00000498905.2_RNA|SBF2-AS1_ENST00000525636.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1727					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1727*(1)		breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GCTGCTCTTCGCTCCACTCCA	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											154	121	132					11																	9806724		2201	4294	6495	9763300	SO:0001587	stop_gained	81846			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.5179C>T	11.37:g.9806724G>A	ENSP00000256190:p.Arg1727*		9763300	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Nonsense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	G	46	12.791679	0.99696	.	.	ENSG00000133812	ENST00000256190;ENST00000532095	.	.	.	6.07	5.11	0.69529	.	0.094578	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	12.6162	0.56578	0.0:0.0:0.6873:0.3127	.	.	.	.	X	1727;115	.	ENSP00000256190:R1727X	R	-	1	2	SBF2	9763300	1.000000	0.71417	0.994000	0.49952	0.803000	0.45373	4.610000	0.61155	2.885000	0.99019	0.655000	0.94253	CGA		0.522	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		A	9806724	G	A	9806724	4	1	61	1	0	0	0	0	0	1	0	0	13896	1095	38	1	386	1	SBF2	11	9806724	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	268968	9806724	125199792	7202	15187										
SBF2	81846	broad.mit.edu	37	chr11	9853897	9853897	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaggcaggcgattgtgtcGatagcagcgagctactcttg	13	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:9853897G>A	ENST00000256190.8	-	27	3663	c.3526C>T	c.(3526-3528)Cga>Tga	p.R1176*		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1176	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1176*(1)		breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CGATTGTGTCGATAGCAGCGA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											121	105	110					11																	9853897		2201	4294	6495	9810473	SO:0001587	stop_gained	81846			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3526C>T	11.37:g.9853897G>A	ENSP00000256190:p.Arg1176*		9810473	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Nonsense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	G	44	10.715846	0.99455	.	.	ENSG00000133812	ENST00000256190	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6961	0.77499	0.0:0.0:0.8625:0.1375	.	.	.	.	X	1176	.	ENSP00000256190:R1176X	R	-	1	2	SBF2	9810473	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.217000	0.58547	2.835000	0.97688	0.591000	0.81541	CGA		0.473	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		A	9853897	G	A	9853897	4	1	61	1	0	0	0	0	0	1	0	0	13896	1066	37	1	2079	1	SBF2	11	9853897	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47173	9853897	125152619	7203	15188										
AMPD3	272	broad.mit.edu	37	chr11	10527315	10527315	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctgaaggaaatgatattCgaaagacaaatgtggctcag	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:10527315C>T	ENST00000396554.3	+	15	2556	c.2215C>T	c.(2215-2217)Cga>Tga	p.R739*	AMPD3_ENST00000444303.2_Nonsense_Mutation_p.R571*	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	730					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.R739*(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		AAATGATATTCGAAAGACAAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											93	90	91					11																	10527315		2201	4294	6495	10483891	SO:0001587	stop_gained	272			M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.2215C>T	11.37:g.10527315C>T	ENSP00000379802:p.Arg739*		10483891	A0AUX0|B7Z2S2|B7Z763|B7Z877	Nonsense_Mutation	SNP	ENST00000396554.3	37	CCDS7802.1	.	.	.	.	.	.	.	.	.	.	C	40	8.196696	0.98701	.	.	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000396553;ENST00000528723;ENST00000529507	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4577	20.3932	0.98965	0.0:1.0:0.0:0.0	.	.	.	.	X	571;739;730;737;730	.	ENSP00000379801:R730X	R	+	1	2	AMPD3	10483891	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.903000	0.56318	2.824000	0.97209	0.655000	0.94253	CGA		0.378	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		T	10527315	C	T	10527315	4	4	61	1	0	0	0	0	0	1	0	0	587	876	31	1	2293	1	AMPD3	11	10527315	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673418	10527315	124479201	7204	15189										
RNF141	50862	broad.mit.edu	37	chr11	10536581	10536581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctccagtcatctgtaggCgacaaatagggcaattcctg	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:10536581C>T	ENST00000265981.2	-	6	717	c.575G>A	c.(574-576)cGc>cAc	p.R192H		NM_016422.3	NP_057506.2	Q8WVD5	RN141_HUMAN	ring finger protein 141	192					protein autoubiquitination (GO:0051865)|regulation of transcription, DNA-templated (GO:0006355)		DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R192H(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9				all cancers(16;4.63e-08)|Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.064)		CATCTGTAGGCGACAAATAGG	0.383																																					Ovarian(8;377 410 25844 26058 41491)											1	Substitution - Missense(1)	large_intestine(1)	11											152	137	142					11																	10536581		2201	4294	6495	10493157	SO:0001583	missense	50862			AF214680	CCDS7803.1	11p15.3	2013-01-09			ENSG00000110315	ENSG00000110315		"RING-type (C3HC4) zinc fingers"	21159	protein-coding gene	gene with protein product						11672448	Standard	NM_016422		Approved	ZFP26, ZNF230	uc001mis.1	Q8WVD5		ENST00000265981.2:c.575G>A	11.37:g.10536581C>T	ENSP00000265981:p.Arg192His		10493157	A8K149|Q9NZB4	Missense_Mutation	SNP	ENST00000265981.2	37	CCDS7803.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297516	0.81025	.	.	ENSG00000110315	ENST00000265981	T	0.61158	0.13	5.7	5.7	0.88788	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	T	0.71937	0.3399	M	0.89414	3.03	0.80722	D	1	D	0.56035	0.974	P	0.47015	0.534	T	0.79004	-0.1980	10	0.72032	D	0.01	-10.379	19.8478	0.96722	0.0:1.0:0.0:0.0	.	192	Q8WVD5	RN141_HUMAN	H	192	ENSP00000265981:R192H	ENSP00000265981:R192H	R	-	2	0	RNF141	10493157	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.067000	0.71193	2.704000	0.92352	0.650000	0.86243	CGC		0.383	RNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385888.1	NM_016422		T	10536581	C	T	10536581	3	4	61	1	0	0	0	0	1	0	0	0	13481	768	27	1	121	1	RNF141	11	10536581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9266	10536581	124469935	7205	15190										
MRVI1	10335	broad.mit.edu	37	chr11	10647979	10647979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctaggcctttgggtgtgGtctcggggtactggagggga	20	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:10647979G>A	ENST00000436272.1	-	8	899	c.821C>T	c.(820-822)aCc>aTc	p.T274I	MRVI1_ENST00000531107.1_Missense_Mutation_p.T293I|MRVI1_ENST00000558540.1_5'UTR|MRVI1_ENST00000424001.1_5'UTR|MRVI1_ENST00000421747.1_Missense_Mutation_p.T292I|MRVI1_ENST00000527509.2_Missense_Mutation_p.T210I|MRVI1_ENST00000423302.2_Missense_Mutation_p.T301I|MRVI1_ENST00000545852.1_5'UTR|MRVI1_ENST00000547195.1_Missense_Mutation_p.T210I|MRVI1_ENST00000552103.1_Missense_Mutation_p.T210I|MRVI1_ENST00000534266.2_5'UTR|MRVI1_ENST00000541483.1_Intron			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	274					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)		p.T274I(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TTTGGGTGTGGTCTCGGGGTA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11											91	98	96					11																	10647979		1933	4141	6074	10604555	SO:0001583	missense	10335			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.821C>T	11.37:g.10647979G>A	ENSP00000412229:p.Thr274Ile		10604555	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37		.	.	.	.	.	.	.	.	.	.	G	7.546	0.661772	0.14645	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000423302;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T	0.14766	3.06;3.08;2.48;2.48;2.88;3.06;2.48	5.56	4.58	0.56647	.	0.366702	0.27664	N	0.018363	T	0.09202	0.0227	N	0.14661	0.345	0.80722	D	1	B;B;B	0.22983	0.047;0.047;0.078	B;B;B	0.24394	0.024;0.024;0.053	T	0.22906	-1.0203	10	0.32370	T	0.25	-3.8868	13.6673	0.62403	0.0:0.0:0.7324:0.2676	.	274;293;292	Q9Y6F6;E9PQY6;Q9Y6F6-4	MRVI1_HUMAN;.;.	I	292;275;274;210;210;301;293;210	ENSP00000414598:T292I;ENSP00000412229:T274I;ENSP00000448278:T210I;ENSP00000446764:T210I;ENSP00000412130:T301I;ENSP00000432436:T293I;ENSP00000432067:T210I	ENSP00000307885:T275I	T	-	2	0	MRVI1	10604555	1.000000	0.71417	0.998000	0.56505	0.014000	0.08584	2.280000	0.43443	2.630000	0.89119	0.563000	0.77884	ACC		0.567	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		A	10647979	G	A	10647979	3	1	61	1	0	0	0	0	1	0	0	0	9883	1261	44	3	1888	3	MRVI1	11	10647979	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111398	10647979	124358537	7206	15191										
GALNTL4	374378	broad.mit.edu	37	chr11	11292769	11292769	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaacaccagctggaagccGaactccaggtcgctattctc	9	14	1	0	rs372239180		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:11292769G>A	ENST00000227756.4	-	11	2157	c.1746C>T	c.(1744-1746)ttC>ttT	p.F582F		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	582	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.F582F(1)									GCTGGAAGCCGAACTCCAGGT	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	11								0,4402		0,0,2201	96	88	91		1746	-3.5	1	11		91	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous	GALNTL4	NM_198516.2		0,1,6494	AA,AG,GG		0.0116,0.0,0.0077		582/608	11292769	1,12989	2201	4294	6495	11249345	SO:0001819	synonymous_variant	374378			AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"Glycosyltransferase family 2 domain containing"	30488	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 18"	615136	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.1746C>T	11.37:g.11292769G>A			11249345	O95903|Q8NDY9	Silent	SNP	ENST00000227756.4	37	CCDS7807.1																																																																																				0.637	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		A	11292769	G	A	11292769	2	1	61	1	0	0	0	0	0	0	0	1	6243	1049	37	1		1	GALNTL4	11	11292769	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	644790	11292769	123713747	7207	15192										
GALNTL4	374378	broad.mit.edu	37	chr11	11398896	11398896	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatgatccgcttccggttCtccttgatgcgggtgagtac	13	10	1	4	rs373136641		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:11398896C>A	ENST00000227756.4	-	5	1221	c.810G>T	c.(808-810)gaG>gaT	p.E270D		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	270					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.E270D(1)									GCTTCCGGTTCTCCTTGATGC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											70	63	65					11																	11398896		2201	4294	6495	11355472	SO:0001583	missense	374378			AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"Glycosyltransferase family 2 domain containing"	30488	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 18"	615136	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.810G>T	11.37:g.11398896C>A	ENSP00000227756:p.Glu270Asp		11355472	O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	37	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084842	0.76642	.	.	ENSG00000110328	ENST00000227756	T	0.59502	0.26	5.52	2.15	0.27550	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.70168	0.3193	M	0.75777	2.31	0.53005	D	0.999961	D	0.63046	0.992	D	0.77004	0.989	T	0.69435	-0.5146	10	0.72032	D	0.01	.	7.056	0.25099	0.0:0.5492:0.0:0.4508	.	270	Q6P9A2	GLTL4_HUMAN	D	270	ENSP00000227756:E270D	ENSP00000227756:E270D	E	-	3	2	GALNTL4	11355472	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.736000	0.38187	0.679000	0.31345	0.655000	0.94253	GAG		0.517	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		A	11398896	C	A	11398896	3	1	61	1	0	0	0	0	1	0	0	0	6243	912	32	2	1041	2	GALNTL4	11	11398896	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106127	11398896	123607620	7208	15193										
USP47	55031	broad.mit.edu	37	chr11	11957967	11957967	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatacaccaatggggcttCtactaggtggcgtcaagtca	11	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:11957967C>A	ENST00000399455.2	+	18	2167	c.2047C>A	c.(2047-2049)Cta>Ata	p.L683I	USP47_ENST00000527733.1_Missense_Mutation_p.L663I|USP47_ENST00000339865.5_Missense_Mutation_p.L595I|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	683					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)	p.L595I(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		AATGGGGCTTCTACTAGGTGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											118	106	110					11																	11957967		1852	4087	5939	11914543	SO:0001583	missense	55031			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.2047C>A	11.37:g.11957967C>A	ENSP00000382382:p.Leu683Ile		11914543	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	C	11.43	1.635552	0.29068	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455	T;T;T	0.04970	3.53;3.53;3.52	5.48	2.55	0.30701	.	0.136492	0.50627	D	0.000107	T	0.04452	0.0122	L	0.31752	0.955	0.54753	D	0.999982	B;B	0.31435	0.217;0.323	B;B	0.31751	0.064;0.135	T	0.44452	-0.9327	10	0.09843	T	0.71	.	8.7172	0.34419	0.0:0.6247:0.0:0.3753	.	663;595	E9PM46;Q96K76-2	.;.	I	595;663;683	ENSP00000339957:L595I;ENSP00000433146:L663I;ENSP00000382382:L683I	ENSP00000339957:L595I	L	+	1	2	USP47	11914543	1.000000	0.71417	0.512000	0.27736	0.993000	0.82548	1.781000	0.38644	0.250000	0.21479	0.655000	0.94253	CTA		0.418	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		A	11957967	C	A	11957967	3	1	61	1	0	0	0	0	1	0	0	0	17118	912	32	2	1845	2	USP47	11	11957967	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	559071	11957967	123048549	7209	15194										
USP47	55031	broad.mit.edu	37	chr11	11969590	11969590	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctctcacttcaaggtctttCgagtgtatgccagcaatcaa	7	12	4	0	rs375838732		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:11969590C>T	ENST00000399455.2	+	22	3370	c.3250C>T	c.(3250-3252)Cga>Tga	p.R1084*	USP47_ENST00000527733.1_Nonsense_Mutation_p.R1064*|USP47_ENST00000339865.5_Nonsense_Mutation_p.R996*|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1084					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)	p.R996*(2)		breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		CAAGGTCTTTCGAGTGTATGC	0.398																																																2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	11											154	143	146					11																	11969590		1846	4095	5941	11926166	SO:0001587	stop_gained	55031			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3250C>T	11.37:g.11969590C>T	ENSP00000382382:p.Arg1084*		11926166	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Nonsense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	C	45	11.420015	0.99558	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7803	0.69760	0.1449:0.8551:0.0:0.0	.	.	.	.	X	996;1064;1084	.	ENSP00000339957:R996X	R	+	1	2	USP47	11926166	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.113000	0.57851	2.520000	0.84964	0.591000	0.81541	CGA		0.398	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		T	11969590	C	T	11969590	4	4	61	1	0	0	0	0	0	1	0	0	17118	876	31	1	3064	1	USP47	11	11969590	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11623	11969590	123036926	7210	15195										
USP47	55031	broad.mit.edu	37	chr11	11976696	11976696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatatctgtgatgatggtgCggtcatattttataggtaac	10	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:11976696C>T	ENST00000399455.2	+	28	4058	c.3938C>T	c.(3937-3939)gCg>gTg	p.A1313V	USP47_ENST00000527733.1_Missense_Mutation_p.A1293V|USP47_ENST00000305481.6_3'UTR|USP47_ENST00000339865.5_Missense_Mutation_p.A1225V|USP47_ENST00000539466.1_Missense_Mutation_p.A95V	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1313				A -> G (in Ref. 1; BAA91348). {ECO:0000305}.	base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)	p.A1225V(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		GATGATGGTGCGGTCATATTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	11											182	166	171					11																	11976696		1867	4107	5974	11933272	SO:0001583	missense	55031			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3938C>T	11.37:g.11976696C>T	ENSP00000382382:p.Ala1313Val		11933272	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	C	25.9	4.685511	0.88639	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000539466;ENST00000399455	T;T;T	0.04551	3.6;3.6;3.6	5.95	5.04	0.67666	.	0.049287	0.85682	N	0.000000	T	0.06462	0.0166	L	0.46157	1.445	0.58432	D	0.999995	B;B	0.27264	0.173;0.168	B;B	0.17979	0.013;0.02	T	0.17899	-1.0354	10	0.51188	T	0.08	.	14.5519	0.68073	0.0:0.9294:0.0:0.0706	.	1293;1225	E9PM46;Q96K76-2	.;.	V	1225;1293;95;1313	ENSP00000339957:A1225V;ENSP00000433146:A1293V;ENSP00000382382:A1313V	ENSP00000339957:A1225V	A	+	2	0	USP47	11933272	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	6.087000	0.71362	1.516000	0.48900	0.650000	0.86243	GCG		0.343	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		T	11976696	C	T	11976696	3	4	61	1	0	0	0	0	1	0	0	0	17118	768	27	1	3776	1	USP47	11	11976696	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7106	11976696	123029820	7211	15196										
MICALCL	84953	broad.mit.edu	37	chr11	12316281	12316281	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggaaggtgctgcctgaaGatagtgcgcaggccctggag	17	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:12316281G>T	ENST00000256186.2	+	3	1594	c.1303G>T	c.(1303-1305)Gat>Tat	p.D435Y		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	435					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.D435Y(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		GCTGCCTGAAGATAGTGCGCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	66	65					11																	12316281		1969	4138	6107	12272857	SO:0001583	missense	84953			BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1303G>T	11.37:g.12316281G>T	ENSP00000256186:p.Asp435Tyr		12272857	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504688	0.44558	.	.	ENSG00000133808	ENST00000256186	T	0.12672	2.66	5.8	1.68	0.24146	.	0.584295	0.15221	N	0.273927	T	0.16385	0.0394	L	0.56769	1.78	0.09310	N	1	D	0.57899	0.981	P	0.47744	0.556	T	0.12293	-1.0553	10	0.56958	D	0.05	.	4.9078	0.13807	0.2627:0.1544:0.5829:0.0	.	435	Q6ZW33	MICLK_HUMAN	Y	435	ENSP00000256186:D435Y	ENSP00000256186:D435Y	D	+	1	0	MICALCL	12272857	0.006000	0.16342	0.000000	0.03702	0.005000	0.04900	0.535000	0.23114	0.048000	0.15891	0.460000	0.39030	GAT		0.557	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		T	12316281	G	T	12316281	3	4	61	1	0	0	0	0	1	0	0	0	9602	942	33	2	1309	2	MICALCL	11	12316281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	339585	12316281	122690235	7212	15197										
ARNTL	406	broad.mit.edu	37	chr11	13375869	13375869	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatccaatggcagaccagaGaatggacatttcttcaacca	7	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:13375869G>T	ENST00000403290.1	+	5	369	c.14G>T	c.(13-15)aGa>aTa	p.R5I	ARNTL_ENST00000389708.3_Missense_Mutation_p.R5I|ARNTL_ENST00000389707.4_Missense_Mutation_p.R5I|ARNTL_ENST00000396441.3_Missense_Mutation_p.R5I|ARNTL_ENST00000361003.4_Missense_Mutation_p.R5I|ARNTL_ENST00000403510.3_5'UTR|RN7SKP151_ENST00000410230.1_RNA|ARNTL_ENST00000403482.3_5'Flank|ARNTL_ENST00000401424.1_5'UTR			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	5					circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R5I(1)		breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		gcagaccagagaatggacatt	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	72	76					11																	13375869		2200	4294	6494	13332445	SO:0001583	missense	406			D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.14G>T	11.37:g.13375869G>T	ENSP00000384517:p.Arg5Ile		13332445	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Missense_Mutation	SNP	ENST00000403290.1	37		.	.	.	.	.	.	.	.	.	.	G	26.9	4.780132	0.90195	.	.	ENSG00000133794	ENST00000529050;ENST00000534544;ENST00000527998;ENST00000396441;ENST00000533520;ENST00000389707;ENST00000529388;ENST00000403290;ENST00000361003;ENST00000389708;ENST00000531665	T;T;T;T;T;T	0.55760	2.81;2.81;0.5;2.82;2.47;2.65	5.71	4.79	0.61399	.	0.051780	0.85682	N	0.000000	T	0.60011	0.2236	L	0.27053	0.805	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.80764	0.986;0.994	T	0.64162	-0.6472	10	0.66056	D	0.02	.	13.9591	0.64168	0.0:0.0:0.8479:0.1521	.	5;5	O00327;O00327-8	BMAL1_HUMAN;.	I	5	ENSP00000379718:R5I;ENSP00000374357:R5I;ENSP00000433571:R5I;ENSP00000384517:R5I;ENSP00000354278:R5I;ENSP00000374358:R5I	ENSP00000354278:R5I	R	+	2	0	ARNTL	13332445	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.528000	0.90598	1.392000	0.46585	0.655000	0.94253	AGA		0.493	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		T	13375869	G	T	13375869	3	4	61	1	0	0	0	0	1	0	0	0	968	942	33	2	16	2	ARNTL	11	13375869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1059588	13375869	121630647	7213	15198										
ARNTL	406	broad.mit.edu	37	chr11	13395673	13395673	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttggcatatttaccacaaGaacttctaggcacatcgtgt	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:13395673G>T	ENST00000403290.1	+	14	1454	c.1099G>T	c.(1099-1101)Gaa>Taa	p.E367*	ARNTL_ENST00000389708.3_Nonsense_Mutation_p.E367*|ARNTL_ENST00000389707.4_Nonsense_Mutation_p.E366*|ARNTL_ENST00000396441.3_Nonsense_Mutation_p.E366*|ARNTL_ENST00000361003.4_Intron|ARNTL_ENST00000403510.3_Nonsense_Mutation_p.E323*|ARNTL_ENST00000403482.3_Nonsense_Mutation_p.E365*|ARNTL_ENST00000401424.1_Nonsense_Mutation_p.E324*			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	367	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E366*(1)		breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		TTTACCACAAGAACTTCTAGG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											140	132	135					11																	13395673		2200	4294	6494	13352249	SO:0001587	stop_gained	406			D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1099G>T	11.37:g.13395673G>T	ENSP00000384517:p.Glu367*		13352249	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Nonsense_Mutation	SNP	ENST00000403290.1	37		.	.	.	.	.	.	.	.	.	.	G	44	10.610343	0.99437	.	.	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000389708;ENST00000403510;ENST00000339640;ENST00000403482	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.0286	0.89276	0.0:0.0:1.0:0.0	.	.	.	.	X	366;366;324;367;367;323;323;365	.	ENSP00000340289:E323X	E	+	1	0	ARNTL	13352249	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.476000	0.97823	2.346000	0.79739	0.561000	0.74099	GAA		0.353	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		T	13395673	G	T	13395673	4	4	61	1	0	0	0	0	0	1	0	0	968	943	33	2	1149	2	ARNTL	11	13395673	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19804	13395673	121610843	7214	15199										
ARNTL	406	broad.mit.edu	37	chr11	13397239	13397239	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttatcacactacggagtCgatggttcagtttcatgaac	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:13397239C>T	ENST00000403290.1	+	15	1610	c.1255C>T	c.(1255-1257)Cga>Tga	p.R419*	ARNTL_ENST00000389708.3_Nonsense_Mutation_p.R419*|ARNTL_ENST00000389707.4_Nonsense_Mutation_p.R418*|ARNTL_ENST00000396441.3_Nonsense_Mutation_p.R418*|ARNTL_ENST00000361003.4_Nonsense_Mutation_p.R301*|ARNTL_ENST00000403510.3_Nonsense_Mutation_p.R375*|ARNTL_ENST00000403482.3_Nonsense_Mutation_p.R417*|ARNTL_ENST00000401424.1_Nonsense_Mutation_p.R376*			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	419	PAC.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R418*(1)		breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		ACTACGGAGTCGATGGTTCAG	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											95	82	86					11																	13397239		2200	4294	6494	13353815	SO:0001587	stop_gained	406			D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1255C>T	11.37:g.13397239C>T	ENSP00000384517:p.Arg419*		13353815	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Nonsense_Mutation	SNP	ENST00000403290.1	37		.	.	.	.	.	.	.	.	.	.	C	43	10.356614	0.99390	.	.	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000389708;ENST00000403510;ENST00000339640;ENST00000403482	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	13.1548	0.59511	0.0:0.9224:0.0:0.0776	.	.	.	.	X	418;418;376;419;301;419;375;375;417	.	ENSP00000340289:R375X	R	+	1	2	ARNTL	13353815	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.644000	0.54381	2.515000	0.84797	0.561000	0.74099	CGA		0.328	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		T	13397239	C	T	13397239	4	4	61	1	0	0	0	0	0	1	0	0	968	876	31	1	1309	1	ARNTL	11	13397239	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1566	13397239	121609277	7215	15200										
PTH	5741	broad.mit.edu	37	chr11	13514157	13514157	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccattctactctctccatcGagttcagatgttttcccagg	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:13514157G>A	ENST00000282091.1	-	3	257	c.143C>T	c.(142-144)tCg>tTg	p.S48L	PTH_ENST00000529816.1_Missense_Mutation_p.S48L	NM_000315.2	NP_000306.1	P01270	PTHY_HUMAN	parathyroid hormone	48					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|bone resorption (GO:0045453)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular macromolecule biosynthetic process (GO:0034645)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to lead ion (GO:0010288)|response to parathyroid hormone (GO:0071107)|response to vitamin D (GO:0033280)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	p.S48L(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(625;0.00116)|Epithelial(150;0.0357)|LUSC - Lung squamous cell carcinoma(625;0.0836)		TCTCTCCATCGAGTTCAGATG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											86	88	88					11																	13514157		2200	4294	6494	13470733	SO:0001583	missense	5741			J00301	CCDS7812.1	11p15.3-p15.1	2013-02-28				ENSG00000152266		"Endogenous ligands"	9606	protein-coding gene	gene with protein product	"parathyrin", "parathormone", "parathyroid hormone 1", "preproparathyroid hormone", "prepro-PTH"	168450				1672845	Standard	NM_000315		Approved	PTH1	uc001mlb.3	P01270		ENST00000282091.1:c.143C>T	11.37:g.13514157G>A	ENSP00000282091:p.Ser48Leu		13470733	Q4VB48|Q9UD38	Missense_Mutation	SNP	ENST00000282091.1	37	CCDS7812.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351603	0.24512	.	.	ENSG00000152266	ENST00000282091;ENST00000529816	D;D	0.83163	-1.69;-1.69	5.24	2.14	0.27477	.	0.777662	0.12188	N	0.491515	T	0.73984	0.3657	L	0.53249	1.67	0.09310	N	1	B	0.24576	0.106	B	0.15484	0.013	T	0.57312	-0.7833	10	0.19147	T	0.46	0.4047	6.0101	0.19571	0.1794:0.0:0.6676:0.1529	.	48	P01270	PTHY_HUMAN	L	48	ENSP00000282091:S48L;ENSP00000433208:S48L	ENSP00000282091:S48L	S	-	2	0	PTH	13470733	0.000000	0.05858	0.012000	0.15200	0.961000	0.63080	0.642000	0.24735	1.354000	0.45846	0.650000	0.86243	TCG		0.498	PTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386198.1	NM_000315		A	13514157	G	A	13514157	3	1	61	1	0	0	0	0	1	0	0	0	12792	1059	37	1	208	1	PTH	11	13514157	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116918	13514157	121492359	7216	15201										
SPON1	10418	broad.mit.edu	37	chr11	14096949	14096949	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgagggctctctgaccaaGaaactttgtgaacaaggtaa	11	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:14096949G>T	ENST00000310358.7	+	0	1075							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)		p.K179N(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		CTCTGACCAAGAAACTTTGTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											46	41	43					11																	14096949		1891	4099	5990	14053525			10418			AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"spondin 1, (f-spondin) extracellular matrix protein"			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		11.37:g.14096949G>T			14053525	A8K6W5|O94862|Q8NCD7|Q8WUR5	Missense_Mutation	SNP	ENST00000310358.7	37		.	.	.	.	.	.	.	.	.	.	G	19.05	3.751233	0.69533	.	.	ENSG00000152268	ENST00000310358	.	.	.	6.03	5.11	0.69529	Reeler domain (1);	0.229807	0.41500	D	0.000871	T	0.51635	0.1686	M	0.82193	2.58	0.58432	D	0.999993	P	0.52316	0.952	B	0.34779	0.189	T	0.72487	-0.4278	8	0.56958	D	0.05	.	12.9645	0.58475	0.0778:0.0:0.9222:0.0	.	179	Q9HCB6	SPON1_HUMAN	N	179	.	ENSP00000309297:K179N	K	+	3	2	SPON1	14053525	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.625000	0.61262	1.547000	0.49401	0.655000	0.94253	AAG		0.517	SPON1-201	KNOWN	basic	processed_transcript	processed_transcript		NM_145584		T	14096949	G	T	14096949	1	4	61	0	1	0	0	0	0	0	0	0	15121	933	33	2		2	SPON1	11	14096949	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	582792	14096949	120909567	7217	15202										
RRAS2	22800	broad.mit.edu	37	chr11	14317365	14317365	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactgctttgtgtaagaatCttcaatggttggatcataat	8	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:14317365C>A	ENST00000256196.4	-	2	458	c.145G>T	c.(145-147)Gat>Tat	p.D49Y	RRAS2_ENST00000529237.1_5'UTR|RRAS2_ENST00000545643.1_Missense_Mutation_p.D55Y|RRAS2_ENST00000414023.2_5'UTR|RRAS2_ENST00000532814.1_5'UTR|RRAS2_ENST00000537760.1_Missense_Mutation_p.D14Y|RRAS2_ENST00000526063.1_5'UTR|RRAS2_ENST00000534746.1_5'UTR			P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2	49					osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D49Y(1)		breast(3)|endometrium(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	12				Epithelial(150;0.203)		GTGTAAGAATCTTCAATGGTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	11											129	132	131					11																	14317365		2200	4294	6494	14273941	SO:0001583	missense	22800			M31468	CCDS7814.1, CCDS44544.1, CCDS53603.1	11p15.2	2014-05-09			ENSG00000133818	ENSG00000133818			17271	protein-coding gene	gene with protein product		600098				2108320, 8052619	Standard	NM_012250		Approved	TC21	uc001mlf.4	P62070	OTTHUMG00000165756	ENST00000256196.4:c.145G>T	11.37:g.14317365C>A	ENSP00000256196:p.Asp49Tyr		14273941	B2R9Z3|B7Z5Z2|B7Z6C4|B7Z7H6|P17082	Missense_Mutation	SNP	ENST00000256196.4	37	CCDS7814.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487131	0.84854	.	.	ENSG00000133818	ENST00000537760;ENST00000545643;ENST00000256196;ENST00000531807	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	4.82	4.82	0.62117	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.94745	0.8304	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	D	0.96887	0.9650	10	0.87932	D	0	.	17.8569	0.88767	0.0:1.0:0.0:0.0	.	55;49	B7Z5Z2;P62070	.;RRAS2_HUMAN	Y	14;55;49;30	ENSP00000437547:D14Y;ENSP00000441722:D55Y;ENSP00000256196:D49Y;ENSP00000435453:D30Y	ENSP00000256196:D49Y	D	-	1	0	RRAS2	14273941	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.531000	0.81973	2.382000	0.81193	0.313000	0.20887	GAT		0.343	RRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386035.1	NM_012250		A	14317365	C	A	14317365	3	1	61	1	0	0	0	0	1	0	0	0	13714	913	32	2	489	2	RRAS2	11	14317365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220416	14317365	120689151	7218	15203										
COPB1	1315	broad.mit.edu	37	chr11	14501200	14501200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcgctgaatggcttcacGaacaaactccaagacatcag	8	11	2	2	rs377571611		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:14501200G>A	ENST00000249923.3	-	11	1573	c.1273C>T	c.(1273-1275)Cgt>Tgt	p.R425C	RNU7-49P_ENST00000516182.1_RNA|COPB1_ENST00000439561.2_Missense_Mutation_p.R425C	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	425					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.R425C(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						ATGGCTTCACGAACAAACTCC	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	11						G	CYS/ARG,CYS/ARG,CYS/ARG	0,4400		0,0,2200	73	74	74		1273,1273,1273	5.9	1	11		74	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense,missense	COPB1	NM_001144061.1,NM_001144062.1,NM_016451.4	180,180,180	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	425/954,425/954,425/954	14501200	1,12987	2200	4294	6494	14457776	SO:0001583	missense	1315			BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.1273C>T	11.37:g.14501200G>A	ENSP00000249923:p.Arg425Cys		14457776	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	G	34	5.373147	0.95923	0.0	1.16E-4	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	T;T;T	0.27557	1.66;1.66;1.66	5.92	5.92	0.95590	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69593	0.3128	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77451	-0.2583	10	0.87932	D	0	-0.1037	20.3343	0.98733	0.0:0.0:1.0:0.0	.	425	P53618	COPB_HUMAN	C	425	ENSP00000249923:R425C;ENSP00000397873:R425C;ENSP00000436383:R425C	ENSP00000249923:R425C	R	-	1	0	COPB1	14457776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.932000	0.87634	2.822000	0.97130	0.650000	0.86243	CGT		0.343	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		A	14501200	G	A	14501200	3	1	61	1	0	0	0	0	1	0	0	0	3734	1058	37	1	1636	1	COPB1	11	14501200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	183835	14501200	120505316	7219	15204										
COPB1	1315	broad.mit.edu	37	chr11	14515779	14515779	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtatgcatcacatacaaGgatcatctcatgtaaaagtc	6	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:14515779G>T	ENST00000249923.3	-	3	598	c.298C>A	c.(298-300)Ctt>Att	p.L100I	COPB1_ENST00000439561.2_Missense_Mutation_p.L100I|PSMA1_ENST00000555531.1_3'UTR|PSMA1_ENST00000419365.2_3'UTR	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	100					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.L100I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						TCACATACAAGGATCATCTCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	76	75					11																	14515779		2198	4294	6492	14472355	SO:0001583	missense	1315			BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.298C>A	11.37:g.14515779G>T	ENSP00000249923:p.Leu100Ile		14472355	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.695772	0.88830	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234;ENST00000529866;ENST00000534771	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.48	5.48	0.80851	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84840	0.0807	10	0.87932	D	0	.	19.3442	0.94357	0.0:0.0:1.0:0.0	.	100	P53618	COPB_HUMAN	I	100	ENSP00000249923:L100I;ENSP00000397873:L100I;ENSP00000436383:L100I;ENSP00000431530:L100I;ENSP00000436401:L100I	ENSP00000249923:L100I	L	-	1	0	COPB1	14472355	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.657000	0.67996	2.567000	0.86603	0.655000	0.94253	CTT		0.328	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		T	14515779	G	T	14515779	3	4	61	1	0	0	0	0	1	0	0	0	3734	1000	35	2	2643	2	COPB1	11	14515779	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14579	14515779	120490737	7220	15205										
CALCB	797	broad.mit.edu	37	chr11	15096614	15096614	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccttccacaggtctgccCtggagagcagcccagacccg	10	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:15096614C>A	ENST00000533448.1	+	3	205	c.94C>A	c.(94-96)Ctg>Atg	p.L32M	CALCB_ENST00000324229.6_Missense_Mutation_p.L32M|CALCB_ENST00000523376.1_Missense_Mutation_p.L43M			P10092	CALCB_HUMAN	calcitonin-related polypeptide beta	32					cellular calcium ion homeostasis (GO:0006874)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)	p.L32M(1)		endometrium(1)|large_intestine(1)|lung(1)|skin(2)	5						CAGGTCTGCCCTGGAGAGCAG	0.617											OREG0020793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											53	56	55					11																	15096614		2200	4294	6494	15053190	SO:0001583	missense	797				CCDS7820.1	11p14.2-p12	2013-02-25	2008-02-20			ENSG00000175868		"Endogenous ligands"	1438	protein-coding gene	gene with protein product		114160	"calcitonin 2"	CALC2			Standard	NM_000728		Approved	FLJ30166, CGRP-II	uc001mlx.1	P10092		ENST00000533448.1:c.94C>A	11.37:g.15096614C>A	ENSP00000433490:p.Leu32Met	700	15053190	A8K573|D3DQX4|Q569I0|Q9UCN9	Missense_Mutation	SNP	ENST00000533448.1	37	CCDS7820.1	.	.	.	.	.	.	.	.	.	.	C	19.51	3.841245	0.71488	.	.	ENSG00000175868	ENST00000523376;ENST00000324229;ENST00000533448	T;T;T	0.37058	1.22;1.22;1.22	5.41	-5.49	0.02584	.	0.562827	0.14959	N	0.288462	T	0.50069	0.1594	M	0.89414	3.03	0.09310	N	0.999997	P	0.51147	0.942	P	0.62014	0.897	T	0.44112	-0.9349	10	0.66056	D	0.02	-3.0046	1.8752	0.03217	0.2077:0.3556:0.1148:0.3218	.	32	P10092	CALCB_HUMAN	M	43;32;32	ENSP00000428882:L43M;ENSP00000346017:L32M;ENSP00000433490:L32M	ENSP00000346017:L32M	L	+	1	2	CALCB	15053190	0.734000	0.28142	0.002000	0.10522	0.394000	0.30568	0.527000	0.22987	-1.237000	0.02539	0.561000	0.74099	CTG		0.617	CALCB-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387433.1	NM_000728		A	15096614	C	A	15096614	3	1	61	1	0	0	0	0	1	0	0	0	2582	680	24	2	100	2	CALCB	11	15096614	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	580835	15096614	119909902	7221	15206										
SOX6	55553	broad.mit.edu	37	chr11	16362605	16362605	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcccagtcagcatcttgttGaatggtactgacaagtgttg	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:16362605G>T	ENST00000352083.6	-	2	267	c.190C>A	c.(190-192)Caa>Aaa	p.Q64K	SOX6_ENST00000533658.1_5'UTR|SOX6_ENST00000316399.6_Missense_Mutation_p.Q64K|SOX6_ENST00000528252.1_Missense_Mutation_p.Q64K|SOX6_ENST00000528429.1_Missense_Mutation_p.Q64K|SOX6_ENST00000396356.3_Missense_Mutation_p.Q64K|SOX6_ENST00000527619.1_Missense_Mutation_p.Q67K			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	64					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.Q64K(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						GCATCTTGTTGAATGGTACTG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											251	198	216					11																	16362605		2200	4294	6494	16319181	SO:0001583	missense	55553			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.190C>A	11.37:g.16362605G>T	ENSP00000339876:p.Gln64Lys		16319181	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	G	17.31	3.357342	0.61293	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429;ENST00000533411;ENST00000526673;ENST00000529469	D;D;D;D;D;D	0.97598	-4.45;-4.44;-4.45;-4.44;-4.44;-4.44	5.18	5.18	0.71444	.	0.075171	0.56097	D	0.000035	D	0.93838	0.8029	L	0.27053	0.805	0.45867	D	0.99872	B;B;B;B;B	0.33549	0.07;0.114;0.162;0.07;0.417	B;B;B;B;B	0.30495	0.033;0.033;0.048;0.039;0.116	D	0.93259	0.6641	10	0.49607	T	0.09	.	18.2917	0.90133	0.0:0.0:1.0:0.0	.	64;64;64;64;67	E9PQ78;E9PQL4;P35712-3;P35712;P35712-2	.;.;.;SOX6_HUMAN;.	K	64;64;64;64;67;64;64;64;64	ENSP00000324948:Q64K;ENSP00000339876:Q64K;ENSP00000379644:Q64K;ENSP00000432134:Q64K;ENSP00000434455:Q67K;ENSP00000433233:Q64K	ENSP00000324948:Q64K	Q	-	1	0	SOX6	16319181	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.397000	0.81536	0.467000	0.42956	CAA		0.478	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		T	16362605	G	T	16362605	3	4	61	1	0	0	0	0	1	0	0	0	14992	1299	45	2	2398	2	SOX6	11	16362605	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1265991	16362605	118643911	7222	15207										
PLEKHA7	144100	broad.mit.edu	37	chr11	16816563	16816563	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttctgtatctgcgatttCtcctgaggaagacgaagtgg	11	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:16816563C>A	ENST00000355661.3	-	18	2422	c.2412G>T	c.(2410-2412)gaG>gaT	p.E804D	PLEKHA7_ENST00000448080.2_Missense_Mutation_p.E804D|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Missense_Mutation_p.E804D			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	804					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)	p.E804D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						TCTGCGATTTCTCCTGAGGAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											162	145	151					11																	16816563		2200	4294	6494	16773139	SO:0001583	missense	144100			BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2412G>T	11.37:g.16816563C>A	ENSP00000347883:p.Glu804Asp		16773139	B4DK33|B4DWC3|Q86VZ7	Missense_Mutation	SNP	ENST00000355661.3	37	CCDS31434.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.64|16.64	3.179336|3.179336	0.57800|0.57800	.|.	.|.	ENSG00000166689|ENSG00000166689	ENST00000531066;ENST00000355661;ENST00000448080;ENST00000525581|ENST00000530489	T;T;T;T|.	0.41758|.	1.15;1.15;1.15;0.99|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.088563|.	0.85682|.	N|.	0.000000|.	T|T	0.65626|0.65626	0.2709|0.2709	L|L	0.60455|0.60455	1.87|1.87	0.46203|0.46203	D|D	0.998924|0.998924	B;B;P;B|.	0.43094|.	0.111;0.162;0.799;0.313|.	B;B;B;B|.	0.37650|.	0.148;0.051;0.255;0.133|.	T|T	0.62329|0.62329	-0.6877|-0.6877	10|5	0.21014|.	T|.	0.42|.	-33.2724|-33.2724	13.3367|13.3367	0.60522|0.60522	0.0:0.9276:0.0:0.0724|0.0:0.9276:0.0:0.0724	.|.	378;804;804;804|.	Q6IQ23-3;E9PKC0;Q6IQ23;Q6IQ23-2|.	.;.;PKHA7_HUMAN;.|.	D|I	804;804;804;135|435	ENSP00000435389:E804D;ENSP00000347883:E804D;ENSP00000416895:E804D;ENSP00000431455:E135D|.	ENSP00000347883:E804D|.	E|R	-|-	3|2	2|0	PLEKHA7|PLEKHA7	16773139|16773139	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	2.418000|2.418000	0.44662|0.44662	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAG|AGA		0.448	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		A	16816563	C	A	16816563	3	1	61	1	0	0	0	0	1	0	0	0	12092	912	32	2	977	2	PLEKHA7	11	16816563	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	453958	16816563	118189953	7223	15208										
PIK3C2A	5286	broad.mit.edu	37	chr11	17121459	17121459	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttggggttgaagtgcatCtctaacgtatttcaaatctt	9	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17121459C>A	ENST00000265970.7	-	25	4065	c.4066G>T	c.(4066-4068)Gat>Tat	p.D1356Y	PIK3C2A_ENST00000540361.1_Missense_Mutation_p.D976Y|PIK3C2A_ENST00000531428.1_5'UTR	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1356	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.D1356Y(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TGAAGTGCATCTCTAACGTAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	11											125	127	126					11																	17121459		2200	4292	6492	17078035	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.4066G>T	11.37:g.17121459C>A	ENSP00000265970:p.Asp1356Tyr		17078035	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.310439	0.81358	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	D;D	0.82893	-1.66;-1.66	5.43	5.43	0.79202	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.086868	0.85682	D	0.000000	D	0.93112	0.7807	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93965	0.7244	10	0.87932	D	0	-6.2936	19.6092	0.95599	0.0:1.0:0.0:0.0	.	1356	O00443	P3C2A_HUMAN	Y	1356;976	ENSP00000265970:D1356Y;ENSP00000438687:D976Y	ENSP00000265970:D1356Y	D	-	1	0	PIK3C2A	17078035	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.666000	0.83877	2.711000	0.92665	0.655000	0.94253	GAT		0.313	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		A	17121459	C	A	17121459	3	1	61	1	0	0	0	0	1	0	0	0	11940	913	32	2	1026	2	PIK3C2A	11	17121459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	304896	17121459	117885057	7224	15209										
PIK3C2A	5286	broad.mit.edu	37	chr11	17140199	17140199	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaaatcttaccaatataAattgtgtgctatctggatat	5	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17140199A>G	ENST00000265970.7	-	17	3027	c.3028T>C	c.(3028-3030)Tta>Cta	p.L1010L	PIK3C2A_ENST00000540361.1_Silent_p.L630L|PIK3C2A_ENST00000531428.1_Intron|RNU6-593P_ENST00000364716.1_RNA	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1010	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.L1010L(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TACCAATATAAATTGTGTGCT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	11											74	79	77					11																	17140199		2200	4281	6481	17096775	SO:0001819	synonymous_variant	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3028T>C	11.37:g.17140199A>G			17096775	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																				0.318	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17140199	A	G	17140199	2	3	61	1	0	0	0	0	0	0	0	1	11940	11	1	4		4	PIK3C2A	11	17140199	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18740	17140199	117866317	7225	15210										
NUCB2	4925	broad.mit.edu	37	chr11	17351716	17351716	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagaggaagaactaaaaGaatatgaaaatattattgct	7	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17351716G>T	ENST00000529010.1	+	12	1264	c.1045G>T	c.(1045-1047)Gaa>Taa	p.E349*	NUCB2_ENST00000458064.2_Nonsense_Mutation_p.E319*|NUCB2_ENST00000323688.6_Nonsense_Mutation_p.E349*	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	349	Binds to necdin. {ECO:0000250}.					cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)	p.E349*(1)		kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AGAACTAAAAGAATATGAAAA	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											31	29	30					11																	17351716		1818	4073	5891	17308292	SO:0001587	stop_gained	4925			AF052642	CCDS41623.1	11p15.1	2013-01-10						"EF-hand domain containing"	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1045G>T	11.37:g.17351716G>T	ENSP00000436455:p.Glu349*		17308292	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation	SNP	ENST00000529010.1	37	CCDS41623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.842348|6.842348	0.97877|0.97877	.|.	.|.	ENSG00000070081|ENSG00000070081	ENST00000323688;ENST00000529010;ENST00000458064|ENST00000527580	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.046069|.	0.85682|.	D|.	0.000000|.	.|T	.|0.63733	.|0.2536	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69087	.|-0.5238	.|3	0.42905|.	T|.	0.14|.	-14.1579|-14.1579	13.0867|13.0867	0.59144|0.59144	0.0732:0.0:0.9268:0.0|0.0732:0.0:0.9268:0.0	.|.	.|.	.|.	.|.	X|I	349;349;319|126	.|.	ENSP00000320168:E349X|.	E|R	+|+	1|2	0|0	NUCB2|NUCB2	17308292|17308292	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.024000|7.024000	0.76443|0.76443	2.692000|2.692000	0.91855|0.91855	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.308	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013		T	17351716	G	T	17351716	4	4	61	1	0	0	0	0	0	1	0	0	10750	943	33	2	1083	2	NUCB2	11	17351716	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211517	17351716	117654800	7226	15211										
ABCC8	6833	broad.mit.edu	37	chr11	17415271	17415271	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaccacagtgcggtctgcGaaggctgtcatcaccacctt	11	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17415271G>A	ENST00000389817.3	-	38	4649	c.4581C>T	c.(4579-4581)ttC>ttT	p.F1527F	ABCC8_ENST00000302539.4_Silent_p.F1528F			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1527	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.F1527F(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TGCGGTCTGCGAAGGCTGTCA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	11											224	187	199					11																	17415271		2200	4293	6493	17371847	SO:0001819	synonymous_variant	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4581C>T	11.37:g.17415271G>A			17371847	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1																																																																																				0.617	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17415271	G	A	17415271	2	1	61	1	0	0	0	0	0	0	0	1	58	1049	37	1		1	ABCC8	11	17415271	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63555	17415271	117591245	7227	15212										
USH1C	10083	broad.mit.edu	37	chr11	17531073	17531073	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcgggtgggagtgaggtCttgggtgggaacggatggcg	24	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17531073C>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000005226.7_Missense_Mutation_p.D615Y|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)	p.D615Y(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GGAGTGAGGTCTTGGGTGGGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											34	35	35					11																	17531073		2200	4293	6493	17487649	SO:0001627	intron_variant	10083			AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1285-7546G>T	11.37:g.17531073C>A			17487649	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.110624	0.37242	.	.	ENSG00000006611	ENST00000005226	T	0.40756	1.02	5.93	4.08	0.47627	.	0.462111	0.24518	N	0.037827	T	0.27967	0.0689	.	.	.	0.25312	N	0.989197	P	0.41265	0.744	B	0.34038	0.174	T	0.23332	-1.0191	9	0.56958	D	0.05	.	7.9787	0.30170	0.0:0.6095:0.3104:0.0801	.	615	Q7RTU8	.	Y	615	ENSP00000005226:D615Y	ENSP00000005226:D615Y	D	-	1	0	USH1C	17487649	0.993000	0.37304	1.000000	0.80357	0.984000	0.73092	0.248000	0.18198	1.534000	0.49203	-0.188000	0.12872	GAC		0.642	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		A	17531073	C	A	17531073	1	1	61	0	1	0	0	0	0	0	0	0	17074	913	32	2		2	USH1C	11	17531073	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115802	17531073	117475443	7228	15213										
USH1C	10083	broad.mit.edu	37	chr11	17532023	17532023	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcctctccacccaatattGaatcttttccgattcttcaa	4	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17532023G>T	ENST00000318024.4	-	15	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000005226.7_Missense_Mutation_p.Q487K|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)	p.Q487K(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						ACCCAATATTGAATCTTTTCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	65	68					11																	17532023		2200	4293	6493	17488599	SO:0001627	intron_variant	10083			AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1284+6924C>A	11.37:g.17532023G>T			17488599	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323364	0.95708	.	.	ENSG00000006611	ENST00000005226	T	0.63580	-0.05	5.92	5.92	0.95590	.	0.167646	0.39985	N	0.001210	T	0.80099	0.4561	.	.	.	0.45541	D	0.998491	D	0.63880	0.993	D	0.67548	0.952	T	0.80834	-0.1205	9	0.66056	D	0.02	.	19.0921	0.93231	0.0:0.0:1.0:0.0	.	487	Q7RTU8	.	K	487	ENSP00000005226:Q487K	ENSP00000005226:Q487K	Q	-	1	0	USH1C	17488599	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.570000	0.90748	2.813000	0.96785	0.561000	0.74099	CAA		0.493	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		T	17532023	G	T	17532023	1	4	61	0	1	0	0	0	0	0	0	0	17074	1299	45	2		2	USH1C	11	17532023	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	950	17532023	117474493	7229	15214										
USH1C	10083	broad.mit.edu	37	chr11	17542514	17542514	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcttcttcccattgcttCttaaacttctcttcctcctc	2	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17542514C>A	ENST00000318024.4	-	14	1221	c.1113G>T	c.(1111-1113)aaG>aaT	p.K371N	USH1C_ENST00000527020.1_Missense_Mutation_p.K352N|USH1C_ENST00000005226.7_Missense_Mutation_p.K371N|USH1C_ENST00000527720.1_Missense_Mutation_p.K340N	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	371					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)	p.K371N(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CCCATTGCTTCTTAAACTTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											423	434	430					11																	17542514		2200	4293	6493	17499090	SO:0001583	missense	10083			AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1113G>T	11.37:g.17542514C>A	ENSP00000317018:p.Lys371Asn		17499090	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.804117	0.50315	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226	T;T;T;T	0.66099	1.7;1.68;1.86;-0.19	5.88	4.96	0.65561	.	0.410430	0.31370	N	0.007778	T	0.44953	0.1318	N	0.19112	0.55	0.31537	N	0.660447	B;B;B	0.14438	0.01;0.006;0.004	B;B;B	0.12837	0.006;0.004;0.008	T	0.46498	-0.9187	10	0.37606	T	0.19	.	10.2257	0.43225	0.0:0.8568:0.0:0.1432	.	352;371;371	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	N	371;340;352;371	ENSP00000317018:K371N;ENSP00000432944:K340N;ENSP00000436934:K352N;ENSP00000005226:K371N	ENSP00000005226:K371N	K	-	3	2	USH1C	17499090	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	0.812000	0.27211	2.790000	0.95986	0.591000	0.81541	AAG		0.502	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		A	17542514	C	A	17542514	3	1	61	1	0	0	0	0	1	0	0	0	17074	912	32	2	1720	2	USH1C	11	17542514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10491	17542514	117464002	7230	15215										
KCNC1	3746	broad.mit.edu	37	chr11	17794164	17794164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtaggaaacctcttagagGcatgtcgatctgacctttca	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:17794164G>A	ENST00000379472.3	+	2	1553	c.1523G>A	c.(1522-1524)gGc>gAc	p.G508D	KCNC1_ENST00000265969.6_Intron	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	508					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.G508D(1)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	CCTCTTAGAGGCATGTCGATC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											59	60	60					11																	17794164		2200	4290	6490	17750740	SO:0001583	missense	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.1523G>A	11.37:g.17794164G>A	ENSP00000368785:p.Gly508Asp		17750740	K4DI87	Missense_Mutation	SNP	ENST00000379472.3	37	CCDS7827.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703908	0.48412	.	.	ENSG00000129159	ENST00000379472	D	0.97138	-4.26	5.42	5.42	0.78866	.	2.715750	0.00897	N	0.002306	D	0.98036	0.9353	M	0.75264	2.295	0.47737	D	0.999506	D	0.61080	0.989	P	0.49665	0.618	D	0.90470	0.4452	9	.	.	.	.	19.2221	0.93801	0.0:0.0:1.0:0.0	.	508	P48547	KCNC1_HUMAN	D	508	ENSP00000368785:G508D	.	G	+	2	0	KCNC1	17750740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.976000	0.63785	2.530000	0.85305	0.561000	0.74099	GGC		0.522	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		A	17794164	G	A	17794164	3	1	61	1	0	0	0	0	1	0	0	0	8035	1203	42	3	1529	3	KCNC1	11	17794164	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	251650	17794164	117212352	7231	15216										
SERGEF	26297	broad.mit.edu	37	chr11	18014478	18014478	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaagagctggtacctacCtgttaatgaagctgagtggt	13	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18014478C>A	ENST00000265965.5	-	7	836	c.685G>T	c.(685-687)Gat>Tat	p.D229Y	SERGEF_ENST00000532265.1_Splice_Site_p.D115Y|SERGEF_ENST00000528200.1_Splice_Site_p.D229Y	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	229					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.D229Y(1)		autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						TGGTACCTACCTGTTAATGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											121	107	112					11																	18014478		2200	4293	6493	17971054	SO:0001630	splice_region_variant	26297			AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.685+1G>T	11.37:g.18014478C>A			17971054	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	37	CCDS7828.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.78|18.78|18.78	3.696965|3.696965|3.696965	0.68386|0.68386|0.68386	.|.|.	.|.|.	ENSG00000129158|ENSG00000129158|ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000532265;ENST00000529728;ENST00000530613;ENST00000532389|ENST00000525920|ENST00000529151	T;T;T;T;T;T|T|.	0.80994|0.33654|.	-1.44;-1.44;-1.44;-1.44;-1.44;-1.44|1.4|.	5.19|5.19|5.19	5.19|5.19|5.19	0.71726|0.71726|0.71726	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);|.|.	0.355374|.|.	0.32608|.|.	N|.|.	0.005867|.|.	T|T|T	0.70850|0.70850|0.70850	0.3271|0.3271|0.3271	L|L|L	0.60067|0.60067|0.60067	1.865|1.865|1.865	0.45272|0.45272|0.45272	D|D|D	0.998278|0.998278|0.998278	D;D;D;D|.|.	0.89917|.|.	0.994;0.999;0.997;1.0|.|.	D;D;D;D|.|.	0.79108|.|.	0.925;0.983;0.916;0.992|.|.	T|T|T	0.67787|0.67787|0.67787	-0.5580|-0.5580|-0.5580	9|6|5	.|.|.	.|.|.	.|.|.	-17.8917|-17.8917|-17.8917	16.1002|16.1002|16.1002	0.81166|0.81166|0.81166	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	115;115;229;229|.|.	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8|.|.	.;.;.;SRGEF_HUMAN|.|.	Y|C|H	229;229;115;115;115;115|99|92	ENSP00000265965:D229Y;ENSP00000434188:D229Y;ENSP00000431314:D115Y;ENSP00000437297:D115Y;ENSP00000436080:D115Y;ENSP00000435898:D115Y|ENSP00000436648:G99C|.	.|.|.	D|G|Q	-|-|-	1|1|3	0|0|2	SERGEF|SERGEF|SERGEF	17971054|17971054|17971054	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.738000|0.738000|0.738000	0.42128|0.42128|0.42128	4.473000|4.473000|4.473000	0.60196|0.60196|0.60196	2.865000|2.865000|2.865000	0.98341|0.98341|0.98341	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAT|GGT|CAG		0.383	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	Missense_Mutation	A	18014478	C	A	18014478	5	1	61	1	0	0	0	0	0	0	1	0	14114	695	24	2	711	2	SERGEF	11	18014478	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220314	18014478	116992038	7232	15217										
TPH1	7166	broad.mit.edu	37	chr11	18062235	18062235	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagtcctccaacttcattCtttaaggaaaaaatgagact	5	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18062235C>A	ENST00000250018.2	-	1	637	c.75G>T	c.(73-75)aaG>aaT	p.K25N	TPH1_ENST00000341556.2_Missense_Mutation_p.K25N	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	25	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.				aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.K25N(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	CAACTTCATTCTTTAAGGAAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											51	47	49					11																	18062235		2198	4290	6488	18018811	SO:0001583	missense	7166			X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"tryptophan 5-monooxygenase"	191060	"tryptophan hydroxylase (tryptophan 5-monooxygenase)"	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.75G>T	11.37:g.18062235C>A	ENSP00000250018:p.Lys25Asn		18018811	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Missense_Mutation	SNP	ENST00000250018.2	37	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.318953	0.41096	.	.	ENSG00000129167	ENST00000250018;ENST00000341556;ENST00000528338	D;D;D	0.99143	-5.48;-5.48;-5.48	5.28	2.31	0.28768	Amino acid-binding ACT (1);	0.089139	0.85682	D	0.000000	D	0.97161	0.9072	M	0.62723	1.935	0.52099	D	0.999942	B	0.14438	0.01	B	0.21917	0.037	D	0.93215	0.6603	10	0.41790	T	0.15	-7.232	6.0048	0.19541	0.1299:0.6457:0.0:0.2244	.	25	P17752	TPH1_HUMAN	N	25;25;35	ENSP00000250018:K25N;ENSP00000343550:K25N;ENSP00000436081:K35N	ENSP00000250018:K25N	K	-	3	2	TPH1	18018811	0.998000	0.40836	0.999000	0.59377	0.716000	0.41182	0.702000	0.25631	0.194000	0.20326	-0.424000	0.05967	AAG		0.323	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179		A	18062235	C	A	18062235	3	1	61	1	0	0	0	0	1	0	0	0	16441	912	32	2	1299	2	TPH1	11	18062235	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47757	18062235	116944281	7233	15218										
SAAL1	113174	broad.mit.edu	37	chr11	18105238	18105238	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgacactgttccatattTtgtaagacccgaatgaggct	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18105238T>G	ENST00000524803.1	-	10	1132	c.1083A>C	c.(1081-1083)caA>caC	p.Q361H	SAAL1_ENST00000300013.4_Missense_Mutation_p.Q360H|SAAL1_ENST00000529318.1_Missense_Mutation_p.Q363H			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	361								p.Q361H(1)		breast(2)|large_intestine(5)|lung(8)	15						GTTCCATATTTTGTAAGACCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	11											111	106	108					11																	18105238		2200	4293	6493	18061814	SO:0001583	missense	113174			AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.1083A>C	11.37:g.18105238T>G	ENSP00000432487:p.Gln361His		18061814	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	37	CCDS31439.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.515746	0.44763	.	.	ENSG00000166788	ENST00000524803;ENST00000300013;ENST00000529318	T;T;T	0.36340	1.34;1.34;1.26	5.99	4.81	0.61882	Armadillo-like helical (1);	0.844921	0.11039	N	0.606397	T	0.29126	0.0724	L	0.27053	0.805	0.28564	N	0.910983	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.004	T	0.10683	-1.0619	10	0.45353	T	0.12	-1.2183	13.3415	0.60547	0.0:0.0:0.14:0.86	.	363;361;361	E9PRZ1;G1UCX3;Q96ER3	.;.;SAAL1_HUMAN	H	361;360;363	ENSP00000432487:Q361H;ENSP00000300013:Q360H;ENSP00000432216:Q363H	ENSP00000300013:Q360H	Q	-	3	2	SAAL1	18061814	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	1.958000	0.40402	2.291000	0.77112	0.533000	0.62120	CAA		0.368	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		G	18105238	T	G	18105238	3	3	61	1	0	0	0	0	1	0	0	0	13838	1838	64	4	353	4	SAAL1	11	18105238	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	43003	18105238	116901278	7234	15219										
MRGPRX3	117195	broad.mit.edu	37	chr11	18159482	18159482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttttccaggatccacctgGattggaaagtcttattttgt	9	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18159482G>A	ENST00000396275.2	+	3	1094	c.733G>A	c.(733-735)Gat>Aat	p.D245N		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D245N(2)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GATCCACCTGGATTGGAAAGT	0.512																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	11											107	103	105					11																	18159482		2200	4293	6493	18116058	SO:0001583	missense	117195				CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.733G>A	11.37:g.18159482G>A	ENSP00000379571:p.Asp245Asn		18116058	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	.	.	.	.	.	.	.	.	.	.	G	8.145	0.786108	0.16189	.	.	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.70986	-0.53;4.24	0.956	0.956	0.19608	GPCR, rhodopsin-like superfamily (1);	2.700440	0.01045	N	0.004375	T	0.54870	0.1885	N	0.20357	0.565	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.38112	-0.9676	10	0.22706	T	0.39	.	5.2081	0.15302	0.0:0.0:1.0:0.0	.	245	Q96LB0	MRGX3_HUMAN	N	245	ENSP00000379571:D245N;ENSP00000436242:D245N	ENSP00000379571:D245N	D	+	1	0	MRGPRX3	18116058	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	-1.323000	0.02692	0.796000	0.33947	0.195000	0.17529	GAT		0.512	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		A	18159482	G	A	18159482	3	1	61	1	0	0	0	0	1	0	0	0	9798	1174	41	3	735	3	MRGPRX3	11	18159482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54244	18159482	116847034	7235	15220										
SAA4	6291	broad.mit.edu	37	chr11	18257431	18257431	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctttcactggtgactcCcatgaccaaggagcagaaaa	9	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18257431C>A	ENST00000278222.4	-	2	223	c.43G>T	c.(43-45)Gga>Tga	p.G15*	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	15					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)		p.G15*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CTGGTGACTCCCATGACCAAG	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											121	116	117					11																	18257431		2199	4293	6492	18214007	SO:0001587	stop_gained	6291			M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.43G>T	11.37:g.18257431C>A	ENSP00000278222:p.Gly15*		18214007	Q6FHJ4	Nonsense_Mutation	SNP	ENST00000278222.4	37	CCDS7832.1	.	.	.	.	.	.	.	.	.	.	C	34	5.305145	0.95601	.	.	ENSG00000148965	ENST00000278222	.	.	.	3.81	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-0.4048	8.7793	0.34781	0.2268:0.7732:0.0:0.0	.	.	.	.	X	15	.	ENSP00000278222:G15X	G	-	1	0	SAA4	18214007	0.047000	0.20315	0.620000	0.29132	0.327000	0.28475	0.919000	0.28692	0.834000	0.34852	0.585000	0.79938	GGA		0.468	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512		A	18257431	C	A	18257431	4	1	61	1	0	0	0	0	0	1	0	0	13837	632	22	2	361	2	SAA4	11	18257431	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97949	18257431	116749085	7236	15221										
SAA1	6288	broad.mit.edu	37	chr11	18288472	18288472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggttttctgctccttggTcctgggtgtcagcagccgaa	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18288472T>C	ENST00000405158.2	+	2	222	c.38T>C	c.(37-39)gTc>gCc	p.V13A	SAA1_ENST00000532858.1_Missense_Mutation_p.V13A|SAA1_ENST00000356524.4_Missense_Mutation_p.V13A|RNA5SP334_ENST00000364825.1_RNA	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	13					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)	p.V13A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	TGCTCCTTGGTCCTGGGTGTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											138	123	128					11																	18288472		2198	4291	6489	18245048	SO:0001583	missense	6288			M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"Endogenous ligands"	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.38T>C	11.37:g.18288472T>C	ENSP00000384906:p.Val13Ala		18245048	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Missense_Mutation	SNP	ENST00000405158.2	37	CCDS7835.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.284077	0.23392	.	.	ENSG00000173432	ENST00000356524;ENST00000532858;ENST00000405158	T;T;T	0.10288	2.89;2.89;2.89	3.67	1.24	0.21308	.	0.282600	0.28042	N	0.016840	T	0.11410	0.0278	M	0.75085	2.285	0.09310	N	1	B;B	0.22909	0.001;0.077	B;B	0.18263	0.001;0.021	T	0.22173	-1.0224	10	0.59425	D	0.04	.	3.8316	0.08876	0.0:0.1178:0.2194:0.6629	.	13;13	D3DQX7;P02735	.;SAA_HUMAN	A	13	ENSP00000348918:V13A;ENSP00000436866:V13A;ENSP00000384906:V13A	ENSP00000348918:V13A	V	+	2	0	SAA1	18245048	0.403000	0.25319	0.001000	0.08648	0.087000	0.18053	0.704000	0.25661	0.254000	0.21573	0.374000	0.22700	GTC		0.522	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161		C	18288472	T	C	18288472	3	2	61	1	0	0	0	0	1	0	0	0	13835	1667	58	4	40	4	SAA1	11	18288472	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31041	18288472	116718044	7237	15222										
HPS5	11234	broad.mit.edu	37	chr11	18318408	18318408	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgctgtgaggtgaattCtttaaatctctcatcttctg	7	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18318408C>A	ENST00000349215.3	-	12	1724	c.1447G>T	c.(1447-1449)Gaa>Taa	p.E483*	HPS5_ENST00000396253.3_Nonsense_Mutation_p.E369*|HPS5_ENST00000438420.2_Nonsense_Mutation_p.E369*|HPS5_ENST00000352460.3_5'Flank|HPS5_ENST00000531848.1_Nonsense_Mutation_p.E369*	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	483					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.E483*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GAGGTGAATTCTTTAAATCTC	0.448									Hermansky-Pudlak syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	11											188	174	179					11																	18318408		2199	4293	6492	18274984	SO:0001587	stop_gained	11234	Familial Cancer Database	HPS, HPS1-8	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1447G>T	11.37:g.18318408C>A	ENSP00000265967:p.Glu483*		18274984	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Nonsense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	C	40	8.447732	0.98815	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	.	.	.	5.71	5.71	0.89125	.	0.107759	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.8493	0.96733	0.0:1.0:0.0:0.0	.	.	.	.	X	369;369;483;369	.	ENSP00000265967:E483X	E	-	1	0	HPS5	18274984	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.487000	0.81328	2.701000	0.92244	0.563000	0.77884	GAA		0.448	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		A	18318408	C	A	18318408	4	1	61	1	0	0	0	0	0	1	0	0	7363	922	32	2	1990	2	HPS5	11	18318408	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29936	18318408	116688108	7238	15223										
GTF2H1	2965	broad.mit.edu	37	chr11	18373950	18373950	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattattaattcttttcaaaGtattagacaagaaatggaag	6	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18373950G>T	ENST00000265963.4	+	11	1377	c.1217G>T	c.(1216-1218)aGt>aTt	p.S406I	GTF2H1_ENST00000453096.2_Missense_Mutation_p.S406I|GTF2H1_ENST00000530496.2_Missense_Mutation_p.S94I|GTF2H1_ENST00000526630.2_5'UTR|GTF2H1_ENST00000534641.1_Missense_Mutation_p.S290I	NM_005316.3	NP_005307.1	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1, 62kDa	406					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S406I(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						TCTTTTCAAAGTATTAGACAA	0.383								Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	11											153	152	153					11																	18373950		2199	4293	6492	18330526	SO:0001583	missense	2965				CCDS7838.1	11p15.1-p14	2012-11-05	2002-08-29		ENSG00000110768	ENSG00000110768		"General transcription factors", "General transcription factor IIH complex subunits"	4655	protein-coding gene	gene with protein product		189972	"general transcription factor IIH, polypeptide 1 (62kD subunit)"			1529339, 8162052	Standard	NM_005316		Approved	BTF2, P62, TFIIH	uc001moh.2	P32780	OTTHUMG00000167690	ENST00000265963.4:c.1217G>T	11.37:g.18373950G>T	ENSP00000265963:p.Ser406Ile		18330526	B3KXE0|D3DQY2|Q6I9Y7|Q9H5K5|Q9NQD9	Missense_Mutation	SNP	ENST00000265963.4	37	CCDS7838.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.104998	0.37145	.	.	ENSG00000110768	ENST00000453096;ENST00000534641;ENST00000265963;ENST00000530496	T;T;T;T	0.49139	1.85;1.84;1.85;0.79	6.06	6.06	0.98353	.	0.210279	0.56097	D	0.000031	T	0.43456	0.1248	L	0.36672	1.1	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.12656	-1.0539	10	0.33940	T	0.23	-18.2595	20.6208	0.99490	0.0:0.0:1.0:0.0	.	406	P32780	TF2H1_HUMAN	I	406;290;406;94	ENSP00000393638:S406I;ENSP00000435375:S290I;ENSP00000265963:S406I;ENSP00000433133:S94I	ENSP00000265963:S406I	S	+	2	0	GTF2H1	18330526	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.002000	0.40835	2.882000	0.98803	0.655000	0.94253	AGT		0.383	GTF2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395627.2	NM_005316		T	18373950	G	T	18373950	3	4	61	1	0	0	0	0	1	0	0	0	6881	1029	36	2	1255	2	GTF2H1	11	18373950	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55542	18373950	116632566	7239	15224										
LDHAL6A	160287	broad.mit.edu	37	chr11	18500331	18500331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtatcacagacctcataAaagtaaaactgactcttgaa	6	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18500331A>C	ENST00000280706.2	+	7	1710	c.913A>C	c.(913-915)Aaa>Caa	p.K305Q	LDHAL6A_ENST00000396213.3_Missense_Mutation_p.K305Q|TSG101_ENST00000536719.1_Intron	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	305					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)	p.K305Q(1)		large_intestine(3)|lung(9)|urinary_tract(1)	13						AGACCTCATAAAAGTAAAACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											148	160	156					11																	18500331		2199	4293	6492	18456907	SO:0001583	missense	160287			AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.913A>C	11.37:g.18500331A>C	ENSP00000280706:p.Lys305Gln		18456907	D3DQY5	Missense_Mutation	SNP	ENST00000280706.2	37	CCDS7841.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241403	0.22711	.	.	ENSG00000166800	ENST00000396213;ENST00000280706	T;T	0.67171	-0.25;-0.25	4.42	1.96	0.26148	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.340955	0.26840	U	0.022225	T	0.65069	0.2656	L	0.42686	1.345	0.29043	N	0.884999	P	0.50272	0.933	P	0.54544	0.755	T	0.59532	-0.7437	10	0.46703	T	0.11	.	6.5816	0.22598	0.6854:0.1607:0.0:0.1539	.	305	Q6ZMR3	LDH6A_HUMAN	Q	305	ENSP00000379516:K305Q;ENSP00000280706:K305Q	ENSP00000280706:K305Q	K	+	1	0	LDHAL6A	18456907	0.985000	0.35326	0.003000	0.11579	0.197000	0.23852	3.831000	0.55776	0.091000	0.17302	0.454000	0.30748	AAA		0.393	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972		C	18500331	A	C	18500331	3	2	61	1	0	0	0	0	1	0	0	0	8721	15	1	4	939	4	LDHAL6A	11	18500331	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	126381	18500331	116506185	7240	15225										
UEVLD	55293	broad.mit.edu	37	chr11	18566206	18566206	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgccaataacccatacttCtttgcctgaagtctgtgcct	6	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18566206C>A	ENST00000541984.1	-	6	615	c.553G>T	c.(553-555)Gaa>Taa	p.E185*	UEVLD_ENST00000543987.1_Nonsense_Mutation_p.E342*|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Nonsense_Mutation_p.E304*|UEVLD_ENST00000320750.6_Nonsense_Mutation_p.E320*|UEVLD_ENST00000396197.3_Nonsense_Mutation_p.E342*|UEVLD_ENST00000379387.4_Nonsense_Mutation_p.E320*	NM_001261386.1	NP_001248315.1			UEV and lactate/malate dehyrogenase domains									p.E342*(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						ACCCATACTTCTTTGCCTGAA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											212	199	204					11																	18566206		2199	4293	6492	18522782	SO:0001587	stop_gained	55293			AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000541984.1:c.553G>T	11.37:g.18566206C>A	ENSP00000437538:p.Glu185*		18522782		Nonsense_Mutation	SNP	ENST00000541984.1	37	CCDS58125.1	.	.	.	.	.	.	.	.	.	.	C	35	5.480500	0.96307	.	.	ENSG00000151116	ENST00000543987;ENST00000535484;ENST00000396197;ENST00000320750;ENST00000379387;ENST00000540110;ENST00000541984	.	.	.	5.74	2.84	0.33178	.	0.527621	0.21618	N	0.071686	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.716	11.1296	0.48339	0.0:0.6816:0.2528:0.0656	.	.	.	.	X	342;304;342;320;320;119;185	.	ENSP00000323353:E320X	E	-	1	0	UEVLD	18522782	1.000000	0.71417	0.985000	0.45067	0.963000	0.63663	2.403000	0.44530	0.344000	0.23847	-0.142000	0.14014	GAA		0.418	UEVLD-015	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000395928.1	NM_018314		A	18566206	C	A	18566206	4	1	61	1	0	0	0	0	0	1	0	0	16973	922	32	2	407	2	UEVLD	11	18566206	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65875	18566206	116440310	7241	15226										
SPTY2D1	144108	broad.mit.edu	37	chr11	18631437	18631437	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcagcttcttggcccttcGacgttgcatttcttcttctt	6	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18631437G>A	ENST00000336349.5	-	6	2264	c.2029C>T	c.(2029-2031)Cga>Tga	p.R677*	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	677								p.R677*(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TTGGCCCTTCGACGTTGCATT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											210	201	204					11																	18631437		2199	4293	6492	18588013	SO:0001587	stop_gained	144108			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.2029C>T	11.37:g.18631437G>A	ENSP00000337991:p.Arg677*		18588013	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Nonsense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	G	39	7.356335	0.98231	.	.	ENSG00000179119	ENST00000336349	.	.	.	5.69	1.28	0.21552	.	0.233173	0.31636	N	0.007301	.	.	.	.	.	.	0.45962	D	0.998788	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-6.7607	14.1144	0.65144	0.0:0.0:0.3067:0.6933	.	.	.	.	X	677	.	ENSP00000337991:R677X	R	-	1	2	SPTY2D1	18588013	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	2.293000	0.43558	0.279000	0.22186	0.655000	0.94253	CGA		0.418	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		A	18631437	G	A	18631437	4	1	61	1	0	0	0	0	0	1	0	0	15165	1066	37	1	32	1	SPTY2D1	11	18631437	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65231	18631437	116375079	7242	15227										
SPTY2D1	144108	broad.mit.edu	37	chr11	18633993	18633993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcttcctcttcatattctCgctgccttttgtaaccagta	4	13	4	0	rs368321001		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18633993C>T	ENST00000336349.5	-	4	1989	c.1754G>A	c.(1753-1755)cGa>cAa	p.R585Q	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	585								p.R585Q(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TTCATATTCTCGCTGCCTTTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	GLN/ARG	0,4398		0,0,2199	116	109	111		1754	4.1	0.9	11		111	1,8585	1.2+/-3.3	0,1,4292	no	missense	SPTY2D1	NM_194285.2	43	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	585/686	18633993	1,12983	2199	4293	6492	18590569	SO:0001583	missense	144108			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1754G>A	11.37:g.18633993C>T	ENSP00000337991:p.Arg585Gln		18590569	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692650	0.68271	0.0	1.16E-4	ENSG00000179119	ENST00000336349	T	0.46451	0.87	5.99	4.13	0.48395	.	0.644446	0.15580	N	0.254991	T	0.37972	0.1023	N	0.22421	0.69	0.28869	N	0.895078	D	0.71674	0.998	P	0.57009	0.811	T	0.13308	-1.0514	10	0.22706	T	0.39	-3.7749	5.9502	0.19242	0.1624:0.6789:0.0:0.1587	.	585	Q68D10	SPT2_HUMAN	Q	585	ENSP00000337991:R585Q	ENSP00000337991:R585Q	R	-	2	0	SPTY2D1	18590569	0.989000	0.36119	0.932000	0.37286	0.959000	0.62525	2.162000	0.42367	0.869000	0.35703	0.655000	0.94253	CGA		0.368	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		T	18633993	C	T	18633993	3	4	61	1	0	0	0	0	1	0	0	0	15165	884	31	1	315	1	SPTY2D1	11	18633993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2556	18633993	116372523	7243	15228										
SPTY2D1	144108	broad.mit.edu	37	chr11	18636920	18636920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtttgtcgtggccctcacGaagtgagggttgggagctat	16	7	1	1	rs138155181	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18636920G>A	ENST00000336349.5	-	3	1136	c.901C>T	c.(901-903)Cgt>Tgt	p.R301C	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	301	Ser-rich.							p.R301C(3)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TGGCCCTCACGAAGTGAGGGT	0.507																																																3	Substitution - Missense(3)	cervix(1)|large_intestine(1)|lung(1)	11						G	CYS/ARG	0,4398		0,0,2199	97	95	96		901	1.5	0.3	11	dbSNP_134	96	5,8581	4.3+/-15.6	0,5,4288	yes	missense	SPTY2D1	NM_194285.2	180	0,5,6487	AA,AG,GG		0.0582,0.0,0.0385	probably-damaging	301/686	18636920	5,12979	2199	4293	6492	18593496	SO:0001583	missense	144108			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.901C>T	11.37:g.18636920G>A	ENSP00000337991:p.Arg301Cys		18593496	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	G	9.141	1.013773	0.19277	0.0	5.82E-4	ENSG00000179119	ENST00000336349;ENST00000333429	T	0.23552	1.9	5.74	1.53	0.23141	.	0.456273	0.21728	N	0.070016	T	0.13243	0.0321	L	0.27053	0.805	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.15037	-1.0451	10	0.51188	T	0.08	-1.2027	1.2617	0.02002	0.1644:0.2187:0.3716:0.2453	.	301	Q68D10	SPT2_HUMAN	C	301	ENSP00000337991:R301C	ENSP00000331447:R301C	R	-	1	0	SPTY2D1	18593496	0.000000	0.05858	0.295000	0.24960	0.762000	0.43233	0.407000	0.21049	0.785000	0.33685	0.563000	0.77884	CGT		0.507	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		A	18636920	G	A	18636920	3	1	61	1	0	0	0	0	1	0	0	0	15165	1058	37	1	1172	1	SPTY2D1	11	18636920	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2927	18636920	116369596	7244	15229										
IGSF22	283284	broad.mit.edu	37	chr11	18731034	18731034	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagtatttctgcctctcGatgagtcctcccactgtgta	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18731034G>A	ENST00000513874.1	-	18	3037	c.2898C>T	c.(2896-2898)atC>atT	p.I966I	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	865								p.I865I(1)|p.I966I(1)		NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TCTGCCTCTCGATGAGTCCTC	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	11											110	114	113					11																	18731034		1959	4149	6108	18687610	SO:0001819	synonymous_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2898C>T	11.37:g.18731034G>A			18687610	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																				0.567	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18731034	G	A	18731034	2	1	61	1	0	0	0	0	0	0	0	1	7621	1048	37	1		1	IGSF22	11	18731034	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94114	18731034	116275482	7245	15230										
IGSF22	283284	broad.mit.edu	37	chr11	18735888	18735888	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgtacttgccctcgtgCtcagggcccatactgggaaa	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18735888C>T	ENST00000513874.1	-	13	1873	c.1734G>A	c.(1732-1734)gaG>gaA	p.E578E	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	578								p.E578E(2)		NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGCCCTCGTGCTCAGGGCCCA	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	11											81	85	84					11																	18735888		2050	4186	6236	18692464	SO:0001819	synonymous_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1734G>A	11.37:g.18735888C>T			18692464	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																				0.562	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		T	18735888	C	T	18735888	2	4	61	1	0	0	0	0	0	0	0	1	7621	796	28	3		3	IGSF22	11	18735888	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4854	18735888	116270628	7246	15231										
MRGPRX1	259249	broad.mit.edu	37	chr11	18956050	18956050	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggatagaggattttagaGatggtatgggggatactgat	15	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:18956050G>T	ENST00000302797.3	-	1	506	c.282C>A	c.(280-282)atC>atA	p.I94I	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	94					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I94I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GGATTTTAGAGATGGTATGGG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	11											134	135	134					11																	18956050		2194	4287	6481	18912626	SO:0001819	synonymous_variant	259249				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.282C>A	11.37:g.18956050G>T			18912626	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																				0.522	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18956050	G	T	18956050	2	4	61	1	0	0	0	0	0	0	0	1	9796	932	33	2		2	MRGPRX1	11	18956050	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	220162	18956050	116050466	7247	15232										
E2F8	79733	broad.mit.edu	37	chr11	19259671	19259671	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttatgtggctcacaaaaGagattttcctggtttaaaaa	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:19259671G>T	ENST00000527884.1	-	3	256	c.24C>A	c.(22-24)ctC>ctA	p.L8L	E2F8_ENST00000250024.4_Silent_p.L8L|RP11-428C19.4_ENST00000527978.1_RNA	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	8					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.L8L(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GCTCACAAAAGAGATTTTCCT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	11											54	57	56					11																	19259671		2199	4293	6492	19216247	SO:0001819	synonymous_variant	79733				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.24C>A	11.37:g.19259671G>T			19216247	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Silent	SNP	ENST00000527884.1	37	CCDS7849.1																																																																																				0.368	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		T	19259671	G	T	19259671	2	4	61	1	0	0	0	0	0	0	0	1	4884	929	33	2		2	E2F8	11	19259671	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	303621	19259671	115746845	7248	15233										
NAV2	89797	broad.mit.edu	37	chr11	19955232	19955232	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaccaacaagaagagttCtctgaaaggcaatgagaaag	10	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:19955232C>A	ENST00000396087.3	+	8	1610	c.1511C>A	c.(1510-1512)tCt>tAt	p.S504Y	NAV2_ENST00000360655.4_Missense_Mutation_p.S417Y|NAV2_ENST00000540292.1_Missense_Mutation_p.S435Y|NAV2_ENST00000396085.1_Missense_Mutation_p.S481Y|NAV2_ENST00000349880.4_Missense_Mutation_p.S481Y|NAV2_ENST00000527559.2_Missense_Mutation_p.S433Y	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	504					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.S504Y(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						AAGAAGAGTTCTCTgaaaggc	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											73	87	82					11																	19955232		2199	4293	6492	19911808	SO:0001583	missense	89797			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.1511C>A	11.37:g.19955232C>A	ENSP00000379396:p.Ser504Tyr		19911808	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.287550	0.59976	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.34472	1.36;1.46;1.47;1.46;1.36;1.36	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000012	T	0.52191	0.1719	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.986;0.996	T	0.45512	-0.9256	9	.	.	.	.	12.551	0.56225	0.0:0.9237:0.0:0.0763	.	481;417	Q8IVL1-3;Q8IVL1-4	.;.	Y	417;481;481;504;433;435	ENSP00000353871:S417Y;ENSP00000379394:S481Y;ENSP00000309577:S481Y;ENSP00000379396:S504Y;ENSP00000435395:S433Y;ENSP00000443489:S435Y	.	S	+	2	0	NAV2	19911808	1.000000	0.71417	0.987000	0.45799	0.976000	0.68499	7.481000	0.81124	2.548000	0.85928	0.455000	0.32223	TCT		0.537	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19955232	C	A	19955232	3	1	61	1	0	0	0	0	1	0	0	0	10214	913	32	2	1547	2	NAV2	11	19955232	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	695561	19955232	115051284	7249	15234										
NAV2	89797	broad.mit.edu	37	chr11	20070336	20070336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgaaaacatgaaaaattCggtggtcatctccaatcctc	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20070336C>T	ENST00000396087.3	+	16	4133	c.4034C>T	c.(4033-4035)tCg>tTg	p.S1345L	NAV2_ENST00000360655.4_Missense_Mutation_p.S1258L|NAV2_ENST00000540292.1_Missense_Mutation_p.S1276L|NAV2_ENST00000396085.1_Missense_Mutation_p.S1322L|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000311043.8_Missense_Mutation_p.S408L|NAV2_ENST00000349880.4_Missense_Mutation_p.S1322L|NAV2_ENST00000533917.1_Missense_Mutation_p.S408L|NAV2_ENST00000527559.2_Missense_Mutation_p.S1274L	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1345					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.S1345L(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ATGAAAAATTCGGTGGTCATC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											119	102	108					11																	20070336		2203	4300	6503	20026912	SO:0001583	missense	89797			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.4034C>T	11.37:g.20070336C>T	ENSP00000379396:p.Ser1345Leu		20026912	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397524	0.62177	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000525322;ENST00000311043;ENST00000536595	T;T;T;T;T;T;T;T;T	0.31769	1.49;1.59;1.6;1.58;1.48;1.48;3.12;1.76;3.12	5.87	4.02	0.46733	.	0.340395	0.25692	N	0.028928	T	0.31482	0.0798	L	0.46157	1.445	0.58432	D	0.999999	P;P;D;P;P;P	0.62365	0.791;0.787;0.991;0.854;0.786;0.579	B;B;P;B;B;B	0.46237	0.273;0.185;0.508;0.195;0.314;0.138	T	0.03051	-1.1078	9	.	.	.	.	12.743	0.57264	0.0:0.8674:0.0:0.1326	.	1322;1345;408;408;1322;1258	A7E2D6;Q8IVL1;Q8IVL1-5;E9PNV5;Q8IVL1-3;Q8IVL1-4	.;NAV2_HUMAN;.;.;.;.	L	1258;1322;1322;1345;1274;1276;408;408;408;408	ENSP00000353871:S1258L;ENSP00000379394:S1322L;ENSP00000309577:S1322L;ENSP00000379396:S1345L;ENSP00000435395:S1274L;ENSP00000443489:S1276L;ENSP00000437316:S408L;ENSP00000437136:S408L;ENSP00000312169:S408L	.	S	+	2	0	NAV2	20026912	1.000000	0.71417	0.008000	0.14137	0.982000	0.71751	4.732000	0.62029	0.944000	0.37579	0.655000	0.94253	TCG		0.532	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20070336	C	T	20070336	3	4	61	1	0	0	0	0	1	0	0	0	10214	893	31	1	4132	1	NAV2	11	20070336	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115104	20070336	114936180	7250	15235										
DBX1	120237	broad.mit.edu	37	chr11	20180780	20180780	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggctgaaaagacccttcGaagtagggaaaggcgaaggt	14	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20180780G>A	ENST00000524983.2	-	2	714	c.426C>T	c.(424-426)ttC>ttT	p.F142F	DBX1_ENST00000227256.3_Silent_p.F142F			A6NMT0	DBX1_HUMAN	developing brain homeobox 1	142					regulation of transcription from RNA polymerase II promoter (GO:0006357)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.F142F(2)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)	21						AAGACCCTTCGAAGTAGGGAA	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	11											135	129	131					11																	20180780		2203	4300	6503	20137356	SO:0001819	synonymous_variant	120237					11p15.1	2011-06-20				ENSG00000109851		"Homeoboxes / ANTP class : NKL subclass"	33185	protein-coding gene	gene with protein product						11239429	Standard	NM_001029865		Approved		uc021qey.1	A6NMT0		ENST00000524983.2:c.426C>T	11.37:g.20180780G>A			20137356		Silent	SNP	ENST00000524983.2	37																																																																																					0.602	DBX1-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387585.2	NM_001029865		A	20180780	G	A	20180780	2	1	61	1	0	0	0	0	0	0	0	1	4265	1049	37	1		1	DBX1	11	20180780	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110444	20180780	114825736	7251	15236										
HTATIP2	10553	broad.mit.edu	37	chr11	20388726	20388726	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtccttgcctagaatcaaGaagtggtggactttgaaaag	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20388726G>T	ENST00000451739.2	+	2	643	c.202G>T	c.(202-204)Gaa>Taa	p.E68*	HTATIP2_ENST00000443524.2_Nonsense_Mutation_p.E68*|HTATIP2_ENST00000532505.1_Nonsense_Mutation_p.E68*|HTATIP2_ENST00000532081.1_Nonsense_Mutation_p.E68*|HTATIP2_ENST00000531058.1_Nonsense_Mutation_p.E68*|HTATIP2_ENST00000419348.2_Nonsense_Mutation_p.E102*|HTATIP2_ENST00000530266.1_Nonsense_Mutation_p.E68*|HTATIP2_ENST00000421577.2_Nonsense_Mutation_p.E68*	NM_001098522.1	NP_001091992.1			HIV-1 Tat interactive protein 2, 30kDa									p.E68*(1)		large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						CTAGAATCAAGAAGTGGTGGA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											157	153	155					11																	20388726		2203	4300	6503	20345302	SO:0001587	stop_gained	10553			AF039103	CCDS7852.1, CCDS44553.1, CCDS53613.1	11p15.1	2011-09-14	2002-08-29		ENSG00000109854	ENSG00000109854	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	16637	protein-coding gene	gene with protein product	"Tat-interacting protein (30kD)", "short chain dehydrogenase/reductase family 44U, member 1"	605628	"HIV-1 Tat interactive protein 2, 30 kDa"			9482853, 9174052, 19027726	Standard	NM_006410		Approved	TIP30, CC3, FLJ26963, SDR44U1	uc001mpx.2	Q9BUP3	OTTHUMG00000166015	ENST00000451739.2:c.202G>T	11.37:g.20388726G>T	ENSP00000394259:p.Glu68*		20345302		Nonsense_Mutation	SNP	ENST00000451739.2	37	CCDS7852.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803738	0.70682	.	.	ENSG00000109854	ENST00000530266;ENST00000421577;ENST00000443524;ENST00000419348;ENST00000451739;ENST00000532505;ENST00000532081;ENST00000531058	.	.	.	5.71	4.8	0.61643	.	0.135685	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-0.8883	12.5013	0.55957	0.081:0.0:0.919:0.0	.	.	.	.	X	68;68;68;102;68;68;68;68	.	ENSP00000392985:E102X	E	+	1	0	HTATIP2	20345302	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	3.799000	0.55529	1.424000	0.47217	0.555000	0.69702	GAA		0.428	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521		T	20388726	G	T	20388726	4	4	61	1	0	0	0	0	0	1	0	0	7453	943	33	2	314	2	HTATIP2	11	20388726	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207946	20388726	114617790	7252	15237										
PRMT3	10196	broad.mit.edu	37	chr11	20448392	20448392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgtagaaaaagtagatgTtatcatatctgagtggatgg	11	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20448392T>C	ENST00000331079.6	+	10	1191	c.974T>C	c.(973-975)gTt>gCt	p.V325A	PRMT3_ENST00000437750.2_Missense_Mutation_p.V263A	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	325	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)	p.V325A(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						AAAGTAGATGTTATCATATCT	0.244																																																1	Substitution - Missense(1)	large_intestine(1)	11											54	59	58					11																	20448392		2186	4284	6470	20404968	SO:0001583	missense	10196			AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"Protein arginine methyltransferases"	30163	protein-coding gene	gene with protein product		603190	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.974T>C	11.37:g.20448392T>C	ENSP00000331879:p.Val325Ala		20404968	B4DUC7	Missense_Mutation	SNP	ENST00000331079.6	37	CCDS7853.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044560	0.55110	.	.	ENSG00000185238	ENST00000331079;ENST00000541255;ENST00000437750	T;T	0.80824	-1.42;-1.42	5.46	5.46	0.80206	.	0.117031	0.64402	D	0.000018	D	0.82360	0.5020	L	0.35593	1.075	0.51767	D	0.999939	B;D	0.54964	0.403;0.969	P;P	0.62435	0.503;0.902	T	0.82092	-0.0628	10	0.40728	T	0.16	-24.2648	13.0519	0.58960	0.0:0.0:0.0:1.0	.	263;325	O60678-2;O60678	.;ANM3_HUMAN	A	325;325;263	ENSP00000331879:V325A;ENSP00000397766:V263A	ENSP00000331879:V325A	V	+	2	0	PRMT3	20404968	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.235000	0.72332	2.074000	0.62210	0.528000	0.53228	GTT		0.244	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788		C	20448392	T	C	20448392	3	2	61	1	0	0	0	0	1	0	0	0	12572	1725	60	4	1012	4	PRMT3	11	20448392	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	59666	20448392	114558124	7253	15238										
SLC6A5	9152	broad.mit.edu	37	chr11	20625954	20625954	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggtttccctacctggcCttccagaacgggggaggtat	14	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20625954C>A	ENST00000525748.1	+	3	936	c.663C>A	c.(661-663)gcC>gcA	p.A221A		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	221					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A221A(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CCTACCTGGCCTTCCAGAACG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	11											114	111	112					11																	20625954		2203	4300	6503	20582530	SO:0001819	synonymous_variant	9152			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.663C>A	11.37:g.20625954C>A			20582530	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																				0.647	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		A	20625954	C	A	20625954	2	1	61	1	0	0	0	0	0	0	0	1	14724	668	24	2		2	SLC6A5	11	20625954	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177562	20625954	114380562	7254	15239										
SLC6A5	9152	broad.mit.edu	37	chr11	20668408	20668408	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattctgtgaagatatagaGatgatgattggattccagcc	11	5	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20668408G>T	ENST00000525748.1	+	14	2271	c.1998G>T	c.(1996-1998)gaG>gaT	p.E666D	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	666					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.E666D(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	AAGATATAGAGATGATGATTG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											129	115	120					11																	20668408		2203	4300	6503	20624984	SO:0001583	missense	9152			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1998G>T	11.37:g.20668408G>T	ENSP00000434364:p.Glu666Asp		20624984	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874427	0.72180	.	.	ENSG00000165970	ENST00000525748	T	0.75154	-0.91	5.86	1.42	0.22433	.	0.142736	0.64402	D	0.000007	T	0.79305	0.4423	M	0.68728	2.09	0.50313	D	0.999864	P	0.50156	0.932	P	0.57009	0.811	T	0.78814	-0.2056	10	0.72032	D	0.01	.	9.9906	0.41868	0.429:0.0:0.571:0.0	.	666	Q9Y345	SC6A5_HUMAN	D	666	ENSP00000434364:E666D	ENSP00000434364:E666D	E	+	3	2	SLC6A5	20624984	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.162000	0.42367	0.400000	0.25396	-0.768000	0.03414	GAG		0.453	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		T	20668408	G	T	20668408	3	4	61	1	0	0	0	0	1	0	0	0	14724	933	33	2	2052	2	SLC6A5	11	20668408	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42454	20668408	114338108	7255	15240										
NELL1	4745	broad.mit.edu	37	chr11	20805360	20805360	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggagtgatactgtccattCgagaactggagcacaggtaa	12	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:20805360C>T	ENST00000357134.5	+	3	471	c.319C>T	c.(319-321)Cga>Tga	p.R107*	NELL1_ENST00000325319.5_Nonsense_Mutation_p.R107*|NELL1_ENST00000298925.5_Nonsense_Mutation_p.R135*|NELL1_ENST00000532434.1_Nonsense_Mutation_p.R107*	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	107	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)	p.R107*(1)		NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						ACTGTCCATTCGAGAACTGGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											109	98	102					11																	20805360		2203	4300	6503	20761936	SO:0001587	stop_gained	4745			AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.319C>T	11.37:g.20805360C>T	ENSP00000349654:p.Arg107*		20761936	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Nonsense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	C	38	7.162540	0.98107	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	.	.	.	6.17	3.2	0.36748	.	0.218765	0.39475	N	0.001349	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-0.518	12.9657	0.58483	0.1213:0.6457:0.233:0.0	.	.	.	.	X	135;107;107;107	.	ENSP00000298925:R135X	R	+	1	2	NELL1	20761936	1.000000	0.71417	0.948000	0.38648	0.512000	0.34134	3.144000	0.50616	0.432000	0.26286	0.655000	0.94253	CGA		0.418	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		T	20805360	C	T	20805360	4	4	61	1	0	0	0	0	0	1	0	0	10364	876	31	1	329	1	NELL1	11	20805360	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136952	20805360	114201156	7256	15241										
NELL1	4745	broad.mit.edu	37	chr11	21556024	21556024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaagcggtttccatgacGatgggacctattcactgtcc	11	11	1	2	rs201961389		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:21556024G>A	ENST00000357134.5	+	16	1902	c.1750G>A	c.(1750-1752)Gat>Aat	p.D584N	NELL1_ENST00000325319.5_Missense_Mutation_p.D527N|NELL1_ENST00000298925.5_Missense_Mutation_p.D612N|NELL1_ENST00000532434.1_Intron|NELL1_ENST00000529218.1_3'UTR	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	584	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)	p.D584N(1)		NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TTTCCATGACGATGGGACCTA	0.532													G|||	1	0.000199681	0	0	5008	,	,		16743	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						G	ASN/ASP,	0,4406		0,0,2203	182	148	159		1750,	4.7	1	11		159	2,8598	2.2+/-6.3	0,2,4298	no	missense,intron	NELL1	NM_006157.3,NM_201551.1	23,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,	584/811,	21556024	2,13004	2203	4300	6503	21512600	SO:0001583	missense	4745			AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1750G>A	11.37:g.21556024G>A	ENSP00000349654:p.Asp584Asn		21512600	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.09	1.254131	0.22965	0.0	2.33E-4	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319	D;D;D	0.87887	-2.31;-2.31;-2.31	5.74	4.73	0.59995	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.073055	0.51477	D	0.000082	T	0.70988	0.3287	N	0.25286	0.73	0.39307	D	0.965017	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.62358	-0.6871	10	0.05620	T	0.96	-18.7381	3.7779	0.08668	0.3339:0.0:0.6661:0.0	.	527;612;584	F5H6I3;B3KXR2;Q92832	.;.;NELL1_HUMAN	N	612;584;527	ENSP00000298925:D612N;ENSP00000349654:D584N;ENSP00000317837:D527N	ENSP00000298925:D612N	D	+	1	0	NELL1	21512600	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.966000	0.76073	2.714000	0.92807	0.585000	0.79938	GAT		0.532	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		A	21556024	G	A	21556024	3	1	61	1	0	0	0	0	1	0	0	0	10364	1058	37	1	1812	1	NELL1	11	21556024	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	750664	21556024	113450492	7257	15242										
ANO5	203859	broad.mit.edu	37	chr11	22294425	22294425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtagagattcgagtggatGcctggaaacttaccactcaa	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:22294425G>A	ENST00000324559.8	+	19	2442	c.2125G>A	c.(2125-2127)Gcc>Acc	p.A709T	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	709					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)	p.A709T(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCGAGTGGATGCCTGGAAACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											151	139	143					11																	22294425		2203	4300	6503	22251001	SO:0001583	missense	203859			AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2125G>A	11.37:g.22294425G>A	ENSP00000315371:p.Ala709Thr		22251001		Missense_Mutation	SNP	ENST00000324559.8	37	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.367341	0.82463	.	.	ENSG00000171714	ENST00000324559	T	0.69561	-0.41	5.57	3.4	0.38934	.	0.146155	0.64402	D	0.000007	D	0.83459	0.5259	M	0.93808	3.46	0.42502	D	0.992934	B	0.34147	0.438	P	0.52481	0.7	D	0.86645	0.1894	10	0.87932	D	0	.	12.2277	0.54470	0.0:0.0:0.4365:0.5635	.	709	Q75V66	ANO5_HUMAN	T	709	ENSP00000315371:A709T	ENSP00000315371:A709T	A	+	1	0	ANO5	22251001	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.832000	0.62759	1.465000	0.48006	-0.187000	0.12897	GCC		0.393	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		A	22294425	G	A	22294425	3	1	61	1	0	0	0	0	1	0	0	0	700	1319	46	3	2199	3	ANO5	11	22294425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	738401	22294425	112712091	7258	15243										
SLC17A6	57084	broad.mit.edu	37	chr11	22384327	22384327	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaatgcctttagctggcaTtcttgtgcagtacactggct	10	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:22384327T>G	ENST00000263160.3	+	6	1141	c.704T>G	c.(703-705)aTt>aGt	p.I235S	CTD-2140G10.4_ENST00000534543.1_RNA	NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	235					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.I235S(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						TTAGCTGGCATTCTTGTGCAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											251	212	225					11																	22384327		2203	4300	6503	22340903	SO:0001583	missense	57084			AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.704T>G	11.37:g.22384327T>G	ENSP00000263160:p.Ile235Ser		22340903	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	37	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.970454	0.92919	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.59638	0.25	5.53	5.53	0.82687	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.60945	0.2308	L	0.52823	1.66	0.80722	D	1	P	0.37015	0.578	B	0.43018	0.405	T	0.63444	-0.6636	10	0.54805	T	0.06	.	15.9669	0.79979	0.0:0.0:0.0:1.0	.	235	Q9P2U8	VGLU2_HUMAN	S	235;123	ENSP00000263160:I235S	ENSP00000263160:I235S	I	+	2	0	SLC17A6	22340903	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.997000	0.88414	2.236000	0.73375	0.533000	0.62120	ATT		0.383	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		G	22384327	T	G	22384327	3	3	61	1	0	0	0	0	1	0	0	0	14458	1493	52	4	726	4	SLC17A6	11	22384327	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	89902	22384327	112622189	7259	15244										
SLC17A6	57084	broad.mit.edu	37	chr11	22391672	22391672	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcagaagctggacttttTatttattgcttattagtcag	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:22391672T>C	ENST00000263160.3	+	8	1416	c.979T>C	c.(979-981)Tat>Cat	p.Y327H		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	327					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.Y327H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						CTGGACTTTTTATTTATTGCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	72	72					11																	22391672		2202	4298	6500	22348248	SO:0001583	missense	57084			AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.979T>C	11.37:g.22391672T>C	ENSP00000263160:p.Tyr327His		22348248	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	37	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.619034	0.87460	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.61859	0.07	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78162	0.4240	M	0.84433	2.695	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.82358	-0.0497	10	0.87932	D	0	.	15.7332	0.77822	0.0:0.0:0.0:1.0	.	327	Q9P2U8	VGLU2_HUMAN	H	327;215	ENSP00000263160:Y327H	ENSP00000263160:Y327H	Y	+	1	0	SLC17A6	22348248	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.182000	0.69389	0.482000	0.46254	TAT		0.328	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		C	22391672	T	C	22391672	3	2	61	1	0	0	0	0	1	0	0	0	14458	1754	61	4	1009	4	SLC17A6	11	22391672	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7345	22391672	112614844	7260	15245										
FANCF	2188	broad.mit.edu	37	chr11	22647289	22647289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcggggtcccaggtgctgAcgtaggtagtgcttgagacc	17	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:22647289A>G	ENST00000327470.3	-	1	98	c.68T>C	c.(67-69)gTc>gCc	p.V23A	AC103801.2_ENST00000428556.2_3'UTR	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	23					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)	p.V23A(1)		kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						CCAGGTGCTGACGTAGGTAGT	0.647			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	1	Substitution - Missense(1)	large_intestine(1)	11											42	45	44					11																	22647289		2203	4300	6503	22603865	SO:0001583	missense	2188	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.68T>C	11.37:g.22647289A>G	ENSP00000330875:p.Val23Ala		22603865	Q52LM0	Missense_Mutation	SNP	ENST00000327470.3	37	CCDS7857.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961848	0.53400	.	.	ENSG00000183161	ENST00000327470	T	0.39056	1.1	5.39	4.23	0.50019	.	0.071524	0.56097	D	0.000037	T	0.53449	0.1797	L	0.59436	1.845	0.80722	D	1	D	0.67145	0.996	P	0.60345	0.873	T	0.56854	-0.7910	10	0.87932	D	0	-15.5941	10.3287	0.43809	0.9239:0.0:0.0761:0.0	.	23	Q9NPI8	FANCF_HUMAN	A	23	ENSP00000330875:V23A	ENSP00000330875:V23A	V	-	2	0	FANCF	22603865	0.754000	0.28360	0.342000	0.25602	0.042000	0.13812	2.557000	0.45871	2.266000	0.75297	0.533000	0.62120	GTC		0.647	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		G	22647289	A	G	22647289	3	3	61	1	0	0	0	0	1	0	0	0	5686	275	10	4	1060	4	FANCF	11	22647289	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	255617	22647289	112359227	7261	15246										
SVIP	258010	broad.mit.edu	37	chr11	22848810	22848810	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgtttttctattttttcCtttttctttctcttttcttg	2	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:22848810C>A	ENST00000354193.4	-	3	278	c.162G>T	c.(160-162)aaG>aaT	p.K54N	RP11-17A1.3_ENST00000525963.1_RNA|SVIP_ENST00000533774.1_5'UTR|RP11-17A1.3_ENST00000499625.1_RNA|RP11-17A1.3_ENST00000528701.1_RNA	NM_148893.1	NP_683691.1	Q8NHG7	SVIP_HUMAN	small VCP/p97-interacting protein	54					negative regulation of ER-associated ubiquitin-dependent protein catabolic process (GO:1903070)|negative regulation of protein complex assembly (GO:0031333)|positive regulation of autophagy (GO:0010508)|positive regulation of protein lipidation (GO:1903061)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	protein self-association (GO:0043621)	p.K54N(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	3						CTATTTTTTCCTTTTTCTTTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	11											108	110	110					11																	22848810		1781	4056	5837	22805386	SO:0001583	missense	258010			AF527534	CCDS41627.1	11p14.2	2009-03-10				ENSG00000198168			25238	protein-coding gene	gene with protein product						18793143, 17872946, 12529442	Standard	NM_148893		Approved	DKFZp313A2432	uc001mqp.4	Q8NHG7		ENST00000354193.4:c.162G>T	11.37:g.22848810C>A	ENSP00000346130:p.Lys54Asn		22805386		Missense_Mutation	SNP	ENST00000354193.4	37	CCDS41627.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254286	0.22965	.	.	ENSG00000198168	ENST00000354193	.	.	.	4.73	1.78	0.24846	.	0.249635	0.28156	N	0.016393	T	0.30355	0.0762	.	.	.	0.28977	N	0.8889	B	0.29301	0.241	B	0.32022	0.139	T	0.17592	-1.0364	8	0.42905	T	0.14	-9.7148	7.3283	0.26567	0.0:0.7122:0.0:0.2878	.	54	Q8NHG7	SVIP_HUMAN	N	54	.	ENSP00000346130:K54N	K	-	3	2	SVIP	22805386	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	0.584000	0.23864	0.153000	0.19213	-0.142000	0.14014	AAG		0.343	SVIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387725.2	NM_148893		A	22848810	C	A	22848810	3	1	61	1	0	0	0	0	1	0	0	0	15461	680	24	2	79	2	SVIP	11	22848810	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201521	22848810	112157706	7262	15247										
LUZP2	338645	broad.mit.edu	37	chr11	24750803	24750803	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgacaaagacatcaagaGaacttgatggaattaaagtc	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:24750803G>T	ENST00000336930.6	+	2	217	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	LUZP2_ENST00000533227.1_5'UTR|LUZP2_ENST00000531187.1_3'UTR			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	51						extracellular region (GO:0005576)		p.E51*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GACATCAAGAGAACTTGATGG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											72	74	74					11																	24750803		2203	4299	6502	24707379	SO:0001587	stop_gained	338645			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.151G>T	11.37:g.24750803G>T	ENSP00000336817:p.Glu51*		24707379	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Nonsense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	G	37	6.057223	0.97241	.	.	ENSG00000187398	ENST00000336930;ENST00000529015	.	.	.	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-24.839	17.923	0.88973	0.0:0.0:1.0:0.0	.	.	.	.	X	51	.	ENSP00000336817:E51X	E	+	1	0	LUZP2	24707379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.890000	0.92477	2.839000	0.97877	0.650000	0.86243	GAA		0.408	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		T	24750803	G	T	24750803	4	4	61	1	0	0	0	0	0	1	0	0	9116	943	33	2	157	2	LUZP2	11	24750803	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1901993	24750803	110255713	7263	15248										
MUC15	143662	broad.mit.edu	37	chr11	26587324	26587324	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctgtgttgtgtttatgtCttgattttcttttccatggc	9	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:26587324C>A	ENST00000455601.2	-	2	200	c.82G>T	c.(82-84)Gac>Tac	p.D28Y	ANO3_ENST00000525139.1_Intron|ANO3_ENST00000537978.1_Intron|MUC15_ENST00000527569.1_Missense_Mutation_p.D55Y|ANO3_ENST00000256737.3_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.D55Y|ANO3_ENST00000531568.1_Intron|MUC15_ENST00000281268.8_Missense_Mutation_p.D55Y|MUC15_ENST00000529533.1_Missense_Mutation_p.D55Y	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	28					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D28Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						GTGTTTATGTCTTGATTTTCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											81	77	78					11																	26587324		2203	4299	6502	26543900	SO:0001583	missense	143662			AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"Mucins"	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.82G>T	11.37:g.26587324C>A	ENSP00000397339:p.Asp28Tyr		26543900	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.377941	0.24944	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.25085	1.85;1.83;1.82;1.83;1.82	4.61	-2.25	0.06888	.	1.637990	0.03274	N	0.185197	T	0.15609	0.0376	N	0.22421	0.69	0.09310	N	1	B;B;B	0.17268	0.021;0.007;0.007	B;B;B	0.10450	0.005;0.002;0.002	T	0.24870	-1.0148	10	0.66056	D	0.02	-12.8881	1.2508	0.01982	0.1438:0.3667:0.1405:0.3491	.	55;28;55	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	Y	28;55;55;55;55	ENSP00000397339:D28Y;ENSP00000416753:D55Y;ENSP00000281268:D55Y;ENSP00000431983:D55Y;ENSP00000431945:D55Y	ENSP00000281268:D55Y	D	-	1	0	MUC15	26543900	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.712000	0.05013	-0.553000	0.06158	0.555000	0.69702	GAC		0.328	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		A	26587324	C	A	26587324	3	1	61	1	0	0	0	0	1	0	0	0	10002	913	32	2	934	2	MUC15	11	26587324	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1836521	26587324	108419192	7264	15249										
ANO3	63982	broad.mit.edu	37	chr11	26619919	26619919	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatattttatagccacagtCttcctggagttttggaaaag	8	6	1	0	rs375881108		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:26619919C>A	ENST00000256737.3	+	15	2307	c.1455C>A	c.(1453-1455)gtC>gtA	p.V485V	ANO3_ENST00000525139.1_Silent_p.V469V|ANO3_ENST00000537978.1_Silent_p.V469V|ANO3_ENST00000531568.1_Silent_p.V339V	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	485					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.V485V(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						TAGCCACAGTCTTCCTGGAGT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	11											84	86	85					11																	26619919		2203	4299	6502	26576495	SO:0001819	synonymous_variant	63982			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1455C>A	11.37:g.26619919C>A			26576495	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																				0.318	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26619919	C	A	26619919	2	1	61	1	0	0	0	0	0	0	0	1	698	900	32	2		2	ANO3	11	26619919	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32595	26619919	108386597	7265	15250										
ANO3	63982	broad.mit.edu	37	chr11	26664809	26664809	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgttaaacaatatcattGaaatcaggctggatgcatac	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:26664809G>A	ENST00000256737.3	+	23	3208	c.2356G>A	c.(2356-2358)Gaa>Aaa	p.E786K	ANO3_ENST00000525139.1_Missense_Mutation_p.E770K|ANO3_ENST00000537978.1_Missense_Mutation_p.E770K|ANO3_ENST00000531568.1_Missense_Mutation_p.E640K	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	786					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.E786K(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						CAATATCATTGAAATCAGGCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											109	101	104					11																	26664809		2203	4299	6502	26621385	SO:0001583	missense	63982			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2356G>A	11.37:g.26664809G>A	ENSP00000256737:p.Glu786Lys		26621385	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	37	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	G	36	5.721785	0.96839	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.88332	0.6408	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.90065	0.4159	10	0.87932	D	0	.	19.9738	0.97296	0.0:0.0:1.0:0.0	.	688;786	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	K	770;770;786;688;640	ENSP00000440737:E770K;ENSP00000432576:E770K;ENSP00000256737:E786K;ENSP00000432394:E640K	ENSP00000256737:E786K	E	+	1	0	ANO3	26621385	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.799000	0.99117	2.732000	0.93576	0.655000	0.94253	GAA		0.408	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26664809	G	A	26664809	3	1	61	1	0	0	0	0	1	0	0	0	698	1291	45	3	2446	3	ANO3	11	26664809	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44890	26664809	108341707	7266	15251										
SLC5A12	159963	broad.mit.edu	37	chr11	26694954	26694954	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacatcagctcacctgctCtgtcccactgtcatgctgaa	6	15	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:26694954C>T	ENST00000396005.3	-	14	2011	c.1702G>A	c.(1702-1704)Gag>Aag	p.E568K		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	568					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.E568K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						CTCACCTGCTCTGTCCCACTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											153	156	155					11																	26694954		2067	4228	6295	26651530	SO:0001583	missense	159963			BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1702G>A	11.37:g.26694954C>T	ENSP00000379326:p.Glu568Lys		26651530	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	C	10.89	1.478143	0.26511	.	.	ENSG00000148942	ENST00000396005	D	0.85013	-1.93	5.62	2.09	0.27110	.	1.202440	0.06292	U	0.699335	T	0.69142	0.3078	N	0.11313	0.125	0.30755	N	0.744687	B	0.20887	0.049	B	0.19666	0.026	T	0.60286	-0.7293	10	0.08179	T	0.78	.	7.1549	0.25632	0.0:0.3734:0.5142:0.1124	.	568	Q1EHB4	SC5AC_HUMAN	K	568	ENSP00000379326:E568K	ENSP00000379326:E568K	E	-	1	0	SLC5A12	26651530	0.949000	0.32298	0.664000	0.29753	0.650000	0.38633	0.735000	0.26115	0.786000	0.33708	0.585000	0.79938	GAG		0.418	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		T	26694954	C	T	26694954	3	4	61	1	0	0	0	0	1	0	0	0	14701	922	32	3	162	3	SLC5A12	11	26694954	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30145	26694954	108311562	7267	15252										
SLC5A12	159963	broad.mit.edu	37	chr11	26743181	26743181	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctctccttaatggcaaaGaacaccccaattccagagga	6	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:26743181G>T	ENST00000396005.3	-	1	390	c.81C>A	c.(79-81)ttC>ttA	p.F27L	SLC5A12_ENST00000280467.6_Missense_Mutation_p.F27L	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	27					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.F27L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TAATGGCAAAGAACACCCCAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	82	82					11																	26743181		2203	4299	6502	26699757	SO:0001583	missense	159963			BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.81C>A	11.37:g.26743181G>T	ENSP00000379326:p.Phe27Leu		26699757	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	G	22.5	4.292137	0.80914	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.85258	-1.96;-1.59	5.59	1.51	0.23008	.	0.059311	0.64402	D	0.000003	D	0.88202	0.6373	M	0.82056	2.57	0.42217	D	0.991836	P;D	0.59357	0.938;0.985	P;P	0.54815	0.755;0.761	D	0.86775	0.1975	10	0.87932	D	0	.	8.2565	0.31760	0.4714:0.0:0.5286:0.0	.	27;27	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	L	27	ENSP00000379326:F27L;ENSP00000280467:F27L	ENSP00000280467:F27L	F	-	3	2	SLC5A12	26699757	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.589000	0.36644	0.276000	0.22118	0.585000	0.79938	TTC		0.468	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		T	26743181	G	T	26743181	3	4	61	1	0	0	0	0	1	0	0	0	14701	933	33	2	1835	2	SLC5A12	11	26743181	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48227	26743181	108263335	7268	15253										
BBOX1	8424	broad.mit.edu	37	chr11	27114906	27114906	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtttcctctatctcacaTtttatgggtgagtcaccaaa	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:27114906T>G	ENST00000529202.1	+	4	865	c.526T>G	c.(526-528)Ttt>Gtt	p.F176V	BBOX1_ENST00000528583.1_Missense_Mutation_p.F176V|BBOX1_ENST00000263182.3_Missense_Mutation_p.F176V|RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000525090.1_Missense_Mutation_p.F176V|BBOX1_ENST00000527505.1_Intron|RP11-1L12.3_ENST00000526061.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	176					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)	p.F176V(2)		breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	CTATCTCACATTTTATGGGTG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	11											80	84	82					11																	27114906		2202	4299	6501	27071482	SO:0001583	missense	8424			AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.526T>G	11.37:g.27114906T>G	ENSP00000435781:p.Phe176Val		27071482	B2R8L7|D3DQZ1|Q6IBJ2	Missense_Mutation	SNP	ENST00000529202.1	37	CCDS7862.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.880959	0.72294	.	.	ENSG00000129151	ENST00000529202;ENST00000263182;ENST00000528583;ENST00000525090	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.81216	0.4776	M	0.68952	2.095	0.53688	D	0.999979	P	0.42161	0.772	B	0.41088	0.347	T	0.78795	-0.2064	10	0.19147	T	0.46	.	13.6181	0.62121	0.0:0.0:0.0:1.0	.	176	O75936	BODG_HUMAN	V	176	ENSP00000435781:F176V;ENSP00000263182:F176V;ENSP00000434918:F176V;ENSP00000433772:F176V	ENSP00000263182:F176V	F	+	1	0	BBOX1	27071482	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.463000	0.66712	2.087000	0.62958	0.528000	0.53228	TTT		0.428	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		G	27114906	T	G	27114906	3	3	61	1	0	0	0	0	1	0	0	0	1335	1493	52	4	536	4	BBOX1	11	27114906	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	371725	27114906	107891610	7269	15254										
CCDC34	91057	broad.mit.edu	37	chr11	27379058	27379058	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcgcacctgtttctgttcTtcttggttattttctgattc	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:27379058T>G	ENST00000328697.6	-	2	1063	c.390A>C	c.(388-390)gaA>gaC	p.E130D	CCDC34_ENST00000317945.6_Missense_Mutation_p.E130D	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	130								p.E130D(1)		endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						GTTTCTGTTCTTCTTGGTTAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											142	130	134					11																	27379058		2202	4299	6501	27335634	SO:0001583	missense	91057			AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.390A>C	11.37:g.27379058T>G	ENSP00000330240:p.Glu130Asp		27335634	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.026757	0.35797	.	.	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.24350	1.86;1.86	5.53	1.86	0.25419	.	0.310256	0.25747	N	0.028573	T	0.20901	0.0503	L	0.53249	1.67	0.18873	N	0.999985	B;B	0.19331	0.035;0.024	B;B	0.24848	0.056;0.018	T	0.13072	-1.0523	10	0.37606	T	0.19	-4.5093	5.0648	0.14576	0.0:0.1692:0.1568:0.674	.	130;130	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	D	130	ENSP00000330240:E130D;ENSP00000321563:E130D	ENSP00000321563:E130D	E	-	3	2	CCDC34	27335634	0.476000	0.25901	0.982000	0.44146	0.784000	0.44337	0.328000	0.19681	1.035000	0.39972	0.533000	0.62120	GAA		0.433	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771		G	27379058	T	G	27379058	3	3	61	1	0	0	0	0	1	0	0	0	2813	1606	56	4	835	4	CCDC34	11	27379058	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	264152	27379058	107627458	7270	15255										
LGR4	55366	broad.mit.edu	37	chr11	27390507	27390507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggatgccagtatagattCccatgaataagttagacaca	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:27390507C>T	ENST00000379214.4	-	18	2206	c.1763G>A	c.(1762-1764)gGa>gAa	p.G588E	LGR4_ENST00000389858.4_Missense_Mutation_p.G564E	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	588					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.G588E(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AGTATAGATTCCCATGAATAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	86	86					11																	27390507		2202	4299	6501	27347083	SO:0001583	missense	55366			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1763G>A	11.37:g.27390507C>T	ENSP00000368516:p.Gly588Glu		27347083	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069726	0.76301	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	D;D	0.93712	-3.27;-3.27	5.95	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.048732	0.85682	N	0.000000	D	0.96315	0.8798	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96766	0.9565	10	0.87932	D	0	.	15.0393	0.71777	0.0:0.9321:0.0:0.0679	.	564;588	G5E9B3;Q9BXB1	.;LGR4_HUMAN	E	588;564	ENSP00000368516:G588E;ENSP00000374508:G564E	ENSP00000368516:G588E	G	-	2	0	LGR4	27347083	1.000000	0.71417	0.980000	0.43619	0.973000	0.67179	6.081000	0.71309	1.518000	0.48934	0.650000	0.86243	GGA		0.413	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		T	27390507	C	T	27390507	3	4	61	1	0	0	0	0	1	0	0	0	8779	855	30	3	1096	3	LGR4	11	27390507	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11449	27390507	107616009	7271	15256										
LGR4	55366	broad.mit.edu	37	chr11	27395535	27395535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttacaggttagttattgGcccaagtgtggcaaaagctc	10	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:27395535G>A	ENST00000379214.4	-	14	1683	c.1240C>T	c.(1240-1242)Cca>Tca	p.P414S	LGR4_ENST00000389858.4_Missense_Mutation_p.P390S	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	414					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.P414S(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						TTAGTTATTGGCCCAAGTGTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											232	234	234					11																	27395535		2202	4299	6501	27352111	SO:0001583	missense	55366			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1240C>T	11.37:g.27395535G>A	ENSP00000368516:p.Pro414Ser		27352111	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	G	0.796	-0.756995	0.03019	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.20200	4.55;2.09	5.15	1.6	0.23607	.	0.291939	0.32218	N	0.006401	T	0.01800	0.0057	N	0.00011	-3	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34650	-0.9820	10	0.02654	T	1	.	2.8934	0.05684	0.2543:0.4973:0.1126:0.1357	.	390;414	G5E9B3;Q9BXB1	.;LGR4_HUMAN	S	414;390	ENSP00000368516:P414S;ENSP00000374508:P390S	ENSP00000368516:P414S	P	-	1	0	LGR4	27352111	0.950000	0.32346	0.999000	0.59377	0.996000	0.88848	1.613000	0.36900	0.038000	0.15604	0.650000	0.86243	CCA		0.328	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		A	27395535	G	A	27395535	3	1	61	1	0	0	0	0	1	0	0	0	8779	1203	42	3	1635	3	LGR4	11	27395535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5028	27395535	107610981	7272	15257										
KIF18A	81930	broad.mit.edu	37	chr11	28104408	28104408	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgtaatgtttacctttcGatttctttttcctgagggtt	7	6	1	1	rs370457263		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:28104408G>A	ENST00000263181.6	-	9	1547	c.1257C>T	c.(1255-1257)atC>atT	p.I419I		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	419					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.I419I(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TTTACCTTTCGATTTCTTTTT	0.249																																																1	Substitution - coding silent(1)	large_intestine(1)	11						G		0,4394		0,0,2197	78	79	79		1257	-6.8	0.8	11		79	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous	KIF18A	NM_031217.3		0,1,6489	AA,AG,GG		0.0116,0.0,0.0077		419/899	28104408	1,12979	2197	4293	6490	28060984	SO:0001819	synonymous_variant	81930			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.1257C>T	11.37:g.28104408G>A			28060984	Q4VPE3|Q86VS5|Q9H0F3	Silent	SNP	ENST00000263181.6	37	CCDS7867.1																																																																																				0.249	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		A	28104408	G	A	28104408	2	1	61	1	0	0	0	0	0	0	0	1	8301	1048	37	1		1	KIF18A	11	28104408	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	708873	28104408	106902108	7273	15258										
KIF18A	81930	broad.mit.edu	37	chr11	28119446	28119446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgttttccggacgtacacGaactactactttcatatggt	8	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:28119446G>A	ENST00000263181.6	-	2	339	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.R17C(3)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						GGACGTACACGAACTACTACT	0.363																																																3	Substitution - Missense(3)	large_intestine(3)	11											166	158	161					11																	28119446		2202	4299	6501	28076022	SO:0001583	missense	81930			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.49C>T	11.37:g.28119446G>A	ENSP00000263181:p.Arg17Cys		28076022	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537380	0.85917	.	.	ENSG00000121621	ENST00000263181	D	0.86694	-2.16	5.53	5.53	0.82687	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.96833	0.8966	H	0.99336	4.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98173	1.0453	10	0.87932	D	0	.	19.823	0.96605	0.0:0.0:1.0:0.0	.	17;17	B2R6H3;Q8NI77	.;KI18A_HUMAN	C	17	ENSP00000263181:R17C	ENSP00000263181:R17C	R	-	1	0	KIF18A	28076022	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.205000	0.77881	2.770000	0.95276	0.650000	0.86243	CGT		0.363	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		A	28119446	G	A	28119446	3	1	61	1	0	0	0	0	1	0	0	0	8301	1058	37	1	2711	1	KIF18A	11	28119446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15038	28119446	106887070	7274	15259										
KCNA4	3739	broad.mit.edu	37	chr11	30032434	30032434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaagaagtagagctccGaaatttcttgagcaaattag	11	5	1	4	rs371670338		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:30032434G>A	ENST00000328224.6	-	2	3025	c.1792C>T	c.(1792-1794)Cgg>Tgg	p.R598W	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	598					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.R598W(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GTAGAGCTCCGAAATTTCTTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	TRP/ARG	1,3765		0,1,1882	84	84	84		1792	3.6	1	11		84	0,8236		0,0,4118	no	missense	KCNA4	NM_002233.3	101	0,1,6000	AA,AG,GG		0.0,0.0266,0.0083	probably-damaging	598/654	30032434	1,12001	1883	4118	6001	29989010	SO:0001583	missense	3739			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1792C>T	11.37:g.30032434G>A	ENSP00000328511:p.Arg598Trp		29989010		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747679	0.49257	2.66E-4	0.0	ENSG00000182255	ENST00000328224	D	0.97089	-4.24	5.55	3.56	0.40772	.	0.889912	0.09660	N	0.772636	D	0.97167	0.9074	L	0.57536	1.79	0.47476	D	0.999439	D	0.65815	0.995	P	0.53809	0.735	D	0.94895	0.8051	10	0.87932	D	0	.	13.7446	0.62868	0.0:0.0:0.5674:0.4326	.	598	P22459	KCNA4_HUMAN	W	598	ENSP00000328511:R598W	ENSP00000328511:R598W	R	-	1	2	KCNA4	29989010	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	4.414000	0.59802	1.325000	0.45301	0.655000	0.94253	CGG		0.458	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30032434	G	A	30032434	3	1	61	1	0	0	0	0	1	0	0	0	8026	1057	37	1	173	1	KCNA4	11	30032434	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1912988	30032434	104974082	7275	15260										
KCNA4	3739	broad.mit.edu	37	chr11	30033500	30033500	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggggacattgactggcctCttcaggcggcctcctgattg	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:30033500C>T	ENST00000328224.6	-	2	1959	c.726G>A	c.(724-726)aaG>aaA	p.K242K	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	242					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.K242K(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	TGACTGGCCTCTTCAGGCGGC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	11											96	87	90					11																	30033500		1868	4122	5990	29990076	SO:0001819	synonymous_variant	3739			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.726G>A	11.37:g.30033500C>T			29990076		Silent	SNP	ENST00000328224.6	37	CCDS41629.1																																																																																				0.493	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		T	30033500	C	T	30033500	2	4	61	1	0	0	0	0	0	0	0	1	8026	912	32	3		3	KCNA4	11	30033500	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1066	30033500	104973016	7276	15261										
PAX6	5080	broad.mit.edu	37	chr11	31815292	31815292	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgttgctggcctgtcttCtctgattcctcagtttttct	9	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:31815292C>A	ENST00000379132.3	-	9	1104	c.824G>T	c.(823-825)aGa>aTa	p.R275I	PAX6_ENST00000379115.4_Missense_Mutation_p.R289I|PAX6_ENST00000419022.1_Missense_Mutation_p.R289I|PAX6_ENST00000379111.2_Missense_Mutation_p.R275I|PAX6_ENST00000379107.2_Missense_Mutation_p.R289I|PAX6_ENST00000241001.8_Missense_Mutation_p.R275I|PAX6_ENST00000379129.2_Missense_Mutation_p.R289I|PAX6_ENST00000379123.5_Missense_Mutation_p.R275I			P26367	PAX6_HUMAN	paired box 6	275					astrocyte differentiation (GO:0048708)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|cerebral cortex regionalization (GO:0021796)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|cornea development in camera-type eye (GO:0061303)|dorsal/ventral axis specification (GO:0009950)|embryonic camera-type eye morphogenesis (GO:0048596)|eye development (GO:0001654)|eye photoreceptor cell development (GO:0042462)|forebrain anterior/posterior pattern specification (GO:0021797)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain-midbrain boundary formation (GO:0021905)|glucose homeostasis (GO:0042593)|hindbrain development (GO:0030902)|iris morphogenesis (GO:0061072)|keratinocyte differentiation (GO:0030216)|lacrimal gland development (GO:0032808)|lens development in camera-type eye (GO:0002088)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|neuron migration (GO:0001764)|oligodendrocyte cell fate specification (GO:0021778)|organ morphogenesis (GO:0009887)|pancreatic A cell development (GO:0003322)|pituitary gland development (GO:0021983)|positive regulation of cell fate specification (GO:0042660)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of gene expression (GO:0010628)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to organelle (GO:0033365)|protein ubiquitination (GO:0016567)|regulation of cell migration (GO:0030334)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment (GO:0021918)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|salivary gland morphogenesis (GO:0007435)|signal transduction involved in regulation of gene expression (GO:0023019)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell differentiation (GO:0003309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.R289I(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)	35	Lung SC(675;0.225)					GGCCTGTCTTCTCTGATTCCT	0.468									Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation																																							1	Substitution - Missense(1)	large_intestine(1)	11											283	287	286					11																	31815292		2202	4299	6501	31771868	SO:0001583	missense	5080	Familial Cancer Database	WAGR syndrome	AY707088	CCDS31451.1, CCDS31452.1	11p13	2014-09-17	2007-07-12		ENSG00000007372	ENSG00000007372		"Paired boxes", "Homeoboxes / PRD class"	8620	protein-coding gene	gene with protein product	"aniridia, keratitis"	607108	"paired box gene 6 (aniridia, keratitis)"	AN2		1302030	Standard	NM_001127612		Approved	D11S812E, AN, WAGR	uc021qfm.1	P26367	OTTHUMG00000041447	ENST00000379132.3:c.824G>T	11.37:g.31815292C>A	ENSP00000368427:p.Arg275Ile		31771868	Q6N006|Q99413	Missense_Mutation	SNP	ENST00000379132.3	37	CCDS31451.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504209	0.96371	.	.	ENSG00000007372	ENST00000419022;ENST00000379132;ENST00000379129;ENST00000531633;ENST00000379107;ENST00000464174;ENST00000241001;ENST00000379115;ENST00000379111;ENST00000379123;ENST00000494377;ENST00000470027;ENST00000379109;ENST00000533333;ENST00000530373;ENST00000531910	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.09;-3.46;-3.11;-3.46;-3.46;-3.46;-3.46;-2.96;-2.96;-3.46;-3.21;-3.0;-2.95	5.94	5.94	0.96194	.	0.044813	0.85682	D	0.000000	D	0.97942	0.9323	M	0.90369	3.11	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.996	D	0.98156	1.0444	10	0.87932	D	0	.	20.3674	0.98886	0.0:1.0:0.0:0.0	.	289;275	F1T0F8;P26367	.;PAX6_HUMAN	I	289;275;289;104;289;74;275;289;275;275;139;139;275;230;74;139	ENSP00000404100:R289I;ENSP00000368427:R275I;ENSP00000368424:R289I;ENSP00000451885:R104I;ENSP00000368401:R289I;ENSP00000431961:R74I;ENSP00000241001:R275I;ENSP00000368410:R289I;ENSP00000368406:R275I;ENSP00000368418:R275I;ENSP00000451901:R139I;ENSP00000450775:R139I;ENSP00000368403:R275I;ENSP00000451372:R230I;ENSP00000452202:R74I;ENSP00000452558:R139I	ENSP00000241001:R275I	R	-	2	0	PAX6	31771868	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.449000	0.80643	2.805000	0.96524	0.643000	0.83706	AGA		0.468	PAX6-008	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000099293.4	NM_001604		A	31815292	C	A	31815292	3	1	61	1	0	0	0	0	1	0	0	0	11514	913	32	2	460	2	PAX6	11	31815292	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1781792	31815292	103191224	7277	15262										
PAX6	5080	broad.mit.edu	37	chr11	31816274	31816274	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttgagcctcatctgaatCttctccgttggaactgatgg	9	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:31816274C>A	ENST00000379132.3	-	7	866	c.586G>T	c.(586-588)Gat>Tat	p.D196Y	PAX6_ENST00000379115.4_Missense_Mutation_p.D210Y|PAX6_ENST00000419022.1_Missense_Mutation_p.D210Y|PAX6_ENST00000379111.2_Missense_Mutation_p.D196Y|PAX6_ENST00000379107.2_Missense_Mutation_p.D210Y|PAX6_ENST00000241001.8_Missense_Mutation_p.D196Y|PAX6_ENST00000379129.2_Missense_Mutation_p.D210Y|PAX6_ENST00000379123.5_Missense_Mutation_p.D196Y			P26367	PAX6_HUMAN	paired box 6	196	Gln/Gly-rich.				astrocyte differentiation (GO:0048708)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|cerebral cortex regionalization (GO:0021796)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|cornea development in camera-type eye (GO:0061303)|dorsal/ventral axis specification (GO:0009950)|embryonic camera-type eye morphogenesis (GO:0048596)|eye development (GO:0001654)|eye photoreceptor cell development (GO:0042462)|forebrain anterior/posterior pattern specification (GO:0021797)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain-midbrain boundary formation (GO:0021905)|glucose homeostasis (GO:0042593)|hindbrain development (GO:0030902)|iris morphogenesis (GO:0061072)|keratinocyte differentiation (GO:0030216)|lacrimal gland development (GO:0032808)|lens development in camera-type eye (GO:0002088)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|neuron migration (GO:0001764)|oligodendrocyte cell fate specification (GO:0021778)|organ morphogenesis (GO:0009887)|pancreatic A cell development (GO:0003322)|pituitary gland development (GO:0021983)|positive regulation of cell fate specification (GO:0042660)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of gene expression (GO:0010628)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to organelle (GO:0033365)|protein ubiquitination (GO:0016567)|regulation of cell migration (GO:0030334)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment (GO:0021918)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|salivary gland morphogenesis (GO:0007435)|signal transduction involved in regulation of gene expression (GO:0023019)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell differentiation (GO:0003309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.D210Y(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)	35	Lung SC(675;0.225)					TCATCTGAATCTTCTCCGTTG	0.463									Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation																																							1	Substitution - Missense(1)	large_intestine(1)	11											131	117	122					11																	31816274		2202	4299	6501	31772850	SO:0001583	missense	5080	Familial Cancer Database	WAGR syndrome	AY707088	CCDS31451.1, CCDS31452.1	11p13	2014-09-17	2007-07-12		ENSG00000007372	ENSG00000007372		"Paired boxes", "Homeoboxes / PRD class"	8620	protein-coding gene	gene with protein product	"aniridia, keratitis"	607108	"paired box gene 6 (aniridia, keratitis)"	AN2		1302030	Standard	NM_001127612		Approved	D11S812E, AN, WAGR	uc021qfm.1	P26367	OTTHUMG00000041447	ENST00000379132.3:c.586G>T	11.37:g.31816274C>A	ENSP00000368427:p.Asp196Tyr		31772850	Q6N006|Q99413	Missense_Mutation	SNP	ENST00000379132.3	37	CCDS31451.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972312	0.74246	.	.	ENSG00000007372	ENST00000419022;ENST00000379132;ENST00000379129;ENST00000531633;ENST00000379107;ENST00000241001;ENST00000379115;ENST00000379111;ENST00000379123;ENST00000494377;ENST00000470027;ENST00000379109;ENST00000533333;ENST00000531910;ENST00000471303	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	5.76	5.76	0.90799	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97145	0.9067	M	0.64170	1.965	0.80722	D	1	D;P	0.65815	0.995;0.939	D;P	0.64042	0.921;0.781	D	0.97294	0.9926	10	0.72032	D	0.01	.	19.9583	0.97232	0.0:1.0:0.0:0.0	.	210;196	F1T0F8;P26367	.;PAX6_HUMAN	Y	210;196;210;25;210;196;210;196;196;60;60;196;151;60;60	ENSP00000404100:D210Y;ENSP00000368427:D196Y;ENSP00000368424:D210Y;ENSP00000451885:D25Y;ENSP00000368401:D210Y;ENSP00000241001:D196Y;ENSP00000368410:D210Y;ENSP00000368406:D196Y;ENSP00000368418:D196Y;ENSP00000451901:D60Y;ENSP00000450775:D60Y;ENSP00000368403:D196Y;ENSP00000451372:D151Y;ENSP00000452558:D60Y;ENSP00000435884:D60Y	ENSP00000241001:D196Y	D	-	1	0	PAX6	31772850	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.453000	0.80700	2.716000	0.92895	0.655000	0.94253	GAT		0.463	PAX6-008	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000099293.4	NM_001604		A	31816274	C	A	31816274	3	1	61	1	0	0	0	0	1	0	0	0	11514	913	32	2	706	2	PAX6	11	31816274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	982	31816274	103190242	7278	15263										
RCN1	5954	broad.mit.edu	37	chr11	32118795	32118795	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatacatctttgataatgtCgccaaagtctggaaggatta	9	6	2	2	rs141697360		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32118795C>T	ENST00000054950.3	+	2	653	c.360C>T	c.(358-360)gtC>gtT	p.V120V	RCN1_ENST00000532942.1_Silent_p.V69V|RP1-65P5.3_ENST00000533009.1_RNA	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	120	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)	p.V120V(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					TTGATAATGTCGCCAAAGTCT	0.423													.|||	1	0.000199681	8e-04	0	5008	,	,		19997	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		3,4401	6.2+/-15.9	0,3,2199	69	63	65		360	-1.2	1	11	dbSNP_134	65	0,8594		0,0,4297	no	coding-synonymous	RCN1	NM_002901.2		0,3,6496	TT,TC,CC		0.0,0.0681,0.0231		120/332	32118795	3,12995	2202	4297	6499	32075371	SO:0001819	synonymous_variant	5954			D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"EF-hand domain containing"	9934	protein-coding gene	gene with protein product	"proliferation-inducing gene 20"	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.360C>T	11.37:g.32118795C>T			32075371	B7Z1M1|D3DR00	Silent	SNP	ENST00000054950.3	37	CCDS7876.1																																																																																				0.423	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901		T	32118795	C	T	32118795	2	4	61	1	0	0	0	0	0	0	0	1	13216	871	31	1		1	RCN1	11	32118795	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	302521	32118795	102887721	7279	15264										
WT1	7490	broad.mit.edu	37	chr11	32421570	32421570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcgttgtgtggttatcgCtctcgtaccctgtgctgtgg	15	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32421570C>T	ENST00000379079.2	-	6	659	c.386G>A	c.(385-387)aGc>aAc	p.S129N	WT1_ENST00000448076.3_Missense_Mutation_p.S341N|WT1_ENST00000530998.1_Missense_Mutation_p.S112N|WT1_ENST00000332351.3_Missense_Mutation_p.S341N	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	273					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S273N(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GTGGTTATCGCTCTCGTACCC	0.537			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	1	Substitution - Missense(1)	large_intestine(1)	11											267	225	239					11																	32421570		2202	4299	6501	32378146	SO:0001583	missense	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.386G>A	11.37:g.32421570C>T	ENSP00000368370:p.Ser129Asn		32378146	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	37	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.349018	0.24426	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527775	D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.98	3.91	0.45181	Wilm&apos (1);s tumour protein, N-terminal (1);	0.126809	0.51477	U	0.000100	T	0.66237	0.2769	N	0.04355	-0.22	0.35555	D	0.804189	B;B;B;B;B	0.13145	0.007;0.003;0.004;0.0;0.001	B;B;B;B;B	0.19666	0.02;0.026;0.026;0.009;0.011	T	0.64685	-0.6349	10	0.32370	T	0.25	.	6.6096	0.22743	0.0:0.6541:0.0:0.3459	.	329;273;346;112;129	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	N	129;341;112;324;341;92	ENSP00000368370:S129N;ENSP00000331327:S341N;ENSP00000435307:S112N;ENSP00000415516:S324N;ENSP00000413452:S341N;ENSP00000435351:S92N	ENSP00000331327:S341N	S	-	2	0	WT1	32378146	0.944000	0.32072	0.890000	0.34922	0.672000	0.39443	1.864000	0.39469	1.529000	0.49120	0.650000	0.86243	AGC		0.537	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		T	32421570	C	T	32421570	3	4	61	1	0	0	0	0	1	0	0	0	17448	797	28	3	551	3	WT1	11	32421570	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	302775	32421570	102584946	7280	15265										
CCDC73	493860	broad.mit.edu	37	chr11	32632747	32632747	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcttcactgggttctccCttgggatctggatggatact	10	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32632747C>A	ENST00000335185.5	-	17	3004	c.2961G>T	c.(2959-2961)aaG>aaT	p.K987N		NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	987								p.K987N(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TGGGTTCTCCCTTGGGATCTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											171	161	164					11																	32632747		1860	4108	5968	32589323	SO:0001583	missense	493860			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.2961G>T	11.37:g.32632747C>A	ENSP00000335325:p.Lys987Asn		32589323	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901564	0.33535	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.56	4.65	0.58169	.	0.301266	0.28436	N	0.015358	T	0.54127	0.1839	L	0.55481	1.735	0.80722	D	1	B	0.34200	0.441	B	0.35312	0.2	T	0.58634	-0.7602	9	0.87932	D	0	.	12.5305	0.56111	0.0:0.9233:0.0:0.0767	.	987	Q6ZRK6	CCD73_HUMAN	N	987	.	ENSP00000335325:K987N	K	-	3	2	CCDC73	32589323	1.000000	0.71417	0.994000	0.49952	0.621000	0.37620	2.378000	0.44309	1.349000	0.45751	0.655000	0.94253	AAG		0.388	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		A	32632747	C	A	32632747	3	1	61	1	0	0	0	0	1	0	0	0	2852	680	24	2	286	2	CCDC73	11	32632747	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211177	32632747	102373769	7281	15266										
CCDC73	493860	broad.mit.edu	37	chr11	32636084	32636084	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctcattttcagaaacatCtttattattattgtgatatg	6	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32636084C>A	ENST00000335185.5	-	16	1823	c.1780G>T	c.(1780-1782)Gat>Tat	p.D594Y	CCDC73_ENST00000534415.1_5'Flank	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	594								p.D594Y(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TCAGAAACATCTTTATTATTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											82	75	77					11																	32636084		1831	4082	5913	32592660	SO:0001583	missense	493860			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1780G>T	11.37:g.32636084C>A	ENSP00000335325:p.Asp594Tyr		32592660	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	C	8.629	0.893152	0.17613	.	.	ENSG00000186714	ENST00000335185	.	.	.	4.89	0.771	0.18504	.	0.236936	0.29444	N	0.012129	T	0.31451	0.0797	L	0.59436	1.845	0.09310	N	1	B	0.20261	0.043	B	0.21546	0.035	T	0.31861	-0.9928	9	0.56958	D	0.05	.	0.997	0.01469	0.1564:0.3873:0.1531:0.3033	.	594	Q6ZRK6	CCD73_HUMAN	Y	594	.	ENSP00000335325:D594Y	D	-	1	0	CCDC73	32592660	0.000000	0.05858	0.003000	0.11579	0.152000	0.21847	-0.069000	0.11542	-0.050000	0.13356	-0.274000	0.10170	GAT		0.333	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		A	32636084	C	A	32636084	3	1	61	1	0	0	0	0	1	0	0	0	2852	913	32	2	1471	2	CCDC73	11	32636084	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3337	32636084	102370432	7282	15267										
CCDC73	493860	broad.mit.edu	37	chr11	32663596	32663596	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcattttcttttaccttCtccctttgcagctcattatc	2	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32663596C>A	ENST00000335185.5	-	13	1015	c.972G>T	c.(970-972)gaG>gaT	p.E324D	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	324								p.E324D(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CTTTTACCTTCTCCCTTTGCA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	70	72					11																	32663596		1788	4054	5842	32620172	SO:0001583	missense	493860			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.972G>T	11.37:g.32663596C>A	ENSP00000335325:p.Glu324Asp		32620172	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472903	0.63737	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.43	5.43	0.79202	.	0.308452	0.32473	N	0.006047	T	0.70378	0.3217	M	0.61703	1.905	0.80722	D	1	P;D	0.69078	0.873;0.997	P;D	0.66196	0.517;0.942	T	0.71381	-0.4610	9	0.52906	T	0.07	.	12.5824	0.56397	0.0:0.9237:0.0:0.0763	.	314;324	Q6ZRK6-2;Q6ZRK6	.;CCD73_HUMAN	D	324	.	ENSP00000335325:E324D	E	-	3	2	CCDC73	32620172	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.963000	0.49184	2.538000	0.85594	0.467000	0.42956	GAG		0.279	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		A	32663596	C	A	32663596	3	1	61	1	0	0	0	0	1	0	0	0	2852	912	32	2	2291	2	CCDC73	11	32663596	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27512	32663596	102342920	7283	15268										
CCDC73	493860	broad.mit.edu	37	chr11	32697142	32697142	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatatttcagcttcttgtTttttatttaaagctgaaagt	6	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32697142T>G	ENST00000335185.5	-	9	657	c.614A>C	c.(613-615)aAa>aCa	p.K205T	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	205								p.K205T(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					AGCTTCTTGTTTTTTATTTAA	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	11											32	31	31					11																	32697142		1787	4031	5818	32653718	SO:0001583	missense	493860			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.614A>C	11.37:g.32697142T>G	ENSP00000335325:p.Lys205Thr		32653718	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.061052	0.36373	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.1	3.9	0.45041	.	.	.	.	.	T	0.46737	0.1408	L	0.54323	1.7	0.80722	D	1	B;B	0.27932	0.041;0.194	B;B	0.26094	0.019;0.066	T	0.45026	-0.9289	8	0.32370	T	0.25	.	5.0666	0.14585	0.0:0.1244:0.178:0.6976	.	205;205	Q6ZRK6-2;Q6ZRK6	.;CCD73_HUMAN	T	205	.	ENSP00000335325:K205T	K	-	2	0	CCDC73	32653718	0.958000	0.32768	0.995000	0.50966	0.851000	0.48451	1.558000	0.36309	1.928000	0.55862	0.397000	0.26171	AAA		0.269	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		G	32697142	T	G	32697142	3	3	61	1	0	0	0	0	1	0	0	0	2852	1841	64	4	2665	4	CCDC73	11	32697142	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33546	32697142	102309374	7284	15269										
QSER1	79832	broad.mit.edu	37	chr11	32954325	32954325	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtataaaacattgactttTtctgggtcatctcagactgt	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32954325T>G	ENST00000399302.2	+	4	1469	c.1134T>G	c.(1132-1134)ttT>ttG	p.F378L	QSER1_ENST00000527788.1_Intron	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	378	Ser-rich.							p.F378L(1)		breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					CATTGACTTTTTCTGGGTCAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											105	97	99					11																	32954325		1828	4077	5905	32910901	SO:0001583	missense	79832			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.1134T>G	11.37:g.32954325T>G	ENSP00000382241:p.Phe378Leu		32910901	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722575	0.48728	.	.	ENSG00000060749	ENST00000399302	T	0.48522	0.81	4.89	3.76	0.43208	.	0.000000	0.43260	U	0.000586	T	0.28034	0.0691	N	0.19112	0.55	0.80722	D	1	B	0.32071	0.355	B	0.29267	0.1	T	0.04128	-1.0975	10	0.12766	T	0.61	.	10.6649	0.45723	0.0:0.0763:0.0:0.9236	.	378	Q2KHR3	QSER1_HUMAN	L	378	ENSP00000382241:F378L	ENSP00000382241:F378L	F	+	3	2	QSER1	32910901	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.463000	0.45058	0.825000	0.34637	0.482000	0.46254	TTT		0.378	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		G	32954325	T	G	32954325	3	3	61	1	0	0	0	0	1	0	0	0	12919	1838	64	4	1140	4	QSER1	11	32954325	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	257183	32954325	102052191	7285	15270										
QSER1	79832	broad.mit.edu	37	chr11	32997884	32997884	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattttctttttttagatttCttcggtgcagaaaaaaaatg	7	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:32997884C>A	ENST00000399302.2	+	13	5407	c.5072C>A	c.(5071-5073)tCt>tAt	p.S1691Y	QSER1_ENST00000527788.1_Missense_Mutation_p.S1452Y	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1691								p.S1691Y(1)		breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TTTTAGATTTCTTCGGTGCAG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	11											49	48	49					11																	32997884		1795	4055	5850	32954460	SO:0001583	missense	79832			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.5072C>A	11.37:g.32997884C>A	ENSP00000382241:p.Ser1691Tyr		32954460	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.422482	0.25639	.	.	ENSG00000060749	ENST00000399302;ENST00000527788	T;T	0.25414	2.13;1.8	5.78	4.86	0.63082	.	0.000000	0.41712	U	0.000839	T	0.20981	0.0505	L	0.43152	1.355	0.43647	D	0.996052	B;B	0.13145	0.007;0.004	B;B	0.15484	0.013;0.006	T	0.08827	-1.0703	10	0.02654	T	1	.	16.2413	0.82409	0.134:0.866:0.0:0.0	.	1452;1691	Q2KHR3-2;Q2KHR3	.;QSER1_HUMAN	Y	1691;1452	ENSP00000382241:S1691Y;ENSP00000432766:S1452Y	ENSP00000382241:S1691Y	S	+	2	0	QSER1	32954460	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	3.785000	0.55424	1.445000	0.47624	0.563000	0.77884	TCT		0.294	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		A	32997884	C	A	32997884	3	1	61	1	0	0	0	0	1	0	0	0	12919	913	32	2	5114	2	QSER1	11	32997884	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43559	32997884	102008632	7286	15271										
CSTF3	1479	broad.mit.edu	37	chr11	33107279	33107279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttggtatcttgcatcttCggaaaatttccatcagttca	6	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33107279C>T	ENST00000323959.4	-	20	2070	c.1931G>A	c.(1930-1932)cGa>cAa	p.R644Q	TCP11L1_ENST00000324357.9_Intron	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	644					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R644Q(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						CTTGCATCTTCGGAAAATTTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											146	137	140					11																	33107279		2202	4298	6500	33063855	SO:0001583	missense	1479			U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.1931G>A	11.37:g.33107279C>T	ENSP00000315791:p.Arg644Gln		33063855	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Missense_Mutation	SNP	ENST00000323959.4	37	CCDS7883.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.077977	0.76528	.	.	ENSG00000176102	ENST00000323959;ENST00000537832	.	.	.	5.88	5.88	0.94601	Suppressor of forked (1);	0.055348	0.64402	D	0.000001	T	0.54759	0.1878	L	0.59436	1.845	0.80722	D	1	P	0.44429	0.835	B	0.37550	0.253	T	0.52924	-0.8510	9	0.21014	T	0.42	.	20.2381	0.98363	0.0:1.0:0.0:0.0	.	644	Q12996	CSTF3_HUMAN	Q	644;577	.	ENSP00000315791:R644Q	R	-	2	0	CSTF3	33063855	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.336000	0.79245	2.779000	0.95612	0.650000	0.86243	CGA		0.358	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326		T	33107279	C	T	33107279	3	4	61	1	0	0	0	0	1	0	0	0	3992	884	31	1	230	1	CSTF3	11	33107279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109395	33107279	101899237	7287	15272										
HIPK3	10114	broad.mit.edu	37	chr11	33361005	33361005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgattgatgcagatttaaGaattactccagctgagaccc	9	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33361005G>T	ENST00000303296.4	+	6	1843	c.1538G>T	c.(1537-1539)aGa>aTa	p.R513I	HIPK3_ENST00000525975.1_Missense_Mutation_p.R513I|HIPK3_ENST00000379016.3_Missense_Mutation_p.R513I|HIPK3_ENST00000456517.1_Missense_Mutation_p.R513I	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	513	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R513I(1)		endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						GCAGATTTAAGAATTACTCCA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											212	218	216					11																	33361005		2202	4298	6500	33317581	SO:0001583	missense	10114			AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1538G>T	11.37:g.33361005G>T	ENSP00000304226:p.Arg513Ile		33317581	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	37	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	34	5.412374	0.96072	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.93	5.93	0.95920	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.080808	0.53938	D	0.000058	D	0.90407	0.6997	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92722	0.6192	10	0.87932	D	0	.	20.3465	0.98790	0.0:0.0:1.0:0.0	.	513;513	Q9H422-2;Q9H422	.;HIPK3_HUMAN	I	513	ENSP00000431710:R513I;ENSP00000304226:R513I;ENSP00000368301:R513I;ENSP00000398241:R513I	ENSP00000304226:R513I	R	+	2	0	HIPK3	33317581	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.798000	0.96311	0.655000	0.94253	AGA		0.353	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		T	33361005	G	T	33361005	3	4	61	1	0	0	0	0	1	0	0	0	7139	942	33	2	1556	2	HIPK3	11	33361005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253726	33361005	101645511	7288	15273										
HIPK3	10114	broad.mit.edu	37	chr11	33370113	33370113	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccacattcagcatttatTtctccaaagataattaatgg	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33370113T>C	ENST00000303296.4	+	13	2720	c.2415T>C	c.(2413-2415)atT>atC	p.I805I	HIPK3_ENST00000525975.1_Silent_p.I784I|HIPK3_ENST00000379016.3_Silent_p.I784I|HIPK3_ENST00000456517.1_Silent_p.I784I	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	805	Interaction with AR. {ECO:0000250}.|Interaction with FAS. {ECO:0000250}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I805I(1)		endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						CAGCATTTATTTCTCCAAAGA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	11											38	41	40					11																	33370113		2201	4297	6498	33326689	SO:0001819	synonymous_variant	10114			AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.2415T>C	11.37:g.33370113T>C			33326689	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	37	CCDS7884.1																																																																																				0.313	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33370113	T	C	33370113	2	2	61	1	0	0	0	0	0	0	0	1	7139	1829	64	4		4	HIPK3	11	33370113	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9108	33370113	101636403	7289	15274										
C11orf41	25758	broad.mit.edu	37	chr11	33564420	33564420	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaccagcagaaagctagcCtctgccactgcaaatgactc	8	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33564420C>A	ENST00000321505.4	+	1	600	c.420C>A	c.(418-420)gcC>gcA	p.A140A	KIAA1549L_ENST00000265654.5_Silent_p.A140A|KIAA1549L_ENST00000389726.3_Silent_p.A140A			Q6ZVL6	K154L_HUMAN	KIAA1549-like	140						integral component of membrane (GO:0016021)		p.A140A(2)									GAAAGCTAGCCTCTGCCACTG	0.517											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - coding silent(2)	large_intestine(2)	11											53	53	53					11																	33564420		1910	4109	6019	33520996	SO:0001819	synonymous_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.420C>A	11.37:g.33564420C>A		841	33520996	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																				0.517	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33564420	C	A	33564420	2	1	61	1	0	0	0	0	0	0	0	1	1644	668	24	2		2	C11orf41	11	33564420	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	194307	33564420	101442096	7290	15275										
C11orf41	25758	broad.mit.edu	37	chr11	33564564	33564564	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggtcaagagcaagccatCctttctggggcggttcccgc	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33564564C>A	ENST00000321505.4	+	1	744	c.564C>A	c.(562-564)atC>atA	p.I188I	KIAA1549L_ENST00000265654.5_Silent_p.I188I|KIAA1549L_ENST00000389726.3_Silent_p.I188I			Q6ZVL6	K154L_HUMAN	KIAA1549-like	188						integral component of membrane (GO:0016021)		p.I188I(2)									AGCAAGCCATCCTTTCTGGGG	0.557											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - coding silent(2)	large_intestine(2)	11											153	151	152					11																	33564564		2008	4148	6156	33521140	SO:0001819	synonymous_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.564C>A	11.37:g.33564564C>A		841	33521140	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																				0.557	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33564564	C	A	33564564	2	1	61	1	0	0	0	0	0	0	0	1	1644	845	30	2		2	C11orf41	11	33564564	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	144	33564564	101441952	7291	15276										
C11orf41	25758	broad.mit.edu	37	chr11	33565195	33565195	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagcaaccacagatgttTtctggagttctctttcagca	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33565195T>G	ENST00000321505.4	+	1	1375	c.1195T>G	c.(1195-1197)Ttc>Gtc	p.F399V	KIAA1549L_ENST00000265654.5_Missense_Mutation_p.F399V|KIAA1549L_ENST00000389726.3_Missense_Mutation_p.F399V			Q6ZVL6	K154L_HUMAN	KIAA1549-like	399						integral component of membrane (GO:0016021)		p.F399V(2)									CACAGATGTTTTCTGGAGTTC	0.408											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	11											34	34	34					11																	33565195		1861	4106	5967	33521771	SO:0001583	missense	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.1195T>G	11.37:g.33565195T>G	ENSP00000315295:p.Phe399Val	841	33521771	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	T	15.12	2.738588	0.49045	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.	.	.	5.65	5.65	0.86999	.	0.432330	0.22293	N	0.061966	T	0.52709	0.1751	M	0.62723	1.935	0.32973	D	0.522586	P;P	0.42296	0.651;0.775	B;B	0.43916	0.162;0.436	T	0.60647	-0.7222	9	0.14252	T	0.57	-3.4441	13.3966	0.60856	0.0:0.0:0.0:1.0	.	399;399	E9PAT2;Q6ZVL6-2	.;.	V	399;399;399;239	.	ENSP00000265654:F399V	F	+	1	0	C11orf41	33521771	0.921000	0.31238	0.959000	0.39883	0.944000	0.59088	1.191000	0.32138	2.149000	0.67028	0.454000	0.30748	TTC		0.408	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		G	33565195	T	G	33565195	3	3	61	1	0	0	0	0	1	0	0	0	1644	1841	64	4	1197	4	C11orf41	11	33565195	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	631	33565195	101441321	7292	15277										
C11orf41	25758	broad.mit.edu	37	chr11	33565376	33565376	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgccgatgccataaaatCtcaggatttcaaagatactg	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33565376C>A	ENST00000321505.4	+	1	1556	c.1376C>A	c.(1375-1377)tCt>tAt	p.S459Y	KIAA1549L_ENST00000265654.5_Missense_Mutation_p.S459Y|KIAA1549L_ENST00000389726.3_Missense_Mutation_p.S459Y			Q6ZVL6	K154L_HUMAN	KIAA1549-like	459						integral component of membrane (GO:0016021)		p.S459Y(2)									GCCATAAAATCTCAGGATTTC	0.448											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	11											138	133	135					11																	33565376		1871	4113	5984	33521952	SO:0001583	missense	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.1376C>A	11.37:g.33565376C>A	ENSP00000315295:p.Ser459Tyr	841	33521952	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	0.026	-1.368050	0.01225	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.	.	.	5.35	0.999	0.19862	.	0.719740	0.13072	N	0.416001	T	0.30008	0.0751	L	0.50333	1.59	0.09310	N	1	B;B	0.23806	0.004;0.091	B;B	0.17433	0.003;0.018	T	0.30937	-0.9961	9	0.54805	T	0.06	2.8877	1.4142	0.02298	0.1401:0.4041:0.1364:0.3194	.	459;459	E9PAT2;Q6ZVL6-2	.;.	Y	459;459;459;299	.	ENSP00000265654:S459Y	S	+	2	0	C11orf41	33521952	0.000000	0.05858	0.004000	0.12327	0.913000	0.54294	-0.377000	0.07456	0.627000	0.30340	0.442000	0.29010	TCT		0.448	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33565376	C	A	33565376	3	1	61	1	0	0	0	0	1	0	0	0	1644	913	32	2	1378	2	C11orf41	11	33565376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	181	33565376	101441140	7293	15278										
C11orf41	25758	broad.mit.edu	37	chr11	33581404	33581404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctcctcagccagctctCggctgagctggtgggattct	12	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33581404C>T	ENST00000321505.4	+	6	3254	c.3074C>T	c.(3073-3075)tCg>tTg	p.S1025L	KIAA1549L_ENST00000265654.5_Missense_Mutation_p.S1031L|KIAA1549L_ENST00000389726.3_Missense_Mutation_p.S1031L			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1025						integral component of membrane (GO:0016021)		p.S1031L(1)|p.S1025L(1)									AGCCAGCTCTCGGCTGAGCTG	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	11											115	121	119					11																	33581404		2134	4229	6363	33537980	SO:0001583	missense	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3074C>T	11.37:g.33581404C>T	ENSP00000315295:p.Ser1025Leu		33537980	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.553505|5.553505	0.96501|0.96501	.|.	.|.	ENSG00000110427|ENSG00000110427	ENST00000526400|ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.|.	.|.	.|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	.|0.119448	.|0.64402	.|D	.|0.000014	D|D	0.83151|0.83151	0.5192|0.5192	M|M	0.77103|0.77103	2.36|2.36	0.41093|0.41093	D|D	0.985616|0.985616	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.84883|0.84883	0.0832|0.0832	5|9	.|0.87932	.|D	.|0	-13.0799|-13.0799	19.6376|19.6376	0.95740|0.95740	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1031;1031	.|E9PAT2;Q6ZVL6-2	.|.;.	W|L	423|1025;1031;1031;864	.|.	.|ENSP00000265654:S1031L	R|S	+|+	1|2	2|0	C11orf41|C11orf41	33537980|33537980	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.982000|0.982000	0.71751|0.71751	7.430000|7.430000	0.80321|0.80321	2.715000|2.715000	0.92844|0.92844	0.573000|0.573000	0.79308|0.79308	CGG|TCG		0.602	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33581404	C	T	33581404	3	4	61	1	0	0	0	0	1	0	0	0	1644	893	31	1	3114	1	C11orf41	11	33581404	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16028	33581404	101425112	7294	15279										
LMO2	4005	broad.mit.edu	37	chr11	33880946	33880946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactcgtagatgtcctgttCgcacactatgtcagagttga	9	11	1	3	rs374739443		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:33880946C>T	ENST00000395833.3	-	3	862	c.433G>A	c.(433-435)Gaa>Aaa	p.E145K	LMO2_ENST00000257818.2_Missense_Mutation_p.E214K	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	145	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)	p.E145K(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						ATGTCCTGTTCGCACACTATG	0.502			T	TRD@	T-ALL																																		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	1	Substitution - Missense(1)	large_intestine(1)	11						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4404		0,0,2202	134	109	117		433,433,640	5.4	1	11		117	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	LMO2	NM_001142315.1,NM_001142316.1,NM_005574.3	56,56,56	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	145/159,145/159,214/228	33880946	1,12999	2202	4298	6500	33837522	SO:0001583	missense	4005			X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"T-cell translocation gene 2", "rhombotin-like 1"	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.433G>A	11.37:g.33880946C>T	ENSP00000379175:p.Glu145Lys		33837522	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	37	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411241	0.83340	0.0	1.16E-4	ENSG00000135363	ENST00000395833;ENST00000257818	D;D	0.86164	-2.08;-2.08	5.36	5.36	0.76844	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	L	0.31845	0.965	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.70227	0.947;0.968	T	0.82959	-0.0198	10	0.06891	T	0.86	.	19.4655	0.94935	0.0:1.0:0.0:0.0	.	214;145	P25791-3;P25791	.;RBTN2_HUMAN	K	145;214	ENSP00000379175:E145K;ENSP00000257818:E214K	ENSP00000257818:E214K	E	-	1	0	LMO2	33837522	1.000000	0.71417	0.982000	0.44146	0.985000	0.73830	7.577000	0.82486	2.692000	0.91855	0.491000	0.48974	GAA		0.502	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574		T	33880946	C	T	33880946	3	4	61	1	0	0	0	0	1	0	0	0	8876	893	31	1	47	1	LMO2	11	33880946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	299542	33880946	101125570	7295	15280										
CAPRIN1	4076	broad.mit.edu	37	chr11	34101238	34101238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactttgacagcacccacaAccaccagaatgggctgtgtg	9	13	0	2	rs201905401		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34101238A>G	ENST00000341394.4	+	7	941	c.752A>G	c.(751-753)aAc>aGc	p.N251S	CAPRIN1_ENST00000532820.1_Missense_Mutation_p.N251S|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.N170S|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.N251S|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.N251S	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	251					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.N251S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				AGCACCCACAACCACCAGAAT	0.408													A|||	1	0.000199681	0	0	5008	,	,		15582	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											98	91	93					11																	34101238		2202	4298	6500	34057814	SO:0001583	missense	4076			BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.752A>G	11.37:g.34101238A>G	ENSP00000340329:p.Asn251Ser		34057814	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	37	CCDS31453.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	7.556	0.663728	0.14710	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.56	4.44	0.53790	.	0.183072	0.64402	D	0.000016	T	0.17280	0.0415	N	0.17474	0.49	0.34977	D	0.753702	B;B	0.18968	0.032;0.016	B;B	0.14023	0.007;0.01	T	0.17198	-1.0377	10	0.10902	T	0.67	-6.8484	11.6166	0.51094	0.9303:0.0:0.0697:0.0	.	251;251	Q14444;Q14444-2	CAPR1_HUMAN;.	S	251;251;251;251;170	ENSP00000340329:N251S;ENSP00000374296:N251S;ENSP00000434150:N251S;ENSP00000434204:N251S;ENSP00000431581:N170S	ENSP00000340329:N251S	N	+	2	0	CAPRIN1	34057814	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	5.266000	0.65525	1.056000	0.40484	-0.270000	0.10280	AAC		0.408	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		G	34101238	A	G	34101238	3	3	61	1	0	0	0	0	1	0	0	0	2641	43	2	4	774	4	CAPRIN1	11	34101238	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	220292	34101238	100905278	7296	15281										
CAPRIN1	4076	broad.mit.edu	37	chr11	34104523	34104523	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaaatagacagttcatgGcagaaacacagttcaccagt	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34104523G>A	ENST00000341394.4	+	9	1090	c.901G>A	c.(901-903)Gca>Aca	p.A301T	CAPRIN1_ENST00000532820.1_Missense_Mutation_p.A301T|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.A220T|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.A301T|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.A301T	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	301					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A301T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				ACAGTTCATGGCAGAAACACA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											195	203	200					11																	34104523		2202	4298	6500	34061099	SO:0001583	missense	4076			BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.901G>A	11.37:g.34104523G>A	ENSP00000340329:p.Ala301Thr		34061099	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	37	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	G	6.645	0.487455	0.12641	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	6.17	6.17	0.99709	.	0.251234	0.47852	D	0.000210	T	0.17746	0.0426	N	0.13235	0.315	0.36451	D	0.866064	B;B	0.21147	0.031;0.052	B;B	0.16289	0.006;0.015	T	0.16867	-1.0388	10	0.09843	T	0.71	-8.4438	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	301;301	Q14444;Q14444-2	CAPR1_HUMAN;.	T	301;301;301;301;220	ENSP00000340329:A301T;ENSP00000374296:A301T;ENSP00000434150:A301T;ENSP00000434204:A301T;ENSP00000431581:A220T	ENSP00000340329:A301T	A	+	1	0	CAPRIN1	34061099	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	3.333000	0.52090	2.941000	0.99782	0.655000	0.94253	GCA		0.378	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		A	34104523	G	A	34104523	3	1	61	1	0	0	0	0	1	0	0	0	2641	1203	42	3	931	3	CAPRIN1	11	34104523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3285	34104523	100901993	7297	15282										
NAT10	55226	broad.mit.edu	37	chr11	34133608	34133608	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgattgcagtcaccggaaGaaaagaatgcgacagctgca	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34133608G>T	ENST00000257829.3	+	4	416	c.210G>T	c.(208-210)aaG>aaT	p.K70N	NAT10_ENST00000527971.1_Missense_Mutation_p.K70N|NAT10_ENST00000531159.2_5'UTR	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	70						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)	p.K70N(1)		endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				GTCACCGGAAGAAAAGAATGC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											63	58	60					11																	34133608		2202	4298	6500	34090184	SO:0001583	missense	55226			AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.210G>T	11.37:g.34133608G>T	ENSP00000257829:p.Lys70Asn		34090184	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	37	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.350459	0.61183	.	.	ENSG00000135372	ENST00000257829;ENST00000529523;ENST00000527971	T;T;T	0.33865	1.39;1.39;1.39	5.31	3.44	0.39384	.	0.047342	0.85682	D	0.000000	T	0.66208	0.2766	H	0.94503	3.545	0.80722	D	1	D	0.63880	0.993	D	0.69479	0.964	T	0.71593	-0.4546	10	0.87932	D	0	-21.3798	10.0077	0.41968	0.2189:0.0:0.7811:0.0	.	70	Q9H0A0	NAT10_HUMAN	N	70	ENSP00000257829:K70N;ENSP00000435569:K70N;ENSP00000437324:K70N	ENSP00000257829:K70N	K	+	3	2	NAT10	34090184	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	4.632000	0.61311	0.629000	0.30376	-0.150000	0.13652	AAG		0.483	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		T	34133608	G	T	34133608	3	4	61	1	0	0	0	0	1	0	0	0	10204	933	33	2	220	2	NAT10	11	34133608	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29085	34133608	100872908	7298	15283										
NAT10	55226	broad.mit.edu	37	chr11	34152464	34152464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgagaataagaccacgaCgacagccagattggcatcag	11	10	1	3	rs148211973	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34152464C>T	ENST00000257829.3	+	13	1555	c.1349C>T	c.(1348-1350)aCg>aTg	p.T450M	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.T378M	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	450						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)	p.T450M(1)		endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				AAGACCACGACGACAGCCAGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	MET/THR,MET/THR	0,4404		0,0,2202	102	89	93		1133,1349	4.4	0	11	dbSNP_134	93	11,8585	8.4+/-32.0	0,11,4287	yes	missense,missense	NAT10	NM_001144030.1,NM_024662.2	81,81	0,11,6489	TT,TC,CC		0.128,0.0,0.0846	possibly-damaging,possibly-damaging	378/954,450/1026	34152464	11,12989	2202	4298	6500	34109040	SO:0001583	missense	55226			AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1349C>T	11.37:g.34152464C>T	ENSP00000257829:p.Thr450Met		34109040	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	37	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780205	0.31502	0.0	0.00128	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.31769	1.49;1.48	5.33	4.42	0.53409	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.496991	0.25798	N	0.028233	T	0.26484	0.0647	L	0.38175	1.15	0.20403	N	0.999903	B	0.19583	0.037	B	0.18871	0.023	T	0.18304	-1.0341	10	0.49607	T	0.09	-3.8836	14.0935	0.65006	0.0:0.9274:0.0:0.0726	.	450	Q9H0A0	NAT10_HUMAN	M	450;378	ENSP00000257829:T450M;ENSP00000433011:T378M	ENSP00000257829:T450M	T	+	2	0	NAT10	34109040	0.002000	0.14202	0.014000	0.15608	0.986000	0.74619	1.493000	0.35605	1.386000	0.46466	0.561000	0.74099	ACG		0.592	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		T	34152464	C	T	34152464	3	4	61	1	0	0	0	0	1	0	0	0	10204	536	19	1	1395	1	NAT10	11	34152464	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18856	34152464	100854052	7299	15284										
CAT	847	broad.mit.edu	37	chr11	34477737	34477737	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttttccatttaatccattCgatctcaccaaggtgagtca	5	11	2	1	rs373984976		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34477737C>T	ENST00000241052.4	+	7	980	c.891C>T	c.(889-891)ttC>ttT	p.F297F		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	297					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.F297F(1)		breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	TTAATCCATTCGATCTCACCA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C		0,4404		0,0,2202	47	49	49		891	1.1	1	11		49	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	CAT	NM_001752.3		0,2,6498	TT,TC,CC		0.0233,0.0,0.0154		297/528	34477737	2,12998	2202	4298	6500	34434313	SO:0001819	synonymous_variant	847			AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.891C>T	11.37:g.34477737C>T			34434313	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Silent	SNP	ENST00000241052.4	37	CCDS7891.1																																																																																				0.328	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		T	34477737	C	T	34477737	2	4	61	1	0	0	0	0	0	0	0	1	2692	883	31	1		1	CAT	11	34477737	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	325273	34477737	100528779	7300	15285										
PDHX	8050	broad.mit.edu	37	chr11	34999702	34999702	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcagtaaatgattttatCatcaaggcagcagctgttac	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:34999702C>A	ENST00000227868.4	+	8	1080	c.996C>A	c.(994-996)atC>atA	p.I332I	PDHX_ENST00000448838.3_Silent_p.I317I|PDHX_ENST00000430469.2_Intron			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	332					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)	p.I332I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	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)			ATGATTTTATCATCAAGGCAG	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	11											133	137	136					11																	34999702		2202	4293	6495	34956278	SO:0001819	synonymous_variant	8050			U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.996C>A	11.37:g.34999702C>A			34956278	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	C	9.989	1.230393	0.22542	.	.	ENSG00000110435	ENST00000526309	.	.	.	5.74	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.3292	4.9812	0.14166	0.171:0.6154:0.0:0.2137	.	.	.	.	X	20	.	.	S	+	2	0	PDHX	34956278	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.321000	0.33678	0.764000	0.33197	0.655000	0.94253	TCA		0.289	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		A	34999702	C	A	34999702	2	1	61	1	0	0	0	0	0	0	0	1	11698	816	29	2		2	PDHX	11	34999702	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	521965	34999702	100006814	7301	15286										
SLC1A2	6506	broad.mit.edu	37	chr11	35333783	35333783	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaggttttcagggaagaGatttcgaataaggtccagga	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:35333783G>T	ENST00000278379.3	-	4	805	c.523C>A	c.(523-525)Ctc>Atc	p.L175I	SLC1A2_ENST00000395753.1_Missense_Mutation_p.L166I|SLC1A2_ENST00000606205.1_Missense_Mutation_p.L175I|SLC1A2_ENST00000395750.1_Missense_Mutation_p.L166I	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	175					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.L175I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			TCAGGGAAGAGATTTCGAATA	0.478																																					NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)											1	Substitution - Missense(1)	large_intestine(1)	11											212	208	209					11																	35333783		2202	4298	6500	35290359	SO:0001583	missense	6506			AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.523C>A	11.37:g.35333783G>T	ENSP00000278379:p.Leu175Ile		35290359	B4DQE9|Q14417|Q541G6|U3KQQ4	Missense_Mutation	SNP	ENST00000278379.3	37	CCDS31459.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.918662	0.73098	.	.	ENSG00000110436	ENST00000278379;ENST00000395750;ENST00000395753;ENST00000449068	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.76	3.87	0.44632	.	0.000000	0.85682	D	0.000000	T	0.48466	0.1501	N	0.26042	0.785	0.58432	D	0.999999	P;P	0.41978	0.767;0.642	B;P	0.47528	0.348;0.549	T	0.39761	-0.9598	10	0.32370	T	0.25	-19.1331	8.7425	0.34567	0.1262:0.0:0.7461:0.1277	.	175;175	B4DQE9;P43004	.;EAA2_HUMAN	I	175;166;166;171	ENSP00000278379:L175I;ENSP00000379099:L166I;ENSP00000379102:L166I;ENSP00000406133:L171I	ENSP00000278379:L175I	L	-	1	0	SLC1A2	35290359	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.743000	0.74848	1.432000	0.47375	0.462000	0.41574	CTC		0.478	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		T	35333783	G	T	35333783	3	4	61	1	0	0	0	0	1	0	0	0	14469	942	33	2	1233	2	SLC1A2	11	35333783	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334081	35333783	99672733	7302	15287										
PAMR1	25891	broad.mit.edu	37	chr11	35456131	35456131	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaaaacaactttcaggtCtgctgtcttgatcatggtga	8	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:35456131C>A	ENST00000378880.2	-	10	2000	c.1555G>T	c.(1555-1557)Gac>Tac	p.D519Y	PAMR1_ENST00000278360.3_Missense_Mutation_p.D536Y|PAMR1_ENST00000532848.1_Missense_Mutation_p.D479Y|PAMR1_ENST00000378878.3_Missense_Mutation_p.D408Y	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	519	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.D536Y(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						ACTTTCAGGTCTGCTGTCTTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											133	118	123					11																	35456131		2202	4298	6500	35412707	SO:0001583	missense	25891				CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1555G>T	11.37:g.35456131C>A	ENSP00000368158:p.Asp519Tyr		35412707	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.235824	0.58886	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	5.36	5.36	0.76844	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.252679	0.45867	D	0.000339	D	0.91851	0.7421	L	0.41632	1.29	0.44890	D	0.9979	D;D;P	0.71674	0.998;0.963;0.955	D;P;P	0.65323	0.934;0.776;0.748	D	0.92704	0.6177	10	0.87932	D	0	.	19.0909	0.93227	0.0:1.0:0.0:0.0	.	408;519;536	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	Y	536;519;408;479;496	ENSP00000278360:D536Y;ENSP00000368158:D519Y;ENSP00000368156:D408Y;ENSP00000433868:D479Y;ENSP00000432591:D496Y	ENSP00000278360:D536Y	D	-	1	0	PAMR1	35412707	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	3.087000	0.50167	2.526000	0.85167	0.555000	0.69702	GAC		0.547	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35456131	C	A	35456131	3	1	61	1	0	0	0	0	1	0	0	0	11444	913	32	2	615	2	PAMR1	11	35456131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122348	35456131	99550385	7303	15288										
RAG1	5896	broad.mit.edu	37	chr11	36595361	36595361	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaggcagatgttgactcGatccaccccactgagttctg	11	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:36595361G>A	ENST00000299440.5	+	2	619	c.507G>A	c.(505-507)tcG>tcA	p.S169S		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	169	Interaction with importin alpha-1.		S -> L (in dbSNP:rs4151027).		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S169S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				ATGTTGACTCGATCCACCCCA	0.512									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - coding silent(1)	large_intestine(1)	11											84	76	79					11																	36595361		2202	4298	6500	36551937	SO:0001819	synonymous_variant	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.507G>A	11.37:g.36595361G>A			36551937	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	37	CCDS7902.1																																																																																				0.512	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		A	36595361	G	A	36595361	2	1	61	1	0	0	0	0	0	0	0	1	13040	1045	37	1		1	RAG1	11	36595361	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1139230	36595361	98411155	7304	15289										
RAG1	5896	broad.mit.edu	37	chr11	36596514	36596514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggatgattacccagtgGacaccattgcaaagaggttc	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:36596514G>A	ENST00000299440.5	+	2	1772	c.1660G>A	c.(1660-1662)Gac>Aac	p.D554N		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	554					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D554N(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				TTACCCAGTGGACACCATTGC	0.478									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - Missense(1)	large_intestine(1)	11											107	92	97					11																	36596514		2202	4298	6500	36553090	SO:0001583	missense	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1660G>A	11.37:g.36596514G>A	ENSP00000299440:p.Asp554Asn		36553090	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411725	0.83340	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	D;D	0.86097	-2.07;-2.07	5.58	5.58	0.84498	.	0.157978	0.53938	D	0.000044	D	0.89781	0.6814	M	0.76838	2.35	0.58432	D	0.999999	P	0.42010	0.768	P	0.47891	0.56	D	0.90679	0.4604	10	0.87932	D	0	.	19.6271	0.95682	0.0:0.0:1.0:0.0	.	554	P15918	RAG1_HUMAN	N	554	ENSP00000434610:D554N;ENSP00000299440:D554N	ENSP00000299440:D554N	D	+	1	0	RAG1	36553090	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.649000	0.89929	0.650000	0.86243	GAC		0.478	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		A	36596514	G	A	36596514	3	1	61	1	0	0	0	0	1	0	0	0	13040	1174	41	3	1662	3	RAG1	11	36596514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1153	36596514	98410002	7305	15290										
LRRC4C	57689	broad.mit.edu	37	chr11	40136877	40136877	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggcacaacaagctgtgttCgagggggccatgtcttttat	13	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:40136877C>T	ENST00000278198.2	-	2	2929	c.966G>A	c.(964-966)tcG>tcA	p.S322S	LRRC4C_ENST00000527150.1_Silent_p.S322S|LRRC4C_ENST00000528697.1_Silent_p.S322S|LRRC4C_ENST00000530763.1_Silent_p.S322S			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	322	LRRCT.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.S322S(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				AAGCTGTGTTCGAGGGGGCCA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	11											92	80	84					11																	40136877		2203	4300	6503	40093453	SO:0001819	synonymous_variant	57689			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.966G>A	11.37:g.40136877C>T			40093453	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																				0.493	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		T	40136877	C	T	40136877	2	4	61	1	0	0	0	0	0	0	0	1	9037	871	31	1		1	LRRC4C	11	40136877	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3540363	40136877	94869639	7306	15291										
HSD17B12	51144	broad.mit.edu	37	chr11	43876282	43876282	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagtgtcctgccatacttCgtagctacaaaactggctaa	8	10	0	1	rs574266495		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:43876282C>T	ENST00000278353.4	+	10	821	c.702C>T	c.(700-702)ttC>ttT	p.F234F	RP11-613D13.5_ENST00000530450.1_RNA	NM_016142.2	NP_057226.1	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	234					cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)	p.F234F(1)		endometrium(2)|large_intestine(4)|lung(4)	10						TGCCATACTTCGTAGCTACAA	0.478													C|||	1	0.000199681	0	0.0014	5008	,	,		17933	0		0	False		,,,				2504	0				Ovarian(58;548 1143 13948 16572 34258)											1	Substitution - coding silent(1)	large_intestine(1)	11											114	118	117					11																	43876282		2203	4300	6503	43832858	SO:0001819	synonymous_variant	51144			AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	18646	protein-coding gene	gene with protein product	"3-ketoacyl-CoA reductase", "short chain dehydrogenase/reductase family 12C, member 1"	609574				12482854, 19027726	Standard	NM_016142		Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000278353.4:c.702C>T	11.37:g.43876282C>T			43832858	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	Silent	SNP	ENST00000278353.4	37	CCDS7905.1																																																																																				0.478	HSD17B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389594.1			T	43876282	C	T	43876282	2	4	61	1	0	0	0	0	0	0	0	1	7402	883	31	1		1	HSD17B12	11	43876282	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3739405	43876282	91130234	7307	15292										
ACCSL	390110	broad.mit.edu	37	chr11	44075001	44075001	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcaaccctcagaatcctCtgggtgacatctactcccca	5	15	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44075001C>A	ENST00000378832.1	+	8	1050	c.994C>A	c.(994-996)Ctg>Atg	p.L332M		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	332					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)	p.L332M(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						TCAGAATCCTCTGGGTGACAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											113	104	107					11																	44075001		1858	4091	5949	44031577	SO:0001583	missense	390110				CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.994C>A	11.37:g.44075001C>A	ENSP00000368109:p.Leu332Met		44031577		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	C	9.649	1.141170	0.21205	.	.	ENSG00000205126	ENST00000378832	T	0.24908	1.83	4.45	-3.46	0.04767	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.242590	0.35525	N	0.003157	T	0.46756	0.1409	M	0.92691	3.335	0.36093	D	0.843598	D	0.65815	0.995	D	0.68943	0.961	T	0.51140	-0.8743	10	0.87932	D	0	-5.117	3.0703	0.06229	0.1057:0.4545:0.145:0.2948	.	332	Q4AC99	1A1L2_HUMAN	M	332	ENSP00000368109:L332M	ENSP00000368109:L332M	L	+	1	2	ACCSL	44031577	0.009000	0.17119	0.002000	0.10522	0.001000	0.01503	0.081000	0.14823	-0.726000	0.04895	-2.744000	0.00126	CTG		0.433	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		A	44075001	C	A	44075001	3	1	61	1	0	0	0	0	1	0	0	0	134	912	32	2	1024	2	ACCSL	11	44075001	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	198719	44075001	90931515	7308	15293										
ACCSL	390110	broad.mit.edu	37	chr11	44081394	44081394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaaccctctagctatgcGtcggttctgtgatgtgctgc	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44081394G>A	ENST00000378832.1	+	14	1687	c.1631G>A	c.(1630-1632)cGt>cAt	p.R544H		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	544					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)	p.R544H(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CTAGCTATGCGTCGGTTCTGT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											348	343	345					11																	44081394		2009	4179	6188	44037970	SO:0001583	missense	390110				CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.1631G>A	11.37:g.44081394G>A	ENSP00000368109:p.Arg544His		44037970		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	G	7.574	0.667313	0.14710	.	.	ENSG00000205126	ENST00000378832	T	0.23950	1.88	3.74	-3.63	0.04529	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.721314	0.13634	N	0.373461	T	0.13243	0.0321	L	0.28608	0.87	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.22208	-1.0223	10	0.26408	T	0.33	0.9755	5.1411	0.14959	0.3484:0.0:0.4859:0.1657	.	544	Q4AC99	1A1L2_HUMAN	H	544	ENSP00000368109:R544H	ENSP00000368109:R544H	R	+	2	0	ACCSL	44037970	0.000000	0.05858	0.002000	0.10522	0.223000	0.24884	-0.069000	0.11542	-0.750000	0.04740	-0.310000	0.09108	CGT		0.512	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		A	44081394	G	A	44081394	3	1	61	1	0	0	0	0	1	0	0	0	134	1145	40	1	1685	1	ACCSL	11	44081394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6393	44081394	90925122	7309	15294										
ACCS	84680	broad.mit.edu	37	chr11	44089232	44089232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccacctgtctgggccccAcctgcatgcaggacctgggc	11	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44089232A>G	ENST00000263776.8	+	2	489	c.55A>G	c.(55-57)Acc>Gcc	p.T19A	ACCS_ENST00000432284.2_Missense_Mutation_p.T19A|ACCS_ENST00000533208.1_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	19					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.T19A(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCTGGGCCCCACCTGCATGCA	0.557																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											1	Substitution - Missense(1)	large_intestine(1)	11											69	73	72					11																	44089232		2203	4300	6503	44045808	SO:0001583	missense	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.55A>G	11.37:g.44089232A>G	ENSP00000263776:p.Thr19Ala		44045808	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	G	0.417	-0.910247	0.02434	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.59364	0.97;0.27;0.97;1.07	5.43	0.0996	0.14503	.	0.861636	0.10406	N	0.678505	T	0.26738	0.0654	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-0.427	7.4529	0.27248	0.2042:0.1334:0.6623:0.0	.	19;19	B4E219;Q96QU6	.;1A1L1_HUMAN	A	19	ENSP00000434156:T19A;ENSP00000263776:T19A;ENSP00000391775:T19A;ENSP00000435919:T19A	ENSP00000263776:T19A	T	+	1	0	ACCS	44045808	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.167000	0.09940	-0.164000	0.10927	-3.370000	0.00041	ACC		0.557	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		G	44089232	A	G	44089232	3	3	61	1	0	0	0	0	1	0	0	0	133	159	6	4	57	4	ACCS	11	44089232	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7838	44089232	90917284	7310	15295										
ACCS	84680	broad.mit.edu	37	chr11	44089380	44089380	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacctgtcctctagaggaaGaatgattaaatggttctggg	11	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44089380G>T	ENST00000263776.8	+	2	637	c.203G>T	c.(202-204)aGa>aTa	p.R68I	ACCS_ENST00000432284.2_Missense_Mutation_p.R68I|ACCS_ENST00000533208.1_Intron	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	68					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.R68I(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCTAGAGGAAGAATGATTAAA	0.517																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											1	Substitution - Missense(1)	large_intestine(1)	11											84	75	78					11																	44089380		2203	4300	6503	44045956	SO:0001583	missense	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.203G>T	11.37:g.44089380G>T	ENSP00000263776:p.Arg68Ile		44045956	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.659664	0.29515	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.60797	0.93;0.16;0.93;0.66	5.57	0.586	0.17434	Pyridoxal phosphate-dependent transferase, major domain (1);	0.547984	0.20511	N	0.090885	T	0.47783	0.1464	N	0.25647	0.755	0.09310	N	0.999995	D;B	0.60575	0.988;0.0	P;B	0.51324	0.666;0.002	T	0.40850	-0.9541	9	.	.	.	-0.0063	8.2894	0.31948	0.5857:0.0:0.4143:0.0	.	68;68	B4E219;Q96QU6	.;1A1L1_HUMAN	I	68	ENSP00000434156:R68I;ENSP00000263776:R68I;ENSP00000391775:R68I;ENSP00000435919:R68I	.	R	+	2	0	ACCS	44045956	0.016000	0.18221	0.009000	0.14445	0.995000	0.86356	1.051000	0.30417	0.064000	0.16427	0.655000	0.94253	AGA		0.517	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		T	44089380	G	T	44089380	3	4	61	1	0	0	0	0	1	0	0	0	133	942	33	2	205	2	ACCS	11	44089380	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148	44089380	90917136	7311	15296										
ACCS	84680	broad.mit.edu	37	chr11	44101168	44101168	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcagtgtcctaagcctggaAaggtgaggctccctgacaca	12	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44101168A>C	ENST00000263776.8	+	10	1355	c.921A>C	c.(919-921)gaA>gaC	p.E307D		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	307					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.E307D(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TAAGCCTGGAAAGGTGAGGCT	0.582																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											1	Substitution - Missense(1)	large_intestine(1)	11											170	119	136					11																	44101168		2203	4300	6503	44057744	SO:0001583	missense	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.921A>C	11.37:g.44101168A>C	ENSP00000263776:p.Glu307Asp		44057744	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	A	8.421	0.846383	0.16963	.	.	ENSG00000110455	ENST00000263776	D	0.90620	-2.7	5.84	-2.88	0.05682	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.151648	0.56097	N	0.000024	T	0.68081	0.2962	N	0.02721	-0.515	0.80722	D	1	B	0.13594	0.008	B	0.23150	0.044	T	0.49890	-0.8891	10	0.10636	T	0.68	-6.2727	2.7898	0.05384	0.4796:0.2717:0.1569:0.0918	.	307	Q96QU6	1A1L1_HUMAN	D	307	ENSP00000263776:E307D	ENSP00000263776:E307D	E	+	3	2	ACCS	44057744	0.560000	0.26570	0.773000	0.31616	0.113000	0.19764	-0.165000	0.09968	-0.391000	0.07763	-0.333000	0.08304	GAA		0.582	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		C	44101168	A	C	44101168	3	2	61	1	0	0	0	0	1	0	0	0	133	11	1	4	955	4	ACCS	11	44101168	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11788	44101168	90905348	7312	15297										
ACCS	84680	broad.mit.edu	37	chr11	44104770	44104770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgcccggctcaaggctgCccacacctatgtctcagaag	9	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44104770C>T	ENST00000263776.8	+	13	1597	c.1163C>T	c.(1162-1164)gCc>gTc	p.A388V		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	388					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.A388V(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CTCAAGGCTGCCCACACCTAT	0.527																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											1	Substitution - Missense(1)	large_intestine(1)	11											121	118	119					11																	44104770		2203	4300	6503	44061346	SO:0001583	missense	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.1163C>T	11.37:g.44104770C>T	ENSP00000263776:p.Ala388Val		44061346	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.895603	0.91962	.	.	ENSG00000110455	ENST00000263776	T	0.22134	1.97	5.77	5.77	0.91146	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.52661	0.1748	M	0.87547	2.89	0.80722	D	1	D	0.65815	0.995	D	0.65323	0.934	T	0.54603	-0.8269	10	0.46703	T	0.11	-23.0706	19.5934	0.95525	0.0:1.0:0.0:0.0	.	388	Q96QU6	1A1L1_HUMAN	V	388	ENSP00000263776:A388V	ENSP00000263776:A388V	A	+	2	0	ACCS	44061346	1.000000	0.71417	0.992000	0.48379	0.539000	0.34962	4.469000	0.60169	2.724000	0.93272	0.561000	0.74099	GCC		0.527	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		T	44104770	C	T	44104770	3	4	61	1	0	0	0	0	1	0	0	0	133	739	26	3	1209	3	ACCS	11	44104770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3602	44104770	90901746	7313	15298										
EXT2	2132	broad.mit.edu	37	chr11	44165823	44165823	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaaccagccaggagagaGaactggtcagctgctaatca	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44165823G>T	ENST00000343631.3	+	7	1302				EXT2_ENST00000358681.4_Missense_Mutation_p.E400D|EXT2_ENST00000395673.3_Intron|EXT2_ENST00000533608.1_Intron			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2						carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)	p.E400D(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						CCAGGAGAGAGAACTGGTCAG	0.453			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																													yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	1	Substitution - Missense(1)	large_intestine(1)	11											196	182	186					11																	44165823		876	1990	2866	44122399	SO:0001627	intron_variant	2132	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.1173+14135G>T	11.37:g.44165823G>T			44122399	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	37	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	G	8.796	0.931770	0.18131	.	.	ENSG00000151348	ENST00000358681	D	0.94723	-3.5	5.52	3.63	0.41609	.	.	.	.	.	D	0.86539	0.5957	N	0.08118	0	0.19775	N	0.999957	B	0.02656	0.0	B	0.06405	0.002	T	0.77838	-0.2439	9	0.66056	D	0.02	.	8.0902	0.30797	0.249:0.0:0.751:0.0	.	400	C9JU51	.	D	400	ENSP00000351509:E400D	ENSP00000351509:E400D	E	+	3	2	EXT2	44122399	0.183000	0.23186	0.025000	0.17156	0.738000	0.42128	0.579000	0.23788	0.680000	0.31366	0.650000	0.86243	GAG		0.453	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		T	44165823	G	T	44165823	1	4	61	0	1	0	0	0	0	0	0	0	5337	933	33	2		2	EXT2	11	44165823	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61053	44165823	90840693	7314	15299										
TSPAN18	90139	broad.mit.edu	37	chr11	44941422	44941422	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagtttgcatctgtgtttCgactcctgaccctggatagt	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:44941422C>T	ENST00000520358.2	+	8	902	c.487C>T	c.(487-489)Cga>Tga	p.R163*	TSPAN18_ENST00000340160.3_Nonsense_Mutation_p.R163*			Q96SJ8	TSN18_HUMAN	tetraspanin 18	163						integral component of membrane (GO:0016021)		p.R163*(1)		endometrium(1)|large_intestine(6)|lung(3)	10						ATCTGTGTTTCGACTCCTGAC	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											147	149	149					11																	44941422		2203	4299	6502	44897998	SO:0001587	stop_gained	90139			AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"Tetraspanins"	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.487C>T	11.37:g.44941422C>T	ENSP00000429993:p.Arg163*		44897998	Q6UY44|Q8NBI9	Nonsense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.40|16.40	3.111874|3.111874	0.56398|0.56398	.|.	.|.	ENSG00000157570|ENSG00000157570	ENST00000533080;ENST00000520358;ENST00000340160|ENST00000518429	.|.	.|.	.|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	3.893800|.	0.00763|.	N|.	0.001152|.	.|T	.|0.74114	.|0.3674	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72811	.|-0.4180	.|4	0.02654|.	T|.	1|.	.|.	18.0206|18.0206	0.89253|0.89253	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	98;163;163|166	.|.	ENSP00000339820:R163X|.	R|S	+|+	1|2	2|0	TSPAN18|TSPAN18	44897998|44897998	1.000000|1.000000	0.71417|0.71417	0.207000|0.207000	0.23584|0.23584	0.102000|0.102000	0.19082|0.19082	4.208000|4.208000	0.58486|0.58486	2.619000|2.619000	0.88677|0.88677	0.561000|0.561000	0.74099|0.74099	CGA|TCG		0.607	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783		T	44941422	C	T	44941422	4	4	61	1	0	0	0	0	0	1	0	0	16682	876	31	1	505	1	TSPAN18	11	44941422	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	775599	44941422	90065094	7315	15300										
PEX16	9409	broad.mit.edu	37	chr11	45937274	45937274	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggccagctggacgagggcGatgacaagccagcggcccac	15	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:45937274G>A	ENST00000378750.5	-	4	582	c.339C>T	c.(337-339)atC>atT	p.I113I	PEX16_ENST00000532681.1_Silent_p.I18I|PEX16_ENST00000241041.3_Silent_p.I113I|PEX16_ENST00000532554.1_Intron			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	113					ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)	p.I113I(1)		large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		GGACGAGGGCGATGACAAGCC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	11											149	144	146					11																	45937274		2203	4299	6502	45893850	SO:0001819	synonymous_variant	9409			AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.339C>T	11.37:g.45937274G>A			45893850	Q9BWB9	Silent	SNP	ENST00000378750.5	37	CCDS31472.1																																																																																				0.612	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174		A	45937274	G	A	45937274	2	1	61	1	0	0	0	0	0	0	0	1	11774	1048	37	1		1	PEX16	11	45937274	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	995852	45937274	89069242	7316	15301										
GYLTL1B	120071	broad.mit.edu	37	chr11	45949913	45949913	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggcccacattgtggagcTggatgcccaggtgaggaggg	18	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:45949913T>G	ENST00000531526.1	+	13	2051	c.1940T>G	c.(1939-1941)cTg>cGg	p.L647R	GYLTL1B_ENST00000401752.1_Missense_Mutation_p.L647R|GYLTL1B_ENST00000536139.1_Missense_Mutation_p.L616R|GYLTL1B_ENST00000325468.5_Missense_Mutation_p.L647R|GYLTL1B_ENST00000529052.1_Missense_Mutation_p.L616R	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	647					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.L647R(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		ATTGTGGAGCTGGATGCCCAG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											105	103	104					11																	45949913		2203	4299	6502	45906489	SO:0001583	missense	120071				CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1940T>G	11.37:g.45949913T>G	ENSP00000432869:p.Leu647Arg		45906489	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Missense_Mutation	SNP	ENST00000531526.1	37	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.530514	0.85706	.	.	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000325468;ENST00000536139	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.67258	0.2874	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.997	T	0.77918	-0.2408	10	0.87932	D	0	-15.5126	15.7274	0.77774	0.0:0.0:0.0:1.0	.	616;616;647	B3KP69;E9PIZ2;Q8N3Y3	.;.;LARG2_HUMAN	R	616;647;647;647;616	ENSP00000431932:L616R;ENSP00000432869:L647R;ENSP00000385235:L647R;ENSP00000324570:L647R;ENSP00000445044:L616R	ENSP00000324570:L647R	L	+	2	0	GYLTL1B	45906489	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	7.698000	0.84413	2.110000	0.64415	0.459000	0.35465	CTG		0.602	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		G	45949913	T	G	45949913	3	3	61	1	0	0	0	0	1	0	0	0	6928	1580	55	4	1986	4	GYLTL1B	11	45949913	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12639	45949913	89056603	7317	15302										
PHF21A	51317	broad.mit.edu	37	chr11	45991374	45991374	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtttactcacctgtggaaGaaagtttggacgtggagtga	14	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:45991374G>T	ENST00000418153.2	-	8	890	c.691C>A	c.(691-693)Ctt>Att	p.L231I	PHF21A_ENST00000257821.4_Missense_Mutation_p.L232I|PHF21A_ENST00000323180.6_Missense_Mutation_p.L232I			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	231					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L232I(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						ACCTGTGGAAGAAAGTTTGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											102	95	97					11																	45991374		2202	4299	6501	45947950	SO:0001583	missense	51317			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.691C>A	11.37:g.45991374G>T	ENSP00000398824:p.Leu231Ile		45947950	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	37	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	G	35	5.467073	0.96257	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153	T;T;T	0.49720	0.77;0.77;0.77	5.5	5.5	0.81552	.	0.067855	0.64402	D	0.000005	T	0.58278	0.2111	M	0.66939	2.045	0.53688	D	0.99997	D;D	0.63046	0.989;0.992	P;P	0.51385	0.572;0.668	T	0.53795	-0.8388	10	0.23302	T	0.38	-7.6421	19.3979	0.94614	0.0:0.0:1.0:0.0	.	231;232	Q96BD5;Q96BD5-2	PF21A_HUMAN;.	I	232;232;231	ENSP00000257821:L232I;ENSP00000323152:L232I;ENSP00000398824:L231I	ENSP00000257821:L232I	L	-	1	0	PHF21A	45947950	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.074000	0.93998	2.595000	0.87683	0.655000	0.94253	CTT		0.463	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		T	45991374	G	T	45991374	3	4	61	1	0	0	0	0	1	0	0	0	11864	942	33	2	1422	2	PHF21A	11	45991374	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41461	45991374	89015142	7318	15303										
CHRM4	1132	broad.mit.edu	37	chr11	46406921	46406921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcgttcgtgtcactttgCgctcccgggccgccatctgc	11	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:46406921C>T	ENST00000433765.2	-	1	1186	c.1187G>A	c.(1186-1188)cGc>cAc	p.R396H		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	396					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.R396H(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TGTCACTTTGCGCTCCCGGGC	0.632																																					Esophageal Squamous(171;1020 1936 4566 30205 42542)											1	Substitution - Missense(1)	large_intestine(1)	11											83	87	86					11																	46406921		2189	4297	6486	46363497	SO:0001583	missense	1132			M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1953	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 4"	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.1187G>A	11.37:g.46406921C>T	ENSP00000409378:p.Arg396His		46363497	B2RPP4|Q0VD60|Q4VBK7	Missense_Mutation	SNP	ENST00000433765.2	37	CCDS44581.1	.	.	.	.	.	.	.	.	.	.	c	17.80	3.477497	0.63849	.	.	ENSG00000180720	ENST00000433765	T	0.73681	-0.77	4.58	4.58	0.56647	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.58864	0.2152	N	0.20845	0.615	0.33116	D	0.541173	P	0.52463	0.953	B	0.43386	0.418	T	0.68891	-0.5289	9	0.87932	D	0	-14.6387	5.431	0.16454	0.0:0.7546:0.0:0.2454	.	396	P08173	ACM4_HUMAN	H	396	ENSP00000409378:R396H	ENSP00000409378:R396H	R	-	2	0	CHRM4	46363497	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.167000	0.50793	2.395000	0.81488	0.457000	0.33378	CGC		0.632	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334985.1	NM_000741		T	46406921	C	T	46406921	3	4	61	1	0	0	0	0	1	0	0	0	3385	768	27	1	256	1	CHRM4	11	46406921	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	415547	46406921	88599595	7319	15304										
KIAA0652	9776	broad.mit.edu	37	chr11	46693837	46693837	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagctggctgtgcatgaGaagaatgtccgcgagtttga	15	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:46693837G>T	ENST00000434074.1	+	17	2198	c.1509G>T	c.(1507-1509)gaG>gaT	p.E503D	ATG13_ENST00000359513.4_Missense_Mutation_p.E503D|ATG13_ENST00000451945.1_Missense_Mutation_p.E466D|ATG13_ENST00000524625.1_Missense_Mutation_p.E466D|ATG13_ENST00000312040.4_Missense_Mutation_p.E503D|ATG13_ENST00000528494.1_Missense_Mutation_p.E536D|ATG13_ENST00000529655.1_Missense_Mutation_p.E466D|ATG13_ENST00000526508.1_Missense_Mutation_p.E503D|ATG13_ENST00000530500.1_Missense_Mutation_p.E387D	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	503					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)	p.E466D(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						CTGTGCATGAGAAGAATGTCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											190	186	187					11																	46693837		2201	4299	6500	46650413	SO:0001583	missense	9776			AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"KIAA0652", "ATG13 autophagy related 13 homolog (S. cerevisiae)"	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.1509G>T	11.37:g.46693837G>T	ENSP00000400642:p.Glu503Asp		46650413	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	37	CCDS44582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.0|28.0	4.882900|4.882900	0.91740|0.91740	.|.	.|.	ENSG00000175224|ENSG00000175224	ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494|ENST00000531933	.|.	.|.	.|.	5.87|5.87	4.96|4.96	0.65561|0.65561	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.65831|.	0.2729|.	L|L	0.61218|0.61218	1.895|1.895	0.53688|0.53688	D|D	0.999978|0.999978	P;D;D;D|.	0.71674|.	0.849;0.998;0.998;0.997|.	B;D;D;D|.	0.77557|.	0.386;0.986;0.99;0.99|.	T|.	0.68903|.	-0.5286|.	9|.	0.87932|0.87932	D|D	0|0	-22.0275|-22.0275	10.9019|10.9019	0.47056|0.47056	0.1423:0.0:0.8577:0.0|0.1423:0.0:0.8577:0.0	.|.	387;503;536;466|.	B4DFI4;O75143;E9PQZ8;O75143-2|.	.;ATG13_HUMAN;.;.|.	D|X	503;503;466;466;387;503;466;503;536|33	.|.	ENSP00000310321:E503D|ENSP00000434125:E33X	E|E	+|+	3|1	2|0	ATG13|ATG13	46650413|46650413	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.562000|5.562000	0.67346|0.67346	1.495000|1.495000	0.48549|0.48549	0.655000|0.655000	0.94253|0.94253	GAG|GAA		0.547	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		T	46693837	G	T	46693837	3	4	61	1	0	0	0	0	1	0	0	0	8209	933	33	2	1571	2	KIAA0652	11	46693837	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	286916	46693837	88312679	7320	15305										
F2	2147	broad.mit.edu	37	chr11	46760879	46760879	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgaaggctgtgaccgggAtgggaaatatggcttctaca	16	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:46760879A>G	ENST00000311907.5	+	14	1846	c.1790A>G	c.(1789-1791)gAt>gGt	p.D597G	F2_ENST00000530231.1_Missense_Mutation_p.D558G	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	597	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)	p.D597G(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	TGTGACCGGGATGGGAAATAT	0.488																																					Esophageal Squamous(147;1147 1808 2148 38609 51144)											1	Substitution - Missense(1)	large_intestine(1)	11											131	130	130					11																	46760879		2201	4299	6500	46717455	SO:0001583	missense	2147			M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"Endogenous ligands"	3535	protein-coding gene	gene with protein product	"prepro-coagulation factor II"	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.1790A>G	11.37:g.46760879A>G	ENSP00000308541:p.Asp597Gly		46717455	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	37	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582365	0.86748	.	.	ENSG00000180210	ENST00000311907;ENST00000530231	D;D	0.87650	-2.28;-2.28	5.34	5.34	0.76211	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.204996	0.49916	D	0.000128	D	0.82490	0.5048	N	0.02876	-0.465	0.58432	D	0.999993	P	0.44627	0.839	P	0.55260	0.772	D	0.87694	0.2556	10	0.87932	D	0	.	15.3645	0.74510	1.0:0.0:0.0:0.0	.	597	P00734	THRB_HUMAN	G	597;558	ENSP00000308541:D597G;ENSP00000433907:D558G	ENSP00000308541:D597G	D	+	2	0	F2	46717455	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.339000	0.96797	2.027000	0.59764	0.456000	0.33151	GAT		0.488	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			G	46760879	A	G	46760879	3	3	61	1	0	0	0	0	1	0	0	0	5355	333	12	4	1844	4	F2	11	46760879	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	67042	46760879	88245637	7321	15306										
LRP4	4038	broad.mit.edu	37	chr11	46903303	46903303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaattgtcttcatgccggCgtcagcccagtatagacgct	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:46903303C>T	ENST00000378623.1	-	20	3006	c.2764G>A	c.(2764-2766)Gcc>Acc	p.A922T		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	922					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.A922T(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TTCATGCCGGCGTCAGCCCAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											136	127	130					11																	46903303		2201	4299	6500	46859879	SO:0001583	missense	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.2764G>A	11.37:g.46903303C>T	ENSP00000367888:p.Ala922Thr		46859879	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	34	5.328550	0.95733	.	.	ENSG00000134569	ENST00000378623	D	0.96427	-4.01	5.81	5.81	0.92471	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.97942	0.9323	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.97933	1.0321	10	0.54805	T	0.06	.	20.0734	0.97734	0.0:1.0:0.0:0.0	.	922	O75096	LRP4_HUMAN	T	922	ENSP00000367888:A922T	ENSP00000367888:A922T	A	-	1	0	LRP4	46859879	1.000000	0.71417	0.997000	0.53966	0.747000	0.42532	7.779000	0.85648	2.751000	0.94390	0.555000	0.69702	GCC		0.498	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46903303	C	T	46903303	3	4	61	1	0	0	0	0	1	0	0	0	8988	768	27	1	3029	1	LRP4	11	46903303	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142424	46903303	88103213	7322	15307										
ARFGAP2	84364	broad.mit.edu	37	chr11	47193020	47193020	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacctttctgcctgctctcGcttcttcccttccagattct	4	17	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47193020G>A	ENST00000524782.1	-	10	1126	c.898C>T	c.(898-900)Cga>Tga	p.R300*	ARFGAP2_ENST00000395449.3_5'UTR|ARFGAP2_ENST00000319543.6_Nonsense_Mutation_p.R31*|ARFGAP2_ENST00000426335.2_Nonsense_Mutation_p.R164*|RP11-390K5.6_ENST00000524412.1_RNA|ARFGAP2_ENST00000419701.2_Nonsense_Mutation_p.R193*	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	300	Required for interaction with coatomer.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R300*(1)		breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						GCCTGCTCTCGCTTCTTCCCT	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											276	263	267					11																	47193020		2201	4299	6500	47149596	SO:0001587	stop_gained	84364			AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"ADP-ribosylation factor GTPase activating proteins"	13504	protein-coding gene	gene with protein product		606908	"zinc finger protein 289, ID1 regulated"	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.898C>T	11.37:g.47193020G>A	ENSP00000434442:p.Arg300*		47149596	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Nonsense_Mutation	SNP	ENST00000524782.1	37	CCDS7926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.5|26.5	4.744011|4.744011	0.89663|0.89663	.|.	.|.	ENSG00000149182|ENSG00000149182	ENST00000527776|ENST00000426335;ENST00000524782;ENST00000319543;ENST00000419701;ENST00000527927;ENST00000525398	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|0.106715	.|0.64402	.|D	.|0.000006	T|.	0.53658|.	0.1810|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42085|.	-0.9472|.	3|.	.|0.07325	.|T	.|0.83	-0.5127|-0.5127	19.756|19.756	0.96291|0.96291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	30|164;300;31;193;164;314	.|.	.|ENSP00000327309:R31X	A|R	-|-	2|1	0|2	ARFGAP2|ARFGAP2	47149596|47149596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.633000|4.633000	0.61318|0.61318	2.665000|2.665000	0.90641|0.90641	0.655000|0.655000	0.94253|0.94253	GCG|CGA		0.552	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389		A	47193020	G	A	47193020	4	1	61	1	0	0	0	0	0	1	0	0	850	1095	38	1	695	1	ARFGAP2	11	47193020	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	289717	47193020	87813496	7323	15308										
DDB2	1643	broad.mit.edu	37	chr11	47259489	47259489	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaggacgatcgacgtgttCgatggaaactcagggaagat	14	6	1	2	rs185380045		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47259489C>T	ENST00000256996.4	+	8	1320	c.1125C>T	c.(1123-1125)ttC>ttT	p.F375F	DDB2_ENST00000378603.3_Silent_p.F311F|DDB2_ENST00000378600.3_Silent_p.F186F|DDB2_ENST00000378601.3_3'UTR|ACP2_ENST00000525230.1_5'Flank	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	375					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.F375F(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						TCGACGTGTTCGATGGAAACT	0.488			"Mis, N"			"skin basal cell, skin squamous cell, melanoma"		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	1	0.000199681	0	0.0014	5008	,	,		21341	0		0	False		,,,				2504	0					yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	1	Substitution - coding silent(1)	large_intestine(1)	11											119	108	111					11																	47259489		2201	4298	6499	47216065	SO:0001819	synonymous_variant	1643	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"WD repeat domain containing"	2718	protein-coding gene	gene with protein product	"xeroderma pigmentosum group E protein", "UV-damaged DNA-binding protein 2", "DDB p48 subunit"	600811	"damage-specific DNA binding protein 2 (48kD)"			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.1125C>T	11.37:g.47259489C>T			47216065	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Silent	SNP	ENST00000256996.4	37	CCDS7927.1																																																																																				0.488	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107		T	47259489	C	T	47259489	2	4	61	1	0	0	0	0	0	0	0	1	4330	883	31	1		1	DDB2	11	47259489	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66469	47259489	87747027	7324	15309										
MADD	8567	broad.mit.edu	37	chr11	47331142	47331142	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacttctgcacaacctcatCtcctacatgctgctgatgaa	5	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47331142C>A	ENST00000311027.5	+	28	4302	c.4137C>A	c.(4135-4137)atC>atA	p.I1379I	MADD_ENST00000342922.4_Silent_p.I1320I|MADD_ENST00000405573.2_Silent_p.I189I|MADD_ENST00000406482.1_Silent_p.I1277I|MADD_ENST00000402192.2_Silent_p.I1319I|MADD_ENST00000407859.3_Silent_p.I1297I|MADD_ENST00000395344.3_Silent_p.I1273I|MADD_ENST00000402799.1_Silent_p.I1277I|MADD_ENST00000349238.3_Silent_p.I1340I|MADD_ENST00000395336.3_Silent_p.I1379I	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.I1379I(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		ACAACCTCATCTCCTACATGC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	11											150	132	138					11																	47331142		2201	4298	6499	47287718	SO:0001819	synonymous_variant	8567			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4137C>A	11.37:g.47331142C>A			47287718		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																				0.507	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			A	47331142	C	A	47331142	2	1	61	1	0	0	0	0	0	0	0	1	9182	903	32	2		2	MADD	11	47331142	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71653	47331142	87675374	7325	15310										
MADD	8567	broad.mit.edu	37	chr11	47333316	47333316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatccgcaagaaggtgaggCgcctaatgggaaagtcgcac	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47333316C>T	ENST00000311027.5	+	29	4357	c.4192C>T	c.(4192-4194)Cgc>Tgc	p.R1398C	MADD_ENST00000342922.4_Missense_Mutation_p.R1339C|MADD_ENST00000405573.2_Missense_Mutation_p.R208C|MADD_ENST00000406482.1_Missense_Mutation_p.R1296C|MADD_ENST00000402192.2_Missense_Mutation_p.R1338C|MADD_ENST00000407859.3_Missense_Mutation_p.R1316C|MADD_ENST00000395344.3_Missense_Mutation_p.R1292C|MADD_ENST00000402799.1_Missense_Mutation_p.R1296C|MADD_ENST00000349238.3_Missense_Mutation_p.R1359C|MADD_ENST00000395336.3_Missense_Mutation_p.R1398C	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.R1398C(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAAGGTGAGGCGCCTAATGGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											109	98	102					11																	47333316		2201	4298	6499	47289892	SO:0001583	missense	8567			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4192C>T	11.37:g.47333316C>T	ENSP00000310933:p.Arg1398Cys		47289892		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.925140	0.92319	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192;ENST00000405573	T;T;T;T;T;T;T;T;T;T	0.61274	2.6;2.43;2.45;2.57;2.55;2.45;2.47;2.57;2.6;0.12	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.75635	0.3876	M	0.66297	2.02	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.983;0.983;0.999;0.993;0.993;0.993;0.999;0.999;0.998;0.999	T	0.78548	-0.2162	10	0.87932	D	0	-11.9969	18.6155	0.91302	0.0:1.0:0.0:0.0	.	208;1292;1292;1398;1296;1296;1296;1359;1316;1398;1339	F8W8U2;B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;.;MADD_HUMAN;.	C	1339;1296;1296;1296;1359;1398;1316;1292;1398;1338;208	ENSP00000343902:R1339C;ENSP00000385585:R1296C;ENSP00000384435:R1296C;ENSP00000304505:R1359C;ENSP00000310933:R1398C;ENSP00000384204:R1316C;ENSP00000378753:R1292C;ENSP00000378745:R1398C;ENSP00000384287:R1338C;ENSP00000384483:R208C	ENSP00000310933:R1398C	R	+	1	0	MADD	47289892	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.375000	0.79646	2.378000	0.81104	0.563000	0.77884	CGC		0.502	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			T	47333316	C	T	47333316	3	4	61	1	0	0	0	0	1	0	0	0	9182	768	27	1	4302	1	MADD	11	47333316	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2174	47333316	87673200	7326	15311										
AGBL2	79841	broad.mit.edu	37	chr11	47688556	47688556	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggtaaaaaactggaattCtctgagtttttgaaaaaggt	9	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47688556C>A	ENST00000525123.1	-	17	2685	c.2400G>T	c.(2398-2400)gaG>gaT	p.E800D	AGBL2_ENST00000528244.1_Missense_Mutation_p.E762D|AGBL2_ENST00000357610.3_Missense_Mutation_p.E802D|AGBL2_ENST00000298861.4_Missense_Mutation_p.E800D|AGBL2_ENST00000529712.1_5'Flank	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	800						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.E800D(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AACTGGAATTCTCTGAGTTTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	11											66	67	67					11																	47688556		2201	4298	6499	47645132	SO:0001583	missense	79841				CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.2400G>T	11.37:g.47688556C>A	ENSP00000435582:p.Glu800Asp		47645132	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060989	0.36373	.	.	ENSG00000165923	ENST00000528609;ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244	T;T;T;T	0.10960	2.86;2.86;2.86;2.82	5.3	2.43	0.29744	.	0.284037	0.25270	N	0.031895	T	0.10981	0.0268	L	0.60455	1.87	0.22354	N	0.999178	P;P	0.46395	0.731;0.877	B;B	0.40901	0.343;0.257	T	0.14699	-1.0463	10	0.41790	T	0.15	-18.0701	7.5365	0.27712	0.0:0.7304:0.0:0.2696	.	762;800	F6U0I4;Q5U5Z8	.;CBPC2_HUMAN	D	183;800;802;800;762	ENSP00000435582:E800D;ENSP00000350228:E802D;ENSP00000298861:E800D;ENSP00000436630:E762D	ENSP00000298861:E800D	E	-	3	2	AGBL2	47645132	0.808000	0.29022	0.074000	0.20217	0.242000	0.25591	1.311000	0.33562	0.328000	0.23435	-0.218000	0.12543	GAG		0.343	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		A	47688556	C	A	47688556	3	1	61	1	0	0	0	0	1	0	0	0	376	912	32	2	320	2	AGBL2	11	47688556	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	355240	47688556	87317960	7327	15312										
AGBL2	79841	broad.mit.edu	37	chr11	47698868	47698868	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcactccaacttccttctAaatctacatcttgtccaagt	3	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47698868A>C	ENST00000525123.1	-	14	2387	c.2102T>G	c.(2101-2103)tTa>tGa	p.L701*	AGBL2_ENST00000528244.1_Nonsense_Mutation_p.L663*|AGBL2_ENST00000357610.3_Nonsense_Mutation_p.L701*|AGBL2_ENST00000298861.4_Nonsense_Mutation_p.L701*|AGBL2_ENST00000529712.1_Intron	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	701						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.L701*(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						ACTTCCTTCTAAATCTACATC	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											90	83	85					11																	47698868		2201	4298	6499	47655444	SO:0001587	stop_gained	79841				CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.2102T>G	11.37:g.47698868A>C	ENSP00000435582:p.Leu701*		47655444	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Nonsense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	.	.	.	.	.	.	.	.	.	.	A	38	6.887491	0.97912	.	.	ENSG00000165923	ENST00000528609;ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244	.	.	.	6.03	6.03	0.97812	.	0.509299	0.20538	N	0.090374	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-12.5547	7.5872	0.27999	0.8488:0.0:0.1512:0.0	.	.	.	.	X	84;701;701;701;663	.	ENSP00000298861:L701X	L	-	2	0	AGBL2	47655444	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	2.316000	0.43761	2.313000	0.78055	0.454000	0.30748	TTA		0.348	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		C	47698868	A	C	47698868	4	2	61	1	0	0	0	0	0	1	0	0	376	372	13	4	630	4	AGBL2	11	47698868	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10312	47698868	87307648	7328	15313										
AGBL2	79841	broad.mit.edu	37	chr11	47701597	47701597	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaaggacttcagatcttcGatggtaaagtgggtgtctct	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47701597G>A	ENST00000525123.1	-	13	2229	c.1944C>T	c.(1942-1944)atC>atT	p.I648I	AGBL2_ENST00000528244.1_Silent_p.I610I|AGBL2_ENST00000357610.3_Silent_p.I648I|AGBL2_ENST00000298861.4_Silent_p.I648I|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	648						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.I648I(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						TCAGATCTTCGATGGTAAAGT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	11											93	87	89					11																	47701597		2201	4298	6499	47658173	SO:0001819	synonymous_variant	79841				CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1944C>T	11.37:g.47701597G>A			47658173	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Silent	SNP	ENST00000525123.1	37	CCDS7944.1																																																																																				0.353	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		A	47701597	G	A	47701597	2	1	61	1	0	0	0	0	0	0	0	1	376	1048	37	1		1	AGBL2	11	47701597	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2729	47701597	87304919	7329	15314										
AGBL2	79841	broad.mit.edu	37	chr11	47707499	47707499	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagactcgttcatgaagccaGtatttgcgattgttgttatt	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:47707499G>A	ENST00000525123.1	-	11	2019	c.1734C>T	c.(1732-1734)taC>taT	p.Y578Y	AGBL2_ENST00000528244.1_Silent_p.Y540Y|AGBL2_ENST00000357610.3_Silent_p.Y578Y|AGBL2_ENST00000298861.4_Silent_p.Y578Y|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	578						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.Y578Y(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						CATGAAGCCAGTATTTGCGAT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	11											228	209	215					11																	47707499		2201	4298	6499	47664075	SO:0001819	synonymous_variant	79841				CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1734C>T	11.37:g.47707499G>A			47664075	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Silent	SNP	ENST00000525123.1	37	CCDS7944.1																																																																																				0.373	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		A	47707499	G	A	47707499	2	1	61	1	0	0	0	0	0	0	0	1	376	1024	36	3		3	AGBL2	11	47707499	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5902	47707499	87299017	7330	15315										
PTPRJ	5795	broad.mit.edu	37	chr11	48161171	48161171	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggagcctggaacaatgcGacccacctggagagctgctc	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48161171G>A	ENST00000418331.2	+	11	2638	c.2286G>A	c.(2284-2286)gcG>gcA	p.A762A		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	762	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.A762A(1)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GGAACAATGCGACCCACCTGG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	11											91	85	87					11																	48161171		2201	4298	6499	48117747	SO:0001819	synonymous_variant	5795			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.2286G>A	11.37:g.48161171G>A			48117747	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																				0.537	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48161171	G	A	48161171	2	1	61	1	0	0	0	0	0	0	0	1	12841	1045	37	1		1	PTPRJ	11	48161171	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	453672	48161171	86845345	7331	15316										
PTPRJ	5795	broad.mit.edu	37	chr11	48171733	48171733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggttcgcagaggaatacGaagtatgttgctgtaaatac	13	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48171733G>A	ENST00000418331.2	+	18	3488	c.3136G>A	c.(3136-3138)Gaa>Aaa	p.E1046K		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	1046	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.E1046K(1)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						AGAGGAATACGAAGTATGTTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											112	117	115					11																	48171733		2201	4298	6499	48128309	SO:0001583	missense	5795			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.3136G>A	11.37:g.48171733G>A	ENSP00000400010:p.Glu1046Lys		48128309	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	G	36	5.606047	0.96626	.	.	ENSG00000149177	ENST00000418331	T	0.13778	2.56	5.5	5.5	0.81552	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	.	.	.	.	T	0.31263	0.0791	L	0.43598	1.365	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.01056	-1.1466	9	0.87932	D	0	.	16.8782	0.86057	0.0:0.0:1.0:0.0	.	1046	Q12913	PTPRJ_HUMAN	K	1046	ENSP00000400010:E1046K	ENSP00000400010:E1046K	E	+	1	0	PTPRJ	48128309	1.000000	0.71417	0.225000	0.23894	0.292000	0.27327	9.201000	0.95017	2.575000	0.86900	0.561000	0.74099	GAA		0.443	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48171733	G	A	48171733	3	1	61	1	0	0	0	0	1	0	0	0	12841	1059	37	1	3215	1	PTPRJ	11	48171733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10562	48171733	86834783	7332	15317										
OR4B1	119765	broad.mit.edu	37	chr11	48238765	48238765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattatatgaacattatcaGtcgtcaactgtgtcaccttc	5	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48238765G>A	ENST00000309562.2	+	1	422	c.404G>A	c.(403-405)aGt>aAt	p.S135N		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S135N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						AACATTATCAGTCGTCAACTG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											109	104	106					11																	48238765		2201	4298	6499	48195341	SO:0001583	missense	119765			AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"GPCR / Class A : Olfactory receptors"	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.404G>A	11.37:g.48238765G>A	ENSP00000311605:p.Ser135Asn		48195341	Q6IF75|Q96R64	Missense_Mutation	SNP	ENST00000309562.2	37	CCDS31485.1	.	.	.	.	.	.	.	.	.	.	G	0.151	-1.090979	0.01858	.	.	ENSG00000175619	ENST00000309562	T	0.38887	1.11	5.38	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	0.199636	0.35585	N	0.003115	T	0.14830	0.0358	N	0.04636	-0.2	0.19775	N	0.999957	B	0.06786	0.001	B	0.15870	0.014	T	0.33240	-0.9876	10	0.02654	T	1	.	7.469	0.27338	0.4763:0.0:0.5237:0.0	.	135	Q8NGF8	OR4B1_HUMAN	N	135	ENSP00000311605:S135N	ENSP00000311605:S135N	S	+	2	0	OR4B1	48195341	0.000000	0.05858	0.329000	0.25429	0.871000	0.50021	-0.847000	0.04331	0.167000	0.19631	0.494000	0.49563	AGT		0.463	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470		A	48238765	G	A	48238765	3	1	61	1	0	0	0	0	1	0	0	0	11075	1029	36	3	406	3	OR4B1	11	48238765	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67032	48238765	86767751	7333	15318										
OR4X2	119764	broad.mit.edu	37	chr11	48266818	48266818	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcccccatgtacttcttcCtcagctacctctccttcatg	4	17	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48266818C>A	ENST00000302329.3	+	1	211	c.163C>A	c.(163-165)Ctc>Atc	p.L55I		NM_001004727.1	NP_001004727.1	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X, member 2	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L55I(1)		breast(1)|large_intestine(4)|lung(12)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	20						GTACTTCTTCCTCAGCTACCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											186	172	177					11																	48266818		2201	4298	6499	48223394	SO:0001583	missense	119764			AB065847	CCDS31486.1	11p11.2	2012-08-09			ENSG00000172208	ENSG00000172208		"GPCR / Class A : Olfactory receptors"	15184	protein-coding gene	gene with protein product							Standard	NM_001004727		Approved		uc001ngs.1	Q8NGF9	OTTHUMG00000165302	ENST00000302329.3:c.163C>A	11.37:g.48266818C>A	ENSP00000307751:p.Leu55Ile		48223394	B2RNK3|Q6IF73|Q96R63	Missense_Mutation	SNP	ENST00000302329.3	37	CCDS31486.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827866	0.71143	.	.	ENSG00000172208	ENST00000302329	T	0.13778	2.56	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000195	T	0.41419	0.1158	M	0.81179	2.53	0.30506	N	0.769889	D	0.89917	1.0	D	0.83275	0.996	T	0.46400	-0.9194	10	0.87932	D	0	.	16.612	0.84885	0.0:1.0:0.0:0.0	.	55	Q8NGF9	OR4X2_HUMAN	I	55	ENSP00000307751:L55I	ENSP00000307751:L55I	L	+	1	0	OR4X2	48223394	0.257000	0.24022	0.998000	0.56505	0.931000	0.56810	0.048000	0.14078	2.496000	0.84212	0.650000	0.86243	CTC		0.493	OR4X2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383376.2	NM_001004727		A	48266818	C	A	48266818	3	1	61	1	0	0	0	0	1	0	0	0	11116	681	24	2	165	2	OR4X2	11	48266818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28053	48266818	86739698	7334	15319										
OR4C3	256144	broad.mit.edu	37	chr11	48347317	48347317	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattgttgttgccttgttCtttgtgccctgtatatttac	7	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48347317C>A	ENST00000319856.4	+	1	846	c.825C>A	c.(823-825)ttC>ttA	p.F275L		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F275L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TTGCCTTGTTCTTTGTGCCCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											286	258	268					11																	48347317		2201	4298	6499	48303893	SO:0001583	missense	256144			AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"GPCR / Class A : Olfactory receptors"	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.825C>A	11.37:g.48347317C>A	ENSP00000321419:p.Phe275Leu		48303893	B2RNF2|Q6IFB3	Missense_Mutation	SNP	ENST00000319856.4	37	CCDS31489.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.968411	0.34754	.	.	ENSG00000176547	ENST00000319856;ENST00000395239	T	0.00285	8.3	5.97	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000041	T	0.00328	0.0010	M	0.75615	2.305	0.31598	N	0.653069	B	0.25206	0.12	B	0.34873	0.191	T	0.04840	-1.0923	10	0.72032	D	0.01	.	9.6035	0.39619	0.0:0.8424:0.0:0.1576	.	248	Q8NH37	OR4C3_HUMAN	L	275;138	ENSP00000321419:F275L	ENSP00000321419:F275L	F	+	3	2	OR4C3	48303893	0.002000	0.14202	1.000000	0.80357	0.388000	0.30384	-0.210000	0.09345	2.838000	0.97847	0.561000	0.74099	TTC		0.418	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		A	48347317	C	A	48347317	3	1	61	1	0	0	0	0	1	0	0	0	11081	912	32	2	827	2	OR4C3	11	48347317	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80499	48347317	86659199	7335	15320										
OR4A47	403253	broad.mit.edu	37	chr11	48510852	48510852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcccattctgtggccccAatgtcattgatcattttttc	7	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:48510852A>T	ENST00000446524.1	+	1	584	c.508A>T	c.(508-510)Aat>Tat	p.N170Y		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N170Y(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						CTGTGGCCCCAATGTCATTGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											149	142	144					11																	48510852		2201	4295	6496	48467428	SO:0001583	missense	403253			BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"GPCR / Class A : Olfactory receptors"	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.508A>T	11.37:g.48510852A>T	ENSP00000412752:p.Asn170Tyr		48467428		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	9.908	1.208681	0.22205	.	.	ENSG00000237388	ENST00000446524	T	0.00262	8.4	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000019	T	0.00666	0.0022	M	0.92923	3.36	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.29305	-1.0016	10	0.72032	D	0.01	.	7.231	0.26043	0.8995:0.0:0.1005:0.0	.	170	Q6IF82	O4A47_HUMAN	Y	170	ENSP00000412752:N170Y	ENSP00000412752:N170Y	N	+	1	0	OR4A47	48467428	0.087000	0.21565	0.470000	0.27216	0.058000	0.15608	2.786000	0.47790	1.799000	0.52666	0.418000	0.28097	AAT		0.463	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		T	48510852	A	T	48510852	3	4	61	1	0	0	0	0	1	0	0	0	11073	130	5	5	510	5	OR4A47	11	48510852	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	163535	48510852	86495664	7336	15321										
OR4C13	283092	broad.mit.edu	37	chr11	49974602	49974602	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatatgcctgttaaactgtCtcttgctcctggtctcctgc	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:49974602C>A	ENST00000555099.1	+	1	660	c.628C>A	c.(628-630)Ctc>Atc	p.L210I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L210I(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						GTTAAACTGTCTCTTGCTCCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											202	165	177					11																	49974602		2201	4296	6497	49931178	SO:0001583	missense	283092			AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.628C>A	11.37:g.49974602C>A	ENSP00000452277:p.Leu210Ile		49931178	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	0.164	-1.078144	0.01903	.	.	ENSG00000258817	ENST00000555099	T	0.38401	1.14	2.7	1.74	0.24563	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	D	0.000759	T	0.25082	0.0609	L	0.41573	1.285	0.09310	N	1	B	0.13145	0.007	B	0.21151	0.033	T	0.16988	-1.0384	9	.	.	.	.	7.2289	0.26030	0.4779:0.5221:0.0:0.0	.	210	Q8NGP0	OR4CD_HUMAN	I	210	ENSP00000452277:L210I	.	L	+	1	0	OR4C13	49931178	0.000000	0.05858	0.573000	0.28510	0.136000	0.21042	-1.409000	0.02483	0.445000	0.26639	0.186000	0.17326	CTC		0.493	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		A	49974602	C	A	49974602	3	1	61	1	0	0	0	0	1	0	0	0	11078	913	32	2	630	2	OR4C13	11	49974602	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1463750	49974602	85031914	7337	15322										
OR4C12	283093	broad.mit.edu	37	chr11	50003563	50003563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagccatactgtaaagaGaatctgaatagttgcatgaa	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:50003563G>T	ENST00000335238.4	-	1	508	c.475C>A	c.(475-477)Ctc>Atc	p.L159I		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L159I(1)		NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						ACTGTAAAGAGAATCTGAATA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											131	135	134					11																	50003563		2201	4296	6497	49960139	SO:0001583	missense	283093			BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"GPCR / Class A : Olfactory receptors"	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.475C>A	11.37:g.50003563G>T	ENSP00000334418:p.Leu159Ile		49960139	B2RNF0|Q6IF49	Missense_Mutation	SNP	ENST00000335238.4	37	CCDS31496.1	.	.	.	.	.	.	.	.	.	.	.	12.25	1.883045	0.33255	.	.	ENSG00000221954	ENST00000335238	T	0.38722	1.12	2.98	2.98	0.34508	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37761	U	0.001941	T	0.34366	0.0895	N	0.21097	0.63	0.23454	N	0.997645	P	0.40000	0.698	P	0.48524	0.58	T	0.09378	-1.0677	10	0.31617	T	0.26	.	8.2721	0.31851	0.0:0.2467:0.7533:0.0	.	159	Q96R67	OR4CC_HUMAN	I	159	ENSP00000334418:L159I	ENSP00000334418:L159I	L	-	1	0	OR4C12	49960139	0.000000	0.05858	0.856000	0.33681	0.722000	0.41435	-0.345000	0.07770	1.698000	0.51180	0.398000	0.26397	CTC		0.468	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1	NM_001005270		T	50003563	G	T	50003563	3	4	61	1	0	0	0	0	1	0	0	0	11077	942	33	2	458	2	OR4C12	11	50003563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28961	50003563	85002953	7338	15323										
OR4A5	81318	broad.mit.edu	37	chr11	51412360	51412360	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcctgagaaaagcccagGaggacaaattctgtaatatt	10	7	1	1	rs141556662		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:51412360G>A	ENST00000319760.6	-	1	88	c.36C>T	c.(34-36)ctC>ctT	p.L12L		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	12						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L12L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AAAAGCCCAGGAGGACAAATT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	11						G		5,4393		0,5,2194	32	30	31		36	0	0.2	11	dbSNP_134	31	0,8588		0,0,4294	no	coding-synonymous	OR4A5	NM_001005272.3		0,5,6488	AA,AG,GG		0.0,0.1137,0.0385		12/316	51412360	5,12981	2199	4294	6493	51268936	SO:0001819	synonymous_variant	81318			AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.36C>T	11.37:g.51412360G>A			51268936	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																				0.428	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51412360	G	A	51412360	2	1	61	1	0	0	0	0	0	0	0	1	11074	1161	41	3		3	OR4A5	11	51412360	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1408797	51412360	83594156	7339	15324										
OR4C15	81309	broad.mit.edu	37	chr11	55322127	55322127	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtctcctatgtacttcttCttgggcttcctgtccttcct	7	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55322127C>A	ENST00000314644.2	+	1	345	c.345C>A	c.(343-345)ttC>ttA	p.F115L		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F115L(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						TGTACTTCTTCTTGGGCTTCC	0.443										HNSCC(20;0.049)																																						1	Substitution - Missense(1)	large_intestine(1)	11											181	144	156					11																	55322127		2201	4296	6497	55078703	SO:0001583	missense	81309			BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.345C>A	11.37:g.55322127C>A	ENSP00000324958:p.Phe115Leu		55078703	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712413	0.48517	.	.	ENSG00000181939	ENST00000314644	T	0.13778	2.56	5.08	0.318	0.15867	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.33702	0.0872	M	0.76838	2.35	0.19775	N	0.999952	D	0.89917	1.0	D	0.87578	0.998	T	0.07947	-1.0746	9	0.72032	D	0.01	.	8.2242	0.31560	0.0:0.4542:0.0:0.5458	.	61	Q8NGM1	OR4CF_HUMAN	L	115	ENSP00000324958:F115L	ENSP00000324958:F115L	F	+	3	2	OR4C15	55078703	0.794000	0.28838	0.140000	0.22221	0.605000	0.37080	0.352000	0.20113	0.010000	0.14839	0.379000	0.24179	TTC		0.443	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		A	55322127	C	A	55322127	3	1	61	1	0	0	0	0	1	0	0	0	11079	912	32	2	347	2	OR4C15	11	55322127	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3909767	55322127	79684389	7340	15325										
OR4C15	81309	broad.mit.edu	37	chr11	55322732	55322732	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatacacgacctccatctgCtttttcccttgacaaaatgg	5	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55322732C>A	ENST00000314644.2	+	1	950	c.950C>A	c.(949-951)gCt>gAt	p.A317D		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A317D(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						CCTCCATCTGCTTTTTCCCTT	0.408										HNSCC(20;0.049)																																						1	Substitution - Missense(1)	large_intestine(1)	11											215	213	214					11																	55322732		2201	4296	6497	55079308	SO:0001583	missense	81309			BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.950C>A	11.37:g.55322732C>A	ENSP00000324958:p.Ala317Asp		55079308	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.281019	0.40394	.	.	ENSG00000181939	ENST00000314644	T	0.37584	1.19	4.92	4.92	0.64577	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.38639	0.1048	N	0.16166	0.38	0.09310	N	1	P	0.49783	0.928	P	0.55260	0.772	T	0.34502	-0.9826	9	0.72032	D	0.01	.	15.6476	0.77068	0.0:1.0:0.0:0.0	.	263	Q8NGM1	OR4CF_HUMAN	D	317	ENSP00000324958:A317D	ENSP00000324958:A317D	A	+	2	0	OR4C15	55079308	0.000000	0.05858	0.166000	0.22797	0.224000	0.24922	-0.298000	0.08265	2.561000	0.86390	0.385000	0.25706	GCT		0.408	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		A	55322732	C	A	55322732	3	1	61	1	0	0	0	0	1	0	0	0	11079	797	28	2	952	2	OR4C15	11	55322732	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	605	55322732	79683784	7341	15326										
OR4C15	81309	broad.mit.edu	37	chr11	55322892	55322892	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaagaaaatattaaactTtaaaaaatccaaagttaaga	5	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55322892T>G	ENST00000314644.2	+	1	1110	c.1110T>G	c.(1108-1110)ctT>ctG	p.L370L		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L370L(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						ATATTAAACTTTAAAAAATCC	0.308										HNSCC(20;0.049)																																						1	Substitution - coding silent(1)	large_intestine(1)	11											19	19	19					11																	55322892		2151	4261	6412	55079468	SO:0001819	synonymous_variant	81309			BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.1110T>G	11.37:g.55322892T>G			55079468	Q6IFE2	Silent	SNP	ENST00000314644.2	37	CCDS31501.1																																																																																				0.308	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		G	55322892	T	G	55322892	2	3	61	1	0	0	0	0	0	0	0	1	11079	1855	64	4		4	OR4C15	11	55322892	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160	55322892	79683624	7342	15327										
OR4C6	219432	broad.mit.edu	37	chr11	55433491	55433491	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacccatgttaaatcccttGatctatacactgaggaatgc	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55433491G>T	ENST00000314259.3	+	1	878	c.849G>T	c.(847-849)ttG>ttT	p.L283F		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L283F(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TAAATCCCTTGATCTATACAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	86	87					11																	55433491		2200	4296	6496	55190067	SO:0001583	missense	219432			CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"GPCR / Class A : Olfactory receptors"	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.849G>T	11.37:g.55433491G>T	ENSP00000324769:p.Leu283Phe		55190067	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	CCDS31506.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.613156	0.28712	.	.	ENSG00000181903	ENST00000314259	T	0.38887	1.11	4.0	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31199	N	0.008063	T	0.35711	0.0941	L	0.60455	1.87	0.24623	N	0.993662	B	0.21309	0.054	B	0.27170	0.077	T	0.33777	-0.9855	10	0.54805	T	0.06	.	4.9123	0.13829	0.1964:0.3374:0.4662:0.0	.	283	Q8NH72	OR4C6_HUMAN	F	283	ENSP00000324769:L283F	ENSP00000324769:L283F	L	+	3	2	OR4C6	55190067	0.000000	0.05858	0.971000	0.41717	0.810000	0.45777	-3.820000	0.00358	0.190000	0.20209	0.530000	0.56133	TTG		0.458	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		T	55433491	G	T	55433491	3	4	61	1	0	0	0	0	1	0	0	0	11083	1281	45	2	851	2	OR4C6	11	55433491	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110599	55433491	79573025	7343	15328										
OR5D13	390142	broad.mit.edu	37	chr11	55541691	55541691	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatggaactatccttttcCtttactgtgttcctaatcct	4	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55541691C>A	ENST00000361760.1	+	1	778	c.778C>A	c.(778-780)Ctt>Att	p.L260I		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L260I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				TATCCTTTTCCTTTACTGTGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											123	100	108					11																	55541691		2200	4296	6496	55298267	SO:0001583	missense	390142			BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.778C>A	11.37:g.55541691C>A	ENSP00000354800:p.Leu260Ile		55298267	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	37	CCDS31507.1	.	.	.	.	.	.	.	.	.	.	C	4.462	0.085504	0.08583	.	.	ENSG00000198877	ENST00000361760	T	0.00115	8.71	3.82	1.59	0.23543	GPCR, rhodopsin-like superfamily (1);	0.285343	0.18785	N	0.131239	T	0.00210	0.0006	L	0.33137	0.985	0.09310	N	1	P	0.40681	0.727	P	0.57324	0.818	T	0.44452	-0.9327	10	0.45353	T	0.12	-11.7571	6.4132	0.21702	0.4932:0.3554:0.1514:0.0	.	260	Q8NGL4	OR5DD_HUMAN	I	260	ENSP00000354800:L260I	ENSP00000354800:L260I	L	+	1	0	OR5D13	55298267	0.000000	0.05858	0.009000	0.14445	0.219000	0.24729	-0.316000	0.08071	0.677000	0.31305	0.486000	0.48141	CTT		0.453	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		A	55541691	C	A	55541691	3	1	61	1	0	0	0	0	1	0	0	0	11185	681	24	2	780	2	OR5D13	11	55541691	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108200	55541691	79464825	7344	15329										
OR5L1	219437	broad.mit.edu	37	chr11	55579153	55579153	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacttgtcctctgtagatTtctgctactcctcaataatt	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55579153T>G	ENST00000333973.2	+	1	300	c.211T>G	c.(211-213)Ttc>Gtc	p.F71V		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F71V(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CTCTGTAGATTTCTGCTACTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											249	227	235					11																	55579153		2200	4296	6496	55335729	SO:0001583	missense	219437			AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.211T>G	11.37:g.55579153T>G	ENSP00000335529:p.Phe71Val		55335729	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	t	6.564	0.472408	0.12461	.	.	ENSG00000186117	ENST00000333973	T	0.02606	4.23	4.32	1.79	0.24919	GPCR, rhodopsin-like superfamily (1);	0.123623	0.37261	N	0.002172	T	0.02193	0.0068	N	0.26130	0.795	0.09310	N	0.999999	B	0.26975	0.165	B	0.29176	0.099	T	0.45249	-0.9274	10	0.33940	T	0.23	-44.2963	5.3665	0.16117	0.0:0.1074:0.377:0.5156	.	71	Q8NGL2	OR5L1_HUMAN	V	71	ENSP00000335529:F71V	ENSP00000335529:F71V	F	+	1	0	OR5L1	55335729	0.000000	0.05858	0.191000	0.23289	0.235000	0.25334	-2.460000	0.00999	0.546000	0.28920	0.358000	0.22013	TTC		0.458	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		G	55579153	T	G	55579153	3	3	61	1	0	0	0	0	1	0	0	0	11201	1841	64	4	213	4	OR5L1	11	55579153	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37462	55579153	79427363	7345	15330										
OR5L1	219437	broad.mit.edu	37	chr11	55579581	55579581	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagtgttaccatcatgatCatcctcacctcctacctgct	6	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55579581C>T	ENST00000333973.2	+	1	728	c.639C>T	c.(637-639)atC>atT	p.I213I		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I213I(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CCATCATGATCATCCTCACCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	11											243	194	211					11																	55579581		2200	4296	6496	55336157	SO:0001819	synonymous_variant	219437			AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.639C>T	11.37:g.55579581C>T			55336157	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																				0.502	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579581	C	T	55579581	2	4	61	1	0	0	0	0	0	0	0	1	11201	816	29	3		3	OR5L1	11	55579581	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	428	55579581	79426935	7346	15331										
OR5L1	219437	broad.mit.edu	37	chr11	55579726	55579726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttccatttattgcaggCccagttcaggcaatagtgga	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55579726C>T	ENST00000333973.2	+	1	873	c.784C>T	c.(784-786)Ccc>Tcc	p.P262S		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	262						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P262S(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TTATTGCAGGCCCAGTTCAGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											112	96	101					11																	55579726		2200	4296	6496	55336302	SO:0001583	missense	219437			AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.784C>T	11.37:g.55579726C>T	ENSP00000335529:p.Pro262Ser		55336302	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	c	13.72	2.321834	0.41096	.	.	ENSG00000186117	ENST00000333973	T	0.00262	8.4	4.12	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.124690	0.37012	N	0.002285	T	0.00241	0.0007	L	0.50333	1.59	0.23602	N	0.997313	B	0.28082	0.2	B	0.37780	0.258	T	0.23332	-1.0191	10	0.72032	D	0.01	-31.8335	11.0165	0.47691	0.0:0.9045:0.0:0.0955	.	262	Q8NGL2	OR5L1_HUMAN	S	262	ENSP00000335529:P262S	ENSP00000335529:P262S	P	+	1	0	OR5L1	55336302	0.007000	0.16637	0.008000	0.14137	0.108000	0.19459	2.322000	0.43814	0.714000	0.32081	0.428000	0.28381	CCC		0.507	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579726	C	T	55579726	3	4	61	1	0	0	0	0	1	0	0	0	11201	739	26	3	786	3	OR5L1	11	55579726	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145	55579726	79426790	7347	15332										
OR5D18	219438	broad.mit.edu	37	chr11	55587651	55587651	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcacttcttctgtgagttCtcctcactactctccctttc	3	15	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55587651C>A	ENST00000333976.4	+	1	566	c.546C>A	c.(544-546)ttC>ttA	p.F182L		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F182L(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TCTGTGAGTTCTCCTCACTAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											222	201	208					11																	55587651		2200	4296	6496	55344227	SO:0001583	missense	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.546C>A	11.37:g.55587651C>A	ENSP00000335025:p.Phe182Leu		55344227	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.389435	0.00200	.	.	ENSG00000186119	ENST00000333976	T	0.35605	1.3	4.85	1.82	0.25136	GPCR, rhodopsin-like superfamily (1);	0.371554	0.20025	N	0.100833	T	0.08358	0.0208	N	0.01128	-1	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.30504	-0.9976	10	0.06625	T	0.88	-17.1055	2.0126	0.03491	0.1722:0.4769:0.1692:0.1816	.	182	Q8NGL1	OR5DI_HUMAN	L	182	ENSP00000335025:F182L	ENSP00000335025:F182L	F	+	3	2	OR5D18	55344227	0.000000	0.05858	0.644000	0.29465	0.082000	0.17680	-2.938000	0.00684	0.585000	0.29608	-1.932000	0.00510	TTC		0.428	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		A	55587651	C	A	55587651	3	1	61	1	0	0	0	0	1	0	0	0	11188	912	32	2	548	2	OR5D18	11	55587651	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7925	55587651	79418865	7348	15333										
OR5L2	26338	broad.mit.edu	37	chr11	55595161	55595161	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgtgggacggtgtgttCtctgattcactcgtccttag	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55595161C>A	ENST00000378397.1	+	1	467	c.467C>A	c.(466-468)tCt>tAt	p.S156Y		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S156Y(1)		breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				ACGGTGTGTTCTCTGATTCAC	0.488										HNSCC(27;0.073)																																						1	Substitution - Missense(1)	large_intestine(1)	11											220	189	200					11																	55595161		2200	4296	6496	55351737	SO:0001583	missense	26338			AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"GPCR / Class A : Olfactory receptors"	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.467C>A	11.37:g.55595161C>A	ENSP00000367650:p.Ser156Tyr		55351737	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	12.71	2.020326	0.35606	.	.	ENSG00000205030	ENST00000378397	T	0.45668	0.89	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000080	T	0.67505	0.2900	M	0.88377	2.95	0.21579	N	0.99964	D	0.89917	1.0	D	0.80764	0.994	T	0.64179	-0.6468	10	0.87932	D	0	-36.82	11.3343	0.49494	0.0:0.9155:0.0:0.0845	.	156	Q8NGL0	OR5L2_HUMAN	Y	156	ENSP00000367650:S156Y	ENSP00000367650:S156Y	S	+	2	0	OR5L2	55351737	0.003000	0.15002	0.925000	0.36789	0.057000	0.15508	1.637000	0.37155	2.613000	0.88420	0.626000	0.83405	TCT		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		A	55595161	C	A	55595161	3	1	61	1	0	0	0	0	1	0	0	0	11202	913	32	2	469	2	OR5L2	11	55595161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7510	55595161	79411355	7349	15334										
SPRYD5	84767	broad.mit.edu	37	chr11	55658984	55658984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccagcacagtaggattatTcctggattgtgaaggtagaa	11	6	0	2	rs138269041		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55658984T>C	ENST00000449290.2	+	7	1327	c.1235T>C	c.(1234-1236)tTc>tCc	p.F412S	TRIM51_ENST00000244891.3_Missense_Mutation_p.F269S	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	412	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.F253S(1)|p.F412S(1)									GTAGGATTATTCCTGGATTGT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	11											74	70	71					11																	55658984		2174	4221	6395	55415560	SO:0001583	missense	84767			BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.1235T>C	11.37:g.55658984T>C	ENSP00000395086:p.Phe412Ser		55415560	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		.	.	.	.	.	.	.	.	.	.	.	14.79	2.640770	0.47153	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.65178	-0.14;-0.14	1.36	1.36	0.22044	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.80507	0.4636	M	0.93808	3.46	0.26691	N	0.971346	D	0.89917	1.0	D	0.91635	0.999	T	0.66874	-0.5813	9	0.87932	D	0	.	5.1325	0.14917	0.0:0.0:0.0:1.0	.	412	Q9BSJ1	SPRY5_HUMAN	S	412;269	ENSP00000395086:F412S;ENSP00000244891:F269S	ENSP00000244891:F269S	F	+	2	0	SPRYD5	55415560	0.990000	0.36364	0.015000	0.15790	0.171000	0.22731	-0.102000	0.10956	0.540000	0.28808	0.136000	0.15936	TTC		0.473	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		C	55658984	T	C	55658984	3	2	61	1	0	0	0	0	1	0	0	0	15150	1783	62	4	1257	4	SPRYD5	11	55658984	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	63823	55658984	79347532	7350	15335										
OR5W2	390148	broad.mit.edu	37	chr11	55681565	55681565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacccacagaagcataggCggaaggccagtgtcatatgt	12	9	1	2	rs148084259		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55681565C>T	ENST00000344514.1	-	1	493	c.494G>A	c.(493-495)cGc>cAc	p.R165H		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R165H(4)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GAAGCATAGGCGGAAGGCCAG	0.428																																					Melanoma(48;171 1190 15239 43886 49348)											4	Substitution - Missense(4)	cervix(1)|large_intestine(1)|stomach(1)|kidney(1)	11						C	HIS/ARG	2,4400	4.2+/-10.8	0,2,2199	87	77	80		494	1.5	0	11	dbSNP_134	80	0,8592		0,0,4296	yes	missense	OR5W2	NM_001001960.1	29	0,2,6495	TT,TC,CC		0.0,0.0454,0.0154	benign	165/311	55681565	2,12992	2201	4296	6497	55438141	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.494G>A	11.37:g.55681565C>T	ENSP00000342448:p.Arg165His		55438141		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	3.073	-0.190656	0.06299	4.54E-4	0.0	ENSG00000187612	ENST00000344514	T	0.00169	8.63	4.77	1.52	0.23074	GPCR, rhodopsin-like superfamily (1);	0.602095	0.13398	N	0.390838	T	0.00144	0.0004	L	0.35341	1.055	0.09310	N	1	B	0.13145	0.007	B	0.15870	0.014	T	0.18085	-1.0348	10	0.41790	T	0.15	.	5.688	0.17813	0.0:0.5609:0.1582:0.2809	.	165	Q8NH69	OR5W2_HUMAN	H	165	ENSP00000342448:R165H	ENSP00000342448:R165H	R	-	2	0	OR5W2	55438141	0.000000	0.05858	0.019000	0.16419	0.048000	0.14542	-3.276000	0.00530	0.435000	0.26365	0.549000	0.68633	CGC		0.428	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		T	55681565	C	T	55681565	3	4	61	1	0	0	0	0	1	0	0	0	11216	768	27	1	440	1	OR5W2	11	55681565	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22581	55681565	79324951	7351	15336										
OR5I1	10798	broad.mit.edu	37	chr11	55703223	55703223	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagaatgaaaaagtaggaGatgatgatgatgataaaaca	11	1	0	8			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55703223G>T	ENST00000301532.3	-	1	653	c.654C>A	c.(652-654)atC>atA	p.I218I		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	218					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I218I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AAAAGTAGGAGATGATGATGA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	11											46	49	48					11																	55703223		2200	4295	6495	55459799	SO:0001819	synonymous_variant	10798			BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"GPCR / Class A : Olfactory receptors"	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.654C>A	11.37:g.55703223G>T			55459799	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																				0.438	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		T	55703223	G	T	55703223	2	4	61	1	0	0	0	0	0	0	0	1	11195	932	33	2		2	OR5I1	11	55703223	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21658	55703223	79303293	7352	15337										
OR5F1	338674	broad.mit.edu	37	chr11	55761584	55761584	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagaagaagtgatggatgAcattggagtcacagaatgac	12	6	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55761584A>G	ENST00000278409.1	-	1	517	c.518T>C	c.(517-519)gTc>gCc	p.V173A		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	173					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V173A(1)		endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					GTGATGGATGACATTGGAGTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	83	85					11																	55761584		2201	4296	6497	55518160	SO:0001583	missense	338674			AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.518T>C	11.37:g.55761584A>G	ENSP00000278409:p.Val173Ala		55518160	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.823083	0.32237	.	.	ENSG00000149133	ENST00000278409	T	0.00169	8.63	3.03	-1.58	0.08479	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	L	0.59912	1.85	0.09310	N	1	P	0.38300	0.626	B	0.43508	0.422	T	0.25813	-1.0121	9	0.52906	T	0.07	.	0.6583	0.00838	0.4076:0.1601:0.1164:0.3158	.	173	O95221	OR5F1_HUMAN	A	173	ENSP00000278409:V173A	ENSP00000278409:V173A	V	-	2	0	OR5F1	55518160	0.000000	0.05858	0.033000	0.17914	0.694000	0.40290	-0.290000	0.08354	0.181000	0.19994	0.247000	0.18012	GTC		0.458	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		G	55761584	A	G	55761584	3	3	61	1	0	0	0	0	1	0	0	0	11189	275	10	4	429	4	OR5F1	11	55761584	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	58361	55761584	79244932	7353	15338										
OR5F1	338674	broad.mit.edu	37	chr11	55761802	55761802	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggagataaagaagtacatCtgtaggaagcagccagcaaa	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55761802C>A	ENST00000278409.1	-	1	299	c.300G>T	c.(298-300)caG>caT	p.Q100H		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	100					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q100H(1)		endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AGAAGTACATCTGTAGGAAGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											86	83	84					11																	55761802		2201	4296	6497	55518378	SO:0001583	missense	338674			AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.300G>T	11.37:g.55761802C>A	ENSP00000278409:p.Gln100His		55518378	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.228898	0.39399	.	.	ENSG00000149133	ENST00000278409	T	0.02121	4.44	3.03	-1.52	0.08637	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.16171	0.0389	H	0.96365	3.81	0.21527	N	0.999659	D	0.89917	1.0	D	0.87578	0.998	T	0.01460	-1.1349	9	0.87932	D	0	.	8.0412	0.30523	0.0:0.5682:0.0:0.4318	.	100	O95221	OR5F1_HUMAN	H	100	ENSP00000278409:Q100H	ENSP00000278409:Q100H	Q	-	3	2	OR5F1	55518378	0.000000	0.05858	0.755000	0.31263	0.811000	0.45836	-1.304000	0.02741	-0.309000	0.08779	0.297000	0.19635	CAG		0.468	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		A	55761802	C	A	55761802	3	1	61	1	0	0	0	0	1	0	0	0	11189	912	32	2	647	2	OR5F1	11	55761802	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	218	55761802	79244714	7354	15339										
OR5AS1	219447	broad.mit.edu	37	chr11	55798272	55798272	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaccgctatgcagccatCtgcaacccactgctctatac	6	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55798272C>A	ENST00000313555.1	+	1	378	c.378C>A	c.(376-378)atC>atA	p.I126I		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I126I(1)		endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					ATGCAGCCATCTGCAACCCAC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	11											146	118	128					11																	55798272		2201	4296	6497	55554848	SO:0001819	synonymous_variant	219447			AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.378C>A	11.37:g.55798272C>A			55554848	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																				0.463	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		A	55798272	C	A	55798272	2	1	61	1	0	0	0	0	0	0	0	1	11177	903	32	2		2	OR5AS1	11	55798272	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36470	55798272	79208244	7355	15340										
OR8H3	390152	broad.mit.edu	37	chr11	55890405	55890405	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacacttccccaattttagCtctgtcctgcactgacacag	6	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55890405C>A	ENST00000313472.3	+	1	557	c.557C>A	c.(556-558)gCt>gAt	p.A186D		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A186D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					CCAATTTTAGCTCTGTCCTGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											236	216	223					11																	55890405		2201	4296	6497	55646981	SO:0001583	missense	390152			AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.557C>A	11.37:g.55890405C>A	ENSP00000323928:p.Ala186Asp		55646981	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.021530	0.35701	.	.	ENSG00000181761	ENST00000313472	T	0.00115	8.71	3.62	1.41	0.22369	GPCR, rhodopsin-like superfamily (1);	0.387872	0.22363	N	0.061043	T	0.00241	0.0007	L	0.59436	1.845	0.09310	N	1	P	0.50528	0.936	P	0.58266	0.836	T	0.46414	-0.9193	10	0.46703	T	0.11	.	4.6704	0.12685	0.3534:0.4599:0.0:0.1867	.	186	Q8N146	OR8H3_HUMAN	D	186	ENSP00000323928:A186D	ENSP00000323928:A186D	A	+	2	0	OR8H3	55646981	0.000000	0.05858	0.946000	0.38457	0.447000	0.32167	-0.946000	0.03905	0.600000	0.29862	0.173000	0.16961	GCT		0.413	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		A	55890405	C	A	55890405	3	1	61	1	0	0	0	0	1	0	0	0	11270	797	28	2	559	2	OR8H3	11	55890405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92133	55890405	79116111	7356	15341										
OR5J2	282775	broad.mit.edu	37	chr11	55944804	55944804	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcaggcagacagcaagcCttctccacctgtgcctctca	8	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:55944804C>A	ENST00000312298.1	+	1	711	c.711C>A	c.(709-711)gcC>gcA	p.A237A		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A237A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					GACAGCAAGCCTTCTCCACCT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11											142	122	129					11																	55944804		2201	4296	6497	55701380	SO:0001819	synonymous_variant	282775			AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.711C>A	11.37:g.55944804C>A			55701380	Q6IEU5	Silent	SNP	ENST00000312298.1	37	CCDS31522.1																																																																																				0.468	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		A	55944804	C	A	55944804	2	1	61	1	0	0	0	0	0	0	0	1	11196	668	24	2		2	OR5J2	11	55944804	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54399	55944804	79061712	7357	15342										
OR5T3	390154	broad.mit.edu	37	chr11	56019969	56019969	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttagtgttttatcattCttggatgcttgctattctac	6	7	4	0	rs573806981		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56019969C>A	ENST00000303059.3	+	1	294	c.294C>A	c.(292-294)ttC>ttA	p.F98L		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F98L(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					TTTTATCATTCTTGGATGCTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											100	100	100					11																	56019969		2201	4296	6497	55776545	SO:0001583	missense	390154			AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.294C>A	11.37:g.56019969C>A	ENSP00000305403:p.Phe98Leu		55776545	Q6IFC7	Missense_Mutation	SNP	ENST00000303059.3	37	CCDS31524.1	.	.	.	.	.	.	.	.	.	.	c	5.301	0.240902	0.10077	.	.	ENSG00000172489	ENST00000303059	T	0.00966	5.49	4.55	-2.89	0.05665	GPCR, rhodopsin-like superfamily (1);	0.433220	0.17255	U	0.180992	T	0.00815	0.0027	L	0.45137	1.4	0.09310	N	1	B	0.14012	0.009	B	0.16722	0.016	T	0.48080	-0.9066	10	0.13470	T	0.59	.	6.244	0.20807	0.0:0.3758:0.2183:0.4059	.	98	Q8NGG3	OR5T3_HUMAN	L	98	ENSP00000305403:F98L	ENSP00000305403:F98L	F	+	3	2	OR5T3	55776545	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-4.264000	0.00263	-0.408000	0.07565	0.643000	0.83706	TTC		0.383	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		A	56019969	C	A	56019969	3	1	61	1	0	0	0	0	1	0	0	0	11214	912	32	2	296	2	OR5T3	11	56019969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75165	56019969	78986547	7358	15343										
OR5T3	390154	broad.mit.edu	37	chr11	56020105	56020105	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaactacagaatgttttCtcttggctgcaatggcttat	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56020105C>A	ENST00000303059.3	+	1	430	c.430C>A	c.(430-432)Ctc>Atc	p.L144I		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L144I(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					AGAATGTTTTCTCTTGGCTGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											197	188	191					11																	56020105		2201	4295	6496	55776681	SO:0001583	missense	390154			AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.430C>A	11.37:g.56020105C>A	ENSP00000305403:p.Leu144Ile		55776681	Q6IFC7	Missense_Mutation	SNP	ENST00000303059.3	37	CCDS31524.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.428389	0.25726	.	.	ENSG00000172489	ENST00000303059	T	0.03496	3.91	4.55	1.19	0.21007	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	U	0.000853	T	0.05090	0.0136	L	0.53780	1.695	0.09310	N	1	B	0.24132	0.098	B	0.34138	0.176	T	0.28744	-1.0034	10	0.59425	D	0.04	.	5.683	0.17786	0.2696:0.5658:0.0:0.1646	.	144	Q8NGG3	OR5T3_HUMAN	I	144	ENSP00000305403:L144I	ENSP00000305403:L144I	L	+	1	0	OR5T3	55776681	0.000000	0.05858	0.524000	0.27887	0.344000	0.29017	-3.007000	0.00649	0.566000	0.29273	0.643000	0.83706	CTC		0.403	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		A	56020105	C	A	56020105	3	1	61	1	0	0	0	0	1	0	0	0	11214	913	32	2	432	2	OR5T3	11	56020105	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136	56020105	78986411	7359	15344										
OR8H1	219469	broad.mit.edu	37	chr11	56057622	56057622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacctggagtcctgtcttCtctgcatgactctaatgaga	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56057622C>A	ENST00000313022.2	-	1	944	c.917G>T	c.(916-918)aGa>aTa	p.R306I		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R306I(1)		NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					GTCCTGTCTTCTCTGCATGAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	99	95					11																	56057622		2201	4295	6496	55814198	SO:0001583	missense	219469			AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.917G>T	11.37:g.56057622C>A	ENSP00000323595:p.Arg306Ile		55814198	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	C	9.349	1.065025	0.20067	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.39229	1.09	3.45	1.0	0.19881	.	0.401911	0.21353	N	0.075935	T	0.39655	0.1086	M	0.77712	2.385	0.09310	N	1	B	0.15473	0.013	B	0.17098	0.017	T	0.42103	-0.9471	10	0.72032	D	0.01	.	5.4074	0.16328	0.0:0.2713:0.0:0.7287	.	306	Q8NGG4	OR8H1_HUMAN	I	306;302	ENSP00000323595:R306I	ENSP00000323595:R306I	R	-	2	0	OR8H1	55814198	0.000000	0.05858	0.002000	0.10522	0.042000	0.13812	-0.565000	0.05929	0.056000	0.16144	-0.410000	0.06199	AGA		0.338	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		A	56057622	C	A	56057622	3	1	61	1	0	0	0	0	1	0	0	0	11268	913	32	2	20	2	OR8H1	11	56057622	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37517	56057622	78948894	7360	15345										
OR8J1	219477	broad.mit.edu	37	chr11	56128214	56128214	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtttcatcttatgtattCtctgtgtcttattgctcttc	7	8	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56128214C>A	ENST00000303039.3	+	1	524	c.492C>A	c.(490-492)ttC>ttA	p.F164L		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F164L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					CTTATGTATTCTCTGTGTCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											114	104	107					11																	56128214		2201	4296	6497	55884790	SO:0001583	missense	219477			AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.492C>A	11.37:g.56128214C>A	ENSP00000304060:p.Phe164Leu		55884790	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	C	9.764	1.170994	0.21621	.	.	ENSG00000172487	ENST00000303039	T	0.00145	8.67	3.91	-0.338	0.12651	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00271	0.0008	L	0.51914	1.62	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52403	-0.8580	10	0.29301	T	0.29	.	10.7095	0.45975	0.0:0.6482:0.0:0.3518	.	164	Q8NGP2	OR8J1_HUMAN	L	164	ENSP00000304060:F164L	ENSP00000304060:F164L	F	+	3	2	OR8J1	55884790	0.000000	0.05858	0.995000	0.50966	0.061000	0.15899	-1.656000	0.01980	0.063000	0.16370	-1.197000	0.01672	TTC		0.408	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		A	56128214	C	A	56128214	3	1	61	1	0	0	0	0	1	0	0	0	11272	912	32	2	494	2	OR8J1	11	56128214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70592	56128214	78878302	7361	15346										
OR8J1	219477	broad.mit.edu	37	chr11	56128426	56128426	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgttcatcagaaggaaggaAaaaagccttttctacctgtg	9	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56128426A>C	ENST00000303039.3	+	1	736	c.704A>C	c.(703-705)aAa>aCa	p.K235T		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K235T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					GAAGGAAGGAAAAAAGCCTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											113	107	109					11																	56128426		2201	4296	6497	55885002	SO:0001583	missense	219477			AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.704A>C	11.37:g.56128426A>C	ENSP00000304060:p.Lys235Thr		55885002	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.463727	0.26335	.	.	ENSG00000172487	ENST00000303039	T	0.00130	8.69	3.9	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.383998	0.25106	N	0.033088	T	0.00178	0.0005	L	0.54908	1.71	0.09310	N	0.999998	P	0.38863	0.65	P	0.45913	0.497	T	0.22765	-1.0207	10	0.40728	T	0.16	.	3.3582	0.07177	0.6468:0.0:0.1589:0.1944	.	235	Q8NGP2	OR8J1_HUMAN	T	235	ENSP00000304060:K235T	ENSP00000304060:K235T	K	+	2	0	OR8J1	55885002	0.000000	0.05858	0.994000	0.49952	0.606000	0.37113	-0.269000	0.08596	0.632000	0.30432	0.443000	0.29094	AAA		0.353	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		C	56128426	A	C	56128426	3	2	61	1	0	0	0	0	1	0	0	0	11272	14	1	4	706	4	OR8J1	11	56128426	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	212	56128426	78878090	7362	15347										
OR5M9	390162	broad.mit.edu	37	chr11	56230655	56230655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagcattttgggggtaaCgttggaggagaagcacacgt	14	7	0	1	rs367845258		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56230655C>T	ENST00000279791.1	-	1	222	c.223G>A	c.(223-225)Gtt>Att	p.V75I		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V75I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					TTGGGGGTAACGTTGGAGGAG	0.438													c|||	1	0.000199681	0	0	5008	,	,		21609	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	11						C	ILE/VAL	0,4402		0,0,2201	85	87	87		223	1.9	0.1	11		87	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR5M9	NM_001004743.1	29	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	benign	75/311	56230655	1,12993	2201	4296	6497	55987231	SO:0001583	missense	390162			AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"GPCR / Class A : Olfactory receptors"	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.223G>A	11.37:g.56230655C>T	ENSP00000279791:p.Val75Ile		55987231	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	CCDS31531.1	.	.	.	.	.	.	.	.	.	.	C	4.132	0.022778	0.08006	0.0	1.16E-4	ENSG00000150269	ENST00000279791	T	0.01406	4.93	4.85	1.88	0.25563	GPCR, rhodopsin-like superfamily (1);	0.172757	0.27518	N	0.019017	T	0.00784	0.0026	N	0.10837	0.055	0.09310	N	1	B	0.32101	0.356	B	0.29785	0.107	T	0.48614	-0.9020	10	0.08179	T	0.78	-18.8969	7.3237	0.26542	0.0:0.6235:0.0:0.3765	.	75	Q8NGP3	OR5M9_HUMAN	I	75	ENSP00000279791:V75I	ENSP00000279791:V75I	V	-	1	0	OR5M9	55987231	0.000000	0.05858	0.076000	0.20297	0.837000	0.47467	0.439000	0.21575	0.566000	0.29273	0.549000	0.68633	GTT		0.438	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743		T	56230655	C	T	56230655	3	4	61	1	0	0	0	0	1	0	0	0	11208	536	19	1	711	1	OR5M9	11	56230655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102229	56230655	78775861	7363	15348										
OR5M3	219482	broad.mit.edu	37	chr11	56237674	56237674	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacaagagcaatgaagaaGaaacactgtactaaacaacc	8	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56237674G>T	ENST00000312240.2	-	1	340	c.300C>A	c.(298-300)ttC>ttA	p.F100L		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F100L(1)		NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CAATGAAGAAGAAACACTGTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	84	85					11																	56237674		2201	4295	6496	55994250	SO:0001583	missense	219482			AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.300C>A	11.37:g.56237674G>T	ENSP00000312208:p.Phe100Leu		55994250	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527260	0.27299	.	.	ENSG00000174937	ENST00000312240	T	0.00448	7.38	5.13	-4.52	0.03472	GPCR, rhodopsin-like superfamily (1);	0.138136	0.33457	N	0.004892	T	0.00271	0.0008	L	0.39566	1.225	0.09310	N	0.999996	B	0.29571	0.249	B	0.32677	0.15	T	0.44097	-0.9350	10	0.37606	T	0.19	-18.3376	8.9423	0.35738	0.6127:0.1079:0.2794:0.0	.	100	Q8NGP4	OR5M3_HUMAN	L	100	ENSP00000312208:F100L	ENSP00000312208:F100L	F	-	3	2	OR5M3	55994250	0.000000	0.05858	0.838000	0.33150	0.927000	0.56198	-0.832000	0.04400	-0.804000	0.04410	0.478000	0.44815	TTC		0.363	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		T	56237674	G	T	56237674	3	4	61	1	0	0	0	0	1	0	0	0	11206	933	33	2	625	2	OR5M3	11	56237674	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7019	56237674	78768842	7364	15349										
OR5M8	219484	broad.mit.edu	37	chr11	56258164	56258164	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcctgccctctgtagagCgaatctttaaaatagcaggg	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56258164C>T	ENST00000327216.2	-	1	707	c.683G>A	c.(682-684)cGc>cAc	p.R228H		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R228H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					CTCTGTAGAGCGAATCTTTAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											40	43	42					11																	56258164		2201	4296	6497	56014740	SO:0001583	missense	219484			AB065744	CCDS31533.1	11q11	2012-08-09			ENSG00000181371	ENSG00000181371		"GPCR / Class A : Olfactory receptors"	14846	protein-coding gene	gene with protein product							Standard	NM_001005282		Approved		uc001nix.1	Q8NGP6	OTTHUMG00000166877	ENST00000327216.2:c.683G>A	11.37:g.56258164C>T	ENSP00000323354:p.Arg228His		56014740	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	37	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	C	0.231	-1.021371	0.02061	.	.	ENSG00000181371	ENST00000327216	T	0.39229	1.09	4.35	-3.88	0.04205	GPCR, rhodopsin-like superfamily (1);	0.560040	0.14923	N	0.290544	T	0.22205	0.0535	L	0.35793	1.09	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.30563	-0.9974	10	0.11182	T	0.66	-0.053	4.7083	0.12860	0.2608:0.231:0.0:0.5082	.	228	Q8NGP6	OR5M8_HUMAN	H	228	ENSP00000323354:R228H	ENSP00000323354:R228H	R	-	2	0	OR5M8	56014740	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.341000	0.01100	-0.810000	0.04375	-0.211000	0.12701	CGC		0.408	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		T	56258164	C	T	56258164	3	4	61	1	0	0	0	0	1	0	0	0	11207	768	27	1	256	1	OR5M8	11	56258164	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20490	56258164	78748352	7365	15350										
OR5M10	390167	broad.mit.edu	37	chr11	56344667	56344667	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggaggatcagcgcagtaGaaatgattgatttcaaggga	14	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56344667G>T	ENST00000526812.2	-	1	596	c.531C>A	c.(529-531)ttC>ttA	p.F177L		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F177L(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						CAGCGCAGTAGAAATGATTGA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	86	87					11																	56344667		1953	4131	6084	56101243	SO:0001583	missense	390167			BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.531C>A	11.37:g.56344667G>T	ENSP00000436004:p.Phe177Leu		56101243	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	14.45	2.540404	0.45176	.	.	ENSG00000254834	ENST00000526812	T	0.00137	8.68	4.04	1.96	0.26148	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00496	0.0016	M	0.88377	2.95	0.30633	N	0.757273	D	0.89917	1.0	D	0.97110	1.0	T	0.25152	-1.0140	9	0.72032	D	0.01	.	8.1009	0.30857	0.2259:0.0:0.7741:0.0	.	177	Q6IEU7	OR5MA_HUMAN	L	177	ENSP00000436004:F177L	ENSP00000436004:F177L	F	-	3	2	OR5M10	56101243	0.989000	0.36119	0.995000	0.50966	0.244000	0.25665	0.928000	0.28831	0.364000	0.24374	0.632000	0.83419	TTC		0.473	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		T	56344667	G	T	56344667	3	4	61	1	0	0	0	0	1	0	0	0	11204	933	33	2	420	2	OR5M10	11	56344667	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86503	56344667	78661849	7366	15351										
OR5M1	390168	broad.mit.edu	37	chr11	56380921	56380921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcttctctagcactgggtCgtctgtcagtcccaagagaa	10	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:56380921C>T	ENST00000526538.1	-	1	57	c.58G>A	c.(58-60)Gac>Aac	p.D20N		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D20N(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						AGCACTGGGTCGTCTGTCAGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											170	158	162					11																	56380921		1920	4127	6047	56137497	SO:0001583	missense	390168			AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"GPCR / Class A : Olfactory receptors"	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.58G>A	11.37:g.56380921C>T	ENSP00000435416:p.Asp20Asn		56137497	Q6IF60|Q96RB6	Missense_Mutation	SNP	ENST00000526538.1	37	CCDS53631.1	.	.	.	.	.	.	.	.	.	.	C	7.229	0.598893	0.13939	.	.	ENSG00000255012	ENST00000526538	T	0.01084	5.36	3.71	-3.9	0.04181	.	1.024230	0.07826	N	0.960527	T	0.00875	0.0029	N	0.24115	0.695	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.46803	-0.9165	10	0.21540	T	0.41	-5.7979	6.4189	0.21732	0.0:0.23:0.148:0.622	.	20	Q8NGP8	OR5M1_HUMAN	N	20	ENSP00000435416:D20N	ENSP00000435416:D20N	D	-	1	0	OR5M1	56137497	0.000000	0.05858	0.001000	0.08648	0.661000	0.39034	-2.385000	0.01062	-0.534000	0.06315	0.280000	0.19369	GAC		0.458	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740		T	56380921	C	T	56380921	3	4	61	1	0	0	0	0	1	0	0	0	11203	884	31	1	893	1	OR5M1	11	56380921	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36254	56380921	78625595	7367	15352										
TNKS1BP1	85456	broad.mit.edu	37	chr11	57077719	57077719	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggctttccaactacccgGtcctgggctgtgagcacccc	11	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57077719G>A	ENST00000532437.1	-	5	2777	c.2466C>T	c.(2464-2466)gaC>gaT	p.D822D	TNKS1BP1_ENST00000358252.3_Silent_p.D822D|TNKS1BP1_ENST00000530920.1_5'UTR			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	822	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)	p.D822D(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CAACTACCCGGTCCTGGGCTG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	11											106	111	109					11																	57077719		2201	4296	6497	56834295	SO:0001819	synonymous_variant	85456			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2466C>T	11.37:g.57077719G>A			56834295	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																				0.612	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57077719	G	A	57077719	2	1	61	1	0	0	0	0	0	0	0	1	16359	1252	44	3		3	TNKS1BP1	11	57077719	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	696798	57077719	77928797	7368	15353										
SSRP1	6749	broad.mit.edu	37	chr11	57094285	57094285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttagctgccttgaggacgaCttggatgatgagcccctaga	12	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57094285C>A	ENST00000278412.2	-	16	2216	c.1950G>T	c.(1948-1950)aaG>aaT	p.K650N	TNKS1BP1_ENST00000358252.3_5'Flank|snoU13_ENST00000459327.1_RNA|RP11-872D17.4_ENST00000534162.1_RNA	NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	650	Ser-rich.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.K650N(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TTGAGGACGACTTGGATGATG	0.463																																					Colon(89;1000 1340 6884 23013 41819)											1	Substitution - Missense(1)	large_intestine(1)	11											169	144	152					11																	57094285		2201	4296	6497	56850861	SO:0001583	missense	6749			M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 80 kDa subunit"	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.1950G>T	11.37:g.57094285C>A	ENSP00000278412:p.Lys650Asn		56850861	Q5BJG8	Missense_Mutation	SNP	ENST00000278412.2	37	CCDS7952.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.238538	0.22711	.	.	ENSG00000149136	ENST00000278412	D	0.93247	-3.19	5.06	4.14	0.48551	.	0.192855	0.44902	D	0.000406	D	0.85687	0.5754	N	0.08118	0	0.44175	D	0.996988	P	0.41978	0.767	B	0.43445	0.42	D	0.84277	0.0492	10	0.40728	T	0.16	.	9.3284	0.38008	0.0:0.8352:0.0:0.1648	.	650	Q08945	SSRP1_HUMAN	N	650	ENSP00000278412:K650N	ENSP00000278412:K650N	K	-	3	2	SSRP1	56850861	1.000000	0.71417	0.975000	0.42487	0.407000	0.30961	2.369000	0.44231	1.133000	0.42147	0.462000	0.41574	AAG		0.463	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		A	57094285	C	A	57094285	3	1	61	1	0	0	0	0	1	0	0	0	15233	564	20	2	187	2	SSRP1	11	57094285	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16566	57094285	77912231	7369	15354										
PRG3	10394	broad.mit.edu	37	chr11	57147240	57147240	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagatcctggcctaggtcTgcctgtgtctctaggctctc	10	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57147240T>G	ENST00000287143.2	-	3	211	c.102A>C	c.(100-102)gcA>gcC	p.A34A		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.A34A(1)		large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						GGCCTAGGTCTGCCTGTGTCT	0.557																																					Melanoma(154;1456 2519 19358 45229)											1	Substitution - coding silent(1)	large_intestine(1)	11											78	73	75					11																	57147240		2201	4296	6497	56903816	SO:0001819	synonymous_variant	10394			AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.102A>C	11.37:g.57147240T>G			56903816	Q5VX23|Q9NXE2	Silent	SNP	ENST00000287143.2	37	CCDS7954.1																																																																																				0.557	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093		G	57147240	T	G	57147240	2	3	61	1	0	0	0	0	0	0	0	1	12514	1567	55	4		4	PRG3	11	57147240	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	52955	57147240	77859276	7370	15355										
PRG2	5553	broad.mit.edu	37	chr11	57156692	57156692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctcctcttcctccagctCcctgcaaggggtctcctcca	6	20	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57156692C>T	ENST00000311862.5	-	3	230	c.157G>A	c.(157-159)Gag>Aag	p.E53K	PRG2_ENST00000525955.1_Missense_Mutation_p.E53K|PRG2_ENST00000533605.1_Missense_Mutation_p.E53K|RP11-872D17.8_ENST00000529411.1_Missense_Mutation_p.E158K	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	53					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.E53K(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				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)	Sargramostim(DB00020)	TCCTCCAGCTCCCTGCAAGGG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	90	90					11																	57156692		2201	4296	6497	56913268	SO:0001583	missense	5553			BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.157G>A	11.37:g.57156692C>T	ENSP00000312134:p.Glu53Lys		56913268	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000311862.5	37	CCDS7955.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021457	0.54576	.	.	ENSG00000186652;ENSG00000186652;ENSG00000186652;ENSG00000254979	ENST00000311862;ENST00000533605;ENST00000525955;ENST00000529411	T;T;T;T	0.43688	2.94;2.63;2.94;0.94	5.41	2.52	0.30459	.	0.328449	0.21115	U	0.079906	T	0.31979	0.0814	L	0.50333	1.59	0.09310	N	1	B;B	0.30584	0.158;0.286	B;B	0.27887	0.062;0.084	T	0.21621	-1.0240	10	0.51188	T	0.08	-16.0453	5.6709	0.17721	0.0:0.6627:0.161:0.1763	.	53;53	A6XMW0;P13727	.;PRG2_HUMAN	K	53;53;53;158	ENSP00000312134:E53K;ENSP00000433231:E53K;ENSP00000433016:E53K;ENSP00000431536:E158K	ENSP00000312134:E53K	E	-	1	0	RP11-872D17.8;PRG2	56913268	0.008000	0.16893	0.000000	0.03702	0.045000	0.14185	0.619000	0.24388	0.256000	0.21614	0.609000	0.83330	GAG		0.547	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728		T	57156692	C	T	57156692	3	4	61	1	0	0	0	0	1	0	0	0	12513	864	30	3	527	3	PRG2	11	57156692	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9452	57156692	77849824	7371	15356										
SERPING1	710	broad.mit.edu	37	chr11	57367425	57367425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtttgcaagacagaggcgAagggaaggtcgcaacaacag	15	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57367425A>G	ENST00000278407.4	+	3	352	c.125A>G	c.(124-126)gAa>gGa	p.E42G	SERPING1_ENST00000340687.6_Missense_Mutation_p.E42G|SERPING1_ENST00000403558.1_Missense_Mutation_p.E76G|SERPING1_ENST00000378323.4_Missense_Mutation_p.E47G|SERPING1_ENST00000378324.2_5'UTR	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	42					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E42G(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						GACAGAGGCGAAGGGAAGGTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											165	160	162					11																	57367425		2201	4296	6497	57124001	SO:0001583	missense	710			X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.125A>G	11.37:g.57367425A>G	ENSP00000278407:p.Glu42Gly		57124001	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	37	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.099175	0.37048	.	.	ENSG00000149131	ENST00000405496;ENST00000278407;ENST00000457869;ENST00000340687;ENST00000378323;ENST00000403558;ENST00000433668	D;D;T;D;D;D	0.90385	-2.66;-1.98;-1.48;-2.04;-1.99;-2.08	4.85	1.19	0.21007	.	1.226530	0.05647	N	0.584429	D	0.85362	0.5679	L	0.48642	1.525	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.69587	-0.5105	10	0.66056	D	0.02	.	0.8222	0.01113	0.4952:0.1665:0.1771:0.1612	.	47;76;42;42	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	G	42;42;76;42;47;76;42	ENSP00000384561:E42G;ENSP00000278407:E42G;ENSP00000399746:E76G;ENSP00000341861:E42G;ENSP00000367574:E47G;ENSP00000384420:E76G	ENSP00000278407:E42G	E	+	2	0	SERPING1	57124001	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.037000	0.12164	0.098000	0.17522	0.459000	0.35465	GAA		0.488	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		G	57367425	A	G	57367425	3	3	61	1	0	0	0	0	1	0	0	0	14153	246	9	4	131	4	SERPING1	11	57367425	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	210733	57367425	77639091	7372	15357										
ZDHHC5	25921	broad.mit.edu	37	chr11	57461380	57461380	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccagggagagctgaggaGaacaaaggtgaggaatttag	15	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57461380G>T	ENST00000287169.3	+	8	2240	c.878G>T	c.(877-879)aGa>aTa	p.R293I	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.R240I	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	293					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.R293I(1)		endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						GAGCTGAGGAGAACAAAGGTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											76	71	73					11																	57461380		2201	4296	6497	57217956	SO:0001583	missense	25921			AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.878G>T	11.37:g.57461380G>T	ENSP00000287169:p.Arg293Ile		57217956	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	37	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112219	0.77210	.	.	ENSG00000156599	ENST00000527985;ENST00000287169;ENST00000529447	T;T;D	0.85411	0.07;1.07;-1.98	5.42	5.42	0.78866	.	0.063062	0.64402	D	0.000016	D	0.87744	0.6254	L	0.49778	1.585	0.80722	D	1	P	0.46457	0.878	P	0.51170	0.661	D	0.88412	0.3022	10	0.72032	D	0.01	-8.0311	18.9933	0.92803	0.0:0.0:1.0:0.0	.	293	Q9C0B5	ZDHC5_HUMAN	I	240;293;127	ENSP00000432202:R240I;ENSP00000287169:R293I;ENSP00000435722:R127I	ENSP00000287169:R293I	R	+	2	0	ZDHHC5	57217956	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.207000	0.89746	2.820000	0.97059	0.650000	0.86243	AGA		0.428	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		T	57461380	G	T	57461380	3	4	61	1	0	0	0	0	1	0	0	0	17657	942	33	2	904	2	ZDHHC5	11	57461380	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93955	57461380	77545136	7373	15358										
TMX2	51075	broad.mit.edu	37	chr11	57506212	57506212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctaatgactgccaatcatTtgcccctatctatgctgacc	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57506212T>G	ENST00000278422.4	+	5	530	c.518T>G	c.(517-519)tTt>tGt	p.F173C	C11orf31_ENST00000388857.4_5'Flank|C11orf31_ENST00000534355.1_5'Flank|TMX2_ENST00000378312.4_Missense_Mutation_p.F135C|TMX2-CTNND1_ENST00000528395.1_Intron	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	173	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.F173C(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						TGCCAATCATTTGCCCCTATC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											189	172	178					11																	57506212		2201	4296	6497	57262788	SO:0001583	missense	51075			AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"Protein disulfide isomerases"	30739	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 12"		"thioredoxin domain containing 14"	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.518T>G	11.37:g.57506212T>G	ENSP00000278422:p.Phe173Cys		57262788	B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Missense_Mutation	SNP	ENST00000278422.4	37	CCDS7967.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416427	0.83449	.	.	ENSG00000213593	ENST00000378312;ENST00000278422	T;T	0.03468	3.92;3.92	5.95	5.95	0.96441	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	U	0.000000	T	0.22898	0.0553	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.00950	-1.1503	10	0.72032	D	0.01	-14.3507	16.0852	0.81042	0.0:0.0:0.0:1.0	.	135;173	Q9Y320-2;Q9Y320	.;TMX2_HUMAN	C	135;173	ENSP00000367562:F135C;ENSP00000278422:F173C	ENSP00000278422:F173C	F	+	2	0	TMX2	57262788	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.484000	0.81180	2.279000	0.76181	0.533000	0.62120	TTT		0.473	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		G	57506212	T	G	57506212	3	3	61	1	0	0	0	0	1	0	0	0	16306	1841	64	4	536	4	TMX2	11	57506212	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	44832	57506212	77500304	7374	15359										
CTNND1	1500	broad.mit.edu	37	chr11	57569383	57569383	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgccatgcttggattccgcTtggatgctgtcaagtccaat	10	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57569383T>G	ENST00000399050.4	+	7	1671	c.1135T>G	c.(1135-1137)Ttg>Gtg	p.L379V	CTNND1_ENST00000530748.1_Missense_Mutation_p.L325V|CTNND1_ENST00000360682.6_Missense_Mutation_p.L379V|CTNND1_ENST00000361391.6_Missense_Mutation_p.L379V|CTNND1_ENST00000361332.4_Missense_Mutation_p.L379V|CTNND1_ENST00000428599.2_Missense_Mutation_p.L379V|CTNND1_ENST00000532245.1_Missense_Mutation_p.L278V|CTNND1_ENST00000532649.1_Missense_Mutation_p.L325V|CTNND1_ENST00000529919.1_Missense_Mutation_p.L379V|CTNND1_ENST00000532787.1_Missense_Mutation_p.L278V|CTNND1_ENST00000529526.1_Missense_Mutation_p.L325V|CTNND1_ENST00000399039.4_Missense_Mutation_p.L379V|CTNND1_ENST00000529986.1_Missense_Mutation_p.L278V|CTNND1_ENST00000426142.2_Missense_Mutation_p.L278V|CTNND1_ENST00000361796.4_Missense_Mutation_p.L379V|CTNND1_ENST00000532844.1_Missense_Mutation_p.L325V|CTNND1_ENST00000529873.1_Missense_Mutation_p.L325V|CTNND1_ENST00000533667.1_Missense_Mutation_p.L56V|CTNND1_ENST00000534579.1_Missense_Mutation_p.L325V|CTNND1_ENST00000530094.1_Missense_Mutation_p.L278V|CTNND1_ENST00000524630.1_Missense_Mutation_p.L379V|CTNND1_ENST00000358694.6_Missense_Mutation_p.L379V|CTNND1_ENST00000526772.1_Missense_Mutation_p.L56V|CTNND1_ENST00000528232.1_Missense_Mutation_p.L278V|CTNND1_ENST00000526357.1_Missense_Mutation_p.L325V|CTNND1_ENST00000528621.1_Missense_Mutation_p.L325V|CTNND1_ENST00000531014.1_Missense_Mutation_p.L56V|CTNND1_ENST00000526938.1_Missense_Mutation_p.L379V|CTNND1_ENST00000532463.1_Missense_Mutation_p.L278V|CTNND1_ENST00000525902.1_Missense_Mutation_p.L56V|CTNND1_ENST00000415361.2_Missense_Mutation_p.L278V|CTNND1_ENST00000527467.1_Missense_Mutation_p.L56V	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	379					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)	p.L379V(1)		breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				TGGATTCCGCTTGGATGCTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											98	97	97					11																	57569383		2051	4214	6265	57325959	SO:0001583	missense	1500			AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.1135T>G	11.37:g.57569383T>G	ENSP00000382004:p.Leu379Val		57325959	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.179708	0.38511	.	.	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000533189;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000533667;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000527467;ENST00000528232;ENST00000531014;ENST00000526772;ENST00000529873;ENST00000525902;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.51325	0.85;0.85;0.85;0.71;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.58	-7.96	0.01144	Armadillo-like helical (1);Armadillo-type fold (1);	0.069969	0.56097	D	0.000023	T	0.51109	0.1655	L	0.31752	0.955	0.31175	N	0.702734	D;D;D;D;D;D;P;D;D	0.71674	0.998;0.998;0.997;0.998;0.998;0.998;0.537;0.998;0.997	D;D;D;D;D;D;B;D;D	0.83275	0.996;0.996;0.991;0.996;0.996;0.996;0.219;0.996;0.991	T	0.60424	-0.7266	10	0.21014	T	0.42	-4.7807	22.8404	0.99976	0.0:0.813:0.0:0.187	.	379;379;379;278;325;325;379;379;379	O60716-3;O60716-2;O60716;O60716-18;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.;.	V	379;379;379;56;379;379;325;278;379;379;379;278;278;379;278;56;325;325;325;379;56;278;56;56;325;56;325;325;278;278;278;325;379	ENSP00000436543:L379V;ENSP00000434808:L379V;ENSP00000381996:L379V;ENSP00000435242:L56V;ENSP00000353902:L379V;ENSP00000354907:L379V;ENSP00000436323:L325V;ENSP00000409930:L278V;ENSP00000382004:L379V;ENSP00000354785:L379V;ENSP00000354823:L379V;ENSP00000432075:L278V;ENSP00000437156:L278V;ENSP00000351527:L379V;ENSP00000434949:L278V;ENSP00000437051:L56V;ENSP00000435379:L325V;ENSP00000432243:L325V;ENSP00000436744:L325V;ENSP00000413586:L379V;ENSP00000434900:L56V;ENSP00000435266:L278V;ENSP00000432623:L56V;ENSP00000433158:L56V;ENSP00000435494:L325V;ENSP00000434672:L56V;ENSP00000433276:L325V;ENSP00000433334:L325V;ENSP00000437327:L278V;ENSP00000403518:L278V;ENSP00000434017:L278V;ENSP00000435789:L325V;ENSP00000432041:L379V	ENSP00000351527:L379V	L	+	1	2	CTNND1	57325959	0.000000	0.05858	0.290000	0.24890	0.953000	0.61014	-0.233000	0.09041	-1.540000	0.01730	0.455000	0.32223	TTG		0.537	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		G	57569383	T	G	57569383	3	3	61	1	0	0	0	0	1	0	0	0	4025	1606	56	4	1153	4	CTNND1	11	57569383	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	63171	57569383	77437133	7375	15360										
OR9Q1	219956	broad.mit.edu	37	chr11	57947558	57947558	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcttccatggtggtgatCttggtgtcctacctgtttat	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57947558C>A	ENST00000335397.3	+	3	958	c.642C>A	c.(640-642)atC>atA	p.I214I		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, member 1	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I214I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Breast(21;0.222)				TGGTGGTGATCTTGGTGTCCT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	11											234	192	206					11																	57947558		2201	4296	6497	57704134	SO:0001819	synonymous_variant	219956			AB065734	CCDS31543.1	11q12.1	2012-08-09				ENSG00000186509		"GPCR / Class A : Olfactory receptors"	14724	protein-coding gene	gene with protein product							Standard	NM_001005212		Approved		uc001nmj.3	Q8NGQ5		ENST00000335397.3:c.642C>A	11.37:g.57947558C>A			57704134	Q2TAN3|Q96RA7	Silent	SNP	ENST00000335397.3	37	CCDS31543.1																																																																																				0.512	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212		A	57947558	C	A	57947558	2	1	61	1	0	0	0	0	0	0	0	1	11286	903	32	2		2	OR9Q1	11	57947558	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	378175	57947558	77058958	7376	15361										
OR1S1	219959	broad.mit.edu	37	chr11	57982522	57982522	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaatattcaaaccaagagTcaatccatctcttatgagag	7	8	3	3	rs367962921		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:57982522T>C	ENST00000309433.6	+	1	306	c.306T>C	c.(304-306)agT>agC	p.S102S		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S102S(4)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				AAACCAAGAGTCAATCCATCT	0.423													T|||	1	0.000199681	0	0	5008	,	,		22479	0.001		0	False		,,,				2504	0															4	Substitution - coding silent(4)	endometrium(3)|large_intestine(1)	11											206	197	200					11																	57982522		2201	4296	6497	57739098	SO:0001819	synonymous_variant	219959			BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"GPCR / Class A : Olfactory receptors"	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.306T>C	11.37:g.57982522T>C			57739098	Q6IFG3	Silent	SNP	ENST00000309433.6	37	CCDS31546.1																																																																																				0.423	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458		C	57982522	T	C	57982522	2	2	61	1	0	0	0	0	0	0	0	1	11003	1664	58	4		4	OR1S1	11	57982522	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34964	57982522	77023994	7377	15362										
OR5B3	441608	broad.mit.edu	37	chr11	58170314	58170314	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacaagctcgctaatatgtCtatcagagcaagagagaacc	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58170314C>A	ENST00000309403.2	-	1	568	c.569G>T	c.(568-570)aGa>aTa	p.R190I		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R190I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GCTAATATGTCTATCAGAGCA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	82	83					11																	58170314		2201	4295	6496	57926890	SO:0001583	missense	441608			AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"GPCR / Class A : Olfactory receptors"	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.569G>T	11.37:g.58170314C>A	ENSP00000308270:p.Arg190Ile		57926890	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	.	.	.	.	.	.	.	.	.	.	c	0.260	-1.000512	0.02128	.	.	ENSG00000172769	ENST00000309403	T	0.00058	8.79	4.05	-0.167	0.13347	GPCR, rhodopsin-like superfamily (1);	0.266449	0.26975	N	0.021547	T	0.00039	0.0001	N	0.00215	-1.835	0.09310	N	1	B	0.12013	0.005	B	0.18561	0.022	T	0.37549	-0.9701	10	0.34782	T	0.22	-8.5078	0.5215	0.00613	0.2586:0.2882:0.2496:0.2036	.	190	Q8NH48	OR5B3_HUMAN	I	190	ENSP00000308270:R190I	ENSP00000308270:R190I	R	-	2	0	OR5B3	57926890	0.000000	0.05858	0.004000	0.12327	0.148000	0.21650	-0.215000	0.09279	0.118000	0.18165	0.650000	0.86243	AGA		0.378	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469		A	58170314	C	A	58170314	3	1	61	1	0	0	0	0	1	0	0	0	11183	913	32	2	377	2	OR5B3	11	58170314	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187792	58170314	76836202	7378	15363										
OR5B12	390191	broad.mit.edu	37	chr11	58207141	58207141	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctacagaaggagagcctgaAagtgttcccagtatgaatgg	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58207141A>T	ENST00000302572.2	-	1	505	c.484T>A	c.(484-486)Ttc>Atc	p.F162I		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F162I(1)		large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GAGAGCCTGAAAGTGTTCCCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											126	117	120					11																	58207141		2201	4295	6496	57963717	SO:0001583	missense	390191			AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.484T>A	11.37:g.58207141A>T	ENSP00000306657:p.Phe162Ile		57963717	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.702377	0.48307	.	.	ENSG00000172362	ENST00000302572	T	0.00241	8.46	4.44	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000063	T	0.00328	0.0010	M	0.62154	1.92	0.09310	N	1	D	0.63046	0.992	P	0.62184	0.899	T	0.47045	-0.9147	10	0.87932	D	0	-28.1969	4.7075	0.12856	0.742:0.0:0.0896:0.1684	.	162	Q96R08	OR5BC_HUMAN	I	162	ENSP00000306657:F162I	ENSP00000306657:F162I	F	-	1	0	OR5B12	57963717	0.003000	0.15002	0.465000	0.27155	0.866000	0.49608	1.699000	0.37804	0.806000	0.34183	0.379000	0.24179	TTC		0.448	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		T	58207141	A	T	58207141	3	4	61	1	0	0	0	0	1	0	0	0	11179	14	1	5	464	5	OR5B12	11	58207141	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	36827	58207141	76799375	7379	15364										
OR5B12	390191	broad.mit.edu	37	chr11	58207353	58207353	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtggcacaagcattatatAatatgaatttgtctcctgtg	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58207353A>T	ENST00000302572.2	-	1	293	c.272T>A	c.(271-273)tTa>tAa	p.L91*		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L91*(1)		large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AGCATTATATAATATGAATTT	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											69	66	67					11																	58207353		2201	4295	6496	57963929	SO:0001587	stop_gained	390191			AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.272T>A	11.37:g.58207353A>T	ENSP00000306657:p.Leu91*		57963929	B2RNL2|Q6IEV5	Nonsense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	A	7.830	0.719602	0.15372	.	.	ENSG00000172362	ENST00000302572	.	.	.	4.75	2.82	0.32997	.	0.273813	0.26439	N	0.024378	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-15.2856	8.2311	0.31599	0.0847:0.0:0.7594:0.1558	.	.	.	.	X	91	.	ENSP00000306657:L91X	L	-	2	0	OR5B12	57963929	0.695000	0.27747	0.002000	0.10522	0.000000	0.00434	3.749000	0.55150	0.669000	0.31146	-0.468000	0.05107	TTA		0.448	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		T	58207353	A	T	58207353	4	4	61	1	0	0	0	0	0	1	0	0	11179	372	13	5	676	5	OR5B12	11	58207353	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	212	58207353	76799163	7380	15365										
OR5B21	219968	broad.mit.edu	37	chr11	58275056	58275056	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggaatgtcacagaagaAatgattaatctcattagaac	10	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58275056A>C	ENST00000360374.2	-	1	522	c.523T>G	c.(523-525)Ttc>Gtc	p.F175V		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F175V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TCACAGAAGAAATGATTAATC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	11											61	56	58					11																	58275056		2201	4295	6496	58031632	SO:0001583	missense	219968				CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.523T>G	11.37:g.58275056A>C	ENSP00000353537:p.Phe175Val		58031632		Missense_Mutation	SNP	ENST00000360374.2	37	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	A	15.05	2.717775	0.48622	.	.	ENSG00000198283	ENST00000360374	T	0.00350	7.98	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37857	U	0.001907	T	0.01061	0.0035	M	0.90814	3.15	0.28821	N	0.897676	D	0.89917	1.0	D	0.97110	1.0	T	0.20638	-1.0269	10	0.54805	T	0.06	-16.0353	14.3011	0.66352	1.0:0.0:0.0:0.0	.	175	A6NL26	OR5BL_HUMAN	V	175	ENSP00000353537:F175V	ENSP00000353537:F175V	F	-	1	0	OR5B21	58031632	0.080000	0.21391	0.746000	0.31095	0.674000	0.39518	2.440000	0.44855	2.248000	0.74166	0.533000	0.62120	TTC		0.493	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		C	58275056	A	C	58275056	3	2	61	1	0	0	0	0	1	0	0	0	11182	14	1	4	408	4	OR5B21	11	58275056	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	67703	58275056	76731460	7381	15366										
LPXN	9404	broad.mit.edu	37	chr11	58295000	58295000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccctgaaaatgcccttcGacaactgtgtcaggcagaaa	9	12	1	2	rs149511007		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58295000G>A	ENST00000395074.2	-	9	1176	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	LPXN_ENST00000528489.1_Missense_Mutation_p.S343L|LPXN_ENST00000528954.1_Missense_Mutation_p.S368L	NM_004811.2	NP_004802.1	O60711	LPXN_HUMAN	leupaxin	363	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell adhesion (GO:0007162)|protein complex assembly (GO:0006461)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|podosome (GO:0002102)	transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)	p.S363L(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				AATGCCCTTCGACAACTGTGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	LEU/SER,LEU/SER	0,4402		0,0,2201	101	89	93		1103,1088	4	1	11	dbSNP_134	93	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense	LPXN	NM_001143995.1,NM_004811.2	145,145	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	368/392,363/387	58295000	1,12991	2201	4295	6496	58051576	SO:0001583	missense	9404			AF062075	CCDS7969.1, CCDS53635.1	11q12.1	2013-09-20			ENSG00000110031	ENSG00000110031			14061	protein-coding gene	gene with protein product		605390				9565592	Standard	NM_004811		Approved	LDPL	uc001nmw.3	O60711	OTTHUMG00000167466	ENST00000395074.2:c.1088C>T	11.37:g.58295000G>A	ENSP00000378512:p.Ser363Leu		58051576	B2R8B4|B4DV71|Q53FW6|Q6FI07	Missense_Mutation	SNP	ENST00000395074.2	37	CCDS7969.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241584	0.79912	0.0	1.16E-4	ENSG00000110031	ENST00000528954;ENST00000395074	D;D	0.87809	-2.3;-2.3	6.03	3.95	0.45737	Zinc finger, LIM-type (4);	0.625127	0.17490	N	0.172369	D	0.82600	0.5072	L	0.56396	1.775	0.35584	D	0.806537	P;P;P	0.51057	0.941;0.938;0.933	B;B;B	0.40199	0.322;0.196;0.284	D	0.85805	0.1376	10	0.49607	T	0.09	.	9.4025	0.38442	0.0:0.1184:0.5723:0.3092	.	343;368;363	B7Z5P7;B4DV71;O60711	.;.;LPXN_HUMAN	L	368;363	ENSP00000431284:S368L;ENSP00000378512:S363L	ENSP00000378512:S363L	S	-	2	0	LPXN	58051576	0.885000	0.30320	0.972000	0.41901	0.989000	0.77384	3.365000	0.52335	2.868000	0.98415	0.557000	0.71058	TCG		0.498	LPXN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394709.1	NM_004811		A	58295000	G	A	58295000	3	1	61	1	0	0	0	0	1	0	0	0	8958	1059	37	1	76	1	LPXN	11	58295000	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19944	58295000	76711516	7382	15367										
ZFP91	80829	broad.mit.edu	37	chr11	58385068	58385068	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatggctgatgggaagatCtttgtgggaagcggcagcag	17	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58385068C>A	ENST00000316059.6	+	11	1773	c.1602C>A	c.(1600-1602)atC>atA	p.I534I	ZFP91-CNTF_ENST00000389919.4_Intron	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	534					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)	p.I534I(1)		cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				ATGGGAAGATCTTTGTGGGAA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	11											92	87	89					11																	58385068		2201	4295	6496	58141644	SO:0001819	synonymous_variant	80829			AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1602C>A	11.37:g.58385068C>A			58141644	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Silent	SNP	ENST00000316059.6	37	CCDS31553.1																																																																																				0.512	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		A	58385068	C	A	58385068	2	1	61	1	0	0	0	0	0	0	0	1	17694	903	32	2		2	ZFP91	11	58385068	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90068	58385068	76621448	7383	15368										
GLYATL2	219970	broad.mit.edu	37	chr11	58604538	58604538	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttgtcattacttgaggtCttgtgtttctttggtaattc	8	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58604538C>A	ENST00000287275.1	-	5	816	c.426G>T	c.(424-426)aaG>aaT	p.K142N	GLYATL2_ENST00000533636.1_5'UTR|GLYATL2_ENST00000532258.1_Missense_Mutation_p.K142N	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	142						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.K142N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	TACTTGAGGTCTTGTGTTTCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											188	172	177					11																	58604538		1894	4116	6010	58361114	SO:0001583	missense	219970			AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.426G>T	11.37:g.58604538C>A	ENSP00000287275:p.Lys142Asn		58361114	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	37	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	C	0.078	-1.189633	0.01607	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.19532	2.14;2.14	1.61	-0.508	0.11980	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	1.396910	0.04800	N	0.433361	T	0.11067	0.0270	N	0.16790	0.44	0.09310	N	1	B	0.25272	0.122	B	0.15870	0.014	T	0.25950	-1.0117	10	0.27082	T	0.32	.	3.0687	0.06222	0.0:0.5241:0.285:0.1909	.	142	Q8WU03	GLYL2_HUMAN	N	142	ENSP00000287275:K142N;ENSP00000434277:K142N	ENSP00000287275:K142N	K	-	3	2	GLYATL2	58361114	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	-0.268000	0.08607	-0.114000	0.11936	-1.006000	0.02489	AAG		0.358	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016		A	58604538	C	A	58604538	3	1	61	1	0	0	0	0	1	0	0	0	6501	912	32	2	466	2	GLYATL2	11	58604538	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219470	58604538	76401978	7384	15369										
GLYATL1	92292	broad.mit.edu	37	chr11	58722327	58722327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcagaagaagttttgaaaAattgtgagatcgtaaactgg	10	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58722327A>G	ENST00000317391.4	+	6	611	c.271A>G	c.(271-273)Aat>Gat	p.N91D	GLYATL1_ENST00000300079.5_Missense_Mutation_p.N122D|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	91						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)	p.N122D(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	AGTTTTGAAAAATTGTGAGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	77	78					11																	58722327		2201	4295	6496	58478903	SO:0001583	missense	92292			AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.271A>G	11.37:g.58722327A>G	ENSP00000322223:p.Asn91Asp		58478903	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	37	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	5.247	0.231123	0.09969	.	.	ENSG00000166840	ENST00000526351;ENST00000444580;ENST00000317391;ENST00000300079	T;T;T	0.13778	2.56;2.56;2.56	2.37	-4.73	0.03259	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	1.167940	0.06758	U	0.781200	T	0.08670	0.0215	N	0.25647	0.755	0.09310	N	1	P;P	0.50710	0.938;0.862	B;P	0.45474	0.444;0.482	T	0.10314	-1.0635	10	0.15952	T	0.53	.	4.4696	0.11706	0.218:0.0:0.1362:0.6458	.	122;91	Q969I3-2;Q969I3	.;GLYL1_HUMAN	D	114;68;91;122	ENSP00000434652:N114D;ENSP00000322223:N91D;ENSP00000300079:N122D	ENSP00000300079:N122D	N	+	1	0	GLYATL1	58478903	0.000000	0.05858	0.000000	0.03702	0.177000	0.22998	-1.617000	0.02051	-1.786000	0.01269	0.164000	0.16699	AAT		0.383	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		G	58722327	A	G	58722327	3	3	61	1	0	0	0	0	1	0	0	0	6500	14	1	4	382	4	GLYATL1	11	58722327	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	117789	58722327	76284189	7385	15370										
GLYATL1	92292	broad.mit.edu	37	chr11	58723383	58723383	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaatattccattttacatCtctgtgttggaagaaaatga	7	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58723383C>A	ENST00000317391.4	+	8	1132	c.792C>A	c.(790-792)atC>atA	p.I264I	GLYATL1_ENST00000300079.5_Silent_p.I295I|RP11-142C4.6_ENST00000533954.1_RNA|RP11-142C4.6_ENST00000525714.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	264						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)	p.I295I(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	CATTTTACATCTCTGTGTTGG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11											72	69	70					11																	58723383		2201	4295	6496	58479959	SO:0001819	synonymous_variant	92292			AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.792C>A	11.37:g.58723383C>A			58479959	A6NDT0|Q7Z510|Q8NAW8	Silent	SNP	ENST00000317391.4	37	CCDS55768.1																																																																																				0.468	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		A	58723383	C	A	58723383	2	1	61	1	0	0	0	0	0	0	0	1	6500	903	32	2		2	GLYATL1	11	58723383	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1056	58723383	76283133	7386	15371										
FAM111B	374393	broad.mit.edu	37	chr11	58891794	58891794	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcagaatccaaatttgaAcaataaagaatgttgtttca	6	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58891794A>C	ENST00000343597.3	+	4	415	c.224A>C	c.(223-225)aAc>aCc	p.N75T	FAM111B_ENST00000411426.1_Missense_Mutation_p.N45T|FAM111B_ENST00000529618.1_Missense_Mutation_p.N45T	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	75							catalytic activity (GO:0003824)	p.N75T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						CCAAATTTGAACAATAAAGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											120	113	115					11																	58891794		2201	4295	6496	58648370	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.224A>C	11.37:g.58891794A>C	ENSP00000341565:p.Asn75Thr		58648370	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	A	0.030	-1.341824	0.01277	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000534403;ENST00000343597	T;T;T	0.30981	1.52;1.52;1.51	2.75	-0.896	0.10557	.	1.277380	0.06005	N	0.648489	T	0.12732	0.0309	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.26360	-1.0105	10	0.10902	T	0.67	.	4.0486	0.09785	0.3521:0.2164:0.4314:0.0	.	75	Q6SJ93	F111B_HUMAN	T	45;45;45;75	ENSP00000393855:N45T;ENSP00000432875:N45T;ENSP00000341565:N75T	ENSP00000341565:N75T	N	+	2	0	FAM111B	58648370	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.863000	0.04259	-0.159000	0.11021	-0.256000	0.11100	AAC		0.378	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		C	58891794	A	C	58891794	3	2	61	1	0	0	0	0	1	0	0	0	5416	43	2	4	230	4	FAM111B	11	58891794	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	168411	58891794	76114722	7387	15372										
FAM111B	374393	broad.mit.edu	37	chr11	58892158	58892158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctataggaaggacaagaaaGaagattgttaagatcaacga	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58892158G>T	ENST00000343597.3	+	4	779	c.588G>T	c.(586-588)aaG>aaT	p.K196N	FAM111B_ENST00000411426.1_Missense_Mutation_p.K166N|FAM111B_ENST00000529618.1_Missense_Mutation_p.K166N	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	196							catalytic activity (GO:0003824)	p.K196N(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						GGACAAGAAAGAAGATTGTTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											106	102	103					11																	58892158		2201	4294	6495	58648734	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.588G>T	11.37:g.58892158G>T	ENSP00000341565:p.Lys196Asn		58648734	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752686	0.49362	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	T;T;T	0.37235	1.23;1.23;1.21	4.52	0.00148	0.14046	.	0.331184	0.21983	U	0.066267	T	0.44787	0.1310	M	0.70275	2.135	0.09310	N	1	D	0.62365	0.991	P	0.58013	0.831	T	0.30001	-0.9993	10	0.87932	D	0	.	3.8874	0.09103	0.5571:0.0:0.26:0.183	.	196	Q6SJ93	F111B_HUMAN	N	166;166;196	ENSP00000393855:K166N;ENSP00000432875:K166N;ENSP00000341565:K196N	ENSP00000341565:K196N	K	+	3	2	FAM111B	58648734	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.481000	0.06552	0.121000	0.18284	0.655000	0.94253	AAG		0.373	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		T	58892158	G	T	58892158	3	4	61	1	0	0	0	0	1	0	0	0	5416	933	33	2	594	2	FAM111B	11	58892158	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	364	58892158	76114358	7388	15373										
FAM111B	374393	broad.mit.edu	37	chr11	58892819	58892819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgggtaagaaaatattttCgggaagaacaaaagagaatg	12	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58892819C>T	ENST00000343597.3	+	4	1440	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	FAM111B_ENST00000411426.1_Missense_Mutation_p.R387W|FAM111B_ENST00000529618.1_Missense_Mutation_p.R387W	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	417							catalytic activity (GO:0003824)	p.R417W(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						AAAATATTTTCGGGAAGAACA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	11											64	69	68					11																	58892819		2200	4294	6494	58649395	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1249C>T	11.37:g.58892819C>T	ENSP00000341565:p.Arg417Trp		58649395	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.529875	0.27387	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	T;T;T	0.33216	1.42;1.42;1.42	3.85	-4.95	0.03048	.	1.340670	0.05675	N	0.589333	T	0.18173	0.0436	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38222	-0.9671	10	0.72032	D	0.01	.	5.8326	0.18588	0.5503:0.2761:0.0:0.1736	.	417	Q6SJ93	F111B_HUMAN	W	387;387;417	ENSP00000393855:R387W;ENSP00000432875:R387W;ENSP00000341565:R417W	ENSP00000341565:R417W	R	+	1	2	FAM111B	58649395	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.625000	0.02036	-0.669000	0.05289	-0.894000	0.02916	CGG		0.343	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		T	58892819	C	T	58892819	3	4	61	1	0	0	0	0	1	0	0	0	5416	875	31	1	1255	1	FAM111B	11	58892819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	661	58892819	76113697	7389	15374										
FAM111B	374393	broad.mit.edu	37	chr11	58893108	58893108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatataattagcaaatgtgCgaaggtaaccttcacttata	7	6	1	1	rs139496218		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58893108C>T	ENST00000343597.3	+	4	1729	c.1538C>T	c.(1537-1539)gCg>gTg	p.A513V	FAM111B_ENST00000411426.1_Missense_Mutation_p.A483V|FAM111B_ENST00000529618.1_Missense_Mutation_p.A483V	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	513							catalytic activity (GO:0003824)	p.A513V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						AGCAAATGTGCGAAGGTAACC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	VAL/ALA,VAL/ALA,VAL/ALA	0,4402		0,0,2201	105	101	102		1448,1448,1538	-2.3	0	11	dbSNP_134	102	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense,missense	FAM111B	NM_001142703.1,NM_001142704.1,NM_198947.3	64,64,64	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	483/705,483/705,513/735	58893108	1,12989	2201	4294	6495	58649684	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1538C>T	11.37:g.58893108C>T	ENSP00000341565:p.Ala513Val		58649684	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	4.837	0.155598	0.09236	0.0	1.16E-4	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	D;D;D	0.88586	-2.4;-2.4;-2.4	4.63	-2.27	0.06846	Peptidase cysteine/serine, trypsin-like (1);	0.579805	0.15421	N	0.263247	T	0.63663	0.2530	N	0.04636	-0.2	0.09310	N	1	P	0.36647	0.563	B	0.31751	0.135	T	0.67581	-0.5634	10	0.02654	T	1	.	4.7182	0.12904	0.1419:0.4201:0.0:0.438	.	513	Q6SJ93	F111B_HUMAN	V	483;483;513	ENSP00000393855:A483V;ENSP00000432875:A483V;ENSP00000341565:A513V	ENSP00000341565:A513V	A	+	2	0	FAM111B	58649684	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	-0.128000	0.10531	-0.273000	0.09246	-0.150000	0.13652	GCG		0.393	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		T	58893108	C	T	58893108	3	4	61	1	0	0	0	0	1	0	0	0	5416	768	27	1	1544	1	FAM111B	11	58893108	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	289	58893108	76113408	7390	15375										
FAM111B	374393	broad.mit.edu	37	chr11	58893641	58893641	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttattctatggattctattCtttgtgatattaaaaagaca	6	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58893641C>A	ENST00000343597.3	+	4	2262	c.2071C>A	c.(2071-2073)Ctt>Att	p.L691I	FAM111B_ENST00000411426.1_Missense_Mutation_p.L661I|FAM111B_ENST00000529618.1_Missense_Mutation_p.L661I	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	691							catalytic activity (GO:0003824)	p.L691I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						GGATTCTATTCTTTGTGATAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											83	84	83					11																	58893641		2201	4295	6496	58650217	SO:0001583	missense	374393			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.2071C>A	11.37:g.58893641C>A	ENSP00000341565:p.Leu691Ile		58650217	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	37	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	9.047	0.991149	0.18966	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	T;T;T	0.36340	1.26;1.26;1.26	4.36	1.27	0.21489	Peptidase cysteine/serine, trypsin-like (1);	0.433027	0.17855	N	0.159729	T	0.33847	0.0877	L	0.61387	1.9	0.09310	N	1	P	0.41673	0.759	B	0.40565	0.333	T	0.16600	-1.0397	10	0.59425	D	0.04	.	8.2939	0.31973	0.2981:0.5522:0.1497:0.0	.	691	Q6SJ93	F111B_HUMAN	I	661;661;691	ENSP00000393855:L661I;ENSP00000432875:L661I;ENSP00000341565:L691I	ENSP00000341565:L691I	L	+	1	0	FAM111B	58650217	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.922000	0.04004	0.167000	0.19631	0.650000	0.86243	CTT		0.333	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		A	58893641	C	A	58893641	3	1	61	1	0	0	0	0	1	0	0	0	5416	913	32	2	2077	2	FAM111B	11	58893641	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	533	58893641	76112875	7391	15376										
FAM111A	63901	broad.mit.edu	37	chr11	58919840	58919840	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatggcagatttctttcCtttctggagaatgatgattg	11	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58919840C>A	ENST00000528737.1	+	5	3517	c.699C>A	c.(697-699)tcC>tcA	p.S233S	FAM111A_ENST00000533703.1_Silent_p.S233S|FAM111A_ENST00000420244.1_Silent_p.S233S|FAM111A_ENST00000531147.1_Silent_p.S233S|FAM111A_ENST00000361723.3_Silent_p.S233S			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	233					defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.S233S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				GATTTCTTTCCTTTCTGGAGA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	11											120	120	120					11																	58919840		2201	4295	6496	58676416	SO:0001819	synonymous_variant	63901			AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.699C>A	11.37:g.58919840C>A			58676416	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Silent	SNP	ENST00000528737.1	37	CCDS7973.1																																																																																				0.413	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		A	58919840	C	A	58919840	2	1	61	1	0	0	0	0	0	0	0	1	5415	668	24	2		2	FAM111A	11	58919840	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26199	58919840	76086676	7392	15377										
FAM111A	63901	broad.mit.edu	37	chr11	58920755	58920755	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgacactgaatttttcttTggggcttccggctcccctgt	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:58920755T>C	ENST00000528737.1	+	5	4432	c.1614T>C	c.(1612-1614)ttT>ttC	p.F538F	FAM111A_ENST00000533703.1_Silent_p.F538F|FAM111A_ENST00000420244.1_Silent_p.F538F|FAM111A_ENST00000531147.1_Silent_p.F538F|FAM111A_ENST00000361723.3_Silent_p.F538F			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	538	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.F538F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				AATTTTTCTTTGGGGCTTCCG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	11											98	104	102					11																	58920755		2201	4295	6496	58677331	SO:0001819	synonymous_variant	63901			AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1614T>C	11.37:g.58920755T>C			58677331	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Silent	SNP	ENST00000528737.1	37	CCDS7973.1																																																																																				0.413	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		C	58920755	T	C	58920755	2	2	61	1	0	0	0	0	0	0	0	1	5415	1809	63	4		4	FAM111A	11	58920755	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	915	58920755	76085761	7393	15378										
OR4D6	219983	broad.mit.edu	37	chr11	59224526	59224526	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcttgtttgtggtcttCtttgctgtgtatgtagcaac	9	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59224526C>A	ENST00000300127.2	+	1	116	c.93C>A	c.(91-93)ttC>ttA	p.F31L		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F31L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						TTGTGGTCTTCTTTGCTGTGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											244	223	230					11																	59224526		2201	4295	6496	58981102	SO:0001583	missense	219983			AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"GPCR / Class A : Olfactory receptors"	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.93C>A	11.37:g.59224526C>A	ENSP00000300127:p.Phe31Leu		58981102	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.493590	0.26774	.	.	ENSG00000166884	ENST00000300127	T	0.04454	3.62	5.9	1.79	0.24919	.	0.000000	0.56097	D	0.000033	T	0.04724	0.0128	L	0.47716	1.5	0.09310	N	0.999997	B	0.13145	0.007	B	0.15484	0.013	T	0.35822	-0.9773	10	0.41790	T	0.15	-23.6324	5.8416	0.18637	0.2694:0.5785:0.0:0.1521	.	31	Q8NGJ1	OR4D6_HUMAN	L	31	ENSP00000300127:F31L	ENSP00000300127:F31L	F	+	3	2	OR4D6	58981102	0.000000	0.05858	0.065000	0.19835	0.943000	0.58893	-1.199000	0.03032	0.068000	0.16574	0.655000	0.94253	TTC		0.468	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708		A	59224526	C	A	59224526	3	1	61	1	0	0	0	0	1	0	0	0	11089	912	32	2	95	2	OR4D6	11	59224526	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	303771	59224526	75781990	7394	15379										
OR4D10	390197	broad.mit.edu	37	chr11	59244933	59244933	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaactgcaccagggtaaaaGaatttattttccttggcctg	8	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59244933G>T	ENST00000530162.1	+	1	88	c.31G>T	c.(31-33)Gaa>Taa	p.E11*		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E9*(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CAGGGTAAAAGAATTTATTTT	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											68	68	68					11																	59244933		1918	4127	6045	59001509	SO:0001587	stop_gained	390197			AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"GPCR / Class A : Olfactory receptors"	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.31G>T	11.37:g.59244933G>T	ENSP00000436424:p.Glu11*		59001509	B2RNH6	Nonsense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605045	0.66445	.	.	ENSG00000254466	ENST00000530162	.	.	.	4.02	3.1	0.35709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	10.5802	0.45250	0.0985:0.0:0.9015:0.0	.	.	.	.	X	11	.	ENSP00000436424:E11X	E	+	1	0	OR4D10	59001509	1.000000	0.71417	0.071000	0.20095	0.050000	0.14768	4.272000	0.58908	0.782000	0.33613	0.655000	0.94253	GAA		0.388	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705		T	59244933	G	T	59244933	4	4	61	1	0	0	0	0	0	1	0	0	11085	943	33	2	33	2	OR4D10	11	59244933	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20407	59244933	75761583	7395	15380										
OR4D10	390197	broad.mit.edu	37	chr11	59245240	59245240	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattggaggggtggatgtatTttctctttcggtgatggcat	14	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59245240T>G	ENST00000530162.1	+	1	395	c.338T>G	c.(337-339)tTt>tGt	p.F113C		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F111C(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTGGATGTATTTTCTCTTTCG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											81	83	83					11																	59245240		2164	4280	6444	59001816	SO:0001583	missense	390197			AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"GPCR / Class A : Olfactory receptors"	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.338T>G	11.37:g.59245240T>G	ENSP00000436424:p.Phe113Cys		59001816	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	T	5.241	0.229970	0.09969	.	.	ENSG00000254466	ENST00000530162	T	0.06449	3.3	4.4	-1.05	0.10036	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.06826	0.0174	L	0.56340	1.77	0.09310	N	1	B	0.21905	0.062	B	0.30316	0.114	T	0.43925	-0.9361	9	0.66056	D	0.02	.	1.5171	0.02508	0.1395:0.1644:0.1448:0.5513	.	113	Q8NGI6	OR4DA_HUMAN	C	113	ENSP00000436424:F113C	ENSP00000436424:F113C	F	+	2	0	OR4D10	59001816	0.000000	0.05858	0.006000	0.13384	0.032000	0.12392	0.557000	0.23454	-0.431000	0.07307	0.533000	0.62120	TTT		0.463	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705		G	59245240	T	G	59245240	3	3	61	1	0	0	0	0	1	0	0	0	11085	1841	64	4	340	4	OR4D10	11	59245240	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	307	59245240	75761276	7396	15381										
OR4D11	219986	broad.mit.edu	37	chr11	59271355	59271355	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcatgacacagatatttCtcttccacctccttggtggg	9	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59271355C>A	ENST00000313253.1	+	1	307	c.307C>A	c.(307-309)Ctc>Atc	p.L103I		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L103I(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						ACAGATATTTCTCTTCCACCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											186	175	179					11																	59271355		2201	4295	6496	59027931	SO:0001583	missense	219986			AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"GPCR / Class A : Olfactory receptors"	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.307C>A	11.37:g.59271355C>A	ENSP00000320077:p.Leu103Ile		59027931		Missense_Mutation	SNP	ENST00000313253.1	37	CCDS31563.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.727901	0.30593	.	.	ENSG00000176200	ENST00000313253	T	0.00406	7.55	5.44	3.11	0.35812	GPCR, rhodopsin-like superfamily (1);	0.243896	0.29165	N	0.012946	T	0.00241	0.0007	N	0.16862	0.45	0.21950	N	0.999456	B	0.15930	0.015	B	0.23150	0.044	T	0.41610	-0.9499	10	0.36615	T	0.2	-47.4943	4.3623	0.11208	0.0:0.1943:0.168:0.6377	.	103	Q8NGI4	OR4DB_HUMAN	I	103	ENSP00000320077:L103I	ENSP00000320077:L103I	L	+	1	0	OR4D11	59027931	0.000000	0.05858	0.974000	0.42286	0.988000	0.76386	0.064000	0.14437	0.368000	0.24481	-0.484000	0.04775	CTC		0.468	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706		A	59271355	C	A	59271355	3	1	61	1	0	0	0	0	1	0	0	0	11086	913	32	2	309	2	OR4D11	11	59271355	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26115	59271355	75735161	7397	15382										
OR4D9	390199	broad.mit.edu	37	chr11	59282396	59282396	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgattcaatggatcagaGaaattacaccagagtgaaag	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59282396G>A	ENST00000329328.3	+	1	11	c.11G>A	c.(10-12)aGa>aAa	p.R4K		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R4K(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						ATGGATCAGAGAAATTACACC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											85	84	84					11																	59282396		2201	4294	6495	59038972	SO:0001583	missense	390199			AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"GPCR / Class A : Olfactory receptors"	15178	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily D, member 9 pseudogene"				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.11G>A	11.37:g.59282396G>A	ENSP00000328563:p.Arg4Lys		59038972	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	.	.	.	.	.	.	.	.	.	.	G	0.046	-1.267075	0.01433	.	.	ENSG00000172742	ENST00000329328	T	0.00253	8.43	3.76	2.84	0.33178	.	1.671880	0.04014	U	0.298698	T	0.00109	0.0003	N	0.13299	0.325	0.19945	N	0.999942	B	0.02656	0.0	B	0.01281	0.0	T	0.38222	-0.9671	10	0.07813	T	0.8	.	6.2286	0.20722	0.3214:0.0:0.6786:0.0	.	4	Q8NGE8	OR4D9_HUMAN	K	4	ENSP00000328563:R4K	ENSP00000328563:R4K	R	+	2	0	OR4D9	59038972	0.016000	0.18221	0.599000	0.28851	0.314000	0.28054	0.724000	0.25954	0.681000	0.31386	-0.189000	0.12847	AGA		0.373	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		A	59282396	G	A	59282396	3	1	61	1	0	0	0	0	1	0	0	0	11090	942	33	3	13	3	OR4D9	11	59282396	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11041	59282396	75724120	7398	15383										
STX3	6809	broad.mit.edu	37	chr11	59560961	59560961	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcacgacatgtttatgGacatcgccatgctggtggag	12	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59560961G>T	ENST00000337979.4	+	8	1196	c.649G>T	c.(649-651)Gac>Tac	p.D217Y	STX3_ENST00000437946.2_Missense_Mutation_p.D120Y|STX3_ENST00000300150.7_Missense_Mutation_p.D186Y|STX3_ENST00000529177.1_Missense_Mutation_p.D217Y|STX3_ENST00000535361.1_Missense_Mutation_p.D217Y	NM_001178040.1|NM_004177.4	NP_001171511.1|NP_004168.1	Q13277	STX3_HUMAN	syntaxin 3	217	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|long-term synaptic potentiation (GO:0060291)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|neurotransmitter transport (GO:0006836)	apical plasma membrane (GO:0016324)|azurophil granule (GO:0042582)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|vacuole (GO:0005773)	arachidonic acid binding (GO:0050544)	p.D217Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|skin(1)	13						CATGTTTATGGACATCGCCAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											130	105	113					11																	59560961		2201	4295	6496	59317537	SO:0001583	missense	6809			AJ002076	CCDS7975.1, CCDS53637.1	11q12.1	2008-02-05	2006-04-25	2006-04-25	ENSG00000166900	ENSG00000166900			11438	protein-coding gene	gene with protein product		600876	"syntaxin 3A"	STX3A		16598260, 16339081	Standard	NM_004177		Approved		uc001nog.3	Q13277	OTTHUMG00000167353	ENST00000337979.4:c.649G>T	11.37:g.59560961G>T	ENSP00000338562:p.Asp217Tyr		59317537	B4DME0|O43750|O43751|Q15360	Missense_Mutation	SNP	ENST00000337979.4	37	CCDS7975.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993773	0.74703	.	.	ENSG00000166900	ENST00000300150;ENST00000337979;ENST00000535361;ENST00000437946;ENST00000529177;ENST00000528805;ENST00000530221	T;T;T;T;T;T;T	0.35421	1.44;1.44;1.44;1.44;1.44;1.44;1.31	5.34	4.43	0.53597	t-SNARE (1);Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.086033	0.85682	D	0.000000	T	0.68522	0.3010	H	0.95504	3.68	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	T	0.74657	-0.3592	10	0.33940	T	0.23	-2.3346	12.528	0.56098	0.0815:0.0:0.9185:0.0	.	120;217;217;217	E7ET77;B4DME0;Q13277-2;Q13277	.;.;.;STX3_HUMAN	Y	186;217;217;120;217;169;4	ENSP00000300150:D186Y;ENSP00000338562:D217Y;ENSP00000441649:D217Y;ENSP00000393536:D120Y;ENSP00000433248:D217Y;ENSP00000431386:D169Y;ENSP00000434836:D4Y	ENSP00000300150:D186Y	D	+	1	0	STX3	59317537	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	9.273000	0.95719	1.229000	0.43630	0.650000	0.86243	GAC		0.537	STX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394264.1	NM_004177		T	59560961	G	T	59560961	3	4	61	1	0	0	0	0	1	0	0	0	15385	1174	41	2	679	2	STX3	11	59560961	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	278565	59560961	75445555	7399	15384										
GIF	2694	broad.mit.edu	37	chr11	59599178	59599178	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggtgttacaccactaaGaaactgccagtatgtcttgt	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59599178G>T	ENST00000257248.2	-	8	1212	c.1165C>A	c.(1165-1167)Ctt>Att	p.L389I	GIF_ENST00000541311.1_Missense_Mutation_p.L364I	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	389	Cobalamin binding.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)	p.L389I(1)		large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	ACACCACTAAGAAACTGCCAG	0.358																																					NSCLC(53;1139 1245 16872 38474 42853)											1	Substitution - Missense(1)	large_intestine(1)	11											117	106	110					11																	59599178		2201	4295	6496	59355754	SO:0001583	missense	2694			X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.1165C>A	11.37:g.59599178G>T	ENSP00000257248:p.Leu389Ile		59355754	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	CCDS7977.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167494	0.78339	.	.	ENSG00000134812	ENST00000257248;ENST00000541311	T;T	0.52057	0.79;0.68	5.41	5.41	0.78517	.	0.108239	0.40385	N	0.001112	T	0.56615	0.1997	M	0.79011	2.435	0.37681	D	0.923487	P	0.44946	0.846	P	0.46110	0.504	T	0.66460	-0.5918	10	0.52906	T	0.07	-13.1848	14.7112	0.69232	0.0:0.0:1.0:0.0	.	389	P27352	IF_HUMAN	I	389;364	ENSP00000257248:L389I;ENSP00000440427:L364I	ENSP00000257248:L389I	L	-	1	0	GIF	59355754	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	2.416000	0.44644	2.532000	0.85374	0.655000	0.94253	CTT		0.358	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		T	59599178	G	T	59599178	3	4	61	1	0	0	0	0	1	0	0	0	6396	942	33	2	96	2	GIF	11	59599178	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38217	59599178	75407338	7400	15385										
GIF	2694	broad.mit.edu	37	chr11	59610014	59610014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggcacagtgccaagatcGctagactgggcccatagaag	12	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59610014G>A	ENST00000257248.2	-	4	460	c.413C>T	c.(412-414)gCg>gTg	p.A138V	GIF_ENST00000541311.1_Missense_Mutation_p.A113V	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	138					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)	p.A138V(1)		large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	TGCCAAGATCGCTAGACTGGG	0.557																																					NSCLC(53;1139 1245 16872 38474 42853)											1	Substitution - Missense(1)	large_intestine(1)	11											92	78	83					11																	59610014		2201	4295	6496	59366590	SO:0001583	missense	2694			X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.413C>T	11.37:g.59610014G>A	ENSP00000257248:p.Ala138Val		59366590	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	CCDS7977.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.599931	0.87055	.	.	ENSG00000134812	ENST00000257248;ENST00000541311	T;T	0.37411	1.2;1.2	5.63	4.67	0.58626	.	0.181621	0.38663	N	0.001607	T	0.49881	0.1583	M	0.65975	2.015	0.39727	D	0.971558	D	0.76494	0.999	P	0.56648	0.803	T	0.48080	-0.9066	10	0.41790	T	0.15	-15.2944	13.1224	0.59334	0.0:0.161:0.8389:0.0	.	138	P27352	IF_HUMAN	V	138;113	ENSP00000257248:A138V;ENSP00000440427:A113V	ENSP00000257248:A138V	A	-	2	0	GIF	59366590	0.978000	0.34361	0.984000	0.44739	0.969000	0.65631	1.859000	0.39418	2.826000	0.97356	0.655000	0.94253	GCG		0.557	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		A	59610014	G	A	59610014	3	1	61	1	0	0	0	0	1	0	0	0	6396	1087	38	1	864	1	GIF	11	59610014	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10836	59610014	75396502	7401	15386										
TCN1	6947	broad.mit.edu	37	chr11	59626700	59626700	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccatttattagactcttCttcacacaggtcagagccag	7	12	4	2	rs200450074		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59626700C>A	ENST00000257264.3	-	5	701	c.597G>T	c.(595-597)aaG>aaT	p.K199N	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	199	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)	p.K199N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTAGACTCTTCTTCACACAGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											180	160	167					11																	59626700		2201	4295	6496	59383276	SO:0001583	missense	6947			J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"haptocorin", "haptocorrin"	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.597G>T	11.37:g.59626700C>A	ENSP00000257264:p.Lys199Asn		59383276	A8KAC5|Q8WV77	Missense_Mutation	SNP	ENST00000257264.3	37	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.545591	0.27652	.	.	ENSG00000134827	ENST00000257264	T	0.40476	1.03	4.92	-4.72	0.03269	.	0.904208	0.09325	N	0.817645	T	0.39911	0.1096	L	0.56769	1.78	0.09310	N	1	P	0.49307	0.922	P	0.49953	0.627	T	0.39210	-0.9625	10	0.19590	T	0.45	.	7.2377	0.26079	0.0:0.2845:0.4578:0.2577	.	199	P20061	TCO1_HUMAN	N	199	ENSP00000257264:K199N	ENSP00000257264:K199N	K	-	3	2	TCN1	59383276	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-1.482000	0.02320	-0.707000	0.05022	-1.954000	0.00483	AAG		0.428	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		A	59626700	C	A	59626700	3	1	61	1	0	0	0	0	1	0	0	0	15745	912	32	2	724	2	TCN1	11	59626700	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16686	59626700	75379816	7402	15387										
MS4A2	2206	broad.mit.edu	37	chr11	59857288	59857288	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaaaaagagcaggagttCctgggggtgagtgagcctcc	15	7	0	4	rs267603048		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59857288C>T	ENST00000278888.3	+	2	282	c.180C>T	c.(178-180)ttC>ttT	p.F60F		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	60					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.F60F(1)		endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	AGCAGGAGTTCCTGGGGGTGA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	11											64	63	63					11																	59857288		2201	4295	6496	59613864	SO:0001819	synonymous_variant	2206			M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.180C>T	11.37:g.59857288C>T			59613864	Q54A81	Silent	SNP	ENST00000278888.3	37	CCDS7980.1																																																																																				0.458	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59857288	C	T	59857288	2	4	61	1	0	0	0	0	0	0	0	1	9890	854	30	3		3	MS4A2	11	59857288	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230588	59857288	75149228	7403	15388										
MS4A2	2206	broad.mit.edu	37	chr11	59861518	59861518	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatctgtggagctggggaaGaactcaaaggaaacaaggta	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:59861518G>T	ENST00000278888.3	+	6	721	c.619G>T	c.(619-621)Gaa>Taa	p.E207*		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	207					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.E207*(1)		endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	AGCTGGGGAAGAACTCAAAGG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											106	95	99					11																	59861518		2201	4295	6496	59618094	SO:0001587	stop_gained	2206			M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.619G>T	11.37:g.59861518G>T	ENSP00000278888:p.Glu207*		59618094	Q54A81	Nonsense_Mutation	SNP	ENST00000278888.3	37	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.478973	0.26511	.	.	ENSG00000149534	ENST00000278888	.	.	.	4.32	-6.03	0.02185	.	1.713730	0.03534	N	0.222830	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	0.1268	1.0545	0.01587	0.1611:0.112:0.3391:0.3878	.	.	.	.	X	207	.	ENSP00000278888:E207X	E	+	1	0	MS4A2	59618094	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-2.207000	0.01230	-1.251000	0.02494	0.637000	0.83480	GAA		0.403	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59861518	G	T	59861518	4	4	61	1	0	0	0	0	0	1	0	0	9890	943	33	2	692	2	MS4A2	11	59861518	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4230	59861518	75144998	7404	15389										
MS4A4A	51338	broad.mit.edu	37	chr11	60064746	60064746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggcatctaatacttatgGaagtaaccctatttccgtgt	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60064746G>A	ENST00000337908.4	+	3	368	c.278G>A	c.(277-279)gGa>gAa	p.G93E	MS4A4A_ENST00000395016.3_Missense_Mutation_p.G74E|MS4A4A_ENST00000355131.3_Missense_Mutation_p.G74E|MS4A4A_ENST00000532114.1_Missense_Mutation_p.G93E	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	93						integral component of membrane (GO:0016021)		p.G74E(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						AATACTTATGGAAGTAACCCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											174	148	157					11																	60064746		2203	4300	6503	59821322	SO:0001583	missense	51338			AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"membrane-spanning 4-domains, subfamily A, member 4"	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.278G>A	11.37:g.60064746G>A	ENSP00000338648:p.Gly93Glu		59821322	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	37	CCDS7982.1	.	.	.	.	.	.	.	.	.	.	G	0.338	-0.951895	0.02285	.	.	ENSG00000110079	ENST00000532114;ENST00000337908;ENST00000355131;ENST00000395016	T;T;T;T	0.18657	2.2;3.1;3.12;3.12	4.07	-8.13	0.01073	.	3.721670	0.01263	N	0.009254	T	0.11665	0.0284	N	0.10945	0.07	0.09310	N	1	B;B	0.12013	0.002;0.005	B;B	0.14578	0.003;0.011	T	0.12041	-1.0563	10	0.29301	T	0.29	7.1007	13.1781	0.59639	0.7576:0.0:0.2424:0.0	.	93;93	Q96JQ5-2;Q96JQ5	.;M4A4A_HUMAN	E	93;93;74;74	ENSP00000434506:G93E;ENSP00000338648:G93E;ENSP00000347252:G74E;ENSP00000378462:G74E	ENSP00000338648:G93E	G	+	2	0	MS4A4A	59821322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.894000	0.01607	-1.970000	0.01003	-1.462000	0.01023	GGA		0.378	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			A	60064746	G	A	60064746	3	1	61	1	0	0	0	0	1	0	0	0	9892	1174	41	3	288	3	MS4A4A	11	60064746	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203228	60064746	74941770	7405	15390										
MS4A4A	51338	broad.mit.edu	37	chr11	60068514	60068514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaattgcagcaggaattaGaactacaaaaggcctggtga	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60068514G>T	ENST00000337908.4	+	4	461	c.371G>T	c.(370-372)aGa>aTa	p.R124I	MS4A4A_ENST00000395016.3_Missense_Mutation_p.R105I|MS4A4A_ENST00000355131.3_Missense_Mutation_p.R105I|MS4A4A_ENST00000532114.1_Missense_Mutation_p.R124I	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	124						integral component of membrane (GO:0016021)		p.R105I(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						GCAGGAATTAGAACTACAAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	74	74					11																	60068514		2203	4299	6502	59825090	SO:0001583	missense	51338			AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"membrane-spanning 4-domains, subfamily A, member 4"	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.371G>T	11.37:g.60068514G>T	ENSP00000338648:p.Arg124Ile		59825090	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	37	CCDS7982.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864444	0.51482	.	.	ENSG00000110079	ENST00000532114;ENST00000337908;ENST00000355131;ENST00000395016	T;T;T;T	0.02606	4.23;4.23;4.23;4.23	4.3	3.39	0.38822	.	1.316680	0.05234	N	0.510874	T	0.09905	0.0243	M	0.67953	2.075	0.39160	D	0.962398	D;P	0.55605	0.972;0.938	P;P	0.53549	0.729;0.726	T	0.06752	-1.0809	10	0.54805	T	0.06	-10.4007	8.3998	0.32579	0.1092:0.0:0.8908:0.0	.	124;124	Q96JQ5-2;Q96JQ5	.;M4A4A_HUMAN	I	124;124;105;105	ENSP00000434506:R124I;ENSP00000338648:R124I;ENSP00000347252:R105I;ENSP00000378462:R105I	ENSP00000338648:R124I	R	+	2	0	MS4A4A	59825090	0.119000	0.22226	0.771000	0.31576	0.831000	0.47069	0.086000	0.14935	1.172000	0.42781	0.467000	0.42956	AGA		0.313	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			T	60068514	G	T	60068514	3	4	61	1	0	0	0	0	1	0	0	0	9892	942	33	2	385	2	MS4A4A	11	60068514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3768	60068514	74938002	7406	15391										
MS4A14	84689	broad.mit.edu	37	chr11	60183576	60183576	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatgacatgacatcccaaGatatgcaatccctagatatg	6	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60183576G>T	ENST00000300187.6	+	5	1412	c.1135G>T	c.(1135-1137)Gat>Tat	p.D379Y	MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000395005.2_Missense_Mutation_p.D362Y|MS4A14_ENST00000531783.1_Missense_Mutation_p.D412Y|MS4A14_ENST00000531787.1_Missense_Mutation_p.D267Y	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	379						integral component of membrane (GO:0016021)		p.D379Y(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						gacatcccaagatatgcaatc	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											141	109	120					11																	60183576		2203	4300	6503	59940152	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1135G>T	11.37:g.60183576G>T	ENSP00000300187:p.Asp379Tyr		59940152	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	6.317	0.426653	0.11987	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.33865	1.39;2.63;1.4;2.97	2.97	-1.22	0.09494	.	4.068660	0.00639	N	0.000518	T	0.44350	0.1289	L	0.34521	1.04	0.09310	N	0.999998	D;D	0.67145	0.996;0.994	D;P	0.66847	0.947;0.885	T	0.28744	-1.0034	10	0.51188	T	0.08	0.0019	3.5797	0.07947	0.3819:0.2171:0.401:0.0	.	362;379	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	Y	267;379;362;412	ENSP00000437222:D267Y;ENSP00000300187:D379Y;ENSP00000378453:D362Y;ENSP00000433761:D412Y	ENSP00000300187:D379Y	D	+	1	0	MS4A14	59940152	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.874000	0.04210	-0.262000	0.09392	-0.300000	0.09419	GAT		0.458	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			T	60183576	G	T	60183576	3	4	61	1	0	0	0	0	1	0	0	0	9888	942	33	2	1153	2	MS4A14	11	60183576	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115062	60183576	74822940	7407	15392										
MS4A14	84689	broad.mit.edu	37	chr11	60183940	60183940	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccttgcaatacttaaggaGacattctttagacgtgcaag	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60183940G>T	ENST00000300187.6	+	5	1776	c.1499G>T	c.(1498-1500)aGa>aTa	p.R500I	MS4A14_ENST00000395005.2_Missense_Mutation_p.R483I|MS4A14_ENST00000531783.1_Missense_Mutation_p.R533I|MS4A14_ENST00000531787.1_Missense_Mutation_p.R388I	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	500	Gln-rich.					integral component of membrane (GO:0016021)		p.R500I(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						TACTTAAGGAGACATTCTTTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	91	90					11																	60183940		2203	4300	6503	59940516	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1499G>T	11.37:g.60183940G>T	ENSP00000300187:p.Arg500Ile		59940516	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	7.178	0.589052	0.13812	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.35605	1.3;2.49;1.3;2.85	2.66	-3.74	0.04385	.	6.479460	0.00166	N	0.000014	T	0.24928	0.0605	L	0.49126	1.545	0.09310	N	1	P;P	0.37548	0.599;0.464	B;B	0.20184	0.028;0.012	T	0.20207	-1.0282	10	0.40728	T	0.16	-0.0023	4.8077	0.13328	0.4644:0.3461:0.1895:0.0	.	483;500	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	I	388;500;483;533	ENSP00000437222:R388I;ENSP00000300187:R500I;ENSP00000378453:R483I;ENSP00000433761:R533I	ENSP00000300187:R500I	R	+	2	0	MS4A14	59940516	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.028000	0.13644	-0.808000	0.04387	-1.342000	0.01247	AGA		0.433	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			T	60183940	G	T	60183940	3	4	61	1	0	0	0	0	1	0	0	0	9888	942	33	2	1517	2	MS4A14	11	60183940	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	364	60183940	74822576	7408	15393										
MS4A5	64232	broad.mit.edu	37	chr11	60215195	60215195	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctttctcaattttggggtGccactcagaggattgtgatt	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60215195G>T	ENST00000300190.2	+	5	652	c.566G>T	c.(565-567)tGc>tTc	p.C189F		NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	189						integral component of membrane (GO:0016021)		p.C189F(1)		large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						ATTTTGGGGTGCCACTCAGAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											174	175	175					11																	60215195		2203	4300	6503	59971771	SO:0001583	missense	64232			AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.566G>T	11.37:g.60215195G>T	ENSP00000300190:p.Cys189Phe		59971771	Q9BZH1	Missense_Mutation	SNP	ENST00000300190.2	37	CCDS7987.1	.	.	.	.	.	.	.	.	.	.	G	0.032	-1.329983	0.01298	.	.	ENSG00000166930	ENST00000300190	T	0.03065	4.06	4.22	0.118	0.14667	.	0.100234	0.40640	U	0.001050	T	0.05044	0.0135	M	0.83012	2.62	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.35895	-0.9770	10	0.52906	T	0.07	2.7918	0.9163	0.01305	0.2117:0.1853:0.4121:0.1909	.	189	Q9H3V2	MS4A5_HUMAN	F	189	ENSP00000300190:C189F	ENSP00000300190:C189F	C	+	2	0	MS4A5	59971771	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.764000	0.04735	0.150000	0.19136	0.467000	0.42956	TGC		0.333	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1			T	60215195	G	T	60215195	3	4	61	1	0	0	0	0	1	0	0	0	9893	1319	46	2	584	2	MS4A5	11	60215195	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31255	60215195	74791321	7409	15394										
MS4A1	931	broad.mit.edu	37	chr11	60235878	60235878	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaagaagaaacagagacGaactttccagaacctcccca	8	11	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60235878G>A	ENST00000534668.1	+	7	1120	c.831G>A	c.(829-831)acG>acA	p.T277T	MS4A1_ENST00000345732.4_Silent_p.T277T|MS4A1_ENST00000389939.2_Silent_p.T277T|MS4A1_ENST00000532073.1_Silent_p.T264T|MS4A1_ENST00000528313.1_Silent_p.T110T	NM_152866.2	NP_690605.1	P11836	CD20_HUMAN	membrane-spanning 4-domains, subfamily A, member 1	277					B cell proliferation (GO:0042100)|humoral immune response (GO:0006959)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	MHC class II protein complex binding (GO:0023026)	p.T277T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24					Ibritumomab(DB00078)|Obinutuzumab(DB08935)|Rituximab(DB00073)|Tositumomab(DB00081)	AAACAGAGACGAACTTTCCAG	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	11											105	102	103					11																	60235878		2203	4300	6503	59992454	SO:0001819	synonymous_variant	931			M27394	CCDS31570.1	11q12-q13.1	2014-09-17				ENSG00000156738		"CD molecules"	7315	protein-coding gene	gene with protein product		112210		CD20		2448768	Standard	NM_152866		Approved	B1, Bp35, MS4A2	uc001npq.3	P11836		ENST00000534668.1:c.831G>A	11.37:g.60235878G>A			59992454	A6NMS4|B4DT24|P08984|Q13963	Silent	SNP	ENST00000534668.1	37	CCDS31570.1																																																																																				0.378	MS4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395402.1			A	60235878	G	A	60235878	2	1	61	1	0	0	0	0	0	0	0	1	9884	1045	37	1		1	MS4A1	11	60235878	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20683	60235878	74770638	7410	15395										
MS4A8B	83661	broad.mit.edu	37	chr11	60468341	60468341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcttggcagcatgaattCgatgacttcagcagttccgg	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60468341C>T	ENST00000300226.2	+	2	211	c.8C>T	c.(7-9)tCg>tTg	p.S3L		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	3						integral component of membrane (GO:0016021)		p.S3L(2)									AGCATGAATTCGATGACTTCA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	11											140	140	140					11																	60468341		2203	4300	6503	60224917	SO:0001583	missense	83661			AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"membrane-spanning 4-domains, subfamily A, member 8B"	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.8C>T	11.37:g.60468341C>T	ENSP00000300226:p.Ser3Leu		60224917	Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	37	CCDS7990.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.879347	0.33162	.	.	ENSG00000166959	ENST00000300226;ENST00000529752	T;T	0.16743	3.22;2.32	3.42	2.49	0.30216	.	1.016890	0.07937	N	0.978600	T	0.15003	0.0362	L	0.40543	1.245	0.09310	N	1	B;B	0.21452	0.056;0.015	B;B	0.12156	0.007;0.001	T	0.26883	-1.0090	10	0.59425	D	0.04	0.4409	6.9132	0.24346	0.0:0.8677:0.0:0.1323	.	3;3	E9PQE1;Q9BY19	.;M4A8B_HUMAN	L	3	ENSP00000300226:S3L;ENSP00000436857:S3L	ENSP00000300226:S3L	S	+	2	0	MS4A8B	60224917	0.001000	0.12720	0.015000	0.15790	0.052000	0.14988	1.420000	0.34804	0.775000	0.33450	-0.320000	0.08662	TCG		0.458	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			T	60468341	C	T	60468341	3	4	61	1	0	0	0	0	1	0	0	0	9897	893	31	1	10	1	MS4A8B	11	60468341	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	232463	60468341	74538175	7411	15396										
MS4A15	219995	broad.mit.edu	37	chr11	60541334	60541334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacaggggctatctggccGtgcttactatcttcactgtc	11	11	3	0	rs200402929		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60541334G>A	ENST00000405633.3	+	6	602	c.523G>A	c.(523-525)Gtg>Atg	p.V175M	MS4A15_ENST00000337911.4_Missense_Mutation_p.V82M|MS4A15_ENST00000528170.1_Missense_Mutation_p.V134M	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	175						integral component of membrane (GO:0016021)		p.V82M(1)		breast(1)|large_intestine(2)|lung(3)	6						CTATCTGGCCGTGCTTACTAT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	11											247	192	210					11																	60541334		2203	4300	6503	60297910	SO:0001583	missense	219995			AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.523G>A	11.37:g.60541334G>A	ENSP00000386022:p.Val175Met		60297910	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.913197	0.33815	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.19250	2.19;2.16;2.48	4.83	4.83	0.62350	.	0.132904	0.49305	D	0.000143	T	0.40196	0.1107	M	0.62016	1.91	0.37912	D	0.931418	D;D	0.89917	0.959;1.0	B;D	0.80764	0.362;0.994	T	0.27571	-1.0070	10	0.20519	T	0.43	-25.2779	13.4224	0.61005	0.0:0.0:1.0:0.0	.	134;175	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	M	134;82;175	ENSP00000434165:V134M;ENSP00000338692:V82M;ENSP00000386022:V175M	ENSP00000338692:V82M	V	+	1	0	MS4A15	60297910	0.960000	0.32886	0.981000	0.43875	0.074000	0.17049	1.506000	0.35747	2.243000	0.73865	0.555000	0.69702	GTG		0.577	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			A	60541334	G	A	60541334	3	1	61	1	0	0	0	0	1	0	0	0	9889	1145	40	1	541	1	MS4A15	11	60541334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72993	60541334	74465182	7412	15397										
MS4A15	219995	broad.mit.edu	37	chr11	60543093	60543093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcctgtgatcttcctgCcaaacgccttcagcgcagac	9	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60543093C>T	ENST00000405633.3	+	7	707	c.628C>T	c.(628-630)Cca>Tca	p.P210S	MS4A15_ENST00000337911.4_Missense_Mutation_p.P117S|MS4A15_ENST00000528170.1_Missense_Mutation_p.P169S	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	210						integral component of membrane (GO:0016021)		p.P117S(1)		breast(1)|large_intestine(2)|lung(3)	6						GATCTTCCTGCCAAACGCCTT	0.572											OREG0020991	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											148	150	150					11																	60543093		2203	4300	6503	60299669	SO:0001583	missense	219995			AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.628C>T	11.37:g.60543093C>T	ENSP00000386022:p.Pro210Ser	1046	60299669	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.173715	0.57692	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.27720	1.72;1.65;1.94	5.43	5.43	0.79202	.	1.137480	0.06514	N	0.738526	T	0.61615	0.2361	M	0.77103	2.36	0.39901	D	0.973894	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.46498	-0.9187	10	0.56958	D	0.05	-15.5389	14.7453	0.69485	0.0:1.0:0.0:0.0	.	169;210	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	S	169;117;210	ENSP00000434165:P169S;ENSP00000338692:P117S;ENSP00000386022:P210S	ENSP00000338692:P117S	P	+	1	0	MS4A15	60299669	1.000000	0.71417	0.993000	0.49108	0.251000	0.25915	3.656000	0.54467	2.538000	0.85594	0.643000	0.83706	CCA		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			T	60543093	C	T	60543093	3	4	61	1	0	0	0	0	1	0	0	0	9889	739	26	3	650	3	MS4A15	11	60543093	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1759	60543093	74463423	7413	15398										
MS4A10	341116	broad.mit.edu	37	chr11	60558512	60558512	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctggcctctatagtcaaGaaccttcacctggtggtgct	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60558512G>A	ENST00000308287.1	+	3	345	c.249G>A	c.(247-249)aaG>aaA	p.K83K		NM_206893.3	NP_996776.2	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member 10	83						integral component of membrane (GO:0016021)		p.K83K(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|skin(2)	21						CTATAGTCAAGAACCTTCACC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											136	134	135					11																	60558512		2203	4300	6503	60315088	SO:0001819	synonymous_variant	341116			AK122633	CCDS7992.1	11q12.2	2008-02-05				ENSG00000172689			13368	protein-coding gene	gene with protein product		608403				11486273, 11401424	Standard	NM_206893		Approved	CD20L7, MS4A9	uc001npz.1	Q96PG2		ENST00000308287.1:c.249G>A	11.37:g.60558512G>A			60315088	B2RP45|Q96PG3	Silent	SNP	ENST00000308287.1	37	CCDS7992.1																																																																																				0.582	MS4A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395619.1	NM_206893		A	60558512	G	A	60558512	2	1	61	1	0	0	0	0	0	0	0	1	9885	933	33	3		3	MS4A10	11	60558512	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15419	60558512	74448004	7414	15399										
CCDC86	79080	broad.mit.edu	37	chr11	60610023	60610023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggagttggcccagaataaGgaggagctgaccccgggggc	17	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60610023G>T	ENST00000227520.5	+	1	480	c.426G>T	c.(424-426)aaG>aaT	p.K142N	RP11-804A23.2_ENST00000539897.1_RNA|RP11-804A23.4_ENST00000538705.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	142	Pro-rich.				viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K142N(1)		endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						CCCAGAATAAGGAGGAGCTGA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											38	41	40					11																	60610023		2203	4298	6501	60366599	SO:0001583	missense	79080			AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.426G>T	11.37:g.60610023G>T	ENSP00000227520:p.Lys142Asn		60366599	B4DY99	Missense_Mutation	SNP	ENST00000227520.5	37	CCDS7993.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.941479	0.53079	.	.	ENSG00000110104	ENST00000227520;ENST00000339492	T	0.52754	0.65	3.71	-2.41	0.06562	.	0.789446	0.11341	N	0.574012	T	0.31949	0.0813	L	0.60455	1.87	0.09310	N	0.999999	P	0.36535	0.557	B	0.32864	0.154	T	0.17684	-1.0361	10	0.28530	T	0.3	-4.0133	1.6851	0.02840	0.2871:0.1397:0.4314:0.1418	.	142	Q9H6F5	CCD86_HUMAN	N	142;106	ENSP00000227520:K142N	ENSP00000227520:K142N	K	+	3	2	CCDC86	60366599	0.002000	0.14202	0.002000	0.10522	0.037000	0.13140	-0.642000	0.05427	-0.239000	0.09710	0.561000	0.74099	AAG		0.637	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098		T	60610023	G	T	60610023	3	4	61	1	0	0	0	0	1	0	0	0	2867	991	35	2	428	2	CCDC86	11	60610023	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51511	60610023	74396493	7415	15400										
ZP1	22917	broad.mit.edu	37	chr11	60635212	60635212	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccaggccaggccagactCtccgcttcaaggtggtgggt	13	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60635212C>T	ENST00000278853.5	+	1	178	c.178C>T	c.(178-180)Ctc>Ttc	p.L60F		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	60					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)		p.L60F(1)		breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						AGGCCAGACTCTCCGCTTCAA	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	11											67	48	54					11																	60635212		2203	4299	6502	60391788	SO:0001583	missense	22917			BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.178C>T	11.37:g.60635212C>T	ENSP00000278853:p.Leu60Phe		60391788		Missense_Mutation	SNP	ENST00000278853.5	37	CCDS31572.1	.	.	.	.	.	.	.	.	.	.	C	4.562	0.104372	0.08731	.	.	ENSG00000149506	ENST00000278853	T	0.23147	1.92	3.71	-7.43	0.01383	.	1.391850	0.05101	N	0.487031	T	0.06554	0.0168	N	0.02539	-0.55	0.09310	N	0.999999	B	0.29432	0.244	B	0.26310	0.068	T	0.19128	-1.0315	10	0.09843	T	0.71	-3.5511	2.7148	0.05184	0.4574:0.1145:0.3157:0.1125	.	60	P60852	ZP1_HUMAN	F	60	ENSP00000278853:L60F	ENSP00000278853:L60F	L	+	1	0	ZP1	60391788	0.000000	0.05858	0.003000	0.11579	0.173000	0.22820	-1.206000	0.03011	-1.785000	0.01271	-1.498000	0.00962	CTC		0.677	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		T	60635212	C	T	60635212	3	4	61	1	0	0	0	0	1	0	0	0	18254	913	32	3	180	3	ZP1	11	60635212	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25189	60635212	74371304	7416	15401										
ZP1	22917	broad.mit.edu	37	chr11	60638578	60638578	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacggaagctttcgtggtCttctacttccctctcaccca	6	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60638578C>A	ENST00000278853.5	+	5	975	c.975C>A	c.(973-975)gtC>gtA	p.V325V		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	325	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)		p.V325V(1)		breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CTTTCGTGGTCTTCTACTTCC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	11											106	95	99					11																	60638578		2203	4299	6502	60395154	SO:0001819	synonymous_variant	22917			BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.975C>A	11.37:g.60638578C>A			60395154		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																				0.597	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		A	60638578	C	A	60638578	2	1	61	1	0	0	0	0	0	0	0	1	18254	900	32	2		2	ZP1	11	60638578	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3366	60638578	74367938	7417	15402										
TMEM109	79073	broad.mit.edu	37	chr11	60689289	60689289	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctcagccctggccaggtCcagaccttcctgctgtgggg	13	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60689289C>T	ENST00000227525.3	+	4	787	c.384C>T	c.(382-384)gtC>gtT	p.V128V	TMEM109_ENST00000536171.1_Silent_p.V128V|TMEM132A_ENST00000453848.2_5'Flank|RP11-881M11.4_ENST00000543907.1_RNA|TMEM132A_ENST00000005286.4_5'Flank	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	128					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)		p.V128V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						CTGGCCAGGTCCAGACCTTCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	11											102	105	104					11																	60689289		2203	4299	6502	60445865	SO:0001819	synonymous_variant	79073				CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.384C>T	11.37:g.60689289C>T			60445865		Silent	SNP	ENST00000227525.3	37	CCDS7996.1																																																																																				0.637	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092		T	60689289	C	T	60689289	2	4	61	1	0	0	0	0	0	0	0	1	16064	842	30	3		3	TMEM109	11	60689289	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50711	60689289	74317227	7418	15403										
TMEM132A	54972	broad.mit.edu	37	chr11	60704344	60704344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggaccctgaggagcttCgcaactacatggagaggatc	13	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60704344C>T	ENST00000453848.2	+	11	3195	c.3037C>T	c.(3037-3039)Cgc>Tgc	p.R1013C	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R1014C			Q24JP5	T132A_HUMAN	transmembrane protein 132A	1013	Confers cellular localization similar to full-length form. {ECO:0000250}.					endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R1014C(1)		breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						TGAGGAGCTTCGCAACTACAT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											31	38	36					11																	60704344		2201	4294	6495	60460920	SO:0001583	missense	54972			AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.3037C>T	11.37:g.60704344C>T	ENSP00000405823:p.Arg1013Cys		60460920	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881188	0.72294	.	.	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.13538	2.59;2.58	4.55	3.56	0.40772	.	0.101149	0.41294	D	0.000905	T	0.35856	0.0946	M	0.75085	2.285	0.52099	D	0.999945	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	T	0.22487	-1.0215	10	0.87932	D	0	-16.1454	14.3582	0.66752	0.1482:0.8518:0.0:0.0	.	1013;1014	Q24JP5;Q24JP5-2	T132A_HUMAN;.	C	764;1013;1014	ENSP00000405823:R1013C;ENSP00000005286:R1014C	ENSP00000005286:R1014C	R	+	1	0	TMEM132A	60460920	0.238000	0.23825	0.998000	0.56505	0.994000	0.84299	1.069000	0.30641	2.537000	0.85549	0.655000	0.94253	CGC		0.647	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		T	60704344	C	T	60704344	3	4	61	1	0	0	0	0	1	0	0	0	16084	884	31	1	3082	1	TMEM132A	11	60704344	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15055	60704344	74302172	7419	15404										
CD5	921	broad.mit.edu	37	chr11	60886814	60886814	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcagctatgaggcccaggAcaagacccaggacctggaga	12	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60886814A>G	ENST00000347785.3	+	5	738	c.572A>G	c.(571-573)gAc>gGc	p.D191G		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	191	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.D191G(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		GAGGCCCAGGACAAGACCCAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											67	70	69					11																	60886814		2203	4299	6502	60643390	SO:0001583	missense	921			X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"CD molecules"	1685	protein-coding gene	gene with protein product		153340	"CD5 antigen (p56-62)"	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.572A>G	11.37:g.60886814A>G	ENSP00000342681:p.Asp191Gly		60643390	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.63|12.63	1.996321|1.996321	0.35226|0.35226	.|.	.|.	ENSG00000110448|ENSG00000110448	ENST00000347785|ENST00000544014	T|T	0.02280|0.03330	4.36|3.97	5.4|5.4	0.243|0.243	0.15503|0.15503	Speract/scavenger receptor (1);|.	0.566946|.	0.16535|.	N|.	0.210200|.	T|T	0.03871|0.03871	0.0109|0.0109	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	B|.	0.28378|.	0.209|.	B|.	0.18561|.	0.022|.	T|T	0.44772|0.44772	-0.9306|-0.9306	10|7	0.66056|0.08179	D|T	0.02|0.78	-14.4616|-14.4616	7.5011|7.5011	0.27518|0.27518	0.345:0.5613:0.0938:0.0|0.345:0.5613:0.0938:0.0	.|.	191|.	P06127|.	CD5_HUMAN|.	G|A	191|160	ENSP00000342681:D191G|ENSP00000440899:T160A	ENSP00000342681:D191G|ENSP00000440899:T160A	D|T	+|+	2|1	0|0	CD5|CD5	60643390|60643390	0.040000|0.040000	0.19996|0.19996	0.002000|0.002000	0.10522|0.10522	0.016000|0.016000	0.09150|0.09150	0.688000|0.688000	0.25422|0.25422	0.028000|0.028000	0.15324|0.15324	-0.387000|-0.387000	0.06579|0.06579	GAC|ACA		0.617	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207		G	60886814	A	G	60886814	3	3	61	1	0	0	0	0	1	0	0	0	3027	275	10	4	590	4	CD5	11	60886814	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	182470	60886814	74119702	7420	15405										
CD5	921	broad.mit.edu	37	chr11	60892516	60892516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccagtgtctttccatcGcaaccacacggcaaccgtcc	7	18	1	0	rs139956085		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60892516G>A	ENST00000347785.3	+	9	1458	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	431					apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.R431H(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		TCTTTCCATCGCAACCACACG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	HIS/ARG	0,4406		0,0,2203	204	134	158		1292	5.1	1	11	dbSNP_134	158	1,8597	1.2+/-3.3	0,1,4298	no	missense	CD5	NM_014207.3	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	431/496	60892516	1,13003	2203	4299	6502	60649092	SO:0001583	missense	921			X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"CD molecules"	1685	protein-coding gene	gene with protein product		153340	"CD5 antigen (p56-62)"	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.1292G>A	11.37:g.60892516G>A	ENSP00000342681:p.Arg431His		60649092	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271893	0.59649	0.0	1.16E-4	ENSG00000110448	ENST00000347785	T	0.30448	1.53	5.05	5.05	0.67936	.	0.000000	0.53938	D	0.000046	T	0.44498	0.1296	L	0.34521	1.04	0.42913	D	0.994269	D	0.89917	1.0	D	0.87578	0.998	T	0.43294	-0.9400	10	0.87932	D	0	-38.409	13.8954	0.63768	0.0:0.0:1.0:0.0	.	431	P06127	CD5_HUMAN	H	431	ENSP00000342681:R431H	ENSP00000342681:R431H	R	+	2	0	CD5	60649092	1.000000	0.71417	1.000000	0.80357	0.220000	0.24768	5.137000	0.64789	2.356000	0.79943	0.462000	0.41574	CGC		0.562	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207		A	60892516	G	A	60892516	3	1	61	1	0	0	0	0	1	0	0	0	3027	1087	38	1	1326	1	CD5	11	60892516	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5702	60892516	74114000	7421	15406										
VPS37C	55048	broad.mit.edu	37	chr11	60901570	60901570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagctcctggtatctatccGagaggtttgagcggctgatc	14	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:60901570G>A	ENST00000301765.5	-	3	435	c.203C>T	c.(202-204)tCg>tTg	p.S68L		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	68					endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)		p.S68L(1)		breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						GTATCTATCCGAGAGGTTTGA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											73	75	74					11																	60901570		2203	4299	6502	60658146	SO:0001583	missense	55048			AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.203C>T	11.37:g.60901570G>A	ENSP00000301765:p.Ser68Leu		60658146	Q8N3K4	Missense_Mutation	SNP	ENST00000301765.5	37	CCDS31573.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.432421	0.25813	.	.	ENSG00000167987	ENST00000301765;ENST00000540084;ENST00000538036	T;T	0.76968	-1.06;-1.06	5.3	4.19	0.49359	Modifier of rudimentary, Modr (1);	0.232990	0.37348	N	0.002124	T	0.58935	0.2157	N	0.17474	0.49	0.33019	D	0.528575	B;B	0.30973	0.302;0.056	B;B	0.18871	0.023;0.016	T	0.65384	-0.6181	10	0.24483	T	0.36	-16.1477	13.0898	0.59160	0.0887:0.0:0.9113:0.0	.	68;68	B4DYD9;A5D8V6	.;VP37C_HUMAN	L	68	ENSP00000301765:S68L;ENSP00000446013:S68L	ENSP00000301765:S68L	S	-	2	0	VPS37C	60658146	0.976000	0.34144	0.948000	0.38648	0.274000	0.26718	1.799000	0.38824	2.496000	0.84212	0.491000	0.48974	TCG		0.612	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966		A	60901570	G	A	60901570	3	1	61	1	0	0	0	0	1	0	0	0	17247	1059	37	1	876	1	VPS37C	11	60901570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9054	60901570	74104946	7422	15407										
DDB1	1642	broad.mit.edu	37	chr11	61089810	61089810	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtccaccacgcacatatcGacaatgggtcctaagttggt	10	11	0	0	rs146385795		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61089810G>A	ENST00000301764.7	-	9	1477	c.1080C>T	c.(1078-1080)gtC>gtT	p.V360V	DDB1_ENST00000545930.1_5'UTR|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	360	Interaction with CDT1.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.V360V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CGCACATATCGACAATGGGTC	0.473								Nucleotide excision repair (NER)					G|||	1	0.000199681	8e-04	0	5008	,	,		19766	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						G		1,4405	2.1+/-5.4	0,1,2202	157	132	141		1080	2.4	1	11	dbSNP_134	141	0,8598		0,0,4299	no	coding-synonymous	DDB1	NM_001923.3		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		360/1141	61089810	1,13003	2203	4299	6502	60846386	SO:0001819	synonymous_variant	1642			AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.1080C>T	11.37:g.61089810G>A			60846386	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	37	CCDS31576.1																																																																																				0.473	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		A	61089810	G	A	61089810	2	1	61	1	0	0	0	0	0	0	0	1	4329	1045	37	1		1	DDB1	11	61089810	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188240	61089810	73916706	7423	15408										
DDB1	1642	broad.mit.edu	37	chr11	61090520	61090520	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacccaggcgagacccgacaAacacaacaccattatcaagg	7	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61090520A>C	ENST00000301764.7	-	8	1365	c.968T>G	c.(967-969)tTt>tGt	p.F323C	DDB1_ENST00000545930.1_5'UTR|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	323	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.F323C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						AGACCCGACAAACACAACACC	0.448								Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	11											101	84	90					11																	61090520		2203	4299	6502	60847096	SO:0001583	missense	1642			AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.968T>G	11.37:g.61090520A>C	ENSP00000301764:p.Phe323Cys		60847096	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	37	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303550	0.81136	.	.	ENSG00000167986	ENST00000301764;ENST00000539739;ENST00000535174;ENST00000541513	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.66	5.66	0.87406	.	0.047947	0.85682	D	0.000000	T	0.70945	0.3282	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.965;0.997	T	0.75614	-0.3257	10	0.87932	D	0	-16.1257	15.9004	0.79369	1.0:0.0:0.0:0.0	.	323;323;323	F5GY55;B7Z2A1;Q16531	.;.;DDB1_HUMAN	C	323;42;106;138	ENSP00000301764:F323C;ENSP00000445563:F42C;ENSP00000446044:F106C;ENSP00000442660:F138C	ENSP00000301764:F323C	F	-	2	0	DDB1	60847096	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.102000	0.77005	2.167000	0.68274	0.533000	0.62120	TTT		0.448	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		C	61090520	A	C	61090520	3	2	61	1	0	0	0	0	1	0	0	0	4329	14	1	4	2534	4	DDB1	11	61090520	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	710	61090520	73915996	7424	15409										
TMEM138	51524	broad.mit.edu	37	chr11	61133520	61133520	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttatgtctacagcatCcaggatattgcagtcctctt	6	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61133520C>A	ENST00000278826.6	+	3	691	c.132C>A	c.(130-132)atC>atA	p.I44I	TMEM138_ENST00000540194.1_3'UTR|TMEM138_ENST00000542946.1_Silent_p.I44I|TMEM138_ENST00000381787.2_5'UTR	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	44					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)		p.I44I(1)		central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						TCTACAGCATCCAGGATATTG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11											243	224	231					11																	61133520		2203	4299	6502	60890096	SO:0001819	synonymous_variant	51524			AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.132C>A	11.37:g.61133520C>A			60890096	A6NGA7|B4E044|Q5JPE1	Silent	SNP	ENST00000278826.6	37	CCDS8005.1																																																																																				0.468	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464		A	61133520	C	A	61133520	2	1	61	1	0	0	0	0	0	0	0	1	16092	845	30	2		2	TMEM138	11	61133520	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43000	61133520	73872996	7425	15410										
CPSF7	79869	broad.mit.edu	37	chr11	61183740	61183740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtaatcgaggaggtggggGcatgagatgctggtagtgga	20	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61183740G>A	ENST00000394888.4	-	6	974	c.802C>T	c.(802-804)Ccc>Tcc	p.P268S	CPSF7_ENST00000448745.1_Missense_Mutation_p.P259S|CPSF7_ENST00000340437.4_Missense_Mutation_p.P311S|CPSF7_ENST00000439958.3_Missense_Mutation_p.P259S	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	268	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P268S(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GGAGGTGGGGGCATGAGATGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											51	55	53					11																	61183740		2202	4299	6501	60940316	SO:0001583	missense	79869				CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.802C>T	11.37:g.61183740G>A	ENSP00000378352:p.Pro268Ser		60940316	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	37	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647690	0.67358	.	.	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000544147;ENST00000539952	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.29	5.29	0.74685	.	0.064918	0.64402	D	0.000007	T	0.80874	0.4707	L	0.28400	0.85	0.80722	D	1	B;B;B;B	0.21606	0.035;0.02;0.058;0.034	B;B;B;B	0.25291	0.012;0.011;0.059;0.025	T	0.75396	-0.3332	10	0.23302	T	0.38	-4.5797	15.0193	0.71617	0.0:0.1427:0.8573:0.0	.	259;268;311;259	B4DGF8;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	S	311;268;259;259;34;259	ENSP00000345412:P311S;ENSP00000378352:P268S;ENSP00000397203:P259S;ENSP00000407394:P259S	ENSP00000345412:P311S	P	-	1	0	CPSF7	60940316	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.109000	0.50345	2.465000	0.83290	0.650000	0.86243	CCC		0.612	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		A	61183740	G	A	61183740	3	1	61	1	0	0	0	0	1	0	0	0	3836	1203	42	3	629	3	CPSF7	11	61183740	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50220	61183740	73822776	7426	15411										
SDHAF2	54949	broad.mit.edu	37	chr11	61205131	61205131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcacagcctattgtctcCtttgctcagtgtgacatcat	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61205131C>A	ENST00000543265.1	+	2	74	c.71C>A	c.(70-72)cCt>cAt	p.P24H	RP11-286N22.8_ENST00000543044.1_Missense_Mutation_p.P12H|SDHAF2_ENST00000534878.1_Missense_Mutation_p.P24H|RP11-286N22.8_ENST00000544880.1_3'UTR|SDHAF2_ENST00000537782.1_Missense_Mutation_p.P24H|SDHAF2_ENST00000301761.2_Missense_Mutation_p.P24H|SDHAF2_ENST00000542074.1_Intron					succinate dehydrogenase complex assembly factor 2									p.P24H(1)		large_intestine(3)|lung(4)|ovary(2)	9						CTATTGTCTCCTTTGCTCAGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	11											200	196	197					11																	61205131		2202	4299	6501	60961707	SO:0001583	missense	54949			AK000494	CCDS8007.1	11q12.2	2014-09-17	2009-08-10	2009-08-10	ENSG00000167985	ENSG00000167985		"Mitochondrial respiratory chain complex assembly factors"	26034	protein-coding gene	gene with protein product		613019	"paraganglioma or familial glomus tumors 2", "chromosome 11 open reading frame 79"	PGL2, C11orf79		19628817	Standard	NM_017841		Approved	FLJ20487, SDH5	uc001nrt.3	Q9NX18	OTTHUMG00000168279	ENST00000543265.1:c.71C>A	11.37:g.61205131C>A	ENSP00000443660:p.Pro24His		60961707		Missense_Mutation	SNP	ENST00000543265.1	37		.	.	.	.	.	.	.	.	.	.	C	18.46	3.628788	0.67015	.	.	ENSG00000256591;ENSG00000167985;ENSG00000167985	ENST00000541135;ENST00000301761;ENST00000543265	T;T;T	0.79749	-1.2;-1.13;-1.3	5.65	4.74	0.60224	.	0.101972	0.64402	D	0.000001	T	0.74943	0.3783	M	0.63428	1.95	0.34193	D	0.672257	B	0.21821	0.061	B	0.20767	0.031	T	0.76537	-0.2923	10	0.41790	T	0.15	-14.3468	7.0779	0.25215	0.1706:0.745:0.0:0.0844	.	24	Q9NX18	SDHF2_HUMAN	H	24	ENSP00000443130:P24H;ENSP00000301761:P24H;ENSP00000443660:P24H	ENSP00000440939:P24H	P	+	2	0	SDHAF2;RP11-286N22.8	60961707	0.362000	0.24980	0.492000	0.27490	0.180000	0.23129	2.567000	0.45956	1.620000	0.50308	0.655000	0.94253	CCT		0.433	SDHAF2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000398484.1	NM_017841		A	61205131	C	A	61205131	3	1	61	1	0	0	0	0	1	0	0	0	14001	681	24	2	77	2	SDHAF2	11	61205131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21391	61205131	73801385	7427	15412										
C11orf66	220004	broad.mit.edu	37	chr11	61249334	61249334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttatgtgaagatgagttCggggggctacacggaccccc	13	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61249334C>T	ENST00000338608.2	+	2	178	c.53C>T	c.(52-54)tCg>tTg	p.S18L	RP11-286N22.8_ENST00000543044.1_3'UTR|PPP1R32_ENST00000432063.2_Missense_Mutation_p.S18L|RP11-286N22.8_ENST00000544880.1_Intron	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	18							phosphatase binding (GO:0019902)	p.S18L(1)									AAGATGAGTTCGGGGGGCTAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											33	35	34					11																	61249334		2202	4299	6501	61005910	SO:0001583	missense	220004			AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.53C>T	11.37:g.61249334C>T	ENSP00000344140:p.Ser18Leu		61005910	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941536	0.73557	.	.	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.46451	0.87;1.44	4.9	3.97	0.46021	.	0.131532	0.34700	N	0.003758	T	0.50120	0.1597	L	0.48877	1.53	0.80722	D	1	P;D	0.89917	0.757;1.0	B;D	0.83275	0.135;0.996	T	0.39663	-0.9603	10	0.09084	T	0.74	-11.93	10.8813	0.46939	0.0:0.9073:0.0:0.0927	.	18;18	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	L	18	ENSP00000391560:S18L;ENSP00000344140:S18L	ENSP00000344140:S18L	S	+	2	0	C11orf66	61005910	0.983000	0.35010	0.979000	0.43373	0.996000	0.88848	2.681000	0.46926	2.278000	0.76064	0.511000	0.50034	TCG		0.627	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		T	61249334	C	T	61249334	3	4	61	1	0	0	0	0	1	0	0	0	1660	893	31	1	55	1	C11orf66	11	61249334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44203	61249334	73757182	7428	15413										
C11orf9	745	broad.mit.edu	37	chr11	61541497	61541497	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacttttcggtgggcgacGacgcctttgtgtgccagaag	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61541497G>A	ENST00000278836.5	+	8	1270	c.1174G>A	c.(1174-1176)Gac>Aac	p.D392N	MYRF_ENST00000327797.1_Missense_Mutation_p.D19N|TMEM258_ENST00000535042.1_5'UTR|MYRF_ENST00000265460.5_Missense_Mutation_p.D383N	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	392					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D383N(1)									GGTGGGCGACGACGCCTTTGT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	67	72					11																	61541497		2202	4299	6501	61298073	SO:0001583	missense	745				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.1174G>A	11.37:g.61541497G>A	ENSP00000278836:p.Asp392Asn		61298073	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	37	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.066422	0.76187	.	.	ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000327797	T;T;T	0.42131	1.55;1.55;0.98	4.43	4.43	0.53597	NDT80 DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);	0.124581	0.56097	D	0.000023	T	0.43389	0.1245	L	0.59436	1.845	0.80722	D	1	P;B	0.42357	0.777;0.414	B;B	0.40444	0.329;0.126	T	0.45071	-0.9286	10	0.39692	T	0.17	-27.6325	17.6067	0.88040	0.0:0.0:1.0:0.0	.	383;392	Q9Y2G1-2;Q9Y2G1	.;MRF_HUMAN	N	392;383;19	ENSP00000278836:D392N;ENSP00000265460:D383N;ENSP00000333261:D19N	ENSP00000265460:D383N	D	+	1	0	C11orf9	61298073	1.000000	0.71417	0.971000	0.41717	0.525000	0.34531	9.204000	0.95041	2.484000	0.83849	0.462000	0.41574	GAC		0.642	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		A	61541497	G	A	61541497	3	1	61	1	0	0	0	0	1	0	0	0	1675	1058	37	1	1227	1	C11orf9	11	61541497	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	292163	61541497	73465019	7429	15414										
FEN1	2237	broad.mit.edu	37	chr11	61563819	61563819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggggtcaagaggctgaGtaagagccgccaaggcagca	16	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61563819G>A	ENST00000305885.2	+	2	1399	c.986G>A	c.(985-987)aGt>aAt	p.S329N	FADS2_ENST00000574708.1_Intron	NM_004111.5	NP_004102.1			flap structure-specific endonuclease 1									p.S329N(1)		endometrium(1)|large_intestine(4)|lung(1)|ovary(1)	7						AAGAGGCTGAGTAAGAGCCGC	0.552								Editing and processing nucleases																																								1	Substitution - Missense(1)	large_intestine(1)	11											37	40	39					11																	61563819		2202	4299	6501	61320395	SO:0001583	missense	2237			L37374	CCDS8010.1	11q12	2013-05-08			ENSG00000168496	ENSG00000168496			3650	protein-coding gene	gene with protein product	"maturation factor-1", "DNase IV"	600393		RAD2		7774922	Standard	NM_004111		Approved	FEN-1, MF1	uc001nsg.3	P39748	OTTHUMG00000168162	ENST00000305885.2:c.986G>A	11.37:g.61563819G>A	ENSP00000305480:p.Ser329Asn		61320395		Missense_Mutation	SNP	ENST00000305885.2	37	CCDS8010.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.549212	0.27652	.	.	ENSG00000168496	ENST00000305885	T	0.29397	1.57	5.44	3.56	0.40772	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.431794	0.27841	N	0.017629	T	0.18130	0.0435	L	0.29908	0.895	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07158	-1.0787	10	0.15499	T	0.54	-16.621	6.4987	0.22155	0.2129:0.1305:0.6566:0.0	.	329	P39748	FEN1_HUMAN	N	329	ENSP00000305480:S329N	ENSP00000305480:S329N	S	+	2	0	FEN1	61320395	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.033000	0.49743	0.768000	0.33290	0.561000	0.74099	AGT		0.552	FEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398526.1	NM_004111		A	61563819	G	A	61563819	3	1	61	1	0	0	0	0	1	0	0	0	5831	1029	36	3	988	3	FEN1	11	61563819	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22322	61563819	73442697	7430	15415										
SCGB1D1	10648	broad.mit.edu	37	chr11	61960885	61960885	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagggaaaaatagcagaGaaatgtgatcgctgagatgt	12	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:61960885G>T	ENST00000306238.3	+	3	327	c.258G>T	c.(256-258)gaG>gaT	p.E86D		NM_006552.1	NP_006543.1	O95968	SG1D1_HUMAN	secretoglobin, family 1D, member 1	86						extracellular space (GO:0005615)	protein heterodimerization activity (GO:0046982)	p.E86D(1)		endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	9						AAATAGCAGAGAAATGTGATC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											160	150	153					11																	61960885		2202	4299	6501	61717461	SO:0001583	missense	10648			AJ224171	CCDS8015.1	11q13	2011-12-14			ENSG00000168515	ENSG00000168515		"Secretoglobins"	18395	protein-coding gene	gene with protein product	"prostatein-like lipophilin A", "lipophilin A (uteroglobin family member)"	615060				9720917, 10066439, 22155607	Standard	NM_006552		Approved	LPHA, LIPA, MGC71958	uc001nsz.1	O95968	OTTHUMG00000167505	ENST00000306238.3:c.258G>T	11.37:g.61960885G>T	ENSP00000303070:p.Glu86Asp		61717461		Missense_Mutation	SNP	ENST00000306238.3	37	CCDS8015.1	.	.	.	.	.	.	.	.	.	.	G	2.153	-0.394026	0.04899	.	.	ENSG00000168515	ENST00000306238	T	0.14144	2.53	2.72	-3.59	0.04583	.	4.184240	0.01265	U	0.009294	T	0.07593	0.0191	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21724	-1.0237	9	0.35671	T	0.21	.	0.2403	0.00191	0.2367:0.167:0.2575:0.3388	.	86	O95968	SG1D1_HUMAN	D	86	ENSP00000303070:E86D	ENSP00000303070:E86D	E	+	3	2	SCGB1D1	61717461	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.033000	0.01425	-0.924000	0.03780	-0.282000	0.10007	GAG		0.413	SCGB1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394856.1	NM_006552		T	61960885	G	T	61960885	3	4	61	1	0	0	0	0	1	0	0	0	13933	933	33	2	268	2	SCGB1D1	11	61960885	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	397066	61960885	73045631	7431	15416										
AHNAK	79026	broad.mit.edu	37	chr11	62286253	62286253	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccagtcccacgctgggGacatcaccctttatctttgg	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62286253G>A	ENST00000378024.4	-	5	15910	c.15636C>T	c.(15634-15636)gtC>gtT	p.V5212V	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5212					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V5212V(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CCACGCTGGGGACATCACCCT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	11											100	88	92					11																	62286253		2202	4299	6501	62042829	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15636C>T	11.37:g.62286253G>A			62042829	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62286253	G	A	62286253	2	1	61	1	0	0	0	0	0	0	0	1	414	1161	41	3		3	AHNAK	11	62286253	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325368	62286253	72720263	7432	15417										
AHNAK	79026	broad.mit.edu	37	chr11	62286315	62286315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagggatggagacttgagGggcagaaatgccgaaggacg	17	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62286315G>A	ENST00000378024.4	-	5	15848	c.15574C>T	c.(15574-15576)Cct>Tct	p.P5192S	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5192					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.P5192S(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GAGACTTGAGGGGCAGAAATG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	83	85					11																	62286315		2202	4299	6501	62042891	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15574C>T	11.37:g.62286315G>A	ENSP00000367263:p.Pro5192Ser		62042891	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	G	14.45	2.540372	0.45176	.	.	ENSG00000124942	ENST00000378024	T	0.04654	3.58	4.84	3.92	0.45320	.	0.138507	0.33272	N	0.005092	T	0.18087	0.0434	M	0.88105	2.93	0.41929	D	0.990553	P	0.41345	0.746	P	0.49451	0.611	T	0.02437	-1.1159	10	0.51188	T	0.08	-3.1713	14.4349	0.67274	0.0:0.0:0.8512:0.1488	.	5192	Q09666	AHNK_HUMAN	S	5192	ENSP00000367263:P5192S	ENSP00000367263:P5192S	P	-	1	0	AHNAK	62042891	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	3.346000	0.52190	1.142000	0.42291	0.643000	0.83706	CCT		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62286315	G	A	62286315	3	1	61	1	0	0	0	0	1	0	0	0	414	1232	43	3	2218	3	AHNAK	11	62286315	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62	62286315	72720201	7433	15418										
AHNAK	79026	broad.mit.edu	37	chr11	62286994	62286994	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttaacatctggcccttcGatgttaatatctgggctgtc	8	9	2	0	rs537813230		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62286994G>A	ENST00000378024.4	-	5	15169	c.14895C>T	c.(14893-14895)atC>atT	p.I4965I	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4965					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.I4965I(2)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTGGCCCTTCGATGTTAATAT	0.453													G|||	1	0.000199681	0	0	5008	,	,		19357	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	11											91	89	90					11																	62286994		2202	4299	6501	62043570	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.14895C>T	11.37:g.62286994G>A			62043570	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.453	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62286994	G	A	62286994	2	1	61	1	0	0	0	0	0	0	0	1	414	1048	37	1		1	AHNAK	11	62286994	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	679	62286994	72719522	7434	15419										
AHNAK	79026	broad.mit.edu	37	chr11	62290273	62290273	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaatgtcaggcatggagatCttgggggctttgatgttcat	13	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62290273C>A	ENST00000378024.4	-	5	11890	c.11616G>T	c.(11614-11616)aaG>aaT	p.K3872N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3872					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.K3872N(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCATGGAGATCTTGGGGGCTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											224	232	230					11																	62290273		2202	4299	6501	62046849	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11616G>T	11.37:g.62290273C>A	ENSP00000367263:p.Lys3872Asn		62046849	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	14.57	2.575459	0.45902	.	.	ENSG00000124942	ENST00000378024	T	0.01252	5.1	4.48	3.57	0.40892	.	0.000000	0.43260	D	0.000588	T	0.03695	0.0105	M	0.88906	2.99	0.42482	D	0.99286	B	0.27316	0.175	B	0.27887	0.084	T	0.09487	-1.0672	10	0.51188	T	0.08	.	10.4956	0.44775	0.0:0.9084:0.0:0.0916	.	3872	Q09666	AHNK_HUMAN	N	3872	ENSP00000367263:K3872N	ENSP00000367263:K3872N	K	-	3	2	AHNAK	62046849	0.008000	0.16893	0.998000	0.56505	0.918000	0.54935	-1.043000	0.03535	1.130000	0.42092	0.537000	0.68136	AAG		0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62290273	C	A	62290273	3	1	61	1	0	0	0	0	1	0	0	0	414	912	32	2	6176	2	AHNAK	11	62290273	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3279	62290273	72716243	7435	15420										
AHNAK	79026	broad.mit.edu	37	chr11	62290725	62290725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatttaccctctgagccttCgatgttaatgtcaggagtgt	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62290725C>T	ENST00000378024.4	-	5	11438	c.11164G>A	c.(11164-11166)Gaa>Aaa	p.E3722K	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3722					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.E3722K(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCTGAGCCTTCGATGTTAATG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											131	139	136					11																	62290725		2202	4299	6501	62047301	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11164G>A	11.37:g.62290725C>T	ENSP00000367263:p.Glu3722Lys		62047301	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	15.45	2.838388	0.51057	.	.	ENSG00000124942	ENST00000378024	T	0.05786	3.39	5.32	4.35	0.52113	.	0.608457	0.13581	N	0.377359	T	0.19604	0.0471	M	0.73430	2.235	0.39039	D	0.960091	D	0.76494	0.999	D	0.74023	0.982	T	0.02625	-1.1132	10	0.17369	T	0.5	.	8.7771	0.34769	0.0:0.7676:0.1525:0.0798	.	3722	Q09666	AHNK_HUMAN	K	3722	ENSP00000367263:E3722K	ENSP00000367263:E3722K	E	-	1	0	AHNAK	62047301	0.447000	0.25673	0.946000	0.38457	0.071000	0.16799	0.417000	0.21214	2.492000	0.84095	0.579000	0.79373	GAA		0.458	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62290725	C	T	62290725	3	4	61	1	0	0	0	0	1	0	0	0	414	893	31	1	6628	1	AHNAK	11	62290725	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	452	62290725	72715791	7436	15421										
AHNAK	79026	broad.mit.edu	37	chr11	62293792	62293792	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggggctttgatattcatCtctggcatcttgaacttagg	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62293792C>A	ENST00000378024.4	-	5	8371	c.8097G>T	c.(8095-8097)gaG>gaT	p.E2699D	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2699					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.E2699D(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGATATTCATCTCTGGCATCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											191	189	189					11																	62293792		2202	4299	6501	62050368	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.8097G>T	11.37:g.62293792C>A	ENSP00000367263:p.Glu2699Asp		62050368	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	7.613	0.675144	0.14841	.	.	ENSG00000124942	ENST00000378024	T	0.03004	4.08	4.61	-4.26	0.03755	.	.	.	.	.	T	0.04137	0.0115	N	0.13272	0.32	0.09310	N	1	D	0.67145	0.996	D	0.77557	0.99	T	0.34304	-0.9834	9	0.15499	T	0.54	-3.8156	1.9367	0.03338	0.1118:0.2704:0.3315:0.2862	.	2699	Q09666	AHNK_HUMAN	D	2699	ENSP00000367263:E2699D	ENSP00000367263:E2699D	E	-	3	2	AHNAK	62050368	0.000000	0.05858	0.007000	0.13788	0.732000	0.41865	-9.647000	0.00010	-0.428000	0.07339	0.473000	0.43528	GAG		0.453	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62293792	C	A	62293792	3	1	61	1	0	0	0	0	1	0	0	0	414	912	32	2	9695	2	AHNAK	11	62293792	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3067	62293792	72712724	7437	15422										
AHNAK	79026	broad.mit.edu	37	chr11	62296327	62296327	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccacatcaggcatggagatCttgggggccttgaagtgcat	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62296327C>A	ENST00000378024.4	-	5	5836	c.5562G>T	c.(5560-5562)aaG>aaT	p.K1854N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1854					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.K1854N(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCATGGAGATCTTGGGGGCCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											193	204	201					11																	62296327		2202	4297	6499	62052903	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5562G>T	11.37:g.62296327C>A	ENSP00000367263:p.Lys1854Asn		62052903	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	8.185	0.794700	0.16327	.	.	ENSG00000124942	ENST00000378024	T	0.01379	4.96	3.04	3.04	0.35103	.	0.000000	0.42294	D	0.000731	T	0.08133	0.0203	M	0.93978	3.48	0.26841	N	0.968378	D	0.71674	0.998	D	0.64321	0.924	T	0.11641	-1.0579	10	0.25106	T	0.35	.	7.5486	0.27781	0.0:0.8697:0.0:0.1303	.	1854	Q09666	AHNK_HUMAN	N	1854	ENSP00000367263:K1854N	ENSP00000367263:K1854N	K	-	3	2	AHNAK	62052903	0.852000	0.29690	0.782000	0.31804	0.027000	0.11550	-0.100000	0.10990	1.394000	0.46624	0.205000	0.17691	AAG		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62296327	C	A	62296327	3	1	61	1	0	0	0	0	1	0	0	0	414	912	32	2	12230	2	AHNAK	11	62296327	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2535	62296327	72710189	7438	15423										
AHNAK	79026	broad.mit.edu	37	chr11	62297539	62297539	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacatctggtatggatatCttctgaggctttatactcat	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62297539C>A	ENST00000378024.4	-	5	4624	c.4350G>T	c.(4348-4350)aaG>aaT	p.K1450N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1450					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.K1450N(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTATGGATATCTTCTGAGGCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											193	202	199					11																	62297539		2202	4299	6501	62054115	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.4350G>T	11.37:g.62297539C>A	ENSP00000367263:p.Lys1450Asn		62054115	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	N	10.39	1.337219	0.24253	.	.	ENSG00000124942	ENST00000378024	T	0.01252	5.1	4.38	3.45	0.39498	.	.	.	.	.	T	0.05686	0.0149	M	0.88377	2.95	0.28658	N	0.906276	P	0.46142	0.873	P	0.50352	0.638	T	0.02983	-1.1086	9	0.48119	T	0.1	.	8.5657	0.33538	0.0:0.8177:0.0:0.1823	.	1450	Q09666	AHNK_HUMAN	N	1450	ENSP00000367263:K1450N	ENSP00000367263:K1450N	K	-	3	2	AHNAK	62054115	0.876000	0.30132	0.994000	0.49952	0.076000	0.17211	0.878000	0.28126	2.007000	0.58848	0.550000	0.68814	AAG		0.378	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62297539	C	A	62297539	3	1	61	1	0	0	0	0	1	0	0	0	414	912	32	2	13442	2	AHNAK	11	62297539	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1212	62297539	72708977	7439	15424										
AHNAK	79026	broad.mit.edu	37	chr11	62297650	62297650	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatccattttgggtcctgaGacatcaacgtcagctttggg	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62297650G>A	ENST00000378024.4	-	5	4513	c.4239C>T	c.(4237-4239)gtC>gtT	p.V1413V	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1413					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V1413V(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGGGTCCTGAGACATCAACGT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11											191	204	200					11																	62297650		2202	4299	6501	62054226	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.4239C>T	11.37:g.62297650G>A			62054226	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.468	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62297650	G	A	62297650	2	1	61	1	0	0	0	0	0	0	0	1	414	929	33	3		3	AHNAK	11	62297650	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111	62297650	72708866	7440	15425										
AHNAK	79026	broad.mit.edu	37	chr11	62299529	62299529	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcacatcaggagcagtaAcatctatcttgggcccggaa	10	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62299529A>C	ENST00000378024.4	-	5	2634	c.2360T>G	c.(2359-2361)gTt>gGt	p.V787G	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	787					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V787G(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AGGAGCAGTAACATCTATCTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											137	142	141					11																	62299529		2202	4299	6501	62056105	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.2360T>G	11.37:g.62299529A>C	ENSP00000367263:p.Val787Gly		62056105	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.455937	0.26161	.	.	ENSG00000124942	ENST00000378024	T	0.01228	5.14	5.46	5.46	0.80206	.	0.361502	0.19065	N	0.123669	T	0.08313	0.0207	M	0.86097	2.795	0.09310	N	0.999993	D	0.61697	0.99	D	0.64042	0.921	T	0.27400	-1.0075	10	0.25106	T	0.35	-7.0466	14.3616	0.66776	1.0:0.0:0.0:0.0	.	787	Q09666	AHNK_HUMAN	G	787	ENSP00000367263:V787G	ENSP00000367263:V787G	V	-	2	0	AHNAK	62056105	0.140000	0.22579	0.003000	0.11579	0.138000	0.21146	2.458000	0.45014	2.085000	0.62840	0.374000	0.22700	GTT		0.498	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62299529	A	C	62299529	3	2	61	1	0	0	0	0	1	0	0	0	414	43	2	4	15432	4	AHNAK	11	62299529	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1879	62299529	72706987	7441	15426										
AHNAK	79026	broad.mit.edu	37	chr11	62303454	62303454	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcgggccgcaggggagttCtgcgtcacctcctgcacaaa	14	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62303454C>A	ENST00000378024.4	-	3	391	c.117G>T	c.(115-117)caG>caT	p.Q39H	AHNAK_ENST00000530124.1_Missense_Mutation_p.Q39H|RP11-864I4.3_ENST00000544108.1_RNA|AHNAK_ENST00000257247.7_Missense_Mutation_p.Q39H	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	39	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.Q39H(2)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAGGGGAGTTCTGCGTCACCT	0.682																																																2	Substitution - Missense(2)	large_intestine(2)	11											59	56	57					11																	62303454		2202	4299	6501	62060030	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.117G>T	11.37:g.62303454C>A	ENSP00000367263:p.Gln39His		62060030	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476433	0.63737	.	.	ENSG00000124942	ENST00000530124;ENST00000257247;ENST00000533365;ENST00000378024;ENST00000530285;ENST00000528508;ENST00000531324	T;T;T;T;T;T;T	0.41758	1.69;1.69;1.69;0.99;1.69;1.69;1.69	5.36	4.43	0.53597	PDZ/DHR/GLGF (3);	0.485483	0.16646	U	0.205411	T	0.35537	0.0935	L	0.29908	0.895	0.23023	N	0.998414	P;P	0.41569	0.755;0.602	B;B	0.44224	0.444;0.353	T	0.18967	-1.0320	10	0.72032	D	0.01	-2.2412	9.0778	0.36534	0.0:0.7678:0.151:0.0812	.	39;39	Q09666;A1A586	AHNK_HUMAN;.	H	39	ENSP00000433789:Q39H;ENSP00000257247:Q39H;ENSP00000433635:Q39H;ENSP00000367263:Q39H;ENSP00000433286:Q39H;ENSP00000435357:Q39H;ENSP00000436845:Q39H	ENSP00000257247:Q39H	Q	-	3	2	AHNAK	62060030	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	0.526000	0.22971	1.221000	0.43506	0.655000	0.94253	CAG		0.682	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62303454	C	A	62303454	3	1	61	1	0	0	0	0	1	0	0	0	414	912	32	2	17683	2	AHNAK	11	62303454	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3925	62303454	72703062	7442	15427										
B3GAT3	26229	broad.mit.edu	37	chr11	62384514	62384514	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcagcaaagtagacgactCcttgggtccctggtggtggt	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62384514C>A	ENST00000265471.5	-	3	790	c.563G>T	c.(562-564)gGa>gTa	p.G188V	B3GAT3_ENST00000531383.1_Missense_Mutation_p.G188V|B3GAT3_ENST00000534026.1_Missense_Mutation_p.G188V	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	188					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)	p.G188V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						GTAGACGACTCCTTGGGTCCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											114	115	115					11																	62384514		2202	4299	6501	62141090	SO:0001583	missense	26229			AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"Beta-1,3-glucuronyltransferases"	923	protein-coding gene	gene with protein product	"glucuronosyltransferase I", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"	606374	"beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.563G>T	11.37:g.62384514C>A	ENSP00000265471:p.Gly188Val		62141090	B7ZAB3|Q96I06|Q9UEP0	Missense_Mutation	SNP	ENST00000265471.5	37	CCDS8025.1	.	.	.	.	.	.	.	.	.	.	c	19.92	3.915899	0.73098	.	.	ENSG00000149541	ENST00000265471;ENST00000531383;ENST00000534026;ENST00000534715	D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79	5.56	5.56	0.83823	.	0.159130	0.56097	N	0.000039	D	0.96744	0.8937	H	0.94925	3.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97623	1.0137	10	0.87932	D	0	.	17.0258	0.86446	0.0:1.0:0.0:0.0	.	188;194;188	B7ZAB3;Q5U676;O94766	.;.;B3GA3_HUMAN	V	188;188;188;211	ENSP00000265471:G188V;ENSP00000431359:G188V;ENSP00000432474:G188V;ENSP00000432854:G211V	ENSP00000265471:G188V	G	-	2	0	B3GAT3	62141090	0.995000	0.38212	0.998000	0.56505	0.970000	0.65996	3.026000	0.49689	2.616000	0.88540	0.556000	0.70494	GGA		0.647	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200		A	62384514	C	A	62384514	3	1	61	1	0	0	0	0	1	0	0	0	1256	855	30	2	456	2	B3GAT3	11	62384514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81060	62384514	72622002	7443	15428										
NXF1	10482	broad.mit.edu	37	chr11	62566033	62566033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgtagtaacttgggaaatCgttcgcgaatggcgctgtca	14	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62566033C>T	ENST00000532297.1	-	12	1660	c.1031G>A	c.(1030-1032)cGa>cAa	p.R344Q	NXF1_ENST00000533048.1_5'Flank|NXF1_ENST00000531709.2_3'UTR|NXF1_ENST00000294172.2_Missense_Mutation_p.R344Q			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	344					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R344Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTTGGGAAATCGTTCGCGAAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											143	135	137					11																	62566033		2201	4299	6500	62322609	SO:0001583	missense	10482			AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"tip associating protein"	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.1031G>A	11.37:g.62566033C>T	ENSP00000436679:p.Arg344Gln		62322609	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.260539	0.80246	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	T;T;T	0.41400	1.0;1.0;1.0	5.77	5.77	0.91146	U2A&apos (1);/phosphoprotein 32 family A, C-terminal (1);	0.058428	0.64402	D	0.000002	T	0.58963	0.2159	M	0.82630	2.6	0.80722	D	1	D;D	0.71674	0.987;0.998	B;P	0.51974	0.382;0.686	T	0.59037	-0.7529	10	0.30854	T	0.27	-2.9944	17.535	0.87827	0.0:1.0:0.0:0.0	.	387;344	E9PIN3;Q9UBU9	.;NXF1_HUMAN	Q	344;344;387	ENSP00000294172:R344Q;ENSP00000436679:R344Q;ENSP00000435742:R387Q	ENSP00000294172:R344Q	R	-	2	0	NXF1	62322609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.356000	0.59430	2.751000	0.94390	0.650000	0.86243	CGA		0.473	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		T	62566033	C	T	62566033	3	4	61	1	0	0	0	0	1	0	0	0	10813	884	31	1	872	1	NXF1	11	62566033	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	181519	62566033	72440483	7444	15429										
SLC22A6	9356	broad.mit.edu	37	chr11	62747001	62747001	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagtatacaggaagatGcagttgaaggaggcagccag	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62747001G>A	ENST00000377871.3	-	8	1586	c.1320C>T	c.(1318-1320)tgC>tgT	p.C440C	SLC22A6_ENST00000360421.4_Silent_p.C440C|SLC22A6_ENST00000421062.2_Silent_p.C440C|SLC22A6_ENST00000537349.1_5'Flank|SLC22A6_ENST00000458333.2_Silent_p.C440C	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	440					alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.C440C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	ACAGGAAGATGCAGTTGAAGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	11											80	69	73					11																	62747001		2201	4298	6499	62503577	SO:0001819	synonymous_variant	9356			AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901		"Solute carriers"	10970	protein-coding gene	gene with protein product		607582				9762842, 9950961	Standard	NM_004790		Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000377871.3:c.1320C>T	11.37:g.62747001G>A			62503577	A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	Silent	SNP	ENST00000377871.3	37	CCDS31591.1																																																																																				0.517	SLC22A6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396186.1	NM_004790		A	62747001	G	A	62747001	2	1	61	1	0	0	0	0	0	0	0	1	14495	1311	46	3		3	SLC22A6	11	62747001	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	180968	62747001	72259515	7445	15430										
SLC22A25	387601	broad.mit.edu	37	chr11	62995978	62995978	+	De_novo_Start_OutOfFrame	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctcccaccatcattccaGccatgaatagaaatttagct	5	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62995978G>T	ENST00000403374.2	-	0	8				SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron|SLC22A25_ENST00000306494.6_Missense_Mutation_p.A154D					solute carrier family 22, member 25									p.A154D(1)		NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CATCATTCCAGCCATGAATAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											112	101	105					11																	62995978		2201	4298	6499	62752554			387601			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000403374.2:c.-296C>A	11.37:g.62995978G>T			62752554		Missense_Mutation	SNP	ENST00000403374.2	37		.	.	.	.	.	.	.	.	.	.	G	13.92	2.380181	0.42207	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.78707	-1.2	3.47	-3.8	0.04307	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.269718	0.34932	U	0.003569	D	0.84311	0.5444	M	0.89163	3.01	0.09310	N	0.999996	D;D	0.59357	0.985;0.958	D;P	0.69142	0.962;0.821	T	0.75396	-0.3332	10	0.72032	D	0.01	.	5.2475	0.15504	0.4171:0.1451:0.4378:0.0	.	152;154	A4IF29;Q6T423	.;S22AP_HUMAN	D	154	ENSP00000307443:A154D	ENSP00000307443:A154D	A	-	2	0	SLC22A25	62752554	0.733000	0.28132	0.001000	0.08648	0.017000	0.09413	0.082000	0.14847	-0.555000	0.06142	0.478000	0.44815	GCT		0.423	SLC22A25-201	KNOWN	basic	protein_coding	protein_coding		NM_199352		T	62995978	G	T	62995978	1	4	61	1	0	1	0	0	0	0	0	0	14491	971	34	2		2	SLC22A25	11	62995978	De_novo_Start_OutOfFrame	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248977	62995978	72010538	7446	15431										
SLC22A25	387601	broad.mit.edu	37	chr11	62997109	62997109	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccaacttgatctaggaGgtcctgaaaggccattgagg	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:62997109G>T	ENST00000306494.6	-	1	15	c.16C>A	c.(16-18)Ctc>Atc	p.L6I	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25									p.L6I(1)		NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TGATCTAGGAGGTCCTGAAAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											42	46	45					11																	62997109		2201	4298	6499	62753685	SO:0001583	missense	387601			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.16C>A	11.37:g.62997109G>T	ENSP00000307443:p.Leu6Ile		62753685		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.515822	0.27123	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.39787	1.06	3.98	3.02	0.34903	.	0.069188	0.64402	D	0.000015	T	0.59169	0.2174	M	0.67625	2.065	0.80722	D	1	D;D	0.89917	0.989;1.0	D;D	0.91635	0.922;0.999	T	0.59440	-0.7454	10	0.56958	D	0.05	.	10.8623	0.46833	0.0:0.0:0.8098:0.1902	.	4;6	A4IF29;Q6T423	.;S22AP_HUMAN	I	6	ENSP00000307443:L6I	ENSP00000307443:L6I	L	-	1	0	SLC22A25	62753685	0.977000	0.34250	0.015000	0.15790	0.157000	0.22087	1.770000	0.38532	0.741000	0.32674	0.472000	0.43445	CTC		0.418	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		T	62997109	G	T	62997109	3	4	61	1	0	0	0	0	1	0	0	0	14491	1000	35	2	1663	2	SLC22A25	11	62997109	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1131	62997109	72009407	7447	15432										
LGALS12	85329	broad.mit.edu	37	chr11	63283095	63283095	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacactcagggcctccttCgcagacagaactctggcctg	11	14	2	3	rs36007310	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63283095C>T	ENST00000394618.3	+	8	1065	c.774C>T	c.(772-774)ttC>ttT	p.F258F	LGALS12_ENST00000340246.5_Silent_p.F259F|LGALS12_ENST00000255684.5_Silent_p.F249F|LGALS12_ENST00000425950.2_Silent_p.F188F|LGALS12_ENST00000415491.2_Silent_p.F197F	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	258	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.F258F(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						GGGCCTCCTTCGCAGACAGAA	0.567													C|||	16	0.00319489	0.0121	0	5008	,	,		20315	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C	,,,,	48,4354	50.2+/-85.5	0,48,2153	68	65	66		777,747,591,564,774	1.8	0.4	11	dbSNP_126	66	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LGALS12	NM_001142535.1,NM_001142536.1,NM_001142537.1,NM_001142538.1,NM_033101.3	,,,,	0,48,6451	TT,TC,CC		0.0,1.0904,0.3693	,,,,	259/338,249/328,197/276,188/267,258/337	63283095	48,12950	2201	4298	6499	63039671	SO:0001819	synonymous_variant	85329			AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.774C>T	11.37:g.63283095C>T			63039671	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	ENST00000394618.3	37	CCDS8045.1																																																																																				0.567	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		T	63283095	C	T	63283095	2	4	61	1	0	0	0	0	0	0	0	1	8761	883	31	1		1	LGALS12	11	63283095	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	285986	63283095	71723421	7448	15433										
ATL3	25923	broad.mit.edu	37	chr11	63403807	63403807	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaattcaccagcaatatCtgttcacaggacgacaaaga	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63403807C>A	ENST00000398868.3	-	9	1127		c.e9-1		ATL3_ENST00000332645.4_Splice_Site|ATL3_ENST00000538786.1_Splice_Site|RP11-697H9.2_ENST00000540307.1_RNA	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3						endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.?(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						CCAGCAATATCTGTTCACAGG	0.403											OREG0021036	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Unknown(1)	large_intestine(1)	11											122	111	114					11																	63403807		1889	4132	6021	63160383	SO:0001630	splice_region_variant	25923				CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.851-1G>T	11.37:g.63403807C>A		1068	63160383	Q8N7W5|Q9H8Q5|Q9UFL1	Splice_Site	SNP	ENST00000398868.3	37	CCDS41663.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.241035	0.79912	.	.	ENSG00000184743	ENST00000398868;ENST00000332645;ENST00000538786	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3466	0.87311	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATL3	63160383	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.818000	0.86416	2.767000	0.95098	0.563000	0.77884	.		0.403	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459	Intron	A	63403807	C	A	63403807	5	1	61	1	0	0	0	0	0	0	1	0	1109	927	32	2	795	2	ATL3	11	63403807	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120712	63403807	71602709	7449	15434										
RTN3	10313	broad.mit.edu	37	chr11	63486240	63486240	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttcttcctttctttcatCttctgaaatacataacactg	3	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63486240C>A	ENST00000377819.5	+	3	420	c.266C>A	c.(265-267)tCt>tAt	p.S89Y	RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.S70Y|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000540798.1_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	89					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.S70Y(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TTTCTTTCATCTTCTGAAATA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	11											48	46	47					11																	63486240		2201	4298	6499	63242816	SO:0001583	missense	10313			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.266C>A	11.37:g.63486240C>A	ENSP00000367050:p.Ser89Tyr		63242816	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.051361	0.55218	.	.	ENSG00000133318	ENST00000377819;ENST00000339997	T;T	0.35605	1.3;1.32	5.3	4.37	0.52481	.	0.324031	0.22726	N	0.056387	T	0.47820	0.1466	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.48103	-0.9064	10	0.87932	D	0	-9.3634	11.9164	0.52767	0.0:0.8245:0.1755:0.0	.	89;70	O95197;O95197-2	RTN3_HUMAN;.	Y	89;70	ENSP00000367050:S89Y;ENSP00000344106:S70Y	ENSP00000344106:S70Y	S	+	2	0	RTN3	63242816	0.990000	0.36364	0.999000	0.59377	0.903000	0.53119	2.044000	0.41241	1.197000	0.43143	0.591000	0.81541	TCT		0.368	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		A	63486240	C	A	63486240	3	1	61	1	0	0	0	0	1	0	0	0	13764	913	32	2	276	2	RTN3	11	63486240	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82433	63486240	71520276	7450	15435										
RTN3	10313	broad.mit.edu	37	chr11	63488381	63488381	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcaagaatggatctgatCttgggatttcccagaagccc	10	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63488381C>A	ENST00000377819.5	+	3	2561	c.2407C>A	c.(2407-2409)Ctt>Att	p.L803I	RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.L784I|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000540798.1_Missense_Mutation_p.L691I	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	803					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.L784I(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TGGATCTGATCTTGGGATTTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	71	71					11																	63488381		2201	4298	6499	63244957	SO:0001583	missense	10313			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.2407C>A	11.37:g.63488381C>A	ENSP00000367050:p.Leu803Ile		63244957	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424747	0.62733	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	T;T;T	0.32753	1.44;1.45;1.48	5.67	4.74	0.60224	.	2.937730	0.01078	N	0.004935	T	0.41903	0.1179	L	0.32530	0.975	0.80722	D	1	D;D;D	0.59767	0.986;0.976;0.986	P;P;P	0.56163	0.793;0.626;0.793	T	0.31861	-0.9928	10	0.13853	T	0.58	-13.6471	12.8375	0.57782	0.0:0.8359:0.1641:0.0	.	691;803;784	F5H774;O95197;O95197-2	.;RTN3_HUMAN;.	I	803;784;691	ENSP00000367050:L803I;ENSP00000344106:L784I;ENSP00000442733:L691I	ENSP00000344106:L784I	L	+	1	0	RTN3	63244957	0.999000	0.42202	0.996000	0.52242	0.819000	0.46315	0.475000	0.22164	1.495000	0.48549	0.655000	0.94253	CTT		0.418	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		A	63488381	C	A	63488381	3	1	61	1	0	0	0	0	1	0	0	0	13764	913	32	2	2417	2	RTN3	11	63488381	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2141	63488381	71518135	7451	15436										
MARK2	2011	broad.mit.edu	37	chr11	63667414	63667414	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggcttcagcaatgaattCacctttgggaacaagctgga	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63667414C>T	ENST00000509502.2	+	8	964	c.501C>T	c.(499-501)ttC>ttT	p.F167F	MARK2_ENST00000361128.5_Silent_p.F200F|MARK2_ENST00000413835.2_Silent_p.F200F|MARK2_ENST00000377810.3_Silent_p.F167F|MARK2_ENST00000502399.3_Silent_p.F200F|MARK2_ENST00000315032.8_Silent_p.F200F|MARK2_ENST00000408948.3_Silent_p.F167F|MARK2_ENST00000508192.1_Silent_p.F200F|MARK2_ENST00000425897.2_Silent_p.F167F|MARK2_ENST00000402010.2_Silent_p.F200F|MARK2_ENST00000350490.7_Silent_p.F200F|MARK2_ENST00000377809.4_Silent_p.F200F|MARK2_ENST00000513765.2_Silent_p.F167F	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2									p.F167F(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						GCAATGAATTCACCTTTGGGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	11											156	150	152					11																	63667414		2201	4297	6498	63423990	SO:0001819	synonymous_variant	2011			BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.501C>T	11.37:g.63667414C>T			63423990		Silent	SNP	ENST00000509502.2	37	CCDS41665.1																																																																																				0.488	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		T	63667414	C	T	63667414	2	4	61	1	0	0	0	0	0	0	0	1	9343	825	29	3		3	MARK2	11	63667414	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179033	63667414	71339102	7452	15437										
MARK2	2011	broad.mit.edu	37	chr11	63668075	63668075	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaataccgtattccattCtacatgtccacggactgtga	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63668075C>A	ENST00000509502.2	+	9	1177	c.714C>A	c.(712-714)ttC>ttA	p.F238L	MARK2_ENST00000361128.5_Missense_Mutation_p.F271L|MARK2_ENST00000413835.2_Missense_Mutation_p.F271L|MARK2_ENST00000377810.3_Missense_Mutation_p.F238L|MARK2_ENST00000502399.3_Missense_Mutation_p.F271L|MARK2_ENST00000315032.8_Missense_Mutation_p.F271L|MARK2_ENST00000408948.3_Missense_Mutation_p.F238L|MARK2_ENST00000508192.1_Missense_Mutation_p.F271L|MARK2_ENST00000425897.2_Missense_Mutation_p.F238L|MARK2_ENST00000402010.2_Missense_Mutation_p.F271L|MARK2_ENST00000350490.7_Missense_Mutation_p.F271L|MARK2_ENST00000377809.4_Missense_Mutation_p.F271L|MARK2_ENST00000513765.2_Missense_Mutation_p.F238L	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2									p.F238L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						GTATTCCATTCTACATGTCCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											179	206	197					11																	63668075		2201	4297	6498	63424651	SO:0001583	missense	2011			BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.714C>A	11.37:g.63668075C>A	ENSP00000423974:p.Phe238Leu		63424651		Missense_Mutation	SNP	ENST00000509502.2	37	CCDS41665.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731578	0.89390	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	T;T;T;T;T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	N	0.05031	-0.125	0.80722	D	1	D;D;D;D;D;D	0.67145	0.996;0.974;0.97;0.99;0.974;0.985	D;P;P;D;P;P	0.68765	0.932;0.511;0.75;0.96;0.638;0.81	T	0.19257	-1.0311	10	0.87932	D	0	.	11.2533	0.49039	0.0:0.9158:0.0:0.0842	.	238;238;271;271;271;271	E7ETY4;Q7KZI7-14;Q7KZI7-15;Q7KZI7-5;Q7KZI7;Q7KZI7-16	.;.;.;.;MARK2_HUMAN;.	L	271;271;271;271;238;271;271;271;271;238;238;238;238	ENSP00000385751:F271L;ENSP00000326632:F271L;ENSP00000367040:F271L;ENSP00000389184:F271L;ENSP00000367041:F238L;ENSP00000425765:F271L;ENSP00000355091:F271L;ENSP00000294247:F271L;ENSP00000423974:F238L;ENSP00000421075:F238L;ENSP00000386128:F238L;ENSP00000415494:F238L	ENSP00000326632:F271L	F	+	3	2	MARK2	63424651	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.246000	0.51414	2.732000	0.93576	0.557000	0.71058	TTC		0.488	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		A	63668075	C	A	63668075	3	1	61	1	0	0	0	0	1	0	0	0	9343	912	32	2	847	2	MARK2	11	63668075	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	661	63668075	71338441	7453	15438										
RCOR2	283248	broad.mit.edu	37	chr11	63681556	63681556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtgggcgacgccgggttCgcaagggatggtggcggtac	21	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63681556C>T	ENST00000301459.4	-	8	1148	c.761G>A	c.(760-762)cGa>cAa	p.R254Q	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	254					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R254Q(2)		kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						ACGCCGGGTTCGCAAGGGATG	0.637																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	11											105	97	100					11																	63681556		2201	4297	6498	63438132	SO:0001583	missense	283248			BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.761G>A	11.37:g.63681556C>T	ENSP00000301459:p.Arg254Gln		63438132	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	37	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.136161	0.77662	.	.	ENSG00000167771	ENST00000301459	T	0.46451	0.87	4.58	4.58	0.56647	.	0.162858	0.43747	D	0.000524	T	0.60599	0.2281	M	0.76574	2.34	0.51482	D	0.999924	D	0.76494	0.999	P	0.58331	0.837	T	0.66164	-0.5992	10	0.66056	D	0.02	.	16.6689	0.85260	0.0:1.0:0.0:0.0	.	254	Q8IZ40	RCOR2_HUMAN	Q	254	ENSP00000301459:R254Q	ENSP00000301459:R254Q	R	-	2	0	RCOR2	63438132	0.998000	0.40836	0.363000	0.25875	0.076000	0.17211	5.842000	0.69417	2.532000	0.85374	0.561000	0.74099	CGA		0.637	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		T	63681556	C	T	63681556	3	4	61	1	0	0	0	0	1	0	0	0	13220	884	31	1	830	1	RCOR2	11	63681556	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13481	63681556	71324960	7454	15439										
RCOR2	283248	broad.mit.edu	37	chr11	63681949	63681949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtccatcacactagttCggctgcgggtcttcttccaa	9	13	4	0	rs140081088		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63681949C>T	ENST00000301459.4	-	6	932	c.545G>A	c.(544-546)cGa>cAa	p.R182Q	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	182					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R182Q(1)		kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						CACACTAGTTCGGCTGCGGGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	GLN/ARG	0,4402		0,0,2201	61	72	68		545	3.5	1	11	dbSNP_134	68	1,8593	1.2+/-3.3	0,1,4296	no	missense	RCOR2	NM_173587.3	43	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	182/524	63681949	1,12995	2201	4297	6498	63438525	SO:0001583	missense	283248			BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.545G>A	11.37:g.63681949C>T	ENSP00000301459:p.Arg182Gln		63438525	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	37	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150138	0.78001	0.0	1.16E-4	ENSG00000167771	ENST00000301459	T	0.28895	1.59	4.37	3.46	0.39613	Homeodomain-like (1);	0.068380	0.52532	D	0.000070	T	0.52108	0.1714	M	0.83774	2.66	0.52501	D	0.999955	D	0.76494	0.999	P	0.61132	0.884	T	0.56613	-0.7950	10	0.51188	T	0.08	.	11.6708	0.51399	0.0:0.9104:0.0:0.0896	.	182	Q8IZ40	RCOR2_HUMAN	Q	182	ENSP00000301459:R182Q	ENSP00000301459:R182Q	R	-	2	0	RCOR2	63438525	0.993000	0.37304	0.971000	0.41717	0.984000	0.73092	4.858000	0.62947	0.964000	0.38108	0.561000	0.74099	CGA		0.597	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		T	63681949	C	T	63681949	3	4	61	1	0	0	0	0	1	0	0	0	13220	884	31	1	1054	1	RCOR2	11	63681949	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	393	63681949	71324567	7455	15440										
STIP1	10963	broad.mit.edu	37	chr11	63965024	63965024	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttgtgagaaggccattGaagtggggagagaaaaccga	15	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63965024G>T	ENST00000305218.4	+	7	1006	c.859G>T	c.(859-861)Gaa>Taa	p.E287*	STIP1_ENST00000538945.1_Nonsense_Mutation_p.E263*|STIP1_ENST00000358794.5_Nonsense_Mutation_p.E334*	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	287					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E287*(1)		endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						GAAGGCCATTGAAGTGGGGAG	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											67	69	69					11																	63965024		2201	4297	6498	63721600	SO:0001587	stop_gained	10963			BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.859G>T	11.37:g.63965024G>T	ENSP00000305958:p.Glu287*		63721600	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Nonsense_Mutation	SNP	ENST00000305218.4	37	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	G	37	6.281134	0.97440	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945	.	.	.	5.73	5.73	0.89815	.	0.199495	0.51477	D	0.000085	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-24.2585	19.059	0.93080	0.0:0.0:1.0:0.0	.	.	.	.	X	334;287;263	.	ENSP00000305958:E287X	E	+	1	0	STIP1	63721600	1.000000	0.71417	0.961000	0.40146	0.851000	0.48451	7.320000	0.79064	2.882000	0.98803	0.655000	0.94253	GAA		0.498	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		T	63965024	G	T	63965024	4	4	61	1	0	0	0	0	0	1	0	0	15324	1291	45	2	885	2	STIP1	11	63965024	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283075	63965024	71041492	7456	15441										
NUDT22	84304	broad.mit.edu	37	chr11	63995105	63995105	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctggtggtacatgaactCttttccagtgtccttcagga	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:63995105C>A	ENST00000279206.3	+	3	702	c.546C>A	c.(544-546)ctC>ctA	p.L182L	DNAJC4_ENST00000355040.4_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|DNAJC4_ENST00000321685.3_5'Flank|TRPT1_ENST00000546133.1_5'Flank|NUDT22_ENST00000441250.2_Intron|TRPT1_ENST00000317459.6_5'Flank|TRPT1_ENST00000540472.1_5'Flank|TRPT1_ENST00000394547.3_5'Flank|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000394546.2_5'Flank|TRPT1_ENST00000546089.1_5'Flank	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	182	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.						hydrolase activity (GO:0016787)	p.L182L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						TACATGAACTCTTTTCCAGTG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	11											110	98	102					11																	63995105		2201	4297	6498	63751681	SO:0001819	synonymous_variant	84304			BC006129	CCDS8061.1, CCDS44640.1	11q13.1	2008-02-05			ENSG00000149761	ENSG00000149761		"Nudix motif containing"	28189	protein-coding gene	gene with protein product						12477932	Standard	NM_032344		Approved	MGC13045	uc009ype.4	Q9BRQ3	OTTHUMG00000167791	ENST00000279206.3:c.546C>A	11.37:g.63995105C>A			63751681	C9JY06|Q71RD5	Silent	SNP	ENST00000279206.3	37	CCDS8061.1																																																																																				0.597	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344		A	63995105	C	A	63995105	2	1	61	1	0	0	0	0	0	0	0	1	10770	900	32	2		2	NUDT22	11	63995105	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30081	63995105	71011411	7457	15442										
KCNK4	50801	broad.mit.edu	37	chr11	64064727	64064727	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccctgcgccatggcatCggtcacattgaagccatctt	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64064727C>T	ENST00000539216.1	+	3	810	c.450C>T	c.(448-450)atC>atT	p.I150I	Y_RNA_ENST00000384297.1_RNA|KCNK4_ENST00000394525.2_Silent_p.I150I|KCNK4_ENST00000422670.2_Silent_p.I150I|KCNK4_ENST00000538767.1_Missense_Mutation_p.S84L|RP11-783K16.10_ENST00000539086.1_RNA|KCNK4_ENST00000539651.1_3'UTR			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	150					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.I150I(1)		breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						GCCATGGCATCGGTCACATTG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	11											47	47	47					11																	64064727		2201	4297	6498	63821303	SO:0001819	synonymous_variant	50801			AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.450C>T	11.37:g.64064727C>T			63821303	B5TJL1|Q96T94	Silent	SNP	ENST00000539216.1	37	CCDS8067.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320064	0.41096	.	.	ENSG00000182450	ENST00000538767	.	.	.	5.05	-2.44	0.06502	.	.	.	.	.	T	0.49949	0.1587	.	.	.	0.80722	D	1	B;B	0.20780	0.048;0.048	B;B	0.11329	0.006;0.006	T	0.36817	-0.9732	7	0.87932	D	0	.	10.8859	0.46965	0.0:0.5438:0.0:0.4562	.	123;84	B4DJC9;F5GYE0	.;.	L	84	.	ENSP00000446454:S84L	S	+	2	0	KCNK4	63821303	0.030000	0.19436	0.729000	0.30791	0.995000	0.86356	-0.960000	0.03849	-0.504000	0.06577	0.561000	0.74099	TCG		0.627	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311		T	64064727	C	T	64064727	2	4	61	1	0	0	0	0	0	0	0	1	8089	874	31	1		1	KCNK4	11	64064727	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69622	64064727	70941789	7458	15443										
KCNK4	50801	broad.mit.edu	37	chr11	64064980	64064980	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtaagagtgctgtcggcGatgcttttcctgctgatcgg	13	9	0	2	rs147311763	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64064980G>A	ENST00000539216.1	+	4	876	c.516G>A	c.(514-516)gcG>gcA	p.A172A	Y_RNA_ENST00000384297.1_RNA|TEX40_ENST00000328404.6_5'Flank|KCNK4_ENST00000394525.2_Silent_p.A172A|KCNK4_ENST00000422670.2_Silent_p.A172A|KCNK4_ENST00000538767.1_Intron|RP11-783K16.10_ENST00000539086.1_RNA|KCNK4_ENST00000539651.1_Intron|TEX40_ENST00000539943.1_5'Flank			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	172					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A172A(1)		breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						TGCTGTCGGCGATGCTTTTCC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	11											128	102	110					11																	64064980		2201	4297	6498	63821556	SO:0001819	synonymous_variant	50801			AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.516G>A	11.37:g.64064980G>A			63821556	B5TJL1|Q96T94	Silent	SNP	ENST00000539216.1	37	CCDS8067.1																																																																																				0.577	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311		A	64064980	G	A	64064980	2	1	61	1	0	0	0	0	0	0	0	1	8089	1045	37	1		1	KCNK4	11	64064980	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253	64064980	70941536	7459	15444										
SLC22A11	55867	broad.mit.edu	37	chr11	64331885	64331885	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggccacaaggaggccaaGaacctgaccatagaggtgag	13	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64331885G>T	ENST00000301891.4	+	5	1301	c.927G>T	c.(925-927)aaG>aaT	p.K309N	SLC22A11_ENST00000377581.3_Missense_Mutation_p.K309N|SLC22A11_ENST00000377585.3_Missense_Mutation_p.K309N|SLC22A11_ENST00000490834.1_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	309					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.K309N(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	AGGAGGCCAAGAACCTGACCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											93	86	88					11																	64331885		2201	4297	6498	64088461	SO:0001583	missense	55867			AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"Solute carriers"	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.927G>T	11.37:g.64331885G>T	ENSP00000301891:p.Lys309Asn		64088461	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Missense_Mutation	SNP	ENST00000301891.4	37	CCDS8074.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871796	0.33069	.	.	ENSG00000168065	ENST00000301891;ENST00000377585;ENST00000377581	T;T;T	0.75154	-0.91;-0.91;-0.91	4.31	-4.06	0.03986	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.546580	0.04187	U	0.327503	T	0.61590	0.2359	N	0.05351	-0.065	0.09310	N	1	D;D;P;P	0.58970	0.958;0.984;0.889;0.889	P;P;P;P	0.57846	0.676;0.828;0.659;0.524	T	0.53697	-0.8402	10	0.27785	T	0.31	.	1.7548	0.02980	0.1652:0.3717:0.2116:0.2515	.	309;103;309;309	Q9NSA0-2;Q8NBZ3;A6NCG2;Q9NSA0	.;.;.;S22AB_HUMAN	N	309	ENSP00000301891:K309N;ENSP00000366809:K309N;ENSP00000366804:K309N	ENSP00000301891:K309N	K	+	3	2	SLC22A11	64088461	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	0.232000	0.17891	-0.515000	0.06479	-0.302000	0.09304	AAG		0.562	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484		T	64331885	G	T	64331885	3	4	61	1	0	0	0	0	1	0	0	0	14479	933	33	2	945	2	SLC22A11	11	64331885	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	266905	64331885	70674631	7460	15445										
NRXN2	9379	broad.mit.edu	37	chr11	64418761	64418761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgacaatgaagtcattgcCgttgcccgagttgaacagaa	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64418761C>T	ENST00000377551.1	-	13	3095	c.2884G>A	c.(2884-2886)Ggc>Agc	p.G962S	NRXN2_ENST00000265459.6_Missense_Mutation_p.G962S|AP001092.4_ENST00000433606.1_RNA|NRXN2_ENST00000409571.1_Missense_Mutation_p.G955S|NRXN2_ENST00000377559.3_Missense_Mutation_p.G922S			Q9P2S2	NRX2A_HUMAN	neurexin 2	962	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)	p.G962S(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						AAGTCATTGCCGTTGCCCGAG	0.587											OREG0004037|OREG0021057	type=REGULATORY REGION|Gene=AL137356|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(1)|skin(1)	11											67	55	59					11																	64418761		2201	4297	6498	64175337	SO:0001583	missense	9379				CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.2884G>A	11.37:g.64418761C>T	ENSP00000366774:p.Gly962Ser	1076	64175337	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855841	0.71834	.	.	ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571	T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25	4.2	4.2	0.49525	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.290921	0.18872	N	0.128818	D	0.84370	0.5457	L	0.52759	1.655	0.54753	D	0.999983	D;B;B	0.89917	1.0;0.424;0.02	D;B;B	0.97110	1.0;0.377;0.009	D	0.85476	0.1176	10	0.66056	D	0.02	.	14.0926	0.65000	0.0:1.0:0.0:0.0	.	922;962;708	Q9P2S2-2;Q9P2S2;E7EV67	.;NRX2A_HUMAN;.	S	962;922;962;922;955	ENSP00000366774:G962S;ENSP00000366782:G922S;ENSP00000265459:G962S;ENSP00000386416:G955S	ENSP00000265459:G962S	G	-	1	0	NRXN2	64175337	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.610000	0.82949	2.172000	0.68678	0.561000	0.74099	GGC		0.587	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64418761	C	T	64418761	3	4	61	1	0	0	0	0	1	0	0	0	10697	652	23	1	2563	1	NRXN2	11	64418761	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86876	64418761	70587755	7461	15446										
RASGRP2	10235	broad.mit.edu	37	chr11	64503026	64503026	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctcacctccaccatcttCtcgatgtgctccaccacgag	7	17	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64503026C>A	ENST00000354024.3	-	11	1536	c.1284G>T	c.(1282-1284)gaG>gaT	p.E428D	RASGRP2_ENST00000394432.3_Missense_Mutation_p.E428D|RASGRP2_ENST00000377494.1_Missense_Mutation_p.E428D|RASGRP2_ENST00000377497.3_Missense_Mutation_p.E428D	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	428	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.E490D(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCACCATCTTCTCGATGTGCT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											60	56	57					11																	64503026		2201	4297	6498	64259602	SO:0001583	missense	10235			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"EF-hand domain containing"	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1284G>T	11.37:g.64503026C>A	ENSP00000338864:p.Glu428Asp		64259602	A6NDC7|O00538|Q9UL65	Missense_Mutation	SNP	ENST00000354024.3	37	CCDS31598.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296169	0.81025	.	.	ENSG00000068831	ENST00000377494;ENST00000394432;ENST00000377497;ENST00000354024	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.9	3.99	0.46301	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.33556	0.0867	L	0.53249	1.67	0.80722	D	1	P;P	0.44734	0.842;0.495	B;B	0.33750	0.169;0.169	T	0.26849	-1.0091	10	0.59425	D	0.04	-8.5918	11.2484	0.49010	0.0:0.9095:0.0:0.0905	.	428;428	Q7LDG7;A6NDC7	GRP2_HUMAN;.	D	428	ENSP00000366714:E428D;ENSP00000377953:E428D;ENSP00000366717:E428D;ENSP00000338864:E428D	ENSP00000338864:E428D	E	-	3	2	RASGRP2	64259602	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.060000	0.41394	1.212000	0.43366	0.561000	0.74099	GAG		0.647	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819		A	64503026	C	A	64503026	3	1	61	1	0	0	0	0	1	0	0	0	13112	912	32	2	569	2	RASGRP2	11	64503026	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84265	64503026	70503490	7462	15447										
RASGRP2	10235	broad.mit.edu	37	chr11	64503052	64503052	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctccaccacgagggcctGatccagcttgggtttggcag	14	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64503052G>A	ENST00000354024.3	-	11	1510	c.1258C>T	c.(1258-1260)Cag>Tag	p.Q420*	RASGRP2_ENST00000394432.3_Nonsense_Mutation_p.Q420*|RASGRP2_ENST00000377494.1_Nonsense_Mutation_p.Q420*|RASGRP2_ENST00000377497.3_Nonsense_Mutation_p.Q420*	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	420					blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.Q482*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACGAGGGCCTGATCCAGCTTG	0.647																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											57	52	54					11																	64503052		2201	4297	6498	64259628	SO:0001587	stop_gained	10235			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"EF-hand domain containing"	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1258C>T	11.37:g.64503052G>A	ENSP00000338864:p.Gln420*		64259628	A6NDC7|O00538|Q9UL65	Nonsense_Mutation	SNP	ENST00000354024.3	37	CCDS31598.1	.	.	.	.	.	.	.	.	.	.	G	39	7.418785	0.98272	.	.	ENSG00000068831	ENST00000377494;ENST00000394432;ENST00000377497;ENST00000354024	.	.	.	4.9	4.9	0.64082	.	0.060349	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-20.7837	15.9583	0.79906	0.0:0.0:1.0:0.0	.	.	.	.	X	420	.	ENSP00000338864:Q420X	Q	-	1	0	RASGRP2	64259628	1.000000	0.71417	0.992000	0.48379	0.982000	0.71751	6.810000	0.75216	2.446000	0.82766	0.561000	0.74099	CAG		0.647	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819		A	64503052	G	A	64503052	4	1	61	1	0	0	0	0	0	1	0	0	13112	1299	45	3	595	3	RASGRP2	11	64503052	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26	64503052	70503464	7463	15448										
PYGM	5837	broad.mit.edu	37	chr11	64519471	64519471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccgcttcacctggatgtCgaagagtgagttggggttga	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64519471C>T	ENST00000164139.3	-	14	2091	c.1693G>A	c.(1693-1695)Gac>Aac	p.D565N	PYGM_ENST00000377432.3_Missense_Mutation_p.D477N|PYGM_ENST00000462303.1_5'UTR	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	565					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)	p.D565N(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACCTGGATGTCGAAGAGTGAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											218	185	196					11																	64519471		2201	4297	6498	64276047	SO:0001583	missense	5837				CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1693G>A	11.37:g.64519471C>T	ENSP00000164139:p.Asp565Asn		64276047	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	35	5.501420	0.96371	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.96200	-3.94;-3.94	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000012	D	0.98469	0.9490	H	0.95645	3.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	D	0.99449	1.0940	10	0.87932	D	0	-44.0514	17.3513	0.87324	0.0:1.0:0.0:0.0	.	477;565	A6NDY6;P11217	.;PYGM_HUMAN	N	477;565;546	ENSP00000366650:D477N;ENSP00000164139:D565N	ENSP00000164139:D565N	D	-	1	0	PYGM	64276047	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.783000	0.85696	2.698000	0.92095	0.561000	0.74099	GAC		0.517	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64519471	C	T	64519471	3	4	61	1	0	0	0	0	1	0	0	0	12899	884	31	1	863	1	PYGM	11	64519471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16419	64519471	70487045	7464	15449										
SF1	7536	broad.mit.edu	37	chr11	64537040	64537040	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcccccggatcataatcTtggcattgcactccttctct	5	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64537040T>G	ENST00000377390.3	-	6	858	c.521A>C	c.(520-522)aAg>aCg	p.K174T	SF1_ENST00000489544.1_5'UTR|SF1_ENST00000227503.9_Missense_Mutation_p.K174T|SF1_ENST00000334944.5_Missense_Mutation_p.K174T|SF1_ENST00000422298.2_Missense_Mutation_p.K59T|SF1_ENST00000433274.2_Missense_Mutation_p.K148T|SF1_ENST00000377387.1_Missense_Mutation_p.K299T|SF1_ENST00000377394.3_Missense_Mutation_p.K174T	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	174	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.K174T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						GATCATAATCTTGGCATTGCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											224	228	227					11																	64537040		2201	4297	6498	64293616	SO:0001583	missense	7536			D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.521A>C	11.37:g.64537040T>G	ENSP00000366607:p.Lys174Thr		64293616	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	37	CCDS31599.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.986590	0.93106	.	.	ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000377394;ENST00000334944;ENST00000422298;ENST00000433274	T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39	6.04	6.04	0.98038	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.85197	2.74	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.996;0.997;0.996;0.998;0.997;0.997	T	0.70425	-0.4875	10	0.87932	D	0	.	14.5406	0.67990	0.0:0.0:0.0:1.0	.	59;174;174;174;174;299	B4DX42;Q15637-6;Q15637-4;Q15637;Q15637-2;Q15637-5	.;.;.;SF01_HUMAN;.;.	T	299;174;174;174;174;59;148	ENSP00000366604:K299T;ENSP00000366607:K174T;ENSP00000227503:K174T;ENSP00000366611:K174T;ENSP00000334414:K174T;ENSP00000413084:K59T;ENSP00000396793:K148T	ENSP00000227503:K174T	K	-	2	0	SF1	64293616	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.670000	0.83925	2.317000	0.78254	0.460000	0.39030	AAG		0.483	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		G	64537040	T	G	64537040	3	3	61	1	0	0	0	0	1	0	0	0	14182	1609	56	4	1568	4	SF1	11	64537040	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	17569	64537040	70469476	7465	15450										
EHD1	10938	broad.mit.edu	37	chr11	64622929	64622929	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacattgggcatctctttCttgagggagctgatgatgta	12	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64622929C>A	ENST00000320631.3	-	4	1199	c.945G>T	c.(943-945)aaG>aaT	p.K315N	EHD1_ENST00000488711.1_5'Flank|EHD1_ENST00000359393.2_Missense_Mutation_p.K315N	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	315					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)	p.K315N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						GCATCTCTTTCTTGAGGGAGC	0.547											OREG0004024	type=REGULATORY REGION|Gene=EHD1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Missense(1)	large_intestine(1)	11											151	140	144					11																	64622929		2201	4297	6498	64379505	SO:0001583	missense	10938			AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"EF-hand domain containing"	3242	protein-coding gene	gene with protein product	"testilin"	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.945G>T	11.37:g.64622929C>A	ENSP00000320516:p.Lys315Asn	1078	64379505	O14611|Q2M3Q4|Q9UNR3	Missense_Mutation	SNP	ENST00000320631.3	37	CCDS8084.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.362391	0.82353	.	.	ENSG00000110047	ENST00000320631;ENST00000359393;ENST00000541001;ENST00000421303;ENST00000421510;ENST00000433803	T;T;T;T	0.51574	2.0;2.0;0.7;1.3	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.92412	3.305	0.58432	D	0.999998	P;P	0.49358	0.923;0.923	P;P	0.52957	0.714;0.714	T	0.78590	-0.2145	10	0.87932	D	0	.	15.0511	0.71872	0.0:1.0:0.0:0.0	.	315;315	B2R5U3;Q9H4M9	.;EHD1_HUMAN	N	315;315;291;329;179;329	ENSP00000320516:K315N;ENSP00000352354:K315N;ENSP00000391429:K179N;ENSP00000404944:K329N	ENSP00000320516:K315N	K	-	3	2	EHD1	64379505	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.439000	0.44846	2.420000	0.82092	0.561000	0.74099	AAG		0.547	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795		A	64622929	C	A	64622929	3	1	61	1	0	0	0	0	1	0	0	0	4988	912	32	2	667	2	EHD1	11	64622929	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85889	64622929	70383587	7466	15451										
PPP2R5B	5526	broad.mit.edu	37	chr11	64697809	64697809	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggttcatctatgaattCgagcacttcaatggtgtggc	11	8	3	1	rs186585758		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64697809C>T	ENST00000164133.2	+	7	1360	c.738C>T	c.(736-738)ttC>ttT	p.F246F		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	246					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.F246F(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						TCTATGAATTCGAGCACTTCA	0.582													c|||	1	0.000199681	0	0	5008	,	,		19032	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11											125	110	115					11																	64697809		2201	4297	6498	64454385	SO:0001819	synonymous_variant	5526			L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9310	protein-coding gene	gene with protein product	"PP2A, B subunit, B' beta isoform", "PP2A, B subunit, B56 beta isoform", "PP2A, B subunit, PR61 beta isoform", "PP2A, B subunit, R5 beta isoform", "serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"	601644	"protein phosphatase 2, regulatory subunit B (B56), beta isoform", "protein phosphatase 2, regulatory subunit B', beta isoform"			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.738C>T	11.37:g.64697809C>T			64454385	Q13853	Silent	SNP	ENST00000164133.2	37	CCDS8085.1																																																																																				0.582	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244		T	64697809	C	T	64697809	2	4	61	1	0	0	0	0	0	0	0	1	12427	883	31	1		1	PPP2R5B	11	64697809	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74880	64697809	70308707	7467	15452										
ZFPL1	7542	broad.mit.edu	37	chr11	64853947	64853947	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaccccgaaacacggcacCtgccggctatcagtgcccca	9	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64853947C>A	ENST00000294258.3	+	4	427	c.275C>A	c.(274-276)cCt>cAt	p.P92H	CDCA5_ENST00000275517.3_5'Flank|AP003068.6_ENST00000525544.2_5'Flank|CDCA5_ENST00000404147.3_5'Flank	NM_006782.3	NP_006773.2	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	92					regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.P92H(1)		breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11						AACACGGCACCTGCCGGCTAT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											145	153	151					11																	64853947		2201	4297	6498	64610523	SO:0001583	missense	7542				CCDS8092.1	11q13	2013-01-08			ENSG00000162300	ENSG00000162300			12868	protein-coding gene	gene with protein product	"zinc-finger protein in MEN1 region"					9653652	Standard	NM_006782		Approved	D11S750, MCG4	uc001ocq.1	O95159	OTTHUMG00000165597	ENST00000294258.3:c.275C>A	11.37:g.64853947C>A	ENSP00000294258:p.Pro92His		64610523	A8K7E9|O14616|Q9UID0	Missense_Mutation	SNP	ENST00000294258.3	37	CCDS8092.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.659672	0.88154	.	.	ENSG00000162300	ENST00000294258;ENST00000526334;ENST00000526945;ENST00000532200	D;D;D	0.96232	-3.95;-3.95;-3.95	5.49	5.49	0.81192	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.051783	0.85682	D	0.000000	D	0.98353	0.9453	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99232	1.0882	10	0.72032	D	0.01	-7.8398	16.8521	0.85996	0.0:1.0:0.0:0.0	.	92	O95159	ZFPL1_HUMAN	H	92;92;86;92	ENSP00000294258:P92H;ENSP00000434454:P92H;ENSP00000437090:P92H	ENSP00000294258:P92H	P	+	2	0	ZFPL1	64610523	1.000000	0.71417	0.998000	0.56505	0.885000	0.51271	6.990000	0.76225	2.578000	0.87016	0.462000	0.41574	CCT		0.617	ZFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385196.1	NM_006782		A	64853947	C	A	64853947	3	1	61	1	0	0	0	0	1	0	0	0	17695	681	24	2	285	2	ZFPL1	11	64853947	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156138	64853947	70152569	7468	15453										
SYVN1	84447	broad.mit.edu	37	chr11	64896042	64896042	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatcacacctacctggaggCctttccatttcaggggctgg	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64896042C>T	ENST00000377190.3	-	15	1834	c.1740G>A	c.(1738-1740)agG>agA	p.R580R	SYVN1_ENST00000526060.1_Silent_p.R579R|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000307289.6_Silent_p.R528R|SYVN1_ENST00000294256.8_Silent_p.R579R	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	580					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)	p.R580R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TACCTGGAGGCCTTTCCATTT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	11											50	59	56					11																	64896042		2201	4297	6498	64652618	SO:0001819	synonymous_variant	84447			AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1740G>A	11.37:g.64896042C>T			64652618	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Silent	SNP	ENST00000377190.3	37	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	c	0.304	-0.971915	0.02215	.	.	ENSG00000162298	ENST00000434219	.	.	.	4.73	1.83	0.25207	.	.	.	.	.	T	0.52709	0.1751	.	.	.	0.49798	D	0.999824	.	.	.	.	.	.	T	0.41502	-0.9505	5	0.35671	T	0.21	-4.6004	4.6044	0.12371	0.0:0.6:0.1982:0.2018	.	.	.	.	D	580	.	ENSP00000412962:G580D	G	-	2	0	SYVN1	64652618	0.834000	0.29399	0.747000	0.31113	0.231000	0.25187	0.854000	0.27791	0.218000	0.20820	0.550000	0.68814	GGC		0.617	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		T	64896042	C	T	64896042	2	4	61	1	0	0	0	0	0	0	0	1	15526	738	26	3		3	SYVN1	11	64896042	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42095	64896042	70110474	7469	15454										
SLC22A20	440044	broad.mit.edu	37	chr11	64990004	64990004	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcccagttagctgtacaGaatctgcagaaggtggctgc	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:64990004G>T	ENST00000525437.1	+	0	902							A6NK97	S22AK_HUMAN	solute carrier family 22, member 20						ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.E234*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)	8						TAGCTGTACAGAATCTGCAGA	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											64	62	62					11																	64990004		2040	4202	6242	64746580			440044			DQ053017		11q13.1	2014-02-20			ENSG00000197847	ENSG00000197847		"Solute carriers"	29867	other	unknown		611696				15369770, 16478971	Standard	NM_001004326		Approved	Oat6, FLJ16331	uc021qlh.1	A6NK97	OTTHUMG00000165615		11.37:g.64990004G>T			64746580	B9EJB2|Q6ZN88	Nonsense_Mutation	SNP	ENST00000525437.1	37																																																																																					0.587	SLC22A20-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000385336.1	NM_001004326		T	64990004	G	T	64990004	1	4	61	0	1	0	0	0	0	0	0	0	14488	943	33	2		2	SLC22A20	11	64990004	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93962	64990004	70016512	7470	15455										
KAT5	10524	broad.mit.edu	37	chr11	65482032	65482032	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcagcctggtgtctgatCgaagccacgacgacatcgtc	12	13	1	1	rs4645921		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:65482032C>T	ENST00000377046.3	+	8	930	c.658C>T	c.(658-660)Cga>Tga	p.R220*	KAT5_ENST00000352980.4_Nonsense_Mutation_p.R168*|KAT5_ENST00000341318.4_Nonsense_Mutation_p.R253*|KAT5_ENST00000530446.1_Nonsense_Mutation_p.R201*|KAT5_ENST00000534650.1_Nonsense_Mutation_p.R9*	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	220					androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)	p.R253*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						GGTGTCTGATCGAAGCCACGA	0.582																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											98	78	85					11																	65482032		2201	4297	6498	65238608	SO:0001587	stop_gained	10524			U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.658C>T	11.37:g.65482032C>T	ENSP00000366245:p.Arg220*		65238608	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Nonsense_Mutation	SNP	ENST00000377046.3	37	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732762	0.30684	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000534104;ENST00000528198;ENST00000531880;ENST00000534650;ENST00000534681	.	.	.	4.97	3.03	0.35002	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-17.2735	7.9251	0.29870	0.1839:0.6388:0.1772:0.0	.	.	.	.	X	220;168;253;201;9;162;214;9;9	.	ENSP00000340330:R253X	R	+	1	2	KAT5	65238608	1.000000	0.71417	0.998000	0.56505	0.129000	0.20672	3.322000	0.52007	0.632000	0.30432	-0.305000	0.09177	CGA		0.582	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		T	65482032	C	T	65482032	4	4	61	1	0	0	0	0	0	1	0	0	8004	876	31	1	783	1	KAT5	11	65482032	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	492028	65482032	69524484	7471	15456										
SNX32	254122	broad.mit.edu	37	chr11	65620387	65620387	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggtctcctcttttcgaaaGaatctcattgagctggcaga	10	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:65620387G>T	ENST00000308342.6	+	12	1541	c.1116G>T	c.(1114-1116)aaG>aaT	p.K372N		NM_152760.2	NP_689973.2	Q86XE0	SNX32_HUMAN	sorting nexin 32	372					intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)	p.K372N(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				READ - Rectum adenocarcinoma(159;0.171)		CTTTTCGAAAGAATCTCATTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	93	91					11																	65620387		2201	4297	6498	65376963	SO:0001583	missense	254122			AK055496	CCDS8113.2	11q13.1	2008-03-11	2008-03-11	2008-03-11	ENSG00000172803	ENSG00000172803		"Sorting nexins"	26423	protein-coding gene	gene with protein product			"sorting nexin 6B"	SNX6B		16782399	Standard	XM_005273871		Approved	FLJ30934	uc001ofr.3	Q86XE0	OTTHUMG00000128491	ENST00000308342.6:c.1116G>T	11.37:g.65620387G>T	ENSP00000310620:p.Lys372Asn		65376963	Q8IW53|Q96NG4	Missense_Mutation	SNP	ENST00000308342.6	37	CCDS8113.2	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650807	0.67472	.	.	ENSG00000172803	ENST00000308342	T	0.20332	2.08	3.88	1.92	0.25849	.	0.148826	0.31113	N	0.008240	T	0.40619	0.1124	M	0.79475	2.455	0.35826	D	0.824947	D	0.76494	0.999	D	0.67900	0.954	T	0.52859	-0.8519	10	0.87932	D	0	-21.2832	8.2013	0.31426	0.211:0.0:0.789:0.0	.	372	Q86XE0	SNX32_HUMAN	N	372	ENSP00000310620:K372N	ENSP00000310620:K372N	K	+	3	2	SNX32	65376963	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	2.118000	0.41949	0.840000	0.34995	0.561000	0.74099	AAG		0.627	SNX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250295.3	NM_152760		T	65620387	G	T	65620387	3	4	61	1	0	0	0	0	1	0	0	0	14939	933	33	2	1162	2	SNX32	11	65620387	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138355	65620387	69386129	7472	15457										
BANF1	8815	broad.mit.edu	37	chr11	65771217	65771217	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggactgcttcggatgccttCgagagtggtgcgacgccttc	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:65771217C>T	ENST00000312175.2	+	3	752	c.244C>T	c.(244-246)Cga>Tga	p.R82*	EIF1AD_ENST00000533544.1_5'Flank|BANF1_ENST00000445560.2_Nonsense_Mutation_p.R82*|BANF1_ENST00000527348.1_Nonsense_Mutation_p.R82*|BANF1_ENST00000533166.1_Nonsense_Mutation_p.R82*|EIF1AD_ENST00000527249.1_5'Flank|EIF1AD_ENST00000526451.1_5'Flank|BANF1_ENST00000524628.1_3'UTR|EIF1AD_ENST00000529964.1_5'Flank|EIF1AD_ENST00000312234.2_5'Flank|EIF1AD_ENST00000525767.1_5'Flank	NM_001143985.1|NM_003860.3	NP_001137457.1|NP_003851.1	O75531	BAF_HUMAN	barrier to autointegration factor 1	82					DNA integration (GO:0015074)|establishment of integrated proviral latency (GO:0075713)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|response to virus (GO:0009615)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R82*(1)		large_intestine(2)|prostate(1)	3						CGGATGCCTTCGAGAGTGGTG	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											73	69	70					11																	65771217		2201	4296	6497	65527793	SO:0001587	stop_gained	8815			AF068235	CCDS8125.1	11q13.1	2012-04-19			ENSG00000175334	ENSG00000175334			17397	protein-coding gene	gene with protein product		603811				9465049	Standard	NM_003860		Approved	BAF	uc001ogp.3	O75531	OTTHUMG00000166749	ENST00000312175.2:c.244C>T	11.37:g.65771217C>T	ENSP00000310275:p.Arg82*		65527793	O60558|Q6FGG7	Nonsense_Mutation	SNP	ENST00000312175.2	37	CCDS8125.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708975	0.89018	.	.	ENSG00000175334	ENST00000312175;ENST00000445560;ENST00000533166;ENST00000527348	.	.	.	4.91	4.01	0.46588	.	0.191724	0.43260	D	0.000596	.	.	.	.	.	.	0.49130	D	0.999757	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-18.1095	6.1307	0.20203	0.1848:0.7214:0.0:0.0938	.	.	.	.	X	82	.	ENSP00000310275:R82X	R	+	1	2	BANF1	65527793	0.991000	0.36638	0.950000	0.38849	0.053000	0.15095	3.250000	0.51445	1.323000	0.45263	-0.142000	0.14014	CGA		0.567	BANF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391340.1	NM_003860		T	65771217	C	T	65771217	4	4	61	1	0	0	0	0	0	1	0	0	1308	876	31	1	250	1	BANF1	11	65771217	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150830	65771217	69235299	7473	15458										
CATSPER1	117144	broad.mit.edu	37	chr11	65787826	65787826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcctttgaacagcgccgTctggaagctatccaccagga	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:65787826T>C	ENST00000312106.5	-	8	2163	c.2026A>G	c.(2026-2028)Acg>Gcg	p.T676A		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	676					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.T676A(1)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						AACAGCGCCGTCTGGAAGCTA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											116	112	113					11																	65787826		2201	4296	6497	65544402	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2026A>G	11.37:g.65787826T>C	ENSP00000309052:p.Thr676Ala		65544402	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	T	9.926	1.213396	0.22289	.	.	ENSG00000175294	ENST00000312106	D	0.96427	-4.01	5.14	5.14	0.70334	.	0.195350	0.25386	U	0.031058	D	0.88815	0.6539	N	0.08118	0	0.21933	N	0.999461	B	0.10296	0.003	B	0.09377	0.004	T	0.74393	-0.3680	10	0.09338	T	0.73	-20.654	11.34	0.49527	0.0:0.0:0.0:1.0	.	676	Q8NEC5	CTSR1_HUMAN	A	676	ENSP00000309052:T676A	ENSP00000309052:T676A	T	-	1	0	CATSPER1	65544402	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	1.341000	0.33907	1.936000	0.56123	0.402000	0.26972	ACG		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		C	65787826	T	C	65787826	3	2	61	1	0	0	0	0	1	0	0	0	2693	1667	58	4	336	4	CATSPER1	11	65787826	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	16609	65787826	69218690	7474	15459										
PACS1	55690	broad.mit.edu	37	chr11	65977848	65977848	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagggttcaaaaagaattCttcgctccaacgagatcgtc	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:65977848C>A	ENST00000320580.4	+	3	493	c.460C>A	c.(460-462)Ctt>Att	p.L154I		NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	154					protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)	p.L154I(1)	RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						AAAAAGAATTCTTCGCTCCAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											133	118	123					11																	65977848		2201	4295	6496	65734424	SO:0001583	missense	55690			AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115			30032	protein-coding gene	gene with protein product		607492				12855553, 14608369	Standard	NM_018026		Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.460C>A	11.37:g.65977848C>A	ENSP00000316454:p.Leu154Ile		65734424	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Missense_Mutation	SNP	ENST00000320580.4	37	CCDS8129.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356807	0.82243	.	.	ENSG00000175115	ENST00000320580;ENST00000533756;ENST00000527380	T	0.57907	0.37	5.28	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.87456	2.885	0.80722	D	1	D;D	0.67145	0.993;0.996	D;D	0.80764	0.987;0.994	T	0.76063	-0.3096	10	0.87932	D	0	-10.7761	9.2592	0.37601	0.0:0.832:0.0:0.168	.	154;154	Q6VY07;Q6VY07-2	PACS1_HUMAN;.	I	154;51;56	ENSP00000316454:L154I	ENSP00000316454:L154I	L	+	1	0	PACS1	65734424	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.896000	0.56266	1.228000	0.43614	0.585000	0.79938	CTT		0.507	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026		A	65977848	C	A	65977848	3	1	61	1	0	0	0	0	1	0	0	0	11403	913	32	2	470	2	PACS1	11	65977848	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	190022	65977848	69028668	7475	15460										
SLC29A2	3177	broad.mit.edu	37	chr11	66136895	66136895	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaggggcagctgggacaGcagcgtcacccaattgttga	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66136895G>A	ENST00000357440.2	-	3	448	c.220C>T	c.(220-222)Ctg>Ttg	p.L74L	SLC29A2_ENST00000546034.1_Silent_p.L74L|SLC29A2_ENST00000311161.7_Silent_p.L74L|SLC29A2_ENST00000544554.1_Silent_p.L74L	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	74					cell proliferation (GO:0008283)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)	p.L74L(1)		breast(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10					Didanosine(DB00900)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Zalcitabine(DB00943)|Zidovudine(DB00495)	AGCTGGGACAGCAGCGTCACC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	11											180	161	168					11																	66136895		2200	4295	6495	65893471	SO:0001819	synonymous_variant	3177			X86681	CCDS8137.1, CCDS73326.1	11q13	2013-07-17	2013-07-17		ENSG00000174669	ENSG00000174669		"Solute carriers"	11004	protein-coding gene	gene with protein product		602110	"solute carrier family 29 (nucleoside transporters), member 2"	ENT2, HNP36		9192854, 9478986	Standard	NM_001532		Approved	DER12	uc001oht.3	Q14542	OTTHUMG00000169056	ENST00000357440.2:c.220C>T	11.37:g.66136895G>A			65893471	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Silent	SNP	ENST00000357440.2	37	CCDS8137.1																																																																																				0.647	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532		A	66136895	G	A	66136895	2	1	61	1	0	0	0	0	0	0	0	1	14572	962	34	3		3	SLC29A2	11	66136895	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159047	66136895	68869621	7476	15461										
NPAS4	266743	broad.mit.edu	37	chr11	66191166	66191166	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagagggacccattactgCcaataactacccaatcaggt	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66191166C>G	ENST00000311034.2	+	6	1102	c.926C>G	c.(925-927)gCc>gGc	p.A309G		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	309	PAC.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.A309G(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CCCATTACTGCCAATAACTAC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											75	74	74					11																	66191166		2200	4295	6495	65947742	SO:0001583	missense	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.926C>G	11.37:g.66191166C>G	ENSP00000311196:p.Ala309Gly		65947742	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.641565	0.29157	.	.	ENSG00000174576	ENST00000311034	T	0.49139	0.79	4.97	4.97	0.65823	.	0.119241	0.38217	N	0.001776	T	0.34366	0.0895	N	0.14661	0.345	0.36269	D	0.855056	B	0.16396	0.017	B	0.20767	0.031	T	0.39542	-0.9609	10	0.66056	D	0.02	-6.2824	15.7617	0.78087	0.0:1.0:0.0:0.0	.	309	Q8IUM7	NPAS4_HUMAN	G	309	ENSP00000311196:A309G	ENSP00000311196:A309G	A	+	2	0	NPAS4	65947742	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.395000	0.59678	2.566000	0.86566	0.561000	0.74099	GCC		0.532	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		G	66191166	C	G	66191166	3	3	61	1	0	0	0	0	1	0	0	0	10596	739	26	5	948	5	NPAS4	11	66191166	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54271	66191166	68815350	7477	15462										
NPAS4	266743	broad.mit.edu	37	chr11	66192122	66192122	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtaatggggactgcacGctcttggccctagcccagct	12	14	1	0	rs373430880		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66192122G>A	ENST00000311034.2	+	7	1937	c.1761G>A	c.(1759-1761)acG>acA	p.T587T		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	587					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.T587T(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GGGACTGCACGCTCTTGGCCC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	11											77	86	83					11																	66192122		2200	4295	6495	65948698	SO:0001819	synonymous_variant	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1761G>A	11.37:g.66192122G>A			65948698	B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	CCDS8138.1																																																																																				0.607	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		A	66192122	G	A	66192122	2	1	61	1	0	0	0	0	0	0	0	1	10596	1074	38	1		1	NPAS4	11	66192122	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	956	66192122	68814394	7478	15463										
PELI3	246330	broad.mit.edu	37	chr11	66240754	66240754	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattgacttcgtggtaacaGacacgtcccctggaggaggg	14	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66240754G>T	ENST00000320740.7	+	6	659	c.499G>T	c.(499-501)Gac>Tac	p.D167Y	CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000533502.1_RNA|PELI3_ENST00000349459.6_Missense_Mutation_p.D143Y|PELI3_ENST00000524466.1_Missense_Mutation_p.D167Y|CTD-3074O7.5_ENST00000602951.1_RNA|PELI3_ENST00000531856.1_Intron	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	167					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.D167Y(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						CGTGGTAACAGACACGTCCCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	11											72	69	70					11																	66240754		2200	4295	6495	65997330	SO:0001583	missense	246330			AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"Pellino homologs"	30010	protein-coding gene	gene with protein product		609827	"pellino homolog 3 (Drosophila)"			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.499G>T	11.37:g.66240754G>T	ENSP00000322532:p.Asp167Tyr		65997330	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Missense_Mutation	SNP	ENST00000320740.7	37	CCDS31615.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862613	0.91511	.	.	ENSG00000174516	ENST00000349459;ENST00000320740;ENST00000524466;ENST00000526296	T;T;T;T	0.62105	0.05;0.05;0.05;0.05	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.82287	0.5004	M	0.88181	2.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;0.998;1.0	D	0.85504	0.1193	10	0.87932	D	0	-39.4691	16.2303	0.82332	0.0:0.0:1.0:0.0	.	143;167;167	Q8N2H9-2;Q8N2H9;Q8N2H9-4	.;PELI3_HUMAN;.	Y	143;167;167;60	ENSP00000309848:D143Y;ENSP00000322532:D167Y;ENSP00000434677:D167Y;ENSP00000436722:D60Y	ENSP00000322532:D167Y	D	+	1	0	PELI3	65997330	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.657000	0.98554	2.688000	0.91661	0.655000	0.94253	GAC		0.607	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065		T	66240754	G	T	66240754	3	4	61	1	0	0	0	0	1	0	0	0	11754	942	33	2	517	2	PELI3	11	66240754	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48632	66240754	68765762	7479	15464										
DPP3	10072	broad.mit.edu	37	chr11	66260299	66260299	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacctttgagaaggacaaGttcctcacccctgacttcac	6	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66260299G>T	ENST00000360510.2	+	10	1166	c.1101G>T	c.(1099-1101)aaG>aaT	p.K367N	DPP3_ENST00000530165.1_Missense_Mutation_p.K337N|DPP3_ENST00000531863.1_Missense_Mutation_p.K387N|DPP3_ENST00000532677.1_Missense_Mutation_p.K386N|DPP3_ENST00000453114.1_Missense_Mutation_p.K367N|DPP3_ENST00000541961.1_Missense_Mutation_p.K367N|DPP3_ENST00000533799.1_3'UTR			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	367					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.K367N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						AGAAGGACAAGTTCCTCACCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											94	92	93					11																	66260299		2200	4295	6495	66016875	SO:0001583	missense	10072			AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.1101G>T	11.37:g.66260299G>T	ENSP00000353701:p.Lys367Asn		66016875	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018360	0.35606	.	.	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000530165;ENST00000543807	T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85	5.26	3.37	0.38596	.	0.171337	0.50627	D	0.000107	T	0.25005	0.0607	L	0.58354	1.805	0.33356	D	0.5717	B;B	0.20671	0.035;0.047	B;B	0.30029	0.028;0.11	T	0.26018	-1.0115	10	0.49607	T	0.09	.	6.1119	0.20106	0.1725:0.1535:0.674:0.0	.	386;367	G3V1D3;Q9NY33	.;DPP3_HUMAN	N	387;386;367;367;367;337;265	ENSP00000432782:K387N;ENSP00000435284:K386N;ENSP00000353701:K367N;ENSP00000389943:K367N;ENSP00000440502:K367N;ENSP00000436941:K337N	ENSP00000353701:K367N	K	+	3	2	DPP3	66016875	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	1.230000	0.32612	1.219000	0.43474	-0.140000	0.14226	AAG		0.602	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			T	66260299	G	T	66260299	3	4	61	1	0	0	0	0	1	0	0	0	4739	1020	36	2	1135	2	DPP3	11	66260299	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19545	66260299	68746217	7480	15465										
ACTN3	8722	broad.mit.edu	37	chr11	66329762	66329762	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggagcctgatgacttccGagcttgcctcatctccatgg	11	12	2	2	rs114618009	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66329762G>A	ENST00000310325.5	-	0	2035				CTD-3074O7.2_ENST00000504911.1_lincRNA|ACTN3_ENST00000502692.1_RNA|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GATGACTTCCGAGCTTGCCTC	0.577													G|||	45	0.00898562	0.0333	0	5008	,	,		18503	0		0.001	False		,,,				2504	0															0			11						G	GLN/ARG	74,4118		1,72,2023	126	141	136		2357	5.7	1	11	dbSNP_132	136	1,8467		0,1,4233	yes	missense	ACTN3	NM_001104.1	43	1,73,6256	AA,AG,GG		0.0118,1.7653,0.5924	possibly-damaging	786/902	66329762	75,12585	2096	4234	6330	66086338	SO:0001628	intergenic_variant	89			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090		11.37:g.66329762G>A			66086338	B2R964|O95240|Q9NSU4|Q9UKQ5	Missense_Mutation	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																				0.577	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		A	66329762	G	A	66329762	1	1	61	0	1	0	0	0	0	0	0	0	206	1058	37	1		1	ACTN3	11	66329762	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69463	66329762	68676754	7481	15466										
ACTN3	8722	broad.mit.edu	37	chr11	66330556	66330556	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctccctgccaagcaggcCgagtactgcatccgccgtat	11	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66330556C>T	ENST00000310325.5	-	0	2035				CTD-3074O7.2_ENST00000504911.1_lincRNA|ACTN3_ENST00000502692.1_RNA|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CCAAGCAGGCCGAGTACTGCA	0.672																																																0			11											38	44	42					11																	66330556		1991	4146	6137	66087132	SO:0001628	intergenic_variant	89			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090		11.37:g.66330556C>T			66087132	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																				0.672	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		T	66330556	C	T	66330556	1	4	61	0	1	0	0	0	0	0	0	0	206	639	23	1		1	ACTN3	11	66330556	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	794	66330556	68675960	7482	15467										
CTSF	8722	broad.mit.edu	37	chr11	66334760	66334760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttataggtaatgacaaagttCttgaagattgaagccatctt	8	5	2	4	rs140630766		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66334760C>A	ENST00000310325.5	-	4	673	c.564G>T	c.(562-564)aaG>aaT	p.K188N	CTSF_ENST00000533168.1_5'UTR	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	188					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)	p.K188N(1)		endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TGACAAAGTTCTTGAAGATTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											135	129	131					11																	66334760		2200	4295	6495	66091336	SO:0001583	missense	8722			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.564G>T	11.37:g.66334760C>A	ENSP00000310832:p.Lys188Asn		66091336	B2R964|O95240|Q9NSU4|Q9UKQ5	Missense_Mutation	SNP	ENST00000310325.5	37	CCDS8144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.72|14.72	2.620951|2.620951	0.46736|0.46736	.|.	.|.	ENSG00000174080|ENSG00000174080	ENST00000524994|ENST00000310325;ENST00000526010	.|D;T	.|0.84589	.|-1.87;0.51	5.14|5.14	4.23|4.23	0.50019|0.50019	.|Proteinase inhibitor I29, cathepsin propeptide (2);	.|0.111799	.|0.64402	.|D	.|0.000013	.|T	.|0.81470	.|0.4829	L|L	0.53561|0.53561	1.675|1.675	0.49483|0.49483	D|D	0.99979|0.99979	.|B	.|0.22604	.|0.072	.|B	.|0.25614	.|0.062	.|T	.|0.77115	.|-0.2707	.|10	.|0.36615	.|T	.|0.2	.|.	11.8491|11.8491	0.52401|0.52401	0.0:0.9135:0.0:0.0865|0.0:0.9135:0.0:0.0865	.|.	.|188	.|Q9UBX1	.|CATF_HUMAN	X|N	37|188;96	.|ENSP00000310832:K188N;ENSP00000435822:K96N	.|ENSP00000310832:K188N	E|K	-|-	1|3	0|2	CTSF|CTSF	66091336|66091336	0.996000|0.996000	0.38824|0.38824	0.922000|0.922000	0.36590|0.36590	0.739000|0.739000	0.42172|0.42172	1.159000|1.159000	0.31749|0.31749	1.292000|1.292000	0.44672|0.44672	0.462000|0.462000	0.41574|0.41574	GAA|AAG		0.498	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		A	66334760	C	A	66334760	3	1	61	1	0	0	0	0	1	0	0	0	4040	912	32	2	930	2	CTSF	11	66334760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4204	66334760	68671756	7483	15468										
CCDC87	55231	broad.mit.edu	37	chr11	66360129	66360129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctcgctgctcagcagcaCgtaggcctcgagccgcttcc	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66360129C>T	ENST00000333861.3	-	1	425	c.358G>A	c.(358-360)Gtg>Atg	p.V120M	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	120					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)			p.V120M(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CTCAGCAGCACGTAGGCCTCG	0.622											OREG0021111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											49	51	51					11																	66360129		2200	4295	6495	66116705	SO:0001583	missense	55231			BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.358G>A	11.37:g.66360129C>T	ENSP00000328487:p.Val120Met	1091	66116705	Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	37	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242120	0.79912	.	.	ENSG00000182791	ENST00000333861	T	0.39592	1.07	5.11	5.11	0.69529	.	0.000000	0.43919	D	0.000508	T	0.63943	0.2554	M	0.73962	2.25	0.38601	D	0.950674	D	0.89917	1.0	D	0.85130	0.997	T	0.69390	-0.5158	10	0.72032	D	0.01	.	13.8971	0.63778	0.0:1.0:0.0:0.0	.	120	Q9NVE4	CCD87_HUMAN	M	120	ENSP00000328487:V120M	ENSP00000328487:V120M	V	-	1	0	CCDC87	66116705	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	0.981000	0.29526	2.650000	0.89964	0.655000	0.94253	GTG		0.622	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		T	66360129	C	T	66360129	3	4	61	1	0	0	0	0	1	0	0	0	2868	536	19	1	2195	1	CCDC87	11	66360129	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25369	66360129	68646387	7484	15469										
RBM14	10432	broad.mit.edu	37	chr11	66391988	66391988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccttctttggtcgcgaccGcagccctctgcgccgttcac	9	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66391988G>A	ENST00000310137.4	+	2	780	c.641G>A	c.(640-642)cGc>cAc	p.R214H	RBM14-RBM4_ENST00000500635.2_Intron|RBM14_ENST00000409372.1_3'UTR|RBM4_ENST00000514361.3_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000412278.2_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	214					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)	p.R214H(1)	RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GGTCGCGACCGCAGCCCTCTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											43	44	44					11																	66391988		2200	4295	6495	66148564	SO:0001583	missense	10432			AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.641G>A	11.37:g.66391988G>A	ENSP00000311747:p.Arg214His		66148564	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	37	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271789	0.59649	.	.	ENSG00000239306	ENST00000310137	D	0.84800	-1.9	5.45	4.54	0.55810	.	0.281210	0.30989	N	0.008462	T	0.74974	0.3787	N	0.19112	0.55	0.80722	D	1	B	0.19331	0.035	B	0.06405	0.002	T	0.71457	-0.4587	10	0.59425	D	0.04	-1.0761	12.1185	0.53878	0.0836:0.0:0.9164:0.0	.	214	Q96PK6	RBM14_HUMAN	H	214	ENSP00000311747:R214H	ENSP00000311747:R214H	R	+	2	0	RBM14	66148564	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.297000	0.78799	1.317000	0.45149	0.655000	0.94253	CGC		0.637	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66391988	G	A	66391988	3	1	61	1	0	0	0	0	1	0	0	0	13152	1087	38	1	647	1	RBM14	11	66391988	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31859	66391988	68614528	7485	15470										
RBM4	5936	broad.mit.edu	37	chr11	66407465	66407465	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcaccaataaggagcttCgagccaagtttgaggagtat	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66407465C>T	ENST00000409406.1	+	1	1060	c.283C>T	c.(283-285)Cga>Tga	p.R95*	RBM4_ENST00000408993.2_Nonsense_Mutation_p.R95*|RBM4_ENST00000398692.4_Nonsense_Mutation_p.R95*|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000530235.1_Nonsense_Mutation_p.R95*|RBM4_ENST00000514361.3_Intron|RBM4_ENST00000578778.1_Nonsense_Mutation_p.R95*|RBM4_ENST00000503028.2_Nonsense_Mutation_p.R95*|RBM4_ENST00000532968.1_Nonsense_Mutation_p.R95*|RBM4_ENST00000310092.7_Nonsense_Mutation_p.R95*|RBM4_ENST00000506523.2_Nonsense_Mutation_p.R95*|RBM4_ENST00000483858.1_Nonsense_Mutation_p.R95*|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000396053.4_Nonsense_Mutation_p.R95*			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	95	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R95*(1)		endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		TAAGGAGCTTCGAGCCAAGTT	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											185	171	176					11																	66407465		2200	4295	6495	66164041	SO:0001587	stop_gained	5936			U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.283C>T	11.37:g.66407465C>T	ENSP00000386894:p.Arg95*		66164041	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Nonsense_Mutation	SNP	ENST00000409406.1	37	CCDS41676.1	.	.	.	.	.	.	.	.	.	.	C	39	7.294978	0.98192	.	.	ENSG00000248643;ENSG00000248643;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933	ENST00000503028;ENST00000514361;ENST00000310092;ENST00000396053;ENST00000408993;ENST00000483858;ENST00000398692;ENST00000510173;ENST00000506523;ENST00000530235;ENST00000532968;ENST00000409406	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7462	16.141	0.81522	0.0:1.0:0.0:0.0	.	.	.	.	X	95	.	ENSP00000425760:R95X	R	+	1	2	RBM4;RBM14-RBM4	66164041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.765000	0.47621	2.485000	0.83878	0.650000	0.86243	CGA		0.502	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896		T	66407465	C	T	66407465	4	4	61	1	0	0	0	0	0	1	0	0	13171	876	31	1	285	1	RBM4	11	66407465	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15477	66407465	68599051	7486	15471										
RBM4B	83759	broad.mit.edu	37	chr11	66436474	66436474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcagaagccgctgccgccGctgctactgcctcataagag	11	14	1	2	rs146310422		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66436474G>A	ENST00000525754.1	-	2	1369	c.701C>T	c.(700-702)gCg>gTg	p.A234V	RBM4B_ENST00000531969.1_Intron|RBM4B_ENST00000310046.4_Missense_Mutation_p.A234V|RBM4B_ENST00000529195.2_5'Flank|RP11-658F2.8_ENST00000548810.1_RNA|RBM4B_ENST00000524637.1_3'UTR|RP11-658F2.8_ENST00000550837.1_RNA			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	234	Interaction with TNPO3. {ECO:0000250}.|Poly-Ala.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A234V(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						CGCTGCCGCCGCTGCTACTGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	VAL/ALA	0,4400		0,0,2200	76	71	73		701	5.9	0.8	11	dbSNP_134	73	1,8589	1.2+/-3.3	0,1,4294	no	missense	RBM4B	NM_031492.2	64	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	benign	234/360	66436474	1,12989	2200	4295	6495	66193050	SO:0001583	missense	83759			AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	28842	protein-coding gene	gene with protein product			"RNA binding motif protein 30"	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.701C>T	11.37:g.66436474G>A	ENSP00000433071:p.Ala234Val		66193050	B3KT83	Missense_Mutation	SNP	ENST00000525754.1	37	CCDS8149.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775930	0.49786	0.0	1.16E-4	ENSG00000173914	ENST00000525754;ENST00000310046	T;T	0.25912	1.77;1.77	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000005	T	0.19644	0.0472	L	0.36672	1.1	0.80722	D	1	B	0.33841	0.428	B	0.19391	0.025	T	0.05435	-1.0885	10	0.13470	T	0.59	-22.4295	19.1058	0.93294	0.0:0.0:1.0:0.0	.	234	Q9BQ04	RBM4B_HUMAN	V	234	ENSP00000433071:A234V;ENSP00000310471:A234V	ENSP00000310471:A234V	A	-	2	0	RBM4B	66193050	0.989000	0.36119	0.750000	0.31169	0.541000	0.35023	4.927000	0.63440	2.822000	0.97130	0.650000	0.86243	GCG		0.527	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492		A	66436474	G	A	66436474	3	1	61	1	0	0	0	0	1	0	0	0	13179	1087	38	1	382	1	RBM4B	11	66436474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29009	66436474	68570042	7487	15472										
SPTBN2	6712	broad.mit.edu	37	chr11	66454566	66454566	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtggtatggcactcccgcGctggctgccttggcatcctt	12	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66454566G>A	ENST00000533211.1	-	36	7126	c.6795C>T	c.(6793-6795)agC>agT	p.S2265S	SPTBN2_ENST00000529997.1_Silent_p.S2265S|SPTBN2_ENST00000309996.2_Silent_p.S2265S			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	2265	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.S2265S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCACTCCCGCGCTGGCTGCCT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	11											81	74	76					11																	66454566		2200	4295	6495	66211142	SO:0001819	synonymous_variant	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.6795C>T	11.37:g.66454566G>A			66211142	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																				0.632	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66454566	G	A	66454566	2	1	61	1	0	0	0	0	0	0	0	1	15159	1078	38	1		1	SPTBN2	11	66454566	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18092	66454566	68551950	7488	15473										
SPTBN2	6712	broad.mit.edu	37	chr11	66456216	66456216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatgaggctctcaacttCgtcgaccgtgcaacccagct	9	14	1	2	rs201985455		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66456216C>T	ENST00000533211.1	-	31	6470	c.6139G>A	c.(6139-6141)Gaa>Aaa	p.E2047K	SPTBN2_ENST00000529997.1_Missense_Mutation_p.E2047K|SPTBN2_ENST00000309996.2_Missense_Mutation_p.E2047K			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	2047					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.E2047K(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTCTCAACTTCGTCGACCGTG	0.617																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	11						C	LYS/GLU	0,4400		0,0,2200	69	59	62		6139	4.8	0.9	11		62	1,8589	1.2+/-3.3	0,1,4294	yes	missense	SPTBN2	NM_006946.2	56	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2047/2391	66456216	1,12989	2200	4295	6495	66212792	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.6139G>A	11.37:g.66456216C>T	ENSP00000432568:p.Glu2047Lys		66212792	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466577	0.84425	0.0	1.16E-4	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.67698	-0.28;-0.28;-0.28	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.81527	0.4841	M	0.82323	2.585	0.80722	D	1	D	0.71674	0.998	D	0.63381	0.914	D	0.83940	0.0311	10	0.54805	T	0.06	.	16.7389	0.85454	0.0:1.0:0.0:0.0	.	2047	O15020	SPTN2_HUMAN	K	2047	ENSP00000432568:E2047K;ENSP00000311489:E2047K;ENSP00000433593:E2047K	ENSP00000311489:E2047K	E	-	1	0	SPTBN2	66212792	1.000000	0.71417	0.851000	0.33527	0.058000	0.15608	7.604000	0.82830	2.477000	0.83638	0.591000	0.81541	GAA		0.617	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66456216	C	T	66456216	3	4	61	1	0	0	0	0	1	0	0	0	15159	893	31	1	1065	1	SPTBN2	11	66456216	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1650	66456216	68550300	7489	15474										
SPTBN2	6712	broad.mit.edu	37	chr11	66482812	66482812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttgaggaactgcagtgCcttgtccacgttctccaggc	10	14	1	1	rs376084729		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66482812C>T	ENST00000533211.1	-	5	695	c.364G>A	c.(364-366)Gca>Aca	p.A122T	SPTBN2_ENST00000309996.2_Missense_Mutation_p.A122T|SPTBN2_ENST00000529997.1_Missense_Mutation_p.A122T|RN7SL12P_ENST00000473849.2_RNA			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	122	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.A122T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						AACTGCAGTGCCTTGTCCACG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	THR/ALA	0,4400		0,0,2200	152	126	135		364	4.7	0.9	11		135	1,8589	1.2+/-3.3	0,1,4294	no	missense	SPTBN2	NM_006946.2	58	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	122/2391	66482812	1,12989	2200	4295	6495	66239388	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.364G>A	11.37:g.66482812C>T	ENSP00000432568:p.Ala122Thr		66239388	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387890	0.82902	0.0	1.16E-4	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262	T;T;T	0.64085	-0.08;-0.08;-0.08	4.65	4.65	0.58169	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.83658	0.5302	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88085	0.2809	10	0.87932	D	0	.	16.4528	0.83997	0.0:1.0:0.0:0.0	.	122	O15020	SPTN2_HUMAN	T	122	ENSP00000432568:A122T;ENSP00000311489:A122T;ENSP00000433593:A122T	ENSP00000311489:A122T	A	-	1	0	SPTBN2	66239388	1.000000	0.71417	0.936000	0.37596	0.158000	0.22134	7.604000	0.82830	2.417000	0.82017	0.561000	0.74099	GCA		0.587	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66482812	C	T	66482812	3	4	61	1	0	0	0	0	1	0	0	0	15159	739	26	3	6944	3	SPTBN2	11	66482812	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26596	66482812	68523704	7490	15475										
RCE1	9986	broad.mit.edu	37	chr11	66613522	66613522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagccttcccctttgtgtgCttttggagcgggcaggggac	15	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:66613522C>A	ENST00000309657.3	+	8	990	c.946C>A	c.(946-948)Ctt>Att	p.L316I	RCE1_ENST00000525356.1_Missense_Mutation_p.L193I|PC_ENST00000528224.1_5'Flank|RCE1_ENST00000524506.1_Missense_Mutation_p.L295I	NM_001032279.1|NM_005133.2	NP_001027450.1|NP_005124.1	Q9Y256	FACE2_HUMAN	Ras converting CAAX endopeptidase 1	316					CAAX-box protein processing (GO:0071586)|proteolysis (GO:0006508)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|metalloendopeptidase activity (GO:0004222)	p.L316I(1)		breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10						CCTTTGTGTGCTTTTGGAGCG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											60	65	64					11																	66613522		2200	4295	6495	66370098	SO:0001583	missense	9986			AF121951	CCDS8151.1	11q13	2013-10-18	2013-10-18	2001-06-29	ENSG00000173653	ENSG00000173653			13721	protein-coding gene	gene with protein product	"farnesylated protein-converting enzyme 2", "prenyl protein-specific endoprotease 2", "RCE1 homolog, prenyl protein protease", "CAAX prenyl protease 2"	605385	"RCE1 (S. Cerevisiae) homolog, prenyl protein protease", "RCE1 homolog, prenyl protein peptidase (S. cerevisiae)", "RCE1 homolog, prenyl protein protease (S. cerevisiae)"	RCE1A, RCE1B		10085068, 10373325	Standard	NM_005133		Approved	hRCE1, FACE-2, FACE2	uc001ojk.1	Q9Y256	OTTHUMG00000167098	ENST00000309657.3:c.946C>A	11.37:g.66613522C>A	ENSP00000309163:p.Leu316Ile		66370098	Q52LZ9	Missense_Mutation	SNP	ENST00000309657.3	37	CCDS8151.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936295	0.73442	.	.	ENSG00000173653	ENST00000309657;ENST00000524506;ENST00000525356	.	.	.	5.04	4.09	0.47781	.	0.078219	0.49916	N	0.000134	T	0.69405	0.3107	L	0.57536	1.79	0.39712	D	0.97134	D	0.63880	0.993	D	0.73708	0.981	T	0.72934	-0.4141	9	0.87932	D	0	-10.623	10.3161	0.43738	0.1964:0.8036:0.0:0.0	.	316	Q9Y256	FACE2_HUMAN	I	316;295;193	.	ENSP00000309163:L316I	L	+	1	0	RCE1	66370098	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	4.469000	0.60169	1.278000	0.44430	0.655000	0.94253	CTT		0.637	RCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393105.1	NM_005133		A	66613522	C	A	66613522	3	1	61	1	0	0	0	0	1	0	0	0	13213	797	28	2	976	2	RCE1	11	66613522	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130710	66613522	68392994	7491	15476										
CABP4	57010	broad.mit.edu	37	chr11	67225907	67225907	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcggtaccggctctgctCggggagccgctggcgggtcc	19	13	1	0	rs145493184	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:67225907C>T	ENST00000325656.5	+	5	794	c.717C>T	c.(715-717)ctC>ctT	p.L239L	CABP4_ENST00000438189.2_Silent_p.L134L|CTC-1337H24.1_ENST00000602912.1_lincRNA	NM_145200.3	NP_660201.1	P57796	CABP4_HUMAN	calcium binding protein 4	239	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				photoreceptor cell morphogenesis (GO:0008594)|phototransduction (GO:0007602)|retinal bipolar neuron differentiation (GO:0060040)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytosol (GO:0005829)|extracellular region (GO:0005576)|synapse (GO:0045202)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)	p.L239L(1)		central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CGGCTCTGCTCGGGGAGCCGC	0.637													C|||	2	0.000399361	0.0015	0	5008	,	,		9576	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11						C		4,4396	8.1+/-20.4	0,4,2196	51	58	55		717	-9.7	0.4	11	dbSNP_134	55	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CABP4	NM_145200.3		0,5,6490	TT,TC,CC		0.0116,0.0909,0.0385		239/276	67225907	5,12985	2200	4295	6495	66982483	SO:0001819	synonymous_variant	57010			AC005849	CCDS8166.1, CCDS73333.1	11q13.2	2013-09-20			ENSG00000175544	ENSG00000175544		"EF-hand domain containing"	1386	protein-coding gene	gene with protein product		608965				10625670, 16960802	Standard	NM_145200		Approved	CSNB2B	uc001olo.3	P57796	OTTHUMG00000168033	ENST00000325656.5:c.717C>T	11.37:g.67225907C>T			66982483	Q8N4Z2|Q8WWY5	Silent	SNP	ENST00000325656.5	37	CCDS8166.1																																																																																				0.637	CABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397624.2			T	67225907	C	T	67225907	2	4	61	1	0	0	0	0	0	0	0	1	2539	871	31	1		1	CABP4	11	67225907	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	612385	67225907	67780609	7492	15477										
ALDH3B2	222	broad.mit.edu	37	chr11	67434115	67434115	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagggtgcgatgatgagGaccaggccaaagggttcctt	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:67434115G>A	ENST00000349015.3	-	4	519	c.81C>T	c.(79-81)gtC>gtT	p.V27V	ALDH3B2_ENST00000530069.1_Silent_p.V27V|ALDH3B2_ENST00000531881.1_5'UTR	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	27					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)	p.V27V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CGATGATGAGGACCAGGCCAA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	11											101	97	98					11																	67434115		2200	4294	6494	67190691	SO:0001819	synonymous_variant	222			U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"Aldehyde dehydrogenases"	411	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 8", "acetaldehyde dehydrogenase 8"	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.81C>T	11.37:g.67434115G>A			67190691	Q53Y98|Q8NAL5|Q96IB2	Silent	SNP	ENST00000349015.3	37	CCDS31622.1																																																																																				0.622	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695		A	67434115	G	A	67434115	2	1	61	1	0	0	0	0	0	0	0	1	500	1161	41	3		3	ALDH3B2	11	67434115	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208208	67434115	67572401	7493	15478										
SUV420H1	51111	broad.mit.edu	37	chr11	67925807	67925807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaccgacgggtgaaggaGcacagtctgtgtagctcaca	12	10	2	1	rs377489614		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:67925807G>A	ENST00000304363.4	-	11	2359	c.2006C>T	c.(2005-2007)gCt>gTt	p.A669V		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	669					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)	p.A669V(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GGGTGAAGGAGCACAGTCTGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											90	80	83					11																	67925807		2200	4294	6494	67682383	SO:0001583	missense	51111			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.2006C>T	11.37:g.67925807G>A	ENSP00000305899:p.Ala669Val		67682383	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	37	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.825095	0.50739	.	.	ENSG00000110066	ENST00000304363	T	0.43294	0.95	5.04	4.05	0.47172	.	0.374676	0.33144	N	0.005230	T	0.23965	0.0580	N	0.19112	0.55	0.22771	N	0.99875	B	0.06786	0.001	B	0.08055	0.003	T	0.05937	-1.0855	10	0.25106	T	0.35	-8.1964	7.4362	0.27156	0.1735:0.0:0.8265:0.0	.	669	Q4FZB7	SV421_HUMAN	V	669	ENSP00000305899:A669V	ENSP00000305899:A669V	A	-	2	0	SUV420H1	67682383	0.095000	0.21747	0.198000	0.23420	0.938000	0.57974	3.266000	0.51569	2.623000	0.88846	0.491000	0.48974	GCT		0.498	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		A	67925807	G	A	67925807	3	1	61	1	0	0	0	0	1	0	0	0	15453	971	34	3	655	3	SUV420H1	11	67925807	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	491692	67925807	67080709	7494	15479										
SUV420H1	51111	broad.mit.edu	37	chr11	67939085	67939085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtacatgacactgaagtCgttttctccatgtctaagta	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:67939085C>T	ENST00000304363.4	-	7	1098	c.745G>A	c.(745-747)Gac>Aac	p.D249N	SUV420H1_ENST00000405515.1_Missense_Mutation_p.D249N|SUV420H1_ENST00000402789.1_Missense_Mutation_p.D249N|SUV420H1_ENST00000402185.2_Missense_Mutation_p.D226N|SUV420H1_ENST00000401547.2_Missense_Mutation_p.D249N	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	249	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)	p.D249N(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						ACACTGAAGTCGTTTTCTCCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											129	128	128					11																	67939085		2200	4294	6494	67695661	SO:0001583	missense	51111			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.745G>A	11.37:g.67939085C>T	ENSP00000305899:p.Asp249Asn		67695661	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	37	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139032	0.94560	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185	D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99	5.73	4.82	0.62117	SET domain (2);	0.133067	0.64402	N	0.000002	D	0.90017	0.6883	L	0.52011	1.625	0.80722	D	1	D;D;D;B	0.89917	1.0;1.0;0.999;0.343	D;D;D;B	0.91635	0.994;0.999;0.994;0.145	D	0.91014	0.4852	10	0.72032	D	0.01	-32.9519	15.2633	0.73640	0.0:0.9324:0.0:0.0676	.	226;249;249;249	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	N	249;249;249;249;226	ENSP00000305899:D249N;ENSP00000385965:D249N;ENSP00000385640:D249N;ENSP00000385005:D249N;ENSP00000384724:D226N	ENSP00000305899:D249N	D	-	1	0	SUV420H1	67695661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	1.552000	0.49463	0.655000	0.94253	GAC		0.413	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		T	67939085	C	T	67939085	3	4	61	1	0	0	0	0	1	0	0	0	15453	884	31	1	1940	1	SUV420H1	11	67939085	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13278	67939085	67067431	7495	15480										
SUV420H1	51111	broad.mit.edu	37	chr11	67957497	67957497	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacaacttgcctccatttCtcctgccattcaccaccatg	4	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:67957497C>A	ENST00000304363.4	-	2	400	c.47G>T	c.(46-48)aGa>aTa	p.R16I	SUV420H1_ENST00000405515.1_Missense_Mutation_p.R16I|SUV420H1_ENST00000402789.1_Missense_Mutation_p.R16I|SUV420H1_ENST00000402185.2_Missense_Mutation_p.R16I|SUV420H1_ENST00000401547.2_Missense_Mutation_p.R16I	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	16					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)	p.R16I(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GCCTCCATTTCTCCTGCCATT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											299	255	270					11																	67957497		2200	4294	6494	67714073	SO:0001583	missense	51111			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.47G>T	11.37:g.67957497C>A	ENSP00000305899:p.Arg16Ile		67714073	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	37	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	C	35	5.432194	0.96150	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000434573	T;T;T;T;T;T	0.61158	0.96;0.96;0.96;0.96;0.13;0.96	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.72145	0.3424	L	0.43152	1.355	0.80722	D	1	D;D;D;D	0.76494	0.99;0.995;0.997;0.999	D;D;D;D	0.85130	0.944;0.986;0.994;0.997	T	0.72491	-0.4277	10	0.87932	D	0	-36.7089	20.3559	0.98840	0.0:1.0:0.0:0.0	.	16;16;16;16	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	I	16	ENSP00000305899:R16I;ENSP00000385965:R16I;ENSP00000385640:R16I;ENSP00000385005:R16I;ENSP00000384724:R16I;ENSP00000402921:R16I	ENSP00000305899:R16I	R	-	2	0	SUV420H1	67714073	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.556000	0.67307	2.890000	0.99128	0.585000	0.79938	AGA		0.478	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		A	67957497	C	A	67957497	3	1	61	1	0	0	0	0	1	0	0	0	15453	913	32	2	2658	2	SUV420H1	11	67957497	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18412	67957497	67049019	7496	15481										
SAPS3	55291	broad.mit.edu	37	chr11	68369342	68369342	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgaaagcacaaaagattCtttaaggagtaattctccag	7	6	2	2	rs555381830		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:68369342C>A	ENST00000393800.2	+	21	2458	c.2204C>A	c.(2203-2205)tCt>tAt	p.S735Y	PPP6R3_ENST00000265636.5_Missense_Mutation_p.S655Y|PPP6R3_ENST00000265637.4_Missense_Mutation_p.S689Y|PPP6R3_ENST00000393799.2_Missense_Mutation_p.S735Y|PPP6R3_ENST00000393801.3_Missense_Mutation_p.S735Y|PPP6R3_ENST00000529710.1_Missense_Mutation_p.S655Y|PPP6R3_ENST00000527403.2_Missense_Mutation_p.S700Y|PPP6R3_ENST00000524845.1_Missense_Mutation_p.S706Y|PPP6R3_ENST00000534534.1_Missense_Mutation_p.S503Y|PPP6R3_ENST00000524904.1_Missense_Mutation_p.S729Y	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	735					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.S735Y(1)|p.S655Y(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						ACAAAAGATTCTTTAAGGAGT	0.458													C|||	1	0.000199681	0	0	5008	,	,		22664	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	11											93	103	99					11																	68369342		2200	4294	6494	68125918	SO:0001583	missense	55291			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2204C>A	11.37:g.68369342C>A	ENSP00000377389:p.Ser735Tyr		68125918	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.246018	0.59103	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.91	2.98	0.34508	.	0.222920	0.48286	D	0.000188	T	0.58764	0.2145	L	0.36672	1.1	0.37118	D	0.900651	B;B;D;D;D;P;D;D	0.58620	0.232;0.187;0.98;0.964;0.964;0.939;0.983;0.964	B;B;P;P;P;P;P;P	0.59889	0.229;0.172;0.694;0.601;0.847;0.615;0.865;0.709	T	0.66681	-0.5862	10	0.62326	D	0.03	.	14.9506	0.71071	0.0:0.7283:0.2717:0.0	.	418;503;655;706;729;735;735;655	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	Y	735;735;503;706;689;729;735;655;655;700;442	ENSP00000377388:S735Y;ENSP00000377389:S735Y;ENSP00000434429:S503Y;ENSP00000431415:S706Y;ENSP00000265637:S689Y;ENSP00000433058:S729Y;ENSP00000377390:S735Y;ENSP00000265636:S655Y;ENSP00000437329:S655Y;ENSP00000433565:S700Y;ENSP00000436209:S442Y	ENSP00000265636:S655Y	S	+	2	0	PPP6R3	68125918	1.000000	0.71417	0.696000	0.30242	0.989000	0.77384	5.144000	0.64832	0.623000	0.30267	-0.282000	0.10007	TCT		0.458	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68369342	C	A	68369342	3	1	61	1	0	0	0	0	1	0	0	0	13875	913	32	2	2278	2	SAPS3	11	68369342	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	411845	68369342	66637174	7497	15482										
CPT1A	1374	broad.mit.edu	37	chr11	68527092	68527092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattgatgaggttctctcccAcaaggatgtacgacacacca	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:68527092A>G	ENST00000265641.5	-	18	2334	c.2180T>C	c.(2179-2181)gTg>gCg	p.V727A	CPT1A_ENST00000540367.1_Missense_Mutation_p.V727A|CPT1A_ENST00000539743.1_Missense_Mutation_p.V727A|CPT1A_ENST00000376618.2_Missense_Mutation_p.V727A	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	727					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)	p.V727A(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GTTCTCTCCCACAAGGATGTA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	11											92	89	90					11																	68527092		2200	4294	6494	68283668	SO:0001583	missense	1374			L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.2180T>C	11.37:g.68527092A>G	ENSP00000265641:p.Val727Ala		68283668	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	37	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	A	1.083	-0.666482	0.03428	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	4.75	3.57	0.40892	.	0.425291	0.22855	N	0.054807	T	0.79493	0.4455	N	0.17278	0.47	0.37139	D	0.901608	B;B	0.27380	0.177;0.02	B;B	0.36092	0.217;0.02	T	0.70644	-0.4815	10	0.06236	T	0.91	.	10.7691	0.46312	0.8577:0.0:0.0:0.1423	.	727;727	P50416;P50416-2	CPT1A_HUMAN;.	A	727	ENSP00000439084:V727A;ENSP00000365803:V727A;ENSP00000265641:V727A;ENSP00000446108:V727A	ENSP00000265641:V727A	V	-	2	0	CPT1A	68283668	0.999000	0.42202	0.501000	0.27601	0.415000	0.31203	8.656000	0.91102	0.901000	0.36495	0.459000	0.35465	GTG		0.428	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		G	68527092	A	G	68527092	3	3	61	1	0	0	0	0	1	0	0	0	3837	159	6	4	189	4	CPT1A	11	68527092	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	157750	68527092	66479424	7498	15483										
MRGPRD	116512	broad.mit.edu	37	chr11	68748274	68748274	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgaggatatagatgcagAaggggttcctgtgcattcga	15	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:68748274A>C	ENST00000309106.3	-	1	181	c.182T>G	c.(181-183)tTc>tGc	p.F61C		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	61						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F61C(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			ATAGATGCAGAAGGGGTTCCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11											66	68	67					11																	68748274		2200	4294	6494	68504850	SO:0001583	missense	116512			AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"GPCR / Class A : Orphans"	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.182T>G	11.37:g.68748274A>C	ENSP00000310631:p.Phe61Cys		68504850	Q8NGK7	Missense_Mutation	SNP	ENST00000309106.3	37	CCDS31625.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946445	0.34377	.	.	ENSG00000172938	ENST00000309106	T	0.16073	2.37	5.17	-0.534	0.11883	GPCR, rhodopsin-like superfamily (1);	0.517384	0.15912	U	0.238573	T	0.29749	0.0743	M	0.91920	3.255	0.26931	N	0.96646	P	0.40970	0.734	P	0.48571	0.582	T	0.21109	-1.0255	10	0.52906	T	0.07	-23.5033	1.5691	0.02611	0.3509:0.1631:0.0815:0.4045	.	61	Q8TDS7	MRGRD_HUMAN	C	61	ENSP00000310631:F61C	ENSP00000310631:F61C	F	-	2	0	MRGPRD	68504850	0.258000	0.24033	0.414000	0.26521	0.020000	0.10135	0.118000	0.15605	-0.036000	0.13669	0.383000	0.25322	TTC		0.592	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923		C	68748274	A	C	68748274	3	2	61	1	0	0	0	0	1	0	0	0	9793	246	9	4	786	4	MRGPRD	11	68748274	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	221182	68748274	66258242	7499	15484										
FGF19	9965	broad.mit.edu	37	chr11	69514117	69514117	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggtctccaggggcgaagaGaacatgtcagattccaagtg	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:69514117G>T	ENST00000294312.3	-	3	1329	c.564C>A	c.(562-564)ttC>ttA	p.F188L		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	188					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)	p.F188L(1)		large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			GGGGCGAAGAGAACATGTCAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	100	101					11																	69514117		2200	4294	6494	69223298	SO:0001583	missense	9965			AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.564C>A	11.37:g.69514117G>T	ENSP00000294312:p.Phe188Leu		69223298		Missense_Mutation	SNP	ENST00000294312.3	37	CCDS8193.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416264	0.42918	.	.	ENSG00000162344	ENST00000294312	T	0.76316	-1.01	5.22	-1.64	0.08318	.	1.049570	0.07421	N	0.894011	T	0.55862	0.1947	N	0.17082	0.46	0.09310	N	1	P	0.37330	0.59	B	0.30251	0.113	T	0.43393	-0.9394	10	0.27082	T	0.32	-26.5021	7.774	0.29026	0.2071:0.233:0.5599:0.0	.	188	O95750	FGF19_HUMAN	L	188	ENSP00000294312:F188L	ENSP00000294312:F188L	F	-	3	2	FGF19	69223298	0.026000	0.19158	0.001000	0.08648	0.405000	0.30901	0.127000	0.15790	0.104000	0.17725	0.555000	0.69702	TTC		0.572	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117		T	69514117	G	T	69514117	3	4	61	1	0	0	0	0	1	0	0	0	5866	933	33	2	90	2	FGF19	11	69514117	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	765843	69514117	65492399	7500	15485										
PPFIA1	8500	broad.mit.edu	37	chr11	70172707	70172707	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttccccctatcagagatCttctgatggttctttaagcc	6	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:70172707C>A	ENST00000253925.7	+	7	928	c.713C>A	c.(712-714)tCt>tAt	p.S238Y	CTA-797E19.2_ENST00000526017.1_RNA|AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.S238Y	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	238					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.S238Y(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TATCAGAGATCTTCTGATGGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											174	192	186					11																	70172707		2200	4294	6494	69850355	SO:0001583	missense	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.713C>A	11.37:g.70172707C>A	ENSP00000253925:p.Ser238Tyr		69850355	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	C	6.985	0.551764	0.13374	.	.	ENSG00000131626	ENST00000253925;ENST00000389547	T;T	0.39997	1.05;1.05	4.67	4.67	0.58626	.	0.414999	0.23797	U	0.044467	T	0.32315	0.0825	N	0.14661	0.345	0.29078	N	0.882889	B;B	0.26744	0.158;0.001	B;B	0.32149	0.141;0.016	T	0.29792	-1.0000	10	0.42905	T	0.14	.	17.9762	0.89128	0.0:1.0:0.0:0.0	.	238;238	Q13136;Q13136-2	LIPA1_HUMAN;.	Y	238	ENSP00000253925:S238Y;ENSP00000374198:S238Y	ENSP00000253925:S238Y	S	+	2	0	PPFIA1	69850355	0.914000	0.31030	0.976000	0.42696	0.810000	0.45777	1.974000	0.40559	2.309000	0.77851	0.655000	0.94253	TCT		0.353	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		A	70172707	C	A	70172707	3	1	61	1	0	0	0	0	1	0	0	0	12340	913	32	2	735	2	PPFIA1	11	70172707	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	658590	70172707	64833809	7501	15486										
PPFIA1	8500	broad.mit.edu	37	chr11	70224285	70224285	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccctctatgcagccaaaGaagatgcagatggacggtat	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:70224285G>T	ENST00000253925.7	+	26	3749	c.3534G>T	c.(3532-3534)aaG>aaT	p.K1178N	AP000487.5_ENST00000500185.2_RNA|PPFIA1_ENST00000530548.1_3'UTR|AP000487.5_ENST00000530690.1_RNA|AP000487.5_ENST00000524619.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.K1178N	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	1178					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.K1178N(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGCAGCCAAAGAAGATGCAGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											127	112	117					11																	70224285		2200	4294	6494	69901933	SO:0001583	missense	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.3534G>T	11.37:g.70224285G>T	ENSP00000253925:p.Lys1178Asn		69901933	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	33	5.216298	0.95104	.	.	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950;ENST00000528853	T;T	0.20463	2.13;2.07	4.55	4.55	0.56014	.	0.062566	0.64402	U	0.000007	T	0.30696	0.0773	L	0.59436	1.845	0.50171	D	0.999854	B;B;P	0.40731	0.019;0.104;0.728	B;B;P	0.44359	0.019;0.059;0.447	T	0.16988	-1.0384	10	0.87932	D	0	.	17.3212	0.87236	0.0:0.0:1.0:0.0	.	675;1178;1178	F5H1G2;Q13136;Q13136-2	.;LIPA1_HUMAN;.	N	1178;1178;675;34	ENSP00000253925:K1178N;ENSP00000374198:K1178N	ENSP00000253925:K1178N	K	+	3	2	PPFIA1	69901933	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.662000	0.83803	2.095000	0.63458	0.561000	0.74099	AAG		0.488	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		T	70224285	G	T	70224285	3	4	61	1	0	0	0	0	1	0	0	0	12340	933	33	2	3632	2	PPFIA1	11	70224285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51578	70224285	64782231	7502	15487										
CTTN	2017	broad.mit.edu	37	chr11	70265868	70265868	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagattactccaaaggtttCggcggcaaatacggtatcga	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:70265868C>T	ENST00000301843.8	+	9	791	c.585C>T	c.(583-585)ttC>ttT	p.F195F	CTTN_ENST00000538675.1_5'Flank|CTTN_ENST00000346329.3_Silent_p.F195F|CTTN_ENST00000376561.3_Silent_p.F195F	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	195					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)		p.F195F(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		CCAAAGGTTTCGGCGGCAAAT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	11											63	61	62					11																	70265868		2200	4294	6494	69943516	SO:0001819	synonymous_variant	2017			AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.585C>T	11.37:g.70265868C>T			69943516	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	C	2.422	-0.332785	0.05314	.	.	ENSG00000085733	ENST00000415461	.	.	.	5.01	-1.48	0.08745	.	.	.	.	.	T	0.57213	0.2038	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52419	-0.8578	4	.	.	.	-19.8223	10.8041	0.46507	0.0:0.335:0.0:0.665	.	.	.	.	L	177	.	.	S	+	2	0	CTTN	69943516	0.175000	0.23083	0.715000	0.30552	0.153000	0.21895	-0.539000	0.06113	-0.480000	0.06803	-1.074000	0.02243	TCG		0.398	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		T	70265868	C	T	70265868	2	4	61	1	0	0	0	0	0	0	0	1	4050	883	31	1		1	CTTN	11	70265868	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41583	70265868	64740648	7503	15488										
CTTN	2017	broad.mit.edu	37	chr11	70279774	70279774	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagcacctacgatgagtAcgagaacgatctggggatca	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:70279774A>G	ENST00000301843.8	+	17	1672	c.1466A>G	c.(1465-1467)tAc>tGc	p.Y489C	CTTN_ENST00000538675.1_Missense_Mutation_p.Y173C|CTTN_ENST00000346329.3_Missense_Mutation_p.Y452C|CTTN_ENST00000376561.3_Missense_Mutation_p.Y452C	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	489					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)		p.Y489C(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		TACGATGAGTACGAGAACGAT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											153	147	149					11																	70279774		2200	4294	6494	69957422	SO:0001583	missense	2017			AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.1466A>G	11.37:g.70279774A>G	ENSP00000301843:p.Tyr489Cys		69957422	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597268	0.46318	.	.	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561;ENST00000538675;ENST00000529736	T;T;T;T;T	0.33865	1.44;1.45;1.39;1.77;1.76	4.96	3.83	0.44106	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	M	0.68593	2.085	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;P	0.91635	0.999;0.995;0.972;0.887	T	0.50898	-0.8773	10	0.41790	T	0.15	-18.6328	10.5254	0.44945	0.9235:0.0:0.0765:0.0	.	173;452;489;452	B4E358;Q96H99;Q14247;Q8N707	.;.;SRC8_HUMAN;.	C	452;489;452;173;146	ENSP00000317189:Y452C;ENSP00000301843:Y489C;ENSP00000365745:Y452C;ENSP00000439762:Y173C;ENSP00000431421:Y146C	ENSP00000301843:Y489C	Y	+	2	0	CTTN	69957422	1.000000	0.71417	0.052000	0.19188	0.506000	0.33950	6.409000	0.73289	0.741000	0.32674	0.529000	0.55759	TAC		0.547	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		G	70279774	A	G	70279774	3	3	61	1	0	0	0	0	1	0	0	0	4050	391	14	4	1524	4	CTTN	11	70279774	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13906	70279774	64726742	7504	15489										
IL18BP	10068	broad.mit.edu	37	chr11	71712298	71712298	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccgcttccccaacttcaGcatcctctactggctgggca	8	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:71712298G>T	ENST00000393703.4	+	4	824	c.287G>T	c.(286-288)aGc>aTc	p.S96I	IL18BP_ENST00000393707.4_Intron|IL18BP_ENST00000260049.5_Missense_Mutation_p.S96I|IL18BP_ENST00000393705.4_Missense_Mutation_p.S96I|IL18BP_ENST00000497194.2_Missense_Mutation_p.S96I|IL18BP_ENST00000531053.1_Missense_Mutation_p.S96I|IL18BP_ENST00000404792.1_Missense_Mutation_p.S96I|IL18BP_ENST00000337131.5_Missense_Mutation_p.S96I	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	96	Ig-like C2-type.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)	p.S96I(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						CCCAACTTCAGCATCCTCTAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	11											53	57	56					11																	71712298		2096	4207	6303	71389946	SO:0001583	missense	10068			AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5987	protein-coding gene	gene with protein product	"MC51L-53L-54L homolog gene product"	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.287G>T	11.37:g.71712298G>T	ENSP00000377306:p.Ser96Ile		71389946	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332104	0.60853	.	.	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049	T;T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71;1.71	4.64	0.5	0.16919	Immunoglobulin-like (1);	0.445990	0.22959	N	0.053571	T	0.42314	0.1197	M	0.71581	2.175	0.29485	N	0.856037	D;D	0.76494	0.998;0.999	D;D	0.67548	0.93;0.952	T	0.35001	-0.9806	10	0.87932	D	0	-3.9242	7.9028	0.29744	0.4682:0.0:0.5318:0.0	.	96;96	G3V1C5;O95998	.;I18BP_HUMAN	I	96	ENSP00000377306:S96I;ENSP00000434717:S96I;ENSP00000377308:S96I;ENSP00000338723:S96I;ENSP00000434835:S96I;ENSP00000384212:S96I;ENSP00000260049:S96I	ENSP00000260049:S96I	S	+	2	0	IL18BP	71389946	0.649000	0.27322	0.994000	0.49952	0.864000	0.49448	0.452000	0.21795	-0.067000	0.12976	0.561000	0.74099	AGC		0.612	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		T	71712298	G	T	71712298	3	4	61	1	0	0	0	0	1	0	0	0	7667	971	34	2	297	2	IL18BP	11	71712298	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1432524	71712298	63294218	7505	15490										
NUMA1	4926	broad.mit.edu	37	chr11	71728806	71728806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccactcctgagtggccttgCtgtgctcctccgtcagctca	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:71728806C>A	ENST00000393695.3	-	13	1377	c.1046G>T	c.(1045-1047)aGc>aTc	p.S349I	NUMA1_ENST00000351960.6_Missense_Mutation_p.S349I|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.S349I	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1									p.S349I(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						AGTGGCCTTGCTGTGCTCCTC	0.607			T	RARA	APL																																		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	1	Substitution - Missense(1)	large_intestine(1)	11											81	72	75					11																	71728806		2200	4293	6493	71406454	SO:0001583	missense	4926			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.1046G>T	11.37:g.71728806C>A	ENSP00000377298:p.Ser349Ile		71406454		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940767	0.52972	.	.	ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000542977;ENST00000537217	T;T;T;T;T	0.46819	2.19;2.66;2.66;1.44;0.86	5.35	4.24	0.50183	.	0.551376	0.20904	N	0.083595	T	0.51719	0.1691	L	0.53249	1.67	0.26471	N	0.975282	P;D;D;P;P;B	0.56968	0.898;0.978;0.978;0.514;0.874;0.32	P;P;P;B;B;B	0.55508	0.736;0.777;0.777;0.264;0.347;0.147	T	0.48547	-0.9026	10	0.62326	D	0.03	.	6.0444	0.19752	0.0:0.6552:0.1753:0.1695	.	349;349;349;349;349;349	F5H6Y5;F5H4J1;A8K394;Q14980-2;Q14980;Q9BTE9	.;.;.;.;NUMA1_HUMAN;.	I	349	ENSP00000260051:S349I;ENSP00000351851:S349I;ENSP00000377298:S349I;ENSP00000444880:S349I;ENSP00000442936:S349I	ENSP00000260051:S349I	S	-	2	0	NUMA1	71406454	0.739000	0.28196	1.000000	0.80357	0.359000	0.29487	0.248000	0.18198	2.504000	0.84457	0.655000	0.94253	AGC		0.607	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			A	71728806	C	A	71728806	3	1	61	1	0	0	0	0	1	0	0	0	10781	797	28	2	5361	2	NUMA1	11	71728806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16508	71728806	63277710	7506	15491										
FOLR2	2350	broad.mit.edu	37	chr11	71932698	71932698	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccccaacgaggaagtggcGaggttctatgctgcagccat	12	11	1	0	rs1803567		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:71932698G>A	ENST00000298223.6	+	5	847	c.660G>A	c.(658-660)gcG>gcA	p.A220A	FOLR2_ENST00000449475.2_Silent_p.A216A|FOLR2_ENST00000454954.2_Silent_p.A179A	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	220					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)	p.A220A(1)		breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	AGGAAGTGGCGAGGTTCTATG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											94	91	92					11																	71932698		2200	4293	6493	71610346	SO:0001819	synonymous_variant	2350			AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.660G>A	11.37:g.71932698G>A			71610346	Q05CA5|Q6GTE8	Silent	SNP	ENST00000298223.6	37	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	g	3.165	-0.171168	0.06421	.	.	ENSG00000165457	ENST00000413873	.	.	.	4.58	-9.15	0.00698	.	.	.	.	.	T	0.49712	0.1573	.	.	.	0.49915	D	0.999833	.	.	.	.	.	.	T	0.61997	-0.6947	5	0.87932	D	0	.	3.0134	0.06052	0.2068:0.4228:0.1118:0.2586	.	.	.	.	Q	234	.	ENSP00000412980:R234Q	R	+	2	0	FOLR2	71610346	0.000000	0.05858	0.018000	0.16275	0.548000	0.35241	-4.792000	0.00185	-1.783000	0.01274	-1.244000	0.01528	CGA		0.582	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		A	71932698	G	A	71932698	2	1	61	1	0	0	0	0	0	0	0	1	6001	1045	37	1		1	FOLR2	11	71932698	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203892	71932698	63073818	7507	15492										
FCHSD2	9873	broad.mit.edu	37	chr11	72553794	72553794	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcatcatcttggttttCtttgttcaagatacggatta	7	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:72553794C>A	ENST00000409418.4	-	17	2181	c.1798G>T	c.(1798-1800)Gaa>Taa	p.E600*	FCHSD2_ENST00000311172.7_Nonsense_Mutation_p.E544*|FCHSD2_ENST00000458644.2_Nonsense_Mutation_p.E464*|FCHSD2_ENST00000409314.1_Nonsense_Mutation_p.E624*|FCHSD2_ENST00000409263.1_Intron|ATG16L2_ENST00000534905.1_3'UTR	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	600	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.							p.E544*(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TCTTGGTTTTCTTTGTTCAAG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											137	133	134					11																	72553794		2200	4293	6493	72231442	SO:0001587	stop_gained	9873			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.1798G>T	11.37:g.72553794C>A	ENSP00000386722:p.Glu600*		72231442	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Nonsense_Mutation	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	C	42	9.202047	0.99099	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644	.	.	.	6.03	6.03	0.97812	.	0.163796	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-21.3241	19.5548	0.95338	0.0:1.0:0.0:0.0	.	.	.	.	X	544;624;600;464	.	ENSP00000308978:E544X	E	-	1	0	FCHSD2	72231442	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.697000	0.68295	2.854000	0.98071	0.655000	0.94253	GAA		0.428	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		A	72553794	C	A	72553794	4	1	61	1	0	0	0	0	0	1	0	0	5809	922	32	2	440	2	FCHSD2	11	72553794	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	621096	72553794	62452722	7508	15493										
FCHSD2	9873	broad.mit.edu	37	chr11	72560840	72560840	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggtgagtggataatttCttaaggtgccagaagggctg	15	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:72560840C>A	ENST00000409418.4	-	14	1786	c.1403G>T	c.(1402-1404)aGa>aTa	p.R468I	FCHSD2_ENST00000311172.7_Missense_Mutation_p.R412I|FCHSD2_ENST00000458644.2_Missense_Mutation_p.R332I|FCHSD2_ENST00000409314.1_Missense_Mutation_p.R492I|FCHSD2_ENST00000409853.1_Missense_Mutation_p.R412I	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	468								p.R412I(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TGGATAATTTCTTAAGGTGCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	11											145	154	151					11																	72560840		2200	4293	6493	72238488	SO:0001583	missense	9873			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.1403G>T	11.37:g.72560840C>A	ENSP00000386722:p.Arg468Ile		72238488	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	C	31	5.062240	0.93846	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644;ENST00000409853	T;T;T;T;T	0.50548	2.36;2.49;2.51;2.37;0.74	5.33	5.33	0.75918	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.67335	0.2882	M	0.74258	2.255	0.80722	D	1	D;D;D	0.69078	0.997;0.988;0.993	P;P;P	0.62298	0.83;0.797;0.9	T	0.69815	-0.5043	10	0.54805	T	0.06	-5.7345	18.0092	0.89218	0.0:1.0:0.0:0.0	.	332;468;412	E7ENZ2;O94868;O94868-3	.;FCSD2_HUMAN;.	I	412;492;468;332;412	ENSP00000308978:R412I;ENSP00000386987:R492I;ENSP00000386722:R468I;ENSP00000402972:R332I;ENSP00000386314:R412I	ENSP00000308978:R412I	R	-	2	0	FCHSD2	72238488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.730000	0.68546	2.490000	0.84030	0.650000	0.86243	AGA		0.373	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		A	72560840	C	A	72560840	3	1	61	1	0	0	0	0	1	0	0	0	5809	913	32	2	847	2	FCHSD2	11	72560840	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7046	72560840	62445676	7509	15494										
FCHSD2	9873	broad.mit.edu	37	chr11	72579065	72579065	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggcttcagctttcaattTaattatctagagaaccaaga	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:72579065T>G	ENST00000409418.4	-	13	1536	c.1153A>C	c.(1153-1155)Aaa>Caa	p.K385Q	FCHSD2_ENST00000311172.7_Missense_Mutation_p.K329Q|FCHSD2_ENST00000458644.2_Missense_Mutation_p.K249Q|FCHSD2_ENST00000409314.1_Missense_Mutation_p.K409Q|FCHSD2_ENST00000409853.1_Missense_Mutation_p.K329Q|RNU6-672P_ENST00000383911.1_RNA	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	385								p.K329Q(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			GCTTTCAATTTAATTATCTAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											29	29	29					11																	72579065		2162	4217	6379	72256713	SO:0001583	missense	9873			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.1153A>C	11.37:g.72579065T>G	ENSP00000386722:p.Lys385Gln		72256713	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	T	18.18	3.567559	0.65651	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644;ENST00000409853	T;T;T;T;T	0.54071	2.17;2.24;2.42;2.09;0.59	5.87	5.87	0.94306	.	0.101328	0.64402	D	0.000002	T	0.66489	0.2794	L	0.49640	1.575	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.994;0.997	T	0.62586	-0.6823	10	0.28530	T	0.3	-19.4599	15.4512	0.75274	0.0:0.0:0.0:1.0	.	249;385;329	E7ENZ2;O94868;O94868-3	.;FCSD2_HUMAN;.	Q	329;409;385;249;329	ENSP00000308978:K329Q;ENSP00000386987:K409Q;ENSP00000386722:K385Q;ENSP00000402972:K249Q;ENSP00000386314:K329Q	ENSP00000308978:K329Q	K	-	1	0	FCHSD2	72256713	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.698000	0.84413	2.248000	0.74166	0.533000	0.62120	AAA		0.403	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		G	72579065	T	G	72579065	3	3	61	1	0	0	0	0	1	0	0	0	5809	1763	61	4	1101	4	FCHSD2	11	72579065	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18225	72579065	62427451	7510	15495										
FCHSD2	9873	broad.mit.edu	37	chr11	72700017	72700017	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaacacatactttgcctcGatgtcagctttctctcgtac	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:72700017G>A	ENST00000409418.4	-	6	896	c.513C>T	c.(511-513)atC>atT	p.I171I	FCHSD2_ENST00000311172.7_Silent_p.I115I|FCHSD2_ENST00000458644.2_Silent_p.I11I|FCHSD2_ENST00000409314.1_Silent_p.I171I|FCHSD2_ENST00000409853.1_Silent_p.I115I	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	171								p.I115I(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			ACTTTGCCTCGATGTCAGCTT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	11											194	164	174					11																	72700017		2198	4291	6489	72377665	SO:0001819	synonymous_variant	9873			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.513C>T	11.37:g.72700017G>A			72377665	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Silent	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	G	9.397	1.077133	0.20227	.	.	ENSG00000137478	ENST00000543644	.	.	.	5.5	2.18	0.27775	.	.	.	.	.	T	0.46927	0.1418	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31916	-0.9926	4	.	.	.	-28.9911	4.3027	0.10932	0.3258:0.0:0.5124:0.1618	.	.	.	.	L	14	.	.	S	-	2	0	FCHSD2	72377665	0.118000	0.22208	1.000000	0.80357	0.985000	0.73830	-0.552000	0.06020	0.709000	0.31976	0.462000	0.41574	TCG		0.343	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		A	72700017	G	A	72700017	2	1	61	1	0	0	0	0	0	0	0	1	5809	1048	37	1		1	FCHSD2	11	72700017	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120952	72700017	62306499	7511	15496										
ARHGEF17	9828	broad.mit.edu	37	chr11	73020614	73020614	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggactgcaggcctgacagtGatgggttaaatctaagcagc	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73020614G>A	ENST00000263674.3	+	1	1281	c.931G>A	c.(931-933)Gat>Aat	p.D311N	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	311					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D311N(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						GCCTGACAGTGATGGGTTAAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											46	58	54					11																	73020614		2198	4291	6489	72698262	SO:0001583	missense	9828			AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.931G>A	11.37:g.73020614G>A	ENSP00000263674:p.Asp311Asn		72698262	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615845	0.46631	.	.	ENSG00000110237	ENST00000263674	T	0.58506	0.33	4.72	3.77	0.43336	.	0.626707	0.13224	N	0.404124	T	0.42426	0.1202	N	0.19112	0.55	0.29512	N	0.854118	B	0.19583	0.037	B	0.18871	0.023	T	0.37865	-0.9687	10	0.42905	T	0.14	-1.937	10.8288	0.46649	0.0:0.0:0.7699:0.2301	.	311	Q96PE2	ARHGH_HUMAN	N	311	ENSP00000263674:D311N	ENSP00000263674:D311N	D	+	1	0	ARHGEF17	72698262	0.999000	0.42202	0.992000	0.48379	0.665000	0.39181	1.995000	0.40767	0.895000	0.36342	0.313000	0.20887	GAT		0.617	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73020614	G	A	73020614	3	1	61	1	0	0	0	0	1	0	0	0	900	1290	45	3	933	3	ARHGEF17	11	73020614	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	320597	73020614	61985902	7512	15497										
PLEKHB1	58473	broad.mit.edu	37	chr11	73372620	73372620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggggcggcgctgggctcGctcatgtggtcgccctgctg	17	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73372620G>A	ENST00000354190.5	+	8	1136	c.705G>A	c.(703-705)tcG>tcA	p.S235S	PLEKHB1_ENST00000535129.1_Silent_p.S181S|PLEKHB1_ENST00000398492.4_Silent_p.S200S|PLEKHB1_ENST00000227214.6_Silent_p.S181S|PLEKHB1_ENST00000398494.4_Silent_p.S216S|PLEKHB1_ENST00000543085.1_Silent_p.S130S|Y_RNA_ENST00000516923.1_RNA	NM_021200.2	NP_067023.1	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B (evectins) member 1	235					multicellular organismal development (GO:0007275)|phototransduction (GO:0007602)|regulation of cell differentiation (GO:0045595)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)	p.S235S(1)		endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	7						CGCTGGGCTCGCTCATGTGGT	0.667											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	11											52	59	57					11																	73372620		2039	4190	6229	73050268	SO:0001819	synonymous_variant	58473			AF081583	CCDS44672.1, CCDS44673.1, CCDS44674.1, CCDS44675.1	11q13.5-q14.1	2013-01-10	2002-11-04	2002-11-08	ENSG00000021300	ENSG00000021300		"Pleckstrin homology (PH) domain containing"	19079	protein-coding gene	gene with protein product		607651	"PH domain containing, retinal 1"	PHRET1		10585447	Standard	NM_021200		Approved	PHR1, KPL1	uc001ouc.3	Q9UF11	OTTHUMG00000168030	ENST00000354190.5:c.705G>A	11.37:g.73372620G>A		1144	73050268	A8K0Q5|B2RBP1|B7Z716|Q9UBF5|Q9UI37|Q9UI44	Silent	SNP	ENST00000354190.5	37	CCDS44672.1																																																																																				0.667	PLEKHB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397593.1			A	73372620	G	A	73372620	2	1	61	1	0	0	0	0	0	0	0	1	12095	1074	38	1		1	PLEKHB1	11	73372620	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	352006	73372620	61633896	7513	15498										
C2CD3	26005	broad.mit.edu	37	chr11	73753122	73753122	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaagtcagaatggaggtTtgggaggacaaaggtgatgt	17	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73753122T>G	ENST00000334126.7	-	29	5863	c.5637A>C	c.(5635-5637)caA>caC	p.Q1879H	C2CD3_ENST00000313663.7_Missense_Mutation_p.Q1879H			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1879					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.Q1879H(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GAATGGAGGTTTGGGAGGACA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											210	179	189					11																	73753122		2200	4293	6493	73430770	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5637A>C	11.37:g.73753122T>G	ENSP00000334379:p.Gln1879His		73430770	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.809|7.809	0.715271|0.715271	0.15306|0.15306	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000538361|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	.|T;T;T	.|0.14144	.|2.95;2.95;2.53	5.82|5.82	-1.66|-1.66	0.08265|0.08265	.|.	.|0.635660	.|0.17829	.|N	.|0.160603	T|T	0.03136|0.03136	0.0092|0.0092	N|N	0.01267|0.01267	-0.92|-0.92	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.39722|0.39722	-0.9600|-0.9600	5|10	.|0.22109	.|T	.|0.4	2.7702|2.7702	3.9707|3.9707	0.09452|0.09452	0.3051:0.1154:0.4586:0.1209|0.3051:0.1154:0.4586:0.1209	.|.	.|1879	.|Q4AC94-1	.|.	H|H	113|1879;1879;1860;687	.|ENSP00000334379:Q1879H;ENSP00000323339:Q1879H;ENSP00000388750:Q687H	.|ENSP00000323339:Q1879H	N|Q	-|-	1|3	0|2	C2CD3|C2CD3	73430770|73430770	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.967000|0.967000	0.64934|0.64934	-2.877000|-2.877000	0.00717|0.00717	-0.294000|-0.294000	0.08973|0.08973	-0.672000|-0.672000	0.03802|0.03802	AAC|CAA		0.483	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73753122	T	G	73753122	3	3	61	1	0	0	0	0	1	0	0	0	2160	1838	64	4	266	4	C2CD3	11	73753122	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	380502	73753122	61253394	7514	15499										
C2CD3	26005	broad.mit.edu	37	chr11	73789470	73789470	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaggtagcaatatgtattCttatgaatgtggttgtggcc	12	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73789470C>A	ENST00000334126.7	-	23	4519	c.4293G>T	c.(4291-4293)aaG>aaT	p.K1431N	C2CD3_ENST00000313663.7_Missense_Mutation_p.K1431N			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1431					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.K1431N(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AATATGTATTCTTATGAATGT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	66	68					11																	73789470		2200	4293	6493	73467118	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4293G>T	11.37:g.73789470C>A	ENSP00000334379:p.Lys1431Asn		73467118	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	16.74	3.206047	0.58234	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	D;D;D	0.87571	-2.27;-2.27;-2.27	5.35	5.35	0.76521	.	0.172954	0.51477	D	0.000089	D	0.89719	0.6796	L	0.60455	1.87	0.32017	N	0.601329	D	0.71674	0.998	D	0.64237	0.923	D	0.90145	0.4216	10	0.66056	D	0.02	-11.1805	7.3573	0.26727	0.0:0.7921:0.0:0.2079	.	1431	Q4AC94-1	.	N	1431;1431;1412;239	ENSP00000334379:K1431N;ENSP00000323339:K1431N;ENSP00000388750:K239N	ENSP00000323339:K1431N	K	-	3	2	C2CD3	73467118	1.000000	0.71417	0.994000	0.49952	0.674000	0.39518	1.953000	0.40352	2.502000	0.84385	0.650000	0.86243	AAG		0.478	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73789470	C	A	73789470	3	1	61	1	0	0	0	0	1	0	0	0	2160	912	32	2	1634	2	C2CD3	11	73789470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36348	73789470	61217046	7515	15500										
C2CD3	26005	broad.mit.edu	37	chr11	73789536	73789536	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccacagccttggggtggaGatggtgacagtggctggctc	17	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73789536G>A	ENST00000334126.7	-	23	4453	c.4227C>T	c.(4225-4227)atC>atT	p.I1409I	C2CD3_ENST00000313663.7_Silent_p.I1409I			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1409					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.I1409I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTGGGGTGGAGATGGTGACAG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	11											66	62	63					11																	73789536		2200	4293	6493	73467184	SO:0001819	synonymous_variant	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4227C>T	11.37:g.73789536G>A			73467184	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																					0.502	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73789536	G	A	73789536	2	1	61	1	0	0	0	0	0	0	0	1	2160	932	33	3		3	C2CD3	11	73789536	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66	73789536	61216980	7516	15501										
C2CD3	26005	broad.mit.edu	37	chr11	73829279	73829279	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagagcagctcacctatttCtcttgcctgctgacctcttc	6	15	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:73829279C>A	ENST00000334126.7	-	9	1740	c.1514G>T	c.(1513-1515)aGa>aTa	p.R505I	C2CD3_ENST00000313663.7_Missense_Mutation_p.R505I			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	505					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.R505I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TCACCTATTTCTCTTGCCTGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											105	99	101					11																	73829279		2200	4293	6493	73506927	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1514G>T	11.37:g.73829279C>A	ENSP00000334379:p.Arg505Ile		73506927	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	12.57	1.976596	0.34848	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.09538	2.97;2.97	5.78	2.2	0.27929	.	0.222683	0.44285	D	0.000466	T	0.05686	0.0149	N	0.08118	0	0.20489	N	0.999899	B;P	0.35923	0.003;0.528	B;B	0.37943	0.004;0.261	T	0.32929	-0.9888	10	0.40728	T	0.16	-5.5186	8.3545	0.32323	0.0:0.3013:0.0:0.6987	.	505;505	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	I	505	ENSP00000334379:R505I;ENSP00000323339:R505I	ENSP00000323339:R505I	R	-	2	0	C2CD3	73506927	0.999000	0.42202	0.772000	0.31596	0.747000	0.42532	1.304000	0.33482	0.127000	0.18452	-1.273000	0.01405	AGA		0.423	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73829279	C	A	73829279	3	1	61	1	0	0	0	0	1	0	0	0	2160	913	32	2	4469	2	C2CD3	11	73829279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39743	73829279	61177237	7517	15502										
P4HA3	283208	broad.mit.edu	37	chr11	74015429	74015429	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggggttgttgaatcctCatgcaaagaaagtaccttgt	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74015429C>A	ENST00000331597.4	-	2	274	c.229G>T	c.(229-231)Gag>Tag	p.E77*	P4HA3_ENST00000427714.2_Nonsense_Mutation_p.E77*	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	77						endoplasmic reticulum (GO:0005783)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.E77*(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(1)	15	Breast(11;2.31e-05)					GTTGAATCCTCATGCAAAGAA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											140	134	136					11																	74015429		2200	4293	6493	73693077	SO:0001587	stop_gained	283208			AY327887	CCDS8230.1, CCDS73347.1	11q13	2008-12-09	2008-12-09			ENSG00000149380			30135	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(III)"	608987	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III"			14500733	Standard	XM_005273924		Approved	C-P4Halpha(III)	uc001ouz.3	Q7Z4N8		ENST00000331597.4:c.229G>T	11.37:g.74015429C>A	ENSP00000332170:p.Glu77*		73693077	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Nonsense_Mutation	SNP	ENST00000331597.4	37	CCDS8230.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755832	0.49362	.	.	ENSG00000149380	ENST00000331597;ENST00000427714	.	.	.	5.79	2.71	0.32032	.	0.486061	0.22798	N	0.055518	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-26.1017	6.0909	0.19993	0.0:0.5794:0.2534:0.1672	.	.	.	.	X	77	.	ENSP00000332170:E77X	E	-	1	0	P4HA3	73693077	0.984000	0.35163	1.000000	0.80357	0.158000	0.22134	0.958000	0.29227	1.439000	0.47511	-0.140000	0.14226	GAG		0.483	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		A	74015429	C	A	74015429	4	1	61	1	0	0	0	0	0	1	0	0	11389	835	29	2	1453	2	P4HA3	11	74015429	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	186150	74015429	60991087	7518	15503										
PGM2L1	283209	broad.mit.edu	37	chr11	74047777	74047777	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaatgagtttcttcagttCttcctccagtaaagcagtgt	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74047777C>A	ENST00000298198.4	-	14	2100	c.1789G>T	c.(1789-1791)Gaa>Taa	p.E597*		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	597					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)	p.E597*(1)		NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					TTCTTCAGTTCTTCCTCCAGT	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											107	96	100					11																	74047777		2200	4293	6493	73725425	SO:0001587	stop_gained	283209			AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"glucose-1,6-bisphosphate synthase"	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.1789G>T	11.37:g.74047777C>A	ENSP00000298198:p.Glu597*		73725425	Q96MQ7|Q9UIK3	Nonsense_Mutation	SNP	ENST00000298198.4	37	CCDS8231.1	.	.	.	.	.	.	.	.	.	.	C	39	7.845117	0.98522	.	.	ENSG00000165434	ENST00000298198	.	.	.	5.38	4.45	0.53987	.	0.053464	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-17.3654	14.0603	0.64795	0.0:0.8476:0.1524:0.0	.	.	.	.	X	597	.	ENSP00000298198:E597X	E	-	1	0	PGM2L1	73725425	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.437000	0.52863	1.359000	0.45940	0.563000	0.77884	GAA		0.338	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582		A	74047777	C	A	74047777	4	1	61	1	0	0	0	0	0	1	0	0	11830	922	32	2	83	2	PGM2L1	11	74047777	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32348	74047777	60958739	7519	15504										
PGM2L1	283209	broad.mit.edu	37	chr11	74056556	74056556	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcaattgccttcagaatTttagaagagactgtggtggc	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74056556T>G	ENST00000298198.4	-	9	1487	c.1176A>C	c.(1174-1176)aaA>aaC	p.K392N		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	392					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)	p.K392N(1)		NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					CCTTCAGAATTTTAGAAGAGA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	98	99					11																	74056556		2200	4293	6493	73734204	SO:0001583	missense	283209			AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"glucose-1,6-bisphosphate synthase"	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.1176A>C	11.37:g.74056556T>G	ENSP00000298198:p.Lys392Asn		73734204	Q96MQ7|Q9UIK3	Missense_Mutation	SNP	ENST00000298198.4	37	CCDS8231.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757239	0.69648	.	.	ENSG00000165434	ENST00000298198	T	0.42900	0.96	5.25	5.25	0.73442	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (1);	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	L	0.48174	1.505	0.47584	D	0.999464	P	0.37731	0.607	B	0.42163	0.378	T	0.25847	-1.0120	10	0.34782	T	0.22	-21.6555	13.4021	0.60889	0.0:0.0:0.0:1.0	.	392	Q6PCE3	PGM2L_HUMAN	N	392	ENSP00000298198:K392N	ENSP00000298198:K392N	K	-	3	2	PGM2L1	73734204	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.689000	0.25437	2.096000	0.63516	0.528000	0.53228	AAA		0.318	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582		G	74056556	T	G	74056556	3	3	61	1	0	0	0	0	1	0	0	0	11830	1838	64	4	716	4	PGM2L1	11	74056556	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8779	74056556	60949960	7520	15505										
POLD3	10714	broad.mit.edu	37	chr11	74329822	74329822	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagaaaccaacaaggaaacGaaaacagaggctaaagaagt	9	7	0	3	rs370291355		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74329822G>A	ENST00000263681.2	+	6	762	c.633G>A	c.(631-633)acG>acA	p.T211T	POLD3_ENST00000527458.1_Silent_p.T172T|POLD3_ENST00000532497.1_Silent_p.T105T	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	211					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.T211T(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					ACAAGGAAACGAAAACAGAGG	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	11						G		0,4400		0,0,2200	72	69	70		633	-0.1	1	11		70	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous	POLD3	NM_006591.1		0,1,6492	AA,AG,GG		0.0116,0.0,0.0077		211/467	74329822	1,12985	2200	4293	6493	74007470	SO:0001819	synonymous_variant	10714			D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"DNA polymerases"	20932	protein-coding gene	gene with protein product	"DNA polymerase delta subunit p66", "Pol delta C subunit (p66)", "protein phosphatase 1, regulatory subunit 128"	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.633G>A	11.37:g.74329822G>A			74007470	B7ZAI6|Q32MZ9|Q32N00	Silent	SNP	ENST00000263681.2	37	CCDS8233.1																																																																																				0.443	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591		A	74329822	G	A	74329822	2	1	61	1	0	0	0	0	0	0	0	1	12223	1045	37	1		1	POLD3	11	74329822	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273266	74329822	60676694	7521	15506										
CHRDL2	25884	broad.mit.edu	37	chr11	74429789	74429789	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcaggtacagcgcaggcaGtacatcaggccttgtggctc	14	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74429789G>T	ENST00000376332.3	-	2	667	c.171C>A	c.(169-171)taC>taA	p.Y57*	CHRDL2_ENST00000263671.5_Nonsense_Mutation_p.Y57*|MIR4696_ENST00000581431.1_RNA|SNORD43_ENST00000390975.1_RNA|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	57	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)		p.Y57*(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					AGCGCAGGCAGTACATCAGGC	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											80	61	68					11																	74429789		2200	4293	6493	74107437	SO:0001587	stop_gained	25884			AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.171C>A	11.37:g.74429789G>T	ENSP00000365510:p.Tyr57*		74107437	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Nonsense_Mutation	SNP	ENST00000376332.3	37		.	.	.	.	.	.	.	.	.	.	G	40	8.369798	0.98781	.	.	ENSG00000054938	ENST00000263671;ENST00000376332;ENST00000528789	.	.	.	5.47	2.61	0.31194	.	0.073354	0.56097	D	0.000022	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-30.4021	8.9331	0.35684	0.2453:0.0:0.7547:0.0	.	.	.	.	X	57	.	ENSP00000263671:Y57X	Y	-	3	2	CHRDL2	74107437	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.311000	0.59147	0.294000	0.22547	0.561000	0.74099	TAC		0.587	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1			T	74429789	G	T	74429789	4	4	61	1	0	0	0	0	0	1	0	0	3380	1024	36	2	1228	2	CHRDL2	11	74429789	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99967	74429789	60576727	7522	15507										
RNF169	254225	broad.mit.edu	37	chr11	74546777	74546777	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcaatgacagcatctccGaagaactaaaccatttcaag	7	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74546777G>A	ENST00000299563.4	+	6	1142	c.1129G>A	c.(1129-1131)Gaa>Aaa	p.E377K		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	377					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)	p.E377K(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CAGCATCTCCGAAGAACTAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											169	174	172					11																	74546777		2046	4200	6246	74224425	SO:0001583	missense	254225			AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"RING-type (C3HC4) zinc fingers"	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1129G>A	11.37:g.74546777G>A	ENSP00000299563:p.Glu377Lys		74224425	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	37	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094166	0.94149	.	.	ENSG00000166439	ENST00000299563	T	0.56611	0.45	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.74465	0.3720	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.75941	-0.3140	10	0.87932	D	0	-39.5918	18.1147	0.89549	0.0:0.0:1.0:0.0	.	377	Q8NCN4	RN169_HUMAN	K	377	ENSP00000299563:E377K	ENSP00000299563:E377K	E	+	1	0	RNF169	74224425	1.000000	0.71417	0.969000	0.41365	0.983000	0.72400	9.164000	0.94755	2.882000	0.98803	0.655000	0.94253	GAA		0.502	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886		A	74546777	G	A	74546777	3	1	61	1	0	0	0	0	1	0	0	0	13497	1059	37	1	1151	1	RNF169	11	74546777	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116988	74546777	60459739	7523	15508										
XRRA1	143570	broad.mit.edu	37	chr11	74570303	74570303	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggaaggatctcgaatatgGgaggaagtgaacatatcttg	13	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74570303G>T	ENST00000340360.6	-	12	1377	c.1046C>A	c.(1045-1047)cCc>cAc	p.P349H	XRRA1_ENST00000527087.1_Intron|XRRA1_ENST00000321448.8_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1									p.P349H(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						CTCGAATATGGGAGGAAGTGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											61	61	61					11																	74570303		1876	4103	5979	74247951	SO:0001583	missense	143570			AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1046C>A	11.37:g.74570303G>T	ENSP00000339918:p.Pro349His		74247951		Missense_Mutation	SNP	ENST00000340360.6	37	CCDS44680.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405714	0.62288	.	.	ENSG00000166435	ENST00000340360;ENST00000344880	T	0.52295	0.67	5.97	5.97	0.96955	.	.	.	.	.	T	0.60728	0.2291	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	P	0.58820	0.846	T	0.60244	-0.7301	9	0.59425	D	0.04	-13.1437	15.924	0.79597	0.0:0.0:1.0:0.0	.	349	Q6P2D8	XRRA1_HUMAN	H	349;335	ENSP00000339918:P349H	ENSP00000339918:P349H	P	-	2	0	XRRA1	74247951	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	4.489000	0.60309	2.828000	0.97474	0.655000	0.94253	CCC		0.478	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		T	74570303	G	T	74570303	3	4	61	1	0	0	0	0	1	0	0	0	17501	1232	43	2	1364	2	XRRA1	11	74570303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23526	74570303	60436213	7524	15509										
XRRA1	143570	broad.mit.edu	37	chr11	74618254	74618254	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgttgtcatccagcatcaGtgtctccagcgctgggaacc	10	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74618254G>A	ENST00000340360.6	-	9	1028	c.697C>T	c.(697-699)Ctg>Ttg	p.L233L	XRRA1_ENST00000533598.1_5'Flank|XRRA1_ENST00000527087.1_Silent_p.L233L|RP11-147I3.1_ENST00000533875.1_RNA|XRRA1_ENST00000321448.8_5'UTR	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1									p.L233L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TCCAGCATCAGTGTCTCCAGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	11											129	132	131					11																	74618254		2037	4206	6243	74295902	SO:0001819	synonymous_variant	143570			AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.697C>T	11.37:g.74618254G>A			74295902		Silent	SNP	ENST00000340360.6	37	CCDS44680.1																																																																																				0.542	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		A	74618254	G	A	74618254	2	1	61	1	0	0	0	0	0	0	0	1	17501	1020	36	3		3	XRRA1	11	74618254	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47951	74618254	60388262	7525	15510										
SLCO2B1	11309	broad.mit.edu	37	chr11	74880776	74880776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgggcagcctcatgctgCgcctttatgtggacattaac	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:74880776C>T	ENST00000289575.5	+	6	1143	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	SLCO2B1_ENST00000454962.2_Intron|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.R228C|SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000341411.4_Intron|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.R106C|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.R134C	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	250					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R250C(1)		breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	CCTCATGCTGCGCCTTTATGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											128	120	123					11																	74880776		2200	4293	6493	74558424	SO:0001583	missense	11309			AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.748C>T	11.37:g.74880776C>T	ENSP00000289575:p.Arg250Cys		74558424	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	37	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650407	0.67472	.	.	ENSG00000137491	ENST00000289575;ENST00000532236;ENST00000525650;ENST00000428359;ENST00000526839	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	4.83	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	0.060626	0.64402	D	0.000004	T	0.64000	0.2559	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.984;0.99	T	0.69569	-0.5110	10	0.72032	D	0.01	.	11.6849	0.51481	0.326:0.674:0.0:0.0	.	106;250	E9PPU8;O94956	.;SO2B1_HUMAN	C	250;134;106;228;126	ENSP00000289575:R250C;ENSP00000434112:R134C;ENSP00000436324:R106C;ENSP00000388912:R228C;ENSP00000434742:R126C	ENSP00000289575:R250C	R	+	1	0	SLCO2B1	74558424	0.932000	0.31603	0.996000	0.52242	0.937000	0.57800	1.528000	0.35985	1.218000	0.43458	0.650000	0.86243	CGC		0.542	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		T	74880776	C	T	74880776	3	4	61	1	0	0	0	0	1	0	0	0	14764	768	27	1	770	1	SLCO2B1	11	74880776	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	262522	74880776	60125740	7526	15511										
MAP6	4135	broad.mit.edu	37	chr11	75298463	75298463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgccacaactgcagaatCgtgaacctttgcatgctctg	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:75298463C>T	ENST00000304771.3	-	4	2833	c.2083G>A	c.(2083-2085)Gat>Aat	p.D695N	MAP6_ENST00000526689.1_5'Flank|CTD-2530H12.4_ENST00000527803.1_RNA|MAP6_ENST00000526740.1_Missense_Mutation_p.D366N	NM_033063.1	NP_149052.1	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6	695	Pro-rich.				dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)		p.D695N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	19	Ovarian(111;0.11)					ACTGCAGAATCGTGAACCTTT	0.488																																					Esophageal Squamous(181;1115 2007 8647 17065 22697)											1	Substitution - Missense(1)	large_intestine(1)	11											173	169	171					11																	75298463		2200	4293	6493	74976111	SO:0001583	missense	4135			AK123340	CCDS31641.1, CCDS44686.1	11q13.5	2005-10-11			ENSG00000171533	ENSG00000171533			6868	protein-coding gene	gene with protein product		601783				10516426, 12231625	Standard	NM_207577		Approved	KIAA1878, STOP, FLJ41346	uc001owu.3	Q96JE9	OTTHUMG00000165343	ENST00000304771.3:c.2083G>A	11.37:g.75298463C>T	ENSP00000307093:p.Asp695Asn		74976111	A7E2A1|Q6P3T0|Q6ZWB8	Missense_Mutation	SNP	ENST00000304771.3	37	CCDS31641.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904430	0.33628	.	.	ENSG00000171533	ENST00000304771;ENST00000526740;ENST00000545476	T	0.55760	0.5	5.01	4.09	0.47781	.	1.620210	0.03501	N	0.218036	T	0.37544	0.1007	L	0.39898	1.24	0.29829	N	0.830197	P	0.44006	0.824	B	0.30251	0.113	T	0.34428	-0.9829	10	0.16420	T	0.52	0.5423	6.6494	0.22953	0.0:0.8127:0.0:0.1872	.	695	Q96JE9	MAP6_HUMAN	N	695;366;366	ENSP00000307093:D695N	ENSP00000307093:D695N	D	-	1	0	MAP6	74976111	0.001000	0.12720	0.006000	0.13384	0.231000	0.25187	1.235000	0.32671	2.723000	0.93209	0.655000	0.94253	GAT		0.488	MAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383527.1	NM_033063		T	75298463	C	T	75298463	3	4	61	1	0	0	0	0	1	0	0	0	9294	884	31	1	362	1	MAP6	11	75298463	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	417687	75298463	59708053	7527	15512										
DGAT2	84649	broad.mit.edu	37	chr11	75511508	75511508	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctcttcgacaagcacaaGaccaagttcggcctcccgga	9	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:75511508G>T	ENST00000228027.7	+	8	1382	c.1122G>T	c.(1120-1122)aaG>aaT	p.K374N	DGAT2_ENST00000376262.3_Missense_Mutation_p.K331N|RP11-535A19.2_ENST00000533945.1_RNA|RP11-535A19.1_ENST00000534354.1_RNA|RP11-535A19.2_ENST00000533590.1_RNA	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	374					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)	p.K374N(1)		endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					ACAAGCACAAGACCAAGTTCG	0.567																																					Melanoma(35;811 1096 8354 24009 39363)											1	Substitution - Missense(1)	large_intestine(1)	11											102	82	88					11																	75511508		2200	4293	6493	75189156	SO:0001583	missense	84649				CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.1122G>T	11.37:g.75511508G>T	ENSP00000228027:p.Lys374Asn		75189156	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Missense_Mutation	SNP	ENST00000228027.7	37	CCDS31642.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091651	0.76756	.	.	ENSG00000062282	ENST00000228027;ENST00000376262	T;T	0.26223	1.75;1.75	5.55	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.56016	0.1957	M	0.91196	3.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.62784	-0.6781	10	0.62326	D	0.03	-34.9708	10.4695	0.44629	0.1672:0.0:0.8328:0.0	.	331;374	Q96PD7-2;Q96PD7	.;DGAT2_HUMAN	N	374;331	ENSP00000228027:K374N;ENSP00000365438:K331N	ENSP00000228027:K374N	K	+	3	2	DGAT2	75189156	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.575000	0.60908	2.622000	0.88805	0.655000	0.94253	AAG		0.567	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		T	75511508	G	T	75511508	3	4	61	1	0	0	0	0	1	0	0	0	4469	933	33	2	1152	2	DGAT2	11	75511508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213045	75511508	59495008	7528	15513										
UVRAG	7405	broad.mit.edu	37	chr11	75590944	75590944	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccacgtggcgaagtctcGattttggaattatgccagac	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:75590944G>A	ENST00000356136.3	+	4	533	c.292G>A	c.(292-294)Gat>Aat	p.D98N	UVRAG_ENST00000528420.1_5'UTR	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	98	C2.				DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)		p.D98N(1)		central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						GCGAAGTCTCGATTTTGGAAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	11											249	239	242					11																	75590944		2200	4293	6493	75268592	SO:0001583	missense	7405			X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.292G>A	11.37:g.75590944G>A	ENSP00000348455:p.Asp98Asn		75268592	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	G	35	5.462927	0.96257	.	.	ENSG00000198382	ENST00000356136	T	0.41758	0.99	5.65	5.65	0.86999	C2 calcium-dependent membrane targeting (1);	0.000000	0.85682	D	0.000000	T	0.62478	0.2431	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.60772	-0.7197	10	0.51188	T	0.08	-20.5642	18.3143	0.90213	0.0:0.0:1.0:0.0	.	98	Q9P2Y5	UVRAG_HUMAN	N	98	ENSP00000348455:D98N	ENSP00000348455:D98N	D	+	1	0	UVRAG	75268592	1.000000	0.71417	0.970000	0.41538	0.995000	0.86356	9.410000	0.97335	2.678000	0.91216	0.655000	0.94253	GAT		0.398	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		A	75590944	G	A	75590944	3	1	61	1	0	0	0	0	1	0	0	0	17148	1058	37	1	306	1	UVRAG	11	75590944	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79436	75590944	59415572	7529	15514										
C11orf30	56946	broad.mit.edu	37	chr11	76162982	76162982	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagaaagatcttcttggaGaactatcaaaagttcttagg	8	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:76162982G>T	ENST00000529032.1	+	2	151	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	C11orf30_ENST00000525959.1_3'UTR|C11orf30_ENST00000525038.1_Nonsense_Mutation_p.E51*|C11orf30_ENST00000524490.1_Nonsense_Mutation_p.E51*|C11orf30_ENST00000524767.1_Nonsense_Mutation_p.E51*|C11orf30_ENST00000343878.3_Nonsense_Mutation_p.E51*|C11orf30_ENST00000533248.1_Nonsense_Mutation_p.E51*|C11orf30_ENST00000525919.1_Nonsense_Mutation_p.E51*|C11orf30_ENST00000334736.3_Nonsense_Mutation_p.E51*|C11orf30_ENST00000533988.1_Nonsense_Mutation_p.E51*			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	51	ENT. {ECO:0000255|PROSITE- ProRule:PRU00476}.|Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.E51*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						TCTTCTTGGAGAACTATCAAA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											33	33	33					11																	76162982		2200	4292	6492	75840630	SO:0001587	stop_gained	56946			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.151G>T	11.37:g.76162982G>T	ENSP00000432327:p.Glu51*		75840630	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Nonsense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	G	33	5.210486	0.95069	.	.	ENSG00000158636	ENST00000533988;ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	.	.	.	5.7	5.7	0.88788	.	0.201106	0.50627	D	0.000107	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-9.507	19.8297	0.96630	0.0:0.0:1.0:0.0	.	.	.	.	X	51	.	ENSP00000334130:E51X	E	+	1	0	C11orf30	75840630	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.923000	0.87546	2.697000	0.92050	0.557000	0.71058	GAA		0.338	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		T	76162982	G	T	76162982	4	4	61	1	0	0	0	0	0	1	0	0	1640	943	33	2	157	2	C11orf30	11	76162982	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	572038	76162982	58843534	7530	15515										
TSKU	25987	broad.mit.edu	37	chr11	76507335	76507335	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcattggtccgggtgccttCgcggggctgggaggccttac	17	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:76507335C>T	ENST00000527881.1	+	2	1701	c.675C>T	c.(673-675)ttC>ttT	p.F225F	TSKU_ENST00000333090.4_Silent_p.F225F			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	225					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)		p.F225F(1)		NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					CGGGTGCCTTCGCGGGGCTGG	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	11											67	69	69					11																	76507335		2200	4289	6489	76184983	SO:0001819	synonymous_variant	25987			AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.675C>T	11.37:g.76507335C>T			76184983	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Silent	SNP	ENST00000527881.1	37	CCDS8246.1																																																																																				0.672	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		T	76507335	C	T	76507335	2	4	61	1	0	0	0	0	0	0	0	1	16667	883	31	1		1	TSKU	11	76507335	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	344353	76507335	58499181	7531	15516										
RSF1	51773	broad.mit.edu	37	chr11	77378474	77378474	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcttcggccccgctttcGaactgaccgctttgattctt	9	13	1	2	rs374487749		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77378474G>A	ENST00000308488.6	-	16	4116	c.3814C>T	c.(3814-3816)Cga>Tga	p.R1272*	RSF1_ENST00000360355.2_Nonsense_Mutation_p.R1241*|RSF1_ENST00000480887.1_Nonsense_Mutation_p.R1020*			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1272					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.R1272*(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	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)			CCCCGCTTTCGAACTGACCGC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											74	74	74					11																	77378474		2200	4292	6492	77056122	SO:0001587	stop_gained	51773			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3814C>T	11.37:g.77378474G>A	ENSP00000311513:p.Arg1272*		77056122	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Nonsense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	G	48	13.910734	0.99770	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355	.	.	.	5.13	4.22	0.49857	.	0.182394	0.26987	N	0.021485	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4901	13.1533	0.59503	0.0776:0.0:0.9223:0.0	.	.	.	.	X	1272;1020;1241	.	ENSP00000311513:R1272X	R	-	1	2	RSF1	77056122	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.917000	0.56424	1.397000	0.46682	0.462000	0.41574	CGA		0.483	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		A	77378474	G	A	77378474	4	1	61	1	0	0	0	0	0	1	0	0	13736	1066	37	1	515	1	RSF1	11	77378474	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	871139	77378474	57628042	7532	15517										
RSF1	51773	broad.mit.edu	37	chr11	77387910	77387910	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtccagatcatttaatcGccggcgtttcttccttcgag	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77387910G>A	ENST00000308488.6	-	13	3570	c.3268C>T	c.(3268-3270)Cga>Tga	p.R1090*	RSF1_ENST00000360355.2_Nonsense_Mutation_p.R1059*|RSF1_ENST00000480887.1_Nonsense_Mutation_p.R838*			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1090					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.R1090*(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	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)			TCATTTAATCGCCGGCGTTTC	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											169	157	161					11																	77387910		2200	4292	6492	77065558	SO:0001587	stop_gained	51773			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3268C>T	11.37:g.77387910G>A	ENSP00000311513:p.Arg1090*		77065558	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Nonsense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	G	49	16.000178	0.99851	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000531026	.	.	.	4.8	4.8	0.61643	.	0.000000	0.41001	D	0.000964	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4603	18.0227	0.89259	0.0:0.0:1.0:0.0	.	.	.	.	X	1090;838;1059;199	.	ENSP00000311513:R1090X	R	-	1	2	RSF1	77065558	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.920000	0.92779	2.670000	0.90874	0.655000	0.94253	CGA		0.473	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		A	77387910	G	A	77387910	4	1	61	1	0	0	0	0	0	1	0	0	13736	1095	38	1	1073	1	RSF1	11	77387910	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9436	77387910	57618606	7533	15518										
RSF1	51773	broad.mit.edu	37	chr11	77411962	77411962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcttaaagtacgacccAcatttgttttctcctcttcc	3	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77411962A>G	ENST00000308488.6	-	6	2614	c.2312T>C	c.(2311-2313)gTg>gCg	p.V771A	RSF1_ENST00000360355.2_Missense_Mutation_p.V740A|RSF1_ENST00000480887.1_Missense_Mutation_p.V519A			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	771					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.V771A(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	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)			AGTACGACCCACATTTGTTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											173	172	172					11																	77411962		2200	4292	6492	77089610	SO:0001583	missense	51773			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2312T>C	11.37:g.77411962A>G	ENSP00000311513:p.Val771Ala		77089610	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.522|6.522	0.464567|0.464567	0.12402|0.12402	.|.	.|.	ENSG00000048649|ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324|ENST00000532556	D;D;D;D|.	0.84800|.	-1.88;-1.89;-1.88;-1.9|.	5.82|5.82	4.69|4.69	0.59074|0.59074	.|.	0.455473|.	0.18596|.	N|.	0.136613|.	T|T	0.43389|0.43389	0.1245|0.1245	L|L	0.27053|0.27053	0.805|0.805	0.35330|0.35330	D|D	0.785491|0.785491	B|.	0.10296|.	0.003|.	B|.	0.09377|.	0.004|.	T|T	0.51317|0.51317	-0.8721|-0.8721	10|5	0.30078|.	T|.	0.28|.	-6.3117|-6.3117	8.6157|8.6157	0.33831|0.33831	0.8826:0.0:0.1174:0.0|0.8826:0.0:0.1174:0.0	.|.	771|.	Q96T23|.	RSF1_HUMAN|.	A|R	771;519;740;572|28	ENSP00000311513:V771A;ENSP00000434509:V519A;ENSP00000353511:V740A;ENSP00000432022:V572A|.	ENSP00000311513:V771A|.	V|W	-|-	2|1	0|0	RSF1|RSF1	77089610|77089610	0.001000|0.001000	0.12720|0.12720	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.166000|1.166000	0.31834|0.31834	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	GTG|TGG		0.418	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		G	77411962	A	G	77411962	3	3	61	1	0	0	0	0	1	0	0	0	13736	159	6	4	2057	4	RSF1	11	77411962	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24052	77411962	57594554	7534	15519										
INTS4	92105	broad.mit.edu	37	chr11	77649828	77649828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccactggaaaactcccccGaactgtaaagttccttggca	8	13	0	0	rs151018256	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77649828G>A	ENST00000534064.1	-	10	1068	c.1034C>T	c.(1033-1035)tCg>tTg	p.S345L	INTS4_ENST00000525931.1_5'Flank|INTS4_ENST00000529807.1_Missense_Mutation_p.S345L	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	345					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.S345L(1)	INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			AAACTCCCCCGAACTGTAAAG	0.483													G|||	2	0.000399361	0	0	5008	,	,		19414	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						G	LEU/SER	1,4399	2.1+/-5.4	0,1,2199	82	81	81		1034	4.2	1	11	dbSNP_134	81	8,8576	6.4+/-24.3	0,8,4284	yes	missense	INTS4	NM_033547.3	145	0,9,6483	AA,AG,GG		0.0932,0.0227,0.0693	possibly-damaging	345/964	77649828	9,12975	2200	4292	6492	77327476	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1034C>T	11.37:g.77649828G>A	ENSP00000434466:p.Ser345Leu		77327476	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	23.8	4.456243	0.84317	2.27E-4	9.32E-4	ENSG00000149262	ENST00000534064;ENST00000354849;ENST00000529807	D;D	0.85556	-2.0;-2.0	4.17	4.17	0.49024	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90776	0.7104	M	0.74881	2.28	0.80722	D	1	D	0.64830	0.994	P	0.61201	0.885	D	0.91551	0.5257	10	0.51188	T	0.08	-11.4634	16.6644	0.85248	0.0:0.0:1.0:0.0	.	345	Q96HW7	INT4_HUMAN	L	345;196;345	ENSP00000434466:S345L;ENSP00000433644:S345L	ENSP00000346913:S196L	S	-	2	0	INTS4	77327476	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.864000	0.92294	2.140000	0.66376	0.471000	0.43371	TCG		0.483	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77649828	G	A	77649828	3	1	61	1	0	0	0	0	1	0	0	0	7801	1059	37	1	1913	1	INTS4	11	77649828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	237866	77649828	57356688	7535	15520										
ALG8	79053	broad.mit.edu	37	chr11	77812074	77812074	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacatacagtttgaaccaaGcatatgtgatgcctactgca	7	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77812074G>T	ENST00000299626.5	-	13	1588	c.1517C>A	c.(1516-1518)gCt>gAt	p.A506D	ALG8_ENST00000532552.2_5'Flank|ALG8_ENST00000376156.3_3'UTR	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	506					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)	p.A506D(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			TTTGAACCAAGCATATGTGAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											149	140	143					11																	77812074		2200	4292	6492	77489722	SO:0001583	missense	79053			AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	608103	"asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1517C>A	11.37:g.77812074G>T	ENSP00000299626:p.Ala506Asp		77489722	A6NDW6|O60860	Missense_Mutation	SNP	ENST00000299626.5	37	CCDS8258.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.04|19.04	3.750845|3.750845	0.69533|0.69533	.|.	.|.	ENSG00000159063|ENSG00000159063	ENST00000299626;ENST00000526849|ENST00000530608	D;D|.	0.83992|.	-1.79;-1.79|.	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	0.300661|.	0.36972|.	N|.	0.002315|.	T|T	0.75539|0.75539	0.3863|0.3863	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	B;B|.	0.27013|.	0.166;0.154|.	B;B|.	0.36567|.	0.148;0.228|.	T|T	0.74615|0.74615	-0.3606|-0.3606	10|5	0.35671|.	T|.	0.21|.	-7.0463|-7.0463	18.7487|18.7487	0.91804|0.91804	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	506;506|.	B3KQL8;Q9BVK2|.	.;ALG8_HUMAN|.	D|I	506;177|208	ENSP00000299626:A506D;ENSP00000434388:A177D|.	ENSP00000299626:A506D|.	A|L	-|-	2|1	0|0	ALG8|ALG8	77489722|77489722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.337000|6.337000	0.72958|0.72958	2.724000|2.724000	0.93272|0.93272	0.563000|0.563000	0.77884|0.77884	GCT|CTT		0.393	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		T	77812074	G	T	77812074	3	4	61	1	0	0	0	0	1	0	0	0	523	971	34	2	67	2	ALG8	11	77812074	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	162246	77812074	57194442	7536	15521										
ALG8	79053	broad.mit.edu	37	chr11	77815466	77815466	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtcagaatcagaaaaatCgaagcgtctcctgcttttcc	9	10	3	2	rs200575151		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77815466C>A	ENST00000299626.5	-	11	1283	c.1212G>T	c.(1210-1212)tcG>tcT	p.S404S	ALG8_ENST00000532552.2_5'UTR|ALG8_ENST00000376156.3_Silent_p.S404S	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	404					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)	p.S404S(2)		NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			TCAGAAAAATCGAAGCGTCTC	0.353													C|||	1	0.000199681	0	0.0014	5008	,	,		16672	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	11											65	66	65					11																	77815466		2200	4292	6492	77493114	SO:0001819	synonymous_variant	79053			AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	608103	"asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1212G>T	11.37:g.77815466C>A			77493114	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	37	CCDS8258.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	0.092	-1.165148	0.01673	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	4.94	-9.88	0.00467	.	.	.	.	.	T	0.43523	0.1251	.	.	.	0.53688	D	0.999977	.	.	.	.	.	.	T	0.55140	-0.8187	4	.	.	.	-5.1213	5.9378	0.19175	0.0678:0.5041:0.2167:0.2114	.	.	.	.	L	106;191	.	.	R	-	2	0	ALG8	77493114	0.001000	0.12720	0.010000	0.14722	0.206000	0.24218	-1.893000	0.01609	-3.612000	0.00132	-2.926000	0.00089	CGA		0.353	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		A	77815466	C	A	77815466	2	1	61	1	0	0	0	0	0	0	0	1	523	871	31	2		2	ALG8	11	77815466	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3392	77815466	57191050	7537	15522										
KCTD21	283219	broad.mit.edu	37	chr11	77884838	77884838	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgtaccgtattaatcGaataatcttattgttcataa	4	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77884838G>A	ENST00000340067.3	-	2	1041	c.763C>T	c.(763-765)Cga>Tga	p.R255*	KCTD21-AS1_ENST00000530261.1_RNA|KCTD21-AS1_ENST00000600795.1_RNA|KCTD21-AS1_ENST00000528468.1_RNA|KCTD21-AS1_ENST00000523626.2_RNA	NM_001029859.1	NP_001025030.1	Q4G0X4	KCD21_HUMAN	potassium channel tetramerization domain containing 21	255					protein homooligomerization (GO:0051260)			p.R255*(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(2)	11	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)			CGTATTAATCGAATAATCTTA	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											107	112	110					11																	77884838		2200	4292	6492	77562486	SO:0001587	stop_gained	283219			AK095233	CCDS31645.1	11q14.1	2013-06-20	2013-06-20			ENSG00000188997			27452	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 21"			21472142	Standard	XM_005273925		Approved	KCASH2	uc001ozb.3	Q4G0X4		ENST00000340067.3:c.763C>T	11.37:g.77884838G>A	ENSP00000339340:p.Arg255*		77562486	B4DTR0	Nonsense_Mutation	SNP	ENST00000340067.3	37	CCDS31645.1	.	.	.	.	.	.	.	.	.	.	G	37	6.081195	0.97267	.	.	ENSG00000188997	ENST00000340067	.	.	.	5.5	5.5	0.81552	.	0.000000	0.47852	D	0.000203	.	.	.	.	.	.	0.44711	D	0.997706	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.7606	0.88463	0.0:0.0:1.0:0.0	.	.	.	.	X	255	.	ENSP00000339340:R255X	R	-	1	2	KCTD21	77562486	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.230000	0.65321	2.861000	0.98227	0.655000	0.94253	CGA		0.488	KCTD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390057.1	NM_001029859		A	77884838	G	A	77884838	4	1	61	1	0	0	0	0	0	1	0	0	8130	1066	37	1	23	1	KCTD21	11	77884838	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69372	77884838	57121678	7538	15523										
KCTD21	283219	broad.mit.edu	37	chr11	77885445	77885445	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatagcggaacactttgccGtcacggtcaatgaagcagtt	10	9	2	1	rs575414089		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77885445G>A	ENST00000340067.3	-	2	434	c.156C>T	c.(154-156)gaC>gaT	p.D52D	KCTD21-AS1_ENST00000530261.1_RNA|KCTD21-AS1_ENST00000600795.1_RNA|KCTD21-AS1_ENST00000528468.1_RNA|KCTD21-AS1_ENST00000523626.2_RNA	NM_001029859.1	NP_001025030.1	Q4G0X4	KCD21_HUMAN	potassium channel tetramerization domain containing 21	52	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein homooligomerization (GO:0051260)			p.D52D(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(2)	11	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)			ACACTTTGCCGTCACGGTCAA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	11											148	113	124					11																	77885445		2200	4292	6492	77563093	SO:0001819	synonymous_variant	283219			AK095233	CCDS31645.1	11q14.1	2013-06-20	2013-06-20			ENSG00000188997			27452	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 21"			21472142	Standard	XM_005273925		Approved	KCASH2	uc001ozb.3	Q4G0X4		ENST00000340067.3:c.156C>T	11.37:g.77885445G>A			77563093	B4DTR0	Silent	SNP	ENST00000340067.3	37	CCDS31645.1																																																																																				0.607	KCTD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390057.1	NM_001029859		A	77885445	G	A	77885445	2	1	61	1	0	0	0	0	0	0	0	1	8130	1136	40	1		1	KCTD21	11	77885445	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	607	77885445	57121071	7539	15524										
USP35	57558	broad.mit.edu	37	chr11	77911746	77911746	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctggtcaaggaggactcGaactcggggaccagctgcct	13	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77911746G>A	ENST00000529308.1	+	6	1350	c.1089G>A	c.(1087-1089)tcG>tcA	p.S363S	USP35_ENST00000530535.1_Intron|USP35_ENST00000526425.1_Silent_p.S94S|USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530267.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.S119S(1)|p.S363S(1)		endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	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;1.04e-25)			AGGAGGACTCGAACTCGGGGA	0.647																																																2	Substitution - coding silent(2)	large_intestine(2)	11											46	53	51					11																	77911746		1949	4116	6065	77589394	SO:0001819	synonymous_variant	57558			AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"Ubiquitin-specific peptidases"	20061	protein-coding gene	gene with protein product			"ubiquitin specific protease 35"			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1089G>A	11.37:g.77911746G>A			77589394		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																				0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		A	77911746	G	A	77911746	2	1	61	1	0	0	0	0	0	0	0	1	17106	1045	37	1		1	USP35	11	77911746	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26301	77911746	57094770	7540	15525										
USP35	57558	broad.mit.edu	37	chr11	77921074	77921074	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtggagaaggagacagaaAaggaggctgagcaggaaaag	18	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:77921074A>T	ENST00000529308.1	+	10	2434	c.2173A>T	c.(2173-2175)Aag>Tag	p.K725*	USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Nonsense_Mutation_p.K456*|USP35_ENST00000441408.2_Nonsense_Mutation_p.K311*|USP35_ENST00000530267.1_Nonsense_Mutation_p.K293*	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	725	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.K725*(1)|p.K481*(1)		endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	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;1.04e-25)			ggagacagaaaaggaggctga	0.602																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											70	92	85					11																	77921074		2090	4222	6312	77598722	SO:0001587	stop_gained	57558			AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"Ubiquitin-specific peptidases"	20061	protein-coding gene	gene with protein product			"ubiquitin specific protease 35"			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2173A>T	11.37:g.77921074A>T	ENSP00000431876:p.Lys725*		77598722		Nonsense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	A	39	7.750077	0.98468	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	.	.	.	5.11	-6.11	0.02131	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1561	7.5767	0.27939	0.6327:0.2342:0.1331:0.0	.	.	.	.	X	293;725;311;456	.	ENSP00000400825:K311X	K	+	1	0	USP35	77598722	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.508000	0.06344	-1.090000	0.03069	0.496000	0.49642	AAG		0.602	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		T	77921074	A	T	77921074	4	4	61	1	0	0	0	0	0	1	0	0	17106	15	1	5	2207	5	USP35	11	77921074	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9328	77921074	57085442	7541	15526										
NARS2	79731	broad.mit.edu	37	chr11	78277216	78277216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagctgtcgcttcactgcGaatcctcaatatagaaccca	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78277216G>A	ENST00000281038.5	-	4	850	c.475C>T	c.(475-477)Cgc>Tgc	p.R159C	NARS2_ENST00000528850.1_5'UTR	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	159					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.R159C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GCTTCACTGCGAATCCTCAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											115	115	115					11																	78277216		2200	4291	6491	77954864	SO:0001583	missense	79731			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.475C>T	11.37:g.78277216G>A	ENSP00000281038:p.Arg159Cys		77954864	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609169	0.87258	.	.	ENSG00000137513	ENST00000281038;ENST00000529880	D;D	0.85861	-2.04;-2.04	5.13	5.13	0.70059	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.000000	0.85682	D	0.000000	D	0.94850	0.8336	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96217	0.9157	10	0.87932	D	0	-9.3895	17.7175	0.88342	0.0:0.0:1.0:0.0	.	159	Q96I59	SYNM_HUMAN	C	159	ENSP00000281038:R159C;ENSP00000432240:R159C	ENSP00000281038:R159C	R	-	1	0	NARS2	77954864	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.731000	0.74785	2.547000	0.85894	0.655000	0.94253	CGC		0.383	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		A	78277216	G	A	78277216	3	1	61	1	0	0	0	0	1	0	0	0	10201	1058	37	1	1002	1	NARS2	11	78277216	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356142	78277216	56729300	7542	15527										
NARS2	79731	broad.mit.edu	37	chr11	78285492	78285492	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggaagggggcggaggaAcagaagcgcacggaccgcag	20	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78285492A>G	ENST00000281038.5	-	1	417	c.42T>C	c.(40-42)tgT>tgC	p.C14C	NARS2_ENST00000528850.1_5'Flank	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	14					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.C14C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GGGCGGAGGAACAGAAGCGCA	0.692																																																1	Substitution - coding silent(1)	large_intestine(1)	11											43	44	43					11																	78285492		2200	4291	6491	77963140	SO:0001819	synonymous_variant	79731			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.42T>C	11.37:g.78285492A>G			77963140	G3V178	Silent	SNP	ENST00000281038.5	37	CCDS8261.1																																																																																				0.692	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		G	78285492	A	G	78285492	2	3	61	1	0	0	0	0	0	0	0	1	10201	41	2	4		4	NARS2	11	78285492	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	8276	78285492	56721024	7543	15528										
ODZ4	26011	broad.mit.edu	37	chr11	78380283	78380283	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaaacctgttccactaaaGacagcaagaggggtcccgat	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78380283G>T	ENST00000278550.7	-	32	7569	c.7107C>A	c.(7105-7107)gtC>gtA	p.V2369V		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2369					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.V2369V(2)									TTCCACTAAAGACAGCAAGAG	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	11											90	91	91					11																	78380283		1988	4162	6150	78057931	SO:0001819	synonymous_variant	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7107C>A	11.37:g.78380283G>T			78057931	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																				0.478	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78380283	G	T	78380283	2	4	61	1	0	0	0	0	0	0	0	1	10868	929	33	2		2	ODZ4	11	78380283	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94791	78380283	56626233	7544	15529										
ODZ4	26011	broad.mit.edu	37	chr11	78381069	78381069	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacatcatcatagcgataGagatcaatgggcagtggggt	13	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78381069G>T	ENST00000278550.7	-	32	6783	c.6321C>A	c.(6319-6321)ctC>ctA	p.L2107L		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2107					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.L2107L(2)									CATAGCGATAGAGATCAATGG	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	11											60	62	61					11																	78381069		2074	4207	6281	78058717	SO:0001819	synonymous_variant	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6321C>A	11.37:g.78381069G>T			78058717	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																				0.488	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78381069	G	T	78381069	2	4	61	1	0	0	0	0	0	0	0	1	10868	929	33	2		2	ODZ4	11	78381069	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	786	78381069	56625447	7545	15530										
ODZ4	26011	broad.mit.edu	37	chr11	78381549	78381549	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaggcggtcattcttgtcGaactcaaagatatactgcct	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78381549G>A	ENST00000278550.7	-	32	6303	c.5841C>T	c.(5839-5841)ttC>ttT	p.F1947F		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1947					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.F1947F(4)									CATTCTTGTCGAACTCAAAGA	0.532																																																4	Substitution - coding silent(4)	large_intestine(4)	11											71	74	73					11																	78381549		2006	4165	6171	78059197	SO:0001819	synonymous_variant	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5841C>T	11.37:g.78381549G>A			78059197	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																				0.532	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78381549	G	A	78381549	2	1	61	1	0	0	0	0	0	0	0	1	10868	1049	37	1		1	ODZ4	11	78381549	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	480	78381549	56624967	7546	15531										
ODZ4	26011	broad.mit.edu	37	chr11	78433868	78433868	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgttgcagctggggcaggaGatgcttctccggcgcccatt	14	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:78433868G>T	ENST00000278550.7	-	24	4107	c.3645C>A	c.(3643-3645)atC>atA	p.I1215I		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1215					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.I1215I(2)									TGGGGCAGGAGATGCTTCTCC	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	11											59	65	63					11																	78433868		2035	4184	6219	78111516	SO:0001819	synonymous_variant	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3645C>A	11.37:g.78433868G>T			78111516	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																				0.602	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78433868	G	T	78433868	2	4	61	1	0	0	0	0	0	0	0	1	10868	932	33	2		2	ODZ4	11	78433868	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52319	78433868	56572648	7547	15532										
C11orf82	220042	broad.mit.edu	37	chr11	82643396	82643396	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagttaatgactctaattTattctctttggaaatgcgag	9	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:82643396T>G	ENST00000533655.1	+	6	1228	c.1016T>G	c.(1015-1017)tTa>tGa	p.L339*	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000329143.3_Nonsense_Mutation_p.L38*|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000430323.2_Nonsense_Mutation_p.L339*	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		339					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L339*(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						GACTCTAATTTATTCTCTTTG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											80	87	84					11																	82643396		2203	4300	6503	82321044	SO:0001587	stop_gained	220042																														ENST00000533655.1:c.1016T>G	11.37:g.82643396T>G	ENSP00000435421:p.Leu339*		82321044	Q96LK6|Q9H856	Nonsense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	T	33	5.278698	0.95459	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	.	.	.	5.52	5.52	0.82312	.	0.978397	0.08372	N	0.955970	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0399	0.53446	0.0:0.0:0.0:1.0	.	.	.	.	X	339;339;38	.	.	L	+	2	0	C11orf82	82321044	0.097000	0.21791	0.030000	0.17652	0.223000	0.24884	1.897000	0.39799	2.109000	0.64355	0.416000	0.27883	TTA		0.408	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			G	82643396	T	G	82643396	4	3	61	1	0	0	0	0	0	1	0	0	1669	1764	61	4	1030	4	C11orf82	11	82643396	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4209528	82643396	52363120	7548	15533										
RAB30	27314	broad.mit.edu	37	chr11	82708346	82708346	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaacaggaaatcataatCttccatactcatttacacag	4	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:82708346C>A	ENST00000533486.1	-	3	297	c.13G>T	c.(13-15)Gat>Tat	p.D5Y	RAB30_ENST00000527633.1_Missense_Mutation_p.D5Y|RAB30_ENST00000532548.1_Missense_Mutation_p.D5Y|RAB30_ENST00000534141.1_Missense_Mutation_p.D5Y|RP11-659G9.3_ENST00000527550.1_RNA|RAB30_ENST00000260056.2_Missense_Mutation_p.D5Y|RAB30_ENST00000525117.1_Missense_Mutation_p.D5Y	NM_014488.3	NP_055303.2	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family	5					Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cis-Golgi network (GO:0005801)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D5Y(1)		endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						AAATCATAATCTTCCATACTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											83	76	78					11																	82708346		2203	4300	6503	82385994	SO:0001583	missense	27314			U57092	CCDS8264.1	11q12-q14	2008-07-21				ENSG00000137502		"RAB, member RAS oncogene"	9770	protein-coding gene	gene with protein product		605693				8863739, 9792283	Standard	NM_014488		Approved		uc001ozu.3	Q15771		ENST00000533486.1:c.13G>T	11.37:g.82708346C>A	ENSP00000435189:p.Asp5Tyr		82385994	Q6FGK1|Q6MZH2|Q96CI8	Missense_Mutation	SNP	ENST00000533486.1	37	CCDS8264.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.961546	0.92791	.	.	ENSG00000137502	ENST00000533486;ENST00000534141;ENST00000260056;ENST00000527633;ENST00000531021;ENST00000534301;ENST00000525117;ENST00000532548;ENST00000526205;ENST00000534103;ENST00000530224;ENST00000533276;ENST00000528379	T;T;T;T;T;T;T;T;T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.89160	0.6636	M	0.69463	2.115	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.966;0.987;0.994	D	0.87631	0.2516	9	.	.	.	.	20.0609	0.97674	0.0:1.0:0.0:0.0	.	5;5;5	E9PLM3;Q6MZH2;Q15771	.;.;RAB30_HUMAN	Y	5	ENSP00000435189:D5Y;ENSP00000434974:D5Y;ENSP00000260056:D5Y;ENSP00000435089:D5Y;ENSP00000434953:D5Y;ENSP00000432193:D5Y;ENSP00000433243:D5Y;ENSP00000437235:D5Y;ENSP00000432336:D5Y;ENSP00000435542:D5Y;ENSP00000436282:D5Y;ENSP00000434528:D5Y;ENSP00000434106:D5Y	.	D	-	1	0	RAB30	82385994	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.763000	0.85283	2.755000	0.94549	0.655000	0.94253	GAT		0.483	RAB30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392141.1	NM_014488		A	82708346	C	A	82708346	3	1	61	1	0	0	0	0	1	0	0	0	12956	913	32	2	614	2	RAB30	11	82708346	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64950	82708346	52298170	7549	15534										
DLG2	1740	broad.mit.edu	37	chr11	83641486	83641486	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggagaagcaggcttatCacatagtttgttcacagtgc	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:83641486C>T	ENST00000532653.1	-	10	1368	c.1066G>A	c.(1066-1068)Gat>Aat	p.D356N	DLG2_ENST00000398301.2_Missense_Mutation_p.D395N|DLG2_ENST00000376104.2_Missense_Mutation_p.D461N|DLG2_ENST00000398309.2_Missense_Mutation_p.D356N|DLG2_ENST00000418306.2_Intron|DLG2_ENST00000531015.1_Missense_Mutation_p.D323N|DLG2_ENST00000537455.1_Missense_Mutation_p.D110N|DLG2_ENST00000280241.8_Missense_Mutation_p.D395N|DLG2_ENST00000543673.1_Missense_Mutation_p.D461N|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000330014.6_Missense_Mutation_p.D295N|DLG2_ENST00000524982.1_Missense_Mutation_p.D356N			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.D356N(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GCAGGCTTATCACATAGTTTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											162	166	165					11																	83641486		1996	4190	6186	83319134	SO:0001583	missense	1740			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.1066G>A	11.37:g.83641486C>T	ENSP00000435849:p.Asp356Asn		83319134	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	C	18.32	3.598710	0.66332	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000537455;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301	T;T;T;T;T;T;T;T;T;T	0.20069	2.64;2.66;2.66;2.61;2.56;2.42;2.65;2.6;2.47;2.1	5.78	5.78	0.91487	.	0.082208	0.46145	D	0.000320	T	0.16085	0.0387	N	0.14661	0.345	0.80722	D	1	P;B;B;P;B;P;B	0.40731	0.598;0.319;0.319;0.598;0.204;0.728;0.319	B;B;B;B;B;B;B	0.39339	0.19;0.111;0.111;0.19;0.046;0.297;0.111	T	0.05370	-1.0889	9	.	.	.	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	323;356;356;295;395;461;356	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700	.;.;.;.;.;.;DLG2_HUMAN	N	356;461;461;395;295;110;356;356;461;323;395	ENSP00000381355:D356N;ENSP00000365272:D461N;ENSP00000441994:D461N;ENSP00000280241:D395N;ENSP00000381353:D295N;ENSP00000443248:D110N;ENSP00000432894:D356N;ENSP00000435849:D356N;ENSP00000433848:D323N;ENSP00000381346:D395N	.	D	-	1	0	DLG2	83319134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.344000	0.79328	2.730000	0.93505	0.655000	0.94253	GAT		0.488	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		T	83641486	C	T	83641486	3	4	61	1	0	0	0	0	1	0	0	0	4566	826	29	3	1652	3	DLG2	11	83641486	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	933140	83641486	51365030	7550	15535										
SYTL2	54843	broad.mit.edu	37	chr11	85409098	85409098	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcacccagatgtgcacttCtccagttgtaggaagctttt	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85409098C>A	ENST00000528231.1	-	16	2654	c.2377G>T	c.(2377-2379)Gaa>Taa	p.E793*	SYTL2_ENST00000527523.1_Nonsense_Mutation_p.E761*|SYTL2_ENST00000525702.1_Nonsense_Mutation_p.E235*|SYTL2_ENST00000354566.3_Nonsense_Mutation_p.E1131*|SYTL2_ENST00000359152.5_Nonsense_Mutation_p.E1639*|SYTL2_ENST00000525423.1_Nonsense_Mutation_p.E1115*|SYTL2_ENST00000529581.1_Nonsense_Mutation_p.E235*|SYTL2_ENST00000524452.1_Nonsense_Mutation_p.E769*|SYTL2_ENST00000316356.4_Nonsense_Mutation_p.E794*|SYTL2_ENST00000389960.4_Nonsense_Mutation_p.E769*|SYTL2_ENST00000533892.1_Nonsense_Mutation_p.E195*|SYTL2_ENST00000389958.3_Nonsense_Mutation_p.E224*	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	793	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.E1131*(1)|p.E794*(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		ATGTGCACTTCTCCAGTTGTA	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											90	84	86					11																	85409098		2203	4299	6502	85086746	SO:0001587	stop_gained	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.2377G>T	11.37:g.85409098C>A	ENSP00000431701:p.Glu793*		85086746	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Nonsense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	39	7.537714	0.98345	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.3912	19.8241	0.96610	0.0:1.0:0.0:0.0	.	.	.	.	X	769;1639;1131;794;235;1115;235;224;510;793;195;761;769	.	.	E	-	1	0	SYTL2	85086746	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.350000	0.79385	2.758000	0.94735	0.655000	0.94253	GAA		0.398	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		A	85409098	C	A	85409098	4	1	61	1	0	0	0	0	0	1	0	0	15522	922	32	2	439	2	SYTL2	11	85409098	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1767612	85409098	49597418	7551	15536										
SYTL2	54843	broad.mit.edu	37	chr11	85437122	85437122	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaacaatcccttccgtattCttttccacattttcctttga	3	12	1	1	rs574962856		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85437122C>A	ENST00000528231.1	-	7	1737				SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000354566.3_Missense_Mutation_p.K126N|SYTL2_ENST00000359152.5_Missense_Mutation_p.K650N|SYTL2_ENST00000525423.1_Missense_Mutation_p.K126N|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000389960.4_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.K126N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTTCCGTATTCTTTTCCACAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											161	158	159					11																	85437122		2203	4299	6502	85114770	SO:0001627	intron_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+1816G>T	11.37:g.85437122C>A			85114770	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	9.494	1.101434	0.20632	.	.	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.34072	1.4;1.38;1.39	5.32	1.79	0.24919	.	0.374949	0.23007	N	0.053005	T	0.21841	0.0526	L	0.32530	0.975	0.09310	N	1	B;B;B	0.24368	0.102;0.102;0.047	B;B;B	0.25759	0.063;0.063;0.032	T	0.15780	-1.0425	9	.	.	.	-3.8828	4.0897	0.09963	0.0:0.3835:0.1902:0.4263	.	126;126;126	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	N	650;126;126	ENSP00000352065:K650N;ENSP00000346576:K126N;ENSP00000432694:K126N	.	K	-	3	2	SYTL2	85114770	0.837000	0.29446	0.684000	0.30055	0.100000	0.18952	-0.039000	0.12124	0.166000	0.19597	0.655000	0.94253	AAG		0.358	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		A	85437122	C	A	85437122	1	1	61	0	1	0	0	0	0	0	0	0	15522	912	32	2		2	SYTL2	11	85437122	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28024	85437122	49569394	7552	15537										
SYTL2	54843	broad.mit.edu	37	chr11	85459427	85459427	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccattggccactcatattCttcagctgctggtcatcctt	6	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85459427C>A	ENST00000528231.1	-	2	418	c.141G>T	c.(139-141)aaG>aaT	p.K47N	SYTL2_ENST00000527523.1_5'UTR|SYTL2_ENST00000524452.1_Missense_Mutation_p.K47N|SYTL2_ENST00000316356.4_Missense_Mutation_p.K47N|SYTL2_ENST00000389960.4_Missense_Mutation_p.K47N	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	47	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.K47N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTCATATTCTTCAGCTGCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											148	137	141					11																	85459427		2203	4299	6502	85137075	SO:0001583	missense	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.141G>T	11.37:g.85459427C>A	ENSP00000431701:p.Lys47Asn		85137075	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.260422	0.80246	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000524452	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.05	4.12	0.48240	Rab-binding domain (1);	.	.	.	.	D	0.84392	0.5462	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.982;0.94;0.973	D	0.83633	0.0146	8	.	.	.	.	10.3881	0.44152	0.0:0.9067:0.0:0.0933	.	47;47;47	Q9HCH5-6;Q9HCH5;Q9HCH5-13	.;SYTL2_HUMAN;.	N	47	ENSP00000374610:K47N;ENSP00000318803:K47N;ENSP00000431701:K47N;ENSP00000435238:K47N	.	K	-	3	2	SYTL2	85137075	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.407000	0.44565	2.513000	0.84729	0.655000	0.94253	AAG		0.393	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		A	85459427	C	A	85459427	3	1	61	1	0	0	0	0	1	0	0	0	15522	912	32	2	5215	2	SYTL2	11	85459427	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22305	85459427	49547089	7553	15538										
SYTL2	54843	broad.mit.edu	37	chr11	85468684	85468684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgactctctcttcttCggccctcttcagagcagcat	6	15	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85468684C>T	ENST00000528231.1	-	1	362	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K	SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Missense_Mutation_p.E29K|SYTL2_ENST00000316356.4_Missense_Mutation_p.E29K|SYTL2_ENST00000389960.4_Missense_Mutation_p.E29K	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	29	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.E29K(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTCTCTTCTTCGGCCCTCTTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											235	239	238					11																	85468684		2203	4299	6502	85146332	SO:0001583	missense	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.85G>A	11.37:g.85468684C>T	ENSP00000431701:p.Glu29Lys		85146332	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479921	0.96307	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000524452	D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98	5.6	5.6	0.85130	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	D	0.90604	0.7054	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.79784	0.99;0.878;0.993	D	0.89426	0.3713	8	.	.	.	.	18.3897	0.90478	0.0:1.0:0.0:0.0	.	29;29;29	Q9HCH5-6;Q9HCH5;Q9HCH5-13	.;SYTL2_HUMAN;.	K	29	ENSP00000374610:E29K;ENSP00000318803:E29K;ENSP00000431701:E29K;ENSP00000435238:E29K	.	E	-	1	0	SYTL2	85146332	1.000000	0.71417	0.957000	0.39632	0.985000	0.73830	6.404000	0.73268	2.626000	0.88956	0.650000	0.86243	GAA		0.478	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85468684	C	T	85468684	3	4	61	1	0	0	0	0	1	0	0	0	15522	893	31	1	5275	1	SYTL2	11	85468684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9257	85468684	49537832	7554	15539										
CCDC83	220047	broad.mit.edu	37	chr11	85606366	85606366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcactctggaagatactaGaaagaaaataatcaaggaaa	7	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85606366G>T	ENST00000342404.3	+	6	758	c.542G>T	c.(541-543)aGa>aTa	p.R181I	CCDC83_ENST00000529676.2_3'UTR|CCDC83_ENST00000376067.1_Missense_Mutation_p.R82I|CCDC83_ENST00000280245.4_Missense_Mutation_p.R181I			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	181								p.R181I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GAAGATACTAGAAAGAAAATA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	11											41	46	44					11																	85606366		2202	4292	6494	85284014	SO:0001583	missense	220047			AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.542G>T	11.37:g.85606366G>T	ENSP00000344512:p.Arg181Ile		85284014	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Missense_Mutation	SNP	ENST00000342404.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.648|6.648	0.488028|0.488028	0.12641|0.12641	.|.	.|.	ENSG00000150676|ENSG00000150676	ENST00000526729|ENST00000280245;ENST00000376067;ENST00000342404	.|T;T;T	.|0.42900	.|0.96;0.96;0.96	4.65|4.65	0.199|0.199	0.15175|0.15175	.|.	.|0.235291	.|0.35936	.|N	.|0.002886	.|T	.|0.44286	.|0.1286	L|L	0.55481|0.55481	1.735|1.735	0.26230|0.26230	N|N	0.979027|0.979027	.|D;B;P	.|0.59767	.|0.986;0.225;0.454	.|P;B;B	.|0.58454	.|0.839;0.048;0.082	.|T	.|0.21930	.|-1.0231	.|9	.|.	.|.	.|.	-11.4535|-11.4535	3.2357|3.2357	0.06763|0.06763	0.3705:0.0:0.4491:0.1804|0.3705:0.0:0.4491:0.1804	.|.	.|82;181;181	.|Q8IWF9-3;Q8IWF9;Q8IWF9-2	.|.;CCD83_HUMAN;.	X|I	87|181;82;181	.|ENSP00000280245:R181I;ENSP00000365235:R82I;ENSP00000344512:R181I	.|.	E|R	+|+	1|2	0|0	CCDC83|CCDC83	85284014|85284014	0.967000|0.967000	0.33354|0.33354	0.560000|0.560000	0.28344|0.28344	0.148000|0.148000	0.21650|0.21650	0.487000|0.487000	0.22356|0.22356	0.463000|0.463000	0.27118|0.27118	0.563000|0.563000	0.77884|0.77884	GAA|AGA		0.274	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		T	85606366	G	T	85606366	3	4	61	1	0	0	0	0	1	0	0	0	2863	942	33	2	560	2	CCDC83	11	85606366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137682	85606366	49400150	7555	15540										
CCDC83	220047	broad.mit.edu	37	chr11	85622351	85622351	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacaggaaggaagttgaaGaattaaaaaatgctattcat	8	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85622351G>T	ENST00000342404.3	+	8	916	c.700G>T	c.(700-702)Gaa>Taa	p.E234*	CCDC83_ENST00000529676.2_3'UTR|CCDC83_ENST00000376067.1_Nonsense_Mutation_p.E135*|CCDC83_ENST00000280245.4_Nonsense_Mutation_p.E234*			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	234								p.E234*(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGAAGTTGAAGAATTAAAAAA	0.333																																																2	Substitution - Nonsense(2)	large_intestine(2)	11											100	110	107					11																	85622351		2203	4299	6502	85299999	SO:0001587	stop_gained	220047			AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.700G>T	11.37:g.85622351G>T	ENSP00000344512:p.Glu234*		85299999	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Nonsense_Mutation	SNP	ENST00000342404.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.456155|6.456155	0.97581|0.97581	.|.	.|.	ENSG00000150676|ENSG00000150676	ENST00000280245;ENST00000376067;ENST00000342404|ENST00000526729	.|.	.|.	.|.	5.08|5.08	2.2|2.2	0.27929|0.27929	.|.	0.453670|.	0.22269|.	N|.	0.062282|.	.|T	.|0.42177	.|0.1191	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.48603	.|-0.9021	.|3	.|.	.|.	.|.	-0.4613|-0.4613	7.0839|7.0839	0.25247|0.25247	0.2838:0.0:0.7162:0.0|0.2838:0.0:0.7162:0.0	.|.	.|.	.|.	.|.	X|N	234;135;234|139	.|.	.|.	E|K	+|+	1|3	0|2	CCDC83|CCDC83	85299999|85299999	0.129000|0.129000	0.22400|0.22400	0.536000|0.536000	0.28039|0.28039	0.283000|0.283000	0.27025|0.27025	-0.609000|-0.609000	0.05635|0.05635	0.192000|0.192000	0.20272|0.20272	0.313000|0.313000	0.20887|0.20887	GAA|AAG		0.333	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		T	85622351	G	T	85622351	4	4	61	1	0	0	0	0	0	1	0	0	2863	943	33	2	726	2	CCDC83	11	85622351	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15985	85622351	49384165	7556	15541										
CCDC83	220047	broad.mit.edu	37	chr11	85627112	85627112	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagaagtagaaagtagaGacttgatgtcctcatcagat	9	8	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:85627112G>A	ENST00000342404.3	+	10	1132	c.916G>A	c.(916-918)Gac>Aac	p.D306N	RP11-90K17.2_ENST00000531414.1_RNA|CCDC83_ENST00000376067.1_Missense_Mutation_p.D206N|CCDC83_ENST00000280245.4_Missense_Mutation_p.D337N			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	306								p.D337N(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AGAAAGTAGAGACTTGATGTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											116	117	116					11																	85627112		2203	4299	6502	85304760	SO:0001583	missense	220047			AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.916G>A	11.37:g.85627112G>A	ENSP00000344512:p.Asp306Asn		85304760	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Missense_Mutation	SNP	ENST00000342404.3	37		.	.	.	.	.	.	.	.	.	.	G	8.358	0.832543	0.16820	.	.	ENSG00000150676	ENST00000280245;ENST00000376067;ENST00000342404	T;T;T	0.42131	0.98;0.98;0.98	4.87	-0.91	0.10511	.	0.840949	0.10708	N	0.643167	T	0.29620	0.0739	L	0.46157	1.445	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.10450	0.004;0.005;0.005	T	0.25152	-1.0140	9	.	.	.	-1.4926	4.3272	0.11046	0.2958:0.3162:0.388:0.0	.	206;306;337	Q8IWF9-3;Q8IWF9;Q8IWF9-2	.;CCD83_HUMAN;.	N	337;206;306	ENSP00000280245:D337N;ENSP00000365235:D206N;ENSP00000344512:D306N	.	D	+	1	0	CCDC83	85304760	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.235000	0.09016	0.027000	0.15297	-0.216000	0.12614	GAC		0.323	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		A	85627112	G	A	85627112	3	1	61	1	0	0	0	0	1	0	0	0	2863	942	33	3	1047	3	CCDC83	11	85627112	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4761	85627112	49379404	7557	15542										
CCDC81	60494	broad.mit.edu	37	chr11	86111738	86111738	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatatctcatcacccaaaaGacttcgagatagacaagctt	6	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:86111738G>T	ENST00000445632.2	+	7	1048	c.776G>T	c.(775-777)aGa>aTa	p.R259I	CCDC81_ENST00000528728.1_Missense_Mutation_p.R42I|CCDC81_ENST00000278487.3_Missense_Mutation_p.R42I|CCDC81_ENST00000354755.1_Missense_Mutation_p.R169I	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	259								p.R169I(2)		kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				TCACCCAAAAGACTTCGAGAT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	11											127	130	129					11																	86111738		2202	4299	6501	85789386	SO:0001583	missense	60494			AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.776G>T	11.37:g.86111738G>T	ENSP00000415528:p.Arg259Ile		85789386	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331174	0.24167	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.63	-5.64	0.02466	.	0.626680	0.15431	N	0.262736	T	0.19805	0.0476	L	0.43152	1.355	0.20926	N	0.99983	P;P;B	0.42961	0.617;0.795;0.002	B;B;B	0.39805	0.105;0.31;0.007	T	0.08289	-1.0729	9	.	.	.	0.0039	1.9419	0.03348	0.3826:0.0904:0.333:0.194	.	42;259;169	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	I	169;42;259;42	ENSP00000346800:R169I;ENSP00000278487:R42I;ENSP00000415528:R259I;ENSP00000437165:R42I	.	R	+	2	0	CCDC81	85789386	0.000000	0.05858	0.003000	0.11579	0.139000	0.21198	-1.163000	0.03138	-0.957000	0.03627	0.655000	0.94253	AGA		0.398	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		T	86111738	G	T	86111738	3	4	61	1	0	0	0	0	1	0	0	0	2861	942	33	2	802	2	CCDC81	11	86111738	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	484626	86111738	48894778	7558	15543										
FZD4	8322	broad.mit.edu	37	chr11	86663064	86663064	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggtaggaaaacctagaaGaatcgatcaggaaggtcagt	13	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:86663064G>T	ENST00000531380.1	-	2	1039	c.734C>A	c.(733-735)tCt>tAt	p.S245Y	PRSS23_ENST00000533902.2_3'UTR	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	245					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S245Y(1)		breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAACCTAGAAGAATCGATCAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	60	61					11																	86663064		2201	4299	6500	86340712	SO:0001583	missense	8322			AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.734C>A	11.37:g.86663064G>T	ENSP00000434034:p.Ser245Tyr		86340712	A8K9Q3|Q14C97|Q6S9E4	Missense_Mutation	SNP	ENST00000531380.1	37	CCDS8279.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.270816	0.59540	.	.	ENSG00000174804	ENST00000531380	T	0.48836	0.8	5.69	5.69	0.88448	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	L	0.54323	1.7	0.80722	D	1	P	0.52463	0.953	P	0.59761	0.863	T	0.57590	-0.7785	9	.	.	.	.	19.8211	0.96595	0.0:0.0:1.0:0.0	.	245	Q9ULV1	FZD4_HUMAN	Y	245	ENSP00000434034:S245Y	.	S	-	2	0	FZD4	86340712	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	8.062000	0.89475	2.687000	0.91594	0.655000	0.94253	TCT		0.478	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		T	86663064	G	T	86663064	3	4	61	1	0	0	0	0	1	0	0	0	6151	942	33	2	883	2	FZD4	11	86663064	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	551326	86663064	48343452	7559	15544										
TMEM135	65084	broad.mit.edu	37	chr11	86782644	86782644	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttatgtggccattctcattGaaagaaaaagcaggtaaaat	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:86782644G>T	ENST00000305494.5	+	3	388	c.349G>T	c.(349-351)Gaa>Taa	p.E117*	TMEM135_ENST00000340353.7_Nonsense_Mutation_p.E117*|TMEM135_ENST00000355734.4_Nonsense_Mutation_p.E117*|TMEM135_ENST00000535167.1_5'UTR|TMEM135_ENST00000532959.1_Intron	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	117					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)		p.E117*(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CATTCTCATTGAAAGAAAAAG	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											56	59	58					11																	86782644		2199	4299	6498	86460292	SO:0001587	stop_gained	65084			BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.349G>T	11.37:g.86782644G>T	ENSP00000306344:p.Glu117*		86460292	Q6AW91|Q8ND01|Q9H6M3	Nonsense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	G	39	7.746110	0.98465	.	.	ENSG00000166575	ENST00000340353;ENST00000525018;ENST00000355734;ENST00000305494	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.5349	18.035	0.89298	0.0:0.0:1.0:0.0	.	.	.	.	X	117	.	.	E	+	1	0	TMEM135	86460292	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.846000	0.92159	2.509000	0.84616	0.655000	0.94253	GAA		0.348	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		T	86782644	G	T	86782644	4	4	61	1	0	0	0	0	0	1	0	0	16090	1291	45	2	359	2	TMEM135	11	86782644	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119580	86782644	48223872	7560	15545										
CTSC	1075	broad.mit.edu	37	chr11	88045581	88045581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaattcttaaggtgtgCtatgttgacatacacattct	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:88045581C>T	ENST00000227266.5	-	3	574	c.460G>A	c.(460-462)Gca>Aca	p.A154T		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	154					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)	p.A154T(1)		large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTAAGGTGTGCTATGTTGACA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											159	155	157					11																	88045581		2201	4299	6500	87685229	SO:0001583	missense	1075			AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"Cathepsins"	2528	protein-coding gene	gene with protein product	"dipeptidyl peptidase 1"	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.460G>A	11.37:g.88045581C>T	ENSP00000227266:p.Ala154Thr		87685229	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	37	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	C	7.577	0.667917	0.14710	.	.	ENSG00000109861	ENST00000393302;ENST00000227266	T	0.69926	-0.44	5.75	1.7	0.24286	.	0.966433	0.08595	N	0.922410	T	0.60366	0.2263	M	0.68317	2.08	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48352	-0.9043	9	.	.	.	.	4.9518	0.14019	0.0:0.4666:0.2451:0.2883	.	154	P53634	CATC_HUMAN	T	137;154	ENSP00000227266:A154T	.	A	-	1	0	CTSC	87685229	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.138000	0.16016	0.372000	0.24591	0.655000	0.94253	GCA		0.408	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		T	88045581	C	T	88045581	3	4	61	1	0	0	0	0	1	0	0	0	4037	797	28	3	951	3	CTSC	11	88045581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1262937	88045581	46960935	7561	15546										
GRM5	2915	broad.mit.edu	37	chr11	88337993	88337993	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccgtccatcaattggcttCatggcatcacagagtcctgc	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:88337993C>A	ENST00000305447.4	-	4	1436	c.1287G>T	c.(1285-1287)atG>atT	p.M429I	GRM5_ENST00000455756.2_Missense_Mutation_p.M429I|GRM5_ENST00000305432.5_Missense_Mutation_p.M429I|GRM5_ENST00000393297.1_Missense_Mutation_p.M429I|GRM5_ENST00000418177.2_Missense_Mutation_p.M429I	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	429					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.M429I(1)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	CAATTGGCTTCATGGCATCAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											82	75	77					11																	88337993		2201	4299	6500	87977641	SO:0001583	missense	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1287G>T	11.37:g.88337993C>A	ENSP00000306138:p.Met429Ile		87977641	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	C	32	5.135751	0.94517	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.77	5.77	0.91146	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90823	0.7118	M	0.71581	2.175	0.80722	D	1	D;D	0.57257	0.979;0.965	D;D	0.74674	0.98;0.984	D	0.89486	0.3753	9	.	.	.	.	19.984	0.97341	0.0:1.0:0.0:0.0	.	429;429	P41594-2;P41594	.;GRM5_HUMAN	I	429	ENSP00000402912:M429I;ENSP00000405690:M429I;ENSP00000305905:M429I;ENSP00000306138:M429I;ENSP00000376975:M429I	.	M	-	3	0	GRM5	87977641	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.818000	0.86416	2.734000	0.93682	0.446000	0.29264	ATG		0.473	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88337993	C	A	88337993	3	1	61	1	0	0	0	0	1	0	0	0	6821	826	29	2	2375	2	GRM5	11	88337993	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	292412	88337993	46668523	7562	15547										
NOX4	50507	broad.mit.edu	37	chr11	89135607	89135607	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaggttcatgaaaatgttCtgagaaatactctggtaagg	11	4	3	2	rs201436866		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:89135607C>A	ENST00000263317.4	-	9	971	c.733G>T	c.(733-735)Gaa>Taa	p.E245*	NOX4_ENST00000525196.1_Intron|NOX4_ENST00000534731.1_Nonsense_Mutation_p.E245*|NOX4_ENST00000528341.1_Nonsense_Mutation_p.E220*|NOX4_ENST00000413594.2_Nonsense_Mutation_p.E266*|NOX4_ENST00000532825.1_Nonsense_Mutation_p.E221*|NOX4_ENST00000424319.1_Nonsense_Mutation_p.E221*|NOX4_ENST00000527956.1_Nonsense_Mutation_p.E221*|NOX4_ENST00000542487.1_Nonsense_Mutation_p.E221*|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000535633.1_Nonsense_Mutation_p.E221*|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000527626.1_Nonsense_Mutation_p.E79*|NOX4_ENST00000343727.5_Nonsense_Mutation_p.E221*			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	245	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.E245*(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TGAAAATGTTCTGAGAAATAC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											94	104	101					11																	89135607		2201	4298	6499	88775255	SO:0001587	stop_gained	50507			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.733G>T	11.37:g.89135607C>A	ENSP00000263317:p.Glu245*		88775255	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Nonsense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	37	5.985175	0.97173	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594	.	.	.	4.76	1.53	0.23141	.	0.997777	0.08115	N	0.995556	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.4074	6.9078	0.24319	0.0:0.5756:0.2708:0.1535	.	.	.	.	X	221;221;221;245;245;221;221;221;79;220;266	.	.	E	-	1	0	NOX4	88775255	0.388000	0.25197	0.934000	0.37439	0.914000	0.54420	1.424000	0.34848	0.512000	0.28257	0.467000	0.42956	GAA		0.428	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		A	89135607	C	A	89135607	4	1	61	1	0	0	0	0	0	1	0	0	10589	922	32	2	1043	2	NOX4	11	89135607	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	797614	89135607	45870909	7563	15548										
NOX4	50507	broad.mit.edu	37	chr11	89173876	89173876	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttgtgaagagaagttttCtaggatcctgagaaaaagaa	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:89173876C>A	ENST00000263317.4	-	6	693	c.455G>T	c.(454-456)aGa>aTa	p.R152I	NOX4_ENST00000525196.1_Missense_Mutation_p.R152I|NOX4_ENST00000534731.1_Missense_Mutation_p.R152I|NOX4_ENST00000528341.1_Missense_Mutation_p.R127I|NOX4_ENST00000413594.2_Missense_Mutation_p.R173I|NOX4_ENST00000532825.1_Missense_Mutation_p.R128I|NOX4_ENST00000424319.1_Missense_Mutation_p.R128I|NOX4_ENST00000527956.1_Missense_Mutation_p.R128I|NOX4_ENST00000542487.1_Missense_Mutation_p.R128I|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000535633.1_Missense_Mutation_p.R128I|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000527626.1_Intron|NOX4_ENST00000343727.5_Missense_Mutation_p.R128I			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	152	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.R152I(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAGAAGTTTTCTAGGATCCTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											38	38	38					11																	89173876		2201	4298	6499	88813524	SO:0001583	missense	50507			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.455G>T	11.37:g.89173876C>A	ENSP00000263317:p.Arg152Ile		88813524	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016493	0.54468	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.95377	-3.62;-3.62;-3.62;-3.6;-3.62;-3.55;-3.69;-3.62;-3.62;-3.58;-3.66	5.92	5.92	0.95590	Flavoprotein transmembrane component (1);	0.231983	0.40728	N	0.001029	D	0.95082	0.8407	N	0.17474	0.49	0.80722	D	1	B;P;D;B;P	0.67145	0.198;0.8;0.996;0.009;0.623	B;P;D;B;B	0.75020	0.326;0.474;0.985;0.007;0.268	D	0.94168	0.7420	9	.	.	.	-18.5498	17.2374	0.87002	0.0:1.0:0.0:0.0	.	128;127;152;152;152	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	I	128;128;128;152;152;152;128;128;128;127;173	ENSP00000412446:R128I;ENSP00000440172:R128I;ENSP00000344747:R128I;ENSP00000436892:R152I;ENSP00000436716:R152I;ENSP00000263317:R152I;ENSP00000434924:R128I;ENSP00000433797:R128I;ENSP00000439373:R128I;ENSP00000436970:R127I;ENSP00000405705:R173I	.	R	-	2	0	NOX4	88813524	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.991000	0.49409	2.809000	0.96659	0.655000	0.94253	AGA		0.333	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		A	89173876	C	A	89173876	3	1	61	1	0	0	0	0	1	0	0	0	10589	913	32	2	1333	2	NOX4	11	89173876	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38269	89173876	45832640	7564	15549										
TRIM49	57093	broad.mit.edu	37	chr11	89537438	89537438	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcttcttcaaatgaatgTtggttttgaggtttatctgc	8	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:89537438T>C	ENST00000329758.1	-	3	528	c.200A>G	c.(199-201)aAc>aGc	p.N67S	TRIM49_ENST00000532501.2_Missense_Mutation_p.N67S	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	67						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.N67S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CAAATGAATGTTGGTTTTGAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											91	83	86					11																	89537438		2191	4296	6487	89177086	SO:0001583	missense	57093			AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13431	protein-coding gene	gene with protein product		606124	"ring finger protein 18", "tripartite motif-containing 49"	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.200A>G	11.37:g.89537438T>C	ENSP00000327604:p.Asn67Ser		89177086	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000329758.1	37	CCDS8287.1	.	.	.	.	.	.	.	.	.	.	T	9.641	1.138980	0.21123	.	.	ENSG00000168930	ENST00000329758;ENST00000532501	D	0.84146	-1.81	0.821	-0.817	0.10836	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	T	0.64103	0.2568	N	0.08118	0	0.09310	N	1	P	0.36577	0.558	B	0.35899	0.213	T	0.56092	-0.8036	8	.	.	.	.	2.7916	0.05390	0.415:0.0:0.0:0.585	.	67	P0CI25	TRI49_HUMAN	S	67	ENSP00000327604:N67S	.	N	-	2	0	TRIM49	89177086	0.010000	0.17322	0.000000	0.03702	0.005000	0.04900	1.001000	0.29783	-0.241000	0.09681	0.163000	0.16589	AAC		0.458	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358		C	89537438	T	C	89537438	3	2	61	1	0	0	0	0	1	0	0	0	16564	1725	60	4	1182	4	TRIM49	11	89537438	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	363562	89537438	45469078	7565	15550										
FAT3	120114	broad.mit.edu	37	chr11	92085332	92085332	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcctcctgcttgttgcctCatcctcctgcttttcaagct	7	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92085332C>A	ENST00000298047.6	+	1	71	c.54C>A	c.(52-54)ctC>ctA	p.L18L	FAT3_ENST00000525166.1_5'Flank|FAT3_ENST00000409404.2_Silent_p.L18L|FAT3_ENST00000541502.1_Silent_p.L18L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	18					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L18L(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CTTGTTGCCTCATCCTCCTGC	0.507										TCGA Ovarian(4;0.039)																																						2	Substitution - coding silent(2)	large_intestine(2)	11											50	52	51					11																	92085332		1960	4140	6100	91724980	SO:0001819	synonymous_variant	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.54C>A	11.37:g.92085332C>A			91724980	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.507	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92085332	C	A	92085332	2	1	61	1	0	0	0	0	0	0	0	1	5710	813	29	2		2	FAT3	11	92085332	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2547894	92085332	42921184	7566	15551										
FAT3	120114	broad.mit.edu	37	chr11	92086402	92086402	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagacactgtccccattaGatttgaaaaagaagtgtacg	9	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92086402G>T	ENST00000298047.6	+	1	1141	c.1124G>T	c.(1123-1125)aGa>aTa	p.R375I	FAT3_ENST00000525166.1_Missense_Mutation_p.R225I|FAT3_ENST00000409404.2_Missense_Mutation_p.R375I|FAT3_ENST00000541502.1_Missense_Mutation_p.R375I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	375	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R375I(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GTCCCCATTAGATTTGAAAAA	0.413										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											82	78	79					11																	92086402		1893	4129	6022	91726050	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1124G>T	11.37:g.92086402G>T	ENSP00000298047:p.Arg375Ile		91726050	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	9.667	1.145751	0.21288	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	4.9	-1.87	0.07737	.	.	.	.	.	T	0.39886	0.1095	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.30880	-0.9963	9	0.52906	T	0.07	.	10.7402	0.46149	0.7067:0.0:0.2933:0.0	.	375	Q8TDW7-3	.	I	375;375;375;225	ENSP00000298047:R375I;ENSP00000387040:R375I;ENSP00000443786:R375I;ENSP00000432586:R225I	ENSP00000298047:R375I	R	+	2	0	FAT3	91726050	0.000000	0.05858	0.081000	0.20488	0.961000	0.63080	-0.227000	0.09126	-0.318000	0.08665	0.655000	0.94253	AGA		0.413	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92086402	G	T	92086402	3	4	61	1	0	0	0	0	1	0	0	0	5710	942	33	2	1126	2	FAT3	11	92086402	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1070	92086402	42920114	7567	15552										
FAT3	120114	broad.mit.edu	37	chr11	92086977	92086977	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaggtcaatgtgactattCgaataggaaatgtcaacgac	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92086977C>T	ENST00000298047.6	+	1	1716	c.1699C>T	c.(1699-1701)Cga>Tga	p.R567*	FAT3_ENST00000525166.1_Nonsense_Mutation_p.R417*|FAT3_ENST00000409404.2_Nonsense_Mutation_p.R567*|FAT3_ENST00000541502.1_Nonsense_Mutation_p.R567*			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	567	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R567*(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGTGACTATTCGAATAGGAAA	0.438										TCGA Ovarian(4;0.039)																																						2	Substitution - Nonsense(2)	large_intestine(2)	11											80	81	81					11																	92086977		1870	4110	5980	91726625	SO:0001587	stop_gained	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1699C>T	11.37:g.92086977C>T	ENSP00000298047:p.Arg567*		91726625	B5MDB0|Q96AU6	Nonsense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	38	6.764816	0.97821	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	.	.	.	5.82	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	5.4691	0.16660	0.1745:0.6751:0.0:0.1504	.	.	.	.	X	567;567;567;417	.	ENSP00000298047:R567X	R	+	1	2	FAT3	91726625	0.044000	0.20184	0.292000	0.24919	0.993000	0.82548	2.385000	0.44371	1.450000	0.47717	0.591000	0.81541	CGA		0.438	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92086977	C	T	92086977	4	4	61	1	0	0	0	0	0	1	0	0	5710	876	31	1	1701	1	FAT3	11	92086977	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	575	92086977	42919539	7568	15553										
FAT3	120114	broad.mit.edu	37	chr11	92087131	92087131	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtacaaaatcatttctgGaaatgaacttggcttctttt	6	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92087131G>A	ENST00000298047.6	+	1	1870	c.1853G>A	c.(1852-1854)gGa>gAa	p.G618E	FAT3_ENST00000525166.1_Missense_Mutation_p.G468E|FAT3_ENST00000409404.2_Missense_Mutation_p.G618E|FAT3_ENST00000541502.1_Missense_Mutation_p.G618E			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	618	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G618E(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATCATTTCTGGAAATGAACTT	0.363										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											38	39	38					11																	92087131		1842	4085	5927	91726779	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1853G>A	11.37:g.92087131G>A	ENSP00000298047:p.Gly618Glu		91726779	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	19.14	3.769402	0.69992	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.74	5.74	0.90152	.	.	.	.	.	T	0.69151	0.3079	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70479	-0.4860	9	0.51188	T	0.08	.	18.8971	0.92427	0.0:0.0:1.0:0.0	.	618	Q8TDW7-3	.	E	618;618;618;468	ENSP00000298047:G618E;ENSP00000387040:G618E;ENSP00000443786:G618E;ENSP00000432586:G468E	ENSP00000298047:G618E	G	+	2	0	FAT3	91726779	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.787000	0.99055	2.709000	0.92574	0.591000	0.81541	GGA		0.363	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92087131	G	A	92087131	3	1	61	1	0	0	0	0	1	0	0	0	5710	1174	41	3	1855	3	FAT3	11	92087131	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154	92087131	42919385	7569	15554										
FAT3	120114	broad.mit.edu	37	chr11	92498146	92498146	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctataccattgaccttCgatgagccgttttataactt	5	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92498146C>T	ENST00000298047.6	+	5	4103	c.4086C>T	c.(4084-4086)ttC>ttT	p.F1362F	FAT3_ENST00000525166.1_Silent_p.F1212F|FAT3_ENST00000409404.2_Silent_p.F1362F|RP11-203F8.1_ENST00000529884.1_RNA			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1362					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F1362F(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CATTGACCTTCGATGAGCCGT	0.498										TCGA Ovarian(4;0.039)																																						2	Substitution - coding silent(2)	large_intestine(2)	11											127	122	124					11																	92498146		1893	4104	5997	92137794	SO:0001819	synonymous_variant	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4086C>T	11.37:g.92498146C>T			92137794	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92498146	C	T	92498146	2	4	61	1	0	0	0	0	0	0	0	1	5710	883	31	1		1	FAT3	11	92498146	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	411015	92498146	42508370	7570	15555										
FAT3	120114	broad.mit.edu	37	chr11	92507291	92507291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggatgcagagcagaggtCcatctataatatgagtgtgg	13	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92507291C>T	ENST00000298047.6	+	6	4297	c.4280C>T	c.(4279-4281)tCc>tTc	p.S1427F	FAT3_ENST00000525166.1_Missense_Mutation_p.S1277F|FAT3_ENST00000409404.2_Missense_Mutation_p.S1427F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1427	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S1427F(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GAGCAGAGGTCCATCTATAAT	0.443										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											93	92	93					11																	92507291		1911	4118	6029	92146939	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4280C>T	11.37:g.92507291C>T	ENSP00000298047:p.Ser1427Phe		92146939	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	27.3	4.823041	0.90873	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.03181	4.02;4.02;4.02	5.59	5.59	0.84812	.	.	.	.	.	T	0.27663	0.0680	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.18272	-1.0342	9	0.87932	D	0	.	19.5708	0.95413	0.0:1.0:0.0:0.0	.	1427	Q8TDW7-3	.	F	1427;1427;1277	ENSP00000298047:S1427F;ENSP00000387040:S1427F;ENSP00000432586:S1277F	ENSP00000298047:S1427F	S	+	2	0	FAT3	92146939	1.000000	0.71417	0.956000	0.39512	0.972000	0.66771	5.614000	0.67695	2.625000	0.88918	0.650000	0.86243	TCC		0.443	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92507291	C	T	92507291	3	4	61	1	0	0	0	0	1	0	0	0	5710	855	30	3	4302	3	FAT3	11	92507291	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9145	92507291	42499225	7571	15556										
FAT3	120114	broad.mit.edu	37	chr11	92531061	92531061	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcatcaccatttgcaaaGaaccagacatgacgacgatg	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92531061G>T	ENST00000298047.6	+	9	4899	c.4882G>T	c.(4882-4884)Gaa>Taa	p.E1628*	FAT3_ENST00000525166.1_Nonsense_Mutation_p.E1478*|FAT3_ENST00000409404.2_Nonsense_Mutation_p.E1628*			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1628	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1628*(2)|p.E1628K(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CATTTGCAAAGAACCAGACAT	0.458										TCGA Ovarian(4;0.039)																																						3	Substitution - Nonsense(2)|Substitution - Missense(1)	large_intestine(2)|NS(1)	11											125	121	122					11																	92531061		2002	4164	6166	92170709	SO:0001587	stop_gained	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4882G>T	11.37:g.92531061G>T	ENSP00000298047:p.Glu1628*		92170709	B5MDB0|Q96AU6	Nonsense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	45	11.541347	0.99574	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	20.0805	0.97772	0.0:0.0:1.0:0.0	.	.	.	.	X	1628;1628;1478	.	ENSP00000298047:E1628X	E	+	1	0	FAT3	92170709	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	6.643000	0.74334	2.755000	0.94549	0.650000	0.86243	GAA		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92531061	G	T	92531061	4	4	61	1	0	0	0	0	0	1	0	0	5710	943	33	2	4916	2	FAT3	11	92531061	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23770	92531061	42475455	7572	15557										
FAT3	120114	broad.mit.edu	37	chr11	92532619	92532619	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaaggaagcattcaactCtgacttgtccaacattgagt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92532619C>T	ENST00000298047.6	+	9	6457	c.6440C>T	c.(6439-6441)tCt>tTt	p.S2147F	FAT3_ENST00000525166.1_Missense_Mutation_p.S1997F|FAT3_ENST00000409404.2_Missense_Mutation_p.S2147F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2147	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S2147F(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GCATTCAACTCTGACTTGTCC	0.433										TCGA Ovarian(4;0.039)																																						2	Substitution - Missense(2)	large_intestine(2)	11											42	42	42					11																	92532619		1915	4129	6044	92172267	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6440C>T	11.37:g.92532619C>T	ENSP00000298047:p.Ser2147Phe		92172267	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	11.43	1.637380	0.29157	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01838	4.61;4.61;4.61	5.78	5.78	0.91487	.	.	.	.	.	T	0.04497	0.0123	N	0.05554	-0.025	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	T	0.67711	-0.5600	9	0.11182	T	0.66	.	20.0124	0.97464	0.0:1.0:0.0:0.0	.	2147	Q8TDW7-3	.	F	2147;2147;1997	ENSP00000298047:S2147F;ENSP00000387040:S2147F;ENSP00000432586:S1997F	ENSP00000298047:S2147F	S	+	2	0	FAT3	92172267	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	7.755000	0.85180	2.749000	0.94314	0.655000	0.94253	TCT		0.433	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92532619	C	T	92532619	3	4	61	1	0	0	0	0	1	0	0	0	5710	913	32	3	6474	3	FAT3	11	92532619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1558	92532619	42473897	7573	15558										
FAT3	120114	broad.mit.edu	37	chr11	92623844	92623844	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccctcatgaagaggagttCttgagtcaggaccagctgcc	11	13	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92623844C>A	ENST00000298047.6	+	27	13352	c.13335C>A	c.(13333-13335)ttC>ttA	p.F4445L	FAT3_ENST00000525166.1_Missense_Mutation_p.F4295L|FAT3_ENST00000409404.2_Missense_Mutation_p.F4413L|FAT3_ENST00000533797.1_Missense_Mutation_p.F748L|FAT3_ENST00000489716.1_3'UTR			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4445	Pro-rich.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F4413L(1)|p.F1020L(1)|p.F4445L(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAGAGGAGTTCTTGAGTCAGG	0.592										TCGA Ovarian(4;0.039)																																						3	Substitution - Missense(3)	large_intestine(3)	11											42	48	46					11																	92623844		2034	4188	6222	92263492	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.13335C>A	11.37:g.92623844C>A	ENSP00000298047:p.Phe4445Leu		92263492	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	15.47	2.843796	0.51164	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.66	3.47	0.39725	.	.	.	.	.	T	0.57621	0.2066	M	0.78456	2.415	0.80722	D	1	P;B	0.42871	0.792;0.025	B;B	0.38264	0.269;0.017	T	0.60031	-0.7342	9	0.45353	T	0.12	.	6.4806	0.22061	0.0:0.6369:0.0:0.3631	.	4413;4445	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	L	4445;4413;4295;748	ENSP00000298047:F4445L;ENSP00000387040:F4413L;ENSP00000432586:F4295L;ENSP00000436399:F748L	ENSP00000298047:F4445L	F	+	3	2	FAT3	92263492	0.961000	0.32948	0.965000	0.40720	0.940000	0.58332	2.077000	0.41557	1.400000	0.46741	-0.136000	0.14681	TTC		0.592	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92623844	C	A	92623844	3	1	61	1	0	0	0	0	1	0	0	0	5710	912	32	2	13337	2	FAT3	11	92623844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91225	92623844	42382672	7574	15559										
SLC36A4	120103	broad.mit.edu	37	chr11	92881895	92881895	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catatattataatgttccttCgaaaatgtaagaatttcaac	4	6	1	1	rs142625181	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:92881895C>T	ENST00000326402.4	-	11	1453	c.1323G>A	c.(1321-1323)tcG>tcA	p.S441S	SLC36A4_ENST00000529184.1_Silent_p.S306S	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	441					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.S441S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AATGTTCCTTCGAAAATGTAA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	11											60	66	64					11																	92881895		2201	4298	6499	92521543	SO:0001819	synonymous_variant	120103			AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.1323G>A	11.37:g.92881895C>T			92521543	Q86X30|Q8IVM5|Q8N8S6	Silent	SNP	ENST00000326402.4	37	CCDS8291.1																																																																																				0.368	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2			T	92881895	C	T	92881895	2	4	61	1	0	0	0	0	0	0	0	1	14633	871	31	1		1	SLC36A4	11	92881895	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258051	92881895	42124621	7575	15560										
HEPHL1	341208	broad.mit.edu	37	chr11	93800715	93800715	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcctgatatgtgtgttggaGaatctgtgtcctggcaccta	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:93800715G>T	ENST00000315765.9	+	5	870	c.862G>T	c.(862-864)Gaa>Taa	p.E288*		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	288	Plastocyanin-like 2.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.E289*(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GTGTGTTGGAGAATCTGTGTC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											155	156	155					11																	93800715		1933	4118	6051	93440363	SO:0001587	stop_gained	341208			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.862G>T	11.37:g.93800715G>T	ENSP00000313699:p.Glu288*		93440363	Q3C1W7	Nonsense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	35	5.574583	0.96553	.	.	ENSG00000181333	ENST00000315765	.	.	.	5.36	5.36	0.76844	.	0.495174	0.23824	N	0.044202	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	13.2185	0.59873	0.0829:0.0:0.9171:0.0	.	.	.	.	X	288	.	ENSP00000313699:E288X	E	+	1	0	HEPHL1	93440363	0.943000	0.32029	0.993000	0.49108	0.940000	0.58332	2.003000	0.40844	2.670000	0.90874	0.561000	0.74099	GAA		0.483	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93800715	G	T	93800715	4	4	61	1	0	0	0	0	0	1	0	0	7076	943	33	2	880	2	HEPHL1	11	93800715	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	918820	93800715	41205801	7576	15561										
HEPHL1	341208	broad.mit.edu	37	chr11	93815698	93815698	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccttcagcattgacaaaGaagataaagagtttgtgaaa	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:93815698G>T	ENST00000315765.9	+	10	1839	c.1831G>T	c.(1831-1833)Gaa>Taa	p.E611*		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	611	Plastocyanin-like 4.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.E615*(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				CATTGACAAAGAAGATAAAGA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											64	58	60					11																	93815698		1831	4082	5913	93455346	SO:0001587	stop_gained	341208			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.1831G>T	11.37:g.93815698G>T	ENSP00000313699:p.Glu611*		93455346	Q3C1W7	Nonsense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	38	7.257642	0.98168	.	.	ENSG00000181333	ENST00000315765	.	.	.	5.59	4.69	0.59074	.	0.382752	0.27088	N	0.020984	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	11.2582	0.49067	0.1578:0.0:0.8422:0.0	.	.	.	.	X	611	.	ENSP00000313699:E611X	E	+	1	0	HEPHL1	93455346	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	5.153000	0.64888	1.370000	0.46153	0.655000	0.94253	GAA		0.373	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93815698	G	T	93815698	4	4	61	1	0	0	0	0	0	1	0	0	7076	943	33	2	1869	2	HEPHL1	11	93815698	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14983	93815698	41190818	7577	15562										
HEPHL1	341208	broad.mit.edu	37	chr11	93826685	93826685	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacatggagatatatttatGaaccgcactgaaaattggat	9	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:93826685G>A	ENST00000315765.9	+	13	2321	c.2313G>A	c.(2311-2313)atG>atA	p.M771I		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	771	Plastocyanin-like 5.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.M775I(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				ATATATTTATGAACCGCACTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											188	181	183					11																	93826685		1850	4100	5950	93466333	SO:0001583	missense	341208			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2313G>A	11.37:g.93826685G>A	ENSP00000313699:p.Met771Ile		93466333	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951293	0.53186	.	.	ENSG00000181333	ENST00000315765	D	0.98849	-5.18	5.35	5.35	0.76521	Cupredoxin (2);	0.162309	0.56097	D	0.000023	D	0.96534	0.8869	L	0.32530	0.975	0.40108	D	0.976458	B	0.12630	0.006	B	0.12837	0.008	D	0.94349	0.7577	10	0.49607	T	0.09	.	16.1601	0.81698	0.0:0.133:0.867:0.0	.	771	Q6MZM0	HPHL1_HUMAN	I	771	ENSP00000313699:M771I	ENSP00000313699:M771I	M	+	3	0	HEPHL1	93466333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.867000	0.39499	2.510000	0.84645	0.542000	0.68232	ATG		0.418	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		A	93826685	G	A	93826685	3	1	61	1	0	0	0	0	1	0	0	0	7076	1290	45	3	2363	3	HEPHL1	11	93826685	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10987	93826685	41179831	7578	15563										
HEPHL1	341208	broad.mit.edu	37	chr11	93844085	93844085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagatagataaatcttaccGagaagatgtgtatgatctct	9	6	2	5	rs554555752	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:93844085G>A	ENST00000315765.9	+	18	3070	c.3062G>A	c.(3061-3063)cGa>cAa	p.R1021Q		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1021	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.R1025Q(2)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				AAATCTTACCGAGAAGATGTG	0.403													G|||	2	0.000399361	0	0	5008	,	,		21305	0		0	False		,,,				2504	0.002															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	11											101	93	96					11																	93844085		1968	4159	6127	93483733	SO:0001583	missense	341208			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3062G>A	11.37:g.93844085G>A	ENSP00000313699:p.Arg1021Gln		93483733	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141572	0.94560	.	.	ENSG00000181333	ENST00000315765	D	0.99735	-6.58	5.97	5.03	0.67393	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.000000	0.85682	D	0.000000	D	0.99674	0.9878	M	0.85859	2.78	0.39215	D	0.963395	D	0.89917	1.0	D	0.79108	0.992	D	0.98294	1.0515	10	0.44086	T	0.13	-7.2308	16.6592	0.85237	0.0:0.0:0.8698:0.1302	.	1021	Q6MZM0	HPHL1_HUMAN	Q	1021	ENSP00000313699:R1021Q	ENSP00000313699:R1021Q	R	+	2	0	HEPHL1	93483733	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.361000	0.79497	2.840000	0.97914	0.655000	0.94253	CGA		0.403	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		A	93844085	G	A	93844085	3	1	61	1	0	0	0	0	1	0	0	0	7076	1058	37	1	3132	1	HEPHL1	11	93844085	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17400	93844085	41162431	7579	15564										
MRE11A	4361	broad.mit.edu	37	chr11	94153324	94153324	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttaaagaactagtgttCataaaaggatcatcatcatc	5	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94153324C>A	ENST00000323929.3	-	20	2316	c.2094G>T	c.(2092-2094)atG>atT	p.M698I	MRE11A_ENST00000323977.3_Missense_Mutation_p.M670I|MRE11A_ENST00000393241.4_Missense_Mutation_p.M697I|MRE11A_ENST00000407439.3_Missense_Mutation_p.M701I	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	698			M -> V (in dbSNP:rs1805362). {ECO:0000269|Ref.6}.		base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.M670I(1)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				AACTAGTGTTCATAAAAGGAT	0.318								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																																							1	Substitution - Missense(1)	large_intestine(1)	11											93	91	91					11																	94153324		2197	4283	6480	93792972	SO:0001583	missense	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.2094G>T	11.37:g.94153324C>A	ENSP00000325863:p.Met698Ile		93792972	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	C	14.25	2.479138	0.44044	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241	T;T;T;T	0.74209	-0.8;-0.8;-0.82;-0.8	5.4	5.4	0.78164	.	0.047526	0.85682	D	0.000000	T	0.68412	0.2998	L	0.44542	1.39	0.80722	D	1	B;B;B	0.14805	0.011;0.006;0.011	B;B;B	0.17433	0.018;0.009;0.01	T	0.64266	-0.6448	10	0.46703	T	0.11	-14.1581	15.0286	0.71687	0.0:1.0:0.0:0.0	.	701;670;698	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	I	698;701;670;697	ENSP00000325863:M698I;ENSP00000385614:M701I;ENSP00000326094:M670I;ENSP00000376933:M697I	ENSP00000325863:M698I	M	-	3	0	MRE11A	93792972	1.000000	0.71417	0.999000	0.59377	0.764000	0.43329	3.627000	0.54252	2.691000	0.91804	0.557000	0.71058	ATG		0.318	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		A	94153324	C	A	94153324	3	1	61	1	0	0	0	0	1	0	0	0	9789	826	29	2	36	2	MRE11A	11	94153324	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	309239	94153324	40853192	7580	15565										
MRE11A	4361	broad.mit.edu	37	chr11	94170365	94170365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaataattcttagtagtgAcatttcgggaaggctgctgt	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94170365A>G	ENST00000323929.3	-	17	2126	c.1904T>C	c.(1903-1905)gTc>gCc	p.V635A	MRE11A_ENST00000323977.3_Missense_Mutation_p.V607A|MRE11A_ENST00000393241.4_Missense_Mutation_p.V634A|MRE11A_ENST00000407439.3_Missense_Mutation_p.V638A	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	635					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.V607A(1)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				CTTAGTAGTGACATTTCGGGA	0.284								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																																							1	Substitution - Missense(1)	large_intestine(1)	11											72	75	74					11																	94170365		2201	4295	6496	93810013	SO:0001583	missense	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.1904T>C	11.37:g.94170365A>G	ENSP00000325863:p.Val635Ala		93810013	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	A	4.922	0.171301	0.09391	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241	T;T;T;T	0.73897	-0.79;-0.79;-0.78;-0.79	5.69	0.0407	0.14210	.	0.451973	0.21788	N	0.069119	T	0.48077	0.1480	N	0.21448	0.665	0.09310	N	0.999998	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.17107	-1.0380	10	0.08179	T	0.78	-14.0396	2.3532	0.04289	0.5997:0.1264:0.1504:0.1236	.	638;607;635	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	A	635;638;607;634	ENSP00000325863:V635A;ENSP00000385614:V638A;ENSP00000326094:V607A;ENSP00000376933:V634A	ENSP00000325863:V635A	V	-	2	0	MRE11A	93810013	0.015000	0.18098	0.685000	0.30070	0.267000	0.26476	0.061000	0.14366	0.060000	0.16281	0.533000	0.62120	GTC		0.284	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		G	94170365	A	G	94170365	3	3	61	1	0	0	0	0	1	0	0	0	9789	275	10	4	238	4	MRE11A	11	94170365	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	17041	94170365	40836151	7581	15566										
MRE11A	4361	broad.mit.edu	37	chr11	94189500	94189500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctggtttctctgaaacgaCgtacctagatcataacagag	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94189500C>T	ENST00000323929.3	-	14	1727	c.1505G>A	c.(1504-1506)cGt>cAt	p.R502H	MRE11A_ENST00000323977.3_Missense_Mutation_p.R502H|MRE11A_ENST00000393241.4_Missense_Mutation_p.R502H|MRE11A_ENST00000407439.3_Missense_Mutation_p.R505H	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	502					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.R502H(1)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				TCTGAAACGACGTACCTAGAT	0.313								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																																							1	Substitution - Missense(1)	large_intestine(1)	11											128	128	128					11																	94189500		2200	4298	6498	93829148	SO:0001583	missense	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.1505G>A	11.37:g.94189500C>T	ENSP00000325863:p.Arg502His		93829148	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.058253	0.55325	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	5.78	5.78	0.91487	.	0.149506	0.64402	D	0.000006	T	0.72162	0.3426	M	0.66939	2.045	0.80722	D	1	B;B;B	0.24675	0.109;0.106;0.109	B;B;B	0.18561	0.022;0.017;0.012	T	0.69269	-0.5189	10	0.48119	T	0.1	-14.7923	14.1901	0.65633	0.0:0.9287:0.0:0.0713	.	505;502;502	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	H	502;505;502;502	ENSP00000325863:R502H;ENSP00000385614:R505H;ENSP00000326094:R502H;ENSP00000376933:R502H	ENSP00000325863:R502H	R	-	2	0	MRE11A	93829148	1.000000	0.71417	0.983000	0.44433	0.850000	0.48378	2.868000	0.48436	2.738000	0.93877	0.591000	0.81541	CGT		0.313	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		T	94189500	C	T	94189500	3	4	61	1	0	0	0	0	1	0	0	0	9789	536	19	1	649	1	MRE11A	11	94189500	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19135	94189500	40817016	7582	15567										
MRE11A	4361	broad.mit.edu	37	chr11	94224094	94224094	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cataaatccaagatgaatatCtgttgcaactaatattttaa	4	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94224094C>A	ENST00000323929.3	-	3	280	c.58G>T	c.(58-60)Gat>Tat	p.D20Y	MRE11A_ENST00000323977.3_Missense_Mutation_p.D20Y|MRE11A_ENST00000393241.4_Missense_Mutation_p.D20Y|ANKRD49_ENST00000544612.1_5'Flank|MRE11A_ENST00000536144.1_5'UTR|MRE11A_ENST00000407439.3_Missense_Mutation_p.D23Y|MRE11A_ENST00000540013.1_Missense_Mutation_p.D20Y	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	20					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.D20Y(1)		breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				AGATGAATATCTGTTGCAACT	0.284								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																																							1	Substitution - Missense(1)	large_intestine(1)	11											82	78	79					11																	94224094		2201	4298	6499	93863742	SO:0001583	missense	4361	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.58G>T	11.37:g.94224094C>A	ENSP00000325863:p.Asp20Tyr		93863742	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.161204	0.78226	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241;ENST00000540013;ENST00000536754;ENST00000538923	D;D;D;D;D;D;D	0.99981	-10.53;-10.53;-10.53;-10.53;-10.53;-10.53;-10.53	4.46	4.46	0.54185	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.99984	0.9995	H	0.96080	3.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.987;0.99	D	0.98173	1.0453	10	0.87932	D	0	-19.9319	17.1299	0.86724	0.0:1.0:0.0:0.0	.	23;20;20	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	Y	20;23;20;20;20;20;20	ENSP00000325863:D20Y;ENSP00000385614:D23Y;ENSP00000326094:D20Y;ENSP00000376933:D20Y;ENSP00000440986:D20Y;ENSP00000439511:D20Y;ENSP00000442809:D20Y	ENSP00000325863:D20Y	D	-	1	0	MRE11A	93863742	1.000000	0.71417	0.948000	0.38648	0.986000	0.74619	7.091000	0.76923	2.029000	0.59856	0.462000	0.41574	GAT		0.284	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		A	94224094	C	A	94224094	3	1	61	1	0	0	0	0	1	0	0	0	9789	913	32	2	2140	2	MRE11A	11	94224094	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34594	94224094	40782422	7583	15568										
ANKRD49	54851	broad.mit.edu	37	chr11	94231625	94231625	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaactgcatttgatattgCcaggaggacaagtatctatc	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94231625C>G	ENST00000544612.1	+	3	1144	c.647C>G	c.(646-648)gCc>gGc	p.A216G	ANKRD49_ENST00000538535.1_3'UTR|ANKRD49_ENST00000302755.4_Missense_Mutation_p.A216G|ANKRD49_ENST00000544253.1_3'UTR	NM_017704.2	NP_060174.2	Q8WVL7	ANR49_HUMAN	ankyrin repeat domain 49	216					positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)		p.A216G(1)		autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|urinary_tract(1)	12		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTTGATATTGCCAGGAGGACA	0.408																																					Melanoma(113;823 1621 4352 9582 22033)											1	Substitution - Missense(1)	large_intestine(1)	11											75	77	76					11																	94231625		2201	4298	6499	93871273	SO:0001583	missense	54851			AF025354	CCDS8300.1	11q21	2013-01-10				ENSG00000168876		"Ankyrin repeat domain containing"	25970	protein-coding gene	gene with protein product						11162141	Standard	NM_017704		Approved	FLJ20189, FGIF, GBIF	uc001pew.3	Q8WVL7		ENST00000544612.1:c.647C>G	11.37:g.94231625C>G	ENSP00000440396:p.Ala216Gly		93871273	Q8NDF2|Q96JE5|Q9NXK7	Missense_Mutation	SNP	ENST00000544612.1	37	CCDS8300.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772757	0.90108	.	.	ENSG00000168876	ENST00000544612;ENST00000302755	D;D	0.82255	-1.59;-1.59	5.64	5.64	0.86602	Ankyrin repeat-containing domain (2);	0.103596	0.64402	D	0.000003	D	0.93207	0.7836	M	0.92923	3.36	0.80722	D	1	D	0.76494	0.999	D	0.66497	0.944	D	0.94306	0.7541	10	0.87932	D	0	-6.4911	19.6932	0.96010	0.0:1.0:0.0:0.0	.	216	Q8WVL7	ANR49_HUMAN	G	216	ENSP00000440396:A216G;ENSP00000303518:A216G	ENSP00000303518:A216G	A	+	2	0	ANKRD49	93871273	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	7.185000	0.77714	2.664000	0.90586	0.655000	0.94253	GCC		0.408	ANKRD49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396314.2	NM_017704		G	94231625	C	G	94231625	3	3	61	1	0	0	0	0	1	0	0	0	675	739	26	5	653	5	ANKRD49	11	94231625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7531	94231625	40774891	7584	15569										
PIWIL4	143689	broad.mit.edu	37	chr11	94331025	94331025	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgcattttggaagccagAtatctctgactggccggatt	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94331025A>G	ENST00000299001.6	+	11	1535	c.1324A>G	c.(1324-1326)Ata>Gta	p.I442V	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	442					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)	p.I442V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGGAAGCCAGATATCTCTGAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	11											99	103	102					11																	94331025		2201	4298	6499	93970673	SO:0001583	missense	143689			AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1324A>G	11.37:g.94331025A>G	ENSP00000299001:p.Ile442Val		93970673	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.669015	0.29604	.	.	ENSG00000134627	ENST00000299001	T	0.03717	3.83	4.83	-4.13	0.03904	Ribonuclease H-like (1);	0.639867	0.15408	N	0.263946	T	0.01695	0.0054	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49952	-0.8884	10	0.08381	T	0.77	-4.7809	7.2884	0.26352	0.3253:0.2793:0.3954:0.0	.	442	Q7Z3Z4	PIWL4_HUMAN	V	442	ENSP00000299001:I442V	ENSP00000299001:I442V	I	+	1	0	PIWIL4	93970673	0.138000	0.22547	0.978000	0.43139	0.836000	0.47400	-0.570000	0.05895	-0.609000	0.05724	0.482000	0.46254	ATA		0.338	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		G	94331025	A	G	94331025	3	3	61	1	0	0	0	0	1	0	0	0	11991	333	12	4	1366	4	PIWIL4	11	94331025	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	99400	94331025	40675491	7585	15570										
AMOTL1	154810	broad.mit.edu	37	chr11	94533042	94533042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaccagtcagaagtcccGaactgaggggaggcccactg	15	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94533042G>A	ENST00000433060.2	+	3	827	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	AMOTL1_ENST00000317837.9_Missense_Mutation_p.R229Q|AMOTL1_ENST00000317829.8_Missense_Mutation_p.R179Q	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	229					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.R229Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CAGAAGTCCCGAACTGAGGGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											24	27	26					11																	94533042		2101	4220	6321	94172690	SO:0001583	missense	154810			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.686G>A	11.37:g.94533042G>A	ENSP00000387739:p.Arg229Gln		94172690	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.813199	0.70912	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T	0.44083	0.93;0.93;0.93	5.28	5.28	0.74379	.	0.080141	0.50627	D	0.000112	T	0.50701	0.1631	M	0.74881	2.28	0.48975	D	0.999734	D;P	0.63880	0.993;0.944	P;B	0.49276	0.605;0.34	T	0.54255	-0.8321	9	.	.	.	-28.3066	12.2812	0.54765	0.078:0.0:0.922:0.0	.	179;229	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	Q	179;235;229;229	ENSP00000320968:R179Q;ENSP00000323474:R229Q;ENSP00000387739:R229Q	.	R	+	2	0	AMOTL1	94172690	1.000000	0.71417	0.989000	0.46669	0.947000	0.59692	5.105000	0.64591	2.472000	0.83506	0.555000	0.69702	CGA		0.637	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94533042	G	A	94533042	3	1	61	1	0	0	0	0	1	0	0	0	583	1058	37	1	696	1	AMOTL1	11	94533042	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202017	94533042	40473474	7586	15571										
AMOTL1	154810	broad.mit.edu	37	chr11	94602626	94602626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccagcggccaaagggaccGcagagaaactgggtatgtgg	15	10	0	1	rs77127753	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:94602626G>A	ENST00000433060.2	+	12	2893	c.2752G>A	c.(2752-2754)Gca>Aca	p.A918T	AMOTL1_ENST00000317837.9_Missense_Mutation_p.A505T|AMOTL1_ENST00000317829.8_Missense_Mutation_p.A868T	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	918					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.A919T(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CAAAGGGACCGCAGAGAAACT	0.602													G|||	3	0.000599042	0.0015	0	5008	,	,		17533	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						G	THR/ALA	6,3886		0,6,1940	16	19	18		2752	2.4	0	11	dbSNP_131	18	0,8262		0,0,4131	yes	missense	AMOTL1	NM_130847.2	58	0,6,6071	AA,AG,GG		0.0,0.1542,0.0494	benign	918/957	94602626	6,12148	1946	4131	6077	94242274	SO:0001583	missense	154810			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2752G>A	11.37:g.94602626G>A	ENSP00000387739:p.Ala918Thr		94242274	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.82	2.351981	0.41700	0.001542	0.0	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.44083	2.26;0.93;2.25	5.26	2.41	0.29592	.	0.552954	0.18358	N	0.143664	T	0.20333	0.0489	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15037	-1.0451	10	0.52906	T	0.07	-0.3659	5.633	0.17522	0.2675:0.0:0.6053:0.1273	.	868;918	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	T	868;505;918	ENSP00000320968:A868T;ENSP00000323474:A505T;ENSP00000387739:A918T	ENSP00000320968:A868T	A	+	1	0	AMOTL1	94242274	0.001000	0.12720	0.001000	0.08648	0.171000	0.22731	0.261000	0.18442	0.252000	0.21531	-0.215000	0.12644	GCA		0.602	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94602626	G	A	94602626	3	1	61	1	0	0	0	0	1	0	0	0	583	1087	38	1	2798	1	AMOTL1	11	94602626	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69584	94602626	40403890	7587	15572										
CEP57	9702	broad.mit.edu	37	chr11	95562478	95562478	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaccaaataactaaagttCgaaaataccaagcccaggta	5	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:95562478C>T	ENST00000325542.5	+	10	1493	c.1255C>T	c.(1255-1257)Cga>Tga	p.R419*	CEP57_ENST00000537677.1_Nonsense_Mutation_p.R392*|CEP57_ENST00000541150.1_Nonsense_Mutation_p.R410*|CEP57_ENST00000325486.5_Nonsense_Mutation_p.R393*	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	419	Mediates interaction with microtubules. {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)	p.R419*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AACTAAAGTTCGAAAATACCA	0.368									Mosaic Variegated Aneuploidy Syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	11											175	181	179					11																	95562478		2201	4298	6499	95202126	SO:0001587	stop_gained	9702	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1255C>T	11.37:g.95562478C>T	ENSP00000317902:p.Arg419*		95202126	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Nonsense_Mutation	SNP	ENST00000325542.5	37	CCDS8304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.150626|6.150626	0.97329|0.97329	.|.	.|.	ENSG00000166037|ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150|ENST00000535224	.|.	.|.	.|.	5.54|5.54	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.64402|.	D|.	0.000006|.	.|T	.|0.71117	.|0.3302	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70687	.|-0.4803	.|4	0.87932|.	D|.	0|.	-11.8853|-11.8853	15.6938|15.6938	0.77477|0.77477	0.1381:0.8619:0.0:0.0|0.1381:0.8619:0.0:0.0	.|.	.|.	.|.	.|.	X|L	392;419;393;410|208	.|.	ENSP00000317487:R393X|.	R|S	+|+	1|2	2|0	CEP57|CEP57	95202126|95202126	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.836000|2.836000	0.48183|0.48183	1.320000|1.320000	0.45209|0.45209	0.491000|0.491000	0.48974|0.48974	CGA|TCG		0.368	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		T	95562478	C	T	95562478	4	4	61	1	0	0	0	0	0	1	0	0	3262	876	31	1	1293	1	CEP57	11	95562478	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	959852	95562478	39444038	7588	15573										
MTMR2	8898	broad.mit.edu	37	chr11	95578127	95578127	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttacttactagttgaaatCgatgtccaaaacttagccat	5	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:95578127C>T	ENST00000346299.5	-	11	1716	c.1376G>A	c.(1375-1377)cGa>cAa	p.R459Q	MTMR2_ENST00000393223.3_Missense_Mutation_p.R387Q|MTMR2_ENST00000409459.1_Missense_Mutation_p.R387Q|MTMR2_ENST00000352297.7_Missense_Mutation_p.R387Q	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	459	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R387Q(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TAGTTGAAATCGATGTCCAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											102	91	95					11																	95578127		2201	4298	6499	95217775	SO:0001583	missense	8898			U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1376G>A	11.37:g.95578127C>T	ENSP00000345752:p.Arg459Gln		95217775	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925006	0.52759	.	.	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297;ENST00000444541	D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19	5.66	4.75	0.60458	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.92244	0.7540	L	0.37561	1.115	0.80722	D	1	D;B	0.57257	0.979;0.429	P;B	0.50970	0.655;0.124	D	0.92554	0.6052	10	0.59425	D	0.04	.	14.8028	0.69929	0.0:0.9304:0.0:0.0696	.	459;459	A8K5G2;Q13614	.;MTMR2_HUMAN	Q	459;387;387;387;387	ENSP00000345752:R459Q;ENSP00000376915:R387Q;ENSP00000386882:R387Q;ENSP00000343737:R387Q;ENSP00000396020:R387Q	ENSP00000345752:R459Q	R	-	2	0	MTMR2	95217775	1.000000	0.71417	0.973000	0.42090	0.680000	0.39746	4.922000	0.63404	1.392000	0.46585	0.462000	0.41574	CGA		0.383	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		T	95578127	C	T	95578127	3	4	61	1	0	0	0	0	1	0	0	0	9974	884	31	1	575	1	MTMR2	11	95578127	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15649	95578127	39428389	7589	15574										
CCDC82	79780	broad.mit.edu	37	chr11	96117829	96117829	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatactacttcttttagttCgcctccaatcaactcgagat	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:96117829C>T	ENST00000278520.5	-	3	511	c.83G>A	c.(82-84)cGa>cAa	p.R28Q	CCDC82_ENST00000525786.1_5'Flank|CCDC82_ENST00000423339.2_Missense_Mutation_p.R28Q|CCDC82_ENST00000542662.1_Missense_Mutation_p.R28Q			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	28								p.R28Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		TCTTTTAGTTCGCCTCCAATC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	11											96	90	92					11																	96117829		2201	4295	6496	95757477	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.83G>A	11.37:g.96117829C>T	ENSP00000278520:p.Arg28Gln		95757477	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088786	0.94100	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339;ENST00000538597;ENST00000530203	T;T;T;T	0.56611	0.59;0.59;0.59;0.45	5.77	5.77	0.91146	.	0.000000	0.52532	D	0.000065	T	0.73032	0.3535	M	0.70595	2.14	0.39958	D	0.974627	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.75371	-0.3341	10	0.87932	D	0	-11.4971	18.1503	0.89672	0.0:1.0:0.0:0.0	.	28;28	Q8N4S0-2;Q8N4S0	.;CCD82_HUMAN	Q	28	ENSP00000278520:R28Q;ENSP00000444010:R28Q;ENSP00000397156:R28Q;ENSP00000442723:R28Q	ENSP00000278520:R28Q	R	-	2	0	CCDC82	95757477	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.436000	0.59948	2.885000	0.99019	0.655000	0.94253	CGA		0.353	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		T	96117829	C	T	96117829	3	4	61	1	0	0	0	0	1	0	0	0	2862	884	31	1	1579	1	CCDC82	11	96117829	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	539702	96117829	38888687	7590	15575										
JRKL	8690	broad.mit.edu	37	chr11	96125030	96125030	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgatgttgaagatatttCtgtggctactgtggctgcca	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:96125030C>A	ENST00000332349.4	+	2	1464	c.1217C>A	c.(1216-1218)tCt>tAt	p.S406Y	JRKL_ENST00000546177.1_Intron|JRKL_ENST00000458427.1_Missense_Mutation_p.S406Y|CCDC82_ENST00000525786.1_5'Flank|CCDC82_ENST00000542662.1_5'Flank	NM_001261833.1	NP_001248762.1	Q9Y4A0	JERKL_HUMAN	JRK-like	406					central nervous system development (GO:0007417)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S406Y(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)		BRCA - Breast invasive adenocarcinoma(274;0.148)		GAAGATATTTCTGTGGCTACT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	89	89					11																	96125030		2201	4298	6499	95764678	SO:0001583	missense	8690			AF004715	CCDS8308.1	11q21	2014-03-28	2014-03-28		ENSG00000183340	ENSG00000183340			6200	protein-coding gene	gene with protein product		603211	"erky (mouse) homolog-like", "jerky homolog-like (mouse)"			9240447	Standard	NM_003772		Approved	HHMJG	uc009ywu.4	Q9Y4A0	OTTHUMG00000154950	ENST00000332349.4:c.1217C>A	11.37:g.96125030C>A	ENSP00000333350:p.Ser406Tyr		95764678	A8K3G4|B2RAJ3|Q32MC2	Missense_Mutation	SNP	ENST00000332349.4	37	CCDS8308.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.789330	0.31685	.	.	ENSG00000183340	ENST00000332349;ENST00000458427	T;T	0.25414	1.8;1.8	4.79	3.88	0.44766	.	0.462473	0.16139	N	0.227830	T	0.23370	0.0565	L	0.40543	1.245	0.27034	N	0.964171	D	0.57899	0.981	P	0.44597	0.454	T	0.07271	-1.0781	10	0.59425	D	0.04	-8.6915	9.4023	0.38440	0.0:0.8991:0.0:0.1009	.	406	Q9Y4A0	JERKL_HUMAN	Y	406	ENSP00000333350:S406Y;ENSP00000389989:S406Y	ENSP00000333350:S406Y	S	+	2	0	JRKL	95764678	0.991000	0.36638	0.585000	0.28666	0.968000	0.65278	3.743000	0.55104	1.137000	0.42214	0.462000	0.41574	TCT		0.413	JRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337775.2	NM_003772		A	96125030	C	A	96125030	3	1	61	1	0	0	0	0	1	0	0	0	7986	913	32	2	1219	2	JRKL	11	96125030	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7201	96125030	38881486	7591	15576										
CNTN5	53942	broad.mit.edu	37	chr11	99827692	99827692	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtgaaaaacacagtgacGaatgctagagtccttagtcc	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:99827692G>A	ENST00000524871.1	+	8	1118	c.828G>A	c.(826-828)acG>acA	p.T276T	CNTN5_ENST00000527185.1_Silent_p.T276T|CNTN5_ENST00000528682.1_Silent_p.T276T|CNTN5_ENST00000279463.3_Silent_p.T276T|CNTN5_ENST00000418526.2_Silent_p.T202T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	276	Ig-like C2-type 2.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.T276T(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		ACACAGTGACGAATGCTAGAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	11											52	51	51					11																	99827692		1953	4138	6091	99332902	SO:0001819	synonymous_variant	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.828G>A	11.37:g.99827692G>A			99332902	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																				0.448	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	99827692	G	A	99827692	2	1	61	1	0	0	0	0	0	0	0	1	3650	1045	37	1		1	CNTN5	11	99827692	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3702662	99827692	35178824	7592	15577										
TRPC6	7225	broad.mit.edu	37	chr11	101323728	101323728	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggttccatggataatttCtctccaagttctctaataag	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101323728C>A	ENST00000344327.3	-	13	3178	c.2754G>T	c.(2752-2754)gaG>gaT	p.E918D	TRPC6_ENST00000532133.1_Missense_Mutation_p.E840D|TRPC6_ENST00000360497.4_Missense_Mutation_p.E863D|TRPC6_ENST00000348423.4_Missense_Mutation_p.E802D	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	918					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.E918D(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TGGATAATTTCTCTCCAAGTT	0.353																																					Colon(166;1315 1927 11094 12848 34731)											1	Substitution - Missense(1)	large_intestine(1)	11											186	186	186					11																	101323728		2202	4300	6502	100828938	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2754G>T	11.37:g.101323728C>A	ENSP00000340913:p.Glu918Asp		100828938	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.227361	0.39399	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.79454	-1.13;-1.21;-1.02;-1.27	5.65	2.73	0.32206	.	0.218369	0.46758	D	0.000266	T	0.65004	0.2650	L	0.31065	0.9	0.39260	D	0.964197	B;P	0.48911	0.074;0.917	B;B	0.44278	0.023;0.445	T	0.61417	-0.7067	10	0.41790	T	0.15	-19.5621	5.8836	0.18868	0.0:0.591:0.1387:0.2703	.	802;918	Q9Y210-2;Q9Y210	.;TRPC6_HUMAN	D	918;840;802;863	ENSP00000340913:E918D;ENSP00000435574:E840D;ENSP00000343672:E802D;ENSP00000353687:E863D	ENSP00000340913:E918D	E	-	3	2	TRPC6	100828938	1.000000	0.71417	0.989000	0.46669	0.971000	0.66376	1.050000	0.30404	0.320000	0.23234	-0.145000	0.13849	GAG		0.353	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101323728	C	A	101323728	3	1	61	1	0	0	0	0	1	0	0	0	16623	912	32	2	45	2	TRPC6	11	101323728	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1496036	101323728	33682788	7593	15578										
TRPC6	7225	broad.mit.edu	37	chr11	101324431	101324431	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgggcctgcagtacatatCttttaatgagccttttcatt	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101324431C>T	ENST00000344327.3	-	12	3018	c.2594G>A	c.(2593-2595)aGa>aAa	p.R865K	TRPC6_ENST00000532133.1_Missense_Mutation_p.R787K|TRPC6_ENST00000360497.4_Missense_Mutation_p.R810K|TRPC6_ENST00000348423.4_Missense_Mutation_p.R749K	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	865					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R865K(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CAGTACATATCTTTTAATGAG	0.408																																					Colon(166;1315 1927 11094 12848 34731)											1	Substitution - Missense(1)	large_intestine(1)	11											165	145	152					11																	101324431		2202	4300	6502	100829641	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2594G>A	11.37:g.101324431C>T	ENSP00000340913:p.Arg865Lys		100829641	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	36	5.816497	0.96982	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29	6.04	6.04	0.98038	.	0.086933	0.85682	D	0.000000	D	0.94765	0.8310	M	0.86343	2.81	0.58432	D	0.999999	D;D;D	0.71674	0.998;0.998;0.996	D;D;D	0.80764	0.994;0.994;0.986	D	0.94577	0.7776	10	0.87932	D	0	-10.2182	20.6437	0.99549	0.0:1.0:0.0:0.0	.	810;749;865	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	K	865;787;749;810	ENSP00000340913:R865K;ENSP00000435574:R787K;ENSP00000343672:R749K;ENSP00000353687:R810K	ENSP00000340913:R865K	R	-	2	0	TRPC6	100829641	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.515000	0.81761	2.890000	0.99128	0.650000	0.86243	AGA		0.408	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		T	101324431	C	T	101324431	3	4	61	1	0	0	0	0	1	0	0	0	16623	913	32	3	209	3	TRPC6	11	101324431	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	703	101324431	33682085	7594	15579										
TRPC6	7225	broad.mit.edu	37	chr11	101344387	101344387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtgatatctgcagaggtCcaaagctttcatttgctggt	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101344387C>T	ENST00000344327.3	-	7	2286	c.1862G>A	c.(1861-1863)gGa>gAa	p.G621E	TRPC6_ENST00000532133.1_Missense_Mutation_p.G543E|TRPC6_ENST00000360497.4_Missense_Mutation_p.G566E|TRPC6_ENST00000348423.4_Missense_Mutation_p.G505E	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	621					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.G621E(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CTGCAGAGGTCCAAAGCTTTC	0.358																																					Colon(166;1315 1927 11094 12848 34731)											1	Substitution - Missense(1)	large_intestine(1)	11											97	95	96					11																	101344387		2203	4298	6501	100849597	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1862G>A	11.37:g.101344387C>T	ENSP00000340913:p.Gly621Glu		100849597	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872623	0.91587	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	D;D;D;D	0.98493	-2.48;-4.96;-4.96;-4.96	5.91	5.91	0.95273	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99360	0.9775	H	0.95187	3.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98748	1.0719	10	0.87932	D	0	-9.3113	20.2985	0.98592	0.0:1.0:0.0:0.0	.	566;505;621	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	E	621;543;505;566	ENSP00000340913:G621E;ENSP00000435574:G543E;ENSP00000343672:G505E;ENSP00000353687:G566E	ENSP00000340913:G621E	G	-	2	0	TRPC6	100849597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.807000	0.86032	2.793000	0.96121	0.655000	0.94253	GGA		0.358	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		T	101344387	C	T	101344387	3	4	61	1	0	0	0	0	1	0	0	0	16623	855	30	3	961	3	TRPC6	11	101344387	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19956	101344387	33662129	7595	15580										
ANGPTL5	253935	broad.mit.edu	37	chr11	101762130	101762130	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgcaagcaattttccagaGaagtgatgaatgccatttag	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101762130G>T	ENST00000334289.3	-	9	1642	c.1047C>A	c.(1045-1047)ttC>ttA	p.F349L		NM_178127.4	NP_835228.2	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5	349	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)		p.F349L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(2)|skin(3)	29		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		ATTTTCCAGAGAAGTGATGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											171	170	170					11																	101762130		2203	4299	6502	101267340	SO:0001583	missense	253935			BC049170	CCDS8312.1	11q22.2	2013-02-06				ENSG00000187151		"Fibrinogen C domain containing"	19705	protein-coding gene	gene with protein product		607666				12624729	Standard	NM_178127		Approved		uc001pgl.3	Q86XS5		ENST00000334289.3:c.1047C>A	11.37:g.101762130G>T	ENSP00000335255:p.Phe349Leu		101267340	A8K658|Q86VR9	Missense_Mutation	SNP	ENST00000334289.3	37	CCDS8312.1	.	.	.	.	.	.	.	.	.	.	G	9.414	1.081351	0.20309	.	.	ENSG00000187151	ENST00000334289	T	0.76578	-1.03	5.25	0.125	0.14718	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.620223	0.17419	N	0.174893	T	0.51975	0.1706	N	0.05078	-0.115	0.09310	N	1	B	0.19331	0.035	B	0.24394	0.053	T	0.38265	-0.9669	10	0.11182	T	0.66	.	9.1231	0.36799	0.3713:0.0:0.6287:0.0	.	349	Q86XS5	ANGL5_HUMAN	L	349	ENSP00000335255:F349L	ENSP00000335255:F349L	F	-	3	2	ANGPTL5	101267340	0.015000	0.18098	0.011000	0.14972	0.934000	0.57294	0.154000	0.16343	-0.020000	0.14032	0.650000	0.86243	TTC		0.418	ANGPTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394138.1	NM_178127		T	101762130	G	T	101762130	3	4	61	1	0	0	0	0	1	0	0	0	617	933	33	2	123	2	ANGPTL5	11	101762130	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	417743	101762130	33244386	7596	15581										
KIAA1377	57562	broad.mit.edu	37	chr11	101833848	101833848	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtccagggaggattctatCtctgaaaatgttacgacttt	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101833848C>A	ENST00000263468.8	+	6	2352	c.2082C>A	c.(2080-2082)atC>atA	p.I694I	KIAA1377_ENST00000537689.1_Silent_p.I495I	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	694								p.I694I(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AGGATTCTATCTCTGAAAATG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	11											102	102	102					11																	101833848		2203	4299	6502	101339058	SO:0001819	synonymous_variant	57562			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2082C>A	11.37:g.101833848C>A			101339058	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																				0.398	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		A	101833848	C	A	101833848	2	1	61	1	0	0	0	0	0	0	0	1	8248	903	32	2		2	KIAA1377	11	101833848	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71718	101833848	33172668	7597	15582										
KIAA1377	57562	broad.mit.edu	37	chr11	101852681	101852681	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaactacaaggggtacttCttatattgaagaaggtatgt	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:101852681C>A	ENST00000263468.8	+	8	3290	c.3020C>A	c.(3019-3021)tCt>tAt	p.S1007Y	KIAA1377_ENST00000537689.1_Missense_Mutation_p.S808Y	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	1007								p.S1007Y(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AGGGGTACTTCTTATATTGAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	11											38	37	37					11																	101852681		2202	4292	6494	101357891	SO:0001583	missense	57562			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.3020C>A	11.37:g.101852681C>A	ENSP00000263468:p.Ser1007Tyr		101357891	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.663|8.663	0.900920|0.900920	0.17760|0.17760	.|.	.|.	ENSG00000110318|ENSG00000110318	ENST00000532077|ENST00000263468;ENST00000537689	.|T;T	.|0.08546	.|3.08;3.08	4.8|4.8	3.87|3.87	0.44632|0.44632	.|.	.|0.434122	.|0.22024	.|N	.|0.065685	T|T	0.17195|0.17195	0.0413|0.0413	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	1|1	.|D	.|0.64830	.|0.994	.|P	.|0.60682	.|0.878	T|T	0.02288|0.02288	-1.1182|-1.1182	5|10	.|0.87932	.|D	.|0	-0.2998|-0.2998	10.8853|10.8853	0.46964|0.46964	0.0:0.8085:0.1915:0.0|0.0:0.8085:0.1915:0.0	.|.	.|1007	.|Q9P2H0	.|K1377_HUMAN	L|Y	40|1007;808	.|ENSP00000263468:S1007Y;ENSP00000443184:S808Y	.|ENSP00000263468:S1007Y	F|S	+|+	3|2	2|0	KIAA1377|KIAA1377	101357891|101357891	0.347000|0.347000	0.24853|0.24853	0.015000|0.015000	0.15790|0.15790	0.023000|0.023000	0.10783|0.10783	0.951000|0.951000	0.29135|0.29135	0.962000|0.962000	0.38057|0.38057	0.655000|0.655000	0.94253|0.94253	TTC|TCT		0.303	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		A	101852681	C	A	101852681	3	1	61	1	0	0	0	0	1	0	0	0	8248	913	32	2	3050	2	KIAA1377	11	101852681	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18833	101852681	33153835	7598	15583										
BIRC3	330	broad.mit.edu	37	chr11	102195260	102195260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaacatagtagaaaacaGcatattcttatcaaatttga	5	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102195260G>T	ENST00000263464.3	+	2	2770	c.20G>T	c.(19-21)aGc>aTc	p.S7I	BIRC3_ENST00000532808.1_Missense_Mutation_p.S7I	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	7					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S7I(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GTAGAAAACAGCATATTCTTA	0.373			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	1	Substitution - Missense(1)	large_intestine(1)	11											97	92	94					11																	102195260		2203	4299	6502	101700470	SO:0001583	missense	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.20G>T	11.37:g.102195260G>T	ENSP00000263464:p.Ser7Ile		101700470	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957975	0.34565	.	.	ENSG00000023445	ENST00000263464;ENST00000532808	T;T	0.23950	1.88;1.88	6.06	5.12	0.69794	.	0.144353	0.85682	D	0.000000	T	0.27594	0.0678	L	0.48362	1.52	0.46260	D	0.99895	B	0.27951	0.195	B	0.31245	0.126	T	0.05886	-1.0858	10	0.87932	D	0	-23.7445	15.1265	0.72486	0.0:0.0:0.7473:0.2527	.	7	Q13489	BIRC3_HUMAN	I	7	ENSP00000263464:S7I;ENSP00000432907:S7I	ENSP00000263464:S7I	S	+	2	0	BIRC3	101700470	0.994000	0.37717	0.869000	0.34112	0.331000	0.28603	3.102000	0.50291	2.871000	0.98454	0.655000	0.94253	AGC		0.373	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102195260	G	T	102195260	3	4	61	1	0	0	0	0	1	0	0	0	1437	971	34	2	22	2	BIRC3	11	102195260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	342579	102195260	32811256	7599	15584										
BIRC3	330	broad.mit.edu	37	chr11	102195755	102195755	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaataacgaaaatgccaGattacttacttttcagacat	5	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102195755G>T	ENST00000263464.3	+	2	3265	c.515G>T	c.(514-516)aGa>aTa	p.R172I	BIRC3_ENST00000532808.1_Missense_Mutation_p.R172I	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	172					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R172I(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GAAAATGCCAGATTACTTACT	0.423			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	1	Substitution - Missense(1)	large_intestine(1)	11											126	129	128					11																	102195755		2203	4299	6502	101700965	SO:0001583	missense	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.515G>T	11.37:g.102195755G>T	ENSP00000263464:p.Arg172Ile		101700965	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453939	0.63290	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	D;D	0.96300	-3.97;-3.97	5.4	5.4	0.78164	Baculoviral inhibition of apoptosis protein repeat (5);	0.000000	0.85682	D	0.000000	D	0.99190	0.9719	H	0.99705	4.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98554	1.0638	10	0.87932	D	0	.	19.3682	0.94473	0.0:0.0:1.0:0.0	.	172	Q13489	BIRC3_HUMAN	I	172;172;21	ENSP00000263464:R172I;ENSP00000432907:R172I	ENSP00000263464:R172I	R	+	2	0	BIRC3	101700965	1.000000	0.71417	0.850000	0.33497	0.019000	0.09904	9.191000	0.94940	2.818000	0.97014	0.591000	0.81541	AGA		0.423	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102195755	G	T	102195755	3	4	61	1	0	0	0	0	1	0	0	0	1437	942	33	2	517	2	BIRC3	11	102195755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	495	102195755	32810761	7600	15585										
BIRC3	330	broad.mit.edu	37	chr11	102201750	102201750	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatccattttgaacctggaGaagaccattcagaagatgca	8	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102201750G>T	ENST00000263464.3	+	6	3852	c.1102G>T	c.(1102-1104)Gaa>Taa	p.E368*	BIRC3_ENST00000532808.1_Nonsense_Mutation_p.E368*	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	368					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E368K(1)|p.E368*(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TGAACCTGGAGAAGACCATTC	0.333			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	11											69	72	71					11																	102201750		2203	4299	6502	101706960	SO:0001587	stop_gained	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1102G>T	11.37:g.102201750G>T	ENSP00000263464:p.Glu368*		101706960	Q16628|Q9HC27|Q9UP46	Nonsense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764626	0.69878	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000527309	.	.	.	5.28	5.28	0.74379	.	0.042995	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	12.4164	0.55496	0.0763:0.0:0.9237:0.0	.	.	.	.	X	368;368;172	.	ENSP00000263464:E368X	E	+	1	0	BIRC3	101706960	1.000000	0.71417	0.970000	0.41538	0.204000	0.24138	7.315000	0.78998	2.741000	0.93983	0.561000	0.74099	GAA		0.333	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102201750	G	T	102201750	4	4	61	1	0	0	0	0	0	1	0	0	1437	943	33	2	1120	2	BIRC3	11	102201750	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5995	102201750	32804766	7601	15586										
BIRC2	329	broad.mit.edu	37	chr11	102248244	102248244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatgatttgtcattaattCggaagaacagaatggctctc	9	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102248244C>T	ENST00000227758.2	+	7	2783	c.1384C>T	c.(1384-1386)Cgg>Tgg	p.R462W	BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.R413W|BIRC2_ENST00000532672.1_Missense_Mutation_p.R441W	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	462	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R462W(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		GTCATTAATTCGGAAGAACAG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	11											69	73	72					11																	102248244		2194	4294	6488	101753454	SO:0001583	missense	329			L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.1384C>T	11.37:g.102248244C>T	ENSP00000227758:p.Arg462Trp		101753454	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.710948	0.68730	.	.	ENSG00000110330	ENST00000530675;ENST00000533742;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	6.04	6.04	0.98038	DEATH-like (2);Caspase Recruitment (3);	0.050625	0.85682	D	0.000000	T	0.44477	0.1295	M	0.80028	2.48	0.53005	D	0.999969	B	0.30326	0.276	B	0.42163	0.378	T	0.40194	-0.9576	10	0.87932	D	0	-19.651	16.1156	0.81304	0.1342:0.8658:0.0:0.0	.	462	Q13490	BIRC2_HUMAN	W	413;124;462;462;441	ENSP00000431723:R413W;ENSP00000433851:R124W;ENSP00000227758:R462W;ENSP00000434979:R441W	ENSP00000227758:R462W	R	+	1	2	BIRC2	101753454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.168000	0.42424	2.876000	0.98609	0.650000	0.86243	CGG		0.303	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		T	102248244	C	T	102248244	3	4	61	1	0	0	0	0	1	0	0	0	1436	875	31	1	1406	1	BIRC2	11	102248244	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46494	102248244	32758272	7602	15587										
TMEM123	114908	broad.mit.edu	37	chr11	102272375	102272375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccaccaacaaagctcccaGtatcaaattttgatcctttc	3	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102272375G>T	ENST00000398136.2	-	4	917	c.497C>A	c.(496-498)aCt>aAt	p.T166N	TMEM123_ENST00000525577.1_5'Flank|TMEM123_ENST00000532161.1_Missense_Mutation_p.T78N|TMEM123_ENST00000361236.3_Missense_Mutation_p.T147N	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	166					oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.T166N(1)		breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		AAAGCTCCCAGTATCAAATTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	84	85					11																	102272375		1802	4078	5880	101777585	SO:0001583	missense	114908			AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"pro oncosis receptor inducing membrane injury gene"	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.497C>A	11.37:g.102272375G>T	ENSP00000381204:p.Thr166Asn		101777585	Q8IWS2|Q96QV2	Missense_Mutation	SNP	ENST00000398136.2	37	CCDS41702.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495044	0.64186	.	.	ENSG00000152558	ENST00000361236;ENST00000398136;ENST00000532161;ENST00000528969	T;T;T;T	0.42900	0.96;1.89;0.96;0.96	6.04	-2.25	0.06888	.	0.713366	0.13176	N	0.407844	T	0.48804	0.1520	L	0.39898	1.24	0.09310	N	0.999999	D;D	0.76494	0.998;0.999	D;D	0.67548	0.914;0.952	T	0.48340	-0.9044	10	0.52906	T	0.07	-5.7603	11.5771	0.50869	0.5644:0.0:0.4356:0.0	.	147;166	Q8N131-2;Q8N131	.;PORIM_HUMAN	N	147;166;78;78	ENSP00000355285:T147N;ENSP00000381204:T166N;ENSP00000435331:T78N;ENSP00000434976:T78N	ENSP00000355285:T147N	T	-	2	0	TMEM123	101777585	0.026000	0.19158	0.687000	0.30102	0.984000	0.73092	0.301000	0.19174	-0.339000	0.08401	0.563000	0.77884	ACT		0.328	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932		T	102272375	G	T	102272375	3	4	61	1	0	0	0	0	1	0	0	0	16075	1029	36	2	137	2	TMEM123	11	102272375	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24131	102272375	32734141	7603	15588										
MMP27	64066	broad.mit.edu	37	chr11	102562686	102562686	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatgattcgggtaatattCtttgtcttaatgtcgtattc	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102562686C>A	ENST00000260229.4	-	10	1444	c.1353G>T	c.(1351-1353)aaG>aaT	p.K451N		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	451					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K451N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GGGTAATATTCTTTGTCTTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	93	97					11																	102562686		2203	4296	6499	102067896	SO:0001583	missense	64066			AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1353G>T	11.37:g.102562686C>A	ENSP00000260229:p.Lys451Asn		102067896	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.255944	0.39896	.	.	ENSG00000137675	ENST00000260229	T	0.14893	2.47	5.97	4.84	0.62591	Hemopexin/matrixin (2);	0.000000	0.64402	D	0.000002	T	0.16642	0.0400	M	0.64170	1.965	0.46823	D	0.999217	B	0.34161	0.439	B	0.32677	0.15	T	0.04440	-1.0951	10	0.38643	T	0.18	.	6.3648	0.21449	0.0:0.6628:0.1417:0.1955	.	451	Q9H306	MMP27_HUMAN	N	451	ENSP00000260229:K451N	ENSP00000260229:K451N	K	-	3	2	MMP27	102067896	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	1.195000	0.32186	1.178000	0.42870	0.591000	0.81541	AAG		0.338	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		A	102562686	C	A	102562686	3	1	61	1	0	0	0	0	1	0	0	0	9694	912	32	2	192	2	MMP27	11	102562686	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	290311	102562686	32443830	7604	15589										
MMP8	4317	broad.mit.edu	37	chr11	102586132	102586132	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaaataaaattcatttcGactctttgtagctgaggatg	9	5	2	2	rs530920765		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102586132G>A	ENST00000236826.3	-	7	1037	c.939C>T	c.(937-939)gtC>gtT	p.V313V		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	313					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.V313V(1)		autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	AATTCATTTCGACTCTTTGTA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	11											107	96	100					11																	102586132		2203	4299	6502	102091342	SO:0001819	synonymous_variant	4317			J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.939C>T	11.37:g.102586132G>A			102091342	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	.	.	.	.	.	.	.	.	.	.	G	3.447	-0.112775	0.06881	.	.	ENSG00000118113	ENST00000438475	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1067	0.30890	0.5878:0.2137:0.1393:0.0592	.	.	.	.	X	289	.	.	R	-	1	2	MMP8	102091342	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.508000	0.00447	-3.667000	0.00124	-0.157000	0.13467	CGA		0.398	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		A	102586132	G	A	102586132	2	1	61	1	0	0	0	0	0	0	0	1	9698	1045	37	1		1	MMP8	11	102586132	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23446	102586132	32420384	7605	15590										
MMP10	4319	broad.mit.edu	37	chr11	102647027	102647027	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacctgtctttaaagaacaGatattctcccctcagagtgc	7	11	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102647027G>T	ENST00000279441.4	-	6	952	c.916C>A	c.(916-918)Ctg>Atg	p.L306M		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	306					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L306M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TTAAAGAACAGATATTCTCCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	73	74					11																	102647027		2203	4299	6502	102152237	SO:0001583	missense	4319			X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.916C>A	11.37:g.102647027G>T	ENSP00000279441:p.Leu306Met		102152237	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	G	2.558	-0.302485	0.05495	.	.	ENSG00000166670	ENST00000279441	T	0.02525	4.26	4.33	1.44	0.22558	Hemopexin/matrixin (2);	0.429445	0.16950	N	0.192930	T	0.05410	0.0143	L	0.39326	1.205	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.34750	-0.9816	10	0.09843	T	0.71	.	2.7164	0.05188	0.4103:0.0:0.3834:0.2063	.	306	P09238	MMP10_HUMAN	M	306	ENSP00000279441:L306M	ENSP00000279441:L306M	L	-	1	2	MMP10	102152237	0.000000	0.05858	0.708000	0.30435	0.315000	0.28087	-0.499000	0.06413	0.576000	0.29452	-0.151000	0.13558	CTG		0.418	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			T	102647027	G	T	102647027	3	4	61	1	0	0	0	0	1	0	0	0	9679	933	33	2	534	2	MMP10	11	102647027	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60895	102647027	32359489	7606	15591										
MMP10	4319	broad.mit.edu	37	chr11	102647132	102647132	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtgggcaccaggggttCctcagtagaggcagggggag	18	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102647132C>A	ENST00000279441.4	-	6	847	c.811G>T	c.(811-813)Gaa>Taa	p.E271*		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	271					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E271*(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	ACCAGGGGTTCCTCAGTAGAG	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											74	72	73					11																	102647132		2203	4299	6502	102152342	SO:0001587	stop_gained	4319			X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.811G>T	11.37:g.102647132C>A	ENSP00000279441:p.Glu271*		102152342	B2R9X9|Q53HH9	Nonsense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.770973	0.69992	.	.	ENSG00000166670	ENST00000279441	.	.	.	4.27	3.31	0.37934	.	1.648230	0.03703	N	0.248851	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5387	0.22369	0.0:0.7093:0.1806:0.1101	.	.	.	.	X	271	.	ENSP00000279441:E271X	E	-	1	0	MMP10	102152342	0.000000	0.05858	0.003000	0.11579	0.150000	0.21749	0.780000	0.26760	1.047000	0.40274	0.650000	0.86243	GAA		0.478	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			A	102647132	C	A	102647132	4	1	61	1	0	0	0	0	0	1	0	0	9679	864	30	2	639	2	MMP10	11	102647132	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105	102647132	32359384	7607	15592										
MMP1	4312	broad.mit.edu	37	chr11	102661215	102661215	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcgttttaggatcaaaTttgtattgtcttgttccatg	7	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102661215T>G	ENST00000315274.6	-	10	1405	c.1338A>C	c.(1336-1338)aaA>aaC	p.K446N	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	446					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K446N(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	TAGGATCAAATTTGTATTGTC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	11											107	101	103					11																	102661215		2202	4299	6501	102166425	SO:0001583	missense	4312			X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"Endogenous ligands"	7155	protein-coding gene	gene with protein product		120353	"matrix metalloproteinase 1 (interstitial collagenase)"	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1338A>C	11.37:g.102661215T>G	ENSP00000322788:p.Lys446Asn		102166425	P08156	Missense_Mutation	SNP	ENST00000315274.6	37	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	t	19.77	3.889718	0.72524	.	.	ENSG00000196611	ENST00000315274	T	0.02763	4.17	6.17	5.05	0.67936	Hemopexin/matrixin (2);	0.329841	0.29900	N	0.010903	T	0.12135	0.0295	M	0.83223	2.63	0.27137	N	0.961748	D	0.56521	0.976	P	0.59221	0.854	T	0.07195	-1.0785	10	0.72032	D	0.01	.	8.8409	0.35142	0.0:0.1561:0.0:0.8439	.	446	P03956	MMP1_HUMAN	N	446	ENSP00000322788:K446N	ENSP00000322788:K446N	K	-	3	2	MMP1	102166425	0.988000	0.35896	1.000000	0.80357	0.951000	0.60555	1.135000	0.31454	1.161000	0.42604	-0.250000	0.11733	AAA		0.299	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421		G	102661215	T	G	102661215	3	3	61	1	0	0	0	0	1	0	0	0	9678	1490	52	4	75	4	MMP1	11	102661215	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	14083	102661215	32345301	7608	15593										
MMP3	4314	broad.mit.edu	37	chr11	102709431	102709431	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatttcctctgatagcccaGaattgatttcctgttaaata	5	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102709431G>T	ENST00000299855.5	-	8	1336	c.1080C>A	c.(1078-1080)ttC>ttA	p.F360L	WTAPP1_ENST00000525739.2_RNA	NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	360					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.F360L(1)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TGATAGCCCAGAATTGATTTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											60	57	58					11																	102709431		2203	4299	6502	102214641	SO:0001583	missense	4314			X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.1080C>A	11.37:g.102709431G>T	ENSP00000299855:p.Phe360Leu		102214641	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	37	CCDS8323.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.08|16.08	3.022908|3.022908	0.54683|0.54683	.|.	.|.	ENSG00000149968|ENSG00000149968	ENST00000299855|ENST00000434103	T|.	0.03035|.	4.07|.	5.07|5.07	5.07|5.07	0.68467|0.68467	Hemopexin/matrixin (2);|.	0.232955|.	0.21996|.	U|.	0.066071|.	T|T	0.79417|0.79417	0.4442|0.4442	M|M	0.88377|0.88377	2.95|2.95	0.38296|0.38296	D|D	0.942841|0.942841	B|.	0.16603|.	0.018|.	B|.	0.35688|.	0.208|.	D|D	0.83792|0.83792	0.0231|0.0231	10|5	0.66056|.	D|.	0.02|.	.|.	13.3264|13.3264	0.60463|0.60463	0.0758:0.0:0.9242:0.0|0.0758:0.0:0.9242:0.0	.|.	360|.	P08254|.	MMP3_HUMAN|.	L|Y	360|4	ENSP00000299855:F360L|.	ENSP00000299855:F360L|.	F|S	-|-	3|2	2|0	MMP3|MMP3	102214641|102214641	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.797000|0.797000	0.45037|0.45037	3.500000|3.500000	0.53318|0.53318	2.793000|2.793000	0.96121|0.96121	0.591000|0.591000	0.81541|0.81541	TTC|TCT		0.393	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422		T	102709431	G	T	102709431	3	4	61	1	0	0	0	0	1	0	0	0	9696	933	33	2	365	2	MMP3	11	102709431	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48216	102709431	32297085	7609	15594										
MMP13	4322	broad.mit.edu	37	chr11	102822868	102822868	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagacctaaggagtggccGaactcatgcgcagcaacaag	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102822868G>A	ENST00000260302.3	-	5	700	c.672C>T	c.(670-672)ttC>ttT	p.F224F	MMP13_ENST00000340273.4_Silent_p.F224F	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	224	Interaction with TIMP2.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.F224F(2)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	AGGAGTGGCCGAACTCATGCG	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	11											167	158	161					11																	102822868		2202	4299	6501	102328078	SO:0001819	synonymous_variant	4322			X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.672C>T	11.37:g.102822868G>A			102328078	A8K846|B2RCZ3|Q6NWN6	Silent	SNP	ENST00000260302.3	37	CCDS8324.1																																																																																				0.443	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		A	102822868	G	A	102822868	2	1	61	1	0	0	0	0	0	0	0	1	9682	1049	37	1		1	MMP13	11	102822868	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113437	102822868	32183648	7610	15595										
DYNC2H1	79659	broad.mit.edu	37	chr11	102984323	102984323	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcaagctgcgacctgaaGtaattactgatgagaatcta	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102984323G>T	ENST00000375735.2	+	2	397	c.253G>T	c.(253-255)Gta>Tta	p.V85L	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.V85L|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.V85L	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	85	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.V85L(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GCGACCTGAAGTAATTACTGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											166	162	163					11																	102984323		1861	4106	5967	102489533	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.253G>T	11.37:g.102984323G>T	ENSP00000364887:p.Val85Leu		102489533	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205376	0.58234	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.33216	1.67;1.42;1.67	6.17	6.17	0.99709	.	0.000000	0.51477	U	0.000081	T	0.35008	0.0917	M	0.76002	2.32	0.47949	D	0.999554	P;B;B	0.36990	0.577;0.077;0.098	B;B;B	0.34301	0.179;0.068;0.099	T	0.08086	-1.0739	10	0.32370	T	0.25	.	14.9567	0.71120	0.0674:0.0:0.9326:0.0	.	85;85;85	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	L	85	ENSP00000364887:V85L;ENSP00000334021:V85L;ENSP00000381167:V85L	ENSP00000334021:V85L	V	+	1	0	DYNC2H1	102489533	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.205000	0.72148	2.941000	0.99782	0.655000	0.94253	GTA		0.333	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	102984323	G	T	102984323	3	4	61	1	0	0	0	0	1	0	0	0	4857	1029	36	2	259	2	DYNC2H1	11	102984323	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161455	102984323	32022193	7611	15596										
DYNC2H1	79659	broad.mit.edu	37	chr11	102985944	102985944	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagttccagttttggataGaacaagctcaccgtggaaat	10	7	1	2	rs35318378		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:102985944G>T	ENST00000375735.2	+	4	685	c.541G>T	c.(541-543)Gaa>Taa	p.E181*	DYNC2H1_ENST00000398093.3_Nonsense_Mutation_p.E181*|DYNC2H1_ENST00000334267.7_Nonsense_Mutation_p.E181*	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	181	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E181*(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GTTTTGGATAGAACAAGCTCA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											65	54	58					11																	102985944		1809	4070	5879	102491154	SO:0001587	stop_gained	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.541G>T	11.37:g.102985944G>T	ENSP00000364887:p.Glu181*		102491154	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Nonsense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	37	6.186634	0.97357	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	.	.	.	5.28	4.35	0.52113	.	0.293642	0.25564	U	0.029814	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	15.1972	0.73100	0.0:0.0:0.858:0.142	.	.	.	.	X	181	.	ENSP00000334021:E181X	E	+	1	0	DYNC2H1	102491154	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.909000	0.92647	1.199000	0.43173	0.655000	0.94253	GAA		0.313	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	102985944	G	T	102985944	4	4	61	1	0	0	0	0	0	1	0	0	4857	943	33	2	555	2	DYNC2H1	11	102985944	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1621	102985944	32020572	7612	15597										
DYNC2H1	79659	broad.mit.edu	37	chr11	103019293	103019293	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgccccagtctgtggaaGaaattggtgatgcaaatcta	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103019293G>T	ENST00000375735.2	+	20	3037	c.2893G>T	c.(2893-2895)Gaa>Taa	p.E965*	DYNC2H1_ENST00000398093.3_Nonsense_Mutation_p.E965*|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	965	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GTCTGTGGAAGAAATTGGTGA	0.338																																																0			11											68	59	62					11																	103019293		1823	4081	5904	102524503	SO:0001587	stop_gained	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2893G>T	11.37:g.103019293G>T	ENSP00000364887:p.Glu965*		102524503	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Nonsense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	42	9.346498	0.99143	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	.	.	.	5.75	5.75	0.90469	.	0.324591	0.26345	U	0.024915	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	19.9462	0.97183	0.0:0.0:1.0:0.0	.	.	.	.	X	965	.	ENSP00000364887:E965X	E	+	1	0	DYNC2H1	102524503	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.648000	0.91062	2.717000	0.92951	0.585000	0.79938	GAA		0.338	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103019293	G	T	103019293	4	4	61	1	0	0	0	0	0	1	0	0	4857	943	33	2	2971	2	DYNC2H1	11	103019293	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33349	103019293	31987223	7613	15598										
DYNC2H1	79659	broad.mit.edu	37	chr11	103029471	103029471	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactactcatgctggaataaGaaattctctactaacaatac	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103029471G>T	ENST00000375735.2	+	27	4337	c.4193G>T	c.(4192-4194)aGa>aTa	p.R1398I	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R1398I|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1398	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GCTGGAATAAGAAATTCTCTA	0.264																																																0			11											15	15	15					11																	103029471		1769	4010	5779	102534681	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4193G>T	11.37:g.103029471G>T	ENSP00000364887:p.Arg1398Ile		102534681	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.060462	0.55432	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.60548	0.18;0.18	5.49	5.49	0.81192	Dynein heavy chain, domain-2 (1);	0.381500	0.16297	U	0.220631	T	0.59473	0.2196	L	0.58302	1.8	0.80722	D	1	P;P	0.43231	0.589;0.801	B;P	0.45449	0.392;0.481	T	0.53837	-0.8382	10	0.23302	T	0.38	.	14.5747	0.68238	0.0719:0.0:0.9281:0.0	.	1398;1398	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	I	1398	ENSP00000364887:R1398I;ENSP00000381167:R1398I	ENSP00000364887:R1398I	R	+	2	0	DYNC2H1	102534681	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.150000	0.64869	2.582000	0.87167	0.655000	0.94253	AGA		0.264	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103029471	G	T	103029471	3	4	61	1	0	0	0	0	1	0	0	0	4857	942	33	2	4299	2	DYNC2H1	11	103029471	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10178	103029471	31977045	7614	15599										
DYNC2H1	79659	broad.mit.edu	37	chr11	103040901	103040901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttaactctcactcaagCcatgaagatgggacttggag	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103040901C>A	ENST00000375735.2	+	33	5177	c.5033C>A	c.(5032-5034)gCc>gAc	p.A1678D	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.A1678D|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1678	AAA 1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTCACTCAAGCCATGAAGATG	0.418																																																0			11											87	83	84					11																	103040901		1884	4109	5993	102546111	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.5033C>A	11.37:g.103040901C>A	ENSP00000364887:p.Ala1678Asp		102546111	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450861	0.84209	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.10099	2.91;2.91	5.54	5.54	0.83059	.	.	.	.	.	T	0.51432	0.1674	H	0.97340	3.985	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.78314	0.991;0.975	T	0.70117	-0.4960	9	0.87932	D	0	.	19.4742	0.94979	0.0:1.0:0.0:0.0	.	1678;1678	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	D	1678	ENSP00000364887:A1678D;ENSP00000381167:A1678D	ENSP00000364887:A1678D	A	+	2	0	DYNC2H1	102546111	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.995000	0.70631	2.602000	0.87976	0.585000	0.79938	GCC		0.418	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	103040901	C	A	103040901	3	1	61	1	0	0	0	0	1	0	0	0	4857	739	26	2	5163	2	DYNC2H1	11	103040901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11430	103040901	31965615	7615	15600										
DYNC2H1	79659	broad.mit.edu	37	chr11	103075663	103075663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgccaggtgttgtggatGgagggttggtccaatagcag	16	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103075663G>T	ENST00000375735.2	+	52	8568	c.8424G>T	c.(8422-8424)atG>atT	p.M2808I	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.M2808I|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2808	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.M241I(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGTTGTGGATGGAGGGTTGGT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	11											58	55	56					11																	103075663		1830	4077	5907	102580873	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8424G>T	11.37:g.103075663G>T	ENSP00000364887:p.Met2808Ile		102580873	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720926	0.48728	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.37235	1.21;1.21	4.85	4.85	0.62838	Dynein heavy chain, P-loop containing D4 domain (1);	0.065981	0.56097	U	0.000023	T	0.39410	0.1077	M	0.64567	1.98	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.15870	0.014;0.007	T	0.32640	-0.9899	10	0.59425	D	0.04	.	16.1472	0.81578	0.0:0.0:1.0:0.0	.	2808;2808	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	I	2808	ENSP00000364887:M2808I;ENSP00000381167:M2808I	ENSP00000364887:M2808I	M	+	3	0	DYNC2H1	102580873	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.568000	0.98166	2.245000	0.73994	0.655000	0.94253	ATG		0.313	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103075663	G	T	103075663	3	4	61	1	0	0	0	0	1	0	0	0	4857	1348	47	2	8630	2	DYNC2H1	11	103075663	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34762	103075663	31930853	7616	15601										
DYNC2H1	79659	broad.mit.edu	37	chr11	103093773	103093773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtattcccatgtcttggAacgaattcatcctttggaaa	7	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103093773A>G	ENST00000375735.2	+	59	9455	c.9311A>G	c.(9310-9312)gAa>gGa	p.E3104G	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.E3104G|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3104	Stalk. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E537G(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CATGTCTTGGAACGAATTCAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	69	71					11																	103093773		1861	4110	5971	102598983	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.9311A>G	11.37:g.103093773A>G	ENSP00000364887:p.Glu3104Gly		102598983	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.841841	0.91197	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.73789	-0.78;-0.78	5.81	5.81	0.92471	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	D	0.88164	0.6363	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.995;0.995	D	0.89448	0.3728	10	0.51188	T	0.08	.	16.1501	0.81611	1.0:0.0:0.0:0.0	.	3104;3104	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	G	3104	ENSP00000364887:E3104G;ENSP00000381167:E3104G	ENSP00000364887:E3104G	E	+	2	0	DYNC2H1	102598983	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.870000	0.92336	2.219000	0.72066	0.533000	0.62120	GAA		0.393	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103093773	A	G	103093773	3	3	61	1	0	0	0	0	1	0	0	0	4857	246	9	4	9545	4	DYNC2H1	11	103093773	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18110	103093773	31912743	7617	15602										
DYNC2H1	79659	broad.mit.edu	37	chr11	103182627	103182627	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctccaggtttaaagaaGaatttaatgcgtacttatga	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103182627G>T	ENST00000375735.2	+	79	11658	c.11514G>T	c.(11512-11514)aaG>aaT	p.K3838N	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.K3845N|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3838	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.K1278N(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GTTTAAAGAAGAATTTAATGC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											56	53	54					11																	103182627		1811	4074	5885	102687837	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11514G>T	11.37:g.103182627G>T	ENSP00000364887:p.Lys3838Asn		102687837	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.174737	0.57692	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621	T;T	0.08458	3.09;3.09	4.69	3.78	0.43462	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.11281	0.0275	L	0.49571	1.57	0.53005	D	0.999966	P;P	0.41131	0.624;0.739	B;B	0.42692	0.395;0.343	T	0.02950	-1.1090	10	0.56958	D	0.05	.	11.2189	0.48842	0.1557:0.0:0.8443:0.0	.	3838;3845	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	N	3838;3845;84	ENSP00000364887:K3838N;ENSP00000381167:K3845N	ENSP00000364887:K3838N	K	+	3	2	DYNC2H1	102687837	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	3.072000	0.50049	0.963000	0.38082	0.555000	0.69702	AAG		0.323	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103182627	G	T	103182627	3	4	61	1	0	0	0	0	1	0	0	0	4857	933	33	2	11853	2	DYNC2H1	11	103182627	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88854	103182627	31823889	7618	15603										
DDI1	414301	broad.mit.edu	37	chr11	103908679	103908679	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggatggtaagtgggcaaGatgagtcttcggacaaggaa	15	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:103908679G>A	ENST00000302259.3	+	1	1372	c.1129G>A	c.(1129-1131)Gat>Aat	p.D377N	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	377							aspartic-type endopeptidase activity (GO:0004190)	p.D377N(2)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AAGTGGGCAAGATGAGTCTTC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	11											62	63	63					11																	103908679		2202	4299	6501	103413889	SO:0001583	missense	414301				CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.1129G>A	11.37:g.103908679G>A	ENSP00000302805:p.Asp377Asn		103413889	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.905993	0.33628	.	.	ENSG00000170967	ENST00000302259	T	0.23348	1.91	4.86	3.94	0.45596	.	0.180454	0.46442	D	0.000285	T	0.23330	0.0564	L	0.47716	1.5	0.29947	N	0.820538	P	0.34800	0.469	B	0.36378	0.223	T	0.11036	-1.0604	10	0.32370	T	0.25	-1.7126	11.3731	0.49711	0.0:0.1825:0.8175:0.0	.	377	Q8WTU0	DDI1_HUMAN	N	377	ENSP00000302805:D377N	ENSP00000302805:D377N	D	+	1	0	DDI1	103413889	1.000000	0.71417	0.030000	0.17652	0.005000	0.04900	3.719000	0.54926	1.402000	0.46780	0.655000	0.94253	GAT		0.448	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		A	103908679	G	A	103908679	3	1	61	1	0	0	0	0	1	0	0	0	4334	942	33	3	1131	3	DDI1	11	103908679	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	726052	103908679	31097837	7619	15604										
CASP4	837	broad.mit.edu	37	chr11	104820490	104820490	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtagcaaatgccctcagCgctgactccatatcctgtaa	8	13	1	1	rs538762722	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:104820490C>T	ENST00000444739.2	-	5	1471	c.561G>A	c.(559-561)gcG>gcA	p.A187A	CASP4_ENST00000393150.3_Silent_p.A131A|CASP4_ENST00000531333.1_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	187					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)	p.A187A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		ATGCCCTCAGCGCTGACTCCA	0.473													.|||	3	0.000599042	0	0	5008	,	,		20573	0		0	False		,,,				2504	0.0031															1	Substitution - coding silent(1)	large_intestine(1)	11											113	101	105					11																	104820490		2202	4299	6501	104325700	SO:0001819	synonymous_variant	837			U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.561G>A	11.37:g.104820490C>T			104325700	A2NHL8|A2NHM0	Silent	SNP	ENST00000444739.2	37	CCDS8327.1																																																																																				0.473	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		T	104820490	C	T	104820490	2	4	61	1	0	0	0	0	0	0	0	1	2679	755	27	1		1	CASP4	11	104820490	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	911811	104820490	30186026	7620	15605										
CASP4	837	broad.mit.edu	37	chr11	104825474	104825474	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaaaaaatccagtcttacCttttttattgggggatattt	7	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:104825474C>A	ENST00000444739.2	-	2	1172	c.262G>T	c.(262-264)Gct>Tct	p.A88S	CASP4_ENST00000393150.3_Splice_Site_p.A32S|CASP4_ENST00000531333.1_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	88	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)	p.A88S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		CCAGTCTTACCTTTTTTATTG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	11											98	102	101					11																	104825474		2201	4299	6500	104330684	SO:0001630	splice_region_variant	837			U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.262+1G>T	11.37:g.104825474C>A			104330684	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.291502	0.23564	.	.	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546;ENST00000417440	T;T;T	0.09445	4.74;4.32;2.98	3.6	3.6	0.41247	DEATH-like (1);Caspase Recruitment (1);	0.273585	0.34362	N	0.004023	T	0.09202	0.0227	L	0.31926	0.97	0.54753	D	0.999986	P;B;B	0.42078	0.77;0.025;0.005	B;B;B	0.42087	0.375;0.1;0.047	T	0.21177	-1.0253	9	.	.	.	.	9.1965	0.37231	0.0:0.7765:0.2235:0.0	.	88;88;88	B4DJH5;B4E2D2;P49662	.;.;CASP4_HUMAN	S	88;32;41;88	ENSP00000388566:A88S;ENSP00000376857:A32S;ENSP00000401673:A88S	.	A	-	1	0	CASP4	104330684	0.982000	0.34865	0.885000	0.34714	0.049000	0.14656	0.791000	0.26915	1.988000	0.58038	0.655000	0.94253	GCT		0.393	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	Missense_Mutation	A	104825474	C	A	104825474	5	1	61	1	0	0	0	0	0	0	1	0	2679	695	24	2	899	2	CASP4	11	104825474	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4984	104825474	30181042	7621	15606										
CASP4	837	broad.mit.edu	37	chr11	104825607	104825607	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttagcatcgtaatatttCtttttttcctcttccttcca	3	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:104825607C>A	ENST00000444739.2	-	2	1039	c.129G>T	c.(127-129)aaG>aaT	p.K43N	CASP4_ENST00000393150.3_5'UTR|CASP4_ENST00000531333.1_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	43	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)	p.K43N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		CGTAATATTTCTTTTTTTCCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											211	196	202					11																	104825607		2202	4299	6501	104330817	SO:0001583	missense	837			U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.129G>T	11.37:g.104825607C>A	ENSP00000388566:p.Lys43Asn		104330817	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872435	0.33069	.	.	ENSG00000196954	ENST00000444739;ENST00000417440	T;T	0.21031	2.03;2.03	3.6	1.3	0.21679	DEATH-like (2);Caspase Recruitment (3);	0.879225	0.09919	N	0.738728	T	0.27866	0.0686	L	0.43923	1.385	0.09310	N	0.999995	D;D;P	0.63880	0.993;0.966;0.473	P;P;P	0.60345	0.873;0.666;0.449	T	0.14254	-1.0479	10	0.45353	T	0.12	.	2.9929	0.05989	0.0:0.2698:0.2338:0.4963	.	43;43;43	B4DJH5;B4E2D2;P49662	.;.;CASP4_HUMAN	N	43	ENSP00000388566:K43N;ENSP00000401673:K43N	ENSP00000401673:K43N	K	-	3	2	CASP4	104330817	0.004000	0.15560	0.017000	0.16124	0.001000	0.01503	0.271000	0.18626	0.558000	0.29135	-0.302000	0.09304	AAG		0.408	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		A	104825607	C	A	104825607	3	1	61	1	0	0	0	0	1	0	0	0	2679	912	32	2	1032	2	CASP4	11	104825607	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133	104825607	30180909	7622	15607										
GRIA4	2893	broad.mit.edu	37	chr11	105483062	105483062	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcgattagcaatttttCttcataacaccagccccaat	3	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105483062C>T	ENST00000530497.1	+	2	148	c.148C>T	c.(148-150)Ctt>Ttt	p.L50F	GRIA4_ENST00000428631.2_Missense_Mutation_p.L50F|GRIA4_ENST00000527669.1_Missense_Mutation_p.L50F|GRIA4_ENST00000282499.5_Missense_Mutation_p.L50F|GRIA4_ENST00000525187.1_Missense_Mutation_p.L50F|GRIA4_ENST00000393125.2_Missense_Mutation_p.L50F|GRIA4_ENST00000393127.2_Missense_Mutation_p.L50F			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	50					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.L50F(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AGCAATTTTTCTTCATAACAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	11											145	125	132					11																	105483062		2202	4299	6501	104988272	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.148C>T	11.37:g.105483062C>T	ENSP00000435775:p.Leu50Phe		104988272	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507128	0.85282	.	.	ENSG00000152578	ENST00000527177;ENST00000393125;ENST00000531986;ENST00000282499;ENST00000393127;ENST00000527669;ENST00000525921;ENST00000428631;ENST00000531011;ENST00000530497;ENST00000525187	D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	5.81	5.81	0.92471	Extracellular ligand-binding receptor (1);	0.203425	0.33792	N	0.004551	D	0.88119	0.6351	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D	0.89917	0.996;1.0;1.0;0.999;0.997	D;D;D;D;D	0.97110	0.96;0.999;1.0;0.988;0.986	D	0.87487	0.2424	10	0.49607	T	0.09	.	20.0784	0.97758	0.0:1.0:0.0:0.0	.	50;50;80;50;50	P48058;G3V164;Q59GL7;Q86XE8;E9PQN1	GRIA4_HUMAN;.;.;.;.	F	50	ENSP00000376833:L50F;ENSP00000282499:L50F;ENSP00000376835:L50F;ENSP00000415551:L50F;ENSP00000432443:L50F;ENSP00000435775:L50F;ENSP00000432180:L50F	ENSP00000282499:L50F	L	+	1	0	GRIA4	104988272	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.066000	0.71185	2.736000	0.93811	0.655000	0.94253	CTT		0.423	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105483062	C	T	105483062	3	4	61	1	0	0	0	0	1	0	0	0	6791	913	32	3	154	3	GRIA4	11	105483062	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	657455	105483062	29523454	7623	15608										
GRIA4	2893	broad.mit.edu	37	chr11	105795128	105795128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttttttctcttatagaaaGcagagattgctattgcccct	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105795128G>A	ENST00000530497.1	+	11	1480	c.1480G>A	c.(1480-1482)Gca>Aca	p.A494T	GRIA4_ENST00000282499.5_Missense_Mutation_p.A494T|GRIA4_ENST00000525187.1_Missense_Mutation_p.A494T|GRIA4_ENST00000393127.2_Missense_Mutation_p.A494T			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	494					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.A494T(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CTTATAGAAAGCAGAGATTGC	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	11											87	89	88					11																	105795128		2202	4299	6501	105300338	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1480G>A	11.37:g.105795128G>A	ENSP00000435775:p.Ala494Thr		105300338	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	33	5.233082	0.95207	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.76	5.76	0.90799	Ionotropic glutamate receptor (1);	0.000000	0.64402	D	0.000002	T	0.73353	0.3576	M	0.89904	3.07	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.987;0.998	T	0.77683	-0.2496	10	0.87932	D	0	.	20.3242	0.98691	0.0:0.0:1.0:0.0	.	494;494	P48058;G3V164	GRIA4_HUMAN;.	T	494	ENSP00000282499:A494T;ENSP00000376835:A494T;ENSP00000435775:A494T;ENSP00000432180:A494T	ENSP00000282499:A494T	A	+	1	0	GRIA4	105300338	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.813000	0.99286	2.882000	0.98803	0.655000	0.94253	GCA		0.388	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105795128	G	A	105795128	3	1	61	1	0	0	0	0	1	0	0	0	6791	971	34	3	1559	3	GRIA4	11	105795128	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	312066	105795128	29211388	7624	15609										
GRIA4	2893	broad.mit.edu	37	chr11	105797481	105797481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttagatccctctcaggtcGaattgttggaggtgtttggt	13	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105797481G>A	ENST00000530497.1	+	12	1862	c.1862G>A	c.(1861-1863)cGa>cAa	p.R621Q	GRIA4_ENST00000282499.5_Missense_Mutation_p.R621Q|GRIA4_ENST00000525187.1_Missense_Mutation_p.R621Q|GRIA4_ENST00000393127.2_Missense_Mutation_p.R621Q			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	621					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R621Q(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CTCTCAGGTCGAATTGTTGGA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	11											124	124	124					11																	105797481		2202	4298	6500	105302691	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1862G>A	11.37:g.105797481G>A	ENSP00000435775:p.Arg621Gln		105302691	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	35	5.481846	0.96307	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	5.6	5.6	0.85130	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000010	D	0.91002	0.7170	H	0.95114	3.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.92915	0.6350	10	0.87932	D	0	.	19.9855	0.97347	0.0:0.0:1.0:0.0	.	621;621	P48058;G3V164	GRIA4_HUMAN;.	Q	621	ENSP00000282499:R621Q;ENSP00000376835:R621Q;ENSP00000435775:R621Q;ENSP00000432180:R621Q	ENSP00000282499:R621Q	R	+	2	0	GRIA4	105302691	1.000000	0.71417	0.997000	0.53966	0.924000	0.55760	9.813000	0.99286	2.806000	0.96561	0.655000	0.94253	CGA		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105797481	G	A	105797481	3	1	61	1	0	0	0	0	1	0	0	0	6791	1058	37	1	1945	1	GRIA4	11	105797481	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2353	105797481	29209035	7625	15610										
GRIA4	2893	broad.mit.edu	37	chr11	105804508	105804508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgatcagcagagccatcaGtattcactaggactacagct	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105804508G>T	ENST00000530497.1	+	13	2107	c.2107G>T	c.(2107-2109)Gta>Tta	p.V703L	GRIA4_ENST00000282499.5_Missense_Mutation_p.V703L|AP000673.1_ENST00000583628.1_RNA|GRIA4_ENST00000525187.1_Missense_Mutation_p.V703L|GRIA4_ENST00000393127.2_Missense_Mutation_p.V703L			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	703					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.V703L(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AGAGCCATCAGTATTCACTAG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	11											64	58	60					11																	105804508		2202	4299	6501	105309718	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2107G>T	11.37:g.105804508G>T	ENSP00000435775:p.Val703Leu		105309718	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620340	0.87460	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187;ENST00000539249	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.51	5.51	0.81932	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000017	T	0.66436	0.2789	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.995	T	0.68903	-0.5286	10	0.87932	D	0	.	19.4254	0.94740	0.0:0.0:1.0:0.0	.	703;703	P48058;G3V164	GRIA4_HUMAN;.	L	703;703;703;703;8	ENSP00000282499:V703L;ENSP00000376835:V703L;ENSP00000435775:V703L;ENSP00000432180:V703L	ENSP00000282499:V703L	V	+	1	0	GRIA4	105309718	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	9.754000	0.98908	2.595000	0.87683	0.591000	0.81541	GTA		0.413	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105804508	G	T	105804508	3	4	61	1	0	0	0	0	1	0	0	0	6791	1029	36	2	2194	2	GRIA4	11	105804508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7027	105804508	29202008	7626	15611										
GRIA4	2893	broad.mit.edu	37	chr11	105850445	105850445	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagttcaggattggctgtCattgcatcggacctaccata	9	10	2	0	rs149657082		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105850445C>A	ENST00000530497.1	+	16	2688	c.2688C>A	c.(2686-2688)gtC>gtA	p.V896V	GRIA4_ENST00000282499.5_Silent_p.V896V|GRIA4_ENST00000533094.1_3'UTR|GRIA4_ENST00000525187.1_3'UTR|GRIA4_ENST00000393127.2_3'UTR			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	896					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.V896V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GATTGGCTGTCATTGCATCGG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	11											72	61	64					11																	105850445		2201	4299	6500	105355655	SO:0001819	synonymous_variant	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2688C>A	11.37:g.105850445C>A			105355655	Q86XE8	Silent	SNP	ENST00000530497.1	37	CCDS8333.1																																																																																				0.502	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105850445	C	A	105850445	2	1	61	1	0	0	0	0	0	0	0	1	6791	813	29	2		2	GRIA4	11	105850445	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45937	105850445	29156071	7627	15612										
KBTBD3	143879	broad.mit.edu	37	chr11	105923757	105923757	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcaccacctaatatataAattttatcttcaattccaat	0	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105923757A>G	ENST00000526793.1	-	3	1818	c.1659T>C	c.(1657-1659)atT>atC	p.I553I	KBTBD3_ENST00000531837.1_Silent_p.I553I|KBTBD3_ENST00000534815.1_Silent_p.I474I	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	549								p.I553I(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		CTAATATATAAATTTTATCTT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	11											75	76	76					11																	105923757		2201	4298	6499	105428967	SO:0001819	synonymous_variant	143879			AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1659T>C	11.37:g.105923757A>G			105428967	Q6N066|Q86X38|Q96NK5	Silent	SNP	ENST00000526793.1	37	CCDS8334.1																																																																																				0.398	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		G	105923757	A	G	105923757	2	3	61	1	0	0	0	0	0	0	0	1	8015	10	1	4		4	KBTBD3	11	105923757	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73312	105923757	29082759	7628	15613										
KBTBD3	143879	broad.mit.edu	37	chr11	105924155	105924155	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaagattcaacatctaagaGacttttaatgtcccgggatc	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105924155G>T	ENST00000526793.1	-	3	1420	c.1261C>A	c.(1261-1263)Ctc>Atc	p.L421I	KBTBD3_ENST00000531837.1_Missense_Mutation_p.L421I|KBTBD3_ENST00000534815.1_Missense_Mutation_p.L342I	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	417								p.L421I(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		ACATCTAAGAGACTTTTAATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											45	44	44					11																	105924155		2201	4296	6497	105429365	SO:0001583	missense	143879			AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1261C>A	11.37:g.105924155G>T	ENSP00000436262:p.Leu421Ile		105429365	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	37	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.286647	0.40494	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.81330	-1.48;-1.48;-1.48	5.97	5.97	0.96955	Kelch-type beta propeller (1);	0.112845	0.64402	D	0.000008	D	0.85978	0.5823	M	0.65975	2.015	0.45390	D	0.998373	P;P	0.43431	0.807;0.767	P;P	0.49752	0.497;0.621	D	0.85532	0.1210	10	0.56958	D	0.05	.	20.4135	0.99023	0.0:0.0:1.0:0.0	.	421;417	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	I	342;421;421	ENSP00000431910:L342I;ENSP00000436262:L421I;ENSP00000432163:L421I	ENSP00000436262:L421I	L	-	1	0	KBTBD3	105429365	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	3.446000	0.52928	2.835000	0.97688	0.591000	0.81541	CTC		0.388	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		T	105924155	G	T	105924155	3	4	61	1	0	0	0	0	1	0	0	0	8015	942	33	2	581	2	KBTBD3	11	105924155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	398	105924155	29082361	7629	15614										
KBTBD3	143879	broad.mit.edu	37	chr11	105924350	105924350	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatgcagtcgaaccgttcGacaacatttccctttgcaac	6	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105924350G>A	ENST00000526793.1	-	3	1225	c.1066C>T	c.(1066-1068)Cga>Tga	p.R356*	KBTBD3_ENST00000531837.1_Nonsense_Mutation_p.R356*|KBTBD3_ENST00000534815.1_Nonsense_Mutation_p.R277*	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	352								p.R356*(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		CGAACCGTTCGACAACATTTC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											101	93	96					11																	105924350		2201	4298	6499	105429560	SO:0001587	stop_gained	143879			AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1066C>T	11.37:g.105924350G>A	ENSP00000436262:p.Arg356*		105429560	Q6N066|Q86X38|Q96NK5	Nonsense_Mutation	SNP	ENST00000526793.1	37	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	G	38	6.732021	0.97796	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	.	.	.	5.97	2.17	0.27698	.	0.083093	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4766	0.67551	0.0:0.0:0.4791:0.5209	.	.	.	.	X	277;356;356	.	ENSP00000436262:R356X	R	-	1	2	KBTBD3	105429560	1.000000	0.71417	0.999000	0.59377	0.283000	0.27025	2.078000	0.41567	0.489000	0.27749	-0.335000	0.08231	CGA		0.423	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		A	105924350	G	A	105924350	4	1	61	1	0	0	0	0	0	1	0	0	8015	1066	37	1	776	1	KBTBD3	11	105924350	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	195	105924350	29082166	7630	15615										
AASDHPPT	60496	broad.mit.edu	37	chr11	105950319	105950319	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactcatcgaatccttacccGaatttcaactttaacatctc	3	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:105950319G>A	ENST00000278618.4	+	2	531	c.309G>A	c.(307-309)ccG>ccA	p.P103P	KBTBD3_ENST00000531837.1_5'Flank|KBTBD3_ENST00000526793.1_5'Flank|KBTBD3_ENST00000534815.1_5'Flank	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	103					macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)	p.P103P(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		ATCCTTACCCGAATTTCAACT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	11											110	109	109					11																	105950319		2201	4299	6500	105455529	SO:0001819	synonymous_variant	60496			AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.309G>A	11.37:g.105950319G>A			105455529	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Silent	SNP	ENST00000278618.4	37	CCDS31664.1																																																																																				0.393	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423		A	105950319	G	A	105950319	2	1	61	1	0	0	0	0	0	0	0	1	23	1045	37	1		1	AASDHPPT	11	105950319	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25969	105950319	29056197	7631	15616										
GUCY1A2	2977	broad.mit.edu	37	chr11	106681181	106681181	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgattctggaacatggatCatttgtcctttgacttccat	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:106681181C>A	ENST00000526355.2	-	5	1698	c.1230G>T	c.(1228-1230)atG>atT	p.M410I	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.M431I|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.M410I	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	410					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.M410I(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	GAACATGGATCATTTGTCCTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											73	78	77					11																	106681181		2201	4298	6499	106186391	SO:0001583	missense	2977			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.1230G>T	11.37:g.106681181C>A	ENSP00000431245:p.Met410Ile		106186391	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861269	0.51482	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.92446	-3.04;-3.04;-3.04	5.49	5.49	0.81192	Haem NO binding associated (1);	0.000000	0.52532	U	0.000066	D	0.96116	0.8734	M	0.87827	2.91	0.80722	D	1	D;P;P	0.65815	0.995;0.911;0.476	P;P;B	0.60012	0.867;0.756;0.159	D	0.96458	0.9339	10	0.66056	D	0.02	.	18.3596	0.90371	0.0:1.0:0.0:0.0	.	431;410;410	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	I	410;410;431	ENSP00000431245:M410I;ENSP00000282249:M410I;ENSP00000344874:M431I	ENSP00000282249:M410I	M	-	3	0	GUCY1A2	106186391	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	7.487000	0.81328	2.563000	0.86464	0.650000	0.86243	ATG		0.378	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106681181	C	A	106681181	3	1	61	1	0	0	0	0	1	0	0	0	6914	826	29	2	984	2	GUCY1A2	11	106681181	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	730862	106681181	28325335	7632	15617										
GUCY1A2	2977	broad.mit.edu	37	chr11	106810509	106810509	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatattagtattttcacattCtttgataaggaaagtaagac	7	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:106810509C>A	ENST00000526355.2	-	4	1351	c.883G>T	c.(883-885)Gaa>Taa	p.E295*	GUCY1A2_ENST00000347596.2_Nonsense_Mutation_p.E295*|GUCY1A2_ENST00000282249.2_Nonsense_Mutation_p.E295*	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	295					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.E295*(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TTTTCACATTCTTTGATAAGG	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											92	91	91					11																	106810509		2201	4298	6499	106315719	SO:0001587	stop_gained	2977			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.883G>T	11.37:g.106810509C>A	ENSP00000431245:p.Glu295*		106315719	A1L4C4|B7ZLT5	Nonsense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	40	8.476145	0.98827	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	.	.	.	5.45	4.54	0.55810	.	0.144593	0.30383	U	0.009750	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	15.0332	0.71723	0.0:0.8476:0.1524:0.0	.	.	.	.	X	295	.	ENSP00000282249:E295X	E	-	1	0	GUCY1A2	106315719	1.000000	0.71417	0.998000	0.56505	0.898000	0.52572	3.102000	0.50291	1.298000	0.44778	0.591000	0.81541	GAA		0.443	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106810509	C	A	106810509	4	1	61	1	0	0	0	0	0	1	0	0	6914	922	32	2	1335	2	GUCY1A2	11	106810509	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	129328	106810509	28196007	7633	15618										
GUCY1A2	2977	broad.mit.edu	37	chr11	106810884	106810884	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttcaccaaatcttttttGaatttcctcaaacttcaaac	1	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:106810884G>T	ENST00000526355.2	-	4	976	c.508C>A	c.(508-510)Caa>Aaa	p.Q170K	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.Q170K|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.Q170K	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	170					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.Q170K(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	AATCTTTTTTGAATTTCCTCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	11											35	41	39					11																	106810884		2137	4284	6421	106316094	SO:0001583	missense	2977			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.508C>A	11.37:g.106810884G>T	ENSP00000431245:p.Gln170Lys		106316094	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	7.304	0.613620	0.14066	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	T;T;T	0.43294	0.95;0.95;0.95	5.17	5.17	0.71159	Heme-NO binding (1);NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.42053	U	0.000768	T	0.28665	0.0710	N	0.12746	0.255	0.53005	D	0.999967	P;B;B	0.40144	0.704;0.019;0.201	B;B;B	0.39217	0.294;0.028;0.087	T	0.07271	-1.0781	10	0.25106	T	0.35	.	17.6474	0.88152	0.0:0.0:1.0:0.0	.	170;170;170	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	K	170	ENSP00000431245:Q170K;ENSP00000282249:Q170K;ENSP00000344874:Q170K	ENSP00000282249:Q170K	Q	-	1	0	GUCY1A2	106316094	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.670000	0.83925	2.400000	0.81607	0.591000	0.81541	CAA		0.328	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			T	106810884	G	T	106810884	3	4	61	1	0	0	0	0	1	0	0	0	6914	1299	45	2	1710	2	GUCY1A2	11	106810884	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	375	106810884	28195632	7634	15619										
CWF19L2	143884	broad.mit.edu	37	chr11	107205633	107205633	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgatatcttttgaagagaGatctatcaacttcttgttca	6	7	6	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:107205633G>A	ENST00000282251.5	-	16	2440	c.2413C>T	c.(2413-2415)Ctc>Ttc	p.L805F		NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	805							catalytic activity (GO:0003824)	p.L651F(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		TTTGAAGAGAGATCTATCAAC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	11											109	119	115					11																	107205633		2201	4297	6498	106710843	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2413C>T	11.37:g.107205633G>A	ENSP00000282251:p.Leu805Phe		106710843	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	G	19.76	3.888038	0.72524	.	.	ENSG00000152404	ENST00000282251;ENST00000409771	T	0.28666	1.6	5.24	2.33	0.28932	Histidine triad-like motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.40119	0.1104	L	0.49256	1.55	0.80722	D	1	P	0.51240	0.943	P	0.59221	0.854	T	0.05289	-1.0894	10	0.38643	T	0.18	-5.864	8.9033	0.35507	0.2441:0.0:0.7559:0.0	.	805	Q2TBE0	C19L2_HUMAN	F	805;63	ENSP00000282251:L805F	ENSP00000282251:L805F	L	-	1	0	CWF19L2	106710843	1.000000	0.71417	0.845000	0.33349	0.894000	0.52154	4.753000	0.62183	0.208000	0.20626	0.655000	0.94253	CTC		0.318	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		A	107205633	G	A	107205633	3	1	61	1	0	0	0	0	1	0	0	0	4078	942	33	3	283	3	CWF19L2	11	107205633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	394749	107205633	27800883	7635	15620										
CWF19L2	143884	broad.mit.edu	37	chr11	107263525	107263525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctgtctctttcttcttcCtccttgtgattccagagatt	5	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:107263525C>T	ENST00000282251.5	-	11	1741	c.1714G>A	c.(1714-1716)Gga>Aga	p.G572R	CWF19L2_ENST00000433523.1_Missense_Mutation_p.G572R	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	572							catalytic activity (GO:0003824)	p.G418R(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		TTTCTTCTTCCTCCTTGTGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											116	111	112					11																	107263525		2201	4298	6499	106768735	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1714G>A	11.37:g.107263525C>T	ENSP00000282251:p.Gly572Arg		106768735	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	C	13.49	2.254096	0.39896	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.19669	2.85;2.13	6.03	4.16	0.48862	.	0.052725	0.85682	D	0.000000	T	0.21103	0.0508	L	0.58428	1.81	0.45946	D	0.998779	B	0.14805	0.011	B	0.17722	0.019	T	0.03077	-1.1075	10	0.31617	T	0.26	-14.9163	10.0893	0.42436	0.0:0.7865:0.1385:0.075	.	572	Q2TBE0	C19L2_HUMAN	R	572	ENSP00000282251:G572R;ENSP00000387533:G572R	ENSP00000282251:G572R	G	-	1	0	CWF19L2	106768735	1.000000	0.71417	0.964000	0.40570	0.864000	0.49448	1.214000	0.32419	0.869000	0.35703	0.557000	0.71058	GGA		0.383	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		T	107263525	C	T	107263525	3	4	61	1	0	0	0	0	1	0	0	0	4078	690	24	3	1002	3	CWF19L2	11	107263525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57892	107263525	27742991	7636	15621										
CWF19L2	143884	broad.mit.edu	37	chr11	107299946	107299946	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagacccaggtctcttatCtttttcatcaccaataaatt	3	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:107299946C>A	ENST00000282251.5	-	8	1039	c.1012G>T	c.(1012-1014)Gat>Tat	p.D338Y	CWF19L2_ENST00000433523.1_Missense_Mutation_p.D338Y	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	338							catalytic activity (GO:0003824)	p.D184Y(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		GGTCTCTTATCTTTTTCATCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	11											102	103	102					11																	107299946		2201	4298	6499	106805156	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1012G>T	11.37:g.107299946C>A	ENSP00000282251:p.Asp338Tyr		106805156	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859231	0.32884	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.23147	1.92;1.92	5.38	4.47	0.54385	.	0.488362	0.23157	N	0.051293	T	0.24005	0.0581	L	0.55103	1.725	0.32434	N	0.547689	B	0.13594	0.008	B	0.15870	0.014	T	0.20773	-1.0265	10	0.21014	T	0.42	-0.1024	11.6612	0.51347	0.0:0.9173:0.0:0.0827	.	338	Q2TBE0	C19L2_HUMAN	Y	338	ENSP00000282251:D338Y;ENSP00000387533:D338Y	ENSP00000282251:D338Y	D	-	1	0	CWF19L2	106805156	0.959000	0.32827	0.702000	0.30337	0.075000	0.17131	1.961000	0.40432	1.393000	0.46605	0.591000	0.81541	GAT		0.333	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		A	107299946	C	A	107299946	3	1	61	1	0	0	0	0	1	0	0	0	4078	913	32	2	1716	2	CWF19L2	11	107299946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36421	107299946	27706570	7637	15622										
CWF19L2	143884	broad.mit.edu	37	chr11	107300048	107300048	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattttactaagtctgattCtctactttcttgacaatttt	3	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:107300048C>A	ENST00000282251.5	-	8	937	c.910G>T	c.(910-912)Gaa>Taa	p.E304*	CWF19L2_ENST00000433523.1_Nonsense_Mutation_p.E304*	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	304							catalytic activity (GO:0003824)	p.E150*(1)		endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		AAGTCTGATTCTCTACTTTCT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											85	81	82					11																	107300048		2201	4293	6494	106805258	SO:0001587	stop_gained	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.910G>T	11.37:g.107300048C>A	ENSP00000282251:p.Glu304*		106805258	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Nonsense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564545	0.86439	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	.	.	.	5.38	1.79	0.24919	.	1.224140	0.05213	N	0.507049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-4.1984	7.5964	0.28050	0.0:0.2459:0.0:0.7541	.	.	.	.	X	304	.	ENSP00000282251:E304X	E	-	1	0	CWF19L2	106805258	0.980000	0.34600	0.515000	0.27774	0.916000	0.54674	1.978000	0.40598	0.421000	0.25980	-0.383000	0.06682	GAA		0.343	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		A	107300048	C	A	107300048	4	1	61	1	0	0	0	0	0	1	0	0	4078	922	32	2	1818	2	CWF19L2	11	107300048	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102	107300048	27706468	7638	15623										
ELMOD1	55531	broad.mit.edu	37	chr11	107502319	107502319	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccagctgttgcagacttCtgtgagtgttcaccccgacg	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:107502319C>A	ENST00000265840.7	+	5	471	c.206C>A	c.(205-207)tCt>tAt	p.S69Y	ELMOD1_ENST00000531234.1_Missense_Mutation_p.S63Y|ELMOD1_ENST00000443271.2_Missense_Mutation_p.S69Y	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	69					phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)	p.S69Y(1)		endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		TTGCAGACTTCTGTGAGTGTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	11											60	55	56					11																	107502319		1848	4071	5919	107007529	SO:0001583	missense	55531			AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"ELMO domain containing 1"			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.206C>A	11.37:g.107502319C>A	ENSP00000265840:p.Ser69Tyr		107007529	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	37	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.166052	0.38217	.	.	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.66	5.66	0.87406	.	0.180158	0.49305	D	0.000149	T	0.40956	0.1138	N	0.08118	0	0.50313	D	0.999869	P;P	0.47604	0.836;0.898	B;P	0.45343	0.285;0.477	T	0.33777	-0.9855	9	0.29301	T	0.29	.	19.736	0.96205	0.0:1.0:0.0:0.0	.	69;69	Q8N336;G5E9S5	ELMD1_HUMAN;.	Y	63;69;69	.	ENSP00000265840:S69Y	S	+	2	0	ELMOD1	107007529	1.000000	0.71417	0.980000	0.43619	0.906000	0.53458	5.364000	0.66110	2.669000	0.90835	0.591000	0.81541	TCT		0.363	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712		A	107502319	C	A	107502319	3	1	61	1	0	0	0	0	1	0	0	0	5081	913	32	2	220	2	ELMOD1	11	107502319	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	202271	107502319	27504197	7639	15624										
NPAT	4863	broad.mit.edu	37	chr11	108032275	108032275	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttttgaattttctggatTtttctgtctttctacatcgc	6	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108032275T>G	ENST00000278612.8	-	17	3643	c.3538A>C	c.(3538-3540)Aat>Cat	p.N1180H		NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	1180					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.N1180H(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		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)		TTTTCTGGATTTTTCTGTCTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	11											200	193	195					11																	108032275		1818	4078	5896	107537485	SO:0001583	missense	4863			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.3538A>C	11.37:g.108032275T>G	ENSP00000278612:p.Asn1180His		107537485	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.78|17.78	3.472361|3.472361	0.63737|0.63737	.|.	.|.	ENSG00000149308|ENSG00000149308	ENST00000527296|ENST00000278612	T|T	0.55760|0.04317	0.5|3.65	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	.|0.315620	.|0.34879	.|N	.|0.003609	T|T	0.13286|0.13286	0.0322|0.0322	L|L	0.60455|0.60455	1.87|1.87	0.37943|0.37943	D|D	0.932406|0.932406	.|P	.|0.50617	.|0.937	.|P	.|0.55999	.|0.789	T|T	0.03364|0.03364	-1.1044|-1.1044	7|10	0.66056|0.38643	D|T	0.02|0.18	-16.1374|-16.1374	12.471|12.471	0.55787|0.55787	0.0:0.0:0.1394:0.8606|0.0:0.0:0.1394:0.8606	.|.	.|1180	.|Q14207	.|NPAT_HUMAN	N|H	178|1180	ENSP00000436510:K178N|ENSP00000278612:N1180H	ENSP00000436510:K178N|ENSP00000278612:N1180H	K|N	-|-	3|1	2|0	NPAT|NPAT	107537485|107537485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	2.532000|2.532000	0.45659|0.45659	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	AAA|AAT		0.363	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		G	108032275	T	G	108032275	3	3	61	1	0	0	0	0	1	0	0	0	10597	1841	64	4	753	4	NPAT	11	108032275	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	529956	108032275	26974241	7640	15625										
NPAT	4863	broad.mit.edu	37	chr11	108043304	108043304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggctgaatcccctacttCggcatatacaacagcaccta	7	13	0	2	rs200624398		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108043304C>T	ENST00000278612.8	-	13	2512	c.2407G>A	c.(2407-2409)Gaa>Aaa	p.E803K	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	803					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.E803K(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		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)		TCCCCTACTTCGGCATATACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	LYS/GLU	0,3690		0,0,1845	71	65	67		2407	5.8	0.9	11		67	1,8209		0,1,4104	no	missense	NPAT	NM_002519.2	56	0,1,5949	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	803/1428	108043304	1,11899	1845	4105	5950	107548514	SO:0001583	missense	4863			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.2407G>A	11.37:g.108043304C>T	ENSP00000278612:p.Glu803Lys		107548514	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.144256	0.57044	0.0	1.22E-4	ENSG00000149308	ENST00000278612	T	0.04360	3.64	5.83	5.83	0.93111	.	0.309039	0.30969	N	0.008512	T	0.03871	0.0109	N	0.08118	0	0.29333	N	0.86655	D;D	0.56287	0.975;0.975	B;B	0.42851	0.4;0.4	T	0.44862	-0.9300	10	0.27082	T	0.32	-8.1251	17.6048	0.88035	0.0:1.0:0.0:0.0	.	803;803	B9EG70;Q14207	.;NPAT_HUMAN	K	803	ENSP00000278612:E803K	ENSP00000278612:E803K	E	-	1	0	NPAT	107548514	0.998000	0.40836	0.923000	0.36655	0.605000	0.37080	3.708000	0.54845	2.747000	0.94245	0.650000	0.86243	GAA		0.368	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		T	108043304	C	T	108043304	3	4	61	1	0	0	0	0	1	0	0	0	10597	893	31	1	1900	1	NPAT	11	108043304	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11029	108043304	26963212	7641	15626										
ATM	472	broad.mit.edu	37	chr11	108139322	108139322	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctagaacctaccaaatccCtccacctgcatatggtgagt	7	14	0	2	rs3218688	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108139322C>A	ENST00000452508.2	+	19	3013	c.2824C>A	c.(2824-2826)Ctc>Atc	p.L942I	AP001925.1_ENST00000596081.1_5'Flank|ATM_ENST00000278616.4_Missense_Mutation_p.L942I			Q13315	ATM_HUMAN	ATM serine/threonine kinase	942			L -> F (in dbSNP:rs3218688).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L942I(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TACCAAATCCCTCCACCTGCA	0.393			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											125	116	119					11																	108139322		2201	4298	6499	107644532	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2824C>A	11.37:g.108139322C>A	ENSP00000388058:p.Leu942Ile		107644532	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	9.356	1.066667	0.20067	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74209	-0.82;-0.82;-0.82	5.86	3.96	0.45880	Armadillo-type fold (1);	0.062472	0.64402	D	0.000004	T	0.71476	0.3344	M	0.72894	2.215	0.25225	N	0.989879	B	0.26672	0.156	B	0.30646	0.118	T	0.65809	-0.6078	10	0.62326	D	0.03	.	7.7634	0.28965	0.1188:0.6863:0.1287:0.0662	.	942	Q13315	ATM_HUMAN	I	942	ENSP00000435747:L942I;ENSP00000278616:L942I;ENSP00000388058:L942I	ENSP00000278616:L942I	L	+	1	0	ATM	107644532	0.785000	0.28726	0.055000	0.19348	0.097000	0.18754	1.342000	0.33919	0.781000	0.33589	-0.181000	0.13052	CTC		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108139322	C	A	108139322	3	1	61	1	0	0	0	0	1	0	0	0	1110	681	24	2	2890	2	ATM	11	108139322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96018	108139322	26867194	7642	15627										
ATM	472	broad.mit.edu	37	chr11	108151768	108151768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggatgaaatttataataGaaaatctgttttactgacgt	7	3	1	3	rs555219189	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108151768G>T	ENST00000452508.2	+	25	3638	c.3449G>T	c.(3448-3450)aGa>aTa	p.R1150I	ATM_ENST00000278616.4_Missense_Mutation_p.R1150I			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1150					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R1150I(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATTTATAATAGAAAATCTGTT	0.318			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											90	95	93					11																	108151768		2201	4298	6499	107656978	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3449G>T	11.37:g.108151768G>T	ENSP00000388058:p.Arg1150Ile		107656978	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	34	5.381142	0.95945	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.72282	-0.64;-0.64;-0.64	6.08	6.08	0.98989	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84092	0.5396	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	D	0.83986	0.0335	10	0.72032	D	0.01	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1150	Q13315	ATM_HUMAN	I	1150	ENSP00000435747:R1150I;ENSP00000278616:R1150I;ENSP00000388058:R1150I	ENSP00000278616:R1150I	R	+	2	0	ATM	107656978	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.790000	0.75115	2.894000	0.99253	0.655000	0.94253	AGA		0.318	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108151768	G	T	108151768	3	4	61	1	0	0	0	0	1	0	0	0	1110	942	33	2	3539	2	ATM	11	108151768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12446	108151768	26854748	7643	15628										
ATM	472	broad.mit.edu	37	chr11	108153509	108153509	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcatctcatttagattatCtggttttggaatggctaaat	9	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108153509C>A	ENST00000452508.2	+	26	3838	c.3649C>A	c.(3649-3651)Ctg>Atg	p.L1217M	ATM_ENST00000278616.4_Missense_Mutation_p.L1217M			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1217					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L1217M(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTAGATTATCTGGTTTTGGA	0.299			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											90	92	91					11																	108153509		2199	4292	6491	107658719	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3649C>A	11.37:g.108153509C>A	ENSP00000388058:p.Leu1217Met		107658719	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393920	0.62066	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.73258	-0.73;-0.73;-0.73	5.38	0.262	0.15597	Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.72898	0.3518	L	0.36672	1.1	0.33686	D	0.61268	D	0.89917	1.0	D	0.78314	0.991	T	0.75929	-0.3144	10	0.49607	T	0.09	.	10.1084	0.42548	0.0:0.5564:0.0:0.4436	.	1217	Q13315	ATM_HUMAN	M	1217	ENSP00000435747:L1217M;ENSP00000278616:L1217M;ENSP00000388058:L1217M	ENSP00000278616:L1217M	L	+	1	2	ATM	107658719	0.999000	0.42202	0.906000	0.35671	0.990000	0.78478	1.107000	0.31110	0.014000	0.14944	0.591000	0.81541	CTG		0.299	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108153509	C	A	108153509	3	1	61	1	0	0	0	0	1	0	0	0	1110	912	32	2	3743	2	ATM	11	108153509	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1741	108153509	26853007	7644	15629										
ATM	472	broad.mit.edu	37	chr11	108159816	108159816	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaagcattttagaaattCtttccaaaagccctgtaagt	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108159816C>A	ENST00000452508.2	+	29	4411	c.4222C>A	c.(4222-4224)Ctt>Att	p.L1408I	ATM_ENST00000278616.4_Missense_Mutation_p.L1408I			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1408					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L1408I(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTAGAAATTCTTTCCAAAAG	0.303			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											43	42	42					11																	108159816		2200	4295	6495	107665026	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4222C>A	11.37:g.108159816C>A	ENSP00000388058:p.Leu1408Ile		107665026	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.29|18.29	3.592175|3.592175	0.66219|0.66219	.|.	.|.	ENSG00000149311|ENSG00000149311	ENST00000531525|ENST00000278616;ENST00000452508;ENST00000389511	.|T;T	.|0.74421	.|-0.84;-0.84	5.36|5.36	5.36|5.36	0.76844|0.76844	.|Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83390|0.83390	0.5244|0.5244	M|M	0.65498|0.65498	2.005|2.005	0.48762|0.48762	D|D	0.999707|0.999707	.|D;D	.|0.89917	.|0.998;1.0	.|D;D	.|0.91635	.|0.996;0.999	T|T	0.82606|0.82606	-0.0374|-0.0374	5|10	.|0.40728	.|T	.|0.16	.|.	12.4398|12.4398	0.55619|0.55619	0.0:0.9232:0.0:0.0768|0.0:0.9232:0.0:0.0768	.|.	.|60;1408	.|E7EV38;Q13315	.|.;ATM_HUMAN	L|I	77|1408;1408;60	.|ENSP00000278616:L1408I;ENSP00000388058:L1408I	.|ENSP00000278616:L1408I	F|L	+|+	3|1	2|0	ATM|ATM	107665026|107665026	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	5.403000|5.403000	0.66338|0.66338	2.497000|2.497000	0.84241|0.84241	0.650000|0.650000	0.86243|0.86243	TTC|CTT		0.303	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108159816	C	A	108159816	3	1	61	1	0	0	0	0	1	0	0	0	1110	913	32	2	4328	2	ATM	11	108159816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6307	108159816	26846700	7645	15630										
ATM	472	broad.mit.edu	37	chr11	108160488	108160488	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcttgggcctttgttcttCgagacgttatttatactttg	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108160488C>T	ENST00000452508.2	+	30	4585	c.4396C>T	c.(4396-4398)Cga>Tga	p.R1466*	ATM_ENST00000278616.4_Nonsense_Mutation_p.R1466*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1466					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R1466*(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTTTGTTCTTCGAGACGTTAT	0.308			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Nonsense(1)	large_intestine(1)	11	GRCh37	CM990210	ATM	M							69	71	70					11																	108160488		2201	4298	6499	107665698	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4396C>T	11.37:g.108160488C>T	ENSP00000388058:p.Arg1466*		107665698	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	46	12.612048	0.99682	.	.	ENSG00000149311	ENST00000278616;ENST00000452508;ENST00000389511	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7116	0.69238	0.1449:0.8551:0.0:0.0	.	.	.	.	X	1466;1466;118	.	ENSP00000278616:R1466X	R	+	1	2	ATM	107665698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.837000	0.48191	2.781000	0.95711	0.650000	0.86243	CGA		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108160488	C	T	108160488	4	4	61	1	0	0	0	0	0	1	0	0	1110	876	31	1	4506	1	ATM	11	108160488	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	672	108160488	26846028	7646	15631										
ATM	472	broad.mit.edu	37	chr11	108163373	108163373	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatcatggatgtgtcattAcgtagcttctccctttgttg	9	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108163373A>G	ENST00000452508.2	+	31	4653	c.4464A>G	c.(4462-4464)ttA>ttG	p.L1488L	ATM_ENST00000278616.4_Silent_p.L1488L			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1488					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L1488L(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATGTGTCATTACGTAGCTTCT	0.368			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - coding silent(1)	large_intestine(1)	11											249	232	238					11																	108163373		2201	4298	6499	107668583	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4464A>G	11.37:g.108163373A>G			107668583	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.368	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108163373	A	G	108163373	2	3	61	1	0	0	0	0	0	0	0	1	1110	388	14	4		4	ATM	11	108163373	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2885	108163373	26843143	7647	15632										
ATM	472	broad.mit.edu	37	chr11	108172385	108172385	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttcagtgtcaaagttCgatcagcagctgttacctgt	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108172385C>T	ENST00000452508.2	+	36	5377	c.5188C>T	c.(5188-5190)Cga>Tga	p.R1730*	ATM_ENST00000278616.4_Nonsense_Mutation_p.R1730*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1730					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R1730*(2)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGTCAAAGTTCGATCAGCAGC	0.343			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	2	Substitution - Nonsense(2)	large_intestine(2)	11	GRCh37	CM990211	ATM	M							125	124	125					11																	108172385		2201	4298	6499	107677595	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5188C>T	11.37:g.108172385C>T	ENSP00000388058:p.Arg1730*		107677595	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	47	13.596063	0.99752	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	.	.	.	4.9	3.95	0.45737	.	0.056256	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	12.8088	0.57628	0.358:0.642:0.0:0.0	.	.	.	.	X	1730	.	ENSP00000278616:R1730X	R	+	1	2	ATM	107677595	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.479000	0.45197	1.136000	0.42199	0.460000	0.39030	CGA		0.343	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108172385	C	T	108172385	4	4	61	1	0	0	0	0	0	1	0	0	1110	876	31	1	5322	1	ATM	11	108172385	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9012	108172385	26834131	7648	15633										
ATM	472	broad.mit.edu	37	chr11	108190772	108190772	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctacattttatgaaagtCtcaaatatgccaggtattat	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108190772C>A	ENST00000452508.2	+	45	6628	c.6439C>A	c.(6439-6441)Ctc>Atc	p.L2147I	ATM_ENST00000278616.4_Missense_Mutation_p.L2147I|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2147	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L2147I(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTATGAAAGTCTCAAATATGC	0.313			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											80	84	83					11																	108190772		2201	4295	6496	107695982	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.6439C>A	11.37:g.108190772C>A	ENSP00000388058:p.Leu2147Ile		107695982	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444585	0.43429	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.55588	0.51;0.51	5.47	5.47	0.80525	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.181981	0.49305	D	0.000145	T	0.37046	0.0989	L	0.36672	1.1	0.80722	D	1	P	0.42827	0.791	B	0.40066	0.318	T	0.21484	-1.0244	10	0.07644	T	0.81	.	8.65	0.34029	0.1519:0.7722:0.0:0.0758	.	2147	Q13315	ATM_HUMAN	I	2147	ENSP00000278616:L2147I;ENSP00000388058:L2147I	ENSP00000278616:L2147I	L	+	1	0	ATM	107695982	0.998000	0.40836	1.000000	0.80357	0.960000	0.62799	3.244000	0.51399	2.581000	0.87130	0.655000	0.94253	CTC		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108190772	C	A	108190772	3	1	61	1	0	0	0	0	1	0	0	0	1110	913	32	2	6609	2	ATM	11	108190772	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18387	108190772	26815744	7649	15634										
ATM	472	broad.mit.edu	37	chr11	108196215	108196215	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatgtattaaggacattCtcaccaaacaccttgtagaa	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108196215C>A	ENST00000452508.2	+	47	6940	c.6751C>A	c.(6751-6753)Ctc>Atc	p.L2251I	ATM_ENST00000278616.4_Missense_Mutation_p.L2251I|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2251	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.		CIKDILT -> H (in AT).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L2251I(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TAAGGACATTCTCACCAAACA	0.388			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	large_intestine(1)	11											106	103	104					11																	108196215		2201	4298	6499	107701425	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.6751C>A	11.37:g.108196215C>A	ENSP00000388058:p.Leu2251Ile		107701425	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.953369	0.53293	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.70399	-0.48;-0.48	5.06	4.13	0.48395	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.119376	0.64402	D	0.000017	T	0.79155	0.4398	L	0.58669	1.825	0.80722	D	1	D	0.63880	0.993	D	0.65573	0.936	T	0.76498	-0.2937	10	0.25751	T	0.34	.	15.094	0.72220	0.1431:0.8569:0.0:0.0	.	2251	Q13315	ATM_HUMAN	I	2251	ENSP00000278616:L2251I;ENSP00000388058:L2251I	ENSP00000278616:L2251I	L	+	1	0	ATM	107701425	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	5.419000	0.66435	1.231000	0.43661	-0.181000	0.13052	CTC		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108196215	C	A	108196215	3	1	61	1	0	0	0	0	1	0	0	0	1110	913	32	2	6929	2	ATM	11	108196215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5443	108196215	26810301	7650	15635										
C11orf65	160140	broad.mit.edu	37	chr11	108253807	108253807	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggttcttgataaacatTttcatagtaagtatcatctg	6	5	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108253807T>G	ENST00000529391.1	-	8	892	c.883A>C	c.(883-885)Aat>Cat	p.N295H	C11orf65_ENST00000393084.1_Missense_Mutation_p.N295H|C11orf65_ENST00000525729.1_Intron|C11orf65_ENST00000526725.1_Intron			Q8NCR3	CK065_HUMAN	chromosome 11 open reading frame 65	295								p.N295H(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(2)	10		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		TGATAAACATTTTCATAGTAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	11											172	174	174					11																	108253807		2201	4298	6499	107759017	SO:0001583	missense	160140			BC059411	CCDS8340.1	11q22.3	2012-05-30			ENSG00000166323	ENSG00000166323			28519	protein-coding gene	gene with protein product						12477932	Standard	NM_152587		Approved	MGC33948	uc001pkh.3	Q8NCR3	OTTHUMG00000166489	ENST00000529391.1:c.883A>C	11.37:g.108253807T>G	ENSP00000436400:p.Asn295His		107759017	B4DZU4|Q6PCA8	Missense_Mutation	SNP	ENST00000529391.1	37	CCDS8340.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056759	0.55325	.	.	ENSG00000166323	ENST00000529391;ENST00000393084	.	.	.	4.46	4.46	0.54185	.	0.096879	0.43110	D	0.000619	T	0.52709	0.1751	L	0.51422	1.61	0.09310	N	1	D	0.69078	0.997	D	0.63192	0.912	T	0.44019	-0.9355	9	0.66056	D	0.02	-37.1275	10.4312	0.44409	0.0:0.0:0.0:1.0	.	295	Q8NCR3	CK065_HUMAN	H	295	.	ENSP00000376799:N295H	N	-	1	0	C11orf65	107759017	0.024000	0.19004	0.121000	0.21740	0.020000	0.10135	1.707000	0.37888	2.238000	0.73509	0.533000	0.62120	AAT		0.318	C11orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390010.3	NM_152587		G	108253807	T	G	108253807	3	3	61	1	0	0	0	0	1	0	0	0	1659	1841	64	4	62	4	C11orf65	11	108253807	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	57592	108253807	26752709	7651	15636										
EXPH5	23086	broad.mit.edu	37	chr11	108382635	108382635	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaaagagcaaatacacttCtcctggaggcagccatttta	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108382635C>A	ENST00000265843.4	-	6	3709	c.3599G>T	c.(3598-3600)aGa>aTa	p.R1200I	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.R1193I|EXPH5_ENST00000443411.1_Missense_Mutation_p.R1012I|EXPH5_ENST00000428840.1_Missense_Mutation_p.R1124I	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1200					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.R1200I(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AAATACACTTCTCCTGGAGGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											96	97	97					11																	108382635		2201	4298	6499	107887845	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.3599G>T	11.37:g.108382635C>A	ENSP00000265843:p.Arg1200Ile		107887845	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627036	0.28978	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03982	4.32;4.25;4.1;4.32;4.17;3.74	5.61	1.65	0.23941	.	0.600185	0.15909	N	0.238696	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.43925	-0.9361	10	0.44086	T	0.13	0.0867	4.9634	0.14078	0.2609:0.1626:0.5764:0.0	.	1200	Q8NEV8	EXPH5_HUMAN	I	1200;1124;1012;1193;1124;1012	ENSP00000265843:R1200I;ENSP00000391966:R1124I;ENSP00000411390:R1012I;ENSP00000432546:R1193I;ENSP00000432683:R1124I;ENSP00000446434:R1012I	ENSP00000265843:R1200I	R	-	2	0	EXPH5	107887845	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	-0.147000	0.10234	0.055000	0.16094	-0.165000	0.13383	AGA		0.383	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		A	108382635	C	A	108382635	3	1	61	1	0	0	0	0	1	0	0	0	5335	913	32	2	2374	2	EXPH5	11	108382635	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128828	108382635	26623881	7652	15637										
EXPH5	23086	broad.mit.edu	37	chr11	108385085	108385085	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaggaactcttcctggttCtccctgtctctagaggaatc	8	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108385085C>A	ENST00000265843.4	-	6	1259	c.1149G>T	c.(1147-1149)gaG>gaT	p.E383D	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000525344.1_Missense_Mutation_p.E376D|EXPH5_ENST00000443411.1_Missense_Mutation_p.E195D|EXPH5_ENST00000428840.1_Missense_Mutation_p.E307D	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	383					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.E383D(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTTCCTGGTTCTCCCTGTCTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											173	175	175					11																	108385085		2201	4298	6499	107890295	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1149G>T	11.37:g.108385085C>A	ENSP00000265843:p.Glu383Asp		107890295	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558429	0.27827	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04015	4.32;4.25;4.1;4.32;4.17;3.73	5.66	4.75	0.60458	.	0.231645	0.30620	N	0.009224	T	0.03390	0.0098	N	0.08118	0	0.24566	N	0.993949	B	0.22604	0.072	B	0.18871	0.023	T	0.40701	-0.9549	10	0.59425	D	0.04	-1.4571	13.8774	0.63662	0.0:0.9239:0.0:0.0761	.	383	Q8NEV8	EXPH5_HUMAN	D	383;307;195;376;227;307;195	ENSP00000265843:E383D;ENSP00000391966:E307D;ENSP00000411390:E195D;ENSP00000432546:E376D;ENSP00000432683:E307D;ENSP00000446434:E195D	ENSP00000265843:E383D	E	-	3	2	EXPH5	107890295	0.072000	0.21174	0.969000	0.41365	0.057000	0.15508	1.289000	0.33307	2.667000	0.90743	0.491000	0.48974	GAG		0.458	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		A	108385085	C	A	108385085	3	1	61	1	0	0	0	0	1	0	0	0	5335	912	32	2	4824	2	EXPH5	11	108385085	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2450	108385085	26621431	7653	15638										
EXPH5	23086	broad.mit.edu	37	chr11	108398882	108398882	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagcagctcccctcacaGgcataggaggtcctgcatgg	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108398882G>T	ENST00000265843.4	-	4	583	c.473C>A	c.(472-474)cCt>cAt	p.P158H	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000525344.1_Missense_Mutation_p.P151H|EXPH5_ENST00000443411.1_Intron|EXPH5_ENST00000428840.1_Missense_Mutation_p.P82H	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	158					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.P158H(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TCCCCTCACAGGCATAGGAGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	87	87					11																	108398882		2201	4298	6499	107904092	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.473C>A	11.37:g.108398882G>T	ENSP00000265843:p.Pro158His		107904092	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.672420	0.67928	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000439956;ENST00000526312	T;T;T;T	0.03035	4.23;4.15;4.23;4.07	5.1	5.1	0.69264	.	0.396531	0.21909	N	0.067337	T	0.07279	0.0184	N	0.22421	0.69	0.80722	D	1	D	0.67145	0.996	P	0.56216	0.794	T	0.29701	-1.0003	10	0.72032	D	0.01	-3.2193	14.3958	0.67010	0.0:0.0:1.0:0.0	.	158	Q8NEV8	EXPH5_HUMAN	H	158;82;151;2;82	ENSP00000265843:P158H;ENSP00000391966:P82H;ENSP00000432546:P151H;ENSP00000432683:P82H	ENSP00000265843:P158H	P	-	2	0	EXPH5	107904092	0.234000	0.23783	0.060000	0.19600	0.191000	0.23601	4.489000	0.60309	2.536000	0.85505	0.491000	0.48974	CCT		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108398882	G	T	108398882	3	4	61	1	0	0	0	0	1	0	0	0	5335	1000	35	2	5508	2	EXPH5	11	108398882	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13797	108398882	26607634	7654	15639										
DDX10	1662	broad.mit.edu	37	chr11	108544240	108544240	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagattttcccttgtccaAaaaaacattgaaaggtaagt	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108544240A>G	ENST00000322536.3	+	2	362	c.233A>G	c.(232-234)aAa>aGa	p.K78R	DDX10_ENST00000526794.1_Missense_Mutation_p.K78R	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	78					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.K78R(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CCCTTGTCCAAAAAAACATTG	0.338			T	NUP98	AML*																																		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	1	Substitution - Missense(1)	large_intestine(1)	11											98	98	98					11																	108544240		2197	4297	6494	108049450	SO:0001583	missense	1662			U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.233A>G	11.37:g.108544240A>G	ENSP00000314348:p.Lys78Arg		108049450	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.636963	0.29157	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.39997	1.05;1.05	5.84	3.22	0.36961	RNA helicase, DEAD-box type, Q motif (1);	0.168762	0.64402	N	0.000006	T	0.28433	0.0703	N	0.25380	0.74	0.58432	D	0.999997	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.004	T	0.06092	-1.0846	10	0.33141	T	0.24	-12.9042	10.9204	0.47161	0.8527:0.0:0.1473:0.0	.	78;78	Q13206;E9PIF2	DDX10_HUMAN;.	R	78	ENSP00000314348:K78R;ENSP00000432032:K78R	ENSP00000314348:K78R	K	+	2	0	DDX10	108049450	1.000000	0.71417	0.482000	0.27366	0.677000	0.39632	4.606000	0.61126	1.043000	0.40175	-0.326000	0.08463	AAA		0.338	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		G	108544240	A	G	108544240	3	3	61	1	0	0	0	0	1	0	0	0	4348	14	1	4	239	4	DDX10	11	108544240	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	145358	108544240	26462276	7655	15640										
DDX10	1662	broad.mit.edu	37	chr11	108559740	108559740	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgctgtattcctttttgaGaagccatctgaagaagaaga	10	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108559740G>T	ENST00000322536.3	+	7	1055	c.926G>T	c.(925-927)aGa>aTa	p.R309I	DDX10_ENST00000526794.1_Missense_Mutation_p.R309I	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	309	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.R309I(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TCCTTTTTGAGAAGCCATCTG	0.388			T	NUP98	AML*																																		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	1	Substitution - Missense(1)	large_intestine(1)	11											231	231	231					11																	108559740		2201	4298	6499	108064950	SO:0001583	missense	1662			U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.926G>T	11.37:g.108559740G>T	ENSP00000314348:p.Arg309Ile		108064950	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.030610	0.75504	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.05025	3.51;3.51	5.61	4.69	0.59074	Helicase, C-terminal (1);	0.127154	0.64402	D	0.000002	T	0.15739	0.0379	M	0.77712	2.385	0.80722	D	1	P;P	0.48998	0.918;0.84	P;P	0.47827	0.558;0.558	T	0.00440	-1.1738	10	0.87932	D	0	-16.1575	14.7812	0.69769	0.07:0.0:0.93:0.0	.	309;309	Q13206;E9PIF2	DDX10_HUMAN;.	I	309;215;309	ENSP00000314348:R309I;ENSP00000432032:R309I	ENSP00000314348:R309I	R	+	2	0	DDX10	108064950	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	3.073000	0.50057	2.637000	0.89404	0.655000	0.94253	AGA		0.388	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		T	108559740	G	T	108559740	3	4	61	1	0	0	0	0	1	0	0	0	4348	942	33	2	952	2	DDX10	11	108559740	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15500	108559740	26446776	7656	15641										
DDX10	1662	broad.mit.edu	37	chr11	108593863	108593863	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccaatgacgaagtggaaGaatttagagcctacttcaat	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:108593863G>T	ENST00000322536.3	+	13	1768	c.1639G>T	c.(1639-1641)Gaa>Taa	p.E547*	DDX10_ENST00000526794.1_Nonsense_Mutation_p.E547*	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	547					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.E547*(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CGAAGTGGAAGAATTTAGAGC	0.433			T	NUP98	AML*																																		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	1	Substitution - Nonsense(1)	large_intestine(1)	11											59	59	59					11																	108593863		2201	4298	6499	108099073	SO:0001587	stop_gained	1662			U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.1639G>T	11.37:g.108593863G>T	ENSP00000314348:p.Glu547*		108099073	B2RCQ3|Q5BJD8	Nonsense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	38	6.777047	0.97829	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	.	.	.	4.9	3.98	0.46160	.	0.284853	0.41938	D	0.000783	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-11.7223	8.5076	0.33197	0.237:0.0:0.763:0.0	.	.	.	.	X	547;453;547	.	ENSP00000314348:E547X	E	+	1	0	DDX10	108099073	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.406000	0.34646	1.181000	0.42912	0.484000	0.47621	GAA		0.433	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		T	108593863	G	T	108593863	4	4	61	1	0	0	0	0	0	1	0	0	4348	943	33	2	1689	2	DDX10	11	108593863	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34123	108593863	26412653	7657	15642										
ZC3H12C	85463	broad.mit.edu	37	chr11	110035566	110035566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatgtgactcacctgtcGacatcggatattattccatg	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110035566G>A	ENST00000278590.3	+	6	1807	c.1756G>A	c.(1756-1758)Gac>Aac	p.D586N	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.D555N|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.D587N	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	586							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.D586N(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		CTCACCTGTCGACATCGGATA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	80	82					11																	110035566		1977	4143	6120	109540776	SO:0001583	missense	85463				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1756G>A	11.37:g.110035566G>A	ENSP00000278590:p.Asp586Asn		109540776	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474618	0.84640	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.41065	1.01;1.01;1.03	6.04	6.04	0.98038	.	0.145935	0.64402	D	0.000011	T	0.66426	0.2788	M	0.69823	2.125	0.46260	D	0.998955	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.99;0.99	T	0.60939	-0.7163	10	0.39692	T	0.17	-26.2426	20.5792	0.99380	0.0:0.0:1.0:0.0	.	587;586;586	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	N	586;587;555	ENSP00000278590:D586N;ENSP00000431821:D587N;ENSP00000413094:D555N	ENSP00000278590:D586N	D	+	1	0	ZC3H12C	109540776	1.000000	0.71417	0.305000	0.25099	0.966000	0.64601	7.639000	0.83342	2.873000	0.98535	0.561000	0.74099	GAC		0.423	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		A	110035566	G	A	110035566	3	1	61	1	0	0	0	0	1	0	0	0	17602	1058	37	1	1778	1	ZC3H12C	11	110035566	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1441703	110035566	24970950	7658	15643										
ZC3H12C	85463	broad.mit.edu	37	chr11	110036163	110036163	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggccaggctatgggatcGacgcctatgggtaccggcag	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110036163G>A	ENST00000278590.3	+	6	2404	c.2353G>A	c.(2353-2355)Gac>Aac	p.D785N	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.D754N|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.D786N	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	785							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.D785N(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		CTATGGGATCGACGCCTATGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	81	80					11																	110036163		1958	4150	6108	109541373	SO:0001583	missense	85463				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2353G>A	11.37:g.110036163G>A	ENSP00000278590:p.Asp785Asn		109541373	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.608448	0.28623	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.36157	1.27;1.27;1.28	5.77	5.77	0.91146	.	0.265656	0.36374	N	0.002638	T	0.36082	0.0954	L	0.59436	1.845	0.31930	N	0.612349	P;P;P	0.36483	0.555;0.555;0.555	B;B;B	0.23852	0.033;0.049;0.033	T	0.52343	-0.8588	10	0.72032	D	0.01	-11.0983	19.9981	0.97395	0.0:0.0:1.0:0.0	.	786;785;785	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	N	785;786;754	ENSP00000278590:D785N;ENSP00000431821:D786N;ENSP00000413094:D754N	ENSP00000278590:D785N	D	+	1	0	ZC3H12C	109541373	1.000000	0.71417	0.080000	0.20451	0.074000	0.17049	5.780000	0.68956	2.729000	0.93468	0.655000	0.94253	GAC		0.552	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		A	110036163	G	A	110036163	3	1	61	1	0	0	0	0	1	0	0	0	17602	1058	37	1	2375	1	ZC3H12C	11	110036163	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	597	110036163	24970353	7659	15644										
ARHGAP20	57569	broad.mit.edu	37	chr11	110450744	110450744	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagcctgaaaagtgcaatCtattggagaggaagtctcag	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110450744C>A	ENST00000260283.4	-	16	3210	c.2926G>T	c.(2926-2928)Gat>Tat	p.D976Y	ARHGAP20_ENST00000533353.1_Missense_Mutation_p.D950Y|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.D940Y|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.D953Y|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.D519Y|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.D950Y|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.D940Y	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	976					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.D976Y(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AAAGTGCAATCTATTGGAGAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	57	57					11																	110450744		2201	4298	6499	109955954	SO:0001583	missense	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2926G>T	11.37:g.110450744C>A	ENSP00000260283:p.Asp976Tyr		109955954	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.495044	0.64186	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.27;2.23;2.24;2.23;2.24	5.9	3.97	0.46021	.	0.218578	0.37304	N	0.002141	T	0.38904	0.1058	M	0.65975	2.015	0.32324	N	0.562061	D;D;D	0.71674	0.998;0.996;0.998	D;P;P	0.63877	0.919;0.754;0.875	T	0.56165	-0.8024	10	0.87932	D	0	.	16.5404	0.84383	0.0:0.7533:0.2467:0.0	.	950;976;953	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	Y	976;950;519;953;940;950;940	ENSP00000260283:D976Y;ENSP00000349660:D950Y;ENSP00000437905:D519Y;ENSP00000432076:D953Y;ENSP00000436319:D940Y;ENSP00000436522:D950Y;ENSP00000431399:D940Y	ENSP00000260283:D976Y	D	-	1	0	ARHGAP20	109955954	1.000000	0.71417	0.827000	0.32855	0.960000	0.62799	5.550000	0.67268	0.800000	0.34041	0.650000	0.86243	GAT		0.502	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		A	110450744	C	A	110450744	3	1	61	1	0	0	0	0	1	0	0	0	870	913	32	2	653	2	ARHGAP20	11	110450744	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	414581	110450744	24555772	7660	15645										
ARHGAP20	57569	broad.mit.edu	37	chr11	110451265	110451265	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggactataagatgccacaGaaatggccactggcttagac	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110451265G>T	ENST00000260283.4	-	16	2689	c.2405C>A	c.(2404-2406)tCt>tAt	p.S802Y	ARHGAP20_ENST00000533353.1_Missense_Mutation_p.S776Y|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.S766Y|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.S779Y|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.S345Y|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.S776Y|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.S766Y	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	802					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.S802Y(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AGATGCCACAGAAATGGCCAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											116	114	114					11																	110451265		2201	4298	6499	109956475	SO:0001583	missense	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2405C>A	11.37:g.110451265G>T	ENSP00000260283:p.Ser802Tyr		109956475	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220393	0.58560	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.17854	2.25;2.25;2.26;2.25;2.26;2.25;2.26	5.46	5.46	0.80206	.	0.100598	0.45126	D	0.000394	T	0.42698	0.1214	M	0.69823	2.125	0.36727	D	0.881523	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.987;0.994	T	0.45352	-0.9267	10	0.49607	T	0.09	.	17.4961	0.87718	0.0:0.0:1.0:0.0	.	776;802;779	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	Y	802;776;345;779;766;776;766	ENSP00000260283:S802Y;ENSP00000349660:S776Y;ENSP00000437905:S345Y;ENSP00000432076:S779Y;ENSP00000436319:S766Y;ENSP00000436522:S776Y;ENSP00000431399:S766Y	ENSP00000260283:S802Y	S	-	2	0	ARHGAP20	109956475	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	4.966000	0.63715	2.567000	0.86603	0.655000	0.94253	TCT		0.438	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		T	110451265	G	T	110451265	3	4	61	1	0	0	0	0	1	0	0	0	870	942	33	2	1174	2	ARHGAP20	11	110451265	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	521	110451265	24555251	7661	15646										
ARHGAP20	57569	broad.mit.edu	37	chr11	110451545	110451545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctttgaatccagatagtCgatgctgggctctgagcaac	11	9	1	3	rs368565272		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110451545C>T	ENST00000260283.4	-	16	2409	c.2125G>A	c.(2125-2127)Gac>Aac	p.D709N	ARHGAP20_ENST00000533353.1_Missense_Mutation_p.D683N|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.D673N|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.D686N|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.D252N|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.D683N|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.D673N	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	709					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.D709N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TCCAGATAGTCGATGCTGGGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	ASN/ASP	2,4400	4.2+/-10.8	0,2,2199	63	64	63		2125	1.6	0	11		63	0,8596		0,0,4298	no	missense	ARHGAP20	NM_020809.2	23	0,2,6497	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	709/1192	110451545	2,12996	2201	4298	6499	109956755	SO:0001583	missense	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2125G>A	11.37:g.110451545C>T	ENSP00000260283:p.Asp709Asn		109956755	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189592	0.38707	4.54E-4	0.0	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.11385	2.81;2.81;2.78;2.81;2.82;2.81;2.82	5.71	1.65	0.23941	.	0.226096	0.37483	N	0.002070	T	0.08223	0.0205	M	0.63428	1.95	0.09310	N	1	P;B;B	0.38167	0.621;0.291;0.414	B;B;B	0.30782	0.12;0.01;0.034	T	0.27123	-1.0083	10	0.33141	T	0.24	.	3.3184	0.07041	0.1512:0.5722:0.1303:0.1464	.	683;709;686	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	N	709;683;252;686;673;683;673	ENSP00000260283:D709N;ENSP00000349660:D683N;ENSP00000437905:D252N;ENSP00000432076:D686N;ENSP00000436319:D673N;ENSP00000436522:D683N;ENSP00000431399:D673N	ENSP00000260283:D709N	D	-	1	0	ARHGAP20	109956755	0.711000	0.27906	0.000000	0.03702	0.946000	0.59487	1.193000	0.32162	0.047000	0.15862	-0.274000	0.10170	GAC		0.502	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		T	110451545	C	T	110451545	3	4	61	1	0	0	0	0	1	0	0	0	870	884	31	1	1454	1	ARHGAP20	11	110451545	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280	110451545	24554971	7662	15647										
ARHGAP20	57569	broad.mit.edu	37	chr11	110462842	110462842	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccagaaggcccagtttatGatagatcttctccttttaaa	7	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:110462842G>T	ENST00000260283.4	-	11	1286	c.1002C>A	c.(1000-1002)atC>atA	p.I334I	ARHGAP20_ENST00000533353.1_Silent_p.I308I|ARHGAP20_ENST00000528829.1_Silent_p.I298I|ARHGAP20_ENST00000524756.1_Silent_p.I311I|ARHGAP20_ENST00000529591.1_5'Flank|ARHGAP20_ENST00000357139.3_Silent_p.I308I|ARHGAP20_ENST00000527598.1_Silent_p.I298I	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	334					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.I334I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CCCAGTTTATGATAGATCTTC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	11											156	151	153					11																	110462842		2201	4298	6499	109968052	SO:0001819	synonymous_variant	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.1002C>A	11.37:g.110462842G>T			109968052	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Silent	SNP	ENST00000260283.4	37	CCDS31673.1																																																																																				0.403	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		T	110462842	G	T	110462842	2	4	61	1	0	0	0	0	0	0	0	1	870	1280	45	2		2	ARHGAP20	11	110462842	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11297	110462842	24543674	7663	15648										
BTG4	54766	broad.mit.edu	37	chr11	111369408	111369408	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagatcgtcatcagcttttCtgcaaagtcttctatttgct	6	10	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111369408C>A	ENST00000356018.2	-	2	293	c.94G>T	c.(94-96)Gaa>Taa	p.E32*	BTG4_ENST00000525791.1_Nonsense_Mutation_p.E32*	NM_017589.3	NP_060059.1	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4	32					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|neuron differentiation (GO:0030182)			p.E32*(1)		large_intestine(2)|upper_aerodigestive_tract(1)	3		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		ATCAGCTTTTCTGCAAAGTCT	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											133	112	119					11																	111369408		2201	4297	6498	110874618	SO:0001587	stop_gained	54766			AJ271351	CCDS8346.1	11q23	2008-05-27				ENSG00000137707			13862	protein-coding gene	gene with protein product		605673				10995567	Standard	NM_017589		Approved	PC3B	uc001plj.3	Q9NY30		ENST00000356018.2:c.94G>T	11.37:g.111369408C>A	ENSP00000348300:p.Glu32*		110874618	Q8NEH7	Nonsense_Mutation	SNP	ENST00000356018.2	37	CCDS8346.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373455	0.95923	.	.	ENSG00000137707	ENST00000356018;ENST00000525791;ENST00000456861	.	.	.	5.47	4.54	0.55810	.	0.262067	0.43416	D	0.000574	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	11.2646	0.49104	0.1389:0.7187:0.1425:0.0	.	.	.	.	X	32	.	ENSP00000348300:E32X	E	-	1	0	BTG4	110874618	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	1.862000	0.39448	1.282000	0.44496	0.591000	0.81541	GAA		0.383	BTG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391177.1			A	111369408	C	A	111369408	4	1	61	1	0	0	0	0	0	1	0	0	1559	922	32	2	597	2	BTG4	11	111369408	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	906566	111369408	23637108	7664	15649										
C11orf88	399949	broad.mit.edu	37	chr11	111385659	111385659	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtcgatgtatccccctagCgaatctcagctggtgctgcg	12	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111385659C>T	ENST00000375618.4	+	1	150	c.150C>T	c.(148-150)agC>agT	p.S50S	MIR34C_ENST00000384831.1_RNA|RP11-794P6.6_ENST00000530283.1_RNA|MIR34B_ENST00000385076.1_RNA|C11orf88_ENST00000529167.1_Silent_p.S50S|C11orf88_ENST00000332814.6_Silent_p.S50S|BTG4_ENST00000356018.2_5'Flank|BTG4_ENST00000525791.1_5'Flank	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	50								p.S50S(1)		endometrium(1)|large_intestine(3)|lung(2)	6						ATCCCCCTAGCGAATCTCAGC	0.592											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	11											58	64	62					11																	111385659		2110	4246	6356	110890869	SO:0001819	synonymous_variant	399949			BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"hypothetical gene supported by BC039505"					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.150C>T	11.37:g.111385659C>T		1434	110890869	E9PAN0|Q6ZRL3	Silent	SNP	ENST00000375618.4	37	CCDS41713.1																																																																																				0.592	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388		T	111385659	C	T	111385659	2	4	61	1	0	0	0	0	0	0	0	1	1674	767	27	1		1	C11orf88	11	111385659	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16251	111385659	23620857	7665	15650										
C11orf88	399949	broad.mit.edu	37	chr11	111386829	111386829	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagaaagtaaagtatctCcaaaaggtaggccaatattt	10	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111386829C>T	ENST00000375618.4	+	3	333	c.333C>T	c.(331-333)ctC>ctT	p.L111L	MIR34C_ENST00000384831.1_RNA|RP11-794P6.6_ENST00000530283.1_RNA|C11orf88_ENST00000529167.1_Silent_p.L111L|C11orf88_ENST00000332814.6_Silent_p.L111L	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	111								p.L111L(1)		endometrium(1)|large_intestine(3)|lung(2)	6						TAAAGTATCTCCAAAAGGTAG	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	11											70	70	70					11																	111386829		1806	4058	5864	110892039	SO:0001819	synonymous_variant	399949			BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"hypothetical gene supported by BC039505"					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.333C>T	11.37:g.111386829C>T			110892039	E9PAN0|Q6ZRL3	Silent	SNP	ENST00000375618.4	37	CCDS41713.1																																																																																				0.303	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388		T	111386829	C	T	111386829	2	4	61	1	0	0	0	0	0	0	0	1	1674	842	30	3		3	C11orf88	11	111386829	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1170	111386829	23619687	7666	15651										
SIK2	23235	broad.mit.edu	37	chr11	111491117	111491117	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatatgccaaaaatggaGaaatttttggtaagcttttt	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111491117G>T	ENST00000304987.3	+	3	480	c.307G>T	c.(307-309)Gaa>Taa	p.E103*		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	103	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.E103*(1)		breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						CAAAAATGGAGAAATTTTTGG	0.284																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											72	78	76					11																	111491117		2201	4291	6492	110996327	SO:0001587	stop_gained	23235			AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.307G>T	11.37:g.111491117G>T	ENSP00000305976:p.Glu103*		110996327	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Nonsense_Mutation	SNP	ENST00000304987.3	37	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	G	38	6.812793	0.97857	.	.	ENSG00000170145	ENST00000304987	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.1569	0.89694	0.0:0.0:1.0:0.0	.	.	.	.	X	103	.	ENSP00000305976:E103X	E	+	1	0	SIK2	110996327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.567000	0.90737	2.575000	0.86900	0.650000	0.86243	GAA		0.284	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		T	111491117	G	T	111491117	4	4	61	1	0	0	0	0	0	1	0	0	14355	943	33	2	317	2	SIK2	11	111491117	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104288	111491117	23515399	7667	15652										
SIK2	23235	broad.mit.edu	37	chr11	111571629	111571629	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttcggttttggaaatttCtttaaaagtggtgaactgct	10	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111571629C>A	ENST00000304987.3	+	5	671	c.498C>A	c.(496-498)ttC>ttA	p.F166L		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	166	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.F166L(2)		breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						TTGGAAATTTCTTTAAAAGTG	0.398																																																2	Substitution - Missense(2)	cervix(1)|large_intestine(1)	11											71	73	72					11																	111571629		2201	4297	6498	111076839	SO:0001583	missense	23235			AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.498C>A	11.37:g.111571629C>A	ENSP00000305976:p.Phe166Leu		111076839	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	ENST00000304987.3	37	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842676	0.71488	.	.	ENSG00000170145	ENST00000304987	T	0.63580	-0.05	5.32	4.4	0.53042	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.089754	0.85682	D	0.000000	T	0.53012	0.1770	N	0.11255	0.115	0.58432	D	0.99999	P	0.51933	0.949	P	0.61132	0.884	T	0.48399	-0.9039	10	0.13108	T	0.6	.	8.6979	0.34307	0.1525:0.7719:0.0:0.0756	.	166	Q9H0K1	SIK2_HUMAN	L	166	ENSP00000305976:F166L	ENSP00000305976:F166L	F	+	3	2	SIK2	111076839	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.584000	0.46102	1.469000	0.48083	0.603000	0.83216	TTC		0.398	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		A	111571629	C	A	111571629	3	1	61	1	0	0	0	0	1	0	0	0	14355	912	32	2	516	2	SIK2	11	111571629	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80512	111571629	23434887	7668	15653										
FDXACB1	91893	broad.mit.edu	37	chr11	111745900	111745900	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgatctatccaaaaacTaacatcatgcacataacatg	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111745900T>G	ENST00000260257.4	-	5	1668	c.1621A>C	c.(1621-1623)Agt>Cgt	p.S541R	FDXACB1_ENST00000542429.1_Missense_Mutation_p.S392R|ALG9_ENST00000524880.1_Intron|ALG9_ENST00000527377.1_Intron	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	541	FDX-ACB. {ECO:0000255|PROSITE- ProRule:PRU00778}.				phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)	p.S541R(2)		endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						ATCCAAAAACTAACATCATGC	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	11											58	57	57					11																	111745900		1868	4102	5970	111251110	SO:0001583	missense	91893				CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.1621A>C	11.37:g.111745900T>G	ENSP00000260257:p.Ser541Arg		111251110	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	37	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181776	0.78677	.	.	ENSG00000255561	ENST00000260257;ENST00000542429	T;T	0.80824	-1.42;-1.42	6.17	6.17	0.99709	Phenylalanyl-tRNA synthetase, beta subunit, ferrodoxin-fold anticodon-binding (5);	0.000000	0.85682	D	0.000000	D	0.91998	0.7465	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93452	0.6803	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	541	Q9BRP7	FDXA1_HUMAN	R	541;392	ENSP00000260257:S541R;ENSP00000441304:S392R	ENSP00000260257:S541R	S	-	1	0	FDXACB1	111251110	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.430000	0.73391	2.371000	0.80710	0.533000	0.62120	AGT		0.388	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111745900	T	G	111745900	3	3	61	1	0	0	0	0	1	0	0	0	5825	1522	53	4	257	4	FDXACB1	11	111745900	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	174271	111745900	23260616	7669	15654										
HSPB2	3316	broad.mit.edu	37	chr11	111784266	111784266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagggcaggggcctccGagcttaggctcagtgagggc	18	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111784266G>A	ENST00000304298.3	+	2	784	c.196G>A	c.(196-198)Gag>Aag	p.E66K	CRYAB_ENST00000227251.3_5'Flank|CRYAB_ENST00000526180.1_5'Flank|HSPB2_ENST00000537382.1_Missense_Mutation_p.E66K|HSPB2-C11orf52_ENST00000534100.1_Intron|CRYAB_ENST00000525823.1_5'Flank|CRYAB_ENST00000533971.1_5'Flank|CRYAB_ENST00000533280.1_5'Flank|CRYAB_ENST00000527950.1_Intron|CRYAB_ENST00000531198.1_5'Flank|CRYAB_ENST00000533475.1_Intron	NM_001541.3	NP_001532.1	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	66					positive regulation of catalytic activity (GO:0043085)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)	p.E66K(1)		large_intestine(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-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;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		AGGGGCCTCCGAGCTTAGGCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											92	95	94					11																	111784266		2201	4297	6498	111289476	SO:0001583	missense	3316			U75898	CCDS8352.1	11q22-q23	2011-09-02	2002-08-29			ENSG00000170276		"Heat shock proteins / HSPB"	5247	protein-coding gene	gene with protein product		602179	"heat shock 27kD protein 2"			9344664, 9490724	Standard	NM_001541		Approved	Hs.78846, MKBP	uc001pmg.2	Q16082		ENST00000304298.3:c.196G>A	11.37:g.111784266G>A	ENSP00000302476:p.Glu66Lys		111289476	Q6I9U7	Missense_Mutation	SNP	ENST00000304298.3	37	CCDS8352.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471878	0.63737	.	.	ENSG00000170276	ENST00000304298;ENST00000537382	D;D	0.90324	-2.65;-2.65	4.84	4.84	0.62591	Heat shock protein Hsp20 (1);HSP20-like chaperone (1);	0.220264	0.38548	N	0.001651	D	0.91630	0.7355	M	0.72576	2.205	0.37244	D	0.906252	D	0.59357	0.985	P	0.47206	0.541	D	0.92911	0.6347	10	0.42905	T	0.14	-13.2361	18.4921	0.90852	0.0:0.0:1.0:0.0	.	66	Q16082	HSPB2_HUMAN	K	66	ENSP00000302476:E66K;ENSP00000445585:E66K	ENSP00000302476:E66K	E	+	1	0	HSPB2	111289476	1.000000	0.71417	0.959000	0.39883	0.985000	0.73830	5.482000	0.66833	2.688000	0.91661	0.650000	0.86243	GAG		0.617	HSPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391669.1			A	111784266	G	A	111784266	3	1	61	1	0	0	0	0	1	0	0	0	7441	1059	37	1	202	1	HSPB2	11	111784266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38366	111784266	23222250	7670	15655										
DIXDC1	85458	broad.mit.edu	37	chr11	111844961	111844961	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccgatcaggacgggatgtCtttcgatatagacagaggta	12	8	2	2	rs587683500		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111844961C>A	ENST00000529225.1	+	5	808	c.528C>A	c.(526-528)gtC>gtA	p.V176V	DIXDC1_ENST00000389821.4_3'UTR|DIXDC1_ENST00000531396.1_Silent_p.V177V|DIXDC1_ENST00000440460.2_Silent_p.V177V	NM_001278542.1	NP_001265471.1	Q155Q3	DIXC1_HUMAN	DIX domain containing 1	177	Actin-binding.				camera-type eye development (GO:0043010)|cell cycle (GO:0007049)|cerebellar cortex development (GO:0021695)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain development (GO:0030900)|forebrain ventricular zone progenitor cell division (GO:0021869)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of axonogenesis (GO:0050772)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JNK cascade (GO:0046330)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of JNK cascade (GO:0046328)|regulation of microtubule cytoskeleton organization (GO:0070507)|Wnt signaling pathway (GO:0016055)	axon terminus (GO:0043679)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytosol (GO:0005829)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	gamma-tubulin binding (GO:0043015)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)	p.V177V(1)		cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		GACGGGATGTCTTTCGATATA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	11											46	44	45					11																	111844961		2003	4167	6170	111350171	SO:0001819	synonymous_variant	85458			AB051522	CCDS60957.1, CCDS73381.1, CCDS73382.1	11q23.1	2014-03-20			ENSG00000150764	ENSG00000150764			23695	protein-coding gene	gene with protein product		610493				12792787	Standard	NM_001037954		Approved	KIAA1735, Dixin	uc001pmm.3	Q155Q3	OTTHUMG00000166912	ENST00000529225.1:c.528C>A	11.37:g.111844961C>A			111350171	A1A5D8|E9PRV4|Q6P2J8|Q6PIK4|Q86SR7|Q8IVY4|Q96N69|Q9C0C8	Silent	SNP	ENST00000529225.1	37																																																																																					0.507	DIXDC1-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000391831.1	NM_001037954		A	111844961	C	A	111844961	2	1	61	1	0	0	0	0	0	0	0	1	4552	900	32	2		2	DIXDC1	11	111844961	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60695	111844961	23161555	7671	15656										
DIXDC1	85458	broad.mit.edu	37	chr11	111853173	111853173	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaagaatatttagaaaaaGaaatggaggaagcaaagaaa	9	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111853173G>T	ENST00000440460.2	+	8	1174	c.877G>T	c.(877-879)Gaa>Taa	p.E293*	DIXDC1_ENST00000389821.4_3'UTR|DIXDC1_ENST00000315253.5_Nonsense_Mutation_p.E82*	NM_001037954.2	NP_001033043.1	Q155Q3	DIXC1_HUMAN	DIX domain containing 1	294	Actin-binding.				camera-type eye development (GO:0043010)|cell cycle (GO:0007049)|cerebellar cortex development (GO:0021695)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain development (GO:0030900)|forebrain ventricular zone progenitor cell division (GO:0021869)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of axonogenesis (GO:0050772)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JNK cascade (GO:0046330)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of JNK cascade (GO:0046328)|regulation of microtubule cytoskeleton organization (GO:0070507)|Wnt signaling pathway (GO:0016055)	axon terminus (GO:0043679)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytosol (GO:0005829)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	gamma-tubulin binding (GO:0043015)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)	p.E293*(1)		cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		TTTAGAAAAAGAAATGGAGGA	0.413											OREG0021331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	11											72	71	71					11																	111853173		1845	4082	5927	111358383	SO:0001587	stop_gained	85458			AB051522	CCDS60957.1, CCDS73381.1, CCDS73382.1	11q23.1	2014-03-20			ENSG00000150764	ENSG00000150764			23695	protein-coding gene	gene with protein product		610493				12792787	Standard	NM_001037954		Approved	KIAA1735, Dixin	uc001pmm.3	Q155Q3	OTTHUMG00000166912	ENST00000440460.2:c.877G>T	11.37:g.111853173G>T	ENSP00000394352:p.Glu293*	1438	111358383	A1A5D8|E9PRV4|Q6P2J8|Q6PIK4|Q86SR7|Q8IVY4|Q96N69|Q9C0C8	Nonsense_Mutation	SNP	ENST00000440460.2	37		.	.	.	.	.	.	.	.	.	.	G	40	8.004905	0.98605	.	.	ENSG00000150764	ENST00000440460;ENST00000315253	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-1.4699	19.4432	0.94831	0.0:0.0:1.0:0.0	.	.	.	.	X	293;82	.	ENSP00000314068:E82X	E	+	1	0	DIXDC1	111358383	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.781000	0.85668	2.941000	0.99782	0.655000	0.94253	GAA		0.413	DIXDC1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037954		T	111853173	G	T	111853173	4	4	61	1	0	0	0	0	0	1	0	0	4552	933	33	2	932	2	DIXDC1	11	111853173	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8212	111853173	23153343	7672	15657										
DLAT	1737	broad.mit.edu	37	chr11	111896976	111896977	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcaccatagcccgttgggINSaaaaaaaagagggggacaaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:111896976_111896977insA	ENST00000280346.6	+	2	993_994	c.334_335insA	c.(334-336)gaafs	p.E112fs	DLAT_ENST00000393051.1_Frame_Shift_Ins_p.E112fs|DLAT_ENST00000537636.1_Frame_Shift_Ins_p.E10fs	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	112	Lipoyl-binding 1. {ECO:0000255|PROSITE- ProRule:PRU01066}.			E -> K (in Ref. 4; CAA68787). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)	p.E115fs*10(1)|p.E115fs*7(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		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)		AGCCCGTTGGGAAAAAAAAGAG	0.332																																																2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	11																																								111402187	SO:0001589	frameshift_variant	1737			Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"E2 component of pyruvate dehydrogenase complex"	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.342dupA	11.37:g.111896984_111896984dupA	ENSP00000280346:p.Glu112fs		111402186	Q16783|Q53EP3	Frame_Shift_Ins	INS	ENST00000280346.6	37	CCDS8354.1																																																																																				0.332	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931		A	111896977	-	A	111896976	7	5	61	1	0	1	1	0	0	0	0	0	4560	1175	41	0	340	0	DLAT	11	111896976	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	43803	111896976	23109540	7673	15658										
NCAM1	4684	broad.mit.edu	37	chr11	113102410	113102410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtagccatgcccgtgtgtCgtcgctgaccctgaagagca	13	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113102410C>T	ENST00000533760.1	+	9	1348	c.749C>T	c.(748-750)tCg>tTg	p.S250L	NCAM1_ENST00000401611.2_Missense_Mutation_p.S377L|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000316851.7_Missense_Mutation_p.S368L	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	378	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.S377L(1)|p.S368L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GCCCGTGTGTCGTCGCTGACC	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	11											64	67	66					11																	113102410		2169	4271	6440	112607620	SO:0001583	missense	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.749C>T	11.37:g.113102410C>T	ENSP00000473281:p.Ser250Leu		112607620	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.433755	0.96150	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.68181	-0.31;-0.31	4.81	4.81	0.61882	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000001	D	0.83008	0.5161	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	D	0.85262	0.1051	9	0.72032	D	0.01	-45.9617	18.4173	0.90575	0.0:1.0:0.0:0.0	.	378;368;378;368	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	L	250;377;368	ENSP00000384055:S377L;ENSP00000318472:S368L	ENSP00000318472:S368L	S	+	2	0	NCAM1	112607620	1.000000	0.71417	0.962000	0.40283	0.972000	0.66771	7.581000	0.82535	2.659000	0.90383	0.561000	0.74099	TCG		0.612	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113102410	C	T	113102410	3	4	61	1	0	0	0	0	1	0	0	0	10233	893	31	1	1172	1	NCAM1	11	113102410	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1205434	113102410	21904106	7674	15659										
NCAM1	4684	broad.mit.edu	37	chr11	113102999	113102999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccacgatctcatggtttCgggatggccagctgctgcca	13	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113102999C>T	ENST00000533760.1	+	10	1563	c.964C>T	c.(964-966)Cgg>Tgg	p.R322W	NCAM1_ENST00000401611.2_Missense_Mutation_p.R449W|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000316851.7_Missense_Mutation_p.R440W	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	450	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.R449W(3)|p.R440W(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CTCATGGTTTCGGGATGGCCA	0.552																																																5	Substitution - Missense(5)	large_intestine(5)	11											72	73	73					11																	113102999		2026	4193	6219	112608209	SO:0001583	missense	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.964C>T	11.37:g.113102999C>T	ENSP00000473281:p.Arg322Trp		112608209	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	C	20.7	4.038920	0.75617	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.74002	-0.8;-0.8	5.73	4.8	0.61643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.071293	0.53938	U	0.000042	D	0.85396	0.5687	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.86032	0.1514	9	0.46703	T	0.11	-39.5648	14.0331	0.64629	0.3884:0.6116:0.0:0.0	.	450;440;450;440	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	W	322;449;440	ENSP00000384055:R449W;ENSP00000318472:R440W	ENSP00000318472:R440W	R	+	1	2	NCAM1	112608209	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	2.277000	0.43417	1.520000	0.48965	0.557000	0.71058	CGG		0.552	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113102999	C	T	113102999	3	4	61	1	0	0	0	0	1	0	0	0	10233	875	31	1	1391	1	NCAM1	11	113102999	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	589	113102999	21903517	7675	15660										
NCAM1	4684	broad.mit.edu	37	chr11	113140937	113140937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccccacctcaggcctgaGcaccggggccatcgtgggca	13	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113140937G>A	ENST00000316851.7	+	16	2129	c.2129G>A	c.(2128-2130)aGc>aAc	p.S710N	NCAM1-AS1_ENST00000526229.1_RNA|NCAM1_ENST00000397957.4_3'UTR|NCAM1-AS1_ENST00000533638.1_RNA	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	720					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.S719N(1)|p.S710N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		TCAGGCCTGAGCACCGGGGCC	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	11											114	134	127					11																	113140937		2119	4256	6375	112646147	SO:0001583	missense	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000316851.7:c.2129G>A	11.37:g.113140937G>A	ENSP00000318472:p.Ser710Asn		112646147	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000316851.7	37		.	.	.	.	.	.	.	.	.	.	G	16.86	3.238193	0.58886	.	.	ENSG00000149294	ENST00000531044;ENST00000316851;ENST00000433634	T	0.65549	-0.16	5.53	5.53	0.82687	.	0.065479	0.64402	U	0.000012	T	0.52289	0.1725	.	.	.	0.45284	D	0.99828	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.09377	0.001;0.004;0.003	T	0.44590	-0.9318	9	0.19147	T	0.46	-16.9625	19.4657	0.94939	0.0:0.0:1.0:0.0	.	592;710;720	E9PLH7;P13591-1;P13591	.;.;NCAM1_HUMAN	N	592;710;175	ENSP00000318472:S710N	ENSP00000318472:S710N	S	+	2	0	NCAM1	112646147	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.611000	0.74183	2.579000	0.87056	0.563000	0.77884	AGC		0.587	NCAM1-201	KNOWN	basic	protein_coding	protein_coding		NM_000615		A	113140937	G	A	113140937	3	1	61	1	0	0	0	0	1	0	0	0	10233	971	34	3	2427	3	NCAM1	11	113140937	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37938	113140937	21865579	7676	15661										
DRD2	1813	broad.mit.edu	37	chr11	113281523	113281523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagatgatggggttcacggCgctgttgacatagcccagcc	14	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113281523C>T	ENST00000362072.3	-	8	1602	c.1258G>A	c.(1258-1260)Gcc>Acc	p.A420T	DRD2_ENST00000542968.1_Missense_Mutation_p.A420T|DRD2_ENST00000544518.1_Missense_Mutation_p.A419T|DRD2_ENST00000538967.1_Missense_Mutation_p.A422T|DRD2_ENST00000355319.2_Missense_Mutation_p.A422T|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000346454.3_Missense_Mutation_p.A391T	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	420					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)	p.A420T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		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)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGGTTCACGGCGCTGTTGACA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11											269	197	221					11																	113281523		2201	4296	6497	112786733	SO:0001583	missense	1813			M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.1258G>A	11.37:g.113281523C>T	ENSP00000354859:p.Ala420Thr		112786733	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	37	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	C	35	5.511316	0.96386	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66499	0.2795	M	0.69523	2.12	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.97110	1.0;0.977;0.977	T	0.67803	-0.5576	10	0.66056	D	0.02	.	19.6513	0.95812	0.0:1.0:0.0:0.0	.	419;391;420	F8VUV1;P14416-2;P14416	.;.;DRD2_HUMAN	T	422;391;420;419;420;422	ENSP00000347474:A422T;ENSP00000278597:A391T;ENSP00000354859:A420T;ENSP00000441068:A419T;ENSP00000442172:A420T;ENSP00000438215:A422T	ENSP00000278597:A391T	A	-	1	0	DRD2	112786733	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.803000	0.85983	2.651000	0.90000	0.655000	0.94253	GCC		0.567	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113281523	C	T	113281523	3	4	61	1	0	0	0	0	1	0	0	0	4768	768	27	1	77	1	DRD2	11	113281523	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140586	113281523	21724993	7677	15662										
DRD2	1813	broad.mit.edu	37	chr11	113283595	113283595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccagctcctgggctcgcCgggcagcctcctgcaccaga	11	18	1	1	rs200184730		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113283595C>T	ENST00000362072.3	-	7	1165	c.821G>A	c.(820-822)cGg>cAg	p.R274Q	DRD2_ENST00000542968.1_Missense_Mutation_p.R274Q|DRD2_ENST00000544518.1_Missense_Mutation_p.R273Q|DRD2_ENST00000538967.1_Missense_Mutation_p.R276Q|DRD2_ENST00000355319.2_Missense_Mutation_p.R276Q|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000346454.3_Missense_Mutation_p.R245Q|DRD2_ENST00000535984.1_5'Flank	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	274	Interaction with PPP1R9B. {ECO:0000250}.				activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)	p.R274Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		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)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CTGGGCTCGCCGGGCAGCCTC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	GLN/ARG,GLN/ARG	1,4391		0,1,2195	18	18	18		821,734	5.7	1	11		18	1,8577		0,1,4288	no	missense,missense	DRD2	NM_000795.3,NM_016574.3	43,43	0,2,6483	TT,TC,CC		0.0117,0.0228,0.0154	benign,benign	274/444,245/415	113283595	2,12968	2196	4289	6485	112788805	SO:0001583	missense	1813			M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.821G>A	11.37:g.113283595C>T	ENSP00000354859:p.Arg274Gln		112788805	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	37	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723344	0.30503	2.28E-4	1.17E-4	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967	T;T;T;T;T;T	0.72394	-0.61;-0.65;-0.58;-0.62;-0.58;-0.61	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.322809	0.33217	N	0.005149	T	0.38453	0.1041	N	0.01219	-0.95	0.30454	N	0.774972	B;B;B	0.17465	0.022;0.022;0.007	B;B;B	0.16289	0.007;0.003;0.015	T	0.37150	-0.9718	10	0.13470	T	0.59	.	9.6654	0.39981	0.0:0.8084:0.0:0.1916	.	273;245;274	F8VUV1;P14416-2;P14416	.;.;DRD2_HUMAN	Q	276;245;274;273;274;276	ENSP00000347474:R276Q;ENSP00000278597:R245Q;ENSP00000354859:R274Q;ENSP00000441068:R273Q;ENSP00000442172:R274Q;ENSP00000438215:R276Q	ENSP00000278597:R245Q	R	-	2	0	DRD2	112788805	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.588000	0.46137	2.722000	0.93159	0.655000	0.94253	CGG		0.662	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113283595	C	T	113283595	3	4	61	1	0	0	0	0	1	0	0	0	4768	652	23	1	518	1	DRD2	11	113283595	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2072	113283595	21722921	7678	15663										
ZW10	9183	broad.mit.edu	37	chr11	113608326	113608326	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattttgccaatgacctcagAaattgctgtattgagtaaag	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113608326A>C	ENST00000200135.3	-	14	2128	c.1984T>G	c.(1984-1986)Tct>Gct	p.S662A		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	662					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)	p.S662A(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		ATGACCTCAGAAATTGCTGTA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											156	145	148					11																	113608326		2201	4296	6497	113113536	SO:0001583	missense	9183			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1984T>G	11.37:g.113608326A>C	ENSP00000200135:p.Ser662Ala		113113536	A1A528	Missense_Mutation	SNP	ENST00000200135.3	37	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	A	7.497	0.651800	0.14516	.	.	ENSG00000086827	ENST00000200135	T	0.46063	0.88	5.27	0.982	0.19762	.	0.474577	0.25723	N	0.028740	T	0.17789	0.0427	N	0.08118	0	0.24908	N	0.992068	B	0.06786	0.001	B	0.04013	0.001	T	0.26985	-1.0087	10	0.07644	T	0.81	-6.6622	9.9714	0.41757	0.377:0.5272:0.0:0.0958	.	662	O43264	ZW10_HUMAN	A	662	ENSP00000200135:S662A	ENSP00000200135:S662A	S	-	1	0	ZW10	113113536	0.941000	0.31946	0.985000	0.45067	0.996000	0.88848	0.323000	0.19593	0.350000	0.24002	0.533000	0.62120	TCT		0.438	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		C	113608326	A	C	113608326	3	2	61	1	0	0	0	0	1	0	0	0	18286	246	9	4	367	4	ZW10	11	113608326	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	324731	113608326	21398190	7679	15664										
CLDN25	644672	broad.mit.edu	37	chr11	113650533	113650533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactatggcctggagtttcCgtgcaaaagtccagctcggg	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113650533C>A	ENST00000453129.2	+	1	65	c.16C>A	c.(16-18)Cgt>Agt	p.R6S		NM_001101389.1	NP_001094859.1	C9JDP6	CLD25_HUMAN	claudin 25	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.R6S(1)		large_intestine(1)|lung(6)|ovary(1)|urinary_tract(2)	10						CTGGAGTTTCCGTGCAAAAGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											79	84	83					11																	113650533		1998	4174	6172	113155743	SO:0001583	missense	644672				CCDS44736.1	11q23.2	2009-09-22			ENSG00000228607	ENSG00000228607			37218	protein-coding gene	gene with protein product							Standard	NM_001101389		Approved		uc009yyw.1	C9JDP6	OTTHUMG00000168193	ENST00000453129.2:c.16C>A	11.37:g.113650533C>A	ENSP00000396304:p.Arg6Ser		113155743		Missense_Mutation	SNP	ENST00000453129.2	37	CCDS44736.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403365	0.25291	.	.	ENSG00000228607	ENST00000453129	T	0.62498	0.02	5.04	2.99	0.34606	.	.	.	.	.	T	0.37376	0.1001	N	0.03194	-0.395	0.09310	N	1	P	0.46621	0.881	B	0.44108	0.441	T	0.08452	-1.0721	9	0.16896	T	0.51	.	8.3573	0.32338	0.2372:0.676:0.0:0.0868	.	6	C9JDP6	CLD25_HUMAN	S	6	ENSP00000396304:R6S	ENSP00000396304:R6S	R	+	1	0	CLDN25	113155743	0.000000	0.05858	0.085000	0.20634	0.059000	0.15707	-0.142000	0.10311	1.322000	0.45245	0.655000	0.94253	CGT		0.547	CLDN25-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398706.1	NM_001101389		A	113650533	C	A	113650533	3	1	61	1	0	0	0	0	1	0	0	0	3491	652	23	2	18	2	CLDN25	11	113650533	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42207	113650533	21355983	7680	15665										
USP28	57646	broad.mit.edu	37	chr11	113670059	113670059	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattgggtcgaattgttggaGgctctttcaagacgatgatt	12	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113670059G>T	ENST00000003302.4	-	25	3205	c.3137C>A	c.(3136-3138)cCt>cAt	p.P1046H	USP28_ENST00000545540.1_Missense_Mutation_p.P889H|USP28_ENST00000260188.5_Missense_Mutation_p.P1014H|USP28_ENST00000544967.1_Missense_Mutation_p.P722H	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	1046					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.P1046H(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		AATTGTTGGAGGCTCTTTCAA	0.458																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											1	Substitution - Missense(1)	large_intestine(1)	11											122	124	123					11																	113670059		2201	4296	6497	113175269	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.3137C>A	11.37:g.113670059G>T	ENSP00000003302:p.Pro1046His		113175269	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916822	0.92249	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	T;T;T;T	0.60171	0.69;0.75;0.21;0.78	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.76428	0.3986	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.993;0.999	T	0.77501	-0.2564	10	0.87932	D	0	-21.4559	19.8677	0.96824	0.0:0.0:1.0:0.0	.	889;1046;722	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	H	1046;1014;722;889	ENSP00000003302:P1046H;ENSP00000260188:P1014H;ENSP00000442431:P722H;ENSP00000444991:P889H	ENSP00000003302:P1046H	P	-	2	0	USP28	113175269	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.361000	0.97122	2.709000	0.92574	0.655000	0.94253	CCT		0.458	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113670059	G	T	113670059	3	4	61	1	0	0	0	0	1	0	0	0	17098	1000	35	2	100	2	USP28	11	113670059	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19526	113670059	21336457	7681	15666										
HTR3B	9177	broad.mit.edu	37	chr11	113802485	113802485	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctactactaacaggtctgGaatgatgaatttttatcctg	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:113802485G>T	ENST00000260191.2	+	4	521	c.264G>T	c.(262-264)tgG>tgT	p.W88C	HTR3B_ENST00000537778.1_Missense_Mutation_p.W77C	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	88					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)	p.W88C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	AACAGGTCTGGAATGATGAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11											103	99	100					11																	113802485		2201	4296	6497	113307695	SO:0001583	missense	9177			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.264G>T	11.37:g.113802485G>T	ENSP00000260191:p.Trp88Cys		113307695	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.22|19.22	3.785241|3.785241	0.70337|0.70337	.|.	.|.	ENSG00000149305|ENSG00000149305	ENST00000543092|ENST00000260191;ENST00000537778	.|D;D	.|0.98684	.|-5.07;-5.07	5.41|5.41	5.41|5.41	0.78517|0.78517	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99465|0.99465	0.9810|0.9810	H|H	0.96861|0.96861	3.895|3.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	D|D	0.98333|0.98333	1.0534|1.0534	5|10	.|0.87932	.|D	.|0	-8.1494|-8.1494	17.0425|17.0425	0.86493|0.86493	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|77;88	.|O95264-2;O95264	.|.;5HT3B_HUMAN	V|C	17|88;77	.|ENSP00000260191:W88C;ENSP00000443118:W77C	.|ENSP00000260191:W88C	G|W	+|+	2|3	0|0	HTR3B|HTR3B	113307695|113307695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	9.150000|9.150000	0.94667|0.94667	2.697000|2.697000	0.92050|0.92050	0.563000|0.563000	0.77884|0.77884	GGA|TGG		0.383	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		T	113802485	G	T	113802485	3	4	61	1	0	0	0	0	1	0	0	0	7466	1183	41	2	278	2	HTR3B	11	113802485	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132426	113802485	21204031	7682	15667										
ZBTB16	7704	broad.mit.edu	37	chr11	114057719	114057719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtgcggtgcacagttttCgaaggaggatgccctggaga	15	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114057719C>T	ENST00000335953.4	+	4	1792	c.1412C>T	c.(1411-1413)tCg>tTg	p.S471L	ZBTB16_ENST00000392996.2_Missense_Mutation_p.S471L	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	471					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S471L(1)		central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GCACAGTTTTCGAAGGAGGAT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	11											196	162	174					11																	114057719		2201	4296	6497	113562929	SO:0001583	missense	7704			Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1412C>T	11.37:g.114057719C>T	ENSP00000338157:p.Ser471Leu		113562929	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153583	0.78114	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.35789	1.29;1.29	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.393893	0.23532	N	0.047163	T	0.46795	0.1411	L	0.54863	1.705	0.41574	D	0.988708	P;D	0.58268	0.95;0.982	B;P	0.49361	0.398;0.608	T	0.49072	-0.8977	10	0.62326	D	0.03	-4.2661	19.1808	0.93622	0.0:1.0:0.0:0.0	.	471;476	Q05516;Q59H43	ZBT16_HUMAN;.	L	471;471;348	ENSP00000338157:S471L;ENSP00000376721:S471L	ENSP00000309507:S348L	S	+	2	0	ZBTB16	113562929	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	4.872000	0.63050	2.518000	0.84900	0.655000	0.94253	TCG		0.527	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		T	114057719	C	T	114057719	3	4	61	1	0	0	0	0	1	0	0	0	17565	893	31	1	1422	1	ZBTB16	11	114057719	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	255234	114057719	20948797	7683	15668										
ZBTB16	7704	broad.mit.edu	37	chr11	114112956	114112956	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcagagcgcactgcagcaGcacatggaggtccacgcggg	16	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114112956G>A	ENST00000335953.4	+	5	1901	c.1521G>A	c.(1519-1521)caG>caA	p.Q507Q	ZBTB16_ENST00000535379.1_3'UTR|RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000392996.2_Silent_p.Q507Q	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	507					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q507Q(1)		central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		CACTGCAGCAGCACATGGAGG	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	11											79	58	65					11																	114112956		2201	4296	6497	113618166	SO:0001819	synonymous_variant	7704			Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1521G>A	11.37:g.114112956G>A			113618166	Q8TAL4	Silent	SNP	ENST00000335953.4	37	CCDS8367.1																																																																																				0.627	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		A	114112956	G	A	114112956	2	1	61	1	0	0	0	0	0	0	0	1	17565	962	34	3		3	ZBTB16	11	114112956	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55237	114112956	20893560	7684	15669										
NNMT	4837	broad.mit.edu	37	chr11	114167342	114167342	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaccctcgggattacctaGaaaaatattacaagtttggt	7	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114167342G>T	ENST00000535401.1	+	3	328	c.64G>T	c.(64-66)Gaa>Taa	p.E22*	RP11-64D24.2_ENST00000544925.1_RNA|NNMT_ENST00000545255.1_5'Flank|NNMT_ENST00000541754.1_5'Flank|NNMT_ENST00000542647.1_5'Flank|NNMT_ENST00000299964.3_Nonsense_Mutation_p.E22*			P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	22					methylation (GO:0032259)|organ regeneration (GO:0031100)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	nicotinamide N-methyltransferase activity (GO:0008112)	p.E22*(1)		kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		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)	GGATTACCTAGAAAAATATTA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											78	74	75					11																	114167342		2201	4296	6497	113672552	SO:0001587	stop_gained	4837			U08021	CCDS8368.1	11q23.1	2007-08-15					2.1.1.1		7861	protein-coding gene	gene with protein product		600008				8575745	Standard	NM_006169		Approved		uc001pos.1	P40261		ENST00000535401.1:c.64G>T	11.37:g.114167342G>T	ENSP00000441434:p.Glu22*		113672552		Nonsense_Mutation	SNP	ENST00000535401.1	37	CCDS8368.1	.	.	.	.	.	.	.	.	.	.	G	43	10.316718	0.99381	.	.	ENSG00000166741	ENST00000535401;ENST00000299964	.	.	.	5.36	4.41	0.53225	.	0.317482	0.29438	N	0.012145	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-1.8274	12.6455	0.56731	0.0:0.3045:0.6955:0.0	.	.	.	.	X	22	.	ENSP00000299964:E22X	E	+	1	0	NNMT	113672552	1.000000	0.71417	0.998000	0.56505	0.854000	0.48673	1.343000	0.33930	2.526000	0.85167	0.591000	0.81541	GAA		0.428	NNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398951.1	NM_006169		T	114167342	G	T	114167342	4	4	61	1	0	0	0	0	0	1	0	0	10540	943	33	2	66	2	NNMT	11	114167342	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54386	114167342	20839174	7685	15670										
NNMT	4837	broad.mit.edu	37	chr11	114183101	114183101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggctggctacacaatcGaatggtttgaggtgatctcg	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114183101G>A	ENST00000535401.1	+	5	961	c.697G>A	c.(697-699)Gaa>Aaa	p.E233K	RP11-64D24.2_ENST00000544925.1_RNA|NNMT_ENST00000545255.1_Missense_Mutation_p.E38K|NNMT_ENST00000541754.1_Missense_Mutation_p.E38K|NNMT_ENST00000542647.1_Missense_Mutation_p.E38K|NNMT_ENST00000299964.3_Missense_Mutation_p.E233K			P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	233					methylation (GO:0032259)|organ regeneration (GO:0031100)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	nicotinamide N-methyltransferase activity (GO:0008112)	p.E233K(1)		kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		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)	CTACACAATCGAATGGTTTGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	79	80					11																	114183101		2201	4296	6497	113688311	SO:0001583	missense	4837			U08021	CCDS8368.1	11q23.1	2007-08-15					2.1.1.1		7861	protein-coding gene	gene with protein product		600008				8575745	Standard	NM_006169		Approved		uc001pos.1	P40261		ENST00000535401.1:c.697G>A	11.37:g.114183101G>A	ENSP00000441434:p.Glu233Lys		113688311		Missense_Mutation	SNP	ENST00000535401.1	37	CCDS8368.1	.	.	.	.	.	.	.	.	.	.	G	4.164	0.029023	0.08054	.	.	ENSG00000166741	ENST00000535401;ENST00000299964;ENST00000541754;ENST00000542647;ENST00000545255	T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83	4.93	-2.62	0.06152	.	0.346100	0.26286	N	0.025255	T	0.04724	0.0128	N	0.25647	0.755	0.09310	N	0.999999	B	0.20988	0.05	B	0.17722	0.019	T	0.44922	-0.9296	10	0.06099	T	0.92	-13.079	7.0651	0.25147	0.242:0.4781:0.2799:0.0	.	233	P40261	NNMT_HUMAN	K	233;233;38;38;38	ENSP00000441434:E233K;ENSP00000299964:E233K;ENSP00000445680:E38K;ENSP00000445994:E38K;ENSP00000445248:E38K	ENSP00000299964:E233K	E	+	1	0	NNMT	113688311	0.019000	0.18553	0.000000	0.03702	0.018000	0.09664	0.138000	0.16016	-0.098000	0.12285	0.563000	0.77884	GAA		0.542	NNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398951.1	NM_006169		A	114183101	G	A	114183101	3	1	61	1	0	0	0	0	1	0	0	0	10540	1059	37	1	707	1	NNMT	11	114183101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15759	114183101	20823415	7686	15671										
FAM55D	54827	broad.mit.edu	37	chr11	114441904	114441904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccatagtgtctgggcttCtcagaagaagatgctgaatg	11	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114441904C>A	ENST00000375478.3	-	6	1571	c.1391G>T	c.(1390-1392)aGa>aTa	p.R464I	NXPE4_ENST00000424261.2_Missense_Mutation_p.R180I	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	464						extracellular vesicular exosome (GO:0070062)		p.R464I(1)									GTCTGGGCTTCTCAGAAGAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											143	129	133					11																	114441904		1888	4119	6007	113947114	SO:0001583	missense	54827			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1391G>T	11.37:g.114441904C>A	ENSP00000364627:p.Arg464Ile		113947114	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.194800	0.78902	.	.	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.25579	1.79;1.79	5.39	3.52	0.40303	.	0.000000	0.64402	D	0.000008	T	0.58637	0.2136	M	0.93763	3.455	0.50632	D	0.999883	D	0.89917	1.0	D	0.85130	0.997	T	0.66806	-0.5830	10	0.87932	D	0	.	11.1514	0.48462	0.0:0.8481:0.0:0.1519	.	464	Q6UWF7	FA55D_HUMAN	I	180;464	ENSP00000401503:R180I;ENSP00000364627:R464I	ENSP00000364627:R464I	R	-	2	0	FAM55D	113947114	0.998000	0.40836	0.992000	0.48379	0.995000	0.86356	3.146000	0.50631	0.765000	0.33221	0.655000	0.94253	AGA		0.408	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		A	114441904	C	A	114441904	3	1	61	1	0	0	0	0	1	0	0	0	5606	913	32	2	247	2	FAM55D	11	114441904	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258803	114441904	20564612	7687	15672										
FAM55D	54827	broad.mit.edu	37	chr11	114441972	114441972	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaaaacatcaatgggaaaGggtctgaaatgctggcccag	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114441972G>T	ENST00000375478.3	-	6	1503	c.1323C>A	c.(1321-1323)ccC>ccA	p.P441P	NXPE4_ENST00000424261.2_Silent_p.P157P	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	441						extracellular vesicular exosome (GO:0070062)		p.P441P(1)									CAATGGGAAAGGGTCTGAAAT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	11											144	134	138					11																	114441972		1865	4087	5952	113947182	SO:0001819	synonymous_variant	54827			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1323C>A	11.37:g.114441972G>T			113947182	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																				0.448	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		T	114441972	G	T	114441972	2	4	61	1	0	0	0	0	0	0	0	1	5606	987	35	2		2	FAM55D	11	114441972	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68	114441972	20564544	7688	15673										
FAM55D	54827	broad.mit.edu	37	chr11	114442144	114442144	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcctatccaaatccacaGcaagctggtgttgcaatttt	7	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:114442144G>T	ENST00000375478.3	-	6	1331	c.1151C>A	c.(1150-1152)gCt>gAt	p.A384D	NXPE4_ENST00000424261.2_Missense_Mutation_p.A100D	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	384						extracellular vesicular exosome (GO:0070062)		p.A384D(1)									CAAATCCACAGCAAGCTGGTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	11											210	187	194					11																	114442144		1912	4138	6050	113947354	SO:0001583	missense	54827			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1151C>A	11.37:g.114442144G>T	ENSP00000364627:p.Ala384Asp		113947354	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.618233	0.66787	.	.	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.19105	2.17;2.23	5.44	2.05	0.26809	.	0.317840	0.25912	N	0.027496	T	0.46190	0.1380	M	0.90870	3.155	0.33784	D	0.624576	D	0.64830	0.994	D	0.67725	0.953	T	0.58707	-0.7589	10	0.35671	T	0.21	.	7.4306	0.27126	0.1957:0.1388:0.6655:0.0	.	384	Q6UWF7	FA55D_HUMAN	D	100;384	ENSP00000401503:A100D;ENSP00000364627:A384D	ENSP00000364627:A384D	A	-	2	0	FAM55D	113947354	1.000000	0.71417	0.700000	0.30305	0.994000	0.84299	1.798000	0.38814	0.777000	0.33496	0.609000	0.83330	GCT		0.398	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		T	114442144	G	T	114442144	3	4	61	1	0	0	0	0	1	0	0	0	5606	971	34	2	487	2	FAM55D	11	114442144	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172	114442144	20564372	7689	15674										
CADM1	23705	broad.mit.edu	37	chr11	115049434	115049434	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaacaccaccaccgccacGacgccaccgatcacggcatg	9	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:115049434G>A	ENST00000452722.3	-	9	1160	c.1140C>T	c.(1138-1140)gtC>gtT	p.V380V	CADM1_ENST00000537058.1_Silent_p.V391V|CADM1_ENST00000536727.1_Silent_p.V381V|CADM1_ENST00000331581.6_Silent_p.V409V|CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000542447.2_Silent_p.V352V	NM_014333.3	NP_055148.3			cell adhesion molecule 1									p.V380V(1)		cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		CCACCGCCACGACGCCACCGA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	11											131	114	119					11																	115049434		2201	4296	6497	114554644	SO:0001819	synonymous_variant	23705			AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1140C>T	11.37:g.115049434G>A			114554644		Silent	SNP	ENST00000452722.3	37	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	G	5.211	0.224538	0.09916	.	.	ENSG00000182985	ENST00000545380	.	.	.	5.0	3.08	0.35506	.	.	.	.	.	T	0.57036	0.2026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53422	-0.8441	4	.	.	.	.	8.3511	0.32303	0.3017:0.0:0.6983:0.0	.	.	.	.	C	351	.	.	R	-	1	0	CADM1	114554644	0.948000	0.32251	1.000000	0.80357	0.996000	0.88848	0.079000	0.14782	1.349000	0.45751	0.655000	0.94253	CGT		0.517	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		A	115049434	G	A	115049434	2	1	61	1	0	0	0	0	0	0	0	1	2572	1045	37	1		1	CADM1	11	115049434	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	607290	115049434	19957082	7690	15675										
ZNF259	8882	broad.mit.edu	37	chr11	116656573	116656573	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaatgaactcatcaattCtttcagctgtagcatctttg	6	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:116656573C>A	ENST00000227322.3	-	5	580	c.521G>T	c.(520-522)aGa>aTa	p.R174I		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		174					apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)	p.R174I(2)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		CTCATCAATTCTTTCAGCTGT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	11											171	143	153					11																	116656573		2201	4296	6497	116161783	SO:0001583	missense	8882																														ENST00000227322.3:c.521G>T	11.37:g.116656573C>A	ENSP00000227322:p.Arg174Ile		116161783	Q2TAA0	Missense_Mutation	SNP	ENST00000227322.3	37	CCDS8375.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	26.3|26.3|26.3	4.725364|4.725364|4.725364	0.89298|0.89298|0.89298	.|.|.	.|.|.	ENSG00000109917|ENSG00000109917|ENSG00000109917	ENST00000444935|ENST00000429220|ENST00000227322	.|.|T	.|.|0.47177	.|.|0.85	5.61|5.61|5.61	4.48|4.48|4.48	0.54585|0.54585|0.54585	.|.|Zinc finger, ZPR1-type (3);	.|.|0.079874	.|.|0.85682	.|.|D	.|.|0.000000	.|T|T	.|0.39937|0.39937	.|0.1097|0.1097	L|L|L	0.52011|0.52011|0.52011	1.625|1.625|1.625	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|P;P	.|.|0.39883	.|.|0.564;0.693	.|.|B;B	.|.|0.41374	.|.|0.242;0.355	.|T|T	.|0.42799|0.42799	.|-0.9430|-0.9430	.|5|10	.|.|0.72032	.|.|D	.|.|0.01	-6.4738|-6.4738|-6.4738	4.1595|4.1595|4.1595	0.10277|0.10277|0.10277	0.0:0.6884:0.0:0.3116|0.0:0.6884:0.0:0.3116|0.0:0.6884:0.0:0.3116	.|.|.	.|.|123;174	.|.|B4DVT8;O75312	.|.|.;ZPR1_HUMAN	X|N|I	174|116|174	.|.|ENSP00000227322:R174I	.|.|ENSP00000227322:R174I	E|K|R	-|-|-	1|3|2	0|2|0	ZNF259|ZNF259|ZNF259	116161783|116161783|116161783	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	5.009000|5.009000|5.009000	0.63998|0.63998|0.63998	2.808000|2.808000|2.808000	0.96608|0.96608|0.96608	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|AAG|AGA		0.483	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2			A	116656573	C	A	116656573	3	1	61	1	0	0	0	0	1	0	0	0	17840	913	32	2	898	2	ZNF259	11	116656573	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1607139	116656573	18349943	7691	15676										
SIK3	23387	broad.mit.edu	37	chr11	116728696	116728696	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctttggtcaatgtacttGaactcttactgtcttggaag	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:116728696G>T	ENST00000292055.4	-	20	3202	c.3167C>A	c.(3166-3168)tCa>tAa	p.S1056*	SIK3_ENST00000375300.1_Nonsense_Mutation_p.S1114*|SIK3_ENST00000446921.2_Nonsense_Mutation_p.S1054*|SIK3_ENST00000375288.1_Nonsense_Mutation_p.S391*|SIK3_ENST00000542607.1_Nonsense_Mutation_p.S996*|SIK3_ENST00000434315.2_Nonsense_Mutation_p.S895*|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000488337.1_5'UTR	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1056					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S1162*(2)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						CAATGTACTTGAACTCTTACT	0.547																																																2	Substitution - Nonsense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	11											93	93	93					11																	116728696		2201	4296	6497	116233906	SO:0001587	stop_gained	23387			AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.3167C>A	11.37:g.116728696G>T	ENSP00000292055:p.Ser1056*		116233906	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Nonsense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.105833|7.105833	0.98066|0.98066	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000445177;ENST00000446921|ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315	.|.	.|.	.|.	5.54|5.54	3.6|3.6	0.41247|0.41247	.|.	.|0.505775	.|0.14661	.|U	.|0.305982	T|.	0.16685|.	0.0401|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.30297|.	-0.9983|.	3|.	.|0.02654	.|T	.|1	.|.	6.3893|6.3893	0.21577|0.21577	0.1655:0.1489:0.6856:0.0|0.1655:0.1489:0.6856:0.0	.|.	.|.	.|.	.|.	L|X	1155;1018|1114;1056;391;996;895	.|.	.|ENSP00000292055:S1056X	F|S	-|-	3|2	2|0	SIK3|SIK3	116233906|116233906	0.086000|0.086000	0.21541|0.21541	0.001000|0.001000	0.08648|0.08648	0.061000|0.061000	0.15899|0.15899	2.639000|2.639000	0.46570|0.46570	0.617000|0.617000	0.30160|0.30160	0.563000|0.563000	0.77884|0.77884	TTC|TCA		0.547	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		T	116728696	G	T	116728696	4	4	61	1	0	0	0	0	0	1	0	0	14356	1294	45	2	640	2	SIK3	11	116728696	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72123	116728696	18277820	7692	15677										
TAGLN	6876	broad.mit.edu	37	chr11	117073799	117073799	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcgagaagaagtatgacGaggagctggaggagcggctg	17	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:117073799G>A	ENST00000532870.1	+	1	1211	c.70G>A	c.(70-72)Gag>Aag	p.E24K	TAGLN_ENST00000392951.4_Missense_Mutation_p.E24K|TAGLN_ENST00000530649.1_Missense_Mutation_p.E24K|PCSK7_ENST00000529458.1_5'Flank			Q01995	TAGL_HUMAN	transgelin	24	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)		p.E24K(1)		central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		GAAGTATGACGAGGAGCTGGA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11											69	60	63					11																	117073799		2201	4296	6497	116579009	SO:0001583	missense	6876			M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"SM22-alpha", "transgelin variant 2"	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.70G>A	11.37:g.117073799G>A	ENSP00000432282:p.Glu24Lys		116579009	O15542	Missense_Mutation	SNP	ENST00000532870.1	37	CCDS8381.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680653	0.47886	.	.	ENSG00000149591	ENST00000392951;ENST00000525531;ENST00000278968;ENST00000529792;ENST00000530649;ENST00000532870	T;T;T;T;T;T	0.44083	1.59;1.59;1.59;0.93;1.59;1.59	4.74	4.74	0.60224	Calponin homology domain (3);	0.270867	0.42294	D	0.000740	T	0.29389	0.0732	N	0.16743	0.435	0.48288	D	0.99962	B	0.06786	0.001	B	0.04013	0.001	T	0.04708	-1.0932	10	0.27082	T	0.32	.	17.2567	0.87059	0.0:0.0:1.0:0.0	.	24	Q01995	TAGL_HUMAN	K	24	ENSP00000376678:E24K;ENSP00000432054:E24K;ENSP00000278968:E24K;ENSP00000431862:E24K;ENSP00000431941:E24K;ENSP00000432282:E24K	ENSP00000278968:E24K	E	+	1	0	TAGLN	116579009	1.000000	0.71417	0.996000	0.52242	0.679000	0.39708	4.379000	0.59575	2.619000	0.88677	0.561000	0.74099	GAG		0.597	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522		A	117073799	G	A	117073799	3	1	61	1	0	0	0	0	1	0	0	0	15577	1059	37	1	72	1	TAGLN	11	117073799	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	345103	117073799	17932717	7693	15678										
RNF214	257160	broad.mit.edu	37	chr11	117150911	117150911	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcactagagagccggaaaGagttactggtactgaaacta	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:117150911G>T	ENST00000531452.1	+	8	1127	c.1081G>T	c.(1081-1083)Gag>Tag	p.E361*	RNF214_ENST00000530849.1_Nonsense_Mutation_p.E206*|RNF214_ENST00000300650.4_Nonsense_Mutation_p.E361*|RNF214_ENST00000531287.1_Nonsense_Mutation_p.E206*	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	361							zinc ion binding (GO:0008270)	p.E361*(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		GAGCCGGAAAGAGTTACTGGT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											141	130	134					11																	117150911		1827	4090	5917	116656121	SO:0001587	stop_gained	257160			AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.1081G>T	11.37:g.117150911G>T	ENSP00000431643:p.Glu361*		116656121	B2RUW0|B4DTD1	Nonsense_Mutation	SNP	ENST00000531452.1	37	CCDS41720.1	.	.	.	.	.	.	.	.	.	.	G	36	5.826242	0.96996	.	.	ENSG00000167257	ENST00000531287;ENST00000531452;ENST00000530849;ENST00000300650	.	.	.	5.5	5.5	0.81552	.	0.283001	0.39083	N	0.001472	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-10.6764	18.7341	0.91748	0.0:0.0:1.0:0.0	.	.	.	.	X	206;361;206;361	.	ENSP00000300650:E361X	E	+	1	0	RNF214	116656121	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.481000	0.73608	2.732000	0.93576	0.655000	0.94253	GAG		0.353	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		T	117150911	G	T	117150911	4	4	61	1	0	0	0	0	0	1	0	0	13515	943	33	2	1107	2	RNF214	11	117150911	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77112	117150911	17855605	7694	15679										
CEP164	22897	broad.mit.edu	37	chr11	117280659	117280659	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggacgacttcctgttggaGaagtggcgcaagtattttcc	13	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:117280659G>T	ENST00000278935.3	+	30	4221	c.4074G>T	c.(4072-4074)gaG>gaT	p.E1358D	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1358					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.E1358D(1)		breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		TCCTGTTGGAGAAGTGGCGCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											51	53	53					11																	117280659		2201	4296	6497	116785869	SO:0001583	missense	22897			AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.4074G>T	11.37:g.117280659G>T	ENSP00000278935:p.Glu1358Asp		116785869	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.570105	0.65765	.	.	ENSG00000110274	ENST00000278935	T	0.36157	1.27	4.4	2.5	0.30297	.	0.000000	0.48767	D	0.000166	T	0.53174	0.1780	M	0.72894	2.215	0.32756	N	0.505796	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	T	0.62863	-0.6764	10	0.62326	D	0.03	-19.4746	8.0169	0.30387	0.1927:0.0:0.8073:0.0	.	1358;1353	Q9UPV0;Q9UPV0-2	CE164_HUMAN;.	D	1358	ENSP00000278935:E1358D	ENSP00000278935:E1358D	E	+	3	2	CEP164	116785869	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.132000	0.57977	0.848000	0.35191	0.561000	0.74099	GAG		0.587	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		T	117280659	G	T	117280659	3	4	61	1	0	0	0	0	1	0	0	0	3255	933	33	2	4184	2	CEP164	11	117280659	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129748	117280659	17725857	7695	15680										
TMPRSS13	84000	broad.mit.edu	37	chr11	117772978	117772978	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattttctgaatcgcacctcGctctgaggaagagaatggga	12	8	2	3	rs190994759		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:117772978G>A	ENST00000524993.1	-	13	1737	c.1680C>T	c.(1678-1680)agC>agT	p.S560S	TMPRSS13_ENST00000528626.1_Silent_p.S525S	NM_001077263.2	NP_001070731.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	0						blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.S560S(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		ATCGCACCTCGCTCTGAGGAA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	11											49	54	52					11																	117772978		1985	4179	6164	117278188	SO:0001819	synonymous_variant	84000			AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000524993.1:c.1680C>T	11.37:g.117772978G>A			117278188	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000524993.1	37	CCDS41721.1																																																																																				0.577	TMPRSS13-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392317.1	NM_032046		A	117772978	G	A	117772978	2	1	61	1	0	0	0	0	0	0	0	1	16284	1078	38	1		1	TMPRSS13	11	117772978	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	492319	117772978	17233538	7696	15681										
TMPRSS4	56649	broad.mit.edu	37	chr11	117978571	117978571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaacagccaggagcttCgcatgcggaactcaagtggg	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:117978571C>T	ENST00000437212.3	+	6	737	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C	TMPRSS4_ENST00000522824.1_Missense_Mutation_p.R170C|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.R28C|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.R135C|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.R173C			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	175	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.R175C(2)		breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	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)		CCAGGAGCTTCGCATGCGGAA	0.542																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	11											72	64	67					11																	117978571		2200	4296	6496	117483781	SO:0001583	missense	56649			AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"Serine peptidases / Transmembrane"	11878	protein-coding gene	gene with protein product	"transmembrane serine protease 3", "membrane-type serine protease 2", "type II membrane serine protease"	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.523C>T	11.37:g.117978571C>T	ENSP00000416037:p.Arg175Cys		117483781	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.98|12.98	2.100554|2.100554	0.37048|0.37048	.|.	.|.	ENSG00000137648|ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151|ENST00000517544	T;D;T;T;T;T|.	0.88896|.	0.74;-2.44;0.74;0.74;0.74;0.74|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Speract/scavenger receptor-related (2);|.	0.611504|.	0.15422|.	N|.	0.263216|.	T|T	0.41396|0.41396	0.1157|0.1157	L|L	0.34521|0.34521	1.04|1.04	0.23754|0.23754	N|N	0.996939|0.996939	D;D;D;P;D|.	0.62365|.	0.964;0.978;0.991;0.951;0.987|.	B;B;B;B;P|.	0.46825|.	0.232;0.328;0.328;0.394;0.528|.	T|T	0.30995|0.30995	-0.9959|-0.9959	10|5	0.40728|.	T|.	0.16|.	.|.	14.4689|14.4689	0.67501|0.67501	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	150;135;28;175;173|.	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3|.	.;.;.;TMPS4_HUMAN;.|.	C|L	173;28;135;175;170;122|141	ENSP00000435184:R173C;ENSP00000428814:R28C;ENSP00000429209:R135C;ENSP00000416037:R175C;ENSP00000430547:R170C;ENSP00000428407:R122C|.	ENSP00000416037:R175C|.	R|S	+|+	1|2	0|0	TMPRSS4|TMPRSS4	117483781|117483781	0.997000|0.997000	0.39634|0.39634	0.943000|0.943000	0.38184|0.38184	0.040000|0.040000	0.13550|0.13550	3.827000|3.827000	0.55745|0.55745	2.472000|2.472000	0.83506|0.83506	0.585000|0.585000	0.79938|0.79938	CGC|TCG		0.542	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		T	117978571	C	T	117978571	3	4	61	1	0	0	0	0	1	0	0	0	16288	884	31	1	545	1	TMPRSS4	11	117978571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205593	117978571	17027945	7697	15682										
AMICA1	120425	broad.mit.edu	37	chr11	118074365	118074365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagtttgtggtagtaacGaaatacaatctcctcctaga	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118074365G>A	ENST00000356289.5	-	6	723	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	AMICA1_ENST00000533261.1_Missense_Mutation_p.R173C|AMICA1_ENST00000292067.7_Missense_Mutation_p.R174C|AMICA1_ENST00000526620.1_Missense_Mutation_p.R145C	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	184	Ig-like V-type 2.				blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)	p.R174G(1)|p.R174C(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	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;3.4e-05)		TGGTAGTAACGAAATACAATC	0.502																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	11											78	78	78					11																	118074365		2200	4296	6496	117579575	SO:0001583	missense	120425			AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"Immunoglobulin superfamily / V-set domain containing"	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.550C>T	11.37:g.118074365G>A	ENSP00000348635:p.Arg184Cys		117579575	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	37	CCDS41723.1	.	.	.	.	.	.	.	.	.	.	G	8.409	0.843756	0.16963	.	.	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620;ENST00000537867	D;D;D;D	0.94723	-3.5;-3.5;-3.47;-3.5	4.26	-0.719	0.11201	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.534510	0.03913	N	0.282253	D	0.88074	0.6339	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.22346	0.068;0.068;0.068;0.068;0.055	B;B;B;B;B	0.20184	0.028;0.028;0.028;0.028;0.016	T	0.76520	-0.2929	10	0.44086	T	0.13	0.8174	2.4244	0.04455	0.2793:0.0:0.3162:0.4045	.	184;145;184;173;174	B4DVI6;E9PKK2;Q86YT9;E9PR26;Q86YT9-2	.;.;JAML1_HUMAN;.;.	C	184;174;173;145;145	ENSP00000348635:R184C;ENSP00000292067:R174C;ENSP00000436117:R173C;ENSP00000431218:R145C	ENSP00000292067:R174C	R	-	1	0	AMICA1	117579575	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.403000	0.02497	0.011000	0.14865	0.491000	0.48974	CGT		0.502	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206		A	118074365	G	A	118074365	3	1	61	1	0	0	0	0	1	0	0	0	574	1058	37	1	654	1	AMICA1	11	118074365	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95794	118074365	16932151	7698	15683										
MPZL2	10205	broad.mit.edu	37	chr11	118134857	118134857	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaccgcacgagtagagctCttgccatacatgagggaaac	11	11	1	2	rs200147114	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118134857C>A	ENST00000278937.2	-	1	140	c.12G>T	c.(10-12)aaG>aaT	p.K4N	MPZL2_ENST00000438295.2_Missense_Mutation_p.K4N|MPZL2_ENST00000525647.1_5'UTR	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	4					anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K4N(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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;3.04e-05)		GAGTAGAGCTCTTGCCATACA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	11											84	75	78					11																	118134857		2200	4296	6496	117640067	SO:0001583	missense	10205			AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"Immunoglobulin superfamily / V-set domain containing"	3496	protein-coding gene	gene with protein product		604873	"epithelial V-like antigen 1"	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.12G>T	11.37:g.118134857C>A	ENSP00000278937:p.Lys4Asn		117640067	A8K2R1	Missense_Mutation	SNP	ENST00000278937.2	37	CCDS8393.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.195232	0.78902	.	.	ENSG00000149573	ENST00000278937;ENST00000438295	D;D	0.97480	-4.4;-4.4	5.35	4.38	0.52667	.	1.221950	0.05569	N	0.570665	D	0.94918	0.8357	L	0.36672	1.1	0.23784	N	0.99686	B	0.19583	0.037	B	0.19391	0.025	D	0.86715	0.1938	10	0.59425	D	0.04	.	11.1875	0.48666	0.0:0.8147:0.1853:0.0	.	4	O60487	MPZL2_HUMAN	N	4	ENSP00000278937:K4N;ENSP00000408362:K4N	ENSP00000278937:K4N	K	-	3	2	MPZL2	117640067	0.372000	0.25064	0.447000	0.26932	0.988000	0.76386	0.747000	0.26290	2.516000	0.84829	0.591000	0.81541	AAG		0.592	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797		A	118134857	C	A	118134857	3	1	61	1	0	0	0	0	1	0	0	0	9780	912	32	2	655	2	MPZL2	11	118134857	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60492	118134857	16871659	7699	15684										
UBE4A	9354	broad.mit.edu	37	chr11	118239408	118239408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagagcctggatgaattcGattactctgtggctgagatt	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118239408G>A	ENST00000431736.2	+	3	256	c.184G>A	c.(184-186)Gat>Aat	p.D62N	UBE4A_ENST00000252108.3_Missense_Mutation_p.D62N					ubiquitination factor E4A									p.D62N(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	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;3.28e-05)		GGATGAATTCGATTACTCTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											222	217	219					11																	118239408		2200	4296	6496	117744618	SO:0001583	missense	9354			D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.184G>A	11.37:g.118239408G>A	ENSP00000387362:p.Asp62Asn		117744618		Missense_Mutation	SNP	ENST00000431736.2	37	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146829	0.77888	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.46063	0.88;0.88	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	L	0.38838	1.175	0.80722	D	1	P;D	0.63880	0.893;0.993	B;P	0.51806	0.259;0.68	T	0.27123	-1.0083	10	0.35671	T	0.21	-13.7985	18.8905	0.92399	0.0:0.0:1.0:0.0	.	62;62	Q14139;Q14139-2	UBE4A_HUMAN;.	N	62	ENSP00000252108:D62N;ENSP00000387362:D62N	ENSP00000252108:D62N	D	+	1	0	UBE4A	117744618	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.947000	0.93000	2.707000	0.92482	0.655000	0.94253	GAT		0.438	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		A	118239408	G	A	118239408	3	1	61	1	0	0	0	0	1	0	0	0	16922	1058	37	1	190	1	UBE4A	11	118239408	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104551	118239408	16767108	7700	15685										
ATP5L	10632	broad.mit.edu	37	chr11	118277667	118277667	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagctgctgtgacttactCgaagcctcgattggccacat	9	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118277667C>T	ENST00000300688.3	+	2	580	c.68C>T	c.(67-69)tCg>tTg	p.S23L	ATP5L_ENST00000524422.1_Missense_Mutation_p.S23L|ATP5L_ENST00000529770.1_3'UTR	NM_006476.4	NP_006467.4	O75964	ATP5L_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G	23					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)	p.S23L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)	7	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;3.07e-05)		GTGACTTACTCGAAGCCTCGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											36	31	32					11																	118277667		2200	4296	6496	117782877	SO:0001583	missense	10632			AF092124	CCDS8397.1	11q23.3	2012-10-12	2010-06-11		ENSG00000167283	ENSG00000167283		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	14247	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G"			11230166, 11042152	Standard	NR_033759		Approved	ATP5JG	uc001psx.3	O75964		ENST00000300688.3:c.68C>T	11.37:g.118277667C>T	ENSP00000300688:p.Ser23Leu		117782877	A8K0K3|Q96BV6|Q9UBZ7	Missense_Mutation	SNP	ENST00000300688.3	37	CCDS8397.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604391	0.66445	.	.	ENSG00000167283	ENST00000300688;ENST00000524422	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.67344	0.2883	L	0.56769	1.78	0.80722	D	1	B	0.13594	0.008	B	0.20577	0.03	T	0.60697	-0.7212	9	0.42905	T	0.14	0.2161	20.0338	0.97549	0.0:1.0:0.0:0.0	.	23	O75964	ATP5L_HUMAN	L	23	.	ENSP00000300688:S23L	S	+	2	0	ATP5L	117782877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.157000	0.77461	2.836000	0.97738	0.655000	0.94253	TCG		0.458	ATP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389220.1	NM_006476		T	118277667	C	T	118277667	3	4	61	1	0	0	0	0	1	0	0	0	1161	893	31	1	74	1	ATP5L	11	118277667	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38259	118277667	16728849	7701	15686										
MLL	4297	broad.mit.edu	37	chr11	118343215	118343215	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgattagagtctacaccGaatagtagattcagtgcccc	9	12	2	2	rs542752721		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118343215G>A	ENST00000389506.5	+	3	1341	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	KMT2A_ENST00000354520.4_Silent_p.P447P|KMT2A_ENST00000534358.1_Silent_p.P447P			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	447					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.P447P(1)									AGTCTACACCGAATAGTAGAT	0.463													G|||	1	0.000199681	0	0	5008	,	,		16755	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	11											116	128	124					11																	118343215		2200	4296	6496	117848425	SO:0001819	synonymous_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.1341G>A	11.37:g.118343215G>A			117848425	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.463	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118343215	G	A	118343215	2	1	61	1	0	0	0	0	0	0	0	1	9650	1045	37	1		1	MLL	11	118343215	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65548	118343215	16663301	7702	15687										
MLL	4297	broad.mit.edu	37	chr11	118344081	118344081	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagtatccaatagaaaaaGgaaaagaaaagtgtttagtc	10	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118344081G>T	ENST00000389506.5	+	3	2207	c.2207G>T	c.(2206-2208)aGg>aTg	p.R736M	KMT2A_ENST00000354520.4_Missense_Mutation_p.R736M|KMT2A_ENST00000534358.1_Missense_Mutation_p.R736M			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	736					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R736M(1)									AATAGAAAAAGGAAAAGAAAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											82	77	79					11																	118344081		2200	4296	6496	117849291	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.2207G>T	11.37:g.118344081G>T	ENSP00000374157:p.Arg736Met		117849291	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.027118	0.35797	.	.	ENSG00000118058	ENST00000534358;ENST00000531904;ENST00000389506;ENST00000354520	D;T;D;D	0.84442	-1.84;1.93;-1.85;-1.84	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.86535	0.5956	L	0.27053	0.805	0.46954	D	0.999263	D;D;D	0.67145	0.991;0.991;0.996	P;P;P	0.56700	0.687;0.687;0.804	D	0.87789	0.2617	10	0.87932	D	0	.	20.1894	0.98226	0.0:0.0:1.0:0.0	.	736;736;769	E9PQG7;Q03164;E9PR05	.;MLL1_HUMAN;.	M	736;769;736;736	ENSP00000436786:R736M;ENSP00000432391:R769M;ENSP00000374157:R736M;ENSP00000346516:R736M	ENSP00000346516:R736M	R	+	2	0	MLL	117849291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.077000	0.71275	2.781000	0.95711	0.591000	0.81541	AGG		0.418	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118344081	G	T	118344081	3	4	61	1	0	0	0	0	1	0	0	0	9650	1000	35	2	2217	2	MLL	11	118344081	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	866	118344081	16662435	7703	15688										
MLL	4297	broad.mit.edu	37	chr11	118359410	118359410	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctctggaggaccagctgGaaaattggtgttgtcgtcgt	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118359410G>T	ENST00000389506.5	+	11	4414	c.4414G>T	c.(4414-4416)Gaa>Taa	p.E1472*	KMT2A_ENST00000354520.4_Nonsense_Mutation_p.E1434*|KMT2A_ENST00000534358.1_Nonsense_Mutation_p.E1472*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1472					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.E1472*(1)									GGACCAGCTGGAAAATTGGTG	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											123	108	113					11																	118359410		2200	4296	6496	117864620	SO:0001587	stop_gained	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.4414G>T	11.37:g.118359410G>T	ENSP00000374157:p.Glu1472*		117864620	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	44	10.836978	0.99476	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313;ENST00000392873	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.8024	0.96513	0.0:0.0:1.0:0.0	.	.	.	.	X	1472;1472;1434;382;184	.	ENSP00000346516:E1434X	E	+	1	0	MLL	117864620	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.416000	0.97383	2.752000	0.94435	0.655000	0.94253	GAA		0.458	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118359410	G	T	118359410	4	4	61	1	0	0	0	0	0	1	0	0	9650	1175	41	2	4456	2	MLL	11	118359410	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15329	118359410	16647106	7704	15689										
MLL	4297	broad.mit.edu	37	chr11	118373354	118373354	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaaagtagttgatcatgtCttagggccactgaattcaag	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118373354C>A	ENST00000389506.5	+	27	6738	c.6738C>A	c.(6736-6738)gtC>gtA	p.V2246V	KMT2A_ENST00000354520.4_Silent_p.V2208V|KMT2A_ENST00000534358.1_Silent_p.V2249V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2246					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.V2246V(1)									TTGATCATGTCTTAGGGCCAC	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	11											102	96	98					11																	118373354		2200	4296	6496	117878564	SO:0001819	synonymous_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.6738C>A	11.37:g.118373354C>A			117878564	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.423	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118373354	C	A	118373354	2	1	61	1	0	0	0	0	0	0	0	1	9650	900	32	2		2	MLL	11	118373354	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13944	118373354	16633162	7705	15690										
MLL	4297	broad.mit.edu	37	chr11	118375900	118375900	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgttctccaaactcttcCaaatggagtgacccaaaaaa	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118375900C>A	ENST00000389506.5	+	27	9284	c.9284C>A	c.(9283-9285)cCa>cAa	p.P3095Q	KMT2A_ENST00000354520.4_Missense_Mutation_p.P3057Q|KMT2A_ENST00000534358.1_Missense_Mutation_p.P3098Q			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3095					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.P3095Q(1)									CAAACTCTTCCAAATGGAGTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											140	145	143					11																	118375900		2200	4295	6495	117881110	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.9284C>A	11.37:g.118375900C>A	ENSP00000374157:p.Pro3095Gln		117881110	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.577604	0.45902	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.91237	-2.81;-2.81;-2.73	6.08	6.08	0.98989	.	0.053101	0.85682	D	0.000000	D	0.94245	0.8152	M	0.68952	2.095	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.58721	0.844;0.844	D	0.93965	0.7244	10	0.87932	D	0	.	20.6721	0.99693	0.0:1.0:0.0:0.0	.	3098;3095	E9PQG7;Q03164	.;MLL1_HUMAN	Q	3098;3095;3057;2005	ENSP00000436786:P3098Q;ENSP00000374157:P3095Q;ENSP00000346516:P3057Q	ENSP00000346516:P3057Q	P	+	2	0	MLL	117881110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.894000	0.99253	0.591000	0.81541	CCA		0.473	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118375900	C	A	118375900	3	1	61	1	0	0	0	0	1	0	0	0	9650	594	21	2	9390	2	MLL	11	118375900	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2546	118375900	16630616	7706	15691										
MLL	4297	broad.mit.edu	37	chr11	118376743	118376743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttggtaccccagatattgGctcaataagcaatcttttaa	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118376743G>A	ENST00000389506.5	+	27	10127	c.10127G>A	c.(10126-10128)gGc>gAc	p.G3376D	KMT2A_ENST00000354520.4_Missense_Mutation_p.G3338D|KMT2A_ENST00000534358.1_Missense_Mutation_p.G3379D			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3376					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.G3376D(1)									CCAGATATTGGCTCAATAAGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											141	147	145					11																	118376743		2200	4295	6495	117881953	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10127G>A	11.37:g.118376743G>A	ENSP00000374157:p.Gly3376Asp		117881953	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.321434	0.60634	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.86432	-2.12;-2.12;-2.08	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.83797	0.5332	L	0.46157	1.445	0.58432	D	0.99999	P;P	0.43352	0.804;0.804	B;B	0.41412	0.356;0.356	T	0.82502	-0.0425	10	0.34782	T	0.22	.	13.5041	0.61474	0.071:0.0:0.929:0.0	.	3379;3376	E9PQG7;Q03164	.;MLL1_HUMAN	D	3379;3376;3338;2286	ENSP00000436786:G3379D;ENSP00000374157:G3376D;ENSP00000346516:G3338D	ENSP00000346516:G3338D	G	+	2	0	MLL	117881953	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.690000	0.84178	2.809000	0.96659	0.467000	0.42956	GGC		0.488	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118376743	G	A	118376743	3	1	61	1	0	0	0	0	1	0	0	0	9650	1203	42	3	10233	3	MLL	11	118376743	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	843	118376743	16629773	7707	15692										
ARCN1	372	broad.mit.edu	37	chr11	118452034	118452034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtttgtggaaatgacccGaactcggattgagggcttat	12	7	0	2	rs367554879		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118452034G>A	ENST00000264028.4	+	2	172	c.77G>A	c.(76-78)cGa>cAa	p.R26Q	ARCN1_ENST00000359415.4_Missense_Mutation_p.R67Q|ARCN1_ENST00000534182.2_Missense_Mutation_p.R26Q|ARCN1_ENST00000392859.3_Intron	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	26					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.R26Q(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		GAAATGACCCGAACTCGGATT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	GLN/ARG,	0,4400		0,0,2200	122	113	116		77,	4.6	1	11		116	1,8589	1.2+/-3.3	0,1,4294	no	missense,intron	ARCN1	NM_001655.4,NM_001142281.1	43,	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	26/512,	118452034	1,12989	2200	4295	6495	117957244	SO:0001583	missense	372			X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"coatomer protein complex, subunit delta"	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.77G>A	11.37:g.118452034G>A	ENSP00000264028:p.Arg26Gln		117957244	B4E1X2|E9PEU4|Q52M80	Missense_Mutation	SNP	ENST00000264028.4	37	CCDS8400.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217482	0.95104	0.0	1.16E-4	ENSG00000095139	ENST00000359415;ENST00000542521;ENST00000534182;ENST00000264028	T;T	0.37058	1.22;1.25	5.55	4.64	0.57946	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.91140	3.18	0.80722	D	1	D;D;D	0.89917	0.993;1.0;1.0	P;D;D	0.78314	0.713;0.991;0.991	T	0.75994	-0.3121	10	0.72032	D	0.01	-14.2731	14.5029	0.67734	0.0705:0.0:0.9294:0.0	.	26;67;26	E9PK34;B0YIW6;P48444	.;.;COPD_HUMAN	Q	67;26;26;26	ENSP00000352385:R67Q;ENSP00000264028:R26Q	ENSP00000264028:R26Q	R	+	2	0	ARCN1	117957244	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.390000	0.97246	1.365000	0.46057	0.643000	0.83706	CGA		0.443	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			A	118452034	G	A	118452034	3	1	61	1	0	0	0	0	1	0	0	0	842	1058	37	1	83	1	ARCN1	11	118452034	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75291	118452034	16554482	7708	15693										
BCL9L	283149	broad.mit.edu	37	chr11	118773063	118773063	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaagggttcctcatatttCttcagcccgctgggaggggc	13	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118773063C>A	ENST00000334801.3	-	6	2353	c.1389G>T	c.(1387-1389)aaG>aaT	p.K463N	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	463	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.K463N(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CCTCATATTTCTTCAGCCCGC	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	11											26	34	31					11																	118773063		2088	4086	6174	118278273	SO:0001583	missense	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1389G>T	11.37:g.118773063C>A	ENSP00000335320:p.Lys463Asn		118278273	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	12.75	2.030578	0.35797	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	T	0.78481	-1.18	4.62	4.62	0.57501	.	0.000000	0.45867	D	0.000326	D	0.84538	0.5494	L	0.58101	1.795	0.54753	D	0.999987	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.941	D	0.85967	0.1474	10	0.87932	D	0	-18.1729	13.078	0.59097	0.0:0.9193:0.0:0.0807	.	458;463	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	N	463;426;463;463	ENSP00000335320:K463N	ENSP00000335320:K463N	K	-	3	2	BCL9L	118278273	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	1.758000	0.38410	2.402000	0.81655	0.305000	0.20034	AAG		0.687	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118773063	C	A	118773063	3	1	61	1	0	0	0	0	1	0	0	0	1383	912	32	2	3122	2	BCL9L	11	118773063	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	321029	118773063	16233453	7709	15694										
FOXR1	283150	broad.mit.edu	37	chr11	118850248	118850248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctccagagtcggaggcttCggcaagccagcagccaggcg	14	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:118850248C>T	ENST00000317011.3	+	4	706	c.481C>T	c.(481-483)Cgg>Tgg	p.R161W		NM_181721.2	NP_859072.1	Q6PIV2	FOXR1_HUMAN	forkhead box R1	161					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R161W(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		TCGGAGGCTTCGGCAAGCCAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	11											42	48	46					11																	118850248		2200	4295	6495	118355458	SO:0001583	missense	283150			AB094092	CCDS31688.1	11q23.3	2008-02-05			ENSG00000176302	ENSG00000176302		"Forkhead boxes"	29980	protein-coding gene	gene with protein product		615755				15067358	Standard	XM_005271514		Approved	DLNB13, FOXN5	uc001pui.3	Q6PIV2	OTTHUMG00000166347	ENST00000317011.3:c.481C>T	11.37:g.118850248C>T	ENSP00000314806:p.Arg161Trp		118355458	B0YJ15|Q08AS8|Q86UT9|Q8IXX2	Missense_Mutation	SNP	ENST00000317011.3	37	CCDS31688.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.396586	0.62177	.	.	ENSG00000176302	ENST00000317011	D	0.95377	-3.69	5.61	5.61	0.85477	.	0.915017	0.09436	N	0.802382	D	0.95778	0.8626	L	0.45698	1.435	0.26818	N	0.968843	D	0.76494	0.999	P	0.53689	0.732	D	0.90523	0.4490	10	0.48119	T	0.1	.	15.5123	0.75793	0.0:1.0:0.0:0.0	.	161	Q6PIV2	FOXR1_HUMAN	W	161	ENSP00000314806:R161W	ENSP00000314806:R161W	R	+	1	2	FOXR1	118355458	1.000000	0.71417	0.967000	0.41034	0.998000	0.95712	2.724000	0.47285	2.826000	0.97356	0.655000	0.94253	CGG		0.607	FOXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389312.1	NM_181721		T	118850248	C	T	118850248	3	4	61	1	0	0	0	0	1	0	0	0	6050	875	31	1	495	1	FOXR1	11	118850248	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77185	118850248	16156268	7710	15695										
CBL	867	broad.mit.edu	37	chr11	119103391	119103391	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaaagaatgtatgaggaGaattctcagcctaggtaatg	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:119103391G>T	ENST00000264033.4	+	2	805	c.429G>T	c.(427-429)gaG>gaT	p.E143D		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	143	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|Sufficient for interaction with EPHB1.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E143D(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TGTATGAGGAGAATTCTCAGC	0.363			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	1	Substitution - Missense(1)	large_intestine(1)	11											74	73	73					11																	119103391		2199	4295	6494	118608601	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.429G>T	11.37:g.119103391G>T	ENSP00000264033:p.Glu143Asp		118608601	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.385386	0.42308	.	.	ENSG00000110395	ENST00000264033	T	0.77620	-1.11	5.91	5.91	0.95273	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.098718	0.64402	D	0.000002	T	0.80954	0.4723	M	0.80508	2.5	0.80722	D	1	B	0.28128	0.201	B	0.35114	0.196	T	0.79678	-0.1703	10	0.56958	D	0.05	-43.436	13.4877	0.61375	0.0711:0.0:0.9289:0.0	.	143	P22681	CBL_HUMAN	D	143	ENSP00000264033:E143D	ENSP00000264033:E143D	E	+	3	2	CBL	118608601	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.956000	0.49129	2.793000	0.96121	0.655000	0.94253	GAG		0.363	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119103391	G	T	119103391	3	4	61	1	0	0	0	0	1	0	0	0	2706	933	33	2	435	2	CBL	11	119103391	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253143	119103391	15903125	7711	15696										
CBL	867	broad.mit.edu	37	chr11	119142447	119142447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattctgatcatttgtaggcGaaacctaaccaaactgtccc	6	12	2	1	rs199739868		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:119142447G>A	ENST00000264033.4	+	3	822	c.446G>A	c.(445-447)cGa>cAa	p.R149Q		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	149	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|Sufficient for interaction with EPHB1.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R149Q(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		ATTTGTAGGCGAAACCTAACC	0.338			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	1	Substitution - Missense(1)	large_intestine(1)	11											70	72	71					11																	119142447		2199	4295	6494	118647657	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.446G>A	11.37:g.119142447G>A	ENSP00000264033:p.Arg149Gln		118647657	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.412803	0.83340	.	.	ENSG00000110395	ENST00000264033	D	0.84146	-1.81	5.54	5.54	0.83059	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.85682	D	0.000000	D	0.93723	0.7994	M	0.86740	2.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94121	0.7379	10	0.87932	D	0	-51.7478	19.8465	0.96710	0.0:0.0:1.0:0.0	.	149	P22681	CBL_HUMAN	Q	149	ENSP00000264033:R149Q	ENSP00000264033:R149Q	R	+	2	0	CBL	118647657	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	8.013000	0.88655	2.769000	0.95229	0.561000	0.74099	CGA		0.338	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		A	119142447	G	A	119142447	3	1	61	1	0	0	0	0	1	0	0	0	2706	1058	37	1	456	1	CBL	11	119142447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39056	119142447	15864069	7712	15697										
CBL	867	broad.mit.edu	37	chr11	119169179	119169179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccggccgtgctggcccgccGaactctctcagatatctcta	10	16	3	1	rs150811339		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:119169179G>A	ENST00000264033.4	+	15	2739	c.2363G>A	c.(2362-2364)cGa>cAa	p.R788Q		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	788	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R788Q(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CTGGCCCGCCGAACTCTCTCA	0.547			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	1	0.000199681	8e-04	0	5008	,	,		17868	0		0	False		,,,				2504	0						"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	1	Substitution - Missense(1)	large_intestine(1)	11						G	GLN/ARG	4,4394	8.1+/-20.4	0,4,2195	84	82	83		2363	5.6	1	11	dbSNP_134	83	0,8590		0,0,4295	yes	missense	CBL	NM_005188.2	43	0,4,6490	AA,AG,GG		0.0,0.091,0.0308	probably-damaging	788/907	119169179	4,12984	2199	4295	6494	118674389	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2363G>A	11.37:g.119169179G>A	ENSP00000264033:p.Arg788Gln		118674389	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	20.5	4.001384	0.74818	9.1E-4	0.0	ENSG00000110395	ENST00000264033	D	0.84370	-1.84	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.85792	0.5779	L	0.34521	1.04	0.58432	D	0.999999	D	0.71674	0.998	P	0.52627	0.704	D	0.86976	0.2101	10	0.62326	D	0.03	-45.5034	19.6034	0.95572	0.0:0.0:1.0:0.0	.	788	P22681	CBL_HUMAN	Q	788	ENSP00000264033:R788Q	ENSP00000264033:R788Q	R	+	2	0	CBL	118674389	1.000000	0.71417	0.973000	0.42090	0.482000	0.33219	8.599000	0.90856	2.623000	0.88846	0.650000	0.86243	CGA		0.547	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		A	119169179	G	A	119169179	3	1	61	1	0	0	0	0	1	0	0	0	2706	1058	37	1	2421	1	CBL	11	119169179	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26732	119169179	15837337	7713	15698										
PVRL1	5818	broad.mit.edu	37	chr11	119546007	119546007	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctccacacccttggggaGagagccatttagcctgtggg	14	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:119546007G>A	ENST00000264025.3	-	5	1395	c.865C>T	c.(865-867)Ctc>Ttc	p.L289F	PVRL1_ENST00000340882.2_Missense_Mutation_p.L289F|PVRL1_ENST00000524510.1_5'Flank|PVRL1_ENST00000341398.2_Missense_Mutation_p.L289F	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	289	Ig-like C2-type 2.|Interaction with FGFR. {ECO:0000250}.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.L289F(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CCCTTGGGGAGAGAGCCATTT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	11											111	101	104					11																	119546007		2199	4295	6494	119051217	SO:0001583	missense	5818			X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9706	protein-coding gene	gene with protein product	"nectin"	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.865C>T	11.37:g.119546007G>A	ENSP00000264025:p.Leu289Phe		119051217	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011955	0.75046	.	.	ENSG00000110400	ENST00000341398;ENST00000264025;ENST00000340882	T;T;T	0.16457	2.34;2.34;2.34	5.46	5.46	0.80206	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	M	0.80028	2.48	0.52501	D	0.999952	D;D;D	0.71674	0.992;0.998;0.987	P;D;P	0.70935	0.897;0.971;0.854	T	0.24476	-1.0159	10	0.19147	T	0.46	.	18.3075	0.90188	0.0:0.0:1.0:0.0	.	289;289;289	Q15223-3;Q15223;Q15223-2	.;PVRL1_HUMAN;.	F	289	ENSP00000344974:L289F;ENSP00000264025:L289F;ENSP00000345289:L289F	ENSP00000264025:L289F	L	-	1	0	PVRL1	119051217	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	3.475000	0.53136	2.559000	0.86315	0.655000	0.94253	CTC		0.582	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			A	119546007	G	A	119546007	3	1	61	1	0	0	0	0	1	0	0	0	12876	942	33	3	1142	3	PVRL1	11	119546007	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	376828	119546007	15460509	7714	15699										
TRIM29	23650	broad.mit.edu	37	chr11	119986076	119986076	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttgccagatttccaagtCtggggctgggccttggggct	15	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:119986076C>A	ENST00000341846.5	-	8	2095	c.1674G>T	c.(1672-1674)caG>caT	p.Q558H	TRIM29_ENST00000529044.1_Missense_Mutation_p.Q297H|TRIM29_ENST00000524816.3_Missense_Mutation_p.Q124H|TRIM29_ENST00000528870.1_Missense_Mutation_p.Q91H|TRIM29_ENST00000525887.1_5'UTR|TRIM29_ENST00000541857.1_Missense_Mutation_p.Q291H	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	558					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q558H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		ATTTCCAAGTCTGGGGCTGGG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	55	56					11																	119986076		2199	4295	6494	119491286	SO:0001583	missense	23650			AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"Tripartite motif containing / Tripartite motif containing"	17274	protein-coding gene	gene with protein product	"tripartite motif protein TRIM29", "ataxia-telangiectasia group D-associated protein"	610658	"tripartite motif-containing 29"			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1674G>T	11.37:g.119986076C>A	ENSP00000343129:p.Gln558His		119491286	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.52|18.52	3.642069|3.642069	0.67244|0.67244	.|.	.|.	ENSG00000137699|ENSG00000137699	ENST00000525327;ENST00000524956|ENST00000341846;ENST00000541857;ENST00000533302;ENST00000524816;ENST00000528870;ENST00000529044;ENST00000526881	.|T	.|0.54675	.|0.56	5.21|5.21	3.32|3.32	0.38043|0.38043	.|.	.|0.000000	.|0.56097	.|D	.|0.000022	T|T	0.56717|0.56717	0.2004|0.2004	L|L	0.32530|0.32530	0.975|0.975	0.34859|0.34859	D|D	0.742375|0.742375	.|D;D;D	.|0.89917	.|0.997;0.997;1.0	.|D;D;D	.|0.83275	.|0.995;0.995;0.996	T|T	0.63229|0.63229	-0.6684|-0.6684	5|9	.|.	.|.	.|.	.|.	8.5224|8.5224	0.33285|0.33285	0.0:0.815:0.0:0.185|0.0:0.815:0.0:0.185	.|.	.|291;297;558	.|B7Z8U9;E9PRL4;Q14134	.|.;.;TRI29_HUMAN	Y|H	151;96|558;291;139;124;91;297;93	.|ENSP00000343129:Q558H	.|.	D|Q	-|-	1|3	0|2	TRIM29|TRIM29	119491286|119491286	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.833000|1.833000	0.39161|0.39161	1.174000|1.174000	0.42811|0.42811	0.462000|0.462000	0.41574|0.41574	GAC|CAG		0.622	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		A	119986076	C	A	119986076	3	1	61	1	0	0	0	0	1	0	0	0	16543	912	32	2	100	2	TRIM29	11	119986076	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	440069	119986076	15020440	7715	15700										
POU2F3	25833	broad.mit.edu	37	chr11	120178283	120178283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagaaacggaccagcatcGagaccaacatccgcctgact	9	13	0	3	rs373394231		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120178283G>A	ENST00000543440.2	+	9	1015	c.865G>A	c.(865-867)Gag>Aag	p.E289K	POU2F3_ENST00000260264.4_Missense_Mutation_p.E291K	NM_014352.3	NP_055167.2	Q9UKI9	PO2F3_HUMAN	POU class 2 homeobox 3	289					epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.E289K(1)		large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)	17		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		GACCAGCATCGAGACCAACAT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11							LYS/GLU	0,4406		0,0,2203	152	137	142		865	5.6	1	11		142	1,8597	1.2+/-3.3	0,1,4298	no	missense	POU2F3	NM_014352.3	56	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	289/437	120178283	1,13003	2203	4299	6502	119683493	SO:0001583	missense	25833			AF133895	CCDS8431.1, CCDS58190.1	11q23.3	2011-06-20	2007-07-13		ENSG00000137709	ENSG00000137709		"Homeoboxes / POU class"	19864	protein-coding gene	gene with protein product		607394	"POU domain class 2, transcription factor 3"			10473598	Standard	NM_014352		Approved	OCT11, PLA-1, Skn-1a, Epoc-1	uc021qrk.1	Q9UKI9	OTTHUMG00000166140	ENST00000543440.2:c.865G>A	11.37:g.120178283G>A	ENSP00000441687:p.Glu289Lys		119683493	A8K7H8|B4DY07|F5GWW6|Q3MIY3|Q9UKR7|Q9Y504	Missense_Mutation	SNP	ENST00000543440.2	37	CCDS8431.1	.	.	.	.	.	.	.	.	.	.	G	36	5.889489	0.97068	0.0	1.16E-4	ENSG00000137709	ENST00000543440;ENST00000260264;ENST00000533620;ENST00000532638	D;D;D;D	0.95554	-3.74;-3.74;-3.74;-3.74	5.62	5.62	0.85841	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97504	0.9183	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67103	0.926;0.949	D	0.97754	1.0216	10	0.66056	D	0.02	.	19.6614	0.95875	0.0:0.0:1.0:0.0	.	243;289	E9PIN6;Q9UKI9	.;PO2F3_HUMAN	K	291;289;243;74	ENSP00000441687:E291K;ENSP00000260264:E289K;ENSP00000435738:E243K;ENSP00000436236:E74K	ENSP00000260264:E289K	E	+	1	0	POU2F3	119683493	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.805000	0.99149	2.633000	0.89246	0.655000	0.94253	GAG		0.572	POU2F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388039.2			A	120178283	G	A	120178283	3	1	61	1	0	0	0	0	1	0	0	0	12304	1059	37	1	899	1	POU2F3	11	120178283	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192207	120178283	14828233	7716	15701										
ARHGEF12	23365	broad.mit.edu	37	chr11	120318989	120318989	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatatgaagcatttgggaGtaaaagtgaaagagcctcga	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120318989G>T	ENST00000397843.2	+	20	1835	c.1669G>T	c.(1669-1671)Gta>Tta	p.V557L	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.V538L|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.V454L	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	557	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V557L(1)		NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GCATTTGGGAGTAAAAGTGAA	0.408			T	MLL	AML																																		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	1	Substitution - Missense(1)	large_intestine(1)	11											93	90	91					11																	120318989		1857	4087	5944	119824199	SO:0001583	missense	23365			AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1669G>T	11.37:g.120318989G>T	ENSP00000380942:p.Val557Leu		119824199	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	35	5.529374	0.96446	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.83506	-1.73;-1.73;-1.73	5.28	5.28	0.74379	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.44483	D	0.000457	D	0.90017	0.6883	M	0.67953	2.075	0.58432	D	0.999999	D;P;P	0.89917	1.0;0.815;0.846	D;P;P	0.91635	0.999;0.646;0.759	D	0.87747	0.2589	10	0.27785	T	0.31	-13.3017	18.915	0.92501	0.0:0.0:1.0:0.0	.	454;538;557	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	L	557;538;454	ENSP00000380942:V557L;ENSP00000349056:V538L;ENSP00000432984:V454L	ENSP00000349056:V538L	V	+	1	0	ARHGEF12	119824199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.430000	0.97488	2.465000	0.83290	0.585000	0.79938	GTA		0.408	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120318989	G	T	120318989	3	4	61	1	0	0	0	0	1	0	0	0	897	1029	36	2	1747	2	ARHGEF12	11	120318989	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140706	120318989	14687527	7717	15702										
ARHGEF12	23365	broad.mit.edu	37	chr11	120329901	120329901	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaattgttctacactgaaaGagctcatgttcgaacactga	8	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120329901G>T	ENST00000397843.2	+	26	2565	c.2399G>T	c.(2398-2400)aGa>aTa	p.R800I	AP000758.1_ENST00000595283.1_Silent_p.L49L|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.R781I|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.R697I	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	800	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R800I(1)		NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TACACTGAAAGAGCTCATGTT	0.393			T	MLL	AML																																		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	1	Substitution - Missense(1)	large_intestine(1)	11											102	98	99					11																	120329901		1846	4112	5958	119835111	SO:0001583	missense	23365			AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.2399G>T	11.37:g.120329901G>T	ENSP00000380942:p.Arg800Ile		119835111	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	35	5.430313	0.96150	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.67523	-0.27;-0.27;-0.27	5.62	5.62	0.85841	Dbl homology (DH) domain (5);	0.000000	0.49305	D	0.000156	T	0.81475	0.4830	M	0.73319	2.225	0.80722	D	1	D;D;D	0.89917	0.958;1.0;1.0	P;D;D	0.91635	0.851;0.999;0.999	T	0.78048	-0.2356	10	0.30854	T	0.27	-18.0044	19.6767	0.95936	0.0:0.0:1.0:0.0	.	697;781;800	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	I	800;781;697	ENSP00000380942:R800I;ENSP00000349056:R781I;ENSP00000432984:R697I	ENSP00000349056:R781I	R	+	2	0	ARHGEF12	119835111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.430000	0.97488	2.634000	0.89283	0.655000	0.94253	AGA		0.393	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120329901	G	T	120329901	3	4	61	1	0	0	0	0	1	0	0	0	897	942	33	2	2501	2	ARHGEF12	11	120329901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10912	120329901	14676615	7718	15703										
GRIK4	2900	broad.mit.edu	37	chr11	120690494	120690494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaagtggccccagaggagTtcgtcaagttccagttccag	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120690494T>C	ENST00000527524.2	+	6	663	c.376T>C	c.(376-378)Ttc>Ctc	p.F126L	GRIK4_ENST00000438375.2_Missense_Mutation_p.F126L	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	126					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.F126L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		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)		CCCAGAGGAGTTCGTCAAGTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											235	241	239					11																	120690494		2203	4299	6502	120195704	SO:0001583	missense	2900			S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.376T>C	11.37:g.120690494T>C	ENSP00000435648:p.Phe126Leu		120195704	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.300088	0.23650	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.21361	2.01;2.01	4.27	4.27	0.50696	Extracellular ligand-binding receptor (1);	0.099966	0.64402	D	0.000002	T	0.12178	0.0296	N	0.16478	0.41	0.38613	D	0.950951	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.003	T	0.09662	-1.0664	10	0.09843	T	0.71	.	13.5674	0.61826	0.0:0.0:0.0:1.0	.	126;126	A6H8K8;Q16099	.;GRIK4_HUMAN	L	126	ENSP00000435648:F126L;ENSP00000404063:F126L	ENSP00000404063:F126L	F	+	1	0	GRIK4	120195704	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	5.933000	0.70130	1.782000	0.52362	0.459000	0.35465	TTC		0.532	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		C	120690494	T	C	120690494	3	2	61	1	0	0	0	0	1	0	0	0	6797	1725	60	4	390	4	GRIK4	11	120690494	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	360593	120690494	14316022	7719	15704										
GRIK4	2900	broad.mit.edu	37	chr11	120823599	120823599	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttctccttcctggacccAttttctccgggcgtctggct	8	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120823599A>C	ENST00000527524.2	+	15	1913	c.1626A>C	c.(1624-1626)ccA>ccC	p.P542P	GRIK4_ENST00000438375.2_Silent_p.P542P	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	542					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.P542P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		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)		TCCTGGACCCATTTTCTCCGG	0.542											OREG0021429	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	11											146	135	139					11																	120823599		2203	4299	6502	120328809	SO:0001819	synonymous_variant	2900			S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1626A>C	11.37:g.120823599A>C		1506	120328809	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																				0.542	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		C	120823599	A	C	120823599	2	2	61	1	0	0	0	0	0	0	0	1	6797	204	8	4		4	GRIK4	11	120823599	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	133105	120823599	14182917	7720	15705										
TBCEL	219899	broad.mit.edu	37	chr11	120929086	120929086	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagacattgataaactaAattcatttcccaaactggaa	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120929086A>C	ENST00000529397.1	+	6	845	c.745A>C	c.(745-747)Aat>Cat	p.N249H	TBCEL_ENST00000422003.2_Missense_Mutation_p.N249H	NM_001130047.1	NP_001123519.1	Q5QJ74	TBCEL_HUMAN	tubulin folding cofactor E-like	249						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.N249H(1)	TECTA/TBCEL(2)	endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		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)		TGATAAACTAAATTCATTTCC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											118	114	116					11																	120929086		2203	4298	6501	120434296	SO:0001583	missense	219899			BC020501	CCDS31692.1	11q23.3	2008-02-05	2006-11-21	2006-11-21		ENSG00000154114			28115	protein-coding gene	gene with protein product		610451	"leucine rich repeat containing 35", "tubulin-specific chaperone e-like"	LRRC35		15728251	Standard	NM_152715		Approved	MGC10233	uc001pxo.3	Q5QJ74		ENST00000529397.1:c.745A>C	11.37:g.120929086A>C	ENSP00000437184:p.Asn249His		120434296	Q0VAN6	Missense_Mutation	SNP	ENST00000529397.1	37	CCDS31692.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.832182	0.50845	.	.	ENSG00000154114	ENST00000529397;ENST00000422003;ENST00000533134;ENST00000533169	T;T;T	0.45276	0.9;0.9;0.9	5.75	5.75	0.90469	.	0.043303	0.85682	D	0.000000	T	0.57577	0.2063	L	0.59436	1.845	0.80722	D	1	D	0.58620	0.983	P	0.58873	0.847	T	0.58825	-0.7568	10	0.54805	T	0.06	0.9399	16.0563	0.80809	1.0:0.0:0.0:0.0	.	249	Q5QJ74	TBCEL_HUMAN	H	249;249;16;52	ENSP00000437184:N249H;ENSP00000403925:N249H;ENSP00000436419:N16H	ENSP00000403925:N249H	N	+	1	0	TBCEL	120434296	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.313000	0.96297	2.183000	0.69458	0.528000	0.53228	AAT		0.378	TBCEL-005	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387688.1	NM_152715		C	120929086	A	C	120929086	3	2	61	1	0	0	0	0	1	0	0	0	15674	14	1	4	763	4	TBCEL	11	120929086	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	105487	120929086	14077430	7721	15706										
TECTA	7007	broad.mit.edu	37	chr11	120980049	120980049	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcacaatggaattcgaggcGagatctattacagagagacc	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120980049G>A	ENST00000392793.1	+	4	599	c.328G>A	c.(328-330)Gag>Aag	p.E110K	TECTA_ENST00000264037.2_Missense_Mutation_p.E110K			O75443	TECTA_HUMAN	tectorin alpha	110	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.E110K(2)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AATTCGAGGCGAGATCTATTA	0.512																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	11											104	99	100					11																	120980049		2203	4299	6502	120485259	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.328G>A	11.37:g.120980049G>A	ENSP00000376543:p.Glu110Lys		120485259		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133159	0.77662	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.33654	1.4;1.4	5.46	5.46	0.80206	Nidogen, extracellular domain (2);	0.053752	0.64402	D	0.000001	T	0.25419	0.0618	N	0.11892	0.195	0.47511	D	0.999442	D	0.53619	0.961	B	0.40134	0.32	T	0.12682	-1.0538	10	0.59425	D	0.04	.	19.3216	0.94243	0.0:0.0:1.0:0.0	.	110	O75443	TECTA_HUMAN	K	110	ENSP00000376543:E110K;ENSP00000264037:E110K	ENSP00000264037:E110K	E	+	1	0	TECTA	120485259	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.835000	0.86780	2.573000	0.86826	0.655000	0.94253	GAG		0.512	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	120980049	G	A	120980049	3	1	61	1	0	0	0	0	1	0	0	0	15786	1059	37	1	338	1	TECTA	11	120980049	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50963	120980049	14026467	7722	15707										
TECTA	7007	broad.mit.edu	37	chr11	120983872	120983872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactggaccacggggacggCgagtggcggcgaccccctga	16	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:120983872C>T	ENST00000392793.1	+	5	849	c.578C>T	c.(577-579)gCg>gTg	p.A193V	TECTA_ENST00000264037.2_Missense_Mutation_p.A193V			O75443	TECTA_HUMAN	tectorin alpha	193	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.A193V(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		ACGGGGACGGCGAGTGGCGGC	0.572											OREG0021430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											81	76	78					11																	120983872		2203	4299	6502	120489082	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.578C>T	11.37:g.120983872C>T	ENSP00000376543:p.Ala193Val	1508	120489082		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357218	0.41801	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.72615	-0.67;-0.67	5.37	4.46	0.54185	Nidogen, extracellular domain (3);	0.182139	0.47852	N	0.000204	T	0.65450	0.2692	M	0.75777	2.31	0.50171	D	0.999855	P	0.41214	0.742	B	0.31191	0.125	T	0.67417	-0.5676	10	0.30854	T	0.27	.	14.2309	0.65892	0.0:0.929:0.0:0.071	.	193	O75443	TECTA_HUMAN	V	193	ENSP00000376543:A193V;ENSP00000264037:A193V	ENSP00000264037:A193V	A	+	2	0	TECTA	120489082	1.000000	0.71417	0.124000	0.21820	0.002000	0.02628	7.603000	0.82811	1.501000	0.48654	-0.145000	0.13849	GCG		0.572	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	120983872	C	T	120983872	3	4	61	1	0	0	0	0	1	0	0	0	15786	768	27	1	592	1	TECTA	11	120983872	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3823	120983872	14022644	7723	15708										
TECTA	7007	broad.mit.edu	37	chr11	121000473	121000473	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagtactcagacataggtCtattgtacatccggctgtcc	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:121000473C>A	ENST00000392793.1	+	10	2765	c.2494C>A	c.(2494-2496)Cta>Ata	p.L832I	TECTA_ENST00000264037.2_Missense_Mutation_p.L832I			O75443	TECTA_HUMAN	tectorin alpha	832	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.L832I(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGACATAGGTCTATTGTACAT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											169	161	164					11																	121000473		2203	4299	6502	120505683	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2494C>A	11.37:g.121000473C>A	ENSP00000376543:p.Leu832Ile		120505683		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	10.00	1.233163	0.22626	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.59502	0.26;0.26	5.56	3.6	0.41247	von Willebrand factor, type D domain (3);	0.224058	0.38837	N	0.001551	T	0.53094	0.1775	M	0.69823	2.125	0.30435	N	0.776784	B	0.21905	0.062	B	0.29267	0.1	T	0.48822	-0.9001	10	0.25751	T	0.34	.	7.9369	0.29935	0.1215:0.6914:0.118:0.0691	.	832	O75443	TECTA_HUMAN	I	832	ENSP00000376543:L832I;ENSP00000264037:L832I	ENSP00000264037:L832I	L	+	1	2	TECTA	120505683	0.079000	0.21365	0.897000	0.35233	0.370000	0.29829	0.552000	0.23376	2.630000	0.89119	0.563000	0.77884	CTA		0.502	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121000473	C	A	121000473	3	1	61	1	0	0	0	0	1	0	0	0	15786	912	32	2	2528	2	TECTA	11	121000473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16601	121000473	14006043	7724	15709										
TECTA	7007	broad.mit.edu	37	chr11	121000676	121000676	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaggcctgcaacaatgaCtcggagctgctcaagtttta	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:121000676C>A	ENST00000392793.1	+	10	2968	c.2697C>A	c.(2695-2697)gaC>gaA	p.D899E	TECTA_ENST00000264037.2_Missense_Mutation_p.D899E			O75443	TECTA_HUMAN	tectorin alpha	899	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.D899E(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GCAACAATGACTCGGAGCTGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											71	68	69					11																	121000676		2203	4299	6502	120505886	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2697C>A	11.37:g.121000676C>A	ENSP00000376543:p.Asp899Glu		120505886		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697637	0.68386	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.35236	1.32;1.32	5.65	1.64	0.23874	von Willebrand factor, type D domain (1);	0.000000	0.64402	D	0.000003	T	0.49508	0.1561	L	0.53249	1.67	0.32667	N	0.517313	D	0.64830	0.994	D	0.72625	0.978	T	0.57429	-0.7813	10	0.36615	T	0.2	.	11.1389	0.48392	0.0:0.7489:0.0:0.2511	.	899	O75443	TECTA_HUMAN	E	899	ENSP00000376543:D899E;ENSP00000264037:D899E	ENSP00000264037:D899E	D	+	3	2	TECTA	120505886	1.000000	0.71417	0.951000	0.38953	0.865000	0.49528	2.254000	0.43214	0.333000	0.23563	0.557000	0.71058	GAC		0.562	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121000676	C	A	121000676	3	1	61	1	0	0	0	0	1	0	0	0	15786	564	20	2	2731	2	TECTA	11	121000676	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203	121000676	14005840	7725	15710										
TECTA	7007	broad.mit.edu	37	chr11	121008365	121008365	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggacctggactgccagatCttctgctattgcagtggcac	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:121008365C>A	ENST00000392793.1	+	11	3448	c.3177C>A	c.(3175-3177)atC>atA	p.I1059I	TECTA_ENST00000264037.2_Silent_p.I1059I			O75443	TECTA_HUMAN	tectorin alpha	1059					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.I1059I(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		ACTGCCAGATCTTCTGCTATT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	11											109	89	96					11																	121008365		2203	4299	6502	120513575	SO:0001819	synonymous_variant	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.3177C>A	11.37:g.121008365C>A			120513575		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																				0.567	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121008365	C	A	121008365	2	1	61	1	0	0	0	0	0	0	0	1	15786	903	32	2		2	TECTA	11	121008365	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7689	121008365	13998151	7726	15711										
SC5DL	6309	broad.mit.edu	37	chr11	121175083	121175083	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagaatcaagtccgtcGagagattaagtttactgtcc	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:121175083G>A	ENST00000392789.2	+	3	461	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	SC5D_ENST00000534230.1_Missense_Mutation_p.R75Q|SC5D_ENST00000264027.4_Missense_Mutation_p.R75Q	NM_001024956.2	NP_001020127.1	O75845	SC5D_HUMAN	sterol-C5-desaturase	75					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via lathosterol (GO:0033490)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	C-5 sterol desaturase activity (GO:0000248)|iron ion binding (GO:0005506)|lathosterol oxidase activity (GO:0050046)	p.R75Q(1)									CAAGTCCGTCGAGAGATTAAG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	11											122	118	119					11																	121175083		2203	4299	6502	120680293	SO:0001583	missense	6309				CCDS8435.1	11q23.3	2013-03-04	2013-03-04	2013-03-04	ENSG00000109929	ENSG00000109929	1.14.21.6	"Fatty acid hydroxylase domain containing"	10547	protein-coding gene	gene with protein product	"lathosterol oxidase"	602286	"sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like"	SC5DL		8976377	Standard	NM_006918		Approved		uc001pxu.3	O75845	OTTHUMG00000166068	ENST00000392789.2:c.224G>A	11.37:g.121175083G>A	ENSP00000376539:p.Arg75Gln		120680293	O00119|Q6GTM5|Q9UK15	Missense_Mutation	SNP	ENST00000392789.2	37	CCDS8435.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.028673	0.54790	.	.	ENSG00000109929	ENST00000264027;ENST00000527762;ENST00000534230;ENST00000392789	D;D;D;D	0.86030	-1.64;-1.63;-2.06;-1.64	6.07	4.23	0.50019	.	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	L	0.43923	1.385	0.34515	D	0.707556	B;D	0.56287	0.032;0.975	B;B	0.40782	0.008;0.34	T	0.77996	-0.2377	10	0.12766	T	0.61	-1.0569	12.2355	0.54514	0.1395:0.0:0.8605:0.0	.	75;75	O75845;E9PQ91	SC5D_HUMAN;.	Q	75;82;75;75	ENSP00000264027:R75Q;ENSP00000436290:R82Q;ENSP00000432550:R75Q;ENSP00000376539:R75Q	ENSP00000264027:R75Q	R	+	2	0	SC5DL	120680293	1.000000	0.71417	0.532000	0.27989	0.933000	0.57130	5.652000	0.67959	0.913000	0.36797	-0.136000	0.14681	CGA		0.348	SC5D-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387702.1	NM_001024956		A	121175083	G	A	121175083	3	1	61	1	0	0	0	0	1	0	0	0	13903	1058	37	1	230	1	SC5DL	11	121175083	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166718	121175083	13831433	7727	15712										
C11orf63	79864	broad.mit.edu	37	chr11	122756701	122756701	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttggaatctgattcagaAagcctcacgcaagagattat	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:122756701A>C	ENST00000531316.1	+	1	236	c.144A>C	c.(142-144)gaA>gaC	p.E48D	C11orf63_ENST00000227349.2_Missense_Mutation_p.E48D|C11orf63_ENST00000307257.6_Missense_Mutation_p.E48D			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	48					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.E48D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		CTGATTCAGAAAGCCTCACGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											95	98	97					11																	122756701		2202	4299	6501	122261911	SO:0001583	missense	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.144A>C	11.37:g.122756701A>C	ENSP00000431669:p.Glu48Asp		122261911	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.028937	0.54790	.	.	ENSG00000109944	ENST00000307257;ENST00000227349;ENST00000531316	T;T	0.65364	-0.15;-0.15	5.57	4.42	0.53409	.	0.220192	0.31031	N	0.008393	T	0.70885	0.3275	M	0.64997	1.995	0.38024	D	0.934949	D;D	0.69078	0.997;0.997	P;P	0.61800	0.894;0.894	T	0.73585	-0.3936	10	0.51188	T	0.08	-9.9487	9.1979	0.37240	0.9132:0.0:0.0868:0.0	.	48;48	Q6NUN7;Q6NUN7-2	CK063_HUMAN;.	D	48	ENSP00000227349:E48D;ENSP00000431669:E48D	ENSP00000227349:E48D	E	+	3	2	C11orf63	122261911	1.000000	0.71417	0.979000	0.43373	0.786000	0.44442	1.600000	0.36762	0.910000	0.36722	0.533000	0.62120	GAA		0.468	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		C	122756701	A	C	122756701	3	2	61	1	0	0	0	0	1	0	0	0	1658	11	1	4	146	4	C11orf63	11	122756701	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1581618	122756701	12249815	7728	15713										
C11orf63	79864	broad.mit.edu	37	chr11	122775092	122775092	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgggattacccaccccGaaaacggactcttatcttca	6	13	3	0	rs149285900		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:122775092G>A	ENST00000531316.1	+	2	896	c.804G>A	c.(802-804)ccG>ccA	p.P268P	C11orf63_ENST00000227349.2_Silent_p.P268P|C11orf63_ENST00000307257.6_Silent_p.P268P			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	268					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.P268P(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		TACCCACCCCGAAAACGGACT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	11											149	166	161					11																	122775092		2202	4299	6501	122280302	SO:0001819	synonymous_variant	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.804G>A	11.37:g.122775092G>A			122280302	A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	ENST00000531316.1	37	CCDS8438.1																																																																																				0.423	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		A	122775092	G	A	122775092	2	1	61	1	0	0	0	0	0	0	0	1	1658	1045	37	1		1	C11orf63	11	122775092	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18391	122775092	12231424	7729	15714										
BSX	390259	broad.mit.edu	37	chr11	122848592	122848592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgccggttctggaaccacGttttcacctgatttcgggga	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:122848592G>A	ENST00000343035.2	-	3	515	c.467C>T	c.(466-468)aCg>aTg	p.T156M		NM_001098169.1	NP_001091639.1	Q3C1V8	BSH_HUMAN	brain-specific homeobox	156					eating behavior (GO:0042755)|locomotory behavior (GO:0007626)|mammary gland involution (GO:0060056)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T156M(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	10		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)		CTGGAACCACGTTTTCACCTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											58	62	61					11																	122848592		1903	4144	6047	122353802	SO:0001583	missense	390259				CCDS41728.1	11q24.1	2011-07-19			ENSG00000188909	ENSG00000188909		"Homeoboxes / ANTP class : NKL subclass"	20450	protein-coding gene	gene with protein product		611074					Standard	NM_001098169		Approved	BSX1	uc010rzs.2	Q3C1V8	OTTHUMG00000150247	ENST00000343035.2:c.467C>T	11.37:g.122848592G>A	ENSP00000344285:p.Thr156Met		122353802		Missense_Mutation	SNP	ENST00000343035.2	37	CCDS41728.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965847	0.92855	.	.	ENSG00000188909	ENST00000343035	D	0.96232	-3.95	5.53	5.53	0.82687	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98692	0.9561	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99180	1.0867	10	0.59425	D	0.04	.	19.472	0.94966	0.0:0.0:1.0:0.0	.	156	Q3C1V8	BSH_HUMAN	M	156	ENSP00000344285:T156M	ENSP00000344285:T156M	T	-	2	0	BSX	122353802	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.102000	0.94226	2.585000	0.87301	0.655000	0.94253	ACG		0.512	BSX-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317076.1	NM_001098169		A	122848592	G	A	122848592	3	1	61	1	0	0	0	0	1	0	0	0	1538	1145	40	1	237	1	BSX	11	122848592	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73500	122848592	12157924	7730	15715										
HSPA8	3312	broad.mit.edu	37	chr11	122930366	122930366	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctactgggtccagggtgCcacggaacaggtcagcattc	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:122930366C>G	ENST00000532636.1	-	5	1054	c.935G>C	c.(934-936)gGc>gCc	p.G312A	HSPA8_ENST00000526862.1_5'UTR|HSPA8_ENST00000227378.3_Missense_Mutation_p.G312A|HSPA8_ENST00000534319.1_Missense_Mutation_p.G76A|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.G293A|HSPA8_ENST00000534624.1_Missense_Mutation_p.G312A|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.G312A|HSPA8_ENST00000533540.1_Missense_Mutation_p.G166A|SNORD14E_ENST00000364009.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	312	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.G312A(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GTCCAGGGTGCCACGGAACAG	0.483																																					Colon(21;486 594 5900 6733 14272)											1	Substitution - Missense(1)	large_intestine(1)	11											49	51	50					11																	122930366		2202	4299	6501	122435576	SO:0001583	missense	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.935G>C	11.37:g.122930366C>G	ENSP00000437125:p.Gly312Ala		122435576	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911379	0.92178	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000528292	T;T;T;T;T;T;T;T	0.00932	5.53;5.53;5.53;5.53;5.53;5.53;5.53;5.53	4.65	4.65	0.58169	.	0.056048	0.64402	D	0.000002	T	0.03095	0.0091	L	0.31420	0.93	0.80722	D	1	B;D;D;B	0.89917	0.006;1.0;1.0;0.006	B;D;D;B	0.80764	0.029;0.994;0.99;0.029	T	0.63862	-0.6541	10	0.87932	D	0	-18.0675	17.9506	0.89052	0.0:1.0:0.0:0.0	.	312;312;312;312	Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;HSP7C_HUMAN	A	312;166;312;312;312;76;293;252	ENSP00000437125:G312A;ENSP00000437189:G166A;ENSP00000432083:G312A;ENSP00000404372:G312A;ENSP00000227378:G312A;ENSP00000433316:G76A;ENSP00000433584:G293A;ENSP00000432884:G252A	ENSP00000227378:G312A	G	-	2	0	HSPA8	122435576	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.672000	0.83956	2.308000	0.77769	0.556000	0.70494	GGC		0.483	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			G	122930366	C	G	122930366	3	3	61	1	0	0	0	0	1	0	0	0	7437	739	26	5	1025	5	HSPA8	11	122930366	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81774	122930366	12076150	7731	15716										
GRAMD1B	57476	broad.mit.edu	37	chr11	123480967	123480967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccgaagtcctcacccacGacgtgccctaccatgactac	7	17	1	1	rs542866239		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123480967G>A	ENST00000529750.1	+	13	1738	c.1411G>A	c.(1411-1413)Gac>Aac	p.D471N	GRAMD1B_ENST00000322282.7_Missense_Mutation_p.D471N|GRAMD1B_ENST00000450171.2_Missense_Mutation_p.D162N|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.D478N	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	471						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.D471N(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CCTCACCCACGACGTGCCCTA	0.537													G|||	1	0.000199681	8e-04	0	5008	,	,		17879	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											120	119	119					11																	123480967		2071	4205	6276	122986177	SO:0001583	missense	57476			AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1411G>A	11.37:g.123480967G>A	ENSP00000436500:p.Asp471Asn		122986177	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	37	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	G	33	5.265394	0.95399	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000450171	T;T;T;T;T	0.54279	1.47;1.45;1.44;1.44;0.58	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.72566	0.3476	M	0.79123	2.44	0.80722	D	1	D;D;D;D	0.89917	0.995;1.0;0.998;0.995	P;D;P;P	0.65874	0.837;0.939;0.825;0.837	T	0.73623	-0.3924	10	0.45353	T	0.12	.	18.5888	0.91200	0.0:0.0:1.0:0.0	.	431;162;471;478	B7Z4N9;Q3KR37-3;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	N	478;478;471;471;431;162	ENSP00000402457:D478N;ENSP00000325628:D471N;ENSP00000436500:D471N;ENSP00000432987:D431N;ENSP00000388458:D162N	ENSP00000325628:D471N	D	+	1	0	GRAMD1B	122986177	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.456000	0.80751	2.554000	0.86153	0.561000	0.74099	GAC		0.537	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		A	123480967	G	A	123480967	3	1	61	1	0	0	0	0	1	0	0	0	6769	1058	37	1	1461	1	GRAMD1B	11	123480967	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	550601	123480967	11525549	7732	15717										
GRAMD1B	57476	broad.mit.edu	37	chr11	123483532	123483532	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaaacgttcatcgagaaGaacttctggagtgggctgga	14	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123483532G>T	ENST00000529750.1	+	14	1881	c.1554G>T	c.(1552-1554)aaG>aaT	p.K518N	GRAMD1B_ENST00000322282.7_Missense_Mutation_p.K518N|GRAMD1B_ENST00000450171.2_Missense_Mutation_p.K209N|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.K525N	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	518						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.K518N(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		TCATCGAGAAGAACTTCTGGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											54	55	55					11																	123483532		1943	4131	6074	122988742	SO:0001583	missense	57476			AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1554G>T	11.37:g.123483532G>T	ENSP00000436500:p.Lys518Asn		122988742	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	37	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117656	0.77323	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000450171	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.42	4.49	0.54785	.	0.049931	0.85682	D	0.000000	T	0.48786	0.1519	M	0.65975	2.015	0.58432	D	0.999995	D;D;D;D	0.71674	0.998;0.996;0.986;0.983	D;P;P;D	0.69307	0.963;0.866;0.722;0.938	T	0.41574	-0.9501	10	0.49607	T	0.09	.	10.2129	0.43152	0.1486:0.0:0.8514:0.0	.	478;209;518;525	B7Z4N9;Q3KR37-3;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	N	525;525;518;518;478;209	ENSP00000402457:K525N;ENSP00000325628:K518N;ENSP00000436500:K518N;ENSP00000432987:K478N;ENSP00000388458:K209N	ENSP00000325628:K518N	K	+	3	2	GRAMD1B	122988742	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.040000	0.41203	2.699000	0.92147	0.563000	0.77884	AAG		0.537	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		T	123483532	G	T	123483532	3	4	61	1	0	0	0	0	1	0	0	0	6769	933	33	2	1608	2	GRAMD1B	11	123483532	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2565	123483532	11522984	7733	15718										
SCN3B	55800	broad.mit.edu	37	chr11	123524498	123524498	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaggggaaacaatctattGaaggcaggcatcttctgggg	14	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123524498G>T	ENST00000392770.2	-	1	814	c.12C>A	c.(10-12)ttC>ttA	p.F4L	SCN3B_ENST00000299333.3_Missense_Mutation_p.F4L|SCN3B_ENST00000530277.1_Missense_Mutation_p.F4L	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	4					atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.F4L(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	ACAATCTATTGAAGGCAGGCA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											160	163	162					11																	123524498		2202	4299	6501	123029708	SO:0001583	missense	55800			AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.12C>A	11.37:g.123524498G>T	ENSP00000376523:p.Phe4Leu		123029708	A5H1I5|Q17RL3|Q9ULR2	Missense_Mutation	SNP	ENST00000392770.2	37	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.508101	0.44660	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836;ENST00000528267	D;D;D;D;D	0.97710	-3.74;-3.74;-3.74;-4.5;-3.2	4.97	4.97	0.65823	.	0.644653	0.16577	N	0.208372	D	0.91012	0.7173	N	0.03608	-0.345	0.38616	D	0.951018	B	0.02656	0.0	B	0.01281	0.0	D	0.87245	0.2269	10	0.06365	T	0.9	-0.0117	14.1029	0.65068	0.0:0.0:1.0:0.0	.	4	Q9NY72	SCN3B_HUMAN	L	4	ENSP00000376523:F4L;ENSP00000299333:F4L;ENSP00000432785:F4L;ENSP00000435554:F4L;ENSP00000434363:F4L	ENSP00000299333:F4L	F	-	3	2	SCN3B	123029708	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.912000	0.48782	2.452000	0.82932	0.591000	0.81541	TTC		0.517	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		T	123524498	G	T	123524498	3	4	61	1	0	0	0	0	1	0	0	0	13956	1281	45	2	655	2	SCN3B	11	123524498	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40966	123524498	11482018	7734	15719										
ZNF202	7753	broad.mit.edu	37	chr11	123601563	123601563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattccctcttcttcccaaaGatcctggtcctctggttcca	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123601563G>T	ENST00000529691.1	-	2	253	c.34C>A	c.(34-36)Ctt>Att	p.L12I	ZNF202_ENST00000336139.4_Missense_Mutation_p.L12I|ZNF202_ENST00000530393.1_Missense_Mutation_p.L12I			O95125	ZN202_HUMAN	zinc finger protein 202	12					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L12I(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		TCTTCCCAAAGATCCTGGTCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											82	86	85					11																	123601563		2202	4299	6501	123106773	SO:0001583	missense	7753			AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.34C>A	11.37:g.123601563G>T	ENSP00000433881:p.Leu12Ile		123106773	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	37	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660252	0.67586	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691;ENST00000533463;ENST00000528306	T;T;T;T	0.06068	3.35;3.35;3.35;3.38	4.7	4.7	0.59300	.	0.000000	0.44483	D	0.000457	T	0.08891	0.0220	N	0.08118	0	0.34011	D	0.651478	D	0.63880	0.993	D	0.67548	0.952	T	0.44952	-0.9294	10	0.22706	T	0.39	-15.7215	13.0223	0.58796	0.0:0.0:1.0:0.0	.	12	O95125	ZN202_HUMAN	I	12	ENSP00000337724:L12I;ENSP00000432504:L12I;ENSP00000433881:L12I;ENSP00000431223:L12I	ENSP00000337724:L12I	L	-	1	0	ZNF202	123106773	0.953000	0.32496	0.999000	0.59377	0.998000	0.95712	1.900000	0.39828	2.438000	0.82558	0.555000	0.69702	CTT		0.537	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		T	123601563	G	T	123601563	3	4	61	1	0	0	0	0	1	0	0	0	17802	942	33	2	1936	2	ZNF202	11	123601563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77065	123601563	11404953	7735	15720										
OR6X1	390260	broad.mit.edu	37	chr11	123624672	123624672	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctggtgtctatgcaggcGgctttcaaactgggcccaac	12	11	2	0	rs570526906		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123624672G>A	ENST00000327930.2	-	1	581	c.555C>T	c.(553-555)gcC>gcT	p.A185A		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A185A(1)		breast(3)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)	23		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CTATGCAGGCGGCTTTCAAAC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	11											89	91	90					11																	123624672		2202	4299	6501	123129882	SO:0001819	synonymous_variant	390260			AB065510	CCDS31695.1	11q24.1	2012-08-09			ENSG00000221931	ENSG00000221931		"GPCR / Class A : Olfactory receptors"	14737	protein-coding gene	gene with protein product							Standard	NM_001005188		Approved		uc010rzy.2	Q8NH79	OTTHUMG00000166011	ENST00000327930.2:c.555C>T	11.37:g.123624672G>A			123129882	B9EGW9|Q6IFA0	Silent	SNP	ENST00000327930.2	37	CCDS31695.1																																																																																				0.443	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	NM_001005188		A	123624672	G	A	123624672	2	1	61	1	0	0	0	0	0	0	0	1	11243	1103	39	1		1	OR6X1	11	123624672	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23109	123624672	11381844	7736	15721										
OR6M1	390261	broad.mit.edu	37	chr11	123676685	123676685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgtagtgcagtgggtcgcAgatagccatgtagcggtcaa	15	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123676685A>G	ENST00000309154.2	-	1	410	c.373T>C	c.(373-375)Tgc>Cgc	p.C125R		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C125R(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		AGTGGGTCGCAGATAGCCATG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	11											50	51	51					11																	123676685		2202	4299	6501	123181895	SO:0001583	missense	390261			AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.373T>C	11.37:g.123676685A>G	ENSP00000311038:p.Cys125Arg		123181895	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.553480	0.45487	.	.	ENSG00000196099	ENST00000309154	T	0.06218	3.33	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002874	T	0.30166	0.0756	M	0.92317	3.295	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.20207	-1.0282	10	0.87932	D	0	.	10.3296	0.43814	1.0:0.0:0.0:0.0	.	125	Q8NGM8	OR6M1_HUMAN	R	125	ENSP00000311038:C125R	ENSP00000311038:C125R	C	-	1	0	OR6M1	123181895	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	4.276000	0.58933	1.518000	0.48934	0.533000	0.62120	TGC		0.517	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		G	123676685	A	G	123676685	3	3	61	1	0	0	0	0	1	0	0	0	11236	188	7	4	571	4	OR6M1	11	123676685	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52013	123676685	11329831	7737	15722										
TMEM225	338661	broad.mit.edu	37	chr11	123755265	123755265	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaatcagataggtgaatTtcatacccaggattaagtta	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123755265T>G	ENST00000375026.2	-	2	476	c.260A>C	c.(259-261)aAa>aCa	p.K87T		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	87					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.K87T(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						ATAGGTGAATTTCATACCCAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											120	123	122					11																	123755265		2202	4299	6501	123260475	SO:0001583	missense	338661			AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"PMP22 claudin domain containing", "protein phosphatase 1, regulatory subunit 154"						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.260A>C	11.37:g.123755265T>G	ENSP00000364166:p.Lys87Thr		123260475		Missense_Mutation	SNP	ENST00000375026.2	37	CCDS31697.1	.	.	.	.	.	.	.	.	.	.	T	11.91	1.780341	0.31502	.	.	ENSG00000204300	ENST00000375026;ENST00000528595	T;T	0.69926	-0.44;-0.44	5.17	2.82	0.32997	.	0.466873	0.18539	N	0.138247	T	0.49457	0.1558	N	0.19112	0.55	0.18873	N	0.999983	P	0.39216	0.664	B	0.41723	0.365	T	0.43015	-0.9417	10	0.66056	D	0.02	-6.3863	4.2122	0.10517	0.1774:0.0941:0.0:0.7286	.	87	Q6GV28	TM225_HUMAN	T	87;37	ENSP00000364166:K87T;ENSP00000431282:K37T	ENSP00000364166:K87T	K	-	2	0	TMEM225	123260475	0.559000	0.26562	0.435000	0.26784	0.101000	0.19017	1.021000	0.30040	0.420000	0.25954	0.533000	0.62120	AAA		0.418	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743		G	123755265	T	G	123755265	3	3	61	1	0	0	0	0	1	0	0	0	16186	1841	64	4	429	4	TMEM225	11	123755265	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	78580	123755265	11251251	7738	15723										
OR4D5	219875	broad.mit.edu	37	chr11	123811218	123811218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagtgatcatggccatgAagaagctgtggaggaggaaa	16	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123811218A>G	ENST00000307033.2	+	1	969	c.895A>G	c.(895-897)Aag>Gag	p.K299E		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K299E(1)		autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CATGGCCATGAAGAAGCTGTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											88	87	87					11																	123811218		2202	4299	6501	123316428	SO:0001583	missense	219875			BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"GPCR / Class A : Olfactory receptors"	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.895A>G	11.37:g.123811218A>G	ENSP00000305970:p.Lys299Glu		123316428	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	37	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.862578	0.51482	.	.	ENSG00000171014	ENST00000307033	T	0.42900	0.96	5.29	5.29	0.74685	.	0.176563	0.26867	U	0.022087	T	0.38983	0.1061	L	0.41079	1.255	0.34585	D	0.71485	P	0.39404	0.672	B	0.39904	0.313	T	0.57423	-0.7814	10	0.62326	D	0.03	-9.998	14.8805	0.70528	1.0:0.0:0.0:0.0	.	299	Q8NGN0	OR4D5_HUMAN	E	299	ENSP00000305970:K299E	ENSP00000305970:K299E	K	+	1	0	OR4D5	123316428	0.714000	0.27936	1.000000	0.80357	0.225000	0.24961	1.730000	0.38125	1.994000	0.58287	0.528000	0.53228	AAG		0.507	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965		G	123811218	A	G	123811218	3	3	61	1	0	0	0	0	1	0	0	0	11088	247	9	4	897	4	OR4D5	11	123811218	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	55953	123811218	11195298	7739	15724										
OR10S1	219873	broad.mit.edu	37	chr11	123848354	123848354	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacagtctggttggggttCtccgttgtcatggtcatctt	11	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123848354C>A	ENST00000531945.1	-	1	134	c.45G>T	c.(43-45)gaG>gaT	p.E15D		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E15D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GGTTGGGGTTCTCCGTTGTCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											85	85	85					11																	123848354		2202	4299	6501	123353564	SO:0001583	missense	219873			BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.45G>T	11.37:g.123848354C>A	ENSP00000431914:p.Glu15Asp		123353564	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.775503	0.31411	.	.	ENSG00000196248	ENST00000531945	T	0.00457	7.29	4.75	-3.66	0.04489	.	0.353602	0.19897	U	0.103603	T	0.00210	0.0006	N	0.25094	0.71	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43294	-0.9400	10	0.30854	T	0.27	-1.8337	1.9994	0.03463	0.1724:0.3577:0.094:0.3759	.	15	Q8NGN2	O10S1_HUMAN	D	15	ENSP00000431914:E15D	ENSP00000431914:E15D	E	-	3	2	OR10S1	123353564	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.373000	0.02568	-1.021000	0.03350	-0.164000	0.13417	GAG		0.478	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		A	123848354	C	A	123848354	3	1	61	1	0	0	0	0	1	0	0	0	10949	912	32	2	954	2	OR10S1	11	123848354	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37136	123848354	11158162	7740	15725										
OR10G8	219869	broad.mit.edu	37	chr11	123900516	123900516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgtactacttcctcaccAacctgtcgttcattgacatg	5	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123900516A>G	ENST00000431524.1	+	1	220	c.187A>G	c.(187-189)Aac>Gac	p.N63D		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N63D(1)		breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CTTCCTCACCAACCTGTCGTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											263	209	227					11																	123900516		2201	4299	6500	123405726	SO:0001583	missense	219869			AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.187A>G	11.37:g.123900516A>G	ENSP00000389072:p.Asn63Asp		123405726	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.176160	0.57692	.	.	ENSG00000234560	ENST00000431524	T	0.12672	2.66	2.95	1.66	0.24008	GPCR, rhodopsin-like superfamily (1);	0.422805	0.19930	N	0.102892	T	0.28863	0.0716	M	0.88031	2.925	0.26731	N	0.970597	P	0.45474	0.859	P	0.53809	0.735	T	0.05750	-1.0866	10	0.54805	T	0.06	.	4.4751	0.11731	0.6221:0.1908:0.0:0.187	.	63	Q8NGN5	O10G8_HUMAN	D	63	ENSP00000389072:N63D	ENSP00000389072:N63D	N	+	1	0	OR10G8	123405726	0.000000	0.05858	1.000000	0.80357	0.971000	0.66376	0.862000	0.27899	1.337000	0.45525	0.477000	0.44152	AAC		0.537	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		G	123900516	A	G	123900516	3	3	61	1	0	0	0	0	1	0	0	0	10934	130	5	4	189	4	OR10G8	11	123900516	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52162	123900516	11106000	7741	15726										
VWA5A	4013	broad.mit.edu	37	chr11	123994469	123994469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatcttggcaccactccaGaacatttacaggggaccctc	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:123994469G>T	ENST00000456829.2	+	10	1373	c.1122G>T	c.(1120-1122)caG>caT	p.Q374H	VWA5A_ENST00000392748.1_Missense_Mutation_p.Q374H|VWA5A_ENST00000361352.5_Missense_Mutation_p.Q374H|VWA5A_ENST00000449321.1_Missense_Mutation_p.Q374H|VWA5A_ENST00000360334.4_Missense_Mutation_p.Q374H|VWA5A_ENST00000392744.4_Missense_Mutation_p.Q390H	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	374	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.							p.Q374H(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						CACCACTCCAGAACATTTACA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	61	61					11																	123994469		2201	4298	6499	123499679	SO:0001583	missense	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1122G>T	11.37:g.123994469G>T	ENSP00000407726:p.Gln374His		123499679	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.045582	0.55110	.	.	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.08807	3.05;3.05;3.05;3.05;3.05;3.05	5.64	1.52	0.23074	von Willebrand factor, type A (3);	1.015120	0.07871	N	0.967939	T	0.15392	0.0371	L	0.47716	1.5	0.09310	N	1	P;P	0.49358	0.923;0.923	P;P	0.56343	0.726;0.796	T	0.24476	-1.0159	10	0.41790	T	0.15	-0.5001	5.3667	0.16117	0.233:0.0:0.6098:0.1571	.	390;374	B4DHS6;O00534	.;VMA5A_HUMAN	H	374;374;374;374;374;390	ENSP00000407726:Q374H;ENSP00000353485:Q374H;ENSP00000376504:Q374H;ENSP00000355070:Q374H;ENSP00000404683:Q374H;ENSP00000376501:Q390H	ENSP00000353485:Q374H	Q	+	3	2	VWA5A	123499679	0.000000	0.05858	0.000000	0.03702	0.679000	0.39708	0.443000	0.21644	0.023000	0.15187	0.644000	0.83932	CAG		0.512	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		T	123994469	G	T	123994469	3	4	61	1	0	0	0	0	1	0	0	0	17282	933	33	2	1152	2	VWA5A	11	123994469	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93953	123994469	11012047	7742	15727										
VWA5A	4013	broad.mit.edu	37	chr11	124006949	124006949	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagaacagactgtcatCtttaggggtcagagattaat	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124006949C>A	ENST00000456829.2	+	13	1724	c.1473C>A	c.(1471-1473)atC>atA	p.I491I	VWA5A_ENST00000392748.1_Silent_p.I491I|VWA5A_ENST00000360334.4_Intron	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	491								p.I491I(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						AGACTGTCATCTTTAGGGGTC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	11											115	106	109					11																	124006949		2201	4299	6500	123512159	SO:0001819	synonymous_variant	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1473C>A	11.37:g.124006949C>A			123512159	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	37	CCDS8444.1																																																																																				0.493	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		A	124006949	C	A	124006949	2	1	61	1	0	0	0	0	0	0	0	1	17282	903	32	2		2	VWA5A	11	124006949	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12480	124006949	10999567	7743	15728										
VWA5A	4013	broad.mit.edu	37	chr11	124016640	124016640	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatctgtggatcctgctatCtttgccttttgaagatacca	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124016640C>A	ENST00000456829.2	+	19	2600	c.2349C>A	c.(2347-2349)atC>atA	p.I783I	VWA5A_ENST00000392748.1_Silent_p.I783I|VWA5A_ENST00000360334.4_3'UTR	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	783								p.I783I(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						ATCCTGCTATCTTTGCCTTTT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	11											138	113	122					11																	124016640		2200	4296	6496	123521850	SO:0001819	synonymous_variant	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.2349C>A	11.37:g.124016640C>A			123521850	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	37	CCDS8444.1																																																																																				0.418	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		A	124016640	C	A	124016640	2	1	61	1	0	0	0	0	0	0	0	1	17282	903	32	2		2	VWA5A	11	124016640	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9691	124016640	10989876	7744	15729										
OR8B3	390271	broad.mit.edu	37	chr11	124266631	124266631	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaactgggtaccatgataTtaatacccacaacaatgaga	6	9	0	2	rs374508700		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124266631T>G	ENST00000354597.3	-	1	633	c.617A>C	c.(616-618)aAt>aCt	p.N206T		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N206T(1)		kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TACCATGATATTAATACCCAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											157	163	161					11																	124266631		2201	4299	6500	123771841	SO:0001583	missense	390271			AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"GPCR / Class A : Olfactory receptors"	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.617A>C	11.37:g.124266631T>G	ENSP00000346611:p.Asn206Thr		123771841	Q6IFQ8|Q8NGH1	Missense_Mutation	SNP	ENST00000354597.3	37	CCDS31709.1	.	.	.	.	.	.	.	.	.	.	N	6.519	0.463978	0.12402	.	.	ENSG00000196661	ENST00000354597	T	0.00076	8.76	3.62	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	T	0.00241	0.0007	L	0.46567	1.45	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.50466	-0.8825	10	0.59425	D	0.04	.	0.477	0.00541	0.1758:0.2036:0.1825:0.4381	.	206	Q8NGG8	OR8B3_HUMAN	T	206	ENSP00000346611:N206T	ENSP00000346611:N206T	N	-	2	0	OR8B3	123771841	0.000000	0.05858	0.602000	0.28890	0.028000	0.11728	-0.296000	0.08287	0.759000	0.33084	0.454000	0.30748	AAT		0.418	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467		G	124266631	T	G	124266631	3	3	61	1	0	0	0	0	1	0	0	0	11259	1493	52	4	326	4	OR8B3	11	124266631	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	249991	124266631	10739885	7745	15730										
OR8B8	26493	broad.mit.edu	37	chr11	124310880	124310880	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaccacagtgaccacgtaGaagcctagaaacaggaagaa	9	12	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124310880G>T	ENST00000328064.2	-	1	174	c.102C>A	c.(100-102)ttC>ttA	p.F34L		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	34					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F34L(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TGACCACGTAGAAGCCTAGAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											79	79	79					11																	124310880		2201	4299	6500	123816090	SO:0001583	missense	26493			AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.102C>A	11.37:g.124310880G>T	ENSP00000330280:p.Phe34Leu		123816090	A1L446|Q96RC8	Missense_Mutation	SNP	ENST00000328064.2	37	CCDS8446.1	.	.	.	.	.	.	.	.	.	.	G	10.18	1.279724	0.23392	.	.	ENSG00000197125	ENST00000328064	T	0.00625	6.14	3.73	1.74	0.24563	.	0.831471	0.10292	N	0.692187	T	0.00384	0.0012	N	0.02103	-0.685	0.24195	N	0.995533	B	0.19073	0.033	B	0.21151	0.033	T	0.47368	-0.9123	10	0.87932	D	0	.	3.7861	0.08702	0.3129:0.0:0.5162:0.1708	.	34	Q15620	OR8B8_HUMAN	L	34	ENSP00000330280:F34L	ENSP00000330280:F34L	F	-	3	2	OR8B8	123816090	0.029000	0.19370	0.088000	0.20740	0.643000	0.38383	-0.252000	0.08806	0.483000	0.27608	0.557000	0.71058	TTC		0.507	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310880	G	T	124310880	3	4	61	1	0	0	0	0	1	0	0	0	11261	933	33	2	836	2	OR8B8	11	124310880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44249	124310880	10695636	7746	15731										
SIAE	54414	broad.mit.edu	37	chr11	124508521	124508521	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccttgtgagccaagagttCtatcttctcaggcagtggtc	10	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124508521C>A	ENST00000263593.3	-	9	1409	c.1237G>T	c.(1237-1239)Gaa>Taa	p.E413*	RNA5SP352_ENST00000363408.1_RNA|SIAE_ENST00000545756.1_Nonsense_Mutation_p.E378*			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	413					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)	p.E413*(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		GCCAAGAGTTCTATCTTCTCA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											133	117	123					11																	124508521		2201	4299	6500	124013731	SO:0001587	stop_gained	54414			AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"sialic acid-specific acetylesterase II"	610079	"Ysg2 homolog (mouse)"	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.1237G>T	11.37:g.124508521C>A	ENSP00000263593:p.Glu413*		124013731	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Nonsense_Mutation	SNP	ENST00000263593.3	37	CCDS8449.1	.	.	.	.	.	.	.	.	.	.	C	36	5.613441	0.96637	.	.	ENSG00000110013	ENST00000263593;ENST00000545756	.	.	.	5.44	4.51	0.55191	.	0.472295	0.22152	N	0.063911	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-13.5951	14.8376	0.70194	0.0:0.8549:0.1451:0.0	.	.	.	.	X	413;378	.	ENSP00000263593:E413X	E	-	1	0	SIAE	124013731	0.045000	0.20229	0.290000	0.24890	0.448000	0.32197	1.162000	0.31786	1.250000	0.43966	0.655000	0.94253	GAA		0.468	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601		A	124508521	C	A	124508521	4	1	61	1	0	0	0	0	0	1	0	0	14335	922	32	2	342	2	SIAE	11	124508521	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	197641	124508521	10497995	7747	15732										
VSIG2	23584	broad.mit.edu	37	chr11	124620809	124620809	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagatggccattggtgaaGtacaggatctggggagaggc	16	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124620809G>T	ENST00000326621.5	-	3	328	c.228C>A	c.(226-228)taC>taA	p.Y76*	VSIG2_ENST00000403470.1_Nonsense_Mutation_p.Y76*	NM_014312.3	NP_055127.2	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	76	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.Y76*(1)		central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(5)	19	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		CATTGGTGAAGTACAGGATCT	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											71	63	66					11																	124620809		2201	4299	6500	124126019	SO:0001587	stop_gained	23584			AF061022	CCDS8452.1	11q24	2013-01-11			ENSG00000019102	ENSG00000019102		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	17149	protein-coding gene	gene with protein product		606011				9862345	Standard	NM_014312		Approved	CTXL, CTH	uc001qas.3	Q96IQ7	OTTHUMG00000150357	ENST00000326621.5:c.228C>A	11.37:g.124620809G>T	ENSP00000318684:p.Tyr76*		124126019	O95791|Q9NX42	Nonsense_Mutation	SNP	ENST00000326621.5	37	CCDS8452.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.783107	0.90282	.	.	ENSG00000019102	ENST00000326621;ENST00000403470	.	.	.	5.28	2.23	0.28157	.	0.214441	0.32161	N	0.006488	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3558	0.32329	0.2801:0.0:0.7199:0.0	.	.	.	.	X	76	.	ENSP00000318684:Y76X	Y	-	3	2	VSIG2	124126019	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.431000	0.34925	0.810000	0.34279	0.655000	0.94253	TAC		0.527	VSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317785.1	NM_014312		T	124620809	G	T	124620809	4	4	61	1	0	0	0	0	0	1	0	0	17264	1024	36	2	775	2	VSIG2	11	124620809	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112288	124620809	10385707	7748	15733										
ROBO3	64221	broad.mit.edu	37	chr11	124742277	124742277	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccttgctctgtccccagGtcctgcttttccccagtcag	8	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124742277G>A	ENST00000397801.1	+	8	1351	c.1159G>A	c.(1159-1161)Gtc>Atc	p.V387I	ROBO3_ENST00000538940.1_Splice_Site_p.V365I	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	387	Ig-like C2-type 4.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)		p.V387I(2)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		CTGTCCCCAGGTCCTGCTTTT	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	11											69	70	69					11																	124742277		1979	4154	6133	124247487	SO:0001630	splice_region_variant	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1159-1G>A	11.37:g.124742277G>A			124247487		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.472527	0.43942	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.65364	-0.15;-0.15	5.7	4.69	0.59074	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.200534	0.24597	N	0.037176	T	0.33731	0.0873	N	0.05414	-0.055	0.80722	D	1	B	0.15473	0.013	B	0.09377	0.004	T	0.29579	-1.0007	9	.	.	.	.	4.0117	0.09626	0.3219:0.0:0.6781:0.0	.	387	Q96MS0	ROBO3_HUMAN	I	387;365	ENSP00000380903:V387I;ENSP00000441797:V365I	.	V	+	1	0	ROBO3	124247487	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.302000	0.65733	2.695000	0.91970	0.655000	0.94253	GTC		0.567	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	Missense_Mutation	A	124742277	G	A	124742277	5	1	61	1	0	0	0	0	0	0	1	0	13552	1275	44	3	1189	3	ROBO3	11	124742277	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121468	124742277	10264239	7749	15734										
ROBO3	64221	broad.mit.edu	37	chr11	124745200	124745200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggggctgggggctgaaaGcctctctgtgaccaggagca	18	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124745200G>A	ENST00000397801.1	+	14	2459	c.2267G>A	c.(2266-2268)aGc>aAc	p.S756N	ROBO3_ENST00000543966.1_5'Flank|ROBO3_ENST00000538940.1_Missense_Mutation_p.S734N	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	756	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)		p.S756N(2)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		GGGGCTGAAAGCCTCTCTGTG	0.607																																																2	Substitution - Missense(2)	large_intestine(2)	11											70	71	70					11																	124745200		1932	4149	6081	124250410	SO:0001583	missense	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.2267G>A	11.37:g.124745200G>A	ENSP00000380903:p.Ser756Asn		124250410		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.356244	0.61293	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.71103	-0.54;-0.54	5.47	5.47	0.80525	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.45361	D	0.000380	D	0.82820	0.5120	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84426	0.0574	10	0.87932	D	0	.	16.0553	0.80798	0.0:0.0:1.0:0.0	.	756	Q96MS0	ROBO3_HUMAN	N	756;734	ENSP00000380903:S756N;ENSP00000441797:S734N	ENSP00000380903:S756N	S	+	2	0	ROBO3	124250410	1.000000	0.71417	0.970000	0.41538	0.039000	0.13416	7.772000	0.85439	2.559000	0.86315	0.650000	0.86243	AGC		0.607	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		A	124745200	G	A	124745200	3	1	61	1	0	0	0	0	1	0	0	0	13552	971	34	3	2321	3	ROBO3	11	124745200	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2923	124745200	10261316	7750	15735										
ROBO4	54538	broad.mit.edu	37	chr11	124764191	124764191	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcctggcatatgggtggcGatttccagctgggtctgctc	15	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124764191G>A	ENST00000306534.3	-	8	1709	c.1224C>T	c.(1222-1224)atC>atT	p.I408I	ROBO4_ENST00000533054.1_Silent_p.I263I|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	408	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.I408I(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		TATGGGTGGCGATTTCCAGCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	11											123	94	104					11																	124764191		2201	4299	6500	124269401	SO:0001819	synonymous_variant	54538			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1224C>T	11.37:g.124764191G>A			124269401	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																				0.592	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124764191	G	A	124764191	2	1	61	1	0	0	0	0	0	0	0	1	13553	1048	37	1		1	ROBO4	11	124764191	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18991	124764191	10242325	7751	15736										
SLC37A2	219855	broad.mit.edu	37	chr11	124953755	124953755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacctgtctacactcttcGatgttggtggcatcataggt	12	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:124953755G>A	ENST00000403796.2	+	11	1322	c.1021G>A	c.(1021-1023)Gat>Aat	p.D341N	SLC37A2_ENST00000298280.5_Missense_Mutation_p.D341N|SLC37A2_ENST00000525837.1_3'UTR|SLC37A2_ENST00000407458.1_Missense_Mutation_p.D341N|SLC37A2_ENST00000308074.4_Missense_Mutation_p.D341N	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	341					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.D341N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TACACTCTTCGATGTTGGTGG	0.562																																					Melanoma(11;373 620 21213 26083 47768)											1	Substitution - Missense(1)	large_intestine(1)	11											147	112	124					11																	124953755		2201	4299	6500	124458965	SO:0001583	missense	219855			AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"Solute carriers"	20644	protein-coding gene	gene with protein product			"solute carrier family 37 (glycerol-3-phosphate transporter), member 2"				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.1021G>A	11.37:g.124953755G>A	ENSP00000384407:p.Asp341Asn		124458965	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831891	0.71258	.	.	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.57436	0.4;0.4;0.44;0.4	4.97	4.97	0.65823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.82506	-0.0423	10	0.87932	D	0	-23.194	18.0204	0.89253	0.0:0.0:1.0:0.0	.	341;341	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	N	341	ENSP00000384407:D341N;ENSP00000385126:D341N;ENSP00000298280:D341N;ENSP00000311833:D341N	ENSP00000298280:D341N	D	+	1	0	SLC37A2	124458965	1.000000	0.71417	0.943000	0.38184	0.194000	0.23727	9.214000	0.95140	2.583000	0.87209	0.655000	0.94253	GAT		0.562	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		A	124953755	G	A	124953755	3	1	61	1	0	0	0	0	1	0	0	0	14635	1058	37	1	1063	1	SLC37A2	11	124953755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189564	124953755	10052761	7752	15737										
PKNOX2	63876	broad.mit.edu	37	chr11	125281716	125281716	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgaggagtcttgcccaaGcatgccaccaatataatgcg	9	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125281716G>A	ENST00000298282.9	+	10	1162	c.891G>A	c.(889-891)aaG>aaA	p.K297K	PKNOX2_ENST00000530517.1_3'UTR|PKNOX2_ENST00000542175.1_Silent_p.K233K	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	297					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.K297K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TCTTGCCCAAGCATGCCACCA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	11											144	142	143					11																	125281716		2069	4226	6295	124786926	SO:0001819	synonymous_variant	63876			AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.891G>A	11.37:g.125281716G>A			124786926	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Silent	SNP	ENST00000298282.9	37	CCDS41730.1																																																																																				0.507	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			A	125281716	G	A	125281716	2	1	61	1	0	0	0	0	0	0	0	1	12014	962	34	3		3	PKNOX2	11	125281716	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	327961	125281716	9724800	7753	15738										
PKNOX2	63876	broad.mit.edu	37	chr11	125301174	125301174	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggatgggacagaagaagaGgatgaggatgagatggaaga	18	1	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125301174G>T	ENST00000298282.9	+	13	1576	c.1305G>T	c.(1303-1305)gaG>gaT	p.E435D	PKNOX2_ENST00000530517.1_3'UTR|PKNOX2_ENST00000542175.1_Missense_Mutation_p.E371D	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	435	Asp/Glu-rich (acidic).				regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.E435D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		CAgaagaagaggatgaggatg	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	11											48	53	51					11																	125301174		2165	4274	6439	124806384	SO:0001583	missense	63876			AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.1305G>T	11.37:g.125301174G>T	ENSP00000298282:p.Glu435Asp		124806384	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	37	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521381	0.44866	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175	D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.93	4.56	2.68	0.31781	.	0.290613	0.31134	N	0.008192	T	0.77294	0.4109	N	0.02247	-0.625	0.51767	D	0.999937	D;D;D	0.61697	0.99;0.984;0.984	D;D;D	0.70935	0.971;0.935;0.935	T	0.71609	-0.4541	10	0.15499	T	0.54	-16.6369	10.3701	0.44049	0.1614:0.0:0.8386:0.0	.	371;406;435	F5GZ15;B7Z3G7;Q96KN3	.;.;PKNX2_HUMAN	D	406;406;435;371	ENSP00000434732:E406D;ENSP00000433971:E406D;ENSP00000298282:E435D;ENSP00000441470:E371D	ENSP00000298282:E435D	E	+	3	2	PKNOX2	124806384	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.465000	0.35299	0.649000	0.30751	0.655000	0.94253	GAG		0.567	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			T	125301174	G	T	125301174	3	4	61	1	0	0	0	0	1	0	0	0	12014	991	35	2	1343	2	PKNOX2	11	125301174	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19458	125301174	9705342	7754	15739										
FEZ1	9638	broad.mit.edu	37	chr11	125359541	125359541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagaaaaattctcaagctCggagagggaggggtcctcga	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125359541C>T	ENST00000278919.3	-	2	367	c.133G>A	c.(133-135)Gag>Aag	p.E45K	FEZ1_ENST00000524435.1_Missense_Mutation_p.E45K|FEZ1_ENST00000366139.3_Missense_Mutation_p.E45K	NM_005103.4	NP_005094.1	Q99689	FEZ1_HUMAN	fasciculation and elongation protein zeta 1 (zygin I)	45					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|establishment of mitochondrion localization (GO:0051654)|nervous system development (GO:0007399)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|transport (GO:0006810)	axon (GO:0030424)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)		p.E45K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	24	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0934)		TTCTCAAGCTCGGAGAGGGAG	0.502																																					Melanoma(180;509 2033 10762 15939 24711)											1	Substitution - Missense(1)	large_intestine(1)	11											62	69	67					11																	125359541		2201	4299	6500	124864751	SO:0001583	missense	9638			U60060	CCDS31716.1, CCDS44758.1	11q24.2	2005-09-29			ENSG00000149557	ENSG00000149557			3659	protein-coding gene	gene with protein product		604825				9096408, 15843383	Standard	NM_005103		Approved		uc001qbx.3	Q99689	OTTHUMG00000165886	ENST00000278919.3:c.133G>A	11.37:g.125359541C>T	ENSP00000278919:p.Glu45Lys		124864751	O00679|O00728|Q6IBI7	Missense_Mutation	SNP	ENST00000278919.3	37	CCDS31716.1	.	.	.	.	.	.	.	.	.	.	C	36	5.796840	0.96952	.	.	ENSG00000149557	ENST00000278919;ENST00000529053;ENST00000366139;ENST00000524435;ENST00000527534	T	0.32272	1.46	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.44117	0.1278	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.98	T	0.08848	-1.0702	10	0.17369	T	0.5	-14.48	19.5568	0.95354	0.0:1.0:0.0:0.0	.	45;45	B4DKG5;Q99689	.;FEZ1_HUMAN	K	45	ENSP00000278919:E45K	ENSP00000278919:E45K	E	-	1	0	FEZ1	124864751	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	7.670000	0.83925	2.722000	0.93159	0.650000	0.86243	GAG		0.502	FEZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386875.1	NM_005103		T	125359541	C	T	125359541	3	4	61	1	0	0	0	0	1	0	0	0	5842	893	31	1	1085	1	FEZ1	11	125359541	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58367	125359541	9646975	7755	15740										
EI24	9538	broad.mit.edu	37	chr11	125448072	125448072	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttggtcgtggctggaattCttcctcacgtcaattttcag	10	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125448072C>A	ENST00000278903.6	+	6	602	c.360C>A	c.(358-360)ttC>ttA	p.F120L	EI24_ENST00000530985.1_3'UTR|EI24_ENST00000343678.4_Missense_Mutation_p.F120L|STT3A-AS1_ENST00000532714.1_RNA|STT3A-AS1_ENST00000530526.1_RNA	NM_004879.3	NP_004870.3	O14681	EI24_HUMAN	etoposide induced 2.4	120					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.F120L(2)		large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		GGCTGGAATTCTTCCTCACGT	0.453																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	11											204	186	192					11																	125448072		1918	4151	6069	124953282	SO:0001583	missense	9538			AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"ectopic P-granules autophagy protein 4 homolog (C. elegans)"	605170	"etoposide induced 2.4 mRNA"			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000278903.6:c.360C>A	11.37:g.125448072C>A	ENSP00000278903:p.Phe120Leu		124953282	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000278903.6	37		.	.	.	.	.	.	.	.	.	.	C	12.66	2.003675	0.35320	.	.	ENSG00000149547	ENST00000278903;ENST00000343678;ENST00000524723;ENST00000527842;ENST00000527131	.	.	.	5.83	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.61135	0.2323	L	0.39633	1.23	0.58432	D	0.999993	D;D;D;D	0.69078	0.997;0.997;0.979;0.997	D;D;D;D	0.77004	0.989;0.989;0.982;0.989	T	0.55289	-0.8164	9	0.11485	T	0.65	-8.3033	10.8227	0.46614	0.0:0.7108:0.0:0.2892	.	106;120;120;120	B4DKL6;E9PM05;A6NES3;O14681	.;.;.;EI24_HUMAN	L	120;120;163;120;120	.	ENSP00000278903:F120L	F	+	3	2	EI24	124953282	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	0.706000	0.25690	0.813000	0.34350	0.655000	0.94253	TTC		0.453	EI24-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_004879		A	125448072	C	A	125448072	3	1	61	1	0	0	0	0	1	0	0	0	4996	912	32	2	378	2	EI24	11	125448072	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88531	125448072	9558444	7756	15741										
PATE2	399967	broad.mit.edu	37	chr11	125647896	125647896	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcataacacattatttcagtCgctgccagatacaaaaagag	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125647896C>T	ENST00000358524.3	-	3	123	c.78G>A	c.(76-78)gcG>gcA	p.A26A	PATE2_ENST00000436890.2_Intron	NM_212555.2	NP_997720.1	Q6UY27	PATE2_HUMAN	prostate and testis expressed 2	26						extracellular space (GO:0005615)		p.A26A(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)	6						TTATTTCAGTCGCTGCCAGAT	0.438																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	11											99	91	94					11																	125647896		2201	4299	6500	125153106	SO:0001630	splice_region_variant	399967			AY358105	CCDS8465.1	11q24.2	2008-12-17	2008-12-17	2008-12-17		ENSG00000196844		"PATE family"	32249	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 38"	C11orf38			Standard	NM_212555		Approved	UNQ3112, LVLF3112, PATE-M	uc001qcu.3	Q6UY27		ENST00000358524.3:c.77-1G>A	11.37:g.125647896C>T			125153106	B2RNZ2|B7ZMG4	Silent	SNP	ENST00000358524.3	37	CCDS8465.1																																																																																				0.438	PATE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386729.1	NM_212555	Silent	T	125647896	C	T	125647896	5	4	61	1	0	0	0	0	0	0	1	0	11505	898	31	1	271	1	PATE2	11	125647896	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	199824	125647896	9358620	7757	15742										
PUS3	83480	broad.mit.edu	37	chr11	125765145	125765145	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggcttttggggatttttCtctatattcagcagctcatc	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125765145C>A	ENST00000530811.1	-	2	963	c.918G>T	c.(916-918)gaG>gaT	p.E306D	PUS3_ENST00000227474.3_Missense_Mutation_p.E306D|HYLS1_ENST00000425380.2_Intron|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	306					tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.E306D(1)		NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		GGGGATTTTTCTCTATATTCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											77	82	80					11																	125765145		2201	4299	6500	125270355	SO:0001583	missense	83480			BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.918G>T	11.37:g.125765145C>A	ENSP00000432386:p.Glu306Asp		125270355	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.452062	0.43531	.	.	ENSG00000110060	ENST00000227474;ENST00000530811	T;T	0.19250	2.16;2.16	5.73	1.67	0.24075	Pseudouridine synthase I, TruA, C-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.320500	0.36482	N	0.002568	T	0.22205	0.0535	L	0.52905	1.665	0.41015	D	0.98503	B	0.24483	0.104	B	0.37731	0.257	T	0.05354	-1.0890	10	0.38643	T	0.18	-5.1744	6.039	0.19724	0.0:0.6041:0.1308:0.2651	.	306	Q9BZE2	PUS3_HUMAN	D	306	ENSP00000227474:E306D;ENSP00000432386:E306D	ENSP00000227474:E306D	E	-	3	2	PUS3	125270355	0.997000	0.39634	1.000000	0.80357	0.972000	0.66771	0.521000	0.22893	0.727000	0.32360	0.591000	0.81541	GAG		0.408	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		A	125765145	C	A	125765145	3	1	61	1	0	0	0	0	1	0	0	0	12869	912	32	2	535	2	PUS3	11	125765145	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117249	125765145	9241371	7758	15743										
HYLS1	219844	broad.mit.edu	37	chr11	125769968	125769968	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtgaagatcatagaaaGgaattacgctggggtgtccg	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125769968G>T	ENST00000425380.2	+	3	1486	c.705G>T	c.(703-705)aaG>aaT	p.K235N	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Missense_Mutation_p.K235N|HYLS1_ENST00000356438.3_Missense_Mutation_p.K235N	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	235						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K235N(1)		breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		ATCATAGAAAGGAATTACGCT	0.478																																					Esophageal Squamous(172;2590 2636 8884 10471)											1	Substitution - Missense(1)	large_intestine(1)	11											81	74	76					11																	125769968		2201	4299	6500	125275178	SO:0001583	missense	219844			AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.705G>T	11.37:g.125769968G>T	ENSP00000414884:p.Lys235Asn		125275178	B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	37	CCDS8467.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.948111	0.53186	.	.	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.77877	-1.13;-1.13;-1.13	6.02	2.73	0.32206	.	0.149329	0.43416	D	0.000561	T	0.82204	0.4986	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.81728	-0.0800	10	0.52906	T	0.07	.	11.7312	0.51737	0.2703:0.0:0.7297:0.0	.	235	Q96M11	HYLS1_HUMAN	N	235	ENSP00000348815:K235N;ENSP00000414884:K235N;ENSP00000436833:K235N	ENSP00000348815:K235N	K	+	3	2	HYLS1	125275178	0.999000	0.42202	1.000000	0.80357	0.821000	0.46438	0.317000	0.19487	0.884000	0.36064	-0.140000	0.14226	AAG		0.478	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014		T	125769968	G	T	125769968	3	4	61	1	0	0	0	0	1	0	0	0	7490	991	35	2	707	2	HYLS1	11	125769968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4823	125769968	9236548	7759	15744										
DDX25	29118	broad.mit.edu	37	chr11	125786921	125786921	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcacagagctctaccctcCgaatgccaaatgctcctctt	5	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125786921C>T	ENST00000263576.6	+	9	968	c.813C>T	c.(811-813)tcC>tcT	p.S271S	RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	271	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.S157S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		CTCTACCCTCCGAATGCCAAA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	11											83	84	84					11																	125786921		2080	4224	6304	125292131	SO:0001819	synonymous_variant	29118			AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"DEAD-boxes"	18698	protein-coding gene	gene with protein product	"gonadotropin-regulated testicular RNA helicase"	607663	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.813C>T	11.37:g.125786921C>T			125292131	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	37	CCDS44766.1																																																																																				0.507	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		T	125786921	C	T	125786921	2	4	61	1	0	0	0	0	0	0	0	1	4358	639	23	1		1	DDX25	11	125786921	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16953	125786921	9219595	7760	15745										
CDON	50937	broad.mit.edu	37	chr11	125864237	125864237	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatctgttggtcggtaataGatataaaatccttgaatggg	10	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:125864237G>T	ENST00000392693.3	-	14	2719	c.2592C>A	c.(2590-2592)atC>atA	p.I864I	CDON_ENST00000531738.1_Silent_p.I241I|CDON_ENST00000263577.7_Silent_p.I864I	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	864	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I864I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GTCGGTAATAGATATAAAATC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	11											116	106	110					11																	125864237		2201	4299	6500	125369447	SO:0001819	synonymous_variant	50937			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.2592C>A	11.37:g.125864237G>T			125369447	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																				0.388	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		T	125864237	G	T	125864237	2	4	61	1	0	0	0	0	0	0	0	1	3176	932	33	2		2	CDON	11	125864237	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77316	125864237	9142279	7761	15746										
FAM118B	79607	broad.mit.edu	37	chr11	126104960	126104960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggattcttcaacgatggcGaacctcccaccaaaaagccc	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:126104960G>A	ENST00000533050.1	+	3	557	c.64G>A	c.(64-66)Gaa>Aaa	p.E22K	FAM118B_ENST00000529731.1_Missense_Mutation_p.E22K|FAM118B_ENST00000360194.4_Missense_Mutation_p.E22K|FAM118B_ENST00000525728.1_Intron	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	22								p.E22K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		CAACGATGGCGAACCTCCCAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											76	81	79					11																	126104960		2201	4299	6500	125610170	SO:0001583	missense	79607			BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.64G>A	11.37:g.126104960G>A	ENSP00000433343:p.Glu22Lys		125610170	Q9H7B0	Missense_Mutation	SNP	ENST00000533050.1	37	CCDS8470.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.296043	0.23650	.	.	ENSG00000197798	ENST00000533050;ENST00000528985;ENST00000529731;ENST00000360194;ENST00000530043;ENST00000525338	T;T;T;T;T;T	0.42513	1.56;1.56;0.97;1.56;0.98;0.97	6.17	4.31	0.51392	.	0.481200	0.24158	N	0.041005	T	0.18045	0.0433	N	0.08118	0	0.22803	N	0.998715	B;B;B	0.17852	0.024;0.014;0.014	B;B;B	0.12156	0.007;0.003;0.004	T	0.21759	-1.0236	10	0.12103	T	0.63	-10.7204	4.7513	0.13063	0.2217:0.0:0.62:0.1583	.	22;22;22	G3V179;E9PMJ2;Q9BPY3	.;.;F118B_HUMAN	K	22	ENSP00000433343:E22K;ENSP00000434952:E22K;ENSP00000432712:E22K;ENSP00000353321:E22K;ENSP00000437285:E22K;ENSP00000435754:E22K	ENSP00000353321:E22K	E	+	1	0	FAM118B	125610170	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.335000	0.43929	0.932000	0.37266	0.655000	0.94253	GAA		0.413	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		A	126104960	G	A	126104960	3	1	61	1	0	0	0	0	1	0	0	0	5428	1059	37	1	66	1	FAM118B	11	126104960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	240723	126104960	8901556	7762	15747										
FAM118B	79607	broad.mit.edu	37	chr11	126126690	126126690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatggagatgactatgccGatcttccagaatatttcaag	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:126126690G>A	ENST00000533050.1	+	7	1418	c.925G>A	c.(925-927)Gat>Aat	p.D309N	FAM118B_ENST00000529731.1_Missense_Mutation_p.D233N|FAM118B_ENST00000360194.4_Missense_Mutation_p.D309N	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	309								p.D309N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TGACTATGCCGATCTTCCAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											166	173	171					11																	126126690		2201	4299	6500	125631900	SO:0001583	missense	79607			BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.925G>A	11.37:g.126126690G>A	ENSP00000433343:p.Asp309Asn		125631900	Q9H7B0	Missense_Mutation	SNP	ENST00000533050.1	37	CCDS8470.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.863536	0.71949	.	.	ENSG00000197798	ENST00000533050;ENST00000528985;ENST00000529731;ENST00000360194;ENST00000525338	T;T;T;T;T	0.48836	1.58;1.58;1.58;1.58;0.8	5.04	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.51363	0.1670	N	0.19112	0.55	0.54753	D	0.999984	P;D;D	0.76494	0.516;0.999;0.998	B;D;D	0.72625	0.064;0.978;0.909	T	0.50825	-0.8782	10	0.36615	T	0.2	-25.2598	13.5572	0.61765	0.0748:0.0:0.9252:0.0	.	233;309;309	G3V179;E9PMJ2;Q9BPY3	.;.;F118B_HUMAN	N	309;309;233;309;233	ENSP00000433343:D309N;ENSP00000434952:D309N;ENSP00000432712:D233N;ENSP00000353321:D309N;ENSP00000435754:D233N	ENSP00000353321:D309N	D	+	1	0	FAM118B	125631900	1.000000	0.71417	0.998000	0.56505	0.903000	0.53119	7.433000	0.80362	1.343000	0.45638	0.591000	0.81541	GAT		0.453	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		A	126126690	G	A	126126690	3	1	61	1	0	0	0	0	1	0	0	0	5428	1058	37	1	943	1	FAM118B	11	126126690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21730	126126690	8879826	7763	15748										
ETS1	2113	broad.mit.edu	37	chr11	128391833	128391833	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggggaaaagctccagatcGactttttccgtcttgatgat	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:128391833G>T	ENST00000319397.6	-	1	366	c.57C>A	c.(55-57)gtC>gtA	p.V19V	ETS1_ENST00000531611.1_Silent_p.V19V|ETS1_ENST00000392668.4_Intron|ETS1_ENST00000345075.4_Silent_p.V19V|ETS1_ENST00000535549.1_Silent_p.V19V|ETS1_ENST00000526145.2_Silent_p.V19V	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	19					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.V19V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		GCTCCAGATCGACTTTTTCCG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	11											54	56	55					11																	128391833		2201	4297	6498	127897043	SO:0001819	synonymous_variant	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.57C>A	11.37:g.128391833G>T			127897043	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Silent	SNP	ENST00000319397.6	37	CCDS8475.1																																																																																				0.632	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		T	128391833	G	T	128391833	2	4	61	1	0	0	0	0	0	0	0	1	5288	1045	37	2		2	ETS1	11	128391833	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2265143	128391833	6614683	7764	15749										
FLI1	2313	broad.mit.edu	37	chr11	128680588	128680588	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaaagtgcacggcaaaaGatatgcttacaaatttgact	8	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:128680588G>T	ENST00000527786.2	+	9	1553	c.1064G>T	c.(1063-1065)aGa>aTa	p.R355I	FLI1_ENST00000344954.6_Missense_Mutation_p.R322I|FLI1_ENST00000534087.2_Missense_Mutation_p.R322I|FLI1_ENST00000525560.1_Missense_Mutation_p.R162I|FLI1_ENST00000281428.8_Missense_Mutation_p.R289I	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	355					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R355I(1)	EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		CACGGCAAAAGATATGCTTAC	0.488			T	EWSR1	Ewing sarcoma																																		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	1	Substitution - Missense(1)	large_intestine(1)	11											64	71	69					11																	128680588		2183	4289	6472	128185798	SO:0001583	missense	2313			M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"Friend leukemia virus integration 1"			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.1064G>T	11.37:g.128680588G>T	ENSP00000433488:p.Arg355Ile		128185798	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Missense_Mutation	SNP	ENST00000527786.2	37	CCDS44768.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238786	0.79800	.	.	ENSG00000151702	ENST00000525560;ENST00000344954;ENST00000429175;ENST00000534087;ENST00000281428	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.23	5.23	0.72850	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.67702	0.2921	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.76793	-0.2828	10	0.87932	D	0	.	18.9989	0.92824	0.0:0.0:1.0:0.0	.	355;162;289	Q01543;B4DFV4;Q01543-2	FLI1_HUMAN;.;.	I	162;322;355;322;289	ENSP00000437124:R162I;ENSP00000339627:R322I;ENSP00000399985:R355I;ENSP00000432950:R322I;ENSP00000281428:R289I	ENSP00000281428:R289I	R	+	2	0	FLI1	128185798	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.595000	0.98260	2.719000	0.93026	0.650000	0.86243	AGA		0.488	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017		T	128680588	G	T	128680588	3	4	61	1	0	0	0	0	1	0	0	0	5943	942	33	2	1098	2	FLI1	11	128680588	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288755	128680588	6325928	7765	15750										
ARHGAP32	9743	broad.mit.edu	37	chr11	128842602	128842602	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtgctggtattctcttCgggggacccagaaggagggt	17	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:128842602C>T	ENST00000310343.9	-	21	3756	c.3757G>A	c.(3757-3759)Gaa>Aaa	p.E1253K	ARHGAP32_ENST00000392657.3_Missense_Mutation_p.E904K|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.E904K|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1253					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)	p.E1253K(2)|p.E904K(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GTATTCTCTTCGGGGGACCCA	0.483																																																4	Substitution - Missense(4)	large_intestine(4)	11											101	105	104					11																	128842602		2201	4297	6498	128347812	SO:0001583	missense	9743			AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.3757G>A	11.37:g.128842602C>T	ENSP00000310561:p.Glu1253Lys		128347812	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.060806	0.76074	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.09163	3.02;3.01;3.01	5.71	5.71	0.89125	.	0.308092	0.28077	N	0.016682	T	0.12689	0.0308	M	0.63428	1.95	0.35537	D	0.80273	P	0.48640	0.913	B	0.34038	0.174	T	0.23940	-1.0174	10	0.36615	T	0.2	.	18.0404	0.89317	0.0:1.0:0.0:0.0	.	1253	A7KAX9	RHG32_HUMAN	K	1253;904;904	ENSP00000310561:E1253K;ENSP00000376425:E904K;ENSP00000432862:E904K	ENSP00000310561:E1253K	E	-	1	0	ARHGAP32	128347812	0.990000	0.36364	0.996000	0.52242	0.991000	0.79684	3.103000	0.50298	2.710000	0.92621	0.655000	0.94253	GAA		0.483	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128842602	C	T	128842602	3	4	61	1	0	0	0	0	1	0	0	0	881	893	31	1	2514	1	ARHGAP32	11	128842602	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162014	128842602	6163914	7766	15751										
ARHGAP32	9743	broad.mit.edu	37	chr11	128844371	128844371	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaatttccgtcctatcttCggagagaaagcatagacgac	8	10	1	2	rs537107666		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:128844371C>T	ENST00000310343.9	-	20	2678	c.2679G>A	c.(2677-2679)ccG>ccA	p.P893P	ARHGAP32_ENST00000392657.3_Silent_p.P544P|ARHGAP32_ENST00000527272.1_Silent_p.P544P|ARHGAP32_ENST00000524655.1_Silent_p.P819P	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	893					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)	p.P893P(1)|p.P544P(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GTCCTATCTTCGGAGAGAAAG	0.438													C|||	1	0.000199681	0	0	5008	,	,		23392	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	11											176	160	165					11																	128844371		2201	4297	6498	128349581	SO:0001819	synonymous_variant	9743			AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.2679G>A	11.37:g.128844371C>T			128349581	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																				0.438	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128844371	C	T	128844371	2	4	61	1	0	0	0	0	0	0	0	1	881	871	31	1		1	ARHGAP32	11	128844371	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1769	128844371	6162145	7767	15752										
TMEM45B	120224	broad.mit.edu	37	chr11	129722522	129722522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcgtctcgagatcgtcGaagccgcaattaggactttg	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:129722522G>A	ENST00000524567.1	+	2	426	c.145G>A	c.(145-147)Gaa>Aaa	p.E49K	TMEM45B_ENST00000281441.3_Missense_Mutation_p.E49K			Q96B21	TM45B_HUMAN	transmembrane protein 45B	49						integral component of membrane (GO:0016021)		p.E49K(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		CGAGATCGTCGAAGCCGCAAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	11											133	125	127					11																	129722522		2201	4297	6498	129227732	SO:0001583	missense	120224			AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.145G>A	11.37:g.129722522G>A	ENSP00000436293:p.Glu49Lys		129227732	A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	37	CCDS8482.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283590	0.80803	.	.	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.38560	1.13;1.13	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	M	0.90145	3.09	0.80722	D	1	D	0.76494	0.999	P	0.60789	0.879	T	0.76468	-0.2948	10	0.87932	D	0	-2.7805	18.2812	0.90098	0.0:0.0:1.0:0.0	.	49	Q96B21	TM45B_HUMAN	K	49	ENSP00000281441:E49K;ENSP00000436293:E49K	ENSP00000281441:E49K	E	+	1	0	TMEM45B	129227732	1.000000	0.71417	0.930000	0.37139	0.035000	0.12851	8.834000	0.92094	2.653000	0.90120	0.655000	0.94253	GAA		0.473	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		A	129722522	G	A	129722522	3	1	61	1	0	0	0	0	1	0	0	0	16209	1059	37	1	147	1	TMEM45B	11	129722522	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	878151	129722522	5283994	7768	15753										
PRDM10	56980	broad.mit.edu	37	chr11	129772231	129772231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtttggtgatatgcacttCgctgcttccgttcccgttgg	12	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:129772231C>T	ENST00000360871.3	-	21	3679	c.3448G>A	c.(3448-3450)Gaa>Aaa	p.E1150K	PRDM10_ENST00000526082.1_Missense_Mutation_p.E1068K|PRDM10_ENST00000528746.1_Missense_Mutation_p.E1111K|PRDM10_ENST00000304538.6_Missense_Mutation_p.E1017K|PRDM10_ENST00000423662.2_Missense_Mutation_p.E1055K|PRDM10_ENST00000358825.5_Missense_Mutation_p.E1154K	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	1141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.E1150K(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		ATATGCACTTCGCTGCTTCCG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	11											329	288	302					11																	129772231		2201	4297	6498	129277441	SO:0001583	missense	56980			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.3448G>A	11.37:g.129772231C>T	ENSP00000354118:p.Glu1150Lys		129277441	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087018	0.94100	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082	T;T;T;T;T;T	0.18960	2.48;2.18;2.48;2.49;2.56;2.47	5.66	5.66	0.87406	.	0.052499	0.85682	D	0.000000	T	0.23727	0.0574	L	0.32530	0.975	0.80722	D	1	P;P;P;D;P;P	0.56035	0.956;0.935;0.893;0.974;0.935;0.935	B;B;B;P;B;B	0.44696	0.27;0.364;0.2;0.458;0.364;0.364	T	0.01121	-1.1445	10	0.87932	D	0	-19.895	19.3454	0.94361	0.0:1.0:0.0:0.0	.	1064;1150;1141;1068;1017;1055	B7ZL72;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;PRD10_HUMAN;.;.;.	K	1154;1017;1150;1055;1111;1068	ENSP00000351686:E1154K;ENSP00000302669:E1017K;ENSP00000354118:E1150K;ENSP00000398431:E1055K;ENSP00000431262:E1111K;ENSP00000432237:E1068K	ENSP00000302669:E1017K	E	-	1	0	PRDM10	129277441	1.000000	0.71417	0.947000	0.38551	0.850000	0.48378	7.128000	0.77217	2.689000	0.91719	0.591000	0.81541	GAA		0.542	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		T	129772231	C	T	129772231	3	4	61	1	0	0	0	0	1	0	0	0	12485	893	31	1	26	1	PRDM10	11	129772231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49709	129772231	5234285	7769	15754										
PRDM10	56980	broad.mit.edu	37	chr11	129784892	129784892	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactctggatgcttctttcGaatgtgctggaccatcttgg	11	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:129784892G>A	ENST00000360871.3	-	17	2779	c.2548C>T	c.(2548-2550)Cga>Tga	p.R850*	PRDM10_ENST00000526082.1_Nonsense_Mutation_p.R768*|PRDM10_ENST00000528746.1_Nonsense_Mutation_p.R824*|PRDM10_ENST00000304538.6_Nonsense_Mutation_p.R764*|PRDM10_ENST00000423662.2_Nonsense_Mutation_p.R768*|PRDM10_ENST00000358825.5_Nonsense_Mutation_p.R854*	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	854					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.R850*(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGCTTCTTTCGAATGTGCTGG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											101	101	101					11																	129784892		2201	4297	6498	129290102	SO:0001587	stop_gained	56980			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2548C>T	11.37:g.129784892G>A	ENSP00000354118:p.Arg850*		129290102	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Nonsense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	G	39	7.803198	0.98498	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	.	.	.	5.76	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.8327	17.516	0.87773	0.0:0.0:0.8677:0.1323	.	.	.	.	X	854;764;850;768;824;768;567	.	ENSP00000302669:R764X	R	-	1	2	PRDM10	129290102	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.661000	0.61518	2.718000	0.92993	0.655000	0.94253	CGA		0.433	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129784892	G	A	129784892	4	1	61	1	0	0	0	0	0	1	0	0	12485	1066	37	1	942	1	PRDM10	11	129784892	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12661	129784892	5221624	7770	15755										
ST14	6768	broad.mit.edu	37	chr11	130078361	130078361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgcacgaccagagccagcGcagcgcccctggggtgcagg	15	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130078361G>A	ENST00000278742.5	+	17	2469	c.2051G>A	c.(2050-2052)cGc>cAc	p.R684H		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	684	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R684H(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CAGAGCCAGCGCAGCGCCCCT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	56	56					11																	130078361		2201	4297	6498	129583571	SO:0001583	missense	6768			AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"Serine peptidases / Transmembrane"	11344	protein-coding gene	gene with protein product	"epithin", "matriptase"	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.2051G>A	11.37:g.130078361G>A	ENSP00000278742:p.Arg684His		129583571	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429018	0.62844	.	.	ENSG00000149418	ENST00000278742;ENST00000525779	D	0.88818	-2.43	5.4	4.46	0.54185	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.38663	N	0.001620	D	0.88381	0.6421	L	0.42529	1.33	0.40323	D	0.978843	D	0.76494	0.999	P	0.51974	0.686	D	0.87949	0.2722	10	0.44086	T	0.13	.	12.7428	0.57264	0.0:0.0:0.701:0.299	.	684	Q9Y5Y6	ST14_HUMAN	H	684;586	ENSP00000278742:R684H	ENSP00000278742:R684H	R	+	2	0	ST14	129583571	0.179000	0.23135	0.998000	0.56505	0.648000	0.38561	0.784000	0.26816	1.237000	0.43756	0.313000	0.20887	CGC		0.632	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			A	130078361	G	A	130078361	3	1	61	1	0	0	0	0	1	0	0	0	15250	1087	38	1	2117	1	ST14	11	130078361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293469	130078361	4928155	7771	15756										
ZBTB44	29068	broad.mit.edu	37	chr11	130130756	130130756	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaggcattatacctataGaggaagactgtggactaatc	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130130756G>T	ENST00000357899.4	-	2	1285	c.1013C>A	c.(1012-1014)tCt>tAt	p.S338Y	ZBTB44_ENST00000397753.1_Missense_Mutation_p.S338Y|ZBTB44_ENST00000530205.1_Missense_Mutation_p.S338Y|ZBTB44_ENST00000525842.1_Missense_Mutation_p.S338Y			Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	338					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S338Y(1)		autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		TATACCTATAGAGGAAGACTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											85	79	81					11																	130130756		1881	4106	5987	129635966	SO:0001583	missense	29068			AK024659	CCDS44776.1, CCDS73414.1, CCDS73415.1	11q24.3	2013-01-08	2006-09-19	2006-09-19		ENSG00000196323		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	25001	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 15"	BTBD15		11042152	Standard	NM_014155		Approved	HSPC063, ZNF851	uc001qgb.4	Q8NCP5		ENST00000357899.4:c.1013C>A	11.37:g.130130756G>T	ENSP00000350574:p.Ser338Tyr		129635966	Q6IPT8|Q86VJ7|Q86XX5	Missense_Mutation	SNP	ENST00000357899.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.02|19.02	3.745368|3.745368	0.69418|0.69418	.|.	.|.	ENSG00000196323|ENSG00000196323	ENST00000529982|ENST00000525842;ENST00000397753;ENST00000445008;ENST00000357899;ENST00000530205	.|T;T;T;T;T	.|0.15256	.|2.44;2.77;2.5;2.77;2.44	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	.|0.049920	.|0.85682	.|D	.|0.000000	T|T	0.32041|0.32041	0.0816|0.0816	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.69078	.|0.997;0.997;0.995;0.997	.|D;D;D;D	.|0.80764	.|0.994;0.994;0.979;0.994	T|T	0.05886|0.05886	-1.0858|-1.0858	5|10	.|0.62326	.|D	.|0.03	.|.	19.3282|19.3282	0.94273|0.94273	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|338;338;338;338	.|Q8NCP5-4;Q8NCP5-3;Q8NCP5;Q8NCP5-2	.|.;.;ZBT44_HUMAN;.	I|Y	192|338	.|ENSP00000433457:S338Y;ENSP00000380861:S338Y;ENSP00000408079:S338Y;ENSP00000350574:S338Y;ENSP00000434177:S338Y	.|ENSP00000350574:S338Y	L|S	-|-	1|2	2|0	ZBTB44|ZBTB44	129635966|129635966	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	9.434000|9.434000	0.97515|0.97515	2.566000|2.566000	0.86566|0.86566	0.563000|0.563000	0.77884|0.77884	CTA|TCT		0.408	ZBTB44-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000386126.1	NM_014155		T	130130756	G	T	130130756	3	4	61	1	0	0	0	0	1	0	0	0	17584	942	33	2	368	2	ZBTB44	11	130130756	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52395	130130756	4875760	7772	15757										
ZBTB44	29068	broad.mit.edu	37	chr11	130131186	130131186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgtgccacactttacagGactttcaggagacataacaa	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130131186G>A	ENST00000357899.4	-	2	855	c.583C>T	c.(583-585)Cct>Tct	p.P195S	ZBTB44_ENST00000397753.1_Missense_Mutation_p.P195S|ZBTB44_ENST00000530205.1_Missense_Mutation_p.P195S|ZBTB44_ENST00000525842.1_Missense_Mutation_p.P195S			Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P195S(1)		autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		CACTTTACAGGACTTTCAGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											87	83	84					11																	130131186		1928	4133	6061	129636396	SO:0001583	missense	29068			AK024659	CCDS44776.1, CCDS73414.1, CCDS73415.1	11q24.3	2013-01-08	2006-09-19	2006-09-19		ENSG00000196323		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	25001	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 15"	BTBD15		11042152	Standard	NM_014155		Approved	HSPC063, ZNF851	uc001qgb.4	Q8NCP5		ENST00000357899.4:c.583C>T	11.37:g.130131186G>A	ENSP00000350574:p.Pro195Ser		129636396	Q6IPT8|Q86VJ7|Q86XX5	Missense_Mutation	SNP	ENST00000357899.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.020861|4.020861	0.75275|0.75275	.|.	.|.	ENSG00000196323|ENSG00000196323	ENST00000525842;ENST00000397753;ENST00000445008;ENST00000357899;ENST00000530205;ENST00000338191|ENST00000527478	T;T;T;T;T|T	0.59364|0.55760	0.27;0.27;0.27;0.27;0.27|0.5	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54663|0.54663	0.1872|0.1872	L|L	0.27053|0.27053	0.805|0.805	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	0.996;0.996;0.993;1.0|.	D;D;D;D|.	0.87578|.	0.986;0.986;0.968;0.998|.	T|T	0.51741|0.51741	-0.8667|-0.8667	10|7	0.87932|0.39692	D|T	0|0.17	.|.	19.4488|19.4488	0.94859|0.94859	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	195;195;195;195|.	Q8NCP5-4;Q8NCP5-3;Q8NCP5;Q8NCP5-2|.	.;.;ZBT44_HUMAN;.|.	S|F	195;195;195;195;195;107|191	ENSP00000433457:P195S;ENSP00000380861:P195S;ENSP00000408079:P195S;ENSP00000350574:P195S;ENSP00000434177:P195S|ENSP00000436187:S191F	ENSP00000341618:P107S|ENSP00000436187:S191F	P|S	-|-	1|2	0|0	ZBTB44|ZBTB44	129636396|129636396	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.187000|9.187000	0.94912|0.94912	2.586000|2.586000	0.87340|0.87340	0.655000|0.655000	0.94253|0.94253	CCT|TCC		0.458	ZBTB44-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000386126.1	NM_014155		A	130131186	G	A	130131186	3	1	61	1	0	0	0	0	1	0	0	0	17584	1174	41	3	798	3	ZBTB44	11	130131186	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	430	130131186	4875330	7773	15758										
ADAMTS15	170689	broad.mit.edu	37	chr11	130341198	130341198	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgggaacctgggctccaaGaagagattcgacaagtgtgg	15	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130341198G>T	ENST00000299164.2	+	7	1998	c.1998G>T	c.(1996-1998)aaG>aaT	p.K666N		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	666	Cys-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K666N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		TGGGCTCCAAGAAGAGATTCG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	11											136	133	134					11																	130341198		2201	4297	6498	129846408	SO:0001583	missense	170689			AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"ADAM metallopeptidases with thrombospondin type 1 motif"	16305	protein-coding gene	gene with protein product		607509	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.1998G>T	11.37:g.130341198G>T	ENSP00000299164:p.Lys666Asn		129846408	Q32MI6	Missense_Mutation	SNP	ENST00000299164.2	37	CCDS8488.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.812056	0.32053	.	.	ENSG00000166106	ENST00000299164	T	0.66099	-0.19	5.97	4.12	0.48240	.	.	.	.	.	T	0.38772	0.1053	N	0.11023	0.085	0.43647	D	0.996052	B	0.02656	0.0	B	0.04013	0.001	T	0.10917	-1.0609	9	0.20519	T	0.43	.	8.8375	0.35121	0.2788:0.0:0.7212:0.0	.	666	Q8TE58	ATS15_HUMAN	N	666	ENSP00000299164:K666N	ENSP00000299164:K666N	K	+	3	2	ADAMTS15	129846408	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.318000	0.33643	0.868000	0.35678	0.655000	0.94253	AAG		0.572	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		T	130341198	G	T	130341198	3	4	61	1	0	0	0	0	1	0	0	0	260	933	33	2	2024	2	ADAMTS15	11	130341198	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210012	130341198	4665318	7774	15759										
SNX19	399979	broad.mit.edu	37	chr11	130784604	130784604	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaccatctttgggttccaGagcctgggaactctctaggg	11	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130784604G>T	ENST00000265909.4	-	1	1800	c.1231C>A	c.(1231-1233)Ctg>Atg	p.L411M	SNX19_ENST00000528555.1_Intron|SNX19_ENST00000539184.1_De_novo_Start_OutOfFrame|SNX19_ENST00000530356.1_De_novo_Start_OutOfFrame|SNX19_ENST00000533214.1_Missense_Mutation_p.L411M|SNX19_ENST00000533318.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	411					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.L411M(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TTGGGTTCCAGAGCCTGGGAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	11											57	55	56					11																	130784604		2201	4297	6498	130289814	SO:0001583	missense	399979			D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1231C>A	11.37:g.130784604G>T	ENSP00000265909:p.Leu411Met		130289814	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.531405	0.27387	.	.	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.24350	1.86;1.86	4.88	1.91	0.25777	.	1.256370	0.05410	N	0.542200	T	0.15609	0.0376	L	0.32530	0.975	0.09310	N	0.999997	P;B	0.40083	0.702;0.451	B;B	0.32149	0.141;0.086	T	0.23190	-1.0195	10	0.52906	T	0.07	-4.2499	0.7336	0.00961	0.3131:0.1615:0.3593:0.1662	.	411;411	E9PKB9;Q92543	.;SNX19_HUMAN	M	411	ENSP00000265909:L411M;ENSP00000435390:L411M	ENSP00000265909:L411M	L	-	1	2	SNX19	130289814	0.095000	0.21747	0.353000	0.25747	0.529000	0.34654	0.671000	0.25172	0.238000	0.21222	0.650000	0.86243	CTG		0.552	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		T	130784604	G	T	130784604	3	4	61	1	0	0	0	0	1	0	0	0	14927	933	33	2	1791	2	SNX19	11	130784604	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	443406	130784604	4221912	7775	15760										
SNX19	399979	broad.mit.edu	37	chr11	130784751	130784751	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acataagaacaggggacctcGaacatttggctgtaggaaat	11	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:130784751G>A	ENST00000265909.4	-	1	1653	c.1084C>T	c.(1084-1086)Cga>Tga	p.R362*	SNX19_ENST00000528555.1_Intron|SNX19_ENST00000539184.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000533214.1_Nonsense_Mutation_p.R362*|SNX19_ENST00000533318.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	362					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.R362*(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		AGGGGACCTCGAACATTTGGC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											66	65	65					11																	130784751		2201	4297	6498	130289961	SO:0001587	stop_gained	399979			D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1084C>T	11.37:g.130784751G>A	ENSP00000265909:p.Arg362*		130289961	E9PKB9|Q8IV55	Nonsense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	G	39	7.328037	0.98214	.	.	ENSG00000120451	ENST00000265909;ENST00000533214	.	.	.	5.23	3.22	0.36961	.	0.463174	0.19793	N	0.105939	.	.	.	.	.	.	0.47009	D	0.999288	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-1.1055	13.0527	0.58964	0.0:0.0:0.5805:0.4195	.	.	.	.	X	362	.	ENSP00000265909:R362X	R	-	1	2	SNX19	130289961	0.954000	0.32549	0.791000	0.31998	0.300000	0.27592	2.330000	0.43885	1.175000	0.42826	0.644000	0.83932	CGA		0.483	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130784751	G	A	130784751	4	1	61	1	0	0	0	0	0	1	0	0	14927	1066	37	1	1938	1	SNX19	11	130784751	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147	130784751	4221765	7776	15761										
OPCML	4978	broad.mit.edu	37	chr11	132306105	132306105	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcggcctttgttttcaatcCtcattccatccagaccagtg	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:132306105C>A	ENST00000331898.7	-	6	1390	c.812G>T	c.(811-813)aGg>aTg	p.R271M	OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Missense_Mutation_p.R230M|OPCML_ENST00000524381.1_Missense_Mutation_p.R264M|OPCML_ENST00000541867.1_Missense_Mutation_p.R271M	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	271	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.R271M(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GTTTTCAATCCTCATTCCATC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											154	141	145					11																	132306105		2201	4297	6498	131811315	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.812G>T	11.37:g.132306105C>A	ENSP00000330862:p.Arg271Met		131811315	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831818	0.71258	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.91	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.091270	0.85682	D	0.000000	T	0.75525	0.3861	M	0.64997	1.995	0.43047	D	0.994641	D;P;P;P	0.55800	0.973;0.921;0.921;0.921	P;P;P;P	0.56343	0.796;0.796;0.796;0.796	T	0.78807	-0.2059	10	0.66056	D	0.02	-19.6951	14.6617	0.68876	0.0:0.9297:0.0:0.0703	.	271;264;270;271	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	M	271;264;230;238;271	ENSP00000330862:R271M;ENSP00000434750:R264M;ENSP00000363910:R230M;ENSP00000445496:R271M	ENSP00000330862:R271M	R	-	2	0	OPCML	131811315	1.000000	0.71417	0.993000	0.49108	0.794000	0.44872	3.504000	0.53347	1.502000	0.48669	0.650000	0.86243	AGG		0.448	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		A	132306105	C	A	132306105	3	1	61	1	0	0	0	0	1	0	0	0	10905	681	24	2	233	2	OPCML	11	132306105	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1521354	132306105	2700411	7777	15762										
SPATA19	219938	broad.mit.edu	37	chr11	133712402	133712402	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtctcacctgctctattcGatctcgcatgatgtcctctg	7	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:133712402G>A	ENST00000299140.3	-	5	469	c.415C>T	c.(415-417)Cga>Tga	p.R139*	SPATA19_ENST00000532889.1_Nonsense_Mutation_p.R139*	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	139					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)		p.R139*(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		TGCTCTATTCGATCTCGCATG	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											275	212	233					11																	133712402		2201	4297	6498	133217612	SO:0001587	stop_gained	219938			AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"spergen 1", "cancer/testis antigen 132"	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.415C>T	11.37:g.133712402G>A	ENSP00000299140:p.Arg139*		133217612	Q8N7A9	Nonsense_Mutation	SNP	ENST00000299140.3	37	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128968	0.94473	.	.	ENSG00000166118	ENST00000299140;ENST00000532889	.	.	.	5.66	2.52	0.30459	.	0.000000	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2355	7.7475	0.28877	0.0:0.1299:0.416:0.4541	.	.	.	.	X	139	.	ENSP00000299140:R139X	R	-	1	2	SPATA19	133217612	0.958000	0.32768	0.501000	0.27601	0.935000	0.57460	1.624000	0.37018	0.751000	0.32900	0.462000	0.41574	CGA		0.517	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927		A	133712402	G	A	133712402	4	1	61	1	0	0	0	0	0	1	0	0	15043	1066	37	1	96	1	SPATA19	11	133712402	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1406297	133712402	1294114	7778	15763										
ACAD8	27034	broad.mit.edu	37	chr11	134128487	134128487	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccgctctgtaccatggaGaagtttgcttcctactgcct	8	14	1	1	rs35423297		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:134128487G>T	ENST00000281182.4	+	4	565	c.459G>T	c.(457-459)gaG>gaT	p.E153D	ACAD8_ENST00000374752.4_Intron|ACAD8_ENST00000543332.1_Missense_Mutation_p.E55D|ACAD8_ENST00000524547.1_Intron|ACAD8_ENST00000537423.1_Missense_Mutation_p.E76D	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	153					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.E153D(1)		endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GTACCATGGAGAAGTTTGCTT	0.488																																					GBM(65;238 1125 33403 41853 48889)											1	Substitution - Missense(1)	large_intestine(1)	11											129	90	103					11																	134128487		2201	4297	6498	133633697	SO:0001583	missense	27034			AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.459G>T	11.37:g.134128487G>T	ENSP00000281182:p.Glu153Asp		133633697	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.260296	0.39995	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000537915	D;D;D	0.99201	-5.55;-5.55;-5.55	5.56	5.56	0.83823	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.099177	0.64402	D	0.000002	D	0.96355	0.8811	L	0.37507	1.11	0.43988	D	0.996683	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.001	B;B;B;B;B	0.10450	0.003;0.005;0.001;0.001;0.005	D	0.91859	0.5498	10	0.37606	T	0.19	.	5.7791	0.18295	0.1166:0.0:0.6944:0.189	.	94;76;55;55;153	B7Z767;B7Z5W4;B7Z9L5;B7Z7F1;Q9UKU7	.;.;.;.;ACAD8_HUMAN	D	153;76;55;115	ENSP00000281182:E153D;ENSP00000443763:E76D;ENSP00000438302:E55D	ENSP00000281182:E153D	E	+	3	2	ACAD8	133633697	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.909000	0.39917	2.605000	0.88082	0.655000	0.94253	GAG		0.488	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		T	134128487	G	T	134128487	3	4	61	1	0	0	0	0	1	0	0	0	110	933	33	2	473	2	ACAD8	11	134128487	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	416085	134128487	878029	7779	15764										
GLB1L3	112937	broad.mit.edu	37	chr11	134183914	134183914	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagatgaaaatgagcttCtttgagaggtatgctccagc	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr11:134183914C>A	ENST00000431683.2	+	17	1659	c.1659C>A	c.(1657-1659)ttC>ttA	p.F553L		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	553					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)	p.F553L(1)|p.F214L(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		AAATGAGCTTCTTTGAGAGGT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	11											70	65	67					11																	134183914		1895	4115	6010	133689124	SO:0001583	missense	112937				CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1659C>A	11.37:g.134183914C>A	ENSP00000396615:p.Phe553Leu		133689124	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561484	0.45590	.	.	ENSG00000166105	ENST00000431683	D	0.94092	-3.35	4.78	3.87	0.44632	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.92084	0.7491	M	0.77313	2.365	0.40809	D	0.983401	B	0.24368	0.102	B	0.23419	0.046	D	0.90706	0.4624	10	0.56958	D	0.05	.	10.7441	0.46170	0.0:0.9092:0.0:0.0908	.	553	Q8NCI6	GLBL3_HUMAN	L	553	ENSP00000396615:F553L	ENSP00000396615:F553L	F	+	3	2	GLB1L3	133689124	1.000000	0.71417	0.510000	0.27712	0.012000	0.07955	1.548000	0.36201	1.361000	0.45981	0.563000	0.77884	TTC		0.478	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		A	134183914	C	A	134183914	3	1	61	1	0	0	0	0	1	0	0	0	6450	912	32	2	1725	2	GLB1L3	11	134183914	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55427	134183914	822602	7780	15765										
IQSEC3	440073	broad.mit.edu	37	chr12	250337	250337	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctcacgcggcttcatccCggacacccccatcggtgtgg	11	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:250337C>T	ENST00000538872.1	+	5	2157	c.2039C>T	c.(2038-2040)cCg>cTg	p.P680L	IQSEC3_ENST00000326261.4_Missense_Mutation_p.P680L|IQSEC3_ENST00000382841.2_Missense_Mutation_p.P377L|RP11-598F7.4_ENST00000505893.2_RNA|RP11-598F7.4_ENST00000508953.2_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	680	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P377L(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		GGCTTCATCCCGGACACCCCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12											117	109	112					12																	250337		2203	4300	6503	120598	SO:0001583	missense	440073			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2039C>T	12.37:g.250337C>T	ENSP00000437554:p.Pro680Leu		120598	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	37	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.391108	0.82902	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.76839	-1.05;-1.05;-1.05	5.76	5.76	0.90799	SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.78071	0.4226	L	0.58354	1.805	0.80722	D	1	B;P	0.38129	0.45;0.619	B;B	0.37780	0.258;0.119	T	0.79992	-0.1569	10	0.87932	D	0	.	19.973	0.97292	0.0:1.0:0.0:0.0	.	680;377	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	L	680;680;377	ENSP00000437554:P680L;ENSP00000315662:P680L;ENSP00000372292:P377L	ENSP00000315662:P680L	P	+	2	0	IQSEC3	120598	1.000000	0.71417	0.967000	0.41034	0.345000	0.29048	7.818000	0.86416	2.729000	0.93468	0.511000	0.50034	CCG		0.587	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		T	250337	C	T	250337	3	4	61	1	0	0	0	0	1	0	0	0	7840	652	23	1	2057	1	IQSEC3	12	250337	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		250337	133601558	7781	15766										
IQSEC3	440073	broad.mit.edu	37	chr12	274617	274617	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagattctcaaactttgcccGaagaagaagagctcctccac	7	13	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:274617G>A	ENST00000538872.1	+	10	2845	c.2727G>A	c.(2725-2727)ccG>ccA	p.P909P	RP11-598F7.5_ENST00000540136.1_RNA|IQSEC3_ENST00000326261.4_Silent_p.P909P|IQSEC3_ENST00000382841.2_Silent_p.P606P|RP11-598F7.6_ENST00000537295.1_lincRNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	909	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P606P(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AACTTTGCCCGAAGAAGAAGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	12											182	171	174					12																	274617		2203	4300	6503	144878	SO:0001819	synonymous_variant	440073			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2727G>A	12.37:g.274617G>A			144878	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																				0.522	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		A	274617	G	A	274617	2	1	61	1	0	0	0	0	0	0	0	1	7840	1045	37	1		1	IQSEC3	12	274617	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24280	274617	133577278	7782	15767										
SLC6A12	6539	broad.mit.edu	37	chr12	304439	304439	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaatgacaggaacagcaGgcatatgccactggaagcat	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:304439G>A	ENST00000428720.1	-	13	2124	c.1381C>T	c.(1381-1383)Ctg>Ttg	p.L461L	RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Silent_p.L461L|SLC6A12_ENST00000424061.2_Silent_p.L461L|SLC6A12_ENST00000359674.4_Silent_p.L461L|SLC6A12_ENST00000538272.1_5'Flank|SLC6A12_ENST00000397296.2_Silent_p.L461L	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	461					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.L461L(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGGAACAGCAGGCATATGCCA	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	12											258	214	229					12																	304439		2203	4300	6503	174700	SO:0001819	synonymous_variant	6539			L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1381C>T	12.37:g.304439G>A			174700	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																				0.567	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		A	304439	G	A	304439	2	1	61	1	0	0	0	0	0	0	0	1	14712	991	35	3		3	SLC6A12	12	304439	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29822	304439	133547456	7783	15768										
SLC6A12	6539	broad.mit.edu	37	chr12	307996	307996	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcggaacaaatctggcttCaagtagtagatgatgccctg	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:307996C>A	ENST00000428720.1	-	8	1556	c.813G>T	c.(811-813)ttG>ttT	p.L271F	SLC6A12_ENST00000536824.1_Missense_Mutation_p.L271F|SLC6A12_ENST00000424061.2_Missense_Mutation_p.L271F|SLC6A12_ENST00000359674.4_Missense_Mutation_p.L271F|SLC6A12_ENST00000538272.1_5'UTR|SLC6A12_ENST00000397296.2_Missense_Mutation_p.L271F	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	271					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.L271F(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AATCTGGCTTCAAGTAGTAGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											147	123	131					12																	307996		2203	4300	6503	178257	SO:0001583	missense	6539			L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.813G>T	12.37:g.307996C>A	ENSP00000388184:p.Leu271Phe		178257	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163215	0.57476	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	4.44	3.54	0.40534	.	0.000000	0.64402	D	0.000006	D	0.82852	0.5127	L	0.53561	1.675	0.54753	D	0.999988	D	0.56287	0.975	D	0.68621	0.959	T	0.82900	-0.0228	10	0.87932	D	0	.	9.4566	0.38758	0.1413:0.781:0.0:0.0778	.	271	P48065	S6A12_HUMAN	F	271	ENSP00000352702:L271F;ENSP00000380464:L271F;ENSP00000388184:L271F;ENSP00000399136:L271F;ENSP00000444268:L271F	ENSP00000352702:L271F	L	-	3	2	SLC6A12	178257	0.986000	0.35501	0.999000	0.59377	0.844000	0.47949	0.340000	0.19892	0.969000	0.38237	0.655000	0.94253	TTG		0.527	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		A	307996	C	A	307996	3	1	61	1	0	0	0	0	1	0	0	0	14712	825	29	2	1067	2	SLC6A12	12	307996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3557	307996	133543899	7784	15769										
KDM5A	5927	broad.mit.edu	37	chr12	416835	416835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctctccttcaggcaaccGtacgggcaacttctgaaggg	12	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:416835G>A	ENST00000399788.2	-	23	4077	c.3715C>T	c.(3715-3717)Cgg>Tgg	p.R1239W	KDM5A_ENST00000382815.4_Missense_Mutation_p.R1239W	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1239					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R1239W(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						TCAGGCAACCGTACGGGCAAC	0.512			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	2	Substitution - Missense(2)	large_intestine(2)	12											76	76	76					12																	416835		1921	4126	6047	287096	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.3715C>T	12.37:g.416835G>A	ENSP00000382688:p.Arg1239Trp		287096	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011070	0.75046	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	T;T	0.01209	5.17;5.17	5.66	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.05044	0.0135	L	0.56199	1.76	0.58432	D	0.999999	D;D	0.67145	0.993;0.996	P;D	0.68353	0.832;0.957	T	0.34551	-0.9824	10	0.87932	D	0	-14.4907	15.3118	0.74039	0.0:0.0:0.8315:0.1685	.	1239;1239	P29375;P29375-2	KDM5A_HUMAN;.	W	1239	ENSP00000382688:R1239W;ENSP00000372265:R1239W	ENSP00000372265:R1239W	R	-	1	2	KDM5A	287096	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.803000	0.55560	1.354000	0.45846	0.585000	0.79938	CGG		0.512	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		A	416835	G	A	416835	3	1	61	1	0	0	0	0	1	0	0	0	8154	1144	40	1	1381	1	KDM5A	12	416835	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108839	416835	133435060	7785	15770										
KDM5A	5927	broad.mit.edu	37	chr12	430229	430229	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacaaaggccttcaattCttccactgtcagtttggtcc	8	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:430229C>A	ENST00000399788.2	-	18	2835	c.2473G>T	c.(2473-2475)Gaa>Taa	p.E825*	KDM5A_ENST00000382815.4_Nonsense_Mutation_p.E825*	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	825					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E825*(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GCCTTCAATTCTTCCACTGTC	0.398			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	2	Substitution - Nonsense(2)	large_intestine(2)	12											173	175	175					12																	430229		1908	4112	6020	300490	SO:0001587	stop_gained	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.2473G>T	12.37:g.430229C>A	ENSP00000382688:p.Glu825*		300490	A8MV76|Q4LE72|Q86XZ1	Nonsense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	C	44	10.954680	0.99494	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-23.4619	19.9434	0.97174	0.0:1.0:0.0:0.0	.	.	.	.	X	444;784;825;825;444	.	ENSP00000261253:E444X	E	-	1	0	KDM5A	300490	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.461000	0.80834	2.710000	0.92621	0.563000	0.77884	GAA		0.398	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		A	430229	C	A	430229	4	1	61	1	0	0	0	0	0	1	0	0	8154	922	32	2	2643	2	KDM5A	12	430229	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13394	430229	133421666	7786	15771										
KDM5A	5927	broad.mit.edu	37	chr12	443441	443441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggaataactccagtgatCctcaatgtgccagcaaaaag	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:443441C>T	ENST00000399788.2	-	11	1818	c.1456G>A	c.(1456-1458)Gat>Aat	p.D486N	KDM5A_ENST00000382815.4_Missense_Mutation_p.D486N	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	486	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.D486N(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CTCCAGTGATCCTCAATGTGC	0.413			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	2	Substitution - Missense(2)	large_intestine(2)	12											156	150	152					12																	443441		2117	4252	6369	313702	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1456G>A	12.37:g.443441C>T	ENSP00000382688:p.Asp486Asn		313702	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	C	36	5.600127	0.96614	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.72725	-0.68;-0.68;-0.68	5.22	5.22	0.72569	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;0.999;1.0;1.0	D	0.90606	0.4548	10	0.87932	D	0	-17.5632	18.7848	0.91949	0.0:1.0:0.0:0.0	.	105;486;486;486	B4DVX3;F5H1F7;P29375;P29375-2	.;.;KDM5A_HUMAN;.	N	105;445;486;486;105	ENSP00000382688:D486N;ENSP00000372265:D486N;ENSP00000440622:D105N	ENSP00000261253:D105N	D	-	1	0	KDM5A	313702	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.772000	0.85439	2.459000	0.83118	0.655000	0.94253	GAT		0.413	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		T	443441	C	T	443441	3	4	61	1	0	0	0	0	1	0	0	0	8154	855	30	3	3688	3	KDM5A	12	443441	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13212	443441	133408454	7787	15772										
KDM5A	5927	broad.mit.edu	37	chr12	465663	465663	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccccaaaaatctgaagtTtcttcagttccgtgtttcta	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:465663T>G	ENST00000399788.2	-	6	1075	c.713A>C	c.(712-714)aAa>aCa	p.K238T	KDM5A_ENST00000382815.4_Missense_Mutation_p.K238T	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	238					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.K238T(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						AATCTGAAGTTTCTTCAGTTC	0.353			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	2	Substitution - Missense(2)	large_intestine(2)	12											89	86	87					12																	465663		1807	4079	5886	335924	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.713A>C	12.37:g.465663T>G	ENSP00000382688:p.Lys238Thr		335924	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.024695	0.54683	.	.	ENSG00000073614	ENST00000399787;ENST00000399788;ENST00000382815	D;D	0.85861	-2.04;-1.85	5.77	5.77	0.91146	.	0.312435	0.37219	N	0.002199	D	0.84451	0.5475	M	0.64997	1.995	0.37039	D	0.897054	B;B;B	0.29671	0.033;0.085;0.254	B;B;B	0.32022	0.049;0.032;0.139	D	0.86378	0.1727	10	0.87932	D	0	-20.5152	14.6651	0.68901	0.0:0.0:0.0:1.0	.	238;238;238	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	T	197;238;238	ENSP00000382688:K238T;ENSP00000372265:K238T	ENSP00000372265:K238T	K	-	2	0	KDM5A	335924	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.632000	0.46511	2.190000	0.69967	0.533000	0.62120	AAA		0.353	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		G	465663	T	G	465663	3	3	61	1	0	0	0	0	1	0	0	0	8154	1841	64	4	4451	4	KDM5A	12	465663	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22222	465663	133386232	7788	15773										
CCDC77	84318	broad.mit.edu	37	chr12	547544	547544	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatgagagcaccaaagatTttctgcaactcagatctgaa	7	9	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:547544T>G	ENST00000239830.4	+	10	1044	c.865T>G	c.(865-867)Ttt>Gtt	p.F289V	CCDC77_ENST00000412006.2_Missense_Mutation_p.F257V|CCDC77_ENST00000422000.1_Missense_Mutation_p.F257V|CCDC77_ENST00000540180.1_Missense_Mutation_p.F257V	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	289						centrosome (GO:0005813)|membrane (GO:0016020)		p.F289V(1)		cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			CACCAAAGATTTTCTGCAACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											89	89	89					12																	547544		2203	4300	6503	417805	SO:0001583	missense	84318			AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.865T>G	12.37:g.547544T>G	ENSP00000239830:p.Phe289Val		417805	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	37	CCDS8503.1	.	.	.	.	.	.	.	.	.	.	t	16.19	3.053661	0.55218	.	.	ENSG00000120647	ENST00000540180;ENST00000422000;ENST00000543504;ENST00000239830;ENST00000412006	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.04	5.04	0.67666	.	0.103334	0.64402	D	0.000002	T	0.48169	0.1485	M	0.69358	2.11	0.43271	D	0.995227	D	0.69078	0.997	P	0.61132	0.884	T	0.39583	-0.9607	10	0.21540	T	0.41	-18.7523	15.0787	0.72096	0.0:0.0:0.0:1.0	.	289	Q9BR77	CCD77_HUMAN	V	257;257;257;289;257	ENSP00000440554:F257V;ENSP00000391870:F257V;ENSP00000445873:F257V;ENSP00000239830:F289V;ENSP00000412925:F257V	ENSP00000239830:F289V	F	+	1	0	CCDC77	417805	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	5.760000	0.68793	2.025000	0.59659	0.454000	0.30748	TTT		0.393	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358		G	547544	T	G	547544	3	3	61	1	0	0	0	0	1	0	0	0	2857	1841	64	4	895	4	CCDC77	12	547544	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	81881	547544	133304351	7789	15774										
CCDC77	84318	broad.mit.edu	37	chr12	551073	551073	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttggtctggagaatgaacTtagactctgttaatgtctac	10	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:551073T>G	ENST00000239830.4	+	13	1633	c.1454T>G	c.(1453-1455)cTt>cGt	p.L485R	CCDC77_ENST00000412006.2_Missense_Mutation_p.L453R|CCDC77_ENST00000422000.1_Missense_Mutation_p.L453R|CCDC77_ENST00000540180.1_Missense_Mutation_p.L453R	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	485						centrosome (GO:0005813)|membrane (GO:0016020)		p.L485R(1)		cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			GAGAATGAACTTAGACTCTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	144	149					12																	551073		2203	4300	6503	421334	SO:0001583	missense	84318			AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.1454T>G	12.37:g.551073T>G	ENSP00000239830:p.Leu485Arg		421334	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	37	CCDS8503.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.413551	0.83449	.	.	ENSG00000120647	ENST00000540180;ENST00000422000;ENST00000239830;ENST00000412006	T;T;T;T	0.59638	0.25;0.25;0.78;0.25	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.77579	0.4151	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81064	-0.1102	10	0.87932	D	0	-12.805	15.9677	0.79987	0.0:0.0:0.0:1.0	.	485	Q9BR77	CCD77_HUMAN	R	453;453;485;453	ENSP00000440554:L453R;ENSP00000391870:L453R;ENSP00000239830:L485R;ENSP00000412925:L453R	ENSP00000239830:L485R	L	+	2	0	CCDC77	421334	1.000000	0.71417	0.990000	0.47175	0.851000	0.48451	7.197000	0.77814	2.227000	0.72691	0.460000	0.39030	CTT		0.438	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358		G	551073	T	G	551073	3	3	61	1	0	0	0	0	1	0	0	0	2857	1609	56	4	1496	4	CCDC77	12	551073	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3529	551073	133300822	7790	15775										
WNK1	65125	broad.mit.edu	37	chr12	977741	977741	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgtctttgttcctcattCtgcgcctgctgtgttaactc	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:977741C>A	ENST00000315939.6	+	9	2782				WNK1_ENST00000574564.1_Missense_Mutation_p.S249Y|WNK1_ENST00000530271.2_Missense_Mutation_p.S1035Y|WNK1_ENST00000537687.1_Missense_Mutation_p.S950Y|WNK1_ENST00000340908.4_Intron|WNK1_ENST00000535572.1_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.S950Y(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTTCCTCATTCTGCGCCTGCT	0.453																																					Colon(19;451 567 6672 12618 28860)											1	Substitution - Missense(1)	large_intestine(1)	12											52	53	53					12																	977741		1905	4107	6012	848002	SO:0001627	intron_variant	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2140-2690C>A	12.37:g.977741C>A			848002	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524519	0.64747	.	.	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.18810	2.19;2.19	5.36	5.36	0.76844	.	.	.	.	.	T	0.50837	0.1639	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.52711	-0.8539	8	0.66056	D	0.02	.	19.4469	0.94851	0.0:1.0:0.0:0.0	.	1035	F5H2M7	.	Y	950;1035	ENSP00000444465:S950Y;ENSP00000433548:S1035Y	ENSP00000433548:S1035Y	S	+	2	0	WNK1	848002	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.125000	0.57931	2.659000	0.90383	0.563000	0.77884	TCT		0.453	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	977741	C	A	977741	1	1	61	0	1	0	0	0	0	0	0	0	17417	913	32	2		2	WNK1	12	977741	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426668	977741	132874154	7791	15776										
RAD52	5893	broad.mit.edu	37	chr12	1042192	1042192	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcaggatggctgtcacgTcctccaagaattgcttcctc	10	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:1042192T>C	ENST00000358495.3	-	2	171	c.33A>G	c.(31-33)ggA>ggG	p.G11G	RAD52_ENST00000539046.1_Intron|RAD52_ENST00000544742.1_Silent_p.G11G|RAD52_ENST00000536177.1_Silent_p.G11G|RAD52_ENST00000545564.1_Silent_p.G11G|RAD52_ENST00000430095.2_Silent_p.G11G|RAD52_ENST00000541619.1_Silent_p.G11G	NM_134424.2	NP_602296.2	P43351	RAD52_HUMAN	RAD52 homolog (S. cerevisiae)	11					DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)	p.G11G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			GGCTGTCACGTCCTCCAAGAA	0.443								Homologous recombination																																								1	Substitution - coding silent(1)	large_intestine(1)	12											205	206	206					12																	1042192		2203	4300	6503	912453	SO:0001819	synonymous_variant	5893				CCDS8507.2	12p13-p12.2	2008-08-05	2001-11-28		ENSG00000002016	ENSG00000002016			9824	protein-coding gene	gene with protein product		600392	"RAD52 (S. cerevisiae) homolog"			7774919, 18313388	Standard	XM_005253721		Approved		uc001qis.1	P43351	OTTHUMG00000090361	ENST00000358495.3:c.33A>G	12.37:g.1042192T>C			912453	Q13205|Q9Y5T7|Q9Y5T8|Q9Y5T9	Silent	SNP	ENST00000358495.3	37	CCDS8507.2																																																																																				0.443	RAD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206733.2	NM_134424		C	1042192	T	C	1042192	2	2	61	1	0	0	0	0	0	0	0	1	13028	1654	58	4		4	RAD52	12	1042192	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	64451	1042192	132809703	7792	15777										
ERC1	23085	broad.mit.edu	37	chr12	1137559	1137559	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgaaggaagtattaagaGaaaatgatctcttgcggaag	12	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:1137559G>T	ENST00000397203.2	+	2	896	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	ERC1_ENST00000589028.1_Nonsense_Mutation_p.E164*|ERC1_ENST00000543086.3_Nonsense_Mutation_p.E164*|ERC1_ENST00000355446.5_Nonsense_Mutation_p.E164*|ERC1_ENST00000546231.2_Nonsense_Mutation_p.E164*|ERC1_ENST00000360905.4_Nonsense_Mutation_p.E164*			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	164					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)	p.E164*(1)		NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			AGTATTAAGAGAAAATGATCT	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											115	107	109					12																	1137559		2203	4300	6503	1007820	SO:0001587	stop_gained	23085			AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.490G>T	12.37:g.1137559G>T	ENSP00000380386:p.Glu164*		1007820	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Nonsense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	36	5.730181	0.96856	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-22.055	19.7395	0.96220	0.0:0.0:1.0:0.0	.	.	.	.	X	164	.	ENSP00000299183:E164X	E	+	1	0	ERC1	1007820	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	8.207000	0.89746	2.669000	0.90835	0.655000	0.94253	GAA		0.463	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1137559	G	T	1137559	4	4	61	1	0	0	0	0	0	1	0	0	5223	943	33	2	492	2	ERC1	12	1137559	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95367	1137559	132714336	7793	15778										
ERC1	23085	broad.mit.edu	37	chr12	1192486	1192486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttcatgctgagcatgagCggcaggccaaagagctgttt	14	9	1	3	rs199966368		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:1192486C>T	ENST00000397203.2	+	3	1232	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	ERC1_ENST00000589028.1_Missense_Mutation_p.R276W|ERC1_ENST00000543086.3_Missense_Mutation_p.R276W|ERC1_ENST00000355446.5_Missense_Mutation_p.R276W|ERC1_ENST00000546231.2_Missense_Mutation_p.R276W|ERC1_ENST00000360905.4_Missense_Mutation_p.R276W			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	276					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)	p.R276W(1)		NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			TGAGCATGAGCGGCAGGCCAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											65	61	62					12																	1192486		2203	4300	6503	1062747	SO:0001583	missense	23085			AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.826C>T	12.37:g.1192486C>T	ENSP00000380386:p.Arg276Trp		1062747	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.992923	0.74703	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51	5.62	-0.491	0.12045	.	0.000000	0.85682	D	0.000000	T	0.68577	0.3016	M	0.68593	2.085	0.53688	D	0.999972	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;0.998;1.0	T	0.73655	-0.3914	10	0.87932	D	0	-17.0348	16.7633	0.85517	0.6221:0.3779:0.0:0.0	.	52;276;276;276	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	W	276;276;276;276;276;276;276;276;276;276;52	ENSP00000340054:R276W;ENSP00000380386:R276W;ENSP00000438546:R276W;ENSP00000445336:R276W;ENSP00000442739:R276W;ENSP00000347621:R276W;ENSP00000354158:R276W;ENSP00000410064:R276W	ENSP00000340054:R276W	R	+	1	2	ERC1	1062747	0.998000	0.40836	0.997000	0.53966	0.999000	0.98932	1.186000	0.32078	-0.003000	0.14444	0.655000	0.94253	CGG		0.493	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1192486	C	T	1192486	3	4	61	1	0	0	0	0	1	0	0	0	5223	759	27	1	832	1	ERC1	12	1192486	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54927	1192486	132659409	7794	15779										
ERC1	23085	broad.mit.edu	37	chr12	1192680	1192680	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacgactggcagaggcagaGatgcacgttcatcacctaga	12	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:1192680G>T	ENST00000397203.2	+	3	1426	c.1020G>T	c.(1018-1020)gaG>gaT	p.E340D	ERC1_ENST00000589028.1_Missense_Mutation_p.E340D|ERC1_ENST00000543086.3_Missense_Mutation_p.E340D|ERC1_ENST00000355446.5_Missense_Mutation_p.E340D|ERC1_ENST00000546231.2_Missense_Mutation_p.E340D|ERC1_ENST00000360905.4_Missense_Mutation_p.E340D			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	340					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)	p.E340D(1)		NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			CAGAGGCAGAGATGCACGTTC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											99	94	96					12																	1192680		2203	4300	6503	1062941	SO:0001583	missense	23085			AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.1020G>T	12.37:g.1192680G>T	ENSP00000380386:p.Glu340Asp		1062941	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267566	0.80469	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.56	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.64594	0.2612	M	0.68593	2.085	0.53005	D	0.999969	D;D;D;D	0.89917	1.0;0.997;0.997;0.998	D;D;D;D	0.91635	0.999;0.99;0.99;0.966	T	0.65689	-0.6107	10	0.49607	T	0.09	-25.0619	11.6838	0.51474	0.1433:0.0:0.8567:0.0	.	116;340;340;340	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	D	340;340;340;340;340;340;340;340;340;340;116	ENSP00000340054:E340D;ENSP00000380386:E340D;ENSP00000438546:E340D;ENSP00000445336:E340D;ENSP00000442739:E340D;ENSP00000347621:E340D;ENSP00000354158:E340D;ENSP00000410064:E340D	ENSP00000340054:E340D	E	+	3	2	ERC1	1062941	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.384000	0.44362	1.467000	0.48044	0.655000	0.94253	GAG		0.423	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1192680	G	T	1192680	3	4	61	1	0	0	0	0	1	0	0	0	5223	933	33	2	1026	2	ERC1	12	1192680	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194	1192680	132659215	7795	15780										
ADIPOR2	79602	broad.mit.edu	37	chr12	1893207	1893207	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgctgcccggatccccGaacgctttttccctggcaaa	9	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:1893207G>A	ENST00000357103.4	+	7	1251	c.1000G>A	c.(1000-1002)Gaa>Aaa	p.E334K		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	334					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)	p.E334K(1)		endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			CCGGATCCCCGAACGCTTTTT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	12											82	76	78					12																	1893207		2203	4300	6503	1763468	SO:0001583	missense	79602			AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"GPCR / Unclassified : Adiponectin receptors"	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.1000G>A	12.37:g.1893207G>A	ENSP00000349616:p.Glu334Lys		1763468	Q53YY5|Q9H737	Missense_Mutation	SNP	ENST00000357103.4	37	CCDS8511.1	.	.	.	.	.	.	.	.	.	.	G	36	5.775868	0.96922	.	.	ENSG00000006831	ENST00000357103	T	0.60299	0.2	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	H	0.98525	4.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91648	0.5332	10	0.87932	D	0	-12.5939	19.2986	0.94134	0.0:0.0:1.0:0.0	.	334	Q86V24	ADR2_HUMAN	K	334	ENSP00000349616:E334K	ENSP00000349616:E334K	E	+	1	0	ADIPOR2	1763468	1.000000	0.71417	0.925000	0.36789	0.975000	0.68041	9.869000	0.99810	2.555000	0.86185	0.655000	0.94253	GAA		0.542	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551		A	1893207	G	A	1893207	3	1	61	1	0	0	0	0	1	0	0	0	319	1059	37	1	1022	1	ADIPOR2	12	1893207	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	700527	1893207	131958688	7796	15781										
DCP1B	196513	broad.mit.edu	37	chr12	2062038	2062038	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtactctgaagtttctcGaacaggttctgagttctgga	13	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2062038G>A	ENST00000280665.6	-	7	1147	c.1068C>T	c.(1066-1068)ttC>ttT	p.F356F	DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000540622.1_Silent_p.F230F|DCP1B_ENST00000397173.4_Silent_p.F254F	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	356					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)	p.F356F(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			GAAGTTTCTCGAACAGGTTCT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											74	82	80					12																	2062038		2203	4300	6503	1932299	SO:0001819	synonymous_variant	196513			AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.1068C>T	12.37:g.2062038G>A			1932299	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	37	CCDS31727.1																																																																																				0.532	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		A	2062038	G	A	2062038	2	1	61	1	0	0	0	0	0	0	0	1	4305	1049	37	1		1	DCP1B	12	2062038	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168831	2062038	131789857	7797	15782										
CACNA1C	775	broad.mit.edu	37	chr12	2692029	2692029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattcggtgatgtatgatggGatcatggcttatggcggccc	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2692029G>A	ENST00000347598.4	+	15	2145	c.2145G>A	c.(2143-2145)ggG>ggA	p.G715G	CACNA1C_ENST00000399617.1_Silent_p.G715G|CACNA1C_ENST00000480911.1_Silent_p.G715G|CACNA1C_ENST00000399595.1_Silent_p.G715G|CACNA1C_ENST00000399601.1_Silent_p.G715G|CACNA1C_ENST00000399591.1_Silent_p.G715G|CACNA1C_ENST00000399603.1_Silent_p.G715G|CACNA1C_ENST00000399637.1_Silent_p.G715G|CACNA1C_ENST00000399606.1_Silent_p.G715G|CACNA1C_ENST00000344100.3_Silent_p.G715G|CACNA1C_ENST00000399649.1_Silent_p.G715G|CACNA1C_ENST00000399638.1_Silent_p.G715G|CACNA1C_ENST00000406454.3_Silent_p.G715G|CACNA1C_ENST00000399641.1_Silent_p.G715G|CACNA1C_ENST00000335762.5_Silent_p.G740G|CACNA1C_ENST00000399629.1_Silent_p.G715G|CACNA1C_ENST00000327702.7_Silent_p.G715G|CACNA1C_ENST00000399655.1_Silent_p.G715G|CACNA1C_ENST00000399621.1_Silent_p.G715G|CACNA1C_ENST00000402845.3_Silent_p.G715G|CACNA1C_ENST00000399644.1_Silent_p.G715G|CACNA1C_ENST00000399634.1_Silent_p.G715G|CACNA1C_ENST00000399597.1_Silent_p.G715G	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	715					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G715G(1)|p.G745G(1)|p.G250G(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTATGATGGGATCATGGCTT	0.488																																																3	Substitution - coding silent(3)	large_intestine(3)	12											123	140	134					12																	2692029		2090	4247	6337	2562290	SO:0001819	synonymous_variant	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.2145G>A	12.37:g.2692029G>A			2562290	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																				0.488	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2692029	G	A	2692029	2	1	61	1	0	0	0	0	0	0	0	1	2546	1161	41	3		3	CACNA1C	12	2692029	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	629991	2692029	131159866	7798	15783										
CACNA1C	775	broad.mit.edu	37	chr12	2711054	2711054	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctttcttgcacaagggttCtttctgccggaactacttca	9	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2711054C>A	ENST00000347598.4	+	23	2948	c.2948C>A	c.(2947-2949)tCt>tAt	p.S983Y	CACNA1C_ENST00000399617.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000480911.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399595.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399601.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399591.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399603.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399637.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399606.1_Missense_Mutation_p.S983Y|CACNA1C_ENST00000344100.3_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399649.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399638.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000406454.3_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399641.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000335762.5_Missense_Mutation_p.S988Y|CACNA1C_ENST00000399629.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000327702.7_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399655.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399621.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000402845.3_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399644.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399634.1_Missense_Mutation_p.S963Y|CACNA1C_ENST00000399597.1_Missense_Mutation_p.S963Y|CACNA1C-AS3_ENST00000543559.1_RNA	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	983					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S498Y(1)|p.S963Y(1)|p.S1013Y(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CACAAGGGTTCTTTCTGCCGG	0.577																																																3	Substitution - Missense(3)	large_intestine(3)	12											153	156	155					12																	2711054		2203	4300	6503	2581315	SO:0001583	missense	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.2948C>A	12.37:g.2711054C>A	ENSP00000266376:p.Ser983Tyr		2581315	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521095	0.85495	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97114	-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25;-4.25	4.54	4.54	0.55810	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98632	0.9542	M	0.89478	3.035	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;1.0;0.999;0.991;0.999;0.999;0.999;0.998;0.999;0.999;0.999;0.998;0.995;0.999;0.995;0.998;0.999;0.999;0.999;0.994;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.996;0.998;0.99;0.996;0.998;0.998;0.999;0.952;0.987;0.998;0.996;0.987;0.999;0.998;0.999;0.992;0.974;0.998;0.974;0.992;0.998;0.998;0.992;0.989;0.997	D	0.99647	1.0990	10	0.87932	D	0	.	17.8378	0.88706	0.0:1.0:0.0:0.0	.	963;960;983;963;963;963;963;963;963;983;963;934;983;963;963;963;963;963;963;963;963;963;963;963;963	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	Y	988;963;963;963;963;963;963;963;963;963;983;983;963;963;963;963;963;963;963;963;963;963;963;804	ENSP00000336982:S988Y;ENSP00000382563:S963Y;ENSP00000437936:S963Y;ENSP00000382552:S963Y;ENSP00000382547:S963Y;ENSP00000382506:S963Y;ENSP00000382530:S963Y;ENSP00000382546:S963Y;ENSP00000382500:S963Y;ENSP00000382549:S963Y;ENSP00000266376:S983Y;ENSP00000382515:S983Y;ENSP00000382510:S963Y;ENSP00000341092:S963Y;ENSP00000382537:S963Y;ENSP00000329877:S963Y;ENSP00000382557:S963Y;ENSP00000385724:S963Y;ENSP00000382512:S963Y;ENSP00000382542:S963Y;ENSP00000382526:S963Y;ENSP00000385896:S963Y;ENSP00000382504:S963Y	ENSP00000323129:S804Y	S	+	2	0	CACNA1C	2581315	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	7.598000	0.82745	2.521000	0.84997	0.655000	0.94253	TCT		0.577	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2711054	C	A	2711054	3	1	61	1	0	0	0	0	1	0	0	0	2546	913	32	2	3146	2	CACNA1C	12	2711054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19025	2711054	131140841	7799	15784										
ITFG2	55846	broad.mit.edu	37	chr12	2929370	2929370	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagctggtgtccctcaaGaaatggatgctggagggtca	16	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2929370G>T	ENST00000228799.2	+	5	664	c.525G>T	c.(523-525)aaG>aaT	p.K175N	ITFG2_ENST00000542548.1_Missense_Mutation_p.K63N|ITFG2_ENST00000419778.2_5'UTR	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	175					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.K175N(1)|p.K175K(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TGTCCCTCAAGAAATGGATGC	0.602																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	12											74	54	61					12																	2929370		2203	4300	6503	2799631	SO:0001583	missense	55846			AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.525G>T	12.37:g.2929370G>T	ENSP00000228799:p.Lys175Asn		2799631	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Missense_Mutation	SNP	ENST00000228799.2	37	CCDS8513.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457049	0.84317	.	.	ENSG00000111203	ENST00000228799;ENST00000542548	T;T	0.70516	-0.49;2.29	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	L	0.43701	1.375	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.73322	-0.4019	10	0.21540	T	0.41	-7.7262	16.5494	0.84464	0.0:0.0:1.0:0.0	.	175	Q969R8	ITFG2_HUMAN	N	175;63	ENSP00000228799:K175N;ENSP00000437870:K63N	ENSP00000228799:K175N	K	+	3	2	ITFG2	2799631	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.540000	0.73861	2.384000	0.81235	0.561000	0.74099	AAG		0.602	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		T	2929370	G	T	2929370	3	4	61	1	0	0	0	0	1	0	0	0	7891	933	33	2	543	2	ITFG2	12	2929370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218316	2929370	130922525	7800	15785										
FOXM1	2305	broad.mit.edu	37	chr12	2968603	2968603	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcctcccaggagtgagatGattcctctttgaaagatggg	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2968603G>T	ENST00000359843.3	-	9	1561	c.1493C>A	c.(1492-1494)tCa>tAa	p.S498*	FOXM1_ENST00000361953.3_Nonsense_Mutation_p.S483*|FOXM1_ENST00000342628.2_Nonsense_Mutation_p.S536*|AC005841.1_ENST00000382678.3_5'Flank|ITFG2_ENST00000545509.1_Intron|Y_RNA_ENST00000410561.1_RNA	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	498	Glu/Pro/Ser/Thr-rich.				cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S536*(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GGAGTGAGATGATTCCTCTTT	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											91	97	95					12																	2968603		2203	4300	6503	2838864	SO:0001587	stop_gained	2305			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"Forkhead boxes"	3818	protein-coding gene	gene with protein product	"M-phase phosphoprotein 2"	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1493C>A	12.37:g.2968603G>T	ENSP00000352901:p.Ser498*		2838864	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Nonsense_Mutation	SNP	ENST00000359843.3	37	CCDS8515.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801051	0.70567	.	.	ENSG00000111206	ENST00000342628;ENST00000361953;ENST00000359843	.	.	.	4.28	-1.95	0.07548	.	1.858790	0.03073	N	0.157456	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	9.3087	0.37891	0.5391:0.0:0.4609:0.0	.	.	.	.	X	536;483;498	.	ENSP00000342307:S536X	S	-	2	0	FOXM1	2838864	0.000000	0.05858	0.000000	0.03702	0.443000	0.32047	-0.173000	0.09854	-0.282000	0.09128	0.462000	0.41574	TCA		0.572	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		T	2968603	G	T	2968603	4	4	61	1	0	0	0	0	0	1	0	0	6037	1294	45	2	802	2	FOXM1	12	2968603	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39233	2968603	130883292	7801	15786										
FOXM1	2305	broad.mit.edu	37	chr12	2981354	2981354	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcagaactcatctttcGaagccactggatgttggata	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:2981354G>A	ENST00000359843.3	-	3	630	c.562C>T	c.(562-564)Cga>Tga	p.R188*	FOXM1_ENST00000361953.3_Nonsense_Mutation_p.R188*|FOXM1_ENST00000537018.1_5'UTR|FOXM1_ENST00000342628.2_Nonsense_Mutation_p.R188*	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	188					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R188*(2)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			CTCATCTTTCGAAGCCACTGG	0.498																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											183	160	168					12																	2981354		2203	4300	6503	2851615	SO:0001587	stop_gained	2305			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"Forkhead boxes"	3818	protein-coding gene	gene with protein product	"M-phase phosphoprotein 2"	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.562C>T	12.37:g.2981354G>A	ENSP00000352901:p.Arg188*		2851615	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Nonsense_Mutation	SNP	ENST00000359843.3	37	CCDS8515.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.824801	0.71143	.	.	ENSG00000111206	ENST00000342628;ENST00000361953;ENST00000359843	.	.	.	5.7	3.83	0.44106	.	0.160788	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	15.2014	0.73139	0.0:0.7204:0.2796:0.0	.	.	.	.	X	188	.	ENSP00000342307:R188X	R	-	1	2	FOXM1	2851615	0.560000	0.26570	0.930000	0.37139	0.029000	0.11900	1.754000	0.38369	0.714000	0.32081	-0.165000	0.13383	CGA		0.498	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		A	2981354	G	A	2981354	4	1	61	1	0	0	0	0	0	1	0	0	6037	1066	37	1	1875	1	FOXM1	12	2981354	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12751	2981354	130870541	7802	15787										
TSPAN9	10867	broad.mit.edu	37	chr12	3390929	3390929	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaggtgaagatgtggttCgatgacaataagcacgtgct	13	5	0	3	rs201166747		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:3390929C>T	ENST00000011898.5	+	8	755	c.594C>T	c.(592-594)ttC>ttT	p.F198F	TSPAN9_ENST00000537971.1_Silent_p.F198F|TSPAN9_ENST00000407263.1_Silent_p.F198F	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	198						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)		p.F198F(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			AGATGTGGTTCGATGACAATA	0.632													C|||	1	0.000199681	0	0.0014	5008	,	,		19195	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											143	111	122					12																	3390929		2203	4300	6503	3261190	SO:0001819	synonymous_variant	10867			AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"Tetraspanins"	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.594C>T	12.37:g.3390929C>T			3261190	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																				0.632	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675		T	3390929	C	T	3390929	2	4	61	1	0	0	0	0	0	0	0	1	16694	883	31	1		1	TSPAN9	12	3390929	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	409575	3390929	130460966	7803	15788										
PRMT8	56341	broad.mit.edu	37	chr12	3662819	3662819	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctatgccctttccagatCgaatgctccagtatttctga	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:3662819C>T	ENST00000382622.3	+	4	810	c.420C>T	c.(418-420)atC>atT	p.I140I	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Silent_p.I131I	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	140	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.I140I(2)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			CTTTCCAGATCGAATGCTCCA	0.483																																																2	Substitution - coding silent(2)	large_intestine(2)	12											118	106	110					12																	3662819		2203	4300	6503	3533080	SO:0001819	synonymous_variant	56341			AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.420C>T	12.37:g.3662819C>T			3533080	B2RDP0|Q8TBJ8	Silent	SNP	ENST00000382622.3	37	CCDS8521.2																																																																																				0.483	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		T	3662819	C	T	3662819	2	4	61	1	0	0	0	0	0	0	0	1	12576	874	31	1		1	PRMT8	12	3662819	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271890	3662819	130189076	7804	15789										
PARP11	57097	broad.mit.edu	37	chr12	3939099	3939099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctgccaagtaaaaccagCcccactgggtatctgacgtg	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:3939099C>T	ENST00000228820.4	-	2	248	c.104G>A	c.(103-105)gGc>gAc	p.G35D	PARP11_ENST00000447133.3_5'UTR|PARP11_ENST00000427057.2_5'UTR|PARP11_ENST00000397096.2_Missense_Mutation_p.G28D	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	28	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.G28D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			GTAAAACCAGCCCCACTGGGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											183	164	171					12																	3939099		2203	4300	6503	3809360	SO:0001583	missense	57097			AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.104G>A	12.37:g.3939099C>T	ENSP00000228820:p.Gly35Asp		3809360	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	37	CCDS8523.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.48|18.48	3.632998|3.632998	0.67015|0.67015	.|.	.|.	ENSG00000111224|ENSG00000111224	ENST00000450737|ENST00000397096;ENST00000228820	.|T;T	.|0.41400	.|1.0;1.0	5.52|5.52	4.63|4.63	0.57726|0.57726	.|WWE domain (2);	.|0.050111	.|0.85682	.|D	.|0.000000	T|T	0.33962|0.33962	0.0881|0.0881	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B;B	.|0.12013	.|0.004;0.005	.|B;B	.|0.17433	.|0.011;0.018	T|T	0.11397|0.11397	-1.0589|-1.0589	6|10	0.87932|0.12430	D|T	0|0.62	.|.	12.1031|12.1031	0.53796|0.53796	0.0:0.9181:0.0:0.0819|0.0:0.9181:0.0:0.0819	.|.	.|35;28	.|Q9NR21-4;Q9NR21	.|.;PAR11_HUMAN	T|D	14|28;35	.|ENSP00000380284:G28D;ENSP00000228820:G35D	ENSP00000387481:A14T|ENSP00000228820:G35D	A|G	-|-	1|2	0|0	PARP11|PARP11	3809360|3809360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.180000|5.180000	0.65048|0.65048	1.576000|1.576000	0.49790|0.49790	0.563000|0.563000	0.77884|0.77884	GCT|GGC		0.413	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			T	3939099	C	T	3939099	3	4	61	1	0	0	0	0	1	0	0	0	11487	739	26	3	940	3	PARP11	12	3939099	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	276280	3939099	129912796	7805	15790										
RAD51AP1	10635	broad.mit.edu	37	chr12	4655578	4655578	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatgtgcagaactctcaaGataaaagtaactttattttc	5	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4655578G>A	ENST00000544927.1	+	4	323	c.313G>A	c.(313-315)Gat>Aat	p.D105N	RAD51AP1_ENST00000543041.1_Intron|RAD51AP1_ENST00000228843.9_Missense_Mutation_p.D122N|RAD51AP1_ENST00000321524.7_Missense_Mutation_p.D122N|RAD51AP1_ENST00000352618.4_Missense_Mutation_p.D105N					RAD51 associated protein 1									p.D105N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			GAACTCTCAAGATAAAAGTAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											66	69	68					12																	4655578		2203	4300	6503	4525839	SO:0001583	missense	10635			AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000544927.1:c.313G>A	12.37:g.4655578G>A	ENSP00000446296:p.Asp105Asn		4525839		Missense_Mutation	SNP	ENST00000544927.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.16|17.16	3.319116|3.319116	0.60524|0.60524	.|.	.|.	ENSG00000111247|ENSG00000111247	ENST00000321524;ENST00000228843;ENST00000352618;ENST00000544927|ENST00000536117	T;T;T;T|.	0.32272|.	1.46;1.46;1.46;1.46|.	5.47|5.47	3.66|3.66	0.41972|0.41972	.|.	1.272510|.	0.04832|.	N|.	0.438830|.	T|T	0.39172|0.39172	0.1068|0.1068	L|L	0.44542|0.44542	1.39|1.39	0.09310|0.09310	N|N	0.999994|0.999994	B;B;B|.	0.20671|.	0.009;0.009;0.047|.	B;B;B|.	0.16289|.	0.011;0.007;0.015|.	T|T	0.22173|0.22173	-1.0224|-1.0224	10|5	0.42905|.	T|.	0.14|.	-0.6802|-0.6802	8.4187|8.4187	0.32687|0.32687	0.1796:0.0:0.8204:0.0|0.1796:0.0:0.8204:0.0	.|.	122;122;105|.	Q96B01;A8K313;Q96B01-2|.	R51A1_HUMAN;.;.|.	N|K	122;122;105;105|99	ENSP00000323750:D122N;ENSP00000228843:D122N;ENSP00000309479:D105N;ENSP00000446296:D105N|.	ENSP00000228843:D122N|.	D|R	+|+	1|2	0|0	RAD51AP1|RAD51AP1	4525839|4525839	0.216000|0.216000	0.23585|0.23585	0.001000|0.001000	0.08648|0.08648	0.329000|0.329000	0.28539|0.28539	2.677000|2.677000	0.46892|0.46892	0.708000|0.708000	0.31955|0.31955	0.491000|0.491000	0.48974|0.48974	GAT|AGA		0.368	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	NM_006479		A	4655578	G	A	4655578	3	1	61	1	0	0	0	0	1	0	0	0	13023	942	33	3	382	3	RAD51AP1	12	4655578	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	716479	4655578	129196317	7806	15791										
DYRK4	8798	broad.mit.edu	37	chr12	4722902	4722902	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcaagaacacaaacgttTtaccccctattgtatgacct	4	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4722902T>G	ENST00000540757.2	+	13	1706	c.1546T>G	c.(1546-1548)Tta>Gta	p.L516V	DYRK4_ENST00000545342.1_Missense_Mutation_p.L153V|DYRK4_ENST00000010132.5_Missense_Mutation_p.L516V|RP11-500M8.7_ENST00000536588.1_Intron|DYRK4_ENST00000543431.1_Missense_Mutation_p.L515V	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	516						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.L917V(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			CACAAACGTTTTACCCCCTAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	12											66	69	68					12																	4722902		2203	4300	6503	4593163	SO:0001583	missense	8798			Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.1546T>G	12.37:g.4722902T>G	ENSP00000441755:p.Leu516Val		4593163	A8K8F7|Q8NEF2|Q92631	Missense_Mutation	SNP	ENST00000540757.2	37	CCDS8530.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927847	0.34002	.	.	ENSG00000010219	ENST00000540757;ENST00000010132;ENST00000543431;ENST00000545342	T;T;T;T	0.68331	-0.32;-0.32;-0.32;0.11	5.24	2.9	0.33743	.	0.445638	0.18176	N	0.149291	T	0.73434	0.3586	L	0.54323	1.7	0.58432	D	0.999993	D;D;D	0.76494	0.999;0.996;0.993	D;D;D	0.80764	0.991;0.994;0.987	T	0.69003	-0.5260	10	0.46703	T	0.11	.	6.6469	0.22941	0.0:0.1853:0.0:0.8147	.	229;515;516	B4E1A4;Q9NR20-2;Q9NR20	.;.;DYRK4_HUMAN	V	516;516;515;153	ENSP00000441755:L516V;ENSP00000010132:L516V;ENSP00000439697:L515V;ENSP00000446005:L153V	ENSP00000010132:L516V	L	+	1	2	DYRK4	4593163	0.763000	0.28462	0.379000	0.26080	0.170000	0.22686	0.753000	0.26376	0.457000	0.26962	-0.297000	0.09499	TTA		0.483	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2			G	4722902	T	G	4722902	3	3	61	1	0	0	0	0	1	0	0	0	4869	1838	64	4	1588	4	DYRK4	12	4722902	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	67324	4722902	129128993	7807	15792										
AKAP3	10566	broad.mit.edu	37	chr12	4736321	4736321	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccttcttttctgcttgttCttggtcacctacaatgggag	9	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4736321C>A	ENST00000545990.2	-	5	2271	c.1747G>T	c.(1747-1749)Gaa>Taa	p.E583*	AKAP3_ENST00000228850.1_Nonsense_Mutation_p.E583*|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	583					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.E583*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TCTGCTTGTTCTTGGTCACCT	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											74	72	72					12																	4736321		2203	4300	6503	4606582	SO:0001587	stop_gained	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1747G>T	12.37:g.4736321C>A	ENSP00000440994:p.Glu583*		4606582	O75945|Q86X01|Q9UM61	Nonsense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	42	9.740506	0.99252	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	.	.	.	5.95	5.95	0.96441	.	0.295817	0.30060	N	0.010506	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.3022	0.87185	0.0:1.0:0.0:0.0	.	.	.	.	X	583	.	ENSP00000228850:E583X	E	-	1	0	AKAP3	4606582	0.967000	0.33354	0.897000	0.35233	0.832000	0.47134	2.072000	0.41510	2.825000	0.97269	0.655000	0.94253	GAA		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4736321	C	A	4736321	4	1	61	1	0	0	0	0	0	1	0	0	452	922	32	2	822	2	AKAP3	12	4736321	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13419	4736321	129115574	7808	15793										
AKAP3	10566	broad.mit.edu	37	chr12	4737562	4737562	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctatcttactgaggcttTtggtgggtgtgggttcattc	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4737562T>G	ENST00000545990.2	-	5	1030	c.506A>C	c.(505-507)aAa>aCa	p.K169T	AKAP3_ENST00000228850.1_Missense_Mutation_p.K169T|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	169					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.K169T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ACTGAGGCTTTTGGTGGGTGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											178	169	172					12																	4737562		2203	4300	6503	4607823	SO:0001583	missense	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.506A>C	12.37:g.4737562T>G	ENSP00000440994:p.Lys169Thr		4607823	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	T	4.599	0.111380	0.08831	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07908	3.15;3.15	4.76	2.47	0.30058	A-kinase anchor 110kDa, C-terminal (1);	0.382658	0.23157	N	0.051300	T	0.12263	0.0298	L	0.50919	1.6	0.09310	N	1	D	0.56746	0.977	P	0.55785	0.784	T	0.12785	-1.0534	10	0.19590	T	0.45	.	5.6221	0.17463	0.0:0.2118:0.0:0.7882	.	169	O75969	AKAP3_HUMAN	T	169	ENSP00000228850:K169T;ENSP00000440994:K169T	ENSP00000228850:K169T	K	-	2	0	AKAP3	4607823	0.846000	0.29590	0.147000	0.22382	0.030000	0.12068	0.718000	0.25866	0.956000	0.37904	0.533000	0.62120	AAA		0.493	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		G	4737562	T	G	4737562	3	3	61	1	0	0	0	0	1	0	0	0	452	1841	64	4	2063	4	AKAP3	12	4737562	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1241	4737562	129114333	7809	15794										
AKAP3	10566	broad.mit.edu	37	chr12	4737701	4737701	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttagcatagaaggaaacttCatctactgaactcccgttgc	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4737701C>A	ENST00000545990.2	-	5	891	c.367G>T	c.(367-369)Gaa>Taa	p.E123*	AKAP3_ENST00000228850.1_Nonsense_Mutation_p.E123*|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	123					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.E123*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						AAGGAAACTTCATCTACTGAA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											126	116	119					12																	4737701		2203	4300	6503	4607962	SO:0001587	stop_gained	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.367G>T	12.37:g.4737701C>A	ENSP00000440994:p.Glu123*		4607962	O75945|Q86X01|Q9UM61	Nonsense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	19.77	3.888613	0.72524	.	.	ENSG00000111254	ENST00000228850;ENST00000545990;ENST00000540967	.	.	.	4.7	4.7	0.59300	.	0.097636	0.45361	D	0.000364	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.9948	0.71421	0.0:1.0:0.0:0.0	.	.	.	.	X	123	.	ENSP00000228850:E123X	E	-	1	0	AKAP3	4607962	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.921000	0.40035	2.583000	0.87209	0.655000	0.94253	GAA		0.483	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4737701	C	A	4737701	4	1	61	1	0	0	0	0	0	1	0	0	452	835	29	2	2202	2	AKAP3	12	4737701	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139	4737701	129114194	7810	15795										
AKAP3	10566	broad.mit.edu	37	chr12	4747301	4747301	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcttggttgtctccaggaGaatagacatcaactttgcat	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4747301G>A	ENST00000545990.2	-	4	586	c.62C>T	c.(61-63)tCt>tTt	p.S21F	AKAP3_ENST00000228850.1_Missense_Mutation_p.S21F|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	21					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.S21F(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GTCTCCAGGAGAATAGACATC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											243	235	238					12																	4747301		2203	4300	6503	4617562	SO:0001583	missense	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.62C>T	12.37:g.4747301G>A	ENSP00000440994:p.Ser21Phe		4617562	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945889	0.73672	.	.	ENSG00000111254	ENST00000228850;ENST00000545990;ENST00000540967;ENST00000536414	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	5.51	5.51	0.81932	.	0.524430	0.17425	N	0.174699	T	0.51381	0.1671	M	0.68952	2.095	0.37598	D	0.920441	P	0.52316	0.952	P	0.52267	0.694	T	0.58188	-0.7680	10	0.87932	D	0	-9.2632	16.4468	0.83936	0.0:0.0:1.0:0.0	.	21	O75969	AKAP3_HUMAN	F	21	ENSP00000228850:S21F;ENSP00000440994:S21F;ENSP00000442376:S21F;ENSP00000439382:S21F	ENSP00000228850:S21F	S	-	2	0	AKAP3	4617562	0.968000	0.33430	0.993000	0.49108	0.826000	0.46750	1.728000	0.38105	2.868000	0.98415	0.557000	0.71058	TCT		0.423	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4747301	G	A	4747301	3	1	61	1	0	0	0	0	1	0	0	0	452	942	33	3	2511	3	AKAP3	12	4747301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9600	4747301	129104594	7811	15796										
GALNT8	26290	broad.mit.edu	37	chr12	4829869	4829869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttggaggaaactccccaAagccctcttcattgggctga	10	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4829869A>G	ENST00000252318.2	+	1	363	c.26A>G	c.(25-27)aAa>aGa	p.K9R	RP11-234B24.2_ENST00000527518.1_lincRNA|RP11-234B24.6_ENST00000544741.2_Intron	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	9					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.K9R(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						AAACTCCCCAAAGCCCTCTTC	0.507																																					Colon(108;631 1558 7270 20097 39846)											1	Substitution - Missense(1)	large_intestine(1)	12											103	96	98					12																	4829869		2203	4300	6503	4700130	SO:0001583	missense	26290			AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4130	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 8"	606250	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.26A>G	12.37:g.4829869A>G	ENSP00000252318:p.Lys9Arg		4700130	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	A	9.709	1.156491	0.21454	.	.	ENSG00000130035	ENST00000252318	T	0.53206	0.63	4.04	1.7	0.24286	.	7.665550	0.00166	N	0.000000	T	0.32971	0.0847	L	0.29908	0.895	0.09310	N	1	B	0.28082	0.2	B	0.21917	0.037	T	0.11470	-1.0586	10	0.09843	T	0.71	.	5.2235	0.15381	0.7578:0.0:0.2422:0.0	.	9	Q9NY28	GALT8_HUMAN	R	9	ENSP00000252318:K9R	ENSP00000252318:K9R	K	+	2	0	GALNT8	4700130	0.001000	0.12720	0.006000	0.13384	0.135000	0.20990	0.547000	0.23299	0.167000	0.19631	0.374000	0.22700	AAA		0.507	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417		G	4829869	A	G	4829869	3	3	61	1	0	0	0	0	1	0	0	0	6239	14	1	4	28	4	GALNT8	12	4829869	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	82568	4829869	129022026	7812	15797										
KCNA6	3742	broad.mit.edu	37	chr12	4919466	4919466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaacgagtacttcttcGaccgcaaccggcccagcttc	10	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:4919466G>A	ENST00000280684.3	+	1	1125	c.259G>A	c.(259-261)Gac>Aac	p.D87N	KCNA6_ENST00000433855.1_Missense_Mutation_p.D87N|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	87					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.D87N(1)		NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	GTACTTCTTCGACCGCAACCG	0.637										HNSCC(72;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											50	53	52					12																	4919466		2203	4300	6503	4789727	SO:0001583	missense	3742			X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.259G>A	12.37:g.4919466G>A	ENSP00000280684:p.Asp87Asn		4789727		Missense_Mutation	SNP	ENST00000280684.3	37	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.897607	0.91962	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	D;D	0.85484	-1.99;-1.99	4.45	4.45	0.53987	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.050251	0.85682	D	0.000000	D	0.93618	0.7962	M	0.91140	3.18	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.95073	0.8206	10	0.87932	D	0	.	15.826	0.78706	0.0:0.0:1.0:0.0	.	87	P17658	KCNA6_HUMAN	N	87	ENSP00000408321:D87N;ENSP00000280684:D87N	ENSP00000280684:D87N	D	+	1	0	KCNA6	4789727	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.458000	0.97634	2.291000	0.77112	0.462000	0.41574	GAC		0.637	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		A	4919466	G	A	4919466	3	1	61	1	0	0	0	0	1	0	0	0	8028	1058	37	1	261	1	KCNA6	12	4919466	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89597	4919466	128932429	7813	15798										
KCNA5	3741	broad.mit.edu	37	chr12	5154030	5154030	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgccaggtgtggcttatCttcgagtatccggagagctc	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:5154030C>A	ENST00000252321.3	+	1	946	c.717C>A	c.(715-717)atC>atA	p.I239I		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	239					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)	p.I239I(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	TGTGGCTTATCTTCGAGTATC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	12											93	103	100					12																	5154030		2203	4300	6503	5024291	SO:0001819	synonymous_variant	3741			M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.717C>A	12.37:g.5154030C>A			5024291	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Silent	SNP	ENST00000252321.3	37	CCDS8536.1																																																																																				0.602	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		A	5154030	C	A	5154030	2	1	61	1	0	0	0	0	0	0	0	1	8027	903	32	2		2	KCNA5	12	5154030	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	234564	5154030	128697865	7814	15799										
KCNA5	3741	broad.mit.edu	37	chr12	5154807	5154807	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggcaagatcgtgggctcGctgtgtgccatcgccggggt	19	10	0	1	rs576837393		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:5154807G>A	ENST00000252321.3	+	1	1723	c.1494G>A	c.(1492-1494)tcG>tcA	p.S498S		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	498					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)	p.S498S(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	TCGTGGGCTCGCTGTGTGCCA	0.612													G|||	1	0.000199681	0	0	5008	,	,		18810	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	12											117	107	110					12																	5154807		2203	4300	6503	5025068	SO:0001819	synonymous_variant	3741			M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1494G>A	12.37:g.5154807G>A			5025068	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Silent	SNP	ENST00000252321.3	37	CCDS8536.1																																																																																				0.612	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		A	5154807	G	A	5154807	2	1	61	1	0	0	0	0	0	0	0	1	8027	1074	38	1		1	KCNA5	12	5154807	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	777	5154807	128697088	7815	15800										
ANO2	57101	broad.mit.edu	37	chr12	5685016	5685016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctgcagaactgaacctCctggtcaaactgtgagtttt	8	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:5685016C>T	ENST00000356134.5	-	25	2679	c.2608G>A	c.(2608-2610)Gag>Aag	p.E870K	ANO2_ENST00000327087.8_Missense_Mutation_p.E869K|ANO2_ENST00000546188.1_Missense_Mutation_p.E870K	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	874					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.E870K(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						AACTGAACCTCCTGGTCAAAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											62	63	62					12																	5685016		1939	4132	6071	5555277	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2608G>A	12.37:g.5685016C>T	ENSP00000348453:p.Glu870Lys		5555277	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	C	13.35	2.211430	0.39102	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.65732	-0.17;-0.16;-0.16	5.28	5.28	0.74379	.	0.263406	0.38778	N	0.001568	T	0.48943	0.1528	L	0.34521	1.04	0.36648	D	0.877239	B	0.15473	0.013	B	0.17979	0.02	T	0.49826	-0.8898	10	0.20046	T	0.44	.	11.7169	0.51659	0.0:0.9194:0.0:0.0806	.	869	Q9NQ90-3	.	K	869;870;870;874	ENSP00000314048:E869K;ENSP00000348453:E870K;ENSP00000440981:E870K	ENSP00000314048:E869K	E	-	1	0	ANO2	5555277	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.810000	0.47979	2.621000	0.88768	0.650000	0.86243	GAG		0.498	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		T	5685016	C	T	5685016	3	4	61	1	0	0	0	0	1	0	0	0	697	864	30	3	403	3	ANO2	12	5685016	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	530209	5685016	128166879	7816	15801										
ANO2	57101	broad.mit.edu	37	chr12	5708757	5708757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcagtttctccagcttcgGtctcatctttcagctttcga	7	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:5708757G>A	ENST00000356134.5	-	22	2200	c.2129C>T	c.(2128-2130)aCc>aTc	p.T710I	ANO2_ENST00000327087.8_Missense_Mutation_p.T709I|ANO2_ENST00000546188.1_Missense_Mutation_p.T710I	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	714					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.T710I(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCCAGCTTCGGTCTCATCTTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											151	149	150					12																	5708757		2112	4237	6349	5579018	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2129C>T	12.37:g.5708757G>A	ENSP00000348453:p.Thr710Ile		5579018	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	G	11.88	1.770599	0.31320	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.63744	-0.06;-0.06;-0.06	5.74	4.85	0.62838	.	0.129128	0.56097	D	0.000024	T	0.50446	0.1616	L	0.41492	1.28	0.33233	D	0.55622	B	0.25609	0.13	B	0.18561	0.022	T	0.58607	-0.7607	10	0.34782	T	0.22	.	11.789	0.52059	0.084:0.0:0.916:0.0	.	709	Q9NQ90-3	.	I	709;710;710;714	ENSP00000314048:T709I;ENSP00000348453:T710I;ENSP00000440981:T710I	ENSP00000314048:T709I	T	-	2	0	ANO2	5579018	0.892000	0.30473	0.988000	0.46212	0.820000	0.46376	3.890000	0.56220	2.717000	0.92951	0.563000	0.77884	ACC		0.453	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		A	5708757	G	A	5708757	3	1	61	1	0	0	0	0	1	0	0	0	697	1261	44	3	894	3	ANO2	12	5708757	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23741	5708757	128143138	7817	15802										
ANO2	57101	broad.mit.edu	37	chr12	5721837	5721837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacgggactccaatctcaAagatgttgttctggatcaac	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:5721837A>G	ENST00000356134.5	-	21	2146	c.2075T>C	c.(2074-2076)tTt>tCt	p.F692S	ANO2_ENST00000327087.8_Missense_Mutation_p.F691S|ANO2_ENST00000546188.1_Missense_Mutation_p.F692S	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	696					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.F692S(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCCAATCTCAAAGATGTTGTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											74	74	74					12																	5721837		1924	4146	6070	5592098	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2075T>C	12.37:g.5721837A>G	ENSP00000348453:p.Phe692Ser		5592098	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	A	18.70	3.679832	0.68042	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.62232	0.04;0.04;0.04	4.56	4.56	0.56223	.	0.151263	0.64402	D	0.000015	T	0.67552	0.2905	L	0.46157	1.445	0.58432	D	0.999993	D	0.57257	0.979	P	0.60609	0.877	T	0.63825	-0.6549	10	0.25751	T	0.34	.	12.1615	0.54107	1.0:0.0:0.0:0.0	.	691	Q9NQ90-3	.	S	691;692;692;696	ENSP00000314048:F691S;ENSP00000348453:F692S;ENSP00000440981:F692S	ENSP00000314048:F691S	F	-	2	0	ANO2	5592098	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.781000	0.91805	2.050000	0.60909	0.533000	0.62120	TTT		0.517	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		G	5721837	A	G	5721837	3	3	61	1	0	0	0	0	1	0	0	0	697	14	1	4	952	4	ANO2	12	5721837	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13080	5721837	128130058	7818	15803										
ANO2	57101	broad.mit.edu	37	chr12	6030319	6030319	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtcccagctcaatgtcacCtgggcccccagcatgaggct	11	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6030319C>A	ENST00000356134.5	-	3	480	c.409G>T	c.(409-411)Ggt>Tgt	p.G137C	ANO2_ENST00000327087.8_Missense_Mutation_p.G137C|ANO2_ENST00000546188.1_Missense_Mutation_p.G137C	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	141					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.G137C(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCAATGTCACCTGGGCCCCCA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	12											70	67	68					12																	6030319		2008	4156	6164	5900580	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.409G>T	12.37:g.6030319C>A	ENSP00000348453:p.Gly137Cys		5900580	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	C	9.472	1.095906	0.20552	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.66815	-0.23;-0.23;-0.23	4.03	3.14	0.36123	.	0.319446	0.28671	N	0.014532	T	0.61009	0.2313	L	0.46157	1.445	0.09310	N	0.999997	D	0.55800	0.973	P	0.46479	0.518	T	0.55016	-0.8206	10	0.54805	T	0.06	.	8.9666	0.35881	0.0:0.8966:0.0:0.1034	.	137	Q9NQ90-3	.	C	137;137;137;141	ENSP00000314048:G137C;ENSP00000348453:G137C;ENSP00000440981:G137C	ENSP00000314048:G137C	G	-	1	0	ANO2	5900580	0.000000	0.05858	0.641000	0.29422	0.039000	0.13416	0.382000	0.20635	0.903000	0.36546	0.563000	0.77884	GGT		0.627	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		A	6030319	C	A	6030319	3	1	61	1	0	0	0	0	1	0	0	0	697	681	24	2	2683	2	ANO2	12	6030319	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308482	6030319	127821576	7819	15804										
VWF	7450	broad.mit.edu	37	chr12	6085413	6085413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagggtagatggtgcttCggtggacacacacctgtaga	13	10	0	2	rs370600984		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6085413C>T	ENST00000261405.5	-	43	7555	c.7301G>A	c.(7300-7302)cGa>cAa	p.R2434Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2434	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.R2434Q(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GATGGTGCTTCGGTGGACACA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	88	70	76		7301	-0.5	1	12		76	0,8600		0,0,4300	no	missense	VWF	NM_000552.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2434/2814	6085413	1,13005	2203	4300	6503	5955674	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7301G>A	12.37:g.6085413C>T	ENSP00000261405:p.Arg2434Gln		5955674	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912436	0.33721	2.27E-4	0.0	ENSG00000110799	ENST00000261405	T	0.64260	-0.09	5.19	-0.517	0.11947	von Willebrand factor, type C (3);	0.319527	0.18110	N	0.151391	T	0.40015	0.1100	N	0.24115	0.695	0.53688	D	0.999971	B	0.22346	0.068	B	0.13407	0.009	T	0.09509	-1.0671	10	0.17369	T	0.5	.	8.8775	0.35354	0.0:0.4529:0.0:0.5471	.	2434	P04275	VWF_HUMAN	Q	2434	ENSP00000261405:R2434Q	ENSP00000261405:R2434Q	R	-	2	0	VWF	5955674	0.159000	0.22864	0.989000	0.46669	0.914000	0.54420	-0.037000	0.12164	-0.023000	0.13963	-0.229000	0.12294	CGA		0.547	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6085413	C	T	6085413	3	4	61	1	0	0	0	0	1	0	0	0	17286	884	31	1	1180	1	VWF	12	6085413	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55094	6085413	127766482	7820	15805										
VWF	7450	broad.mit.edu	37	chr12	6128534	6128534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaggccacctggctgccCgcatacttcacctggctggc	13	15	1	0	rs143459496	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6128534C>T	ENST00000261405.5	-	28	4304	c.4050G>A	c.(4048-4050)gcG>gcA	p.A1350A		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1350	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.A1350A(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCTGGCTGCCCGCATACTTCA	0.622													C|||	6	0.00119808	0.0045	0	5008	,	,		18705	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						C		7,4399		0,7,2196	54	49	51		4050	-2.2	0.9	12	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	VWF	NM_000552.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		1350/2814	6128534	7,12999	2203	4300	6503	5998795	SO:0001819	synonymous_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4050G>A	12.37:g.6128534C>T			5998795	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.622	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6128534	C	T	6128534	2	4	61	1	0	0	0	0	0	0	0	1	17286	639	23	1		1	VWF	12	6128534	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43121	6128534	127723361	7821	15806										
VWF	7450	broad.mit.edu	37	chr12	6135135	6135135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagtccacagggtcttcCtccacttggaggttgctgct	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6135135C>T	ENST00000261405.5	-	23	3299	c.3045G>A	c.(3043-3045)gaG>gaA	p.E1015E		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1015	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.E1015E(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CAGGGTCTTCCTCCACTTGGA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	12											94	88	90					12																	6135135		2203	4300	6503	6005396	SO:0001819	synonymous_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.3045G>A	12.37:g.6135135C>T			6005396	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.527	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6135135	C	T	6135135	2	4	61	1	0	0	0	0	0	0	0	1	17286	680	24	3		3	VWF	12	6135135	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6601	6135135	127716760	7822	15807										
VWF	7450	broad.mit.edu	37	chr12	6167022	6167022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggttcacatactcatgcgCgggttgagggcgcagggatc	16	10	2	1	rs368329035		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6167022C>T	ENST00000261405.5	-	14	1976	c.1722G>A	c.(1720-1722)ccG>ccA	p.P574P		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	574	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.P574P(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TACTCATGCGCGGGTTGAGGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C		0,4402		0,0,2201	71	72	72		1722	1.4	1	12		72	2,8594		0,2,4296	no	coding-synonymous	VWF	NM_000552.3		0,2,6497	TT,TC,CC		0.0233,0.0,0.0154		574/2814	6167022	2,12996	2201	4298	6499	6037283	SO:0001819	synonymous_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1722G>A	12.37:g.6167022C>T			6037283	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.662	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6167022	C	T	6167022	2	4	61	1	0	0	0	0	0	0	0	1	17286	755	27	1		1	VWF	12	6167022	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31887	6167022	127684873	7823	15808										
VWF	7450	broad.mit.edu	37	chr12	6184622	6184622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacactcacacaaagtcttCtcacacagggccacaaaagg	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6184622C>A	ENST00000261405.5	-	7	1007	c.753G>T	c.(751-753)gaG>gaT	p.E251D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	251					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.E251D(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ACAAAGTCTTCTCACACAGGG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	59	61					12																	6184622		2203	4300	6503	6054883	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.753G>T	12.37:g.6184622C>A	ENSP00000261405:p.Glu251Asp		6054883	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735822	0.49045	.	.	ENSG00000110799	ENST00000261405	T	0.76709	-1.04	4.71	1.18	0.20946	Uncharacterised domain, cysteine-rich (2);	0.000000	0.41396	D	0.000894	D	0.85470	0.5704	M	0.88570	2.965	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.74348	0.973;0.983	T	0.81258	-0.1014	10	0.27082	T	0.32	.	5.7704	0.18249	0.0:0.4239:0.0:0.5761	.	251;251	B4DNX0;P04275	.;VWF_HUMAN	D	251	ENSP00000261405:E251D	ENSP00000261405:E251D	E	-	3	2	VWF	6054883	0.062000	0.20869	0.777000	0.31699	0.269000	0.26545	0.258000	0.18387	0.470000	0.27294	0.561000	0.74099	GAG		0.647	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6184622	C	A	6184622	3	1	61	1	0	0	0	0	1	0	0	0	17286	912	32	2	7872	2	VWF	12	6184622	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17600	6184622	127667273	7824	15809										
SCNN1A	6337	broad.mit.edu	37	chr12	6457333	6457333	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaccagcaggtcaaagacGagctcagccatctccaccac	8	15	3	2	rs559461583		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6457333G>A	ENST00000228916.2	-	13	1814	c.1716C>T	c.(1714-1716)ctC>ctT	p.L572L	SCNN1A_ENST00000358945.3_Silent_p.L594L|SCNN1A_ENST00000543768.1_Silent_p.L595L|SCNN1A_ENST00000396966.2_3'UTR|SCNN1A_ENST00000360168.3_Silent_p.L631L|SCNN1A_ENST00000540037.1_Silent_p.L272L	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	572					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)	p.L572L(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GGTCAAAGACGAGCTCAGCCA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	12											76	73	74					12																	6457333		2203	4300	6503	6327594	SO:0001819	synonymous_variant	6337			Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1716C>T	12.37:g.6457333G>A			6327594	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	CCDS8543.1																																																																																				0.607	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6457333	G	A	6457333	2	1	61	1	0	0	0	0	0	0	0	1	13964	1045	37	1		1	SCNN1A	12	6457333	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272711	6457333	127394562	7825	15810										
LTBR	4055	broad.mit.edu	37	chr12	6494471	6494471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagccgggaatgttctgtgCtgcctgggccctcgagtgta	14	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6494471C>T	ENST00000228918.4	+	4	724	c.398C>T	c.(397-399)gCt>gTt	p.A133V	LTBR_ENST00000543190.1_Missense_Mutation_p.A26V|LTBR_ENST00000539925.1_Missense_Mutation_p.A114V|LTBR_ENST00000541102.1_Missense_Mutation_p.A26V	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	133					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.A133V(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						ATGTTCTGTGCTGCCTGGGCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	12											54	56	55					12																	6494471		2203	4300	6503	6364732	SO:0001583	missense	4055			L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"Tumor necrosis factor receptor superfamily"	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.398C>T	12.37:g.6494471C>T	ENSP00000228918:p.Ala133Val		6364732	B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	37	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	C	7.818	0.717093	0.15372	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000536876;ENST00000543190;ENST00000541102	T;T;T;T;D	0.97430	0.14;0.14;0.14;-0.69;-4.38	4.02	1.28	0.21552	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.795910	0.11764	N	0.531793	D	0.88295	0.6398	N	0.03917	-0.325	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.79210	-0.1897	9	.	.	.	0.6293	4.7513	0.13063	0.0:0.4784:0.0:0.5216	.	114;114;133	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	V	114;133;26;128;26;26	ENSP00000440875:A114V;ENSP00000228918:A133V;ENSP00000437647:A128V;ENSP00000438955:A26V;ENSP00000438605:A26V	.	A	+	2	0	LTBR	6364732	0.000000	0.05858	0.006000	0.13384	0.570000	0.35934	0.403000	0.20982	0.054000	0.16065	0.561000	0.74099	GCT		0.637	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			T	6494471	C	T	6494471	3	4	61	1	0	0	0	0	1	0	0	0	9106	797	28	3	412	3	LTBR	12	6494471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37138	6494471	127357424	7826	15811										
TAPBPL	55080	broad.mit.edu	37	chr12	6562874	6562874	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcccccaggggactgtgcGaactgcaggtaagaaaatga	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6562874G>A	ENST00000266556.7	+	3	722	c.557G>A	c.(556-558)cGa>cAa	p.R186Q	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Missense_Mutation_p.R109Q|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	186	Ig-like V-type.				negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)	p.R186Q(1)		endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GGGACTGTGCGAACTGCAGGT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											21	22	22					12																	6562874		2203	4300	6503	6433135	SO:0001583	missense	55080			AK001005	CCDS8546.1	12p13.31	2013-01-11						"Immunoglobulin superfamily / C1-set domain containing"	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.557G>A	12.37:g.6562874G>A	ENSP00000266556:p.Arg186Gln		6433135	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	.	.	.	.	.	.	.	.	.	.	G	5.436	0.265526	0.10294	.	.	ENSG00000139192	ENST00000544021;ENST00000266556	T;T	0.42900	0.96;3.18	4.56	-9.12	0.00707	Immunoglobulin-like (1);	0.969423	0.08513	N	0.934583	T	0.09862	0.0242	N	0.01576	-0.805	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.16988	-1.0384	10	0.17369	T	0.5	-0.1374	1.6673	0.02805	0.5092:0.098:0.142:0.2508	.	186	Q9BX59	TPSNR_HUMAN	Q	109;186	ENSP00000445341:R109Q;ENSP00000266556:R186Q	ENSP00000266556:R186Q	R	+	2	0	TAPBPL	6433135	0.000000	0.05858	0.047000	0.18901	0.134000	0.20937	-1.273000	0.02823	-1.597000	0.01609	-0.320000	0.08662	CGA		0.557	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009		A	6562874	G	A	6562874	3	1	61	1	0	0	0	0	1	0	0	0	15592	1058	37	1	567	1	TAPBPL	12	6562874	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68403	6562874	127289021	7827	15812										
NOP2	4839	broad.mit.edu	37	chr12	6672891	6672891	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgactcaggggtcacttCtttctcttcctcctcgtcct	7	16	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6672891C>A	ENST00000322166.5	-	7	698	c.577G>T	c.(577-579)Gaa>Taa	p.E193*	NOP2_ENST00000545200.1_Nonsense_Mutation_p.E189*|NOP2_ENST00000541778.1_Nonsense_Mutation_p.E189*|NOP2_ENST00000382421.3_Nonsense_Mutation_p.E226*|NOP2_ENST00000537442.1_Nonsense_Mutation_p.E193*|NOP2_ENST00000399466.2_Nonsense_Mutation_p.E189*|NOP2_ENST00000542015.1_Intron	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	193					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.E189*(1)		breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						GGGGTCACTTCTTTCTCTTCC	0.552											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	12											51	53	52					12																	6672891		1939	4126	6065	6543152	SO:0001587	stop_gained	4839				CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.577G>T	12.37:g.6672891C>A	ENSP00000313272:p.Glu193*	635	6543152	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Nonsense_Mutation	SNP	ENST00000322166.5	37	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.445916	0.63178	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867	.	.	.	2.86	-5.72	0.02406	.	1.681900	0.04492	N	0.379709	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	3.274	7.5914	0.28023	0.0:0.7371:0.1241:0.1389	.	.	.	.	X	193;226;189;189;193;189;69;189	.	ENSP00000313272:E193X	E	-	1	0	NOP2	6543152	0.000000	0.05858	0.000000	0.03702	0.319000	0.28217	-0.865000	0.04250	-1.520000	0.01773	0.134000	0.15878	GAA		0.552	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		A	6672891	C	A	6672891	4	1	61	1	0	0	0	0	0	1	0	0	10569	922	32	2	1901	2	NOP2	12	6672891	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110017	6672891	127179004	7828	15813										
CHD4	1108	broad.mit.edu	37	chr12	6701197	6701197	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgagtgcttcaaaatttCgagtgaggatgtacttgtag	11	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6701197C>T	ENST00000357008.2	-	20	3138	c.2975G>A	c.(2974-2976)cGa>cAa	p.R992Q	CHD4_ENST00000544484.1_Missense_Mutation_p.R989Q|CHD4_ENST00000309577.6_Missense_Mutation_p.R992Q|CHD4_ENST00000544040.1_Missense_Mutation_p.R985Q	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	992					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R992Q(2)		central_nervous_system(2)	2						TTCAAAATTTCGAGTGAGGAT	0.453																																					Colon(32;586 792 4568 16848 45314)											2	Substitution - Missense(2)	large_intestine(2)	12											148	145	146					12																	6701197		2203	4300	6503	6571458	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2975G>A	12.37:g.6701197C>T	ENSP00000349508:p.Arg992Gln		6571458	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	33	5.258054	0.95368	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	4.59	4.59	0.56863	SNF2-related (1);	0.087525	0.46145	D	0.000316	T	0.81093	0.4751	L	0.35723	1.085	0.80722	D	1	D;D;D	0.71674	0.985;0.982;0.998	P;P;D	0.75484	0.642;0.791;0.986	D	0.83720	0.0192	10	0.87932	D	0	.	17.5807	0.87966	0.0:1.0:0.0:0.0	.	992;992;985	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	Q	989;985;992;992;966	ENSP00000440392:R989Q;ENSP00000440542:R985Q;ENSP00000312419:R992Q;ENSP00000349508:R992Q	ENSP00000312419:R992Q	R	-	2	0	CHD4	6571458	1.000000	0.71417	0.953000	0.39169	0.981000	0.71138	7.601000	0.82783	2.362000	0.80069	0.563000	0.77884	CGA		0.453	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		T	6701197	C	T	6701197	3	4	61	1	0	0	0	0	1	0	0	0	3333	884	31	1	2847	1	CHD4	12	6701197	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28306	6701197	127150698	7829	15814										
ACRBP	84519	broad.mit.edu	37	chr12	6753361	6753361	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatatttcattcatttcatCtatttcctgggctgatcgaa	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6753361C>A	ENST00000229243.2	-	5	979	c.886G>T	c.(886-888)Gat>Tat	p.D296Y	ACRBP_ENST00000542357.1_5'Flank|ACRBP_ENST00000414226.2_Missense_Mutation_p.D263Y|ACRBP_ENST00000536350.1_Missense_Mutation_p.D296Y	NM_032489.2	NP_115878.2			acrosin binding protein									p.D296Y(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						TTCATTTCATCTATTTCCTGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	96	96					12																	6753361		2203	4300	6503	6623622	SO:0001583	missense	84519			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"proacrosin binding protein sp32", "cancer/testis antigen 23"	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.886G>T	12.37:g.6753361C>A	ENSP00000229243:p.Asp296Tyr		6623622		Missense_Mutation	SNP	ENST00000229243.2	37	CCDS8554.1	.	.	.	.	.	.	.	.	.	.	C	8.087	0.773587	0.16051	.	.	ENSG00000111644	ENST00000229243;ENST00000414226;ENST00000536350	T;T	0.50813	0.75;0.73	4.25	3.35	0.38373	.	0.733950	0.12675	N	0.448450	T	0.49558	0.1564	L	0.57536	1.79	0.31600	N	0.652832	P;D	0.55385	0.948;0.971	P;P	0.49561	0.52;0.615	T	0.54741	-0.8248	10	0.40728	T	0.16	-0.4485	8.1816	0.31313	0.0:0.8897:0.0:0.1103	.	263;296	E7EP66;Q8NEB7	.;ACRBP_HUMAN	Y	296;263;296	ENSP00000229243:D296Y;ENSP00000402725:D263Y	ENSP00000229243:D296Y	D	-	1	0	ACRBP	6623622	0.991000	0.36638	0.969000	0.41365	0.103000	0.19146	1.953000	0.40352	1.132000	0.42129	0.561000	0.74099	GAT		0.453	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489		A	6753361	C	A	6753361	3	1	61	1	0	0	0	0	1	0	0	0	170	913	32	2	769	2	ACRBP	12	6753361	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52164	6753361	127098534	7830	15815										
ACRBP	84519	broad.mit.edu	37	chr12	6754442	6754442	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtgagacttcagctgaaGcttctatctccttgagagtg	12	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6754442G>T	ENST00000229243.2	-	4	512	c.419C>A	c.(418-420)gCt>gAt	p.A140D	ACRBP_ENST00000542357.1_5'Flank|ACRBP_ENST00000414226.2_Missense_Mutation_p.A140D|ACRBP_ENST00000536350.1_Missense_Mutation_p.A140D	NM_032489.2	NP_115878.2			acrosin binding protein									p.A140D(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						TTCAGCTGAAGCTTCTATCTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											158	154	155					12																	6754442		2203	4300	6503	6624703	SO:0001583	missense	84519			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"proacrosin binding protein sp32", "cancer/testis antigen 23"	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.419C>A	12.37:g.6754442G>T	ENSP00000229243:p.Ala140Asp		6624703		Missense_Mutation	SNP	ENST00000229243.2	37	CCDS8554.1	.	.	.	.	.	.	.	.	.	.	G	9.941	1.217541	0.22373	.	.	ENSG00000111644	ENST00000229243;ENST00000414226;ENST00000536350;ENST00000546114	T;T	0.46819	0.92;0.86	4.41	1.57	0.23409	.	1.096420	0.07004	N	0.823883	T	0.33323	0.0859	N	0.22421	0.69	0.09310	N	1	B;B	0.26708	0.077;0.157	B;B	0.28553	0.042;0.091	T	0.36261	-0.9755	10	0.72032	D	0.01	-0.0223	4.4347	0.11545	0.2015:0.1864:0.6121:0.0	.	140;140	E7EP66;Q8NEB7	.;ACRBP_HUMAN	D	140	ENSP00000229243:A140D;ENSP00000402725:A140D	ENSP00000229243:A140D	A	-	2	0	ACRBP	6624703	0.001000	0.12720	0.000000	0.03702	0.052000	0.14988	0.607000	0.24209	0.363000	0.24346	0.561000	0.74099	GCT		0.532	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489		T	6754442	G	T	6754442	3	4	61	1	0	0	0	0	1	0	0	0	170	971	34	2	1240	2	ACRBP	12	6754442	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1081	6754442	127097453	7831	15816										
ACRBP	84519	broad.mit.edu	37	chr12	6755661	6755661	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctcaccttggcatagtaGacgtggttggagcaacggta	14	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6755661G>T	ENST00000229243.2	-	3	438	c.345C>A	c.(343-345)gtC>gtA	p.V115V	ACRBP_ENST00000542357.1_5'Flank|ACRBP_ENST00000414226.2_Silent_p.V115V|ACRBP_ENST00000536350.1_Silent_p.V115V	NM_032489.2	NP_115878.2			acrosin binding protein									p.V115V(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						TGGCATAGTAGACGTGGTTGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											137	124	129					12																	6755661		2203	4300	6503	6625922	SO:0001819	synonymous_variant	84519			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"proacrosin binding protein sp32", "cancer/testis antigen 23"	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.345C>A	12.37:g.6755661G>T			6625922		Silent	SNP	ENST00000229243.2	37	CCDS8554.1																																																																																				0.577	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489		T	6755661	G	T	6755661	2	4	61	1	0	0	0	0	0	0	0	1	170	929	33	2		2	ACRBP	12	6755661	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1219	6755661	127096234	7832	15817										
GPR162	27239	broad.mit.edu	37	chr12	6936003	6936003	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttggaggacgaggaggaCgaggaagaggctgaaggtgg	22	3	0	2	rs141548833		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6936003C>T	ENST00000311268.3	+	5	2188	c.1401C>T	c.(1399-1401)gaC>gaT	p.D467D	LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000396725.2_RNA|GPR162_ENST00000382315.3_Silent_p.D163D|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000428545.2_Silent_p.D183D	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	467						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D467D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						ACGAGGAGGACGAGGAAGAGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	2,4404	4.2+/-10.8	0,2,2201	50	62	58		549,1401	-9.6	0	12	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	183/305,467/589	6936003	2,13004	2203	4300	6503	6806264	SO:0001819	synonymous_variant	27239			U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1401C>T	12.37:g.6936003C>T			6806264	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																				0.652	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		T	6936003	C	T	6936003	2	4	61	1	0	0	0	0	0	0	0	1	6686	535	19	1		1	GPR162	12	6936003	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180342	6936003	126915892	7833	15818										
USP5	8078	broad.mit.edu	37	chr12	6970161	6970161	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaatgaagtgttccgcttCttggtggaggaaaagatcaa	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:6970161C>A	ENST00000229268.8	+	12	1441	c.1389C>A	c.(1387-1389)ttC>ttA	p.F463L	USP5_ENST00000389231.5_Missense_Mutation_p.F463L|USP5_ENST00000541969.1_3'UTR	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	463	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)	p.F463L(1)		breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						TGTTCCGCTTCTTGGTGGAGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											194	195	195					12																	6970161		2203	4300	6503	6840422	SO:0001583	missense	8078			U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1389C>A	12.37:g.6970161C>A	ENSP00000229268:p.Phe463Leu		6840422	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	37	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235153	0.79800	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.74209	-0.82;-0.82	5.14	4.24	0.50183	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.87196	0.6117	M	0.90595	3.13	0.80722	D	1	D;P	0.76494	0.999;0.72	D;P	0.91635	0.999;0.447	D	0.88520	0.3095	10	0.62326	D	0.03	-5.808	11.0035	0.47620	0.0:0.8359:0.0:0.1641	.	463;463	P45974;P45974-2	UBP5_HUMAN;.	L	463	ENSP00000229268:F463L;ENSP00000373883:F463L	ENSP00000229268:F463L	F	+	3	2	USP5	6840422	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.510000	0.35790	1.361000	0.45981	0.561000	0.74099	TTC		0.552	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			A	6970161	C	A	6970161	3	1	61	1	0	0	0	0	1	0	0	0	17121	912	32	2	1435	2	USP5	12	6970161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34158	6970161	126881734	7834	15819										
ATN1	1822	broad.mit.edu	37	chr12	7050633	7050633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtcagctgagctgcagcGcttggcgctggaacagcagc	14	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7050633G>A	ENST00000356654.4	+	9	3692	c.3455G>A	c.(3454-3456)cGc>cAc	p.R1152H	U47924.31_ENST00000607421.1_RNA|C12orf57_ENST00000540506.2_5'Flank|C12orf57_ENST00000544681.1_5'Flank|C12orf57_ENST00000229281.5_5'Flank|RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000537087.1_5'Flank|ATN1_ENST00000396684.2_Missense_Mutation_p.R1152H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	1152					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)	p.R1152H(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						GAGCTGCAGCGCTTGGCGCTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											49	50	49					12																	7050633		2203	4297	6500	6920894	SO:0001583	missense	1822			U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.3455G>A	12.37:g.7050633G>A	ENSP00000349076:p.Arg1152His		6920894	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	37	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647780	0.87958	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.62232	0.04;0.04;0.04	4.32	3.43	0.39272	.	0.000000	0.34555	U	0.003865	T	0.74749	0.3757	M	0.64170	1.965	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.77392	-0.2605	10	0.87932	D	0	.	12.5227	0.56069	0.0809:0.0:0.9191:0.0	.	1152	P54259	ATN1_HUMAN	H	1152;1152;1152;737	ENSP00000349076:R1152H;ENSP00000379915:R1152H;ENSP00000441744:R1152H	ENSP00000229279:R737H	R	+	2	0	ATN1	6920894	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	9.657000	0.98554	1.192000	0.43071	0.655000	0.94253	CGC		0.652	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		A	7050633	G	A	7050633	3	1	61	1	0	0	0	0	1	0	0	0	1112	1087	38	1	3485	1	ATN1	12	7050633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80472	7050633	126801262	7835	15820										
C1S	716	broad.mit.edu	37	chr12	7173871	7173871	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattctgtttgggagcctgcGaaggcaaaatatgtctttag	11	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7173871G>A	ENST00000406697.1	+	11	1549	c.921G>A	c.(919-921)gcG>gcA	p.A307A	C1S_ENST00000360817.5_Silent_p.A307A|C1S_ENST00000328916.3_Silent_p.A307A|C1S_ENST00000402681.3_Silent_p.A140A			P09871	C1S_HUMAN	complement component 1, s subcomponent	307	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)	p.A307A(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GGGAGCCTGCGAAGGCAAAAT	0.458																																					GBM(156;750 1943 12971 24779 31015)											1	Substitution - coding silent(1)	large_intestine(1)	12											113	114	114					12																	7173871		2203	4300	6503	7044132	SO:0001819	synonymous_variant	716				CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.921G>A	12.37:g.7173871G>A			7044132	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Silent	SNP	ENST00000406697.1	37	CCDS31735.1																																																																																				0.458	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		A	7173871	G	A	7173871	2	1	61	1	0	0	0	0	0	0	0	1	1980	1045	37	1		1	C1S	12	7173871	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123238	7173871	126678024	7836	15821										
C1S	716	broad.mit.edu	37	chr12	7174350	7174350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattattctccagggacgtgTtggtgcaacatctttctatt	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7174350T>C	ENST00000406697.1	+	12	1623	c.995T>C	c.(994-996)gTt>gCt	p.V332A	C1S_ENST00000360817.5_Missense_Mutation_p.V332A|C1S_ENST00000328916.3_Missense_Mutation_p.V332A|C1S_ENST00000402681.3_Missense_Mutation_p.V165A			P09871	C1S_HUMAN	complement component 1, s subcomponent	332	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)	p.V332A(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	CAGGGACGTGTTGGTGCAACA	0.383																																					GBM(156;750 1943 12971 24779 31015)											1	Substitution - Missense(1)	large_intestine(1)	12											151	137	142					12																	7174350		2203	4300	6503	7044611	SO:0001583	missense	716				CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.995T>C	12.37:g.7174350T>C	ENSP00000385035:p.Val332Ala		7044611	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	T	7.171	0.587567	0.13812	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02	5.74	2.21	0.28008	Complement control module (2);Sushi/SCR/CCP (3);	0.194329	0.25509	N	0.030194	T	0.68778	0.3038	L	0.51914	1.62	0.09310	N	1	B	0.26120	0.142	B	0.36030	0.216	T	0.52238	-0.8602	10	0.09084	T	0.74	.	6.5942	0.22664	0.0:0.2696:0.0:0.7304	.	332	P09871	C1S_HUMAN	A	332;332;332;320;165	ENSP00000385035:V332A;ENSP00000328173:V332A;ENSP00000354057:V332A;ENSP00000384171:V165A	ENSP00000328173:V332A	V	+	2	0	C1S	7044611	0.000000	0.05858	0.025000	0.17156	0.425000	0.31504	0.131000	0.15870	0.461000	0.27071	0.459000	0.35465	GTT		0.383	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		C	7174350	T	C	7174350	3	2	61	1	0	0	0	0	1	0	0	0	1980	1725	60	4	1025	4	C1S	12	7174350	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	479	7174350	126677545	7837	15822										
C1R	715	broad.mit.edu	37	chr12	7188279	7188279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttccagctccagcagggCgatgtccccctcaaaattgt	8	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7188279C>T	ENST00000542285.1	-	11	1668	c.1519G>A	c.(1519-1521)Gcc>Acc	p.A507T				P00736	C1R_HUMAN	complement component 1, r subcomponent	559	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A522T(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|pancreas(1)	16					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TCCAGCAGGGCGATGTCCCCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	12											99	106	104					12																	7188279		2187	4291	6478	7058534	SO:0001583	missense	715			M14058		12p13.31	2014-05-14			ENSG00000159403	ENSG00000159403	3.4.21.41	"Complement system"	1246	protein-coding gene	gene with protein product		613785					Standard	NM_001733		Approved		uc010sfy.2	P00736	OTTHUMG00000168149	ENST00000542285.1:c.1519G>A	12.37:g.7188279C>T	ENSP00000438615:p.Ala507Thr		7058534	A6NJQ8|Q68D77|Q8J012	Missense_Mutation	SNP	ENST00000542285.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.632016	0.96682	.	.	ENSG00000159403	ENST00000290575;ENST00000542285	T	0.68479	-0.33	5.64	5.64	0.86602	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000001	D	0.83737	0.5319	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85296	0.1070	9	0.87932	D	0	.	19.7027	0.96062	0.0:1.0:0.0:0.0	.	559	P00736	C1R_HUMAN	T	522;507	ENSP00000438615:A507T	ENSP00000290575:A522T	A	-	1	0	C1R	7058534	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	7.534000	0.82004	2.646000	0.89796	0.655000	0.94253	GCC		0.567	C1R-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001733		T	7188279	C	T	7188279	3	4	61	1	0	0	0	0	1	0	0	0	1978	768	27	1	446	1	C1R	12	7188279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13929	7188279	126663616	7838	15823										
CLSTN3	9746	broad.mit.edu	37	chr12	7286336	7286336	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgactgtggcgagggccccGacggggccaacaccaagaag	15	12	0	2	rs144627317	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7286336G>A	ENST00000266546.6	+	3	805	c.355G>A	c.(355-357)Gac>Aac	p.D119N	RP11-273B20.1_ENST00000538062.1_RNA|CLSTN3_ENST00000537408.1_Missense_Mutation_p.D131N	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	119	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.D119N(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CGAGGGCCCCGACGGGGCCAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/ASP	4,4402	8.1+/-20.4	0,4,2199	46	41	43		355	5.1	0.5	12	dbSNP_134	43	0,8600		0,0,4300	yes	missense	CLSTN3	NM_014718.3	23	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	benign	119/957	7286336	4,13002	2203	4300	6503	7177603	SO:0001583	missense	9746			AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.355G>A	12.37:g.7286336G>A	ENSP00000266546:p.Asp119Asn		7177603	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332175	0.81801	9.08E-4	0.0	ENSG00000139182	ENST00000541953;ENST00000266546;ENST00000545663;ENST00000535452;ENST00000534830;ENST00000539982;ENST00000537408	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.07	5.07	0.68467	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	L	0.31294	0.92	0.80722	D	1	D;P	0.76494	0.999;0.573	D;B	0.75020	0.985;0.087	T	0.56044	-0.8044	10	0.51188	T	0.08	-23.6201	18.4631	0.90746	0.0:0.0:1.0:0.0	.	131;119	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	N	119;119;82;82;82;102;131	ENSP00000443959:D119N;ENSP00000266546:D119N;ENSP00000442612:D82N;ENSP00000443468:D82N;ENSP00000443490:D82N;ENSP00000442801:D102N;ENSP00000440679:D131N	ENSP00000266546:D119N	D	+	1	0	CLSTN3	7177603	1.000000	0.71417	0.477000	0.27303	0.982000	0.71751	9.476000	0.97823	2.347000	0.79759	0.561000	0.74099	GAC		0.627	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		A	7286336	G	A	7286336	3	1	61	1	0	0	0	0	1	0	0	0	3569	1058	37	1	365	1	CLSTN3	12	7286336	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98057	7286336	126565559	7839	15824										
CLSTN3	9746	broad.mit.edu	37	chr12	7288882	7288882	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcctggagacctgtgatGaaccactctggaacattcag	10	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7288882G>T	ENST00000266546.6	+	6	1273	c.823G>T	c.(823-825)Gaa>Taa	p.E275*	CLSTN3_ENST00000537408.1_Nonsense_Mutation_p.E287*	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	275					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.E275*(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						GACCTGTGATGAACCACTCTG	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											110	97	101					12																	7288882		2203	4300	6503	7180149	SO:0001587	stop_gained	9746			AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.823G>T	12.37:g.7288882G>T	ENSP00000266546:p.Glu275*		7180149	D3DUT6|O94831|Q2T9J5|Q5UE57	Nonsense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	G	44	11.250452	0.99537	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-18.2836	19.0734	0.93150	0.0:0.0:1.0:0.0	.	.	.	.	X	275;287	.	ENSP00000266546:E275X	E	+	1	0	CLSTN3	7180149	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	9.869000	0.99810	2.756000	0.94617	0.561000	0.74099	GAA		0.562	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		T	7288882	G	T	7288882	4	4	61	1	0	0	0	0	0	1	0	0	3569	1291	45	2	845	2	CLSTN3	12	7288882	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2546	7288882	126563013	7840	15825										
ACSM4	341392	broad.mit.edu	37	chr12	7459190	7459190	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaaaggggatgaggtaaAatggagcttcagagaactgg	16	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7459190A>C	ENST00000399422.4	+	2	311	c.263A>C	c.(262-264)aAa>aCa	p.K88T		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	88					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						GATGAGGTAAAATGGAGCTTC	0.562																																																0			12											59	70	66					12																	7459190		2085	4253	6338	7350457	SO:0001583	missense	341392				CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"Acyl-CoA synthetase family"	32016	protein-coding gene	gene with protein product	"similar to olfactory specific medium-chain acyl CoA synthetase"	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.263A>C	12.37:g.7459190A>C	ENSP00000382349:p.Lys88Thr		7350457	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	37	CCDS44825.1	.	.	.	.	.	.	.	.	.	.	A	17.02	3.281617	0.59758	.	.	ENSG00000215009	ENST00000399422	T	0.39592	1.07	5.13	3.99	0.46301	.	0.000000	0.40640	U	0.001046	T	0.43722	0.1260	N	0.25992	0.78	0.33303	D	0.565039	D	0.67145	0.996	P	0.61477	0.889	T	0.54125	-0.8340	10	0.37606	T	0.19	-1.7466	9.21	0.37313	0.9121:0.0:0.0879:0.0	.	88	P0C7M7	ACSM4_HUMAN	T	88	ENSP00000382349:K88T	ENSP00000382349:K88T	K	+	2	0	ACSM4	7350457	0.972000	0.33761	0.999000	0.59377	0.994000	0.84299	2.215000	0.42862	0.911000	0.36747	0.533000	0.62120	AAA		0.562	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		C	7459190	A	C	7459190	3	2	61	1	0	0	0	0	1	0	0	0	186	14	1	4	269	4	ACSM4	12	7459190	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	170308	7459190	126392705	7841	15826										
ACSM4	341392	broad.mit.edu	37	chr12	7475017	7475017	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactctgtctctccagataTaaattcaagagtctgcggca	7	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7475017T>C	ENST00000399422.4	+	7	1053	c.1005T>C	c.(1003-1005)taT>taC	p.Y335Y		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	335					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						TCTCCAGATATAAATTCAAGA	0.507																																																0			12											52	52	52					12																	7475017		1904	4124	6028	7366284	SO:0001819	synonymous_variant	341392				CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"Acyl-CoA synthetase family"	32016	protein-coding gene	gene with protein product	"similar to olfactory specific medium-chain acyl CoA synthetase"	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.1005T>C	12.37:g.7475017T>C			7366284	A8MTI6	Silent	SNP	ENST00000399422.4	37	CCDS44825.1																																																																																				0.507	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		C	7475017	T	C	7475017	2	2	61	1	0	0	0	0	0	0	0	1	186	1413	49	4		4	ACSM4	12	7475017	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	15827	7475017	126376878	7842	15827										
ACSM4	341392	broad.mit.edu	37	chr12	7479625	7479625	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaagtcctacaacccagaGaaattaactcttgaacttca	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7479625G>A	ENST00000399422.4	+	12	1638	c.1590G>A	c.(1588-1590)gaG>gaA	p.E530E		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	530					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						ACAACCCAGAGAAATTAACTC	0.373																																																0			12											67	61	63					12																	7479625		1830	4093	5923	7370892	SO:0001819	synonymous_variant	341392				CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"Acyl-CoA synthetase family"	32016	protein-coding gene	gene with protein product	"similar to olfactory specific medium-chain acyl CoA synthetase"	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.1590G>A	12.37:g.7479625G>A			7370892	A8MTI6	Silent	SNP	ENST00000399422.4	37	CCDS44825.1																																																																																				0.373	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		A	7479625	G	A	7479625	2	1	61	1	0	0	0	0	0	0	0	1	186	933	33	3		3	ACSM4	12	7479625	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4608	7479625	126372270	7843	15828										
CD163L1	283316	broad.mit.edu	37	chr12	7510025	7510025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtggcttcagaggcaggaAgaactcccaacagcgatgtg	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7510025A>C	ENST00000313599.3	-	19	4394	c.4337T>G	c.(4336-4338)cTt>cGt	p.L1446R	CD163L1_ENST00000396630.1_Missense_Mutation_p.L1414R|CD163L1_ENST00000416109.2_Missense_Mutation_p.L1456R			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1446						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.L1446R(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						AGAGGCAGGAAGAACTCCCAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											96	91	93					12																	7510025		2203	4300	6503	7401292	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4337T>G	12.37:g.7510025A>C	ENSP00000315945:p.Leu1446Arg		7401292	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	A	7.404	0.633426	0.14322	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.02763	4.83;4.82;4.17	1.07	-0.484	0.12071	.	.	.	.	.	T	0.03434	0.0099	N	0.08118	0	0.09310	N	0.999998	D;D	0.71674	0.998;0.968	D;P	0.77557	0.99;0.452	T	0.45687	-0.9244	9	0.25106	T	0.35	.	3.1544	0.06499	0.6017:0.0:0.3983:0.0	.	1456;1446	E7EVK4;Q9NR16	.;C163B_HUMAN	R	1446;1456;1414	ENSP00000315945:L1446R;ENSP00000393474:L1456R;ENSP00000379871:L1414R	ENSP00000315945:L1446R	L	-	2	0	CD163L1	7401292	0.080000	0.21391	0.264000	0.24511	0.183000	0.23260	-0.074000	0.11450	-0.156000	0.11079	0.448000	0.29417	CTT		0.418	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7510025	A	C	7510025	3	2	61	1	0	0	0	0	1	0	0	0	2974	72	3	4	28	4	CD163L1	12	7510025	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	30400	7510025	126341870	7844	15829										
CD163L1	283316	broad.mit.edu	37	chr12	7527940	7527940	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctccaagaactgtcatttGacagttatccagaagtgact	8	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7527940G>A	ENST00000313599.3	-	11	2995	c.2938C>T	c.(2938-2940)Caa>Taa	p.Q980*	CD163L1_ENST00000396630.1_Nonsense_Mutation_p.Q980*|CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Nonsense_Mutation_p.Q990*			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	980	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.Q980*(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ACTGTCATTTGACAGTTATCC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											94	82	86					12																	7527940		2203	4300	6503	7419207	SO:0001587	stop_gained	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.2938C>T	12.37:g.7527940G>A	ENSP00000315945:p.Gln980*		7419207	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Nonsense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	38	6.639636	0.97726	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	.	.	.	2.29	2.29	0.28610	.	0.437595	0.18575	U	0.137211	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	4.9677	0.14098	0.174:0.0:0.826:0.0	.	.	.	.	X	980;990;980	.	ENSP00000315945:Q980X	Q	-	1	0	CD163L1	7419207	0.000000	0.05858	0.004000	0.12327	0.652000	0.38707	-0.127000	0.10547	1.577000	0.49804	0.455000	0.32223	CAA		0.423	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7527940	G	A	7527940	4	1	61	1	0	0	0	0	0	1	0	0	2974	1299	45	3	1459	3	CD163L1	12	7527940	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17915	7527940	126323955	7845	15830										
CD163L1	283316	broad.mit.edu	37	chr12	7559282	7559282	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaatgaggcaagccagcGaagtgaagtgcggttccaca	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7559282G>A	ENST00000313599.3	-	5	990	c.933C>T	c.(931-933)ttC>ttT	p.F311F	CD163L1_ENST00000396630.1_Silent_p.F311F|CD163L1_ENST00000416109.2_Silent_p.F321F			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	311	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.F311F(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						GCAAGCCAGCGAAGTGAAGTG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	12											289	222	244					12																	7559282		2203	4300	6503	7450549	SO:0001819	synonymous_variant	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.933C>T	12.37:g.7559282G>A			7450549	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																				0.507	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7559282	G	A	7559282	2	1	61	1	0	0	0	0	0	0	0	1	2974	1049	37	1		1	CD163L1	12	7559282	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31342	7559282	126292613	7846	15831										
GDF3	9573	broad.mit.edu	37	chr12	7842521	7842521	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtcttcataatgtcgtaGaatgacattgtcattattgt	7	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7842521G>T	ENST00000329913.3	-	2	1095	c.1048C>A	c.(1048-1050)Cta>Ata	p.L350I		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	350					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.L350I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						TAATGTCGTAGAATGACATTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											109	99	102					12																	7842521		2203	4300	6503	7733788	SO:0001583	missense	9573			AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"Endogenous ligands"	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.1048C>A	12.37:g.7842521G>T	ENSP00000331745:p.Leu350Ile		7733788	Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	37	CCDS8581.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199477	0.58126	.	.	ENSG00000184344	ENST00000329913	T	0.77620	-1.11	3.78	0.668	0.17912	Transforming growth factor-beta, C-terminal (3);	0.067888	0.64402	N	0.000010	D	0.83119	0.5185	M	0.69823	2.125	0.54753	D	0.999989	D	0.64830	0.994	D	0.91635	0.999	T	0.79487	-0.1783	10	0.87932	D	0	.	5.3109	0.15829	0.2215:0.1786:0.5999:0.0	.	350	Q9NR23	GDF3_HUMAN	I	350	ENSP00000331745:L350I	ENSP00000331745:L350I	L	-	1	2	GDF3	7733788	0.992000	0.36948	0.306000	0.25113	0.966000	0.64601	2.103000	0.41806	0.002000	0.14630	-0.258000	0.10820	CTA		0.448	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			T	7842521	G	T	7842521	3	4	61	1	0	0	0	0	1	0	0	0	6335	933	33	2	50	2	GDF3	12	7842521	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	283239	7842521	126009374	7847	15832										
CLEC4C	170482	broad.mit.edu	37	chr12	7894042	7894042	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcctttccttccatgacGcaggtcaggcttggatgata	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7894042G>A	ENST00000542353.1	-	4	700	c.210C>T	c.(208-210)tgC>tgT	p.C70C	CLEC4C_ENST00000354629.5_Silent_p.C39C|CLEC4C_ENST00000540085.1_Silent_p.C39C|CLEC4C_ENST00000360345.3_Silent_p.C70C	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	70					innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.C70C(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		CTTCCATGACGCAGGTCAGGC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	12											195	165	175					12																	7894042		2203	4300	6503	7785309	SO:0001819	synonymous_variant	170482			AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"C-type lectin domain containing", "CD molecules"	13258	protein-coding gene	gene with protein product		606677	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.210C>T	12.37:g.7894042G>A			7785309	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Silent	SNP	ENST00000542353.1	37	CCDS8583.1																																																																																				0.413	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503		A	7894042	G	A	7894042	2	1	61	1	0	0	0	0	0	0	0	1	3519	1079	38	1		1	CLEC4C	12	7894042	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51521	7894042	125957853	7848	15833										
SLC2A14	144195	broad.mit.edu	37	chr12	7970528	7970528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggccctggctgaagagttCggccacaataaaccagggaa	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7970528C>T	ENST00000543909.1	-	15	2002	c.1243G>A	c.(1243-1245)Gaa>Aaa	p.E415K	SLC2A14_ENST00000539924.1_Missense_Mutation_p.E430K|SLC2A14_ENST00000431042.2_Missense_Mutation_p.E392K|SLC2A14_ENST00000535295.1_Missense_Mutation_p.E306K|SLC2A14_ENST00000542546.1_Missense_Mutation_p.E306K|SLC2A14_ENST00000340749.5_Missense_Mutation_p.E392K|SLC2A14_ENST00000396589.2_Missense_Mutation_p.E415K|SLC2A14_ENST00000542505.1_Missense_Mutation_p.E56K			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	415					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)	p.E415K(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		CTGAAGAGTTCGGCCACAATA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											35	38	37					12																	7970528		2203	4298	6501	7861795	SO:0001583	missense	144195			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1243G>A	12.37:g.7970528C>T	ENSP00000440480:p.Glu415Lys		7861795	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240840	0.79912	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	D;D;D;D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94;-1.94;-1.94;-1.94	3.31	3.31	0.37934	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.94285	0.8164	H	0.97214	3.96	0.58432	D	0.999999	D;D;D;D	0.69078	0.997;0.976;0.984;0.987	P;P;P;D	0.66847	0.84;0.672;0.855;0.947	D	0.95525	0.8598	10	0.87932	D	0	.	12.4172	0.55500	0.0:1.0:0.0:0.0	.	430;306;392;415	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	K	392;415;392;56;415;306;306;430	ENSP00000340450:E392K;ENSP00000440480:E415K;ENSP00000407287:E392K;ENSP00000438484:E56K;ENSP00000379834:E415K;ENSP00000440492:E306K;ENSP00000443903:E306K;ENSP00000445929:E430K	ENSP00000340450:E392K	E	-	1	0	SLC2A14	7861795	1.000000	0.71417	0.989000	0.46669	0.805000	0.45488	6.898000	0.75676	1.546000	0.49388	0.195000	0.17529	GAA		0.557	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		T	7970528	C	T	7970528	3	4	61	1	0	0	0	0	1	0	0	0	14580	893	31	1	327	1	SLC2A14	12	7970528	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76486	7970528	125881367	7849	15834										
SLC2A14	144195	broad.mit.edu	37	chr12	7972173	7972173	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcctgccctttccaccaGaaatagctggaagaagaata	7	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:7972173G>T	ENST00000543909.1	-	14	1804	c.1045C>A	c.(1045-1047)Ctg>Atg	p.L349M	SLC2A14_ENST00000539924.1_Missense_Mutation_p.L364M|SLC2A14_ENST00000431042.2_Missense_Mutation_p.L326M|SLC2A14_ENST00000535295.1_Missense_Mutation_p.L240M|SLC2A14_ENST00000542546.1_Missense_Mutation_p.L240M|SLC2A14_ENST00000340749.5_Missense_Mutation_p.L326M|SLC2A14_ENST00000396589.2_Missense_Mutation_p.L349M|SLC2A14_ENST00000542505.1_De_novo_Start_InFrame			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	349					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)	p.L349M(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		CTTTCCACCAGAAATAGCTGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											29	25	27					12																	7972173		2201	4278	6479	7863440	SO:0001583	missense	144195			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1045C>A	12.37:g.7972173G>T	ENSP00000440480:p.Leu349Met		7863440	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032097	0.35893	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	D;D;D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02;-2.02;-2.02	2.56	1.64	0.23874	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.166104	0.42420	D	0.000710	D	0.91392	0.7284	M	0.94021	3.485	0.45108	D	0.998126	D;D;D;D	0.55385	0.971;0.971;0.964;0.971	D;D;P;P	0.64506	0.926;0.926;0.841;0.902	D	0.87874	0.2673	10	0.66056	D	0.02	.	3.1801	0.06582	0.1538:0.0:0.5874:0.2588	.	364;240;326;349	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	M	326;349;326;349;240;240;364	ENSP00000340450:L326M;ENSP00000440480:L349M;ENSP00000407287:L326M;ENSP00000379834:L349M;ENSP00000440492:L240M;ENSP00000443903:L240M;ENSP00000445929:L364M	ENSP00000340450:L326M	L	-	1	2	SLC2A14	7863440	0.878000	0.30173	0.845000	0.33349	0.308000	0.27856	0.298000	0.19120	0.405000	0.25532	0.184000	0.17185	CTG		0.423	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		T	7972173	G	T	7972173	3	4	61	1	0	0	0	0	1	0	0	0	14580	933	33	2	529	2	SLC2A14	12	7972173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1645	7972173	125879722	7850	15835										
C3AR1	719	broad.mit.edu	37	chr12	8211979	8211979	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggaaacccactggggattTtaggtgagaccacatcagca	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8211979T>G	ENST00000307637.4	-	2	1006	c.803A>C	c.(802-804)aAa>aCa	p.K268T		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	268					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.K268T(1)		breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		ACTGGGGATTTTAGGTGAGAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											66	69	68					12																	8211979		2203	4300	6503	8103246	SO:0001583	missense	719			U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.803A>C	12.37:g.8211979T>G	ENSP00000302079:p.Lys268Thr		8103246	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	37	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	T	0.269	-0.994034	0.02145	.	.	ENSG00000171860	ENST00000307637	T	0.71222	-0.55	4.63	-2.18	0.07037	GPCR, rhodopsin-like superfamily (1);	1.876120	0.03022	N	0.150913	T	0.43787	0.1263	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15378	-1.0439	10	0.21540	T	0.41	.	1.6782	0.02826	0.2839:0.1819:0.4086:0.1257	.	268	Q16581	C3AR_HUMAN	T	268	ENSP00000302079:K268T	ENSP00000302079:K268T	K	-	2	0	C3AR1	8103246	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.857000	0.04286	-0.289000	0.09038	-1.096000	0.02151	AAA		0.428	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			G	8211979	T	G	8211979	3	3	61	1	0	0	0	0	1	0	0	0	2211	1841	64	4	649	4	C3AR1	12	8211979	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	239806	8211979	125639916	7851	15836										
C3AR1	719	broad.mit.edu	37	chr12	8212307	8212307	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgaagatttcccggtacaCgaacacaggaatgcacatca	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8212307C>T	ENST00000307637.4	-	2	678	c.475G>A	c.(475-477)Gtg>Atg	p.V159M		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	159					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.V159M(1)		breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		TCCCGGTACACGAACACAGGA	0.448													C|||	1	0.000199681	0	0	5008	,	,		-128	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	12											182	151	161					12																	8212307		2203	4300	6503	8103574	SO:0001583	missense	719			U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.475G>A	12.37:g.8212307C>T	ENSP00000302079:p.Val159Met		8103574	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	37	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	C	2.629	-0.286726	0.05605	.	.	ENSG00000171860	ENST00000307637	T	0.72505	-0.66	5.46	-10.9	0.00192	GPCR, rhodopsin-like superfamily (1);	2.176640	0.02069	N	0.051428	T	0.53932	0.1827	L	0.38953	1.18	0.09310	N	1	B	0.23377	0.084	B	0.25291	0.059	T	0.35968	-0.9767	10	0.29301	T	0.29	.	6.8046	0.23770	0.0969:0.529:0.1505:0.2236	.	159	Q16581	C3AR_HUMAN	M	159	ENSP00000302079:V159M	ENSP00000302079:V159M	V	-	1	0	C3AR1	8103574	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.941000	0.01542	-2.638000	0.00430	-1.202000	0.01658	GTG		0.448	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			T	8212307	C	T	8212307	3	4	61	1	0	0	0	0	1	0	0	0	2211	536	19	1	977	1	C3AR1	12	8212307	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	328	8212307	125639588	7852	15837										
ZNF705A	440077	broad.mit.edu	37	chr12	8329638	8329638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttttgaatgtaatgattCgggagaagattgcactcaca	9	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8329638C>T	ENST00000359286.4	+	5	451	c.362C>T	c.(361-363)tCg>tTg	p.S121L		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	121					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S121L(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		TGTAATGATTCGGGAGAAGAT	0.388													c|||	2	0.000399361	0.0015	0	5008	,	,		-128	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											86	88	87					12																	8329638		2202	4291	6493	8220905	SO:0001583	missense	440077			AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"Zinc fingers, C2H2-type", "-"	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.362C>T	12.37:g.8329638C>T	ENSP00000352233:p.Ser121Leu		8220905		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	.	.	.	.	.	.	.	.	.	.	.	2.620	-0.288826	0.05605	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.01560	4.77;4.77	1.35	0.0886	0.14455	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01254	0.0041	N	0.14661	0.345	0.24768	N	0.992889	B	0.02656	0.0	B	0.01281	0.0	T	0.46247	-0.9205	9	0.56958	D	0.05	.	4.8955	0.13748	0.0:0.1923:0.0:0.8077	.	121	Q6ZN79	Z705A_HUMAN	L	121	ENSP00000379816:S121L;ENSP00000352233:S121L	ENSP00000352233:S121L	S	+	2	0	ZNF705A	8220905	0.865000	0.29922	0.060000	0.19600	0.032000	0.12392	1.279000	0.33191	0.021000	0.15133	-0.939000	0.02691	TCG		0.388	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328		T	8329638	C	T	8329638	3	4	61	1	0	0	0	0	1	0	0	0	18147	893	31	1	380	1	ZNF705A	12	8329638	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117331	8329638	125522257	7853	15838										
CLEC4E	26253	broad.mit.edu	37	chr12	8688692	8688692	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagggtaattacctcagaGactttgtcaaaggtgtgccg	13	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8688692G>T	ENST00000299663.3	-	5	647	c.482C>A	c.(481-483)tCt>tAt	p.S161Y	CLEC4E_ENST00000545274.1_Missense_Mutation_p.S116Y|CLEC4E_ENST00000446457.2_Intron	NM_014358.2	NP_055173.1	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E	161	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.S161Y(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Lung SC(5;0.184)					TTACCTCAGAGACTTTGTCAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	82	84					12																	8688692		2203	4300	6503	8579959	SO:0001583	missense	26253			AB024718	CCDS8594.1	12p13.31	2005-02-09		2005-02-09	ENSG00000166523	ENSG00000166523		"C-type lectin domain containing"	14555	protein-coding gene	gene with protein product		609962	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 9"	CLECSF9		10528209	Standard	NM_014358		Approved	mincle	uc001quo.1	Q9ULY5	OTTHUMG00000168675	ENST00000299663.3:c.482C>A	12.37:g.8688692G>T	ENSP00000299663:p.Ser161Tyr		8579959	B2R6Q6	Missense_Mutation	SNP	ENST00000299663.3	37	CCDS8594.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.599443	0.66332	.	.	ENSG00000166523	ENST00000299663;ENST00000545274	T;T	0.20463	2.15;2.07	5.53	2.48	0.30137	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.566609	0.16128	N	0.228344	T	0.30262	0.0759	L	0.38175	1.15	0.09310	N	1	D	0.59767	0.986	D	0.64237	0.923	T	0.04178	-1.0971	10	0.72032	D	0.01	.	8.7848	0.34814	0.0:0.1443:0.5587:0.2969	.	161	Q9ULY5	CLC4E_HUMAN	Y	161;116	ENSP00000299663:S161Y;ENSP00000443034:S116Y	ENSP00000299663:S161Y	S	-	2	0	CLEC4E	8579959	0.049000	0.20398	0.341000	0.25589	0.779000	0.44077	1.330000	0.33781	0.784000	0.33661	0.585000	0.79938	TCT		0.443	CLEC4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400566.1	NM_014358		T	8688692	G	T	8688692	3	4	61	1	0	0	0	0	1	0	0	0	3521	942	33	2	185	2	CLEC4E	12	8688692	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	359054	8688692	125163203	7854	15839										
RIMKLB	57494	broad.mit.edu	37	chr12	8902460	8902460	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatttatatatttcaggtCtgcggatcaatggagagcta	10	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8902460C>A	ENST00000538135.1	+	3	1003	c.178C>A	c.(178-180)Ctg>Atg	p.L60M	RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000535829.1_Missense_Mutation_p.L60M|RIMKLB_ENST00000357529.3_Missense_Mutation_p.L60M			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	60					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.L60M(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TATTTCAGGTCTGCGGATCAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											33	32	32					12																	8902460		1872	4103	5975	8793727	SO:0001583	missense	57494			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"N-acetylaspartyl-glutamate synthetase"	614054	"family with sequence similarity 80, member B"	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.178C>A	12.37:g.8902460C>A	ENSP00000440943:p.Leu60Met		8793727	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	37	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	C	8.623	0.891763	0.17613	.	.	ENSG00000166532	ENST00000541044;ENST00000539923;ENST00000537189;ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	5.47	2.63	0.31362	.	0.000000	0.56097	U	0.000031	T	0.37544	0.1007	L	0.38838	1.175	0.45318	D	0.998315	B;B	0.31009	0.303;0.061	B;B	0.29942	0.109;0.034	T	0.15925	-1.0420	9	0.59425	D	0.04	.	5.2434	0.15483	0.1422:0.6254:0.0:0.2324	.	60;60	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	M	60;60;121;60;60;60	.	ENSP00000350136:L60M	L	+	1	2	RIMKLB	8793727	1.000000	0.71417	0.570000	0.28473	0.274000	0.26718	2.910000	0.48766	0.266000	0.21894	0.591000	0.81541	CTG		0.403	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		A	8902460	C	A	8902460	3	1	61	1	0	0	0	0	1	0	0	0	13403	912	32	2	184	2	RIMKLB	12	8902460	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213768	8902460	124949435	7855	15840										
RIMKLB	57494	broad.mit.edu	37	chr12	8902618	8902618	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaagccatcctgaactgCgttaataagttctggacatt	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8902618C>T	ENST00000538135.1	+	3	1161	c.336C>T	c.(334-336)tgC>tgT	p.C112C	RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000535829.1_Silent_p.C112C|RIMKLB_ENST00000357529.3_Silent_p.C112C			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	112					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.C112C(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCCTGAACTGCGTTAATAAGT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	12											99	93	95					12																	8902618		1924	4115	6039	8793885	SO:0001819	synonymous_variant	57494			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"N-acetylaspartyl-glutamate synthetase"	614054	"family with sequence similarity 80, member B"	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.336C>T	12.37:g.8902618C>T			8793885	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Silent	SNP	ENST00000538135.1	37	CCDS41748.1																																																																																				0.473	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		T	8902618	C	T	8902618	2	4	61	1	0	0	0	0	0	0	0	1	13403	776	27	1		1	RIMKLB	12	8902618	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158	8902618	124949277	7856	15841										
A2ML1	144568	broad.mit.edu	37	chr12	8975916	8975916	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacccagaagttgctagaAtactctggactgaagaagag	11	7	1	6	rs371564965		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8975916A>C	ENST00000299698.7	+	2	381	c.201A>C	c.(199-201)gaA>gaC	p.E67D	A2ML1-AS2_ENST00000394240.3_RNA|A2ML1-AS1_ENST00000537288.1_RNA	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.E67D(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AGTTGCTAGAATACTCTGGAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											99	99	99					12																	8975916		1932	4131	6063	8867183	SO:0001583	missense	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.201A>C	12.37:g.8975916A>C	ENSP00000299698:p.Glu67Asp		8867183		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	A	12.09	1.834747	0.32421	.	.	ENSG00000166535	ENST00000299698;ENST00000539161	T	0.34072	1.38	4.25	1.85	0.25348	.	0.355450	0.21084	N	0.080427	T	0.15565	0.0375	N	0.08118	0	0.31747	N	0.635077	B	0.23490	0.086	B	0.24269	0.052	T	0.10730	-1.0617	10	0.30854	T	0.27	.	4.4525	0.11628	0.6969:0.1993:0.1038:0.0	.	67	A8K2U0	A2ML1_HUMAN	D	67	ENSP00000299698:E67D	ENSP00000299698:E67D	E	+	3	2	A2ML1	8867183	0.080000	0.21391	0.164000	0.22755	0.950000	0.60333	0.625000	0.24477	0.397000	0.25310	0.460000	0.39030	GAA		0.473	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		C	8975916	A	C	8975916	3	2	61	1	0	0	0	0	1	0	0	0	5	98	4	4	207	4	A2ML1	12	8975916	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73298	8975916	124875979	7857	15842										
A2ML1	144568	broad.mit.edu	37	chr12	8995759	8995759	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatggaagacttagtataTaatccggaacaagtgccacg	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:8995759T>C	ENST00000299698.7	+	12	1458	c.1278T>C	c.(1276-1278)taT>taC	p.Y426Y	A2ML1_ENST00000539547.1_5'Flank	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.Y426Y(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ACTTAGTATATAATCCGGAAC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	12											87	88	87					12																	8995759		1937	4137	6074	8887026	SO:0001819	synonymous_variant	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1278T>C	12.37:g.8995759T>C			8887026		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																				0.478	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		C	8995759	T	C	8995759	2	2	61	1	0	0	0	0	0	0	0	1	5	1413	49	4		4	A2ML1	12	8995759	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19843	8995759	124856136	7858	15843										
A2ML1	144568	broad.mit.edu	37	chr12	9001387	9001387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtatgatcagtgtccagtGtctggcccatgggactttcc	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9001387G>A	ENST00000299698.7	+	16	2085	c.1905G>A	c.(1903-1905)gtG>gtA	p.V635V	A2ML1_ENST00000539547.1_Silent_p.V144V|A2ML1_ENST00000540049.1_3'UTR	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.V635V(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AGTGTCCAGTGTCTGGCCCAT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											187	174	178					12																	9001387		1977	4154	6131	8892654	SO:0001819	synonymous_variant	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1905G>A	12.37:g.9001387G>A			8892654		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																				0.532	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		A	9001387	G	A	9001387	2	1	61	1	0	0	0	0	0	0	0	1	5	1364	48	3		3	A2ML1	12	9001387	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5628	9001387	124850508	7859	15844										
A2ML1	144568	broad.mit.edu	37	chr12	9007408	9007408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtggagaagacacacagCtcattgctgtgcccaaaagg	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9007408C>T	ENST00000299698.7	+	22	2925	c.2745C>T	c.(2743-2745)agC>agT	p.S915S	A2ML1_ENST00000539547.1_Silent_p.S424S	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.S915S(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AGACACACAGCTCATTGCTGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	12											85	86	86					12																	9007408		1953	4154	6107	8898675	SO:0001819	synonymous_variant	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2745C>T	12.37:g.9007408C>T			8898675		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																				0.443	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9007408	C	T	9007408	2	4	61	1	0	0	0	0	0	0	0	1	5	796	28	3		3	A2ML1	12	9007408	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6021	9007408	124844487	7860	15845										
A2ML1	144568	broad.mit.edu	37	chr12	9016534	9016534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgactcaaaaggagatagCgaaggccactagcatagtgg	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9016534C>T	ENST00000299698.7	+	29	3827	c.3647C>T	c.(3646-3648)gCg>gTg	p.A1216V	A2ML1_ENST00000539547.1_Missense_Mutation_p.A725V	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.A1216V(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AAGGAGATAGCGAAGGCCACT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											71	72	72					12																	9016534		1959	4131	6090	8907801	SO:0001583	missense	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3647C>T	12.37:g.9016534C>T	ENSP00000299698:p.Ala1216Val		8907801		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991770	0.54041	.	.	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.38077	1.16;1.16;1.16	4.38	2.52	0.30459	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.545863	0.16521	N	0.210810	T	0.28300	0.0699	L	0.28458	0.855	0.23162	N	0.9982	P	0.51147	0.942	P	0.48627	0.584	T	0.06006	-1.0851	10	0.40728	T	0.16	.	4.3714	0.11249	0.1613:0.592:0.1567:0.09	.	1216	A8K2U0	A2ML1_HUMAN	V	1216;1216;766;725	ENSP00000299698:A1216V;ENSP00000443174:A766V;ENSP00000438292:A725V	ENSP00000299698:A1216V	A	+	2	0	A2ML1	8907801	0.000000	0.05858	0.995000	0.50966	0.952000	0.60782	-0.043000	0.12043	1.173000	0.42796	0.591000	0.81541	GCG		0.532	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9016534	C	T	9016534	3	4	61	1	0	0	0	0	1	0	0	0	5	768	27	1	3761	1	A2ML1	12	9016534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9126	9016534	124835361	7861	15846										
A2M	2	broad.mit.edu	37	chr12	9232361	9232361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctctccacagccataggGcatctggagaagattttgtg	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9232361G>A	ENST00000318602.7	-	24	3212	c.2905C>T	c.(2905-2907)Ccc>Tcc	p.P969S	A2M_ENST00000542567.1_5'UTR	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	969					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.P969S(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CAGCCATAGGGCATCTGGAGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											111	106	107					12																	9232361		2067	4240	6307	9123628	SO:0001583	missense	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2905C>T	12.37:g.9232361G>A	ENSP00000323929:p.Pro969Ser		9123628	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034824	0.93575	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	D	0.95821	-3.82	5.08	5.08	0.68730	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);Alpha-2-macroglobulin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98735	0.9575	H	0.97962	4.115	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99671	1.0996	10	0.87932	D	0	.	18.4343	0.90638	0.0:0.0:1.0:0.0	.	969	P01023	A2MG_HUMAN	S	969;984	ENSP00000323929:P969S	ENSP00000323929:P969S	P	-	1	0	A2M	9123628	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.570000	0.98174	2.525000	0.85131	0.467000	0.42956	CCC		0.423	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9232361	G	A	9232361	3	1	61	1	0	0	0	0	1	0	0	0	4	1203	42	3	1571	3	A2M	12	9232361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215827	9232361	124619534	7862	15847										
A2M	2	broad.mit.edu	37	chr12	9243030	9243030	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaggcgcttgttccttctCcactgggacagctaggaagg	14	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9243030C>A	ENST00000318602.7	-	20	2825	c.2518G>T	c.(2518-2520)Gag>Tag	p.E840*		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	840					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.E840*(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TGTTCCTTCTCCACTGGGACA	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											103	107	105					12																	9243030		2125	4266	6391	9134297	SO:0001587	stop_gained	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2518G>T	12.37:g.9243030C>A	ENSP00000323929:p.Glu840*		9134297	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Nonsense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.24|12.24	1.879375|1.879375	0.33162|0.33162	.|.	.|.	ENSG00000175899|ENSG00000175899	ENST00000318602;ENST00000540099|ENST00000543436	.|.	.|.	.|.	5.23|5.23	3.33|3.33	0.38152|0.38152	.|.	0.453502|.	0.20600|.	N|.	0.089169|.	.|T	.|0.43743	.|0.1261	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.52132	.|-0.8616	.|3	0.07644|.	T|.	0.81|.	.|.	7.6277|7.6277	0.28222|0.28222	0.0:0.7224:0.0:0.2776|0.0:0.7224:0.0:0.2776	.|.	.|.	.|.	.|.	X|C	840;855|87	.|.	ENSP00000323929:E840X|.	E|W	-|-	1|3	0|0	A2M|A2M	9134297|9134297	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.054000|0.054000	0.15201|0.15201	0.683000|0.683000	0.25349|0.25349	0.642000|0.642000	0.30620|0.30620	0.655000|0.655000	0.94253|0.94253	GAG|TGG		0.532	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9243030	C	A	9243030	4	1	61	1	0	0	0	0	0	1	0	0	4	864	30	2	1974	2	A2M	12	9243030	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10669	9243030	124608865	7863	15848										
PZP	5858	broad.mit.edu	37	chr12	9305864	9305864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgaatcctgaacggtgaCctgtgcagttttctcagttc	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9305864C>T	ENST00000261336.2	-	30	3878	c.3850G>A	c.(3850-3852)Gtc>Atc	p.V1284I	PZP_ENST00000381997.2_Missense_Mutation_p.V1070I	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1284					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.V1284I(1)|p.V1070I(1)|p.V1070F(1)|p.V1284F(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TGAACGGTGACCTGTGCAGTT	0.507																																					Melanoma(125;1402 1695 4685 34487 38571)											4	Substitution - Missense(4)	large_intestine(2)|lung(2)	12											107	108	108					12																	9305864		2203	4300	6503	9197131	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3850G>A	12.37:g.9305864C>T	ENSP00000261336:p.Val1284Ile		9197131	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827486	0.71143	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.43294	1.05;0.95	3.92	3.92	0.45320	.	0.351376	0.22503	U	0.059214	T	0.68467	0.3004	M	0.87900	2.915	0.37903	D	0.931099	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.972	T	0.77354	-0.2619	10	0.51188	T	0.08	.	16.3675	0.83338	0.0:1.0:0.0:0.0	.	1070;1284	P20742-2;P20742	.;PZP_HUMAN	I	1284;1070	ENSP00000261336:V1284I;ENSP00000371427:V1070I	ENSP00000261336:V1284I	V	-	1	0	PZP	9197131	0.002000	0.14202	0.024000	0.17045	0.002000	0.02628	0.986000	0.29590	2.135000	0.66039	0.557000	0.71058	GTC		0.507	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9305864	C	T	9305864	3	4	61	1	0	0	0	0	1	0	0	0	12906	507	18	3	626	3	PZP	12	9305864	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62834	9305864	124546031	7864	15849										
PZP	5858	broad.mit.edu	37	chr12	9318677	9318677	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaactcccagatccaagtCtcaggaaaatagcttcgcac	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9318677C>A	ENST00000261336.2	-	18	2257	c.2229G>T	c.(2227-2229)gaG>gaT	p.E743D	PZP_ENST00000381997.2_Missense_Mutation_p.E612D|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	743					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E743D(1)|p.E612D(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						AGATCCAAGTCTCAGGAAAAT	0.428																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											151	142	145					12																	9318677		2203	4300	6503	9209944	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2229G>T	12.37:g.9318677C>A	ENSP00000261336:p.Glu743Asp		9209944	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.722294	0.48728	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.54675	0.78;0.56	3.58	1.7	0.24286	.	0.000000	0.64402	U	0.000015	T	0.53384	0.1793	L	0.29908	0.895	0.22096	N	0.999369	D;D;D	0.76494	0.999;0.985;0.999	D;P;D	0.70227	0.968;0.882;0.968	T	0.34279	-0.9835	10	0.62326	D	0.03	.	6.5173	0.22254	0.0:0.7552:0.0:0.2448	.	743;612;743	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	D	743;612	ENSP00000261336:E743D;ENSP00000371427:E612D	ENSP00000261336:E743D	E	-	3	2	PZP	9209944	0.972000	0.33761	1.000000	0.80357	0.661000	0.39034	0.087000	0.14958	0.798000	0.33994	0.467000	0.42956	GAG		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9318677	C	A	9318677	3	1	61	1	0	0	0	0	1	0	0	0	12906	912	32	2	2295	2	PZP	12	9318677	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12813	9318677	124533218	7865	15850										
PZP	5858	broad.mit.edu	37	chr12	9346787	9346787	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtcattcacagagatgaaGaagagtttattggggatggg	15	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9346787G>T	ENST00000261336.2	-	11	1168	c.1140C>A	c.(1138-1140)ttC>ttA	p.F380L	PZP_ENST00000381997.2_Missense_Mutation_p.F249L	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	380					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F249L(1)|p.F380L(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CAGAGATGAAGAAGAGTTTAT	0.423																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											179	166	171					12																	9346787		2203	4300	6503	9238054	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1140C>A	12.37:g.9346787G>T	ENSP00000261336:p.Phe380Leu		9238054	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.132971	0.37630	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.30714	1.72;1.52	3.53	2.63	0.31362	.	0.322334	0.20700	U	0.087284	T	0.09158	0.0226	N	0.00841	-1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24941	-1.0146	10	0.34782	T	0.22	.	7.4433	0.27196	0.1312:0.0:0.8688:0.0	.	249;380	P20742-2;P20742	.;PZP_HUMAN	L	380;249	ENSP00000261336:F380L;ENSP00000371427:F249L	ENSP00000261336:F380L	F	-	3	2	PZP	9238054	0.001000	0.12720	0.121000	0.21740	0.443000	0.32047	-0.209000	0.09358	0.788000	0.33755	0.557000	0.71058	TTC		0.423	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9346787	G	T	9346787	3	4	61	1	0	0	0	0	1	0	0	0	12906	933	33	2	3412	2	PZP	12	9346787	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28110	9346787	124505108	7866	15851										
PZP	5858	broad.mit.edu	37	chr12	9353924	9353924	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactttttctgatacttaccTcaaggtatatcagtggaatc	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9353924T>G	ENST00000261336.2	-	5	528	c.500A>C	c.(499-501)gAg>gCg	p.E167A	PZP_ENST00000381997.2_Splice_Site_p.E36A	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	167					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E36A(1)|p.E167A(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GATACTTACCTCAAGGTATAT	0.318																																					Melanoma(125;1402 1695 4685 34487 38571)											2	Substitution - Missense(2)	large_intestine(2)	12											50	53	52					12																	9353924		2203	4294	6497	9245191	SO:0001630	splice_region_variant	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.501+1A>C	12.37:g.9353924T>G			9245191	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.389302	0.42410	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.74209	-0.82;-0.82	2.19	2.19	0.27852	Alpha-2-macroglobulin, N-terminal (1);	0.352956	0.20219	U	0.096738	T	0.79155	0.4398	M	0.82517	2.595	0.23198	N	0.998137	P;P	0.48911	0.917;0.873	P;P	0.51945	0.62;0.685	T	0.69859	-0.5031	10	0.72032	D	0.01	.	6.3433	0.21335	0.0:0.0:0.0:1.0	.	36;167	P20742-2;P20742	.;PZP_HUMAN	A	167;36	ENSP00000261336:E167A;ENSP00000371427:E36A	ENSP00000261336:E167A	E	-	2	0	PZP	9245191	1.000000	0.71417	0.984000	0.44739	0.054000	0.15201	2.923000	0.48868	1.271000	0.44313	0.460000	0.39030	GAG		0.318	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	Missense_Mutation	G	9353924	T	G	9353924	5	3	61	1	0	0	0	0	0	0	1	0	12906	1565	54	4	4076	4	PZP	12	9353924	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7137	9353924	124497971	7867	15852										
KLRB1	3820	broad.mit.edu	37	chr12	9747911	9747911	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctcacaggtgttagttCtttttggcagatccatctga	8	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9747911C>A	ENST00000229402.3	-	6	683	c.637G>T	c.(637-639)Gaa>Taa	p.E213*		NM_002258.2	NP_002249.1	Q12918	KLRB1_HUMAN	killer cell lectin-like receptor subfamily B, member 1	213					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.E213*(1)		endometrium(2)|large_intestine(6)|lung(4)	12						GGTGTTAGTTCTTTTTGGCAG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											174	157	163					12																	9747911		2203	4300	6503	9639178	SO:0001587	stop_gained	3820			U11276	CCDS8601.1	12p13	2014-05-22			ENSG00000111796	ENSG00000111796		"Killer cell lectin-like receptors", "CD molecules", "C-type lectin domain containing"	6373	protein-coding gene	gene with protein product		602890		NKR		8077657	Standard	NM_002258		Approved	CD161, NKR-P1, NKR-P1A, hNKR-P1A, CLEC5B	uc010sgt.2	Q12918	OTTHUMG00000168581	ENST00000229402.3:c.637G>T	12.37:g.9747911C>A	ENSP00000229402:p.Glu213*		9639178	Q24K24	Nonsense_Mutation	SNP	ENST00000229402.3	37	CCDS8601.1	.	.	.	.	.	.	.	.	.	.	.	12.94	2.089361	0.36855	.	.	ENSG00000111796	ENST00000229402	.	.	.	3.11	1.22	0.21188	.	0.423542	0.17374	N	0.176559	.	.	.	.	.	.	0.40040	D	0.975648	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-2.104	4.4567	0.11647	0.0:0.6358:0.232:0.1323	.	.	.	.	X	213	.	ENSP00000229402:E213X	E	-	1	0	KLRB1	9639178	0.889000	0.30405	0.551000	0.28230	0.023000	0.10783	0.156000	0.16382	0.335000	0.23614	-0.300000	0.09419	GAA		0.378	KLRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400280.1	NM_002258		A	9747911	C	A	9747911	4	1	61	1	0	0	0	0	0	1	0	0	8435	922	32	2	43	2	KLRB1	12	9747911	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	393987	9747911	124103984	7868	15853										
KLRB1	3820	broad.mit.edu	37	chr12	9760354	9760354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattaaagccacttaccccGaggaagagatgaaggtgaag	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9760354G>A	ENST00000229402.3	-	1	128	c.82C>T	c.(82-84)Cgg>Tgg	p.R28W		NM_002258.2	NP_002249.1	Q12918	KLRB1_HUMAN	killer cell lectin-like receptor subfamily B, member 1	28					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R28W(1)		endometrium(2)|large_intestine(6)|lung(4)	12						CACTTACCCCGAGGAAGAGAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											160	135	143					12																	9760354		2203	4300	6503	9651621	SO:0001583	missense	3820			U11276	CCDS8601.1	12p13	2014-05-22			ENSG00000111796	ENSG00000111796		"Killer cell lectin-like receptors", "CD molecules", "C-type lectin domain containing"	6373	protein-coding gene	gene with protein product		602890		NKR		8077657	Standard	NM_002258		Approved	CD161, NKR-P1, NKR-P1A, hNKR-P1A, CLEC5B	uc010sgt.2	Q12918	OTTHUMG00000168581	ENST00000229402.3:c.82C>T	12.37:g.9760354G>A	ENSP00000229402:p.Arg28Trp		9651621	Q24K24	Missense_Mutation	SNP	ENST00000229402.3	37	CCDS8601.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.446558	0.63178	.	.	ENSG00000111796	ENST00000229402	T	0.29917	1.55	2.89	1.0	0.19881	.	1.643360	0.04072	N	0.308271	T	0.25901	0.0631	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.53988	0.739	T	0.16541	-1.0399	10	0.66056	D	0.02	.	4.1234	0.10116	0.1401:0.2435:0.6164:0.0	.	28	Q12918	KLRB1_HUMAN	W	28	ENSP00000229402:R28W	ENSP00000229402:R28W	R	-	1	2	KLRB1	9651621	0.997000	0.39634	0.091000	0.20842	0.745000	0.42441	2.282000	0.43461	0.262000	0.21774	0.591000	0.81541	CGG		0.413	KLRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400280.1	NM_002258		A	9760354	G	A	9760354	3	1	61	1	0	0	0	0	1	0	0	0	8435	1057	37	1	618	1	KLRB1	12	9760354	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12443	9760354	124091541	7869	15854										
KLRF1	51348	broad.mit.edu	37	chr12	9984941	9984941	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacgttgcactggtataaaAtcttactgggaatatctgga	10	6	2	1	rs373947558		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:9984941A>C	ENST00000279544.3	+	2	179	c.115A>C	c.(115-117)Atc>Ctc	p.I39L	KLRF1_ENST00000354855.3_Missense_Mutation_p.I39L|KLRF1_ENST00000324214.4_Missense_Mutation_p.I39L|KLRF1_ENST00000537723.1_Missense_Mutation_p.I39L	NM_016523.1	NP_057607	Q9NZS2	KLRF1_HUMAN	killer cell lectin-like receptor subfamily F, member 1	39					cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|MHC class I receptor activity (GO:0032393)|transmembrane signaling receptor activity (GO:0004888)	p.I39L(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(6)	13						CTGGTATAAAATCTTACTGGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											138	130	132					12																	9984941		1819	4083	5902	9876208	SO:0001583	missense	51348			AF175206	CCDS41750.1	12p13.31	2011-08-30			ENSG00000150045	ENSG00000150045		"Killer cell lectin-like receptors", "C-type lectin domain containing"	13342	protein-coding gene	gene with protein product		605029				10671213	Standard	NM_001291823		Approved	CLEC5C, NKp80	uc021qux.1	Q9NZS2		ENST00000279544.3:c.115A>C	12.37:g.9984941A>C	ENSP00000279544:p.Ile39Leu		9876208	Q4KMT5|Q96PR2|Q96PR3|Q9NZS1	Missense_Mutation	SNP	ENST00000279544.3	37	CCDS41750.1	.	.	.	.	.	.	.	.	.	.	A	6.338	0.430468	0.12045	.	.	ENSG00000150045	ENST00000354855;ENST00000324214;ENST00000279544;ENST00000537723	T;T;T	0.53423	4.72;5.04;0.62	2.92	0.501	0.16925	.	.	.	.	.	T	0.27027	0.0662	L	0.27053	0.805	0.09310	N	1	B;B;B	0.32101	0.062;0.356;0.057	B;B;B	0.26614	0.015;0.071;0.023	T	0.12734	-1.0536	8	.	.	.	.	4.822	0.13396	0.7187:0.0:0.2813:0.0	.	39;39;39	Q9NZS2;Q4KN30;Q9NZS2-2	KLRF1_HUMAN;.;.	L	39	ENSP00000322487:I39L;ENSP00000279544:I39L;ENSP00000443054:I39L	.	I	+	1	0	KLRF1	9876208	0.755000	0.28372	0.092000	0.20876	0.194000	0.23727	0.930000	0.28858	0.101000	0.17610	0.528000	0.53228	ATC		0.323	KLRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399535.1	NM_016523		C	9984941	A	C	9984941	3	2	61	1	0	0	0	0	1	0	0	0	8441	101	4	4	121	4	KLRF1	12	9984941	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	224587	9984941	123866954	7870	15855										
CLEC1B	51266	broad.mit.edu	37	chr12	10145858	10145858	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaataagcacaattcatatTtccttttccatcttccaaaa	1	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10145858T>G	ENST00000298527.6	-	6	753	c.574A>C	c.(574-576)Aat>Cat	p.N192H	CLEC1B_ENST00000428126.2_Missense_Mutation_p.N159H|CLEC1B_ENST00000348658.4_Missense_Mutation_p.N159H	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	192	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.N101H(1)|p.N192H(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CAATTCATATTTCCTTTTCCA	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	12											100	91	94					12																	10145858		1848	4086	5934	10037125	SO:0001583	missense	51266			AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.574A>C	12.37:g.10145858T>G	ENSP00000298527:p.Asn192His		10037125	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	T	12.64	1.998903	0.35226	.	.	ENSG00000165682	ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939	T;T;T	0.19105	2.17;2.17;2.17	4.17	2.8	0.32819	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.289707	0.25241	N	0.032087	T	0.40645	0.1125	M	0.81497	2.545	0.31529	N	0.661413	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.47005	-0.9150	10	0.62326	D	0.03	.	4.2016	0.10469	0.0:0.2072:0.0:0.7928	.	159;192	Q9P126-2;Q9P126	.;CLC1B_HUMAN	H	159;192;159;101	ENSP00000406338:N159H;ENSP00000298527:N192H;ENSP00000327169:N159H	ENSP00000298527:N192H	N	-	1	0	CLEC1B	10037125	0.954000	0.32549	0.999000	0.59377	0.295000	0.27426	0.788000	0.26872	1.633000	0.50488	0.402000	0.26972	AAT		0.368	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		G	10145858	T	G	10145858	3	3	61	1	0	0	0	0	1	0	0	0	3512	1841	64	4	119	4	CLEC1B	12	10145858	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160917	10145858	123706037	7871	15856										
CLEC1B	51266	broad.mit.edu	37	chr12	10147815	10147815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgagataatccgacccaacGaattaaatgagtcctggctt	9	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10147815G>A	ENST00000298527.6	-	5	648	c.469C>T	c.(469-471)Cgt>Tgt	p.R157C	CLEC1B_ENST00000428126.2_Missense_Mutation_p.R124C|CLEC1B_ENST00000348658.4_Missense_Mutation_p.R124C	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	157	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R157C(1)|p.?(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CCGACCCAACGAATTAAATGA	0.418																																																2	Substitution - Missense(1)|Unknown(1)	large_intestine(2)	12											258	248	251					12																	10147815		1853	4089	5942	10039082	SO:0001583	missense	51266			AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.469C>T	12.37:g.10147815G>A	ENSP00000298527:p.Arg157Cys		10039082	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.26|16.26	3.072111|3.072111	0.55646|0.55646	.|.	.|.	ENSG00000165682|ENSG00000165682	ENST00000398939|ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658	.|T;T;T;T	.|0.18338	.|2.22;2.22;2.22;2.22	3.83|3.83	3.83|3.83	0.44106|0.44106	.|C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.|0.000000	.|0.48767	.|D	.|0.000165	.|T	.|0.37433	.|0.1003	M|M	0.69823|0.69823	2.125|2.125	0.50632|0.50632	D|D	0.999883|0.999883	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	.|T	.|0.08953	.|-1.0697	.|10	.|0.40728	.|T	.|0.16	.|.	11.1397|11.1397	0.48396|0.48396	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|124;157	.|Q9P126-2;Q9P126	.|.;CLC1B_HUMAN	.|C	-1|64;124;157;124	.|ENSP00000381910:R64C;ENSP00000406338:R124C;ENSP00000298527:R157C;ENSP00000327169:R124C	.|ENSP00000298527:R157C	.|R	-|-	.|1	.|0	CLEC1B|CLEC1B	10039082|10039082	0.999000|0.999000	0.42202|0.42202	0.960000|0.960000	0.40013|0.40013	0.644000|0.644000	0.38419|0.38419	4.365000|4.365000	0.59486|0.59486	1.954000|1.954000	0.56735|0.56735	0.298000|0.298000	0.19748|0.19748	.|CGT		0.418	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		A	10147815	G	A	10147815	3	1	61	1	0	0	0	0	1	0	0	0	3512	1058	37	1	228	1	CLEC1B	12	10147815	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1957	10147815	123704080	7872	15857										
CLEC1A	51267	broad.mit.edu	37	chr12	10228193	10228193	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacttttgctgtctttataGaactggtagcaattgtctcc	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10228193G>T	ENST00000315330.4	-	4	515	c.453C>A	c.(451-453)ttC>ttA	p.F151L	CLEC1A_ENST00000457018.2_Missense_Mutation_p.F118L|CLEC1A_ENST00000420265.2_Missense_Mutation_p.F59L	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	151	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.F151L(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						TGTCTTTATAGAACTGGTAGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											139	133	135					12																	10228193		2203	4300	6503	10119460	SO:0001583	missense	51267			AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.453C>A	12.37:g.10228193G>T	ENSP00000326407:p.Phe151Leu		10119460	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	37	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789295	0.70337	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.19394	2.15;2.15;2.15	5.06	2.21	0.28008	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.64402	D	0.000017	T	0.34019	0.0883	L	0.58428	1.81	0.30502	N	0.770263	B;D;P	0.63880	0.296;0.993;0.869	B;D;P	0.68192	0.097;0.956;0.751	T	0.14980	-1.0453	10	0.41790	T	0.15	.	6.3919	0.21591	0.3012:0.0:0.6988:0.0	.	59;118;151	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	L	151;118;59	ENSP00000326407:F151L;ENSP00000415048:F118L;ENSP00000417010:F59L	ENSP00000326407:F151L	F	-	3	2	CLEC1A	10119460	0.929000	0.31497	0.929000	0.37066	0.954000	0.61252	0.534000	0.23098	0.654000	0.30846	0.655000	0.94253	TTC		0.383	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		T	10228193	G	T	10228193	3	4	61	1	0	0	0	0	1	0	0	0	3511	933	33	2	401	2	CLEC1A	12	10228193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80378	10228193	123623702	7873	15858										
CLEC7A	64581	broad.mit.edu	37	chr12	10282677	10282677	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctaaatcaggatgatatTccattgttcttgagagcccc	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10282677T>G	ENST00000304084.8	-	1	159	c.5A>C	c.(4-6)gAa>gCa	p.E2A	CLEC7A_ENST00000396484.2_Missense_Mutation_p.E2A|CLEC7A_ENST00000525605.1_Missense_Mutation_p.E2A|CLEC7A_ENST00000298523.5_Missense_Mutation_p.E2A|CLEC7A_ENST00000533022.1_Missense_Mutation_p.E2A|CLEC7A_ENST00000353231.5_Missense_Mutation_p.E2A|CLEC7A_ENST00000310002.4_Missense_Mutation_p.E2A	NM_197947.2	NP_922938.1	Q9BXN2	CLC7A_HUMAN	C-type lectin domain family 7, member A	2					carbohydrate mediated signaling (GO:0009756)|cell recognition (GO:0008037)|defense response to protozoan (GO:0042832)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|MHC protein binding (GO:0042287)|signaling pattern recognition receptor activity (GO:0008329)	p.E2A(2)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						AGGATGATATTCCATTGTTCT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	12											93	85	88					12																	10282677		2201	4300	6501	10173944	SO:0001583	missense	64581			AY009090	CCDS8613.1, CCDS8614.1, CCDS8617.1, CCDS41753.1, CCDS41754.1, CCDS53744.1	12p13.2-p12.3	2014-09-17		2005-02-09	ENSG00000172243	ENSG00000172243		"C-type lectin domain containing"	14558	protein-coding gene	gene with protein product		606264	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 12"	CLECSF12			Standard	XM_005253468		Approved	dectin-1, hDectin-1	uc001qxg.2	Q9BXN2	OTTHUMG00000133597	ENST00000304084.8:c.5A>C	12.37:g.10282677T>G	ENSP00000302569:p.Glu2Ala		10173944	B2R861|B7Z494|B7Z5A9|B7Z5B9|Q6IPS7|Q96D32|Q96DR9|Q96LD3|Q96PA4|Q96PA5|Q96PA6|Q96PA7|Q96PA8|Q9H1K3	Missense_Mutation	SNP	ENST00000304084.8	37	CCDS41753.1	.	.	.	.	.	.	.	.	.	.	T	8.578	0.881540	0.17467	.	.	ENSG00000172243	ENST00000353231;ENST00000298523;ENST00000396484;ENST00000304084;ENST00000533022;ENST00000310002;ENST00000525605	T;T;T;T;T	0.08458	4.84;3.23;4.72;3.09;3.09	4.24	3.07	0.35406	.	0.589948	0.15319	N	0.268640	T	0.08447	0.0210	L	0.42245	1.32	0.19945	N	0.999948	B;B;B;B;B;B;B;B	0.19073	0.033;0.027;0.011;0.019;0.014;0.011;0.002;0.001	B;B;B;B;B;B;B;B	0.19946	0.027;0.015;0.009;0.012;0.014;0.009;0.001;0.002	T	0.23154	-1.0196	10	0.72032	D	0.01	.	7.8602	0.29506	0.0:0.0:0.211:0.789	.	2;2;2;2;2;2;2;2	Q96D32;Q9BXN2-6;Q9BXN2-4;Q9BXN2-5;Q9BXN2-3;Q9BXN2-7;Q9BXN2;Q9BXN2-2	.;.;.;.;.;.;CLC7A_HUMAN;.	A	2	ENSP00000266456:E2A;ENSP00000298523:E2A;ENSP00000379743:E2A;ENSP00000302569:E2A;ENSP00000431461:E2A	ENSP00000298523:E2A	E	-	2	0	CLEC7A	10173944	0.392000	0.25229	0.694000	0.30210	0.433000	0.31745	0.528000	0.23002	0.930000	0.37217	-0.446000	0.05623	GAA		0.393	CLEC7A-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390772.1	NM_197954		G	10282677	T	G	10282677	3	3	61	1	0	0	0	0	1	0	0	0	3527	1783	62	4	798	4	CLEC7A	12	10282677	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	54484	10282677	123569218	7874	15859										
KLRC3	3823	broad.mit.edu	37	chr12	10570992	10570992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactagaagagttctttgaaGcacaggcctgcaaactctct	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10570992G>A	ENST00000396439.2	-	4	481	c.437C>T	c.(436-438)gCt>gTt	p.A146V	KLRC3_ENST00000381903.2_Missense_Mutation_p.A146V|KLRC3_ENST00000381904.2_Missense_Mutation_p.A146V|NKG2-E_ENST00000539033.1_Missense_Mutation_p.A146V	NM_002261.2	NP_002252.2	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C, member 3	146	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular defense response (GO:0006968)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.A146V(1)		large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						GTTCTTTGAAGCACAGGCCTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											158	165	163					12																	10570992		2203	4300	6503	10462259	SO:0001583	missense	3823			L14542	CCDS31744.1, CCDS41755.1	12p13	2008-08-05			ENSG00000205810	ENSG00000205810		"Killer cell lectin-like receptors"	6376	protein-coding gene	gene with protein product		602892				9598306	Standard	NM_002261		Approved	NKG2-E	uc001qyi.1	Q07444	OTTHUMG00000167149	ENST00000396439.2:c.437C>T	12.37:g.10570992G>A	ENSP00000379716:p.Ala146Val		10462259	Q8WXA4|Q96RL0|Q9UP04	Missense_Mutation	SNP	ENST00000396439.2	37	CCDS41755.1	.	.	.	.	.	.	.	.	.	.	g	11.92	1.782504	0.31502	.	.	ENSG00000255641;ENSG00000205810;ENSG00000205810;ENSG00000205810	ENST00000539033;ENST00000396439;ENST00000381904;ENST00000381903	T;T;T;T	0.05855	3.38;3.38;3.38;3.38	2.34	0.377	0.16198	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.662784	0.13524	N	0.381459	T	0.11024	0.0269	M	0.71206	2.165	0.09310	N	1	P;P;P	0.41393	0.51;0.748;0.526	B;P;P	0.48368	0.382;0.575;0.472	T	0.15065	-1.0450	10	0.38643	T	0.18	.	4.1468	0.10220	0.3944:0.0:0.6056:0.0	.	146;146;146	Q07444-2;F5H6K3;Q07444	.;.;NKG2E_HUMAN	V	146	ENSP00000437563:A146V;ENSP00000379716:A146V;ENSP00000371329:A146V;ENSP00000371328:A146V	ENSP00000371328:A146V	A	-	2	0	KLRC3;RP11-277P12.6	10462259	0.001000	0.12720	0.093000	0.20910	0.006000	0.05464	0.504000	0.22626	0.097000	0.17492	0.454000	0.30748	GCT		0.358	KLRC3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393471.1	NM_002261		A	10570992	G	A	10570992	3	1	61	1	0	0	0	0	1	0	0	0	8438	971	34	3	397	3	KLRC3	12	10570992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288315	10570992	123280903	7875	15860										
MAGOHB	55110	broad.mit.edu	37	chr12	10758956	10758956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaccaaatagtaaaatactCgaaggccttcaggatcccta	7	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10758956C>T	ENST00000320756.2	-	5	455	c.365G>A	c.(364-366)cGa>cAa	p.R122Q	MAGOHB_ENST00000539554.1_Missense_Mutation_p.R76Q|MAGOHB_ENST00000381881.2_Missense_Mutation_p.R85Q	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	122					mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R122Q(1)		breast(2)|large_intestine(2)	4						GTAAAATACTCGAAGGCCTTC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	12											29	28	28					12																	10758956		2194	4272	6466	10650223	SO:0001583	missense	55110				CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.365G>A	12.37:g.10758956C>T	ENSP00000319240:p.Arg122Gln		10650223		Missense_Mutation	SNP	ENST00000320756.2	37	CCDS8628.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580203	0.65992	.	.	ENSG00000111196	ENST00000539554;ENST00000320756;ENST00000381881	.	.	.	4.23	4.23	0.50019	.	0.082787	0.46442	U	0.000289	T	0.72128	0.3422	M	0.90650	3.135	0.80722	D	1	B	0.28082	0.2	B	0.27715	0.082	T	0.74940	-0.3493	9	0.44086	T	0.13	.	14.9007	0.70678	0.0:1.0:0.0:0.0	.	122	Q96A72	MGN2_HUMAN	Q	76;122;85	.	ENSP00000319240:R122Q	R	-	2	0	MAGOHB	10650223	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.785000	0.75089	2.615000	0.88500	0.655000	0.94253	CGA		0.279	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		T	10758956	C	T	10758956	3	4	61	1	0	0	0	0	1	0	0	0	9225	884	31	1	85	1	MAGOHB	12	10758956	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187964	10758956	123092939	7876	15861										
TAS2R7	50837	broad.mit.edu	37	chr12	10954720	10954720	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaatcagcgttcaaattCtcagtggctggaaggctaat	10	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10954720C>A	ENST00000240687.2	-	1	506	c.450G>T	c.(448-450)gaG>gaT	p.E150D		NM_023919.2	NP_076408.1	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	150					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.E150D(1)		kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3)	10						CGTTCAAATTCTCAGTGGCTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											106	98	101					12																	10954720		2203	4300	6503	10845987	SO:0001583	missense	50837			AF227133	CCDS8631.1	12p13	2012-08-22			ENSG00000121377	ENSG00000121377		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14913	protein-coding gene	gene with protein product		604793				10761934, 10766242	Standard	NM_023919		Approved	T2R7, TRB4	uc001qyv.3	Q9NYW3	OTTHUMG00000168505	ENST00000240687.2:c.450G>T	12.37:g.10954720C>A	ENSP00000240687:p.Glu150Asp		10845987	Q645Y1	Missense_Mutation	SNP	ENST00000240687.2	37	CCDS8631.1	.	.	.	.	.	.	.	.	.	.	C	0.090	-1.168365	0.01660	.	.	ENSG00000121377	ENST00000240687	T	0.37058	1.22	5.27	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.972564	0.08452	N	0.943826	T	0.30541	0.0768	L	0.47716	1.5	0.09310	N	1	B	0.16166	0.016	B	0.18263	0.021	T	0.34329	-0.9833	10	0.12766	T	0.61	.	8.9883	0.36008	0.0:0.809:0.0:0.191	.	150	Q9NYW3	TA2R7_HUMAN	D	150	ENSP00000240687:E150D	ENSP00000240687:E150D	E	-	3	2	TAS2R7	10845987	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	-0.204000	0.09425	0.692000	0.31613	0.650000	0.86243	GAG		0.423	TAS2R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399931.1			A	10954720	C	A	10954720	3	1	61	1	0	0	0	0	1	0	0	0	15625	912	32	2	510	2	TAS2R7	12	10954720	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	195764	10954720	122897175	7877	15862										
TAS2R9	50835	broad.mit.edu	37	chr12	10962478	10962478	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagagcagcataaagaagCcatctaatgatattacacac	7	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10962478C>A	ENST00000240691.2	-	1	289	c.197G>T	c.(196-198)gGc>gTc	p.G66V	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	66					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)	p.G66V(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CATAAAGAAGCCATCTAATGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	101	102					12																	10962478		2203	4300	6503	10853745	SO:0001583	missense	50835			AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.197G>T	12.37:g.10962478C>A	ENSP00000240691:p.Gly66Val		10853745	Q502V7|Q50KT0|Q50KT1|Q645W9	Missense_Mutation	SNP	ENST00000240691.2	37	CCDS8633.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037904	0.54896	.	.	ENSG00000121381	ENST00000240691	T	0.35236	1.32	4.66	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.317042	0.24107	U	0.041481	T	0.41834	0.1176	M	0.70842	2.15	0.31320	N	0.686175	P	0.44309	0.832	P	0.47346	0.544	T	0.49390	-0.8945	10	0.37606	T	0.19	.	8.1749	0.31276	0.1792:0.6474:0.1734:0.0	.	66	Q9NYW1	TA2R9_HUMAN	V	66	ENSP00000240691:G66V	ENSP00000240691:G66V	G	-	2	0	TAS2R9	10853745	0.000000	0.05858	0.281000	0.24762	0.520000	0.34377	-1.121000	0.03270	1.052000	0.40392	0.585000	0.79938	GGC		0.403	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1			A	10962478	C	A	10962478	3	1	61	1	0	0	0	0	1	0	0	0	15627	739	26	2	745	2	TAS2R9	12	10962478	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7758	10962478	122889417	7878	15863										
TAS2R10	50839	broad.mit.edu	37	chr12	10978744	10978744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtgagaataaagccaatcGtagataacttattcttggca	9	7	1	2	rs371389147		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:10978744G>A	ENST00000240619.2	-	1	213	c.125C>T	c.(124-126)aCg>aTg	p.T42M		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	42					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.T42M(1)		breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						AAAGCCAATCGTAGATAACTT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	MET/THR	0,4406		0,0,2203	71	66	68		125	-4.3	0	12		68	1,8599	1.2+/-3.3	0,1,4299	no	missense	TAS2R10	NM_023921.1	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	42/308	10978744	1,13005	2203	4300	6503	10870011	SO:0001583	missense	50839			AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.125C>T	12.37:g.10978744G>A	ENSP00000240619:p.Thr42Met		10870011	Q3MIM9|Q6NTD9	Missense_Mutation	SNP	ENST00000240619.2	37	CCDS8634.1	.	.	.	.	.	.	.	.	.	.	G	2.031	-0.422409	0.04734	0.0	1.16E-4	ENSG00000121318	ENST00000240619	T	0.38077	1.16	4.34	-4.28	0.03732	.	1.601890	0.05141	N	0.494339	T	0.25419	0.0618	L	0.31157	0.91	0.09310	N	1	B	0.33379	0.41	B	0.29524	0.103	T	0.32188	-0.9916	10	0.44086	T	0.13	.	12.0872	0.53704	0.3995:0.0:0.6005:0.0	.	42	Q9NYW0	T2R10_HUMAN	M	42	ENSP00000240619:T42M	ENSP00000240619:T42M	T	-	2	0	TAS2R10	10870011	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.476000	0.06591	-0.560000	0.06102	-0.423000	0.05987	ACG		0.328	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			A	10978744	G	A	10978744	3	1	61	1	0	0	0	0	1	0	0	0	15605	1145	40	1	802	1	TAS2R10	12	10978744	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16266	10978744	122873151	7879	15864										
TAS2R13	50838	broad.mit.edu	37	chr12	11061085	11061085	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtggcttgaaggagagaaGactccaatcgtctcacaaag	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:11061085G>T	ENST00000390677.2	-	1	1076	c.813C>A	c.(811-813)gtC>gtA	p.V271V	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	271					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.V271V(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						AAGGAGAGAAGACTCCAATCG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											86	78	81					12																	11061085		2203	4300	6503	10952352	SO:0001819	synonymous_variant	50838			AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.813C>A	12.37:g.11061085G>T			10952352	Q4G0I5|Q502V8|Q645X2	Silent	SNP	ENST00000390677.2	37	CCDS8635.1																																																																																				0.408	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			T	11061085	G	T	11061085	2	4	61	1	0	0	0	0	0	0	0	1	15606	929	33	2		2	TAS2R13	12	11061085	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82341	11061085	122790810	7880	15865										
TAS2R20	259295	broad.mit.edu	37	chr12	11150221	11150221	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttactgcccaggcattaGaaataaaaattattactttt	6	6	0	1	rs193920802		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:11150221G>T	ENST00000538986.1	-	1	253	c.254C>A	c.(253-255)tCt>tAt	p.S85Y	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	85					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S85Y(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						CCAGGCATTAGAAATAAAAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											47	52	51					12																	11150221		2186	4292	6478	11041488	SO:0001583	missense	259295			AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19109	protein-coding gene	gene with protein product		613962	"taste receptor, type 2, member 49"	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.254C>A	12.37:g.11150221G>T	ENSP00000441624:p.Ser85Tyr		11041488	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.811001	0.00074	.	.	ENSG00000255837	ENST00000538986	T	0.37752	1.18	2.77	-5.53	0.02552	.	3.284530	0.02183	U	0.060660	T	0.13798	0.0334	N	0.11427	0.14	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.33343	-0.9872	10	0.02654	T	1	.	1.2232	0.01928	0.2429:0.1958:0.3836:0.1777	.	85	P59543	T2R20_HUMAN	Y	85	ENSP00000441624:S85Y	ENSP00000441624:S85Y	S	-	2	0	TAS2R20	11041488	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.480000	0.02325	-2.954000	0.00292	-0.282000	0.10007	TCT		0.348	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889		T	11150221	G	T	11150221	3	4	61	1	0	0	0	0	1	0	0	0	15610	942	33	2	679	2	TAS2R20	12	11150221	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89136	11150221	122701674	7881	15866										
TAS2R46	259292	broad.mit.edu	37	chr12	11214292	11214292	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgagatgtttacacagaGaacagattaacagcagaaaa	8	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:11214292G>T	ENST00000533467.1	-	1	601	c.602C>A	c.(601-603)tCt>tAt	p.S201Y	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	201					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.S201Y(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TTTACACAGAGAACAGATTAA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	12											176	181	179					12																	11214292		2203	4299	6502	11105559	SO:0001583	missense	259292			AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.602C>A	12.37:g.11214292G>T	ENSP00000436450:p.Ser201Tyr		11105559	P59548|Q645X6	Missense_Mutation	SNP	ENST00000533467.1	37	CCDS53748.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.821386	0.32237	.	.	ENSG00000226761	ENST00000533467	T	0.01629	4.72	2.54	1.62	0.23740	.	.	.	.	.	T	0.15003	0.0362	H	0.97587	4.035	0.22066	N	0.99938	D	0.89917	1.0	D	0.79108	0.992	T	0.05053	-1.0909	9	0.87932	D	0	.	7.0832	0.25244	0.1496:0.0:0.8504:0.0	.	201	P59540	T2R46_HUMAN	Y	201	ENSP00000436450:S201Y	ENSP00000436450:S201Y	S	-	2	0	TAS2R46	11105559	0.626000	0.27120	0.130000	0.21974	0.015000	0.08874	2.100000	0.41777	0.411000	0.25702	0.194000	0.17425	TCT		0.428	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887		T	11214292	G	T	11214292	3	4	61	1	0	0	0	0	1	0	0	0	15621	942	33	2	331	2	TAS2R46	12	11214292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64071	11214292	122637603	7882	15867										
PRB4	5545	broad.mit.edu	37	chr12	11462308	11462308	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaattgggatttacctgaTattaggaagagagattcttc	10	4	1	4	rs376674559		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:11462308T>G	ENST00000535904.1	-	2	129	c.96A>C	c.(94-96)atA>atC	p.I32I	PRB4_ENST00000445719.2_Silent_p.I32I|PRB4_ENST00000279575.1_Silent_p.I32I			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	32				LIS -> PPP (in Ref. 6; AAB50687). {ECO:0000305}.|LISGKPEGR -> IIPPKPPG (in Ref. 5; AA sequence). {ECO:0000305}.		extracellular region (GO:0005576)		p.I32I(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						ATTTACCTGATATTAGGAAGA	0.378										HNSCC(22;0.051)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											169	146	154					12																	11462308		2203	4300	6503	11353575	SO:0001819	synonymous_variant	5545				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.96A>C	12.37:g.11462308T>G			11353575	A1L439|O00600|P02813|P10161|P10162|P81489	Silent	SNP	ENST00000535904.1	37	CCDS8641.1																																																																																				0.378	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		G	11462308	T	G	11462308	2	3	61	1	0	0	0	0	0	0	0	1	12479	1396	49	4		4	PRB4	12	11462308	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	248016	11462308	122389587	7883	15868										
PRB1	5542	broad.mit.edu	37	chr12	11507489	11507489	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattcttcctggctgacatCtagaagagaagcacaggatg	11	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:11507489C>A	ENST00000500254.2	-	2	102		c.e2-1		PRB1_ENST00000545626.1_Splice_Site|PRB1_ENST00000546254.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)		p.?(1)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			TGGCTGACATCTAGAAGAGAA	0.438																																																1	Unknown(1)	large_intestine(1)	12											186	175	179					12																	11507489		2179	4277	6456	11398756	SO:0001630	splice_region_variant	5542				CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.65-1G>T	12.37:g.11507489C>A			11398756	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Splice_Site	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	C	3.706	-0.060587	0.07317	.	.	ENSG00000251655	ENST00000545626;ENST00000500254	.	.	.	1.7	1.7	0.24286	.	.	.	.	.	.	.	.	.	.	.	0.22127	N	0.999342	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9445	0.24510	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRB1	11398756	0.346000	0.24844	0.098000	0.21074	0.006000	0.05464	1.273000	0.33121	1.265000	0.44215	0.558000	0.71614	.		0.438	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	Intron	A	11507489	C	A	11507489	5	1	61	1	0	0	0	0	0	0	1	0	12476	927	32	2	939	2	PRB1	12	11507489	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45181	11507489	122344406	7884	15869										
ETV6	2120	broad.mit.edu	37	chr12	12038864	12038864	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttgaacaaacagaacaGaacaaacatgacctatgaga	6	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12038864G>T	ENST00000396373.4	+	7	1431	c.1157G>T	c.(1156-1158)aGa>aTa	p.R386I		NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	386					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R386I(1)	ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				AAACAGAACAGAACAAACATG	0.418			T	"NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"	"congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"																																		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"L, E, M"	1	Substitution - Missense(1)	large_intestine(1)	12											103	97	99					12																	12038864		2203	4300	6503	11930131	SO:0001583	missense	2120			BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"TEL oncogene"	600618	"ets variant gene 6 (TEL oncogene)"			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.1157G>T	12.37:g.12038864G>T	ENSP00000379658:p.Arg386Ile		11930131	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Missense_Mutation	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.933552	0.92458	.	.	ENSG00000139083	ENST00000396373	T	0.27256	1.68	5.1	5.1	0.69264	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66622	-0.5877	10	0.87932	D	0	.	18.4712	0.90776	0.0:0.0:1.0:0.0	.	386	P41212	ETV6_HUMAN	I	386	ENSP00000379658:R386I	ENSP00000379658:R386I	R	+	2	0	ETV6	11930131	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.541000	0.85698	0.655000	0.94253	AGA		0.418	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987		T	12038864	G	T	12038864	3	4	61	1	0	0	0	0	1	0	0	0	5296	942	33	2	1183	2	ETV6	12	12038864	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	531375	12038864	121813031	7885	15870										
BCL2L14	79370	broad.mit.edu	37	chr12	12232252	12232252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcccaacatgtgtagcaccAgtgggtgtgacctggaagaa	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12232252A>G	ENST00000308721.5	+	2	219	c.13A>G	c.(13-15)Agt>Ggt	p.S5G	BCL2L14_ENST00000589718.1_Missense_Mutation_p.S5G|BCL2L14_ENST00000396369.1_Missense_Mutation_p.S5G|BCL2L14_ENST00000396367.1_Missense_Mutation_p.S5G|BCL2L14_ENST00000586576.1_Missense_Mutation_p.S38G|BCL2L14_ENST00000266434.4_Missense_Mutation_p.S5G	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	5					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)	p.S5G(2)		large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		GTGTAGCACCAGTGGGTGTGA	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	12											141	126	131					12																	12232252		2203	4300	6503	12123519	SO:0001583	missense	79370			AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.13A>G	12.37:g.12232252A>G	ENSP00000309132:p.Ser5Gly		12123519	A8KAD0|Q96QR5|Q9BZR7	Missense_Mutation	SNP	ENST00000308721.5	37	CCDS8645.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.043381	0.36085	.	.	ENSG00000121380	ENST00000464885;ENST00000461264;ENST00000308721;ENST00000266434;ENST00000396369;ENST00000396367	.	.	.	4.11	0.335	0.15953	.	0.398924	0.24568	N	0.037404	T	0.55513	0.1925	M	0.73962	2.25	0.27251	N	0.958892	P;D	0.71674	0.703;0.998	B;D	0.80764	0.203;0.994	T	0.46345	-0.9198	9	0.87932	D	0	-6.0632	4.628	0.12488	0.5266:0.3667:0.1066:0.0	.	5;5	Q9BZR8-2;Q9BZR8	.;B2L14_HUMAN	G	5;8;5;5;5;5	.	ENSP00000266434:S5G	S	+	1	0	BCL2L14	12123519	0.619000	0.27059	0.748000	0.31131	0.351000	0.29236	0.976000	0.29462	0.056000	0.16144	0.460000	0.39030	AGT		0.483	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766		G	12232252	A	G	12232252	3	3	61	1	0	0	0	0	1	0	0	0	1373	188	7	4	15	4	BCL2L14	12	12232252	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	193388	12232252	121619643	7886	15871										
LRP6	4040	broad.mit.edu	37	chr12	12317235	12317235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatatcagtccaataaattCggttgtctgtcacatcaaaa	5	8	4	0	rs376188127		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12317235C>T	ENST00000261349.4	-	9	2100	c.2024G>A	c.(2023-2025)cGa>cAa	p.R675Q	LRP6_ENST00000543091.1_Missense_Mutation_p.R675Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	675	Beta-propeller 3.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R675Q(3)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CCAATAAATTCGGTTGTCTGT	0.358																																																3	Substitution - Missense(3)	large_intestine(3)	12						C	GLN/ARG	1,4403	2.1+/-5.4	0,1,2201	85	87	86		2024	5.4	1	12		86	0,8600		0,0,4300	no	missense	LRP6	NM_002336.2	43	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	675/1614	12317235	1,13003	2202	4300	6502	12208502	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.2024G>A	12.37:g.12317235C>T	ENSP00000261349:p.Arg675Gln		12208502	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132673	0.94517	2.27E-4	0.0	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96802	-4.13;-4.13	5.41	5.41	0.78517	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.50627	U	0.000115	D	0.97785	0.9273	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.941	D	0.96857	0.9629	10	0.31617	T	0.26	.	19.571	0.95419	0.0:1.0:0.0:0.0	.	675;675	F5H7J9;O75581	.;LRP6_HUMAN	Q	675	ENSP00000261349:R675Q;ENSP00000442472:R675Q	ENSP00000261349:R675Q	R	-	2	0	LRP6	12208502	1.000000	0.71417	0.966000	0.40874	0.987000	0.75469	6.013000	0.70776	2.709000	0.92574	0.655000	0.94253	CGA		0.358	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12317235	C	T	12317235	3	4	61	1	0	0	0	0	1	0	0	0	8991	884	31	1	2877	1	LRP6	12	12317235	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84983	12317235	121534660	7887	15872										
LRP6	4040	broad.mit.edu	37	chr12	12317322	12317322	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattattgtttgtttccagaGaaattcgtctgatatctgct	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12317322G>T	ENST00000261349.4	-	9	2013	c.1937C>A	c.(1936-1938)tCt>tAt	p.S646Y	LRP6_ENST00000543091.1_Missense_Mutation_p.S646Y	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	646	Beta-propeller 3.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S646Y(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TGTTTCCAGAGAAATTCGTCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											104	103	103					12																	12317322		2203	4300	6503	12208589	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1937C>A	12.37:g.12317322G>T	ENSP00000261349:p.Ser646Tyr		12208589	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884412	0.91814	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91740	-2.9;-2.9	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000009	D	0.96256	0.8779	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.952	D	0.94924	0.8076	10	0.38643	T	0.18	.	20.0965	0.97849	0.0:0.0:1.0:0.0	.	646;646	F5H7J9;O75581	.;LRP6_HUMAN	Y	646	ENSP00000261349:S646Y;ENSP00000442472:S646Y	ENSP00000261349:S646Y	S	-	2	0	LRP6	12208589	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.771000	0.98977	2.824000	0.97209	0.655000	0.94253	TCT		0.418	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12317322	G	T	12317322	3	4	61	1	0	0	0	0	1	0	0	0	8991	942	33	2	2964	2	LRP6	12	12317322	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87	12317322	121534573	7888	15873										
LRP6	4040	broad.mit.edu	37	chr12	12356241	12356241	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagtccatttggccagtaAatttcactgtttattataat	6	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12356241A>C	ENST00000261349.4	-	3	619	c.543T>G	c.(541-543)atT>atG	p.I181M	LRP6_ENST00000543091.1_Missense_Mutation_p.I181M	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	181	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.I181M(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TTGGCCAGTAAATTTCACTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	12											130	123	126					12																	12356241		2203	4300	6503	12247508	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.543T>G	12.37:g.12356241A>C	ENSP00000261349:p.Ile181Met		12247508	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.283407	0.59867	.	.	ENSG00000070018	ENST00000261349;ENST00000543091;ENST00000535731	D;D;D	0.96745	-4.11;-4.11;-4.11	5.51	4.35	0.52113	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000007	D	0.97461	0.9169	M	0.75615	2.305	0.52099	D	0.999941	D;D	0.71674	0.997;0.998	D;D	0.85130	0.997;0.997	D	0.96615	0.9455	10	0.45353	T	0.12	.	10.8166	0.46580	0.7487:0.0:0.0:0.2512	.	181;181	F5H7J9;O75581	.;LRP6_HUMAN	M	181;181;30	ENSP00000261349:I181M;ENSP00000442472:I181M;ENSP00000439765:I30M	ENSP00000261349:I181M	I	-	3	3	LRP6	12247508	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.756000	0.38390	0.900000	0.36469	0.459000	0.35465	ATT		0.378	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12356241	A	C	12356241	3	2	61	1	0	0	0	0	1	0	0	0	8991	10	1	4	4382	4	LRP6	12	12356241	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	38919	12356241	121495654	7889	15874										
MANSC1	54682	broad.mit.edu	37	chr12	12483101	12483101	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagcagggacccgataaGaagccatttttcaaatggaa	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12483101G>T	ENST00000535902.1	-	4	1719	c.1156C>A	c.(1156-1158)Ctt>Att	p.L386I	MANSC1_ENST00000396349.3_Missense_Mutation_p.L352I|MANSC1_ENST00000545735.1_Missense_Mutation_p.L305I			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	386						integral component of membrane (GO:0016021)		p.L386I(1)|p.L386V(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		GACCCGATAAGAAGCCATTTT	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											76	78	77					12																	12483101		2203	4300	6503	12374368	SO:0001583	missense	54682			AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.1156C>A	12.37:g.12483101G>T	ENSP00000438205:p.Leu386Ile		12374368	Q8NEC1|Q9NW60	Missense_Mutation	SNP	ENST00000535902.1	37	CCDS8648.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.496059	0.64186	.	.	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000355566;ENST00000545735	T;T;T	0.63744	0.24;0.23;-0.06	5.24	5.24	0.73138	.	0.000000	0.35646	N	0.003069	T	0.78767	0.4335	M	0.78049	2.395	0.35198	D	0.774037	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.987;0.991;0.991	D	0.85835	0.1394	10	0.87932	D	0	-15.4925	14.3004	0.66346	0.0:0.0:1.0:0.0	.	320;352;386	B4DQ82;Q9NW60;Q9H8J5	.;.;MANS1_HUMAN	I	386;352;305;305	ENSP00000438205:L386I;ENSP00000379638:L352I;ENSP00000445303:L305I	ENSP00000347765:L305I	L	-	1	0	MANSC1	12374368	1.000000	0.71417	0.816000	0.32577	0.451000	0.32288	4.742000	0.62103	2.449000	0.82847	0.491000	0.48974	CTT		0.527	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		T	12483101	G	T	12483101	3	4	61	1	0	0	0	0	1	0	0	0	9254	942	33	2	143	2	MANSC1	12	12483101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	126860	12483101	121368794	7890	15875										
DUSP16	80824	broad.mit.edu	37	chr12	12630396	12630396	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccttatcaggactggtttCgggagtctgctccgatagtt	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12630396C>T	ENST00000228862.2	-	7	2000	c.1369G>A	c.(1369-1371)Gaa>Aaa	p.E457K	DUSP16_ENST00000545864.1_5'Flank|DUSP16_ENST00000298573.4_3'UTR	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	457					dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E457K(1)		endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GGACTGGTTTCGGGAGTCTGC	0.527																																					Ovarian(158;443 1896 15437 36069 46477)											1	Substitution - Missense(1)	large_intestine(1)	12											108	107	107					12																	12630396		2203	4300	6503	12521663	SO:0001583	missense	80824			AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	17909	protein-coding gene	gene with protein product	"MAPK phosphatase-7"	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.1369G>A	12.37:g.12630396C>T	ENSP00000228862:p.Glu457Lys		12521663	Q547C7|Q96QS2|Q9C0G3	Missense_Mutation	SNP	ENST00000228862.2	37	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044309	0.55110	.	.	ENSG00000111266	ENST00000228862	T	0.01947	4.54	5.8	5.8	0.92144	.	0.504675	0.19206	N	0.120057	T	0.04137	0.0115	L	0.59436	1.845	0.80722	D	1	P;P	0.50528	0.87;0.936	B;B	0.37144	0.184;0.242	T	0.52079	-0.8623	10	0.44086	T	0.13	.	20.063	0.97692	0.0:1.0:0.0:0.0	.	457;457	Q9BY84;Q96N49	DUS16_HUMAN;.	K	457	ENSP00000228862:E457K	ENSP00000228862:E457K	E	-	1	0	DUSP16	12521663	1.000000	0.71417	0.425000	0.26659	0.215000	0.24574	5.482000	0.66833	2.735000	0.93741	0.655000	0.94253	GAA		0.527	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640		T	12630396	C	T	12630396	3	4	61	1	0	0	0	0	1	0	0	0	4827	893	31	1	632	1	DUSP16	12	12630396	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147295	12630396	121221499	7891	15876										
GPR19	2842	broad.mit.edu	37	chr12	12814224	12814224	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgagtcatagatcgagtCtttggtaatagttttggcca	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:12814224C>A	ENST00000540510.1	-	2	1351	c.1159G>T	c.(1159-1161)Gac>Tac	p.D387Y	GPR19_ENST00000332427.2_Missense_Mutation_p.D387Y			P46093	GPR4_HUMAN	G protein-coupled receptor 19	0					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D387Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		TAGATCGAGTCTTTGGTAATA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											155	143	147					12																	12814224		2203	4300	6503	12705491	SO:0001583	missense	2842				CCDS8652.1	12p12.3	2014-01-30				ENSG00000183150		"GPCR / Class A : Orphans"	4473	protein-coding gene	gene with protein product		602927					Standard	NM_006143		Approved		uc001raq.2	Q15760		ENST00000540510.1:c.1159G>T	12.37:g.12814224C>A	ENSP00000441832:p.Asp387Tyr		12705491	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000540510.1	37	CCDS8652.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996144	0.74703	.	.	ENSG00000183150	ENST00000540510;ENST00000332427	T;T	0.70045	-0.45;-0.45	5.64	5.64	0.86602	.	0.162498	0.51477	D	0.000082	T	0.69860	0.3158	N	0.19112	0.55	0.58432	D	0.999994	D	0.71674	0.998	P	0.60173	0.87	T	0.73512	-0.3959	10	0.62326	D	0.03	-29.1788	19.3003	0.94141	0.0:1.0:0.0:0.0	.	387	Q15760	GPR19_HUMAN	Y	387	ENSP00000441832:D387Y;ENSP00000333744:D387Y	ENSP00000333744:D387Y	D	-	1	0	GPR19	12705491	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.071000	0.71229	2.658000	0.90341	0.650000	0.86243	GAC		0.393	GPR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400662.1	NM_006143		A	12814224	C	A	12814224	3	1	61	1	0	0	0	0	1	0	0	0	6699	913	32	2	92	2	GPR19	12	12814224	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	183828	12814224	121037671	7892	15877										
GPRC5D	55507	broad.mit.edu	37	chr12	13103217	13103217	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtagcagaattgtgaccacGatgccaagtatggccaggga	13	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13103217G>A	ENST00000228887.1	-	1	101	c.102C>T	c.(100-102)atC>atT	p.I34I	RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|GPRC5D_ENST00000396333.3_Silent_p.I34I|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000538231.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I34I(1)		kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		TTGTGACCACGATGCCAAGTA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											109	101	104					12																	13103217		2203	4300	6503	12994484	SO:0001819	synonymous_variant	55507			AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"GPCR / Class C : Orphans"	13310	protein-coding gene	gene with protein product		607437	"G protein-coupled receptor, family C, group 5, member D"				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.102C>T	12.37:g.13103217G>A			12994484	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																				0.532	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1			A	13103217	G	A	13103217	2	1	61	1	0	0	0	0	0	0	0	1	6748	1048	37	1		1	GPRC5D	12	13103217	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288993	13103217	120748678	7893	15878										
HEBP1	50865	broad.mit.edu	37	chr12	13140196	13140196	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaaccagacttttaatttCttctgcagagagccatcttc	7	11	3	2	rs375649105		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13140196C>A	ENST00000014930.4	-	3	446	c.288G>T	c.(286-288)aaG>aaT	p.K96N	RP11-392P7.6_ENST00000499948.2_RNA|HEBP1_ENST00000536942.1_Missense_Mutation_p.K96N	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	96					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)	p.K96N(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CTTTTAATTTCTTCTGCAGAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	89	88					12																	13140196		2203	4300	6503	13031463	SO:0001583	missense	50865			AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.288G>T	12.37:g.13140196C>A	ENSP00000014930:p.Lys96Asn		13031463	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	37	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744729	0.49151	.	.	ENSG00000013583	ENST00000014930;ENST00000535636;ENST00000536942	T;T;T	0.21734	1.99;1.99;1.99	5.66	5.66	0.87406	Regulatory factor, effector, bacterial (1);	0.214710	0.50627	D	0.000109	T	0.20700	0.0498	L	0.43152	1.355	0.38235	D	0.941162	P	0.36144	0.539	B	0.41271	0.352	T	0.05084	-1.0907	10	0.16420	T	0.52	-16.0362	11.3851	0.49780	0.1405:0.7239:0.1356:0.0	.	96	Q9NRV9	HEBP1_HUMAN	N	96;25;96	ENSP00000014930:K96N;ENSP00000442020:K25N;ENSP00000441678:K96N	ENSP00000014930:K96N	K	-	3	2	HEBP1	13031463	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.926000	0.28804	2.830000	0.97506	0.655000	0.94253	AAG		0.473	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			A	13140196	C	A	13140196	3	1	61	1	0	0	0	0	1	0	0	0	7057	912	32	2	289	2	HEBP1	12	13140196	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36979	13140196	120711699	7894	15879										
KIAA1467	57613	broad.mit.edu	37	chr12	13214669	13214669	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtgacagggacacacaaGatgctcagcgcattcaatgc	10	11	2	2	rs371752869		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13214669G>T	ENST00000197268.8	+	4	813	c.693G>T	c.(691-693)aaG>aaT	p.K231N		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	231						integral component of membrane (GO:0016021)		p.K231N(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		GGACACACAAGATGCTCAGCG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/LYS	1,4405	2.1+/-5.4	0,1,2202	90	77	81		693	2.8	1	12		81	0,8600		0,0,4300	no	missense	KIAA1467	NM_020853.1	94	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging	231/623	13214669	1,13005	2203	4300	6503	13105936	SO:0001583	missense	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.693G>T	12.37:g.13214669G>T	ENSP00000197268:p.Lys231Asn		13105936	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	37	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	G	9.455	1.091544	0.20471	2.27E-4	0.0	ENSG00000084444	ENST00000197268;ENST00000537625	T;T	0.39056	1.1;1.79	5.58	2.79	0.32731	Quinonprotein alcohol dehydrogenase-like (1);	0.322809	0.33834	N	0.004502	T	0.50222	0.1603	M	0.70595	2.14	0.37012	D	0.895787	D	0.54601	0.967	P	0.53689	0.732	T	0.51934	-0.8642	10	0.29301	T	0.29	-15.0887	9.7459	0.40446	0.3983:0.0:0.6017:0.0	.	231	A2RU67	K1467_HUMAN	N	231;7	ENSP00000197268:K231N;ENSP00000437974:K7N	ENSP00000197268:K231N	K	+	3	2	KIAA1467	13105936	1.000000	0.71417	0.954000	0.39281	0.048000	0.14542	1.785000	0.38684	0.066000	0.16515	-1.761000	0.00669	AAG		0.463	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		T	13214669	G	T	13214669	3	4	61	1	0	0	0	0	1	0	0	0	8256	933	33	2	707	2	KIAA1467	12	13214669	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74473	13214669	120637226	7895	15880										
KIAA1467	57613	broad.mit.edu	37	chr12	13220194	13220194	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagaatgggaaaagcgaaGatccatcaacctgtctgagc	11	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13220194G>T	ENST00000197268.8	+	7	1226	c.1106G>T	c.(1105-1107)aGa>aTa	p.R369I		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	369						integral component of membrane (GO:0016021)		p.R369I(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		GAAAAGCGAAGATCCATCAAC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	144	149					12																	13220194		2203	4300	6503	13111461	SO:0001583	missense	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.1106G>T	12.37:g.13220194G>T	ENSP00000197268:p.Arg369Ile		13111461	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	37	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.195853	0.78902	.	.	ENSG00000084444	ENST00000197268;ENST00000537625	T	0.42513	0.97	5.44	5.44	0.79542	.	0.091390	0.85682	D	0.000000	T	0.65439	0.2691	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.65923	-0.6050	10	0.48119	T	0.1	-21.4563	17.4632	0.87625	0.0:0.0:1.0:0.0	.	369	A2RU67	K1467_HUMAN	I	369;145	ENSP00000197268:R369I	ENSP00000197268:R369I	R	+	2	0	KIAA1467	13111461	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.257000	0.72480	2.545000	0.85829	0.655000	0.94253	AGA		0.483	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		T	13220194	G	T	13220194	3	4	61	1	0	0	0	0	1	0	0	0	8256	942	33	2	1132	2	KIAA1467	12	13220194	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5525	13220194	120631701	7896	15881										
KIAA1467	57613	broad.mit.edu	37	chr12	13221377	13221377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgagacttcaaggcctgCgcaggtttgcattgtgttcc	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13221377C>T	ENST00000197268.8	+	8	1402	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	428						integral component of membrane (GO:0016021)		p.R428C(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TCAAGGCCTGCGCAGGTTTGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											182	140	154					12																	13221377		2203	4300	6503	13112644	SO:0001583	missense	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.1282C>T	12.37:g.13221377C>T	ENSP00000197268:p.Arg428Cys		13112644	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	37	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.364874	0.41902	.	.	ENSG00000084444	ENST00000197268;ENST00000537625	T	0.30981	1.51	5.42	-0.00166	0.14033	.	0.784398	0.12972	N	0.424079	T	0.19327	0.0464	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22068	-1.0227	10	0.37606	T	0.19	-5.9399	0.9814	0.01437	0.329:0.3332:0.1103:0.2275	.	428	A2RU67	K1467_HUMAN	C	428;204	ENSP00000437974:R204C	ENSP00000197268:R428C	R	+	1	0	KIAA1467	13112644	0.005000	0.15991	0.362000	0.25862	0.647000	0.38526	0.117000	0.15583	0.255000	0.21593	-0.182000	0.12963	CGC		0.448	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		T	13221377	C	T	13221377	3	4	61	1	0	0	0	0	1	0	0	0	8256	768	27	1	1312	1	KIAA1467	12	13221377	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1183	13221377	120630518	7897	15882										
KIAA1467	57613	broad.mit.edu	37	chr12	13232903	13232903	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccgtggggagctgcgaaGatttctctctaggataaagt	14	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13232903G>T	ENST00000197268.8	+	12	1943	c.1823G>T	c.(1822-1824)aGa>aTa	p.R608I		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	608						integral component of membrane (GO:0016021)		p.R608I(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		GAGCTGCGAAGATTTCTCTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	48	46					12																	13232903		2203	4300	6503	13124170	SO:0001583	missense	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.1823G>T	12.37:g.13232903G>T	ENSP00000197268:p.Arg608Ile		13124170	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	37	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.635909	0.87760	.	.	ENSG00000084444	ENST00000197268	T	0.55234	0.53	5.43	5.43	0.79202	.	0.186836	0.47455	D	0.000234	T	0.69931	0.3166	L	0.60455	1.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	T	0.72020	-0.4416	10	0.72032	D	0.01	-4.7524	17.4437	0.87573	0.0:0.0:1.0:0.0	.	608	A2RU67	K1467_HUMAN	I	608	ENSP00000197268:R608I	ENSP00000197268:R608I	R	+	2	0	KIAA1467	13124170	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.063000	0.71162	2.540000	0.85666	0.650000	0.86243	AGA		0.502	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		T	13232903	G	T	13232903	3	4	61	1	0	0	0	0	1	0	0	0	8256	942	33	2	1869	2	KIAA1467	12	13232903	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11526	13232903	120618992	7898	15883										
GRIN2B	2904	broad.mit.edu	37	chr12	13715728	13715728	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccctcactcagacatcagActcaatactagaaagtttct	4	12	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:13715728A>T	ENST00000609686.1	-	13	4653	c.4444T>A	c.(4444-4446)Tct>Act	p.S1482T		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1482					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.S1482T(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGACATCAGACTCAATACTA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											133	133	133					12																	13715728		2203	4300	6503	13606995	SO:0001583	missense	2904				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.4444T>A	12.37:g.13715728A>T	ENSP00000477455:p.Ser1482Thr		13606995	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.474182	0.63737	.	.	ENSG00000150086	ENST00000279593	T	0.28895	1.59	5.02	5.02	0.67125	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53718	-0.8399	10	0.87932	D	0	.	14.9146	0.70785	1.0:0.0:0.0:0.0	.	1482	Q13224	NMDE2_HUMAN	T	1482	ENSP00000279593:S1482T	ENSP00000279593:S1482T	S	-	1	0	GRIN2B	13606995	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.756000	0.91651	2.108000	0.64289	0.533000	0.62120	TCT		0.532	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			T	13715728	A	T	13715728	3	4	61	1	0	0	0	0	1	0	0	0	6801	275	10	5	14	5	GRIN2B	12	13715728	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	482825	13715728	120136167	7899	15884										
GRIN2B	2904	broad.mit.edu	37	chr12	14019007	14019007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccttgatggccacctcgtCggaagtgcccacgaggatga	12	12	0	2	rs370809599		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14019007C>T	ENST00000609686.1	-	2	345	c.136G>A	c.(136-138)Gac>Aac	p.D46N		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	46					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.D46N(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCCACCTCGTCGGAAGTGCCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	90	85	87		136	5.7	1	12		87	0,8600		0,0,4300	no	missense	GRIN2B	NM_000834.3	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	46/1485	14019007	1,13005	2203	4300	6503	13910274	SO:0001583	missense	2904				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.136G>A	12.37:g.14019007C>T	ENSP00000477455:p.Asp46Asn		13910274	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469691	0.26423	2.27E-4	0.0	ENSG00000150086	ENST00000279593	T	0.11063	2.81	5.69	5.69	0.88448	.	0.102768	0.64402	D	0.000003	T	0.06735	0.0172	N	0.08118	0	0.36504	D	0.869188	B	0.12013	0.005	B	0.01281	0.0	T	0.29518	-1.0009	10	0.08599	T	0.76	.	19.8218	0.96599	0.0:1.0:0.0:0.0	.	46	Q13224	NMDE2_HUMAN	N	46	ENSP00000279593:D46N	ENSP00000279593:D46N	D	-	1	0	GRIN2B	13910274	1.000000	0.71417	0.974000	0.42286	0.976000	0.68499	3.837000	0.55820	2.676000	0.91093	0.557000	0.71058	GAC		0.587	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			T	14019007	C	T	14019007	3	4	61	1	0	0	0	0	1	0	0	0	6801	884	31	1	4366	1	GRIN2B	12	14019007	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	303279	14019007	119832888	7900	15885										
ATF7IP	55729	broad.mit.edu	37	chr12	14589105	14589105	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtacagtctaaacgtcgtCgatatatggaagaagaatat	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14589105C>T	ENST00000540793.1	+	3	1866	c.1711C>T	c.(1711-1713)Cga>Tga	p.R571*	ATF7IP_ENST00000261168.4_Nonsense_Mutation_p.R571*|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000536444.1_Nonsense_Mutation_p.R570*|ATF7IP_ENST00000544627.1_Nonsense_Mutation_p.R579*|ATF7IP_ENST00000543189.1_Nonsense_Mutation_p.R570*			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	571	Glu-rich.|Interaction with SETDB1.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.R571*(2)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TAAACGTCGTCGATATATGGA	0.358																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											120	121	120					12																	14589105		2203	4300	6503	14480372	SO:0001587	stop_gained	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1711C>T	12.37:g.14589105C>T	ENSP00000444589:p.Arg571*		14480372	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Nonsense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	39	7.746878	0.98468	.	.	ENSG00000171681	ENST00000261168;ENST00000538511;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000540793	.	.	.	5.48	4.57	0.56435	.	0.000000	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.5873	15.4187	0.74995	0.1404:0.8596:0.0:0.0	.	.	.	.	X	571;10;570;570;579;571	.	ENSP00000261168:R571X	R	+	1	2	ATF7IP	14480372	1.000000	0.71417	0.974000	0.42286	0.989000	0.77384	3.412000	0.52679	1.401000	0.46761	0.585000	0.79938	CGA		0.358	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		T	14589105	C	T	14589105	4	4	61	1	0	0	0	0	0	1	0	0	1088	876	31	1	1721	1	ATF7IP	12	14589105	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	570098	14589105	119262790	7901	15886										
ATF7IP	55729	broad.mit.edu	37	chr12	14631268	14631268	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaccccaaaaaactaaatCacactcctgtatcaaccatg	3	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14631268C>A	ENST00000540793.1	+	11	3114	c.2959C>A	c.(2959-2961)Cac>Aac	p.H987N	ATF7IP_ENST00000261168.4_Missense_Mutation_p.H987N|ATF7IP_ENST00000536444.1_Missense_Mutation_p.H986N|ATF7IP_ENST00000544627.1_Missense_Mutation_p.H995N|ATF7IP_ENST00000543189.1_Missense_Mutation_p.H986N			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	987					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.H987N(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AAAACTAAATCACACTCCTGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											135	130	132					12																	14631268		2203	4300	6503	14522535	SO:0001583	missense	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.2959C>A	12.37:g.14631268C>A	ENSP00000444589:p.His987Asn		14522535	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	9.832	1.188797	0.21954	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	5.28	5.28	0.74379	.	0.447046	0.20993	N	0.081987	T	0.15955	0.0384	L	0.40543	1.245	0.09310	N	1	B;B;P	0.45827	0.257;0.257;0.867	B;B;B	0.41510	0.098;0.098;0.359	T	0.16928	-1.0386	10	0.22706	T	0.39	-5.1952	14.1632	0.65459	0.1498:0.8502:0.0:0.0	.	986;987;986	G3V1U0;Q6VMQ6;Q6VMQ6-2	.;MCAF1_HUMAN;.	N	987;986;986;995;987	ENSP00000261168:H987N;ENSP00000443179:H986N;ENSP00000445955:H986N;ENSP00000440440:H995N;ENSP00000444589:H987N	ENSP00000261168:H987N	H	+	1	0	ATF7IP	14522535	0.448000	0.25681	0.028000	0.17463	0.805000	0.45488	3.348000	0.52209	2.629000	0.89072	0.650000	0.86243	CAC		0.403	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		A	14631268	C	A	14631268	3	1	61	1	0	0	0	0	1	0	0	0	1088	826	29	2	3001	2	ATF7IP	12	14631268	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42163	14631268	119220627	7902	15887										
PLBD1	79887	broad.mit.edu	37	chr12	14706146	14706146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggggcagtgaggtaaccctCcaaaaagccagccacaaaca	10	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14706146C>T	ENST00000240617.5	-	2	968	c.316G>A	c.(316-318)Gag>Aag	p.E106K	RN7SKP134_ENST00000363960.1_RNA	NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	106					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.E106K(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						AGGTAACCCTCCAAAAAGCCA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											76	67	70					12																	14706146		2203	4300	6503	14597413	SO:0001583	missense	79887			BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"PLB homolog 1 (Dictyostelium)"					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.316G>A	12.37:g.14706146C>T	ENSP00000240617:p.Glu106Lys		14597413	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	37	CCDS31751.1	.	.	.	.	.	.	.	.	.	.	C	35	5.517151	0.96416	.	.	ENSG00000121316	ENST00000240617;ENST00000540572	T;T	0.23348	1.91;1.91	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.67059	0.2853	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76495	-0.2938	10	0.87932	D	0	-30.6198	19.0599	0.93085	0.0:1.0:0.0:0.0	.	106	Q6P4A8	PLBL1_HUMAN	K	106;59	ENSP00000240617:E106K;ENSP00000438367:E59K	ENSP00000240617:E106K	E	-	1	0	PLBD1	14597413	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.736000	0.74811	2.941000	0.99782	0.655000	0.94253	GAG		0.537	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829		T	14706146	C	T	14706146	3	4	61	1	0	0	0	0	1	0	0	0	12056	864	30	3	1385	3	PLBD1	12	14706146	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74878	14706146	119145749	7903	15888										
C12orf69	440087	broad.mit.edu	37	chr12	14959262	14959262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcttctcccaggatgaccGaaataaccttttgcactatt	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14959262G>A	ENST00000316048.2	-	2	425	c.353C>T	c.(352-354)tCg>tTg	p.S118L	C12orf60_ENST00000527783.1_Intron|WBP11_ENST00000261167.2_5'Flank|C12orf60_ENST00000330828.2_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	118						integral component of membrane (GO:0016021)		p.S118L(1)									CAGGATGACCGAAATAACCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											135	127	130					12																	14959262		1938	4145	6083	14850529	SO:0001583	missense	440087				CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 69"	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.353C>T	12.37:g.14959262G>A	ENSP00000381895:p.Ser118Leu		14850529	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	37	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537371	0.65085	.	.	ENSG00000179256	ENST00000316048	T	0.18338	2.22	5.04	5.04	0.67666	.	0.000000	0.35096	U	0.003455	T	0.27663	0.0680	N	0.24115	0.695	0.35737	D	0.818369	D	0.71674	0.998	D	0.75484	0.986	T	0.24657	-1.0154	10	0.87932	D	0	-9.9982	13.7537	0.62923	0.0:0.0:1.0:0.0	.	118	A2RU48	CL069_HUMAN	L	118	ENSP00000381895:S118L	ENSP00000381895:S118L	S	-	2	0	C12orf69	14850529	1.000000	0.71417	0.945000	0.38365	0.621000	0.37620	4.691000	0.61738	2.611000	0.88343	0.561000	0.74099	TCG		0.413	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698		A	14959262	G	A	14959262	3	1	61	1	0	0	0	0	1	0	0	0	1715	1059	37	1	328	1	C12orf69	12	14959262	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	253116	14959262	118892633	7904	15889										
ART4	420	broad.mit.edu	37	chr12	14993621	14993621	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggagaggaattggccaAatcgaatggtggcccctgtg	15	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:14993621A>C	ENST00000228936.4	-	2	992	c.611T>G	c.(610-612)tTt>tGt	p.F204C	C12orf60_ENST00000527783.1_Intron|RP11-233G1.4_ENST00000444324.2_RNA	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	204					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)	p.F204C(1)		large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						GAATTGGCCAAATCGAATGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	103	104					12																	14993621		2203	4300	6503	14884888	SO:0001583	missense	420			X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"CD molecules", "Blood group antigens"	726	protein-coding gene	gene with protein product		110600	"Dombrock blood group", "ADP-ribosyltransferase 4 (DO blood group)", "ADP-ribosyltransferase 4"	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.611T>G	12.37:g.14993621A>C	ENSP00000228936:p.Phe204Cys		14884888	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	37	CCDS8668.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.452117	0.63290	.	.	ENSG00000111339	ENST00000228936;ENST00000420600	T;T	0.10288	2.89;2.89	4.35	4.35	0.52113	.	0.107302	0.64402	D	0.000004	T	0.41581	0.1165	M	0.93328	3.405	0.44956	D	0.997977	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.53823	-0.8384	10	0.87932	D	0	0.0497	12.1614	0.54105	1.0:0.0:0.0:0.0	.	204;204	A8K6J7;Q93070	.;NAR4_HUMAN	C	204;187	ENSP00000228936:F204C;ENSP00000405689:F187C	ENSP00000228936:F204C	F	-	2	0	ART4	14884888	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	6.846000	0.75399	2.193000	0.70182	0.460000	0.39030	TTT		0.493	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071		C	14993621	A	C	14993621	3	2	61	1	0	0	0	0	1	0	0	0	1000	14	1	4	341	4	ART4	12	14993621	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	34359	14993621	118858274	7905	15890										
EPS8	2059	broad.mit.edu	37	chr12	15822654	15822654	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccacttgaagaatcatatCttgagtccacactttgccct	5	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:15822654C>A	ENST00000281172.5	-	5	746	c.310G>T	c.(310-312)Gat>Tat	p.D104Y	EPS8_ENST00000543612.1_Missense_Mutation_p.D104Y|EPS8_ENST00000543523.1_Missense_Mutation_p.D104Y|RNU6-251P_ENST00000363235.1_RNA	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	104	PH; first part.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)	p.D104Y(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		AGAATCATATCTTGAGTCCAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											123	107	112					12																	15822654		2203	4300	6503	15713921	SO:0001583	missense	2059			U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.310G>T	12.37:g.15822654C>A	ENSP00000281172:p.Asp104Tyr		15713921	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	37	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.393714	0.83011	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000543223;ENST00000546311;ENST00000535752	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.08	5.08	0.68730	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.051712	0.85682	D	0.000000	T	0.67822	0.2934	M	0.65975	2.015	0.80722	D	1	D	0.64830	0.994	D	0.68943	0.961	T	0.71224	-0.4656	10	0.87932	D	0	-22.2539	18.8402	0.92180	0.0:1.0:0.0:0.0	.	104	Q12929	EPS8_HUMAN	Y	104	ENSP00000441867:D104Y;ENSP00000281172:D104Y;ENSP00000442388:D104Y;ENSP00000445235:D104Y;ENSP00000440591:D104Y	ENSP00000281172:D104Y	D	-	1	0	EPS8	15713921	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.771000	0.85420	2.528000	0.85240	0.650000	0.86243	GAT		0.373	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			A	15822654	C	A	15822654	3	1	61	1	0	0	0	0	1	0	0	0	5207	913	32	2	2226	2	EPS8	12	15822654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	829033	15822654	118029241	7906	15891										
DERA	51071	broad.mit.edu	37	chr12	16189274	16189275	+	Nonsense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgaagccagaactctttCgaataggtgccagtactctg					rs376413295		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:16189274_16189275CG>TA	ENST00000428559.2	+	8	1071_1072	c.859_860CG>TA	c.(859-861)CGa>TAa	p.R287*	DERA_ENST00000532573.1_3'UTR|DERA_ENST00000532964.1_Nonsense_Mutation_p.R244*|DERA_ENST00000526530.1_Nonsense_Mutation_p.R199*	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	287					deoxyribonucleoside catabolic process (GO:0046121)|deoxyribonucleotide catabolic process (GO:0009264)|deoxyribose phosphate catabolic process (GO:0046386)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	deoxyribose-phosphate aldolase activity (GO:0004139)	p.R287>?(1)		endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		Hepatocellular(102;0.121)				AGAACTCTTTCGAATAGGTGCC	0.455																																																1	Complex(1)	large_intestine(1)	12																																								16080542	SO:0001587	stop_gained	51071			AF132960	CCDS44838.1, CCDS73451.1	12p12.3	2010-06-24	2010-06-24		ENSG00000023697	ENSG00000023697	4.1.2.4		24269	protein-coding gene	gene with protein product			"2-deoxyribose-5-phosphate aldolase homolog (C. elegans)"			12546782	Standard	XM_006719083		Approved	CGI-26, DEOC	uc001rde.3	Q9Y315	OTTHUMG00000165537	Exception_encountered	12.37:g.16189274_16189275delinsTA	ENSP00000416583:p.Arg287*		16080541	Q53HN9|Q6PHW2	Nonsense_Mutation	DNP	ENST00000428559.2	37	CCDS44838.1																																																																																				0.455	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954		TA	16189275	CG	TA	16189274	4	4	61	1	0	0	0	0	0	1	0	0	4456	876	31	1	889	1	DERA	12	16189274	Nonsense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	366620	16189274	117662621	7907	15892										
LMO3	55885	broad.mit.edu	37	chr12	16704219	16704219	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtagtccgtctggcaaagGatcatgttattctttaggaa	10	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:16704219G>A	ENST00000320122.6	-	4	897	c.375C>T	c.(373-375)atC>atT	p.I125I	LMO3_ENST00000534946.1_Silent_p.I125I|LMO3_ENST00000447609.1_Silent_p.I125I|LMO3_ENST00000541846.1_Silent_p.I125I|LMO3_ENST00000541295.1_Silent_p.I143I|LMO3_ENST00000535535.1_Silent_p.I125I|LMO3_ENST00000540848.1_Silent_p.I125I|LMO3_ENST00000354662.1_Silent_p.I125I|LMO3_ENST00000537304.1_Silent_p.I125I|LMO3_ENST00000540445.1_Silent_p.I147I|LMO3_ENST00000441439.2_Silent_p.I125I|LMO3_ENST00000261169.6_Silent_p.I136I	NM_001243611.1	NP_001230540.1	Q8TAP4	LMO3_HUMAN	LIM domain only 3 (rhombotin-like 2)	125	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)	p.I125I(1)		endometrium(2)|large_intestine(2)|skin(1)	5		Hepatocellular(102;0.244)				TCTGGCAAAGGATCATGTTAT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	12											148	137	141					12																	16704219		2203	4300	6503	16595486	SO:0001819	synonymous_variant	55885			BC026311	CCDS8678.1, CCDS58210.1, CCDS58211.1, CCDS58212.1	12p13	2004-05-19			ENSG00000048540	ENSG00000048540			6643	protein-coding gene	gene with protein product		180386		RBTNL2		11489251	Standard	NM_018640		Approved	Rhom-3, DAT1	uc010shy.2	Q8TAP4	OTTHUMG00000168837	ENST00000320122.6:c.375C>T	12.37:g.16704219G>A			16595486	B4DG90|B4DH35|Q58A66|Q58A67|Q8N974|Q9UDD5	Silent	SNP	ENST00000320122.6	37	CCDS8678.1																																																																																				0.353	LMO3-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401279.1	NM_018640		A	16704219	G	A	16704219	2	1	61	1	0	0	0	0	0	0	0	1	8877	1164	41	3		3	LMO3	12	16704219	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	514945	16704219	117147676	7908	15893										
PIK3C2G	5288	broad.mit.edu	37	chr12	18435102	18435102	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatttctctttgtaaatcaAccccattcttctagccaagt	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:18435102A>G	ENST00000266497.5	+	1	125	c.87A>G	c.(85-87)caA>caG	p.Q29Q	PIK3C2G_ENST00000433979.1_Silent_p.Q29Q|PIK3C2G_ENST00000535651.1_Silent_p.Q29Q|PIK3C2G_ENST00000538779.1_Silent_p.Q29Q|RERGL_ENST00000541632.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	29					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.Q29Q(2)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTGTAAATCAACCCCATTCTT	0.368																																																2	Substitution - coding silent(2)	large_intestine(2)	12											64	61	62					12																	18435102		1867	4106	5973	18326369	SO:0001819	synonymous_variant	5288			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.87A>G	12.37:g.18435102A>G			18326369	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																				0.368	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18435102	A	G	18435102	2	3	61	1	0	0	0	0	0	0	0	1	11942	40	2	4		4	PIK3C2G	12	18435102	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1730883	18435102	115416793	7909	15894										
PIK3C2G	5288	broad.mit.edu	37	chr12	18443905	18443905	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtttaatatacatatttTtattgataactcaacacaac	2	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:18443905T>G	ENST00000266497.5	+	3	916	c.878T>G	c.(877-879)tTt>tGt	p.F293C	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.F293C|PIK3C2G_ENST00000536967.1_3'UTR|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.F293C|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.F293C|RERGL_ENST00000541632.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	293	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.F293C(2)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				ATACATATTTTTATTGATAAC	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	12											49	47	47					12																	18443905		1813	4076	5889	18335172	SO:0001583	missense	5288			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.878T>G	12.37:g.18443905T>G	ENSP00000266497:p.Phe293Cys		18335172	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	6.178	0.400974	0.11696	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.07	-0.175	0.13315	Phosphoinositide 3-kinase, ras-binding (2);	2.486070	0.01200	N	0.007559	T	0.28599	0.0708	N	0.22421	0.69	0.09310	N	1	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.08055	0.003;0.002;0.002	T	0.12477	-1.0546	10	0.38643	T	0.18	-1.3011	3.5529	0.07853	0.0:0.3073:0.2277:0.465	.	292;293;293	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	C	293	ENSP00000443850:F293C;ENSP00000404845:F293C;ENSP00000266497:F293C;ENSP00000445381:F293C	ENSP00000266497:F293C	F	+	2	0	PIK3C2G	18335172	0.507000	0.26146	0.013000	0.15412	0.008000	0.06430	0.366000	0.20365	-0.017000	0.14103	0.524000	0.50904	TTT		0.368	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18443905	T	G	18443905	3	3	61	1	0	0	0	0	1	0	0	0	11942	1841	64	4	888	4	PIK3C2G	12	18443905	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8803	18443905	115407990	7910	15895										
PLCZ1	89869	broad.mit.edu	37	chr12	18852769	18852769	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcttgtgtctccccaataGaattattttcattaaattgc	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:18852769G>T	ENST00000538330.1	-	6	860	c.479C>A	c.(478-480)tCt>tAt	p.S160Y	PLCZ1_ENST00000435379.1_Missense_Mutation_p.S183Y|PLCZ1_ENST00000541695.1_Missense_Mutation_p.S241Y|PLCZ1_ENST00000539875.1_Missense_Mutation_p.S185Y|PLCZ1_ENST00000266505.7_Missense_Mutation_p.S378Y|PLCZ1_ENST00000542762.1_5'UTR|PLCZ1_ENST00000447925.2_Missense_Mutation_p.S376Y					phospholipase C, zeta 1									p.S378Y(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CTCCCCAATAGAATTATTTTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											44	49	47					12																	18852769		2202	4295	6497	18744036	SO:0001583	missense	89869			AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.479C>A	12.37:g.18852769G>T	ENSP00000445880:p.Ser160Tyr		18744036		Missense_Mutation	SNP	ENST00000538330.1	37		.	.	.	.	.	.	.	.	.	.	G	22.4	4.280378	0.80692	.	.	ENSG00000139151	ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000541695;ENST00000539875;ENST00000540421;ENST00000543242	T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;0.05	5.88	5.88	0.94601	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	D	0.93051	0.7788	H	0.98351	4.21	0.50313	D	0.999864	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95215	0.8329	10	0.87932	D	0	.	16.9709	0.86298	0.0:0.0:1.0:0.0	.	378;160	Q86YW0;Q8N7S5	PLCZ1_HUMAN;.	Y	160;378;376;183;241;185;113;119	ENSP00000445880:S160Y;ENSP00000266505:S378Y;ENSP00000402358:S376Y;ENSP00000400504:S183Y;ENSP00000443349:S241Y;ENSP00000445026:S185Y;ENSP00000445889:S113Y;ENSP00000443762:S119Y	ENSP00000266505:S378Y	S	-	2	0	PLCZ1	18744036	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	6.980000	0.76160	2.779000	0.95612	0.650000	0.86243	TCT		0.328	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		T	18852769	G	T	18852769	3	4	61	1	0	0	0	0	1	0	0	0	12075	942	33	2	717	2	PLCZ1	12	18852769	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	408864	18852769	114999126	7911	15896										
CAPZA3	93661	broad.mit.edu	37	chr12	18891302	18891302	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtaaatgcctttgatgatCtctgtctgcttatccgtgat	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:18891302C>A	ENST00000317658.3	+	1	258	c.100C>A	c.(100-102)Ctc>Atc	p.L34I	PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	34					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)		p.L34I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTTTGATGATCTCTGTCTGCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											108	101	103					12																	18891302		2203	4299	6502	18782569	SO:0001583	missense	93661			AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.100C>A	12.37:g.18891302C>A	ENSP00000326238:p.Leu34Ile		18782569	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.534818	0.64972	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.8	4.8	0.61643	.	0.085593	0.48286	D	0.000200	T	0.65217	0.2670	L	0.31664	0.95	0.38538	D	0.949152	D	0.69078	0.997	D	0.85130	0.997	T	0.69232	-0.5199	9	0.54805	T	0.06	-5.9873	14.7244	0.69332	0.0:1.0:0.0:0.0	.	34	Q96KX2	CAZA3_HUMAN	I	34	.	ENSP00000326238:L34I	L	+	1	0	CAPZA3	18782569	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.062000	0.49971	2.498000	0.84270	0.563000	0.77884	CTC		0.468	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		A	18891302	C	A	18891302	3	1	61	1	0	0	0	0	1	0	0	0	2648	913	32	2	102	2	CAPZA3	12	18891302	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38533	18891302	114960593	7912	15897										
SLCO1C1	53919	broad.mit.edu	37	chr12	20852529	20852529	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatggacacttcatccaaaGaaaatatccagttgttctgc	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:20852529G>T	ENST00000266509.2	+	2	387	c.19G>T	c.(19-21)Gaa>Taa	p.E7*	SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000381552.1_Nonsense_Mutation_p.E7*|SLCO1C1_ENST00000545604.1_Nonsense_Mutation_p.E7*|SLCO1C1_ENST00000540354.1_Nonsense_Mutation_p.E7*	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	7					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.E7*(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TTCATCCAAAGAAAATATCCA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											59	59	59					12																	20852529		2203	4299	6502	20743796	SO:0001587	stop_gained	53919			AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.19G>T	12.37:g.20852529G>T	ENSP00000266509:p.Glu7*		20743796	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Nonsense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	G	37	6.059751	0.97246	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	.	.	.	4.86	3.97	0.46021	.	1.245850	0.05226	N	0.509429	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	11.3881	0.49798	0.0835:0.0:0.9165:0.0	.	.	.	.	X	7	.	ENSP00000266509:E7X	E	+	1	0	SLCO1C1	20743796	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.111000	0.50360	1.285000	0.44548	0.655000	0.94253	GAA		0.333	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		T	20852529	G	T	20852529	4	4	61	1	0	0	0	0	0	1	0	0	14762	943	33	2	21	2	SLCO1C1	12	20852529	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1961227	20852529	112999366	7913	15898										
SLCO1B3	28234	broad.mit.edu	37	chr12	21015486	21015486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaggacattcttccttgTatttaggtaacgtacagaat	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21015486T>C	ENST00000381545.3	+	7	841	c.622T>C	c.(622-624)Tat>Cat	p.Y208H	SLCO1B7_ENST00000554957.1_Intron|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.Y208H|LST3_ENST00000540229.1_Missense_Mutation_p.Y208H|LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.Y208H	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	208					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)	p.Y208H(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTCTTCCTTGTATTTAGGTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	93	93					12																	21015486		2203	4300	6503	20906753	SO:0001583	missense	28234				CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.622T>C	12.37:g.21015486T>C	ENSP00000370956:p.Tyr208His		20906753	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.642557	0.29246	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	3.9	2.68	0.31781	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.188484	0.48286	N	0.000198	T	0.63402	0.2508	M	0.86097	2.795	0.29923	N	0.822574	P;P;P	0.51933	0.864;0.949;0.949	P;P;P	0.60415	0.663;0.874;0.874	T	0.62058	-0.6934	10	0.52906	T	0.07	.	7.059	0.25115	0.0:0.1872:0.0:0.8128	.	208;208;208	Q5JAR4;B3KP78;Q9NPD5	.;.;SO1B3_HUMAN	H	208;208;208;208;32;208	ENSP00000442000:Y208H;ENSP00000261196:Y208H;ENSP00000370956:Y208H;ENSP00000451758:Y208H;ENSP00000443225:Y32H;ENSP00000441269:Y208H	ENSP00000441269:Y208H	Y	+	1	0	SLCO1B3;RP11-545J16.1	20906753	1.000000	0.71417	0.012000	0.15200	0.378000	0.30076	4.746000	0.62133	0.352000	0.24053	0.377000	0.23210	TAT		0.338	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		C	21015486	T	C	21015486	3	2	61	1	0	0	0	0	1	0	0	0	14761	1638	57	4	640	4	SLCO1B3	12	21015486	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162957	21015486	112836409	7914	15899										
LST-3TM12	338821	broad.mit.edu	37	chr12	21172237	21172237	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatctaaactacacagaccGaagttaattggaattggttg	10	6	1	1	rs267603415		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21172237G>A	ENST00000421593.2	+	2	141	c.141G>A	c.(139-141)ccG>ccA	p.P47P	SLCO1B7_ENST00000554957.1_Intron|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000540229.1_Intron|LST3_ENST00000381541.3_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.P47P(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TACACAGACCGAAGTTAATTG	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	12											178	171	173					12																	21172237		2203	4299	6502	21063504	SO:0001819	synonymous_variant	338821			AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"Solute carriers"	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.141G>A	12.37:g.21172237G>A			21063504	Q71QF0	Silent	SNP	ENST00000421593.2	37	CCDS44843.1																																																																																				0.328	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562		A	21172237	G	A	21172237	2	1	61	1	0	0	0	0	0	0	0	1	9095	1045	37	1		1	LST-3TM12	12	21172237	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	156751	21172237	112679658	7915	15900										
SLCO1B1	10599	broad.mit.edu	37	chr12	21327517	21327517	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttccctttctaggaaattTgcttgtgattgtatttgtga	9	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21327517T>C	ENST00000256958.2	+	4	329	c.233T>C	c.(232-234)tTg>tCg	p.L78S		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	78					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.L78S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	CTAGGAAATTTGCTTGTGATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											169	150	156					12																	21327517		2203	4300	6503	21218784	SO:0001583	missense	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.233T>C	12.37:g.21327517T>C	ENSP00000256958:p.Leu78Ser		21218784	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.399537	0.62177	.	.	ENSG00000134538	ENST00000256958	T	0.45276	0.9	3.66	3.66	0.41972	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	T	0.62282	0.2415	M	0.78049	2.395	0.47153	D	0.99933	D	0.76494	0.999	D	0.75484	0.986	T	0.66472	-0.5915	10	0.62326	D	0.03	.	11.3015	0.49309	0.0:0.0:0.0:1.0	.	78	Q9Y6L6	SO1B1_HUMAN	S	78	ENSP00000256958:L78S	ENSP00000256958:L78S	L	+	2	0	SLCO1B1	21218784	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	7.047000	0.76599	1.656000	0.50722	0.254000	0.18369	TTG		0.353	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		C	21327517	T	C	21327517	3	2	61	1	0	0	0	0	1	0	0	0	14760	1821	63	4	243	4	SLCO1B1	12	21327517	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	155280	21327517	112524378	7916	15901										
SLCO1B1	10599	broad.mit.edu	37	chr12	21329726	21329726	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagttacaggtattctaaaGaaactaatatcaattcatca	4	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21329726G>T	ENST00000256958.2	+	5	472	c.376G>T	c.(376-378)Gaa>Taa	p.E126*		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	126					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.E126*(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GTATTCTAAAGAAACTAATAT	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											70	72	71					12																	21329726		2198	4285	6483	21220993	SO:0001587	stop_gained	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.376G>T	12.37:g.21329726G>T	ENSP00000256958:p.Glu126*		21220993	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Nonsense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757409	0.49468	.	.	ENSG00000134538	ENST00000256958	.	.	.	3.52	3.52	0.40303	.	1.140570	0.06248	N	0.691668	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	10.71	0.45977	0.0:0.0:1.0:0.0	.	.	.	.	X	126	.	ENSP00000256958:E126X	E	+	1	0	SLCO1B1	21220993	0.909000	0.30893	0.763000	0.31416	0.142000	0.21351	3.123000	0.50453	1.955000	0.56771	0.305000	0.20034	GAA		0.303	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		T	21329726	G	T	21329726	4	4	61	1	0	0	0	0	0	1	0	0	14760	943	33	2	390	2	SLCO1B1	12	21329726	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2209	21329726	112522169	7917	15902										
SLCO1B1	10599	broad.mit.edu	37	chr12	21331626	21331626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttacattgatgatttcGctaaagaaggacattcttct	6	7	3	3	rs540112224		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21331626G>A	ENST00000256958.2	+	6	694	c.598G>A	c.(598-600)Gct>Act	p.A200T		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	200					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.A200T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TGATGATTTCGCTAAAGAAGG	0.353													G|||	1	0.000199681	0	0	5008	,	,		15195	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	12											120	111	114					12																	21331626		2203	4300	6503	21222893	SO:0001583	missense	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.598G>A	12.37:g.21331626G>A	ENSP00000256958:p.Ala200Thr		21222893	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089140	0.36855	.	.	ENSG00000134538	ENST00000256958	T	0.60171	0.21	3.71	3.71	0.42584	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.242240	0.42053	D	0.000764	T	0.71953	0.3401	M	0.85299	2.745	0.38461	D	0.94722	D	0.67145	0.996	D	0.66497	0.944	T	0.75693	-0.3229	10	0.56958	D	0.05	.	6.1548	0.20332	0.0945:0.0:0.5958:0.3097	.	200	Q9Y6L6	SO1B1_HUMAN	T	200	ENSP00000256958:A200T	ENSP00000256958:A200T	A	+	1	0	SLCO1B1	21222893	1.000000	0.71417	0.991000	0.47740	0.181000	0.23173	1.791000	0.38744	2.065000	0.61736	0.313000	0.20887	GCT		0.353	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		A	21331626	G	A	21331626	3	1	61	1	0	0	0	0	1	0	0	0	14760	1087	38	1	616	1	SLCO1B1	12	21331626	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1900	21331626	112520269	7918	15903										
SLCO1B1	10599	broad.mit.edu	37	chr12	21370160	21370160	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgtacaaggaaattttaCttttttgttgcaatacaagt	7	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21370160C>A	ENST00000256958.2	+	12	1701	c.1605C>A	c.(1603-1605)taC>taA	p.Y535*		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	535					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.Y535*(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GGAAATTTTACTTTTTTGTTG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											142	144	143					12																	21370160		2203	4300	6503	21261427	SO:0001587	stop_gained	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1605C>A	12.37:g.21370160C>A	ENSP00000256958:p.Tyr535*		21261427	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Nonsense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143978	0.77888	.	.	ENSG00000134538	ENST00000256958	.	.	.	3.84	1.23	0.21249	.	0.504913	0.20650	N	0.088222	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.6646	0.12659	0.0:0.3403:0.0:0.6597	.	.	.	.	X	535	.	ENSP00000256958:Y535X	Y	+	3	2	SLCO1B1	21261427	0.000000	0.05858	0.059000	0.19551	0.013000	0.08279	-0.015000	0.12634	0.572000	0.29383	0.491000	0.48974	TAC		0.368	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		A	21370160	C	A	21370160	4	1	61	1	0	0	0	0	0	1	0	0	14760	576	20	2	1647	2	SLCO1B1	12	21370160	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38534	21370160	112481735	7919	15904										
RECQL	5965	broad.mit.edu	37	chr12	21630862	21630862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcagcccaattagtgatgCgttagggaactgccgcttta	11	9	1	1	rs202110155		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21630862C>T	ENST00000444129.2	-	7	1210	c.742G>A	c.(742-744)Gca>Aca	p.A248T	RECQL_ENST00000421138.2_Missense_Mutation_p.A248T	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	248	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.A248T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						ATTAGTGATGCGTTAGGGAAC	0.358								Other identified genes with known or suspected DNA repair function					C|||	1	0.000199681	0	0	5008	,	,		17226	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											94	94	94					12																	21630862		2203	4300	6503	21522129	SO:0001583	missense	5965			D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"DNA helicase Q1-like"	600537	"RecQ protein-like (DNA helicase Q1-like)"			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.742G>A	12.37:g.21630862C>T	ENSP00000416739:p.Ala248Thr		21522129	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	3.419	-0.118657	0.06838	.	.	ENSG00000004700	ENST00000444129;ENST00000421138	T;T	0.76316	-1.01;-1.01	4.8	-1.99	0.07457	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.498949	0.24050	N	0.042011	T	0.47154	0.1430	N	0.02765	-0.5	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.35301	-0.9794	10	0.39692	T	0.17	-7.3848	6.1865	0.20500	0.2292:0.4425:0.0:0.3283	.	248	P46063	RECQ1_HUMAN	T	248	ENSP00000416739:A248T;ENSP00000395449:A248T	ENSP00000395449:A248T	A	-	1	0	RECQL	21522129	0.876000	0.30132	0.004000	0.12327	0.001000	0.01503	1.209000	0.32357	-0.425000	0.07371	-1.107000	0.02091	GCA		0.358	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		T	21630862	C	T	21630862	3	4	61	1	0	0	0	0	1	0	0	0	13238	768	27	1	1243	1	RECQL	12	21630862	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	260702	21630862	112221033	7920	15905										
GYS2	2998	broad.mit.edu	37	chr12	21712623	21712623	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttttttccaaacttttcCttcacagaatgtgcaacatc	4	10	1	1	rs368757293		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21712623C>A	ENST00000261195.2	-	9	1445	c.1191G>T	c.(1189-1191)aaG>aaT	p.K397N		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	397					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.K397N(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CAAACTTTTCCTTCACAGAAT	0.294																																					Colon(149;9 1820 3690 10544 50424)											1	Substitution - Missense(1)	large_intestine(1)	12											101	108	106					12																	21712623		2202	4294	6496	21603890	SO:0001583	missense	2998				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1191G>T	12.37:g.21712623C>A	ENSP00000261195:p.Lys397Asn		21603890	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.118153	0.56505	.	.	ENSG00000111713	ENST00000261195	T	0.65732	-0.17	5.01	1.12	0.20585	.	0.000000	0.85682	D	0.000000	T	0.66992	0.2846	L	0.40543	1.245	0.58432	D	0.999991	D	0.89917	1.0	D	0.85130	0.997	T	0.64071	-0.6493	10	0.59425	D	0.04	-29.6354	8.9657	0.35874	0.0:0.5473:0.0:0.4527	.	397	P54840	GYS2_HUMAN	N	397	ENSP00000261195:K397N	ENSP00000261195:K397N	K	-	3	2	GYS2	21603890	0.998000	0.40836	0.998000	0.56505	0.923000	0.55619	0.518000	0.22847	0.101000	0.17610	-0.251000	0.11542	AAG		0.294	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		A	21712623	C	A	21712623	3	1	61	1	0	0	0	0	1	0	0	0	6934	680	24	2	952	2	GYS2	12	21712623	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81761	21712623	112139272	7921	15906										
GYS2	2998	broad.mit.edu	37	chr12	21721869	21721869	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgtggtgaacacgtgagcGcaatgaacggaagctcgctc	13	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21721869G>A	ENST00000261195.2	-	5	1007	c.753C>T	c.(751-753)tgC>tgT	p.C251C		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	251					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.C251C(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ACACGTGAGCGCAATGAACGG	0.423																																					Colon(149;9 1820 3690 10544 50424)											1	Substitution - coding silent(1)	large_intestine(1)	12											173	164	167					12																	21721869		2203	4300	6503	21613136	SO:0001819	synonymous_variant	2998				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.753C>T	12.37:g.21721869G>A			21613136	A0AVD8	Silent	SNP	ENST00000261195.2	37	CCDS8690.1																																																																																				0.423	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		A	21721869	G	A	21721869	2	1	61	1	0	0	0	0	0	0	0	1	6934	1079	38	1		1	GYS2	12	21721869	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9246	21721869	112130026	7922	15907										
GYS2	2998	broad.mit.edu	37	chr12	21728967	21728967	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccacataaggacttccttCtatcagccatcttccaaaat	3	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21728967C>A	ENST00000261195.2	-	3	582	c.328G>T	c.(328-330)Gaa>Taa	p.E110*		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	110					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.E110*(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGACTTCCTTCTATCAGCCAT	0.443																																					Colon(149;9 1820 3690 10544 50424)											1	Substitution - Nonsense(1)	large_intestine(1)	12											105	96	99					12																	21728967		2203	4300	6503	21620234	SO:0001587	stop_gained	2998				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.328G>T	12.37:g.21728967C>A	ENSP00000261195:p.Glu110*		21620234	A0AVD8	Nonsense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	39	7.416544	0.98272	.	.	ENSG00000111713	ENST00000261195	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.9305	18.9212	0.92526	0.0:1.0:0.0:0.0	.	.	.	.	X	110	.	ENSP00000261195:E110X	E	-	1	0	GYS2	21620234	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.265000	0.78442	2.781000	0.95711	0.650000	0.86243	GAA		0.443	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		A	21728967	C	A	21728967	4	1	61	1	0	0	0	0	0	1	0	0	6934	922	32	2	1839	2	GYS2	12	21728967	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7098	21728967	112122928	7923	15908										
LDHB	3945	broad.mit.edu	37	chr12	21791301	21791301	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttacctttcaaccaccatCttatgcacttccttccaatt	1	15	2	0	rs375806839		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21791301C>A	ENST00000396076.1	-	6	1031	c.699G>T	c.(697-699)aaG>aaT	p.K233N	LDHB_ENST00000350669.1_Missense_Mutation_p.K233N	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	233					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)	p.K233N(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						CAACCACCATCTTATGCACTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											125	122	123					12																	21791301		2203	4300	6503	21682568	SO:0001583	missense	3945				CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.699G>T	12.37:g.21791301C>A	ENSP00000379386:p.Lys233Asn		21682568		Missense_Mutation	SNP	ENST00000396076.1	37	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364735	0.82463	.	.	ENSG00000111716	ENST00000396076;ENST00000350669	T;T	0.68025	-0.3;-0.3	5.11	4.19	0.49359	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.80454	0.4626	M	0.77616	2.38	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.82022	-0.0663	10	0.62326	D	0.03	.	12.6257	0.56628	0.0:0.9159:0.0:0.0841	.	233	P07195	LDHB_HUMAN	N	233	ENSP00000379386:K233N;ENSP00000229319:K233N	ENSP00000229319:K233N	K	-	3	2	LDHB	21682568	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.207000	0.42788	1.087000	0.41251	0.655000	0.94253	AAG		0.373	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300		A	21791301	C	A	21791301	3	1	61	1	0	0	0	0	1	0	0	0	8723	912	32	2	317	2	LDHB	12	21791301	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62334	21791301	112060594	7924	15909										
LDHB	3945	broad.mit.edu	37	chr12	21794978	21794978	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggtagcgaaatctagcaGaatccagattacatccactt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21794978G>T	ENST00000396076.1	-	5	835	c.503C>A	c.(502-504)tCt>tAt	p.S168Y	LDHB_ENST00000350669.1_Missense_Mutation_p.S168Y	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	168					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)	p.S168Y(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						AAATCTAGCAGAATCCAGATT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											110	100	103					12																	21794978		2203	4300	6503	21686245	SO:0001583	missense	3945				CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.503C>A	12.37:g.21794978G>T	ENSP00000379386:p.Ser168Tyr		21686245		Missense_Mutation	SNP	ENST00000396076.1	37	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	G	31	5.062905	0.93898	.	.	ENSG00000111716	ENST00000396076;ENST00000350669;ENST00000396075	T;T;T	0.67698	-0.28;-0.28;-0.28	5.67	5.67	0.87782	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.105298	0.64402	D	0.000002	D	0.90638	0.7064	H	0.99425	4.56	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94411	0.7632	10	0.87932	D	0	.	19.8346	0.96650	0.0:0.0:1.0:0.0	.	168	P07195	LDHB_HUMAN	Y	168	ENSP00000379386:S168Y;ENSP00000229319:S168Y;ENSP00000379385:S168Y	ENSP00000229319:S168Y	S	-	2	0	LDHB	21686245	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.848000	0.99507	2.679000	0.91253	0.644000	0.83932	TCT		0.423	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300		T	21794978	G	T	21794978	3	4	61	1	0	0	0	0	1	0	0	0	8723	942	33	2	517	2	LDHB	12	21794978	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3677	21794978	112056917	7925	15910										
KCNJ8	3764	broad.mit.edu	37	chr12	21918737	21918737	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggaagaattgttccttcGgatagaattgttcctcctca	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21918737G>A	ENST00000240662.2	-	3	1540	c.1195C>T	c.(1195-1197)Cga>Tga	p.R399*	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	399					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.R399*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	TTGTTCCTTCGGATAGAATTG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											144	139	140					12																	21918737		2203	4300	6503	21810004	SO:0001587	stop_gained	3764			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.1195C>T	12.37:g.21918737G>A	ENSP00000240662:p.Arg399*		21810004	O00657	Nonsense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	G	37	6.454116	0.97581	.	.	ENSG00000121361	ENST00000240662;ENST00000539350	.	.	.	5.86	3.84	0.44239	.	0.408001	0.25397	N	0.030967	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0294	0.80567	0.0:0.0:0.6537:0.3462	.	.	.	.	X	399	.	ENSP00000240662:R399X	R	-	1	2	KCNJ8	21810004	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	1.655000	0.37345	1.456000	0.47831	0.655000	0.94253	CGA		0.418	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		A	21918737	G	A	21918737	4	1	61	1	0	0	0	0	0	1	0	0	8077	1124	39	1	83	1	KCNJ8	12	21918737	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123759	21918737	111933158	7926	15911										
KCNJ8	3764	broad.mit.edu	37	chr12	21918957	21918957	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcctcagtcacaatggaCacaaagcggtggccccattg	9	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21918957C>T	ENST00000240662.2	-	3	1320	c.975G>A	c.(973-975)gtG>gtA	p.V325V	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	325					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.V325V(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	TCACAATGGACACAAAGCGGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	12											99	91	94					12																	21918957		2203	4300	6503	21810224	SO:0001819	synonymous_variant	3764			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.975G>A	12.37:g.21918957C>T			21810224	O00657	Silent	SNP	ENST00000240662.2	37	CCDS8692.1																																																																																				0.493	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		T	21918957	C	T	21918957	2	4	61	1	0	0	0	0	0	0	0	1	8077	465	17	3		3	KCNJ8	12	21918957	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220	21918957	111932938	7927	15912										
KCNJ8	3764	broad.mit.edu	37	chr12	21919461	21919461	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atattctggagaatcaaaacCgtgatggccaaagggcattc	10	8	2	2	rs143319002	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21919461C>T	ENST00000240662.2	-	3	816	c.471G>A	c.(469-471)acG>acA	p.T157T	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	157					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.T157T(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	GAATCAAAACCGTGATGGCCA	0.438													C|||	3	0.000599042	0.0023	0	5008	,	,		21056	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											100	88	92					12																	21919461		2203	4300	6503	21810728	SO:0001819	synonymous_variant	3764			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.471G>A	12.37:g.21919461C>T			21810728	O00657	Silent	SNP	ENST00000240662.2	37	CCDS8692.1																																																																																				0.438	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		T	21919461	C	T	21919461	2	4	61	1	0	0	0	0	0	0	0	1	8077	639	23	1		1	KCNJ8	12	21919461	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	504	21919461	111932434	7928	15913										
KCNJ8	3764	broad.mit.edu	37	chr12	21926499	21926499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgcgcaggttctctgcggCgatgcgcgccagcacatact	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21926499C>T	ENST00000240662.2	-	2	397	c.52G>A	c.(52-54)Gcc>Acc	p.A18T		NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	18					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.A18T(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	TTCTCTGCGGCGATGCGCGCC	0.622											OREG0021704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											74	77	76					12																	21926499		2203	4299	6502	21817766	SO:0001583	missense	3764			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.52G>A	12.37:g.21926499C>T	ENSP00000240662:p.Ala18Thr	752	21817766	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	C	34	5.297749	0.95574	.	.	ENSG00000121361	ENST00000240662;ENST00000539350;ENST00000537950	D;D	0.92805	-2.52;-3.11	4.88	4.88	0.63580	.	0.270973	0.36200	N	0.002721	D	0.89757	0.6807	L	0.29908	0.895	0.50813	D	0.999894	D	0.62365	0.991	P	0.47075	0.536	D	0.90735	0.4645	10	0.52906	T	0.07	.	18.2172	0.89890	0.0:1.0:0.0:0.0	.	18	Q15842	IRK8_HUMAN	T	18	ENSP00000240662:A18T;ENSP00000440012:A18T	ENSP00000240662:A18T	A	-	1	0	KCNJ8	21817766	1.000000	0.71417	0.997000	0.53966	0.955000	0.61496	7.638000	0.83328	2.531000	0.85337	0.591000	0.81541	GCC		0.622	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		T	21926499	C	T	21926499	3	4	61	1	0	0	0	0	1	0	0	0	8077	768	27	1	1230	1	KCNJ8	12	21926499	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7038	21926499	111925396	7929	15914										
ABCC9	10060	broad.mit.edu	37	chr12	21953992	21953992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actccttcacatgtctgcgcGaacaaaagaagcaaatactc	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21953992G>A	ENST00000261200.4	-	38	4635	c.4636C>T	c.(4636-4638)Cgc>Tgc	p.R1546C		NM_020297.2	NP_064693.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	0	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.R1546C(1)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	ATGTCTGCGCGAACAAAAGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											91	85	87					12																	21953992		2203	4300	6503	21845259	SO:0001583	missense	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261200.4:c.4636C>T	12.37:g.21953992G>A	ENSP00000261200:p.Arg1546Cys		21845259	O60707	Missense_Mutation	SNP	ENST00000261200.4	37	CCDS8693.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905144	0.72868	.	.	ENSG00000069431	ENST00000261200	D	0.90900	-2.75	4.88	4.88	0.63580	.	0.116707	0.56097	D	0.000021	D	0.91479	0.7310	L	0.56396	1.775	0.80722	D	1	D;P	0.58970	0.984;0.952	P;P	0.48795	0.59;0.556	D	0.92624	0.6110	10	0.87932	D	0	-2.9795	18.5784	0.91163	0.0:0.0:1.0:0.0	.	1546;117	O60706-2;Q8N9N1	.;.	C	1546	ENSP00000261200:R1546C	ENSP00000261200:R1546C	R	-	1	0	ABCC9	21845259	0.979000	0.34478	1.000000	0.80357	0.951000	0.60555	3.657000	0.54474	2.695000	0.91970	0.650000	0.86243	CGC		0.383	ABCC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402228.1	NM_005691		A	21953992	G	A	21953992	3	1	61	1	0	0	0	0	1	0	0	0	59	1058	37	1	17	1	ABCC9	12	21953992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27493	21953992	111897903	7930	15915										
ABCC9	10060	broad.mit.edu	37	chr12	21960388	21960388	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgtccaacgctaaaattCtccccaccttcagtgacaac	4	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21960388C>A	ENST00000261201.4	-	36	4340	c.4341G>T	c.(4339-4341)gaG>gaT	p.E1447D	ABCC9_ENST00000345162.2_Missense_Mutation_p.E1411D|ABCC9_ENST00000261200.4_Missense_Mutation_p.E1447D	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1447	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.E1447D(1)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CGCTAAAATTCTCCCCACCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											125	111	116					12																	21960388		2203	4300	6503	21851655	SO:0001583	missense	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4341G>T	12.37:g.21960388C>A	ENSP00000261201:p.Glu1447Asp		21851655	O60707	Missense_Mutation	SNP	ENST00000261201.4	37	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952851	0.53293	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31	5.02	4.05	0.47172	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.87593	0.6216	N	0.10916	0.065	0.45515	D	0.99847	P;B	0.35107	0.484;0.259	B;B	0.42916	0.402;0.227	D	0.85576	0.1237	10	0.30078	T	0.28	-16.9376	12.84	0.57797	0.0:0.8657:0.0:0.1343	.	1447;1447	O60706;O60706-2	ABCC9_HUMAN;.	D	1447;1074;1447;1411	ENSP00000261200:E1447D;ENSP00000440521:E1074D;ENSP00000261201:E1447D;ENSP00000261202:E1411D	ENSP00000261200:E1447D	E	-	3	2	ABCC9	21851655	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.006000	0.40874	2.585000	0.87301	0.561000	0.74099	GAG		0.413	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	21960388	C	A	21960388	3	1	61	1	0	0	0	0	1	0	0	0	59	912	32	2	462	2	ABCC9	12	21960388	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6396	21960388	111891507	7931	15916										
ABCC9	10060	broad.mit.edu	37	chr12	21962852	21962852	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaaggcttcccagagtcTgtcatctgtgcatttgcact	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:21962852T>G	ENST00000261201.4	-	35	4248	c.4249A>C	c.(4249-4251)Aga>Cga	p.R1417R	ABCC9_ENST00000345162.2_Silent_p.R1381R|ABCC9_ENST00000261200.4_Silent_p.R1417R	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1417	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.R1417R(1)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TCCCAGAGTCTGTCATCTGTG	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	12											89	91	90					12																	21962852		2203	4300	6503	21854119	SO:0001819	synonymous_variant	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4249A>C	12.37:g.21962852T>G			21854119	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																				0.308	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		G	21962852	T	G	21962852	2	3	61	1	0	0	0	0	0	0	0	1	59	1588	55	4		4	ABCC9	12	21962852	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2464	21962852	111889043	7932	15917										
ABCC9	10060	broad.mit.edu	37	chr12	22028606	22028606	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgttggaattcgaatatCtatattggataatgtagcta	8	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22028606C>A	ENST00000261201.4	-	15	2073	c.2074G>T	c.(2074-2076)Gat>Tat	p.D692Y	ABCC9_ENST00000345162.2_Missense_Mutation_p.D656Y|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Missense_Mutation_p.D692Y	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	692	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.D692H(2)|p.D692Y(1)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	ATTCGAATATCTATATTGGAT	0.308																																																3	Substitution - Missense(3)	urinary_tract(2)|large_intestine(1)	12											77	77	77					12																	22028606		2203	4300	6503	21919873	SO:0001583	missense	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.2074G>T	12.37:g.22028606C>A	ENSP00000261201:p.Asp692Tyr		21919873	O60707	Missense_Mutation	SNP	ENST00000261201.4	37	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922576	0.52653	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.94092	-3.35;-3.35;-3.35;-3.35	5.55	3.74	0.42951	ABC transporter-like (1);	0.189340	0.56097	D	0.000035	D	0.93416	0.7900	M	0.68593	2.085	0.35187	D	0.773038	P;P	0.48503	0.773;0.911	P;P	0.49953	0.492;0.627	D	0.94638	0.7828	10	0.72032	D	0.01	-12.656	10.5036	0.44821	0.0:0.7832:0.0:0.2168	.	692;692	O60706;O60706-2	ABCC9_HUMAN;.	Y	692;319;692;656	ENSP00000261200:D692Y;ENSP00000440521:D319Y;ENSP00000261201:D692Y;ENSP00000261202:D656Y	ENSP00000261200:D692Y	D	-	1	0	ABCC9	21919873	1.000000	0.71417	0.999000	0.59377	0.793000	0.44817	1.238000	0.32707	0.708000	0.31955	0.484000	0.47621	GAT		0.308	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	22028606	C	A	22028606	3	1	61	1	0	0	0	0	1	0	0	0	59	913	32	2	2813	2	ABCC9	12	22028606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65754	22028606	111823289	7933	15918										
ABCC9	10060	broad.mit.edu	37	chr12	22078907	22078907	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggaaaatttgatgtttcGatattatgataatacactat	6	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22078907G>A	ENST00000261201.4	-	3	374	c.375C>T	c.(373-375)atC>atT	p.I125I	ABCC9_ENST00000345162.2_Silent_p.I125I|ABCC9_ENST00000326684.4_Silent_p.I125I|ABCC9_ENST00000538350.1_Silent_p.I125I|ABCC9_ENST00000261200.4_Silent_p.I125I	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	125					defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.I125I(2)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TTGATGTTTCGATATTATGAT	0.383																																																2	Substitution - coding silent(2)	large_intestine(2)	12											104	103	103					12																	22078907		2203	4300	6503	21970174	SO:0001819	synonymous_variant	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.375C>T	12.37:g.22078907G>A			21970174	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																				0.383	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	22078907	G	A	22078907	2	1	61	1	0	0	0	0	0	0	0	1	59	1048	37	1		1	ABCC9	12	22078907	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50301	22078907	111772988	7934	15919										
CMAS	55907	broad.mit.edu	37	chr12	22208151	22208151	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggtgcacaagttcatcGaagaagttctgaagtttcaa	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22208151G>A	ENST00000229329.2	+	2	459	c.329G>A	c.(328-330)cGa>cAa	p.R110Q		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	110					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)	p.R110Q(2)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						CAAGTTCATCGAAGAAGTTCT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	12											83	80	81					12																	22208151		2203	4300	6503	22099418	SO:0001583	missense	55907			AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.329G>A	12.37:g.22208151G>A	ENSP00000229329:p.Arg110Gln		22099418	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	37	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239638	0.79800	.	.	ENSG00000111726	ENST00000229329	.	.	.	5.54	5.54	0.83059	.	0.080030	0.49305	D	0.000153	T	0.61400	0.2344	M	0.77486	2.375	0.52099	D	0.999946	P	0.50443	0.935	B	0.42163	0.378	T	0.63804	-0.6554	9	0.29301	T	0.29	-16.0592	17.6578	0.88182	0.0:0.0:1.0:0.0	.	110	Q8NFW8	NEUA_HUMAN	Q	110	.	ENSP00000229329:R110Q	R	+	2	0	CMAS	22099418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.000000	0.70678	2.597000	0.87782	0.591000	0.81541	CGA		0.338	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		A	22208151	G	A	22208151	3	1	61	1	0	0	0	0	1	0	0	0	3581	1058	37	1	335	1	CMAS	12	22208151	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129244	22208151	111643744	7935	15920										
CMAS	55907	broad.mit.edu	37	chr12	22214246	22214246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcaaagagaagcttaagGaaataaaacttttggtttgc	10	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22214246G>A	ENST00000229329.2	+	6	950	c.820G>A	c.(820-822)Gaa>Aaa	p.E274K		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	274					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)	p.E274K(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						GAAGCTTAAGGAAATAAAACT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	111	109					12																	22214246		2203	4300	6503	22105513	SO:0001583	missense	55907			AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.820G>A	12.37:g.22214246G>A	ENSP00000229329:p.Glu274Lys		22105513	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	37	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854340	0.32791	.	.	ENSG00000111726	ENST00000229329	T	0.21361	2.01	5.97	5.97	0.96955	HAD-like domain (2);	0.054903	0.64402	D	0.000001	T	0.11750	0.0286	N	0.04959	-0.14	0.50632	D	0.999881	B	0.06786	0.001	B	0.04013	0.001	T	0.16719	-1.0393	10	0.06625	T	0.88	-16.8083	20.4135	0.99023	0.0:0.0:1.0:0.0	.	274	Q8NFW8	NEUA_HUMAN	K	274	ENSP00000229329:E274K	ENSP00000229329:E274K	E	+	1	0	CMAS	22105513	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.821000	0.48065	2.835000	0.97688	0.591000	0.81541	GAA		0.343	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		A	22214246	G	A	22214246	3	1	61	1	0	0	0	0	1	0	0	0	3581	1175	41	3	842	3	CMAS	12	22214246	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6095	22214246	111637649	7936	15921										
CMAS	55907	broad.mit.edu	37	chr12	22218082	22218082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtctgatgaagagtgctTgaagagagtgggcctaagtg	16	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22218082T>C	ENST00000229329.2	+	8	1272	c.1142T>C	c.(1141-1143)tTg>tCg	p.L381S		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	381					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)	p.L381S(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						GAAGAGTGCTTGAAGAGAGTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											186	192	190					12																	22218082		2203	4300	6503	22109349	SO:0001583	missense	55907			AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.1142T>C	12.37:g.22218082T>C	ENSP00000229329:p.Leu381Ser		22109349	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	37	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033576	0.75504	.	.	ENSG00000111726	ENST00000229329	T	0.23147	1.92	5.53	5.53	0.82687	HAD-like domain (2);	0.000000	0.64402	D	0.000001	T	0.57577	0.2063	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66368	-0.5941	10	0.87932	D	0	-7.2675	14.2141	0.65781	0.0:0.0:0.0:1.0	.	381	Q8NFW8	NEUA_HUMAN	S	381	ENSP00000229329:L381S	ENSP00000229329:L381S	L	+	2	0	CMAS	22109349	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.877000	0.69675	2.085000	0.62840	0.455000	0.32223	TTG		0.428	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		C	22218082	T	C	22218082	3	2	61	1	0	0	0	0	1	0	0	0	3581	1821	63	4	1172	4	CMAS	12	22218082	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3836	22218082	111633813	7937	15922										
KIAA0528	9847	broad.mit.edu	37	chr12	22643136	22643136	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctgtgccagatgcagataAaatgcagacctcttcactat	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22643136A>C	ENST00000333957.4	-	12	1534	c.1279T>G	c.(1279-1281)Tta>Gta	p.L427V	C2CD5_ENST00000544930.1_Missense_Mutation_p.L242V|C2CD5_ENST00000396028.2_Missense_Mutation_p.L418V|C2CD5_ENST00000446597.1_Missense_Mutation_p.L427V|C2CD5_ENST00000542676.1_Missense_Mutation_p.L427V|C2CD5_ENST00000545552.1_Missense_Mutation_p.L440V|C2CD5_ENST00000536386.1_Missense_Mutation_p.L429V	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	427					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)	p.L427V(1)									GATGCAGATAAAATGCAGACC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	63	64					12																	22643136		2203	4300	6503	22534403	SO:0001583	missense	9847			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.1279T>G	12.37:g.22643136A>C	ENSP00000334229:p.Leu427Val		22534403	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	37	CCDS31758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.68|16.68	3.191755|3.191755	0.58017|0.58017	.|.	.|.	ENSG00000111731|ENSG00000111731	ENST00000535555|ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930	.|T;T;T;T;T;T;T	.|0.80033	.|0.28;0.28;0.28;0.28;0.28;0.28;-1.33	5.58|5.58	3.27|3.27	0.37495|0.37495	.|.	.|0.092352	.|0.44902	.|N	.|0.000409	D|D	0.88518|0.88518	0.6458|0.6458	M|M	0.84773|0.84773	2.715|2.715	0.42668|0.42668	D|D	0.993503|0.993503	.|P;B;B;B;B;D	.|0.76494	.|0.569;0.189;0.104;0.035;0.013;0.999	.|B;B;B;B;B;D	.|0.80764	.|0.251;0.051;0.088;0.05;0.021;0.994	D|D	0.88276|0.88276	0.2933|0.2933	5|10	.|0.87932	.|D	.|0	-6.804|-6.804	8.2032|8.2032	0.31436|0.31436	0.8446:0.0:0.1554:0.0|0.8446:0.0:0.1554:0.0	.|.	.|429;427;242;429;418;427	.|F5H2A1;B4DRN7;F5H3N1;B7ZLL0;Q86YS7-2;Q86YS7	.|.;.;.;.;.;K0528_HUMAN	C|V	124|427;427;429;418;427;440;242	.|ENSP00000334229:L427V;ENSP00000388756:L427V;ENSP00000439392:L429V;ENSP00000379345:L418V;ENSP00000441951:L427V;ENSP00000443204:L440V;ENSP00000445288:L242V	.|ENSP00000334229:L427V	F|L	-|-	2|1	0|2	KIAA0528|KIAA0528	22534403|22534403	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.768000|2.768000	0.47645|0.47645	0.962000|0.962000	0.38057|0.38057	0.477000|0.477000	0.44152|0.44152	TTT|TTA		0.403	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22643136	A	C	22643136	3	2	61	1	0	0	0	0	1	0	0	0	8203	11	1	4	1779	4	KIAA0528	12	22643136	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	425054	22643136	111208759	7938	15923										
KIAA0528	9847	broad.mit.edu	37	chr12	22677465	22677465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcccttggtgtgcgaattCgatcaatccactgatattct	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:22677465C>T	ENST00000333957.4	-	6	797	c.542G>A	c.(541-543)cGa>cAa	p.R181Q	C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000540703.1_5'UTR|C2CD5_ENST00000396028.2_Missense_Mutation_p.R181Q|C2CD5_ENST00000446597.1_Missense_Mutation_p.R181Q|C2CD5_ENST00000542676.1_Missense_Mutation_p.R181Q|C2CD5_ENST00000545552.1_Missense_Mutation_p.R181Q|C2CD5_ENST00000536386.1_Missense_Mutation_p.R181Q	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	181					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)	p.R181Q(2)									TGTGCGAATTCGATCAATCCA	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	12											134	120	125					12																	22677465		2203	4300	6503	22568732	SO:0001583	missense	9847			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.542G>A	12.37:g.22677465C>T	ENSP00000334229:p.Arg181Gln		22568732	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	37	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.939001	0.92526	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	4.95	4.02	0.46733	.	0.000000	0.64402	D	0.000001	T	0.48484	0.1502	L	0.48642	1.525	0.80722	D	1	D;P;P;D;P	0.69078	0.963;0.827;0.899;0.997;0.719	B;B;B;P;B	0.53722	0.432;0.119;0.17;0.733;0.119	T	0.51340	-0.8718	10	0.54805	T	0.06	-8.7416	14.6419	0.68732	0.146:0.854:0.0:0.0	.	181;181;181;181;181	F5H2A1;B4DRN7;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;K0528_HUMAN	Q	181	ENSP00000334229:R181Q;ENSP00000388756:R181Q;ENSP00000439392:R181Q;ENSP00000379345:R181Q;ENSP00000441951:R181Q;ENSP00000443204:R181Q	ENSP00000334229:R181Q	R	-	2	0	KIAA0528	22568732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.985000	0.70556	2.306000	0.77630	0.585000	0.79938	CGA		0.368	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22677465	C	T	22677465	3	4	61	1	0	0	0	0	1	0	0	0	8203	884	31	1	2540	1	KIAA0528	12	22677465	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34329	22677465	111174430	7939	15924										
SOX5	6660	broad.mit.edu	37	chr12	23716202	23716202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaactgaccttttctgttCggcagttattgagacccaga	9	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:23716202C>A	ENST00000451604.2	-	11	1579	c.1478G>T	c.(1477-1479)cGa>cTa	p.R493L	SOX5_ENST00000381381.2_Intron|SOX5_ENST00000396007.2_Missense_Mutation_p.R107L|SOX5_ENST00000537393.1_Missense_Mutation_p.R458L|SOX5_ENST00000309359.1_Missense_Mutation_p.R480L|SOX5_ENST00000546136.1_Missense_Mutation_p.R480L|SOX5_ENST00000541536.1_Intron|SOX5_ENST00000545921.1_Missense_Mutation_p.R483L			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	493					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R493Q(1)|p.R493L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						CTTTTCTGTTCGGCAGTTATT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	12											129	118	122					12																	23716202		2203	4300	6503	23607469	SO:0001583	missense	6660			AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1478G>T	12.37:g.23716202C>A	ENSP00000398273:p.Arg493Leu		23607469	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174612	0.78452	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000396007;ENST00000545921	T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.58850	0.2151	L	0.52905	1.665	0.80722	D	1	P;B;D	0.56287	0.747;0.37;0.975	P;B;P	0.53185	0.567;0.13;0.72	T	0.52343	-0.8588	10	0.36615	T	0.2	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	458;493;107	F5H0I3;P35711;P35711-3	.;SOX5_HUMAN;.	L	480;480;493;445;458;107;483	ENSP00000437487:R480L;ENSP00000308927:R480L;ENSP00000398273:R493L;ENSP00000439832:R458L;ENSP00000379328:R107L;ENSP00000443520:R483L	ENSP00000308927:R480L	R	-	2	0	SOX5	23607469	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	7.474000	0.81024	2.789000	0.95967	0.591000	0.81541	CGA		0.368	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		A	23716202	C	A	23716202	3	1	61	1	0	0	0	0	1	0	0	0	14991	884	31	2	833	2	SOX5	12	23716202	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1038737	23716202	110135693	7940	15925										
LRMP	55259	broad.mit.edu	37	chr12	25260946	25260946	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacgtctctagaacatatCttgtggccatttaccagact	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:25260946C>A	ENST00000320267.9	-	0	2361				LRMP_ENST00000354454.3_Silent_p.I484I|LRMP_ENST00000547044.1_Silent_p.I484I|LRMP_ENST00000548766.1_Silent_p.I484I	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1									p.I484I(1)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	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)			TAGAACATATCTTGTGGCCAT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	12											110	106	107					12																	25260946		2203	4300	6503	25152213	SO:0001628	intergenic_variant	4033			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195		12.37:g.25260946C>A			25152213	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Silent	SNP	ENST00000320267.9	37	CCDS41762.1																																																																																				0.463	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		A	25260946	C	A	25260946	1	1	61	0	1	0	0	0	0	0	0	0	8979	903	32	2		2	LRMP	12	25260946	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1544744	25260946	108590949	7941	15926										
CASC1	55259	broad.mit.edu	37	chr12	25297395	25297395	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttgtttggactcttcttcGacctccttgctgattgcttt	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:25297395G>A	ENST00000320267.9	-	8	969	c.888C>T	c.(886-888)gtC>gtT	p.V296V	CASC1_ENST00000545133.1_Silent_p.V237V|CASC1_ENST00000537577.1_Silent_p.V184V|CASC1_ENST00000395990.2_Silent_p.V256V|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Silent_p.V302V|CASC1_ENST00000354189.5_Silent_p.V360V	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	296								p.V302V(1)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	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)			ACTCTTCTTCGACCTCCTTGC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	12											218	204	209					12																	25297395		2203	4300	6503	25188662	SO:0001819	synonymous_variant	55259			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.888C>T	12.37:g.25297395G>A			25188662	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Silent	SNP	ENST00000320267.9	37	CCDS41762.1																																																																																				0.388	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		A	25297395	G	A	25297395	2	1	61	1	0	0	0	0	0	0	0	1	2666	1045	37	1		1	CASC1	12	25297395	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36449	25297395	108554500	7942	15927										
CASC1	55259	broad.mit.edu	37	chr12	25308325	25308325	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaataaagttcttcaagttCttcatttctcctttctagat	3	8	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:25308325C>T	ENST00000320267.9	-	4	283	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	CASC1_ENST00000545133.1_Missense_Mutation_p.E9K|CASC1_ENST00000537577.1_5'UTR|CASC1_ENST00000395990.2_Missense_Mutation_p.E28K|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Missense_Mutation_p.E74K|CASC1_ENST00000354189.5_Missense_Mutation_p.E132K	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	68	Glu-rich.							p.E74K(1)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	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)			TCTTCAAGTTCTTCATTTCTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											99	101	101					12																	25308325		2203	4297	6500	25199592	SO:0001583	missense	55259			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.202G>A	12.37:g.25308325C>T	ENSP00000313141:p.Glu68Lys		25199592	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.274919|4.274919	0.80580|0.80580	.|.	.|.	ENSG00000118307|ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000395992;ENST00000545133;ENST00000389246;ENST00000554347|ENST00000556006	T;T;T;T;T;T|.	0.28895|.	1.59;1.9;1.9;1.9;1.9;1.97|.	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71863|0.71863	0.3390|0.3390	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;0.999;1.0|.	D;D;D;D|.	0.87578|.	0.998;0.997;0.994;0.997|.	T|T	0.71431|0.71431	-0.4595|-0.4595	10|5	0.25106|.	T|.	0.35|.	-27.0216|-27.0216	13.345|13.345	0.60566|0.60566	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	9;132;68;74|.	F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9|.	.;.;CASC1_HUMAN;.|.	K|K	132;74;68;28;74;9;28;28|43	ENSP00000346126:E132K;ENSP00000379310:E74K;ENSP00000313141:E68K;ENSP00000379313:E28K;ENSP00000437373:E9K;ENSP00000451232:E28K|.	ENSP00000313141:E68K|.	E|R	-|-	1|2	0|0	CASC1|CASC1	25199592|25199592	0.997000|0.997000	0.39634|0.39634	0.656000|0.656000	0.29637|0.29637	0.995000|0.995000	0.86356|0.86356	4.035000|4.035000	0.57297|0.57297	2.609000|2.609000	0.88269|0.88269	0.643000|0.643000	0.83706|0.83706	GAA|AGA		0.338	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		T	25308325	C	T	25308325	3	4	61	1	0	0	0	0	1	0	0	0	2666	922	32	3	1996	3	CASC1	12	25308325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10930	25308325	108543570	7943	15928										
CASC1	55259	broad.mit.edu	37	chr12	25311443	25311443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatttttctttctcaattCgctgtatttcaagcctttcc	4	12	3	0	rs140615558		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:25311443C>T	ENST00000320267.9	-	3	224	c.143G>A	c.(142-144)cGa>cAa	p.R48Q	CASC1_ENST00000545133.1_Intron|CASC1_ENST00000537577.1_Intron|CASC1_ENST00000395990.2_Missense_Mutation_p.R8Q|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Missense_Mutation_p.R54Q|CASC1_ENST00000354189.5_Missense_Mutation_p.R112Q	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	48	Glu-rich.							p.R54Q(2)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	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)			TTTCTCAATTCGCTGTATTTC	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	12						C	GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	127	120	122		335,143,,23,161	2.2	0	12	dbSNP_134	122	0,8598		0,0,4299	no	missense,missense,intron,missense,missense	CASC1	NM_001082972.1,NM_001082973.1,NM_001204101.1,NM_001204102.1,NM_018272.3	43,43,,43,43	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	112/691,48/717,,8/677,54/723	25311443	1,13003	2203	4299	6502	25202710	SO:0001583	missense	55259			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.143G>A	12.37:g.25311443C>T	ENSP00000313141:p.Arg48Gln		25202710	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	.	.	.	.	.	.	.	.	.	.	C	9.107	1.005716	0.19199	2.27E-4	0.0	ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000395992;ENST00000389246;ENST00000554347	T;T;T;T;T	0.53640	2.19;1.33;1.32;0.61;2.13	5.42	2.15	0.27550	.	0.324209	0.26967	N	0.021590	T	0.30603	0.0770	L	0.40543	1.245	0.21897	N	0.99948	P;B;B	0.34615	0.459;0.056;0.179	B;B;B	0.23018	0.024;0.006;0.043	T	0.12785	-1.0534	10	0.39692	T	0.17	-9.9041	8.0894	0.30793	0.0:0.7029:0.0:0.2971	.	112;48;54	Q6TDU7-3;Q6TDU7;F8W8F9	.;CASC1_HUMAN;.	Q	112;54;48;8;54;8;8	ENSP00000346126:R112Q;ENSP00000379310:R54Q;ENSP00000313141:R48Q;ENSP00000379313:R8Q;ENSP00000451232:R8Q	ENSP00000313141:R48Q	R	-	2	0	CASC1	25202710	0.833000	0.29383	0.013000	0.15412	0.751000	0.42716	1.928000	0.40104	0.659000	0.30945	0.573000	0.79308	CGA		0.299	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		T	25311443	C	T	25311443	3	4	61	1	0	0	0	0	1	0	0	0	2666	884	31	1	2059	1	CASC1	12	25311443	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3118	25311443	108540452	7944	15929										
SSPN	8082	broad.mit.edu	37	chr12	26383754	26383754	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacctgtgagaccacactCgactcttgccagtgcaaact	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26383754C>T	ENST00000242729.2	+	3	654	c.477C>T	c.(475-477)ctC>ctT	p.L159L	RP11-283G6.5_ENST00000541940.1_RNA|SSPN_ENST00000540266.1_Silent_p.L56L|RP11-283G6.4_ENST00000540392.1_RNA|SSPN_ENST00000422622.2_Silent_p.L56L|RP11-283G6.5_ENST00000540625.1_RNA|SSPN_ENST00000535504.1_Intron|RP11-283G6.5_ENST00000537525.1_RNA	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	159					cell adhesion (GO:0007155)|muscle contraction (GO:0006936)	cell junction (GO:0030054)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)		p.L159L(1)		kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					AGACCACACTCGACTCTTGCC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	12											125	109	115					12																	26383754		2203	4300	6503	26275021	SO:0001819	synonymous_variant	8082			AF016028	CCDS8707.1, CCDS44850.1	12p11.2	2014-09-17	2012-03-14			ENSG00000123096			11322	protein-coding gene	gene with protein product		601599	"Kras oncogene-associated gene"	KRAG		9395445, 8661122	Standard	NM_005086		Approved	SPN1, SPN2	uc001rhe.3	Q14714		ENST00000242729.2:c.477C>T	12.37:g.26383754C>T			26275021	B3KS67	Silent	SNP	ENST00000242729.2	37	CCDS8707.1																																																																																				0.587	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086		T	26383754	C	T	26383754	2	4	61	1	0	0	0	0	0	0	0	1	15227	871	31	1		1	SSPN	12	26383754	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1072311	26383754	107468141	7945	15930										
ITPR2	3709	broad.mit.edu	37	chr12	26648163	26648163	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatcacctttaaagtatcGattcagaagtatctttctta	4	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26648163G>A	ENST00000381340.3	-	38	5520	c.5104C>T	c.(5104-5106)Cga>Tga	p.R1702*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1702					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.R1702*(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTAAAGTATCGATTCAGAAGT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											129	118	122					12																	26648163		1848	4099	5947	26539430	SO:0001587	stop_gained	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5104C>T	12.37:g.26648163G>A	ENSP00000370744:p.Arg1702*		26539430	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	49	15.374899	0.99831	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.63	4.63	0.57726	.	0.065913	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3957	0.90497	0.0:0.0:1.0:0.0	.	.	.	.	X	1702	.	ENSP00000370744:R1702X	R	-	1	2	ITPR2	26539430	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	4.977000	0.63792	2.503000	0.84419	0.591000	0.81541	CGA		0.353	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26648163	G	A	26648163	4	1	61	1	0	0	0	0	0	1	0	0	7942	1066	37	1	3081	1	ITPR2	12	26648163	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	264409	26648163	107203732	7946	15931										
ITPR2	3709	broad.mit.edu	37	chr12	26748460	26748460	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggttacttgtatagatttCtttcatttccacttcagtgt	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26748460C>A	ENST00000381340.3	-	32	4734	c.4318G>T	c.(4318-4320)Gaa>Taa	p.E1440*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1440					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.E1440*(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GTATAGATTTCTTTCATTTCC	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											118	111	114					12																	26748460		1811	4069	5880	26639727	SO:0001587	stop_gained	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4318G>T	12.37:g.26748460C>A	ENSP00000370744:p.Glu1440*		26639727	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	48	14.215293	0.99785	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.71	4.71	0.59529	.	0.049391	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.2156	0.89884	0.0:1.0:0.0:0.0	.	.	.	.	X	1440	.	ENSP00000370744:E1440X	E	-	1	0	ITPR2	26639727	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.596000	0.82721	2.611000	0.88343	0.563000	0.77884	GAA		0.323	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26748460	C	A	26748460	4	1	61	1	0	0	0	0	0	1	0	0	7942	922	32	2	3891	2	ITPR2	12	26748460	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100297	26748460	107103435	7947	15932										
ITPR2	3709	broad.mit.edu	37	chr12	26749869	26749869	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactatgtcgtccagcgggaGaagggaattacacttgattt	11	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26749869G>T	ENST00000381340.3	-	31	4617	c.4201C>A	c.(4201-4203)Ctc>Atc	p.L1401I		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1401					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.L1401I(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TCCAGCGGGAGAAGGGAATTA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											96	97	97					12																	26749869		2065	4212	6277	26641136	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4201C>A	12.37:g.26749869G>T	ENSP00000370744:p.Leu1401Ile		26641136	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546605	0.65198	.	.	ENSG00000123104	ENST00000381340	D	0.94613	-3.47	4.44	3.53	0.40419	.	0.077705	0.53938	D	0.000054	D	0.95329	0.8484	M	0.62016	1.91	0.80722	D	1	D	0.57571	0.98	P	0.61477	0.889	D	0.93567	0.6900	10	0.30078	T	0.28	.	11.8292	0.52285	0.0872:0.0:0.9128:0.0	.	1401	Q14571	ITPR2_HUMAN	I	1401	ENSP00000370744:L1401I	ENSP00000370744:L1401I	L	-	1	0	ITPR2	26641136	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.077000	0.50089	1.171000	0.42768	0.650000	0.86243	CTC		0.493	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26749869	G	T	26749869	3	4	61	1	0	0	0	0	1	0	0	0	7942	942	33	2	4012	2	ITPR2	12	26749869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1409	26749869	107102026	7948	15933										
ITPR2	3709	broad.mit.edu	37	chr12	26775310	26775310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgtcctgcctccttcatCgtcaagttgaactggatttt	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26775310C>T	ENST00000381340.3	-	25	3567	c.3151G>A	c.(3151-3153)Gat>Aat	p.D1051N	ITPR2_ENST00000545902.1_5'UTR|RP11-666F17.1_ENST00000414098.2_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1051					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.D1051N(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CCTCCTTCATCGTCAAGTTGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	99	100					12																	26775310		1890	4117	6007	26666577	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3151G>A	12.37:g.26775310C>T	ENSP00000370744:p.Asp1051Asn		26666577	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366938	0.82463	.	.	ENSG00000123104	ENST00000381340	T	0.64618	-0.11	5.11	5.11	0.69529	.	0.091655	0.85682	D	0.000000	T	0.76744	0.4030	M	0.77313	2.365	0.80722	D	1	D	0.69078	0.997	P	0.59357	0.856	T	0.74853	-0.3523	10	0.30854	T	0.27	.	18.7307	0.91734	0.0:1.0:0.0:0.0	.	1051	Q14571	ITPR2_HUMAN	N	1051	ENSP00000370744:D1051N	ENSP00000370744:D1051N	D	-	1	0	ITPR2	26666577	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	7.541000	0.82084	2.659000	0.90383	0.650000	0.86243	GAT		0.388	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26775310	C	T	26775310	3	4	61	1	0	0	0	0	1	0	0	0	7942	884	31	1	5086	1	ITPR2	12	26775310	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25441	26775310	107076585	7949	15934										
ITPR2	3709	broad.mit.edu	37	chr12	26812056	26812056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttcaaaccttggctcccGatttctcctgagtaaactga	6	12	2	2	rs566154914		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:26812056G>A	ENST00000381340.3	-	16	2292	c.1876C>T	c.(1876-1878)Cgg>Tgg	p.R626W		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	626					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.R626W(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CTTGGCTCCCGATTTCTCCTG	0.338													G|||	1	0.000199681	0	0	5008	,	,		17495	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											183	163	169					12																	26812056		1826	4081	5907	26703323	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1876C>T	12.37:g.26812056G>A	ENSP00000370744:p.Arg626Trp		26703323	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200488	0.79015	.	.	ENSG00000123104	ENST00000381340	D	0.96651	-4.08	4.79	4.79	0.61399	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.96131	0.8739	N	0.17379	0.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97564	1.0100	10	0.87932	D	0	.	18.0473	0.89336	0.0:0.0:1.0:0.0	.	626	Q14571	ITPR2_HUMAN	W	626	ENSP00000370744:R626W	ENSP00000370744:R626W	R	-	1	2	ITPR2	26703323	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	3.750000	0.55157	2.481000	0.83766	0.650000	0.86243	CGG		0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26812056	G	A	26812056	3	1	61	1	0	0	0	0	1	0	0	0	7942	1057	37	1	6397	1	ITPR2	12	26812056	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36746	26812056	107039839	7950	15935										
C12orf11	55726	broad.mit.edu	37	chr12	27075611	27075611	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccacatcataattggcaGatgtgttagcatgctgttct	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27075611G>T	ENST00000261191.7	-	8	1363	c.827C>A	c.(826-828)tCt>tAt	p.S276Y	ASUN_ENST00000539625.1_Missense_Mutation_p.S175Y	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	276					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S276Y(1)									ATAATTGGCAGATGTGTTAGC	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	12											130	122	125					12																	27075611		2203	4300	6503	26966878	SO:0001583	missense	55726			AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.827C>A	12.37:g.27075611G>T	ENSP00000261191:p.Ser276Tyr		26966878	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Missense_Mutation	SNP	ENST00000261191.7	37	CCDS8708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.7|28.7	4.940863|4.940863	0.92526|0.92526	.|.	.|.	ENSG00000064102|ENSG00000064102	ENST00000536232|ENST00000261191;ENST00000539625	.|T;T	.|0.62788	.|0.0;0.0	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81692|0.81692	0.4876|0.4876	M|M	0.79693|0.79693	2.465|2.465	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.83275	.|0.996	T|T	0.82859|0.82859	-0.0249|-0.0249	5|10	.|0.87932	.|D	.|0	-17.4127|-17.4127	20.1751|20.1751	0.98176|0.98176	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|276	.|Q9NVM9	.|M89BB_HUMAN	M|Y	34|276;175	.|ENSP00000261191:S276Y;ENSP00000443724:S175Y	.|ENSP00000261191:S276Y	L|S	-|-	1|2	2|0	C12orf11|C12orf11	26966878|26966878	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.447000|9.447000	0.97595|0.97595	2.855000|2.855000	0.98099|0.98099	0.585000|0.585000	0.79938|0.79938	CTG|TCT		0.284	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		T	27075611	G	T	27075611	3	4	61	1	0	0	0	0	1	0	0	0	1679	942	33	2	1333	2	C12orf11	12	27075611	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	263555	27075611	106776284	7951	15936										
FGFR1OP2	26127	broad.mit.edu	37	chr12	27113500	27113500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttccttgatgcatctcGacacatccttgaagcacctc	5	14	2	2	rs144332739	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27113500G>A	ENST00000229395.3	+	5	791	c.449G>A	c.(448-450)cGa>cAa	p.R150Q	FGFR1OP2_ENST00000327214.5_Intron|FGFR1OP2_ENST00000546072.1_Missense_Mutation_p.R150Q	NM_015633.2	NP_056448.1	Q9NVK5	FGOP2_HUMAN	FGFR1 oncogene partner 2	150					wound healing (GO:0042060)	cytosol (GO:0005829)		p.R150Q(1)		cervix(1)|large_intestine(4)|lung(1)|prostate(2)	8	Colorectal(261;0.0847)					GATGCATCTCGACACATCCTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	112	93	99		,449,449	3.3	1	12	dbSNP_134	99	0,8600		0,0,4300	no	intron,missense,missense	FGFR1OP2	NM_001171887.1,NM_001171888.1,NM_015633.2	,43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,probably-damaging,probably-damaging	,150/173,150/254	27113500	2,13004	2203	4300	6503	27004767	SO:0001583	missense	26127			AF161472	CCDS8709.1, CCDS53766.1, CCDS53767.1	12p12.1	2014-01-28			ENSG00000111790	ENSG00000111790			23098	protein-coding gene	gene with protein product		608858				15034873	Standard	NM_015633		Approved	DKFZp564O1863	uc001rhm.3	Q9NVK5		ENST00000229395.3:c.449G>A	12.37:g.27113500G>A	ENSP00000229395:p.Arg150Gln		27004767	Q6R955|Q8N5L7|Q9P034|Q9UFK8	Missense_Mutation	SNP	ENST00000229395.3	37	CCDS8709.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386795	0.42308	4.54E-4	0.0	ENSG00000111790	ENST00000229395;ENST00000546072	.	.	.	5.23	3.35	0.38373	.	0.170408	0.28425	N	0.015391	T	0.14743	0.0356	N	0.08118	0	0.80722	D	1	B;P	0.50617	0.005;0.937	B;B	0.29077	0.004;0.098	T	0.04664	-1.0935	9	0.32370	T	0.25	-8.621	6.9964	0.24784	0.0904:0.0:0.7373:0.1723	.	150;150	Q9NVK5;Q9NVK5-3	FGOP2_HUMAN;.	Q	150	.	ENSP00000229395:R150Q	R	+	2	0	FGFR1OP2	27004767	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.895000	0.28363	0.818000	0.34468	0.655000	0.94253	CGA		0.403	FGFR1OP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402961.1	NM_015633		A	27113500	G	A	27113500	3	1	61	1	0	0	0	0	1	0	0	0	5884	1058	37	1	463	1	FGFR1OP2	12	27113500	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37889	27113500	106738395	7952	15937										
STK38L	23012	broad.mit.edu	37	chr12	27468021	27468021	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggactgaattttatagaaAtctcacacacaacccaccaa	4	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27468021A>C	ENST00000389032.3	+	8	915	c.746A>C	c.(745-747)aAt>aCt	p.N249T	STK38L_ENST00000539577.1_Missense_Mutation_p.N156T	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like									p.N249T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TTTTATAGAAATCTCACACAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	100	99					12																	27468021		2203	4300	6503	27359288	SO:0001583	missense	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.746A>C	12.37:g.27468021A>C	ENSP00000373684:p.Asn249Thr		27359288		Missense_Mutation	SNP	ENST00000389032.3	37	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.257708	0.59321	.	.	ENSG00000211455	ENST00000389032;ENST00000545470;ENST00000539577	T;T;T	0.63913	0.3;-0.07;0.36	4.32	4.32	0.51571	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049029	0.85682	D	0.000000	T	0.54679	0.1873	L	0.28344	0.845	0.80722	D	1	B;B	0.30973	0.302;0.302	B;B	0.39339	0.232;0.297	T	0.56878	-0.7906	10	0.41790	T	0.15	.	13.9591	0.64168	1.0:0.0:0.0:0.0	.	156;249	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	T	249;208;156	ENSP00000373684:N249T;ENSP00000439457:N208T;ENSP00000446386:N156T	ENSP00000373684:N249T	N	+	2	0	STK38L	27359288	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	9.067000	0.93955	1.952000	0.56665	0.533000	0.62120	AAT		0.343	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		C	27468021	A	C	27468021	3	2	61	1	0	0	0	0	1	0	0	0	15343	101	4	4	772	4	STK38L	12	27468021	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	354521	27468021	106383874	7953	15938										
ARNTL2	56938	broad.mit.edu	37	chr12	27543126	27543126	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggataaagagttgtaaaatCtctgtcaaagaagagcatgg	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27543126C>A	ENST00000266503.5	+	9	891	c.873C>A	c.(871-873)atC>atA	p.I291I	ARNTL2_ENST00000311001.5_Silent_p.I277I|ARNTL2_ENST00000542388.1_Silent_p.I206I|ARNTL2_ENST00000546179.1_Silent_p.I254I|ARNTL2_ENST00000261178.5_Silent_p.I243I|ARNTL2_ENST00000395901.2_Silent_p.I254I|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000544915.1_Silent_p.I257I			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	291					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.I291I(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					GTTGTAAAATCTCTGTCAAAG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	12											102	100	101					12																	27543126		2203	4300	6503	27434393	SO:0001819	synonymous_variant	56938			AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"Basic helix-loop-helix proteins"	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.873C>A	12.37:g.27543126C>A			27434393	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Silent	SNP	ENST00000266503.5	37	CCDS8712.1	.	.	.	.	.	.	.	.	.	.	C	7.359	0.624546	0.14193	.	.	ENSG00000029153	ENST00000457040	.	.	.	3.71	1.69	0.24217	.	.	.	.	.	T	0.32285	0.0824	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21999	-1.0229	4	.	.	.	.	6.9736	0.24662	0.1703:0.7333:0.0:0.0964	.	.	.	.	Y	243	.	.	S	+	2	0	ARNTL2	27434393	0.000000	0.05858	0.557000	0.28306	0.961000	0.63080	0.116000	0.15561	0.912000	0.36772	-0.136000	0.14681	TCT		0.393	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		A	27543126	C	A	27543126	2	1	61	1	0	0	0	0	0	0	0	1	969	903	32	2		2	ARNTL2	12	27543126	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75105	27543126	106308769	7954	15939										
PPFIBP1	8496	broad.mit.edu	37	chr12	27830005	27830005	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatatctgaagatcgtaaaCgaagtgccagtgcacccacc	10	11	1	2	rs371335870		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27830005C>T	ENST00000318304.8	+	18	1916				PPFIBP1_ENST00000228425.6_Nonsense_Mutation_p.R531*|PPFIBP1_ENST00000542629.1_Intron|PPFIBP1_ENST00000537927.1_Intron	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)						cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.R531*(2)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AGATCGTAAACGAAGTGCCAG	0.502																																																2	Substitution - Nonsense(2)	large_intestine(2)	12						C	,,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	347	286	307		,,1591,	5.4	1	12		307	0,8600		0,0,4300	no	intron,intron,stop-gained,intron	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	,,531/1006,	27830005	1,13005	2203	4300	6503	27721272	SO:0001627	intron_variant	8496			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1633+473C>T	12.37:g.27830005C>T			27721272	O75336|Q86X70|Q9NY03|Q9ULJ0	Nonsense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381988	0.98786	2.27E-4	0.0	ENSG00000110841	ENST00000228425	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	19.0495	0.93038	0.0:1.0:0.0:0.0	.	.	.	.	X	531	.	ENSP00000228425:R531X	R	+	1	2	PPFIBP1	27721272	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.205000	0.42770	2.832000	0.97577	0.655000	0.94253	CGA		0.502	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		T	27830005	C	T	27830005	1	4	61	0	1	0	0	0	0	0	0	0	12344	528	19	1		1	PPFIBP1	12	27830005	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	286879	27830005	106021890	7955	15940										
PPFIBP1	8496	broad.mit.edu	37	chr12	27841951	27841951	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttctttaaacaggttCtagagcctcgttttaacgta	6	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:27841951C>A	ENST00000318304.8	+	26	2801	c.2518C>A	c.(2518-2520)Cta>Ata	p.L840I	PPFIBP1_ENST00000228425.6_Missense_Mutation_p.L834I|PPFIBP1_ENST00000542629.1_Missense_Mutation_p.L809I|PPFIBP1_ENST00000537927.1_Missense_Mutation_p.L687I	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	840	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.L840I(1)|p.L834I(1)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TAAACAGGTTCTAGAGCCTCG	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	12											63	59	61					12																	27841951		2203	4300	6503	27733218	SO:0001583	missense	8496			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.2518C>A	12.37:g.27841951C>A	ENSP00000314724:p.Leu840Ile		27733218	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.0|21.0	4.076167|4.076167	0.76415|0.76415	.|.	.|.	ENSG00000110841|ENSG00000110841	ENST00000539326|ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	.|T;T;T;T;T	.|0.46819	.|0.86;0.86;0.86;0.86;0.86	5.18|5.18	4.25|4.25	0.50352|0.50352	.|Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (1);Sterile alpha motif, type 2 (1);	.|0.000000	.|0.28436	.|U	.|0.015357	T|T	0.66386|0.66386	0.2784|0.2784	M|M	0.83118|0.83118	2.625|2.625	0.54753|0.54753	D|D	0.999989|0.999989	.|D;D;D;D;D	.|0.89917	.|1.0;0.998;1.0;1.0;0.999	.|D;D;D;D;D	.|0.97110	.|1.0;0.996;0.999;0.999;0.999	T|T	0.69423|0.69423	-0.5149|-0.5149	5|10	.|0.72032	.|D	.|0.01	-10.575|-10.575	7.1826|7.1826	0.25780|0.25780	0.1614:0.7226:0.0:0.116|0.1614:0.7226:0.0:0.116	.|.	.|687;671;840;834;809	.|Q86W92-3;F5GZP6;Q86W92;Q86W92-2;Q86W92-4	.|.;.;LIPB1_HUMAN;.;.	L|I	70|671;687;840;809;834	.|ENSP00000444304:L671I;ENSP00000445425:L687I;ENSP00000314724:L840I;ENSP00000443442:L809I;ENSP00000228425:L834I	.|ENSP00000228425:L834I	F|L	+|+	3|1	2|2	PPFIBP1|PPFIBP1	27733218|27733218	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	1.568000|1.568000	0.36418|0.36418	2.418000|2.418000	0.82041|0.82041	0.591000|0.591000	0.81541|0.81541	TTC|CTA		0.353	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		A	27841951	C	A	27841951	3	1	61	1	0	0	0	0	1	0	0	0	12344	912	32	2	2640	2	PPFIBP1	12	27841951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11946	27841951	106009944	7956	15941										
CCDC91	55297	broad.mit.edu	37	chr12	28460625	28460625	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtcttagaaaaaggcttTctaaaagaaaaagagcaaga	8	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:28460625T>C	ENST00000545336.1	+	9	938	c.519T>C	c.(517-519)ttT>ttC	p.F173F	CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000306172.5_Silent_p.F143F|CCDC91_ENST00000381259.1_Silent_p.F173F|CCDC91_ENST00000539107.1_Silent_p.F173F|CCDC91_ENST00000381256.1_Silent_p.F173F			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	173					protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)		p.F173F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AAAAAGGCTTTCTAAAAGAAA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	12											61	63	63					12																	28460625		2203	4293	6496	28351892	SO:0001819	synonymous_variant	55297			AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"GGA binding partner"					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.519T>C	12.37:g.28460625T>C			28351892	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Silent	SNP	ENST00000545336.1	37	CCDS8716.1																																																																																				0.284	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318		C	28460625	T	C	28460625	2	2	61	1	0	0	0	0	0	0	0	1	2876	1780	62	4		4	CCDC91	12	28460625	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	618674	28460625	105391270	7957	15942										
FAR2	55711	broad.mit.edu	37	chr12	29469918	29469918	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccattatctatgactgctAtctgcggctcactggaagga	10	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:29469918A>G	ENST00000536681.3	+	9	1346	c.1100A>G	c.(1099-1101)tAt>tGt	p.Y367C	RP11-996F15.2_ENST00000553105.1_RNA|FAR2_ENST00000182377.4_Missense_Mutation_p.Y367C|FAR2_ENST00000547116.1_Missense_Mutation_p.Y270C	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	367					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)	p.Y367C(1)		central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						TATGACTGCTATCTGCGGCTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	12											130	132	131					12																	29469918		2203	4300	6503	29361185	SO:0001583	missense	55711			AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.1100A>G	12.37:g.29469918A>G	ENSP00000443291:p.Tyr367Cys		29361185	F8VV73|Q9H0D5|Q9NVW8	Missense_Mutation	SNP	ENST00000536681.3	37	CCDS8717.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.036024	0.35893	.	.	ENSG00000064763	ENST00000536681;ENST00000182377;ENST00000547116	T;T;T	0.31247	1.93;1.93;1.5	4.44	4.44	0.53790	.	0.258720	0.32273	N	0.006332	T	0.24198	0.0586	L	0.29908	0.895	0.43368	D	0.995451	B	0.25206	0.12	B	0.27715	0.082	T	0.07481	-1.0770	10	0.56958	D	0.05	-11.7982	11.7233	0.51696	1.0:0.0:0.0:0.0	.	367	Q96K12	FACR2_HUMAN	C	367;367;270	ENSP00000443291:Y367C;ENSP00000182377:Y367C;ENSP00000449349:Y270C	ENSP00000182377:Y367C	Y	+	2	0	FAR2	29361185	0.987000	0.35691	0.881000	0.34555	0.854000	0.48673	2.601000	0.46249	1.866000	0.54105	0.383000	0.25322	TAT		0.507	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		G	29469918	A	G	29469918	3	3	61	1	0	0	0	0	1	0	0	0	5694	449	16	4	1130	4	FAR2	12	29469918	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1009293	29469918	104381977	7958	15943										
OVCH1	341350	broad.mit.edu	37	chr12	29648248	29648248	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgttttagatacagcaGtgcaatatcaggactcatat	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:29648248G>T	ENST00000318184.5	-	4	423	c.424C>A	c.(424-426)Ctg>Atg	p.L142M		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	142	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.L142M(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGATACAGCAGTGCAATATCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											204	193	196					12																	29648248		1850	4085	5935	29539515	SO:0001583	missense	341350			BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.424C>A	12.37:g.29648248G>T	ENSP00000326708:p.Leu142Met		29539515		Missense_Mutation	SNP	ENST00000318184.5	37		.	.	.	.	.	.	.	.	.	.	G	13.69	2.312676	0.40895	.	.	ENSG00000187950	ENST00000318184	D	0.97505	-4.41	2.89	2.0	0.26442	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.97324	0.9125	M	0.76727	2.345	0.09310	N	0.999999	D	0.71674	0.998	D	0.65874	0.939	D	0.91262	0.5037	9	0.52906	T	0.07	.	4.2879	0.10863	0.1345:0.2381:0.6274:0.0	.	142	Q7RTY7	OVCH1_HUMAN	M	142	ENSP00000326708:L142M	ENSP00000326708:L142M	L	-	1	2	OVCH1	29539515	0.555000	0.26530	0.561000	0.28357	0.994000	0.84299	1.121000	0.31283	0.787000	0.33731	0.655000	0.94253	CTG		0.348	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		T	29648248	G	T	29648248	3	4	61	1	0	0	0	0	1	0	0	0	11354	1020	36	2	3080	2	OVCH1	12	29648248	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178330	29648248	104203647	7959	15944										
TMTC1	83857	broad.mit.edu	37	chr12	29689219	29689219	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatggaatccttcagtaAggtgatagcttcttcctttt	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:29689219A>C	ENST00000539277.1	-	11	1766	c.1708T>G	c.(1708-1710)Tta>Gta	p.L570V	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000381224.2_Missense_Mutation_p.L524V|TMTC1_ENST00000551659.1_Missense_Mutation_p.L632V|TMTC1_ENST00000552618.1_Missense_Mutation_p.L594V|TMTC1_ENST00000256062.5_Missense_Mutation_p.L462V	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	570						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.L462V(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TCCTTCAGTAAGGTGATAGCT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											177	166	170					12																	29689219		2203	4300	6503	29580486	SO:0001583	missense	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1708T>G	12.37:g.29689219A>C	ENSP00000442046:p.Leu570Val		29580486	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.856319	0.51376	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.63744	-0.06;0.59;0.24;0.59;-0.06	5.6	4.47	0.54385	Tetratricopeptide-like helical (1);PIK-related kinase, FAT (1);Tetratricopeptide repeat-containing (1);	0.272597	0.30930	N	0.008590	T	0.53530	0.1802	L	0.45470	1.425	0.30323	N	0.787418	P;B;B	0.36712	0.566;0.304;0.138	B;B;B	0.40101	0.319;0.047;0.044	T	0.54774	-0.8243	9	.	.	.	-9.0507	6.64	0.22904	0.874:0.0:0.126:0.0	.	524;570;632	Q8IUR5-3;Q8IUR5;F8VTQ9	.;TMTC1_HUMAN;.	V	333;462;632;594;570;524	ENSP00000256062:L462V;ENSP00000448112:L632V;ENSP00000449043:L594V;ENSP00000442046:L570V;ENSP00000370622:L524V	.	L	-	1	2	TMTC1	29580486	0.481000	0.25941	0.641000	0.29422	0.970000	0.65996	0.862000	0.27899	0.960000	0.38005	0.533000	0.62120	TTA		0.388	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		C	29689219	A	C	29689219	3	2	61	1	0	0	0	0	1	0	0	0	16299	69	3	4	972	4	TMTC1	12	29689219	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40971	29689219	104162676	7960	15945										
TMTC1	83857	broad.mit.edu	37	chr12	29904729	29904729	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttcccattctcccggtGaggatggcctggcagtgagg	14	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:29904729G>T	ENST00000539277.1	-	5	866	c.808C>A	c.(808-810)Cac>Aac	p.H270N	TMTC1_ENST00000381224.2_Missense_Mutation_p.H162N|TMTC1_ENST00000551659.1_Missense_Mutation_p.H270N|TMTC1_ENST00000552618.1_Missense_Mutation_p.H270N|TMTC1_ENST00000256062.5_Missense_Mutation_p.H162N	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	270						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.H162N(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TTCTCCCGGTGAGGATGGCCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	12											40	37	38					12																	29904729		2203	4299	6502	29795996	SO:0001583	missense	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.808C>A	12.37:g.29904729G>T	ENSP00000442046:p.His270Asn		29795996	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	G	5.978	0.364331	0.11296	.	.	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.67523	-0.27;0.0;-0.25;-0.14;1.58	4.83	4.83	0.62350	.	0.986824	0.08272	N	0.971348	T	0.56187	0.1968	L	0.29908	0.895	0.19775	N	0.99996	B;B	0.26547	0.152;0.039	B;B	0.18871	0.023;0.006	T	0.36529	-0.9744	9	.	.	.	-0.33	14.1526	0.65395	0.0:0.0:1.0:0.0	.	162;270	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	N	162;270;270;270;162	ENSP00000256062:H162N;ENSP00000448112:H270N;ENSP00000449043:H270N;ENSP00000442046:H270N;ENSP00000370622:H162N	.	H	-	1	0	TMTC1	29795996	0.420000	0.25457	0.016000	0.15963	0.175000	0.22909	0.709000	0.25734	2.610000	0.88304	0.555000	0.69702	CAC		0.627	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		T	29904729	G	T	29904729	3	4	61	1	0	0	0	0	1	0	0	0	16299	1290	45	2	1896	2	TMTC1	12	29904729	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215510	29904729	103947166	7961	15946										
TMTC1	83857	broad.mit.edu	37	chr12	29911645	29911645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctacacatacctgttgtaCgagagaaaggccaatagaaa	9	8	0	2	rs146162779	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:29911645C>T	ENST00000539277.1	-	3	604	c.546G>A	c.(544-546)tcG>tcA	p.S182S	TMTC1_ENST00000381224.2_Silent_p.S74S|TMTC1_ENST00000551659.1_Silent_p.S182S|TMTC1_ENST00000552618.1_Silent_p.S182S|TMTC1_ENST00000256062.5_Silent_p.S74S	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	182						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.S74S(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ACCTGTTGTACGAGAGAAAGG	0.478													C|||	2	0.000399361	8e-04	0	5008	,	,		19194	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	3,4403	6.2+/-15.9	0,3,2200	117	84	95		546,222	3.8	1	12	dbSNP_134	95	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TMTC1	NM_001193451.1,NM_175861.3	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	182/883,74/775	29911645	3,13003	2203	4300	6503	29802912	SO:0001819	synonymous_variant	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.546G>A	12.37:g.29911645C>T			29802912	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	37	CCDS53772.1																																																																																				0.478	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		T	29911645	C	T	29911645	2	4	61	1	0	0	0	0	0	0	0	1	16299	523	19	1		1	TMTC1	12	29911645	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6916	29911645	103940250	7962	15947										
IPO8	10526	broad.mit.edu	37	chr12	30827624	30827624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagctacaatatgcagtgCccacttcttacacttccacc	5	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:30827624C>T	ENST00000256079.4	-	7	1131	c.793G>A	c.(793-795)Gca>Aca	p.A265T	IPO8_ENST00000544829.1_Missense_Mutation_p.A60T	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	265					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)	p.A265T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ATATGCAGTGCCCACTTCTTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											261	248	252					12																	30827624		2203	4300	6503	30718891	SO:0001583	missense	10526			U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.793G>A	12.37:g.30827624C>T	ENSP00000256079:p.Ala265Thr		30718891	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	37	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	C	33	5.225470	0.95173	.	.	ENSG00000133704	ENST00000256079;ENST00000544829;ENST00000542464	T;T;T	0.74209	-0.82;-0.82;-0.82	3.99	3.99	0.46301	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	D	0.84556	0.5498	M	0.70903	2.155	0.80722	D	1	D;D	0.89917	1.0;0.988	D;D	0.79108	0.992;0.934	D	0.85003	0.0901	10	0.41790	T	0.15	-12.3262	16.6289	0.85011	0.0:1.0:0.0:0.0	.	60;265	B7Z7M3;O15397	.;IPO8_HUMAN	T	265;60;79	ENSP00000256079:A265T;ENSP00000444520:A60T;ENSP00000439556:A79T	ENSP00000256079:A265T	A	-	1	0	IPO8	30718891	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	5.687000	0.68219	2.202000	0.70862	0.563000	0.77884	GCA		0.393	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		T	30827624	C	T	30827624	3	4	61	1	0	0	0	0	1	0	0	0	7819	739	26	3	2396	3	IPO8	12	30827624	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	915979	30827624	103024271	7963	15948										
CAPRIN2	65981	broad.mit.edu	37	chr12	30882056	30882056	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctctgttctaaggaaacTgcaggcttggatacctcctg	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:30882056T>G	ENST00000395805.2	-	8	1855	c.1308A>C	c.(1306-1308)gcA>gcC	p.A436A	CAPRIN2_ENST00000298892.5_Silent_p.A436A|CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000308433.5_Silent_p.A103A|CAPRIN2_ENST00000251071.5_Silent_p.A436A|CAPRIN2_ENST00000417045.1_Silent_p.A436A	NM_001206856.1	NP_001193785.1			caprin family member 2									p.A436A(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					CTAAGGAAACTGCAGGCTTGG	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	12											120	114	116					12																	30882056		2203	4300	6503	30773323	SO:0001819	synonymous_variant	65981			AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.1308A>C	12.37:g.30882056T>G			30773323		Silent	SNP	ENST00000395805.2	37	CCDS55816.1																																																																																				0.483	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		G	30882056	T	G	30882056	2	3	61	1	0	0	0	0	0	0	0	1	2642	1567	55	4		4	CAPRIN2	12	30882056	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	54432	30882056	102969839	7964	15949										
CAPRIN2	65981	broad.mit.edu	37	chr12	30887963	30887963	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaatgaggtagtcaagttCttttgaaggcaaatacactg	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:30887963C>A	ENST00000395805.2	-	4	1295	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	CAPRIN2_ENST00000298892.5_Nonsense_Mutation_p.E250*|CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000251071.5_Nonsense_Mutation_p.E250*|CAPRIN2_ENST00000417045.1_Nonsense_Mutation_p.E250*	NM_001206856.1	NP_001193785.1			caprin family member 2									p.E250*(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TAGTCAAGTTCTTTTGAAGGC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											169	167	168					12																	30887963		2203	4300	6503	30779230	SO:0001587	stop_gained	65981			AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.748G>T	12.37:g.30887963C>A	ENSP00000379150:p.Glu250*		30779230		Nonsense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	C	39	7.325092	0.98214	.	.	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000537108;ENST00000541765;ENST00000543380;ENST00000542550	.	.	.	4.72	3.83	0.44106	.	0.378221	0.30011	N	0.010631	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-7.3822	13.0598	0.59000	0.0:0.9222:0.0:0.0778	.	.	.	.	X	250;250;250;250;169;47;47;169	.	ENSP00000251071:E250X	E	-	1	0	CAPRIN2	30779230	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.681000	0.54648	1.205000	0.43262	0.591000	0.81541	GAA		0.373	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		A	30887963	C	A	30887963	4	1	61	1	0	0	0	0	0	1	0	0	2642	922	32	2	2695	2	CAPRIN2	12	30887963	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5907	30887963	102963932	7965	15950										
CAPRIN2	65981	broad.mit.edu	37	chr12	30906661	30906661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttccacagaagtgagctCgaaacccaatgatgcttgag	9	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:30906661C>T	ENST00000395805.2	-	1	584	c.37G>A	c.(37-39)Gag>Aag	p.E13K	CAPRIN2_ENST00000298892.5_Missense_Mutation_p.E13K|CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.E13K|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.E13K|RP11-77I22.2_ENST00000500076.2_lincRNA	NM_001206856.1	NP_001193785.1			caprin family member 2									p.E13K(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GAAGTGAGCTCGAAACCCAAT	0.408											OREG0021723	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	12											103	104	104					12																	30906661		2202	4299	6501	30797928	SO:0001583	missense	65981			AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.37G>A	12.37:g.30906661C>T	ENSP00000379150:p.Glu13Lys	820	30797928		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416424	0.42918	.	.	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045	T;T;T;T	0.72942	-0.7;2.78;-0.65;2.78	3.72	2.83	0.33086	.	.	.	.	.	T	0.45115	0.1326	N	0.08118	0	0.19575	N	0.999964	B;B;B;B	0.13145	0.004;0.007;0.002;0.003	B;B;B;B	0.08055	0.001;0.003;0.001;0.001	T	0.25328	-1.0135	8	.	.	.	0.5218	5.7801	0.18301	0.0:0.7584:0.0:0.2416	.	13;13;13;13	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2	.;.;CAPR2_HUMAN;.	K	13	ENSP00000298892:E13K;ENSP00000379150:E13K;ENSP00000251071:E13K;ENSP00000391479:E13K	.	E	-	1	0	CAPRIN2	30797928	0.001000	0.12720	0.056000	0.19401	0.500000	0.33767	0.235000	0.17948	0.783000	0.33636	0.563000	0.77884	GAG		0.408	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		T	30906661	C	T	30906661	3	4	61	1	0	0	0	0	1	0	0	0	2642	893	31	1	3418	1	CAPRIN2	12	30906661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18698	30906661	102945234	7966	15951										
DDX11	1663	broad.mit.edu	37	chr12	31247735	31247735	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttccagagccagatCgacaacatcaacctgttcaa	5	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:31247735C>T	ENST00000407793.2	+	14	1712	c.1461C>T	c.(1459-1461)atC>atT	p.I487I	DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.I487I|DDX11_ENST00000545668.1_Silent_p.I487I|DDX11_ENST00000542838.1_Silent_p.I487I|DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000228264.6_Silent_p.I461I	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	487					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.I487I(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AGAGCCAGATCGACAACATCA	0.483										Multiple Myeloma(12;0.14)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											52	52	52					12																	31247735		2203	4297	6500	31139002	SO:0001819	synonymous_variant	1663			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1461C>T	12.37:g.31247735C>T			31139002	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																				0.483	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		T	31247735	C	T	31247735	2	4	61	1	0	0	0	0	0	0	0	1	4349	874	31	1		1	DDX11	12	31247735	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	341074	31247735	102604160	7967	15952										
DENND5B	160518	broad.mit.edu	37	chr12	31577526	31577526	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaggtcacaaaggctggcGatcaaggtgttctcctccag	12	11	3	0	rs187555875	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:31577526G>A	ENST00000389082.5	-	10	2598	c.2334C>T	c.(2332-2334)atC>atT	p.I778I	DENND5B_ENST00000536562.1_Silent_p.I813I|DENND5B_ENST00000306833.6_Silent_p.I813I	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	778	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.I778I(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						AAAGGCTGGCGATCAAGGTGT	0.532													G|||	5	0.000998403	0.0038	0	5008	,	,		17205	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						G		13,4127		0,13,2057	182	178	179		2334	-4.1	0.7	12		179	0,8456		0,0,4228	yes	coding-synonymous	DENND5B	NM_144973.3		0,13,6285	AA,AG,GG		0.0,0.314,0.1032		778/1275	31577526	13,12583	2070	4228	6298	31468793	SO:0001819	synonymous_variant	160518			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2334C>T	12.37:g.31577526G>A			31468793	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	37	CCDS44857.1																																																																																				0.532	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31577526	G	A	31577526	2	1	61	1	0	0	0	0	0	0	0	1	4448	1048	37	1		1	DENND5B	12	31577526	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	329791	31577526	102274369	7968	15953										
AMN1	196394	broad.mit.edu	37	chr12	31854856	31854856	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaatttaatttcttcagtTttctacagttagacaggtgc	6	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:31854856T>G	ENST00000281471.6	-	3	422	c.257A>C	c.(256-258)aAa>aCa	p.K86T	AMN1_ENST00000537562.1_Missense_Mutation_p.K68T|AMN1_ENST00000536761.1_Missense_Mutation_p.K68T|AMN1_ENST00000541931.1_5'UTR|AMN1_ENST00000542781.1_5'UTR	NM_001113402.1|NM_001278411.1|NM_001278412.1	NP_001106873.1|NP_001265340.1|NP_001265341.1	Q8IY45	AMN1_HUMAN	antagonist of mitotic exit network 1 homolog (S. cerevisiae)	86								p.K86T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	7	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			TTTCTTCAGTTTTCTACAGTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	42	42					12																	31854856		1834	4083	5917	31746123	SO:0001583	missense	196394				CCDS44858.1, CCDS61089.1	12p11.21	2010-07-19			ENSG00000151743	ENSG00000151743			27281	protein-coding gene	gene with protein product							Standard	NM_001113402		Approved		uc001rkq.4	Q8IY45	OTTHUMG00000169192	ENST00000281471.6:c.257A>C	12.37:g.31854856T>G	ENSP00000281471:p.Lys86Thr		31746123	B7Z7J3|Q6NVU4|Q86X98	Missense_Mutation	SNP	ENST00000281471.6	37	CCDS44858.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.410486	0.42715	.	.	ENSG00000151743	ENST00000281471;ENST00000537562;ENST00000536761;ENST00000535408;ENST00000537960;ENST00000506446	T;T;T;T;T;T	0.17528	3.63;3.63;3.63;3.63;2.28;2.27	5.37	5.37	0.77165	.	0.215397	0.40469	N	0.001096	T	0.17577	0.0422	M	0.72479	2.2	0.80722	D	1	P	0.40144	0.704	B	0.27380	0.079	T	0.07829	-1.0752	10	0.21540	T	0.41	.	15.6746	0.77307	0.0:0.0:0.0:1.0	.	86	Q8IY45	AMN1_HUMAN	T	86;68;68;68;68;88	ENSP00000281471:K86T;ENSP00000441419:K68T;ENSP00000440967:K68T;ENSP00000438990:K68T;ENSP00000441846:K68T;ENSP00000439438:K88T	ENSP00000281471:K86T	K	-	2	0	AMN1	31746123	1.000000	0.71417	1.000000	0.80357	0.466000	0.32739	4.774000	0.62339	2.164000	0.68074	0.533000	0.62120	AAA		0.353	AMN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402807.2	NR_004854		G	31854856	T	G	31854856	3	3	61	1	0	0	0	0	1	0	0	0	581	1841	64	4	539	4	AMN1	12	31854856	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	277330	31854856	101997039	7969	15954										
H3F3C	440093	broad.mit.edu	37	chr12	31944983	31944983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacggtcccaggcctgtagcGatgaggcttcaccccgcagg	13	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:31944983G>A	ENST00000340398.3	-	1	192	c.118C>T	c.(118-120)Cgc>Tgc	p.R40C		NM_001013699.2	NP_001013721.2	Q6NXT2	H3C_HUMAN	H3 histone, family 3C	40					positive regulation of cell growth (GO:0030307)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	nucleosomal DNA binding (GO:0031492)	p.R40C(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	18						GGCCTGTAGCGATGAGGCTTC	0.607										HNSCC(67;0.2)																																						1	Substitution - Missense(1)	large_intestine(1)	12											59	57	57					12																	31944983		2203	4300	6503	31836250	SO:0001583	missense	440093			BC066906	CCDS31769.1	12p11.21	2012-02-15			ENSG00000188375	ENSG00000188375		"Histones / Replication-independent"	33164	protein-coding gene	gene with protein product						21274551	Standard	NM_001013699		Approved	H3.5	uc001rkr.3	Q6NXT2	OTTHUMG00000157811	ENST00000340398.3:c.118C>T	12.37:g.31944983G>A	ENSP00000339835:p.Arg40Cys		31836250	E9P281	Missense_Mutation	SNP	ENST00000340398.3	37	CCDS31769.1	.	.	.	.	.	.	.	.	.	.	G	5.552	0.286808	0.10513	.	.	ENSG00000188375	ENST00000340398	T	0.52295	0.67	0.999	-2.0	0.07433	Histone-fold (2);	0.398688	0.19628	N	0.109742	T	0.51143	0.1657	M	0.93550	3.43	0.39901	D	0.973893	B	0.24132	0.098	B	0.22753	0.041	T	0.43523	-0.9386	10	0.62326	D	0.03	.	6.32	0.21213	0.3436:0.0:0.6564:0.0	.	40	Q6NXT2	H3C_HUMAN	C	40	ENSP00000339835:R40C	ENSP00000339835:R40C	R	-	1	0	H3F3C	31836250	1.000000	0.71417	0.000000	0.03702	0.028000	0.11728	3.716000	0.54904	-0.641000	0.05487	-0.506000	0.04501	CGC		0.607	H3F3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349653.1	NM_001013699		A	31944983	G	A	31944983	3	1	61	1	0	0	0	0	1	0	0	0	6956	1058	37	1	293	1	H3F3C	12	31944983	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90127	31944983	101906912	7970	15955										
C12orf35	55196	broad.mit.edu	37	chr12	32134898	32134898	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcagcacaattggaaatTtcactaacttgaaagtaaat	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32134898T>G	ENST00000312561.4	+	4	1423	c.1009T>G	c.(1009-1011)Ttc>Gtc	p.F337V	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	337								p.F337V(1)									AATTGGAAATTTCACTAACTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	84	85					12																	32134898		2203	4300	6503	32026165	SO:0001583	missense	55196			AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1009T>G	12.37:g.32134898T>G	ENSP00000310338:p.Phe337Val		32026165	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	T	12.52	1.961331	0.34565	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.07216	3.83;3.21	5.45	1.91	0.25777	.	0.655283	0.14267	N	0.330452	T	0.04861	0.0131	N	0.24115	0.695	0.09310	N	1	B	0.29432	0.244	B	0.28553	0.091	T	0.40478	-0.9561	9	.	.	.	.	4.3731	0.11258	0.0:0.238:0.167:0.5949	.	337	Q9HCM1	CL035_HUMAN	V	337	ENSP00000310338:F337V;ENSP00000370442:F337V	.	F	+	1	0	C12orf35	32026165	0.003000	0.15002	0.009000	0.14445	0.202000	0.24057	-0.216000	0.09266	0.901000	0.36495	0.454000	0.30748	TTC		0.398	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		G	32134898	T	G	32134898	3	3	61	1	0	0	0	0	1	0	0	0	1686	1841	64	4	1011	4	C12orf35	12	32134898	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	189915	32134898	101716997	7971	15956										
C12orf35	55196	broad.mit.edu	37	chr12	32136876	32136876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagttattctagagaaaaGtagtttggagcatgccactg	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32136876G>A	ENST00000312561.4	+	4	3401	c.2987G>A	c.(2986-2988)aGt>aAt	p.S996N	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	996								p.S996N(1)									CTAGAGAAAAGTAGTTTGGAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											45	47	46					12																	32136876		2203	4298	6501	32028143	SO:0001583	missense	55196			AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.2987G>A	12.37:g.32136876G>A	ENSP00000310338:p.Ser996Asn		32028143	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	11.42	1.634634	0.29068	.	.	ENSG00000174718	ENST00000312561	T	0.12361	2.69	5.69	3.69	0.42338	.	0.811662	0.11391	N	0.568821	T	0.13713	0.0332	L	0.59436	1.845	0.09310	N	1	B	0.15141	0.012	B	0.20184	0.028	T	0.34329	-0.9833	9	.	.	.	.	4.3014	0.10927	0.5697:0.0:0.4303:0.0	.	996	Q9HCM1	CL035_HUMAN	N	996	ENSP00000310338:S996N	.	S	+	2	0	C12orf35	32028143	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-0.023000	0.12456	0.651000	0.30788	0.655000	0.94253	AGT		0.398	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		A	32136876	G	A	32136876	3	1	61	1	0	0	0	0	1	0	0	0	1686	1029	36	3	2989	3	C12orf35	12	32136876	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1978	32136876	101715019	7972	15957										
BICD1	636	broad.mit.edu	37	chr12	32369294	32369294	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttactatctggggaagatCttggagatgcagaacgagct	13	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32369294C>A	ENST00000281474.5	+	2	430	c.327C>A	c.(325-327)atC>atA	p.I109I	BICD1_ENST00000548411.1_Silent_p.I109I	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	109					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.I109I(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			TGGGGAAGATCTTGGAGATGC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	12											110	102	105					12																	32369294		2203	4300	6503	32260561	SO:0001819	synonymous_variant	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.327C>A	12.37:g.32369294C>A			32260561	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																				0.547	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		A	32369294	C	A	32369294	2	1	61	1	0	0	0	0	0	0	0	1	1429	903	32	2		2	BICD1	12	32369294	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	232418	32369294	101482601	7973	15958										
FGD4	121512	broad.mit.edu	37	chr12	32734932	32734932	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatttgaagaaagagtctgCtgtgaacctaaatgctccta	9	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32734932C>A	ENST00000427716.2	+	4	555	c.131C>A	c.(130-132)gCt>gAt	p.A44D	FGD4_ENST00000546442.1_5'UTR|FGD4_ENST00000531134.1_Missense_Mutation_p.A129D|FGD4_ENST00000534526.2_Missense_Mutation_p.A181D|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000472289.1_Missense_Mutation_p.A44D|FGD4_ENST00000525053.1_Missense_Mutation_p.A156D	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	44	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.A44D(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAAGAGTCTGCTGTGAACCTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											86	87	87					12																	32734932		2203	4300	6503	32626199	SO:0001583	missense	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.131C>A	12.37:g.32734932C>A	ENSP00000394487:p.Ala44Asp		32626199	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	C	12.37	1.917412	0.33815	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000472289;ENST00000427716;ENST00000525053;ENST00000395742	T;T;T;T	0.70045	-0.45;-0.44;-0.44;-0.44	4.63	3.72	0.42706	.	0.406760	0.20662	N	0.088008	T	0.57388	0.2050	N	0.08118	0	0.80722	D	1	B;B;B;D	0.55385	0.201;0.037;0.09;0.971	B;B;B;P	0.52957	0.051;0.035;0.036;0.714	T	0.64398	-0.6417	10	0.62326	D	0.03	-3.3341	13.2827	0.60224	0.0:0.8408:0.1592:0.0	.	156;129;44;44	E9PJX4;B7Z493;Q96M96;E9PQT1	.;.;FGD4_HUMAN;.	D	181;129;44;44;156;25	ENSP00000449273:A181D;ENSP00000431323:A129D;ENSP00000394487:A44D;ENSP00000433666:A156D	ENSP00000379089:A44D	A	+	2	0	FGD4	32626199	0.289000	0.24334	0.962000	0.40283	0.578000	0.36192	3.098000	0.50259	1.039000	0.40074	0.563000	0.77884	GCT		0.393	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		A	32734932	C	A	32734932	3	1	61	1	0	0	0	0	1	0	0	0	5854	797	28	2	137	2	FGD4	12	32734932	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	365638	32734932	101116963	7974	15959										
YARS2	51067	broad.mit.edu	37	chr12	32908661	32908661	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccgtctccgggaagaagtCcttgaacagacctcgagcct	10	15	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32908661C>A	ENST00000324868.8	-	1	175	c.148G>T	c.(148-150)Gac>Tac	p.D50Y		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	50					gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)	p.D50Y(1)		endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GGGAAGAAGTCCTTGAACAGA	0.577											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											100	108	105					12																	32908661		2203	4300	6503	32799928	SO:0001583	missense	51067			AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"Aminoacyl tRNA synthetases / Class I"	24249	protein-coding gene	gene with protein product	"tyrosine tRNA ligase 2, mitochondrial"	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.148G>T	12.37:g.32908661C>A	ENSP00000320658:p.Asp50Tyr	836	32799928	D3DUW8|Q9H817	Missense_Mutation	SNP	ENST00000324868.8	37	CCDS31770.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427699	0.83667	.	.	ENSG00000139131	ENST00000324868	T	0.74106	-0.81	5.1	4.22	0.49857	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.402823	0.29246	N	0.012704	T	0.73760	0.3628	L	0.27053	0.805	0.40331	D	0.97892	D	0.65815	0.995	P	0.56788	0.806	T	0.78016	-0.2369	10	0.87932	D	0	-8.2383	13.0532	0.58966	0.0:0.9229:0.0:0.0771	.	50	Q9Y2Z4	SYYM_HUMAN	Y	50	ENSP00000320658:D50Y	ENSP00000320658:D50Y	D	-	1	0	YARS2	32799928	1.000000	0.71417	0.994000	0.49952	0.974000	0.67602	5.330000	0.65899	1.401000	0.46761	0.650000	0.86243	GAC		0.577	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936		A	32908661	C	A	32908661	3	1	61	1	0	0	0	0	1	0	0	0	17508	855	30	2	1305	2	YARS2	12	32908661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173729	32908661	100943234	7975	15960										
PKP2	5318	broad.mit.edu	37	chr12	32977061	32977061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccgtcacatcttctcatcGcttttctcccatcagcgcca	5	17	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:32977061G>A	ENST00000070846.6	-	8	1748	c.1724C>T	c.(1723-1725)gCg>gTg	p.A575V	PKP2_ENST00000340811.4_Missense_Mutation_p.A531V	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	575					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.A575V(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TCTTCTCATCGCTTTTCTCCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											147	124	132					12																	32977061		2203	4300	6503	32868328	SO:0001583	missense	5318			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1724C>T	12.37:g.32977061G>A	ENSP00000070846:p.Ala575Val		32868328	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	1.724	-0.495897	0.04291	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.75260	-0.92;-0.92	5.53	1.72	0.24424	Armadillo-like helical (1);Armadillo-type fold (1);	0.700493	0.14412	N	0.321211	T	0.51075	0.1653	N	0.17631	0.505	0.30227	N	0.7963	B;B;B	0.14805	0.004;0.002;0.011	B;B;B	0.09377	0.004;0.002;0.001	T	0.36383	-0.9750	10	0.14252	T	0.57	-4.7271	3.599	0.08018	0.4871:0.0:0.2671:0.2457	.	531;531;575	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	V	531;575;575	ENSP00000342800:A531V;ENSP00000070846:A575V	ENSP00000070846:A575V	A	-	2	0	PKP2	32868328	0.837000	0.29446	0.919000	0.36401	0.348000	0.29142	0.755000	0.26405	0.401000	0.25424	-0.482000	0.04802	GCG		0.403	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		A	32977061	G	A	32977061	3	1	61	1	0	0	0	0	1	0	0	0	12016	1087	38	1	949	1	PKP2	12	32977061	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68400	32977061	100874834	7976	15961										
ALG10B	144245	broad.mit.edu	37	chr12	38714050	38714050	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaacttcctttattatacaGaagcaggatctatgtttttt	5	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:38714050G>A	ENST00000308742.4	+	3	773	c.457G>A	c.(457-459)Gaa>Aaa	p.E153K	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	153					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)	p.E153K(1)		breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TTATTATACAGAAGCAGGATC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											114	118	117					12																	38714050		2203	4299	6502	37000317	SO:0001583	missense	144245			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.457G>A	12.37:g.38714050G>A	ENSP00000310120:p.Glu153Lys		37000317	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	g	21.6	4.176107	0.78564	.	.	ENSG00000175548	ENST00000308742	T	0.57595	0.39	3.26	3.26	0.37387	.	0.046320	0.85682	D	0.000000	T	0.57095	0.2030	L	0.55481	1.735	0.80722	D	1	P	0.41080	0.737	P	0.49140	0.601	T	0.63928	-0.6526	10	0.87932	D	0	.	12.7892	0.57523	0.0:0.0:1.0:0.0	.	153	Q5I7T1	AG10B_HUMAN	K	153	ENSP00000310120:E153K	ENSP00000310120:E153K	E	+	1	0	ALG10B	37000317	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.211000	0.95120	2.124000	0.65301	0.561000	0.74099	GAA		0.348	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		A	38714050	G	A	38714050	3	1	61	1	0	0	0	0	1	0	0	0	512	943	33	3	467	3	ALG10B	12	38714050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5736989	38714050	95137845	7977	15962										
ALG10B	144245	broad.mit.edu	37	chr12	38714425	38714425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtggaattgttattggcGatcggagtagtcatgaagcc	14	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:38714425G>A	ENST00000308742.4	+	3	1148	c.832G>A	c.(832-834)Gat>Aat	p.D278N	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	278					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)	p.D278N(1)		breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TGTTATTGGCGATCGGAGTAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											157	156	156					12																	38714425		2203	4295	6498	37000692	SO:0001583	missense	144245			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.832G>A	12.37:g.38714425G>A	ENSP00000310120:p.Asp278Asn		37000692	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	g	21.2	4.108245	0.77096	.	.	ENSG00000175548	ENST00000308742	T	0.60920	0.15	3.24	3.24	0.37175	.	0.000000	0.85682	D	0.000000	T	0.80210	0.4581	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85069	0.0939	10	0.66056	D	0.02	.	12.7668	0.57396	0.0:0.0:1.0:0.0	.	278	Q5I7T1	AG10B_HUMAN	N	278	ENSP00000310120:D278N	ENSP00000310120:D278N	D	+	1	0	ALG10B	37000692	1.000000	0.71417	0.712000	0.30502	0.802000	0.45316	9.132000	0.94455	2.113000	0.64589	0.655000	0.94253	GAT		0.368	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		A	38714425	G	A	38714425	3	1	61	1	0	0	0	0	1	0	0	0	512	1058	37	1	842	1	ALG10B	12	38714425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	375	38714425	95137470	7978	15963										
ALG10B	144245	broad.mit.edu	37	chr12	38714509	38714509	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttttttcttttcctcatCtcctgtctcctagcaaaatt	2	12	5	0	rs143124122	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:38714509C>A	ENST00000308742.4	+	3	1232	c.916C>A	c.(916-918)Ctc>Atc	p.L306I	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	306					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)	p.L306I(1)		breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TTTTCCTCATCTCCTGTCTCC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											128	135	133					12																	38714509		2203	4299	6502	37000776	SO:0001583	missense	144245			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.916C>A	12.37:g.38714509C>A	ENSP00000310120:p.Leu306Ile		37000776	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	c	6.641	0.486818	0.12641	.	.	ENSG00000175548	ENST00000308742	T	0.55760	0.5	3.34	-0.516	0.11950	.	0.146147	0.47852	D	0.000214	T	0.40862	0.1134	L	0.51422	1.61	0.80722	D	1	P	0.39883	0.693	B	0.39840	0.311	T	0.11324	-1.0592	10	0.29301	T	0.29	.	7.455	0.27261	0.0:0.579:0.0:0.421	.	306	Q5I7T1	AG10B_HUMAN	I	306	ENSP00000310120:L306I	ENSP00000310120:L306I	L	+	1	0	ALG10B	37000776	1.000000	0.71417	0.439000	0.26833	0.438000	0.31896	1.180000	0.32005	-0.117000	0.11872	-0.136000	0.14681	CTC		0.348	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		A	38714509	C	A	38714509	3	1	61	1	0	0	0	0	1	0	0	0	512	913	32	2	926	2	ALG10B	12	38714509	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84	38714509	95137386	7979	15964										
KIF21A	55605	broad.mit.edu	37	chr12	39716680	39716680	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagtggtggttctccttCgggcctagtcaaagaatgga	13	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:39716680C>T	ENST00000361418.5	-	27	3476	c.3461G>A	c.(3460-3462)cGa>cAa	p.R1154Q	KIF21A_ENST00000395670.3_Missense_Mutation_p.R1154Q|KIF21A_ENST00000361961.3_Missense_Mutation_p.R1141Q|KIF21A_ENST00000541463.2_Missense_Mutation_p.R1118Q|KIF21A_ENST00000547745.1_5'Flank|KIF21A_ENST00000544797.2_Missense_Mutation_p.R1134Q			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1154					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1141Q(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GGTTCTCCTTCGGGCCTAGTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											123	117	119					12																	39716680		2203	4300	6503	38002947	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3461G>A	12.37:g.39716680C>T	ENSP00000354878:p.Arg1154Gln		38002947	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.071814|5.071814	0.93950|0.93950	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000552961|ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.|T;T;T;T;T;T	.|0.73047	.|-0.64;-0.63;-0.1;-0.71;-0.55;-0.6	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.158511	.|0.29730	.|N	.|0.011353	D|D	0.84051|0.84051	0.5387|0.5387	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|P;D;B;P;P;D	.|0.71674	.|0.951;0.998;0.226;0.802;0.934;0.983	.|B;D;B;B;B;P	.|0.75484	.|0.242;0.986;0.032;0.131;0.409;0.612	D|D	0.85442|0.85442	0.1155|0.1155	5|10	.|0.72032	.|D	.|0.01	.|.	19.0969|19.0969	0.93255|0.93255	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1134;1118;1154;1141;1154;201	.|F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3;F5H0V8	.|.;.;KI21A_HUMAN;.;.;.	K|Q	502|1141;1154;1154;201;195;1134;1154;1118	.|ENSP00000354851:R1141Q;ENSP00000379029:R1154Q;ENSP00000448792:R195Q;ENSP00000445606:R1134Q;ENSP00000354878:R1154Q;ENSP00000438075:R1118Q	.|ENSP00000344501:R1154Q	E|R	-|-	1|2	0|0	KIF21A|KIF21A	38002947|38002947	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.332000|7.332000	0.79203|0.79203	2.496000|2.496000	0.84212|0.84212	0.650000|0.650000	0.86243|0.86243	GAA|CGA		0.438	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		T	39716680	C	T	39716680	3	4	61	1	0	0	0	0	1	0	0	0	8309	884	31	1	1611	1	KIF21A	12	39716680	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1002171	39716680	94135215	7980	15965										
KIF21A	55605	broad.mit.edu	37	chr12	39726186	39726186	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttttgaaagtttctctcGtctttttgtgagttcctccc	6	10	3	2	rs142292357		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:39726186G>A	ENST00000361418.5	-	21	2896	c.2881C>T	c.(2881-2883)Cga>Tga	p.R961*	KIF21A_ENST00000395670.3_Nonsense_Mutation_p.R961*|KIF21A_ENST00000361961.3_Nonsense_Mutation_p.R948*|KIF21A_ENST00000541463.2_Nonsense_Mutation_p.R925*|KIF21A_ENST00000544797.2_Nonsense_Mutation_p.R948*			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	961					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R948*(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				AGTTTCTCTCGTCTTTTTGTG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	12						G	stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	203	190	195		2842,2881,2773,2842	3.7	1	12	dbSNP_134	195	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained,stop-gained	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	948/1638,961/1675,925/1622,948/1662	39726186	1,13005	2203	4300	6503	38012453	SO:0001587	stop_gained	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2881C>T	12.37:g.39726186G>A	ENSP00000354878:p.Arg961*		38012453	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Nonsense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	G	36	5.643258	0.96704	0.0	1.16E-4	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.	.	.	5.67	3.66	0.41972	.	0.000000	0.47852	D	0.000208	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.1304	0.53940	0.0:0.0:0.4186:0.5814	.	.	.	.	X	948;961;961;15;9;948;961;925	.	ENSP00000344501:R961X	R	-	1	2	KIF21A	38012453	0.991000	0.36638	0.998000	0.56505	0.991000	0.79684	1.953000	0.40352	1.357000	0.45904	0.557000	0.71058	CGA		0.398	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39726186	G	A	39726186	4	1	61	1	0	0	0	0	0	1	0	0	8309	1153	40	1	2215	1	KIF21A	12	39726186	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9506	39726186	94125709	7981	15966										
KIF21A	55605	broad.mit.edu	37	chr12	39745603	39745603	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcttcctcttttcttttCttttcaacttctctaaatct	0	11	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:39745603C>A	ENST00000361418.5	-	11	1664	c.1649G>T	c.(1648-1650)aGa>aTa	p.R550I	KIF21A_ENST00000395670.3_Missense_Mutation_p.R550I|KIF21A_ENST00000361961.3_Missense_Mutation_p.R550I|KIF21A_ENST00000541463.2_Missense_Mutation_p.R550I|KIF21A_ENST00000544797.2_Missense_Mutation_p.R550I			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	550					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R550I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				CTTTTCTTTTCTTTTCAACTT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	66	64					12																	39745603		2203	4300	6503	38031870	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1649G>T	12.37:g.39745603C>A	ENSP00000354878:p.Arg550Ile		38031870	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919924	0.52653	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	5.85	5.85	0.93711	.	0.103999	0.41938	D	0.000794	T	0.62307	0.2417	L	0.47716	1.5	0.43959	D	0.996636	D;P;P;P;P	0.53151	0.958;0.8;0.874;0.8;0.874	P;B;B;B;B	0.47981	0.563;0.203;0.387;0.143;0.277	T	0.62661	-0.6807	10	0.41790	T	0.15	.	7.6781	0.28497	0.0:0.8082:0.0:0.1918	.	550;550;550;550;550	F5H219;B9EGE4;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;.;KI21A_HUMAN;.	I	550	ENSP00000354851:R550I;ENSP00000379029:R550I;ENSP00000445606:R550I;ENSP00000354878:R550I;ENSP00000438075:R550I	ENSP00000344501:R550I	R	-	2	0	KIF21A	38031870	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.246000	0.58740	2.768000	0.95171	0.655000	0.94253	AGA		0.308	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39745603	C	A	39745603	3	1	61	1	0	0	0	0	1	0	0	0	8309	913	32	2	3487	2	KIF21A	12	39745603	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19417	39745603	94106292	7982	15967										
KIF21A	55605	broad.mit.edu	37	chr12	39751232	39751232	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccctcttcgtcaattattCttttaccctagtaaaggaaa	4	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:39751232C>A	ENST00000361418.5	-	9	1238	c.1223G>T	c.(1222-1224)aGa>aTa	p.R408I	KIF21A_ENST00000395670.3_Missense_Mutation_p.R408I|KIF21A_ENST00000361961.3_Missense_Mutation_p.R408I|KIF21A_ENST00000541463.2_Missense_Mutation_p.R408I|KIF21A_ENST00000544797.2_Missense_Mutation_p.R408I			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	408					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R408I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GTCAATTATTCTTTTACCCTA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											90	83	85					12																	39751232		2203	4300	6503	38037499	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1223G>T	12.37:g.39751232C>A	ENSP00000354878:p.Arg408Ile		38037499	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.674069	0.88445	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463;ENST00000552908	T;T;T;T;T;D	0.83419	-0.63;-0.6;-0.63;-0.54;-0.59;-1.72	4.55	4.55	0.56014	.	0.000000	0.56097	D	0.000026	D	0.89753	0.6806	M	0.64404	1.975	0.80722	D	1	B;D;B;D;B	0.89917	0.383;0.996;0.175;1.0;0.126	B;D;B;D;B	0.85130	0.259;0.974;0.188;0.997;0.241	D	0.90197	0.4254	10	0.51188	T	0.08	.	17.6979	0.88286	0.0:1.0:0.0:0.0	.	408;408;408;408;408	F5H219;B9EGE4;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;.;KI21A_HUMAN;.	I	408;408;408;408;408;408;231	ENSP00000354851:R408I;ENSP00000379029:R408I;ENSP00000445606:R408I;ENSP00000354878:R408I;ENSP00000438075:R408I;ENSP00000449700:R231I	ENSP00000344501:R408I	R	-	2	0	KIF21A	38037499	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.574000	0.82434	2.236000	0.73375	0.655000	0.94253	AGA		0.343	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39751232	C	A	39751232	3	1	61	1	0	0	0	0	1	0	0	0	8309	913	32	2	3921	2	KIF21A	12	39751232	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5629	39751232	94100663	7983	15968										
C12orf40	283461	broad.mit.edu	37	chr12	40076564	40076564	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaaaggaagtttcaaatTttcttgaagatgtgaaccag	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40076564T>G	ENST00000324616.5	+	8	992	c.838T>G	c.(838-840)Ttt>Gtt	p.F280V	C12orf40_ENST00000405531.3_Missense_Mutation_p.F280V|C12orf40_ENST00000398716.1_Missense_Mutation_p.F203V	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	280								p.F280V(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AGTTTCAAATTTTCTTGAAGA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											139	136	137					12																	40076564		1837	4082	5919	38362831	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.838T>G	12.37:g.40076564T>G	ENSP00000317671:p.Phe280Val		38362831	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.426960	0.25726	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.57752	0.38;0.41	4.9	4.9	0.64082	.	0.342750	0.24952	N	0.034281	T	0.51092	0.1654	L	0.32530	0.975	0.09310	N	1	D	0.57257	0.979	P	0.54270	0.747	T	0.47623	-0.9103	10	0.87932	D	0	.	7.8732	0.29578	0.0:0.0956:0.0:0.9044	.	280	Q86WS4	CL040_HUMAN	V	280;203;280	ENSP00000383897:F280V;ENSP00000317671:F280V	ENSP00000317671:F280V	F	+	1	0	C12orf40	38362831	0.723000	0.28027	0.296000	0.24974	0.105000	0.19272	3.283000	0.51701	2.143000	0.66587	0.482000	0.46254	TTT		0.338	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		G	40076564	T	G	40076564	3	3	61	1	0	0	0	0	1	0	0	0	1690	1841	64	4	868	4	C12orf40	12	40076564	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	325332	40076564	93775331	7984	15969										
C12orf40	283461	broad.mit.edu	37	chr12	40085881	40085881	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaggaggaatatattctTtaaaaagcaagcgaatatct	8	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40085881T>G	ENST00000324616.5	+	11	1532	c.1378T>G	c.(1378-1380)Tta>Gta	p.L460V	C12orf40_ENST00000405531.3_Missense_Mutation_p.L460V	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	460								p.L460V(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AATATATTCTTTAAAAAGCAA	0.244																																																1	Substitution - Missense(1)	large_intestine(1)	12											29	29	29					12																	40085881		1771	3971	5742	38372148	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1378T>G	12.37:g.40085881T>G	ENSP00000317671:p.Leu460Val		38372148	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	6.731	0.503665	0.12822	.	.	ENSG00000180116	ENST00000405531;ENST00000324616	T;T	0.60299	0.2;0.27	3.09	1.9	0.25705	.	0.195695	0.24766	N	0.035777	T	0.38108	0.1028	L	0.34521	1.04	0.58432	D	0.999999	P	0.52061	0.95	B	0.41466	0.358	T	0.12915	-1.0529	10	0.18276	T	0.48	.	5.5079	0.16864	0.2466:0.0:0.0:0.7534	.	460	Q86WS4	CL040_HUMAN	V	460	ENSP00000383897:L460V;ENSP00000317671:L460V	ENSP00000317671:L460V	L	+	1	2	C12orf40	38372148	0.996000	0.38824	0.826000	0.32828	0.097000	0.18754	0.942000	0.29017	0.547000	0.28938	0.379000	0.24179	TTA		0.244	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		G	40085881	T	G	40085881	3	3	61	1	0	0	0	0	1	0	0	0	1690	1838	64	4	1420	4	C12orf40	12	40085881	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9317	40085881	93766014	7985	15970										
SLC2A13	114134	broad.mit.edu	37	chr12	40422198	40422198	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgcatctgagataaaattCtacgggccttctgagtctgt	9	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40422198C>A	ENST00000280871.4	-	3	880	c.830G>T	c.(829-831)aGa>aTa	p.R277I	SLC2A13_ENST00000380858.1_Missense_Mutation_p.R277I	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	277					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.R258I(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				AGATAAAATTCTACGGGCCTT	0.433										HNSCC(50;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	12											106	111	109					12																	40422198		2203	4300	6503	38708465	SO:0001583	missense	114134			AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.830G>T	12.37:g.40422198C>A	ENSP00000280871:p.Arg277Ile		38708465	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	37	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783546	0.70222	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	T;T	0.75704	-0.96;-0.96	5.54	5.54	0.83059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.144833	0.64402	D	0.000011	T	0.78362	0.4271	L	0.49455	1.56	0.58432	D	0.999993	B;P	0.44241	0.171;0.829	B;P	0.48488	0.149;0.579	T	0.79517	-0.1771	10	0.66056	D	0.02	-20.8508	19.8499	0.96734	0.0:1.0:0.0:0.0	.	277;277	Q96QE2;E9PE47	MYCT_HUMAN;.	I	277	ENSP00000280871:R277I;ENSP00000370239:R277I	ENSP00000280871:R277I	R	-	2	0	SLC2A13	38708465	0.620000	0.27068	0.964000	0.40570	0.963000	0.63663	2.744000	0.47450	2.779000	0.95612	0.591000	0.81541	AGA		0.433	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			A	40422198	C	A	40422198	3	1	61	1	0	0	0	0	1	0	0	0	14579	913	32	2	1148	2	SLC2A13	12	40422198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336317	40422198	93429697	7986	15971										
LRRK2	120892	broad.mit.edu	37	chr12	40645086	40645086	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaagaatgagaatcaagaGaatgatgatgagggggaaga	15	1	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40645086G>T	ENST00000298910.7	+	9	1069	c.1011G>T	c.(1009-1011)gaG>gaT	p.E337D	LRRK2_ENST00000343742.2_Missense_Mutation_p.E337D	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	337					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.E337D(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGAATCAAGAGAATGATGATG	0.323											OREG0003829	type=REGULATORY REGION|Gene=LRRK2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				2	Substitution - Missense(2)	large_intestine(2)	12											54	59	57					12																	40645086		2203	4300	6503	38931353	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1011G>T	12.37:g.40645086G>T	ENSP00000298910:p.Glu337Asp	895	38931353	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	6.806	0.517776	0.13005	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.34859	1.34;1.34	4.79	1.77	0.24775	Armadillo-type fold (1);	0.515626	0.17869	N	0.159253	T	0.24044	0.0582	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.16928	-1.0386	10	0.30854	T	0.27	.	4.2256	0.10579	0.2688:0.0:0.5562:0.1749	.	337	Q5S007	LRRK2_HUMAN	D	337	ENSP00000341930:E337D;ENSP00000298910:E337D	ENSP00000298910:E337D	E	+	3	2	LRRK2	38931353	0.009000	0.17119	0.000000	0.03702	0.438000	0.31896	-0.174000	0.09839	0.235000	0.21160	0.655000	0.94253	GAG		0.323	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40645086	G	T	40645086	3	4	61	1	0	0	0	0	1	0	0	0	9062	933	33	2	1045	2	LRRK2	12	40645086	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	222888	40645086	93206809	7987	15972										
LRRK2	120892	broad.mit.edu	37	chr12	40646787	40646787	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagttttccaggcatctgcGaatgcattgtcaactctctt	8	10	3	0	rs200357353		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40646787G>A	ENST00000298910.7	+	11	1315	c.1257G>A	c.(1255-1257)gcG>gcA	p.A419A	LRRK2_ENST00000343742.2_Silent_p.A419A	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	419			A -> V (in dbSNP:rs34594498). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.A419A(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGGCATCTGCGAATGCATTGT	0.363																																																2	Substitution - coding silent(2)	large_intestine(2)	12											74	71	72					12																	40646787		2203	4300	6503	38933054	SO:0001819	synonymous_variant	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1257G>A	12.37:g.40646787G>A			38933054	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	0.203	-1.043116	0.01997	.	.	ENSG00000188906	ENST00000416796	T	0.64803	-0.12	5.12	-10.2	0.00374	.	.	.	.	.	T	0.29423	0.0733	.	.	.	0.54753	D	0.999981	.	.	.	.	.	.	T	0.30387	-0.9980	6	0.07482	T	0.82	.	3.9133	0.09213	0.2111:0.142:0.4341:0.2128	.	.	.	.	K	211	ENSP00000398726:E211K	ENSP00000398726:E211K	E	+	1	0	LRRK2	38933054	0.006000	0.16342	0.000000	0.03702	0.022000	0.10575	-2.038000	0.01419	-3.279000	0.00197	-3.753000	0.00022	GAA		0.363	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40646787	G	A	40646787	2	1	61	1	0	0	0	0	0	0	0	1	9062	1045	37	1		1	LRRK2	12	40646787	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1701	40646787	93205108	7988	15973										
LRRK2	120892	broad.mit.edu	37	chr12	40687400	40687400	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaattcaattagtgtaggaGaattttaccgagatgccgta	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40687400G>T	ENST00000298910.7	+	21	2801	c.2743G>T	c.(2743-2745)Gaa>Taa	p.E915*	LRRK2_ENST00000343742.2_Nonsense_Mutation_p.E915*	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	915					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.E915*(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TAGTGTAGGAGAATTTTACCG	0.323																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											86	83	84					12																	40687400		2202	4299	6501	38973667	SO:0001587	stop_gained	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2743G>T	12.37:g.40687400G>T	ENSP00000298910:p.Glu915*		38973667	A6NJU2|Q6ZS50|Q8NCX9	Nonsense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	40	8.420233	0.98803	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	.	.	.	5.03	5.03	0.67393	.	0.347464	0.30338	N	0.009841	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	12.1414	0.54000	0.079:0.0:0.921:0.0	.	.	.	.	X	915	.	ENSP00000298910:E915X	E	+	1	0	LRRK2	38973667	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.972000	0.63756	2.471000	0.83476	0.650000	0.86243	GAA		0.323	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40687400	G	T	40687400	4	4	61	1	0	0	0	0	0	1	0	0	9062	943	33	2	2825	2	LRRK2	12	40687400	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40613	40687400	93164495	7989	15974										
LRRK2	120892	broad.mit.edu	37	chr12	40699758	40699758	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atataggatgtaaagccaaaGacatcataaggttagataat	8	4	1	2	rs573327331		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40699758G>T	ENST00000298910.7	+	28	4007	c.3949G>T	c.(3949-3951)Gac>Tac	p.D1317Y		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1317					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.D1317Y(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TAAAGCCAAAGACATCATAAG	0.289													G|||	1	0.000199681	0	0.0014	5008	,	,		19582	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12											47	45	46					12																	40699758		2203	4299	6502	38986025	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.3949G>T	12.37:g.40699758G>T	ENSP00000298910:p.Asp1317Tyr		38986025	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538913	0.85917	.	.	ENSG00000188906	ENST00000298910	T	0.74315	-0.83	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.81375	0.4809	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.82866	-0.0245	10	0.87932	D	0	.	19.9738	0.97296	0.0:0.0:1.0:0.0	.	1317;1317	Q17RV3;Q5S007	.;LRRK2_HUMAN	Y	1317	ENSP00000298910:D1317Y	ENSP00000298910:D1317Y	D	+	1	0	LRRK2	38986025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.352000	0.97076	2.732000	0.93576	0.655000	0.94253	GAC		0.289	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40699758	G	T	40699758	3	4	61	1	0	0	0	0	1	0	0	0	9062	942	33	2	4059	2	LRRK2	12	40699758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12358	40699758	93152137	7990	15975										
LRRK2	120892	broad.mit.edu	37	chr12	40716990	40716990	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagtaaatccagatcaaccAaggctcaccattccaatatc	4	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:40716990A>C	ENST00000298910.7	+	38	5596	c.5538A>C	c.(5536-5538)ccA>ccC	p.P1846P		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1846					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.P1809P(1)|p.P1846P(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CAGATCAACCAAGGCTCACCA	0.328																																																2	Substitution - coding silent(2)	large_intestine(2)	12											74	73	73					12																	40716990		2203	4300	6503	39003257	SO:0001819	synonymous_variant	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5538A>C	12.37:g.40716990A>C			39003257	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																				0.328	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		C	40716990	A	C	40716990	2	2	61	1	0	0	0	0	0	0	0	1	9062	117	5	4		4	LRRK2	12	40716990	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	17232	40716990	93134905	7991	15976										
CNTN1	1272	broad.mit.edu	37	chr12	41323661	41323661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcacaatggataaacggcGatttgtgtctcagacaaatg	9	7	2	1	rs4408370		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41323661G>A	ENST00000551295.2	+	7	677	c.560G>A	c.(559-561)cGa>cAa	p.R187Q	CNTN1_ENST00000347616.1_Missense_Mutation_p.R187Q|CNTN1_ENST00000547849.1_Missense_Mutation_p.R187Q|CNTN1_ENST00000348761.2_Missense_Mutation_p.R176Q|CNTN1_ENST00000360099.3_Missense_Mutation_p.R187Q|CNTN1_ENST00000547702.1_Missense_Mutation_p.R187Q	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	187	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R187Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GATAAACGGCGATTTGTGTCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											122	121	121					12																	41323661		2203	4299	6502	39609928	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.560G>A	12.37:g.41323661G>A	ENSP00000447006:p.Arg187Gln		39609928	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	35	5.499137	0.96355	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.39	5.39	0.77823	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89210	0.6650	M	0.84156	2.68	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.976;0.986	D	0.88446	0.3045	10	0.42905	T	0.14	.	19.5309	0.95228	0.0:0.0:1.0:0.0	rs4408370;rs4408370	187;176;187	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	Q	187;187;187;187;187;176	ENSP00000448004:R187Q;ENSP00000447006:R187Q;ENSP00000448653:R187Q;ENSP00000325660:R187Q;ENSP00000353213:R187Q;ENSP00000261160:R176Q	ENSP00000325660:R187Q	R	+	2	0	CNTN1	39609928	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.476000	0.97823	2.699000	0.92147	0.655000	0.94253	CGA		0.368	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41323661	G	A	41323661	3	1	61	1	0	0	0	0	1	0	0	0	3646	1058	37	1	582	1	CNTN1	12	41323661	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	606671	41323661	92528234	7992	15977										
CNTN1	1272	broad.mit.edu	37	chr12	41327267	41327267	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttaatattaggaacAacaaaaccatatcctgctga	4	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41327267A>G	ENST00000551295.2	+	8	825	c.708A>G	c.(706-708)acA>acG	p.T236T	CNTN1_ENST00000347616.1_Silent_p.T236T|CNTN1_ENST00000547849.1_Silent_p.T236T|CNTN1_ENST00000348761.2_Silent_p.T225T|CNTN1_ENST00000360099.3_Silent_p.T236T|CNTN1_ENST00000547702.1_Silent_p.T236T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	236					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.T236T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TATTAGGAACAACAAAACCAT	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	12											120	120	120					12																	41327267		2203	4300	6503	39613534	SO:0001819	synonymous_variant	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.708A>G	12.37:g.41327267A>G			39613534	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	37	CCDS8737.1																																																																																				0.338	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41327267	A	G	41327267	2	3	61	1	0	0	0	0	0	0	0	1	3646	117	5	4		4	CNTN1	12	41327267	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3606	41327267	92524628	7993	15978										
CNTN1	1272	broad.mit.edu	37	chr12	41374826	41374826	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctaaatacactatccaGaccaagactattctttcaga	3	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41374826G>A	ENST00000551295.2	+	16	2037	c.1920G>A	c.(1918-1920)caG>caA	p.Q640Q	CNTN1_ENST00000347616.1_Silent_p.Q640Q|CNTN1_ENST00000348761.2_Silent_p.Q629Q	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	640	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.Q640Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				ACACTATCCAGACCAAGACTA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	12											125	128	127					12																	41374826		2203	4300	6503	39661093	SO:0001819	synonymous_variant	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1920G>A	12.37:g.41374826G>A			39661093	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	37	CCDS8737.1																																																																																				0.393	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41374826	G	A	41374826	2	1	61	1	0	0	0	0	0	0	0	1	3646	933	33	3		3	CNTN1	12	41374826	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47559	41374826	92477069	7994	15979										
PDZRN4	29951	broad.mit.edu	37	chr12	41966705	41966705	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcatgatggaggattccgGaattataacaccagcataga	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41966705G>A	ENST00000402685.2	+	10	2132	c.2124G>A	c.(2122-2124)cgG>cgA	p.R708R	PDZRN4_ENST00000539469.2_Silent_p.R450R|PDZRN4_ENST00000298919.7_Silent_p.R448R	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	708							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R450R(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GAGGATTCCGGAATTATAACA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	12											98	101	100					12																	41966705		2203	4300	6503	40252972	SO:0001819	synonymous_variant	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2124G>A	12.37:g.41966705G>A			40252972	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																				0.448	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41966705	G	A	41966705	2	1	61	1	0	0	0	0	0	0	0	1	11741	1161	41	3		3	PDZRN4	12	41966705	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	591879	41966705	91885190	7995	15980										
PDZRN4	29951	broad.mit.edu	37	chr12	41967301	41967301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcacaaagagacccgtgcGagaccgaatcctgaaggaac	10	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41967301G>A	ENST00000402685.2	+	10	2728	c.2720G>A	c.(2719-2721)cGa>cAa	p.R907Q	PDZRN4_ENST00000539469.2_Missense_Mutation_p.R649Q|PDZRN4_ENST00000298919.7_Missense_Mutation_p.R647Q	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	907							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R649Q(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AGACCCGTGCGAGACCGAATC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	90	93					12																	41967301		2203	4300	6503	40253568	SO:0001583	missense	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2720G>A	12.37:g.41967301G>A	ENSP00000384197:p.Arg907Gln		40253568	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000397	0.93227	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.49139	0.79;0.79;0.79	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000004	T	0.74030	0.3663	M	0.85373	2.75	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	T	0.77289	-0.2643	10	0.87932	D	0	-20.1324	19.939	0.97151	0.0:0.0:1.0:0.0	.	907;647;649	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	Q	907;649;647	ENSP00000384197:R907Q;ENSP00000439990:R649Q;ENSP00000298919:R647Q	ENSP00000298919:R647Q	R	+	2	0	PDZRN4	40253568	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.813000	0.99286	2.890000	0.99128	0.650000	0.86243	CGA		0.517	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41967301	G	A	41967301	3	1	61	1	0	0	0	0	1	0	0	0	11741	1058	37	1	2831	1	PDZRN4	12	41967301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	596	41967301	91884594	7996	15981										
PDZRN4	29951	broad.mit.edu	37	chr12	41967475	41967475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgccgtgagttcatgatgcGaagcaggttagagtgtctca	13	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:41967475G>A	ENST00000402685.2	+	10	2902	c.2894G>A	c.(2893-2895)cGa>cAa	p.R965Q	PDZRN4_ENST00000539469.2_Missense_Mutation_p.R707Q|PDZRN4_ENST00000298919.7_Missense_Mutation_p.R705Q	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	965							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R707Q(2)|p.R965Q(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TTCATGATGCGAAGCAGGTTA	0.507																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	12											69	64	66					12																	41967475		2203	4300	6503	40253742	SO:0001583	missense	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2894G>A	12.37:g.41967475G>A	ENSP00000384197:p.Arg965Gln		40253742	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	1.545	-0.540706	0.04053	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.75704	-0.96;-0.96;-0.96	4.9	4.9	0.64082	.	0.000000	0.64402	D	0.000001	T	0.40719	0.1128	N	0.00801	-1.175	0.80722	D	1	P;B;B	0.45986	0.87;0.032;0.032	B;B;B	0.36504	0.226;0.012;0.012	T	0.61387	-0.7073	10	0.02654	T	1	-25.0878	18.9769	0.92740	0.0:0.0:1.0:0.0	.	965;705;707	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	Q	965;707;705	ENSP00000384197:R965Q;ENSP00000439990:R707Q;ENSP00000298919:R705Q	ENSP00000298919:R705Q	R	+	2	0	PDZRN4	40253742	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	4.735000	0.62051	2.656000	0.90262	0.557000	0.71058	CGA		0.507	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41967475	G	A	41967475	3	1	61	1	0	0	0	0	1	0	0	0	11741	1058	37	1	3005	1	PDZRN4	12	41967475	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	174	41967475	91884420	7997	15982										
PRICKLE1	144165	broad.mit.edu	37	chr12	42860028	42860028	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggtttcacagtactccGcatagagagactcaaaacag	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:42860028G>A	ENST00000455697.1	-	6	1028	c.743C>T	c.(742-744)gCg>gTg	p.A248V	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.A248V|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.A248V|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.A248V|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.A248V	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	248	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.A248V(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ACAGTACTCCGCATAGAGAGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	12											76	73	74					12																	42860028		2203	4300	6503	41146295	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.743C>T	12.37:g.42860028G>A	ENSP00000401060:p.Ala248Val		41146295	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	36	5.711645	0.96830	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.18	5.18	0.71444	Zinc finger, LIM-type (2);	0.094019	0.64402	D	0.000001	D	0.94551	0.8245	M	0.89968	3.075	0.80722	D	1	D	0.55800	0.973	P	0.55508	0.777	D	0.95474	0.8554	10	0.87932	D	0	-4.697	19.0641	0.93103	0.0:0.0:1.0:0.0	.	248	Q96MT3	PRIC1_HUMAN	V	248	ENSP00000401060:A248V;ENSP00000398947:A248V;ENSP00000448359:A248V;ENSP00000345064:A248V;ENSP00000449819:A248V	ENSP00000345064:A248V	A	-	2	0	PRICKLE1	41146295	1.000000	0.71417	0.663000	0.29738	0.994000	0.84299	9.813000	0.99286	2.590000	0.87494	0.561000	0.74099	GCG		0.522	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42860028	G	A	42860028	3	1	61	1	0	0	0	0	1	0	0	0	12520	1087	38	1	1764	1	PRICKLE1	12	42860028	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	892553	42860028	90991867	7998	15983										
PRICKLE1	144165	broad.mit.edu	37	chr12	42862517	42862517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgataaaaatagatgaggtCgaccagcagctcattacacg	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:42862517C>T	ENST00000455697.1	-	5	784	c.499G>A	c.(499-501)Gac>Aac	p.D167N	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.D167N|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.D167N|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.D167N|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.D167N	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	167	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.D167N(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TAGATGAGGTCGACCAGCAGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	92	93					12																	42862517		2203	4300	6503	41148784	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.499G>A	12.37:g.42862517C>T	ENSP00000401060:p.Asp167Asn		41148784	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	C	36	5.954499	0.97139	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24	5.56	5.56	0.83823	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.93766	0.8007	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93424	0.6779	10	0.56958	D	0.05	-22.1322	19.8898	0.96926	0.0:1.0:0.0:0.0	.	167	Q96MT3	PRIC1_HUMAN	N	167	ENSP00000401060:D167N;ENSP00000398947:D167N;ENSP00000448359:D167N;ENSP00000345064:D167N;ENSP00000449819:D167N	ENSP00000345064:D167N	D	-	1	0	PRICKLE1	41148784	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.775000	0.95449	0.655000	0.94253	GAC		0.502	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			T	42862517	C	T	42862517	3	4	61	1	0	0	0	0	1	0	0	0	12520	884	31	1	2012	1	PRICKLE1	12	42862517	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2489	42862517	90989378	7999	15984										
ADAMTS20	80070	broad.mit.edu	37	chr12	43777454	43777454	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgaagaattatagactatTtcattcacttgtctgatttg	7	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:43777454T>C	ENST00000389420.3	-	31	4703	c.4704A>G	c.(4702-4704)gaA>gaG	p.E1568E		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1568	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E1568E(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		TATAGACTATTTCATTCACTT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	12											150	138	142					12																	43777454		2203	4300	6503	42063721	SO:0001819	synonymous_variant	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.4704A>G	12.37:g.43777454T>C			42063721	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																				0.373	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43777454	T	C	43777454	2	2	61	1	0	0	0	0	0	0	0	1	266	1838	64	4		4	ADAMTS20	12	43777454	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	914937	43777454	90074441	8000	15985										
ADAMTS20	80070	broad.mit.edu	37	chr12	43823520	43823520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgagcaaggtgtaagtAcacagctctgttcagaagaa	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:43823520A>G	ENST00000389420.3	-	24	3388	c.3389T>C	c.(3388-3390)gTa>gCa	p.V1130A	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.V1130A|ADAMTS20_ENST00000395541.2_Intron	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1130	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V1130A(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		AGGTGTAAGTACACAGCTCTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											49	46	47					12																	43823520		2202	4299	6501	42109787	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3389T>C	12.37:g.43823520A>G	ENSP00000374071:p.Val1130Ala		42109787	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	4.029	0.002854	0.07866	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.52526	0.66;0.66	4.69	2.1	0.27182	.	1.394090	0.04985	N	0.466388	T	0.24198	0.0586	N	0.05306	-0.075	0.23346	N	0.997867	B	0.25667	0.131	B	0.29440	0.102	T	0.31641	-0.9936	10	0.08179	T	0.78	.	3.7924	0.08726	0.6397:0.0:0.1026:0.2577	.	1130	P59510	ATS20_HUMAN	A	1130	ENSP00000374071:V1130A;ENSP00000448341:V1130A	ENSP00000374068:V1130A	V	-	2	0	ADAMTS20	42109787	0.102000	0.21896	0.034000	0.17996	0.034000	0.12701	1.026000	0.30103	0.879000	0.35944	0.482000	0.46254	GTA		0.353	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43823520	A	G	43823520	3	3	61	1	0	0	0	0	1	0	0	0	266	391	14	4	2406	4	ADAMTS20	12	43823520	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	46066	43823520	90028375	8001	15986										
ADAMTS20	80070	broad.mit.edu	37	chr12	43847741	43847741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcgcctggttgcactttCgattccgcctccacatgttc	8	15	0	0	rs143824237	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:43847741C>T	ENST00000389420.3	-	12	1728	c.1729G>A	c.(1729-1731)Gaa>Aaa	p.E577K	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E577K	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	577	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E577K(2)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		GTTGCACTTTCGATTCCGCCT	0.413													C|||	4	0.000798722	0.0023	0	5008	,	,		16287	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12											114	90	98					12																	43847741		2203	4300	6503	42134008	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1729G>A	12.37:g.43847741C>T	ENSP00000374071:p.Glu577Lys		42134008	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	8	0.003663003663003663	7	0.014227642276422764	0	0.0	1	0.0017482517482517483	0	0.0	C	3.133	-0.178037	0.06380	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.50001	0.76;0.76	4.77	3.63	0.41609	.	0.382752	0.21292	N	0.076950	T	0.10508	0.0257	N	0.00885	-1.115	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.21449	-1.0245	10	0.02654	T	1	.	10.2372	0.43290	0.0:0.082:0.0:0.918	.	577	P59510	ATS20_HUMAN	K	577	ENSP00000374071:E577K;ENSP00000448341:E577K	ENSP00000374068:E577K	E	-	1	0	ADAMTS20	42134008	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	2.252000	0.43196	0.930000	0.37217	-0.482000	0.04802	GAA		0.413	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43847741	C	T	43847741	3	4	61	1	0	0	0	0	1	0	0	0	266	893	31	1	4114	1	ADAMTS20	12	43847741	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24221	43847741	90004154	8002	15987										
PUS7L	83448	broad.mit.edu	37	chr12	44139911	44139912	+	Missense_Mutation	DNP	TT	TT	GC													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagaatcatttatttgttTttttaaatttctaatgacaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	TT	TT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44139911_44139912TT>GC	ENST00000416848.2	-	4	1688_1689	c.1200_1201AA>GC	c.(1198-1203)aaAAaa>aaGCaa	p.K401Q	PUS7L_ENST00000431332.3_Missense_Mutation_p.K88Q|PUS7L_ENST00000344862.5_Missense_Mutation_p.K401Q|PUS7L_ENST00000551923.1_Missense_Mutation_p.K401Q	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	401					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.K400>?(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TTTATTTGTTTTTTTAAATTTC	0.317																																																1	Complex(1)	large_intestine(1)	12																																								42426179	SO:0001583	missense	83448			BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1200_1201delinsGC	12.37:g.44139911_44139912delinsGC	ENSP00000415899:p.Lys401Gln		42426178	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	DNP	ENST00000416848.2	37	CCDS8743.1																																																																																				0.317	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		GC	44139912	TT	GC	44139911	3	3	61	1	0	0	0	0	1	0	0	0	12871	1850	64	4	928	4	PUS7L	12	44139911	Missense_Mutation	DNP	TT	TCGA-AG-A002-01A-01W-A00K-09	292170	44139911	89711984	8003	15988										
PUS7L	83448	broad.mit.edu	37	chr12	44148436	44148436	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agataccaaatgacaaagttCtttatattcaagatttggtt	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44148436C>A	ENST00000416848.2	-	2	1101	c.613G>T	c.(613-615)Gaa>Taa	p.E205*	PUS7L_ENST00000553166.1_Nonsense_Mutation_p.E205*|PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000344862.5_Nonsense_Mutation_p.E205*|PUS7L_ENST00000551923.1_Nonsense_Mutation_p.E205*	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	205					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.E205*(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TGACAAAGTTCTTTATATTCA	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											50	51	51					12																	44148436		2203	4299	6502	42434703	SO:0001587	stop_gained	83448			BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.613G>T	12.37:g.44148436C>A	ENSP00000415899:p.Glu205*		42434703	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Nonsense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	.	.	.	.	.	.	.	.	.	.	C	41	8.579854	0.98872	.	.	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-34.3818	19.9585	0.97232	0.0:1.0:0.0:0.0	.	.	.	.	X	205	.	ENSP00000343081:E205X	E	-	1	0	PUS7L	42434703	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.439000	0.59968	2.894000	0.99253	0.655000	0.94253	GAA		0.303	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44148436	C	A	44148436	4	1	61	1	0	0	0	0	0	1	0	0	12871	922	32	2	1524	2	PUS7L	12	44148436	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8525	44148436	89703459	8004	15989										
IRAK4	51135	broad.mit.edu	37	chr12	44176112	44176112	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttacatttttttcagtgCaaatatcttactggatgaag	6	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44176112C>A	ENST00000448290.2	+	9	1015	c.944C>A	c.(943-945)gCa>gAa	p.A315E	IRAK4_ENST00000440781.2_Missense_Mutation_p.A191E|IRAK4_ENST00000431837.1_Missense_Mutation_p.A191E|IRAK4_ENST00000551736.1_Missense_Mutation_p.A315E	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	315	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A315E(1)				all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		TTTTTCAGTGCAAATATCTTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											57	58	58					12																	44176112		2203	4300	6503	42462379	SO:0001583	missense	51135			AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.944C>A	12.37:g.44176112C>A	ENSP00000390651:p.Ala315Glu		42462379	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	C	32	5.124005	0.94429	.	.	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06	5.62	5.62	0.85841	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94928	0.8360	L	0.46567	1.45	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95174	0.8293	10	0.87932	D	0	-25.5481	19.6622	0.95877	0.0:1.0:0.0:0.0	.	315	Q9NWZ3	IRAK4_HUMAN	E	191;191;315;315	ENSP00000408734:A191E;ENSP00000390327:A191E;ENSP00000390651:A315E;ENSP00000446490:A315E	ENSP00000390327:A191E	A	+	2	0	IRAK4	42462379	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.641000	0.54360	2.637000	0.89404	0.585000	0.79938	GCA		0.363	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			A	44176112	C	A	44176112	3	1	61	1	0	0	0	0	1	0	0	0	7846	710	25	2	974	2	IRAK4	12	44176112	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27676	44176112	89675783	8005	15990										
TWF1	5756	broad.mit.edu	37	chr12	44189457	44189457	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcctctttttcctgcaggAccttttggttttgcaaaact	6	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44189457A>G	ENST00000395510.2	-	9	1113	c.984T>C	c.(982-984)ggT>ggC	p.G328G	TWF1_ENST00000552521.1_Silent_p.G230G|TWF1_ENST00000548315.1_Silent_p.G335G|TWF1_ENST00000325127.4_Silent_p.G362G	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	328					barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.G328G(1)		endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		TTCCTGCAGGACCTTTTGGTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											102	98	100					12																	44189457		2203	4300	6503	42475724	SO:0001819	synonymous_variant	5756			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"protein tyrosine kinase 9", "PTK9 protein tyrosine kinase 9", "twinfilin, actin-binding protein, homolog 1 (Drosophila)"	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.984T>C	12.37:g.44189457A>G			42475724	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																				0.408	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822		G	44189457	A	G	44189457	2	3	61	1	0	0	0	0	0	0	0	1	16821	262	10	4		4	TWF1	12	44189457	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13345	44189457	89662438	8006	15991										
TWF1	5756	broad.mit.edu	37	chr12	44190794	44190794	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctacctttctaattacatcCatttgtagttgtctttctac	4	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44190794C>A	ENST00000395510.2	-	8	996	c.867G>T	c.(865-867)atG>atT	p.M289I	TWF1_ENST00000552521.1_Missense_Mutation_p.M191I|TWF1_ENST00000548315.1_Missense_Mutation_p.M296I|TWF1_ENST00000325127.4_Missense_Mutation_p.M323I	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	289	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.M289I(1)		endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		TAATTACATCCATTTGTAGTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											81	85	84					12																	44190794		2203	4299	6502	42477061	SO:0001583	missense	5756			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"protein tyrosine kinase 9", "PTK9 protein tyrosine kinase 9", "twinfilin, actin-binding protein, homolog 1 (Drosophila)"	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.867G>T	12.37:g.44190794C>A	ENSP00000378886:p.Met289Ile		42477061	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Missense_Mutation	SNP	ENST00000395510.2	37	CCDS31780.2	.	.	.	.	.	.	.	.	.	.	C	5.837	0.338626	0.11069	.	.	ENSG00000151239	ENST00000552521;ENST00000395510;ENST00000325127;ENST00000548315	T;T;T;T	0.25749	1.78;2.54;2.53;2.53	5.55	5.55	0.83447	Actin-binding, cofilin/tropomyosin type (2);	0.118606	0.85682	D	0.000000	T	0.11410	0.0278	N	0.02181	-0.65	0.50039	D	0.999846	B;B	0.06786	0.001;0.0	B;B	0.17433	0.01;0.018	T	0.19321	-1.0309	10	0.06757	T	0.87	-29.9587	19.5094	0.95135	0.0:1.0:0.0:0.0	.	296;289	Q12792-3;Q12792	.;TWF1_HUMAN	I	191;289;323;296	ENSP00000448750:M191I;ENSP00000378886:M289I;ENSP00000321058:M323I;ENSP00000449428:M296I	ENSP00000321058:M323I	M	-	3	0	TWF1	42477061	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.898000	0.39809	2.620000	0.88729	0.591000	0.81541	ATG		0.333	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822		A	44190794	C	A	44190794	3	1	61	1	0	0	0	0	1	0	0	0	16821	594	21	2	193	2	TWF1	12	44190794	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1337	44190794	89661101	8007	15992										
TWF1	5756	broad.mit.edu	37	chr12	44193279	44193279	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgtgacagcaagtatttTttatatccatgtaatgatac	7	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44193279T>G	ENST00000395510.2	-	5	534	c.405A>C	c.(403-405)aaA>aaC	p.K135N	TWF1_ENST00000552521.1_Missense_Mutation_p.K37N|TWF1_ENST00000548315.1_Missense_Mutation_p.K135N|TWF1_ENST00000325127.4_Missense_Mutation_p.K169N|TWF1_ENST00000547564.1_5'Flank	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	135	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.K135N(1)		endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		GCAAGTATTTTTTATATCCAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											71	70	71					12																	44193279		2203	4300	6503	42479546	SO:0001583	missense	5756			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"protein tyrosine kinase 9", "PTK9 protein tyrosine kinase 9", "twinfilin, actin-binding protein, homolog 1 (Drosophila)"	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.405A>C	12.37:g.44193279T>G	ENSP00000378886:p.Lys135Asn		42479546	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Missense_Mutation	SNP	ENST00000395510.2	37	CCDS31780.2	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731105	0.48939	.	.	ENSG00000151239	ENST00000552521;ENST00000395510;ENST00000325127;ENST00000548315;ENST00000546662;ENST00000548403	D;T;T;T;T;T	0.83163	-1.69;1.47;1.47;1.47;1.42;1.44	5.95	2.33	0.28932	Actin-binding, cofilin/tropomyosin type (2);	0.408692	0.31922	N	0.006846	T	0.80449	0.4625	M	0.80183	2.485	0.44149	D	0.996949	B;B	0.31730	0.101;0.337	B;B	0.33196	0.099;0.159	T	0.72896	-0.4153	10	0.44086	T	0.13	-26.8428	5.7793	0.18297	0.0:0.2003:0.1292:0.6705	.	135;135	Q12792-3;Q12792	.;TWF1_HUMAN	N	37;135;169;135;173;109	ENSP00000448750:K37N;ENSP00000378886:K135N;ENSP00000321058:K169N;ENSP00000449428:K135N;ENSP00000448221:K173N;ENSP00000446696:K109N	ENSP00000321058:K169N	K	-	3	2	TWF1	42479546	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	0.713000	0.25794	0.161000	0.19458	0.533000	0.62120	AAA		0.353	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822		G	44193279	T	G	44193279	3	3	61	1	0	0	0	0	1	0	0	0	16821	1838	64	4	667	4	TWF1	12	44193279	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2485	44193279	89658616	8008	15993										
NELL2	4753	broad.mit.edu	37	chr12	44913950	44913950	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagcactcattctctggGagaatgctgaattcacactc	10	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44913950G>A	ENST00000429094.2	-	19	2742	c.2238C>T	c.(2236-2238)ctC>ctT	p.L746L	NELL2_ENST00000549027.1_Silent_p.L745L|NELL2_ENST00000437801.2_Silent_p.L796L|NELL2_ENST00000395487.2_Silent_p.L745L|NELL2_ENST00000551601.1_Silent_p.L698L|NELL2_ENST00000452445.2_Silent_p.L746L|NELL2_ENST00000333837.4_Silent_p.L769L	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	746	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L746L(1)|p.L796L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CATTCTCTGGGAGAATGCTGA	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	12											80	67	71					12																	44913950		2203	4300	6503	43200217	SO:0001819	synonymous_variant	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2238C>T	12.37:g.44913950G>A			43200217	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000429094.2	37	CCDS8746.1																																																																																				0.547	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		A	44913950	G	A	44913950	2	1	61	1	0	0	0	0	0	0	0	1	10365	1161	41	3		3	NELL2	12	44913950	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	720671	44913950	88937945	8009	15994										
NELL2	4753	broad.mit.edu	37	chr12	44915902	44915902	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattcagggcagcaaaaaaGatcaactgtgggattctcac	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44915902G>T	ENST00000429094.2	-	18	2560	c.2056C>A	c.(2056-2058)Ctt>Att	p.L686I	NELL2_ENST00000549027.1_Missense_Mutation_p.L685I|NELL2_ENST00000437801.2_Missense_Mutation_p.L736I|NELL2_ENST00000395487.2_Missense_Mutation_p.L685I|NELL2_ENST00000551601.1_Missense_Mutation_p.L638I|NELL2_ENST00000452445.2_Missense_Mutation_p.L686I|NELL2_ENST00000333837.4_Missense_Mutation_p.L709I	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	686	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L686I(1)|p.L736I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CAGCAAAAAAGATCAACTGTG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	12											122	111	115					12																	44915902		2203	4300	6503	43202169	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2056C>A	12.37:g.44915902G>T	ENSP00000390680:p.Leu686Ile		43202169	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316418	0.60524	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	D;D;T;D;D;D;D	0.82619	-1.57;-1.55;-1.25;-1.55;-1.57;-1.51;-1.63	5.7	5.7	0.88788	von Willebrand factor, type C (2);	0.063717	0.64402	D	0.000004	D	0.84124	0.5403	M	0.62723	1.935	0.49798	D	0.999824	P;D;P;P;P	0.56968	0.894;0.978;0.879;0.595;0.94	B;P;B;B;P	0.50136	0.437;0.632;0.36;0.123;0.495	T	0.81733	-0.0798	10	0.25751	T	0.34	-14.6968	14.0416	0.64678	0.0717:0.0:0.9283:0.0	.	709;736;638;686;685	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	I	685;686;638;686;685;709;736	ENSP00000378866:L685I;ENSP00000390680:L686I;ENSP00000449332:L638I;ENSP00000394612:L686I;ENSP00000447927:L685I;ENSP00000327988:L709I;ENSP00000416341:L736I	ENSP00000327988:L709I	L	-	1	0	NELL2	43202169	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.482000	0.66833	2.683000	0.91414	0.650000	0.86243	CTT		0.428	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		T	44915902	G	T	44915902	3	4	61	1	0	0	0	0	1	0	0	0	10365	942	33	2	406	2	NELL2	12	44915902	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1952	44915902	88935993	8010	15995										
NELL2	4753	broad.mit.edu	37	chr12	44917116	44917116	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcattttccaacacccaAatctgaccattgtgcttaac	4	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:44917116A>C	ENST00000429094.2	-	17	2460	c.1956T>G	c.(1954-1956)atT>atG	p.I652M	NELL2_ENST00000549027.1_Missense_Mutation_p.I651M|NELL2_ENST00000437801.2_Missense_Mutation_p.I702M|NELL2_ENST00000395487.2_Missense_Mutation_p.I651M|NELL2_ENST00000551601.1_Missense_Mutation_p.I604M|NELL2_ENST00000452445.2_Missense_Mutation_p.I652M|NELL2_ENST00000333837.4_Missense_Mutation_p.I675M	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	652	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.I652M(1)|p.I702M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CCAACACCCAAATCTGACCAT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	12											173	166	168					12																	44917116		2203	4300	6503	43203383	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1956T>G	12.37:g.44917116A>C	ENSP00000390680:p.Ile652Met		43203383	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.11|19.11	3.764295|3.764295	0.69878|0.69878	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801|ENST00000550139	T;T;T;T;T;T;D|.	0.81739|.	-1.48;-1.46;-1.19;-1.46;-1.48;-1.42;-1.53|.	5.69|5.69	-5.27|-5.27	0.02763|0.02763	von Willebrand factor, type C (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.45034|0.45034	0.1322|0.1322	L|L	0.41573|0.41573	1.285|1.285	0.46798|0.46798	D|D	0.9992|0.9992	D;D;D;D;D|.	0.76494|.	0.994;0.992;0.999;0.999;0.992|.	P;D;D;D;D|.	0.73708|.	0.88;0.923;0.981;0.916;0.923|.	T|T	0.43718|0.43718	-0.9374|-0.9374	10|5	0.33940|.	T|.	0.23|.	-17.6086|-17.6086	5.1665|5.1665	0.15088|0.15088	0.3015:0.1082:0.4842:0.1061|0.3015:0.1082:0.4842:0.1061	.|.	675;702;604;652;651|.	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2|.	.;.;.;NELL2_HUMAN;.|.	M|V	651;652;604;652;651;675;702|65	ENSP00000378866:I651M;ENSP00000390680:I652M;ENSP00000449332:I604M;ENSP00000394612:I652M;ENSP00000447927:I651M;ENSP00000327988:I675M;ENSP00000416341:I702M|.	ENSP00000327988:I675M|.	I|L	-|-	3|1	3|2	NELL2|NELL2	43203383|43203383	0.994000|0.994000	0.37717|0.37717	0.966000|0.966000	0.40874|0.40874	0.982000|0.982000	0.71751|0.71751	0.439000|0.439000	0.21575|0.21575	-0.827000|-0.827000	0.04278|0.04278	0.448000|0.448000	0.29417|0.29417	ATT|TTG		0.378	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		C	44917116	A	C	44917116	3	2	61	1	0	0	0	0	1	0	0	0	10365	10	1	4	510	4	NELL2	12	44917116	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1214	44917116	88934779	8011	15996										
NELL2	4753	broad.mit.edu	37	chr12	45097553	45097553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagccctaaaaccatctCgacagctacaaacagccctg	7	14	1	1	rs114802162		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:45097553C>T	ENST00000429094.2	-	12	1778	c.1274G>A	c.(1273-1275)cGa>cAa	p.R425Q	NELL2_ENST00000549027.1_Missense_Mutation_p.R424Q|NELL2_ENST00000437801.2_Missense_Mutation_p.R475Q|NELL2_ENST00000395487.2_Missense_Mutation_p.R424Q|NELL2_ENST00000551601.1_Missense_Mutation_p.R424Q|NELL2_ENST00000452445.2_Missense_Mutation_p.R425Q|NELL2_ENST00000333837.4_Missense_Mutation_p.R448Q	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	425	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R475Q(1)|p.R425Q(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		AAAACCATCTCGACAGCTACA	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		15632	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12											93	87	89					12																	45097553		2203	4300	6503	43383820	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1274G>A	12.37:g.45097553C>T	ENSP00000390680:p.Arg425Gln		43383820	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.34|15.34	2.805758|2.805758	0.50421|0.50421	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000550313|ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684	.|D;D;T;D;D;D;D	.|0.95622	.|-3.28;-3.28;-0.62;-3.28;-3.28;-2.2;-3.76	5.6|5.6	4.52|4.52	0.55395|0.55395	.|Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.|0.199086	.|0.43416	.|D	.|0.000564	D|D	0.90714|0.90714	0.7086|0.7086	L|L	0.29908|0.29908	0.895|0.895	0.46317|0.46317	D|D	0.998989|0.998989	.|B;B;B;B;B;B	.|0.22146	.|0.019;0.051;0.04;0.016;0.024;0.065	.|B;B;B;B;B;B	.|0.14578	.|0.003;0.011;0.011;0.003;0.003;0.01	D|D	0.86854|0.86854	0.2025|0.2025	5|10	.|0.16420	.|T	.|0.52	-10.4736|-10.4736	15.3805|15.3805	0.74651|0.74651	0.0:0.9222:0.0:0.0778|0.0:0.9222:0.0:0.0778	.|.	.|448;475;424;425;425;424	.|B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2	.|.;.;.;.;NELL2_HUMAN;.	K|Q	169|424;425;424;425;424;448;475;424	.|ENSP00000378866:R424Q;ENSP00000390680:R425Q;ENSP00000449332:R424Q;ENSP00000394612:R425Q;ENSP00000447927:R424Q;ENSP00000327988:R448Q;ENSP00000416341:R475Q	.|ENSP00000327988:R448Q	E|R	-|-	1|2	0|0	NELL2|NELL2	43383820|43383820	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.339000|2.339000	0.43965|0.43965	2.641000|2.641000	0.89580|0.89580	0.650000|0.650000	0.86243|0.86243	GAG|CGA		0.393	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		T	45097553	C	T	45097553	3	4	61	1	0	0	0	0	1	0	0	0	10365	884	31	1	1212	1	NELL2	12	45097553	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180437	45097553	88754342	8012	15997										
NELL2	4753	broad.mit.edu	37	chr12	45171048	45171048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattaagatctgggcactgaGcaataaatccctggggcatg	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:45171048G>A	ENST00000429094.2	-	6	1160	c.656C>T	c.(655-657)gCt>gTt	p.A219V	NELL2_ENST00000549027.1_Missense_Mutation_p.A218V|NELL2_ENST00000547172.1_5'Flank|NELL2_ENST00000437801.2_Missense_Mutation_p.A269V|NELL2_ENST00000395487.2_Missense_Mutation_p.A218V|NELL2_ENST00000551601.1_Missense_Mutation_p.A218V|NELL2_ENST00000452445.2_Missense_Mutation_p.A219V|NELL2_ENST00000333837.4_Missense_Mutation_p.A242V	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	219	Laminin G-like.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.A219V(1)|p.A269V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		TGGGCACTGAGCAATAAATCC	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	12											137	129	132					12																	45171048		2203	4300	6503	43457315	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.656C>T	12.37:g.45171048G>A	ENSP00000390680:p.Ala219Val		43457315	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.573286	0.45902	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684;ENST00000552993	T;T;T;T;T;T;T;T	0.02763	4.17;4.17;4.17;4.17;4.17;4.17;4.17;4.17	5.62	2.44	0.29823	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.449943	0.25792	N	0.028276	T	0.01222	0.0040	N	0.01352	-0.895	0.30565	N	0.764059	B;B;B;B;B;B	0.14012	0.0;0.009;0.007;0.0;0.003;0.005	B;B;B;B;B;B	0.14023	0.001;0.006;0.01;0.001;0.002;0.004	T	0.34030	-0.9845	10	0.30854	T	0.27	-4.7424	9.9699	0.41747	0.2477:0.0:0.7523:0.0	.	242;269;218;219;219;218	B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2	.;.;.;.;NELL2_HUMAN;.	V	218;219;218;219;218;242;269;218;219	ENSP00000378866:A218V;ENSP00000390680:A219V;ENSP00000449332:A218V;ENSP00000394612:A219V;ENSP00000447927:A218V;ENSP00000327988:A242V;ENSP00000416341:A269V;ENSP00000447085:A219V	ENSP00000327988:A242V	A	-	2	0	NELL2	43457315	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.812000	0.47994	0.556000	0.29098	0.655000	0.94253	GCT		0.378	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		A	45171048	G	A	45171048	3	1	61	1	0	0	0	0	1	0	0	0	10365	971	34	3	1854	3	NELL2	12	45171048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73495	45171048	88680847	8013	15998										
ANO6	196527	broad.mit.edu	37	chr12	45742071	45742071	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagttgatagagatgctttCttcaatccagccaccagaag	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:45742071C>A	ENST00000320560.8	+	5	808	c.606C>A	c.(604-606)ttC>ttA	p.F202L	ANO6_ENST00000423947.3_Missense_Mutation_p.F223L|ANO6_ENST00000425752.2_Missense_Mutation_p.F202L|ANO6_ENST00000441606.2_Missense_Mutation_p.F184L|ANO6_ENST00000435642.1_Missense_Mutation_p.F202L|ANO6_ENST00000426898.2_3'UTR	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	202					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)	p.F202L(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GAGATGCTTTCTTCAATCCAG	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	12											104	105	104					12																	45742071		2203	4300	6503	44028338	SO:0001583	missense	196527			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.606C>A	12.37:g.45742071C>A	ENSP00000320087:p.Phe202Leu		44028338	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	37	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029431	0.54790	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67	5.3	5.3	0.74995	.	0.048749	0.85682	D	0.000000	T	0.71239	0.3316	M	0.65498	2.005	0.58432	D	0.999998	B;B;B;P	0.43287	0.394;0.101;0.075;0.802	B;B;B;B	0.43225	0.165;0.082;0.025;0.412	T	0.73767	-0.3879	10	0.52906	T	0.07	.	13.6522	0.62318	0.0:0.9179:0.0:0.0821	.	184;223;202;202	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	L	202;223;202;202;184	ENSP00000391417:F202L;ENSP00000409126:F223L;ENSP00000413840:F202L;ENSP00000320087:F202L;ENSP00000413137:F184L	ENSP00000320087:F202L	F	+	3	2	ANO6	44028338	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	1.624000	0.37018	2.861000	0.98227	0.655000	0.94253	TTC		0.418	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		A	45742071	C	A	45742071	3	1	61	1	0	0	0	0	1	0	0	0	701	912	32	2	644	2	ANO6	12	45742071	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	571023	45742071	88109824	8014	15999										
ANO6	196527	broad.mit.edu	37	chr12	45823010	45823010	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttcatgagaatcacctCaaagatatgacgaaaaatat	5	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:45823010C>A	ENST00000320560.8	+	20	2851	c.2649C>A	c.(2647-2649)ctC>ctA	p.L883L	ANO6_ENST00000423947.3_Silent_p.L904L|ANO6_ENST00000425752.2_Intron|ANO6_ENST00000441606.2_Silent_p.L865L|ANO6_ENST00000435642.1_Intron	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	883					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)	p.L883L(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AGAATCACCTCAAAGATATGA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	12											54	52	53					12																	45823010		2203	4300	6503	44109277	SO:0001819	synonymous_variant	196527			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.2649C>A	12.37:g.45823010C>A			44109277	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Silent	SNP	ENST00000320560.8	37	CCDS31782.1																																																																																				0.373	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		A	45823010	C	A	45823010	2	1	61	1	0	0	0	0	0	0	0	1	701	813	29	2		2	ANO6	12	45823010	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80939	45823010	88028885	8015	16000										
ARID2	196528	broad.mit.edu	37	chr12	46215240	46215240	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtatttggagaagaatgGaaagagaagactgatagaga	13	2	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46215240G>A	ENST00000334344.6	+	6	847	c.675G>A	c.(673-675)tgG>tgA	p.W225*	ARID2_ENST00000422737.1_Nonsense_Mutation_p.W76*	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	225					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W225*(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GAGAAGAATGGAAAGAGAAGA	0.279			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Nonsense(1)	large_intestine(1)	12											70	76	74					12																	46215240		2203	4292	6495	44501507	SO:0001587	stop_gained	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.675G>A	12.37:g.46215240G>A	ENSP00000335044:p.Trp225*		44501507	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	38	6.729098	0.97796	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-2.6626	19.9024	0.96993	0.0:0.0:1.0:0.0	.	.	.	.	X	225;76	.	ENSP00000335044:W225X	W	+	3	0	ARID2	44501507	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.858000	0.75461	2.775000	0.95449	0.650000	0.86243	TGG		0.279	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46215240	G	A	46215240	4	1	61	1	0	0	0	0	0	1	0	0	915	1183	41	3	697	3	ARID2	12	46215240	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	392230	46215240	87636655	8016	16001										
ARID2	196528	broad.mit.edu	37	chr12	46231286	46231286	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtatgtttttcaggcatgGaaattttgggaaatctttgc	10	4	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46231286G>T	ENST00000334344.6	+	10	1298	c.1126G>T	c.(1126-1128)Gaa>Taa	p.E376*	ARID2_ENST00000444670.1_Nonsense_Mutation_p.E5*|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Nonsense_Mutation_p.E227*	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	376					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E376*(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTCAGGCATGGAAATTTTGGG	0.303			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Nonsense(1)	large_intestine(1)	12											88	88	88					12																	46231286		2203	4300	6503	44517553	SO:0001587	stop_gained	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1126G>T	12.37:g.46231286G>T	ENSP00000335044:p.Glu376*		44517553	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	38	6.798440	0.97845	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.8766	19.024	0.92925	0.0:0.0:1.0:0.0	.	.	.	.	X	376;227;5	.	ENSP00000335044:E376X	E	+	1	0	ARID2	44517553	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	9.869000	0.99810	2.486000	0.83907	0.313000	0.20887	GAA		0.303	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46231286	G	T	46231286	4	4	61	1	0	0	0	0	0	1	0	0	915	1175	41	2	1164	2	ARID2	12	46231286	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16046	46231286	87620609	8017	16002										
ARID2	196528	broad.mit.edu	37	chr12	46243461	46243461	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaaaacggagggctatacCacttcccattcagatgtact	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46243461C>A	ENST00000334344.6	+	14	1986	c.1814C>A	c.(1813-1815)cCa>cAa	p.P605Q	ARID2_ENST00000444670.1_Missense_Mutation_p.P215Q|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Missense_Mutation_p.P456Q	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	605					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P605Q(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AGGGCTATACCACTTCCCATT	0.458			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)	12											318	289	299					12																	46243461		2203	4300	6503	44529728	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1814C>A	12.37:g.46243461C>A	ENSP00000335044:p.Pro605Gln		44529728	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244234	0.79912	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.63255	-0.03	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.72590	0.3479	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.74396	-0.3679	10	0.87932	D	0	-10.3507	20.2985	0.98592	0.0:1.0:0.0:0.0	.	605;605	Q68CP9-3;Q68CP9	.;ARID2_HUMAN	Q	605;456;215	ENSP00000335044:P605Q	ENSP00000335044:P605Q	P	+	2	0	ARID2	44529728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.214000	0.77958	2.793000	0.96121	0.655000	0.94253	CCA		0.458	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46243461	C	A	46243461	3	1	61	1	0	0	0	0	1	0	0	0	915	594	21	2	1868	2	ARID2	12	46243461	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12175	46243461	87608434	8018	16003										
ARID2	196528	broad.mit.edu	37	chr12	46244929	46244929	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactgtcagtcaaatgttatCtgtgaaaaggcagcaacagc	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46244929C>A	ENST00000334344.6	+	15	3195	c.3023C>A	c.(3022-3024)tCt>tAt	p.S1008Y	ARID2_ENST00000444670.1_Missense_Mutation_p.S618Y|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Missense_Mutation_p.S859Y	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1008	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S1008Y(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAAATGTTATCTGTGAAAAGG	0.502			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)	12											204	166	179					12																	46244929		2203	4300	6503	44531196	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3023C>A	12.37:g.46244929C>A	ENSP00000335044:p.Ser1008Tyr		44531196	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225146	0.58668	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.49720	0.77	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.60881	0.2303	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.998;0.998;0.991	T	0.63184	-0.6694	10	0.87932	D	0	-10.6988	19.9335	0.97129	0.0:1.0:0.0:0.0	.	1008;618;1008	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	Y	1008;125;125;859;618	ENSP00000335044:S1008Y	ENSP00000335044:S1008Y	S	+	2	0	ARID2	44531196	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.263000	0.78421	2.722000	0.93159	0.462000	0.41574	TCT		0.502	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46244929	C	A	46244929	3	1	61	1	0	0	0	0	1	0	0	0	915	913	32	2	3081	2	ARID2	12	46244929	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1468	46244929	87606966	8019	16004										
ARID2	196528	broad.mit.edu	37	chr12	46246051	46246051	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattccaaatcataaaacttCcaatcatgtaggaaatggtg	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46246051C>G	ENST00000334344.6	+	15	4317	c.4145C>G	c.(4144-4146)tCc>tGc	p.S1382C	ARID2_ENST00000444670.1_Missense_Mutation_p.S992C|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Missense_Mutation_p.S1233C	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1382					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S1382C(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CATAAAACTTCCAATCATGTA	0.348			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)	12											69	66	67					12																	46246051		2203	4300	6503	44532318	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4145C>G	12.37:g.46246051C>G	ENSP00000335044:p.Ser1382Cys		44532318	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.426003	0.25726	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.51071	0.72	6.07	5.17	0.71159	.	0.046027	0.85682	N	0.000000	T	0.42063	0.1186	L	0.32530	0.975	0.80722	D	1	B;B;B	0.18166	0.01;0.026;0.009	B;B;B	0.19391	0.025;0.025;0.004	T	0.24368	-1.0162	10	0.56958	D	0.05	-1.9405	17.6457	0.88148	0.0:0.8772:0.1228:0.0	.	1382;992;1382	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	C	1382;499;499;1233;992	ENSP00000335044:S1382C	ENSP00000335044:S1382C	S	+	2	0	ARID2	44532318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.559000	0.67326	1.552000	0.49463	0.655000	0.94253	TCC		0.348	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46246051	C	G	46246051	3	3	61	1	0	0	0	0	1	0	0	0	915	855	30	5	4203	5	ARID2	12	46246051	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1122	46246051	87605844	8020	16005										
SFRS2IP	9169	broad.mit.edu	37	chr12	46318817	46318817	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttataggtagctgagaAccatcaacttgctggtttgt	9	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46318817A>G	ENST00000369367.3	-	12	3833	c.3600T>C	c.(3598-3600)ggT>ggC	p.G1200G	SCAF11_ENST00000419565.2_Silent_p.G1200G|SCAF11_ENST00000549162.1_Silent_p.G1008G|SCAF11_ENST00000465950.1_Silent_p.G885G|SCAF11_ENST00000550629.1_5'Flank	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1200					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G1200G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GTAGCTGAGAACCATCAACTT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	12											130	124	126					12																	46318817		2203	4300	6503	44605084	SO:0001819	synonymous_variant	9169			Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.3600T>C	12.37:g.46318817A>G			44605084	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																				0.353	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		G	46318817	A	G	46318817	2	3	61	1	0	0	0	0	0	0	0	1	14214	30	2	4		4	SFRS2IP	12	46318817	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72766	46318817	87533078	8021	16006										
SLC38A1	81539	broad.mit.edu	37	chr12	46582775	46582775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggccttcgtcactactcGatgagcaggcccagtcatag	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46582775G>A	ENST00000398637.5	-	17	2136	c.1442C>T	c.(1441-1443)tCg>tTg	p.S481L	SLC38A1_ENST00000546893.1_Missense_Mutation_p.S481L|SLC38A1_ENST00000439706.1_Missense_Mutation_p.S481L|SLC38A1_ENST00000549049.1_Missense_Mutation_p.S481L	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	481					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.S481L(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	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)			GTCACTACTCGATGAGCAGGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											89	93	92					12																	46582775		1995	4187	6182	44869042	SO:0001583	missense	81539			AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.1442C>T	12.37:g.46582775G>A	ENSP00000381634:p.Ser481Leu		44869042	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	g	11.86	1.765437	0.31228	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893	T;T;T;T	0.05925	3.37;3.37;3.37;3.37	5.33	3.34	0.38264	.	.	.	.	.	T	0.05181	0.0138	L	0.27053	0.805	0.09310	N	0.999999	B	0.18610	0.029	B	0.12156	0.007	T	0.35847	-0.9772	9	0.31617	T	0.26	1.4316	8.8779	0.35356	0.0:0.2454:0.5323:0.2223	.	481	Q9H2H9	S38A1_HUMAN	L	481	ENSP00000449607:S481L;ENSP00000398142:S481L;ENSP00000381634:S481L;ENSP00000447853:S481L	ENSP00000381634:S481L	S	-	2	0	SLC38A1	44869042	0.191000	0.23288	0.042000	0.18584	0.776000	0.43924	3.003000	0.49505	1.334000	0.45468	0.586000	0.80456	TCG		0.527	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			A	46582775	G	A	46582775	3	1	61	1	0	0	0	0	1	0	0	0	14638	1059	37	1	25	1	SLC38A1	12	46582775	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	263958	46582775	87269120	8022	16007										
SLC38A1	81539	broad.mit.edu	37	chr12	46602843	46602843	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcctcagcttacctgtttCttttgaacagatcaatagga	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46602843C>A	ENST00000398637.5	-	6	1076	c.382G>T	c.(382-384)Gaa>Taa	p.E128*	SLC38A1_ENST00000546893.1_Nonsense_Mutation_p.E128*|SLC38A1_ENST00000439706.1_Nonsense_Mutation_p.E128*|SLC38A1_ENST00000549049.1_Nonsense_Mutation_p.E128*|SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000552197.1_Nonsense_Mutation_p.E128*	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	128					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.E128*(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	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)			TTACCTGTTTCTTTTGAACAG	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											65	57	59					12																	46602843		1805	4078	5883	44889110	SO:0001587	stop_gained	81539			AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.382G>T	12.37:g.46602843C>A	ENSP00000381634:p.Glu128*		44889110	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Nonsense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	42	9.557203	0.99204	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197	.	.	.	5.71	3.86	0.44501	.	0.160447	0.43416	D	0.000569	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-22.1614	12.5506	0.56223	0.0:0.8144:0.1196:0.0661	.	.	.	.	X	128	.	ENSP00000381634:E128X	E	-	1	0	SLC38A1	44889110	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.103000	0.57783	1.554000	0.49487	0.650000	0.86243	GAA		0.323	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			A	46602843	C	A	46602843	4	1	61	1	0	0	0	0	0	1	0	0	14638	922	32	2	1129	2	SLC38A1	12	46602843	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20068	46602843	87249052	8023	16008										
SLC38A1	81539	broad.mit.edu	37	chr12	46633487	46633487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctgaccattttctacttCggtgaaatcattggagtcat	7	8	4	2	rs75571325		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:46633487C>T	ENST00000398637.5	-	3	791	c.97G>A	c.(97-99)Gaa>Aaa	p.E33K	SLC38A1_ENST00000546893.1_Missense_Mutation_p.E33K|SLC38A1_ENST00000439706.1_Missense_Mutation_p.E33K|SLC38A1_ENST00000549049.1_Missense_Mutation_p.E33K|SLC38A1_ENST00000549633.1_Intron|SLC38A1_ENST00000552197.1_Missense_Mutation_p.E33K	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	33					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.E33K(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	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)			TTTTCTACTTCGGTGAAATCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											161	149	153					12																	46633487		1876	4126	6002	44919754	SO:0001583	missense	81539			AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.97G>A	12.37:g.46633487C>T	ENSP00000381634:p.Glu33Lys		44919754	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607894	0.46527	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197;ENST00000550173	T;T;T;T;T	0.07216	3.37;3.37;3.37;3.37;3.21	4.93	4.93	0.64822	.	0.000000	0.53938	D	0.000048	T	0.04952	0.0133	N	0.08118	0	0.42346	D	0.992353	D;B	0.60160	0.987;0.429	P;B	0.44696	0.458;0.028	T	0.53683	-0.8404	10	0.13108	T	0.6	-19.218	11.959	0.52997	0.0:0.9201:0.0:0.0799	.	33;33	F8VX04;Q9H2H9	.;S38A1_HUMAN	K	33	ENSP00000449607:E33K;ENSP00000398142:E33K;ENSP00000381634:E33K;ENSP00000447853:E33K;ENSP00000449756:E33K	ENSP00000381634:E33K	E	-	1	0	SLC38A1	44919754	0.991000	0.36638	0.936000	0.37596	0.963000	0.63663	3.119000	0.50422	2.438000	0.82558	0.585000	0.79938	GAA		0.388	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			T	46633487	C	T	46633487	3	4	61	1	0	0	0	0	1	0	0	0	14638	893	31	1	1426	1	SLC38A1	12	46633487	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30644	46633487	87218408	8024	16009										
SLC38A4	55089	broad.mit.edu	37	chr12	47168838	47168838	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttatgtacttactgggaaGaggacaatgggcacagttag	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:47168838G>T	ENST00000447411.1	-	13	1499	c.1293C>A	c.(1291-1293)ctC>ctA	p.L431L	SLC38A4_ENST00000266579.4_Silent_p.L431L	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	431					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)	p.L431L(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					TTACTGGGAAGAGGACAATGG	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											181	165	170					12																	47168838		2203	4300	6503	45455105	SO:0001819	synonymous_variant	55089			AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.1293C>A	12.37:g.47168838G>T			45455105	A8K553	Silent	SNP	ENST00000447411.1	37	CCDS8750.1																																																																																				0.408	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			T	47168838	G	T	47168838	2	4	61	1	0	0	0	0	0	0	0	1	14643	929	33	2		2	SLC38A4	12	47168838	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	535351	47168838	86683057	8025	16010										
AMIGO2	91523	broad.mit.edu	37	chr12	47471880	47471880	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaccatcagtctttccccGacctgagcctcatgaataaa	7	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:47471880G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000266581.4_Silent_p.V302V|AMIGO2_ENST00000429635.1_Silent_p.V302V|AMIGO2_ENST00000321382.3_Silent_p.V302V|AMIGO2_ENST00000550413.1_Silent_p.V302V			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)	p.V302V(1)									GTCTTTCCCCGACCTGAGCCT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	12											151	147	148					12																	47471880		2203	4300	6503	45758147	SO:0001631	upstream_gene_variant	347902			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		12.37:g.47471880G>A	Exception_encountered		45758147	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																				0.488	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47471880	G	A	47471880	1	1	61	0	1	0	0	0	0	0	0	0	576	1045	37	1		1	AMIGO2	12	47471880	5'Flank	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	303042	47471880	86380015	8026	16011										
FAM113B	91523	broad.mit.edu	37	chr12	47628897	47628897	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgcttcacaataagttCgtggtcatcctgggggactc	11	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:47628897C>T	ENST00000546455.1	+	4	782	c.51C>T	c.(49-51)ttC>ttT	p.F17F	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Silent_p.F17F			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	17							hydrolase activity (GO:0016787)	p.F17F(2)									ACAATAAGTTCGTGGTCATCC	0.592																																																2	Substitution - coding silent(2)	large_intestine(2)	12											66	65	65					12																	47628897		2203	4300	6503	45915164	SO:0001819	synonymous_variant	91523			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.51C>T	12.37:g.47628897C>T			45915164	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																				0.592	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		T	47628897	C	T	47628897	2	4	61	1	0	0	0	0	0	0	0	1	5418	883	31	1		1	FAM113B	12	47628897	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157017	47628897	86222998	8027	16012										
RPAP3	79657	broad.mit.edu	37	chr12	48062853	48062853	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattttctcgctgtaagacTgacatacatcctgcttcaaa	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48062853T>G	ENST00000005386.3	-	14	1674	c.1559A>C	c.(1558-1560)cAg>cCg	p.Q520P	RPAP3_ENST00000380650.4_Missense_Mutation_p.Q486P|RPAP3_ENST00000432584.3_Missense_Mutation_p.Q361P	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	520								p.Q520P(1)		endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					GCTGTAAGACTGACATACATC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											155	155	155					12																	48062853		2203	4300	6503	46349120	SO:0001583	missense	79657			AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"Tetratricopeptide (TTC) repeat domain containing"	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.1559A>C	12.37:g.48062853T>G	ENSP00000005386:p.Gln520Pro		46349120	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	37	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	T	8.704	0.910471	0.17833	.	.	ENSG00000005175	ENST00000005386;ENST00000432584;ENST00000380650	T;T;T	0.15487	2.83;2.42;2.87	5.9	4.76	0.60689	.	1.982520	0.02035	N	0.048895	T	0.23249	0.0562	L	0.60455	1.87	0.30603	N	0.760336	B;B	0.19445	0.028;0.036	B;B	0.18561	0.022;0.022	T	0.23904	-1.0175	10	0.52906	T	0.07	.	7.4042	0.26981	0.0:0.0758:0.1442:0.78	.	486;520	Q9H6T3-2;Q9H6T3	.;RPAP3_HUMAN	P	520;361;486	ENSP00000005386:Q520P;ENSP00000401823:Q361P;ENSP00000370024:Q486P	ENSP00000005386:Q520P	Q	-	2	0	RPAP3	46349120	1.000000	0.71417	0.478000	0.27316	0.235000	0.25334	1.854000	0.39368	1.064000	0.40671	0.523000	0.50628	CAG		0.408	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		G	48062853	T	G	48062853	3	3	61	1	0	0	0	0	1	0	0	0	13580	1580	55	4	454	4	RPAP3	12	48062853	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	433956	48062853	85789042	8028	16013										
RPAP3	79657	broad.mit.edu	37	chr12	48096599	48096599	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcacttgtagttgtaattCgattgctttatttgctgaag	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48096599C>T	ENST00000005386.3	-	2	140	c.25G>A	c.(25-27)Gaa>Aaa	p.E9K	RPAP3_ENST00000380650.4_Missense_Mutation_p.E9K|RPAP3_ENST00000432584.3_Intron	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	9								p.E9K(1)		endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					AGTTGTAATTCGATTGCTTTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											163	143	150					12																	48096599		2202	4298	6500	46382866	SO:0001583	missense	79657			AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"Tetratricopeptide (TTC) repeat domain containing"	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.25G>A	12.37:g.48096599C>T	ENSP00000005386:p.Glu9Lys		46382866	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	37	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466317	0.84425	.	.	ENSG00000005175	ENST00000005386;ENST00000380650	T;T	0.62498	0.02;0.02	5.12	5.12	0.69794	.	0.700302	0.14566	N	0.311741	T	0.78117	0.4233	M	0.64676	1.99	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.74674	0.96;0.984	T	0.78578	-0.2150	10	0.72032	D	0.01	.	17.9142	0.88944	0.0:1.0:0.0:0.0	.	9;9	Q9H6T3-2;Q9H6T3	.;RPAP3_HUMAN	K	9	ENSP00000005386:E9K;ENSP00000370024:E9K	ENSP00000005386:E9K	E	-	1	0	RPAP3	46382866	1.000000	0.71417	0.960000	0.40013	0.482000	0.33219	7.102000	0.77005	2.527000	0.85204	0.650000	0.86243	GAA		0.338	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		T	48096599	C	T	48096599	3	4	61	1	0	0	0	0	1	0	0	0	13580	893	31	1	2036	1	RPAP3	12	48096599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33746	48096599	85755296	8029	16014										
RAPGEF3	10411	broad.mit.edu	37	chr12	48134163	48134163	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaagaaggaattgagattCttctgctccttgaggctgtg	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48134163C>A	ENST00000449771.2	-	22	2335	c.2247G>T	c.(2245-2247)aaG>aaT	p.K749N	RAPGEF3_ENST00000405493.2_Missense_Mutation_p.K707N|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.K749N|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.K707N|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.K707N|RAPGEF3_ENST00000548919.1_Intron|RP1-197B17.3_ENST00000547799.1_lincRNA			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	749	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.K707N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		AATTGAGATTCTTCTGCTCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	57	58					12																	48134163		2203	4300	6503	46420430	SO:0001583	missense	10411			AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.2247G>T	12.37:g.48134163C>A	ENSP00000395708:p.Lys749Asn		46420430	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308953	0.81247	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	4.42	4.42	0.53409	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.055984	0.64402	D	0.000002	T	0.24122	0.0584	N	0.11106	0.095	0.49687	D	0.99981	D	0.52996	0.957	P	0.57057	0.812	T	0.04373	-1.0956	10	0.87932	D	0	.	9.9112	0.41406	0.0:0.9055:0.0:0.0945	.	749	O95398	RPGF3_HUMAN	N	707;749;396;707;707;707;749	ENSP00000384521:K707N;ENSP00000395708:K749N;ENSP00000448619:K707N;ENSP00000171000:K707N;ENSP00000373864:K749N	ENSP00000171000:K707N	K	-	3	2	RAPGEF3	46420430	0.988000	0.35896	1.000000	0.80357	0.998000	0.95712	0.310000	0.19356	2.476000	0.83614	0.650000	0.86243	AAG		0.597	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		A	48134163	C	A	48134163	3	1	61	1	0	0	0	0	1	0	0	0	13082	912	32	2	552	2	RAPGEF3	12	48134163	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37564	48134163	85717732	8030	16015										
COL2A1	1280	broad.mit.edu	37	chr12	48371108	48371108	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaggatacttacagcttCtcctctgtctccttgcttgc	6	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48371108C>A	ENST00000380518.3	-	46	3432	c.3268G>T	c.(3268-3270)Gaa>Taa	p.E1090*	COL2A1_ENST00000337299.6_Nonsense_Mutation_p.E1021*|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	1090	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.E1021*(1)|p.E1090*(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTTACAGCTTCTCCTCTGTCT	0.622																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											71	83	79					12																	48371108		2203	4300	6503	46657375	SO:0001587	stop_gained	1280			X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.3268G>T	12.37:g.48371108C>A	ENSP00000369889:p.Glu1090*		46657375	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Nonsense_Mutation	SNP	ENST00000380518.3	37	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	44	11.172230	0.99526	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	18.2304	0.89933	0.0:1.0:0.0:0.0	.	.	.	.	X	1090;1021;1021	.	ENSP00000338213:E1021X	E	-	1	0	COL2A1	46657375	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.917000	0.63369	2.401000	0.81631	0.563000	0.77884	GAA		0.622	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48371108	C	A	48371108	4	1	61	1	0	0	0	0	0	1	0	0	3693	922	32	2	1231	2	COL2A1	12	48371108	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	236945	48371108	85480787	8031	16016										
COL2A1	1280	broad.mit.edu	37	chr12	48393715	48393715	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaaccactggcagtggcGaggtcagttgggcagatggg	16	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48393715G>A	ENST00000380518.3	-	2	443	c.279C>T	c.(277-279)ctC>ctT	p.L93L	COL2A1_ENST00000337299.6_Intron	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	93					axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.L93L(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TGGCAGTGGCGAGGTCAGTTG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	12											70	77	75					12																	48393715		2060	4205	6265	46679982	SO:0001819	synonymous_variant	1280			X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.279C>T	12.37:g.48393715G>A			46679982	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																				0.498	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48393715	G	A	48393715	2	1	61	1	0	0	0	0	0	0	0	1	3693	1045	37	1		1	COL2A1	12	48393715	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22607	48393715	85458180	8032	16017										
SENP1	29843	broad.mit.edu	37	chr12	48468157	48468157	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctggctgatgtggaacaGagtggtgatgatggggatga	17	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48468157G>T	ENST00000004980.5	-	8	1368	c.890C>A	c.(889-891)tCt>tAt	p.S297Y	SENP1_ENST00000448372.1_Missense_Mutation_p.S297Y|SENP1_ENST00000549518.1_Missense_Mutation_p.S297Y|SENP1_ENST00000339976.6_3'UTR|SENP1_ENST00000551330.1_Missense_Mutation_p.S297Y|SENP1_ENST00000549595.1_Missense_Mutation_p.S297Y			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	297	His-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)	p.S297Y(1)		large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				ATGTGGAACAGAGTGGTGATG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											189	184	186					12																	48468157		1983	4162	6145	46754424	SO:0001583	missense	29843			AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.890C>A	12.37:g.48468157G>T	ENSP00000004980:p.Ser297Tyr		46754424	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	37	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	G	9.270	1.045542	0.19748	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	4.14	3.22	0.36961	.	0.649356	0.14034	N	0.345887	T	0.08891	0.0220	N	0.14661	0.345	0.09310	N	0.999998	P;P	0.37276	0.454;0.589	B;B	0.34931	0.094;0.192	T	0.16748	-1.0392	10	0.08599	T	0.76	-0.0189	11.8125	0.52192	0.0:0.3394:0.6606:0.0	.	297;297	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	Y	297	ENSP00000004980:S297Y;ENSP00000394791:S297Y;ENSP00000446681:S297Y;ENSP00000450076:S297Y;ENSP00000447328:S297Y	ENSP00000004980:S297Y	S	-	2	0	SENP1	46754424	0.997000	0.39634	0.076000	0.20297	0.936000	0.57629	2.804000	0.47931	1.066000	0.40716	0.655000	0.94253	TCT		0.393	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		T	48468157	G	T	48468157	3	4	61	1	0	0	0	0	1	0	0	0	14083	942	33	2	1085	2	SENP1	12	48468157	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74442	48468157	85383738	8033	16018										
PFKM	29843	broad.mit.edu	37	chr12	48501166	48501166	+	5'Flank	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggcagccatgcataaaGacgagtttcatctgaaattt	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48501166G>T	ENST00000004980.5	-	0	0				PFKM_ENST00000340802.6_Missense_Mutation_p.D4Y|SENP1_ENST00000448372.1_5'Flank|SENP1_ENST00000551330.1_5'Flank|SENP1_ENST00000549518.1_5'Flank|SENP1_ENST00000339976.6_5'Flank			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				CATGCATAAAGACGAGTTTCA	0.443																																																0			12											198	173	181					12																	48501166		1568	3582	5150	46787433	SO:0001631	upstream_gene_variant	5213			AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896		12.37:g.48501166G>T	Exception_encountered		46787433	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	37	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989061	0.35131	.	.	ENSG00000152556	ENST00000340802;ENST00000546755;ENST00000549366;ENST00000552792;ENST00000548288	T;D;D;D	0.89123	-1.49;-2.44;-2.47;-2.46	3.92	-0.986	0.10252	.	0.904422	0.09104	N	0.848059	T	0.74261	0.3693	N	0.08118	0	0.80722	D	1	B	0.32876	0.388	B	0.28011	0.085	T	0.60535	-0.7244	10	0.56958	D	0.05	-0.3606	7.1759	0.25744	0.5415:0.0:0.4585:0.0	.	4	Q6ZTT1	.	Y	4	ENSP00000345771:D4Y;ENSP00000449622:D4Y;ENSP00000448940:D4Y;ENSP00000448018:D4Y	ENSP00000345771:D4Y	D	+	1	0	PFKM	46787433	0.829000	0.29322	0.843000	0.33291	0.544000	0.35116	0.128000	0.15810	-0.205000	0.10219	-0.218000	0.12543	GAC		0.443	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		T	48501166	G	T	48501166	1	4	61	0	1	0	0	0	0	0	0	0	11796	942	33	2		2	PFKM	12	48501166	5'Flank	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33009	48501166	85350729	8034	16019										
PFKM	5213	broad.mit.edu	37	chr12	48528785	48528785	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgagggtgcaattgacaaGaatggaaaaccaatcacctc	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48528785G>T	ENST00000312352.7	+	9	846	c.807G>T	c.(805-807)aaG>aaT	p.K269N	PFKM_ENST00000551804.1_Missense_Mutation_p.K269N|PFKM_ENST00000340802.6_Missense_Mutation_p.K340N|PFKM_ENST00000395233.2_Missense_Mutation_p.K269N|PFKM_ENST00000547587.1_Missense_Mutation_p.K269N|PFKM_ENST00000359794.5_Missense_Mutation_p.K269N	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	269	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.K269N(1)		NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CAATTGACAAGAATGGAAAAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	113	115					12																	48528785		2203	4300	6503	46815052	SO:0001583	missense	5213			M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.807G>T	12.37:g.48528785G>T	ENSP00000309438:p.Lys269Asn		46815052	J3KNX3|Q16814|Q16815|Q6ZTT1	Missense_Mutation	SNP	ENST00000312352.7	37	CCDS8760.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307311	0.40795	.	.	ENSG00000152556	ENST00000340802;ENST00000359794;ENST00000395233;ENST00000551804;ENST00000547587;ENST00000312352	T;T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35;-1.35	4.64	0.778	0.18543	Phosphofructokinase domain (2);	0.515072	0.20312	N	0.094814	T	0.68641	0.3023	N	0.17674	0.51	0.30275	N	0.79191	B;B;B	0.33266	0.143;0.173;0.404	B;B;B	0.38755	0.098;0.158;0.281	T	0.65524	-0.6147	10	0.46703	T	0.11	-6.5557	10.5991	0.45356	0.2613:0.0:0.7387:0.0	.	269;269;340	P08237-2;P08237;Q6ZTT1	.;K6PF_HUMAN;.	N	340;269;269;269;269;269	ENSP00000345771:K340N;ENSP00000352842:K269N;ENSP00000378656:K269N;ENSP00000448177:K269N;ENSP00000449426:K269N;ENSP00000309438:K269N	ENSP00000309438:K269N	K	+	3	2	PFKM	46815052	0.000000	0.05858	0.394000	0.26270	0.852000	0.48524	0.340000	0.19892	0.136000	0.18733	0.650000	0.86243	AAG		0.458	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		T	48528785	G	T	48528785	3	4	61	1	0	0	0	0	1	0	0	0	11796	933	33	2	1058	2	PFKM	12	48528785	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27619	48528785	85323110	8035	16020										
PFKM	5213	broad.mit.edu	37	chr12	48535535	48535535	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaactaggactctacccaaGaagagctttgaacagatcag	8	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48535535G>T	ENST00000312352.7	+	16	1464	c.1425G>T	c.(1423-1425)aaG>aaT	p.K475N	PFKM_ENST00000551804.1_Missense_Mutation_p.K444N|PFKM_ENST00000340802.6_Missense_Mutation_p.K546N|PFKM_ENST00000395233.2_Missense_Mutation_p.K444N|PFKM_ENST00000547587.1_Missense_Mutation_p.K475N|PFKM_ENST00000359794.5_Missense_Mutation_p.K475N	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	475	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.K475N(1)		NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CTCTACCCAAGAAGAGCTTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											155	161	159					12																	48535535		2203	4300	6503	46821802	SO:0001583	missense	5213			M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.1425G>T	12.37:g.48535535G>T	ENSP00000309438:p.Lys475Asn		46821802	J3KNX3|Q16814|Q16815|Q6ZTT1	Missense_Mutation	SNP	ENST00000312352.7	37	CCDS8760.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.532771	0.27387	.	.	ENSG00000152556	ENST00000340802;ENST00000359794;ENST00000395233;ENST00000551804;ENST00000547587;ENST00000312352;ENST00000546465	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	4.97	4.04	0.47022	Phosphofructokinase domain (2);	0.261911	0.44483	D	0.000443	T	0.49081	0.1536	N	0.02181	-0.65	0.50467	D	0.99987	B;B;B	0.11235	0.001;0.001;0.004	B;B;B	0.23716	0.003;0.006;0.048	T	0.43507	-0.9387	10	0.30854	T	0.27	-9.4898	12.0229	0.53354	0.0899:0.0:0.9101:0.0	.	444;475;546	P08237-2;P08237;Q6ZTT1	.;K6PF_HUMAN;.	N	546;475;444;444;475;475;90	ENSP00000345771:K546N;ENSP00000352842:K475N;ENSP00000378656:K444N;ENSP00000448177:K444N;ENSP00000449426:K475N;ENSP00000309438:K475N;ENSP00000446519:K90N	ENSP00000309438:K475N	K	+	3	2	PFKM	46821802	0.962000	0.33011	1.000000	0.80357	0.989000	0.77384	0.403000	0.20982	1.385000	0.46445	0.563000	0.77884	AAG		0.473	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		T	48535535	G	T	48535535	3	4	61	1	0	0	0	0	1	0	0	0	11796	933	33	2	1704	2	PFKM	12	48535535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6750	48535535	85316360	8036	16021										
OR10AD1	121275	broad.mit.edu	37	chr12	48596302	48596302	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgggggttcatgtaagaGaacatagctgaagtgtagag	15	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48596302G>T	ENST00000310248.2	-	1	868	c.774C>A	c.(772-774)ttC>ttA	p.F258L		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F258L(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						TCATGTAAGAGAACATAGCTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	86	85					12																	48596302		2203	4300	6503	46882569	SO:0001583	missense	121275				CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"GPCR / Class A : Olfactory receptors"	14819	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily AD, member 1 pseudogene"	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.774C>A	12.37:g.48596302G>T	ENSP00000308689:p.Phe258Leu		46882569	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.417858	0.42918	.	.	ENSG00000172640	ENST00000310248	T	0.00241	8.46	4.69	1.79	0.24919	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41001	D	0.000968	T	0.00178	0.0005	M	0.66378	2.025	0.28162	N	0.928958	B	0.25007	0.116	B	0.22601	0.04	T	0.22347	-1.0219	10	0.46703	T	0.11	-37.9722	6.3856	0.21559	0.311:0.0:0.689:0.0	.	258	Q8NGE0	O10AD_HUMAN	L	258	ENSP00000308689:F258L	ENSP00000308689:F258L	F	-	3	2	OR10AD1	46882569	0.447000	0.25673	1.000000	0.80357	0.962000	0.63368	0.401000	0.20948	0.660000	0.30964	0.561000	0.74099	TTC		0.498	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1			T	48596302	G	T	48596302	3	4	61	1	0	0	0	0	1	0	0	0	10927	933	33	2	183	2	OR10AD1	12	48596302	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60767	48596302	85255593	8037	16022										
H1FNT	341567	broad.mit.edu	37	chr12	48723339	48723339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctccgaaacgccggctacGaagtgcgcaggaagagcggc	15	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:48723339G>A	ENST00000335017.1	+	1	577	c.265G>A	c.(265-267)Gaa>Aaa	p.E89K		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	89					chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.E89K(1)		endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						CGCCGGCTACGAAGTGCGCAG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	12											20	24	23					12																	48723339		2200	4299	6499	47009606	SO:0001583	missense	341567			AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"Histones / Replication-independent"	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.265G>A	12.37:g.48723339G>A	ENSP00000334805:p.Glu89Lys		47009606	Q147U8|Q5GKZ5|Q7Z694	Missense_Mutation	SNP	ENST00000335017.1	37	CCDS8762.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768323	0.90020	.	.	ENSG00000187166	ENST00000335017	T	0.20069	2.1	5.39	-6.04	0.02178	.	.	.	.	.	T	0.18841	0.0452	L	0.52573	1.65	0.24824	N	0.992569	D	0.53885	0.963	B	0.42030	0.373	T	0.38394	-0.9663	9	0.87932	D	0	-7.1868	13.346	0.60573	0.1363:0.6025:0.2612:0.0	.	89	Q75WM6	H1FNT_HUMAN	K	89	ENSP00000334805:E89K	ENSP00000334805:E89K	E	+	1	0	H1FNT	47009606	1.000000	0.71417	0.288000	0.24862	0.975000	0.68041	0.999000	0.29757	-0.665000	0.05317	0.650000	0.86243	GAA		0.667	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788		A	48723339	G	A	48723339	3	1	61	1	0	0	0	0	1	0	0	0	6942	1059	37	1	267	1	H1FNT	12	48723339	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127037	48723339	85128556	8038	16023										
CCDC65	85478	broad.mit.edu	37	chr12	49298245	49298245	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaggctcctcagccagttCttgaaggtgatggccttttg	13	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49298245C>A	ENST00000320516.4	+	1	314	c.126C>A	c.(124-126)ttC>ttA	p.F42L	CCDC65_ENST00000266984.5_Missense_Mutation_p.F42L|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	42								p.F42L(1)		breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						TCAGCCAGTTCTTGAAGGTGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											109	124	119					12																	49298245		2203	4300	6503	47584512	SO:0001583	missense	85478				CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.126C>A	12.37:g.49298245C>A	ENSP00000312706:p.Phe42Leu		47584512	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129755	0.77549	.	.	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	T;T;T	0.48522	1.54;0.81;1.55	5.06	5.06	0.68205	.	0.057305	0.64402	D	0.000001	T	0.55369	0.1916	L	0.55103	1.725	0.44880	D	0.997894	D	0.69078	0.997	D	0.63957	0.92	T	0.45323	-0.9269	10	0.10636	T	0.68	-12.1964	11.2037	0.48756	0.0:0.9149:0.0:0.0851	.	42	Q8IXS2	CCD65_HUMAN	L	42	ENSP00000266984:F42L;ENSP00000446569:F42L;ENSP00000312706:F42L	ENSP00000266984:F42L	F	+	3	2	CCDC65	47584512	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.694000	0.54742	2.808000	0.96608	0.655000	0.94253	TTC		0.552	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124		A	49298245	C	A	49298245	3	1	61	1	0	0	0	0	1	0	0	0	2843	912	32	2	128	2	CCDC65	12	49298245	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	574906	49298245	84553650	8039	16024										
CCDC65	85478	broad.mit.edu	37	chr12	49310836	49310836	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagcagaactatatagattCtgagtatgaaagcaagctgg	12	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49310836C>A	ENST00000320516.4	+	4	742	c.554C>A	c.(553-555)tCt>tAt	p.S185Y	CCDC65_ENST00000266984.5_Missense_Mutation_p.S185Y|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	185								p.S185Y(1)		breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						TATATAGATTCTGAGTATGAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											107	96	100					12																	49310836		2203	4300	6503	47597103	SO:0001583	missense	85478				CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.554C>A	12.37:g.49310836C>A	ENSP00000312706:p.Ser185Tyr		47597103	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.806052	0.50421	.	.	ENSG00000139537	ENST00000266984;ENST00000320516	T;T	0.02525	4.26;4.26	5.22	4.34	0.51931	.	0.735545	0.13661	N	0.371611	T	0.05227	0.0139	L	0.56769	1.78	0.30351	N	0.784736	P	0.46220	0.874	B	0.44224	0.444	T	0.10497	-1.0627	10	0.59425	D	0.04	-1.4545	7.9324	0.29909	0.0:0.656:0.2594:0.0846	.	185	Q8IXS2	CCD65_HUMAN	Y	185	ENSP00000266984:S185Y;ENSP00000312706:S185Y	ENSP00000266984:S185Y	S	+	2	0	CCDC65	47597103	0.000000	0.05858	0.192000	0.23308	0.996000	0.88848	0.393000	0.20817	1.593000	0.50029	0.655000	0.94253	TCT		0.428	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124		A	49310836	C	A	49310836	3	1	61	1	0	0	0	0	1	0	0	0	2843	913	32	2	568	2	CCDC65	12	49310836	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12591	49310836	84541059	8040	16025										
FKBP11	51303	broad.mit.edu	37	chr12	49317628	49317628	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggaatgattgcccttcGcttctctctgagggaaggaa	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49317628G>A	ENST00000550765.1	-	5	723	c.325C>T	c.(325-327)Cga>Tga	p.R109*	FKBP11_ENST00000444214.2_Nonsense_Mutation_p.R7*|CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_Intron|FKBP11_ENST00000453172.2_Nonsense_Mutation_p.R109*|FKBP11_ENST00000552878.1_Nonsense_Mutation_p.R109*|RP11-302B13.5_ENST00000398092.4_Intron	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	109	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R109*(1)		kidney(1)|large_intestine(3)|lung(1)	5						ATTGCCCTTCGCTTCTCTCTG	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											135	116	122					12																	49317628		2203	4300	6503	47603895	SO:0001587	stop_gained	51303			AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"FK506 binding protein 11 (19 kDa)"			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.325C>T	12.37:g.49317628G>A	ENSP00000449751:p.Arg109*		47603895	B4DWB7	Nonsense_Mutation	SNP	ENST00000550765.1	37	CCDS8773.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382216	0.82792	.	.	ENSG00000134285	ENST00000444214;ENST00000550765;ENST00000552878;ENST00000453172	.	.	.	5.16	4.26	0.50523	.	0.114128	0.49305	D	0.000147	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4339	14.3998	0.67034	0.0:0.0:0.8512:0.1488	.	.	.	.	X	7;109;109;109	.	ENSP00000412403:R7X	R	-	1	2	FKBP11	47603895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.884000	0.48562	1.282000	0.44496	0.650000	0.86243	CGA		0.522	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		A	49317628	G	A	49317628	4	1	61	1	0	0	0	0	0	1	0	0	5922	1095	38	1	345	1	FKBP11	12	49317628	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6792	49317628	84534267	8041	16026										
WNT10B	7480	broad.mit.edu	37	chr12	49362094	49362094	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaaggaaaaagcactttCtcggaaacctggggatgaga	14	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49362094C>A	ENST00000301061.4	-	4	694	c.346G>T	c.(346-348)Gaa>Taa	p.E116*	WNT10B_ENST00000403957.1_Nonsense_Mutation_p.E116*|WNT10B_ENST00000407467.1_Nonsense_Mutation_p.E116*	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	116					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.E116*(1)		central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						AAAGCACTTTCTCGGAAACCT	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											62	58	59					12																	49362094		2203	4300	6503	47648361	SO:0001587	stop_gained	7480			X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"Wingless-type MMTV integration sites"	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.346G>T	12.37:g.49362094C>A	ENSP00000301061:p.Glu116*		47648361	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Nonsense_Mutation	SNP	ENST00000301061.4	37	CCDS8775.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.275783|5.275783	0.95459|0.95459	.|.	.|.	ENSG00000169884|ENSG00000169884	ENST00000413630|ENST00000301061;ENST00000407467;ENST00000403957	T|.	0.78924|.	-1.22|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.76898|.	0.4052|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.80854|.	-0.1196|.	6|.	0.35671|0.87932	T|D	0.21|0	.|.	17.4835|17.4835	0.87680|0.87680	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	127|116	ENSP00000398473:E127D|.	ENSP00000398473:E127D|ENSP00000301061:E116X	E|E	-|-	3|1	2|0	WNT10B|WNT10B	47648361|47648361	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.959000|0.959000	0.62525|0.62525	7.783000|7.783000	0.85696|0.85696	2.504000|2.504000	0.84457|0.84457	0.491000|0.491000	0.48974|0.48974	GAG|GAA		0.572	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394		A	49362094	C	A	49362094	4	1	61	1	0	0	0	0	0	1	0	0	17423	922	32	2	831	2	WNT10B	12	49362094	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44466	49362094	84489801	8042	16027										
DHH	50846	broad.mit.edu	37	chr12	49488038	49488038	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttctcctcatccttgaaGatgatgtcggggttgtagtt	11	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49488038G>T	ENST00000266991.2	-	1	564	c.258C>A	c.(256-258)atC>atA	p.I86I	RP11-386G11.8_ENST00000548030.1_RNA|RP11-386G11.8_ENST00000553174.1_RNA	NM_021044.2	NP_066382.1	O43323	DHH_HUMAN	desert hedgehog	86					cell-cell signaling (GO:0007267)|Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|myelination (GO:0042552)|regulation of steroid biosynthetic process (GO:0050810)|response to estradiol (GO:0032355)|spermatid development (GO:0007286)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.I86I(1)		breast(1)|large_intestine(3)|lung(4)	8						CATCCTTGAAGATGATGTCGG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	12											84	83	84					12																	49488038		2203	4300	6503	47774305	SO:0001819	synonymous_variant	50846			AB010994	CCDS8779.1	12q13.1	2010-06-24	2010-06-24			ENSG00000139549			2865	protein-coding gene	gene with protein product		605423	"desert hedgehog (Drosophila) homolog"			10773676, 10640830	Standard	NM_021044		Approved	HHG-3, MGC35145	uc001rtf.3	O43323	OTTHUMG00000170408	ENST00000266991.2:c.258C>A	12.37:g.49488038G>T			47774305	Q15794	Silent	SNP	ENST00000266991.2	37	CCDS8779.1																																																																																				0.667	DHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408973.1	NM_021044		T	49488038	G	T	49488038	2	4	61	1	0	0	0	0	0	0	0	1	4494	932	33	2		2	DHH	12	49488038	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125944	49488038	84363857	8043	16028										
TUBA1B	10376	broad.mit.edu	37	chr12	49523033	49523033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggtgcttaccagcttgcGaattcggtccaacacaaggt	11	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49523033G>A	ENST00000336023.5	-	3	461	c.367C>T	c.(367-369)Cgc>Tgc	p.R123C	RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000551496.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	123					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R123C(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						ACCAGCTTGCGAATTCGGTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											162	148	153					12																	49523033		2203	4300	6503	47809300	SO:0001583	missense	10376			AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"Tubulins"	18809	protein-coding gene	gene with protein product	"tubulin, alpha, ubiquitous"	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.367C>T	12.37:g.49523033G>A	ENSP00000336799:p.Arg123Cys		47809300	P04687|P05209|Q27I68|Q8WU19	Missense_Mutation	SNP	ENST00000336023.5	37	CCDS31792.1	.	.	.	.	.	.	.	.	.	.	g	13.46	2.244498	0.39697	.	.	ENSG00000123416	ENST00000336023;ENST00000550367	T;T	0.73789	-0.78;-0.78	4.59	4.59	0.56863	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.45867	U	0.000336	D	0.88916	0.6567	H	0.98218	4.175	0.80722	D	1	D	0.69078	0.997	P	0.58130	0.833	D	0.92146	0.5724	10	0.72032	D	0.01	.	12.0702	0.53611	0.0:0.0:0.8269:0.1731	.	123	P68363	TBA1B_HUMAN	C	123	ENSP00000336799:R123C;ENSP00000449325:R123C	ENSP00000336799:R123C	R	-	1	0	TUBA1B	47809300	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.416000	0.66417	2.115000	0.64714	0.558000	0.71614	CGC		0.468	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082		A	49523033	G	A	49523033	3	1	61	1	0	0	0	0	1	0	0	0	16784	1058	37	1	996	1	TUBA1B	12	49523033	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34995	49523033	84328862	8044	16029										
TUBA1C	84790	broad.mit.edu	37	chr12	49666312	49666312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctgtcgtagaaacctcGatatcgagcgcccaacctac	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49666312G>A	ENST00000301072.6	+	4	927	c.652G>A	c.(652-654)Gat>Aat	p.D218N	RP11-161H23.5_ENST00000550468.2_RNA|TUBA1C_ENST00000541364.1_Missense_Mutation_p.D288N	NM_032704.3	NP_116093.1	Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	218					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.D218N(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						TAGAAACCTCGATATCGAGCG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											12	18	16					12																	49666312		2168	4266	6434	47952579	SO:0001583	missense	84790			BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553		"Tubulins"	20768	protein-coding gene	gene with protein product			"tubulin, alpha 6"	TUBA6		7821789	Standard	NM_032704		Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000301072.6:c.652G>A	12.37:g.49666312G>A	ENSP00000301072:p.Asp218Asn		47952579		Missense_Mutation	SNP	ENST00000301072.6	37	CCDS8782.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.792532	0.31685	.	.	ENSG00000167553	ENST00000541364;ENST00000301072	T;T	0.69435	-0.4;-0.4	4.63	3.71	0.42584	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000001	T	0.57110	0.2031	L	0.33093	0.98	0.80722	D	1	B;B	0.15719	0.014;0.004	B;B	0.21360	0.034;0.011	T	0.57957	-0.7721	10	0.72032	D	0.01	.	14.1653	0.65473	0.0:0.1522:0.8478:0.0	.	288;218	F5H5D3;Q9BQE3	.;TBA1C_HUMAN	N	288;218	ENSP00000443475:D288N;ENSP00000301072:D218N	ENSP00000301072:D218N	D	+	1	0	TUBA1C	47952579	1.000000	0.71417	0.399000	0.26333	0.969000	0.65631	6.345000	0.72995	1.220000	0.43490	0.549000	0.68633	GAT		0.498	TUBA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404424.1	NM_032704		A	49666312	G	A	49666312	3	1	61	1	0	0	0	0	1	0	0	0	16785	1058	37	1	666	1	TUBA1C	12	49666312	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143279	49666312	84185583	8045	16030										
KCNH3	23416	broad.mit.edu	37	chr12	49948260	49948260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagccttgcgctgtaccccGagtttgccccgcgcttcagt	10	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49948260G>A	ENST00000257981.6	+	11	2319	c.2059G>A	c.(2059-2061)Gag>Aag	p.E687K		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	687					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.E687K(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GCTGTACCCCGAGTTTGCCCC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											61	60	60					12																	49948260		2203	4300	6503	48234527	SO:0001583	missense	23416			AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2059G>A	12.37:g.49948260G>A	ENSP00000257981:p.Glu687Lys		48234527	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	G	35	5.526473	0.96431	.	.	ENSG00000135519	ENST00000257981	D	0.96940	-4.18	4.81	4.81	0.61882	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (1);	0.000000	0.47455	D	0.000230	D	0.95639	0.8582	M	0.85462	2.755	0.58432	D	0.999999	P	0.40515	0.719	B	0.34093	0.175	D	0.96485	0.9359	10	0.72032	D	0.01	.	16.1975	0.82042	0.0:0.0:1.0:0.0	.	687	Q9ULD8	KCNH3_HUMAN	K	687	ENSP00000257981:E687K	ENSP00000257981:E687K	E	+	1	0	KCNH3	48234527	1.000000	0.71417	0.999000	0.59377	0.920000	0.55202	9.789000	0.99068	2.628000	0.89032	0.563000	0.77884	GAG		0.632	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		A	49948260	G	A	49948260	3	1	61	1	0	0	0	0	1	0	0	0	8054	1059	37	1	2101	1	KCNH3	12	49948260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281948	49948260	83903635	8046	16031										
FAM186B	84070	broad.mit.edu	37	chr12	49993495	49993495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagggccaggtcagccttCggatggatgtcccagtgaca	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49993495C>T	ENST00000257894.2	-	4	2089	c.1928G>A	c.(1927-1929)cGa>cAa	p.R643Q	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R553Q	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	643						protein complex (GO:0043234)		p.R643Q(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTCAGCCTTCGGATGGATGT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	73	75					12																	49993495		2203	4300	6503	48279762	SO:0001583	missense	84070			AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1928G>A	12.37:g.49993495C>T	ENSP00000257894:p.Arg643Gln		48279762	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	C	9.533	1.111269	0.20714	.	.	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.12147	2.71;2.71;2.91	4.73	-1.54	0.08584	.	1.189380	0.06442	N	0.726104	T	0.04272	0.0118	N	0.03115	-0.41	0.09310	N	1	B;B	0.25351	0.124;0.028	B;B	0.14578	0.011;0.008	T	0.38650	-0.9651	9	.	.	.	-0.1014	0.8277	0.01124	0.16:0.3474:0.1566:0.336	.	553;643	B4DZ15;Q8IYM0	.;F186B_HUMAN	Q	553;256;643	ENSP00000438569:R553Q;ENSP00000436995:R256Q;ENSP00000257894:R643Q	.	R	-	2	0	FAM186B	48279762	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.406000	0.07187	-0.082000	0.12640	-0.812000	0.03155	CGA		0.532	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		T	49993495	C	T	49993495	3	4	61	1	0	0	0	0	1	0	0	0	5528	884	31	1	769	1	FAM186B	12	49993495	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45235	49993495	83858400	8047	16032										
FAM186B	84070	broad.mit.edu	37	chr12	49994866	49994866	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggctgaggatgggatggaGatgtctgtgggcttcttccc	17	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:49994866G>T	ENST00000257894.2	-	4	718	c.557C>A	c.(556-558)tCt>tAt	p.S186Y	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Missense_Mutation_p.S186Y|FAM186B_ENST00000544141.1_Missense_Mutation_p.S96Y	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	186						protein complex (GO:0043234)		p.S186Y(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATGGGATGGAGATGTCTGTGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											112	76	88					12																	49994866		2203	4300	6503	48281133	SO:0001583	missense	84070			AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.557C>A	12.37:g.49994866G>T	ENSP00000257894:p.Ser186Tyr		48281133	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451066	0.43531	.	.	ENSG00000135436	ENST00000544141;ENST00000551047;ENST00000257894	T;T;T	0.48201	2.62;0.82;2.82	4.98	0.906	0.19314	.	1.248190	0.05817	N	0.615076	T	0.48484	0.1502	L	0.44542	1.39	0.09310	N	1	D;D	0.54207	0.965;0.965	P;P	0.54312	0.748;0.748	T	0.27331	-1.0077	9	.	.	.	1.5783	1.9535	0.03371	0.1796:0.1508:0.5031:0.1665	.	96;186	B4DZ15;Q8IYM0	.;F186B_HUMAN	Y	96;186;186	ENSP00000438569:S96Y;ENSP00000448656:S186Y;ENSP00000257894:S186Y	.	S	-	2	0	FAM186B	48281133	0.013000	0.17824	0.000000	0.03702	0.010000	0.07245	1.489000	0.35562	-0.023000	0.13963	-0.312000	0.09012	TCT		0.557	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		T	49994866	G	T	49994866	3	4	61	1	0	0	0	0	1	0	0	0	5528	942	33	2	2140	2	FAM186B	12	49994866	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1371	49994866	83857029	8048	16033										
PRPF40B	25766	broad.mit.edu	37	chr12	50031567	50031567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggaggagttgaaggcacGattccatgatgaaaagaaga	14	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50031567G>A	ENST00000380281.1	+	17	1725	c.1661G>A	c.(1660-1662)cGa>cAa	p.R554Q	FMNL3_ENST00000550668.1_5'Flank|PRPF40B_ENST00000548825.2_Missense_Mutation_p.R576Q|PRPF40B_ENST00000261897.1_Missense_Mutation_p.R548Q			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	554	FF 5.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)		p.R554Q(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						TTGAAGGCACGATTCCATGAT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											120	109	113					12																	50031567		2203	4300	6503	48317834	SO:0001583	missense	25766			AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"Huntingtin interacting protein C"		"PRP40 pre-mRNA processing factor 40 homolog B (yeast)"			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.1661G>A	12.37:g.50031567G>A	ENSP00000369634:p.Arg554Gln		48317834	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	37		.	.	.	.	.	.	.	.	.	.	G	29.9	5.049508	0.93740	.	.	ENSG00000110844	ENST00000261897;ENST00000380281	T;T	0.22539	1.96;1.95	4.98	4.98	0.66077	.	0.106734	0.38720	N	0.001594	T	0.31420	0.0796	M	0.67517	2.055	0.80722	D	1	P;P;P	0.50272	0.791;0.733;0.933	B;B;P	0.46253	0.312;0.329;0.509	T	0.03503	-1.1030	9	.	.	.	-6.1859	17.5414	0.87849	0.0:0.0:1.0:0.0	.	554;548;554	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	Q	548;554	ENSP00000261897:R548Q;ENSP00000369634:R554Q	.	R	+	2	0	PRPF40B	48317834	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.298000	0.96132	2.753000	0.94483	0.655000	0.94253	CGA		0.552	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		A	50031567	G	A	50031567	3	1	61	1	0	0	0	0	1	0	0	0	12606	1058	37	1	1727	1	PRPF40B	12	50031567	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36701	50031567	83820328	8049	16034										
FMNL3	91010	broad.mit.edu	37	chr12	50062278	50062278	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagatcagatcccatttCttctcattgtcatactgccg	5	13	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50062278C>A	ENST00000293590.5	-	2	419	c.186G>T	c.(184-186)aaG>aaT	p.K62N	FMNL3_ENST00000550488.1_Missense_Mutation_p.K62N|FMNL3_ENST00000335154.5_Missense_Mutation_p.K62N|FMNL3_ENST00000352151.5_Missense_Mutation_p.K62N			Q8IVF7	FMNL3_HUMAN	formin-like 3	62	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)	p.K62N(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GATCCCATTTCTTCTCATTGT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											158	160	159					12																	50062278		1906	4126	6032	48348545	SO:0001583	missense	91010			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.186G>T	12.37:g.50062278C>A	ENSP00000293590:p.Lys62Asn		48348545	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	ENST00000293590.5	37		.	.	.	.	.	.	.	.	.	.	C	32	5.110384	0.94292	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590;ENST00000550424	D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.41	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.96278	0.8786	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.80764	0.994;0.99	D	0.96567	0.9420	10	0.87932	D	0	.	18.6701	0.91507	0.0:1.0:0.0:0.0	.	62;62	Q8IVF7-2;Q8IVF7-3	.;.	N	62;62;62;62;31	ENSP00000335655:K62N;ENSP00000447479:K62N;ENSP00000344311:K62N;ENSP00000293590:K62N;ENSP00000448939:K31N	ENSP00000293590:K62N	K	-	3	2	FMNL3	48348545	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.843000	0.55865	2.882000	0.98803	0.655000	0.94253	AAG		0.552	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		A	50062278	C	A	50062278	3	1	61	1	0	0	0	0	1	0	0	0	5972	912	32	2	2997	2	FMNL3	12	50062278	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30711	50062278	83789617	8050	16035										
NCKAP5L	57701	broad.mit.edu	37	chr12	50190423	50190423	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccagcacccatgaacatgCtaaggaaggggaggggcccc	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50190423C>A	ENST00000335999.6	-	8	1421	c.1220G>T	c.(1219-1221)aGc>aTc	p.S407I		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	403	Pro-rich.							p.S407I(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CATGAACATGCTAAGGAAGGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	12											18	20	19					12																	50190423		1838	4049	5887	48476690	SO:0001583	missense	57701			AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1220G>T	12.37:g.50190423C>A	ENSP00000337998:p.Ser407Ile		48476690	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	37	CCDS41781.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.44|12.44	1.940094|1.940094	0.34283|0.34283	.|.	.|.	ENSG00000167566|ENSG00000167566	ENST00000335999;ENST00000354423|ENST00000433948	T|.	0.54279|.	0.58|.	4.25|4.25	4.25|4.25	0.50352|0.50352	.|.	0.000000|.	0.50627|.	D|.	0.000117|.	T|.	0.33933|.	0.0880|.	N|N	0.08118|0.08118	0|0	0.33787|0.33787	D|D	0.625003|0.625003	D|.	0.64830|.	0.994|.	P|.	0.62649|.	0.905|.	T|.	0.45279|.	-0.9272|.	10|.	0.87932|.	D|.	0|.	-14.3536|-14.3536	15.8311|15.8311	0.78752|0.78752	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	403|.	E2QRB5|.	.|.	I|Y	407;403|121	ENSP00000337998:S407I|.	ENSP00000337998:S407I|.	S|X	-|-	2|3	0|2	NCKAP5L|NCKAP5L	48476690|48476690	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.306000|0.306000	0.27790|0.27790	2.812000|2.812000	0.47994|0.47994	2.102000|2.102000	0.63906|0.63906	0.561000|0.561000	0.74099|0.74099	AGC|TAG		0.637	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		A	50190423	C	A	50190423	3	1	61	1	0	0	0	0	1	0	0	0	10255	797	28	2	2808	2	NCKAP5L	12	50190423	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128145	50190423	83661472	8051	16036										
BCDIN3D	144233	broad.mit.edu	37	chr12	50232726	50232726	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagaggagacggaattCtcttgaggcatctgagcagg	15	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50232726C>A	ENST00000333924.4	-	2	348	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	103	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)	p.E103*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						AGACGGAATTCTCTTGAGGCA	0.488											OREG0021805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	12											87	83	84					12																	50232726		2203	4300	6503	48518993	SO:0001587	stop_gained	144233				CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.307G>T	12.37:g.50232726C>A	ENSP00000335201:p.Glu103*	968	48518993	A8K829	Nonsense_Mutation	SNP	ENST00000333924.4	37	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424409	0.83667	.	.	ENSG00000186666	ENST00000333924	.	.	.	5.37	4.48	0.54585	.	0.302658	0.40818	N	0.001016	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	11.9233	0.52803	0.0:0.9149:0.0:0.0851	.	.	.	.	X	103	.	ENSP00000335201:E103X	E	-	1	0	BCDIN3D	48518993	0.622000	0.27085	0.985000	0.45067	0.990000	0.78478	1.522000	0.35921	1.395000	0.46643	0.591000	0.81541	GAA		0.488	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		A	50232726	C	A	50232726	4	1	61	1	0	0	0	0	0	1	0	0	1358	922	32	2	575	2	BCDIN3D	12	50232726	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42303	50232726	83619169	8052	16037										
SMARCD1	6602	broad.mit.edu	37	chr12	50480578	50480578	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcccaggcctatatggatCtcttggcttttgaaaggaaa	9	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50480578C>A	ENST00000394963.4	+	4	846	c.448C>A	c.(448-450)Ctc>Atc	p.L150I	SMARCD1_ENST00000548573.1_5'Flank|SMARCD1_ENST00000381513.4_Missense_Mutation_p.L150I	NM_003076.4	NP_003067.3			SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1									p.L111I(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	18						CTATATGGATCTCTTGGCTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	102	103					12																	50480578		2203	4300	6503	48766845	SO:0001583	missense	6602			U66617	CCDS8797.2, CCDS8798.2	12q13-q14	2008-08-05			ENSG00000066117	ENSG00000066117			11106	protein-coding gene	gene with protein product		601735				8804307, 9693044, 12917342	Standard	NM_003076		Approved	BAF60A, Rsc6p, CRACD1	uc001rvx.4	Q96GM5	OTTHUMG00000150194	ENST00000394963.4:c.448C>A	12.37:g.50480578C>A	ENSP00000378414:p.Leu150Ile		48766845		Missense_Mutation	SNP	ENST00000394963.4	37	CCDS8797.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055921	0.76074	.	.	ENSG00000066117	ENST00000394963;ENST00000381513;ENST00000551966;ENST00000550477;ENST00000551497	T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.78886	0.4354	M	0.88704	2.975	0.80722	D	1	D;D;D	0.71674	0.998;0.994;0.995	D;D;D	0.91635	0.999;0.966;0.968	T	0.82028	-0.0660	10	0.87932	D	0	-11.4566	13.5587	0.61775	0.0:0.9257:0.0:0.0743	.	150;150;150	B4DF50;Q96GM5-2;Q96GM5	.;.;SMRD1_HUMAN	I	150;150;150;150;88	ENSP00000378414:L150I;ENSP00000370924:L150I;ENSP00000447386:L150I;ENSP00000448030:L150I;ENSP00000449825:L88I	ENSP00000370924:L150I	L	+	1	0	SMARCD1	48766845	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.522000	0.45572	2.873000	0.98535	0.561000	0.74099	CTC		0.418	SMARCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316759.2	NM_003076		A	50480578	C	A	50480578	3	1	61	1	0	0	0	0	1	0	0	0	14814	913	32	2	462	2	SMARCD1	12	50480578	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	247852	50480578	83371317	8053	16038										
SMARCD1	6602	broad.mit.edu	37	chr12	50481162	50481162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcaaaaacggaagctgcGaattttcatttctaacactt	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50481162G>A	ENST00000394963.4	+	5	946	c.548G>A	c.(547-549)cGa>cAa	p.R183Q	SMARCD1_ENST00000548573.1_5'Flank|SMARCD1_ENST00000381513.4_Missense_Mutation_p.R183Q	NM_003076.4	NP_003067.3			SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1									p.R144Q(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	18						CGGAAGCTGCGAATTTTCATT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											179	185	183					12																	50481162		2203	4300	6503	48767429	SO:0001583	missense	6602			U66617	CCDS8797.2, CCDS8798.2	12q13-q14	2008-08-05			ENSG00000066117	ENSG00000066117			11106	protein-coding gene	gene with protein product		601735				8804307, 9693044, 12917342	Standard	NM_003076		Approved	BAF60A, Rsc6p, CRACD1	uc001rvx.4	Q96GM5	OTTHUMG00000150194	ENST00000394963.4:c.548G>A	12.37:g.50481162G>A	ENSP00000378414:p.Arg183Gln		48767429		Missense_Mutation	SNP	ENST00000394963.4	37	CCDS8797.2	.	.	.	.	.	.	.	.	.	.	G	31	5.075018	0.94000	.	.	ENSG00000066117	ENST00000394963;ENST00000381513	T;T	0.52526	0.66;0.66	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.75133	0.3808	M	0.88842	2.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.99	T	0.79509	-0.1774	10	0.87932	D	0	-7.3085	19.2785	0.94042	0.0:0.0:1.0:0.0	.	183;183;183	B4DF50;Q96GM5-2;Q96GM5	.;.;SMRD1_HUMAN	Q	183	ENSP00000378414:R183Q;ENSP00000370924:R183Q	ENSP00000370924:R183Q	R	+	2	0	SMARCD1	48767429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.559000	0.98135	2.873000	0.98535	0.561000	0.74099	CGA		0.517	SMARCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316759.2	NM_003076		A	50481162	G	A	50481162	3	1	61	1	0	0	0	0	1	0	0	0	14814	1058	37	1	566	1	SMARCD1	12	50481162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	584	50481162	83370733	8054	16039										
LIMA1	51474	broad.mit.edu	37	chr12	50570879	50570879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatcctcatcataataccGatttctctttatctgttctt	2	12	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50570879G>A	ENST00000341247.4	-	11	2397	c.2248C>T	c.(2248-2250)Cgg>Tgg	p.R750W	LIMA1_ENST00000552783.1_Missense_Mutation_p.R591W|LIMA1_ENST00000394943.3_Missense_Mutation_p.R751W|LIMA1_ENST00000547825.1_Missense_Mutation_p.R448W|LIMA1_ENST00000552823.1_Missense_Mutation_p.R590W|LIMA1_ENST00000552909.1_Missense_Mutation_p.R589W|LIMA1_ENST00000552491.1_Missense_Mutation_p.R447W	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	750					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.R750W(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TCATAATACCGATTTCTCTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											310	302	304					12																	50570879		2203	4300	6503	48857146	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.2248C>T	12.37:g.50570879G>A	ENSP00000340184:p.Arg750Trp		48857146	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480316	0.84747	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	D;D;D;D;D;D;D	0.95069	-2.87;-2.86;-3.26;-3.6;-2.87;-3.25;-3.25	6.02	6.02	0.97574	.	0.062767	0.64402	D	0.000004	D	0.96987	0.9016	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.97048	0.9762	10	0.87932	D	0	.	16.0721	0.80941	0.0:0.0:0.8655:0.1345	.	760;750;589	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	W	447;448;590;751;750;591;589;669	ENSP00000448463:R447W;ENSP00000448706:R448W;ENSP00000450266:R590W;ENSP00000378400:R751W;ENSP00000340184:R750W;ENSP00000448779:R591W;ENSP00000450087:R589W	ENSP00000340184:R750W	R	-	1	2	LIMA1	48857146	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.028000	0.57246	2.865000	0.98341	0.655000	0.94253	CGG		0.428	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50570879	G	A	50570879	3	1	61	1	0	0	0	0	1	0	0	0	8819	1057	37	1	35	1	LIMA1	12	50570879	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89717	50570879	83281016	8055	16040										
LIMA1	51474	broad.mit.edu	37	chr12	50615895	50615895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgcccgaagcatctgtgTtttcactgatttctgatttt	7	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50615895T>C	ENST00000341247.4	-	4	688	c.539A>G	c.(538-540)aAc>aGc	p.N180S	RP3-405J10.4_ENST00000551284.1_RNA|LIMA1_ENST00000552008.1_5'Flank|LIMA1_ENST00000552783.1_Missense_Mutation_p.N20S|LIMA1_ENST00000394943.3_Missense_Mutation_p.N180S|LIMA1_ENST00000552823.1_Missense_Mutation_p.N20S|LIMA1_ENST00000552909.1_Missense_Mutation_p.N20S	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	180					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.N180S(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						AGCATCTGTGTTTTCACTGAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											196	196	196					12																	50615895		2203	4300	6503	48902162	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.539A>G	12.37:g.50615895T>C	ENSP00000340184:p.Asn180Ser		48902162	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595989	0.46318	.	.	ENSG00000050405	ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;D;T;T;T	0.84370	-1.39;-1.84;-1.1;-1.39;-1.39	6.17	3.85	0.44370	.	0.358324	0.32244	N	0.006364	T	0.75162	0.3812	M	0.67953	2.075	0.21386	N	0.999709	B;B;P	0.41848	0.304;0.304;0.763	B;B;B	0.33392	0.139;0.106;0.163	T	0.63812	-0.6552	10	0.07990	T	0.79	.	5.3248	0.15901	0.0:0.2065:0.1426:0.6509	.	189;180;20	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	S	20;180;180;20;20;99	ENSP00000450266:N20S;ENSP00000378400:N180S;ENSP00000340184:N180S;ENSP00000448779:N20S;ENSP00000450087:N20S	ENSP00000340184:N180S	N	-	2	0	LIMA1	48902162	0.977000	0.34250	0.772000	0.31596	0.934000	0.57294	1.048000	0.30379	1.149000	0.42402	0.533000	0.62120	AAC		0.368	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		C	50615895	T	C	50615895	3	2	61	1	0	0	0	0	1	0	0	0	8819	1725	60	4	1775	4	LIMA1	12	50615895	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	45016	50615895	83236000	8056	16041										
LIMA1	51474	broad.mit.edu	37	chr12	50616203	50616203	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctcccagccctgggttCtcccacttcttctttaacac	5	17	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:50616203C>A	ENST00000341247.4	-	4	380	c.231G>T	c.(229-231)gaG>gaT	p.E77D	RP3-405J10.4_ENST00000551284.1_RNA|LIMA1_ENST00000552008.1_5'Flank|LIMA1_ENST00000552783.1_5'UTR|LIMA1_ENST00000394943.3_Missense_Mutation_p.E77D|LIMA1_ENST00000552823.1_5'Flank|LIMA1_ENST00000552909.1_5'Flank	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	77					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.E77D(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GCCCTGGGTTCTCCCACTTCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											111	108	109					12																	50616203		2203	4300	6503	48902470	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.231G>T	12.37:g.50616203C>A	ENSP00000340184:p.Glu77Asp		48902470	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764838	0.90020	.	.	ENSG00000050405	ENST00000394943;ENST00000341247;ENST00000551691;ENST00000550592	D;D	0.90004	-2.6;-1.86	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94496	0.8228	M	0.72894	2.215	0.80722	D	1	D;P	0.76494	0.999;0.929	D;P	0.78314	0.991;0.811	D	0.93855	0.7148	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	86;77	Q59FE8;Q9UHB6	.;LIMA1_HUMAN	D	77	ENSP00000378400:E77D;ENSP00000340184:E77D	ENSP00000340184:E77D	E	-	3	2	LIMA1	48902470	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.826000	0.48104	2.941000	0.99782	0.655000	0.94253	GAG		0.493	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50616203	C	A	50616203	3	1	61	1	0	0	0	0	1	0	0	0	8819	912	32	2	2083	2	LIMA1	12	50616203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308	50616203	83235692	8057	16042										
DIP2B	57609	broad.mit.edu	37	chr12	51065176	51065176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgtatttgccaatactcGaataggtaggagctggatct	11	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51065176G>A	ENST00000301180.5	+	5	669	c.635G>A	c.(634-636)cGa>cAa	p.R212Q		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	212	Ser-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.R212Q(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GCCAATACTCGAATAGGTAGG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											81	75	77					12																	51065176		2203	4300	6503	49351443	SO:0001583	missense	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.635G>A	12.37:g.51065176G>A	ENSP00000301180:p.Arg212Gln		49351443	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.045042	0.55110	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.22134	1.97	5.3	5.3	0.74995	.	0.115976	0.64402	N	0.000011	T	0.09468	0.0233	N	0.19112	0.55	0.54753	D	0.999987	B;P	0.45348	0.007;0.856	B;B	0.33254	0.002;0.16	T	0.14200	-1.0481	10	0.05620	T	0.96	-4.3495	12.4674	0.55766	0.0761:0.0:0.9239:0.0	.	212;222	Q9P265;E9PHD6	DIP2B_HUMAN;.	Q	222;212	ENSP00000301180:R212Q	ENSP00000301180:R212Q	R	+	2	0	DIP2B	49351443	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.178000	0.77657	2.762000	0.94881	0.591000	0.81541	CGA		0.453	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51065176	G	A	51065176	3	1	61	1	0	0	0	0	1	0	0	0	4539	1058	37	1	653	1	DIP2B	12	51065176	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	448973	51065176	82786719	8058	16043										
DIP2B	57609	broad.mit.edu	37	chr12	51092171	51092171	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcaatgaatggattgagCtatggggtaatacgggtcaa	12	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51092171C>A	ENST00000301180.5	+	18	2143	c.2109C>A	c.(2107-2109)agC>agA	p.S703R		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	703						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.S703R(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						ATGGATTGAGCTATGGGGTAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											106	100	102					12																	51092171		2203	4300	6503	49378438	SO:0001583	missense	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2109C>A	12.37:g.51092171C>A	ENSP00000301180:p.Ser703Arg		49378438	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365488	0.61513	.	.	ENSG00000066084	ENST00000301180	T	0.25579	1.79	5.2	3.22	0.36961	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	M	0.79926	2.475	0.58432	D	0.999997	P	0.44816	0.844	P	0.58130	0.833	T	0.30446	-0.9978	10	0.45353	T	0.12	-14.7795	4.4345	0.11544	0.0:0.5838:0.0:0.4162	.	703	Q9P265	DIP2B_HUMAN	R	703	ENSP00000301180:S703R	ENSP00000301180:S703R	S	+	3	2	DIP2B	49378438	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.498000	0.22530	1.413000	0.46997	0.591000	0.81541	AGC		0.468	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51092171	C	A	51092171	3	1	61	1	0	0	0	0	1	0	0	0	4539	796	28	2	2179	2	DIP2B	12	51092171	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26995	51092171	82759724	8059	16044										
DIP2B	57609	broad.mit.edu	37	chr12	51126253	51126253	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaagctcttcaaagacatCgggctgtccccgcgggctgt	11	13	3	1	rs143164072		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51126253C>T	ENST00000301180.5	+	32	3949	c.3915C>T	c.(3913-3915)atC>atT	p.I1305I		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1305						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.I1305I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						TCAAAGACATCGGGCTGTCCC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C		1,4405	2.1+/-5.4	0,1,2202	93	83	86		3915	-2.9	0.8	12	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DIP2B	NM_173602.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		1305/1577	51126253	2,13004	2203	4300	6503	49412520	SO:0001819	synonymous_variant	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.3915C>T	12.37:g.51126253C>T			49412520	Q6B011|Q8N1L5|Q8NB38	Silent	SNP	ENST00000301180.5	37	CCDS31799.1																																																																																				0.542	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		T	51126253	C	T	51126253	2	4	61	1	0	0	0	0	0	0	0	1	4539	874	31	1		1	DIP2B	12	51126253	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34082	51126253	82725642	8060	16045										
SLC11A2	4891	broad.mit.edu	37	chr12	51398584	51398584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcaccttgggatactgaCggtgacatacttcagcaaga	10	10	2	3	rs368158015		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51398584C>T	ENST00000262051.7	-	5	503	c.416G>A	c.(415-417)cGt>cAt	p.R139H	SLC11A2_ENST00000541174.2_Missense_Mutation_p.R139H|SLC11A2_ENST00000549193.1_5'Flank|SLC11A2_ENST00000545993.2_Missense_Mutation_p.R135H|SLC11A2_ENST00000394904.3_Missense_Mutation_p.R168H|SLC11A2_ENST00000262052.5_Missense_Mutation_p.R139H|SLC11A2_ENST00000547198.1_Missense_Mutation_p.R139H|SLC11A2_ENST00000547688.1_Missense_Mutation_p.R168H|SLC11A2_ENST00000546743.1_Missense_Mutation_p.R60H	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	139					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.R139H(1)		breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						GGGATACTGACGGTGACATAC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	87	59	68		416,503,416,416,416,416,404	4.4	1	12		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	29,29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign,benign	139/562,168/591,139/569,139/569,139/562,139/562,135/558	51398584	1,13005	2203	4300	6503	49684851	SO:0001583	missense	4891			AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"Solute carriers"	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.416G>A	12.37:g.51398584C>T	ENSP00000262051:p.Arg139His		49684851	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288616	0.59976	0.0	1.16E-4	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743;ENST00000547579;ENST00000550714;ENST00000547732;ENST00000549110;ENST00000548193	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5	5.35	4.45	0.53987	.	0.060946	0.64402	D	0.000004	T	0.62392	0.2424	L	0.39020	1.185	0.58432	D	0.999999	B;B;B;B;B	0.18741	0.015;0.012;0.03;0.029;0.018	B;B;B;B;B	0.21546	0.035;0.02;0.033;0.02;0.013	T	0.60541	-0.7243	10	0.59425	D	0.04	-6.3187	13.3033	0.60338	0.0:0.9216:0.0:0.0784	.	102;135;168;139;139	B7Z9M2;F5H741;P49281-3;P49281-2;P49281	.;.;.;.;NRAM2_HUMAN	H	139;139;139;168;168;139;135;60;60;92;60;60;139	ENSP00000262051:R139H;ENSP00000446769:R139H;ENSP00000262052:R139H;ENSP00000378364:R168H;ENSP00000449200:R168H;ENSP00000444542:R139H;ENSP00000442810:R135H;ENSP00000446914:R60H;ENSP00000447482:R60H;ENSP00000446984:R92H;ENSP00000447102:R60H;ENSP00000447334:R60H;ENSP00000449209:R139H	ENSP00000262051:R139H	R	-	2	0	SLC11A2	49684851	0.983000	0.35010	1.000000	0.80357	0.998000	0.95712	2.153000	0.42282	1.233000	0.43693	0.650000	0.86243	CGT		0.532	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1			T	51398584	C	T	51398584	3	4	61	1	0	0	0	0	1	0	0	0	14418	536	19	1	1399	1	SLC11A2	12	51398584	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	272331	51398584	82453311	8061	16046										
LETMD1	25875	broad.mit.edu	37	chr12	51442819	51442819	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgatcttccttgtaggtCttcaaagcttcacctttctc	5	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51442819C>A	ENST00000262055.4	+	2	164	c.125C>A	c.(124-126)tCt>tAt	p.S42Y	LETMD1_ENST00000547008.1_Missense_Mutation_p.S42Y|LETMD1_ENST00000380123.2_Missense_Mutation_p.S42Y|LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000552739.1_Intron|LETMD1_ENST00000550929.1_5'UTR|LETMD1_ENST00000418425.2_Missense_Mutation_p.S42Y	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	42	Required and sufficient for mitochondrial import.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)		p.S42Y(1)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						CCTTGTAGGTCTTCAAAGCTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	95	97					12																	51442819		2203	4300	6503	49729086	SO:0001583	missense	25875			AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"cervical cancer 1 protooncogene"					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.125C>A	12.37:g.51442819C>A	ENSP00000262055:p.Ser42Tyr		49729086	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Missense_Mutation	SNP	ENST00000262055.4	37	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836035	0.71373	.	.	ENSG00000050426	ENST00000551477;ENST00000262055;ENST00000550442;ENST00000549340;ENST00000548209;ENST00000548251;ENST00000380123;ENST00000548401;ENST00000418425;ENST00000448283;ENST00000547008	T;T;T;T;T;T;T;T;T;T	0.55413	0.64;0.67;0.64;0.52;0.57;0.57;0.59;0.78;0.67;0.59	4.86	4.86	0.63082	.	0.149916	0.31760	N	0.007102	T	0.43831	0.1265	N	0.24115	0.695	0.32400	N	0.552028	B;B;P;B;B;P	0.52842	0.356;0.102;0.94;0.057;0.005;0.956	B;B;P;B;B;P	0.48030	0.197;0.046;0.564;0.075;0.015;0.564	T	0.55915	-0.8065	10	0.52906	T	0.07	-9.2798	10.8632	0.46839	0.1879:0.8121:0.0:0.0	.	42;42;42;42;42;42	B7Z9A7;F8VVQ3;B3KXK7;F8W6J0;F8W1Z2;Q6P1Q0	.;.;.;.;.;LTMD1_HUMAN	Y	9;42;42;42;42;42;42;49;42;42;42	ENSP00000446862:S9Y;ENSP00000262055:S42Y;ENSP00000448110:S42Y;ENSP00000449896:S42Y;ENSP00000450275:S42Y;ENSP00000447166:S42Y;ENSP00000369466:S42Y;ENSP00000450082:S49Y;ENSP00000389903:S42Y;ENSP00000447419:S42Y	ENSP00000262055:S42Y	S	+	2	0	LETMD1	49729086	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.206000	0.42779	2.685000	0.91497	0.655000	0.94253	TCT		0.433	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416		A	51442819	C	A	51442819	3	1	61	1	0	0	0	0	1	0	0	0	8758	913	32	2	131	2	LETMD1	12	51442819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44235	51442819	82409076	8062	16047										
TFCP2	7024	broad.mit.edu	37	chr12	51497497	51497497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgtagaaaaacgatttCgatgcaaccactgctgagct	9	8	0	3	rs563834540		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51497497C>T	ENST00000257915.5	-	10	1474	c.1016G>A	c.(1015-1017)cGa>cAa	p.R339Q	TFCP2_ENST00000549867.1_Intron|TFCP2_ENST00000307660.4_Missense_Mutation_p.R288Q|TFCP2_ENST00000548115.1_Missense_Mutation_p.R288Q	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	339	DNA-binding.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R339Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AAAACGATTTCGATGCAACCA	0.373													C|||	1	0.000199681	0	0	5008	,	,		19876	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											165	161	162					12																	51497497		2203	4300	6503	49783764	SO:0001583	missense	7024			U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.1016G>A	12.37:g.51497497C>T	ENSP00000257915:p.Arg339Gln		49783764	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	37	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.741597	0.69304	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000548115;ENST00000548108	T;T;T;T	0.46451	2.21;0.88;0.87;2.22	5.32	4.43	0.53597	Sterile alpha motif/pointed domain (1);	0.000000	0.85682	D	0.000000	T	0.53400	0.1794	L	0.52573	1.65	0.52099	D	0.999941	D;B;B	0.71674	0.998;0.448;0.194	D;B;B	0.66497	0.944;0.062;0.038	T	0.47275	-0.9130	10	0.20519	T	0.43	-11.1708	13.552	0.61738	0.0:0.9237:0.0:0.0763	.	288;339;339	Q12800-2;Q12800;Q12800-4	.;TFCP2_HUMAN;.	Q	339;288;288;241	ENSP00000257915:R339Q;ENSP00000304411:R288Q;ENSP00000447991:R288Q;ENSP00000449280:R241Q	ENSP00000257915:R339Q	R	-	2	0	TFCP2	49783764	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	3.125000	0.50469	1.626000	0.50381	0.655000	0.94253	CGA		0.373	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		T	51497497	C	T	51497497	3	4	61	1	0	0	0	0	1	0	0	0	15834	884	31	1	516	1	TFCP2	12	51497497	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54678	51497497	82354398	8063	16048										
BIN2	51411	broad.mit.edu	37	chr12	51690946	51690946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtcacatagcagccaataCgactattaggaagcaaaacc	8	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51690946C>T	ENST00000267012.4	-	8	666	c.605G>A	c.(604-606)cGt>cAt	p.R202H	BIN2_ENST00000604560.1_Missense_Mutation_p.R175H|BIN2_ENST00000544402.1_Missense_Mutation_p.R176H|BIN2_ENST00000452142.2_Missense_Mutation_p.R170H	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	202	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)	p.R202H(1)		NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						GCAGCCAATACGACTATTAGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											97	86	90					12																	51690946		2203	4300	6503	49977213	SO:0001583	missense	51411			AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.605G>A	12.37:g.51690946C>T	ENSP00000267012:p.Arg202His		49977213	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	CCDS8811.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669160	0.88348	.	.	ENSG00000110934	ENST00000452142;ENST00000267012;ENST00000544402	T;T;T	0.64803	-0.12;-0.12;-0.12	4.78	3.89	0.44902	BAR (3);	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	M	0.86651	2.83	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.83734	0.0200	10	0.87932	D	0	-5.6463	12.4407	0.55623	0.0:0.9168:0.0:0.0832	.	176;170;202	F5H0W4;Q9UBW5-2;Q9UBW5	.;.;BIN2_HUMAN	H	170;202;176	ENSP00000410217:R170H;ENSP00000267012:R202H;ENSP00000445874:R176H	ENSP00000267012:R202H	R	-	2	0	BIN2	49977213	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.248000	0.78268	1.381000	0.46364	0.557000	0.71058	CGT		0.438	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1			T	51690946	C	T	51690946	3	4	61	1	0	0	0	0	1	0	0	0	1434	536	19	1	1116	1	BIN2	12	51690946	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	193449	51690946	82160949	8064	16049										
GALNT6	11226	broad.mit.edu	37	chr12	51773511	51773511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaggaagagcacaaaggCgcagcccaccatggccaggc	14	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51773511C>T	ENST00000543196.2	-	2	260	c.55G>A	c.(55-57)Gcc>Acc	p.A19T	GALNT6_ENST00000603203.1_5'Flank|GALNT6_ENST00000356317.3_Missense_Mutation_p.A19T			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	19					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A19T(1)		endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						AGCACAAAGGCGCAGCCCACC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											32	35	34					12																	51773511		2203	4300	6503	50059778	SO:0001583	missense	11226			Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.55G>A	12.37:g.51773511C>T	ENSP00000444171:p.Ala19Thr		50059778	Q8IYH4|Q9H6G2|Q9UIV5	Missense_Mutation	SNP	ENST00000543196.2	37	CCDS8813.1	.	.	.	.	.	.	.	.	.	.	C	9.976	1.226881	0.22542	.	.	ENSG00000139629	ENST00000543196;ENST00000356317;ENST00000546163	T;T	0.29655	1.56;1.56	4.52	1.74	0.24563	.	0.378318	0.30383	N	0.009760	T	0.16428	0.0395	N	0.11427	0.14	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.18967	-1.0320	10	0.38643	T	0.18	.	12.7228	0.57152	0.0:0.8403:0.0:0.1597	.	19	Q8NCL4	GALT6_HUMAN	T	19	ENSP00000444171:A19T;ENSP00000348668:A19T	ENSP00000348668:A19T	A	-	1	0	GALNT6	50059778	0.001000	0.12720	0.430000	0.26722	0.758000	0.43043	-0.127000	0.10547	0.410000	0.25675	-0.940000	0.02684	GCC		0.632	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		T	51773511	C	T	51773511	3	4	61	1	0	0	0	0	1	0	0	0	6237	768	27	1	1853	1	GALNT6	12	51773511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82565	51773511	82078384	8065	16050										
SLC4A8	9498	broad.mit.edu	37	chr12	51851155	51851155	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgatcctggatcagcaaGaactgtccagtgacctgaat	9	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51851155G>T	ENST00000453097.2	+	6	812	c.595G>T	c.(595-597)Gaa>Taa	p.E199*	SLC4A8_ENST00000535225.2_Nonsense_Mutation_p.E146*|SLC4A8_ENST00000394856.1_Nonsense_Mutation_p.E146*|SLC4A8_ENST00000514353.3_Nonsense_Mutation_p.E146*|SLC4A8_ENST00000358657.3_Nonsense_Mutation_p.E226*	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.E146*(1)|p.E199*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		GGATCAGCAAGAACTGTCCAG	0.468																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											107	94	98					12																	51851155		2203	4300	6503	50137422	SO:0001587	stop_gained	9498			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.595G>T	12.37:g.51851155G>T	ENSP00000405812:p.Glu199*		50137422		Nonsense_Mutation	SNP	ENST00000453097.2	37	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	G	37	6.394359	0.97533	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	.	.	.	5.29	5.29	0.74685	.	0.142257	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.8094	0.85715	0.0:0.0:1.0:0.0	.	.	.	.	X	146;226;199;146;199;146;146;146	.	ENSP00000315789:E199X	E	+	1	0	SLC4A8	50137422	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.705000	0.74644	2.635000	0.89317	0.655000	0.94253	GAA		0.468	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51851155	G	T	51851155	4	4	61	1	0	0	0	0	0	1	0	0	14696	943	33	2	617	2	SLC4A8	12	51851155	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77644	51851155	82000740	8066	16051										
SLC4A8	9498	broad.mit.edu	37	chr12	51851238	51851238	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatcatcagaatgaaaaGaagagaaacaacctcattcc	5	10	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51851238G>T	ENST00000453097.2	+	6	895	c.678G>T	c.(676-678)aaG>aaT	p.K226N	SLC4A8_ENST00000535225.2_Missense_Mutation_p.K173N|SLC4A8_ENST00000394856.1_Missense_Mutation_p.K173N|SLC4A8_ENST00000514353.3_Missense_Mutation_p.K173N|SLC4A8_ENST00000358657.3_Missense_Mutation_p.K253N	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.K173N(1)|p.K226N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AGAATGAAAAGAAGAGAAACA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	12											165	146	152					12																	51851238		2203	4300	6503	50137505	SO:0001583	missense	9498			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.678G>T	12.37:g.51851238G>T	ENSP00000405812:p.Lys226Asn		50137505		Missense_Mutation	SNP	ENST00000453097.2	37	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.621134	0.87460	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.29	4.37	0.52481	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.089250	0.85682	D	0.000000	T	0.70605	0.3243	M	0.63428	1.95	0.58432	D	0.999991	P;B;B;B;B;P;P	0.51147	0.942;0.077;0.174;0.024;0.038;0.469;0.627	P;B;B;B;B;B;B	0.51079	0.658;0.069;0.106;0.049;0.238;0.315;0.17	T	0.73433	-0.3984	10	0.66056	D	0.02	.	11.2712	0.49140	0.0939:0.0:0.9061:0.0	.	173;253;173;226;226;226;173	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6;F8VSA8	.;.;.;S4A8_HUMAN;.;.;.	N	173;253;226;173;226;173;173;173	ENSP00000441520:K173N;ENSP00000351483:K253N;ENSP00000405812:K226N;ENSP00000378325:K173N;ENSP00000442561:K173N	ENSP00000315789:K226N	K	+	3	2	SLC4A8	50137505	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.400000	0.44504	1.299000	0.44798	0.655000	0.94253	AAG		0.433	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51851238	G	T	51851238	3	4	61	1	0	0	0	0	1	0	0	0	14696	933	33	2	700	2	SLC4A8	12	51851238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83	51851238	82000657	8067	16052										
SLC4A8	9498	broad.mit.edu	37	chr12	51856209	51856209	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtgggatccctccattaGaattgagccacccaaaaatg	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:51856209G>T	ENST00000453097.2	+	10	1434	c.1217G>T	c.(1216-1218)aGa>aTa	p.R406I	SLC4A8_ENST00000535225.2_Missense_Mutation_p.R353I|SLC4A8_ENST00000394856.1_Missense_Mutation_p.R353I|SLC4A8_ENST00000514353.3_Missense_Mutation_p.R353I|SLC4A8_ENST00000358657.3_Missense_Mutation_p.R433I	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.R406I(1)|p.R353I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		CCCTCCATTAGAATTGAGCCA	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	12											97	91	93					12																	51856209		2203	4300	6503	50142476	SO:0001583	missense	9498			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1217G>T	12.37:g.51856209G>T	ENSP00000405812:p.Arg406Ile		50142476		Missense_Mutation	SNP	ENST00000453097.2	37	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	G	33	5.282272	0.95489	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000551071	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35	5.33	5.33	0.75918	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.91998	0.7465	M	0.91140	3.18	0.80722	D	1	D;P;P;P;D;P	0.71674	0.998;0.69;0.951;0.82;0.971;0.887	D;P;P;P;P;D	0.78314	0.991;0.508;0.784;0.852;0.891;0.929	D	0.93136	0.6537	10	0.87932	D	0	.	18.6579	0.91460	0.0:0.0:1.0:0.0	.	353;433;353;406;406;406	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6	.;.;.;S4A8_HUMAN;.;.	I	353;433;406;353;406;353;353	ENSP00000441520:R353I;ENSP00000351483:R433I;ENSP00000405812:R406I;ENSP00000378325:R353I;ENSP00000442561:R353I	ENSP00000315789:R406I	R	+	2	0	SLC4A8	50142476	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.809000	0.99208	2.866000	0.98385	0.650000	0.86243	AGA		0.502	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51856209	G	T	51856209	3	4	61	1	0	0	0	0	1	0	0	0	14696	942	33	2	1255	2	SLC4A8	12	51856209	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4971	51856209	81995686	8068	16053										
SCN8A	6334	broad.mit.edu	37	chr12	52156381	52156381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttggaacatttttgacgGatttattgtctccctcagtt	9	7	2	1	rs368457455		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52156381G>A	ENST00000354534.6	+	15	2643	c.2465G>A	c.(2464-2466)gGa>gAa	p.G822E	SCN8A_ENST00000550891.1_Missense_Mutation_p.G822E|SCN8A_ENST00000545061.1_Missense_Mutation_p.G822E	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	822					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.G822E(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	ATTTTTGACGGATTTATTGTC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	12											159	158	159					12																	52156381		1892	4142	6034	50442648	SO:0001583	missense	6334			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.2465G>A	12.37:g.52156381G>A	ENSP00000346534:p.Gly822Glu		50442648	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930636	0.73327	.	.	ENSG00000196876	ENST00000550891;ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94	4.23	4.23	0.50019	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98738	0.9576	M	0.77712	2.385	0.80722	D	1	D;D;D	0.69078	0.995;0.992;0.997	P;P;D	0.68039	0.889;0.774;0.955	D	0.99110	1.0846	10	0.59425	D	0.04	.	17.9135	0.88942	0.0:0.0:1.0:0.0	.	822;822;822	F8VWM7;F8VRN5;Q9UQD0	.;.;SCN8A_HUMAN	E	822;822;822;822;735	ENSP00000448415:G822E;ENSP00000346534:G822E;ENSP00000440360:G822E;ENSP00000347255:G822E	ENSP00000346534:G822E	G	+	2	0	SCN8A	50442648	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.601000	0.98297	2.632000	0.89209	0.455000	0.32223	GGA		0.413	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52156381	G	A	52156381	3	1	61	1	0	0	0	0	1	0	0	0	13961	1174	41	3	2519	3	SCN8A	12	52156381	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	300172	52156381	81695514	8069	16054										
SCN8A	6334	broad.mit.edu	37	chr12	52200541	52200541	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatctctttcctaattgtCgtgaacatgtacattgccat	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52200541C>T	ENST00000354534.6	+	27	5449	c.5271C>T	c.(5269-5271)gtC>gtT	p.V1757V	RP11-923I11.3_ENST00000565518.1_lincRNA|SCN8A_ENST00000545061.1_Silent_p.V1716V	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1757					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.V1757V(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	TCCTAATTGTCGTGAACATGT	0.463																																																2	Substitution - coding silent(2)	large_intestine(2)	12											131	139	136					12																	52200541		2198	4300	6498	50486808	SO:0001819	synonymous_variant	6334			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.5271C>T	12.37:g.52200541C>T			50486808	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																				0.463	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		T	52200541	C	T	52200541	2	4	61	1	0	0	0	0	0	0	0	1	13961	871	31	1		1	SCN8A	12	52200541	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44160	52200541	81651354	8070	16055										
KRT7	3855	broad.mit.edu	37	chr12	52636858	52636858	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccggaatacccggaatgaGatttcagagatgaaccgggc	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52636858G>T	ENST00000331817.5	+	6	1104	c.921G>T	c.(919-921)gaG>gaT	p.E307D	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	307	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.E307D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	CCCGGAATGAGATTTCAGAGA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											76	70	72					12																	52636858		2203	4300	6503	50923125	SO:0001583	missense	3855				CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"-", "Intermediate filaments type II, keratins (basic)"	6445	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 7", "cytokeratin 7", "sarcolectin", "keratin, 55K type II cytoskeletal"	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.921G>T	12.37:g.52636858G>T	ENSP00000329243:p.Glu307Asp		50923125	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	37	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.619297	0.66787	.	.	ENSG00000135480	ENST00000331817;ENST00000422319;ENST00000551537	D	0.92752	-3.1	3.94	3.94	0.45596	Prefoldin (1);Filament (1);	0.000000	0.38326	N	0.001737	D	0.93851	0.8033	M	0.89534	3.04	0.54753	D	0.999986	B;P	0.41546	0.349;0.754	P;B	0.44860	0.462;0.4	D	0.94873	0.8032	10	0.87932	D	0	.	12.2178	0.54416	0.0865:0.0:0.9135:0.0	.	307;307	F8VZY5;P08729	.;K2C7_HUMAN	D	307;283;307	ENSP00000329243:E307D	ENSP00000329243:E307D	E	+	3	2	KRT7	50923125	1.000000	0.71417	0.986000	0.45419	0.764000	0.43329	2.733000	0.47360	2.219000	0.72066	0.561000	0.74099	GAG		0.577	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		T	52636858	G	T	52636858	3	4	61	1	0	0	0	0	1	0	0	0	8504	933	33	2	943	2	KRT7	12	52636858	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436317	52636858	81215037	8071	16056										
KRT84	3890	broad.mit.edu	37	chr12	52776228	52776228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaaccctcacctccatgTaaagcgtttttagaaagtca	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52776228T>C	ENST00000257951.3	-	4	971	c.905A>G	c.(904-906)tAc>tGc	p.Y302C	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	302	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.Y302C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CACCTCCATGTAAAGCGTTTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											126	108	114					12																	52776228		2203	4300	6503	51062495	SO:0001583	missense	3890			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.905A>G	12.37:g.52776228T>C	ENSP00000257951:p.Tyr302Cys		51062495	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.238065	0.39598	.	.	ENSG00000161849	ENST00000257951	D	0.90261	-2.64	4.34	3.16	0.36331	Filament (1);	0.183599	0.26887	N	0.021997	D	0.94932	0.8361	M	0.90369	3.11	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	D	0.87827	0.2642	10	0.87932	D	0	.	6.7566	0.23518	0.1499:0.0:0.1563:0.6938	.	302	Q9NSB2	KRT84_HUMAN	C	302	ENSP00000257951:Y302C	ENSP00000257951:Y302C	Y	-	2	0	KRT84	51062495	1.000000	0.71417	0.003000	0.11579	0.784000	0.44337	5.403000	0.66338	0.784000	0.33661	0.533000	0.62120	TAC		0.453	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		C	52776228	T	C	52776228	3	2	61	1	0	0	0	0	1	0	0	0	8519	1638	57	4	921	4	KRT84	12	52776228	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	139370	52776228	81075667	8072	16057										
KRT84	3890	broad.mit.edu	37	chr12	52777552	52777552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctccacttggtctctaGgagcttattctgctgctcta	9	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52777552G>T	ENST00000257951.3	-	2	643	c.577C>A	c.(577-579)Cta>Ata	p.L193I	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	193	Coil 1A.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.L193I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TTGGTCTCTAGGAGCTTATTC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											68	68	68					12																	52777552		2203	4300	6503	51063819	SO:0001583	missense	3890			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.577C>A	12.37:g.52777552G>T	ENSP00000257951:p.Leu193Ile		51063819	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228328	0.58777	.	.	ENSG00000161849	ENST00000257951	D	0.95307	-3.67	5.32	0.209	0.15226	Filament (1);	0.000000	0.39020	N	0.001493	D	0.97498	0.9181	H	0.95504	3.68	0.33239	D	0.557001	D	0.76494	0.999	D	0.91635	0.999	D	0.97148	0.9829	10	0.87932	D	0	.	9.9637	0.41712	0.3444:0.0:0.6556:0.0	.	193	Q9NSB2	KRT84_HUMAN	I	193	ENSP00000257951:L193I	ENSP00000257951:L193I	L	-	1	2	KRT84	51063819	1.000000	0.71417	0.309000	0.25155	0.558000	0.35554	4.734000	0.62043	-0.048000	0.13401	-0.345000	0.07892	CTA		0.498	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		T	52777552	G	T	52777552	3	4	61	1	0	0	0	0	1	0	0	0	8519	991	35	2	1257	2	KRT84	12	52777552	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1324	52777552	81074343	8073	16058										
KRT84	3890	broad.mit.edu	37	chr12	52779051	52779051	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccactgccagctccaaAgcccagaccaacacagctgt	7	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52779051A>C	ENST00000257951.3	-	1	385	c.319T>G	c.(319-321)Ttt>Gtt	p.F107V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	107	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.F107V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAGCTCCAAAGCCCAGACCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12											183	171	175					12																	52779051		2203	4300	6503	51065318	SO:0001583	missense	3890			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.319T>G	12.37:g.52779051A>C	ENSP00000257951:p.Phe107Val		51065318	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.337101	0.24253	.	.	ENSG00000161849	ENST00000257951	T	0.80909	-1.43	5.01	5.01	0.66863	.	0.262503	0.27710	N	0.018170	T	0.75781	0.3896	L	0.56280	1.765	0.09310	N	1	B	0.23442	0.085	B	0.19666	0.026	T	0.61931	-0.6961	10	0.21540	T	0.41	.	15.189	0.73028	1.0:0.0:0.0:0.0	.	107	Q9NSB2	KRT84_HUMAN	V	107	ENSP00000257951:F107V	ENSP00000257951:F107V	F	-	1	0	KRT84	51065318	0.422000	0.25473	0.425000	0.26659	0.007000	0.05969	1.746000	0.38288	2.230000	0.72887	0.496000	0.49642	TTT		0.587	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		C	52779051	A	C	52779051	3	2	61	1	0	0	0	0	1	0	0	0	8519	72	3	4	1519	4	KRT84	12	52779051	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1499	52779051	81072844	8074	16059										
KRT75	9119	broad.mit.edu	37	chr12	52822462	52822462	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatgcggttcatttcagaGatctcttgtttggtgtttcg	10	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52822462G>T	ENST00000252245.5	-	6	1321	c.1101C>A	c.(1099-1101)atC>atA	p.I367I	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	367	Coil 2.|Rod.		I -> V (in dbSNP:rs2232402).		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.I367I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TCATTTCAGAGATCTCTTGTT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	12											193	158	170					12																	52822462		2203	4300	6503	51108729	SO:0001819	synonymous_variant	9119			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1101C>A	12.37:g.52822462G>T			51108729	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																				0.512	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		T	52822462	G	T	52822462	2	4	61	1	0	0	0	0	0	0	0	1	8509	932	33	2		2	KRT75	12	52822462	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43411	52822462	81029433	8075	16060										
KRT6A	3853	broad.mit.edu	37	chr12	52881633	52881633	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactgaagccacctccaacGccaagaccactgccatagga	8	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52881633G>A	ENST00000330722.6	-	9	1634	c.1566C>T	c.(1564-1566)ggC>ggT	p.G522G		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	522	Tail.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.G522G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACCTCCAACGCCAAGACCAC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	12											87	96	93					12																	52881633		2203	4300	6503	51167900	SO:0001819	synonymous_variant	3853			BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.1566C>T	12.37:g.52881633G>A			51167900	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																				0.612	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		A	52881633	G	A	52881633	2	1	61	1	0	0	0	0	0	0	0	1	8501	1074	38	1		1	KRT6A	12	52881633	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59171	52881633	80970262	8076	16061										
KRT5	3852	broad.mit.edu	37	chr12	52913636	52913636	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggttgaggggagtcaggaGactctggttgacagtgacct	16	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52913636G>T	ENST00000252242.4	-	1	835	c.445C>A	c.(445-447)Ctc>Atc	p.L149I		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	149	Head.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.L149I(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGAGTCAGGAGACTCTGGTTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12											176	165	169					12																	52913636		2203	4300	6503	51199903	SO:0001583	missense	3852				CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.445C>A	12.37:g.52913636G>T	ENSP00000252242:p.Leu149Ile		51199903	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668075	0.88348	.	.	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000549420;ENST00000551275	D;T;D	0.91996	-2.95;-1.06;-2.95	5.53	4.64	0.57946	.	0.000000	0.51477	D	0.000092	D	0.96651	0.8907	M	0.91717	3.235	0.41445	D	0.987944	D	0.89917	1.0	D	0.91635	0.999	D	0.97475	1.0043	10	0.87932	D	0	.	13.859	0.63548	0.0742:0.0:0.9258:0.0	.	149	P13647	K2C5_HUMAN	I	149;114;39;114	ENSP00000252242:L149I;ENSP00000447209:L39I;ENSP00000448041:L114I	ENSP00000252242:L149I	L	-	1	0	KRT5	51199903	.	.	0.544000	0.28141	0.997000	0.91878	.	.	1.336000	0.45506	0.563000	0.77884	CTC		0.592	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			T	52913636	G	T	52913636	3	4	61	1	0	0	0	0	1	0	0	0	8500	942	33	2	1363	2	KRT5	12	52913636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32003	52913636	80938259	8077	16062										
KRT5	3852	broad.mit.edu	37	chr12	52913943	52913943	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgcaaggctgaccctgccGaagccaccaccaccgccacc	8	22	0	1	rs201458850	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52913943G>A	ENST00000252242.4	-	1	528	c.138C>T	c.(136-138)ttC>ttT	p.F46F		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	46	Gly-rich.|Head.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.F46F(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGACCCTGCCGAAGCCACCAC	0.652													G|||	2	0.000399361	0	0	5008	,	,		15824	0.001		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											35	48	44					12																	52913943		2203	4294	6497	51200210	SO:0001819	synonymous_variant	3852				CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.138C>T	12.37:g.52913943G>A			51200210	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																				0.652	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			A	52913943	G	A	52913943	2	1	61	1	0	0	0	0	0	0	0	1	8500	1049	37	1		1	KRT5	12	52913943	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	307	52913943	80937952	8078	16063										
KRT71	112802	broad.mit.edu	37	chr12	52941659	52941659	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgcttcttcacgttctcGatctctgagcggattctctg	8	13	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52941659G>A	ENST00000267119.5	-	6	1155	c.1086C>T	c.(1084-1086)atC>atT	p.I362I		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	362	Coil 2.|Rod.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.I362I(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		TCACGTTCTCGATCTCTGAGC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	12											189	182	184					12																	52941659		2203	4300	6503	51227926	SO:0001819	synonymous_variant	112802			AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"-", "Intermediate filaments type II, keratins (basic)"	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.1086C>T	12.37:g.52941659G>A			51227926	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																				0.562	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		A	52941659	G	A	52941659	2	1	61	1	0	0	0	0	0	0	0	1	8505	1048	37	1		1	KRT71	12	52941659	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27716	52941659	80910236	8079	16064										
KRT74	121391	broad.mit.edu	37	chr12	52967109	52967109	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttgtcaatgaaggaggcGaacttgtcgttcagcacctt	10	10	2	1	rs531125952		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:52967109G>A	ENST00000305620.2	-	1	500	c.453C>T	c.(451-453)ttC>ttT	p.F151F	KRT74_ENST00000549343.1_Silent_p.F151F	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	151	Coil 1A.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)	p.F151F(1)		kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		TGAAGGAGGCGAACTTGTCGT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	12											125	116	119					12																	52967109		2203	4300	6503	51253376	SO:0001819	synonymous_variant	121391			BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"-", "Intermediate filaments type II, keratins (basic)"	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.453C>T	12.37:g.52967109G>A			51253376	B5MD61|Q86Y45	Silent	SNP	ENST00000305620.2	37	CCDS8832.1																																																																																				0.592	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053		A	52967109	G	A	52967109	2	1	61	1	0	0	0	0	0	0	0	1	8508	1049	37	1		1	KRT74	12	52967109	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25450	52967109	80884786	8080	16065										
KRT73	319101	broad.mit.edu	37	chr12	53005048	53005048	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagacgggtcagctctgaGatctcatttttggtgtgttt	12	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53005048G>A	ENST00000305748.3	-	6	1084	c.1050C>T	c.(1048-1050)atC>atT	p.I350I	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	350	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.I350I(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCAGCTCTGAGATCTCATTTT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	12											165	139	148					12																	53005048		2203	4300	6503	51291315	SO:0001819	synonymous_variant	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.1050C>T	12.37:g.53005048G>A			51291315	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																				0.527	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		A	53005048	G	A	53005048	2	1	61	1	0	0	0	0	0	0	0	1	8507	932	33	3		3	KRT73	12	53005048	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37939	53005048	80846847	8081	16066										
KRT1	3848	broad.mit.edu	37	chr12	53071971	53071971	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatggtcacaaattcattCtctgcatttgtccgcttgtt	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53071971C>A	ENST00000252244.3	-	3	901	c.843G>T	c.(841-843)gaG>gaT	p.E281D		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	281	Coil 1B.|Rod.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.E281E(1)|p.E281D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CAAATTCATTCTCTGCATTTG	0.403																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	12											156	125	135					12																	53071971		2203	4300	6503	51358238	SO:0001583	missense	3848			X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.843G>T	12.37:g.53071971C>A	ENSP00000252244:p.Glu281Asp		51358238	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.907262	0.72868	.	.	ENSG00000167768	ENST00000252244	D	0.94330	-3.4	5.17	2.27	0.28462	Filament (1);	.	.	.	.	D	0.97235	0.9096	H	0.96333	3.805	0.34284	D	0.682432	D	0.89917	1.0	D	0.97110	1.0	D	0.96904	0.9662	9	0.87932	D	0	.	8.2714	0.31846	0.0:0.6035:0.0:0.3965	.	281	P04264	K2C1_HUMAN	D	281	ENSP00000252244:E281D	ENSP00000252244:E281D	E	-	3	2	KRT1	51358238	0.987000	0.35691	1.000000	0.80357	0.999000	0.98932	0.349000	0.20055	0.256000	0.21614	0.655000	0.94253	GAG		0.403	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53071971	C	A	53071971	3	1	61	1	0	0	0	0	1	0	0	0	8468	912	32	2	1119	2	KRT1	12	53071971	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66923	53071971	80779924	8082	16067										
KRT3	3850	broad.mit.edu	37	chr12	53189607	53189607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcctccagcccgggagcCgccagctgccacgctgatgg	13	16	0	1	rs557308178		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53189607C>A	ENST00000417996.2	-	1	294	c.220G>T	c.(220-222)Ggc>Tgc	p.G74C	KRT3_ENST00000309505.3_Missense_Mutation_p.G74C	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	74	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.G74C(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						GCCCGGGAGCCGCCAGCTGCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											72	99	90					12																	53189607		2203	4300	6503	51475874	SO:0001583	missense	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.220G>T	12.37:g.53189607C>A	ENSP00000413479:p.Gly74Cys		51475874	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	c	10.48	1.362238	0.24684	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.95554	-3.74;-3.74	4.98	2.07	0.26955	.	0.140616	0.32901	N	0.005512	D	0.91479	0.7310	L	0.58354	1.805	0.30672	N	0.75331	B	0.24483	0.104	B	0.24269	0.052	D	0.85108	0.0961	10	0.45353	T	0.12	.	3.1397	0.06451	0.1431:0.5648:0.1385:0.1535	.	74	P12035	K2C3_HUMAN	C	74	ENSP00000413479:G74C;ENSP00000312206:G74C	ENSP00000312206:G74C	G	-	1	0	KRT3	51475874	0.811000	0.29063	0.927000	0.36925	0.625000	0.37756	1.848000	0.39309	0.209000	0.20645	-0.300000	0.09419	GGC		0.652	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53189607	C	A	53189607	3	1	61	1	0	0	0	0	1	0	0	0	8487	652	23	2	1702	2	KRT3	12	53189607	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117636	53189607	80662288	8083	16068										
KRT79	338785	broad.mit.edu	37	chr12	53227866	53227866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccccaagttatagaggcttCggctgccaaagccacctgtg	10	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53227866C>T	ENST00000330553.5	-	1	213	c.179G>A	c.(178-180)cGa>cAa	p.R60Q		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	60	Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)	p.R60Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ATAGAGGCTTCGGCTGCCAAA	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	12											24	31	29					12																	53227866		2191	4283	6474	51514133	SO:0001583	missense	338785			AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.179G>A	12.37:g.53227866C>T	ENSP00000328358:p.Arg60Gln		51514133	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.601071	0.46423	.	.	ENSG00000185640	ENST00000330553	T	0.42900	0.96	4.22	2.32	0.28847	.	0.360362	0.20805	N	0.085354	T	0.34077	0.0885	L	0.58810	1.83	0.28616	N	0.908436	B	0.33748	0.423	B	0.25405	0.06	T	0.30679	-0.9970	10	0.62326	D	0.03	.	9.3387	0.38067	0.0:0.8088:0.0:0.1912	.	60	Q5XKE5	K2C79_HUMAN	Q	60	ENSP00000328358:R60Q	ENSP00000328358:R60Q	R	-	2	0	KRT79	51514133	0.005000	0.15991	0.999000	0.59377	0.980000	0.70556	1.053000	0.30442	0.679000	0.31345	0.655000	0.94253	CGA		0.662	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		T	53227866	C	T	53227866	3	4	61	1	0	0	0	0	1	0	0	0	8513	884	31	1	1464	1	KRT79	12	53227866	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38259	53227866	80624029	8084	16069										
KRT78	196374	broad.mit.edu	37	chr12	53237996	53237996	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcagacacctgaagttCctggtactgagaggggaaca	14	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53237996C>A	ENST00000304620.4	-	6	991	c.928G>T	c.(928-930)Gaa>Taa	p.E310*	KRT78_ENST00000359499.4_Nonsense_Mutation_p.E200*	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	310	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.E310*(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						ACCTGAAGTTCCTGGTACTGA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											137	125	129					12																	53237996		2203	4300	6503	51524263	SO:0001587	stop_gained	196374			AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"-", "Intermediate filaments type II, keratins (basic)"	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.928G>T	12.37:g.53237996C>A	ENSP00000306261:p.Glu310*		51524263	A8K4D6|Q5HYM7|Q7RTT2	Nonsense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.095878	0.36952	.	.	ENSG00000170423	ENST00000359499;ENST00000304620;ENST00000539860	.	.	.	4.54	3.63	0.41609	.	0.333140	0.17355	N	0.177261	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.2924	0.54825	0.0:0.828:0.172:0.0	.	.	.	.	X	200;310;81	.	ENSP00000306261:E310X	E	-	1	0	KRT78	51524263	0.999000	0.42202	1.000000	0.80357	0.047000	0.14425	1.415000	0.34748	1.197000	0.43143	0.558000	0.71614	GAA		0.507	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352		A	53237996	C	A	53237996	4	1	61	1	0	0	0	0	0	1	0	0	8512	864	30	2	650	2	KRT78	12	53237996	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10130	53237996	80613899	8085	16070										
EIF4B	1975	broad.mit.edu	37	chr12	53412779	53412779	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcaattaaggaattctttCgaggattaaatgtaagtgta	9	3	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53412779C>T	ENST00000262056.9	+	3	675	c.349C>T	c.(349-351)Cga>Tga	p.R117*	EIF4B_ENST00000551527.1_3'UTR|EIF4B_ENST00000416762.3_Nonsense_Mutation_p.R117*|RP11-983P16.4_ENST00000549388.1_RNA|RP11-983P16.4_ENST00000552905.1_RNA|EIF4B_ENST00000420463.3_Nonsense_Mutation_p.R117*	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	117	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)	p.R117*(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						GGAATTCTTTCGAGGATTAAA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											40	37	38					12																	53412779		1809	4072	5881	51699046	SO:0001587	stop_gained	1975			X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.349C>T	12.37:g.53412779C>T	ENSP00000262056:p.Arg117*		51699046	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Nonsense_Mutation	SNP	ENST00000262056.9	37	CCDS41788.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.734160	0.89482	.	.	ENSG00000063046	ENST00000262056;ENST00000551002;ENST00000420463;ENST00000430205;ENST00000416762;ENST00000549481;ENST00000552490	.	.	.	4.78	2.22	0.28083	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9775	0.47475	0.6183:0.3817:0.0:0.0	.	.	.	.	X	117;71;117;117;117;117;117	.	ENSP00000262056:R117X	R	+	1	2	EIF4B	51699046	0.997000	0.39634	1.000000	0.80357	0.897000	0.52465	1.715000	0.37971	0.921000	0.36994	-0.335000	0.08231	CGA		0.368	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		T	53412779	C	T	53412779	4	4	61	1	0	0	0	0	0	1	0	0	5040	876	31	1	359	1	EIF4B	12	53412779	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174783	53412779	80439116	8086	16071										
TENC1	23371	broad.mit.edu	37	chr12	53454966	53454966	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggaccctggggcccagaGcaggcatcatcgccagccag	13	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53454966G>A	ENST00000314250.6	+	20	3566	c.3276G>A	c.(3274-3276)gaG>gaA	p.E1092E	TENC1_ENST00000552570.1_Silent_p.E1092E|TENC1_ENST00000546602.1_Silent_p.E995E|TENC1_ENST00000379902.3_Silent_p.E968E|TENC1_ENST00000549700.1_Silent_p.E1027E|TENC1_ENST00000314276.3_Silent_p.E1102E|TENC1_ENST00000451358.1_Silent_p.E1082E	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1092	Pro-rich.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.E1092E(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						GGGGCCCAGAGCAGGCATCAT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	12											55	67	63					12																	53454966		2203	4299	6502	51741233	SO:0001819	synonymous_variant	23371			AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.3276G>A	12.37:g.53454966G>A			51741233	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	37	CCDS8843.1																																																																																				0.617	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		A	53454966	G	A	53454966	2	1	61	1	0	0	0	0	0	0	0	1	15797	962	34	3		3	TENC1	12	53454966	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42187	53454966	80396929	8087	16072										
CSAD	51380	broad.mit.edu	37	chr12	53552392	53552392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccacacggaagaagttgCcccgggtcccgtggggctgg	15	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53552392C>T	ENST00000444623.1	-	17	1652	c.1385G>A	c.(1384-1386)gGc>gAc	p.G462D	CSAD_ENST00000267085.4_Missense_Mutation_p.G489D|CSAD_ENST00000379843.3_Missense_Mutation_p.G315D|CSAD_ENST00000379846.1_Missense_Mutation_p.G315D|RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000453446.2_Missense_Mutation_p.G462D	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	462					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)	p.G462D(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	GAAGAAGTTGCCCCGGGTCCC	0.612																																					Ovarian(109;252 1546 16882 28524 44645)											1	Substitution - Missense(1)	large_intestine(1)	12											80	61	67					12																	53552392		2203	4300	6503	51838659	SO:0001583	missense	51380			AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1385G>A	12.37:g.53552392C>T	ENSP00000415485:p.Gly462Asp		51838659	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	37	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286700	0.23478	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	4.49	-3.72	0.04411	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.777054	0.11752	N	0.532902	T	0.35068	0.0919	M	0.66297	2.02	0.50813	D	0.999893	B;B;P	0.35894	0.367;0.117;0.526	B;B;B	0.31245	0.08;0.037;0.126	T	0.38394	-0.9663	10	0.39692	T	0.17	-2.9217	11.5724	0.50841	0.2818:0.1482:0.57:0.0	.	489;462;315	Q9Y600-3;Q9Y600;Q9Y600-2	.;CSAD_HUMAN;.	D	551;315;489;315;462;423;462	ENSP00000369172:G315D;ENSP00000267085:G489D;ENSP00000369175:G315D;ENSP00000415485:G462D;ENSP00000410648:G462D	ENSP00000267085:G489D	G	-	2	0	CSAD	51838659	0.877000	0.30153	0.425000	0.26659	0.198000	0.23893	0.331000	0.19733	-0.403000	0.07622	0.442000	0.29010	GGC		0.612	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		T	53552392	C	T	53552392	3	4	61	1	0	0	0	0	1	0	0	0	3931	739	26	3	100	3	CSAD	12	53552392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97426	53552392	80299503	8088	16073										
AAAS	8086	broad.mit.edu	37	chr12	53701481	53701481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcgggatgtgggcaattCggcctgtggaccagccctgc	15	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53701481C>T	ENST00000209873.4	-	16	1598	c.1433G>A	c.(1432-1434)cGa>cAa	p.R478Q	AAAS_ENST00000394384.3_Missense_Mutation_p.R445Q|AAAS_ENST00000550286.1_Missense_Mutation_p.R354Q|AAAS_ENST00000549983.1_5'Flank	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	478					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)		p.R478Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						GTGGGCAATTCGGCCTGTGGA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											77	77	77					12																	53701481		2202	4300	6502	51987748	SO:0001583	missense	8086			AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"WD repeat domain containing"	13666	protein-coding gene	gene with protein product	"aladin", "Allgrove, triple-A"	605378	"achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.1433G>A	12.37:g.53701481C>T	ENSP00000209873:p.Arg478Gln		51987748	Q5JB47|Q9NWI6|Q9UG19	Missense_Mutation	SNP	ENST00000209873.4	37	CCDS8856.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592810	0.86953	.	.	ENSG00000094914	ENST00000209873;ENST00000394384;ENST00000550286	D;D;D	0.84298	-1.83;-1.66;-1.78	4.49	4.49	0.54785	.	0.139179	0.47852	D	0.000201	T	0.80737	0.4680	N	0.24115	0.695	0.47994	D	0.999567	D;D	0.67145	0.996;0.99	P;P	0.48921	0.595;0.551	T	0.82116	-0.0616	10	0.45353	T	0.12	-5.5162	15.0872	0.72165	0.0:1.0:0.0:0.0	.	445;478	Q5JB47;Q9NRG9	.;AAAS_HUMAN	Q	478;445;354	ENSP00000209873:R478Q;ENSP00000377908:R445Q;ENSP00000446885:R354Q	ENSP00000209873:R478Q	R	-	2	0	AAAS	51987748	0.569000	0.26643	0.992000	0.48379	0.998000	0.95712	0.887000	0.28254	2.504000	0.84457	0.655000	0.94253	CGA		0.602	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405632.1			T	53701481	C	T	53701481	3	4	61	1	0	0	0	0	1	0	0	0	8	884	31	1	211	1	AAAS	12	53701481	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149089	53701481	80150414	8089	16074										
SP7	121340	broad.mit.edu	37	chr12	53722275	53722275	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggcctctcgcctgtgtgCcagcgcaagtgggccttcag	14	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53722275C>T	ENST00000536324.2	-	3	1234	c.951G>A	c.(949-951)tgG>tgA	p.W317*	SP7_ENST00000537210.2_Nonsense_Mutation_p.W299*|SP7_ENST00000303846.3_Nonsense_Mutation_p.W317*	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	317					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W317*(1)		cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						CGCCTGTGTGCCAGCGCAAGT	0.637																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											49	55	53					12																	53722275		2203	4300	6503	52008542	SO:0001587	stop_gained	121340			AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.951G>A	12.37:g.53722275C>T	ENSP00000443827:p.Trp317*		52008542	B3KY26|Q3MJ72|Q7Z718	Nonsense_Mutation	SNP	ENST00000536324.2	37	CCDS44897.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149243	0.94645	.	.	ENSG00000170374	ENST00000536324;ENST00000303846;ENST00000537210	.	.	.	4.33	4.33	0.51752	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4596	0.84032	0.0:1.0:0.0:0.0	.	.	.	.	X	317;317;299	.	ENSP00000302812:W317X	W	-	3	0	SP7	52008542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.754000	0.85163	2.344000	0.79699	0.491000	0.48974	TGG		0.637	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53722275	C	T	53722275	4	4	61	1	0	0	0	0	0	1	0	0	15006	740	26	3	348	3	SP7	12	53722275	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20794	53722275	80129620	8090	16075										
MAP3K12	7786	broad.mit.edu	37	chr12	53878118	53878118	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgcagcaggatctgtcGgaatgatgggcgatttcgtg	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:53878118G>A	ENST00000267079.2	-	8	1297	c.1072C>T	c.(1072-1074)Cga>Tga	p.R358*	MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547488.1_Nonsense_Mutation_p.R391*|MAP3K12_ENST00000547035.1_Nonsense_Mutation_p.R391*	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	358	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.R358*(1)		NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						AGGATCTGTCGGAATGATGGG	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											168	115	133					12																	53878118		2203	4300	6503	52164385	SO:0001587	stop_gained	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1072C>T	12.37:g.53878118G>A	ENSP00000267079:p.Arg358*		52164385	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Nonsense_Mutation	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	G	38	6.771929	0.97825	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	.	.	.	5.27	4.26	0.50523	.	0.000000	0.34268	N	0.004105	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.441	0.67318	0.0:0.0:0.818:0.182	.	.	.	.	X	358;391;391	.	ENSP00000267079:R358X	R	-	1	2	MAP3K12	52164385	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.461000	0.45040	2.653000	0.90120	0.561000	0.74099	CGA		0.493	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		A	53878118	G	A	53878118	4	1	61	1	0	0	0	0	0	1	0	0	9276	1124	39	1	1539	1	MAP3K12	12	53878118	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155843	53878118	79973777	8091	16076										
ATP5G2	517	broad.mit.edu	37	chr12	54063039	54063039	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaacttggctgctgtgtcGatgtcccttgaaatggcgct	12	9	0	2	rs371876915		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54063039G>A	ENST00000549164.1	-	4	391	c.204C>T	c.(202-204)atC>atT	p.I68I	ATP5G2_ENST00000550241.1_5'Flank|ATP5G2_ENST00000338662.5_Silent_p.I84I|ATP5G2_ENST00000602871.1_Silent_p.I68I|ATP5G2_ENST00000394349.3_Silent_p.I125I			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	68					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.I84I(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						CTGCTGTGTCGATGTCCCTTG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	12						G	,	0,4406		0,0,2203	67	63	64		252,375	-8.8	0.2	12		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATP5G2	NM_001002031.2,NM_005176.5	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	84/158,125/199	54063039	1,13005	2203	4300	6503	52349306	SO:0001819	synonymous_variant	517			X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	842	protein-coding gene	gene with protein product		603193	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.204C>T	12.37:g.54063039G>A			52349306	B3KQQ6	Silent	SNP	ENST00000549164.1	37																																																																																					0.552	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176		A	54063039	G	A	54063039	2	1	61	1	0	0	0	0	0	0	0	1	1155	1048	37	1		1	ATP5G2	12	54063039	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184921	54063039	79788856	8092	16077										
HOXC13	3229	broad.mit.edu	37	chr12	54339018	54339018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggtcagcaaatcgaaagCgcctcatctccactccacct	8	15	3	0	rs201149022	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54339018C>T	ENST00000243056.3	+	2	1127	c.971C>T	c.(970-972)gCg>gTg	p.A324V		NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	324					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|hair follicle development (GO:0001942)|nail development (GO:0035878)|tongue morphogenesis (GO:0043587)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.A324V(1)		breast(1)|large_intestine(1)|skin(1)	3						AAATCGAAAGCGCCTCATCTC	0.582			T	NUP98	AML								C|||	2	0.000399361	0	0	5008	,	,		13896	0.002		0	False		,,,				2504	0						Dom	yes		12	12q13.3	3229	homeo box C13		L	1	Substitution - Missense(1)	large_intestine(1)	12											71	71	71					12																	54339018		2203	4300	6503	52625285	SO:0001583	missense	3229				CCDS8865.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123364	ENSG00000123364		"Homeoboxes / ANTP class : HOXL subclass"	5125	protein-coding gene	gene with protein product		142976	"homeo box C13"	HOX3, HOX3G		1973146, 1358459	Standard	NM_017410		Approved		uc001sei.3	P31276	OTTHUMG00000160008	ENST00000243056.3:c.971C>T	12.37:g.54339018C>T	ENSP00000243056:p.Ala324Val		52625285	Q5BL02|Q96J32|Q9NR24|Q9NYD5	Missense_Mutation	SNP	ENST00000243056.3	37	CCDS8865.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	18.84	3.709081	0.68615	.	.	ENSG00000123364	ENST00000243056	D	0.93366	-3.21	5.1	5.1	0.69264	Homeodomain-like (1);	0.390431	0.26627	N	0.023334	D	0.89143	0.6631	L	0.34521	1.04	0.38510	D	0.948454	B	0.30211	0.273	B	0.17098	0.017	D	0.88582	0.3137	10	0.62326	D	0.03	.	17.8201	0.88648	0.0:1.0:0.0:0.0	.	324	P31276	HXC13_HUMAN	V	324	ENSP00000243056:A324V	ENSP00000243056:A324V	A	+	2	0	HOXC13	52625285	0.899000	0.30636	1.000000	0.80357	0.997000	0.91878	5.481000	0.66826	2.825000	0.97269	0.655000	0.94253	GCG		0.582	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			T	54339018	C	T	54339018	3	4	61	1	0	0	0	0	1	0	0	0	7333	768	27	1	977	1	HOXC13	12	54339018	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	275979	54339018	79512877	8093	16078										
HOXC10	3226	broad.mit.edu	37	chr12	54379432	54379432	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccgaggcagctctctactCccaccccttgccggagtcct	8	20	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54379432C>A	ENST00000303460.4	+	1	463	c.389C>A	c.(388-390)tCc>tAc	p.S130Y	HOXC-AS3_ENST00000567780.1_RNA|HOXC-AS3_ENST00000514702.1_RNA|RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000513165.1_RNA|HOXC-AS3_ENST00000509870.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	130					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.S130Y(1)		endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						GCTCTCTACTCCCACCCCTTG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	12											39	40	40					12																	54379432		2203	4300	6503	52665699	SO:0001583	missense	3226				CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.389C>A	12.37:g.54379432C>A	ENSP00000307321:p.Ser130Tyr		52665699	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	37	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169658	0.38315	.	.	ENSG00000180818	ENST00000515593;ENST00000303460	D	0.92397	-3.03	4.45	4.45	0.53987	.	0.297521	0.38548	N	0.001660	D	0.84790	0.5550	L	0.34521	1.04	0.42219	D	0.991841	B	0.27656	0.184	B	0.09377	0.004	T	0.81293	-0.0998	10	0.05833	T	0.94	.	16.2355	0.82371	0.0:1.0:0.0:0.0	.	130	Q9NYD6	HXC10_HUMAN	Y	18;130	ENSP00000307321:S130Y	ENSP00000307321:S130Y	S	+	2	0	HOXC10	52665699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.066000	0.41452	2.199000	0.70637	0.505000	0.49811	TCC		0.642	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			A	54379432	C	A	54379432	3	1	61	1	0	0	0	0	1	0	0	0	7330	855	30	2	391	2	HOXC10	12	54379432	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40414	54379432	79472463	8094	16079										
HOXC4	3221	broad.mit.edu	37	chr12	54447806	54447806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctacatccctgaacacagtCcggaatattacggccggacc	9	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54447806C>A	ENST00000430889.2	+	1	146	c.100C>A	c.(100-102)Ccg>Acg	p.P34T	HOXC4_ENST00000303406.4_Missense_Mutation_p.P34T|HOXC4_ENST00000609810.1_Missense_Mutation_p.P34T	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	34					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P34T(1)		cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						TGAACACAGTCCGGAATATTA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											129	134	133					12																	54447806		2203	4300	6503	52734073	SO:0001583	missense	3221				CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.100C>A	12.37:g.54447806C>A	ENSP00000399808:p.Pro34Thr		52734073		Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.871962	0.51695	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.84944	-1.92;-1.92	3.41	3.41	0.39046	.	0.299133	0.30538	N	0.009411	D	0.82291	0.5005	L	0.56340	1.77	0.58432	D	0.999997	P	0.51791	0.948	B	0.43082	0.407	D	0.83824	0.0248	10	0.42905	T	0.14	.	14.7795	0.69754	0.0:1.0:0.0:0.0	.	34	P09017	HXC4_HUMAN	T	34	ENSP00000305973:P34T;ENSP00000399808:P34T	ENSP00000305973:P34T	P	+	1	0	HOXC4	52734073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.798000	0.38814	2.187000	0.69744	0.462000	0.41574	CCG		0.517	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447806	C	A	54447806	3	1	61	1	0	0	0	0	1	0	0	0	7334	855	30	2	102	2	HOXC4	12	54447806	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68374	54447806	79404089	8095	16080										
SMUG1	23583	broad.mit.edu	37	chr12	54577615	54577615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcagctcagcattgagcCgaagctcctcctccaggaag	11	14	2	1	rs376491349		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54577615C>T	ENST00000508394.2	-	2	172	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	SMUG1_ENST00000243112.5_Missense_Mutation_p.R37Q|SMUG1_ENST00000506595.1_Missense_Mutation_p.R37Q|SMUG1_ENST00000513838.1_Missense_Mutation_p.R37Q|SMUG1_ENST00000401977.2_Missense_Mutation_p.R37Q|SMUG1_ENST00000514685.1_Missense_Mutation_p.R37Q|SMUG1_ENST00000337581.3_Missense_Mutation_p.R37Q|SMUG1_ENST00000514196.1_Missense_Mutation_p.R37Q|SMUG1_ENST00000505128.1_Missense_Mutation_p.R37Q|SMUG1_ENST00000505662.1_5'UTR	NM_001243787.1|NM_001243788.1|NM_014311.2	NP_001230716.1|NP_001230717.1|NP_055126.1	Q53HV7	SMUG1_HUMAN	single-strand-selective monofunctional uracil-DNA glycosylase 1	37					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA N-glycosylase activity (GO:0019104)|oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity (GO:0000703)|single-strand selective uracil DNA N-glycosylase activity (GO:0017065)|uracil DNA N-glycosylase activity (GO:0004844)	p.R37Q(1)		kidney(1)|large_intestine(4)|lung(1)	6						AGCATTGAGCCGAAGCTCCTC	0.597								Base excision repair (BER), DNA glycosylases																																								1	Substitution - Missense(1)	large_intestine(1)	12						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	53	47	49		110	4	1	12		49	0,8600		0,0,4300	no	missense	SMUG1	NM_014311.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	37/271	54577615	1,13005	2203	4300	6503	52863882	SO:0001583	missense	23583			AF125182	CCDS8874.1, CCDS58239.1	12q13.13	2013-10-28			ENSG00000123415	ENSG00000123415			17148	protein-coding gene	gene with protein product		607753				10074426, 11526119	Standard	NM_014311		Approved	UNG3, FDG, HMUDG	uc009znf.2	Q53HV7	OTTHUMG00000160068	ENST00000508394.2:c.110G>A	12.37:g.54577615C>T	ENSP00000424191:p.Arg37Gln		52863882	A8K2K9|O95862|Q0D2M0|Q8NB71|Q9BWC8	Missense_Mutation	SNP	ENST00000508394.2	37	CCDS8874.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.226290	0.39300	2.27E-4	0.0	ENSG00000123415	ENST00000506595;ENST00000514685;ENST00000505128;ENST00000337581;ENST00000508394;ENST00000513838;ENST00000243112;ENST00000401977;ENST00000514196;ENST00000504338;ENST00000507904;ENST00000503447;ENST00000504797;ENST00000506169;ENST00000503306	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	4.85	3.96	0.45880	Uracil-DNA glycosylase-like (2);	0.195941	0.44688	D	0.000426	T	0.41190	0.1148	L	0.48642	1.525	0.30799	N	0.740033	P;D;B	0.71674	0.763;0.998;0.239	B;P;B	0.54312	0.044;0.748;0.034	T	0.40232	-0.9574	10	0.22706	T	0.39	.	4.6936	0.12793	0.1737:0.6491:0.0:0.1772	.	37;37;37	Q53HV7;D6RAI1;Q53HV7-2	SMUG1_HUMAN;.;.	Q	37	ENSP00000421206:R37Q;ENSP00000421139:R37Q;ENSP00000421894:R37Q;ENSP00000338606:R37Q;ENSP00000424191:R37Q;ENSP00000423629:R37Q;ENSP00000243112:R37Q;ENSP00000384828:R37Q;ENSP00000425974:R37Q;ENSP00000423083:R37Q;ENSP00000423457:R37Q;ENSP00000421790:R37Q;ENSP00000427547:R37Q;ENSP00000425426:R37Q	ENSP00000243112:R37Q	R	-	2	0	SMUG1	52863882	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	1.648000	0.37271	1.402000	0.46780	0.591000	0.81541	CGG		0.597	SMUG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359074.3	NM_014311		T	54577615	C	T	54577615	3	4	61	1	0	0	0	0	1	0	0	0	14855	652	23	1	710	1	SMUG1	12	54577615	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	129809	54577615	79274280	8096	16081										
GPR84	53831	broad.mit.edu	37	chr12	54756701	54756701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcaccttcccaaattccGatgaagaatccggagctctt	8	12	2	2	rs139990475		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54756701G>A	ENST00000551809.1	-	1	1570	c.935C>T	c.(934-936)tCg>tTg	p.S312L	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|GPR84_ENST00000267015.3_Missense_Mutation_p.S312L			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.S312L(1)		NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						CCCAAATTCCGATGAAGAATC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	LEU/SER	3,4403	6.2+/-15.9	0,3,2200	133	134	134		935	4.8	0	12	dbSNP_134	134	0,8600		0,0,4300	yes	missense	GPR84	NM_020370.2	145	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	312/397	54756701	3,13003	2203	4300	6503	53042968	SO:0001583	missense	53831			AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.935C>T	12.37:g.54756701G>A	ENSP00000450310:p.Ser312Leu		53042968	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	37	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	G	9.462	1.093319	0.20471	6.81E-4	0.0	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.38887	1.11;1.11	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.324438	0.24879	N	0.034869	T	0.37348	0.1000	L	0.45228	1.405	0.09310	N	0.999998	D	0.53745	0.962	B	0.42495	0.389	T	0.30208	-0.9986	10	0.29301	T	0.29	-1.0246	15.6317	0.76917	0.0:0.0:1.0:0.0	.	312	Q9NQS5	GPR84_HUMAN	L	312	ENSP00000267015:S312L;ENSP00000450310:S312L	ENSP00000267015:S312L	S	-	2	0	GPR84	53042968	0.981000	0.34729	0.033000	0.17914	0.094000	0.18550	4.869000	0.63028	2.359000	0.80004	0.561000	0.74099	TCG		0.502	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			A	54756701	G	A	54756701	3	1	61	1	0	0	0	0	1	0	0	0	6734	1059	37	1	259	1	GPR84	12	54756701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	179086	54756701	79095194	8097	16082										
GPR84	53831	broad.mit.edu	37	chr12	54757609	54757609	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagactcatggtagcaggaGaagttggcgtcagagctgtt	14	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54757609G>T	ENST00000551809.1	-	1	662	c.27C>A	c.(25-27)ttC>ttA	p.F9L	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|GPR84_ENST00000267015.3_Missense_Mutation_p.F9L			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.F9L(1)		NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						GGTAGCAGGAGAAGTTGGCGT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	67	76					12																	54757609		2203	4300	6503	53043876	SO:0001583	missense	53831			AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.27C>A	12.37:g.54757609G>T	ENSP00000450310:p.Phe9Leu		53043876	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	37	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.545822	0.45280	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.34667	1.35;1.35	4.81	1.78	0.24846	.	0.000000	0.64402	D	0.000001	T	0.37404	0.1002	L	0.29908	0.895	0.47094	D	0.999311	D	0.76494	0.999	D	0.78314	0.991	T	0.26155	-1.0111	10	0.10636	T	0.68	-27.1533	7.0545	0.25091	0.4184:0.0:0.5816:0.0	.	9	Q9NQS5	GPR84_HUMAN	L	9	ENSP00000267015:F9L;ENSP00000450310:F9L	ENSP00000267015:F9L	F	-	3	2	GPR84	53043876	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	1.753000	0.38359	0.233000	0.21120	0.555000	0.69702	TTC		0.527	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			T	54757609	G	T	54757609	3	4	61	1	0	0	0	0	1	0	0	0	6734	933	33	2	1167	2	GPR84	12	54757609	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	908	54757609	79094286	8098	16083										
ZNF385A	25946	broad.mit.edu	37	chr12	54769632	54769632	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttggcttcttacctgaGaattgaagcggatttgacag	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54769632G>T	ENST00000338010.5	-	3	307	c.254C>A	c.(253-255)tCt>tAt	p.S85Y	ZNF385A_ENST00000352268.6_Missense_Mutation_p.S85Y|ZNF385A_ENST00000551771.1_Missense_Mutation_p.S65Y|ZNF385A_ENST00000394313.2_Missense_Mutation_p.S65Y|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|ZNF385A_ENST00000546970.1_Missense_Mutation_p.S65Y|ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000551109.1_Missense_Mutation_p.S65Y	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	85					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S65Y(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						TCTTACCTGAGAATTGAAGCG	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	12											70	62	64					12																	54769632		2203	4300	6503	53055899	SO:0001583	missense	25946			AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"zinc finger protein 385"	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.254C>A	12.37:g.54769632G>T	ENSP00000338927:p.Ser85Tyr		53055899	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Missense_Mutation	SNP	ENST00000338010.5	37	CCDS44911.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227888	0.79576	.	.	ENSG00000161642	ENST00000551109;ENST00000352268;ENST00000394313;ENST00000338010;ENST00000546970;ENST00000551771;ENST00000546919;ENST00000549937;ENST00000547210;ENST00000550774	T;T;T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	3.68	3.68	0.42216	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.59972	0.2233	M	0.64170	1.965	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999	D;D;D;D;D	0.87578	0.996;0.991;0.996;0.998;0.998	T	0.64833	-0.6314	10	0.87932	D	0	-9.4009	13.2995	0.60317	0.0:0.0:1.0:0.0	.	65;65;65;65;65	Q96PM9-2;F8VSJ1;F8VRY0;Q96PM9;F1T0F1	.;.;.;Z385A_HUMAN;.	Y	65;85;65;85;65;65;65;47;65;65	ENSP00000449161:S65Y;ENSP00000293385:S85Y;ENSP00000377849:S65Y;ENSP00000338927:S85Y;ENSP00000446913:S65Y;ENSP00000447162:S65Y;ENSP00000448466:S65Y;ENSP00000448567:S47Y;ENSP00000448264:S65Y;ENSP00000449462:S65Y	ENSP00000338927:S85Y	S	-	2	0	ZNF385A	53055899	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.192000	0.94947	2.068000	0.61886	0.491000	0.48974	TCT		0.562	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481		T	54769632	G	T	54769632	3	4	61	1	0	0	0	0	1	0	0	0	17915	942	33	2	930	2	ZNF385A	12	54769632	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12023	54769632	79082263	8099	16084										
ITGA5	3678	broad.mit.edu	37	chr12	54794765	54794765	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctggctaatggagctgggGccttggttgatgagctgagg	17	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54794765G>A	ENST00000293379.4	-	25	2769	c.2508C>T	c.(2506-2508)ggC>ggT	p.G836G	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	836					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.G836G(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						TGGAGCTGGGGCCTTGGTTGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	12											68	61	64					12																	54794765		2203	4300	6503	53081032	SO:0001819	synonymous_variant	3678				CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.2508C>T	12.37:g.54794765G>A			53081032	Q96HA5	Silent	SNP	ENST00000293379.4	37	CCDS8880.1																																																																																				0.542	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			A	54794765	G	A	54794765	2	1	61	1	0	0	0	0	0	0	0	1	7900	1190	42	3		3	ITGA5	12	54794765	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25133	54794765	79057130	8100	16085										
ITGA5	3678	broad.mit.edu	37	chr12	54805673	54805673	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggctggcaccccaaggacaGaggtagacagcaccaccctg	13	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54805673G>T	ENST00000293379.4	-	2	555	c.294C>A	c.(292-294)ctC>ctA	p.L98L	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|ITGA5_ENST00000547744.1_5'Flank	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	98					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.L98L(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						CCCAAGGACAGAGGTAGACAG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	12											59	56	57					12																	54805673		2203	4300	6503	53091940	SO:0001819	synonymous_variant	3678				CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.294C>A	12.37:g.54805673G>T			53091940	Q96HA5	Silent	SNP	ENST00000293379.4	37	CCDS8880.1																																																																																				0.607	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			T	54805673	G	T	54805673	2	4	61	1	0	0	0	0	0	0	0	1	7900	929	33	2		2	ITGA5	12	54805673	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10908	54805673	79046222	8101	16086										
NCKAP1L	3071	broad.mit.edu	37	chr12	54894350	54894350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacatcgtgaaaaagccGagataattagattcctcacc	7	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54894350G>A	ENST00000293373.6	+	3	326	c.247G>A	c.(247-249)Gag>Aag	p.E83K	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.E33K|RP11-753H16.3_ENST00000550474.1_RNA	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	83					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)	p.E83K(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TGAAAAAGCCGAGATAATTAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											180	171	174					12																	54894350		2203	4300	6503	53180617	SO:0001583	missense	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.247G>A	12.37:g.54894350G>A	ENSP00000293373:p.Glu83Lys		53180617	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.558194	0.86231	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.34472	1.36;1.36	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.57036	0.2026	M	0.73598	2.24	0.58432	D	0.999997	D	0.69078	0.997	P	0.59424	0.857	T	0.61068	-0.7137	10	0.62326	D	0.03	-20.3422	16.5054	0.84271	0.0:0.0:1.0:0.0	.	83	P55160	NCKPL_HUMAN	K	83;33	ENSP00000293373:E83K;ENSP00000445596:E33K	ENSP00000293373:E83K	E	+	1	0	NCKAP1L	53180617	1.000000	0.71417	0.984000	0.44739	0.964000	0.63967	9.051000	0.93849	2.554000	0.86153	0.460000	0.39030	GAG		0.383	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		A	54894350	G	A	54894350	3	1	61	1	0	0	0	0	1	0	0	0	10253	1059	37	1	257	1	NCKAP1L	12	54894350	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88677	54894350	78957545	8102	16087										
NCKAP1L	3071	broad.mit.edu	37	chr12	54902257	54902257	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttctgtcacggattgaaGatcggcggatactcattggc	11	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54902257G>T	ENST00000293373.6	+	5	527	c.448G>T	c.(448-450)Gat>Tat	p.D150Y	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.D100Y	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	150					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)	p.D150Y(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						ACGGATTGAAGATCGGCGGAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											267	247	253					12																	54902257		2203	4300	6503	53188524	SO:0001583	missense	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.448G>T	12.37:g.54902257G>T	ENSP00000293373:p.Asp150Tyr		53188524	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014311	0.93404	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.37752	1.18;1.18	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.63943	0.2554	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.65948	-0.6044	10	0.87932	D	0	-16.5712	18.1531	0.89682	0.0:0.0:1.0:0.0	.	150	P55160	NCKPL_HUMAN	Y	150;100	ENSP00000293373:D150Y;ENSP00000445596:D100Y	ENSP00000293373:D150Y	D	+	1	0	NCKAP1L	53188524	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.490000	0.97952	2.885000	0.99019	0.655000	0.94253	GAT		0.418	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		T	54902257	G	T	54902257	3	4	61	1	0	0	0	0	1	0	0	0	10253	942	33	2	466	2	NCKAP1L	12	54902257	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7907	54902257	78949638	8103	16088										
PDE1B	5153	broad.mit.edu	37	chr12	54967393	54967393	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttttatgtccgctcagaGaactccgagccctggtcatt	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:54967393G>A	ENST00000243052.3	+	10	1400	c.964G>A	c.(964-966)Gaa>Aaa	p.E322K	PDE1B_ENST00000538346.1_Splice_Site_p.E281K|PDE1B_ENST00000550620.1_Splice_Site_p.E302K|PDE1B_ENST00000394277.3_3'UTR	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	322	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.E322K(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	TCCGCTCAGAGAACTCCGAGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	12											156	143	148					12																	54967393		2203	4300	6503	53253660	SO:0001630	splice_region_variant	5153			U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"Phosphodiesterases"	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.963-1G>A	12.37:g.54967393G>A			53253660	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	37	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331245	0.95733	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	T;T;T	0.81247	-1.47;-1.47;-1.47	5.1	5.1	0.69264	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.84234	0.5427	L	0.48642	1.525	0.80722	D	1	P;P	0.48016	0.883;0.904	P;P	0.56216	0.794;0.792	D	0.85409	0.1136	10	0.62326	D	0.03	.	16.4016	0.83642	0.0:0.0:1.0:0.0	.	302;322	Q01064-2;Q01064	.;PDE1B_HUMAN	K	322;281;302	ENSP00000243052:E322K;ENSP00000442559:E281K;ENSP00000448519:E302K	ENSP00000243052:E322K	E	+	1	0	PDE1B	53253660	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	7.896000	0.87350	2.549000	0.85964	0.561000	0.74099	GAA		0.522	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1		Missense_Mutation	A	54967393	G	A	54967393	5	1	61	1	0	0	0	0	0	0	1	0	11665	956	33	3	1055	3	PDE1B	12	54967393	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65136	54967393	78884502	8104	16089										
KIAA0748	9840	broad.mit.edu	37	chr12	55357630	55357630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagggggtggtgaaaaatCgggcgggtatccgagaagtg	20	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55357630C>T	ENST00000449076.1	-	8	683	c.551G>A	c.(550-552)cGa>cAa	p.R184Q	TESPA1_ENST00000531122.1_Missense_Mutation_p.R46Q|TESPA1_ENST00000532804.1_Missense_Mutation_p.R46Q|TESPA1_ENST00000316577.8_Missense_Mutation_p.R184Q|TESPA1_ENST00000524959.1_5'UTR|TESPA1_ENST00000524622.1_Missense_Mutation_p.R46Q	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	184					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R46Q(1)|p.R184Q(1)									GGTGAAAAATCGGGCGGGTAT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	12											116	120	119					12																	55357630		1893	4104	5997	53643897	SO:0001583	missense	9840			AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.551G>A	12.37:g.55357630C>T	ENSP00000400892:p.Arg184Gln		53643897	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	37	CCDS44913.1	.	.	.	.	.	.	.	.	.	.	C	35	5.421957	0.96111	.	.	ENSG00000135426	ENST00000524622;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000532757;ENST00000531122;ENST00000526532;ENST00000533446	T;T;T;T;T	0.76839	-1.05;-1.05;-0.39;-0.39;-1.05	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.87042	0.6079	M	0.68952	2.095	0.51482	D	0.999928	D	0.89917	1.0	D	0.91635	0.999	D	0.87774	0.2607	10	0.87932	D	0	-19.5321	17.0763	0.86587	0.0:1.0:0.0:0.0	.	184	A2RU30	K0748_HUMAN	Q	46;46;184;184;46;46;46;46	ENSP00000435622:R46Q;ENSP00000432030:R46Q;ENSP00000400892:R184Q;ENSP00000312679:R184Q;ENSP00000433098:R46Q	ENSP00000312679:R184Q	R	-	2	0	KIAA0748	53643897	0.991000	0.36638	0.998000	0.56505	0.969000	0.65631	6.989000	0.76219	2.821000	0.97095	0.561000	0.74099	CGA		0.517	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		T	55357630	C	T	55357630	3	4	61	1	0	0	0	0	1	0	0	0	8211	884	31	1	1026	1	KIAA0748	12	55357630	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	390237	55357630	78494265	8105	16090										
NEUROD4	58158	broad.mit.edu	37	chr12	55420451	55420451	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggtcccaagaaaaagaaGatgaccaaagctcgccttga	11	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55420451G>T	ENST00000242994.3	+	2	606	c.228G>T	c.(226-228)aaG>aaT	p.K76N		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	76					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K76N(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						AGAAAAAGAAGATGACCAAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	56	57					12																	55420451		2203	4300	6503	53706718	SO:0001583	missense	58158			AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.228G>T	12.37:g.55420451G>T	ENSP00000242994:p.Lys76Asn		53706718	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.007962	0.54361	.	.	ENSG00000123307	ENST00000242994	D	0.96232	-3.95	5.37	3.55	0.40652	.	0.000000	0.85682	D	0.000000	D	0.97021	0.9027	M	0.82716	2.605	0.52099	D	0.999947	D	0.71674	0.998	P	0.57425	0.82	D	0.96089	0.9060	10	0.87932	D	0	-13.4445	7.8856	0.29648	0.2529:0.0:0.7471:0.0	.	76	Q9HD90	NDF4_HUMAN	N	76	ENSP00000242994:K76N	ENSP00000242994:K76N	K	+	3	2	NEUROD4	53706718	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.808000	0.38912	0.771000	0.33359	-0.150000	0.13652	AAG		0.498	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			T	55420451	G	T	55420451	3	4	61	1	0	0	0	0	1	0	0	0	10381	933	33	2	230	2	NEUROD4	12	55420451	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62821	55420451	78431444	8106	16091										
NEUROD4	58158	broad.mit.edu	37	chr12	55420598	55420598	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacccaaaaactttccaaGatagagactcttagactggc	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55420598G>A	ENST00000242994.3	+	2	753	c.375G>A	c.(373-375)aaG>aaA	p.K125K		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	125	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K125K(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						AACTTTCCAAGATAGAGACTC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	12											81	85	84					12																	55420598		2203	4300	6503	53706865	SO:0001819	synonymous_variant	58158			AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.375G>A	12.37:g.55420598G>A			53706865	B2RAC9	Silent	SNP	ENST00000242994.3	37	CCDS8886.1																																																																																				0.498	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			A	55420598	G	A	55420598	2	1	61	1	0	0	0	0	0	0	0	1	10381	933	33	3		3	NEUROD4	12	55420598	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147	55420598	78431297	8107	16092										
NEUROD4	58158	broad.mit.edu	37	chr12	55421035	55421035	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaagcaagatgggtctcCtgacctagaaaaatcctaca	8	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55421035C>A	ENST00000242994.3	+	2	1190	c.812C>A	c.(811-813)cCt>cAt	p.P271H		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	271					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P271H(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						GATGGGTCTCCTGACCTAGAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	153	155					12																	55421035		2203	4300	6503	53707302	SO:0001583	missense	58158			AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.812C>A	12.37:g.55421035C>A	ENSP00000242994:p.Pro271His		53707302	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357545	0.82243	.	.	ENSG00000123307	ENST00000242994	D	0.96041	-3.89	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.97303	0.9118	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	D	0.97360	0.9969	10	0.72032	D	0.01	-11.168	18.0364	0.89305	0.0:1.0:0.0:0.0	.	271	Q9HD90	NDF4_HUMAN	H	271	ENSP00000242994:P271H	ENSP00000242994:P271H	P	+	2	0	NEUROD4	53707302	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.082000	0.71318	2.941000	0.99782	0.655000	0.94253	CCT		0.532	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			A	55421035	C	A	55421035	3	1	61	1	0	0	0	0	1	0	0	0	10381	681	24	2	814	2	NEUROD4	12	55421035	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	437	55421035	78430860	8108	16093										
OR6C6	283365	broad.mit.edu	37	chr12	55688836	55688836	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaaggagaaattacggaGaaagaaatacattggcgtct	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55688836G>T	ENST00000358433.2	-	1	180	c.181C>A	c.(181-183)Ctc>Atc	p.L61I		NM_001005493.1	NP_001005493.1	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C, member 6	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L61I(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						AAATTACGGAGAAAGAAATAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											68	71	70					12																	55688836		2203	4300	6503	53975103	SO:0001583	missense	283365				CCDS31817.1	12q13.13	2012-08-09			ENSG00000188324	ENSG00000188324		"GPCR / Class A : Olfactory receptors"	31293	protein-coding gene	gene with protein product							Standard	NM_001005493		Approved		uc010sph.2	A6NF89	OTTHUMG00000168101	ENST00000358433.2:c.181C>A	12.37:g.55688836G>T	ENSP00000351211:p.Leu61Ile		53975103		Missense_Mutation	SNP	ENST00000358433.2	37	CCDS31817.1	.	.	.	.	.	.	.	.	.	.	-	12.08	1.830366	0.32329	.	.	ENSG00000188324	ENST00000358433	T	0.13778	2.56	4.24	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41194	D	0.000924	T	0.35711	0.0941	M	0.83012	2.62	0.18873	N	0.999988	D	0.63046	0.992	P	0.62649	0.905	T	0.16305	-1.0407	10	0.87932	D	0	.	12.0973	0.53763	0.0869:0.0:0.9131:0.0	.	61	A6NF89	OR6C6_HUMAN	I	61	ENSP00000351211:L61I	ENSP00000351211:L61I	L	-	1	0	OR6C6	53975103	0.907000	0.30839	0.423000	0.26634	0.103000	0.19146	0.501000	0.22578	1.132000	0.42129	0.580000	0.79431	CTC		0.388	OR6C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398151.1			T	55688836	G	T	55688836	3	4	61	1	0	0	0	0	1	0	0	0	11225	942	33	2	765	2	OR6C6	12	55688836	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	267801	55688836	78163059	8109	16094										
OR6C6	283365	broad.mit.edu	37	chr12	55688976	55688976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtgggtcatctgtcaatCctaggagaatgaactctatt	9	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55688976C>T	ENST00000358433.2	-	1	40	c.41G>A	c.(40-42)gGa>gAa	p.G14E		NM_001005493.1	NP_001005493.1	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C, member 6	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G14E(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						ATCTGTCAATCCTAGGAGAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											107	107	107					12																	55688976		2203	4300	6503	53975243	SO:0001583	missense	283365				CCDS31817.1	12q13.13	2012-08-09			ENSG00000188324	ENSG00000188324		"GPCR / Class A : Olfactory receptors"	31293	protein-coding gene	gene with protein product							Standard	NM_001005493		Approved		uc010sph.2	A6NF89	OTTHUMG00000168101	ENST00000358433.2:c.41G>A	12.37:g.55688976C>T	ENSP00000351211:p.Gly14Glu		53975243		Missense_Mutation	SNP	ENST00000358433.2	37	CCDS31817.1	.	.	.	.	.	.	.	.	.	.	-	10.82	1.458965	0.26248	.	.	ENSG00000188324	ENST00000358433	T	0.02301	4.35	4.24	4.24	0.50183	.	0.000000	0.45867	D	0.000334	T	0.14960	0.0361	M	0.92784	3.345	0.38962	D	0.958562	D	0.64830	0.994	P	0.62382	0.901	T	0.02546	-1.1143	10	0.87932	D	0	.	13.7506	0.62906	0.0:0.8444:0.1556:0.0	.	14	A6NF89	OR6C6_HUMAN	E	14	ENSP00000351211:G14E	ENSP00000351211:G14E	G	-	2	0	OR6C6	53975243	0.247000	0.23920	0.110000	0.21437	0.011000	0.07611	1.173000	0.31920	2.359000	0.80004	0.580000	0.79431	GGA		0.348	OR6C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398151.1			T	55688976	C	T	55688976	3	4	61	1	0	0	0	0	1	0	0	0	11225	855	30	3	905	3	OR6C6	12	55688976	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140	55688976	78162919	8110	16095										
OR6C3	254786	broad.mit.edu	37	chr12	55726054	55726054	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatcttgttcagatacatgGctcctagaagtaattggttt	8	7	2	2	rs147847006	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55726054G>A	ENST00000379667.1	+	1	570	c.570G>A	c.(568-570)tgG>tgA	p.W190*		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	190					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W190*(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						CAGATACATGGCTCCTAGAAG	0.373													G|||	2	0.000399361	0	0	5008	,	,		21611	0.001		0.001	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	12											253	246	248					12																	55726054		2203	4300	6503	54012321	SO:0001587	stop_gained	254786			AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"GPCR / Class A : Olfactory receptors"	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.570G>A	12.37:g.55726054G>A	ENSP00000368989:p.Trp190*		54012321		Nonsense_Mutation	SNP	ENST00000379667.1	37	CCDS31819.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	7.958	0.746263	0.15710	.	.	ENSG00000205329	ENST00000379667	.	.	.	5.27	2.37	0.29283	.	0.494226	0.17235	N	0.181799	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	3.8498	0.08949	0.0764:0.313:0.3627:0.248	.	.	.	.	X	190	.	ENSP00000368989:W190X	W	+	3	0	OR6C3	54012321	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.590000	0.00899	0.421000	0.25980	0.650000	0.86243	TGG		0.373	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1			A	55726054	G	A	55726054	4	1	61	1	0	0	0	0	0	1	0	0	11223	1212	42	3	572	3	OR6C3	12	55726054	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37078	55726054	78125841	8111	16096										
OR6C2	341416	broad.mit.edu	37	chr12	55846219	55846219	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtctcatttactacagtCtgcattcccagattcttgta	6	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55846219C>A	ENST00000322678.1	+	1	222	c.222C>A	c.(220-222)gtC>gtA	p.V74V	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_054105.1	NP_473446.1	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C, member 2	74					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V74V(1)		kidney(2)|large_intestine(5)|lung(8)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	23						TTACTACAGTCTGCATTCCCA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	12											115	118	117					12																	55846219		2203	4300	6503	54132486	SO:0001819	synonymous_variant	341416			AF179766	CCDS31824.1	12q13.2	2012-08-09				ENSG00000179695		"GPCR / Class A : Olfactory receptors"	15436	protein-coding gene	gene with protein product							Standard	NM_054105		Approved	OR6C67	uc001sgz.1	Q9NZP2	OTTHUMG00000169957	ENST00000322678.1:c.222C>A	12.37:g.55846219C>A			54132486		Silent	SNP	ENST00000322678.1	37	CCDS31824.1																																																																																				0.373	OR6C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406676.1	NM_054105		A	55846219	C	A	55846219	2	1	61	1	0	0	0	0	0	0	0	1	11222	900	32	2		2	OR6C2	12	55846219	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120165	55846219	78005676	8112	16097										
OR6C70	390327	broad.mit.edu	37	chr12	55863008	55863008	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtctgaagcagaaaatatCtttctaaatacagctttgaa	6	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55863008C>A	ENST00000327335.4	-	1	914	c.915G>T	c.(913-915)aaG>aaT	p.K305N	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K305N(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						CAGAAAATATCTTTCTAAATA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	12											42	43	43					12																	55863008		2203	4299	6502	54149275	SO:0001583	missense	390327				CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"GPCR / Class A : Olfactory receptors"	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.915G>T	12.37:g.55863008C>A	ENSP00000329153:p.Lys305Asn		54149275		Missense_Mutation	SNP	ENST00000327335.4	37	CCDS31825.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.099271	0.37048	.	.	ENSG00000184954	ENST00000327335	T	0.38887	1.11	4.0	2.16	0.27623	.	0.256722	0.27482	N	0.019165	T	0.28466	0.0704	N	0.25957	0.775	0.09310	N	1	B	0.17268	0.021	B	0.17979	0.02	T	0.27331	-1.0077	10	0.87932	D	0	.	9.0748	0.36515	0.0:0.7921:0.0:0.2079	.	305	A6NIJ9	O6C70_HUMAN	N	305	ENSP00000329153:K305N	ENSP00000329153:K305N	K	-	3	2	OR6C70	54149275	0.001000	0.12720	0.001000	0.08648	0.539000	0.34962	0.207000	0.17395	0.499000	0.27970	0.633000	0.83428	AAG		0.313	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1			A	55863008	C	A	55863008	3	1	61	1	0	0	0	0	1	0	0	0	11228	912	32	2	25	2	OR6C70	12	55863008	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16789	55863008	77988887	8113	16098										
OR6C4	341418	broad.mit.edu	37	chr12	55945217	55945217	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttctccttcttagaaatTtccttcacatccatttttat	1	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55945217T>G	ENST00000394256.2	+	1	235	c.207T>G	c.(205-207)atT>atG	p.I69M	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I69M(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TCTTAGAAATTTCCTTCACAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	118	116					12																	55945217		2202	4300	6502	54231484	SO:0001583	missense	341418			BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.207T>G	12.37:g.55945217T>G	ENSP00000377799:p.Ile69Met		54231484	A8MZG7|B2RNN2|Q6IFK1	Missense_Mutation	SNP	ENST00000394256.2	37	CCDS31827.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.730142	0.30684	.	.	ENSG00000179626	ENST00000394256	T	0.04809	3.55	4.77	0.979	0.19745	GPCR, rhodopsin-like superfamily (1);	0.585977	0.15051	N	0.283339	T	0.05823	0.0152	L	0.59912	1.85	0.09310	N	1	B	0.28636	0.218	B	0.32149	0.141	T	0.33266	-0.9875	10	0.72032	D	0.01	.	3.3943	0.07300	0.1243:0.0755:0.256:0.5442	.	69	Q8NGE1	OR6C4_HUMAN	M	69	ENSP00000377799:I69M	ENSP00000377799:I69M	I	+	3	3	OR6C4	54231484	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	-1.039000	0.03550	0.353000	0.24079	0.524000	0.50904	ATT		0.413	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			G	55945217	T	G	55945217	3	3	61	1	0	0	0	0	1	0	0	0	11224	1829	64	4	209	4	OR6C4	12	55945217	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	82209	55945217	77906678	8114	16099										
OR6C4	341418	broad.mit.edu	37	chr12	55945508	55945508	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatgacccaggtagatttCtgtgtctccaacattctgaa	8	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:55945508C>T	ENST00000394256.2	+	1	526	c.498C>T	c.(496-498)ttC>ttT	p.F166F	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F166L(1)|p.F166F(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						AGGTAGATTTCTGTGTCTCCA	0.478																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	12											132	131	132					12																	55945508		2203	4300	6503	54231775	SO:0001819	synonymous_variant	341418			BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.498C>T	12.37:g.55945508C>T			54231775	A8MZG7|B2RNN2|Q6IFK1	Silent	SNP	ENST00000394256.2	37	CCDS31827.1																																																																																				0.478	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			T	55945508	C	T	55945508	2	4	61	1	0	0	0	0	0	0	0	1	11224	912	32	3		3	OR6C4	12	55945508	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	291	55945508	77906387	8115	16100										
METTL7B	196410	broad.mit.edu	37	chr12	56077829	56077829	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatgggaaaggctgtcaAataatctttcccaagctcca	7	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56077829A>C	ENST00000394252.3	+	2	940	c.731A>C	c.(730-732)aAa>aCa	p.K244T		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	244							methyltransferase activity (GO:0008168)	p.K194T(1)		kidney(1)|large_intestine(1)|lung(4)	6						AAGGCTGTCAAATAATCTTTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											79	68	72					12																	56077829		2203	4300	6503	54364096	SO:0001583	missense	196410				CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"associated with lipid droplets 1"					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.731A>C	12.37:g.56077829A>C	ENSP00000377796:p.Lys244Thr		54364096	A8K247|Q8WUI1	Missense_Mutation	SNP	ENST00000394252.3	37	CCDS8887.2	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943796	0.73672	.	.	ENSG00000170439	ENST00000394252	T	0.59083	0.29	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.79251	0.4414	M	0.92317	3.295	0.58432	D	0.999999	D	0.89917	1.0	D	0.75020	0.985	D	0.83710	0.0187	10	0.87932	D	0	-34.9058	11.205	0.48765	1.0:0.0:0.0:0.0	.	244	Q6UX53	MET7B_HUMAN	T	244	ENSP00000377796:K244T	ENSP00000377796:K244T	K	+	2	0	METTL7B	54364096	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	7.930000	0.87610	1.744000	0.51775	0.459000	0.35465	AAA		0.527	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637		C	56077829	A	C	56077829	3	2	61	1	0	0	0	0	1	0	0	0	9536	14	1	4	737	4	METTL7B	12	56077829	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	132321	56077829	77774066	8116	16101										
ITGA7	3679	broad.mit.edu	37	chr12	56087081	56087081	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagagcccagggttctgagCgactggccttggttggaaac	15	10	1	2	rs138301131		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56087081C>T	ENST00000555728.1	-	21	2716	c.2688G>A	c.(2686-2688)tcG>tcA	p.S896S	ITGA7_ENST00000257880.7_Silent_p.S896S|ITGA7_ENST00000394230.2_Silent_p.S856S|ITGA7_ENST00000452168.2_Silent_p.S759S|ITGA7_ENST00000553804.1_Silent_p.S856S|ITGA7_ENST00000347027.6_Silent_p.S846S|ITGA7_ENST00000394229.2_Silent_p.S852S|ITGA7_ENST00000257879.6_Silent_p.S852S			Q13683	ITA7_HUMAN	integrin, alpha 7	896					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.S852S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GGGTTCTGAGCGACTGGCCTT	0.468													C|||	1	0.000199681	0	0	5008	,	,		17004	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	12						C	,,	1,4405	2.1+/-5.4	0,1,2202	57	58	58		2568,2277,2556	-9.7	0.5	12	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGA7	NM_001144996.1,NM_001144997.1,NM_002206.2	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	856/1142,759/1045,852/1138	56087081	1,13005	2203	4300	6503	54373348	SO:0001819	synonymous_variant	3679				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2688G>A	12.37:g.56087081C>T			54373348	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																					0.468	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		T	56087081	C	T	56087081	2	4	61	1	0	0	0	0	0	0	0	1	7902	755	27	1		1	ITGA7	12	56087081	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9252	56087081	77764814	8117	16102										
DNAJC14	85406	broad.mit.edu	37	chr12	56221644	56221644	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgagatggccacaagtttCtacgtactctcccaccaata	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56221644C>A	ENST00000357606.3	-	3	1088	c.799G>T	c.(799-801)Gaa>Taa	p.E267*	TMEM198B_ENST00000478241.1_RNA|DNAJC14_ENST00000317287.5_Nonsense_Mutation_p.E267*|DNAJC14_ENST00000317269.3_Nonsense_Mutation_p.E267*|RP11-762I7.5_ENST00000546837.1_5'Flank			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	267					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.E267*(1)		breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						CCACAAGTTTCTACGTACTCT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											93	76	81					12																	56221644		2203	4300	6503	54507911	SO:0001587	stop_gained	85406			AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.799G>T	12.37:g.56221644C>A	ENSP00000350223:p.Glu267*		54507911	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Nonsense_Mutation	SNP	ENST00000357606.3	37	CCDS8894.1	.	.	.	.	.	.	.	.	.	.	C	39	7.849381	0.98525	.	.	ENSG00000135392	ENST00000357606;ENST00000317269;ENST00000317287	.	.	.	5.18	5.18	0.71444	.	0.198193	0.42682	D	0.000673	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.7301	16.5686	0.84605	0.0:1.0:0.0:0.0	.	.	.	.	X	267	.	.	E	-	1	0	DNAJC14	54507911	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	4.577000	0.60922	2.572000	0.86782	0.655000	0.94253	GAA		0.522	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		A	56221644	C	A	56221644	4	1	61	1	0	0	0	0	0	1	0	0	4644	922	32	2	1333	2	DNAJC14	12	56221644	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	134563	56221644	77630251	8118	16103										
MMP19	4327	broad.mit.edu	37	chr12	56233466	56233466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcccctcagtccagaactCgtcttcgtcgaagtgcacac	9	15	2	1	rs536616162		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56233466C>T	ENST00000322569.4	-	5	671	c.580G>A	c.(580-582)Gag>Aag	p.E194K	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000409200.3_Intron|MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000548629.1_Missense_Mutation_p.E171K	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	194					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E194K(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	GTCCAGAACTCGTCTTCGTCG	0.602													C|||	1	0.000199681	0	0.0014	5008	,	,		20234	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											81	61	67					12																	56233466		2203	4300	6503	54519733	SO:0001583	missense	4327			X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.580G>A	12.37:g.56233466C>T	ENSP00000313437:p.Glu194Lys		54519733	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	37	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105465	0.77096	.	.	ENSG00000123342	ENST00000322569;ENST00000548629	T;T	0.30714	1.52;1.52	5.22	5.22	0.72569	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.094766	0.64402	D	0.000001	T	0.62109	0.2401	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	T	0.69540	-0.5118	10	0.87932	D	0	.	17.7115	0.88323	0.0:1.0:0.0:0.0	.	194	Q99542	MMP19_HUMAN	K	194;171	ENSP00000313437:E194K;ENSP00000446979:E171K	ENSP00000313437:E194K	E	-	1	0	MMP19	54519733	1.000000	0.71417	0.998000	0.56505	0.067000	0.16453	7.288000	0.78691	2.721000	0.93114	0.511000	0.50034	GAG		0.602	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		T	56233466	C	T	56233466	3	4	61	1	0	0	0	0	1	0	0	0	9687	893	31	1	966	1	MMP19	12	56233466	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11822	56233466	77618429	8119	16104										
WIBG	84305	broad.mit.edu	37	chr12	56296005	56296005	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcctttcgcttcaggttaCgtttggctgtcttggagagg	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56296005C>T	ENST00000408946.2	-	3	417	c.266G>A	c.(265-267)cGt>cAt	p.R89H	WIBG_ENST00000547925.1_3'UTR|WIBG_ENST00000557259.1_3'UTR|WIBG_ENST00000398213.4_Missense_Mutation_p.R88H|WIBG_ENST00000302533.6_5'UTR	NM_032345.2	NP_115721.1	Q9BRP8	WIBG_HUMAN	within bgcn homolog (Drosophila)	89					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|exon-exon junction complex (GO:0035145)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.R89H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CTTCAGGTTACGTTTGGCTGT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											76	74	75					12																	56296005		1981	4162	6143	54582272	SO:0001583	missense	84305			BC014976	CCDS41795.1, CCDS44916.1	12q13.2	2008-02-05				ENSG00000170473			30258	protein-coding gene	gene with protein product						12438415, 12483225	Standard	NM_032345		Approved	PYM	uc001sif.1	Q9BRP8	OTTHUMG00000170220	ENST00000408946.2:c.266G>A	12.37:g.56296005C>T	ENSP00000386156:p.Arg89His		54582272	B6ZDM5|Q8IXJ8|Q8N8E7	Missense_Mutation	SNP	ENST00000408946.2	37	CCDS41795.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041020	0.55003	.	.	ENSG00000170473	ENST00000408946;ENST00000398213	T;T	0.34275	1.37;1.38	5.26	3.43	0.39272	.	0.105395	0.64402	D	0.000005	T	0.34513	0.0900	M	0.62723	1.935	0.80722	D	1	B;B	0.11235	0.004;0.001	B;B	0.08055	0.003;0.003	T	0.18272	-1.0342	10	0.66056	D	0.02	.	9.6866	0.40103	0.1408:0.784:0.0:0.0752	.	89;88	Q9BRP8;Q9BRP8-2	WIBG_HUMAN;.	H	89;88	ENSP00000386156:R89H;ENSP00000381271:R88H	ENSP00000381271:R88H	R	-	2	0	WIBG	54582272	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.822000	0.69265	0.719000	0.32188	0.655000	0.94253	CGT		0.582	WIBG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408079.1	NM_032345		T	56296005	C	T	56296005	3	4	61	1	0	0	0	0	1	0	0	0	17405	536	19	1	352	1	WIBG	12	56296005	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62539	56296005	77555890	8120	16105										
ESYT1	23344	broad.mit.edu	37	chr12	56537081	56537081	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctgtcaagtctaattcCtccttcatgtcaagagagcg	8	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56537081C>A	ENST00000394048.5	+	29	3453	c.3189C>A	c.(3187-3189)tcC>tcA	p.S1063S	ESYT1_ENST00000541590.1_Silent_p.S1073S|ESYT1_ENST00000267113.4_Silent_p.S1073S	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	1063	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.S1063S(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						AGTCTAATTCCTCCTTCATGT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	12											108	103	104					12																	56537081		2203	4300	6503	54823348	SO:0001819	synonymous_variant	23344			AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.3189C>A	12.37:g.56537081C>A			54823348	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Silent	SNP	ENST00000394048.5	37	CCDS8904.1																																																																																				0.567	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		A	56537081	C	A	56537081	2	1	61	1	0	0	0	0	0	0	0	1	5277	668	24	2		2	ESYT1	12	56537081	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241076	56537081	77314814	8121	16106										
SLC39A5	283375	broad.mit.edu	37	chr12	56630474	56630474	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagggtggcactgatatcaCgtggatggtcctcctgggag	15	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56630474C>T	ENST00000266980.4	+	8	1444	c.1151C>T	c.(1150-1152)aCg>aTg	p.T384M	SLC39A5_ENST00000419232.1_3'UTR|ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Missense_Mutation_p.T384M	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	384					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.T383M(1)		NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						ACTGATATCACGTGGATGGTC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	12											128	109	115					12																	56630474		2203	4300	6503	54916741	SO:0001583	missense	283375				CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"Solute carriers"	20502	protein-coding gene	gene with protein product		608730	"solute carrier family 39 (metal ion transporter), member 5"				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1151C>T	12.37:g.56630474C>T	ENSP00000266980:p.Thr384Met		54916741	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652237	0.47362	.	.	ENSG00000139540	ENST00000454355;ENST00000266980	T;T	0.49432	0.78;0.78	4.82	3.93	0.45458	.	0.296949	0.28853	N	0.013932	T	0.47414	0.1444	L	0.46157	1.445	0.32509	N	0.537799	D	0.53462	0.96	P	0.50270	0.636	T	0.60712	-0.7209	10	0.59425	D	0.04	-10.51	8.6797	0.34201	0.0:0.8242:0.0:0.1758	.	384	Q6ZMH5	S39A5_HUMAN	M	384	ENSP00000405360:T384M;ENSP00000266980:T384M	ENSP00000266980:T384M	T	+	2	0	SLC39A5	54916741	0.032000	0.19561	0.372000	0.25991	0.197000	0.23852	1.486000	0.35530	1.405000	0.46838	0.561000	0.74099	ACG		0.637	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		T	56630474	C	T	56630474	3	4	61	1	0	0	0	0	1	0	0	0	14658	536	19	1	1177	1	SLC39A5	12	56630474	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93393	56630474	77221421	8122	16107										
SLC39A5	283375	broad.mit.edu	37	chr12	56631497	56631497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaggagcggctactgccCgtgaccactgagggctgatg	16	11	0	3	rs150715610		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56631497C>T	ENST00000266980.4	+	11	1898	c.1605C>T	c.(1603-1605)ccC>ccT	p.P535P	SLC39A5_ENST00000419232.1_3'UTR|ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Silent_p.P535P	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	535					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.P534P(1)		NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGCTACTGCCCGTGACCACTG	0.677													C|||	1	0.000199681	8e-04	0	5008	,	,		14860	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	1,4401		0,1,2200	24	23	24		1605,1605	2.3	0.7	12	dbSNP_134	24	3,8593		0,3,4295	no	coding-synonymous,coding-synonymous	SLC39A5	NM_001135195.1,NM_173596.2	,	0,4,6495	TT,TC,CC		0.0349,0.0227,0.0308	,	535/541,535/541	56631497	4,12994	2201	4298	6499	54917764	SO:0001819	synonymous_variant	283375				CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"Solute carriers"	20502	protein-coding gene	gene with protein product		608730	"solute carrier family 39 (metal ion transporter), member 5"				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1605C>T	12.37:g.56631497C>T			54917764	B2R808|Q8N6Y3	Silent	SNP	ENST00000266980.4	37	CCDS8912.2																																																																																				0.677	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		T	56631497	C	T	56631497	2	4	61	1	0	0	0	0	0	0	0	1	14658	639	23	1		1	SLC39A5	12	56631497	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1023	56631497	77220398	8123	16108										
COQ10A	93058	broad.mit.edu	37	chr12	56663986	56663986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctggccaccatgttttTtgatgaggttgtcaaacaga	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56663986T>C	ENST00000308197.5	+	5	890	c.629T>C	c.(628-630)tTt>tCt	p.F210S	COQ10A_ENST00000546544.1_Missense_Mutation_p.F193S|COQ10A_ENST00000433805.2_Missense_Mutation_p.F178S|RP11-977G19.14_ENST00000546464.1_RNA	NM_144576.3	NP_653177.3	Q96MF6	CQ10A_HUMAN	coenzyme Q10 homolog A (S. cerevisiae)	210						mitochondrial inner membrane (GO:0005743)		p.F210S(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	8						ACCATGTTTTTTGATGAGGTT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	12											196	191	193					12																	56663986		1980	4143	6123	54950253	SO:0001583	missense	93058			AK057003	CCDS41796.1, CCDS44921.1	12q13.3	2011-09-16	2006-04-04		ENSG00000135469	ENSG00000135469			26515	protein-coding gene	gene with protein product			"coenzyme Q10 homolog A (yeast)"				Standard	NM_144576		Approved	FLJ32452	uc001sko.4	Q96MF6	OTTHUMG00000170283	ENST00000308197.5:c.629T>C	12.37:g.56663986T>C	ENSP00000312587:p.Phe210Ser		54950253	Q6GMR6|Q6UWB9|Q86X16|Q8TAL2|Q96MF1|Q9BUP4	Missense_Mutation	SNP	ENST00000308197.5	37	CCDS41796.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.712061	0.89112	.	.	ENSG00000135469	ENST00000308197;ENST00000433805;ENST00000546544	T;T;T	0.29397	1.57;1.61;1.59	4.96	4.96	0.65561	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.68168	-0.5480	10	0.87932	D	0	.	14.057	0.64776	0.0:0.0:0.0:1.0	.	193;215;210	Q96MF6-2;Q8TAL2;Q96MF6	.;.;CQ10A_HUMAN	S	210;178;193	ENSP00000312587:F210S;ENSP00000407843:F178S;ENSP00000446723:F193S	ENSP00000312587:F210S	F	+	2	0	COQ10A	54950253	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.548000	0.82154	2.217000	0.71921	0.533000	0.62120	TTT		0.488	COQ10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408332.1	NM_144576		C	56663986	T	C	56663986	3	2	61	1	0	0	0	0	1	0	0	0	3749	1841	64	4	689	4	COQ10A	12	56663986	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32489	56663986	77187909	8124	16109										
STAT2	6773	broad.mit.edu	37	chr12	56740375	56740375	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgactgcagcacctccttcGtgtacggttgcacagagtag	12	11	0	2	rs143059589		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56740375G>A	ENST00000314128.4	-	21	1918	c.1895C>T	c.(1894-1896)aCg>aTg	p.T632M	STAT2_ENST00000557235.1_Missense_Mutation_p.T628M|STAT2_ENST00000556539.1_5'UTR			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	632	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.T632M(1)		NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						CACCTCCTTCGTGTACGGTTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	MET/THR,MET/THR	0,4406		0,0,2203	91	77	82		1895,1883	5.7	1	12	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	STAT2	NM_005419.3,NM_198332.1	81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	632/852,628/848	56740375	1,13005	2203	4300	6503	55026642	SO:0001583	missense	6773			BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"SH2 domain containing"	11363	protein-coding gene	gene with protein product		600556	"signal transducer and activator of transcription 2, 113kD"			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1895C>T	12.37:g.56740375G>A	ENSP00000315768:p.Thr632Met		55026642	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595877	0.86953	0.0	1.16E-4	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.97378	-4.36;-4.36	5.71	5.71	0.89125	SH2 motif (4);	0.048701	0.85682	D	0.000000	D	0.98717	0.9569	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.961;1.0	D	0.99421	1.0933	10	0.87932	D	0	-17.8663	19.0174	0.92900	0.0:0.0:1.0:0.0	.	628;632	G3V2M6;P52630	.;STAT2_HUMAN	M	632;628	ENSP00000315768:T632M;ENSP00000450751:T628M	ENSP00000315768:T632M	T	-	2	0	STAT2	55026642	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	9.535000	0.98064	2.873000	0.98535	0.561000	0.74099	ACG		0.547	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419		A	56740375	G	A	56740375	3	1	61	1	0	0	0	0	1	0	0	0	15304	1145	40	1	676	1	STAT2	12	56740375	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76389	56740375	77111520	8125	16110										
SPRYD4	283377	broad.mit.edu	37	chr12	56862398	56862398	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgctgctttttgcacgttCtttgcgcttgtgccgctggg	14	11	1	0	rs148775301		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:56862398C>A	ENST00000338146.5	+	1	98	c.23C>A	c.(22-24)tCt>tAt	p.S8Y	MIP_ENST00000555551.1_Intron	NM_207344.3	NP_997227	Q8WW59	SPRY4_HUMAN	SPRY domain containing 4	8						mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S8Y(1)		kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)	7						TTTGCACGTTCTTTGCGCTTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	TYR/SER	0,4406		0,0,2203	145	132	136		23	2.5	0	12	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	missense	SPRYD4	NM_207344.3	144	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	8/208	56862398	1,13005	2203	4300	6503	55148665	SO:0001583	missense	283377			AL832247	CCDS8920.1	12q13.3	2006-03-09				ENSG00000176422			27468	protein-coding gene	gene with protein product							Standard	NM_207344		Approved	DKFZp686N0877	uc001sli.4	Q8WW59		ENST00000338146.5:c.23C>A	12.37:g.56862398C>A	ENSP00000338034:p.Ser8Tyr		55148665	A8K7A5	Missense_Mutation	SNP	ENST00000338146.5	37	CCDS8920.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.816796	0.32145	0.0	1.16E-4	ENSG00000176422	ENST00000338146	T	0.64803	-0.12	5.36	2.45	0.29901	.	0.952345	0.08818	N	0.889240	T	0.46464	0.1394	N	0.22421	0.69	0.09310	N	1	B	0.32693	0.38	B	0.31016	0.123	T	0.33599	-0.9862	10	0.49607	T	0.09	-0.0183	7.7856	0.29091	0.0:0.5897:0.3235:0.0868	.	8	Q8WW59	SPRY4_HUMAN	Y	8	ENSP00000338034:S8Y	ENSP00000338034:S8Y	S	+	2	0	SPRYD4	55148665	0.000000	0.05858	0.000000	0.03702	0.979000	0.70002	0.215000	0.17562	0.308000	0.22923	-0.300000	0.09419	TCT		0.572	SPRYD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_207344		A	56862398	C	A	56862398	3	1	61	1	0	0	0	0	1	0	0	0	15149	913	32	2	25	2	SPRYD4	12	56862398	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122023	56862398	76989497	8126	16111										
BAZ2A	11176	broad.mit.edu	37	chr12	57005692	57005692	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagttacgggagaggcttTtggggatgtcactgaagccg	17	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57005692T>G	ENST00000551812.1	-	6	1673	c.1480A>C	c.(1480-1482)Aaa>Caa	p.K494Q	BAZ2A_ENST00000179765.5_Missense_Mutation_p.K462Q|BAZ2A_ENST00000379441.3_Missense_Mutation_p.K464Q|BAZ2A_ENST00000549884.1_Missense_Mutation_p.K492Q	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	494					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K494Q(2)		breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GGAGAGGCTTTTGGGGATGTC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	12											49	52	51					12																	57005692		1944	4154	6098	55291959	SO:0001583	missense	11176			AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.1480A>C	12.37:g.57005692T>G	ENSP00000446880:p.Lys494Gln		55291959	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.244|8.244	0.807579|0.807579	0.16467|0.16467	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884|ENST00000551996	T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2|.	5.09|5.09	2.68|2.68	0.31781|0.31781	.|.	0.750279|.	0.12806|.	N|.	0.437571|.	T|T	0.10078|0.10078	0.0247|0.0247	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.09022|.	0.002;0.001|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.21793|0.21793	-1.0235|-1.0235	10|5	0.08599|.	T|.	0.76|.	.|.	1.5553|1.5553	0.02583|0.02583	0.1607:0.0959:0.2651:0.4783|0.1607:0.0959:0.2651:0.4783	.|.	492;494|.	F8VU39;Q9UIF9|.	.;BAZ2A_HUMAN|.	Q|H	464;462;494;492|141	ENSP00000368754:K464Q;ENSP00000179765:K462Q;ENSP00000446880:K494Q;ENSP00000447941:K492Q|.	ENSP00000179765:K462Q|.	K|Q	-|-	1|3	0|2	BAZ2A|BAZ2A	55291959|55291959	0.005000|0.005000	0.15991|0.15991	0.192000|0.192000	0.23308|0.23308	0.817000|0.817000	0.46193|0.46193	0.445000|0.445000	0.21677|0.21677	0.944000|0.944000	0.37579|0.37579	0.459000|0.459000	0.35465|0.35465	AAA|CAA		0.542	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	57005692	T	G	57005692	3	3	61	1	0	0	0	0	1	0	0	0	1332	1850	64	4	4333	4	BAZ2A	12	57005692	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	143294	57005692	76846203	8127	16112										
TAC3	6866	broad.mit.edu	37	chr12	57407147	57407147	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagagggtacttacgtttCtcgggagatgttgattcctt	12	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57407147C>T	ENST00000458521.2	-	4	393	c.234G>A	c.(232-234)gaG>gaA	p.E78E	TAC3_ENST00000441881.1_Silent_p.E78E|TAC3_ENST00000415231.1_Silent_p.E78E	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	78					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)	p.E78E(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						ACTTACGTTTCTCGGGAGATG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	12											148	132	138					12																	57407147		2203	4300	6503	55693414	SO:0001819	synonymous_variant	6866			AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"Endogenous ligands"	11521	protein-coding gene	gene with protein product	"preprotachykinin-B"	162330	"neuromedin K", "neurokinin beta"	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.234G>A	12.37:g.57407147C>T			55693414	Q6IAG2|Q71BC6|Q71BC9	Silent	SNP	ENST00000458521.2	37	CCDS8928.1																																																																																				0.522	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667		T	57407147	C	T	57407147	2	4	61	1	0	0	0	0	0	0	0	1	15538	912	32	3		3	TAC3	12	57407147	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	401455	57407147	76444748	8128	16113										
MYO1A	4640	broad.mit.edu	37	chr12	57424932	57424932	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtggatggcaaattgttCttcagccccagtaggaattt	10	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57424932C>A	ENST00000442789.2	-	24	2663	c.2376G>T	c.(2374-2376)aaG>aaT	p.K792N	TAC3_ENST00000415231.1_5'Flank|MYO1A_ENST00000300119.3_Missense_Mutation_p.K792N|MYO1A_ENST00000544473.1_Missense_Mutation_p.K630N	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	792					microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K792N(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						GCAAATTGTTCTTCAGCCCCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	12											106	98	100					12																	57424932		2203	4300	6503	55711199	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2376G>T	12.37:g.57424932C>A	ENSP00000393392:p.Lys792Asn		55711199	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058404	0.76074	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.87650	-2.23;-2.23;-2.28	4.66	4.66	0.58398	.	0.116780	0.56097	D	0.000037	D	0.84866	0.5567	M	0.71581	2.175	0.43179	D	0.994996	P	0.36282	0.546	B	0.31812	0.136	D	0.86425	0.1757	10	0.56958	D	0.05	.	13.0595	0.59000	0.0:1.0:0.0:0.0	.	792	Q9UBC5	MYO1A_HUMAN	N	792;792;630	ENSP00000300119:K792N;ENSP00000393392:K792N;ENSP00000440514:K630N	ENSP00000300119:K792N	K	-	3	2	MYO1A	55711199	0.998000	0.40836	0.974000	0.42286	0.990000	0.78478	1.859000	0.39418	2.123000	0.65237	0.563000	0.77884	AAG		0.522	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57424932	C	A	57424932	3	1	61	1	0	0	0	0	1	0	0	0	10098	912	32	2	779	2	MYO1A	12	57424932	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17785	57424932	76426963	8129	16114										
MYO1A	4640	broad.mit.edu	37	chr12	57430157	57430157	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaaatatttgcgataattCtttcgggcctggcagaaaag	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57430157C>A	ENST00000442789.2	-	23	2570	c.2283G>T	c.(2281-2283)aaG>aaT	p.K761N	MYO1A_ENST00000300119.3_Missense_Mutation_p.K761N|MYO1A_ENST00000544473.1_Missense_Mutation_p.K599N|MYO1A_ENST00000476795.1_5'Flank	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	761	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K761N(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						TGCGATAATTCTTTCGGGCCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	107	107					12																	57430157		2203	4300	6503	55716424	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2283G>T	12.37:g.57430157C>A	ENSP00000393392:p.Lys761Asn		55716424	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065002	0.55432	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	T;T;T	0.37058	1.22;1.22;1.22	4.79	4.79	0.61399	.	0.397164	0.26251	N	0.025450	T	0.55625	0.1932	M	0.79475	2.455	0.42246	D	0.991958	D	0.69078	0.997	D	0.63793	0.918	T	0.53380	-0.8447	10	0.24483	T	0.36	.	13.2045	0.59787	0.0:1.0:0.0:0.0	.	761	Q9UBC5	MYO1A_HUMAN	N	761;761;599	ENSP00000300119:K761N;ENSP00000393392:K761N;ENSP00000440514:K599N	ENSP00000300119:K761N	K	-	3	2	MYO1A	55716424	0.987000	0.35691	1.000000	0.80357	0.642000	0.38348	1.932000	0.40143	2.484000	0.83849	0.563000	0.77884	AAG		0.453	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57430157	C	A	57430157	3	1	61	1	0	0	0	0	1	0	0	0	10098	912	32	2	876	2	MYO1A	12	57430157	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5225	57430157	76421738	8130	16115										
MYO1A	4640	broad.mit.edu	37	chr12	57441147	57441147	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagttcacctgctctccttTcccacagacggcagccacat	7	16	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57441147T>C	ENST00000442789.2	-	6	657	c.370A>G	c.(370-372)Aaa>Gaa	p.K124E	MYO1A_ENST00000300119.3_Missense_Mutation_p.K124E|MYO1A_ENST00000544473.1_5'UTR	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	124	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K124E(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						TGCTCTCCTTTCCCACAGACG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											88	79	82					12																	57441147		2203	4300	6503	55727414	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.370A>G	12.37:g.57441147T>C	ENSP00000393392:p.Lys124Glu		55727414	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.889494	0.72524	.	.	ENSG00000166866	ENST00000300119;ENST00000442789	D;D	0.87179	-2.22;-2.22	5.19	2.6	0.31112	Myosin head, motor domain (2);	0.049980	0.85682	D	0.000000	D	0.89497	0.6732	L	0.58810	1.83	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.86236	0.1640	10	0.35671	T	0.21	.	6.5204	0.22272	0.0:0.0857:0.1554:0.7588	.	124	Q9UBC5	MYO1A_HUMAN	E	124	ENSP00000300119:K124E;ENSP00000393392:K124E	ENSP00000300119:K124E	K	-	1	0	MYO1A	55727414	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	4.083000	0.57643	0.901000	0.36495	0.533000	0.62120	AAA		0.577	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		C	57441147	T	C	57441147	3	2	61	1	0	0	0	0	1	0	0	0	10098	1792	62	4	2857	4	MYO1A	12	57441147	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10990	57441147	76410748	8131	16116										
TMEM194A	23306	broad.mit.edu	37	chr12	57453782	57453782	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccctaatccatactcctgCtcatggacagaaacttcatt	4	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57453782C>A	ENST00000300128.4	-	9	1238	c.1215G>T	c.(1213-1215)gaG>gaT	p.E405D	TMEM194A_ENST00000379391.3_Missense_Mutation_p.E332D	NM_001130963.1	NP_001124435.1	O14524	T194A_HUMAN	transmembrane protein 194A	405						integral component of membrane (GO:0016021)		p.E332D(1)|p.E405D(1)		endometrium(3)|large_intestine(3)|lung(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CATACTCCTGCTCATGGACAG	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	12											101	91	94					12																	57453782		2203	4300	6503	55740049	SO:0001583	missense	23306			AB006624	CCDS31841.1, CCDS44927.1	12q13.3	2008-06-10	2008-06-10	2008-06-10		ENSG00000166881			29001	protein-coding gene	gene with protein product			"transmembrane protein 194"	TMEM194			Standard	NM_015257		Approved	KIAA0286	uc001smy.3	O14524		ENST00000300128.4:c.1215G>T	12.37:g.57453782C>A	ENSP00000300128:p.Glu405Asp		55740049	Q17R72|Q68DH0|Q6IQ25	Missense_Mutation	SNP	ENST00000300128.4	37	CCDS44927.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.017562	0.54576	.	.	ENSG00000166881	ENST00000379391;ENST00000300128	T;T	0.52983	0.72;0.64	5.61	3.78	0.43462	.	0.288557	0.38663	N	0.001607	T	0.55194	0.1905	L	0.54323	1.7	0.39620	D	0.97001	P;D	0.67145	0.726;0.996	B;P	0.59056	0.222;0.851	T	0.53697	-0.8402	10	0.37606	T	0.19	-13.1948	9.8949	0.41311	0.0:0.833:0.0:0.167	.	405;332	O14524;O14524-2	T194A_HUMAN;.	D	332;405	ENSP00000368701:E332D;ENSP00000300128:E405D	ENSP00000300128:E405D	E	-	3	2	TMEM194A	55740049	0.640000	0.27243	1.000000	0.80357	0.997000	0.91878	-0.195000	0.09546	0.718000	0.32166	0.561000	0.74099	GAG		0.448	TMEM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411272.1	NM_015257		A	57453782	C	A	57453782	3	1	61	1	0	0	0	0	1	0	0	0	16155	796	28	2	123	2	TMEM194A	12	57453782	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12635	57453782	76398113	8132	16117										
TMEM194A	23306	broad.mit.edu	37	chr12	57466683	57466683	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaagcatgaccacatttAcatcagtttcagctttatgc	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57466683A>G	ENST00000300128.4	-	2	163	c.140T>C	c.(139-141)gTa>gCa	p.V47A	TMEM194A_ENST00000553654.1_5'UTR|TMEM194A_ENST00000379391.3_Missense_Mutation_p.V47A	NM_001130963.1	NP_001124435.1	O14524	T194A_HUMAN	transmembrane protein 194A	47						integral component of membrane (GO:0016021)		p.V47A(2)		endometrium(3)|large_intestine(3)|lung(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GACCACATTTACATCAGTTTC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	12											111	93	99					12																	57466683		2203	4300	6503	55752950	SO:0001583	missense	23306			AB006624	CCDS31841.1, CCDS44927.1	12q13.3	2008-06-10	2008-06-10	2008-06-10		ENSG00000166881			29001	protein-coding gene	gene with protein product			"transmembrane protein 194"	TMEM194			Standard	NM_015257		Approved	KIAA0286	uc001smy.3	O14524		ENST00000300128.4:c.140T>C	12.37:g.57466683A>G	ENSP00000300128:p.Val47Ala		55752950	Q17R72|Q68DH0|Q6IQ25	Missense_Mutation	SNP	ENST00000300128.4	37	CCDS44927.1	.	.	.	.	.	.	.	.	.	.	A	6.746	0.506383	0.12883	.	.	ENSG00000166881	ENST00000379391;ENST00000300128	T;T	0.44482	0.92;0.94	5.05	2.7	0.31948	.	1.614940	0.03661	N	0.242604	T	0.30103	0.0754	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.10450	0.0;0.005	T	0.17592	-1.0364	10	0.07990	T	0.79	1.7095	3.3021	0.06987	0.6447:0.0:0.1848:0.1705	.	47;47	O14524;O14524-2	T194A_HUMAN;.	A	47	ENSP00000368701:V47A;ENSP00000300128:V47A	ENSP00000300128:V47A	V	-	2	0	TMEM194A	55752950	0.000000	0.05858	0.001000	0.08648	0.426000	0.31534	-0.161000	0.10026	0.405000	0.25532	0.482000	0.46254	GTA		0.338	TMEM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411272.1	NM_015257		G	57466683	A	G	57466683	3	3	61	1	0	0	0	0	1	0	0	0	16155	391	14	4	1226	4	TMEM194A	12	57466683	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12901	57466683	76385212	8133	16118										
LRP1	4035	broad.mit.edu	37	chr12	57548340	57548340	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagaaccgcaccaagctCgtcgacagcaagattgtgtt	12	11	0	2	rs147797119	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57548340C>T	ENST00000243077.3	+	8	1549	c.1083C>T	c.(1081-1083)ctC>ctT	p.L361L	LRP1_ENST00000554174.1_Silent_p.L361L	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	361					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.L361L(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCACCAAGCTCGTCGACAGCA	0.517													C|||	2	0.000399361	0	0	5008	,	,		22890	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						C		2,4404	4.2+/-10.8	0,2,2201	116	81	93		1083	0.5	1	12	dbSNP_134	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRP1	NM_002332.2		0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308		361/4545	57548340	4,13002	2203	4300	6503	55834607	SO:0001819	synonymous_variant	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1083C>T	12.37:g.57548340C>T			55834607	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																				0.517	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57548340	C	T	57548340	2	4	61	1	0	0	0	0	0	0	0	1	8980	871	31	1		1	LRP1	12	57548340	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81657	57548340	76303555	8134	16119										
LRP1	4035	broad.mit.edu	37	chr12	57584742	57584742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagctctacttctctgacGccaccctggacaagatcgag	9	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57584742G>A	ENST00000243077.3	+	43	7652	c.7186G>A	c.(7186-7188)Gcc>Acc	p.A2396T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2396					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.A2396T(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTTCTCTGACGCCACCCTGGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	12											91	72	78					12																	57584742		2203	4300	6503	55871009	SO:0001583	missense	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7186G>A	12.37:g.57584742G>A	ENSP00000243077:p.Ala2396Thr		55871009	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	g	24.3	4.514981	0.85389	.	.	ENSG00000123384	ENST00000243077	D	0.96427	-4.01	4.93	4.93	0.64822	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.95538	0.8550	M	0.81497	2.545	0.80722	D	1	B	0.33807	0.426	B	0.28709	0.093	D	0.95507	0.8582	10	0.56958	D	0.05	.	17.1266	0.86716	0.0:0.0:1.0:0.0	.	2396	Q07954	LRP1_HUMAN	T	2396	ENSP00000243077:A2396T	ENSP00000243077:A2396T	A	+	1	0	LRP1	55871009	1.000000	0.71417	0.955000	0.39395	0.954000	0.61252	9.636000	0.98440	2.560000	0.86352	0.537000	0.68136	GCC		0.642	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57584742	G	A	57584742	3	1	61	1	0	0	0	0	1	0	0	0	8980	1087	38	1	7356	1	LRP1	12	57584742	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36402	57584742	76267153	8135	16120										
LRP1	4035	broad.mit.edu	37	chr12	57586646	57586646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgaactctctccatgccGaatcaacaacggtggctgcc	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57586646G>A	ENST00000243077.3	+	45	7914	c.7448G>A	c.(7447-7449)cGa>cAa	p.R2483Q	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2483	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.R2483Q(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TCTCCATGCCGAATCAACAAC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	12											174	132	147					12																	57586646		2203	4300	6503	55872913	SO:0001583	missense	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7448G>A	12.37:g.57586646G>A	ENSP00000243077:p.Arg2483Gln		55872913	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.438694	0.43326	.	.	ENSG00000123384	ENST00000243077	D	0.86694	-2.16	4.3	4.3	0.51218	Six-bladed beta-propeller, TolB-like (1);Epidermal growth factor-like (1);	0.081814	0.48767	D	0.000176	T	0.75817	0.3901	L	0.28192	0.835	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.67787	-0.5580	10	0.12430	T	0.62	.	9.4805	0.38898	0.0988:0.0:0.9012:0.0	.	2483	Q07954	LRP1_HUMAN	Q	2483	ENSP00000243077:R2483Q	ENSP00000243077:R2483Q	R	+	2	0	LRP1	55872913	0.876000	0.30132	0.973000	0.42090	0.907000	0.53573	2.316000	0.43761	2.243000	0.73865	0.514000	0.50259	CGA		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57586646	G	A	57586646	3	1	61	1	0	0	0	0	1	0	0	0	8980	1058	37	1	7626	1	LRP1	12	57586646	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1904	57586646	76265249	8136	16121										
SHMT2	6472	broad.mit.edu	37	chr12	57626051	57626051	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagccacgtccatcttcttCgagtctatgccctataagct	6	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57626051C>T	ENST00000328923.3	+	5	1022	c.570C>T	c.(568-570)ttC>ttT	p.F190F	SHMT2_ENST00000414700.3_Silent_p.F169F|SHMT2_ENST00000393827.4_Missense_Mutation_p.S85L|SHMT2_ENST00000553474.1_Silent_p.F169F|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000449049.3_Silent_p.F169F|SHMT2_ENST00000557487.1_Silent_p.F190F	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	190					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)	p.F190F(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CCATCTTCTTCGAGTCTATGC	0.587																																					Esophageal Squamous(150;1369 2416 49071 49364)											1	Substitution - coding silent(1)	large_intestine(1)	12											166	136	146					12																	57626051		2203	4300	6503	55912318	SO:0001819	synonymous_variant	6472			AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.570C>T	12.37:g.57626051C>T			55912318	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Silent	SNP	ENST00000328923.3	37	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.537921	0.65085	.	.	ENSG00000182199	ENST00000393827	T	0.30981	1.51	4.95	-9.0	0.00747	.	.	.	.	.	T	0.25644	0.0624	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.10683	-1.0619	8	0.59425	D	0.04	-2.2021	19.8812	0.96900	0.0:0.1145:0.0:0.8855	.	85	B4DLV4	.	L	85	ENSP00000377413:S85L	ENSP00000377413:S85L	S	+	2	0	SHMT2	55912318	0.186000	0.23225	0.449000	0.26957	0.984000	0.73092	-0.473000	0.06615	-2.087000	0.00862	-0.793000	0.03317	TCG		0.587	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		T	57626051	C	T	57626051	2	4	61	1	0	0	0	0	0	0	0	1	14323	883	31	1		1	SHMT2	12	57626051	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39405	57626051	76225844	8137	16122										
INHBC	3626	broad.mit.edu	37	chr12	57843533	57843533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgtgagattggctggcacGactggatcatccagcctgag	13	11	1	2	rs149645850		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57843533G>A	ENST00000309668.2	+	2	914	c.787G>A	c.(787-789)Gac>Aac	p.D263N		NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	263					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)	p.D263N(1)		breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						TGGCTGGCACGACTGGATCAT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/ASP	0,4406		0,0,2203	86	73	77		787	4.1	1	12	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	INHBC	NM_005538.2	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	263/353	57843533	1,13005	2203	4300	6503	56129800	SO:0001583	missense	3626				CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.787G>A	12.37:g.57843533G>A	ENSP00000308716:p.Asp263Asn		56129800	A1L3Y2	Missense_Mutation	SNP	ENST00000309668.2	37	CCDS8938.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.596771	0.66332	0.0	1.16E-4	ENSG00000175189	ENST00000309668	T	0.64618	-0.11	4.09	4.09	0.47781	Transforming growth factor-beta, C-terminal (3);	0.048820	0.85682	D	0.000000	T	0.76263	0.3963	M	0.78456	2.415	0.80722	D	1	D	0.76494	0.999	P	0.60682	0.878	T	0.78492	-0.2183	9	.	.	.	-24.0494	16.2822	0.82697	0.0:0.0:1.0:0.0	.	263	P55103	INHBC_HUMAN	N	263	ENSP00000308716:D263N	.	D	+	1	0	INHBC	56129800	1.000000	0.71417	0.970000	0.41538	0.146000	0.21551	7.773000	0.85462	2.591000	0.87537	0.650000	0.86243	GAC		0.547	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538		A	57843533	G	A	57843533	3	1	61	1	0	0	0	0	1	0	0	0	7764	1058	37	1	793	1	INHBC	12	57843533	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	217482	57843533	76008362	8138	16123										
ARHGAP9	64333	broad.mit.edu	37	chr12	57873164	57873164	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctaggatcccccaggaaCttggccaccaccggctggat	11	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57873164C>T	ENST00000356411.2	-	2	164	c.26G>A	c.(25-27)aGt>aAt	p.S9N	ARHGAP9_ENST00000424809.2_Missense_Mutation_p.S9N|ARHGAP9_ENST00000430041.2_5'Flank|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.S80N|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.S9N|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.S88N|ARHGAP9_ENST00000550454.1_5'Flank			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	9					positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)	p.S9N(1)		endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			CCCCCAGGAACTTGGCCACCA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											28	29	29					12																	57873164		2203	4300	6503	56159431	SO:0001583	missense	64333			AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.26G>A	12.37:g.57873164C>T	ENSP00000348782:p.Ser9Asn		56159431	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	C	15.86	2.958137	0.53400	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423	T;T;T;T	0.27720	3.01;3.0;1.65;2.95	4.93	3.09	0.35607	.	0.207462	0.32901	N	0.005518	T	0.24470	0.0593	N	0.24115	0.695	0.23198	N	0.998137	P;B;B;B;B	0.51791	0.948;0.001;0.421;0.001;0.001	P;B;B;B;B	0.48738	0.588;0.008;0.107;0.006;0.003	T	0.06716	-1.0811	10	0.87932	D	0	.	6.4608	0.21956	0.1794:0.7259:0.0:0.0946	.	9;88;9;9;9	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9	.;.;RHG09_HUMAN;.;.	N	9;9;9;80;58	ENSP00000377380:S9N;ENSP00000348782:S9N;ENSP00000394307:S9N;ENSP00000377386:S80N	ENSP00000344852:S58N	S	-	2	0	ARHGAP9	56159431	0.172000	0.23043	1.000000	0.80357	0.989000	0.77384	0.595000	0.24029	0.584000	0.29591	-0.136000	0.14681	AGT		0.602	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		T	57873164	C	T	57873164	3	4	61	1	0	0	0	0	1	0	0	0	889	565	20	3	2237	3	ARHGAP9	12	57873164	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29631	57873164	75978731	8139	16124										
MARS	4141	broad.mit.edu	37	chr12	57884088	57884088	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaacagcaaggtgtcctgGctctccggccttacctccaa	9	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57884088G>A	ENST00000262027.5	+	6	723	c.589G>A	c.(589-591)Gct>Act	p.A197T	MARS_ENST00000315473.5_5'UTR|ARHGAP9_ENST00000393797.2_5'Flank|MARS_ENST00000447721.2_3'UTR|ARHGAP9_ENST00000550288.1_5'Flank	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	197	GST C-terminal.				gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)	p.A197T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	AGGTGTCCTGGCTCTCCGGCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	12											116	124	121					12																	57884088		2203	4300	6503	56170355	SO:0001583	missense	4141			X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.589G>A	12.37:g.57884088G>A	ENSP00000262027:p.Ala197Thr		56170355	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	37	CCDS8942.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.191499|5.191499	0.94923|0.94923	.|.	.|.	ENSG00000166986|ENSG00000166986	ENST00000262027|ENST00000552371	T|.	0.79653|.	-1.29|.	4.53|4.53	4.53|4.53	0.55603|0.55603	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);|.	0.210898|.	0.38778|.	N|.	0.001568|.	T|.	0.58935|.	0.2157|.	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	P;P|.	0.44734|.	0.842;0.563|.	B;B|.	0.40329|.	0.326;0.09|.	T|.	0.54970|.	-0.8213|.	10|.	0.72032|.	D|.	0.01|.	-12.9119|-12.9119	16.5751|16.5751	0.84634|0.84634	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	70;197|.	B4E0E9;P56192|.	.;SYMC_HUMAN|.	T|X	197|68	ENSP00000262027:A197T|.	ENSP00000262027:A197T|.	A|W	+|+	1|3	0|0	MARS|MARS	56170355|56170355	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.992000|0.992000	0.81027|0.81027	5.079000|5.079000	0.64431|0.64431	2.520000|2.520000	0.84964|0.84964	0.514000|0.514000	0.50259|0.50259	GCT|TGG		0.597	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		A	57884088	G	A	57884088	3	1	61	1	0	0	0	0	1	0	0	0	9346	1203	42	3	611	3	MARS	12	57884088	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10924	57884088	75967807	8140	16125										
MARS	4141	broad.mit.edu	37	chr12	57910233	57910233	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttagggaaacattgtccgaGaactgaaagcacaaaaggca	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57910233G>T	ENST00000262027.5	+	21	2706	c.2572G>T	c.(2572-2574)Gaa>Taa	p.E858*	RN7SL312P_ENST00000582079.1_RNA|MIR616_ENST00000385293.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	858	WHEP-TRS.				gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)	p.E858*(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	CATTGTCCGAGAACTGAAAGC	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											63	62	62					12																	57910233		2203	4300	6503	56196500	SO:0001587	stop_gained	4141			X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2572G>T	12.37:g.57910233G>T	ENSP00000262027:p.Glu858*		56196500	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Nonsense_Mutation	SNP	ENST00000262027.5	37	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.502264	0.64298	.	.	ENSG00000166986	ENST00000262027;ENST00000552914	.	.	.	5.47	5.47	0.80525	.	0.179817	0.46442	D	0.000286	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-16.6303	14.7373	0.69424	0.0:0.1456:0.8544:0.0	.	.	.	.	X	858;177	.	ENSP00000262027:E858X	E	+	1	0	MARS	56196500	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.525000	0.53502	2.746000	0.94184	0.561000	0.74099	GAA		0.498	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		T	57910233	G	T	57910233	4	4	61	1	0	0	0	0	0	1	0	0	9346	943	33	2	2654	2	MARS	12	57910233	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26145	57910233	75941662	8141	16126										
KIF5A	3798	broad.mit.edu	37	chr12	57957931	57957931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgatgggaatcattcctcGaattgcccgagacatcttca	9	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57957931G>A	ENST00000455537.2	+	4	606	c.332G>A	c.(331-333)cGa>cAa	p.R111Q	KIF5A_ENST00000286452.5_Intron	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	111	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.R111Q(1)|p.R111L(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						ATCATTCCTCGAATTGCCCGA	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											108	91	96					12																	57957931		2203	4300	6503	56244198	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.332G>A	12.37:g.57957931G>A	ENSP00000408979:p.Arg111Gln		56244198	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741314	0.96873	.	.	ENSG00000155980	ENST00000455537	T	0.76186	-1.0	4.87	4.87	0.63330	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.88738	0.6518	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90848	0.4729	10	0.87932	D	0	.	17.3316	0.87265	0.0:0.0:1.0:0.0	.	111	Q12840	KIF5A_HUMAN	Q	111	ENSP00000408979:R111Q	ENSP00000408979:R111Q	R	+	2	0	KIF5A	56244198	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.431000	0.97494	2.691000	0.91804	0.655000	0.94253	CGA		0.527	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		A	57957931	G	A	57957931	3	1	61	1	0	0	0	0	1	0	0	0	8326	1058	37	1	346	1	KIF5A	12	57957931	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47698	57957931	75893964	8142	16127										
KIF5A	3798	broad.mit.edu	37	chr12	57958276	57958276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttacctggacaaaattCgtgaccttctggatggtgag	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57958276C>T	ENST00000455537.2	+	5	704	c.430C>T	c.(430-432)Cgt>Tgt	p.R144C	KIF5A_ENST00000286452.5_Missense_Mutation_p.R55C	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	144	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.R144C(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GGACAAAATTCGTGACCTTCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											155	157	156					12																	57958276		2203	4300	6503	56244543	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.430C>T	12.37:g.57958276C>T	ENSP00000408979:p.Arg144Cys		56244543	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072439	0.76415	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.74209	-0.82;-0.82	5.05	5.05	0.67936	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.88477	0.6447	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90267	0.4305	10	0.87932	D	0	.	12.7656	0.57391	0.1641:0.8359:0.0:0.0	.	55;144	B7Z2M7;Q12840	.;KIF5A_HUMAN	C	144;55	ENSP00000408979:R144C;ENSP00000286452:R55C	ENSP00000286452:R55C	R	+	1	0	KIF5A	56244543	0.864000	0.29904	0.999000	0.59377	0.991000	0.79684	1.642000	0.37207	2.793000	0.96121	0.655000	0.94253	CGT		0.418	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57958276	C	T	57958276	3	4	61	1	0	0	0	0	1	0	0	0	8326	884	31	1	448	1	KIF5A	12	57958276	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	345	57958276	75893619	8143	16128										
KIF5A	3798	broad.mit.edu	37	chr12	57969442	57969442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatgaggccaagatccgctCgcttacggaatacatgcaga	11	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57969442C>T	ENST00000455537.2	+	17	2199	c.1925C>T	c.(1924-1926)tCg>tTg	p.S642L	KIF5A_ENST00000286452.5_Missense_Mutation_p.S553L	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	642					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.S642L(2)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						AAGATCCGCTCGCTTACGGAA	0.557																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											136	128	131					12																	57969442		2203	4300	6503	56255709	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1925C>T	12.37:g.57969442C>T	ENSP00000408979:p.Ser642Leu		56255709	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247897	0.80024	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.81499	-1.5;-1.5	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.89174	0.6640	M	0.83384	2.64	0.80722	D	1	D;D	0.76494	0.998;0.999	D;P	0.64042	0.921;0.877	D	0.90605	0.4547	10	0.59425	D	0.04	.	16.2291	0.82321	0.0:1.0:0.0:0.0	.	553;642	B7Z2M7;Q12840	.;KIF5A_HUMAN	L	642;553	ENSP00000408979:S642L;ENSP00000286452:S553L	ENSP00000286452:S553L	S	+	2	0	KIF5A	56255709	1.000000	0.71417	0.944000	0.38274	0.919000	0.55068	5.779000	0.68948	2.440000	0.82611	0.655000	0.94253	TCG		0.557	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57969442	C	T	57969442	3	4	61	1	0	0	0	0	1	0	0	0	8326	893	31	1	1991	1	KIF5A	12	57969442	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11166	57969442	75882453	8144	16129										
KIF5A	3798	broad.mit.edu	37	chr12	57969534	57969534	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagctggccaagctccagGcccagggtgaggccttctta	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:57969534G>A	ENST00000455537.2	+	17	2291	c.2017G>A	c.(2017-2019)Gcc>Acc	p.A673T	KIF5A_ENST00000286452.5_Missense_Mutation_p.A584T	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	673					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.A673T(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAAGCTCCAGGCCCAGGGTGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	12											151	147	148					12																	57969534		2203	4300	6503	56255801	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2017G>A	12.37:g.57969534G>A	ENSP00000408979:p.Ala673Thr		56255801	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766671	0.69878	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.85773	-2.03;-2.03	4.52	4.52	0.55395	.	0.217974	0.38272	N	0.001742	D	0.85673	0.5751	M	0.70275	2.135	0.41042	D	0.985233	B;B	0.21821	0.061;0.061	B;B	0.31245	0.126;0.099	T	0.83172	-0.0093	10	0.34782	T	0.22	.	16.5706	0.84611	0.0:0.0:1.0:0.0	.	584;673	B7Z2M7;Q12840	.;KIF5A_HUMAN	T	673;584	ENSP00000408979:A673T;ENSP00000286452:A584T	ENSP00000286452:A584T	A	+	1	0	KIF5A	56255801	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.994000	0.93529	2.517000	0.84864	0.655000	0.94253	GCC		0.507	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		A	57969534	G	A	57969534	3	1	61	1	0	0	0	0	1	0	0	0	8326	1203	42	3	2083	3	KIF5A	12	57969534	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92	57969534	75882361	8145	16130										
DTX3	196403	broad.mit.edu	37	chr12	58000803	58000803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccatcctcatagatggcGagacttctgacatctatgtt	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58000803G>A	ENST00000548198.1	+	3	1661	c.157G>A	c.(157-159)Gag>Aag	p.E53K	DTX3_ENST00000337737.3_Missense_Mutation_p.E53K|DTX3_ENST00000551632.1_Missense_Mutation_p.E56K|DTX3_ENST00000548804.1_Missense_Mutation_p.E53K			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	53					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E53K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					CATAGATGGCGAGACTTCTGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	12											126	134	131					12																	58000803		1912	4123	6035	56287070	SO:0001583	missense	196403			AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.157G>A	12.37:g.58000803G>A	ENSP00000447873:p.Glu53Lys		56287070	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	37	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.657081	0.67586	.	.	ENSG00000178498	ENST00000548804;ENST00000549583;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000548478	T;T;T;T;T;T	0.62232	0.81;0.04;0.81;0.81;0.8;0.07	4.02	4.02	0.46733	.	0.079738	0.47455	D	0.000230	T	0.64768	0.2628	N	0.19112	0.55	0.49483	D	0.999795	D	0.67145	0.996	D	0.68621	0.959	T	0.69232	-0.5199	10	0.56958	D	0.05	-3.044	14.0354	0.64642	0.0:0.0:1.0:0.0	.	53	Q8N9I9	DTX3_HUMAN	K	53;56;53;53;56;46	ENSP00000449294:E53K;ENSP00000449688:E56K;ENSP00000338050:E53K;ENSP00000447873:E53K;ENSP00000448696:E56K;ENSP00000448224:E46K	ENSP00000338050:E53K	E	+	1	0	DTX3	56287070	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	7.651000	0.83577	1.966000	0.57179	0.462000	0.41574	GAG		0.622	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		A	58000803	G	A	58000803	3	1	61	1	0	0	0	0	1	0	0	0	4806	1059	37	1	163	1	DTX3	12	58000803	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31269	58000803	75851092	8146	16131										
SLC26A10	65012	broad.mit.edu	37	chr12	58014221	58014221	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttgctaggtactgggaGacacctgtccacaggtgagt	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58014221G>T	ENST00000320442.4	+	1	529	c.218G>T	c.(217-219)aGa>aTa	p.R73I	AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA|SLC26A10_ENST00000379218.2_Missense_Mutation_p.R73I|AC025165.8_ENST00000593846.1_RNA	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	73						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)	p.R73I(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					GGTACTGGGAGACACCTGTCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											274	272	272					12																	58014221		2203	4300	6503	56300488	SO:0001583	missense	65012				CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.218G>T	12.37:g.58014221G>T	ENSP00000320217:p.Arg73Ile		56300488	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	20.7	4.041249	0.75732	.	.	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.92805	-3.11;-3.11	4.71	4.71	0.59529	.	.	.	.	.	D	0.96244	0.8775	M	0.92507	3.315	0.45056	D	0.998079	D	0.71674	0.998	D	0.72982	0.979	D	0.96083	0.9055	9	0.87932	D	0	.	9.0075	0.36120	0.098:0.0:0.902:0.0	.	73	Q8NG04	S2610_HUMAN	I	73	ENSP00000320217:R73I;ENSP00000368520:R73I	ENSP00000320217:R73I	R	+	2	0	SLC26A10	56300488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.918000	0.63376	2.620000	0.88729	0.655000	0.94253	AGA		0.527	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			T	58014221	G	T	58014221	3	4	61	1	0	0	0	0	1	0	0	0	14552	942	33	2	220	2	SLC26A10	12	58014221	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13418	58014221	75837674	8147	16132										
SLC26A10	65012	broad.mit.edu	37	chr12	58016351	58016351	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttttcaggtgcttctgGcctccgtgctctgcttcacc	8	15	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58016351G>A	ENST00000320442.4	+	5	1029	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	SLC26A10_ENST00000379218.2_Missense_Mutation_p.A240T|AC025165.8_ENST00000593846.1_RNA	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	240						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)	p.A240T(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					GGTGCTTCTGGCCTCCGTGCT	0.512											OREG0021948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											360	341	347					12																	58016351		2203	4300	6503	56302618	SO:0001583	missense	65012				CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.718G>A	12.37:g.58016351G>A	ENSP00000320217:p.Ala240Thr	1027	56302618	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	25.2	4.616591	0.87359	.	.	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.93488	-3.23;-3.23	4.2	3.21	0.36854	Sulphate transporter (1);	.	.	.	.	D	0.93713	0.7991	L	0.37897	1.145	0.41946	D	0.990638	D	0.89917	1.0	D	0.91635	0.999	D	0.92296	0.5845	9	0.40728	T	0.16	.	11.5314	0.50612	0.0:0.1833:0.8167:0.0	.	240	Q8NG04	S2610_HUMAN	T	240	ENSP00000320217:A240T;ENSP00000368520:A240T	ENSP00000320217:A240T	A	+	1	0	SLC26A10	56302618	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	4.707000	0.61852	2.258000	0.74832	0.655000	0.94253	GCC		0.512	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			A	58016351	G	A	58016351	3	1	61	1	0	0	0	0	1	0	0	0	14552	1203	42	3	736	3	SLC26A10	12	58016351	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2130	58016351	75835544	8148	16133										
OS9	10956	broad.mit.edu	37	chr12	58111685	58111685	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtgcaggtcaaagtcattCgaagccctgcggatttgatt	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58111685C>T	ENST00000315970.7	+	10	1119	c.1078C>T	c.(1078-1080)Cga>Tga	p.R360*	OS9_ENST00000413095.2_Nonsense_Mutation_p.R154*|OS9_ENST00000257966.8_Nonsense_Mutation_p.R361*|OS9_ENST00000439210.2_Nonsense_Mutation_p.R301*|OS9_ENST00000551035.1_Nonsense_Mutation_p.R328*|OS9_ENST00000552285.1_Nonsense_Mutation_p.R360*|OS9_ENST00000389142.5_Nonsense_Mutation_p.R360*|OS9_ENST00000435406.2_Nonsense_Mutation_p.R308*|OS9_ENST00000389146.6_Nonsense_Mutation_p.R360*|RP11-571M6.7_ENST00000549477.1_RNA	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	360					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)	p.R360*(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			CAAAGTCATTCGAAGCCCTGC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											114	121	119					12																	58111685		2203	4300	6503	56397952	SO:0001587	stop_gained	10956			AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"endoplasmic reticulum lectin 2", "erlectin 2"	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.1078C>T	12.37:g.58111685C>T	ENSP00000318165:p.Arg360*		56397952	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Nonsense_Mutation	SNP	ENST00000315970.7	37	CCDS31843.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672301	0.88348	.	.	ENSG00000135506	ENST00000552285;ENST00000315970;ENST00000439210;ENST00000389146;ENST00000413095;ENST00000551035;ENST00000257966;ENST00000435406;ENST00000389142	.	.	.	5.39	5.39	0.77823	.	0.056136	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.535	0.67953	0.0:1.0:0.0:0.0	.	.	.	.	X	360;360;301;360;154;328;361;308;360	.	ENSP00000257966:R361X	R	+	1	2	OS9	56397952	0.997000	0.39634	0.996000	0.52242	0.966000	0.64601	3.907000	0.56348	2.804000	0.96469	0.655000	0.94253	CGA		0.383	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812		T	58111685	C	T	58111685	4	4	61	1	0	0	0	0	0	1	0	0	11303	876	31	1	1116	1	OS9	12	58111685	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95334	58111685	75740210	8149	16134										
AGAP2	116986	broad.mit.edu	37	chr12	58124308	58124308	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcgggccaaattccggtCtggcttcagcaggtgtttgg	15	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58124308C>A	ENST00000547588.1	-	12	2397	c.2398G>T	c.(2398-2400)Gac>Tac	p.D800Y	AGAP2_ENST00000257897.3_Missense_Mutation_p.D464Y	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	800	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)	p.D464Y(1)		breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						AAATTCCGGTCTGGCTTCAGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	12											218	219	219					12																	58124308		2203	4300	6503	56410575	SO:0001583	missense	116986			AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.2398G>T	12.37:g.58124308C>A	ENSP00000449241:p.Asp800Tyr		56410575	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	37	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.08|18.08	3.543814|3.543814	0.65198|0.65198	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000257897;ENST00000547588;ENST00000549129|ENST00000328568	T;T|.	0.36157|.	1.42;1.27|.	4.72|4.72	4.72|4.72	0.59763|0.59763	Pleckstrin homology domain (3);|.	1.838160|.	0.02846|.	N|.	0.128515|.	T|T	0.62011|0.62011	0.2393|0.2393	L|L	0.49778|0.49778	1.585|1.585	0.41984|0.41984	D|D	0.990817|0.990817	P;D;D|.	0.64830|.	0.95;0.994;0.965|.	B;P;P|.	0.58820|.	0.397;0.846;0.805|.	T|T	0.59069|0.59069	-0.7523|-0.7523	10|5	0.87932|.	D|.	0|.	.|.	13.3774|13.3774	0.60747|0.60747	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	464;800;800|.	Q99490-2;F8VVT9;Q99490|.	.;.;AGAP2_HUMAN|.	Y|I	464;800;156|663	ENSP00000257897:D464Y;ENSP00000449241:D800Y|.	ENSP00000257897:D464Y|.	D|R	-|-	1|2	0|0	AGAP2|AGAP2	56410575|56410575	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.583000|3.583000	0.53928|0.53928	2.630000|2.630000	0.89119|0.89119	0.561000|0.561000	0.74099|0.74099	GAC|AGA		0.567	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		A	58124308	C	A	58124308	3	1	61	1	0	0	0	0	1	0	0	0	368	913	32	2	1212	2	AGAP2	12	58124308	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12623	58124308	75727587	8150	16135										
AGAP2	116986	broad.mit.edu	37	chr12	58127857	58127857	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcctcgtccctccccgcGaagggaactcagctgcccat	9	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58127857G>A	ENST00000547588.1	-	5	1500	c.1501C>T	c.(1501-1503)Cgc>Tgc	p.R501C	AGAP2_ENST00000257897.3_Missense_Mutation_p.R165C	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	501	G domain.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)	p.R165C(1)		breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CCCTCCCCGCGAAGGGAACTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12											56	45	49					12																	58127857		2203	4300	6503	56414124	SO:0001583	missense	116986			AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.1501C>T	12.37:g.58127857G>A	ENSP00000449241:p.Arg501Cys		56414124	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	37	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	3.996381|3.996381	0.74818|0.74818	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000257897;ENST00000547588|ENST00000328568	T;T|.	0.70282|.	-0.47;-0.47|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Mitochondrial Rho-like (1);|.	0.074808|.	0.52532|.	D|.	0.000075|.	D|D	0.82935|0.82935	0.5145|0.5145	M|M	0.86573|0.86573	2.825|2.825	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.998;1.0;1.0|.	D|D	0.84786|0.84786	0.0776|0.0776	10|5	0.87932|.	D|.	0|.	.|.	17.1186|17.1186	0.86695|0.86695	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	165;501;501|.	Q99490-2;F8VVT9;Q99490|.	.;.;AGAP2_HUMAN|.	C|L	165;501|364	ENSP00000257897:R165C;ENSP00000449241:R501C|.	ENSP00000257897:R165C|.	R|S	-|-	1|2	0|0	AGAP2|AGAP2	56414124|56414124	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.588000|0.588000	0.36517|0.36517	5.314000|5.314000	0.65804|0.65804	2.724000|2.724000	0.93272|0.93272	0.561000|0.561000	0.74099|0.74099	CGC|TCG		0.592	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		A	58127857	G	A	58127857	3	1	61	1	0	0	0	0	1	0	0	0	368	1058	37	1	2137	1	AGAP2	12	58127857	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3549	58127857	75724038	8151	16136										
MARCH9	92979	broad.mit.edu	37	chr12	58151918	58151918	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctccctgacggtcatcGagaaggtccagattgctgcc	10	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58151918G>A	ENST00000266643.5	+	3	972	c.541G>A	c.(541-543)Gag>Aag	p.E181K	MARCH9_ENST00000548358.1_Missense_Mutation_p.E68K	NM_138396.5	NP_612405.2	Q86YJ5	MARH9_HUMAN	membrane-associated ring finger (C3HC4) 9	181					protein ubiquitination (GO:0016567)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E181K(1)|p.E68K(1)		autonomic_ganglia(1)|large_intestine(2)|lung(1)	4	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			GACGGTCATCGAGAAGGTCCA	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	12											117	96	103					12																	58151918		2203	4300	6503	56438185	SO:0001583	missense	92979			BC009489	CCDS31847.1	12q14.1	2013-01-09				ENSG00000139266		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	25139	protein-coding gene	gene with protein product		613336				14722266	Standard	NM_138396		Approved	RNF179, FLJ36578	uc001spx.2	Q86YJ5		ENST00000266643.5:c.541G>A	12.37:g.58151918G>A	ENSP00000266643:p.Glu181Lys		56438185	B2R9U9|Q86VN5|Q96GG2	Missense_Mutation	SNP	ENST00000266643.5	37	CCDS31847.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.897452	0.91962	.	.	ENSG00000139266	ENST00000266643;ENST00000548358	T;T	0.58652	0.32;0.32	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.78259	0.4255	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	T	0.80464	-0.1371	10	0.87932	D	0	.	18.1173	0.89561	0.0:0.0:1.0:0.0	.	68;181	Q86YJ5-2;Q86YJ5	.;MARH9_HUMAN	K	181;68	ENSP00000266643:E181K;ENSP00000446758:E68K	ENSP00000266643:E181K	E	+	1	0	MARCH9	56438185	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.810000	0.96702	0.655000	0.94253	GAG		0.592	MARCH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409244.1	NM_138396		A	58151918	G	A	58151918	3	1	61	1	0	0	0	0	1	0	0	0	9338	1059	37	1	551	1	MARCH9	12	58151918	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24061	58151918	75699977	8152	16137										
MARCH9	92979	broad.mit.edu	37	chr12	58152625	58152625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagctgcggccaccagatgCccgttccagctcccattctg	10	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58152625C>T	ENST00000266643.5	+	4	1417	c.986C>T	c.(985-987)gCc>gTc	p.A329V	MARCH9_ENST00000548358.1_Missense_Mutation_p.A216V	NM_138396.5	NP_612405.2	Q86YJ5	MARH9_HUMAN	membrane-associated ring finger (C3HC4) 9	329					protein ubiquitination (GO:0016567)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A216V(1)|p.A329V(1)		autonomic_ganglia(1)|large_intestine(2)|lung(1)	4	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			CCACCAGATGCCCGTTCCAGC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	12											28	27	27					12																	58152625		2188	4291	6479	56438892	SO:0001583	missense	92979			BC009489	CCDS31847.1	12q14.1	2013-01-09				ENSG00000139266		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	25139	protein-coding gene	gene with protein product		613336				14722266	Standard	NM_138396		Approved	RNF179, FLJ36578	uc001spx.2	Q86YJ5		ENST00000266643.5:c.986C>T	12.37:g.58152625C>T	ENSP00000266643:p.Ala329Val		56438892	B2R9U9|Q86VN5|Q96GG2	Missense_Mutation	SNP	ENST00000266643.5	37	CCDS31847.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.455234	0.26161	.	.	ENSG00000139266	ENST00000266643;ENST00000548358	T;T	0.31510	2.5;1.49	5.56	5.56	0.83823	.	0.272699	0.35436	N	0.003201	T	0.19565	0.0470	N	0.08118	0	0.22954	N	0.998519	B;B	0.28178	0.202;0.021	B;B	0.35550	0.205;0.012	T	0.21348	-1.0248	10	0.41790	T	0.15	.	11.7245	0.51702	0.272:0.728:0.0:0.0	.	216;329	Q86YJ5-2;Q86YJ5	.;MARH9_HUMAN	V	329;216	ENSP00000266643:A329V;ENSP00000446758:A216V	ENSP00000266643:A329V	A	+	2	0	MARCH9	56438892	0.533000	0.26354	1.000000	0.80357	0.975000	0.68041	0.433000	0.21477	2.890000	0.99128	0.655000	0.94253	GCC		0.602	MARCH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409244.1	NM_138396		T	58152625	C	T	58152625	3	4	61	1	0	0	0	0	1	0	0	0	9338	739	26	3	1000	3	MARCH9	12	58152625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	707	58152625	75699270	8153	16138										
TSFM	25895	broad.mit.edu	37	chr12	58176894	58176894	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttcttatctcatctaggCtgggtctcttctgcgtcagt	8	12	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:58176894C>A	ENST00000300209.8	+	0	2563				TSFM_ENST00000323833.8_Splice_Site_p.A20D|TSFM_ENST00000550559.1_Splice_Site_p.A20D|TSFM_ENST00000497617.1_3'UTR|TSFM_ENST00000454289.3_Splice_Site_p.A20D|TSFM_ENST00000543727.1_Splice_Site_p.A20D|RP11-571M6.15_ENST00000553083.1_3'UTR|RP11-571M6.15_ENST00000471530.1_Splice_Site_p.L35M|TSFM_ENST00000548851.1_Splice_Site_p.A20D|TSFM_ENST00000540550.1_Splice_Site_p.A20D|TSFM_ENST00000350762.5_5'UTR	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)	p.A20D(1)		endometrium(1)|lung(1)	2						CTCATCTAGGCTGGGTCTCTT	0.587											OREG0021954	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											48	50	49					12																	58176894		2203	4300	6503	56463161	SO:0001628	intergenic_variant	10102			AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		12.37:g.58176894C>A		1028	56463161	Q9H749|Q9Y3W2	Missense_Mutation	SNP	ENST00000300209.8	37	CCDS8957.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.564207	0.65651	.	.	ENSG00000123297	ENST00000454289;ENST00000543727;ENST00000540550;ENST00000323833;ENST00000550559;ENST00000548851	.	.	.	4.99	3.15	0.36227	.	0.610700	0.14848	N	0.294869	T	0.38878	0.1057	L	0.27053	0.805	0.80722	D	1	B;B;B	0.34372	0.451;0.08;0.418	B;B;B	0.36504	0.203;0.027;0.226	T	0.27773	-1.0064	9	0.72032	D	0.01	.	6.5659	0.22511	0.1765:0.7322:0.0:0.0913	.	20;20;20	B4E391;P43897;P43897-2	.;EFTS_HUMAN;.	D	20	.	ENSP00000313877:A20D	A	+	2	0	TSFM	56463161	0.313000	0.24554	0.681000	0.30009	0.037000	0.13140	0.216000	0.17585	0.801000	0.34066	0.462000	0.41574	GCT		0.587	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		A	58176894	C	A	58176894	1	1	61	0	1	0	0	0	0	0	0	0	16655	811	28	2		2	TSFM	12	58176894	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24269	58176894	75675001	8154	16139										
LRIG3	121227	broad.mit.edu	37	chr12	59268079	59268079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaactgggctcatagtggTccattaaaactgttcttggg	11	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:59268079T>C	ENST00000320743.3	-	18	3159	c.2873A>G	c.(2872-2874)gAc>gGc	p.D958G	LRIG3_ENST00000379141.4_Missense_Mutation_p.D898G	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	958					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D958G(1)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CTCATAGTGGTCCATTAAAAC	0.423			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	1	Substitution - Missense(1)	large_intestine(1)	12											113	107	109					12																	59268079		2203	4300	6503	57554346	SO:0001583	missense	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2873A>G	12.37:g.59268079T>C	ENSP00000326759:p.Asp958Gly		57554346	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375599	0.24857	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.64085	-0.03;-0.08	5.83	5.83	0.93111	.	0.191446	0.25447	N	0.030601	T	0.61489	0.2351	M	0.73962	2.25	0.36112	D	0.844865	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.001	T	0.63892	-0.6534	9	.	.	.	.	12.0356	0.53423	0.0:0.0686:0.0:0.9313	.	898;958	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	G	898;958	ENSP00000368436:D898G;ENSP00000326759:D958G	.	D	-	2	0	LRIG3	57554346	1.000000	0.71417	0.937000	0.37676	0.038000	0.13279	4.248000	0.58760	2.224000	0.72417	0.528000	0.53228	GAC		0.423	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		C	59268079	T	C	59268079	3	2	61	1	0	0	0	0	1	0	0	0	8975	1667	58	4	494	4	LRIG3	12	59268079	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1091185	59268079	74583816	8155	16140										
LRIG3	121227	broad.mit.edu	37	chr12	59271414	59271414	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccaagggtgttagacatCtcacatgtgtatttcccagc	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:59271414C>A	ENST00000320743.3	-	15	2590	c.2304G>T	c.(2302-2304)gaG>gaT	p.E768D	LRIG3_ENST00000379141.4_Missense_Mutation_p.E708D	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	768	Ig-like C2-type 3.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E768D(1)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TGTTAGACATCTCACATGTGT	0.522			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	1	Substitution - Missense(1)	large_intestine(1)	12											175	157	163					12																	59271414		2203	4300	6503	57557681	SO:0001583	missense	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2304G>T	12.37:g.59271414C>A	ENSP00000326759:p.Glu768Asp		57557681	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.460864	0.43736	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.67865	-0.29;-0.29	5.59	0.709	0.18150	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37857	N	0.001902	T	0.74550	0.3731	M	0.70108	2.13	0.51482	D	0.999925	P;D	0.76494	0.863;0.999	P;D	0.80764	0.614;0.994	T	0.69472	-0.5136	9	.	.	.	.	5.8935	0.18927	0.0:0.2045:0.1363:0.6592	.	708;768	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	D	708;768	ENSP00000368436:E708D;ENSP00000326759:E768D	.	E	-	3	2	LRIG3	57557681	0.998000	0.40836	0.890000	0.34922	0.334000	0.28698	0.511000	0.22739	-0.043000	0.13513	0.655000	0.94253	GAG		0.522	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59271414	C	A	59271414	3	1	61	1	0	0	0	0	1	0	0	0	8975	912	32	2	1075	2	LRIG3	12	59271414	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3335	59271414	74580481	8156	16141										
LRIG3	121227	broad.mit.edu	37	chr12	59279668	59279668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagtaatagaacggatccGatttccttggagtatcctgg	10	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:59279668G>A	ENST00000320743.3	-	10	1475	c.1189C>T	c.(1189-1191)Cgg>Tgg	p.R397W	LRIG3_ENST00000379141.4_Missense_Mutation_p.R337W	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	397					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R397W(1)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GAACGGATCCGATTTCCTTGG	0.363			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	1	Substitution - Missense(1)	large_intestine(1)	12											145	163	157					12																	59279668		2203	4300	6503	57565935	SO:0001583	missense	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1189C>T	12.37:g.59279668G>A	ENSP00000326759:p.Arg397Trp		57565935	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.717386	0.30413	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.60548	0.18;0.18	5.93	4.06	0.47325	.	0.000000	0.34178	N	0.004197	T	0.57755	0.2075	M	0.85859	2.78	0.45946	D	0.998771	B;B	0.27264	0.118;0.173	B;B	0.27170	0.033;0.077	T	0.57866	-0.7737	9	.	.	.	.	7.6058	0.28101	0.0776:0.0:0.4676:0.4548	.	337;397	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	W	337;397	ENSP00000368436:R337W;ENSP00000326759:R397W	.	R	-	1	2	LRIG3	57565935	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	1.599000	0.36751	1.458000	0.47871	0.655000	0.94253	CGG		0.363	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59279668	G	A	59279668	3	1	61	1	0	0	0	0	1	0	0	0	8975	1057	37	1	2210	1	LRIG3	12	59279668	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8254	59279668	74572227	8157	16142										
USP15	9958	broad.mit.edu	37	chr12	62749171	62749171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttataagaactatgattattCggaacctggaagaaacaatg	8	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:62749171C>T	ENST00000280377.5	+	8	888	c.830C>T	c.(829-831)tCg>tTg	p.S277L	USP15_ENST00000393654.3_Missense_Mutation_p.S252L|USP15_ENST00000353364.3_Missense_Mutation_p.S248L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	277					BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.S248L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TATGATTATTCGGAACCTGGA	0.358																																					Melanoma(181;615 2041 39364 49691 50001)											1	Substitution - Missense(1)	large_intestine(1)	12											87	83	84					12																	62749171		2203	4300	6503	61035438	SO:0001583	missense	9958			AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.830C>T	12.37:g.62749171C>T	ENSP00000280377:p.Ser277Leu		61035438	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	37	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331588	0.60853	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.20738	2.06;2.06;2.05	5.45	4.57	0.56435	.	0.219510	0.40302	N	0.001128	T	0.15219	0.0367	N	0.25647	0.755	0.58432	D	0.999997	B;B	0.22003	0.063;0.058	B;B	0.18263	0.009;0.021	T	0.05451	-1.0884	9	.	.	.	-2.7678	14.0563	0.64772	0.0:0.9274:0.0:0.0726	.	277;248	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	248;277;252	ENSP00000258123:S248L;ENSP00000280377:S277L;ENSP00000377264:S252L	.	S	+	2	0	USP15	61035438	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.192000	0.58378	1.315000	0.45114	0.557000	0.71058	TCG		0.358	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		T	62749171	C	T	62749171	3	4	61	1	0	0	0	0	1	0	0	0	17086	893	31	1	769	1	USP15	12	62749171	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3469503	62749171	71102724	8158	16143										
USP15	9958	broad.mit.edu	37	chr12	62790089	62790089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagtgacttggatatgtCggaattcttaattaatccaa	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:62790089C>T	ENST00000280377.5	+	20	2643	c.2585C>T	c.(2584-2586)tCg>tTg	p.S862L	USP15_ENST00000393654.3_Missense_Mutation_p.S837L|USP15_ENST00000353364.3_Missense_Mutation_p.S833L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	862	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.S833L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTGGATATGTCGGAATTCTTA	0.378																																					Melanoma(181;615 2041 39364 49691 50001)											1	Substitution - Missense(1)	large_intestine(1)	12											130	124	126					12																	62790089		2203	4300	6503	61076356	SO:0001583	missense	9958			AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2585C>T	12.37:g.62790089C>T	ENSP00000280377:p.Ser862Leu		61076356	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	37	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459069	0.96240	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654;ENST00000549415	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	5.47	5.47	0.80525	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.201380	0.45126	D	0.000388	T	0.62527	0.2435	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.972	T	0.61267	-0.7097	9	.	.	.	-7.7818	19.6937	0.96012	0.0:1.0:0.0:0.0	.	862;833	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	833;862;837;64	ENSP00000258123:S833L;ENSP00000280377:S862L;ENSP00000377264:S837L;ENSP00000448372:S64L	.	S	+	2	0	USP15	61076356	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	6.066000	0.71185	2.720000	0.93068	0.650000	0.86243	TCG		0.378	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		T	62790089	C	T	62790089	3	4	61	1	0	0	0	0	1	0	0	0	17086	893	31	1	2572	1	USP15	12	62790089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40918	62790089	71061806	8159	16144										
MON2	23041	broad.mit.edu	37	chr12	62972263	62972263	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctattcaagagtttcaaaGaaatgaaaatattgatgtcg	7	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:62972263G>T	ENST00000393632.2	+	31	4944	c.4553G>T	c.(4552-4554)aGa>aTa	p.R1518I	MON2_ENST00000546600.1_Missense_Mutation_p.R1518I|MON2_ENST00000393629.2_Missense_Mutation_p.R1512I|MON2_ENST00000280379.6_Missense_Mutation_p.R1519I|MON2_ENST00000552738.1_Missense_Mutation_p.R1489I|MON2_ENST00000393630.3_Missense_Mutation_p.R1519I	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1518					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.R1518I(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAGTTTCAAAGAAATGAAAAT	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	12											30	30	30					12																	62972263		2198	4284	6482	61258530	SO:0001583	missense	23041				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4553G>T	12.37:g.62972263G>T	ENSP00000377252:p.Arg1518Ile		61258530	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865771	0.51588	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.56275	0.47;0.47;0.49;0.49;0.47;0.47	5.66	4.77	0.60923	.	0.097400	0.64402	D	0.000001	T	0.41811	0.1175	L	0.38175	1.15	0.80722	D	1	B;B;B;B;B	0.32573	0.103;0.253;0.253;0.178;0.376	B;B;B;B;B	0.33690	0.035;0.168;0.111;0.049;0.076	T	0.24548	-1.0157	9	.	.	.	-12.146	11.2165	0.48830	0.1588:0.0:0.8412:0.0	.	1512;1489;1518;387;1518	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	I	1518;1519;1519;1518;1489;1512	ENSP00000377252:R1518I;ENSP00000377250:R1519I;ENSP00000280379:R1519I;ENSP00000447407:R1518I;ENSP00000449215:R1489I;ENSP00000377249:R1512I	.	R	+	2	0	MON2	61258530	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.736000	0.62059	1.384000	0.46424	0.650000	0.86243	AGA		0.279	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62972263	G	T	62972263	3	4	61	1	0	0	0	0	1	0	0	0	9730	942	33	2	4675	2	MON2	12	62972263	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182174	62972263	70879632	8160	16145										
MON2	23041	broad.mit.edu	37	chr12	62974131	62974131	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgccaattttattcctaagGaatttgttggtcaaataatg	7	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:62974131G>A	ENST00000393632.2	+	32	5021	c.4630G>A	c.(4630-4632)Gaa>Aaa	p.E1544K	MON2_ENST00000546600.1_Missense_Mutation_p.E1544K|MON2_ENST00000393629.2_Missense_Mutation_p.E1538K|MON2_ENST00000280379.6_Missense_Mutation_p.E1545K|MON2_ENST00000552738.1_Missense_Mutation_p.E1515K|MON2_ENST00000393630.3_Missense_Mutation_p.E1545K	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1544					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.E1544K(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TATTCCTAAGGAATTTGTTGG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	12											92	92	92					12																	62974131		2203	4289	6492	61260398	SO:0001583	missense	23041				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4630G>A	12.37:g.62974131G>A	ENSP00000377252:p.Glu1544Lys		61260398	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668533	0.88348	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23;-0.23	6.07	6.07	0.98685	.	0.160487	0.56097	D	0.000034	T	0.65873	0.2733	L	0.43152	1.355	0.80722	D	1	B;P;B;B;P	0.38129	0.306;0.619;0.433;0.119;0.575	B;B;B;B;B	0.41299	0.11;0.353;0.156;0.073;0.156	T	0.60115	-0.7326	9	.	.	.	-12.4621	20.6593	0.99626	0.0:0.0:1.0:0.0	.	1538;1515;1544;413;1544	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	K	1544;1545;1545;1544;1515;1538	ENSP00000377252:E1544K;ENSP00000377250:E1545K;ENSP00000280379:E1545K;ENSP00000447407:E1544K;ENSP00000449215:E1515K;ENSP00000377249:E1538K	.	E	+	1	0	MON2	61260398	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	GAA		0.294	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		A	62974131	G	A	62974131	3	1	61	1	0	0	0	0	1	0	0	0	9730	1175	41	3	4756	3	MON2	12	62974131	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1868	62974131	70877764	8161	16146										
PPM1H	57460	broad.mit.edu	37	chr12	63226025	63226025	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctcacagctggcttggtCttcattgtgtgtgctcttcc	9	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:63226025C>A	ENST00000228705.6	-	2	580	c.280G>T	c.(280-282)Gac>Tac	p.D94Y		NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	94							phosphoprotein phosphatase activity (GO:0004721)	p.D94Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		CTGGCTTGGTCTTCATTGTGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	59	59					12																	63226025		1961	4163	6124	61512292	SO:0001583	missense	57460			AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.280G>T	12.37:g.63226025C>A	ENSP00000228705:p.Asp94Tyr		61512292	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	37	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.695157	0.88830	.	.	ENSG00000111110	ENST00000228705	T	0.41065	1.01	5.64	5.64	0.86602	Protein phosphatase 2C-like (3);	0.104847	0.64402	D	0.000005	T	0.69450	0.3112	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.72141	-0.4380	9	.	.	.	.	17.8834	0.88848	0.0:1.0:0.0:0.0	.	94	Q9ULR3	PPM1H_HUMAN	Y	94	ENSP00000228705:D94Y	.	D	-	1	0	PPM1H	61512292	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.167000	0.77562	2.670000	0.90874	0.650000	0.86243	GAC		0.542	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		A	63226025	C	A	63226025	3	1	61	1	0	0	0	0	1	0	0	0	12375	913	32	2	1300	2	PPM1H	12	63226025	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	251894	63226025	70625870	8162	16147										
AVPR1A	552	broad.mit.edu	37	chr12	63541422	63541422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgatggtagggttttccGattctgcatgaaaaatataa	11	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:63541422G>A	ENST00000299178.2	-	2	1079	c.974C>T	c.(973-975)tCg>tTg	p.S325L		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	325					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)	p.S325L(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	AGGGTTTTCCGATTCTGCATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											103	101	101					12																	63541422		2203	4300	6503	61827689	SO:0001583	missense	552			L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.974C>T	12.37:g.63541422G>A	ENSP00000299178:p.Ser325Leu		61827689		Missense_Mutation	SNP	ENST00000299178.2	37	CCDS8965.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038365	0.75617	.	.	ENSG00000166148	ENST00000550940;ENST00000299178	T;T	0.70631	-0.5;-0.5	5.82	5.82	0.92795	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81569	0.4850	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.78976	-0.1991	9	.	.	.	-8.4785	19.0835	0.93192	0.0:0.0:1.0:0.0	.	325	P37288	V1AR_HUMAN	L	106;325	ENSP00000449822:S106L;ENSP00000299178:S325L	.	S	-	2	0	AVPR1A	61827689	1.000000	0.71417	0.837000	0.33122	0.273000	0.26683	7.888000	0.87302	2.767000	0.95098	0.655000	0.94253	TCG		0.363	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			A	63541422	G	A	63541422	3	1	61	1	0	0	0	0	1	0	0	0	1232	1059	37	1	286	1	AVPR1A	12	63541422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	315397	63541422	70310473	8163	16148										
DPY19L2	283417	broad.mit.edu	37	chr12	63991659	63991659	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaatctgtataccttaagAttctggctgctataagatca	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:63991659A>G	ENST00000324472.4	-	14	1574	c.1391T>C	c.(1390-1392)aTc>aCc	p.I464T		NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	464					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.I464T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		ATACCTTAAGATTCTGGCTGC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											46	52	50					12																	63991659		2201	4285	6486	62277926	SO:0001583	missense	283417				CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.1391T>C	12.37:g.63991659A>G	ENSP00000315988:p.Ile464Thr		62277926	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.217477	0.58560	.	.	ENSG00000177990	ENST00000324472	T	0.56941	0.43	3.14	3.14	0.36123	.	0.057547	0.64402	D	0.000001	T	0.49457	0.1558	L	0.60455	1.87	0.80722	D	1	P	0.37731	0.607	B	0.42692	0.395	T	0.45512	-0.9256	9	.	.	.	.	7.9714	0.30130	1.0:0.0:0.0:0.0	.	464	Q6NUT2	D19L2_HUMAN	T	464	ENSP00000315988:I464T	.	I	-	2	0	DPY19L2	62277926	1.000000	0.71417	0.905000	0.35620	0.979000	0.70002	5.266000	0.65525	1.427000	0.47276	0.473000	0.43528	ATC		0.323	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		G	63991659	A	G	63991659	3	3	61	1	0	0	0	0	1	0	0	0	4752	333	12	4	921	4	DPY19L2	12	63991659	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	450237	63991659	69860236	8164	16149										
SRGAP1	57522	broad.mit.edu	37	chr12	64377749	64377749	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcgagctcaactggtagaAcaacaaaaatgcctggagca	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:64377749A>G	ENST00000355086.3	+	2	614	c.90A>G	c.(88-90)gaA>gaG	p.E30E	SRGAP1_ENST00000357825.3_Silent_p.E30E|SRGAP1_ENST00000543397.1_5'UTR	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	30	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.E30E(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		AACTGGTAGAACAACAAAAAT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	12											75	80	79					12																	64377749		2203	4300	6503	62664016	SO:0001819	synonymous_variant	57522			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.90A>G	12.37:g.64377749A>G			62664016	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	37	CCDS8967.1																																																																																				0.403	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			G	64377749	A	G	64377749	2	3	61	1	0	0	0	0	0	0	0	1	15184	40	2	4		4	SRGAP1	12	64377749	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	386090	64377749	69474146	8165	16150										
SRGAP1	57522	broad.mit.edu	37	chr12	64458903	64458903	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattctccatcaggtgtgCcaggtcagtgcccagcagcc	10	15	4	0	rs200749162		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:64458903C>T	ENST00000355086.3	+	8	1553	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000357825.3_Silent_p.C343C|SRGAP1_ENST00000543397.1_Silent_p.C303C	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	343	F-BAR domain.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.C343C(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		ATCAGGTGTGCCAGGTCAGTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	12											91	67	75					12																	64458903		2203	4300	6503	62745170	SO:0001819	synonymous_variant	57522			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1029C>T	12.37:g.64458903C>T			62745170	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	37	CCDS8967.1																																																																																				0.517	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64458903	C	T	64458903	2	4	61	1	0	0	0	0	0	0	0	1	15184	747	26	3		3	SRGAP1	12	64458903	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81154	64458903	69392992	8166	16151										
SRGAP1	57522	broad.mit.edu	37	chr12	64488754	64488754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattgtggaaagctgtattCggttcatcaatctctatggt	9	7	4	0	rs377564318		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:64488754C>T	ENST00000355086.3	+	13	2106	c.1582C>T	c.(1582-1584)Cgg>Tgg	p.R528W	RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000357825.3_Missense_Mutation_p.R505W|SRGAP1_ENST00000543397.1_Missense_Mutation_p.R465W	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	528	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.R528W(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		AAGCTGTATTCGGTTCATCAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	141	138	139		1582	2.9	1	12		139	1,8599	1.2+/-3.3	0,1,4299	no	missense	SRGAP1	NM_020762.2	101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	528/1086	64488754	2,13004	2203	4300	6503	62775021	SO:0001583	missense	57522			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1582C>T	12.37:g.64488754C>T	ENSP00000347198:p.Arg528Trp		62775021	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.625959	0.66901	2.27E-4	1.16E-4	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.19669	2.13;2.13;2.13	5.05	2.88	0.33553	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.31335	U	0.007833	T	0.56572	0.1994	H	0.95294	3.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.70988	-0.4722	9	.	.	.	.	12.9014	0.58126	0.4416:0.5584:0.0:0.0	.	528;465	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	W	528;505;465	ENSP00000347198:R528W;ENSP00000350480:R505W;ENSP00000437948:R465W	.	R	+	1	2	SRGAP1	62775021	1.000000	0.71417	0.990000	0.47175	0.955000	0.61496	2.625000	0.46452	1.231000	0.43661	0.460000	0.39030	CGG		0.383	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64488754	C	T	64488754	3	4	61	1	0	0	0	0	1	0	0	0	15184	875	31	1	1632	1	SRGAP1	12	64488754	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29851	64488754	69363141	8167	16152										
C12orf56	115749	broad.mit.edu	37	chr12	64746797	64746797	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaatgtgttggctgatttCtctatctggcgaactcaaaa	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:64746797C>A	ENST00000543942.2	-	2	918	c.292G>T	c.(292-294)Gaa>Taa	p.E98*	snoU13_ENST00000459220.1_RNA|RPS11P6_ENST00000535684.1_RNA|C12orf56_ENST00000333722.5_Nonsense_Mutation_p.E98*	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56	98								p.E98*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		TGGCTGATTTCTCTATCTGGC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											116	109	111					12																	64746797		1824	4076	5900	63033064	SO:0001587	stop_gained	115749				CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306			26967	protein-coding gene	gene with protein product							Standard	NM_001099676		Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782	ENST00000543942.2:c.292G>T	12.37:g.64746797C>A	ENSP00000446101:p.Glu98*		63033064		Nonsense_Mutation	SNP	ENST00000543942.2	37		.	.	.	.	.	.	.	.	.	.	c	19.18	3.777400	0.70107	.	.	ENSG00000185306	ENST00000333722;ENST00000543942;ENST00000433716;ENST00000543259	.	.	.	3.73	3.73	0.42828	.	0.295721	0.25089	N	0.033239	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.9387	11.3191	0.49410	0.0:1.0:0.0:0.0	.	.	.	.	X	98;98;98;85	.	.	E	-	1	0	C12orf56	63033064	1.000000	0.71417	0.999000	0.59377	0.085000	0.17905	2.862000	0.48388	2.382000	0.81193	0.651000	0.88453	GAA		0.333	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000401058.2	NM_001099676		A	64746797	C	A	64746797	4	1	61	1	0	0	0	0	0	1	0	0	1704	922	32	2	1624	2	C12orf56	12	64746797	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	258043	64746797	69105098	8168	16153										
TBK1	29110	broad.mit.edu	37	chr12	64878130	64878130	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaacaaaccaaaattatttCttcaaatcaagaacttatct	1	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:64878130C>A	ENST00000331710.5	+	9	1379	c.1040C>A	c.(1039-1041)tCt>tAt	p.S347Y		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	347	Ubiquitin-like.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S347Y(2)		breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		AAAATTATTTCTTCAAATCAA	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	12											52	52	52					12																	64878130		2203	4300	6503	63164397	SO:0001583	missense	29110			AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1040C>A	12.37:g.64878130C>A	ENSP00000329967:p.Ser347Tyr		63164397	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	37	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737255	0.49045	.	.	ENSG00000183735	ENST00000331710	T	0.67523	-0.27	5.0	5.0	0.66597	.	0.165439	0.53938	D	0.000042	T	0.58235	0.2108	L	0.40543	1.245	0.46336	D	0.998993	P	0.36438	0.553	B	0.32465	0.146	T	0.56920	-0.7899	9	.	.	.	-10.5686	19.186	0.93644	0.0:1.0:0.0:0.0	.	347	Q9UHD2	TBK1_HUMAN	Y	347	ENSP00000329967:S347Y	.	S	+	2	0	TBK1	63164397	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	3.713000	0.54882	2.706000	0.92434	0.563000	0.77884	TCT		0.368	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		A	64878130	C	A	64878130	3	1	61	1	0	0	0	0	1	0	0	0	15676	913	32	2	1070	2	TBK1	12	64878130	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131333	64878130	68973765	8169	16154										
GNS	2799	broad.mit.edu	37	chr12	65110564	65110564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgagtcctgacactgccgCgattgctgaacatgagacgg	12	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:65110564C>T	ENST00000258145.3	-	14	1786	c.1616G>A	c.(1615-1617)cGc>cAc	p.R539H	GNS_ENST00000418919.2_Missense_Mutation_p.R483H|GNS_ENST00000542058.1_Missense_Mutation_p.R519H|GNS_ENST00000543646.1_Missense_Mutation_p.R571H	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	539					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)	p.R539H(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		GACACTGCCGCGATTGCTGAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											95	83	87					12																	65110564		2203	4300	6503	63396831	SO:0001583	missense	2799				CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.1616G>A	12.37:g.65110564C>T	ENSP00000258145:p.Arg539His		63396831	B4DYH8|Q53F05	Missense_Mutation	SNP	ENST00000258145.3	37	CCDS8970.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.856433	0.00558	.	.	ENSG00000135677	ENST00000418919;ENST00000258145;ENST00000543646;ENST00000542058;ENST00000539825	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.31	4.18	0.49190	.	0.899364	0.09943	N	0.735687	T	0.30759	0.0775	N	0.00926	-1.1	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.18808	-1.0325	9	.	.	.	-6.1081	9.3492	0.38126	0.0:0.0831:0.0:0.9169	.	519;571;539;483	B4DYH8;F6S8M0;P15586;Q7Z3X3	.;.;GNS_HUMAN;.	H	483;539;571;519;456	ENSP00000413130:R483H;ENSP00000258145:R539H;ENSP00000438497:R571H;ENSP00000444819:R519H	.	R	-	2	0	GNS	63396831	0.819000	0.29175	0.069000	0.20011	0.018000	0.09664	1.147000	0.31602	0.969000	0.38237	-0.378000	0.06908	CGC		0.468	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			T	65110564	C	T	65110564	3	4	61	1	0	0	0	0	1	0	0	0	6570	768	27	1	46	1	GNS	12	65110564	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	232434	65110564	68741331	8170	16155										
GNS	2799	broad.mit.edu	37	chr12	65116805	65116805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatacgccaggactcaggGaagggcatgttgggtcagtg	16	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:65116805G>A	ENST00000258145.3	-	11	1459	c.1289C>T	c.(1288-1290)tCc>tTc	p.S430F	GNS_ENST00000418919.2_Missense_Mutation_p.S374F|GNS_ENST00000542058.1_Missense_Mutation_p.S410F|GNS_ENST00000543646.1_Missense_Mutation_p.S462F	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	430					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)	p.S430F(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		AGGACTCAGGGAAGGGCATGT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	12											229	182	198					12																	65116805		2203	4300	6503	63403072	SO:0001583	missense	2799				CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.1289C>T	12.37:g.65116805G>A	ENSP00000258145:p.Ser430Phe		63403072	B4DYH8|Q53F05	Missense_Mutation	SNP	ENST00000258145.3	37	CCDS8970.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495073	0.26774	.	.	ENSG00000135677	ENST00000418919;ENST00000258145;ENST00000543646;ENST00000542058;ENST00000539825	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.06	4.18	0.49190	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.605492	0.18615	N	0.136055	T	0.51075	0.1653	L	0.39898	1.24	0.25713	N	0.985465	P;P;B;B	0.40050	0.469;0.7;0.195;0.111	B;B;B;B	0.38194	0.232;0.267;0.222;0.057	T	0.40608	-0.9554	9	.	.	.	-7.6206	10.448	0.44505	0.0764:0.1436:0.7799:0.0	.	410;462;430;374	B4DYH8;F6S8M0;P15586;Q7Z3X3	.;.;GNS_HUMAN;.	F	374;430;462;410;347	ENSP00000413130:S374F;ENSP00000258145:S430F;ENSP00000438497:S462F;ENSP00000444819:S410F	.	S	-	2	0	GNS	63403072	0.870000	0.30015	0.585000	0.28666	0.611000	0.37282	3.686000	0.54685	1.294000	0.44707	-0.339000	0.08088	TCC		0.483	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			A	65116805	G	A	65116805	3	1	61	1	0	0	0	0	1	0	0	0	6570	1174	41	3	385	3	GNS	12	65116805	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6241	65116805	68735090	8171	16156										
GNS	2799	broad.mit.edu	37	chr12	65134422	65134422	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctaaaaactgtattgaaGaattagtcattggagtcttg	8	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:65134422G>T	ENST00000258145.3	-	7	1009	c.839C>A	c.(838-840)tCt>tAt	p.S280Y	GNS_ENST00000418919.2_Missense_Mutation_p.S224Y|GNS_ENST00000542058.1_Missense_Mutation_p.S260Y|GNS_ENST00000543646.1_Missense_Mutation_p.S312Y	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	280					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)	p.S280Y(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		CTGTATTGAAGAATTAGTCAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											128	125	126					12																	65134422		2203	4299	6502	63420689	SO:0001583	missense	2799				CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.839C>A	12.37:g.65134422G>T	ENSP00000258145:p.Ser280Tyr		63420689	B4DYH8|Q53F05	Missense_Mutation	SNP	ENST00000258145.3	37	CCDS8970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.78|16.78	3.217716|3.217716	0.58560|0.58560	.|.	.|.	ENSG00000135677|ENSG00000135677	ENST00000540196|ENST00000418919;ENST00000258145;ENST00000543646;ENST00000542058;ENST00000539825;ENST00000545471;ENST00000545273	.|D;D;D;D;D	.|0.99891	.|-4.66;-5.06;-4.7;-4.75;-7.56	5.47|5.47	5.47|5.47	0.80525|0.80525	.|Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	.|0.099172	.|0.64402	.|D	.|0.000001	D|D	0.99846|0.99846	0.9929|0.9929	M|M	0.72894|0.72894	2.215|2.215	0.58432|0.58432	D|D	0.999999|0.999999	.|B;D;B;P	.|0.69078	.|0.24;0.997;0.142;0.454	.|B;D;B;B	.|0.63597	.|0.166;0.916;0.14;0.176	D|D	0.97232|0.97232	0.9885|0.9885	5|9	.|.	.|.	.|.	-23.2391|-23.2391	19.7308|19.7308	0.96181|0.96181	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|260;312;280;224	.|B4DYH8;F6S8M0;P15586;Q7Z3X3	.|.;.;GNS_HUMAN;.	L|Y	99|224;280;312;260;197;217;204	.|ENSP00000413130:S224Y;ENSP00000258145:S280Y;ENSP00000438497:S312Y;ENSP00000444819:S260Y;ENSP00000445055:S204Y	.|.	F|S	-|-	3|2	2|0	GNS|GNS	63420689|63420689	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	6.476000|6.476000	0.73587|0.73587	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	TTC|TCT		0.353	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			T	65134422	G	T	65134422	3	4	61	1	0	0	0	0	1	0	0	0	6570	942	33	2	851	2	GNS	12	65134422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17617	65134422	68717473	8172	16157										
LEMD3	23592	broad.mit.edu	37	chr12	65564368	65564368	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccgggagtctagacaggaGccgaaacctcgaagaggcgg	16	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:65564368G>T	ENST00000308330.2	+	1	1018	c.992G>T	c.(991-993)aGc>aTc	p.S331I	LEMD3_ENST00000541171.1_Intron	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	331					negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)	p.S331I(1)		breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		CTAGACAGGAGCCGAAACCTC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	12											24	29	27					12																	65564368		2203	4299	6502	63850635	SO:0001583	missense	23592			AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.992G>T	12.37:g.65564368G>T	ENSP00000308369:p.Ser331Ile		63850635	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	37	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.556073	0.65425	.	.	ENSG00000174106	ENST00000308330	T	0.50548	0.74	3.26	3.26	0.37387	.	0.443226	0.20432	N	0.092457	T	0.48642	0.1511	N	0.19112	0.55	0.36519	D	0.870059	D	0.61697	0.99	D	0.66497	0.944	T	0.52426	-0.8577	9	.	.	.	-11.2019	12.3297	0.55033	0.0:0.0:1.0:0.0	.	331	Q9Y2U8	MAN1_HUMAN	I	331	ENSP00000308369:S331I	.	S	+	2	0	LEMD3	63850635	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.735000	0.47377	2.127000	0.65507	0.462000	0.41574	AGC		0.622	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			T	65564368	G	T	65564368	3	4	61	1	0	0	0	0	1	0	0	0	8743	971	34	2	994	2	LEMD3	12	65564368	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	429946	65564368	68287527	8173	16158										
IRAK3	11213	broad.mit.edu	37	chr12	66597574	66597574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtggaacaagagaattaCtttggtcctgggcacagaaa	11	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:66597574C>T	ENST00000261233.4	+	2	638	c.217C>T	c.(217-219)Ctt>Ttt	p.L73F	IRAK3_ENST00000457197.2_Intron	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3									p.L73F(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		AAGAGAATTACTTTGGTCCTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	99	101					12																	66597574		2203	4300	6503	64883841	SO:0001583	missense	11213			AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.217C>T	12.37:g.66597574C>T	ENSP00000261233:p.Leu73Phe		64883841		Missense_Mutation	SNP	ENST00000261233.4	37	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198170	0.79015	.	.	ENSG00000090376	ENST00000261233	D	0.97041	-4.22	5.81	5.81	0.92471	Death (3);DEATH-like (2);	0.084638	0.48286	D	0.000188	D	0.98160	0.9392	M	0.75085	2.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98085	1.0406	9	.	.	.	-18.8496	15.575	0.76368	0.0:1.0:0.0:0.0	.	73	Q9Y616	IRAK3_HUMAN	F	73	ENSP00000261233:L73F	.	L	+	1	0	IRAK3	64883841	0.961000	0.32948	0.823000	0.32752	0.854000	0.48673	2.872000	0.48467	2.759000	0.94783	0.591000	0.81541	CTT		0.423	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1			T	66597574	C	T	66597574	3	4	61	1	0	0	0	0	1	0	0	0	7845	565	20	3	223	3	IRAK3	12	66597574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1033206	66597574	67254321	8174	16159										
IRAK3	11213	broad.mit.edu	37	chr12	66622063	66622063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccactcccttggcacattcGaatcggtatattaataggaa	7	11	0	0	rs371798024		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:66622063G>A	ENST00000261233.4	+	8	1221	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	IRAK3_ENST00000457197.2_Missense_Mutation_p.R206Q	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3									p.R267Q(2)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		TGGCACATTCGAATCGGTATA	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	12											201	182	189					12																	66622063		2203	4300	6503	64908330	SO:0001583	missense	11213			AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.800G>A	12.37:g.66622063G>A	ENSP00000261233:p.Arg267Gln		64908330		Missense_Mutation	SNP	ENST00000261233.4	37	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.630710	0.67015	.	.	ENSG00000090376	ENST00000261233;ENST00000457197	T;T	0.65364	-0.15;-0.15	5.88	5.88	0.94601	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.87378	0.6162	H	0.98426	4.23	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91551	0.5257	9	.	.	.	-9.8002	15.7406	0.77891	0.0:0.0:1.0:0.0	.	206;267	Q9Y616-2;Q9Y616	.;IRAK3_HUMAN	Q	267;206	ENSP00000261233:R267Q;ENSP00000409852:R206Q	.	R	+	2	0	IRAK3	64908330	0.998000	0.40836	1.000000	0.80357	0.024000	0.10985	3.811000	0.55620	2.797000	0.96272	0.561000	0.74099	CGA		0.413	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1			A	66622063	G	A	66622063	3	1	61	1	0	0	0	0	1	0	0	0	7845	1058	37	1	830	1	IRAK3	12	66622063	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24489	66622063	67229832	8175	16160										
HELB	92797	broad.mit.edu	37	chr12	66703893	66703893	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcacaccacaaaacctgaGaattcaagcgatgatgcatt	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:66703893G>T	ENST00000247815.4	+	4	1244	c.1185G>T	c.(1183-1185)gaG>gaT	p.E395D		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	395					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)	p.E395D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		CAAAACCTGAGAATTCAAGCG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											181	172	175					12																	66703893		2203	4300	6503	64990160	SO:0001583	missense	92797			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1185G>T	12.37:g.66703893G>T	ENSP00000247815:p.Glu395Asp		64990160	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.486100	0.26686	.	.	ENSG00000127311	ENST00000247815	T	0.12361	2.69	6.17	4.34	0.51931	.	0.804346	0.11782	N	0.530090	T	0.15478	0.0373	L	0.54323	1.7	0.09310	N	1	B	0.26318	0.146	B	0.24974	0.057	T	0.19386	-1.0307	9	.	.	.	-4.0563	11.2266	0.48888	0.0:0.124:0.6184:0.2576	.	395	Q8NG08	HELB_HUMAN	D	395	ENSP00000247815:E395D	.	E	+	3	2	HELB	64990160	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.085000	0.14912	0.916000	0.36871	0.655000	0.94253	GAG		0.418	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			T	66703893	G	T	66703893	3	4	61	1	0	0	0	0	1	0	0	0	7066	933	33	2	1199	2	HELB	12	66703893	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81830	66703893	67148002	8176	16161										
GRIP1	23426	broad.mit.edu	37	chr12	66935705	66935705	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccttcttcatcagctcGacgactgtggagcccttgaa	8	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:66935705G>A	ENST00000398016.3	-	3	230	c.162C>T	c.(160-162)gtC>gtT	p.V54V	GRIP1_ENST00000359742.4_Silent_p.V54V|GRIP1_ENST00000286445.7_Silent_p.V54V	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.V54V(1)		NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TCATCAGCTCGACGACTGTGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	12											222	215	217					12																	66935705		1904	4116	6020	65221972	SO:0001819	synonymous_variant	23426			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.162C>T	12.37:g.66935705G>A			65221972	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	ENST00000398016.3	37	CCDS41807.1																																																																																				0.458	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66935705	G	A	66935705	2	1	61	1	0	0	0	0	0	0	0	1	6808	1045	37	1		1	GRIP1	12	66935705	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231812	66935705	66916190	8177	16162										
CAND1	55832	broad.mit.edu	37	chr12	67691631	67691631	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctttgaatcatttgtaagAaggtaagtttttaagatctc	8	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:67691631A>G	ENST00000545606.1	+	6	1289	c.852A>G	c.(850-852)agA>agG	p.R284R		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	284					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.R284R(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		CATTTGTAAGAAGGTAAGTTT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	12											67	72	70					12																	67691631		2201	4296	6497	65977898	SO:0001819	synonymous_variant	55832				CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.852A>G	12.37:g.67691631A>G			65977898	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																				0.323	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		G	67691631	A	G	67691631	2	3	61	1	0	0	0	0	0	0	0	1	2621	243	9	4		4	CAND1	12	67691631	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	755926	67691631	66160264	8178	16163										
CAND1	55832	broad.mit.edu	37	chr12	67699030	67699030	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctccagtggtggcttgtGttggagacccattttacaaa	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:67699030G>A	ENST00000545606.1	+	10	2019	c.1582G>A	c.(1582-1584)Gtt>Att	p.V528I		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	528					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.V528I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		GGTGGCTTGTGTTGGAGACCC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											196	172	180					12																	67699030		2203	4300	6503	65985297	SO:0001583	missense	55832				CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1582G>A	12.37:g.67699030G>A	ENSP00000442318:p.Val528Ile		65985297	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	37	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.360606	0.41801	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.64085	-0.08	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57330	0.2046	L	0.43152	1.355	0.80722	D	1	B	0.20988	0.05	B	0.21708	0.036	T	0.50955	-0.8766	9	.	.	.	-23.0958	19.5723	0.95425	0.0:0.0:1.0:0.0	.	528	Q86VP6	CAND1_HUMAN	I	528;528;370	ENSP00000442318:V528I	.	V	+	1	0	CAND1	65985297	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.899000	0.87370	2.695000	0.91970	0.557000	0.71058	GTT		0.433	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67699030	G	A	67699030	3	1	61	1	0	0	0	0	1	0	0	0	2621	1377	48	3	1620	3	CAND1	12	67699030	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7399	67699030	66152865	8179	16164										
NUP107	57122	broad.mit.edu	37	chr12	69103821	69103821	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagagtattgccaaagatGaaattggagaattttctgat	10	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:69103821G>T	ENST00000229179.4	+	10	1170	c.838G>T	c.(838-840)Gaa>Taa	p.E280*	NUP107_ENST00000378905.2_Nonsense_Mutation_p.E129*|NUP107_ENST00000539906.1_Nonsense_Mutation_p.E251*	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	280					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)	p.E280*(1)	NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TGCCAAAGATGAAATTGGAGA	0.279																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											83	88	86					12																	69103821		2203	4299	6502	67390088	SO:0001587	stop_gained	57122			AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.838G>T	12.37:g.69103821G>T	ENSP00000229179:p.Glu280*		67390088	B4DZ67|Q6PJE1	Nonsense_Mutation	SNP	ENST00000229179.4	37	CCDS8985.1	.	.	.	.	.	.	.	.	.	.	G	39	7.744869	0.98465	.	.	ENSG00000111581	ENST00000229179;ENST00000378905;ENST00000539906	.	.	.	5.22	5.22	0.72569	.	0.211270	0.48767	D	0.000175	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.5863	18.7588	0.91842	0.0:0.0:1.0:0.0	.	.	.	.	X	280;129;251	.	.	E	+	1	0	NUP107	67390088	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	6.834000	0.75339	2.601000	0.87937	0.557000	0.71058	GAA		0.279	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		T	69103821	G	T	69103821	4	4	61	1	0	0	0	0	0	1	0	0	10784	1291	45	2	876	2	NUP107	12	69103821	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1404791	69103821	64748074	8180	16165										
YEATS4	8089	broad.mit.edu	37	chr12	69759619	69759619	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacaggatggggtgaattCgaaataatcatcaaaatatt	9	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:69759619C>T	ENST00000247843.2	+	4	558	c.288C>T	c.(286-288)ttC>ttT	p.F96F	YEATS4_ENST00000548020.1_Intron	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4	96	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)	p.F96F(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			GGGGTGAATTCGAAATAATCA	0.284																																																1	Substitution - coding silent(1)	large_intestine(1)	12											72	76	74					12																	69759619		2203	4292	6495	68045886	SO:0001819	synonymous_variant	8089			AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.288C>T	12.37:g.69759619C>T			68045886	Q9NQD0	Silent	SNP	ENST00000247843.2	37	CCDS8990.1																																																																																				0.284	YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530		T	69759619	C	T	69759619	2	4	61	1	0	0	0	0	0	0	0	1	17513	883	31	1		1	YEATS4	12	69759619	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	655798	69759619	64092276	8181	16166										
FRS2	10818	broad.mit.edu	37	chr12	69965161	69965161	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagagccagttgtagaaaGaaataatcatcagacagaat	10	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:69965161G>T	ENST00000550389.1	+	5	605	c.359G>T	c.(358-360)aGa>aTa	p.R120I	FRS2_ENST00000549921.1_Missense_Mutation_p.R120I|FRS2_ENST00000299293.2_Missense_Mutation_p.R120I|FRS2_ENST00000397997.2_Missense_Mutation_p.R120I	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	120					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R120I(2)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GTTGTAGAAAGAAATAATCAT	0.368											OREG0021986	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	12											101	93	96					12																	69965161		1863	4096	5959	68251428	SO:0001583	missense	10818			AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.359G>T	12.37:g.69965161G>T	ENSP00000447241:p.Arg120Ile	1118	68251428	B0LPF2|B2R684|O43558|Q7LDQ6	Missense_Mutation	SNP	ENST00000550389.1	37	CCDS41809.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275874	0.80580	.	.	ENSG00000166225	ENST00000299293;ENST00000549921;ENST00000550389;ENST00000397997;ENST00000551325	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	5.71	5.71	0.89125	.	0.249234	0.37955	N	0.001874	D	0.88592	0.6478	L	0.47190	1.495	0.80722	D	1	D	0.54397	0.966	D	0.68943	0.961	D	0.86384	0.1731	9	.	.	.	-12.7779	19.9325	0.97124	0.0:0.0:1.0:0.0	.	120	Q8WU20	FRS2_HUMAN	I	120	ENSP00000299293:R120I;ENSP00000450048:R120I;ENSP00000447241:R120I;ENSP00000381083:R120I;ENSP00000449432:R120I	.	R	+	2	0	FRS2	68251428	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.546000	0.90661	2.720000	0.93068	0.650000	0.86243	AGA		0.368	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654		T	69965161	G	T	69965161	3	4	61	1	0	0	0	0	1	0	0	0	6080	942	33	2	369	2	FRS2	12	69965161	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205542	69965161	63886734	8182	16167										
FRS2	10818	broad.mit.edu	37	chr12	69968178	69968178	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaggggtcaggagaggtCgtctgacatccaccagtacc	12	13	3	2	rs550828203		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:69968178C>T	ENST00000550389.1	+	7	1216	c.970C>T	c.(970-972)Cgt>Tgt	p.R324C	FRS2_ENST00000549921.1_Missense_Mutation_p.R324C|FRS2_ENST00000299293.2_Missense_Mutation_p.R324C|FRS2_ENST00000397997.2_Missense_Mutation_p.R324C	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	324					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R324C(2)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			CAGGAGAGGTCGTCTGACATC	0.433													C|||	1	0.000199681	0	0	5008	,	,		21130	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12											74	74	74					12																	69968178		1937	4132	6069	68254445	SO:0001583	missense	10818			AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.970C>T	12.37:g.69968178C>T	ENSP00000447241:p.Arg324Cys		68254445	B0LPF2|B2R684|O43558|Q7LDQ6	Missense_Mutation	SNP	ENST00000550389.1	37	CCDS41809.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397125	0.62177	.	.	ENSG00000166225	ENST00000299293;ENST00000549921;ENST00000550389;ENST00000397997	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	6.04	6.04	0.98038	.	0.130904	0.53938	D	0.000052	T	0.32734	0.0839	L	0.39898	1.24	0.80722	D	1	D	0.76494	0.999	P	0.48677	0.586	T	0.00426	-1.1746	9	.	.	.	-10.0024	20.6396	0.99537	0.0:1.0:0.0:0.0	.	324	Q8WU20	FRS2_HUMAN	C	324	ENSP00000299293:R324C;ENSP00000450048:R324C;ENSP00000447241:R324C;ENSP00000381083:R324C	.	R	+	1	0	FRS2	68254445	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.961000	0.56759	2.881000	0.98747	0.650000	0.86243	CGT		0.433	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654		T	69968178	C	T	69968178	3	4	61	1	0	0	0	0	1	0	0	0	6080	884	31	1	988	1	FRS2	12	69968178	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3017	69968178	63883717	8183	16168										
CCT2	10576	broad.mit.edu	37	chr12	69991759	69991759	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatctttaggctgttctgagAtgttgatggctcatgctgtg	12	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:69991759A>C	ENST00000299300.6	+	13	1431	c.1243A>C	c.(1243-1245)Atg>Ctg	p.M415L	CCT2_ENST00000544368.2_Missense_Mutation_p.M415L|CCT2_ENST00000543146.2_Missense_Mutation_p.M368L	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	415					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)	p.M415L(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	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)			CTGTTCTGAGATGTTGATGGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											45	40	42					12																	69991759		2203	4300	6503	68278026	SO:0001583	missense	10576			AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"Heat Shock Proteins / Chaperonins"	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.1243A>C	12.37:g.69991759A>C	ENSP00000299300:p.Met415Leu		68278026	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Missense_Mutation	SNP	ENST00000299300.6	37	CCDS8991.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.762368	0.69763	.	.	ENSG00000166226	ENST00000299300;ENST00000544368;ENST00000543146	T;T;T	0.75367	-0.93;-0.93;-0.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	L	0.48642	1.525	0.58432	D	0.999999	B;B	0.27700	0.186;0.132	B;B	0.30401	0.07;0.115	T	0.64984	-0.6278	9	.	.	.	-32.8856	15.0521	0.71881	1.0:0.0:0.0:0.0	.	415;415	F5GWF6;P78371	.;TCPB_HUMAN	L	415;415;368	ENSP00000299300:M415L;ENSP00000441847:M415L;ENSP00000445471:M368L	.	M	+	1	0	CCT2	68278026	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.685000	0.91246	2.371000	0.80710	0.533000	0.62120	ATG		0.373	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431		C	69991759	A	C	69991759	3	2	61	1	0	0	0	0	1	0	0	0	2959	333	12	4	1293	4	CCT2	12	69991759	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	23581	69991759	63860136	8184	16169										
RAB3IP	117177	broad.mit.edu	37	chr12	70209221	70209221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttatttcaaagaggaaCtctgatgctctgcgtgggac	13	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:70209221C>A	ENST00000247833.7	+	11	1754	c.1378C>A	c.(1378-1380)Ctc>Atc	p.L460I	RAB3IP_ENST00000362025.5_3'UTR|RAB3IP_ENST00000550536.1_Missense_Mutation_p.L476I|RAB3IP_ENST00000325555.9_Missense_Mutation_p.L254I|AC025263.3_ENST00000550437.1_Intron|RAB3IP_ENST00000553099.1_Missense_Mutation_p.L254I|RAB3IP_ENST00000483530.2_3'UTR|RAB3IP_ENST00000550847.1_Missense_Mutation_p.L167I|RAB3IP_ENST00000551641.1_Missense_Mutation_p.L254I					RAB3A interacting protein									p.L476I(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			CAAAGAGGAACTCTGATGCTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											174	163	167					12																	70209221		2203	4300	6503	68495488	SO:0001583	missense	117177				CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"rabin3"	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.1378C>A	12.37:g.70209221C>A	ENSP00000247833:p.Leu460Ile		68495488		Missense_Mutation	SNP	ENST00000247833.7	37	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041529	0.75732	.	.	ENSG00000127328	ENST00000247833;ENST00000325555;ENST00000550536;ENST00000551641;ENST00000553099;ENST00000550847	T;T;T;T;T;T	0.57436	0.44;0.73;0.4;0.73;0.73;0.67	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.68787	0.3039	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.68481	-0.5397	10	0.66056	D	0.02	.	20.1882	0.98224	0.0:1.0:0.0:0.0	.	476	Q96QF0	RAB3I_HUMAN	I	460;254;476;254;254;167	ENSP00000247833:L460I;ENSP00000323349:L254I;ENSP00000447300:L476I;ENSP00000448773:L254I;ENSP00000448027:L254I;ENSP00000448102:L167I	ENSP00000247833:L460I	L	+	1	0	RAB3IP	68495488	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	4.252000	0.58785	2.783000	0.95769	0.591000	0.81541	CTC		0.398	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456		A	70209221	C	A	70209221	3	1	61	1	0	0	0	0	1	0	0	0	12975	565	20	2	1468	2	RAB3IP	12	70209221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	217462	70209221	63642674	8185	16170										
KCNMB4	27345	broad.mit.edu	37	chr12	70824427	70824427	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatgaagaagcgcaagttCtcttaaaggggaaggaggct	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:70824427C>A	ENST00000258111.4	+	3	1086	c.627C>A	c.(625-627)ttC>ttA	p.F209L		NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	209					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)	p.F209L(2)		kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	AGCGCAAGTTCTCTTAAAGGG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	12											66	58	61					12																	70824427		2203	4300	6503	69110694	SO:0001583	missense	27345			AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643		"Potassium channels"	6289	protein-coding gene	gene with protein product		605223				10692449, 10828459	Standard	NM_014505		Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.627C>A	12.37:g.70824427C>A	ENSP00000258111:p.Phe209Leu		69110694	Q8IVR3|Q9NPA4|Q9P0G5	Missense_Mutation	SNP	ENST00000258111.4	37	CCDS8997.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096601	0.56075	.	.	ENSG00000135643	ENST00000258111	T	0.11169	2.8	6.06	6.06	0.98353	.	0.347490	0.30528	N	0.009429	T	0.05640	0.0148	N	0.08118	0	0.41397	D	0.987653	B	0.17038	0.02	B	0.17433	0.018	T	0.44267	-0.9339	10	0.11794	T	0.64	-28.0105	11.7861	0.52043	0.0:0.8653:0.0:0.1347	.	209	Q86W47	KCMB4_HUMAN	L	209	ENSP00000258111:F209L	ENSP00000258111:F209L	F	+	3	2	KCNMB4	69110694	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.250000	0.32850	2.882000	0.98803	0.655000	0.94253	TTC		0.557	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395208.1	NM_014505		A	70824427	C	A	70824427	3	1	61	1	0	0	0	0	1	0	0	0	8098	912	32	2	637	2	KCNMB4	12	70824427	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	615206	70824427	63027468	8186	16171										
PTPRB	5787	broad.mit.edu	37	chr12	70929847	70929847	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaccatgacgatgttgtgAacgttttgttcccacaccat	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:70929847A>C	ENST00000261266.5	-	27	5414	c.5385T>G	c.(5383-5385)gtT>gtG	p.V1795V	RP11-588H23.3_ENST00000548687.1_RNA|RP11-588H23.3_ENST00000549460.1_RNA|RP11-588H23.3_ENST00000551438.1_RNA|RP11-588H23.3_ENST00000546836.1_RNA|PTPRB_ENST00000538708.1_Silent_p.V1705V|RP11-588H23.3_ENST00000547656.1_RNA|PTPRB_ENST00000550857.1_Silent_p.V1705V|PTPRB_ENST00000451516.2_Silent_p.V1705V|PTPRB_ENST00000550358.1_Silent_p.V1925V|PTPRB_ENST00000334414.6_Silent_p.V2013V	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1795	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V2013V(1)|p.V1795V(1)		breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CGATGTTGTGAACGTTTTGTT	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	12											141	136	138					12																	70929847		1982	4170	6152	69216114	SO:0001819	synonymous_variant	5787			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5385T>G	12.37:g.70929847A>C			69216114	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																				0.488	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			C	70929847	A	C	70929847	2	2	61	1	0	0	0	0	0	0	0	1	12833	233	9	4		4	PTPRB	12	70929847	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	105420	70929847	62922048	8187	16172										
PTPRB	5787	broad.mit.edu	37	chr12	70986105	70986105	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagcagacagttcaccagaGacacagctgacagtaacttg	10	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:70986105G>T	ENST00000261266.5	-	5	1112	c.1083C>A	c.(1081-1083)gtC>gtA	p.V361V	PTPRB_ENST00000551525.1_Silent_p.V578V|PTPRB_ENST00000538708.1_Silent_p.V361V|PTPRB_ENST00000550857.1_Silent_p.V361V|PTPRB_ENST00000451516.2_Silent_p.V361V|PTPRB_ENST00000550358.1_Silent_p.V579V|PTPRB_ENST00000334414.6_Silent_p.V579V|PTPRB_ENST00000538174.2_5'UTR	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	361	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V361V(1)|p.V579V(1)		breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GTTCACCAGAGACACAGCTGA	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	12											101	99	99					12																	70986105		1973	4152	6125	69272372	SO:0001819	synonymous_variant	5787			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1083C>A	12.37:g.70986105G>T			69272372	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																				0.468	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70986105	G	T	70986105	2	4	61	1	0	0	0	0	0	0	0	1	12833	929	33	2		2	PTPRB	12	70986105	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56258	70986105	62865790	8188	16173										
PTPRR	5801	broad.mit.edu	37	chr12	71050494	71050494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacactcacctatccatacGaagctggcagacaatgctta	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:71050494G>A	ENST00000283228.2	-	13	2322	c.1870C>T	c.(1870-1872)Cgt>Tgt	p.R624C	PTPRR_ENST00000549308.1_Missense_Mutation_p.R379C|PTPRR_ENST00000342084.4_Missense_Mutation_p.R512C|PTPRR_ENST00000440835.2_Missense_Mutation_p.R379C|PTPRR_ENST00000378778.1_Missense_Mutation_p.R418C|PTPRR_ENST00000537619.2_5'UTR	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	624	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R624C(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		CTATCCATACGAAGCTGGCAG	0.458																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	12											199	153	168					12																	71050494		2203	4300	6503	69336761	SO:0001583	missense	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1870C>T	12.37:g.71050494G>A	ENSP00000283228:p.Arg624Cys		69336761	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074974	0.76415	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;-2.87	5.48	5.48	0.80851	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.52532	D	0.000073	D	0.97005	0.9022	H	0.97440	4.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.97988	1.0353	10	0.87932	D	0	-12.1384	14.2232	0.65841	0.0:0.0:0.8507:0.1493	.	512;418;624	F5GXR7;Q15256-4;Q15256	.;.;PTPRR_HUMAN	C	379;624;418;512;379	ENSP00000391750:R379C;ENSP00000283228:R624C;ENSP00000368054:R418C;ENSP00000339605:R512C;ENSP00000446943:R379C	ENSP00000283228:R624C	R	-	1	0	PTPRR	69336761	1.000000	0.71417	0.998000	0.56505	0.805000	0.45488	9.099000	0.94207	2.573000	0.86826	0.655000	0.94253	CGT		0.458	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71050494	G	A	71050494	3	1	61	1	0	0	0	0	1	0	0	0	12847	1058	37	1	111	1	PTPRR	12	71050494	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64389	71050494	62801401	8189	16174										
PTPRR	5801	broad.mit.edu	37	chr12	71056292	71056292	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctttaagacaaggtttcGaatggtgtagttatcacatt	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:71056292G>A	ENST00000283228.2	-	11	2043	c.1591C>T	c.(1591-1593)Cga>Tga	p.R531*	PTPRR_ENST00000549308.1_Nonsense_Mutation_p.R286*|PTPRR_ENST00000342084.4_Nonsense_Mutation_p.R419*|PTPRR_ENST00000440835.2_Nonsense_Mutation_p.R286*|PTPRR_ENST00000378778.1_Nonsense_Mutation_p.R325*|PTPRR_ENST00000537619.2_5'UTR	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	531	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R531*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		ACAAGGTTTCGAATGGTGTAG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											115	101	106					12																	71056292		2203	4299	6502	69342559	SO:0001587	stop_gained	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1591C>T	12.37:g.71056292G>A	ENSP00000283228:p.Arg531*		69342559	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Nonsense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	G	39	7.291274	0.98189	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	.	.	.	5.87	2.91	0.33838	.	0.000000	0.48286	D	0.000197	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.4113	15.15	0.72689	0.0:0.0:0.6304:0.3696	.	.	.	.	X	286;531;325;419;286	.	ENSP00000283228:R531X	R	-	1	2	PTPRR	69342559	1.000000	0.71417	0.684000	0.30055	0.981000	0.71138	4.091000	0.57700	0.407000	0.25591	-0.182000	0.12963	CGA		0.353	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71056292	G	A	71056292	4	1	61	1	0	0	0	0	0	1	0	0	12847	1066	37	1	398	1	PTPRR	12	71056292	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5798	71056292	62795603	8190	16175										
PTPRR	5801	broad.mit.edu	37	chr12	71077918	71077918	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcatacctcatttttttCtttgagttttgtgatcataa	5	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:71077918C>A	ENST00000283228.2	-	10	1938	c.1486G>T	c.(1486-1488)Gaa>Taa	p.E496*	PTPRR_ENST00000549308.1_Nonsense_Mutation_p.E251*|PTPRR_ENST00000342084.4_Nonsense_Mutation_p.E384*|PTPRR_ENST00000440835.2_Nonsense_Mutation_p.E251*|PTPRR_ENST00000378778.1_Nonsense_Mutation_p.E290*	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	496	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E496*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TCATTTTTTTCTTTGAGTTTT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											92	79	84					12																	71077918		2203	4300	6503	69364185	SO:0001587	stop_gained	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1486G>T	12.37:g.71077918C>A	ENSP00000283228:p.Glu496*		69364185	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Nonsense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	39	7.802260	0.98498	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	.	.	.	5.83	5.83	0.93111	.	0.000000	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-22.2902	19.7442	0.96245	0.0:1.0:0.0:0.0	.	.	.	.	X	251;496;290;384;251	.	ENSP00000283228:E496X	E	-	1	0	PTPRR	69364185	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.770000	0.95276	0.655000	0.94253	GAA		0.398	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71077918	C	A	71077918	4	1	61	1	0	0	0	0	0	1	0	0	12847	922	32	2	507	2	PTPRR	12	71077918	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21626	71077918	62773977	8191	16176										
PTPRR	5801	broad.mit.edu	37	chr12	71092068	71092068	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaaatggtcttatagcgaTttttagttccatgacgcgga	10	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:71092068T>G	ENST00000283228.2	-	8	1708	c.1256A>C	c.(1255-1257)aAt>aCt	p.N419T	PTPRR_ENST00000549308.1_Missense_Mutation_p.N174T|PTPRR_ENST00000342084.4_Missense_Mutation_p.N307T|PTPRR_ENST00000440835.2_Missense_Mutation_p.N174T|PTPRR_ENST00000378778.1_Missense_Mutation_p.N213T	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	419	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.N419T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		CTTATAGCGATTTTTAGTTCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	85	84					12																	71092068		2202	4300	6502	69378335	SO:0001583	missense	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1256A>C	12.37:g.71092068T>G	ENSP00000283228:p.Asn419Thr		69378335	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420442	0.83559	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308;ENST00000550661	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	5.79	5.79	0.91817	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.104826	0.41001	D	0.000971	D	0.82866	0.5130	H	0.99379	4.54	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.996;0.998;0.999	D	0.90578	0.4527	10	0.87932	D	0	-16.0463	16.1323	0.81449	0.0:0.0:0.0:1.0	.	268;307;213;419	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	T	174;419;213;307;174;174	ENSP00000391750:N174T;ENSP00000283228:N419T;ENSP00000368054:N213T;ENSP00000339605:N307T;ENSP00000446943:N174T;ENSP00000449616:N174T	ENSP00000283228:N419T	N	-	2	0	PTPRR	69378335	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.940000	0.75917	2.223000	0.72356	0.454000	0.30748	AAT		0.343	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		G	71092068	T	G	71092068	3	3	61	1	0	0	0	0	1	0	0	0	12847	1493	52	4	745	4	PTPRR	12	71092068	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	14150	71092068	62759827	8192	16177										
TSPAN8	7103	broad.mit.edu	37	chr12	71533570	71533570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgatgatggcacctacaGcaatcaatatgtccacagca	7	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:71533570G>A	ENST00000393330.2	-	7	734	c.182C>T	c.(181-183)gCt>gTt	p.A61V	TSPAN8_ENST00000546561.1_Missense_Mutation_p.A61V|TSPAN8_ENST00000552128.1_5'Flank|TSPAN8_ENST00000552786.1_5'Flank|TSPAN8_ENST00000247829.3_Missense_Mutation_p.A61V			P19075	TSN8_HUMAN	tetraspanin 8	61					negative regulation of blood coagulation (GO:0030195)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.A61V(1)		breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(7)|skin(3)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			GGCACCTACAGCAATCAATAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											151	145	147					12																	71533570		2203	4300	6503	69819837	SO:0001583	missense	7103			M35252	CCDS8999.1	12q14.1-q21.1	2013-02-14	2005-03-21	2005-03-21		ENSG00000127324		"Tetraspanins"	11855	protein-coding gene	gene with protein product		600769	"transmembrane 4 superfamily member 3"	TM4SF3		2395876	Standard	NM_004616		Approved	CO-029	uc001swj.1	P19075		ENST00000393330.2:c.182C>T	12.37:g.71533570G>A	ENSP00000377003:p.Ala61Val		69819837	B2R7T7|Q9BS78	Missense_Mutation	SNP	ENST00000393330.2	37	CCDS8999.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995259	0.54147	.	.	ENSG00000127324	ENST00000393330;ENST00000247829;ENST00000546561	T;T;T	0.78364	-1.17;-1.17;-1.17	5.18	3.25	0.37280	.	0.228623	0.44483	D	0.000460	T	0.79441	0.4446	L	0.48218	1.51	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.73972	-0.3814	10	0.09084	T	0.74	.	9.6025	0.39612	0.1816:0.0:0.8184:0.0	.	61	P19075	TSN8_HUMAN	V	61	ENSP00000377003:A61V;ENSP00000247829:A61V;ENSP00000447160:A61V	ENSP00000247829:A61V	A	-	2	0	TSPAN8	69819837	0.911000	0.30947	0.958000	0.39756	0.088000	0.18126	3.698000	0.54771	0.605000	0.29947	0.655000	0.94253	GCT		0.418	TSPAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404737.1	NM_004616		A	71533570	G	A	71533570	3	1	61	1	0	0	0	0	1	0	0	0	16693	971	34	3	555	3	TSPAN8	12	71533570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	441502	71533570	62318325	8193	16178										
ZFC3H1	196441	broad.mit.edu	37	chr12	72013718	72013718	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttttacctgtaagatgaaGaatttgcacatatgataaaa	6	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72013718G>T	ENST00000378743.3	-	26	5395	c.5037C>A	c.(5035-5037)ttC>ttA	p.F1679L		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1679					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F1679L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GTAAGATGAAGAATTTGCACA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	55	57					12																	72013718		1827	4078	5905	70299985	SO:0001583	missense	196441			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5037C>A	12.37:g.72013718G>T	ENSP00000368017:p.Phe1679Leu		70299985	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570094	0.45798	.	.	ENSG00000133858	ENST00000378743	T	0.33438	1.41	5.67	1.78	0.24846	Tetratricopeptide-like helical (1);	0.182763	0.48286	N	0.000181	T	0.15739	0.0379	L	0.29908	0.895	0.80722	D	1	B	0.31077	0.307	B	0.27380	0.079	T	0.11743	-1.0575	10	0.08599	T	0.76	.	6.8661	0.24094	0.2811:0.1275:0.5913:0.0	.	1679	O60293	ZC3H1_HUMAN	L	1679	ENSP00000368017:F1679L	ENSP00000368017:F1679L	F	-	3	2	ZFC3H1	70299985	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	1.373000	0.34272	0.045000	0.15804	0.650000	0.86243	TTC		0.348	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72013718	G	T	72013718	3	4	61	1	0	0	0	0	1	0	0	0	17672	933	33	2	972	2	ZFC3H1	12	72013718	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	480148	72013718	61838177	8194	16179										
ZFC3H1	196441	broad.mit.edu	37	chr12	72013875	72013875	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggacatgattccaataaaGatttacaaagctccattgca	6	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72013875G>T	ENST00000378743.3	-	26	5238	c.4880C>A	c.(4879-4881)tCt>tAt	p.S1627Y		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1627					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S1627Y(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTCCAATAAAGATTTACAAAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											63	57	59					12																	72013875		1847	4099	5946	70300142	SO:0001583	missense	196441			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4880C>A	12.37:g.72013875G>T	ENSP00000368017:p.Ser1627Tyr		70300142	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.337491	0.24253	.	.	ENSG00000133858	ENST00000378743	T	0.35048	1.33	5.56	-4.67	0.03319	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.537042	0.20991	N	0.082030	T	0.24967	0.0606	L	0.27053	0.805	0.09310	N	1	P	0.52842	0.956	P	0.48030	0.564	T	0.30880	-0.9963	10	0.56958	D	0.05	.	9.0566	0.36410	0.0:0.2011:0.2818:0.5171	.	1627	O60293	ZC3H1_HUMAN	Y	1627	ENSP00000368017:S1627Y	ENSP00000368017:S1627Y	S	-	2	0	ZFC3H1	70300142	0.012000	0.17670	0.014000	0.15608	0.736000	0.42039	0.555000	0.23422	-0.776000	0.04578	-0.830000	0.03078	TCT		0.363	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72013875	G	T	72013875	3	4	61	1	0	0	0	0	1	0	0	0	17672	942	33	2	1129	2	ZFC3H1	12	72013875	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157	72013875	61838020	8195	16180										
ZFC3H1	196441	broad.mit.edu	37	chr12	72027185	72027185	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcttgttgcactaaattCtttaaaacagattcatcttt	4	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72027185C>A	ENST00000378743.3	-	13	2902	c.2544G>T	c.(2542-2544)aaG>aaT	p.K848N		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	848					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.K848N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GCACTAAATTCTTTAAAACAG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	12											42	38	39					12																	72027185		1791	4058	5849	70313452	SO:0001583	missense	196441			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.2544G>T	12.37:g.72027185C>A	ENSP00000368017:p.Lys848Asn		70313452	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.213825	0.39102	.	.	ENSG00000133858	ENST00000378743	T	0.37752	1.18	5.04	2.05	0.26809	.	0.207171	0.40818	N	0.001017	T	0.27205	0.0667	N	0.19112	0.55	0.80722	D	1	P	0.51791	0.948	P	0.49528	0.614	T	0.01961	-1.1239	10	0.32370	T	0.25	.	8.0166	0.30385	0.0:0.4869:0.0:0.5131	.	848	O60293	ZC3H1_HUMAN	N	848	ENSP00000368017:K848N	ENSP00000368017:K848N	K	-	3	2	ZFC3H1	70313452	1.000000	0.71417	0.999000	0.59377	0.844000	0.47949	0.612000	0.24283	0.099000	0.17552	0.460000	0.39030	AAG		0.303	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72027185	C	A	72027185	3	1	61	1	0	0	0	0	1	0	0	0	17672	912	32	2	3517	2	ZFC3H1	12	72027185	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13310	72027185	61824710	8196	16181										
ZFC3H1	196441	broad.mit.edu	37	chr12	72028527	72028527	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatattcaatcttcttttCttcaggcaaagcctccggtg	6	11	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72028527C>A	ENST00000378743.3	-	11	2675	c.2317G>T	c.(2317-2319)Gaa>Taa	p.E773*		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	773					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.E773*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATCTTCTTTTCTTCAGGCAAA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											81	74	76					12																	72028527		1799	4060	5859	70314794	SO:0001587	stop_gained	196441			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.2317G>T	12.37:g.72028527C>A	ENSP00000368017:p.Glu773*		70314794	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Nonsense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	C	42	9.608956	0.99219	.	.	ENSG00000133858	ENST00000378743	.	.	.	5.55	5.55	0.83447	.	0.129578	0.49305	D	0.000147	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.5027	0.95103	0.0:1.0:0.0:0.0	.	.	.	.	X	773	.	ENSP00000368017:E773X	E	-	1	0	ZFC3H1	70314794	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.407000	0.80029	2.610000	0.88304	0.655000	0.94253	GAA		0.313	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72028527	C	A	72028527	4	1	61	1	0	0	0	0	0	1	0	0	17672	922	32	2	3752	2	ZFC3H1	12	72028527	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1342	72028527	61823368	8197	16182										
THAP2	83591	broad.mit.edu	37	chr12	72068116	72068116	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacctaacaggacaaactCgacgacttaaaatggatgct	8	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72068116C>T	ENST00000308086.2	+	2	1706	c.205C>T	c.(205-207)Cga>Tga	p.R69*	RP11-293I14.2_ENST00000548802.1_Nonsense_Mutation_p.R45*	NM_031435.3	NP_113623.1	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated protein 2	69						nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R69*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	10						AGGACAAACTCGACGACTTAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											124	122	122					12																	72068116		2203	4300	6503	70354383	SO:0001587	stop_gained	83591			BC008358	CCDS9001.1	12q21.1	2013-01-25				ENSG00000173451		"THAP (C2CH-type zinc finger) domain containing"	20854	protein-coding gene	gene with protein product		612531				12575992	Standard	NM_031435		Approved	DKFZP564I0422	uc001swq.3	Q9H0W7	OTTHUMG00000169556	ENST00000308086.2:c.205C>T	12.37:g.72068116C>T	ENSP00000310796:p.Arg69*		70354383	B2R8P3	Nonsense_Mutation	SNP	ENST00000308086.2	37	CCDS9001.1	.	.	.	.	.	.	.	.	.	.	C	49	15.776912	0.99845	.	.	ENSG00000173451	ENST00000308086	.	.	.	6.08	1.43	0.22495	.	0.203595	0.31519	N	0.007503	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4775	0.11750	0.5421:0.2695:0.1088:0.0796	.	.	.	.	X	69	.	ENSP00000310796:R69X	R	+	1	2	THAP2	70354383	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	0.435000	0.21510	0.307000	0.22880	0.655000	0.94253	CGA		0.378	THAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404796.1	NM_031435		T	72068116	C	T	72068116	4	4	61	1	0	0	0	0	0	1	0	0	15883	876	31	1	211	1	THAP2	12	72068116	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39589	72068116	61783779	8198	16183										
THAP2	83591	broad.mit.edu	37	chr12	72070853	72070853	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagataaaacactgctaagtCtaaatctaaaacagaccaag	5	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72070853C>A	ENST00000308086.2	+	3	2153	c.652C>A	c.(652-654)Cta>Ata	p.L218I	RP11-293I14.2_ENST00000548802.1_Intron	NM_031435.3	NP_113623.1	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated protein 2	218						nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L218I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	10						ACTGCTAAGTCTAAATCTAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	59	59					12																	72070853		2203	4298	6501	70357120	SO:0001583	missense	83591			BC008358	CCDS9001.1	12q21.1	2013-01-25				ENSG00000173451		"THAP (C2CH-type zinc finger) domain containing"	20854	protein-coding gene	gene with protein product		612531				12575992	Standard	NM_031435		Approved	DKFZP564I0422	uc001swq.3	Q9H0W7	OTTHUMG00000169556	ENST00000308086.2:c.652C>A	12.37:g.72070853C>A	ENSP00000310796:p.Leu218Ile		70357120	B2R8P3	Missense_Mutation	SNP	ENST00000308086.2	37	CCDS9001.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585589	0.28268	.	.	ENSG00000173451	ENST00000308086	D	0.96232	-3.95	5.8	3.0	0.34707	.	0.524779	0.14718	N	0.302481	D	0.87865	0.6285	N	0.08118	0	0.80722	D	1	B	0.30793	0.295	B	0.32211	0.142	T	0.78580	-0.2149	10	0.25106	T	0.35	.	1.9381	0.03341	0.1423:0.4953:0.1376:0.2248	.	218	Q9H0W7	THAP2_HUMAN	I	218	ENSP00000310796:L218I	ENSP00000310796:L218I	L	+	1	2	THAP2	70357120	0.994000	0.37717	0.932000	0.37286	0.678000	0.39670	0.427000	0.21379	0.371000	0.24564	-0.261000	0.10672	CTA		0.353	THAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404796.1	NM_031435		A	72070853	C	A	72070853	3	1	61	1	0	0	0	0	1	0	0	0	15883	912	32	2	662	2	THAP2	12	72070853	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2737	72070853	61781042	8199	16184										
TBC1D15	64786	broad.mit.edu	37	chr12	72290536	72290536	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagtaccaaggaggaaaGaacccaattacaaaagcaaa	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72290536G>T	ENST00000550746.1	+	10	1179	c.1115G>T	c.(1114-1116)aGa>aTa	p.R372I	TBC1D15_ENST00000393309.3_Missense_Mutation_p.R126I|TBC1D15_ENST00000319106.8_Missense_Mutation_p.R363I|TBC1D15_ENST00000485960.2_Missense_Mutation_p.R355I	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	372	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)	p.R372I(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AAGGAGGAAAGAACCCAATTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											88	90	89					12																	72290536		2203	4300	6503	70576803	SO:0001583	missense	64786			AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1115G>T	12.37:g.72290536G>T	ENSP00000448182:p.Arg372Ile		70576803	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Missense_Mutation	SNP	ENST00000550746.1	37	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543368	0.86022	.	.	ENSG00000121749	ENST00000550746;ENST00000491063;ENST00000319106;ENST00000485960;ENST00000393309	T;T;T;T;T	0.04809	3.55;3.55;3.55;3.55;3.55	5.87	4.05	0.47172	Rab-GAP/TBC domain (4);	0.046933	0.85682	D	0.000000	T	0.24509	0.0594	M	0.91818	3.245	0.80722	D	1	D;D;D	0.60160	0.987;0.971;0.971	D;P;P	0.64506	0.926;0.879;0.9	T	0.08973	-1.0696	10	0.87932	D	0	-19.3556	12.0146	0.53307	0.1384:0.0:0.8616:0.0	.	363;355;372	E9PH93;Q8TC07-2;Q8TC07	.;.;TBC15_HUMAN	I	372;256;363;355;126	ENSP00000448182:R372I;ENSP00000418091:R256I;ENSP00000318262:R363I;ENSP00000420678:R355I;ENSP00000376986:R126I	ENSP00000318262:R363I	R	+	2	0	TBC1D15	70576803	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.903000	0.87398	1.492000	0.48499	0.650000	0.86243	AGA		0.363	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771		T	72290536	G	T	72290536	3	4	61	1	0	0	0	0	1	0	0	0	15643	942	33	2	1277	2	TBC1D15	12	72290536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219683	72290536	61561359	8200	16185										
TBC1D15	64786	broad.mit.edu	37	chr12	72315181	72315181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccatgaaaattgatgtgGaagatatactctgcaaggca	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72315181G>A	ENST00000550746.1	+	17	1865	c.1801G>A	c.(1801-1803)Gaa>Aaa	p.E601K	TBC1D15_ENST00000393309.3_Missense_Mutation_p.E355K|TBC1D15_ENST00000319106.8_Missense_Mutation_p.E592K|TBC1D15_ENST00000485960.2_Missense_Mutation_p.E584K	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	601					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)	p.E601K(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AATTGATGTGGAAGATATACT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	12											109	118	115					12																	72315181		2203	4300	6503	70601448	SO:0001583	missense	64786			AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1801G>A	12.37:g.72315181G>A	ENSP00000448182:p.Glu601Lys		70601448	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Missense_Mutation	SNP	ENST00000550746.1	37	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.700326	0.68501	.	.	ENSG00000121749	ENST00000550746;ENST00000319106;ENST00000485960;ENST00000393309	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.29	5.29	0.74685	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.32194	0.0821	L	0.46157	1.445	0.58432	D	0.999996	D;D;P	0.56746	0.962;0.977;0.877	P;P;B	0.51487	0.448;0.671;0.265	T	0.01036	-1.1473	10	0.37606	T	0.19	-21.8889	12.6268	0.56634	0.0762:0.0:0.9238:0.0	.	592;584;601	E9PH93;Q8TC07-2;Q8TC07	.;.;TBC15_HUMAN	K	601;592;584;355	ENSP00000448182:E601K;ENSP00000318262:E592K;ENSP00000420678:E584K;ENSP00000376986:E355K	ENSP00000318262:E592K	E	+	1	0	TBC1D15	70601448	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.645000	0.83430	2.646000	0.89796	0.591000	0.81541	GAA		0.299	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771		A	72315181	G	A	72315181	3	1	61	1	0	0	0	0	1	0	0	0	15643	1175	41	3	1991	3	TBC1D15	12	72315181	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24645	72315181	61536714	8201	16186										
TPH2	121278	broad.mit.edu	37	chr12	72332842	72332842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctggattcagcagtgcccGaagagcatcagctacttggc	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72332842G>A	ENST00000333850.3	+	1	217	c.76G>A	c.(76-78)Gaa>Aaa	p.E26K	TPH2_ENST00000546576.1_3'UTR	NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	26					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.E26K(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	AGCAGTGCCCGAAGAGCATCA	0.468											OREG0021996	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											120	104	110					12																	72332842		2203	4300	6503	70619109	SO:0001583	missense	121278			AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.76G>A	12.37:g.72332842G>A	ENSP00000329093:p.Glu26Lys	1136	70619109	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	37	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.672513	0.47781	.	.	ENSG00000139287	ENST00000333850;ENST00000266669	D	0.99466	-5.95	5.6	5.6	0.85130	.	0.246896	0.37761	N	0.001957	D	0.97554	0.9199	L	0.27053	0.805	0.35742	D	0.818787	B	0.09022	0.002	B	0.04013	0.001	D	0.98223	1.0479	10	0.30078	T	0.28	-16.665	14.2983	0.66329	0.0:0.148:0.852:0.0	.	26	Q8IWU9	TPH2_HUMAN	K	26	ENSP00000329093:E26K	ENSP00000266669:E26K	E	+	1	0	TPH2	70619109	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	4.961000	0.63681	2.649000	0.89929	0.650000	0.86243	GAA		0.468	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		A	72332842	G	A	72332842	3	1	61	1	0	0	0	0	1	0	0	0	16442	1059	37	1	78	1	TPH2	12	72332842	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17661	72332842	61519053	8202	16187										
TPH2	121278	broad.mit.edu	37	chr12	72425140	72425140	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagcctactttgtttcaGaaagttttgaagaagccaaa	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72425140G>T	ENST00000333850.3	+	10	1408	c.1267G>T	c.(1267-1269)Gaa>Taa	p.E423*		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	423					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.E423*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CTTTGTTTCAGAAAGTTTTGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											101	107	105					12																	72425140		2203	4300	6503	70711407	SO:0001587	stop_gained	121278			AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1267G>T	12.37:g.72425140G>T	ENSP00000329093:p.Glu423*		70711407	A6NGA4|Q14CB0	Nonsense_Mutation	SNP	ENST00000333850.3	37	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	G	39	7.658789	0.98415	.	.	ENSG00000139287	ENST00000333850	.	.	.	5.43	5.43	0.79202	.	0.112865	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-19.2914	19.589	0.95499	0.0:0.0:1.0:0.0	.	.	.	.	X	423	.	ENSP00000329093:E423X	E	+	1	0	TPH2	70711407	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.813000	0.99286	2.709000	0.92574	0.491000	0.48974	GAA		0.383	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		T	72425140	G	T	72425140	4	4	61	1	0	0	0	0	0	1	0	0	16442	943	33	2	1305	2	TPH2	12	72425140	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92298	72425140	61426755	8203	16188										
TRHDE	29953	broad.mit.edu	37	chr12	72667273	72667273	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgaagattatctacaacGcgctcatcgagaatgagctc	8	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72667273G>A	ENST00000261180.4	+	1	811	c.715G>A	c.(715-717)Gcg>Acg	p.A239T	TRHDE-AS1_ENST00000435350.1_RNA|TRHDE-AS1_ENST00000550334.1_RNA|TRHDE-AS1_ENST00000426250.3_RNA	NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	239					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A239T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						TATCTACAACGCGCTCATCGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12											55	56	56					12																	72667273		2202	4300	6502	70953540	SO:0001583	missense	29953			AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.715G>A	12.37:g.72667273G>A	ENSP00000261180:p.Ala239Thr		70953540	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.032915|4.032915	0.75504|0.75504	.|.	.|.	ENSG00000072657|ENSG00000072657	ENST00000261180|ENST00000547300	T|.	0.02974|.	4.09|.	5.1|5.1	5.1|5.1	0.69264|0.69264	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73690|0.73690	0.3619|0.3619	M|M	0.67569|0.67569	2.06|2.06	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.65573|.	0.936|.	T|T	0.73322|0.73322	-0.4019|-0.4019	10|5	0.72032|.	D|.	0.01|.	.|.	17.2833|17.2833	0.87134|0.87134	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	239|.	Q9UKU6|.	TRHDE_HUMAN|.	T|H	239|4	ENSP00000261180:A239T|.	ENSP00000261180:A239T|.	A|R	+|+	1|2	0|0	TRHDE|TRHDE	70953540|70953540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.524000|0.524000	0.34500|0.34500	9.104000|9.104000	0.94239|0.94239	2.358000|2.358000	0.79984|0.79984	0.514000|0.514000	0.50259|0.50259	GCG|CGC		0.572	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		A	72667273	G	A	72667273	3	1	61	1	0	0	0	0	1	0	0	0	16519	1087	38	1	717	1	TRHDE	12	72667273	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	242133	72667273	61184622	8204	16189										
TRHDE	29953	broad.mit.edu	37	chr12	72680634	72680634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggaagatggatgggttaCggatcacttttcacagaccc	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72680634C>T	ENST00000261180.4	+	2	1049	c.953C>T	c.(952-954)aCg>aTg	p.T318M		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	318					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T318M(3)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GGATGGGTTACGGATCACTTT	0.413																																																3	Substitution - Missense(3)	large_intestine(1)|lung(1)|endometrium(1)	12											157	147	151					12																	72680634		2203	4300	6503	70966901	SO:0001583	missense	29953			AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.953C>T	12.37:g.72680634C>T	ENSP00000261180:p.Thr318Met		70966901	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753464	0.69648	.	.	ENSG00000072657	ENST00000261180	T	0.05025	3.51	6.17	6.17	0.99709	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.22627	0.0546	L	0.49256	1.55	0.58432	D	0.999999	D	0.89917	1.0	D	0.71414	0.973	T	0.00002	-1.2612	10	0.56958	D	0.05	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	318	Q9UKU6	TRHDE_HUMAN	M	318	ENSP00000261180:T318M	ENSP00000261180:T318M	T	+	2	0	TRHDE	70966901	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.089000	0.71384	2.941000	0.99782	0.655000	0.94253	ACG		0.413	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		T	72680634	C	T	72680634	3	4	61	1	0	0	0	0	1	0	0	0	16519	536	19	1	959	1	TRHDE	12	72680634	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13361	72680634	61171261	8205	16190										
TRHDE	29953	broad.mit.edu	37	chr12	72771779	72771779	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatatttttaattaggtacGattatatgcaagacctgatg	7	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:72771779G>A	ENST00000261180.4	+	3	1154	c.1058G>A	c.(1057-1059)cGa>cAa	p.R353Q		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	353					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R353Q(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						aattaGGTACGATTATATGCA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	12											33	35	34					12																	72771779		2203	4293	6496	71058046	SO:0001583	missense	29953			AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.1058G>A	12.37:g.72771779G>A	ENSP00000261180:p.Arg353Gln		71058046	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.636728	0.87760	.	.	ENSG00000072657	ENST00000261180	T	0.03152	4.03	5.57	5.57	0.84162	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.18964	0.0455	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.00146	-1.1992	10	0.39692	T	0.17	.	19.5437	0.95283	0.0:0.0:1.0:0.0	.	353	Q9UKU6	TRHDE_HUMAN	Q	353	ENSP00000261180:R353Q	ENSP00000261180:R353Q	R	+	2	0	TRHDE	71058046	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	9.235000	0.95353	2.645000	0.89757	0.585000	0.79938	CGA		0.313	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		A	72771779	G	A	72771779	3	1	61	1	0	0	0	0	1	0	0	0	16519	1058	37	1	1068	1	TRHDE	12	72771779	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91145	72771779	61080116	8206	16191										
KCNC2	3747	broad.mit.edu	37	chr12	75444659	75444659	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcattagtactagctcGaagagtatgtccaagcaccc	7	10	1	1	rs200951837		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:75444659G>A	ENST00000549446.1	-	3	1806	c.1126C>T	c.(1126-1128)Cga>Tga	p.R376*	KCNC2_ENST00000341669.3_Nonsense_Mutation_p.R376*|KCNC2_ENST00000548243.1_5'UTR|KCNC2_ENST00000548513.1_Nonsense_Mutation_p.R376*|KCNC2_ENST00000350228.2_Nonsense_Mutation_p.R376*|KCNC2_ENST00000393288.2_Nonsense_Mutation_p.R376*|KCNC2_ENST00000540018.1_Nonsense_Mutation_p.R376*|KCNC2_ENST00000550433.1_Nonsense_Mutation_p.R376*|KCNC2_ENST00000298972.1_Nonsense_Mutation_p.R376*	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	376					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R376*(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GTACTAGCTCGAAGAGTATGT	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											53	50	51					12																	75444659		2203	4300	6503	73730926	SO:0001587	stop_gained	3747			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1126C>T	12.37:g.75444659G>A	ENSP00000449253:p.Arg376*		73730926	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Nonsense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	G	42	9.583643	0.99211	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	.	.	.	6.06	6.06	0.98353	.	0.000000	0.53938	D	0.000058	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.8785	0.86058	0.0:0.0:0.8713:0.1287	.	.	.	.	X	376	.	ENSP00000298972:R376X	R	-	1	2	KCNC2	73730926	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.969000	0.56816	2.880000	0.98712	0.650000	0.86243	CGA		0.453	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75444659	G	A	75444659	4	1	61	1	0	0	0	0	0	1	0	0	8036	1066	37	1	868	1	KCNC2	12	75444659	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2672880	75444659	58407236	8207	16192										
KCNC2	3747	broad.mit.edu	37	chr12	75444845	75444845	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtcaatgatattcaagaGatttttgatgaattcaagtt	7	3	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:75444845G>T	ENST00000549446.1	-	3	1620	c.940C>A	c.(940-942)Ctc>Atc	p.L314I	KCNC2_ENST00000341669.3_Missense_Mutation_p.L314I|KCNC2_ENST00000548243.1_5'Flank|KCNC2_ENST00000548513.1_Missense_Mutation_p.L314I|KCNC2_ENST00000350228.2_Missense_Mutation_p.L314I|KCNC2_ENST00000393288.2_Missense_Mutation_p.L314I|KCNC2_ENST00000540018.1_Missense_Mutation_p.L314I|KCNC2_ENST00000550433.1_Missense_Mutation_p.L314I|KCNC2_ENST00000298972.1_Missense_Mutation_p.L314I	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	314					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.L314I(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	ATATTCAAGAGATTTTTGATG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	12											95	91	92					12																	75444845		2203	4300	6503	73731112	SO:0001583	missense	3747			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.940C>A	12.37:g.75444845G>T	ENSP00000449253:p.Leu314Ile		73731112	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198039	0.22037	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	D;D;D;D;D;D;D;D	0.98550	-4.99;-4.99;-4.99;-4.99;-4.99;-4.99;-4.99;-4.99	5.76	5.76	0.90799	Ion transport (1);	0.000000	0.64402	D	0.000017	D	0.94411	0.8202	N	0.11284	0.12	0.41275	D	0.986874	B;B;B;B;B	0.32051	0.185;0.354;0.015;0.185;0.006	B;B;B;B;B	0.31547	0.086;0.132;0.017;0.086;0.01	D	0.93096	0.6504	10	0.17369	T	0.5	.	19.5587	0.95364	0.0:0.0:1.0:0.0	.	314;314;314;314;314	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	I	314	ENSP00000448301:L314I;ENSP00000449941:L314I;ENSP00000449253:L314I;ENSP00000340121:L314I;ENSP00000298972:L314I;ENSP00000319877:L314I;ENSP00000438423:L314I;ENSP00000376966:L314I	ENSP00000298972:L314I	L	-	1	0	KCNC2	73731112	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.532000	0.45659	2.718000	0.92993	0.650000	0.86243	CTC		0.403	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		T	75444845	G	T	75444845	3	4	61	1	0	0	0	0	1	0	0	0	8036	942	33	2	1054	2	KCNC2	12	75444845	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186	75444845	58407050	8208	16193										
KCNC2	3747	broad.mit.edu	37	chr12	75601256	75601256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaatgaggtcgggggtctCgaagatgtccagcgcctcct	14	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:75601256C>T	ENST00000549446.1	-	2	1188	c.508G>A	c.(508-510)Gag>Aag	p.E170K	KCNC2_ENST00000341669.3_Missense_Mutation_p.E170K|KCNC2_ENST00000548513.1_Missense_Mutation_p.E170K|KCNC2_ENST00000350228.2_Missense_Mutation_p.E170K|KCNC2_ENST00000393288.2_Missense_Mutation_p.E170K|KCNC2_ENST00000540018.1_Missense_Mutation_p.E170K|KCNC2_ENST00000550433.1_Missense_Mutation_p.E170K|KCNC2_ENST00000298972.1_Missense_Mutation_p.E170K	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	170					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.E170K(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	TCGGGGGTCTCGAAGATGTCC	0.726																																																2	Substitution - Missense(2)	large_intestine(2)	12											24	27	26					12																	75601256		2203	4299	6502	73887523	SO:0001583	missense	3747			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.508G>A	12.37:g.75601256C>T	ENSP00000449253:p.Glu170Lys		73887523	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.693895	0.68386	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	D;D;D;D;D;D;D;D	0.97553	-4.42;-4.42;-4.42;-4.42;-4.42;-4.4;-4.39;-4.43	3.69	3.69	0.42338	.	0.000000	0.47093	D	0.000254	D	0.93906	0.8050	L	0.46670	1.46	0.80722	D	1	B;B;B;B;P	0.37997	0.347;0.347;0.259;0.157;0.614	B;B;B;B;B	0.26770	0.054;0.054;0.049;0.031;0.073	D	0.94776	0.7949	10	0.72032	D	0.01	.	15.9794	0.80094	0.0:1.0:0.0:0.0	.	170;170;170;170;170	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	K	170	ENSP00000448301:E170K;ENSP00000449941:E170K;ENSP00000449253:E170K;ENSP00000340121:E170K;ENSP00000298972:E170K;ENSP00000319877:E170K;ENSP00000438423:E170K;ENSP00000376966:E170K	ENSP00000298972:E170K	E	-	1	0	KCNC2	73887523	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.513000	0.60476	2.047000	0.60756	0.563000	0.77884	GAG		0.726	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		T	75601256	C	T	75601256	3	4	61	1	0	0	0	0	1	0	0	0	8036	893	31	1	1490	1	KCNC2	12	75601256	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156411	75601256	58250639	8209	16194										
KRR1	11103	broad.mit.edu	37	chr12	75897824	75897824	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgatcgtaattcagaatCttttgccaactctctcttaa	5	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:75897824C>A	ENST00000229214.4	-	7	714	c.691G>T	c.(691-693)Gat>Tat	p.D231Y	KRR1_ENST00000438169.2_Intron	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	231					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.D231Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						AATTCAGAATCTTTTGCCAAC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											121	114	116					12																	75897824		2203	4300	6503	74184091	SO:0001583	missense	11103			U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.691G>T	12.37:g.75897824C>A	ENSP00000229214:p.Asp231Tyr		74184091	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Missense_Mutation	SNP	ENST00000229214.4	37	CCDS9012.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856356	0.91355	.	.	ENSG00000111615	ENST00000229214	T	0.31510	1.49	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.67869	0.2939	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74965	-0.3484	10	0.87932	D	0	-14.7821	20.1951	0.98241	0.0:1.0:0.0:0.0	.	231	Q13601	KRR1_HUMAN	Y	231	ENSP00000229214:D231Y	ENSP00000229214:D231Y	D	-	1	0	KRR1	74184091	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.395000	0.66291	2.780000	0.95670	0.585000	0.79938	GAT		0.323	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043		A	75897824	C	A	75897824	3	1	61	1	0	0	0	0	1	0	0	0	8467	913	32	2	470	2	KRR1	12	75897824	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296568	75897824	57954071	8210	16195										
PHLDA1	22822	broad.mit.edu	37	chr12	76424734	76424734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcttgcgggcaccgaaagTcgatctccttgccctctgcc	11	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:76424734T>C	ENST00000266671.5	-	1	2978	c.788A>G	c.(787-789)gAc>gGc	p.D263G	RP11-290L1.3_ENST00000552367.1_RNA|PHLDA1_ENST00000602540.1_Missense_Mutation_p.D122G|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	263	PH.				apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)		p.D263G(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				GCACCGAAAGTCGATCTCCTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	77	85					12																	76424734		2203	4300	6503	74711001	SO:0001583	missense	22822			Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.788A>G	12.37:g.76424734T>C	ENSP00000266671:p.Asp263Gly		74711001	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	ENST00000266671.5	37	CCDS31861.1	.	.	.	.	.	.	.	.	.	.	T	33	5.224522	0.95139	.	.	ENSG00000139289	ENST00000266671;ENST00000421361	T	0.78126	-1.15	4.97	4.97	0.65823	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	D	0.86066	0.5844	M	0.62088	1.915	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87685	0.2550	10	0.87932	D	0	-24.549	14.8172	0.70045	0.0:0.0:0.0:1.0	.	263	Q8WV24	PHLA1_HUMAN	G	263;122	ENSP00000266671:D263G	ENSP00000266671:D263G	D	-	2	0	PHLDA1	74711001	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.631000	0.83237	2.087000	0.62958	0.459000	0.35465	GAC		0.567	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		C	76424734	T	C	76424734	3	2	61	1	0	0	0	0	1	0	0	0	11879	1667	58	4	421	4	PHLDA1	12	76424734	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	526910	76424734	57427161	8211	16196										
E2F7	144455	broad.mit.edu	37	chr12	77427749	77427749	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagcttctgttttgcacaGacttgaatctggccatatgt	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:77427749G>T	ENST00000322886.7	-	8	1432	c.1197C>A	c.(1195-1197)gtC>gtA	p.V399V	E2F7_ENST00000416496.2_Silent_p.V399V	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	399					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.V399V(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GTTTTGCACAGACTTGAATCT	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	12											108	98	101					12																	77427749		2203	4300	6503	75951880	SO:0001819	synonymous_variant	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1197C>A	12.37:g.77427749G>T			75951880	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																				0.443	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		T	77427749	G	T	77427749	2	4	61	1	0	0	0	0	0	0	0	1	4883	929	33	2		2	E2F7	12	77427749	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1003015	77427749	56424146	8212	16197										
E2F7	144455	broad.mit.edu	37	chr12	77439840	77439840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggacagtcgggttcagaGaaatccagtaactgttgttc	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:77439840G>T	ENST00000322886.7	-	5	1042	c.807C>A	c.(805-807)ttC>ttA	p.F269L	E2F7_ENST00000416496.2_Missense_Mutation_p.F269L	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	269					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.F269L(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CGGGTTCAGAGAAATCCAGTA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	12											129	122	124					12																	77439840		2203	4300	6503	75963971	SO:0001583	missense	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.807C>A	12.37:g.77439840G>T	ENSP00000323246:p.Phe269Leu		75963971	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.102|6.102	0.387127|0.387127	0.11581|0.11581	.|.	.|.	ENSG00000165891|ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669|ENST00000551058	T;T;T|.	0.15952|.	2.65;2.38;2.39|.	6.04|6.04	3.22|3.22	0.36961|0.36961	.|.	0.302784|.	0.38272|.	N|.	0.001743|.	T|T	0.46927|0.46927	0.1418|0.1418	L|L	0.48877|0.48877	1.53|1.53	0.34661|0.34661	D|D	0.722701|0.722701	B;P|.	0.34864|.	0.347;0.473|.	B;B|.	0.35353|.	0.069;0.201|.	T|T	0.54186|0.54186	-0.8331|-0.8331	10|5	0.22706|.	T|.	0.39|.	-20.0438|-20.0438	4.0837|4.0837	0.09937|0.09937	0.3288:0.1682:0.503:0.0|0.3288:0.1682:0.503:0.0	.|.	269;269|.	F8VSE7;Q96AV8|.	.;E2F7_HUMAN|.	L|Y	269|147	ENSP00000323246:F269L;ENSP00000393639:F269L;ENSP00000448245:F269L|.	ENSP00000323246:F269L|.	F|S	-|-	3|2	2|0	E2F7|E2F7	75963971|75963971	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.868000|0.868000	0.49771|0.49771	1.877000|1.877000	0.39598|0.39598	0.873000|0.873000	0.35799|0.35799	0.561000|0.561000	0.74099|0.74099	TTC|TCT		0.433	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		T	77439840	G	T	77439840	3	4	61	1	0	0	0	0	1	0	0	0	4883	933	33	2	1964	2	E2F7	12	77439840	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12091	77439840	56412055	8213	16198										
NAV3	89795	broad.mit.edu	37	chr12	78400518	78400518	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggactgctttacgccccccGcagcctcccagttcaggacc	9	19	1	0	rs202050601		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78400518G>A	ENST00000397909.2	+	8	1373	c.1200G>A	c.(1198-1200)ccG>ccA	p.P400P	NAV3_ENST00000536525.2_Silent_p.P400P|NAV3_ENST00000228327.6_Silent_p.P400P|NAV3_ENST00000266692.7_Silent_p.P400P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	400						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P400P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TACGCCCCCCGCAGCCTCCCA	0.502										HNSCC(70;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											93	94	93					12																	78400518		1968	4151	6119	76924649	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1200G>A	12.37:g.78400518G>A			76924649	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	0.032	-1.326686	0.01309	.	.	ENSG00000067798	ENST00000550503	.	.	.	5.74	-11.5	0.00074	.	.	.	.	.	T	0.41351	0.1155	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57625	-0.7779	4	.	.	.	-7.5483	5.7999	0.18408	0.127:0.1988:0.4878:0.1863	.	.	.	.	T	224	.	.	A	+	1	0	NAV3	76924649	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-3.348000	0.00503	-4.130000	0.00071	-1.642000	0.00770	GCA		0.502	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78400518	G	A	78400518	2	1	61	1	0	0	0	0	0	0	0	1	10215	1074	38	1		1	NAV3	12	78400518	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	960678	78400518	55451377	8214	16199										
NAV3	89795	broad.mit.edu	37	chr12	78400774	78400774	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactgaaaaaccagtcaaaGaagagaaggatcaggtgaca	11	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78400774G>T	ENST00000397909.2	+	8	1629	c.1456G>T	c.(1456-1458)Gaa>Taa	p.E486*	NAV3_ENST00000536525.2_Nonsense_Mutation_p.E486*|NAV3_ENST00000228327.6_Nonsense_Mutation_p.E486*|NAV3_ENST00000266692.7_Nonsense_Mutation_p.E486*			Q8IVL0	NAV3_HUMAN	neuron navigator 3	486						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.E486*(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ACCAGTCAAAGAAGAGAAGGA	0.398										HNSCC(70;0.22)																																						1	Substitution - Nonsense(1)	large_intestine(1)	12											74	72	73					12																	78400774		1860	4099	5959	76924905	SO:0001587	stop_gained	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1456G>T	12.37:g.78400774G>T	ENSP00000381007:p.Glu486*		76924905	Q8NFW7|Q9Y2E7	Nonsense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	36	5.723323	0.96847	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	.	.	.	5.73	5.73	0.89815	.	0.172417	0.25555	U	0.029863	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-3.7061	19.9161	0.97063	0.0:0.0:1.0:0.0	.	.	.	.	X	486	.	ENSP00000228327:E486X	E	+	1	0	NAV3	76924905	1.000000	0.71417	0.998000	0.56505	0.057000	0.15508	7.827000	0.86722	2.710000	0.92621	0.650000	0.86243	GAA		0.398	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78400774	G	T	78400774	4	4	61	1	0	0	0	0	0	1	0	0	10215	943	33	2	1486	2	NAV3	12	78400774	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	256	78400774	55451121	8215	16200										
NAV3	89795	broad.mit.edu	37	chr12	78511824	78511824	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgaggacagattcagaGaaacgctccaccacagacga	10	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78511824G>T	ENST00000397909.2	+	14	2960	c.2787G>T	c.(2785-2787)gaG>gaT	p.E929D	NAV3_ENST00000536525.2_Missense_Mutation_p.E929D|NAV3_ENST00000228327.6_Missense_Mutation_p.E929D|NAV3_ENST00000266692.7_Missense_Mutation_p.E929D			Q8IVL0	NAV3_HUMAN	neuron navigator 3	929						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.E929D(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CAGATTCAGAGAAACGCTCCA	0.383										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											114	118	117					12																	78511824		1864	4110	5974	77035955	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.2787G>T	12.37:g.78511824G>T	ENSP00000381007:p.Glu929Asp		77035955	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.03|17.03	3.283327|3.283327	0.59867|0.59867	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000552895	T;T;T;T|.	0.35048|.	1.33;1.33;1.33;1.33|.	6.04|6.04	3.26|3.26	0.37387|0.37387	.|.	0.000000|0.000000	0.40385|0.40385	U|U	0.001109|0.001109	T|.	0.61375|.	0.2342|.	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	P;P;D|.	0.67145|.	0.761;0.85;0.996|.	B;B;D|.	0.76071|.	0.277;0.374;0.987|.	T|.	0.56214|.	-0.8016|.	10|.	0.56958|.	D|.	0.05|.	-23.164|-23.164	9.2273|9.2273	0.37414|0.37414	0.2713:0.0:0.7287:0.0|0.2713:0.0:0.7287:0.0	.|.	929;929;929|.	E7EUC6;Q8IVL0;Q8IVL0-2|.	.;NAV3_HUMAN;.|.	D|X	929|1	ENSP00000446132:E929D;ENSP00000381007:E929D;ENSP00000228327:E929D;ENSP00000266692:E929D|.	ENSP00000228327:E929D|.	E|E	+|+	3|1	2|0	NAV3|NAV3	77035955|77035955	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.457000|0.457000	0.32468|0.32468	2.898000|2.898000	0.48672|0.48672	0.451000|0.451000	0.26802|0.26802	0.563000|0.563000	0.77884|0.77884	GAG|GAA		0.383	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78511824	G	T	78511824	3	4	61	1	0	0	0	0	1	0	0	0	10215	933	33	2	2841	2	NAV3	12	78511824	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111050	78511824	55340071	8216	16201										
NAV3	89795	broad.mit.edu	37	chr12	78562590	78562590	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctgaaggctcagaattCtgctgcccaggcggctattc	11	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78562590C>T	ENST00000397909.2	+	24	5098	c.4925C>T	c.(4924-4926)tCt>tTt	p.S1642F	NAV3_ENST00000536525.2_Missense_Mutation_p.S1642F|NAV3_ENST00000228327.6_Missense_Mutation_p.S1642F|NAV3_ENST00000266692.7_Missense_Mutation_p.S1465F			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1642						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.S1642F(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTCAGAATTCTGCTGCCCAG	0.403										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											80	81	81					12																	78562590		1818	4077	5895	77086721	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4925C>T	12.37:g.78562590C>T	ENSP00000381007:p.Ser1642Phe		77086721	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	C	21.2	4.110816	0.77210	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29	5.41	5.41	0.78517	.	0.000000	0.40064	U	0.001192	D	0.93184	0.7829	L	0.46157	1.445	0.80722	D	1	P;P;B;P	0.48503	0.556;0.681;0.384;0.911	B;B;B;P	0.47981	0.211;0.372;0.081;0.563	D	0.93629	0.6954	10	0.66056	D	0.02	-13.6274	19.559	0.95364	0.0:1.0:0.0:0.0	.	1642;1465;1642;1642	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.;.;NAV3_HUMAN;.	F	1642;1642;1642;1465;263;271	ENSP00000446132:S1642F;ENSP00000381007:S1642F;ENSP00000228327:S1642F;ENSP00000266692:S1465F;ENSP00000448303:S271F	ENSP00000228327:S1642F	S	+	2	0	NAV3	77086721	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.050000	0.71063	2.706000	0.92434	0.650000	0.86243	TCT		0.403	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78562590	C	T	78562590	3	4	61	1	0	0	0	0	1	0	0	0	10215	913	32	3	5019	3	NAV3	12	78562590	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50766	78562590	55289305	8217	16202										
NAV3	89795	broad.mit.edu	37	chr12	78573312	78573312	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtttccttcttcaggatCtgtgaatgcacagaagctga	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78573312C>T	ENST00000397909.2	+	29	5540	c.5367C>T	c.(5365-5367)atC>atT	p.I1789I	NAV3_ENST00000536525.2_Silent_p.I1767I|NAV3_ENST00000228327.6_Silent_p.I1767I|NAV3_ENST00000266692.7_Silent_p.I1590I			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1789						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.I1767I(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TCTTCAGGATCTGTGAATGCA	0.463										HNSCC(70;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											56	57	57					12																	78573312		1859	4107	5966	77097443	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5367C>T	12.37:g.78573312C>T			77097443	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																					0.463	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78573312	C	T	78573312	2	4	61	1	0	0	0	0	0	0	0	1	10215	903	32	3		3	NAV3	12	78573312	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10722	78573312	55278583	8218	16203										
NAV3	89795	broad.mit.edu	37	chr12	78582427	78582427	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatacatccactagccttggTctgagctctgactgcattgc	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78582427T>C	ENST00000397909.2	+	33	6098	c.5925T>C	c.(5923-5925)ggT>ggC	p.G1975G	NAV3_ENST00000536525.2_Silent_p.G1953G|NAV3_ENST00000552300.1_Intron|NAV3_ENST00000228327.6_Silent_p.G1953G|NAV3_ENST00000266692.7_Silent_p.G1776G			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1975						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.G1953G(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTAGCCTTGGTCTGAGCTCTG	0.393										HNSCC(70;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											127	121	123					12																	78582427		1909	4136	6045	77106558	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5925T>C	12.37:g.78582427T>C			77106558	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	T	10.03	1.239274	0.22711	.	.	ENSG00000067798	ENST00000552895	.	.	.	5.95	3.52	0.40303	.	.	.	.	.	T	0.53400	0.1794	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45440	-0.9261	4	.	.	.	-9.8262	4.5841	0.12273	0.1405:0.1547:0.0:0.7048	.	.	.	.	P	848	.	.	S	+	1	0	NAV3	77106558	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.691000	0.25467	0.457000	0.26962	0.533000	0.62120	TCT		0.393	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		C	78582427	T	C	78582427	2	2	61	1	0	0	0	0	0	0	0	1	10215	1654	58	4		4	NAV3	12	78582427	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9115	78582427	55269468	8219	16204										
NAV3	89795	broad.mit.edu	37	chr12	78591108	78591108	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcccagttgtaataattCttgataatcttcatcatgtg	6	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78591108C>A	ENST00000397909.2	+	35	6546	c.6373C>A	c.(6373-6375)Ctt>Att	p.L2125I	NAV3_ENST00000536525.2_Missense_Mutation_p.L2103I|NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000228327.6_Missense_Mutation_p.L2103I|NAV3_ENST00000266692.7_Missense_Mutation_p.L1926I			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2125						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.L2103I(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TGTAATAATTCTTGATAATCT	0.333										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											127	115	119					12																	78591108		1836	4082	5918	77115239	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6373C>A	12.37:g.78591108C>A	ENSP00000381007:p.Leu2125Ile		77115239	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.316216|4.316216	0.81469|0.81469	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	D;D;D;D;D|.	0.88586|.	-2.4;-2.4;-2.4;-2.4;-2.4|.	5.35|5.35	5.35|5.35	0.76521|0.76521	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);|.	0.000000|.	0.35378|.	U|.	0.003241|.	T|T	0.57577|0.57577	0.2063|0.2063	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;0.996;1.0;0.998|.	D;D;D;D|.	0.91635|.	0.999;0.986;0.999;0.996|.	T|T	0.51482|0.51482	-0.8700|-0.8700	10|5	0.48119|.	T|.	0.1|.	-12.6085|-12.6085	19.4322|19.4322	0.94775|0.94775	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2103;1926;2125;2103|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	I|Y	2103;2125;2103;1926;717;725|997	ENSP00000446132:L2103I;ENSP00000381007:L2125I;ENSP00000228327:L2103I;ENSP00000266692:L1926I;ENSP00000448303:L725I|.	ENSP00000228327:L2103I|.	L|S	+|+	1|2	0|0	NAV3|NAV3	77115239|77115239	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.965000|0.965000	0.64279|0.64279	6.013000|6.013000	0.70776|0.70776	2.649000|2.649000	0.89929|0.89929	0.655000|0.655000	0.94253|0.94253	CTT|TCT		0.333	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78591108	C	A	78591108	3	1	61	1	0	0	0	0	1	0	0	0	10215	913	32	2	6441	2	NAV3	12	78591108	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8681	78591108	55260787	8220	16205										
NAV3	89795	broad.mit.edu	37	chr12	78592401	78592401	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagtccatatattattggaAcaatgaatcagggagtttct	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78592401A>T	ENST00000397909.2	+	36	6636	c.6463A>T	c.(6463-6465)Aca>Tca	p.T2155S	NAV3_ENST00000536525.2_Missense_Mutation_p.T2133S|NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000228327.6_Missense_Mutation_p.T2133S|NAV3_ENST00000266692.7_Missense_Mutation_p.T1956S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2155						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.T2133S(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TATTATTGGAACAATGAATCA	0.269										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											77	73	74					12																	78592401		1791	4064	5855	77116532	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6463A>T	12.37:g.78592401A>T	ENSP00000381007:p.Thr2155Ser		77116532	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.4|27.4	4.832241|4.832241	0.91036|0.91036	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000552895|ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	.|D;D;D;D;D	.|0.92805	.|-3.11;-3.11;-3.11;-3.11;-3.11	6.16|6.16	6.16|6.16	0.99307|0.99307	.|ATPase, AAA+ type, core (1);	.|0.389468	.|0.18389	.|U	.|0.142707	D|D	0.96247|0.96247	0.8776|0.8776	M|M	0.80847|0.80847	2.515|2.515	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.996;1.0;0.998	.|D;D;D;D	.|0.87578	.|0.998;0.98;0.998;0.994	D|D	0.96361|0.96361	0.9266|0.9266	5|10	.|0.87932	.|D	.|0	-19.2583|-19.2583	16.4795|16.4795	0.84153|0.84153	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2133;1956;2155;2133	.|E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.|.;.;NAV3_HUMAN;.	I|S	1027|2133;2155;2133;1956;747;755	.|ENSP00000446132:T2133S;ENSP00000381007:T2155S;ENSP00000228327:T2133S;ENSP00000266692:T1956S;ENSP00000448303:T755S	.|ENSP00000228327:T2133S	N|T	+|+	2|1	0|0	NAV3|NAV3	77116532|77116532	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.108000|9.108000	0.94275|0.94275	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	AAC|ACA		0.269	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78592401	A	T	78592401	3	4	61	1	0	0	0	0	1	0	0	0	10215	43	2	5	6535	5	NAV3	12	78592401	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1293	78592401	55259494	8221	16206										
NAV3	89795	broad.mit.edu	37	chr12	78598832	78598832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttcagctgcgaccagaaGatgttgggtatgaaagctgc	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:78598832G>T	ENST00000397909.2	+	39	7125	c.6952G>T	c.(6952-6954)Gat>Tat	p.D2318Y	NAV3_ENST00000536525.2_Missense_Mutation_p.D2296Y|NAV3_ENST00000541270.1_Missense_Mutation_p.D148Y|NAV3_ENST00000228327.6_Missense_Mutation_p.D2296Y|NAV3_ENST00000266692.7_Missense_Mutation_p.D2119Y			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2318						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.D2296Y(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCGACCAGAAGATGTTGGGTA	0.502										HNSCC(70;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	12											79	83	81					12																	78598832		2060	4195	6255	77122963	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6952G>T	12.37:g.78598832G>T	ENSP00000381007:p.Asp2318Tyr		77122963	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.77|16.77	3.214654|3.214654	0.58452|0.58452	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000541270|ENST00000552895;ENST00000551162	T;T;T;T;T|.	0.57436|.	1.16;1.14;1.16;1.15;0.4|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.000000|.	0.41396|.	U|.	0.000894|.	D|D	0.83727|0.83727	0.5317|0.5317	M|M	0.86651|0.86651	2.83|2.83	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.998;0.999;0.999|.	D|D	0.85547|0.85547	0.1219|0.1219	10|5	0.87932|.	D|.	0|.	-19.6489|-19.6489	19.1641|19.1641	0.93546|0.93546	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2296;2119;2318;2296|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	Y|I	2296;2318;2296;2119;148|1190;185	ENSP00000446132:D2296Y;ENSP00000381007:D2318Y;ENSP00000228327:D2296Y;ENSP00000266692:D2119Y;ENSP00000444918:D148Y|.	ENSP00000228327:D2296Y|.	D|R	+|+	1|2	0|0	NAV3|NAV3	77122963|77122963	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.009000|0.009000	0.06853|0.06853	9.869000|9.869000	0.99810|0.99810	2.532000|2.532000	0.85374|0.85374	0.591000|0.591000	0.81541|0.81541	GAT|AGA		0.502	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78598832	G	T	78598832	3	4	61	1	0	0	0	0	1	0	0	0	10215	942	33	2	7036	2	NAV3	12	78598832	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6431	78598832	55253063	8222	16207										
PAWR	5074	broad.mit.edu	37	chr12	79990394	79990394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacccacttctatctgttCgagaatatctacttgagaca	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:79990394C>T	ENST00000328827.4	-	5	1100	c.728G>A	c.(727-729)cGa>cAa	p.R243Q		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	243					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)	p.R243Q(1)		NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						TCTATCTGTTCGAGAATATCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	98	100					12																	79990394		2203	4300	6503	78514525	SO:0001583	missense	5074			U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.728G>A	12.37:g.79990394C>T	ENSP00000328088:p.Arg243Gln		78514525	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	37	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.774007	0.69992	.	.	ENSG00000177425	ENST00000328827	T	0.20598	2.06	5.51	4.61	0.57282	.	0.619252	0.14866	N	0.293831	T	0.31451	0.0797	L	0.43152	1.355	0.30948	N	0.725072	D	0.76494	0.999	P	0.58266	0.836	T	0.15321	-1.0441	9	.	.	.	-0.7603	10.2474	0.43350	0.2667:0.604:0.1293:0.0	.	243	Q96IZ0	PAWR_HUMAN	Q	243	ENSP00000328088:R243Q	.	R	-	2	0	PAWR	78514525	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.730000	0.62015	1.299000	0.44798	0.585000	0.79938	CGA		0.363	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		T	79990394	C	T	79990394	3	4	61	1	0	0	0	0	1	0	0	0	11508	884	31	1	306	1	PAWR	12	79990394	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1391562	79990394	53861501	8223	16208										
MYF6	4618	broad.mit.edu	37	chr12	81102357	81102357	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagtggccaagtgtttccGatcattccagggggctcgtg	13	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:81102357G>A	ENST00000228641.3	+	2	796	c.574G>A	c.(574-576)Gat>Aat	p.D192N		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	192					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D192N(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						AAGTGTTTCCGATCATTCCAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	12											67	73	71					12																	81102357		2203	4300	6503	79626488	SO:0001583	missense	4618				CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"Basic helix-loop-helix proteins"	7566	protein-coding gene	gene with protein product	"muscle-specific regulatory factor 4"	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.574G>A	12.37:g.81102357G>A	ENSP00000228641:p.Asp192Asn		79626488	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	37	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.279542	0.40294	.	.	ENSG00000111046	ENST00000228641	D	0.96200	-3.94	5.36	4.47	0.54385	.	0.135378	0.64402	N	0.000004	D	0.95881	0.8659	M	0.73962	2.25	0.42796	D	0.993913	D	0.69078	0.997	P	0.53760	0.734	D	0.94834	0.7999	10	0.38643	T	0.18	-29.7936	11.4501	0.50147	0.0847:0.0:0.9153:0.0	.	192	P23409	MYF6_HUMAN	N	192	ENSP00000228641:D192N	ENSP00000228641:D192N	D	+	1	0	MYF6	79626488	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.261000	0.51530	1.384000	0.46424	-0.140000	0.14226	GAT		0.562	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469		A	81102357	G	A	81102357	3	1	61	1	0	0	0	0	1	0	0	0	10058	1058	37	1	580	1	MYF6	12	81102357	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1111963	81102357	52749538	8224	16209										
PPFIA2	8499	broad.mit.edu	37	chr12	81688688	81688688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctaatcgaagttttaagcGatgcagtggattgctgattc	11	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:81688688G>A	ENST00000549396.1	-	24	3011	c.2851C>T	c.(2851-2853)Cgc>Tgc	p.R951C	PPFIA2_ENST00000550359.2_Missense_Mutation_p.R798C|PPFIA2_ENST00000541570.2_Missense_Mutation_p.R518C|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R852C|PPFIA2_ENST00000552948.1_Missense_Mutation_p.R951C|PPFIA2_ENST00000550584.2_Missense_Mutation_p.R951C|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000541017.1_Missense_Mutation_p.R168C|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R936C|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R936C|RP11-121G22.3_ENST00000549161.1_lincRNA|PPFIA2_ENST00000407050.4_Missense_Mutation_p.R877C|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R951C	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	951	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.R951C(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						AGTTTTAAGCGATGCAGTGGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											129	128	128					12																	81688688		2059	4223	6282	80212819	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2851C>T	12.37:g.81688688G>A	ENSP00000450337:p.Arg951Cys		80212819	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.124018|5.124018	0.94429|0.94429	.|.	.|.	ENSG00000139220|ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000541017;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948|ENST00000551147	T;T;T;T;T;T;T;T;T|.	0.58210|.	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35|.	5.62|5.62	5.62|5.62	0.85841|0.85841	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83303|0.83303	0.5225|0.5225	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.84458|0.84458	0.0592|0.0592	10|5	0.87932|.	D|.	0|.	-6.6626|-6.6626	19.6517|19.6517	0.95819|0.95819	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	951|.	O75334|.	LIPA2_HUMAN|.	C|L	951;936;518;168;877;962;936;951;852;951|116	ENSP00000450337:R951C;ENSP00000450298:R936C;ENSP00000438337:R518C;ENSP00000445532:R168C;ENSP00000385093:R877C;ENSP00000327416:R936C;ENSP00000449338:R951C;ENSP00000388373:R852C;ENSP00000447868:R951C|.	ENSP00000327416:R936C|.	R|S	-|-	1|2	0|0	PPFIA2|PPFIA2	80212819|80212819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.932000|7.932000	0.87634|0.87634	2.662000|2.662000	0.90505|0.90505	0.655000|0.655000	0.94253|0.94253	CGC|TCG		0.493	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81688688	G	A	81688688	3	1	61	1	0	0	0	0	1	0	0	0	12341	1058	37	1	958	1	PPFIA2	12	81688688	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	586331	81688688	52163207	8225	16210										
PPFIA2	8499	broad.mit.edu	37	chr12	81732974	81732974	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacggagctgcccaagtcGagctttttcttttttaccaa	7	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:81732974G>A	ENST00000549396.1	-	21	2693	c.2533C>T	c.(2533-2535)Cga>Tga	p.R845*	PPFIA2_ENST00000550359.2_Nonsense_Mutation_p.R692*|PPFIA2_ENST00000541570.2_Nonsense_Mutation_p.R412*|PPFIA2_ENST00000443686.3_Nonsense_Mutation_p.R746*|PPFIA2_ENST00000552948.1_Nonsense_Mutation_p.R845*|PPFIA2_ENST00000550584.2_Nonsense_Mutation_p.R845*|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000541017.1_Nonsense_Mutation_p.R62*|PPFIA2_ENST00000549325.1_Nonsense_Mutation_p.R827*|PPFIA2_ENST00000333447.7_Nonsense_Mutation_p.R827*|PPFIA2_ENST00000407050.4_Nonsense_Mutation_p.R771*|PPFIA2_ENST00000548586.1_Nonsense_Mutation_p.R845*	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	845					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.R845*(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TGCCCAAGTCGAGCTTTTTCT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											197	195	196					12																	81732974		1863	4103	5966	80257105	SO:0001587	stop_gained	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2533C>T	12.37:g.81732974G>A	ENSP00000450337:p.Arg845*		80257105	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Nonsense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.981454|3.981454	0.74474|0.74474	.|.	.|.	ENSG00000139220|ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000541017;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948|ENST00000551147	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79805	.|0.4509	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77905	.|-0.2413	.|3	0.02654|.	T|.	1|.	-9.8226|-9.8226	19.7201|19.7201	0.96139|0.96139	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	845;827;412;62;771;856;827;845;746;845|7	.|.	ENSP00000327416:R827X|.	R|S	-|-	1|2	2|0	PPFIA2|PPFIA2	80257105|80257105	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.679000|0.679000	0.39708|0.39708	3.168000|3.168000	0.50801|0.50801	2.661000|2.661000	0.90470|0.90470	0.561000|0.561000	0.74099|0.74099	CGA|TCG		0.413	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81732974	G	A	81732974	4	1	61	1	0	0	0	0	0	1	0	0	12341	1066	37	1	1288	1	PPFIA2	12	81732974	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44286	81732974	52118921	8226	16211										
PPFIA2	8499	broad.mit.edu	37	chr12	82070589	82070589	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggtggatcagcccccttaGaaccagccagccctcctgtt	9	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:82070589G>T	ENST00000549396.1	-	4	444	c.284C>A	c.(283-285)tCt>tAt	p.S95Y	PPFIA2_ENST00000552948.1_Missense_Mutation_p.S95Y|PPFIA2_ENST00000550584.2_Missense_Mutation_p.S95Y|PPFIA2_ENST00000549325.1_Intron|PPFIA2_ENST00000333447.7_Intron|PPFIA2_ENST00000548586.1_Missense_Mutation_p.S95Y	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	95					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.S95Y(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						AGCCCCCTTAGAACCAGCCAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	61	61					12																	82070589		1848	4086	5934	80594720	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.284C>A	12.37:g.82070589G>T	ENSP00000450337:p.Ser95Tyr		80594720	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.763252	0.49574	.	.	ENSG00000139220	ENST00000549396;ENST00000541501;ENST00000548586;ENST00000552948;ENST00000547623	T;T;T;T	0.42131	1.31;1.31;1.31;0.98	5.97	5.97	0.96955	.	0.364665	0.26203	N	0.025739	T	0.46034	0.1372	N	0.14661	0.345	0.80722	D	1	P	0.52842	0.956	P	0.61397	0.888	T	0.45977	-0.9224	10	0.54805	T	0.06	.	15.9389	0.79739	0.0:0.0:1.0:0.0	.	95	O75334	LIPA2_HUMAN	Y	95;106;95;95;95	ENSP00000450337:S95Y;ENSP00000449338:S95Y;ENSP00000447868:S95Y;ENSP00000447918:S95Y	ENSP00000439748:S106Y	S	-	2	0	PPFIA2	80594720	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.489000	0.60309	2.836000	0.97738	0.655000	0.94253	TCT		0.423	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	82070589	G	T	82070589	3	4	61	1	0	0	0	0	1	0	0	0	12341	942	33	2	3605	2	PPFIA2	12	82070589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	337615	82070589	51781306	8227	16212										
C12orf26	84190	broad.mit.edu	37	chr12	82796816	82796816	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctggctccaaatactttgCgaatatttacctccaactct	4	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:82796816C>T	ENST00000248306.3	+	5	1255	c.1186C>T	c.(1186-1188)Cga>Tga	p.R396*	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	396							methyltransferase activity (GO:0008168)	p.R396*(1)									AAATACTTTGCGAATATTTAC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											94	91	92					12																	82796816		2203	4300	6503	81320947	SO:0001587	stop_gained	84190			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1186C>T	12.37:g.82796816C>T	ENSP00000248306:p.Arg396*		81320947	Q9H5Y3	Nonsense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659609	0.47467	.	.	ENSG00000127720	ENST00000248306;ENST00000550298	.	.	.	5.49	0.0525	0.14302	.	0.061591	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2559	16.8327	0.85949	0.4112:0.5888:0.0:0.0	.	.	.	.	X	396;31	.	ENSP00000248306:R396X	R	+	1	2	C12orf26	81320947	1.000000	0.71417	0.993000	0.49108	0.249000	0.25844	1.157000	0.31724	0.003000	0.14656	-3.060000	0.00068	CGA		0.373	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		T	82796816	C	T	82796816	4	4	61	1	0	0	0	0	0	1	0	0	1683	760	27	1	1204	1	C12orf26	12	82796816	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726227	82796816	51055079	8228	16213										
C12orf26	84190	broad.mit.edu	37	chr12	82850527	82850527	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcggcatgttggtaaaatTtattccaaatgttcttcttt	7	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:82850527T>G	ENST00000248306.3	+	9	1569	c.1500T>G	c.(1498-1500)atT>atG	p.I500M	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	500							methyltransferase activity (GO:0008168)	p.I500M(1)									TTGGTAAAATTTATTCCAAAT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	12											75	71	72					12																	82850527		2201	4296	6497	81374658	SO:0001583	missense	84190			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1500T>G	12.37:g.82850527T>G	ENSP00000248306:p.Ile500Met		81374658	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.125041	0.56721	.	.	ENSG00000127720	ENST00000248306	T	0.32753	1.44	5.86	2.1	0.27182	.	0.112616	0.64402	D	0.000010	T	0.33789	0.0875	L	0.56769	1.78	0.36813	D	0.88598	D	0.58620	0.983	P	0.54856	0.762	T	0.33497	-0.9866	10	0.32370	T	0.25	-7.9364	1.9312	0.03328	0.2776:0.0766:0.1442:0.5016	.	500	Q8N6Q8	CL026_HUMAN	M	500	ENSP00000248306:I500M	ENSP00000248306:I500M	I	+	3	3	C12orf26	81374658	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	0.060000	0.14342	0.106000	0.17784	0.528000	0.53228	ATT		0.284	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		G	82850527	T	G	82850527	3	3	61	1	0	0	0	0	1	0	0	0	1683	1829	64	4	1534	4	C12orf26	12	82850527	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	53711	82850527	51001368	8229	16214										
C12orf26	84190	broad.mit.edu	37	chr12	82871104	82871104	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagactttgattcttctGgatcgactttgttacctgaa	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:82871104G>T	ENST00000248306.3	+	11	1761	c.1692G>T	c.(1690-1692)ctG>ctT	p.L564L		NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	564							methyltransferase activity (GO:0008168)	p.L564L(1)									TGATTCTTCTGGATCGACTTT	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	12											87	95	92					12																	82871104		2203	4293	6496	81395235	SO:0001819	synonymous_variant	84190			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1692G>T	12.37:g.82871104G>T			81395235	Q9H5Y3	Silent	SNP	ENST00000248306.3	37	CCDS9024.1																																																																																				0.299	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		T	82871104	G	T	82871104	2	4	61	1	0	0	0	0	0	0	0	1	1683	1335	47	2		2	C12orf26	12	82871104	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20577	82871104	50980791	8230	16215										
TMTC2	160335	broad.mit.edu	37	chr12	83424585	83424585	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtttttcaagggtcgtaaGagtgaggctgaaaagctctt	12	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:83424585G>T	ENST00000321196.3	+	9	2786	c.2079G>T	c.(2077-2079)aaG>aaT	p.K693N	TMTC2_ENST00000549919.1_Missense_Mutation_p.K687N	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	693					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.K693N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						AGGGTCGTAAGAGTGAGGCTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											182	165	171					12																	83424585		2203	4300	6503	81948716	SO:0001583	missense	160335			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2079G>T	12.37:g.83424585G>T	ENSP00000322300:p.Lys693Asn		81948716	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	g	13.35	2.209793	0.39003	.	.	ENSG00000179104	ENST00000321196;ENST00000549919;ENST00000546590	D;D	0.88354	-2.37;-2.37	5.53	2.68	0.31781	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.132010	0.64402	D	0.000002	D	0.87819	0.6273	L	0.46819	1.47	0.42202	D	0.991774	D	0.53312	0.959	P	0.54815	0.761	D	0.83827	0.0250	10	0.27785	T	0.31	-4.0833	8.2402	0.31656	0.1448:0.0:0.7247:0.1305	.	693	Q8N394	TMTC2_HUMAN	N	693;687;448	ENSP00000322300:K693N;ENSP00000447609:K687N	ENSP00000322300:K693N	K	+	3	2	TMTC2	81948716	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	2.006000	0.40874	0.821000	0.34540	-0.224000	0.12420	AAG		0.423	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83424585	G	T	83424585	3	4	61	1	0	0	0	0	1	0	0	0	16300	933	33	2	2113	2	TMTC2	12	83424585	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	553481	83424585	50427310	8231	16216										
TMTC2	160335	broad.mit.edu	37	chr12	83526117	83526117	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacacagtccaatctccgCaaactgtggaacatcatgga	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:83526117C>T	ENST00000321196.3	+	12	3167	c.2460C>T	c.(2458-2460)cgC>cgT	p.R820R	TMTC2_ENST00000549919.1_Silent_p.R814R	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	820					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.R820R(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CCAATCTCCGCAAACTGTGGA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	12											98	79	85					12																	83526117		2203	4300	6503	82050248	SO:0001819	synonymous_variant	160335			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2460C>T	12.37:g.83526117C>T			82050248	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	37	CCDS9025.1																																																																																				0.517	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83526117	C	T	83526117	2	4	61	1	0	0	0	0	0	0	0	1	16300	697	25	3		3	TMTC2	12	83526117	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101532	83526117	50325778	8232	16217										
SLC6A15	55117	broad.mit.edu	37	chr12	85266480	85266480	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcataaactaaatgataatcTtctgcagtaacagttgaaag	6	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85266480T>G	ENST00000266682.5	-	8	1744	c.1203A>C	c.(1201-1203)gaA>gaC	p.E401D	SLC6A15_ENST00000309283.7_Missense_Mutation_p.E109D|SLC6A15_ENST00000552192.1_Missense_Mutation_p.E294D|SLC6A15_ENST00000551388.1_5'Flank	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	401					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.E401D(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AATGATAATCTTCTGCAGTAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	12											75	77	77					12																	85266480		2203	4297	6500	83790611	SO:0001583	missense	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1203A>C	12.37:g.85266480T>G	ENSP00000266682:p.Glu401Asp		83790611	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	8.742	0.919214	0.17982	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000318721;ENST00000552192;ENST00000551818	T;T;T	0.78364	-1.17;-0.75;-0.94	5.46	0.789	0.18607	.	0.344782	0.30762	N	0.008935	T	0.58949	0.2158	L	0.31371	0.925	0.80722	D	1	B;B	0.12013	0.001;0.005	B;B	0.15870	0.005;0.014	T	0.37526	-0.9702	10	0.18276	T	0.48	.	5.7965	0.18389	0.1257:0.1693:0.0:0.705	.	109;401	F8WJN6;Q9H2J7	.;S6A15_HUMAN	D	109;401;117;294;109	ENSP00000311645:E109D;ENSP00000266682:E401D;ENSP00000450145:E294D	ENSP00000266682:E401D	E	-	3	2	SLC6A15	83790611	0.998000	0.40836	0.981000	0.43875	0.793000	0.44817	0.366000	0.20365	0.369000	0.24510	0.460000	0.39030	GAA		0.318	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		G	85266480	T	G	85266480	3	3	61	1	0	0	0	0	1	0	0	0	14715	1606	56	4	1009	4	SLC6A15	12	85266480	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1740363	85266480	48585415	8233	16218										
SLC6A15	55117	broad.mit.edu	37	chr12	85266553	85266553	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttccccattttcaaaaatTtcatgatcgtctctgaattt	4	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85266553T>G	ENST00000266682.5	-	8	1671	c.1130A>C	c.(1129-1131)aAa>aCa	p.K377T	SLC6A15_ENST00000309283.7_Missense_Mutation_p.K85T|SLC6A15_ENST00000552192.1_Missense_Mutation_p.K270T|SLC6A15_ENST00000551388.1_5'Flank	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	377					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.K377T(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TTTCAAAAATTTCATGATCGT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	12											48	49	49					12																	85266553		2202	4298	6500	83790684	SO:0001583	missense	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1130A>C	12.37:g.85266553T>G	ENSP00000266682:p.Lys377Thr		83790684	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	8.918	0.960326	0.18507	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000318721;ENST00000552192;ENST00000551818	T;T;T	0.78126	-1.15;-0.7;-0.9	5.68	0.52	0.17040	.	0.315984	0.34580	N	0.003849	T	0.58524	0.2128	L	0.28556	0.865	0.09310	N	0.999994	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.005	T	0.35126	-0.9801	10	0.13853	T	0.58	.	6.1806	0.20470	0.0:0.1343:0.2541:0.6115	.	85;377	F8WJN6;Q9H2J7	.;S6A15_HUMAN	T	85;377;93;270;85	ENSP00000311645:K85T;ENSP00000266682:K377T;ENSP00000450145:K270T	ENSP00000266682:K377T	K	-	2	0	SLC6A15	83790684	0.000000	0.05858	0.000000	0.03702	0.951000	0.60555	-0.012000	0.12699	0.059000	0.16252	0.383000	0.25322	AAA		0.318	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		G	85266553	T	G	85266553	3	3	61	1	0	0	0	0	1	0	0	0	14715	1841	64	4	1082	4	SLC6A15	12	85266553	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	73	85266553	48585342	8234	16219										
TSPAN19	144448	broad.mit.edu	37	chr12	85423699	85423699	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattaagaaagtacttaataAttattgttttgttatttctt	5	2	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85423699A>C	ENST00000532498.2	-	2	106	c.26T>G	c.(25-27)aTt>aGt	p.I9S	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	9						integral component of membrane (GO:0016021)		p.I9S(1)		ovary(1)	1						GTACTTAATAATTATTGTTTT	0.244																																																1	Substitution - Missense(1)	large_intestine(1)	12											17	16	17					12																	85423699		1714	3862	5576	83947830	SO:0001583	missense	144448				CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"Tetraspanins"	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.26T>G	12.37:g.85423699A>C	ENSP00000433816:p.Ile9Ser		83947830		Missense_Mutation	SNP	ENST00000532498.2	37	CCDS44949.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.901371	0.33535	.	.	ENSG00000231738	ENST00000532498;ENST00000547836	T	0.42513	0.97	4.49	4.49	0.54785	.	.	.	.	.	T	0.39279	0.1072	N	0.08118	0	0.27535	N	0.950966	D	0.56746	0.977	P	0.59357	0.856	T	0.27191	-1.0081	9	0.87932	D	0	.	10.7543	0.46228	1.0:0.0:0.0:0.0	.	9	P0C672	TSN19_HUMAN	S	9	ENSP00000433816:I9S	ENSP00000408184:I9S	I	-	2	0	TSPAN19	83947830	0.915000	0.31059	0.705000	0.30386	0.223000	0.24884	1.963000	0.40452	1.974000	0.57490	0.379000	0.24179	ATT		0.244	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917		C	85423699	A	C	85423699	3	2	61	1	0	0	0	0	1	0	0	0	16683	101	4	4	752	4	TSPAN19	12	85423699	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	157146	85423699	48428196	8235	16220										
LRRIQ1	84125	broad.mit.edu	37	chr12	85492678	85492678	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatcttgttttactaagaGaattgcacttggatgataac	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85492678G>T	ENST00000393217.2	+	13	3176	c.3115G>T	c.(3115-3117)Gaa>Taa	p.E1039*		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1039								p.E1039*(3)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTTACTAAGAGAATTGCACTT	0.294																																																3	Substitution - Nonsense(3)	large_intestine(3)	12											82	85	84					12																	85492678		2202	4294	6496	84016809	SO:0001587	stop_gained	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3115G>T	12.37:g.85492678G>T	ENSP00000376910:p.Glu1039*		84016809	Q567P4|Q9BS17|Q9HA36	Nonsense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	G	40	8.443873	0.98813	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	.	.	.	5.4	5.4	0.78164	.	0.056303	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.9326	0.70929	0.0:0.0:0.848:0.152	.	.	.	.	X	1039;1014;1039	.	ENSP00000256007:E1039X	E	+	1	0	LRRIQ1	84016809	1.000000	0.71417	0.998000	0.56505	0.796000	0.44982	2.903000	0.48711	2.521000	0.84997	0.585000	0.79938	GAA		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85492678	G	T	85492678	4	4	61	1	0	0	0	0	0	1	0	0	9058	943	33	2	3161	2	LRRIQ1	12	85492678	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68979	85492678	48359217	8236	16221										
LRRIQ1	84125	broad.mit.edu	37	chr12	85518255	85518255	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagtagtaatgacaaattCtttgctgaggaatcaccaaa	9	6	2	2	rs141671586		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85518255C>A	ENST00000393217.2	+	17	4026	c.3965C>A	c.(3964-3966)tCt>tAt	p.S1322Y		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1322								p.S1322Y(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ATGACAAATTCTTTGCTGAGG	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	12											135	154	147					12																	85518255		2203	4299	6502	84042386	SO:0001583	missense	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3965C>A	12.37:g.85518255C>A	ENSP00000376910:p.Ser1322Tyr		84042386	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	C	10.32	1.318999	0.23994	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.58652	0.32	4.81	-0.495	0.12030	.	0.780949	0.11050	N	0.605142	T	0.29556	0.0737	N	0.14661	0.345	0.09310	N	1	P;P	0.41947	0.766;0.766	B;B	0.37047	0.24;0.24	T	0.13629	-1.0502	10	0.33141	T	0.24	.	0.7746	0.01030	0.37:0.2758:0.1143:0.2399	.	1322;1297	Q96JM4;C9JI57	LRIQ1_HUMAN;.	Y	1322;1297;1322	ENSP00000376910:S1322Y	ENSP00000256007:S1322Y	S	+	2	0	LRRIQ1	84042386	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.064000	0.11636	0.065000	0.16485	-0.923000	0.02734	TCT		0.328	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85518255	C	A	85518255	3	1	61	1	0	0	0	0	1	0	0	0	9058	913	32	2	4027	2	LRRIQ1	12	85518255	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25577	85518255	48333640	8237	16222										
LRRIQ1	84125	broad.mit.edu	37	chr12	85547514	85547515	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgctaaaatctgaaaaagINSaaaaaaaaatttcagaagaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85547514_85547515insA	ENST00000393217.2	+	22	4676_4677	c.4615_4616insA	c.(4615-4617)gaafs	p.E1539fs		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1539								p.I1542fs*8(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ATCTGAAAAAGAAAAAAAAATT	0.287																																																1	Insertion - Frameshift(1)	large_intestine(1)	12								14,3396		0,14,1691						5.7	1			17	51,7677		1,49,3814	no	frameshift	LRRIQ1	NM_001079910.1		1,63,5505	A1A1,A1R,RR		0.6599,0.4106,0.5836				65,11073				84071646	SO:0001589	frameshift_variant	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4624dupA	12.37:g.85547523_85547523dupA	ENSP00000376910:p.Glu1539fs		84071645	Q567P4|Q9BS17|Q9HA36	Frame_Shift_Ins	INS	ENST00000393217.2	37	CCDS41816.1																																																																																				0.287	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85547515	-	A	85547514	7	5	61	1	0	1	1	0	0	0	0	0	9058	943	33	0	4701	0	LRRIQ1	12	85547514	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	29259	85547514	48304381	8238	16223										
ALX1	8092	broad.mit.edu	37	chr12	85677605	85677605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattacccggatgtgtatgTcagagaacagcttgctctga	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:85677605T>C	ENST00000316824.3	+	2	637	c.482T>C	c.(481-483)gTc>gCc	p.V161A		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	161					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.V161A(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		GATGTGTATGTCAGAGAACAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	108	107					12																	85677605		2203	4300	6503	84201736	SO:0001583	missense	8092			U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"Homeoboxes / PRD class"	1494	protein-coding gene	gene with protein product		601527	"cartilage paired-class homeoprotein 1"	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.482T>C	12.37:g.85677605T>C	ENSP00000315417:p.Val161Ala		84201736	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275942	0.23307	.	.	ENSG00000180318	ENST00000316824	D	0.95205	-3.64	5.63	5.63	0.86233	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.85353	0.5677	N	0.02011	-0.69	0.80722	D	1	B	0.23249	0.082	B	0.29663	0.105	T	0.82277	-0.0537	10	0.14656	T	0.56	.	16.1307	0.81436	0.0:0.0:0.0:1.0	.	161	Q15699	ALX1_HUMAN	A	161	ENSP00000315417:V161A	ENSP00000315417:V161A	V	+	2	0	ALX1	84201736	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.278000	0.43426	2.263000	0.75096	0.533000	0.62120	GTC		0.498	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		C	85677605	T	C	85677605	3	2	61	1	0	0	0	0	1	0	0	0	556	1667	58	4	488	4	ALX1	12	85677605	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	130091	85677605	48174290	8239	16224										
RASSF9	9182	broad.mit.edu	37	chr12	86199586	86199586	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcttccccagaagaaatcGtttctctccaaacgtagcct	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:86199586G>A	ENST00000361228.3	-	2	570	c.202C>T	c.(202-204)Cga>Tga	p.R68*		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	68	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.R68*(2)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGAAGAAATCGTTTCTCTCCA	0.488																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											114	113	114					12																	86199586		1924	4151	6075	84723717	SO:0001587	stop_gained	9182				CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.202C>T	12.37:g.86199586G>A	ENSP00000354884:p.Arg68*		84723717	B3KMQ4|Q8N5U8	Nonsense_Mutation	SNP	ENST00000361228.3	37	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	G	36	5.964432	0.97151	.	.	ENSG00000198774	ENST00000361228	.	.	.	4.82	3.92	0.45320	.	0.336013	0.23175	N	0.051097	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-11.4453	12.0462	0.53480	0.0:0.0:0.5223:0.4777	.	.	.	.	X	68	.	ENSP00000354884:R68X	R	-	1	2	RASSF9	84723717	0.994000	0.37717	0.997000	0.53966	0.889000	0.51656	3.302000	0.51849	1.149000	0.42402	-0.426000	0.05927	CGA		0.488	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			A	86199586	G	A	86199586	4	1	61	1	0	0	0	0	0	1	0	0	13130	1153	40	1	1109	1	RASSF9	12	86199586	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	521981	86199586	47652309	8240	16225										
NTS	4922	broad.mit.edu	37	chr12	86276136	86276136	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctacatactcaaaagaGattcttactattactgagag	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:86276136G>T	ENST00000256010.6	+	4	603	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	NTS_ENST00000551529.1_Missense_Mutation_p.D91Y	NM_006183.4	NP_006174.1	P30990	NEUT_HUMAN	neurotensin	166					regulation of blood vessel size (GO:0050880)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)		p.D166Y(1)		large_intestine(2)|lung(6)	8						ACTCAAAAGAGATTCTTACTA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	12											90	104	100					12																	86276136		2201	4294	6495	84800267	SO:0001583	missense	4922				CCDS9029.1	12q21.31	2013-02-26			ENSG00000133636	ENSG00000133636		"Endogenous ligands"	8038	protein-coding gene	gene with protein product	"neuromedin N", "pro-neurotensin/neuromedin"	162650					Standard	NM_006183		Approved		uc001tag.3	P30990	OTTHUMG00000169832	ENST00000256010.6:c.496G>T	12.37:g.86276136G>T	ENSP00000256010:p.Asp166Tyr		84800267		Missense_Mutation	SNP	ENST00000256010.6	37	CCDS9029.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.168372	0.38315	.	.	ENSG00000133636	ENST00000551529;ENST00000256010;ENST00000550879	.	.	.	5.84	3.8	0.43715	.	0.479844	0.23975	N	0.042726	T	0.16085	0.0387	N	0.08118	0	0.24387	N	0.994769	P	0.40834	0.73	B	0.41440	0.357	T	0.04915	-1.0918	9	0.51188	T	0.08	-0.5009	6.4088	0.21680	0.3166:0.0:0.6834:0.0	.	166	P30990	NEUT_HUMAN	Y	91;166;111	.	ENSP00000256010:D166Y	D	+	1	0	NTS	84800267	1.000000	0.71417	0.997000	0.53966	0.932000	0.56968	2.725000	0.47294	1.492000	0.48499	0.591000	0.81541	GAT		0.299	NTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406111.2			T	86276136	G	T	86276136	3	4	61	1	0	0	0	0	1	0	0	0	10740	942	33	2	510	2	NTS	12	86276136	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76550	86276136	47575759	8241	16226										
MGAT4C	25834	broad.mit.edu	37	chr12	86373678	86373678	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgataaaacattaataAaaaatgggccaaacgtggga	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:86373678A>C	ENST00000604798.1	-	8	2030	c.826T>G	c.(826-828)Tta>Gta	p.L276V	MGAT4C_ENST00000393205.2_Missense_Mutation_p.L305V|MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000332156.1_Missense_Mutation_p.L276V|MGAT4C_ENST00000548651.1_Missense_Mutation_p.L276V|MGAT4C_ENST00000552808.2_Missense_Mutation_p.L276V|MGAT4C_ENST00000549405.2_Missense_Mutation_p.L276V			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	276					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.L276V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AACATTAATAAAAAATGGGCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	60	60					12																	86373678		2203	4300	6503	84897809	SO:0001583	missense	25834				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.826T>G	12.37:g.86373678A>C	ENSP00000474896:p.Leu276Val		84897809	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370153	0.24771	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	5.75	4.61	0.57282	.	0.082464	0.52532	D	0.000075	T	0.64505	0.2604	M	0.71206	2.165	0.47374	D	0.999403	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63088	-0.6715	10	0.39692	T	0.17	-12.6387	10.4604	0.44577	0.8652:0.0:0.1348:0.0	.	305;276	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	V	276;305;276;276;276;276;276	ENSP00000331664:L276V;ENSP00000376900:L305V;ENSP00000449022:L276V;ENSP00000446647:L276V;ENSP00000447253:L276V;ENSP00000449172:L276V	ENSP00000331664:L276V	L	-	1	2	MGAT4C	84897809	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	5.037000	0.64170	1.002000	0.39104	-0.296000	0.09543	TTA		0.383	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		C	86373678	A	C	86373678	3	2	61	1	0	0	0	0	1	0	0	0	9577	11	1	4	614	4	MGAT4C	12	86373678	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	97542	86373678	47478217	8242	16227										
MGAT4C	25834	broad.mit.edu	37	chr12	86383263	86383263	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacactgtagaacgttttCtcaggcatctcattttatca	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:86383263C>A	ENST00000604798.1	-	6	1266	c.62G>T	c.(61-63)aGa>aTa	p.R21I	MGAT4C_ENST00000393205.2_Missense_Mutation_p.R50I|MGAT4C_ENST00000552435.2_Missense_Mutation_p.R21I|MGAT4C_ENST00000332156.1_Missense_Mutation_p.R21I|MGAT4C_ENST00000548651.1_Missense_Mutation_p.R21I|MGAT4C_ENST00000552808.2_Missense_Mutation_p.R21I|MGAT4C_ENST00000549405.2_Missense_Mutation_p.R21I			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	21					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.R21I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AGAACGTTTTCTCAGGCATCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											80	70	73					12																	86383263		2202	4300	6502	84907394	SO:0001583	missense	25834				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.62G>T	12.37:g.86383263C>A	ENSP00000474896:p.Arg21Ile		84907394	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.851544	0.71719	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225;ENST00000552435	T;T;T;T;T;T	0.48522	1.39;1.34;1.39;1.39;1.39;0.81	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000001	T	0.61324	0.2338	L	0.34521	1.04	0.80722	D	1	D;B	0.76494	0.999;0.099	D;B	0.80764	0.994;0.04	T	0.62690	-0.6801	10	0.66056	D	0.02	-6.1035	19.8034	0.96518	0.0:1.0:0.0:0.0	.	50;21	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	I	21;50;21;21;21;21;21;21	ENSP00000331664:R21I;ENSP00000376900:R50I;ENSP00000449022:R21I;ENSP00000446647:R21I;ENSP00000447253:R21I;ENSP00000449172:R21I	ENSP00000331664:R21I	R	-	2	0	MGAT4C	84907394	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.179000	0.77665	2.669000	0.90835	0.655000	0.94253	AGA		0.328	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		A	86383263	C	A	86383263	3	1	61	1	0	0	0	0	1	0	0	0	9577	913	32	2	1386	2	MGAT4C	12	86383263	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9585	86383263	47468632	8243	16228										
C12orf29	91298	broad.mit.edu	37	chr12	88439529	88439529	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaacactggaactcataGgaacaaatatcaatggaaac	6	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88439529G>T	ENST00000356891.3	+	5	795	c.592G>T	c.(592-594)Gga>Tga	p.G198*	C12orf29_ENST00000548757.2_3'UTR	NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	198					hematopoietic progenitor cell differentiation (GO:0002244)			p.G198*(1)		large_intestine(3)|lung(1)|ovary(1)	5						GGAACTCATAGGAACAAATAT	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											73	71	72					12																	88439529		2203	4299	6502	86963660	SO:0001587	stop_gained	91298			AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.592G>T	12.37:g.88439529G>T	ENSP00000349358:p.Gly198*		86963660	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Nonsense_Mutation	SNP	ENST00000356891.3	37	CCDS31866.1	.	.	.	.	.	.	.	.	.	.	G	36	5.957725	0.97145	.	.	ENSG00000133641	ENST00000356891	.	.	.	5.64	5.64	0.86602	.	0.051237	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.3003	17.8768	0.88827	0.0:0.0:1.0:0.0	.	.	.	.	X	198	.	ENSP00000349358:G198X	G	+	1	0	C12orf29	86963660	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.872000	0.92352	2.666000	0.90696	0.655000	0.94253	GGA		0.353	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894		T	88439529	G	T	88439529	4	4	61	1	0	0	0	0	0	1	0	0	1684	1001	35	2	610	2	C12orf29	12	88439529	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2056266	88439529	45412366	8244	16229										
CEP290	80184	broad.mit.edu	37	chr12	88465129	88465129	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttttaattcttccaattCtttttctgactccaaagctc	2	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88465129C>A	ENST00000552810.1	-	43	6296	c.5953G>T	c.(5953-5955)Gaa>Taa	p.E1985*	CEP290_ENST00000547691.2_Nonsense_Mutation_p.E1045*|CEP290_ENST00000309041.7_Nonsense_Mutation_p.E1987*|CEP290_ENST00000397838.3_Nonsense_Mutation_p.E1045*	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1985					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.E1987*(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TCTTCCAATTCTTTTTCTGAC	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											114	100	104					12																	88465129		1797	4068	5865	86989260	SO:0001587	stop_gained	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5953G>T	12.37:g.88465129C>A	ENSP00000448012:p.Glu1985*		86989260	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	49	15.160921	0.99824	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	.	.	.	5.23	5.23	0.72850	.	0.044989	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	19.1622	0.93537	0.0:1.0:0.0:0.0	.	.	.	.	X	1045;1985;1987;1045	.	ENSP00000308021:E1987X	E	-	1	0	CEP290	86989260	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.087000	0.57671	2.608000	0.88229	0.484000	0.47621	GAA		0.343	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88465129	C	A	88465129	4	1	61	1	0	0	0	0	0	1	0	0	3259	922	32	2	1534	2	CEP290	12	88465129	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25600	88465129	45386766	8245	16230										
CEP290	80184	broad.mit.edu	37	chr12	88465636	88465636	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctcttttaacttgtttCgaattccttctattttggct	4	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88465636C>T	ENST00000552810.1	-	42	6120	c.5777G>A	c.(5776-5778)cGa>cAa	p.R1926Q	CEP290_ENST00000547691.2_Missense_Mutation_p.R986Q|CEP290_ENST00000309041.7_Missense_Mutation_p.R1928Q|CEP290_ENST00000397838.3_Missense_Mutation_p.R986Q	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1926					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.R1928Q(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TAACTTGTTTCGAATTCCTTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											104	93	97					12																	88465636		1805	4068	5873	86989767	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5777G>A	12.37:g.88465636C>T	ENSP00000448012:p.Arg1926Gln		86989767	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275118	0.80580	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.66815	0.29;-0.23;-0.23;0.29	5.34	5.34	0.76211	.	0.118436	0.56097	D	0.000027	T	0.78227	0.4250	M	0.72118	2.19	0.47949	D	0.99955	D	0.89917	1.0	D	0.72625	0.978	T	0.73310	-0.4023	10	0.02654	T	1	.	19.0366	0.92982	0.0:1.0:0.0:0.0	.	1926	O15078	CE290_HUMAN	Q	986;1926;1928;986	ENSP00000446905:R986Q;ENSP00000448012:R1926Q;ENSP00000308021:R1928Q;ENSP00000380938:R986Q	ENSP00000308021:R1928Q	R	-	2	0	CEP290	86989767	0.976000	0.34144	0.993000	0.49108	0.740000	0.42216	3.380000	0.52448	2.498000	0.84270	0.460000	0.39030	CGA		0.328	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88465636	C	T	88465636	3	4	61	1	0	0	0	0	1	0	0	0	3259	884	31	1	1714	1	CEP290	12	88465636	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	507	88465636	45386259	8246	16231										
CEP290	80184	broad.mit.edu	37	chr12	88505621	88505621	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaagattccttctgcattCtttgattctatagcctagca	5	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88505621C>A	ENST00000552810.1	-	21	2410	c.2067G>T	c.(2065-2067)aaG>aaT	p.K689N	CEP290_ENST00000309041.7_Missense_Mutation_p.K691N|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	689					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.K691N(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CTTCTGCATTCTTTGATTCTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											29	26	27					12																	88505621		1785	4062	5847	87029752	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2067G>T	12.37:g.88505621C>A	ENSP00000448012:p.Lys689Asn		87029752	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.457990|5.457990	0.96240|0.96240	.|.	.|.	ENSG00000198707|ENSG00000198707	ENST00000545139|ENST00000552810;ENST00000309041;ENST00000536998	.|T;T	.|0.78816	.|-1.21;-1.21	5.75|5.75	0.879|0.879	0.19155|0.19155	.|.	.|0.268680	.|0.37053	.|N	.|0.002271	.|T	.|0.73583	.|0.3605	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|P;P	.|0.46142	.|0.873;0.804	.|P;P	.|0.47376	.|0.447;0.545	.|T	.|0.68557	.|-0.5377	.|10	0.66056|0.38643	D|T	0.02|0.18	.|.	9.9222|9.9222	0.41470|0.41470	0.0:0.6703:0.0:0.3297|0.0:0.6703:0.0:0.3297	.|.	.|689;689	.|Q05BJ6;O15078	.|.;CE290_HUMAN	X|N	544|689;691;689	.|ENSP00000448012:K689N;ENSP00000308021:K691N	ENSP00000444813:E544X|ENSP00000308021:K691N	E|K	-|-	1|3	0|2	CEP290|CEP290	87029752|87029752	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.988000|0.988000	0.76386|0.76386	0.743000|0.743000	0.26231|0.26231	0.100000|0.100000	0.17581|0.17581	-0.244000|-0.244000	0.11960|0.11960	GAA|AAG		0.338	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88505621	C	A	88505621	3	1	61	1	0	0	0	0	1	0	0	0	3259	912	32	2	5508	2	CEP290	12	88505621	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39985	88505621	45346274	8247	16232										
CEP290	80184	broad.mit.edu	37	chr12	88512329	88512329	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttcagatcaagtcgttCttcctctagactttcaatct	4	10	6	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88512329C>A	ENST00000552810.1	-	17	1985	c.1642G>T	c.(1642-1644)Gaa>Taa	p.E548*	CEP290_ENST00000309041.7_Nonsense_Mutation_p.E550*|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	548					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.E550*(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TCAAGTCGTTCTTCCTCTAGA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											69	60	62					12																	88512329		1800	4050	5850	87036460	SO:0001587	stop_gained	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1642G>T	12.37:g.88512329C>A	ENSP00000448012:p.Glu548*		87036460	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	41	9.091683	0.99062	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	12.7687	0.57408	0.0:0.9255:0.0:0.0745	.	.	.	.	X	548;550;548;450	.	ENSP00000308021:E550X	E	-	1	0	CEP290	87036460	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.443000	0.66581	2.601000	0.87937	0.585000	0.79938	GAA		0.323	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88512329	C	A	88512329	4	1	61	1	0	0	0	0	0	1	0	0	3259	922	32	2	5949	2	CEP290	12	88512329	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6708	88512329	45339566	8248	16233										
CEP290	80184	broad.mit.edu	37	chr12	88514015	88514015	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatttggtttttacaattCtttatttcaacgacagcatc	4	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88514015C>A	ENST00000552810.1	-	15	1741	c.1398G>T	c.(1396-1398)aaG>aaT	p.K466N	CEP290_ENST00000309041.7_Missense_Mutation_p.K466N|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	466					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.K466N(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTTACAATTCTTTATTTCAA	0.249																																																1	Substitution - Missense(1)	large_intestine(1)	12											58	50	53					12																	88514015		1786	4040	5826	87038146	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1398G>T	12.37:g.88514015C>A	ENSP00000448012:p.Lys466Asn		87038146	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454440	0.43634	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.71579	-0.58;-0.55	5.51	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	M	0.70275	2.135	0.80722	D	1	B;B	0.27997	0.082;0.197	B;B	0.28465	0.058;0.09	T	0.63497	-0.6624	10	0.34782	T	0.22	.	8.5795	0.33619	0.0:0.7298:0.1276:0.1426	.	466;466	Q05BJ6;O15078	.;CE290_HUMAN	N	466;466;466;368	ENSP00000448012:K466N;ENSP00000308021:K466N	ENSP00000308021:K466N	K	-	3	2	CEP290	87038146	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.210000	0.32370	1.335000	0.45486	0.650000	0.86243	AAG		0.249	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88514015	C	A	88514015	3	1	61	1	0	0	0	0	1	0	0	0	3259	912	32	2	6201	2	CEP290	12	88514015	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1686	88514015	45337880	8249	16234										
TMTC3	160418	broad.mit.edu	37	chr12	88547113	88547113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaacagtattgacatttCgcttaaattatttgttaagt	5	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88547113C>T	ENST00000266712.6	+	3	455	c.235C>T	c.(235-237)Cgc>Tgc	p.R79C		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	79					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)		p.R79C(1)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						ATTGACATTTCGCTTAAATTA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											107	95	99					12																	88547113		2203	4299	6502	87071244	SO:0001583	missense	160418				CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.235C>T	12.37:g.88547113C>T	ENSP00000266712:p.Arg79Cys		87071244	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	C	33	5.285838	0.95517	.	.	ENSG00000139324	ENST00000549011;ENST00000266712	D;T	0.94897	-3.55;-0.32	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.97851	0.9294	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97832	1.0263	10	0.66056	D	0.02	-7.7387	20.4324	0.99085	0.0:1.0:0.0:0.0	.	79	Q6ZXV5-2	.	C	79	ENSP00000447640:R79C;ENSP00000266712:R79C	ENSP00000266712:R79C	R	+	1	0	TMTC3	87071244	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.689000	0.68234	2.833000	0.97629	0.585000	0.79938	CGC		0.353	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		T	88547113	C	T	88547113	3	4	61	1	0	0	0	0	1	0	0	0	16301	884	31	1	241	1	TMTC3	12	88547113	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33098	88547113	45304782	8250	16235										
TMTC3	160418	broad.mit.edu	37	chr12	88586433	88586433	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaagcaaaggaagcatatCttaaagcactagagctggac	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88586433C>A	ENST00000266712.6	+	13	1979	c.1759C>A	c.(1759-1761)Ctt>Att	p.L587I		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	587					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)		p.L587I(1)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						GGAAGCATATCTTAAAGCACT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											84	87	86					12																	88586433		2203	4299	6502	87110564	SO:0001583	missense	160418				CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1759C>A	12.37:g.88586433C>A	ENSP00000266712:p.Leu587Ile		87110564	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431844	0.43122	.	.	ENSG00000139324	ENST00000266712	T	0.60040	0.22	5.71	5.71	0.89125	.	0.058070	0.64402	D	0.000001	T	0.52256	0.1723	L	0.48935	1.535	0.44798	D	0.997809	B	0.11235	0.004	B	0.17722	0.019	T	0.44967	-0.9293	10	0.39692	T	0.17	-17.0777	14.6645	0.68896	0.1454:0.8546:0.0:0.0	.	587	Q6ZXV5-2	.	I	587	ENSP00000266712:L587I	ENSP00000266712:L587I	L	+	1	0	TMTC3	87110564	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.733000	0.62036	2.705000	0.92388	0.585000	0.79938	CTT		0.333	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		A	88586433	C	A	88586433	3	1	61	1	0	0	0	0	1	0	0	0	16301	913	32	2	1805	2	TMTC3	12	88586433	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39320	88586433	45265462	8251	16236										
TMTC3	160418	broad.mit.edu	37	chr12	88588653	88588653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaagctagaaaacgacttCtaagttatataaatgaagag	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88588653C>A	ENST00000266712.6	+	14	2192	c.1972C>A	c.(1972-1974)Cta>Ata	p.L658I		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	659					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)		p.L658I(1)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						AAAACGACTTCTAAGTTATAT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	12											71	74	73					12																	88588653		2203	4299	6502	87112784	SO:0001583	missense	160418				CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1972C>A	12.37:g.88588653C>A	ENSP00000266712:p.Leu658Ile		87112784	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265010	0.59431	.	.	ENSG00000139324	ENST00000266712	T	0.64803	-0.12	5.83	2.04	0.26737	.	0.000000	0.85682	D	0.000000	T	0.69269	0.3092	M	0.66939	2.045	0.44694	D	0.997684	D	0.58620	0.983	P	0.58820	0.846	T	0.64558	-0.6379	10	0.34782	T	0.22	-11.3065	9.7638	0.40548	0.0:0.6021:0.0:0.3979	.	658	Q6ZXV5-2	.	I	658	ENSP00000266712:L658I	ENSP00000266712:L658I	L	+	1	2	TMTC3	87112784	0.943000	0.32029	0.970000	0.41538	0.986000	0.74619	0.209000	0.17435	0.112000	0.17975	0.591000	0.81541	CTA		0.313	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		A	88588653	C	A	88588653	3	1	61	1	0	0	0	0	1	0	0	0	16301	912	32	2	2022	2	TMTC3	12	88588653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2220	88588653	45263242	8252	16237										
KITLG	4254	broad.mit.edu	37	chr12	88912555	88912555	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatggaataattactcaaGccttcagaaatatttgaaaa	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:88912555G>T	ENST00000228280.5	-	4	464	c.282C>A	c.(280-282)ggC>ggA	p.G94G	KITLG_ENST00000357116.4_Intron|KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000347404.5_Silent_p.G94G	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	94					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)	p.G94G(1)		kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						AATTACTCAAGCCTTCAGAAA	0.378									Testicular Cancer, Familial Clustering of																																							1	Substitution - coding silent(1)	large_intestine(1)	12											115	110	112					12																	88912555		2203	4300	6503	87436686	SO:0001819	synonymous_variant	4254	Familial Cancer Database		M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"mast cell growth factor", "stem cell factor", "steel factor", "familial progressive hyperpigmentation 2"	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.282C>A	12.37:g.88912555G>T			87436686	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Silent	SNP	ENST00000228280.5	37	CCDS31868.1																																																																																				0.378	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994		T	88912555	G	T	88912555	2	4	61	1	0	0	0	0	0	0	0	1	8351	958	34	2		2	KITLG	12	88912555	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	323902	88912555	44939340	8253	16238										
POC1B	282809	broad.mit.edu	37	chr12	89918951	89918951	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgatcgcagctttgtggcCtttgaaataacgctccagaa	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:89918951C>A	ENST00000313546.3	-	2	174	c.46G>T	c.(46-48)Ggc>Tgc	p.G16C	POC1B_ENST00000541909.1_De_novo_Start_InFrame|POC1B-GALNT4_ENST00000547474.1_Missense_Mutation_p.G16C|POC1B_ENST00000549504.1_De_novo_Start_InFrame|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000549035.1_De_novo_Start_OutOfFrame|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.G16C|GALNT4_ENST00000529983.2_5'Flank|GALNT4_ENST00000413530.1_Missense_Mutation_p.K102N|POC1B_ENST00000393179.4_De_novo_Start_InFrame	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	16					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)		p.K102N(1)|p.G16C(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						GCTTTGTGGCCTTTGAAATAA	0.498											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	12											107	93	98					12																	89918951		2203	4300	6503	88443082	SO:0001583	missense	282809			AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"WD repeat domain containing"	30836	protein-coding gene	gene with protein product		614784	"WD repeat domain 51B", "POC1 centriolar protein homolog B (Chlamydomonas)"	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.46G>T	12.37:g.89918951C>A	ENSP00000323302:p.Gly16Cys	1271	88443082	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	37	CCDS31869.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.527716|4.527716	0.85706|0.85706	.|.	.|.	ENSG00000139323;ENSG00000259075;ENSG00000259075|ENSG00000259075	ENST00000313546;ENST00000548729;ENST00000547474|ENST00000413530	T;T;D|T	0.85411|0.73047	-0.51;-0.03;-1.98|-0.71	4.61|4.61	4.61|4.61	0.57282|0.57282	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.056051|.	0.64402|.	D|.	0.000001|.	D|D	0.84920|0.84920	0.5579|0.5579	M|M	0.91768|0.91768	3.24|3.24	0.29016|0.29016	N|N	0.886608|0.886608	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.995|.	T|T	0.81627|0.81627	-0.0847|-0.0847	10|7	0.87932|0.66056	D|D	0|0.02	.|.	14.2869|14.2869	0.66251|0.66251	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	16;16|.	F8VUJ3;Q8TC44|.	.;POC1B_HUMAN|.	C|N	16|102	ENSP00000323302:G16C;ENSP00000447852:G16C;ENSP00000447754:G16C|ENSP00000389686:K102N	ENSP00000323302:G16C|ENSP00000389686:K102N	G|K	-|-	1|3	0|2	POC1B;RP11-1109F11.4|RP11-1109F11.4	88443082|88443082	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	4.287000|4.287000	0.59001|0.59001	2.377000|2.377000	0.81083|0.81083	0.555000|0.555000	0.69702|0.69702	GGC|AAG		0.498	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240		A	89918951	C	A	89918951	3	1	61	1	0	0	0	0	1	0	0	0	12207	681	24	2	1434	2	POC1B	12	89918951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1006396	89918951	43932944	8254	16239										
ATP2B1	490	broad.mit.edu	37	chr12	90013815	90013815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcacccttgctgaatattCgataacttccatctgaattt	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:90013815C>T	ENST00000428670.3	-	11	2246	c.1790G>A	c.(1789-1791)cGa>cAa	p.R597Q	ATP2B1_ENST00000359142.3_Missense_Mutation_p.R597Q|ATP2B1_ENST00000348959.3_Missense_Mutation_p.R597Q|ATP2B1_ENST00000261173.2_Missense_Mutation_p.R597Q|ATP2B1_ENST00000393164.2_Missense_Mutation_p.R340Q			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	597					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.R597Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						GCTGAATATTCGATAACTTCC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	110	111					12																	90013815		2203	4300	6503	88537946	SO:0001583	missense	490			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1790G>A	12.37:g.90013815C>T	ENSP00000392043:p.Arg597Gln		88537946	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	C	34	5.374897	0.95923	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.97498	0.9181	M	0.72624	2.21	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.994	D;P;P	0.77557	0.99;0.747;0.516	D	0.97880	1.0291	10	0.66056	D	0.02	-38.6369	19.3416	0.94344	0.0:1.0:0.0:0.0	.	597;597;597	P20020-3;P20020-2;P20020-6	.;.;.	Q	597;597;597;597;340	ENSP00000261173:R597Q;ENSP00000343599:R597Q;ENSP00000352054:R597Q;ENSP00000392043:R597Q;ENSP00000376869:R340Q	ENSP00000261173:R597Q	R	-	2	0	ATP2B1	88537946	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	6.086000	0.71352	2.560000	0.86352	0.467000	0.42956	CGA		0.353	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		T	90013815	C	T	90013815	3	4	61	1	0	0	0	0	1	0	0	0	1140	884	31	1	2074	1	ATP2B1	12	90013815	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94864	90013815	43838080	8255	16240										
ATP2B1	490	broad.mit.edu	37	chr12	90049477	90049477	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattgggagatgttttcaAtttggtgcaaattccataga	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:90049477A>C	ENST00000428670.3	-	2	643	c.187T>G	c.(187-189)Ttg>Gtg	p.L63V	ATP2B1_ENST00000359142.3_Missense_Mutation_p.L63V|ATP2B1_ENST00000348959.3_Missense_Mutation_p.L63V|ATP2B1_ENST00000261173.2_Missense_Mutation_p.L63V			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	63					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.L63V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						GATGTTTTCAATTTGGTGCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											73	71	72					12																	90049477		2203	4300	6503	88573608	SO:0001583	missense	490			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.187T>G	12.37:g.90049477A>C	ENSP00000392043:p.Leu63Val		88573608	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.436710	0.62955	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000551310	D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03	5.48	4.33	0.51752	.	0.000000	0.85682	D	0.000000	D	0.91432	0.7296	M	0.81341	2.54	0.58432	D	0.999991	D;P	0.71674	0.998;0.71	D;P	0.77557	0.99;0.71	D	0.91045	0.4874	9	.	.	.	-20.2277	11.3987	0.49858	0.9287:0.0:0.0713:0.0	.	63;63	P20020-3;P20020-2	.;.	V	63	ENSP00000261173:L63V;ENSP00000343599:L63V;ENSP00000352054:L63V;ENSP00000392043:L63V	.	L	-	1	2	ATP2B1	88573608	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.245000	0.58734	1.011000	0.39340	0.482000	0.46254	TTG		0.393	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	90049477	A	C	90049477	3	2	61	1	0	0	0	0	1	0	0	0	1140	98	4	4	3713	4	ATP2B1	12	90049477	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	35662	90049477	43802418	8256	16241										
C12orf12	196477	broad.mit.edu	37	chr12	91347473	91347473	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcccctctctgctcgttCtcctccaggacctcctcttc	4	20	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91347473C>A	ENST00000358859.2	-	1	1480	c.1047G>T	c.(1045-1047)gaG>gaT	p.E349D	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	349	Glu-rich.							p.E349D(1)									TCTGCTCGTTCTCCTCCAGGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											189	164	172					12																	91347473		2203	4300	6503	89871604	SO:0001583	missense	196477			BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.1047G>T	12.37:g.91347473C>A	ENSP00000351727:p.Glu349Asp		89871604	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	37	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	C	9.247	1.039767	0.19669	.	.	ENSG00000197651	ENST00000358859	T	0.25579	1.79	5.04	3.2	0.36748	.	0.787422	0.10360	N	0.684115	T	0.15046	0.0363	N	0.24115	0.695	0.09310	N	1	P	0.36144	0.539	B	0.30179	0.112	T	0.16188	-1.0411	10	0.54805	T	0.06	-6.0543	6.0762	0.19917	0.1861:0.719:0.0:0.0948	.	349	Q8TC90	CL012_HUMAN	D	349	ENSP00000351727:E349D	ENSP00000351727:E349D	E	-	3	2	C12orf12	89871604	0.002000	0.14202	0.112000	0.21494	0.086000	0.17979	0.065000	0.14466	0.705000	0.31890	0.460000	0.39030	GAG		0.493	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		A	91347473	C	A	91347473	3	1	61	1	0	0	0	0	1	0	0	0	1680	912	32	2	177	2	C12orf12	12	91347473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1297996	91347473	42504422	8257	16242										
EPYC	1833	broad.mit.edu	37	chr12	91358079	91358079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacattgcagaacgtatcttCgtgcatttccagaatgttgt	8	8	1	2	rs138857092		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91358079C>T	ENST00000261172.3	-	7	915	c.823G>A	c.(823-825)Gaa>Aaa	p.E275K		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	275					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)	p.E275K(2)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						AACGTATCTTCGTGCATTTCC	0.338																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	12						C	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	95	88	90		823	5.5	1	12	dbSNP_134	90	0,8600		0,0,4300	no	missense	EPYC	NM_004950.4	56	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	275/323	91358079	2,13004	2203	4300	6503	89882210	SO:0001583	missense	1833			AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.823G>A	12.37:g.91358079C>T	ENSP00000261172:p.Glu275Lys		89882210	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169056	0.78339	4.54E-4	0.0	ENSG00000083782	ENST00000261172	T	0.02421	4.3	5.54	5.54	0.83059	.	0.043221	0.85682	D	0.000000	T	0.04724	0.0128	L	0.52364	1.645	0.80722	D	1	P	0.38335	0.627	B	0.35073	0.195	T	0.54636	-0.8264	10	0.25106	T	0.35	.	19.5595	0.95367	0.0:1.0:0.0:0.0	.	275	Q99645	EPYC_HUMAN	K	275	ENSP00000261172:E275K	ENSP00000261172:E275K	E	-	1	0	EPYC	89882210	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.690000	0.68241	2.613000	0.88420	0.586000	0.80456	GAA		0.338	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950		T	91358079	C	T	91358079	3	4	61	1	0	0	0	0	1	0	0	0	5214	893	31	1	149	1	EPYC	12	91358079	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10606	91358079	42493816	8258	16243										
EPYC	1833	broad.mit.edu	37	chr12	91363821	91363821	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttactggtagactcctacCtggaggtgaagggctcgtag	13	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91363821C>A	ENST00000261172.3	-	6	890	c.798G>T	c.(796-798)caG>caT	p.Q266H		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	266					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)	p.Q266H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						AGACTCCTACCTGGAGGTGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											184	185	185					12																	91363821		2203	4300	6503	89887952	SO:0001630	splice_region_variant	1833			AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.798+1G>T	12.37:g.91363821C>A			89887952	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490229	0.64074	.	.	ENSG00000083782	ENST00000261172	T	0.02446	4.29	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.06781	0.0173	M	0.64404	1.975	0.80722	D	1	P	0.50066	0.931	P	0.48089	0.566	T	0.19943	-1.0290	9	.	.	.	.	12.3739	0.55269	0.0:0.9229:0.0:0.0771	.	266	Q99645	EPYC_HUMAN	H	266	ENSP00000261172:Q266H	.	Q	-	3	2	EPYC	89887952	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	5.639000	0.67868	2.491000	0.84063	0.467000	0.42956	CAG		0.478	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950	Missense_Mutation	A	91363821	C	A	91363821	5	1	61	1	0	0	0	0	0	0	1	0	5214	695	24	2	178	2	EPYC	12	91363821	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5742	91363821	42488074	8259	16244										
KERA	11081	broad.mit.edu	37	chr12	91449223	91449223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcagatgagcactgattCggggaacctttgtgagttga	14	7	0	5	rs371954775		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91449223C>T	ENST00000266719.3	-	2	1083	c.836G>A	c.(835-837)cGa>cAa	p.R279Q		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	279					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.R279Q(1)		breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						AGCACTGATTCGGGGAACCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12						C	GLN/ARG	0,4406		0,0,2203	121	114	116		836	5	1	12		116	1,8597	1.2+/-3.3	0,1,4298	no	missense	KERA	NM_007035.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	279/353	91449223	1,13003	2203	4299	6502	89973354	SO:0001583	missense	11081			AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.836G>A	12.37:g.91449223C>T	ENSP00000266719:p.Arg279Gln		89973354		Missense_Mutation	SNP	ENST00000266719.3	37	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	C	8.688	0.906658	0.17833	0.0	1.16E-4	ENSG00000139330	ENST00000266719	T	0.17854	2.25	5.91	4.97	0.65823	.	0.676237	0.15520	N	0.258104	T	0.09730	0.0239	N	0.21373	0.66	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.36480	-0.9746	10	0.13853	T	0.58	-11.0118	5.2909	0.15727	0.1222:0.6232:0.1722:0.0824	.	279	O60938	KERA_HUMAN	Q	279	ENSP00000266719:R279Q	ENSP00000266719:R279Q	R	-	2	0	KERA	89973354	0.055000	0.20627	0.999000	0.59377	0.651000	0.38670	0.858000	0.27845	1.405000	0.46838	0.655000	0.94253	CGA		0.408	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		T	91449223	C	T	91449223	3	4	61	1	0	0	0	0	1	0	0	0	8164	884	31	1	230	1	KERA	12	91449223	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85402	91449223	42402672	8260	16245										
KERA	11081	broad.mit.edu	37	chr12	91449839	91449839	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttgaagataaagataccAaattcttgaaggaatagcag	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91449839A>C	ENST00000266719.3	-	2	467	c.220T>G	c.(220-222)Tgg>Ggg	p.W74G		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	74					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.W74G(1)		breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						TAAAGATACCAAATTCTTGAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	92	94					12																	91449839		2203	4297	6500	89973970	SO:0001583	missense	11081			AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.220T>G	12.37:g.91449839A>C	ENSP00000266719:p.Trp74Gly		89973970		Missense_Mutation	SNP	ENST00000266719.3	37	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480151	0.44044	.	.	ENSG00000139330	ENST00000266719	T	0.17691	2.26	5.84	2.02	0.26589	Leucine-rich repeat-containing N-terminal (1);	0.050640	0.85682	D	0.000000	T	0.07188	0.0182	N	0.02247	-0.625	0.58432	D	0.999999	B	0.26809	0.16	B	0.37989	0.262	T	0.35699	-0.9778	10	0.20519	T	0.43	-0.1214	5.5058	0.16854	0.685:0.0:0.1972:0.1178	.	74	O60938	KERA_HUMAN	G	74	ENSP00000266719:W74G	ENSP00000266719:W74G	W	-	1	0	KERA	89973970	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.980000	0.49321	0.096000	0.17463	0.529000	0.55759	TGG		0.373	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		C	91449839	A	C	91449839	3	2	61	1	0	0	0	0	1	0	0	0	8164	130	5	4	846	4	KERA	12	91449839	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	616	91449839	42402056	8261	16246										
LUM	4060	broad.mit.edu	37	chr12	91502039	91502039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattccactatcagccagttCgttgtgagataaacgcagat	8	9	1	2	rs267603717		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:91502039C>T	ENST00000266718.4	-	2	1172	c.718G>A	c.(718-720)Gaa>Aaa	p.E240K	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	240					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.E240K(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						TCAGCCAGTTCGTTGTGAGAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	149	152					12																	91502039		2203	4300	6503	90026170	SO:0001583	missense	4060			BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.718G>A	12.37:g.91502039C>T	ENSP00000266718:p.Glu240Lys		90026170	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	37	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	6.330	0.429002	0.11987	.	.	ENSG00000139329	ENST00000266718	T	0.56444	0.46	5.57	4.65	0.58169	.	0.103471	0.64402	D	0.000005	T	0.16214	0.0390	N	0.01003	-1.06	0.42346	D	0.992353	B	0.09022	0.002	B	0.09377	0.004	T	0.37641	-0.9697	10	0.02654	T	1	-31.9346	5.1455	0.14983	0.0:0.6323:0.188:0.1797	.	240	P51884	LUM_HUMAN	K	240	ENSP00000266718:E240K	ENSP00000266718:E240K	E	-	1	0	LUM	90026170	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	2.455000	0.44988	2.614000	0.88457	0.557000	0.71058	GAA		0.388	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		T	91502039	C	T	91502039	3	4	61	1	0	0	0	0	1	0	0	0	9114	893	31	1	306	1	LUM	12	91502039	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52200	91502039	42349856	8262	16247										
PLEKHG7	440107	broad.mit.edu	37	chr12	93157910	93157910	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggttcgtgtacagtactcGatcagcctattccactagat	9	10	1	1	rs375510513		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:93157910G>A	ENST00000344636.3	+	10	1058	c.874G>A	c.(874-876)Gat>Aat	p.D292N		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	292	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D292N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						TACAGTACTCGATCAGCCTAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	222	213	216		874	4.9	0.8	12		216	0,8600		0,0,4300	no	missense	PLEKHG7	NM_001004330.2	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	292/380	93157910	1,13005	2203	4300	6503	91682041	SO:0001583	missense	440107			AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.874G>A	12.37:g.93157910G>A	ENSP00000344961:p.Asp292Asn		91682041	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	37	CCDS31873.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657141	0.29425	2.27E-4	0.0	ENSG00000187510	ENST00000344636	T	0.63255	-0.03	5.82	4.94	0.65067	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.138800	0.64402	D	0.000005	T	0.60919	0.2306	M	0.63428	1.95	0.44771	D	0.997777	D	0.60160	0.987	B	0.43155	0.41	T	0.66081	-0.6012	10	0.56958	D	0.05	-6.5921	13.2984	0.60311	0.0732:0.0:0.9268:0.0	.	292	Q6ZR37	PKHG7_HUMAN	N	292	ENSP00000344961:D292N	ENSP00000344961:D292N	D	+	1	0	PLEKHG7	91682041	1.000000	0.71417	0.812000	0.32479	0.130000	0.20726	5.113000	0.64640	1.466000	0.48025	0.650000	0.86243	GAT		0.413	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330		A	93157910	G	A	93157910	3	1	61	1	0	0	0	0	1	0	0	0	12106	1058	37	1	908	1	PLEKHG7	12	93157910	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1655871	93157910	40693985	8263	16248										
EEA1	8411	broad.mit.edu	37	chr12	93213196	93213196	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctttttctagtaatgaaAtattttctttactcttctgt	3	6	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:93213196A>G	ENST00000322349.8	-	14	1880	c.1616T>C	c.(1615-1617)aTt>aCt	p.I539T		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	539	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.I539T(1)		endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TAGTAATGAAATATTTTCTTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	59	59					12																	93213196		2202	4296	6498	91737327	SO:0001583	missense	8411			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.1616T>C	12.37:g.93213196A>G	ENSP00000317955:p.Ile539Thr		91737327	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.511871	0.44660	.	.	ENSG00000102189	ENST00000322349	T	0.78707	-1.2	5.55	3.2	0.36748	.	0.237591	0.28946	N	0.013633	T	0.61426	0.2346	L	0.27053	0.805	0.35167	D	0.771209	B	0.06786	0.001	B	0.04013	0.001	T	0.55829	-0.8079	10	0.14252	T	0.57	.	9.6148	0.39685	0.858:0.0:0.142:0.0	.	539	Q15075	EEA1_HUMAN	T	539	ENSP00000317955:I539T	ENSP00000317955:I539T	I	-	2	0	EEA1	91737327	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	6.284000	0.72652	0.411000	0.25702	0.377000	0.23210	ATT		0.338	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		G	93213196	A	G	93213196	3	3	61	1	0	0	0	0	1	0	0	0	4932	101	4	4	2683	4	EEA1	12	93213196	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	55286	93213196	40638699	8264	16249										
EEA1	8411	broad.mit.edu	37	chr12	93226457	93226457	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttagttctacatgtattCtatgcagtgaggtttcagat	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:93226457C>A	ENST00000322349.8	-	11	1349	c.1085G>T	c.(1084-1086)aGa>aTa	p.R362I		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	362					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.R362I(1)		endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TACATGTATTCTATGCAGTGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											149	140	143					12																	93226457		2203	4300	6503	91750588	SO:0001583	missense	8411			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.1085G>T	12.37:g.93226457C>A	ENSP00000317955:p.Arg362Ile		91750588	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526100	0.44969	.	.	ENSG00000102189	ENST00000322349	T	0.66815	-0.23	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000017	T	0.72795	0.3505	L	0.29908	0.895	0.58432	D	0.999999	D	0.71674	0.998	D	0.78314	0.991	T	0.74275	-0.3718	10	0.54805	T	0.06	.	14.9913	0.71390	0.0:0.8579:0.1421:0.0	.	362	Q15075	EEA1_HUMAN	I	362	ENSP00000317955:R362I	ENSP00000317955:R362I	R	-	2	0	EEA1	91750588	0.998000	0.40836	0.947000	0.38551	0.028000	0.11728	3.804000	0.55568	2.577000	0.86979	0.655000	0.94253	AGA		0.388	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		A	93226457	C	A	93226457	3	1	61	1	0	0	0	0	1	0	0	0	4932	913	32	2	3226	2	EEA1	12	93226457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13261	93226457	40625438	8265	16250										
SOCS2	8835	broad.mit.edu	37	chr12	93968937	93968937	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaaagattacttggaagaAtataaattccaggtataaat	6	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:93968937A>C	ENST00000340600.2	+	3	1177	c.579A>C	c.(577-579)gaA>gaC	p.E193D	SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000536696.2_Missense_Mutation_p.E193D|SOCS2_ENST00000551556.1_Missense_Mutation_p.E193D|SOCS2_ENST00000549206.1_Missense_Mutation_p.E193D|SOCS2_ENST00000549122.1_Missense_Mutation_p.E193D	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	O14508	SOCS2_HUMAN	suppressor of cytokine signaling 2	193	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to hormone stimulus (GO:0032870)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of signal transduction (GO:0009967)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of signal transduction (GO:0009966)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	growth hormone receptor binding (GO:0005131)|insulin-like growth factor receptor binding (GO:0005159)|JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)	p.E193D(1)		cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)	14						ACTTGGAAGAATATAAATTCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											40	38	39					12																	93968937		2203	4300	6503	92493068	SO:0001583	missense	8835			AF037989	CCDS9047.1	12q	2013-02-14			ENSG00000120833	ENSG00000120833		"Suppressors of cytokine signaling", "SH2 domain containing"	19382	protein-coding gene	gene with protein product	"STAT-induced STAT inhibitor-2"	605117				9344848, 9266833	Standard	NM_003877		Approved	STATI2, SSI2, SOCS-2, SSI-2, CIS2, Cish2	uc031qjc.1	O14508		ENST00000340600.2:c.579A>C	12.37:g.93968937A>C	ENSP00000339428:p.Glu193Asp		92493068	A8K3D1|O14542|O95102|Q9UKS5	Missense_Mutation	SNP	ENST00000340600.2	37	CCDS9047.1	.	.	.	.	.	.	.	.	.	.	A	7.889	0.731836	0.15507	.	.	ENSG00000120833	ENST00000340600;ENST00000549206;ENST00000536696;ENST00000539385;ENST00000549122;ENST00000551556	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.84	-0.588	0.11687	SOCS protein, C-terminal (4);	0.142496	0.64402	D	0.000007	T	0.18130	0.0435	N	0.21097	0.63	0.43304	D	0.995302	B	0.06786	0.001	B	0.08055	0.003	T	0.07233	-1.0783	10	0.33141	T	0.24	-2.0415	11.3885	0.49800	0.5843:0.0:0.4157:0.0	.	193	O14508	SOCS2_HUMAN	D	193;193;193;141;193;193	ENSP00000339428:E193D;ENSP00000448815:E193D;ENSP00000442898:E193D;ENSP00000447161:E193D;ENSP00000449227:E193D	ENSP00000339428:E193D	E	+	3	2	SOCS2	92493068	0.796000	0.28864	0.992000	0.48379	0.984000	0.73092	-0.031000	0.12287	-0.328000	0.08539	-0.899000	0.02877	GAA		0.393	SOCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407731.2			C	93968937	A	C	93968937	3	2	61	1	0	0	0	0	1	0	0	0	14951	98	4	4	585	4	SOCS2	12	93968937	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	742480	93968937	39882958	8266	16251										
CRADD	8738	broad.mit.edu	37	chr12	94072802	94072802	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtttccctgggtcagggaGaagctgaagaaggcaaggga	17	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94072802G>A	ENST00000542893.2	+	2	570	c.252G>A	c.(250-252)gaG>gaA	p.E84E	CRADD_ENST00000552033.1_Silent_p.E84E|CRADD_ENST00000548483.1_Silent_p.E84E|CRADD_ENST00000332896.3_Silent_p.E84E|CRADD_ENST00000552983.1_Silent_p.E84E|CRADD_ENST00000541813.1_Silent_p.E84E			P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with death domain	84	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death domain binding (GO:0070513)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)	p.E84E(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)	8						GGGTCAGGGAGAAGCTGAAGA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	12											60	62	61					12																	94072802		2203	4300	6503	92596933	SO:0001819	synonymous_variant	8738			U84388	CCDS9048.1	12q21.33-q23.1	2008-08-04				ENSG00000169372			2340	protein-coding gene	gene with protein product	"RIP-associated ICH1/CED3-homologous protein with death domain"	603454				8985253, 9044836	Standard	NM_003805		Approved	RAIDD	uc001tda.3	P78560		ENST00000542893.2:c.252G>A	12.37:g.94072802G>A			92596933	B7Z2Q5	Silent	SNP	ENST00000542893.2	37	CCDS9048.1																																																																																				0.502	CRADD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408515.1	NM_003805		A	94072802	G	A	94072802	2	1	61	1	0	0	0	0	0	0	0	1	3851	933	33	3		3	CRADD	12	94072802	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103865	94072802	39779093	8267	16252										
PLXNC1	10154	broad.mit.edu	37	chr12	94580195	94580195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caataaacataaatcctgttCggagtgtttaacagccacag	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94580195C>T	ENST00000258526.4	+	4	1634	c.1385C>T	c.(1384-1386)tCg>tTg	p.S462L	RP11-74K11.2_ENST00000550759.1_RNA	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	462					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.S462L(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AAATCCTGTTCGGAGTGTTTA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	12											133	116	122					12																	94580195		2203	4300	6503	93104326	SO:0001583	missense	10154			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.1385C>T	12.37:g.94580195C>T	ENSP00000258526:p.Ser462Leu		93104326	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	37	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.423077	0.25639	.	.	ENSG00000136040	ENST00000258526;ENST00000551850	T;T	0.20463	2.07;2.07	5.51	-3.88	0.04205	.	1.955300	0.02302	N	0.071282	T	0.14184	0.0343	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15752	-1.0426	10	0.33940	T	0.23	.	1.7802	0.03030	0.18:0.2594:0.1096:0.4509	.	462	O60486	PLXC1_HUMAN	L	462;78	ENSP00000258526:S462L;ENSP00000447843:S78L	ENSP00000258526:S462L	S	+	2	0	PLXNC1	93104326	0.000000	0.05858	0.000000	0.03702	0.984000	0.73092	-0.497000	0.06428	-0.789000	0.04498	0.561000	0.74099	TCG		0.418	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94580195	C	T	94580195	3	4	61	1	0	0	0	0	1	0	0	0	12157	893	31	1	1399	1	PLXNC1	12	94580195	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	507393	94580195	39271700	8268	16253										
PLXNC1	10154	broad.mit.edu	37	chr12	94673260	94673260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgcaggcattaaacgtcGtctttgaaaaaatcccggaa	8	9	2	1	rs139894368		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94673260G>A	ENST00000258526.4	+	22	3859	c.3610G>A	c.(3610-3612)Gtc>Atc	p.V1204I	RP11-1105G2.4_ENST00000550111.1_RNA|PLXNC1_ENST00000545312.1_5'UTR|PLXNC1_ENST00000547057.1_Missense_Mutation_p.V251I|RP11-1105G2.3_ENST00000547927.1_5'Flank|RP11-1105G2.3_ENST00000551941.1_Intron	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1204					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.V1204I(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ATTAAACGTCGTCTTTGAAAA	0.403													G|||	1	0.000199681	8e-04	0	5008	,	,		15569	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	81	78	79		3610	1.6	1	12	dbSNP_134	79	0,8600		0,0,4300	no	missense	PLXNC1	NM_005761.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1204/1569	94673260	1,13005	2203	4300	6503	93197391	SO:0001583	missense	10154			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.3610G>A	12.37:g.94673260G>A	ENSP00000258526:p.Val1204Ile		93197391	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	37	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.579105	0.28180	2.27E-4	0.0	ENSG00000136040	ENST00000258526;ENST00000547057	T;T	0.10860	2.83;2.83	5.81	1.63	0.23807	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.592975	0.14030	N	0.346224	T	0.05686	0.0149	N	0.13140	0.3	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.001;0.002	T	0.37753	-0.9692	10	0.12430	T	0.62	.	9.1544	0.36983	0.4301:0.0:0.5699:0.0	.	251;1204	B4DHQ7;O60486	.;PLXC1_HUMAN	I	1204;251	ENSP00000258526:V1204I;ENSP00000446720:V251I	ENSP00000258526:V1204I	V	+	1	0	PLXNC1	93197391	0.125000	0.22332	0.996000	0.52242	0.900000	0.52787	0.089000	0.15002	0.020000	0.15106	-0.126000	0.14955	GTC		0.403	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			A	94673260	G	A	94673260	3	1	61	1	0	0	0	0	1	0	0	0	12157	1145	40	1	3696	1	PLXNC1	12	94673260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93065	94673260	39178635	8269	16254										
PLXNC1	10154	broad.mit.edu	37	chr12	94688288	94688288	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggatccactataaaagtCtttaagaagatagcaaattt	6	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94688288C>A	ENST00000258526.4	+	24	4155	c.3906C>A	c.(3904-3906)gtC>gtA	p.V1302V	PLXNC1_ENST00000545312.1_Silent_p.V41V|PLXNC1_ENST00000547057.1_Silent_p.V349V	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1302					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.V1302V(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTATAAAAGTCTTTAAGAAGA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	12											35	38	37					12																	94688288		2194	4295	6489	93212419	SO:0001819	synonymous_variant	10154			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.3906C>A	12.37:g.94688288C>A			93212419	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																				0.313	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			A	94688288	C	A	94688288	2	1	61	1	0	0	0	0	0	0	0	1	12157	900	32	2		2	PLXNC1	12	94688288	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15028	94688288	39163607	8270	16255										
CCDC41	51134	broad.mit.edu	37	chr12	94761717	94761717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatctgttctcgagttctAacctaaaacaagagatcata	5	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94761717A>G	ENST00000397809.5	-	11	1745	c.1196T>C	c.(1195-1197)tTa>tCa	p.L399S	CCDC41_ENST00000397807.2_Missense_Mutation_p.L366S|CCDC41_ENST00000339839.5_Missense_Mutation_p.L399S|CCDC41_ENST00000549352.1_5'Flank	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		391					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)		p.L399S(1)		breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						CTCGAGTTCTAACCTAAAACA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											122	107	111					12																	94761717		1838	4087	5925	93285848	SO:0001583	missense	51134																														ENST00000397809.5:c.1196T>C	12.37:g.94761717A>G	ENSP00000380911:p.Leu399Ser		93285848	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194625	0.78902	.	.	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807	T;T;T	0.57273	0.56;0.56;0.41	5.83	5.83	0.93111	.	.	.	.	.	T	0.63486	0.2515	L	0.53249	1.67	0.44562	D	0.997524	D;D	0.59767	0.986;0.966	D;P	0.63957	0.92;0.836	T	0.58216	-0.7675	9	0.09590	T	0.72	-2.3285	16.2127	0.82178	1.0:0.0:0.0:0.0	.	366;391	Q9Y592-2;Q9Y592	.;CCD41_HUMAN	S	399;399;366	ENSP00000344655:L399S;ENSP00000380911:L399S;ENSP00000380909:L366S	ENSP00000344655:L399S	L	-	2	0	CCDC41	93285848	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.429000	0.80309	2.236000	0.73375	0.533000	0.62120	TTA		0.338	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			G	94761717	A	G	94761717	3	3	61	1	0	0	0	0	1	0	0	0	2819	372	13	4	937	4	CCDC41	12	94761717	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73429	94761717	39090178	8271	16256										
CCDC41	51134	broad.mit.edu	37	chr12	94805517	94805517	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagttttctctactaattCtcctcttagttcttcaagca	3	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94805517C>A	ENST00000397809.5	-	4	829	c.280G>T	c.(280-282)Gaa>Taa	p.E94*	CCDC41_ENST00000547575.1_Nonsense_Mutation_p.E94*|CCDC41_ENST00000397807.2_Nonsense_Mutation_p.E61*|CCDC41_ENST00000339839.5_Nonsense_Mutation_p.E94*	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		86					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)		p.E94*(2)		breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						TCTACTAATTCTCCTCTTAGT	0.338																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											107	99	102					12																	94805517		1804	4059	5863	93329648	SO:0001587	stop_gained	51134																														ENST00000397809.5:c.280G>T	12.37:g.94805517C>A	ENSP00000380911:p.Glu94*		93329648	A4FVB1|Q08AP1	Nonsense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	.	.	.	.	.	.	.	.	.	.	C	38	6.885434	0.97908	.	.	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	.	.	.	4.88	3.96	0.45880	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-6.964	14.4521	0.67392	0.0:0.7204:0.2795:0.0	.	.	.	.	X	94;94;61;94	.	ENSP00000344655:E94X	E	-	1	0	CCDC41	93329648	0.997000	0.39634	0.827000	0.32855	0.294000	0.27393	3.669000	0.54561	1.137000	0.42214	0.655000	0.94253	GAA		0.338	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			A	94805517	C	A	94805517	4	1	61	1	0	0	0	0	0	1	0	0	2819	922	32	2	1881	2	CCDC41	12	94805517	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43800	94805517	39046378	8272	16257										
TMCC3	57458	broad.mit.edu	37	chr12	94972183	94972183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtacctggatgtcccgcGagcgctcgtaggcctggtag	15	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:94972183G>A	ENST00000261226.4	-	3	1249	c.1118C>T	c.(1117-1119)tCg>tTg	p.S373L	TMCC3_ENST00000551457.1_Missense_Mutation_p.S342L	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	373						integral component of membrane (GO:0016021)		p.S373L(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GATGTCCCGCGAGCGCTCGTA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											95	88	90					12																	94972183		2203	4300	6503	93496314	SO:0001583	missense	57458			AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1118C>T	12.37:g.94972183G>A	ENSP00000261226:p.Ser373Leu		93496314	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	37	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806299	0.31961	.	.	ENSG00000057704	ENST00000261226;ENST00000551457	T;T	0.39787	1.06;1.06	5.7	5.7	0.88788	.	0.160465	0.56097	D	0.000028	T	0.25494	0.0620	N	0.12569	0.235	0.58432	D	0.999999	P	0.37176	0.586	B	0.35655	0.207	T	0.10989	-1.0606	10	0.02654	T	1	-5.3234	19.8333	0.96644	0.0:0.0:1.0:0.0	.	373	Q9ULS5	TMCC3_HUMAN	L	373;342	ENSP00000261226:S373L;ENSP00000449888:S342L	ENSP00000261226:S373L	S	-	2	0	TMCC3	93496314	1.000000	0.71417	0.488000	0.27440	0.188000	0.23474	9.869000	0.99810	2.698000	0.92095	0.491000	0.48974	TCG		0.537	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94972183	G	A	94972183	3	1	61	1	0	0	0	0	1	0	0	0	16033	1059	37	1	323	1	TMCC3	12	94972183	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	166666	94972183	38879712	8273	16258										
NR2C1	7181	broad.mit.edu	37	chr12	95434360	95434360	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggtactcaggcataggaGaaggcatggtgagctagtat	14	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95434360G>A	ENST00000333003.5	-	10	1475	c.1145C>T	c.(1144-1146)tCt>tTt	p.S382F	NR2C1_ENST00000545833.1_5'UTR|NR2C1_ENST00000330677.7_Missense_Mutation_p.S382F|NR2C1_ENST00000393101.3_Missense_Mutation_p.S382F	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	382					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S382F(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						AGGCATAGGAGAAGGCATGGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											131	113	119					12																	95434360		2203	4300	6503	93958491	SO:0001583	missense	7181			M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1145C>T	12.37:g.95434360G>A	ENSP00000333275:p.Ser382Phe		93958491	A8K5K4|Q15625|Q15626	Missense_Mutation	SNP	ENST00000333003.5	37	CCDS9051.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201277	0.58234	.	.	ENSG00000120798	ENST00000333003;ENST00000393101;ENST00000330677	D;D;D	0.96830	-4.14;-4.14;-4.14	6.06	6.06	0.98353	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.171825	0.53938	D	0.000049	D	0.98131	0.9383	M	0.79475	2.455	0.49798	D	0.999822	D;D;D;D	0.71674	0.998;0.994;0.995;0.995	D;P;P;P	0.78314	0.991;0.83;0.893;0.861	D	0.97781	1.0232	10	0.51188	T	0.08	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	382;382;382;382	B6ZGT7;P13056-3;P13056-2;P13056	.;.;.;NR2C1_HUMAN	F	382	ENSP00000333275:S382F;ENSP00000376813:S382F;ENSP00000328843:S382F	ENSP00000328843:S382F	S	-	2	0	NR2C1	93958491	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.782000	0.62396	2.882000	0.98803	0.655000	0.94253	TCT		0.398	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		A	95434360	G	A	95434360	3	1	61	1	0	0	0	0	1	0	0	0	10653	942	33	3	764	3	NR2C1	12	95434360	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	462177	95434360	38417535	8274	16259										
NR2C1	7181	broad.mit.edu	37	chr12	95442870	95442870	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctacatgtgaatcgctgaGaagtggcccctctttttcgg	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95442870G>A	ENST00000333003.5	-	9	1435	c.1105C>T	c.(1105-1107)Ctc>Ttc	p.L369F	NR2C1_ENST00000545833.1_5'UTR|NR2C1_ENST00000330677.7_Missense_Mutation_p.L369F|NR2C1_ENST00000393101.3_Missense_Mutation_p.L369F	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	369					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.L369F(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						GAATCGCTGAGAAGTGGCCCC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											140	123	129					12																	95442870		2203	4300	6503	93967001	SO:0001583	missense	7181			M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1105C>T	12.37:g.95442870G>A	ENSP00000333275:p.Leu369Phe		93967001	A8K5K4|Q15625|Q15626	Missense_Mutation	SNP	ENST00000333003.5	37	CCDS9051.1	.	.	.	.	.	.	.	.	.	.	G	31	5.062323	0.93898	.	.	ENSG00000120798	ENST00000333003;ENST00000393101;ENST00000330677	D;D;D	0.92805	-3.11;-2.91;-2.89	6.05	6.05	0.98169	Nuclear hormone receptor, ligand-binding (1);	0.184650	0.50627	D	0.000119	D	0.96200	0.8761	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	0.999;0.998;1.0;0.981	D;D;D;P	0.83275	0.994;0.996;0.985;0.832	D	0.95733	0.8776	10	0.72032	D	0.01	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	369;369;369;369	B6ZGT7;P13056-3;P13056-2;P13056	.;.;.;NR2C1_HUMAN	F	369	ENSP00000333275:L369F;ENSP00000376813:L369F;ENSP00000328843:L369F	ENSP00000328843:L369F	L	-	1	0	NR2C1	93967001	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.875000	0.87205	2.878000	0.98634	0.650000	0.86243	CTC		0.403	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		A	95442870	G	A	95442870	3	1	61	1	0	0	0	0	1	0	0	0	10653	942	33	3	808	3	NR2C1	12	95442870	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8510	95442870	38409025	8275	16260										
FGD6	55785	broad.mit.edu	37	chr12	95488460	95488460	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctagccattcatccctttCtgtggcagaactgttggggg	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95488460C>A	ENST00000343958.4	-	15	3731	c.3508G>T	c.(3508-3510)Gaa>Taa	p.E1170*	FGD6_ENST00000549499.1_Nonsense_Mutation_p.E1170*|FGD6_ENST00000546711.1_Nonsense_Mutation_p.E1170*	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1170	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.E1170*(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TCATCCCTTTCTGTGGCAGAA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											143	137	139					12																	95488460		2203	4300	6503	94012591	SO:0001587	stop_gained	55785			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3508G>T	12.37:g.95488460C>A	ENSP00000344446:p.Glu1170*		94012591	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Nonsense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	C	36	5.654532	0.96724	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000551521;ENST00000549499	.	.	.	6.04	6.04	0.98038	.	0.000000	0.50627	D	0.000115	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.9704	20.5792	0.99380	0.0:1.0:0.0:0.0	.	.	.	.	X	1170;1170;166;1170	.	ENSP00000344446:E1170X	E	-	1	0	FGD6	94012591	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.226000	0.78060	2.873000	0.98535	0.561000	0.74099	GAA		0.423	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		A	95488460	C	A	95488460	4	1	61	1	0	0	0	0	0	1	0	0	5856	922	32	2	812	2	FGD6	12	95488460	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45590	95488460	38363435	8276	16261										
FGD6	55785	broad.mit.edu	37	chr12	95602980	95602980	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattccaggctatagttttCtgtggaatatgccttgatgg	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95602980C>A	ENST00000343958.4	-	2	2303	c.2080G>T	c.(2080-2082)Gaa>Taa	p.E694*	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Nonsense_Mutation_p.E694*|FGD6_ENST00000546711.1_Nonsense_Mutation_p.E694*	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	694					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.E694*(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTATAGTTTTCTGTGGAATAT	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											141	153	149					12																	95602980		2203	4300	6503	94127111	SO:0001587	stop_gained	55785			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.2080G>T	12.37:g.95602980C>A	ENSP00000344446:p.Glu694*		94127111	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Nonsense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	C	38	6.932626	0.97944	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	.	.	.	6.04	6.04	0.98038	.	0.395855	0.21714	N	0.070234	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-14.9575	20.5792	0.99380	0.0:1.0:0.0:0.0	.	.	.	.	X	694	.	ENSP00000344446:E694X	E	-	1	0	FGD6	94127111	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	5.359000	0.66074	2.873000	0.98535	0.561000	0.74099	GAA		0.488	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		A	95602980	C	A	95602980	4	1	61	1	0	0	0	0	0	1	0	0	5856	922	32	2	2292	2	FGD6	12	95602980	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114520	95602980	38248915	8277	16262										
FGD6	55785	broad.mit.edu	37	chr12	95603586	95603586	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttggggacaattcgtaGagaattttcctcttttataa	7	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95603586G>T	ENST00000343958.4	-	2	1697	c.1474C>A	c.(1474-1476)Cta>Ata	p.L492I	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.L492I|FGD6_ENST00000546711.1_Missense_Mutation_p.L492I	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	492					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.L492I(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						ACAATTCGTAGAGAATTTTCC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											68	74	72					12																	95603586		2203	4300	6503	94127717	SO:0001583	missense	55785			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1474C>A	12.37:g.95603586G>T	ENSP00000344446:p.Leu492Ile		94127717	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	G	0.072	-1.200268	0.01581	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.66815	-0.13;-0.23;-0.15	6.04	2.28	0.28536	.	1.166620	0.06515	N	0.738640	T	0.38904	0.1058	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27971	-1.0058	10	0.26408	T	0.33	-0.5237	2.6243	0.04925	0.4119:0.0:0.3564:0.2317	.	492	Q6ZV73	FGD6_HUMAN	I	492	ENSP00000344446:L492I;ENSP00000450342:L492I;ENSP00000449005:L492I	ENSP00000344446:L492I	L	-	1	2	FGD6	94127717	0.985000	0.35326	0.484000	0.27391	0.331000	0.28603	1.951000	0.40333	1.125000	0.41998	-0.367000	0.07326	CTA		0.413	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		T	95603586	G	T	95603586	3	4	61	1	0	0	0	0	1	0	0	0	5856	933	33	2	2898	2	FGD6	12	95603586	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	606	95603586	38248309	8278	16263										
FGD6	55785	broad.mit.edu	37	chr12	95604098	95604098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgtaacagacgagcagttCgtgtctttctgggcttggga	15	8	2	1	rs148149725		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95604098C>T	ENST00000343958.4	-	2	1185	c.962G>A	c.(961-963)cGa>cAa	p.R321Q	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.R321Q|FGD6_ENST00000546711.1_Missense_Mutation_p.R321Q	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	321					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.R321Q(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						ACGAGCAGTTCGTGTCTTTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	117	116					12																	95604098		2203	4300	6503	94128229	SO:0001583	missense	55785			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.962G>A	12.37:g.95604098C>T	ENSP00000344446:p.Arg321Gln		94128229	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467774	0.26335	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.70516	-0.38;-0.49;-0.43	5.29	1.34	0.21922	.	0.486350	0.17439	N	0.174198	T	0.57272	0.2042	L	0.48642	1.525	0.18873	N	0.999981	D	0.56746	0.977	B	0.41646	0.362	T	0.49707	-0.8911	10	0.33141	T	0.24	0.0201	6.121	0.20154	0.1317:0.6523:0.0:0.2159	.	321	Q6ZV73	FGD6_HUMAN	Q	321	ENSP00000344446:R321Q;ENSP00000450342:R321Q;ENSP00000449005:R321Q	ENSP00000344446:R321Q	R	-	2	0	FGD6	94128229	0.293000	0.24371	0.007000	0.13788	0.378000	0.30076	0.626000	0.24492	-0.027000	0.13873	-0.224000	0.12420	CGA		0.423	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		T	95604098	C	T	95604098	3	4	61	1	0	0	0	0	1	0	0	0	5856	884	31	1	3410	1	FGD6	12	95604098	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	512	95604098	38247797	8279	16264										
VEZT	55591	broad.mit.edu	37	chr12	95694139	95694139	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtaaaaataaagataattCttcaaatgaagtcttccccc	5	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95694139C>A	ENST00000436874.1	+	12	2135	c.2030C>A	c.(2029-2031)tCt>tAt	p.S677Y	VEZT_ENST00000261219.6_Missense_Mutation_p.S629Y|VEZT_ENST00000356859.4_3'UTR	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	677					chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)		p.S677Y(2)		endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						AAAGATAATTCTTCAAATGAA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	12											43	41	41					12																	95694139		1866	4097	5963	94218270	SO:0001583	missense	55591			AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.2030C>A	12.37:g.95694139C>A	ENSP00000410083:p.Ser677Tyr		94218270	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	37	CCDS44954.1	.	.	.	.	.	.	.	.	.	.	C	2.086	-0.409649	0.04799	.	.	ENSG00000028203	ENST00000436874;ENST00000261219;ENST00000397792;ENST00000397796	T;T;T	0.15952	2.38;2.38;2.38	6.02	4.16	0.48862	.	0.379957	0.30473	N	0.009549	T	0.16938	0.0407	L	0.54323	1.7	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.18555	-1.0333	10	0.59425	D	0.04	-42.1416	8.3762	0.32445	0.1196:0.7019:0.1153:0.0632	.	677	Q9HBM0	VEZA_HUMAN	Y	677;629;633;677	ENSP00000410083:S677Y;ENSP00000261219:S629Y;ENSP00000380894:S633Y	ENSP00000261219:S629Y	S	+	2	0	VEZT	94218270	0.001000	0.12720	0.008000	0.14137	0.030000	0.12068	1.237000	0.32695	0.827000	0.34685	0.650000	0.86243	TCT		0.388	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599		A	95694139	C	A	95694139	3	1	61	1	0	0	0	0	1	0	0	0	17196	913	32	2	2076	2	VEZT	12	95694139	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90041	95694139	38157756	8280	16265										
METAP2	10988	broad.mit.edu	37	chr12	95869931	95869931	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatcagcattggaagataAagaaagagatgaagatgatg	12	2	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95869931A>C	ENST00000323666.5	+	2	465	c.236A>C	c.(235-237)aAa>aCa	p.K79T	METAP2_ENST00000546753.1_Missense_Mutation_p.K79T|METAP2_ENST00000261220.9_Missense_Mutation_p.K78T|METAP2_ENST00000551840.1_Missense_Mutation_p.K78T|METAP2_ENST00000550777.1_Intron	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2									p.K79T(1)		endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						TTGGAAGATAAAGAAAGAGAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											134	126	129					12																	95869931		2203	4300	6503	94394062	SO:0001583	missense	10988			U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.236A>C	12.37:g.95869931A>C	ENSP00000325312:p.Lys79Thr		94394062		Missense_Mutation	SNP	ENST00000323666.5	37	CCDS9052.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.866221	0.51588	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000549502;ENST00000553151;ENST00000551840	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.47655	0.1457	N	0.08118	0	0.50813	D	0.999896	P;D;D;D	0.56968	0.759;0.978;0.978;0.963	B;P;P;P	0.59115	0.143;0.852;0.852;0.715	T	0.50268	-0.8848	9	0.29301	T	0.29	-4.0048	14.1236	0.65205	1.0:0.0:0.0:0.0	.	79;78;78;79	B4DUX5;G3XA91;F8VQZ7;P50579	.;.;.;AMPM2_HUMAN	T	79;79;78;79;55;78	.	ENSP00000261220:K78T	K	+	2	0	METAP2	94394062	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	3.703000	0.54808	1.973000	0.57446	0.528000	0.53228	AAA		0.403	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		C	95869931	A	C	95869931	3	2	61	1	0	0	0	0	1	0	0	0	9517	14	1	4	242	4	METAP2	12	95869931	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	175792	95869931	37981964	8281	16266										
USP44	84101	broad.mit.edu	37	chr12	95927737	95927737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggcacttaatgtacgtCgtagtaacttcaggtctcca	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:95927737C>T	ENST00000258499.3	-	2	584	c.296G>A	c.(295-297)cGa>cAa	p.R99Q	USP44_ENST00000393091.2_Missense_Mutation_p.R99Q|USP44_ENST00000552440.1_Missense_Mutation_p.R99Q|USP44_ENST00000537435.2_Missense_Mutation_p.R99Q	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	99					mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R99Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TAATGTACGTCGTAGTAACTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											166	140	149					12																	95927737		2203	4300	6503	94451868	SO:0001583	missense	84101			AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.296G>A	12.37:g.95927737C>T	ENSP00000258499:p.Arg99Gln		94451868	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.492395	0.84962	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435;ENST00000551837;ENST00000549639	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.12	5.12	0.69794	Zinc finger, RING/FYVE/PHD-type (1);	0.119106	0.64402	D	0.000014	T	0.57095	0.2030	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.56848	-0.7911	10	0.44086	T	0.13	.	18.9309	0.92564	0.0:1.0:0.0:0.0	.	99	Q9H0E7	UBP44_HUMAN	Q	99	ENSP00000258499:R99Q;ENSP00000376806:R99Q;ENSP00000448670:R99Q;ENSP00000442629:R99Q;ENSP00000448601:R99Q;ENSP00000449635:R99Q	ENSP00000258499:R99Q	R	-	2	0	USP44	94451868	1.000000	0.71417	0.999000	0.59377	0.744000	0.42396	7.445000	0.80570	2.536000	0.85505	0.561000	0.74099	CGA		0.388	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		T	95927737	C	T	95927737	3	4	61	1	0	0	0	0	1	0	0	0	17115	884	31	1	1862	1	USP44	12	95927737	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57806	95927737	37924158	8282	16267										
NTN4	59277	broad.mit.edu	37	chr12	96104370	96104370	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcccacacattaacgtcGaagtgacaggtatcagcatg	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:96104370G>A	ENST00000343702.4	-	5	1477	c.1029C>T	c.(1027-1029)ttC>ttT	p.F343F	NTN4_ENST00000538383.1_Silent_p.F306F|NTN4_ENST00000553059.1_Silent_p.F343F|NTN4_ENST00000344911.4_Silent_p.F306F|NTN4_ENST00000552603.1_5'Flank	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	343	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)		p.F343F(1)		NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CATTAACGTCGAAGTGACAGG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	12											149	107	121					12																	96104370		2203	4300	6503	94628501	SO:0001819	synonymous_variant	59277			AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"Netrins"	13658	protein-coding gene	gene with protein product	"beta-netrin", "Netrin-4"	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.1029C>T	12.37:g.96104370G>A			94628501	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Silent	SNP	ENST00000343702.4	37	CCDS9054.1																																																																																				0.453	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229		A	96104370	G	A	96104370	2	1	61	1	0	0	0	0	0	0	0	1	10733	1049	37	1		1	NTN4	12	96104370	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176633	96104370	37747525	8283	16268										
NTN4	59277	broad.mit.edu	37	chr12	96181127	96181127	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgtagaagcagtacagttCggtagcattctgaccgcagg	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:96181127C>T	ENST00000343702.4	-	2	623	c.175G>A	c.(175-177)Gaa>Aaa	p.E59K	NTN4_ENST00000538383.1_Missense_Mutation_p.E22K|NTN4_ENST00000553059.1_Missense_Mutation_p.E59K|NTN4_ENST00000344911.4_Missense_Mutation_p.E22K	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	59	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)		p.E59K(2)		NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CAGTACAGTTCGGTAGCATTC	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	12											101	80	87					12																	96181127		2203	4300	6503	94705258	SO:0001583	missense	59277			AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"Netrins"	13658	protein-coding gene	gene with protein product	"beta-netrin", "Netrin-4"	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.175G>A	12.37:g.96181127C>T	ENSP00000340998:p.Glu59Lys		94705258	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	C	32	5.129331	0.94473	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059;ENST00000547980	T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28	5.77	5.77	0.91146	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93077	0.7796	H	0.94222	3.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.987	D	0.94001	0.7275	10	0.62326	D	0.03	.	19.9883	0.97356	0.0:1.0:0.0:0.0	.	59;59	Q9HB63-2;Q9HB63	.;NET4_HUMAN	K	59;22;22;59;22	ENSP00000340998:E59K;ENSP00000339436:E22K;ENSP00000444432:E22K;ENSP00000447292:E59K;ENSP00000447594:E22K	ENSP00000340998:E59K	E	-	1	0	NTN4	94705258	1.000000	0.71417	0.962000	0.40283	0.988000	0.76386	7.294000	0.78760	2.722000	0.93159	0.555000	0.69702	GAA		0.537	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229		T	96181127	C	T	96181127	3	4	61	1	0	0	0	0	1	0	0	0	10733	893	31	1	1747	1	NTN4	12	96181127	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76757	96181127	37670768	8284	16269										
HAL	3034	broad.mit.edu	37	chr12	96374440	96374440	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggattgcagagccgctcGattcttctctcactgattgc	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:96374440G>A	ENST00000261208.3	-	17	1781	c.1413C>T	c.(1411-1413)atC>atT	p.I471I	HAL_ENST00000541929.1_Silent_p.I263I|HAL_ENST00000538703.1_Silent_p.I471I	NM_002108.3	NP_002099.1	P42357	HUTH_HUMAN	histidine ammonia-lyase	471					biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	histidine ammonia-lyase activity (GO:0004397)	p.I471I(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	34					L-Histidine(DB00117)	AGAGCCGCTCGATTCTTCTCT	0.522																																					NSCLC(169;943 2815 23563 30031)											1	Substitution - coding silent(1)	large_intestine(1)	12											147	130	136					12																	96374440		2203	4300	6503	94898571	SO:0001819	synonymous_variant	3034				CCDS9058.1, CCDS58264.1, CCDS58265.1	12q22-q24.1	1991-07-12				ENSG00000084110	4.3.1.3		4806	protein-coding gene	gene with protein product		609457		HIS			Standard	NM_002108		Approved		uc001tem.2	P42357	OTTHUMG00000170354	ENST00000261208.3:c.1413C>T	12.37:g.96374440G>A			94898571	B4DQC1|B4E0V8|F5GXF2|F5H1U5|Q4VB92|Q4VB93	Silent	SNP	ENST00000261208.3	37	CCDS9058.1	.	.	.	.	.	.	.	.	.	.	G	3.287	-0.145707	0.06627	.	.	ENSG00000084110	ENST00000548808	.	.	.	5.66	-2.15	0.07102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.4502	6.4683	0.21993	0.5434:0.0:0.2457:0.211	.	.	.	.	X	3	.	.	R	-	1	2	HAL	94898571	0.006000	0.16342	0.982000	0.44146	0.231000	0.25187	-0.914000	0.04038	-0.445000	0.07159	-0.140000	0.14226	CGA		0.522	HAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408644.1			A	96374440	G	A	96374440	2	1	61	1	0	0	0	0	0	0	0	1	6968	1048	37	1		1	HAL	12	96374440	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	193313	96374440	37477455	8285	16270										
HAL	3034	broad.mit.edu	37	chr12	96384285	96384285	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcaccaacggttcctttCtctgggacatagggcaggca	12	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:96384285C>A	ENST00000261208.3	-	10	1109	c.741G>T	c.(739-741)gaG>gaT	p.E247D	HAL_ENST00000541929.1_Missense_Mutation_p.E39D|HAL_ENST00000538703.1_Missense_Mutation_p.E247D|HAL_ENST00000551562.1_5'UTR	NM_002108.3	NP_002099.1	P42357	HUTH_HUMAN	histidine ammonia-lyase	247					biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	histidine ammonia-lyase activity (GO:0004397)	p.E247D(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	34					L-Histidine(DB00117)	CGGTTCCTTTCTCTGGGACAT	0.552																																					NSCLC(169;943 2815 23563 30031)											1	Substitution - Missense(1)	large_intestine(1)	12											124	109	114					12																	96384285		2203	4300	6503	94908416	SO:0001583	missense	3034				CCDS9058.1, CCDS58264.1, CCDS58265.1	12q22-q24.1	1991-07-12				ENSG00000084110	4.3.1.3		4806	protein-coding gene	gene with protein product		609457		HIS			Standard	NM_002108		Approved		uc001tem.2	P42357	OTTHUMG00000170354	ENST00000261208.3:c.741G>T	12.37:g.96384285C>A	ENSP00000261208:p.Glu247Asp		94908416	B4DQC1|B4E0V8|F5GXF2|F5H1U5|Q4VB92|Q4VB93	Missense_Mutation	SNP	ENST00000261208.3	37	CCDS9058.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735235	0.89482	.	.	ENSG00000084110	ENST00000261208;ENST00000541929;ENST00000538703;ENST00000552509;ENST00000546579	T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2	5.44	4.55	0.56014	L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87676	0.6237	M	0.84948	2.725	0.58432	D	0.999999	D;P	0.54772	0.968;0.955	P;D	0.63113	0.72;0.911	D	0.89115	0.3499	10	0.59425	D	0.04	-21.5762	14.0935	0.65006	0.0:0.9276:0.0:0.0724	.	247;247	F5GXF2;P42357	.;HUTH_HUMAN	D	247;39;247;235;157	ENSP00000261208:E247D;ENSP00000446364:E39D;ENSP00000440861:E247D;ENSP00000450372:E235D;ENSP00000447543:E157D	ENSP00000261208:E247D	E	-	3	2	HAL	94908416	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.005000	0.49521	1.314000	0.45095	0.555000	0.69702	GAG		0.552	HAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408644.1			A	96384285	C	A	96384285	3	1	61	1	0	0	0	0	1	0	0	0	6968	912	32	2	1280	2	HAL	12	96384285	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9845	96384285	37467610	8286	16271										
NEDD1	121441	broad.mit.edu	37	chr12	97328953	97328953	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccataggcttggataaaaGaatcatcctctatgacactt	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:97328953G>T	ENST00000266742.4	+	7	1028	c.689G>T	c.(688-690)aGa>aTa	p.R230I	NEDD1_ENST00000411739.2_Missense_Mutation_p.R141I|NEDD1_ENST00000457368.2_Missense_Mutation_p.R141I|NEDD1_ENST00000555114.1_3'UTR|NEDD1_ENST00000557644.1_Missense_Mutation_p.R237I|NEDD1_ENST00000429527.2_Missense_Mutation_p.R230I	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	230					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)		p.R230I(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						TTGGATAAAAGAATCATCCTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											146	143	144					12																	97328953		2203	4300	6503	95853084	SO:0001583	missense	121441				CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"WD repeat domain containing"	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.689G>T	12.37:g.97328953G>T	ENSP00000266742:p.Arg230Ile		95853084	B0AZN0|B4E145|G3V3F1|Q8NA30	Missense_Mutation	SNP	ENST00000266742.4	37	CCDS9063.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178478	0.78564	.	.	ENSG00000139350	ENST00000266742;ENST00000429527;ENST00000411739;ENST00000553609;ENST00000557644;ENST00000457368	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.71	3.88	0.44766	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.131325	0.64402	D	0.000001	T	0.49270	0.1547	L	0.56396	1.775	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.941	T	0.40776	-0.9545	10	0.45353	T	0.12	.	12.1339	0.53959	0.1389:0.0:0.8611:0.0	.	237;230	G3V3F1;Q8NHV4	.;NEDD1_HUMAN	I	230;230;141;141;237;141	ENSP00000266742:R230I;ENSP00000404978:R230I;ENSP00000411307:R141I;ENSP00000451830:R141I;ENSP00000451211:R237I;ENSP00000407964:R141I	ENSP00000266742:R230I	R	+	2	0	NEDD1	95853084	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.639000	0.61361	0.753000	0.32945	0.650000	0.86243	AGA		0.358	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1			T	97328953	G	T	97328953	3	4	61	1	0	0	0	0	1	0	0	0	10340	942	33	2	732	2	NEDD1	12	97328953	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	944668	97328953	36522942	8287	16272										
NEDD1	121441	broad.mit.edu	37	chr12	97339533	97339533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactctcagaaaaaatagccGacagcattggaaataaccgg	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:97339533G>A	ENST00000266742.4	+	14	2056	c.1717G>A	c.(1717-1719)Gac>Aac	p.D573N	NEDD1_ENST00000411739.2_Missense_Mutation_p.D484N|NEDD1_ENST00000457368.2_Missense_Mutation_p.D484N|NEDD1_ENST00000557644.1_Missense_Mutation_p.D580N|NEDD1_ENST00000429527.2_Missense_Mutation_p.D573N	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	573					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)		p.D573N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						AAAAATAGCCGACAGCATTGG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											101	94	96					12																	97339533		2203	4300	6503	95863664	SO:0001583	missense	121441				CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"WD repeat domain containing"	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.1717G>A	12.37:g.97339533G>A	ENSP00000266742:p.Asp573Asn		95863664	B0AZN0|B4E145|G3V3F1|Q8NA30	Missense_Mutation	SNP	ENST00000266742.4	37	CCDS9063.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609787	0.66558	.	.	ENSG00000139350	ENST00000266742;ENST00000429527;ENST00000411739;ENST00000557644;ENST00000457368	T;T;T;T;T	0.50548	0.74;0.74;1.58;0.74;1.58	5.87	4.99	0.66335	.	0.144183	0.64402	D	0.000008	T	0.63070	0.2480	L	0.56769	1.78	0.40167	D	0.977137	D;D	0.76494	0.999;0.998	D;P	0.63703	0.917;0.75	T	0.68017	-0.5520	10	0.72032	D	0.01	.	14.9712	0.71235	0.0681:0.0:0.9319:0.0	.	580;573	G3V3F1;Q8NHV4	.;NEDD1_HUMAN	N	573;573;484;580;484	ENSP00000266742:D573N;ENSP00000404978:D573N;ENSP00000411307:D484N;ENSP00000451211:D580N;ENSP00000407964:D484N	ENSP00000266742:D573N	D	+	1	0	NEDD1	95863664	1.000000	0.71417	0.817000	0.32601	0.378000	0.30076	5.806000	0.69150	1.497000	0.48584	0.655000	0.94253	GAC		0.358	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1			A	97339533	G	A	97339533	3	1	61	1	0	0	0	0	1	0	0	0	10340	1058	37	1	1788	1	NEDD1	12	97339533	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10580	97339533	36512362	8288	16273										
TMPO	7112	broad.mit.edu	37	chr12	98925613	98925613	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagatacagtgacaatgaaGaaggtaaaattttaaatgat	8	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:98925613G>T	ENST00000556029.1	+	3	918	c.562G>T	c.(562-564)Gaa>Taa	p.E188*	TMPO_ENST00000266732.4_Nonsense_Mutation_p.E188*|TMPO_ENST00000393053.2_Nonsense_Mutation_p.E188*|TMPO_ENST00000261210.5_Nonsense_Mutation_p.E188*|TMPO_ENST00000343315.5_Nonsense_Mutation_p.E188*	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	188	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)	p.E188*(2)		breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGACAATGAAGAAGGTAAAAT	0.308																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											49	52	51					12																	98925613		2203	4300	6503	97449744	SO:0001587	stop_gained	7112				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.562G>T	12.37:g.98925613G>T	ENSP00000450627:p.Glu188*		97449744	A2T926|Q14861	Nonsense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	37	6.227727	0.97394	.	.	ENSG00000120802	ENST00000556029;ENST00000343315;ENST00000266732;ENST00000393053;ENST00000261210;ENST00000556678	.	.	.	5.4	5.4	0.78164	.	0.047126	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	18.779	0.91924	0.0:0.0:1.0:0.0	.	.	.	.	X	188;188;188;188;188;95	.	ENSP00000261210:E188X	E	+	1	0	TMPO	97449744	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.275000	0.89892	2.523000	0.85059	0.655000	0.94253	GAA		0.308	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		T	98925613	G	T	98925613	4	4	61	1	0	0	0	0	0	1	0	0	16276	943	33	2	572	2	TMPO	12	98925613	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1586080	98925613	34926282	8289	16274										
TMPO	7112	broad.mit.edu	37	chr12	98927458	98927458	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactcactaccttaggtctaGaagtggctaagcaatcacag	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:98927458G>T	ENST00000556029.1	+	3	921				TMPO_ENST00000266732.4_Nonsense_Mutation_p.E475*|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000261210.5_Intron|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)	p.E475*(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CTTAGGTCTAGAAGTGGCTAA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											139	120	126					12																	98927458		2203	4300	6503	97451589	SO:0001627	intron_variant	7112				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.565+1842G>T	12.37:g.98927458G>T			97451589	A2T926|Q14861	Nonsense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.259473	0.80246	.	.	ENSG00000120802	ENST00000266732	.	.	.	5.65	5.65	0.86999	.	0.215070	0.39274	N	0.001413	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-16.9242	15.5961	0.76583	0.0:0.0:1.0:0.0	.	.	.	.	X	475	.	ENSP00000266732:E475X	E	+	1	0	TMPO	97451589	1.000000	0.71417	0.979000	0.43373	0.082000	0.17680	4.431000	0.59915	2.827000	0.97445	0.650000	0.86243	GAA		0.388	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		T	98927458	G	T	98927458	1	4	61	0	1	0	0	0	0	0	0	0	16276	943	33	2		2	TMPO	12	98927458	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1845	98927458	34924437	8290	16275										
TMPO	7112	broad.mit.edu	37	chr12	98940155	98940155	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgggagaaaaaacagagGaaagaagagtagaaagggat	16	1	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:98940155G>T	ENST00000556029.1	+	8	1365	c.1009G>T	c.(1009-1011)Gaa>Taa	p.E337*	TMPO_ENST00000393053.2_Nonsense_Mutation_p.E228*|TMPO_ENST00000343315.5_Nonsense_Mutation_p.E297*|TMPO_ENST00000548223.1_3'UTR	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	337	Binds lamins B.|NAKAP95-binding C.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)	p.E337*(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AAAAACAGAGGAAAGAAGAGT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											128	128	128					12																	98940155		2203	4299	6502	97464286	SO:0001587	stop_gained	7112				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.1009G>T	12.37:g.98940155G>T	ENSP00000450627:p.Glu337*		97464286	A2T926|Q14861	Nonsense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	38	7.139340	0.98088	.	.	ENSG00000120802	ENST00000556029;ENST00000343315;ENST00000393053;ENST00000556678	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	19.5665	0.95395	0.0:0.0:1.0:0.0	.	.	.	.	X	337;297;228;172	.	ENSP00000340251:E337X	E	+	1	0	TMPO	97464286	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.894000	0.75655	2.699000	0.92147	0.655000	0.94253	GAA		0.308	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		T	98940155	G	T	98940155	4	4	61	1	0	0	0	0	0	1	0	0	16276	1175	41	2	2563	2	TMPO	12	98940155	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12697	98940155	34911740	8291	16276										
SLC25A3	5250	broad.mit.edu	37	chr12	98995180	98995180	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtttgcccgtatcatcatGattggtaccctgactgcact	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:98995180G>T	ENST00000228318.3	+	8	1083	c.963G>T	c.(961-963)atG>atT	p.M321I	SLC25A3_ENST00000548847.1_Missense_Mutation_p.M283I|SLC25A3_ENST00000551917.1_Missense_Mutation_p.M321I|SLC25A3_ENST00000552981.1_Missense_Mutation_p.M320I|SLC25A3_ENST00000401722.3_Missense_Mutation_p.M320I|SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Missense_Mutation_p.M320I|SLC25A3_ENST00000549338.1_Missense_Mutation_p.M320I	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	321					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)	p.M321I(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		GTATCATCATGATTGGTACCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											172	164	167					12																	98995180		2203	4300	6503	97519311	SO:0001583	missense	5250				CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"Solute carriers"	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.963G>T	12.37:g.98995180G>T	ENSP00000228318:p.Met321Ile		97519311	B3KS34|Q7Z7N7|Q96A03	Missense_Mutation	SNP	ENST00000228318.3	37	CCDS9066.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840001	0.91117	.	.	ENSG00000075415	ENST00000401722;ENST00000188376;ENST00000228318;ENST00000551917;ENST00000552981;ENST00000549338;ENST00000548847	T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.48	5.48	0.80851	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.63721	0.2535	M	0.93507	3.425	0.80722	D	1	D;D;D;D	0.65815	0.995;0.984;0.978;0.991	D;D;D;D	0.71184	0.972;0.937;0.948;0.948	T	0.73408	-0.3992	10	0.87932	D	0	-33.2784	19.7153	0.96115	0.0:0.0:1.0:0.0	.	283;320;321;320	F8VVM2;B2RE88;Q00325;Q00325-2	.;.;MPCP_HUMAN;.	I	320;320;321;321;320;320;283	ENSP00000383898:M320I;ENSP00000188376:M320I;ENSP00000228318:M321I;ENSP00000447310:M321I;ENSP00000448708:M320I;ENSP00000447740:M320I;ENSP00000449166:M283I	ENSP00000188376:M320I	M	+	3	0	SLC25A3	97519311	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.173000	0.94815	2.731000	0.93534	0.655000	0.94253	ATG		0.448	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		T	98995180	G	T	98995180	3	4	61	1	0	0	0	0	1	0	0	0	14530	1290	45	2	1115	2	SLC25A3	12	98995180	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55025	98995180	34856715	8292	16277										
IKBIP	121457	broad.mit.edu	37	chr12	99007832	99007832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttctagttcttgcacaGaatctgtcaatgatattaca	5	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:99007832G>T	ENST00000342502.2	-	3	995	c.584C>A	c.(583-585)tCt>tAt	p.S195Y	IKBIP_ENST00000393042.3_3'UTR|IKBIP_ENST00000420861.1_Missense_Mutation_p.S89Y	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	195					response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S195Y(1)		NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						TTCTTGCACAGAATCTGTCAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											57	54	55					12																	99007832		2203	4298	6501	97531963	SO:0001583	missense	121457			AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"I kappa B kinase interacting protein"	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.584C>A	12.37:g.99007832G>T	ENSP00000343471:p.Ser195Tyr		97531963	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Missense_Mutation	SNP	ENST00000342502.2	37	CCDS9067.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.089229	0.55968	.	.	ENSG00000166130	ENST00000342502;ENST00000420861	T;T	0.49720	0.83;0.77	5.48	5.48	0.80851	.	.	.	.	.	T	0.62146	0.2404	L	0.56769	1.78	0.27665	N	0.946945	D	0.56968	0.978	P	0.58873	0.847	T	0.58278	-0.7664	9	0.72032	D	0.01	.	15.0204	0.71627	0.0:0.0:0.8571:0.1429	.	195	Q70UQ0	IKIP_HUMAN	Y	195;89	ENSP00000343471:S195Y;ENSP00000398023:S89Y	ENSP00000343471:S195Y	S	-	2	0	IKBIP	97531963	1.000000	0.71417	0.997000	0.53966	0.707000	0.40811	4.466000	0.60148	2.577000	0.86979	0.655000	0.94253	TCT		0.328	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687		T	99007832	G	T	99007832	3	4	61	1	0	0	0	0	1	0	0	0	7630	942	33	2	472	2	IKBIP	12	99007832	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12652	99007832	34844063	8293	16278										
ANKS1B	56899	broad.mit.edu	37	chr12	99145259	99145259	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctagctggtaagcgacttcGaatgcctgtcccagggttag	13	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:99145259G>A	ENST00000547776.2	-	25	3545	c.3546C>T	c.(3544-3546)ttC>ttT	p.F1182F	ANKS1B_ENST00000549493.2_Silent_p.F432F|ANKS1B_ENST00000549025.2_Silent_p.F280F|ANKS1B_ENST00000547010.1_Silent_p.F698F|ANKS1B_ENST00000341752.7_Silent_p.F188F|ANKS1B_ENST00000546568.1_Silent_p.F348F|ANKS1B_ENST00000329257.7_Silent_p.F1182F|ANKS1B_ENST00000333732.7_Silent_p.F212F|ANKS1B_ENST00000546960.1_Silent_p.F408F|ANKS1B_ENST00000332712.7_Silent_p.F372F|ANKS1B_ENST00000550693.2_Silent_p.F372F|ANKS1B_ENST00000549558.2_Silent_p.F348F|ANKS1B_ENST00000547446.1_Silent_p.F317F	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	1182	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.F1182F(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		AAGCGACTTCGAATGCCTGTC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	12											169	169	169					12																	99145259		1902	4104	6006	97669390	SO:0001819	synonymous_variant	56899			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3546C>T	12.37:g.99145259G>A			97669390	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	9.276	1.047023	0.19827	.	.	ENSG00000185046	ENST00000550778	.	.	.	5.08	-2.15	0.07102	.	.	.	.	.	T	0.55162	0.1903	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52548	-0.8561	4	.	.	.	-11.2089	10.1709	0.42908	0.6505:0.0:0.3495:0.0	.	.	.	.	L	454	.	.	S	-	2	0	ANKS1B	97669390	1.000000	0.71417	0.993000	0.49108	0.890000	0.51754	1.140000	0.31516	-0.252000	0.09528	-1.069000	0.02264	TCG		0.458	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	99145259	G	A	99145259	2	1	61	1	0	0	0	0	0	0	0	1	689	1049	37	1		1	ANKS1B	12	99145259	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137427	99145259	34706636	8294	16279										
ANKS1B	56899	broad.mit.edu	37	chr12	100169438	100169438	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccacgccttctaaataCtctgtgtgtatacatttttg	5	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100169438C>T	ENST00000547776.2	-	7	848	c.849G>A	c.(847-849)gaG>gaA	p.E283E	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Splice_Site_p.E283E	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	283						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.E283E(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CTTCTAAATACTCTGTGTGTA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	12											101	87	91					12																	100169438		1834	4077	5911	98693569	SO:0001630	splice_region_variant	56899			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.848-1G>A	12.37:g.100169438C>T			98693569	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1																																																																																				0.333	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	Silent	T	100169438	C	T	100169438	5	4	61	1	0	0	0	0	0	0	1	0	689	579	20	3	3265	3	ANKS1B	12	100169438	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1024179	100169438	33682457	8295	16280										
ACTR6	64431	broad.mit.edu	37	chr12	100603985	100603985	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaaaagaagcaattattCggtgagttgtatttaatttt	8	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100603985C>T	ENST00000188312.2	+	5	1279	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W	ACTR6_ENST00000551617.1_Splice_Site_p.R90W|ACTR6_ENST00000546902.1_Splice_Site_p.R90W|ACTR6_ENST00000552376.1_Splice_Site_p.R172W	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	172						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R172W(1)		autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						AGCAATTATTCGGTGAGTTGT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	108	106					12																	100603985		2203	4299	6502	99128116	SO:0001630	splice_region_variant	64431			AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.515+1C>T	12.37:g.100603985C>T			99128116	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Missense_Mutation	SNP	ENST00000188312.2	37	CCDS9074.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.388786	0.61956	.	.	ENSG00000075089	ENST00000551652;ENST00000188312;ENST00000546902;ENST00000552376;ENST00000551617	D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64	4.82	1.84	0.25277	.	0.000000	0.85682	D	0.000000	D	0.97857	0.9296	H	0.95260	3.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98278	1.0507	10	0.87932	D	0	.	14.3133	0.66432	0.5732:0.4268:0.0:0.0	.	90;172;172	F8VSD1;F8W057;Q9GZN1	.;.;ARP6_HUMAN	W	184;172;90;172;90	ENSP00000448508:R184W;ENSP00000188312:R172W;ENSP00000448669:R90W;ENSP00000447237:R172W;ENSP00000448356:R90W	ENSP00000188312:R172W	R	+	1	2	ACTR6	99128116	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.957000	0.56730	0.270000	0.21984	-0.169000	0.13324	CGG		0.303	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408159.1	NM_022496	Missense_Mutation	T	100603985	C	T	100603985	5	4	61	1	0	0	0	0	0	0	1	0	216	898	31	1	532	1	ACTR6	12	100603985	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	434547	100603985	33247910	8296	16281										
SCYL2	55681	broad.mit.edu	37	chr12	100676756	100676756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatattgcagccatggagtCcatgcttaataaattgaaga	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100676756C>A	ENST00000360820.2	+	2	445	c.8C>A	c.(7-9)tCc>tAc	p.S3Y	SCYL2_ENST00000550067.1_3'UTR	NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	3					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)	p.S3Y(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GCCATGGAGTCCATGCTTAAT	0.353																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											67	63	64					12																	100676756		2203	4300	6503	99200887	SO:0001583	missense	55681			AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.8C>A	12.37:g.100676756C>A	ENSP00000354061:p.Ser3Tyr		99200887	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686795	0.68157	.	.	ENSG00000136021	ENST00000549687;ENST00000360820	T;T	0.37235	1.71;1.21	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.24160	0.0585	N	0.08118	0	0.80722	D	1	B	0.26081	0.141	B	0.20767	0.031	T	0.10019	-1.0648	10	0.72032	D	0.01	.	19.0444	0.93013	0.0:1.0:0.0:0.0	.	3	Q6P3W7	SCYL2_HUMAN	Y	3	ENSP00000448366:S3Y;ENSP00000354061:S3Y	ENSP00000354061:S3Y	S	+	2	0	SCYL2	99200887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.551000	0.82182	2.490000	0.84030	0.591000	0.81541	TCC		0.353	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		A	100676756	C	A	100676756	3	1	61	1	0	0	0	0	1	0	0	0	13985	855	30	2	10	2	SCYL2	12	100676756	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72771	100676756	33175139	8297	16282										
SLC17A8	246213	broad.mit.edu	37	chr12	100797822	100797822	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcccttccaggtgggtCtcttgtcagcagtcccacac	8	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100797822C>A	ENST00000323346.5	+	9	1373	c.1060C>A	c.(1060-1062)Ctc>Atc	p.L354I	SLC17A8_ENST00000392989.3_Missense_Mutation_p.L304I|snoU13_ENST00000459038.1_RNA	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	354					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.L354I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						CCAGGTGGGTCTCTTGTCAGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											110	111	111					12																	100797822		2203	4300	6503	99321953	SO:0001583	missense	246213			AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1060C>A	12.37:g.100797822C>A	ENSP00000316909:p.Leu354Ile		99321953	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	37	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904165	0.33628	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.62639	0.01;0.01	5.64	5.64	0.86602	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.120420	0.56097	D	0.000021	T	0.45538	0.1347	N	0.16233	0.39	0.48632	D	0.999681	B;B	0.10296	0.002;0.003	B;B	0.17979	0.02;0.013	T	0.34428	-0.9829	10	0.23302	T	0.38	.	12.9643	0.58475	0.0:0.9262:0.0:0.0738	.	354;304	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	I	354;304	ENSP00000316909:L354I;ENSP00000376715:L304I	ENSP00000316909:L354I	L	+	1	0	SLC17A8	99321953	0.959000	0.32827	1.000000	0.80357	0.978000	0.69477	2.111000	0.41883	2.658000	0.90341	0.563000	0.77884	CTC		0.468	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		A	100797822	C	A	100797822	3	1	61	1	0	0	0	0	1	0	0	0	14460	913	32	2	1094	2	SLC17A8	12	100797822	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121066	100797822	33054073	8298	16283										
SLC17A8	246213	broad.mit.edu	37	chr12	100813904	100813904	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagctgacatcctaccaGaatgaagagagaaacttctc	9	9	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100813904G>T	ENST00000323346.5	+	12	2050	c.1737G>T	c.(1735-1737)caG>caT	p.Q579H	SLC17A8_ENST00000392989.3_Missense_Mutation_p.Q529H	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	579					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.Q579H(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						CATCCTACCAGAATGAAGAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											72	64	67					12																	100813904		2203	4300	6503	99338035	SO:0001583	missense	246213			AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1737G>T	12.37:g.100813904G>T	ENSP00000316909:p.Gln579His		99338035	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	37	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.819277	0.32145	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.69435	0.02;-0.4	4.8	3.9	0.45041	.	0.351400	0.30085	N	0.010446	T	0.48909	0.1526	N	0.22421	0.69	0.31073	N	0.712835	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.50684	-0.8799	10	0.41790	T	0.15	.	8.8587	0.35245	0.0822:0.0:0.7576:0.1602	.	579;529	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	H	579;529	ENSP00000316909:Q579H;ENSP00000376715:Q529H	ENSP00000316909:Q579H	Q	+	3	2	SLC17A8	99338035	0.997000	0.39634	0.992000	0.48379	0.912000	0.54170	0.412000	0.21131	2.388000	0.81334	0.591000	0.81541	CAG		0.438	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		T	100813904	G	T	100813904	3	4	61	1	0	0	0	0	1	0	0	0	14460	933	33	2	1783	2	SLC17A8	12	100813904	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16082	100813904	33037991	8299	16284										
NR1H4	9971	broad.mit.edu	37	chr12	100934588	100934588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctattggaagaaagaattcGaaatagtggtaagtgatttg	11	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:100934588G>A	ENST00000551379.1	+	7	1128	c.1100G>A	c.(1099-1101)cGa>cAa	p.R367Q	NR1H4_ENST00000548884.1_Missense_Mutation_p.R353Q|NR1H4_ENST00000188403.7_Missense_Mutation_p.R363Q|NR1H4_ENST00000549996.1_Missense_Mutation_p.R306Q|NR1H4_ENST00000392986.3_Missense_Mutation_p.R357Q			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	367	Ligand-binding.				bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R353Q(2)		NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	GAAAGAATTCGAAATAGTGGT	0.413																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											105	103	104					12																	100934588		2203	4300	6503	99458719	SO:0001583	missense	9971			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.1100G>A	12.37:g.100934588G>A	ENSP00000447149:p.Arg367Gln		99458719	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	37	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091893	0.76756	.	.	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.96685	-4.09;-4.09;-4.09;-4.09;-4.09	5.05	4.15	0.48705	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.055575	0.64402	D	0.000002	D	0.96892	0.8985	L	0.56340	1.77	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.993;1.0;1.0;0.972	P;P;P;P;B	0.62435	0.892;0.657;0.854;0.902;0.358	D	0.96490	0.9363	10	0.48119	T	0.1	.	15.4862	0.75569	0.0:0.1391:0.8609:0.0	.	306;367;363;357;353	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	Q	353;357;306;367;363	ENSP00000448506:R353Q;ENSP00000376712:R357Q;ENSP00000448978:R306Q;ENSP00000447149:R367Q;ENSP00000188403:R363Q	ENSP00000188403:R363Q	R	+	2	0	NR1H4	99458719	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	7.547000	0.82146	1.110000	0.41699	0.585000	0.79938	CGA		0.413	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		A	100934588	G	A	100934588	3	1	61	1	0	0	0	0	1	0	0	0	10650	1058	37	1	1084	1	NR1H4	12	100934588	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120684	100934588	32917307	8300	16285										
ANO4	121601	broad.mit.edu	37	chr12	101490408	101490408	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagctccacattttacatCgcattcttcctcggaaggta	6	12	1	0	rs200172974		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101490408C>T	ENST00000392977.3	+	19	2043	c.1833C>T	c.(1831-1833)atC>atT	p.I611I	ANO4_ENST00000299222.9_Silent_p.I131I|ANO4_ENST00000550015.1_Silent_p.I131I|ANO4_ENST00000392979.3_Silent_p.I576I			Q32M45	ANO4_HUMAN	anoctamin 4	611					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.I576I(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						CATTTTACATCGCATTCTTCC	0.502										HNSCC(74;0.22)			C|||	1	0.000199681	0	0.0014	5008	,	,		20949	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											120	108	112					12																	101490408		2203	4300	6503	100014539	SO:0001819	synonymous_variant	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1833C>T	12.37:g.101490408C>T			100014539	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																					0.502	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		T	101490408	C	T	101490408	2	4	61	1	0	0	0	0	0	0	0	1	699	874	31	1		1	ANO4	12	101490408	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	555820	101490408	32361487	8301	16286										
SLC5A8	160728	broad.mit.edu	37	chr12	101552062	101552062	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaattggataaaaagtcctCtttggttagtatgtatctgg	9	4	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101552062C>A	ENST00000536262.2	-	14	2233	c.1675G>T	c.(1675-1677)Gag>Tag	p.E559*		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8									p.E559*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAAAAGTCCTCTTTGGTTAGT	0.343																																					GBM(60;420 1056 13605 22380 47675)											1	Substitution - Nonsense(1)	large_intestine(1)	12											134	163	153					12																	101552062		2202	4299	6501	100076193	SO:0001587	stop_gained	160728			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1675G>T	12.37:g.101552062C>A	ENSP00000445340:p.Glu559*		100076193		Nonsense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	C	42	9.767185	0.99259	.	.	ENSG00000256870	ENST00000536262	.	.	.	5.66	3.78	0.43462	.	0.300312	0.30649	N	0.009175	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	14.8271	0.70122	0.0:0.575:0.4249:0.0	.	.	.	.	X	559	.	ENSP00000445340:E559X	E	-	1	0	SLC5A8	100076193	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.923000	0.48868	0.693000	0.31634	0.555000	0.69702	GAG		0.343	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101552062	C	A	101552062	4	1	61	1	0	0	0	0	0	1	0	0	14708	922	32	2	165	2	SLC5A8	12	101552062	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61654	101552062	32299833	8302	16287										
SLC5A8	160728	broad.mit.edu	37	chr12	101555773	101555773	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttgataaactgacaagtaTccccactaataatgttacca	5	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101555773T>G	ENST00000536262.2	-	13	2167	c.1609A>C	c.(1609-1611)Ata>Cta	p.I537L		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8									p.I537L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTGACAAGTATCCCCACTAAT	0.323																																					GBM(60;420 1056 13605 22380 47675)											1	Substitution - Missense(1)	large_intestine(1)	12											174	179	178					12																	101555773		2203	4300	6503	100079904	SO:0001583	missense	160728			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1609A>C	12.37:g.101555773T>G	ENSP00000445340:p.Ile537Leu		100079904		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	T	0.298	-0.975615	0.02215	.	.	ENSG00000256870	ENST00000536262	T	0.60171	0.21	5.5	3.04	0.35103	.	0.633297	0.17747	N	0.163380	T	0.28962	0.0719	N	0.13198	0.31	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	10	0.02654	T	1	.	4.1279	0.10136	0.1566:0.1562:0.0:0.6871	.	537	Q8N695	SC5A8_HUMAN	L	537	ENSP00000445340:I537L	ENSP00000445340:I537L	I	-	1	0	SLC5A8	100079904	0.119000	0.22226	0.833000	0.33012	0.419000	0.31324	0.765000	0.26546	2.098000	0.63641	0.477000	0.44152	ATA		0.323	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		G	101555773	T	G	101555773	3	3	61	1	0	0	0	0	1	0	0	0	14708	1435	50	4	235	4	SLC5A8	12	101555773	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3711	101555773	32296122	8303	16288										
SLC5A8	160728	broad.mit.edu	37	chr12	101577979	101577979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggataatcttgcagaatgtCcagtaccaaataaggcatga	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101577979C>T	ENST00000536262.2	-	8	1543	c.985G>A	c.(985-987)Gac>Aac	p.D329N		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8									p.D329N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGCAGAATGTCCAGTACCAAA	0.348																																					GBM(60;420 1056 13605 22380 47675)											1	Substitution - Missense(1)	large_intestine(1)	12											71	69	69					12																	101577979		2203	4300	6503	100102110	SO:0001583	missense	160728			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.985G>A	12.37:g.101577979C>T	ENSP00000445340:p.Asp329Asn		100102110		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	C	35	5.516742	0.96402	.	.	ENSG00000256870	ENST00000536262	D	0.87650	-2.28	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.90017	0.6883	M	0.63843	1.955	0.80722	D	1	P	0.44344	0.833	P	0.49085	0.6	D	0.89899	0.4043	10	0.54805	T	0.06	.	19.7537	0.96281	0.0:1.0:0.0:0.0	.	329	Q8N695	SC5A8_HUMAN	N	329	ENSP00000445340:D329N	ENSP00000445340:D329N	D	-	1	0	SLC5A8	100102110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.806000	0.86020	2.676000	0.91093	0.655000	0.94253	GAC		0.348	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		T	101577979	C	T	101577979	3	4	61	1	0	0	0	0	1	0	0	0	14708	855	30	3	879	3	SLC5A8	12	101577979	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22206	101577979	32273916	8304	16289										
SLC5A8	160728	broad.mit.edu	37	chr12	101598313	101598313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggactgttccacagagacGaacacatttgttaaatcgaa	9	8	0	1	rs555404331	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101598313G>A	ENST00000536262.2	-	2	940	c.382C>T	c.(382-384)Cgt>Tgt	p.R128C		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8									p.R128C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CCACAGAGACGAACACATTTG	0.333													G|||	2	0.000399361	0	0	5008	,	,		17203	0.002		0	False		,,,				2504	0				GBM(60;420 1056 13605 22380 47675)											1	Substitution - Missense(1)	large_intestine(1)	12											62	62	62					12																	101598313		2203	4300	6503	100122444	SO:0001583	missense	160728			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.382C>T	12.37:g.101598313G>A	ENSP00000445340:p.Arg128Cys		100122444		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.392976	0.83011	.	.	ENSG00000256870	ENST00000536262	D	0.88975	-2.45	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.94404	0.8200	H	0.97186	3.955	0.80722	D	1	P	0.47253	0.892	P	0.44990	0.466	D	0.95881	0.8899	10	0.87932	D	0	.	19.7423	0.96237	0.0:0.0:1.0:0.0	.	128	Q8N695	SC5A8_HUMAN	C	128	ENSP00000445340:R128C	ENSP00000445340:R128C	R	-	1	0	SLC5A8	100122444	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.894000	0.87336	2.676000	0.91093	0.555000	0.69702	CGT		0.333	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101598313	G	A	101598313	3	1	61	1	0	0	0	0	1	0	0	0	14708	1058	37	1	1506	1	SLC5A8	12	101598313	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20334	101598313	32253582	8305	16290										
UTP20	27340	broad.mit.edu	37	chr12	101702017	101702017	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatattacgccaggcagaaCttgttccagcaactgtgaat	8	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101702017C>T	ENST00000261637.4	+	18	2224	c.2050C>T	c.(2050-2052)Ctt>Ttt	p.L684F		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	684					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.L684F(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CCAGGCAGAACTTGTTCCAGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	100	101					12																	101702017		2203	4300	6503	100226148	SO:0001583	missense	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.2050C>T	12.37:g.101702017C>T	ENSP00000261637:p.Leu684Phe		100226148	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665668	0.88251	.	.	ENSG00000120800	ENST00000261637	T	0.18502	2.21	5.91	5.91	0.95273	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.17048	-1.0382	10	0.59425	D	0.04	-16.5707	20.2985	0.98592	0.0:1.0:0.0:0.0	.	684	O75691	UTP20_HUMAN	F	684	ENSP00000261637:L684F	ENSP00000261637:L684F	L	+	1	0	UTP20	100226148	1.000000	0.71417	0.977000	0.42913	0.928000	0.56348	4.938000	0.63519	2.793000	0.96121	0.655000	0.94253	CTT		0.443	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101702017	C	T	101702017	3	4	61	1	0	0	0	0	1	0	0	0	17139	565	20	3	2120	3	UTP20	12	101702017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103704	101702017	32149878	8306	16291										
UTP20	27340	broad.mit.edu	37	chr12	101728223	101728223	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcaggcttggatctgaGagtcaatattctcctactcc	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101728223G>T	ENST00000261637.4	+	29	3756	c.3582G>T	c.(3580-3582)gaG>gaT	p.E1194D		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1194					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.E1194D(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TTGGATCTGAGAGTCAATATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											89	78	82					12																	101728223		2203	4300	6503	100252354	SO:0001583	missense	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.3582G>T	12.37:g.101728223G>T	ENSP00000261637:p.Glu1194Asp		100252354	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907314	0.72868	.	.	ENSG00000120800	ENST00000261637	T	0.39056	1.1	5.62	2.84	0.33178	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57066	0.2028	M	0.66939	2.045	0.49483	D	0.999791	D	0.76494	0.999	D	0.77004	0.989	T	0.52373	-0.8584	10	0.45353	T	0.12	-22.4177	8.6484	0.34020	0.3532:0.0:0.6468:0.0	.	1194	O75691	UTP20_HUMAN	D	1194	ENSP00000261637:E1194D	ENSP00000261637:E1194D	E	+	3	2	UTP20	100252354	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.350000	0.44063	0.336000	0.23639	0.650000	0.86243	GAG		0.358	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101728223	G	T	101728223	3	4	61	1	0	0	0	0	1	0	0	0	17139	933	33	2	3696	2	UTP20	12	101728223	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26206	101728223	32123672	8307	16292										
UTP20	27340	broad.mit.edu	37	chr12	101736730	101736730	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttatagcttaacgccttCgatcaaagacatcttgatga	6	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101736730C>T	ENST00000261637.4	+	35	4482	c.4308C>T	c.(4306-4308)ttC>ttT	p.F1436F		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1436					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.F1436F(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TTAACGCCTTCGATCAAAGAC	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	12											110	107	108					12																	101736730		2203	4300	6503	100260861	SO:0001819	synonymous_variant	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4308C>T	12.37:g.101736730C>T			100260861	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																				0.328	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101736730	C	T	101736730	2	4	61	1	0	0	0	0	0	0	0	1	17139	883	31	1		1	UTP20	12	101736730	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8507	101736730	32115165	8308	16293										
UTP20	27340	broad.mit.edu	37	chr12	101773211	101773211	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcacagcagcccagattTttggattactctttgcctct	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101773211T>G	ENST00000261637.4	+	57	7633	c.7459T>G	c.(7459-7461)Ttt>Gtt	p.F2487V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2487					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.F2487V(1)		NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AGCCCAGATTTTTGGATTACT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											86	85	85					12																	101773211		2203	4300	6503	100297342	SO:0001583	missense	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.7459T>G	12.37:g.101773211T>G	ENSP00000261637:p.Phe2487Val		100297342	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601325	0.87055	.	.	ENSG00000120800	ENST00000261637	T	0.04970	3.52	6.04	6.04	0.98038	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.18551	0.0445	M	0.64404	1.975	0.80722	D	1	D	0.64830	0.994	D	0.66351	0.943	T	0.09618	-1.0666	10	0.07175	T	0.84	-27.324	16.5757	0.84637	0.0:0.0:0.0:1.0	.	2487	O75691	UTP20_HUMAN	V	2487	ENSP00000261637:F2487V	ENSP00000261637:F2487V	F	+	1	0	UTP20	100297342	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	5.600000	0.67599	2.317000	0.78254	0.523000	0.50628	TTT		0.453	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101773211	T	G	101773211	3	3	61	1	0	0	0	0	1	0	0	0	17139	1841	64	4	7685	4	UTP20	12	101773211	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	36481	101773211	32078684	8309	16294										
ARL1	400	broad.mit.edu	37	chr12	101796696	101796696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaatttaaggtttttgtaCgtcaccgtctctacattaaa	7	7	2	0	rs375724509		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101796696C>T	ENST00000261636.8	-	3	345	c.171G>A	c.(169-171)acG>acA	p.T57T	ARL1_ENST00000549302.1_5'Flank|ARL1_ENST00000536227.1_Silent_p.T40T|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000551828.1_Silent_p.T40T|ARL1_ENST00000551671.1_Silent_p.T57T|ARL1_ENST00000539055.1_Silent_p.T11T	NM_001177.4	NP_001168.1	P40616	ARL1_HUMAN	ADP-ribosylation factor-like 1	57					activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.T57T(1)		central_nervous_system(1)|upper_aerodigestive_tract(1)	2		Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163)		GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125)		GGTTTTTGTACGTCACCGTCT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C		1,3651		0,1,1825	139	131	134		171	0.1	1	12		134	0,8172		0,0,4086	no	coding-synonymous	ARL1	NM_001177.4		0,1,5911	TT,TC,CC		0.0,0.0274,0.0085		57/182	101796696	1,11823	1826	4086	5912	100320827	SO:0001819	synonymous_variant	400			BX537387	CCDS44958.1, CCDS73510.1	12q23.3	2014-05-09						"ADP-ribosylation factors-like", "ADP-ribosylation factors"	692	protein-coding gene	gene with protein product		603425					Standard	XM_005268869		Approved	ARFL1	uc001tib.3	P40616	OTTHUMG00000170271	ENST00000261636.8:c.171G>A	12.37:g.101796696C>T			100320827	B4DWW1|P80417|Q53XB1	Silent	SNP	ENST00000261636.8	37	CCDS44958.1																																																																																				0.358	ARL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408246.1	NM_001177		T	101796696	C	T	101796696	2	4	61	1	0	0	0	0	0	0	0	1	925	523	19	1		1	ARL1	12	101796696	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23485	101796696	32055199	8310	16295										
ARL1	400	broad.mit.edu	37	chr12	101799708	101799708	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatcccaaaattaaaattCtcatttcccgagttccaaac	2	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:101799708C>T	ENST00000261636.8	-	2	230	c.56G>A	c.(55-57)aGa>aAa	p.R19K	RP11-321F8.4_ENST00000547360.1_lincRNA|ARL1_ENST00000549302.1_5'UTR|ARL1_ENST00000536227.1_Missense_Mutation_p.R2K|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000551828.1_Missense_Mutation_p.R2K|ARL1_ENST00000551671.1_Missense_Mutation_p.R19K|ARL1_ENST00000539055.1_Intron	NM_001177.4	NP_001168.1	P40616	ARL1_HUMAN	ADP-ribosylation factor-like 1	19					activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.R19K(1)		central_nervous_system(1)|upper_aerodigestive_tract(1)	2		Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163)		GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125)		AATTAAAATTCTCATTTCCCG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	12											63	53	56					12																	101799708		1806	4059	5865	100323839	SO:0001583	missense	400			BX537387	CCDS44958.1, CCDS73510.1	12q23.3	2014-05-09						"ADP-ribosylation factors-like", "ADP-ribosylation factors"	692	protein-coding gene	gene with protein product		603425					Standard	XM_005268869		Approved	ARFL1	uc001tib.3	P40616	OTTHUMG00000170271	ENST00000261636.8:c.56G>A	12.37:g.101799708C>T	ENSP00000261636:p.Arg19Lys		100323839	B4DWW1|P80417|Q53XB1	Missense_Mutation	SNP	ENST00000261636.8	37	CCDS44958.1	.	.	.	.	.	.	.	.	.	.	C	36	5.730942	0.96856	.	.	ENSG00000120805	ENST00000261636;ENST00000536227;ENST00000551828;ENST00000551671;ENST00000548070	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.79	5.79	0.91817	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89368	0.6695	M	0.79693	2.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89792	0.3969	10	0.87932	D	0	-17.8979	20.0946	0.97833	0.0:1.0:0.0:0.0	.	19;19	F8VYN9;P40616	.;ARL1_HUMAN	K	19;2;2;19;2	ENSP00000261636:R19K;ENSP00000441808:R2K;ENSP00000448850:R2K;ENSP00000448912:R19K;ENSP00000450315:R2K	ENSP00000261636:R19K	R	-	2	0	ARL1	100323839	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	7.711000	0.84669	2.761000	0.94854	0.644000	0.83932	AGA		0.318	ARL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408246.1	NM_001177		T	101799708	C	T	101799708	3	4	61	1	0	0	0	0	1	0	0	0	925	913	32	3	509	3	ARL1	12	101799708	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3012	101799708	32052187	8311	16296										
MYBPC1	4604	broad.mit.edu	37	chr12	102061599	102061599	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgcaaagatctttgtgCgtgtgaaggctgttaatgca	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102061599C>T	ENST00000550270.1	+	22	2425	c.2425C>T	c.(2425-2427)Cgt>Tgt	p.R809C	MYBPC1_ENST00000392934.3_Missense_Mutation_p.R778C|MYBPC1_ENST00000360610.2_Missense_Mutation_p.R809C|MYBPC1_ENST00000551300.1_Missense_Mutation_p.R692C|MYBPC1_ENST00000361685.2_Missense_Mutation_p.R816C|MYBPC1_ENST00000549145.1_Missense_Mutation_p.R822C|MYBPC1_ENST00000547509.1_Missense_Mutation_p.R777C|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000553190.1_Missense_Mutation_p.R791C|MYBPC1_ENST00000541119.1_Missense_Mutation_p.R779C|MYBPC1_ENST00000361466.2_Missense_Mutation_p.R816C|MYBPC1_ENST00000545503.2_Missense_Mutation_p.R791C|MYBPC1_ENST00000547405.1_Missense_Mutation_p.R765C|MYBPC1_ENST00000441232.1_Missense_Mutation_p.R809C|MYBPC1_ENST00000452455.2_Missense_Mutation_p.R809C|MYBPC1_ENST00000536007.1_Missense_Mutation_p.R772C			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	809	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.R816C(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GATCTTTGTGCGTGTGAAGGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											107	91	96					12																	102061599		2203	4300	6503	100585730	SO:0001583	missense	4604				CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.2425C>T	12.37:g.102061599C>T	ENSP00000449702:p.Arg809Cys		100585730	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412318	0.62511	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.73	4.77	0.60923	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000172	T	0.76637	0.4015	M	0.82923	2.615	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.994;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.932;0.999;1.0;0.999;1.0;0.978;0.999	T	0.79783	-0.1658	10	0.87932	D	0	.	13.4713	0.61283	0.266:0.734:0.0:0.0	.	772;779;809;791;778;765;791;809;816;816	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.	C	765;809;809;809;778;777;816;822;791;791;772;779;816;692;809	ENSP00000448175:R765C;ENSP00000400908:R809C;ENSP00000388989:R809C;ENSP00000353822:R809C;ENSP00000376665:R778C;ENSP00000447362:R777C;ENSP00000354845:R816C;ENSP00000447660:R822C;ENSP00000447900:R791C;ENSP00000440034:R791C;ENSP00000446128:R772C;ENSP00000442847:R779C;ENSP00000354849:R816C;ENSP00000447116:R692C;ENSP00000449702:R809C	ENSP00000353822:R809C	R	+	1	0	MYBPC1	100585730	1.000000	0.71417	0.997000	0.53966	0.718000	0.41266	3.046000	0.49846	2.699000	0.92147	0.650000	0.86243	CGT		0.468	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102061599	C	T	102061599	3	4	61	1	0	0	0	0	1	0	0	0	10041	768	27	1	2594	1	MYBPC1	12	102061599	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	261891	102061599	31790296	8312	16297										
CHPT1	56994	broad.mit.edu	37	chr12	102120171	102120171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagactgcatgtcatcaaGcacctgaacaggttcacaag	8	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102120171G>A	ENST00000229266.3	+	8	1400	c.1165G>A	c.(1165-1167)Gca>Aca	p.A389T	CHPT1_ENST00000549872.1_Missense_Mutation_p.A389T	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	389					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)	p.A389T(1)		kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						ATGTCATCAAGCACCTGAACA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											108	104	106					12																	102120171		2203	4300	6503	100644302	SO:0001583	missense	56994				CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"phosphatidylcholine synthesizing enzyme"					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.1165G>A	12.37:g.102120171G>A	ENSP00000229266:p.Ala389Thr		100644302	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Missense_Mutation	SNP	ENST00000229266.3	37	CCDS9086.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679262	0.68042	.	.	ENSG00000111666	ENST00000229266;ENST00000549872;ENST00000543999	T;T	0.46819	0.94;0.86	6.17	5.29	0.74685	.	0.287809	0.38720	N	0.001589	T	0.43344	0.1243	L	0.44542	1.39	0.42529	D	0.993034	B;B	0.23990	0.095;0.026	B;B	0.25884	0.064;0.035	T	0.29822	-0.9999	10	0.39692	T	0.17	-1.0466	15.7563	0.78030	0.065:0.0:0.935:0.0	.	389;389	F8W1B3;Q8WUD6	.;CHPT1_HUMAN	T	389;389;222	ENSP00000229266:A389T;ENSP00000448766:A389T	ENSP00000229266:A389T	A	+	1	0	CHPT1	100644302	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	5.700000	0.68318	1.626000	0.50381	0.655000	0.94253	GCA		0.398	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244		A	102120171	G	A	102120171	3	1	61	1	0	0	0	0	1	0	0	0	3376	971	34	3	1195	3	CHPT1	12	102120171	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58572	102120171	31731724	8313	16298										
GNPTAB	79158	broad.mit.edu	37	chr12	102159074	102159074	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcactttatacaattcatGaaaatgatctagaggaaaaa	6	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102159074G>T	ENST00000299314.7	-	13	1883	c.1621C>A	c.(1621-1623)Cat>Aat	p.H541N	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	541					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)	p.H541N(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TACAATTCATGAAAATGATCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	61	60					12																	102159074		2202	4300	6502	100683205	SO:0001583	missense	79158			AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.1621C>A	12.37:g.102159074G>T	ENSP00000299314:p.His541Asn		100683205	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	37	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	G	7.544	0.661235	0.14645	.	.	ENSG00000111670	ENST00000299314	D	0.95821	-3.82	5.96	5.06	0.68205	Notch domain (1);	0.430200	0.27600	N	0.018648	D	0.88055	0.6334	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.82493	-0.0430	10	0.07482	T	0.82	-26.237	13.4043	0.60903	0.0:0.3714:0.6286:0.0	.	541	Q3T906	GNPTA_HUMAN	N	541	ENSP00000299314:H541N	ENSP00000299314:H541N	H	-	1	0	GNPTAB	100683205	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.662000	0.46766	2.832000	0.97577	0.655000	0.94253	CAT		0.338	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			T	102159074	G	T	102159074	3	4	61	1	0	0	0	0	1	0	0	0	6565	1290	45	2	2185	2	GNPTAB	12	102159074	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38903	102159074	31692821	8314	16299										
CCDC53	51019	broad.mit.edu	37	chr12	102439876	102439876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttcaatttgttggatacGaagtgaaaggtctgccagtt	11	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102439876G>A	ENST00000240079.6	-	3	333	c.172C>T	c.(172-174)Cgt>Tgt	p.R58C	CCDC53_ENST00000545679.1_Missense_Mutation_p.R58C|CCDC53_ENST00000539515.1_5'UTR	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	58						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)		p.R58C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						TGTTGGATACGAAGTGAAAGG	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	12											47	43	44					12																	102439876		1796	4062	5858	100964006	SO:0001583	missense	51019			AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.172C>T	12.37:g.102439876G>A	ENSP00000240079:p.Arg58Cys		100964006	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	37	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323109	0.81580	.	.	ENSG00000120860	ENST00000240079;ENST00000545679;ENST00000542923	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	M	0.87547	2.89	0.80722	D	1	P;D	0.54207	0.836;0.965	B;B	0.43194	0.212;0.411	T	0.76828	-0.2815	9	0.52906	T	0.07	-11.4463	16.3866	0.83507	0.0:0.0:1.0:0.0	.	58;58	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	C	58;58;8	.	ENSP00000240079:R58C	R	-	1	0	CCDC53	100964006	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.063000	0.64332	2.659000	0.90383	0.655000	0.94253	CGT		0.294	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053		A	102439876	G	A	102439876	3	1	61	1	0	0	0	0	1	0	0	0	2829	1058	37	1	363	1	CCDC53	12	102439876	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	280802	102439876	31412019	8315	16300										
C12orf48	55010	broad.mit.edu	37	chr12	102558231	102558231	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggtgcagctgctagcaAggaaaattatcttttcatat	8	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102558231A>C	ENST00000358383.5	+	5	556	c.511A>C	c.(511-513)Agg>Cgg	p.R171R	PARPBP_ENST00000541394.1_Silent_p.R248R|PARPBP_ENST00000392911.2_Silent_p.R90R|PARPBP_ENST00000543784.1_Silent_p.R57R|PARPBP_ENST00000327680.2_Silent_p.R90R|PARPBP_ENST00000378128.3_Silent_p.R171R|PARPBP_ENST00000535811.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	171					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R90R(1)		endometrium(1)|lung(8)|urinary_tract(2)	11						GCTGCTAGCAAGGAAAATTAT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	12											65	72	69					12																	102558231		2202	4300	6502	101082361	SO:0001819	synonymous_variant	55010			AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"PARP-1 binding protein"	613687	"chromosome 12 open reading frame 48"	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.511A>C	12.37:g.102558231A>C			101082361	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Silent	SNP	ENST00000358383.5	37	CCDS9090.2																																																																																				0.318	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		C	102558231	A	C	102558231	2	2	61	1	0	0	0	0	0	0	0	1	1696	63	3	4		4	C12orf48	12	102558231	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	118355	102558231	31293664	8316	16301										
IGF1	3479	broad.mit.edu	37	chr12	102869449	102869449	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcccctgtctccacacacGaactgaagagcatccaccag	7	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:102869449G>A	ENST00000307046.8	-	2	373	c.192C>T	c.(190-192)ttC>ttT	p.F64F	IGF1_ENST00000337514.6_Silent_p.F64F|IGF1_ENST00000392904.1_Silent_p.F64F|IGF1_ENST00000456098.1_Silent_p.F64F|IGF1_ENST00000424202.2_Silent_p.F48F	NM_001111285.1	NP_001104755.1	P05019	IGF1_HUMAN	insulin-like growth factor 1 (somatomedin C)	64	B.				blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|bone mineralization involved in bone maturation (GO:0035630)|branching morphogenesis of an epithelial tube (GO:0048754)|cell activation (GO:0001775)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|DNA replication (GO:0006260)|exocrine pancreas development (GO:0031017)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|glial cell differentiation (GO:0010001)|glycolate metabolic process (GO:0009441)|inner ear development (GO:0048839)|insulin-like growth factor receptor signaling pathway (GO:0048009)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mammary gland development (GO:0030879)|multicellular organism growth (GO:0035264)|muscle hypertrophy (GO:0014896)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|myoblast proliferation (GO:0051450)|myotube cell development (GO:0014904)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate gland growth (GO:0060736)|prostate gland stromal morphogenesis (GO:0060741)|proteoglycan biosynthetic process (GO:0030166)|Ras protein signal transduction (GO:0007265)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of multicellular organism growth (GO:0040014)|signal transduction (GO:0007165)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|skeletal system development (GO:0001501)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)|water homeostasis (GO:0030104)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|insulin-like growth factor binding protein complex (GO:0016942)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	hormone activity (GO:0005179)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|integrin binding (GO:0005178)	p.F64F(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)	11						CTCCACACACGAACTGAAGAG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	12											72	73	73					12																	102869449		2203	4300	6503	101393579	SO:0001819	synonymous_variant	3479			X00173	CCDS9091.1, CCDS44960.1, CCDS44961.1, CCDS44962.1	12q23.2	2014-09-16			ENSG00000017427	ENSG00000017427		"Endogenous ligands"	5464	protein-coding gene	gene with protein product		147440				2982726, 6358902	Standard	NM_001111283		Approved	IGF1A, IGFI, IGF-I	uc001tjp.4	P05019	OTTHUMG00000149910	ENST00000307046.8:c.192C>T	12.37:g.102869449G>A			101393579	B2RWM7|E9PD02|P01343|Q14620	Silent	SNP	ENST00000307046.8	37	CCDS44962.1																																																																																				0.557	IGF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313855.1	NM_000618		A	102869449	G	A	102869449	2	1	61	1	0	0	0	0	0	0	0	1	7591	1049	37	1		1	IGF1	12	102869449	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	311218	102869449	30982446	8317	16302										
STAB2	55576	broad.mit.edu	37	chr12	104049338	104049338	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatgaaggacggcactctCgattacctcctttctccaga	7	13	2	2	rs559457405		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104049338C>T	ENST00000388887.2	+	15	1917	c.1713C>T	c.(1711-1713)ctC>ctT	p.L571L	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.L571L(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ACGGCACTCTCGATTACCTCC	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	12											175	141	153					12																	104049338		2203	4300	6503	102573468	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1713C>T	12.37:g.104049338C>T			102573468		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.453	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104049338	C	T	104049338	2	4	61	1	0	0	0	0	0	0	0	1	15277	871	31	1		1	STAB2	12	104049338	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1179889	104049338	29802557	8318	16303										
STAB2	55576	broad.mit.edu	37	chr12	104063378	104063378	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccagtgtccaggaggcttCtcaaatccatgctcaggaaa	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104063378C>A	ENST00000388887.2	+	21	2436	c.2232C>A	c.(2230-2232)ttC>ttA	p.F744L	RP11-341G23.3_ENST00000550175.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.F744L(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CAGGAGGCTTCTCAAATCCAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	111	111					12																	104063378		2203	4300	6503	102587508	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2232C>A	12.37:g.104063378C>A	ENSP00000373539:p.Phe744Leu		102587508		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.371128	0.61624	.	.	ENSG00000136011	ENST00000388887	D	0.83673	-1.75	5.44	4.44	0.53790	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.243673	0.40818	N	0.001009	T	0.71854	0.3389	L	0.56396	1.775	0.41810	D	0.989969	B	0.28512	0.214	B	0.17433	0.018	T	0.63037	-0.6726	10	0.10636	T	0.68	.	4.2761	0.10809	0.0:0.6921:0.0:0.3079	.	744	Q8WWQ8	STAB2_HUMAN	L	744	ENSP00000373539:F744L	ENSP00000373539:F744L	F	+	3	2	STAB2	102587508	0.729000	0.28090	0.972000	0.41901	0.972000	0.66771	1.255000	0.32909	2.568000	0.86640	0.650000	0.86243	TTC		0.418	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104063378	C	A	104063378	3	1	61	1	0	0	0	0	1	0	0	0	15277	912	32	2	2314	2	STAB2	12	104063378	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14040	104063378	29788517	8319	16304										
STAB2	55576	broad.mit.edu	37	chr12	104100656	104100656	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgctttggtaatggcatCtgtttggatggagtgaatgg	15	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104100656C>A	ENST00000388887.2	+	38	4287	c.4083C>A	c.(4081-4083)atC>atA	p.I1361I		NM_017564.9	NP_060034.9			stabilin 2									p.I1361I(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GTAATGGCATCTGTTTGGATG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											134	116	122					12																	104100656		2203	4300	6503	102624786	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4083C>A	12.37:g.104100656C>A			102624786		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.577	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104100656	C	A	104100656	2	1	61	1	0	0	0	0	0	0	0	1	15277	903	32	2		2	STAB2	12	104100656	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37278	104100656	29751239	8320	16305										
STAB2	55576	broad.mit.edu	37	chr12	104121053	104121053	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcccacaggagcatttCgtgaaagatctggtcggccc	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104121053C>T	ENST00000388887.2	+	47	5064	c.4860C>T	c.(4858-4860)ttC>ttT	p.F1620F		NM_017564.9	NP_060034.9			stabilin 2									p.F1620F(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AGGAGCATTTCGTGAAAGATC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	12											244	238	240					12																	104121053		2203	4300	6503	102645183	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4860C>T	12.37:g.104121053C>T			102645183		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.512	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104121053	C	T	104121053	2	4	61	1	0	0	0	0	0	0	0	1	15277	883	31	1		1	STAB2	12	104121053	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20397	104121053	29730842	8321	16306										
HSP90B1	7184	broad.mit.edu	37	chr12	104331554	104331554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaatattcacagttcatAaactttcctatttatgtatg	3	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104331554A>G	ENST00000299767.5	+	6	1007	c.825A>G	c.(823-825)atA>atG	p.I275M		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	275					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)	p.I275M(1)		central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CACAGTTCATAAACTTTCCTA	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	12											45	46	46					12																	104331554		2202	4299	6501	102855684	SO:0001583	missense	7184			AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.825A>G	12.37:g.104331554A>G	ENSP00000299767:p.Ile275Met		102855684	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.091738	0.55968	.	.	ENSG00000166598	ENST00000299767;ENST00000537375	T	0.15603	2.41	5.67	0.246	0.15516	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.41743	0.1172	H	0.98295	4.195	0.80722	D	1	B;P	0.49862	0.224;0.929	B;P	0.48089	0.351;0.566	T	0.58352	-0.7651	10	0.72032	D	0.01	.	10.1979	0.43065	0.3959:0.491:0.0:0.1131	.	301;275	Q59FC6;P14625	.;ENPL_HUMAN	M	275	ENSP00000299767:I275M	ENSP00000299767:I275M	I	+	3	3	HSP90B1	102855684	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.936000	0.48971	-0.191000	0.10448	0.533000	0.62120	ATA		0.289	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		G	104331554	A	G	104331554	3	3	61	1	0	0	0	0	1	0	0	0	7424	352	13	4	847	4	HSP90B1	12	104331554	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	210501	104331554	29520341	8322	16307										
HSP90B1	7184	broad.mit.edu	37	chr12	104333311	104333311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaaactgtctgggactggGaacttatgaatgatatcaaa	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104333311G>A	ENST00000299767.5	+	8	1182	c.1000G>A	c.(1000-1002)Gaa>Aaa	p.E334K		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	334					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)	p.E334K(1)		central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CTGGGACTGGGAACTTATGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											110	115	113					12																	104333311		2203	4300	6503	102857441	SO:0001583	missense	7184			AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1000G>A	12.37:g.104333311G>A	ENSP00000299767:p.Glu334Lys		102857441	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	G	34	5.405242	0.96051	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	T	0.13778	2.56	5.5	5.5	0.81552	ATPase-like, ATP-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.36908	0.0984	M	0.85777	2.775	0.80722	D	1	P	0.45569	0.861	P	0.51918	0.684	T	0.26503	-1.0101	10	0.66056	D	0.02	.	19.4074	0.94653	0.0:0.0:1.0:0.0	.	334	P14625	ENPL_HUMAN	K	334;84	ENSP00000299767:E334K	ENSP00000299767:E334K	E	+	1	0	HSP90B1	102857441	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.731000	0.98807	2.568000	0.86640	0.650000	0.86243	GAA		0.353	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		A	104333311	G	A	104333311	3	1	61	1	0	0	0	0	1	0	0	0	7424	1175	41	3	1030	3	HSP90B1	12	104333311	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1757	104333311	29518584	8323	16308										
HSP90B1	7184	broad.mit.edu	37	chr12	104336389	104336389	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatgatactttttggaaaGaatttggtaccaacatcaag	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104336389G>T	ENST00000299767.5	+	12	1641	c.1459G>T	c.(1459-1461)Gaa>Taa	p.E487*		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	487					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)	p.E487*(1)		central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	TTTTTGGAAAGAATTTGGTAC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											101	100	100					12																	104336389		2203	4300	6503	102860519	SO:0001587	stop_gained	7184			AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1459G>T	12.37:g.104336389G>T	ENSP00000299767:p.Glu487*		102860519	Q96A97	Nonsense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	G	41	8.564876	0.98866	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	.	.	.	X	487;237	.	ENSP00000299767:E487X	E	+	1	0	HSP90B1	102860519	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.879000	0.98667	0.650000	0.86243	GAA		0.383	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		T	104336389	G	T	104336389	4	4	61	1	0	0	0	0	0	1	0	0	7424	943	33	2	1505	2	HSP90B1	12	104336389	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3078	104336389	29515506	8324	16309										
GLT8D2	83468	broad.mit.edu	37	chr12	104408801	104408801	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgctcacctgcgtcattCttgggcacagtccccttatg	9	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104408801C>A	ENST00000360814.4	-	4	507	c.102G>T	c.(100-102)aaG>aaT	p.K34N	GLT8D2_ENST00000547583.1_Missense_Mutation_p.K34N|GLT8D2_ENST00000546436.1_Missense_Mutation_p.K34N|GLT8D2_ENST00000548660.1_Missense_Mutation_p.K34N	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	34						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.K34N(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						CTGCGTCATTCTTGGGCACAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											98	84	89					12																	104408801		2203	4300	6503	102932931	SO:0001583	missense	83468			BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"Glycosyltransferase family 8 domain containing"	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.102G>T	12.37:g.104408801C>A	ENSP00000354053:p.Lys34Asn		102932931	Q96KA2	Missense_Mutation	SNP	ENST00000360814.4	37	CCDS9096.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514968	0.27123	.	.	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660;ENST00000547583	T;T;T;T	0.52526	1.35;1.35;1.35;0.66	5.19	4.28	0.50868	.	0.559280	0.20856	N	0.084422	T	0.34803	0.0910	L	0.29908	0.895	0.09310	N	0.999996	B	0.24186	0.099	B	0.17098	0.017	T	0.14699	-1.0463	10	0.27785	T	0.31	.	12.7777	0.57457	0.0:0.8345:0.1655:0.0	.	34	Q9H1C3	GL8D2_HUMAN	N	34	ENSP00000354053:K34N;ENSP00000449750:K34N;ENSP00000447450:K34N;ENSP00000448065:K34N	ENSP00000354053:K34N	K	-	3	2	GLT8D2	102932931	0.017000	0.18338	0.003000	0.11579	0.048000	0.14542	1.307000	0.33516	1.121000	0.41925	0.655000	0.94253	AAG		0.443	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302		A	104408801	C	A	104408801	3	1	61	1	0	0	0	0	1	0	0	0	6490	912	32	2	979	2	GLT8D2	12	104408801	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72412	104408801	29443094	8325	16310										
GLT8D2	83468	broad.mit.edu	37	chr12	104408872	104408872	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgatcagaaggaacagcaGcacctgattaactgaaatag	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104408872G>A	ENST00000360814.4	-	4	436	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	GLT8D2_ENST00000547583.1_Silent_p.L11L|GLT8D2_ENST00000546436.1_Silent_p.L11L|GLT8D2_ENST00000548660.1_Silent_p.L11L	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	11						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.L11L(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						AGGAACAGCAGCACCTGATTA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	12											109	95	100					12																	104408872		2203	4300	6503	102933002	SO:0001819	synonymous_variant	83468			BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"Glycosyltransferase family 8 domain containing"	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.31C>T	12.37:g.104408872G>A			102933002	Q96KA2	Silent	SNP	ENST00000360814.4	37	CCDS9096.1																																																																																				0.428	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302		A	104408872	G	A	104408872	2	1	61	1	0	0	0	0	0	0	0	1	6490	962	34	3		3	GLT8D2	12	104408872	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71	104408872	29443023	8326	16311										
HCFC2	29915	broad.mit.edu	37	chr12	104461860	104461860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcctggcaaacgaaagcGaagattcaaacaataatgtt	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104461860G>A	ENST00000229330.4	+	3	552	c.448G>A	c.(448-450)Gaa>Aaa	p.E150K		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	150					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)	p.E150K(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AAACGAAAGCGAAGATTCAAA	0.383																																					Esophageal Squamous(184;1814 2036 4771 6974 15702)											1	Substitution - Missense(1)	large_intestine(1)	12											169	164	166					12																	104461860		2203	4300	6503	102985990	SO:0001583	missense	29915			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.448G>A	12.37:g.104461860G>A	ENSP00000229330:p.Glu150Lys		102985990	B2R8Q5|C0H5X3	Missense_Mutation	SNP	ENST00000229330.4	37	CCDS9097.1	.	.	.	.	.	.	.	.	.	.	G	34	5.374295	0.95923	.	.	ENSG00000111727	ENST00000229330;ENST00000550444	T	0.73789	-0.78	5.45	5.45	0.79879	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.84902	0.5575	M	0.62723	1.935	0.58432	D	0.999999	D	0.89917	1.0	D	0.75484	0.986	T	0.83216	-0.0071	10	0.40728	T	0.16	-26.7769	19.6392	0.95751	0.0:0.0:1.0:0.0	.	150	Q9Y5Z7	HCFC2_HUMAN	K	150;61	ENSP00000229330:E150K	ENSP00000229330:E150K	E	+	1	0	HCFC2	102985990	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.722000	0.93159	0.491000	0.48974	GAA		0.383	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		A	104461860	G	A	104461860	3	1	61	1	0	0	0	0	1	0	0	0	7014	1059	37	1	458	1	HCFC2	12	104461860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52988	104461860	29390035	8327	16312										
HCFC2	29915	broad.mit.edu	37	chr12	104497010	104497010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaccagctacacaagttCggtggcttcaaggtaacaat	10	9	1	0	rs201154697		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104497010C>T	ENST00000229330.4	+	15	2442	c.2338C>T	c.(2338-2340)Cgg>Tgg	p.R780W	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	780	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)	p.R780W(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TACACAAGTTCGGTGGCTTCA	0.358																																					Esophageal Squamous(184;1814 2036 4771 6974 15702)											1	Substitution - Missense(1)	large_intestine(1)	12											94	91	92					12																	104497010		2203	4300	6503	103021140	SO:0001583	missense	29915			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.2338C>T	12.37:g.104497010C>T	ENSP00000229330:p.Arg780Trp		103021140	B2R8Q5|C0H5X3	Missense_Mutation	SNP	ENST00000229330.4	37	CCDS9097.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.619540	0.66787	.	.	ENSG00000111727	ENST00000229330	T	0.54479	0.57	5.9	4.99	0.66335	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.075560	0.52532	D	0.000065	T	0.70500	0.3231	M	0.74467	2.265	0.46981	D	0.999273	D	0.89917	1.0	D	0.67900	0.954	T	0.74830	-0.3531	10	0.87932	D	0	-7.4402	13.8708	0.63617	0.2776:0.7224:0.0:0.0	.	780	Q9Y5Z7	HCFC2_HUMAN	W	780	ENSP00000229330:R780W	ENSP00000229330:R780W	R	+	1	2	HCFC2	103021140	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	3.008000	0.49544	1.438000	0.47492	0.650000	0.86243	CGG		0.358	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		T	104497010	C	T	104497010	3	4	61	1	0	0	0	0	1	0	0	0	7014	875	31	1	2396	1	HCFC2	12	104497010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35150	104497010	29354885	8328	16313										
EID3	493861	broad.mit.edu	37	chr12	104698266	104698266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgttctgcaccaaagccccGacttgaacaccagaaaaaag	7	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104698266G>A	ENST00000527879.1	+	1	750	c.554G>A	c.(553-555)cGa>cAa	p.R185Q	TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000529546.1_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3									p.R185Q(1)		large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CCAAAGCCCCGACTTGAACAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											118	117	117					12																	104698266		1885	4114	5999	103222396	SO:0001583	missense	493861			BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.554G>A	12.37:g.104698266G>A	ENSP00000435619:p.Arg185Gln		103222396		Missense_Mutation	SNP	ENST00000527879.1	37	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982186	0.74474	.	.	ENSG00000255150	ENST00000527879	T	0.53640	0.61	4.94	4.04	0.47022	.	.	.	.	.	T	0.65831	0.2729	M	0.74647	2.275	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54951	-0.8216	9	0.37606	T	0.19	.	10.8797	0.46931	0.0:0.0:0.8124:0.1876	.	185	Q8N140	EID3_HUMAN	Q	185	ENSP00000435619:R185Q	ENSP00000435619:R185Q	R	+	2	0	EID3	103222396	0.536000	0.26378	0.017000	0.16124	0.232000	0.25224	3.036000	0.49767	1.449000	0.47699	0.555000	0.69702	CGA		0.423	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394		A	104698266	G	A	104698266	3	1	61	1	0	0	0	0	1	0	0	0	5000	1058	37	1	556	1	EID3	12	104698266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	201256	104698266	29153629	8329	16314										
CHST11	50515	broad.mit.edu	37	chr12	104995690	104995690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctttcctcagtcatgcGgaggaatccctttggtgtgg	11	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:104995690G>A	ENST00000303694.5	+	2	564	c.125G>A	c.(124-126)cGg>cAg	p.R42Q	CHST11_ENST00000547956.1_Missense_Mutation_p.R42Q|CHST11_ENST00000546689.1_Missense_Mutation_p.R37Q|CHST11_ENST00000549260.1_Missense_Mutation_p.R37Q	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	42					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)	p.R42Q(2)		breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						TCAGTCATGCGGAGGAATCCC	0.498																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	12											86	78	80					12																	104995690		2203	4300	6503	103519820	SO:0001583	missense	50515			AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"Sulfotransferases, membrane-bound"	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.125G>A	12.37:g.104995690G>A	ENSP00000305725:p.Arg42Gln		103519820	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	37	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.543720	0.65198	.	.	ENSG00000171310	ENST00000547956;ENST00000549260;ENST00000303694;ENST00000546689;ENST00000549016	T;T;T	0.67865	-0.29;-0.27;-0.22	5.73	4.84	0.62591	.	0.462257	0.22116	N	0.064416	T	0.48447	0.1500	L	0.29908	0.895	0.44660	D	0.99764	B;B	0.27765	0.188;0.009	B;B	0.19148	0.024;0.002	T	0.39313	-0.9620	10	0.11485	T	0.65	-12.461	10.2124	0.43150	0.1538:0.0:0.8462:0.0	.	37;42	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	Q	42;37;42;37;2	ENSP00000450004:R37Q;ENSP00000305725:R42Q;ENSP00000449095:R2Q	ENSP00000305725:R42Q	R	+	2	0	CHST11	103519820	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	5.144000	0.64832	1.567000	0.49668	-0.136000	0.14681	CGG		0.498	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		A	104995690	G	A	104995690	3	1	61	1	0	0	0	0	1	0	0	0	3405	1116	39	1	131	1	CHST11	12	104995690	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297424	104995690	28856205	8330	16315										
SLC41A2	84102	broad.mit.edu	37	chr12	105238336	105238336	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaatgaatagtgtagaGgaaaattaaatgtccaggaa	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105238336G>A	ENST00000258538.3	-	9	1577	c.1450C>T	c.(1450-1452)Ctc>Ttc	p.L484F		NM_032148.3	NP_115524.3	Q96JW4	S41A2_HUMAN	solute carrier family 41 (magnesium transporter), member 2	484					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.L401F(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	22						ATAGTGTAGAGGAAAATTAAA	0.284																																					Esophageal Squamous(195;176 2919 4272 35572)											1	Substitution - Missense(1)	large_intestine(1)	12											66	74	71					12																	105238336		2203	4297	6500	103762466	SO:0001583	missense	84102			BC036734	CCDS9100.2	12q24.11	2013-07-17	2013-07-17		ENSG00000136052	ENSG00000136052		"Solute carriers"	31045	protein-coding gene	gene with protein product		610802	"solute carrier family 41, member 2"				Standard	NM_032148		Approved	DKFZP434K0427	uc001tla.3	Q96JW4	OTTHUMG00000156965	ENST00000258538.3:c.1450C>T	12.37:g.105238336G>A	ENSP00000258538:p.Leu484Phe		103762466	Q3KP68|Q9H0E5	Missense_Mutation	SNP	ENST00000258538.3	37	CCDS9100.2	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681444	0.68042	.	.	ENSG00000136052	ENST00000258538	T	0.33654	1.4	5.59	5.59	0.84812	MgtE magnesium transporter, integral membrane (1);	0.000000	0.85682	D	0.000000	T	0.55609	0.1931	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.53019	-0.8497	10	0.36615	T	0.2	-4.2263	10.6719	0.45764	0.1158:0.0:0.8842:0.0	.	484	Q96JW4	S41A2_HUMAN	F	484	ENSP00000258538:L484F	ENSP00000258538:L484F	L	-	1	0	SLC41A2	103762466	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.742000	0.62103	2.634000	0.89283	0.655000	0.94253	CTC		0.284	SLC41A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346850.3	NM_032148		A	105238336	G	A	105238336	3	1	61	1	0	0	0	0	1	0	0	0	14667	1000	35	3	279	3	SLC41A2	12	105238336	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	242646	105238336	28613559	8331	16316										
ALDH1L2	160428	broad.mit.edu	37	chr12	105424187	105424187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttccacatctgtgaacaCggtcggctccatgaaaaagc	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105424187C>T	ENST00000258494.9	-	21	2571	c.2431G>A	c.(2431-2433)Gtg>Atg	p.V811M	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	811	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.V811M(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						TCTGTGAACACGGTCGGCTCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	83	84					12																	105424187		2203	4300	6503	103948317	SO:0001583	missense	160428			AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2431G>A	12.37:g.105424187C>T	ENSP00000258494:p.Val811Met		103948317	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	37	CCDS31891.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.560897|4.560897	0.86335|0.86335	.|.	.|.	ENSG00000136010|ENSG00000136010	ENST00000548418|ENST00000258494	.|D	.|0.82081	.|-1.57	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93383|0.93383	0.7890|0.7890	H|H	0.95645|0.95645	3.7|3.7	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.68353	.|0.957	D|D	0.94563|0.94563	0.7764|0.7764	5|10	.|0.87932	.|D	.|0	.|.	14.7322|14.7322	0.69391|0.69391	0.0:0.9314:0.0:0.0686|0.0:0.9314:0.0:0.0686	.|.	.|811	.|Q3SY69	.|AL1L2_HUMAN	H|M	63|811	.|ENSP00000258494:V811M	.|ENSP00000258494:V811M	R|V	-|-	2|1	0|0	ALDH1L2|ALDH1L2	103948317|103948317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.849000|0.849000	0.48306|0.48306	5.970000|5.970000	0.70431|0.70431	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.373	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		T	105424187	C	T	105424187	3	4	61	1	0	0	0	0	1	0	0	0	495	536	19	1	352	1	ALDH1L2	12	105424187	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	185851	105424187	28427708	8332	16317										
ALDH1L2	160428	broad.mit.edu	37	chr12	105428095	105428095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccactcttgtcacaaattCgtcgtggatggattcttcca	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105428095C>T	ENST00000258494.9	-	19	2367	c.2227G>A	c.(2227-2229)Gaa>Aaa	p.E743K	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	743	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.E743K(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						GTCACAAATTCGTCGTGGATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	85	92					12																	105428095		2203	4300	6503	103952225	SO:0001583	missense	160428			AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2227G>A	12.37:g.105428095C>T	ENSP00000258494:p.Glu743Lys		103952225	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	37	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508300	0.64410	.	.	ENSG00000136010	ENST00000258494	T	0.17854	2.25	5.36	5.36	0.76844	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.044515	0.85682	D	0.000000	T	0.16854	0.0405	L	0.41236	1.265	0.80722	D	1	B	0.32604	0.377	B	0.25405	0.06	T	0.02269	-1.1185	10	0.45353	T	0.12	.	19.4661	0.94943	0.0:1.0:0.0:0.0	.	743	Q3SY69	AL1L2_HUMAN	K	743	ENSP00000258494:E743K	ENSP00000258494:E743K	E	-	1	0	ALDH1L2	103952225	1.000000	0.71417	0.996000	0.52242	0.774000	0.43823	3.819000	0.55686	2.672000	0.90937	0.555000	0.69702	GAA		0.423	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		T	105428095	C	T	105428095	3	4	61	1	0	0	0	0	1	0	0	0	495	893	31	1	564	1	ALDH1L2	12	105428095	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3908	105428095	28423800	8333	16318										
ALDH1L2	160428	broad.mit.edu	37	chr12	105431886	105431886	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaccctctcttaccattcGcacagccttgtcaagttcac	5	15	3	1	rs376554461		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105431886G>A	ENST00000258494.9	-	18	2280	c.2140C>T	c.(2140-2142)Cga>Tga	p.R714*	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	714	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.R714*(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CTTACCATTCGCACAGCCTTG	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											88	80	83					12																	105431886		2203	4300	6503	103956016	SO:0001587	stop_gained	160428			AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2140C>T	12.37:g.105431886G>A	ENSP00000258494:p.Arg714*		103956016	Q3SY68|Q68D62|Q6AI55|Q8N922	Nonsense_Mutation	SNP	ENST00000258494.9	37	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	G	40	8.097870	0.98651	.	.	ENSG00000136010	ENST00000258494	.	.	.	5.47	-0.542	0.11854	.	0.051011	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7513	0.85487	0.0:0.0:0.1923:0.8077	.	.	.	.	X	714	.	ENSP00000258494:R714X	R	-	1	2	ALDH1L2	103956016	0.998000	0.40836	0.938000	0.37757	0.995000	0.86356	0.415000	0.21181	-0.013000	0.14199	0.650000	0.86243	CGA		0.478	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		A	105431886	G	A	105431886	4	1	61	1	0	0	0	0	0	1	0	0	495	1095	38	1	655	1	ALDH1L2	12	105431886	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3791	105431886	28420009	8334	16319										
KIAA1033	23325	broad.mit.edu	37	chr12	105543428	105543428	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtttttgaaaaagaagttCtatatatttagccaatttat	5	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105543428C>A	ENST00000332180.5	+	25	2637	c.2550C>A	c.(2548-2550)ttC>ttA	p.F850L		NM_015275.1	NP_056090.1			KIAA1033									p.F850L(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						AAAAGAAGTTCTATATATTTA	0.234																																																1	Substitution - Missense(1)	large_intestine(1)	12											51	52	52					12																	105543428		1777	4026	5803	104067558	SO:0001583	missense	23325			AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2550C>A	12.37:g.105543428C>A	ENSP00000328062:p.Phe850Leu		104067558		Missense_Mutation	SNP	ENST00000332180.5	37	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.704082	0.48412	.	.	ENSG00000136051	ENST00000332180	T	0.43688	0.94	5.67	2.79	0.32731	.	0.045348	0.85682	D	0.000000	T	0.32496	0.0831	L	0.47716	1.5	0.53005	D	0.999965	P;P	0.35011	0.48;0.48	B;B	0.31495	0.131;0.131	T	0.09250	-1.0683	10	0.72032	D	0.01	.	8.5872	0.33666	0.0:0.6075:0.0:0.3925	.	851;850	B7ZKT9;Q2M389	.;WASH7_HUMAN	L	850	ENSP00000328062:F850L	ENSP00000328062:F850L	F	+	3	2	KIAA1033	104067558	0.956000	0.32656	1.000000	0.80357	0.991000	0.79684	0.086000	0.14935	0.295000	0.22570	0.557000	0.71058	TTC		0.234	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		A	105543428	C	A	105543428	3	1	61	1	0	0	0	0	1	0	0	0	8227	912	32	2	2648	2	KIAA1033	12	105543428	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111542	105543428	28308467	8335	16320										
KIAA1033	23325	broad.mit.edu	37	chr12	105553811	105553811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcctcagtgatcacacacGaaattctgccgaaggcacag	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105553811G>A	ENST00000332180.5	+	29	3032	c.2945G>A	c.(2944-2946)cGa>cAa	p.R982Q		NM_015275.1	NP_056090.1			KIAA1033									p.R982Q(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						GATCACACACGAAATTCTGCC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											91	92	92					12																	105553811		1806	4074	5880	104077941	SO:0001583	missense	23325			AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2945G>A	12.37:g.105553811G>A	ENSP00000328062:p.Arg982Gln		104077941		Missense_Mutation	SNP	ENST00000332180.5	37	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409055	0.62399	.	.	ENSG00000136051	ENST00000332180;ENST00000551224	T;T	0.75938	-0.98;-0.98	4.98	4.98	0.66077	.	0.050555	0.85682	D	0.000000	T	0.53045	0.1772	N	0.02391	-0.57	0.58432	D	0.999995	B;B	0.15930	0.015;0.015	B;B	0.11329	0.006;0.006	T	0.50162	-0.8860	10	0.32370	T	0.25	.	18.2844	0.90110	0.0:0.0:1.0:0.0	.	983;982	B7ZKT9;Q2M389	.;WASH7_HUMAN	Q	982;60	ENSP00000328062:R982Q;ENSP00000447015:R60Q	ENSP00000328062:R982Q	R	+	2	0	KIAA1033	104077941	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.433000	0.73404	2.314000	0.78098	0.484000	0.47621	CGA		0.363	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		A	105553811	G	A	105553811	3	1	61	1	0	0	0	0	1	0	0	0	8227	1058	37	1	3059	1	KIAA1033	12	105553811	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10383	105553811	28298084	8336	16321										
APPL2	55198	broad.mit.edu	37	chr12	105582196	105582196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccattgatcccaaaaaccGaactataaacatctgctgca	5	12	1	1	rs536236110		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105582196G>A	ENST00000258530.3	-	17	1714	c.1489C>T	c.(1489-1491)Cgg>Tgg	p.R497W	APPL2_ENST00000539978.2_Missense_Mutation_p.R454W|APPL2_ENST00000551662.1_Missense_Mutation_p.R503W	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.R497W(2)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CCCAAAAACCGAACTATAAAC	0.423													G|||	1	0.000199681	0	0	5008	,	,		21010	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	12											93	91	92					12																	105582196		2203	4300	6503	104106326	SO:0001583	missense	55198			AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"Pleckstrin homology (PH) domain containing"	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1489C>T	12.37:g.105582196G>A	ENSP00000258530:p.Arg497Trp		104106326	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000258530.3	37	CCDS9101.1	.	.	.	.	.	.	.	.	.	.	G	32	5.175533	0.94807	.	.	ENSG00000136044	ENST00000258530;ENST00000539978;ENST00000551662	T;T;T	0.24908	1.83;1.83;1.83	5.35	5.35	0.76521	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.054287	0.85682	D	0.000000	T	0.54013	0.1832	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;P;D	0.69654	0.946;0.727;0.965	T	0.58825	-0.7568	10	0.87932	D	0	-21.6286	19.0617	0.93096	0.0:0.0:1.0:0.0	.	503;454;497	F8W1P5;B7Z1Q8;Q8NEU8	.;.;DP13B_HUMAN	W	497;454;503	ENSP00000258530:R497W;ENSP00000444472:R454W;ENSP00000446917:R503W	ENSP00000258530:R497W	R	-	1	2	APPL2	104106326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.497000	0.84241	0.637000	0.83480	CGG		0.423	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171		A	105582196	G	A	105582196	3	1	61	1	0	0	0	0	1	0	0	0	818	1057	37	1	525	1	APPL2	12	105582196	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28385	105582196	28269699	8337	16322										
APPL2	55198	broad.mit.edu	37	chr12	105593257	105593257	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatcaacagaaagtaattCttgctgggacacccgcatct	7	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:105593257C>A	ENST00000258530.3	-	10	982	c.757G>T	c.(757-759)Gaa>Taa	p.E253*	APPL2_ENST00000539978.2_Nonsense_Mutation_p.E210*|APPL2_ENST00000551662.1_Nonsense_Mutation_p.E259*|APPL2_ENST00000549573.1_5'UTR	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0	Asp/Glu-rich (highly acidic).				cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.E253*(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAAAGTAATTCTTGCTGGGAC	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											132	119	124					12																	105593257		2203	4300	6503	104117387	SO:0001587	stop_gained	55198			AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"Pleckstrin homology (PH) domain containing"	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.757G>T	12.37:g.105593257C>A	ENSP00000258530:p.Glu253*		104117387	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Nonsense_Mutation	SNP	ENST00000258530.3	37	CCDS9101.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430200	0.83776	.	.	ENSG00000136044	ENST00000258530;ENST00000539978;ENST00000551662	.	.	.	5.93	5.93	0.95920	.	0.045908	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-29.1572	20.3539	0.98825	0.0:1.0:0.0:0.0	.	.	.	.	X	253;210;259	.	ENSP00000258530:E253X	E	-	1	0	APPL2	104117387	1.000000	0.71417	0.826000	0.32828	0.399000	0.30720	7.298000	0.78815	2.826000	0.97356	0.655000	0.94253	GAA		0.493	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171		A	105593257	C	A	105593257	4	1	61	1	0	0	0	0	0	1	0	0	818	922	32	2	1285	2	APPL2	12	105593257	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11061	105593257	28258638	8338	16323										
NUAK1	9891	broad.mit.edu	37	chr12	106464625	106464625	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgtgatcgaaaccatcGaagggcattgttccataaac	8	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:106464625G>A	ENST00000261402.2	-	6	2138	c.759C>T	c.(757-759)ttC>ttT	p.F253F		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.F253F(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						CGAAACCATCGAAGGGCATTG	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	12											114	101	105					12																	106464625		2203	4300	6503	104988755	SO:0001819	synonymous_variant	9891			AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.759C>T	12.37:g.106464625G>A			104988755	A7MD39|Q96KA8	Silent	SNP	ENST00000261402.2	37	CCDS31892.1																																																																																				0.547	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		A	106464625	G	A	106464625	2	1	61	1	0	0	0	0	0	0	0	1	10743	1049	37	1		1	NUAK1	12	106464625	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	871368	106464625	27387270	8339	16324										
CKAP4	10970	broad.mit.edu	37	chr12	106633632	106633632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttgaggctcaccagctCgcggacctcggtgtagatgt	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:106633632C>T	ENST00000378026.4	-	2	1115	c.979G>A	c.(979-981)Gag>Aag	p.E327K	CKAP4_ENST00000552828.1_5'Flank	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	327						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.E327K(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						CTCACCAGCTCGCGGACCTCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											37	38	38					12																	106633632		2203	4300	6503	105157762	SO:0001583	missense	10970			X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.979G>A	12.37:g.106633632C>T	ENSP00000367265:p.Glu327Lys		105157762	Q504S5|Q53ES6	Missense_Mutation	SNP	ENST00000378026.4	37	CCDS9103.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488809	0.84962	.	.	ENSG00000136026	ENST00000378026	T	0.78246	-1.16	5.58	5.58	0.84498	.	0.105878	0.64402	D	0.000006	D	0.84151	0.5409	M	0.76328	2.33	0.49130	D	0.99975	D	0.65815	0.995	P	0.56216	0.794	T	0.83003	-0.0176	10	0.33940	T	0.23	-30.1539	15.1073	0.72332	0.0:0.859:0.141:0.0	.	327	Q07065	CKAP4_HUMAN	K	327	ENSP00000367265:E327K	ENSP00000367265:E327K	E	-	1	0	CKAP4	105157762	1.000000	0.71417	0.990000	0.47175	0.852000	0.48524	5.037000	0.64170	2.641000	0.89580	0.563000	0.77884	GAG		0.602	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1			T	106633632	C	T	106633632	3	4	61	1	0	0	0	0	1	0	0	0	3450	893	31	1	833	1	CKAP4	12	106633632	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	169007	106633632	27218263	8340	16325										
POLR3B	55703	broad.mit.edu	37	chr12	106772092	106772092	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagttattcttatccaaGagcagctgtctaagaacagg	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:106772092G>T	ENST00000228347.4	+	8	766	c.544G>T	c.(544-546)Gag>Tag	p.E182*	POLR3B_ENST00000539066.1_Nonsense_Mutation_p.E124*	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	182					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.E182*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						TCTTATCCAAGAGCAGCTGTC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											148	141	143					12																	106772092		2203	4300	6503	105296222	SO:0001587	stop_gained	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.544G>T	12.37:g.106772092G>T	ENSP00000228347:p.Glu182*		105296222	A8K6H0|B3KV73|F5H1E6|Q9NW59	Nonsense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	39	7.786786	0.98489	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.7127	19.49	0.95047	0.0:0.0:1.0:0.0	.	.	.	.	X	182;182;124	.	ENSP00000228347:E182X	E	+	1	0	POLR3B	105296222	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.703000	0.98714	2.704000	0.92352	0.650000	0.86243	GAG		0.418	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		T	106772092	G	T	106772092	4	4	61	1	0	0	0	0	0	1	0	0	12260	943	33	2	574	2	POLR3B	12	106772092	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138460	106772092	27079803	8341	16326										
POLR3B	55703	broad.mit.edu	37	chr12	106824068	106824068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggaaattggtctttaaaGagatttaaaatggaccgcca	10	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:106824068G>T	ENST00000228347.4	+	14	1503	c.1281G>T	c.(1279-1281)aaG>aaT	p.K427N	POLR3B_ENST00000539066.1_Missense_Mutation_p.K369N	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	427					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.K427N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GGTCTTTAAAGAGATTTAAAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											101	111	107					12																	106824068		2203	4300	6503	105348198	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1281G>T	12.37:g.106824068G>T	ENSP00000228347:p.Lys427Asn		105348198	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.860949	0.71949	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.77489	-1.1;-1.1	5.71	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.86863	0.6035	H	0.95187	3.635	0.80722	D	1	P	0.52842	0.956	P	0.50136	0.632	D	0.89441	0.3723	10	0.87932	D	0	-27.3411	10.7865	0.46409	0.1442:0.0:0.8558:0.0	.	427	Q9NW08	RPC2_HUMAN	N	427;427;369	ENSP00000228347:K427N;ENSP00000445721:K369N	ENSP00000228347:K427N	K	+	3	2	POLR3B	105348198	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.643000	0.46604	1.412000	0.46977	-0.136000	0.14681	AAG		0.433	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		T	106824068	G	T	106824068	3	4	61	1	0	0	0	0	1	0	0	0	12260	933	33	2	1335	2	POLR3B	12	106824068	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51976	106824068	27027827	8342	16327										
POLR3B	55703	broad.mit.edu	37	chr12	106827518	106827518	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacatcttaggtgtcattcGagaccacaaaaagctagtga	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:106827518G>A	ENST00000228347.4	+	16	1871	c.1649G>A	c.(1648-1650)cGa>cAa	p.R550Q	POLR3B_ENST00000539066.1_Missense_Mutation_p.R492Q	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	550					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.R550Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GGTGTCATTCGAGACCACAAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											106	103	104					12																	106827518		2203	4300	6503	105351648	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1649G>A	12.37:g.106827518G>A	ENSP00000228347:p.Arg550Gln		105351648	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267008	0.80469	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.77098	-1.07;-1.07	6.03	6.03	0.97812	RNA polymerase Rpb2, domain 4 (1);	0.000000	0.85682	D	0.000000	T	0.76622	0.4013	L	0.46614	1.455	0.80722	D	1	B	0.21225	0.053	B	0.26693	0.072	T	0.70342	-0.4898	10	0.52906	T	0.07	-11.3506	20.5666	0.99351	0.0:0.0:1.0:0.0	.	550	Q9NW08	RPC2_HUMAN	Q	550;550;492	ENSP00000228347:R550Q;ENSP00000445721:R492Q	ENSP00000228347:R550Q	R	+	2	0	POLR3B	105351648	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.588000	0.82629	2.854000	0.98071	0.655000	0.94253	CGA		0.328	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		A	106827518	G	A	106827518	3	1	61	1	0	0	0	0	1	0	0	0	12260	1058	37	1	1711	1	POLR3B	12	106827518	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3450	106827518	27024377	8343	16328										
RFX4	5992	broad.mit.edu	37	chr12	107103124	107103124	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagcttaactcaggtgattCgaaagtttgccaagcaactg	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107103124C>T	ENST00000392842.1	+	9	1264	c.850C>T	c.(850-852)Cga>Tga	p.R284*	RFX4_ENST00000229387.5_Nonsense_Mutation_p.R190*|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Nonsense_Mutation_p.R293*	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	284					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R293*(1)|p.R284*(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TCAGGTGATTCGAAAGTTTGC	0.448																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											92	81	85					12																	107103124		2203	4300	6503	105627254	SO:0001587	stop_gained	5992			AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.850C>T	12.37:g.107103124C>T	ENSP00000376585:p.Arg284*		105627254	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Nonsense_Mutation	SNP	ENST00000392842.1	37	CCDS9106.1	.	.	.	.	.	.	.	.	.	.	C	38	7.256001	0.98168	.	.	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000266774;ENST00000551640;ENST00000229387	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.9846	13.9022	0.63812	0.2673:0.7327:0.0:0.0	.	.	.	.	X	284;293;293;229;190	.	ENSP00000229387:R190X	R	+	1	2	RFX4	105627254	0.974000	0.33945	1.000000	0.80357	0.995000	0.86356	1.605000	0.36815	2.682000	0.91365	0.650000	0.86243	CGA		0.448	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		T	107103124	C	T	107103124	4	4	61	1	0	0	0	0	0	1	0	0	13302	876	31	1	1057	1	RFX4	12	107103124	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	275606	107103124	26748771	8344	16329										
RFX4	5992	broad.mit.edu	37	chr12	107103204	107103204	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttgcgaaacatcaagttCgaatgtaagtactgagttga	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107103204C>T	ENST00000392842.1	+	9	1344	c.930C>T	c.(928-930)ttC>ttT	p.F310F	RFX4_ENST00000229387.5_Silent_p.F216F|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Silent_p.F319F	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	310					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.F310F(1)|p.F319F(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						ACATCAAGTTCGAATGTAAGT	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	12											79	69	72					12																	107103204		2203	4300	6503	105627334	SO:0001819	synonymous_variant	5992			AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.930C>T	12.37:g.107103204C>T			105627334	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																				0.408	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		T	107103204	C	T	107103204	2	4	61	1	0	0	0	0	0	0	0	1	13302	883	31	1		1	RFX4	12	107103204	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80	107103204	26748691	8345	16330										
RIC8B	55188	broad.mit.edu	37	chr12	107177781	107177781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttccccctcagcataggGctactttcaaatttgaatca	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107177781G>A	ENST00000392839.2	+	2	197	c.91G>A	c.(91-93)Gct>Act	p.A31T	RIC8B_ENST00000392837.4_Missense_Mutation_p.A31T|RIC8B_ENST00000549643.1_Intron|RIC8B_ENST00000355478.2_5'UTR	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	31					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.A31T(1)		kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TCAGCATAGGGCTACTTTCAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											134	129	131					12																	107177781		2203	4300	6503	105701911	SO:0001583	missense	55188			AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.91G>A	12.37:g.107177781G>A	ENSP00000376583:p.Ala31Thr		105701911	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Missense_Mutation	SNP	ENST00000392839.2	37	CCDS9109.2	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629075	0.46944	.	.	ENSG00000111785	ENST00000392837;ENST00000392839	.	.	.	5.48	4.58	0.56647	.	0.548643	0.20031	N	0.100715	T	0.35508	0.0934	N	0.08118	0	0.80722	D	1	B;B	0.16396	0.001;0.017	B;B	0.11329	0.001;0.006	T	0.12578	-1.0542	9	0.21014	T	0.42	-0.026	11.9737	0.53078	0.0:0.0:0.8264:0.1736	.	31;31	Q9NVN3;B7WPL0	RIC8B_HUMAN;.	T	31	.	ENSP00000376582:A31T	A	+	1	0	RIC8B	105701911	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.270000	0.43355	1.421000	0.47157	0.557000	0.71058	GCT		0.333	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157		A	107177781	G	A	107177781	3	1	61	1	0	0	0	0	1	0	0	0	13393	1203	42	3	97	3	RIC8B	12	107177781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74577	107177781	26674114	8346	16331										
RIC8B	55188	broad.mit.edu	37	chr12	107219576	107219576	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcgtaggtccaactgaaGacaaaacagaagagctacac	8	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107219576G>T	ENST00000392839.2	+	4	920	c.814G>T	c.(814-816)Gac>Tac	p.D272Y	RIC8B_ENST00000392837.4_Missense_Mutation_p.D272Y|RIC8B_ENST00000549643.1_Intron|RIC8B_ENST00000355478.2_Missense_Mutation_p.D232Y	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	272					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.D272Y(1)		kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TCCAACTGAAGACAAAACAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	105	110					12																	107219576		2203	4300	6503	105743706	SO:0001583	missense	55188			AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.814G>T	12.37:g.107219576G>T	ENSP00000376583:p.Asp272Tyr		105743706	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Missense_Mutation	SNP	ENST00000392839.2	37	CCDS9109.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.120853|4.120853	0.77436|0.77436	.|.	.|.	ENSG00000111785|ENSG00000111785	ENST00000392837;ENST00000392839;ENST00000355478|ENST00000548914	T;T;T|.	0.56611|.	0.45;0.45;0.45|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Armadillo-type fold (1);|.	0.044998|.	0.85682|.	D|.	0.000000|.	T|T	0.74741|0.74741	0.3756|0.3756	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	D;D;D|.	0.69078|.	0.993;0.997;0.997|.	P;D;D|.	0.69479|.	0.858;0.964;0.964|.	T|T	0.74340|0.74340	-0.3697|-0.3697	10|5	0.56958|.	D|.	0.05|.	-2.4789|-2.4789	17.0142|17.0142	0.86414|0.86414	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	232;272;272|.	Q9NVN3-3;Q9NVN3;B7WPL0|.	.;RIC8B_HUMAN;.|.	Y|N	272;272;232|96	ENSP00000376582:D272Y;ENSP00000376583:D272Y;ENSP00000347662:D232Y|.	ENSP00000347662:D232Y|.	D|K	+|+	1|3	0|2	RIC8B|RIC8B	105743706|105743706	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.018000|6.018000	0.70811|0.70811	2.535000|2.535000	0.85469|0.85469	0.591000|0.591000	0.81541|0.81541	GAC|AAG		0.388	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157		T	107219576	G	T	107219576	3	4	61	1	0	0	0	0	1	0	0	0	13393	942	33	2	828	2	RIC8B	12	107219576	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41795	107219576	26632319	8347	16332										
MTERFD3	80298	broad.mit.edu	37	chr12	107371395	107371395	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccttacttttttggcctgAattttgccaaaattagcttc	7	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107371395A>G	ENST00000552029.1	-	2	3166	c.1098T>C	c.(1096-1098)atT>atC	p.I366I	MTERFD3_ENST00000240050.4_Silent_p.I366I|MTERFD3_ENST00000392830.2_Silent_p.I366I|C12orf23_ENST00000551237.1_Intron			Q49AM1	MTEF2_HUMAN		366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)	p.I366I(1)		breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						TTTTGGCCTGAATTTTGCCAA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	12											142	138	139					12																	107371395		2203	4300	6503	105895525	SO:0001819	synonymous_variant	80298																														ENST00000552029.1:c.1098T>C	12.37:g.107371395A>G			105895525	Q53HM2|Q9H4L6|Q9H7Y9	Silent	SNP	ENST00000552029.1	37	CCDS9111.1																																																																																				0.378	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			G	107371395	A	G	107371395	2	3	61	1	0	0	0	0	0	0	0	1	9951	242	9	4		4	MTERFD3	12	107371395	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	151819	107371395	26480500	8348	16333										
CRY1	1407	broad.mit.edu	37	chr12	107393758	107393758	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtttgaagtaaaacagtcGacatgacaaacaaccaaatc	6	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107393758G>A	ENST00000008527.5	-	6	1654	c.787C>T	c.(787-789)Cga>Tga	p.R263*		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	263					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.R263*(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						TAAAACAGTCGACATGACAAA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											67	68	68					12																	107393758		2203	4300	6503	105917888	SO:0001587	stop_gained	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.787C>T	12.37:g.107393758G>A	ENSP00000008527:p.Arg263*		105917888		Nonsense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	G	45	11.598548	0.99580	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.82	4.91	0.64330	.	0.056923	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.14	15.7241	0.77740	0.0:0.0:0.8524:0.1475	.	.	.	.	X	263	.	ENSP00000008527:R263X	R	-	1	2	CRY1	105917888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.411000	0.73298	1.387000	0.46486	0.650000	0.86243	CGA		0.338	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		A	107393758	G	A	107393758	4	1	61	1	0	0	0	0	0	1	0	0	3909	1066	37	1	1001	1	CRY1	12	107393758	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22363	107393758	26458137	8349	16334										
CRY1	1407	broad.mit.edu	37	chr12	107415962	107415962	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagatcctcaagacactgaAgcaaaaatctagagagaaga	8	8	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:107415962A>C	ENST00000008527.5	-	2	1034	c.167T>G	c.(166-168)cTt>cGt	p.L56R		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	56	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.L56R(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						AAGACACTGAAGCAAAAATCT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	12											65	71	69					12																	107415962		2203	4300	6503	105940092	SO:0001583	missense	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.167T>G	12.37:g.107415962A>C	ENSP00000008527:p.Leu56Arg		105940092		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.490404	0.84962	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.38	5.38	0.77491	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87370	0.6160	H	0.96604	3.85	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.91021	0.4857	9	0.54805	T	0.06	-18.2268	15.049	0.71850	1.0:0.0:0.0:0.0	.	56	Q16526	CRY1_HUMAN	R	56	.	ENSP00000008527:L56R	L	-	2	0	CRY1	105940092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.010000	0.93611	2.036000	0.60181	0.528000	0.53228	CTT		0.313	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		C	107415962	A	C	107415962	3	2	61	1	0	0	0	0	1	0	0	0	3909	72	3	4	1637	4	CRY1	12	107415962	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22204	107415962	26435933	8350	16335										
PWP1	11137	broad.mit.edu	37	chr12	108082481	108082481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacccaggcacgcccaagagAgcccctggaggatggtgacc	13	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:108082481A>G	ENST00000412830.3	+	3	389	c.221A>G	c.(220-222)gAg>gGg	p.E74G	PWP1_ENST00000541166.1_Missense_Mutation_p.E12G	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	74					transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.E74G(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						CGCCCAAGAGAGCCCCTGGAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											127	119	122					12																	108082481		2203	4300	6503	106606611	SO:0001583	missense	11137			BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"WD repeat domain containing"	17015	protein-coding gene	gene with protein product	"endonuclein"					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.221A>G	12.37:g.108082481A>G	ENSP00000387365:p.Glu74Gly		106606611	A8K3R6|Q7Z3X9	Missense_Mutation	SNP	ENST00000412830.3	37	CCDS9114.1	.	.	.	.	.	.	.	.	.	.	.	13.31	2.199572	0.38806	.	.	ENSG00000136045	ENST00000412830;ENST00000547995;ENST00000258531;ENST00000546068;ENST00000538327;ENST00000541166	T;T	0.71934	-0.61;-0.6	5.69	5.69	0.88448	.	0.311853	0.32081	N	0.006616	T	0.61540	0.2355	L	0.41961	1.31	0.23984	N	0.996266	B	0.33694	0.421	B	0.29785	0.107	T	0.53872	-0.8377	10	0.23302	T	0.38	.	14.9158	0.70795	1.0:0.0:0.0:0.0	.	74	Q13610	PWP1_HUMAN	G	74;12;74;74;74;12	ENSP00000387365:E74G;ENSP00000445249:E12G	ENSP00000258531:E74G	E	+	2	0	PWP1	106606611	0.629000	0.27146	0.896000	0.35187	0.956000	0.61745	2.111000	0.41883	2.158000	0.67659	0.391000	0.25812	GAG		0.537	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062		G	108082481	A	G	108082481	3	3	61	1	0	0	0	0	1	0	0	0	12880	304	11	4	231	4	PWP1	12	108082481	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	666519	108082481	25769414	8351	16336										
PRDM4	11108	broad.mit.edu	37	chr12	108145836	108145836	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagtctattgaaacaatgCctggttctaatccaacattt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:108145836C>G	ENST00000228437.5	-	5	941	c.482G>C	c.(481-483)gGc>gCc	p.G161A	RP11-864J10.4_ENST00000546714.1_RNA|PRDM4_ENST00000547268.1_5'Flank	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	161					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)	p.G161A(1)		biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						TGAAACAATGCCTGGTTCTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											160	148	152					12																	108145836		2203	4300	6503	106669966	SO:0001583	missense	11108			AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"Zinc fingers, C2H2-type"	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.482G>C	12.37:g.108145836C>G	ENSP00000228437:p.Gly161Ala		106669966	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	37	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.594090	0.66219	.	.	ENSG00000110851	ENST00000228437	D	0.81739	-1.53	5.66	5.66	0.87406	.	0.050500	0.85682	D	0.000000	T	0.68229	0.2978	L	0.27053	0.805	0.80722	D	1	P	0.37525	0.598	B	0.29077	0.098	T	0.73433	-0.3984	10	0.87932	D	0	-17.7265	13.9724	0.64250	0.0:0.9278:0.0:0.0722	.	161	Q9UKN5	PRDM4_HUMAN	A	161	ENSP00000228437:G161A	ENSP00000228437:G161A	G	-	2	0	PRDM4	106669966	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.282000	0.58971	2.656000	0.90262	0.655000	0.94253	GGC		0.433	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		G	108145836	C	G	108145836	3	3	61	1	0	0	0	0	1	0	0	0	12493	739	26	5	1955	5	PRDM4	12	108145836	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63355	108145836	25706059	8352	16337										
SART3	9733	broad.mit.edu	37	chr12	108923999	108923999	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgatctttttcttctttTttaacgctttcttctcagcc	3	12	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:108923999T>G	ENST00000228284.3	-	15	2069	c.1835A>C	c.(1834-1836)aAa>aCa	p.K612T	SART3_ENST00000431469.2_Missense_Mutation_p.K576T	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	612	Poly-Lys.|Required for nuclear localization.				cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K612T(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						TTTCTTCTTTTTTAACGCTTT	0.478									Porokeratosis																																							1	Substitution - Missense(1)	large_intestine(1)	12											142	129	134					12																	108923999		2203	4300	6503	107448129	SO:0001583	missense	9733	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"RNA binding motif (RRM) containing"	16860	protein-coding gene	gene with protein product		611684	"squamous cell carcinoma antigen recognised by T cells 3"			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.1835A>C	12.37:g.108923999T>G	ENSP00000228284:p.Lys612Thr		107448129	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Missense_Mutation	SNP	ENST00000228284.3	37	CCDS9117.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.227569	0.39399	.	.	ENSG00000075856	ENST00000228284;ENST00000431469;ENST00000535329;ENST00000412617;ENST00000546815	T;T;T	0.59083	2.32;2.15;0.29	6.03	3.7	0.42460	.	0.241652	0.48767	D	0.000177	T	0.56321	0.1977	N	0.24115	0.695	0.80722	D	1	D;D;P;P	0.64830	0.985;0.994;0.941;0.819	P;P;P;B	0.60682	0.801;0.878;0.536;0.435	T	0.52771	-0.8531	10	0.40728	T	0.16	-11.6946	9.8033	0.40777	0.0:0.1377:0.0:0.8623	.	560;630;576;612	E7EMI4;F8VV04;B7ZKM0;Q15020	.;.;.;SART3_HUMAN	T	612;576;188;560;630	ENSP00000228284:K612T;ENSP00000414453:K576T;ENSP00000449386:K630T	ENSP00000228284:K612T	K	-	2	0	SART3	107448129	1.000000	0.71417	0.446000	0.26920	0.250000	0.25880	3.142000	0.50601	0.533000	0.28675	0.533000	0.62120	AAA		0.478	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1			G	108923999	T	G	108923999	3	3	61	1	0	0	0	0	1	0	0	0	13884	1841	64	4	1076	4	SART3	12	108923999	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	778163	108923999	24927896	8353	16338										
SELPLG	6404	broad.mit.edu	37	chr12	109017951	109017951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatctaggtactcatattCggtggcctgtctccggtccc	9	12	3	0	rs372642040		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109017951C>T	ENST00000550948.1	-	2	357	c.133G>A	c.(133-135)Gaa>Aaa	p.E45K	SELPLG_ENST00000388962.3_Missense_Mutation_p.E45K|SELPLG_ENST00000228463.6_Missense_Mutation_p.E61K			Q14242	SELPL_HUMAN	selectin P ligand	45					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.E45K(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						TACTCATATTCGGTGGCCTGT	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	12						C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	83	79	80		181,133	-2.5	0	12		80	0,8600		0,0,4300	no	missense,missense	SELPLG	NM_001206609.1,NM_003006.4	56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	61/429,45/413	109017951	1,13005	2203	4300	6503	107542080	SO:0001583	missense	6404				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.133G>A	12.37:g.109017951C>T	ENSP00000447752:p.Glu45Lys		107542080	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040434	0.35989	2.27E-4	0.0	ENSG00000110876	ENST00000388962;ENST00000550948;ENST00000228463	T;T;T	0.35048	1.34;1.33;1.35	3.11	-2.52	0.06346	.	.	.	.	.	T	0.15089	0.0364	N	0.24115	0.695	0.09310	N	1	P;P;P	0.47677	0.899;0.815;0.815	B;B;B	0.35510	0.204;0.121;0.121	T	0.13575	-1.0504	9	0.52906	T	0.07	5.6865	0.3006	0.00272	0.2733:0.3036:0.1542:0.2689	.	61;45;45	B7Z5C7;Q14242;B4DHR9	.;SELPL_HUMAN;.	K	45;45;61	ENSP00000373614:E45K;ENSP00000447752:E45K;ENSP00000228463:E61K	ENSP00000228463:E61K	E	-	1	0	SELPLG	107542080	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.838000	0.04372	-0.604000	0.05760	-0.314000	0.08810	GAA		0.587	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			T	109017951	C	T	109017951	3	4	61	1	0	0	0	0	1	0	0	0	14057	893	31	1	1083	1	SELPLG	12	109017951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93952	109017951	24833944	8354	16339										
CORO1C	23603	broad.mit.edu	37	chr12	109042426	109042426	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggatgctgatcaggtcGcacttcttgtttgcagtggg	15	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109042426G>A	ENST00000261401.3	-	10	1432	c.1260C>T	c.(1258-1260)tgC>tgT	p.C420C	CORO1C_ENST00000420959.2_Silent_p.C473C|CORO1C_ENST00000541050.1_Silent_p.C420C|CORO1C_ENST00000549772.1_Silent_p.C426C|CORO1C_ENST00000549384.1_5'UTR|CORO1C_ENST00000421578.2_Silent_p.C315C	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	420					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.C420C(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						TGATCAGGTCGCACTTCTTGT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	12											273	217	236					12																	109042426		2203	4300	6503	107566555	SO:0001819	synonymous_variant	23603			BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"Coronins", "WD repeat domain containing"	2254	protein-coding gene	gene with protein product		605269	"coronin, actin-binding protein, 1C"			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.1260C>T	12.37:g.109042426G>A			107566555	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Silent	SNP	ENST00000261401.3	37	CCDS9120.1																																																																																				0.517	CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325		A	109042426	G	A	109042426	2	1	61	1	0	0	0	0	0	0	0	1	3761	1079	38	1		1	CORO1C	12	109042426	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24475	109042426	24809469	8355	16340										
CORO1C	23603	broad.mit.edu	37	chr12	109042528	109042528	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtgcttcaaggagatgagGattgggtctgcattcttgcc	13	9	3	2	rs537326835		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109042528G>T	ENST00000261401.3	-	10	1330	c.1158C>A	c.(1156-1158)atC>atA	p.I386I	CORO1C_ENST00000420959.2_Silent_p.I439I|CORO1C_ENST00000541050.1_Silent_p.I386I|CORO1C_ENST00000549772.1_Silent_p.I392I|CORO1C_ENST00000549384.1_5'UTR|CORO1C_ENST00000421578.2_Silent_p.I281I	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	386					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.I386I(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						AGGAGATGAGGATTGGGTCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	12											219	163	182					12																	109042528		2203	4300	6503	107566657	SO:0001819	synonymous_variant	23603			BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"Coronins", "WD repeat domain containing"	2254	protein-coding gene	gene with protein product		605269	"coronin, actin-binding protein, 1C"			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.1158C>A	12.37:g.109042528G>T			107566657	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Silent	SNP	ENST00000261401.3	37	CCDS9120.1																																																																																				0.517	CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325		T	109042528	G	T	109042528	2	4	61	1	0	0	0	0	0	0	0	1	3761	1164	41	2		2	CORO1C	12	109042528	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102	109042528	24809367	8356	16341										
SSH1	54434	broad.mit.edu	37	chr12	109192845	109192845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttggggcgcgtgatgctgCgcttctgctttacatagtta	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109192845C>T	ENST00000326495.5	-	13	1373	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	SSH1_ENST00000551165.1_Missense_Mutation_p.R427H|SSH1_ENST00000360239.3_Missense_Mutation_p.R115H|SSH1_ENST00000326470.5_Missense_Mutation_p.R438H	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	427	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R427H(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CGTGATGCTGCGCTTCTGCTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	74	76					12																	109192845		2203	4300	6503	107716974	SO:0001583	missense	54434			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1280G>A	12.37:g.109192845C>T	ENSP00000315713:p.Arg427His		107716974	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186623	0.94885	.	.	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	T;T;T;T	0.78126	0.48;-1.15;-1.15;-1.15	5.11	5.11	0.69529	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.91157	0.7215	M	0.92367	3.3	0.58432	D	0.999995	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	D	0.93124	0.6527	10	0.87932	D	0	-30.9629	18.9257	0.92544	0.0:1.0:0.0:0.0	.	438;427;427;115	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	H	115;427;427;438	ENSP00000353374:R115H;ENSP00000315713:R427H;ENSP00000448824:R427H;ENSP00000326107:R438H	ENSP00000326107:R438H	R	-	2	0	SSH1	107716974	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.818000	0.86416	2.554000	0.86153	0.655000	0.94253	CGC		0.537	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		T	109192845	C	T	109192845	3	4	61	1	0	0	0	0	1	0	0	0	15223	768	27	1	2067	1	SSH1	12	109192845	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150317	109192845	24659050	8357	16342										
DAO	1610	broad.mit.edu	37	chr12	109278918	109278918	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccccactcaccaccaccGacgtggctgccggcctctgg	9	20	3	0	rs375063129		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109278918G>A	ENST00000228476.3	+	2	340	c.136G>A	c.(136-138)Gac>Aac	p.D46N	DAO_ENST00000551281.1_Missense_Mutation_p.D46N	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	46					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)	p.D46N(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	CACCACCACCGACGTGGCTGC	0.632													G|||	1	0.000199681	8e-04	0	5008	,	,		18282	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	86	83	84		136	5.6	0.5	12		84	0,8600		0,0,4300	no	missense	DAO	NM_001917.4	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	46/348	109278918	1,13005	2203	4300	6503	107803047	SO:0001583	missense	1610			D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.136G>A	12.37:g.109278918G>A	ENSP00000228476:p.Asp46Asn		107803047	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645408	0.67358	2.27E-4	0.0	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547166	T;T;T	0.81415	-1.49;-1.49;-1.49	5.58	5.58	0.84498	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.89694	0.6789	M	0.82923	2.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.86659	0.1903	10	0.16420	T	0.52	-12.7685	18.1463	0.89656	0.0:0.0:1.0:0.0	.	46;46	P14920;Q7Z312	OXDA_HUMAN;.	N	46	ENSP00000446853:D46N;ENSP00000228476:D46N;ENSP00000447104:D46N	ENSP00000228476:D46N	D	+	1	0	DAO	107803047	1.000000	0.71417	0.461000	0.27105	0.009000	0.06853	7.935000	0.87658	2.628000	0.89032	0.591000	0.81541	GAC		0.632	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			A	109278918	G	A	109278918	3	1	61	1	0	0	0	0	1	0	0	0	4237	1058	37	1	138	1	DAO	12	109278918	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86073	109278918	24572977	8358	16343										
DAO	1610	broad.mit.edu	37	chr12	109294270	109294270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctctttgggagaatcctgGaagaaaagaaattgtccaga	11	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109294270G>A	ENST00000228476.3	+	11	1207	c.1003G>A	c.(1003-1005)Gaa>Aaa	p.E335K	DAO_ENST00000551281.1_Missense_Mutation_p.E269K	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	335					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)	p.E335K(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	GAGAATCCTGGAAGAAAAGAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	89	93					12																	109294270		2203	4300	6503	107818399	SO:0001583	missense	1610			D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.1003G>A	12.37:g.109294270G>A	ENSP00000228476:p.Glu335Lys		107818399	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.140875	0.37825	.	.	ENSG00000110887	ENST00000551281;ENST00000228476	T;T	0.43294	0.96;0.95	4.73	4.73	0.59995	NAD(P)-binding domain (1);	0.242140	0.40385	N	0.001116	T	0.29976	0.0750	L	0.33339	1.005	0.42377	D	0.992475	B;B	0.21309	0.054;0.024	B;B	0.09377	0.004;0.004	T	0.10359	-1.0633	10	0.08381	T	0.77	-11.5925	15.2271	0.73359	0.0:0.0:1.0:0.0	.	335;318	P14920;Q7Z312	OXDA_HUMAN;.	K	269;335	ENSP00000446853:E269K;ENSP00000228476:E335K	ENSP00000228476:E335K	E	+	1	0	DAO	107818399	1.000000	0.71417	0.971000	0.41717	0.597000	0.36814	4.256000	0.58810	2.169000	0.68431	0.561000	0.74099	GAA		0.557	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			A	109294270	G	A	109294270	3	1	61	1	0	0	0	0	1	0	0	0	4237	1175	41	3	1041	3	DAO	12	109294270	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15352	109294270	24557625	8359	16344										
USP30	84749	broad.mit.edu	37	chr12	109494587	109494587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattacagaaagaaagaagCgtagaaaaggtaagaatgag	11	4	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109494587C>T	ENST00000257548.5	+	2	277	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C	USP30-AS1_ENST00000478808.2_RNA|USP30_ENST00000392784.2_Missense_Mutation_p.R31C	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	62					mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R53C(1)		endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						AAGAAAGAAGCGTAGAAAAGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											117	124	121					12																	109494587		2203	4300	6503	107978970	SO:0001583	missense	84749			BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.184C>T	12.37:g.109494587C>T	ENSP00000257548:p.Arg62Cys		107978970	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	37	CCDS9123.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128988	0.77549	.	.	ENSG00000135093	ENST00000392784;ENST00000257548;ENST00000536723;ENST00000536393;ENST00000539121	T;T;T;T	0.37235	1.22;1.21;1.32;1.41	5.88	5.0	0.66597	.	0.256489	0.44285	D	0.000472	T	0.35480	0.0933	N	0.24115	0.695	0.46499	D	0.999075	D	0.76494	0.999	P	0.54706	0.759	T	0.16364	-1.0405	10	0.54805	T	0.06	-10.7143	9.2279	0.37418	0.0:0.837:0.0:0.163	.	62	Q70CQ3	UBP30_HUMAN	C	31;62;31;62;36	ENSP00000376535:R31C;ENSP00000257548:R62C;ENSP00000443678:R31C;ENSP00000440837:R36C	ENSP00000257548:R62C	R	+	1	0	USP30	107978970	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.401000	0.52601	1.484000	0.48361	0.655000	0.94253	CGT		0.423	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		T	109494587	C	T	109494587	3	4	61	1	0	0	0	0	1	0	0	0	17101	768	27	1	190	1	USP30	12	109494587	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200317	109494587	24357308	8360	16345										
ACACB	32	broad.mit.edu	37	chr12	109679060	109679060	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacatcagcctctacaaaGaagtgactgactccagatct	8	11	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109679060G>T	ENST00000338432.7	+	36	5115	c.4996G>T	c.(4996-4998)Gaa>Taa	p.E1666*	ACACB_ENST00000543201.1_Nonsense_Mutation_p.E332*|ACACB_ENST00000377854.5_Nonsense_Mutation_p.E1596*|ACACB_ENST00000377848.3_Nonsense_Mutation_p.E1666*			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1666					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.E1666*(1)		NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CCTCTACAAAGAAGTGACTGA	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											150	146	147					12																	109679060		2203	4300	6503	108163443	SO:0001587	stop_gained	32			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.4996G>T	12.37:g.109679060G>T	ENSP00000341044:p.Glu1666*		108163443	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Nonsense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	37	6.440083	0.97568	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.2868	0.90117	0.0:0.0:1.0:0.0	.	.	.	.	X	1666;1666;1596;897;332	.	ENSP00000341044:E1666X	E	+	1	0	ACACB	108163443	1.000000	0.71417	0.952000	0.39060	0.642000	0.38348	9.810000	0.99221	2.407000	0.81776	0.561000	0.74099	GAA		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109679060	G	T	109679060	4	4	61	1	0	0	0	0	0	1	0	0	107	943	33	2	5134	2	ACACB	12	109679060	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184473	109679060	24172835	8361	16346										
FOXN4	121643	broad.mit.edu	37	chr12	109719222	109719222	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcctcaccctgcagagcGaagtccatgatgctcgggtc	11	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109719222G>A	ENST00000299162.5	-	9	1388	c.1284C>T	c.(1282-1284)ttC>ttT	p.F428F	FOXN4_ENST00000355216.1_Silent_p.F248F	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	428					amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F428F(1)|p.F248F(1)		large_intestine(5)|lung(9)|ovary(2)	16						CCTGCAGAGCGAAGTCCATGA	0.607																																																2	Substitution - coding silent(2)	large_intestine(2)	12											72	71	71					12																	109719222		2203	4300	6503	108203605	SO:0001819	synonymous_variant	121643			AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"Forkhead boxes"	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.1284C>T	12.37:g.109719222G>A			108203605	Q6ZMR4|Q96NZ0	Silent	SNP	ENST00000299162.5	37	CCDS9126.2																																																																																				0.607	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735		A	109719222	G	A	109719222	2	1	61	1	0	0	0	0	0	0	0	1	6041	1049	37	1		1	FOXN4	12	109719222	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40162	109719222	24132673	8362	16347										
MYO1H	283446	broad.mit.edu	37	chr12	109834299	109834299	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagaggcctccaagaaaaTtctcgagtattttgcagtga	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109834299T>G	ENST00000431443.2	+	3	353	c.353T>G	c.(352-354)aTt>aGt	p.I118S	MYO1H_ENST00000310903.5_Missense_Mutation_p.I118S	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	118	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.I118S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TCCAAGAAAATTCTCGAGTAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											67	68	68					12																	109834299		1882	4112	5994	108318682	SO:0001583	missense	283446				CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.353T>G	12.37:g.109834299T>G	ENSP00000444076:p.Ile118Ser		108318682	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	37		.	.	.	.	.	.	.	.	.	.	T	22.6	4.312306	0.81358	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.89746	-2.56;-2.56	4.8	4.8	0.61643	.	.	.	.	.	D	0.95456	0.8524	H	0.95645	3.7	0.49798	D	0.999821	D	0.67145	0.996	P	0.61397	0.888	D	0.96711	0.9525	9	0.87932	D	0	.	14.2704	0.66149	0.0:0.0:0.0:1.0	.	118	F5H3C6	.	S	118	ENSP00000439182:I118S;ENSP00000444076:I118S	ENSP00000439182:I118S	I	+	2	0	MYO1H	108318682	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	7.945000	0.87732	2.112000	0.64535	0.524000	0.50904	ATT		0.493	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		G	109834299	T	G	109834299	3	3	61	1	0	0	0	0	1	0	0	0	10105	1493	52	4	363	4	MYO1H	12	109834299	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	115077	109834299	24017596	8363	16348										
MYO1H	283446	broad.mit.edu	37	chr12	109883334	109883334	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtttacagttttttattAgtccgggaaaagaaggcaca	9	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109883334A>C	ENST00000431443.2	+	30	2992	c.2992A>C	c.(2992-2994)Agt>Cgt	p.S998R	MYO1H_ENST00000310903.5_Missense_Mutation_p.S988R|RP11-256L11.3_ENST00000539987.1_RNA	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	998	Myosin tail. {ECO:0000255}.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S988R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GTTTTTTATTAGTCCGGGAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											129	122	124					12																	109883334		1830	4082	5912	108367717	SO:0001583	missense	283446				CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.2992A>C	12.37:g.109883334A>C	ENSP00000444076:p.Ser998Arg		108367717	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	37		.	.	.	.	.	.	.	.	.	.	A	15.96	2.987274	0.53934	.	.	ENSG00000174527	ENST00000310903;ENST00000431443;ENST00000542268	T;T	0.35048	1.33;1.33	5.97	3.64	0.41730	Myosin tail 2 (1);	.	.	.	.	T	0.22704	0.0548	L	0.27053	0.805	0.27651	N	0.947393	B;B	0.25169	0.119;0.098	B;B	0.27715	0.082;0.03	T	0.24333	-1.0163	9	0.16420	T	0.52	.	6.1611	0.20364	0.752:0.0:0.248:0.0	.	998;988	Q8N1T3;F5H3C6	MYO1H_HUMAN;.	R	988;998;179	ENSP00000439182:S988R;ENSP00000444076:S998R	ENSP00000439182:S988R	S	+	1	0	MYO1H	108367717	0.108000	0.22018	0.987000	0.45799	0.985000	0.73830	0.603000	0.24149	1.072000	0.40860	0.528000	0.53228	AGT		0.348	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		C	109883334	A	C	109883334	3	2	61	1	0	0	0	0	1	0	0	0	10105	420	15	4	3080	4	MYO1H	12	109883334	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	49035	109883334	23968561	8364	16349										
UBE3B	89910	broad.mit.edu	37	chr12	109935660	109935660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttctcagacaatctgattCggccgttcctcatccacatc	6	14	3	2	rs200362048		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109935660C>T	ENST00000342494.3	+	10	1346	c.751C>T	c.(751-753)Cgg>Tgg	p.R251W	UBE3B_ENST00000280774.5_Missense_Mutation_p.R251W|UBE3B_ENST00000434735.2_Missense_Mutation_p.R251W	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	251					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R251W(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						CAATCTGATTCGGCCGTTCCT	0.512													C|||	1	0.000199681	0	0	5008	,	,		18849	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											252	191	212					12																	109935660		2203	4300	6503	108420043	SO:0001583	missense	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.751C>T	12.37:g.109935660C>T	ENSP00000340596:p.Arg251Trp		108420043	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	19.97	3.924522	0.73213	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.46819	1.19;0.86;1.45;1.19	5.95	5.05	0.67936	.	0.099482	0.64402	D	0.000003	T	0.44265	0.1285	L	0.57536	1.79	0.58432	D	0.999995	P	0.49185	0.92	B	0.38712	0.28	T	0.51585	-0.8687	10	0.72032	D	0.01	-20.4626	13.9029	0.63817	0.2908:0.7092:0.0:0.0	.	251	Q7Z3V4	UBE3B_HUMAN	W	251	ENSP00000391529:R251W;ENSP00000280774:R251W;ENSP00000443131:R251W;ENSP00000340596:R251W	ENSP00000280774:R251W	R	+	1	2	UBE3B	108420043	0.850000	0.29656	0.761000	0.31378	0.964000	0.63967	1.184000	0.32053	1.486000	0.48398	0.585000	0.79938	CGG		0.512	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109935660	C	T	109935660	3	4	61	1	0	0	0	0	1	0	0	0	16920	875	31	1	781	1	UBE3B	12	109935660	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52326	109935660	23916235	8365	16350										
UBE3B	89910	broad.mit.edu	37	chr12	109947484	109947484	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctcctctttcctgaattCttttgtgtttaagatgatct	5	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109947484C>A	ENST00000342494.3	+	16	2301	c.1706C>A	c.(1705-1707)tCt>tAt	p.S569Y	UBE3B_ENST00000280774.5_Missense_Mutation_p.S569Y|UBE3B_ENST00000434735.2_Missense_Mutation_p.S569Y|UBE3B_ENST00000535900.1_Intron	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	569					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S569Y(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TTCCTGAATTCTTTTGTGTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											164	151	155					12																	109947484		2203	4300	6503	108431867	SO:0001583	missense	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1706C>A	12.37:g.109947484C>A	ENSP00000340596:p.Ser569Tyr		108431867	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316185	0.81469	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.44881	1.22;0.91;1.49;1.22	5.81	4.92	0.64577	.	0.263303	0.44483	D	0.000459	T	0.34803	0.0910	N	0.22421	0.69	0.49389	D	0.999788	B	0.21381	0.055	B	0.28849	0.095	T	0.14531	-1.0469	10	0.54805	T	0.06	-17.7548	15.868	0.79080	0.0:0.864:0.1359:0.0	.	569	Q7Z3V4	UBE3B_HUMAN	Y	569	ENSP00000391529:S569Y;ENSP00000280774:S569Y;ENSP00000443131:S569Y;ENSP00000340596:S569Y	ENSP00000280774:S569Y	S	+	2	0	UBE3B	108431867	1.000000	0.71417	0.998000	0.56505	0.868000	0.49771	4.649000	0.61433	1.463000	0.47967	-0.133000	0.14855	TCT		0.403	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		A	109947484	C	A	109947484	3	1	61	1	0	0	0	0	1	0	0	0	16920	913	32	2	1760	2	UBE3B	12	109947484	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11824	109947484	23904411	8366	16351										
UBE3B	89910	broad.mit.edu	37	chr12	109964214	109964214	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccattcctgttacaaatGaaaataagtgagtatagcaa	7	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109964214G>T	ENST00000342494.3	+	24	3215	c.2620G>T	c.(2620-2622)Gaa>Taa	p.E874*	UBE3B_ENST00000434735.2_Nonsense_Mutation_p.E874*	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	874	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.E874*(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TGTTACAAATGAAAATAAGTG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											105	101	103					12																	109964214		2203	4300	6503	108448597	SO:0001587	stop_gained	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.2620G>T	12.37:g.109964214G>T	ENSP00000340596:p.Glu874*		108448597	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Nonsense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	50	16.147771	0.99855	.	.	ENSG00000151148	ENST00000434735;ENST00000342494;ENST00000538070	.	.	.	5.71	5.71	0.89125	.	0.045759	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-4.7963	18.828	0.92125	0.0:0.0:1.0:0.0	.	.	.	.	X	874;874;169	.	ENSP00000340596:E874X	E	+	1	0	UBE3B	108448597	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.229000	0.95273	2.697000	0.92050	0.655000	0.94253	GAA		0.393	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109964214	G	T	109964214	4	4	61	1	0	0	0	0	0	1	0	0	16920	1291	45	2	2706	2	UBE3B	12	109964214	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16730	109964214	23887681	8367	16352										
MMAB	326625	broad.mit.edu	37	chr12	109994869	109994869	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggccgatgggtcatttttCatgtatattttctcttgatt	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:109994869C>A	ENST00000545712.2	-	9	1110	c.717G>T	c.(715-717)atG>atT	p.M239I	MMAB_ENST00000540016.1_Missense_Mutation_p.M187I|MMAB_ENST00000266839.5_Missense_Mutation_p.M148I	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	239			M -> K (common polymorphism; dbSNP:rs9593). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)	p.M239I(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGTCATTTTTCATGTATATTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											124	110	114					12																	109994869		2203	4300	6503	108479252	SO:0001583	missense	326625			AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"ATP:cob(I)alamin adenosyltransferase", "cilia and flagella associated protein 23"	607568	"methylmalonic aciduria (cobalamin deficiency) type B"			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.717G>T	12.37:g.109994869C>A	ENSP00000445920:p.Met239Ile		108479252	C5HU05|Q9BSH0	Missense_Mutation	SNP	ENST00000545712.2	37	CCDS9131.1	.	.	.	.	.	.	.	.	.	.	C	9.394	1.076185	0.20227	.	.	ENSG00000139428	ENST00000545712;ENST00000266839	D;D	0.89343	-2.5;-2.42	5.43	4.53	0.55603	Adenosylcobalamin biosynthesis, ATP:cob(I)alamin adenosyltransferase-like (2);	0.390145	0.26616	N	0.023396	T	0.71204	0.3312	N	0.01779	-0.725	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.60566	-0.7238	10	0.38643	T	0.18	-9.3558	8.9329	0.35682	0.0:0.8374:0.0:0.1626	.	239	Q96EY8	MMAB_HUMAN	I	239;148	ENSP00000445920:M239I;ENSP00000266839:M148I	ENSP00000266839:M148I	M	-	3	0	MMAB	108479252	0.973000	0.33851	0.987000	0.45799	0.216000	0.24613	1.017000	0.29989	2.527000	0.85204	0.561000	0.74099	ATG		0.517	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2			A	109994869	C	A	109994869	3	1	61	1	0	0	0	0	1	0	0	0	9670	826	29	2	39	2	MMAB	12	109994869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30655	109994869	23857026	8368	16353										
TRPV4	59341	broad.mit.edu	37	chr12	110230181	110230181	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcacctgaagcgtagccGatcatgaagagcaagtagac	11	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110230181G>T	ENST00000418703.2	-	11	1972	c.1878C>A	c.(1876-1878)atC>atA	p.I626I	TRPV4_ENST00000541794.1_Silent_p.I579I|TRPV4_ENST00000261740.2_Silent_p.I626I|TRPV4_ENST00000392719.2_Silent_p.I579I|TRPV4_ENST00000536838.1_Silent_p.I592I|TRPV4_ENST00000544971.1_Silent_p.I519I|TRPV4_ENST00000346520.2_Silent_p.I566I|TRPV4_ENST00000537083.1_Silent_p.I566I	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	626					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)	p.I626I(3)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						AAGCGTAGCCGATCATGAAGA	0.532																																																3	Substitution - coding silent(3)	skin(2)|large_intestine(1)	12											69	67	67					12																	110230181		2203	4300	6503	108714564	SO:0001819	synonymous_variant	59341			AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1878C>A	12.37:g.110230181G>T			108714564	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																				0.532	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		T	110230181	G	T	110230181	2	4	61	1	0	0	0	0	0	0	0	1	16638	1048	37	2		2	TRPV4	12	110230181	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	235312	110230181	23621714	8369	16354										
GIT2	9815	broad.mit.edu	37	chr12	110370842	110370842	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggcagccttggcgatgtCgtacgcacactggatgacct	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110370842C>T	ENST00000355312.3	-	20	2220	c.2221G>A	c.(2221-2223)Gac>Aac	p.D741N	GIT2_ENST00000338373.5_Missense_Mutation_p.D643N|GIT2_ENST00000551209.1_Missense_Mutation_p.D690N|GIT2_ENST00000343646.5_Missense_Mutation_p.D631N|GIT2_ENST00000356259.4_Missense_Mutation_p.D628N|GIT2_ENST00000548655.1_5'Flank|GIT2_ENST00000457474.2_Missense_Mutation_p.D663N|GIT2_ENST00000354574.4_Missense_Mutation_p.D663N|GIT2_ENST00000361006.5_Missense_Mutation_p.D711N|GIT2_ENST00000360185.4_Missense_Mutation_p.D691N|GIT2_ENST00000553118.1_Missense_Mutation_p.D613N	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	741					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.D741N(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TTGGCGATGTCGTACGCACAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12											162	135	144					12																	110370842		2203	4300	6503	108855225	SO:0001583	missense	9815			AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.2221G>A	12.37:g.110370842C>T	ENSP00000347464:p.Asp741Asn		108855225	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Missense_Mutation	SNP	ENST00000355312.3	37	CCDS9138.1	.	.	.	.	.	.	.	.	.	.	C	37	6.124210	0.97305	.	.	ENSG00000139436	ENST00000355312;ENST00000360185;ENST00000354574;ENST00000338373;ENST00000343646;ENST00000356259;ENST00000457474;ENST00000361006;ENST00000553118;ENST00000551209	T;T;T;T;T;T;T;T;T;T	0.80909	-1.18;-1.4;-1.16;-1.07;-1.3;-1.02;-1.12;-1.12;-1.18;-1.43	5.53	5.53	0.82687	G protein-coupled receptor kinase-interacting protein 1 C term (1);	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.81942	2.565	0.45330	D	0.998326	D;D;D;D;D	0.89917	0.998;0.989;1.0;0.991;0.977	D;D;D;D;P	0.85130	0.969;0.969;0.997;0.963;0.866	D	0.91207	0.4996	10	0.72032	D	0.01	.	18.4469	0.90688	0.0:1.0:0.0:0.0	.	663;663;613;741;711	Q14161-10;F8WAK2;Q14161-11;Q14161;Q14161-5	.;.;.;GIT2_HUMAN;.	N	741;691;663;643;631;628;663;711;613;690	ENSP00000347464:D741N;ENSP00000353312:D691N;ENSP00000346585:D663N;ENSP00000340342:D643N;ENSP00000340938:D631N;ENSP00000348595:D628N;ENSP00000391813:D663N;ENSP00000354282:D711N;ENSP00000447465:D613N;ENSP00000448832:D690N	ENSP00000340342:D643N	D	-	1	0	GIT2	108855225	1.000000	0.71417	0.971000	0.41717	0.981000	0.71138	7.818000	0.86416	2.593000	0.87608	0.455000	0.32223	GAC		0.572	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		T	110370842	C	T	110370842	3	4	61	1	0	0	0	0	1	0	0	0	6417	884	31	1	62	1	GIT2	12	110370842	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140661	110370842	23481053	8370	16355										
GIT2	9815	broad.mit.edu	37	chr12	110377017	110377017	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtgttgtcgtagtcactCtcaggtgtgctgttctgctt	13	8	3	0	rs541055586		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110377017C>T	ENST00000355312.3	-	17	1766	c.1767G>A	c.(1765-1767)gaG>gaA	p.E589E	TCHP_ENST00000550780.1_Intron|GIT2_ENST00000338373.5_Silent_p.E491E|GIT2_ENST00000551209.1_Silent_p.E538E|GIT2_ENST00000343646.5_Silent_p.E479E|GIT2_ENST00000356259.4_Silent_p.E476E|GIT2_ENST00000548655.1_5'UTR|GIT2_ENST00000457474.2_Silent_p.E511E|GIT2_ENST00000354574.4_Silent_p.E511E|GIT2_ENST00000361006.5_Silent_p.E559E|GIT2_ENST00000360185.4_Silent_p.E539E|GIT2_ENST00000553118.1_Silent_p.E461E	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	589					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.E589E(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						CGTAGTCACTCTCAGGTGTGC	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	12											300	237	259					12																	110377017		2203	4300	6503	108861400	SO:0001819	synonymous_variant	9815			AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1767G>A	12.37:g.110377017C>T			108861400	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	37	CCDS9138.1																																																																																				0.567	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		T	110377017	C	T	110377017	2	4	61	1	0	0	0	0	0	0	0	1	6417	912	32	3		3	GIT2	12	110377017	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6175	110377017	23474878	8371	16356										
ANKRD13A	88455	broad.mit.edu	37	chr12	110449927	110449927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgtgacaaaagaaaatCgccagggatggacaggtaag	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110449927C>T	ENST00000261739.4	+	2	380	c.214C>T	c.(214-216)Cgc>Tgc	p.R72C	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	72						endosome (GO:0005768)|plasma membrane (GO:0005886)		p.R72C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						AAAAGAAAATCGCCAGGGATG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	73	75					12																	110449927		2203	4300	6503	108934310	SO:0001583	missense	88455			AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.214C>T	12.37:g.110449927C>T	ENSP00000261739:p.Arg72Cys		108934310	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.390313	0.25118	.	.	ENSG00000076513	ENST00000261739	T	0.65178	-0.14	6.17	-0.492	0.12041	Ankyrin repeat-containing domain (3);	0.601650	0.18704	N	0.133517	T	0.51635	0.1686	L	0.49640	1.575	0.09310	N	0.999999	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.06405	0.001;0.001;0.002	T	0.45220	-0.9276	10	0.52906	T	0.07	9.9977	9.9583	0.41680	0.09:0.3437:0.5042:0.0621	.	72;72;72	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	C	72	ENSP00000261739:R72C	ENSP00000261739:R72C	R	+	1	0	ANKRD13A	108934310	0.038000	0.19896	0.017000	0.16124	0.949000	0.60115	0.488000	0.22371	-0.368000	0.08040	0.655000	0.94253	CGC		0.408	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		T	110449927	C	T	110449927	3	4	61	1	0	0	0	0	1	0	0	0	641	884	31	1	220	1	ANKRD13A	12	110449927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72910	110449927	23401968	8372	16357										
ANKRD13A	88455	broad.mit.edu	37	chr12	110461908	110461908	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaagttgttaatggttaCgaagcaaaggtaaaaggaaa	12	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110461908C>T	ENST00000261739.4	+	7	958	c.792C>T	c.(790-792)taC>taT	p.Y264Y		NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	264						endosome (GO:0005768)|plasma membrane (GO:0005886)		p.Y264Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						TTAATGGTTACGAAGCAAAGG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	12											164	181	175					12																	110461908		2203	4300	6503	108946291	SO:0001819	synonymous_variant	88455			AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.792C>T	12.37:g.110461908C>T			108946291	O60736	Silent	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	C	8.325	0.825125	0.16678	.	.	ENSG00000076513	ENST00000547639	.	.	.	6.05	6.05	0.98169	.	.	.	.	.	T	0.60805	0.2297	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58584	-0.7611	4	.	.	.	-23.4219	8.9076	0.35532	0.0:0.8439:0.0:0.1561	.	.	.	.	M	118	.	.	T	+	2	0	ANKRD13A	108946291	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.697000	0.47060	2.878000	0.98634	0.650000	0.86243	ACG		0.343	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		T	110461908	C	T	110461908	2	4	61	1	0	0	0	0	0	0	0	1	641	547	19	1		1	ANKRD13A	12	110461908	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11981	110461908	23389987	8373	16358										
ANKRD13A	88455	broad.mit.edu	37	chr12	110471670	110471670	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgaatcttactatgttcaaGacaatggcagaaatgtgcat	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110471670G>T	ENST00000261739.4	+	13	1583	c.1417G>T	c.(1417-1419)Gac>Tac	p.D473Y	C12orf76_ENST00000546651.2_Intron	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	473						endosome (GO:0005768)|plasma membrane (GO:0005886)		p.D473Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CTATGTTCAAGACAATGGCAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											181	162	168					12																	110471670		2203	4300	6503	108956053	SO:0001583	missense	88455			AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.1417G>T	12.37:g.110471670G>T	ENSP00000261739:p.Asp473Tyr		108956053	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	G	34	5.320690	0.95682	.	.	ENSG00000076513	ENST00000261738;ENST00000261739;ENST00000547419;ENST00000553251;ENST00000549826	T	0.57907	0.37	5.63	5.63	0.86233	.	0.141387	0.64402	D	0.000004	T	0.68732	0.3033	M	0.68317	2.08	0.80722	D	1	D;D;D	0.62365	0.991;0.991;0.981	P;P;P	0.58721	0.832;0.844;0.656	T	0.71454	-0.4588	10	0.87932	D	0	-2.4762	18.6977	0.91607	0.0:0.0:1.0:0.0	.	472;219;473	B4DYP5;E9PGV0;Q8IZ07	.;.;AN13A_HUMAN	Y	219;473;111;111;111	ENSP00000261739:D473Y	ENSP00000261738:D219Y	D	+	1	0	ANKRD13A	108956053	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.335000	0.65929	2.652000	0.90054	0.655000	0.94253	GAC		0.438	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		T	110471670	G	T	110471670	3	4	61	1	0	0	0	0	1	0	0	0	641	942	33	2	1467	2	ANKRD13A	12	110471670	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9762	110471670	23380225	8374	16359										
C12orf76	400073	broad.mit.edu	37	chr12	110495068	110495069	+	Missense_Mutation	DNP	CC	CC	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctctgcagggaggatgtgCctttcagcaaagttcctctc					rs142398265		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110495068_110495069CC>TA	ENST00000309050.5	-	4	588_589	c.224_225GG>TA	c.(223-225)aGG>aTA	p.R75I	C12orf76_ENST00000548936.1_Intron|C12orf76_ENST00000548191.1_Intron	NM_207435.1	NP_997318.1	Q8N812	CL076_HUMAN	chromosome 12 open reading frame 76	75								p.R75>?(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6						GGAGGATGTGCCTTTCAGCAAA	0.495																																																1	Complex(1)	large_intestine(1)	12																																								108979452	SO:0001583	missense	400073			BC041968	CCDS9141.1	12q24.11	2012-08-16			ENSG00000174456	ENSG00000174456			33790	protein-coding gene	gene with protein product							Standard	NM_207435		Approved	FLJ40142	uc001tqe.2	Q8N812	OTTHUMG00000169315	ENST00000309050.5:c.224_225delinsTA	12.37:g.110495068_110495069delinsTA	ENSP00000308368:p.Arg75Ile		108979451		Missense_Mutation	DNP	ENST00000309050.5	37	CCDS9141.1																																																																																				0.495	C12orf76-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403439.2	NM_207435		TA	110495069	CC	TA	110495068	3	4	61	1	0	0	0	0	1	0	0	0	1719	738	26	3	190	3	C12orf76	12	110495068	Missense_Mutation	DNP	CC	TCGA-AG-A002-01A-01W-A00K-09	23398	110495068	23356827	8375	16360										
ATP2A2	488	broad.mit.edu	37	chr12	110783824	110783824	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttgtccgaaaaccagtcCttgctgaggatgcccccctg	10	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110783824C>A	ENST00000539276.2	+	19	2869	c.2760C>A	c.(2758-2760)tcC>tcA	p.S920S	ATP2A2_ENST00000395494.2_Silent_p.S893S|ATP2A2_ENST00000308664.6_Silent_p.S920S			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	920			S -> Y (in DD; mild/moderate/severe form; one patient with epilepsy).		blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)	p.S920S(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						AAAACCAGTCCTTGCTGAGGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											178	138	152					12																	110783824		2203	4300	6503	109268207	SO:0001819	synonymous_variant	488				CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2760C>A	12.37:g.110783824C>A			109268207	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	37	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	C	3.938	-0.014842	0.07681	.	.	ENSG00000174437	ENST00000548169	.	.	.	6.17	2.12	0.27331	.	.	.	.	.	T	0.51500	0.1678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39603	-0.9606	4	.	.	.	.	4.6528	0.12603	0.2295:0.5093:0.0:0.2612	.	.	.	.	I	811	.	.	L	+	1	0	ATP2A2	109268207	0.352000	0.24895	0.981000	0.43875	0.998000	0.95712	0.128000	0.15810	0.464000	0.27142	0.655000	0.94253	CTT		0.577	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		A	110783824	C	A	110783824	2	1	61	1	0	0	0	0	0	0	0	1	1138	668	24	2		2	ATP2A2	12	110783824	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	288756	110783824	23068071	8376	16361										
C12orf24	29902	broad.mit.edu	37	chr12	110924385	110924385	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttagctcccgttactcacaGaaacagcattacccttgcac	5	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110924385G>T	ENST00000377673.5	+	5	995	c.483G>T	c.(481-483)caG>caT	p.Q161H		NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	161								p.Q161H(1)									GTTACTCACAGAAACAGCATT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											162	168	166					12																	110924385		2203	4300	6503	109408768	SO:0001583	missense	29902			U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.483G>T	12.37:g.110924385G>T	ENSP00000366901:p.Gln161His		109408768	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	37	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058642	0.55325	.	.	ENSG00000204856	ENST00000377673;ENST00000538285;ENST00000548869	T	0.56611	0.45	3.9	3.01	0.34805	.	0.215935	0.23644	N	0.045995	T	0.56124	0.1964	L	0.56769	1.78	0.80722	D	1	P;P;P	0.52061	0.828;0.95;0.899	P;P;P	0.52881	0.474;0.712;0.571	T	0.57347	-0.7827	10	0.66056	D	0.02	-4.7572	7.6795	0.28505	0.1179:0.0:0.8821:0.0	.	161;161;161	B4DJX7;F5GZE4;Q8WUB2	.;.;CL024_HUMAN	H	161;161;67	ENSP00000366901:Q161H	ENSP00000366901:Q161H	Q	+	3	2	C12orf24	109408768	1.000000	0.71417	0.996000	0.52242	0.960000	0.62799	1.299000	0.33424	0.976000	0.38417	0.467000	0.42956	CAG		0.473	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		T	110924385	G	T	110924385	3	4	61	1	0	0	0	0	1	0	0	0	1682	933	33	2	501	2	C12orf24	12	110924385	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	140561	110924385	22927510	8377	16362										
VPS29	51699	broad.mit.edu	37	chr12	110933823	110933823	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaatacatcacctcatcGaagtctcctctcacaatatg	6	12	4	0	rs369133923		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110933823G>A	ENST00000549578.1	-	2	254	c.189C>T	c.(187-189)ttC>ttT	p.F63F	VPS29_ENST00000360579.7_Silent_p.F67F|SNORD50_ENST00000365465.1_RNA|VPS29_ENST00000546588.1_Silent_p.F95F|VPS29_ENST00000552130.2_5'UTR|VPS29_ENST00000551655.1_5'Flank|VPS29_ENST00000549970.1_5'UTR|VPS29_ENST00000447578.2_5'UTR	NM_016226.3	NP_057310.1	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 homolog (S. cerevisiae)	63					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphoserine phosphatase activity (GO:0004647)	p.F63F(1)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						TCACCTCATCGAAGTCTCCTC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	12						G	,	0,3790		0,0,1895	143	127	132		189,201	-5	0.9	12		132	1,8243		0,1,4121	no	coding-synonymous,coding-synonymous	VPS29	NM_016226.3,NM_057180.1	,	0,1,6016	AA,AG,GG		0.0121,0.0,0.0083	,	63/183,67/187	110933823	1,12033	1895	4122	6017	109418206	SO:0001819	synonymous_variant	51699			AF193795	CCDS41832.1, CCDS53832.1, CCDS73525.1	12q24	2006-12-19	2006-12-19			ENSG00000111237			14340	protein-coding gene	gene with protein product		606932	"vacuolar protein sorting 29 (yeast homolog)", "vacuolar protein sorting 29 (yeast)"			11062004	Standard	NM_001282151		Approved	PEP11, DC7, DC15	uc001tqx.3	Q9UBQ0	OTTHUMG00000169527	ENST00000549578.1:c.189C>T	12.37:g.110933823G>A			109418206	Q502Y5|Q6FIF8|Q6IAH3|Q9H0W0|Q9NRP1|Q9NRU7	Silent	SNP	ENST00000549578.1	37	CCDS41832.1	.	.	.	.	.	.	.	.	.	.	G	9.246	1.039560	0.19669	0.0	1.21E-4	ENSG00000111237	ENST00000360579	.	.	.	5.91	-4.98	0.03019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.4894	16.464	0.84073	0.8487:0.0:0.1513:0.0	.	.	.	.	X	80	.	.	R	-	1	2	VPS29	109418206	0.989000	0.36119	0.854000	0.33618	0.971000	0.66376	0.430000	0.21428	-0.888000	0.03956	-0.793000	0.03317	CGA		0.393	VPS29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404623.1			A	110933823	G	A	110933823	2	1	61	1	0	0	0	0	0	0	0	1	17240	1049	37	1		1	VPS29	12	110933823	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9438	110933823	22918072	8378	16363										
RAD9B	144715	broad.mit.edu	37	chr12	110950593	110950593	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttttaaggtattaaaaGaactcataatatatgttttc	4	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110950593G>T	ENST00000392672.4	+	5	497	c.398G>T	c.(397-399)aGa>aTa	p.R133I	RAD9B_ENST00000409246.1_Missense_Mutation_p.R61I|RAD9B_ENST00000409425.1_Missense_Mutation_p.R61I|RAD9B_ENST00000433301.1_Intron|RAD9B_ENST00000409300.1_Missense_Mutation_p.R133I|RAD9B_ENST00000409778.3_Intron	NM_152442.3	NP_689655.3	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	130					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)		p.R133I(1)		endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						GGTATTAAAAGAACTCATAAT	0.269											OREG0022115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											74	62	66					12																	110950593		692	1588	2280	109434976	SO:0001583	missense	144715				CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000392672.4:c.398G>T	12.37:g.110950593G>T	ENSP00000376440:p.Arg133Ile	1431	109434976	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000392672.4	37	CCDS9148.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116992	0.77323	.	.	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	5.74	-1.13	0.09775	.	0.228599	0.42172	D	0.000741	T	0.30885	0.0779	L	0.46157	1.445	0.53688	D	0.999971	P;P	0.52316	0.952;0.952	P;P	0.54815	0.761;0.761	T	0.07908	-1.0748	10	0.87932	D	0	-8.0762	9.9589	0.41684	0.7247:0.0:0.2753:0.0	.	133;130	B4DX60;Q6WBX8	.;RAD9B_HUMAN	I	61;133;133;61	ENSP00000387329:R61I;ENSP00000376440:R133I;ENSP00000386434:R133I;ENSP00000386629:R61I	ENSP00000376440:R133I	R	+	2	0	RAD9B	109434976	1.000000	0.71417	0.740000	0.30986	0.967000	0.64934	1.697000	0.37784	-0.095000	0.12351	0.542000	0.68232	AGA		0.269	RAD9B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328756.2	NM_152442		T	110950593	G	T	110950593	3	4	61	1	0	0	0	0	1	0	0	0	13033	942	33	2	416	2	RAD9B	12	110950593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16770	110950593	22901302	8379	16364										
RAD9B	144715	broad.mit.edu	37	chr12	110956536	110956536	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcagatgagtttgacttCtttcaaattggaatggacac	10	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110956536C>A	ENST00000409778.3	+	5	468	c.444C>A	c.(442-444)ttC>ttA	p.F148L	RAD9B_ENST00000409246.1_Missense_Mutation_p.F145L|RAD9B_ENST00000409425.1_Missense_Mutation_p.F145L|RAD9B_ENST00000392672.4_Missense_Mutation_p.F217L|RAD9B_ENST00000409300.1_Missense_Mutation_p.F217L			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	168					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)		p.F217L(1)|p.F59L(1)		endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						AGTTTGACTTCTTTCAAATTG	0.289																																																2	Substitution - Missense(2)	large_intestine(2)	12											82	82	82					12																	110956536		2203	4299	6502	109440919	SO:0001583	missense	144715				CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.444C>A	12.37:g.110956536C>A	ENSP00000386697:p.Phe148Leu		109440919	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000409778.3	37		.	.	.	.	.	.	.	.	.	.	C	13.61	2.289485	0.40494	.	.	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425;ENST00000409778	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	5.77	4.88	0.63580	.	0.187707	0.47455	D	0.000221	T	0.17704	0.0425	L	0.43152	1.355	0.28873	N	0.894843	B;B;B	0.18166	0.026;0.001;0.001	B;B;B	0.18561	0.022;0.004;0.007	T	0.11421	-1.0588	9	.	.	.	-5.9168	10.0966	0.42480	0.0:0.8455:0.0:0.1545	.	148;217;214	B4DYM6;B4DX60;Q6WBX8	.;.;RAD9B_HUMAN	L	145;217;217;145;148	ENSP00000387329:F145L;ENSP00000376440:F217L;ENSP00000386434:F217L;ENSP00000386629:F145L;ENSP00000386697:F148L	.	F	+	3	2	RAD9B	109440919	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	2.398000	0.44486	1.435000	0.47434	0.460000	0.39030	TTC		0.289	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442		A	110956536	C	A	110956536	3	1	61	1	0	0	0	0	1	0	0	0	13033	912	32	2	677	2	RAD9B	12	110956536	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5943	110956536	22895359	8380	16365										
RAD9B	160760	broad.mit.edu	37	chr12	110969393	110969393	+	3'UTR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcagtgtgctgcaggaaaGaatttaatggaagtgatgcc	13	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110969393G>T	ENST00000354300.3	-	0	6652				RAD9B_ENST00000409246.1_3'UTR|RAD9B_ENST00000409425.1_3'UTR|RAD9B_ENST00000392672.4_Nonsense_Mutation_p.E417*|RAD9B_ENST00000409300.1_3'UTR|RAD9B_ENST00000409778.3_Missense_Mutation_p.K311N	NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)							mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.E417*(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						CTGCAGGAAAGAATTTAATGG	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											97	84	88					12																	110969393		1568	3582	5150	109453776	SO:0001624	3_prime_UTR_variant	144715			AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"T cell activation protein phosphatase 2C"	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.*5449C>A	12.37:g.110969393G>T			109453776	B3KWC5|Q68DZ7|Q6UY82	Nonsense_Mutation	SNP	ENST00000354300.3	37	CCDS9149.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.96|13.96	2.392638|2.392638	0.42410|0.42410	.|.	.|.	ENSG00000151164|ENSG00000151164	ENST00000392672|ENST00000409778	.|T	.|0.19669	.|2.13	4.43|4.43	-5.49|-5.49	0.02584|0.02584	.|.	102.590000|.	0.04352|.	U|.	0.355933|.	.|T	.|0.11793	.|0.0287	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	.|T	.|0.31138	.|-0.9954	.|8	0.39692|0.62326	T|D	0.17|0.03	9.7323|9.7323	4.3078|4.3078	0.10956|0.10956	0.3114:0.0:0.2117:0.4769|0.3114:0.0:0.2117:0.4769	.|.	.|311	.|B4DYM6	.|.	X|N	417|311	.|ENSP00000386697:K311N	ENSP00000376440:E417X|ENSP00000386697:K311N	E|K	+|+	1|3	0|2	RAD9B|RAD9B	109453776|109453776	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.340000|0.340000	0.28889|0.28889	-0.801000|-0.801000	0.04550|0.04550	-1.396000|-1.396000	0.02071|0.02071	-1.853000|-1.853000	0.00566|0.00566	GAA|AAG		0.348	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283		T	110969393	G	T	110969393	1	4	61	0	1	0	0	0	0	0	0	0	13033	943	33	2		2	RAD9B	12	110969393	3'UTR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12857	110969393	22882502	8381	16366										
PPTC7	160760	broad.mit.edu	37	chr12	110989718	110989718	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccgcattaaagtccctgaGaattgagatggatcaactcc	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:110989718G>T	ENST00000354300.3	-	2	567	c.279C>A	c.(277-279)ttC>ttA	p.F93L		NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)	93	PP2C-like.					mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.F93L(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						AAGTCCCTGAGAATTGAGATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											104	93	97					12																	110989718		2203	4300	6503	109474101	SO:0001583	missense	160760			AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"T cell activation protein phosphatase 2C"	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.279C>A	12.37:g.110989718G>T	ENSP00000346255:p.Phe93Leu		109474101	B3KWC5|Q68DZ7|Q6UY82	Missense_Mutation	SNP	ENST00000354300.3	37	CCDS9149.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.868619	0.91587	.	.	ENSG00000196850	ENST00000354300	.	.	.	5.96	5.96	0.96718	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.77598	0.4154	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78804	-0.2060	9	0.72032	D	0.01	-15.9739	13.5885	0.61946	0.0707:0.0:0.9293:0.0	.	93	Q8NI37	PPTC7_HUMAN	L	93	.	ENSP00000346255:F93L	F	-	3	2	PPTC7	109474101	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.586000	0.60984	2.814000	0.96858	0.655000	0.94253	TTC		0.423	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283		T	110989718	G	T	110989718	3	4	61	1	0	0	0	0	1	0	0	0	12447	933	33	2	655	2	PPTC7	12	110989718	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20325	110989718	22862177	8382	16367										
PPP1CC	5501	broad.mit.edu	37	chr12	111160414	111160414	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcggggtcagaccacaaaaGatcacaaagaagaccttgat	9	9	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:111160414G>T	ENST00000335007.5	-	5	800	c.610C>A	c.(610-612)Ctt>Att	p.L204I	PPP1CC_ENST00000546933.1_Missense_Mutation_p.L213I|PPP1CC_ENST00000550991.1_Missense_Mutation_p.L204I|PPP1CC_ENST00000340766.5_Missense_Mutation_p.L204I|PPP1CC_ENST00000551676.1_Missense_Mutation_p.L204I	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	204					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)	p.L204I(1)		central_nervous_system(1)|large_intestine(2)|lung(3)	6						GACCACAAAAGATCACAAAGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											108	101	103					12																	111160414		2203	4300	6503	109644797	SO:0001583	missense	5501				CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9283	protein-coding gene	gene with protein product		176914	"protein phosphatase 1, catalytic subunit, gamma isoform"				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.610C>A	12.37:g.111160414G>T	ENSP00000335084:p.Leu204Ile		109644797		Missense_Mutation	SNP	ENST00000335007.5	37	CCDS9150.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550252	0.65311	.	.	ENSG00000186298	ENST00000335007;ENST00000340766;ENST00000550261;ENST00000553024;ENST00000546933;ENST00000550991;ENST00000551676	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;3.09	5.79	5.79	0.91817	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.116023	0.64402	N	0.000017	T	0.63319	0.2501	M	0.73217	2.22	0.50313	D	0.999868	B	0.31274	0.317	P	0.44447	0.45	T	0.64765	-0.6330	10	0.72032	D	0.01	-4.7656	13.5916	0.61964	0.071:0.0:0.929:0.0	.	204	P36873	PP1G_HUMAN	I	204;204;63;22;213;204;204	ENSP00000335084:L204I;ENSP00000341779:L204I;ENSP00000447122:L213I;ENSP00000448981:L204I;ENSP00000448437:L204I	ENSP00000335084:L204I	L	-	1	0	PPP1CC	109644797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.108000	0.50337	2.899000	0.99337	0.655000	0.94253	CTT		0.433	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1			T	111160414	G	T	111160414	3	4	61	1	0	0	0	0	1	0	0	0	12385	942	33	2	373	2	PPP1CC	12	111160414	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170696	111160414	22691481	8383	16368										
CCDC63	160762	broad.mit.edu	37	chr12	111342432	111342432	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgacctgctgctgttggaGacctacaggcgcatcctgga	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:111342432G>T	ENST00000308208.5	+	11	1625	c.1383G>T	c.(1381-1383)gaG>gaT	p.E461D	CCDC63_ENST00000545036.1_Missense_Mutation_p.E421D|CCDC63_ENST00000552694.1_Missense_Mutation_p.E382D	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	461								p.E461D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TGCTGTTGGAGACCTACAGGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	12											82	80	81					12																	111342432		2203	4300	6503	109826815	SO:0001583	missense	160762			AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1383G>T	12.37:g.111342432G>T	ENSP00000312399:p.Glu461Asp		109826815	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	37	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	g	16.16	3.045192	0.55110	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.33654	1.41;1.4;1.41	4.99	1.57	0.23409	.	0.112392	0.64402	D	0.000013	T	0.51278	0.1665	M	0.77820	2.39	0.18873	N	0.999982	D	0.76494	0.999	D	0.73380	0.98	T	0.31943	-0.9925	10	0.30854	T	0.27	.	5.6415	0.17567	0.4065:0.0:0.5935:0.0	.	461	Q8NA47	CCD63_HUMAN	D	421;461;382	ENSP00000445881:E421D;ENSP00000312399:E461D;ENSP00000450217:E382D	ENSP00000312399:E461D	E	+	3	2	CCDC63	109826815	0.914000	0.31030	0.128000	0.21923	0.114000	0.19823	0.756000	0.26419	0.629000	0.30376	-0.238000	0.12139	GAG		0.597	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		T	111342432	G	T	111342432	3	4	61	1	0	0	0	0	1	0	0	0	2840	933	33	2	1421	2	CCDC63	12	111342432	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	182018	111342432	22509463	8384	16369										
CUX2	23316	broad.mit.edu	37	chr12	111742014	111742014	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgtccccttctccccagCgagctgaggctgcccagcgg	11	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:111742014C>T	ENST00000261726.6	+	10	908	c.754C>T	c.(754-756)Cga>Tga	p.R252*	AC002979.1_ENST00000408459.1_RNA	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	252					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.R252*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						TTCTCCCCAGCGAGCTGAGGC	0.657																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											26	32	30					12																	111742014		2036	4181	6217	110226397	SO:0001630	splice_region_variant	23316			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.754-1C>T	12.37:g.111742014C>T			110226397	A7E2Y4	Nonsense_Mutation	SNP	ENST00000261726.6	37	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	C	37	5.987049	0.97173	.	.	ENSG00000111249	ENST00000261726	.	.	.	4.79	1.27	0.21489	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.2961	13.9261	0.63964	0.5615:0.4385:0.0:0.0	.	.	.	.	X	252	.	.	R	+	1	2	CUX2	110226397	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.481000	0.45215	0.523000	0.28482	0.460000	0.39030	CGA		0.657	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	Nonsense_Mutation	T	111742014	C	T	111742014	5	4	61	1	0	0	0	0	0	0	1	0	4071	782	27	1	792	1	CUX2	12	111742014	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	399582	111742014	22109881	8385	16370										
CUX2	23316	broad.mit.edu	37	chr12	111779793	111779793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccctcgcagcagaccatcGagctcctctccttccagctc	6	20	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:111779793G>A	ENST00000261726.6	+	21	3749	c.3595G>A	c.(3595-3597)Gag>Aag	p.E1199K	RNA5SP373_ENST00000517271.1_RNA	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1199					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.E1199K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						GCAGACCATCGAGCTCCTCTC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	78	73					12																	111779793		2195	4300	6495	110264176	SO:0001583	missense	23316			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3595G>A	12.37:g.111779793G>A	ENSP00000261726:p.Glu1199Lys		110264176	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	37	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	35	5.556105	0.96514	.	.	ENSG00000111249	ENST00000261726	D	0.96554	-4.05	5.1	5.1	0.69264	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96784	0.8950	L	0.57536	1.79	0.80722	D	1	P	0.44690	0.841	P	0.53689	0.732	D	0.96079	0.9052	10	0.34782	T	0.22	-29.9019	18.528	0.90980	0.0:0.0:1.0:0.0	.	1199	O14529	CUX2_HUMAN	K	1199	ENSP00000261726:E1199K	ENSP00000261726:E1199K	E	+	1	0	CUX2	110264176	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.787000	0.99055	2.377000	0.81083	0.462000	0.41574	GAG		0.612	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111779793	G	A	111779793	3	1	61	1	0	0	0	0	1	0	0	0	4071	1059	37	1	3677	1	CUX2	12	111779793	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37779	111779793	22072102	8386	16371										
ATXN2	6311	broad.mit.edu	37	chr12	111951295	111951295	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacccctcccagcagaaactCtgtgatttcgaggatgtcgc	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:111951295C>A	ENST00000377617.3	-	11	2065	c.1904G>T	c.(1903-1905)aGa>aTa	p.R635I	ATXN2_ENST00000608853.1_Missense_Mutation_p.R475I|ATXN2_ENST00000389153.4_Missense_Mutation_p.R370I|ATXN2_ENST00000542287.2_Missense_Mutation_p.R370I|ATXN2_ENST00000550104.1_Missense_Mutation_p.R635I|ATXN2_ENST00000535949.1_Missense_Mutation_p.R346I	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	635	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.R635I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						AGCAGAAACTCTGTGATTTCG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	68	72					12																	111951295		2203	4300	6503	110435678	SO:0001583	missense	6311			U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1904G>T	12.37:g.111951295C>A	ENSP00000366843:p.Arg635Ile		110435678	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.209665|5.209665	0.95069|0.95069	.|.	.|.	ENSG00000204842|ENSG00000204842	ENST00000481331|ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949;ENST00000492467;ENST00000550236	.|T;T	.|0.72394	.|-0.51;-0.65	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.77611	.|0.4156	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.998;0.998;0.995;0.999	.|D;D;D;D	.|0.85130	.|0.991;0.991;0.986;0.997	.|T	.|0.79024	.|-0.1972	.|10	0.87932|0.54805	D|T	0|0.06	-10.9441|-10.9441	19.4538|19.4538	0.94878|0.94878	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|370;635;346;370	.|B3KT59;Q99700;Q24JQ7;F8VQP2	.|.;ATX2_HUMAN;.;.	X|I	19|370;635;635;370;346;25;50	.|ENSP00000366843:R635I;ENSP00000446576:R635I	ENSP00000449850:E19X|ENSP00000366843:R635I	E|R	-|-	1|2	0|0	ATXN2|ATXN2	110435678|110435678	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.733000|5.733000	0.68571|0.68571	2.604000|2.604000	0.88044|0.88044	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.498	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		A	111951295	C	A	111951295	3	1	61	1	0	0	0	0	1	0	0	0	1212	913	32	2	2097	2	ATXN2	12	111951295	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171502	111951295	21900600	8387	16372										
BRAP	8315	broad.mit.edu	37	chr12	112093396	112093396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtgtccttctctatccGaactatcttgttttcccagt	6	12	2	0	rs377591727		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112093396G>A	ENST00000327551.6	-	10	1335	c.1195C>T	c.(1195-1197)Cgg>Tgg	p.R399W	BRAP_ENST00000539060.1_Missense_Mutation_p.R250W|BRAP_ENST00000419234.4_Missense_Mutation_p.R429W			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R429W(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TTCTCTATCCGAACTATCTTG	0.443																																					Pancreas(146;846 1904 7830 25130 26065)											1	Substitution - Missense(1)	large_intestine(1)	12											202	164	177					12																	112093396		2203	4300	6503	110577779	SO:0001583	missense	8315			AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1195C>T	12.37:g.112093396G>A	ENSP00000330813:p.Arg399Trp		110577779	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	37		.	.	.	.	.	.	.	.	.	.	G	25.3	4.621825	0.87460	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.49432	0.78;0.8;0.79	5.16	4.26	0.50523	.	0.162750	0.56097	D	0.000036	T	0.61763	0.2373	M	0.78916	2.43	0.58432	D	0.999997	P;D	0.69078	0.946;0.997	B;P	0.53313	0.18;0.723	T	0.69401	-0.5155	10	0.87932	D	0	-15.2067	15.0653	0.71989	0.0:0.0:0.857:0.143	.	250;429	B4DRM1;Q7Z569	.;BRAP_HUMAN	W	429;250;399;211	ENSP00000403524:R429W;ENSP00000441659:R250W;ENSP00000330813:R399W	ENSP00000330813:R399W	R	-	1	2	BRAP	110577779	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	7.317000	0.79018	1.157000	0.42530	0.561000	0.74099	CGG		0.443	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112093396	G	A	112093396	3	1	61	1	0	0	0	0	1	0	0	0	1500	1057	37	1	505	1	BRAP	12	112093396	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142101	112093396	21758499	8388	16373										
ACAD10	80724	broad.mit.edu	37	chr12	112167698	112167698	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagccatggagaggctgatCgaatggctgcccctccatct	11	14	1	2	rs540444011	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112167698C>T	ENST00000313698.4	+	10	1487	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000392636.2_Silent_p.I46I|ACAD10_ENST00000549590.1_Silent_p.I444I|ACAD10_ENST00000455480.2_Silent_p.I475I	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	444						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.I444I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						AGAGGCTGATCGAATGGCTGC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	12											71	60	64					12																	112167698		2203	4300	6503	110652081	SO:0001819	synonymous_variant	80724			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.1332C>T	12.37:g.112167698C>T			110652081	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Silent	SNP	ENST00000313698.4	37	CCDS31903.1																																																																																				0.557	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		T	112167698	C	T	112167698	2	4	61	1	0	0	0	0	0	0	0	1	108	874	31	1		1	ACAD10	12	112167698	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74302	112167698	21684197	8389	16374										
TMEM116	89894	broad.mit.edu	37	chr12	112375047	112375047	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaatagcagaggtatcagGctgggagggaaaaaaagtat	13	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112375047G>T	ENST00000550831.3	-	6	458	c.90C>A	c.(88-90)agC>agA	p.S30R	TMEM116_ENST00000354825.3_Splice_Site_p.S30R|TMEM116_ENST00000549537.2_5'UTR|TMEM116_ENST00000437003.2_Splice_Site_p.S30R|TMEM116_ENST00000355445.3_Splice_Site_p.S87R|TMEM116_ENST00000552374.2_Splice_Site_p.S122R	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	30						integral component of membrane (GO:0016021)		p.S30R(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						GAGGTATCAGGCTGGGAGGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											102	99	100					12																	112375047		2203	4300	6503	110859430	SO:0001630	splice_region_variant	89894			AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.90-1C>A	12.37:g.112375047G>T			110859430	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	37	CCDS9157.1	.	.	.	.	.	.	.	.	.	.	g	16.18	3.050587	0.55218	.	.	ENSG00000198270	ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	T;T;T;T;T;T	0.40225	1.21;1.21;1.21;1.21;1.21;1.04	4.9	3.05	0.35203	.	0.054274	0.64402	D	0.000001	T	0.54095	0.1837	L	0.59436	1.845	0.39796	D	0.9725	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.85130	0.996;0.974;0.997;0.974	T	0.52011	-0.8632	10	0.31617	T	0.26	.	8.2608	0.31783	0.2556:0.0:0.7444:0.0	.	122;87;122;30	F8VNZ8;G5E985;G3V1W7;Q8NCL8	.;.;.;TM116_HUMAN	R	87;30;30;30;122;122	ENSP00000347620:S87R;ENSP00000346883:S30R;ENSP00000450377:S30R;ENSP00000395861:S30R;ENSP00000447731:S122R;ENSP00000446516:S122R	ENSP00000346883:S30R	S	-	3	2	TMEM116	110859430	1.000000	0.71417	0.990000	0.47175	0.821000	0.46438	2.130000	0.42064	1.075000	0.40932	0.467000	0.42956	AGC		0.408	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341	Missense_Mutation	T	112375047	G	T	112375047	5	4	61	1	0	0	0	0	0	0	1	0	16069	1217	42	2	667	2	TMEM116	12	112375047	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207349	112375047	21476848	8390	16375										
TMEM116	89894	broad.mit.edu	37	chr12	112375987	112375987	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagaaaacaaaggccatttGacaaactcgacaagtataat	7	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112375987G>T	ENST00000550831.3	-	5	435	c.67C>A	c.(67-69)Caa>Aaa	p.Q23K	TMEM116_ENST00000354825.3_Missense_Mutation_p.Q23K|TMEM116_ENST00000549537.2_5'UTR|TMEM116_ENST00000437003.2_Missense_Mutation_p.Q23K|TMEM116_ENST00000355445.3_Missense_Mutation_p.Q80K|TMEM116_ENST00000552374.2_Missense_Mutation_p.Q115K	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	23						integral component of membrane (GO:0016021)		p.Q23K(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						AAGGCCATTTGACAAACTCGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											76	78	77					12																	112375987		2203	4300	6503	110860370	SO:0001583	missense	89894			AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.67C>A	12.37:g.112375987G>T	ENSP00000450377:p.Gln23Lys		110860370	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	37	CCDS9157.1	.	.	.	.	.	.	.	.	.	.	g	13.96	2.391542	0.42410	.	.	ENSG00000198270	ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	T;T;T;T;T;T	0.42131	1.34;1.34;1.34;1.34;1.34;0.98	5.65	2.41	0.29592	.	0.437844	0.22605	N	0.057917	T	0.24044	0.0582	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.17268	0.021;0.001;0.005;0.005	B;B;B;B	0.15484	0.013;0.001;0.002;0.002	T	0.09100	-1.0690	10	0.15066	T	0.55	0.3337	3.8787	0.09068	0.2033:0.0:0.6064:0.1903	.	115;80;115;23	F8VNZ8;G5E985;G3V1W7;Q8NCL8	.;.;.;TM116_HUMAN	K	80;23;23;23;115;115	ENSP00000347620:Q80K;ENSP00000346883:Q23K;ENSP00000450377:Q23K;ENSP00000395861:Q23K;ENSP00000447731:Q115K;ENSP00000446516:Q115K	ENSP00000346883:Q23K	Q	-	1	0	TMEM116	110860370	0.995000	0.38212	0.804000	0.32291	0.758000	0.43043	1.152000	0.31663	1.375000	0.46248	0.467000	0.42956	CAA		0.333	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341		T	112375987	G	T	112375987	3	4	61	1	0	0	0	0	1	0	0	0	16069	1299	45	2	694	2	TMEM116	12	112375987	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	940	112375987	21475908	8391	16376										
NAA25	80018	broad.mit.edu	37	chr12	112486159	112486159	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacttgtgcaaaatgaagaGaattattcagcctgttccta	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112486159G>T	ENST00000261745.4	-	16	2065	c.1817C>A	c.(1816-1818)tCt>tAt	p.S606Y		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	606						cytoplasm (GO:0005737)		p.S606Y(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						AAAATGAAGAGAATTATTCAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	111	114					12																	112486159		2203	4300	6503	110970542	SO:0001583	missense	80018			AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.1817C>A	12.37:g.112486159G>T	ENSP00000261745:p.Ser606Tyr		110970542	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375120	0.82682	.	.	ENSG00000111300	ENST00000261745	T	0.72615	-0.67	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.86628	0.5978	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88211	0.2890	10	0.87932	D	0	-12.1628	19.584	0.95484	0.0:0.0:1.0:0.0	.	606;606	A8K8X0;Q14CX7	.;NAA25_HUMAN	Y	606	ENSP00000261745:S606Y	ENSP00000261745:S606Y	S	-	2	0	NAA25	110970542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.604000	0.88044	0.655000	0.94253	TCT		0.373	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112486159	G	T	112486159	3	4	61	1	0	0	0	0	1	0	0	0	10151	942	33	2	1137	2	NAA25	12	112486159	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110172	112486159	21365736	8392	16377										
TRAFD1	10906	broad.mit.edu	37	chr12	112578959	112578959	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgagagcctttgaatcaGatgttttccacaatagaact	7	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112578959G>T	ENST00000257604.5	+	5	1191	c.574G>T	c.(574-576)Gat>Tat	p.D192Y	TRAFD1_ENST00000412615.2_Missense_Mutation_p.D192Y	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	192					negative regulation of innate immune response (GO:0045824)|response to cytokine (GO:0034097)		metal ion binding (GO:0046872)	p.D192Y(1)		kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						CTTTGAATCAGATGTTTTCCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											49	48	48					12																	112578959		2203	4300	6503	111063342	SO:0001583	missense	10906			AB007447	CCDS9160.1	12q24.13	2013-01-25			ENSG00000135148	ENSG00000135148			24808	protein-coding gene	gene with protein product		613197				12477932	Standard	NM_006700		Approved	FLN29	uc001ttp.3	O14545	OTTHUMG00000169640	ENST00000257604.5:c.574G>T	12.37:g.112578959G>T	ENSP00000257604:p.Asp192Tyr		111063342	A8K5L6|B4DI89	Missense_Mutation	SNP	ENST00000257604.5	37	CCDS9160.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958393	0.53400	.	.	ENSG00000135148	ENST00000412615;ENST00000257604;ENST00000552896	T;T;T	0.03212	4.01;4.01;4.01	5.2	5.2	0.72013	.	0.695263	0.14601	N	0.309604	T	0.10680	0.0261	L	0.57536	1.79	0.25380	N	0.98862	P;D	0.54964	0.904;0.969	P;P	0.51135	0.66;0.563	T	0.03068	-1.1076	10	0.66056	D	0.02	-12.0598	16.4935	0.84208	0.0:0.0:1.0:0.0	.	192;192	F8VNX8;O14545	.;TRAD1_HUMAN	Y	192	ENSP00000396526:D192Y;ENSP00000257604:D192Y;ENSP00000450357:D192Y	ENSP00000257604:D192Y	D	+	1	0	TRAFD1	111063342	0.890000	0.30428	0.187000	0.23214	0.683000	0.39861	5.182000	0.65059	2.812000	0.96745	0.563000	0.77884	GAT		0.473	TRAFD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405214.1	NM_006700		T	112578959	G	T	112578959	3	4	61	1	0	0	0	0	1	0	0	0	16487	942	33	2	588	2	TRAFD1	12	112578959	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92800	112578959	21272936	8393	16378										
C12orf51	283450	broad.mit.edu	37	chr12	112654696	112654696	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggtgtctccataggaaacGatttcaatttcccagtaaaa	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112654696G>A	ENST00000430131.2	-	46	7145	c.6000C>T	c.(5998-6000)atC>atT	p.I2000I	HECTD4_ENST00000377560.5_Silent_p.I2250I|HECTD4_ENST00000550722.1_Silent_p.I2276I			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2000					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I2000I(1)|p.I2250I(1)									CATAGGAAACGATTTCAATTT	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	12											82	79	80					12																	112654696		1881	4119	6000	111139079	SO:0001819	synonymous_variant	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.6000C>T	12.37:g.112654696G>A			111139079	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	G	7.712	0.695384	0.15106	.	.	ENSG00000173064	ENST00000550968	.	.	.	5.81	-2.65	0.06095	.	.	.	.	.	T	0.38295	0.1035	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32375	-0.9909	4	.	.	.	.	1.042	0.01561	0.2983:0.095:0.2412:0.3655	.	.	.	.	L	167	.	.	S	-	2	0	C12orf51	111139079	0.993000	0.37304	0.975000	0.42487	0.753000	0.42808	0.467000	0.22035	-0.331000	0.08501	-1.707000	0.00718	TCG		0.493	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112654696	G	A	112654696	2	1	61	1	0	0	0	0	0	0	0	1	1700	1048	37	1		1	C12orf51	12	112654696	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75737	112654696	21197199	8394	16379										
C12orf51	283450	broad.mit.edu	37	chr12	112684854	112684854	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagggtttctgaataagaGaattcacttcttgtaggaac	11	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112684854G>T	ENST00000430131.2	-	28	4243	c.3098C>A	c.(3097-3099)tCt>tAt	p.S1033Y	HECTD4_ENST00000377560.5_Missense_Mutation_p.S1283Y|HECTD4_ENST00000550722.1_Missense_Mutation_p.S1309Y			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1033					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S1033Y(1)|p.S1283Y(1)									CTGAATAAGAGAATTCACTTC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	12											70	66	67					12																	112684854		1844	4084	5928	111169237	SO:0001583	missense	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.3098C>A	12.37:g.112684854G>T	ENSP00000404379:p.Ser1033Tyr		111169237	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	G	17.00	3.276361	0.59649	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51817	0.69;0.69;0.69	5.72	5.72	0.89469	.	.	.	.	.	T	0.39036	0.1063	N	0.19112	0.55	0.54753	D	0.999983	P	0.41041	0.736	B	0.38712	0.28	T	0.40997	-0.9533	9	0.87932	D	0	.	19.8937	0.96942	0.0:0.0:1.0:0.0	.	1033	Q9Y4D8	K0614_HUMAN	Y	1283;1033;1309	ENSP00000366783:S1283Y;ENSP00000404379:S1033Y;ENSP00000449784:S1309Y	ENSP00000366783:S1283Y	S	-	2	0	C12orf51	111169237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.545000	0.60698	2.716000	0.92895	0.650000	0.86243	TCT		0.393	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112684854	G	T	112684854	3	4	61	1	0	0	0	0	1	0	0	0	1700	942	33	2	9084	2	C12orf51	12	112684854	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30158	112684854	21167041	8395	16380										
RPL6	6128	broad.mit.edu	37	chr12	112843733	112843733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcttgaagtaagcatcaGtaagatgttttgggattttt	9	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112843733G>A	ENST00000424576.2	-	6	823	c.638C>T	c.(637-639)aCt>aTt	p.T213I	RPL6_ENST00000202773.9_Missense_Mutation_p.T213I	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	213					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.T213I(1)		cervix(1)|large_intestine(6)|lung(3)	10						GTAAGCATCAGTAAGATGTTT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	67	66					12																	112843733		2203	4297	6500	111328116	SO:0001583	missense	6128			X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"L ribosomal proteins"	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.638C>T	12.37:g.112843733G>A	ENSP00000403172:p.Thr213Ile		111328116	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494199	0.64186	.	.	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.33654	1.4;1.4	5.05	4.15	0.48705	Translation protein SH3-like, subgroup (1);	0.092162	0.64402	D	0.000001	T	0.54711	0.1875	M	0.89785	3.06	0.34808	D	0.737478	P	0.45715	0.865	P	0.48089	0.566	T	0.74383	-0.3683	10	0.72032	D	0.01	.	13.3275	0.60467	0.0:0.0:0.7129:0.2871	.	213	Q02878	RL6_HUMAN	I	213;213;153	ENSP00000202773:T213I;ENSP00000403172:T213I	ENSP00000202773:T213I	T	-	2	0	RPL6	111328116	1.000000	0.71417	0.889000	0.34880	0.966000	0.64601	3.079000	0.50104	1.097000	0.41459	0.591000	0.81541	ACT		0.418	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1			A	112843733	G	A	112843733	3	1	61	1	0	0	0	0	1	0	0	0	13635	1029	36	3	236	3	RPL6	12	112843733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	158879	112843733	21008162	8396	16381										
PTPN11	5781	broad.mit.edu	37	chr12	112942550	112942550	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtgggcctgatgcaacaGcagaaaagtttcagatgaga	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:112942550G>T	ENST00000351677.2	+	15	1962	c.1764G>T	c.(1762-1764)caG>caT	p.Q588H		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	592					abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.Q588H(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TGATGCAACAGCAGAAAAGTT	0.368			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	12											55	51	52					12																	112942550		2203	4300	6503	111426933	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1764G>T	12.37:g.112942550G>T	ENSP00000340944:p.Gln588His		111426933	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583432	0.86748	.	.	ENSG00000179295	ENST00000351677	T	0.10668	2.85	5.65	5.65	0.86999	.	0.059730	0.64402	D	0.000002	T	0.15349	0.0370	N	0.08118	0	0.80722	D	1	D	0.60575	0.988	D	0.72338	0.977	T	0.15321	-1.0441	10	0.66056	D	0.02	.	12.9894	0.58610	0.0736:0.0:0.9264:0.0	.	588	Q06124-2	.	H	588	ENSP00000340944:Q588H	ENSP00000340944:Q588H	Q	+	3	2	PTPN11	111426933	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.620000	0.67736	2.647000	0.89833	0.650000	0.86243	CAG		0.368	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112942550	G	T	112942550	3	4	61	1	0	0	0	0	1	0	0	0	12815	962	34	2	1822	2	PTPN11	12	112942550	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98817	112942550	20909345	8397	16382										
RPH3A	22895	broad.mit.edu	37	chr12	113327845	113327845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagatgaaacgtgctgggaCcaccgggtcagcccgaggca	14	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113327845C>T	ENST00000389385.4	+	18	2077	c.1580C>T	c.(1579-1581)aCc>aTc	p.T527I	RPH3A_ENST00000447659.2_Missense_Mutation_p.T478I|RPH3A_ENST00000543106.2_Missense_Mutation_p.T527I|RPH3A_ENST00000415485.3_Missense_Mutation_p.T527I|RPH3A_ENST00000548866.1_Missense_Mutation_p.T478I|RPH3A_ENST00000420983.2_Missense_Mutation_p.T527I|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000551052.1_Missense_Mutation_p.T523I	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	527					intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)	p.T523I(1)		breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CGTGCTGGGACCACCGGGTCA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	12											186	191	189					12																	113327845		2203	4300	6503	111812228	SO:0001583	missense	22895			AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1580C>T	12.37:g.113327845C>T	ENSP00000374036:p.Thr527Ile		111812228	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.628341	0.28978	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983;ENST00000549913	T;T;T;T;T;T;T	0.62788	0.01;0.01;0.01;0.01;0.01;0.0;0.01	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000006	T	0.58595	0.2133	L	0.47716	1.5	0.80722	D	1	B;B;B;B	0.31680	0.335;0.23;0.23;0.335	B;B;B;B	0.32022	0.139;0.085;0.085;0.139	T	0.58607	-0.7607	10	0.44086	T	0.13	.	18.0793	0.89438	0.0:1.0:0.0:0.0	.	478;527;527;523	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	I	527;527;478;523;527;478;527;179	ENSP00000440384:T527I;ENSP00000374036:T527I;ENSP00000413254:T478I;ENSP00000448297:T523I;ENSP00000405357:T527I;ENSP00000450347:T478I;ENSP00000408889:T527I	ENSP00000374036:T527I	T	+	2	0	RPH3A	111812228	1.000000	0.71417	0.999000	0.59377	0.046000	0.14306	4.376000	0.59556	2.625000	0.88918	0.655000	0.94253	ACC		0.493	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		T	113327845	C	T	113327845	3	4	61	1	0	0	0	0	1	0	0	0	13588	507	18	3	1642	3	RPH3A	12	113327845	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385295	113327845	20524050	8398	16383										
OAS3	4940	broad.mit.edu	37	chr12	113398993	113398993	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcggaggaacttcatgaAcattcgccctgtcaagctga	11	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113398993A>G	ENST00000228928.7	+	8	1954	c.1775A>G	c.(1774-1776)aAc>aGc	p.N592S	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	592	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)	p.N592S(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						AACTTCATGAACATTCGCCCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											60	63	62					12																	113398993		2026	4191	6217	111883376	SO:0001583	missense	4940			AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"2'-5'-oligoadenylate synthetase 3 (100 kD)"			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1775A>G	12.37:g.113398993A>G	ENSP00000228928:p.Asn592Ser		111883376	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.804246	0.50315	.	.	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.08193	3.12	4.64	3.51	0.40186	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.21962	0.0529	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.00626	-1.1638	9	0.44086	T	0.13	.	6.7037	0.23238	0.8928:0.0:0.1072:0.0	.	592	Q9Y6K5	OAS3_HUMAN	S	592;591	ENSP00000228928:N592S	ENSP00000228928:N592S	N	+	2	0	OAS3	111883376	0.005000	0.15991	0.945000	0.38365	0.548000	0.35241	1.151000	0.31651	0.813000	0.34350	0.533000	0.62120	AAC		0.582	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			G	113398993	A	G	113398993	3	3	61	1	0	0	0	0	1	0	0	0	10832	43	2	4	1805	4	OAS3	12	113398993	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	71148	113398993	20452902	8399	16384										
OAS2	4939	broad.mit.edu	37	chr12	113446959	113446959	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaccgttggtgttggcatCttctggcaaaagaagcaaag	14	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113446959C>A	ENST00000342315.4	+	10	2177	c.1963C>A	c.(1963-1965)Ctt>Att	p.L655I	OAS2_ENST00000392583.2_Missense_Mutation_p.L655I|RP1-71H24.1_ENST00000552784.1_RNA	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	655	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.L655I(1)		NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GTGTTGGCATCTTCTGGCAAA	0.512																																					Pancreas(199;709 2232 18410 33584 35052)											1	Substitution - Missense(1)	large_intestine(1)	12											260	245	250					12																	113446959		2203	4300	6503	111931342	SO:0001583	missense	4939			M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1963C>A	12.37:g.113446959C>A	ENSP00000342278:p.Leu655Ile		111931342	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	37	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	15.50	2.851884	0.51270	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.46063	0.88;0.88	4.39	1.38	0.22167	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	0.000000	0.33235	N	0.005127	T	0.46833	0.1413	L	0.56199	1.76	0.09310	N	1	D;D	0.63046	0.992;0.99	P;P	0.61477	0.889;0.822	T	0.22800	-1.0206	10	0.42905	T	0.14	-27.2982	3.7912	0.08721	0.1909:0.5973:0.0:0.2118	.	655;655	P29728;P29728-2	OAS2_HUMAN;.	I	655	ENSP00000342278:L655I;ENSP00000376362:L655I	ENSP00000342278:L655I	L	+	1	0	OAS2	111931342	0.043000	0.20138	0.388000	0.26195	0.884000	0.51177	1.296000	0.33389	0.484000	0.27630	0.655000	0.94253	CTT		0.512	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			A	113446959	C	A	113446959	3	1	61	1	0	0	0	0	1	0	0	0	10831	913	32	2	2072	2	OAS2	12	113446959	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47966	113446959	20404936	8400	16385										
RASAL1	8437	broad.mit.edu	37	chr12	113556972	113556972	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcccaccatgtcccagtcCcagagctccacccgcagtgg	9	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113556972C>A	ENST00000261729.5	-	8	918	c.603G>T	c.(601-603)tgG>tgT	p.W201C	RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000446861.3_Missense_Mutation_p.W201C|RASAL1_ENST00000546530.1_Missense_Mutation_p.W201C|RASAL1_ENST00000548055.1_Missense_Mutation_p.W201C			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	201	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)	p.W201C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TGTCCCAGTCCCAGAGCTCCA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	12											104	91	95					12																	113556972		2203	4300	6503	112041355	SO:0001583	missense	8437			AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.603G>T	12.37:g.113556972C>A	ENSP00000261729:p.Trp201Cys		112041355	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.527331	0.85706	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	5.55	5.55	0.83447	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.062215	0.64402	D	0.000002	D	0.90672	0.7074	M	0.82923	2.615	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;0.998;0.998;0.998;0.981;0.998;1.0	D;D;D;D;P;D;D	0.83275	0.974;0.974;0.956;0.974;0.905;0.98;0.996	D	0.91646	0.5331	10	0.87932	D	0	.	18.2814	0.90099	0.0:1.0:0.0:0.0	.	201;201;201;213;201;201;201	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	C	201	ENSP00000450244:W201C;ENSP00000261729:W201C;ENSP00000395920:W201C;ENSP00000448510:W201C	ENSP00000261729:W201C	W	-	3	0	RASAL1	112041355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.389000	0.79806	2.627000	0.88993	0.561000	0.74099	TGG		0.607	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		A	113556972	C	A	113556972	3	1	61	1	0	0	0	0	1	0	0	0	13100	624	22	2	1871	2	RASAL1	12	113556972	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110013	113556972	20294923	8401	16386										
C12orf52	84934	broad.mit.edu	37	chr12	113629616	113629616	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaccaaagcccccttgGaaatgatactctttcatcag	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113629616G>T	ENST00000548278.1	+	4	1496	c.804G>T	c.(802-804)tgG>tgT	p.W268C	C12orf52_ENST00000552495.1_Missense_Mutation_p.W292C|RP11-545P7.4_ENST00000552525.1_RNA|C12orf52_ENST00000549621.1_Missense_Mutation_p.W268C	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		268	Interaction with tubulin.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)	p.W268C(1)		large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						AGCCCCCTTGGAAATGATACT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12											38	42	41					12																	113629616		2200	4297	6497	112113999	SO:0001583	missense	84934																														ENST00000548278.1:c.804G>T	12.37:g.113629616G>T	ENSP00000449841:p.Trp268Cys		112113999	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	37	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242252	0.58995	.	.	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000266813	T;T;T	0.60299	0.33;0.33;0.2	4.65	4.65	0.58169	.	0.378754	0.20555	N	0.090025	T	0.72961	0.3526	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75379	-0.3338	10	0.87932	D	0	-9.6299	12.8999	0.58119	0.0:0.0:1.0:0.0	.	292;268	F8VRG5;Q96K30	.;RITA_HUMAN	C	268;268;292;268;265	ENSP00000448289:W268C;ENSP00000449841:W268C;ENSP00000448680:W292C	ENSP00000266813:W265C	W	+	3	0	C12orf52	112113999	1.000000	0.71417	0.988000	0.46212	0.719000	0.41307	5.019000	0.64060	2.404000	0.81709	0.655000	0.94253	TGG		0.592	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1			T	113629616	G	T	113629616	3	4	61	1	0	0	0	0	1	0	0	0	1701	1183	41	2	810	2	C12orf52	12	113629616	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72644	113629616	20222279	8402	16387										
IQCD	115811	broad.mit.edu	37	chr12	113645763	113645763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgttggatgccacatacGacagcaaggtcaccagctcc	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113645763G>A	ENST00000416617.2	-	2	399	c.209C>T	c.(208-210)tCg>tTg	p.S70L	IQCD_ENST00000546692.1_Missense_Mutation_p.S70L|IQCD_ENST00000299732.2_Missense_Mutation_p.S70L			Q96DY2	IQCD_HUMAN	IQ motif containing D	70								p.S70L(1)		endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TGCCACATACGACAGCAAGGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											264	221	236					12																	113645763		2203	4300	6503	112130146	SO:0001583	missense	115811			BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 10"					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.209C>T	12.37:g.113645763G>A	ENSP00000400669:p.Ser70Leu		112130146	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	37		.	.	.	.	.	.	.	.	.	.	G	8.148	0.786769	0.16189	.	.	ENSG00000166578	ENST00000299732;ENST00000416617;ENST00000546692;ENST00000392574	T;T;T	0.09538	2.97;2.97;2.97	4.58	2.63	0.31362	.	0.530546	0.17771	N	0.162586	T	0.26122	0.0637	M	0.69823	2.125	0.09310	N	0.999996	D;D	0.89917	1.0;0.996	D;P	0.67900	0.954;0.707	T	0.03576	-1.1023	10	0.42905	T	0.14	-1.6489	8.6645	0.34112	0.0:0.3143:0.5238:0.1619	.	70;70	F8VZV9;Q96DY2-2	.;.	L	70	ENSP00000299732:S70L;ENSP00000400669:S70L;ENSP00000446623:S70L	ENSP00000299732:S70L	S	-	2	0	IQCD	112130146	0.983000	0.35010	0.178000	0.23040	0.046000	0.14306	2.216000	0.42871	0.488000	0.27723	0.563000	0.77884	TCG		0.537	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451		A	113645763	G	A	113645763	3	1	61	1	0	0	0	0	1	0	0	0	7826	1059	37	1	842	1	IQCD	12	113645763	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16147	113645763	20206132	8403	16388										
TPCN1	53373	broad.mit.edu	37	chr12	113698285	113698285	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaattaccaagaggcagcAatctacctccaggtgagtat	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:113698285A>C	ENST00000335509.6	+	3	539	c.225A>C	c.(223-225)gcA>gcC	p.A75A	TPCN1_ENST00000392569.4_Silent_p.A7A|TPCN1_ENST00000541517.1_Silent_p.A147A|TPCN1_ENST00000550785.1_Silent_p.A147A	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	75					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)	p.A75A(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						AAGAGGCAGCAATCTACCTCC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	12											52	50	51					12																	113698285		2203	4300	6503	112182668	SO:0001819	synonymous_variant	53373			AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.225A>C	12.37:g.113698285A>C			112182668	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																				0.587	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		C	113698285	A	C	113698285	2	2	61	1	0	0	0	0	0	0	0	1	16435	117	5	4		4	TPCN1	12	113698285	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52522	113698285	20153610	8404	16389										
TBX5	6910	broad.mit.edu	37	chr12	114841671	114841671	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggctccagaggcgtgtgCgccaggccaaagccctcgtc	13	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:114841671C>T	ENST00000310346.4	-	2	699	c.33G>A	c.(31-33)gcG>gcA	p.A11A	TBX5_ENST00000349716.5_Intron|TBX5_ENST00000405440.2_Silent_p.A11A|TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000526441.1_Silent_p.A11A	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	11				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.A11A(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GAGGCGTGTGCGCCAGGCCAA	0.697																																					NSCLC(152;1358 1980 4050 23898 40356)											1	Substitution - coding silent(1)	large_intestine(1)	12											25	30	28					12																	114841671		2202	4299	6501	113326054	SO:0001819	synonymous_variant	6910			U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.33G>A	12.37:g.114841671C>T			113326054	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	37	CCDS9173.1																																																																																				0.697	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		T	114841671	C	T	114841671	2	4	61	1	0	0	0	0	0	0	0	1	15700	755	27	1		1	TBX5	12	114841671	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1143386	114841671	19010224	8405	16390										
TBX3	6926	broad.mit.edu	37	chr12	115120687	115120687	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagttctttagcctccaGgtgcaccttggggtcgtcct	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:115120687G>T	ENST00000257566.3	-	1	708	c.319C>A	c.(319-321)Ctg>Atg	p.L107M	TBX3_ENST00000349155.2_Missense_Mutation_p.L107M	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	107					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L107M(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TTAGCCTCCAGGTGCACCTTG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	12											48	50	50					12																	115120687		2203	4300	6503	113605070	SO:0001583	missense	6926			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.319C>A	12.37:g.115120687G>T	ENSP00000257566:p.Leu107Met		113605070	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	G	19.50	3.838926	0.71373	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.93859	-3.3;-3.3	5.32	5.32	0.75619	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.98349	0.9452	H	0.98833	4.345	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.999	D	0.99795	1.1033	10	0.87932	D	0	.	19.0084	0.92861	0.0:0.0:1.0:0.0	.	107;107;107	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	M	107	ENSP00000257567:L107M;ENSP00000257566:L107M	ENSP00000257566:L107M	L	-	1	2	TBX3	113605070	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.486000	0.60286	2.489000	0.83994	0.655000	0.94253	CTG		0.602	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		T	115120687	G	T	115120687	3	4	61	1	0	0	0	0	1	0	0	0	15698	991	35	2	1944	2	TBX3	12	115120687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	279016	115120687	18731208	8406	16391										
MED13L	23389	broad.mit.edu	37	chr12	116446735	116446735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctccatgcataattcttCggccacagagggcctatggt	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:116446735C>T	ENST00000281928.3	-	10	1689	c.1483G>A	c.(1483-1485)Gaa>Aaa	p.E495K		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	495						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.E495K(1)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CATAATTCTTCGGCCACAGAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	12											197	187	191					12																	116446735		2203	4300	6503	114931118	SO:0001583	missense	23389			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1483G>A	12.37:g.116446735C>T	ENSP00000281928:p.Glu495Lys		114931118	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.664949	0.47572	.	.	ENSG00000123066	ENST00000281928	T	0.75477	-0.94	5.76	5.76	0.90799	.	0.281278	0.41194	D	0.000928	T	0.67822	0.2934	L	0.53249	1.67	0.36414	D	0.863906	B	0.23806	0.091	B	0.17098	0.017	T	0.66630	-0.5875	10	0.20519	T	0.43	.	13.2077	0.59807	0.0:0.9274:0.0:0.0726	.	495	Q71F56	MD13L_HUMAN	K	495	ENSP00000281928:E495K	ENSP00000281928:E495K	E	-	1	0	MED13L	114931118	0.999000	0.42202	0.993000	0.49108	0.869000	0.49853	3.893000	0.56243	2.732000	0.93576	0.655000	0.94253	GAA		0.453	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116446735	C	T	116446735	3	4	61	1	0	0	0	0	1	0	0	0	9461	893	31	1	5237	1	MED13L	12	116446735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1326048	116446735	17405160	8407	16392										
MED13L	23389	broad.mit.edu	37	chr12	116457644	116457644	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaactcgtcttcctctttCgattcttctttcttttttag	3	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:116457644C>T	ENST00000281928.3	-	6	965	c.759G>A	c.(757-759)tcG>tcA	p.S253S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	253						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.S253S(2)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTTCCTCTTTCGATTCTTCTT	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	12											180	163	169					12																	116457644		2203	4300	6503	114942027	SO:0001819	synonymous_variant	23389			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.759G>A	12.37:g.116457644C>T			114942027	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																				0.398	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116457644	C	T	116457644	2	4	61	1	0	0	0	0	0	0	0	1	9461	871	31	1		1	MED13L	12	116457644	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10909	116457644	17394251	8408	16393										
FBXW8	26259	broad.mit.edu	37	chr12	117365904	117365904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatatatttcagtatctggAcaggaaagaactaggaagat	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117365904A>G	ENST00000309909.5	+	2	477	c.395A>G	c.(394-396)gAc>gGc	p.D132G	FBXW8_ENST00000455858.2_Missense_Mutation_p.D66G			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	132	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)		p.D132G(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		CAGTATCTGGACAGGAAAGAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	103	106					12																	117365904		2203	4300	6503	115850287	SO:0001583	missense	26259			AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"F-boxes / WD-40 domains", "WD repeat domain containing"	13597	protein-coding gene	gene with protein product		609073	"F-box only protein 29", "F-box and WD-40 domain protein 8"	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.395A>G	12.37:g.117365904A>G	ENSP00000310686:p.Asp132Gly		115850287	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	.	.	.	.	.	.	.	.	.	.	A	8.460	0.855141	0.17106	.	.	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.28666	1.6;1.6	5.73	0.915	0.19366	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.685741	0.14579	N	0.311010	T	0.22627	0.0546	L	0.48174	1.505	0.25367	N	0.988731	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.25813	-1.0121	10	0.17832	T	0.49	-6.8055	8.4099	0.32638	0.5964:0.0:0.4036:0.0	.	132;66	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	G	132;66;66	ENSP00000310686:D132G;ENSP00000389144:D66G	ENSP00000310686:D132G	D	+	2	0	FBXW8	115850287	0.996000	0.38824	0.915000	0.36163	0.994000	0.84299	0.618000	0.24373	0.448000	0.26722	0.454000	0.30748	GAC		0.383	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		G	117365904	A	G	117365904	3	3	61	1	0	0	0	0	1	0	0	0	5789	275	10	4	401	4	FBXW8	12	117365904	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	908260	117365904	16485991	8409	16394										
TESC	54997	broad.mit.edu	37	chr12	117494618	117494618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaacgcccacctgttgtCgaagaaggcacgaacaattt	10	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117494618C>T	ENST00000335209.7	-	3	388	c.202G>A	c.(202-204)Gac>Aac	p.D68N	TESC_ENST00000541210.1_Intron|TESC_ENST00000535198.1_5'Flank|TESC_ENST00000392545.4_Missense_Mutation_p.D121N			Q96BS2	CHP3_HUMAN	tescalcin	68					cell differentiation (GO:0030154)|cellular response to retinoic acid (GO:0071300)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell proliferation (GO:0008285)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of sodium:proton antiporter activity (GO:0032417)|positive regulation of transcription, DNA-templated (GO:0045893)|protein maturation (GO:0051604)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of cell adhesion mediated by integrin (GO:0033628)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphatase inhibitor activity (GO:0019212)|protein homodimerization activity (GO:0042803)|protein kinase inhibitor activity (GO:0004860)	p.D121N(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		CACCTGTTGTCGAAGAAGGCA	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	12											150	116	127					12																	117494618		2203	4300	6503	115979001	SO:0001583	missense	54997			AF443207	CCDS9183.2, CCDS9183.3, CCDS53835.1	12q24.22	2013-01-10			ENSG00000088992	ENSG00000088992		"EF-hand domain containing"	26065	protein-coding gene	gene with protein product	"calcineurin-like EF hand protein 3"	611585				11145610, 11696366, 12809501, 14661968	Standard	NM_017899		Approved	TSC, FLJ20607, CHP3	uc001twh.3	Q96BS2	OTTHUMG00000144168	ENST00000335209.7:c.202G>A	12.37:g.117494618C>T	ENSP00000334785:p.Asp68Asn		115979001	F5H1Y5|Q9NWT9	Missense_Mutation	SNP	ENST00000335209.7	37	CCDS9183.3	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892513	0.91889	.	.	ENSG00000088992	ENST00000335209;ENST00000392545	T;T	0.54479	0.57;0.57	5.17	5.17	0.71159	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.72803	0.3506	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.72626	-0.4236	10	0.33940	T	0.23	-48.5903	17.4632	0.87625	0.0:1.0:0.0:0.0	.	68	Q96BS2	TESC_HUMAN	N	68;121	ENSP00000334785:D68N;ENSP00000376328:D121N	ENSP00000334785:D68N	D	-	1	0	TESC	115979001	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.745000	0.68672	2.401000	0.81631	0.655000	0.94253	GAC		0.517	TESC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291363.2	NM_017899		T	117494618	C	T	117494618	3	4	61	1	0	0	0	0	1	0	0	0	15805	884	31	1	466	1	TESC	12	117494618	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128714	117494618	16357277	8410	16395										
FBXO21	23014	broad.mit.edu	37	chr12	117627100	117627100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctaacccagctttttgccGaactttatactcttccaacc	3	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117627100G>A	ENST00000330622.5	-	2	306	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W	FBXO21_ENST00000427718.2_Missense_Mutation_p.R103W|FBXO21_ENST00000549689.1_5'Flank			O94952	FBX21_HUMAN	F-box protein 21	103					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)	p.R103W(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|pancreas(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	29	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		GCTTTTTGCCGAACTTTATAC	0.478																																					GBM(168;452 2038 13535 17701 43680)											1	Substitution - Missense(1)	large_intestine(1)	12											173	160	164					12																	117627100		2203	4300	6503	116111483	SO:0001583	missense	23014			AB020682	CCDS9184.1, CCDS44989.1	12q24.23	2004-06-15	2004-06-15					"F-boxes /  "other""	13592	protein-coding gene	gene with protein product		609095	"F-box only protein 21"			10048485, 10531035	Standard	NM_033624		Approved	FBX21, KIAA0875	uc001twk.3	O94952	OTTHUMG00000169495	ENST00000330622.5:c.307C>T	12.37:g.117627100G>A	ENSP00000328187:p.Arg103Trp		116111483	B3KMF0|Q5BJG0|Q9H087	Missense_Mutation	SNP	ENST00000330622.5	37	CCDS9184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.176842|5.176842	0.94846|0.94846	.|.	.|.	ENSG00000135108|ENSG00000135108	ENST00000427718;ENST00000257563;ENST00000535590;ENST00000330622|ENST00000550180	T;T|.	0.23147|.	1.92;1.92|.	4.95|4.95	4.95|4.95	0.65309|0.65309	F-box domain, Skp2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74268|0.74268	0.3694|0.3694	M|M	0.68952|0.68952	2.095|2.095	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;0.985;1.0|.	T|T	0.73811|0.73811	-0.3865|-0.3865	10|5	0.87932|.	D|.	0|.	-24.9799|-24.9799	18.144|18.144	0.89649|0.89649	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	19;103;103|.	Q8IUQ5;O94952;O94952-1|.	.;FBX21_HUMAN;.|.	W|L	103;19;19;103|46	ENSP00000414468:R103W;ENSP00000328187:R103W|.	ENSP00000257563:R19W|.	R|S	-|-	1|2	2|0	FBXO21|FBXO21	116111483|116111483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.076000|5.076000	0.64413|0.64413	2.442000|2.442000	0.82660|0.82660	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.478	FBXO21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404409.1	NM_033624		A	117627100	G	A	117627100	3	1	61	1	0	0	0	0	1	0	0	0	5752	1057	37	1	1623	1	FBXO21	12	117627100	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	132482	117627100	16224795	8411	16396										
NOS1	4842	broad.mit.edu	37	chr12	117657968	117657968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatggctttgaggacatcaGcagccatggtgacgtcccca	13	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117657968G>A	ENST00000338101.4	-	27	4188	c.4184C>T	c.(4183-4185)gCt>gTt	p.A1395V	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.A1361V			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.A1361V(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GAGGACATCAGCAGCCATGGT	0.612																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - Missense(1)	large_intestine(1)	12											134	147	142					12																	117657968		2199	4295	6494	116142351	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4184C>T	12.37:g.117657968G>A	ENSP00000337459:p.Ala1395Val		116142351		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.264449	0.59431	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	D;D	0.86865	-2.18;-2.18	4.44	4.44	0.53790	Oxidoreductase FAD/NAD(P)-binding (1);	0.055324	0.64402	D	0.000001	T	0.80959	0.4724	L	0.40543	1.245	0.80722	D	1	P	0.34699	0.464	B	0.33846	0.171	T	0.79569	-0.1749	10	0.35671	T	0.21	-21.7721	11.8385	0.52340	0.0:0.3356:0.6644:0.0	.	1361	P29475	NOS1_HUMAN	V	1256;1361;1395	ENSP00000320758:A1361V;ENSP00000337459:A1395V	ENSP00000320758:A1361V	A	-	2	0	NOS1	116142351	1.000000	0.71417	0.925000	0.36789	0.948000	0.59901	6.681000	0.74523	2.310000	0.77875	0.561000	0.74099	GCT		0.612	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117657968	G	A	117657968	3	1	61	1	0	0	0	0	1	0	0	0	10572	971	34	3	234	3	NOS1	12	117657968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30868	117657968	16193927	8412	16397										
NOS1	4842	broad.mit.edu	37	chr12	117672562	117672562	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcacgaagatagttgaccGactgcaggaaattgcagagg	13	8	0	3	rs565699307		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117672562G>A	ENST00000338101.4	-	21	3149	c.3145C>T	c.(3145-3147)Cgg>Tgg	p.R1049W	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Splice_Site_p.R1015W			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.R1015W(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		ATAGTTGACCGACTGCAGGAA	0.552																																					Esophageal Squamous(162;1748 2599 51982 52956)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											31	33	32					12																	117672562		2021	4188	6209	116156945	SO:0001630	splice_region_variant	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3144-1C>T	12.37:g.117672562G>A			116156945		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377548	0.61735	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.78364	-1.17;-1.17	4.65	4.65	0.58169	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.91469	0.7307	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93812	0.7111	10	0.87932	D	0	-14.5882	18.067	0.89394	0.0:0.0:1.0:0.0	.	1015	P29475	NOS1_HUMAN	W	910;1015;1015;1049	ENSP00000320758:R1015W;ENSP00000337459:R1049W	ENSP00000320758:R1015W	R	-	1	2	NOS1	116156945	1.000000	0.71417	0.989000	0.46669	0.022000	0.10575	7.511000	0.81718	2.568000	0.86640	0.561000	0.74099	CGG		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		Missense_Mutation	A	117672562	G	A	117672562	5	1	61	1	0	0	0	0	0	0	1	0	10572	1072	37	1	1297	1	NOS1	12	117672562	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14594	117672562	16179333	8413	16398										
NOS1	4842	broad.mit.edu	37	chr12	117698402	117698402	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccccatcagcttggccgaGaacttgacagctctggaggg	13	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117698402G>T	ENST00000338101.4	-	13	2239	c.2235C>A	c.(2233-2235)ttC>ttA	p.F745L	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.F745L			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.F745L(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCTTGGCCGAGAACTTGACAG	0.517																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - Missense(1)	large_intestine(1)	12											71	69	70					12																	117698402		1934	4162	6096	116182785	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2235C>A	12.37:g.117698402G>T	ENSP00000337459:p.Phe745Leu		116182785		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113672	0.56398	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.01446	4.91;4.88	5.11	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.04048	0.0113	M	0.76002	2.32	0.80722	D	1	P	0.37824	0.609	B	0.40864	0.342	T	0.28004	-1.0057	10	0.66056	D	0.02	-32.7639	9.8821	0.41240	0.155:0.0:0.845:0.0	.	745	P29475	NOS1_HUMAN	L	640;745;745;745	ENSP00000320758:F745L;ENSP00000337459:F745L	ENSP00000320758:F745L	F	-	3	2	NOS1	116182785	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.635000	0.46537	1.385000	0.46445	0.655000	0.94253	TTC		0.517	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117698402	G	T	117698402	3	4	61	1	0	0	0	0	1	0	0	0	10572	933	33	2	2133	2	NOS1	12	117698402	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25840	117698402	16153493	8414	16399										
NOS1	4842	broad.mit.edu	37	chr12	117703130	117703130	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggaaggacctggtattcGaaggagggggtgagccggta	19	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117703130G>A	ENST00000338101.4	-	11	2131	c.2127C>T	c.(2125-2127)ttC>ttT	p.F709F	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.F709F			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.F709F(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCTGGTATTCGAAGGAGGGGG	0.557																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - coding silent(1)	large_intestine(1)	12											28	33	31					12																	117703130		2068	4238	6306	116187513	SO:0001819	synonymous_variant	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2127C>T	12.37:g.117703130G>A			116187513		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																				0.557	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117703130	G	A	117703130	2	1	61	1	0	0	0	0	0	0	0	1	10572	1049	37	1		1	NOS1	12	117703130	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4728	117703130	16148765	8415	16400										
NOS1	4842	broad.mit.edu	37	chr12	117723132	117723132	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtgcagtcacgggcatcGaatacctggaagaggcacag	15	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117723132G>A	ENST00000338101.4	-	6	1300	c.1296C>T	c.(1294-1296)ttC>ttT	p.F432F	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.F432F			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.F432F(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CACGGGCATCGAATACCTGGA	0.552																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - coding silent(1)	large_intestine(1)	12											76	80	79					12																	117723132		2051	4200	6251	116207515	SO:0001819	synonymous_variant	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1296C>T	12.37:g.117723132G>A			116207515		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																				0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117723132	G	A	117723132	2	1	61	1	0	0	0	0	0	0	0	1	10572	1049	37	1		1	NOS1	12	117723132	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20002	117723132	16128763	8416	16401										
NOS1	4842	broad.mit.edu	37	chr12	117726001	117726001	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatgatggagcccatgcaGatgtactcagtgcatcccgt	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117726001G>T	ENST00000344089.3	-	6	1746	c.1061C>A	c.(1060-1062)tCt>tAt	p.S354Y	NOS1_ENST00000317775.6_Silent_p.I335I|NOS1_ENST00000338101.4_Silent_p.I335I	NM_001204213.1|NM_001204214.1	NP_001191142.1|NP_001191143.1	Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.I335I(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		AGCCCATGCAGATGTACTCAG	0.507																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - coding silent(1)	large_intestine(1)	12											112	110	111					12																	117726001		1964	4157	6121	116210384	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000344089.3:c.1061C>A	12.37:g.117726001G>T	ENSP00000339862:p.Ser354Tyr		116210384		Silent	SNP	ENST00000344089.3	37		.	.	.	.	.	.	.	.	.	.	G	14.76	2.631664	0.46944	.	.	ENSG00000089250	ENST00000344089	T	0.08008	3.14	5.93	4.09	0.47781	.	.	.	.	.	T	0.13286	0.0322	.	.	.	0.25252	N	0.989661	.	.	.	.	.	.	T	0.10847	-1.0612	6	0.87932	D	0	-28.8057	8.7034	0.34340	0.0682:0.0:0.6604:0.2714	.	.	.	.	Y	354	ENSP00000339862:S354Y	ENSP00000339862:S354Y	S	-	2	0	NOS1	116210384	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	1.332000	0.33805	0.831000	0.34780	0.563000	0.77884	TCT		0.507	NOS1-201	KNOWN	basic	protein_coding	protein_coding				T	117726001	G	T	117726001	3	4	61	1	0	0	0	0	1	0	0	0	10572	932	33	2	3399	2	NOS1	12	117726001	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2869	117726001	16125894	8417	16402										
KSR2	283455	broad.mit.edu	37	chr12	117914280	117914280	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacttacccaagggcaaaGacgtcagagtgcttggagaa	11	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117914280G>T	ENST00000339824.5	-	17	3298	c.2571C>A	c.(2569-2571)gtC>gtA	p.V857V	KSR2_ENST00000425217.1_Silent_p.V828V|KSR2_ENST00000302438.5_3'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	857	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.V889V(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAAGGGCAAAGACGTCAGAGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	12											52	61	58					12																	117914280		1980	4154	6134	116398663	SO:0001819	synonymous_variant	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2571C>A	12.37:g.117914280G>T			116398663	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					0.597	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		T	117914280	G	T	117914280	2	4	61	1	0	0	0	0	0	0	0	1	8604	929	33	2		2	KSR2	12	117914280	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	188279	117914280	15937615	8418	16403										
KSR2	283455	broad.mit.edu	37	chr12	117962842	117962842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcggccgtggtacacttgCccaaagcggccctttccaat	10	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:117962842C>T	ENST00000339824.5	-	14	2761	c.2034G>A	c.(2032-2034)ggG>ggA	p.G678G	KSR2_ENST00000425217.1_Silent_p.G649G|KSR2_ENST00000302438.5_Silent_p.G375G|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	678	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.G710G(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGTACACTTGCCCAAAGCGGC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	12											56	61	59					12																	117962842		2090	4205	6295	116447225	SO:0001819	synonymous_variant	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2034G>A	12.37:g.117962842C>T			116447225	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					0.607	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		T	117962842	C	T	117962842	2	4	61	1	0	0	0	0	0	0	0	1	8604	726	26	3		3	KSR2	12	117962842	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48562	117962842	15889053	8419	16404										
KSR2	283455	broad.mit.edu	37	chr12	118105456	118105456	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaagggtttgctcttctTcttggctctgaaagggagac	12	8	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:118105456T>G	ENST00000339824.5	-	5	1721	c.994A>C	c.(994-996)Aag>Cag	p.K332Q	KSR2_ENST00000425217.1_Missense_Mutation_p.K303Q|KSR2_ENST00000302438.5_Missense_Mutation_p.K29Q|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	332					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.K364Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTGCTCTTCTTCTTGGCTCTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	12											46	47	47					12																	118105456		1926	4132	6058	116589839	SO:0001583	missense	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.994A>C	12.37:g.118105456T>G	ENSP00000339952:p.Lys332Gln		116589839	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	37		.	.	.	.	.	.	.	.	.	.	T	16.83	3.230337	0.58777	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	T;T;T	0.51574	0.7;0.7;0.7	4.9	4.9	0.64082	.	0.138655	0.47455	D	0.000234	T	0.60792	0.2296	L	0.46157	1.445	0.46954	D	0.99926	D	0.57899	0.981	D	0.69824	0.966	T	0.63010	-0.6732	10	0.59425	D	0.04	.	13.8297	0.63373	0.0:0.0:0.0:1.0	.	332	Q6VAB6	KSR2_HUMAN	Q	303;332;29;4	ENSP00000389715:K303Q;ENSP00000339952:K332Q;ENSP00000305466:K29Q	ENSP00000305466:K29Q	K	-	1	0	KSR2	116589839	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.613000	0.82986	1.966000	0.57179	0.460000	0.39030	AAG		0.542	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		G	118105456	T	G	118105456	3	3	61	1	0	0	0	0	1	0	0	0	8604	1792	62	4	1922	4	KSR2	12	118105456	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	142614	118105456	15746439	8420	16405										
RFC5	5985	broad.mit.edu	37	chr12	118457550	118457550	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagctatataaagacaaaGaatttggctccatggtcttg	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:118457550G>T	ENST00000454402.2	+	3	362	c.244G>T	c.(244-246)Gaa>Taa	p.E82*	RFC5_ENST00000229043.3_5'UTR|RFC5_ENST00000392542.2_Nonsense_Mutation_p.E61*	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	82					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.E82*(2)		NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAAAGACAAAGAATTTGGCTC	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											89	83	85					12																	118457550		2203	4300	6503	116941933	SO:0001587	stop_gained	5985				CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.244G>T	12.37:g.118457550G>T	ENSP00000408295:p.Glu82*		116941933	A8MZ62|B3KSX8	Nonsense_Mutation	SNP	ENST00000454402.2	37	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	G	36	5.937311	0.97122	.	.	ENSG00000111445	ENST00000484086;ENST00000420967;ENST00000454402;ENST00000392542;ENST00000535092	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-0.9433	17.519	0.87782	0.0:0.0:1.0:0.0	.	.	.	.	X	114;61;82;61;61	.	ENSP00000376325:E61X	E	+	1	0	RFC5	116941933	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	9.454000	0.97621	2.669000	0.90835	0.655000	0.94253	GAA		0.423	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		T	118457550	G	T	118457550	4	4	61	1	0	0	0	0	0	1	0	0	13285	943	33	2	260	2	RFC5	12	118457550	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	352094	118457550	15394345	8421	16406										
CCDC60	160777	broad.mit.edu	37	chr12	119909831	119909831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctgtgaagataggccgtgGatattttgctattctgaggg	14	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:119909831G>A	ENST00000327554.2	+	3	668	c.203G>A	c.(202-204)gGa>gAa	p.G68E	CCDC60_ENST00000546345.1_3'UTR|RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	68								p.G68E(1)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ATAGGCCGTGGATATTTTGCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	97	98					12																	119909831		2203	4300	6503	118394214	SO:0001583	missense	160777			BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.203G>A	12.37:g.119909831G>A	ENSP00000333374:p.Gly68Glu		118394214		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.321055	0.23994	.	.	ENSG00000183273	ENST00000327554	T	0.26810	1.71	5.22	5.22	0.72569	.	0.401293	0.21849	N	0.068205	T	0.38852	0.1056	L	0.50333	1.59	0.80722	D	1	D	0.59357	0.985	P	0.57009	0.811	T	0.04128	-1.0975	9	.	.	.	-12.5009	14.2748	0.66173	0.0:0.0:1.0:0.0	.	68	Q8IWA6	CCD60_HUMAN	E	68	ENSP00000333374:G68E	.	G	+	2	0	CCDC60	118394214	0.749000	0.28305	0.014000	0.15608	0.048000	0.14542	4.411000	0.59781	2.407000	0.81776	0.514000	0.50259	GGA		0.468	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119909831	G	A	119909831	3	1	61	1	0	0	0	0	1	0	0	0	2837	1174	41	3	213	3	CCDC60	12	119909831	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1452281	119909831	13942064	8422	16407										
PRKAB1	5564	broad.mit.edu	37	chr12	120112250	120112250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggattcccaaaagtgctccGatgtgtctggtatgaacaca	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:120112250G>A	ENST00000229328.5	+	4	1015	c.523G>A	c.(523-525)Gat>Aat	p.D175N	PRKAB1_ENST00000540121.1_Missense_Mutation_p.D9N|PRKAB1_ENST00000541640.1_Missense_Mutation_p.D175N	NM_006253.4	NP_006244.2	Q9Y478	AAKB1_HUMAN	protein kinase, AMP-activated, beta 1 non-catalytic subunit	175					cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein kinase activity (GO:0004672)	p.D175N(1)		endometrium(2)|large_intestine(3)|lung(5)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Metformin(DB00331)	AAAGTGCTCCGATGTGTCTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											134	122	126					12																	120112250		2203	4300	6503	118596633	SO:0001583	missense	5564			BC001823	CCDS9191.1	12q24.1-q24.3	2008-05-14			ENSG00000111725	ENSG00000111725			9378	protein-coding gene	gene with protein product	"AMPK beta 1"	602740				8557660	Standard	NM_006253		Approved		uc001txg.3	Q9Y478	OTTHUMG00000168954	ENST00000229328.5:c.523G>A	12.37:g.120112250G>A	ENSP00000229328:p.Asp175Asn		118596633	Q9UBV0|Q9UE20|Q9UEX2|Q9Y6V8	Missense_Mutation	SNP	ENST00000229328.5	37	CCDS9191.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562807	0.65538	.	.	ENSG00000111725	ENST00000229328;ENST00000541640;ENST00000539596;ENST00000540121;ENST00000545223	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.67116	0.2859	M	0.62016	1.91	0.80722	D	1	B	0.27416	0.178	B	0.29524	0.103	T	0.61252	-0.7100	9	0.21014	T	0.42	-21.5678	20.422	0.99049	0.0:0.0:1.0:0.0	.	175	Q9Y478	AAKB1_HUMAN	N	175;175;138;9;9	.	ENSP00000229328:D175N	D	+	1	0	PRKAB1	118596633	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.832000	0.97577	0.655000	0.94253	GAT		0.428	PRKAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401731.2	NM_006253		A	120112250	G	A	120112250	3	1	61	1	0	0	0	0	1	0	0	0	12529	1058	37	1	537	1	PRKAB1	12	120112250	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202419	120112250	13739645	8423	16408										
CIT	11113	broad.mit.edu	37	chr12	120173072	120173072	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggcgccagaagcctcatCgagttgtttggacaagtaga	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:120173072C>T	ENST00000261833.7	-	24	2975	c.2923G>A	c.(2923-2925)Gat>Aat	p.D975N	CIT_ENST00000392521.2_Missense_Mutation_p.D1017N|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	975					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.D975N(1)|p.D1018N(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GAAGCCTCATCGAGTTGTTTG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	12											234	210	218					12																	120173072		2203	4300	6503	118657455	SO:0001583	missense	11113			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.2923G>A	12.37:g.120173072C>T	ENSP00000261833:p.Asp975Asn		118657455	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799838	0.70567	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.66460	-0.13;-0.21	5.23	5.23	0.72850	.	0.114632	0.64402	D	0.000017	T	0.59197	0.2176	N	0.24115	0.695	0.49915	D	0.999831	D;P;D	0.56287	0.968;0.824;0.975	B;B;P	0.49085	0.37;0.105;0.6	T	0.60271	-0.7296	10	0.42905	T	0.14	.	12.5166	0.56036	0.0:0.9232:0.0:0.0768	.	1017;975;508	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	N	1017;975	ENSP00000376306:D1017N;ENSP00000261833:D975N	ENSP00000261833:D975N	D	-	1	0	CIT	118657455	1.000000	0.71417	0.996000	0.52242	0.586000	0.36452	6.051000	0.71072	2.587000	0.87381	0.655000	0.94253	GAT		0.517	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120173072	C	T	120173072	3	4	61	1	0	0	0	0	1	0	0	0	3444	884	31	1	3256	1	CIT	12	120173072	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60822	120173072	13678823	8424	16409										
CCDC64	92558	broad.mit.edu	37	chr12	120518740	120518740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaaaagaggagagagaccGactcagagtcacttctgagg	12	9	3	5	rs373275826		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:120518740G>A	ENST00000397558.2	+	7	1358	c.1358G>A	c.(1357-1359)cGa>cAa	p.R453Q	CCDC64_ENST00000446727.2_Missense_Mutation_p.R124Q|CCDC64_ENST00000257583.4_Missense_Mutation_p.R150Q	NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	453					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)	p.R453Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGAGAGACCGACTCAGAGTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12						G	GLN/ARG	1,4103		0,1,2051	71	78	76		1358	3.5	1	12		76	0,8390		0,0,4195	no	missense	CCDC64	NM_207311.2	43	0,1,6246	AA,AG,GG		0.0,0.0244,0.0080	possibly-damaging	453/574	120518740	1,12493	2052	4195	6247	119003123	SO:0001583	missense	92558			U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.1358G>A	12.37:g.120518740G>A	ENSP00000380690:p.Arg453Gln		119003123	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	37	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.646918	0.47258	2.44E-4	0.0	ENSG00000135127	ENST00000397558;ENST00000446727;ENST00000548673;ENST00000257583	T;T;T	0.04706	3.59;3.6;3.57	5.32	3.48	0.39840	.	0.346876	0.28641	N	0.014638	T	0.04048	0.0113	L	0.39467	1.215	0.38678	D	0.952472	B;B;P	0.39624	0.236;0.433;0.681	B;B;B	0.26614	0.016;0.044;0.071	T	0.51116	-0.8746	10	0.38643	T	0.18	0.1625	11.9701	0.53060	0.1425:0.0:0.8575:0.0	.	150;124;453	B4DWL0;B4DNE7;Q6ZP65	.;.;BICR1_HUMAN	Q	453;124;171;150	ENSP00000380690:R453Q;ENSP00000399658:R124Q;ENSP00000447477:R171Q	ENSP00000257583:R150Q	R	+	2	0	CCDC64	119003123	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.269000	0.65542	0.619000	0.30197	0.561000	0.74099	CGA		0.527	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311		A	120518740	G	A	120518740	3	1	61	1	0	0	0	0	1	0	0	0	2841	1058	37	1	1384	1	CCDC64	12	120518740	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	345668	120518740	13333155	8425	16410										
SIRT4	23409	broad.mit.edu	37	chr12	120741624	120741624	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttatgcccgcactgaccGcaggcccatccagcatggtg	11	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:120741624G>A	ENST00000202967.4	+	2	319	c.260G>A	c.(259-261)cGc>cAc	p.R87H		NM_012240.2	NP_036372.1			sirtuin 4									p.R87H(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGCACTGACCGCAGGCCCATC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12											55	51	52					12																	120741624		2203	4300	6503	119226007	SO:0001583	missense	23409			AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.260G>A	12.37:g.120741624G>A	ENSP00000202967:p.Arg87His		119226007		Missense_Mutation	SNP	ENST00000202967.4	37	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	G	8.712	0.912308	0.17907	.	.	ENSG00000089163	ENST00000536460;ENST00000202967	T;T	0.17854	2.25;2.25	5.39	3.51	0.40186	.	0.097314	0.64402	D	0.000002	T	0.06050	0.0157	N	0.02751	-0.505	0.51233	D	0.999913	B	0.14012	0.009	B	0.12156	0.007	T	0.25572	-1.0128	10	0.05525	T	0.97	-22.2578	11.4148	0.49945	0.1517:0.0:0.8483:0.0	.	87	Q9Y6E7	SIRT4_HUMAN	H	28;87	ENSP00000444838:R28H;ENSP00000202967:R87H	ENSP00000202967:R87H	R	+	2	0	SIRT4	119226007	1.000000	0.71417	0.799000	0.32177	0.971000	0.66376	5.419000	0.66435	0.732000	0.32470	0.644000	0.83932	CGC		0.572	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		A	120741624	G	A	120741624	3	1	61	1	0	0	0	0	1	0	0	0	14377	1087	38	1	262	1	SIRT4	12	120741624	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	222884	120741624	13110271	8426	16411										
RNF10	9921	broad.mit.edu	37	chr12	121013487	121013487	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcccaaaactgctccaaaGaaaggtgaggatggtccact	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121013487G>T	ENST00000325954.4	+	15	2657	c.2196G>T	c.(2194-2196)aaG>aaT	p.K732N	RNF10_ENST00000413266.2_Missense_Mutation_p.K737N|RNF10_ENST00000542701.1_3'UTR	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	732					negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K732N(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTGCTCCAAAGAAAGGTGAGG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											101	102	102					12																	121013487		2203	4300	6503	119497870	SO:0001583	missense	9921			AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"RING-type (C3HC4) zinc fingers"	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.2196G>T	12.37:g.121013487G>T	ENSP00000322242:p.Lys732Asn		119497870	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	37	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.821027	0.71028	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000538254	D;D	0.89939	-2.59;-2.59	5.39	-0.864	0.10666	.	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	L	0.55481	1.735	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.85807	0.1377	10	0.23891	T	0.37	.	10.7077	0.45965	0.3824:0.0:0.6176:0.0	.	737;732	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	N	732;732;737;67	ENSP00000322242:K732N;ENSP00000415682:K737N	ENSP00000322242:K732N	K	+	3	2	RNF10	119497870	1.000000	0.71417	0.977000	0.42913	0.983000	0.72400	2.411000	0.44600	-0.191000	0.10448	-0.150000	0.13652	AAG		0.443	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			T	121013487	G	T	121013487	3	4	61	1	0	0	0	0	1	0	0	0	13459	933	33	2	2254	2	RNF10	12	121013487	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	271863	121013487	12838408	8427	16412										
ACADS	35	broad.mit.edu	37	chr12	121164911	121164911	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacaccagatgttgctccaGacatgccgggactttgccga	10	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121164911G>A	ENST00000242592.4	+	2	280	c.129G>A	c.(127-129)caG>caA	p.Q43Q	ACADS_ENST00000411593.2_Silent_p.Q43Q	NM_000017.2	NP_000008.1	P16219	ACADS_HUMAN	acyl-CoA dehydrogenase, C-2 to C-3 short chain	43					butyrate catabolic process (GO:0046359)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|protein homotetramerization (GO:0051289)|response to glucocorticoid (GO:0051384)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|butyryl-CoA dehydrogenase activity (GO:0004085)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)	p.Q43Q(1)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			Flavin adenine dinucleotide(DB03147)	TGTTGCTCCAGACATGCCGGG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											192	181	185					12																	121164911		2203	4300	6503	119649294	SO:0001819	synonymous_variant	35			M26393	CCDS9207.1	12q24.31	2012-07-13	2010-04-30		ENSG00000122971	ENSG00000122971	1.3.8.1		90	protein-coding gene	gene with protein product		606885	"acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain"			2565344	Standard	NM_000017		Approved	SCAD, ACAD3	uc001tza.4	P16219	OTTHUMG00000169203	ENST00000242592.4:c.129G>A	12.37:g.121164911G>A			119649294	P78331	Silent	SNP	ENST00000242592.4	37	CCDS9207.1																																																																																				0.577	ACADS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402861.1	NM_000017		A	121164911	G	A	121164911	2	1	61	1	0	0	0	0	0	0	0	1	114	933	33	3		3	ACADS	12	121164911	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151424	121164911	12686984	8428	16413										
OASL	8638	broad.mit.edu	37	chr12	121458598	121458598	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccatcaggattcttcacGaagacctggatctcggaggg	11	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121458598G>A	ENST00000257570.5	-	6	1581	c.1311C>T	c.(1309-1311)ttC>ttT	p.F437F	OASL_ENST00000339275.5_3'UTR	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	437	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)	p.F437F(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GATTCTTCACGAAGACCTGGA	0.542																																					Colon(192;517 2041 31392 31913 39966)											1	Substitution - coding silent(1)	large_intestine(1)	12											91	88	89					12																	121458598		2203	4300	6503	119942981	SO:0001819	synonymous_variant	8638			AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.1311C>T	12.37:g.121458598G>A			119942981	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Silent	SNP	ENST00000257570.5	37	CCDS9211.1																																																																																				0.542	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		A	121458598	G	A	121458598	2	1	61	1	0	0	0	0	0	0	0	1	10833	1049	37	1		1	OASL	12	121458598	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293687	121458598	12393297	8429	16414										
OASL	8638	broad.mit.edu	37	chr12	121469315	121469315	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgatgtttcacgaaatttCtctgcagctcgctgaaggat	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121469315C>A	ENST00000257570.5	-	3	857	c.587G>T	c.(586-588)aGa>aTa	p.R196I	OASL_ENST00000339275.5_Missense_Mutation_p.R196I	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	196					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)	p.R196I(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACGAAATTTCTCTGCAGCTC	0.577																																					Colon(192;517 2041 31392 31913 39966)											1	Substitution - Missense(1)	large_intestine(1)	12											102	94	96					12																	121469315		2203	4300	6503	119953698	SO:0001583	missense	8638			AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.587G>T	12.37:g.121469315C>A	ENSP00000257570:p.Arg196Ile		119953698	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	37	CCDS9211.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.28|17.28	3.349537|3.349537	0.61183|0.61183	.|.	.|.	ENSG00000135114|ENSG00000135114	ENST00000543677|ENST00000257570;ENST00000339275	.|T;T	.|0.51325	.|0.71;0.71	5.65|5.65	2.69|2.69	0.31865|0.31865	.|-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.|0.226336	.|0.30227	.|N	.|0.010109	.|T	.|0.67230	.|0.2871	M|M	0.87269|0.87269	2.87|2.87	0.30271|0.30271	N|N	0.792216|0.792216	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.87578	.|0.979;0.998	.|T	.|0.65730	.|-0.6097	.|10	.|0.87932	.|D	.|0	-24.4989|-24.4989	6.647|6.647	0.22941|0.22941	0.0:0.7105:0.0:0.2895|0.0:0.7105:0.0:0.2895	.|.	.|196;196	.|Q15646-2;Q15646	.|.;OASL_HUMAN	X|I	94|196	.|ENSP00000257570:R196I;ENSP00000341125:R196I	.|ENSP00000257570:R196I	E|R	-|-	1|2	0|0	OASL|OASL	119953698|119953698	0.833000|0.833000	0.29383|0.29383	0.675000|0.675000	0.29917|0.29917	0.736000|0.736000	0.42039|0.42039	0.662000|0.662000	0.25038|0.25038	0.952000|0.952000	0.37798|0.37798	-0.150000|-0.150000	0.13652|0.13652	GAA|AGA		0.577	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		A	121469315	C	A	121469315	3	1	61	1	0	0	0	0	1	0	0	0	10833	913	32	2	973	2	OASL	12	121469315	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10717	121469315	12382580	8430	16415										
P2RX4	5025	broad.mit.edu	37	chr12	121659733	121659733	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggaggaaaactccctcttCgtcatgaccaacgtgatcct	8	13	2	2	rs371199627		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121659733C>T	ENST00000337233.4	+	3	608	c.300C>T	c.(298-300)ttC>ttT	p.F100F	P2RX4_ENST00000541532.1_Silent_p.F100F|P2RX4_ENST00000359949.7_Silent_p.F116F|P2RX4_ENST00000540930.1_3'UTR|P2RX4_ENST00000543171.1_5'UTR	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	100					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.F100F(1)		breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACTCCCTCTTCGTCATGACCA	0.627													C|||	1	0.000199681	8e-04	0	5008	,	,		14862	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						C		1,4405	2.1+/-5.4	0,1,2202	177	159	165		300	1.8	1	12		165	0,8600		0,0,4300	no	coding-synonymous	P2RX4	NM_002560.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		100/389	121659733	1,13005	2203	4300	6503	120144116	SO:0001819	synonymous_variant	5025			Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.300C>T	12.37:g.121659733C>T			120144116	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Silent	SNP	ENST00000337233.4	37	CCDS9214.1																																																																																				0.627	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		T	121659733	C	T	121659733	2	4	61	1	0	0	0	0	0	0	0	1	11373	883	31	1		1	P2RX4	12	121659733	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	190418	121659733	12192162	8431	16416										
P2RX4	5025	broad.mit.edu	37	chr12	121666358	121666358	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttttttaaaggctgcaGaaaacttcactcttttggtt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121666358G>T	ENST00000337233.4	+	6	855	c.547G>T	c.(547-549)Gaa>Taa	p.E183*	P2RX4_ENST00000541532.1_3'UTR|P2RX4_ENST00000359949.7_Nonsense_Mutation_p.E199*|P2RX4_ENST00000540930.1_3'UTR|P2RX4_ENST00000543171.1_Nonsense_Mutation_p.E82*	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	183					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.E183*(1)		breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AAAGGCTGCAGAAAACTTCAC	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											77	74	75					12																	121666358		2203	4299	6502	120150741	SO:0001587	stop_gained	5025			Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.547G>T	12.37:g.121666358G>T	ENSP00000336607:p.Glu183*		120150741	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Nonsense_Mutation	SNP	ENST00000337233.4	37	CCDS9214.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252397	0.80135	.	.	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000543171;ENST00000538701;ENST00000542067	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-24.5745	18.2117	0.89872	0.0:0.0:1.0:0.0	.	.	.	.	X	183;199;82;53;156	.	ENSP00000336607:E183X	E	+	1	0	P2RX4	120150741	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.450000	0.80656	2.619000	0.88677	0.462000	0.41574	GAA		0.338	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		T	121666358	G	T	121666358	4	4	61	1	0	0	0	0	0	1	0	0	11373	943	33	2	569	2	P2RX4	12	121666358	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6625	121666358	12185537	8432	16417										
KDM2B	84678	broad.mit.edu	37	chr12	121881589	121881589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccgggggacgtttgaagcGatgaggcctaaaggggggtg	19	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:121881589G>A	ENST00000377071.4	-	17	2531	c.2459C>T	c.(2458-2460)tCg>tTg	p.S820L	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Intron|KDM2B_ENST00000542973.1_Missense_Mutation_p.S188L	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	820					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)	p.S459L(1)|p.S820L(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGTTTGAAGCGATGAGGCCTA	0.607											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	12											36	42	40					12																	121881589		1972	4154	6126	120365972	SO:0001583	missense	84678			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2459C>T	12.37:g.121881589G>A	ENSP00000366271:p.Ser820Leu	1514	120365972	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.201087	0.38905	.	.	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377071;ENST00000540043;ENST00000261824	T;T	0.22945	2.24;1.93	4.86	3.9	0.45041	.	0.357803	0.20448	N	0.092149	T	0.10981	0.0268	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.18310	0.009;0.027;0.027	B;B;B	0.12156	0.007;0.007;0.007	T	0.12502	-1.0545	10	0.30854	T	0.27	-12.2278	9.8788	0.41220	0.0:0.0:0.7966:0.2034	.	260;820;263	B7ZB05;Q8NHM5;B4DSN4	.;KDM2B_HUMAN;.	L	820;188;820;263;823	ENSP00000437821:S188L;ENSP00000366271:S820L	ENSP00000261824:S823L	S	-	2	0	KDM2B	120365972	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.385000	0.52485	2.698000	0.92095	0.561000	0.74099	TCG		0.607	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		A	121881589	G	A	121881589	3	1	61	1	0	0	0	0	1	0	0	0	8146	1059	37	1	1631	1	KDM2B	12	121881589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215231	121881589	11970306	8433	16418										
TMEM120B	144404	broad.mit.edu	37	chr12	122199565	122199565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgcacagggtgactgacGaagtcttcaacttcctgctg	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122199565G>A	ENST00000449592.2	+	6	573	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	TMEM120B_ENST00000540377.1_5'UTR	NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	158						integral component of membrane (GO:0016021)		p.E158K(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		GGTGACTGACGAAGTCTTCAA	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	12											93	89	91					12																	122199565		2052	4195	6247	120683948	SO:0001583	missense	144404			BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.472G>A	12.37:g.122199565G>A	ENSP00000404991:p.Glu158Lys		120683948	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	37	CCDS41852.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.108179	0.77096	.	.	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.29917	1.55;1.55	5.62	4.67	0.58626	.	0.053460	0.85682	D	0.000000	T	0.29749	0.0743	M	0.72118	2.19	0.80722	D	1	P	0.47484	0.896	B	0.40199	0.322	T	0.10405	-1.0631	10	0.09843	T	0.71	-8.5011	13.0689	0.59048	0.0:0.0:0.8385:0.1614	.	158	A0PK00	T120B_HUMAN	K	158;137	ENSP00000404991:E158K;ENSP00000442105:E137K	ENSP00000345152:E158K	E	+	1	0	TMEM120B	120683948	1.000000	0.71417	0.870000	0.34147	0.750000	0.42670	7.536000	0.82023	2.655000	0.90218	0.650000	0.86243	GAA		0.592	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825		A	122199565	G	A	122199565	3	1	61	1	0	0	0	0	1	0	0	0	16073	1059	37	1	494	1	TMEM120B	12	122199565	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	317976	122199565	11652330	8434	16419										
HPD	3242	broad.mit.edu	37	chr12	122286961	122286961	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccacaatgtggtcgatCatctccagactgcatttggg	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122286961C>A	ENST00000289004.4	-	9	575	c.540G>T	c.(538-540)atG>atT	p.M180I	HPD_ENST00000543163.1_Missense_Mutation_p.M141I|HPD_ENST00000543869.2_5'UTR	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	180					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)	p.M180I(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	TGTGGTCGATCATCTCCAGAC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											162	119	134					12																	122286961		2203	4300	6503	120771344	SO:0001583	missense	3242			BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.540G>T	12.37:g.122286961C>A	ENSP00000289004:p.Met180Ile		120771344	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	37	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	C	7.906	0.735498	0.15574	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.62364	0.03;0.03	5.64	-11.3	0.00108	.	0.368486	0.33553	N	0.004788	T	0.18299	0.0439	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	10	0.22706	T	0.39	-3.5749	8.6557	0.34062	0.1486:0.1878:0.5514:0.1121	.	180	P32754	HPPD_HUMAN	I	180;177;141	ENSP00000289004:M180I;ENSP00000441677:M141I	ENSP00000289004:M180I	M	-	3	0	HPD	120771344	0.010000	0.17322	0.000000	0.03702	0.034000	0.12701	-1.247000	0.02893	-4.043000	0.00079	-1.092000	0.02172	ATG		0.557	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		A	122286961	C	A	122286961	3	1	61	1	0	0	0	0	1	0	0	0	7353	826	29	2	665	2	HPD	12	122286961	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87396	122286961	11564934	8435	16420										
WDR66	144406	broad.mit.edu	37	chr12	122398570	122398570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtacttagcaagacttcGctctcatcgcaaaagcattc	8	11	1	1	rs200928405		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122398570G>A	ENST00000288912.4	+	14	3067	c.2213G>A	c.(2212-2214)cGc>cAc	p.R738H	WDR66_ENST00000397454.2_Missense_Mutation_p.R738H	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	738							calcium ion binding (GO:0005509)	p.R738H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GCAAGACTTCGCTCTCATCGC	0.488																																					Esophageal Squamous(85;849 1794 49757 52143)											1	Substitution - Missense(1)	large_intestine(1)	12											146	143	144					12																	122398570		1951	4153	6104	120882953	SO:0001583	missense	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2213G>A	12.37:g.122398570G>A	ENSP00000288912:p.Arg738His		120882953	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.141426	0.37825	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.63580	0.91;-0.05	4.82	3.91	0.45181	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.183177	0.47852	D	0.000202	T	0.48642	0.1511	L	0.31926	0.97	0.24698	N	0.993275	P	0.42296	0.775	B	0.40636	0.335	T	0.42565	-0.9444	10	0.33940	T	0.23	.	9.5498	0.39304	0.1761:0.0:0.8239:0.0	.	738	Q8TBY9	WDR66_HUMAN	H	738	ENSP00000288912:R738H;ENSP00000380595:R738H	ENSP00000288912:R738H	R	+	2	0	WDR66	120882953	0.045000	0.20229	0.205000	0.23548	0.916000	0.54674	1.443000	0.35057	2.382000	0.81193	0.655000	0.94253	CGC		0.488	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		A	122398570	G	A	122398570	3	1	61	1	0	0	0	0	1	0	0	0	17357	1087	38	1	2263	1	WDR66	12	122398570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111609	122398570	11453325	8436	16421										
BCL7A	605	broad.mit.edu	37	chr12	122481882	122481882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccgctccagagcccaactCggctgtgcccagcgacggca	11	19	0	1	rs538468428		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122481882C>T	ENST00000261822.4	+	4	568	c.362C>T	c.(361-363)tCg>tTg	p.S121L	BCL7A_ENST00000538010.1_Missense_Mutation_p.S121L	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	121					negative regulation of transcription, DNA-templated (GO:0045892)			p.S121L(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		GAGCCCAACTCGGCTGTGCCC	0.632			T	MYC	BNHL								C|||	1	0.000199681	0	0.0014	5008	,	,		17829	0		0	False		,,,				2504	0				GBM(17;197 467 16477 23242 44349)		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	1	Substitution - Missense(1)	large_intestine(1)	12											126	109	115					12																	122481882		2203	4300	6503	120966265	SO:0001583	missense	605			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.362C>T	12.37:g.122481882C>T	ENSP00000261822:p.Ser121Leu		120966265	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.991537	0.35131	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.47177	0.87;0.85	5.54	4.65	0.58169	.	0.544904	0.20291	N	0.095224	T	0.30479	0.0766	N	0.19112	0.55	0.09310	N	1	B;B	0.15719	0.003;0.014	B;B	0.11329	0.001;0.006	T	0.14643	-1.0465	10	0.27785	T	0.31	.	8.817	0.35002	0.0:0.7701:0.0:0.2299	.	121;121	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	L	121	ENSP00000445868:S121L;ENSP00000261822:S121L	ENSP00000261822:S121L	S	+	2	0	BCL7A	120966265	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.943000	0.29030	1.346000	0.45694	0.650000	0.86243	TCG		0.632	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			T	122481882	C	T	122481882	3	4	61	1	0	0	0	0	1	0	0	0	1379	893	31	1	376	1	BCL7A	12	122481882	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83312	122481882	11370013	8437	16422										
BCL7A	605	broad.mit.edu	37	chr12	122492891	122492891	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggagcccattgggttgtCgggggtacgttgaaaggtgt	18	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122492891C>T	ENST00000261822.4	+	5	767				BCL7A_ENST00000538010.1_Missense_Mutation_p.S207L	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A						negative regulation of transcription, DNA-templated (GO:0045892)			p.S207L(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		ATTGGGTTGTCGGGGGTACGT	0.542			T	MYC	BNHL						OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(17;197 467 16477 23242 44349)		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	1	Substitution - Missense(1)	large_intestine(1)	12											64	67	66					12																	122492891		2203	4300	6503	120977274	SO:0001627	intron_variant	605			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.561+59C>T	12.37:g.122492891C>T		1519	120977274	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846205	0.32606	.	.	ENSG00000110987	ENST00000538010	T	0.47869	0.83	5.1	-4.65	0.03339	.	2.819560	0.00924	N	0.002629	T	0.28400	0.0702	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07481	-1.0770	9	0.30854	T	0.27	.	3.5867	0.07973	0.1038:0.4454:0.1025:0.3482	.	207	Q4VC05-2	.	L	207	ENSP00000445868:S207L	ENSP00000445868:S207L	S	+	2	0	BCL7A	120977274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.477000	0.02331	-0.815000	0.04346	-2.183000	0.00315	TCG		0.542	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			T	122492891	C	T	122492891	1	4	61	0	1	0	0	0	0	0	0	0	1379	893	31	1		1	BCL7A	12	122492891	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11009	122492891	11359004	8438	16423										
MLXIP	22877	broad.mit.edu	37	chr12	122618047	122618047	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatccagcccacggacttCggtccctcagagccgccact	8	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122618047C>T	ENST00000319080.7	+	9	1377	c.1245C>T	c.(1243-1245)ttC>ttT	p.F415F	MLXIP_ENST00000538698.1_Silent_p.F22F|MLXIP_ENST00000377037.2_Silent_p.F22F					MLX interacting protein									p.F415F(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		CCACGGACTTCGGTCCCTCAG	0.672																																					Esophageal Squamous(105;787 1493 16200 18566 52466)											1	Substitution - coding silent(1)	large_intestine(1)	12											15	19	18					12																	122618047		2081	4194	6275	121184000	SO:0001819	synonymous_variant	22877			AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"Basic helix-loop-helix proteins"	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1245C>T	12.37:g.122618047C>T			121184000		Silent	SNP	ENST00000319080.7	37																																																																																					0.672	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		T	122618047	C	T	122618047	2	4	61	1	0	0	0	0	0	0	0	1	9666	883	31	1		1	MLXIP	12	122618047	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	125156	122618047	11233848	8439	16424										
IL31	386653	broad.mit.edu	37	chr12	122658409	122658409	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctttcaaaagcatcttCgagagggactgtaattcctc	7	10	3	1	rs141921768		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122658409C>T	ENST00000377035.1	-	2	173	c.147G>A	c.(145-147)tcG>tcA	p.S49S		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	49					immune system process (GO:0002376)	extracellular space (GO:0005615)		p.S49S(1)		central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		AAAGCATCTTCGAGAGGGACT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	2,4404	4.2+/-10.8	0,2,2201	110	101	104		147,	-8.3	0	12	dbSNP_134	104	0,8600		0,0,4300	no	coding-synonymous,intron	LRRC43,IL31	NM_001014336.1,NM_152759.4	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	49/165,	122658409	2,13004	2203	4300	6503	121224362	SO:0001819	synonymous_variant	386653			AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"Interleukins and interleukin receptors"	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.147G>A	12.37:g.122658409C>T			121224362	A2RUQ1	Silent	SNP	ENST00000377035.1	37	CCDS31919.1																																																																																				0.483	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336		T	122658409	C	T	122658409	2	4	61	1	0	0	0	0	0	0	0	1	7711	871	31	1		1	IL31	12	122658409	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40362	122658409	11193486	8440	16425										
LRRC43	254050	broad.mit.edu	37	chr12	122669073	122669073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgccactgcagaataagtCgcgctttcttcctcaaactt	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122669073C>T	ENST00000339777.4	+	2	186	c.158C>T	c.(157-159)tCg>tTg	p.S53L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	53								p.S53L(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	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)		CAGAATAAGTCGCGCTTTCTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	12											40	41	41					12																	122669073		1956	4147	6103	121235026	SO:0001583	missense	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.158C>T	12.37:g.122669073C>T	ENSP00000344233:p.Ser53Leu		121235026	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010416	0.54361	.	.	ENSG00000158113	ENST00000339777	T	0.60040	0.22	4.94	4.04	0.47022	.	.	.	.	.	T	0.72317	0.3445	M	0.67953	2.075	0.58432	D	0.999994	D	0.76494	0.999	D	0.77557	0.99	T	0.75830	-0.3179	9	0.87932	D	0	-1.7082	13.2026	0.59776	0.0:0.9202:0.0:0.0798	.	53	Q8N309	LRC43_HUMAN	L	53	ENSP00000344233:S53L	ENSP00000344233:S53L	S	+	2	0	LRRC43	121235026	0.982000	0.34865	0.060000	0.19600	0.253000	0.25986	3.123000	0.50453	2.272000	0.75746	0.462000	0.41574	TCG		0.547	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122669073	C	T	122669073	3	4	61	1	0	0	0	0	1	0	0	0	9030	893	31	1	164	1	LRRC43	12	122669073	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10664	122669073	11182822	8441	16426										
LRRC43	254050	broad.mit.edu	37	chr12	122685168	122685168	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacaagaaagggaaggaGaaagacaggacggggaaagg	17	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122685168G>T	ENST00000339777.4	+	9	1609	c.1581G>T	c.(1579-1581)gaG>gaT	p.E527D	LRRC43_ENST00000425921.1_Missense_Mutation_p.E342D|B3GNT4_ENST00000324189.4_5'Flank|LRRC43_ENST00000537733.1_3'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	527	Lys-rich.							p.E527D(1)|p.E342D(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	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)		aagggaaggagaaagacagga	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	12											92	109	104					12																	122685168		1966	4129	6095	121251121	SO:0001583	missense	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1581G>T	12.37:g.122685168G>T	ENSP00000344233:p.Glu527Asp		121251121	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	G	7.327	0.618242	0.14129	.	.	ENSG00000158113	ENST00000339777;ENST00000289014;ENST00000425921	T;T	0.56275	0.47;0.88	4.4	1.41	0.22369	.	0.781535	0.10513	N	0.665870	T	0.37732	0.1014	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.24048	-1.0171	10	0.35671	T	0.21	-1.416	7.6994	0.28613	0.0892:0.312:0.5988:0.0	.	527	Q8N309	LRC43_HUMAN	D	527;398;342	ENSP00000344233:E527D;ENSP00000416628:E342D	ENSP00000289014:E398D	E	+	3	2	LRRC43	121251121	0.325000	0.24660	0.000000	0.03702	0.003000	0.03518	0.777000	0.26718	0.166000	0.19597	0.650000	0.86243	GAG		0.587	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122685168	G	T	122685168	3	4	61	1	0	0	0	0	1	0	0	0	9030	933	33	2	1615	2	LRRC43	12	122685168	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16095	122685168	11166727	8442	16427										
CLIP1	6249	broad.mit.edu	37	chr12	122794329	122794329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttgatgacttgtgacttCgtccctgcttctccccagct	7	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122794329C>T	ENST00000540338.1	-	19	3615	c.3574G>A	c.(3574-3576)Gaa>Aaa	p.E1192K	CLIP1_ENST00000545889.1_Missense_Mutation_p.E767K|CLIP1_ENST00000361654.4_Missense_Mutation_p.E1070K|CLIP1_ENST00000358808.2_Missense_Mutation_p.E1181K|CLIP1_ENST00000537178.1_Missense_Mutation_p.E1146K|CLIP1_ENST00000302528.7_Missense_Mutation_p.E1181K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1192					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.E1181K(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTTGTGACTTCGTCCCTGCTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											202	126	152					12																	122794329		2203	4300	6503	121360282	SO:0001583	missense	6249				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.3574G>A	12.37:g.122794329C>T	ENSP00000439093:p.Glu1192Lys		121360282	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438276	0.43326	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000392458;ENST00000537178;ENST00000540338	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	5.57	3.67	0.42095	.	0.667620	0.16017	N	0.233512	T	0.25791	0.0628	L	0.27053	0.805	0.42513	D	0.992971	B;B;B	0.23591	0.088;0.088;0.025	B;B;B	0.25614	0.062;0.038;0.007	T	0.03268	-1.1054	10	0.17832	T	0.49	-10.0363	12.3337	0.55054	0.1345:0.7362:0.1292:0.0	.	1146;1181;1192	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	K	767;1181;1181;911;223;1146;1192	ENSP00000438743:E767K;ENSP00000303585:E1181K;ENSP00000351665:E1181K;ENSP00000445531:E1146K;ENSP00000439093:E1192K	ENSP00000303585:E1181K	E	-	1	0	CLIP1	121360282	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.546000	0.45778	0.652000	0.30806	0.555000	0.69702	GAA		0.557	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122794329	C	T	122794329	3	4	61	1	0	0	0	0	1	0	0	0	3538	893	31	1	770	1	CLIP1	12	122794329	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109161	122794329	11057566	8443	16428										
ZCCHC8	55596	broad.mit.edu	37	chr12	122966082	122966082	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actataccttttccatcataGagtgcaagccccgaattctc	5	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122966082G>T	ENST00000336229.4	-	10	1135	c.1005C>A	c.(1003-1005)ctC>ctA	p.L335L	ZCCHC8_ENST00000543897.1_Silent_p.L97L|ZCCHC8_ENST00000536306.1_Silent_p.L97L	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	335					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L335L(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TTCCATCATAGAGTGCAAGCC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											129	125	126					12																	122966082		1829	4079	5908	121532035	SO:0001819	synonymous_variant	55596			BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.1005C>A	12.37:g.122966082G>T			121532035	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Silent	SNP	ENST00000336229.4	37																																																																																					0.408	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		T	122966082	G	T	122966082	2	4	61	1	0	0	0	0	0	0	0	1	17633	929	33	2		2	ZCCHC8	12	122966082	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	171753	122966082	10885813	8444	16429										
ZCCHC8	55596	broad.mit.edu	37	chr12	122975067	122975067	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctgctgttcctcaaatCtttttactaaatttgataca	3	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122975067C>A	ENST00000336229.4	-	4	495	c.365G>T	c.(364-366)aGa>aTa	p.R122I	ZCCHC8_ENST00000543897.1_5'UTR|SNORA9_ENST00000516383.1_RNA|ZCCHC8_ENST00000536306.1_5'UTR	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	122					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R122I(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TTCCTCAAATCTTTTTACTAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	12											67	63	64					12																	122975067		1807	4068	5875	121541020	SO:0001583	missense	55596			BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.365G>T	12.37:g.122975067C>A	ENSP00000337313:p.Arg122Ile		121541020	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	C	16.83	3.231215	0.58777	.	.	ENSG00000033030	ENST00000336229	T	0.50813	0.73	5.83	4.94	0.65067	.	0.041724	0.85682	D	0.000000	T	0.41858	0.1177	L	0.54323	1.7	0.51482	D	0.99992	B	0.31009	0.303	B	0.31495	0.131	T	0.42481	-0.9449	10	0.59425	D	0.04	-22.8154	8.7725	0.34742	0.0:0.7958:0.0:0.2042	.	122	Q6NZY4	ZCHC8_HUMAN	I	122	ENSP00000337313:R122I	ENSP00000337313:R122I	R	-	2	0	ZCCHC8	121541020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.485000	0.45250	2.763000	0.94921	0.563000	0.77884	AGA		0.328	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		A	122975067	C	A	122975067	3	1	61	1	0	0	0	0	1	0	0	0	17633	913	32	2	1802	2	ZCCHC8	12	122975067	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8985	122975067	10876828	8445	16430										
RSRC2	65117	broad.mit.edu	37	chr12	122999749	122999749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttctgctaaatcttctcgGcttttcaattctcttctttc	3	12	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:122999749G>A	ENST00000331738.7	-	6	773	c.628C>T	c.(628-630)Ccg>Tcg	p.P210S	RSRC2_ENST00000392442.2_5'Flank|RSRC2_ENST00000354654.2_Missense_Mutation_p.P162S	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2	210							poly(A) RNA binding (GO:0044822)	p.P210S(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		AATCTTCTCGGCTTTTCAATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	12											203	197	199					12																	122999749		2203	4300	6503	121565702	SO:0001583	missense	65117			AF161432	CCDS31920.1	12q24.31	2007-02-13			ENSG00000111011	ENSG00000111011			30559	protein-coding gene	gene with protein product						17203224	Standard	NM_023012		Approved	FLJ11021	uc001ucr.3	Q7L4I2	OTTHUMG00000167572	ENST00000331738.7:c.628C>T	12.37:g.122999749G>A	ENSP00000330188:p.Pro210Ser		121565702	Q6N040|Q6NW16|Q9H864	Missense_Mutation	SNP	ENST00000331738.7	37	CCDS31920.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037158	0.35893	.	.	ENSG00000111011	ENST00000331738;ENST00000354654;ENST00000418773;ENST00000344591	T;T;T	0.14516	2.5;2.5;2.5	5.63	5.63	0.86233	.	0.259597	0.45867	D	0.000332	T	0.09686	0.0238	N	0.14661	0.345	0.37299	D	0.90862	B;B;B;B	0.17268	0.021;0.009;0.021;0.003	B;B;B;B	0.16289	0.015;0.003;0.015;0.003	T	0.21449	-1.0245	10	0.09338	T	0.73	.	20.0442	0.97604	0.0:0.0:1.0:0.0	.	210;162;210;151	F5GXM2;Q7L4I2-2;Q7L4I2;E1B6W4	.;.;RSRC2_HUMAN;.	S	210;162;210;151	ENSP00000330188:P210S;ENSP00000346678:P162S;ENSP00000343315:P151S	ENSP00000330188:P210S	P	-	1	0	RSRC2	121565702	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.974000	0.56852	2.814000	0.96858	0.655000	0.94253	CCG		0.378	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	NM_023012		A	122999749	G	A	122999749	3	1	61	1	0	0	0	0	1	0	0	0	13752	1203	42	3	696	3	RSRC2	12	122999749	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24682	122999749	10852146	8446	16431										
KNTC1	9735	broad.mit.edu	37	chr12	123058871	123058871	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagtccacatcactctttGaaacagcatgggaagcaaag	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123058871G>T	ENST00000333479.7	+	27	2503	c.2326G>T	c.(2326-2328)Gaa>Taa	p.E776*	KNTC1_ENST00000450485.2_Nonsense_Mutation_p.E739*	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	776					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.E776*(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	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)		ATCACTCTTTGAAACAGCATG	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											80	76	77					12																	123058871		1900	4131	6031	121624824	SO:0001587	stop_gained	9735				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2326G>T	12.37:g.123058871G>T	ENSP00000328236:p.Glu776*		121624824	A7E2C4|B3KSG2	Nonsense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	41	8.708985	0.98922	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	.	.	.	5.61	5.61	0.85477	.	0.193029	0.36066	N	0.002813	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-11.7798	19.6299	0.95698	0.0:0.0:1.0:0.0	.	.	.	.	X	739;776	.	ENSP00000328236:E776X	E	+	1	0	KNTC1	121624824	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.541000	0.82084	2.640000	0.89533	0.563000	0.77884	GAA		0.343	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123058871	G	T	123058871	4	4	61	1	0	0	0	0	0	1	0	0	8449	1291	45	2	2428	2	KNTC1	12	123058871	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59122	123058871	10793024	8447	16432										
KNTC1	9735	broad.mit.edu	37	chr12	123098300	123098300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggaaaaaccacagccacGagtccatggtaggtacacct	10	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123098300G>A	ENST00000333479.7	+	55	6046	c.5869G>A	c.(5869-5871)Gag>Aag	p.E1957K	KNTC1_ENST00000450485.2_Missense_Mutation_p.E882K|KNTC1_ENST00000537348.1_Missense_Mutation_p.E382K|KNTC1_ENST00000436959.3_5'UTR	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1957					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.E1957K(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	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)		CCACAGCCACGAGTCCATGGT	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											72	66	68					12																	123098300		1877	4117	5994	121664253	SO:0001583	missense	9735				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.5869G>A	12.37:g.123098300G>A	ENSP00000328236:p.Glu1957Lys		121664253	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028668	0.75390	.	.	ENSG00000184445	ENST00000450485;ENST00000333479;ENST00000537348;ENST00000546125	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.81	5.81	0.92471	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.54679	0.1873	M	0.71581	2.175	0.54753	D	0.999987	D;D	0.67145	0.996;0.994	P;P	0.61874	0.895;0.872	T	0.47947	-0.9077	10	0.29301	T	0.29	-26.5803	14.2655	0.66116	0.0708:0.0:0.9292:0.0	.	882;1957	E7ES84;P50748	.;KNTC1_HUMAN	K	882;1957;382;118	ENSP00000397992:E882K;ENSP00000328236:E1957K;ENSP00000443622:E382K;ENSP00000439119:E118K	ENSP00000328236:E1957K	E	+	1	0	KNTC1	121664253	1.000000	0.71417	0.168000	0.22838	0.556000	0.35491	7.489000	0.81451	2.752000	0.94435	0.557000	0.71058	GAG		0.438	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			A	123098300	G	A	123098300	3	1	61	1	0	0	0	0	1	0	0	0	8449	1059	37	1	6083	1	KNTC1	12	123098300	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39429	123098300	10753595	8448	16433										
KNTC1	9735	broad.mit.edu	37	chr12	123107101	123107101	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatgttgaagatgcatgcGatgaataccaacaatatcac	7	8	1	3	rs538519234		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123107101G>A	ENST00000333479.7	+	62	6639	c.6462G>A	c.(6460-6462)gcG>gcA	p.A2154A	KNTC1_ENST00000450485.2_Silent_p.A1079A|KNTC1_ENST00000537348.1_3'UTR|HCAR1_ENST00000356987.2_Intron|KNTC1_ENST00000436959.3_Silent_p.A75A|KNTC1_ENST00000534995.1_Silent_p.A75A	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	2154					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.A2154A(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	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)		AGATGCATGCGATGAATACCA	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	12											45	43	43					12																	123107101		1848	4085	5933	121673054	SO:0001819	synonymous_variant	9735				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.6462G>A	12.37:g.123107101G>A			121673054	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	37	CCDS45002.1																																																																																				0.294	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			A	123107101	G	A	123107101	2	1	61	1	0	0	0	0	0	0	0	1	8449	1045	37	1		1	KNTC1	12	123107101	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8801	123107101	10744794	8449	16434										
GPR109A	338442	broad.mit.edu	37	chr12	123186843	123186843	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggggtcccctgtgagctCgacgctcgtgctgcggttat	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123186843C>T	ENST00000328880.5	-	1	1047	c.988G>A	c.(988-990)Gag>Aag	p.E330K	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	330					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)	p.E330K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	CCTGTGAGCTCGACGCTCGTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											126	116	119					12																	123186843		2203	4300	6503	121752796	SO:0001583	missense	338442			AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.988G>A	12.37:g.123186843C>T	ENSP00000375066:p.Glu330Lys		121752796	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	37	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828834	0.32329	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.61742	0.08	5.5	3.47	0.39725	.	0.215234	0.29451	U	0.012119	T	0.33818	0.0876	L	0.44542	1.39	0.31309	N	0.687409	P	0.45348	0.856	B	0.27608	0.081	T	0.42103	-0.9471	10	0.08599	T	0.76	-23.8309	6.944	0.24508	0.166:0.7379:0.0:0.0961	.	330	Q8TDS4	HCAR2_HUMAN	K	330	ENSP00000375066:E330K	ENSP00000375066:E330K	E	-	1	0	HCAR2	121752796	0.698000	0.27777	0.655000	0.29622	0.162000	0.22319	1.008000	0.29872	0.655000	0.30866	0.563000	0.77884	GAG		0.577	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		T	123186843	C	T	123186843	3	4	61	1	0	0	0	0	1	0	0	0	6645	893	31	1	107	1	GPR109A	12	123186843	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79742	123186843	10665052	8450	16435										
DENR	8562	broad.mit.edu	37	chr12	123253328	123253328	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctttttttaaaaaaataGaaattgatcttaaagaagca	4	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123253328G>T	ENST00000280557.6	+	7	598		c.e7-1		DENR_ENST00000455982.2_Splice_Site|Y_RNA_ENST00000384187.1_RNA	NM_003677.3	NP_003668.2	O43583	DENR_HUMAN	density-regulated protein						formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)		translation initiation factor activity (GO:0003743)	p.?(1)		kidney(1)|large_intestine(1)|urinary_tract(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.28e-05)|Epithelial(86;6.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.199)		TAAAAAAATAGAAATTGATCT	0.299																																																1	Unknown(1)	large_intestine(1)	12											12	11	11					12																	123253328		1773	4028	5801	121819281	SO:0001630	splice_region_variant	8562			AF038554	CCDS45003.1	12q24.31	1999-06-17			ENSG00000139726	ENSG00000139726			2769	protein-coding gene	gene with protein product		604550				9628587	Standard	NM_003677		Approved	DRP, DRP1, SMAP-3	uc001uda.3	O43583	OTTHUMG00000168844	ENST00000280557.6:c.413-1G>T	12.37:g.123253328G>T			121819281	Q9H3U6|Q9UKZ0	Splice_Site	SNP	ENST00000280557.6	37	CCDS45003.1	.	.	.	.	.	.	.	.	.	.	.	19.76	3.887536	0.72410	.	.	ENSG00000139726	ENST00000280557;ENST00000455982	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5949	0.91226	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DENR	121819281	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.689000	0.98673	2.458000	0.83093	0.638000	0.83543	.		0.299	DENR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401336.1	NM_003677	Intron	T	123253328	G	T	123253328	5	4	61	1	0	0	0	0	0	0	1	0	4449	956	33	2	434	2	DENR	12	123253328	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66485	123253328	10598567	8451	16436										
MPHOSPH9	10198	broad.mit.edu	37	chr12	123645694	123645694	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttttacctggtccttttCttttgtaagttcatcaaaaa	5	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123645694C>A	ENST00000606320.1	-	22	3576	c.3370G>T	c.(3370-3372)Gaa>Taa	p.E1124*	MPHOSPH9_ENST00000392425.3_Nonsense_Mutation_p.E972*|MPHOSPH9_ENST00000302349.5_Nonsense_Mutation_p.E972*|MPHOSPH9_ENST00000541076.2_Nonsense_Mutation_p.E1094*			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	1124						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E972*(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		TGGTCCTTTTCTTTTGTAAGT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											56	55	55					12																	123645694		2203	4300	6503	122211647	SO:0001587	stop_gained	10198			X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.3370G>T	12.37:g.123645694C>A	ENSP00000475489:p.Glu1124*		122211647	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Nonsense_Mutation	SNP	ENST00000606320.1	37		.	.	.	.	.	.	.	.	.	.	C	41	8.549335	0.98859	.	.	ENSG00000051825	ENST00000541603;ENST00000302349;ENST00000541076	.	.	.	5.8	5.8	0.92144	.	0.135962	0.48767	D	0.000163	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.0215	20.0693	0.97712	0.0:1.0:0.0:0.0	.	.	.	.	X	150;972;972	.	ENSP00000303597:E972X	E	-	1	0	MPHOSPH9	122211647	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.747000	0.68689	2.758000	0.94735	0.563000	0.77884	GAA		0.343	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2			A	123645694	C	A	123645694	4	1	61	1	0	0	0	0	0	1	0	0	9758	922	32	2	193	2	MPHOSPH9	12	123645694	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	392366	123645694	10206201	8452	16437										
SBNO1	55206	broad.mit.edu	37	chr12	123808274	123808274	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaaggactatctcttggcGaactgttgttacttggagct	10	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123808274G>A	ENST00000602398.1	-	16	2205	c.2078C>T	c.(2077-2079)tCg>tTg	p.S693L	SBNO1_ENST00000602750.1_Missense_Mutation_p.S692L|SBNO1_ENST00000267176.4_Missense_Mutation_p.S692L|SBNO1_ENST00000420886.2_Missense_Mutation_p.S693L			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	693					regulation of transcription, DNA-templated (GO:0006355)			p.S692L(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ATCTCTTGGCGAACTGTTGTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	60	59					12																	123808274		2203	4300	6503	122374227	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2078C>T	12.37:g.123808274G>A	ENSP00000473665:p.Ser693Leu		122374227	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.158682	0.57368	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	T;T	0.31769	1.48;1.48	5.79	5.79	0.91817	.	0.216427	0.41294	D	0.000918	T	0.26666	0.0652	L	0.47716	1.5	0.51767	D	0.999932	P;P;P	0.46327	0.659;0.844;0.876	B;B;B	0.32864	0.056;0.154;0.131	T	0.05007	-1.0912	10	0.27785	T	0.31	-17.0946	20.04	0.97581	0.0:0.0:1.0:0.0	.	693;692;691	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	L	693;692;692	ENSP00000387361:S693L;ENSP00000267176:S692L	ENSP00000267176:S692L	S	-	2	0	SBNO1	122374227	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.577000	0.82486	2.733000	0.93635	0.655000	0.94253	TCG		0.388	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123808274	G	A	123808274	3	1	61	1	0	0	0	0	1	0	0	0	13899	1059	37	1	2171	1	SBNO1	12	123808274	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	162580	123808274	10043621	8453	16438										
SBNO1	55206	broad.mit.edu	37	chr12	123815832	123815832	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaataattttcatagatgaTtcctgctatcgtccttcctt	4	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:123815832T>G	ENST00000602398.1	-	8	1127	c.1000A>C	c.(1000-1002)Atc>Ctc	p.I334L	SBNO1_ENST00000602750.1_Missense_Mutation_p.I333L|SBNO1_ENST00000267176.4_Missense_Mutation_p.I333L|SBNO1_ENST00000420886.2_Missense_Mutation_p.I334L			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	334					regulation of transcription, DNA-templated (GO:0006355)			p.I333L(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TCATAGATGATTCCTGCTATC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	141	147					12																	123815832		2203	4300	6503	122381785	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1000A>C	12.37:g.123815832T>G	ENSP00000473665:p.Ile334Leu		122381785	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270237	0.59540	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.92348	-3.02;-3.02	5.83	4.68	0.58851	Helicase/UvrB domain (1);	0.053100	0.64402	D	0.000001	D	0.90518	0.7029	M	0.67700	2.07	0.58432	D	0.999999	B;B;B	0.23128	0.08;0.032;0.047	B;B;B	0.26864	0.074;0.044;0.023	D	0.86892	0.2049	10	0.46703	T	0.11	-16.3253	11.8661	0.52495	0.0:0.0681:0.0:0.9319	.	334;333;332	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	L	334;333;333	ENSP00000387361:I334L;ENSP00000267176:I333L	ENSP00000267176:I333L	I	-	1	0	SBNO1	122381785	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.423000	0.52756	1.032000	0.39892	0.459000	0.35465	ATC		0.438	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		G	123815832	T	G	123815832	3	3	61	1	0	0	0	0	1	0	0	0	13899	1493	52	4	3281	4	SBNO1	12	123815832	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7558	123815832	10036063	8454	16439										
TCTN2	79867	broad.mit.edu	37	chr12	124163819	124163819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctggagcctgtgatgttCgctgctgctgtgaccaggta	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124163819C>T	ENST00000303372.5	+	5	675	c.547C>T	c.(547-549)Cgc>Tgc	p.R183C	TCTN2_ENST00000426174.2_Missense_Mutation_p.R182C	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	183	Cys-rich.				cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.R183C(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		CTGTGATGTTCGCTGCTGCTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											218	192	201					12																	124163819		2203	4300	6503	122729772	SO:0001583	missense	79867			AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.547C>T	12.37:g.124163819C>T	ENSP00000304941:p.Arg183Cys		122729772	A8K7Y8|B3KPW5|Q9H966	Missense_Mutation	SNP	ENST00000303372.5	37	CCDS9253.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233387	0.79688	.	.	ENSG00000168778	ENST00000426174;ENST00000303372	D;D	0.83250	-1.7;-1.7	5.05	5.05	0.67936	Domain of unknown function DUF1619 (1);	0.074229	0.56097	D	0.000037	D	0.90089	0.6904	M	0.76574	2.34	0.54753	D	0.999987	D;D	0.76494	0.999;0.999	D;D	0.63033	0.91;0.91	D	0.90990	0.4834	10	0.59425	D	0.04	-12.1279	18.0585	0.89370	0.0:1.0:0.0:0.0	.	182;183	A8K7Y8;Q96GX1	.;TECT2_HUMAN	C	182;183	ENSP00000395171:R182C;ENSP00000304941:R183C	ENSP00000304941:R183C	R	+	1	0	TCTN2	122729772	0.998000	0.40836	0.978000	0.43139	0.967000	0.64934	3.938000	0.56583	2.343000	0.79666	0.416000	0.27883	CGC		0.448	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		T	124163819	C	T	124163819	3	4	61	1	0	0	0	0	1	0	0	0	15762	884	31	1	565	1	TCTN2	12	124163819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	347987	124163819	9688076	8455	16440										
DNAH10	196385	broad.mit.edu	37	chr12	124256209	124256209	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaacagagaggatgaagaAatggacaaagagatttcaga	11	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124256209A>C	ENST00000409039.3	+	3	202	c.177A>C	c.(175-177)gaA>gaC	p.E59D		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	59	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E59D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGGATGAAGAAATGGACAAAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	12											85	78	81					12																	124256209		1853	4091	5944	122822162	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.177A>C	12.37:g.124256209A>C	ENSP00000386770:p.Glu59Asp		122822162	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	8.346	0.829883	0.16749	.	.	ENSG00000197653	ENST00000409039	T	0.22539	1.95	3.85	-6.99	0.01605	.	.	.	.	.	T	0.08223	0.0205	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38802	-0.9644	9	0.10902	T	0.67	.	3.7268	0.08477	0.2825:0.5005:0.0955:0.1215	.	59	Q8IVF4	DYH10_HUMAN	D	59	ENSP00000386770:E59D	ENSP00000386770:E59D	E	+	3	2	DNAH10	122822162	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.067000	0.00620	-1.026000	0.03330	0.482000	0.46254	GAA		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124256209	A	C	124256209	3	2	61	1	0	0	0	0	1	0	0	0	4609	11	1	4	187	4	DNAH10	12	124256209	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	92390	124256209	9595686	8456	16441										
DNAH10	196385	broad.mit.edu	37	chr12	124265846	124265846	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccatgcagcaacttgaaGgtaaggtttcattttcctcc	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124265846G>A	ENST00000409039.3	+	6	683	c.658G>A	c.(658-660)Ggt>Agt	p.G220S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	220	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G38S(1)|p.G220S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCAACTTGAAGGTAAGGTTTC	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	12											87	92	90					12																	124265846		2203	4300	6503	122831799	SO:0001630	splice_region_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.658+1G>A	12.37:g.124265846G>A			122831799	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.53	2.562831	0.45694	.	.	ENSG00000197653	ENST00000409039	T	0.26067	1.76	4.99	4.99	0.66335	.	0.416726	0.20369	U	0.093681	T	0.31104	0.0786	L	0.59436	1.845	0.80722	D	1	B	0.23185	0.081	B	0.24269	0.052	T	0.09552	-1.0669	10	0.52906	T	0.07	.	17.9259	0.88983	0.0:0.0:1.0:0.0	.	220	Q8IVF4	DYH10_HUMAN	S	220	ENSP00000386770:G220S	ENSP00000386770:G220S	G	+	1	0	DNAH10	122831799	1.000000	0.71417	0.992000	0.48379	0.373000	0.29922	7.436000	0.80404	2.324000	0.78689	0.436000	0.28706	GGT		0.353	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation	A	124265846	G	A	124265846	5	1	61	1	0	0	0	0	0	0	1	0	4609	1014	35	3	680	3	DNAH10	12	124265846	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9637	124265846	9586049	8457	16442										
DNAH10	196385	broad.mit.edu	37	chr12	124281300	124281300	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaatatactgggaacgatCtctgttctttcggattaagc	9	8	2	0	rs137932597	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124281300C>A	ENST00000409039.3	+	12	1755	c.1730C>A	c.(1729-1731)tCt>tAt	p.S577Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	577	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S395Y(1)|p.S577Y(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGGGAACGATCTCTGTTCTTT	0.418													C|||	2	0.000399361	0	0.0029	5008	,	,		17682	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12						C	TYR/SER	0,4406		0,0,2203	150	131	138		1730	5.3	0.1	12	dbSNP_134	138	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DNAH10	NM_207437.3	144	0,5,6498	AA,AC,CC		0.0581,0.0,0.0384	possibly-damaging	577/4472	124281300	5,13001	2203	4300	6503	122847253	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1730C>A	12.37:g.124281300C>A	ENSP00000386770:p.Ser577Tyr		122847253	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	13.32	2.201059	0.38905	0.0	5.81E-4	ENSG00000197653	ENST00000409039	T	0.57907	0.37	5.35	5.35	0.76521	Dynein heavy chain, domain-1 (1);	0.244211	0.26923	N	0.021813	T	0.77445	0.4131	M	0.87758	2.905	0.36991	D	0.894791	D;D;P	0.76494	0.999;0.999;0.871	D;D;P	0.79784	0.973;0.993;0.673	D	0.83622	0.0140	10	0.62326	D	0.03	.	19.0759	0.93161	0.0:1.0:0.0:0.0	.	577;452;577	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	Y	577	ENSP00000386770:S577Y	ENSP00000386770:S577Y	S	+	2	0	DNAH10	122847253	0.952000	0.32445	0.143000	0.22291	0.053000	0.15095	2.356000	0.44116	2.506000	0.84524	0.650000	0.86243	TCT		0.418	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124281300	C	A	124281300	3	1	61	1	0	0	0	0	1	0	0	0	4609	913	32	2	1776	2	DNAH10	12	124281300	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15454	124281300	9570595	8458	16443										
DNAH10	196385	broad.mit.edu	37	chr12	124293364	124293364	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacttgcagtcttttaattCtttgatccttggaaatgtcc	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124293364C>A	ENST00000409039.3	+	18	2679	c.2654C>A	c.(2653-2655)tCt>tAt	p.S885Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	885	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S703Y(1)|p.S885Y(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TCTTTTAATTCTTTGATCCTT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	12											302	278	286					12																	124293364		2203	4300	6503	122859317	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2654C>A	12.37:g.124293364C>A	ENSP00000386770:p.Ser885Tyr		122859317	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	9.934	1.215573	0.22373	.	.	ENSG00000197653	ENST00000409039	T	0.22743	1.94	5.72	4.82	0.62117	.	0.996867	0.08124	N	0.994237	T	0.35422	0.0931	L	0.50333	1.59	0.09310	N	1	P;P;P	0.50943	0.94;0.829;0.833	P;B;B	0.49953	0.627;0.396;0.372	T	0.39502	-0.9611	10	0.72032	D	0.01	.	16.6635	0.85247	0.0:0.8701:0.1299:0.0	.	885;760;885	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	Y	885	ENSP00000386770:S885Y	ENSP00000386770:S885Y	S	+	2	0	DNAH10	122859317	0.000000	0.05858	0.003000	0.11579	0.171000	0.22731	1.236000	0.32683	1.400000	0.46741	0.655000	0.94253	TCT		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124293364	C	A	124293364	3	1	61	1	0	0	0	0	1	0	0	0	4609	913	32	2	2724	2	DNAH10	12	124293364	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12064	124293364	9558531	8459	16444										
DNAH10	196385	broad.mit.edu	37	chr12	124297904	124297904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatctacaaaaatggaagcGgtatcgacctctctggaaat	9	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124297904G>A	ENST00000409039.3	+	19	3009	c.2984G>A	c.(2983-2985)cGg>cAg	p.R995Q		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	995	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R813Q(1)|p.R995Q(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AAATGGAAGCGGTATCGACCT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	12											133	129	131					12																	124297904		2203	4300	6503	122863857	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2984G>A	12.37:g.124297904G>A	ENSP00000386770:p.Arg995Gln		122863857	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483443	0.63962	.	.	ENSG00000197653	ENST00000409039	T	0.21361	2.01	5.83	4.02	0.46733	.	0.495836	0.17768	N	0.162679	T	0.42245	0.1194	M	0.82056	2.57	0.30791	N	0.740882	D;D;B	0.62365	0.991;0.987;0.359	P;P;B	0.59288	0.855;0.769;0.032	T	0.49021	-0.8982	10	0.42905	T	0.14	.	11.6895	0.51508	0.1964:0.0:0.8036:0.0	.	995;870;995	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	Q	995	ENSP00000386770:R995Q	ENSP00000386770:R995Q	R	+	2	0	DNAH10	122863857	0.997000	0.39634	0.805000	0.32314	0.940000	0.58332	2.793000	0.47845	0.821000	0.34540	0.563000	0.77884	CGG		0.393	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124297904	G	A	124297904	3	1	61	1	0	0	0	0	1	0	0	0	4609	1116	39	1	3058	1	DNAH10	12	124297904	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4540	124297904	9553991	8460	16445										
DNAH10	196385	broad.mit.edu	37	chr12	124319972	124319972	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttggatgttggttcagaGaaaatggatgtatcttgaaa	12	2	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124319972G>T	ENST00000409039.3	+	27	4470	c.4445G>T	c.(4444-4446)aGa>aTa	p.R1482I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1482	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R74I(1)|p.R1482I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TTGGTTCAGAGAAAATGGATG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	12											124	111	115					12																	124319972		1873	4108	5981	122885925	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4445G>T	12.37:g.124319972G>T	ENSP00000386770:p.Arg1482Ile		122885925	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.228404	0.79576	.	.	ENSG00000197653	ENST00000409039	T	0.64618	-0.11	5.69	5.69	0.88448	Dynein heavy chain, domain-2 (1);	0.073622	0.52532	U	0.000069	D	0.84547	0.5496	M	0.93150	3.385	0.80722	D	1	D	0.56746	0.977	D	0.65323	0.934	D	0.87870	0.2670	10	0.72032	D	0.01	.	19.8155	0.96566	0.0:0.0:1.0:0.0	.	1482	Q8IVF4	DYH10_HUMAN	I	1482	ENSP00000386770:R1482I	ENSP00000386770:R1482I	R	+	2	0	DNAH10	122885925	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.396000	0.73234	2.682000	0.91365	0.650000	0.86243	AGA		0.378	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124319972	G	T	124319972	3	4	61	1	0	0	0	0	1	0	0	0	4609	942	33	2	4551	2	DNAH10	12	124319972	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22068	124319972	9531923	8461	16446										
DNAH10	196385	broad.mit.edu	37	chr12	124325937	124325937	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaactggtgtccgcgatGatttcagcagaaggagaagt	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124325937G>T	ENST00000409039.3	+	29	4876	c.4851G>T	c.(4849-4851)atG>atT	p.M1617I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1617	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.M209I(1)|p.M1617I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGTCCGCGATGATTTCAGCAG	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	12											239	240	240					12																	124325937		2026	4168	6194	122891890	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4851G>T	12.37:g.124325937G>T	ENSP00000386770:p.Met1617Ile		122891890	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	15.59	2.878401	0.51801	.	.	ENSG00000197653	ENST00000409039	T	0.65178	-0.14	5.23	5.23	0.72850	Dynein heavy chain, domain-2 (1);	0.130953	0.49305	U	0.000144	T	0.72622	0.3483	M	0.79614	2.46	0.53688	D	0.999976	P	0.50272	0.933	P	0.49477	0.612	T	0.75642	-0.3247	10	0.48119	T	0.1	.	18.7853	0.91952	0.0:0.0:1.0:0.0	.	1617	Q8IVF4	DYH10_HUMAN	I	1617	ENSP00000386770:M1617I	ENSP00000386770:M1617I	M	+	3	0	DNAH10	122891890	1.000000	0.71417	0.997000	0.53966	0.377000	0.30045	7.634000	0.83273	2.457000	0.83068	0.561000	0.74099	ATG		0.502	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124325937	G	T	124325937	3	4	61	1	0	0	0	0	1	0	0	0	4609	1290	45	2	4965	2	DNAH10	12	124325937	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5965	124325937	9525958	8462	16447										
DNAH10	196385	broad.mit.edu	37	chr12	124337884	124337884	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgagctgaagagaggctcCtctgaccttagggaggtagg	17	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124337884C>A	ENST00000409039.3	+	35	6094	c.6069C>A	c.(6067-6069)tcC>tcA	p.S2023S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2023					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S615S(1)|p.S2023S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGAGAGGCTCCTCTGACCTTA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	12											41	44	43					12																	124337884		2024	4188	6212	122903837	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6069C>A	12.37:g.124337884C>A			122903837	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.552	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124337884	C	A	124337884	2	1	61	1	0	0	0	0	0	0	0	1	4609	668	24	2		2	DNAH10	12	124337884	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11947	124337884	9514011	8463	16448										
DNAH10	196385	broad.mit.edu	37	chr12	124349171	124349171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgatggtgatgtggatgCtctatgggtggaaaacatga	14	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124349171C>T	ENST00000409039.3	+	39	6609	c.6584C>T	c.(6583-6585)gCt>gTt	p.A2195V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2195	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A787V(1)|p.A2195V(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GATGTGGATGCTCTATGGGTG	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	12											156	152	153					12																	124349171		1980	4175	6155	122915124	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6584C>T	12.37:g.124349171C>T	ENSP00000386770:p.Ala2195Val		122915124	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	33	5.259740	0.95368	.	.	ENSG00000197653	ENST00000409039	D	0.90788	-2.73	5.46	5.46	0.80206	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.64402	U	0.000001	D	0.97343	0.9131	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98459	1.0595	10	0.72032	D	0.01	.	19.3147	0.94207	0.0:1.0:0.0:0.0	.	2195	Q8IVF4	DYH10_HUMAN	V	2195	ENSP00000386770:A2195V	ENSP00000386770:A2195V	A	+	2	0	DNAH10	122915124	1.000000	0.71417	0.779000	0.31741	0.783000	0.44284	7.818000	0.86416	2.559000	0.86315	0.563000	0.77884	GCT		0.478	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124349171	C	T	124349171	3	4	61	1	0	0	0	0	1	0	0	0	4609	797	28	3	6738	3	DNAH10	12	124349171	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11287	124349171	9502724	8464	16449										
DNAH10	196385	broad.mit.edu	37	chr12	124358157	124358157	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgtccatggatatccaaaGaaatttagaagcaaatgtgg	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124358157G>T	ENST00000409039.3	+	45	7509	c.7484G>T	c.(7483-7485)aGa>aTa	p.R2495I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2495	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2495I(1)|p.R1087I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GATATCCAAAGAAATTTAGAA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	12											73	68	69					12																	124358157		1913	4136	6049	122924110	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7484G>T	12.37:g.124358157G>T	ENSP00000386770:p.Arg2495Ile		122924110	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889393	0.91889	.	.	ENSG00000197653	ENST00000409039	T	0.49720	0.77	5.51	5.51	0.81932	ATPase, AAA+ type, core (1);	0.000000	0.85682	U	0.000000	T	0.61388	0.2343	M	0.87547	2.89	0.80722	D	1	P	0.42871	0.792	B	0.43194	0.411	T	0.67968	-0.5533	10	0.49607	T	0.09	.	19.4169	0.94704	0.0:0.0:1.0:0.0	.	2495	Q8IVF4	DYH10_HUMAN	I	2495	ENSP00000386770:R2495I	ENSP00000386770:R2495I	R	+	2	0	DNAH10	122924110	1.000000	0.71417	0.980000	0.43619	0.961000	0.63080	9.808000	0.99193	2.599000	0.87857	0.561000	0.74099	AGA		0.458	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124358157	G	T	124358157	3	4	61	1	0	0	0	0	1	0	0	0	4609	942	33	2	7662	2	DNAH10	12	124358157	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8986	124358157	9493738	8465	16450										
DNAH10	196385	broad.mit.edu	37	chr12	124362407	124362407	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattacatcttcaaccttcGagatctctcacgggttttta	5	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124362407G>A	ENST00000409039.3	+	47	7995	c.7970G>A	c.(7969-7971)cGa>cAa	p.R2657Q		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2657	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2657Q(1)|p.R1249Q(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TTCAACCTTCGAGATCTCTCA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	12											171	175	174					12																	124362407		1967	4148	6115	122928360	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7970G>A	12.37:g.124362407G>A	ENSP00000386770:p.Arg2657Gln		122928360	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	36	5.646461	0.96704	.	.	ENSG00000197653	ENST00000409039	T	0.67698	-0.28	5.46	5.46	0.80206	.	0.000000	0.64402	U	0.000005	D	0.89904	0.6850	H	0.98818	4.34	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.93874	0.7165	10	0.87932	D	0	.	18.9035	0.92452	0.0:0.0:1.0:0.0	.	2657	Q8IVF4	DYH10_HUMAN	Q	2657	ENSP00000386770:R2657Q	ENSP00000386770:R2657Q	R	+	2	0	DNAH10	122928360	1.000000	0.71417	0.542000	0.28115	0.918000	0.54935	9.679000	0.98649	2.572000	0.86782	0.555000	0.69702	CGA		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124362407	G	A	124362407	3	1	61	1	0	0	0	0	1	0	0	0	4609	1058	37	1	8156	1	DNAH10	12	124362407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4250	124362407	9489488	8466	16451										
DNAH10	196385	broad.mit.edu	37	chr12	124364286	124364286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttccagatggctctgcacGaaggagaaccacgcatttat	9	11	1	2	rs191652249		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124364286G>A	ENST00000409039.3	+	49	8243	c.8218G>A	c.(8218-8220)Gaa>Aaa	p.E2740K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2740					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E2740K(1)|p.E1332K(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GGCTCTGCACGAAGGAGAACC	0.527													G|||	1	0.000199681	0	0	5008	,	,		16837	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	12											244	234	237					12																	124364286		2056	4193	6249	122930239	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.8218G>A	12.37:g.124364286G>A	ENSP00000386770:p.Glu2740Lys		122930239	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.03	1.814453	0.32053	.	.	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.76	5.76	0.90799	.	0.477764	0.18074	U	0.152535	T	0.32823	0.0842	L	0.60904	1.88	0.48762	D	0.999708	B	0.18461	0.028	B	0.21360	0.034	T	0.05194	-1.0900	10	0.49607	T	0.09	.	19.9616	0.97254	0.0:0.0:1.0:0.0	.	2740	Q8IVF4	DYH10_HUMAN	K	2740	ENSP00000386770:E2740K	ENSP00000386770:E2740K	E	+	1	0	DNAH10	122930239	1.000000	0.71417	0.772000	0.31596	0.044000	0.14063	6.192000	0.72069	2.724000	0.93272	0.561000	0.74099	GAA		0.527	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124364286	G	A	124364286	3	1	61	1	0	0	0	0	1	0	0	0	4609	1059	37	1	8412	1	DNAH10	12	124364286	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1879	124364286	9487609	8467	16452										
DNAH10	196385	broad.mit.edu	37	chr12	124382417	124382417	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagccaacagtttctacaGaaattgaggcgcagcaacta	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124382417G>T	ENST00000409039.3	+	54	9052	c.9027G>T	c.(9025-9027)caG>caT	p.Q3009H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3009	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Q3009H(1)|p.Q1601H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGTTTCTACAGAAATTGAGGC	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	12											79	79	79					12																	124382417		1864	4111	5975	122948370	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9027G>T	12.37:g.124382417G>T	ENSP00000386770:p.Gln3009His		122948370	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557502	0.27827	.	.	ENSG00000197653	ENST00000409039	T	0.42513	0.97	4.92	3.95	0.45737	Dynein heavy chain, P-loop containing D4 domain (1);	0.181088	0.49916	D	0.000136	T	0.59797	0.2220	M	0.84511	2.7	0.45161	D	0.99817	P	0.37176	0.586	P	0.49637	0.617	T	0.63457	-0.6633	10	0.45353	T	0.12	.	13.8137	0.63278	0.0856:0.0:0.9144:0.0	.	3009	Q8IVF4	DYH10_HUMAN	H	3009	ENSP00000386770:Q3009H	ENSP00000386770:Q3009H	Q	+	3	2	DNAH10	122948370	1.000000	0.71417	0.998000	0.56505	0.085000	0.17905	2.359000	0.44142	2.549000	0.85964	0.561000	0.74099	CAG		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124382417	G	T	124382417	3	4	61	1	0	0	0	0	1	0	0	0	4609	933	33	2	9241	2	DNAH10	12	124382417	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18131	124382417	9469478	8468	16453										
DNAH10	196385	broad.mit.edu	37	chr12	124395209	124395209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagagaaatcaagcccaAaagagagaaggtattgcccg	10	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124395209A>G	ENST00000409039.3	+	58	9795	c.9770A>G	c.(9769-9771)aAa>aGa	p.K3257R		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3257	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K3257R(1)|p.K1849R(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ATCAAGCCCAAAAGAGAGAAG	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	12											66	68	67					12																	124395209		1960	4145	6105	122961162	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9770A>G	12.37:g.124395209A>G	ENSP00000386770:p.Lys3257Arg		122961162	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.11|18.11	3.550414|3.550414	0.65311|0.65311	.|.	.|.	ENSG00000197653|ENSG00000197653	ENST00000540041|ENST00000409039	T|T	0.80033|0.79653	-1.33|-1.29	4.96|4.96	3.8|3.8	0.43715|0.43715	.|Dynein heavy chain, coiled coil stalk (1);	0.114956|0.114956	0.56097|0.56097	N|N	0.000021|0.000021	D|D	0.92182|0.92182	0.7521|0.7521	H|H	0.97635|0.97635	4.045|4.045	0.43593|0.43593	D|D	0.995946|0.995946	.|D	.|0.76494	.|0.999	.|D	.|0.77557	.|0.99	D|D	0.91668|0.91668	0.5348|0.5348	8|10	0.87932|0.41790	D|T	0|0.15	.|.	10.5915|10.5915	0.45312|0.45312	0.9235:0.0:0.0765:0.0|0.9235:0.0:0.0765:0.0	.|.	.|3257	.|Q8IVF4	.|DYH10_HUMAN	E|R	185|3257	ENSP00000445308:K185E|ENSP00000386770:K3257R	ENSP00000445308:K185E|ENSP00000386770:K3257R	K|K	+|+	1|2	0|0	DNAH10|DNAH10	122961162|122961162	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.756000|0.756000	0.42949|0.42949	7.229000|7.229000	0.78088|0.78088	0.737000|0.737000	0.32582|0.32582	0.533000|0.533000	0.62120|0.62120	AAA|AAA		0.453	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			G	124395209	A	G	124395209	3	3	61	1	0	0	0	0	1	0	0	0	4609	14	1	4	10000	4	DNAH10	12	124395209	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12792	124395209	9456686	8469	16454										
DNAH10	196385	broad.mit.edu	37	chr12	124401112	124401112	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacatcgatcctgtgattGacaacgtcttagaaaaaaat	6	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124401112G>T	ENST00000409039.3	+	62	10502	c.10477G>T	c.(10477-10479)Gac>Tac	p.D3493Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3493	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D3493Y(1)|p.D2085Y(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TCCTGTGATTGACAACGTCTT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	12											100	99	99					12																	124401112		1909	4115	6024	122967065	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10477G>T	12.37:g.124401112G>T	ENSP00000386770:p.Asp3493Tyr		122967065	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425846	0.43020	.	.	ENSG00000197653	ENST00000409039	T	0.27720	1.65	4.47	4.47	0.54385	.	0.116934	0.56097	D	0.000029	T	0.56062	0.1960	M	0.71296	2.17	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	T	0.62868	-0.6763	10	0.87932	D	0	.	17.1377	0.86744	0.0:0.0:1.0:0.0	.	3493	Q8IVF4	DYH10_HUMAN	Y	3493	ENSP00000386770:D3493Y	ENSP00000386770:D3493Y	D	+	1	0	DNAH10	122967065	1.000000	0.71417	0.606000	0.28943	0.070000	0.16714	8.010000	0.88615	2.033000	0.60031	0.561000	0.74099	GAC		0.423	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124401112	G	T	124401112	3	4	61	1	0	0	0	0	1	0	0	0	4609	1290	45	2	10723	2	DNAH10	12	124401112	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5903	124401112	9450783	8470	16455										
CCDC92	80212	broad.mit.edu	37	chr12	124422300	124422300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaacaactcagcattttCgttctctttcactttcagtt	3	11	5	0	rs184378821		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124422300C>T	ENST00000238156.3	-	5	655	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	RP11-380L11.3_ENST00000602292.1_RNA|CCDC92_ENST00000545135.1_Missense_Mutation_p.E84K|CCDC92_ENST00000545891.1_Missense_Mutation_p.E84K|DNAH10OS_ENST00000514254.2_5'Flank|CCDC92_ENST00000544798.1_Intron	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	101						centriole (GO:0005814)		p.E101K(1)		large_intestine(5)|lung(2)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		TCAGCATTTTCGTTCTCTTTC	0.453													C|||	1	0.000199681	0	0.0014	5008	,	,		21761	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12											242	229	233					12																	124422300		2203	4300	6503	122988253	SO:0001583	missense	80212			AK026124	CCDS9256.1	12q24.31	2011-09-02			ENSG00000119242	ENSG00000119242			29563	protein-coding gene	gene with protein product	"limkain beta 2"					12477932	Standard	NM_025140		Approved	FLJ22471	uc001ufw.1	Q53HC0	OTTHUMG00000168725	ENST00000238156.3:c.301G>A	12.37:g.124422300C>T	ENSP00000238156:p.Glu101Lys		122988253	B3KNQ0|Q9H697	Missense_Mutation	SNP	ENST00000238156.3	37	CCDS9256.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	25.9	4.688280	0.88639	.	.	ENSG00000119242	ENST00000238156;ENST00000545135;ENST00000545891;ENST00000539761;ENST00000535556	T;T;T;T;T	0.49432	1.71;1.72;1.72;0.78;0.87	5.17	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.68924	0.3054	M	0.83118	2.625	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.70699	-0.4800	10	0.35671	T	0.21	-24.9873	13.9509	0.64116	0.0:0.9266:0.0:0.0734	.	101	Q53HC0	CCD92_HUMAN	K	101;84;84;101;84	ENSP00000238156:E101K;ENSP00000439526:E84K;ENSP00000440024:E84K;ENSP00000439441:E101K;ENSP00000438281:E84K	ENSP00000238156:E101K	E	-	1	0	CCDC92	122988253	1.000000	0.71417	0.054000	0.19295	0.005000	0.04900	7.713000	0.84693	1.310000	0.45006	0.555000	0.69702	GAA		0.453	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140		T	124422300	C	T	124422300	3	4	61	1	0	0	0	0	1	0	0	0	2877	893	31	1	698	1	CCDC92	12	124422300	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21188	124422300	9429595	8471	16456										
ZNF664	144348	broad.mit.edu	37	chr12	124496743	124496743	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctctgagagagcagatCtttttatgcatcagaaaatt	7	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:124496743C>A	ENST00000539644.1	+	6	1882	c.52C>A	c.(52-54)Ctt>Att	p.L18I	ZNF664_ENST00000538932.2_Missense_Mutation_p.L18I|ZNF664_ENST00000392404.3_Missense_Mutation_p.L18I|FAM101A_ENST00000545615.1_Intron|ZNF664_ENST00000337815.4_Missense_Mutation_p.L18I			Q8N3J9	ZN664_HUMAN	zinc finger protein 664	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L18I(1)		breast(1)|large_intestine(5)|lung(6)|skin(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		GAGAGCAGATCTTTTTATGCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	12											63	68	66					12																	124496743		2203	4300	6503	123062696	SO:0001583	missense	144348				CCDS9257.1	12q24.31	2013-05-10			ENSG00000179195	ENSG00000179195		"Zinc fingers, C2H2-type"	25406	protein-coding gene	gene with protein product			"zinc finger protein 176"	ZNF176		12477932	Standard	NM_001204298		Approved	ZFOC1, DKFZp761B128	uc001uga.3	Q8N3J9	OTTHUMG00000168596	ENST00000539644.1:c.52C>A	12.37:g.124496743C>A	ENSP00000441405:p.Leu18Ile		123062696	B3KP97|Q15914|Q3ZCQ7	Missense_Mutation	SNP	ENST00000539644.1	37	CCDS9257.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903918	0.72754	.	.	ENSG00000179195	ENST00000539644;ENST00000392404;ENST00000538932;ENST00000337815	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.4	4.4	0.53042	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36200	N	0.002733	T	0.51517	0.1679	M	0.87180	2.865	0.35143	D	0.769058	B	0.10296	0.003	B	0.35727	0.209	T	0.59783	-0.7389	9	.	.	.	-23.8451	8.5154	0.33242	0.0:0.8985:0.0:0.1015	.	18	Q8N3J9	ZN664_HUMAN	I	18	ENSP00000441405:L18I;ENSP00000376205:L18I;ENSP00000440645:L18I;ENSP00000337320:L18I	.	L	+	1	0	ZNF664	123062696	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	3.651000	0.54431	2.728000	0.93425	0.655000	0.94253	CTT		0.358	ZNF664-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400365.1	NM_152437		A	124496743	C	A	124496743	3	1	61	1	0	0	0	0	1	0	0	0	18111	913	32	2	54	2	ZNF664	12	124496743	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74443	124496743	9355152	8472	16457										
SCARB1	949	broad.mit.edu	37	chr12	125302241	125302241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggacaggctactggggtCgatgcgcacgttctgcaggg	17	9	1	0	rs371712274		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:125302241C>T	ENST00000415380.2	-	2	264	c.139G>A	c.(139-141)Gac>Aac	p.D47N	SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000261693.6_Missense_Mutation_p.D47N|SCARB1_ENST00000541205.1_Missense_Mutation_p.D6N|SCARB1_ENST00000546215.1_Missense_Mutation_p.D47N|SCARB1_ENST00000376788.1_Intron|SCARB1_ENST00000544327.1_5'UTR|SCARB1_ENST00000540495.1_Missense_Mutation_p.D10N|SCARB1_ENST00000339570.5_Missense_Mutation_p.D47N			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	47					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.D47N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	CTACTGGGGTCGATGCGCACG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											111	113	112					12																	125302241		2203	4300	6503	123868194	SO:0001583	missense	949			Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.139G>A	12.37:g.125302241C>T	ENSP00000414979:p.Asp47Asn		123868194	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		.	.	.	.	.	.	.	.	.	.	C	17.47	3.396507	0.62177	.	.	ENSG00000073060	ENST00000339570;ENST00000415380;ENST00000261693;ENST00000546215;ENST00000541205;ENST00000540495;ENST00000545493	T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.29	3.42	0.39159	.	0.050196	0.85682	D	0.000000	T	0.61388	0.2343	L	0.46885	1.475	0.51012	D	0.999904	P;P;P;P;B;B	0.49358	0.736;0.494;0.923;0.923;0.171;0.439	B;B;B;B;B;B	0.40534	0.297;0.196;0.332;0.332;0.07;0.086	T	0.63184	-0.6694	10	0.46703	T	0.11	-58.0068	11.068	0.47987	0.0:0.8013:0.128:0.0707	.	6;47;47;47;47;47	B3KW46;B7ZKQ9;B4E3I1;Q8WTV0;F8W8N0;Q8WTV0-2	.;.;.;SCRB1_HUMAN;.;.	N	47;47;47;47;6;10;47	ENSP00000343795:D47N;ENSP00000414979:D47N;ENSP00000261693:D47N;ENSP00000442862:D47N;ENSP00000446107:D6N;ENSP00000443286:D10N;ENSP00000443454:D47N	ENSP00000261693:D47N	D	-	1	0	SCARB1	123868194	0.985000	0.35326	1.000000	0.80357	0.992000	0.81027	2.663000	0.46774	1.211000	0.43351	0.555000	0.69702	GAC		0.582	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		T	125302241	C	T	125302241	3	4	61	1	0	0	0	0	1	0	0	0	13918	884	31	1	1558	1	SCARB1	12	125302241	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	805498	125302241	8549654	8473	16458										
DHX37	57647	broad.mit.edu	37	chr12	125470724	125470724	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcttcttctccttcttcGacaggggaggggctttggtc	14	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:125470724G>A	ENST00000308736.2	-	2	292	c.194C>T	c.(193-195)tCg>tTg	p.S65L		NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	65							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.S65L(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CTCCTTCTTCGACAGGGGAGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	12											159	154	156					12																	125470724		2203	4300	6503	124036677	SO:0001583	missense	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.194C>T	12.37:g.125470724G>A	ENSP00000311135:p.Ser65Leu		124036677	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	G	5.546	0.285652	0.10513	.	.	ENSG00000150990	ENST00000308736	T	0.10005	2.92	3.82	3.82	0.43975	.	1.082840	0.07061	N	0.833758	T	0.12433	0.0302	L	0.59436	1.845	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25916	-1.0118	10	0.31617	T	0.26	2.2816	5.7929	0.18371	0.1103:0.2005:0.6892:0.0	.	65	Q8IY37	DHX37_HUMAN	L	65	ENSP00000311135:S65L	ENSP00000311135:S65L	S	-	2	0	DHX37	124036677	0.025000	0.19082	0.011000	0.14972	0.247000	0.25773	2.140000	0.42159	1.835000	0.53391	0.491000	0.48974	TCG		0.507	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125470724	G	A	125470724	3	1	61	1	0	0	0	0	1	0	0	0	4521	1059	37	1	3383	1	DHX37	12	125470724	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168483	125470724	8381171	8474	16459										
TMEM132B	114795	broad.mit.edu	37	chr12	126128824	126128824	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcccggttgctgccaacaGaaggtgaggaatcaaagaga	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:126128824G>T	ENST00000299308.3	+	6	1633	c.1625G>T	c.(1624-1626)aGa>aTa	p.R542I	TMEM132B_ENST00000535886.1_Missense_Mutation_p.R54I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	542						integral component of membrane (GO:0016021)		p.R542I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		GCTGCCAACAGAAGGTGAGGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12											37	39	39					12																	126128824		1934	4150	6084	124694777	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1625G>T	12.37:g.126128824G>T	ENSP00000299308:p.Arg542Ile		124694777	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015590	0.35511	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.20463	2.07;2.07	5.52	1.1	0.20463	.	0.275183	0.30519	N	0.009451	T	0.20047	0.0482	L	0.52905	1.665	0.54753	D	0.999986	P	0.49559	0.925	P	0.44990	0.466	T	0.02081	-1.1217	10	0.45353	T	0.12	.	6.834	0.23925	0.6314:0.0:0.3686:0.0	.	542	Q14DG7	T132B_HUMAN	I	542;54	ENSP00000299308:R542I;ENSP00000440436:R54I	ENSP00000299308:R542I	R	+	2	0	TMEM132B	124694777	1.000000	0.71417	0.407000	0.26434	0.027000	0.11550	2.944000	0.49034	0.296000	0.22592	-0.150000	0.13652	AGA		0.572	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	126128824	G	T	126128824	3	4	61	1	0	0	0	0	1	0	0	0	16085	942	33	2	1647	2	TMEM132B	12	126128824	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	658100	126128824	7723071	8475	16460										
GLT1D1	144423	broad.mit.edu	37	chr12	129373226	129373226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctttggtggaactgatgTaaatgaagatgccaaccagg	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:129373226T>C	ENST00000442111.2	+	3	348	c.260T>C	c.(259-261)gTa>gCa	p.V87A	GLT1D1_ENST00000537468.1_Missense_Mutation_p.V76A|GLT1D1_ENST00000542193.1_5'UTR|GLT1D1_ENST00000281703.6_Missense_Mutation_p.V87A			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	87					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)	p.V87A(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GGAACTGATGTAAATGAAGAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											108	95	99					12																	129373226		2203	4300	6503	127939179	SO:0001583	missense	144423				CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"Glycosyltransferase group 1 domain containing"	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.260T>C	12.37:g.129373226T>C	ENSP00000394692:p.Val87Ala		127939179	Q86XG8	Missense_Mutation	SNP	ENST00000442111.2	37		.	.	.	.	.	.	.	.	.	.	T	10.64	1.407290	0.25378	.	.	ENSG00000151948	ENST00000442111;ENST00000281703;ENST00000537468	T;T;T	0.78924	-1.22;0.7;-1.22	5.4	5.4	0.78164	.	0.178001	0.46442	D	0.000300	T	0.66147	0.2760	N	0.24115	0.695	0.80722	D	1	P;B	0.35242	0.492;0.287	B;B	0.35607	0.206;0.053	T	0.64795	-0.6323	10	0.25106	T	0.35	-3.5586	14.6068	0.68486	0.0:0.0:0.0:1.0	.	76;87	F5H088;Q96MS3-2	.;.	A	87;87;76	ENSP00000394692:V87A;ENSP00000281703:V87A;ENSP00000438158:V76A	ENSP00000281703:V87A	V	+	2	0	GLT1D1	127939179	1.000000	0.71417	0.810000	0.32431	0.264000	0.26372	4.902000	0.63266	2.039000	0.60335	0.528000	0.53228	GTA		0.448	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669		C	129373226	T	C	129373226	3	2	61	1	0	0	0	0	1	0	0	0	6485	1638	57	4	270	4	GLT1D1	12	129373226	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3244402	129373226	4478669	8476	16461										
GLT1D1	144423	broad.mit.edu	37	chr12	129431920	129431920	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattggagagatgcctcaaGaagatctgcacgcggtggtg	15	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:129431920G>T	ENST00000442111.2	+	10	785	c.697G>T	c.(697-699)Gaa>Taa	p.E233*	GLT1D1_ENST00000537468.1_Nonsense_Mutation_p.E238*|GLT1D1_ENST00000542193.1_Nonsense_Mutation_p.E150*|GLT1D1_ENST00000281703.6_Nonsense_Mutation_p.E153*			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	233					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)	p.E153*(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GATGCCTCAAGAAGATCTGCA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											178	144	155					12																	129431920		2203	4300	6503	127997873	SO:0001587	stop_gained	144423				CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"Glycosyltransferase group 1 domain containing"	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.697G>T	12.37:g.129431920G>T	ENSP00000394692:p.Glu233*		127997873	Q86XG8	Nonsense_Mutation	SNP	ENST00000442111.2	37		.	.	.	.	.	.	.	.	.	.	G	15.24	2.775336	0.49786	.	.	ENSG00000151948	ENST00000442111;ENST00000281703;ENST00000537468;ENST00000542193	.	.	.	5.66	5.66	0.87406	.	1.449630	0.03730	N	0.253234	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-5.4445	13.4863	0.61369	0.0:0.0:0.8435:0.1565	.	.	.	.	X	233;153;238;150	.	ENSP00000281703:E153X	E	+	1	0	GLT1D1	127997873	0.976000	0.34144	0.034000	0.17996	0.001000	0.01503	2.145000	0.42207	2.648000	0.89879	0.655000	0.94253	GAA		0.498	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669		T	129431920	G	T	129431920	4	4	61	1	0	0	0	0	0	1	0	0	6485	943	33	2	479	2	GLT1D1	12	129431920	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58694	129431920	4419975	8477	16462										
TMEM132D	121256	broad.mit.edu	37	chr12	129559186	129559186	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccatgagtcccatagaaGaactgccatagtactgtcct	7	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:129559186G>T	ENST00000422113.2	-	9	2860	c.2534C>A	c.(2533-2535)tCt>tAt	p.S845Y	TMEM132D_ENST00000389441.4_Missense_Mutation_p.S383Y	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	845					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.S845Y(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		TCCCATAGAAGAACTGCCATA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	113	115					12																	129559186		2203	4300	6503	128125139	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2534C>A	12.37:g.129559186G>T	ENSP00000408581:p.Ser845Tyr		128125139	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.491380	0.26774	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.10763	2.84;3.63	4.2	2.17	0.27698	.	0.547632	0.17493	N	0.172271	T	0.18467	0.0443	M	0.80746	2.51	0.09310	N	1	P;P	0.47350	0.867;0.894	P;P	0.46362	0.509;0.514	T	0.05818	-1.0862	9	.	.	.	-5.4767	9.3608	0.38195	0.0864:0.1483:0.7653:0.0	.	845;383	Q14C87;Q14C87-2	T132D_HUMAN;.	Y	383;845	ENSP00000374092:S383Y;ENSP00000408581:S845Y	.	S	-	2	0	TMEM132D	128125139	0.995000	0.38212	0.164000	0.22755	0.170000	0.22686	5.191000	0.65110	2.033000	0.60031	0.462000	0.41574	TCT		0.527	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	129559186	G	T	129559186	3	4	61	1	0	0	0	0	1	0	0	0	16086	942	33	2	769	2	TMEM132D	12	129559186	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127266	129559186	4292709	8478	16463										
TMEM132D	121256	broad.mit.edu	37	chr12	130184826	130184826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcaaagaccctcaggcacGgcagcttctccccggcgctg	11	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130184826G>A	ENST00000422113.2	-	2	823	c.497C>T	c.(496-498)cCg>cTg	p.P166L	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	166					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.P166L(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		CCTCAGGCACGGCAGCTTCTC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	12											19	21	20					12																	130184826		2203	4297	6500	128750779	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.497C>T	12.37:g.130184826G>A	ENSP00000408581:p.Pro166Leu		128750779	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.040712	0.93685	.	.	ENSG00000151952	ENST00000422113	T	0.15372	2.43	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000009	T	0.49949	0.1587	M	0.86864	2.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56092	-0.8036	9	.	.	.	-37.7966	19.0288	0.92946	0.0:0.0:1.0:0.0	.	166	Q14C87	T132D_HUMAN	L	166	ENSP00000408581:P166L	.	P	-	2	0	TMEM132D	128750779	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.553000	0.98118	2.472000	0.83506	0.555000	0.69702	CCG		0.662	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130184826	G	A	130184826	3	1	61	1	0	0	0	0	1	0	0	0	16086	1116	39	1	2834	1	TMEM132D	12	130184826	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	625640	130184826	3667069	8479	16464										
TMEM132D	121256	broad.mit.edu	37	chr12	130185032	130185032	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcgatggagaaaggcccGtagctggcattgaggacagg	16	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130185032G>A	ENST00000422113.2	-	2	617	c.291C>T	c.(289-291)taC>taT	p.Y97Y	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	97					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.Y97Y(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		AGAAAGGCCCGTAGCTGGCAT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	12											65	65	65					12																	130185032		2203	4300	6503	128750985	SO:0001819	synonymous_variant	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.291C>T	12.37:g.130185032G>A			128750985	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.488	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130185032	G	A	130185032	2	1	61	1	0	0	0	0	0	0	0	1	16086	1140	40	1		1	TMEM132D	12	130185032	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206	130185032	3666863	8480	16465										
FZD10	11211	broad.mit.edu	37	chr12	130647677	130647677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacgagaaccagcgcgagGcagccatccagttgcacgag	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130647677G>A	ENST00000229030.4	+	1	674	c.190G>A	c.(190-192)Gca>Aca	p.A64T	FZD10_ENST00000539839.1_Missense_Mutation_p.G31D|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	64	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A64T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CCAGCGCGAGGCAGCCATCCA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	12																																								129213630	SO:0001583	missense	11211			AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.190G>A	12.37:g.130647677G>A	ENSP00000229030:p.Ala64Thr		129213630		Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.32|11.32	1.605241|1.605241	0.28623|0.28623	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000229030|ENST00000539839	T|.	0.81415|.	-1.49|.	4.4|4.4	3.51|3.51	0.40186|0.40186	Frizzled domain (5);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.79185|0.79185	0.4403|0.4403	M|M	0.89534|0.89534	3.04|3.04	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.82484|0.82484	-0.0434|-0.0434	10|6	0.87932|0.87932	D|D	0|0	.|.	12.1678|12.1678	0.54139|0.54139	0.0844:0.0:0.9156:0.0|0.0844:0.0:0.9156:0.0	.|.	64|.	Q9ULW2|.	FZD10_HUMAN|.	T|D	64|31	ENSP00000229030:A64T|.	ENSP00000229030:A64T|ENSP00000438460:G31D	A|G	+|+	1|2	0|0	FZD10|FZD10	129213630|129213630	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.744000|0.744000	0.42396|0.42396	7.429000|7.429000	0.80309|0.80309	0.833000|0.833000	0.34828|0.34828	0.561000|0.561000	0.74099|0.74099	GCA|GGC		0.627	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	130647677	G	A	130647677	3	1	61	1	0	0	0	0	1	0	0	0	6148	1203	42	3	192	3	FZD10	12	130647677	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	462645	130647677	3204218	8481	16466										
FZD10	11211	broad.mit.edu	37	chr12	130648241	130648241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtgctcaccttcctcatcGacccggcccgcttccgctac	7	21	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130648241G>A	ENST00000229030.4	+	1	1238	c.754G>A	c.(754-756)Gac>Aac	p.D252N	FZD10_ENST00000539839.1_Missense_Mutation_p.R219Q|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	252					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.D252N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CTTCCTCATCGACCCGGCCCG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	12											116	101	106					12																	130648241		2203	4300	6503	129214194	SO:0001583	missense	11211			AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.754G>A	12.37:g.130648241G>A	ENSP00000229030:p.Asp252Asn		129214194		Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.34|16.34	3.095534|3.095534	0.56075|0.56075	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000229030|ENST00000539839	D|.	0.86562|.	-2.14|.	4.96|4.96	4.96|4.96	0.65561|0.65561	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.78188|0.78188	0.4244|0.4244	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	D|.	0.55800|.	0.973|.	P|.	0.47430|.	0.547|.	T|T	0.81904|0.81904	-0.0719|-0.0719	10|6	0.87932|0.87932	D|D	0|0	.|.	18.2056|18.2056	0.89853|0.89853	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	252|.	Q9ULW2|.	FZD10_HUMAN|.	N|Q	252|219	ENSP00000229030:D252N|.	ENSP00000229030:D252N|ENSP00000438460:R219Q	D|R	+|+	1|2	0|0	FZD10|FZD10	129214194|129214194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.636000|9.636000	0.98440|0.98440	2.285000|2.285000	0.76669|0.76669	0.561000|0.561000	0.74099|0.74099	GAC|CGA		0.657	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	130648241	G	A	130648241	3	1	61	1	0	0	0	0	1	0	0	0	6148	1058	37	1	756	1	FZD10	12	130648241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	564	130648241	3203654	8482	16467										
FZD10	11211	broad.mit.edu	37	chr12	130648738	130648738	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttcatcctctcgggcttCgtggccctgttccacatccg	8	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130648738C>T	ENST00000229030.4	+	1	1735	c.1251C>T	c.(1249-1251)ttC>ttT	p.F417F	FZD10_ENST00000539839.1_Missense_Mutation_p.R385C|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	417					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.F417F(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TCTCGGGCTTCGTGGCCCTGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	12											148	135	140					12																	130648738		2203	4300	6503	129214691	SO:0001819	synonymous_variant	11211			AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1251C>T	12.37:g.130648738C>T			129214691		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	C	9.612	1.131531	0.21041	.	.	ENSG00000111432	ENST00000539839	.	.	.	5.21	3.37	0.38596	.	.	.	.	.	T	0.64057	0.2564	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63844	-0.6545	5	0.87932	D	0	.	8.2495	0.31708	0.0:0.613:0.0:0.387	.	.	.	.	C	385	.	ENSP00000438460:R385C	R	+	1	0	FZD10	129214691	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	0.344000	0.19962	0.573000	0.29400	0.561000	0.74099	CGT		0.617	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	130648738	C	T	130648738	2	4	61	1	0	0	0	0	0	0	0	1	6148	883	31	1		1	FZD10	12	130648738	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	497	130648738	3203157	8483	16468										
PIWIL1	9271	broad.mit.edu	37	chr12	130833931	130833931	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcagacagaagaacataaAtttcaagaacaagtttccaa	5	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130833931A>C	ENST00000245255.3	+	8	1154	c.882A>C	c.(880-882)aaA>aaC	p.K294N		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	294	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.K294N(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		AAGAACATAAATTTCAAGAAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	12											70	67	68					12																	130833931		2203	4300	6503	129399884	SO:0001583	missense	9271			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.882A>C	12.37:g.130833931A>C	ENSP00000245255:p.Lys294Asn		129399884	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	A	1.638	-0.517168	0.04171	.	.	ENSG00000125207	ENST00000245255	T	0.13307	2.6	5.85	-0.294	0.12831	Argonaute/Dicer protein, PAZ (4);	0.384439	0.32970	N	0.005425	T	0.04543	0.0124	N	0.04768	-0.165	0.31859	N	0.621184	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.40117	-0.9580	10	0.13108	T	0.6	-12.1051	5.5201	0.16927	0.4721:0.1476:0.3803:0.0	.	294;294	Q96J94;Q96J94-2	PIWL1_HUMAN;.	N	294	ENSP00000245255:K294N	ENSP00000245255:K294N	K	+	3	2	PIWIL1	129399884	0.516000	0.26218	0.537000	0.28052	0.939000	0.58152	0.383000	0.20651	-0.285000	0.09089	-0.274000	0.10170	AAA		0.338	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			C	130833931	A	C	130833931	3	2	61	1	0	0	0	0	1	0	0	0	11988	98	4	4	908	4	PIWIL1	12	130833931	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	185193	130833931	3017964	8484	16469										
PIWIL1	9271	broad.mit.edu	37	chr12	130839474	130839474	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgattttaacgtgatgaaaGacttagccgttcatacaaga	8	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130839474G>T	ENST00000245255.3	+	11	1485	c.1213G>T	c.(1213-1215)Gac>Tac	p.D405Y		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	405					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.D405Y(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CGTGATGAAAGACTTAGCCGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											152	140	144					12																	130839474		2203	4300	6503	129405427	SO:0001583	missense	9271			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1213G>T	12.37:g.130839474G>T	ENSP00000245255:p.Asp405Tyr		129405427	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673482	0.67928	.	.	ENSG00000125207	ENST00000245255	T	0.14640	2.49	5.38	5.38	0.77491	Argonaute/Dicer protein, PAZ (3);	0.094101	0.64402	D	0.000001	T	0.44932	0.1317	M	0.89715	3.055	0.80722	D	1	D;B	0.56746	0.977;0.286	D;B	0.63381	0.914;0.364	T	0.54642	-0.8263	10	0.72032	D	0.01	-9.3986	18.1727	0.89751	0.0:0.0:1.0:0.0	.	405;405	Q96J94;Q96J94-2	PIWL1_HUMAN;.	Y	405	ENSP00000245255:D405Y	ENSP00000245255:D405Y	D	+	1	0	PIWIL1	129405427	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.806000	0.86020	2.516000	0.84829	0.558000	0.71614	GAC		0.353	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			T	130839474	G	T	130839474	3	4	61	1	0	0	0	0	1	0	0	0	11988	942	33	2	1251	2	PIWIL1	12	130839474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5543	130839474	3012421	8485	16470										
RIMBP2	23504	broad.mit.edu	37	chr12	130892274	130892274	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtttggctggtacctcGacatcgacgttgggcgagct	14	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130892274G>A	ENST00000261655.4	-	16	3085	c.2922C>T	c.(2920-2922)gtC>gtT	p.V974V		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	974	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.V974V(2)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTGGTACCTCGACATCGACGT	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	12											469	360	397					12																	130892274		2203	4300	6503	129458227	SO:0001819	synonymous_variant	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2922C>T	12.37:g.130892274G>A			129458227	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																				0.567	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130892274	G	A	130892274	2	1	61	1	0	0	0	0	0	0	0	1	13400	1045	37	1		1	RIMBP2	12	130892274	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52800	130892274	2959621	8486	16471										
RIMBP2	23504	broad.mit.edu	37	chr12	130907040	130907040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggacctctgaggaccagCgctgccacggggaaacctcc	13	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:130907040C>T	ENST00000261655.4	-	13	2591	c.2428G>A	c.(2428-2430)Gct>Act	p.A810T	RP11-117L5.4_ENST00000539532.1_lincRNA	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	810					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.A810T(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TGAGGACCAGCGCTGCCACGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	12											49	42	44					12																	130907040		2203	4300	6503	129472993	SO:0001583	missense	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2428G>A	12.37:g.130907040C>T	ENSP00000261655:p.Ala810Thr		129472993	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	C	7.363	0.625315	0.14257	.	.	ENSG00000060709	ENST00000261655	T	0.20463	2.07	4.9	2.07	0.26955	.	0.991588	0.08197	N	0.982914	T	0.15219	0.0367	L	0.36672	1.1	0.80722	D	1	B	0.11235	0.004	B	0.08055	0.003	T	0.15009	-1.0452	10	0.09084	T	0.74	-0.9191	8.3202	0.32124	0.0:0.7288:0.128:0.1432	.	810	O15034	RIMB2_HUMAN	T	810	ENSP00000261655:A810T	ENSP00000261655:A810T	A	-	1	0	RIMBP2	129472993	0.090000	0.21635	0.001000	0.08648	0.338000	0.28826	0.670000	0.25157	0.127000	0.18452	-1.332000	0.01269	GCT		0.572	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130907040	C	T	130907040	3	4	61	1	0	0	0	0	1	0	0	0	13400	768	27	1	758	1	RIMBP2	12	130907040	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14766	130907040	2944855	8487	16472										
RAN	5901	broad.mit.edu	37	chr12	131359223	131359223	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaacaaagtggatattaAggacaggaaagtgaaggcga	14	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:131359223A>C	ENST00000543796.1	+	5	638	c.380A>C	c.(379-381)aAg>aCg	p.K127T	RAN_ENST00000392369.2_Missense_Mutation_p.K127T|RAN_ENST00000254675.3_Missense_Mutation_p.K39T|RAN_ENST00000392367.3_Missense_Mutation_p.K144T|RAN_ENST00000541630.1_Missense_Mutation_p.K39T			P62826	RAN_HUMAN	RAN, member RAS oncogene family	127					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.K127T(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		GTGGATATTAAGGACAGGAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	12											113	98	103					12																	131359223		2203	4300	6503	129925176	SO:0001583	missense	5901			M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341			9846	protein-coding gene	gene with protein product		601179				8421051	Standard	XM_005253592		Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.380A>C	12.37:g.131359223A>C	ENSP00000446215:p.Lys127Thr		129925176	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	37	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492325	0.64074	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	4.07	4.07	0.47477	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.71796	0.3382	L	0.35542	1.07	0.80722	D	1	B;B	0.23854	0.092;0.092	B;B	0.34873	0.191;0.191	T	0.72581	-0.4250	10	0.87932	D	0	-17.8637	12.5276	0.56096	1.0:0.0:0.0:0.0	.	127;127	A8K3Z8;P62826	.;RAN_HUMAN	T	127;145;39;127;39;123;144	ENSP00000446215:K127T;ENSP00000396127:K145T;ENSP00000441210:K39T;ENSP00000376176:K127T;ENSP00000254675:K39T;ENSP00000444042:K123T;ENSP00000376174:K144T	ENSP00000254675:K39T	K	+	2	0	RAN	129925176	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.805000	0.91925	1.611000	0.50210	0.533000	0.62120	AAG		0.408	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		C	131359223	A	C	131359223	3	2	61	1	0	0	0	0	1	0	0	0	13061	72	3	4	394	4	RAN	12	131359223	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	452183	131359223	2492672	8488	16473										
SFRS8	6433	broad.mit.edu	37	chr12	132212883	132212883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccctcgcagcacttgttCgtaaggcacaggctgacagt	10	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:132212883C>T	ENST00000261674.4	+	7	1132	c.991C>T	c.(991-993)Cgt>Tgt	p.R331C	SFSWAP_ENST00000541286.1_Missense_Mutation_p.R331C	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	331					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.R331C(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						AGCACTTGTTCGTAAGGCACA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	12											189	150	163					12																	132212883		2203	4300	6503	130778836	SO:0001583	missense	6433			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)"	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.991C>T	12.37:g.132212883C>T	ENSP00000261674:p.Arg331Cys		130778836	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.847898	0.71603	.	.	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000535236;ENST00000541286	T;T;T	0.24723	2.84;1.84;2.83	5.61	5.61	0.85477	.	0.103312	0.64402	D	0.000003	T	0.48822	0.1521	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.67725	0.953;0.855;0.938	T	0.40232	-0.9574	10	0.54805	T	0.06	-14.7473	17.8127	0.88620	0.0:1.0:0.0:0.0	.	331;331;268	F5H6B8;Q12872;F5H525	.;SFSWA_HUMAN;.	C	331;268;124;331	ENSP00000261674:R331C;ENSP00000443045:R124C;ENSP00000437738:R331C	ENSP00000261674:R331C	R	+	1	0	SFSWAP	130778836	1.000000	0.71417	0.854000	0.33618	0.408000	0.30992	6.425000	0.73370	2.652000	0.90054	0.655000	0.94253	CGT		0.552	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		T	132212883	C	T	132212883	3	4	61	1	0	0	0	0	1	0	0	0	14220	884	31	1	1017	1	SFRS8	12	132212883	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	853660	132212883	1639012	8489	16474										
SFRS8	6433	broad.mit.edu	37	chr12	132249130	132249130	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagaaggccaagaaagttCtagtagtgctgcaaacacta	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:132249130C>A	ENST00000261674.4	+	12	1991	c.1850C>A	c.(1849-1851)tCt>tAt	p.S617Y	SFSWAP_ENST00000541286.1_Missense_Mutation_p.S617Y	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	617	Poly-Ser.				mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.S617Y(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CAAGAAAGTTCTAGTAGTGCT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	12											109	90	96					12																	132249130		2203	4300	6503	130815083	SO:0001583	missense	6433			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)"	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1850C>A	12.37:g.132249130C>A	ENSP00000261674:p.Ser617Tyr		130815083	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928631	0.34002	.	.	ENSG00000061936	ENST00000261674;ENST00000535236;ENST00000541286	T;T;T	0.25085	2.8;1.82;2.82	5.29	-0.0915	0.13661	.	1.214880	0.05399	N	0.540265	T	0.19927	0.0479	L	0.36672	1.1	0.09310	N	1	B;B	0.23806	0.091;0.055	B;B	0.23716	0.048;0.021	T	0.31138	-0.9954	10	0.48119	T	0.1	-0.1436	4.4065	0.11411	0.1149:0.354:0.397:0.1341	.	617;617	F5H6B8;Q12872	.;SFSWA_HUMAN	Y	617;410;617	ENSP00000261674:S617Y;ENSP00000443045:S410Y;ENSP00000437738:S617Y	ENSP00000261674:S617Y	S	+	2	0	SFSWAP	130815083	0.000000	0.05858	0.000000	0.03702	0.992000	0.81027	0.380000	0.20602	-0.235000	0.09767	0.561000	0.74099	TCT		0.448	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		A	132249130	C	A	132249130	3	1	61	1	0	0	0	0	1	0	0	0	14220	913	32	2	1896	2	SFRS8	12	132249130	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36247	132249130	1602765	8490	16475										
P2RX2	22953	broad.mit.edu	37	chr12	133197092	133197092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacgttccacgaggcctccGacctctactgccccatcttc	7	19	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133197092G>A	ENST00000389110.3	+	7	734	c.697G>A	c.(697-699)Gac>Aac	p.D233N	P2RX2_ENST00000352418.4_Missense_Mutation_p.D161N|P2RX2_ENST00000351222.4_Missense_Mutation_p.D141N|P2RX2_ENST00000449132.2_Missense_Mutation_p.R197Q|P2RX2_ENST00000348800.5_Missense_Mutation_p.D233N|P2RX2_ENST00000350048.5_Missense_Mutation_p.D209N|P2RX2_ENST00000343948.4_Missense_Mutation_p.D233N	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	233					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)	p.D233N(1)		NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		CGAGGCCTCCGACCTCTACTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											74	68	70					12																	133197092		2203	4300	6503	131707165	SO:0001583	missense	22953			AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.697G>A	12.37:g.133197092G>A	ENSP00000373762:p.Asp233Asn		131707165	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Missense_Mutation	SNP	ENST00000389110.3	37	CCDS31931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.41|10.41	1.341788|1.341788	0.24339|0.24339	.|.	.|.	ENSG00000187848|ENSG00000187848	ENST00000389110;ENST00000343948;ENST00000352418;ENST00000350048;ENST00000351222;ENST00000348800|ENST00000449132	T;T;T;T;T;T|T	0.03951|0.09445	3.75;3.75;3.75;3.75;3.75;3.75|2.98	5.58|5.58	3.54|3.54	0.40534|0.40534	.|.	0.437004|.	0.26442|.	N|.	0.024355|.	T|T	0.08758|0.08758	0.0217|0.0217	L|L	0.41027|0.41027	1.25|1.25	0.34661|0.34661	D|D	0.722699|0.722699	B;B;P;B;B;B;B|B	0.41214|0.19445	0.137;0.191;0.742;0.038;0.117;0.227;0.066|0.036	B;B;B;B;B;B;B|B	0.18263|0.08055	0.014;0.012;0.013;0.014;0.012;0.021;0.005|0.003	T|T	0.10520|0.10520	-1.0626|-1.0626	10|9	0.12766|0.59425	T|D	0.61|0.04	-16.0764|-16.0764	5.0848|5.0848	0.14676|0.14676	0.0847:0.1548:0.6226:0.1378|0.0847:0.1548:0.6226:0.1378	.|.	233;141;161;209;233;233;233|197	Q32MC3;Q9UBL9-5;Q9UBL9-6;Q9UBL9-3;Q9UBL9-4;Q9UBL9;Q9UBL9-2|Q9UBL9-7	.;.;.;.;.;P2RX2_HUMAN;.|.	N|Q	233;233;161;209;141;233|197	ENSP00000373762:D233N;ENSP00000343339:D233N;ENSP00000341419:D161N;ENSP00000343904:D209N;ENSP00000344502:D141N;ENSP00000345095:D233N|ENSP00000405531:R197Q	ENSP00000343339:D233N|ENSP00000405531:R197Q	D|R	+|+	1|2	0|0	P2RX2|P2RX2	131707165|131707165	0.020000|0.020000	0.18652|0.18652	0.295000|0.295000	0.24960|0.24960	0.232000|0.232000	0.25224|0.25224	0.997000|0.997000	0.29731|0.29731	0.555000|0.555000	0.29079|0.29079	0.555000|0.555000	0.69702|0.69702	GAC|CGA		0.632	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			A	133197092	G	A	133197092	3	1	61	1	0	0	0	0	1	0	0	0	11371	1058	37	1	723	1	P2RX2	12	133197092	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	947962	133197092	654803	8491	16476										
POLE	5426	broad.mit.edu	37	chr12	133218337	133218337	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcctgctggatcacgtcGaagctgatccccatgctgtc	12	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133218337G>A	ENST00000320574.5	-	39	5317	c.5274C>T	c.(5272-5274)ttC>ttT	p.F1758F	POLE_ENST00000535270.1_Silent_p.F1731F|POLE_ENST00000434528.3_5'Flank	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1758					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.F1758F(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GGATCACGTCGAAGCTGATCC	0.602								DNA polymerases (catalytic subunits)																																								1	Substitution - coding silent(1)	large_intestine(1)	12											107	89	95					12																	133218337		2203	4300	6503	131728410	SO:0001819	synonymous_variant	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.5274C>T	12.37:g.133218337G>A			131728410	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																				0.602	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133218337	G	A	133218337	2	1	61	1	0	0	0	0	0	0	0	1	12227	1049	37	1		1	POLE	12	133218337	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21245	133218337	633558	8492	16477										
POLE	5426	broad.mit.edu	37	chr12	133236066	133236066	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggttctcagagatgagctcGaatagctcagagtcaggcat	12	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133236066G>A	ENST00000320574.5	-	26	3133	c.3090C>T	c.(3088-3090)ttC>ttT	p.F1030F	POLE_ENST00000535270.1_Silent_p.F1003F	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1030					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.F1030F(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	AGATGAGCTCGAATAGCTCAG	0.532								DNA polymerases (catalytic subunits)																																								1	Substitution - coding silent(1)	large_intestine(1)	12											67	61	63					12																	133236066		2203	4300	6503	131746139	SO:0001819	synonymous_variant	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3090C>T	12.37:g.133236066G>A			131746139	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																				0.532	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133236066	G	A	133236066	2	1	61	1	0	0	0	0	0	0	0	1	12227	1049	37	1		1	POLE	12	133236066	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17729	133236066	615829	8493	16478										
POLE	5426	broad.mit.edu	37	chr12	133249847	133249847	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcgacagcatctgacacaGaatacgtggccagagtctga	12	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133249847G>A	ENST00000320574.5	-	14	1419	c.1376C>T	c.(1375-1377)tCt>tTt	p.S459F	POLE_ENST00000535270.1_Missense_Mutation_p.S432F	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	459			S -> F (found in a colorectal sample; somatic mutation). {ECO:0000269|PubMed:23263490}.		base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.S459F(2)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	ATCTGACACAGAATACGTGGC	0.527								DNA polymerases (catalytic subunits)																																								2	Substitution - Missense(2)	large_intestine(2)	12											185	156	166					12																	133249847		2203	4300	6503	131759920	SO:0001583	missense	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.1376C>T	12.37:g.133249847G>A	ENSP00000322570:p.Ser459Phe		131759920	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145562	0.57044	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577;ENST00000535934	T;T;T;T	0.44083	4.77;4.77;4.77;0.93	5.37	4.47	0.54385	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.74007	0.3660	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82255	-0.0548	10	0.87932	D	0	.	13.4599	0.61221	0.0755:0.0:0.9245:0.0	.	432;459	F5H1D6;Q07864	.;DPOE1_HUMAN	F	459;470;432;239;394;77	ENSP00000322570:S459F;ENSP00000406383:S470F;ENSP00000445753:S432F;ENSP00000442519:S239F	ENSP00000322570:S459F	S	-	2	0	POLE	131759920	1.000000	0.71417	0.176000	0.23000	0.185000	0.23345	7.962000	0.87912	2.524000	0.85096	0.313000	0.20887	TCT		0.527	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133249847	G	A	133249847	3	1	61	1	0	0	0	0	1	0	0	0	12227	942	33	3	5628	3	POLE	12	133249847	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13781	133249847	602048	8494	16479										
POLE	5426	broad.mit.edu	37	chr12	133256213	133256213	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagcctgatgtaatttcGcttcaaacccaccaagtgat	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133256213G>A	ENST00000320574.5	-	6	491	c.448C>T	c.(448-450)Cga>Tga	p.R150*	POLE_ENST00000535270.1_Nonsense_Mutation_p.R123*	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	150					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.R150*(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	ATGTAATTTCGCTTCAAACCC	0.478								DNA polymerases (catalytic subunits)																																								1	Substitution - Nonsense(1)	large_intestine(1)	12											122	100	108					12																	133256213		2203	4300	6503	131766286	SO:0001587	stop_gained	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.448C>T	12.37:g.133256213G>A	ENSP00000322570:p.Arg150*		131766286	Q13533|Q86VH9	Nonsense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.797508	0.90538	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000376577	.	.	.	6.04	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6914	0.77457	0.0:0.0:0.7512:0.2488	.	.	.	.	X	150;161;123;85	.	ENSP00000322570:R150X	R	-	1	2	POLE	131766286	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	3.873000	0.56093	1.551000	0.49450	0.561000	0.74099	CGA		0.478	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133256213	G	A	133256213	4	1	61	1	0	0	0	0	0	1	0	0	12227	1095	38	1	6588	1	POLE	12	133256213	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6366	133256213	595682	8495	16480										
ANKLE2	23141	broad.mit.edu	37	chr12	133319798	133319798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaatcaaatggtgtgacGaaagcacgttgactacatct	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133319798G>A	ENST00000357997.5	-	6	1384	c.1295C>T	c.(1294-1296)tCg>tTg	p.S432L	ANKLE2_ENST00000337516.5_Missense_Mutation_p.S432L|ANKLE2_ENST00000539605.1_Missense_Mutation_p.S370L	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	432					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)	p.S432L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		ATGGTGTGACGAAAGCACGTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											127	114	118					12																	133319798		1884	4104	5988	131829871	SO:0001583	missense	23141			AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1295C>T	12.37:g.133319798G>A	ENSP00000350686:p.Ser432Leu		131829871	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	g	12.97	2.097258	0.37048	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516;ENST00000545623	T;T;T;T	0.54479	1.64;1.64;0.57;0.57	4.71	4.71	0.59529	Ankyrin repeat-containing domain (2);	0.218384	0.47093	D	0.000249	T	0.20941	0.0504	N	0.00041	-2.485	0.31442	N	0.671815	D;D	0.64830	0.993;0.994	P;P	0.51550	0.457;0.673	T	0.42816	-0.9429	10	0.27082	T	0.32	-12.0326	13.4826	0.61345	0.0:0.1571:0.8429:0.0	.	432;432	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	L	370;432;432;202	ENSP00000446268:S370L;ENSP00000350686:S432L;ENSP00000337651:S432L;ENSP00000438515:S202L	ENSP00000337651:S432L	S	-	2	0	ANKLE2	131829871	1.000000	0.71417	0.998000	0.56505	0.035000	0.12851	6.674000	0.74487	2.161000	0.67846	0.639000	0.83563	TCG		0.353	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			A	133319798	G	A	133319798	3	1	61	1	0	0	0	0	1	0	0	0	633	1059	37	1	1553	1	ANKLE2	12	133319798	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63585	133319798	532097	8496	16481										
CHFR	55743	broad.mit.edu	37	chr12	133448903	133448903	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattcttcctgtacaccaagTagatgacatccccagtctgt	6	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133448903T>C	ENST00000432561.2	-	4	384	c.311A>G	c.(310-312)tAc>tGc	p.Y104C	CHFR_ENST00000266880.7_Missense_Mutation_p.Y104C|CHFR_ENST00000443047.2_Missense_Mutation_p.Y104C|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000315585.7_Missense_Mutation_p.Y104C|CHFR_ENST00000450056.2_Missense_Mutation_p.Y104C			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	104					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Y104C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		GTACACCAAGTAGATGACATC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											200	168	179					12																	133448903		2203	4300	6503	131958976	SO:0001583	missense	55743			AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"RING-type (C3HC4) zinc fingers"	20455	protein-coding gene	gene with protein product		605209	"checkpoint with forkhead and ring finger domains"			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.311A>G	12.37:g.133448903T>C	ENSP00000392395:p.Tyr104Cys		131958976	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Missense_Mutation	SNP	ENST00000432561.2	37	CCDS53849.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512575	0.85389	.	.	ENSG00000072609	ENST00000315585;ENST00000443047;ENST00000450056;ENST00000266880;ENST00000432561;ENST00000540963	D;D;D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12;-2.12;-2.12	5.7	5.7	0.88788	Forkhead-associated (FHA) domain (2);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	D	0.87180	0.6113	N	0.11106	0.095	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	D	0.89770	0.3953	10	0.59425	D	0.04	-22.2202	15.6259	0.76855	0.0:0.0:0.0:1.0	.	104;104;104;104;104	Q96EP1-5;Q96EP1-4;Q96EP1;Q96EP1-2;Q96EP1-3	.;.;CHFR_HUMAN;.;.	C	104	ENSP00000320557:Y104C;ENSP00000416431:Y104C;ENSP00000398735:Y104C;ENSP00000266880:Y104C;ENSP00000392395:Y104C;ENSP00000441837:Y104C	ENSP00000266880:Y104C	Y	-	2	0	CHFR	131958976	1.000000	0.71417	0.989000	0.46669	0.975000	0.68041	7.038000	0.76537	2.174000	0.68829	0.496000	0.49642	TAC		0.498	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2			C	133448903	T	C	133448903	3	2	61	1	0	0	0	0	1	0	0	0	3343	1638	57	4	1840	4	CHFR	12	133448903	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	129105	133448903	402992	8497	16482										
ZNF140	7699	broad.mit.edu	37	chr12	133682122	133682122	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcaagtggtgagatcaaaGacttttcaccaaaaaatgtc	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr12:133682122G>T	ENST00000355557.2	+	5	1542	c.259G>T	c.(259-261)Gac>Tac	p.D87Y	ZNF140_ENST00000440550.2_Intron|ZNF140_ENST00000544426.1_5'UTR|ZNF140_ENST00000319849.3_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D87Y(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TGAGATCAAAGACTTTTCACC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12																																								132192195	SO:0001583	missense	7699			U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.259G>T	12.37:g.133682122G>T	ENSP00000347755:p.Asp87Tyr		132192195	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	37	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	G	3.003	-0.205629	0.06180	.	.	ENSG00000196387	ENST00000355557;ENST00000356456;ENST00000412146;ENST00000429434	T;T;T;T	0.05199	3.48;6.02;4.77;6.09	4.09	3.19	0.36642	.	1.410700	0.05197	N	0.504298	T	0.08802	0.0218	L	0.45352	1.415	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.33574	-0.9863	10	0.62326	D	0.03	.	9.8224	0.40891	0.1039:0.0:0.8961:0.0	.	87	P52738	ZN140_HUMAN	Y	87;87;53;103	ENSP00000347755:D87Y;ENSP00000444905:D87Y;ENSP00000389566:D53Y;ENSP00000415499:D103Y	ENSP00000347755:D87Y	D	+	1	0	ZNF140	132192195	0.001000	0.12720	0.001000	0.08648	0.210000	0.24377	0.947000	0.29082	1.062000	0.40625	0.455000	0.32223	GAC		0.343	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		T	133682122	G	T	133682122	3	4	61	1	0	0	0	0	1	0	0	0	17768	942	33	2	273	2	ZNF140	12	133682122	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	233219	133682122	169773	8498	16483										
TPTE2	93492	broad.mit.edu	37	chr13	20025334	20025334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagactcgatagtggtttCgatgtttcttatctagaaac	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20025334C>T	ENST00000400230.2	-	11	817	c.773G>A	c.(772-774)cGa>cAa	p.R258Q	TPTE2_ENST00000255310.6_Missense_Mutation_p.R181Q|TPTE2_ENST00000390680.2_Missense_Mutation_p.R181Q|TPTE2_ENST00000382977.4_Missense_Mutation_p.R258Q|TPTE2_ENST00000382978.1_Missense_Mutation_p.R218Q|TPTE2_ENST00000400103.2_Missense_Mutation_p.R147Q|TPTE2_ENST00000457266.2_Missense_Mutation_p.R147Q|TPTE2_ENST00000382975.4_Missense_Mutation_p.R218Q			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	258	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R181Q(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ATAGTGGTTTCGATGTTTCTT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	13											131	116	121					13																	20025334		2203	4299	6502	18923334	SO:0001583	missense	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.773G>A	13.37:g.20025334C>T	ENSP00000383089:p.Arg258Gln		18923334	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	c	0.190	-1.054100	0.01965	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	2.63	-3.6	0.04570	Phosphatase tensin type (1);	0.996918	0.08131	N	0.993126	T	0.11067	0.0270	N	0.03948	-0.315	0.09310	N	1	B;B;B	0.12013	0.005;0.002;0.003	B;B;B	0.14023	0.01;0.006;0.01	T	0.33777	-0.9855	9	.	.	.	-0.2719	6.4557	0.21928	0.0:0.4108:0.3389:0.2504	.	147;181;258	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	Q	218;147;258;181;181;258;218;147;258;127	ENSP00000372438:R218Q;ENSP00000382974:R147Q;ENSP00000383089:R258Q;ENSP00000255310:R181Q;ENSP00000375098:R181Q;ENSP00000372437:R258Q;ENSP00000372435:R218Q;ENSP00000442218:R147Q	.	R	-	2	0	TPTE2	18923334	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	-2.361000	0.01083	-0.977000	0.03537	-1.247000	0.01520	CGA		0.363	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		T	20025334	C	T	20025334	3	4	61	1	0	0	0	0	1	0	0	0	16471	884	31	1	835	1	TPTE2	13	20025334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		20025334	95144544	8499	16484										
PSPC1	55269	broad.mit.edu	37	chr13	20333550	20333550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttccacaatgactggaCgaggggtcctggataggtat	15	7	0	1	rs370840309		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20333550C>T	ENST00000338910.4	-	3	842	c.683G>A	c.(682-684)cGt>cAt	p.R228H		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	228	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficient for paraspeckles localization.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R228H(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AATGACTGGACGAGGGGTCCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	HIS/ARG	0,3716		0,0,1858	91	85	87		683	5.5	1	13		87	1,8225		0,1,4112	no	missense	PSPC1	NM_001042414.2	29	0,1,5970	TT,TC,CC		0.0122,0.0,0.0084	possibly-damaging	228/524	20333550	1,11941	1858	4113	5971	19231550	SO:0001583	missense	55269			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.683G>A	13.37:g.20333550C>T	ENSP00000343966:p.Arg228His		19231550	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.117425	0.77323	0.0	1.22E-4	ENSG00000121390	ENST00000338910;ENST00000422828;ENST00000427943	T;T	0.19938	2.11;2.39	5.48	5.48	0.80851	RNA recognition motif domain (2);	0.056960	0.64402	D	0.000001	T	0.23727	0.0574	L	0.49778	1.585	0.80722	D	1	B	0.31859	0.343	B	0.24701	0.055	T	0.03483	-1.1032	10	0.87932	D	0	-11.6278	19.3434	0.94355	0.0:1.0:0.0:0.0	.	228	Q8WXF1	PSPC1_HUMAN	H	228;168;228	ENSP00000343966:R228H;ENSP00000393069:R228H	ENSP00000343966:R228H	R	-	2	0	PSPC1	19231550	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.818000	0.86416	2.580000	0.87095	0.557000	0.71058	CGT		0.338	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			T	20333550	C	T	20333550	3	4	61	1	0	0	0	0	1	0	0	0	12750	536	19	1	916	1	PSPC1	13	20333550	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308216	20333550	94836328	8500	16485										
PSPC1	55269	broad.mit.edu	37	chr13	20346427	20346427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacatctttccagagcctttCgtgcaggaggttttgctgca	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20346427C>T	ENST00000338910.4	-	2	788	c.629G>A	c.(628-630)cGa>cAa	p.R210Q		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	210	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficient for paraspeckles localization.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R210Q(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CAGAGCCTTTCGTGCAGGAGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											105	96	99					13																	20346427		1919	4142	6061	19244427	SO:0001583	missense	55269			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.629G>A	13.37:g.20346427C>T	ENSP00000343966:p.Arg210Gln		19244427	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996105	0.74703	.	.	ENSG00000121390	ENST00000338910;ENST00000422828;ENST00000427943	T;T	0.15487	2.42;2.42	5.88	5.88	0.94601	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.08044	0.0201	N	0.02011	-0.69	0.80722	D	1	B	0.26744	0.158	B	0.18561	0.022	T	0.41124	-0.9526	10	0.16896	T	0.51	-14.2049	20.2405	0.98372	0.0:1.0:0.0:0.0	.	210	Q8WXF1	PSPC1_HUMAN	Q	210;150;210	ENSP00000343966:R210Q;ENSP00000393069:R210Q	ENSP00000343966:R210Q	R	-	2	0	PSPC1	19244427	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.756000	0.85195	2.797000	0.96272	0.561000	0.74099	CGA		0.438	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			T	20346427	C	T	20346427	3	4	61	1	0	0	0	0	1	0	0	0	12750	884	31	1	974	1	PSPC1	13	20346427	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12877	20346427	94823451	8501	16486										
ZMYM5	9205	broad.mit.edu	37	chr13	20399217	20399217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccacattctactgaaagCtgtagctgtgaagtcttttc	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20399217C>A	ENST00000337963.4	-	8	1674	c.1410G>T	c.(1408-1410)caG>caT	p.Q470H		NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	470						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.Q470H(1)		kidney(1)|large_intestine(5)|lung(9)	15		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)		ctactgaaagctgtagctgtg	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	13											88	77	81					13																	20399217		1568	3582	5150	19297217	SO:0001583	missense	9205			AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1410G>T	13.37:g.20399217C>A	ENSP00000337034:p.Gln470His		19297217	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		.	.	.	.	.	.	.	.	.	.	C	0.055	-1.238622	0.01493	.	.	ENSG00000132950	ENST00000337963;ENST00000502168	T;T	0.18016	2.24;2.24	2.62	-1.57	0.08506	.	0.197095	0.43416	N	0.000566	T	0.12518	0.0304	L	0.44542	1.39	0.09310	N	1	P	0.40144	0.704	B	0.41571	0.36	T	0.13872	-1.0493	10	0.42905	T	0.14	.	4.5528	0.12123	0.0:0.454:0.1729:0.3731	.	470	Q9UJ78	ZMYM5_HUMAN	H	470;460	ENSP00000337034:Q470H;ENSP00000445779:Q460H	ENSP00000337034:Q470H	Q	-	3	2	ZMYM5	19297217	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.923000	0.04000	-0.916000	0.03818	-2.270000	0.00275	CAG		0.363	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		A	20399217	C	A	20399217	3	1	61	1	0	0	0	0	1	0	0	0	17742	796	28	2	603	2	ZMYM5	13	20399217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52790	20399217	94770661	8502	16487										
ZMYM5	9205	broad.mit.edu	37	chr13	20412858	20412858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttttacatattatgcttCgtgtgttttgagtacgttta	7	5	0	1	rs114493699		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20412858C>T	ENST00000337963.4	-	5	1118	c.854G>A	c.(853-855)cGa>cAa	p.R285Q	ZMYM5_ENST00000382907.4_Intron|ZMYM5_ENST00000382905.4_Missense_Mutation_p.R285Q	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	285						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R285Q(2)		kidney(1)|large_intestine(5)|lung(9)	15		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)		TATTATGCTTCGTGTGTTTTG	0.383													C|||	1	0.000199681	0	0	5008	,	,		19863	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	13											156	144	148					13																	20412858		2203	4300	6503	19310858	SO:0001583	missense	9205			AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.854G>A	13.37:g.20412858C>T	ENSP00000337034:p.Arg285Gln		19310858	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.486	0.861004	0.17178	.	.	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382905	T;T;T	0.22743	2.27;2.27;1.94	4.68	-0.87	0.10646	.	0.460476	0.24443	N	0.038492	T	0.09862	0.0242	N	0.25485	0.75	0.25346	N	0.988904	B;B	0.13145	0.002;0.007	B;B	0.10450	0.002;0.005	T	0.30679	-0.9970	10	0.14252	T	0.57	-0.0124	4.4145	0.11450	0.249:0.3746:0.0:0.3764	.	285;285	Q9UJ78;Q9UJ78-1	ZMYM5_HUMAN;.	Q	285;275;285	ENSP00000337034:R285Q;ENSP00000445779:R275Q;ENSP00000372361:R285Q	ENSP00000337034:R285Q	R	-	2	0	ZMYM5	19310858	1.000000	0.71417	0.060000	0.19600	0.612000	0.37316	1.086000	0.30853	-0.022000	0.13986	-1.069000	0.02264	CGA		0.383	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		T	20412858	C	T	20412858	3	4	61	1	0	0	0	0	1	0	0	0	17742	884	31	1	1282	1	ZMYM5	13	20412858	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13641	20412858	94757020	8503	16488										
ZMYM5	9205	broad.mit.edu	37	chr13	20412933	20412933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtgagctgatccttttCgttgataagctgtctgtccc	11	9	1	4	rs143728763		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20412933C>T	ENST00000337963.4	-	5	1043	c.779G>A	c.(778-780)cGa>cAa	p.R260Q	ZMYM5_ENST00000382907.4_Intron|ZMYM5_ENST00000382905.4_Missense_Mutation_p.R260Q	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	260						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R260Q(2)		kidney(1)|large_intestine(5)|lung(9)	15		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)		TGATCCTTTTCGTTGATAAGC	0.398													C|||	1	0.000199681	0	0	5008	,	,		19797	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	13											254	233	240					13																	20412933		2203	4300	6503	19310933	SO:0001583	missense	9205			AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.779G>A	13.37:g.20412933C>T	ENSP00000337034:p.Arg260Gln		19310933	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	27.8	4.862248	0.91511	.	.	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382905	T;T;T	0.53857	0.6;0.6;0.6	4.67	3.83	0.44106	TRASH (1);Zinc finger, MYM-type (1);	0.000000	0.85682	D	0.000000	T	0.69762	0.3147	M	0.71036	2.16	0.52099	D	0.999949	D;P	0.89917	1.0;0.931	D;B	0.85130	0.997;0.23	T	0.73646	-0.3917	10	0.72032	D	0.01	-8.2739	13.043	0.58910	0.0:0.922:0.0:0.078	.	260;260	Q9UJ78;Q9UJ78-1	ZMYM5_HUMAN;.	Q	260;250;260	ENSP00000337034:R260Q;ENSP00000445779:R250Q;ENSP00000372361:R260Q	ENSP00000337034:R260Q	R	-	2	0	ZMYM5	19310933	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.571000	0.67404	1.329000	0.45376	0.555000	0.69702	CGA		0.398	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		T	20412933	C	T	20412933	3	4	61	1	0	0	0	0	1	0	0	0	17742	884	31	1	1357	1	ZMYM5	13	20412933	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75	20412933	94756945	8504	16489										
GJB6	10804	broad.mit.edu	37	chr13	20797482	20797482	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacgaagtcctcttgctcGtcaccccacacttcctgggc	8	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:20797482G>A	ENST00000356192.6	-	5	758	c.138C>T	c.(136-138)gaC>gaT	p.D46D	GJB6_ENST00000241124.6_Silent_p.D46D|GJB6_ENST00000400065.3_Silent_p.D46D|GJB6_ENST00000400066.3_Silent_p.D46D	NM_001110219.2	NP_001103689.1	O95452	CXB6_HUMAN	gap junction protein, beta 6, 30kDa	46					apoptotic process (GO:0006915)|cell communication (GO:0007154)|ear morphogenesis (GO:0042471)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|sensory perception of sound (GO:0007605)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)		p.D46D(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	9		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)		CCTCTTGCTCGTCACCCCACA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	13											119	97	105					13																	20797482		2203	4300	6503	19695482	SO:0001819	synonymous_variant	10804			AJ005585	CCDS9291.1	13q12	2010-01-06	2007-11-06		ENSG00000121742	ENSG00000121742		"Ion channels / Gap junction proteins (connexins)"	4288	protein-coding gene	gene with protein product	"connexin 30"	604418	"ectodermal dysplasia 2, hidrotic (Clouston syndrome)", "gap junction protein, beta 6 (connexin 30)", "gap junction protein, beta 6"	DFNA3, ED2		10471490, 8845850	Standard	NM_006783		Approved	EDH, HED, CX30	uc001und.4	O95452	OTTHUMG00000016515	ENST00000356192.6:c.138C>T	13.37:g.20797482G>A			19695482	B3KQN2|Q5Q1H9|Q5Q1I0|Q5Q1I1|Q5T5U0|Q8IUP0	Silent	SNP	ENST00000356192.6	37	CCDS9291.1																																																																																				0.542	GJB6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272906.1			A	20797482	G	A	20797482	2	1	61	1	0	0	0	0	0	0	0	1	6432	1136	40	1		1	GJB6	13	20797482	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	384549	20797482	94372396	8505	16490										
IFT88	8100	broad.mit.edu	37	chr13	21265282	21265282	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaggatgattttgctgatGaagaattaggagatgatttg	13	1	0	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21265282G>T	ENST00000319980.6	+	28	2797	c.2470G>T	c.(2470-2472)Gaa>Taa	p.E824*	IFT88_ENST00000537103.1_Nonsense_Mutation_p.E796*|IFT88_ENST00000382778.4_3'UTR|IFT88_ENST00000351808.5_Nonsense_Mutation_p.E815*	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	824					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)		p.E824*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		TTTTGCTGATGAAGAATTAGG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											81	84	83					13																	21265282		2203	4300	6503	20163282	SO:0001587	stop_gained	8100			AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.2470G>T	13.37:g.21265282G>T	ENSP00000323580:p.Glu824*		20163282	A2A491|B4DUS2|Q5SZJ6|Q8N719	Nonsense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	G	41	8.995534	0.99029	.	.	ENSG00000032742	ENST00000351808;ENST00000319980;ENST00000537103	.	.	.	5.56	5.56	0.83823	.	0.104567	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-28.0999	19.1155	0.93336	0.0:0.0:1.0:0.0	.	.	.	.	X	815;824;796	.	ENSP00000323580:E824X	E	+	1	0	IFT88	20163282	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.949000	0.93012	2.598000	0.87819	0.655000	0.94253	GAA		0.378	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		T	21265282	G	T	21265282	4	4	61	1	0	0	0	0	0	1	0	0	7587	1291	45	2	2572	2	IFT88	13	21265282	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	467800	21265282	93904596	8506	16491										
XPO4	64328	broad.mit.edu	37	chr13	21381614	21381614	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctaatcacagaatctgttCtgttgtaccctgggatggaa	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21381614C>T	ENST00000255305.6	-	13	1870	c.1799G>A	c.(1798-1800)aGa>aAa	p.R600K	XPO4_ENST00000400602.2_Missense_Mutation_p.R600K			Q9C0E2	XPO4_HUMAN	exportin 4	600					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R573K(1)		breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		AGAATCTGTTCTGTTGTACCC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13											118	107	111					13																	21381614		1823	4079	5902	20279614	SO:0001583	missense	64328			AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.1799G>A	13.37:g.21381614C>T	ENSP00000255305:p.Arg600Lys		20279614	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	37	CCDS41872.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527172	0.27299	.	.	ENSG00000132953	ENST00000400602;ENST00000456108;ENST00000255305	T;T	0.51071	0.72;0.72	5.74	5.74	0.90152	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	N	0.14661	0.345	0.58432	D	0.999994	B	0.22746	0.074	B	0.22601	0.04	T	0.20240	-1.0281	10	0.05959	T	0.93	-10.14	19.9173	0.97066	0.0:1.0:0.0:0.0	.	600	Q9C0E2	XPO4_HUMAN	K	600;470;600	ENSP00000383444:R600K;ENSP00000255305:R600K	ENSP00000255305:R600K	R	-	2	0	XPO4	20279614	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.707000	0.92482	0.563000	0.77884	AGA		0.353	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		T	21381614	C	T	21381614	3	4	61	1	0	0	0	0	1	0	0	0	17486	913	32	3	1700	3	XPO4	13	21381614	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116332	21381614	93788264	8507	16492										
LATS2	26524	broad.mit.edu	37	chr13	21562238	21562238	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcctttgtcccccttggCgcttttgcggctcttgtcgc	10	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21562238C>T	ENST00000382592.4	-	4	2086	c.1681G>A	c.(1681-1683)Gcc>Acc	p.A561T	LATS2_ENST00000472754.1_5'Flank|LATS2_ENST00000542899.1_Missense_Mutation_p.A561T	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2									p.A561T(1)		breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TCCCCCTTGGCGCTTTTGCGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	13											143	141	142					13																	21562238		2203	4300	6503	20460238	SO:0001583	missense	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.1681G>A	13.37:g.21562238C>T	ENSP00000372035:p.Ala561Thr		20460238		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	c	5.761	0.324720	0.10900	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.59083	0.29;0.29	5.12	-4.0	0.04057	.	0.806598	0.11396	N	0.568284	T	0.25754	0.0627	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.17137	-1.0379	10	0.16420	T	0.52	.	3.264	0.06859	0.2146:0.1472:0.098:0.5402	.	561	Q9NRM7	LATS2_HUMAN	T	561	ENSP00000372035:A561T;ENSP00000441817:A561T	ENSP00000372035:A561T	A	-	1	0	LATS2	20460238	0.000000	0.05858	0.000000	0.03702	0.361000	0.29550	-0.791000	0.04599	-0.675000	0.05246	-0.233000	0.12211	GCC		0.607	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			T	21562238	C	T	21562238	3	4	61	1	0	0	0	0	1	0	0	0	8669	768	27	1	1605	1	LATS2	13	21562238	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180624	21562238	93607640	8508	16493										
LATS2	26524	broad.mit.edu	37	chr13	21620068	21620068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcgggtagcccctgaaccGaagacttggatggctgtttt	13	10	0	2	rs139154828		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21620068G>A	ENST00000382592.4	-	2	503	c.98C>T	c.(97-99)tCg>tTg	p.S33L	LATS2_ENST00000542899.1_Missense_Mutation_p.S33L	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2									p.S33L(1)		breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CCCCTGAACCGAAGACTTGGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	LEU/SER	0,4406		0,0,2203	107	102	104		98	3.9	0	13	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	missense	LATS2	NM_014572.2	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	33/1089	21620068	1,13005	2203	4300	6503	20518068	SO:0001583	missense	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.98C>T	13.37:g.21620068G>A	ENSP00000372035:p.Ser33Leu		20518068		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	G	9.712	1.157409	0.21454	0.0	1.16E-4	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.36520	1.25;1.25	5.66	3.9	0.45041	.	0.517239	0.19226	N	0.119536	T	0.32466	0.0830	L	0.54323	1.7	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29761	-1.0001	10	0.66056	D	0.02	.	8.3095	0.32062	0.1399:0.13:0.73:0.0	.	33	Q9NRM7	LATS2_HUMAN	L	33	ENSP00000372035:S33L;ENSP00000441817:S33L	ENSP00000372035:S33L	S	-	2	0	LATS2	20518068	0.536000	0.26378	0.000000	0.03702	0.042000	0.13812	2.909000	0.48758	0.722000	0.32252	0.655000	0.94253	TCG		0.542	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			A	21620068	G	A	21620068	3	1	61	1	0	0	0	0	1	0	0	0	8669	1059	37	1	3196	1	LATS2	13	21620068	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57830	21620068	93549810	8509	16494										
SKA3	221150	broad.mit.edu	37	chr13	21742259	21742259	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatttttagtgcacattttGgagtttttagtacttttact	6	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21742259G>T	ENST00000314759.5	-	4	735	c.611C>A	c.(610-612)cCa>cAa	p.P204Q	SKA3_ENST00000400018.3_Missense_Mutation_p.P204Q	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	204					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.P204Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TGCACATTTTGGAGTTTTTAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											185	201	196					13																	21742259		2203	4300	6503	20640259	SO:0001583	missense	221150			AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.611C>A	13.37:g.21742259G>T	ENSP00000319417:p.Pro204Gln		20640259	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.624860	0.66901	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.69561	-0.41;-0.41	5.88	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.78997	0.4372	M	0.68952	2.095	0.42298	D	0.992163	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.99	T	0.81382	-0.0958	10	0.87932	D	0	-15.4198	12.1607	0.54103	0.0795:0.0:0.9205:0.0	.	204;204	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	Q	204	ENSP00000319417:P204Q;ENSP00000382896:P204Q	ENSP00000319417:P204Q	P	-	2	0	SKA3	20640259	1.000000	0.71417	0.139000	0.22197	0.862000	0.49288	5.574000	0.67424	1.491000	0.48482	0.655000	0.94253	CCA		0.358	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061		T	21742259	G	T	21742259	3	4	61	1	0	0	0	0	1	0	0	0	14391	1348	47	2	698	2	SKA3	13	21742259	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122191	21742259	93427619	8510	16495										
ZDHHC20	253832	broad.mit.edu	37	chr13	21955619	21955619	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattctccagccactgagaTtcactgtccaacaagcggtt	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21955619T>G	ENST00000400590.3	-	11	1212	c.1014A>C	c.(1012-1014)gaA>gaC	p.E338D	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.E338D|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.E275D|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.E337D|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000320220.9_3'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	338					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.E338D(1)|p.E337D(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		GCCACTGAGATTCACTGTCCA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	13											79	76	77					13																	21955619		1878	4113	5991	20853619	SO:0001583	missense	253832			AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"Zinc fingers, DHHC-type"	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.1014A>C	13.37:g.21955619T>G	ENSP00000383433:p.Glu338Asp		20853619	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	T	11.72	1.721750	0.30503	.	.	ENSG00000180776	ENST00000400590;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T	0.52754	0.91;0.92;0.65;0.91	5.65	-8.35	0.00984	.	0.795430	0.12307	N	0.480573	T	0.18130	0.0435	N	0.13352	0.335	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.001;0.005	T	0.09552	-1.0669	10	0.21540	T	0.41	-0.3633	2.0911	0.03657	0.174:0.2396:0.3593:0.2271	.	275;337	B4DRN8;Q5W0Z9-3	.;.	D	338;337;275;338	ENSP00000383433:E338D;ENSP00000371905:E337D;ENSP00000443236:E275D;ENSP00000401232:E338D	ENSP00000371905:E337D	E	-	3	2	ZDHHC20	20853619	0.698000	0.27777	0.892000	0.35008	0.995000	0.86356	-0.519000	0.06260	-1.100000	0.03030	-0.313000	0.08912	GAA		0.398	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		G	21955619	T	G	21955619	3	3	61	1	0	0	0	0	1	0	0	0	17650	1490	52	4	61	4	ZDHHC20	13	21955619	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	213360	21955619	93214259	8511	16496										
ZDHHC20	253832	broad.mit.edu	37	chr13	21974523	21974523	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacttaccgtccaaaattTtataaagtactctaaaactg	4	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:21974523T>G	ENST00000400590.3	-	7	781	c.583A>C	c.(583-585)Aaa>Caa	p.K195Q	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.K195Q|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.K132Q|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.K195Q|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.K195Q			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	195					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.K195Q(2)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		GTCCAAAATTTTATAAAGTAC	0.289																																																2	Substitution - Missense(2)	large_intestine(2)	13											23	22	22					13																	21974523		1792	4049	5841	20872523	SO:0001583	missense	253832			AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"Zinc fingers, DHHC-type"	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.583A>C	13.37:g.21974523T>G	ENSP00000383433:p.Lys195Gln		20872523	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	T	16.23	3.063975	0.55432	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	5.74	5.74	0.90152	.	0.204842	0.52532	D	0.000063	T	0.23572	0.0570	L	0.35288	1.05	0.80722	D	1	B;B	0.21688	0.059;0.021	B;B	0.28465	0.038;0.09	T	0.04268	-1.0964	10	0.25106	T	0.35	-11.3104	16.042	0.80691	0.0:0.0:0.0:1.0	.	132;195	B4DRN8;Q5W0Z9-3	.;.	Q	195;195;195;132;195	ENSP00000383433:K195Q;ENSP00000313583:K195Q;ENSP00000371905:K195Q;ENSP00000443236:K132Q;ENSP00000401232:K195Q	ENSP00000313583:K195Q	K	-	1	0	ZDHHC20	20872523	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.586000	0.82596	2.188000	0.69820	0.459000	0.35465	AAA		0.289	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		G	21974523	T	G	21974523	3	3	61	1	0	0	0	0	1	0	0	0	17650	1850	64	4	505	4	ZDHHC20	13	21974523	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18904	21974523	93195355	8512	16497										
EFHA1	221154	broad.mit.edu	37	chr13	22069459	22069460	+	Splice_Site	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctctcttaaactccgctINSaaaaaacaaacataaaacaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:22069459_22069460insA	ENST00000382374.4	-	11	1108		c.e11-2		MICU2_ENST00000479790.1_5'UTR	NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2						mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)	p.?(1)									TAAACTCCGCTAAAAAACAAAC	0.292																																																1	Unknown(1)	large_intestine(1)	13																																								20967460	SO:0001630	splice_region_variant	221154			AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.1043-2->T	13.37:g.22069465_22069465dupA			20967459	Q8N0T6|Q8NAX8	Splice_Site	INS	ENST00000382374.4	37	CCDS9297.1																																																																																				0.292	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726	Intron	A	22069460	-	A	22069459	8	5	61	1	0	1	1	0	0	0	1	0	4954	1536	53	0	271	0	EFHA1	13	22069459	Splice_Site	INS	-	TCGA-AG-A002-01A-01W-A00K-09	94936	22069459	93100419	8513	16498										
SGCG	6445	broad.mit.edu	37	chr13	23777840	23777840	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactccgtggcagatggtgCgtgagcagtacactacagcc	12	12	0	2	rs140310896		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23777840C>T	ENST00000218867.3	+	2	131	c.7C>T	c.(7-9)Cgt>Tgt	p.R3C	SGCG_ENST00000537476.1_Missense_Mutation_p.R3C|SGCG_ENST00000545013.1_Missense_Mutation_p.R3C	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	3					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.R3C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		GCAGATGGTGCGTGAGCAGTA	0.473													C|||	1	0.000199681	0	0	5008	,	,		16327	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	124	102	110		7	1.7	0	13	dbSNP_134	110	0,8598		0,0,4299	no	missense	SGCG	NM_000231.2	180	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	3/292	23777840	1,13003	2203	4299	6502	22675840	SO:0001583	missense	6445			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.7C>T	13.37:g.23777840C>T	ENSP00000218867:p.Arg3Cys		22675840	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	37	CCDS9299.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.952	0.745062	0.15710	2.27E-4	0.0	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.88354	-2.37;-2.37;-2.37	5.46	1.66	0.24008	.	0.212558	0.49916	N	0.000125	T	0.80476	0.4630	L	0.34521	1.04	0.29964	N	0.819134	B	0.20164	0.042	B	0.14023	0.01	T	0.71593	-0.4546	10	0.62326	D	0.03	-0.0501	6.8499	0.24008	0.1226:0.5756:0.2367:0.0651	.	3	Q13326	SGCG_HUMAN	C	3	ENSP00000218867:R3C;ENSP00000444100:R3C;ENSP00000442232:R3C	ENSP00000218867:R3C	R	+	1	0	SGCG	22675840	0.994000	0.37717	0.001000	0.08648	0.068000	0.16541	3.416000	0.52707	-0.005000	0.14395	-0.175000	0.13238	CGT		0.473	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		T	23777840	C	T	23777840	3	4	61	1	0	0	0	0	1	0	0	0	14240	768	27	1	9	1	SGCG	13	23777840	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1708381	23777840	91392038	8514	16499										
SGCG	6445	broad.mit.edu	37	chr13	23808842	23808842	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtatgccaaagaaatacaCtccagagtggtaagaaaatg	9	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23808842C>A	ENST00000218867.3	+	3	412	c.288C>A	c.(286-288)caC>caA	p.H96Q	SGCG_ENST00000537476.1_Missense_Mutation_p.H96Q|SGCG_ENST00000545013.1_Missense_Mutation_p.H96Q	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	96					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.H96Q(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		AAGAAATACACTCCAGAGTGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											105	109	107					13																	23808842		2203	4300	6503	22706842	SO:0001583	missense	6445			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.288C>A	13.37:g.23808842C>A	ENSP00000218867:p.His96Gln		22706842	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	37	CCDS9299.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.695662	0.30052	.	.	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.94457	-3.43;-3.43;-3.43	5.55	5.55	0.83447	.	0.181977	0.64402	D	0.000015	D	0.91036	0.7180	L	0.39245	1.2	0.44275	D	0.997139	P	0.36354	0.549	B	0.37650	0.255	D	0.88915	0.3362	10	0.09084	T	0.74	1.2825	17.0082	0.86399	0.0:1.0:0.0:0.0	.	96	Q13326	SGCG_HUMAN	Q	96	ENSP00000218867:H96Q;ENSP00000444100:H96Q;ENSP00000442232:H96Q	ENSP00000218867:H96Q	H	+	3	2	SGCG	22706842	0.999000	0.42202	1.000000	0.80357	0.921000	0.55340	0.580000	0.23803	2.613000	0.88420	0.585000	0.79938	CAC		0.338	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		A	23808842	C	A	23808842	3	1	61	1	0	0	0	0	1	0	0	0	14240	564	20	2	294	2	SGCG	13	23808842	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31002	23808842	91361036	8515	16500										
SGCG	6445	broad.mit.edu	37	chr13	23894856	23894856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacgctgggaaaattgaggCgctttctcaaatggatattc	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23894856C>T	ENST00000218867.3	+	7	783	c.659C>T	c.(658-660)gCg>gTg	p.A220V	SGCG_ENST00000537476.1_Missense_Mutation_p.A220V|SGCG_ENST00000545013.1_Missense_Mutation_p.A220V	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	220					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.A220V(2)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		AAAATTGAGGCGCTTTCTCAA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	13											94	94	94					13																	23894856		2203	4300	6503	22792856	SO:0001583	missense	6445			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.659C>T	13.37:g.23894856C>T	ENSP00000218867:p.Ala220Val		22792856	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	37	CCDS9299.1	.	.	.	.	.	.	.	.	.	.	C	7.835	0.720641	0.15372	.	.	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.94092	-3.35;-3.35;-3.35	5.62	2.95	0.34219	.	0.359451	0.32401	N	0.006155	D	0.85767	0.5773	L	0.35723	1.085	0.32340	N	0.559927	B	0.16802	0.019	B	0.16722	0.016	T	0.75536	-0.3283	10	0.09843	T	0.71	-11.4823	5.7878	0.18343	0.0:0.5251:0.2669:0.208	.	220	Q13326	SGCG_HUMAN	V	220	ENSP00000218867:A220V;ENSP00000444100:A220V;ENSP00000442232:A220V	ENSP00000218867:A220V	A	+	2	0	SGCG	22792856	0.071000	0.21146	0.994000	0.49952	0.001000	0.01503	0.217000	0.17603	0.743000	0.32719	-0.822000	0.03109	GCG		0.448	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		T	23894856	C	T	23894856	3	4	61	1	0	0	0	0	1	0	0	0	14240	768	27	1	681	1	SGCG	13	23894856	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86014	23894856	91275022	8516	16501										
SACS	26278	broad.mit.edu	37	chr13	23905110	23905110	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttaagatttctggtaaaGaattaaccttaagctttttg	6	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23905110G>T	ENST00000382292.3	-	9	13178	c.12905C>A	c.(12904-12906)tCt>tAt	p.S4302Y	SACS_ENST00000402364.1_Missense_Mutation_p.S3552Y|SACS_ENST00000382298.3_Missense_Mutation_p.S4302Y			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4302					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.S4155Y(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTCTGGTAAAGAATTAACCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	13											90	100	96					13																	23905110		2202	4300	6502	22803110	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12905C>A	13.37:g.23905110G>T	ENSP00000371729:p.Ser4302Tyr		22803110	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	16.06	3.017201	0.54576	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88741	-2.27;-2.42;-2.27	5.83	4.98	0.66077	Heat shock protein DnaJ, N-terminal (2);	0.227144	0.47852	D	0.000214	D	0.85457	0.5701	L	0.39898	1.24	0.30394	N	0.780724	B	0.31009	0.303	B	0.33890	0.172	D	0.85296	0.1070	10	0.87932	D	0	.	14.3544	0.66727	0.0707:0.0:0.9293:0.0	.	4302	Q9NZJ4	SACS_HUMAN	Y	4302;3552;4302	ENSP00000371729:S4302Y;ENSP00000385844:S3552Y;ENSP00000371735:S4302Y	ENSP00000371729:S4302Y	S	-	2	0	SACS	22803110	1.000000	0.71417	0.996000	0.52242	0.929000	0.56500	8.017000	0.88712	2.746000	0.94184	0.563000	0.77884	TCT		0.428	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23905110	G	T	23905110	3	4	61	1	0	0	0	0	1	0	0	0	13841	942	33	2	838	2	SACS	13	23905110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10254	23905110	91264768	8517	16502										
SACS	26278	broad.mit.edu	37	chr13	23905348	23905348	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatctatctgatatatctTtcctagaaaactagaattgt	4	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23905348T>G	ENST00000382292.3	-	9	12940	c.12667A>C	c.(12667-12669)Aag>Cag	p.K4223Q	SACS_ENST00000402364.1_Missense_Mutation_p.K3473Q|SACS_ENST00000382298.3_Missense_Mutation_p.K4223Q			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4223					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.K4076Q(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGATATATCTTTCCTAGAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	13											44	48	47					13																	23905348		2203	4299	6502	22803348	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12667A>C	13.37:g.23905348T>G	ENSP00000371729:p.Lys4223Gln		22803348	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	17.97	3.519179	0.64634	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88664	-2.26;-2.41;-2.26	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.90184	0.6932	L	0.33485	1.01	0.50813	D	0.999896	D	0.71674	0.998	P	0.61874	0.895	D	0.90186	0.4246	10	0.42905	T	0.14	.	15.4983	0.75673	0.0:0.0:0.0:1.0	.	4223	Q9NZJ4	SACS_HUMAN	Q	4223;3473;4223	ENSP00000371729:K4223Q;ENSP00000385844:K3473Q;ENSP00000371735:K4223Q	ENSP00000371729:K4223Q	K	-	1	0	SACS	22803348	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	8.036000	0.88901	2.049000	0.60858	0.460000	0.39030	AAG		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23905348	T	G	23905348	3	3	61	1	0	0	0	0	1	0	0	0	13841	1850	64	4	1076	4	SACS	13	23905348	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	238	23905348	91264530	8518	16503										
SACS	26278	broad.mit.edu	37	chr13	23907021	23907021	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatattgaggatgaaatCtaatgaattccgcgggggcc	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23907021C>A	ENST00000382292.3	-	9	11267	c.10994G>T	c.(10993-10995)aGa>aTa	p.R3665I	SACS_ENST00000402364.1_Missense_Mutation_p.R2915I|SACS_ENST00000382298.3_Missense_Mutation_p.R3665I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3665					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.R3518I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AGGATGAAATCTAATGAATTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											64	68	66					13																	23907021		2203	4299	6502	22805021	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10994G>T	13.37:g.23907021C>A	ENSP00000371729:p.Arg3665Ile		22805021	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.557372	0.86231	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87729	-2.14;-2.29;-2.14	5.95	5.95	0.96441	.	0.050119	0.64402	D	0.000001	D	0.85102	0.5620	N	0.24115	0.695	0.44685	D	0.997672	P	0.49961	0.93	P	0.48030	0.564	D	0.85764	0.1351	10	0.52906	T	0.07	.	20.3748	0.98911	0.0:1.0:0.0:0.0	.	3665	Q9NZJ4	SACS_HUMAN	I	3665;2915;3665	ENSP00000371729:R3665I;ENSP00000385844:R2915I;ENSP00000371735:R3665I	ENSP00000371729:R3665I	R	-	2	0	SACS	22805021	0.296000	0.24398	0.817000	0.32601	0.843000	0.47879	3.253000	0.51469	2.817000	0.96982	0.563000	0.77884	AGA		0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23907021	C	A	23907021	3	1	61	1	0	0	0	0	1	0	0	0	13841	913	32	2	2749	2	SACS	13	23907021	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1673	23907021	91262857	8519	16504										
SACS	26278	broad.mit.edu	37	chr13	23907090	23907090	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagttctttcagaaaatttCcagataacaaatccattcgt	4	8	2	2	rs148349355		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23907090C>A	ENST00000382292.3	-	9	11198	c.10925G>T	c.(10924-10926)gGa>gTa	p.G3642V	SACS_ENST00000402364.1_Missense_Mutation_p.G2892V|SACS_ENST00000382298.3_Missense_Mutation_p.G3642V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3642					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.G3495V(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CAGAAAATTTCCAGATAACAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											38	43	42					13																	23907090		2203	4298	6501	22805090	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10925G>T	13.37:g.23907090C>A	ENSP00000371729:p.Gly3642Val		22805090	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768476	0.69878	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87650	-2.13;-2.28;-2.13	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.90435	0.7005	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89228	0.3575	10	0.41790	T	0.15	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	3642	Q9NZJ4	SACS_HUMAN	V	3642;2892;3642	ENSP00000371729:G3642V;ENSP00000385844:G2892V;ENSP00000371735:G3642V	ENSP00000371729:G3642V	G	-	2	0	SACS	22805090	1.000000	0.71417	0.946000	0.38457	0.720000	0.41350	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GGA		0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23907090	C	A	23907090	3	1	61	1	0	0	0	0	1	0	0	0	13841	855	30	2	2818	2	SACS	13	23907090	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69	23907090	91262788	8520	16505										
SACS	26278	broad.mit.edu	37	chr13	23907566	23907566	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagagagattttcaattttTggtaagaggtgtttcaaata	9	2	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23907566T>G	ENST00000382292.3	-	9	10722	c.10449A>C	c.(10447-10449)ccA>ccC	p.P3483P	SACS_ENST00000402364.1_Silent_p.P2733P|SACS_ENST00000382298.3_Silent_p.P3483P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3483					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.P3336P(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTCAATTTTTGGTAAGAGGT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	13											53	55	54					13																	23907566		2198	4292	6490	22805566	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10449A>C	13.37:g.23907566T>G			22805566	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																				0.323	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23907566	T	G	23907566	2	3	61	1	0	0	0	0	0	0	0	1	13841	1799	63	4		4	SACS	13	23907566	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	476	23907566	91262312	8521	16506										
SACS	26278	broad.mit.edu	37	chr13	23908736	23908736	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctgatatcagcaggggtCacataactaacaggaatatc	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23908736C>A	ENST00000382292.3	-	9	9552	c.9279G>T	c.(9277-9279)gtG>gtT	p.V3093V	SACS_ENST00000402364.1_Silent_p.V2343V|SACS_ENST00000382298.3_Silent_p.V3093V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3093					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.V2946V(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CAGCAGGGGTCACATAACTAA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											68	65	66					13																	23908736		2203	4300	6503	22806736	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9279G>T	13.37:g.23908736C>A			22806736	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																				0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23908736	C	A	23908736	2	1	61	1	0	0	0	0	0	0	0	1	13841	813	29	2		2	SACS	13	23908736	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1170	23908736	91261142	8522	16507										
SACS	26278	broad.mit.edu	37	chr13	23908898	23908898	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatattataatctgcattTttaaggtgttgtaattcatc	7	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23908898T>G	ENST00000382292.3	-	9	9390	c.9117A>C	c.(9115-9117)aaA>aaC	p.K3039N	SACS_ENST00000402364.1_Missense_Mutation_p.K2289N|SACS_ENST00000382298.3_Missense_Mutation_p.K3039N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3039					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.K2892N(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AATCTGCATTTTTAAGGTGTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	13											104	102	103					13																	23908898		2203	4299	6502	22806898	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9117A>C	13.37:g.23908898T>G	ENSP00000371729:p.Lys3039Asn		22806898	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	16.19	3.053188	0.55218	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88201	-2.21;-2.35;-2.21	5.64	3.25	0.37280	.	0.000000	0.85682	D	0.000000	D	0.88463	0.6443	L	0.40543	1.245	0.38650	D	0.951823	D	0.63880	0.993	P	0.59948	0.866	D	0.84248	0.0476	10	0.18276	T	0.48	.	10.1503	0.42788	0.0:0.1192:0.0:0.8808	.	3039	Q9NZJ4	SACS_HUMAN	N	3039;2289;3039	ENSP00000371729:K3039N;ENSP00000385844:K2289N;ENSP00000371735:K3039N	ENSP00000371729:K3039N	K	-	3	2	SACS	22806898	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.655000	0.46707	0.436000	0.26393	0.454000	0.30748	AAA		0.318	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23908898	T	G	23908898	3	3	61	1	0	0	0	0	1	0	0	0	13841	1838	64	4	4626	4	SACS	13	23908898	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162	23908898	91260980	8523	16508										
SACS	26278	broad.mit.edu	37	chr13	23909113	23909113	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatctggctgtagatcaaGacggttaactgggaaaaacg	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23909113G>T	ENST00000382292.3	-	9	9175	c.8902C>A	c.(8902-8904)Ctt>Att	p.L2968I	SACS_ENST00000402364.1_Missense_Mutation_p.L2218I|SACS_ENST00000382298.3_Missense_Mutation_p.L2968I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2968					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.L2821I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGTAGATCAAGACGGTTAACT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											89	91	91					13																	23909113		2203	4299	6502	22807113	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8902C>A	13.37:g.23909113G>T	ENSP00000371729:p.Leu2968Ile		22807113	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	11.88	1.769318	0.31320	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87179	-2.08;-2.22;-2.08	5.64	5.64	0.86602	.	0.067372	0.64402	D	0.000011	T	0.82213	0.4988	L	0.36672	1.1	0.36072	D	0.842162	D	0.57571	0.98	B	0.44315	0.446	D	0.84089	0.0389	10	0.29301	T	0.29	.	12.9722	0.58520	0.0738:0.0:0.9262:0.0	.	2968	Q9NZJ4	SACS_HUMAN	I	2968;2218;2968	ENSP00000371729:L2968I;ENSP00000385844:L2218I;ENSP00000371735:L2968I	ENSP00000371729:L2968I	L	-	1	0	SACS	22807113	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.348000	0.66004	2.653000	0.90120	0.555000	0.69702	CTT		0.383	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23909113	G	T	23909113	3	4	61	1	0	0	0	0	1	0	0	0	13841	942	33	2	4841	2	SACS	13	23909113	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215	23909113	91260765	8524	16509										
SACS	26278	broad.mit.edu	37	chr13	23909694	23909694	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattgtttccttttcaatCtgtctccatctgtgattttg	6	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23909694C>A	ENST00000382292.3	-	9	8594	c.8321G>T	c.(8320-8322)aGa>aTa	p.R2774I	SACS_ENST00000402364.1_Missense_Mutation_p.R2024I|SACS_ENST00000382298.3_Missense_Mutation_p.R2774I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2774					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.R2627I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CCTTTTCAATCTGTCTCCATC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	13											100	92	95					13																	23909694		2203	4299	6502	22807694	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8321G>T	13.37:g.23909694C>A	ENSP00000371729:p.Arg2774Ile		22807694	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.855606	0.91355	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88354	-2.18;-2.37;-2.18	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.91418	0.7292	L	0.43152	1.355	0.80722	D	1	D	0.67145	0.996	P	0.59546	0.859	D	0.91770	0.5427	10	0.56958	D	0.05	.	19.0749	0.93156	0.0:1.0:0.0:0.0	.	2774	Q9NZJ4	SACS_HUMAN	I	2774;2024;2774	ENSP00000371729:R2774I;ENSP00000385844:R2024I;ENSP00000371735:R2774I	ENSP00000371729:R2774I	R	-	2	0	SACS	22807694	1.000000	0.71417	0.689000	0.30133	0.991000	0.79684	7.445000	0.80570	2.584000	0.87258	0.462000	0.41574	AGA		0.333	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23909694	C	A	23909694	3	1	61	1	0	0	0	0	1	0	0	0	13841	913	32	2	5422	2	SACS	13	23909694	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	581	23909694	91260184	8525	16510										
SACS	26278	broad.mit.edu	37	chr13	23911196	23911196	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttaacagccaatgacacTgaaccacaacctctaaaaga	4	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23911196T>G	ENST00000382292.3	-	9	7092	c.6819A>C	c.(6817-6819)tcA>tcC	p.S2273S	SACS_ENST00000402364.1_Silent_p.S1523S|SACS_ENST00000382298.3_Silent_p.S2273S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2273					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.S2126S(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CCAATGACACTGAACCACAAC	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	13											48	50	49					13																	23911196		2203	4299	6502	22809196	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6819A>C	13.37:g.23911196T>G			22809196	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																				0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23911196	T	G	23911196	2	3	61	1	0	0	0	0	0	0	0	1	13841	1567	55	4		4	SACS	13	23911196	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1502	23911196	91258682	8526	16511										
SACS	26278	broad.mit.edu	37	chr13	23913102	23913102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaagggttccattatagCtgtaaggtgcttctacagtc	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23913102C>T	ENST00000382292.3	-	9	5186	c.4913G>A	c.(4912-4914)aGc>aAc	p.S1638N	SACS_ENST00000402364.1_Missense_Mutation_p.S888N|SACS_ENST00000382298.3_Missense_Mutation_p.S1638N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1638					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.S1491N(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TCCATTATAGCTGTAAGGTGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											136	128	131					13																	23913102		2203	4299	6502	22811102	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.4913G>A	13.37:g.23913102C>T	ENSP00000371729:p.Ser1638Asn		22811102	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	10.43	1.347853	0.24426	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88975	-2.45;-2.45;-2.45	5.84	5.84	0.93424	ATPase-like, ATP-binding domain (2);	0.088957	0.85682	D	0.000000	T	0.80706	0.4674	N	0.16368	0.405	0.33638	D	0.606938	P	0.38922	0.651	B	0.32677	0.15	T	0.81899	-0.0721	10	0.21540	T	0.41	.	20.1551	0.98106	0.0:1.0:0.0:0.0	.	1638	Q9NZJ4	SACS_HUMAN	N	1638;888;1638	ENSP00000371729:S1638N;ENSP00000385844:S888N;ENSP00000371735:S1638N	ENSP00000371729:S1638N	S	-	2	0	SACS	22811102	1.000000	0.71417	1.000000	0.80357	0.208000	0.24298	5.393000	0.66279	2.760000	0.94817	0.655000	0.94253	AGC		0.358	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23913102	C	T	23913102	3	4	61	1	0	0	0	0	1	0	0	0	13841	797	28	3	8830	3	SACS	13	23913102	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1906	23913102	91256776	8527	16512										
SACS	26278	broad.mit.edu	37	chr13	23913434	23913434	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgaatctgagaattgagaAttgttgaatgaccacaaagc	9	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23913434A>G	ENST00000382292.3	-	9	4854	c.4581T>C	c.(4579-4581)aaT>aaC	p.N1527N	SACS_ENST00000402364.1_Silent_p.N777N|SACS_ENST00000382298.3_Silent_p.N1527N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1527					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.N1380N(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AGAATTGAGAATTGTTGAATG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											62	58	60					13																	23913434		2203	4300	6503	22811434	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.4581T>C	13.37:g.23913434A>G			22811434	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																				0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23913434	A	G	23913434	2	3	61	1	0	0	0	0	0	0	0	1	13841	98	4	4		4	SACS	13	23913434	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	332	23913434	91256444	8528	16513										
SACS	26278	broad.mit.edu	37	chr13	23914615	23914615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgtgattcttatttaaaaCcagtaagagggttttggctt	10	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23914615C>T	ENST00000382292.3	-	9	3673	c.3400G>A	c.(3400-3402)Gtt>Att	p.V1134I	SACS_ENST00000402364.1_Missense_Mutation_p.V384I|SACS_ENST00000382298.3_Missense_Mutation_p.V1134I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1134					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.V987I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTATTTAAAACCAGTAAGAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											115	120	118					13																	23914615		2203	4300	6503	22812615	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.3400G>A	13.37:g.23914615C>T	ENSP00000371729:p.Val1134Ile		22812615	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	6.760	0.509055	0.12883	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87412	-2.1;-2.25;-2.1	6.16	5.32	0.75619	.	0.122006	0.56097	N	0.000028	T	0.74989	0.3789	N	0.21448	0.665	0.35087	D	0.763973	B	0.02656	0.0	B	0.01281	0.0	T	0.70421	-0.4876	10	0.13108	T	0.6	.	7.2921	0.26372	0.0:0.7278:0.0:0.2722	.	1134	Q9NZJ4	SACS_HUMAN	I	1134;384;1134	ENSP00000371729:V1134I;ENSP00000385844:V384I;ENSP00000371735:V1134I	ENSP00000371729:V1134I	V	-	1	0	SACS	22812615	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	3.829000	0.55760	1.623000	0.50342	0.650000	0.86243	GTT		0.393	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23914615	C	T	23914615	3	4	61	1	0	0	0	0	1	0	0	0	13841	507	18	3	10343	3	SACS	13	23914615	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1181	23914615	91255263	8529	16514										
SACS	26278	broad.mit.edu	37	chr13	23915071	23915071	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctttaactgttctatttTcaacatgtttgccagacgaa	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23915071T>G	ENST00000382292.3	-	9	3217	c.2944A>C	c.(2944-2946)Aaa>Caa	p.K982Q	SACS_ENST00000402364.1_Missense_Mutation_p.K232Q|SACS_ENST00000382298.3_Missense_Mutation_p.K982Q			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	982					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.K835Q(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGTTCTATTTTCAACATGTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	74	74					13																	23915071		2203	4300	6503	22813071	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.2944A>C	13.37:g.23915071T>G	ENSP00000371729:p.Lys982Gln		22813071	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	14.98	2.698327	0.48307	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87650	-2.13;-2.28;-2.13	6.05	6.05	0.98169	.	0.046859	0.85682	D	0.000000	T	0.81607	0.4858	L	0.29908	0.895	0.37528	D	0.917824	B	0.23650	0.089	B	0.16722	0.016	T	0.79391	-0.1823	10	0.41790	T	0.15	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	982	Q9NZJ4	SACS_HUMAN	Q	982;232;982	ENSP00000371729:K982Q;ENSP00000385844:K232Q;ENSP00000371735:K982Q	ENSP00000371729:K982Q	K	-	1	0	SACS	22813071	1.000000	0.71417	1.000000	0.80357	0.578000	0.36192	5.978000	0.70501	2.320000	0.78422	0.528000	0.53228	AAA		0.358	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23915071	T	G	23915071	3	3	61	1	0	0	0	0	1	0	0	0	13841	1792	62	4	10799	4	SACS	13	23915071	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	456	23915071	91254807	8530	16515										
SACS	26278	broad.mit.edu	37	chr13	23929770	23929770	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcactctaaacaccagtttCtctgttccgtcagcctctcg	6	15	5	0	rs370395358		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:23929770C>A	ENST00000382292.3	-	7	1254	c.981G>T	c.(979-981)gaG>gaT	p.E327D	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Missense_Mutation_p.E327D			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	327					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.E180D(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ACACCAGTTTCTCTGTTCCGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	76	78	78		981	4.9	0.9	13		78	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	45	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	possibly-damaging	327/4580	23929770	1,13005	2203	4300	6503	22827770	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.981G>T	13.37:g.23929770C>A	ENSP00000371729:p.Glu327Asp		22827770	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.79|13.79	2.342142|2.342142	0.41498|0.41498	2.27E-4|2.27E-4	0.0|0.0	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298|ENST00000455470	D;D|.	0.87491|.	-2.26;-2.26|.	5.72|5.72	4.86|4.86	0.63082|0.63082	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.58807|.	0.2148|.	M|M	0.71206|0.71206	2.165|2.165	0.38838|0.38838	D|D	0.956|0.956	D;P;P|.	0.64830|.	0.994;0.589;0.548|.	P;P;B|.	0.62184|.	0.899;0.544;0.415|.	T|.	0.57242|.	-0.7845|.	10|.	0.41790|0.06757	T|T	0.15|0.87	.|.	10.392|10.392	0.44179|0.44179	0.0:0.8493:0.0:0.1507|0.0:0.8493:0.0:0.1507	.|.	226;114;327|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	D|X	327|227	ENSP00000371729:E327D;ENSP00000371735:E327D|.	ENSP00000371729:E327D|ENSP00000406565:E227X	E|E	-|-	3|1	2|0	SACS|SACS	22827770|22827770	0.994000|0.994000	0.37717|0.37717	0.868000|0.868000	0.34077|0.34077	0.106000|0.106000	0.19336|0.19336	0.913000|0.913000	0.28611|0.28611	1.525000|1.525000	0.49052|0.49052	0.650000|0.650000	0.86243|0.86243	GAG|GAA		0.433	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23929770	C	A	23929770	3	1	61	1	0	0	0	0	1	0	0	0	13841	912	32	2	12770	2	SACS	13	23929770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14699	23929770	91240108	8531	16516										
MIPEP	4285	broad.mit.edu	37	chr13	24334343	24334343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccacgaggtggctgaatCgcagctgccaggcctgccaa	12	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:24334343C>T	ENST00000382172.3	-	17	1960	c.1862G>A	c.(1861-1863)cGa>cAa	p.R621Q		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	621					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R621Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		GTGGCTGAATCGCAGCTGCCA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	13											82	80	81					13																	24334343		2203	4300	6503	23232343	SO:0001583	missense	4285				CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1862G>A	13.37:g.24334343C>T	ENSP00000371607:p.Arg621Gln		23232343	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.192669|5.192669	0.94960|0.94960	.|.	.|.	ENSG00000027001|ENSG00000027001	ENST00000433710|ENST00000382172	.|T	.|0.11495	.|2.77	5.56|5.56	5.56|5.56	0.83823|0.83823	.|Neurolysin/Thimet oligopeptidase, domain 2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.23014|0.23014	0.0556|0.0556	L|L	0.41632|0.41632	1.29|1.29	0.80722|0.80722	D|D	1|1	.|D	.|0.64830	.|0.994	.|P	.|0.58520	.|0.84	T|T	0.00124|0.00124	-1.2023|-1.2023	6|10	0.87932|0.51188	D|T	0|0.08	-20.6263|-20.6263	19.1287|19.1287	0.93396|0.93396	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|621	.|Q99797	.|MIPEP_HUMAN	N|Q	19|621	.|ENSP00000371607:R621Q	ENSP00000397404:D19N|ENSP00000371607:R621Q	D|R	-|-	1|2	0|0	MIPEP|MIPEP	23232343|23232343	1.000000|1.000000	0.71417|0.71417	0.639000|0.639000	0.29394|0.29394	0.788000|0.788000	0.44548|0.44548	5.652000|5.652000	0.67959|0.67959	2.631000|2.631000	0.89168|0.89168	0.462000|0.462000	0.41574|0.41574	GAT|CGA		0.512	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			T	24334343	C	T	24334343	3	4	61	1	0	0	0	0	1	0	0	0	9622	884	31	1	291	1	MIPEP	13	24334343	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	404573	24334343	90835535	8532	16517										
MIPEP	4285	broad.mit.edu	37	chr13	24443524	24443524	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctctgctgctgagcaattCttctaaacatttcaattgac	5	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:24443524C>A	ENST00000382172.3	-	7	948	c.850G>T	c.(850-852)Gaa>Taa	p.E284*		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	284					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.E284*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		CTGAGCAATTCTTCTAAACAT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											78	79	78					13																	24443524		2203	4300	6503	23341524	SO:0001587	stop_gained	4285				CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.850G>T	13.37:g.24443524C>A	ENSP00000371607:p.Glu284*		23341524	Q5JV15|Q5T9Q9|Q96G65	Nonsense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	C	39	7.796665	0.98495	.	.	ENSG00000027001	ENST00000382172	.	.	.	5.9	5.04	0.67666	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	16.9456	0.86229	0.0:0.8722:0.1278:0.0	.	.	.	.	X	284	.	ENSP00000371607:E284X	E	-	1	0	MIPEP	23341524	1.000000	0.71417	0.521000	0.27850	0.936000	0.57629	7.222000	0.78025	1.453000	0.47775	0.561000	0.74099	GAA		0.398	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			A	24443524	C	A	24443524	4	1	61	1	0	0	0	0	0	1	0	0	9622	922	32	2	1343	2	MIPEP	13	24443524	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109181	24443524	90726354	8533	16518										
PARP4	143	broad.mit.edu	37	chr13	25060323	25060323	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccgacacaagattcccacGatgttttgtacaggagaacc	8	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25060323G>A	ENST00000381989.3	-	11	1440	c.1335C>T	c.(1333-1335)atC>atT	p.I445I		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	445	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.I445I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGATTCCCACGATGTTTTGTA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											105	92	97					13																	25060323		2203	4300	6503	23958323	SO:0001819	synonymous_variant	143			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1335C>T	13.37:g.25060323G>A			23958323	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																				0.373	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		A	25060323	G	A	25060323	2	1	61	1	0	0	0	0	0	0	0	1	11494	1048	37	1		1	PARP4	13	25060323	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	616799	25060323	90109555	8534	16519										
ATP12A	479	broad.mit.edu	37	chr13	25263463	25263463	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatctttgcttattaccaaGaggcaaaaagcaccaacatc	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25263463G>T	ENST00000381946.3	+	5	663	c.496G>T	c.(496-498)Gag>Tag	p.E166*	ATP12A_ENST00000218548.6_Nonsense_Mutation_p.E166*			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	166					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.E166*(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTATTACCAAGAGGCAAAAAG	0.522																																					Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - Nonsense(1)	large_intestine(1)	13											219	205	210					13																	25263463		2203	4300	6503	24161463	SO:0001587	stop_gained	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.496G>T	13.37:g.25263463G>T	ENSP00000371372:p.Glu166*		24161463	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Nonsense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	41	8.556387	0.98861	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	.	.	.	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.1375	0.81497	0.0:0.0:1.0:0.0	.	.	.	.	X	166	.	ENSP00000218548:E166X	E	+	1	0	ATP12A	24161463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.163000	0.77524	2.680000	0.91292	0.561000	0.74099	GAG		0.522	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25263463	G	T	25263463	4	4	61	1	0	0	0	0	0	1	0	0	1123	943	33	2	514	2	ATP12A	13	25263463	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203140	25263463	89906415	8535	16520										
ATP12A	479	broad.mit.edu	37	chr13	25266635	25266635	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaagaacctggaggctgtGgagaccctcggctccacctc	13	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25266635G>T	ENST00000381946.3	+	9	1304	c.1137G>T	c.(1135-1137)gtG>gtT	p.V379V	ATP12A_ENST00000218548.6_Silent_p.V385V			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	379					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.V379V(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TGGAGGCTGTGGAGACCCTCG	0.557																																					Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - coding silent(1)	large_intestine(1)	13											90	81	84					13																	25266635		2203	4300	6503	24164635	SO:0001819	synonymous_variant	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1137G>T	13.37:g.25266635G>T			24164635	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																				0.557	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25266635	G	T	25266635	2	4	61	1	0	0	0	0	0	0	0	1	1123	1335	47	2		2	ATP12A	13	25266635	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3172	25266635	89903243	8536	16521										
ATP12A	479	broad.mit.edu	37	chr13	25268621	25268621	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcagaaactgctcttttaAaattctcagaggtcattttg	6	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25268621A>C	ENST00000381946.3	+	11	1584	c.1417A>C	c.(1417-1419)Aaa>Caa	p.K473Q	ATP12A_ENST00000218548.6_Missense_Mutation_p.K479Q			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	473					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.K473Q(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TGCTCTTTTAAAATTCTCAGA	0.368											OREG0022298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - Missense(1)	large_intestine(1)	13											116	126	123					13																	25268621		2203	4300	6503	24166621	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1417A>C	13.37:g.25268621A>C	ENSP00000371372:p.Lys473Gln	777	24166621	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.131487	0.77549	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.79845	-1.31;-1.31	5.55	5.55	0.83447	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.86180	0.5871	L	0.49455	1.56	0.58432	D	0.999994	D;D	0.76494	0.999;0.996	D;P	0.70227	0.968;0.892	D	0.87477	0.2418	10	0.87932	D	0	.	13.6515	0.62314	1.0:0.0:0.0:0.0	.	479;473	P54707-2;P54707	.;AT12A_HUMAN	Q	479;473	ENSP00000218548:K479Q;ENSP00000371372:K473Q	ENSP00000218548:K479Q	K	+	1	0	ATP12A	24166621	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.121000	0.77160	2.117000	0.64856	0.460000	0.39030	AAA		0.368	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		C	25268621	A	C	25268621	3	2	61	1	0	0	0	0	1	0	0	0	1123	15	1	4	1477	4	ATP12A	13	25268621	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1986	25268621	89901257	8537	16522										
ATP12A	479	broad.mit.edu	37	chr13	25272866	25272866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaagggggcccctgagcGcatcctagagaaatgcagca	14	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25272866G>A	ENST00000381946.3	+	12	1750	c.1583G>A	c.(1582-1584)cGc>cAc	p.R528H	ATP12A_ENST00000218548.6_Missense_Mutation_p.R534H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	528					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.R528H(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GCCCCTGAGCGCATCCTAGAG	0.572																																					Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - Missense(1)	large_intestine(1)	13											99	95	97					13																	25272866		2203	4300	6503	24170866	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1583G>A	13.37:g.25272866G>A	ENSP00000371372:p.Arg528His		24170866	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572470	0.65765	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.80480	-1.38;-1.38	5.72	4.88	0.63580	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.062472	0.64402	D	0.000006	D	0.88190	0.6370	M	0.88450	2.955	0.58432	D	0.999999	D;D	0.71674	0.998;0.988	P;P	0.55055	0.767;0.598	D	0.90082	0.4171	10	0.87932	D	0	.	12.5302	0.56111	0.0806:0.0:0.9194:0.0	.	534;528	P54707-2;P54707	.;AT12A_HUMAN	H	534;528	ENSP00000218548:R534H;ENSP00000371372:R528H	ENSP00000218548:R534H	R	+	2	0	ATP12A	24170866	1.000000	0.71417	0.985000	0.45067	0.124000	0.20399	7.849000	0.86908	1.430000	0.47334	0.655000	0.94253	CGC		0.572	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25272866	G	A	25272866	3	1	61	1	0	0	0	0	1	0	0	0	1123	1087	38	1	1647	1	ATP12A	13	25272866	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4245	25272866	89897012	8538	16523										
ATP12A	479	broad.mit.edu	37	chr13	25275049	25275049	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcaccaaatgccggagtGcagggatcaaggtgggagtt	15	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25275049G>A	ENST00000381946.3	+	13	2037	c.1870G>A	c.(1870-1872)Gca>Aca	p.A624T	ATP12A_ENST00000218548.6_Missense_Mutation_p.A630T|RNY1P7_ENST00000384743.1_RNA			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	624					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.A624T(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		ATGCCGGAGTGCAGGGATCAA	0.453																																					Pancreas(156;1582 1935 18898 22665 26498)											1	Substitution - Missense(1)	large_intestine(1)	13											109	98	102					13																	25275049		2203	4300	6503	24173049	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1870G>A	13.37:g.25275049G>A	ENSP00000371372:p.Ala624Thr		24173049	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029468	0.75504	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.96940	-4.18;-4.18	6.17	6.17	0.99709	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.071421	0.64402	D	0.000020	D	0.99029	0.9668	H	0.98446	4.235	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.97;1.0	D	0.99120	1.0849	10	0.87932	D	0	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	630;624	P54707-2;P54707	.;AT12A_HUMAN	T	630;624	ENSP00000218548:A630T;ENSP00000371372:A624T	ENSP00000218548:A630T	A	+	1	0	ATP12A	24173049	1.000000	0.71417	0.964000	0.40570	0.004000	0.04260	9.751000	0.98889	2.941000	0.99782	0.655000	0.94253	GCA		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25275049	G	A	25275049	3	1	61	1	0	0	0	0	1	0	0	0	1123	1319	46	3	1938	3	ATP12A	13	25275049	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2183	25275049	89894829	8539	16524										
RNF17	56163	broad.mit.edu	37	chr13	25362132	25362132	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcttaaatgaaggaaaaaGaacctgtgtgaagaatttgc	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25362132G>T	ENST00000255324.5	+	7	670	c.618G>T	c.(616-618)aaG>aaT	p.K206N	RNF17_ENST00000381921.1_Missense_Mutation_p.K206N|RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000255325.6_Missense_Mutation_p.K206N	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	206					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.K206N(2)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GAAGGAAAAAGAACCTGTGTG	0.269																																																2	Substitution - Missense(2)	large_intestine(2)	13											50	56	54					13																	25362132		2187	4289	6476	24260132	SO:0001583	missense	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.618G>T	13.37:g.25362132G>T	ENSP00000255324:p.Lys206Asn		24260132	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	14.07	2.426353	0.43020	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325;ENST00000255326	T;T;T	0.18960	3.43;3.43;2.18	4.62	3.68	0.42216	.	0.225076	0.30920	N	0.008608	T	0.24084	0.0583	L	0.29908	0.895	0.27653	N	0.947321	P;P;D	0.67145	0.651;0.651;0.996	B;B;P	0.59948	0.216;0.165;0.866	T	0.03384	-1.1042	10	0.49607	T	0.09	.	5.5109	0.16880	0.1943:0.0:0.8057:0.0	.	206;206;206	B7Z7S1;Q9BXT8;Q9BXT8-2	.;RNF17_HUMAN;.	N	206;206;65;207;206	ENSP00000255324:K206N;ENSP00000371346:K206N;ENSP00000255325:K207N	ENSP00000255324:K206N	K	+	3	2	RNF17	24260132	1.000000	0.71417	0.995000	0.50966	0.953000	0.61014	2.204000	0.42761	2.399000	0.81585	0.557000	0.71058	AAG		0.269	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25362132	G	T	25362132	3	4	61	1	0	0	0	0	1	0	0	0	13498	933	33	2	644	2	RNF17	13	25362132	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87083	25362132	89807746	8540	16525										
RNF17	56163	broad.mit.edu	37	chr13	25367367	25367367	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtacatttagaagcaaaaAacttccagccacagaaagac	6	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25367367A>C	ENST00000255324.5	+	10	1175	c.1123A>C	c.(1123-1125)Aac>Cac	p.N375H	RNF17_ENST00000381921.1_Missense_Mutation_p.N375H|RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000255325.6_Missense_Mutation_p.N375H	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	375					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.N375H(2)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		AGAAGCAAAAAACTTCCAGCC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	13											154	146	149					13																	25367367		2203	4300	6503	24265367	SO:0001583	missense	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1123A>C	13.37:g.25367367A>C	ENSP00000255324:p.Asn375His		24265367	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	A	6.387	0.439464	0.12104	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325;ENST00000255326	T;T;T	0.18960	3.43;3.44;2.18	5.15	0.866	0.19079	.	1.903360	0.02243	N	0.065922	T	0.15998	0.0385	N	0.14661	0.345	0.09310	N	1	B;B;B	0.30709	0.291;0.291;0.25	B;B;B	0.37047	0.125;0.125;0.24	T	0.25398	-1.0133	10	0.37606	T	0.19	.	5.3465	0.16012	0.5728:0.3221:0.105:0.0	.	375;375;375	B7Z7S1;Q9BXT8;Q9BXT8-2	.;RNF17_HUMAN;.	H	375;375;234;376;375	ENSP00000255324:N375H;ENSP00000371346:N375H;ENSP00000255325:N376H	ENSP00000255324:N375H	N	+	1	0	RNF17	24265367	0.000000	0.05858	0.001000	0.08648	0.246000	0.25737	0.348000	0.20031	0.001000	0.14605	0.528000	0.53228	AAC		0.423	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		C	25367367	A	C	25367367	3	2	61	1	0	0	0	0	1	0	0	0	13498	14	1	4	1161	4	RNF17	13	25367367	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5235	25367367	89802511	8541	16526										
RNF17	56163	broad.mit.edu	37	chr13	25399853	25399853	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcctctgtccagttcaaGatcaagcctgtgtagctaaa	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25399853G>T	ENST00000255324.5	+	16	2240	c.2188G>T	c.(2188-2190)Gat>Tat	p.D730Y	RNF17_ENST00000381921.1_Missense_Mutation_p.D730Y	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	730	Tudor 1. {ECO:0000255|PROSITE- ProRule:PRU00211}.				multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.D730Y(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TCCAGTTCAAGATCAAGCCTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											101	98	99					13																	25399853		2203	4300	6503	24297853	SO:0001583	missense	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2188G>T	13.37:g.25399853G>T	ENSP00000255324:p.Asp730Tyr		24297853	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196457	0.58126	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.12465	2.68;2.68;2.68	4.69	2.91	0.33838	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.813267	0.10890	N	0.622764	T	0.23210	0.0561	L	0.49778	1.585	0.80722	D	1	P;D	0.58620	0.954;0.983	P;P	0.55222	0.771;0.663	T	0.01532	-1.1331	10	0.87932	D	0	.	8.0305	0.30461	0.188:0.0:0.812:0.0	.	730;730	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	Y	730;730;589;54	ENSP00000255324:D730Y;ENSP00000371346:D730Y;ENSP00000388892:D54Y	ENSP00000255324:D730Y	D	+	1	0	RNF17	24297853	1.000000	0.71417	0.996000	0.52242	0.931000	0.56810	1.824000	0.39072	0.492000	0.27815	0.491000	0.48974	GAT		0.383	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25399853	G	T	25399853	3	4	61	1	0	0	0	0	1	0	0	0	13498	942	33	2	2250	2	RNF17	13	25399853	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32486	25399853	89770025	8542	16527										
RNF17	56163	broad.mit.edu	37	chr13	25418008	25418008	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctacctaatgagaatttTcagtcactttataataagga	5	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25418008T>G	ENST00000255324.5	+	20	2782	c.2730T>G	c.(2728-2730)ttT>ttG	p.F910L	RNF17_ENST00000381921.1_Missense_Mutation_p.F910L|RNF17_ENST00000339524.3_5'Flank	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	910					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.F910L(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		ATGAGAATTTTCAGTCACTTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	13											56	58	57					13																	25418008		2203	4293	6496	24316008	SO:0001583	missense	56163			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2730T>G	13.37:g.25418008T>G	ENSP00000255324:p.Phe910Leu		24316008	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	T	1.848	-0.465720	0.04476	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.10763	3.6;3.6;2.84	4.72	1.68	0.24146	.	0.776710	0.12173	N	0.492811	T	0.03651	0.0104	N	0.04203	-0.255	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.001	B;B;B	0.09377	0.004;0.001;0.002	T	0.37549	-0.9701	10	0.10111	T	0.7	-0.0208	3.4584	0.07524	0.1548:0.4167:0.3343:0.0942	.	910;910;910	B7Z7S1;Q9BXT8-5;Q9BXT8	.;.;RNF17_HUMAN	L	910;910;769;234	ENSP00000255324:F910L;ENSP00000371346:F910L;ENSP00000388892:F234L	ENSP00000255324:F910L	F	+	3	2	RNF17	24316008	0.352000	0.24895	1.000000	0.80357	0.929000	0.56500	-0.432000	0.06956	0.681000	0.31386	-0.285000	0.09966	TTT		0.318	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25418008	T	G	25418008	3	3	61	1	0	0	0	0	1	0	0	0	13498	1780	62	4	2808	4	RNF17	13	25418008	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	18155	25418008	89751870	8543	16528										
CENPJ	55835	broad.mit.edu	37	chr13	25457389	25457389	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accggatctgtacttcgtttCttgatgaccgtttgcatata	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25457389C>A	ENST00000381884.4	-	17	4128	c.3943G>T	c.(3943-3945)Gaa>Taa	p.E1315*	CENPJ_ENST00000545981.1_3'UTR|CENPJ_ENST00000493190.1_5'Flank	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1315					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)	p.E1315*(1)		endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TACTTCGTTTCTTGATGACCG	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											345	293	311					13																	25457389		2203	4300	6503	24355389	SO:0001587	stop_gained	55835			AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.3943G>T	13.37:g.25457389C>A	ENSP00000371308:p.Glu1315*		24355389	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Nonsense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	C	43	10.153419	0.99348	.	.	ENSG00000151849	ENST00000381884	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.0075	0.92857	0.0:1.0:0.0:0.0	.	.	.	.	X	1315	.	ENSP00000371308:E1315X	E	-	1	0	CENPJ	24355389	1.000000	0.71417	0.940000	0.37924	0.833000	0.47200	7.113000	0.77095	2.791000	0.96007	0.591000	0.81541	GAA		0.443	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25457389	C	A	25457389	4	1	61	1	0	0	0	0	0	1	0	0	3240	922	32	2	77	2	CENPJ	13	25457389	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39381	25457389	89712489	8544	16529										
CENPJ	55835	broad.mit.edu	37	chr13	25473704	25473704	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttttgctttctgttgttcGaagtctgcaatttctttcct	6	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:25473704G>A	ENST00000381884.4	-	9	3029	c.2844C>T	c.(2842-2844)ttC>ttT	p.F948F	CENPJ_ENST00000545981.1_Silent_p.F948F	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	948					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)	p.F948F(1)		endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TCTGTTGTTCGAAGTCTGCAA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	13											86	78	81					13																	25473704		2202	4298	6500	24371704	SO:0001819	synonymous_variant	55835			AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.2844C>T	13.37:g.25473704G>A			24371704	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	G	8.571	0.880147	0.17467	.	.	ENSG00000151849	ENST00000418179	.	.	.	5.25	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1184	0.42605	0.9192:0.0:0.0808:0.0	.	.	.	.	X	30	.	.	R	-	1	2	CENPJ	24371704	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.486000	0.45259	0.843000	0.35070	-0.259000	0.10710	CGA		0.378	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25473704	G	A	25473704	2	1	61	1	0	0	0	0	0	0	0	1	3240	1049	37	1		1	CENPJ	13	25473704	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16315	25473704	89696174	8545	16530										
ATP8A2	51761	broad.mit.edu	37	chr13	26129171	26129171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgacactcctgccatgGccaggacatcaaaccttaat	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:26129171G>A	ENST00000381655.2	+	13	1370	c.1228G>A	c.(1228-1230)Gcc>Acc	p.A410T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.A370T	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	370					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.A410T(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TCCTGCCATGGCCAGGACATC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											104	101	102					13																	26129171		1840	4099	5939	25027171	SO:0001583	missense	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.1228G>A	13.37:g.26129171G>A	ENSP00000371070:p.Ala410Thr		25027171	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	G	33	5.275722	0.95459	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	D;D	0.88664	-2.41;-2.41	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.93226	0.7842	L	0.53671	1.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;1.0	D	0.93612	0.6940	10	0.72032	D	0.01	.	18.6642	0.91483	0.0:0.0:1.0:0.0	.	370;370;370	B7Z880;Q9NTI2-3;Q9NTI2	.;.;AT8A2_HUMAN	T	410;370;190	ENSP00000371070:A410T;ENSP00000255283:A370T	ENSP00000255283:A370T	A	+	1	0	ATP8A2	25027171	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.493000	0.97960	2.656000	0.90262	0.637000	0.83480	GCC		0.418	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		A	26129171	G	A	26129171	3	1	61	1	0	0	0	0	1	0	0	0	1194	1203	42	3	1278	3	ATP8A2	13	26129171	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	655467	26129171	89040707	8546	16531										
ATP8A2	51761	broad.mit.edu	37	chr13	26155966	26155966	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaatgtagaatttgctgCtacttggagccacagccata	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:26155966C>A	ENST00000381655.2	+	23	2159	c.2017C>A	c.(2017-2019)Cta>Ata	p.L673I	ATP8A2_ENST00000255283.8_Missense_Mutation_p.L633I|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	633					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.L673I(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GAATTTGCTGCTACTTGGAGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	13											84	78	80					13																	26155966		1860	4100	5960	25053966	SO:0001583	missense	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2017C>A	13.37:g.26155966C>A	ENSP00000371070:p.Leu673Ile		25053966	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808897	0.50421	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.72051	-0.62;-0.62	6.17	-5.31	0.02730	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.64402	D	0.000001	D	0.83170	0.5196	M	0.83312	2.635	0.51233	D	0.999917	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.84804	0.0786	10	0.87932	D	0	.	20.4787	0.99198	0.0:0.8433:0.0:0.1567	.	633;453;633	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	I	673;633;453	ENSP00000371070:L673I;ENSP00000255283:L633I	ENSP00000255283:L633I	L	+	1	2	ATP8A2	25053966	0.999000	0.42202	0.518000	0.27811	0.206000	0.24218	0.984000	0.29565	-0.876000	0.04017	-0.768000	0.03414	CTA		0.403	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		A	26155966	C	A	26155966	3	1	61	1	0	0	0	0	1	0	0	0	1194	796	28	2	2107	2	ATP8A2	13	26155966	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26795	26155966	89013912	8547	16532										
ATP8A2	51761	broad.mit.edu	37	chr13	26535765	26535765	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgggattatttctggttcCtactgcctgtttgattgaag	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:26535765C>A	ENST00000381655.2	+	34	3378	c.3236C>A	c.(3235-3237)cCt>cAt	p.P1079H	ATP8A2_ENST00000255283.8_Missense_Mutation_p.P1014H	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1039					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.P1079H(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TTTCTGGTTCCTACTGCCTGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	13											200	183	188					13																	26535765		1929	4138	6067	25433765	SO:0001583	missense	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3236C>A	13.37:g.26535765C>A	ENSP00000371070:p.Pro1079His		25433765	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595455	0.66219	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.58652	0.32;0.32	5.48	5.48	0.80851	.	0.141452	0.48286	D	0.000194	T	0.80523	0.4639	M	0.88181	2.935	0.49798	D	0.999825	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.83854	0.0264	10	0.87932	D	0	.	17.4784	0.87667	0.0:1.0:0.0:0.0	.	1014;1039	B7Z880;Q9NTI2	.;AT8A2_HUMAN	H	1079;1014;859	ENSP00000371070:P1079H;ENSP00000255283:P1014H	ENSP00000255283:P1014H	P	+	2	0	ATP8A2	25433765	0.991000	0.36638	0.918000	0.36340	0.608000	0.37181	3.020000	0.49643	2.722000	0.93159	0.650000	0.86243	CCT		0.453	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		A	26535765	C	A	26535765	3	1	61	1	0	0	0	0	1	0	0	0	1194	681	24	2	3370	2	ATP8A2	13	26535765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	379799	26535765	88634113	8548	16533										
CDK8	1024	broad.mit.edu	37	chr13	26967555	26967555	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actactaacgtcagaaccaaTatttcactgtcgacaagagg	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:26967555T>G	ENST00000381527.3	+	7	1201	c.698T>G	c.(697-699)aTa>aGa	p.I233R	CDK8_ENST00000536792.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.I233R(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TCAGAACCAATATTTCACTGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	13											169	160	163					13																	26967555		2203	4300	6503	25865555	SO:0001583	missense	1024			X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.698T>G	13.37:g.26967555T>G	ENSP00000370938:p.Ile233Arg		25865555	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	37	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.220566	0.79464	.	.	ENSG00000132964	ENST00000381527	T	0.66280	-0.2	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77438	0.4130	M	0.71296	2.17	0.80722	D	1	D;D	0.57257	0.974;0.979	D;D	0.66979	0.913;0.948	T	0.80448	-0.1378	10	0.87932	D	0	-16.1545	15.5584	0.76219	0.0:0.0:0.0:1.0	.	233;233	P49336-2;P49336	.;CDK8_HUMAN	R	233	ENSP00000370938:I233R	ENSP00000370938:I233R	I	+	2	0	CDK8	25865555	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.655000	0.83696	2.122000	0.65172	0.528000	0.53228	ATA		0.343	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			G	26967555	T	G	26967555	3	3	61	1	0	0	0	0	1	0	0	0	3156	1406	49	4	724	4	CDK8	13	26967555	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	431790	26967555	88202323	8549	16534										
USP12	219333	broad.mit.edu	37	chr13	27690731	27690731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaatgccgaagcattggcGccctataaaatgaaaaacaa	7	9	1	1	rs367930012		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:27690731G>A	ENST00000282344.6	-	2	307	c.51C>T	c.(49-51)ggC>ggT	p.G17G		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	17					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G17G(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AAGCATTGGCGCCCTATAAAA	0.388																																					Ovarian(37;808 911 7590 44442 44991)											1	Substitution - coding silent(1)	large_intestine(1)	13						G		1,4405	2.1+/-5.4	0,1,2202	56	54	55		51	5.3	1	13		55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	USP12	NM_182488.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		17/371	27690731	2,13004	2203	4300	6503	26588731	SO:0001819	synonymous_variant	219333			AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.51C>T	13.37:g.27690731G>A			26588731	A8K0X0|Q5VZV3|Q8TC49	Silent	SNP	ENST00000282344.6	37	CCDS31952.1																																																																																				0.388	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		A	27690731	G	A	27690731	2	1	61	1	0	0	0	0	0	0	0	1	17083	1074	38	1		1	USP12	13	27690731	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	723176	27690731	87479147	8550	16535										
LNX2	222484	broad.mit.edu	37	chr13	28127379	28127379	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacatgacccatgatggggAccaactggcatcatactcat	8	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28127379A>G	ENST00000316334.3	-	8	1873	c.1744T>C	c.(1744-1746)Tcc>Ccc	p.S582P		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	582					protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)	p.S582P(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CATGATGGGGACCAACTGGCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	13											106	94	98					13																	28127379		2203	4300	6503	27025379	SO:0001583	missense	222484			AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1744T>C	13.37:g.28127379A>G	ENSP00000325929:p.Ser582Pro		27025379	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	.	.	.	.	.	.	.	.	.	.	A	30	5.053344	0.93793	.	.	ENSG00000139517	ENST00000316334	T	0.06449	3.3	6.05	6.05	0.98169	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.14184	0.0343	M	0.82056	2.57	0.80722	D	1	P	0.37525	0.598	B	0.37601	0.254	T	0.00516	-1.1694	10	0.66056	D	0.02	.	16.5993	0.84807	1.0:0.0:0.0:0.0	.	582	Q8N448	LNX2_HUMAN	P	582	ENSP00000325929:S582P	ENSP00000325929:S582P	S	-	1	0	LNX2	27025379	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.957000	0.93082	2.311000	0.77944	0.528000	0.53228	TCC		0.498	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			G	28127379	A	G	28127379	3	3	61	1	0	0	0	0	1	0	0	0	8890	275	10	4	340	4	LNX2	13	28127379	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	436648	28127379	87042499	8551	16536										
FLT3	2322	broad.mit.edu	37	chr13	28601234	28601234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctcttacctggaatttGgatgtgattggaaagtgggg	14	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28601234G>T	ENST00000241453.7	-	17	2279	c.2198C>A	c.(2197-2199)cCa>cAa	p.P733Q	FLT3_ENST00000380982.4_Missense_Mutation_p.P733Q|FLT3_ENST00000537084.1_Missense_Mutation_p.P733Q	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	733	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.P733Q(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCTGGAATTTGGATGTGATTG	0.388			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	1	Substitution - Missense(1)	large_intestine(1)	13											161	165	163					13																	28601234		2203	4300	6503	27499234	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2198C>A	13.37:g.28601234G>T	ENSP00000241453:p.Pro733Gln		27499234	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	4.277	0.050513	0.08243	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.76316	-0.94;-1.01;-0.78	5.73	5.73	0.89815	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.474234	0.21792	N	0.069049	T	0.70640	0.3247	L	0.47716	1.5	0.09310	N	1	B;B	0.14012	0.009;0.007	B;B	0.12156	0.007;0.004	T	0.55321	-0.8159	10	0.23302	T	0.38	.	13.2333	0.59955	0.0:0.0:0.7407:0.2593	.	733;733	P36888-2;P36888	.;FLT3_HUMAN	Q	733	ENSP00000241453:P733Q;ENSP00000370369:P733Q;ENSP00000438139:P733Q	ENSP00000241453:P733Q	P	-	2	0	FLT3	27499234	0.918000	0.31147	0.962000	0.40283	0.922000	0.55478	1.584000	0.36589	2.861000	0.98227	0.655000	0.94253	CCA		0.388	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			T	28601234	G	T	28601234	3	4	61	1	0	0	0	0	1	0	0	0	5961	1348	47	2	815	2	FLT3	13	28601234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	473855	28601234	86568644	8552	16537										
FLT3	2322	broad.mit.edu	37	chr13	28636159	28636160	+	Missense_Mutation	DNP	GC	GC	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcgtacactgtccctgaGctctggggtctcaacgcaca							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28636159_28636160GC>TA	ENST00000241453.7	-	3	293_294	c.212_213GC>TA	c.(211-213)aGC>aTA	p.S71I	FLT3_ENST00000380982.4_Missense_Mutation_p.S71I|FLT3_ENST00000537084.1_Missense_Mutation_p.S71I	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	71				S -> N (in Ref. 5; AAI44040). {ECO:0000305}.	B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.S71>?(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGTCCCTGAGCTCTGGGGTCT	0.53			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	1	Complex(1)	large_intestine(1)	13																																								27534160	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.212_213delinsTA	13.37:g.28636159_28636160delinsTA	ENSP00000241453:p.Ser71Ile		27534159	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	DNP	ENST00000241453.7	37	CCDS31953.1																																																																																				0.53	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			TA	28636160	GC	TA	28636159	3	4	61	1	0	0	0	0	1	0	0	0	5961	962	34	2	2856	2	FLT3	13	28636159	Missense_Mutation	DNP	GC	TCGA-AG-A002-01A-01W-A00K-09	34925	28636159	86533719	8553	16538										
PAN3	255967	broad.mit.edu	37	chr13	28841485	28841485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggagaaactatgatgaGcagacactttaatgacccta	10	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28841485G>A	ENST00000380958.3	+	12	1891	c.1739G>A	c.(1738-1740)aGc>aAc	p.S580N	PAN3_ENST00000399613.1_Missense_Mutation_p.S380N|PAN3_ENST00000282391.5_Missense_Mutation_p.S268N	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit									p.S380N(2)		endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	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)		ACTATGATGAGCAGACACTTT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	13											134	125	128					13																	28841485		2203	4300	6503	27739485	SO:0001583	missense	255967			AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.1739G>A	13.37:g.28841485G>A	ENSP00000370345:p.Ser580Asn		27739485		Missense_Mutation	SNP	ENST00000380958.3	37	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295351	0.40594	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.20069	2.1;2.1;2.1	5.56	4.72	0.59763	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115505	0.85682	N	0.000000	T	0.16599	0.0399	L	0.28344	0.845	0.80722	D	1	B;B;B;B	0.31790	0.34;0.314;0.015;0.112	B;B;B;B	0.33846	0.171;0.075;0.009;0.048	T	0.05666	-1.0871	10	0.22706	T	0.39	-4.8908	14.5814	0.68295	0.0704:0.0:0.9296:0.0	.	580;580;268;526	Q58A45-4;Q58A45;Q58A45-2;Q58A45-3	.;PAN3_HUMAN;.;.	N	580;380;268	ENSP00000370345:S580N;ENSP00000382522:S380N;ENSP00000282391:S268N	ENSP00000282391:S268N	S	+	2	0	PAN3	27739485	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	1.359000	0.45940	-0.157000	0.13467	AGC		0.368	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		A	28841485	G	A	28841485	3	1	61	1	0	0	0	0	1	0	0	0	11446	971	34	3	1785	3	PAN3	13	28841485	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205326	28841485	86328393	8554	16539										
PAN3	255967	broad.mit.edu	37	chr13	28851448	28851448	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcaggaattcagcgagaGaatttacagaaagccatgga	12	6	1	2	rs148327218		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28851448G>T	ENST00000380958.3	+	15	2276	c.2124G>T	c.(2122-2124)gaG>gaT	p.E708D	PAN3_ENST00000399613.1_Missense_Mutation_p.E508D|PAN3_ENST00000282391.5_Missense_Mutation_p.E396D	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit									p.E508D(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	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)		TTCAGCGAGAGAATTTACAGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	114	117	116		2124	1.3	1	13	dbSNP_134	116	0,8600		0,0,4300	no	missense	PAN3	NM_175854.7	45	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	benign	708/888	28851448	1,13005	2203	4300	6503	27749448	SO:0001583	missense	255967			AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.2124G>T	13.37:g.28851448G>T	ENSP00000370345:p.Glu708Asp		27749448		Missense_Mutation	SNP	ENST00000380958.3	37	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	G	9.476	1.096794	0.20552	2.27E-4	0.0	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.46819	0.86;0.86;0.86	5.81	1.28	0.21552	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043570	0.85682	N	0.000000	T	0.22589	0.0545	N	0.13168	0.305	0.58432	D	0.999998	P;B;P	0.36315	0.547;0.023;0.487	B;B;B	0.37989	0.262;0.015;0.122	T	0.22417	-1.0217	10	0.02654	T	1	-8.5289	6.638	0.22893	0.3084:0.0:0.5691:0.1225	.	708;396;654	Q58A45;Q58A45-2;Q58A45-3	PAN3_HUMAN;.;.	D	708;508;396	ENSP00000370345:E708D;ENSP00000382522:E508D;ENSP00000282391:E396D	ENSP00000282391:E396D	E	+	3	2	PAN3	27749448	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.900000	0.28431	0.286000	0.22352	0.655000	0.94253	GAG		0.348	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		T	28851448	G	T	28851448	3	4	61	1	0	0	0	0	1	0	0	0	11446	933	33	2	2182	2	PAN3	13	28851448	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9963	28851448	86318430	8555	16540										
FLT1	2321	broad.mit.edu	37	chr13	28901613	28901613	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttaccttgttgagaaaaaAtaagtcacgtttgctcttga	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28901613A>C	ENST00000282397.4	-	20	3033	c.2782T>G	c.(2782-2784)Ttt>Gtt	p.F928V	FLT1_ENST00000540678.1_Missense_Mutation_p.F146V	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	928	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.F928V(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTGAGAAAAAATAAGTCACGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											79	77	78					13																	28901613		2203	4300	6503	27799613	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2782T>G	13.37:g.28901613A>C	ENSP00000282397:p.Phe928Val		27799613	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.513142	0.85389	.	.	ENSG00000102755	ENST00000282397;ENST00000540678	D;D	0.88741	-2.42;-2.42	5.8	5.8	0.92144	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92309	0.7560	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93147	0.6546	10	0.87932	D	0	.	16.1412	0.81522	1.0:0.0:0.0:0.0	.	928	P17948	VGFR1_HUMAN	V	928;146	ENSP00000282397:F928V;ENSP00000443311:F146V	ENSP00000282397:F928V	F	-	1	0	FLT1	27799613	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.339000	0.96797	2.216000	0.71823	0.402000	0.26972	TTT		0.373	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28901613	A	C	28901613	3	2	61	1	0	0	0	0	1	0	0	0	5960	101	4	4	1278	4	FLT1	13	28901613	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	50165	28901613	86268265	8556	16541										
FLT1	2321	broad.mit.edu	37	chr13	28959097	28959097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaccattagcatgacagtCtaaagtggtggaactgctga	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:28959097C>A	ENST00000282397.4	-	14	2292	c.2041G>T	c.(2041-2043)Gac>Tac	p.D681Y	FLT1_ENST00000541932.1_Missense_Mutation_p.D681Y	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	681	Ig-like C2-type 7.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.D681Y(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCATGACAGTCTAAAGTGGTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	13											215	193	200					13																	28959097		2203	4300	6503	27857097	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2041G>T	13.37:g.28959097C>A	ENSP00000282397:p.Asp681Tyr		27857097	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.218592	0.39201	.	.	ENSG00000102755	ENST00000282397;ENST00000541932	T;T	0.68025	-0.3;-0.3	5.72	4.86	0.63082	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.384025	0.29653	N	0.011546	T	0.64114	0.2569	N	0.25647	0.755	0.80722	D	1	P;P	0.52170	0.951;0.946	P;P	0.55455	0.672;0.776	T	0.58352	-0.7651	10	0.11794	T	0.64	.	14.4437	0.67336	0.0:0.8175:0.1825:0.0	.	681;681	P17948-3;P17948	.;VGFR1_HUMAN	Y	681	ENSP00000282397:D681Y;ENSP00000437631:D681Y	ENSP00000282397:D681Y	D	-	1	0	FLT1	27857097	0.979000	0.34478	0.869000	0.34112	0.229000	0.25112	1.484000	0.35508	1.311000	0.45024	0.655000	0.94253	GAC		0.443	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28959097	C	A	28959097	3	1	61	1	0	0	0	0	1	0	0	0	5960	913	32	2	2133	2	FLT1	13	28959097	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57484	28959097	86210781	8557	16542										
SLC46A3	283537	broad.mit.edu	37	chr13	29287375	29287375	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtcaatgatagctattcGaattgttttttgtttgtgtt	8	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29287375G>A	ENST00000266943.6	-	3	871	c.502C>T	c.(502-504)Cga>Tga	p.R168*	SLC46A3_ENST00000380814.4_Nonsense_Mutation_p.R168*	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	168					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R168*(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		ATAGCTATTCGAATTGTTTTT	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											62	60	61					13																	29287375		2203	4300	6503	28185375	SO:0001587	stop_gained	283537				CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.502C>T	13.37:g.29287375G>A	ENSP00000266943:p.Arg168*		28185375	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Nonsense_Mutation	SNP	ENST00000266943.6	37	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	G	39	7.373792	0.98245	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	.	.	.	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1697	17.0043	0.86388	0.0:0.0:0.872:0.128	.	.	.	.	X	168	.	ENSP00000266943:R168X	R	-	1	2	SLC46A3	28185375	1.000000	0.71417	0.997000	0.53966	0.462000	0.32619	5.976000	0.70484	2.941000	0.99782	0.655000	0.94253	CGA		0.373	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		A	29287375	G	A	29287375	4	1	61	1	0	0	0	0	0	1	0	0	14683	1066	37	1	913	1	SLC46A3	13	29287375	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	328278	29287375	85882503	8558	16543										
MTUS2	23281	broad.mit.edu	37	chr13	29598891	29598891	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactcagttgcgggacaacaGaaatgcagcaagaaataata	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29598891G>T	ENST00000431530.3	+	1	144	c.86G>T	c.(85-87)aGa>aTa	p.R29I		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	19						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.R29I(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CGGGACAACAGAAATGCAGCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	72	73					13																	29598891		1918	4134	6052	28496891	SO:0001583	missense	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.86G>T	13.37:g.29598891G>T	ENSP00000392057:p.Arg29Ile		28496891	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	15.51	2.856341	0.51376	.	.	ENSG00000132938	ENST00000431530	T	0.19105	2.17	5.84	4.11	0.48088	.	0.106937	0.37955	N	0.001866	T	0.38558	0.1045	M	0.62723	1.935	0.80722	D	1	D	0.61080	0.989	D	0.63192	0.912	T	0.06807	-1.0806	9	.	.	.	.	11.8423	0.52361	0.1418:0.0:0.8582:0.0	.	19	Q5JR59	MTUS2_HUMAN	I	29	ENSP00000392057:R29I	.	R	+	2	0	MTUS2	28496891	1.000000	0.71417	0.968000	0.41197	0.171000	0.22731	1.376000	0.34306	0.808000	0.34231	0.563000	0.77884	AGA		0.458	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29598891	G	T	29598891	3	4	61	1	0	0	0	0	1	0	0	0	9996	942	33	2	88	2	MTUS2	13	29598891	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	311516	29598891	85570987	8559	16544										
MTUS2	23281	broad.mit.edu	37	chr13	29599124	29599124	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggctctgccagcctgaaaGattttagactttcttcaacc	7	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29599124G>A	ENST00000431530.3	+	1	377	c.319G>A	c.(319-321)Gat>Aat	p.D107N		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	97						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.D107N(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CAGCCTGAAAGATTTTAGACT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	13											38	38	38					13																	29599124		1859	4088	5947	28497124	SO:0001583	missense	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.319G>A	13.37:g.29599124G>A	ENSP00000392057:p.Asp107Asn		28497124	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	14.69	2.610545	0.46527	.	.	ENSG00000132938	ENST00000431530	T	0.15487	2.42	5.37	5.37	0.77165	.	0.664002	0.13608	N	0.375324	T	0.32912	0.0845	L	0.51422	1.61	0.80722	D	1	D	0.56746	0.977	P	0.55923	0.787	T	0.01027	-1.1476	9	.	.	.	.	18.0886	0.89466	0.0:0.0:1.0:0.0	.	97	Q5JR59	MTUS2_HUMAN	N	107	ENSP00000392057:D107N	.	D	+	1	0	MTUS2	28497124	0.996000	0.38824	0.019000	0.16419	0.018000	0.09664	3.934000	0.56553	2.509000	0.84616	0.563000	0.77884	GAT		0.488	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		A	29599124	G	A	29599124	3	1	61	1	0	0	0	0	1	0	0	0	9996	942	33	3	321	3	MTUS2	13	29599124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	233	29599124	85570754	8560	16545										
MTUS2	23281	broad.mit.edu	37	chr13	29600045	29600045	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagggctctgcttccttaGgaggggctgataatcagccc	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29600045G>T	ENST00000431530.3	+	1	1298	c.1240G>T	c.(1240-1242)Gga>Tga	p.G414*		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	404						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.G414*(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						TGCTTCCTTAGGAGGGGCTGA	0.537																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											32	34	33					13																	29600045		1919	4144	6063	28498045	SO:0001587	stop_gained	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1240G>T	13.37:g.29600045G>T	ENSP00000392057:p.Gly414*		28498045	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Nonsense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	37	6.078471	0.97262	.	.	ENSG00000132938	ENST00000431530	.	.	.	5.56	2.85	0.33270	.	1.231650	0.05924	N	0.634004	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4935	0.38974	0.0784:0.4427:0.4789:0.0	.	.	.	.	X	414	.	.	G	+	1	0	MTUS2	28498045	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.211000	0.17474	0.284000	0.22305	0.655000	0.94253	GGA		0.537	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29600045	G	T	29600045	4	4	61	1	0	0	0	0	0	1	0	0	9996	1001	35	2	1242	2	MTUS2	13	29600045	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	921	29600045	85569833	8561	16546										
MTUS2	23281	broad.mit.edu	37	chr13	29600576	29600576	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactgatagtgcacgcttgTtgaacacgtcccccaaagtg	9	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29600576T>C	ENST00000431530.3	+	1	1829	c.1771T>C	c.(1771-1773)Ttg>Ctg	p.L591L		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	581						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.L591L(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						TGCACGCTTGTTGAACACGTC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	13											77	81	80					13																	29600576		1993	4168	6161	28498576	SO:0001819	synonymous_variant	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1771T>C	13.37:g.29600576T>C			28498576	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	37	CCDS45022.1																																																																																				0.557	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		C	29600576	T	C	29600576	2	2	61	1	0	0	0	0	0	0	0	1	9996	1722	60	4		4	MTUS2	13	29600576	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	531	29600576	85569302	8562	16547										
MTUS2	23281	broad.mit.edu	37	chr13	29608168	29608168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccatctgcaaagagcagGattctgattgcaagtcagag	10	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:29608168G>T	ENST00000431530.3	+	2	2440	c.2382G>T	c.(2380-2382)agG>agT	p.R794S		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	784	Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.R794S(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CAAAGAGCAGGATTCTGATTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	13											102	102	102					13																	29608168		2094	4218	6312	28506168	SO:0001583	missense	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2382G>T	13.37:g.29608168G>T	ENSP00000392057:p.Arg794Ser		28506168	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797689	0.70567	.	.	ENSG00000132938	ENST00000431530	T	0.44083	0.93	5.46	3.72	0.42706	.	0.000000	0.64402	D	0.000001	T	0.58424	0.2121	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58222	-0.7674	9	.	.	.	.	8.0174	0.30389	0.2417:0.0:0.7583:0.0	.	784	Q5JR59	MTUS2_HUMAN	S	794	ENSP00000392057:R794S	.	R	+	3	2	MTUS2	28506168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.939000	0.48995	1.288000	0.44600	0.655000	0.94253	AGG		0.517	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29608168	G	T	29608168	3	4	61	1	0	0	0	0	1	0	0	0	9996	1165	41	2	2388	2	MTUS2	13	29608168	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7592	29608168	85561710	8563	16548										
SLC7A1	6541	broad.mit.edu	37	chr13	30107082	30107082	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctgcctatcagctcgtcGaaggtggcgctccaggccct	13	14	2	0	rs144196494		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:30107082G>A	ENST00000380752.5	-	4	794	c.408C>T	c.(406-408)ttC>ttT	p.F136F		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	136					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)	p.F136F(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		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)	TCAGCTCGTCGAAGGTGGCGC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	13						G		0,4406		0,0,2203	71	67	68		408	-2	0.4	13	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC7A1	NM_003045.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		136/630	30107082	1,13005	2203	4300	6503	29005082	SO:0001819	synonymous_variant	6541			AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"Solute carriers"	11057	protein-coding gene	gene with protein product	"ecotropic retroviral receptor", "amino acid transporter, cationic 1"	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.408C>T	13.37:g.30107082G>A			29005082	Q5JR50	Silent	SNP	ENST00000380752.5	37	CCDS9333.1																																																																																				0.562	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		A	30107082	G	A	30107082	2	1	61	1	0	0	0	0	0	0	0	1	14729	1049	37	1		1	SLC7A1	13	30107082	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	498914	30107082	85062796	8564	16549										
UBL3	5412	broad.mit.edu	37	chr13	30351348	30351348	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaagcagaatcgttaggaGaaaacaggaactcttttgtt	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:30351348G>T	ENST00000380680.4	-	2	1225	c.80C>A	c.(79-81)tCt>tAt	p.S27Y		NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	27	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.S27Y(1)		large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		ATCGTTAGGAGAAAACAGGAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	13											100	96	97					13																	30351348		2203	4300	6503	29249348	SO:0001583	missense	5412			AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042			12504	protein-coding gene	gene with protein product		604711		PNSC1		10375635	Standard	NM_007106		Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.80C>A	13.37:g.30351348G>T	ENSP00000370055:p.Ser27Tyr		29249348	B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	Missense_Mutation	SNP	ENST00000380680.4	37	CCDS9334.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.794740	0.90453	.	.	ENSG00000122042	ENST00000380680	.	.	.	5.77	5.77	0.91146	Ubiquitin supergroup (1);	0.000000	0.85682	D	0.000000	T	0.79040	0.4379	M	0.78916	2.43	0.80722	D	1	D	0.64830	0.994	P	0.62560	0.904	T	0.79035	-0.1968	9	0.54805	T	0.06	-21.55	19.335	0.94312	0.0:0.0:1.0:0.0	.	27	O95164	UBL3_HUMAN	Y	27	.	ENSP00000370055:S27Y	S	-	2	0	UBL3	29249348	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.286000	0.95898	2.890000	0.99128	0.650000	0.86243	TCT		0.313	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044342.1	NM_007106		T	30351348	G	T	30351348	3	4	61	1	0	0	0	0	1	0	0	0	16926	942	33	2	289	2	UBL3	13	30351348	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244266	30351348	84818530	8565	16550										
UBL3	5412	broad.mit.edu	37	chr13	30423672	30423672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccgccgggacattactggAcatcttgccgtttgatatac	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:30423672A>G	ENST00000380680.4	-	1	1149	c.4T>C	c.(4-6)Tcc>Ccc	p.S2P		NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	2						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.S2P(1)		large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		ACATTACTGGACATCTTGCCG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											125	114	118					13																	30423672		2203	4300	6503	29321672	SO:0001583	missense	5412			AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042			12504	protein-coding gene	gene with protein product		604711		PNSC1		10375635	Standard	NM_007106		Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.4T>C	13.37:g.30423672A>G	ENSP00000370055:p.Ser2Pro		29321672	B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	Missense_Mutation	SNP	ENST00000380680.4	37	CCDS9334.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.736111	0.49045	.	.	ENSG00000122042	ENST00000380680	.	.	.	4.69	4.69	0.59074	.	0.550372	0.18400	N	0.142394	T	0.46054	0.1373	L	0.50333	1.59	0.32380	N	0.554615	B	0.17268	0.021	B	0.17433	0.018	T	0.53837	-0.8382	9	0.38643	T	0.18	0.0209	10.4608	0.44578	1.0:0.0:0.0:0.0	.	2	O95164	UBL3_HUMAN	P	2	.	ENSP00000370055:S2P	S	-	1	0	UBL3	29321672	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.014000	0.57145	1.970000	0.57323	0.459000	0.35465	TCC		0.393	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044342.1	NM_007106		G	30423672	A	G	30423672	3	3	61	1	0	0	0	0	1	0	0	0	16926	275	10	4	369	4	UBL3	13	30423672	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72324	30423672	84746206	8566	16551										
HMGB1	3146	broad.mit.edu	37	chr13	31036768	31036768	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacatctctcccagtttcttCgcaacatcaccaatggacag	5	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:31036768C>T	ENST00000405805.1	-	4	1318	c.378G>A	c.(376-378)gcG>gcA	p.A126A	HMGB1_ENST00000326004.4_Silent_p.A126A|HMGB1_ENST00000399489.1_Silent_p.A126A|HMGB1_ENST00000399494.1_Silent_p.A126A|HMGB1_ENST00000341423.5_Silent_p.A126A|HMGB1_ENST00000339872.4_Silent_p.A126A|HMGB1_ENST00000468384.1_5'Flank			P09429	HMGB1_HUMAN	high mobility group box 1	126					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)	p.A126A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CCAGTTTCTTCGCAACATCAC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	13											96	88	91					13																	31036768		2202	4280	6482	29934768	SO:0001819	synonymous_variant	3146			D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.378G>A	13.37:g.31036768C>T			29934768	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Silent	SNP	ENST00000405805.1	37	CCDS9335.1																																																																																				0.413	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		T	31036768	C	T	31036768	2	4	61	1	0	0	0	0	0	0	0	1	7246	871	31	1		1	HMGB1	13	31036768	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	613096	31036768	84133110	8567	16552										
USPL1	10208	broad.mit.edu	37	chr13	31216867	31216867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgggactttgaatgttCgcagtgtggacaccaatatc	10	8	1	1	rs528822246	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:31216867C>T	ENST00000255304.4	+	6	1427	c.1085C>T	c.(1084-1086)tCg>tTg	p.S362L		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	362	SUMO-binding.|USP.				Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)	p.S362L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		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)		TTTGAATGTTCGCAGTGTGGA	0.373													C|||	2	0.000399361	0	0	5008	,	,		17987	0		0	False		,,,				2504	0.002				Ovarian(60;318 1180 1554 28110 31601)											1	Substitution - Missense(1)	large_intestine(1)	13											134	134	134					13																	31216867		2202	4300	6502	30114867	SO:0001583	missense	10208			X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1085C>T	13.37:g.31216867C>T	ENSP00000255304:p.Ser362Leu		30114867	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	C	9.008	0.981820	0.18812	.	.	ENSG00000132952	ENST00000255304	T	0.43294	0.95	5.42	4.57	0.56435	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (1);	0.797343	0.11776	N	0.530632	T	0.26991	0.0661	L	0.55481	1.735	0.28322	N	0.922191	P	0.37500	0.597	B	0.26693	0.072	T	0.32824	-0.9892	10	0.02654	T	1	-11.0454	6.7363	0.23411	0.0:0.8096:0.0:0.1904	.	362	Q5W0Q7	USPL1_HUMAN	L	362	ENSP00000255304:S362L	ENSP00000255304:S362L	S	+	2	0	USPL1	30114867	0.987000	0.35691	0.918000	0.36340	0.708000	0.40852	3.077000	0.50089	2.705000	0.92388	0.591000	0.81541	TCG		0.373	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		T	31216867	C	T	31216867	3	4	61	1	0	0	0	0	1	0	0	0	17132	893	31	1	1103	1	USPL1	13	31216867	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180099	31216867	83953011	8568	16553										
C13orf33	84935	broad.mit.edu	37	chr13	31495952	31495952	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatccgaaggagcagtttCtctgaccgaaagttcagtgt	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:31495952C>A	ENST00000380482.4	+	4	1081	c.756C>A	c.(754-756)ttC>ttA	p.F252L	TEX26-AS1_ENST00000588726.1_RNA|TEX26-AS1_ENST00000451495.2_RNA|TEX26-AS1_ENST00000593246.1_RNA|TEX26-AS1_ENST00000585870.1_RNA|TEX26-AS1_ENST00000590344.1_RNA|TEX26-AS1_ENST00000592950.1_RNA|TEX26-AS1_ENST00000588425.1_RNA|TEX26-AS1_ENST00000586973.1_RNA|TEX26-AS1_ENST00000586464.1_RNA|TEX26-AS1_ENST00000590721.1_RNA	NM_032849.3	NP_116238	Q5VYS4	MEDAG_HUMAN	mesenteric estrogen-dependent adipogenesis	252					positive regulation of fat cell differentiation (GO:0045600)	cytoplasm (GO:0005737)		p.F252L(1)									GGAGCAGTTTCTCTGACCGAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											49	51	50					13																	31495952		2203	4300	6503	30393952	SO:0001583	missense	84935			AB055407	CCDS9338.1	13q12.3	2013-10-11	2012-09-26	2012-09-26	ENSG00000102802	ENSG00000102802			25926	protein-coding gene	gene with protein product	"mesenteric estrogen-dependent adipose 4", "activated in W/Wv mouse stomach 3 homolog"		"chromosome 13 open reading frame 33"	C13orf33		22510272	Standard	NM_032849		Approved	FLJ14834, AWMS3, MEDA-4	uc001uth.4	Q5VYS4	OTTHUMG00000016679	ENST00000380482.4:c.756C>A	13.37:g.31495952C>A	ENSP00000369849:p.Phe252Leu		30393952	Q8IXF1|Q96K26|Q96NC8	Missense_Mutation	SNP	ENST00000380482.4	37	CCDS9338.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464506	0.63513	.	.	ENSG00000102802	ENST00000380482	T	0.50813	0.73	5.33	3.6	0.41247	.	0.070853	0.64402	D	0.000013	T	0.49201	0.1543	N	0.24115	0.695	0.31727	N	0.637485	D	0.56035	0.974	D	0.70487	0.969	T	0.54636	-0.8264	10	0.51188	T	0.08	-21.5399	7.4504	0.27235	0.0:0.7333:0.0:0.2667	.	252	Q5VYS4	CM033_HUMAN	L	252	ENSP00000369849:F252L	ENSP00000369849:F252L	F	+	3	2	C13orf33	30393952	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	0.884000	0.28214	0.641000	0.30601	0.462000	0.41574	TTC		0.358	MEDAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044375.1	NM_032849		A	31495952	C	A	31495952	3	1	61	1	0	0	0	0	1	0	0	0	1731	912	32	2	770	2	C13orf33	13	31495952	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279085	31495952	83673926	8569	16554										
RXFP2	122042	broad.mit.edu	37	chr13	32365998	32365998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatgtccgaatatgtatgCccttgacggacggcatttct	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32365998C>T	ENST00000298386.2	+	15	1272	c.1201C>T	c.(1201-1203)Ccc>Tcc	p.P401S	RXFP2_ENST00000380314.1_Missense_Mutation_p.P377S	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	401					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)	p.P401S(1)		cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		AATATGTATGCCCTTGACGGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											184	167	172					13																	32365998		2203	4300	6503	31263998	SO:0001583	missense	122042			AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1201C>T	13.37:g.32365998C>T	ENSP00000298386:p.Pro401Ser		31263998	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819849	0.90873	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.73681	-0.77;-0.72	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.87819	0.6273	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89295	0.3622	10	0.87932	D	0	.	17.1485	0.86772	0.0:1.0:0.0:0.0	.	377;401	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	S	377;401	ENSP00000369670:P377S;ENSP00000298386:P401S	ENSP00000298386:P401S	P	+	1	0	RXFP2	31263998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.906000	0.69900	2.661000	0.90470	0.655000	0.94253	CCC		0.393	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		T	32365998	C	T	32365998	3	4	61	1	0	0	0	0	1	0	0	0	13797	739	26	3	1259	3	RXFP2	13	32365998	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	870046	32365998	82803880	8570	16555										
FRY	10129	broad.mit.edu	37	chr13	32691505	32691505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctccctttctgagtactGcctgccttccattctacgta	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32691505G>A	ENST00000380250.3	+	4	855	c.359G>A	c.(358-360)tGc>tAc	p.C120Y		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	120						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.C120Y(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCTGAGTACTGCCTGCCTTCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											102	96	98					13																	32691505		1913	4146	6059	31589505	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.359G>A	13.37:g.32691505G>A	ENSP00000369600:p.Cys120Tyr		31589505	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759896	0.89932	.	.	ENSG00000073910	ENST00000380250;ENST00000436046;ENST00000267067	T	0.25250	1.81	5.13	5.13	0.70059	.	0.051991	0.85682	D	0.000000	T	0.37625	0.1010	M	0.84082	2.675	0.80722	D	1	P	0.37466	0.596	B	0.35971	0.215	T	0.48670	-0.9015	10	0.87932	D	0	.	18.9435	0.92612	0.0:0.0:1.0:0.0	.	120	Q5TBA9	FRY_HUMAN	Y	120;117;86	ENSP00000369600:C120Y	ENSP00000267067:C86Y	C	+	2	0	FRY	31589505	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.311000	0.96282	2.533000	0.85409	0.655000	0.94253	TGC		0.393	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32691505	G	A	32691505	3	1	61	1	0	0	0	0	1	0	0	0	6082	1319	46	3	373	3	FRY	13	32691505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325507	32691505	82478373	8571	16556										
FRY	10129	broad.mit.edu	37	chr13	32705932	32705932	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaaattctttcgaattaaGatgtatccagtggaggattt	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32705932G>T	ENST00000380250.3	+	8	1336	c.840G>T	c.(838-840)aaG>aaT	p.K280N		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	280						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.K280N(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TTCGAATTAAGATGTATCCAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	13											142	128	132					13																	32705932		1848	4109	5957	31603932	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.840G>T	13.37:g.32705932G>T	ENSP00000369600:p.Lys280Asn		31603932	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820551	0.71028	.	.	ENSG00000073910	ENST00000380250;ENST00000267067	T	0.30981	1.51	5.8	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	M	0.80982	2.52	0.80722	D	1	P	0.51147	0.942	P	0.57244	0.816	T	0.60571	-0.7237	10	0.87932	D	0	.	13.575	0.61868	0.1471:0.0:0.8529:0.0	.	280	Q5TBA9	FRY_HUMAN	N	280;208	ENSP00000369600:K280N	ENSP00000267067:K208N	K	+	3	2	FRY	31603932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.231000	0.51294	1.460000	0.47911	-0.145000	0.13849	AAG		0.423	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32705932	G	T	32705932	3	4	61	1	0	0	0	0	1	0	0	0	6082	933	33	2	870	2	FRY	13	32705932	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14427	32705932	82463946	8572	16557										
FRY	10129	broad.mit.edu	37	chr13	32721488	32721488	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactttgggtttacatgattCgaattaaatgtgaaagcaac	8	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32721488C>T	ENST00000380250.3	+	12	1745	c.1249C>T	c.(1249-1251)Cga>Tga	p.R417*		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	417						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R417*(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TTACATGATTCGAATTAAATG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											95	90	91					13																	32721488		1869	4117	5986	31619488	SO:0001587	stop_gained	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.1249C>T	13.37:g.32721488C>T	ENSP00000369600:p.Arg417*		31619488	Q9Y3N6	Nonsense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	43	10.226233	0.99364	.	.	ENSG00000073910	ENST00000380250;ENST00000267067	.	.	.	5.35	3.29	0.37713	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.0336	0.58856	0.4036:0.5964:0.0:0.0	.	.	.	.	X	417;345	.	ENSP00000267067:R345X	R	+	1	2	FRY	31619488	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.202000	0.32271	1.365000	0.46057	0.561000	0.74099	CGA		0.403	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32721488	C	T	32721488	4	4	61	1	0	0	0	0	0	1	0	0	6082	876	31	1	1295	1	FRY	13	32721488	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15556	32721488	82448390	8573	16558										
FRY	10129	broad.mit.edu	37	chr13	32745149	32745149	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctttattcgtttcacagGctctctattcatatggatga	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32745149G>A	ENST00000380250.3	+	18	2389	c.1893G>A	c.(1891-1893)agG>agA	p.R631R		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	631						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R631R(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGTTTCACAGGCTCTCTATTC	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	13											119	110	113					13																	32745149		1821	4077	5898	31643149	SO:0001630	splice_region_variant	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.1893-1G>A	13.37:g.32745149G>A			31643149	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																				0.323	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	Silent	A	32745149	G	A	32745149	5	1	61	1	0	0	0	0	0	0	1	0	6082	1217	42	3	1963	3	FRY	13	32745149	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23661	32745149	82424729	8574	16559										
FRY	10129	broad.mit.edu	37	chr13	32760504	32760504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgttcactcctctggatCgttacagtgacagaaatcat	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32760504C>T	ENST00000380250.3	+	27	3923	c.3427C>T	c.(3427-3429)Cgt>Tgt	p.R1143C		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1143						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R1143C(2)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCCTCTGGATCGTTACAGTGA	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|NS(1)	13											156	148	151					13																	32760504		1919	4131	6050	31658504	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3427C>T	13.37:g.32760504C>T	ENSP00000369600:p.Arg1143Cys		31658504	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546060	0.86022	.	.	ENSG00000073910	ENST00000380250	T	0.27256	1.68	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.36504	-0.9745	10	0.87932	D	0	.	19.1621	0.93537	0.0:1.0:0.0:0.0	.	1143	Q5TBA9	FRY_HUMAN	C	1143	ENSP00000369600:R1143C	ENSP00000369600:R1143C	R	+	1	0	FRY	31658504	1.000000	0.71417	0.786000	0.31890	0.996000	0.88848	6.021000	0.70832	2.541000	0.85698	0.585000	0.79938	CGT		0.438	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32760504	C	T	32760504	3	4	61	1	0	0	0	0	1	0	0	0	6082	884	31	1	3533	1	FRY	13	32760504	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15355	32760504	82409374	8575	16560										
FRY	10129	broad.mit.edu	37	chr13	32811625	32811625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggcaacaccgcaactgccGaacggagccggcatcaacga	12	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32811625G>A	ENST00000380250.3	+	44	6416	c.5920G>A	c.(5920-5922)Gaa>Aaa	p.E1974K		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1974						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E1974K(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGCAACTGCCGAACGGAGCCG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	13											61	70	67					13																	32811625		2025	4187	6212	31709625	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5920G>A	13.37:g.32811625G>A	ENSP00000369600:p.Glu1974Lys		31709625	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632978	0.47049	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.22539	1.95	6.17	5.31	0.75309	.	0.157630	0.56097	D	0.000033	T	0.15176	0.0366	L	0.34521	1.04	0.80722	D	1	P	0.46656	0.882	B	0.32864	0.154	T	0.02661	-1.1127	10	0.29301	T	0.29	.	17.419	0.87510	0.0:0.1245:0.8754:0.0	.	1974	Q5TBA9	FRY_HUMAN	K	1974;811	ENSP00000369600:E1974K	ENSP00000369600:E1974K	E	+	1	0	FRY	31709625	1.000000	0.71417	0.967000	0.41034	0.862000	0.49288	5.712000	0.68407	1.585000	0.49928	0.655000	0.94253	GAA		0.527	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32811625	G	A	32811625	3	1	61	1	0	0	0	0	1	0	0	0	6082	1059	37	1	6094	1	FRY	13	32811625	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51121	32811625	82358253	8576	16561										
FRY	10129	broad.mit.edu	37	chr13	32813960	32813960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggtcaatgtggtctgtcGataccttcatgaagcatatg	12	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32813960G>A	ENST00000380250.3	+	46	7125	c.6629G>A	c.(6628-6630)cGa>cAa	p.R2210Q		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2210						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R2210Q(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GTGGTCTGTCGATACCTTCAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											96	97	96					13																	32813960		1973	4166	6139	31711960	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.6629G>A	13.37:g.32813960G>A	ENSP00000369600:p.Arg2210Gln		31711960	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	36	5.862075	0.97036	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.23348	1.91	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.51295	0.1666	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.16424	-1.0403	10	0.25751	T	0.34	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	2210	Q5TBA9	FRY_HUMAN	Q	2210;1047	ENSP00000369600:R2210Q	ENSP00000369600:R2210Q	R	+	2	0	FRY	31711960	1.000000	0.71417	0.680000	0.29994	0.991000	0.79684	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	CGA		0.418	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32813960	G	A	32813960	3	1	61	1	0	0	0	0	1	0	0	0	6082	1058	37	1	6811	1	FRY	13	32813960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2335	32813960	82355918	8577	16562										
BRCA2	675	broad.mit.edu	37	chr13	32893291	32893291	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataattctgaacctgcagaaGaatctgaacataaaaacaac	5	8	2	4	rs80358435		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32893291G>T	ENST00000380152.3	+	3	378	c.145G>T	c.(145-147)Gaa>Taa	p.E49*	BRCA2_ENST00000544455.1_Nonsense_Mutation_p.E49*			P51587	BRCA2_HUMAN	breast cancer 2, early onset	49					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.E49*(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ACCTGCAGAAGAATCTGAACA	0.328			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Nonsense(2)	large_intestine(2)	13	GRCh37	CM011914	BRCA2	M	rs80358435						68	74	72					13																	32893291		2203	4300	6503	31791291	SO:0001587	stop_gained	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.145G>T	13.37:g.32893291G>T	ENSP00000369497:p.Glu49*		31791291	O00183|O15008|Q13879|Q5TBJ7	Nonsense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287904	0.80803	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	.	.	.	5.69	5.69	0.88448	.	0.253957	0.34460	N	0.003947	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.7521	0.77994	0.0:0.0:0.863:0.137	.	.	.	.	X	49;49;47	.	ENSP00000369497:E49X	E	+	1	0	BRCA2	31791291	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	3.549000	0.53681	2.840000	0.97914	0.655000	0.94253	GAA		0.328	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32893291	G	T	32893291	4	4	61	1	0	0	0	0	0	1	0	0	1502	943	33	2	151	2	BRCA2	13	32893291	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79331	32893291	82276587	8578	16563										
BRCA2	675	broad.mit.edu	37	chr13	32914129	32914129	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaattaaggaaaacaacgaGaataaatcaaaaatttgcca	6	5	1	1	rs276174860		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32914129G>T	ENST00000380152.3	+	11	5870	c.5637G>T	c.(5635-5637)gaG>gaT	p.E1879D	BRCA2_ENST00000544455.1_Missense_Mutation_p.E1879D			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1879					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.E1879D(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAAACAACGAGAATAAATCAA	0.313			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											43	42	42					13																	32914129		2203	4300	6503	31812129	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5637G>T	13.37:g.32914129G>T	ENSP00000369497:p.Glu1879Asp		31812129	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	9.308	1.054917	0.19907	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.74421	-0.84;-0.84	5.71	1.97	0.26223	.	0.683613	0.14324	N	0.326794	T	0.64416	0.2596	L	0.56769	1.78	0.09310	N	1	B	0.15141	0.012	B	0.13407	0.009	T	0.58194	-0.7679	10	0.62326	D	0.03	.	1.4906	0.02456	0.2015:0.1217:0.426:0.2508	.	1879	P51587	BRCA2_HUMAN	D	1879	ENSP00000369497:E1879D;ENSP00000439902:E1879D	ENSP00000369497:E1879D	E	+	3	2	BRCA2	31812129	0.249000	0.23941	0.000000	0.03702	0.009000	0.06853	1.082000	0.30803	0.058000	0.16222	-0.145000	0.13849	GAG		0.313	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32914129	G	T	32914129	3	4	61	1	0	0	0	0	1	0	0	0	1502	933	33	2	5675	2	BRCA2	13	32914129	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20838	32914129	82255749	8579	16564										
BRCA2	675	broad.mit.edu	37	chr13	32914542	32914542	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttccaaagtattgtttaAaagtaacgaacattcagacc	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32914542A>C	ENST00000380152.3	+	11	6283	c.6050A>C	c.(6049-6051)aAa>aCa	p.K2017T	BRCA2_ENST00000544455.1_Missense_Mutation_p.K2017T			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2017					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.K2017T(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GTATTGTTTAAAAGTAACGAA	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											56	59	58					13																	32914542		2202	4297	6499	31812542	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6050A>C	13.37:g.32914542A>C	ENSP00000369497:p.Lys2017Thr		31812542	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	2.641	-0.284142	0.05642	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00753	5.74;5.74	5.54	1.62	0.23740	.	0.287341	0.30260	N	0.010034	T	0.00608	0.0020	N	0.25485	0.75	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.49978	-0.8881	10	0.51188	T	0.08	.	2.4527	0.04522	0.5265:0.2321:0.1295:0.1119	.	2017	P51587	BRCA2_HUMAN	T	2017	ENSP00000369497:K2017T;ENSP00000439902:K2017T	ENSP00000369497:K2017T	K	+	2	0	BRCA2	31812542	0.018000	0.18449	0.000000	0.03702	0.018000	0.09664	1.955000	0.40372	0.049000	0.15920	-0.291000	0.09656	AAA		0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32914542	A	C	32914542	3	2	61	1	0	0	0	0	1	0	0	0	1502	14	1	4	6088	4	BRCA2	13	32914542	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	413	32914542	82255336	8580	16565										
BRCA2	675	broad.mit.edu	37	chr13	32915144	32915144	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgttctacttactccaaaGattcagaaaactactttgaa	4	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32915144G>T	ENST00000380152.3	+	11	6885	c.6652G>T	c.(6652-6654)Gat>Tat	p.D2218Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.D2218Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2218					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.D2218Y(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTACTCCAAAGATTCAGAAAA	0.338			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13	GRCh37	CI004794	BRCA2	I							63	66	65					13																	32915144		2203	4300	6503	31813144	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6652G>T	13.37:g.32915144G>T	ENSP00000369497:p.Asp2218Tyr		31813144	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.150458	0.57151	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.80738	-1.41;-1.41	5.42	5.42	0.78866	.	0.264614	0.32593	N	0.005885	D	0.85212	0.5645	M	0.68317	2.08	0.25743	N	0.985132	D	0.76494	0.999	P	0.61328	0.887	T	0.78952	-0.2001	10	0.66056	D	0.02	.	8.3602	0.32355	0.1339:0.0:0.8661:0.0	.	2218	P51587	BRCA2_HUMAN	Y	2218	ENSP00000369497:D2218Y;ENSP00000439902:D2218Y	ENSP00000369497:D2218Y	D	+	1	0	BRCA2	31813144	0.912000	0.30974	0.925000	0.36789	0.927000	0.56198	1.149000	0.31626	2.546000	0.85860	0.591000	0.81541	GAT		0.338	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32915144	G	T	32915144	3	4	61	1	0	0	0	0	1	0	0	0	1502	942	33	2	6690	2	BRCA2	13	32915144	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	602	32915144	82254734	8581	16566										
BRCA2	675	broad.mit.edu	37	chr13	32915220	32915220	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgatgaactgacagattCtaaactgccaagtcatgcca	8	9	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32915220C>A	ENST00000380152.3	+	11	6961	c.6728C>A	c.(6727-6729)tCt>tAt	p.S2243Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.S2243Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2243					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.S2243Y(2)|p.S2243C(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CTGACAGATTCTAAACTGCCA	0.363			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	3	Substitution - Missense(3)	large_intestine(2)|lung(1)	13											116	119	118					13																	32915220		2203	4300	6503	31813220	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6728C>A	13.37:g.32915220C>A	ENSP00000369497:p.Ser2243Tyr		31813220	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.891798	0.33442	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.83992	-1.79;-1.79	5.71	1.1	0.20463	.	0.353820	0.26711	N	0.022894	D	0.84737	0.5538	M	0.69823	2.125	0.36311	D	0.85767	D	0.55605	0.972	P	0.53649	0.731	D	0.85252	0.1045	10	0.72032	D	0.01	.	8.6659	0.34121	0.0:0.6384:0.0:0.3616	.	2243	P51587	BRCA2_HUMAN	Y	2243	ENSP00000369497:S2243Y;ENSP00000439902:S2243Y	ENSP00000369497:S2243Y	S	+	2	0	BRCA2	31813220	0.102000	0.21896	0.897000	0.35233	0.256000	0.26092	0.206000	0.17375	0.091000	0.17302	-0.136000	0.14681	TCT		0.363	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32915220	C	A	32915220	3	1	61	1	0	0	0	0	1	0	0	0	1502	913	32	2	6766	2	BRCA2	13	32915220	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76	32915220	82254658	8582	16567										
BRCA2	675	broad.mit.edu	37	chr13	32953980	32953980	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcttgcaacttcaaaatCtaaaagtaaatctgaaagag	5	7	5	2	rs80359736		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:32953980C>A	ENST00000380152.3	+	23	9280	c.9047C>A	c.(9046-9048)tCt>tAt	p.S3016Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.S3016Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	3016					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.S3016Y(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ACTTCAAAATCTAAAAGTAAA	0.323			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											51	51	51					13																	32953980		2203	4294	6497	31851980	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.9047C>A	13.37:g.32953980C>A	ENSP00000369497:p.Ser3016Tyr		31851980	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793373	0.70452	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.73681	-0.77;-0.77	5.66	5.66	0.87406	Nucleic acid-binding, OB-fold-like (1);	0.186310	0.48286	D	0.000182	D	0.86957	0.6058	M	0.77616	2.38	0.39957	D	0.974613	D	0.89917	1.0	D	0.75020	0.985	D	0.87177	0.2225	10	0.54805	T	0.06	.	20.115	0.97926	0.0:1.0:0.0:0.0	.	3016	P51587	BRCA2_HUMAN	Y	3016	ENSP00000369497:S3016Y;ENSP00000439902:S3016Y	ENSP00000369497:S3016Y	S	+	2	0	BRCA2	31851980	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	3.344000	0.52174	2.827000	0.97445	0.655000	0.94253	TCT		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32953980	C	A	32953980	3	1	61	1	0	0	0	0	1	0	0	0	1502	913	32	2	9133	2	BRCA2	13	32953980	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38760	32953980	82215898	8583	16568										
N4BP2L2	10443	broad.mit.edu	37	chr13	33017983	33017983	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggaaactgtctttaggatCtttatttttccatctttttt	5	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33017983C>A	ENST00000504114.1	-	6	737	c.646G>T	c.(646-648)Gat>Tat	p.D216Y	N4BP2L2_ENST00000357505.6_Missense_Mutation_p.D216Y|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000446957.2_Intron|N4BP2L2_ENST00000399396.3_Missense_Mutation_p.D231Y			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.D231Y(1)		kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCTTTAGGATCTTTATTTTTC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	13											71	65	67					13																	33017983		1823	4070	5893	31915983	SO:0001583	missense	10443			U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.646G>T	13.37:g.33017983C>A	ENSP00000427477:p.Asp216Tyr		31915983	A3KME8	Missense_Mutation	SNP	ENST00000504114.1	37		.	.	.	.	.	.	.	.	.	.	C	11.87	1.767748	0.31320	.	.	ENSG00000139617;ENSG00000139617;ENSG00000244754;ENSG00000244754;ENSG00000244754;ENSG00000244754	ENST00000380121;ENST00000503296;ENST00000504114;ENST00000357505;ENST00000399396;ENST00000505213	T	0.47528	0.84	4.6	-2.22	0.06952	.	1.779970	0.02634	N	0.104633	T	0.31136	0.0787	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.23249	0.02;0.02;0.082;0.082	B;B;B;B	0.20384	0.029;0.029;0.029;0.029	T	0.14531	-1.0469	10	0.49607	T	0.09	-0.0027	2.7214	0.05202	0.1308:0.4694:0.1309:0.2688	.	216;231;114;114	B4DPY1;Q92802-3;Q96KV2;Q9Y3H6	.;.;.;.	Y	114;143;216;216;231;660	ENSP00000423362:D660Y	ENSP00000350104:D216Y	D	-	1	0	N4BP2L2;RP11-298P3.4	31915983	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.760000	0.04756	-0.486000	0.06744	0.655000	0.94253	GAT		0.328	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887		A	33017983	C	A	33017983	3	1	61	1	0	0	0	0	1	0	0	0	10142	913	32	2	1579	2	N4BP2L2	13	33017983	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64003	33017983	82151895	8584	16569										
N4BP2L2	10443	broad.mit.edu	37	chr13	33092079	33092079	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaatagaaatggacatttGatattcataacgatccaaca	5	7	1	2	rs11556385		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33092079G>T	ENST00000267068.3	-	6	1776	c.1612C>A	c.(1612-1614)Caa>Aaa	p.Q538K	N4BP2L2_ENST00000357505.6_Missense_Mutation_p.Q94K|N4BP2L2_ENST00000504114.1_Missense_Mutation_p.Q94K|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.Q538K|N4BP2L2_ENST00000399396.3_Missense_Mutation_p.Q109K	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	538					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.Q538K(1)		kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ATGGACATTTGATATTCATAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											144	134	137					13																	33092079		2203	4300	6503	31990079	SO:0001583	missense	10443			U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.1612C>A	13.37:g.33092079G>T	ENSP00000267068:p.Gln538Lys		31990079	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437469	0.43224	.	.	ENSG00000244754	ENST00000504114;ENST00000357505;ENST00000399396;ENST00000446957;ENST00000505213;ENST00000267068	T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32	5.17	-0.522	0.11928	.	0.805990	0.10334	N	0.687157	T	0.25158	0.0611	N	0.22421	0.69	0.22989	N	0.99847	B;P;B;B	0.35872	0.244;0.525;0.022;0.003	B;B;B;B	0.36092	0.217;0.164;0.038;0.004	T	0.19224	-1.0312	10	0.51188	T	0.08	-0.3672	11.4628	0.50221	0.0:0.4635:0.3151:0.2213	.	94;109;538;538	B4DPY1;Q92802-3;Q92802;Q92802-2	.;.;N42L2_HUMAN;.	K	94;94;109;538;538;538	ENSP00000427477:Q94K;ENSP00000350104:Q94K;ENSP00000382328:Q109K;ENSP00000394239:Q538K;ENSP00000423362:Q538K;ENSP00000267068:Q538K	ENSP00000267068:Q538K	Q	-	1	0	N4BP2L2	31990079	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	2.892000	0.48625	-0.038000	0.13624	0.563000	0.77884	CAA		0.408	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		T	33092079	G	T	33092079	3	4	61	1	0	0	0	0	1	0	0	0	10142	1299	45	2	2004	2	N4BP2L2	13	33092079	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74096	33092079	82077799	8585	16570										
PDS5B	23047	broad.mit.edu	37	chr13	33316753	33316753	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctattaaaatgatggttCgatggctacttggaatgaaa	11	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33316753C>T	ENST00000315596.10	+	23	2686	c.2500C>T	c.(2500-2502)Cga>Tga	p.R834*		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	834					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.R834*(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AATGATGGTTCGATGGCTACT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											115	104	107					13																	33316753		1829	4087	5916	32214753	SO:0001587	stop_gained	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2500C>T	13.37:g.33316753C>T	ENSP00000313851:p.Arg834*		32214753	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Nonsense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	C	40	8.066114	0.98638	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.93	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0597	15.133	0.72539	0.0:0.9324:0.0:0.0676	.	.	.	.	X	834	.	ENSP00000313851:R834X	R	+	1	2	PDS5B	32214753	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.703000	0.54808	1.518000	0.48934	0.591000	0.81541	CGA		0.308	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		T	33316753	C	T	33316753	4	4	61	1	0	0	0	0	0	1	0	0	11723	876	31	1	2586	1	PDS5B	13	33316753	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	224674	33316753	81853125	8586	16571										
PDS5B	23047	broad.mit.edu	37	chr13	33344644	33344644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagacaaagtggaaataCggaacagaagtccaaaagca	10	6	0	3	rs201933867		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33344644C>T	ENST00000315596.10	+	32	4196	c.4010C>T	c.(4009-4011)aCg>aTg	p.T1337M		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1337					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.T1337M(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AGTGGAAATACGGAACAGAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	MET/THR	6,3950		0,6,1972	41	41	41		4010	-0.7	0	13		41	0,8342		0,0,4171	yes	missense	PDS5B	NM_015032.3	81	0,6,6143	TT,TC,CC		0.0,0.1517,0.0488	benign	1337/1448	33344644	6,12292	1978	4171	6149	32242644	SO:0001583	missense	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.4010C>T	13.37:g.33344644C>T	ENSP00000313851:p.Thr1337Met		32242644	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	C	2.670	-0.277819	0.05679	0.001517	0.0	ENSG00000083642	ENST00000315596;ENST00000447833	.	.	.	5.98	-0.729	0.11158	.	1.042960	0.07435	N	0.896396	T	0.17874	0.0429	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24368	-1.0162	9	0.44086	T	0.13	-3.2909	5.8458	0.18665	0.0:0.2575:0.1535:0.5889	.	1337	Q9NTI5	PDS5B_HUMAN	M	1337;289	.	ENSP00000313851:T1337M	T	+	2	0	PDS5B	32242644	0.009000	0.17119	0.000000	0.03702	0.161000	0.22273	1.963000	0.40452	-0.075000	0.12798	-0.224000	0.12420	ACG		0.413	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		T	33344644	C	T	33344644	3	4	61	1	0	0	0	0	1	0	0	0	11723	536	19	1	4132	1	PDS5B	13	33344644	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27891	33344644	81825234	8587	16572										
KL	9365	broad.mit.edu	37	chr13	33635145	33635145	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggcagcctatggccccGaaccaaggactgccgcgcct	12	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33635145G>A	ENST00000380099.3	+	4	1937	c.1929G>A	c.(1927-1929)ccG>ccA	p.P643P	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	643	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.P643P(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CTATGGCCCCGAACCAAGGAC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	13											48	50	49					13																	33635145		2203	4300	6503	32533145	SO:0001819	synonymous_variant	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1929G>A	13.37:g.33635145G>A			32533145	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																				0.627	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			A	33635145	G	A	33635145	2	1	61	1	0	0	0	0	0	0	0	1	8352	1045	37	1		1	KL	13	33635145	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	290501	33635145	81534733	8588	16573										
KL	9365	broad.mit.edu	37	chr13	33635558	33635558	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggactggctgaaccaaaGaaacaattttcttcttcctt	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33635558G>T	ENST00000380099.3	+	4	2350	c.2342G>T	c.(2341-2343)aGa>aTa	p.R781I	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	781	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.R781I(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CTGAACCAAAGAAACAATTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	13											63	65	64					13																	33635558		2203	4300	6503	32533558	SO:0001583	missense	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2342G>T	13.37:g.33635558G>T	ENSP00000369442:p.Arg781Ile		32533558	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.788023	0.31593	.	.	ENSG00000133116	ENST00000380099	T	0.34667	1.35	5.91	3.2	0.36748	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.364000	0.32068	N	0.006637	T	0.35998	0.0951	M	0.70787	2.145	0.21147	N	0.999774	B	0.18166	0.026	B	0.27715	0.082	T	0.40961	-0.9535	10	0.87932	D	0	-14.6806	5.7527	0.18156	0.2789:0.0:0.5912:0.1299	.	781	Q9UEF7	KLOT_HUMAN	I	781	ENSP00000369442:R781I	ENSP00000369442:R781I	R	+	2	0	KL	32533558	0.680000	0.27605	0.008000	0.14137	0.927000	0.56198	1.458000	0.35223	0.819000	0.34492	0.655000	0.94253	AGA		0.428	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			T	33635558	G	T	33635558	3	4	61	1	0	0	0	0	1	0	0	0	8352	942	33	2	2356	2	KL	13	33635558	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	413	33635558	81534320	8589	16574										
KL	9365	broad.mit.edu	37	chr13	33638124	33638124	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaaacattacaggaaaaTtattgacagcaatggtttcc	7	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33638124T>G	ENST00000380099.3	+	5	2848	c.2840T>G	c.(2839-2841)aTt>aGt	p.I947S	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	947	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.I947S(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TACAGGAAAATTATTGACAGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	13											124	124	124					13																	33638124		2203	4300	6503	32536124	SO:0001583	missense	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2840T>G	13.37:g.33638124T>G	ENSP00000369442:p.Ile947Ser		32536124	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.122698	0.77436	.	.	ENSG00000133116	ENST00000380099	T	0.36157	1.27	5.52	5.52	0.82312	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.111045	0.64402	D	0.000011	T	0.66509	0.2796	M	0.88842	2.985	0.58432	D	0.999999	D	0.76494	0.999	D	0.76575	0.988	T	0.74219	-0.3736	10	0.87932	D	0	-10.3003	15.6637	0.77209	0.0:0.0:0.0:1.0	.	947	Q9UEF7	KLOT_HUMAN	S	947	ENSP00000369442:I947S	ENSP00000369442:I947S	I	+	2	0	KL	32536124	1.000000	0.71417	0.817000	0.32601	0.950000	0.60333	7.348000	0.79366	2.095000	0.63458	0.533000	0.62120	ATT		0.458	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			G	33638124	T	G	33638124	3	3	61	1	0	0	0	0	1	0	0	0	8352	1493	52	4	2858	4	KL	13	33638124	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2566	33638124	81531754	8590	16575										
KL	9365	broad.mit.edu	37	chr13	33638278	33638278	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctattatttctctctcCcttatattttactactcgaa	2	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:33638278C>A	ENST00000380099.3	+	5	3002	c.2994C>A	c.(2992-2994)tcC>tcA	p.S998S	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	998					acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.S998S(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TTTCTCTCTCCCTTATATTTT	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	13											45	47	46					13																	33638278		2203	4299	6502	32536278	SO:0001819	synonymous_variant	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2994C>A	13.37:g.33638278C>A			32536278	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																				0.328	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			A	33638278	C	A	33638278	2	1	61	1	0	0	0	0	0	0	0	1	8352	610	22	2		2	KL	13	33638278	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154	33638278	81531600	8591	16576										
NBEA	26960	broad.mit.edu	37	chr13	35734058	35734058	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgagtcttctagtagcaaAattgtaccaaatattgatgc	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:35734058A>C	ENST00000400445.3	+	22	4284	c.3750A>C	c.(3748-3750)aaA>aaC	p.K1250N	NBEA_ENST00000310336.4_Missense_Mutation_p.K1250N|NBEA_ENST00000540320.1_Missense_Mutation_p.K1250N|NBEA_ENST00000379939.2_Missense_Mutation_p.K1250N	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1250					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.K1250N(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CTAGTAGCAAAATTGTACCAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											41	44	43					13																	35734058		1849	4086	5935	34632058	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.3750A>C	13.37:g.35734058A>C	ENSP00000383295:p.Lys1250Asn		34632058	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.050361	0.36181	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.91	4.74	0.60224	.	0.105676	0.64402	D	0.000007	T	0.40067	0.1102	L	0.29908	0.895	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.15037	-1.0451	10	0.34782	T	0.22	.	11.7143	0.51643	0.9314:0.0:0.0686:0.0	.	1250	Q5T321	.	N	1250	ENSP00000440951:K1250N;ENSP00000383295:K1250N;ENSP00000369271:K1250N;ENSP00000308534:K1250N	ENSP00000308534:K1250N	K	+	3	2	NBEA	34632058	0.992000	0.36948	0.926000	0.36857	0.967000	0.64934	2.556000	0.45862	1.072000	0.40860	0.528000	0.53228	AAA		0.383	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	35734058	A	C	35734058	3	2	61	1	0	0	0	0	1	0	0	0	10217	11	1	4	3836	4	NBEA	13	35734058	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2095780	35734058	79435820	8592	16577										
NBEA	26960	broad.mit.edu	37	chr13	35758155	35758155	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatccaagtttgaaccatgGattccttgccaagttaattc	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:35758155G>T	ENST00000400445.3	+	30	5408	c.4874G>T	c.(4873-4875)gGa>gTa	p.G1625V	NBEA_ENST00000310336.4_Missense_Mutation_p.G1625V|NBEA_ENST00000540320.1_Missense_Mutation_p.G1625V|NBEA_ENST00000379939.2_Missense_Mutation_p.G1622V	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1625					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.G1625V(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTGAACCATGGATTCCTTGCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											123	111	115					13																	35758155		1893	4124	6017	34656155	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4874G>T	13.37:g.35758155G>T	ENSP00000383295:p.Gly1625Val		34656155	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915398	0.52546	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.49432	0.78;0.79;0.79;0.78	5.82	5.82	0.92795	.	0.165336	0.43747	D	0.000532	T	0.49406	0.1555	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.50783	-0.8787	10	0.23891	T	0.37	.	18.2756	0.90081	0.0:0.0:1.0:0.0	.	1622	Q5T321	.	V	1625;1625;1622;1625	ENSP00000440951:G1625V;ENSP00000383295:G1625V;ENSP00000369271:G1622V;ENSP00000308534:G1625V	ENSP00000308534:G1625V	G	+	2	0	NBEA	34656155	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.069000	0.71209	2.753000	0.94483	0.467000	0.42956	GGA		0.418	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35758155	G	T	35758155	3	4	61	1	0	0	0	0	1	0	0	0	10217	1174	41	2	4992	2	NBEA	13	35758155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24097	35758155	79411723	8593	16578										
NBEA	26960	broad.mit.edu	37	chr13	35770201	35770201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttatccactttgtcatccGaagtgaagaaatcacaagag	7	9	3	3	rs561239166		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:35770201G>A	ENST00000400445.3	+	31	5662	c.5128G>A	c.(5128-5130)Gaa>Aaa	p.E1710K	NBEA_ENST00000310336.4_Missense_Mutation_p.E1710K|NBEA_ENST00000540320.1_Missense_Mutation_p.E1710K|NBEA_ENST00000379939.2_Missense_Mutation_p.E1707K	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1710					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.E1710K(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTTGTCATCCGAAGTGAAGAA	0.428													G|||	1	0.000199681	0	0	5008	,	,		16523	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	13											86	84	85					13																	35770201		1885	4126	6011	34668201	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5128G>A	13.37:g.35770201G>A	ENSP00000383295:p.Glu1710Lys		34668201	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547129	0.65311	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	L	0.48642	1.525	0.80722	D	1	B;D	0.55385	0.181;0.971	B;B	0.44163	0.009;0.443	T	0.51252	-0.8729	10	0.23891	T	0.37	.	20.0979	0.97857	0.0:0.0:1.0:0.0	.	1710;1707	Q8NFP9;Q5T321	NBEA_HUMAN;.	K	1710;1710;1707;1710;337	ENSP00000440951:E1710K;ENSP00000383295:E1710K;ENSP00000369271:E1707K;ENSP00000308534:E1710K	ENSP00000308534:E1710K	E	+	1	0	NBEA	34668201	1.000000	0.71417	0.966000	0.40874	0.949000	0.60115	7.362000	0.79507	2.767000	0.95098	0.585000	0.79938	GAA		0.428	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35770201	G	A	35770201	3	1	61	1	0	0	0	0	1	0	0	0	10217	1059	37	1	5250	1	NBEA	13	35770201	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12046	35770201	79399677	8594	16579										
NBEA	26960	broad.mit.edu	37	chr13	36006473	36006473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgaaggagacgatttgttCgcaatgcatttggctccact	11	9	0	1	rs200761216		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:36006473C>T	ENST00000400445.3	+	39	6781	c.6247C>T	c.(6247-6249)Cgc>Tgc	p.R2083C	NBEA_ENST00000310336.4_Missense_Mutation_p.R2083C|NBEA_ENST00000540320.1_Missense_Mutation_p.R2083C|NBEA_ENST00000379939.2_Missense_Mutation_p.R2080C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2083					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R2083C(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ACGATTTGTTCGCAATGCATT	0.408													C|||	1	0.000199681	0	0.0014	5008	,	,		15220	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	13											121	108	112					13																	36006473		1904	4110	6014	34904473	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6247C>T	13.37:g.36006473C>T	ENSP00000383295:p.Arg2083Cys		34904473	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	24.6	4.549374	0.86127	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.72	5.72	0.89469	Domain of unknown function DUF1088 (1);	0.000000	0.85682	D	0.000000	T	0.70962	0.3284	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.973	T	0.73043	-0.4107	10	0.87932	D	0	.	19.879	0.96888	0.0:1.0:0.0:0.0	.	2083;2080	Q8NFP9;Q5T321	NBEA_HUMAN;.	C	2083;2083;2080;2083;710	ENSP00000440951:R2083C;ENSP00000383295:R2083C;ENSP00000369271:R2080C;ENSP00000308534:R2083C	ENSP00000308534:R2083C	R	+	1	0	NBEA	34904473	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.921000	0.48852	2.695000	0.91970	0.655000	0.94253	CGC		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	36006473	C	T	36006473	3	4	61	1	0	0	0	0	1	0	0	0	10217	884	31	1	6401	1	NBEA	13	36006473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	236272	36006473	79163405	8595	16580										
MAB21L1	4081	broad.mit.edu	37	chr13	36050171	36050171	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacgtcggaaactactttGcagacttcccggatagtttt	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:36050171G>T	ENST00000379919.4	-	1	661	c.105C>A	c.(103-105)tgC>tgA	p.C35*	NBEA_ENST00000310336.4_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000537702.1_5'Flank	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	35					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)		p.C35*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		AAACTACTTTGCAGACTTCCC	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											104	106	105					13																	36050171		2203	4300	6503	34948171	SO:0001587	stop_gained	4081			BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.105C>A	13.37:g.36050171G>T	ENSP00000369251:p.Cys35*		34948171	Q6I9T5	Nonsense_Mutation	SNP	ENST00000379919.4	37	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	G	41	8.542897	0.98857	.	.	ENSG00000180660	ENST00000379919	.	.	.	5.76	4.92	0.64577	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	14.745	0.69483	0.0693:0.0:0.9307:0.0	.	.	.	.	X	35	.	ENSP00000369251:C35X	C	-	3	2	MAB21L1	34948171	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.796000	0.75145	1.459000	0.47892	0.655000	0.94253	TGC		0.517	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		T	36050171	G	T	36050171	4	4	61	1	0	0	0	0	0	1	0	0	9171	1311	46	2	978	2	MAB21L1	13	36050171	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43698	36050171	79119707	8596	16581										
DCLK1	9201	broad.mit.edu	37	chr13	36367513	36367513	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgcttactgctatgacaGaaactccagctgctgtgcta	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:36367513G>T	ENST00000360631.3	-	16	2259	c.2048C>A	c.(2047-2049)tCt>tAt	p.S683Y	DCLK1_ENST00000255448.4_Missense_Mutation_p.S683Y|DCLK1_ENST00000379893.1_Missense_Mutation_p.S376Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	683					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.S683Y(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TGCTATGACAGAAACTCCAGC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	13											201	195	197					13																	36367513		2203	4300	6503	35265513	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.2048C>A	13.37:g.36367513G>T	ENSP00000353846:p.Ser683Tyr		35265513	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	19.53	3.844432	0.71488	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893	T;T;T	0.69175	-0.38;-0.34;-0.36	5.49	5.49	0.81192	Protein kinase-like domain (1);	0.119626	0.64402	D	0.000016	T	0.76615	0.4012	L	0.57536	1.79	0.80722	D	1	D;P;D;P	0.55385	0.966;0.885;0.971;0.813	P;P;P;P	0.61800	0.876;0.691;0.894;0.674	T	0.78383	-0.2225	10	0.72032	D	0.01	.	14.2495	0.66011	0.0:0.0:0.8511:0.1489	.	376;683;683;376	O15075-4;O15075;O15075-2;O15075-3	.;DCLK1_HUMAN;.;.	Y	375;683;683;376	ENSP00000255448:S683Y;ENSP00000353846:S683Y;ENSP00000369223:S376Y	ENSP00000255448:S683Y	S	-	2	0	DCLK1	35265513	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.392000	0.79840	2.575000	0.86900	0.650000	0.86243	TCT		0.443	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		T	36367513	G	T	36367513	3	4	61	1	0	0	0	0	1	0	0	0	4297	942	33	2	153	2	DCLK1	13	36367513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	317342	36367513	78802365	8597	16582										
DCLK1	9201	broad.mit.edu	37	chr13	36396965	36396965	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatcccactggcgtctctCtcggtgtatttgttagtgga	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:36396965C>A	ENST00000360631.3	-	11	1666	c.1455G>T	c.(1453-1455)gaG>gaT	p.E485D	DCLK1_ENST00000255448.4_Missense_Mutation_p.E485D|DCLK1_ENST00000379893.1_Missense_Mutation_p.E178D			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	485	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.E485D(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TGGCGTCTCTCTCGGTGTATT	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	13											210	181	191					13																	36396965		2203	4300	6503	35294965	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1455G>T	13.37:g.36396965C>A	ENSP00000353846:p.Glu485Asp		35294965	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	C	16.44	3.125156	0.56721	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893	T;T;T	0.50001	0.76;0.76;0.76	5.84	3.21	0.36854	.	0.000000	0.85682	D	0.000000	T	0.69169	0.3081	M	0.86097	2.795	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.71303	-0.4633	10	0.87932	D	0	.	11.1118	0.48237	0.0:0.8013:0.0:0.1987	.	178;485;178	O15075-4;O15075-2;O15075-3	.;.;.	D	177;485;485;178	ENSP00000255448:E485D;ENSP00000353846:E485D;ENSP00000369223:E178D	ENSP00000255448:E485D	E	-	3	2	DCLK1	35294965	1.000000	0.71417	0.988000	0.46212	0.184000	0.23303	3.318000	0.51975	0.407000	0.25591	-0.140000	0.14226	GAG		0.522	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36396965	C	A	36396965	3	1	61	1	0	0	0	0	1	0	0	0	4297	912	32	2	766	2	DCLK1	13	36396965	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29452	36396965	78772913	8598	16583										
SPG20	23111	broad.mit.edu	37	chr13	36878765	36878765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttctcctgcattatatcCgtatctttaaaagaaagatt	5	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:36878765C>T	ENST00000451493.1	-	9	1955	c.1738G>A	c.(1738-1740)Gga>Aga	p.G580R	SPG20_ENST00000438666.2_Missense_Mutation_p.G580R|SPG20_ENST00000355182.4_Missense_Mutation_p.G580R|SPG20_ENST00000494062.2_Missense_Mutation_p.G580R	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	580					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)	p.G580R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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)		GCATTATATCCGTATCTTTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											76	66	70					13																	36878765		2203	4300	6503	35776765	SO:0001583	missense	23111			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1738G>A	13.37:g.36878765C>T	ENSP00000414147:p.Gly580Arg		35776765	O60349|Q86Y67|Q9H1T2|Q9H1T3	Missense_Mutation	SNP	ENST00000451493.1	37	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559805	0.45590	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	D;D;D	0.98585	-5.01;-5.01;-5.01	4.86	4.02	0.46733	Senescence/spartin-associated (1);	0.113535	0.64402	D	0.000012	D	0.98585	0.9527	M	0.70842	2.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99425	1.0934	10	0.87932	D	0	-9.1554	13.2441	0.60014	0.0:0.9225:0.0:0.0775	.	580;580	A8K6Q9;Q8N0X7	.;SPG20_HUMAN	R	580	ENSP00000406061:G580R;ENSP00000347314:G580R;ENSP00000414147:G580R	ENSP00000347314:G580R	G	-	1	0	SPG20	35776765	1.000000	0.71417	0.377000	0.26055	0.013000	0.08279	7.202000	0.77856	1.188000	0.43014	0.591000	0.81541	GGA		0.338	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			T	36878765	C	T	36878765	3	4	61	1	0	0	0	0	1	0	0	0	15081	661	23	1	266	1	SPG20	13	36878765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	481800	36878765	78291113	8599	16584										
CCNA1	8900	broad.mit.edu	37	chr13	37006787	37006787	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggctttcccgcaatcatgtAccctggatcttttattgggg	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37006787A>G	ENST00000255465.4	+	1	293	c.29A>G	c.(28-30)tAc>tGc	p.Y10C	CCNA1_ENST00000418263.1_Missense_Mutation_p.Y10C|CCNA1_ENST00000463403.1_Intron|CCNA1_ENST00000440264.1_Intron|CCNA1_ENST00000449823.1_Intron			P78396	CCNA1_HUMAN	cyclin A1	10					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.Y10C(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		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;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GCAATCATGTACCCTGGATCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	13											49	47	47					13																	37006787		2203	4300	6503	35904787	SO:0001583	missense	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.29A>G	13.37:g.37006787A>G	ENSP00000255465:p.Tyr10Cys		35904787	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	37	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.272739	0.23221	.	.	ENSG00000133101	ENST00000418263;ENST00000255465	T;T	0.15139	2.45;2.45	2.9	0.242	0.15498	.	.	.	.	.	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.31724	-0.9933	9	0.87932	D	0	.	4.8886	0.13715	0.706:0.0:0.294:0.0	.	10;10	P78396-2;P78396	.;CCNA1_HUMAN	C	10	ENSP00000396479:Y10C;ENSP00000255465:Y10C	ENSP00000255465:Y10C	Y	+	2	0	CCNA1	35904787	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.080000	0.11339	-0.031000	0.13781	-0.441000	0.05720	TAC		0.592	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		G	37006787	A	G	37006787	3	3	61	1	0	0	0	0	1	0	0	0	2915	391	14	4	31	4	CCNA1	13	37006787	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	128022	37006787	78163091	8600	16585										
CCNA1	8900	broad.mit.edu	37	chr13	37007242	37007242	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgctggctacagtggccCgaggtcccgatgcttgtcag	14	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37007242C>T	ENST00000255465.4	+	2	445	c.181C>T	c.(181-183)Cga>Tga	p.R61*	CCNA1_ENST00000418263.1_Nonsense_Mutation_p.R60*|CCNA1_ENST00000463403.1_3'UTR|CCNA1_ENST00000440264.1_Nonsense_Mutation_p.R17*|CCNA1_ENST00000449823.1_Nonsense_Mutation_p.R17*			P78396	CCNA1_HUMAN	cyclin A1	61					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.R61*(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		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;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TACAGTGGCCCGAGGTCCCGA	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											97	95	96					13																	37007242		2203	4300	6503	35905242	SO:0001587	stop_gained	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.181C>T	13.37:g.37007242C>T	ENSP00000255465:p.Arg61*		35905242	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Nonsense_Mutation	SNP	ENST00000255465.4	37	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	C	37	6.340452	0.97489	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	.	.	.	4.63	0.705	0.18127	.	0.950360	0.08634	N	0.916536	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.6457	0.39865	0.137:0.3797:0.4833:0.0	.	.	.	.	X	17;17;60;61	.	ENSP00000255465:R61X	R	+	1	2	CCNA1	35905242	0.000000	0.05858	0.001000	0.08648	0.159000	0.22180	-0.263000	0.08670	-0.145000	0.11294	-0.280000	0.10049	CGA		0.587	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		T	37007242	C	T	37007242	4	4	61	1	0	0	0	0	0	1	0	0	2915	644	23	1	187	1	CCNA1	13	37007242	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455	37007242	78162636	8601	16586										
C13orf36	400120	broad.mit.edu	37	chr13	37269376	37269376	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcctcagccttttagcgtTtctgcttctgcttttaatca	5	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37269376T>G	ENST00000315190.3	+	2	607	c.161T>G	c.(160-162)tTt>tGt	p.F54C		NM_203451.2	NP_982276.2	A2A2V5	SRTM1_HUMAN	serine-rich and transmembrane domain containing 1	54						integral component of membrane (GO:0016021)		p.F54C(1)									CTTTTAGCGTTTCTGCTTCTG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	13											244	213	223					13																	37269376		2203	4300	6503	36167376	SO:0001583	missense	400120				CCDS9358.1	13q13.3	2011-08-10	2011-08-10	2011-08-09	ENSG00000180440	ENSG00000180440			33792	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 36"	C13orf36			Standard	NM_203451		Approved		uc001uvt.4	A2A2V5	OTTHUMG00000016735	ENST00000315190.3:c.161T>G	13.37:g.37269376T>G	ENSP00000325776:p.Phe54Cys		36167376	Q8N469	Missense_Mutation	SNP	ENST00000315190.3	37	CCDS9358.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046932	0.55110	.	.	ENSG00000180440	ENST00000315190	.	.	.	5.19	5.19	0.71726	.	0.051852	0.85682	D	0.000000	T	0.52517	0.1739	N	0.14661	0.345	0.51012	D	0.999909	D	0.65815	0.995	P	0.59889	0.865	T	0.60767	-0.7198	9	0.87932	D	0	-30.9059	14.2351	0.65922	0.0:0.0:0.0:1.0	.	54	A2A2V5	SRTM1_HUMAN	C	54	.	ENSP00000325776:F54C	F	+	2	0	SERTM1	36167376	1.000000	0.71417	0.843000	0.33291	0.964000	0.63967	7.293000	0.78740	1.946000	0.56461	0.460000	0.39030	TTT		0.493	SERTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044518.2	NM_203451		G	37269376	T	G	37269376	3	3	61	1	0	0	0	0	1	0	0	0	1734	1841	64	4	163	4	C13orf36	13	37269376	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	262134	37269376	77900502	8602	16587										
C13orf36	400120	broad.mit.edu	37	chr13	37269535	37269535	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactttttcaaacctttcatCctgaggaaaatggaagagtc	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37269535C>A	ENST00000315190.3	+	2	766	c.320C>A	c.(319-321)tCc>tAc	p.S107Y		NM_203451.2	NP_982276.2	A2A2V5	SRTM1_HUMAN	serine-rich and transmembrane domain containing 1	107						integral component of membrane (GO:0016021)		p.S107Y(1)									AACCTTTCATCCTGAGGAAAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	13											49	50	49					13																	37269535		2203	4300	6503	36167535	SO:0001583	missense	400120				CCDS9358.1	13q13.3	2011-08-10	2011-08-10	2011-08-09	ENSG00000180440	ENSG00000180440			33792	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 36"	C13orf36			Standard	NM_203451		Approved		uc001uvt.4	A2A2V5	OTTHUMG00000016735	ENST00000315190.3:c.320C>A	13.37:g.37269535C>A	ENSP00000325776:p.Ser107Tyr		36167535	Q8N469	Missense_Mutation	SNP	ENST00000315190.3	37	CCDS9358.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938761	0.52972	.	.	ENSG00000180440	ENST00000315190	.	.	.	5.28	5.28	0.74379	.	0.233501	0.37348	N	0.002136	T	0.36826	0.0981	N	0.14661	0.345	0.40245	D	0.978002	P	0.43352	0.804	B	0.35413	0.202	T	0.48896	-0.8994	9	0.87932	D	0	.	17.9066	0.88920	0.0:1.0:0.0:0.0	.	107	A2A2V5	SRTM1_HUMAN	Y	107	.	ENSP00000325776:S107Y	S	+	2	0	SERTM1	36167535	0.956000	0.32656	0.624000	0.29186	0.727000	0.41649	3.939000	0.56591	2.445000	0.82738	0.557000	0.71058	TCC		0.468	SERTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044518.2	NM_203451		A	37269535	C	A	37269535	3	1	61	1	0	0	0	0	1	0	0	0	1734	855	30	2	322	2	C13orf36	13	37269535	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159	37269535	77900343	8603	16588										
SMAD9	4093	broad.mit.edu	37	chr13	37446795	37446795	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccatagttcttactgacCtgagtgttgatagggactct	10	8	2	4	rs141672146		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37446795C>A	ENST00000399275.2	-	2	809	c.670G>T	c.(670-672)Gtt>Ttt	p.V224F	SMAD9_ENST00000350148.5_Splice_Site_p.D224Y|SMAD9_ENST00000379826.4_Splice_Site_p.V224F			O15198	SMAD9_HUMAN	SMAD family member 9	224					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)	p.D224Y(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		TCTTACTGACCTGAGTGTTGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	13											92	82	85					13																	37446795		2203	4300	6503	36344795	SO:0001630	splice_region_variant	4093				CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.670+1G>T	13.37:g.37446795C>A			36344795	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.35|18.35	3.605392|3.605392	0.66445|0.66445	.|.	.|.	ENSG00000120693|ENSG00000120693	ENST00000350148|ENST00000399275;ENST00000379826	D|D;D	0.97256|0.94092	-4.31|-3.35;-3.35	5.23|5.23	5.23|5.23	0.72850|0.72850	.|SMAD/FHA domain (1);	.|0.312565	.|0.29853	.|U	.|0.011032	D|D	0.93327|0.93327	0.7873|0.7873	M|M	0.81497|0.81497	2.545|2.545	0.54753|0.54753	D|D	0.999984|0.999984	B|B	0.06786|0.29886	0.001|0.26	B|B	0.11329|0.29942	0.006|0.109	D|D	0.91712|0.91712	0.5382|0.5382	8|9	.|.	.|.	.|.	.|.	18.1363|18.1363	0.89620|0.89620	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	224|224	O15198-2|O15198	.|SMAD9_HUMAN	Y|F	224|224	ENSP00000239885:D224Y|ENSP00000382216:V224F;ENSP00000369154:V224F	.|.	D|V	-|-	1|1	0|0	SMAD9|SMAD9	36344795|36344795	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.906000|0.906000	0.53458|0.53458	7.508000|7.508000	0.81686|0.81686	2.589000|2.589000	0.87451|0.87451	0.557000|0.557000	0.71058|0.71058	GAC|GTT		0.507	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905	Missense_Mutation	A	37446795	C	A	37446795	5	1	61	1	0	0	0	0	0	0	1	0	14801	695	24	2	753	2	SMAD9	13	37446795	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177260	37446795	77723083	8604	16589										
ALG5	29880	broad.mit.edu	37	chr13	37524129	37524129	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggcaccagtcaaatatcGaagtcgtataaaaagtaggt	9	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37524129G>A	ENST00000239891.3	-	10	991	c.925C>T	c.(925-927)Cga>Tga	p.R309*	ALG5_ENST00000443765.1_Nonsense_Mutation_p.R279*	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	309					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)	p.R309*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GTCAAATATCGAAGTCGTATA	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											85	83	84					13																	37524129		2203	4300	6503	36422129	SO:0001587	stop_gained	29880			AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"Glycosyltransferase family 2 domain containing"	20266	protein-coding gene	gene with protein product		604565	"asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)", "asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.925C>T	13.37:g.37524129G>A	ENSP00000239891:p.Arg309*		36422129	B4DR37|Q5TBA6	Nonsense_Mutation	SNP	ENST00000239891.3	37	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245912	0.80024	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	.	.	.	5.86	5.01	0.66863	.	0.054432	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6453	0.62277	0.0:0.0:0.6013:0.3987	.	.	.	.	X	279;309	.	ENSP00000239891:R309X	R	-	1	2	ALG5	36422129	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	3.338000	0.52128	1.462000	0.47948	-0.182000	0.12963	CGA		0.358	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338		A	37524129	G	A	37524129	4	1	61	1	0	0	0	0	0	1	0	0	521	1066	37	1	53	1	ALG5	13	37524129	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77334	37524129	77645749	8605	16590										
FAM48A	55578	broad.mit.edu	37	chr13	37598207	37598207	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtgatagggcagctggaGaaagcatgctaacttgattg	14	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37598207G>T	ENST00000350612.6	-	19	1776	c.1556C>A	c.(1555-1557)tCt>tAt	p.S519Y	SUPT20H_ENST00000360252.4_Missense_Mutation_p.S520Y|SUPT20H_ENST00000464744.1_Missense_Mutation_p.S520Y|SUPT20H_ENST00000475892.1_Missense_Mutation_p.S519Y|SUPT20H_ENST00000542180.1_Missense_Mutation_p.S483Y|SUPT20H_ENST00000356185.3_Missense_Mutation_p.S520Y	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	519					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)	p.S519Y(1)									GGCAGCTGGAGAAAGCATGCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											151	148	149					13																	37598207		2203	4300	6503	36496207	SO:0001583	missense	55578			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1556C>A	13.37:g.37598207G>T	ENSP00000218894:p.Ser519Tyr		36496207	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716528	0.89205	.	.	ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180	T;T;T;T;T;T	0.55760	0.84;0.5;1.41;0.84;0.84;0.53	5.4	5.4	0.78164	.	0.233439	0.37136	N	0.002225	T	0.65770	0.2723	L	0.57536	1.79	0.58432	D	0.999999	P;P;P;D;D;D;D	0.61080	0.826;0.826;0.894;0.958;0.989;0.958;0.989	P;P;P;P;P;P;P	0.56514	0.451;0.451;0.548;0.535;0.8;0.635;0.8	T	0.66060	-0.6017	10	0.49607	T	0.09	-8.6031	19.189	0.93656	0.0:0.0:1.0:0.0	.	483;519;519;520;520;519;519	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7;F5GX46	.;.;.;.;.;FA48A_HUMAN;.	Y	520;519;519;520;519;520;483	ENSP00000353388:S520Y;ENSP00000417510:S519Y;ENSP00000218894:S519Y;ENSP00000348512:S520Y;ENSP00000419754:S520Y;ENSP00000439000:S483Y	ENSP00000218894:S519Y	S	-	2	0	FAM48A	36496207	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.278000	0.89899	2.538000	0.85594	0.655000	0.94253	TCT		0.398	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		T	37598207	G	T	37598207	3	4	61	1	0	0	0	0	1	0	0	0	5591	942	33	2	815	2	FAM48A	13	37598207	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74078	37598207	77571671	8606	16591										
FAM48A	55578	broad.mit.edu	37	chr13	37599555	37599555	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcttcattctggactaattCttggtactgattgactaccc	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37599555C>A	ENST00000350612.6	-	17	1451	c.1231G>T	c.(1231-1233)Gaa>Taa	p.E411*	SUPT20H_ENST00000360252.4_Nonsense_Mutation_p.E412*|SUPT20H_ENST00000464744.1_Nonsense_Mutation_p.E412*|SUPT20H_ENST00000475892.1_Nonsense_Mutation_p.E411*|SUPT20H_ENST00000542180.1_Nonsense_Mutation_p.E375*|SUPT20H_ENST00000356185.3_Nonsense_Mutation_p.E412*	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	411					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)	p.E411*(1)									TGGACTAATTCTTGGTACTGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											115	100	105					13																	37599555		2203	4300	6503	36497555	SO:0001587	stop_gained	55578			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1231G>T	13.37:g.37599555C>A	ENSP00000218894:p.Glu411*		36497555	E7ER46|Q71RF3|Q9Y6A6	Nonsense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.448995|7.448995	0.98292|0.98292	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180|ENST00000469488	.|.	.|.	.|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.099985|.	0.64402|.	D|.	0.000002|.	.|T	.|0.79764	.|0.4502	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77824	.|-0.2444	.|3	0.52906|.	T|.	0.07|.	-13.1941|-13.1941	19.7654|19.7654	0.96337|0.96337	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	412;411;411;412;411;412;375|18	.|.	ENSP00000218894:E411X|.	E|K	-|-	1|3	0|2	FAM48A|FAM48A	36497555|36497555	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.544000|0.544000	0.35116|0.35116	6.887000|6.887000	0.75616|0.75616	2.679000|2.679000	0.91253|0.91253	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.383	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		A	37599555	C	A	37599555	4	1	61	1	0	0	0	0	0	1	0	0	5591	922	32	2	1148	2	FAM48A	13	37599555	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1348	37599555	77570323	8607	16592										
CSNK1A1L	122011	broad.mit.edu	37	chr13	37678626	37678626	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtagttcaagtacatggcGaattctgcaggaaacccctt	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:37678626G>A	ENST00000379800.3	-	1	1177	c.768C>T	c.(766-768)ttC>ttT	p.F256F		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F256F(2)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		AGTACATGGCGAATTCTGCAG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	13											133	129	130					13																	37678626		2203	4300	6503	36576626	SO:0001819	synonymous_variant	122011			BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.768C>T	13.37:g.37678626G>A			36576626	Q5T2N2	Silent	SNP	ENST00000379800.3	37	CCDS9363.1																																																																																				0.433	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		A	37678626	G	A	37678626	2	1	61	1	0	0	0	0	0	0	0	1	3957	1049	37	1		1	CSNK1A1L	13	37678626	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79071	37678626	77491252	8608	16593										
TRPC4	7223	broad.mit.edu	37	chr13	38211066	38211066	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgtggtcacgtaatcttCgtgggtgactgtgtctggga	14	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:38211066C>T	ENST00000379705.3	-	11	3765	c.2908G>A	c.(2908-2910)Gaa>Aaa	p.E970K	TRPC4_ENST00000379681.3_Missense_Mutation_p.E975K|TRPC4_ENST00000447043.1_Missense_Mutation_p.E829K|TRPC4_ENST00000379679.1_Missense_Mutation_p.E797K|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000358477.2_Missense_Mutation_p.E886K|TRPC4_ENST00000379673.2_Missense_Mutation_p.E821K|TRPC4_ENST00000338947.5_Missense_Mutation_p.E797K|TRPC4_ENST00000355779.2_Missense_Mutation_p.E829K			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	970	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.E970K(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		ACGTAATCTTCGTGGGTGACT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											125	118	120					13																	38211066		2203	4300	6503	37109066	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2908G>A	13.37:g.38211066C>T	ENSP00000369027:p.Glu970Lys		37109066	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.974194	0.34848	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T;T	0.74526	-0.36;-0.36;-0.17;-0.17;-0.07;-0.51;-0.85;-0.07	5.53	5.53	0.82687	.	0.774326	0.11685	N	0.539469	T	0.76550	0.4003	N	0.14661	0.345	0.80722	D	1	P;B;D;P;P;P	0.61697	0.468;0.257;0.99;0.681;0.531;0.553	B;B;P;B;B;B	0.61722	0.05;0.073;0.893;0.116;0.151;0.034	T	0.78119	-0.2328	10	0.72032	D	0.01	-13.3746	17.6349	0.88119	0.0:1.0:0.0:0.0	.	829;821;975;797;886;970	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	K	970;975;797;797;829;886;821;829	ENSP00000369027:E970K;ENSP00000369003:E975K;ENSP00000342580:E797K;ENSP00000369001:E797K;ENSP00000348025:E829K;ENSP00000351264:E886K;ENSP00000368995:E821K;ENSP00000414316:E829K	ENSP00000342580:E797K	E	-	1	0	TRPC4	37109066	0.840000	0.29493	0.416000	0.26546	0.097000	0.18754	5.038000	0.64177	2.612000	0.88384	0.655000	0.94253	GAA		0.433	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38211066	C	T	38211066	3	4	61	1	0	0	0	0	1	0	0	0	16620	893	31	1	29	1	TRPC4	13	38211066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	532440	38211066	76958812	8609	16594										
TRPC4	7223	broad.mit.edu	37	chr13	38211466	38211466	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatatcggtcacaaaattCacttttctctgcttctccct	4	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:38211466C>A	ENST00000379705.3	-	11	3365	c.2508G>T	c.(2506-2508)gtG>gtT	p.V836V	TRPC4_ENST00000379681.3_Silent_p.V841V|TRPC4_ENST00000447043.1_Intron|TRPC4_ENST00000379679.1_Silent_p.V663V|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000358477.2_Intron|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000338947.5_Silent_p.V663V|TRPC4_ENST00000355779.2_Intron			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	836	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.V836V(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCACAAAATTCACTTTTCTCT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	13											75	76	76					13																	38211466		2203	4300	6503	37109466	SO:0001819	synonymous_variant	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2508G>T	13.37:g.38211466C>A			37109466	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																				0.428	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		A	38211466	C	A	38211466	2	1	61	1	0	0	0	0	0	0	0	1	16620	813	29	2		2	TRPC4	13	38211466	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	400	38211466	76958412	8610	16595										
FREM2	341640	broad.mit.edu	37	chr13	39265478	39265478	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattaatggcaacagatttaGattcagaagacaaatctttg	7	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39265478G>T	ENST00000280481.7	+	1	4213	c.3997G>T	c.(3997-3999)Gat>Tat	p.D1333Y		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1333					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1333Y(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACAGATTTAGATTCAGAAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13											76	80	79					13																	39265478		2203	4300	6503	38163478	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3997G>T	13.37:g.39265478G>T	ENSP00000280481:p.Asp1333Tyr		38163478	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.638705	0.67130	.	.	ENSG00000150893	ENST00000280481	T	0.74106	-0.81	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93768	0.7072	10	0.87932	D	0	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1333	Q5SZK8	FREM2_HUMAN	Y	1333	ENSP00000280481:D1333Y	ENSP00000280481:D1333Y	D	+	1	0	FREM2	38163478	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.864000	0.99589	2.894000	0.99253	0.655000	0.94253	GAT		0.353	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39265478	G	T	39265478	3	4	61	1	0	0	0	0	1	0	0	0	6064	942	33	2	3999	2	FREM2	13	39265478	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1054012	39265478	75904400	8611	16596										
FREM2	341640	broad.mit.edu	37	chr13	39265545	39265545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatggcttattacagagacGaaaacctactggtgcctttg	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39265545G>A	ENST00000280481.7	+	1	4280	c.4064G>A	c.(4063-4065)cGa>cAa	p.R1355Q		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1355					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1355Q(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTACAGAGACGAAAACCTACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	13											64	65	65					13																	39265545		2203	4300	6503	38163545	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4064G>A	13.37:g.39265545G>A	ENSP00000280481:p.Arg1355Gln		38163545	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	0.815	-0.750642	0.03041	.	.	ENSG00000150893	ENST00000280481	T	0.42131	0.98	5.81	-3.79	0.04320	.	0.755679	0.12542	N	0.459858	T	0.25158	0.0611	L	0.37750	1.13	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33266	-0.9875	10	0.12430	T	0.62	.	8.9312	0.35672	0.5521:0.0:0.3399:0.108	.	1355	Q5SZK8	FREM2_HUMAN	Q	1355	ENSP00000280481:R1355Q	ENSP00000280481:R1355Q	R	+	2	0	FREM2	38163545	0.000000	0.05858	0.032000	0.17829	0.842000	0.47809	-1.692000	0.01918	-0.822000	0.04306	-0.768000	0.03414	CGA		0.368	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39265545	G	A	39265545	3	1	61	1	0	0	0	0	1	0	0	0	6064	1058	37	1	4066	1	FREM2	13	39265545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67	39265545	75904333	8612	16597										
FREM2	341640	broad.mit.edu	37	chr13	39450481	39450481	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcacctgcaaccccagaGaacctgtcacctttgacctt	6	16	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39450481G>T	ENST00000280481.7	+	20	8722	c.8506G>T	c.(8506-8508)Gaa>Taa	p.E2836*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2836					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E2836*(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CAACCCCAGAGAACCTGTCAC	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											126	105	112					13																	39450481		2203	4300	6503	38348481	SO:0001587	stop_gained	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8506G>T	13.37:g.39450481G>T	ENSP00000280481:p.Glu2836*		38348481	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	51	17.907791	0.99895	.	.	ENSG00000150893	ENST00000280481	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	19.8108	0.96545	0.0:0.0:1.0:0.0	.	.	.	.	X	2836	.	ENSP00000280481:E2836X	E	+	1	0	FREM2	38348481	1.000000	0.71417	0.996000	0.52242	0.822000	0.46500	9.776000	0.99001	2.698000	0.92095	0.563000	0.77884	GAA		0.463	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39450481	G	T	39450481	4	4	61	1	0	0	0	0	0	1	0	0	6064	943	33	2	8584	2	FREM2	13	39450481	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184936	39450481	75719397	8613	16598										
FREM2	341640	broad.mit.edu	37	chr13	39453093	39453093	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatctgatggatttaaagtCgactcaacaccactctttca	7	10	4	1	rs552170785		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39453093C>T	ENST00000280481.7	+	23	9201	c.8985C>T	c.(8983-8985)gtC>gtT	p.V2995V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2995					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2995V(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GATTTAAAGTCGACTCAACAC	0.418													C|||	1	0.000199681	0	0	5008	,	,		18510	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	13											201	174	184					13																	39453093		2203	4300	6503	38351093	SO:0001819	synonymous_variant	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8985C>T	13.37:g.39453093C>T			38351093	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39453093	C	T	39453093	2	4	61	1	0	0	0	0	0	0	0	1	6064	871	31	1		1	FREM2	13	39453093	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2612	39453093	75716785	8614	16599										
FREM2	341640	broad.mit.edu	37	chr13	39454470	39454470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgatctatacagtgagatCgaaagacaatgccaatcgag	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39454470C>T	ENST00000280481.7	+	24	9272	c.9056C>T	c.(9055-9057)tCg>tTg	p.S3019L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3019					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S3019L(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACAGTGAGATCGAAAGACAAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											96	92	93					13																	39454470		2203	4300	6503	38352470	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9056C>T	13.37:g.39454470C>T	ENSP00000280481:p.Ser3019Leu		38352470	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470783	0.84533	.	.	ENSG00000150893	ENST00000280481	T	0.60171	0.21	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.80849	0.4702	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.82494	-0.0429	10	0.66056	D	0.02	.	20.2562	0.98421	0.0:1.0:0.0:0.0	.	3019	Q5SZK8	FREM2_HUMAN	L	3019	ENSP00000280481:S3019L	ENSP00000280481:S3019L	S	+	2	0	FREM2	38352470	1.000000	0.71417	0.518000	0.27811	0.286000	0.27126	7.593000	0.82686	2.797000	0.96272	0.563000	0.77884	TCG		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39454470	C	T	39454470	3	4	61	1	0	0	0	0	1	0	0	0	6064	893	31	1	9150	1	FREM2	13	39454470	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1377	39454470	75715408	8615	16600										
STOML3	161003	broad.mit.edu	37	chr13	39542553	39542553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttggctctcgcttccCgggtggcctcagcctcggct	11	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:39542553C>T	ENST00000379631.4	-	6	979	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	STOML3_ENST00000423210.1_Missense_Mutation_p.R203Q	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	212					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.R212Q(1)		breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		TCTCGCTTCCCGGGTGGCCTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	13											90	84	86					13																	39542553		2203	4300	6503	38440553	SO:0001583	missense	161003			BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.635G>A	13.37:g.39542553C>T	ENSP00000368952:p.Arg212Gln		38440553	B4E285|Q5JS35	Missense_Mutation	SNP	ENST00000379631.4	37	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.406233	0.62288	.	.	ENSG00000133115	ENST00000379631;ENST00000423210	D;D	0.94330	-3.4;-3.4	5.92	5.92	0.95590	.	0.109676	0.64402	D	0.000006	D	0.96595	0.8889	M	0.91768	3.24	0.80722	D	1	D;D	0.69078	0.985;0.997	P;P	0.58520	0.84;0.84	D	0.96810	0.9596	10	0.72032	D	0.01	-13.843	13.1665	0.59573	0.0:0.9232:0.0:0.0767	.	203;212	B4E285;Q8TAV4	.;STML3_HUMAN	Q	212;203	ENSP00000368952:R212Q;ENSP00000401989:R203Q	ENSP00000368952:R212Q	R	-	2	0	STOML3	38440553	0.962000	0.33011	0.858000	0.33744	0.003000	0.03518	3.088000	0.50175	2.795000	0.96236	0.655000	0.94253	CGG		0.562	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			T	39542553	C	T	39542553	3	4	61	1	0	0	0	0	1	0	0	0	15354	652	23	1	248	1	STOML3	13	39542553	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88083	39542553	75627325	8616	16601										
COG6	57511	broad.mit.edu	37	chr13	40293445	40293445	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgttgctgcgtgaagttTtagcatctcacgattcttca	8	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:40293445T>G	ENST00000455146.3	+	14	1407	c.1357T>G	c.(1357-1359)Tta>Gta	p.L453V	COG6_ENST00000416691.1_Missense_Mutation_p.L453V	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	453					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.L453V(1)		NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		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)		GCGTGAAGTTTTAGCATCTCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	13											142	125	131					13																	40293445		2203	4300	6503	39191445	SO:0001583	missense	57511			AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1357T>G	13.37:g.40293445T>G	ENSP00000397441:p.Leu453Val		39191445	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082000	0.76528	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	T;T	0.61742	0.08;0.08	5.92	-1.26	0.09376	.	0.000000	0.85682	D	0.000000	T	0.69691	0.3139	M	0.72118	2.19	0.53688	D	0.999979	D;D	0.76494	0.999;0.985	D;P	0.72982	0.979;0.81	T	0.69942	-0.5008	10	0.51188	T	0.08	0.04	12.7872	0.57512	0.0:0.6825:0.0:0.3175	.	474;453	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	V	453;484;453	ENSP00000403733:L453V;ENSP00000397441:L453V	ENSP00000255468:L484V	L	+	1	2	COG6	39191445	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	0.675000	0.25232	-0.163000	0.10946	0.533000	0.62120	TTA		0.388	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40293445	T	G	40293445	3	3	61	1	0	0	0	0	1	0	0	0	3668	1838	64	4	1411	4	COG6	13	40293445	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	750892	40293445	74876433	8617	16602										
SLC25A15	10166	broad.mit.edu	37	chr13	41381512	41381512	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactctcaagcactttacttCgagaagtaccaggctatttc	7	11	1	1	rs104894429		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41381512C>T	ENST00000338625.4	+	5	771	c.535C>T	c.(535-537)Cga>Tga	p.R179*	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	179					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|L-ornithine transmembrane transport (GO:1903352)|mitochondrial ornithine transport (GO:0000066)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	L-ornithine transmembrane transporter activity (GO:0000064)	p.R179*(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|stomach(1)|urinary_tract(1)	14		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	CACTTTACTTCGAGAAGTACC	0.448													C|||	1	0.000199681	0	0	5008	,	,		21877	0.001		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	13	GRCh37	CM001338	SLC25A15	M	rs104894429						191	177	182					13																	41381512		2203	4300	6503	40279512	SO:0001587	stop_gained	10166			AF112968	CCDS9373.1	13q14	2013-05-22			ENSG00000102743	ENSG00000102743		"Solute carriers"	10985	protein-coding gene	gene with protein product	"ornithine transporter 1"	603861		ORNT1, HHH		10369256	Standard	NM_014252		Approved	ORC1, D13S327	uc001uxn.3	Q9Y619	OTTHUMG00000016776	ENST00000338625.4:c.535C>T	13.37:g.41381512C>T	ENSP00000342267:p.Arg179*		40279512	Q5VZD8|Q9HC45	Nonsense_Mutation	SNP	ENST00000338625.4	37	CCDS9373.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139146	0.94560	.	.	ENSG00000102743	ENST00000338625;ENST00000379523;ENST00000443985;ENST00000417731	.	.	.	5.22	4.32	0.51571	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8191	0.70059	0.1438:0.8562:0.0:0.0	.	.	.	.	X	179;133;119;133	.	ENSP00000342267:R179X	R	+	1	2	SLC25A15	40279512	0.998000	0.40836	1.000000	0.80357	0.978000	0.69477	2.419000	0.44671	2.597000	0.87782	0.455000	0.32223	CGA		0.448	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252		T	41381512	C	T	41381512	4	4	61	1	0	0	0	0	0	1	0	0	14514	876	31	1	549	1	SLC25A15	13	41381512	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1088067	41381512	73788366	8618	16603										
ELF1	1997	broad.mit.edu	37	chr13	41515075	41515075	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctaatactctgaacggaaGaatttaatgtttcatcctgc	6	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41515075G>T	ENST00000239882.3	-	8	1552	c.1238C>A	c.(1237-1239)tCt>tAt	p.S413Y	ELF1_ENST00000442101.1_Missense_Mutation_p.S389Y|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	413					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S413Y(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CTGAACGGAAGAATTTAATGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	13											101	95	97					13																	41515075		2203	4300	6503	40413075	SO:0001583	missense	1997			M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1238C>A	13.37:g.41515075G>T	ENSP00000239882:p.Ser413Tyr		40413075	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.725157	0.48833	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.49432	0.78;0.78	5.66	5.66	0.87406	.	0.270267	0.36703	N	0.002442	T	0.51873	0.1700	L	0.29908	0.895	0.37128	D	0.901136	D;D	0.59767	0.971;0.986	P;P	0.52514	0.624;0.701	T	0.59059	-0.7525	10	0.87932	D	0	.	20.1253	0.97977	0.0:0.0:1.0:0.0	.	389;413	E9PDQ9;P32519	.;ELF1_HUMAN	Y	389;155;413	ENSP00000405580:S389Y;ENSP00000239882:S413Y	ENSP00000239882:S413Y	S	-	2	0	ELF1	40413075	1.000000	0.71417	0.966000	0.40874	0.106000	0.19336	7.491000	0.81471	2.832000	0.97577	0.655000	0.94253	TCT		0.428	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		T	41515075	G	T	41515075	3	4	61	1	0	0	0	0	1	0	0	0	5066	942	33	2	629	2	ELF1	13	41515075	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133563	41515075	73654803	8619	16604										
KBTBD6	89890	broad.mit.edu	37	chr13	41704633	41704633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgcatttcactgaggcGctacacgcacccaaaaatca	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41704633G>A	ENST00000379485.1	-	1	2249	c.2015C>T	c.(2014-2016)gCg>gTg	p.A672V	KBTBD6_ENST00000499385.2_Missense_Mutation_p.A606V	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	672								p.A672V(1)		NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		TCACTGAGGCGCTACACGCAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											69	69	69					13																	41704633		2203	4300	6503	40602633	SO:0001583	missense	89890			AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.2015C>T	13.37:g.41704633G>A	ENSP00000368799:p.Ala672Val		40602633	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	g	15.47	2.844139	0.51164	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.77750	-1.05;-1.12	3.8	1.94	0.25998	.	0.230218	0.27927	N	0.017292	T	0.66867	0.2833	N	0.24115	0.695	0.09310	N	1	D;D	0.59767	0.986;0.976	P;B	0.50082	0.63;0.427	T	0.59883	-0.7370	10	0.87932	D	0	.	4.6932	0.12791	0.1313:0.2253:0.6434:0.0	.	606;672	F5GZN7;Q86V97	.;KBTB6_HUMAN	V	672;606	ENSP00000368799:A672V;ENSP00000444326:A606V	ENSP00000368799:A672V	A	-	2	0	KBTBD6	40602633	0.009000	0.17119	0.007000	0.13788	0.382000	0.30200	1.037000	0.30241	0.353000	0.24079	0.462000	0.41574	GCG		0.398	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		A	41704633	G	A	41704633	3	1	61	1	0	0	0	0	1	0	0	0	8018	1087	38	1	13	1	KBTBD6	13	41704633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189558	41704633	73465245	8620	16605										
KBTBD6	89890	broad.mit.edu	37	chr13	41705091	41705091	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatctcctcattgaagacGcaggcttcctgaaagtcatt	8	10	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41705091G>A	ENST00000379485.1	-	1	1791	c.1557C>T	c.(1555-1557)tgC>tgT	p.C519C	KBTBD6_ENST00000499385.2_Silent_p.C453C	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	519								p.C519C(1)		NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CATTGAAGACGCAGGCTTCCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	13											96	92	94					13																	41705091		2203	4300	6503	40603091	SO:0001819	synonymous_variant	89890			AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.1557C>T	13.37:g.41705091G>A			40603091	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Silent	SNP	ENST00000379485.1	37	CCDS9376.1																																																																																				0.443	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		A	41705091	G	A	41705091	2	1	61	1	0	0	0	0	0	0	0	1	8018	1079	38	1		1	KBTBD6	13	41705091	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	458	41705091	73464787	8621	16606										
KBTBD7	84078	broad.mit.edu	37	chr13	41766758	41766758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggaatattactaatccGcctccattctcccctagctg	5	14	1	0	rs149586667	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41766758G>A	ENST00000379483.3	-	1	1944	c.1636C>T	c.(1636-1638)Cgg>Tgg	p.R546W		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	546								p.R546W(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		TTACTAATCCGCCTCCATTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	13											128	129	129					13																	41766758		2203	4300	6503	40664758	SO:0001583	missense	84078			AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1636C>T	13.37:g.41766758G>A	ENSP00000368797:p.Arg546Trp		40664758	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	37	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.635184	0.47049	.	.	ENSG00000120696	ENST00000379483;ENST00000501885	T	0.67865	-0.29	5.37	4.52	0.55395	Kelch-type beta propeller (1);	0.067619	0.53938	U	0.000043	T	0.66066	0.2752	L	0.46157	1.445	0.42849	D	0.994071	D	0.65815	0.995	P	0.51170	0.661	T	0.65216	-0.6222	10	0.37606	T	0.19	.	11.1073	0.48210	0.0:0.0:0.6635:0.3364	.	546	Q8WVZ9	KBTB7_HUMAN	W	546;448	ENSP00000368797:R546W	ENSP00000368797:R546W	R	-	1	2	KBTBD7	40664758	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	2.692000	0.47018	1.221000	0.43506	0.557000	0.71058	CGG		0.423	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		A	41766758	G	A	41766758	3	1	61	1	0	0	0	0	1	0	0	0	8019	1086	38	1	422	1	KBTBD7	13	41766758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61667	41766758	73403120	8622	16607										
KBTBD7	84078	broad.mit.edu	37	chr13	41767132	41767132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccctcacgacacagcaagCgatctgcaagttgctgccaa	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41767132C>T	ENST00000379483.3	-	1	1570	c.1262G>A	c.(1261-1263)cGc>cAc	p.R421H		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	421								p.R421H(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		ACACAGCAAGCGATCTGCAAG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	13											119	108	112					13																	41767132		2203	4298	6501	40665132	SO:0001583	missense	84078			AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1262G>A	13.37:g.41767132C>T	ENSP00000368797:p.Arg421His		40665132	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	37	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.795462	0.31777	.	.	ENSG00000120696	ENST00000379483;ENST00000501885	T	0.66460	-0.21	5.05	3.32	0.38043	Kelch-type beta propeller (1);	0.000000	0.64402	D	0.000001	T	0.50086	0.1595	N	0.20986	0.625	0.41065	D	0.985407	B	0.14438	0.01	B	0.08055	0.003	T	0.43475	-0.9389	10	0.59425	D	0.04	.	9.561	0.39369	0.0:0.8263:0.0:0.1737	.	421	Q8WVZ9	KBTB7_HUMAN	H	421;323	ENSP00000368797:R421H	ENSP00000368797:R421H	R	-	2	0	KBTBD7	40665132	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	4.044000	0.57361	0.530000	0.28619	-0.262000	0.10625	CGC		0.493	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		T	41767132	C	T	41767132	3	4	61	1	0	0	0	0	1	0	0	0	8019	768	27	1	796	1	KBTBD7	13	41767132	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	374	41767132	73402746	8623	16608										
MTRF1	9617	broad.mit.edu	37	chr13	41826864	41826864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacatgtcaaatatttctCgggtaaattgttggcagatg	11	5	2	1	rs146179881		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41826864C>T	ENST00000379480.4	-	5	714	c.614G>A	c.(613-615)cGa>cAa	p.R205Q	MTRF1_ENST00000430347.2_Missense_Mutation_p.R218Q|MTRF1_ENST00000239852.6_5'UTR|MTRF1_ENST00000379477.1_Missense_Mutation_p.R205Q	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	205					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)	p.R205Q(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		AAATATTTCTCGGGTAAATTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	GLN/ARG	3,4401	6.2+/-15.9	0,3,2199	61	59	60		614	3.2	1	13	dbSNP_134	60	0,8600		0,0,4300	no	missense	MTRF1	NM_004294.2	43	0,3,6499	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	205/446	41826864	3,13001	2202	4300	6502	40724864	SO:0001583	missense	9617			AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"mitochontrial peptide chain release factor 1"	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.614G>A	13.37:g.41826864C>T	ENSP00000368793:p.Arg205Gln		40724864	B4DG01|Q5T6Y5|Q8IUQ6	Missense_Mutation	SNP	ENST00000379480.4	37	CCDS9378.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516337	0.64634	6.81E-4	0.0	ENSG00000120662	ENST00000379480;ENST00000379477;ENST00000430347;ENST00000452359	T;T;T;T	0.41400	2.82;2.82;2.82;1.0	5.88	3.19	0.36642	Peptide chain release factor (2);	0.293440	0.37136	N	0.002226	T	0.26629	0.0651	L	0.27053	0.805	0.80722	D	1	P;P	0.49090	0.919;0.774	B;B	0.41202	0.35;0.267	T	0.05007	-1.0912	10	0.62326	D	0.03	-6.2204	6.075	0.19911	0.0:0.5884:0.0:0.4116	.	218;205	B4DG01;O75570	.;RF1M_HUMAN	Q	205;205;218;205	ENSP00000368793:R205Q;ENSP00000368790:R205Q;ENSP00000400031:R218Q;ENSP00000399279:R205Q	ENSP00000368790:R205Q	R	-	2	0	MTRF1	40724864	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	0.613000	0.24299	1.494000	0.48533	0.591000	0.81541	CGA		0.353	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294		T	41826864	C	T	41826864	3	4	61	1	0	0	0	0	1	0	0	0	9989	884	31	1	747	1	MTRF1	13	41826864	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59732	41826864	73343014	8624	16609										
NAA16	79612	broad.mit.edu	37	chr13	41899936	41899936	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaatctttggaacatataGaaatgtatgagaaacaaata	8	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41899936G>T	ENST00000379406.3	+	6	964	c.640G>T	c.(640-642)Gaa>Taa	p.E214*	NAA16_ENST00000379367.3_Nonsense_Mutation_p.E214*|NAA16_ENST00000403412.3_Nonsense_Mutation_p.E214*	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	214					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)	p.E214*(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						GGAACATATAGAAATGTATGA	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											70	79	76					13																	41899936		2203	4299	6502	40797936	SO:0001587	stop_gained	79612			AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.640G>T	13.37:g.41899936G>T	ENSP00000368716:p.Glu214*		40797936	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Nonsense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	G	38	6.717307	0.97784	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	.	.	.	5.02	4.15	0.48705	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-11.0825	15.2234	0.73330	0.0:0.1415:0.8585:0.0	.	.	.	.	X	214	.	ENSP00000368674:E214X	E	+	1	0	NAA16	40797936	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	2.562000	0.45914	1.082000	0.41137	0.557000	0.71058	GAA		0.308	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41899936	G	T	41899936	4	4	61	1	0	0	0	0	0	1	0	0	10149	943	33	2	662	2	NAA16	13	41899936	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73072	41899936	73269942	8625	16610										
NAA16	79612	broad.mit.edu	37	chr13	41933037	41933037	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaattccaaatgtgcaaAatacatgcttcgagcaaata	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:41933037A>C	ENST00000379406.3	+	12	1673	c.1349A>C	c.(1348-1350)aAa>aCa	p.K450T	NAA16_ENST00000379367.3_Missense_Mutation_p.K450T	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	450					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)	p.K450T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AAATGTGCAAAATACATGCTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											99	100	100					13																	41933037		2203	4300	6503	40831037	SO:0001583	missense	79612			AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1349A>C	13.37:g.41933037A>C	ENSP00000368716:p.Lys450Thr		40831037	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069751	0.76301	.	.	ENSG00000172766	ENST00000379367;ENST00000379406	T;T	0.57436	0.4;0.4	4.91	4.91	0.64330	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	T	0.78253	0.4254	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.83543	0.0097	10	0.56958	D	0.05	-21.819	14.5277	0.67900	1.0:0.0:0.0:0.0	.	450	Q6N069	NAA16_HUMAN	T	450	ENSP00000368674:K450T;ENSP00000368716:K450T	ENSP00000368674:K450T	K	+	2	0	NAA16	40831037	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.675000	0.91195	1.833000	0.53350	0.459000	0.35465	AAA		0.373	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		C	41933037	A	C	41933037	3	2	61	1	0	0	0	0	1	0	0	0	10149	14	1	4	1428	4	NAA16	13	41933037	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33101	41933037	73236841	8626	16611										
KIAA0564	23078	broad.mit.edu	37	chr13	42275564	42275564	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcacagattatattaatttCatccaatggtattctccatg	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42275564C>A	ENST00000379310.3	-	28	3396	c.3328G>T	c.(3328-3330)Gaa>Taa	p.E1110*		NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1110						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E1110*(1)									ATATTAATTTCATCCAATGGT	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											172	161	164					13																	42275564		1834	4088	5922	41173564	SO:0001587	stop_gained	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3328G>T	13.37:g.42275564C>A	ENSP00000368612:p.Glu1110*		41173564	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Nonsense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	41	8.611181	0.98884	.	.	ENSG00000102763	ENST00000251030;ENST00000379310	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	19.6589	0.95855	0.0:1.0:0.0:0.0	.	.	.	.	X	1014;1110	.	ENSP00000251030:E1014X	E	-	1	0	KIAA0564	41173564	1.000000	0.71417	0.997000	0.53966	0.280000	0.26924	6.664000	0.74437	2.713000	0.92767	0.591000	0.81541	GAA		0.328	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42275564	C	A	42275564	4	1	61	1	0	0	0	0	0	1	0	0	8206	835	29	2	2461	2	KIAA0564	13	42275564	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	342527	42275564	72894314	8627	16612										
KIAA0564	23078	broad.mit.edu	37	chr13	42293873	42293873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagagaccttcagtcggAaatttctgtattaaaaaaaa	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42293873A>G	ENST00000379310.3	-	26	3038	c.2970T>C	c.(2968-2970)ttT>ttC	p.F990F	VWA8_ENST00000281496.6_Silent_p.F990F	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	990						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.F990F(1)									CTTCAGTCGGAAATTTCTGTA	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	13											70	65	67					13																	42293873		2203	4300	6503	41191873	SO:0001819	synonymous_variant	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2970T>C	13.37:g.42293873A>G			41191873	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	37	CCDS41881.1																																																																																				0.299	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42293873	A	G	42293873	2	3	61	1	0	0	0	0	0	0	0	1	8206	243	9	4		4	KIAA0564	13	42293873	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	18309	42293873	72876005	8628	16613										
KIAA0564	23078	broad.mit.edu	37	chr13	42335334	42335334	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaacaatcttgttttttcCtacaccctgtaattacacag	4	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42335334C>A	ENST00000379310.3	-	21	2424	c.2356G>T	c.(2356-2358)Gga>Tga	p.G786*	VWA8_ENST00000281496.6_Nonsense_Mutation_p.G786*	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	786						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.G786*(1)									TTGTTTTTTCCTACACCCTGT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											146	141	142					13																	42335334		2203	4300	6503	41233334	SO:0001587	stop_gained	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2356G>T	13.37:g.42335334C>A	ENSP00000368612:p.Gly786*		41233334	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Nonsense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	42	9.291654	0.99127	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.8048	0.92032	0.0:1.0:0.0:0.0	.	.	.	.	X	690;786;786	.	ENSP00000251030:G690X	G	-	1	0	KIAA0564	41233334	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.440000	0.73435	2.803000	0.96430	0.650000	0.86243	GGA		0.368	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42335334	C	A	42335334	4	1	61	1	0	0	0	0	0	1	0	0	8206	690	24	2	3465	2	KIAA0564	13	42335334	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41461	42335334	72834544	8629	16614										
KIAA0564	23078	broad.mit.edu	37	chr13	42461370	42461370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatatccctggcttgaaatCgagaacgaagaggggggtct	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42461370C>T	ENST00000379310.3	-	6	847	c.779G>A	c.(778-780)cGa>cAa	p.R260Q	VWA8_ENST00000281496.6_Missense_Mutation_p.R260Q	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	260						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R260Q(1)									GGCTTGAAATCGAGAACGAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13											50	55	53					13																	42461370		2203	4300	6503	41359370	SO:0001583	missense	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.779G>A	13.37:g.42461370C>T	ENSP00000368612:p.Arg260Gln		41359370	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919010	0.92249	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.73681	-0.77;-0.77	5.11	4.25	0.50352	ATPase, dynein-related, AAA domain (1);	0.080769	0.44688	D	0.000433	D	0.89632	0.6771	H	0.94264	3.515	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.92471	0.5985	10	0.72032	D	0.01	.	15.2066	0.73183	0.1419:0.8581:0.0:0.0	.	260	A3KMH1	K0564_HUMAN	Q	164;260;260;260	ENSP00000368612:R260Q;ENSP00000281496:R260Q	ENSP00000251030:R164Q	R	-	2	0	KIAA0564	41359370	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.720000	0.84759	1.259000	0.44117	0.650000	0.86243	CGA		0.378	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42461370	C	T	42461370	3	4	61	1	0	0	0	0	1	0	0	0	8206	884	31	1	5102	1	KIAA0564	13	42461370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	126036	42461370	72708508	8630	16615										
KIAA0564	23078	broad.mit.edu	37	chr13	42524079	42524079	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatatttcttactgtagttCtgtggcacaagttctggatt	8	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42524079C>T	ENST00000379310.3	-	2	302	c.234G>A	c.(232-234)caG>caA	p.Q78Q	VWA8_ENST00000281496.6_Silent_p.Q78Q	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	78						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.Q78Q(2)									TACTGTAGTTCTGTGGCACAA	0.249																																																2	Substitution - coding silent(2)	large_intestine(2)	13											22	22	22					13																	42524079		2193	4292	6485	41422079	SO:0001819	synonymous_variant	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.234G>A	13.37:g.42524079C>T			41422079	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	37	CCDS41881.1																																																																																				0.249	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42524079	C	T	42524079	2	4	61	1	0	0	0	0	0	0	0	1	8206	912	32	3		3	KIAA0564	13	42524079	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62709	42524079	72645799	8631	16616										
DGKH	160851	broad.mit.edu	37	chr13	42740747	42740747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagtaaagttcctccgtcGctttaaacagttgctaaatc	9	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42740747G>A	ENST00000337343.4	+	9	1076	c.1055G>A	c.(1054-1056)cGc>cAc	p.R352H	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.R216H|DGKH_ENST00000379274.2_Missense_Mutation_p.R216H|DGKH_ENST00000538674.1_Missense_Mutation_p.R107H|DGKH_ENST00000540693.1_Missense_Mutation_p.R352H|DGKH_ENST00000261491.5_Missense_Mutation_p.R352H	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	352	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R352H(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTCCTCCGTCGCTTTAAACAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	13											128	126	127					13																	42740747		2203	4300	6503	41638747	SO:0001583	missense	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1055G>A	13.37:g.42740747G>A	ENSP00000337572:p.Arg352His		41638747	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.845423	0.71603	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	5.81	4.07	0.47477	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.46927	0.1418	M	0.62723	1.935	0.48040	D	0.999576	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.993;0.992;0.997;0.996	T	0.49409	-0.8943	10	0.87932	D	0	.	12.8356	0.57771	0.134:0.0:0.866:0.0	.	107;216;352;352	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	H	352;352;352;216;216;107	ENSP00000440823:R352H;ENSP00000337572:R352H;ENSP00000261491:R352H;ENSP00000368576:R216H;ENSP00000445114:R216H;ENSP00000441308:R107H	ENSP00000261491:R352H	R	+	2	0	DGKH	41638747	1.000000	0.71417	0.777000	0.31699	0.628000	0.37860	7.841000	0.86834	1.470000	0.48102	-0.142000	0.14014	CGC		0.368	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42740747	G	A	42740747	3	1	61	1	0	0	0	0	1	0	0	0	4481	1087	38	1	1089	1	DGKH	13	42740747	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216668	42740747	72429131	8632	16617										
DGKH	160851	broad.mit.edu	37	chr13	42773954	42773954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatttattttcaggagccGaactaaaaacttgatgtggt	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42773954G>A	ENST00000337343.4	+	20	2423	c.2402G>A	c.(2401-2403)cGa>cAa	p.R801Q	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.R665Q|DGKH_ENST00000379274.2_Missense_Mutation_p.R665Q|DGKH_ENST00000538674.1_Missense_Mutation_p.R556Q|DGKH_ENST00000540693.1_Missense_Mutation_p.R801Q|DGKH_ENST00000261491.5_Missense_Mutation_p.R801Q	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	801					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R801Q(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTCAGGAGCCGAACTAAAAAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	13											47	51	49					13																	42773954		2203	4300	6503	41671954	SO:0001583	missense	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.2402G>A	13.37:g.42773954G>A	ENSP00000337572:p.Arg801Gln		41671954	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015610	0.93404	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	5.79	5.79	0.91817	Diacylglycerol kinase, accessory domain (2);	0.073536	0.56097	D	0.000034	T	0.61986	0.2391	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.992;0.996;0.982;0.997	T	0.62651	-0.6809	10	0.87932	D	0	.	20.0367	0.97561	0.0:0.0:1.0:0.0	.	556;665;801;801	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	Q	801;801;801;665;665;556	ENSP00000440823:R801Q;ENSP00000337572:R801Q;ENSP00000261491:R801Q;ENSP00000368576:R665Q;ENSP00000445114:R665Q;ENSP00000441308:R556Q	ENSP00000261491:R801Q	R	+	2	0	DGKH	41671954	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.956000	0.87863	2.727000	0.93392	0.591000	0.81541	CGA		0.348	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42773954	G	A	42773954	3	1	61	1	0	0	0	0	1	0	0	0	4481	1058	37	1	2480	1	DGKH	13	42773954	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33207	42773954	72395924	8633	16618										
AKAP11	11215	broad.mit.edu	37	chr13	42874681	42874681	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggcatttgatgagctgaGaaggcagcgtgcattttcac	13	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42874681G>T	ENST00000025301.2	+	8	1974	c.1799G>T	c.(1798-1800)aGa>aTa	p.R600I		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	600					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.R600I(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GATGAGCTGAGAAGGCAGCGT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											85	82	83					13																	42874681		2203	4300	6503	41772681	SO:0001583	missense	11215			AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.1799G>T	13.37:g.42874681G>T	ENSP00000025301:p.Arg600Ile		41772681	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707653	0.68615	.	.	ENSG00000023516	ENST00000025301	T	0.16196	2.36	6.07	5.11	0.69529	.	0.123620	0.53938	D	0.000043	T	0.32071	0.0817	M	0.65975	2.015	0.80722	D	1	D	0.53151	0.958	P	0.54312	0.748	T	0.03278	-1.1053	10	0.48119	T	0.1	.	12.9991	0.58666	0.0934:0.0:0.9066:0.0	.	600	Q9UKA4	AKA11_HUMAN	I	600	ENSP00000025301:R600I	ENSP00000025301:R600I	R	+	2	0	AKAP11	41772681	1.000000	0.71417	0.977000	0.42913	0.917000	0.54804	3.908000	0.56355	1.324000	0.45282	0.585000	0.79938	AGA		0.393	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42874681	G	T	42874681	3	4	61	1	0	0	0	0	1	0	0	0	447	942	33	2	1821	2	AKAP11	13	42874681	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100727	42874681	72295197	8634	16619										
AKAP11	11215	broad.mit.edu	37	chr13	42875403	42875403	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatatttgtttaccttcaGaacacaatccaggtaatcag	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:42875403G>A	ENST00000025301.2	+	8	2696	c.2521G>A	c.(2521-2523)Gaa>Aaa	p.E841K		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	841					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.E841K(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTTACCTTCAGAACACAATCC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											41	40	40					13																	42875403		2203	4297	6500	41773403	SO:0001583	missense	11215			AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2521G>A	13.37:g.42875403G>A	ENSP00000025301:p.Glu841Lys		41773403	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.283287	0.40394	.	.	ENSG00000023516	ENST00000025301	T	0.15372	2.43	6.17	5.16	0.70880	.	0.560263	0.18125	N	0.150915	T	0.19248	0.0462	L	0.51422	1.61	0.35054	D	0.760887	P	0.42692	0.787	B	0.39379	0.298	T	0.14811	-1.0459	10	0.52906	T	0.07	.	14.7236	0.69326	0.0772:0.0:0.9228:0.0	.	841	Q9UKA4	AKA11_HUMAN	K	841	ENSP00000025301:E841K	ENSP00000025301:E841K	E	+	1	0	AKAP11	41773403	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.687000	0.54692	2.941000	0.99782	0.655000	0.94253	GAA		0.338	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42875403	G	A	42875403	3	1	61	1	0	0	0	0	1	0	0	0	447	943	33	3	2543	3	AKAP11	13	42875403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	722	42875403	72294475	8635	16620										
ENOX1	55068	broad.mit.edu	37	chr13	43810869	43810869	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcaactgtcaacacattGatttcctataaagttaaaag	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:43810869G>T	ENST00000261488.6	-	15	2194	c.1617C>A	c.(1615-1617)atC>atA	p.I539I	ENOX1_ENST00000412891.1_Silent_p.I539I	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	539					rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)	p.I539I(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TCAACACATTGATTTCCTATA	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	13											95	91	92					13																	43810869		2202	4297	6499	42708869	SO:0001819	synonymous_variant	55068			EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"RNA binding motif (RRM) containing"	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.1617C>A	13.37:g.43810869G>T			42708869	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Silent	SNP	ENST00000261488.6	37	CCDS9389.1																																																																																				0.338	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		T	43810869	G	T	43810869	2	4	61	1	0	0	0	0	0	0	0	1	5139	1280	45	2		2	ENOX1	13	43810869	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	935466	43810869	71359009	8636	16621										
CCDC122	160857	broad.mit.edu	37	chr13	44434060	44434060	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagctttacattttctgaAtgtaaggatttgatttgagt	8	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:44434060A>G	ENST00000444614.3	-	5	561	c.303T>C	c.(301-303)caT>caC	p.H101H	CCDC122_ENST00000281508.3_Silent_p.H101H|CCDC122_ENST00000476570.2_5'UTR	NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	101								p.H101H(1)		endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		CATTTTCTGAATGTAAGGATT	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	13											86	83	84					13																	44434060		2203	4294	6497	43332060	SO:0001819	synonymous_variant	160857			AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.303T>C	13.37:g.44434060A>G			43332060	B2RP70|B7ZMI9|Q96MV0	Silent	SNP	ENST00000444614.3	37	CCDS9390.2																																																																																				0.299	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974		G	44434060	A	G	44434060	2	3	61	1	0	0	0	0	0	0	0	1	2764	98	4	4		4	CCDC122	13	44434060	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	623191	44434060	70735818	8637	16622										
TSC22D1	8848	broad.mit.edu	37	chr13	45149345	45149345	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcacgcatattagtcattAcagatgcaggtgaaccactg	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:45149345A>G	ENST00000458659.2	-	1	1356	c.866T>C	c.(865-867)gTa>gCa	p.V289A	TSC22D1_ENST00000460842.1_5'Flank|TSC22D1_ENST00000501704.2_Missense_Mutation_p.V289A	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	289					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V289A(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		ATTAGTCATTACAGATGCAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											109	102	104					13																	45149345		2203	4300	6503	44047345	SO:0001583	missense	8848			AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"transforming growth factor beta 1 induced transcript 4"	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.866T>C	13.37:g.45149345A>G	ENSP00000397435:p.Val289Ala		44047345	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	A	7.396	0.631741	0.14322	.	.	ENSG00000102804	ENST00000458659;ENST00000501704	T;T	0.46063	0.88;0.88	4.95	3.76	0.43208	.	0.268957	0.25872	N	0.027754	T	0.24851	0.0603	L	0.27053	0.805	0.22401	N	0.999134	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.21793	-1.0235	10	0.07325	T	0.83	.	9.652	0.39904	0.9167:0.0:0.0833:0.0	.	289;289	B3KRL7;Q15714	.;T22D1_HUMAN	A	289	ENSP00000397435:V289A;ENSP00000437414:V289A	ENSP00000397435:V289A	V	-	2	0	TSC22D1	44047345	0.681000	0.27614	0.995000	0.50966	0.494000	0.33585	0.868000	0.27982	0.912000	0.36772	0.459000	0.35465	GTA		0.418	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		G	45149345	A	G	45149345	3	3	61	1	0	0	0	0	1	0	0	0	16647	391	14	4	2496	4	TSC22D1	13	45149345	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	715285	45149345	70020533	8638	16623										
KIAA1704	55425	broad.mit.edu	37	chr13	45602086	45602086	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagccctaataaaaaaatCtagagaactaaacaccagat	4	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:45602086C>A	ENST00000379151.4	+	8	1074	c.971C>A	c.(970-972)tCt>tAt	p.S324Y	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_Missense_Mutation_p.S324Y|GPALPP1_ENST00000357537.3_Missense_Mutation_p.S154Y	NM_018559.2	NP_061029.2	Q8IXQ4	GPAM1_HUMAN	GPALPP motifs containing 1	324								p.S324Y(1)									ATAAAAAAATCTAGAGAACTA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	13											67	78	74					13																	45602086		2203	4298	6501	44500086	SO:0001583	missense	55425			AB051491	CCDS9394.1	13q14.12	2013-08-13	2013-08-12	2013-08-12	ENSG00000133114	ENSG00000133114			20298	protein-coding gene	gene with protein product			"KIAA1704"	KIAA1704		11214970	Standard	NM_018559		Approved	bA245H20.2, AD029, LSR7	uc001uzq.3	Q8IXQ4	OTTHUMG00000016841	ENST00000379151.4:c.971C>A	13.37:g.45602086C>A	ENSP00000368447:p.Ser324Tyr		44500086	A8K8X8|Q05BX8|Q05D87|Q5T3Z3|Q5T3Z5|Q9C0F9|Q9H2R0|Q9P0W6	Missense_Mutation	SNP	ENST00000379151.4	37	CCDS9394.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545404	0.86022	.	.	ENSG00000133114	ENST00000379151;ENST00000361121;ENST00000357537	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.83450	0.5257	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	D	0.84819	0.0795	9	0.87932	D	0	-13.4251	19.0819	0.93186	0.0:1.0:0.0:0.0	.	175;324	Q8IXQ4-2;Q8IXQ4	.;K1704_HUMAN	Y	324;324;154	.	ENSP00000350145:S154Y	S	+	2	0	KIAA1704	44500086	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.335000	0.79234	2.757000	0.94681	0.585000	0.79938	TCT		0.323	GPALPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044749.2	NM_018559		A	45602086	C	A	45602086	3	1	61	1	0	0	0	0	1	0	0	0	8273	913	32	2	1001	2	KIAA1704	13	45602086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	452741	45602086	69567792	8639	16624										
KCTD4	386618	broad.mit.edu	37	chr13	45768399	45768399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgattttctcgaaacccttCgggcaatagaagttctccat	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:45768399C>T	ENST00000379108.1	-	1	453	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K	GTF2F2_ENST00000340473.6_Intron|KCTD4_ENST00000405872.1_Missense_Mutation_p.E102K			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	102	BTB.				protein homooligomerization (GO:0051260)			p.E102K(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		CGAAACCCTTCGGGCAATAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	13											104	102	103					13																	45768399		2203	4300	6503	44666399	SO:0001583	missense	386618			BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.304G>A	13.37:g.45768399C>T	ENSP00000368402:p.Glu102Lys		44666399	Q5W0P9	Missense_Mutation	SNP	ENST00000379108.1	37	CCDS9396.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396005	0.83011	.	.	ENSG00000180332	ENST00000379108;ENST00000405872	T;T	0.76968	-1.06;-1.06	5.96	5.96	0.96718	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.052235	0.85682	D	0.000000	T	0.81245	0.4782	L	0.31065	0.9	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.80986	-0.1137	10	0.49607	T	0.09	.	19.3895	0.94574	0.0:1.0:0.0:0.0	.	102	Q8WVF5	KCTD4_HUMAN	K	102	ENSP00000368402:E102K;ENSP00000385144:E102K	ENSP00000368402:E102K	E	-	1	0	KCTD4	44666399	1.000000	0.71417	0.968000	0.41197	0.972000	0.66771	5.980000	0.70516	2.833000	0.97629	0.591000	0.81541	GAA		0.458	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			T	45768399	C	T	45768399	3	4	61	1	0	0	0	0	1	0	0	0	8132	893	31	1	479	1	KCTD4	13	45768399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166313	45768399	69401479	8640	16625										
GTF2F2	2963	broad.mit.edu	37	chr13	45781630	45781630	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccagtgaaaactacatgCgattaaaaaggttggtgttt	10	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:45781630C>T	ENST00000340473.6	+	5	517	c.376C>T	c.(376-378)Cga>Tga	p.R126*	GTF2F2_ENST00000494087.1_3'UTR	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	126					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)	p.R126*(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		AAACTACATGCGATTAAAAAG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											84	87	86					13																	45781630		2203	4300	6503	44679630	SO:0001587	stop_gained	2963			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342		"General transcription factors"	4653	protein-coding gene	gene with protein product		189969	"general transcription factor IIF, polypeptide 1 (74kD subunit)"			8162052	Standard	NM_004128		Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.376C>T	13.37:g.45781630C>T	ENSP00000340823:p.Arg126*		44679630	A6NNS5|Q5W0H3	Nonsense_Mutation	SNP	ENST00000340473.6	37	CCDS9395.1	.	.	.	.	.	.	.	.	.	.	C	36	5.716407	0.96830	.	.	ENSG00000188342	ENST00000340473	.	.	.	4.98	2.51	0.30379	.	0.326495	0.33144	N	0.005240	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-13.4925	10.9978	0.47587	0.5003:0.4997:0.0:0.0	.	.	.	.	X	126	.	ENSP00000340823:R126X	R	+	1	2	GTF2F2	44679630	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	2.159000	0.42339	0.323000	0.23307	-0.262000	0.10625	CGA		0.388	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044767.2	NM_004128		T	45781630	C	T	45781630	4	4	61	1	0	0	0	0	0	1	0	0	6880	760	27	1	394	1	GTF2F2	13	45781630	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13231	45781630	69388248	8641	16626										
SLC25A30	253512	broad.mit.edu	37	chr13	45971415	45971415	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatattccaaggaccaagtCtcaaccaatttggccaaaag	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:45971415C>A	ENST00000539591.1	-	8	822	c.659G>T	c.(658-660)aGa>aTa	p.R220I				Q5SVS4	KMCP1_HUMAN	solute carrier family 25, member 30	271					mitochondrial transport (GO:0006839)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.R271I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)		AGGACCAAGTCTCAACCAATT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	13											72	74	73					13																	45971415		2203	4300	6503	44869415	SO:0001583	missense	253512			AK074457	CCDS31967.1, CCDS66539.1	13q14	2013-05-22			ENSG00000174032	ENSG00000174032		"Solute carriers"	27371	protein-coding gene	gene with protein product		610793					Standard	XM_005266321		Approved		uc001vag.3	Q5SVS4	OTTHUMG00000016853	ENST00000539591.1:c.659G>T	13.37:g.45971415C>A	ENSP00000443542:p.Arg220Ile		44869415	B2RN96|B4DZK3|F5H8H8	Missense_Mutation	SNP	ENST00000539591.1	37		.	.	.	.	.	.	.	.	.	.	.	29.6	5.018949	0.93404	.	.	ENSG00000174032	ENST00000519676;ENST00000536510;ENST00000539591	D;D	0.81739	-1.53;-1.53	5.62	5.62	0.85841	Mitochondrial carrier domain (2);	0.154274	0.53938	D	0.000057	D	0.92306	0.7559	M	0.92077	3.27	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.93544	0.6880	10	0.87932	D	0	-34.8243	18.5744	0.91149	0.0:1.0:0.0:0.0	.	271	Q5SVS4	KMCP1_HUMAN	I	271;196;220	ENSP00000429168:R271I;ENSP00000443542:R220I	ENSP00000429168:R271I	R	-	2	0	SLC25A30	44869415	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.095000	0.76952	2.795000	0.96236	0.655000	0.94253	AGA		0.308	SLC25A30-201	KNOWN	basic	protein_coding	protein_coding		XM_170736		A	45971415	C	A	45971415	3	1	61	1	0	0	0	0	1	0	0	0	14531	913	32	2	71	2	SLC25A30	13	45971415	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	189785	45971415	69198463	8642	16627										
COG3	83548	broad.mit.edu	37	chr13	46050389	46050389	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcactgcccattgaactGacttcagtagtgcctgaatc	8	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46050389G>T	ENST00000349995.5	+	2	340	c.228G>T	c.(226-228)ctG>ctT	p.L76L		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	76					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.L76L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		CCATTGAACTGACTTCAGTAG	0.393																																					Ovarian(150;1048 1859 18083 21577 42700)											1	Substitution - coding silent(1)	large_intestine(1)	13											106	100	102					13																	46050389		2203	4300	6503	44948390	SO:0001819	synonymous_variant	83548			AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.228G>T	13.37:g.46050389G>T			44948390	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																				0.393	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46050389	G	T	46050389	2	4	61	1	0	0	0	0	0	0	0	1	3665	1277	45	2		2	COG3	13	46050389	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78974	46050389	69119489	8643	16628										
SPERT	220082	broad.mit.edu	37	chr13	46287329	46287329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccgcagaggggcacagccGaacccttcccgaggctccac	11	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46287329G>A	ENST00000310521.1	+	3	249	c.169G>A	c.(169-171)Gaa>Aaa	p.E57K	SPERT_ENST00000378966.3_Missense_Mutation_p.E21K	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	57						cytoplasmic membrane-bounded vesicle (GO:0016023)		p.E57K(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		GGGCACAGCCGAACCCTTCCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	13											21	21	21					13																	46287329		2201	4298	6499	45185330	SO:0001583	missense	220082			AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.169G>A	13.37:g.46287329G>A	ENSP00000309189:p.Glu57Lys		45185330	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247467	0.59103	.	.	ENSG00000174015	ENST00000310521;ENST00000533564;ENST00000378966	T;T	0.57752	0.39;0.38	5.1	5.1	0.69264	.	0.000000	0.48286	D	0.000181	T	0.63651	0.2529	L	0.40543	1.245	0.39134	D	0.961919	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.67601	-0.5629	10	0.87932	D	0	.	13.8953	0.63768	0.0:0.0:1.0:0.0	.	21;57	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	K	57;30;21	ENSP00000309189:E57K;ENSP00000368249:E21K	ENSP00000309189:E57K	E	+	1	0	SPERT	45185330	0.994000	0.37717	0.998000	0.56505	0.231000	0.25187	2.592000	0.46171	2.653000	0.90120	0.650000	0.86243	GAA		0.647	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46287329	G	A	46287329	3	1	61	1	0	0	0	0	1	0	0	0	15078	1059	37	1	179	1	SPERT	13	46287329	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236940	46287329	68882549	8644	16629										
SIAH3	283514	broad.mit.edu	37	chr13	46425654	46425654	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttgtgtgtggggttgacGacacagacaagttgcccggc	16	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46425654G>A	ENST00000400405.2	-	1	217	c.111C>T	c.(109-111)gtC>gtT	p.V37V		NM_198849.2	NP_942146.2	Q8IW03	SIAH3_HUMAN	siah E3 ubiquitin protein ligase family member 3	37					multicellular organismal development (GO:0007275)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.V37V(1)		large_intestine(3)|lung(7)|ovary(1)|skin(1)	12						TGGGGTTGACGACACAGACAA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	13											84	91	89					13																	46425654		1960	4162	6122	45323655	SO:0001819	synonymous_variant	283514				CCDS41883.1	13q14.12	2012-02-23	2012-02-23		ENSG00000215475	ENSG00000215475			30553	protein-coding gene	gene with protein product		615609	"seven in absentia homolog 3 (Drosophila)"			12477932	Standard	NM_198849		Approved	FLJ39203	uc001vap.3	Q8IW03	OTTHUMG00000016862	ENST00000400405.2:c.111C>T	13.37:g.46425654G>A			45323655	B7ZBP0|Q8N8M6	Silent	SNP	ENST00000400405.2	37	CCDS41883.1																																																																																				0.537	SIAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044788.2	NM_198849		A	46425654	G	A	46425654	2	1	61	1	0	0	0	0	0	0	0	1	14338	1045	37	1		1	SIAH3	13	46425654	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138325	46425654	68744224	8645	16630										
ZC3H13	23091	broad.mit.edu	37	chr13	46542124	46542124	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtcgatctgactctggaGaacttcttcttgaactatgg	9	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46542124G>T	ENST00000242848.4	-	15	4184	c.3836C>A	c.(3835-3837)tCt>tAt	p.S1279Y	ZC3H13_ENST00000378921.2_Missense_Mutation_p.S235Y|ZC3H13_ENST00000282007.3_Missense_Mutation_p.S1279Y			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1279	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S1279Y(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		TGACTCTGGAGAACTTCTTCT	0.393																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Missense(1)	large_intestine(1)	13											145	138	141					13																	46542124		2203	4300	6503	45440125	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3836C>A	13.37:g.46542124G>T	ENSP00000242848:p.Ser1279Tyr		45440125	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	17.58	3.425378	0.62733	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	T;T;T	0.55413	1.57;1.9;0.52	5.36	5.36	0.76844	.	0.000000	0.56097	D	0.000026	T	0.71099	0.3300	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.72636	-0.4233	10	0.72032	D	0.01	.	19.4559	0.94889	0.0:0.0:1.0:0.0	.	1279;1279	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	Y	1279;235;1279	ENSP00000242848:S1279Y;ENSP00000368201:S235Y;ENSP00000282007:S1279Y	ENSP00000242848:S1279Y	S	-	2	0	ZC3H13	45440125	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.979000	0.93455	2.669000	0.90835	0.591000	0.81541	TCT		0.393	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46542124	G	T	46542124	3	4	61	1	0	0	0	0	1	0	0	0	17604	942	33	2	870	2	ZC3H13	13	46542124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116470	46542124	68627754	8646	16631										
ZC3H13	23091	broad.mit.edu	37	chr13	46542898	46542898	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacctgaagaagtacttcGactgggttctccacgcttta	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46542898G>A	ENST00000242848.4	-	14	4129	c.3781C>T	c.(3781-3783)Cga>Tga	p.R1261*	ZC3H13_ENST00000378921.2_Nonsense_Mutation_p.R217*|ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.R1261*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1261	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1261*(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		GAAGTACTTCGACTGGGTTCT	0.343																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Nonsense(1)	large_intestine(1)	13											120	123	122					13																	46542898		2203	4300	6503	45440899	SO:0001587	stop_gained	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3781C>T	13.37:g.46542898G>A	ENSP00000242848:p.Arg1261*		45440899	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	46	12.202900	0.99646	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	.	.	.	5.44	4.58	0.56647	.	0.000000	0.50627	D	0.000117	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7476	0.77958	0.0:0.0:0.8622:0.1378	.	.	.	.	X	1261;217;1261	.	ENSP00000242848:R1261X	R	-	1	2	ZC3H13	45440899	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.214000	0.77958	1.403000	0.46800	0.591000	0.81541	CGA		0.343	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46542898	G	A	46542898	4	1	61	1	0	0	0	0	0	1	0	0	17604	1066	37	1	929	1	ZC3H13	13	46542898	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	774	46542898	68626980	8647	16632										
ZC3H13	23091	broad.mit.edu	37	chr13	46543093	46543093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtatgactacggttactccGattgctcccgaggctgctgc	11	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46543093G>A	ENST00000242848.4	-	14	3934	c.3586C>T	c.(3586-3588)Cgg>Tgg	p.R1196W	ZC3H13_ENST00000378921.2_Missense_Mutation_p.R152W|ZC3H13_ENST00000282007.3_Missense_Mutation_p.R1196W			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1196	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1196W(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		CGGTTACTCCGATTGCTCCCG	0.502																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Missense(1)	large_intestine(1)	13											180	169	173					13																	46543093		2203	4300	6503	45441094	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3586C>T	13.37:g.46543093G>A	ENSP00000242848:p.Arg1196Trp		45441094	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	15.24	2.776119	0.49786	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	T;T;T	0.35605	2.3;1.93;1.3	5.63	4.77	0.60923	.	0.000000	0.56097	D	0.000036	T	0.47229	0.1434	L	0.27053	0.805	0.46437	D	0.999044	D;D	0.89917	1.0;1.0	D;D	0.68765	0.913;0.96	T	0.52749	-0.8534	10	0.87932	D	0	.	16.1454	0.81562	0.0:0.0:0.8655:0.1345	.	1196;1196	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	W	1196;152;1196	ENSP00000242848:R1196W;ENSP00000368201:R152W;ENSP00000282007:R1196W	ENSP00000242848:R1196W	R	-	1	2	ZC3H13	45441094	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.937000	0.75898	1.485000	0.48380	0.655000	0.94253	CGG		0.502	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46543093	G	A	46543093	3	1	61	1	0	0	0	0	1	0	0	0	17604	1057	37	1	1124	1	ZC3H13	13	46543093	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	195	46543093	68626785	8648	16633										
ZC3H13	23091	broad.mit.edu	37	chr13	46562970	46562970	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactgtgaagttcgttcatGatcatgtctccctttctctc	7	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46562970G>T	ENST00000242848.4	-	9	1555	c.1207C>A	c.(1207-1209)Cat>Aat	p.H403N	ZC3H13_ENST00000282007.3_Missense_Mutation_p.H403N			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	403	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.H403N(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		GTTCGTTCATGATCATGTCTC	0.438																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Missense(1)	large_intestine(1)	13											154	132	140					13																	46562970		2203	4300	6503	45460971	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1207C>A	13.37:g.46562970G>T	ENSP00000242848:p.His403Asn		45460971	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	13.51	2.259108	0.39896	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	T;T	0.29917	2.57;1.55	5.81	5.81	0.92471	.	0.108387	0.40640	N	0.001049	T	0.19886	0.0478	N	0.19112	0.55	0.80722	D	1	B;P	0.41848	0.255;0.763	B;B	0.35770	0.073;0.21	T	0.02966	-1.1088	10	0.30854	T	0.27	.	14.8686	0.70437	0.0:0.0:0.8565:0.1435	.	403;403	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	N	403;403;219	ENSP00000242848:H403N;ENSP00000282007:H403N	ENSP00000242848:H403N	H	-	1	0	ZC3H13	45460971	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.504000	0.60414	2.738000	0.93877	0.655000	0.94253	CAT		0.438	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46562970	G	T	46562970	3	4	61	1	0	0	0	0	1	0	0	0	17604	1290	45	2	3523	2	ZC3H13	13	46562970	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19877	46562970	68606908	8649	16634										
CPB2	1361	broad.mit.edu	37	chr13	46632342	46632342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggtctttgcttttacttCgtgtataggaatatggaaac	9	6	1	0	rs376421547		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46632342C>T	ENST00000181383.4	-	9	987	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	CPB2_ENST00000439329.3_Missense_Mutation_p.R287Q|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606351.1_RNA|CPB2-AS1_ENST00000606991.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	324		Cleavage; by thrombin.			blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R324Q(1)		NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		GCTTTTACTTCGTGTATAGGA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	169	162	164		971,860	0.8	0.3	13		164	0,8600		0,0,4300	no	missense,missense	CPB2	NM_001872.3,NM_016413.3	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	324/424,287/361	46632342	1,13005	2203	4300	6503	45530343	SO:0001583	missense	1361			M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"thrombin-activatable fibrinolysis inhibitor", "carboxypeptidase U", "plasma carboxypeptidase B", "carboxypeptidase R"	603101	"carboxypeptidase B2 (plasma, carboxypeptidase U)"			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.971G>A	13.37:g.46632342C>T	ENSP00000181383:p.Arg324Gln		45530343	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	37	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	C	8.499	0.863906	0.17250	2.27E-4	0.0	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.11604	2.76;2.76	5.86	0.752	0.18398	Peptidase M14, carboxypeptidase A (2);	0.797322	0.12646	N	0.450853	T	0.09642	0.0237	L	0.45137	1.4	0.09310	N	1	D;B	0.56968	0.978;0.123	P;B	0.47299	0.543;0.009	T	0.20371	-1.0277	10	0.37606	T	0.19	.	1.0087	0.01492	0.178:0.356:0.1745:0.2915	.	287;324	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	Q	324;287	ENSP00000181383:R324Q;ENSP00000400714:R287Q	ENSP00000181383:R324Q	R	-	2	0	CPB2	45530343	0.000000	0.05858	0.312000	0.25196	0.009000	0.06853	-0.734000	0.04893	0.354000	0.24105	-1.105000	0.02106	CGA		0.328	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872		T	46632342	C	T	46632342	3	4	61	1	0	0	0	0	1	0	0	0	3803	884	31	1	312	1	CPB2	13	46632342	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69372	46632342	68537536	8650	16635										
C13orf18	80183	broad.mit.edu	37	chr13	46917591	46917591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgcacaccgggggcactCggaggactggaagcactgtt	14	13	0	0	rs374704916		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:46917591C>T	ENST00000429979.1	-	15	2522	c.1918G>A	c.(1918-1920)Gag>Aag	p.E640K	KIAA0226L_ENST00000378784.4_Missense_Mutation_p.E573K|KIAA0226L_ENST00000378781.3_3'UTR|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.E505K|KIAA0226L_ENST00000378797.2_Silent_p.P588P|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.E483K|KIAA0226L_ENST00000378787.3_Silent_p.P588P|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.E483K|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.E640K	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	640								p.E640K(1)		NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						CGGGGGCACTCGGAGGACTGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	74	68	70		1918	-5.6	0	13		70	0,8600		0,0,4300	no	missense	KIAA0226L	NM_025113.2	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	640/663	46917591	1,13005	2203	4300	6503	45815592	SO:0001583	missense	80183			AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 18"	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1918G>A	13.37:g.46917591C>T	ENSP00000396935:p.Glu640Lys		45815592	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	C	3.669	-0.067958	0.07228	2.27E-4	0.0	ENSG00000102445	ENST00000429979;ENST00000378784;ENST00000389908;ENST00000409879;ENST00000322896;ENST00000534925	T;T;T;T	0.43294	0.96;0.95;0.96;0.96	5.55	-5.64	0.02466	.	.	.	.	.	T	0.22666	0.0547	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.15141	0.012;0.012;0.004;0.003;0.002	B;B;B;B;B	0.11329	0.006;0.006;0.006;0.004;0.003	T	0.37596	-0.9699	9	0.07175	T	0.84	0.0897	7.4501	0.27234	0.0:0.2625:0.3537:0.3838	.	483;483;640;505;573	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3	.;.;K226L_HUMAN;.;.	K	640;573;640;483;483;505	ENSP00000396935:E640K;ENSP00000368061:E573K;ENSP00000374558:E640K;ENSP00000437501:E505K	ENSP00000315633:E483K	E	-	1	0	KIAA0226L	45815592	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.156000	0.03160	-1.978000	0.00993	-1.775000	0.00657	GAG		0.517	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		T	46917591	C	T	46917591	3	4	61	1	0	0	0	0	1	0	0	0	1724	893	31	1	74	1	C13orf18	13	46917591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	285249	46917591	68252287	8651	16636										
LRCH1	23143	broad.mit.edu	37	chr13	47243167	47243167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtattgtctttgcagtcGaaatcagctgtccgccctgc	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:47243167G>A	ENST00000389798.3	+	3	652	c.455G>A	c.(454-456)cGa>cAa	p.R152Q	LRCH1_ENST00000311191.6_Missense_Mutation_p.R152Q|LRCH1_ENST00000389797.3_Missense_Mutation_p.R152Q	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	152								p.R152Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CTTTGCAGTCGAAATCAGCTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											159	149	153					13																	47243167		2203	4300	6503	46141168	SO:0001583	missense	23143			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.455G>A	13.37:g.47243167G>A	ENSP00000374448:p.Arg152Gln		46141168	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	G	36	5.742636	0.96873	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.57273	0.41;0.41;0.41	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000001	T	0.55433	0.1920	N	0.05078	-0.115	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;1.0;0.896	D;D;D;P	0.91635	0.999;0.999;0.998;0.649	T	0.65183	-0.6230	10	0.54805	T	0.06	-23.2914	18.9909	0.92791	0.0:0.0:1.0:0.0	.	152;152;152;152	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	Q	152	ENSP00000308493:R152Q;ENSP00000374448:R152Q;ENSP00000374447:R152Q	ENSP00000308493:R152Q	R	+	2	0	LRCH1	46141168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.733000	0.93635	0.655000	0.94253	CGA		0.433	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		A	47243167	G	A	47243167	3	1	61	1	0	0	0	0	1	0	0	0	8961	1058	37	1	465	1	LRCH1	13	47243167	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325576	47243167	67926711	8652	16637										
HTR2A	3356	broad.mit.edu	37	chr13	47469874	47469874	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgagaggcacccttcacaGgaaaggttggttcgattttc	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:47469874G>T	ENST00000378688.4	-	1	299	c.168C>A	c.(166-168)tcC>tcA	p.S56S	HTR2A_ENST00000542664.1_Silent_p.S56S|HTR2A_ENST00000543956.1_Intron			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	56					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.S56S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCCTTCACAGGAAAGGTTGG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	13											119	115	116					13																	47469874		2203	4300	6503	46367875	SO:0001819	synonymous_variant	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.168C>A	13.37:g.47469874G>T			46367875	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Silent	SNP	ENST00000378688.4	37	CCDS9405.1																																																																																				0.443	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		T	47469874	G	T	47469874	2	4	61	1	0	0	0	0	0	0	0	1	7462	987	35	2		2	HTR2A	13	47469874	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226707	47469874	67700004	8653	16638										
HTR2A	3356	broad.mit.edu	37	chr13	47470013	47470013	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcgtagttgagctcaaaGaagtattttcttcacaaaga	8	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:47470013G>T	ENST00000378688.4	-	1	160	c.29C>A	c.(28-30)tCt>tAt	p.S10Y	HTR2A_ENST00000542664.1_Missense_Mutation_p.S10Y|HTR2A_ENST00000543956.1_Intron			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	10					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.S10Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGAGCTCAAAGAAGTATTTTC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											88	87	87					13																	47470013		2203	4300	6503	46368014	SO:0001583	missense	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.29C>A	13.37:g.47470013G>T	ENSP00000367959:p.Ser10Tyr		46368014	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.439827	0.63067	.	.	ENSG00000102468	ENST00000378688;ENST00000542664	T;T	0.58060	0.36;0.36	5.49	5.49	0.81192	.	0.092127	0.48286	D	0.000181	T	0.40094	0.1103	L	0.27053	0.805	0.37935	D	0.932146	B	0.25719	0.132	B	0.21917	0.037	T	0.44651	-0.9314	10	0.72032	D	0.01	.	11.7818	0.52020	0.0798:0.0:0.9202:0.0	.	10	P28223	5HT2A_HUMAN	Y	10	ENSP00000367959:S10Y;ENSP00000437737:S10Y	ENSP00000367959:S10Y	S	-	2	0	HTR2A	46368014	0.981000	0.34729	0.532000	0.27989	0.997000	0.91878	4.909000	0.63314	2.574000	0.86865	0.585000	0.79938	TCT		0.398	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		T	47470013	G	T	47470013	3	4	61	1	0	0	0	0	1	0	0	0	7462	942	33	2	1398	2	HTR2A	13	47470013	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139	47470013	67699865	8654	16639										
SUCLA2	8803	broad.mit.edu	37	chr13	48528637	48528637	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgtagatcaaagattttCttttggcgataggctgaatt	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48528637C>A	ENST00000378654.3	-	7	914	c.858G>T	c.(856-858)aaG>aaT	p.K286N	SUCLA2_ENST00000544100.1_Missense_Mutation_p.K152N|SUCLA2_ENST00000543413.1_Missense_Mutation_p.K228N|SUCLA2_ENST00000534875.1_Missense_Mutation_p.K228N	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	286	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)	p.K286N(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		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)	CAAAGATTTTCTTTTGGCGAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	75	75					13																	48528637		2203	4299	6502	47426638	SO:0001583	missense	8803			AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.858G>T	13.37:g.48528637C>A	ENSP00000367923:p.Lys286Asn		47426638	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Missense_Mutation	SNP	ENST00000378654.3	37	CCDS9406.1	.	.	.	.	.	.	.	.	.	.	c	17.87	3.496133	0.64186	.	.	ENSG00000136143	ENST00000378654;ENST00000378645;ENST00000378642;ENST00000331052;ENST00000544100;ENST00000534875;ENST00000543413;ENST00000541732;ENST00000434484;ENST00000433022	T;T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44;-0.44	5.67	4.82	0.62117	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.77212	0.4097	M	0.76170	2.325	0.80722	D	1	D	0.58970	0.984	P	0.56514	0.8	T	0.80612	-0.1305	10	0.72032	D	0.01	-12.7903	13.9116	0.63871	0.0:0.9266:0.0:0.0734	.	286	Q9P2R7	SUCB1_HUMAN	N	286;264;216;138;152;228;228;114;216;138	ENSP00000367923:K286N;ENSP00000443412:K152N;ENSP00000438182:K228N;ENSP00000441056:K228N;ENSP00000392771:K216N;ENSP00000415091:K138N	ENSP00000367898:K138N	K	-	3	2	SUCLA2	47426638	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.941000	0.40233	1.523000	0.49018	0.650000	0.86243	AAG		0.383	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1			A	48528637	C	A	48528637	3	1	61	1	0	0	0	0	1	0	0	0	15402	912	32	2	553	2	SUCLA2	13	48528637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1058624	48528637	66641241	8655	16640										
NUDT15	55270	broad.mit.edu	37	chr13	48615145	48615145	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgcctcagttgtgaattCtttcattgagaaggagaatt	9	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48615145C>A	ENST00000258662.2	+	2	428	c.248C>A	c.(247-249)tCt>tAt	p.S83Y		NM_018283.1	NP_060753.1	Q9NV35	NUD15_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 15	83	Interaction with PCNA.|Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				dGTP catabolic process (GO:0006203)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|metal ion binding (GO:0046872)	p.S83Y(2)		endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		GTTGTGAATTCTTTCATTGAG	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	13											73	70	71					13																	48615145		2203	4300	6503	47513146	SO:0001583	missense	55270				CCDS9407.1	13q14.12	2006-04-12			ENSG00000136159	ENSG00000136159		"Nudix motif containing"	23063	protein-coding gene	gene with protein product		615792				12767940	Standard	NM_018283		Approved	MTH2, FLJ10956	uc001vbw.1	Q9NV35	OTTHUMG00000016890	ENST00000258662.2:c.248C>A	13.37:g.48615145C>A	ENSP00000258662:p.Ser83Tyr		47513146	A2RUR6|Q32Q27|Q6P2C9	Missense_Mutation	SNP	ENST00000258662.2	37	CCDS9407.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.192240	0.78902	.	.	ENSG00000136159	ENST00000258662	T	0.12147	2.71	5.66	5.66	0.87406	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.052886	0.85682	D	0.000000	T	0.23289	0.0563	L	0.41027	1.25	0.58432	D	0.999997	D	0.55800	0.973	P	0.54174	0.744	T	0.00107	-1.2052	10	0.44086	T	0.13	-12.6931	17.2999	0.87180	0.0:1.0:0.0:0.0	.	83	Q9NV35	NUD15_HUMAN	Y	83	ENSP00000258662:S83Y	ENSP00000258662:S83Y	S	+	2	0	NUDT15	47513146	1.000000	0.71417	0.990000	0.47175	0.819000	0.46315	3.693000	0.54735	2.676000	0.91093	0.555000	0.69702	TCT		0.388	NUDT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044862.3	NM_018283		A	48615145	C	A	48615145	3	1	61	1	0	0	0	0	1	0	0	0	10762	913	32	2	254	2	NUDT15	13	48615145	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86508	48615145	66554733	8656	16641										
ITM2B	9445	broad.mit.edu	37	chr13	48830429	48830429	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgaagaaaatattaaaatCtttgaagaagaagaagttga	8	1	1	7			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48830429C>A	ENST00000378565.5	+	3	566	c.363C>A	c.(361-363)atC>atA	p.I121I	ITM2B_ENST00000378549.5_Intron	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	121	Necessary for interaction with APP and inhibitor effects on APP processing.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)	p.I121I(1)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		ATATTAAAATCTTTGAAGAAG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	13											79	80	80					13																	48830429		2203	4300	6503	47728430	SO:0001819	synonymous_variant	9445			AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.363C>A	13.37:g.48830429C>A			47728430	Q5W0A3|Q96B24|Q9NYH1	Silent	SNP	ENST00000378565.5	37	CCDS9409.1																																																																																				0.398	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		A	48830429	C	A	48830429	2	1	61	1	0	0	0	0	0	0	0	1	7934	903	32	2		2	ITM2B	13	48830429	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	215284	48830429	66339449	8657	16642										
ITM2B	9445	broad.mit.edu	37	chr13	48835313	48835313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcaattgtttcgcaattCggcattttgaaaacaaattt	6	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48835313C>T	ENST00000378565.5	+	6	957	c.754C>T	c.(754-756)Cgg>Tgg	p.R252W	ITM2B_ENST00000378549.5_Missense_Mutation_p.R146W	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	252					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)	p.R252W(1)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		TTTCGCAATTCGGCATTTTGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	13											54	59	57					13																	48835313		2203	4299	6502	47733314	SO:0001583	missense	9445			AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.754C>T	13.37:g.48835313C>T	ENSP00000367828:p.Arg252Trp		47733314	Q5W0A3|Q96B24|Q9NYH1	Missense_Mutation	SNP	ENST00000378565.5	37	CCDS9409.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460086	0.84317	.	.	ENSG00000136156	ENST00000378565;ENST00000378549	T;T	0.17213	2.29;2.29	5.84	5.84	0.93424	.	0.109133	0.64402	D	0.000005	T	0.40719	0.1128	M	0.79011	2.435	0.58432	D	0.999996	D	0.71674	0.998	P	0.56612	0.802	T	0.24333	-1.0163	10	0.87932	D	0	-13.1067	19.1228	0.93371	0.0:1.0:0.0:0.0	.	252	Q9Y287	ITM2B_HUMAN	W	252;146	ENSP00000367828:R252W;ENSP00000367811:R146W	ENSP00000367811:R146W	R	+	1	2	ITM2B	47733314	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.172000	0.77604	2.765000	0.95021	0.655000	0.94253	CGG		0.313	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		T	48835313	C	T	48835313	3	4	61	1	0	0	0	0	1	0	0	0	7934	875	31	1	776	1	ITM2B	13	48835313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4884	48835313	66334565	8658	16643										
RB1	5925	broad.mit.edu	37	chr13	48937070	48937070	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattgaagttctctgtaaaGaacatgaatgtaatatagat	7	3	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48937070G>T	ENST00000267163.4	+	8	976	c.838G>T	c.(838-840)Gaa>Taa	p.E280*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	280					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)|p.E280*(2)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCTCTGTAAAGAACATGAATG	0.333		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(6)|Substitution - Nonsense(2)	bone(11)|breast(5)|large_intestine(2)|eye(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13	GRCh37	CM025387	RB1	M							72	79	76					13																	48937070		2203	4300	6503	47835071	SO:0001587	stop_gained	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.838G>T	13.37:g.48937070G>T	ENSP00000267163:p.Glu280*		47835071	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.002411	0.93227	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	6.17	6.17	0.99709	.	0.052818	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5813	0.61905	0.0738:0.0:0.9262:0.0	.	.	.	.	X	259;280	.	.	E	+	1	0	RB1	47835071	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.641000	0.61375	2.941000	0.99782	0.655000	0.94253	GAA		0.333	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48937070	G	T	48937070	4	4	61	1	0	0	0	0	0	1	0	0	13135	943	33	2	868	2	RB1	13	48937070	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	101757	48937070	66232808	8659	16644										
RB1	5925	broad.mit.edu	37	chr13	48953748	48953748	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgatacaaacttggagttCgcttgtattaccgagtaatg	10	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48953748C>T	ENST00000267163.4	+	14	1489	c.1351C>T	c.(1351-1353)Cgc>Tgc	p.R451C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	451	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.R451C(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACTTGGAGTTCGCTTGTATTA	0.343		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	26	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(3)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											21	22	22					13																	48953748		2201	4300	6501	47851749	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1351C>T	13.37:g.48953748C>T	ENSP00000267163:p.Arg451Cys		47851749	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190230	0.78789	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.88277	-2.36	5.74	5.74	0.90152	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.140776	0.48286	D	0.000188	D	0.94135	0.8119	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93800	0.7100	10	0.59425	D	0.04	.	19.9145	0.97053	0.0:1.0:0.0:0.0	.	451	P06400	RB_HUMAN	C	430;451	ENSP00000267163:R451C	ENSP00000267163:R451C	R	+	1	0	RB1	47851749	0.999000	0.42202	1.000000	0.80357	0.980000	0.70556	4.397000	0.59690	2.707000	0.92482	0.557000	0.71058	CGC		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48953748	C	T	48953748	3	4	61	1	0	0	0	0	1	0	0	0	13135	884	31	1	1405	1	RB1	13	48953748	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16678	48953748	66216130	8660	16645										
LPAR6	10161	broad.mit.edu	37	chr13	48985559	48985559	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgtcaaatatcttacttTttaaggtctgtaggttatgc	7	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48985559T>G	ENST00000378434.4	-	7	2625	c.1001A>C	c.(1000-1002)aAa>aCa	p.K334T	RB1_ENST00000267163.4_Intron|LPAR6_ENST00000345941.2_Missense_Mutation_p.K334T	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	334						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)|p.K334T(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						TATCTTACTTTTTAAGGTCTG	0.358																																																20	Whole gene deletion(15)|Unknown(4)|Substitution - Missense(1)	bone(10)|breast(4)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											81	87	85					13																	48985559		2203	4300	6503	47883560	SO:0001583	missense	10161			AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.1001A>C	13.37:g.48985559T>G	ENSP00000367691:p.Lys334Thr		47883560	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	ENST00000378434.4	37	CCDS9410.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.867618	0.32977	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.64803	-0.12;-0.12	5.25	5.25	0.73442	.	0.193868	0.40469	N	0.001096	T	0.44973	0.1319	N	0.08118	0	0.53005	D	0.999965	P	0.43094	0.799	B	0.42692	0.395	T	0.43278	-0.9401	10	0.20046	T	0.44	.	15.45	0.75265	0.0:0.0:0.0:1.0	.	334	P43657	LPAR6_HUMAN	T	334	ENSP00000367691:K334T;ENSP00000344353:K334T	ENSP00000344353:K334T	K	-	2	0	LPAR6	47883560	1.000000	0.71417	0.998000	0.56505	0.534000	0.34807	4.805000	0.62561	2.104000	0.64026	0.374000	0.22700	AAA		0.358	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		G	48985559	T	G	48985559	3	3	61	1	0	0	0	0	1	0	0	0	8938	1841	64	4	37	4	LPAR6	13	48985559	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31811	48985559	66184319	8661	16646										
LPAR6	10161	broad.mit.edu	37	chr13	48985676	48985676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaattctgaattgtgtccGatgtaaagtagtaaactata	8	4	1	2	rs367788266		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48985676G>A	ENST00000378434.4	-	7	2508	c.884C>T	c.(883-885)tCg>tTg	p.S295L	RB1_ENST00000267163.4_Intron|LPAR6_ENST00000345941.2_Missense_Mutation_p.S295L	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)|p.S295L(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						AATTGTGTCCGATGTAAAGTA	0.378																																																20	Whole gene deletion(15)|Unknown(4)|Substitution - Missense(1)	bone(10)|breast(4)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											75	80	78					13																	48985676		2203	4300	6503	47883677	SO:0001583	missense	10161			AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.884C>T	13.37:g.48985676G>A	ENSP00000367691:p.Ser295Leu		47883677	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	ENST00000378434.4	37	CCDS9410.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.215812	0.58452	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.43294	0.95;0.95	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	N	0.08118	0	0.80722	D	1	P	0.43024	0.798	B	0.38458	0.274	T	0.13926	-1.0491	10	0.45353	T	0.12	.	19.8171	0.96573	0.0:0.0:1.0:0.0	.	295	P43657	LPAR6_HUMAN	L	295	ENSP00000367691:S295L;ENSP00000344353:S295L	ENSP00000344353:S295L	S	-	2	0	LPAR6	47883677	1.000000	0.71417	0.834000	0.33040	0.977000	0.68977	9.869000	0.99810	2.678000	0.91216	0.455000	0.32223	TCG		0.378	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		A	48985676	G	A	48985676	3	1	61	1	0	0	0	0	1	0	0	0	8938	1059	37	1	154	1	LPAR6	13	48985676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117	48985676	66184202	8662	16647										
LPAR6	10161	broad.mit.edu	37	chr13	48986518	48986518	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatacaaagtgtacttaaaGgagtcattatagaagcagtg	9	6	1	1	rs148227482	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:48986518G>T	ENST00000378434.4	-	7	1666	c.42C>A	c.(40-42)tcC>tcA	p.S14S	RB1_ENST00000267163.4_Intron|LPAR6_ENST00000345941.2_Silent_p.S14S	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)|p.S14S(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						TGTACTTAAAGGAGTCATTAT	0.423																																																20	Whole gene deletion(15)|Unknown(4)|Substitution - coding silent(1)	bone(10)|breast(4)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											96	91	93					13																	48986518		2203	4300	6503	47884519	SO:0001819	synonymous_variant	10161			AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.42C>A	13.37:g.48986518G>T			47884519	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Silent	SNP	ENST00000378434.4	37	CCDS9410.1																																																																																				0.423	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		T	48986518	G	T	48986518	2	4	61	1	0	0	0	0	0	0	0	1	8938	987	35	2		2	LPAR6	13	48986518	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	842	48986518	66183360	8663	16648										
FNDC3A	22862	broad.mit.edu	37	chr13	49742800	49742800	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actccttcagaggctgaaatCtttaccaccttgagctgtga	8	11	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:49742800C>A	ENST00000492622.2	+	10	1394	c.1089C>A	c.(1087-1089)atC>atA	p.I363I	FNDC3A_ENST00000541916.1_Silent_p.I363I|FNDC3A_ENST00000398316.3_Silent_p.I307I	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	363	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)	p.I363I(1)		endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		AGGCTGAAATCTTTACCACCT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											121	123	122					13																	49742800		2203	4300	6503	48640801	SO:0001819	synonymous_variant	22862			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.1089C>A	13.37:g.49742800C>A			48640801	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	37	CCDS41886.1																																																																																				0.373	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		A	49742800	C	A	49742800	2	1	61	1	0	0	0	0	0	0	0	1	5988	903	32	2		2	FNDC3A	13	49742800	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	756282	49742800	65427078	8664	16649										
FNDC3A	22862	broad.mit.edu	37	chr13	49772671	49772671	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagacattgtcaaccgattCtattcagtaccaccttcaga	5	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:49772671C>A	ENST00000492622.2	+	23	3253	c.2948C>A	c.(2947-2949)tCt>tAt	p.S983Y	FNDC3A_ENST00000541916.1_Missense_Mutation_p.S983Y|FNDC3A_ENST00000398316.3_Missense_Mutation_p.S927Y	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	983	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)	p.S983Y(1)		endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TCAACCGATTCTATTCAGTAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											119	105	110					13																	49772671		2203	4300	6503	48670672	SO:0001583	missense	22862			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.2948C>A	13.37:g.49772671C>A	ENSP00000417257:p.Ser983Tyr		48670672	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761540	0.49468	.	.	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.56103	0.48;0.48;0.48	6.06	6.06	0.98353	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.176419	0.39759	N	0.001271	T	0.46889	0.1416	L	0.45581	1.43	0.58432	D	0.999999	B;B	0.21225	0.053;0.033	B;B	0.25759	0.037;0.063	T	0.45026	-0.9289	10	0.02654	T	1	-11.3926	19.6279	0.95687	0.0:1.0:0.0:0.0	.	927;983	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	Y	983;919;983;927	ENSP00000417257:S983Y;ENSP00000441831:S983Y;ENSP00000381362:S927Y	ENSP00000338579:S919Y	S	+	2	0	FNDC3A	48670672	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.487000	0.81328	2.880000	0.98712	0.650000	0.86243	TCT		0.408	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		A	49772671	C	A	49772671	3	1	61	1	0	0	0	0	1	0	0	0	5988	913	32	2	3045	2	FNDC3A	13	49772671	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29871	49772671	65397207	8665	16650										
CDADC1	81602	broad.mit.edu	37	chr13	49841638	49841638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttcagctggagttaaccGaatttcatactggcctgctg	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:49841638G>A	ENST00000251108.6	+	5	556	c.443G>A	c.(442-444)cGa>cAa	p.R148Q	CDADC1_ENST00000444959.1_5'UTR	NM_001193478.1|NM_030911.3	NP_001180407.1|NP_112173.1	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	148							hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)	p.R148Q(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	16		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		GGAGTTAACCGAATTTCATAC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	13											71	71	71					13																	49841638		2203	4300	6503	48739639	SO:0001583	missense	81602			AY027525	CCDS9415.1	13q14.11	2008-02-05			ENSG00000102543	ENSG00000102543			20299	protein-coding gene	gene with protein product							Standard	NM_001193478		Approved	NYD-SP15	uc001vcu.3	Q9BWV3	OTTHUMG00000016913	ENST00000251108.6:c.443G>A	13.37:g.49841638G>A	ENSP00000251108:p.Arg148Gln		48739639	Q49A08|Q4G119|Q5TAW9|Q7Z764|Q9NT36	Missense_Mutation	SNP	ENST00000251108.6	37	CCDS9415.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962364	0.74016	.	.	ENSG00000102543	ENST00000251108	T	0.47869	0.83	5.53	5.53	0.82687	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.254542	0.37715	N	0.001961	T	0.53351	0.1791	L	0.52759	1.655	0.80722	D	1	D;P	0.59767	0.986;0.949	P;P	0.48400	0.576;0.495	T	0.57447	-0.7810	10	0.87932	D	0	-10.2974	18.8171	0.92081	0.0:0.0:1.0:0.0	.	148;148	Q9BWV3;B2R742	CDAC1_HUMAN;.	Q	148	ENSP00000251108:R148Q	ENSP00000251108:R148Q	R	+	2	0	CDADC1	48739639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.611000	0.61162	2.749000	0.94314	0.655000	0.94253	CGA		0.368	CDADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044902.2	NM_030911		A	49841638	G	A	49841638	3	1	61	1	0	0	0	0	1	0	0	0	3059	1058	37	1	461	1	CDADC1	13	49841638	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68967	49841638	65328240	8666	16651										
CAB39L	81617	broad.mit.edu	37	chr13	49957001	49957001	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaggattttcacaatttCtgctggatttttgtgtgatt	8	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:49957001C>A	ENST00000355854.4	-	2	543	c.46G>T	c.(46-48)Gaa>Taa	p.E16*	CAB39L_ENST00000410043.1_Nonsense_Mutation_p.E16*|CAB39L_ENST00000347776.5_Nonsense_Mutation_p.E16*|CAB39L_ENST00000409308.1_Nonsense_Mutation_p.E16*|CAB39L_ENST00000476943.1_5'UTR	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	16					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)		p.E16*(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		TTCACAATTTCTGCTGGATTT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											170	152	157					13																	49957001		1813	4075	5888	48855002	SO:0001587	stop_gained	81617			AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.46G>T	13.37:g.49957001C>A	ENSP00000348113:p.Glu16*		48855002	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Nonsense_Mutation	SNP	ENST00000355854.4	37	CCDS9416.2	.	.	.	.	.	.	.	.	.	.	C	38	7.200580	0.98132	.	.	ENSG00000102547	ENST00000355854;ENST00000347776;ENST00000378341;ENST00000409308;ENST00000410043;ENST00000457041;ENST00000413278;ENST00000409082	.	.	.	5.88	5.88	0.94601	.	0.046805	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.7128	19.2196	0.93791	0.0:1.0:0.0:0.0	.	.	.	.	X	16;16;13;16;16;16;16;16	.	.	E	-	1	0	CAB39L	48855002	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.327000	0.79147	2.789000	0.95967	0.591000	0.81541	GAA		0.308	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925		A	49957001	C	A	49957001	4	1	61	1	0	0	0	0	0	1	0	0	2532	922	32	2	999	2	CAB39L	13	49957001	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115363	49957001	65212877	8667	16652										
SETDB2	83852	broad.mit.edu	37	chr13	50050778	50050778	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctctgcagctgccaatcAaatgtcacttccaaagacga	6	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:50050778A>C	ENST00000317257.8	+	7	1333	c.508A>C	c.(508-510)Aaa>Caa	p.K170Q	SETDB2_ENST00000354234.4_Missense_Mutation_p.K158Q|SETDB2_ENST00000258672.5_Missense_Mutation_p.K158Q	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	170	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)	p.K170Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		GCTGCCAATCAAATGTCACTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											96	92	93					13																	50050778		2203	4300	6503	48948779	SO:0001583	missense	83852			AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"Chromatin-modifying enzymes / K-methyltransferases"	20263	protein-coding gene	gene with protein product		607865	"chromosome 13 open reading frame 4"	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.508A>C	13.37:g.50050778A>C	ENSP00000326477:p.Lys170Gln		48948779	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Missense_Mutation	SNP	ENST00000317257.8	37	CCDS9417.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887872	0.33348	.	.	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	D;D;D	0.99311	-5.73;-5.73;-5.73	5.96	2.03	0.26663	Methyl-CpG DNA binding (2);DNA-binding, integrase-type (1);	0.447241	0.26967	N	0.021592	D	0.94716	0.8295	N	0.03608	-0.345	0.20403	N	0.999906	P;P;P	0.44344	0.763;0.799;0.833	B;B;B	0.43508	0.229;0.297;0.422	D	0.92969	0.6396	10	0.13470	T	0.59	.	6.1774	0.20451	0.364:0.4088:0.0:0.2272	.	170;158;170	Q96T68-3;Q96T68-2;Q96T68	.;.;SETB2_HUMAN	Q	158;170;158	ENSP00000346175:K158Q;ENSP00000326477:K170Q;ENSP00000258672:K158Q	ENSP00000258672:K158Q	K	+	1	0	SETDB2	48948779	0.199000	0.23386	0.988000	0.46212	0.838000	0.47535	1.185000	0.32065	1.048000	0.40298	0.533000	0.62120	AAA		0.438	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915		C	50050778	A	C	50050778	3	2	61	1	0	0	0	0	1	0	0	0	14176	131	5	4	530	4	SETDB2	13	50050778	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	93777	50050778	65119100	8668	16653										
TRIM13	10206	broad.mit.edu	37	chr13	50586951	50586951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggaagacataaaactagTcgatgtggataaactttctt	10	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:50586951T>C	ENST00000378182.3	+	2	1613	c.875T>C	c.(874-876)gTc>gCc	p.V292A	KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000420995.2_Missense_Mutation_p.V292A|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000356017.4_Missense_Mutation_p.V295A|TRIM13_ENST00000298772.5_Missense_Mutation_p.V295A|TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000457662.2_Missense_Mutation_p.V292A	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	292					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V292A(1)		large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		ATAAAACTAGTCGATGTGGAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											173	183	180					13																	50586951		2203	4300	6503	49484952	SO:0001583	missense	10206			AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9976	protein-coding gene	gene with protein product		605661	"ret finger protein 2", "tripartite motif-containing 13"	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.875T>C	13.37:g.50586951T>C	ENSP00000367424:p.Val292Ala		49484952	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Missense_Mutation	SNP	ENST00000378182.3	37	CCDS9423.1	.	.	.	.	.	.	.	.	.	.	T	0.582	-0.836536	0.02692	.	.	ENSG00000204977	ENST00000420995;ENST00000378182;ENST00000356017;ENST00000457662;ENST00000298772	T;T;T;T;T	0.24350	1.86;1.86;2.4;1.86;2.4	5.75	5.75	0.90469	.	0.193579	0.43579	D	0.000548	T	0.15262	0.0368	N	0.24115	0.695	0.29215	N	0.874332	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.12967	-1.0527	9	.	.	.	-5.4112	7.2282	0.26028	0.0:0.0732:0.1472:0.7796	.	292;295	O60858;O60858-3	TRI13_HUMAN;.	A	292;292;295;292;295	ENSP00000412943:V292A;ENSP00000367424:V292A;ENSP00000348299:V295A;ENSP00000399206:V292A;ENSP00000298772:V295A	.	V	+	2	0	TRIM13	49484952	0.994000	0.37717	0.972000	0.41901	0.963000	0.63663	1.617000	0.36943	2.188000	0.69820	0.533000	0.62120	GTC		0.393	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278		C	50586951	T	C	50586951	3	2	61	1	0	0	0	0	1	0	0	0	16528	1667	58	4	890	4	TRIM13	13	50586951	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	536173	50586951	64582927	8669	16654										
TRIM13	10206	broad.mit.edu	37	chr13	50587237	50587237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttcaatgaaagattcaaGaattttactttggtggtact	7	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:50587237G>T	ENST00000378182.3	+	2	1899	c.1161G>T	c.(1159-1161)aaG>aaT	p.K387N	KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000420995.2_Missense_Mutation_p.K387N|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000356017.4_Missense_Mutation_p.K390N|TRIM13_ENST00000298772.5_Missense_Mutation_p.K390N|TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000457662.2_Missense_Mutation_p.K387N	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	387					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K387N(1)		large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		AAAGATTCAAGAATTTTACTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	13											85	93	91					13																	50587237		2203	4299	6502	49485238	SO:0001583	missense	10206			AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9976	protein-coding gene	gene with protein product		605661	"ret finger protein 2", "tripartite motif-containing 13"	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.1161G>T	13.37:g.50587237G>T	ENSP00000367424:p.Lys387Asn		49485238	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Missense_Mutation	SNP	ENST00000378182.3	37	CCDS9423.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.428106	0.25726	.	.	ENSG00000204977	ENST00000420995;ENST00000378182;ENST00000356017;ENST00000457662;ENST00000298772	T;T;T;T;T	0.28255	1.62;1.62;2.16;1.62;2.16	5.81	4.06	0.47325	.	0.249776	0.40908	D	0.001000	T	0.20251	0.0487	L	0.27053	0.805	0.34692	D	0.725879	B;B	0.25609	0.079;0.13	B;B	0.28849	0.044;0.095	T	0.22312	-1.0220	9	.	.	.	-6.5883	8.3216	0.32132	0.3026:0.0:0.6974:0.0	.	387;390	O60858;O60858-3	TRI13_HUMAN;.	N	387;387;390;387;390	ENSP00000412943:K387N;ENSP00000367424:K387N;ENSP00000348299:K390N;ENSP00000399206:K387N;ENSP00000298772:K390N	.	K	+	3	2	TRIM13	49485238	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	1.009000	0.29886	0.775000	0.33450	0.655000	0.94253	AAG		0.318	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278		T	50587237	G	T	50587237	3	4	61	1	0	0	0	0	1	0	0	0	16528	933	33	2	1176	2	TRIM13	13	50587237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	286	50587237	64582641	8670	16655										
FAM124A	220108	broad.mit.edu	37	chr13	51825727	51825727	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggcgtggatccaccccgAcctcccgctgttccgggtgt	12	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:51825727A>G	ENST00000322475.8	+	3	359	c.224A>G	c.(223-225)gAc>gGc	p.D75G	FAM124A_ENST00000280057.6_Missense_Mutation_p.D111G	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	75								p.D111G(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		ATCCACCCCGACCTCCCGCTG	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	13											18	17	18					13																	51825727		2201	4295	6496	50723728	SO:0001583	missense	220108			AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.224A>G	13.37:g.51825727A>G	ENSP00000324625:p.Asp75Gly		50723728	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.493646	0.64186	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.50001	0.76;0.76	5.79	4.61	0.57282	.	0.104679	0.64402	D	0.000006	T	0.54159	0.1841	M	0.61703	1.905	0.54753	D	0.999987	P;B;P	0.51351	0.944;0.197;0.51	P;B;B	0.50825	0.651;0.09;0.23	T	0.57556	-0.7791	10	0.87932	D	0	-5.3193	11.0341	0.47791	0.9275:0.0:0.0725:0.0	.	75;111;75	Q86V42;Q86V42-2;Q86V42-3	F124A_HUMAN;.;.	G	75;111	ENSP00000324625:D75G;ENSP00000280057:D111G	ENSP00000280057:D111G	D	+	2	0	FAM124A	50723728	1.000000	0.71417	0.744000	0.31058	0.753000	0.42808	6.916000	0.75776	1.022000	0.39626	-0.256000	0.11100	GAC		0.692	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		G	51825727	A	G	51825727	3	3	61	1	0	0	0	0	1	0	0	0	5441	275	10	4	346	4	FAM124A	13	51825727	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1238490	51825727	63344151	8671	16656										
INTS6	26512	broad.mit.edu	37	chr13	51950187	51950187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaactatgttctaaccttCgtcctgtcctttcagaaatc	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:51950187C>T	ENST00000311234.4	-	13	2198	c.1726G>A	c.(1726-1728)Gaa>Aaa	p.E576K	INTS6_ENST00000425000.1_Missense_Mutation_p.E144K|INTS6_ENST00000398119.2_Missense_Mutation_p.E563K|INTS6_ENST00000497989.1_Missense_Mutation_p.E398K|INTS6_ENST00000490542.1_Missense_Mutation_p.E260K|INTS6_ENST00000463928.1_Intron	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	576					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.E576K(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		TTCTAACCTTCGTCCTGTCCT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	13											80	79	79					13																	51950187		2203	4300	6503	50848188	SO:0001583	missense	26512			AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"DEAD-boxes"	14879	protein-coding gene	gene with protein product		604331	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.1726G>A	13.37:g.51950187C>T	ENSP00000310260:p.Glu576Lys		50848188	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	37	CCDS9428.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.010326	0.93346	.	.	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989;ENST00000425000;ENST00000490542	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.48	5.48	0.80851	.	0.157109	0.56097	D	0.000023	T	0.40767	0.1130	L	0.45698	1.435	0.80722	D	1	P	0.48162	0.906	B	0.41860	0.368	T	0.18745	-1.0327	10	0.31617	T	0.26	.	18.3392	0.90299	0.0:1.0:0.0:0.0	.	576	Q9UL03	INT6_HUMAN	K	576;563;398;144;260	ENSP00000310260:E576K;ENSP00000381187:E563K;ENSP00000419871:E398K;ENSP00000406915:E144K;ENSP00000419984:E260K	ENSP00000310260:E576K	E	-	1	0	INTS6	50848188	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.987000	0.49378	2.579000	0.87056	0.650000	0.86243	GAA		0.313	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		T	51950187	C	T	51950187	3	4	61	1	0	0	0	0	1	0	0	0	7803	893	31	1	961	1	INTS6	13	51950187	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124460	51950187	63219691	8672	16657										
INTS6	26512	broad.mit.edu	37	chr13	51961531	51961531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtacttactagtgttggCgaattttgatctggccaaaa	10	7	1	1	rs142545429		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:51961531C>T	ENST00000311234.4	-	7	1357	c.885G>A	c.(883-885)tcG>tcA	p.S295S	INTS6_ENST00000420668.2_3'UTR|INTS6_ENST00000425000.1_5'UTR|INTS6_ENST00000398119.2_Silent_p.S282S|INTS6_ENST00000497989.1_Silent_p.S117S|INTS6_ENST00000490542.1_5'Flank|INTS6_ENST00000463928.1_Intron	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	295					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.S295S(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		CTAGTGTTGGCGAATTTTGAT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	13						C	,	2,4404	4.2+/-10.8	0,2,2201	95	87	90		846,885	2.6	1	13	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	INTS6	NM_001039937.1,NM_012141.2	,	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	,	282/875,295/888	51961531	4,13002	2203	4300	6503	50859532	SO:0001819	synonymous_variant	26512			AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"DEAD-boxes"	14879	protein-coding gene	gene with protein product		604331	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.885G>A	13.37:g.51961531C>T			50859532	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Silent	SNP	ENST00000311234.4	37	CCDS9428.1																																																																																				0.378	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		T	51961531	C	T	51961531	2	4	61	1	0	0	0	0	0	0	0	1	7803	755	27	1		1	INTS6	13	51961531	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11344	51961531	63208347	8673	16658										
CCDC70	83446	broad.mit.edu	37	chr13	52439852	52439852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgggaaatggaaaagtCtttcagggaggaagagaaaa	13	4	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52439852C>A	ENST00000242819.4	+	2	634	c.338C>A	c.(337-339)tCt>tAt	p.S113Y		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	113						extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.S113Y(1)		breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		ATGGAAAAGTCTTTCAGGGAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	13											83	97	92					13																	52439852		2203	4300	6503	51337853	SO:0001583	missense	83446				CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.338C>A	13.37:g.52439852C>A	ENSP00000242819:p.Ser113Tyr		51337853	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	37	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	11.92	1.784037	0.31593	.	.	ENSG00000123171	ENST00000242819	T	0.42900	0.96	5.83	3.16	0.36331	.	0.632765	0.15607	N	0.253567	T	0.49712	0.1573	M	0.65975	2.015	0.09310	N	1	D	0.59767	0.986	P	0.54100	0.742	T	0.41324	-0.9515	10	0.72032	D	0.01	-12.9497	5.9485	0.19232	0.1365:0.6436:0.1447:0.0752	.	113	Q6NSX1	CCD70_HUMAN	Y	113	ENSP00000242819:S113Y	ENSP00000242819:S113Y	S	+	2	0	CCDC70	51337853	0.017000	0.18338	0.000000	0.03702	0.000000	0.00434	0.461000	0.21940	0.377000	0.24735	-0.181000	0.13052	TCT		0.468	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290		A	52439852	C	A	52439852	3	1	61	1	0	0	0	0	1	0	0	0	2849	913	32	2	340	2	CCDC70	13	52439852	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	478321	52439852	62730026	8674	16659										
ATP7B	540	broad.mit.edu	37	chr13	52549227	52549227	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatccagaccaccttcataGccaacattgtcaaaagcaaa	4	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52549227G>C	ENST00000242839.4	-	2	285	c.129C>G	c.(127-129)ggC>ggG	p.G43G	ATP7B_ENST00000448424.2_Silent_p.G43G|ATP7B_ENST00000400366.3_Silent_p.G43G|ATP7B_ENST00000542656.1_Silent_p.G11G|ATP7B_ENST00000400370.3_Silent_p.G43G|ATP7B_ENST00000482841.1_5'Flank|ATP7B_ENST00000418097.2_Silent_p.G43G|ATP7B_ENST00000344297.5_Silent_p.G43G	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	43					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)	p.G43G(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CACCTTCATAGCCAACATTGT	0.463									Wilson disease																																							1	Substitution - coding silent(1)	large_intestine(1)	13											100	101	101					13																	52549227		1971	4130	6101	51447228	SO:0001819	synonymous_variant	540	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.129C>G	13.37:g.52549227G>C			51447228	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	37	CCDS41892.1																																																																																				0.463	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		C	52549227	G	C	52549227	2	2	61	1	0	0	0	0	0	0	0	1	1192	958	34	5		5	ATP7B	13	52549227	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109375	52549227	62620651	8675	16660										
UTP14C	9724	broad.mit.edu	37	chr13	52603501	52603501	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcccctggagcaggaaatTtttaacctcctccataagaa	6	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52603501T>G	ENST00000521776.2	+	2	1294	c.561T>G	c.(559-561)atT>atG	p.I187M	ALG11_ENST00000521508.1_3'UTR|ALG11_ENST00000523764.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	187					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.I187M(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		AGCAGGAAATTTTTAACCTCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	76	76					13																	52603501		2203	4300	6503	51501502	SO:0001583	missense	9724			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.561T>G	13.37:g.52603501T>G	ENSP00000428619:p.Ile187Met		51501502	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.682710	0.47991	.	.	ENSG00000253797	ENST00000521776	T	0.26373	1.74	2.24	2.24	0.28232	.	0.260598	0.42964	D	0.000627	T	0.43787	0.1263	M	0.72118	2.19	0.36530	D	0.870685	D	0.67145	0.996	D	0.70227	0.968	T	0.53165	-0.8477	10	0.87932	D	0	-0.606	8.0157	0.30379	0.0:0.0:0.0:1.0	.	187	Q5TAP6	UT14C_HUMAN	M	187	ENSP00000428619:I187M	ENSP00000428619:I187M	I	+	3	3	UTP14C	51501502	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	1.275000	0.33144	1.043000	0.40175	0.368000	0.22195	ATT		0.527	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		G	52603501	T	G	52603501	3	3	61	1	0	0	0	0	1	0	0	0	17136	1829	64	4	563	4	UTP14C	13	52603501	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	54274	52603501	62566377	8676	16661										
UTP14C	9724	broad.mit.edu	37	chr13	52603942	52603942	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaacaaagaactgacacaGaaactccaggtagcctctga	8	10	1	5	rs370282802		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52603942G>T	ENST00000521776.2	+	2	1735	c.1002G>T	c.(1000-1002)caG>caT	p.Q334H		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	334					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.Q334H(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		AACTGACACAGAAACTCCAGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	13											106	104	105					13																	52603942		2203	4300	6503	51501943	SO:0001583	missense	9724			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.1002G>T	13.37:g.52603942G>T	ENSP00000428619:p.Gln334His		51501943	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	.	.	.	.	.	.	.	.	.	.	G	9.857	1.195311	0.22037	.	.	ENSG00000253797	ENST00000521776	T	0.19250	2.16	2.58	2.58	0.30949	.	0.263218	0.39020	N	0.001494	T	0.26593	0.0650	M	0.80028	2.48	0.47511	D	0.999443	B	0.22003	0.063	B	0.27076	0.076	T	0.09552	-1.0669	9	.	.	.	-22.2978	10.8649	0.46849	0.0:0.0:1.0:0.0	.	334	Q5TAP6	UT14C_HUMAN	H	334	ENSP00000428619:Q334H	.	Q	+	3	2	UTP14C	51501943	1.000000	0.71417	0.080000	0.20451	0.331000	0.28603	4.032000	0.57274	1.460000	0.47911	0.448000	0.29417	CAG		0.502	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		T	52603942	G	T	52603942	3	4	61	1	0	0	0	0	1	0	0	0	17136	933	33	2	1004	2	UTP14C	13	52603942	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	441	52603942	62565936	8677	16662										
UTP14C	9724	broad.mit.edu	37	chr13	52604655	52604655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtctccttccgtgaggtCtttggcagttcccacaataa	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52604655C>A	ENST00000521776.2	+	2	2448	c.1715C>A	c.(1714-1716)tCt>tAt	p.S572Y		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	572					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.S572Y(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		TCCGTGAGGTCTTTGGCAGTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	13											90	90	90					13																	52604655		2203	4300	6503	51502656	SO:0001583	missense	9724			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.1715C>A	13.37:g.52604655C>A	ENSP00000428619:p.Ser572Tyr		51502656	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109441	0.37242	.	.	ENSG00000253797	ENST00000521776	T	0.18657	2.2	2.9	2.03	0.26663	.	0.274140	0.42964	D	0.000628	T	0.44008	0.1273	M	0.87180	2.865	0.20196	N	0.999924	D	0.71674	0.998	D	0.71184	0.972	T	0.22836	-1.0205	9	.	.	.	-13.1265	5.9899	0.19454	0.0:0.8443:0.0:0.1557	.	572	Q5TAP6	UT14C_HUMAN	Y	572	ENSP00000428619:S572Y	.	S	+	2	0	UTP14C	51502656	0.003000	0.15002	0.972000	0.41901	0.734000	0.41952	0.732000	0.26072	0.549000	0.28973	0.455000	0.32223	TCT		0.478	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		A	52604655	C	A	52604655	3	1	61	1	0	0	0	0	1	0	0	0	17136	913	32	2	1717	2	UTP14C	13	52604655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	713	52604655	62565223	8678	16663										
UTP14C	9724	broad.mit.edu	37	chr13	52604761	52604761	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatgtcatcagagatttCttgaaagagaagagggaagc	13	4	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52604761C>T	ENST00000521776.2	+	2	2554	c.1821C>T	c.(1819-1821)ttC>ttT	p.F607F		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	607					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.F607F(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		TCAGAGATTTCTTGAAAGAGA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	13											80	87	85					13																	52604761		2203	4297	6500	51502762	SO:0001819	synonymous_variant	9724			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.1821C>T	13.37:g.52604761C>T			51502762	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	37	CCDS31978.1																																																																																				0.517	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		T	52604761	C	T	52604761	2	4	61	1	0	0	0	0	0	0	0	1	17136	912	32	3		3	UTP14C	13	52604761	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106	52604761	62565117	8679	16664										
NEK5	341676	broad.mit.edu	37	chr13	52682524	52682524	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgttccaatacaagttcGagcaagttccatggaactag	10	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52682524G>A	ENST00000355568.4	-	8	623	c.484C>T	c.(484-486)Cga>Tga	p.R162*		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	162	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R219*(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		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)		ATACAAGTTCGAGCAAGTTCC	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											120	115	117					13																	52682524		2203	4300	6503	51580525	SO:0001587	stop_gained	341676			BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)-related kinase 5"			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.484C>T	13.37:g.52682524G>A	ENSP00000347767:p.Arg162*		51580525	Q5TAP5	Nonsense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.368213	0.82463	.	.	ENSG00000197168	ENST00000355568	.	.	.	5.39	1.18	0.20946	.	0.676087	0.12574	N	0.457053	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8458	0.29424	0.1052:0.0:0.4307:0.4641	.	.	.	.	X	162	.	ENSP00000347767:R162X	R	-	1	2	NEK5	51580525	0.969000	0.33509	0.905000	0.35620	0.998000	0.95712	0.452000	0.21795	0.177000	0.19895	0.557000	0.71058	CGA		0.333	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		A	52682524	G	A	52682524	4	1	61	1	0	0	0	0	0	1	0	0	10358	1066	37	1	1702	1	NEK5	13	52682524	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77763	52682524	62487354	8680	16665										
NEK3	4752	broad.mit.edu	37	chr13	52725364	52725364	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggtacaagcaaatgccatCggactaaaaccataaaaagg	8	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:52725364C>T	ENST00000400357.2	-	6	1758	c.465G>A	c.(463-465)ccG>ccA	p.P155P	NEK3_ENST00000339406.3_Silent_p.P155P|NEK3_ENST00000452082.2_Silent_p.P176P|NEK3_ENST00000378101.2_Silent_p.P155P			P51956	NEK3_HUMAN	NIMA-related kinase 3	155	Interaction with VAV2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.P155P(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		CAAATGCCATCGGACTAAAAC	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	13											100	87	91					13																	52725364		1880	4113	5993	51623365	SO:0001819	synonymous_variant	4752			AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"serine/threonine-protein kinase NEK3", "phosphorylase B kinase kinase", "glycogen synthase A kinase", "hydroxyalkyl-protein kinase"	604044	"NIMA (never in mitosis gene a)-related kinase 3"			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.465G>A	13.37:g.52725364C>T			51623365	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Silent	SNP	ENST00000400357.2	37	CCDS53871.1																																																																																				0.373	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			T	52725364	C	T	52725364	2	4	61	1	0	0	0	0	0	0	0	1	10356	871	31	1		1	NEK3	13	52725364	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42840	52725364	62444514	8681	16666										
PCDH8	5100	broad.mit.edu	37	chr13	53418722	53418722	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcattggctcccttcttCggggacaggtacctgccagg	11	12	2	0	rs199906293		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:53418722C>T	ENST00000377942.3	-	3	3389	c.3186G>A	c.(3184-3186)ccG>ccA	p.P1062P	PCDH8_ENST00000338862.4_Silent_p.P965P	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	1062					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.P1062P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CTCCCTTCTTCGGGGACAGGT	0.552																																					GBM(36;25 841 9273 49207)											1	Substitution - coding silent(1)	large_intestine(1)	13						C	,	1,4405	2.1+/-5.4	0,1,2202	57	62	60		3186,2895	-5.8	0.9	13		60	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PCDH8	NM_002590.3,NM_032949.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	1062/1071,965/974	53418722	1,13005	2203	4300	6503	52316723	SO:0001819	synonymous_variant	5100			AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.3186G>A	13.37:g.53418722C>T			52316723	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Silent	SNP	ENST00000377942.3	37	CCDS9438.1																																																																																				0.552	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53418722	C	T	53418722	2	4	61	1	0	0	0	0	0	0	0	1	11548	871	31	1		1	PCDH8	13	53418722	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	693358	53418722	61751156	8682	16667										
PCDH17	27253	broad.mit.edu	37	chr13	58207197	58207197	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgcacctacctgctcacgCgcgacgatcacggcctcttt	8	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:58207197C>T	ENST00000377918.3	+	1	543	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	173	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R173C(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CCTGCTCACGCGCGACGATCA	0.652																																					Melanoma(72;952 1291 1619 12849 33676)											1	Substitution - Missense(1)	large_intestine(1)	13											36	37	37					13																	58207197		2203	4300	6503	57105198	SO:0001583	missense	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.517C>T	13.37:g.58207197C>T	ENSP00000367151:p.Arg173Cys		57105198	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041225	0.75732	.	.	ENSG00000118946	ENST00000377918	T	0.59906	0.23	4.95	4.95	0.65309	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	N	0.02721	-0.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.983;0.995	T	0.60885	-0.7174	9	.	.	.	.	18.3899	0.90479	0.0:1.0:0.0:0.0	.	173;173	O14917-2;O14917	.;PCD17_HUMAN	C	173	ENSP00000367151:R173C	.	R	+	1	0	PCDH17	57105198	1.000000	0.71417	0.996000	0.52242	0.925000	0.55904	4.291000	0.59025	2.589000	0.87451	0.650000	0.86243	CGC		0.652	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58207197	C	T	58207197	3	4	61	1	0	0	0	0	1	0	0	0	11543	768	27	1	519	1	PCDH17	13	58207197	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4788475	58207197	56962681	8683	16668										
PCDH17	27253	broad.mit.edu	37	chr13	58299275	58299275	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcattccagagccagccgGgattccagtgagatgggtgc	15	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:58299275G>T	ENST00000377918.3	+	4	3353	c.3327G>T	c.(3325-3327)cgG>cgT	p.R1109R		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1109					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1109R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GAGCCAGCCGGGATTCCAGTG	0.522																																					Melanoma(72;952 1291 1619 12849 33676)											1	Substitution - coding silent(1)	large_intestine(1)	13											158	160	159					13																	58299275		2203	4300	6503	57197276	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3327G>T	13.37:g.58299275G>T			57197276	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.522	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58299275	G	T	58299275	2	4	61	1	0	0	0	0	0	0	0	1	11543	1219	43	2		2	PCDH17	13	58299275	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92078	58299275	56870603	8684	16669										
TDRD3	81550	broad.mit.edu	37	chr13	61060050	61060050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgaaaagcaaaggacgGctgctattgctgaagttgca	11	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:61060050G>A	ENST00000196169.3	+	7	1194	c.406G>A	c.(406-408)Gct>Act	p.A136T	TDRD3_ENST00000377881.2_Missense_Mutation_p.A136T|TDRD3_ENST00000377894.2_Missense_Mutation_p.A136T|TDRD3_ENST00000535286.1_Missense_Mutation_p.A229T	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	136					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.A136T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GCAAAGGACGGCTGCTATTGC	0.338																																					Colon(36;164 906 35820 50723)											1	Substitution - Missense(1)	large_intestine(1)	13											88	82	84					13																	61060050		2202	4300	6502	59958051	SO:0001583	missense	81550			AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.406G>A	13.37:g.61060050G>A	ENSP00000196169:p.Ala136Thr		59958051	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	33	5.260836	0.95368	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.5	5.54	5.54	0.83059	.	0.052188	0.85682	D	0.000000	D	0.96654	0.8908	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.994;0.993	D	0.94812	0.7979	10	0.20046	T	0.44	-4.1563	19.5087	0.95132	0.0:0.0:1.0:0.0	.	229;135;136	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	T	136;136;136;229	ENSP00000196169:A136T;ENSP00000367113:A136T;ENSP00000367126:A136T;ENSP00000440190:A229T	ENSP00000196169:A136T	A	+	1	0	TDRD3	59958051	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.395000	0.97266	2.610000	0.88304	0.655000	0.94253	GCT		0.338	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61060050	G	A	61060050	3	1	61	1	0	0	0	0	1	0	0	0	15771	1203	42	3	711	3	TDRD3	13	61060050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2760775	61060050	54109828	8685	16670										
TDRD3	81550	broad.mit.edu	37	chr13	61141677	61141677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggaagaaggcacctacGatcaaactctggagttccgt	12	9	2	1	rs544622581		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:61141677G>A	ENST00000196169.3	+	13	2646	c.1858G>A	c.(1858-1860)Gat>Aat	p.D620N	TDRD3_ENST00000535286.1_Missense_Mutation_p.D713N|TDRD3_ENST00000377881.2_Missense_Mutation_p.D620N|TDRD3_ENST00000377894.2_Missense_Mutation_p.D620N	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	620					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.D620N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		AGGCACCTACGATCAAACTCT	0.448													G|||	1	0.000199681	8e-04	0	5008	,	,		14171	0		0	False		,,,				2504	0				Colon(36;164 906 35820 50723)											1	Substitution - Missense(1)	large_intestine(1)	13											77	69	71					13																	61141677		2203	4300	6503	60039678	SO:0001583	missense	81550			AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1858G>A	13.37:g.61141677G>A	ENSP00000196169:p.Asp620Asn		60039678	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.535226	0.64972	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.94417	-3.41;-3.41;-3.41;-3.42	6.17	4.45	0.53987	.	0.150682	0.64402	D	0.000012	D	0.90181	0.6931	N	0.14661	0.345	0.33554	D	0.596531	D;D;D	0.57899	0.98;0.975;0.981	P;P;P	0.48815	0.564;0.56;0.591	D	0.91980	0.5594	10	0.54805	T	0.06	-16.0429	10.9765	0.47469	0.0677:0.0:0.8024:0.1299	.	713;619;620	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	N	620;620;620;713	ENSP00000196169:D620N;ENSP00000367113:D620N;ENSP00000367126:D620N;ENSP00000440190:D713N	ENSP00000196169:D620N	D	+	1	0	TDRD3	60039678	1.000000	0.71417	0.950000	0.38849	0.916000	0.54674	6.885000	0.75606	0.932000	0.37266	0.655000	0.94253	GAT		0.448	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61141677	G	A	61141677	3	1	61	1	0	0	0	0	1	0	0	0	15771	1058	37	1	2187	1	TDRD3	13	61141677	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81627	61141677	54028201	8686	16671										
PCDH9	5101	broad.mit.edu	37	chr13	67800973	67800973	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaatgaatcgttcttgttCttctctgtcaaatactctgg	6	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:67800973C>T	ENST00000377865.2	-	1	1734	c.1600G>A	c.(1600-1602)Gaa>Aaa	p.E534K	PCDH9_ENST00000377861.3_Missense_Mutation_p.E534K|PCDH9_ENST00000456367.1_Missense_Mutation_p.E534K|PCDH9_ENST00000544246.1_Missense_Mutation_p.E534K|PCDH9_ENST00000328454.5_Missense_Mutation_p.E534K			Q9HC56	PCDH9_HUMAN	protocadherin 9	534	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E534K(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CGTTCTTGTTCTTCTCTGTCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	13											89	91	90					13																	67800973		2203	4300	6503	66698974	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1600G>A	13.37:g.67800973C>T	ENSP00000367096:p.Glu534Lys		66698974	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	8.608	0.888550	0.17540	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	6.08	6.08	0.98989	Cadherin (4);Cadherin-like (1);	0.049677	0.85682	D	0.000000	T	0.32675	0.0837	N	0.05510	-0.035	0.80722	D	1	B;B;B;B	0.11235	0.004;0.001;0.001;0.002	B;B;B;B	0.14023	0.01;0.006;0.004;0.006	T	0.10291	-1.0636	10	0.23302	T	0.38	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	534;534;534;534	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	K	534	ENSP00000442186:E534K;ENSP00000367096:E534K;ENSP00000401699:E534K;ENSP00000332060:E534K;ENSP00000367092:E534K	ENSP00000332060:E534K	E	-	1	0	PCDH9	66698974	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.089000	0.71384	2.894000	0.99253	0.655000	0.94253	GAA		0.453	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67800973	C	T	67800973	3	4	61	1	0	0	0	0	1	0	0	0	11549	922	32	3	2129	3	PCDH9	13	67800973	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6659296	67800973	47368905	8687	16672										
PCDH9	5101	broad.mit.edu	37	chr13	67801368	67801368	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggacctctctttcaataAaacagatcactttgccattc	5	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:67801368A>C	ENST00000377865.2	-	1	1339	c.1205T>G	c.(1204-1206)tTt>tGt	p.F402C	PCDH9_ENST00000377861.3_Missense_Mutation_p.F402C|PCDH9_ENST00000456367.1_Missense_Mutation_p.F402C|PCDH9_ENST00000544246.1_Missense_Mutation_p.F402C|PCDH9_ENST00000328454.5_Missense_Mutation_p.F402C			Q9HC56	PCDH9_HUMAN	protocadherin 9	402	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F402C(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TCTTTCAATAAAACAGATCAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	13											95	91	93					13																	67801368		2203	4300	6503	66699369	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1205T>G	13.37:g.67801368A>C	ENSP00000367096:p.Phe402Cys		66699369	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.034658	0.35893	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72211	0.3432	M	0.83012	2.62	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.984;0.992;0.993;0.996	T	0.75139	-0.3423	10	0.56958	D	0.05	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	402;402;402;402	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	C	402	ENSP00000442186:F402C;ENSP00000367096:F402C;ENSP00000401699:F402C;ENSP00000332060:F402C;ENSP00000367092:F402C	ENSP00000332060:F402C	F	-	2	0	PCDH9	66699369	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.327000	0.79147	2.371000	0.80710	0.533000	0.62120	TTT		0.388	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		C	67801368	A	C	67801368	3	2	61	1	0	0	0	0	1	0	0	0	11549	14	1	4	2524	4	PCDH9	13	67801368	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	395	67801368	47368510	8688	16673										
C13orf34	79866	broad.mit.edu	37	chr13	73305523	73305523	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttatacttaagtcattcTcggtaagttttcctttcttg	6	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:73305523T>C	ENST00000390667.5	+	3	355	c.258T>C	c.(256-258)tcT>tcC	p.S86S	BORA_ENST00000464754.1_3'UTR|BORA_ENST00000377815.3_Intron	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	86					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)	p.S86S(1)									TAAGTCATTCTCGGTAAGTTT	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	13											101	93	95					13																	73305523		1815	4075	5890	72203524	SO:0001819	synonymous_variant	79866			BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"chromosome 13 open reading frame 34"	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.258T>C	13.37:g.73305523T>C			72203524	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Silent	SNP	ENST00000390667.5	37	CCDS9446.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.392180	0.42410	.	.	ENSG00000136122	ENST00000377814	T	0.47528	0.84	5.86	1.97	0.26223	.	0.099394	0.64402	D	0.000002	T	0.39517	0.1081	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18398	-1.0338	7	0.33940	T	0.23	-24.5517	1.4822	0.02439	0.1515:0.1231:0.315:0.4104	.	.	.	.	P	64	ENSP00000367045:S64P	ENSP00000367045:S64P	S	+	1	0	BORA	72203524	0.954000	0.32549	1.000000	0.80357	0.996000	0.88848	-0.038000	0.12144	0.506000	0.28125	0.528000	0.53228	TCG		0.338	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808		C	73305523	T	C	73305523	2	2	61	1	0	0	0	0	0	0	0	1	1732	1538	54	4		4	C13orf34	13	73305523	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5504155	73305523	41864355	8689	16674										
DIS3	22894	broad.mit.edu	37	chr13	73347916	73347916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctggtttctatgcgaattCgagggattctcttatcagca	10	8	4	0	rs139907646		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:73347916C>T	ENST00000377767.4	-	8	1245	c.1145G>A	c.(1144-1146)cGa>cAa	p.R382Q	DIS3_ENST00000377780.4_Missense_Mutation_p.R352Q|DIS3_ENST00000545453.1_Missense_Mutation_p.R220Q	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	382					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)	p.R382Q(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		TATGCGAATTCGAGGGATTCT	0.383										Multiple Myeloma(4;0.011)			C|||	1	0.000199681	0	0	5008	,	,		14678	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	13						C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	102	99	100		1055,1145	5.4	1	13	dbSNP_134	100	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	43,43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	352/929,382/959	73347916	3,13003	2203	4300	6503	72245917	SO:0001583	missense	22894			AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1145G>A	13.37:g.73347916C>T	ENSP00000366997:p.Arg382Gln		72245917	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	C	37	5.984270	0.97173	0.0	3.49E-4	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.29655	1.56;1.56;1.56	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.55321	0.1913	M	0.74546	2.27	0.80722	D	1	D;D	0.64830	0.994;0.989	P;P	0.61070	0.883;0.767	T	0.56768	-0.7924	10	0.59425	D	0.04	.	19.6384	0.95746	0.0:1.0:0.0:0.0	.	352;382	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	Q	382;352;220	ENSP00000366997:R382Q;ENSP00000367011:R352Q;ENSP00000440058:R220Q	ENSP00000366997:R382Q	R	-	2	0	DIS3	72245917	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.674000	0.68117	2.703000	0.92315	0.655000	0.94253	CGA		0.383	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		T	73347916	C	T	73347916	3	4	61	1	0	0	0	0	1	0	0	0	4546	884	31	1	1787	1	DIS3	13	73347916	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42393	73347916	41821962	8690	16675										
TBC1D4	9882	broad.mit.edu	37	chr13	75861108	75861108	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttcattttggtctctctCgtcaaaagattttccaggtt	7	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:75861108C>T	ENST00000377636.3	-	21	4063	c.3717G>A	c.(3715-3717)acG>acA	p.T1239T	TBC1D4_ENST00000431480.2_Silent_p.T1231T|TBC1D4_ENST00000377625.2_Silent_p.T1176T|TBC1D4_ENST00000425511.1_Silent_p.T403T	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1239					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.T1239T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TGGTCTCTCTCGTCAAAAGAT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	13											121	114	116					13																	75861108		1814	4082	5896	74759109	SO:0001819	synonymous_variant	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3717G>A	13.37:g.75861108C>T			74759109	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																				0.433	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	75861108	C	T	75861108	2	4	61	1	0	0	0	0	0	0	0	1	15661	871	31	1		1	TBC1D4	13	75861108	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2513192	75861108	39308770	8691	16676										
TBC1D4	9882	broad.mit.edu	37	chr13	75898521	75898521	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctccttgtacatgcgtcGaactgacgaaagattgctga	9	10	1	3	rs61736969	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:75898521G>A	ENST00000377636.3	-	11	2396	c.2050C>T	c.(2050-2052)Cga>Tga	p.R684*	TBC1D4_ENST00000431480.2_Nonsense_Mutation_p.R684*|TBC1D4_ENST00000377625.2_Intron|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	684	Ser-rich.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.R684*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TACATGCGTCGAACTGACGAA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											102	105	104					13																	75898521		1878	4111	5989	74796522	SO:0001587	stop_gained	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2050C>T	13.37:g.75898521G>A	ENSP00000366863:p.Arg684*		74796522	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Nonsense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	G	44	10.749347	0.99460	.	.	ENSG00000136111	ENST00000377636;ENST00000431480	.	.	.	5.47	4.61	0.57282	.	0.431976	0.19338	N	0.116720	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-8.6451	16.3903	0.83532	0.0:0.1316:0.8684:0.0	.	.	.	.	X	684	.	ENSP00000366863:R684X	R	-	1	2	TBC1D4	74796522	1.000000	0.71417	0.916000	0.36221	0.984000	0.73092	2.755000	0.47540	1.293000	0.44690	0.650000	0.86243	CGA		0.388	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		A	75898521	G	A	75898521	4	1	61	1	0	0	0	0	0	1	0	0	15661	1066	37	1	1890	1	TBC1D4	13	75898521	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37413	75898521	39271357	8692	16677										
TBC1D4	9882	broad.mit.edu	37	chr13	75933935	75933935	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagatatctttaaaattCttttctagcacaactgattt	6	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:75933935C>A	ENST00000377636.3	-	3	1486	c.1140G>T	c.(1138-1140)aaG>aaT	p.K380N	TBC1D4_ENST00000431480.2_Missense_Mutation_p.K380N|TBC1D4_ENST00000377625.2_Missense_Mutation_p.K380N|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	380	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.K380N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		CTTTAAAATTCTTTTCTAGCA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	13											72	71	71					13																	75933935		1800	4067	5867	74831936	SO:0001583	missense	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.1140G>T	13.37:g.75933935C>A	ENSP00000366863:p.Lys380Asn		74831936	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	C	32	5.143726	0.94603	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.19532	2.14;2.14;2.14	5.86	5.86	0.93980	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.64402	D	0.000001	T	0.51924	0.1703	M	0.77486	2.375	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.50423	-0.8830	10	0.87932	D	0	-39.2984	20.5632	0.99335	0.0:1.0:0.0:0.0	.	380;380;380	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	N	380	ENSP00000366863:K380N;ENSP00000395986:K380N;ENSP00000366852:K380N	ENSP00000366852:K380N	K	-	3	2	TBC1D4	74831936	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.065000	0.57513	2.937000	0.99478	0.650000	0.86243	AAG		0.303	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		A	75933935	C	A	75933935	3	1	61	1	0	0	0	0	1	0	0	0	15661	912	32	2	2832	2	TBC1D4	13	75933935	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35414	75933935	39235943	8693	16678										
UCHL3	7347	broad.mit.edu	37	chr13	76141439	76141439	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgagccagatacctggaGaactatgatgtcggtacctt	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:76141439G>T	ENST00000377595.3	+	5	447	c.417G>T	c.(415-417)gaG>gaT	p.E139D	RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	139					protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E139D(1)		kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		GATACCTGGAGAACTATGATG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	13											134	132	133					13																	76141439		2203	4300	6503	75039440	SO:0001583	missense	7347			M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.417G>T	13.37:g.76141439G>T	ENSP00000366819:p.Glu139Asp		75039440	B2R970|Q5TBK8|Q6IBE9	Missense_Mutation	SNP	ENST00000377595.3	37	CCDS9453.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165342	0.57476	.	.	ENSG00000118939	ENST00000377595;ENST00000377589;ENST00000419068	T;T	0.56611	0.45;0.45	6.08	4.12	0.48240	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.098362	0.64402	D	0.000001	T	0.53142	0.1778	M	0.86178	2.8	0.58432	D	0.999991	P	0.37663	0.604	B	0.38156	0.266	T	0.59762	-0.7393	10	0.59425	D	0.04	-16.0933	4.5467	0.12085	0.4112:0.0:0.5888:0.0	.	139	P15374	UCHL3_HUMAN	D	139;96;73	ENSP00000366819:E139D;ENSP00000398189:E73D	ENSP00000366813:E96D	E	+	3	2	UCHL3	75039440	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.179000	0.42528	1.586000	0.49944	0.655000	0.94253	GAG		0.403	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002		T	76141439	G	T	76141439	3	4	61	1	0	0	0	0	1	0	0	0	16961	933	33	2	435	2	UCHL3	13	76141439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	207504	76141439	39028439	8694	16679										
LMO7	4008	broad.mit.edu	37	chr13	76374929	76374929	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctccaaggcaccataagaGagaagattcctttgaaagct	8	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:76374929G>T	ENST00000341547.4	+	8	1988	c.728G>T	c.(727-729)aGa>aTa	p.R243I	LMO7_ENST00000526202.1_Missense_Mutation_p.R152I|LMO7_ENST00000357063.3_Missense_Mutation_p.R243I|LMO7_ENST00000377534.3_Missense_Mutation_p.R243I|LMO7_ENST00000465261.2_5'UTR|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000321797.8_5'UTR	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	243					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R243I(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CACCATAAGAGAGAAGATTCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	13											152	154	153					13																	76374929		2203	4300	6503	75272930	SO:0001583	missense	4008			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.728G>T	13.37:g.76374929G>T	ENSP00000342112:p.Arg243Ile		75272930	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	37	CCDS9454.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437578	0.96168	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000526202	T;T;T;T;T	0.55588	1.12;0.84;0.85;0.59;0.51	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.74535	0.3729	M	0.75777	2.31	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.982	D;D;P	0.79108	0.986;0.992;0.73	T	0.75903	-0.3153	10	0.87932	D	0	-19.641	20.089	0.97809	0.0:0.0:1.0:0.0	.	152;243;191	E9PMS6;Q8WWI1-3;F8J2B5	.;.;.	I	243;243;243;191;152	ENSP00000342112:R243I;ENSP00000349571:R243I;ENSP00000366757:R243I;ENSP00000366719:R191I;ENSP00000431129:R152I	ENSP00000342112:R243I	R	+	2	0	LMO7	75272930	1.000000	0.71417	0.962000	0.40283	0.868000	0.49771	6.102000	0.71486	2.765000	0.95021	0.591000	0.81541	AGA		0.512	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358		T	76374929	G	T	76374929	3	4	61	1	0	0	0	0	1	0	0	0	8879	942	33	2	758	2	LMO7	13	76374929	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	233490	76374929	38794949	8695	16680										
LMO7	4008	broad.mit.edu	37	chr13	76379723	76379723	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcaaagacaagaagcatAcccaacattgtaaaggatga	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:76379723A>G	ENST00000321797.8	+	7	1045	c.324A>G	c.(322-324)atA>atG	p.I108M	LMO7_ENST00000526202.1_Intron|LMO7_ENST00000357063.3_Missense_Mutation_p.I393M|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000377534.3_Missense_Mutation_p.I393M|LMO7_ENST00000465261.2_Missense_Mutation_p.I108M|RP11-29G8.3_ENST00000563635.1_RNA			Q8WWI1	LMO7_HUMAN	LIM domain 7	393	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I393M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CAAGAAGCATACCCAACATTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	13											278	248	257					13																	76379723		1568	3582	5150	75277724	SO:0001583	missense	4008			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.324A>G	13.37:g.76379723A>G	ENSP00000317802:p.Ile108Met		75277724	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	A	7.517	0.655916	0.14580	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261;ENST00000526371	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.93	-7.47	0.01365	.	1.031100	0.07598	N	0.923227	T	0.19765	0.0475	N	0.04203	-0.255	0.09310	N	0.999999	B	0.14438	0.01	B	0.11329	0.006	T	0.11567	-1.0582	10	0.30854	T	0.27	0.1788	0.7144	0.00929	0.2258:0.2293:0.2896:0.2553	.	108	E9PLH4	.	M	393;393;108;108;108	ENSP00000349571:I393M;ENSP00000366757:I393M;ENSP00000317802:I108M;ENSP00000433352:I108M;ENSP00000432269:I108M	ENSP00000317802:I108M	I	+	3	3	LMO7	75277724	0.000000	0.05858	0.003000	0.11579	0.770000	0.43624	-2.144000	0.01296	-0.835000	0.04234	0.460000	0.39030	ATA		0.448	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		G	76379723	A	G	76379723	3	3	61	1	0	0	0	0	1	0	0	0	8879	381	14	4	1217	4	LMO7	13	76379723	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4794	76379723	38790155	8696	16681										
KCTD12	115207	broad.mit.edu	37	chr13	77459446	77459446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcggacagcttgtcgaaggCctgctccaggaagttgaact	12	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77459446C>T	ENST00000377474.2	-	1	1079	c.838G>A	c.(838-840)Gcc>Acc	p.A280T	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Missense_Mutation_p.A280T	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	280					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)	p.A280T(1)		kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		TTGTCGAAGGCCTGCTCCAGG	0.632											OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	13											48	41	43					13																	77459446		2203	4300	6503	76357447	SO:0001583	missense	115207			AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"predominantly fetal expressed T1 domain"	610521	"chromosome 13 open reading frame 2", "potassium channel tetramerisation domain containing 12"	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.838G>A	13.37:g.77459446C>T	ENSP00000366694:p.Ala280Thr	1175	76357447		Missense_Mutation	SNP	ENST00000377474.2	37	CCDS9455.1	.	.	.	.	.	.	.	.	.	.	C	33	5.227797	0.95173	.	.	ENSG00000178695	ENST00000377474;ENST00000317765	T;T	0.64085	-0.08;-0.08	4.84	4.84	0.62591	.	0.049892	0.85682	N	0.000000	T	0.80093	0.4560	M	0.78285	2.405	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82772	-0.0292	10	0.66056	D	0.02	.	17.9207	0.88965	0.0:1.0:0.0:0.0	.	280	Q96CX2	KCD12_HUMAN	T	280	ENSP00000366694:A280T;ENSP00000317141:A280T	ENSP00000317141:A280T	A	-	1	0	KCTD12	76357447	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.582000	0.82546	2.399000	0.81585	0.462000	0.41574	GCC		0.632	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444		T	77459446	C	T	77459446	3	4	61	1	0	0	0	0	1	0	0	0	8120	739	26	3	143	3	KCTD12	13	77459446	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1079723	77459446	37710432	8697	16682										
FBXL3	26224	broad.mit.edu	37	chr13	77581687	77581687	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcttcttcatataaaaAaaaatacatcactaagttca	1	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77581687A>C	ENST00000355619.5	-	5	1204	c.880T>G	c.(880-882)Ttt>Gtt	p.F294V	FBXL3_ENST00000477982.1_Intron	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	294					entrainment of circadian clock by photoperiod (GO:0043153)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.F294V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		TCATATAAAAAAAAATACATC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	13											72	73	73					13																	77581687		2203	4300	6503	76479688	SO:0001583	missense	26224			AF129532	CCDS9457.1	13q22	2011-06-09	2004-07-20	2004-07-21	ENSG00000005812	ENSG00000005812		"F-boxes / Leucine-rich repeats"	13599	protein-coding gene	gene with protein product		605653	"F-box and leucine-rich repeat protein 3A"	FBXL3A		10531035, 10828603	Standard	NM_012158		Approved	FBL3, FBL3A	uc001vkd.3	Q9UKT7	OTTHUMG00000017099	ENST00000355619.5:c.880T>G	13.37:g.77581687A>C	ENSP00000347834:p.Phe294Val		76479688	B2RB04|Q9P122	Missense_Mutation	SNP	ENST00000355619.5	37	CCDS9457.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211739	0.58452	.	.	ENSG00000005812	ENST00000355619	T	0.21361	2.01	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.42743	0.1216	M	0.66939	2.045	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.15464	-1.0436	10	0.15952	T	0.53	-24.2553	16.8222	0.85835	1.0:0.0:0.0:0.0	.	294	Q9UKT7	FBXL3_HUMAN	V	294	ENSP00000347834:F294V	ENSP00000347834:F294V	F	-	1	0	FBXL3	76479688	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	TTT		0.413	FBXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045312.3			C	77581687	A	C	77581687	3	2	61	1	0	0	0	0	1	0	0	0	5739	14	1	4	410	4	FBXL3	13	77581687	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	122241	77581687	37588191	8698	16683										
FBXL3	26224	broad.mit.edu	37	chr13	77589659	77589659	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtatcatctatcttaagCgaagacagggatttggagtt	12	5	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77589659C>T	ENST00000355619.5	-	4	852	c.528G>A	c.(526-528)tcG>tcA	p.S176S	FBXL3_ENST00000477982.1_5'UTR	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	176					entrainment of circadian clock by photoperiod (GO:0043153)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.S176S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		CTATCTTAAGCGAAGACAGGG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	13											127	115	119					13																	77589659		2203	4300	6503	76487660	SO:0001819	synonymous_variant	26224			AF129532	CCDS9457.1	13q22	2011-06-09	2004-07-20	2004-07-21	ENSG00000005812	ENSG00000005812		"F-boxes / Leucine-rich repeats"	13599	protein-coding gene	gene with protein product		605653	"F-box and leucine-rich repeat protein 3A"	FBXL3A		10531035, 10828603	Standard	NM_012158		Approved	FBL3, FBL3A	uc001vkd.3	Q9UKT7	OTTHUMG00000017099	ENST00000355619.5:c.528G>A	13.37:g.77589659C>T			76487660	B2RB04|Q9P122	Silent	SNP	ENST00000355619.5	37	CCDS9457.1																																																																																				0.358	FBXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045312.3			T	77589659	C	T	77589659	2	4	61	1	0	0	0	0	0	0	0	1	5739	755	27	1		1	FBXL3	13	77589659	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7972	77589659	37580219	8699	16684										
MYCBP2	23077	broad.mit.edu	37	chr13	77657240	77657240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatggtctgcagcaagcGgtgaaaggtgtgtggtaaag	17	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77657240G>A	ENST00000544440.2	-	63	10866	c.10849C>T	c.(10849-10851)Cgc>Tgc	p.R3617C	MYCBP2-AS2_ENST00000428716.2_RNA|MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2_ENST00000407578.2_Missense_Mutation_p.R3655C|MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2-AS1_ENST00000450627.2_RNA|MYCBP2_ENST00000357337.6_Missense_Mutation_p.R3617C					MYC binding protein 2, E3 ubiquitin protein ligase									p.H3617Y(1)|p.R3655C(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGCAGCAAGCGGTGAAAGGTG	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	13											211	188	196					13																	77657240		2203	4300	6503	76555241	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.10849C>T	13.37:g.77657240G>A	ENSP00000444596:p.Arg3617Cys		76555241		Missense_Mutation	SNP	ENST00000544440.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.59|15.59	2.877842|2.877842	0.51801|0.51801	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000429715|ENST00000357337;ENST00000407578;ENST00000544440	.|T;T;T	.|0.67171	.|-0.25;-0.25;-0.25	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	.|0.062059	.|0.64402	.|D	.|0.000002	T|T	0.47875|0.47875	0.1469|0.1469	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	D|D	1|1	.|B	.|0.11235	.|0.004	.|B	.|0.04013	.|0.001	T|T	0.43750|0.43750	-0.9372|-0.9372	5|10	.|0.51188	.|T	.|0.08	.|.	19.165|19.165	0.93553|0.93553	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|3617	.|O75592	.|MYCB2_HUMAN	L|C	40|3617;3655;3617	.|ENSP00000349892:R3617C;ENSP00000384288:R3655C;ENSP00000444596:R3617C	.|ENSP00000349892:R3617C	P|R	-|-	2|1	0|0	MYCBP2|MYCBP2	76555241|76555241	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.825000|0.825000	0.46686|0.46686	7.984000|7.984000	0.88150|0.88150	2.504000|2.504000	0.84457|0.84457	0.650000|0.650000	0.86243|0.86243	CCG|CGC		0.473	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77657240	G	A	77657240	3	1	61	1	0	0	0	0	1	0	0	0	10048	1116	39	1	3157	1	MYCBP2	13	77657240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67581	77657240	37512638	8700	16685										
MYCBP2	23077	broad.mit.edu	37	chr13	77718581	77718581	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggctttaaagaaaataccGatttcaatgccatcaatggt	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77718581G>A	ENST00000544440.2	-	49	7205	c.7188C>T	c.(7186-7188)atC>atT	p.I2396I	MYCBP2_ENST00000407578.2_Splice_Site_p.I2434I|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Splice_Site_p.I2396I					MYC binding protein 2, E3 ubiquitin protein ligase									p.I2396I(1)|p.I2434I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGAAAATACCGATTTCAATGC	0.363																																																2	Substitution - coding silent(2)	large_intestine(2)	13											127	117	120					13																	77718581		2203	4300	6503	76616582	SO:0001630	splice_region_variant	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.7189+1C>T	13.37:g.77718581G>A			76616582		Silent	SNP	ENST00000544440.2	37																																																																																					0.363	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	Silent	A	77718581	G	A	77718581	5	1	61	1	0	0	0	0	0	0	1	0	10048	1072	37	1	6874	1	MYCBP2	13	77718581	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61341	77718581	37451297	8701	16686										
MYCBP2	23077	broad.mit.edu	37	chr13	77838066	77838066	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagattcaggatacttacatCtcttgaagcagctatctgat	7	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:77838066C>A	ENST00000544440.2	-	9	1332	c.1315G>T	c.(1315-1317)Gat>Tat	p.D439Y	MYCBP2_ENST00000407578.2_Missense_Mutation_p.D477Y|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.D439Y					MYC binding protein 2, E3 ubiquitin protein ligase									p.D439Y(2)|p.D477Y(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATACTTACATCTCTTGAAGCA	0.313																																																3	Substitution - Missense(3)	large_intestine(3)	13											60	64	62					13																	77838066		2201	4300	6501	76736067	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.1315G>T	13.37:g.77838066C>A	ENSP00000444596:p.Asp439Tyr		76736067		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	C	17.33	3.363111	0.61513	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.31247	1.51;1.5;1.51	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	L	0.42245	1.32	0.80722	D	1	P	0.48407	0.91	P	0.51487	0.671	T	0.20338	-1.0278	10	0.87932	D	0	.	19.6731	0.95918	0.0:1.0:0.0:0.0	.	439	O75592	MYCB2_HUMAN	Y	439;477;439	ENSP00000349892:D439Y;ENSP00000384288:D477Y;ENSP00000444596:D439Y	ENSP00000349892:D439Y	D	-	1	0	MYCBP2	76736067	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.113000	0.50376	2.817000	0.96982	0.563000	0.77884	GAT		0.313	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77838066	C	A	77838066	3	1	61	1	0	0	0	0	1	0	0	0	10048	913	32	2	12907	2	MYCBP2	13	77838066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119485	77838066	37331812	8702	16687										
SCEL	8796	broad.mit.edu	37	chr13	78211282	78211282	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaaggatggatatcaggaGaatatctctggaaaatacat	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:78211282G>T	ENST00000349847.3	+	30	1875	c.1791G>T	c.(1789-1791)gaG>gaT	p.E597D	SCEL_ENST00000535157.1_Missense_Mutation_p.E555D|SCEL_ENST00000377246.3_Missense_Mutation_p.E577D	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	597					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)	p.E597D(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		GATATCAGGAGAATATCTCTG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	13											101	95	97					13																	78211282		2203	4298	6501	77109283	SO:0001583	missense	8796			AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1791G>T	13.37:g.78211282G>T	ENSP00000302579:p.Glu597Asp		77109283	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	37	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118055	0.56505	.	.	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.81330	-1.48;-1.48;-1.48	5.93	-3.13	0.05266	.	0.000000	0.56097	D	0.000021	T	0.77123	0.4084	M	0.70595	2.14	0.19575	N	0.999961	B;P;P	0.42375	0.394;0.778;0.453	P;P;P	0.50405	0.461;0.64;0.566	T	0.67601	-0.5629	10	0.16896	T	0.51	-12.9989	4.3679	0.11233	0.6213:0.1191:0.1397:0.12	.	555;577;597	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	D	555;577;597	ENSP00000437895:E555D;ENSP00000366454:E577D;ENSP00000302579:E597D	ENSP00000302579:E597D	E	+	3	2	SCEL	77109283	0.939000	0.31865	0.799000	0.32177	0.835000	0.47333	0.026000	0.13599	-0.452000	0.07087	-0.136000	0.14681	GAG		0.343	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		T	78211282	G	T	78211282	3	4	61	1	0	0	0	0	1	0	0	0	13925	933	33	2	1905	2	SCEL	13	78211282	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	373216	78211282	36958596	8703	16688										
EDNRB	1910	broad.mit.edu	37	chr13	78474009	78474009	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaccttaaagcagtttttGaatcttttgctcaccaaata	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:78474009G>A	ENST00000334286.5	-	6	1415	c.1179C>T	c.(1177-1179)ttC>ttT	p.F393F	EDNRB_ENST00000377211.4_Silent_p.F483F|EDNRB_ENST00000446573.1_Silent_p.F393F	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	393					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.F393F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AGCAGTTTTTGAATCTTTTGC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	13											85	80	81					13																	78474009		2203	4299	6502	77372010	SO:0001819	synonymous_variant	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1179C>T	13.37:g.78474009G>A			77372010	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Silent	SNP	ENST00000334286.5	37	CCDS9461.1																																																																																				0.348	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			A	78474009	G	A	78474009	2	1	61	1	0	0	0	0	0	0	0	1	4931	1281	45	3		3	EDNRB	13	78474009	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	262727	78474009	36695869	8704	16689										
EDNRB	1910	broad.mit.edu	37	chr13	78474696	78474696	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatcattctgattataaaGagtgagcttcagaatcctgc	10	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:78474696G>T	ENST00000334286.5	-	5	1281	c.1045C>A	c.(1045-1047)Ctt>Att	p.L349I	EDNRB_ENST00000377211.4_Missense_Mutation_p.L439I|EDNRB_ENST00000446573.1_Missense_Mutation_p.L349I	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	349					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.L349I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGATTATAAAGAGTGAGCTTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											83	87	86					13																	78474696		2203	4300	6503	77372697	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1045C>A	13.37:g.78474696G>T	ENSP00000335311:p.Leu349Ile		77372697	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	G	9.735	1.163435	0.21538	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.71698	-0.59;-0.59;-0.59	5.62	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.217810	0.45867	N	0.000326	T	0.44393	0.1291	N	0.05078	-0.115	0.31732	N	0.63689	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.005;0.005;0.006	T	0.40942	-0.9536	10	0.16896	T	0.51	-6.993	9.0855	0.36579	0.0694:0.0:0.4439:0.4867	.	349;439;349	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	I	439;349;349	ENSP00000366416:L439I;ENSP00000403401:L349I;ENSP00000335311:L349I	ENSP00000335311:L349I	L	-	1	0	EDNRB	77372697	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.495000	0.35627	0.823000	0.34589	0.650000	0.86243	CTT		0.433	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			T	78474696	G	T	78474696	3	4	61	1	0	0	0	0	1	0	0	0	4931	942	33	2	416	2	EDNRB	13	78474696	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	687	78474696	36695182	8705	16690										
EDNRB	1910	broad.mit.edu	37	chr13	78475268	78475268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaggtcattagtgtataAaaaaatgcagtgatggccaa	9	6	2	1	rs543375862		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:78475268A>C	ENST00000334286.5	-	4	1112	c.876T>G	c.(874-876)ttT>ttG	p.F292L	EDNRB_ENST00000377211.4_Missense_Mutation_p.F382L|EDNRB_ENST00000446573.1_Missense_Mutation_p.F292L	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	292			F -> L (in WS4A). {ECO:0000269|PubMed:12189494}.		aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.F292L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TTAGTGTATAAAAAAATGCAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	13											81	85	84					13																	78475268		2203	4300	6503	77373269	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.876T>G	13.37:g.78475268A>C	ENSP00000335311:p.Phe292Leu		77373269	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284229	0.59867	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.34667	1.35;1.35;1.35	5.55	1.89	0.25635	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	L	0.57130	1.785	0.58432	D	0.99999	D;P;D	0.64830	0.994;0.567;0.99	D;B;D	0.68765	0.96;0.333;0.957	T	0.42749	-0.9433	10	0.87932	D	0	-7.5758	6.4859	0.22089	0.431:0.0:0.569:0.0	.	292;382;292	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	L	382;292;292	ENSP00000366416:F382L;ENSP00000403401:F292L;ENSP00000335311:F292L	ENSP00000335311:F292L	F	-	3	2	EDNRB	77373269	1.000000	0.71417	0.993000	0.49108	0.224000	0.24922	1.199000	0.32235	0.411000	0.25702	-0.411000	0.06167	TTT		0.338	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78475268	A	C	78475268	3	2	61	1	0	0	0	0	1	0	0	0	4931	11	1	4	589	4	EDNRB	13	78475268	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	572	78475268	36694610	8706	16691										
RNF219	79596	broad.mit.edu	37	chr13	79190571	79190571	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttatatcatcttctgaaGaatctttattagaaacattt	3	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:79190571G>T	ENST00000282003.6	-	6	1383	c.1325C>A	c.(1324-1326)tCt>tAt	p.S442Y	RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606429.1_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	442	Ser-rich.						zinc ion binding (GO:0008270)	p.S442Y(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		ATCTTCTGAAGAATCTTTATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											40	43	42					13																	79190571		2203	4300	6503	78088572	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1325C>A	13.37:g.79190571G>T	ENSP00000282003:p.Ser442Tyr		78088572	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.471277	0.26423	.	.	ENSG00000152193	ENST00000282003	T	0.14516	2.5	5.82	4.0	0.46444	.	0.421258	0.25400	N	0.030948	T	0.12135	0.0295	L	0.47716	1.5	0.31613	N	0.651298	B	0.30455	0.28	B	0.27500	0.08	T	0.08207	-1.0733	10	0.72032	D	0.01	-2.7114	7.3228	0.26539	0.15:0.1374:0.7127:0.0	.	442	Q5W0B1	RN219_HUMAN	Y	442	ENSP00000282003:S442Y	ENSP00000282003:S442Y	S	-	2	0	RNF219	78088572	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.985000	0.56930	0.735000	0.32537	0.650000	0.86243	TCT		0.358	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		T	79190571	G	T	79190571	3	4	61	1	0	0	0	0	1	0	0	0	13519	942	33	2	859	2	RNF219	13	79190571	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	715303	79190571	35979307	8707	16692										
RNF219	79596	broad.mit.edu	37	chr13	79190857	79190857	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacattacttctacctgttCttgatataggtctttgttct	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:79190857C>A	ENST00000282003.6	-	6	1097	c.1039G>T	c.(1039-1041)Gaa>Taa	p.E347*	RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606429.1_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	347							zinc ion binding (GO:0008270)	p.E347*(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		TCTACCTGTTCTTGATATAGG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											159	146	151					13																	79190857		2203	4300	6503	78088858	SO:0001587	stop_gained	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1039G>T	13.37:g.79190857C>A	ENSP00000282003:p.Glu347*		78088858	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Nonsense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.584387	0.46110	.	.	ENSG00000152193	ENST00000282003	.	.	.	5.92	3.57	0.40892	.	0.409574	0.25916	N	0.027479	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1281	5.772	0.18259	0.0:0.3086:0.0:0.6914	.	.	.	.	X	347	.	ENSP00000282003:E347X	E	-	1	0	RNF219	78088858	0.593000	0.26840	0.299000	0.25016	0.575000	0.36095	1.522000	0.35921	1.076000	0.40961	-0.238000	0.12139	GAA		0.418	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79190857	C	A	79190857	4	1	61	1	0	0	0	0	0	1	0	0	13519	922	32	2	1145	2	RNF219	13	79190857	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	286	79190857	35979021	8708	16693										
RNF219	79596	broad.mit.edu	37	chr13	79191020	79191020	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcactatcgccttgattCtttgacaccacatcctcctc	5	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:79191020C>A	ENST00000282003.6	-	6	934	c.876G>T	c.(874-876)aaG>aaT	p.K292N	RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606429.1_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	292							zinc ion binding (GO:0008270)	p.K292N(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CGCCTTGATTCTTTGACACCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	13											99	95	96					13																	79191020		2203	4300	6503	78089021	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.876G>T	13.37:g.79191020C>A	ENSP00000282003:p.Lys292Asn		78089021	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	9.396	1.076644	0.20227	.	.	ENSG00000152193	ENST00000282003	.	.	.	6.02	1.02	0.19986	.	0.632498	0.16550	N	0.209521	T	0.26774	0.0655	L	0.43152	1.355	0.22412	N	0.999124	B	0.06786	0.001	B	0.06405	0.002	T	0.14144	-1.0483	9	0.32370	T	0.25	-38.5527	1.2928	0.02063	0.3245:0.3679:0.1605:0.1472	.	292	Q5W0B1	RN219_HUMAN	N	292	.	ENSP00000282003:K292N	K	-	3	2	RNF219	78089021	0.119000	0.22226	0.635000	0.29338	0.939000	0.58152	0.327000	0.19663	0.353000	0.24079	0.655000	0.94253	AAG		0.498	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79191020	C	A	79191020	3	1	61	1	0	0	0	0	1	0	0	0	13519	912	32	2	1308	2	RNF219	13	79191020	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	163	79191020	35978858	8709	16694										
RBM26	64062	broad.mit.edu	37	chr13	79932564	79932564	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtttgttctattaaaatTtggtctgcaaacaaaattca	6	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:79932564T>G	ENST00000438737.2	-	11	1974	c.1534A>C	c.(1534-1536)Aat>Cat	p.N512H	RBM26_ENST00000438724.1_Missense_Mutation_p.N512H|RBM26_ENST00000267229.7_Missense_Mutation_p.N512H			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	512					mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.N512H(2)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		CTATTAAAATTTGGTCTGCAA	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	13											50	53	52					13																	79932564		2199	4298	6497	78830565	SO:0001583	missense	64062			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.1534A>C	13.37:g.79932564T>G	ENSP00000387531:p.Asn512His		78830565	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Missense_Mutation	SNP	ENST00000438737.2	37		.	.	.	.	.	.	.	.	.	.	T	20.8	4.044960	0.75846	.	.	ENSG00000139746	ENST00000267229;ENST00000438737;ENST00000327303;ENST00000438724	T;T	0.48836	0.8;0.81	5.23	5.23	0.72850	.	0.097480	0.64402	D	0.000002	T	0.56514	0.1990	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.997;0.997	T	0.54302	-0.8314	9	.	.	.	-18.7044	15.4171	0.74977	0.0:0.0:0.0:1.0	.	512;512;512	Q5T8P6-2;Q5T8P6;Q5T8P6-3	.;RBM26_HUMAN;.	H	512;513;512;512	ENSP00000267229:N512H;ENSP00000390222:N512H	.	N	-	1	0	RBM26	78830565	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.439000	0.80444	2.088000	0.63022	0.383000	0.25322	AAT		0.303	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		G	79932564	T	G	79932564	3	3	61	1	0	0	0	0	1	0	0	0	13163	1841	64	4	1452	4	RBM26	13	79932564	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	741544	79932564	35237314	8710	16695										
SPRY2	10253	broad.mit.edu	37	chr13	80911714	80911714	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggctctgatctgatccaGagacaagacatgtacctgct	10	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:80911714G>A	ENST00000377102.1	-	2	1104	c.127C>T	c.(127-129)Ctg>Ttg	p.L43L	SPRY2_ENST00000377104.3_Silent_p.L43L|SPRY2_ENST00000540649.1_Silent_p.L43L			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	43					bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)	p.L43L(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		ATCTGATCCAGAGACAAGACA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	13											113	111	112					13																	80911714		2203	4300	6503	79809715	SO:0001819	synonymous_variant	10253			AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.127C>T	13.37:g.80911714G>A			79809715	B2R9J9|Q5T6Z7	Silent	SNP	ENST00000377102.1	37	CCDS9463.1																																																																																				0.632	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			A	80911714	G	A	80911714	2	1	61	1	0	0	0	0	0	0	0	1	15145	933	33	3		3	SPRY2	13	80911714	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	979150	80911714	34258164	8711	16696										
SLITRK1	114798	broad.mit.edu	37	chr13	84454468	84454468	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaatccacaaagtgcgatTttcggatgctgtggatcttg	11	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:84454468T>G	ENST00000377084.2	-	1	2060	c.1175A>C	c.(1174-1176)aAa>aCa	p.K392T		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	392					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.K392T(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		AAAGTGCGATTTTCGGATGCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	13											176	170	172					13																	84454468		2203	4300	6503	83352469	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1175A>C	13.37:g.84454468T>G	ENSP00000366288:p.Lys392Thr		83352469	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.295786	0.23564	.	.	ENSG00000178235	ENST00000377084	T	0.59083	0.29	5.22	4.0	0.46444	.	0.099800	0.64402	D	0.000002	T	0.43389	0.1245	L	0.28504	0.86	0.48975	D	0.999735	B	0.21309	0.054	B	0.25140	0.058	T	0.18178	-1.0345	10	0.22706	T	0.39	-6.6787	10.2014	0.43087	0.0:0.0809:0.0:0.9191	.	392	Q96PX8	SLIK1_HUMAN	T	392	ENSP00000366288:K392T	ENSP00000366288:K392T	K	-	2	0	SLITRK1	83352469	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.963000	0.40452	0.787000	0.33731	0.454000	0.30748	AAA		0.453	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		G	84454468	T	G	84454468	3	3	61	1	0	0	0	0	1	0	0	0	14779	1841	64	4	919	4	SLITRK1	13	84454468	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3542754	84454468	30715410	8712	16697										
SLITRK1	114798	broad.mit.edu	37	chr13	84455190	84455190	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccagcttgttcaagtcCtggaaggcccccgggtctat	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:84455190C>A	ENST00000377084.2	-	1	1338	c.453G>T	c.(451-453)caG>caT	p.Q151H		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	151					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.Q151H(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		TGTTCAAGTCCTGGAAGGCCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	13											72	75	74					13																	84455190		2203	4300	6503	83353191	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.453G>T	13.37:g.84455190C>A	ENSP00000366288:p.Gln151His		83353191	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	C	8.843	0.942833	0.18281	.	.	ENSG00000178235	ENST00000377084	T	0.58210	0.35	4.45	2.61	0.31194	.	0.055638	0.64402	D	0.000002	T	0.39517	0.1081	L	0.37800	1.135	0.43913	D	0.996554	B	0.06786	0.001	B	0.04013	0.001	T	0.18053	-1.0349	10	0.48119	T	0.1	-9.6737	8.7675	0.34711	0.0:0.8014:0.0:0.1986	.	151	Q96PX8	SLIK1_HUMAN	H	151	ENSP00000366288:Q151H	ENSP00000366288:Q151H	Q	-	3	2	SLITRK1	83353191	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.012000	0.40932	0.441000	0.26529	-0.367000	0.07326	CAG		0.483	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84455190	C	A	84455190	3	1	61	1	0	0	0	0	1	0	0	0	14779	680	24	2	1641	2	SLITRK1	13	84455190	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	722	84455190	30714688	8713	16698										
SLITRK6	84189	broad.mit.edu	37	chr13	86370073	86370073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgtaattgatttccacGaagatctagatgggttaaag	10	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:86370073G>A	ENST00000400286.2	-	2	1169	c.571C>T	c.(571-573)Cgt>Tgt	p.R191C		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	191					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.R191C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TGATTTCCACGAAGATCTAGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	13											115	105	108					13																	86370073		1858	4090	5948	85268074	SO:0001583	missense	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.571C>T	13.37:g.86370073G>A	ENSP00000383143:p.Arg191Cys		85268074	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477909	0.63849	.	.	ENSG00000184564	ENST00000400286	T	0.58358	0.34	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.73102	0.3544	M	0.67517	2.055	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72972	-0.4129	10	0.87932	D	0	-18.1278	19.4432	0.94831	0.0:0.0:1.0:0.0	.	191	Q9H5Y7	SLIK6_HUMAN	C	191	ENSP00000383143:R191C	ENSP00000383143:R191C	R	-	1	0	SLITRK6	85268074	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGT		0.388	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		A	86370073	G	A	86370073	3	1	61	1	0	0	0	0	1	0	0	0	14784	1058	37	1	1958	1	SLITRK6	13	86370073	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1914883	86370073	28799805	8714	16699										
GPC5	2262	broad.mit.edu	37	chr13	92408585	92408585	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgactgtacaggtcattCtatggaggtctagctgatca	10	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:92408585C>A	ENST00000377067.3	+	5	1563	c.1191C>A	c.(1189-1191)ttC>ttA	p.F397L	GPC5_ENST00000483422.1_3'UTR	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	397					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.F397L(2)		NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ACAGGTCATTCTATGGAGGTC	0.363																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	13											126	124	124					13																	92408585		2203	4300	6503	91206586	SO:0001583	missense	2262			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1191C>A	13.37:g.92408585C>A	ENSP00000366267:p.Phe397Leu		91206586	B2R726|O60436|Q9BX27	Missense_Mutation	SNP	ENST00000377067.3	37	CCDS9468.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842640	0.71488	.	.	ENSG00000179399	ENST00000377067	T	0.60040	0.22	5.32	3.09	0.35607	.	0.100304	0.64402	D	0.000002	T	0.66327	0.2778	M	0.76002	2.32	0.41513	D	0.988351	P	0.44659	0.84	P	0.55303	0.773	T	0.66709	-0.5855	10	0.52906	T	0.07	-22.7159	7.1073	0.25370	0.0:0.6911:0.0:0.3089	.	397	P78333	GPC5_HUMAN	L	397	ENSP00000366267:F397L	ENSP00000366267:F397L	F	+	3	2	GPC5	91206586	1.000000	0.71417	0.998000	0.56505	0.831000	0.47069	0.498000	0.22530	1.111000	0.41721	0.543000	0.68304	TTC		0.363	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		A	92408585	C	A	92408585	3	1	61	1	0	0	0	0	1	0	0	0	6621	912	32	2	1209	2	GPC5	13	92408585	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6038512	92408585	22761293	8715	16700										
DCT	1638	broad.mit.edu	37	chr13	95092217	95092217	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggggtgtatatccttttcGaagtcttctatattgaagaa	9	5	2	2	rs200349922		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:95092217G>A	ENST00000377028.5	-	8	1908	c.1495C>T	c.(1495-1497)Cga>Tga	p.R499*	DCT_ENST00000446125.1_Nonsense_Mutation_p.R532*	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	499					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)	p.R499*(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		TATCCTTTTCGAAGTCTTCTA	0.458													G|||	1	0.000199681	0	0	5008	,	,		18005	0		0	False		,,,				2504	0.001															1	Substitution - Nonsense(1)	large_intestine(1)	13											109	109	109					13																	95092217		2203	4300	6503	93890218	SO:0001587	stop_gained	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1495C>T	13.37:g.95092217G>A	ENSP00000366227:p.Arg499*		93890218	Q09GT4	Nonsense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	G	39	7.663642	0.98419	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	.	.	.	4.88	1.87	0.25490	.	0.659026	0.15920	N	0.238177	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.5464	4.1965	0.10445	0.0871:0.1327:0.5517:0.2286	.	.	.	.	X	499;532	.	ENSP00000366227:R499X	R	-	1	2	DCT	93890218	0.755000	0.28372	0.273000	0.24645	0.997000	0.91878	1.658000	0.37376	0.540000	0.28808	0.563000	0.77884	CGA		0.458	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			A	95092217	G	A	95092217	4	1	61	1	0	0	0	0	0	1	0	0	4310	1066	37	1	68	1	DCT	13	95092217	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2683632	95092217	20077661	8716	16701										
DCT	1638	broad.mit.edu	37	chr13	95112436	95112436	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaaggctcatcacttgaGaatccagagtcccatctgct	8	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:95112436G>T	ENST00000377028.5	-	6	1501	c.1088C>A	c.(1087-1089)tCt>tAt	p.S363Y	DCT_ENST00000490854.1_5'Flank|DCT_ENST00000446125.1_Missense_Mutation_p.S363Y	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	363					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)	p.S363Y(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CATCACTTGAGAATCCAGAGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											91	85	87					13																	95112436		2203	4300	6503	93910437	SO:0001583	missense	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1088C>A	13.37:g.95112436G>T	ENSP00000366227:p.Ser363Tyr		93910437	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.919700	0.73098	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.98849	-5.18;-5.18	5.52	5.52	0.82312	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.178386	0.52532	D	0.000075	D	0.98985	0.9654	M	0.81341	2.54	0.40894	D	0.98409	D;D	0.76494	0.999;0.998	D;D	0.75020	0.985;0.965	D	0.99834	1.1056	10	0.87932	D	0	-23.9967	13.6898	0.62539	0.0738:0.0:0.9262:0.0	.	363;363	Q09GT4;P40126	.;TYRP2_HUMAN	Y	363	ENSP00000366227:S363Y;ENSP00000392762:S363Y	ENSP00000366227:S363Y	S	-	2	0	DCT	93910437	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	5.308000	0.65768	2.620000	0.88729	0.655000	0.94253	TCT		0.418	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			T	95112436	G	T	95112436	3	4	61	1	0	0	0	0	1	0	0	0	4310	942	33	2	590	2	DCT	13	95112436	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20219	95112436	20057442	8717	16702										
DCT	1638	broad.mit.edu	37	chr13	95118820	95118820	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttgacctacctggagatCtctttccagacacaacaaat	6	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:95118820C>T	ENST00000377028.5	-	3	1101	c.688G>A	c.(688-690)Gat>Aat	p.D230N	AL139318.1_ENST00000390768.1_RNA|DCT_ENST00000490854.1_5'UTR|DCT_ENST00000446125.1_Missense_Mutation_p.D230N	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	230					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)	p.D230N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		ACCTGGAGATCTCTTTCCAGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	13											64	64	64					13																	95118820		2203	4300	6503	93916821	SO:0001583	missense	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.688G>A	13.37:g.95118820C>T	ENSP00000366227:p.Asp230Asn		93916821	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	C	35	5.469311	0.96274	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.98807	-5.15;-5.15	5.7	5.7	0.88788	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.134566	0.64402	D	0.000002	D	0.99102	0.9691	M	0.83603	2.65	0.80722	D	1	D;P	0.56968	0.978;0.954	P;P	0.62491	0.903;0.745	D	0.99782	1.1028	10	0.87932	D	0	-7.2391	19.8418	0.96692	0.0:1.0:0.0:0.0	.	230;230	Q09GT4;P40126	.;TYRP2_HUMAN	N	230	ENSP00000366227:D230N;ENSP00000392762:D230N	ENSP00000366227:D230N	D	-	1	0	DCT	93916821	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.802000	0.85969	2.685000	0.91497	0.561000	0.74099	GAT		0.368	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			T	95118820	C	T	95118820	3	4	61	1	0	0	0	0	1	0	0	0	4310	913	32	3	1002	3	DCT	13	95118820	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6384	95118820	20051058	8718	16703										
TGDS	23483	broad.mit.edu	37	chr13	95243150	95243150	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagtactatatctattttCtctgtttcaaaaagcagttt	5	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:95243150C>A	ENST00000261296.5	-	4	390	c.270G>T	c.(268-270)gaG>gaT	p.E90D	TGDS_ENST00000498294.1_5'UTR	NM_014305.2	NP_055120.1	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase	90					nucleotide-sugar metabolic process (GO:0009225)		coenzyme binding (GO:0050662)|dTDP-glucose 4,6-dehydratase activity (GO:0008460)	p.E90D(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					TATCTATTTTCTCTGTTTCAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											148	146	147					13																	95243150		2203	4300	6503	94041151	SO:0001583	missense	23483			AF048686	CCDS9471.1	13q32.1	2012-02-22			ENSG00000088451	ENSG00000088451	4.2.1.46	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	20324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 2E, member 1"					19027726	Standard	NM_014305		Approved	TDPGD, SDR2E1	uc001vlw.3	O95455	OTTHUMG00000046308	ENST00000261296.5:c.270G>T	13.37:g.95243150C>A	ENSP00000261296:p.Glu90Asp		94041151	Q05DQ3|Q2TU31|Q5T3Z2|Q9H1T9	Missense_Mutation	SNP	ENST00000261296.5	37	CCDS9471.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.175562	0.57692	.	.	ENSG00000088451	ENST00000261296	D	0.88741	-2.42	5.48	4.63	0.57726	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.099925	0.64402	D	0.000002	D	0.93180	0.7828	M	0.73372	2.23	0.43156	D	0.994935	D	0.65815	0.995	D	0.67103	0.949	D	0.93094	0.6502	10	0.87932	D	0	.	13.4279	0.61037	0.0:0.8631:0.0:0.1369	.	90	O95455	TGDS_HUMAN	D	90	ENSP00000261296:E90D	ENSP00000261296:E90D	E	-	3	2	TGDS	94041151	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.430000	0.34914	0.700000	0.31782	-1.134000	0.01955	GAG		0.398	TGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106904.2	NM_014305		A	95243150	C	A	95243150	3	1	61	1	0	0	0	0	1	0	0	0	15853	912	32	2	818	2	TGDS	13	95243150	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124330	95243150	19926728	8719	16704										
SOX21	11166	broad.mit.edu	37	chr13	95364052	95364052	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtccttcttgagcagcgtCttgggcttgcgccgcggccg	14	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:95364052C>T	ENST00000376945.2	-	1	337	c.252G>A	c.(250-252)aaG>aaA	p.K84K	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	84					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K84K(1)		large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					TGAGCAGCGTCTTGGGCTTGC	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	13											70	63	66					13																	95364052		2203	4300	6503	94162053	SO:0001819	synonymous_variant	11166			AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"SRY (sex determining region Y)-boxes"	11197	protein-coding gene	gene with protein product	"SRY-box 21"	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.252G>A	13.37:g.95364052C>T			94162053	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	37	CCDS9473.1																																																																																				0.687	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084		T	95364052	C	T	95364052	2	4	61	1	0	0	0	0	0	0	0	1	14987	912	32	3		3	SOX21	13	95364052	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120902	95364052	19805826	8720	16705										
CLDN10	9071	broad.mit.edu	37	chr13	96212691	96212691	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaaatcacaacggaattCtttgatcctctctttgttga	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96212691C>A	ENST00000299339.2	+	3	467	c.438C>A	c.(436-438)ttC>ttA	p.F146L	CLDN10_ENST00000376873.3_Missense_Mutation_p.F144L|CLDN10_ENST00000376855.1_Missense_Mutation_p.F64L	NM_006984.4	NP_008915.1	P78369	CLD10_HUMAN	claudin 10	146					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|ion transport (GO:0006811)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.F144L(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	15	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			CAACGGAATTCTTTGATCCTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	13											161	150	154					13																	96212691		2203	4300	6503	95010692	SO:0001583	missense	9071			U89916	CCDS9475.1, CCDS9476.1	13q31-q34	2008-07-18			ENSG00000134873	ENSG00000134873		"Claudins"	2033	protein-coding gene	gene with protein product						18025272	Standard	NM_182848		Approved	OSP-L, CPETRL3	uc001vmh.2	P78369	OTTHUMG00000017217	ENST00000299339.2:c.438C>A	13.37:g.96212691C>A	ENSP00000299339:p.Phe146Leu		95010692	Q6IBF9|Q96N78	Missense_Mutation	SNP	ENST00000299339.2	37	CCDS9476.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299175	0.81025	.	.	ENSG00000134873	ENST00000376873;ENST00000299339;ENST00000376855	D;D;D	0.88509	-2.39;-2.39;-2.39	5.75	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.96383	0.8820	H	0.97214	3.96	0.58432	D	0.999998	D;D;D	0.64830	0.994;0.994;0.994	D;D;D	0.69824	0.932;0.932;0.966	D	0.97601	1.0123	10	0.87932	D	0	.	14.6379	0.68702	0.0:0.9306:0.0:0.0694	.	146;146;144	Q6IBF9;P78369;Q96N78	.;CLD10_HUMAN;.	L	144;146;64	ENSP00000366069:F144L;ENSP00000299339:F146L;ENSP00000366051:F64L	ENSP00000299339:F146L	F	+	3	2	CLDN10	95010692	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.381000	0.44336	1.428000	0.47296	0.650000	0.86243	TTC		0.373	CLDN10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045484.1	NM_006984		A	96212691	C	A	96212691	3	1	61	1	0	0	0	0	1	0	0	0	3478	912	32	2	666	2	CLDN10	13	96212691	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	848639	96212691	18957187	8721	16706										
DZIP1	22873	broad.mit.edu	37	chr13	96239899	96239899	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccttgttttgtggtggCggcacaggaagtgggcctgg	17	9	0	0	rs111764824		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96239899C>T	ENST00000376829.2	-	20	2963	c.2112G>A	c.(2110-2112)ccG>ccA	p.P704P	DZIP1_ENST00000361396.2_Silent_p.P685P|DZIP1_ENST00000361156.3_Silent_p.P685P|DZIP1_ENST00000347108.3_Silent_p.P704P	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	704					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P685P(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TTTGTGGTGGCGGCACAGGAA	0.567													C|||	1	0.000199681	0	0	5008	,	,		17885	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13											126	105	112					13																	96239899		2203	4300	6503	95037900	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2112G>A	13.37:g.96239899C>T			95037900	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.567	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		T	96239899	C	T	96239899	2	4	61	1	0	0	0	0	0	0	0	1	4874	755	27	1		1	DZIP1	13	96239899	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27208	96239899	18929979	8722	16707										
DZIP1	22873	broad.mit.edu	37	chr13	96261761	96261761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaagcctgccaggctaaaGgatttcctgaaatgacagaa	9	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96261761G>T	ENST00000376829.2	-	13	2221	c.1370C>A	c.(1369-1371)cCt>cAt	p.P457H	DZIP1_ENST00000361396.2_Intron|DZIP1_ENST00000361156.3_Intron|DZIP1_ENST00000347108.3_Missense_Mutation_p.P457H	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	457					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P457H(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CCAGGCTAAAGGATTTCCTGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13											27	27	27					13																	96261761		2203	4299	6502	95059762	SO:0001583	missense	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1370C>A	13.37:g.96261761G>T	ENSP00000366025:p.Pro457His		95059762	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	G	9.513	1.106189	0.20632	.	.	ENSG00000134874	ENST00000347108;ENST00000376829	T;T	0.08720	3.06;3.06	3.85	-0.0973	0.13633	.	1.235800	0.05343	N	0.530466	T	0.10337	0.0253	L	0.51422	1.61	0.45690	D	0.998604	D	0.58620	0.983	P	0.46975	0.533	T	0.44892	-0.9298	10	0.41790	T	0.15	1.1866	2.1386	0.03769	0.102:0.1707:0.3772:0.3502	.	457	Q86YF9	DZIP1_HUMAN	H	457	ENSP00000257312:P457H;ENSP00000366025:P457H	ENSP00000257312:P457H	P	-	2	0	DZIP1	95059762	0.679000	0.27596	0.456000	0.27044	0.291000	0.27294	1.186000	0.32078	-0.059000	0.13154	-1.132000	0.01976	CCT		0.378	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		T	96261761	G	T	96261761	3	4	61	1	0	0	0	0	1	0	0	0	4874	1000	35	2	1277	2	DZIP1	13	96261761	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21862	96261761	18908117	8723	16708										
DZIP1	22873	broad.mit.edu	37	chr13	96264407	96264407	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatctatcattgaggttcGaagtttctctatatgtgaca	7	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96264407G>A	ENST00000376829.2	-	11	2049	c.1198C>T	c.(1198-1200)Cga>Tga	p.R400*	DZIP1_ENST00000361396.2_Nonsense_Mutation_p.R400*|DZIP1_ENST00000361156.3_Nonsense_Mutation_p.R400*|DZIP1_ENST00000347108.3_Nonsense_Mutation_p.R400*	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	400					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.R400*(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			attgAGGTTCGAAGTTTCTCT	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											112	109	110					13																	96264407		2203	4300	6503	95062408	SO:0001587	stop_gained	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1198C>T	13.37:g.96264407G>A	ENSP00000366025:p.Arg400*		95062408	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Nonsense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	G	45	12.067778	0.99632	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	.	.	.	5.88	5.88	0.94601	.	0.496875	0.21683	N	0.070691	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.2598	12.6734	0.56880	0.0:0.0:0.8353:0.1647	.	.	.	.	X	400	.	ENSP00000257312:R400X	R	-	1	2	DZIP1	95062408	0.998000	0.40836	1.000000	0.80357	0.882000	0.50991	2.949000	0.49074	2.778000	0.95560	0.655000	0.94253	CGA		0.383	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		A	96264407	G	A	96264407	4	1	61	1	0	0	0	0	0	1	0	0	4874	1066	37	1	1457	1	DZIP1	13	96264407	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2646	96264407	18905471	8724	16709										
DZIP1	22873	broad.mit.edu	37	chr13	96282324	96282324	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcttccttcaatacgacGatctcactccggagcttctc	6	15	4	0	rs147346095	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96282324G>A	ENST00000376829.2	-	7	1580	c.729C>T	c.(727-729)atC>atT	p.I243I	DZIP1_ENST00000361396.2_Silent_p.I243I|DZIP1_ENST00000361156.3_Silent_p.I243I|DZIP1_ENST00000347108.3_Silent_p.I243I	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	243					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.I243I(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TCAATACGACGATCTCACTCC	0.468													G|||	4	0.000798722	0	0.0029	5008	,	,		18353	0		0.001	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	13						G	,	1,4405	2.1+/-5.4	0,1,2202	113	90	98		729,729	-8.5	0.4	13	dbSNP_134	98	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	DZIP1	NM_014934.3,NM_198968.2	,	0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538	,	243/849,243/868	96282324	7,12999	2203	4300	6503	95080325	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.729C>T	13.37:g.96282324G>A			95080325	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.468	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		A	96282324	G	A	96282324	2	1	61	1	0	0	0	0	0	0	0	1	4874	1048	37	1		1	DZIP1	13	96282324	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17917	96282324	18887554	8725	16710										
UGGT2	55757	broad.mit.edu	37	chr13	96506694	96506694	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggagctccatccagatcGaaatctcgaagttcttttag	8	9	2	1	rs549305023		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96506694G>A	ENST00000376747.3	-	35	4114	c.4044C>T	c.(4042-4044)ttC>ttT	p.F1348F		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1348	Glucosyltransferase.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.F1348F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						CATCCAGATCGAAATCTCGAA	0.373													G|||	1	0.000199681	0	0	5008	,	,		17432	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13											72	68	70					13																	96506694		2203	4300	6503	95304695	SO:0001819	synonymous_variant	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.4044C>T	13.37:g.96506694G>A			95304695	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	37	CCDS9480.1																																																																																				0.373	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96506694	G	A	96506694	2	1	61	1	0	0	0	0	0	0	0	1	16982	1049	37	1		1	UGGT2	13	96506694	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	224370	96506694	18663184	8726	16711										
UGGT2	55757	broad.mit.edu	37	chr13	96530017	96530017	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcctagtgtgaactgcaGaccccgaggaggctgttctg	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96530017G>T	ENST00000376747.3	-	28	3392	c.3322C>A	c.(3322-3324)Ctg>Atg	p.L1108M		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1108					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.L1108M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						GTGAACTGCAGACCCCGAGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13											134	128	130					13																	96530017		2203	4300	6503	95328018	SO:0001583	missense	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3322C>A	13.37:g.96530017G>T	ENSP00000365938:p.Leu1108Met		95328018	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290089	0.59976	.	.	ENSG00000102595	ENST00000376747	T	0.49139	0.79	5.14	3.4	0.38934	.	0.000000	0.64402	D	0.000002	T	0.69260	0.3091	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.986	T	0.72232	-0.4353	10	0.72032	D	0.01	-6.5715	8.3968	0.32561	0.3048:0.0:0.6952:0.0	.	1108;1108	Q9NV86;Q9NYU1	.;UGGG2_HUMAN	M	1108	ENSP00000365938:L1108M	ENSP00000365938:L1108M	L	-	1	2	UGGT2	95328018	0.983000	0.35010	1.000000	0.80357	0.906000	0.53458	1.928000	0.40104	1.159000	0.42565	0.467000	0.42956	CTG		0.378	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		T	96530017	G	T	96530017	3	4	61	1	0	0	0	0	1	0	0	0	16982	933	33	2	1276	2	UGGT2	13	96530017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23323	96530017	18639861	8727	16712										
UGGT2	55757	broad.mit.edu	37	chr13	96642326	96642326	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaagatctgaatatatttCtctgcatcaaaatattaagt	4	6	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96642326C>A	ENST00000376747.3	-	8	902	c.832G>T	c.(832-834)Gaa>Taa	p.E278*	UGGT2_ENST00000376714.3_Intron|UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000397618.3_Splice_Site_p.E278*	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	278					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.E278*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						GAATATATTTCTCTGCATCAA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											119	121	120					13																	96642326		2203	4296	6499	95440327	SO:0001630	splice_region_variant	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.831-1G>T	13.37:g.96642326C>A			95440327	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Nonsense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049578	0.75846	.	.	ENSG00000102595	ENST00000376747;ENST00000397618	.	.	.	5.37	4.51	0.55191	.	0.179519	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-28.593	7.5591	0.27841	0.0:0.6287:0.2839:0.0874	.	.	.	.	X	278	.	ENSP00000365938:E278X	E	-	1	0	UGGT2	95440327	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	2.407000	0.44565	2.673000	0.90976	0.591000	0.81541	GAA		0.313	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	Nonsense_Mutation	A	96642326	C	A	96642326	5	1	61	1	0	0	0	0	0	0	1	0	16982	927	32	2	3846	2	UGGT2	13	96642326	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	112309	96642326	18527552	8728	16713										
UGGT2	55757	broad.mit.edu	37	chr13	96665596	96665596	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaacatacagaatttcctCattttgagctttttcagaca	5	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:96665596C>A	ENST00000376747.3	-	5	695	c.625G>T	c.(625-627)Gag>Tag	p.E209*	UGGT2_ENST00000376712.4_Nonsense_Mutation_p.E209*|UGGT2_ENST00000376714.3_Nonsense_Mutation_p.E209*|UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000397618.3_Nonsense_Mutation_p.E209*	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	209					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.E209*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AGAATTTCCTCATTTTGAGCT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											104	97	99					13																	96665596		2203	4300	6503	95463597	SO:0001587	stop_gained	55757			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.625G>T	13.37:g.96665596C>A	ENSP00000365938:p.Glu209*		95463597	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Nonsense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	C	38	6.727597	0.97792	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	.	.	.	5.49	4.59	0.56863	.	0.306011	0.35870	N	0.002921	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-3.3781	15.7529	0.78001	0.0:0.8635:0.1365:0.0	.	.	.	.	X	209	.	ENSP00000365902:E209X	E	-	1	0	UGGT2	95463597	0.569000	0.26643	0.095000	0.20976	0.981000	0.71138	3.474000	0.53129	2.576000	0.86940	0.591000	0.81541	GAG		0.343	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96665596	C	A	96665596	4	1	61	1	0	0	0	0	0	1	0	0	16982	835	29	2	4065	2	UGGT2	13	96665596	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23270	96665596	18504282	8729	16714										
MBNL2	10150	broad.mit.edu	37	chr13	97999258	97999258	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccaaaatcaaagctgcGcagcaccaagccaaccaagc	8	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:97999258G>A	ENST00000376673.3	+	5	1522	c.741G>A	c.(739-741)gcG>gcA	p.A247A	MBNL2_ENST00000445661.2_Intron|MBNL2_ENST00000345429.6_Silent_p.A247A|MBNL2_ENST00000397601.1_Silent_p.A247A|MBNL2_ENST00000343600.4_Silent_p.A247A			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	247					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A247A(2)		endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			TCAAAGCTGCGCAGCACCAAG	0.617																																																2	Substitution - coding silent(2)	large_intestine(2)	13											33	34	34					13																	97999258		2203	4300	6503	96797259	SO:0001819	synonymous_variant	10150			AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"Zinc fingers, CCCH-type domain containing"	16746	protein-coding gene	gene with protein product		607327	"muscleblind-like 2 (Drosophila)"			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.741G>A	13.37:g.97999258G>A			96797259	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Silent	SNP	ENST00000376673.3	37																																																																																					0.617	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778		A	97999258	G	A	97999258	2	1	61	1	0	0	0	0	0	0	0	1	9384	1074	38	1		1	MBNL2	13	97999258	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1333662	97999258	17170620	8730	16715										
IPO5	3843	broad.mit.edu	37	chr13	98669038	98669038	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatattttacactcaatatTcagtagctacaaagaaaagg	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:98669038T>G	ENST00000490680.1	+	22	2614	c.2549T>G	c.(2548-2550)tTc>tGc	p.F850C	IPO5_ENST00000539640.1_Missense_Mutation_p.F725C|IPO5_ENST00000261574.5_Missense_Mutation_p.F868C			O00410	IPO5_HUMAN	importin 5	850					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)	p.F868C(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						CACTCAATATTCAGTAGCTAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	13											137	133	135					13																	98669038		2203	4300	6503	97467039	SO:0001583	missense	3843			U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2549T>G	13.37:g.98669038T>G	ENSP00000418393:p.Phe850Cys		97467039	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.1|24.1	4.494312|4.494312	0.85069|0.85069	.|.	.|.	ENSG00000065150|ENSG00000065150	ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640|ENST00000469360	T;T;T;T|.	0.68765|.	-0.35;-0.35;-0.35;-0.35|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.088147|.	0.85682|.	D|.	0.000000|.	T|T	0.78188|0.78188	0.4244|0.4244	M|M	0.83312|0.83312	2.635|2.635	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.80281|0.80281	-0.1448|-0.1448	10|5	0.87932|.	D|.	0|.	-7.3192|-7.3192	15.8357|15.8357	0.78796|0.78796	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	868|.	O00410-3|.	.|.	C|A	868;850;850;725|852	ENSP00000261574:F868C;ENSP00000350219:F850C;ENSP00000418393:F850C;ENSP00000445126:F725C|.	ENSP00000261574:F868C|.	F|S	+|+	2|1	0|0	IPO5|IPO5	97467039|97467039	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.814000|7.814000	0.86154|0.86154	2.136000|2.136000	0.66102|0.66102	0.533000|0.533000	0.62120|0.62120	TTC|TCA		0.313	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		G	98669038	T	G	98669038	3	3	61	1	0	0	0	0	1	0	0	0	7817	1783	62	4	2693	4	IPO5	13	98669038	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	669780	98669038	16500840	8731	16716										
RNF113B	140432	broad.mit.edu	37	chr13	98828770	98828770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcccacttcatggttttCgtcctcgcagatacagtagc	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:98828770C>T	ENST00000267291.6	-	1	749	c.721G>A	c.(721-723)Gaa>Aaa	p.E241K	FARP1_ENST00000595437.1_Intron|FARP1_ENST00000319562.6_Intron|FARP1_ENST00000376581.5_Intron|FARP1_ENST00000376586.2_Intron	NM_178861.4	NP_849192.1	Q8IZP6	R113B_HUMAN	ring finger protein 113B	241							zinc ion binding (GO:0008270)	p.E241K(2)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)			TCATGGTTTTCGTCCTCGCAG	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	13											109	101	104					13																	98828770		2203	4300	6503	97626771	SO:0001583	missense	140432			AF539427	CCDS9486.1	13q32.2	2006-08-22	2005-03-22	2005-03-22	ENSG00000139797	ENSG00000139797		"RING-type (C3HC4) zinc fingers"	17267	protein-coding gene	gene with protein product			"zinc finger protein 183-like 1"	ZNF183L1			Standard	NM_178861		Approved	RNF161	uc001vnk.3	Q8IZP6	OTTHUMG00000017245	ENST00000267291.6:c.721G>A	13.37:g.98828770C>T	ENSP00000267291:p.Glu241Lys		97626771	Q8WWF9|Q96QY9	Missense_Mutation	SNP	ENST00000267291.6	37	CCDS9486.1	.	.	.	.	.	.	.	.	.	.	C	7.669	0.686489	0.14973	.	.	ENSG00000139797	ENST00000267291	T	0.32753	1.44	1.57	1.57	0.23409	.	0.000000	0.85682	U	0.000000	T	0.23572	0.0570	L	0.49699	1.58	0.41607	D	0.988889	D	0.53885	0.963	B	0.43623	0.425	T	0.11867	-1.0570	10	0.10902	T	0.67	.	9.0801	0.36547	0.0:1.0:0.0:0.0	.	241	Q8IZP6	R113B_HUMAN	K	241	ENSP00000267291:E241K	ENSP00000267291:E241K	E	-	1	0	RNF113B	97626771	0.998000	0.40836	0.095000	0.20976	0.004000	0.04260	5.091000	0.64505	1.176000	0.42840	0.591000	0.81541	GAA		0.527	RNF113B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045536.3	NM_178861		T	98828770	C	T	98828770	3	4	61	1	0	0	0	0	1	0	0	0	13465	893	31	1	255	1	RNF113B	13	98828770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159732	98828770	16341108	8732	16717										
FARP1	10160	broad.mit.edu	37	chr13	99099066	99099066	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggaaagcgagtacacgttCgaaaggtagacacccccttc	11	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99099066C>T	ENST00000319562.6	+	26	3316	c.3051C>T	c.(3049-3051)ttC>ttT	p.F1017F	FARP1_ENST00000595437.1_Silent_p.F1048F|FARP1_ENST00000376586.2_Silent_p.F1048F	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	1017	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F1017F(1)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AGTACACGTTCGAAAGGTAGA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	13											146	112	123					13																	99099066		2203	4300	6503	97897067	SO:0001819	synonymous_variant	10160			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.3051C>T	13.37:g.99099066C>T			97897067	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1																																																																																				0.557	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		T	99099066	C	T	99099066	2	4	61	1	0	0	0	0	0	0	0	1	5695	883	31	1		1	FARP1	13	99099066	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	270296	99099066	16070812	8733	16718										
SLC15A1	6564	broad.mit.edu	37	chr13	99338532	99338532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcctgcctgaagcaccGacttcatgttggaaggagcc	11	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99338532G>A	ENST00000376503.5	-	22	1902	c.1847C>T	c.(1846-1848)tCg>tTg	p.S616L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	616					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)	p.S616L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTGAAGCACCGACTTCATGTT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	13											115	79	91					13																	99338532		2203	4300	6503	98136533	SO:0001583	missense	6564			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"Solute carriers"	10920	protein-coding gene	gene with protein product	"peptide transporter HPEPT1", "bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)", "solute carrier family 15 oligopeptide transporter member 1"	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1847C>T	13.37:g.99338532G>A	ENSP00000365686:p.Ser616Leu		98136533	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195300	0.94960	.	.	ENSG00000088386	ENST00000376503	T	0.60548	0.18	5.91	5.91	0.95273	Major facilitator superfamily domain, general substrate transporter (1);	0.128146	0.56097	D	0.000037	D	0.84270	0.5435	H	0.97415	4	0.80722	D	1	D	0.76494	0.999	D	0.63033	0.91	D	0.89347	0.3658	10	0.87932	D	0	-28.1678	19.07	0.93130	0.0:0.0:1.0:0.0	.	616	P46059	S15A1_HUMAN	L	616	ENSP00000365686:S616L	ENSP00000365686:S616L	S	-	2	0	SLC15A1	98136533	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.982000	0.93471	2.793000	0.96121	0.655000	0.94253	TCG		0.582	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073		A	99338532	G	A	99338532	3	1	61	1	0	0	0	0	1	0	0	0	14435	1059	37	1	287	1	SLC15A1	13	99338532	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239466	99338532	15831346	8734	16719										
SLC15A1	6564	broad.mit.edu	37	chr13	99340754	99340754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaactggtatgtgctgGcattgtagctgctgatgttt	12	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99340754G>A	ENST00000376503.5	-	19	1599	c.1544C>T	c.(1543-1545)gCc>gTc	p.A515V		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	515					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)	p.A515V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GTATGTGCTGGCATTGTAGCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											129	129	129					13																	99340754		2203	4300	6503	98138755	SO:0001583	missense	6564			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"Solute carriers"	10920	protein-coding gene	gene with protein product	"peptide transporter HPEPT1", "bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)", "solute carrier family 15 oligopeptide transporter member 1"	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1544C>T	13.37:g.99340754G>A	ENSP00000365686:p.Ala515Val		98138755	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	.	.	.	.	.	.	.	.	.	.	G	0.290	-0.980805	0.02197	.	.	ENSG00000088386	ENST00000376503	T	0.01963	4.53	5.91	4.18	0.49190	Major facilitator superfamily domain, general substrate transporter (1);	0.264293	0.45126	N	0.000395	T	0.01905	0.0060	L	0.40543	1.245	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.37174	-0.9717	10	0.02654	T	1	-33.2304	6.6643	0.23032	0.1548:0.1475:0.6977:0.0	.	515	P46059	S15A1_HUMAN	V	515	ENSP00000365686:A515V	ENSP00000365686:A515V	A	-	2	0	SLC15A1	98138755	0.594000	0.26849	0.993000	0.49108	0.008000	0.06430	0.181000	0.16880	0.830000	0.34757	-0.126000	0.14955	GCC		0.358	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073		A	99340754	G	A	99340754	3	1	61	1	0	0	0	0	1	0	0	0	14435	1203	42	3	602	3	SLC15A1	13	99340754	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2222	99340754	15829124	8735	16720										
SLC15A1	6564	broad.mit.edu	37	chr13	99378638	99378638	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctcgcattccatagtaGgaaaatctttcgcaaaactc	5	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99378638G>T	ENST00000376503.5	-	3	142	c.87C>A	c.(85-87)tcC>tcA	p.S29S		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	29					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)	p.S29S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TTCCATAGTAGGAAAATCTTT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	13											86	80	82					13																	99378638		2203	4300	6503	98176639	SO:0001819	synonymous_variant	6564			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"Solute carriers"	10920	protein-coding gene	gene with protein product	"peptide transporter HPEPT1", "bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)", "solute carrier family 15 oligopeptide transporter member 1"	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.87C>A	13.37:g.99378638G>T			98176639	Q5VW82	Silent	SNP	ENST00000376503.5	37	CCDS9489.1																																																																																				0.448	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073		T	99378638	G	T	99378638	2	4	61	1	0	0	0	0	0	0	0	1	14435	987	35	2		2	SLC15A1	13	99378638	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37884	99378638	15791240	8736	16721										
DOCK9	23348	broad.mit.edu	37	chr13	99515753	99515753	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcagtaacagtcccaccaaGaagtggtttctgcagaactc	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99515753G>T	ENST00000376460.1	-	31	3416	c.3336C>A	c.(3334-3336)ttC>ttA	p.F1112L	DOCK9_ENST00000448493.2_Missense_Mutation_p.F1124L|DOCK9_ENST00000442173.1_Missense_Mutation_p.F1112L|DOCK9_ENST00000339416.2_Missense_Mutation_p.F1113L|DOCK9_ENST00000461998.1_5'UTR	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1113					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F1124L(1)|p.F1113L(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GTCCCACCAAGAAGTGGTTTC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	13											44	42	43					13																	99515753		1845	4080	5925	98313754	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3336C>A	13.37:g.99515753G>T	ENSP00000365643:p.Phe1112Leu		98313754	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398692	0.83120	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000448493;ENST00000442173	D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23	5.72	4.0	0.46444	.	0.000000	0.85682	D	0.000000	D	0.98532	0.9510	M	0.91354	3.2	0.58432	D	0.999999	B;B;D;B;D;D	0.64830	0.029;0.026;0.994;0.058;0.992;0.989	B;B;D;B;D;D	0.72338	0.162;0.027;0.977;0.103;0.924;0.917	D	0.98763	1.0725	10	0.87932	D	0	.	12.2872	0.54798	0.1367:0.0:0.8633:0.0	.	1113;1112;1113;1112;1112;1113	A6H8Z6;E9PFM9;A8MWZ5;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;.;DOCK9_HUMAN	L	1112;1113;1113;1113;1112;43;1113;1124;1112	ENSP00000365643:F1112L;ENSP00000341086:F1113L;ENSP00000401958:F1124L;ENSP00000406883:F1112L	ENSP00000341086:F1113L	F	-	3	2	DOCK9	98313754	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.065000	0.49994	0.767000	0.33267	-0.140000	0.14226	TTC		0.493	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		T	99515753	G	T	99515753	3	4	61	1	0	0	0	0	1	0	0	0	4705	933	33	2	3035	2	DOCK9	13	99515753	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137115	99515753	15654125	8737	16722										
DOCK9	23348	broad.mit.edu	37	chr13	99535321	99535321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtactttacaagttcgtttCctaaggcttgggctccagat	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99535321C>T	ENST00000376460.1	-	23	2614	c.2534G>A	c.(2533-2535)gGa>gAa	p.G845E	DOCK9_ENST00000448493.2_Missense_Mutation_p.G857E|DOCK9_ENST00000442173.1_Missense_Mutation_p.G845E|DOCK9_ENST00000339416.2_Missense_Mutation_p.G846E	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	846					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G846E(1)|p.G857E(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAGTTCGTTTCCTAAGGCTTG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	13											119	107	111					13																	99535321		1854	4103	5957	98333322	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2534G>A	13.37:g.99535321C>T	ENSP00000365643:p.Gly845Glu		98333322	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.529688	0.27387	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.18657	2.55;2.63;2.21;2.2	5.49	5.49	0.81192	.	0.052065	0.85682	D	0.000000	T	0.10937	0.0267	N	0.03071	-0.42	0.58432	D	0.999996	B;B;B;B;B	0.11235	0.0;0.004;0.0;0.001;0.004	B;B;B;B;B	0.12837	0.003;0.005;0.001;0.003;0.008	T	0.24404	-1.0161	10	0.22706	T	0.39	.	17.9237	0.88976	0.0:1.0:0.0:0.0	.	846;845;845;845;846	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	E	845;846;846;846;845;846;857;845	ENSP00000365643:G845E;ENSP00000341086:G846E;ENSP00000401958:G857E;ENSP00000406883:G845E	ENSP00000341086:G846E	G	-	2	0	DOCK9	98333322	1.000000	0.71417	0.992000	0.48379	0.922000	0.55478	4.396000	0.59684	2.750000	0.94351	0.563000	0.77884	GGA		0.403	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		T	99535321	C	T	99535321	3	4	61	1	0	0	0	0	1	0	0	0	4705	855	30	3	3869	3	DOCK9	13	99535321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19568	99535321	15634557	8738	16723										
GPR18	2841	broad.mit.edu	37	chr13	99907895	99907895	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgcataataaaacattcGaaagggtaaagtcattataa	6	4	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:99907895G>A	ENST00000340807.3	-	3	788	c.232C>T	c.(232-234)Cga>Tga	p.R78*	GPR18_ENST00000397473.2_Nonsense_Mutation_p.R78*|GPR18_ENST00000397470.2_Nonsense_Mutation_p.R78*|UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	78					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R78*(1)		endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	TAAAACATTCGAAAGGGTAAA	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											72	73	72					13																	99907895		2203	4300	6503	98705896	SO:0001587	stop_gained	2841			L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.232C>T	13.37:g.99907895G>A	ENSP00000343428:p.Arg78*		98705896	Q6GTM3|Q96HI6|Q9H2L2	Nonsense_Mutation	SNP	ENST00000340807.3	37	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	G	37	6.439455	0.97568	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	.	.	.	6.07	5.22	0.72569	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.5775	16.5987	0.84803	0.0:0.0:0.8687:0.1313	.	.	.	.	X	78	.	.	R	-	1	2	GPR18	98705896	1.000000	0.71417	0.997000	0.53966	0.891000	0.51852	4.969000	0.63735	1.535000	0.49220	0.655000	0.94253	CGA		0.388	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			A	99907895	G	A	99907895	4	1	61	1	0	0	0	0	0	1	0	0	6695	1066	37	1	767	1	GPR18	13	99907895	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	372574	99907895	15261983	8739	16724										
TM9SF2	9375	broad.mit.edu	37	chr13	100211649	100211649	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatggcgttcattccttacGagtggctttactgcagttta	9	9	1	0	rs7330734	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:100211649G>A	ENST00000376387.4	+	16	1975	c.1785G>A	c.(1783-1785)acG>acA	p.T595T		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	595					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.T595T(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CATTCCTTACGAGTGGCTTTA	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	13											147	140	142					13																	100211649		2203	4300	6503	99009650	SO:0001819	synonymous_variant	9375			U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.1785G>A	13.37:g.100211649G>A			99009650	A8K399|Q2TAY5	Silent	SNP	ENST00000376387.4	37	CCDS9493.1																																																																																				0.353	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			A	100211649	G	A	100211649	2	1	61	1	0	0	0	0	0	0	0	1	16017	1045	37	1		1	TM9SF2	13	100211649	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	303754	100211649	14958229	8740	16725										
PCCA	5095	broad.mit.edu	37	chr13	100809577	100809577	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcctttcagaaaacaaaGaatttgccagatgtttggta	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:100809577G>T	ENST00000376285.1	+	6	489	c.451G>T	c.(451-453)Gaa>Taa	p.E151*	PCCA_ENST00000376279.3_Nonsense_Mutation_p.E151*|PCCA_ENST00000485946.1_3'UTR|PCCA_ENST00000376286.4_Nonsense_Mutation_p.E125*	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	151	Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.E151*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	AGAAAACAAAGAATTTGCCAG	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											99	96	97					13																	100809577		2203	4299	6502	99607578	SO:0001587	stop_gained	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.451G>T	13.37:g.100809577G>T	ENSP00000365462:p.Glu151*		99607578	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Nonsense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	G	37	6.622426	0.97714	.	.	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285	.	.	.	5.0	5.0	0.66597	.	0.056971	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	18.267	0.90055	0.0:0.0:1.0:0.0	.	.	.	.	X	125;151;151	.	ENSP00000365456:E151X	E	+	1	0	PCCA	99607578	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.452000	0.90346	2.477000	0.83638	0.561000	0.74099	GAA		0.338	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			T	100809577	G	T	100809577	4	4	61	1	0	0	0	0	0	1	0	0	11535	943	33	2	473	2	PCCA	13	100809577	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	597928	100809577	14360301	8741	16726										
PCCA	5095	broad.mit.edu	37	chr13	100962160	100962160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggataactatgttattcGaggtaaaaacaaagatttgc	8	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:100962160G>A	ENST00000376285.1	+	16	1465	c.1427G>A	c.(1426-1428)cGa>cAa	p.R476Q	PCCA_ENST00000376279.3_Missense_Mutation_p.R476Q|PCCA_ENST00000376286.4_Missense_Mutation_p.R450Q	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	476	Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.R476Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TATGTTATTCGAGGTAAAAAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	13											137	133	134					13																	100962160		2203	4300	6503	99760161	SO:0001583	missense	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1427G>A	13.37:g.100962160G>A	ENSP00000365462:p.Arg476Gln		99760161	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.274669|5.274669	0.95459|0.95459	.|.	.|.	ENSG00000175198|ENSG00000175198	ENST00000443601|ENST00000376286;ENST00000376279;ENST00000376285;ENST00000376254	.|T;T;T	.|0.81247	.|-1.47;-1.47;-1.47	5.36|5.36	5.36|5.36	0.76844|0.76844	.|Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84037|0.84037	0.5384|0.5384	L|L	0.33339|0.33339	1.005|1.005	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.998;0.997;0.998	.|P;P;P	.|0.62184	.|0.846;0.837;0.899	D|D	0.84354|0.84354	0.0534|0.0534	5|10	.|0.46703	.|T	.|0.11	.|.	19.078|19.078	0.93171|0.93171	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|476;450;476	.|C9JPQ8;P05165-2;P05165	.|.;.;PCCA_HUMAN	K|Q	68|450;476;476;67	.|ENSP00000365463:R450Q;ENSP00000365456:R476Q;ENSP00000365462:R476Q	.|ENSP00000365430:R67Q	E|R	+|+	1|2	0|0	PCCA|PCCA	99760161|99760161	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.921000|0.921000	0.55340|0.55340	8.433000|8.433000	0.90291|0.90291	2.491000|2.491000	0.84063|0.84063	0.650000|0.650000	0.86243|0.86243	GAG|CGA		0.403	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			A	100962160	G	A	100962160	3	1	61	1	0	0	0	0	1	0	0	0	11535	1058	37	1	1489	1	PCCA	13	100962160	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152583	100962160	14207718	8742	16727										
PCCA	5095	broad.mit.edu	37	chr13	101179949	101179949	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcagaaggtcaagaaatTtgtgtgattgaagccatgaa	12	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:101179949T>G	ENST00000376285.1	+	23	2099	c.2061T>G	c.(2059-2061)atT>atG	p.I687M	PCCA_ENST00000376279.3_Missense_Mutation_p.I640M|PCCA_ENST00000376286.4_Missense_Mutation_p.I661M	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	687	Biotinyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.I687M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GTCAAGAAATTTGTGTGATTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	13											108	109	109					13																	101179949		2203	4300	6503	99977950	SO:0001583	missense	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.2061T>G	13.37:g.101179949T>G	ENSP00000365462:p.Ile687Met		99977950	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.80|12.80	2.046292|2.046292	0.36085|0.36085	.|.	.|.	ENSG00000175198|ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285;ENST00000376277;ENST00000428969|ENST00000458283	D;D;D;D|.	0.84146|.	-1.81;-1.81;-1.81;-1.81|.	5.55|5.55	-4.92|-4.92	0.03075|0.03075	Single hybrid motif (1);Biotin/lipoyl attachment (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.46927|0.46927	0.1418|0.1418	L|L	0.46885|0.46885	1.475|1.475	0.49687|0.49687	D|D	0.999814|0.999814	B;B;B|.	0.15473|.	0.006;0.01;0.013|.	B;B;B|.	0.28385|.	0.024;0.087;0.089|.	T|T	0.45977|0.45977	-0.9224|-0.9224	10|5	0.62326|.	D|.	0.03|.	.|.	3.7083|3.7083	0.08410|0.08410	0.2155:0.4423:0.1103:0.2319|0.2155:0.4423:0.1103:0.2319	.|.	640;661;687|.	C9JPQ8;P05165-2;P05165|.	.;.;PCCA_HUMAN|.	M|V	661;640;687;79;70|93	ENSP00000365463:I661M;ENSP00000365456:I640M;ENSP00000365462:I687M;ENSP00000399413:I70M|.	ENSP00000365454:I79M|.	I|L	+|+	3|1	3|2	PCCA|PCCA	99977950|99977950	0.751000|0.751000	0.28327|0.28327	0.946000|0.946000	0.38457|0.38457	0.812000|0.812000	0.45895|0.45895	-0.295000|-0.295000	0.08298|0.08298	-0.931000|-0.931000	0.03746|0.03746	-0.429000|-0.429000	0.05907|0.05907	ATT|TTG		0.423	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			G	101179949	T	G	101179949	3	3	61	1	0	0	0	0	1	0	0	0	11535	1829	64	4	2151	4	PCCA	13	101179949	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	217789	101179949	13989929	8743	16728										
NALCN	259232	broad.mit.edu	37	chr13	101760101	101760101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcatctttatttcactgtCttctctttgtgcatttctat	3	9	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:101760101C>A	ENST00000251127.6	-	21	2485	c.2404G>T	c.(2404-2406)Gac>Tac	p.D802Y		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	802					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.D802Y(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ATTTCACTGTCTTCTCTTTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13											202	174	184					13																	101760101		2203	4300	6503	100558102	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2404G>T	13.37:g.101760101C>A	ENSP00000251127:p.Asp802Tyr		100558102	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.095616	0.56075	.	.	ENSG00000102452	ENST00000251127	D	0.97831	-4.56	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.98479	0.9493	M	0.70595	2.14	0.80722	D	1	D	0.67145	0.996	D	0.66602	0.945	D	0.99647	1.0990	10	0.87932	D	0	.	19.5008	0.95093	0.0:1.0:0.0:0.0	.	802	Q8IZF0	NALCN_HUMAN	Y	802	ENSP00000251127:D802Y	ENSP00000251127:D802Y	D	-	1	0	NALCN	100558102	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.743000	0.68655	2.594000	0.87642	0.650000	0.86243	GAC		0.378	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		A	101760101	C	A	101760101	3	1	61	1	0	0	0	0	1	0	0	0	10178	913	32	2	2908	2	NALCN	13	101760101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	580152	101760101	13409777	8744	16729										
NALCN	259232	broad.mit.edu	37	chr13	102029339	102029339	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaatgctcggatcataatCagtggccgtggaatccgcaa	12	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:102029339C>A	ENST00000251127.6	-	5	525	c.444G>T	c.(442-444)ctG>ctT	p.L148L	NALCN_ENST00000376196.3_Silent_p.L148L|NALCN_ENST00000376200.5_Silent_p.L148L|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	148					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.L148L(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGATCATAATCAGTGGCCGTG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	13											74	73	74					13																	102029339		2203	4300	6503	100827340	SO:0001819	synonymous_variant	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.444G>T	13.37:g.102029339C>A			100827340	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																				0.398	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		A	102029339	C	A	102029339	2	1	61	1	0	0	0	0	0	0	0	1	10178	813	29	2		2	NALCN	13	102029339	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	269238	102029339	13140539	8745	16730										
ITGBL1	9358	broad.mit.edu	37	chr13	102231702	102231702	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcatggagataaatgtgaAttccagtgcgatatcacccc	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:102231702A>C	ENST00000376180.3	+	5	870	c.651A>C	c.(649-651)gaA>gaC	p.E217D	ITGBL1_ENST00000545560.2_Missense_Mutation_p.E76D|ITGBL1_ENST00000376162.3_Missense_Mutation_p.E124D	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	217	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)		p.E217D(1)		breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ATAAATGTGAATTCCAGTGCG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											158	147	150					13																	102231702		2203	4300	6503	101029703	SO:0001583	missense	9358			AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.651A>C	13.37:g.102231702A>C	ENSP00000365351:p.Glu217Asp		101029703	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Missense_Mutation	SNP	ENST00000376180.3	37	CCDS9499.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.322809	0.60634	.	.	ENSG00000198542	ENST00000376180;ENST00000537118;ENST00000539955;ENST00000545560;ENST00000376162	D;D;D	0.92595	-3.07;-3.07;-3.07	5.29	4.12	0.48240	.	0.000000	0.85682	D	0.000000	D	0.90331	0.6975	N	0.22421	0.69	0.51482	D	0.999928	P;D	0.65815	0.779;0.995	P;D	0.67382	0.814;0.951	D	0.85614	0.1260	10	0.10111	T	0.7	.	10.5043	0.44823	0.9221:0.0:0.0778:0.0	.	76;217	B3KTP1;O95965	.;ITGBL_HUMAN	D	217;125;76;76;124	ENSP00000365351:E217D;ENSP00000439903:E76D;ENSP00000365332:E124D	ENSP00000365332:E124D	E	+	3	2	ITGBL1	101029703	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.764000	0.38471	0.968000	0.38212	0.460000	0.39030	GAA		0.438	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		C	102231702	A	C	102231702	3	2	61	1	0	0	0	0	1	0	0	0	7923	98	4	4	669	4	ITGBL1	13	102231702	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	202363	102231702	12938176	8746	16731										
FGF14	2259	broad.mit.edu	37	chr13	102568818	102568818	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaccttggcgccgcaaccTgcgcttcttgaggccgaaga	12	14	1	3	rs368619012		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:102568818T>C	ENST00000376143.4	-	1	177	c.178A>G	c.(178-180)Agg>Ggg	p.R60G	FGF14_ENST00000376131.4_Intron	NM_004115.3	NP_004106.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	60					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.R60G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CGCCGCAACCTGCGCTTCTTG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	13											45	46	46					13																	102568818		2203	4300	6503	101366819	SO:0001583	missense	2259				CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466			3671	protein-coding gene	gene with protein product		601515				8790420, 17236779	Standard	NM_175929		Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376143.4:c.178A>G	13.37:g.102568818T>C	ENSP00000365313:p.Arg60Gly		101366819	Q86YN7|Q96QX6	Missense_Mutation	SNP	ENST00000376143.4	37	CCDS9501.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.762031	0.31228	.	.	ENSG00000102466	ENST00000376143	T	0.78595	-1.19	5.36	5.36	0.76844	.	.	.	.	.	T	0.70692	0.3253	L	0.43152	1.355	0.31663	N	0.645386	B	0.22211	0.066	B	0.22753	0.041	T	0.69752	-0.5060	9	0.30078	T	0.28	.	12.5174	0.56040	0.0:0.0:0.1388:0.8612	.	60	Q92915	FGF14_HUMAN	G	60	ENSP00000365313:R60G	ENSP00000365313:R60G	R	-	1	2	FGF14	101366819	1.000000	0.71417	1.000000	0.80357	0.265000	0.26407	3.756000	0.55205	2.023000	0.59567	0.460000	0.39030	AGG		0.657	FGF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045679.2			C	102568818	T	C	102568818	3	2	61	1	0	0	0	0	1	0	0	0	5862	1579	55	4	585	4	FGF14	13	102568818	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	337116	102568818	12601060	8747	16732										
FGF14	2259	broad.mit.edu	37	chr13	103053933	103053933	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttgggcgaaaagcaatcCagcagcttagacaccctgag	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103053933C>A	ENST00000376131.4	-	1	191	c.96G>T	c.(94-96)ctG>ctT	p.L32L	RP11-811P12.3_ENST00000418923.2_RNA	NM_175929.2	NP_787125.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	0					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.L32L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AAAAGCAATCCAGCAGCTTAG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	13											93	86	88					13																	103053933		2203	4300	6503	101851934	SO:0001819	synonymous_variant	2259				CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466			3671	protein-coding gene	gene with protein product		601515				8790420, 17236779	Standard	NM_175929		Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376131.4:c.96G>T	13.37:g.103053933C>A			101851934	Q86YN7|Q96QX6	Silent	SNP	ENST00000376131.4	37	CCDS9500.1																																																																																				0.413	FGF14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045680.5			A	103053933	C	A	103053933	2	1	61	1	0	0	0	0	0	0	0	1	5862	581	21	2		2	FGF14	13	103053933	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	485115	103053933	12115945	8748	16733										
TPP2	7174	broad.mit.edu	37	chr13	103280245	103280245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcttgtcaactacagttaCggagaagcaactcactggcc	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103280245C>T	ENST00000376065.4	+	8	1023	c.987C>T	c.(985-987)taC>taT	p.Y329Y	TPP2_ENST00000376052.3_Silent_p.Y329Y	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	329	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.Y329Y(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACTACAGTTACGGAGAAGCAA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	13											110	101	104					13																	103280245		2203	4300	6503	102078246	SO:0001819	synonymous_variant	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.987C>T	13.37:g.103280245C>T			102078246	Q5VZU8	Silent	SNP	ENST00000376065.4	37	CCDS9502.1																																																																																				0.363	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103280245	C	T	103280245	2	4	61	1	0	0	0	0	0	0	0	1	16452	547	19	1		1	TPP2	13	103280245	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	226312	103280245	11889633	8749	16734										
TPP2	7174	broad.mit.edu	37	chr13	103288611	103288611	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacctcgttcagaatacatCatttgctaataaattaggtt	5	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103288611C>A	ENST00000376065.4	+	13	1583	c.1547C>A	c.(1546-1548)tCa>tAa	p.S516*	TPP2_ENST00000376052.3_Nonsense_Mutation_p.S516*	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	516					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.S516*(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CAGAATACATCATTTGCTAAT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											94	85	88					13																	103288611		2203	4300	6503	102086612	SO:0001587	stop_gained	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.1547C>A	13.37:g.103288611C>A	ENSP00000365233:p.Ser516*		102086612	Q5VZU8	Nonsense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	C	39	7.435403	0.98282	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.96	5.96	0.96718	.	0.193278	0.46145	D	0.000317	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	.	.	.	X	516	.	ENSP00000365220:S516X	S	+	2	0	TPP2	102086612	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.832000	0.97577	0.655000	0.94253	TCA		0.368	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			A	103288611	C	A	103288611	4	1	61	1	0	0	0	0	0	1	0	0	16452	838	29	2	1597	2	TPP2	13	103288611	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8366	103288611	11881267	8750	16735										
TPP2	7174	broad.mit.edu	37	chr13	103317230	103317230	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagccctagcagtttataTtgcaatgaagactgatccca	7	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103317230T>G	ENST00000376065.4	+	26	3323	c.3287T>G	c.(3286-3288)aTt>aGt	p.I1096S	TPP2_ENST00000466153.1_3'UTR|TPP2_ENST00000376052.3_Missense_Mutation_p.I1109S	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1096					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.I1096S(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCAGTTTATATTGCAATGAAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13											78	77	77					13																	103317230		2203	4300	6503	102115231	SO:0001583	missense	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.3287T>G	13.37:g.103317230T>G	ENSP00000365233:p.Ile1096Ser		102115231	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.314154	0.60414	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.72	5.72	0.89469	.	0.219650	0.47852	D	0.000209	T	0.40448	0.1117	N	0.08118	0	0.50039	D	0.999849	B	0.24675	0.109	B	0.19666	0.026	T	0.37572	-0.9700	9	0.72032	D	0.01	.	16.0016	0.80297	0.0:0.0:0.0:1.0	.	1096	P29144	TPP2_HUMAN	S	1096;1109	.	ENSP00000365220:I1109S	I	+	2	0	TPP2	102115231	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.437000	0.80417	2.183000	0.69458	0.533000	0.62120	ATT		0.353	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			G	103317230	T	G	103317230	3	3	61	1	0	0	0	0	1	0	0	0	16452	1493	52	4	3389	4	TPP2	13	103317230	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	28619	103317230	11852648	8751	16736										
C13orf27	93081	broad.mit.edu	37	chr13	103419754	103419754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatacaaatgagaccccGaacaaaatcatcaccatcat	4	11	3	2	rs199524126		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103419754G>A	ENST00000376032.4	-	5	562	c.373C>T	c.(373-375)Cgg>Tgg	p.R125W	TEX30_ENST00000376021.4_Missense_Mutation_p.R84W|TEX30_ENST00000487260.1_5'Flank|TEX30_ENST00000376019.1_Missense_Mutation_p.R84W|TEX30_ENST00000376027.1_Intron|TEX30_ENST00000376029.3_Intron|TEX30_ENST00000376022.1_Intron	NM_138779.3	NP_620134.3	Q5JUR7	TEX30_HUMAN	testis expressed 30	125								p.R84W(2)		lung(1)|urinary_tract(1)	2						ATGAGACCCCGAACAAAATCA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	13						G	TRP/ARG	0,4406		0,0,2203	82	75	77		373	4.6	1	13		77	1,8599	1.2+/-3.3	0,1,4299	no	missense	C13orf27	NM_138779.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/228	103419754	1,13005	2203	4300	6503	102217755	SO:0001583	missense	93081			AF070559	CCDS9503.2, CCDS66577.1, CCDS66578.1	13q33.1	2012-02-09	2012-02-09	2012-02-09	ENSG00000151287	ENSG00000151287			25188	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 27"	C13orf27			Standard	XM_005254097		Approved		uc001vpo.3	Q5JUR7	OTTHUMG00000017306	ENST00000376032.4:c.373C>T	13.37:g.103419754G>A	ENSP00000365200:p.Arg125Trp		102217755	Q5JUR8|Q96KZ8	Missense_Mutation	SNP	ENST00000376032.4	37	CCDS9503.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182178	0.78677	0.0	1.16E-4	ENSG00000151287	ENST00000376019;ENST00000376021;ENST00000376032	T;T;T	0.24350	1.86;1.86;1.86	5.48	4.62	0.57501	.	0.062786	0.64402	D	0.000004	T	0.34978	0.0916	L	0.40543	1.245	0.80722	D	1	D	0.71674	0.998	P	0.54174	0.744	T	0.14952	-1.0454	10	0.66056	D	0.02	-19.9593	15.7952	0.78404	0.0:0.0:0.8627:0.1373	.	125	Q5JUR7	CM027_HUMAN	W	84;84;125	ENSP00000365187:R84W;ENSP00000365189:R84W;ENSP00000365200:R125W	ENSP00000365187:R84W	R	-	1	2	C13orf27	102217755	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.477000	0.60223	1.406000	0.46857	0.591000	0.81541	CGG		0.408	TEX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045691.4	NM_138779		A	103419754	G	A	103419754	3	1	61	1	0	0	0	0	1	0	0	0	1727	1057	37	1	318	1	C13orf27	13	103419754	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102524	103419754	11750124	8752	16737										
KDELC1	79070	broad.mit.edu	37	chr13	103440228	103440228	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatatgtcatcgcccatgaGattatttcttgcaaattctt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103440228G>T	ENST00000376004.4	-	8	1675	c.1339C>A	c.(1339-1341)Ctc>Atc	p.L447I	KDELC1_ENST00000460338.1_5'UTR	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	447						endoplasmic reticulum lumen (GO:0005788)		p.L447I(2)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TCGCCCATGAGATTATTTCTT	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	13											108	101	104					13																	103440228		2202	4299	6501	102238229	SO:0001583	missense	79070			BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.1339C>A	13.37:g.103440228G>T	ENSP00000365172:p.Leu447Ile		102238229	Q53HL3|Q9BVD2	Missense_Mutation	SNP	ENST00000376004.4	37	CCDS9504.1	.	.	.	.	.	.	.	.	.	.	G	34	5.301559	0.95601	.	.	ENSG00000134901	ENST00000376004	T	0.38560	1.13	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.75339	0.3836	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81086	-0.1092	10	0.66056	D	0.02	.	19.888	0.96917	0.0:0.0:1.0:0.0	.	447	Q6UW63	KDEL1_HUMAN	I	447	ENSP00000365172:L447I	ENSP00000365172:L447I	L	-	1	0	KDELC1	102238229	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.622000	0.83099	2.720000	0.93068	0.591000	0.81541	CTC		0.348	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1			T	103440228	G	T	103440228	3	4	61	1	0	0	0	0	1	0	0	0	8138	942	33	2	181	2	KDELC1	13	103440228	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20474	103440228	11729650	8753	16738										
KDELC1	79070	broad.mit.edu	37	chr13	103443320	103443320	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcatcgtgtttaaagaaGaaaaagttggtgaaagcagc	10	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103443320G>A	ENST00000376004.4	-	6	1350	c.1014C>T	c.(1012-1014)ttC>ttT	p.F338F	KDELC1_ENST00000460338.1_5'UTR	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	338						endoplasmic reticulum lumen (GO:0005788)		p.F338F(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GTTTAAAGAAGAAAAAGTTGG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	13											70	73	72					13																	103443320		2203	4300	6503	102241321	SO:0001819	synonymous_variant	79070			BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.1014C>T	13.37:g.103443320G>A			102241321	Q53HL3|Q9BVD2	Silent	SNP	ENST00000376004.4	37	CCDS9504.1																																																																																				0.403	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1			A	103443320	G	A	103443320	2	1	61	1	0	0	0	0	0	0	0	1	8138	933	33	3		3	KDELC1	13	103443320	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3092	103443320	11726558	8754	16739										
BIVM	54841	broad.mit.edu	37	chr13	103459698	103459698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagaaagtcacctgaagaGaatctacaaggtgctgtaaa	11	6	2	3	rs142016216		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103459698G>T	ENST00000257336.1	+	3	760	c.81G>T	c.(79-81)gaG>gaT	p.E27D	BIVM_ENST00000491929.1_3'UTR|BIVM-ERCC5_ENST00000602836.1_5'Flank|BIVM_ENST00000419638.1_Missense_Mutation_p.E27D|BIVM_ENST00000448849.2_Intron	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	27						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.E27D(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CACCTGAAGAGAATCTACAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	13											73	71	72					13																	103459698		2203	4300	6503	102257699	SO:0001583	missense	2073			AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.81G>T	13.37:g.103459698G>T	ENSP00000257336:p.Glu27Asp		102257699	Q2M1J2|Q9NXM4	Missense_Mutation	SNP	ENST00000257336.1	37	CCDS9505.1	.	.	.	.	.	.	.	.	.	.	G	4.983	0.182616	0.09495	.	.	ENSG00000134897	ENST00000257336;ENST00000419638	.	.	.	5.75	3.14	0.36123	.	0.063315	0.64402	N	0.000012	T	0.21881	0.0527	N	0.19112	0.55	0.30232	N	0.795782	B	0.02656	0.0	B	0.04013	0.001	T	0.10268	-1.0637	9	0.33141	T	0.24	.	2.2416	0.04021	0.1409:0.218:0.4238:0.2174	.	27	Q86UB2	BIVM_HUMAN	D	27	.	ENSP00000257336:E27D	E	+	3	2	BIVM	102257699	0.703000	0.27826	0.837000	0.33122	0.482000	0.33219	0.432000	0.21461	0.383000	0.24910	-0.751000	0.03497	GAG		0.438	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2			T	103459698	G	T	103459698	3	4	61	1	0	0	0	0	1	0	0	0	1442	933	33	2	83	2	BIVM	13	103459698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16378	103459698	11710180	8755	16740										
ERCC5	2073	broad.mit.edu	37	chr13	103524735	103524735	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgggggaaacctgatctcGacaaaattagagaatatcct	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:103524735G>A	ENST00000355739.4	+	13	4289	c.2866G>A	c.(2866-2868)Gac>Aac	p.D956N	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.R1381Q|ERCC5_ENST00000375954.1_Missense_Mutation_p.D189N	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	956					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)	p.D956N(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					ACCTGATCTCGACAAAATTAG	0.438			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	1	Substitution - Missense(1)	large_intestine(1)	13											56	54	54					13																	103524735		2203	4300	6503	102322736	SO:0001583	missense	2073	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2866G>A	13.37:g.103524735G>A	ENSP00000347978:p.Asp956Asn		102322736	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.976833	0.53720	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.79454	-1.27;-1.27	5.54	5.54	0.83059	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.532373	0.21339	N	0.076161	T	0.76744	0.4030	L	0.55103	1.725	0.80722	D	1	D;D	0.58620	0.983;0.959	B;B	0.42319	0.359;0.383	T	0.79895	-0.1610	10	0.56958	D	0.05	-5.1094	19.4954	0.95070	0.0:0.0:1.0:0.0	.	956;1381	P28715;Q59FZ7	ERCC5_HUMAN;.	N	1381;956;788;189	ENSP00000347978:D956N;ENSP00000365121:D189N	ENSP00000347978:D956N	D	+	1	0	ERCC5	102322736	1.000000	0.71417	0.014000	0.15608	0.492000	0.33523	6.552000	0.73914	2.607000	0.88179	0.655000	0.94253	GAC		0.438	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103524735	G	A	103524735	3	1	61	1	0	0	0	0	1	0	0	0	5229	1058	37	1	2916	1	ERCC5	13	103524735	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65037	103524735	11645143	8756	16741										
EFNB2	1948	broad.mit.edu	37	chr13	107147256	107147256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttttacaaagggacttgTtgtcgaacttcttccatttg	9	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:107147256T>C	ENST00000245323.4	-	4	735	c.586A>G	c.(586-588)Aca>Gca	p.T196A		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	196					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)	p.T196A(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					AAGGGACTTGTTGTCGAACTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											305	275	285					13																	107147256		2203	4300	6503	105945257	SO:0001583	missense	1948			L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.586A>G	13.37:g.107147256T>C	ENSP00000245323:p.Thr196Ala		105945257	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	37	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	T	3.826	-0.036797	0.07497	.	.	ENSG00000125266	ENST00000245323	D	0.90385	-2.66	6.07	6.07	0.98685	.	0.208574	0.51477	D	0.000097	T	0.80444	0.4624	N	0.11560	0.145	0.58432	D	0.999994	B	0.24092	0.097	B	0.23716	0.048	T	0.76515	-0.2931	10	0.05436	T	0.98	.	16.6277	0.84984	0.0:0.0:0.0:1.0	.	196	P52799	EFNB2_HUMAN	A	196	ENSP00000245323:T196A	ENSP00000245323:T196A	T	-	1	0	EFNB2	105945257	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.505000	0.66981	2.330000	0.79161	0.528000	0.53228	ACA		0.408	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		C	107147256	T	C	107147256	3	2	61	1	0	0	0	0	1	0	0	0	4967	1725	60	4	423	4	EFNB2	13	107147256	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3622521	107147256	8022622	8757	16742										
LIG4	3981	broad.mit.edu	37	chr13	108861527	108861527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctgcaattacacagtacGtgtctgggcctggattttgt	10	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:108861527G>A	ENST00000356922.4	-	2	2362	c.2090C>T	c.(2089-2091)aCg>aTg	p.T697M	LIG4_ENST00000442234.1_Missense_Mutation_p.T697M|LIG4_ENST00000405925.1_Missense_Mutation_p.T697M	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	697	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.T697M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TACACAGTACGTGTCTGGGCC	0.393								Non-homologous end-joining																																								1	Substitution - Missense(1)	large_intestine(1)	13											79	77	78					13																	108861527		2203	4300	6503	107659528	SO:0001583	missense	3981			X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.2090C>T	13.37:g.108861527G>A	ENSP00000349393:p.Thr697Met		107659528	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472941	0.84640	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.12984	2.63;2.63;2.63	5.83	5.83	0.93111	BRCT (4);	0.000000	0.85682	D	0.000000	T	0.42154	0.1190	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.16837	-1.0389	10	0.62326	D	0.03	.	19.1803	0.93620	0.0:0.0:1.0:0.0	.	697	P49917	DNLI4_HUMAN	M	697	ENSP00000385955:T697M;ENSP00000402030:T697M;ENSP00000349393:T697M	ENSP00000349393:T697M	T	-	2	0	LIG4	107659528	1.000000	0.71417	0.966000	0.40874	0.940000	0.58332	9.787000	0.99055	2.775000	0.95449	0.539000	0.68188	ACG		0.393	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		A	108861527	G	A	108861527	3	1	61	1	0	0	0	0	1	0	0	0	8806	1145	40	1	649	1	LIG4	13	108861527	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1714271	108861527	6308351	8758	16743										
ABHD13	84945	broad.mit.edu	37	chr13	108881742	108881742	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatagcaggtattctgtataAattccaggatgtattgcttt	8	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:108881742A>C	ENST00000375898.3	+	2	477	c.176A>C	c.(175-177)aAa>aCa	p.K59T		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	59						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.K59T(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ATTCTGTATAAATTCCAGGAT	0.353																																					Pancreas(22;506 789 38166 45896 51596)											1	Substitution - Missense(1)	large_intestine(1)	13											110	116	114					13																	108881742		2203	4299	6502	107679743	SO:0001583	missense	84945			AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"Abhydrolase domain containing"	20293	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 6"	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	ENST00000375898.3:c.176A>C	13.37:g.108881742A>C	ENSP00000365063:p.Lys59Thr		107679743	B3KWE7|Q8NBW1|Q96JX9	Missense_Mutation	SNP	ENST00000375898.3	37	CCDS32007.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.789755	0.31685	.	.	ENSG00000139826	ENST00000375898	T	0.16897	2.31	5.68	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.14141	0.0342	L	0.45581	1.43	0.58432	D	0.999999	P	0.42649	0.786	B	0.37451	0.25	T	0.06991	-1.0796	10	0.21014	T	0.42	-24.1899	10.7389	0.46141	0.9254:0.0:0.0746:0.0	.	59	Q7L211	ABHDD_HUMAN	T	59	ENSP00000365063:K59T	ENSP00000365063:K59T	K	+	2	0	ABHD13	107679743	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.054000	0.76649	0.969000	0.38237	0.455000	0.32223	AAA		0.353	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045743.1	NM_032859		C	108881742	A	C	108881742	3	2	61	1	0	0	0	0	1	0	0	0	78	14	1	4	178	4	ABHD13	13	108881742	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	20215	108881742	6288136	8759	16744										
TNFSF13B	10673	broad.mit.edu	37	chr13	108959224	108959224	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaacttgcaataccaagaGaaaatgcacaaatatcactg	5	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:108959224G>T	ENST00000375887.4	+	6	974	c.796G>T	c.(796-798)Gaa>Taa	p.E266*	TNFSF13B_ENST00000430559.1_Nonsense_Mutation_p.E247*	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	266					B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.E266*(1)		large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	AATACCAAGAGAAAATGCACA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											143	123	130					13																	108959224		2203	4300	6503	107757225	SO:0001587	stop_gained	10673			AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11929	protein-coding gene	gene with protein product		603969		TNFSF20		10331498, 10359578	Standard	NM_006573		Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.796G>T	13.37:g.108959224G>T	ENSP00000365048:p.Glu266*		107757225	E0ADT7|Q6FHD6|Q7Z5J2	Nonsense_Mutation	SNP	ENST00000375887.4	37	CCDS9509.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700119	0.88924	.	.	ENSG00000102524	ENST00000430559;ENST00000375887	.	.	.	5.49	4.63	0.57726	.	0.540943	0.21152	N	0.079315	.	.	.	.	.	.	0.26442	N	0.975759	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.5953	6.1949	0.20544	0.2349:0.0:0.7651:0.0	.	.	.	.	X	247;266	.	.	E	+	1	0	TNFSF13B	107757225	0.910000	0.30920	0.400000	0.26346	0.857000	0.48899	2.203000	0.42752	2.722000	0.93159	0.591000	0.81541	GAA		0.378	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045739.3			T	108959224	G	T	108959224	4	4	61	1	0	0	0	0	0	1	0	0	16345	943	33	2	818	2	TNFSF13B	13	108959224	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77482	108959224	6210654	8760	16745										
MYO16	23026	broad.mit.edu	37	chr13	109704802	109704802	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaattattggagaaaacaaGaattatctagaacttagtaa	6	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:109704802G>T	ENST00000357550.2	+	24	3002	c.2961G>T	c.(2959-2961)aaG>aaT	p.K987N	MYO16_ENST00000356711.2_Missense_Mutation_p.K987N|MYO16_ENST00000457511.2_Missense_Mutation_p.K499N	NM_001198950.1	NP_001185879.1			myosin XVI									p.K987N(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GAGAAAACAAGAATTATCTAG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	13											75	74	74					13																	109704802		2203	4300	6503	108502803	SO:0001583	missense	23026				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.2961G>T	13.37:g.109704802G>T	ENSP00000350160:p.Lys987Asn		108502803		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846438	0.71603	.	.	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000375857;ENST00000457511	D;D;D	0.87809	-2.3;-2.3;-2.3	5.66	4.8	0.61643	Myosin head, motor domain (2);	0.412552	0.17657	U	0.166471	D	0.87018	0.6073	M	0.62723	1.935	0.45648	D	0.998573	P;B;P	0.40970	0.726;0.328;0.734	P;B;P	0.46049	0.474;0.284;0.502	D	0.85031	0.0917	9	.	.	.	.	10.4446	0.44486	0.1495:0.0:0.8505:0.0	.	499;987;987	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	N	987;987;775;499	ENSP00000349145:K987N;ENSP00000350160:K987N;ENSP00000401633:K499N	.	K	+	3	2	MYO16	108502803	1.000000	0.71417	0.828000	0.32881	0.990000	0.78478	4.205000	0.58466	2.669000	0.90835	0.591000	0.81541	AAG		0.308	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109704802	G	T	109704802	3	4	61	1	0	0	0	0	1	0	0	0	10094	933	33	2	3055	2	MYO16	13	109704802	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	745578	109704802	5465076	8761	16746										
MYO16	23026	broad.mit.edu	37	chr13	109707770	109707770	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatattattggaaaacttcaGaagtgcactccacacttcat	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:109707770G>T	ENST00000357550.2	+	26	3137	c.3096G>T	c.(3094-3096)caG>caT	p.Q1032H	MYO16_ENST00000356711.2_Missense_Mutation_p.Q1032H|MYO16_ENST00000457511.2_Missense_Mutation_p.Q544H	NM_001198950.1	NP_001185879.1			myosin XVI									p.Q1032H(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GAAAACTTCAGAAGTGCACTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	13											74	72	73					13																	109707770		2203	4299	6502	108505771	SO:0001583	missense	23026				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.3096G>T	13.37:g.109707770G>T	ENSP00000350160:p.Gln1032His		108505771		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965788	0.74131	.	.	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000375857;ENST00000457511	D;D;D	0.87491	-2.26;-2.26;-2.26	5.21	4.36	0.52297	Myosin head, motor domain (2);	0.192600	0.25114	U	0.033033	D	0.88526	0.6460	L	0.38531	1.155	0.53005	D	0.99996	P;P;D	0.56746	0.898;0.776;0.977	P;P;P	0.62885	0.805;0.714;0.908	D	0.86798	0.1990	9	.	.	.	.	13.2916	0.60274	0.0773:0.0:0.9227:0.0	.	544;1032;1032	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	H	1032;1032;820;544	ENSP00000349145:Q1032H;ENSP00000350160:Q1032H;ENSP00000401633:Q544H	.	Q	+	3	2	MYO16	108505771	1.000000	0.71417	0.896000	0.35187	0.922000	0.55478	4.660000	0.61511	1.158000	0.42547	0.561000	0.74099	CAG		0.363	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109707770	G	T	109707770	3	4	61	1	0	0	0	0	1	0	0	0	10094	933	33	2	3198	2	MYO16	13	109707770	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2968	109707770	5462108	8762	16747										
MYO16	23026	broad.mit.edu	37	chr13	109772791	109772791	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgcctacagttgcagaGaaaaattataacctgccaaa	7	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:109772791G>T	ENST00000357550.2	+	28	3487	c.3446G>T	c.(3445-3447)aGa>aTa	p.R1149I	MYO16_ENST00000356711.2_Missense_Mutation_p.R1149I|MYO16_ENST00000457511.2_Missense_Mutation_p.R661I	NM_001198950.1	NP_001185879.1			myosin XVI									p.R1149I(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CAGTTGCAGAGAAAAATTATA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	13											111	107	108					13																	109772791		2203	4300	6503	108570792	SO:0001583	missense	23026				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.3446G>T	13.37:g.109772791G>T	ENSP00000350160:p.Arg1149Ile		108570792		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.631771	0.46944	.	.	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000457511	D;D;D	0.95447	-3.71;-3.71;-3.71	5.38	3.61	0.41365	.	0.154989	0.29424	U	0.012187	D	0.89350	0.6690	N	0.24115	0.695	0.52501	D	0.999957	P;P	0.45715	0.865;0.788	B;B	0.42882	0.401;0.293	D	0.84020	0.0353	9	.	.	.	.	4.4853	0.11787	0.2556:0.1711:0.5733:0.0	.	661;1149	F8W883;Q9Y6X6	.;MYO16_HUMAN	I	1149;1149;661	ENSP00000349145:R1149I;ENSP00000350160:R1149I;ENSP00000401633:R661I	.	R	+	2	0	MYO16	108570792	1.000000	0.71417	0.964000	0.40570	0.983000	0.72400	2.453000	0.44970	0.607000	0.29982	0.650000	0.86243	AGA		0.353	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109772791	G	T	109772791	3	4	61	1	0	0	0	0	1	0	0	0	10094	942	33	2	3556	2	MYO16	13	109772791	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65021	109772791	5397087	8763	16748										
MYO16	23026	broad.mit.edu	37	chr13	109777577	109777577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacatggggctgaaaacctAcgatgccctggtcattcaga	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:109777577A>G	ENST00000357550.2	+	29	3628	c.3587A>G	c.(3586-3588)tAc>tGc	p.Y1196C	MYO16_ENST00000356711.2_Missense_Mutation_p.Y1196C|MYO16_ENST00000457511.2_Missense_Mutation_p.Y708C	NM_001198950.1	NP_001185879.1			myosin XVI									p.Y1196C(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CTGAAAACCTACGATGCCCTG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	13											72	67	69					13																	109777577		2203	4300	6503	108575578	SO:0001583	missense	23026				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.3587A>G	13.37:g.109777577A>G	ENSP00000350160:p.Tyr1196Cys		108575578		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254783	0.59212	.	.	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000457511	D;D;D	0.90844	-1.64;-1.64;-2.74	5.23	5.23	0.72850	.	0.000000	0.37095	U	0.002257	D	0.94666	0.8280	M	0.76328	2.33	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.94569	0.7769	9	.	.	.	.	14.4586	0.67433	1.0:0.0:0.0:0.0	.	708;1196	F8W883;Q9Y6X6	.;MYO16_HUMAN	C	1196;1196;708	ENSP00000349145:Y1196C;ENSP00000350160:Y1196C;ENSP00000401633:Y708C	.	Y	+	2	0	MYO16	108575578	1.000000	0.71417	0.913000	0.36048	0.453000	0.32348	7.964000	0.87933	2.194000	0.70268	0.533000	0.62120	TAC		0.488	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		G	109777577	A	G	109777577	3	3	61	1	0	0	0	0	1	0	0	0	10094	391	14	4	3701	4	MYO16	13	109777577	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4786	109777577	5392301	8764	16749										
COL4A1	1282	broad.mit.edu	37	chr13	110847385	110847385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacctttctctccaatttCgcctataaatcctggctgcc	4	15	1	0	rs570739274		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:110847385C>T	ENST00000375820.4	-	22	1487	c.1366G>A	c.(1366-1368)Gaa>Aaa	p.E456K	COL4A1_ENST00000543140.1_Missense_Mutation_p.E456K	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	456	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.E456K(1)|p.E450K(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TCTCCAATTTCGCCTATAAAT	0.443													C|||	1	0.000199681	0	0.0014	5008	,	,		17234	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	13											45	49	47					13																	110847385		2203	4300	6503	109645386	SO:0001583	missense	1282			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1366G>A	13.37:g.110847385C>T	ENSP00000364979:p.Glu456Lys		109645386	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408191	0.42715	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198;ENST00000543140	D;D	0.95205	-3.26;-3.64	5.49	5.49	0.81192	.	0.052786	0.64402	D	0.000001	D	0.94997	0.8381	L	0.42744	1.35	0.58432	D	0.999997	D	0.89917	1.0	D	0.81914	0.995	D	0.91652	0.5335	10	0.06236	T	0.91	.	16.9032	0.86118	0.0:1.0:0.0:0.0	.	456	P02462	CO4A1_HUMAN	K	450;456;456;456	ENSP00000364979:E456K;ENSP00000443348:E456K	ENSP00000364973:E450K	E	-	1	0	COL4A1	109645386	0.994000	0.37717	0.108000	0.21378	0.211000	0.24417	5.003000	0.63959	2.583000	0.87209	0.561000	0.74099	GAA		0.443	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			T	110847385	C	T	110847385	3	4	61	1	0	0	0	0	1	0	0	0	3695	893	31	1	3767	1	COL4A1	13	110847385	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1069808	110847385	4322493	8765	16750										
C13orf16	121793	broad.mit.edu	37	chr13	111980555	111980555	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacgttcctctgtatgacatTtgtgactacaacgtctccag	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:111980555T>G	ENST00000283547.1	+	3	213	c.84T>G	c.(82-84)atT>atG	p.I28M		NM_152324.1	NP_689537.1	Q8N6K0	TEX29_HUMAN	testis expressed 29	28						integral component of membrane (GO:0016021)		p.I28M(1)									TGTATGACATTTGTGACTACA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	13											146	121	130					13																	111980555		2203	4300	6503	110778556	SO:0001583	missense	121793			BC029889	CCDS9522.1	13q34	2012-03-23	2012-02-07	2012-02-07	ENSG00000153495	ENSG00000153495			20370	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 16"	C13orf16			Standard	NM_152324		Approved	bA474D23.1, MGC35169	uc001vsa.3	Q8N6K0	OTTHUMG00000017358	ENST00000283547.1:c.84T>G	13.37:g.111980555T>G	ENSP00000283547:p.Ile28Met		110778556		Missense_Mutation	SNP	ENST00000283547.1	37	CCDS9522.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507735	0.64410	.	.	ENSG00000153495	ENST00000283547	.	.	.	5.32	-4.0	0.04057	.	0.189651	0.25316	N	0.031546	T	0.29458	0.0734	L	0.32530	0.975	0.27840	N	0.941143	D	0.54964	0.969	P	0.56042	0.79	T	0.28490	-1.0042	9	0.87932	D	0	-22.4678	1.3694	0.02207	0.2338:0.3179:0.0904:0.3578	.	28	Q8N6K0	CM016_HUMAN	M	28	.	ENSP00000283547:I28M	I	+	3	3	C13orf16	110778556	0.996000	0.38824	0.951000	0.38953	0.987000	0.75469	0.057000	0.14279	-1.070000	0.03149	0.402000	0.26972	ATT		0.537	TEX29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045812.2	NM_152324		G	111980555	T	G	111980555	3	3	61	1	0	0	0	0	1	0	0	0	1723	1829	64	4	90	4	C13orf16	13	111980555	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1133170	111980555	3189323	8766	16751										
C13orf28	122258	broad.mit.edu	37	chr13	113086765	113086765	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttccccacagaaaagaaTtcaaagaacactcagtatga	6	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113086765T>G	ENST00000283550.3	+	6	520	c.453T>G	c.(451-453)aaT>aaG	p.N151K	SPACA7_ENST00000375699.3_Missense_Mutation_p.N120K	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	151						acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)		p.N151K(1)		large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						CAGAAAAGAATTCAAAGAACA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	13											76	79	78					13																	113086765		2203	4300	6503	112134766	SO:0001583	missense	122258			BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 28"	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.453T>G	13.37:g.113086765T>G	ENSP00000283550:p.Asn151Lys		112134766	Q5T8L1	Missense_Mutation	SNP	ENST00000283550.3	37	CCDS9524.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.203650	0.38905	.	.	ENSG00000153498	ENST00000283550;ENST00000375699	T;T	0.48522	0.84;0.81	3.04	-2.55	0.06288	.	.	.	.	.	T	0.19967	0.0480	N	0.14661	0.345	0.09310	N	1	B	0.33044	0.395	B	0.23574	0.047	T	0.12091	-1.0561	9	0.25751	T	0.34	-1.7748	2.4382	0.04488	0.3678:0.1996:0.0:0.4327	.	151	Q96KW9	SPAC7_HUMAN	K	151;120	ENSP00000283550:N151K;ENSP00000364851:N120K	ENSP00000283550:N151K	N	+	3	2	SPACA7	112134766	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.073000	0.03430	-0.519000	0.06444	0.533000	0.62120	AAT		0.348	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248		G	113086765	T	G	113086765	3	3	61	1	0	0	0	0	1	0	0	0	1728	1490	52	4	475	4	C13orf28	13	113086765	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1106210	113086765	2083113	8767	16752										
TUBGCP3	10426	broad.mit.edu	37	chr13	113219480	113219480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcagcatctgcttctcttCgttgtcgaataactgaaaag	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113219480C>T	ENST00000261965.3	-	3	383	c.197G>A	c.(196-198)cGa>cAa	p.R66Q	TUBGCP3_ENST00000375669.3_Missense_Mutation_p.R66Q	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	66					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R66Q(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	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)					TGCTTCTCTTCGTTGTCGAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	13											165	163	163					13																	113219480		2203	4300	6503	112267481	SO:0001583	missense	10426			AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.197G>A	13.37:g.113219480C>T	ENSP00000261965:p.Arg66Gln		112267481	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	37	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972611	0.53614	.	.	ENSG00000126216	ENST00000261965;ENST00000375669	T;T	0.22134	1.97;1.97	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.36496	0.0969	L	0.57536	1.79	0.58432	D	0.999992	P;D;B;P	0.76494	0.785;0.999;0.108;0.891	B;P;B;B	0.59703	0.255;0.862;0.036;0.172	T	0.09509	-1.0671	10	0.11794	T	0.64	-21.1653	17.687	0.88258	0.0:1.0:0.0:0.0	.	66;66;66;66	B4DYP7;Q96CW5-3;Q96CW5-2;Q96CW5	.;.;.;GCP3_HUMAN	Q	66	ENSP00000261965:R66Q;ENSP00000364821:R66Q	ENSP00000261965:R66Q	R	-	2	0	TUBGCP3	112267481	1.000000	0.71417	0.541000	0.28102	0.671000	0.39405	6.715000	0.74697	2.263000	0.75096	0.638000	0.83543	CGA		0.363	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		T	113219480	C	T	113219480	3	4	61	1	0	0	0	0	1	0	0	0	16807	884	31	1	2606	1	TUBGCP3	13	113219480	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132715	113219480	1950398	8768	16753										
ATP11A	23250	broad.mit.edu	37	chr13	113527934	113527934	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatcaaccattttgtcatCtgggggtcgctgctgttcta	11	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113527934C>T	ENST00000487903.1	+	27	3193	c.3105C>T	c.(3103-3105)atC>atT	p.I1035I	ATP11A_ENST00000375645.3_Silent_p.I1035I|ATP11A_ENST00000375630.2_Silent_p.I1035I|ATP11A_ENST00000283558.8_Silent_p.I1035I			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1035					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.I1035I(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	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_lung(25;0.134)|all_epithelial(44;0.141)				ATTTTGTCATCTGGGGGTCGC	0.423											OREG0003854	type=REGULATORY REGION|Gene=ATP11A|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - coding silent(1)	large_intestine(1)	13											230	191	204					13																	113527934		2203	4300	6503	112575935	SO:0001819	synonymous_variant	23250			AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3105C>T	13.37:g.113527934C>T		1451	112575935	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																				0.423	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		T	113527934	C	T	113527934	2	4	61	1	0	0	0	0	0	0	0	1	1120	903	32	3		3	ATP11A	13	113527934	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308454	113527934	1641944	8769	16754										
F10	2159	broad.mit.edu	37	chr13	113803327	113803327	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaggagacctatgacttCgacatcgccgtgctccggct	10	13	0	2	rs148209958		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113803327C>T	ENST00000375559.3	+	8	1001	c.963C>T	c.(961-963)ttC>ttT	p.F321F	F10_ENST00000375551.3_Missense_Mutation_p.S318L|F10_ENST00000409306.1_Missense_Mutation_p.S320L	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	321	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)	p.F321F(1)		endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	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;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	CCTATGACTTCGACATCGCCG	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	13						C		1,4405	2.1+/-5.4	0,1,2202	202	159	174		963	-2.6	0.2	13	dbSNP_134	174	0,8600		0,0,4300	no	coding-synonymous	F10	NM_000504.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		321/489	113803327	1,13005	2203	4300	6503	112851328	SO:0001819	synonymous_variant	2159				CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.963C>T	13.37:g.113803327C>T			112851328	Q14340	Silent	SNP	ENST00000375559.3	37	CCDS9530.1	.	.	.	.	.	.	.	.	.	.	C	9.254	1.041434	0.19669	2.27E-4	0.0	ENSG00000126218	ENST00000409306;ENST00000375551	D;D	0.96136	-3.86;-3.92	5.25	-2.57	0.06248	.	.	.	.	.	D	0.92280	0.7551	.	.	.	0.80722	D	1	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.78994	-0.1984	8	0.87932	D	0	.	13.6534	0.62325	0.0:0.3075:0.0:0.6925	.	320;318	B7ZBK1;Q5JVE8	.;.	L	320;318	ENSP00000387092:S320L;ENSP00000364701:S318L	ENSP00000364701:S318L	S	+	2	0	F10	112851328	0.000000	0.05858	0.246000	0.24233	0.446000	0.32137	-0.944000	0.03913	-0.888000	0.03956	0.563000	0.77884	TCG		0.642	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			T	113803327	C	T	113803327	2	4	61	1	0	0	0	0	0	0	0	1	5349	883	31	1		1	F10	13	113803327	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	275393	113803327	1366551	8770	16755										
PCID2	55795	broad.mit.edu	37	chr13	113835492	113835492	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagaatcatccttttgttCttctgactagaacggtgaca	7	9	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113835492C>A	ENST00000337344.4	-	10	814	c.738G>T	c.(736-738)aaG>aaT	p.K246N	PCID2_ENST00000375479.2_Missense_Mutation_p.K246N|PCID2_ENST00000375457.2_Missense_Mutation_p.K244N|PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000246505.5_Missense_Mutation_p.K300N|PCID2_ENST00000375459.1_Missense_Mutation_p.K244N|PCID2_ENST00000375477.1_Missense_Mutation_p.K246N	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	246					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)			p.K300N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	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)			TCCTTTTGTTCTTCTGACTAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											146	126	133					13																	113835492		2203	4300	6503	112883493	SO:0001583	missense	55795			AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.738G>T	13.37:g.113835492C>A	ENSP00000337405:p.Lys246Asn		112883493	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	37	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165830	0.38217	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	.	.	.	5.25	4.28	0.50868	PCI/PINT associated module (1);	0.051288	0.85682	D	0.000000	T	0.50051	0.1593	M	0.62088	1.915	0.52501	D	0.999954	B;B	0.23058	0.079;0.003	B;B	0.25405	0.06;0.017	T	0.51301	-0.8723	9	0.37606	T	0.19	-25.154	5.9745	0.19371	0.0:0.6834:0.0:0.3166	.	300;246	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	N	246;246;246;300;244;244;223;246;223	.	ENSP00000246505:K300N	K	-	3	2	PCID2	112883493	1.000000	0.71417	1.000000	0.80357	0.648000	0.38561	2.481000	0.45215	2.445000	0.82738	0.563000	0.77884	AAG		0.433	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386		A	113835492	C	A	113835492	3	1	61	1	0	0	0	0	1	0	0	0	11610	912	32	2	481	2	PCID2	13	113835492	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32165	113835492	1334386	8771	16756										
CUL4A	8451	broad.mit.edu	37	chr13	113897299	113897299	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacttttggaacagcgatCgtaatcaatcctgagaaaga	9	7	1	3	rs146783617	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113897299C>T	ENST00000375440.4	+	11	1137	c.1053C>T	c.(1051-1053)atC>atT	p.I351I	CUL4A_ENST00000375441.3_Silent_p.I251I|CUL4A_ENST00000451881.1_Silent_p.I251I|CUL4A_ENST00000326335.4_Silent_p.I251I	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	351					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)		p.I251I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			GAACAGCGATCGTAATCAATC	0.418													C|||	2	0.000399361	0.0015	0	5008	,	,		17539	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13						C	,	5,4401	8.1+/-20.4	0,5,2198	152	127	136		1053,753	-0.9	1	13	dbSNP_134	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CUL4A	NM_001008895.1,NM_003589.2	,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,	351/760,251/660	113897299	5,13001	2203	4300	6503	112945300	SO:0001819	synonymous_variant	8451			U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1053C>T	13.37:g.113897299C>T			112945300	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Silent	SNP	ENST00000375440.4	37	CCDS41908.1																																																																																				0.418	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		T	113897299	C	T	113897299	2	4	61	1	0	0	0	0	0	0	0	1	4063	874	31	1		1	CUL4A	13	113897299	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61807	113897299	1272579	8772	16757										
LAMP1	3916	broad.mit.edu	37	chr13	113974716	113974716	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcggccagcgggagctgCggcgcccacctggtgactct	14	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113974716C>T	ENST00000332556.4	+	6	1001	c.807C>T	c.(805-807)tgC>tgT	p.C269C	LAMP1_ENST00000397181.3_Silent_p.C216C	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	269	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)	p.C269C(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GCGGGAGCTGCGGCGCCCACC	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	13											111	115	114					13																	113974716		2068	4217	6285	113022717	SO:0001819	synonymous_variant	3916			J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.807C>T	13.37:g.113974716C>T			113022717	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	37	CCDS41909.1																																																																																				0.632	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			T	113974716	C	T	113974716	2	4	61	1	0	0	0	0	0	0	0	1	8639	776	27	1		1	LAMP1	13	113974716	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77417	113974716	1195162	8773	16758										
LAMP1	3916	broad.mit.edu	37	chr13	113975969	113975969	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagcacgtccgtgtcacGaaggcgttttcagtcaatat	12	9	3	0	rs376013627		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:113975969G>A	ENST00000332556.4	+	8	1235	c.1041G>A	c.(1039-1041)acG>acA	p.T347T	LAMP1_ENST00000397181.3_Silent_p.T294T	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	347	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)	p.T347T(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TCCGTGTCACGAAGGCGTTTT	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		17366	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13						G		1,4217		0,1,2108	106	116	112		1041	-10.5	0	13		112	1,8405		0,1,4202	no	coding-synonymous	LAMP1	NM_005561.3		0,2,6310	AA,AG,GG		0.0119,0.0237,0.0158		347/418	113975969	2,12622	2109	4203	6312	113023970	SO:0001819	synonymous_variant	3916			J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.1041G>A	13.37:g.113975969G>A			113023970	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	37	CCDS41909.1																																																																																				0.577	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			A	113975969	G	A	113975969	2	1	61	1	0	0	0	0	0	0	0	1	8639	1045	37	1		1	LAMP1	13	113975969	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1253	113975969	1193909	8774	16759										
ATP4B	496	broad.mit.edu	37	chr13	114307233	114307233	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctttccttcttcaaagccGaagttgggatccgccaggcc	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:114307233G>A	ENST00000335288.4	-	4	551	c.510C>T	c.(508-510)ttC>ttT	p.F170F		NM_000705.3	NP_000696.1	P51164	ATP4B_HUMAN	ATPase, H+/K+ exchanging, beta polypeptide	170					cell adhesion (GO:0007155)|hydrogen ion transmembrane transport (GO:1902600)|ion transmembrane transport (GO:0034220)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	hydrogen:potassium-exchanging ATPase activity (GO:0008900)	p.F170F(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.171)			CTTCAAAGCCGAAGTTGGGAT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	13											78	76	77					13																	114307233		2203	4300	6503	113355234	SO:0001819	synonymous_variant	496				CCDS9539.1	13q34	2011-08-01			ENSG00000186009	ENSG00000186009	3.6.3.10	"ATPases / P-type"	820	protein-coding gene	gene with protein product		137217				1330887, 15057823	Standard	NM_000705		Approved	ATP6B	uc001vtz.3	P51164	OTTHUMG00000140234	ENST00000335288.4:c.510C>T	13.37:g.114307233G>A			113355234	B1B0N8	Silent	SNP	ENST00000335288.4	37	CCDS9539.1																																																																																				0.512	ATP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276703.2	NM_000705		A	114307233	G	A	114307233	2	1	61	1	0	0	0	0	0	0	0	1	1147	1049	37	1		1	ATP4B	13	114307233	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	331264	114307233	862645	8775	16760										
RASA3	22821	broad.mit.edu	37	chr13	114789762	114789762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggttttctcacctgatttCgagcttgtccacgtcttcct	7	13	2	1	rs370747207		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:114789762C>T	ENST00000334062.7	-	8	794	c.673G>A	c.(673-675)Gaa>Aaa	p.E225K	RASA3_ENST00000542651.1_3'UTR|RASA3_ENST00000389544.4_Missense_Mutation_p.E193K	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	225	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.E225K(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CACCTGATTTCGAGCTTGTCC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	LYS/GLU	0,4406		0,0,2203	261	284	276		673	5.4	0.9	13		276	1,8599	1.2+/-3.3	0,1,4299	no	missense	RASA3	NM_007368.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	225/835	114789762	1,13005	2203	4300	6503	113807864	SO:0001583	missense	22821				CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.673G>A	13.37:g.114789762C>T	ENSP00000335029:p.Glu225Lys		113807864	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677331	0.47886	0.0	1.16E-4	ENSG00000185989	ENST00000334062;ENST00000389544	D;D	0.86694	-2.06;-2.16	5.41	5.41	0.78517	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.768732	0.12442	N	0.468638	D	0.87059	0.6083	L	0.38175	1.15	0.80722	D	1	P	0.49635	0.926	P	0.49421	0.61	D	0.84536	0.0636	9	.	.	.	.	17.9483	0.89045	0.0:1.0:0.0:0.0	.	225	Q14644	RASA3_HUMAN	K	225;193	ENSP00000335029:E225K;ENSP00000374195:E193K	.	E	-	1	0	RASA3	113807864	1.000000	0.71417	0.907000	0.35723	0.001000	0.01503	4.503000	0.60407	2.513000	0.84729	0.655000	0.94253	GAA		0.498	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114789762	C	T	114789762	3	4	61	1	0	0	0	0	1	0	0	0	13099	893	31	1	1899	1	RASA3	13	114789762	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	482529	114789762	380116	8776	16761										
CDC16	8881	broad.mit.edu	37	chr13	115024835	115024835	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagccgaaaaatggtttCttgatgctttggaaaaaatt	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:115024835C>A	ENST00000356221.3	+	14	1384	c.1276C>A	c.(1276-1278)Ctt>Att	p.L426I	CDC16_ENST00000375312.3_Missense_Mutation_p.L281I|CDC16_ENST00000360383.3_Missense_Mutation_p.L426I|CDC16_ENST00000252458.6_Missense_Mutation_p.L281I|CDC16_ENST00000375310.1_Missense_Mutation_p.L332I|CDC16_ENST00000375308.1_Missense_Mutation_p.L332I|CDC16_ENST00000252457.5_Missense_Mutation_p.L425I			Q13042	CDC16_HUMAN	cell division cycle 16	426					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)		p.L425I(1)		endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			AAAATGGTTTCTTGATGCTTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	13											86	94	91					13																	115024835		2203	4299	6502	114042937	SO:0001583	missense	8881			U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.1276C>A	13.37:g.115024835C>A	ENSP00000348554:p.Leu426Ile		114042937	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975715	0.53720	.	.	ENSG00000130177	ENST00000360383;ENST00000375312;ENST00000356221;ENST00000375310;ENST00000252457;ENST00000375308;ENST00000252458	T;T;T;T;T;T;T	0.73681	0.59;-0.77;0.59;0.59;0.59;0.59;-0.77	5.43	5.43	0.79202	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.75576	0.3868	L	0.60455	1.87	0.80722	D	1	P;P;P	0.45768	0.866;0.606;0.471	P;P;B	0.48400	0.576;0.529;0.329	T	0.74711	-0.3573	9	.	.	.	-17.3394	12.5606	0.56279	0.0:0.9229:0.0:0.0771	.	374;425;426	Q13042-3;Q13042-2;Q13042	.;.;CDC16_HUMAN	I	426;281;426;332;425;332;281	ENSP00000353549:L426I;ENSP00000364461:L281I;ENSP00000348554:L426I;ENSP00000364459:L332I;ENSP00000252457:L425I;ENSP00000364457:L332I;ENSP00000252458:L281I	.	L	+	1	0	CDC16	114042937	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.095000	0.64529	2.713000	0.92767	0.655000	0.94253	CTT		0.299	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		A	115024835	C	A	115024835	3	1	61	1	0	0	0	0	1	0	0	0	3064	913	32	2	1330	2	CDC16	13	115024835	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235073	115024835	145043	8777	16762										
ZNF828	283489	broad.mit.edu	37	chr13	115089339	115089339	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaagcattccaggaacttCgtaaaccatcagcacgtttg	9	10	1	0	rs371511810		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:115089339C>T	ENST00000361283.1	+	3	331	c.22C>T	c.(22-24)Cgt>Tgt	p.R8C		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	8					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.R8C(1)									CCAGGAACTTCGTAAACCATC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	13						C	CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	124	119	121		22,22,22	5	0	13		121	0,8600		0,0,4300	no	missense,missense,missense	ZNF828	NM_001164144.1,NM_001164145.1,NM_032436.2	180,180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	8/813,8/813,8/813	115089339	1,13005	2203	4300	6503	114107441	SO:0001583	missense	283489			AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.22C>T	13.37:g.115089339C>T	ENSP00000354730:p.Arg8Cys		114107441	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	37	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321379	0.60634	2.27E-4	0.0	ENSG00000198824	ENST00000361283	T	0.01584	4.75	5.83	4.98	0.66077	.	0.387956	0.22343	N	0.061305	T	0.03220	0.0094	L	0.32530	0.975	0.09310	N	0.999998	D	0.64830	0.994	P	0.50049	0.629	T	0.49072	-0.8977	9	.	.	.	-2.2058	14.1691	0.65497	0.2712:0.7288:0.0:0.0	.	8	Q96JM3	ZN828_HUMAN	C	8	ENSP00000354730:R8C	.	R	+	1	0	ZNF828	114107441	0.016000	0.18221	0.004000	0.12327	0.979000	0.70002	2.277000	0.43417	1.453000	0.47775	0.655000	0.94253	CGT		0.378	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		T	115089339	C	T	115089339	3	4	61	1	0	0	0	0	1	0	0	0	18220	884	31	1	24	1	ZNF828	13	115089339	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64504	115089339	80539	8778	16763										
ZNF828	283489	broad.mit.edu	37	chr13	115090672	115090672	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagatctttggaagctttCtcctgatcagcggaaaactt	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr13:115090672C>A	ENST00000361283.1	+	3	1664	c.1355C>A	c.(1354-1356)tCt>tAt	p.S452Y		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	452	Mediates interaction with MAD2L2.|Mediates localization to the spindle and the kinetochore and is required for the attachment of spindle microtubules to the kinetochore.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S452Y(1)									TGGAAGCTTTCTCCTGATCAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	13											130	151	144					13																	115090672		2203	4300	6503	114108774	SO:0001583	missense	283489			AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.1355C>A	13.37:g.115090672C>A	ENSP00000354730:p.Ser452Tyr		114108774	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	37	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.888203	0.52014	.	.	ENSG00000198824	ENST00000361283	T	0.01647	4.71	5.8	5.8	0.92144	.	0.107601	0.41938	D	0.000781	T	0.03651	0.0104	L	0.50333	1.59	0.37409	D	0.913146	D	0.55605	0.972	P	0.50440	0.641	T	0.51293	-0.8724	9	.	.	.	-21.0137	9.0015	0.36085	0.0:0.8766:0.0:0.1234	.	452	Q96JM3	ZN828_HUMAN	Y	452	ENSP00000354730:S452Y	.	S	+	2	0	ZNF828	114108774	0.253000	0.23982	1.000000	0.80357	0.993000	0.82548	0.911000	0.28584	2.741000	0.93983	0.650000	0.86243	TCT		0.512	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		A	115090672	C	A	115090672	3	1	61	1	0	0	0	0	1	0	0	0	18220	913	32	2	1357	2	ZNF828	13	115090672	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1333	115090672	79206	8779	16764										
OR4N2	390429	broad.mit.edu	37	chr14	20296066	20296066	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctgtggcttgggggtttTgtccactccattatccaggt	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20296066T>C	ENST00000315947.1	+	1	459	c.459T>C	c.(457-459)ttT>ttC	p.F153F	OR4N2_ENST00000568211.1_Silent_p.F153F	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F153F(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTGGGGGTTTTGTCCACTCCA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	14											129	141	137					14																	20296066		2203	4300	6503	19365906	SO:0001819	synonymous_variant	390429				CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.459T>C	14.37:g.20296066T>C			19365906	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																				0.527	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			C	20296066	T	C	20296066	2	2	61	1	0	0	0	0	0	0	0	1	11108	1809	63	4		4	OR4N2	14	20296066	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09		20296066	87053474	8780	16765										
OR4K2	390431	broad.mit.edu	37	chr14	20344474	20344474	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgaatttgttttgctgggGctctctaattcctgggaact	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20344474G>A	ENST00000298642.2	+	1	84	c.48G>A	c.(46-48)ggG>ggA	p.G16G		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G16G(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTTGCTGGGGCTCTCTAATT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	14											192	208	203					14																	20344474		2203	4300	6503	19414314	SO:0001819	synonymous_variant	390431				CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.48G>A	14.37:g.20344474G>A			19414314	B2RNK8|Q6IFA5	Silent	SNP	ENST00000298642.2	37	CCDS32023.1																																																																																				0.373	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			A	20344474	G	A	20344474	2	1	61	1	0	0	0	0	0	0	0	1	11103	1190	42	3		3	OR4K2	14	20344474	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48408	20344474	87005066	8781	16766										
OR4K5	79317	broad.mit.edu	37	chr14	20389623	20389623	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgtcctaaaccccattatTtatacactaaggaataggga	6	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20389623T>G	ENST00000315915.4	+	1	883	c.858T>G	c.(856-858)atT>atG	p.I286M		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I286M(2)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ACCCCATTATTTATACACTAA	0.403																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	14											123	135	131					14																	20389623		2203	4300	6503	19459463	SO:0001583	missense	79317			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"GPCR / Class A : Olfactory receptors"	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.858T>G	14.37:g.20389623T>G	ENSP00000319511:p.Ile286Met		19459463	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	10.44	1.349518	0.24426	.	.	ENSG00000176281	ENST00000315915	T	0.57273	0.41	4.28	-0.614	0.11590	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000186	T	0.63022	0.2476	M	0.74546	2.27	0.31540	N	0.660065	D	0.89917	1.0	D	0.76575	0.988	T	0.62927	-0.6750	10	0.87932	D	0	.	3.7476	0.08554	0.1635:0.3316:0.0:0.5049	.	286	Q8NGD3	OR4K5_HUMAN	M	286	ENSP00000319511:I286M	ENSP00000319511:I286M	I	+	3	3	OR4K5	19459463	0.011000	0.17503	0.030000	0.17652	0.196000	0.23810	-1.595000	0.02093	-0.283000	0.09115	0.533000	0.62120	ATT		0.403	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483		G	20389623	T	G	20389623	3	3	61	1	0	0	0	0	1	0	0	0	11104	1829	64	4	860	4	OR4K5	14	20389623	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	45149	20389623	86959917	8782	16767										
OR4K15	81127	broad.mit.edu	37	chr14	20444261	20444261	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatctgccattttgtggtcCtaataaggtagacagttttt	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20444261C>A	ENST00000305051.5	+	1	659	c.584C>A	c.(583-585)cCt>cAt	p.P195H		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P195H(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTTGTGGTCCTAATAAGGTA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											176	168	171					14																	20444261		2203	4299	6502	19514101	SO:0001583	missense	81127				CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"GPCR / Class A : Olfactory receptors"	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.584C>A	14.37:g.20444261C>A	ENSP00000304077:p.Pro195His		19514101	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	.	.	.	.	.	.	.	.	.	.	.	16.79	3.219118	0.58560	.	.	ENSG00000169488	ENST00000305051	T	0.38077	1.16	3.98	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000110	T	0.52948	0.1766	M	0.61703	1.905	0.41567	D	0.988669	D	0.64830	0.994	P	0.61940	0.896	T	0.59337	-0.7473	10	0.87932	D	0	.	13.5924	0.61967	0.0:1.0:0.0:0.0	.	195	Q8NH41	OR4KF_HUMAN	H	195	ENSP00000304077:P195H	ENSP00000304077:P195H	P	+	2	0	OR4K15	19514101	0.005000	0.15991	0.914000	0.36105	0.810000	0.45777	1.273000	0.33121	2.045000	0.60652	0.585000	0.79938	CCT		0.438	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1			A	20444261	C	A	20444261	3	1	61	1	0	0	0	0	1	0	0	0	11101	681	24	2	586	2	OR4K15	14	20444261	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54638	20444261	86905279	8783	16768										
OR4K15	81127	broad.mit.edu	37	chr14	20444436	20444436	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttacagttaggaatcgctcCtctgcaagcatggcgaaggc	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20444436C>A	ENST00000305051.5	+	1	834	c.759C>A	c.(757-759)tcC>tcA	p.S253S		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S253S(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGAATCGCTCCTCTGCAAGCA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	14											125	111	115					14																	20444436		2203	4300	6503	19514276	SO:0001819	synonymous_variant	81127				CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"GPCR / Class A : Olfactory receptors"	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.759C>A	14.37:g.20444436C>A			19514276	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																				0.453	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1			A	20444436	C	A	20444436	2	1	61	1	0	0	0	0	0	0	0	1	11101	668	24	2		2	OR4K15	14	20444436	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	175	20444436	86905104	8784	16769										
OR4K14	122740	broad.mit.edu	37	chr14	20483341	20483341	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgacaccaaggaatagttCtgtgggtccattgcctcagg	11	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20483341C>T	ENST00000305045.2	-	1	11	c.12G>A	c.(10-12)caG>caA	p.Q4Q		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q4Q(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		AGGAATAGTTCTGTGGGTCCA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	14											40	41	41					14																	20483341		2157	4266	6423	19553181	SO:0001819	synonymous_variant	122740				CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"GPCR / Class A : Olfactory receptors"	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.12G>A	14.37:g.20483341C>T			19553181	Q6IEU1|Q96R71	Silent	SNP	ENST00000305045.2	37	CCDS32027.1																																																																																				0.373	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1			T	20483341	C	T	20483341	2	4	61	1	0	0	0	0	0	0	0	1	11100	912	32	3		3	OR4K14	14	20483341	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38905	20483341	86866199	8785	16770										
OR4K13	390433	broad.mit.edu	37	chr14	20502223	20502223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagaaagccttagaggatCgactagcagcacggtaccta	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20502223C>T	ENST00000315693.2	-	1	696	c.695G>A	c.(694-696)cGa>cAa	p.R232Q	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R232Q(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CTTAGAGGATCGACTAGCAGC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	14											139	123	128					14																	20502223		2203	4300	6503	19572063	SO:0001583	missense	390433				CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"GPCR / Class A : Olfactory receptors"	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.695G>A	14.37:g.20502223C>T	ENSP00000319322:p.Arg232Gln		19572063	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	.	.	.	.	.	.	.	.	.	.	.	6.366	0.435699	0.12104	.	.	ENSG00000176253	ENST00000315693	T	0.00076	8.76	3.31	1.34	0.21922	GPCR, rhodopsin-like superfamily (1);	0.393919	0.18036	U	0.153795	T	0.00109	0.0003	N	0.20807	0.61	0.09310	N	1	B	0.27316	0.175	B	0.31016	0.123	T	0.21484	-1.0244	10	0.87932	D	0	.	6.5092	0.22212	0.0:0.5366:0.3568:0.1066	.	232	Q8NH42	OR4KD_HUMAN	Q	232	ENSP00000319322:R232Q	ENSP00000319322:R232Q	R	-	2	0	OR4K13	19572063	0.000000	0.05858	0.006000	0.13384	0.085000	0.17905	0.249000	0.18216	0.095000	0.17434	-0.413000	0.06143	CGA		0.493	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1			T	20502223	C	T	20502223	3	4	61	1	0	0	0	0	1	0	0	0	11099	884	31	1	221	1	OR4K13	14	20502223	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18882	20502223	86847317	8786	16771										
OR4K13	390433	broad.mit.edu	37	chr14	20502705	20502705	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcaaaagaagccaggatCatatcaatgcaggagaggtt	12	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20502705C>A	ENST00000315693.2	-	1	214	c.213G>T	c.(211-213)atG>atT	p.M71I	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M71I(2)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AAGCCAGGATCATATCAATGC	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	14											106	99	101					14																	20502705		2203	4300	6503	19572545	SO:0001583	missense	390433				CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"GPCR / Class A : Olfactory receptors"	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.213G>T	14.37:g.20502705C>A	ENSP00000319322:p.Met71Ile		19572545	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	.	.	.	.	.	.	.	.	.	.	.	2.010	-0.427393	0.04701	.	.	ENSG00000176253	ENST00000315693	T	0.01804	4.63	3.64	1.79	0.24919	GPCR, rhodopsin-like superfamily (1);	0.143817	0.31636	U	0.007306	T	0.00815	0.0027	N	0.02876	-0.465	0.09310	N	1	B	0.16166	0.016	B	0.17979	0.02	T	0.49163	-0.8968	10	0.13470	T	0.59	.	5.6702	0.17717	0.0:0.7424:0.0:0.2576	.	71	Q8NH42	OR4KD_HUMAN	I	71	ENSP00000319322:M71I	ENSP00000319322:M71I	M	-	3	0	OR4K13	19572545	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.868000	0.04236	0.246000	0.21394	-0.335000	0.08231	ATG		0.438	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1			A	20502705	C	A	20502705	3	1	61	1	0	0	0	0	1	0	0	0	11099	826	29	2	703	2	OR4K13	14	20502705	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	482	20502705	86846835	8787	16772										
OR4L1	122742	broad.mit.edu	37	chr14	20528284	20528284	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaacttcaaattttcttCtttgtgacattttccctgat	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20528284C>A	ENST00000315683.1	+	1	81	c.81C>A	c.(79-81)ttC>ttA	p.F27L		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F27L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AAATTTTCTTCTTTGTGACAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	14											167	173	171					14																	20528284		2203	4300	6503	19598124	SO:0001583	missense	122742				CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"GPCR / Class A : Olfactory receptors"	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.81C>A	14.37:g.20528284C>A	ENSP00000319217:p.Phe27Leu		19598124	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	.	.	.	.	.	.	.	.	.	.	.	0.511	-0.866327	0.02590	.	.	ENSG00000176246	ENST00000315683	T	0.00672	5.89	3.84	2.94	0.34122	.	0.236658	0.29783	N	0.011205	T	0.00271	0.0008	N	0.00569	-1.365	0.19575	N	0.999966	B	0.16802	0.019	B	0.16722	0.016	T	0.45071	-0.9286	10	0.02654	T	1	.	6.3094	0.21156	0.0:0.7719:0.0:0.2281	.	27	Q8NH43	OR4L1_HUMAN	L	27	ENSP00000319217:F27L	ENSP00000319217:F27L	F	+	3	2	OR4L1	19598124	0.000000	0.05858	0.996000	0.52242	0.976000	0.68499	-0.491000	0.06474	0.962000	0.38057	0.639000	0.83563	TTC		0.383	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1			A	20528284	C	A	20528284	3	1	61	1	0	0	0	0	1	0	0	0	11105	912	32	2	83	2	OR4L1	14	20528284	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25579	20528284	86821256	8788	16773										
OR4L1	122742	broad.mit.edu	37	chr14	20528521	20528521	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgttcttcatgcacttCtttgggggtgctgagatgac	12	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20528521C>A	ENST00000315683.1	+	1	318	c.318C>A	c.(316-318)ttC>ttA	p.F106L		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F106L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TCATGCACTTCTTTGGGGGTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	14											144	129	134					14																	20528521		2203	4300	6503	19598361	SO:0001583	missense	122742				CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"GPCR / Class A : Olfactory receptors"	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.318C>A	14.37:g.20528521C>A	ENSP00000319217:p.Phe106Leu		19598361	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	.	.	.	.	.	.	.	.	.	.	.	0.124	-1.122401	0.01785	.	.	ENSG00000176246	ENST00000315683	T	0.01323	5.01	3.99	-3.21	0.05140	GPCR, rhodopsin-like superfamily (1);	0.756875	0.12114	N	0.498297	T	0.00637	0.0021	N	0.04636	-0.2	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.45963	-0.9225	10	0.08179	T	0.78	.	6.2385	0.20776	0.123:0.3097:0.4848:0.0824	.	106	Q8NH43	OR4L1_HUMAN	L	106	ENSP00000319217:F106L	ENSP00000319217:F106L	F	+	3	2	OR4L1	19598361	0.000000	0.05858	0.986000	0.45419	0.867000	0.49689	-2.317000	0.01122	-0.524000	0.06400	-0.158000	0.13435	TTC		0.483	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1			A	20528521	C	A	20528521	3	1	61	1	0	0	0	0	1	0	0	0	11105	912	32	2	320	2	OR4L1	14	20528521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	237	20528521	86821019	8789	16774										
OR4L1	122742	broad.mit.edu	37	chr14	20529107	20529107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggccataagaaaattaCggttccaatatgttagttct	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20529107C>T	ENST00000315683.1	+	1	904	c.904C>T	c.(904-906)Cgg>Tgg	p.R302W		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R302W(2)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AAGAAAATTACGGTTCCAATA	0.303																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	14											51	57	55					14																	20529107		2203	4298	6501	19598947	SO:0001583	missense	122742				CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"GPCR / Class A : Olfactory receptors"	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.904C>T	14.37:g.20529107C>T	ENSP00000319217:p.Arg302Trp		19598947	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	.	.	.	.	.	.	.	.	.	.	.	5.014	0.188196	0.09547	.	.	ENSG00000176246	ENST00000315683	T	0.36699	1.24	4.26	-2.56	0.06268	.	2.575630	0.01495	N	0.017262	T	0.14527	0.0351	N	0.02876	-0.465	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.10405	-1.0631	10	0.33141	T	0.24	.	2.0985	0.03674	0.126:0.4334:0.124:0.3165	.	302	Q8NH43	OR4L1_HUMAN	W	302	ENSP00000319217:R302W	ENSP00000319217:R302W	R	+	1	2	OR4L1	19598947	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.922000	0.00170	-0.293000	0.08986	-1.223000	0.01593	CGG		0.303	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1			T	20529107	C	T	20529107	3	4	61	1	0	0	0	0	1	0	0	0	11105	527	19	1	906	1	OR4L1	14	20529107	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	586	20529107	86820433	8790	16775										
OR4K17	390436	broad.mit.edu	37	chr14	20586179	20586179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttgtggtcccaatgtggTagacagcattttttgtgacc	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20586179T>C	ENST00000315543.4	+	1	614	c.614T>C	c.(613-615)gTa>gCa	p.V205A		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V205A(1)		kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		CCCAATGTGGTAGACAGCATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											275	240	252					14																	20586179		2203	4300	6503	19656019	SO:0001583	missense	390436				CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.614T>C	14.37:g.20586179T>C	ENSP00000319197:p.Val205Ala		19656019	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	37	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	16.49	3.138735	0.56936	.	.	ENSG00000176230	ENST00000315543	T	0.00123	8.7	2.86	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30969	U	0.008510	T	0.00412	0.0013	M	0.93328	3.405	0.09310	N	1	P	0.51791	0.948	P	0.52343	0.696	T	0.14035	-1.0487	10	0.87932	D	0	.	10.2538	0.43385	0.0:0.0:0.0:1.0	.	177	Q8NGC6	OR4KH_HUMAN	A	205	ENSP00000319197:V205A	ENSP00000319197:V205A	V	+	2	0	OR4K17	19656019	0.011000	0.17503	0.872000	0.34217	0.741000	0.42261	2.019000	0.41001	1.292000	0.44672	0.332000	0.21555	GTA		0.438	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			C	20586179	T	C	20586179	3	2	61	1	0	0	0	0	1	0	0	0	11102	1638	57	4	616	4	OR4K17	14	20586179	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	57072	20586179	86763361	8791	16776										
OR11G2	390439	broad.mit.edu	37	chr14	20665918	20665918	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcctccagttctactttTtcttctccttgggctctaca	5	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20665918T>G	ENST00000357366.3	+	1	424	c.424T>G	c.(424-426)Ttc>Gtc	p.F142V		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F142V(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GTTCTACTTTTTCTTCTCCTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	14											63	60	61					14																	20665918		2203	4300	6503	19735758	SO:0001583	missense	390439				CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.424T>G	14.37:g.20665918T>G	ENSP00000349930:p.Phe142Val		19735758	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	37	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	t	16.98	3.270750	0.59540	.	.	ENSG00000196832	ENST00000357366	T	0.02258	4.37	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000103	T	0.10852	0.0265	M	0.70903	2.155	0.27059	N	0.963593	D	0.89917	1.0	D	0.72625	0.978	T	0.01413	-1.1361	10	0.52906	T	0.07	.	13.7044	0.62629	0.0:0.0:0.0:1.0	.	142	Q8NGC1	O11G2_HUMAN	V	142	ENSP00000349930:F142V	ENSP00000349930:F142V	F	+	1	0	OR11G2	19735758	0.516000	0.26218	0.999000	0.59377	0.936000	0.57629	1.169000	0.31871	2.073000	0.62155	0.528000	0.53228	TTC		0.483	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			G	20665918	T	G	20665918	3	3	61	1	0	0	0	0	1	0	0	0	10956	1841	64	4	426	4	OR11G2	14	20665918	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	79739	20665918	86683622	8792	16777										
OR11G2	390439	broad.mit.edu	37	chr14	20666352	20666352	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtctcacctggctgtggtTtcactgttctacggctcagt	12	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20666352T>G	ENST00000357366.3	+	1	858	c.858T>G	c.(856-858)gtT>gtG	p.V286V		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V286V(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TGGCTGTGGTTTCACTGTTCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	14											172	164	167					14																	20666352		2203	4300	6503	19736192	SO:0001819	synonymous_variant	390439				CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.858T>G	14.37:g.20666352T>G			19736192	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	37	CCDS32032.1																																																																																				0.507	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			G	20666352	T	G	20666352	2	3	61	1	0	0	0	0	0	0	0	1	10956	1828	64	4		4	OR11G2	14	20666352	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	434	20666352	86683188	8793	16778										
OR11H6	122748	broad.mit.edu	37	chr14	20692499	20692499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggcctgcatctctgctCcttccactgagcttatctgt	7	15	2	1	rs146626346		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20692499C>A	ENST00000315519.2	+	1	709	c.631C>A	c.(631-633)Cct>Act	p.P211T		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P211T(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		CATCTCTGCTCCTTCCACTGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	14											123	113	117					14																	20692499		2203	4300	6503	19762339	SO:0001583	missense	122748				CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"GPCR / Class A : Olfactory receptors"	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.631C>A	14.37:g.20692499C>A	ENSP00000319071:p.Pro211Thr		19762339	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695444	0.48202	.	.	ENSG00000176219	ENST00000315519	T	0.00058	8.79	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000081	T	0.00241	0.0007	N	0.17312	0.475	0.24933	N	0.991905	D	0.71674	0.998	D	0.83275	0.996	T	0.78969	-0.1994	10	0.26408	T	0.33	.	15.8321	0.78760	0.0:1.0:0.0:0.0	.	211	Q8NGC7	O11H6_HUMAN	T	211	ENSP00000319071:P211T	ENSP00000319071:P211T	P	+	1	0	OR11H6	19762339	0.000000	0.05858	0.819000	0.32651	0.962000	0.63368	-0.677000	0.05215	2.592000	0.87571	0.471000	0.43371	CCT		0.493	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			A	20692499	C	A	20692499	3	1	61	1	0	0	0	0	1	0	0	0	10960	855	30	2	633	2	OR11H6	14	20692499	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26147	20692499	86657041	8794	16779										
OR11H6	122748	broad.mit.edu	37	chr14	20692598	20692598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctggtcatcagagctgtgCtttgtattccctctggtgct	10	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20692598C>T	ENST00000315519.2	+	1	808	c.730C>T	c.(730-732)Ctt>Ttt	p.L244F		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L244F(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		CAGAGCTGTGCTTTGTATTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											115	100	105					14																	20692598		2203	4300	6503	19762438	SO:0001583	missense	122748				CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"GPCR / Class A : Olfactory receptors"	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.730C>T	14.37:g.20692598C>T	ENSP00000319071:p.Leu244Phe		19762438	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	.	.	.	.	.	.	.	.	.	.	C	7.062	0.566589	0.13560	.	.	ENSG00000176219	ENST00000315519	T	0.00296	8.24	4.78	-3.09	0.05331	GPCR, rhodopsin-like superfamily (1);	0.166842	0.28371	N	0.015592	T	0.00241	0.0007	M	0.73430	2.235	0.09310	N	1	B	0.14805	0.011	B	0.26969	0.075	T	0.43988	-0.9357	10	0.49607	T	0.09	.	7.0318	0.24970	0.0:0.4535:0.1135:0.4331	.	244	Q8NGC7	O11H6_HUMAN	F	244	ENSP00000319071:L244F	ENSP00000319071:L244F	L	+	1	0	OR11H6	19762438	0.000000	0.05858	0.257000	0.24404	0.743000	0.42351	-1.425000	0.02446	-0.556000	0.06134	-0.373000	0.07131	CTT		0.468	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			T	20692598	C	T	20692598	3	4	61	1	0	0	0	0	1	0	0	0	10960	797	28	3	732	3	OR11H6	14	20692598	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99	20692598	86656942	8795	16780										
TTC5	91875	broad.mit.edu	37	chr14	20768861	20768861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccaggcttccaccagctCgggctccagcttcacagcct	9	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20768861C>T	ENST00000258821.3	-	3	357	c.301G>A	c.(301-303)Gag>Aag	p.E101K		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	101					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E101K(2)		endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		TCCACCAGCTCGGGCTCCAGC	0.542																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	14											119	116	117					14																	20768861		2203	4300	6503	19838701	SO:0001583	missense	91875			BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"Tetratricopeptide (TTC) repeat domain containing"	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.301G>A	14.37:g.20768861C>T	ENSP00000258821:p.Glu101Lys		19838701	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	37	CCDS9546.1	.	.	.	.	.	.	.	.	.	.	C	7.628	0.678289	0.14841	.	.	ENSG00000136319	ENST00000258821	T	0.59906	0.23	5.16	1.14	0.20703	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.327520	0.35646	N	0.003068	T	0.23492	0.0568	N	0.01705	-0.755	0.27219	N	0.959719	B	0.02656	0.0	B	0.01281	0.0	T	0.31861	-0.9928	10	0.02654	T	1	.	11.0909	0.48115	0.0:0.7727:0.0:0.2273	.	101	Q8N0Z6	TTC5_HUMAN	K	101	ENSP00000258821:E101K	ENSP00000258821:E101K	E	-	1	0	TTC5	19838701	0.744000	0.28250	0.944000	0.38274	0.858000	0.48976	1.221000	0.32503	0.025000	0.15241	-0.940000	0.02684	GAG		0.542	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376		T	20768861	C	T	20768861	3	4	61	1	0	0	0	0	1	0	0	0	16751	893	31	1	1053	1	TTC5	14	20768861	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76263	20768861	86580679	8796	16781										
PARP2	10038	broad.mit.edu	37	chr14	20819270	20819270	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaacaaggccaaggaaatCtttcagaagaagtgagtgct	10	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20819270C>A	ENST00000250416.5	+	6	552	c.525C>A	c.(523-525)atC>atA	p.I175I	PARP2_ENST00000527915.1_Silent_p.I175I|PARP2_ENST00000429687.3_Silent_p.I162I	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	175					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.I175I(1)|p.I126I(1)		central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		CCAAGGAAATCTTTCAGAAGA	0.383								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																																								2	Substitution - coding silent(2)	large_intestine(2)	14											75	68	70					14																	20819270		1864	4094	5958	19889110	SO:0001819	synonymous_variant	10038			AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"Poly (ADP-ribose) polymerases"	272	protein-coding gene	gene with protein product		607725	"ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2", "poly (ADP-ribose) polymerase family, member 2"	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.525C>A	14.37:g.20819270C>A			19889110	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	37	CCDS41910.1																																																																																				0.383	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			A	20819270	C	A	20819270	2	1	61	1	0	0	0	0	0	0	0	1	11492	903	32	2		2	PARP2	14	20819270	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50409	20819270	86530270	8797	16782										
PARP2	10038	broad.mit.edu	37	chr14	20820419	20820419	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagattccttgacaaaacGaaaaacaattgggaagatcg	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20820419G>A	ENST00000250416.5	+	7	579	c.552G>A	c.(550-552)acG>acA	p.T184T	PARP2_ENST00000527915.1_Silent_p.T184T|PARP2_ENST00000429687.3_Silent_p.T171T	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	184					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.T135T(1)|p.T184T(1)		central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		TTGACAAAACGAAAAACAATT	0.368								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																																								2	Substitution - coding silent(2)	large_intestine(2)	14											104	94	97					14																	20820419		1829	4087	5916	19890259	SO:0001819	synonymous_variant	10038			AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"Poly (ADP-ribose) polymerases"	272	protein-coding gene	gene with protein product		607725	"ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2", "poly (ADP-ribose) polymerase family, member 2"	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.552G>A	14.37:g.20820419G>A			19890259	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	37	CCDS41910.1																																																																																				0.368	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			A	20820419	G	A	20820419	2	1	61	1	0	0	0	0	0	0	0	1	11492	1045	37	1		1	PARP2	14	20820419	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1149	20820419	86529121	8798	16783										
TEP1	7011	broad.mit.edu	37	chr14	20857405	20857405	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgtactcacttcagtatCgcatcagtacagcctgagag	8	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20857405C>T	ENST00000262715.5	-	17	2557	c.2517G>A	c.(2515-2517)gcG>gcA	p.A839A	TEP1_ENST00000556935.1_Silent_p.A731A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	839					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.A839A(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		ACTTCAGTATCGCATCAGTAC	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	14											167	141	150					14																	20857405		2203	4300	6503	19927245	SO:0001819	synonymous_variant	7011				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.2517G>A	14.37:g.20857405C>T			19927245	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																				0.383	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20857405	C	T	20857405	2	4	61	1	0	0	0	0	0	0	0	1	15798	871	31	1		1	TEP1	14	20857405	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36986	20857405	86492135	8799	16784										
APEX1	328	broad.mit.edu	37	chr14	20925287	20925287	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgctgggatgaagcctttCgcaagttcctgaagggcctg	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20925287C>T	ENST00000216714.3	+	5	845	c.577C>T	c.(577-579)Cgc>Tgc	p.R193C	APEX1_ENST00000557365.1_3'UTR|APEX1_ENST00000557054.1_Silent_p.F11F|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.R193C|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000555414.1_Missense_Mutation_p.R193C	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	193					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)	p.R193C(1)		breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	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)	Lucanthone(DB04967)	TGAAGCCTTTCGCAAGTTCCT	0.542								Other BER factors																																								1	Substitution - Missense(1)	large_intestine(1)	14											71	72	72					14																	20925287		2203	4300	6503	19995127	SO:0001583	missense	328			X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.577C>T	14.37:g.20925287C>T	ENSP00000216714:p.Arg193Cys		19995127	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	37	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.410031	0.42715	.	.	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000553681;ENST00000398030;ENST00000555839	T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45	5.79	3.96	0.45880	Endonuclease/exonuclease/phosphatase (2);	0.107146	0.64402	N	0.000004	T	0.79370	0.4434	M	0.79475	2.455	0.80722	D	1	B	0.17038	0.02	B	0.10450	0.005	T	0.75659	-0.3241	10	0.66056	D	0.02	.	10.2874	0.43575	0.1355:0.7929:0.0:0.0716	.	193	P27695	APEX1_HUMAN	C	193;193;193;193;164	ENSP00000451979:R193C;ENSP00000216714:R193C;ENSP00000451327:R193C;ENSP00000381111:R193C;ENSP00000452460:R164C	ENSP00000216714:R193C	R	+	1	0	APEX1	19995127	1.000000	0.71417	0.888000	0.34837	0.972000	0.66771	3.677000	0.54619	0.775000	0.33450	0.655000	0.94253	CGC		0.542	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641		T	20925287	C	T	20925287	3	4	61	1	0	0	0	0	1	0	0	0	769	884	31	1	591	1	APEX1	14	20925287	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67882	20925287	86424253	8800	16785										
APEX1	328	broad.mit.edu	37	chr14	20925531	20925531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttatatgatgaatgctcGatccaagaatgttggttggc	11	6	0	3	rs374977590		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:20925531G>A	ENST00000216714.3	+	5	1089	c.821G>A	c.(820-822)cGa>cAa	p.R274Q	APEX1_ENST00000557054.1_3'UTR|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.R274Q|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000555414.1_Missense_Mutation_p.R274Q	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	274					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)	p.R274Q(1)		breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	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)	Lucanthone(DB04967)	ATGAATGCTCGATCCAAGAAT	0.502								Other BER factors																																								1	Substitution - Missense(1)	large_intestine(1)	14						G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	252	216	228		821,821,821	5.8	1	14		228	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	APEX1	NM_001641.3,NM_080648.2,NM_080649.2	43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	274/319,274/319,274/319	20925531	1,13005	2203	4300	6503	19995371	SO:0001583	missense	328			X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.821G>A	14.37:g.20925531G>A	ENSP00000216714:p.Arg274Gln		19995371	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	37	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.929193	0.92389	0.0	1.16E-4	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000398030;ENST00000557054	T;T;T	0.65916	-0.18;-0.18;-0.18	5.79	5.79	0.91817	Endonuclease/exonuclease/phosphatase (2);	0.057147	0.64402	D	0.000001	D	0.87204	0.6119	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.91217	0.5003	10	0.87932	D	0	-0.8645	18.8114	0.92059	0.0:0.0:1.0:0.0	.	274	P27695	APEX1_HUMAN	Q	274;274;274;5	ENSP00000451979:R274Q;ENSP00000216714:R274Q;ENSP00000381111:R274Q	ENSP00000216714:R274Q	R	+	2	0	APEX1	19995371	1.000000	0.71417	0.982000	0.44146	0.938000	0.57974	9.317000	0.96327	2.733000	0.93635	0.655000	0.94253	CGA		0.502	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641		A	20925531	G	A	20925531	3	1	61	1	0	0	0	0	1	0	0	0	769	1058	37	1	835	1	APEX1	14	20925531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244	20925531	86424009	8801	16786										
RNASE9	390443	broad.mit.edu	37	chr14	21025021	21025021	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcattccaggttcaataaGgacacgtcttttgacttttt	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21025021G>T	ENST00000557068.1	-	4	1933	c.208C>A	c.(208-210)Ctt>Att	p.L70I	RNASE9_ENST00000555230.1_Missense_Mutation_p.L70I|RNASE9_ENST00000554964.1_Missense_Mutation_p.L70I|RNASE9_ENST00000553541.1_Missense_Mutation_p.L70I|RNASE9_ENST00000429244.2_Missense_Mutation_p.L70I|RNASE9_ENST00000553706.1_Missense_Mutation_p.L75I|RNASE9_ENST00000338904.3_Missense_Mutation_p.L70I|RNASE9_ENST00000556208.1_Missense_Mutation_p.L75I|RNASE9_ENST00000404716.3_Missense_Mutation_p.L75I|RNASE9_ENST00000557209.1_Missense_Mutation_p.L75I			P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)	70						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)	p.L70I(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|ovary(2)|urinary_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)		GGTTCAATAAGGACACGTCTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	14											175	175	175					14																	21025021		2203	4300	6503	20094861	SO:0001583	missense	390443			AY665804	CCDS32036.1, CCDS53883.1, CCDS55904.1	14q11.2	2006-10-31				ENSG00000188655		"Ribonucleases, RNase A"	20673	protein-coding gene	gene with protein product		614014				15676279, 12920233	Standard	NM_001001673		Approved	h461	uc010ahu.3	P60153		ENST00000557068.1:c.208C>A	14.37:g.21025021G>T	ENSP00000451565:p.Leu70Ile		20094861	A2RQR8|A8QJS1|Q5GAN7|Q6KG53	Missense_Mutation	SNP	ENST00000557068.1	37	CCDS32036.1	.	.	.	.	.	.	.	.	.	.	G	0.021	-1.422151	0.01126	.	.	ENSG00000188655	ENST00000338904;ENST00000554964;ENST00000555230;ENST00000557068;ENST00000404716;ENST00000556208;ENST00000553541;ENST00000429244;ENST00000553706;ENST00000557209	T;T;T;T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1;1.1;1.1;1.1;1.1	3.62	-6.29	0.02013	Ribonuclease A, domain (2);	.	.	.	.	T	0.28863	0.0716	L	0.31065	0.9	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.13407	0.005;0.009	T	0.22312	-1.0220	9	0.21540	T	0.41	-11.7085	16.7149	0.85395	0.0:0.0:0.7969:0.2031	.	70;75	P60153;P60153-2	RNAS9_HUMAN;.	I	70;70;70;70;75;75;70;70;75;75	ENSP00000340162:L70I;ENSP00000450599:L70I;ENSP00000450800:L70I;ENSP00000451565:L70I;ENSP00000384683:L75I;ENSP00000451160:L75I;ENSP00000451285:L70I;ENSP00000409504:L70I;ENSP00000450570:L75I;ENSP00000450987:L75I	ENSP00000340162:L70I	L	-	1	0	RNASE9	20094861	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.999000	0.01467	-1.261000	0.02462	-2.838000	0.00105	CTT		0.368	RNASE9-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411094.1	NM_001001673		T	21025021	G	T	21025021	3	4	61	1	0	0	0	0	1	0	0	0	13447	1000	35	2	413	2	RNASE9	14	21025021	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99490	21025021	86324519	8802	16787										
OR6S1	341799	broad.mit.edu	37	chr14	21109054	21109054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccacagaaccactctgcGatggccgcacatagagaaaa	9	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21109054G>A	ENST00000320704.3	-	1	796	c.797C>T	c.(796-798)tCg>tTg	p.S266L		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S266L(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		ACCACTCTGCGATGGCCGCAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	14											154	132	139					14																	21109054		2203	4300	6503	20178894	SO:0001583	missense	341799			AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"GPCR / Class A : Olfactory receptors"	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.797C>T	14.37:g.21109054G>A	ENSP00000313110:p.Ser266Leu		20178894	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407098	0.62399	.	.	ENSG00000181803	ENST00000320704	T	0.00174	8.62	5.7	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41396	D	0.000888	T	0.00356	0.0011	L	0.38733	1.17	0.24214	N	0.995463	D	0.76494	0.999	D	0.70935	0.971	T	0.64394	-0.6418	10	0.87932	D	0	-9.7024	13.1874	0.59688	0.0:0.0:0.8399:0.1601	.	266	Q8NH40	OR6S1_HUMAN	L	266	ENSP00000313110:S266L	ENSP00000313110:S266L	S	-	2	0	OR6S1	20178894	0.002000	0.14202	0.998000	0.56505	0.835000	0.47333	0.484000	0.22308	2.671000	0.90904	0.655000	0.94253	TCG		0.478	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1			A	21109054	G	A	21109054	3	1	61	1	0	0	0	0	1	0	0	0	11240	1059	37	1	202	1	OR6S1	14	21109054	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84033	21109054	86240486	8803	16788										
RNASE2	6036	broad.mit.edu	37	chr14	21423967	21423967	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacttcccaaatttgtctgCttcttctgttggggcttctg	8	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21423967C>T	ENST00000304625.2	+	2	127	c.37C>T	c.(37-39)Ctt>Ttt	p.L13F		NM_002934.2	NP_002925.1	P10153	RNAS2_HUMAN	ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)	13					chemotaxis (GO:0006935)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)|ribonuclease activity (GO:0004540)	p.L13F(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	17	all_cancers(95;0.00381)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)		AATTTGTCTGCTTCTTCTGTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	14											93	100	98					14																	21423967		2203	4297	6500	20493807	SO:0001583	missense	6036			X55988	CCDS9561.1	14q11.2	2014-03-13			ENSG00000169385	ENSG00000169385		"Ribonucleases, RNase A"	10045	protein-coding gene	gene with protein product		131410		RNS2		1577491, 2734298	Standard	NM_002934		Approved	EDN	uc001vyl.1	P10153	OTTHUMG00000029607	ENST00000304625.2:c.37C>T	14.37:g.21423967C>T	ENSP00000303276:p.Leu13Phe		20493807	Q52M39|Q9H2B7|Q9UCG7	Missense_Mutation	SNP	ENST00000304625.2	37	CCDS9561.1	.	.	.	.	.	.	.	.	.	.	c	14.16	2.451184	0.43531	.	.	ENSG00000169385	ENST00000304625	T	0.12672	2.66	2.78	0.837	0.18896	.	0.353829	0.21922	U	0.067153	T	0.24967	0.0606	M	0.79926	2.475	0.09310	N	1	D	0.64830	0.994	P	0.56343	0.796	T	0.09100	-1.0690	10	0.72032	D	0.01	.	3.1381	0.06446	0.263:0.5873:0.0:0.1497	.	13	P10153	RNAS2_HUMAN	F	13	ENSP00000303276:L13F	ENSP00000303276:L13F	L	+	1	0	RNASE2	20493807	0.000000	0.05858	0.003000	0.11579	0.220000	0.24768	-0.423000	0.07034	0.216000	0.20781	0.455000	0.32223	CTT		0.458	RNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073799.2			T	21423967	C	T	21423967	3	4	61	1	0	0	0	0	1	0	0	0	13441	797	28	3	39	3	RNASE2	14	21423967	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314913	21423967	85925573	8804	16789										
SLC39A2	29986	broad.mit.edu	37	chr14	21469640	21469640	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtcaccttcctagaaattCttccacgggagctagctagt	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21469640C>A	ENST00000298681.4	+	4	989	c.832C>A	c.(832-834)Ctt>Att	p.L278I	RP11-84C10.4_ENST00000557335.1_RNA|SLC39A2_ENST00000554422.1_3'UTR	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	278					transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)	p.L278I(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		CCTAGAAATTCTTCCACGGGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											86	91	89					14																	21469640		2203	4300	6503	20539480	SO:0001583	missense	29986			AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"Solute carriers"	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.832C>A	14.37:g.21469640C>A	ENSP00000298681:p.Leu278Ile		20539480	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.890255	0.72524	.	.	ENSG00000165794	ENST00000298681	T	0.60299	0.2	5.8	0.917	0.19380	.	0.000000	0.85682	D	0.000000	T	0.66954	0.2842	L	0.60845	1.875	0.53005	D	0.999969	D	0.89917	1.0	D	0.87578	0.998	T	0.62044	-0.6937	10	0.46703	T	0.11	-9.5291	8.8383	0.35126	0.0:0.6128:0.0:0.3872	.	278	Q9NP94	S39A2_HUMAN	I	278	ENSP00000298681:L278I	ENSP00000298681:L278I	L	+	1	0	SLC39A2	20539480	0.997000	0.39634	0.978000	0.43139	0.926000	0.56050	1.698000	0.37794	-0.097000	0.12307	-0.136000	0.14681	CTT		0.562	SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579		A	21469640	C	A	21469640	3	1	61	1	0	0	0	0	1	0	0	0	14655	913	32	2	846	2	SLC39A2	14	21469640	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45673	21469640	85879900	8805	16790										
RPGRIP1	57096	broad.mit.edu	37	chr14	21762904	21762904	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattggaggacagtttctttCgacttcgcgaagatcacatg	10	8	2	1	rs192003551		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21762904C>T	ENST00000400017.2	+	2	154	c.154C>T	c.(154-156)Cga>Tga	p.R52*	RPGRIP1_ENST00000556336.1_Nonsense_Mutation_p.R52*|RPGRIP1_ENST00000206660.6_Nonsense_Mutation_p.R52*|RPGRIP1_ENST00000557771.1_Nonsense_Mutation_p.R52*	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	52					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.R52*(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAGTTTCTTTCGACTTCGCGA	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		17307	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	14											83	83	83					14																	21762904		1873	4104	5977	20832744	SO:0001587	stop_gained	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.154C>T	14.37:g.21762904C>T	ENSP00000382895:p.Arg52*		20832744	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Nonsense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	26.3	4.725168	0.89298	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	.	.	.	4.52	4.52	0.55395	.	0.786157	0.11179	N	0.591127	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.2507	12.6168	0.56582	0.0:1.0:0.0:0.0	.	.	.	.	X	52	.	ENSP00000206660:R52X	R	+	1	2	RPGRIP1	20832744	1.000000	0.71417	0.971000	0.41717	0.738000	0.42128	3.925000	0.56484	2.341000	0.79615	0.561000	0.74099	CGA		0.393	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21762904	C	T	21762904	4	4	61	1	0	0	0	0	0	1	0	0	13586	876	31	1	160	1	RPGRIP1	14	21762904	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	293264	21762904	85586636	8806	16791										
RPGRIP1	57096	broad.mit.edu	37	chr14	21785901	21785901	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagccccactggagcaacGagctcatagcggaacagcta	11	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21785901G>A	ENST00000400017.2	+	10	1198	c.1198G>A	c.(1198-1200)Gag>Aag	p.E400K	RPGRIP1_ENST00000382933.4_Missense_Mutation_p.E42K|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.E373K|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.E400K|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.E373K	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	400					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.E16K(2)|p.E400K(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CTGGAGCAACGAGCTCATAGC	0.537																																																3	Substitution - Missense(3)	large_intestine(2)|prostate(1)	14											26	26	26					14																	21785901		1989	4165	6154	20855741	SO:0001583	missense	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1198G>A	14.37:g.21785901G>A	ENSP00000382895:p.Glu400Lys		20855741	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	G	0.242	-1.012795	0.02095	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000557351	T;T;T;T;T	0.76709	-0.16;-1.02;-1.04;-1.04;-0.39	4.64	3.72	0.42706	.	1.273330	0.05041	N	0.476245	T	0.78748	0.4332	L	0.39898	1.24	0.26274	N	0.978377	D;D;P	0.69078	0.997;0.982;0.935	P;B;B	0.58520	0.84;0.407;0.238	T	0.62039	-0.6938	10	0.02654	T	1	-8.5731	10.3292	0.43812	0.0:0.1997:0.8003:0.0	.	42;16;400	Q96KN7-4;Q96KN7-5;Q96KN7	.;.;RPGR1_HUMAN	K	373;373;400;400;42;42	ENSP00000450445:E373K;ENSP00000451219:E373K;ENSP00000382895:E400K;ENSP00000206660:E400K;ENSP00000372391:E42K	ENSP00000206660:E400K	E	+	1	0	RPGRIP1	20855741	0.349000	0.24870	0.250000	0.24296	0.329000	0.28539	1.588000	0.36633	1.117000	0.41842	0.467000	0.42956	GAG		0.537	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		A	21785901	G	A	21785901	3	1	61	1	0	0	0	0	1	0	0	0	13586	1059	37	1	1236	1	RPGRIP1	14	21785901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22997	21785901	85563639	8807	16792										
RPGRIP1	57096	broad.mit.edu	37	chr14	21790105	21790105	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcgactactagacctcaaGaataaccgtatcaagcagct	6	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21790105G>T	ENST00000400017.2	+	13	1704	c.1704G>T	c.(1702-1704)aaG>aaT	p.K568N	RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000307974.4_5'Flank|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.K210N|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.K541N|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.K568N|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.K541N	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	568					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.K184N(1)|p.K568N(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TAGACCTCAAGAATAACCGTA	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	14											97	93	94					14																	21790105		1883	4107	5990	20859945	SO:0001583	missense	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1704G>T	14.37:g.21790105G>T	ENSP00000382895:p.Lys568Asn		20859945	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581308	0.46006	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000554303	T;T;T;T;T;T;D	0.81499	-0.35;-1.15;-1.13;-1.13;-0.71;-1.44;-1.5	4.58	4.58	0.56647	.	0.185606	0.47852	D	0.000201	D	0.87669	0.6235	M	0.73598	2.24	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.80764	0.992;0.982;0.994;0.987	D	0.86203	0.1620	10	0.35671	T	0.21	-28.7959	12.3505	0.55144	0.0:0.0:0.8305:0.1695	.	43;210;184;568	G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7	.;.;.;RPGR1_HUMAN	N	541;541;568;568;210;43;41	ENSP00000450445:K541N;ENSP00000451219:K541N;ENSP00000382895:K568N;ENSP00000206660:K568N;ENSP00000372391:K210N;ENSP00000451262:K43N;ENSP00000450426:K41N	ENSP00000206660:K568N	K	+	3	2	RPGRIP1	20859945	1.000000	0.71417	1.000000	0.80357	0.462000	0.32619	1.415000	0.34748	2.538000	0.85594	0.305000	0.20034	AAG		0.443	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21790105	G	T	21790105	3	4	61	1	0	0	0	0	1	0	0	0	13586	933	33	2	1754	2	RPGRIP1	14	21790105	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4204	21790105	85559435	8808	16793										
RPGRIP1	57096	broad.mit.edu	37	chr14	21793997	21793997	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatctttccagttcagatCggagtcttgggaacctcaga	9	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21793997C>T	ENST00000400017.2	+	16	2375	c.2375C>T	c.(2374-2376)tCg>tTg	p.S792L	RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.S151L|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.S792L|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.S754L	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	792					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.S792L(1)|p.S408L(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAGTTCAGATCGGAGTCTTGG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	14											57	54	55					14																	21793997		1997	4164	6161	20863837	SO:0001583	missense	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2375C>T	14.37:g.21793997C>T	ENSP00000382895:p.Ser792Leu		20863837	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	C	6.932	0.541716	0.13250	.	.	ENSG00000092200	ENST00000557771;ENST00000400017;ENST00000206660;ENST00000555587;ENST00000307974	D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94	4.71	1.78	0.24846	C2 calcium/lipid-binding domain, CaLB (1);	0.715884	0.13693	N	0.369403	T	0.79845	0.4516	M	0.62723	1.935	0.22127	N	0.999345	B;B;B;B;B	0.27068	0.015;0.019;0.048;0.061;0.167	B;B;B;B;B	0.17722	0.009;0.008;0.014;0.019;0.008	T	0.63319	-0.6664	10	0.27785	T	0.31	0.1243	8.8884	0.35418	0.0:0.7131:0.0:0.2869	.	175;151;267;408;792	Q96KN7-2;Q96KN7-3;G3V3I7;Q96KN7-5;Q96KN7	.;.;.;.;RPGR1_HUMAN	L	754;792;792;267;151	ENSP00000451219:S754L;ENSP00000382895:S792L;ENSP00000206660:S792L;ENSP00000451262:S267L;ENSP00000309721:S151L	ENSP00000206660:S792L	S	+	2	0	RPGRIP1	20863837	0.036000	0.19791	0.031000	0.17742	0.753000	0.42808	0.110000	0.15437	0.030000	0.15379	-0.797000	0.03246	TCG		0.507	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21793997	C	T	21793997	3	4	61	1	0	0	0	0	1	0	0	0	13586	893	31	1	2437	1	RPGRIP1	14	21793997	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3892	21793997	85555543	8809	16794										
RPGRIP1	57096	broad.mit.edu	37	chr14	21816377	21816377	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctggatgaagaaaagaaaGaatgtgaagaagtgggatat	13	2	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21816377G>T	ENST00000400017.2	+	23	3664	c.3664G>T	c.(3664-3666)Gaa>Taa	p.E1222*	RPGRIP1_ENST00000307974.4_Nonsense_Mutation_p.E581*|RPGRIP1_ENST00000382933.4_Nonsense_Mutation_p.E548*|RPGRIP1_ENST00000556336.1_Nonsense_Mutation_p.E879*|RPGRIP1_ENST00000206660.6_Nonsense_Mutation_p.E1222*|RPGRIP1_ENST00000557771.1_Nonsense_Mutation_p.E1184*	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	1222	Interaction with RPGR. {ECO:0000269|PubMed:24981858}.				eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.E838*(1)|p.E1222*(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		AGAAAAGAAAGAATGTGAAGA	0.353																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											118	111	113					14																	21816377		1865	4100	5965	20886217	SO:0001587	stop_gained	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.3664G>T	14.37:g.21816377G>T	ENSP00000382895:p.Glu1222*		20886217	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Nonsense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119202	0.94385	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000307974	.	.	.	4.69	3.8	0.43715	.	0.138369	0.52532	D	0.000080	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-1.3668	11.871	0.52520	0.0869:0.0:0.9131:0.0	.	.	.	.	X	879;1184;1222;1222;548;697;581	.	ENSP00000206660:E1222X	E	+	1	0	RPGRIP1	20886217	1.000000	0.71417	0.710000	0.30468	0.002000	0.02628	5.565000	0.67365	1.195000	0.43115	-0.140000	0.14226	GAA		0.353	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21816377	G	T	21816377	4	4	61	1	0	0	0	0	0	1	0	0	13586	943	33	2	3754	2	RPGRIP1	14	21816377	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22380	21816377	85533163	8810	16795										
SUPT16H	11198	broad.mit.edu	37	chr14	21820963	21820963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcttcttcctcgtaacGactttctcggtccgctaaat	5	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21820963G>A	ENST00000216297.2	-	26	3351	c.3013C>T	c.(3013-3015)Cgt>Tgt	p.R1005C		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	1005	Glu-rich (acidic).				DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1005C(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TCCTCGTAACGACTTTCTCGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											146	125	132					14																	21820963		2203	4300	6503	20890803	SO:0001583	missense	11198			AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.3013C>T	14.37:g.21820963G>A	ENSP00000216297:p.Arg1005Cys		20890803	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Missense_Mutation	SNP	ENST00000216297.2	37	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.068494	0.76301	.	.	ENSG00000092201	ENST00000216297	.	.	.	5.09	5.09	0.68999	.	0.268795	0.38217	N	0.001773	T	0.47544	0.1451	L	0.43923	1.385	0.80722	D	1	D	0.64830	0.994	B	0.41299	0.353	T	0.54536	-0.8279	9	0.56958	D	0.05	-7.1424	17.4918	0.87705	0.0:0.0:1.0:0.0	.	1005	Q9Y5B9	SP16H_HUMAN	C	1005	.	ENSP00000216297:R1005C	R	-	1	0	SUPT16H	20890803	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.928000	0.56506	2.663000	0.90544	0.650000	0.86243	CGT		0.448	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			A	21820963	G	A	21820963	3	1	61	1	0	0	0	0	1	0	0	0	15435	1058	37	1	134	1	SUPT16H	14	21820963	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4586	21820963	85528577	8811	16796										
CHD8	57680	broad.mit.edu	37	chr14	21873468	21873468	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctttggaaaggaaggaGaaattcttctccaaaatagc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21873468G>T	ENST00000557364.1	-	16	3470	c.3207C>A	c.(3205-3207)ttC>ttA	p.F1069L	CHD8_ENST00000430710.3_Missense_Mutation_p.F790L|CHD8_ENST00000399982.2_Missense_Mutation_p.F1069L|CHD8_ENST00000555962.1_Intron			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1069					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.F1069L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AAAGGAAGGAGAAATTCTTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	14											87	80	82					14																	21873468		1855	4101	5956	20943308	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.3207C>A	14.37:g.21873468G>T	ENSP00000451601:p.Phe1069Leu		20943308	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.87|19.87	3.907681|3.907681	0.72868|0.72868	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	D;D;D|.	0.92699|.	-3.09;-3.09;-3.09|.	5.2|5.2	3.35|3.35	0.38373|0.38373	SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.42630|0.42630	0.1211|0.1211	N|N	0.25485|0.25485	0.75|0.75	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.83275|.	0.996;0.993|.	T|T	0.19516|0.19516	-1.0303|-1.0303	10|5	0.87932|.	D|.	0|.	-15.3028|-15.3028	8.6294|8.6294	0.33911|0.33911	0.2419:0.0:0.7581:0.0|0.2419:0.0:0.7581:0.0	.|.	1069;790|.	Q9HCK8;Q9HCK8-2|.	CHD8_HUMAN;.|.	L|I	790;1069;789;1069|295	ENSP00000406288:F790L;ENSP00000382863:F1069L;ENSP00000451601:F1069L|.	ENSP00000262707:F789L|.	F|L	-|-	3|1	2|0	CHD8|CHD8	20943308|20943308	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.558000|1.558000	0.36309|0.36309	1.436000|1.436000	0.47453|0.47453	0.561000|0.561000	0.74099|0.74099	TTC|CTC		0.403	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21873468	G	T	21873468	3	4	61	1	0	0	0	0	1	0	0	0	3337	933	33	2	4630	2	CHD8	14	21873468	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52505	21873468	85476072	8812	16797										
METTL3	56339	broad.mit.edu	37	chr14	21967202	21967202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgtgtggtcgtccaaatAactcaatcttgcgagtgcca	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:21967202A>G	ENST00000298717.4	-	10	1749	c.1598T>C	c.(1597-1599)tTa>tCa	p.L533S	TOX4_ENST00000405508.1_3'UTR|TOX4_ENST00000262709.3_3'UTR	NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	533					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)	p.L533S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		TCGTCCAAATAACTCAATCTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											174	141	152					14																	21967202		2203	4300	6503	21037042	SO:0001583	missense	56339			AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"N6-adenosine-methyltransferase 70 kDa subunit"	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1598T>C	14.37:g.21967202A>G	ENSP00000298717:p.Leu533Ser		21037042	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	37	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.685564	0.88639	.	.	ENSG00000165819	ENST00000298717	T	0.61274	0.12	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	D	0.83422	0.5251	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88718	0.3227	10	0.87932	D	0	-5.4217	14.96	0.71151	1.0:0.0:0.0:0.0	.	533	Q86U44	MTA70_HUMAN	S	533	ENSP00000298717:L533S	ENSP00000298717:L533S	L	-	2	0	METTL3	21037042	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.653000	0.91088	2.179000	0.69175	0.533000	0.62120	TTA		0.423	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852		G	21967202	A	G	21967202	3	3	61	1	0	0	0	0	1	0	0	0	9531	372	13	4	152	4	METTL3	14	21967202	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	93734	21967202	85382338	8813	16798										
OR10G2	26534	broad.mit.edu	37	chr14	22102678	22102678	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccaggaagtgaaagaaAtacagttgagccacacagcc	10	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:22102678A>C	ENST00000542433.1	-	1	418	c.321T>G	c.(319-321)taT>taG	p.Y107*		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y107*(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		AGTGAAAGAAATACAGTTGAG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											45	46	46					14																	22102678		2203	4299	6502	21172518	SO:0001587	stop_gained	26534				CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"GPCR / Class A : Olfactory receptors"	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.321T>G	14.37:g.22102678A>C	ENSP00000445383:p.Tyr107*		21172518	B2RPD0	Nonsense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.969018	0.74131	.	.	ENSG00000255582	ENST00000542433	.	.	.	3.79	1.27	0.21489	.	0.187027	0.26003	N	0.026932	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-8.0478	4.989	0.14205	0.5986:0.0:0.4014:0.0	.	.	.	.	X	107	.	ENSP00000445383:Y107X	Y	-	3	2	OR10G2	21172518	0.000000	0.05858	0.865000	0.33974	0.671000	0.39405	0.029000	0.13666	0.486000	0.27676	0.460000	0.39030	TAT		0.512	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			C	22102678	A	C	22102678	4	2	61	1	0	0	0	0	0	1	0	0	10930	108	4	4	614	4	OR10G2	14	22102678	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	135476	22102678	85246862	8814	16799										
OR4E2	26686	broad.mit.edu	37	chr14	22134223	22134223	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagacaagtttttttcacGaaatcatatacataatgggc	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:22134223G>A	ENST00000408935.1	+	1	927	c.927G>A	c.(925-927)acG>acA	p.T309T		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T309T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TTTTTTTCACGAAATCATATA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	14											32	29	30					14																	22134223		1917	4141	6058	21204063	SO:0001819	synonymous_variant	26686				CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"GPCR / Class A : Olfactory receptors"	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.927G>A	14.37:g.22134223G>A			21204063	Q6IET6|Q96R62	Silent	SNP	ENST00000408935.1	37	CCDS41916.1																																																																																				0.393	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1			A	22134223	G	A	22134223	2	1	61	1	0	0	0	0	0	0	0	1	11091	1045	37	1		1	OR4E2	14	22134223	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31545	22134223	85215317	8815	16800										
OXA1L	5018	broad.mit.edu	37	chr14	23235782	23235782	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaaatatggccgccaagCtccgttctcttttaccgcct	6	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23235782C>A	ENST00000285848.5	+	1	52	c.52C>A	c.(52-54)Ctc>Atc	p.L18I	OXA1L_ENST00000412791.1_5'Flank|OXA1L_ENST00000604262.1_5'Flank|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000358043.5_5'Flank|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA	NM_005015.3	NP_005006.3	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	0					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)	p.L18I(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		GGCCGCCAAGCTCCGTTCTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	14											118	121	120					14																	23235782		2203	4300	6503	22305622	SO:0001583	missense	5018				CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000285848.5:c.52C>A	14.37:g.23235782C>A	ENSP00000285848:p.Leu18Ile		22305622	B4DPA2	Missense_Mutation	SNP	ENST00000285848.5	37	CCDS9573.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089881	0.36855	.	.	ENSG00000155463	ENST00000285848	T	0.38077	1.16	5.08	-0.548	0.11833	.	.	.	.	.	T	0.16685	0.0401	N	0.08118	0	0.09310	N	0.999995	B	0.26935	0.164	B	0.16722	0.016	T	0.18713	-1.0328	9	0.87932	D	0	-5.5158	6.6098	0.22745	0.0:0.4075:0.4233:0.1692	.	18	Q2M1J6	.	I	18	ENSP00000285848:L18I	ENSP00000285848:L18I	L	+	1	0	OXA1L	22305622	0.000000	0.05858	0.000000	0.03702	0.179000	0.23085	-0.440000	0.06888	0.007000	0.14760	0.655000	0.94253	CTC		0.502	OXA1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071630.2	NM_005015		A	23235782	C	A	23235782	3	1	61	1	0	0	0	0	1	0	0	0	11359	797	28	2	54	2	OXA1L	14	23235782	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1101559	23235782	84113758	8816	16801										
OXA1L	5018	broad.mit.edu	37	chr14	23237225	23237225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagcagtacctgaggtggCttctggagagactgcagatg	14	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23237225C>T	ENST00000604262.1	+	3	307	c.284C>T	c.(283-285)gCt>gTt	p.A95V	OXA1L_ENST00000412791.1_Missense_Mutation_p.A95V|OXA1L_ENST00000285848.5_Missense_Mutation_p.A155V|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000358043.5_Missense_Mutation_p.A79V|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	95					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)	p.A155V(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		CCTGAGGTGGCTTCTGGAGAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	14											53	52	52					14																	23237225		2203	4300	6503	22307065	SO:0001583	missense	5018				CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.284C>T	14.37:g.23237225C>T	ENSP00000474623:p.Ala95Val		22307065	B4DPA2	Missense_Mutation	SNP	ENST00000604262.1	37		.	.	.	.	.	.	.	.	.	.	C	16.94	3.261616	0.59431	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.34472	1.36;1.44;1.39	5.65	3.51	0.40186	.	0.409242	0.28376	N	0.015571	T	0.27134	0.0665	L	0.33753	1.03	0.58432	D	0.999994	P;B;B;B	0.41450	0.75;0.087;0.012;0.087	B;B;B;B	0.38327	0.271;0.03;0.012;0.03	T	0.05937	-1.0855	10	0.41790	T	0.15	-6.7895	12.2102	0.54375	0.0:0.8326:0.0:0.1674	.	95;95;95;155	B4DGZ2;E7EVY0;Q15070;Q2M1J6	.;.;OXA1L_HUMAN;.	V	155;95;79	ENSP00000285848:A155V;ENSP00000387601:A95V;ENSP00000350740:A79V	ENSP00000285848:A155V	A	+	2	0	OXA1L	22307065	0.995000	0.38212	1.000000	0.80357	0.996000	0.88848	1.512000	0.35812	1.386000	0.46466	0.655000	0.94253	GCT		0.512	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468876.1	NM_005015		T	23237225	C	T	23237225	3	4	61	1	0	0	0	0	1	0	0	0	11359	797	28	3	474	3	OXA1L	14	23237225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1443	23237225	84112315	8817	16802										
LRP10	26020	broad.mit.edu	37	chr14	23346015	23346015	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagaagactttcctacagaGaatcctaatgatgtaagtca	8	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23346015G>T	ENST00000359591.4	+	6	2233	c.1542G>T	c.(1540-1542)gaG>gaT	p.E514D	LRP10_ENST00000546834.1_Missense_Mutation_p.E514D|LRP10_ENST00000470660.1_3'UTR	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	514					endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.E514D(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		TTCCTACAGAGAATCCTAATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	14											90	85	86					14																	23346015		2203	4300	6503	22415855	SO:0001583	missense	26020			AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.1542G>T	14.37:g.23346015G>T	ENSP00000352601:p.Glu514Asp		22415855	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	37	CCDS9578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.53|18.53	3.643561|3.643561	0.67244|0.67244	.|.	.|.	ENSG00000197324|ENSG00000197324	ENST00000359591;ENST00000546834|ENST00000551466	D;D|.	0.94092|.	-3.19;-3.35|.	5.54|5.54	4.64|4.64	0.57946|0.57946	.|.	0.105732|0.105732	0.64402|0.64402	D|D	0.000004|0.000004	T|.	0.62588|.	0.2440|.	L|L	0.50333|0.50333	1.59|1.59	0.42656|0.42656	D|D	0.993469|0.993469	D|.	0.63880|.	0.993|.	P|.	0.57548|.	0.823|.	T|.	0.62737|.	-0.6791|.	10|.	0.33940|0.46703	T|T	0.23|0.11	-20.6302|-20.6302	12.7364|12.7364	0.57228|0.57228	0.0804:0.0:0.9196:0.0|0.0804:0.0:0.9196:0.0	.|.	514|.	Q7Z4F1|.	LRP10_HUMAN|.	D|X	514|416	ENSP00000352601:E514D;ENSP00000447559:E514D|.	ENSP00000352601:E514D|ENSP00000447977:E416X	E|E	+|+	3|1	2|0	LRP10|LRP10	22415855|22415855	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	0.381000|0.381000	0.20619|0.20619	2.628000|2.628000	0.89032|0.89032	0.563000|0.563000	0.77884|0.77884	GAG|GAA		0.587	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			T	23346015	G	T	23346015	3	4	61	1	0	0	0	0	1	0	0	0	8981	933	33	2	1564	2	LRP10	14	23346015	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108790	23346015	84003525	8818	16803										
LRP10	26020	broad.mit.edu	37	chr14	23346371	23346371	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctccccttgaggccctaGatggtggcacaggtccagcc	12	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23346371G>T	ENST00000359591.4	+	7	2468	c.1777G>T	c.(1777-1779)Gat>Tat	p.D593Y	LRP10_ENST00000546834.1_Intron|LRP10_ENST00000470660.1_Intron	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	593					endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.D593Y(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		TGAGGCCCTAGATGGTGGCAC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	14											33	40	37					14																	23346371		2200	4295	6495	22416211	SO:0001583	missense	26020			AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.1777G>T	14.37:g.23346371G>T	ENSP00000352601:p.Asp593Tyr		22416211	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	37	CCDS9578.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167431	0.38315	.	.	ENSG00000197324	ENST00000359591	D	0.93076	-3.16	4.9	4.9	0.64082	.	0.420579	0.27249	N	0.020239	D	0.89266	0.6666	L	0.36672	1.1	0.80722	D	1	P	0.44090	0.826	B	0.37833	0.259	D	0.90827	0.4713	10	0.72032	D	0.01	-8.0927	15.4503	0.75268	0.0:0.0:1.0:0.0	.	593	Q7Z4F1	LRP10_HUMAN	Y	593	ENSP00000352601:D593Y	ENSP00000352601:D593Y	D	+	1	0	LRP10	22416211	1.000000	0.71417	0.351000	0.25721	0.040000	0.13550	6.644000	0.74338	2.710000	0.92621	0.462000	0.41574	GAT		0.677	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			T	23346371	G	T	23346371	3	4	61	1	0	0	0	0	1	0	0	0	8981	942	33	2	1803	2	LRP10	14	23346371	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356	23346371	84003169	8819	16804										
CEBPE	1053	broad.mit.edu	37	chr14	23588016	23588016	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgccttcctgtctgggccGaaggtatgtggagggtaggc	17	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23588016G>A	ENST00000206513.5	-	1	809	c.285C>T	c.(283-285)ttC>ttT	p.F95F		NM_001805.3	NP_001796.2	Q15744	CEBPE_HUMAN	CCAAT/enhancer binding protein (C/EBP), epsilon	95					cellular response to lipopolysaccharide (GO:0071222)|cytokine biosynthetic process (GO:0042089)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|macrophage differentiation (GO:0030225)|phagocytosis (GO:0006909)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.F95F(1)		large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0064)		TGTCTGGGCCGAAGGTATGTG	0.697																																					NSCLC(63;1230 1818 14565 22565)											1	Substitution - coding silent(1)	large_intestine(1)	14											25	26	25					14																	23588016		2203	4300	6503	22657856	SO:0001819	synonymous_variant	1053				CCDS9589.1	14q11.2	2014-09-17			ENSG00000092067	ENSG00000092067		"basic leucine zipper proteins"	1836	protein-coding gene	gene with protein product		600749				8661101	Standard	NM_001805		Approved	CRP1	uc001wiv.2	Q15744	OTTHUMG00000028719	ENST00000206513.5:c.285C>T	14.37:g.23588016G>A			22657856	Q15745|Q8IYI2|Q99803	Silent	SNP	ENST00000206513.5	37	CCDS9589.1																																																																																				0.697	CEBPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071716.2	NM_001805		A	23588016	G	A	23588016	2	1	61	1	0	0	0	0	0	0	0	1	3208	1049	37	1		1	CEBPE	14	23588016	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241645	23588016	83761524	8820	16805										
SLC7A8	23428	broad.mit.edu	37	chr14	23635555	23635555	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctcttacccagccagtcCtccgaagatgtccttgacat	6	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23635555C>A	ENST00000316902.7	-	2	1071	c.346G>T	c.(346-348)Gga>Tga	p.G116*	SLC7A8_ENST00000469263.1_Nonsense_Mutation_p.G116*	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	116					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)	p.G116*(1)		autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	CCAGCCAGTCCTCCGAAGATG	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											115	116	116					14																	23635555		2203	4300	6503	22705395	SO:0001587	stop_gained	23428			Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.346G>T	14.37:g.23635555C>A	ENSP00000320378:p.Gly116*		22705395	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Nonsense_Mutation	SNP	ENST00000316902.7	37	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	C	43	10.306840	0.99380	.	.	ENSG00000092068	ENST00000316902;ENST00000469263	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	18.5137	0.90928	0.0:1.0:0.0:0.0	.	.	.	.	X	116	.	ENSP00000320378:G116X	G	-	1	0	SLC7A8	22705395	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.398000	0.79919	2.733000	0.93635	0.655000	0.94253	GGA		0.532	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			A	23635555	C	A	23635555	4	1	61	1	0	0	0	0	0	1	0	0	14741	690	24	2	1301	2	SLC7A8	14	23635555	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47539	23635555	83713985	8821	16806										
MYH6	4624	broad.mit.edu	37	chr14	23851691	23851691	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttgacctgggactcagcGatgtccgcccgctcctctgc	11	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23851691G>A	ENST00000356287.3	-	37	5771	c.5742C>T	c.(5740-5742)atC>atT	p.I1914I	MYH6_ENST00000405093.3_Silent_p.I1914I			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1914					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.I1914I(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGGACTCAGCGATGTCCGCCC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	14											180	158	165					14																	23851691		2203	4300	6503	22921531	SO:0001819	synonymous_variant	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5742C>T	14.37:g.23851691G>A			22921531	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																				0.592	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23851691	G	A	23851691	2	1	61	1	0	0	0	0	0	0	0	1	10068	1048	37	1		1	MYH6	14	23851691	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216136	23851691	83497849	8822	16807										
MYH6	4624	broad.mit.edu	37	chr14	23858216	23858216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtactgctcccgcagcaggtCgcagtcatgccgggccgact	13	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23858216C>T	ENST00000356287.3	-	28	4056	c.4027G>A	c.(4027-4029)Gac>Aac	p.D1343N	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Missense_Mutation_p.D1343N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1343					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.D1343N(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CGCAGCAGGTCGCAGTCATGC	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	14											45	41	43					14																	23858216		2203	4300	6503	22928056	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.4027G>A	14.37:g.23858216C>T	ENSP00000348634:p.Asp1343Asn		22928056	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	N	34	5.410519	0.96072	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.82167	-1.58;-1.58	4.74	4.74	0.60224	Myosin tail (1);	.	.	.	.	D	0.91549	0.7331	M	0.85462	2.755	0.58432	D	0.999998	D	0.71674	0.998	D	0.65874	0.939	D	0.93137	0.6538	9	0.87932	D	0	.	18.113	0.89541	0.0:1.0:0.0:0.0	.	1343	P13533	MYH6_HUMAN	N	1343	ENSP00000386041:D1343N;ENSP00000348634:D1343N	ENSP00000348634:D1343N	D	-	1	0	MYH6	22928056	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.631000	0.83237	2.336000	0.79503	0.650000	0.86243	GAC		0.687	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23858216	C	T	23858216	3	4	61	1	0	0	0	0	1	0	0	0	10068	884	31	1	1836	1	MYH6	14	23858216	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6525	23858216	83491324	8823	16808										
MYH6	4624	broad.mit.edu	37	chr14	23865510	23865510	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctgcgttccactatcttCttgaactcaatgcgcatgag	7	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23865510C>A	ENST00000356287.3	-	19	2441	c.2412G>T	c.(2410-2412)aaG>aaT	p.K804N	MYH6_ENST00000405093.3_Missense_Mutation_p.K804N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	804	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.K804N(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCACTATCTTCTTGAACTCAA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	14											112	100	104					14																	23865510		2203	4300	6503	22935350	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2412G>T	14.37:g.23865510C>A	ENSP00000348634:p.Lys804Asn		22935350	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	8.817	0.936622	0.18206	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.92299	-3.01;-3.01	4.78	2.91	0.33838	.	.	.	.	.	D	0.89979	0.6872	M	0.72894	2.215	0.46542	D	0.999098	B	0.02656	0.0	B	0.06405	0.002	D	0.87473	0.2415	9	0.52906	T	0.07	.	10.529	0.44965	0.0:0.7862:0.0:0.2138	.	804	P13533	MYH6_HUMAN	N	804	ENSP00000386041:K804N;ENSP00000348634:K804N	ENSP00000348634:K804N	K	-	3	2	MYH6	22935350	1.000000	0.71417	1.000000	0.80357	0.142000	0.21351	1.114000	0.31196	1.159000	0.42565	0.650000	0.86243	AAG		0.572	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23865510	C	A	23865510	3	1	61	1	0	0	0	0	1	0	0	0	10068	912	32	2	3487	2	MYH6	14	23865510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7294	23865510	83484030	8824	16809										
MYH7	4625	broad.mit.edu	37	chr14	23886416	23886416	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatgttccagggactcctCataggcgttcttgagtttga	11	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23886416C>A	ENST00000355349.3	-	32	4627	c.4465G>T	c.(4465-4467)Gag>Tag	p.E1489*	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1489					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.E1489*(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		AGGGACTCCTCATAGGCGTTC	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											121	127	125					14																	23886416		2203	4300	6503	22956256	SO:0001587	stop_gained	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4465G>T	14.37:g.23886416C>A	ENSP00000347507:p.Glu1489*		22956256	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Nonsense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	45	12.045298	0.99630	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.0892	0.93219	0.0:1.0:0.0:0.0	.	.	.	.	X	1489;1494	.	ENSP00000347507:E1489X	E	-	1	0	MYH7	22956256	1.000000	0.71417	0.993000	0.49108	0.974000	0.67602	7.359000	0.79477	2.746000	0.94184	0.591000	0.81541	GAG		0.592	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23886416	C	A	23886416	4	1	61	1	0	0	0	0	0	1	0	0	10069	835	29	2	1378	2	MYH7	14	23886416	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20906	23886416	83463124	8825	16810										
MYH7	4625	broad.mit.edu	37	chr14	23902386	23902386	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatgtcctcgattttgtcGaacttgggtgggttctgctg	13	9	1	0	rs267603955		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23902386G>A	ENST00000355349.3	-	4	414	c.252C>T	c.(250-252)ttC>ttT	p.F84F		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	84					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.F84F(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGATTTTGTCGAACTTGGGTG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	14											274	197	223					14																	23902386		2203	4300	6503	22972226	SO:0001819	synonymous_variant	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.252C>T	14.37:g.23902386G>A			22972226	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																				0.587	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23902386	G	A	23902386	2	1	61	1	0	0	0	0	0	0	0	1	10069	1049	37	1		1	MYH7	14	23902386	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15970	23902386	83447154	8826	16811										
MYH7	4625	broad.mit.edu	37	chr14	23902931	23902931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaaagactgccatctccGaatctcccatggctgtgcct	7	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:23902931G>A	ENST00000355349.3	-	3	173	c.11C>T	c.(10-12)tCg>tTg	p.S4L		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	4					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.S4L(2)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TGCCATCTCCGAATCTCCCAT	0.617																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	14											44	45	45					14																	23902931		2203	4300	6503	22972771	SO:0001583	missense	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.11C>T	14.37:g.23902931G>A	ENSP00000347507:p.Ser4Leu		22972771	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.979492	0.34942	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.85484	-1.99	4.11	4.11	0.48088	.	.	.	.	.	T	0.72203	0.3431	N	0.04508	-0.205	0.40138	D	0.976799	B	0.21520	0.057	B	0.23018	0.043	T	0.71276	-0.4641	9	0.54805	T	0.06	.	16.305	0.82844	0.0:0.0:1.0:0.0	.	4	P12883	MYH7_HUMAN	L	4	ENSP00000347507:S4L	ENSP00000347507:S4L	S	-	2	0	MYH7	22972771	0.984000	0.35163	0.333000	0.25482	0.072000	0.16883	5.804000	0.69135	1.988000	0.58038	0.555000	0.69702	TCG		0.617	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23902931	G	A	23902931	3	1	61	1	0	0	0	0	1	0	0	0	10069	1059	37	1	5948	1	MYH7	14	23902931	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	545	23902931	83446609	8827	16812										
AP1G2	8906	broad.mit.edu	37	chr14	24033579	24033579	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgagtaggaagcgaccaaGaatgttgacagctagaacct	12	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24033579G>T	ENST00000308724.5	-	9	1695	c.940C>A	c.(940-942)Ctt>Att	p.L314I	RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Missense_Mutation_p.L314I|AP1G2_ENST00000556277.1_5'Flank	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	314					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)	p.L314I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		AAGCGACCAAGAATGTTGACA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	14											145	118	127					14																	24033579		2203	4300	6503	23103419	SO:0001583	missense	8906			AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.940C>A	14.37:g.24033579G>T	ENSP00000312442:p.Leu314Ile		23103419	D3DS51|O75504	Missense_Mutation	SNP	ENST00000308724.5	37	CCDS9602.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.718295	0.68844	.	.	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	T;T	0.60548	0.18;0.18	4.38	4.38	0.52667	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.74839	0.3769	M	0.85373	2.75	0.49299	D	0.999772	D;D	0.76494	0.998;0.999	D;D	0.83275	0.996;0.996	T	0.77792	-0.2455	10	0.87932	D	0	-8.6008	8.1372	0.31061	0.1069:0.0:0.8931:0.0	.	314;169	O75843;Q86V28	AP1G2_HUMAN;.	I	314;314;83;169	ENSP00000312442:L314I;ENSP00000380309:L314I	ENSP00000312442:L314I	L	-	1	0	AP1G2	23103419	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	3.789000	0.55454	2.269000	0.75478	0.557000	0.71058	CTT		0.527	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		T	24033579	G	T	24033579	3	4	61	1	0	0	0	0	1	0	0	0	733	942	33	2	1469	2	AP1G2	14	24033579	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130648	24033579	83315961	8828	16813										
AP1G2	8906	broad.mit.edu	37	chr14	24033844	24033844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccgcatttccggcatttCggctggtgtccgtgttagtg	14	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24033844C>T	ENST00000308724.5	-	8	1603	c.848G>A	c.(847-849)cGa>cAa	p.R283Q	RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Missense_Mutation_p.R283Q|AP1G2_ENST00000556277.1_5'UTR	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	283					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)	p.R283L(1)|p.R283Q(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TCCGGCATTTCGGCTGGTGTC	0.532																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	14											120	88	99					14																	24033844		2203	4300	6503	23103684	SO:0001583	missense	8906			AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.848G>A	14.37:g.24033844C>T	ENSP00000312442:p.Arg283Gln		23103684	D3DS51|O75504	Missense_Mutation	SNP	ENST00000308724.5	37	CCDS9602.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.950368	0.53186	.	.	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000535852	T;T	0.11930	2.73;2.73	3.98	3.09	0.35607	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.483516	0.20578	N	0.089586	T	0.12902	0.0313	L	0.45352	1.415	0.34864	D	0.742873	P;P	0.40250	0.478;0.709	B;B	0.41917	0.263;0.37	T	0.16808	-1.0390	10	0.72032	D	0.01	0.0	6.0621	0.19844	0.0:0.7694:0.0:0.2306	.	283;138	O75843;Q86V28	AP1G2_HUMAN;.	Q	283;283;138	ENSP00000312442:R283Q;ENSP00000380309:R283Q	ENSP00000312442:R283Q	R	-	2	0	AP1G2	23103684	0.998000	0.40836	0.997000	0.53966	0.437000	0.31866	2.709000	0.47160	0.880000	0.35969	0.313000	0.20887	CGA		0.532	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		T	24033844	C	T	24033844	3	4	61	1	0	0	0	0	1	0	0	0	733	884	31	1	1565	1	AP1G2	14	24033844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	265	24033844	83315696	8829	16814										
DHRS2	10202	broad.mit.edu	37	chr14	24113359	24113359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcttccattgcagcttaTaatccagtagtggtaagtgc	9	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24113359T>C	ENST00000250383.6	+	6	1004	c.528T>C	c.(526-528)taT>taC	p.Y176Y	DHRS2_ENST00000344777.7_Silent_p.Y176Y	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	176					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)	p.Y176Y(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		TTGCAGCTTATAATCCAGTAG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	14											261	217	232					14																	24113359		2203	4300	6503	23183199	SO:0001819	synonymous_variant	10202				CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18349	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 1"	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.528T>C	14.37:g.24113359T>C			23183199	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Silent	SNP	ENST00000250383.6	37	CCDS9604.1	.	.	.	.	.	.	.	.	.	.	T	2.207	-0.381495	0.05000	.	.	ENSG00000100867	ENST00000557535	.	.	.	5.14	0.163	0.14986	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6811	0.28513	0.0:0.5132:0.0:0.4868	.	.	.	.	Q	92	.	.	X	+	1	0	DHRS2	23183199	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.973000	0.03798	-0.113000	0.11958	0.533000	0.62120	TAA		0.478	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		C	24113359	T	C	24113359	2	2	61	1	0	0	0	0	0	0	0	1	4501	1413	49	4		4	DHRS2	14	24113359	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	79515	24113359	83236181	8830	16815										
LRRC16B	90668	broad.mit.edu	37	chr14	24534944	24534944	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagccaagggttggagcttCgatgggaaacgagaggtgag	18	5	0	3	rs370965600		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24534944C>T	ENST00000342740.5	+	34	3664	c.3510C>T	c.(3508-3510)ttC>ttT	p.F1170F	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1170						cytoplasm (GO:0005737)		p.F1170F(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GTTGGAGCTTCGATGGGAAAC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	14						C		0,4406		0,0,2203	123	104	111		3510	2.1	1	14		111	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRRC16B	NM_138360.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		1170/1373	24534944	2,13004	2203	4300	6503	23604784	SO:0001819	synonymous_variant	90668			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3510C>T	14.37:g.24534944C>T			23604784	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																				0.627	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24534944	C	T	24534944	2	4	61	1	0	0	0	0	0	0	0	1	9001	883	31	1		1	LRRC16B	14	24534944	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	421585	24534944	82814596	8831	16816										
DCAF11	80344	broad.mit.edu	37	chr14	24592285	24592285	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaagattgtcagcagttCggtgaggttgcaagggttga	16	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24592285C>T	ENST00000446197.3	+	14	2232	c.1505C>T	c.(1504-1506)tCg>tTg	p.S502L	DCAF11_ENST00000396936.1_Splice_Site_p.S402L|RP11-468E2.6_ENST00000558325.1_Splice_Site_p.F91F|DCAF11_ENST00000396941.4_Splice_Site_p.S476L|DCAF11_ENST00000559115.1_Splice_Site_p.S502L	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	502					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.S502L(1)									GTCAGCAGTTCGGTGAGGTTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	14											140	118	125					14																	24592285		2203	4300	6503	23662125	SO:0001630	splice_region_variant	80344			AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20258	protein-coding gene	gene with protein product		613317	"WD repeat domain 23"	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.1506+1C>T	14.37:g.24592285C>T			23662125	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	37	CCDS9610.1	.	.	.	.	.	.	.	.	.	.	c	31	5.092934	0.94149	.	.	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396936;ENST00000396941	T;T	0.74421	-0.84;-0.84	5.33	5.33	0.75918	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.91395	0.7285	H	0.98027	4.13	0.80722	D	1	D;D;D;D;D	0.89917	0.997;0.988;0.999;1.0;0.996	P;P;D;D;P	0.78314	0.889;0.592;0.937;0.991;0.788	D	0.94078	0.7341	10	0.87932	D	0	-6.6235	16.5604	0.84551	0.0:1.0:0.0:0.0	.	425;476;402;502;502	Q59GN6;Q8TEB1-2;Q8TEB1-3;A8K9T2;Q8TEB1	.;.;.;.;DCA11_HUMAN	L	502;476;402;476	ENSP00000380142:S402L;ENSP00000380146:S476L	ENSP00000323680:S502L	S	+	2	0	DCAF11	23662125	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.737000	0.74816	2.778000	0.95560	0.655000	0.94253	TCG		0.572	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		Missense_Mutation	T	24592285	C	T	24592285	5	4	61	1	0	0	0	0	0	0	1	0	4268	898	31	1	1555	1	DCAF11	14	24592285	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57341	24592285	82757255	8832	16817										
RNF31	55072	broad.mit.edu	37	chr14	24626832	24626832	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcggctgctacaatgcCttttacgccaagaatgtaag	10	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24626832C>A	ENST00000324103.6	+	16	3032	c.2712C>A	c.(2710-2712)gcC>gcA	p.A904A	RP11-468E2.4_ENST00000558468.1_Silent_p.A379A|RNF31_ENST00000559275.1_Silent_p.A753A|RNA5SP383_ENST00000362934.1_RNA|RNF31_ENST00000382687.3_Silent_p.A753A	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	904					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A904A(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GCTACAATGCCTTTTACGCCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	14											104	112	109					14																	24626832		2027	4183	6210	23696672	SO:0001819	synonymous_variant	55072			AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.2712C>A	14.37:g.24626832C>A			23696672	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Silent	SNP	ENST00000324103.6	37	CCDS41931.1																																																																																				0.592	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		A	24626832	C	A	24626832	2	1	61	1	0	0	0	0	0	0	0	1	13524	668	24	2		2	RNF31	14	24626832	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34547	24626832	82722708	8833	16818										
CIDEB	27141	broad.mit.edu	37	chr14	24776619	24776619	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcagctgtcaggcctttCcggatggtccgcttgtgatc	14	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24776619C>T	ENST00000336557.5	-	5	1446	c.144G>A	c.(142-144)cgG>cgA	p.R48R	LTB4R2_ENST00000543919.1_5'Flank|CIDEB_ENST00000554411.1_Silent_p.R48R|LTB4R2_ENST00000533293.1_5'Flank|CIDEB_ENST00000258807.5_Silent_p.R48R|LTB4R2_ENST00000528054.1_5'Flank|NOP9_ENST00000267425.3_3'UTR			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	48	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)	p.R48R(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TCAGGCCTTTCCGGATGGTCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	14											78	77	78					14																	24776619		2203	4300	6503	23846459	SO:0001819	synonymous_variant	27141			AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.144G>A	14.37:g.24776619C>T			23846459	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																				0.572	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			T	24776619	C	T	24776619	2	4	61	1	0	0	0	0	0	0	0	1	3432	842	30	3		3	CIDEB	14	24776619	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149787	24776619	82572921	8834	16819										
LTB4R	1241	broad.mit.edu	37	chr14	24785425	24785425	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcgaggctgtcacgggcTtcctgctgcccttcctggct	11	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24785425T>G	ENST00000396789.4	+	2	2293	c.568T>G	c.(568-570)Ttc>Gtc	p.F190V	LTB4R_ENST00000396782.2_Missense_Mutation_p.F190V|LTB4R_ENST00000345363.3_Missense_Mutation_p.F190V	NM_181657.3	NP_858043.1	Q15722	LT4R1_HUMAN	leukotriene B4 receptor	190					cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|muscle contraction (GO:0006936)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	leukotriene B4 receptor activity (GO:0001632)|leukotriene receptor activity (GO:0004974)|nucleotide binding (GO:0000166)	p.F190V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(265;0.018)		TGTCACGGGCTTCCTGCTGCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	14											47	49	48					14																	24785425		2203	4300	6503	23855265	SO:0001583	missense	1241			X98356	CCDS9626.1	14q11.2-q12	2012-08-10			ENSG00000213903	ENSG00000213903		"GPCR / Class A : Leukotriene receptors"	6713	protein-coding gene	gene with protein product		601531		P2RY7, GPR16, CMKRL1		8921391, 8702478	Standard	NM_181657		Approved	BLTR, P2Y7, LTB4R1	uc001wos.3	Q15722	OTTHUMG00000029346	ENST00000396789.4:c.568T>G	14.37:g.24785425T>G	ENSP00000380008:p.Phe190Val		23855265	Q13305|Q53XV5|Q92641|Q9BSU5	Missense_Mutation	SNP	ENST00000396789.4	37	CCDS9626.1	.	.	.	.	.	.	.	.	.	.	T	32	5.191406	0.94923	.	.	ENSG00000213903	ENST00000345363;ENST00000396789;ENST00000556141;ENST00000396782	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.128895	0.51477	U	0.000086	D	0.89598	0.6761	M	0.90309	3.105	0.58432	D	0.999997	D	0.76494	0.999	D	0.75020	0.985	D	0.91482	0.5205	10	0.72032	D	0.01	.	13.9798	0.64297	0.0:0.0:0.0:1.0	.	190	Q15722	LT4R1_HUMAN	V	190;190;90;190	ENSP00000307445:F190V;ENSP00000380008:F190V;ENSP00000451929:F90V;ENSP00000380002:F190V	ENSP00000307445:F190V	F	+	1	0	LTB4R	23855265	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.065000	0.64344	2.187000	0.69744	0.533000	0.62120	TTC		0.667	LTB4R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073198.4			G	24785425	T	G	24785425	3	3	61	1	0	0	0	0	1	0	0	0	9100	1609	56	4	570	4	LTB4R	14	24785425	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8806	24785425	82564115	8835	16820										
RIPK3	11035	broad.mit.edu	37	chr14	24807498	24807498	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcccacattaggatcccGaagctgcaggagacacaaag	10	12	0	1	rs373410782		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24807498G>A	ENST00000216274.5	-	5	839	c.621C>T	c.(619-621)ttC>ttT	p.F207F	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	207	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)	p.F207F(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TTAGGATCCCGAAGCTGCAGG	0.522																																					Pancreas(58;918 1191 4668 13304 15331)											1	Substitution - coding silent(1)	large_intestine(1)	14						G		0,4406		0,0,2203	96	99	98		621	-6.9	1	14		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RIPK3	NM_006871.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		207/519	24807498	1,13005	2203	4300	6503	23877338	SO:0001819	synonymous_variant	11035			AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.621C>T	14.37:g.24807498G>A			23877338	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	37	CCDS9628.1																																																																																				0.522	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		A	24807498	G	A	24807498	2	1	61	1	0	0	0	0	0	0	0	1	13419	1049	37	1		1	RIPK3	14	24807498	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22073	24807498	82542042	8836	16821										
NYNRIN	57523	broad.mit.edu	37	chr14	24878408	24878408	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggagctcagatgtaaaaGacaaagttagctcggatctc	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24878408G>T	ENST00000382554.3	+	4	1726	c.1408G>T	c.(1408-1410)Gac>Tac	p.D470Y		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	470					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.D470Y(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						AGATGTAAAAGACAAAGTTAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											35	36	36					14																	24878408		1905	4107	6012	23948248	SO:0001583	missense	57523			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.1408G>T	14.37:g.24878408G>T	ENSP00000371994:p.Asp470Tyr		23948248	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318738	0.41096	.	.	ENSG00000205978	ENST00000382554	T	0.12039	2.72	4.79	2.92	0.33932	.	1.316840	0.05341	N	0.530084	T	0.09862	0.0242	N	0.24115	0.695	0.09310	N	1	P	0.40476	0.718	B	0.34138	0.176	T	0.28618	-1.0038	10	0.87932	D	0	.	6.7668	0.23571	0.0937:0.1773:0.729:0.0	.	470	Q9P2P1	NYNRI_HUMAN	Y	470	ENSP00000371994:D470Y	ENSP00000371994:D470Y	D	+	1	0	NYNRIN	23948248	0.996000	0.38824	0.019000	0.16419	0.018000	0.09664	3.817000	0.55668	0.910000	0.36722	0.655000	0.94253	GAC		0.547	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24878408	G	T	24878408	3	4	61	1	0	0	0	0	1	0	0	0	10827	942	33	2	1418	2	NYNRIN	14	24878408	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70910	24878408	82471132	8837	16822										
NYNRIN	57523	broad.mit.edu	37	chr14	24886145	24886145	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccctcaaggagttcatCttcctgcatgggaagaagtg	13	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:24886145C>A	ENST00000382554.3	+	9	5508	c.5190C>A	c.(5188-5190)atC>atA	p.I1730I		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1730	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.				DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.I1730I(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						AGGAGTTCATCTTCCTGCATG	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	14											17	20	19					14																	24886145		1993	4157	6150	23955985	SO:0001819	synonymous_variant	57523			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.5190C>A	14.37:g.24886145C>A			23955985	Q6P153|Q86TR3|Q9HAC4	Silent	SNP	ENST00000382554.3	37	CCDS45090.1																																																																																				0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			A	24886145	C	A	24886145	2	1	61	1	0	0	0	0	0	0	0	1	10827	903	32	2		2	NYNRIN	14	24886145	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7737	24886145	82463395	8838	16823										
STXBP6	29091	broad.mit.edu	37	chr14	25326292	25326292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcatccactgtgatctccGaacaaatgatgtggagcctt	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:25326292G>A	ENST00000323944.5	-	3	677	c.226C>T	c.(226-228)Cgg>Tgg	p.R76W	STXBP6_ENST00000358326.2_Missense_Mutation_p.R76W|STXBP6_ENST00000396700.1_Missense_Mutation_p.R76W|STXBP6_ENST00000548724.1_Missense_Mutation_p.R76W|STXBP6_ENST00000550887.1_Missense_Mutation_p.R76W|STXBP6_ENST00000419632.2_Missense_Mutation_p.R76W|STXBP6_ENST00000546511.1_Missense_Mutation_p.R76W			Q8NFX7	STXB6_HUMAN	syntaxin binding protein 6 (amisyn)	76					negative regulation of exocytosis (GO:0045920)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R76W(1)		central_nervous_system(2)|endometrium(2)|large_intestine(3)	7				GBM - Glioblastoma multiforme(265;0.0296)		TGTGATCTCCGAACAAATGAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	14											237	210	219					14																	25326292		2203	4300	6503	24396132	SO:0001583	missense	29091			AF161505	CCDS9634.1	14q11.2	2002-12-18			ENSG00000168952	ENSG00000168952			19666	protein-coding gene	gene with protein product		607958				12145319	Standard	NM_014178		Approved	amisyn, HSPC156	uc001wpu.3	Q8NFX7	OTTHUMG00000140186	ENST00000323944.5:c.226C>T	14.37:g.25326292G>A	ENSP00000324302:p.Arg76Trp		24396132	D3DS78|Q8N3H1|Q8N8D5|Q96GF3|Q9P008	Missense_Mutation	SNP	ENST00000323944.5	37	CCDS9634.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483334	0.84854	.	.	ENSG00000168952	ENST00000396700;ENST00000548724;ENST00000323944;ENST00000419632;ENST00000546511;ENST00000550887;ENST00000358326	.	.	.	5.84	3.84	0.44239	.	0.100496	0.64402	D	0.000003	T	0.60907	0.2305	L	0.59436	1.845	0.58432	D	0.999996	D	0.69078	0.997	P	0.50617	0.646	T	0.65721	-0.6099	9	0.87932	D	0	-23.6575	12.2439	0.54560	0.0:0.0:0.705:0.295	.	76	Q8NFX7	STXB6_HUMAN	W	76	.	ENSP00000324302:R76W	R	-	1	2	STXBP6	24396132	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	3.721000	0.54941	2.779000	0.95612	0.655000	0.94253	CGG		0.458	STXBP6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409166.1			A	25326292	G	A	25326292	3	1	61	1	0	0	0	0	1	0	0	0	15397	1057	37	1	422	1	STXBP6	14	25326292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	440147	25326292	82023248	8839	16824										
NOVA1	4857	broad.mit.edu	37	chr14	26941547	26941547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattagctctggaggtggtCatgggatcagatggagagga	17	4	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:26941547C>A	ENST00000344429.5	-	4	501	c.498G>T	c.(496-498)atG>atT	p.M166I	NOVA1_ENST00000267422.7_Missense_Mutation_p.M44I|NOVA1_ENST00000547619.1_Missense_Mutation_p.M166I|NOVA1_ENST00000465357.2_Intron|NOVA1_ENST00000539517.2_Missense_Mutation_p.M166I	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	169					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.M166I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		TGGAGGTGGTCATGGGATCAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											223	184	197					14																	26941547		2203	4300	6503	26011387	SO:0001583	missense	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.498G>T	14.37:g.26941547C>A	ENSP00000342387:p.Met166Ile		26011387	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	37	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677498	0.29783	.	.	ENSG00000139910	ENST00000539517;ENST00000267422;ENST00000449198;ENST00000549146;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.97;0.86;0.8	5.92	5.92	0.95590	.	0.412688	0.23191	N	0.050920	T	0.47002	0.1422	N	0.08118	0	0.58432	D	0.99999	B;B;B	0.20780	0.048;0.01;0.025	B;B;B	0.16289	0.015;0.001;0.004	T	0.35325	-0.9793	10	0.41790	T	0.15	-24.0609	20.3343	0.98733	0.0:1.0:0.0:0.0	.	166;169;166	P51513-2;P51513;P51513-4	.;NOVA1_HUMAN;.	I	166;44;125;44;129;166;166	ENSP00000438875:M166I;ENSP00000267422:M44I;ENSP00000408914:M125I;ENSP00000449113:M44I;ENSP00000449185:M129I;ENSP00000342387:M166I;ENSP00000448157:M166I	ENSP00000267422:M44I	M	-	3	0	NOVA1	26011387	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.822000	0.97130	0.650000	0.86243	ATG		0.453	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		A	26941547	C	A	26941547	3	1	61	1	0	0	0	0	1	0	0	0	10585	826	29	2	1064	2	NOVA1	14	26941547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1615255	26941547	80407993	8840	16825										
NOVA1	4857	broad.mit.edu	37	chr14	27064620	27064620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccattgcacctacctggGtaaaaatctttggacttaga	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:27064620G>A	ENST00000344429.5	-	2	279	c.276C>T	c.(274-276)taC>taT	p.Y92Y	NOVA1_ENST00000574031.1_Silent_p.Y92Y|RP11-483C6.1_ENST00000572358.1_RNA|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000547619.1_Silent_p.Y92Y|NOVA1_ENST00000465357.2_Silent_p.Y92Y|NOVA1_ENST00000551754.1_5'UTR|NOVA1-AS1_ENST00000547786.1_RNA|NOVA1_ENST00000539517.2_Silent_p.Y92Y	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	95	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y92Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		ACCTACCTGGGTAAAAATCTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	14											166	157	160					14																	27064620		2203	4300	6503	26134460	SO:0001819	synonymous_variant	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.276C>T	14.37:g.27064620G>A			26134460	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Silent	SNP	ENST00000344429.5	37	CCDS9635.1																																																																																				0.408	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		A	27064620	G	A	27064620	2	1	61	1	0	0	0	0	0	0	0	1	10585	1256	44	3		3	NOVA1	14	27064620	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123073	27064620	80284920	8841	16826										
FOXG1	2290	broad.mit.edu	37	chr14	29237110	29237110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacgctcaacggcatctacGagttcatcatgaagaacttc	7	12	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:29237110G>A	ENST00000313071.4	+	1	824	c.625G>A	c.(625-627)Gag>Aag	p.E209K	RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000549487.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.E209K	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	209					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E209K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CGGCATCTACGAGTTCATCAT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											56	53	54					14																	29237110		2203	4300	6503	28306861	SO:0001583	missense	2290				CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.625G>A	14.37:g.29237110G>A	ENSP00000339004:p.Glu209Lys		28306861	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	37	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524740	0.85600	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.95307	-3.67;-3.67	3.69	2.79	0.32731	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	U	0.000000	D	0.92596	0.7648	N	0.10874	0.06	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.91609	0.5301	10	0.56958	D	0.05	.	10.6273	0.45514	0.0991:0.0:0.9009:0.0	.	209	P55316	FOXG1_HUMAN	K	209	ENSP00000371975:E209K;ENSP00000339004:E209K	ENSP00000339004:E209K	E	+	1	0	FOXG1	28306861	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	6.596000	0.74113	0.527000	0.28560	0.306000	0.20318	GAG		0.562	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237110	G	A	29237110	3	1	61	1	0	0	0	0	1	0	0	0	6026	1059	37	1	627	1	FOXG1	14	29237110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2172490	29237110	78112430	8842	16827										
FOXG1	2290	broad.mit.edu	37	chr14	29237855	29237855	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgccctgtgagtctttaaGaccctctttgccaagtttta	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:29237855G>T	ENST00000313071.4	+	1	1569	c.1370G>T	c.(1369-1371)aGa>aTa	p.R457I	FOXG1_ENST00000382535.3_Missense_Mutation_p.R457I	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	457					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R457I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GAGTCTTTAAGACCCTCTTTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											76	75	76					14																	29237855		2203	4300	6503	28307606	SO:0001583	missense	2290				CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.1370G>T	14.37:g.29237855G>T	ENSP00000339004:p.Arg457Ile		28307606	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	37	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028514	0.75390	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.94758	-3.51;-3.51	4.14	4.14	0.48551	.	0.326841	0.28577	U	0.014853	D	0.94883	0.8346	L	0.27053	0.805	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	D	0.95546	0.8616	10	0.54805	T	0.06	.	16.7792	0.85559	0.0:0.0:1.0:0.0	.	457	P55316	FOXG1_HUMAN	I	457	ENSP00000371975:R457I;ENSP00000339004:R457I	ENSP00000339004:R457I	R	+	2	0	FOXG1	28307606	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.220000	0.95180	2.006000	0.58801	0.491000	0.48974	AGA		0.547	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			T	29237855	G	T	29237855	3	4	61	1	0	0	0	0	1	0	0	0	6026	942	33	2	1372	2	FOXG1	14	29237855	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	745	29237855	78111685	8843	16828										
PRKD1	5587	broad.mit.edu	37	chr14	30066843	30066843	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacagaccacatgtctagaGagcgattgtagcccttgttc	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:30066843G>T	ENST00000331968.5	-	16	2517	c.2288C>A	c.(2287-2289)tCt>tAt	p.S763Y	PRKD1_ENST00000415220.2_Missense_Mutation_p.S771Y	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	763	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.S763Y(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CATGTCTAGAGAGCGATTGTA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	14											145	136	139					14																	30066843		2203	4300	6503	29136594	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2288C>A	14.37:g.30066843G>T	ENSP00000333568:p.Ser763Tyr		29136594	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300251	0.81136	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.83506	-1.73;-1.73	5.72	5.72	0.89469	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90714	0.7086	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.90708	0.4625	10	0.87932	D	0	-13.2176	20.2504	0.98404	0.0:0.0:1.0:0.0	.	763	Q15139	KPCD1_HUMAN	Y	763;771	ENSP00000333568:S763Y;ENSP00000390535:S771Y	ENSP00000333568:S763Y	S	-	2	0	PRKD1	29136594	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	9.813000	0.99286	2.850000	0.98022	0.650000	0.86243	TCT		0.493	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30066843	G	T	30066843	3	4	61	1	0	0	0	0	1	0	0	0	12552	942	33	2	462	2	PRKD1	14	30066843	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	828988	30066843	77282697	8844	16829										
PRKD1	5587	broad.mit.edu	37	chr14	30103685	30103685	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgactgtgctgcttttcCtcttcgtgtgtttgacagac	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:30103685C>A	ENST00000331968.5	-	8	1482	c.1253G>T	c.(1252-1254)aGg>aTg	p.R418M	PRKD1_ENST00000415220.2_Missense_Mutation_p.R426M|PRKD1_ENST00000551644.1_5'Flank	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	418					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.R418K(2)|p.R418M(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GCTGCTTTTCCTCTTCGTGTG	0.443																																																4	Substitution - Missense(4)	large_intestine(2)|NS(2)	14											490	358	403					14																	30103685		2203	4300	6503	29173436	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1253G>T	14.37:g.30103685C>A	ENSP00000333568:p.Arg418Met		29173436	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	32	5.189632	0.94923	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.70631	-0.5;-0.48	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.85906	0.5806	M	0.82323	2.585	0.80722	D	1	D	0.69078	0.997	D	0.66847	0.947	D	0.86522	0.1816	10	0.87932	D	0	-21.3639	20.5407	0.99260	0.0:1.0:0.0:0.0	.	418	Q15139	KPCD1_HUMAN	M	418;426	ENSP00000333568:R418M;ENSP00000390535:R426M	ENSP00000333568:R418M	R	-	2	0	PRKD1	29173436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.710000	0.84655	2.865000	0.98341	0.655000	0.94253	AGG		0.443	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30103685	C	A	30103685	3	1	61	1	0	0	0	0	1	0	0	0	12552	681	24	2	1529	2	PRKD1	14	30103685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36842	30103685	77245855	8845	16830										
G2E3	55632	broad.mit.edu	37	chr14	31062822	31062822	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccttgttgtaagaacgctTggtttcatagagactgttta	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31062822T>C	ENST00000206595.6	+	6	659	c.505T>C	c.(505-507)Tgg>Cgg	p.W169R	G2E3_ENST00000438909.2_Missense_Mutation_p.W123R|G2E3_ENST00000553504.1_Missense_Mutation_p.W199R|G2E3_ENST00000544007.1_3'UTR	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	169					apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.W169R(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						TAAGAACGCTTGGTTTCATAG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	14											65	66	66					14																	31062822		2202	4299	6501	30132573	SO:0001583	missense	55632			AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.505T>C	14.37:g.31062822T>C	ENSP00000206595:p.Trp169Arg		30132573	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	37	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.278674	0.80692	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504;ENST00000547532;ENST00000552515	T;T;T;T	0.78595	-0.52;-0.52;-0.52;-1.19	5.17	5.17	0.71159	Zinc finger, RING-type (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89305	0.6677	M	0.86651	2.83	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.91311	0.5074	10	0.87932	D	0	-7.9491	15.3058	0.73990	0.0:0.0:0.0:1.0	.	123;169	B4DIF9;Q7L622	.;G2E3_HUMAN	R	169;123;199;169;9	ENSP00000206595:W169R;ENSP00000391068:W123R;ENSP00000451653:W199R;ENSP00000446615:W169R	ENSP00000206595:W169R	W	+	1	0	G2E3	30132573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.835000	0.75344	2.078000	0.62432	0.477000	0.44152	TGG		0.303	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		C	31062822	T	C	31062822	3	2	61	1	0	0	0	0	1	0	0	0	6159	1812	63	4	523	4	G2E3	14	31062822	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	959137	31062822	76286718	8846	16831										
COCH	1690	broad.mit.edu	37	chr14	31349680	31349680	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgactaaagaaaacaccCgagaagaaaactggcaataa	7	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31349680C>T	ENST00000396618.3	+	7	515	c.459C>T	c.(457-459)ccC>ccT	p.P153P	COCH_ENST00000382493.4_5'Flank|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000475087.1_Silent_p.P153P|COCH_ENST00000216361.4_Silent_p.P153P|COCH_ENST00000460581.2_Silent_p.P41P	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	153					defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.P153P(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	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;0.00645)		AGAAAACACCCGAGAAGAAAA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	14											136	138	137					14																	31349680		2203	4300	6503	30419431	SO:0001819	synonymous_variant	1690				CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.459C>T	14.37:g.31349680C>T			30419431	A8K9K9|D3DS84|Q96IU6	Silent	SNP	ENST00000396618.3	37	CCDS9640.1																																																																																				0.418	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		T	31349680	C	T	31349680	2	4	61	1	0	0	0	0	0	0	0	1	3662	639	23	1		1	COCH	14	31349680	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	286858	31349680	75999860	8847	16832										
HECTD1	25831	broad.mit.edu	37	chr14	31598438	31598438	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgctgcttccttttctaCttgaggagcctgcagcagca	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31598438C>A	ENST00000399332.1	-	25	4627	c.4139G>T	c.(4138-4140)aGt>aTt	p.S1380I	HECTD1_ENST00000553700.1_Missense_Mutation_p.S1380I	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1380	Ser-rich.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.S1380I(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		TCCTTTTCTACTTGAGGAGCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	14											151	149	149					14																	31598438		2013	4188	6201	30668189	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.4139G>T	14.37:g.31598438C>A	ENSP00000382269:p.Ser1380Ile		30668189	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885989	0.72410	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.49139	0.79;0.79;1.31	5.73	5.73	0.89815	.	0.000000	0.85682	U	0.000000	T	0.51601	0.1684	N	0.08118	0	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.69142	0.962;0.944	T	0.60419	-0.7267	10	0.56958	D	0.05	-11.8156	20.2786	0.98501	0.0:1.0:0.0:0.0	.	1380;1380	D3DS86;Q9ULT8	.;HECD1_HUMAN	I	1380;1382;1380;807	ENSP00000450697:S1380I;ENSP00000382269:S1380I;ENSP00000451860:S807I	ENSP00000261312:S1382I	S	-	2	0	HECTD1	30668189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.252000	0.78309	2.868000	0.98415	0.557000	0.71058	AGT		0.483	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31598438	C	A	31598438	3	1	61	1	0	0	0	0	1	0	0	0	7060	565	20	2	3769	2	HECTD1	14	31598438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	248758	31598438	75751102	8848	16833										
HEATR5A	25938	broad.mit.edu	37	chr14	31771711	31771711	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtacaatatagtagggaGaattgagatgcttcctgtaa	12	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31771711G>T	ENST00000389961.3	-	32	5235	c.5236C>A	c.(5236-5238)Ctc>Atc	p.L1746I	HEATR5A_ENST00000439727.1_Missense_Mutation_p.L1459I|RP11-596D21.1_ENST00000551799.1_RNA|HEATR5A_ENST00000543095.2_Missense_Mutation_p.L1752I|HEATR5A_ENST00000439348.1_Intron			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1746								p.L1746I(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		ATAGTAGGGAGAATTGAGATG	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	14											26	27	27					14																	31771711		1827	4082	5909	30841462	SO:0001583	missense	25938			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.5236C>A	14.37:g.31771711G>T	ENSP00000374611:p.Leu1746Ile		30841462	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		.	.	.	.	.	.	.	.	.	.	G	16.58	3.163604	0.57476	.	.	ENSG00000129493	ENST00000389961;ENST00000439727;ENST00000543095	T;T;T	0.68331	-0.32;-0.32;-0.32	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.81621	0.4861	M	0.81802	2.56	0.80722	D	1	.	.	.	.	.	.	D	0.84567	0.0653	8	0.72032	D	0.01	.	18.41	0.90548	0.0:0.0:1.0:0.0	.	.	.	.	I	1746;1459;1752	ENSP00000374611:L1746I;ENSP00000408681:L1459I;ENSP00000437968:L1752I	ENSP00000374611:L1746I	L	-	1	0	HEATR5A	30841462	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.038000	0.70964	2.441000	0.82636	0.561000	0.74099	CTC		0.408	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		T	31771711	G	T	31771711	3	4	61	1	0	0	0	0	1	0	0	0	7052	942	33	2	902	2	HEATR5A	14	31771711	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173273	31771711	75577829	8849	16834										
HEATR5A	25938	broad.mit.edu	37	chr14	31813174	31813174	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagctgctgaaggcaagaGatggcctgagcttgaacaag	14	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31813174G>T	ENST00000389961.3	-	20	3137	c.3138C>A	c.(3136-3138)atC>atA	p.I1046I	HEATR5A_ENST00000439727.1_Silent_p.I759I|HEATR5A_ENST00000543095.2_Silent_p.I1052I|HEATR5A_ENST00000439348.1_Silent_p.I1046I|HEATR5A_ENST00000404677.3_Silent_p.I1052I			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1046								p.I1046I(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		GAAGGCAAGAGATGGCCTGAG	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	14											85	94	91					14																	31813174		2190	4298	6488	30882925	SO:0001819	synonymous_variant	25938			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.3138C>A	14.37:g.31813174G>T			30882925	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.854|9.854	1.194576|1.194576	0.22037|0.22037	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000550366|ENST00000538864;ENST00000549719	.|.	.|.	.|.	5.98|5.98	5.08|5.08	0.68730|0.68730	.|.	.|.	.|.	.|.	.|.	T|T	0.59088|0.59088	0.2168|0.2168	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57837|0.57837	-0.7742|-0.7742	4|4	.|.	.|.	.|.	.|.	8.024|8.024	0.30425|0.30425	0.1303:0.0:0.7369:0.1327|0.1303:0.0:0.7369:0.1327	.|.	.|.	.|.	.|.	I|Y	695|680;71	.|.	.|.	L|S	-|-	1|2	0|0	HEATR5A|HEATR5A	30882925|30882925	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.376000|2.376000	0.44292|0.44292	1.511000|1.511000	0.48818|0.48818	0.650000|0.650000	0.86243|0.86243	CTC|TCT		0.448	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		T	31813174	G	T	31813174	2	4	61	1	0	0	0	0	0	0	0	1	7052	932	33	2		2	HEATR5A	14	31813174	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41463	31813174	75536366	8850	16835										
HEATR5A	25938	broad.mit.edu	37	chr14	31844094	31844094	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcggctcttttctgtttCtagatctttaggagatgctg	9	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31844094C>A	ENST00000389961.3	-	11	1770	c.1771G>T	c.(1771-1773)Gaa>Taa	p.E591*	HEATR5A_ENST00000439727.1_Nonsense_Mutation_p.E304*|HEATR5A_ENST00000543095.2_Nonsense_Mutation_p.E597*|HEATR5A_ENST00000439348.1_Nonsense_Mutation_p.E591*|HEATR5A_ENST00000404677.3_Nonsense_Mutation_p.E597*			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	591								p.E591*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TTTTCTGTTTCTAGATCTTTA	0.468																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											63	65	64					14																	31844094		1920	4128	6048	30913845	SO:0001587	stop_gained	25938			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1771G>T	14.37:g.31844094C>A	ENSP00000374611:p.Glu591*		30913845	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Nonsense_Mutation	SNP	ENST00000389961.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	40|40|40	8.166897|8.166897|8.166897	0.98686|0.98686|0.98686	.|.|.	.|.|.	ENSG00000129493|ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000550366|ENST00000538864	.|.|.	.|.|.	.|.|.	5.92|5.92|5.92	5.92|5.92|5.92	0.95590|0.95590|0.95590	.|.|.	0.050910|.|.	0.85682|.|.	D|.|.	0.000000|.|.	.|T|.	.|0.80303|.	.|0.4598|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|.	.|0.77824|.	.|-0.2444|.	.|3|.	0.87932|.|.	D|.|.	0|.|.	.|.|.	20.3172|20.3172|20.3172	0.98658|0.98658|0.98658	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|I|Y	591;591;304;597;597|239|224	.|.|.	ENSP00000374611:E591X|.|.	E|R|X	-|-|-	1|2|3	0|0|2	HEATR5A|HEATR5A|HEATR5A	30913845|30913845|30913845	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.792000|7.792000|7.792000	0.85828|0.85828|0.85828	2.801000|2.801000|2.801000	0.96364|0.96364|0.96364	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GAA|AGA|TAG		0.468	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		A	31844094	C	A	31844094	4	1	61	1	0	0	0	0	0	1	0	0	7052	922	32	2	4451	2	HEATR5A	14	31844094	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30920	31844094	75505446	8851	16836										
HEATR5A	25938	broad.mit.edu	37	chr14	31855692	31855692	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtatgagatttccaagttCttgtaaagcacaaaccagca	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31855692C>A	ENST00000389961.3	-	8	1260	c.1261G>T	c.(1261-1263)Gaa>Taa	p.E421*	HEATR5A_ENST00000439727.1_Nonsense_Mutation_p.E134*|HEATR5A_ENST00000543095.2_Nonsense_Mutation_p.E427*|HEATR5A_ENST00000439348.1_Nonsense_Mutation_p.E421*|HEATR5A_ENST00000404677.3_Nonsense_Mutation_p.E427*			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	421								p.E421*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TTTCCAAGTTCTTGTAAAGCA	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											121	118	119					14																	31855692		1883	4118	6001	30925443	SO:0001587	stop_gained	25938			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1261G>T	14.37:g.31855692C>A	ENSP00000374611:p.Glu421*		30925443	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Nonsense_Mutation	SNP	ENST00000389961.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	39|39|39	7.374785|7.374785|7.374785	0.98245|0.98245|0.98245	.|.|.	.|.|.	ENSG00000129493|ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000538864|ENST00000550366	.|.|.	.|.|.	.|.|.	5.93|5.93|5.93	5.93|5.93|5.93	0.95920|0.95920|0.95920	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	.|T|T	.|0.80319|0.80319	.|0.4601|0.4601	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.77781|0.77781	.|-0.2459|-0.2459	.|3|3	0.87932|.|.	D|.|.	0|.|.	.|.|.	20.3495|20.3495|20.3495	0.98807|0.98807|0.98807	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	421;421;134;427;427|54|69	.|.|.	ENSP00000374611:E421X|.|.	E|K|R	-|-|-	1|3|2	0|2|0	HEATR5A|HEATR5A|HEATR5A	30925443|30925443|30925443	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.959000|0.959000|0.959000	0.62525|0.62525|0.62525	7.168000|7.168000|7.168000	0.77570|0.77570|0.77570	2.814000|2.814000|2.814000	0.96858|0.96858|0.96858	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAA|AAG|AGA		0.433	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		A	31855692	C	A	31855692	4	1	61	1	0	0	0	0	0	1	0	0	7052	922	32	2	4973	2	HEATR5A	14	31855692	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11598	31855692	75493848	8852	16837										
C14orf126	112487	broad.mit.edu	37	chr14	31917405	31917405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcctgttcccataagtgCcatgttccactacaacccta	5	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:31917405C>T	ENST00000310850.4	-	3	553	c.437G>A	c.(436-438)gGc>gAc	p.G146D	CTD-2213F21.2_ENST00000502430.2_RNA|DTD2_ENST00000356180.4_Missense_Mutation_p.G146D|RP11-176H8.1_ENST00000547378.1_Intron	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	146					D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.G146D(1)									CCCATAAGTGCCATGTTCCAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											234	231	232					14																	31917405		2203	4300	6503	30987156	SO:0001583	missense	112487			BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.437G>A	14.37:g.31917405C>T	ENSP00000312224:p.Gly146Asp		30987156	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	C	32	5.154213	0.94645	.	.	ENSG00000129480	ENST00000310850;ENST00000356180	T;T	0.77358	-1.09;-1.09	6.04	6.04	0.98038	D-Tyr tRNAtyr deacylase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.90448	0.7009	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90792	0.4687	10	0.87932	D	0	-3.2728	20.5948	0.99439	0.0:1.0:0.0:0.0	.	146	Q96FN9	DTD2_HUMAN	D	146	ENSP00000312224:G146D;ENSP00000348503:G146D	ENSP00000312224:G146D	G	-	2	0	C14orf126	30987156	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.333000	0.79214	2.873000	0.98535	0.563000	0.77884	GGC		0.393	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		T	31917405	C	T	31917405	3	4	61	1	0	0	0	0	1	0	0	0	1747	739	26	3	73	3	C14orf126	14	31917405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61713	31917405	75432135	8853	16838										
ARHGAP5	394	broad.mit.edu	37	chr14	32560992	32560992	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttaatggaaaagagagcaGatttccagttatgttttgtg	11	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:32560992G>A	ENST00000345122.3	+	2	1432	c.1117G>A	c.(1117-1119)Gat>Aat	p.D373N	ARHGAP5_ENST00000556611.1_Missense_Mutation_p.D373N|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.D373N|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.D373N|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	373	FF 2.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.D373N(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AAAGAGAGCAGATTTCCAGTT	0.358																																					NSCLC(9;77 350 3443 29227 41353)											1	Substitution - Missense(1)	large_intestine(1)	14											105	111	109					14																	32560992		2183	4287	6470	31630743	SO:0001583	missense	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1117G>A	14.37:g.32560992G>A	ENSP00000371897:p.Asp373Asn		31630743	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.638647	0.67130	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	5.64	5.64	0.86602	FF domain (1);	0.206005	0.49305	D	0.000146	T	0.15609	0.0376	L	0.52573	1.65	0.80722	D	1	B;B	0.18610	0.029;0.017	B;B	0.28553	0.091;0.042	T	0.06023	-1.0850	10	0.27082	T	0.32	.	19.7009	0.96052	0.0:0.0:1.0:0.0	.	373;373	Q13017-2;Q13017	.;RHG05_HUMAN	N	373	ENSP00000452222:D373N;ENSP00000441692:D373N;ENSP00000371897:D373N;ENSP00000393307:D373N	ENSP00000371897:D373N	D	+	1	0	ARHGAP5	31630743	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.646000	0.89796	0.563000	0.77884	GAT		0.358	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		A	32560992	G	A	32560992	3	1	61	1	0	0	0	0	1	0	0	0	886	942	33	3	1119	3	ARHGAP5	14	32560992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	643587	32560992	74788548	8854	16839										
AKAP6	9472	broad.mit.edu	37	chr14	33016050	33016050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagtccagtatgcctctcGctggcatgaaaaagtatgct	11	9	1	1	rs139751571	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:33016050G>A	ENST00000280979.4	+	4	2361	c.2191G>A	c.(2191-2193)Gct>Act	p.A731T	AKAP6_ENST00000557272.1_Missense_Mutation_p.A731T|AKAP6_ENST00000557354.1_Missense_Mutation_p.A731T	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	731					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.A731T(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TATGCCTCTCGCTGGCATGAA	0.448													G|||	7	0.00139776	0.0053	0	5008	,	,		18479	0		0	False		,,,				2504	0				Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Missense(1)	large_intestine(1)	14						G	THR/ALA	26,4380	34.3+/-65.2	0,26,2177	64	62	62		2191	2.5	1	14	dbSNP_134	62	0,8600		0,0,4300	yes	missense	AKAP6	NM_004274.4	58	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	benign	731/2320	33016050	26,12980	2203	4300	6503	32085801	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2191G>A	14.37:g.33016050G>A	ENSP00000280979:p.Ala731Thr		32085801	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	6.915	0.538489	0.13250	0.005901	0.0	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.30448	1.53;1.53;1.53	6.17	2.52	0.30459	.	0.572707	0.18217	N	0.148006	T	0.10423	0.0255	N	0.08118	0	0.19775	N	0.99995	B;B	0.12630	0.001;0.006	B;B	0.08055	0.001;0.003	T	0.17410	-1.0370	10	0.46703	T	0.11	-1.973	7.7743	0.29029	0.2421:0.0:0.1282:0.6297	.	731;731	A7E242;Q13023	.;AKAP6_HUMAN	T	731	ENSP00000280979:A731T;ENSP00000450531:A731T;ENSP00000451247:A731T	ENSP00000280979:A731T	A	+	1	0	AKAP6	32085801	0.997000	0.39634	0.999000	0.59377	0.103000	0.19146	1.978000	0.40598	0.193000	0.20303	-1.006000	0.02489	GCT		0.448	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		A	33016050	G	A	33016050	3	1	61	1	0	0	0	0	1	0	0	0	455	1087	38	1	2201	1	AKAP6	14	33016050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	455058	33016050	74333490	8855	16840										
AKAP6	9472	broad.mit.edu	37	chr14	33147553	33147553	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctacctggaagcacaaagaGatgctgttgagcagatgtcc	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:33147553G>T	ENST00000280979.4	+	8	2937	c.2767G>T	c.(2767-2769)Gat>Tat	p.D923Y	AKAP6_ENST00000557272.1_Missense_Mutation_p.D923Y|AKAP6_ENST00000557354.1_Missense_Mutation_p.D923Y	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	923					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.D923Y(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AGCACAAAGAGATGCTGTTGA	0.438																																					Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Missense(1)	large_intestine(1)	14											134	117	123					14																	33147553		2203	4300	6503	32217304	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2767G>T	14.37:g.33147553G>T	ENSP00000280979:p.Asp923Tyr		32217304	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.693996	0.68386	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.20332	3.34;2.08;2.09	5.3	5.3	0.74995	.	0.069487	0.64402	D	0.000015	T	0.33411	0.0862	N	0.19112	0.55	0.53005	D	0.999966	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.18871	-1.0323	10	0.72032	D	0.01	-15.3955	17.1295	0.86723	0.0:0.0:1.0:0.0	.	923;923	A7E242;Q13023	.;AKAP6_HUMAN	Y	923	ENSP00000280979:D923Y;ENSP00000450531:D923Y;ENSP00000451247:D923Y	ENSP00000280979:D923Y	D	+	1	0	AKAP6	32217304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.775000	0.75018	2.480000	0.83734	0.585000	0.79938	GAT		0.438	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33147553	G	T	33147553	3	4	61	1	0	0	0	0	1	0	0	0	455	942	33	2	2793	2	AKAP6	14	33147553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131503	33147553	74201987	8856	16841										
AKAP6	9472	broad.mit.edu	37	chr14	33292123	33292123	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgagctctctctttgctcaGaggatattgtgttacacaag	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:33292123G>T	ENST00000280979.4	+	13	5274	c.5104G>T	c.(5104-5106)Gag>Tag	p.E1702*	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1702			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.E1702Q(2)|p.E1702*(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCTTTGCTCAGAGGATATTGT	0.463																																					Melanoma(49;821 1200 7288 13647 42351)											3	Substitution - Missense(2)|Substitution - Nonsense(1)	breast(2)|large_intestine(1)	14											114	105	108					14																	33292123		2203	4300	6503	32361874	SO:0001587	stop_gained	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.5104G>T	14.37:g.33292123G>T	ENSP00000280979:p.Glu1702*		32361874	A7E242|A7E2D4|O15028	Nonsense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	45	11.539272	0.99573	.	.	ENSG00000151320	ENST00000280979	.	.	.	5.98	5.98	0.97165	.	0.049889	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.5256	20.4561	0.99145	0.0:0.0:1.0:0.0	.	.	.	.	X	1702	.	ENSP00000280979:E1702X	E	+	1	0	AKAP6	32361874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.922000	0.92789	2.843000	0.97960	0.650000	0.86243	GAG		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33292123	G	T	33292123	4	4	61	1	0	0	0	0	0	1	0	0	455	943	33	2	5150	2	AKAP6	14	33292123	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144570	33292123	74057417	8857	16842										
AKAP6	9472	broad.mit.edu	37	chr14	33293654	33293654	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgatgcagatacagtggCtctttcaagtccttcctctc	8	11	3	3	rs201151556		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:33293654C>G	ENST00000280979.4	+	13	6805	c.6635C>G	c.(6634-6636)gCt>gGt	p.A2212G	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2212					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.A2212G(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GATACAGTGGCTCTTTCAAGT	0.463													C|||	1	0.000199681	0	0.0014	5008	,	,		21000	0		0	False		,,,				2504	0				Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Missense(1)	large_intestine(1)	14											100	90	93					14																	33293654		2203	4300	6503	32363405	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6635C>G	14.37:g.33293654C>G	ENSP00000280979:p.Ala2212Gly		32363405	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	8.820	0.937427	0.18206	.	.	ENSG00000151320	ENST00000280979	T	0.05139	3.49	5.11	1.97	0.26223	.	0.821838	0.10903	N	0.621432	T	0.05364	0.0142	L	0.51422	1.61	0.09310	N	1	P	0.35433	0.501	B	0.32864	0.154	T	0.38045	-0.9679	10	0.25106	T	0.35	-0.5924	1.5897	0.02651	0.2415:0.4496:0.1242:0.1847	.	2212	Q13023	AKAP6_HUMAN	G	2212	ENSP00000280979:A2212G	ENSP00000280979:A2212G	A	+	2	0	AKAP6	32363405	0.000000	0.05858	0.005000	0.12908	0.124000	0.20399	0.178000	0.16820	0.633000	0.30452	-0.140000	0.14226	GCT		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		G	33293654	C	G	33293654	3	3	61	1	0	0	0	0	1	0	0	0	455	797	28	5	6681	5	AKAP6	14	33293654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1531	33293654	74055886	8858	16843										
NPAS3	64067	broad.mit.edu	37	chr14	34269462	34269462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcggtgctcaagatcaagaCggagatctcagaacccatca	9	12	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:34269462C>T	ENST00000356141.4	+	12	1949	c.1949C>T	c.(1948-1950)aCg>aTg	p.T650M	NPAS3_ENST00000548645.1_Missense_Mutation_p.T620M|NPAS3_ENST00000551492.1_Missense_Mutation_p.T655M|NPAS3_ENST00000346562.2_Missense_Mutation_p.T618M|NPAS3_ENST00000357798.5_Missense_Mutation_p.T637M			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	650					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.T618M(2)		breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AAGATCAAGACGGAGATCTCA	0.632																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	14											56	56	56					14																	34269462		2203	4300	6503	33339213	SO:0001583	missense	64067			AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1949C>T	14.37:g.34269462C>T	ENSP00000348460:p.Thr650Met		33339213	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.478950	0.63849	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.71341	-0.56;2.95;2.96;2.96;2.94;2.81	5.07	5.07	0.68467	.	0.118877	0.56097	D	0.000036	T	0.72653	0.3487	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;P;P;P	0.58077	0.832;0.684;0.832;0.832	T	0.77373	-0.2612	10	0.72032	D	0.01	.	18.4473	0.90690	0.0:1.0:0.0:0.0	.	620;650;618;637	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	M	624;655;618;620;650;637	ENSP00000448373:T624M;ENSP00000450392:T655M;ENSP00000319610:T618M;ENSP00000448916:T620M;ENSP00000348460:T650M;ENSP00000350446:T637M	ENSP00000319610:T618M	T	+	2	0	NPAS3	33339213	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.558000	0.82253	2.329000	0.79093	0.555000	0.69702	ACG		0.632	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	34269462	C	T	34269462	3	4	61	1	0	0	0	0	1	0	0	0	10595	536	19	1	2050	1	NPAS3	14	34269462	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	975808	34269462	73080078	8859	16844										
EAPP	55837	broad.mit.edu	37	chr14	34985664	34985664	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcagcatcttcccggttaGacctcatcttcttatggacc	8	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:34985664G>T	ENST00000250454.3	-	6	791	c.710C>A	c.(709-711)tCt>tAt	p.S237Y		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	237					negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.S237Y(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		TTCCCGGTTAGACCTCATCTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	14											252	247	248					14																	34985664		1964	4134	6098	34055415	SO:0001583	missense	55837			AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"chromosome 14 open reading frame 11"	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.710C>A	14.37:g.34985664G>T	ENSP00000250454:p.Ser237Tyr		34055415	Q9BVF4|Q9NWV5|Q9NZ86	Missense_Mutation	SNP	ENST00000250454.3	37	CCDS41941.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669404	0.47677	.	.	ENSG00000129518	ENST00000250454	T	0.45668	0.89	5.44	5.44	0.79542	.	0.494514	0.23496	N	0.047549	T	0.43567	0.1253	L	0.59436	1.845	0.28779	N	0.899942	P	0.38335	0.627	B	0.40782	0.34	T	0.48658	-0.9016	10	0.48119	T	0.1	-6.3946	12.7433	0.57266	0.0:0.0:0.728:0.272	.	237	Q56P03	EAPP_HUMAN	Y	237	ENSP00000250454:S237Y	ENSP00000250454:S237Y	S	-	2	0	EAPP	34055415	0.630000	0.27155	0.095000	0.20976	0.401000	0.30781	3.835000	0.55805	2.720000	0.93068	0.650000	0.86243	TCT		0.443	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453		T	34985664	G	T	34985664	3	4	61	1	0	0	0	0	1	0	0	0	4888	942	33	2	151	2	EAPP	14	34985664	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	716202	34985664	72363876	8860	16845										
BAZ1A	11177	broad.mit.edu	37	chr14	35234232	35234232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagaaaaaaataccttgaGctttggtcgaacacagtagg	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35234232G>A	ENST00000382422.2	-	21	3871	c.3544C>T	c.(3544-3546)Ctc>Ttc	p.L1182F	BAZ1A_ENST00000358716.4_Missense_Mutation_p.L1150F|BAZ1A_ENST00000360310.1_Missense_Mutation_p.L1182F			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1182					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)	p.L1182F(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		AATACCTTGAGCTTTGGTCGA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	14											92	85	87					14																	35234232		2203	4300	6503	34303983	SO:0001583	missense	11177			AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3544C>T	14.37:g.35234232G>A	ENSP00000371859:p.Leu1182Phe		34303983	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407844	0.83340	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	D;D;D	0.81908	-1.55;-1.55;-1.55	5.67	5.67	0.87782	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.94540	0.7744	10	0.87932	D	0	.	19.7775	0.96400	0.0:0.0:1.0:0.0	.	1150;1182	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	F	1150;1182;1182;834	ENSP00000351555:L1150F;ENSP00000371859:L1182F;ENSP00000353458:L1182F	ENSP00000351555:L1150F	L	-	1	0	BAZ1A	34303983	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.226000	0.72277	2.680000	0.91292	0.655000	0.94253	CTC		0.373	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			A	35234232	G	A	35234232	3	1	61	1	0	0	0	0	1	0	0	0	1330	971	34	3	1150	3	BAZ1A	14	35234232	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248568	35234232	72115308	8861	16846										
BAZ1A	11177	broad.mit.edu	37	chr14	35262071	35262071	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagtcaggaagaaaaaaaGcaattcacacagtgggcctt	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35262071G>T	ENST00000382422.2	-	11	1747	c.1420C>A	c.(1420-1422)Ctt>Att	p.L474I	BAZ1A_ENST00000358716.4_Missense_Mutation_p.L474I|BAZ1A_ENST00000360310.1_Missense_Mutation_p.L474I			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	474	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)	p.L474I(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		AAGAAAAAAAGCAATTCACAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	14											140	130	133					14																	35262071		2203	4300	6503	34331822	SO:0001583	missense	11177			AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1420C>A	14.37:g.35262071G>T	ENSP00000371859:p.Leu474Ile		34331822	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448776	0.84101	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	D;D;D	0.92699	-1.51;-3.09;-3.09	5.08	5.08	0.68730	DDT domain superfamily (1);DDT domain, subgroup (1);DDT domain (1);	0.000000	0.85682	D	0.000000	D	0.94228	0.8147	L	0.52759	1.655	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.99;0.996	D	0.94264	0.7505	10	0.66056	D	0.02	.	13.1995	0.59758	0.0768:0.0:0.9232:0.0	.	474;474	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	I	474;474;474;158	ENSP00000351555:L474I;ENSP00000371859:L474I;ENSP00000353458:L474I	ENSP00000351555:L474I	L	-	1	0	BAZ1A	34331822	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.049000	0.76613	2.527000	0.85204	0.655000	0.94253	CTT		0.388	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			T	35262071	G	T	35262071	3	4	61	1	0	0	0	0	1	0	0	0	1330	971	34	2	3314	2	BAZ1A	14	35262071	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27839	35262071	72087469	8862	16847										
SRP54	6729	broad.mit.edu	37	chr14	35488243	35488243	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcaatggcaaggctaaaGaaattaatgacaataatgga	10	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35488243G>T	ENST00000556994.1	+	14	1516	c.1119G>T	c.(1117-1119)aaG>aaT	p.K373N	SRP54_ENST00000216774.6_Missense_Mutation_p.K373N|SRP54_ENST00000546080.1_Missense_Mutation_p.K324N|SRP54_ENST00000555557.1_Missense_Mutation_p.K309N			P61011	SRP54_HUMAN	signal recognition particle 54kDa	373	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)	p.K373N(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		CAAGGCTAAAGAAATTAATGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	14											102	99	100					14																	35488243		2203	4300	6503	34557994	SO:0001583	missense	6729			X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1119G>T	14.37:g.35488243G>T	ENSP00000451818:p.Lys373Asn		34557994	B2R759|B4DUW6|P13624	Missense_Mutation	SNP	ENST00000556994.1	37	CCDS9652.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028492	0.75390	.	.	ENSG00000100883	ENST00000556994;ENST00000216774;ENST00000546080;ENST00000555557	.	.	.	5.64	2.39	0.29439	Signal recognition particle, SRP54 subunit, M-domain (3);	0.000000	0.85682	D	0.000000	T	0.77350	0.4117	M	0.87381	2.88	0.80722	D	1	D;D	0.67145	0.996;0.992	P;P	0.61328	0.887;0.887	T	0.80432	-0.1385	9	0.59425	D	0.04	-17.4984	12.1763	0.54188	0.2181:0.0:0.7819:0.0	.	324;373	B4DUW6;P61011	.;SRP54_HUMAN	N	373;373;324;309	.	ENSP00000216774:K373N	K	+	3	2	SRP54	34557994	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.896000	0.63222	0.747000	0.32809	0.591000	0.81541	AAG		0.353	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		T	35488243	G	T	35488243	3	4	61	1	0	0	0	0	1	0	0	0	15194	933	33	2	1165	2	SRP54	14	35488243	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	226172	35488243	71861297	8863	16848										
PPP2R3C	55012	broad.mit.edu	37	chr14	35554882	35554882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtccagaagccattcaaatCgattagaatggtggttactg	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35554882C>T	ENST00000261475.5	-	13	1629	c.1276G>A	c.(1276-1278)Gat>Aat	p.D426N		NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	426					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.D426N(1)		central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CCATTCAAATCGATTAGAATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	14											137	128	131					14																	35554882		2203	4300	6503	34624633	SO:0001583	missense	55012			AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.1276G>A	14.37:g.35554882C>T	ENSP00000261475:p.Asp426Asn		34624633	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Missense_Mutation	SNP	ENST00000261475.5	37	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	c	34	5.297435	0.95574	.	.	ENSG00000092020	ENST00000261475;ENST00000555219	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.77458	0.4133	M	0.83774	2.66	0.80722	D	1	D	0.76494	0.999	D	0.67103	0.949	T	0.74487	-0.3649	9	0.02654	T	1	-13.1202	19.3049	0.94157	0.0:1.0:0.0:0.0	.	426	Q969Q6	P2R3C_HUMAN	N	426;101	.	ENSP00000261475:D426N	D	-	1	0	PPP2R3C	34624633	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.626000	0.83164	2.564000	0.86499	0.579000	0.79373	GAT		0.383	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		T	35554882	C	T	35554882	3	4	61	1	0	0	0	0	1	0	0	0	12424	884	31	1	89	1	PPP2R3C	14	35554882	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66639	35554882	71794658	8864	16849										
PPP2R3C	55012	broad.mit.edu	37	chr14	35565773	35565773	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggaacataccataaactcTtagggcagaaggagcagaaa	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35565773T>G	ENST00000261475.5	-	9	1182	c.829A>C	c.(829-831)Aga>Cga	p.R277R		NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	277	EF-hand 1.				activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R277R(1)		central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CCATAAACTCTTAGGGCAGAA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	14											130	117	121					14																	35565773		2203	4300	6503	34635524	SO:0001819	synonymous_variant	55012			AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.829A>C	14.37:g.35565773T>G			34635524	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Silent	SNP	ENST00000261475.5	37	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	T	4.632	0.117482	0.08881	.	.	ENSG00000092020	ENST00000555614	.	.	.	5.01	0.887	0.19200	.	.	.	.	.	T	0.65933	0.2739	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63148	-0.6702	4	.	.	.	-5.9823	12.9564	0.58430	0.0:0.0:0.3799:0.6201	.	.	.	.	T	205	.	.	K	-	2	0	PPP2R3C	34635524	0.998000	0.40836	0.886000	0.34754	0.626000	0.37791	2.148000	0.42235	0.304000	0.22809	0.454000	0.30748	AAG		0.363	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		G	35565773	T	G	35565773	2	3	61	1	0	0	0	0	0	0	0	1	12424	1617	56	4		4	PPP2R3C	14	35565773	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	10891	35565773	71783767	8865	16850										
PPP2R3C	55012	broad.mit.edu	37	chr14	35577367	35577367	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcatgacataattaaaGaactgcatgatggaaattct	6	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35577367G>T	ENST00000261475.5	-	5	833	c.480C>A	c.(478-480)ttC>ttA	p.F160L	PPP2R3C_ENST00000555644.1_Missense_Mutation_p.F160L	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	160					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.F160L(1)		central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CATAATTAAAGAACTGCATGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	14											67	70	69					14																	35577367		2202	4293	6495	34647118	SO:0001583	missense	55012			AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.480C>A	14.37:g.35577367G>T	ENSP00000261475:p.Phe160Leu		34647118	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Missense_Mutation	SNP	ENST00000261475.5	37	CCDS9654.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.77|11.77	1.738081|1.738081	0.30774|0.30774	.|.	.|.	ENSG00000092020|ENSG00000092020	ENST00000261475;ENST00000554361;ENST00000555644;ENST00000557278|ENST00000555614	T;T|.	0.58797|.	0.31;0.31|.	5.8|5.8	4.91|4.91	0.64330|0.64330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.40448|0.40448	0.1117|0.1117	N|N	0.21282|0.21282	0.65|0.65	0.58432|0.58432	D|D	0.999996|0.999996	B;B|.	0.12013|.	0.005;0.002|.	B;B|.	0.15052|.	0.012;0.006|.	T|T	0.25117|0.25117	-1.0141|-1.0141	10|5	0.31617|.	T|.	0.26|.	-7.9479|-7.9479	6.8367|6.8367	0.23941|0.23941	0.2917:0.0:0.7083:0.0|0.2917:0.0:0.7083:0.0	.|.	160;160|.	Q86US5;Q969Q6|.	.;P2R3C_HUMAN|.	L|I	160;132;160;160|89	ENSP00000261475:F160L;ENSP00000450716:F132L|.	ENSP00000261475:F160L|.	F|L	-|-	3|1	2|0	PPP2R3C|PPP2R3C	34647118|34647118	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	2.980000|2.980000	0.49321|0.49321	1.457000|1.457000	0.47850|0.47850	0.650000|0.650000	0.86243|0.86243	TTC|CTT		0.313	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		T	35577367	G	T	35577367	3	4	61	1	0	0	0	0	1	0	0	0	12424	933	33	2	917	2	PPP2R3C	14	35577367	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11594	35577367	71772173	8866	16851										
KIAA0391	9692	broad.mit.edu	37	chr14	35592591	35592591	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccagcagaggttgttttCtcttaaaacaatgtctccac	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35592591C>A	ENST00000557565.1	+	2	521	c.140C>A	c.(139-141)tCt>tAt	p.S47Y	KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000321130.10_Missense_Mutation_p.S47Y|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000603544.1_Missense_Mutation_p.S47Y|KIAA0391_ENST00000603588.1_Intron|PPP2R3C_ENST00000555644.1_5'Flank|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000534898.4_Missense_Mutation_p.S47Y	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	47					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)		p.S47Y(1)		central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		AGGTTGTTTTCTCTTAAAACA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											63	58	60					14																	35592591		2203	4300	6503	34662342	SO:0001583	missense	9692			AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.140C>A	14.37:g.35592591C>A	ENSP00000454657:p.Ser47Tyr		34662342	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	37	CCDS32063.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633505	0.67015	.	.	ENSG00000100890	ENST00000321130;ENST00000534898;ENST00000556121	T;T	0.54279	0.61;0.58	5.25	2.31	0.28768	.	0.292616	0.24912	N	0.034604	T	0.49575	0.1565	M	0.70595	2.14	0.80722	D	1	B;B	0.30281	0.275;0.275	B;B	0.28916	0.096;0.096	T	0.48658	-0.9016	10	0.87932	D	0	-10.4289	9.8369	0.40975	0.1457:0.5913:0.2629:0.0	.	47;47	O15091-2;O15091	.;MRRP3_HUMAN	Y	47	ENSP00000324697:S47Y;ENSP00000440915:S47Y	ENSP00000324697:S47Y	S	+	2	0	KIAA0391	34662342	1.000000	0.71417	0.993000	0.49108	0.798000	0.45092	0.817000	0.27281	0.176000	0.19873	0.563000	0.77884	TCT		0.473	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		A	35592591	C	A	35592591	3	1	61	1	0	0	0	0	1	0	0	0	8193	913	32	2	142	2	KIAA0391	14	35592591	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15224	35592591	71756949	8867	16852										
NFKBIA	4792	broad.mit.edu	37	chr14	35871252	35871252	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctggcctccaaacacacaGtcatcatagggcagctgaaa	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:35871252G>A	ENST00000216797.5	-	6	1022	c.921C>T	c.(919-921)gaC>gaT	p.D307D	NFKBIA_ENST00000557100.1_5'Flank|NFKBIA_ENST00000557389.1_Silent_p.D217D|NFKBIA_ENST00000557140.1_Silent_p.D264D	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	307					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.D307D(1)		breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	CAAACACACAGTCATCATAGG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	14											82	88	86					14																	35871252		2203	4300	6503	34941003	SO:0001819	synonymous_variant	4792				CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.921C>T	14.37:g.35871252G>A			34941003	B2R8L6	Silent	SNP	ENST00000216797.5	37	CCDS9656.1																																																																																				0.453	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		A	35871252	G	A	35871252	2	1	61	1	0	0	0	0	0	0	0	1	10408	1020	36	3		3	NFKBIA	14	35871252	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	278661	35871252	71478288	8868	16853										
INSM2	84684	broad.mit.edu	37	chr14	36004730	36004730	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggtggcaggggatccgaGattttcgtgtgcccatattg	15	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:36004730G>T	ENST00000307169.3	+	1	1483	c.1272G>T	c.(1270-1272)gaG>gaT	p.E424D		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	424					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E424D(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		GGGGATCCGAGATTTTCGTGT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	14											55	65	62					14																	36004730		2194	4299	6493	35074481	SO:0001583	missense	84684			AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"Zinc fingers, C2H2-type"	17539	protein-coding gene	gene with protein product	"mlt 1"	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.1272G>T	14.37:g.36004730G>T	ENSP00000306523:p.Glu424Asp		35074481	A1L432|J9Y024|Q8N8K7|Q96Q84	Missense_Mutation	SNP	ENST00000307169.3	37	CCDS9657.1	.	.	.	.	.	.	.	.	.	.	G	1.269	-0.613563	0.03690	.	.	ENSG00000168348	ENST00000307169	T	0.00902	5.56	4.85	-0.409	0.12378	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.255528	0.20575	N	0.089650	T	0.00906	0.0030	L	0.32530	0.975	0.35963	D	0.834767	B	0.15141	0.012	B	0.12156	0.007	T	0.53012	-0.8498	10	0.72032	D	0.01	-13.2186	7.7136	0.28692	0.2096:0.2194:0.5711:0.0	.	424	Q96T92	INSM2_HUMAN	D	424	ENSP00000306523:E424D	ENSP00000306523:E424D	E	+	3	2	INSM2	35074481	0.999000	0.42202	0.320000	0.25306	0.132000	0.20833	0.478000	0.22212	-0.541000	0.06257	-1.134000	0.01955	GAG		0.652	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1			T	36004730	G	T	36004730	3	4	61	1	0	0	0	0	1	0	0	0	7793	933	33	2	1274	2	INSM2	14	36004730	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133478	36004730	71344810	8869	16854										
RALGAPA1	253959	broad.mit.edu	37	chr14	36104786	36104786	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatccagtccagaaggcagaGaagtaaagatactaccaact	9	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:36104786G>T	ENST00000389698.3	-	31	4567	c.4177C>A	c.(4177-4179)Ctc>Atc	p.L1393I	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.L1440I|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.L1406I|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.L1393I	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1393	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.L1393I(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGAAGGCAGAGAAGTAAAGAT	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	14											48	44	45					14																	36104786		2203	4300	6503	35174537	SO:0001583	missense	253959			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4177C>A	14.37:g.36104786G>T	ENSP00000374348:p.Leu1393Ile		35174537	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.460258	0.63401	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;1.45;-0.26;-0.26	5.27	2.42	0.29668	.	0.000000	0.64402	D	0.000001	T	0.75882	0.3910	L	0.59436	1.845	0.42816	D	0.993977	D;D;D;D	0.76494	0.999;0.997;0.998;0.974	D;D;D;P	0.81914	0.995;0.956;0.959;0.841	T	0.76334	-0.2997	10	0.59425	D	0.04	-7.2736	11.2699	0.49133	0.2101:0.0:0.7899:0.0	.	1440;1406;1393;1393	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	I	1393;1393;1393;1440;31;1406;1440	ENSP00000374348:L1393I;ENSP00000302647:L1393I;ENSP00000258840:L1440I;ENSP00000451133:L31I;ENSP00000371803:L1406I;ENSP00000451877:L1440I	ENSP00000258840:L1440I	L	-	1	0	RALGAPA1	35174537	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.858000	0.55979	0.719000	0.32188	0.563000	0.77884	CTC		0.338	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		T	36104786	G	T	36104786	3	4	61	1	0	0	0	0	1	0	0	0	13050	942	33	2	2126	2	RALGAPA1	14	36104786	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100056	36104786	71244754	8870	16855										
SSTR1	6751	broad.mit.edu	37	chr14	38679126	38679126	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccgtggccaaggtagtaAacctgggcgtgtgggtgcta	15	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:38679126A>C	ENST00000267377.2	+	3	1149	c.532A>C	c.(532-534)Aac>Cac	p.N178H		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	178					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.N178H(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	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)|Pasireotide(DB06663)	CAAGGTAGTAAACCTGGGCGT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	14											76	76	76					14																	38679126		2203	4300	6503	37748877	SO:0001583	missense	6751				CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"GPCR / Class A : Somatostatin receptors"	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.532A>C	14.37:g.38679126A>C	ENSP00000267377:p.Asn178His		37748877		Missense_Mutation	SNP	ENST00000267377.2	37	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299841	0.81136	.	.	ENSG00000139874	ENST00000267377	T	0.71934	-0.61	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	D	0.87034	0.6077	M	0.92970	3.365	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.90131	0.4206	10	0.87932	D	0	.	13.7174	0.62705	1.0:0.0:0.0:0.0	.	178	P30872	SSR1_HUMAN	H	178	ENSP00000267377:N178H	ENSP00000267377:N178H	N	+	1	0	SSTR1	37748877	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.107000	0.94261	2.034000	0.60081	0.459000	0.35465	AAC		0.642	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			C	38679126	A	C	38679126	3	2	61	1	0	0	0	0	1	0	0	0	15236	14	1	4	534	4	SSTR1	14	38679126	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2574340	38679126	68670414	8871	16856										
CLEC14A	161198	broad.mit.edu	37	chr14	38724496	38724496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtacctcccggggcagggAcacaacacatcgcccgagag	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:38724496A>G	ENST00000342213.2	-	1	1078	c.732T>C	c.(730-732)tgT>tgC	p.C244C		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	244						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.C244C(1)		breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	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;0.00439)		CGGGGCAGGGACACAACACAT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	14											119	128	125					14																	38724496		2203	4300	6503	37794247	SO:0001819	synonymous_variant	161198				CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.732T>C	14.37:g.38724496A>G			37794247	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	A	4.420	0.077756	0.08485	.	.	ENSG00000176435	ENST00000546356	.	.	.	3.88	-0.51	0.11973	.	.	.	.	.	T	0.55033	0.1895	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49504	-0.8933	5	0.38643	T	0.18	-8.9553	6.9347	0.24461	0.4782:0.0:0.5218:0.0	.	.	.	.	A	10	.	ENSP00000443662:V10A	V	-	2	0	CLEC14A	37794247	0.994000	0.37717	0.991000	0.47740	0.329000	0.28539	0.138000	0.16016	-0.060000	0.13132	-0.589000	0.04120	GTC		0.617	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		G	38724496	A	G	38724496	2	3	61	1	0	0	0	0	0	0	0	1	3505	273	10	4		4	CLEC14A	14	38724496	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	45370	38724496	68625044	8872	16857										
SEC23A	10484	broad.mit.edu	37	chr14	39509998	39509998	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatctggagtgaagaatttCctgtgcatcatccactgggg	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39509998C>A	ENST00000307712.6	-	18	2597	c.2080G>T	c.(2080-2082)Gaa>Taa	p.E694*	SEC23A_ENST00000536508.1_Nonsense_Mutation_p.E592*|SEC23A_ENST00000537403.1_Nonsense_Mutation_p.E492*|SEC23A_ENST00000545328.2_Nonsense_Mutation_p.E665*	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	694					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)	p.E694*(1)		kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		TGAAGAATTTCCTGTGCATCA	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											126	116	119					14																	39509998		2203	4300	6503	38579749	SO:0001587	stop_gained	10484			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.2080G>T	14.37:g.39509998C>A	ENSP00000306881:p.Glu694*		38579749	B2R5P4|B3KXI2|Q8NE16	Nonsense_Mutation	SNP	ENST00000307712.6	37	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	C	45	11.993167	0.99625	.	.	ENSG00000100934	ENST00000537403;ENST00000307712;ENST00000536508;ENST00000545328	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-17.034	19.9525	0.97208	0.0:1.0:0.0:0.0	.	.	.	.	X	492;694;592;665	.	ENSP00000306881:E694X	E	-	1	0	SEC23A	38579749	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.664000	0.83830	2.719000	0.93026	0.655000	0.94253	GAA		0.438	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			A	39509998	C	A	39509998	4	1	61	1	0	0	0	0	0	1	0	0	14028	864	30	2	229	2	SEC23A	14	39509998	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	785502	39509998	67839542	8873	16858										
SIP1	8487	broad.mit.edu	37	chr14	39587287	39587287	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcacagttttcaactgttCgacaggtaagtgtcatattt	9	7	2	0	rs146348850		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39587287C>T	ENST00000308317.6	+	3	423	c.340C>T	c.(340-342)Cga>Tga	p.R114*	GEMIN2_ENST00000396249.2_Nonsense_Mutation_p.R114*|GEMIN2_ENST00000250379.8_Nonsense_Mutation_p.R114*	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	114					gene expression (GO:0010467)|mRNA processing (GO:0006397)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)		p.R114*(1)									TTCAACTGTTCGACAGGTAAG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	14						C	stop/ARG,stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	57	56	57		340,340,340	6	1	14	dbSNP_134	57	0,8600		0,0,4300	no	stop-gained,stop-gained,stop-gained	GEMIN2	NM_001009182.1,NM_001009183.1,NM_003616.2	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	114/266,114/251,114/281	39587287	1,13005	2203	4300	6503	38657038	SO:0001587	stop_gained	8487			AF027150	CCDS9669.1, CCDS32068.1, CCDS41946.1	14q21.1	2011-08-04	2011-08-04	2011-08-04	ENSG00000092208	ENSG00000092208			10884	protein-coding gene	gene with protein product		602595	"survival of motor neuron protein interacting protein 1"	SIP1		9323130, 9323129, 11121410	Standard	NM_003616		Approved		uc001wuq.3	O14893	OTTHUMG00000028816	ENST00000308317.6:c.340C>T	14.37:g.39587287C>T	ENSP00000308533:p.Arg114*		38657038	B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	Nonsense_Mutation	SNP	ENST00000308317.6	37	CCDS9669.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.590301|5.590301	0.96590|0.96590	2.27E-4|2.27E-4	0.0|0.0	ENSG00000092208|ENSG00000092208	ENST00000308317;ENST00000396249;ENST00000250379|ENST00000534684	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76800	.|0.4038	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73736	.|-0.3889	.|3	0.02654|.	T|.	1|.	-15.979|-15.979	19.3958|19.3958	0.94607|0.94607	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	114|108	.|.	ENSP00000250379:R114X|.	R|S	+|+	1|2	2|0	GEMIN2|GEMIN2	38657038|38657038	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.638000|2.638000	0.46562|0.46562	2.886000|2.886000	0.99085|0.99085	0.644000|0.644000	0.83932|0.83932	CGA|TCG		0.388	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276730.2			T	39587287	C	T	39587287	4	4	61	1	0	0	0	0	0	1	0	0	14364	876	31	1	350	1	SIP1	14	39587287	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77289	39587287	67762253	8874	16859										
PNN	5411	broad.mit.edu	37	chr14	39645740	39645740	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaatttcaggcgtggattCtcagatagtggaggaggacc	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39645740C>A	ENST00000216832.4	+	3	262	c.195C>A	c.(193-195)ttC>ttA	p.F65L	RP11-407N17.4_ENST00000556537.1_lincRNA|PNN_ENST00000553331.1_Missense_Mutation_p.F65L|PNN_ENST00000556530.1_Missense_Mutation_p.F65L	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	65	Necessary for interaction with RNPS1.|Necessary for interactions with KRT8, KRT18 and KRT19.|Necessary for mediating alternative 5' splicing.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.F65L(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		GGCGTGGATTCTCAGATAGTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	14											77	78	78					14																	39645740		2203	4300	6503	38715491	SO:0001583	missense	5411			U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.195C>A	14.37:g.39645740C>A	ENSP00000216832:p.Phe65Leu		38715491	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Missense_Mutation	SNP	ENST00000216832.4	37	CCDS9671.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.962343	0.34659	.	.	ENSG00000100941	ENST00000553331;ENST00000216832;ENST00000556530	T	0.28895	1.59	5.7	5.7	0.88788	Pinin/SDK (2);	0.053822	0.85682	D	0.000000	T	0.13713	0.0332	N	0.01874	-0.695	0.46774	D	0.999196	B	0.15141	0.012	B	0.15052	0.012	T	0.19418	-1.0306	10	0.07325	T	0.83	-4.164	19.4583	0.94904	0.0:1.0:0.0:0.0	.	65	Q9H307	PININ_HUMAN	L	65	ENSP00000216832:F65L	ENSP00000216832:F65L	F	+	3	2	PNN	38715491	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.819000	0.75262	2.681000	0.91329	0.655000	0.94253	TTC		0.368	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		A	39645740	C	A	39645740	3	1	61	1	0	0	0	0	1	0	0	0	12191	912	32	2	205	2	PNN	14	39645740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58453	39645740	67703800	8875	16860										
PNN	5411	broad.mit.edu	37	chr14	39650231	39650231	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagccagataaagaatgtAaaaccctttctcctgggaaa	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39650231A>T	ENST00000216832.4	+	9	1385	c.1318A>T	c.(1318-1320)Aaa>Taa	p.K440*	PNN_ENST00000557680.1_Intron	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	440	Glu-rich.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.K440*(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		TAAAGAATGTAAAACCCTTTC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											60	64	63					14																	39650231		2203	4300	6503	38719982	SO:0001587	stop_gained	5411			U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.1318A>T	14.37:g.39650231A>T	ENSP00000216832:p.Lys440*		38719982	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Nonsense_Mutation	SNP	ENST00000216832.4	37	CCDS9671.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349834	0.82132	.	.	ENSG00000100941	ENST00000216832	.	.	.	5.9	3.48	0.39840	.	0.360068	0.32134	N	0.006521	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-8.396	6.6592	0.23004	0.6297:0.2395:0.1308:0.0	.	.	.	.	X	440	.	ENSP00000216832:K440X	K	+	1	0	PNN	38719982	0.290000	0.24343	1.000000	0.80357	0.984000	0.73092	0.849000	0.27723	0.449000	0.26747	0.528000	0.53228	AAA		0.393	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		T	39650231	A	T	39650231	4	4	61	1	0	0	0	0	0	1	0	0	12191	363	13	5	1352	5	PNN	14	39650231	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	4491	39650231	67699309	8876	16861										
MIA2	117153	broad.mit.edu	37	chr14	39716532	39716532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtacaagaaagctcatttCggagtagaaaaatagcagtg	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39716532C>T	ENST00000280082.3	+	4	953	c.754C>T	c.(754-756)Cgg>Tgg	p.R252W	MIA2_ENST00000556784.1_Missense_Mutation_p.R251W|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R252W	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	252					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)		p.R252W(1)		NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		AAGCTCATTTCGGAGTAGAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											72	73	73					14																	39716532		2203	4300	6503	38786283	SO:0001583	missense	117153			BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.754C>T	14.37:g.39716532C>T	ENSP00000280082:p.Arg252Trp		38786283	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.538941	0.27475	.	.	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.49720	0.77;0.79;3.15	5.66	1.36	0.22044	.	1.285930	0.05614	N	0.578675	T	0.45696	0.1355	L	0.40543	1.245	0.19575	N	0.999969	D;D	0.69078	0.996;0.997	B;P	0.49953	0.424;0.627	T	0.34428	-0.9829	9	.	.	.	-12.6747	5.3675	0.16121	0.2304:0.4799:0.2243:0.0654	.	252;252	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	W	252;251;252	ENSP00000280082:R252W;ENSP00000451934:R251W;ENSP00000452252:R252W	.	R	+	1	2	MIA2;RP11-407N17.3	38786283	0.589000	0.26807	0.658000	0.29665	0.079000	0.17450	0.970000	0.29383	0.703000	0.31848	-0.188000	0.12872	CGG		0.393	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		T	39716532	C	T	39716532	3	4	61	1	0	0	0	0	1	0	0	0	9594	875	31	1	768	1	MIA2	14	39716532	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	66301	39716532	67633008	8877	16862										
MIA2	117153	broad.mit.edu	37	chr14	39716645	39716645	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaattgattcagtgccaaaGacacagtctgaactagcatc	8	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39716645G>T	ENST00000280082.3	+	4	1066	c.867G>T	c.(865-867)aaG>aaT	p.K289N	MIA2_ENST00000556784.1_Missense_Mutation_p.K288N|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K289N	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	289					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)		p.K289N(1)		NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		CAGTGCCAAAGACACAGTCTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	14											114	113	114					14																	39716645		2203	4300	6503	38786396	SO:0001583	missense	117153			BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.867G>T	14.37:g.39716645G>T	ENSP00000280082:p.Lys289Asn		38786396	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	G	3.740	-0.053784	0.07362	.	.	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.46819	0.86;0.86;3.2	5.47	1.47	0.22746	.	1.705140	0.03176	N	0.171376	T	0.44519	0.1297	L	0.60455	1.87	0.09310	N	1	B;B	0.32829	0.267;0.386	B;B	0.33521	0.079;0.165	T	0.22417	-1.0217	9	.	.	.	-8.442	4.0535	0.09806	0.1483:0.1258:0.5963:0.1296	.	289;289	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	N	289;288;289	ENSP00000280082:K289N;ENSP00000451934:K288N;ENSP00000452252:K289N	.	K	+	3	2	MIA2;RP11-407N17.3	38786396	0.001000	0.12720	0.000000	0.03702	0.026000	0.11368	0.268000	0.18571	0.264000	0.21851	-0.188000	0.12872	AAG		0.408	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		T	39716645	G	T	39716645	3	4	61	1	0	0	0	0	1	0	0	0	9594	933	33	2	881	2	MIA2	14	39716645	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113	39716645	67632895	8878	16863										
CTAGE5	4253	broad.mit.edu	37	chr14	39771362	39771362	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgcttgttaaagatgaaAgattgggctgctatgcttgg	13	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:39771362A>C	ENST00000280083.3	+	10	1139	c.825A>C	c.(823-825)aaA>aaC	p.K275N	RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K246N|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K246N|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K810N|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K246N|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K263N|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K200N|CTAGE5_ENST00000348007.3_Missense_Mutation_p.K275N|CTAGE5_ENST00000557038.1_Missense_Mutation_p.K195N|CTAGE5_ENST00000396158.2_Missense_Mutation_p.K280N|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K275N			O15320	CTGE5_HUMAN	CTAGE family, member 5	275					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.K275N(1)	CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TAAAGATGAAAGATTGGGCTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											173	159	164					14																	39771362		2203	4300	6503	38841113	SO:0001583	missense	4253			U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"meningioma expressed antigen 6 (coiled-coil proline-rich)"	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.825A>C	14.37:g.39771362A>C	ENSP00000280083:p.Lys275Asn		38841113	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	.	.	.	.	.	.	.	.	.	.	A	19.83	3.899577	0.72754	.	.	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;D;T;D;D;T;D;T;D;D	0.81908	2.81;-1.55;2.67;-1.55;-1.55;-0.59;-1.55;-0.59;-1.55;-1.55	5.52	1.87	0.25490	.	.	.	.	.	T	0.81635	0.4864	L	0.56199	1.76	0.36214	D	0.85153	P;P;P;P;P;B	0.42941	0.794;0.582;0.673;0.582;0.526;0.428	P;P;P;B;B;B	0.48952	0.523;0.477;0.596;0.331;0.251;0.251	T	0.79669	-0.1707	8	.	.	.	.	7.776	0.29037	0.6619:0.0:0.3381:0.0	.	237;280;275;275;246;263	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	N	810;263;195;237;246;275;280;275;200;275;246	ENSP00000452252:K810N;ENSP00000343897:K263N;ENSP00000450869:K195N;ENSP00000379468:K246N;ENSP00000339286:K275N;ENSP00000379462:K280N;ENSP00000280083:K275N;ENSP00000452562:K200N;ENSP00000343912:K275N;ENSP00000450449:K246N	.	K	+	3	2	CTAGE5;RP11-407N17.3	38841113	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	1.415000	0.34748	0.369000	0.24510	0.528000	0.53228	AAA		0.378	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		C	39771362	A	C	39771362	3	2	61	1	0	0	0	0	1	0	0	0	4000	69	3	4	894	4	CTAGE5	14	39771362	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	54717	39771362	67578178	8879	16864										
FSCB	84075	broad.mit.edu	37	chr14	44973867	44973867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcaccttccaaaacaaccGatcctaattttactgctgga	4	13	1	0	rs201017166	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:44973867G>A	ENST00000340446.4	-	1	2615	c.2324C>T	c.(2323-2325)tCg>tTg	p.S775L	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	775			S -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.S775L(2)		breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CAAAACAACCGATCCTAATTT	0.418													G|||	4	0.000798722	0.003	0	5008	,	,		17064	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|breast(1)	14						G	LEU/SER	7,4399	12.9+/-30.5	0,7,2196	81	89	86		2324	2.3	0	14		86	0,8600		0,0,4300	yes	missense	FSCB	NM_032135.3	145	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging	775/826	44973867	7,12999	2203	4300	6503	44043617	SO:0001583	missense	84075			AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2324C>T	14.37:g.44973867G>A	ENSP00000344579:p.Ser775Leu		44043617	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.552452	0.45487	0.001589	0.0	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.14893	2.47	4.21	2.33	0.28932	.	.	.	.	.	T	0.25306	0.0615	L	0.40543	1.245	0.09310	N	1	D	0.76494	0.999	P	0.60789	0.879	T	0.06607	-1.0817	9	0.59425	D	0.04	-2.1041	7.0569	0.25104	0.0952:0.0:0.7342:0.1706	.	775	Q5H9T9	FSCB_HUMAN	L	775;668	ENSP00000344579:S775L	ENSP00000344579:S775L	S	-	2	0	FSCB	44043617	0.008000	0.16893	0.001000	0.08648	0.012000	0.07955	1.101000	0.31037	0.516000	0.28340	0.430000	0.28490	TCG		0.418	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		A	44973867	G	A	44973867	3	1	61	1	0	0	0	0	1	0	0	0	6085	1059	37	1	157	1	FSCB	14	44973867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5202505	44973867	62375673	8880	16865										
FSCB	84075	broad.mit.edu	37	chr14	44975050	44975050	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagaccgaatttcaccaaGaagctctactgaaggagact	11	9	2	4	rs368327539		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:44975050G>T	ENST00000340446.4	-	1	1432	c.1141C>A	c.(1141-1143)Ctt>Att	p.L381I	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	381	Pro-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.L381I(1)		breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		ATTTCACCAAGAAGCTCTACT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	14											87	100	96					14																	44975050		2203	4300	6503	44044800	SO:0001583	missense	84075			AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1141C>A	14.37:g.44975050G>T	ENSP00000344579:p.Leu381Ile		44044800	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	g	3.730	-0.055816	0.07362	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.15718	2.4	3.87	-0.594	0.11664	.	.	.	.	.	T	0.07593	0.0191	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.41360	-0.9513	9	0.17832	T	0.49	.	4.2796	0.10825	0.2239:0.3706:0.4055:0.0	.	381	Q5H9T9	FSCB_HUMAN	I	381	ENSP00000344579:L381I	ENSP00000344579:L381I	L	-	1	0	FSCB	44044800	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.579000	0.05834	0.068000	0.16574	0.558000	0.71614	CTT		0.527	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		T	44975050	G	T	44975050	3	4	61	1	0	0	0	0	1	0	0	0	6085	942	33	2	1340	2	FSCB	14	44975050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1183	44975050	62374490	8881	16866										
C14orf28	122525	broad.mit.edu	37	chr14	45369915	45369915	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagtttgtagactgttttCtttacttaatggacacctac	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45369915C>A	ENST00000325192.3	+	2	552	c.277C>A	c.(277-279)Ctt>Att	p.L93I	C14orf28_ENST00000557112.1_Missense_Mutation_p.L93I|RP11-857B24.5_ENST00000555157.1_RNA	NM_001017923.1	NP_001017923.1	Q4W4Y0	CN028_HUMAN	chromosome 14 open reading frame 28	93								p.L93I(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(2)	11						AGACTGTTTTCTTTACTTAAT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	14											39	39	39					14																	45369915		2203	4300	6503	44439665	SO:0001583	missense	122525			AA496212	CCDS32069.1	14q21.2	2012-08-16			ENSG00000179476	ENSG00000179476			19834	protein-coding gene	gene with protein product	"dopamine receptor interacting protein 1"						Standard	XM_005267316		Approved	DRIP-1	uc001wvo.3	Q4W4Y0	OTTHUMG00000170722	ENST00000325192.3:c.277C>A	14.37:g.45369915C>A	ENSP00000326846:p.Leu93Ile		44439665		Missense_Mutation	SNP	ENST00000325192.3	37	CCDS32069.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.369840	0.61624	.	.	ENSG00000179476	ENST00000325192;ENST00000557112	T;T	0.33654	1.4;1.4	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.47284	0.1437	N	0.19112	0.55	0.58432	D	0.999998	D	0.67145	0.996	D	0.72625	0.978	T	0.48175	-0.9058	10	0.87932	D	0	.	18.0523	0.89353	0.0:1.0:0.0:0.0	.	93	Q4W4Y0	CN028_HUMAN	I	93	ENSP00000326846:L93I;ENSP00000451791:L93I	ENSP00000326846:L93I	L	+	1	0	C14orf28	44439665	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.452000	0.73485	2.937000	0.99478	0.650000	0.86243	CTT		0.343	C14orf28-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410086.1	NM_001017923		A	45369915	C	A	45369915	3	1	61	1	0	0	0	0	1	0	0	0	1774	913	32	2	279	2	C14orf28	14	45369915	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	394865	45369915	61979625	8882	16867										
KLHL28	54813	broad.mit.edu	37	chr14	45414750	45414750	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatcaagttggctttcaaGaaatgcacaacattctttca	7	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45414750G>T	ENST00000396128.4	-	2	501	c.382C>A	c.(382-384)Ctt>Att	p.L128I	KLHL28_ENST00000355081.2_Missense_Mutation_p.L142I	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	128								p.L128I(1)		breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGGCTTTCAAGAAATGCACAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	14											61	60	60					14																	45414750		2203	4300	6503	44484500	SO:0001583	missense	54813			AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"Kelch-like", "BTB/POZ domain containing"	19741	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 5", "kelch-like 28 (Drosophila)"	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.382C>A	14.37:g.45414750G>T	ENSP00000379434:p.Leu128Ile		44484500	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	37	CCDS9680.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994768	0.74703	.	.	ENSG00000179454	ENST00000396128;ENST00000355081;ENST00000556500	T;T;T	0.81163	-1.46;-1.46;-1.46	5.7	5.7	0.88788	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90003	0.6879	M	0.76433	2.335	0.49130	D	0.999751	D;D	0.89917	1.0;0.979	D;D	0.85130	0.997;0.973	D	0.90450	0.4438	10	0.87932	D	0	.	19.4198	0.94716	0.0:0.0:1.0:0.0	.	128;128	Q9NXS3-2;Q9NXS3	.;KLH28_HUMAN	I	128;142;128	ENSP00000379434:L128I;ENSP00000347193:L142I;ENSP00000452061:L128I	ENSP00000347193:L142I	L	-	1	0	KLHL28	44484500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.997000	0.70646	2.696000	0.92011	0.655000	0.94253	CTT		0.398	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			T	45414750	G	T	45414750	3	4	61	1	0	0	0	0	1	0	0	0	8403	942	33	2	1349	2	KLHL28	14	45414750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44835	45414750	61934790	8883	16868										
FAM179B	23116	broad.mit.edu	37	chr14	45432099	45432099	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggctctgcttgcaacttCtctcggacgttctccggggt	12	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45432099C>A	ENST00000361577.3	+	1	689	c.475C>A	c.(475-477)Ctc>Atc	p.L159I	FAM179B_ENST00000361462.2_Missense_Mutation_p.L159I|KLHL28_ENST00000396128.4_5'Flank|KLHL28_ENST00000355081.2_5'Flank|FAM179B_ENST00000382233.2_Missense_Mutation_p.L159I|KLHL28_ENST00000553817.1_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	159								p.L159I(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						CTTGCAACTTCTCTCGGACGT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											74	82	79					14																	45432099		2203	4300	6503	44501849	SO:0001583	missense	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.475C>A	14.37:g.45432099C>A	ENSP00000355045:p.Leu159Ile		44501849	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859256	0.32884	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.72835	0.95;0.95;-0.69	4.64	3.74	0.42951	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.38058	N	0.001832	T	0.55970	0.1954	N	0.24115	0.695	0.37257	D	0.906835	B;B;B;B	0.25563	0.005;0.129;0.005;0.005	B;B;B;B	0.27608	0.027;0.081;0.017;0.017	T	0.60188	-0.7312	10	0.62326	D	0.03	-1.3755	9.8934	0.41304	0.2036:0.7964:0.0:0.0	.	159;159;159;159	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	I	159	ENSP00000355045:L159I;ENSP00000354917:L159I;ENSP00000371668:L159I	ENSP00000354917:L159I	L	+	1	0	FAM179B	44501849	0.989000	0.36119	0.997000	0.53966	0.912000	0.54170	1.367000	0.34204	1.155000	0.42497	0.655000	0.94253	CTC		0.562	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		A	45432099	C	A	45432099	3	1	61	1	0	0	0	0	1	0	0	0	5522	913	32	2	477	2	FAM179B	14	45432099	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17349	45432099	61917441	8884	16869										
FAM179B	23116	broad.mit.edu	37	chr14	45513967	45513967	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttgcacaaggctggtGaatcaaatacatttataaga	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45513967G>T	ENST00000361577.3	+	13	4262	c.4048G>T	c.(4048-4050)Gaa>Taa	p.E1350*	FAM179B_ENST00000361462.2_Nonsense_Mutation_p.E1350*|FAM179B_ENST00000382233.2_3'UTR|KLHL28_ENST00000553817.1_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1350								p.E1350*(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						CAAGGCTGGTGAATCAAATAC	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											93	91	92					14																	45513967		2203	4300	6503	44583717	SO:0001587	stop_gained	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4048G>T	14.37:g.45513967G>T	ENSP00000355045:p.Glu1350*		44583717	Q68D66|Q6PG27	Nonsense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	G	42	9.576818	0.99210	.	.	ENSG00000198718	ENST00000361577;ENST00000361462	.	.	.	5.83	5.83	0.93111	.	0.049138	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-22.3826	19.7306	0.96180	0.0:0.0:1.0:0.0	.	.	.	.	X	1350	.	ENSP00000354917:E1350X	E	+	1	0	FAM179B	44583717	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	7.617000	0.83032	2.755000	0.94549	0.650000	0.86243	GAA		0.373	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45513967	G	T	45513967	4	4	61	1	0	0	0	0	0	1	0	0	5522	1291	45	2	4098	2	FAM179B	14	45513967	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81868	45513967	61835573	8885	16870										
FAM179B	23116	broad.mit.edu	37	chr14	45514052	45514052	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgcacgtgcagttgtttCtcttatcaatggtggacaaa	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45514052C>A	ENST00000361577.3	+	13	4347	c.4133C>A	c.(4132-4134)tCt>tAt	p.S1378Y	FAM179B_ENST00000361462.2_Missense_Mutation_p.S1378Y|FAM179B_ENST00000382233.2_3'UTR|KLHL28_ENST00000553817.1_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1378								p.S1378Y(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GCAGTTGTTTCTCTTATCAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											76	73	74					14																	45514052		2202	4300	6502	44583802	SO:0001583	missense	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4133C>A	14.37:g.45514052C>A	ENSP00000355045:p.Ser1378Tyr		44583802	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.232225	0.79688	.	.	ENSG00000198718	ENST00000361577;ENST00000361462	T;T	0.66280	2.11;-0.2	5.74	5.74	0.90152	Armadillo-type fold (1);	0.108809	0.64402	D	0.000004	T	0.73737	0.3625	L	0.59436	1.845	0.80722	D	1	P;D	0.58620	0.889;0.983	P;P	0.56278	0.528;0.795	T	0.75246	-0.3385	10	0.72032	D	0.01	-5.322	19.5147	0.95159	0.0:1.0:0.0:0.0	.	1378;1378	G3XAE9;Q9Y4F4	.;F179B_HUMAN	Y	1378	ENSP00000355045:S1378Y;ENSP00000354917:S1378Y	ENSP00000354917:S1378Y	S	+	2	0	FAM179B	44583802	1.000000	0.71417	0.983000	0.44433	0.662000	0.39071	7.027000	0.76463	2.708000	0.92522	0.650000	0.86243	TCT		0.348	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		A	45514052	C	A	45514052	3	1	61	1	0	0	0	0	1	0	0	0	5522	913	32	2	4183	2	FAM179B	14	45514052	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85	45514052	61835488	8886	16871										
FKBP3	2287	broad.mit.edu	37	chr14	45590801	45590801	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctccctttttcagaacaGatttagtatattttggtgga	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45590801G>T	ENST00000216330.3	-	5	751	c.341C>A	c.(340-342)tCt>tAt	p.S114Y	FKBP3_ENST00000396062.3_Missense_Mutation_p.S114Y			Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	114					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)	p.S114Y(1)		NS(1)|biliary_tract(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	12						TTTCAGAACAGATTTAGTATA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											115	108	111					14																	45590801		2203	4300	6503	44660551	SO:0001583	missense	2287			M96256	CCDS9683.1	14q21.2	2008-08-11	2002-08-29		ENSG00000100442	ENSG00000100442			3719	protein-coding gene	gene with protein product		186947	"FK506-binding protein 3 (25kD)"			1374240, 1532945	Standard	NM_002013		Approved	FKBP-25, PPIase	uc010tqf.2	Q00688	OTTHUMG00000140267	ENST00000216330.3:c.341C>A	14.37:g.45590801G>T	ENSP00000216330:p.Ser114Tyr		44660551	B2R4Q9|Q14317	Missense_Mutation	SNP	ENST00000216330.3	37	CCDS9683.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781162	0.90282	.	.	ENSG00000100442	ENST00000216330;ENST00000396062	T;T	0.54479	0.57;0.57	6.17	6.17	0.99709	.	0.107184	0.64402	D	0.000003	T	0.60508	0.2274	L	0.55990	1.75	0.58432	D	0.999998	D	0.64830	0.994	P	0.52598	0.703	T	0.61178	-0.7115	10	0.62326	D	0.03	-16.4342	15.2238	0.73333	0.0:0.0:0.8594:0.1406	.	114	Q00688	FKBP3_HUMAN	Y	114	ENSP00000216330:S114Y;ENSP00000379374:S114Y	ENSP00000216330:S114Y	S	-	2	0	FKBP3	44660551	1.000000	0.71417	0.998000	0.56505	0.944000	0.59088	7.490000	0.81461	2.941000	0.99782	0.655000	0.94253	TCT		0.348	FKBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276796.1	NM_002013		T	45590801	G	T	45590801	3	4	61	1	0	0	0	0	1	0	0	0	5928	942	33	2	349	2	FKBP3	14	45590801	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76749	45590801	61758739	8887	16872										
FANCM	57697	broad.mit.edu	37	chr14	45633685	45633685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcccagaagagcccaattCgtcttgtacaacgaatgggt	9	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45633685C>T	ENST00000267430.5	+	10	1790	c.1705C>T	c.(1705-1707)Cgt>Tgt	p.R569C	FANCM_ENST00000542564.2_Missense_Mutation_p.R543C|FANCM_ENST00000556036.1_Missense_Mutation_p.R569C	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	569	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.R569C(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GAGCCCAATTCGTCTTGTACA	0.433								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	14											82	81	81					14																	45633685		2203	4300	6503	44703435	SO:0001583	missense	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.1705C>T	14.37:g.45633685C>T	ENSP00000267430:p.Arg569Cys		44703435	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132035	0.94473	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.75821	-0.97;-0.97;-0.97	6.07	6.07	0.98685	Helicase, C-terminal (3);	0.104570	0.64402	D	0.000002	D	0.88969	0.6582	M	0.86343	2.81	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.89478	0.3748	10	0.87932	D	0	.	20.2544	0.98414	0.0:1.0:0.0:0.0	.	543;569;569	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	C	569;569;543	ENSP00000450596:R569C;ENSP00000267430:R569C;ENSP00000442493:R543C	ENSP00000267430:R569C	R	+	1	0	FANCM	44703435	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.478000	0.81082	2.885000	0.99019	0.655000	0.94253	CGT		0.433	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45633685	C	T	45633685	3	4	61	1	0	0	0	0	1	0	0	0	5690	884	31	1	1743	1	FANCM	14	45633685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42884	45633685	61715855	8888	16873										
FANCM	57697	broad.mit.edu	37	chr14	45639895	45639895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagtgatgaaattaaagaGataacattgcctcaagttca	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45639895G>T	ENST00000267430.5	+	12	2191	c.2106G>T	c.(2104-2106)gaG>gaT	p.E702D	FANCM_ENST00000542564.2_Missense_Mutation_p.E676D	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	702					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.E702D(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAATTAAAGAGATAACATTGC	0.323								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	14											70	77	75					14																	45639895		2203	4298	6501	44709645	SO:0001583	missense	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2106G>T	14.37:g.45639895G>T	ENSP00000267430:p.Glu702Asp		44709645	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433029	0.25813	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.19806	2.73;2.73;2.12	5.35	0.378	0.16204	.	0.643007	0.16861	N	0.196540	T	0.12902	0.0313	L	0.43923	1.385	0.22213	N	0.999284	B;B	0.28512	0.214;0.105	B;B	0.19391	0.025;0.014	T	0.30416	-0.9979	10	0.17369	T	0.5	.	5.8733	0.18814	0.4478:0.0:0.4247:0.1275	.	676;702	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	D	702;676;218	ENSP00000267430:E702D;ENSP00000442493:E676D;ENSP00000452033:E218D	ENSP00000267430:E702D	E	+	3	2	FANCM	44709645	0.936000	0.31750	0.977000	0.42913	0.975000	0.68041	0.367000	0.20382	-0.105000	0.12132	0.561000	0.74099	GAG		0.323	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45639895	G	T	45639895	3	4	61	1	0	0	0	0	1	0	0	0	5690	933	33	2	2152	2	FANCM	14	45639895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6210	45639895	61709645	8889	16874										
FANCM	57697	broad.mit.edu	37	chr14	45645129	45645129	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaattcacttaaatgtataAattatccatctgaaaaaagt	4	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45645129A>C	ENST00000267430.5	+	14	3257	c.3172A>C	c.(3172-3174)Aat>Cat	p.N1058H	FANCM_ENST00000542564.2_Missense_Mutation_p.N1032H	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1058					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.N1058H(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TAAATGTATAAATTATCCATC	0.323								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	14											23	23	23					14																	45645129		2201	4293	6494	44714879	SO:0001583	missense	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3172A>C	14.37:g.45645129A>C	ENSP00000267430:p.Asn1058His		44714879	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241234	0.22711	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.20332	2.68;2.68;2.08	4.8	4.8	0.61643	.	1.853160	0.02126	N	0.055972	T	0.35335	0.0928	L	0.40543	1.245	0.09310	N	1	P;D	0.55385	0.94;0.971	P;P	0.52710	0.564;0.707	T	0.38908	-0.9639	10	0.59425	D	0.04	.	12.9279	0.58270	1.0:0.0:0.0:0.0	.	1032;1058	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	H	1058;1032;574	ENSP00000267430:N1058H;ENSP00000442493:N1032H;ENSP00000452033:N574H	ENSP00000267430:N1058H	N	+	1	0	FANCM	44714879	0.045000	0.20229	0.003000	0.11579	0.006000	0.05464	2.949000	0.49074	2.091000	0.63221	0.482000	0.46254	AAT		0.323	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		C	45645129	A	C	45645129	3	2	61	1	0	0	0	0	1	0	0	0	5690	14	1	4	3226	4	FANCM	14	45645129	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5234	45645129	61704411	8890	16875										
C14orf106	55320	broad.mit.edu	37	chr14	45686317	45686317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccctcatctgttgcttccTtttaagagttcccactttgg	6	12	2	1	rs141848005	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45686317T>A	ENST00000310806.4	-	13	3366	c.2908A>T	c.(2908-2910)Agg>Tgg	p.R970W		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	970					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R970W(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TGTTGCTTCCTTTTAAGAGTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											165	151	156					14																	45686317		2203	4300	6503	44756067	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2908A>T	14.37:g.45686317T>A	ENSP00000309790:p.Arg970Trp		44756067	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.930461	0.73327	.	.	ENSG00000129534	ENST00000310806	T	0.28895	1.59	5.09	0.912	0.19349	.	0.000000	0.85682	D	0.000000	T	0.49745	0.1575	M	0.68317	2.08	0.47407	D	0.999415	D	0.89917	1.0	D	0.83275	0.996	T	0.55730	-0.8095	10	0.87932	D	0	-12.5808	12.2715	0.54708	0.0:0.0:0.4099:0.5901	.	970	Q6P0N0	M18BP_HUMAN	W	970	ENSP00000309790:R970W	ENSP00000309790:R970W	R	-	1	2	MIS18BP1	44756067	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.727000	0.38095	0.752000	0.32923	0.482000	0.46254	AGG		0.378	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45686317	T	A	45686317	3	1	61	1	0	0	0	0	1	0	0	0	1742	1608	56	5	510	5	C14orf106	14	45686317	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	41188	45686317	61663223	8891	16876										
C14orf106	55320	broad.mit.edu	37	chr14	45693534	45693534	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctacctgattttctattttCttcaattttggtaatagtct	5	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45693534C>A	ENST00000310806.4	-	11	2714	c.2256G>T	c.(2254-2256)aaG>aaT	p.K752N		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	752					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K752N(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TTTCTATTTTCTTCAATTTTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	14											85	88	87					14																	45693534		2203	4300	6503	44763284	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2256G>T	14.37:g.45693534C>A	ENSP00000309790:p.Lys752Asn		44763284	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	C	5.094	0.203012	0.09704	.	.	ENSG00000129534	ENST00000310806	T	0.28454	1.61	5.6	2.77	0.32553	.	0.566724	0.19693	N	0.108218	T	0.23054	0.0557	L	0.48362	1.52	0.09310	N	0.999993	B	0.20368	0.044	B	0.20384	0.029	T	0.19095	-1.0316	10	0.36615	T	0.2	-2.8096	4.7549	0.13078	0.1556:0.6133:0.15:0.0812	.	752	Q6P0N0	M18BP_HUMAN	N	752	ENSP00000309790:K752N	ENSP00000309790:K752N	K	-	3	2	MIS18BP1	44763284	0.296000	0.24398	0.035000	0.18076	0.028000	0.11728	0.293000	0.19029	0.400000	0.25396	0.655000	0.94253	AAG		0.318	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45693534	C	A	45693534	3	1	61	1	0	0	0	0	1	0	0	0	1742	912	32	2	1170	2	C14orf106	14	45693534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7217	45693534	61656006	8892	16877										
C14orf106	55320	broad.mit.edu	37	chr14	45693933	45693933	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatatcaatggatacatcCaattcttcagttgtctcttt	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45693933C>A	ENST00000310806.4	-	11	2315	c.1857G>T	c.(1855-1857)ttG>ttT	p.L619F		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	619					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.L619F(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TGGATACATCCAATTCTTCAG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	14											49	49	49					14																	45693933		2201	4296	6497	44763683	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1857G>T	14.37:g.45693933C>A	ENSP00000309790:p.Leu619Phe		44763683	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406359	0.25378	.	.	ENSG00000129534	ENST00000310806	T	0.20738	2.05	5.18	-5.31	0.02730	.	1.170610	0.06209	N	0.684682	T	0.09686	0.0238	N	0.24115	0.695	0.09310	N	1	B	0.30406	0.278	B	0.24701	0.055	T	0.33189	-0.9878	10	0.10111	T	0.7	4.3482	6.2983	0.21099	0.0:0.1939:0.2548:0.5513	.	619	Q6P0N0	M18BP_HUMAN	F	619	ENSP00000309790:L619F	ENSP00000309790:L619F	L	-	3	2	MIS18BP1	44763683	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	-0.521000	0.06245	-0.770000	0.04614	0.591000	0.81541	TTG		0.289	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45693933	C	A	45693933	3	1	61	1	0	0	0	0	1	0	0	0	1742	593	21	2	1569	2	C14orf106	14	45693933	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	399	45693933	61655607	8893	16878										
C14orf106	55320	broad.mit.edu	37	chr14	45716183	45716183	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatagtttgctttattttTtaatccatccttgttgggct	6	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:45716183T>G	ENST00000310806.4	-	2	765	c.307A>C	c.(307-309)Aaa>Caa	p.K103Q		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	103					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K103Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						GCTTTATTTTTTAATCCATCC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											99	99	99					14																	45716183		2203	4299	6502	44785933	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.307A>C	14.37:g.45716183T>G	ENSP00000309790:p.Lys103Gln		44785933	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.493525	0.44352	.	.	ENSG00000129534	ENST00000310806;ENST00000451174	T	0.22134	1.97	5.55	3.12	0.35913	.	0.732468	0.12921	N	0.428133	T	0.18718	0.0449	L	0.60455	1.87	0.09310	N	1	P	0.47841	0.901	B	0.40565	0.333	T	0.12760	-1.0535	10	0.26408	T	0.33	-10.0478	5.7828	0.18316	0.0:0.0867:0.1682:0.7451	.	103	Q6P0N0	M18BP_HUMAN	Q	103	ENSP00000309790:K103Q	ENSP00000309790:K103Q	K	-	1	0	MIS18BP1	44785933	0.034000	0.19679	0.035000	0.18076	0.732000	0.41865	0.653000	0.24902	0.371000	0.24564	-0.261000	0.10672	AAA		0.323	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			G	45716183	T	G	45716183	3	3	61	1	0	0	0	0	1	0	0	0	1742	1850	64	4	3155	4	C14orf106	14	45716183	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22250	45716183	61633357	8894	16879										
MDGA2	161357	broad.mit.edu	37	chr14	47426586	47426586	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaatcctacctgtaacaaGaaagctgcatctcccagctc	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:47426586G>T	ENST00000399232.2	-	9	2237	c.1873C>A	c.(1873-1875)Ctt>Att	p.L625I	MDGA2_ENST00000426342.1_Missense_Mutation_p.L396I|MDGA2_ENST00000439988.3_Missense_Mutation_p.L694I|MDGA2_ENST00000357362.3_Missense_Mutation_p.L396I	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	625	Ig-like 6.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.L396I(2)|p.L694I(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						CCTGTAACAAGAAAGCTGCAT	0.348																																																3	Substitution - Missense(3)	large_intestine(3)	14											68	67	67					14																	47426586		1834	4087	5921	46496336	SO:0001583	missense	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1873C>A	14.37:g.47426586G>T	ENSP00000382178:p.Leu625Ile		46496336	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	G	16.59	3.164718	0.57476	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.23	5.23	0.72850	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.46758	U	0.000279	T	0.52092	0.1713	L	0.57536	1.79	0.80722	D	1	B;B	0.29552	0.248;0.188	B;B	0.33121	0.098;0.158	T	0.47674	-0.9099	10	0.21014	T	0.42	.	17.3783	0.87398	0.0:0.0:1.0:0.0	.	396;625	F6W3S7;Q7Z553	.;MDGA2_HUMAN	I	625;396;694;396	ENSP00000400011:L625I;ENSP00000405456:L396I;ENSP00000382178:L694I;ENSP00000349925:L396I	ENSP00000349925:L396I	L	-	1	0	MDGA2	46496336	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	5.922000	0.70036	2.447000	0.82792	0.650000	0.86243	CTT		0.348	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47426586	G	T	47426586	3	4	61	1	0	0	0	0	1	0	0	0	9437	942	33	2	1033	2	MDGA2	14	47426586	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1710403	47426586	59922954	8895	16880										
MDGA2	161357	broad.mit.edu	37	chr14	47426796	47426796	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaactcatagtgacacttcGatcctgtccttgccggattt	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:47426796G>A	ENST00000399232.2	-	9	2027	c.1663C>T	c.(1663-1665)Cga>Tga	p.R555*	MDGA2_ENST00000426342.1_Nonsense_Mutation_p.R326*|SNORA25_ENST00000515926.1_RNA|MDGA2_ENST00000439988.3_Nonsense_Mutation_p.R624*|MDGA2_ENST00000357362.3_Nonsense_Mutation_p.R326*	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	555	Ig-like 6.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R326*(2)|p.R624*(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						GTGACACTTCGATCCTGTCCT	0.453																																																3	Substitution - Nonsense(3)	large_intestine(3)	14											90	88	89					14																	47426796		1947	4156	6103	46496546	SO:0001587	stop_gained	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1663C>T	14.37:g.47426796G>A	ENSP00000382178:p.Arg555*		46496546	F6W3S7|J3KPX6	Nonsense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	G	43	10.174959	0.99352	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	.	.	.	5.32	3.41	0.39046	.	0.161338	0.28671	U	0.014537	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8644	0.57932	0.0:0.0:0.6936:0.3064	.	.	.	.	X	555;326;624;326	.	ENSP00000349925:R326X	R	-	1	2	MDGA2	46496546	0.997000	0.39634	0.996000	0.52242	0.972000	0.66771	2.587000	0.46128	0.557000	0.29117	-0.188000	0.12872	CGA		0.453	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		A	47426796	G	A	47426796	4	1	61	1	0	0	0	0	0	1	0	0	9437	1066	37	1	1243	1	MDGA2	14	47426796	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210	47426796	59922744	8896	16881										
MDGA2	161357	broad.mit.edu	37	chr14	47530697	47530697	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacagcttctacttggcaaGatattttcacctcacggcca	7	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:47530697G>T	ENST00000399232.2	-	7	1437	c.1073C>A	c.(1072-1074)tCt>tAt	p.S358Y	MDGA2_ENST00000426342.1_Missense_Mutation_p.S129Y|MDGA2_ENST00000439988.3_Missense_Mutation_p.S427Y|MDGA2_ENST00000357362.3_Missense_Mutation_p.S129Y	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	358	Ig-like 4.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.S129Y(2)|p.S427Y(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						TACTTGGCAAGATATTTTCAC	0.383																																																3	Substitution - Missense(3)	large_intestine(3)	14											90	82	84					14																	47530697		1879	4095	5974	46600447	SO:0001583	missense	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1073C>A	14.37:g.47530697G>T	ENSP00000382178:p.Ser358Tyr		46600447	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	G	27.6	4.849692	0.91277	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.96	5.96	0.96718	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.000000	0.51477	U	0.000088	T	0.82125	0.4969	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82536	-0.0408	10	0.72032	D	0.01	.	18.9858	0.92769	0.0:0.0:1.0:0.0	.	358	Q7Z553	MDGA2_HUMAN	Y	358;129;427;129	ENSP00000400011:S358Y;ENSP00000405456:S129Y;ENSP00000382178:S427Y;ENSP00000349925:S129Y	ENSP00000349925:S129Y	S	-	2	0	MDGA2	46600447	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.852000	0.86927	2.832000	0.97577	0.655000	0.94253	TCT		0.383	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47530697	G	T	47530697	3	4	61	1	0	0	0	0	1	0	0	0	9437	942	33	2	1841	2	MDGA2	14	47530697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103901	47530697	59818843	8897	16882										
C14orf104	55172	broad.mit.edu	37	chr14	50092760	50092760	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatcagagttactacattCttgcaactgtgtcaagagaa	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50092760C>A	ENST00000298292.8	-	3	2094	c.2014G>T	c.(2014-2016)Gaa>Taa	p.E672*	DNAAF2_ENST00000406043.3_Nonsense_Mutation_p.E624*|RP11-649E7.5_ENST00000555043.1_RNA	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	672					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)		p.E163*(1)		kidney(1)|lung(4)	5						TTACTACATTCTTGCAACTGT	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											41	35	37					14																	50092760		2192	4281	6473	49162510	SO:0001587	stop_gained	55172			AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"kintoun"	612517	"chromosome 14 open reading frame 104"	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.2014G>T	14.37:g.50092760C>A	ENSP00000298292:p.Glu672*		49162510	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Nonsense_Mutation	SNP	ENST00000298292.8	37	CCDS9691.2	.	.	.	.	.	.	.	.	.	.	C	38	6.637698	0.97726	.	.	ENSG00000165506	ENST00000298292;ENST00000406043	.	.	.	6.03	5.15	0.70609	.	0.413355	0.23197	N	0.050836	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	11.3791	0.49746	0.0:0.9174:0.0:0.0826	.	.	.	.	X	672;624	.	ENSP00000298292:E672X	E	-	1	0	DNAAF2	49162510	0.999000	0.42202	1.000000	0.80357	0.919000	0.55068	1.828000	0.39111	1.580000	0.49851	0.644000	0.83932	GAA		0.294	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1			A	50092760	C	A	50092760	4	1	61	1	0	0	0	0	0	1	0	0	1740	922	32	2	503	2	C14orf104	14	50092760	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2562063	50092760	57256780	8898	16883										
SDCCAG1	9147	broad.mit.edu	37	chr14	50267191	50267191	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcaggataatttaatgtCtcttccccttcatccttcat	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50267191C>A	ENST00000298310.5	-	23	2768	c.2319G>T	c.(2317-2319)gaG>gaT	p.E773D	NEMF_ENST00000546046.1_Missense_Mutation_p.E752D|NEMF_ENST00000545773.1_Missense_Mutation_p.E731D|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	773					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.E773D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						AATTTAATGTCTCTTCCCCTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	14											141	124	130					14																	50267191		2203	4300	6503	49336941	SO:0001583	missense	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2319G>T	14.37:g.50267191C>A	ENSP00000298310:p.Glu773Asp		49336941	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	C	9.084	1.000096	0.19121	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.47869	0.85;0.83;0.83;0.83	5.37	1.46	0.22682	.	0.260249	0.35838	N	0.002952	T	0.23249	0.0562	N	0.17082	0.46	0.23827	N	0.99673	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.0	T	0.20638	-1.0269	10	0.09843	T	0.71	-7.5381	5.6959	0.17855	0.0:0.5151:0.2637:0.2212	.	752;748;731;773	O60524-3;O60524-5;O60524-4;O60524	.;.;.;NEMF_HUMAN	D	773;731;752;545;731	ENSP00000298310:E773D;ENSP00000438309:E731D;ENSP00000441016:E752D;ENSP00000452540:E731D	ENSP00000298310:E773D	E	-	3	2	NEMF	49336941	0.006000	0.16342	0.095000	0.20976	0.901000	0.52897	-0.148000	0.10219	0.005000	0.14708	-0.384000	0.06662	GAG		0.358	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		A	50267191	C	A	50267191	3	1	61	1	0	0	0	0	1	0	0	0	13994	912	32	2	955	2	SDCCAG1	14	50267191	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174431	50267191	57082349	8899	16884										
SDCCAG1	9147	broad.mit.edu	37	chr14	50295945	50295945	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcaactatttgtaggttCatttctatgagctctccttt	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50295945C>A	ENST00000298310.5	-	13	1508	c.1059G>T	c.(1057-1059)atG>atT	p.M353I	NEMF_ENST00000546046.1_Missense_Mutation_p.M353I|NEMF_ENST00000545773.1_Missense_Mutation_p.M311I|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	353					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.M353I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TTTGTAGGTTCATTTCTATGA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	119	121					14																	50295945		2203	4300	6503	49365695	SO:0001583	missense	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1059G>T	14.37:g.50295945C>A	ENSP00000298310:p.Met353Ile		49365695	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	C	9.907	1.208401	0.22205	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.24	4.33	0.51752	Fibronectin-binding A, N-terminal (1);	0.078463	0.85682	N	0.000000	T	0.41719	0.1171	L	0.58428	1.81	0.80722	D	1	B;B;B;B;B	0.29085	0.232;0.057;0.232;0.232;0.078	B;B;B;B;B	0.30401	0.07;0.07;0.07;0.07;0.115	T	0.26326	-1.0106	10	0.33940	T	0.23	-9.5209	14.8875	0.70582	0.1525:0.8475:0.0:0.0	.	353;124;328;311;353	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	I	353;311;353;124;311	ENSP00000298310:M353I;ENSP00000438309:M311I;ENSP00000441016:M353I;ENSP00000452540:M311I	ENSP00000298310:M353I	M	-	3	0	NEMF	49365695	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.485000	0.53208	1.160000	0.42584	0.591000	0.81541	ATG		0.363	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		A	50295945	C	A	50295945	3	1	61	1	0	0	0	0	1	0	0	0	13994	826	29	2	2255	2	SDCCAG1	14	50295945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28754	50295945	57053595	8900	16885										
SDCCAG1	9147	broad.mit.edu	37	chr14	50296099	50296099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagcttccaatctgttttCgtgatcctttcgaacattat	6	9	1	2	rs147568381	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50296099C>T	ENST00000298310.5	-	12	1440	c.991G>A	c.(991-993)Gaa>Aaa	p.E331K	NEMF_ENST00000546046.1_Missense_Mutation_p.E331K|NEMF_ENST00000545773.1_Missense_Mutation_p.E289K|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	331					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.E331K(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						AATCTGTTTTCGTGATCCTTT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	LYS/GLU	4,4402	8.1+/-20.4	0,4,2199	155	144	148		991	5.3	1	14	dbSNP_134	148	0,8600		0,0,4300	no	missense	NEMF	NM_004713.3	56	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	331/1077	50296099	4,13002	2203	4300	6503	49365849	SO:0001583	missense	9147			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.991G>A	14.37:g.50296099C>T	ENSP00000298310:p.Glu331Lys		49365849	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.207097	0.58343	9.08E-4	0.0	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.34	5.34	0.76211	Fibronectin-binding A, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60117	0.2244	M	0.66378	2.025	0.80722	D	1	P;P;D;P;P	0.56521	0.764;0.782;0.976;0.882;0.833	B;B;P;B;B	0.52598	0.313;0.309;0.703;0.309;0.34	T	0.59279	-0.7484	10	0.37606	T	0.19	-25.3685	19.0478	0.93028	0.0:1.0:0.0:0.0	.	331;102;306;289;331	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	K	331;289;331;102;289	ENSP00000298310:E331K;ENSP00000438309:E289K;ENSP00000441016:E331K;ENSP00000452540:E289K	ENSP00000298310:E331K	E	-	1	0	NEMF	49365849	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.391000	0.59652	2.506000	0.84524	0.585000	0.79938	GAA		0.333	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		T	50296099	C	T	50296099	3	4	61	1	0	0	0	0	1	0	0	0	13994	893	31	1	2327	1	SDCCAG1	14	50296099	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154	50296099	57053441	8901	16886										
C14orf183	196913	broad.mit.edu	37	chr14	50550393	50550393	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatactcagaataagaagtGcacacatttaatagagcagc	7	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50550393G>T	ENST00000305273.1	-	5	950	c.951C>A	c.(949-951)tgC>tgA	p.C317*	RP11-58E21.7_ENST00000556019.2_lincRNA|RP11-58E21.5_ENST00000603228.1_lincRNA	NM_001014830.1	NP_001014830.1	Q8WXQ3	CN183_HUMAN	chromosome 14 open reading frame 183	317								p.C317*(1)		endometrium(2)|large_intestine(2)|lung(3)	7						AATAAGAAGTGCACACATTTA	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											65	71	69					14																	50550393		2005	4190	6195	49620143	SO:0001587	stop_gained	196913			AF390030	CCDS45101.1	14q21.3	2012-09-26			ENSG00000168260	ENSG00000168260			27285	protein-coding gene	gene with protein product							Standard	NM_001014830		Approved		uc010tqk.2	Q8WXQ3	OTTHUMG00000170858	ENST00000305273.1:c.951C>A	14.37:g.50550393G>T	ENSP00000303234:p.Cys317*		49620143		Nonsense_Mutation	SNP	ENST00000305273.1	37	CCDS45101.1	.	.	.	.	.	.	.	.	.	.	G	7.762	0.705646	0.15172	.	.	ENSG00000168260	ENST00000305273	.	.	.	3.94	-0.368	0.12537	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999989	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.5423	0.22387	0.5183:0.0:0.4817:0.0	.	.	.	.	X	317	.	ENSP00000303234:C317X	C	-	3	2	C14orf183	49620143	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.039000	0.13884	-0.065000	0.13021	0.557000	0.71058	TGC		0.512	C14orf183-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000410705.1	NM_001014830		T	50550393	G	T	50550393	4	4	61	1	0	0	0	0	0	1	0	0	1770	1311	46	2	26	2	C14orf183	14	50550393	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	254294	50550393	56799147	8902	16887										
SOS2	6655	broad.mit.edu	37	chr14	50626281	50626281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtcttttactacaaaacGatatacttcaggacttggta	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50626281G>A	ENST00000216373.5	-	10	1994	c.1720C>T	c.(1720-1722)Cgt>Tgt	p.R574C	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Missense_Mutation_p.R541C	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	574					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R574C(2)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					ACTACAAAACGATATACTTCA	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	14											118	121	120					14																	50626281		2203	4300	6503	49696031	SO:0001583	missense	6655			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.1720C>T	14.37:g.50626281G>A	ENSP00000216373:p.Arg574Cys		49696031	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.984420	0.53934	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.32515	1.45;1.45	5.24	4.34	0.51931	Ras guanine nucleotide exchange factor, domain (1);	0.048208	0.85682	N	0.000000	T	0.27967	0.0689	M	0.65975	2.015	0.80722	D	1	P;P;P	0.42357	0.777;0.777;0.607	B;B;B	0.28232	0.059;0.087;0.04	T	0.21075	-1.0256	10	0.54805	T	0.06	.	13.8915	0.63742	0.0737:0.0:0.9263:0.0	.	541;604;574	B7ZKT6;Q59G32;Q07890	.;.;SOS2_HUMAN	C	574;541	ENSP00000216373:R574C;ENSP00000445328:R541C	ENSP00000216373:R574C	R	-	1	0	SOS2	49696031	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.666000	0.61554	1.350000	0.45770	0.585000	0.79938	CGT		0.343	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50626281	G	A	50626281	3	1	61	1	0	0	0	0	1	0	0	0	14974	1058	37	1	2334	1	SOS2	14	50626281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75888	50626281	56723259	8903	16888										
SOS2	6655	broad.mit.edu	37	chr14	50626504	50626504	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtatcttctttatcacaAatttgtattttcctcatgac	3	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50626504A>C	ENST00000216373.5	-	10	1771	c.1497T>G	c.(1495-1497)atT>atG	p.I499M	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Missense_Mutation_p.I466M	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	499	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I499M(2)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CTTTATCACAAATTTGTATTT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	14											84	84	84					14																	50626504		2203	4300	6503	49696254	SO:0001583	missense	6655			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.1497T>G	14.37:g.50626504A>C	ENSP00000216373:p.Ile499Met		49696254	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.830570	0.50845	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	D;D	0.89810	-2.57;-2.57	5.87	1.14	0.20703	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.042154	0.85682	D	0.000000	D	0.91905	0.7437	M	0.83118	2.625	0.53005	D	0.999968	D;P;P	0.61697	0.99;0.949;0.607	D;P;P	0.65773	0.938;0.864;0.674	D	0.88057	0.2791	10	0.87932	D	0	.	3.1272	0.06411	0.2325:0.0846:0.5212:0.1618	.	466;529;499	B7ZKT6;Q59G32;Q07890	.;.;SOS2_HUMAN	M	499;466	ENSP00000216373:I499M;ENSP00000445328:I466M	ENSP00000216373:I499M	I	-	3	3	SOS2	49696254	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	0.922000	0.28734	-0.014000	0.14175	-0.248000	0.11899	ATT		0.353	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			C	50626504	A	C	50626504	3	2	61	1	0	0	0	0	1	0	0	0	14974	10	1	4	2557	4	SOS2	14	50626504	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	223	50626504	56723036	8904	16889										
ATP5S	27109	broad.mit.edu	37	chr14	50792367	50792367	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtgatcttcctggagtaAgagaaaaagaaaatcttgtc	9	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50792367A>C	ENST00000311459.7	+	5	954	c.574A>C	c.(574-576)Aga>Cga	p.R192R	ATP5S_ENST00000245448.6_3'UTR|ATP5S_ENST00000554438.1_3'UTR|ATP5S_ENST00000358473.1_Intron|RP11-247L20.4_ENST00000555403.1_lincRNA	NM_001003803.2	NP_001003803.1	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B)	192					ATP biosynthetic process (GO:0006754)|hydrogen ion transmembrane transport (GO:1902600)|proton transport (GO:0015992)	mitochondrial inner membrane (GO:0005743)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|metal ion binding (GO:0046872)	p.R192R(1)		breast(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	12	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		TCCTGGAGTAAGAGAAAAAGA	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	14											119	126	124					14																	50792367		2203	4298	6501	49862117	SO:0001819	synonymous_variant	27109			U79253	CCDS32075.1, CCDS32076.1, CCDS45102.1	14q21.3	2011-04-13	2010-06-11			ENSG00000125375			18799	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)"			11744738, 8619474	Standard	NM_015684		Approved	HSU79253, ATPW	uc001wxw.2	Q99766		ENST00000311459.7:c.574A>C	14.37:g.50792367A>C			49862117	A8K1U3|D9N156|Q8WWX3|Q96F77	Silent	SNP	ENST00000311459.7	37	CCDS32075.1																																																																																				0.299	ATP5S-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410761.1	NM_015684		C	50792367	A	C	50792367	2	2	61	1	0	0	0	0	0	0	0	1	1164	64	3	4		4	ATP5S	14	50792367	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	165863	50792367	56557173	8905	16890										
CDKL1	8814	broad.mit.edu	37	chr14	50799011	50799011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtaaagcagtggtgctttCggctctttcttagggtcttc	11	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50799011C>T	ENST00000395834.1	-	8	965	c.938G>A	c.(937-939)cGa>cAa	p.R313Q	CDKL1_ENST00000216378.2_3'UTR|ATP5S_ENST00000358473.1_Intron	NM_004196.3	NP_004187.2	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	312					heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R313Q(2)		endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					GTGGTGCTTTCGGCTCTTTCT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	14											285	278	280					14																	50799011		2203	4300	6503	49868761	SO:0001583	missense	8814			AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"Cyclin-dependent kinases"	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000395834.1:c.938G>A	14.37:g.50799011C>T	ENSP00000379176:p.Arg313Gln		49868761	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000395834.1	37	CCDS9699.1	.	.	.	.	.	.	.	.	.	.	C	6.829	0.522196	0.13066	.	.	ENSG00000100490	ENST00000395834	T	0.67171	-0.25	5.33	-1.19	0.09585	Protein kinase-like domain (1);	.	.	.	.	T	0.47600	0.1454	L	0.34521	1.04	0.46586	D	0.999114	B	0.02656	0.0	B	0.04013	0.001	T	0.14476	-1.0471	9	0.22109	T	0.4	.	6.9607	0.24595	0.0:0.5581:0.1076:0.3343	.	312	Q00532	CDKL1_HUMAN	Q	313	ENSP00000379176:R313Q	ENSP00000379176:R313Q	R	-	2	0	CDKL1	49868761	0.177000	0.23109	0.103000	0.21229	0.133000	0.20885	-0.075000	0.11431	-0.331000	0.08501	-1.000000	0.02509	CGA		0.418	CDKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276872.2			T	50799011	C	T	50799011	3	4	61	1	0	0	0	0	1	0	0	0	3159	884	31	1	146	1	CDKL1	14	50799011	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6644	50799011	56550529	8906	16891										
CDKL1	8814	broad.mit.edu	37	chr14	50862439	50862439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgagcattcggatttcccGaagggcaattttctttatga	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:50862439G>A	ENST00000216378.2	-	2	795	c.151C>T	c.(151-153)Cgg>Tgg	p.R51W	CDKL1_ENST00000395834.1_Missense_Mutation_p.R51W|CDKL1_ENST00000356146.1_5'UTR|RP11-247L20.3_ENST00000556713.1_lincRNA	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	50	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R51W(2)		endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					CGGATTTCCCGAAGGGCAATT	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	14											67	73	71					14																	50862439		2203	4300	6503	49932189	SO:0001583	missense	8814			AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"Cyclin-dependent kinases"	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000216378.2:c.151C>T	14.37:g.50862439G>A	ENSP00000216378:p.Arg51Trp		49932189	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	37		.	.	.	.	.	.	.	.	.	.	G	17.54	3.416263	0.62511	.	.	ENSG00000100490	ENST00000395834;ENST00000216378	T;T	0.53857	0.6;0.6	4.34	4.34	0.51931	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.79470	0.4451	M	0.93375	3.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.85794	0.1369	9	0.87932	D	0	.	16.5314	0.84361	0.0:0.0:1.0:0.0	.	240;50	Q00532-2;Q00532	.;CDKL1_HUMAN	W	51	ENSP00000379176:R51W;ENSP00000216378:R51W	ENSP00000216378:R51W	R	-	1	2	CDKL1	49932189	1.000000	0.71417	0.939000	0.37840	0.436000	0.31835	3.350000	0.52224	2.364000	0.80123	0.561000	0.74099	CGG		0.433	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1			A	50862439	G	A	50862439	3	1	61	1	0	0	0	0	1	0	0	0	3159	1057	37	1	961	1	CDKL1	14	50862439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63428	50862439	56487101	8907	16892										
ATL1	51062	broad.mit.edu	37	chr14	51027015	51027015	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcagggacagaaacagttGgggtgagtagcaaatgagaa	15	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:51027015G>A	ENST00000358385.6	+	1	273	c.32G>A	c.(31-33)tGg>tAg	p.W11*	ATL1_ENST00000357032.3_Nonsense_Mutation_p.W11*|ATL1_ENST00000441560.2_Nonsense_Mutation_p.W11*|ATL1_ENST00000354525.4_Nonsense_Mutation_p.W11*|ATL1_ENST00000556478.2_3'UTR	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	11					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.W11*(1)		central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						AGAAACAGTTGGGGTGAGTAG	0.622																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											85	75	78					14																	51027015		2203	4300	6503	50096765	SO:0001587	stop_gained	51062			AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"atlastin"	606439	"spastic paraplegia 3A (autosomal dominant)"	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.32G>A	14.37:g.51027015G>A	ENSP00000351155:p.Trp11*		50096765	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Nonsense_Mutation	SNP	ENST00000358385.6	37	CCDS9700.1	.	.	.	.	.	.	.	.	.	.	G	39	7.453586	0.98292	.	.	ENSG00000198513	ENST00000441560;ENST00000555960;ENST00000553509;ENST00000358385;ENST00000357032;ENST00000354525	.	.	.	5.3	4.4	0.53042	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-3.8529	12.0309	0.53397	0.0:0.1738:0.8262:0.0	.	.	.	.	X	11	.	ENSP00000346522:W11X	W	+	2	0	ATL1	50096765	1.000000	0.71417	0.999000	0.59377	0.798000	0.45092	4.746000	0.62133	1.231000	0.43661	0.491000	0.48974	TGG		0.622	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2			A	51027015	G	A	51027015	4	1	61	1	0	0	0	0	0	1	0	0	1107	1357	47	3	34	3	ATL1	14	51027015	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164576	51027015	56322525	8908	16893										
NIN	51199	broad.mit.edu	37	chr14	51223928	51223928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttattttctagtgcctcatCgtagcgtgtctccatcattc	7	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:51223928C>T	ENST00000382041.3	-	18	4010	c.3820G>A	c.(3820-3822)Gat>Aat	p.D1274N	NIN_ENST00000382043.4_Intron|NIN_ENST00000245441.5_Missense_Mutation_p.D1274N|NIN_ENST00000324330.9_Missense_Mutation_p.D1274N|NIN_ENST00000389868.3_Intron|NIN_ENST00000530997.2_Missense_Mutation_p.D1274N|NIN_ENST00000453196.1_Missense_Mutation_p.D1274N	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1274					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.D1280N(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					AGTGCCTCATCGTAGCGTGTC	0.448			T	PDGFRB	MPD																																		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	1	Substitution - Missense(1)	large_intestine(1)	14											170	172	171					14																	51223928		2203	4300	6503	50293678	SO:0001583	missense	51199			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.3820G>A	14.37:g.51223928C>T	ENSP00000371472:p.Asp1274Asn		50293678	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.274|9.274	1.046302|1.046302	0.19748|0.19748	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196|ENST00000530997;ENST00000389869;ENST00000530853	T;T;T;T|.	0.08546|.	3.35;3.08;3.08;3.09|.	6.06|6.06	4.21|4.21	0.49690|0.49690	.|.	0.961738|.	0.08609|.	N|.	0.920279|.	T|T	0.41213|0.41213	0.1149|0.1149	L|L	0.45581|0.45581	1.43|1.43	0.09310|0.09310	N|N	1|1	D;D;D;D|.	0.56287|.	0.959;0.959;0.975;0.975|.	B;B;P;P|.	0.49528|.	0.375;0.229;0.56;0.614|.	T|T	0.25882|0.25882	-1.0119|-1.0119	10|5	0.26408|.	T|.	0.33|.	-0.3019|-0.3019	8.882|8.882	0.35380|0.35380	0.0:0.7422:0.1334:0.1244|0.0:0.7422:0.1334:0.1244	.|.	1280;1274;1274;1274|.	Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7|.	.;.;NIN_HUMAN;.|.	N|Q	1274;1257;1280;1274;1274;1274|764	ENSP00000245441:D1274N;ENSP00000371472:D1274N;ENSP00000324210:D1274N;ENSP00000412391:D1274N|.	ENSP00000245441:D1274N|.	D|R	-|-	1|2	0|0	NIN|NIN	50293678|50293678	0.035000|0.035000	0.19736|0.19736	0.005000|0.005000	0.12908|0.12908	0.003000|0.003000	0.03518|0.03518	2.182000|2.182000	0.42556|0.42556	1.557000|1.557000	0.49525|0.49525	-0.176000|-0.176000	0.13171|0.13171	GAT|CGA		0.448	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		T	51223928	C	T	51223928	3	4	61	1	0	0	0	0	1	0	0	0	10448	884	31	1	2785	1	NIN	14	51223928	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	196913	51223928	56125612	8909	16894										
NIN	51199	broad.mit.edu	37	chr14	51224741	51224741	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcatctcggctctttctcGatctgctgtctcacaggtcg	9	14	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:51224741G>A	ENST00000382041.3	-	18	3197	c.3007C>T	c.(3007-3009)Cga>Tga	p.R1003*	NIN_ENST00000382043.4_Intron|NIN_ENST00000245441.5_Nonsense_Mutation_p.R1003*|NIN_ENST00000324330.9_Nonsense_Mutation_p.R1003*|NIN_ENST00000389868.3_Intron|NIN_ENST00000530997.2_Nonsense_Mutation_p.R1003*|NIN_ENST00000453196.1_Nonsense_Mutation_p.R1003*	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1003					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.R1009*(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					GCTCTTTCTCGATCTGCTGTC	0.458			T	PDGFRB	MPD																																		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	1	Substitution - Nonsense(1)	large_intestine(1)	14											131	131	131					14																	51224741		2203	4300	6503	50294491	SO:0001587	stop_gained	51199			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.3007C>T	14.37:g.51224741G>A	ENSP00000371472:p.Arg1003*		50294491	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Nonsense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.245357|8.245357	0.98724|0.98724	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196|ENST00000530997;ENST00000389869;ENST00000530853	.|.	.|.	.|.	5.33|5.33	4.35|4.35	0.52113|0.52113	.|.	1.089110|.	0.06954|.	N|.	0.815090|.	.|T	.|0.51449	.|0.1675	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.60131	.|-0.7323	.|3	0.02654|.	T|.	1|.	0.0741|0.0741	8.9599|8.9599	0.35840|0.35840	0.0:0.2239:0.569:0.2071|0.0:0.2239:0.569:0.2071	.|.	.|.	.|.	.|.	X|L	1003;986;1009;1003;1003;1003|493	.|.	ENSP00000245441:R1003X|.	R|S	-|-	1|2	2|0	NIN|NIN	50294491|50294491	0.074000|0.074000	0.21230|0.21230	0.298000|0.298000	0.25002|0.25002	0.688000|0.688000	0.40055|0.40055	1.178000|1.178000	0.31981|0.31981	2.492000|2.492000	0.84095|0.84095	0.563000|0.563000	0.77884|0.77884	CGA|TCG		0.458	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51224741	G	A	51224741	4	1	61	1	0	0	0	0	0	1	0	0	10448	1066	37	1	3598	1	NIN	14	51224741	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	813	51224741	56124799	8910	16895										
NIN	51199	broad.mit.edu	37	chr14	51225321	51225321	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctatttgagaggttctTctattacactctgtttccat	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:51225321T>G	ENST00000382041.3	-	18	2617	c.2427A>C	c.(2425-2427)agA>agC	p.R809S	NIN_ENST00000382043.4_Intron|NIN_ENST00000245441.5_Missense_Mutation_p.R809S|NIN_ENST00000324330.9_Missense_Mutation_p.R809S|NIN_ENST00000389868.3_Intron|NIN_ENST00000530997.2_Missense_Mutation_p.R809S|NIN_ENST00000453196.1_Missense_Mutation_p.R809S	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	809				R -> I (in Ref. 1; AAF23015). {ECO:0000305}.	centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.R815S(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					GAGAGGTTCTTCTATTACACT	0.438			T	PDGFRB	MPD																																		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	1	Substitution - Missense(1)	large_intestine(1)	14											43	45	44					14																	51225321		2203	4300	6503	50295071	SO:0001583	missense	51199			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.2427A>C	14.37:g.51225321T>G	ENSP00000371472:p.Arg809Ser		50295071	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.06|19.06	3.754836|3.754836	0.69648|0.69648	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	.|T;T;T;T	.|0.08370	.|3.37;3.1;3.1;3.11	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|0.250293	.|0.47093	.|D	.|0.000254	T|T	0.26122|0.26122	0.0637|0.0637	M|M	0.69823|0.69823	2.125|2.125	0.33873|0.33873	D|D	0.63517|0.63517	.|D;D;D;D	.|0.89917	.|0.995;0.999;1.0;0.996	.|D;D;D;D	.|0.83275	.|0.939;0.964;0.996;0.99	T|T	0.30149|0.30149	-0.9988|-0.9988	5|10	.|0.13853	.|T	.|0.58	-8.8613|-8.8613	15.5264|15.5264	0.75910|0.75910	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|815;809;809;809	.|Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.|.;.;NIN_HUMAN;.	Q|S	300|809;792;815;809;809;809	.|ENSP00000245441:R809S;ENSP00000371472:R809S;ENSP00000324210:R809S;ENSP00000412391:R809S	.|ENSP00000245441:R809S	K|R	-|-	1|3	0|2	NIN|NIN	50295071|50295071	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.698000|3.698000	0.54771|0.54771	2.261000|2.261000	0.74972|0.74972	0.533000|0.533000	0.62120|0.62120	AAG|AGA		0.438	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		G	51225321	T	G	51225321	3	3	61	1	0	0	0	0	1	0	0	0	10448	1780	62	4	4178	4	NIN	14	51225321	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	580	51225321	56124219	8911	16896										
NIN	51199	broad.mit.edu	37	chr14	51228517	51228517	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggacttactttatcttcGagctccagtctgaggcaaca	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:51228517G>A	ENST00000382041.3	-	16	2077	c.1887C>T	c.(1885-1887)ctC>ctT	p.L629L	NIN_ENST00000382043.4_Silent_p.L629L|NIN_ENST00000245441.5_Silent_p.L629L|NIN_ENST00000324330.9_Silent_p.L629L|NIN_ENST00000389868.3_Silent_p.L629L|NIN_ENST00000530997.2_Silent_p.L629L|NIN_ENST00000453196.1_Silent_p.L629L	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	629					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.L635L(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					CTTTATCTTCGAGCTCCAGTC	0.413			T	PDGFRB	MPD																																		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	1	Substitution - coding silent(1)	large_intestine(1)	14											306	263	278					14																	51228517		2203	4300	6503	50298267	SO:0001819	synonymous_variant	51199			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.1887C>T	14.37:g.51228517G>A			50298267	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	G	2.090	-0.408650	0.04832	.	.	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.48	-3.08	0.05347	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.7406	10.3	0.43646	0.3749:0.5248:0.1002:0.0	.	.	.	.	X	120	.	.	R	-	1	2	NIN	50298267	0.963000	0.33076	0.967000	0.41034	0.272000	0.26649	0.042000	0.13949	-0.853000	0.04136	-0.886000	0.02939	CGA		0.413	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51228517	G	A	51228517	2	1	61	1	0	0	0	0	0	0	0	1	10448	1045	37	1		1	NIN	14	51228517	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3196	51228517	56121023	8912	16897										
FRMD6	122786	broad.mit.edu	37	chr14	52182060	52182060	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggtaagaaatttgagatTttgccagatggcttgccttc	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:52182060T>G	ENST00000344768.5	+	10	1063	c.867T>G	c.(865-867)atT>atG	p.I289M	FRMD6_ENST00000553556.1_5'Flank|FRMD6_ENST00000395718.2_Missense_Mutation_p.I281M|FRMD6_ENST00000554167.1_Missense_Mutation_p.I212M|FRMD6_ENST00000356218.4_Missense_Mutation_p.I281M			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	289	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.I281M(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					AATTTGAGATTTTGCCAGATG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											51	53	53					14																	52182060		2203	4300	6503	51251810	SO:0001583	missense	122786			BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.867T>G	14.37:g.52182060T>G	ENSP00000343899:p.Ile289Met		51251810	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Missense_Mutation	SNP	ENST00000344768.5	37	CCDS58318.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131800	0.56828	.	.	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000555197	D;D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03;-3.03	5.96	2.39	0.29439	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.92489	0.7615	M	0.72479	2.2	0.80722	D	1	D;P;P	0.54047	0.964;0.933;0.684	P;P;P	0.53102	0.596;0.718;0.477	D	0.90007	0.4118	10	0.62326	D	0.03	.	7.8683	0.29549	0.0:0.3792:0.0:0.6208	.	212;289;281	G3V4T7;Q96NE9;Q96NE9-2	.;FRMD6_HUMAN;.	M	281;281;289;212;19	ENSP00000348550:I281M;ENSP00000379068:I281M;ENSP00000343899:I289M;ENSP00000451977:I212M;ENSP00000451157:I19M	ENSP00000343899:I289M	I	+	3	3	FRMD6	51251810	0.999000	0.42202	0.999000	0.59377	0.929000	0.56500	0.626000	0.24492	0.177000	0.19895	-0.250000	0.11733	ATT		0.473	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		G	52182060	T	G	52182060	3	3	61	1	0	0	0	0	1	0	0	0	6073	1829	64	4	877	4	FRMD6	14	52182060	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	953543	52182060	55167480	8913	16898										
FRMD6	122786	broad.mit.edu	37	chr14	52194667	52194667	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtgcatcaacatccaaGatgcttttccagtcaaaaga	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:52194667G>T	ENST00000344768.5	+	14	1985	c.1789G>T	c.(1789-1791)Gat>Tat	p.D597Y	FRMD6_ENST00000553556.1_Missense_Mutation_p.D239Y|FRMD6_ENST00000395718.2_Missense_Mutation_p.D589Y|FRMD6_ENST00000554167.1_Missense_Mutation_p.D520Y|FRMD6_ENST00000356218.4_Missense_Mutation_p.D589Y			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	597					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.D589Y(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					CAACATCCAAGATGCTTTTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											111	93	99					14																	52194667		2203	4300	6503	51264417	SO:0001583	missense	122786			BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1789G>T	14.37:g.52194667G>T	ENSP00000343899:p.Asp597Tyr		51264417	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Missense_Mutation	SNP	ENST00000344768.5	37	CCDS58318.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.797287	0.50208	.	.	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000553556	T;T;T;T	0.78364	-1.17;-1.17;-0.94;-0.75	5.96	5.96	0.96718	.	0.236589	0.42964	D	0.000630	T	0.64416	0.2596	N	0.08118	0	0.31998	N	0.603796	B;B;B	0.32526	0.374;0.004;0.23	B;B;B	0.30495	0.116;0.002;0.116	T	0.70428	-0.4874	10	0.62326	D	0.03	.	20.017	0.97481	0.0:0.0:1.0:0.0	.	520;597;589	G3V4T7;Q96NE9;Q96NE9-2	.;FRMD6_HUMAN;.	Y	589;589;597;520;239	ENSP00000348550:D589Y;ENSP00000379068:D589Y;ENSP00000343899:D597Y;ENSP00000451977:D520Y	ENSP00000343899:D597Y	D	+	1	0	FRMD6	51264417	1.000000	0.71417	0.914000	0.36105	0.986000	0.74619	4.065000	0.57513	2.832000	0.97577	0.655000	0.94253	GAT		0.468	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		T	52194667	G	T	52194667	3	4	61	1	0	0	0	0	1	0	0	0	6073	942	33	2	1815	2	FRMD6	14	52194667	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12607	52194667	55154873	8914	16899										
C14orf166	51637	broad.mit.edu	37	chr14	52460480	52460480	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctttcaagattcaagatCgacaagaagctattgactgg	9	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:52460480C>T	ENST00000261700.3	+	3	391	c.226C>T	c.(226-228)Cga>Tga	p.R76*	C14orf166_ENST00000556760.1_Nonsense_Mutation_p.R76*	NM_016039.2	NP_057123.1	Q9Y224	CN166_HUMAN	chromosome 14 open reading frame 166	76					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA transport (GO:0050658)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core binding (GO:0000993)	p.R76*(1)		endometrium(1)|large_intestine(3)|lung(2)	6	Breast(41;0.0639)|all_epithelial(31;0.101)					GATTCAAGATCGACAAGAAGC	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											144	125	132					14																	52460480		2203	4300	6503	51530230	SO:0001587	stop_gained	51637			AF151857	CCDS9705.1	14q22.1	2014-05-29			ENSG00000087302	ENSG00000087302			23169	protein-coding gene	gene with protein product	"RLL motif containing 1"	610858				10810093, 24608264	Standard	NM_016039		Approved	CGI-99, RLLM1, CLE, CLE7, LCRP369	uc010aod.3	Q9Y224	OTTHUMG00000152332	ENST00000261700.3:c.226C>T	14.37:g.52460480C>T	ENSP00000261700:p.Arg76*		51530230		Nonsense_Mutation	SNP	ENST00000261700.3	37	CCDS9705.1	.	.	.	.	.	.	.	.	.	.	C	37	6.372309	0.97515	.	.	ENSG00000087302	ENST00000261700;ENST00000556760;ENST00000553362	.	.	.	5.53	5.53	0.82687	.	0.103982	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-15.3485	19.4167	0.94704	0.0:1.0:0.0:0.0	.	.	.	.	X	76;76;13	.	ENSP00000261700:R76X	R	+	1	2	C14orf166	51530230	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.982000	0.49337	2.775000	0.95449	0.650000	0.86243	CGA		0.368	C14orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276887.1	NM_016039		T	52460480	C	T	52460480	4	4	61	1	0	0	0	0	0	1	0	0	1760	876	31	1	236	1	C14orf166	14	52460480	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	265813	52460480	54889060	8915	16900										
PTGDR	5729	broad.mit.edu	37	chr14	52741531	52741531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagacctccgagccttgcGatttctatctgtgatttcaa	8	10	3	3	rs143143539		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:52741531G>A	ENST00000306051.2	+	2	1031	c.929G>A	c.(928-930)cGa>cAa	p.R310Q	PTGDR_ENST00000553372.1_3'UTR	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	310					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)	p.R310Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	CGAGCCTTGCGATTTCTATCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											94	88	90					14																	52741531		2203	4300	6503	51811281	SO:0001583	missense	5729			U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"GPCR / Class A : Prostanoid receptors"	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	ENST00000306051.2:c.929G>A	14.37:g.52741531G>A	ENSP00000303424:p.Arg310Gln		51811281	G3V5L3|Q13250|Q13251|Q1ZZ52	Missense_Mutation	SNP	ENST00000306051.2	37	CCDS9707.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.93	3.728383	0.69074	.	.	ENSG00000168229	ENST00000306051	T	0.72167	-0.63	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000157	D	0.84723	0.5535	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85948	0.1462	10	0.72032	D	0.01	-6.3795	18.2013	0.89839	0.0:0.0:1.0:0.0	.	310	Q13258	PD2R_HUMAN	Q	310	ENSP00000303424:R310Q	ENSP00000303424:R310Q	R	+	2	0	PTGDR	51811281	1.000000	0.71417	0.893000	0.35052	0.068000	0.16541	5.443000	0.66581	2.814000	0.96858	0.655000	0.94253	CGA		0.378	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953		A	52741531	G	A	52741531	3	1	61	1	0	0	0	0	1	0	0	0	12775	1058	37	1	935	1	PTGDR	14	52741531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281051	52741531	54608009	8916	16901										
TXNDC16	57544	broad.mit.edu	37	chr14	52955142	52955142	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcctcaatgtgcatattAttttccacatgagatattat	4	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:52955142A>C	ENST00000281741.4	-	12	1418	c.1047T>G	c.(1045-1047)aaT>aaG	p.N349K	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	349					cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)		p.N349K(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					TGTGCATATTATTTTCCACAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	14											139	119	126					14																	52955142		2203	4300	6503	52024892	SO:0001583	missense	57544			AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"KIAA1344"	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.1047T>G	14.37:g.52955142A>C	ENSP00000281741:p.Asn349Lys		52024892	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	.	.	.	.	.	.	.	.	.	.	A	9.258	1.042423	0.19748	.	.	ENSG00000087301	ENST00000281741	T	0.16324	2.35	5.49	3.14	0.36123	Thioredoxin-like fold (1);	0.537462	0.21501	N	0.073533	T	0.12135	0.0295	L	0.41236	1.265	0.23950	N	0.996379	B;B	0.14438	0.01;0.005	B;B	0.09377	0.004;0.003	T	0.33189	-0.9878	10	0.19590	T	0.45	-22.0169	7.1831	0.25784	0.821:0.0:0.179:0.0	.	344;349	B7ZME4;Q9P2K2	.;TXD16_HUMAN	K	349	ENSP00000281741:N349K	ENSP00000281741:N349K	N	-	3	2	TXNDC16	52024892	0.126000	0.22350	0.535000	0.28026	0.517000	0.34286	0.506000	0.22658	0.381000	0.24851	0.455000	0.32223	AAT		0.333	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699		C	52955142	A	C	52955142	3	2	61	1	0	0	0	0	1	0	0	0	16835	446	16	4	1470	4	TXNDC16	14	52955142	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	213611	52955142	54394398	8917	16902										
GPR137C	283554	broad.mit.edu	37	chr14	53066894	53066894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagtggtgaacttgacttgCgcaatgctagttcatggaga	12	6	1	3	rs200637280		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53066894C>T	ENST00000321662.6	+	3	552	c.552C>T	c.(550-552)tgC>tgT	p.C184C		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	184						integral component of membrane (GO:0016021)		p.C184C(1)		NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					ACTTGACTTGCGCAATGCTAG	0.363													C|||	1	0.000199681	0	0	5008	,	,		16532	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14											222	197	204					14																	53066894		1867	4111	5978	52136644	SO:0001819	synonymous_variant	283554			BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.552C>T	14.37:g.53066894C>T			52136644	Q86SM2	Silent	SNP	ENST00000321662.6	37	CCDS45106.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	C|C	8.151|8.151	0.787421|0.787421	0.16258|0.16258	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000555622|ENST00000542169	.|.	.|.	.|.	5.41|5.41	3.03|3.03	0.35002|0.35002	.|.	.|.	.|.	.|.	.|.	T|T	0.58666|0.58666	0.2138|0.2138	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.51880|0.51880	-0.8649|-0.8649	4|4	.|.	.|.	.|.	-35.554|-35.554	9.1975|9.1975	0.37237|0.37237	0.0:0.2094:0.0:0.7906|0.0:0.2094:0.0:0.7906	.|.	.|.	.|.	.|.	V|C	116|138	.|.	.|.	A|R	+|+	2|1	0|0	GPR137C|GPR137C	52136644|52136644	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	1.352000|1.352000	0.34033|0.34033	0.426000|0.426000	0.26116|0.26116	-0.383000|-0.383000	0.06682|0.06682	GCG|CGC		0.363	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		T	53066894	C	T	53066894	2	4	61	1	0	0	0	0	0	0	0	1	6667	776	27	1		1	GPR137C	14	53066894	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111752	53066894	54282646	8918	16903										
ERO1L	30001	broad.mit.edu	37	chr14	53124725	53124725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctcttttttctacacagaGacctaagaaaaagcagtgac	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53124725G>T	ENST00000395686.3	-	11	941	c.718C>A	c.(718-720)Ctc>Atc	p.L240I		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	240					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)	p.L240I(1)	ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					TCTACACAGAGACCTAAGAAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	14											74	73	73					14																	53124725		2202	4297	6499	52194475	SO:0001583	missense	30001			AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"ERO1 (S. cerevisiae)-like"			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.718C>A	14.37:g.53124725G>T	ENSP00000379042:p.Leu240Ile		52194475	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Missense_Mutation	SNP	ENST00000395686.3	37	CCDS9709.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.252331	0.39797	.	.	ENSG00000197930	ENST00000395686	T	0.44083	0.93	5.89	5.0	0.66597	.	0.122224	0.56097	D	0.000028	T	0.57095	0.2030	M	0.80508	2.5	0.44660	D	0.997643	P	0.46142	0.873	P	0.52189	0.692	T	0.62511	-0.6839	10	0.66056	D	0.02	-10.4509	11.5193	0.50541	0.0699:0.1338:0.7963:0.0	.	240	Q96HE7	ERO1A_HUMAN	I	240	ENSP00000379042:L240I	ENSP00000379042:L240I	L	-	1	0	ERO1L	52194475	0.987000	0.35691	0.891000	0.34965	0.753000	0.42808	1.950000	0.40323	1.485000	0.48380	0.655000	0.94253	CTC		0.303	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584		T	53124725	G	T	53124725	3	4	61	1	0	0	0	0	1	0	0	0	5252	942	33	2	712	2	ERO1L	14	53124725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57831	53124725	54224815	8919	16904										
PSMC6	5706	broad.mit.edu	37	chr14	53175094	53175094	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgatctgaaggccctacaGagtgttgggcaggtaggtga	15	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53175094G>A	ENST00000606149.1	+	2	169	c.153G>A	c.(151-153)caG>caA	p.Q51Q	PSMC6_ENST00000445930.2_Silent_p.Q65Q	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	51					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)	p.Q51Q(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					AGGCCCTACAGAGTGTTGGGC	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	14											133	131	132					14																	53175094		2203	4300	6503	52244844	SO:0001819	synonymous_variant	5706				CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.153G>A	14.37:g.53175094G>A			52244844	B2R975|P49719|Q6IBU3|Q92524	Silent	SNP	ENST00000606149.1	37		.	.	.	.	.	.	.	.	.	.	G	6.166	0.398850	0.11696	.	.	ENSG00000100519	ENST00000556813	.	.	.	5.17	0.207	0.15214	.	.	.	.	.	T	0.57213	0.2038	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51196	-0.8736	4	.	.	.	.	9.6137	0.39679	0.5312:0.0:0.4688:0.0	.	.	.	.	K	51	.	.	E	+	1	0	PSMC6	52244844	0.953000	0.32496	1.000000	0.80357	0.799000	0.45148	0.134000	0.15932	0.067000	0.16545	-1.317000	0.01298	GAG		0.343	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		A	53175094	G	A	53175094	2	1	61	1	0	0	0	0	0	0	0	1	12725	933	33	3		3	PSMC6	14	53175094	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50369	53175094	54174446	8920	16905										
PSMC6	5706	broad.mit.edu	37	chr14	53185004	53185004	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtgctcgtttgatcagaGaaatgtttaattatgctaga	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53185004G>T	ENST00000606149.1	+	9	665	c.649G>T	c.(649-651)Gaa>Taa	p.E217*	PSMC6_ENST00000445930.2_Nonsense_Mutation_p.E231*	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	217					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)	p.E217*(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					TTTGATCAGAGAAATGTTTAA	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											100	104	103					14																	53185004		2203	4300	6503	52254754	SO:0001587	stop_gained	5706				CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.649G>T	14.37:g.53185004G>T	ENSP00000475721:p.Glu217*		52254754	B2R975|P49719|Q6IBU3|Q92524	Nonsense_Mutation	SNP	ENST00000606149.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.1|24.1	4.499364|4.499364	0.85069|0.85069	.|.	.|.	ENSG00000100519|ENSG00000100519	ENST00000445930|ENST00000555339;ENST00000556813	.|D;D	.|0.94232	.|-3.38;-3.38	5.03|5.03	5.03|5.03	0.67393|0.67393	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|D	.|0.95903	.|0.8666	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.95309	.|0.8410	.|4	0.87932|.	D|.	0|.	.|.	18.7228|18.7228	0.91702|0.91702	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	231|177;216	.|ENSP00000452048:R177I;ENSP00000451156:R216I	ENSP00000401802:E231X|.	E|R	+|+	1|2	0|0	PSMC6|PSMC6	52254754|52254754	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.435000|9.435000	0.97529|0.97529	2.503000|2.503000	0.84419|0.84419	0.591000|0.591000	0.81541|0.81541	GAA|AGA		0.313	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		T	53185004	G	T	53185004	4	4	61	1	0	0	0	0	0	1	0	0	12725	943	33	2	725	2	PSMC6	14	53185004	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9910	53185004	54164536	8921	16906										
PSMC6	5706	broad.mit.edu	37	chr14	53185747	53185747	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagagagattcagagaacGttaatggaggtaatatttgg	13	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53185747G>A	ENST00000606149.1	+	10	784	c.768G>A	c.(766-768)acG>acA	p.T256T	PSMC6_ENST00000445930.2_Silent_p.T270T	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	256					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)	p.T256T(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					TTCAGAGAACGTTAATGGAGG	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	14											103	105	104					14																	53185747		2203	4300	6503	52255497	SO:0001819	synonymous_variant	5706				CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.768G>A	14.37:g.53185747G>A			52255497	B2R975|P49719|Q6IBU3|Q92524	Silent	SNP	ENST00000606149.1	37																																																																																					0.333	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		A	53185747	G	A	53185747	2	1	61	1	0	0	0	0	0	0	0	1	12725	1132	40	1		1	PSMC6	14	53185747	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	743	53185747	54163793	8922	16907										
PSMC6	5706	broad.mit.edu	37	chr14	53194240	53194240	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcgcaattcgtgctgatCatgattttgtagtacaggaa	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53194240C>A	ENST00000606149.1	+	14	1091	c.1075C>A	c.(1075-1077)Cat>Aat	p.H359N	STYX_ENST00000354586.4_5'Flank|PSMC6_ENST00000557557.1_3'UTR|PSMC6_ENST00000445930.2_Missense_Mutation_p.H373N|STYX_ENST00000442123.2_5'Flank	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	359					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)	p.H359N(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					TCGTGCTGATCATGATTTTGT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											61	58	59					14																	53194240		2203	4300	6503	52263990	SO:0001583	missense	5706				CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.1075C>A	14.37:g.53194240C>A	ENSP00000475721:p.His359Asn		52263990	B2R975|P49719|Q6IBU3|Q92524	Missense_Mutation	SNP	ENST00000606149.1	37		.	.	.	.	.	.	.	.	.	.	C	15.73	2.919574	0.52653	.	.	ENSG00000100519	ENST00000445930	D	0.94687	-3.49	5.3	5.3	0.74995	.	0.096164	0.64402	D	0.000001	D	0.89743	0.6803	N	0.12443	0.215	0.47994	D	0.99956	B	0.09022	0.002	B	0.16722	0.016	D	0.85139	0.0979	10	0.87932	D	0	.	19.3235	0.94252	0.0:1.0:0.0:0.0	.	359	P62333	PRS10_HUMAN	N	373	ENSP00000401802:H373N	ENSP00000401802:H373N	H	+	1	0	PSMC6	52263990	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.526000	0.53509	2.627000	0.88993	0.650000	0.86243	CAT		0.323	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		A	53194240	C	A	53194240	3	1	61	1	0	0	0	0	1	0	0	0	12725	826	29	2	1171	2	PSMC6	14	53194240	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8493	53194240	54155300	8923	16908										
STYX	6815	broad.mit.edu	37	chr14	53224469	53224469	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtttttcaggaaaagttCttgtgcatggaaatgcaggg	12	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53224469C>A	ENST00000354586.4	+	7	642	c.349C>A	c.(349-351)Ctt>Att	p.L117I	STYX_ENST00000556861.1_Intron|STYX_ENST00000442123.2_Missense_Mutation_p.L117I	NM_145251.3	NP_660294.1	Q8WUJ0	STYX_HUMAN	serine/threonine/tyrosine interacting protein	117	Tyrosine-protein phosphatase.				MAPK export from nucleus (GO:0045204)|protein dephosphorylation (GO:0006470)|regulation of ERK1 and ERK2 cascade (GO:0070372)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L117I(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(41;0.176)					AGGAAAAGTTCTTGTGCATGG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	14											69	74	72					14																	53224469		2203	4295	6498	52294219	SO:0001583	missense	6815				CCDS9711.1	14q22.1	2011-06-09	2001-11-29		ENSG00000198252	ENSG00000198252		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	11447	protein-coding gene	gene with protein product		615814	"serine/threonine/tyrosine-interacting protein"			7592916	Standard	NM_145251		Approved		uc010tqy.2	Q8WUJ0	OTTHUMG00000140306	ENST00000354586.4:c.349C>A	14.37:g.53224469C>A	ENSP00000346599:p.Leu117Ile		52294219	B9EJG0|Q99850	Missense_Mutation	SNP	ENST00000354586.4	37	CCDS9711.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963730	0.92791	.	.	ENSG00000198252	ENST00000442123;ENST00000354586	T;T	0.69040	-0.37;-0.37	5.58	5.58	0.84498	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.87321	0.6148	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89824	0.3991	10	0.87932	D	0	.	19.9414	0.97163	0.0:1.0:0.0:0.0	.	117	Q8WUJ0	STYX_HUMAN	I	117	ENSP00000403214:L117I;ENSP00000346599:L117I	ENSP00000346599:L117I	L	+	1	0	STYX	52294219	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.628000	0.74262	2.779000	0.95612	0.650000	0.86243	CTT		0.318	STYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276902.1	NM_145251		A	53224469	C	A	53224469	3	1	61	1	0	0	0	0	1	0	0	0	15399	913	32	2	375	2	STYX	14	53224469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30229	53224469	54125071	8924	16909										
DDHD1	80821	broad.mit.edu	37	chr14	53513548	53513548	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttatacatgaaggttaAaagaaaaagggcaacatcca	8	5	0	2	rs570950752		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53513548A>C	ENST00000323669.5	-	13	2640	c.2641T>G	c.(2641-2643)Tta>Gta	p.L881V	DDHD1_ENST00000395606.1_Missense_Mutation_p.L860V|DDHD1_ENST00000555621.1_5'Flank|DDHD1_ENST00000357758.3_Missense_Mutation_p.L853V	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	881	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.L853V(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					ATGAAGGTTAAAAGAAAAAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	14											148	130	136					14																	53513548		2203	4300	6503	52583298	SO:0001583	missense	80821			AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.2641T>G	14.37:g.53513548A>C	ENSP00000327104:p.Leu881Val		52583298	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	37	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.515119	0.64634	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	5.92	4.78	0.61160	DDHD (2);	0.067206	0.64402	D	0.000008	T	0.67287	0.2877	L	0.56199	1.76	0.46564	D	0.999105	P;D;P	0.76494	0.867;0.999;0.812	P;D;P	0.91635	0.599;0.999;0.61	T	0.67381	-0.5685	9	0.56958	D	0.05	-12.5545	6.4429	0.21859	0.7169:0.0:0.2831:0.0	.	860;881;853	G5E9D1;Q8NEL9;Q8NEL9-2	.;DDHD1_HUMAN;.	V	881;860;853;752	.	ENSP00000327104:L881V	L	-	1	2	DDHD1	52583298	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	2.630000	0.46494	1.067000	0.40740	0.459000	0.35465	TTA		0.418	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			C	53513548	A	C	53513548	3	2	61	1	0	0	0	0	1	0	0	0	4332	11	1	4	65	4	DDHD1	14	53513548	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	289079	53513548	53835992	8925	16910										
DDHD1	80821	broad.mit.edu	37	chr14	53529665	53529665	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaggatattttaccgtcGtttagttatatagagttcat	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:53529665G>A	ENST00000323669.5	-	7	1761	c.1762C>T	c.(1762-1764)Cga>Tga	p.R588*	DDHD1_ENST00000395606.1_Nonsense_Mutation_p.R595*|DDHD1_ENST00000357758.3_Nonsense_Mutation_p.R588*	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	588					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.R588*(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					TTTTACCGTCGTTTAGTTATA	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											75	70	72					14																	53529665		2203	4300	6503	52599415	SO:0001587	stop_gained	80821			AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.1762C>T	14.37:g.53529665G>A	ENSP00000327104:p.Arg588*		52599415	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Nonsense_Mutation	SNP	ENST00000323669.5	37	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.741976	0.89573	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	5.47	4.54	0.55810	.	0.436137	0.24242	N	0.040260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	14.3058	0.66384	0.0:0.0:0.8503:0.1496	.	.	.	.	X	588;595;588;459	.	ENSP00000327104:R588X	R	-	1	2	DDHD1	52599415	0.866000	0.29940	0.100000	0.21137	0.027000	0.11550	3.740000	0.55082	1.210000	0.43336	0.585000	0.79938	CGA		0.333	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			A	53529665	G	A	53529665	4	1	61	1	0	0	0	0	0	1	0	0	4332	1153	40	1	968	1	DDHD1	14	53529665	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16117	53529665	53819875	8926	16911										
GMFB	2764	broad.mit.edu	37	chr14	54947636	54947636	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaggatatgaaactcttCcatcatcatgttgatattta	6	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:54947636C>A	ENST00000358056.3	-	5	507	c.239G>T	c.(238-240)gGa>gTa	p.G80V	GMFB_ENST00000554908.1_3'UTR|GMFB_ENST00000553566.1_5'Flank	NM_004124.2	NP_004115.1	P60983	GMFB_HUMAN	glia maturation factor, beta	80	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of protein kinase activity (GO:0006469)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)|signal transducer activity (GO:0004871)	p.G80V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)	8						TGAAACTCTTCCATCATCATG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	14											79	80	80					14																	54947636		2203	4300	6503	54017386	SO:0001583	missense	2764			M86492	CCDS9718.1	14q22.2	2010-07-06			ENSG00000197045	ENSG00000197045			4373	protein-coding gene	gene with protein product		601713				1712830	Standard	NM_004124		Approved	GMF	uc021rtf.1	P60983	OTTHUMG00000140307	ENST00000358056.3:c.239G>T	14.37:g.54947636C>A	ENSP00000350757:p.Gly80Val		54017386	B2R499|P17774|Q9BS35	Missense_Mutation	SNP	ENST00000358056.3	37	CCDS9718.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745341	0.89663	.	.	ENSG00000197045	ENST00000358056;ENST00000354747;ENST00000553333	T;T	0.37058	1.22;1.22	5.62	5.62	0.85841	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	T	0.72803	0.3506	H	0.94462	3.54	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80144	-0.1505	10	0.87932	D	0	-0.3217	20.0377	0.97569	0.0:1.0:0.0:0.0	.	80	P60983	GMFB_HUMAN	V	80;80;93	ENSP00000350757:G80V;ENSP00000451920:G93V	ENSP00000346789:G80V	G	-	2	0	GMFB	54017386	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.297000	0.78799	2.822000	0.97130	0.650000	0.86243	GGA		0.328	GMFB-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276903.2	NM_004124		A	54947636	C	A	54947636	3	1	61	1	0	0	0	0	1	0	0	0	6509	855	30	2	201	2	GMFB	14	54947636	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1417971	54947636	52401904	8927	16912										
SAMD4A	23034	broad.mit.edu	37	chr14	55203947	55203947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagtggtgggagtgaacaCttagaagatcagaccactgc	14	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55203947C>T	ENST00000554335.1	+	4	1584	c.921C>T	c.(919-921)caC>caT	p.H307H	SAMD4A_ENST00000251091.5_Intron|SAMD4A_ENST00000392067.3_Silent_p.H307H|SAMD4A_ENST00000357634.3_Silent_p.H306H			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	307					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.H306H(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						GGAGTGAACACTTAGAAGATC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	14											158	140	146					14																	55203947		2203	4300	6503	54273697	SO:0001819	synonymous_variant	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.921C>T	14.37:g.55203947C>T			54273697	A8MPZ5|Q0VA96|Q6PEW4	Silent	SNP	ENST00000554335.1	37	CCDS32084.2																																																																																				0.522	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55203947	C	T	55203947	2	4	61	1	0	0	0	0	0	0	0	1	13858	564	20	3		3	SAMD4A	14	55203947	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	256311	55203947	52145593	8928	16913										
SAMD4A	23034	broad.mit.edu	37	chr14	55226887	55226887	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaccgtccaggacatcatCgaggggggcagcctgcgcat	13	14	2	0	rs201991552	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55226887C>T	ENST00000554335.1	+	7	1848	c.1185C>T	c.(1183-1185)atC>atT	p.I395I	SAMD4A_ENST00000251091.5_Silent_p.I307I|SAMD4A_ENST00000555192.1_5'UTR|SAMD4A_ENST00000392067.3_Silent_p.I395I|SAMD4A_ENST00000357634.3_Silent_p.I394I			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	395					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.I394I(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						AGGACATCATCGAGGGGGGCA	0.632													C|||	7	0.00139776	0	0	5008	,	,		15963	0.0069		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14											100	112	108					14																	55226887		2187	4267	6454	54296637	SO:0001819	synonymous_variant	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1185C>T	14.37:g.55226887C>T			54296637	A8MPZ5|Q0VA96|Q6PEW4	Silent	SNP	ENST00000554335.1	37	CCDS32084.2																																																																																				0.632	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55226887	C	T	55226887	2	4	61	1	0	0	0	0	0	0	0	1	13858	874	31	1		1	SAMD4A	14	55226887	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22940	55226887	52122653	8929	16914										
SAMD4A	23034	broad.mit.edu	37	chr14	55236927	55236927	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctagacatatcaggatatCgacagcaaagaaagtatgtt	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55236927C>T	ENST00000554335.1	+	9	2365	c.1702C>T	c.(1702-1704)Cga>Tga	p.R568*	SAMD4A_ENST00000251091.5_Nonsense_Mutation_p.R480*|SAMD4A_ENST00000555192.1_Nonsense_Mutation_p.R159*|SAMD4A_ENST00000392067.3_Nonsense_Mutation_p.R568*|SAMD4A_ENST00000357634.3_Nonsense_Mutation_p.R567*			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	568					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.R567*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						ATCAGGATATCGACAGCAAAG	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											151	146	148					14																	55236927		2203	4300	6503	54306677	SO:0001587	stop_gained	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1702C>T	14.37:g.55236927C>T	ENSP00000452535:p.Arg568*		54306677	A8MPZ5|Q0VA96|Q6PEW4	Nonsense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	39	7.355319	0.98231	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.42	5.42	0.78866	.	0.075963	0.53938	D	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.8228	19.2111	0.93755	0.0:1.0:0.0:0.0	.	.	.	.	X	568;568;480;479;567;159	.	ENSP00000251091:R197X	R	+	1	2	SAMD4A	54306677	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.585000	0.67497	2.551000	0.86045	0.462000	0.41574	CGA		0.463	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55236927	C	T	55236927	4	4	61	1	0	0	0	0	0	1	0	0	13858	876	31	1	1729	1	SAMD4A	14	55236927	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10040	55236927	52112613	8930	16915										
WDHD1	11169	broad.mit.edu	37	chr14	55422389	55422389	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagtttgagaatttcttttCtggaaataggatgctgcaga	10	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55422389C>A	ENST00000360586.3	-	24	3005	c.2940G>T	c.(2938-2940)caG>caT	p.Q980H	WDHD1_ENST00000420358.2_Missense_Mutation_p.Q857H|WDHD1_ENST00000421192.1_Missense_Mutation_p.Q857H|WDHD1_ENST00000359167.4_Missense_Mutation_p.Q498H	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	980					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.Q980H(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						AATTTCTTTTCTGGAAATAGG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	70	70					14																	55422389		2203	4295	6498	54492139	SO:0001583	missense	11169			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2940G>T	14.37:g.55422389C>A	ENSP00000353793:p.Gln980His		54492139	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463786	0.26335	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.62941	0.35;0.83;-0.01	4.71	0.721	0.18219	.	0.261750	0.33057	N	0.005332	T	0.37433	0.1003	N	0.24115	0.695	0.36841	D	0.887414	B;P	0.35527	0.241;0.507	B;B	0.29524	0.103;0.098	T	0.24368	-1.0162	10	0.52906	T	0.07	.	4.2076	0.10497	0.0:0.5345:0.1771:0.2885	.	498;980	F8W7P7;O75717	.;WDHD1_HUMAN	H	980;498;857	ENSP00000353793:Q980H;ENSP00000352085:Q498H;ENSP00000391049:Q857H	ENSP00000352085:Q498H	Q	-	3	2	WDHD1	54492139	1.000000	0.71417	0.994000	0.49952	0.816000	0.46133	0.661000	0.25023	0.267000	0.21916	0.563000	0.77884	CAG		0.303	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		A	55422389	C	A	55422389	3	1	61	1	0	0	0	0	1	0	0	0	17311	912	32	2	461	2	WDHD1	14	55422389	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	185462	55422389	51927151	8931	16916										
WDHD1	11169	broad.mit.edu	37	chr14	55448379	55448379	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtcctctgttaagcattcGaacaattccttctgaatcca	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55448379G>A	ENST00000360586.3	-	16	2007	c.1942C>T	c.(1942-1944)Cga>Tga	p.R648*	WDHD1_ENST00000420358.2_Nonsense_Mutation_p.R525*|WDHD1_ENST00000421192.1_Nonsense_Mutation_p.R525*|WDHD1_ENST00000359167.4_Nonsense_Mutation_p.R166*	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	648					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.R648*(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						TTAAGCATTCGAACAATTCCT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											109	94	99					14																	55448379		2203	4300	6503	54518129	SO:0001587	stop_gained	11169			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.1942C>T	14.37:g.55448379G>A	ENSP00000353793:p.Arg648*		54518129	C9JW18|F6W0U7	Nonsense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	G	42	9.629853	0.99224	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	.	.	.	5.71	4.77	0.60923	.	0.141721	0.47852	D	0.000211	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.3186	14.9058	0.70718	0.0:0.0:0.7814:0.2186	.	.	.	.	X	648;166;525	.	ENSP00000352085:R166X	R	-	1	2	WDHD1	54518129	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.738000	0.55067	2.708000	0.92522	0.585000	0.79938	CGA		0.403	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		A	55448379	G	A	55448379	4	1	61	1	0	0	0	0	0	1	0	0	17311	1066	37	1	1491	1	WDHD1	14	55448379	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25990	55448379	51901161	8932	16917										
WDHD1	11169	broad.mit.edu	37	chr14	55475392	55475392	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgtcctcgaaatgttttCtgttggctgctatccatcac	7	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55475392C>A	ENST00000360586.3	-	5	452	c.387G>T	c.(385-387)caG>caT	p.Q129H	WDHD1_ENST00000420358.2_Missense_Mutation_p.Q6H|WDHD1_ENST00000421192.1_Missense_Mutation_p.Q6H	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	129					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.Q129H(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						GAAATGTTTTCTGTTGGCTGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	14											111	109	110					14																	55475392		2203	4300	6503	54545142	SO:0001583	missense	11169			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.387G>T	14.37:g.55475392C>A	ENSP00000353793:p.Gln129His		54545142	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847190	0.71603	.	.	ENSG00000198554	ENST00000360586;ENST00000421192;ENST00000420358;ENST00000455555	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.15	3.33	0.38152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63450	0.2512	L	0.38175	1.15	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.58707	-0.7589	10	0.33940	T	0.23	.	11.1938	0.48700	0.0:0.8518:0.0:0.1482	.	129	O75717	WDHD1_HUMAN	H	129;6;6;129	ENSP00000353793:Q129H;ENSP00000391049:Q6H;ENSP00000399349:Q6H;ENSP00000413435:Q129H	ENSP00000353793:Q129H	Q	-	3	2	WDHD1	54545142	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.586000	0.53950	0.681000	0.31386	0.591000	0.81541	CAG		0.358	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		A	55475392	C	A	55475392	3	1	61	1	0	0	0	0	1	0	0	0	17311	912	32	2	3090	2	WDHD1	14	55475392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27013	55475392	51874148	8933	16918										
SOCS4	122809	broad.mit.edu	37	chr14	55510690	55510690	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagggtacctttttacttCgagactcagcacaggaagac	10	10	1	3	rs372537919		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55510690C>T	ENST00000395472.2	+	2	1263	c.931C>T	c.(931-933)Cga>Tga	p.R311*	SOCS4_ENST00000555846.1_Nonsense_Mutation_p.R311*|SOCS4_ENST00000339298.2_Nonsense_Mutation_p.R311*	NM_080867.2|NM_199421.1	NP_543143.1|NP_955453.1	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	311	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				intracellular signal transduction (GO:0035556)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)			p.R311*(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	14						CTTTTTACTTCGAGACTCAGC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	14						C	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	121	122	122		931,931	4.9	1	14		122	0,8600		0,0,4300	no	stop-gained,stop-gained	SOCS4	NM_080867.2,NM_199421.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	311/441,311/441	55510690	1,13005	2203	4300	6503	54580443	SO:0001587	stop_gained	122809			AF424815	CCDS9722.1	14q22.1	2013-02-14	2004-02-25	2004-02-27	ENSG00000180008	ENSG00000180008		"Suppressors of cytokine signaling", "SH2 domain containing"	19392	protein-coding gene	gene with protein product			"suppressor of cytokine signaling 7"	SOCS7		12076535, 10500304	Standard	NM_080867		Approved		uc001xbp.3	Q8WXH5	OTTHUMG00000140311	ENST00000395472.2:c.931C>T	14.37:g.55510690C>T	ENSP00000378855:p.Arg311*		54580443		Nonsense_Mutation	SNP	ENST00000395472.2	37	CCDS9722.1	.	.	.	.	.	.	.	.	.	.	C	37	6.115190	0.97296	2.27E-4	0.0	ENSG00000180008	ENST00000395472;ENST00000555846;ENST00000339298	.	.	.	5.77	4.87	0.63330	.	0.000000	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2067	16.1994	0.82060	0.1342:0.8658:0.0:0.0	.	.	.	.	X	311	.	ENSP00000341327:R311X	R	+	1	2	SOCS4	54580443	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.958000	0.56737	1.406000	0.46857	-0.188000	0.12872	CGA		0.418	SOCS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276910.1			T	55510690	C	T	55510690	4	4	61	1	0	0	0	0	0	1	0	0	14953	876	31	1	933	1	SOCS4	14	55510690	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35298	55510690	51838850	8934	16919										
DLGAP5	9787	broad.mit.edu	37	chr14	55625286	55625286	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctgaaaaatccagcatcGaacactattttatcaacttc	3	11	2	1	rs139031197	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55625286G>A	ENST00000247191.2	-	14	2043	c.1827C>T	c.(1825-1827)ttC>ttT	p.F609F	DLGAP5_ENST00000395425.2_Silent_p.F609F	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	609					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)	p.F609F(2)		biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						ATCCAGCATCGAACACTATTT	0.333																																																2	Substitution - coding silent(2)	large_intestine(2)	14						G	,	0,4404		0,0,2202	100	95	97		1827,1827	0	1	14	dbSNP_134	97	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	DLGAP5	NM_001146015.1,NM_014750.4	,	0,3,6499	AA,AG,GG		0.0349,0.0,0.0231	,	609/843,609/847	55625286	3,13001	2202	4300	6502	54695039	SO:0001819	synonymous_variant	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1827C>T	14.37:g.55625286G>A			54695039	A8MTM6|B4DRM8|Q86T11|Q8NG58	Silent	SNP	ENST00000247191.2	37	CCDS9723.1																																																																																				0.333	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55625286	G	A	55625286	2	1	61	1	0	0	0	0	0	0	0	1	4574	1049	37	1		1	DLGAP5	14	55625286	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114596	55625286	51724254	8935	16920										
DLGAP5	9787	broad.mit.edu	37	chr14	55646352	55646352	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttattctctaccttgtCgggttttgtttctacatttt	6	7	2	0	rs368885720		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55646352C>A	ENST00000247191.2	-	7	985	c.769G>T	c.(769-771)Gac>Tac	p.D257Y	DLGAP5_ENST00000395425.2_Missense_Mutation_p.D257Y	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	257					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)	p.D257Y(1)		biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTACCTTGTCGGGTTTTGTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	14											123	109	114					14																	55646352		2203	4300	6503	54716105	SO:0001583	missense	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.769G>T	14.37:g.55646352C>A	ENSP00000247191:p.Asp257Tyr		54716105	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102019	0.37048	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.14022	2.55;2.54	4.37	4.37	0.52481	.	1.643360	0.02844	N	0.128298	T	0.39809	0.1092	M	0.61703	1.905	0.34009	D	0.651259	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.05666	-1.0871	10	0.87932	D	0	.	12.726	0.57170	0.0:1.0:0.0:0.0	.	257;257	A8MTM6;Q15398	.;DLGP5_HUMAN	Y	257	ENSP00000378815:D257Y;ENSP00000247191:D257Y	ENSP00000247191:D257Y	D	-	1	0	DLGAP5	54716105	0.440000	0.25618	0.973000	0.42090	0.086000	0.17979	1.009000	0.29886	2.721000	0.93114	0.655000	0.94253	GAC		0.299	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55646352	C	A	55646352	3	1	61	1	0	0	0	0	1	0	0	0	4574	884	31	2	1918	2	DLGAP5	14	55646352	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21066	55646352	51703188	8936	16921										
DLGAP5	9787	broad.mit.edu	37	chr14	55650280	55650280	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaagacactaaatttacctTttttggctcagctttcacag	5	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55650280T>G	ENST00000247191.2	-	3	646	c.430A>C	c.(430-432)Aag>Cag	p.K144Q	DLGAP5_ENST00000395425.2_Missense_Mutation_p.K144Q	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	144					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)	p.K144Q(1)		biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						AAATTTACCTTTTTTGGCTCA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											74	73	73					14																	55650280		2203	4300	6503	54720033	SO:0001583	missense	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.430A>C	14.37:g.55650280T>G	ENSP00000247191:p.Lys144Gln		54720033	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743451	0.69418	.	.	ENSG00000126787	ENST00000395425;ENST00000247191;ENST00000557645	T;T;T	0.55234	0.53;0.53;0.53	5.02	3.85	0.44370	.	1.130690	0.06517	N	0.739043	T	0.65842	0.2730	L	0.57536	1.79	0.31889	N	0.617428	P;D	0.69078	0.553;0.997	B;P	0.58520	0.203;0.84	T	0.57394	-0.7819	10	0.44086	T	0.13	.	11.1779	0.48610	0.0:0.0:0.1546:0.8454	.	144;144	A8MTM6;Q15398	.;DLGP5_HUMAN	Q	144	ENSP00000378815:K144Q;ENSP00000247191:K144Q;ENSP00000451747:K144Q	ENSP00000247191:K144Q	K	-	1	0	DLGAP5	54720033	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.816000	0.27267	1.017000	0.39495	0.533000	0.62120	AAG		0.323	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		G	55650280	T	G	55650280	3	3	61	1	0	0	0	0	1	0	0	0	4574	1850	64	4	2273	4	DLGAP5	14	55650280	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3928	55650280	51699260	8937	16922										
FBXO34	55030	broad.mit.edu	37	chr14	55819194	55819194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctgccacagctttaatCgggcaatccataagaaagca	8	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:55819194C>T	ENST00000313833.4	+	2	2331	c.2086C>T	c.(2086-2088)Cgg>Tgg	p.R696W	FBXO34_ENST00000440021.1_Missense_Mutation_p.R696W	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	696								p.R696W(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CAGCTTTAATCGGGCAATCCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14											36	36	36					14																	55819194		2203	4300	6503	54888947	SO:0001583	missense	55030			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.2086C>T	14.37:g.55819194C>T	ENSP00000313159:p.Arg696Trp		54888947	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.950415	0.34377	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.20332	2.08;2.08	6.17	4.34	0.51931	.	0.636558	0.13765	N	0.364265	T	0.38612	0.1047	M	0.67953	2.075	0.45318	D	0.998318	D	0.89917	1.0	P	0.62014	0.897	T	0.08229	-1.0732	10	0.72032	D	0.01	.	8.5678	0.33550	0.131:0.7576:0.0:0.1114	.	696	Q9NWN3	FBX34_HUMAN	W	696	ENSP00000313159:R696W;ENSP00000394117:R696W	ENSP00000313159:R696W	R	+	1	2	FBXO34	54888947	0.915000	0.31059	0.996000	0.52242	0.011000	0.07611	1.773000	0.38563	2.941000	0.99782	0.655000	0.94253	CGG		0.488	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			T	55819194	C	T	55819194	3	4	61	1	0	0	0	0	1	0	0	0	5763	875	31	1	2088	1	FBXO34	14	55819194	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168914	55819194	51530346	8938	16923										
KTN1	3895	broad.mit.edu	37	chr14	56083314	56083314	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctccaccaagagactaaAcaagaaagtggatcagggaa	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:56083314A>G	ENST00000395314.3	+	3	671	c.603A>G	c.(601-603)aaA>aaG	p.K201K	KTN1_ENST00000395308.1_Silent_p.K201K|KTN1_ENST00000395311.1_Silent_p.K201K|KTN1_ENST00000413890.2_Silent_p.K201K|KTN1_ENST00000416613.1_Silent_p.K201K|KTN1_ENST00000395309.3_Silent_p.K201K|KTN1_ENST00000438792.2_Silent_p.K201K	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	201					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K201K(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AAGAGACTAAACAAGAAAGTG	0.348			T	RET	papillary thryoid																																		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	2	Substitution - coding silent(2)	large_intestine(2)	14											81	75	77					14																	56083314		2203	4300	6503	55153067	SO:0001819	synonymous_variant	3895				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.603A>G	14.37:g.56083314A>G			55153067	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																				0.348	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56083314	A	G	56083314	2	3	61	1	0	0	0	0	0	0	0	1	8607	40	2	4		4	KTN1	14	56083314	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	264120	56083314	51266226	8939	16924										
KTN1	3895	broad.mit.edu	37	chr14	56118628	56118628	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatctatcacttccaaagtTcaggagcttcagaacttgta	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:56118628T>G	ENST00000395314.3	+	25	2654	c.2586T>G	c.(2584-2586)gtT>gtG	p.V862V	KTN1_ENST00000395308.1_Silent_p.V839V|KTN1_ENST00000395311.1_Silent_p.V839V|Y_RNA_ENST00000363872.1_RNA|KTN1_ENST00000413890.2_Silent_p.V839V|KTN1_ENST00000416613.1_Silent_p.V862V|KTN1_ENST00000395309.3_Silent_p.V862V|KTN1_ENST00000438792.2_Silent_p.V862V|KTN1_ENST00000554507.1_Silent_p.V157V	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	862					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.V862V(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						CTTCCAAAGTTCAGGAGCTTC	0.259			T	RET	papillary thryoid																																		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	2	Substitution - coding silent(2)	large_intestine(2)	14											60	59	60					14																	56118628		2200	4286	6486	55188381	SO:0001819	synonymous_variant	3895				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2586T>G	14.37:g.56118628T>G			55188381	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																				0.259	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56118628	T	G	56118628	2	3	61	1	0	0	0	0	0	0	0	1	8607	1770	62	4		4	KTN1	14	56118628	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	35314	56118628	51230912	8940	16925										
KTN1	3895	broad.mit.edu	37	chr14	56146308	56146308	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgagaaggagacaatgtCtgtaagtctaaatcagactg	10	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:56146308C>A	ENST00000395314.3	+	43	4042	c.3974C>A	c.(3973-3975)tCt>tAt	p.S1325Y	KTN1_ENST00000395308.1_Missense_Mutation_p.S1274Y|KTN1_ENST00000395311.1_Missense_Mutation_p.S1274Y|KTN1_ENST00000413890.2_Missense_Mutation_p.S1274Y|KTN1_ENST00000416613.1_Missense_Mutation_p.S1325Y|KTN1_ENST00000395309.3_Missense_Mutation_p.S1325Y|KTN1_ENST00000555573.1_Missense_Mutation_p.S302Y|KTN1_ENST00000438792.2_Missense_Mutation_p.S1268Y|KTN1_ENST00000554507.1_Missense_Mutation_p.S563Y	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1325					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.S1325Y(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						GAGACAATGTCTGTAAGTCTA	0.393			T	RET	papillary thryoid																																		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	2	Substitution - Missense(2)	large_intestine(2)	14											92	90	91					14																	56146308		2203	4300	6503	55216061	SO:0001583	missense	3895				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3974C>A	14.37:g.56146308C>A	ENSP00000378725:p.Ser1325Tyr		55216061	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.20|18.20	3.570765|3.570765	0.65765|0.65765	.|.	.|.	ENSG00000126777|ENSG00000126777	ENST00000554294|ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507;ENST00000555573	.|T;T;T;T;T;T;T;T;T	.|0.77358	.|1.47;1.44;1.48;1.44;1.47;1.47;1.44;-1.09;-1.09	6.17|6.17	2.38|2.38	0.29361|0.29361	.|.	.|0.380494	.|0.22699	.|N	.|0.056702	T|T	0.76140|0.76140	0.3946|0.3946	N|N	0.24115|0.24115	0.695|0.695	0.25348|0.25348	N|N	0.988892|0.988892	.|D;D;D;D;D;D	.|0.89917	.|0.998;0.998;0.998;1.0;0.996;0.996	.|D;D;D;D;D;D	.|0.87578	.|0.958;0.929;0.958;0.998;0.929;0.929	T|T	0.64516|0.64516	-0.6389|-0.6389	5|10	.|0.59425	.|D	.|0.04	1.2497|1.2497	5.3948|5.3948	0.16263|0.16263	0.1297:0.6016:0.0:0.2687|0.1297:0.6016:0.0:0.2687	.|.	.|302;1297;563;1268;1274;1325	.|B7Z6P3;B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.|.;.;.;.;.;KTN1_HUMAN	M|Y	96|1274;1325;1268;1325;1274;1274;1325;563;302	.|ENSP00000394992:S1274Y;ENSP00000378720:S1325Y;ENSP00000391964:S1268Y;ENSP00000378725:S1325Y;ENSP00000378719:S1274Y;ENSP00000378722:S1274Y;ENSP00000388807:S1325Y;ENSP00000452073:S563Y;ENSP00000451698:S302Y	.|ENSP00000334083:S120Y	L|S	+|+	1|2	2|0	KTN1|KTN1	55216061|55216061	1.000000|1.000000	0.71417|0.71417	0.375000|0.375000	0.26029|0.26029	0.932000|0.932000	0.56968|0.56968	3.187000|3.187000	0.50950|0.50950	0.183000|0.183000	0.20059|0.20059	0.655000|0.655000	0.94253|0.94253	CTG|TCT		0.393	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			A	56146308	C	A	56146308	3	1	61	1	0	0	0	0	1	0	0	0	8607	913	32	2	4140	2	KTN1	14	56146308	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27680	56146308	51203232	8941	16926										
C14orf101	54916	broad.mit.edu	37	chr14	57072378	57072378	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcataataccttggattCtctttcaacttttaaaaaag	5	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:57072378C>A	ENST00000261556.6	+	5	735	c.613C>A	c.(613-615)Ctc>Atc	p.L205I	TMEM260_ENST00000538838.1_Missense_Mutation_p.L205I|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	205						integral component of membrane (GO:0016021)		p.L205I(1)									ACCTTGGATTCTCTTTCAACT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	14											115	124	121					14																	57072378		2202	4298	6500	56142131	SO:0001583	missense	54916			AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.613C>A	14.37:g.57072378C>A	ENSP00000261556:p.Leu205Ile		56142131	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	37	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568338	0.65651	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.54071	1.15;0.59	5.59	5.59	0.84812	.	0.061586	0.64402	D	0.000003	T	0.66934	0.2840	M	0.82323	2.585	0.80722	D	1	D	0.53745	0.962	P	0.53450	0.726	T	0.67864	-0.5560	10	0.36615	T	0.2	-8.3084	13.897	0.63778	0.0:0.9274:0.0:0.0726	.	205	Q9NX78	CN101_HUMAN	I	205	ENSP00000261556:L205I;ENSP00000441934:L205I	ENSP00000261556:L205I	L	+	1	0	C14orf101	56142131	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.739000	0.62080	2.645000	0.89757	0.552000	0.68991	CTC		0.284	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57072378	C	A	57072378	3	1	61	1	0	0	0	0	1	0	0	0	1738	913	32	2	631	2	C14orf101	14	57072378	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	926070	57072378	50277162	8942	16927										
C14orf101	54916	broad.mit.edu	37	chr14	57082687	57082687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtaacaaatatgaggaccGaactctcattcaacatccaa	5	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:57082687G>A	ENST00000261556.6	+	8	1005	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	TMEM260_ENST00000538838.1_Missense_Mutation_p.E295K|TMEM260_ENST00000536419.1_5'UTR|TMEM260_ENST00000553335.1_3'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	295						integral component of membrane (GO:0016021)		p.E295K(2)									TATGAGGACCGAACTCTCATT	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	14											135	139	137					14																	57082687		2203	4299	6502	56152440	SO:0001583	missense	54916			AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.883G>A	14.37:g.57082687G>A	ENSP00000261556:p.Glu295Lys		56152440	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	37	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265191	0.40095	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.46819	1.44;0.86	5.89	4.02	0.46733	.	0.201414	0.51477	D	0.000093	T	0.39600	0.1084	L	0.57536	1.79	0.80722	D	1	B	0.32781	0.384	B	0.19666	0.026	T	0.17198	-1.0377	10	0.14252	T	0.57	-7.4479	14.9773	0.71283	0.0:0.2576:0.7424:0.0	.	295	Q9NX78	CN101_HUMAN	K	295	ENSP00000261556:E295K;ENSP00000441934:E295K	ENSP00000261556:E295K	E	+	1	0	C14orf101	56152440	0.976000	0.34144	0.880000	0.34516	0.620000	0.37586	1.822000	0.39052	0.740000	0.32651	0.585000	0.79938	GAA		0.313	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57082687	G	A	57082687	3	1	61	1	0	0	0	0	1	0	0	0	1738	1059	37	1	913	1	C14orf101	14	57082687	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10309	57082687	50266853	8943	16928										
MUDENG	55745	broad.mit.edu	37	chr14	57736101	57736101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtggcaccgtgagattCtccaggtaaatgcaaatctg	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:57736101C>A	ENST00000261558.3	+	1	475	c.69C>A	c.(67-69)ttC>ttA	p.F23L	AP5M1_ENST00000431972.2_Missense_Mutation_p.F23L|EXOC5_ENST00000340918.7_5'Flank|EXOC5_ENST00000413566.2_5'Flank	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	23					endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)		p.F23L(1)									CCGTGAGATTCTCCAGGTAAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	14											115	108	110					14																	57736101		2203	4300	6503	56805854	SO:0001583	missense	55745			AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.69C>A	14.37:g.57736101C>A	ENSP00000261558:p.Phe23Leu		56805854	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	37	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366150	0.82463	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.33865	1.39;1.41	5.93	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.36496	0.0969	M	0.69823	2.125	0.58432	D	0.999995	B;P	0.40619	0.289;0.724	B;B	0.38458	0.07;0.274	T	0.22800	-1.0206	10	0.66056	D	0.02	.	8.9522	0.35796	0.0:0.771:0.0:0.229	.	23;23	Q9H0R1;Q9H0R1-2	MUDEN_HUMAN;.	L	23	ENSP00000261558:F23L;ENSP00000390531:F23L	ENSP00000261558:F23L	F	+	3	2	MUDENG	56805854	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.273000	0.33121	0.837000	0.34925	0.655000	0.94253	TTC		0.493	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		A	57736101	C	A	57736101	3	1	61	1	0	0	0	0	1	0	0	0	10013	912	32	2	71	2	MUDENG	14	57736101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	653414	57736101	49613439	8944	16929										
SLC35F4	341880	broad.mit.edu	37	chr14	58031063	58031063	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagccaggcggacaacattGaatatcacctcctgctttag	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58031063G>T	ENST00000339762.6	-	8	1355	c.1356C>A	c.(1354-1356)ttC>ttA	p.F452L	SLC35F4_ENST00000554729.1_Missense_Mutation_p.F293L|SLC35F4_ENST00000556826.1_Missense_Mutation_p.F416L			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	452					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.F452L(2)		breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGACAACATTGAATATCACCT	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	14											60	60	60					14																	58031063		1977	4159	6136	57100816	SO:0001583	missense	341880					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"Solute carriers"	19845	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 36"	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.1356C>A	14.37:g.58031063G>T	ENSP00000342518:p.Phe452Leu		57100816	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		.	.	.	.	.	.	.	.	.	.	G	16.57	3.161334	0.57368	.	.	ENSG00000151812	ENST00000556826;ENST00000339762;ENST00000554729	T;T;T	0.48522	0.85;0.81;0.9	5.15	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.46658	0.1404	M	0.68593	2.085	0.80722	D	1	B	0.12013	0.005	B	0.13407	0.009	T	0.41520	-0.9504	10	0.33940	T	0.23	-17.1737	13.9048	0.63828	0.0741:0.0:0.9259:0.0	.	452	A4IF30	S35F4_HUMAN	L	416;452;293	ENSP00000452086:F416L;ENSP00000342518:F452L;ENSP00000451990:F293L	ENSP00000342518:F452L	F	-	3	2	SLC35F4	57100816	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.976000	0.88070	1.295000	0.44724	0.460000	0.39030	TTC		0.443	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260		T	58031063	G	T	58031063	3	4	61	1	0	0	0	0	1	0	0	0	14628	1281	45	2	213	2	SLC35F4	14	58031063	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	294962	58031063	49318477	8945	16930										
SLC35F4	341880	broad.mit.edu	37	chr14	58036615	58036615	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggggtgaaggagatgaaGatcaaattgaagaaacccaa	12	5	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58036615G>T	ENST00000339762.6	-	6	1124	c.1125C>A	c.(1123-1125)atC>atA	p.I375I	SLC35F4_ENST00000554729.1_Silent_p.I216I|SLC35F4_ENST00000556826.1_Silent_p.I339I			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	375					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.I375I(2)		breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGGAGATGAAGATCAAATTGA	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	14											58	64	62					14																	58036615		1942	4143	6085	57106368	SO:0001819	synonymous_variant	341880					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"Solute carriers"	19845	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 36"	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.1125C>A	14.37:g.58036615G>T			57106368	A6NDQ3	Silent	SNP	ENST00000339762.6	37																																																																																					0.478	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260		T	58036615	G	T	58036615	2	4	61	1	0	0	0	0	0	0	0	1	14628	932	33	2		2	SLC35F4	14	58036615	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5552	58036615	49312925	8946	16931										
ACTR10	55860	broad.mit.edu	37	chr14	58698938	58698938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttggcactaagacatttcGaattcatactccacctgcaa	5	12	1	1	rs554639681	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58698938G>A	ENST00000254286.4	+	12	1105	c.1025G>A	c.(1024-1026)cGa>cAa	p.R342Q		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	342					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)		p.R342Q(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						AAGACATTTCGAATTCATACT	0.343													G|||	2	0.000399361	0	0	5008	,	,		12160	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	14											89	98	95					14																	58698938		2203	4300	6503	57768691	SO:0001583	missense	55860			AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.1025G>A	14.37:g.58698938G>A	ENSP00000254286:p.Arg342Gln		57768691	Q9H9Y5|Q9NWY2	Missense_Mutation	SNP	ENST00000254286.4	37	CCDS32090.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.450420	0.63290	.	.	ENSG00000131966	ENST00000254286	D	0.95171	-3.63	5.77	3.91	0.45181	.	0.255144	0.36002	N	0.002853	D	0.86686	0.5992	L	0.31752	0.955	0.40035	D	0.975578	P;P	0.42248	0.774;0.604	B;B	0.34385	0.181;0.095	T	0.82370	-0.0491	9	.	.	.	-4.6272	5.9264	0.19114	0.21:0.0:0.6522:0.1377	.	342;342	Q53H79;Q9NZ32	.;ARP10_HUMAN	Q	342	ENSP00000254286:R342Q	.	R	+	2	0	ACTR10	57768691	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.797000	0.62503	0.869000	0.35703	0.655000	0.94253	CGA		0.343	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1			A	58698938	G	A	58698938	3	1	61	1	0	0	0	0	1	0	0	0	208	1058	37	1	1071	1	ACTR10	14	58698938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	662323	58698938	48650602	8947	16932										
PSMA3	5684	broad.mit.edu	37	chr14	58724656	58724656	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatagcatcttgcagacaGagtggccatgtatgtgcatg	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58724656G>T	ENST00000216455.4	+	5	434	c.344G>T	c.(343-345)aGa>aTa	p.R115I	PSMA3_ENST00000412908.2_Missense_Mutation_p.R115I|PSMA3_ENST00000557508.1_Missense_Mutation_p.R40I	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)	p.R115I(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						CTTGCAGACAGAGTGGCCATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	14											112	109	110					14																	58724656		2203	4300	6503	57794409	SO:0001583	missense	5684				CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"Proteasome (prosome, macropain) subunits"	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.344G>T	14.37:g.58724656G>T	ENSP00000216455:p.Arg115Ile		57794409	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	37	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848322	0.91277	.	.	ENSG00000100567	ENST00000216455;ENST00000412908;ENST00000557508;ENST00000553677	T;T;T	0.23754	1.89;1.89;1.89	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.63873	0.2548	M	0.94142	3.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.70487	0.948;0.969	T	0.75747	-0.3209	10	0.87932	D	0	-5.7676	18.9069	0.92466	0.0:0.0:1.0:0.0	.	115;115	P25788-2;P25788	.;PSA3_HUMAN	I	115;115;40;5	ENSP00000216455:R115I;ENSP00000390491:R115I;ENSP00000452056:R40I	ENSP00000216455:R115I	R	+	2	0	PSMA3	57794409	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.119000	0.94362	2.552000	0.86080	0.655000	0.94253	AGA		0.383	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1	NM_002788		T	58724656	G	T	58724656	3	4	61	1	0	0	0	0	1	0	0	0	12702	942	33	2	362	2	PSMA3	14	58724656	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25718	58724656	48624884	8948	16933										
ARID4A	5926	broad.mit.edu	37	chr14	58833731	58833731	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggagaaaaagattaaaAaagaaagacagggaaggtaa	13	1	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58833731A>C	ENST00000355431.3	+	23	4027	c.3654A>C	c.(3652-3654)aaA>aaC	p.K1218N	ARID4A_ENST00000431317.2_Missense_Mutation_p.K1149N|ARID4A_ENST00000395168.3_Missense_Mutation_p.K1164N|ARID4A_ENST00000348476.3_Missense_Mutation_p.K1149N	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1218					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K1218N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AAAGATTAAAAAAGAAAGACA	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	14											41	47	45					14																	58833731		2196	4273	6469	57903484	SO:0001583	missense	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.3654A>C	14.37:g.58833731A>C	ENSP00000347602:p.Lys1218Asn		57903484	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.015723	0.75161	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317	T;T;T;T	0.27104	1.69;1.97;1.95;1.97	5.59	5.59	0.84812	.	0.043264	0.85682	D	0.000000	T	0.51466	0.1676	M	0.71581	2.175	0.31771	N	0.632157	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.991;0.999	T	0.62859	-0.6765	10	0.87932	D	0	-28.851	15.7641	0.78110	1.0:0.0:0.0:0.0	.	1149;1218;1164	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	N	1218;1149;1164;1149	ENSP00000347602:K1218N;ENSP00000344556:K1149N;ENSP00000378597:K1164N;ENSP00000397368:K1149N	ENSP00000344556:K1149N	K	+	3	2	ARID4A	57903484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.735000	0.68587	2.122000	0.65172	0.477000	0.44152	AAA		0.284	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58833731	A	C	58833731	3	2	61	1	0	0	0	0	1	0	0	0	919	11	1	4	3740	4	ARID4A	14	58833731	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	109075	58833731	48515809	8949	16934										
KIAA0586	9786	broad.mit.edu	37	chr14	58927786	58927786	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagtttatcagggccatcGaagcactcttaaaaaaggac	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58927786G>A	ENST00000556134.1	+	15	2196	c.1922G>A	c.(1921-1923)cGa>cAa	p.R641Q	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Missense_Mutation_p.R580Q|KIAA0586_ENST00000423743.3_Missense_Mutation_p.R612Q|KIAA0586_ENST00000354386.6_Missense_Mutation_p.R709Q	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	641					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.R580Q(1)|p.R709Q(1)		endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CAGGGCCATCGAAGCACTCTT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	14											104	94	97					14																	58927786		1854	4109	5963	57997539	SO:0001583	missense	9786			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.1922G>A	14.37:g.58927786G>A	ENSP00000452351:p.Arg641Gln		57997539	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151484	0.94645	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000002	T	0.66799	0.2826	L	0.36672	1.1	0.47547	D	0.999451	D;D;D;P;D;D	0.89917	1.0;1.0;0.998;0.952;1.0;1.0	D;D;P;P;D;D	0.91635	0.999;0.999;0.845;0.463;0.999;0.999	T	0.67699	-0.5603	10	0.72032	D	0.01	.	20.0589	0.97667	0.0:0.0:1.0:0.0	.	516;516;709;580;641;612	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	Q	709;641;612;580;516	ENSP00000346359:R709Q;ENSP00000452351:R641Q;ENSP00000399427:R612Q;ENSP00000261244:R580Q	ENSP00000261244:R580Q	R	+	2	0	KIAA0586	57997539	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.472000	0.80996	2.732000	0.93576	0.650000	0.86243	CGA		0.378	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		A	58927786	G	A	58927786	3	1	61	1	0	0	0	0	1	0	0	0	8207	1058	37	1	1789	1	KIAA0586	14	58927786	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94055	58927786	48421754	8950	16935										
KIAA0586	9786	broad.mit.edu	37	chr14	58941367	58941367	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagactctgaaccaattCtggagtttaacagaagtgtt	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58941367C>A	ENST00000556134.1	+	20	2906	c.2632C>A	c.(2632-2634)Ctg>Atg	p.L878M	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Missense_Mutation_p.L817M|KIAA0586_ENST00000423743.3_Missense_Mutation_p.L849M|KIAA0586_ENST00000354386.6_Missense_Mutation_p.L946M	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	878					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.L946M(1)|p.L817M(1)		endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGAACCAATTCTGGAGTTTAA	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	14											41	40	40					14																	58941367		1818	4072	5890	58011120	SO:0001583	missense	9786			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.2632C>A	14.37:g.58941367C>A	ENSP00000452351:p.Leu878Met		58011120	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815368	0.50527	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.19	1.65	0.23941	.	0.117279	0.37577	N	0.002022	T	0.73156	0.3551	M	0.74881	2.28	0.31916	N	0.614094	D;D;D;D;D;D	0.89917	0.998;0.998;1.0;1.0;0.998;0.998	D;D;D;D;D;D	0.91635	0.964;0.964;0.999;0.998;0.964;0.964	T	0.73623	-0.3924	10	0.72032	D	0.01	.	6.1661	0.20390	0.0:0.5978:0.1295:0.2728	.	753;753;946;817;878;849	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	M	946;878;849;817;753	ENSP00000346359:L946M;ENSP00000452351:L878M;ENSP00000399427:L849M;ENSP00000261244:L817M	ENSP00000261244:L817M	L	+	1	2	KIAA0586	58011120	0.206000	0.23470	0.996000	0.52242	0.870000	0.49936	0.161000	0.16481	0.314000	0.23086	-0.282000	0.10007	CTG		0.348	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		A	58941367	C	A	58941367	3	1	61	1	0	0	0	0	1	0	0	0	8207	912	32	2	2519	2	KIAA0586	14	58941367	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13581	58941367	48408173	8951	16936										
KIAA0586	9786	broad.mit.edu	37	chr14	58955584	58955584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctgtggtcaaaaattggCccccaagagtaagttaattt	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:58955584C>T	ENST00000556134.1	+	25	4002	c.3728C>T	c.(3727-3729)gCc>gTc	p.A1243V	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Missense_Mutation_p.A1182V|KIAA0586_ENST00000423743.3_Missense_Mutation_p.A1214V|KIAA0586_ENST00000354386.6_Missense_Mutation_p.A1311V	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1243					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.A1311V(1)|p.A1182V(1)		endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CAAAAATTGGCCCCCAAGAGT	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	14											57	57	57					14																	58955584		1806	4074	5880	58025337	SO:0001583	missense	9786			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.3728C>T	14.37:g.58955584C>T	ENSP00000452351:p.Ala1243Val		58025337	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.924314	0.73213	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.38	3.56	0.40772	.	0.256881	0.37095	N	0.002245	T	0.54983	0.1892	.	.	.	0.33561	D	0.597346	P;P;P;B;B	0.51537	0.465;0.946;0.734;0.077;0.077	B;P;B;B;B	0.48677	0.148;0.586;0.203;0.046;0.046	T	0.68595	-0.5367	9	0.56958	D	0.05	.	11.5412	0.50667	0.0:0.8533:0.0:0.1467	.	1118;1311;1182;1243;1214	B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;K0586_HUMAN;.	V	1311;1243;1214;1182	ENSP00000346359:A1311V;ENSP00000452351:A1243V;ENSP00000399427:A1214V;ENSP00000261244:A1182V	ENSP00000261244:A1182V	A	+	2	0	KIAA0586	58025337	0.998000	0.40836	0.155000	0.22561	0.941000	0.58515	2.321000	0.43805	0.766000	0.33244	0.585000	0.79938	GCC		0.318	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		T	58955584	C	T	58955584	3	4	61	1	0	0	0	0	1	0	0	0	8207	739	26	3	3635	3	KIAA0586	14	58955584	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14217	58955584	48393956	8952	16937										
DACT1	51339	broad.mit.edu	37	chr14	59112032	59112032	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaagaccaggcctcagggGcagtttgccgttccctctcc	12	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:59112032G>A	ENST00000335867.4	+	4	715	c.691G>A	c.(691-693)Gca>Aca	p.A231T	DACT1_ENST00000541264.2_Intron|DACT1_ENST00000555845.1_Intron|DACT1_ENST00000395153.3_Intron|DACT1_ENST00000556859.1_Intron			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	231					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)	p.A231T(1)		endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GGCCTCAGGGGCAGTTTGCCG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	115	119					14																	59112032		2203	4300	6503	58181785	SO:0001583	missense	51339			AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.691G>A	14.37:g.59112032G>A	ENSP00000337439:p.Ala231Thr		58181785	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	G	2.705	-0.269987	0.05716	.	.	ENSG00000165617	ENST00000335867	T	0.41758	0.99	5.41	2.55	0.30701	.	0.491785	0.21510	N	0.073384	T	0.16599	0.0399	N	0.10685	0.025	0.09310	N	0.999993	B	0.06786	0.001	B	0.04013	0.001	T	0.25012	-1.0144	10	0.08599	T	0.76	-2.0246	4.4329	0.11536	0.3943:0.0:0.4513:0.1544	.	231	Q9NYF0	DACT1_HUMAN	T	231	ENSP00000337439:A231T	ENSP00000337439:A231T	A	+	1	0	DACT1	58181785	0.344000	0.24827	0.957000	0.39632	0.988000	0.76386	0.460000	0.21924	0.332000	0.23536	0.563000	0.77884	GCA		0.433	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		A	59112032	G	A	59112032	3	1	61	1	0	0	0	0	1	0	0	0	4228	1203	42	3	705	3	DACT1	14	59112032	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	156448	59112032	48237508	8953	16938										
RTN1	6252	broad.mit.edu	37	chr14	60212801	60212801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtctttatcttccagctCggggtgatgttgttcttggt	11	8	3	1	rs370975029		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:60212801C>T	ENST00000267484.5	-	2	975	c.640G>A	c.(640-642)Gag>Aag	p.E214K		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	214					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)		p.E214K(1)		central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCTTCCAGCTCGGGGTGATGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	249	245	246		640	1.1	0	14		246	0,8600		0,0,4300	no	missense	RTN1	NM_021136.2	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	214/777	60212801	1,13005	2203	4300	6503	59282554	SO:0001583	missense	6252			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.640G>A	14.37:g.60212801C>T	ENSP00000267484:p.Glu214Lys		59282554	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	37	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	2.398	-0.338267	0.05278	2.27E-4	0.0	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.21543	2.0	5.7	1.1	0.20463	.	1.068380	0.07080	N	0.836868	T	0.08758	0.0217	N	0.03115	-0.41	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35674	-0.9779	10	0.09084	T	0.74	.	8.8423	0.35148	0.0:0.7084:0.0:0.2916	.	214	Q16799	RTN1_HUMAN	K	214;140	ENSP00000267484:E214K	ENSP00000267484:E214K	E	-	1	0	RTN1	59282554	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.457000	0.21875	0.210000	0.20664	-0.259000	0.10710	GAG		0.468	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			T	60212801	C	T	60212801	3	4	61	1	0	0	0	0	1	0	0	0	13762	893	31	1	1787	1	RTN1	14	60212801	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1100769	60212801	47136739	8954	16939										
C14orf135	64430	broad.mit.edu	37	chr14	60581927	60581927	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattagtcttggctcttttaGaaactagcttgcttcatcac	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:60581927G>T	ENST00000406854.1	+	4	1659	c.1105G>T	c.(1105-1107)Gaa>Taa	p.E369*	PCNXL4_ENST00000317623.4_Nonsense_Mutation_p.E135*|PCNXL4_ENST00000404681.2_Nonsense_Mutation_p.E369*|PCNXL4_ENST00000406949.1_Nonsense_Mutation_p.E135*			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	369						integral component of membrane (GO:0016021)		p.E369*(1)|p.E135*(1)									GGCTCTTTTAGAAACTAGCTT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											157	144	148					14																	60581927		1823	4081	5904	59651680	SO:0001587	stop_gained	64430			AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1105G>T	14.37:g.60581927G>T	ENSP00000384801:p.Glu369*		59651680	A8MXM2|Q9BQG8|Q9H9F2	Nonsense_Mutation	SNP	ENST00000406854.1	37		.	.	.	.	.	.	.	.	.	.	G	42	9.306797	0.99132	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	19.5267	0.95209	0.0:0.0:1.0:0.0	.	.	.	.	X	135;369;135;369	.	ENSP00000317396:E135X	E	+	1	0	C14orf135	59651680	1.000000	0.71417	0.801000	0.32222	0.805000	0.45488	8.837000	0.92110	2.677000	0.91161	0.462000	0.41574	GAA		0.363	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		T	60581927	G	T	60581927	4	4	61	1	0	0	0	0	0	1	0	0	1749	943	33	2	409	2	C14orf135	14	60581927	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	369126	60581927	46767613	8955	16940										
C14orf39	317761	broad.mit.edu	37	chr14	60935224	60935224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttccagagtttctgaaaGagccttagtttcattatgcc	7	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:60935224G>T	ENST00000321731.3	-	9	865	c.706C>A	c.(706-708)Ctt>Att	p.L236I		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	236					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)			p.L236I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GTTTCTGAAAGAGCCTTAGTT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	14											68	71	70					14																	60935224		2199	4282	6481	60004977	SO:0001583	missense	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.706C>A	14.37:g.60935224G>T	ENSP00000324920:p.Leu236Ile		60004977	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.345863	0.24426	.	.	ENSG00000179008	ENST00000321731	T	0.24151	1.87	5.1	4.2	0.49525	.	0.379769	0.22745	N	0.056149	T	0.26521	0.0648	L	0.48362	1.52	0.23132	N	0.998247	P	0.49961	0.93	P	0.47645	0.553	T	0.07347	-1.0777	10	0.32370	T	0.25	-15.2725	8.8344	0.35104	0.1035:0.0:0.8965:0.0	.	236	Q8N1H7	S6OS1_HUMAN	I	236	ENSP00000324920:L236I	ENSP00000324920:L236I	L	-	1	0	C14orf39	60004977	0.964000	0.33143	0.997000	0.53966	0.535000	0.34838	0.799000	0.27028	1.480000	0.48289	0.655000	0.94253	CTT		0.289	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		T	60935224	G	T	60935224	3	4	61	1	0	0	0	0	1	0	0	0	1776	942	33	2	1097	2	C14orf39	14	60935224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	353297	60935224	46414316	8956	16941										
C14orf39	317761	broad.mit.edu	37	chr14	60945052	60945052	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccttgataaacagtaaAttggtcctgcatataatctt	6	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:60945052A>C	ENST00000321731.3	-	5	448	c.289T>G	c.(289-291)Ttt>Gtt	p.F97V		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	97					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)			p.F97V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TAAACAGTAAATTGGTCCTGC	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	14											76	75	75					14																	60945052		2201	4294	6495	60014805	SO:0001583	missense	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.289T>G	14.37:g.60945052A>C	ENSP00000324920:p.Phe97Val		60014805	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	A	4.750	0.139377	0.09083	.	.	ENSG00000179008	ENST00000321731;ENST00000555476	T;T	0.48201	1.86;0.82	5.56	0.459	0.16678	.	0.516547	0.20860	N	0.084363	T	0.38321	0.1036	L	0.56769	1.78	0.09310	N	1	P	0.35575	0.51	B	0.34536	0.185	T	0.24657	-1.0154	10	0.59425	D	0.04	-0.6435	6.4142	0.21708	0.5761:0.1243:0.2995:0.0	.	97	Q8N1H7	S6OS1_HUMAN	V	97;68	ENSP00000324920:F97V;ENSP00000451665:F68V	ENSP00000324920:F97V	F	-	1	0	C14orf39	60014805	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.191000	0.17076	-0.348000	0.08286	-1.162000	0.01777	TTT		0.284	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		C	60945052	A	C	60945052	3	2	61	1	0	0	0	0	1	0	0	0	1776	101	4	4	1530	4	C14orf39	14	60945052	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9828	60945052	46404488	8957	16942										
SIX4	51804	broad.mit.edu	37	chr14	61180285	61180285	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttgttgctttgctctcaGaatttgataagaaattctct	6	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61180285G>A	ENST00000216513.4	-	3	2245	c.2186C>T	c.(2185-2187)tCt>tTt	p.S729F		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	729					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S729F(1)		breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		TTTGCTCTCAGAATTTGATAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											114	110	112					14																	61180285		2203	4300	6503	60250038	SO:0001583	missense	51804			AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.2186C>T	14.37:g.61180285G>A	ENSP00000216513:p.Ser729Phe		60250038	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796743	0.70567	.	.	ENSG00000100625	ENST00000216513;ENST00000554079	D;T	0.93019	-3.15;0.48	5.63	5.63	0.86233	.	0.000000	0.49916	D	0.000135	D	0.93533	0.7936	N	0.19112	0.55	0.80722	D	1	D	0.67145	0.996	P	0.61328	0.887	D	0.94436	0.7654	10	0.87932	D	0	.	20.0396	0.97574	0.0:0.0:1.0:0.0	.	729	Q9UIU6	SIX4_HUMAN	F	729;402	ENSP00000216513:S729F;ENSP00000451537:S402F	ENSP00000216513:S729F	S	-	2	0	SIX4	60250038	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.711000	0.84669	2.814000	0.96858	0.563000	0.77884	TCT		0.423	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			A	61180285	G	A	61180285	3	1	61	1	0	0	0	0	1	0	0	0	14386	942	33	3	163	3	SIX4	14	61180285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	235233	61180285	46169255	8958	16943										
SIX4	51804	broad.mit.edu	37	chr14	61180674	61180674	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgcaggccactccccgaGatgttttcagaagacaggtt	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61180674G>T	ENST00000216513.4	-	3	1856	c.1797C>A	c.(1795-1797)atC>atA	p.I599I		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	599					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I599I(1)		breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		CACTCCCCGAGATGTTTTCAG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	14											66	66	66					14																	61180674		2203	4300	6503	60250427	SO:0001819	synonymous_variant	51804			AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1797C>A	14.37:g.61180674G>T			60250427	Q4QQH5|Q4V764	Silent	SNP	ENST00000216513.4	37	CCDS9749.2																																																																																				0.453	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			T	61180674	G	T	61180674	2	4	61	1	0	0	0	0	0	0	0	1	14386	932	33	2		2	SIX4	14	61180674	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	389	61180674	46168866	8959	16944										
TRMT5	57570	broad.mit.edu	37	chr14	61442504	61442504	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacgtgcacagagggttttCtttcttttgacagacccagc	9	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61442504C>A	ENST00000261249.6	-	4	1517	c.1133G>T	c.(1132-1134)aGa>aTa	p.R378I	RP11-193F5.1_ENST00000553946.1_RNA|RNU6-398P_ENST00000384143.1_RNA	NM_020810.2	NP_065861.2			tRNA methyltransferase 5									p.R378I(1)		NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(1)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0873)		AGAGGGTTTTCTTTCTTTTGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	14											90	90	90					14																	61442504		2203	4300	6503	60512257	SO:0001583	missense	57570			AB037814	CCDS32092.1	14q23.1	2013-06-05	2013-06-05	2005-08-11		ENSG00000126814	2.1.1.228		23141	protein-coding gene	gene with protein product	"tRNA (guanine(37)-N1)-methyltransferase"	611023	"KIAA1393", "tRNA methyltransferase 5 homolog (S. cerevisiae)"	KIAA1393		15248782	Standard	XM_005267916		Approved	TRM5	uc001xff.4	Q32P41		ENST00000261249.6:c.1133G>T	14.37:g.61442504C>A	ENSP00000261249:p.Arg378Ile		60512257		Missense_Mutation	SNP	ENST00000261249.6	37	CCDS32092.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.565883	0.45694	.	.	ENSG00000126814	ENST00000261249	T	0.25085	1.82	6.08	5.18	0.71444	.	0.387375	0.33631	N	0.004707	T	0.17577	0.0422	N	0.17474	0.49	0.37549	D	0.918605	B	0.29432	0.244	B	0.36030	0.216	T	0.18398	-1.0338	10	0.35671	T	0.21	-6.1084	7.9744	0.30147	0.0:0.7225:0.1413:0.1362	.	378	Q32P41	TRM5_HUMAN	I	378	ENSP00000261249:R378I	ENSP00000261249:R378I	R	-	2	0	TRMT5	60512257	0.064000	0.20934	1.000000	0.80357	0.997000	0.91878	0.391000	0.20784	1.560000	0.49568	0.655000	0.94253	AGA		0.458	TRMT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412831.1	NM_02081		A	61442504	C	A	61442504	3	1	61	1	0	0	0	0	1	0	0	0	16607	913	32	2	404	2	TRMT5	14	61442504	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	261830	61442504	45907036	8960	16945										
TRMT5	57570	broad.mit.edu	37	chr14	61442568	61442568	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtccttggaggaagtcttTcccatccaagttgaagactt	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61442568T>G	ENST00000261249.6	-	4	1453	c.1069A>C	c.(1069-1071)Aaa>Caa	p.K357Q	RP11-193F5.1_ENST00000553946.1_RNA|RNU6-398P_ENST00000384143.1_RNA	NM_020810.2	NP_065861.2			tRNA methyltransferase 5									p.K357Q(1)		NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(1)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0873)		AGGAAGTCTTTCCCATCCAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	14											102	102	102					14																	61442568		2203	4300	6503	60512321	SO:0001583	missense	57570			AB037814	CCDS32092.1	14q23.1	2013-06-05	2013-06-05	2005-08-11		ENSG00000126814	2.1.1.228		23141	protein-coding gene	gene with protein product	"tRNA (guanine(37)-N1)-methyltransferase"	611023	"KIAA1393", "tRNA methyltransferase 5 homolog (S. cerevisiae)"	KIAA1393		15248782	Standard	XM_005267916		Approved	TRM5	uc001xff.4	Q32P41		ENST00000261249.6:c.1069A>C	14.37:g.61442568T>G	ENSP00000261249:p.Lys357Gln		60512321		Missense_Mutation	SNP	ENST00000261249.6	37	CCDS32092.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118065	0.56505	.	.	ENSG00000126814	ENST00000261249	T	0.22539	1.95	6.17	0.699	0.18093	.	0.181637	0.56097	N	0.000023	T	0.15825	0.0381	L	0.28400	0.85	0.25954	N	0.982717	B	0.26512	0.151	B	0.33121	0.158	T	0.22243	-1.0222	10	0.66056	D	0.02	-13.3591	8.9335	0.35686	0.0:0.0626:0.3591:0.5783	.	357	Q32P41	TRM5_HUMAN	Q	357	ENSP00000261249:K357Q	ENSP00000261249:K357Q	K	-	1	0	TRMT5	60512321	0.400000	0.25295	0.951000	0.38953	0.990000	0.78478	0.550000	0.23345	0.156000	0.19299	0.533000	0.62120	AAA		0.413	TRMT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412831.1	NM_02081		G	61442568	T	G	61442568	3	3	61	1	0	0	0	0	1	0	0	0	16607	1792	62	4	468	4	TRMT5	14	61442568	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	64	61442568	45906972	8961	16946										
SLC38A6	145389	broad.mit.edu	37	chr14	61497177	61497177	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcagctatgtcatcttatCttttaattattaaaacagag	5	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61497177C>A	ENST00000267488.4	+	6	534	c.418C>A	c.(418-420)Ctt>Att	p.L140I	SLC38A6_ENST00000354886.2_Missense_Mutation_p.L140I|SLC38A6_ENST00000456840.2_Missense_Mutation_p.L117I	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	140					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.L140I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		GTCATCTTATCTTTTAATTAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	14											59	61	60					14																	61497177		2202	4295	6497	60566930	SO:0001583	missense	145389			AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.418C>A	14.37:g.61497177C>A	ENSP00000267488:p.Leu140Ile		60566930	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783896	0.70222	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105	T;T;T;T;T	0.02787	4.16;4.16;4.16;4.16;4.16	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.14485	0.0350	M	0.79475	2.455	0.45528	D	0.998486	D;D;D	0.89917	0.997;0.996;1.0	D;D;D	0.91635	0.957;0.928;0.999	T	0.00019	-1.2362	10	0.72032	D	0.01	.	12.5549	0.56248	0.0:0.9233:0.0:0.0767	.	117;140;140	E7ETF2;Q8IZM9-2;Q8IZM9	.;.;S38A6_HUMAN	I	140;140;135;117;86	ENSP00000346959:L140I;ENSP00000267488:L140I;ENSP00000395851:L135I;ENSP00000413863:L117I;ENSP00000451244:L86I	ENSP00000267488:L140I	L	+	1	0	SLC38A6	60566930	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.779000	0.47734	2.611000	0.88343	0.655000	0.94253	CTT		0.308	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			A	61497177	C	A	61497177	3	1	61	1	0	0	0	0	1	0	0	0	14645	913	32	2	440	2	SLC38A6	14	61497177	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54609	61497177	45852363	8962	16947										
PRKCH	5583	broad.mit.edu	37	chr14	61917629	61917629	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaactacaaagtgccaacaTtctgcgatcactgtggctca	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:61917629T>G	ENST00000332981.5	+	6	1157	c.772T>G	c.(772-774)Ttc>Gtc	p.F258V	PRKCH_ENST00000555082.1_Missense_Mutation_p.F97V	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	258					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)	p.F258V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		AGTGCCAACATTCTGCGATCA	0.473																																					Melanoma(135;863 1779 8064 14443 26348)											1	Substitution - Missense(1)	large_intestine(1)	14											172	137	149					14																	61917629		2203	4300	6503	60987382	SO:0001583	missense	5583			M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.772T>G	14.37:g.61917629T>G	ENSP00000329127:p.Phe258Val		60987382	B4DJN5|Q16246|Q8NE03	Missense_Mutation	SNP	ENST00000332981.5	37	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.992183	0.93167	.	.	ENSG00000027075	ENST00000556778;ENST00000332981;ENST00000555082;ENST00000557585;ENST00000557473	D;D;D;T;D	0.93763	-3.28;-3.28;-3.28;1.07;-1.9	5.79	5.79	0.91817	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.158096	0.44483	D	0.000456	D	0.95576	0.8562	M	0.81112	2.525	0.80722	D	1	P	0.37158	0.585	P	0.48400	0.576	D	0.95834	0.8860	10	0.87932	D	0	.	16.1627	0.81731	0.0:0.0:0.0:1.0	.	258	P24723	KPCL_HUMAN	V	97;258;97;97;97	ENSP00000452055:F97V;ENSP00000329127:F258V;ENSP00000450981:F97V;ENSP00000451930:F97V;ENSP00000452528:F97V	ENSP00000329127:F258V	F	+	1	0	PRKCH	60987382	1.000000	0.71417	0.980000	0.43619	0.907000	0.53573	8.015000	0.88690	2.229000	0.72834	0.472000	0.43445	TTC		0.473	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		G	61917629	T	G	61917629	3	3	61	1	0	0	0	0	1	0	0	0	12547	1493	52	4	794	4	PRKCH	14	61917629	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	420452	61917629	45431911	8963	16948										
HIF1A	3091	broad.mit.edu	37	chr14	62187161	62187161	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagatctcggcgaagtaaaGaatctgaagttttttatgag	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:62187161G>T	ENST00000337138.4	+	2	362	c.97G>T	c.(97-99)Gaa>Taa	p.E33*	HIF1A_ENST00000539097.1_Nonsense_Mutation_p.E57*|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000394997.1_Nonsense_Mutation_p.E34*|HIF1A_ENST00000557538.1_5'UTR|HIF1A_ENST00000557206.1_3'UTR|HIF1A_ENST00000323441.6_Nonsense_Mutation_p.E33*	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	33	Interaction with TSGA10. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.E33*(1)		breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	GCGAAGTAAAGAATCTGAAGT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											101	99	100					14																	62187161		2203	4300	6503	61256914	SO:0001587	stop_gained	3091			U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.97G>T	14.37:g.62187161G>T	ENSP00000338018:p.Glu33*		61256914	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Nonsense_Mutation	SNP	ENST00000337138.4	37	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	G	38	7.027299	0.98013	.	.	ENSG00000100644	ENST00000337138;ENST00000394997;ENST00000323441;ENST00000539097	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.9462	0.97183	0.0:0.0:1.0:0.0	.	.	.	.	X	33;34;33;57	.	ENSP00000323326:E33X	E	+	1	0	HIF1A	61256914	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.717000	0.92951	0.585000	0.79938	GAA		0.418	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		T	62187161	G	T	62187161	4	4	61	1	0	0	0	0	0	1	0	0	7124	943	33	2	103	2	HIF1A	14	62187161	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	269532	62187161	45162379	8964	16949										
HIF1A	3091	broad.mit.edu	37	chr14	62204876	62204876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgctcccctcacccaacGaaaaattacagaatataaat	3	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:62204876G>A	ENST00000337138.4	+	10	1586	c.1321G>A	c.(1321-1323)Gaa>Aaa	p.E441K	HIF1A_ENST00000539097.1_Missense_Mutation_p.E465K|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000394997.1_Missense_Mutation_p.E442K|HIF1A_ENST00000557538.1_Missense_Mutation_p.E382K|HIF1A_ENST00000323441.6_Missense_Mutation_p.E441K|RP11-618G20.1_ENST00000555937.1_RNA	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	441	ODD.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.E441K(1)		breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	CTCACCCAACGAAAAATTACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	14											77	73	75					14																	62204876		2203	4300	6503	61274629	SO:0001583	missense	3091			U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.1321G>A	14.37:g.62204876G>A	ENSP00000338018:p.Glu441Lys		61274629	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	37	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163707	0.57476	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000323441;ENST00000557538;ENST00000539097	T;T;T;T;T	0.55234	0.63;0.63;0.53;0.63;0.62	5.5	5.5	0.81552	.	0.322213	0.30809	N	0.008834	T	0.45438	0.1342	L	0.43152	1.355	0.58432	D	0.999997	B;B;B	0.18166	0.026;0.026;0.026	B;B;B	0.10450	0.003;0.005;0.005	T	0.33752	-0.9856	10	0.45353	T	0.12	.	13.033	0.58854	0.0741:0.0:0.9259:0.0	.	442;441;441	A8MYV6;D0VY79;Q16665	.;.;HIF1A_HUMAN	K	192;382;441;442;441;382;465	ENSP00000338018:E441K;ENSP00000378446:E442K;ENSP00000323326:E441K;ENSP00000451696:E382K;ENSP00000437955:E465K	ENSP00000323326:E441K	E	+	1	0	HIF1A	61274629	1.000000	0.71417	0.991000	0.47740	0.907000	0.53573	6.612000	0.74187	2.734000	0.93682	0.650000	0.86243	GAA		0.413	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		A	62204876	G	A	62204876	3	1	61	1	0	0	0	0	1	0	0	0	7124	1059	37	1	1359	1	HIF1A	14	62204876	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17715	62204876	45144664	8965	16950										
SYT16	83851	broad.mit.edu	37	chr14	62536443	62536443	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagtgacatctgagaaaGgaaagcagacaggattggag	14	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:62536443G>T	ENST00000430451.2	+	2	843	c.646G>T	c.(646-648)Gga>Tga	p.G216*	SYT16_ENST00000446982.2_Nonsense_Mutation_p.G216*|RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	216					exocytosis (GO:0006887)			p.G216*(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		ATCTGAGAAAGGAAAGCAGAC	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											140	135	136					14																	62536443		1937	4135	6072	61606196	SO:0001587	stop_gained	83851			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.646G>T	14.37:g.62536443G>T	ENSP00000394700:p.Gly216*		61606196	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Nonsense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	38	7.258833	0.98168	.	.	ENSG00000139973	ENST00000446982;ENST00000430451	.	.	.	4.8	0.883	0.19177	.	0.586784	0.17464	N	0.173354	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-30.7374	9.4114	0.38494	0.3801:0.0:0.6199:0.0	.	.	.	.	X	216	.	ENSP00000394700:G216X	G	+	1	0	SYT16	61606196	0.998000	0.40836	0.992000	0.48379	0.856000	0.48823	0.830000	0.27462	0.056000	0.16144	0.655000	0.94253	GGA		0.483	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62536443	G	T	62536443	4	4	61	1	0	0	0	0	0	1	0	0	15511	1001	35	2	652	2	SYT16	14	62536443	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	331567	62536443	44813097	8966	16951										
KCNH5	27133	broad.mit.edu	37	chr14	63174365	63174365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggggtacgcttttttccGacagtatttttaaaatttct	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63174365G>A	ENST00000322893.7	-	11	3096	c.2828C>T	c.(2827-2829)tCg>tTg	p.S943L	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	943	CAD (involved in subunit assembly). {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.S943L(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GCTTTTTTCCGACAGTATTTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	14											128	138	135					14																	63174365		2203	4300	6503	62244118	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2828C>T	14.37:g.63174365G>A	ENSP00000321427:p.Ser943Leu		62244118	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	9.665	1.145163	0.21288	.	.	ENSG00000140015	ENST00000322893	D	0.99042	-5.36	5.96	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	N	0.12182	0.205	0.80722	D	1	B	0.15141	0.012	B	0.09377	0.004	D	0.92716	0.6187	10	0.44086	T	0.13	.	14.6071	0.68486	0.0692:0.0:0.9308:0.0	.	943	Q8NCM2	KCNH5_HUMAN	L	943	ENSP00000321427:S943L	ENSP00000321427:S943L	S	-	2	0	KCNH5	62244118	1.000000	0.71417	0.997000	0.53966	0.428000	0.31595	4.695000	0.61767	2.832000	0.97577	0.655000	0.94253	TCG		0.478	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63174365	G	A	63174365	3	1	61	1	0	0	0	0	1	0	0	0	8056	1059	37	1	142	1	KCNH5	14	63174365	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	637922	63174365	44175175	8967	16952										
KCNH5	27133	broad.mit.edu	37	chr14	63447622	63447622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaaaggcattgatgatgtCataaggtaaacaagacagca	9	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63447622C>A	ENST00000322893.7	-	6	1178	c.910G>T	c.(910-912)Gac>Tac	p.D304Y	KCNH5_ENST00000394968.1_Missense_Mutation_p.D246Y|KCNH5_ENST00000420622.2_Missense_Mutation_p.D304Y|KCNH5_ENST00000394964.2_Missense_Mutation_p.D246Y	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	304					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.D304Y(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TTGATGATGTCATAAGGTAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	14											65	57	60					14																	63447622		2203	4300	6503	62517375	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.910G>T	14.37:g.63447622C>A	ENSP00000321427:p.Asp304Tyr		62517375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482638	0.84747	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.98221	-4.8;-4.8;-4.8;-4.8	5.54	5.54	0.83059	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98673	0.9555	L	0.60904	1.88	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.996;0.996;0.999	D	0.99902	1.1165	10	0.87932	D	0	.	19.4888	0.95042	0.0:1.0:0.0:0.0	.	246;246;304;304	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	Y	304;304;246;246	ENSP00000321427:D304Y;ENSP00000395439:D304Y;ENSP00000378419:D246Y;ENSP00000378415:D246Y	ENSP00000321427:D304Y	D	-	1	0	KCNH5	62517375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.764000	0.85297	2.607000	0.88179	0.585000	0.79938	GAC		0.403	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63447622	C	A	63447622	3	1	61	1	0	0	0	0	1	0	0	0	8056	826	29	2	2114	2	KCNH5	14	63447622	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	273257	63447622	43901918	8968	16953										
KCNH5	27133	broad.mit.edu	37	chr14	63447979	63447979	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatatctgatcccagctgaaGaacctaaaagagagaaaatg	9	7	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63447979G>T	ENST00000322893.7	-	6	821	c.553C>A	c.(553-555)Ctt>Att	p.L185I	KCNH5_ENST00000394968.1_Missense_Mutation_p.L127I|KCNH5_ENST00000420622.2_Missense_Mutation_p.L185I|KCNH5_ENST00000394964.2_Missense_Mutation_p.L127I	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	185					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.L185I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CCCAGCTGAAGAACCTAAAAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	14											55	58	57					14																	63447979		2201	4300	6501	62517732	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.553C>A	14.37:g.63447979G>T	ENSP00000321427:p.Leu185Ile		62517732	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.246763	0.80024	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.99051	-5.37;-5.14;-5.15;-5.15	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.98324	0.9444	M	0.71206	2.165	0.80722	D	1	B;B;B;P	0.46784	0.129;0.138;0.317;0.884	B;B;B;B	0.43155	0.046;0.126;0.086;0.41	D	0.99548	1.0965	10	0.52906	T	0.07	.	18.8733	0.92325	0.0:0.0:1.0:0.0	.	127;127;185;185	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	I	185;185;127;127	ENSP00000321427:L185I;ENSP00000395439:L185I;ENSP00000378419:L127I;ENSP00000378415:L127I	ENSP00000321427:L185I	L	-	1	0	KCNH5	62517732	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.887000	0.87295	2.461000	0.83175	0.460000	0.39030	CTT		0.388	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63447979	G	T	63447979	3	4	61	1	0	0	0	0	1	0	0	0	8056	942	33	2	2471	2	KCNH5	14	63447979	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	357	63447979	43901561	8969	16954										
KCNH5	27133	broad.mit.edu	37	chr14	63453860	63453860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagctgctgcaaaacacttCggctatttgtcaaagcccgt	9	11	1	1	rs148002630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63453860C>T	ENST00000322893.7	-	5	747	c.479G>A	c.(478-480)cGa>cAa	p.R160Q	KCNH5_ENST00000394968.1_Missense_Mutation_p.R102Q|KCNH5_ENST00000420622.2_Missense_Mutation_p.R160Q|KCNH5_ENST00000394964.2_Missense_Mutation_p.R102Q	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	160					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.R160Q(2)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CAAAACACTTCGGCTATTTGT	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	14											136	126	129					14																	63453860		2203	4300	6503	62523613	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.479G>A	14.37:g.63453860C>T	ENSP00000321427:p.Arg160Gln		62523613	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089800	0.76756	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.99098	-5.42;-5.18;-5.24;-5.26	5.71	5.71	0.89125	.	0.065171	0.64402	D	0.000009	D	0.98245	0.9419	M	0.82323	2.585	0.80722	D	1	B;B;B;P	0.37612	0.165;0.118;0.237;0.602	B;B;B;B	0.29524	0.017;0.04;0.059;0.103	D	0.99075	1.0835	10	0.59425	D	0.04	.	19.85	0.96736	0.0:1.0:0.0:0.0	.	102;102;160;160	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	Q	160;160;102;102	ENSP00000321427:R160Q;ENSP00000395439:R160Q;ENSP00000378419:R102Q;ENSP00000378415:R102Q	ENSP00000321427:R160Q	R	-	2	0	KCNH5	62523613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.809000	0.69172	2.697000	0.92050	0.563000	0.77884	CGA		0.388	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63453860	C	T	63453860	3	4	61	1	0	0	0	0	1	0	0	0	8056	884	31	1	2549	1	KCNH5	14	63453860	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5881	63453860	43895680	8970	16955										
KCNH5	27133	broad.mit.edu	37	chr14	63511854	63511854	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagcgcctgacgatgttCtccaaaaatgtgttctgcgg	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63511854C>A	ENST00000322893.7	-	1	319	c.51G>T	c.(49-51)gaG>gaT	p.E17D	KCNH5_ENST00000394968.1_Intron|KCNH5_ENST00000420622.2_Missense_Mutation_p.E17D|KCNH5_ENST00000394964.2_Intron	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	17	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.E17D(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TGACGATGTTCTCCAAAAATG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	14											87	71	76					14																	63511854		2203	4300	6503	62581607	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.51G>T	14.37:g.63511854C>A	ENSP00000321427:p.Glu17Asp		62581607	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.688617	0.48097	.	.	ENSG00000140015	ENST00000322893;ENST00000420622	D;D	0.98926	-5.24;-5.06	5.23	4.34	0.51931	PAS (1);	0.049575	0.85682	D	0.000000	D	0.96911	0.8991	N	0.21194	0.64	0.80722	D	1	P;B	0.51147	0.942;0.063	P;B	0.58266	0.836;0.164	D	0.95082	0.8214	10	0.02654	T	1	.	11.949	0.52944	0.0:0.9142:0.0:0.0858	.	17;17	Q8NCM2-2;Q8NCM2	.;KCNH5_HUMAN	D	17	ENSP00000321427:E17D;ENSP00000395439:E17D	ENSP00000321427:E17D	E	-	3	2	KCNH5	62581607	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.861000	0.48380	1.352000	0.45808	0.563000	0.77884	GAG		0.652	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63511854	C	A	63511854	3	1	61	1	0	0	0	0	1	0	0	0	8056	912	32	2	2993	2	KCNH5	14	63511854	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57994	63511854	43837686	8971	16956										
RHOJ	57381	broad.mit.edu	37	chr14	63747757	63747757	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgatctgcttctctgtCgtaaaccctgcctcttacca	5	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:63747757C>T	ENST00000316754.3	+	3	768	c.306C>T	c.(304-306)gtC>gtT	p.V102V	RHOJ_ENST00000555125.1_Silent_p.V102V	NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	102					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.V102V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		GCTTCTCTGTCGTAAACCCTG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	14											221	156	178					14																	63747757		2203	4300	6503	62817510	SO:0001819	synonymous_variant	57381			AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"RAS-like, family 7, member B", "ras homolog gene family, member J"	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.306C>T	14.37:g.63747757C>T			62817510	Q96KC1	Silent	SNP	ENST00000316754.3	37	CCDS9757.1																																																																																				0.537	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3			T	63747757	C	T	63747757	2	4	61	1	0	0	0	0	0	0	0	1	13378	871	31	1		1	RHOJ	14	63747757	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235903	63747757	43601783	8972	16957										
WDR89	112840	broad.mit.edu	37	chr14	64065578	64065578	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggatgctattttcatactCtctttctttgtaaaggtctt	7	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64065578C>A	ENST00000394942.2	-	2	1171	c.1083G>T	c.(1081-1083)gaG>gaT	p.E361D	CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Missense_Mutation_p.E361D	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	361								p.E361D(1)		endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		TTTTCATACTCTCTTTCTTTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	14											118	109	112					14																	64065578		2203	4300	6503	63135331	SO:0001583	missense	112840			AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"WD repeat domain containing"	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.1083G>T	14.37:g.64065578C>A	ENSP00000378399:p.Glu361Asp		63135331		Missense_Mutation	SNP	ENST00000394942.2	37	CCDS9759.1	.	.	.	.	.	.	.	.	.	.	C	0.202	-1.044131	0.01997	.	.	ENSG00000140006	ENST00000394942;ENST00000267522	T;T	0.66995	-0.24;-0.24	5.65	-0.323	0.12709	.	0.318283	0.34628	N	0.003820	T	0.32466	0.0830	N	0.04880	-0.145	0.23501	N	0.997543	B	0.02656	0.0	B	0.01281	0.0	T	0.11131	-1.0600	10	0.11182	T	0.66	.	2.773	0.05340	0.3139:0.2183:0.3727:0.0951	.	361	Q96FK6	WDR89_HUMAN	D	361	ENSP00000378399:E361D;ENSP00000267522:E361D	ENSP00000267522:E361D	E	-	3	2	WDR89	63135331	0.113000	0.22115	0.997000	0.53966	0.647000	0.38526	-0.647000	0.05397	0.018000	0.15052	-0.282000	0.10007	GAG		0.383	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666		A	64065578	C	A	64065578	3	1	61	1	0	0	0	0	1	0	0	0	17376	912	32	2	84	2	WDR89	14	64065578	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	317821	64065578	43283962	8973	16958										
WDR89	112840	broad.mit.edu	37	chr14	64066022	64066022	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactgatgaaattgagttAcaggttgtaaccagtgcatc	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64066022A>G	ENST00000394942.2	-	2	727	c.639T>C	c.(637-639)tgT>tgC	p.C213C	CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Silent_p.C213C	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	213								p.C213C(1)		endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		AAATTGAGTTACAGGTTGTAA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	14											109	105	106					14																	64066022		2203	4300	6503	63135775	SO:0001819	synonymous_variant	112840			AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"WD repeat domain containing"	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.639T>C	14.37:g.64066022A>G			63135775		Silent	SNP	ENST00000394942.2	37	CCDS9759.1																																																																																				0.383	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666		G	64066022	A	G	64066022	2	3	61	1	0	0	0	0	0	0	0	1	17376	389	14	4		4	WDR89	14	64066022	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	444	64066022	43283518	8974	16959										
WDR89	112840	broad.mit.edu	37	chr14	64066562	64066562	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttcctgcttggacagtCtttgatgtgtctataccaag	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64066562C>A	ENST00000394942.2	-	2	187	c.99G>T	c.(97-99)aaG>aaT	p.K33N	CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Missense_Mutation_p.K33N	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	33								p.K33N(1)		endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		CTTGGACAGTCTTTGATGTGT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											78	81	80					14																	64066562		2203	4300	6503	63136315	SO:0001583	missense	112840			AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"WD repeat domain containing"	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.99G>T	14.37:g.64066562C>A	ENSP00000378399:p.Lys33Asn		63136315		Missense_Mutation	SNP	ENST00000394942.2	37	CCDS9759.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.666437	0.29604	.	.	ENSG00000140006	ENST00000394942;ENST00000267522;ENST00000554717	T;T;T	0.68181	-0.31;-0.31;0.89	5.93	1.39	0.22231	.	0.313762	0.31071	N	0.008315	T	0.45357	0.1338	L	0.29908	0.895	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.15292	-1.0442	10	0.17832	T	0.49	.	4.9792	0.14157	0.0:0.4344:0.1517:0.4139	.	33	Q96FK6	WDR89_HUMAN	N	33	ENSP00000378399:K33N;ENSP00000267522:K33N;ENSP00000451702:K33N	ENSP00000267522:K33N	K	-	3	2	WDR89	63136315	0.174000	0.23070	0.386000	0.26170	0.513000	0.34164	0.046000	0.14035	0.364000	0.24374	0.655000	0.94253	AAG		0.348	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666		A	64066562	C	A	64066562	3	1	61	1	0	0	0	0	1	0	0	0	17376	912	32	2	1068	2	WDR89	14	64066562	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	540	64066562	43282978	8975	16960										
SGPP1	81537	broad.mit.edu	37	chr14	64152941	64152941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgtgctgtcttgcttttCgaatatcatcacacggtata	7	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64152941C>T	ENST00000247225.6	-	3	1302	c.1208G>A	c.(1207-1209)cGa>cAa	p.R403Q		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	403					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)	p.R403Q(2)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		TCTTGCTTTTCGAATATCATC	0.348																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	14											153	135	141					14																	64152941		2203	4300	6503	63222694	SO:0001583	missense	81537			AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.1208G>A	14.37:g.64152941C>T	ENSP00000247225:p.Arg403Gln		63222694	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	37	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.449073	0.63178	.	.	ENSG00000126821	ENST00000247225	.	.	.	6.07	6.07	0.98685	.	0.072428	0.56097	D	0.000033	T	0.61887	0.2383	M	0.76002	2.32	0.52501	D	0.999953	D	0.58970	0.984	P	0.47673	0.554	T	0.58792	-0.7574	9	0.14252	T	0.57	-1.5609	14.7663	0.69642	0.0:0.9316:0.0:0.0684	.	403	Q9BX95	SGPP1_HUMAN	Q	403	.	ENSP00000247225:R403Q	R	-	2	0	SGPP1	63222694	1.000000	0.71417	0.999000	0.59377	0.740000	0.42216	4.625000	0.61262	2.885000	0.99019	0.655000	0.94253	CGA		0.348	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791		T	64152941	C	T	64152941	3	4	61	1	0	0	0	0	1	0	0	0	14256	884	31	1	121	1	SGPP1	14	64152941	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86379	64152941	43196599	8976	16961										
SYNE2	23224	broad.mit.edu	37	chr14	64461912	64461912	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccaagggtctcatcaaaGaacatgaggtacaataaagt	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64461912G>T	ENST00000344113.4	+	23	3144	c.2932G>T	c.(2932-2934)Gaa>Taa	p.E978*	SYNE2_ENST00000358025.3_Nonsense_Mutation_p.E978*|SYNE2_ENST00000554584.1_Nonsense_Mutation_p.E978*|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	978					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.E978*(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCTCATCAAAGAACATGAGGT	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											47	46	46					14																	64461912		1842	4074	5916	63531665	SO:0001587	stop_gained	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2932G>T	14.37:g.64461912G>T	ENSP00000341781:p.Glu978*		63531665	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	41	8.628649	0.98892	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.15	3.2	0.36748	.	0.122808	0.35525	N	0.003151	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	13.6024	0.62026	0.0:0.2956:0.7044:0.0	.	.	.	.	X	978	.	ENSP00000261678:E978X	E	+	1	0	SYNE2	63531665	1.000000	0.71417	0.994000	0.49952	0.920000	0.55202	3.190000	0.50973	1.170000	0.42753	0.655000	0.94253	GAA		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64461912	G	T	64461912	4	4	61	1	0	0	0	0	0	1	0	0	15485	943	33	2	3018	2	SYNE2	14	64461912	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	308971	64461912	42887628	8977	16962										
SYNE2	23224	broad.mit.edu	37	chr14	64522810	64522810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttagagatgcctcttcGaaaacaagaggaattggaat	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64522810G>A	ENST00000344113.4	+	49	10105	c.9893G>A	c.(9892-9894)cGa>cAa	p.R3298Q	SYNE2_ENST00000358025.3_Missense_Mutation_p.R3298Q|SYNE2_ENST00000554584.1_Missense_Mutation_p.R3331Q|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3298					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.R3298Q(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATGCCTCTTCGAAAACAAGAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											77	70	72					14																	64522810		1933	4142	6075	63592563	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9893G>A	14.37:g.64522810G>A	ENSP00000341781:p.Arg3298Gln		63592563	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	5.782	0.328636	0.10956	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.34072	1.38;1.38;1.38	5.79	2.92	0.33932	.	1.601550	0.03355	N	0.196692	T	0.17874	0.0429	N	0.08118	0	0.20489	N	0.999896	B;B	0.15719	0.008;0.014	B;B	0.04013	0.001;0.001	T	0.23190	-1.0195	10	0.11794	T	0.64	.	2.3266	0.04224	0.2161:0.1267:0.5186:0.1385	.	3298;3298	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	Q	3298;3298;3331;3331	ENSP00000350719:R3298Q;ENSP00000341781:R3298Q;ENSP00000452570:R3331Q	ENSP00000261678:R3331Q	R	+	2	0	SYNE2	63592563	0.011000	0.17503	0.001000	0.08648	0.182000	0.23217	0.249000	0.18216	0.344000	0.23847	0.491000	0.48974	CGA		0.463	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64522810	G	A	64522810	3	1	61	1	0	0	0	0	1	0	0	0	15485	1058	37	1	10083	1	SYNE2	14	64522810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60898	64522810	42826730	8978	16963										
SYNE2	23224	broad.mit.edu	37	chr14	64610596	64610596	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcaagcgctatgaaagaaCggagtttgcagagcacctgg	13	8	0	3	rs145018323	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64610596C>T	ENST00000344113.4	+	83	15625	c.15413C>T	c.(15412-15414)aCg>aTg	p.T5138M	SYNE2_ENST00000555002.1_Missense_Mutation_p.T1772M|SYNE2_ENST00000358025.3_Missense_Mutation_p.T5138M|SYNE2_ENST00000554584.1_Missense_Mutation_p.T5055M|SYNE2_ENST00000394768.2_Missense_Mutation_p.T1523M|SYNE2_ENST00000357395.3_Missense_Mutation_p.T1523M|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5138					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.T5138M(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TATGAAAGAACGGAGTTTGCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	MET/THR,MET/THR	0,4406		0,0,2203	264	267	266		15413,15413	5.3	0.9	14	dbSNP_134	266	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	81,81	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	5138/6886,5138/6908	64610596	3,13003	2203	4300	6503	63680349	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15413C>T	14.37:g.64610596C>T	ENSP00000341781:p.Thr5138Met		63680349	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927627	0.92389	0.0	3.49E-4	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.52295	1.26;0.73;1.26;1.26;0.67;0.73	5.33	5.33	0.75918	.	0.000000	0.52532	D	0.000074	T	0.72898	0.3518	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.953;0.961	T	0.77094	-0.2715	10	0.72032	D	0.01	.	18.9967	0.92817	0.0:1.0:0.0:0.0	.	1523;5055;5138;5138	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	M	5138;1523;5138;5055;5061;1772;1523	ENSP00000350719:T5138M;ENSP00000349969:T1523M;ENSP00000341781:T5138M;ENSP00000452570:T5055M;ENSP00000450831:T1772M;ENSP00000378249:T1523M	ENSP00000261678:T5061M	T	+	2	0	SYNE2	63680349	1.000000	0.71417	0.886000	0.34754	0.990000	0.78478	5.877000	0.69675	2.479000	0.83701	0.650000	0.86243	ACG		0.468	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64610596	C	T	64610596	3	4	61	1	0	0	0	0	1	0	0	0	15485	536	19	1	15739	1	SYNE2	14	64610596	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	87786	64610596	42738944	8979	16964										
SYNE2	23224	broad.mit.edu	37	chr14	64637010	64637010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgctgtccagggtgttCggcagaggaagggtgacgtt	17	6	0	3	rs540618925		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:64637010C>T	ENST00000344113.4	+	94	17277	c.17065C>T	c.(17065-17067)Cgg>Tgg	p.R5689W	SYNE2_ENST00000555002.1_Missense_Mutation_p.R2323W|SYNE2_ENST00000358025.3_Missense_Mutation_p.R5689W|SYNE2_ENST00000554584.1_Missense_Mutation_p.R5564W|SYNE2_ENST00000394768.2_Missense_Mutation_p.R2074W|SYNE2_ENST00000357395.3_Missense_Mutation_p.R2074W|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5689					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.R5689W(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CCAGGGTGTTCGGCAGAGGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14											155	133	140					14																	64637010		2203	4300	6503	63706763	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17065C>T	14.37:g.64637010C>T	ENSP00000341781:p.Arg5689Trp		63706763	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	9.588	1.125328	0.20959	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.50277	0.75;4.05;0.75;1.3;4.1;4.05	5.56	3.69	0.42338	.	1.047180	0.07564	N	0.917449	T	0.43590	0.1254	L	0.44542	1.39	0.80722	D	1	B;B;B;B;B	0.20887	0.016;0.009;0.007;0.017;0.049	B;B;B;B;B	0.15484	0.013;0.004;0.002;0.004;0.007	T	0.13575	-1.0504	10	0.66056	D	0.02	.	10.8878	0.46976	0.0:0.7982:0.1311:0.0707	.	2074;77;5564;5689;5689	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	W	5689;2074;5689;5564;5570;2323;2074	ENSP00000350719:R5689W;ENSP00000349969:R2074W;ENSP00000341781:R5689W;ENSP00000452570:R5564W;ENSP00000450831:R2323W;ENSP00000378249:R2074W	ENSP00000261678:R5570W	R	+	1	2	SYNE2	63706763	0.365000	0.25006	0.212000	0.23672	0.040000	0.13550	0.834000	0.27518	0.670000	0.31165	0.460000	0.39030	CGG		0.488	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64637010	C	T	64637010	3	4	61	1	0	0	0	0	1	0	0	0	15485	875	31	1	17435	1	SYNE2	14	64637010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26414	64637010	42712530	8980	16965										
FNTB	2342	broad.mit.edu	37	chr14	65511054	65511054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgacaagccggcagatgcGatttgaaggaggatttcagg	16	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:65511054G>A	ENST00000246166.2	+	9	1082	c.848G>A	c.(847-849)cGa>cAa	p.R283Q	MIR4706_ENST00000582134.1_RNA|MAX_ENST00000341653.2_Intron|CHURC1-FNTB_ENST00000549987.1_Missense_Mutation_p.R318Q|FNTB_ENST00000542227.1_Missense_Mutation_p.R237Q|FNTB_ENST00000447296.2_Missense_Mutation_p.R317Q	NM_002028.3	NP_002019.1	P49356	FNTB_HUMAN	farnesyltransferase, CAAX box, beta	283				R -> L (in Ref. 6; AAA86286). {ECO:0000305}.	negative regulation of cell proliferation (GO:0008285)|phototransduction, visible light (GO:0007603)|positive regulation of cell cycle (GO:0045787)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|protein farnesylation (GO:0018343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to cytokine (GO:0034097)|response to inorganic substance (GO:0010035)|response to organic cyclic compound (GO:0014070)|rhodopsin mediated signaling pathway (GO:0016056)|wound healing (GO:0042060)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	farnesyltranstransferase activity (GO:0004311)|protein farnesyltransferase activity (GO:0004660)|zinc ion binding (GO:0008270)	p.R283Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CGGCAGATGCGATTTGAAGGA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	14											145	143	143					14																	65511054		2203	4300	6503	64580807	SO:0001583	missense	2342				CCDS9769.1	14q23.3	2011-09-28			ENSG00000257365	ENSG00000257365			3785	protein-coding gene	gene with protein product		134636				8276393	Standard	NM_002028		Approved	FPTB		P49356	OTTHUMG00000142811	ENST00000246166.2:c.848G>A	14.37:g.65511054G>A	ENSP00000246166:p.Arg283Gln		64580807	B2RDX6|B4E1A0	Missense_Mutation	SNP	ENST00000246166.2	37	CCDS9769.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.664494	0.67700	.	.	ENSG00000125954;ENSG00000125954;ENSG00000125954;ENSG00000125954;ENSG00000257365	ENST00000542227;ENST00000549987;ENST00000447296;ENST00000448390;ENST00000246166	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.67	4.78	0.61160	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.000000	0.85682	D	0.000000	T	0.29491	0.0735	L	0.33485	1.01	0.80722	D	1	B;B;B;B	0.27229	0.172;0.036;0.029;0.1	B;B;B;B	0.14023	0.009;0.01;0.003;0.01	T	0.06516	-1.0822	10	0.13853	T	0.58	-19.2187	13.7462	0.62876	0.0756:0.0:0.9244:0.0	.	286;237;317;283	Q86TX8;B4E1A0;B4DL54;P49356	.;.;.;FNTB_HUMAN	Q	237;318;317;39;283	ENSP00000443140:R237Q;ENSP00000447121:R318Q;ENSP00000406393:R317Q;ENSP00000399362:R39Q;ENSP00000246166:R283Q	ENSP00000246166:R283Q	R	+	2	0	FNTB;AL139022.1	64580807	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.724000	0.74747	1.399000	0.46721	0.511000	0.50034	CGA		0.577	FNTB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000286392.1	NM_002028		A	65511054	G	A	65511054	3	1	61	1	0	0	0	0	1	0	0	0	5997	1058	37	1	882	1	FNTB	14	65511054	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	874044	65511054	41838486	8981	16966										
PLEKHH1	57475	broad.mit.edu	37	chr14	68053937	68053937	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcctgtgctaccaagggGccaacgttgctgtgaatatt	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68053937G>A	ENST00000329153.5	+	29	4212	c.4080G>A	c.(4078-4080)ggG>ggA	p.G1360G	PLEKHH1_ENST00000417684.2_Missense_Mutation_p.A302T	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1360						cytoskeleton (GO:0005856)		p.G1360G(1)		endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CTACCAAGGGGCCAACGTTGC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	14											127	134	131					14																	68053937		1950	4127	6077	67123690	SO:0001819	synonymous_variant	57475			AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.4080G>A	14.37:g.68053937G>A			67123690	A6H8X6|Q6PJL4|Q6ZWC7	Silent	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.460471	0.84317	.	.	ENSG00000054690	ENST00000417684	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	T	0.26991	0.0661	.	.	.	0.24052	N	0.996047	P	0.49253	0.921	B	0.35182	0.197	T	0.30679	-0.9970	7	0.87932	D	0	.	11.9684	0.53049	0.0788:0.0:0.9212:0.0	.	302	E7ESY2	.	T	302	.	ENSP00000397712:A302T	A	+	1	0	PLEKHH1	67123690	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.754000	0.38369	2.837000	0.97791	0.655000	0.94253	GCC		0.512	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68053937	G	A	68053937	2	1	61	1	0	0	0	0	0	0	0	1	12107	1190	42	3		3	PLEKHH1	14	68053937	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2542883	68053937	39295603	8982	16967										
PIGH	5283	broad.mit.edu	37	chr14	68060478	68060478	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatgtaaatggcctcattGatgacaatatccttgacctt	6	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68060478G>T	ENST00000216452.4	-	2	455	c.372C>A	c.(370-372)atC>atA	p.I124I	PIGH_ENST00000560722.1_Silent_p.I124I|PIGH_ENST00000559581.1_Silent_p.I85I	NM_004569.3	NP_004560.1	Q14442	PIGH_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class H	124					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)	p.I124I(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4				all cancers(60;0.000592)|OV - Ovarian serous cystadenocarcinoma(108;0.00395)|BRCA - Breast invasive adenocarcinoma(234;0.00933)		TGGCCTCATTGATGACAATAT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	14											88	69	75					14																	68060478		2203	4300	6503	67130231	SO:0001819	synonymous_variant	5283				CCDS9784.1	14q24.1	2013-02-26	2006-06-28		ENSG00000100564	ENSG00000100564	2.4.1.198	"Phosphatidylinositol glycan anchor biosynthesis"	8964	protein-coding gene	gene with protein product	"phosphatidylinositol N-acetylglucosaminyltransferase subunit"	600154	"phosphatidylinositol glycan, class H"			8204896	Standard	NM_004569		Approved	GPI-H	uc001xjr.1	Q14442	OTTHUMG00000171806	ENST00000216452.4:c.372C>A	14.37:g.68060478G>T			67130231	B2RAA4	Silent	SNP	ENST00000216452.4	37	CCDS9784.1																																																																																				0.403	PIGH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000415189.2	NM_004569		T	68060478	G	T	68060478	2	4	61	1	0	0	0	0	0	0	0	1	11920	1280	45	2		2	PIGH	14	68060478	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6541	68060478	39289062	8983	16968										
ARG2	384	broad.mit.edu	37	chr14	68117554	68117554	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagctttggtcagacaagaGaaggagggcatattgtctat	12	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68117554G>T	ENST00000261783.3	+	8	1162	c.982G>T	c.(982-984)Gaa>Taa	p.E328*	VTI1B_ENST00000554659.1_3'UTR	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	328					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)	p.E328*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	TCAGACAAGAGAAGGAGGGCA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											140	104	116					14																	68117554		2203	4300	6503	67187307	SO:0001587	stop_gained	384			D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"arginase, type II"			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.982G>T	14.37:g.68117554G>T	ENSP00000261783:p.Glu328*		67187307	B2R690|Q6FHY8	Nonsense_Mutation	SNP	ENST00000261783.3	37	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741568	0.96873	.	.	ENSG00000081181	ENST00000261783	.	.	.	5.09	5.09	0.68999	.	0.047889	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.6895	0.91578	0.0:0.0:1.0:0.0	.	.	.	.	X	328	.	ENSP00000261783:E328X	E	+	1	0	ARG2	67187307	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.704000	0.74639	2.661000	0.90470	0.655000	0.94253	GAA		0.463	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172		T	68117554	G	T	68117554	4	4	61	1	0	0	0	0	0	1	0	0	858	943	33	2	1012	2	ARG2	14	68117554	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57076	68117554	39231986	8984	16969										
RDH11	51109	broad.mit.edu	37	chr14	68162372	68162372	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggcgcagccatatacaGaaggaagggcagaaggagga	17	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68162372G>T	ENST00000381346.4	-	1	159	c.49C>A	c.(49-51)Ctg>Atg	p.L17M	RDH11_ENST00000428130.2_Missense_Mutation_p.L17M|RDH11_ENST00000553384.1_Missense_Mutation_p.L17M	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	17					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.L17M(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	GCCATATACAGAAGGAAGGGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											69	61	64					14																	68162372		2203	4300	6503	67232125	SO:0001583	missense	51109			AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.49C>A	14.37:g.68162372G>T	ENSP00000370750:p.Leu17Met		67232125	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	37	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	g	10.92	1.486635	0.26686	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000557273;ENST00000557726	D;D;D;D;D	0.90324	-1.84;-1.54;-1.97;-2.35;-2.65	5.0	5.0	0.66597	.	0.181870	0.35646	N	0.003065	D	0.90456	0.7011	N	0.14661	0.345	0.48185	D	0.9996	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.87578	0.996;0.998;0.996	D	0.90481	0.4460	10	0.42905	T	0.14	.	15.5193	0.75854	0.0:0.0:1.0:0.0	.	17;17;17	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	M	17	ENSP00000370750:L17M;ENSP00000452079:L17M;ENSP00000416395:L17M;ENSP00000450651:L17M;ENSP00000450435:L17M	ENSP00000370750:L17M	L	-	1	2	RDH11	67232125	1.000000	0.71417	0.993000	0.49108	0.007000	0.05969	2.344000	0.44010	2.776000	0.95493	0.651000	0.88453	CTG		0.562	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			T	68162372	G	T	68162372	3	4	61	1	0	0	0	0	1	0	0	0	13227	933	33	2	935	2	RDH11	14	68162372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44818	68162372	39187168	8985	16970										
RDH12	145226	broad.mit.edu	37	chr14	68191929	68191929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcggaaattggacctatccGacaccaaatctatccgagcc	8	13	1	0	rs148334092		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68191929G>A	ENST00000551171.1	+	5	625	c.301G>A	c.(301-303)Gac>Aac	p.D101N	RDH12_ENST00000539142.1_Missense_Mutation_p.D101N|RDH12_ENST00000267502.3_Missense_Mutation_p.D101N	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	101			D -> N. {ECO:0000269|PubMed:16269441}.		photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)	p.D101N(1)		large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	GGACCTATCCGACACCAAATC	0.527													G|||	1	0.000199681	0	0.0014	5008	,	,		19652	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14						G	ASN/ASP	8,4398	14.3+/-33.2	0,8,2195	101	97	98		301	4.6	0.9	14	dbSNP_134	98	0,8600		0,0,4300	yes	missense	RDH12	NM_152443.2	23	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	probably-damaging	101/317	68191929	8,12998	2203	4300	6503	67261682	SO:0001583	missense	145226			AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19977	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 2"	608830	"retinol dehydrogenase 12 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.301G>A	14.37:g.68191929G>A	ENSP00000449079:p.Asp101Asn		67261682	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	37	CCDS9787.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.51	3.638713	0.67130	0.001816	0.0	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.91631	-2.88;-2.88;-2.88	5.52	4.63	0.57726	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95166	0.8433	M	0.73319	2.225	0.47276	D	0.999377	D	0.89917	1.0	D	0.97110	1.0	D	0.95336	0.8434	10	0.66056	D	0.02	.	12.8512	0.57858	0.0746:0.0:0.9254:0.0	.	101	Q96NR8	RDH12_HUMAN	N	101	ENSP00000449079:D101N;ENSP00000267502:D101N;ENSP00000438715:D101N	ENSP00000267502:D101N	D	+	1	0	RDH12	67261682	1.000000	0.71417	0.863000	0.33907	0.319000	0.28217	7.243000	0.78219	1.577000	0.49804	0.563000	0.77884	GAC		0.527	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1			A	68191929	G	A	68191929	3	1	61	1	0	0	0	0	1	0	0	0	13228	1058	37	1	311	1	RDH12	14	68191929	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29557	68191929	39157611	8986	16971										
ZFYVE26	23503	broad.mit.edu	37	chr14	68221958	68221958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacaggtcatggcggcccGaacttggtcctagaagagga	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68221958G>A	ENST00000347230.4	-	37	6934	c.6796C>T	c.(6796-6798)Cgg>Tgg	p.R2266W	ZFYVE26_ENST00000557306.1_Missense_Mutation_p.R112W	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2266					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.R2266W(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		ATGGCGGCCCGAACTTGGTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											87	81	83					14																	68221958		2203	4300	6503	67291711	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.6796C>T	14.37:g.68221958G>A	ENSP00000251119:p.Arg2266Trp		67291711	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178839	0.94846	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000557306	T;T	0.59638	0.86;0.25	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.78622	0.4312	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.79878	-0.1617	10	0.87932	D	0	-23.9975	20.0745	0.97737	0.0:0.0:1.0:0.0	.	112;2266	Q96H43;Q68DK2	.;ZFY26_HUMAN	W	2266;2245;112	ENSP00000251119:R2266W;ENSP00000452142:R112W	ENSP00000251119:R2266W	R	-	1	2	ZFYVE26	67291711	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.869000	0.99810	2.748000	0.94277	0.462000	0.41574	CGG		0.468	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68221958	G	A	68221958	3	1	61	1	0	0	0	0	1	0	0	0	17707	1057	37	1	847	1	ZFYVE26	14	68221958	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30029	68221958	39127582	8987	16972										
ZFYVE26	23503	broad.mit.edu	37	chr14	68274532	68274532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctcaggagatcccagaGcacagagacagcttcggagc	12	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:68274532G>A	ENST00000347230.4	-	5	607	c.469C>T	c.(469-471)Ctc>Ttc	p.L157F	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.L157F	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	157					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.L157F(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AGATCCCAGAGCACAGAGACA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	14											109	110	110					14																	68274532		2203	4300	6503	67344285	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.469C>T	14.37:g.68274532G>A	ENSP00000251119:p.Leu157Phe		67344285	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602805	0.46423	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.58210	0.54;0.35	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.69869	0.3159	M	0.66939	2.045	0.50467	D	0.999875	D;D;B	0.89917	1.0;1.0;0.09	D;D;B	0.91635	0.999;0.999;0.038	T	0.69888	-0.5023	10	0.54805	T	0.06	-14.6528	13.6124	0.62088	0.0705:0.0:0.9295:0.0	.	157;157;157	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	F	157	ENSP00000251119:L157F;ENSP00000450603:L157F	ENSP00000251119:L157F	L	-	1	0	ZFYVE26	67344285	1.000000	0.71417	0.999000	0.59377	0.584000	0.36387	3.140000	0.50585	2.837000	0.97791	0.591000	0.81541	CTC		0.602	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68274532	G	A	68274532	3	1	61	1	0	0	0	0	1	0	0	0	17707	971	34	3	7302	3	ZFYVE26	14	68274532	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52574	68274532	39075008	8988	16973										
ACTN1	87	broad.mit.edu	37	chr14	69351019	69351019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggtctccagcagtttctCggtccgctgggagtgccaaa	12	11	2	0	rs368356125		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:69351019C>T	ENST00000193403.6	-	14	1884	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K	ACTN1_ENST00000376839.3_Missense_Mutation_p.E436K|ACTN1_ENST00000438964.2_Missense_Mutation_p.E501K|ACTN1_ENST00000538545.2_Missense_Mutation_p.E501K|ACTN1_ENST00000394419.4_Missense_Mutation_p.E501K	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	501	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)	p.E501K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AGCAGTTTCTCGGTCCGCTGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	105	88	94		1501,1501,1501	5	1	14		94	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	501/893,501/915,501/888	69351019	1,13005	2203	4300	6503	68420772	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1501G>A	14.37:g.69351019C>T	ENSP00000193403:p.Glu501Lys		68420772	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.577963|5.577963	0.96565|0.96565	0.0|0.0	1.16E-4|1.16E-4	ENSG00000072110|ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000544964|ENST00000553290	T;T;T;T;D;T|.	0.82344|.	-1.41;-1.46;-1.44;-1.48;-1.6;0.74|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.054502|.	0.64402|.	D|.	0.000001|.	T|T	0.77384|0.77384	0.4122|0.4122	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	D|D	1|1	D;P;P;P;P|.	0.55385|.	0.971;0.537;0.82;0.831;0.508|.	P;B;B;B;B|.	0.59643|.	0.861;0.217;0.374;0.37;0.345|.	T|T	0.77707|0.77707	-0.2487|-0.2487	10|5	0.48119|.	T|.	0.1|.	.|.	18.4485|18.4485	0.90695|0.90695	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	132;501;501;501;148|.	B7Z2W3;P12814-2;Q1HE25;P12814;B4DFY0|.	.;.;.;ACTN1_HUMAN;.|.	K|Q	501;501;501;436;501;91|1	ENSP00000193403:E501K;ENSP00000377941:E501K;ENSP00000414272:E501K;ENSP00000366035:E436K;ENSP00000439828:E501K;ENSP00000444422:E91K|.	ENSP00000193403:E501K|.	E|R	-|-	1|2	0|0	ACTN1|ACTN1	68420772|68420772	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.953000|0.953000	0.61014|0.61014	7.651000|7.651000	0.83577|0.83577	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.557	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		T	69351019	C	T	69351019	3	4	61	1	0	0	0	0	1	0	0	0	204	893	31	1	1279	1	ACTN1	14	69351019	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1076487	69351019	37998521	8989	16974										
GALNTL1	57452	broad.mit.edu	37	chr14	69808474	69808474	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctggagaacgtctacccaGagctcacgtgagtgcagccc	11	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:69808474G>T	ENST00000337827.4	+	12	1591	c.1264G>T	c.(1264-1266)Gag>Tag	p.E422*	GALNT16_ENST00000448469.3_Nonsense_Mutation_p.E422*|GALNT16_ENST00000553669.1_Nonsense_Mutation_p.E422*	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	422					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.E422*(1)									CGTCTACCCAGAGCTCACGTG	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											75	49	58					14																	69808474		2203	4300	6503	68878227	SO:0001587	stop_gained	57452			AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23233	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 16"	615132	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.1264G>T	14.37:g.69808474G>T	ENSP00000336729:p.Glu422*		68878227	Q4KMG3|Q58A55|Q9ULT9	Nonsense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	39	7.533575	0.98342	.	.	ENSG00000100626	ENST00000337827;ENST00000536652;ENST00000448469;ENST00000553669	.	.	.	5.48	5.48	0.80851	.	0.051440	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.364	0.94454	0.0:0.0:1.0:0.0	.	.	.	.	X	422;48;422;422	.	ENSP00000336729:E422X	E	+	1	0	GALNTL1	68878227	1.000000	0.71417	0.968000	0.41197	0.954000	0.61252	9.615000	0.98356	2.547000	0.85894	0.655000	0.94253	GAG		0.607	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		T	69808474	G	T	69808474	4	4	61	1	0	0	0	0	0	1	0	0	6241	943	33	2	1310	2	GALNTL1	14	69808474	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	457455	69808474	37541066	8990	16975										
SFRS5	6430	broad.mit.edu	37	chr14	70235943	70235943	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcgtcttatagttgagaAtttatcctcaagagtcagct	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70235943A>C	ENST00000553521.1	+	6	1794	c.341A>C	c.(340-342)aAt>aCt	p.N114T	SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000553635.1_Missense_Mutation_p.N111T|SRSF5_ENST00000394366.2_Missense_Mutation_p.N114T|SRSF5_ENST00000554021.1_Missense_Mutation_p.N114T|SRSF5_ENST00000451983.2_Missense_Mutation_p.N114T|SRSF5_ENST00000555349.1_Missense_Mutation_p.N114T|SRSF5_ENST00000557154.1_Missense_Mutation_p.N114T			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	114	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.N114T(1)		large_intestine(1)|liver(1)	2						ATAGTTGAGAATTTATCCTCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											71	71	71					14																	70235943		2203	4300	6503	69305696	SO:0001583	missense	6430			AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.341A>C	14.37:g.70235943A>C	ENSP00000452123:p.Asn114Thr		69305696	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	37	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.580382	0.65992	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000553369;ENST00000557154;ENST00000451983;ENST00000553635;ENST00000555349;ENST00000554021	T;T;T;T;T;T;T;T	0.38401	1.63;1.63;1.14;1.63;1.14;1.63;1.16;1.14	5.52	5.52	0.82312	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.78704	0.4325	H	0.99820	4.81	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.79108	0.992;0.963	D	0.89026	0.3438	10	0.87932	D	0	.	15.6631	0.77203	1.0:0.0:0.0:0.0	.	111;114	Q13243-3;Q13243	.;SRSF5_HUMAN	T	114;114;114;114;114;111;114;114	ENSP00000452123:N114T;ENSP00000377892:N114T;ENSP00000452449:N114T;ENSP00000451088:N114T;ENSP00000402734:N114T;ENSP00000451391:N111T;ENSP00000452090:N114T;ENSP00000450918:N114T	ENSP00000377892:N114T	N	+	2	0	SRSF5	69305696	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.224000	0.95209	2.088000	0.63022	0.533000	0.62120	AAT		0.348	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		C	70235943	A	C	70235943	3	2	61	1	0	0	0	0	1	0	0	0	14217	101	4	4	355	4	SFRS5	14	70235943	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	427469	70235943	37113597	8991	16976										
SLC10A1	6554	broad.mit.edu	37	chr14	70263850	70263850	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagggtgaagttgaatgggGcagacgcgttgtgggcctcc	18	8	0	3	rs201015997		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70263850G>A	ENST00000216540.4	-	1	156	c.23C>T	c.(22-24)gCc>gTc	p.A8V		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	8					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)	p.A8V(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	GTTGAATGGGGCAGACGCGTT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											75	71	72					14																	70263850		2203	4300	6503	69333603	SO:0001583	missense	6554			L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.23C>T	14.37:g.70263850G>A	ENSP00000216540:p.Ala8Val		69333603	B9EGB6|Q2TU29	Missense_Mutation	SNP	ENST00000216540.4	37	CCDS9797.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902462	0.33628	.	.	ENSG00000100652	ENST00000216540	T	0.08546	3.08	5.23	0.0869	0.14448	.	0.925480	0.09272	N	0.825024	T	0.04588	0.0125	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43048	-0.9415	10	0.48119	T	0.1	-1.2777	1.7573	0.02985	0.2369:0.139:0.4808:0.1433	.	8	Q14973	NTCP_HUMAN	V	8	ENSP00000216540:A8V	ENSP00000216540:A8V	A	-	2	0	SLC10A1	69333603	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.116000	0.15561	-0.146000	0.11274	0.561000	0.74099	GCC		0.562	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			A	70263850	G	A	70263850	3	1	61	1	0	0	0	0	1	0	0	0	14410	1203	42	3	1046	3	SLC10A1	14	70263850	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27907	70263850	37085690	8992	16977										
SLC8A3	6547	broad.mit.edu	37	chr14	70515532	70515532	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacagctgtgactgaatCtttgagaccaatggtgcagc	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70515532C>A	ENST00000381269.2	-	7	3112	c.2359G>T	c.(2359-2361)Gat>Tat	p.D787Y	SLC8A3_ENST00000534137.1_Missense_Mutation_p.D784Y|SLC8A3_ENST00000533541.1_Missense_Mutation_p.D144Y|SLC8A3_ENST00000356921.2_Missense_Mutation_p.D781Y|SLC8A3_ENST00000394330.2_Missense_Mutation_p.D144Y|SLC8A3_ENST00000528359.1_Missense_Mutation_p.D785Y|SLC8A3_ENST00000216568.7_Missense_Mutation_p.D158Y|SLC8A3_ENST00000357887.3_Missense_Mutation_p.D785Y	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	787					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)	p.D787Y(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GTGACTGAATCTTTGAGACCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	14											66	53	58					14																	70515532		2203	4300	6503	69585285	SO:0001583	missense	6547			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.2359G>T	14.37:g.70515532C>A	ENSP00000370669:p.Asp787Tyr		69585285	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.762506	0.89932	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000216568;ENST00000394330;ENST00000534137;ENST00000528359;ENST00000533541	T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;0.52	5.78	5.78	0.91487	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	D	0.87621	0.6223	H	0.97516	4.02	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.999;0.998	D	0.91333	0.5091	10	0.87932	D	0	.	20.0165	0.97478	0.0:1.0:0.0:0.0	.	144;781;787;785;784;158	F2Z391;P57103-2;P57103;Q96QG2;Q96QG1;Q5K3P6	.;.;NAC3_HUMAN;.;.;.	Y	781;787;785;158;144;784;785;144	ENSP00000349392:D781Y;ENSP00000370669:D787Y;ENSP00000350560:D785Y;ENSP00000216568:D158Y;ENSP00000377863:D144Y;ENSP00000436688:D784Y;ENSP00000433531:D785Y;ENSP00000437103:D144Y	ENSP00000216568:D158Y	D	-	1	0	SLC8A3	69585285	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.757000	0.85209	2.740000	0.93945	0.455000	0.32223	GAT		0.532	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70515532	C	A	70515532	3	1	61	1	0	0	0	0	1	0	0	0	14745	913	32	2	432	2	SLC8A3	14	70515532	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	251682	70515532	36834008	8993	16978										
SLC8A3	6547	broad.mit.edu	37	chr14	70515604	70515604	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgagcatgccaatgatgaGgatggagacggcgaagcagg	18	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70515604G>T	ENST00000381269.2	-	7	3040	c.2287C>A	c.(2287-2289)Ctc>Atc	p.L763I	SLC8A3_ENST00000534137.1_Missense_Mutation_p.L760I|SLC8A3_ENST00000533541.1_Missense_Mutation_p.L120I|SLC8A3_ENST00000356921.2_Missense_Mutation_p.L757I|SLC8A3_ENST00000394330.2_Missense_Mutation_p.L120I|SLC8A3_ENST00000528359.1_Missense_Mutation_p.L761I|SLC8A3_ENST00000216568.7_Missense_Mutation_p.L134I|SLC8A3_ENST00000357887.3_Missense_Mutation_p.L761I	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	763					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)	p.L763I(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CCAATGATGAGGATGGAGACG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	14											78	65	69					14																	70515604		2203	4300	6503	69585357	SO:0001583	missense	6547			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.2287C>A	14.37:g.70515604G>T	ENSP00000370669:p.Leu763Ile		69585357	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	9.543	1.113765	0.20795	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000216568;ENST00000394330;ENST00000534137;ENST00000528359;ENST00000533541	T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;0.89	5.52	5.52	0.82312	Sodium/calcium exchanger membrane region (1);	0.131490	0.52532	D	0.000061	T	0.60741	0.2292	N	0.11023	0.085	0.37749	D	0.925915	B;B;B;D;D;B	0.63046	0.0;0.002;0.004;0.979;0.992;0.0	B;B;B;D;D;B	0.76071	0.012;0.008;0.02;0.982;0.987;0.005	T	0.61262	-0.7098	10	0.19590	T	0.45	.	14.2959	0.66314	0.0:0.0:0.8514:0.1486	.	120;757;763;761;760;134	F2Z391;P57103-2;P57103;Q96QG2;Q96QG1;Q5K3P6	.;.;NAC3_HUMAN;.;.;.	I	757;763;761;134;120;760;761;120	ENSP00000349392:L757I;ENSP00000370669:L763I;ENSP00000350560:L761I;ENSP00000216568:L134I;ENSP00000377863:L120I;ENSP00000436688:L760I;ENSP00000433531:L761I;ENSP00000437103:L120I	ENSP00000216568:L134I	L	-	1	0	SLC8A3	69585357	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.951000	0.29135	2.591000	0.87537	0.455000	0.32223	CTC		0.572	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70515604	G	T	70515604	3	4	61	1	0	0	0	0	1	0	0	0	14745	1000	35	2	504	2	SLC8A3	14	70515604	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72	70515604	36833936	8994	16979										
ADAM21	8747	broad.mit.edu	37	chr14	70925820	70925820	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctataaagaaatcaattCtcagggaaaccgttttggtc	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70925820C>A	ENST00000603540.1	+	2	1862	c.1604C>A	c.(1603-1605)tCt>tAt	p.S535Y	ADAM21_ENST00000267499.3_Missense_Mutation_p.S535Y|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	535	Cys-rich.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S535Y(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAAATCAATTCTCAGGGAAAC	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	14											25	50	42					14																	70925820		2112	4251	6363	69995573	SO:0001583	missense	8747			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"ADAM metallopeptidase domain containing"	200	protein-coding gene	gene with protein product		603713	"a disintegrin and metalloproteinase domain 21"			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.1604C>A	14.37:g.70925820C>A	ENSP00000474385:p.Ser535Tyr		69995573	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530998	0.27387	.	.	ENSG00000139985	ENST00000267499	T	0.24538	1.85	4.35	2.47	0.30058	ADAM, cysteine-rich (2);	1.549470	0.04382	U	0.361039	T	0.41050	0.1142	M	0.82823	2.61	0.09310	N	1	B	0.26120	0.142	B	0.32090	0.14	T	0.48647	-0.9017	10	0.87932	D	0	.	11.4816	0.50328	0.0:0.8402:0.0:0.1598	.	535	Q9UKJ8	ADA21_HUMAN	Y	535	ENSP00000267499:S535Y	ENSP00000267499:S535Y	S	+	2	0	ADAM21	69995573	0.000000	0.05858	0.635000	0.29338	0.614000	0.37383	-0.518000	0.06267	1.150000	0.42419	0.460000	0.39030	TCT		0.378	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			A	70925820	C	A	70925820	3	1	61	1	0	0	0	0	1	0	0	0	243	913	32	2	1606	2	ADAM21	14	70925820	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	410216	70925820	36423720	8995	16980										
ADAM21	8747	broad.mit.edu	37	chr14	70926283	70926283	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgccgctgattgtgatTccttctttgtctgttttgac	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:70926283T>C	ENST00000603540.1	+	2	2325	c.2067T>C	c.(2065-2067)atT>atC	p.I689I	ADAM21_ENST00000267499.3_Silent_p.I689I|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	689					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.I689I(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGATTGTGATTCCTTCTTTGT	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	14											79	64	69					14																	70926283		2203	4300	6503	69996036	SO:0001819	synonymous_variant	8747			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"ADAM metallopeptidase domain containing"	200	protein-coding gene	gene with protein product		603713	"a disintegrin and metalloproteinase domain 21"			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.2067T>C	14.37:g.70926283T>C			69996036	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																				0.478	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			C	70926283	T	C	70926283	2	2	61	1	0	0	0	0	0	0	0	1	243	1771	62	4		4	ADAM21	14	70926283	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	463	70926283	36423257	8996	16981										
MAP3K9	4293	broad.mit.edu	37	chr14	71216752	71216752	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctaagccatcaatgcctcGaaagggcacctcaccagtca	8	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:71216752G>A	ENST00000554752.2	-	4	1047	c.1048C>T	c.(1048-1050)Cga>Tga	p.R350*	MAP3K9_ENST00000381250.4_Nonsense_Mutation_p.R350*|MAP3K9_ENST00000555993.2_Nonsense_Mutation_p.R350*|MAP3K9_ENST00000554146.1_Nonsense_Mutation_p.R87*|MAP3K9_ENST00000553414.1_Nonsense_Mutation_p.R44*	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	350	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R350*(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TCAATGCCTCGAAAGGGCACC	0.488																																					GBM(114;411 1587 13539 28235 50070)											1	Substitution - Nonsense(1)	large_intestine(1)	14											131	118	123					14																	71216752		2203	4300	6503	70286505	SO:0001587	stop_gained	4293			AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1048C>T	14.37:g.71216752G>A	ENSP00000451612:p.Arg350*		70286505	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Nonsense_Mutation	SNP	ENST00000554752.2	37		.	.	.	.	.	.	.	.	.	.	G	35	5.482555	0.96307	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	.	.	.	X	350;350;44;350;87;78	.	ENSP00000005198:R350X	R	-	1	2	MAP3K9	70286505	1.000000	0.71417	1.000000	0.80357	0.045000	0.14185	7.953000	0.87836	2.808000	0.96608	0.655000	0.94253	CGA		0.488	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			A	71216752	G	A	71216752	4	1	61	1	0	0	0	0	0	1	0	0	9287	1066	37	1	2348	1	MAP3K9	14	71216752	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	290469	71216752	36132788	8997	16982										
PCNX	22990	broad.mit.edu	37	chr14	71500710	71500710	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatccagaagaccctctatCtgaagtaaaagatccactgc	6	11	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:71500710C>A	ENST00000304743.2	+	18	4177	c.3731C>A	c.(3730-3732)tCt>tAt	p.S1244Y	PCNX_ENST00000238570.5_Missense_Mutation_p.S1244Y|PCNX_ENST00000439984.3_Missense_Mutation_p.S1133Y	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1244						integral component of membrane (GO:0016021)		p.S1244Y(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GACCCTCTATCTGAAGTAAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	14											54	60	58					14																	71500710		2202	4293	6495	70570463	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3731C>A	14.37:g.71500710C>A	ENSP00000304192:p.Ser1244Tyr		70570463	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.8|23.8	4.462138|4.462138	0.84425|0.84425	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.10960	.|3.26;3.24;2.82	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	.|0.122175	.|0.64402	.|D	.|0.000016	T|T	0.31734|0.31734	0.0806|0.0806	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.997;0.981;0.998	.|D;P;D	.|0.80764	.|0.994;0.76;0.928	T|T	0.01945|0.01945	-1.1242|-1.1242	5|10	.|0.72032	.|D	.|0.01	.|.	18.7492|18.7492	0.91807|0.91807	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1244;1133;1244	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	M|Y	303|1244;1244;1133	.|ENSP00000304192:S1244Y;ENSP00000238570:S1244Y;ENSP00000396617:S1133Y	.|ENSP00000238570:S1244Y	L|S	+|+	1|2	2|0	PCNX|PCNX	70570463|70570463	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.081000|7.081000	0.76844|0.76844	2.420000|2.420000	0.82092|0.82092	0.650000|0.650000	0.86243|0.86243	CTG|TCT		0.308	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71500710	C	A	71500710	3	1	61	1	0	0	0	0	1	0	0	0	11622	913	32	2	3801	2	PCNX	14	71500710	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	283958	71500710	35848830	8998	16983										
PCNX	22990	broad.mit.edu	37	chr14	71511997	71511997	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtataatcagtatgaagttCgaagtaagtatttcattagc	8	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:71511997C>T	ENST00000304743.2	+	20	4461	c.4015C>T	c.(4015-4017)Cga>Tga	p.R1339*	PCNX_ENST00000238570.5_Nonsense_Mutation_p.R1339*|PCNX_ENST00000439984.3_Nonsense_Mutation_p.R1228*	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1339						integral component of membrane (GO:0016021)		p.R1339*(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GTATGAAGTTCGAAGTAAGTA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											105	95	98					14																	71511997		2202	4300	6502	70581750	SO:0001587	stop_gained	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4015C>T	14.37:g.71511997C>T	ENSP00000304192:p.Arg1339*		70581750	B2RTR6|O94897|Q96AI7|Q9Y2J9	Nonsense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	C	37	6.158134	0.97334	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	.	.	.	5.72	4.81	0.61882	.	0.121477	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2765	0.82646	0.1336:0.8664:0.0:0.0	.	.	.	.	X	1339;1339;1228	.	ENSP00000238570:R1339X	R	+	1	2	PCNX	70581750	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.069000	0.41481	1.510000	0.48803	0.655000	0.94253	CGA		0.343	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71511997	C	T	71511997	4	4	61	1	0	0	0	0	0	1	0	0	11622	876	31	1	4093	1	PCNX	14	71511997	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11287	71511997	35837543	8999	16984										
PCNX	22990	broad.mit.edu	37	chr14	71513739	71513739	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcttctttttgtggagaaGaatataatctatccattgat	8	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:71513739G>T	ENST00000304743.2	+	21	4523	c.4077G>T	c.(4075-4077)aaG>aaT	p.K1359N	PCNX_ENST00000238570.5_Missense_Mutation_p.K1359N|PCNX_ENST00000439984.3_Missense_Mutation_p.K1248N	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1359						integral component of membrane (GO:0016021)		p.K1359N(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTGTGGAGAAGAATATAATCT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	14											118	108	111					14																	71513739		2203	4300	6503	70583492	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4077G>T	14.37:g.71513739G>T	ENSP00000304192:p.Lys1359Asn		70583492	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.32|15.32	2.797447|2.797447	0.50208|0.50208	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.13420|.	2.94;2.86;2.59|.	4.8|4.8	1.91|1.91	0.25777|0.25777	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71099|0.71099	0.3300|0.3300	M|M	0.81802|0.81802	2.56|2.56	0.58432|0.58432	D|D	0.999991|0.999991	P;D;D|.	0.89917|.	0.944;1.0;0.998|.	P;D;P|.	0.91635|.	0.714;0.999;0.866|.	T|T	0.69420|0.69420	-0.5150|-0.5150	10|5	0.87932|.	D|.	0|.	.|.	8.8391|8.8391	0.35131|0.35131	0.3106:0.0:0.6894:0.0|0.3106:0.0:0.6894:0.0	.|.	1359;1248;1359|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	N|I	1359;1359;1248|418	ENSP00000304192:K1359N;ENSP00000238570:K1359N;ENSP00000396617:K1248N|.	ENSP00000238570:K1359N|.	K|R	+|+	3|2	2|0	PCNX|PCNX	70583492|70583492	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	3.494000|3.494000	0.53273|0.53273	0.542000|0.542000	0.28846|0.28846	0.455000|0.455000	0.32223|0.32223	AAG|AGA		0.368	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71513739	G	T	71513739	3	4	61	1	0	0	0	0	1	0	0	0	11622	933	33	2	4159	2	PCNX	14	71513739	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1742	71513739	35835801	9000	16985										
SIPA1L1	26037	broad.mit.edu	37	chr14	72055295	72055295	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaagatgacaaatctgatCgaggtccaactccaaccaag	7	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72055295C>T	ENST00000555818.1	+	2	1054	c.706C>T	c.(706-708)Cga>Tga	p.R236*	SIPA1L1_ENST00000358550.2_Nonsense_Mutation_p.R236*|SIPA1L1_ENST00000381232.3_Nonsense_Mutation_p.R236*	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	236					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.R236*(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAAATCTGATCGAGGTCCAAC	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											104	93	97					14																	72055295		2203	4300	6503	71125048	SO:0001587	stop_gained	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.706C>T	14.37:g.72055295C>T	ENSP00000450832:p.Arg236*		71125048	J3KP19|O95321|Q9UDU4|Q9UNU4	Nonsense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	40	8.514703	0.98843	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	.	.	.	6.07	5.19	0.71726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8969	19.7327	0.96190	0.1139:0.886:0.0:0.0	.	.	.	.	X	236	.	ENSP00000351352:R236X	R	+	1	2	SIPA1L1	71125048	1.000000	0.71417	0.549000	0.28204	0.001000	0.01503	4.774000	0.62339	0.908000	0.36671	-0.808000	0.03180	CGA		0.433	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72055295	C	T	72055295	4	4	61	1	0	0	0	0	0	1	0	0	14366	876	31	1	708	1	SIPA1L1	14	72055295	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541556	72055295	35294245	9001	16986										
SIPA1L1	26037	broad.mit.edu	37	chr14	72055407	72055407	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacagagagagaacctcaGgctttttaaggaaagggaaa	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72055407G>T	ENST00000555818.1	+	2	1166	c.818G>T	c.(817-819)aGg>aTg	p.R273M	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R273M|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R273M	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	273					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.R273M(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GAGAACCTCAGGCTTTTTAAG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											66	68	67					14																	72055407		2203	4300	6503	71125160	SO:0001583	missense	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.818G>T	14.37:g.72055407G>T	ENSP00000450832:p.Arg273Met		71125160	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153442	0.78114	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.47528	0.84;0.84;0.84	6.07	6.07	0.98685	.	0.130697	0.64402	D	0.000001	T	0.57621	0.2066	L	0.36672	1.1	0.80722	D	1	D;D;D	0.61080	0.972;0.967;0.989	P;P;P	0.59012	0.731;0.78;0.85	T	0.46498	-0.9187	10	0.32370	T	0.25	-32.0357	20.6593	0.99626	0.0:0.0:1.0:0.0	.	273;273;273	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	M	273	ENSP00000370630:R273M;ENSP00000450832:R273M;ENSP00000351352:R273M	ENSP00000351352:R273M	R	+	2	0	SIPA1L1	71125160	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.796000	0.85898	2.885000	0.99019	0.655000	0.94253	AGG		0.438	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72055407	G	T	72055407	3	4	61	1	0	0	0	0	1	0	0	0	14366	1000	35	2	820	2	SIPA1L1	14	72055407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112	72055407	35294133	9002	16987										
SIPA1L1	26037	broad.mit.edu	37	chr14	72055806	72055806	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggaccagggagatgataAaagcaatgagcttgtaatga	12	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72055806A>C	ENST00000555818.1	+	2	1565	c.1217A>C	c.(1216-1218)aAa>aCa	p.K406T	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.K406T|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.K406T	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	406					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.K406T(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GGAGATGATAAAAGCAATGAG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											92	93	92					14																	72055806		2203	4300	6503	71125559	SO:0001583	missense	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1217A>C	14.37:g.72055806A>C	ENSP00000450832:p.Lys406Thr		71125559	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.673927	0.67928	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.79247	-1.25;-1.25;-1.25	5.88	5.88	0.94601	.	0.041708	0.85682	D	0.000000	D	0.86464	0.5939	M	0.67953	2.075	0.80722	D	1	B;P;D	0.71674	0.226;0.712;0.998	B;P;D	0.76071	0.132;0.525;0.987	D	0.85225	0.1029	10	0.34782	T	0.22	-25.9926	16.2792	0.82664	1.0:0.0:0.0:0.0	.	406;406;406	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	T	406	ENSP00000370630:K406T;ENSP00000450832:K406T;ENSP00000351352:K406T	ENSP00000351352:K406T	K	+	2	0	SIPA1L1	71125559	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.528000	0.81941	2.243000	0.73865	0.533000	0.62120	AAA		0.463	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72055806	A	C	72055806	3	2	61	1	0	0	0	0	1	0	0	0	14366	14	1	4	1219	4	SIPA1L1	14	72055806	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	399	72055806	35293734	9003	16988										
SIPA1L1	26037	broad.mit.edu	37	chr14	72055927	72055927	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggatgtgaaagtgcctcCtttgagtctacccttagttc	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72055927C>A	ENST00000555818.1	+	2	1686	c.1338C>A	c.(1336-1338)tcC>tcA	p.S446S	SIPA1L1_ENST00000358550.2_Silent_p.S446S|SIPA1L1_ENST00000381232.3_Silent_p.S446S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	446					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.S446S(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AAAGTGCCTCCTTTGAGTCTA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	14											111	103	106					14																	72055927		2203	4300	6503	71125680	SO:0001819	synonymous_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1338C>A	14.37:g.72055927C>A			71125680	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.448	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72055927	C	A	72055927	2	1	61	1	0	0	0	0	0	0	0	1	14366	668	24	2		2	SIPA1L1	14	72055927	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121	72055927	35293613	9004	16989										
SIPA1L1	26037	broad.mit.edu	37	chr14	72056032	72056032	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatagagtgaaaagatacatCgtggaacacgtagatctggg	13	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72056032C>T	ENST00000555818.1	+	2	1791	c.1443C>T	c.(1441-1443)atC>atT	p.I481I	SIPA1L1_ENST00000358550.2_Silent_p.I481I|SIPA1L1_ENST00000381232.3_Silent_p.I481I	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	481					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.I481I(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AAAGATACATCGTGGAACACG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	14											64	59	61					14																	72056032		2203	4300	6503	71125785	SO:0001819	synonymous_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1443C>T	14.37:g.72056032C>T			71125785	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.398	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72056032	C	T	72056032	2	4	61	1	0	0	0	0	0	0	0	1	14366	874	31	1		1	SIPA1L1	14	72056032	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105	72056032	35293508	9005	16990										
SIPA1L1	26037	broad.mit.edu	37	chr14	72117181	72117181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactattgggagagcgagttCggctcaaaggatttgagaag	14	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72117181C>T	ENST00000555818.1	+	5	2296	c.1948C>T	c.(1948-1950)Cgg>Tgg	p.R650W	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R650W|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R650W|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.R125W	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	650	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.R650W(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGAGCGAGTTCGGCTCAAAGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											101	98	99					14																	72117181		2203	4300	6503	71186934	SO:0001583	missense	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1948C>T	14.37:g.72117181C>T	ENSP00000450832:p.Arg650Trp		71186934	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299765	0.81136	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413;ENST00000555066	D;D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39;-3.39	5.53	4.63	0.57726	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.97511	0.9185	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.989;0.997;1.0;0.998	D	0.98561	1.0641	10	0.72032	D	0.01	-19.617	15.9931	0.80220	0.1358:0.8642:0.0:0.0	.	125;650;125;650;650	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	W	650;650;650;125;166	ENSP00000370630:R650W;ENSP00000450832:R650W;ENSP00000351352:R650W;ENSP00000440682:R125W;ENSP00000452450:R166W	ENSP00000351352:R650W	R	+	1	2	SIPA1L1	71186934	1.000000	0.71417	0.983000	0.44433	0.943000	0.58893	2.939000	0.48995	1.444000	0.47605	0.591000	0.81541	CGG		0.448	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72117181	C	T	72117181	3	4	61	1	0	0	0	0	1	0	0	0	14366	875	31	1	1962	1	SIPA1L1	14	72117181	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61149	72117181	35232359	9006	16991										
SIPA1L1	26037	broad.mit.edu	37	chr14	72138352	72138352	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaacgaggagaatgtgtTtcagtgggtagttttattaa	12	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72138352T>G	ENST00000555818.1	+	8	3120	c.2772T>G	c.(2770-2772)gtT>gtG	p.V924V	SIPA1L1_ENST00000358550.2_Silent_p.V924V|SIPA1L1_ENST00000381232.3_Silent_p.V924V|SIPA1L1_ENST00000537413.1_Silent_p.V399V	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	924					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.V924V(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GAGAATGTGTTTCAGTGGGTA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	14											75	72	73					14																	72138352		2203	4300	6503	71208105	SO:0001819	synonymous_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.2772T>G	14.37:g.72138352T>G			71208105	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.413	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		G	72138352	T	G	72138352	2	3	61	1	0	0	0	0	0	0	0	1	14366	1828	64	4		4	SIPA1L1	14	72138352	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	21171	72138352	35211188	9007	16992										
SIPA1L1	26037	broad.mit.edu	37	chr14	72152162	72152162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaattcaagtttcccttccGaaataataacaagtggcaga	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72152162G>A	ENST00000555818.1	+	10	3536	c.3188G>A	c.(3187-3189)cGa>cAa	p.R1063Q	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R1063Q|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R1063Q|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.R538Q	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1063					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.R1063Q(2)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		TTTCCCTTCCGAAATAATAAC	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	14											98	96	97					14																	72152162		2203	4300	6503	71221915	SO:0001583	missense	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3188G>A	14.37:g.72152162G>A	ENSP00000450832:p.Arg1063Gln		71221915	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	36	5.672643	0.96754	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	D;D;D;D	0.89123	-1.66;-1.64;-1.66;-2.47	5.48	5.48	0.80851	.	0.057524	0.64402	D	0.000001	D	0.93848	0.8032	M	0.72118	2.19	0.80722	D	1	P;B;D;P;D	0.69078	0.892;0.382;0.985;0.943;0.997	P;B;P;P;D	0.67725	0.601;0.043;0.768;0.565;0.953	D	0.92984	0.6409	10	0.45353	T	0.12	-9.3747	19.7112	0.96096	0.0:0.0:1.0:0.0	.	538;1063;538;1063;1063	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	Q	1063;1063;1063;538	ENSP00000370630:R1063Q;ENSP00000450832:R1063Q;ENSP00000351352:R1063Q;ENSP00000440682:R538Q	ENSP00000351352:R1063Q	R	+	2	0	SIPA1L1	71221915	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.742000	0.91588	2.726000	0.93360	0.561000	0.74099	CGA		0.507	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72152162	G	A	72152162	3	1	61	1	0	0	0	0	1	0	0	0	14366	1058	37	1	3222	1	SIPA1L1	14	72152162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13810	72152162	35197378	9008	16993										
SIPA1L1	26037	broad.mit.edu	37	chr14	72171471	72171471	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacctcaggatttcaattCttttgtcctcgagcagcatg	9	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:72171471C>A	ENST00000555818.1	+	13	4028	c.3680C>A	c.(3679-3681)tCt>tAt	p.S1227Y	SIPA1L1_ENST00000554874.1_Intron|SIPA1L1_ENST00000358550.2_Intron|SIPA1L1_ENST00000381232.3_Intron|SIPA1L1_ENST00000537413.1_Intron	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1227					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.S1227Y(2)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GATTTCAATTCTTTTGTCCTC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	14											111	106	108					14																	72171471		2203	4300	6503	71241224	SO:0001583	missense	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3680C>A	14.37:g.72171471C>A	ENSP00000450832:p.Ser1227Tyr		71241224	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292623	0.40594	.	.	ENSG00000197555	ENST00000555818	T	0.54071	0.59	5.73	5.73	0.89815	.	0.230842	0.30134	N	0.010329	T	0.58452	0.2123	N	0.22421	0.69	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.69142	0.962;0.962	T	0.56438	-0.7979	10	0.38643	T	0.18	-13.2603	15.402	0.74849	0.0:1.0:0.0:0.0	.	1227;1227	A6H8W6;O43166	.;SI1L1_HUMAN	Y	1227	ENSP00000450832:S1227Y	ENSP00000351352:S1227Y	S	+	2	0	SIPA1L1	71241224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.676000	0.37565	2.706000	0.92434	0.563000	0.77884	TCT		0.393	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72171471	C	A	72171471	3	1	61	1	0	0	0	0	1	0	0	0	14366	913	32	2	3726	2	SIPA1L1	14	72171471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19309	72171471	35178069	9009	16994										
DPF3	8110	broad.mit.edu	37	chr14	73190389	73190389	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatatcctcttccaaatcCtcttcttcattcccttcttc	2	15	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73190389C>A	ENST00000556509.1	-	5	476	c.477G>T	c.(475-477)gaG>gaT	p.E159D	DPF3_ENST00000557704.1_5'UTR|DPF3_ENST00000541685.1_Missense_Mutation_p.E159D|DPF3_ENST00000546183.1_Missense_Mutation_p.E169D	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	159					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)	p.E158D(1)|p.E159D(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CTTCCAAATCCTCTTCTTCAT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	14											252	251	252					14																	73190389		1870	4113	5983	72260142	SO:0001583	missense	8110			U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.477G>T	14.37:g.73190389C>A	ENSP00000450518:p.Glu159Asp		72260142	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	C	12.10	1.835534	0.32421	.	.	ENSG00000205683	ENST00000540281;ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.90732	-2.72;-0.24;-0.19	5.07	-0.57	0.11753	.	.	.	.	.	T	0.79464	0.4450	N	0.12182	0.205	0.48830	D	0.999712	B;B;B	0.19706	0.038;0.013;0.0	B;B;B	0.24155	0.051;0.021;0.001	T	0.65257	-0.6212	9	0.52906	T	0.07	.	7.1914	0.25828	0.1098:0.383:0.0:0.5072	.	169;159;159	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	D	159;159;158;159;169	ENSP00000450518:E159D;ENSP00000441640:E159D;ENSP00000444662:E169D	ENSP00000381791:E214D	E	-	3	2	DPF3	72260142	0.355000	0.24921	0.997000	0.53966	0.984000	0.73092	-0.577000	0.05847	-0.141000	0.11374	-0.367000	0.07326	GAG		0.423	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			A	73190389	C	A	73190389	3	1	61	1	0	0	0	0	1	0	0	0	4729	680	24	2	616	2	DPF3	14	73190389	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1018918	73190389	34159151	9010	16995										
RBM25	58517	broad.mit.edu	37	chr14	73576125	73576125	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacgagataggaagagagaGaaggaggagcttgaggaaat	17	2	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73576125G>T	ENST00000261973.7	+	14	1902	c.1617G>T	c.(1615-1617)gaG>gaT	p.E539D	RBM25_ENST00000532483.1_3'UTR|RBM25_ENST00000527432.1_Missense_Mutation_p.E539D	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	539	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E539D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		GGAAGAGAGAGAAGGAGGAGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	14											108	109	109					14																	73576125		2203	4300	6503	72645878	SO:0001583	missense	58517			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1617G>T	14.37:g.73576125G>T	ENSP00000261973:p.Glu539Asp		72645878	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294335	0.81025	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.26810	1.71;1.71	5.97	-2.01	0.07410	.	0.000000	0.85682	D	0.000000	T	0.44244	0.1284	M	0.81341	2.54	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.46596	-0.9180	10	0.46703	T	0.11	.	12.1545	0.54068	0.6671:0.0:0.3329:0.0	.	539	P49756	RBM25_HUMAN	D	539	ENSP00000261973:E539D;ENSP00000431150:E539D	ENSP00000261973:E539D	E	+	3	2	RBM25	72645878	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	1.162000	0.31786	-0.252000	0.09528	0.655000	0.94253	GAG		0.478	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		T	73576125	G	T	73576125	3	4	61	1	0	0	0	0	1	0	0	0	13162	933	33	2	1667	2	RBM25	14	73576125	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	385736	73576125	33773415	9011	16996										
RBM25	58517	broad.mit.edu	37	chr14	73578279	73578279	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaattctgtgaagagaaaGaaactacctgtagatagtgt	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73578279G>T	ENST00000261973.7	+	16	2346	c.2061G>T	c.(2059-2061)aaG>aaT	p.K687N	RBM25_ENST00000532483.1_3'UTR|RBM25_ENST00000527432.1_Missense_Mutation_p.K687N	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	687					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K687N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		TGAAGAGAAAGAAACTACCTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											100	99	100					14																	73578279		2203	4300	6503	72648032	SO:0001583	missense	58517			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.2061G>T	14.37:g.73578279G>T	ENSP00000261973:p.Lys687Asn		72648032	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.980537	0.34942	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.14640	2.49;2.49	6.08	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.22166	0.0534	M	0.76574	2.34	0.80722	D	1	P	0.35551	0.509	B	0.38194	0.267	T	0.01648	-1.1304	10	0.39692	T	0.17	.	15.3891	0.74729	0.0663:0.0:0.9337:0.0	.	687	P49756	RBM25_HUMAN	N	687	ENSP00000261973:K687N;ENSP00000431150:K687N	ENSP00000261973:K687N	K	+	3	2	RBM25	72648032	1.000000	0.71417	1.000000	0.80357	0.419000	0.31324	5.627000	0.67784	1.595000	0.50050	-0.229000	0.12294	AAG		0.378	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		T	73578279	G	T	73578279	3	4	61	1	0	0	0	0	1	0	0	0	13162	933	33	2	2119	2	RBM25	14	73578279	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2154	73578279	33771261	9012	16997										
PAPLN	89932	broad.mit.edu	37	chr14	73739302	73739302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcccagctttgtggcaatgAgtattactccagcttctgct	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73739302A>G	ENST00000554301.1	+	26	3930	c.3767A>G	c.(3766-3768)gAg>gGg	p.E1256G	RP4-647C14.3_ENST00000556578.1_RNA|PAPLN_ENST00000340738.5_Missense_Mutation_p.E1229G|PAPLN_ENST00000381166.3_3'UTR|PAPLN_ENST00000555445.1_Missense_Mutation_p.E1240G|PAPLN_ENST00000427855.1_Missense_Mutation_p.E1256G			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	1256	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.E1229G(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TGTGGCAATGAGTATTACTCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	14											122	116	118					14																	73739302		2203	4300	6503	72809055	SO:0001583	missense	89932			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.3767A>G	14.37:g.73739302A>G	ENSP00000451803:p.Glu1256Gly		72809055	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		.	.	.	.	.	.	.	.	.	.	A	20.6	4.020093	0.75275	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.54	5.54	0.83059	PLAC (2);	.	.	.	.	T	0.52175	0.1718	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.99;0.99	D;D;P;P	0.74348	0.971;0.983;0.881;0.894	T	0.56147	-0.8027	9	0.72032	D	0.01	.	15.8465	0.78895	1.0:0.0:0.0:0.0	.	1240;1256;455;1229	O95428-5;O95428;O95428-2;O95428-6	.;PPN_HUMAN;.;.	G	1229;1256;1256;1240	ENSP00000345395:E1229G;ENSP00000403403:E1256G;ENSP00000451803:E1256G;ENSP00000451729:E1240G	ENSP00000345395:E1229G	E	+	2	0	PAPLN	72809055	0.997000	0.39634	1.000000	0.80357	0.944000	0.59088	3.288000	0.51739	2.326000	0.78906	0.533000	0.62120	GAG		0.602	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		G	73739302	A	G	73739302	3	3	61	1	0	0	0	0	1	0	0	0	11459	304	11	4	3784	4	PAPLN	14	73739302	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	161023	73739302	33610238	9013	16998										
HEATR4	399671	broad.mit.edu	37	chr14	73989186	73989186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggggatgccccaggccttCgaggacgcttgctctggatc	15	12	1	0	rs528517201		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73989186C>T	ENST00000553558.1	-	3	992	c.671G>A	c.(670-672)cGa>cAa	p.R224Q	RP3-414A15.2_ENST00000555972.2_RNA|HEATR4_ENST00000560393.1_Missense_Mutation_p.R177Q|RP3-414A15.11_ENST00000553394.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.R224Q	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	224								p.R177Q(2)|p.R224Q(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		CCCAGGCCTTCGAGGACGCTT	0.612													C|||	1	0.000199681	8e-04	0	5008	,	,		19291	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	14											55	54	54					14																	73989186		2203	4300	6503	73058939	SO:0001583	missense	399671			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.671G>A	14.37:g.73989186C>T	ENSP00000450444:p.Arg224Gln		73058939	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	C	2.765	-0.256955	0.05829	.	.	ENSG00000187105	ENST00000553558;ENST00000334988	T;T	0.42131	1.04;0.98	6.07	-12.1	0.00011	.	2.189300	0.01819	N	0.033951	T	0.16938	0.0407	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09378	-1.0677	10	0.22109	T	0.4	0.6839	1.9581	0.03380	0.1368:0.2695:0.3223:0.2715	.	224	Q86WZ0	HEAT4_HUMAN	Q	224;177	ENSP00000450444:R224Q;ENSP00000335447:R177Q	ENSP00000335447:R177Q	R	-	2	0	HEATR4	73058939	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.586000	0.00902	-2.152000	0.00794	-3.449000	0.00036	CGA		0.612	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		T	73989186	C	T	73989186	3	4	61	1	0	0	0	0	1	0	0	0	7051	884	31	1	2473	1	HEATR4	14	73989186	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	249884	73989186	33360354	9014	16999										
HEATR4	399671	broad.mit.edu	37	chr14	73989677	73989677	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccattttcaaatattggctCttgcggtgtagacggtactg	11	8	2	1	rs185514885	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:73989677C>A	ENST00000553558.1	-	3	501	c.180G>T	c.(178-180)aaG>aaT	p.K60N	RP3-414A15.2_ENST00000555972.2_RNA|HEATR4_ENST00000560393.1_Missense_Mutation_p.K13N|RP3-414A15.11_ENST00000553394.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.K60N	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	60								p.K13N(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		AATATTGGCTCTTGCGGTGTA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14											84	88	86					14																	73989677		2203	4300	6503	73059430	SO:0001583	missense	399671			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.180G>T	14.37:g.73989677C>A	ENSP00000450444:p.Lys60Asn		73059430	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211876	0.58452	.	.	ENSG00000187105	ENST00000553558;ENST00000334988;ENST00000556455	T;T	0.16196	2.36;2.36	5.6	1.69	0.24217	.	0.412950	0.21177	N	0.078900	T	0.20333	0.0489	L	0.34521	1.04	0.09310	N	1	D	0.59357	0.985	P	0.55055	0.767	T	0.04900	-1.0919	10	0.72032	D	0.01	-8.278	8.3772	0.32451	0.0:0.6722:0.0:0.3278	.	60	Q86WZ0	HEAT4_HUMAN	N	60;13;60	ENSP00000450444:K60N;ENSP00000452407:K60N	ENSP00000335447:K13N	K	-	3	2	HEATR4	73059430	0.023000	0.18921	0.298000	0.25002	0.018000	0.09664	1.094000	0.30951	0.311000	0.23014	-0.253000	0.11424	AAG		0.488	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		A	73989677	C	A	73989677	3	1	61	1	0	0	0	0	1	0	0	0	7051	912	32	2	2964	2	HEATR4	14	73989677	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	491	73989677	33359863	9015	17000										
ACOT6	641372	broad.mit.edu	37	chr14	74086323	74086323	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagctcatgggaaagaaaGaccccagataatctgttacc	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74086323G>T	ENST00000381139.1	+	2	735	c.404G>T	c.(403-405)aGa>aTa	p.R135I	RP3-414A15.10_ENST00000555011.1_RNA|RP3-414A15.10_ENST00000555500.1_RNA	NM_001037162.1	NP_001032239.1	Q3I5F7	ACOT6_HUMAN	acyl-CoA thioesterase 6	135						cytosol (GO:0005829)	carboxylic ester hydrolase activity (GO:0052689)	p.R135I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00331)		GGGAAAGAAAGACCCCAGATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											72	65	67					14																	74086323		2203	4300	6503	73156076	SO:0001583	missense	641372			DQ082756, BF109853	CCDS32118.1	14q24.3	2011-02-16			ENSG00000205669	ENSG00000205669		"Acyl CoA thioesterases"	33159	protein-coding gene	gene with protein product		614267	"chromosome 14 open reading frame 42"	C14orf42		16940157	Standard	NM_001037162		Approved		uc001xop.3	Q3I5F7		ENST00000381139.1:c.404G>T	14.37:g.74086323G>T	ENSP00000370531:p.Arg135Ile		73156076		Missense_Mutation	SNP	ENST00000381139.1	37	CCDS32118.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.719331	0.68844	.	.	ENSG00000205669	ENST00000554229;ENST00000381139	T;T	0.44482	1.51;0.92	5.8	-1.09	0.09904	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.587166	0.17913	N	0.157771	T	0.44265	0.1285	L	0.54323	1.7	0.45979	D	0.998797	B	0.31705	0.336	B	0.43889	0.435	T	0.48822	-0.9001	10	0.72032	D	0.01	-19.8465	10.2956	0.43623	0.7587:0.0:0.2413:0.0	.	135	Q3I5F7	ACOT6_HUMAN	I	135	ENSP00000451464:R135I;ENSP00000370531:R135I	ENSP00000370531:R135I	R	+	2	0	ACOT6	73156076	0.691000	0.27709	0.955000	0.39395	0.962000	0.63368	0.830000	0.27462	-0.091000	0.12440	0.561000	0.74099	AGA		0.448	ACOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414437.1	NM_001037162		T	74086323	G	T	74086323	3	4	61	1	0	0	0	0	1	0	0	0	154	942	33	2	410	2	ACOT6	14	74086323	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96646	74086323	33263217	9016	17001										
PTGR2	145482	broad.mit.edu	37	chr14	74340905	74340905	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggttattctggatggaaaTagccttgaaaaggtgatata	11	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74340905T>C	ENST00000555661.1	+	4	481	c.336T>C	c.(334-336)aaT>aaC	p.N112N	PTGR2_ENST00000553813.1_Intron|PTGR2_ENST00000555228.1_Silent_p.N112N|PTGR2_ENST00000267568.4_Silent_p.N112N|RP5-1021I20.4_ENST00000556551.2_Silent_p.N112N			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	112					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)	p.N112N(1)		NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	TGGATGGAAATAGCCTTGAAA	0.338																																					Esophageal Squamous(98;1155 1417 16452 47043 47872)											1	Substitution - coding silent(1)	large_intestine(1)	14											74	76	75					14																	74340905		2203	4300	6503	73410658	SO:0001819	synonymous_variant	145482			AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"zinc binding alcohol dehydrogenase domain containing 1"	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.336T>C	14.37:g.74340905T>C			73410658	Q3L8A4|Q6MZH8	Silent	SNP	ENST00000555661.1	37	CCDS9820.1																																																																																				0.338	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1			C	74340905	T	C	74340905	2	2	61	1	0	0	0	0	0	0	0	1	12789	1403	49	4		4	PTGR2	14	74340905	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	254582	74340905	33008635	9017	17002										
PTGR2	145482	broad.mit.edu	37	chr14	74346002	74346002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatcagtgatacagtgatAagtcaggttgtttgctgatt	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74346002A>G	ENST00000555661.1	+	6	868	c.723A>G	c.(721-723)atA>atG	p.I241M	PTGR2_ENST00000553813.1_Missense_Mutation_p.I107M|PTGR2_ENST00000555228.1_Missense_Mutation_p.I241M|PTGR2_ENST00000267568.4_Missense_Mutation_p.I241M|RP5-1021I20.4_ENST00000556551.2_Intron			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	241					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)	p.I241M(1)		NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	ATACAGTGATAAGTCAGGTTG	0.328																																					Esophageal Squamous(98;1155 1417 16452 47043 47872)											1	Substitution - Missense(1)	large_intestine(1)	14											142	134	137					14																	74346002		2203	4300	6503	73415755	SO:0001583	missense	145482			AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"zinc binding alcohol dehydrogenase domain containing 1"	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.723A>G	14.37:g.74346002A>G	ENSP00000452280:p.Ile241Met		73415755	Q3L8A4|Q6MZH8	Missense_Mutation	SNP	ENST00000555661.1	37	CCDS9820.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.739042	0.49045	.	.	ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000258653	ENST00000555228;ENST00000555661;ENST00000267568;ENST00000554885;ENST00000553813	T;T;T;T;T	0.04603	3.59;3.59;3.59;3.59;3.59	5.52	1.65	0.23941	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.040723	0.85682	D	0.000000	T	0.13543	0.0328	L	0.61036	1.89	0.80722	D	1	D	0.67145	0.996	D	0.68483	0.958	T	0.01520	-1.1334	10	0.35671	T	0.21	-21.6402	9.0753	0.36517	0.4129:0.4695:0.0:0.1176	.	241	Q8N8N7	PTGR2_HUMAN	M	241;241;241;192;107	ENSP00000450975:I241M;ENSP00000452280:I241M;ENSP00000267568:I241M;ENSP00000451158:I192M;ENSP00000450824:I107M	ENSP00000267568:I241M	I	+	3	3	RP5-1021I20.4;PTGR2	73415755	0.333000	0.24731	1.000000	0.80357	0.997000	0.91878	0.089000	0.15002	0.377000	0.24735	0.533000	0.62120	ATA		0.328	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1			G	74346002	A	G	74346002	3	3	61	1	0	0	0	0	1	0	0	0	12789	352	13	4	741	4	PTGR2	14	74346002	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5097	74346002	33003538	9018	17003										
FAM161B	145483	broad.mit.edu	37	chr14	74409398	74409398	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctctcatttggatgcgaaTtttcctgaagagctcagctt	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74409398T>G	ENST00000534936.1	-	4	1051	c.946A>C	c.(946-948)Att>Ctt	p.I316L	FAM161B_ENST00000286544.3_Missense_Mutation_p.I379L			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	316								p.I316L(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						TGGATGCGAATTTTCCTGAAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	14											57	62	60					14																	74409398		2203	4300	6503	73479151	SO:0001583	missense	145483			AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 44"	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.946A>C	14.37:g.74409398T>G	ENSP00000445326:p.Ile316Leu		73479151	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	37		.	.	.	.	.	.	.	.	.	.	T	14.94	2.684668	0.47991	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.22743	1.94;1.94	5.5	3.07	0.35406	.	0.290198	0.29376	N	0.012325	T	0.19327	0.0464	L	0.45137	1.4	0.36560	D	0.872391	B	0.25809	0.135	B	0.30251	0.113	T	0.13361	-1.0512	10	0.23891	T	0.37	-3.2196	13.3801	0.60762	0.0:0.0:0.2581:0.7419	.	316	Q96MY7	F161B_HUMAN	L	379;316	ENSP00000286544:I379L;ENSP00000445326:I316L	ENSP00000286544:I379L	I	-	1	0	FAM161B	73479151	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.085000	0.50151	1.071000	0.40834	0.533000	0.62120	ATT		0.532	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		G	74409398	T	G	74409398	3	3	61	1	0	0	0	0	1	0	0	0	5489	1493	52	4	1021	4	FAM161B	14	74409398	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	63396	74409398	32940142	9019	17004										
COQ6	51004	broad.mit.edu	37	chr14	74420205	74420205	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtccaaagaaagtactggaGaaattgtcagaaacttacag	10	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74420205G>T	ENST00000334571.2	+	2	271	c.231G>T	c.(229-231)gaG>gaT	p.E77D	COQ6_ENST00000554920.1_Missense_Mutation_p.E77D|COQ6_ENST00000555552.1_3'UTR|COQ6_ENST00000394026.4_Missense_Mutation_p.E52D|COQ6_ENST00000238709.4_Missense_Mutation_p.R22I	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	77					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)	p.E77D(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		AAGTACTGGAGAAATTGTCAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											100	96	97					14																	74420205		2203	4300	6503	73489958	SO:0001583	missense	51004			AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.231G>T	14.37:g.74420205G>T	ENSP00000333946:p.Glu77Asp		73489958	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	37	CCDS9823.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.32|12.32	1.902410|1.902410	0.33628|0.33628	.|.	.|.	ENSG00000119723|ENSG00000119723	ENST00000394026;ENST00000334571;ENST00000556300;ENST00000554920;ENST00000545052|ENST00000555376;ENST00000238709;ENST00000553462;ENST00000554153;ENST00000557584;ENST00000553922;ENST00000554193;ENST00000554905;ENST00000557205;ENST00000554320;ENST00000555392	T;T|T;T	0.44482|0.61627	0.92;0.95|0.78;0.09	5.37|5.37	4.46|4.46	0.54185|0.54185	.|.	0.255193|.	0.42821|.	N|.	0.000660|.	T|T	0.38188|0.38188	0.1031|0.1031	N|N	0.11201|0.11201	0.11|0.11	0.30884|0.30884	N|N	0.731123|0.731123	B;B;B|B;B;B;B	0.02656|0.17852	0.0;0.0;0.0|0.024;0.023;0.001;0.001	B;B;B|B;B;B;B	0.08055|0.21151	0.003;0.0;0.001|0.022;0.033;0.003;0.001	T|T	0.41770|0.41770	-0.9490|-0.9490	10|9	0.09843|0.87932	T|D	0.71|0	-0.0166|-0.0166	8.4559|8.4559	0.32899|0.32899	0.0:0.2534:0.4877:0.259|0.0:0.2534:0.4877:0.259	.|.	77;52;77|42;42;22;22	B7Z357;B7Z3K8;Q9Y2Z9|B7Z8E9;B7Z262;G3XA86;Q86U30	.;.;COQ6_HUMAN|.;.;.;.	D|I	52;77;77;77;77|22;22;22;42;42;22;42;42;42;22;22	ENSP00000377594:E52D;ENSP00000333946:E77D|ENSP00000238709:R22I;ENSP00000451123:R22I	ENSP00000333946:E77D|ENSP00000238709:R22I	E|R	+|+	3|2	2|0	COQ6|COQ6	73489958|73489958	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	0.971000|0.971000	0.29396|0.29396	1.485000|1.485000	0.48380|0.48380	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.393	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			T	74420205	G	T	74420205	3	4	61	1	0	0	0	0	1	0	0	0	3755	942	33	2	237	2	COQ6	14	74420205	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10807	74420205	32929335	9020	17005										
C14orf45	80127	broad.mit.edu	37	chr14	74516684	74516684	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatactggatgagagaacaGaagtggaaagattcttttta	10	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74516684G>T	ENST00000394009.3	+	8	1195	c.1072G>T	c.(1072-1074)Gaa>Taa	p.E358*	AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_Nonsense_Mutation_p.E83*	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	358					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.E57*(1)|p.E358*(1)									TGAGAGAACAGAAGTGGAAAG	0.418																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											117	110	113					14																	74516684		2203	4300	6503	73586437	SO:0001587	stop_gained	80127			BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 45"	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1072G>T	14.37:g.74516684G>T	ENSP00000377577:p.Glu358*		73586437	Q0P604|Q9H5P8	Nonsense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	.	.	.	.	.	.	.	.	.	.	G	42	9.291873	0.99127	.	.	ENSG00000119636	ENST00000394009;ENST00000553773	.	.	.	5.66	5.66	0.87406	.	0.090906	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.7701	19.7951	0.96477	0.0:0.0:1.0:0.0	.	.	.	.	X	358;83	.	ENSP00000377577:E358X	E	+	1	0	C14orf45	73586437	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.948000	0.93006	2.688000	0.91661	0.549000	0.68633	GAA		0.418	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057		T	74516684	G	T	74516684	4	4	61	1	0	0	0	0	0	1	0	0	1779	943	33	2	1102	2	C14orf45	14	74516684	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96479	74516684	32832856	9021	17006										
ALDH6A1	4329	broad.mit.edu	37	chr14	74534217	74534217	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctgccccaaccagctggTtcagggtattttccttattg	9	11	1	0	rs376852895		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:74534217T>C	ENST00000553458.1	-	8	1006	c.908A>G	c.(907-909)aAc>aGc	p.N303S	ALDH6A1_ENST00000350259.4_Missense_Mutation_p.N290S|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_Intron|ALDH6A1_ENST00000555126.1_Missense_Mutation_p.N20S	NM_001278593.1|NM_005589.2	NP_001265522.1|NP_005580.1	Q02252	MMSA_HUMAN	aldehyde dehydrogenase 6 family, member A1	303					branched-chain amino acid catabolic process (GO:0009083)|brown fat cell differentiation (GO:0050873)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|thymine metabolic process (GO:0019859)|valine catabolic process (GO:0006574)|valine metabolic process (GO:0006573)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fatty-acyl-CoA binding (GO:0000062)|malonate-semialdehyde dehydrogenase (acetylating) activity (GO:0018478)|methylmalonate-semialdehyde dehydrogenase (acylating) activity (GO:0004491)|poly(A) RNA binding (GO:0044822)	p.N303S(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(3)|skin(3)	21				BRCA - Breast invasive adenocarcinoma(234;0.00354)		AACCAGCTGGTTCAGGGTATT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	14						T	SER/ASN	0,4406		0,0,2203	72	71	72		908	5.4	1	14		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	ALDH6A1	NM_005589.2	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	303/536	74534217	1,13005	2203	4300	6503	73603970	SO:0001583	missense	4329			M93405	CCDS9826.1, CCDS61501.1	14q24.3	2014-02-03			ENSG00000119711	ENSG00000119711	1.2.1.27	"Aldehyde dehydrogenases"	7179	protein-coding gene	gene with protein product		603178		MMSDH		1527093	Standard	NM_005589		Approved		uc001xpo.3	Q02252	OTTHUMG00000171203	ENST00000553458.1:c.908A>G	14.37:g.74534217T>C	ENSP00000450436:p.Asn303Ser		73603970	B2R609|B4DFS8|J3KNU8|Q9UKM8	Missense_Mutation	SNP	ENST00000553458.1	37	CCDS9826.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.518791	0.85495	0.0	1.16E-4	ENSG00000119711	ENST00000553458;ENST00000350259;ENST00000555126	T;T;T	0.75260	-0.92;-0.92;-0.92	5.41	5.41	0.78517	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.081136	0.85682	D	0.000000	T	0.77758	0.4178	M	0.78801	2.425	0.80722	D	1	P;P	0.37398	0.593;0.593	B;B	0.40702	0.338;0.338	T	0.78378	-0.2227	10	0.40728	T	0.16	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	290;303	B4DFS8;Q02252	.;MMSA_HUMAN	S	303;290;20	ENSP00000450436:N303S;ENSP00000342564:N290S;ENSP00000452081:N20S	ENSP00000342564:N303S	N	-	2	0	ALDH6A1	73603970	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.855000	0.86950	2.270000	0.75569	0.482000	0.46254	AAC		0.507	ALDH6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412309.1			C	74534217	T	C	74534217	3	2	61	1	0	0	0	0	1	0	0	0	503	1725	60	4	719	4	ALDH6A1	14	74534217	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	17533	74534217	32815323	9022	17007										
KIAA0317	9870	broad.mit.edu	37	chr14	75142629	75142629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtggacacattgcgttCgacgatattcttctcatcct	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75142629C>T	ENST00000356357.4	-	8	1368	c.853G>A	c.(853-855)Gaa>Aaa	p.E285K	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	285					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.E285K(1)									ACATTGCGTTCGACGATATTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	14											126	125	126					14																	75142629		1966	4153	6119	74212382	SO:0001583	missense	9870			AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.853G>A	14.37:g.75142629C>T	ENSP00000348714:p.Glu285Lys		74212382	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	37	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996480	0.93167	.	.	ENSG00000119682	ENST00000356357;ENST00000543377;ENST00000556202	T;T	0.49139	0.79;0.79	5.87	5.87	0.94306	.	0.043569	0.85682	D	0.000000	T	0.46619	0.1402	L	0.40543	1.245	0.80722	D	1	D;B	0.64830	0.994;0.222	P;B	0.45037	0.467;0.019	T	0.26643	-1.0097	10	0.30078	T	0.28	.	20.2147	0.98293	0.0:1.0:0.0:0.0	.	285;285	O15033-2;O15033	.;K0317_HUMAN	K	285;124;124	ENSP00000348714:E285K;ENSP00000452101:E124K	ENSP00000348714:E285K	E	-	1	0	KIAA0317	74212382	1.000000	0.71417	0.971000	0.41717	0.985000	0.73830	7.590000	0.82653	2.785000	0.95823	0.591000	0.81541	GAA		0.413	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		T	75142629	C	T	75142629	3	4	61	1	0	0	0	0	1	0	0	0	8188	893	31	1	1670	1	KIAA0317	14	75142629	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	608412	75142629	32206911	9023	17008										
FCF1	51077	broad.mit.edu	37	chr14	75199495	75199495	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaggaacctatgcagatGactgcttagtacagagagta	10	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75199495G>T	ENST00000341162.4	+	6	481	c.427G>T	c.(427-429)Gac>Tac	p.D143Y	FCF1_ENST00000534938.2_Missense_Mutation_p.D131Y|FCF1_ENST00000553615.1_Missense_Mutation_p.D128Y	NM_015962.4	NP_057046.1	Q9Y324	FCF1_HUMAN	FCF1 rRNA-processing protein	143	PINc.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.D143Y(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.0037)		CTATGCAGATGACTGCTTAGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	14											104	98	100					14																	75199495		2203	4300	6503	74269248	SO:0001583	missense	51077			AF132969	CCDS9832.1	14q24.2	2013-05-03	2013-05-03	2007-01-30	ENSG00000119616	ENSG00000119616			20220	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 111", "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)"	C14orf111		16762320	Standard	XR_245690		Approved	CGI-35, Bka, UTP24	uc001xqh.3	Q9Y324		ENST00000341162.4:c.427G>T	14.37:g.75199495G>T	ENSP00000344393:p.Asp143Tyr		74269248	Q86TW8|Q8TBL8	Missense_Mutation	SNP	ENST00000341162.4	37	CCDS9832.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824814	0.90955	.	.	ENSG00000119616	ENST00000554590;ENST00000341162;ENST00000534938;ENST00000553615	.	.	.	4.77	4.77	0.60923	Nucleotide binding protein, PINc (1);	0.000000	0.85682	D	0.000000	D	0.90820	0.7117	H	0.98802	4.335	0.80722	D	1	D;D	0.76494	0.989;0.999	D;D	0.79784	0.955;0.993	D	0.94476	0.7689	9	0.87932	D	0	.	17.9481	0.89045	0.0:0.0:1.0:0.0	.	143;128	Q9Y324;G3V5S9	FCF1_HUMAN;.	Y	54;143;131;128	.	ENSP00000344393:D143Y	D	+	1	0	FCF1	74269248	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.039000	0.93777	2.627000	0.88993	0.655000	0.94253	GAC		0.343	FCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413622.1	NM_015962		T	75199495	G	T	75199495	3	4	61	1	0	0	0	0	1	0	0	0	5796	1290	45	2	449	2	FCF1	14	75199495	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56866	75199495	32150045	9024	17009										
YLPM1	56252	broad.mit.edu	37	chr14	75247239	75247239	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcacactcagttacagcaGattctacaacagtatcagca	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75247239G>A	ENST00000552421.1	+	3	1366	c.1242G>A	c.(1240-1242)caG>caA	p.Q414Q	YLPM1_ENST00000238571.3_Silent_p.Q414Q|YLPM1_ENST00000325680.7_Silent_p.Q414Q			P49750	YLPM1_HUMAN	YLP motif containing 1	414	Gln-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.Q414Q(2)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		AGTTACAGCAGATTCTACAAC	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	14											173	167	169					14																	75247239		2006	4184	6190	74316992	SO:0001819	synonymous_variant	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1242G>A	14.37:g.75247239G>A			74316992	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000552421.1	37																																																																																					0.493	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		A	75247239	G	A	75247239	2	1	61	1	0	0	0	0	0	0	0	1	17526	933	33	3		3	YLPM1	14	75247239	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47744	75247239	32102301	9025	17010										
YLPM1	56252	broad.mit.edu	37	chr14	75266069	75266069	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggagagaagaaagaaatCgagagcatgggtatgatcga	15	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75266069C>T	ENST00000325680.7	+	5	4193	c.4069C>T	c.(4069-4071)Cga>Tga	p.R1357*	YLPM1_ENST00000552421.1_Intron|YLPM1_ENST00000238571.3_Nonsense_Mutation_p.R1162*	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	1162					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R1357*(1)|p.R1162*(1)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		AGAAAGAAATCGAGAGCATGG	0.473																																																2	Substitution - Nonsense(2)	large_intestine(2)	14											170	160	163					14																	75266069		1882	4122	6004	74335822	SO:0001587	stop_gained	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.4069C>T	14.37:g.75266069C>T	ENSP00000324463:p.Arg1357*		74335822	P49752|Q96I64|Q9P1V7	Nonsense_Mutation	SNP	ENST00000325680.7	37	CCDS45135.1	.	.	.	.	.	.	.	.	.	.	C	37	6.382028	0.97520	.	.	ENSG00000119596	ENST00000325680;ENST00000238571;ENST00000423680	.	.	.	5.97	5.01	0.66863	.	0.000000	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5401	13.708	0.62651	0.2119:0.7881:0.0:0.0	.	.	.	.	X	1357;1162;1070	.	ENSP00000238571:R1162X	R	+	1	2	YLPM1	74335822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.759000	0.47573	2.855000	0.98099	0.537000	0.68136	CGA		0.473	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589		T	75266069	C	T	75266069	4	4	61	1	0	0	0	0	0	1	0	0	17526	876	31	1	4087	1	YLPM1	14	75266069	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18830	75266069	32083471	9026	17011										
PROX2	283571	broad.mit.edu	37	chr14	75329892	75329892	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagctggtgctccagaagGaaggaaactgggcttctcag	14	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75329892G>T	ENST00000445876.1	-	1	645	c.646C>A	c.(646-648)Cct>Act	p.P216T	PROX2_ENST00000556084.2_Missense_Mutation_p.P216T|PROX2_ENST00000556489.2_Missense_Mutation_p.P216T			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	216					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P216T(1)		kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		GCTCCAGAAGGAAGGAAACTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											62	60	61					14																	75329892		1937	4137	6074	74399645	SO:0001583	missense	283571				CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"Homeoboxes / PROS class"	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.646C>A	14.37:g.75329892G>T	ENSP00000405932:p.Pro216Thr		74399645	C9J5W1|Q8N9Q3	Missense_Mutation	SNP	ENST00000445876.1	37	CCDS45136.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.60|13.60	2.286440|2.286440	0.40494|0.40494	.|.	.|.	ENSG00000119608|ENSG00000119608	ENST00000556084|ENST00000556489;ENST00000389664;ENST00000424024;ENST00000445876	.|T;T	.|0.43294	.|0.95;0.95	5.81|5.81	2.71|2.71	0.32032|0.32032	.|.	.|0.418555	.|0.24516	.|N	.|0.037849	T|T	0.30198|0.30198	0.0757|0.0757	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|P;P	.|0.37122	.|0.583;0.583	.|B;B	.|0.38428	.|0.273;0.273	T|T	0.10086|0.10086	-1.0645|-1.0645	5|10	.|0.28530	.|T	.|0.3	-0.4587|-0.4587	9.2899|9.2899	0.37780|0.37780	0.1345:0.0:0.6907:0.1748|0.1345:0.0:0.6907:0.1748	.|.	.|216;216	.|G3V3G0;Q3B8N5-2	.|.;.	L|T	215|216	.|ENSP00000451223:P216T;ENSP00000405932:P216T	.|ENSP00000374315:P216T	F|P	-|-	3|1	2|0	PROX2|PROX2	74399645|74399645	0.010000|0.010000	0.17322|0.17322	0.009000|0.009000	0.14445|0.14445	0.082000|0.082000	0.17680|0.17680	0.728000|0.728000	0.26013|0.26013	0.819000|0.819000	0.34492|0.34492	-0.266000|-0.266000	0.10368|0.10368	TTC|CCT		0.547	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75329892	G	T	75329892	3	4	61	1	0	0	0	0	1	0	0	0	12595	1174	41	2	1148	2	PROX2	14	75329892	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63823	75329892	32019648	9027	17012										
DLST	1743	broad.mit.edu	37	chr14	75355979	75355979	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttgcatttttcctagaGgatgacttggttacagtcaa	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75355979G>T	ENST00000334220.4	+	5	262	c.201G>T	c.(199-201)aaG>aaT	p.K67N	DLST_ENST00000334212.6_5'UTR|DLST_ENST00000555190.1_3'UTR	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	67					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)	p.K67N(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		TTTTCCTAGAGGATGACTTGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	74	73					14																	75355979		2203	4300	6503	74425732	SO:0001630	splice_region_variant	1743				CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.200-1G>T	14.37:g.75355979G>T			74425732	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Missense_Mutation	SNP	ENST00000334220.4	37	CCDS9833.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281925	0.59867	.	.	ENSG00000119689	ENST00000334220;ENST00000554806	T;T	0.16073	2.37;2.91	5.56	5.56	0.83823	Single hybrid motif (1);	0.242944	0.46758	D	0.000261	T	0.14960	0.0361	N	0.19112	0.55	0.80722	D	1	P;B;P	0.50272	0.933;0.258;0.799	B;B;B	0.42692	0.395;0.093;0.202	T	0.03534	-1.1027	10	0.29301	T	0.29	.	19.5174	0.95170	0.0:0.0:1.0:0.0	.	67;67;67	Q6IBS5;B7Z6J1;P36957	.;.;ODO2_HUMAN	N	67;50	ENSP00000335304:K67N;ENSP00000451957:K50N	ENSP00000238671:K50N	K	+	3	2	DLST	74425732	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.617000	0.54181	2.612000	0.88384	0.563000	0.77884	AAG		0.323	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1		Missense_Mutation	T	75355979	G	T	75355979	5	4	61	1	0	0	0	0	0	0	1	0	4580	1014	35	2	219	2	DLST	14	75355979	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26087	75355979	31993561	9028	17013										
PGF	5228	broad.mit.edu	37	chr14	75416114	75416114	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgcagattctcatcgccGcagcagccggtgcagcgcag	13	14	1	1	rs201159181		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75416114G>A	ENST00000405431.2	-	3	260	c.261C>T	c.(259-261)tgC>tgT	p.C87C	PGF_ENST00000555567.1_Silent_p.C87C|PGF_ENST00000553716.1_Silent_p.C87C|PGF_ENST00000238607.6_Silent_p.C86C			P49763	PLGF_HUMAN	placental growth factor	87					branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of morphogenesis of a branching structure (GO:0060688)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.C87C(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.00668)	Aflibercept(DB08885)	TCTCATCGCCGCAGCAGCCGG	0.637																																					GBM(127;389 2301 5452 48547)											1	Substitution - coding silent(1)	large_intestine(1)	14						G	,	2,4404	4.2+/-10.8	0,2,2201	66	56	59		261,261	-2.2	0.1	14		59	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PGF	NM_001207012.1,NM_002632.5	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	87/150,87/171	75416114	2,13004	2203	4300	6503	74485867	SO:0001819	synonymous_variant	5228			S72960	CCDS9835.1, CCDS55932.1, CCDS73664.1	14q24.3	2013-02-18	2008-03-20		ENSG00000119630	ENSG00000119630			8893	protein-coding gene	gene with protein product	"placenta growth factor"	601121	"placental growth factor-like", "placental growth factor, vascular endothelial growth factor-related protein"	PGFL		7681160	Standard	NM_002632		Approved	PLGF, PlGF-2, PlGF, SHGC-10760, D12S1900	uc001xqz.3	P49763	OTTHUMG00000171496	ENST00000405431.2:c.261C>T	14.37:g.75416114G>A			74485867	Q07101|Q9BV78|Q9Y6S8	Silent	SNP	ENST00000405431.2	37	CCDS9835.1																																																																																				0.637	PGF-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414064.1	NM_002632		A	75416114	G	A	75416114	2	1	61	1	0	0	0	0	0	0	0	1	11819	1079	38	1		1	PGF	14	75416114	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60135	75416114	31933426	9029	17014										
MLH3	27030	broad.mit.edu	37	chr14	75497284	75497284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagtagatcttcctctccGaagttcattggcttctcttt	6	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75497284G>A	ENST00000556740.1	-	8	3984	c.3949C>T	c.(3949-3951)Cgg>Tgg	p.R1317W	MLH3_ENST00000556257.1_Missense_Mutation_p.R1139W|MLH3_ENST00000355774.2_Missense_Mutation_p.R1317W|MLH3_ENST00000238662.7_Missense_Mutation_p.R1293W|MLH3_ENST00000380968.2_Missense_Mutation_p.R263W|MLH3_ENST00000544985.1_3'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1317					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.R1293W(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		CTTCCTCTCCGAAGTTCATTG	0.423								Mismatch excision repair (MMR)																																								1	Substitution - Missense(1)	large_intestine(1)	14											254	215	228					14																	75497284		2203	4300	6503	74567037	SO:0001583	missense	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3949C>T	14.37:g.75497284G>A	ENSP00000452316:p.Arg1317Trp		74567037	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.063474	0.76187	.	.	ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000238662;ENST00000556257;ENST00000556740	D;T;D;D;D	0.82619	-1.63;0.5;-1.5;-1.6;-1.63	5.78	4.88	0.63580	MutL, C-terminal, dimerisation (2);	0.137025	0.49916	D	0.000130	D	0.91412	0.7290	M	0.81112	2.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.92694	0.6169	10	0.87932	D	0	-9.6696	16.8517	0.85996	0.0:0.1285:0.8715:0.0	.	1293;1317	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	W	1317;263;1293;1139;1317	ENSP00000348020:R1317W;ENSP00000370355:R263W;ENSP00000238662:R1293W;ENSP00000451540:R1139W;ENSP00000452316:R1317W	ENSP00000238662:R1293W	R	-	1	2	MLH3	74567037	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.009000	0.63998	1.419000	0.47118	0.563000	0.77884	CGG		0.423	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75497284	G	A	75497284	3	1	61	1	0	0	0	0	1	0	0	0	9648	1057	37	1	432	1	MLH3	14	75497284	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81170	75497284	31852256	9030	17015										
MLH3	27030	broad.mit.edu	37	chr14	75513090	75513090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtacttaccattctcaagtAcaacatccacagccacagtt	4	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75513090A>G	ENST00000556740.1	-	1	3304	c.3269T>C	c.(3268-3270)gTa>gCa	p.V1090A	MLH3_ENST00000556257.1_Missense_Mutation_p.V1090A|MLH3_ENST00000355774.2_Missense_Mutation_p.V1090A|MLH3_ENST00000238662.7_Missense_Mutation_p.V1090A|MLH3_ENST00000380968.2_Missense_Mutation_p.V36A|MLH3_ENST00000544985.1_Missense_Mutation_p.V85A|MLH3_ENST00000555671.1_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1090					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.V1090A(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		ATTCTCAAGTACAACATCCAC	0.418								Mismatch excision repair (MMR)																																								1	Substitution - Missense(1)	large_intestine(1)	14											114	97	103					14																	75513090		2203	4300	6503	74582843	SO:0001583	missense	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3269T>C	14.37:g.75513090A>G	ENSP00000452316:p.Val1090Ala		74582843	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.70|12.70	2.016050|2.016050	0.35606|0.35606	.|.	.|.	ENSG00000119684|ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000238662;ENST00000556257;ENST00000556740;ENST00000544985|ENST00000553713	D;T;D;T;D;T|.	0.83591|.	-1.67;0.48;-1.74;-1.49;-1.67;0.25|.	5.49|5.49	4.32|4.32	0.51571|0.51571	.|.	0.648960|.	0.15610|.	N|.	0.253444|.	T|T	0.39835|0.39835	0.1093|0.1093	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	P;B|.	0.39282|.	0.666;0.393|.	B;B|.	0.33620|.	0.167;0.08|.	T|T	0.21793|0.21793	-1.0235|-1.0235	10|5	0.66056|.	D|.	0.02|.	0.0137|0.0137	12.5822|12.5822	0.56397|0.56397	0.8613:0.1387:0.0:0.0|0.8613:0.1387:0.0:0.0	.|.	1090;1090|.	Q9UHC1-2;Q9UHC1|.	.;MLH3_HUMAN|.	A|H	1090;36;1090;1090;1090;85|147	ENSP00000348020:V1090A;ENSP00000370355:V36A;ENSP00000238662:V1090A;ENSP00000451540:V1090A;ENSP00000452316:V1090A;ENSP00000441371:V85A|.	ENSP00000238662:V1090A|.	V|Y	-|-	2|1	0|0	MLH3|MLH3	74582843|74582843	0.520000|0.520000	0.26250|0.26250	0.001000|0.001000	0.08648|0.08648	0.683000|0.683000	0.39861|0.39861	5.485000|5.485000	0.66850|0.66850	1.049000|1.049000	0.40321|0.40321	0.528000|0.528000	0.53228|0.53228	GTA|TAC		0.418	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		G	75513090	A	G	75513090	3	3	61	1	0	0	0	0	1	0	0	0	9648	391	14	4	1140	4	MLH3	14	75513090	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	15806	75513090	31836450	9031	17016										
MLH3	27030	broad.mit.edu	37	chr14	75514048	75514048	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccattactttcctctacttCtgtatccagaggattttcaa	4	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75514048C>A	ENST00000556740.1	-	1	2346	c.2311G>T	c.(2311-2313)Gaa>Taa	p.E771*	MLH3_ENST00000556257.1_Nonsense_Mutation_p.E771*|MLH3_ENST00000355774.2_Nonsense_Mutation_p.E771*|MLH3_ENST00000238662.7_Nonsense_Mutation_p.E771*|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000555671.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	771					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.E771*(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TCCTCTACTTCTGTATCCAGA	0.418								Mismatch excision repair (MMR)																																								1	Substitution - Nonsense(1)	large_intestine(1)	14											137	142	140					14																	75514048		2203	4300	6503	74583801	SO:0001587	stop_gained	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2311G>T	14.37:g.75514048C>A	ENSP00000452316:p.Glu771*		74583801	P49751|Q56DK9|Q9P292|Q9UHC0	Nonsense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606042	0.87157	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	.	.	.	5.93	3.1	0.35709	.	0.525534	0.20379	N	0.093485	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-11.5867	7.6737	0.28473	0.0:0.5383:0.3128:0.1489	.	.	.	.	X	771	.	ENSP00000238662:E771X	E	-	1	0	MLH3	74583801	0.111000	0.22076	0.210000	0.23637	0.026000	0.11368	0.441000	0.21611	0.840000	0.34995	-0.165000	0.13383	GAA		0.418	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75514048	C	A	75514048	4	1	61	1	0	0	0	0	0	1	0	0	9648	922	32	2	2098	2	MLH3	14	75514048	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	958	75514048	31835492	9032	17017										
TMED10	10972	broad.mit.edu	37	chr14	75602511	75602511	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttcatgtaggcaaaatCattaacaatagattctgaaa	5	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75602511C>A	ENST00000303575.4	-	4	541	c.490G>T	c.(490-492)Gat>Tat	p.D164Y	TMED10_ENST00000557670.1_5'UTR|RP11-950C14.7_ENST00000556236.1_RNA	NM_006827.5	NP_006818.3	P49755	TMEDA_HUMAN	transmembrane emp24-like trafficking protein 10 (yeast)	164	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.|Required for TMED10 and TMED2 cis-Golgi network localization.				beta-amyloid formation (GO:0034205)|cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPI-coated vesicle budding (GO:0035964)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|kidney development (GO:0001822)|protein oligomerization (GO:0051259)|regulated secretory pathway (GO:0045055)|response to acid chemical (GO:0001101)|response to alkaloid (GO:0043279)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle targeting, to, from or within Golgi (GO:0048199)	cis-Golgi network (GO:0005801)|COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	syntaxin binding (GO:0019905)	p.D164Y(1)		endometrium(1)|large_intestine(5)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(234;0.0126)		TAGGCAAAATCATTAACAATA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	14											128	110	116					14																	75602511		2203	4300	6503	74672264	SO:0001583	missense	10972			AL832012, X97442	CCDS9840.1	14q24.3	2008-08-11			ENSG00000170348	ENSG00000170348			16998	protein-coding gene	gene with protein product		605406				7596406, 8663407	Standard	NM_006827		Approved	TMP21, P24(DELTA)	uc001xrm.1	P49755		ENST00000303575.4:c.490G>T	14.37:g.75602511C>A	ENSP00000303145:p.Asp164Tyr		74672264	B2R605|Q15602|Q16536|Q86TC2|Q86TS5	Missense_Mutation	SNP	ENST00000303575.4	37	CCDS9840.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090320	0.94149	.	.	ENSG00000170348	ENST00000303575	T	0.17213	2.29	5.72	5.72	0.89469	GOLD (2);	0.000000	0.85682	D	0.000000	T	0.47322	0.1439	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.39143	-0.9628	10	0.49607	T	0.09	-10.1497	19.8938	0.96942	0.0:1.0:0.0:0.0	.	164	P49755	TMEDA_HUMAN	Y	164	ENSP00000303145:D164Y	ENSP00000303145:D164Y	D	-	1	0	TMED10	74672264	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.442000	0.80503	2.703000	0.92315	0.460000	0.39030	GAT		0.418	TMED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415034.1	NM_006827		A	75602511	C	A	75602511	3	1	61	1	0	0	0	0	1	0	0	0	16042	826	29	2	177	2	TMED10	14	75602511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88463	75602511	31747029	9033	17018										
TMED10	10972	broad.mit.edu	37	chr14	75614405	75614405	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccactccatgcttcatgtCtaggatcacgagttggtcag	9	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75614405C>A	ENST00000303575.4	-	3	424	c.373G>T	c.(373-375)Gac>Tac	p.D125Y	TMED10_ENST00000557670.1_5'UTR	NM_006827.5	NP_006818.3	P49755	TMEDA_HUMAN	transmembrane emp24-like trafficking protein 10 (yeast)	125	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.|Required for interaction with STX17.				beta-amyloid formation (GO:0034205)|cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPI-coated vesicle budding (GO:0035964)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|kidney development (GO:0001822)|protein oligomerization (GO:0051259)|regulated secretory pathway (GO:0045055)|response to acid chemical (GO:0001101)|response to alkaloid (GO:0043279)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle targeting, to, from or within Golgi (GO:0048199)	cis-Golgi network (GO:0005801)|COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	syntaxin binding (GO:0019905)	p.D125Y(1)		endometrium(1)|large_intestine(5)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(234;0.0126)		TGCTTCATGTCTAGGATCACG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											254	227	236					14																	75614405		2203	4300	6503	74684158	SO:0001583	missense	10972			AL832012, X97442	CCDS9840.1	14q24.3	2008-08-11			ENSG00000170348	ENSG00000170348			16998	protein-coding gene	gene with protein product		605406				7596406, 8663407	Standard	NM_006827		Approved	TMP21, P24(DELTA)	uc001xrm.1	P49755		ENST00000303575.4:c.373G>T	14.37:g.75614405C>A	ENSP00000303145:p.Asp125Tyr		74684158	B2R605|Q15602|Q16536|Q86TC2|Q86TS5	Missense_Mutation	SNP	ENST00000303575.4	37	CCDS9840.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306070	0.60305	.	.	ENSG00000170348	ENST00000303575	T	0.20463	2.07	6.06	6.06	0.98353	GOLD (2);	0.096682	0.64402	D	0.000001	T	0.40839	0.1133	M	0.93638	3.44	0.58432	D	0.999999	B	0.27140	0.169	B	0.35727	0.209	T	0.48103	-0.9064	10	0.87932	D	0	-24.9813	10.8833	0.46951	0.0:0.8613:0.0:0.1387	.	125	P49755	TMEDA_HUMAN	Y	125	ENSP00000303145:D125Y	ENSP00000303145:D125Y	D	-	1	0	TMED10	74684158	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.685000	0.61693	2.880000	0.98712	0.650000	0.86243	GAC		0.463	TMED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415034.1	NM_006827		A	75614405	C	A	75614405	3	1	61	1	0	0	0	0	1	0	0	0	16042	913	32	2	298	2	TMED10	14	75614405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11894	75614405	31735135	9034	17019										
FOS	2353	broad.mit.edu	37	chr14	75747528	75747528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtctgctttgcagaccGagattgccaacctgctgaag	11	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75747528G>A	ENST00000303562.4	+	4	753	c.544G>A	c.(544-546)Gag>Aag	p.E182K	FOS_ENST00000535987.1_Missense_Mutation_p.E146K|FOS_ENST00000555686.1_Missense_Mutation_p.E68K|FOS_ENST00000555347.1_Missense_Mutation_p.E34K	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN	FBJ murine osteosarcoma viral oncogene homolog	182	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hormone stimulus (GO:0032870)|cellular response to reactive oxygen species (GO:0034614)|conditioned taste aversion (GO:0001661)|DNA methylation (GO:0006306)|Fc-epsilon receptor signaling pathway (GO:0038095)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gravity (GO:0009629)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|skeletal muscle cell differentiation (GO:0035914)|sleep (GO:0030431)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	double-stranded DNA binding (GO:0003690)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E182K(1)		central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)	Nadroparin(DB08813)|Pseudoephedrine(DB00852)	TTTGCAGACCGAGATTGCCAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	14											71	76	75					14																	75747528		2202	4298	6500	74817281	SO:0001583	missense	2353			K00650	CCDS9841.1	14q24.3	2013-01-10	2009-07-23			ENSG00000170345		"basic leucine zipper proteins"	3796	protein-coding gene	gene with protein product		164810	"v-fos FBJ murine osteosarcoma viral oncogene homolog"			16123044, 16055710, 15926923	Standard	NM_005252		Approved	c-fos, AP-1	uc001xrn.3	P01100		ENST00000303562.4:c.544G>A	14.37:g.75747528G>A	ENSP00000306245:p.Glu182Lys		74817281	A8K4E2|B4DQ65|P18849	Missense_Mutation	SNP	ENST00000303562.4	37	CCDS9841.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.406915	0.83230	.	.	ENSG00000170345	ENST00000303562;ENST00000535987;ENST00000555686;ENST00000555672;ENST00000555347	T;T;T;T;T	0.80033	0.28;-1.33;0.28;-1.33;0.28	5.38	5.38	0.77491	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.048986	0.85682	D	0.000000	D	0.90783	0.7106	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	D	0.91680	0.5357	10	0.87932	D	0	-5.0546	19.1116	0.93318	0.0:0.0:1.0:0.0	.	146;182	B4DQ65;P01100	.;FOS_HUMAN	K	182;146;68;32;34	ENSP00000306245:E182K;ENSP00000442268:E146K;ENSP00000452590:E68K;ENSP00000452440:E32K;ENSP00000450886:E34K	ENSP00000306245:E182K	E	+	1	0	FOS	74817281	1.000000	0.71417	0.963000	0.40424	0.987000	0.75469	9.750000	0.98875	2.677000	0.91161	0.563000	0.77884	GAG		0.493	FOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415044.1	NM_005252		A	75747528	G	A	75747528	3	1	61	1	0	0	0	0	1	0	0	0	6004	1059	37	1	558	1	FOS	14	75747528	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133123	75747528	31602012	9035	17020										
BATF	10538	broad.mit.edu	37	chr14	75991472	75991472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagaggagggagaaaaatCgtattgccgcccagaagagc	13	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:75991472C>T	ENST00000286639.6	+	2	367	c.109C>T	c.(109-111)Cgt>Tgt	p.R37C	BATF_ENST00000555504.1_Missense_Mutation_p.R37C|BATF_ENST00000555795.1_3'UTR	NM_006399.3	NP_006390.1	Q16520	BATF_HUMAN	basic leucine zipper transcription factor, ATF-like	37	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hematopoietic stem cell differentiation (GO:0060218)|isotype switching (GO:0045190)|lymphoid progenitor cell differentiation (GO:0002320)|myeloid dendritic cell differentiation (GO:0043011)|T-helper 17 cell differentiation (GO:0072539)|T-helper 17 cell lineage commitment (GO:0072540)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R37C(1)		large_intestine(1)|ovary(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.028)		GGAGAAAAATCGTATTGCCGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	14											88	75	79					14																	75991472		2203	4300	6503	75061225	SO:0001583	missense	10538			AF016898	CCDS9843.1	14q24	2013-01-10				ENSG00000156127		"basic leucine zipper proteins"	958	protein-coding gene	gene with protein product	"activating transcription factor B", "SF-HT-activated gene 2"	612476				8570175, 8630063	Standard	NM_006399		Approved	B-ATF, SFA-2, BATF1	uc001xrr.3	Q16520		ENST00000286639.6:c.109C>T	14.37:g.75991472C>T	ENSP00000286639:p.Arg37Cys		75061225		Missense_Mutation	SNP	ENST00000286639.6	37	CCDS9843.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616930	0.87359	.	.	ENSG00000156127	ENST00000286639;ENST00000555504	T	0.73258	-0.73	5.71	5.71	0.89125	Basic-leucine zipper (bZIP) transcription factor (3);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.84397	0.5463	M	0.81682	2.555	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86011	0.1501	10	0.87932	D	0	-2.7248	14.6782	0.68998	0.1451:0.8549:0.0:0.0	.	37	Q16520	BATF_HUMAN	C	37	ENSP00000286639:R37C	ENSP00000286639:R37C	R	+	1	0	BATF	75061225	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.459000	0.66685	2.709000	0.92574	0.655000	0.94253	CGT		0.522	BATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413669.1	NM_006399		T	75991472	C	T	75991472	3	4	61	1	0	0	0	0	1	0	0	0	1326	884	31	1	115	1	BATF	14	75991472	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	243944	75991472	31358068	9036	17021										
FLVCR2	55640	broad.mit.edu	37	chr14	76088432	76088432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctatagcttggaattgCgattgggttcttggtccctc	10	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:76088432C>T	ENST00000238667.4	+	2	1036	c.680C>T	c.(679-681)gCg>gTg	p.A227V	FLVCR2_ENST00000556856.1_5'Flank|FLVCR2_ENST00000556241.1_3'UTR|FLVCR2_ENST00000539311.1_Missense_Mutation_p.A22V|FLVCR2_ENST00000553587.1_5'UTR	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	227					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)	p.A227V(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CTTGGAATTGCGATTGGGTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	14											318	292	301					14																	76088432		2203	4300	6503	75158185	SO:0001583	missense	55640			AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"Solute carriers"	20105	protein-coding gene	gene with protein product		610865	"chromosome 14 open reading frame 58", "feline leukemia virus subgroup C cellular receptor 2"	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.680C>T	14.37:g.76088432C>T	ENSP00000238667:p.Ala227Val		75158185	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Missense_Mutation	SNP	ENST00000238667.4	37	CCDS9844.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758687	0.89843	.	.	ENSG00000119686	ENST00000238667;ENST00000539311	T;T	0.58210	0.35;0.35	5.86	5.86	0.93980	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.81059	0.4744	H	0.94734	3.575	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.982	D	0.84529	0.0632	10	0.52906	T	0.07	-23.0509	18.9487	0.92632	0.0:1.0:0.0:0.0	.	22;227	B7Z485;Q9UPI3	.;FLVC2_HUMAN	V	227;22	ENSP00000238667:A227V;ENSP00000443439:A22V	ENSP00000238667:A227V	A	+	2	0	AC007182.1	75158185	1.000000	0.71417	0.969000	0.41365	0.567000	0.35839	7.045000	0.76585	2.778000	0.95560	0.655000	0.94253	GCG		0.428	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791		T	76088432	C	T	76088432	3	4	61	1	0	0	0	0	1	0	0	0	5965	768	27	1	686	1	FLVCR2	14	76088432	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96960	76088432	31261108	9037	17022										
C14orf118	55668	broad.mit.edu	37	chr14	76639930	76639930	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctacctggagctgcagctCgatgcctcagaaaggggcga	14	11	2	1	rs377474002		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:76639930C>T	ENST00000261530.7	+	5	1012	c.946C>T	c.(946-948)Cga>Tga	p.R316*	GPATCH2L_ENST00000556663.1_Nonsense_Mutation_p.R316*|GPATCH2L_ENST00000312858.5_Nonsense_Mutation_p.R316*|GPATCH2L_ENST00000557263.1_Nonsense_Mutation_p.R316*	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	316								p.R316*(1)									AGCTGCAGCTCGATGCCTCAG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	14						C	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	138	123	128		946,946	4.8	1	14		128	0,8600		0,0,4300	no	stop-gained,stop-gained	C14orf118	NM_017926.2,NM_017972.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	316/483,316/478	76639930	1,13005	2203	4300	6503	75709683	SO:0001587	stop_gained	55668			AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 118"	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.946C>T	14.37:g.76639930C>T	ENSP00000261530:p.Arg316*		75709683	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Nonsense_Mutation	SNP	ENST00000261530.7	37	CCDS9848.1	.	.	.	.	.	.	.	.	.	.	C	37	6.360632	0.97502	2.27E-4	0.0	ENSG00000089916	ENST00000336993;ENST00000557263;ENST00000312858;ENST00000261530;ENST00000556663	.	.	.	5.71	4.81	0.61882	.	0.259391	0.31051	N	0.008358	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.1686	14.2928	0.66292	0.1486:0.8514:0.0:0.0	.	.	.	.	X	316	.	ENSP00000261530:R316X	R	+	1	2	C14orf118	75709683	1.000000	0.71417	0.980000	0.43619	0.990000	0.78478	3.379000	0.52440	1.368000	0.46115	0.655000	0.94253	CGA		0.483	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		T	76639930	C	T	76639930	4	4	61	1	0	0	0	0	0	1	0	0	1745	876	31	1	960	1	C14orf118	14	76639930	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	551498	76639930	30709610	9038	17023										
C14orf118	55668	broad.mit.edu	37	chr14	76668171	76668171	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttttaaaatgccacaaGaaaagagccctggatacagc	7	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:76668171G>T	ENST00000261530.7	+	10	1492	c.1426G>T	c.(1426-1428)Gaa>Taa	p.E476*	GPATCH2L_ENST00000556675.1_Intron|GPATCH2L_ENST00000312858.5_Nonsense_Mutation_p.E471*	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	476								p.E476*(1)									AATGCCACAAGAAAAGAGCCC	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											98	103	101					14																	76668171		2203	4300	6503	75737924	SO:0001587	stop_gained	55668			AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 118"	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.1426G>T	14.37:g.76668171G>T	ENSP00000261530:p.Glu476*		75737924	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Nonsense_Mutation	SNP	ENST00000261530.7	37	CCDS9848.1	.	.	.	.	.	.	.	.	.	.	G	36	5.700599	0.96802	.	.	ENSG00000089916	ENST00000312858;ENST00000261530	.	.	.	5.95	5.95	0.96441	.	0.319150	0.33309	N	0.005047	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-36.8585	17.5491	0.87871	0.0:0.0:1.0:0.0	.	.	.	.	X	471;476	.	ENSP00000261530:E476X	E	+	1	0	C14orf118	75737924	1.000000	0.71417	0.951000	0.38953	0.732000	0.41865	5.638000	0.67861	2.824000	0.97209	0.655000	0.94253	GAA		0.493	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		T	76668171	G	T	76668171	4	4	61	1	0	0	0	0	0	1	0	0	1745	943	33	2	1504	2	C14orf118	14	76668171	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28241	76668171	30681369	9039	17024										
ANGEL1	23357	broad.mit.edu	37	chr14	77270134	77270134	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacatgtgctcacctgatCtcttggggtgacaggaggtg	15	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77270134C>A	ENST00000251089.2	-	6	1614	c.1502G>T	c.(1501-1503)aGa>aTa	p.R501I	ANGEL1_ENST00000557179.1_Missense_Mutation_p.R66I	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	501								p.R501I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CTCACCTGATCTCTTGGGGTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	14											111	113	112					14																	77270134		2203	4300	6503	76339887	SO:0001583	missense	23357			AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.1502G>T	14.37:g.77270134C>A	ENSP00000251089:p.Arg501Ile		76339887	B4DWL7|O94859|Q8NCS9	Missense_Mutation	SNP	ENST00000251089.2	37	CCDS9852.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284643	0.40394	.	.	ENSG00000013523	ENST00000251089;ENST00000557179	T;T	0.48836	1.86;0.8	5.75	3.78	0.43462	Endonuclease/exonuclease/phosphatase (2);	0.257970	0.40385	N	0.001105	T	0.27594	0.0678	N	0.24115	0.695	0.44462	D	0.997393	B	0.06786	0.001	B	0.13407	0.009	T	0.13388	-1.0511	10	0.35671	T	0.21	0.0037	2.6291	0.04939	0.1921:0.5095:0.1859:0.1125	.	501	Q9UNK9	ANGE1_HUMAN	I	501;66	ENSP00000251089:R501I;ENSP00000451534:R66I	ENSP00000251089:R501I	R	-	2	0	ANGEL1	76339887	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.911000	0.28584	1.389000	0.46526	0.655000	0.94253	AGA		0.517	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305		A	77270134	C	A	77270134	3	1	61	1	0	0	0	0	1	0	0	0	608	913	32	2	530	2	ANGEL1	14	77270134	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	601963	77270134	30079406	9040	17025										
C14orf166B	145497	broad.mit.edu	37	chr14	77311207	77311207	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctcagtcacaaccaattCtctgatgtaggaggggagca	11	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77311207C>A	ENST00000393774.3	+	7	814	c.690C>A	c.(688-690)ttC>ttA	p.F230L	C14orf166B_ENST00000450042.2_3'UTR	NM_194287.2	NP_919263.2												p.F230L(1)		breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		ACAACCAATTCTCTGATGTAG	0.473																																					Ovarian(165;1056 1958 32571 36789 48728)											1	Substitution - Missense(1)	large_intestine(1)	14											57	56	56					14																	77311207		2203	4300	6503	76380960	SO:0001583	missense	145497																														ENST00000393774.3:c.690C>A	14.37:g.77311207C>A	ENSP00000377369:p.Phe230Leu		76380960		Missense_Mutation	SNP	ENST00000393774.3	37	CCDS9853.2	.	.	.	.	.	.	.	.	.	.	C	11.67	1.706386	0.30232	.	.	ENSG00000100565	ENST00000393774	T	0.40756	1.02	5.66	3.6	0.41247	.	0.097237	0.64402	N	0.000001	T	0.27313	0.0670	L	0.33189	0.99	0.80722	D	1	B	0.31485	0.325	B	0.35240	0.198	T	0.03673	-1.1014	10	0.08599	T	0.76	.	6.8553	0.24038	0.0:0.6379:0.0:0.3621	.	230	Q0VAA2	CN16B_HUMAN	L	230	ENSP00000377369:F230L	ENSP00000377369:F230L	F	+	3	2	C14orf166B	76380960	1.000000	0.71417	0.984000	0.44739	0.386000	0.30323	1.157000	0.31724	1.387000	0.46486	0.462000	0.41574	TTC		0.473	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1			A	77311207	C	A	77311207	3	1	61	1	0	0	0	0	1	0	0	0	1761	912	32	2	716	2	C14orf166B	14	77311207	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41073	77311207	30038333	9041	17026										
TMEM63C	57156	broad.mit.edu	37	chr14	77705948	77705948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgcccaccgctggcaggcGccatgccatgcggggccggc	16	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77705948G>A	ENST00000298351.4	+	12	953	c.809G>A	c.(808-810)cGc>cAc	p.R270H		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	270					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)	p.R270H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		GCTGGCAGGCGCCATGCCATG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	14											25	28	27					14																	77705948		1898	4106	6004	76775701	SO:0001583	missense	57156				CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"		"chromosome 14 open reading frame 171"	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.809G>A	14.37:g.77705948G>A	ENSP00000298351:p.Arg270His		76775701	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Missense_Mutation	SNP	ENST00000298351.4	37	CCDS45141.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.309568	0.40895	.	.	ENSG00000165548	ENST00000298351	T	0.42513	0.97	5.17	4.07	0.47477	.	0.052460	0.85682	D	0.000000	T	0.36799	0.0980	L	0.50333	1.59	0.58432	D	0.999997	B	0.30709	0.291	B	0.21917	0.037	T	0.41980	-0.9478	10	0.66056	D	0.02	-25.4703	14.5653	0.68171	0.0835:0.0:0.9165:0.0	.	270	Q9P1W3	TM63C_HUMAN	H	270	ENSP00000298351:R270H	ENSP00000298351:R270H	R	+	2	0	TMEM63C	76775701	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	6.950000	0.75977	2.406000	0.81754	0.462000	0.41574	CGC		0.647	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1			A	77705948	G	A	77705948	3	1	61	1	0	0	0	0	1	0	0	0	16231	1087	38	1	847	1	TMEM63C	14	77705948	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	394741	77705948	29643592	9042	17027										
POMT2	29954	broad.mit.edu	37	chr14	77751926	77751926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatccggtttccaaatttcCtgtttacgacctcaatccgc	6	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77751926C>A	ENST00000261534.4	-	13	1584	c.1382G>T	c.(1381-1383)aGg>aTg	p.R461M		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	461						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)	p.R461M(1)		breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		TCCAAATTTCCTGTTTACGAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	14											301	337	325					14																	77751926		2203	4300	6503	76821679	SO:0001583	missense	29954			AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.1382G>T	14.37:g.77751926C>A	ENSP00000261534:p.Arg461Met		76821679	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	C	34	5.385006	0.95967	.	.	ENSG00000009830	ENST00000261534	D	0.83992	-1.79	5.55	5.55	0.83447	MIR (2);	0.050216	0.85682	D	0.000000	D	0.87939	0.6304	L	0.49778	1.585	0.58432	D	0.999993	D	0.58268	0.982	P	0.59115	0.852	D	0.87593	0.2492	10	0.54805	T	0.06	-14.2534	19.8667	0.96806	0.0:1.0:0.0:0.0	.	461	Q9UKY4	POMT2_HUMAN	M	461	ENSP00000261534:R461M	ENSP00000261534:R461M	R	-	2	0	POMT2	76821679	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.421000	0.80204	2.773000	0.95371	0.655000	0.94253	AGG		0.458	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		A	77751926	C	A	77751926	3	1	61	1	0	0	0	0	1	0	0	0	12277	681	24	2	906	2	POMT2	14	77751926	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45978	77751926	29597614	9043	17028										
TMED8	283578	broad.mit.edu	37	chr14	77808177	77808177	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagggagtaggagttgtcGaacttgagcaggtagatgcc	16	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77808177G>A	ENST00000216468.7	-	6	970	c.915C>T	c.(913-915)ttC>ttT	p.F305F		NM_213601.1	NP_998766.1	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain containing 8	305	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				transport (GO:0006810)	integral component of membrane (GO:0016021)		p.F305F(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)	15			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGGAGTTGTCGAACTTGAGCA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	14											146	126	133					14																	77808177		2203	4300	6503	76877930	SO:0001819	synonymous_variant	283578			AK095650	CCDS32125.1	14q24.3	2005-08-26	2005-08-26	2005-01-07		ENSG00000100580			18633	protein-coding gene	gene with protein product			"family with sequence similarity 15, member B", "transmembrane emp24 domain containing 8"	FAM15B			Standard	NM_213601		Approved		uc001xto.1	Q6PL24		ENST00000216468.7:c.915C>T	14.37:g.77808177G>A			76877930	B3KTI6|Q3MJB0|Q9P1V9	Silent	SNP	ENST00000216468.7	37	CCDS32125.1																																																																																				0.587	TMED8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414100.1	NM_213601		A	77808177	G	A	77808177	2	1	61	1	0	0	0	0	0	0	0	1	16050	1049	37	1		1	TMED8	14	77808177	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	56251	77808177	29541363	9044	17029										
VIPAR	63894	broad.mit.edu	37	chr14	77908963	77908963	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggaagtgaataagatgtCtcagggcaacctgtcgcacc	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77908963C>A	ENST00000553888.1	-	10	1184	c.674G>T	c.(673-675)aGa>aTa	p.R225I	VIPAS39_ENST00000343765.2_Missense_Mutation_p.R225I|VIPAS39_ENST00000448935.2_Missense_Mutation_p.R176I|VIPAS39_ENST00000556412.1_Missense_Mutation_p.R251I|VIPAS39_ENST00000327028.4_Missense_Mutation_p.R212I|VIPAS39_ENST00000557658.1_Missense_Mutation_p.R225I	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	225					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)		p.R225I(1)									AATAAGATGTCTCAGGGCAAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	14											150	155	153					14																	77908963		2203	4300	6503	76978716	SO:0001583	missense	63894			AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.674G>T	14.37:g.77908963C>A	ENSP00000452181:p.Arg225Ile		76978716	B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	37	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330687	0.60853	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61	4.7	3.74	0.42951	.	0.125424	0.64402	D	0.000014	T	0.42517	0.1206	L	0.47716	1.5	0.80722	D	1	P;P	0.40731	0.655;0.728	B;B	0.40410	0.272;0.328	T	0.39921	-0.9590	10	0.36615	T	0.2	-11.2599	13.8849	0.63702	0.0:0.8462:0.1537:0.0	.	176;225	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	I	225;225;212;225;176;251	ENSP00000339122:R225I;ENSP00000452181:R225I;ENSP00000313098:R212I;ENSP00000452191:R225I;ENSP00000404815:R176I;ENSP00000451857:R251I	ENSP00000313098:R212I	R	-	2	0	VIPAR	76978716	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.625000	0.46452	2.146000	0.66826	0.655000	0.94253	AGA		0.413	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		A	77908963	C	A	77908963	3	1	61	1	0	0	0	0	1	0	0	0	17208	913	32	2	851	2	VIPAR	14	77908963	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100786	77908963	29440577	9045	17030										
ISM2	145501	broad.mit.edu	37	chr14	77948669	77948669	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgggggtgctcaccgtaGctgacagaatccttgaagac	13	9	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:77948669G>A	ENST00000342219.4	-	4	1025	c.969C>T	c.(967-969)agC>agT	p.S323S	ISM2_ENST00000493585.1_Intron|ISM2_ENST00000393684.3_Silent_p.S235S|ISM2_ENST00000412904.1_Silent_p.S242S|ISM2_ENST00000429906.1_Silent_p.S242S	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	323						extracellular region (GO:0005576)		p.S323S(1)		endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						GCTCACCGTAGCTGACAGAAT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	14											85	84	84					14																	77948669		2203	4300	6503	77018422	SO:0001819	synonymous_variant	145501			AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"thrombospondin and AMOP containing isthmin-like 1"	612684	"thrombospondin, type I domain-containing 3", "thrombospondin, type I, domain containing 3", "isthmin 2 homolog (zebrafish)"	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.969C>T	14.37:g.77948669G>A			77018422	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Silent	SNP	ENST00000342219.4	37	CCDS9864.1																																																																																				0.597	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509		A	77948669	G	A	77948669	2	1	61	1	0	0	0	0	0	0	0	1	7882	962	34	3		3	ISM2	14	77948669	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39706	77948669	29400871	9046	17031										
NRXN3	9369	broad.mit.edu	37	chr14	79434521	79434521	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactttcctttccaggtgatCtctatatggctggtctggcc	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:79434521C>T	ENST00000554719.1	+	11	2346	c.1855C>T	c.(1855-1857)Ctc>Ttc	p.L619F	NRXN3_ENST00000335750.5_Missense_Mutation_p.L619F	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	223					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.L619F(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TCCAGGTGATCTCTATATGGC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											94	88	90					14																	79434521		2203	4300	6503	78504274	SO:0001583	missense	9369			AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1855C>T	14.37:g.79434521C>T	ENSP00000451648:p.Leu619Phe		78504274	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.029298	0.93518	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	D;D	0.85258	-1.96;-1.96	5.94	5.94	0.96194	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.92799	0.7710	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.987	D	0.91735	0.5399	8	.	.	.	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	992;619	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	F	992;981;619;619	ENSP00000451648:L619F;ENSP00000338349:L619F	.	L	+	1	0	NRXN3	78504274	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.987000	0.70571	2.807000	0.96579	0.591000	0.81541	CTC		0.453	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		T	79434521	C	T	79434521	3	4	61	1	0	0	0	0	1	0	0	0	10698	913	32	3	1889	3	NRXN3	14	79434521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1485852	79434521	27915019	9047	17032										
DIO2	1734	broad.mit.edu	37	chr14	80669434	80669434	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagtttgcggaaggctggCagctggctcgtgaaaggagg	17	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:80669434C>T	ENST00000557010.1	-	4	805	c.420G>A	c.(418-420)ctG>ctA	p.L140L	DIO2_ENST00000422005.3_3'UTR|DIO2_ENST00000555750.1_Silent_p.L176L|DIO2_ENST00000557125.1_Intron|DIO2_ENST00000438257.4_Silent_p.L140L	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	140					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)	p.L140L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		GGAAGGCTGGCAGCTGGCTCG	0.572											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	14											51	56	54					14																	80669434		2081	4228	6309	79739187	SO:0001819	synonymous_variant	1734			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"thyroxine deiodinase, type II", "deiodonase-2", "deiodinase-2"	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.420G>A	14.37:g.80669434C>T		1200	79739187	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Silent	SNP	ENST00000557010.1	37	CCDS45146.1																																																																																				0.572	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			T	80669434	C	T	80669434	2	4	61	1	0	0	0	0	0	0	0	1	4536	697	25	3		3	DIO2	14	80669434	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1234913	80669434	26680106	9048	17033										
C14orf145	145508	broad.mit.edu	37	chr14	81259399	81259399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattctggatctccttaagtCgatccaacatctgcagttgc	8	11	3	0	rs138323270		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:81259399C>T	ENST00000555265.1	-	14	1640	c.1265G>A	c.(1264-1266)cGa>cAa	p.R422Q	CEP128_ENST00000281129.3_Missense_Mutation_p.R422Q			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	422						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)		p.R422Q(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						CTCCTTAAGTCGATCCAACAT	0.453													C|||	1	0.000199681	8e-04	0	5008	,	,		20458	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	14						C	GLN/ARG	0,4406		0,0,2203	168	153	158		1265	-2.5	0.4	14	dbSNP_134	158	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CEP128	NM_152446.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	422/1095	81259399	1,13005	2203	4300	6503	80329152	SO:0001583	missense	145508			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.1265G>A	14.37:g.81259399C>T	ENSP00000451162:p.Arg422Gln		80329152	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	C	0.076	-1.192068	0.01607	0.0	1.16E-4	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.20738	2.05;2.05	5.51	-2.45	0.06481	.	0.557653	0.16862	N	0.196467	T	0.03305	0.0096	N	0.00210	-1.845	0.80722	D	1	B	0.12013	0.005	B	0.04013	0.001	T	0.49643	-0.8918	10	0.02654	T	1	.	10.6187	0.45467	0.0:0.3323:0.0:0.6677	.	422	Q6ZU80	CE128_HUMAN	Q	422	ENSP00000281129:R422Q;ENSP00000451162:R422Q	ENSP00000281129:R422Q	R	-	2	0	CEP128	80329152	0.999000	0.42202	0.450000	0.26969	0.274000	0.26718	1.436000	0.34980	-0.436000	0.07254	-1.000000	0.02509	CGA		0.453	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		T	81259399	C	T	81259399	3	4	61	1	0	0	0	0	1	0	0	0	1753	884	31	1	2067	1	C14orf145	14	81259399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	589965	81259399	26090141	9049	17034										
TSHR	7253	broad.mit.edu	37	chr14	81606200	81606200	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcttttaagaatcagaaGaaaatcagagggtaagtggc	12	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:81606200G>A	ENST00000541158.2	+	10	1192	c.870G>A	c.(868-870)aaG>aaA	p.K290K	TSHR_ENST00000298171.2_Silent_p.K290K|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	290					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.K290K(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	AGAATCAGAAGAAAATCAGAG	0.463			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	1	Substitution - coding silent(1)	large_intestine(1)	14											49	46	47					14																	81606200		2203	4300	6503	80675953	SO:0001819	synonymous_variant	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.870G>A	14.37:g.81606200G>A			80675953	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	CCDS9872.1																																																																																				0.463	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		A	81606200	G	A	81606200	2	1	61	1	0	0	0	0	0	0	0	1	16662	933	33	3		3	TSHR	14	81606200	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346801	81606200	25743340	9050	17035										
STON2	85439	broad.mit.edu	37	chr14	81744852	81744852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttaaatgatcccattgaaTtataaggtacatctgggatc	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:81744852T>C	ENST00000267540.2	-	4	1003	c.803A>G	c.(802-804)aAt>aGt	p.N268S	STON2_ENST00000556280.1_5'UTR|STON2_ENST00000555447.1_Missense_Mutation_p.N268S	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	268					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)		p.N268S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		TCCCATTGAATTATAAGGTAC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											127	129	128					14																	81744852		2203	4300	6503	80814605	SO:0001583	missense	85439			AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.803A>G	14.37:g.81744852T>C	ENSP00000267540:p.Asn268Ser		80814605	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	37	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	T	0.648	-0.810478	0.02798	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.53423	0.62;0.62	6.17	5.03	0.67393	Stonin-2, N-terminal (1);	0.478319	0.24267	N	0.040035	T	0.40473	0.1118	L	0.53249	1.67	0.09310	N	1	B;B	0.19583	0.018;0.037	B;B	0.15870	0.014;0.008	T	0.29518	-1.0009	10	0.32370	T	0.25	-11.6603	8.4031	0.32599	0.0:0.2048:0.0:0.7952	.	268;268	Q8WXE9;G3V2T7	STON2_HUMAN;.	S	268;280;268	ENSP00000450857:N268S;ENSP00000267540:N268S	ENSP00000267540:N268S	N	-	2	0	STON2	80814605	0.985000	0.35326	0.019000	0.16419	0.008000	0.06430	1.169000	0.31871	1.161000	0.42604	-0.250000	0.11733	AAT		0.448	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		C	81744852	T	C	81744852	3	2	61	1	0	0	0	0	1	0	0	0	15357	1493	52	4	1920	4	STON2	14	81744852	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	138652	81744852	25604688	9051	17036										
SEL1L	6400	broad.mit.edu	37	chr14	81950701	81950701	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcggtgccaaacccataGaaatggtagtctccgagctt	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:81950701G>T	ENST00000336735.4	-	19	2030	c.1914C>A	c.(1912-1914)ttC>ttA	p.F638L		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	638	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.F638L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CAAACCCATAGAAATGGTAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	14											122	123	123					14																	81950701		2203	4300	6503	81020454	SO:0001583	missense	6400				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1914C>A	14.37:g.81950701G>T	ENSP00000337053:p.Phe638Leu		81020454	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	37	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.186892	0.57909	.	.	ENSG00000071537	ENST00000336735	T	0.51574	0.7	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);	0.042803	0.85682	D	0.000000	T	0.32882	0.0844	N	0.05124	-0.11	0.80722	D	1	P	0.39376	0.67	B	0.42959	0.403	T	0.18085	-1.0348	10	0.28530	T	0.3	.	15.4023	0.74852	0.0681:0.0:0.9319:0.0	.	638	Q9UBV2	SE1L1_HUMAN	L	638	ENSP00000337053:F638L	ENSP00000337053:F638L	F	-	3	2	SEL1L	81020454	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.401000	0.59716	2.809000	0.96659	0.557000	0.71058	TTC		0.373	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		T	81950701	G	T	81950701	3	4	61	1	0	0	0	0	1	0	0	0	14047	933	33	2	482	2	SEL1L	14	81950701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205849	81950701	25398839	9052	17037										
SEL1L	6400	broad.mit.edu	37	chr14	81956802	81956802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacaatgtcacttccttccGaatacatctggaaaacagat	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:81956802G>A	ENST00000336735.4	-	13	1378	c.1262C>T	c.(1261-1263)tCg>tTg	p.S421L		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	421	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S421L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		ACTTCCTTCCGAATACATCTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	14											126	108	114					14																	81956802		2203	4300	6503	81026555	SO:0001583	missense	6400				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1262C>T	14.37:g.81956802G>A	ENSP00000337053:p.Ser421Leu		81026555	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	37	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466948	0.26335	.	.	ENSG00000071537	ENST00000336735	T	0.46451	0.87	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.22437	0.0541	N	0.03881	-0.34	0.80722	D	1	B	0.23442	0.085	B	0.25140	0.058	T	0.18681	-1.0329	10	0.05351	T	0.99	.	20.1551	0.98106	0.0:0.0:1.0:0.0	.	421	Q9UBV2	SE1L1_HUMAN	L	421	ENSP00000337053:S421L	ENSP00000337053:S421L	S	-	2	0	SEL1L	81026555	1.000000	0.71417	0.989000	0.46669	0.977000	0.68977	8.899000	0.92544	2.760000	0.94817	0.655000	0.94253	TCG		0.403	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		A	81956802	G	A	81956802	3	1	61	1	0	0	0	0	1	0	0	0	14047	1059	37	1	1158	1	SEL1L	14	81956802	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6101	81956802	25392738	9053	17038										
FLRT2	23768	broad.mit.edu	37	chr14	86088162	86088162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatggcaaccaactggacGaattccccatgaaccttccc	7	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:86088162G>A	ENST00000330753.4	+	2	1071	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K	FLRT2_ENST00000554746.1_Missense_Mutation_p.E102K	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	102					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.E102K(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CCAACTGGACGAATTCCCCAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											118	112	114					14																	86088162		2203	4300	6503	85157915	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.304G>A	14.37:g.86088162G>A	ENSP00000332879:p.Glu102Lys		85157915	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535874	0.85812	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.02525	4.26;4.26	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.12646	0.0307	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	T	0.00249	-1.1879	10	0.56958	D	0.05	-14.0584	19.9036	0.96999	0.0:0.0:1.0:0.0	.	102	O43155	FLRT2_HUMAN	K	102	ENSP00000332879:E102K;ENSP00000451050:E102K	ENSP00000332879:E102K	E	+	1	0	FLRT2	85157915	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	9.867000	0.99620	2.706000	0.92434	0.655000	0.94253	GAA		0.468	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86088162	G	A	86088162	3	1	61	1	0	0	0	0	1	0	0	0	5958	1059	37	1	306	1	FLRT2	14	86088162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4131360	86088162	21261378	9054	17039										
FLRT2	23768	broad.mit.edu	37	chr14	86088447	86088447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgaattgctgtcatatccGacatggccttccagaatctc	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:86088447G>A	ENST00000330753.4	+	2	1356	c.589G>A	c.(589-591)Gac>Aac	p.D197N	FLRT2_ENST00000554746.1_Missense_Mutation_p.D197N	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	197					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.D197N(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TGTCATATCCGACATGGCCTT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	14											111	112	112					14																	86088447		2203	4300	6503	85158200	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.589G>A	14.37:g.86088447G>A	ENSP00000332879:p.Asp197Asn		85158200	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135020	0.77662	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.02369	4.32;4.32	5.42	5.42	0.78866	.	0.048991	0.85682	D	0.000000	T	0.03783	0.0107	N	0.16567	0.415	0.58432	D	0.999997	D	0.58268	0.982	P	0.47645	0.553	T	0.66089	-0.6010	10	0.19147	T	0.46	-31.5414	19.5873	0.95495	0.0:0.0:1.0:0.0	.	197	O43155	FLRT2_HUMAN	N	197	ENSP00000332879:D197N;ENSP00000451050:D197N	ENSP00000332879:D197N	D	+	1	0	FLRT2	85158200	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.696000	0.74598	2.702000	0.92279	0.650000	0.86243	GAC		0.512	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86088447	G	A	86088447	3	1	61	1	0	0	0	0	1	0	0	0	5958	1058	37	1	591	1	FLRT2	14	86088447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	285	86088447	21261093	9055	17040										
FLRT2	23768	broad.mit.edu	37	chr14	86088759	86088759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttttgataatctctccAacctgaagcagctcactgct	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:86088759A>G	ENST00000330753.4	+	2	1668	c.901A>G	c.(901-903)Aac>Gac	p.N301D	FLRT2_ENST00000554746.1_Missense_Mutation_p.N301D	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	301					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.N301D(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TAATCTCTCCAACCTGAAGCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											169	178	175					14																	86088759		2203	4300	6503	85158512	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.901A>G	14.37:g.86088759A>G	ENSP00000332879:p.Asn301Asp		85158512	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.190086	0.58017	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.58940	0.3;0.3	5.97	5.97	0.96955	.	0.135238	0.64402	D	0.000003	T	0.55529	0.1926	L	0.49350	1.555	0.39545	D	0.968884	B	0.34372	0.451	B	0.34991	0.193	T	0.60188	-0.7312	10	0.59425	D	0.04	-22.735	16.4473	0.83942	1.0:0.0:0.0:0.0	.	301	O43155	FLRT2_HUMAN	D	301	ENSP00000332879:N301D;ENSP00000451050:N301D	ENSP00000332879:N301D	N	+	1	0	FLRT2	85158512	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.330000	0.72925	2.281000	0.76405	0.533000	0.62120	AAC		0.453	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			G	86088759	A	G	86088759	3	3	61	1	0	0	0	0	1	0	0	0	5958	130	5	4	903	4	FLRT2	14	86088759	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	312	86088759	21260781	9056	17041										
GPR65	8477	broad.mit.edu	37	chr14	88477672	88477672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacagttgttgaatattgcGatgccgaaaagtctaatttt	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:88477672G>A	ENST00000267549.3	+	2	1039	c.481G>A	c.(481-483)Gat>Aat	p.D161N	RP11-300J18.2_ENST00000554433.1_RNA	NM_003608.3	NP_003599.2	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	161					actin cytoskeleton reorganization (GO:0031532)|activation of Rho GTPase activity (GO:0032862)|apoptotic process (GO:0006915)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of stress fiber assembly (GO:0051496)|response to acidic pH (GO:0010447)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D161N(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)	16						TGAATATTGCGATGCCGAAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											148	141	144					14																	88477672		2203	4300	6503	87547425	SO:0001583	missense	8477			U95218	CCDS9879.1	14q31-q32.1	2012-08-21			ENSG00000140030	ENSG00000140030		"GPCR / Class A : Orphans"	4517	protein-coding gene	gene with protein product		604620				9655242	Standard	NM_003608		Approved	hTDAG8, TDAG8	uc001xvv.3	Q8IYL9	OTTHUMG00000028648	ENST00000267549.3:c.481G>A	14.37:g.88477672G>A	ENSP00000267549:p.Asp161Asn		87547425	O75819	Missense_Mutation	SNP	ENST00000267549.3	37	CCDS9879.1	.	.	.	.	.	.	.	.	.	.	G	2.069	-0.413614	0.04799	.	.	ENSG00000140030	ENST00000267549	T	0.36520	1.25	5.82	1.88	0.25563	GPCR, rhodopsin-like superfamily (1);	1.248090	0.05567	N	0.570504	T	0.26011	0.0634	L	0.33485	1.01	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.24548	-1.0157	10	0.15499	T	0.54	.	6.316	0.21190	0.3183:0.1275:0.5542:0.0	.	161	Q8IYL9	PSYR_HUMAN	N	161	ENSP00000267549:D161N	ENSP00000267549:D161N	D	+	1	0	GPR65	87547425	0.000000	0.05858	0.003000	0.11579	0.115000	0.19883	0.234000	0.17930	0.360000	0.24265	0.650000	0.86243	GAT		0.393	GPR65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071564.4			A	88477672	G	A	88477672	3	1	61	1	0	0	0	0	1	0	0	0	6726	1058	37	1	483	1	GPR65	14	88477672	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2388913	88477672	18871868	9057	17042										
PTPN21	11099	broad.mit.edu	37	chr14	88935415	88935415	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagactggatctcttcaaGatatgctgtggaaaatcaat	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:88935415G>T	ENST00000556564.1	-	18	3525	c.3241C>A	c.(3241-3243)Ctt>Att	p.L1081I	PTPN21_ENST00000328736.3_Missense_Mutation_p.L1081I	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	1081	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.L1081I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ATCTCTTCAAGATATGCTGTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	14											83	62	69					14																	88935415		2203	4300	6503	88005168	SO:0001583	missense	11099			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.3241C>A	14.37:g.88935415G>T	ENSP00000452414:p.Leu1081Ile		88005168		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261851	0.59431	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000553531	D;D;D	0.82803	-1.65;-1.65;-1.65	5.79	5.79	0.91817	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000001	D	0.85500	0.5711	L	0.35644	1.08	0.34601	D	0.716548	D	0.71674	0.998	D	0.87578	0.998	D	0.87867	0.2668	10	0.46703	T	0.11	.	10.1168	0.42596	0.1528:0.0:0.8472:0.0	.	1081	Q16825	PTN21_HUMAN	I	1081;1081;42	ENSP00000330276:L1081I;ENSP00000452414:L1081I;ENSP00000450847:L42I	ENSP00000330276:L1081I	L	-	1	0	PTPN21	88005168	1.000000	0.71417	0.998000	0.56505	0.370000	0.29829	2.365000	0.44196	2.733000	0.93635	0.655000	0.94253	CTT		0.448	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			T	88935415	G	T	88935415	3	4	61	1	0	0	0	0	1	0	0	0	12823	942	33	2	291	2	PTPN21	14	88935415	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	457743	88935415	18414125	9058	17043										
PTPN21	11099	broad.mit.edu	37	chr14	88938683	88938683	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagaacatcttggaatcGatttctttctgcattttcag	8	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:88938683G>A	ENST00000556564.1	-	15	3060	c.2776C>T	c.(2776-2778)Cga>Tga	p.R926*	PTPN21_ENST00000328736.3_Nonsense_Mutation_p.R926*	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	926	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.R926*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCTTGGAATCGATTTCTTTCT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											193	168	176					14																	88938683		2203	4300	6503	88008436	SO:0001587	stop_gained	11099			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.2776C>T	14.37:g.88938683G>A	ENSP00000452414:p.Arg926*		88008436		Nonsense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	G	43	10.088578	0.99333	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	.	.	.	5.86	3.84	0.44239	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6719	0.77286	0.0:0.0:0.6766:0.3234	.	.	.	.	X	926	.	ENSP00000330276:R926X	R	-	1	2	PTPN21	88008436	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	3.629000	0.54266	1.441000	0.47550	0.655000	0.94253	CGA		0.403	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			A	88938683	G	A	88938683	4	1	61	1	0	0	0	0	0	1	0	0	12823	1066	37	1	768	1	PTPN21	14	88938683	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3268	88938683	18410857	9059	17044										
PTPN21	11099	broad.mit.edu	37	chr14	88971668	88971668	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggaaacaaggcaaattTctgaagaaagtcctgggatt	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:88971668T>A	ENST00000556564.1	-	5	780	c.496A>T	c.(496-498)Aaa>Taa	p.K166*	PTPN21_ENST00000328736.3_Nonsense_Mutation_p.K166*|RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000554628.1_5'UTR	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	166	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.K166*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AAGGCAAATTTCTGAAGAAAG	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											100	107	104					14																	88971668		2203	4300	6503	88041421	SO:0001587	stop_gained	11099			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.496A>T	14.37:g.88971668T>A	ENSP00000452414:p.Lys166*		88041421		Nonsense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	T	38	7.208056	0.98136	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000555243	.	.	.	5.18	5.18	0.71444	.	0.200155	0.43579	D	0.000558	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3546	0.49609	0.0:0.0:0.1516:0.8483	.	.	.	.	X	166	.	ENSP00000330276:K166X	K	-	1	0	PTPN21	88041421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.659000	0.54489	2.076000	0.62316	0.533000	0.62120	AAA		0.333	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			A	88971668	T	A	88971668	4	1	61	1	0	0	0	0	0	1	0	0	12823	1792	62	5	3088	5	PTPN21	14	88971668	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32985	88971668	18377872	9060	17045										
ZC3H14	79882	broad.mit.edu	37	chr14	89034485	89034485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctagggaacaacacaattcGattcaccgtatggtatgttt	8	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:89034485G>A	ENST00000251038.5	+	3	407	c.182G>A	c.(181-183)cGa>cAa	p.R61Q	ZC3H14_ENST00000555755.1_Missense_Mutation_p.R61Q|ZC3H14_ENST00000393514.5_Missense_Mutation_p.R61Q|ZC3H14_ENST00000359301.3_Missense_Mutation_p.R27Q|ZC3H14_ENST00000557607.1_Intron|ZC3H14_ENST00000336693.4_Missense_Mutation_p.R27Q|ZC3H14_ENST00000302216.8_Missense_Mutation_p.R61Q|ZC3H14_ENST00000556945.1_Missense_Mutation_p.R61Q	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	61						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R61Q(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						AACACAATTCGATTCACCGTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											137	106	116					14																	89034485		2203	4300	6503	88104238	SO:0001583	missense	79882			AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.182G>A	14.37:g.89034485G>A	ENSP00000251038:p.Arg61Gln		88104238	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	37	CCDS32133.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.093410	0.76756	.	.	ENSG00000100722	ENST00000251038;ENST00000393530;ENST00000353091;ENST00000359301;ENST00000302216;ENST00000554602;ENST00000380684;ENST00000556945;ENST00000556158;ENST00000555799;ENST00000555755;ENST00000393514;ENST00000336693;ENST00000557693;ENST00000555120	T;T;T;T;T;T;T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81	5.62	5.62	0.85841	.	0.059107	0.64402	D	0.000003	T	0.66742	0.2820	N	0.19112	0.55	0.38002	D	0.934252	D;D;P;D	0.63880	0.993;0.979;0.919;0.983	P;B;B;P	0.46172	0.506;0.409;0.169;0.49	T	0.66929	-0.5799	10	0.22706	T	0.39	-11.5101	19.6685	0.95901	0.0:0.0:1.0:0.0	.	61;61;61;61	G3V5R4;Q6PJT7-2;Q6PJT7-3;Q6PJT7	.;.;.;ZC3HE_HUMAN	Q	61;61;61;27;61;27;61;61;48;27;61;61;27;27;27	ENSP00000251038:R61Q;ENSP00000352250:R27Q;ENSP00000307025:R61Q;ENSP00000451638:R27Q;ENSP00000450474:R61Q;ENSP00000451389:R48Q;ENSP00000451489:R27Q;ENSP00000452475:R61Q;ENSP00000377150:R61Q;ENSP00000338002:R27Q;ENSP00000452210:R27Q;ENSP00000450451:R27Q	ENSP00000251038:R61Q	R	+	2	0	ZC3H14	88104238	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.874000	0.75546	2.639000	0.89480	0.655000	0.94253	CGA		0.423	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		A	89034485	G	A	89034485	3	1	61	1	0	0	0	0	1	0	0	0	17605	1058	37	1	192	1	ZC3H14	14	89034485	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62817	89034485	18315055	9061	17046										
EML5	161436	broad.mit.edu	37	chr14	89082538	89082538	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgatcaccactggtaaatcGaatatttgtcacatggggcg	10	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:89082538G>A	ENST00000380664.5	-	41	5820	c.5821C>T	c.(5821-5823)Cga>Tga	p.R1941*	EML5_ENST00000352093.5_Nonsense_Mutation_p.R1903*|EML5_ENST00000554922.1_Nonsense_Mutation_p.R1949*			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1941						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)	p.R1949*(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CTGGTAAATCGAATATTTGTC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											164	154	157					14																	89082538		1921	4125	6046	88152291	SO:0001587	stop_gained	161436			AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.5821C>T	14.37:g.89082538G>A	ENSP00000370039:p.Arg1941*		88152291	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Nonsense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	G	48	14.012450	0.99775	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-7.6493	19.3663	0.94464	0.0:0.0:1.0:0.0	.	.	.	.	X	1949;1903;1941	.	ENSP00000298315:R1903X	R	-	1	2	EML5	88152291	1.000000	0.71417	0.988000	0.46212	0.992000	0.81027	9.476000	0.97823	2.564000	0.86499	0.655000	0.94253	CGA		0.428	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89082538	G	A	89082538	4	1	61	1	0	0	0	0	0	1	0	0	5113	1066	37	1	96	1	EML5	14	89082538	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48053	89082538	18267002	9062	17047										
EML5	161436	broad.mit.edu	37	chr14	89087606	89087606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatttttctctccaacttCgattatttcagcattccttg	4	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:89087606C>T	ENST00000380664.5	-	36	5028	c.5029G>A	c.(5029-5031)Gaa>Aaa	p.E1677K	EML5_ENST00000553320.1_5'UTR|EML5_ENST00000352093.5_Missense_Mutation_p.E1639K|EML5_ENST00000554922.1_Missense_Mutation_p.E1685K			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1677						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)	p.E1685K(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TCTCCAACTTCGATTATTTCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	14											151	147	149					14																	89087606		1879	4107	5986	88157359	SO:0001583	missense	161436			AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.5029G>A	14.37:g.89087606C>T	ENSP00000370039:p.Glu1677Lys		88157359	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.342748	0.95783	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664;ENST00000555823	T;T;T;T	0.60548	3.59;3.59;3.59;0.18	5.68	5.68	0.88126	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71576	0.3356	M	0.83223	2.63	0.58432	D	0.999999	D	0.63046	0.992	P	0.54210	0.745	T	0.68554	-0.5378	10	0.13108	T	0.6	-27.2855	19.7763	0.96395	0.0:1.0:0.0:0.0	.	1677	Q05BV3	EMAL5_HUMAN	K	1685;1639;1677;126	ENSP00000451998:E1685K;ENSP00000298315:E1639K;ENSP00000370039:E1677K;ENSP00000452030:E126K	ENSP00000298315:E1639K	E	-	1	0	EML5	88157359	1.000000	0.71417	0.999000	0.59377	0.911000	0.54048	7.421000	0.80204	2.678000	0.91216	0.591000	0.81541	GAA		0.413	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89087606	C	T	89087606	3	4	61	1	0	0	0	0	1	0	0	0	5113	893	31	1	908	1	EML5	14	89087606	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5068	89087606	18261934	9063	17048										
EML5	161436	broad.mit.edu	37	chr14	89091350	89091350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcacgataagtccatctCgcagggtggtgtacatggca	12	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:89091350C>T	ENST00000380664.5	-	34	4837	c.4838G>A	c.(4837-4839)cGa>cAa	p.R1613Q	EML5_ENST00000553320.1_5'UTR|EML5_ENST00000352093.5_Missense_Mutation_p.R1575Q|EML5_ENST00000554922.1_Missense_Mutation_p.R1621Q			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1613						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)	p.R1621Q(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAGTCCATCTCGCAGGGTGGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											71	70	70					14																	89091350		1985	4170	6155	88161103	SO:0001583	missense	161436			AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.4838G>A	14.37:g.89091350C>T	ENSP00000370039:p.Arg1613Gln		88161103	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	35	5.456194	0.96223	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664;ENST00000555823	T;T;T;T	0.58358	3.6;3.6;3.6;0.34	5.01	5.01	0.66863	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.057060	0.64402	D	0.000002	T	0.69459	0.3113	M	0.69358	2.11	0.51482	D	0.999924	D;D	0.89917	0.975;1.0	P;D	0.77557	0.75;0.99	T	0.63576	-0.6606	10	0.17832	T	0.49	-7.9597	18.5013	0.90882	0.0:1.0:0.0:0.0	.	1621;1613	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	Q	1621;1575;1613;62	ENSP00000451998:R1621Q;ENSP00000298315:R1575Q;ENSP00000370039:R1613Q;ENSP00000452030:R62Q	ENSP00000298315:R1575Q	R	-	2	0	EML5	88161103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.171000	0.77595	2.612000	0.88384	0.561000	0.74099	CGA		0.473	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89091350	C	T	89091350	3	4	61	1	0	0	0	0	1	0	0	0	5113	884	31	1	1107	1	EML5	14	89091350	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3744	89091350	18258190	9064	17049										
EML5	161436	broad.mit.edu	37	chr14	89163195	89163195	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaaacagccttacctgaGaaatcaacggcactaacacc	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:89163195G>A	ENST00000380664.5	-	15	2339	c.2340C>T	c.(2338-2340)ttC>ttT	p.F780F	EML5_ENST00000554922.1_Silent_p.F780F|EML5_ENST00000352093.5_Silent_p.F780F			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	780						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)	p.F780F(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCTTACCTGAGAAATCAACGG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	14											68	69	69					14																	89163195		1900	4117	6017	88232948	SO:0001819	synonymous_variant	161436			AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2340C>T	14.37:g.89163195G>A			88232948	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																				0.393	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89163195	G	A	89163195	2	1	61	1	0	0	0	0	0	0	0	1	5113	933	33	3		3	EML5	14	89163195	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71845	89163195	18186345	9065	17050										
C14orf143	90141	broad.mit.edu	37	chr14	90420309	90420309	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaagtcctctctgctgaGatatcctttgtgatcttcat	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:90420309G>T	ENST00000316738.7	-	2	140	c.112C>A	c.(112-114)Ctc>Atc	p.L38I	RP11-33N16.3_ENST00000555070.1_RNA|TDP1_ENST00000393452.3_5'Flank|EFCAB11_ENST00000538485.2_Missense_Mutation_p.L38I|EFCAB11_ENST00000556609.1_5'UTR|TDP1_ENST00000357382.3_5'Flank|TDP1_ENST00000335725.4_5'Flank|EFCAB11_ENST00000555872.1_Missense_Mutation_p.L14I|TDP1_ENST00000393454.2_5'Flank|EFCAB11_ENST00000556005.1_Missense_Mutation_p.L14I|EFCAB11_ENST00000267544.9_5'UTR	NM_001284267.1|NM_145231.3	NP_001271196.1|NP_660274.1	Q9BUY7	EFC11_HUMAN	EF-hand calcium binding domain 11	38	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.L38I(1)		large_intestine(1)|lung(1)	2						TCTCTGCTGAGATATCCTTTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	14											112	109	110					14																	90420309		2203	4300	6503	89490062	SO:0001583	missense	90141			AK094740	CCDS9887.1, CCDS61522.1, CCDS61523.1, CCDS61524.1, CCDS61525.1	14q32.11	2013-01-10	2011-01-31	2011-01-31	ENSG00000140025	ENSG00000140025		"EF-hand domain containing"	20357	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 143"	C14orf143			Standard	NM_145231		Approved		uc001xxt.3	Q9BUY7	OTTHUMG00000148671	ENST00000316738.7:c.112C>A	14.37:g.90420309G>T	ENSP00000326267:p.Leu38Ile		89490062	B3KT10|B7Z5G9|G3V5G1|Q86T09|Q86TV7|Q8NDQ1	Missense_Mutation	SNP	ENST00000316738.7	37	CCDS9887.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745841	0.69418	.	.	ENSG00000140025	ENST00000316738;ENST00000555872;ENST00000538485;ENST00000556005	T;T;T;T	0.74106	0.09;0.09;-0.81;-0.81	5.8	3.95	0.45737	EF-hand-like domain (1);	0.000000	0.56097	D	0.000022	T	0.76572	0.4006	L	0.55834	1.745	0.80722	D	1	D;D;D;D	0.89917	0.964;0.999;1.0;1.0	P;D;D;D	0.74348	0.857;0.959;0.983;0.97	T	0.75243	-0.3386	10	0.02654	T	1	-12.562	8.3489	0.32290	0.2591:0.0:0.7409:0.0	.	38;14;38;14	B7Z5G9;Q9BUY7-3;Q9BUY7;Q9BUY7-2	.;.;EFC11_HUMAN;.	I	38;14;38;14	ENSP00000326267:L38I;ENSP00000452320:L14I;ENSP00000438072:L38I;ENSP00000452143:L14I	ENSP00000326267:L38I	L	-	1	0	EFCAB11	89490062	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	1.049000	0.30392	1.433000	0.47394	0.655000	0.94253	CTC		0.353	EFCAB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309022.2	NM_145231		T	90420309	G	T	90420309	3	4	61	1	0	0	0	0	1	0	0	0	1752	942	33	2	399	2	C14orf143	14	90420309	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1257114	90420309	16929231	9066	17051										
KCNK13	56659	broad.mit.edu	37	chr14	90650753	90650753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcctcatctcttgctgCgcctcagccatgtacacccc	5	19	3	0	rs149915166	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:90650753C>T	ENST00000282146.4	+	2	1074	c.633C>T	c.(631-633)tgC>tgT	p.C211C		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	211					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.C211C(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				TCTCTTGCTGCGCCTCAGCCA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	14						C		1,4405	2.1+/-5.4	0,1,2202	164	139	147		633	-10.6	0	14	dbSNP_134	147	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KCNK13	NM_022054.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		211/409	90650753	2,13004	2203	4300	6503	89720506	SO:0001819	synonymous_variant	56659			AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.633C>T	14.37:g.90650753C>T			89720506	B5TJL8|Q96E79	Silent	SNP	ENST00000282146.4	37	CCDS9889.1																																																																																				0.562	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		T	90650753	C	T	90650753	2	4	61	1	0	0	0	0	0	0	0	1	8082	776	27	1		1	KCNK13	14	90650753	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230444	90650753	16698787	9067	17052										
C14orf102	55051	broad.mit.edu	37	chr14	90770503	90770503	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgtaacaggagccgcatCttccaagtccttcactggta	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:90770503C>A	ENST00000354366.3	-	5	1013	c.781G>T	c.(781-783)Gat>Tat	p.D261Y	NRDE2_ENST00000357904.3_Missense_Mutation_p.D30Y	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	261								p.D261Y(1)									GGAGCCGCATCTTCCAAGTCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	14											149	133	138					14																	90770503		2203	4300	6503	89840256	SO:0001583	missense	55051			AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.781G>T	14.37:g.90770503C>A	ENSP00000346335:p.Asp261Tyr		89840256	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.886128	0.33348	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.34072	1.86;1.38	5.49	5.49	0.81192	.	0.738080	0.13508	N	0.382694	T	0.32102	0.0818	L	0.57536	1.79	0.09310	N	1	P	0.44877	0.845	B	0.34722	0.188	T	0.37641	-0.9697	10	0.48119	T	0.1	-11.581	10.8593	0.46817	0.0:0.8854:0.0:0.1146	.	261	Q9H7Z3	CN102_HUMAN	Y	261;30	ENSP00000346335:D261Y;ENSP00000350579:D30Y	ENSP00000346335:D261Y	D	-	1	0	C14orf102	89840256	0.002000	0.14202	0.089000	0.20774	0.017000	0.09413	1.081000	0.30791	2.746000	0.94184	0.655000	0.94253	GAT		0.473	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		A	90770503	C	A	90770503	3	1	61	1	0	0	0	0	1	0	0	0	1739	913	32	2	2753	2	C14orf102	14	90770503	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119750	90770503	16579037	9068	17053										
TTC7B	145567	broad.mit.edu	37	chr14	91121432	91121432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacatcaacgacagttttgGcaaacttttcagcctcttcc	5	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91121432G>A	ENST00000328459.6	-	12	1485	c.1364C>T	c.(1363-1365)gCc>gTc	p.A455V	TTC7B_ENST00000357056.2_Missense_Mutation_p.A455V	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	455								p.A455V(1)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GACAGTTTTGGCAAACTTTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											97	85	89					14																	91121432		2203	4300	6503	90191185	SO:0001583	missense	145567			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1364C>T	14.37:g.91121432G>A	ENSP00000336127:p.Ala455Val		90191185	Q86U24|Q86VT3	Missense_Mutation	SNP	ENST00000328459.6	37	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	G	32	5.163443	0.94727	.	.	ENSG00000165914	ENST00000555768;ENST00000357056;ENST00000328459;ENST00000540938	T;T	0.77750	-1.12;-1.12	5.91	5.91	0.95273	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.049216	0.85682	D	0.000000	D	0.82563	0.5064	M	0.68593	2.085	0.80722	D	1	P	0.50443	0.935	P	0.48368	0.575	D	0.84168	0.0432	10	0.87932	D	0	-17.7276	20.2985	0.98592	0.0:0.0:1.0:0.0	.	455	Q86TV6	TTC7B_HUMAN	V	353;455;455;197	ENSP00000349564:A455V;ENSP00000336127:A455V	ENSP00000336127:A455V	A	-	2	0	TTC7B	90191185	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.482000	0.73613	2.793000	0.96121	0.655000	0.94253	GCC		0.463	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			A	91121432	G	A	91121432	3	1	61	1	0	0	0	0	1	0	0	0	16753	1203	42	3	1203	3	TTC7B	14	91121432	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	350929	91121432	16228108	9069	17054										
RPS6KA5	9252	broad.mit.edu	37	chr14	91341661	91341661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctggtacacgtcaaacttCggtcatgagattggaaggga	13	8	2	1	rs373786141	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91341661C>T	ENST00000261991.3	-	15	2053	c.1880G>A	c.(1879-1881)cGa>cAa	p.R627Q	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.R548Q	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	627	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R627Q(2)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CGTCAAACTTCGGTCATGAGA	0.428													C|||	14	0.00279553	0	0	5008	,	,		20365	0		0	False		,,,				2504	0.0143															2	Substitution - Missense(2)	large_intestine(2)	14											70	71	71					14																	91341661		2203	4300	6503	90411414	SO:0001583	missense	9252			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.1880G>A	14.37:g.91341661C>T	ENSP00000261991:p.Arg627Gln		90411414	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	37	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851160	0.32699	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	T;T	0.67698	-0.28;-0.28	5.43	3.29	0.37713	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.158248	0.56097	D	0.000031	T	0.44201	0.1282	N	0.20845	0.615	0.80722	D	1	B	0.25441	0.126	B	0.22753	0.041	T	0.13575	-1.0504	10	0.14656	T	0.56	.	6.7976	0.23734	0.0:0.374:0.0:0.626	.	627	O75582	KS6A5_HUMAN	Q	627;548	ENSP00000261991:R627Q;ENSP00000442803:R548Q	ENSP00000261991:R627Q	R	-	2	0	RPS6KA5	90411414	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	1.419000	0.34793	0.581000	0.29539	0.561000	0.74099	CGA		0.428	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		T	91341661	C	T	91341661	3	4	61	1	0	0	0	0	1	0	0	0	13691	884	31	1	540	1	RPS6KA5	14	91341661	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	220229	91341661	16007879	9070	17055										
RPS6KA5	9252	broad.mit.edu	37	chr14	91386570	91386570	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagatatctcagcttgggaAtttttttctccatcaacagt	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91386570A>T	ENST00000261991.3	-	7	959	c.786T>A	c.(784-786)aaT>aaA	p.N262K	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.N183K|RPS6KA5_ENST00000418736.2_Missense_Mutation_p.N262K	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	262	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N262K(2)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CAGCTTGGGAATTTTTTTCTC	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	14											86	93	91					14																	91386570		2203	4298	6501	90456323	SO:0001583	missense	9252			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.786T>A	14.37:g.91386570A>T	ENSP00000261991:p.Asn262Lys		90456323	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	37	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.805124	0.50315	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.64438	-0.1;-0.1;-0.1	5.31	-1.11	0.09840	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047357	0.85682	D	0.000000	T	0.52933	0.1765	N	0.10629	0.01	0.58432	D	0.999997	D;D	0.89917	0.993;1.0	P;D	0.85130	0.885;0.997	T	0.47262	-0.9131	10	0.18276	T	0.48	.	9.7444	0.40437	0.6522:0.0:0.3478:0.0	.	262;262	O75582-2;O75582	.;KS6A5_HUMAN	K	262;183;262	ENSP00000261991:N262K;ENSP00000442803:N183K;ENSP00000402787:N262K	ENSP00000261991:N262K	N	-	3	2	RPS6KA5	90456323	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	2.607000	0.46300	-0.470000	0.06901	-0.256000	0.11100	AAT		0.353	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		T	91386570	A	T	91386570	3	4	61	1	0	0	0	0	1	0	0	0	13691	98	4	5	1672	5	RPS6KA5	14	91386570	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	44909	91386570	15962970	9071	17056										
RPS6KA5	9252	broad.mit.edu	37	chr14	91409509	91409509	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatattctcaagcttaatAtcacgatatataatccccaa	3	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91409509A>G	ENST00000261991.3	-	5	704	c.531T>C	c.(529-531)gaT>gaC	p.D177D	RPS6KA5_ENST00000536315.2_Silent_p.D98D|RPS6KA5_ENST00000418736.2_Silent_p.D177D	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	177	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D177D(2)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CAAGCTTAATATCACGATATA	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	14											65	62	63					14																	91409509		2203	4300	6503	90479262	SO:0001819	synonymous_variant	9252			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.531T>C	14.37:g.91409509A>G			90479262	O95316|Q96AF7	Silent	SNP	ENST00000261991.3	37	CCDS9893.1																																																																																				0.313	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		G	91409509	A	G	91409509	2	3	61	1	0	0	0	0	0	0	0	1	13691	446	16	4		4	RPS6KA5	14	91409509	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22939	91409509	15940031	9072	17057										
RPS6KA5	9252	broad.mit.edu	37	chr14	91413793	91413793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttaccttgtggagatgttCgagggcaagcacaatctctc	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91413793C>T	ENST00000261991.3	-	4	669	c.496G>A	c.(496-498)Gaa>Aaa	p.E166K	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.E87K|RPS6KA5_ENST00000418736.2_Missense_Mutation_p.E166K	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	166	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E166K(4)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		TGGAGATGTTCGAGGGCAAGC	0.378																																																4	Substitution - Missense(4)	large_intestine(4)	14											109	107	108					14																	91413793		2203	4300	6503	90483546	SO:0001583	missense	9252			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.496G>A	14.37:g.91413793C>T	ENSP00000261991:p.Glu166Lys		90483546	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	37	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396017	0.83011	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.65549	-0.16;-0.16;-0.16	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050610	0.85682	D	0.000000	T	0.74489	0.3723	L	0.43701	1.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.965	T	0.76537	-0.2923	10	0.72032	D	0.01	.	19.0272	0.92937	0.0:1.0:0.0:0.0	.	166;166	O75582-2;O75582	.;KS6A5_HUMAN	K	166;87;166	ENSP00000261991:E166K;ENSP00000442803:E87K;ENSP00000402787:E166K	ENSP00000261991:E166K	E	-	1	0	RPS6KA5	90483546	1.000000	0.71417	0.986000	0.45419	0.473000	0.32948	7.440000	0.80464	2.502000	0.84385	0.591000	0.81541	GAA		0.378	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		T	91413793	C	T	91413793	3	4	61	1	0	0	0	0	1	0	0	0	13691	893	31	1	1974	1	RPS6KA5	14	91413793	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4284	91413793	15935747	9073	17058										
C14orf159	80017	broad.mit.edu	37	chr14	91633717	91633717	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaaggtgctatctcagaGaccaggtaaaaagcttgggt	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91633717G>T	ENST00000523771.1	+	4	855	c.252G>T	c.(250-252)gaG>gaT	p.E84D	C14orf159_ENST00000256324.10_Missense_Mutation_p.E84D|C14orf159_ENST00000518868.1_Missense_Mutation_p.E84D|C14orf159_ENST00000525393.2_Intron|C14orf159_ENST00000521077.2_Missense_Mutation_p.E84D|C14orf159_ENST00000412671.2_Missense_Mutation_p.E84D|C14orf159_ENST00000298858.4_Missense_Mutation_p.E84D|C14orf159_ENST00000519019.1_Missense_Mutation_p.E84D|C14orf159_ENST00000520328.1_Missense_Mutation_p.E84D|C14orf159_ENST00000428926.2_Missense_Mutation_p.E84D|C14orf159_ENST00000522322.1_Missense_Mutation_p.E84D|C14orf159_ENST00000518665.2_Missense_Mutation_p.E84D|C14orf159_ENST00000523816.1_Missense_Mutation_p.E84D|C14orf159_ENST00000517877.1_Missense_Mutation_p.E84D			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	84						mitochondrion (GO:0005739)		p.E84D(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CTATCTCAGAGACCAGGTAAA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	14											97	93	95					14																	91633717		2203	4300	6503	90703470	SO:0001583	missense	80017			AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.252G>T	14.37:g.91633717G>T	ENSP00000429655:p.Glu84Asp		90703470	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	G	8.670	0.902658	0.17760	.	.	ENSG00000133943	ENST00000521334;ENST00000522837;ENST00000518871;ENST00000298858;ENST00000520328;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000521077;ENST00000518665;ENST00000518868;ENST00000519019;ENST00000523816;ENST00000517518;ENST00000428926;ENST00000523894;ENST00000522322;ENST00000523771;ENST00000521064;ENST00000412671;ENST00000517877	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.42900	2.04;0.96;2.04;0.97;2.04;2.04;2.04;2.04;2.04;0.97;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;1.2	5.35	-3.96	0.04106	.	0.318283	0.31092	N	0.008262	T	0.06096	0.0158	N	0.00095	-2.16	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.39354	-0.9618	10	0.02654	T	1	.	8.7492	0.34605	0.0:0.3133:0.1128:0.5738	.	84;84;84;84;84;84	Q7Z3D6-6;Q7Z3D6;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	.;CN159_HUMAN;.;.;.;.	D	84	ENSP00000430022:E84D;ENSP00000427971:E84D;ENSP00000429189:E84D;ENSP00000298858:E84D;ENSP00000429453:E84D;ENSP00000256324:E84D;ENSP00000430666:E84D;ENSP00000428296:E84D;ENSP00000430137:E84D;ENSP00000429098:E84D;ENSP00000428263:E84D;ENSP00000430318:E84D;ENSP00000428974:E84D;ENSP00000428652:E84D;ENSP00000404343:E84D;ENSP00000429459:E84D;ENSP00000427953:E84D;ENSP00000429655:E84D;ENSP00000429392:E84D;ENSP00000404196:E84D;ENSP00000429949:E84D	ENSP00000256324:E84D	E	+	3	2	C14orf159	90703470	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.478000	0.06575	-0.896000	0.03915	-0.311000	0.09066	GAG		0.547	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		T	91633717	G	T	91633717	3	4	61	1	0	0	0	0	1	0	0	0	1759	933	33	2	258	2	C14orf159	14	91633717	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	219924	91633717	15715823	9074	17059										
SMEK1	55671	broad.mit.edu	37	chr14	91931745	91931745	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttaatccaataatctttCttttaaaacgaagggcacct	4	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:91931745C>A	ENST00000554943.1	-	11	1794	c.1679G>T	c.(1678-1680)aGa>aTa	p.R560I	SMEK1_ENST00000337238.4_Missense_Mutation_p.R547I|SMEK1_ENST00000555462.1_Missense_Mutation_p.R321I|SMEK1_ENST00000554684.1_Missense_Mutation_p.R547I|SMEK1_ENST00000555718.1_5'UTR|SMEK1_ENST00000428424.2_Missense_Mutation_p.R321I			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	560					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)		p.R560I(1)		NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		AATAATCTTTCTTTTAAAACG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											83	83	83					14																	91931745		2203	4300	6503	91001498	SO:0001583	missense	55671			AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1679G>T	14.37:g.91931745C>A	ENSP00000450883:p.Arg560Ile		91001498	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	37		.	.	.	.	.	.	.	.	.	.	C	17.23	3.337657	0.60963	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	6.15	6.15	0.99193	Armadillo-type fold (1);	0.041374	0.85682	D	0.000000	D	0.98077	0.9366	M	0.86178	2.8	0.80722	D	1	D;D;D	0.89917	0.994;1.0;1.0	D;D;D	0.97110	0.983;0.999;1.0	D	0.97849	1.0273	10	0.62326	D	0.03	-15.6355	20.8387	0.99724	0.0:1.0:0.0:0.0	.	321;560;547	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	I	547;547;321;560;321;547	ENSP00000450864:R547I;ENSP00000337125:R547I;ENSP00000392704:R321I;ENSP00000450883:R560I;ENSP00000450891:R321I;ENSP00000452596:R547I	ENSP00000337125:R547I	R	-	2	0	SMEK1	91001498	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	7.811000	0.86092	2.932000	0.99384	0.643000	0.83706	AGA		0.348	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		A	91931745	C	A	91931745	3	1	61	1	0	0	0	0	1	0	0	0	14830	913	32	2	842	2	SMEK1	14	91931745	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298028	91931745	15417795	9075	17060										
CATSPERB	79820	broad.mit.edu	37	chr14	92054395	92054395	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttctactaattgtttcattCttttaatattttctggcaca	4	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92054395C>A	ENST00000256343.3	-	25	3140	c.2984G>T	c.(2983-2985)aGa>aTa	p.R995I		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	995					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.R995I(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TTGTTTCATTCTTTTAATATT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	126	126					14																	92054395		2203	4298	6501	91124148	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.2984G>T	14.37:g.92054395C>A	ENSP00000256343:p.Arg995Ile		91124148	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332246	0.24167	.	.	ENSG00000133962	ENST00000256343	T	0.52295	0.67	5.27	-3.09	0.05331	.	0.829641	0.10325	N	0.688237	T	0.33904	0.0879	N	0.24115	0.695	0.09310	N	1	P	0.35656	0.514	B	0.38755	0.281	T	0.37619	-0.9698	10	0.72032	D	0.01	-11.7023	11.0107	0.47661	0.0:0.4535:0.0:0.5465	.	995	Q9H7T0	CTSRB_HUMAN	I	995	ENSP00000256343:R995I	ENSP00000256343:R995I	R	-	2	0	CATSPERB	91124148	0.008000	0.16893	0.000000	0.03702	0.001000	0.01503	0.068000	0.14531	-0.511000	0.06514	-2.299000	0.00261	AGA		0.303	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92054395	C	A	92054395	3	1	61	1	0	0	0	0	1	0	0	0	2697	913	32	2	378	2	CATSPERB	14	92054395	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122650	92054395	15295145	9076	17061										
CATSPERB	79820	broad.mit.edu	37	chr14	92058307	92058307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcagttacactcctcccGagtggaaacattagcacact	8	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92058307G>A	ENST00000256343.3	-	23	2905	c.2749C>T	c.(2749-2751)Cgg>Tgg	p.R917W		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	917					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.R917W(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				CACTCCTCCCGAGTGGAAACA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	14											150	148	149					14																	92058307		2203	4300	6503	91128060	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.2749C>T	14.37:g.92058307G>A	ENSP00000256343:p.Arg917Trp		91128060	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655206	0.67472	.	.	ENSG00000133962	ENST00000256343	T	0.61510	0.1	5.27	5.27	0.74061	.	0.000000	0.45361	D	0.000367	T	0.72938	0.3523	M	0.64404	1.975	0.32084	N	0.592741	D	0.89917	1.0	D	0.97110	1.0	T	0.78692	-0.2105	10	0.87932	D	0	-12.25	14.4254	0.67212	0.0:0.0:1.0:0.0	.	917	Q9H7T0	CTSRB_HUMAN	W	917	ENSP00000256343:R917W	ENSP00000256343:R917W	R	-	1	2	CATSPERB	91128060	0.947000	0.32204	0.151000	0.22473	0.637000	0.38172	2.066000	0.41452	2.463000	0.83235	0.467000	0.42956	CGG		0.398	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92058307	G	A	92058307	3	1	61	1	0	0	0	0	1	0	0	0	2697	1057	37	1	621	1	CATSPERB	14	92058307	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3912	92058307	15291233	9077	17062										
CATSPERB	79820	broad.mit.edu	37	chr14	92088187	92088187	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcaatggctaatgcattCttattatctaaaatgcttgt	7	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92088187C>A	ENST00000256343.3	-	19	2181	c.2025G>T	c.(2023-2025)aaG>aaT	p.K675N		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	675					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.K675N(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				CTAATGCATTCTTATTATCTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											95	85	89					14																	92088187		2203	4300	6503	91157940	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.2025G>T	14.37:g.92088187C>A	ENSP00000256343:p.Lys675Asn		91157940	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.630467	0.28978	.	.	ENSG00000133962	ENST00000256343	T	0.44881	0.91	5.43	-1.56	0.08532	.	2.022300	0.02197	N	0.061882	T	0.27349	0.0671	L	0.31926	0.97	0.09310	N	1	B	0.17268	0.021	B	0.16289	0.015	T	0.05566	-1.0877	10	0.22109	T	0.4	0.4772	0.6391	0.00807	0.3474:0.2869:0.122:0.2437	.	675	Q9H7T0	CTSRB_HUMAN	N	675	ENSP00000256343:K675N	ENSP00000256343:K675N	K	-	3	2	CATSPERB	91157940	0.000000	0.05858	0.052000	0.19188	0.160000	0.22226	-0.341000	0.07811	-0.018000	0.14079	0.591000	0.81541	AAG		0.423	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92088187	C	A	92088187	3	1	61	1	0	0	0	0	1	0	0	0	2697	912	32	2	1361	2	CATSPERB	14	92088187	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29880	92088187	15261353	9078	17063										
CATSPERB	79820	broad.mit.edu	37	chr14	92126257	92126257	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaaactatgaaaagtcttCtttatgatatcatcatgaaa	4	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92126257C>A	ENST00000256343.3	-	15	1512	c.1356G>T	c.(1354-1356)aaG>aaT	p.K452N		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	452					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.K452N(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				GAAAAGTCTTCTTTATGATAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	14											77	78	78					14																	92126257		2203	4299	6502	91196010	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1356G>T	14.37:g.92126257C>A	ENSP00000256343:p.Lys452Asn		91196010	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	6.205	0.405946	0.11754	.	.	ENSG00000133962	ENST00000256343	T	0.46063	0.88	4.76	3.87	0.44632	.	1.152260	0.06413	N	0.721012	T	0.43456	0.1248	L	0.50333	1.59	0.09310	N	1	B	0.22983	0.078	B	0.28232	0.087	T	0.39860	-0.9593	10	0.42905	T	0.14	-1.4105	11.4097	0.49919	0.0:0.8173:0.1827:0.0	.	452	Q9H7T0	CTSRB_HUMAN	N	452	ENSP00000256343:K452N	ENSP00000256343:K452N	K	-	3	2	CATSPERB	91196010	0.000000	0.05858	0.002000	0.10522	0.135000	0.20990	0.015000	0.13355	1.116000	0.41820	-0.273000	0.10243	AAG		0.333	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92126257	C	A	92126257	3	1	61	1	0	0	0	0	1	0	0	0	2697	912	32	2	2046	2	CATSPERB	14	92126257	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38070	92126257	15223283	9079	17064										
CATSPERB	79820	broad.mit.edu	37	chr14	92189396	92189396	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agataaaatgtaattaccaaCgttaaattaaagtggaagat	7	3	0	2	rs141312058	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92189396C>A	ENST00000256343.3	-	4	462	c.306G>T	c.(304-306)acG>acT	p.T102T		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	102					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.T102T(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TAATTACCAACGTTAAATTAA	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	14											118	116	116					14																	92189396		2203	4300	6503	91259149	SO:0001819	synonymous_variant	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.306G>T	14.37:g.92189396C>A			91259149	A0AV51	Silent	SNP	ENST00000256343.3	37	CCDS32142.1																																																																																				0.328	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92189396	C	A	92189396	2	1	61	1	0	0	0	0	0	0	0	1	2697	523	19	2		2	CATSPERB	14	92189396	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63139	92189396	15160144	9080	17065										
CATSPERB	79820	broad.mit.edu	37	chr14	92191463	92191463	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaacttgattatttcattCtcttgagggaaccctttgtt	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92191463C>A	ENST00000256343.3	-	3	285	c.129G>T	c.(127-129)gaG>gaT	p.E43D		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	43					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.E43D(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TTATTTCATTCTCTTGAGGGA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	14											73	67	69					14																	92191463		2202	4297	6499	91261216	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.129G>T	14.37:g.92191463C>A	ENSP00000256343:p.Glu43Asp		91261216	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392869	0.25118	.	.	ENSG00000133962	ENST00000256343;ENST00000553329;ENST00000554560;ENST00000556661;ENST00000553676	T	0.44482	0.92	5.0	-4.48	0.03515	.	1.706150	0.03362	N	0.197753	T	0.23886	0.0578	N	0.22421	0.69	0.09310	N	1	B	0.25169	0.119	B	0.21917	0.037	T	0.08680	-1.0710	10	0.20046	T	0.44	0.3217	4.2872	0.10860	0.231:0.2353:0.4464:0.0873	.	43	Q9H7T0	CTSRB_HUMAN	D	43	ENSP00000256343:E43D	ENSP00000256343:E43D	E	-	3	2	CATSPERB	91261216	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.530000	0.06179	-0.654000	0.05394	-0.182000	0.12963	GAG		0.318	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92191463	C	A	92191463	3	1	61	1	0	0	0	0	1	0	0	0	2697	912	32	2	3321	2	CATSPERB	14	92191463	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2067	92191463	15158077	9081	17066										
FBLN5	10516	broad.mit.edu	37	chr14	92343955	92343955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggagcgtcctgacaccacgTccatgtcccggtacaagatg	11	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92343955T>C	ENST00000342058.4	-	10	1654	c.1061A>G	c.(1060-1062)gAc>gGc	p.D354G	FBLN5_ENST00000556154.1_Missense_Mutation_p.D359G|FBLN5_ENST00000267620.10_Missense_Mutation_p.D395G|FBLN5_ENST00000556961.1_5'Flank	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	354					cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)	p.D354G(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				TGACACCACGTCCATGTCCCG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	14											127	110	116					14																	92343955		2203	4300	6503	91413708	SO:0001583	missense	10516			AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.1061A>G	14.37:g.92343955T>C	ENSP00000345008:p.Asp354Gly		91413708	O75966|Q6IAL4|Q6UWA3	Missense_Mutation	SNP	ENST00000342058.4	37	CCDS9898.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.181085|5.181085	0.94846|0.94846	.|.	.|.	ENSG00000140092|ENSG00000140092	ENST00000267620;ENST00000342058;ENST00000556154|ENST00000554121	D;D;D|.	0.82526|.	-1.6;-1.62;-1.58|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61627|0.61627	0.2362|0.2362	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.994;0.99|.	D;P;P|.	0.91635|.	0.999;0.879;0.677|.	T|T	0.57100|0.57100	-0.7869|-0.7869	10|5	0.54805|.	T|.	0.06|.	.|.	16.8222|16.8222	0.85835|0.85835	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	395;359;354|.	G3XA98;G3V4U0;Q9UBX5|.	.;.;FBLN5_HUMAN|.	G|A	395;354;359|63	ENSP00000267620:D395G;ENSP00000345008:D354G;ENSP00000451982:D359G|.	ENSP00000267620:D451G|.	D|T	-|-	2|1	0|0	FBLN5|FBLN5	91413708|91413708	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.996000|0.996000	0.88848|0.88848	5.084000|5.084000	0.64462|0.64462	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAC|ACG		0.542	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			C	92343955	T	C	92343955	3	2	61	1	0	0	0	0	1	0	0	0	5719	1667	58	4	293	4	FBLN5	14	92343955	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	152492	92343955	15005585	9082	17067										
TRIP11	9321	broad.mit.edu	37	chr14	92471598	92471598	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttaatttcctcttcaaGatgttccttgatcgtgttca	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92471598G>T	ENST00000267622.4	-	11	3095	c.2722C>A	c.(2722-2724)Ctt>Att	p.L908I		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	908					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.L908I(1)		breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TCCTCTTCAAGATGTTCCTTG	0.398			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	1	Substitution - Missense(1)	large_intestine(1)	14											196	171	180					14																	92471598		2203	4300	6503	91541351	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.2722C>A	14.37:g.92471598G>T	ENSP00000267622:p.Leu908Ile		91541351	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.99|11.99	1.803580|1.803580	0.31869|0.31869	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.08546|.	3.08|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.458950|.	0.23714|.	N|.	0.045296|.	T|T	0.57388|0.57388	0.2050|0.2050	M|M	0.63843|0.63843	1.955|1.955	0.30036|0.30036	N|N	0.813088|0.813088	D;D|.	0.67145|.	0.972;0.996|.	P;D|.	0.64776|.	0.592;0.929|.	T|T	0.58411|0.58411	-0.7641|-0.7641	10|5	0.52906|.	T|.	0.07|.	.|.	13.7479|13.7479	0.62887|0.62887	0.0698:0.0:0.9302:0.0|0.0698:0.0:0.9302:0.0	.|.	644;908|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	I|Y	908;644|623	ENSP00000267622:L908I|.	ENSP00000267622:L908I|.	L|S	-|-	1|2	0|0	TRIP11|TRIP11	91541351|91541351	1.000000|1.000000	0.71417|0.71417	0.549000|0.549000	0.28204|0.28204	0.327000|0.327000	0.28475|0.28475	3.193000|3.193000	0.50997|0.50997	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	CTT|TCT		0.398	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92471598	G	T	92471598	3	4	61	1	0	0	0	0	1	0	0	0	16595	942	33	2	3261	2	TRIP11	14	92471598	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127643	92471598	14877942	9083	17068										
SLC24A4	123041	broad.mit.edu	37	chr14	92959951	92959951	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaccttcgtcaacttgccGatgtgccgggaagacgatta	10	10	1	1	rs537146844		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:92959951G>A	ENST00000532405.1	+	17	2074	c.1848G>A	c.(1846-1848)ccG>ccA	p.P616P	SLC24A4_ENST00000351924.5_Silent_p.P580P|SLC24A4_ENST00000531433.1_Silent_p.P597P|SLC24A4_ENST00000298877.1_Silent_p.P599P|SLC24A4_ENST00000393265.2_Silent_p.P552P			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	616					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.P599P(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		TCAACTTGCCGATGTGCCGGG	0.562													G|||	1	0.000199681	0	0.0014	5008	,	,		19697	0		0	False		,,,				2504	0				NSCLC(10;315 435 10383 28450 38798)											1	Substitution - coding silent(1)	large_intestine(1)	14											153	123	133					14																	92959951		2203	4300	6503	92029704	SO:0001819	synonymous_variant	123041			AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"Solute carriers"	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1848G>A	14.37:g.92959951G>A			92029704	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Silent	SNP	ENST00000532405.1	37	CCDS9903.2																																																																																				0.562	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646		A	92959951	G	A	92959951	2	1	61	1	0	0	0	0	0	0	0	1	14505	1045	37	1		1	SLC24A4	14	92959951	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	488353	92959951	14389589	9084	17069										
RIN3	79890	broad.mit.edu	37	chr14	93043795	93043795	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagctcggccgaggtgctcGaatacaccattaaggaagaa	11	9	0	1	rs139542247		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93043795G>A	ENST00000216487.7	+	3	499	c.340G>A	c.(340-342)Gaa>Aaa	p.E114K	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	114	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.E114*(1)|p.E114K(1)		endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CGAGGTGCTCGAATACACCAT	0.522																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	14						G	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	107	103	104		340	4	0.2	14	dbSNP_134	104	0,8600		0,0,4300	no	missense	RIN3	NM_024832.3	56	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging	114/986	93043795	2,13004	2203	4300	6503	92113548	SO:0001583	missense	79890			BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.340G>A	14.37:g.93043795G>A	ENSP00000216487:p.Glu114Lys		92113548	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733764	0.30684	4.54E-4	0.0	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.29397	1.57	4.91	4.01	0.46588	SH2 motif (3);	0.338794	0.29273	N	0.012623	T	0.54240	0.1846	M	0.78801	2.425	0.80722	D	1	D;P	0.89917	1.0;0.956	D;B	0.77557	0.99;0.296	T	0.58532	-0.7620	10	0.72032	D	0.01	-15.2306	11.5957	0.50972	0.0:0.18:0.82:0.0	.	39;114	Q6ZRC2;Q8TB24	.;RIN3_HUMAN	K	114	ENSP00000216487:E114K	ENSP00000216487:E114K	E	+	1	0	RIN3	92113548	0.993000	0.37304	0.233000	0.24025	0.004000	0.04260	2.689000	0.46993	1.184000	0.42957	0.655000	0.94253	GAA		0.522	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			A	93043795	G	A	93043795	3	1	61	1	0	0	0	0	1	0	0	0	13410	1059	37	1	350	1	RIN3	14	93043795	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83844	93043795	14305745	9085	17070										
LGMN	5641	broad.mit.edu	37	chr14	93170702	93170702	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacgtggtccatggacaattTtatcctgcgagagacaggaa	11	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93170702T>G	ENST00000393218.2	-	15	1601	c.1264A>C	c.(1264-1266)Aaa>Caa	p.K422Q	LGMN_ENST00000557434.1_Missense_Mutation_p.K365Q|LGMN_ENST00000334869.4_Missense_Mutation_p.K422Q|LGMN_ENST00000555699.1_Missense_Mutation_p.K342T	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	422					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.K422Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		ATGGACAATTTTATCCTGCGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	14											72	64	67					14																	93170702		2203	4300	6503	92240455	SO:0001583	missense	5641			D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"protease, cysteine, 1 (legumain)"	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1264A>C	14.37:g.93170702T>G	ENSP00000376911:p.Lys422Gln		92240455	O00123|Q86TV2|Q86TV3|Q9BTY1	Missense_Mutation	SNP	ENST00000393218.2	37	CCDS9904.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.806|9.806	1.181741|1.181741	0.21787|0.21787	.|.	.|.	ENSG00000100600|ENSG00000100600	ENST00000334869;ENST00000557434;ENST00000262004;ENST00000393218;ENST00000539531;ENST00000535855|ENST00000555699;ENST00000334864	T;T;T|T	0.44881|0.48201	0.94;0.91;0.94|0.82	4.89|4.89	3.69|3.69	0.42338|0.42338	.|.	0.559530|0.559530	0.21173|0.21173	N|N	0.078956|0.078956	T|T	0.35740|0.35740	0.0942|0.0942	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	B;B;B|P	0.12013|0.37914	0.005;0.005;0.003|0.611	B;B;B|B	0.10450|0.35550	0.005;0.005;0.002|0.205	T|T	0.20739|0.20739	-1.0266|-1.0266	10|10	0.25106|0.34782	T|T	0.35|0.22	-17.1113|-17.1113	4.9187|4.9187	0.13858|0.13858	0.2016:0.0895:0.0:0.709|0.2016:0.0895:0.0:0.709	.|.	422;422;365|342	A8K669;Q99538;Q86TV3|Q86TV2	.;LGMN_HUMAN;.|.	Q|T	422;365;365;422;399;387|342	ENSP00000334052:K422Q;ENSP00000452572:K365Q;ENSP00000376911:K422Q|ENSP00000451861:K342T	ENSP00000262004:K365Q|ENSP00000334206:K342T	K|K	-|-	1|2	0|0	LGMN|LGMN	92240455|92240455	0.174000|0.174000	0.23070|0.23070	0.307000|0.307000	0.25127|0.25127	0.484000|0.484000	0.33280|0.33280	0.450000|0.450000	0.21762|0.21762	0.778000|0.778000	0.33520|0.33520	0.449000|0.449000	0.29647|0.29647	AAA|AAA		0.532	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606		G	93170702	T	G	93170702	3	3	61	1	0	0	0	0	1	0	0	0	8778	1850	64	4	41	4	LGMN	14	93170702	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	126907	93170702	14178838	9086	17071										
GOLGA5	9950	broad.mit.edu	37	chr14	93263822	93263822	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctggaaaggcagaagatCttttaaaccgagttgatcaa	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93263822C>A	ENST00000163416.2	+	2	296	c.40C>A	c.(40-42)Ctt>Att	p.L14I	GOLGA5_ENST00000355976.2_Missense_Mutation_p.L14I	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	14					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.L14I(1)		large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		GGCAGAAGATCTTTTAAACCG	0.408			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	1	Substitution - Missense(1)	large_intestine(1)	14											72	65	68					14																	93263822		2203	4300	6503	92333575	SO:0001583	missense	9950			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.40C>A	14.37:g.93263822C>A	ENSP00000163416:p.Leu14Ile		92333575	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.312227	0.81358	.	.	ENSG00000066455	ENST00000163416;ENST00000355976;ENST00000439315	T;T	0.42900	0.97;0.96	5.51	5.51	0.81932	.	0.000000	0.44285	D	0.000477	T	0.50326	0.1609	M	0.65975	2.015	0.38900	D	0.957294	D	0.53745	0.962	P	0.49361	0.608	T	0.56450	-0.7977	10	0.59425	D	0.04	-13.6872	13.0533	0.58966	0.0:0.9263:0.0:0.0737	.	14	Q8TBA6	GOGA5_HUMAN	I	14	ENSP00000163416:L14I;ENSP00000348252:L14I	ENSP00000163416:L14I	L	+	1	0	GOLGA5	92333575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.893000	0.63199	2.738000	0.93877	0.655000	0.94253	CTT		0.408	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			A	93263822	C	A	93263822	3	1	61	1	0	0	0	0	1	0	0	0	6576	913	32	2	42	2	GOLGA5	14	93263822	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93120	93263822	14085718	9087	17072										
GOLGA5	9950	broad.mit.edu	37	chr14	93264120	93264120	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatcccattttgtgcgaaGaaaaaagtcagaacctgatg	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93264120G>T	ENST00000163416.2	+	2	594	c.338G>T	c.(337-339)aGa>aTa	p.R113I	GOLGA5_ENST00000355976.2_Missense_Mutation_p.R113I	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	113					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.R113I(1)		large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		TTTGTGCGAAGAAAAAAGTCA	0.453			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	1	Substitution - Missense(1)	large_intestine(1)	14											91	89	90					14																	93264120		2203	4300	6503	92333873	SO:0001583	missense	9950			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.338G>T	14.37:g.93264120G>T	ENSP00000163416:p.Arg113Ile		92333873	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576348	0.86645	.	.	ENSG00000066455	ENST00000163416;ENST00000355976	T;T	0.34667	1.36;1.35	5.45	5.45	0.79879	.	0.000000	0.53938	D	0.000051	T	0.45895	0.1365	M	0.65975	2.015	0.80722	D	1	P	0.49961	0.93	P	0.44732	0.459	T	0.49916	-0.8888	10	0.59425	D	0.04	-23.2732	19.6558	0.95837	0.0:0.0:1.0:0.0	.	113	Q8TBA6	GOGA5_HUMAN	I	113	ENSP00000163416:R113I;ENSP00000348252:R113I	ENSP00000163416:R113I	R	+	2	0	GOLGA5	92333873	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.811000	0.62606	2.719000	0.93026	0.655000	0.94253	AGA		0.453	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			T	93264120	G	T	93264120	3	4	61	1	0	0	0	0	1	0	0	0	6576	942	33	2	340	2	GOLGA5	14	93264120	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298	93264120	14085420	9088	17073										
GOLGA5	9950	broad.mit.edu	37	chr14	93290922	93290922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatagaagaagatctttatcGaacaaagaacacattgcaaa	6	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93290922G>A	ENST00000163416.2	+	9	1908	c.1652G>A	c.(1651-1653)cGa>cAa	p.R551Q	GOLGA5_ENST00000355976.2_Missense_Mutation_p.R551Q	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	551					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.R551Q(1)		large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		GATCTTTATCGAACAAAGAAC	0.363			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	1	Substitution - Missense(1)	large_intestine(1)	14											94	91	92					14																	93290922		2203	4300	6503	92360675	SO:0001583	missense	9950			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.1652G>A	14.37:g.93290922G>A	ENSP00000163416:p.Arg551Gln		92360675	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990694	0.93106	.	.	ENSG00000066455	ENST00000163416;ENST00000355976;ENST00000439315	T;T	0.42900	0.96;0.96	5.66	4.77	0.60923	.	0.000000	0.37348	N	0.002123	T	0.35770	0.0943	L	0.46614	1.455	0.58432	D	0.99999	P	0.49358	0.923	B	0.41917	0.37	T	0.11227	-1.0596	10	0.32370	T	0.25	-12.9377	10.9682	0.47424	0.1429:0.0:0.8571:0.0	.	551	Q8TBA6	GOGA5_HUMAN	Q	551;551;460	ENSP00000163416:R551Q;ENSP00000348252:R551Q	ENSP00000163416:R551Q	R	+	2	0	GOLGA5	92360675	1.000000	0.71417	0.996000	0.52242	0.933000	0.57130	5.619000	0.67729	1.527000	0.49086	0.655000	0.94253	CGA		0.363	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			A	93290922	G	A	93290922	3	1	61	1	0	0	0	0	1	0	0	0	6576	1058	37	1	1682	1	GOLGA5	14	93290922	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26802	93290922	14058618	9089	17074										
GOLGA5	9950	broad.mit.edu	37	chr14	93299660	93299660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtagtagtaatgggtcttCgattaatatgtctggaattg	11	3	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93299660C>T	ENST00000163416.2	+	10	2169	c.1913C>T	c.(1912-1914)tCg>tTg	p.S638L	GOLGA5_ENST00000355976.2_Missense_Mutation_p.S638L	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	638					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.S638L(1)		large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		AATGGGTCTTCGATTAATATG	0.408			T	RET	papillary thyroid																																		Dom	yes		14	14q	9950	"golgi autoantigen, golgin subfamily a, 5  (PTC5)"		E	1	Substitution - Missense(1)	large_intestine(1)	14											107	107	107					14																	93299660		2203	4300	6503	92369413	SO:0001583	missense	9950			AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"golgi integral membrane protein 5"	606918	"golgi autoantigen, golgin subfamily a, 5"			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.1913C>T	14.37:g.93299660C>T	ENSP00000163416:p.Ser638Leu		92369413	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.51|14.51	2.556183|2.556183	0.45487|0.45487	.|.	.|.	ENSG00000066455|ENSG00000066455	ENST00000554700|ENST00000163416;ENST00000355976;ENST00000439315	.|T;T	.|0.47177	.|0.85;0.85	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	.|0.146686	.|0.31589	.|N	.|0.007383	.|T	.|0.50599	.|0.1625	M|M	0.76170|0.76170	2.325|2.325	0.46725|0.46725	D|D	0.999178|0.999178	.|B	.|0.25667	.|0.131	.|B	.|0.28991	.|0.097	.|T	.|0.50898	.|-0.8773	.|10	.|0.11485	.|T	.|0.65	-4.3359|-4.3359	18.7034|18.7034	0.91629|0.91629	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|638	.|Q8TBA6	.|GOGA5_HUMAN	X|L	64|638;638;547	.|ENSP00000163416:S638L;ENSP00000348252:S638L	.|ENSP00000163416:S638L	R|S	+|+	1|2	2|0	GOLGA5|GOLGA5	92369413|92369413	0.734000|0.734000	0.28142|0.28142	0.013000|0.013000	0.15412|0.15412	0.317000|0.317000	0.28152|0.28152	5.173000|5.173000	0.65010|0.65010	2.417000|2.417000	0.82017|0.82017	0.585000|0.585000	0.79938|0.79938	CGA|TCG		0.408	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1			T	93299660	C	T	93299660	3	4	61	1	0	0	0	0	1	0	0	0	6576	893	31	1	1947	1	GOLGA5	14	93299660	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8738	93299660	14049880	9090	17075										
ITPK1	3705	broad.mit.edu	37	chr14	93460334	93460334	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtctcagggtgggcatcGatgtactcctgaaagggaag	15	7	1	1	rs375334505		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93460334G>A	ENST00000267615.6	-	5	428	c.255C>T	c.(253-255)atC>atT	p.I85I	ITPK1_ENST00000556603.2_Silent_p.I85I|ITPK1_ENST00000556954.1_Intron|ITPK1_ENST00000555495.1_5'UTR|ITPK1_ENST00000354313.3_Silent_p.I85I			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	85					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)	p.I85I(1)		endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GGTGGGCATCGATGTACTCCT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	14											162	123	136					14																	93460334		2203	4300	6503	92530087	SO:0001819	synonymous_variant	3705			U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.255C>T	14.37:g.93460334G>A			92530087	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	37	CCDS9907.1																																																																																				0.597	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		A	93460334	G	A	93460334	2	1	61	1	0	0	0	0	0	0	0	1	7937	1048	37	1		1	ITPK1	14	93460334	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	160674	93460334	13889206	9091	17076										
MOAP1	64112	broad.mit.edu	37	chr14	93649666	93649666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcagattaagctctctgcGaattgttttgtggactgccc	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:93649666G>A	ENST00000556883.1	-	2	1406	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C	TMEM251_ENST00000415050.2_5'Flank|RP11-371E8.4_ENST00000557574.1_5'Flank|MOAP1_ENST00000298894.4_Missense_Mutation_p.R308C|TMEM251_ENST00000283534.4_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	308					apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)	p.R308C(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		agctctctgcgaattgttttg	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	14											106	106	106					14																	93649666		2203	4300	6503	92719419	SO:0001583	missense	64112			BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"Paraneoplastic Ma antigens"	16658	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 4"	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.922C>T	14.37:g.93649666G>A	ENSP00000451594:p.Arg308Cys		92719419	B2RDF6|Q9H833|Q9HAS1	Missense_Mutation	SNP	ENST00000556883.1	37	CCDS9908.1	.	.	.	.	.	.	.	.	.	.	G	7.848	0.723327	0.15439	.	.	ENSG00000165943	ENST00000298894;ENST00000556883	T;T	0.10668	2.85;2.85	3.15	1.18	0.20946	.	.	.	.	.	T	0.18551	0.0445	L	0.40543	1.245	0.09310	N	1	D	0.89917	1.0	D	0.67231	0.95	T	0.10245	-1.0638	9	0.72032	D	0.01	4.1608	5.5827	0.17258	0.0:0.2232:0.547:0.2299	.	308	Q96BY2	MOAP1_HUMAN	C	308	ENSP00000298894:R308C;ENSP00000451594:R308C	ENSP00000298894:R308C	R	-	1	0	MOAP1	92719419	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.075000	0.11431	0.319000	0.23209	-0.188000	0.12872	CGC		0.502	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1			A	93649666	G	A	93649666	3	1	61	1	0	0	0	0	1	0	0	0	9710	1058	37	1	137	1	MOAP1	14	93649666	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	189332	93649666	13699874	9092	17077										
KIAA1409	57578	broad.mit.edu	37	chr14	94008989	94008989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagaccgtatgtgatgttCgcttcgatgtcatggtcatg	12	7	2	3	rs375043069		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94008989C>T	ENST00000393151.2	+	14	1702	c.1702C>T	c.(1702-1704)Cgc>Tgc	p.R568C	UNC79_ENST00000555664.1_Missense_Mutation_p.R568C|UNC79_ENST00000553484.1_Missense_Mutation_p.R568C|UNC79_ENST00000256339.4_Missense_Mutation_p.R391C			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	568					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R391C(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						ATGTGATGTTCGCTTCGATGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	CYS/ARG	0,4406		0,0,2203	283	243	257		1171	5.9	1	14		257	1,8599	1.2+/-3.3	0,1,4299	no	missense	UNC79	NM_020818.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	391/2459	94008989	1,13005	2203	4300	6503	93078742	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1702C>T	14.37:g.94008989C>T	ENSP00000376858:p.Arg568Cys		93078742	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	33	5.244956	0.95272	0.0	1.16E-4	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19105	2.18;2.17;2.18;2.18	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.40979	0.1139	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.10222	-1.0639	10	0.72032	D	0.01	-19.2761	20.3129	0.98645	0.0:1.0:0.0:0.0	.	568	C9JQL1	.	C	391;568;568;568;568	ENSP00000256339:R391C;ENSP00000450868:R568C;ENSP00000451360:R568C;ENSP00000376858:R568C	ENSP00000256339:R391C	R	+	1	0	KIAA1409	93078742	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.049000	0.71053	2.800000	0.96347	0.650000	0.86243	CGC		0.488	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94008989	C	T	94008989	3	4	61	1	0	0	0	0	1	0	0	0	8251	884	31	1	1213	1	KIAA1409	14	94008989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	359323	94008989	13340551	9093	17078										
KIAA1409	57578	broad.mit.edu	37	chr14	94038411	94038411	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagataatcagttaaaaGaattcagggaagtattaagg	9	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94038411G>A	ENST00000393151.2	+	15	1927	c.1927G>A	c.(1927-1929)Gaa>Aaa	p.E643K	UNC79_ENST00000555664.1_Missense_Mutation_p.E643K|UNC79_ENST00000553484.1_Missense_Mutation_p.E643K|UNC79_ENST00000256339.4_Missense_Mutation_p.E466K			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	643					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E466K(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCAGTTAAAAGAATTCAGGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	14											50	52	51					14																	94038411		2203	4300	6503	93108164	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1927G>A	14.37:g.94038411G>A	ENSP00000376858:p.Glu643Lys		93108164	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	G	24.8	4.576260	0.86645	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.24538	1.85;1.86;1.85;1.86	5.73	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.41766	0.1173	L	0.41492	1.28	0.52501	D	0.999954	D	0.61697	0.99	D	0.72982	0.979	T	0.26430	-1.0103	10	0.54805	T	0.06	-6.467	14.5782	0.68265	0.0701:0.0:0.9299:0.0	.	643	C9JQL1	.	K	466;643;643;643;643	ENSP00000256339:E466K;ENSP00000450868:E643K;ENSP00000451360:E643K;ENSP00000376858:E643K	ENSP00000256339:E466K	E	+	1	0	KIAA1409	93108164	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.460000	0.97641	1.429000	0.47314	0.650000	0.86243	GAA		0.408	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94038411	G	A	94038411	3	1	61	1	0	0	0	0	1	0	0	0	8251	943	33	3	1442	3	KIAA1409	14	94038411	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29422	94038411	13311129	9094	17079										
KIAA1409	57578	broad.mit.edu	37	chr14	94044293	94044293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcctttgcgtagtccgtttCgtagccctttcaagaatttt	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94044293C>T	ENST00000393151.2	+	18	2317	c.2317C>T	c.(2317-2319)Cgt>Tgt	p.R773C	UNC79_ENST00000555664.1_Missense_Mutation_p.R773C|UNC79_ENST00000553484.1_Missense_Mutation_p.R773C|UNC79_ENST00000256339.4_Missense_Mutation_p.R596C			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	773					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R596C(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TAGTCCGTTTCGTAGCCCTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											227	208	215					14																	94044293		2203	4300	6503	93114046	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2317C>T	14.37:g.94044293C>T	ENSP00000376858:p.Arg773Cys		93114046	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	21.3	4.127326	0.77549	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.33	5.33	0.75918	.	0.077647	0.53938	D	0.000041	T	0.29256	0.0728	L	0.29908	0.895	0.53688	D	0.999975	D	0.64830	0.994	P	0.53224	0.721	T	0.02081	-1.1217	10	0.59425	D	0.04	-8.5423	19.0159	0.92894	0.0:1.0:0.0:0.0	.	773	C9JQL1	.	C	596;773;773;773;773	ENSP00000256339:R596C;ENSP00000450868:R773C;ENSP00000451360:R773C;ENSP00000376858:R773C	ENSP00000256339:R596C	R	+	1	0	KIAA1409	93114046	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	5.593000	0.67550	2.502000	0.84385	0.650000	0.86243	CGT		0.433	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94044293	C	T	94044293	3	4	61	1	0	0	0	0	1	0	0	0	8251	884	31	1	1844	1	KIAA1409	14	94044293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5882	94044293	13305247	9095	17080										
KIAA1409	57578	broad.mit.edu	37	chr14	94079406	94079406	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgtcaacttgctttaatGcattcattgcaggaattgcc	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94079406G>A	ENST00000393151.2	+	27	4018	c.4018G>A	c.(4018-4020)Gca>Aca	p.A1340T	UNC79_ENST00000555664.1_Missense_Mutation_p.A1340T|UNC79_ENST00000553484.1_Missense_Mutation_p.A1362T|UNC79_ENST00000256339.4_Missense_Mutation_p.A1163T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1340					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A1163T(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TTGCTTTAATGCATTCATTGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											113	96	102					14																	94079406		2203	4300	6503	93149159	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4018G>A	14.37:g.94079406G>A	ENSP00000376858:p.Ala1340Thr		93149159	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	G	32	5.157185	0.94686	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.27104	1.78;1.72;1.69;1.78	5.56	5.56	0.83823	.	0.049628	0.85682	D	0.000000	T	0.49338	0.1551	L	0.55990	1.75	0.49051	D	0.999745	D	0.71674	0.998	D	0.78314	0.991	T	0.45308	-0.9270	10	0.72032	D	0.01	-13.8774	19.5316	0.95231	0.0:0.0:1.0:0.0	.	1362	C9JQL1	.	T	1163;1340;1362;1340;1362	ENSP00000256339:A1163T;ENSP00000450868:A1340T;ENSP00000451360:A1362T;ENSP00000376858:A1340T	ENSP00000256339:A1163T	A	+	1	0	KIAA1409	93149159	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.617000	0.88574	0.650000	0.86243	GCA		0.433	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94079406	G	A	94079406	3	1	61	1	0	0	0	0	1	0	0	0	8251	1319	46	3	3581	3	KIAA1409	14	94079406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35113	94079406	13270134	9096	17081										
KIAA1409	57578	broad.mit.edu	37	chr14	94152982	94152982	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgctggatttcatggcagAcatgcacacgctgaccaaac	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94152982A>G	ENST00000393151.2	+	44	7001	c.7001A>G	c.(7000-7002)gAc>gGc	p.D2334G	UNC79_ENST00000555664.1_Missense_Mutation_p.D2295G|UNC79_ENST00000553484.1_Missense_Mutation_p.D2356G|UNC79_ENST00000256339.4_Missense_Mutation_p.D2157G			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2334					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D2157G(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TTCATGGCAGACATGCACACG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	14											206	140	162					14																	94152982		2203	4300	6503	93222735	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7001A>G	14.37:g.94152982A>G	ENSP00000376858:p.Asp2334Gly		93222735	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	A	19.72	3.880965	0.72294	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.34472	1.37;1.41;1.36;1.38	5.65	5.65	0.86999	.	0.044925	0.85682	D	0.000000	T	0.45696	0.1355	M	0.73962	2.25	0.80722	D	1	B	0.23591	0.088	B	0.31614	0.133	T	0.46233	-0.9206	10	0.72032	D	0.01	-25.3802	15.849	0.78912	1.0:0.0:0.0:0.0	.	2356	C9JQL1	.	G	2157;2295;2356;2334;2356	ENSP00000256339:D2157G;ENSP00000450868:D2295G;ENSP00000451360:D2356G;ENSP00000376858:D2334G	ENSP00000256339:D2157G	D	+	2	0	KIAA1409	93222735	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.842000	0.92136	2.285000	0.76669	0.533000	0.62120	GAC		0.502	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94152982	A	G	94152982	3	3	61	1	0	0	0	0	1	0	0	0	8251	275	10	4	6632	4	KIAA1409	14	94152982	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	73576	94152982	13196558	9097	17082										
FAM181A	90050	broad.mit.edu	37	chr14	94394676	94394676	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctgctgaacttcgtgaaCctggcgtccagcgacatcaa	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94394676C>T	ENST00000267594.5	+	3	538	c.231C>T	c.(229-231)aaC>aaT	p.N77N	FAM181A-AS1_ENST00000554742.1_RNA|FAM181A_ENST00000556222.1_Silent_p.N15N|FAM181A_ENST00000557000.2_Silent_p.N15N|FAM181A_ENST00000557719.1_Silent_p.N15N	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	77								p.N77N(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						ACTTCGTGAACCTGGCGTCCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	14											84	74	77					14																	94394676		2203	4300	6503	93464429	SO:0001819	synonymous_variant	90050			BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 152"	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.231C>T	14.37:g.94394676C>T			93464429	B2RD39|Q96GY1	Silent	SNP	ENST00000267594.5	37	CCDS9914.1																																																																																				0.602	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344		T	94394676	C	T	94394676	2	4	61	1	0	0	0	0	0	0	0	1	5524	506	18	3		3	FAM181A	14	94394676	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241694	94394676	12954864	9098	17083										
FAM181A	90050	broad.mit.edu	37	chr14	94395495	94395495	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccccacccatcttcaatgtCtttggctacctctagccacg	5	18	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94395495C>A	ENST00000267594.5	+	3	1357	c.1050C>A	c.(1048-1050)gtC>gtA	p.V350V	FAM181A-AS1_ENST00000554742.1_RNA|FAM181A_ENST00000556222.1_Silent_p.V288V|FAM181A_ENST00000557000.2_Silent_p.V288V|FAM181A_ENST00000557719.1_Silent_p.V288V	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	350								p.V350V(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						TCTTCAATGTCTTTGGCTACC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	14											28	33	32					14																	94395495		2106	4137	6243	93465248	SO:0001819	synonymous_variant	90050			BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 152"	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.1050C>A	14.37:g.94395495C>A			93465248	B2RD39|Q96GY1	Silent	SNP	ENST00000267594.5	37	CCDS9914.1																																																																																				0.657	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344		A	94395495	C	A	94395495	2	1	61	1	0	0	0	0	0	0	0	1	5524	900	32	2		2	FAM181A	14	94395495	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	819	94395495	12954045	9099	17084										
OTUB2	78990	broad.mit.edu	37	chr14	94505427	94505427	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagagcagggagatcttcaAgtgagtgccggggccccttg	16	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94505427A>C	ENST00000203664.5	+	3	427	c.218A>C	c.(217-219)aAg>aCg	p.K73T	OTUB2_ENST00000553723.1_Missense_Mutation_p.K73T	NM_023112.3	NP_075601.1	Q96DC9	OTUB2_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 2	73	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				cellular amino acid metabolic process (GO:0006520)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)	p.K73T(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(1)	5		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		GAGATCTTCAAGTGAGTGCCG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	14											66	68	67					14																	94505427		2203	4300	6503	93575180	SO:0001630	splice_region_variant	78990			AF318378	CCDS9917.1	14q32.13-q32.2	2014-02-24	2014-02-24	2004-05-28		ENSG00000089723		"OTU domain containing"	20351	protein-coding gene	gene with protein product		608338	"chromosome 14 open reading frame 137", "OTU domain, ubiquitin aldehyde binding 2"	C14orf137		12704427, 19996094	Standard	NM_023112		Approved	FLJ21916, MGC3102	uc001ych.4	Q96DC9		ENST00000203664.5:c.218+1A>C	14.37:g.94505427A>C			93575180	Q6IA10|Q9H6T1	Missense_Mutation	SNP	ENST00000203664.5	37	CCDS9917.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410738	0.42817	.	.	ENSG00000089723	ENST00000203664;ENST00000553723	T	0.43688	0.94	5.36	1.63	0.23807	Ovarian tumour, otubain (1);	0.274273	0.38663	N	0.001613	T	0.30386	0.0763	L	0.32530	0.975	0.33178	D	0.549167	B	0.12013	0.005	B	0.25614	0.062	T	0.25433	-1.0132	10	0.59425	D	0.04	-12.7263	7.8261	0.29315	0.4219:0.0:0.5781:0.0	.	73	Q96DC9	OTUB2_HUMAN	T	73	ENSP00000203664:K73T	ENSP00000203664:K73T	K	+	2	0	OTUB2	93575180	0.999000	0.42202	0.999000	0.59377	0.639000	0.38242	0.456000	0.21859	0.033000	0.15463	0.459000	0.35465	AAG		0.582	OTUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412855.1		Missense_Mutation	C	94505427	A	C	94505427	5	2	61	1	0	0	0	0	0	0	1	0	11343	86	3	4	228	4	OTUB2	14	94505427	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	109932	94505427	12844113	9100	17085										
DDX24	57062	broad.mit.edu	37	chr14	94521491	94521491	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggtagctcgagcagttcGaccacttcggtggacataaa	11	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94521491G>A	ENST00000330836.5	-	7	2160	c.2029C>T	c.(2029-2031)Cga>Tga	p.R677*	DDX24_ENST00000555054.1_Nonsense_Mutation_p.R634*|DDX24_ENST00000544005.1_Nonsense_Mutation_p.R427*	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	677	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.R677*(1)		cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CGAGCAGTTCGACCACTTCGG	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											134	122	126					14																	94521491		2203	4300	6503	93591244	SO:0001587	stop_gained	57062			AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.2029C>T	14.37:g.94521491G>A	ENSP00000328690:p.Arg677*		93591244	E7EMJ4|Q4V9L5	Nonsense_Mutation	SNP	ENST00000330836.5	37	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	G	38	6.799542	0.97849	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	.	.	.	5.43	3.61	0.41365	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0148	6.2943	0.21077	0.1393:0.0:0.6074:0.2534	.	.	.	.	X	677;427;622;303;634;634	.	ENSP00000328690:R677X	R	-	1	2	DDX24	93591244	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	2.727000	0.47311	0.785000	0.33685	-0.136000	0.14681	CGA		0.493	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		A	94521491	G	A	94521491	4	1	61	1	0	0	0	0	0	1	0	0	4357	1066	37	1	562	1	DDX24	14	94521491	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16064	94521491	12828049	9101	17086										
DDX24	57062	broad.mit.edu	37	chr14	94526849	94526849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtggcagaaaaaacaagcGtttgtctctttgggttgtat	12	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94526849G>A	ENST00000330836.5	-	5	1639	c.1508C>T	c.(1507-1509)aCg>aTg	p.T503M	DDX24_ENST00000555054.1_Missense_Mutation_p.T460M|DDX24_ENST00000544005.1_Missense_Mutation_p.T253M	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	503	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.T503M(1)		cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		AAAAACAAGCGTTTGTCTCTT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	14											166	153	157					14																	94526849		2203	4300	6503	93596602	SO:0001583	missense	57062			AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.1508C>T	14.37:g.94526849G>A	ENSP00000328690:p.Thr503Met		93596602	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	37	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.976069	0.74360	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.15952	2.38;2.38;2.38	5.45	5.45	0.79879	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.047609	0.85682	D	0.000000	T	0.31482	0.0798	M	0.63843	1.955	0.53005	D	0.99996	P	0.43909	0.821	P	0.48189	0.57	T	0.01460	-1.1349	10	0.59425	D	0.04	-12.2273	19.661	0.95871	0.0:0.0:1.0:0.0	.	503	Q9GZR7	DDX24_HUMAN	M	503;253;448;129;460;460	ENSP00000328690:T503M;ENSP00000440623:T253M;ENSP00000452145:T460M	ENSP00000328690:T503M	T	-	2	0	DDX24	93596602	1.000000	0.71417	0.956000	0.39512	0.982000	0.71751	5.253000	0.65452	2.714000	0.92807	0.563000	0.77884	ACG		0.478	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		A	94526849	G	A	94526849	3	1	61	1	0	0	0	0	1	0	0	0	4357	1145	40	1	1091	1	DDX24	14	94526849	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5358	94526849	12822691	9102	17087										
PPP4R4	57718	broad.mit.edu	37	chr14	94708199	94708199	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacattgggtttgcaacaaGaaaatggacacaatgaaaac	9	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94708199G>T	ENST00000304338.3	+	10	1205	c.1051G>T	c.(1051-1053)Gaa>Taa	p.E351*		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	351					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)	p.E351*(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						TTTGCAACAAGAAAATGGACA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											65	68	67					14																	94708199		2203	4300	6503	93777952	SO:0001587	stop_gained	57718			AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1051G>T	14.37:g.94708199G>T	ENSP00000305924:p.Glu351*		93777952	Q9BUF8|Q9HCF0	Nonsense_Mutation	SNP	ENST00000304338.3	37	CCDS9921.1	.	.	.	.	.	.	.	.	.	.	G	38	6.945591	0.97956	.	.	ENSG00000119698	ENST00000304338	.	.	.	5.25	5.25	0.73442	.	0.983803	0.08329	N	0.962693	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-21.2123	18.8186	0.92088	0.0:0.0:1.0:0.0	.	.	.	.	X	351	.	ENSP00000305924:E351X	E	+	1	0	PPP4R4	93777952	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.605000	0.82844	2.452000	0.82932	0.591000	0.81541	GAA		0.343	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		T	94708199	G	T	94708199	4	4	61	1	0	0	0	0	0	1	0	0	12439	943	33	2	1162	2	PPP4R4	14	94708199	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	181350	94708199	12641341	9103	17088										
PPP4R4	57718	broad.mit.edu	37	chr14	94716569	94716569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatttttctgcgttataatCgtaaacaagaacagagacat	7	7	1	2	rs201499500		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94716569C>T	ENST00000304338.3	+	15	1826	c.1672C>T	c.(1672-1674)Cgt>Tgt	p.R558C		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	558					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)	p.R558C(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						GCGTTATAATCGTAAACAAGA	0.343													C|||	1	0.000199681	0	0	5008	,	,		18686	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14						C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	133	118	123		1672	5.7	1	14	dbSNP_134	123	0,8600		0,0,4300	yes	missense	PPP4R4	NM_058237.1	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	558/874	94716569	2,13004	2203	4300	6503	93786322	SO:0001583	missense	57718			AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1672C>T	14.37:g.94716569C>T	ENSP00000305924:p.Arg558Cys		93786322	Q9BUF8|Q9HCF0	Missense_Mutation	SNP	ENST00000304338.3	37	CCDS9921.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	25.3	4.629145	0.87560	4.54E-4	0.0	ENSG00000119698	ENST00000304338	T	0.32988	1.43	5.71	5.71	0.89125	Armadillo-like helical (1);Armadillo-type fold (1);	0.049066	0.85682	D	0.000000	T	0.57725	0.2073	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.58205	-0.7677	10	0.66056	D	0.02	-11.8211	19.8403	0.96679	0.0:1.0:0.0:0.0	.	558	Q6NUP7	PP4R4_HUMAN	C	558	ENSP00000305924:R558C	ENSP00000305924:R558C	R	+	1	0	PPP4R4	93786322	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.684000	0.74538	2.692000	0.91855	0.455000	0.32223	CGT		0.343	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		T	94716569	C	T	94716569	3	4	61	1	0	0	0	0	1	0	0	0	12439	884	31	1	1803	1	PPP4R4	14	94716569	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8370	94716569	12632971	9104	17089										
SERPINA1	5265	broad.mit.edu	37	chr14	94849283	94849283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccctccaggatttcatCgtgagtgtcagccttggtcc	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94849283C>T	ENST00000448921.1	-	4	864	c.292G>A	c.(292-294)Gat>Aat	p.D98N	SERPINA1_ENST00000393087.4_Missense_Mutation_p.D98N|SERPINA1_ENST00000404814.4_Missense_Mutation_p.D98N|SERPINA1_ENST00000393088.4_Missense_Mutation_p.D98N|SERPINA1_ENST00000449399.3_Missense_Mutation_p.D98N|SERPINA1_ENST00000437397.1_Missense_Mutation_p.D98N|SERPINA1_ENST00000402629.1_Missense_Mutation_p.D98N|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000355814.4_Missense_Mutation_p.D98N|SERPINA1_ENST00000440909.1_Missense_Mutation_p.D98N	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	98					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D98N(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		AGGATTTCATCGTGAGTGTCA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	14											91	86	88					14																	94849283		2203	4300	6503	93919036	SO:0001583	missense	5265			X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.292G>A	14.37:g.94849283C>T	ENSP00000416066:p.Asp98Asn		93919036	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	.	.	.	.	.	.	.	.	.	.	c	9.002	0.980372	0.18812	.	.	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000554720;ENST00000556091;ENST00000557492;ENST00000556955	D;D;D;D;D;D;D;D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	5.8	0.242	0.15498	Serpin domain (3);	0.768931	0.12004	N	0.508523	T	0.75184	0.3815	L	0.41027	1.25	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.003	T	0.60475	-0.7256	10	0.37606	T	0.19	.	5.2807	0.15674	0.2066:0.2495:0.0:0.5439	.	98;98	P01009-2;P01009	.;A1AT_HUMAN	N	98;98;98;98;98;98;98;98;98;12;98;98;98	ENSP00000390299:D98N;ENSP00000416066:D98N;ENSP00000408474:D98N;ENSP00000348068:D98N;ENSP00000376802:D98N;ENSP00000376803:D98N;ENSP00000385960:D98N;ENSP00000416354:D98N;ENSP00000386094:D98N;ENSP00000450561:D12N;ENSP00000452169:D98N;ENSP00000452452:D98N;ENSP00000451098:D98N	ENSP00000348068:D98N	D	-	1	0	SERPINA1	93919036	0.000000	0.05858	0.032000	0.17829	0.111000	0.19643	-2.322000	0.01118	0.106000	0.17784	-0.405000	0.06341	GAT		0.552	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		T	94849283	C	T	94849283	3	4	61	1	0	0	0	0	1	0	0	0	14123	884	31	1	980	1	SERPINA1	14	94849283	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132714	94849283	12500257	9105	17090										
SERPINA11	256394	broad.mit.edu	37	chr14	94909507	94909507	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaatttggggaagtatgtCttccaggttatatgttccag	10	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94909507C>A	ENST00000334708.3	-	4	1037	c.973G>T	c.(973-975)Gac>Tac	p.D325Y	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	325					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D507Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		GGAAGTATGTCTTCCAGGTTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											115	109	111					14																	94909507		2203	4300	6503	93979260	SO:0001583	missense	256394			BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"Serine (or cysteine) peptidase inhibitors"	19193	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.973G>T	14.37:g.94909507C>A	ENSP00000335024:p.Asp325Tyr		93979260	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	37	CCDS32149.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710122	0.48517	.	.	ENSG00000186910	ENST00000334708	D	0.88896	-2.44	6.04	5.14	0.70334	Serpin domain (3);	0.434725	0.21362	N	0.075787	D	0.92658	0.7667	M	0.80847	2.515	0.33681	D	0.612173	P	0.44659	0.84	P	0.57009	0.811	D	0.95137	0.8260	10	0.72032	D	0.01	.	8.6654	0.34118	0.0:0.7477:0.1522:0.1001	.	325	Q86U17	SPA11_HUMAN	Y	325	ENSP00000335024:D325Y	ENSP00000335024:D325Y	D	-	1	0	SERPINA11	93979260	0.959000	0.32827	0.998000	0.56505	0.356000	0.29392	2.503000	0.45407	1.527000	0.49086	0.563000	0.77884	GAC		0.423	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451		A	94909507	C	A	94909507	3	1	61	1	0	0	0	0	1	0	0	0	14125	913	32	2	303	2	SERPINA11	14	94909507	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60224	94909507	12440033	9106	17091										
SERPINA12	145264	broad.mit.edu	37	chr14	94955986	94955986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaggctgcgatgaggggCgatcttggtgagatcaccat	14	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:94955986C>T	ENST00000341228.2	-	5	1819	c.1024G>A	c.(1024-1026)Gcc>Acc	p.A342T	SERPINA12_ENST00000556881.1_Missense_Mutation_p.A342T	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	342					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A342T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		CGATGAGGGGCGATCTTGGTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	14																																								94025739	SO:0001583	missense	145264			AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.1024G>A	14.37:g.94955986C>T	ENSP00000342109:p.Ala342Thr		94025739		Missense_Mutation	SNP	ENST00000341228.2	37	CCDS9926.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.663149	0.00772	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	D;D	0.83837	-1.77;-1.77	5.16	-4.27	0.03744	Serpin domain (3);	0.846665	0.10446	N	0.673698	T	0.48822	0.1521	N	0.01640	-0.785	0.09310	N	1	B	0.22276	0.067	B	0.12837	0.008	T	0.54296	-0.8315	10	0.02654	T	1	.	7.2237	0.26003	0.2082:0.4868:0.0:0.305	.	342	Q8IW75	SPA12_HUMAN	T	342	ENSP00000451738:A342T;ENSP00000342109:A342T	ENSP00000342109:A342T	A	-	1	0	SERPINA12	94025739	0.037000	0.19845	0.060000	0.19600	0.057000	0.15508	-0.420000	0.07062	-0.232000	0.09811	-0.410000	0.06199	GCC		0.592	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		T	94955986	C	T	94955986	3	4	61	1	0	0	0	0	1	0	0	0	14126	768	27	1	228	1	SERPINA12	14	94955986	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46479	94955986	12393554	9107	17092										
SERPINA4	5267	broad.mit.edu	37	chr14	95033448	95033448	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacagatacttgccctgctCggtgctacggatggattaca	11	10	0	2	rs13306799	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95033448C>A	ENST00000557004.1	+	3	1212	c.791C>A	c.(790-792)tCg>tAg	p.S264*	SERPINA4_ENST00000555095.1_Nonsense_Mutation_p.S264*|SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Nonsense_Mutation_p.S264*			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	264					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S264*(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		TTGCCCTGCTCGGTGCTACGG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											113	98	103					14																	95033448		2203	4300	6503	94103201	SO:0001587	stop_gained	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.791C>A	14.37:g.95033448C>A	ENSP00000450838:p.Ser264*		94103201	Q53XB5|Q86TR9|Q96BZ5	Nonsense_Mutation	SNP	ENST00000557004.1	37	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	C	30	5.057188	0.93846	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	.	.	.	4.56	1.45	0.22620	.	0.301071	0.21998	N	0.066044	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	6.1145	0.20120	0.1152:0.6133:0.1866:0.085	.	.	.	.	X	264	.	ENSP00000298841:S264X	S	+	2	0	SERPINA4	94103201	0.000000	0.05858	0.059000	0.19551	0.163000	0.22366	-0.420000	0.07062	0.445000	0.26639	0.561000	0.74099	TCG		0.483	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		A	95033448	C	A	95033448	4	1	61	1	0	0	0	0	0	1	0	0	14128	893	31	2	797	2	SERPINA4	14	95033448	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77462	95033448	12316092	9108	17093										
SERPINA4	5267	broad.mit.edu	37	chr14	95034505	95034505	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttgcatcttcccaagttCtccatttctggctcctatgt	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95034505C>A	ENST00000557004.1	+	4	1384	c.963C>A	c.(961-963)ttC>ttA	p.F321L	SERPINA4_ENST00000555095.1_Missense_Mutation_p.F321L|SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Missense_Mutation_p.F321L			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	321					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.F321L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		TTCCCAAGTTCTCCATTTCTG	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	14											128	129	129					14																	95034505		2203	4300	6503	94104258	SO:0001583	missense	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.963C>A	14.37:g.95034505C>A	ENSP00000450838:p.Phe321Leu		94104258	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	37	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	C	9.454	1.091233	0.20471	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.88201	-2.35;-2.35;-2.35	5.45	-0.326	0.12698	Serpin domain (3);	0.000000	0.64402	D	0.000016	D	0.89413	0.6708	M	0.63843	1.955	0.80722	D	1	D;P	0.63880	0.993;0.838	D;P	0.67382	0.951;0.576	D	0.84193	0.0446	10	0.22706	T	0.39	.	4.6011	0.12354	0.0:0.2783:0.1777:0.5439	.	321;321	B2R815;P29622	.;KAIN_HUMAN	L	321	ENSP00000450838:F321L;ENSP00000451172:F321L;ENSP00000298841:F321L	ENSP00000298841:F321L	F	+	3	2	SERPINA4	94104258	0.053000	0.20554	1.000000	0.80357	0.847000	0.48162	-0.461000	0.06712	0.289000	0.22422	0.655000	0.94253	TTC		0.463	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		A	95034505	C	A	95034505	3	1	61	1	0	0	0	0	1	0	0	0	14128	912	32	2	973	2	SERPINA4	14	95034505	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1057	95034505	12315035	9109	17094										
SERPINA3	12	broad.mit.edu	37	chr14	95088716	95088716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgccaaagttttccatctCgagggactataacctgaacg	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95088716C>T	ENST00000467132.1	+	4	2104	c.956C>T	c.(955-957)tCg>tTg	p.S319L	SERPINA3_ENST00000482740.1_Missense_Mutation_p.S101L|SERPINA3_ENST00000393078.3_Missense_Mutation_p.S319L|RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393080.4_Missense_Mutation_p.S319L			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	319					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S319L(1)		NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		TTTTCCATCTCGAGGGACTAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	14											134	123	127					14																	95088716		2203	4300	6503	94158469	SO:0001583	missense	12			K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.956C>T	14.37:g.95088716C>T	ENSP00000450540:p.Ser319Leu		94158469	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	37	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.628758	0.46944	.	.	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000467132;ENST00000482740	D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46	4.6	4.6	0.57074	Serpin domain (3);	0.356831	0.24642	N	0.036788	D	0.95796	0.8632	M	0.93594	3.435	0.40033	D	0.975555	D;D	0.89917	1.0;0.994	D;P	0.76071	0.987;0.569	D	0.97274	0.9913	10	0.87932	D	0	.	16.1584	0.81681	0.0:1.0:0.0:0.0	.	319;344	P01011;G3V5I3	AACT_HUMAN;.	L	344;319;319;319;101	ENSP00000452367:S344L;ENSP00000376793:S319L;ENSP00000376795:S319L;ENSP00000450540:S319L;ENSP00000451119:S101L	ENSP00000376793:S319L	S	+	2	0	SERPINA3	94158469	0.743000	0.28239	0.937000	0.37676	0.020000	0.10135	2.164000	0.42387	2.381000	0.81170	0.462000	0.41574	TCG		0.498	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		T	95088716	C	T	95088716	3	4	61	1	0	0	0	0	1	0	0	0	14127	893	31	1	966	1	SERPINA3	14	95088716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54211	95088716	12260824	9110	17095										
CLMN	79789	broad.mit.edu	37	chr14	95670249	95670249	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaggattctggaatcttCgaggattcctgtttctgttc	12	7	3	0	rs576493570|rs201041933	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95670249C>T	ENST00000298912.4	-	9	1550	c.1437G>A	c.(1435-1437)tcG>tcA	p.S479S		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	479					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.S479S(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTGGAATCTTCGAGGATTCCT	0.463													C|||	1	0.000199681	0	0.0014	5008	,	,		19499	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14						C		0,4406		0,0,2203	67	66	66		1437	-11	0	14		66	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CLMN	NM_024734.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		479/1003	95670249	3,13003	2203	4300	6503	94740002	SO:0001819	synonymous_variant	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1437G>A	14.37:g.95670249C>T			94740002	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Silent	SNP	ENST00000298912.4	37	CCDS9933.1																																																																																				0.463	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95670249	C	T	95670249	2	4	61	1	0	0	0	0	0	0	0	1	3548	871	31	1		1	CLMN	14	95670249	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	581533	95670249	11679291	9111	17096										
CLMN	79789	broad.mit.edu	37	chr14	95670573	95670573	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggtggagctgtctgacagCgcatggctggaaacaccatc	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95670573C>T	ENST00000298912.4	-	9	1226	c.1113G>A	c.(1111-1113)gcG>gcA	p.A371A		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	371					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.A371A(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TGTCTGACAGCGCATGGCTGG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	14											122	120	121					14																	95670573		2203	4300	6503	94740326	SO:0001819	synonymous_variant	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1113G>A	14.37:g.95670573C>T			94740326	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Silent	SNP	ENST00000298912.4	37	CCDS9933.1																																																																																				0.542	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95670573	C	T	95670573	2	4	61	1	0	0	0	0	0	0	0	1	3548	755	27	1		1	CLMN	14	95670573	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	324	95670573	11678967	9112	17097										
CLMN	79789	broad.mit.edu	37	chr14	95670764	95670764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcgaacaaaagtggattCgataggaacttctttatctg	10	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:95670764C>T	ENST00000298912.4	-	9	1035	c.922G>A	c.(922-924)Gaa>Aaa	p.E308K		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	308					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.E308K(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		AAAGTGGATTCGATAGGAACT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	75	73					14																	95670764		2201	4300	6501	94740517	SO:0001583	missense	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.922G>A	14.37:g.95670764C>T	ENSP00000298912:p.Glu308Lys		94740517	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519167	0.64634	.	.	ENSG00000165959	ENST00000298912	D	0.92965	-3.14	5.64	5.64	0.86602	.	0.000000	0.42053	D	0.000767	D	0.95284	0.8470	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.63793	0.918	D	0.94534	0.7739	10	0.46703	T	0.11	.	19.7154	0.96115	0.0:1.0:0.0:0.0	.	308	Q96JQ2	CLMN_HUMAN	K	308	ENSP00000298912:E308K	ENSP00000298912:E308K	E	-	1	0	CLMN	94740517	0.999000	0.42202	0.457000	0.27056	0.116000	0.19942	5.251000	0.65438	2.664000	0.90586	0.655000	0.94253	GAA		0.348	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95670764	C	T	95670764	3	4	61	1	0	0	0	0	1	0	0	0	3548	893	31	1	2106	1	CLMN	14	95670764	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191	95670764	11678776	9113	17098										
TCL1A	8115	broad.mit.edu	37	chr14	96178596	96178596	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccagaaactggagtctgaGgatcggtatcgtccatcagg	13	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96178596G>T	ENST00000402399.1	-	2	387	c.258C>A	c.(256-258)tcC>tcA	p.S86S	TCL1A_ENST00000556450.1_Silent_p.S86S|TCL1A_ENST00000555202.1_Silent_p.S86S|RP11-164H13.1_ENST00000553445.1_RNA|TCL1A_ENST00000554012.1_Silent_p.S86S|RP11-164H13.1_ENST00000547644.2_RNA	NM_021966.2	NP_068801.1	P56279	TCL1A_HUMAN	T-cell leukemia/lymphoma 1A	86					multicellular organismal development (GO:0007275)|stem cell maintenance (GO:0019827)	cell cortex (GO:0005938)|endoplasmic reticulum (GO:0005783)|pronucleus (GO:0045120)		p.S86S(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		TGGAGTCTGAGGATCGGTATC	0.572			T	TRA@	T-CLL																																Ovarian(96;1068 2019 35393 39316)		Dom	yes		14	14q32.1	8115	T-cell leukemia/lymphoma 1A		L	1	Substitution - coding silent(1)	large_intestine(1)	14											169	156	161					14																	96178596		2203	4300	6503	95248349	SO:0001819	synonymous_variant	8115			X82240	CCDS9941.1	14q32.1	2008-07-03				ENSG00000100721			11648	protein-coding gene	gene with protein product		186960				2783489, 7809072	Standard	NM_021966		Approved	TCL1	uc001yfb.4	P56279		ENST00000402399.1:c.258C>A	14.37:g.96178596G>T			95248349	Q6IBK7	Silent	SNP	ENST00000402399.1	37	CCDS9941.1	.	.	.	.	.	.	.	.	.	.	G	7.815	0.716497	0.15306	.	.	ENSG00000100721	ENST00000557043	.	.	.	3.61	2.68	0.31781	.	.	.	.	.	T	0.35451	0.0932	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.20605	-1.0270	4	.	.	.	-7.3554	8.3157	0.32100	0.0:0.0:0.7651:0.2349	.	.	.	.	I	61	.	.	L	-	1	0	TCL1A	95248349	0.000000	0.05858	0.002000	0.10522	0.377000	0.30045	0.526000	0.22971	1.058000	0.40530	0.462000	0.41574	CTC		0.572	TCL1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413246.1			T	96178596	G	T	96178596	2	4	61	1	0	0	0	0	0	0	0	1	15743	987	35	2		2	TCL1A	14	96178596	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	507832	96178596	11170944	9114	17099										
BDKRB2	624	broad.mit.edu	37	chr14	96703475	96703475	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggaagatatcaatgtttCtgtctgttcgtgaggactcc	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96703475C>A	ENST00000306005.3	+	2	227	c.31C>A	c.(31-33)Ctg>Atg	p.L11M	BDKRB2_ENST00000542454.2_5'UTR|RP11-404P21.8_ENST00000553811.1_Missense_Mutation_p.L11M|BDKRB2_ENST00000554311.1_Missense_Mutation_p.L11M|BDKRB2_ENST00000539359.1_5'UTR	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	11					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)	p.L11M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	ATCAATGTTTCTGTCTGTTCG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	14											216	172	187					14																	96703475		2203	4300	6503	95773228	SO:0001583	missense	624			S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.31C>A	14.37:g.96703475C>A	ENSP00000307713:p.Leu11Met		95773228		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	C	8.555	0.876353	0.17395	.	.	ENSG00000168398;ENSG00000168398;ENSG00000258691	ENST00000554311;ENST00000306005;ENST00000553811	T;T;T	0.72942	-0.7;-0.7;1.09	3.71	-1.54	0.08584	.	2.102490	0.02714	N	0.113208	T	0.51635	0.1686	N	0.08118	0	0.09310	N	1	P	0.52316	0.952	B	0.43575	0.424	T	0.49341	-0.8950	10	0.51188	T	0.08	.	5.8483	0.18679	0.0:0.3239:0.4787:0.1974	.	11	P30411	BKRB2_HUMAN	M	11	ENSP00000450482:L11M;ENSP00000307713:L11M;ENSP00000450984:L11M	ENSP00000307713:L11M	L	+	1	2	RP11-404P21.8;BDKRB2	95773228	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.622000	0.05553	-0.310000	0.08766	-0.819000	0.03115	CTG		0.522	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			A	96703475	C	A	96703475	3	1	61	1	0	0	0	0	1	0	0	0	1394	912	32	2	33	2	BDKRB2	14	96703475	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	524879	96703475	10646065	9115	17100										
BDKRB2	624	broad.mit.edu	37	chr14	96707028	96707028	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaccatctccaacaacttCgactggctctttggggagac	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96707028C>T	ENST00000306005.3	+	3	559	c.363C>T	c.(361-363)ttC>ttT	p.F121F	BDKRB2_ENST00000542454.2_Silent_p.F94F|RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000554311.1_Silent_p.F121F|BDKRB2_ENST00000539359.1_Silent_p.F94F	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	121					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)	p.F121F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	CCAACAACTTCGACTGGCTCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	14											138	139	139					14																	96707028		2203	4300	6503	95776781	SO:0001819	synonymous_variant	624			S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.363C>T	14.37:g.96707028C>T			95776781		Silent	SNP	ENST00000306005.3	37	CCDS9942.1																																																																																				0.592	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			T	96707028	C	T	96707028	2	4	61	1	0	0	0	0	0	0	0	1	1394	883	31	1		1	BDKRB2	14	96707028	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3553	96707028	10642512	9116	17101										
ATG2B	55102	broad.mit.edu	37	chr14	96761432	96761432	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccagagaaagaaataaccAgatttggctcctttgaggta	10	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96761432A>C	ENST00000359933.4	-	36	6184	c.5291T>G	c.(5290-5292)cTg>cGg	p.L1764R	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1764					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.L1764R(1)		breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGAAATAACCAGATTTGGCTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	14											88	84	85					14																	96761432		2203	4300	6503	95831185	SO:0001583	missense	55102			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.5291T>G	14.37:g.96761432A>C	ENSP00000353010:p.Leu1764Arg		95831185	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	15.98	2.993628	0.54041	.	.	ENSG00000066739	ENST00000359933	T	0.09445	2.98	5.52	4.37	0.52481	.	0.463200	0.21277	N	0.077208	T	0.06280	0.0162	L	0.29908	0.895	0.33160	D	0.54683	B	0.33448	0.412	B	0.30855	0.121	T	0.15037	-1.0451	10	0.16420	T	0.52	.	4.6728	0.12698	0.7325:0.0:0.2675:0.0	.	1764	Q96BY7	ATG2B_HUMAN	R	1764	ENSP00000353010:L1764R	ENSP00000261834:L408R	L	-	2	0	ATG2B	95831185	1.000000	0.71417	0.269000	0.24586	0.994000	0.84299	5.031000	0.64134	2.225000	0.72522	0.459000	0.35465	CTG		0.418	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		C	96761432	A	C	96761432	3	2	61	1	0	0	0	0	1	0	0	0	1095	188	7	4	973	4	ATG2B	14	96761432	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	54404	96761432	10588108	9117	17102										
ATG2B	55102	broad.mit.edu	37	chr14	96798893	96798893	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtatatgtactagttaatGataactcaaggtccatgttt	7	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96798893G>T	ENST00000359933.4	-	9	2200	c.1307C>A	c.(1306-1308)tCa>tAa	p.S436*		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	436					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.S436*(1)		breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ACTAGTTAATGATAACTCAAG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											124	123	123					14																	96798893		1822	4070	5892	95868646	SO:0001587	stop_gained	55102			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1307C>A	14.37:g.96798893G>T	ENSP00000353010:p.Ser436*		95868646	Q6ZRE7|Q96DQ3|Q9NW80	Nonsense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	G	47	13.619558	0.99753	.	.	ENSG00000066739	ENST00000359933	.	.	.	6.06	6.06	0.98353	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	.	.	.	X	436	.	ENSP00000353010:S436X	S	-	2	0	ATG2B	95868646	1.000000	0.71417	0.248000	0.24265	0.996000	0.88848	9.165000	0.94761	2.882000	0.98803	0.655000	0.94253	TCA		0.403	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96798893	G	T	96798893	4	4	61	1	0	0	0	0	0	1	0	0	1095	1294	45	2	5065	2	ATG2B	14	96798893	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37461	96798893	10550647	9118	17103										
C14orf129	51527	broad.mit.edu	37	chr14	96851890	96851890	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcttttgaccaggtagatGatcatttacagactccctac	7	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96851890G>T	ENST00000556095.1	+	4	2101	c.289G>T	c.(289-291)Gat>Tat	p.D97Y	GSKIP_ENST00000438650.1_Missense_Mutation_p.D97Y|GSKIP_ENST00000555181.1_Missense_Mutation_p.D97Y|RNU2-33P_ENST00000410344.1_RNA|GSKIP_ENST00000554182.1_Missense_Mutation_p.D97Y	NM_001271904.1	NP_001258833.1	Q9P0R6	GSKIP_HUMAN	GSK3B interacting protein	97						cytoplasm (GO:0005737)		p.D97Y(1)									CCAGGTAGATGATCATTTACA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											167	148	155					14																	96851890		2203	4300	6503	95921643	SO:0001583	missense	51527			AF151044	CCDS32153.1	14q32.2	2012-09-25	2012-09-25	2012-09-25	ENSG00000100744	ENSG00000100744			20343	protein-coding gene	gene with protein product	"GSK3beta interaction protein"		"chromosome 14 open reading frame 129"	C14orf129		16981698, 21328310	Standard	NM_001271904		Approved		uc031qqf.1	Q9P0R6	OTTHUMG00000171420	ENST00000556095.1:c.289G>T	14.37:g.96851890G>T	ENSP00000451188:p.Asp97Tyr		95921643	B3KSZ0|Q9BST1|Q9NWK0	Missense_Mutation	SNP	ENST00000556095.1	37	CCDS32153.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.235797	0.79800	.	.	ENSG00000100744	ENST00000555181;ENST00000554182;ENST00000556095;ENST00000438650;ENST00000555757	.	.	.	5.54	5.54	0.83059	GSKIP/TIF31 domain (1);	0.202488	0.51477	D	0.000098	T	0.75064	0.3799	L	0.55481	1.735	0.80722	D	1	P	0.42161	0.772	P	0.57425	0.82	T	0.75068	-0.3448	9	0.62326	D	0.03	-26.039	19.4733	0.94973	0.0:0.0:1.0:0.0	.	97	Q9P0R6	GSKIP_HUMAN	Y	97	.	ENSP00000412315:D97Y	D	+	1	0	C14orf129	95921643	1.000000	0.71417	0.189000	0.23252	0.973000	0.67179	6.362000	0.73077	2.609000	0.88269	0.655000	0.94253	GAT		0.423	GSKIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413338.1	NM_016472		T	96851890	G	T	96851890	3	4	61	1	0	0	0	0	1	0	0	0	1748	1290	45	2	295	2	C14orf129	14	96851890	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52997	96851890	10497650	9119	17104										
PAPOLA	10914	broad.mit.edu	37	chr14	96986482	96986482	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttagcagcccccaaggaGactgactgcgtacttacaca	9	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:96986482G>T	ENST00000216277.8	+	2	319	c.99G>T	c.(97-99)gaG>gaT	p.E33D	PAPOLA_ENST00000554130.1_3'UTR|PAPOLA_ENST00000557320.1_Missense_Mutation_p.E33D|PAPOLA_ENST00000557471.1_Missense_Mutation_p.E33D|PAPOLA_ENST00000392990.2_Missense_Mutation_p.E33D	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	33					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.E33D(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		CCCCCAAGGAGACTGACTGCG	0.433																																					NSCLC(19;254 734 11908 35501 39234)											1	Substitution - Missense(1)	large_intestine(1)	14											130	113	119					14																	96986482		2203	4300	6503	96056235	SO:0001583	missense	10914			X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.99G>T	14.37:g.96986482G>T	ENSP00000216277:p.Glu33Asp		96056235	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Missense_Mutation	SNP	ENST00000216277.8	37	CCDS9946.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278791	0.40294	.	.	ENSG00000090060	ENST00000216277;ENST00000557320;ENST00000546064;ENST00000557471;ENST00000556619;ENST00000392990	.	.	.	4.94	4.94	0.65067	Poly(A) polymerase, central domain (1);	0.175194	0.49305	N	0.000160	T	0.51007	0.1649	L	0.35854	1.095	0.45056	D	0.998078	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.002;0.004;0.004;0.001;0.003	T	0.44221	-0.9342	9	0.27082	T	0.32	.	13.5008	0.61454	0.0:0.0:0.8438:0.1562	.	49;49;33;33;49	F5H5I8;B4DYF4;P51003;P51003-2;B4DHB8	.;.;PAPOA_HUMAN;.;.	D	33;33;49;33;33;33	.	ENSP00000216277:E33D	E	+	3	2	PAPOLA	96056235	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.612000	0.46343	2.455000	0.83008	0.650000	0.86243	GAG		0.433	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			T	96986482	G	T	96986482	3	4	61	1	0	0	0	0	1	0	0	0	11460	933	33	2	105	2	PAPOLA	14	96986482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134592	96986482	10363058	9120	17105										
VRK1	7443	broad.mit.edu	37	chr14	97322574	97322574	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatcctaaatatgttagaGattccaaaattaggtaaagg	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:97322574G>T	ENST00000216639.3	+	9	966	c.817G>T	c.(817-819)Gat>Tat	p.D273Y		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	273	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D273Y(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		ATATGTTAGAGATTCCAAAAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	14											85	86	86					14																	97322574		2203	4300	6503	96392327	SO:0001583	missense	7443			AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.817G>T	14.37:g.97322574G>T	ENSP00000216639:p.Asp273Tyr		96392327	Q3SYL2	Missense_Mutation	SNP	ENST00000216639.3	37	CCDS9947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.1|20.1	3.936206|3.936206	0.73442|0.73442	.|.	.|.	ENSG00000100749|ENSG00000100749	ENST00000216639|ENST00000557222;ENST00000557352	T|T;T	0.63913|0.66280	-0.07|-0.2;2.1	5.96|5.96	5.07|5.07	0.68467|0.68467	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.090395|.	0.85682|.	D|.	0.000000|.	T|T	0.55752|0.55752	0.1940|0.1940	L|L	0.31476|0.31476	0.935|0.935	0.80722|0.80722	D|D	1|1	D|.	0.54397|.	0.966|.	P|.	0.50934|.	0.654|.	T|T	0.52741|0.52741	-0.8535|-0.8535	10|6	0.25106|.	T|.	0.35|.	-12.8922|-12.8922	10.7606|10.7606	0.46261|0.46261	0.0682:0.132:0.7998:0.0|0.0682:0.132:0.7998:0.0	.|.	273|.	Q99986|.	VRK1_HUMAN|.	Y|I	273|129;54	ENSP00000216639:D273Y|ENSP00000450820:R129I;ENSP00000451682:R54I	ENSP00000216639:D273Y|.	D|R	+|+	1|2	0|0	VRK1|VRK1	96392327|96392327	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	4.887000|4.887000	0.63156|0.63156	1.492000|1.492000	0.48499|0.48499	0.655000|0.655000	0.94253|0.94253	GAT|AGA		0.328	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384		T	97322574	G	T	97322574	3	4	61	1	0	0	0	0	1	0	0	0	17259	942	33	2	847	2	VRK1	14	97322574	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336092	97322574	10026966	9121	17106										
SETD3	84193	broad.mit.edu	37	chr14	99927567	99927567	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcaaaccaaagccctcttCtttgaagttaaccatttcaa	3	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:99927567C>A	ENST00000331768.5	-	4	466	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	SETD3_ENST00000453938.1_Intron|SETD3_ENST00000329331.3_Nonsense_Mutation_p.E103*|SETD3_ENST00000436070.2_Nonsense_Mutation_p.E103*	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	103	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)	p.E103*(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				AAGCCCTCTTCTTTGAAGTTA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											119	121	120					14																	99927567		2203	4300	6503	98997320	SO:0001587	stop_gained	84193			AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.307G>T	14.37:g.99927567C>A	ENSP00000327436:p.Glu103*		98997320	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Nonsense_Mutation	SNP	ENST00000331768.5	37	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	C	37	6.341539	0.97489	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	.	.	.	5.45	5.45	0.79879	.	0.110848	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-14.1669	19.6632	0.95882	0.0:1.0:0.0:0.0	.	.	.	.	X	103	.	ENSP00000327910:E103X	E	-	1	0	SETD3	98997320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.671000	0.61590	2.716000	0.92895	0.655000	0.94253	GAA		0.398	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		A	99927567	C	A	99927567	4	1	61	1	0	0	0	0	0	1	0	0	14169	922	32	2	1563	2	SETD3	14	99927567	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2604993	99927567	7421973	9122	17107										
EML1	2009	broad.mit.edu	37	chr14	100331887	100331887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctgcctttaagaaccaCggtcaacaatggcactgtgt	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100331887C>T	ENST00000262233.6	+	3	426	c.287C>T	c.(286-288)aCg>aTg	p.T96M	EML1_ENST00000327921.9_Missense_Mutation_p.T65M|EML1_ENST00000334192.4_Missense_Mutation_p.T96M|EML1_ENST00000556758.1_3'UTR	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	96					brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.T96M(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				TTAAGAACCACGGTCAACAAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											98	89	92					14																	100331887		2203	4300	6503	99401640	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.287C>T	14.37:g.100331887C>T	ENSP00000262233:p.Thr96Met		99401640	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799547	0.90538	.	.	ENSG00000066629	ENST00000554479;ENST00000555145;ENST00000327921;ENST00000556199;ENST00000556835;ENST00000262233;ENST00000334192;ENST00000542138;ENST00000556714;ENST00000553720;ENST00000556947	T;T;T;T;T	0.33438	2.81;1.69;1.65;1.68;1.41	5.31	5.31	0.75309	.	0.051703	0.85682	D	0.000000	T	0.47507	0.1449	L	0.47716	1.5	0.58432	D	0.999999	D;D;P;D;D	0.89917	0.996;0.994;0.646;1.0;1.0	P;P;B;P;P	0.60415	0.863;0.733;0.186;0.874;0.81	T	0.41875	-0.9484	10	0.56958	D	0.05	-11.9135	18.9668	0.92700	0.0:1.0:0.0:0.0	.	65;65;96;96;96	F8W717;B7Z650;O00423;O00423-3;B3KXA3	.;.;EMAL1_HUMAN;.;.	M	83;83;65;65;65;96;96;96;65;77;102	ENSP00000451346:T83M;ENSP00000327384:T65M;ENSP00000262233:T96M;ENSP00000334314:T96M;ENSP00000452089:T65M	ENSP00000262233:T96M	T	+	2	0	EML1	99401640	1.000000	0.71417	0.976000	0.42696	0.982000	0.71751	7.027000	0.76463	2.482000	0.83794	0.591000	0.81541	ACG		0.468	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		T	100331887	C	T	100331887	3	4	61	1	0	0	0	0	1	0	0	0	5109	536	19	1	297	1	EML1	14	100331887	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	404320	100331887	7017653	9123	17108										
EML1	2009	broad.mit.edu	37	chr14	100363623	100363623	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgctggccacaacgatgaCgtgaagtggtaagtcctgaa	12	9	0	3	rs200809929		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100363623C>T	ENST00000262233.6	+	7	958	c.819C>T	c.(817-819)gaC>gaT	p.D273D	EML1_ENST00000327921.9_Silent_p.D261D|EML1_ENST00000334192.4_Silent_p.D292D	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	273	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.D292D(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				ACAACGATGACGTGAAGTGGT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	14						C	,	0,4406		0,0,2203	122	94	103		876,819	2.1	1	14		103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	EML1	NM_001008707.1,NM_004434.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	292/835,273/816	100363623	1,13005	2203	4300	6503	99433376	SO:0001819	synonymous_variant	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.819C>T	14.37:g.100363623C>T			99433376	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	37	CCDS32155.1																																																																																				0.552	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		T	100363623	C	T	100363623	2	4	61	1	0	0	0	0	0	0	0	1	5109	535	19	1		1	EML1	14	100363623	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31736	100363623	6985917	9124	17109										
EML1	2009	broad.mit.edu	37	chr14	100375814	100375814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagaagcaaggattattcGaggtaaagttaaattatgat	9	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100375814G>A	ENST00000262233.6	+	11	1376	c.1237G>A	c.(1237-1239)Gag>Aag	p.E413K	EML1_ENST00000327921.9_Missense_Mutation_p.E401K|EML1_ENST00000334192.4_Missense_Mutation_p.E432K	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	413	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.E432K(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGGATTATTCGAGGTAAAGTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	14											113	116	115					14																	100375814		2203	4300	6503	99445567	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1237G>A	14.37:g.100375814G>A	ENSP00000262233:p.Glu413Lys		99445567	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.843439|4.843439	0.91197|0.91197	.|.	.|.	ENSG00000066629|ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138|ENST00000554386	T;T;T|.	0.39592|.	1.07;1.07;1.07|.	5.18|5.18	5.18|5.18	0.71444|0.71444	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83468|0.83468	0.5261|0.5261	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	D;D;P;D;D|.	0.89917|.	1.0;1.0;0.907;1.0;1.0|.	D;D;B;D;D|.	0.85130|.	0.996;0.991;0.241;0.997;0.991|.	D|D	0.85839|0.85839	0.1396|0.1396	10|5	0.54805|.	T|.	0.06|.	-32.8693|-32.8693	18.7108|18.7108	0.91656|0.91656	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	401;401;413;432;432|.	F8W717;B7Z650;O00423;O00423-3;B3KXA3|.	.;.;EMAL1_HUMAN;.;.|.	K|Q	401;413;432;432|105	ENSP00000327384:E401K;ENSP00000262233:E413K;ENSP00000334314:E432K|.	ENSP00000262233:E413K|.	E|R	+|+	1|2	0|0	EML1|EML1	99445567|99445567	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.601000|0.601000	0.36947|0.36947	9.684000|9.684000	0.98659|0.98659	2.425000|2.425000	0.82216|0.82216	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.403	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		A	100375814	G	A	100375814	3	1	61	1	0	0	0	0	1	0	0	0	5109	1059	37	1	1340	1	EML1	14	100375814	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12191	100375814	6973726	9125	17110										
EML1	2009	broad.mit.edu	37	chr14	100376617	100376617	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtcctctgtgtgactttCtctgaaaacggtgacaccat	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100376617C>A	ENST00000262233.6	+	12	1417	c.1278C>A	c.(1276-1278)ttC>ttA	p.F426L	EML1_ENST00000327921.9_Missense_Mutation_p.F414L|EML1_ENST00000334192.4_Missense_Mutation_p.F445L	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	426	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.F445L(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GTGTGACTTTCTCTGAAAACG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	14											100	97	98					14																	100376617		2203	4300	6503	99446370	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1278C>A	14.37:g.100376617C>A	ENSP00000262233:p.Phe426Leu		99446370	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.247126|4.247126	0.80024|0.80024	.|.	.|.	ENSG00000066629|ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138|ENST00000554386	T;T;T|.	0.47869|.	0.83;0.83;0.83|.	5.24|5.24	-0.0777|-0.0777	0.13717|0.13717	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74520|0.74520	0.3727|0.3727	M|M	0.88570|0.88570	2.965|2.965	0.80722|0.80722	D|D	1|1	D;P;D;D|.	0.76494|.	0.996;0.882;0.999;0.994|.	D;P;D;D|.	0.80764|.	0.99;0.596;0.994;0.977|.	T|T	0.74009|0.74009	-0.3802|-0.3802	10|5	0.87932|.	D|.	0|.	-20.6033|-20.6033	9.1326|9.1326	0.36854|0.36854	0.0:0.329:0.0:0.671|0.0:0.329:0.0:0.671	.|.	414;426;445;445|.	F8W717;O00423;O00423-3;B3KXA3|.	.;EMAL1_HUMAN;.;.|.	L|I	414;426;445;445|119	ENSP00000327384:F414L;ENSP00000262233:F426L;ENSP00000334314:F445L|.	ENSP00000262233:F426L|.	F|L	+|+	3|1	2|0	EML1|EML1	99446370|99446370	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.993000|0.993000	0.82548|0.82548	1.396000|1.396000	0.34531|0.34531	0.003000|0.003000	0.14656|0.14656	-0.302000|-0.302000	0.09304|0.09304	TTC|CTC		0.328	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		A	100376617	C	A	100376617	3	1	61	1	0	0	0	0	1	0	0	0	5109	912	32	2	1385	2	EML1	14	100376617	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	803	100376617	6972923	9126	17111										
YY1	7528	broad.mit.edu	37	chr14	100742864	100742864	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggataactcggccatgaGaaaacatctgcacacccacg	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100742864G>T	ENST00000262238.4	+	4	1201	c.941G>T	c.(940-942)aGa>aTa	p.R314I		NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	314	Binding to DNA.|Involved in nuclear matrix association.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R314I(1)		cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				TCGGCCATGAGAAAACATCTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											92	87	88					14																	100742864		2203	4300	6503	99812617	SO:0001583	missense	7528			BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"INO80 complex subunits", "Zinc fingers, C2H2-type"	12856	protein-coding gene	gene with protein product	"INO80 complex subunit S", "Yin and Yang 1 protein"	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.941G>T	14.37:g.100742864G>T	ENSP00000262238:p.Arg314Ile		99812617	Q14935	Missense_Mutation	SNP	ENST00000262238.4	37	CCDS9957.1	.	.	.	.	.	.	.	.	.	.	G	34	5.395858	0.96009	.	.	ENSG00000100811	ENST00000262238	T	0.12672	2.66	5.63	5.63	0.86233	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.31857	0.0810	L	0.39514	1.22	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00405	-1.1760	10	0.46703	T	0.11	.	20.0344	0.97551	0.0:0.0:1.0:0.0	.	314	P25490	TYY1_HUMAN	I	314	ENSP00000262238:R314I	ENSP00000262238:R314I	R	+	2	0	YY1	99812617	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.717000	0.98755	2.803000	0.96430	0.650000	0.86243	AGA		0.438	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		T	100742864	G	T	100742864	3	4	61	1	0	0	0	0	1	0	0	0	17547	942	33	2	955	2	YY1	14	100742864	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	366247	100742864	6606676	9127	17112										
WDR25	79446	broad.mit.edu	37	chr14	100847678	100847678	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctttaagcaagtaaaactCtccaggaactttcccaagtc	6	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:100847678C>A	ENST00000335290.6	+	2	643	c.417C>A	c.(415-417)ctC>ctA	p.L139L	WDR25_ENST00000402312.3_Silent_p.L139L|WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000554175.1_Silent_p.L139L|WDR25_ENST00000554998.1_Silent_p.L139L	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	139								p.L139L(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				AAGTAAAACTCTCCAGGAACT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	14											67	74	72					14																	100847678		2203	4300	6503	99917431	SO:0001819	synonymous_variant	79446			BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"WD repeat domain containing"	21064	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 67"	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.417C>A	14.37:g.100847678C>A			99917431	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																				0.483	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		A	100847678	C	A	100847678	2	1	61	1	0	0	0	0	0	0	0	1	17322	900	32	2		2	WDR25	14	100847678	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104814	100847678	6501862	9128	17113										
DIO3	1735	broad.mit.edu	37	chr14	102028404	102028404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactaagtaccagcgcgacGtcgacttcctcatcatctac	6	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102028404G>A	ENST00000510508.4	+	1	717	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	DIO3_ENST00000359323.3_Missense_Mutation_p.V165I|DIO3OS_ENST00000408206.1_lincRNA			P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	191					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|positive regulation of multicellular organism growth (GO:0040018)|small molecule metabolic process (GO:0044281)|thyroid hormone catabolic process (GO:0042404)|thyroid hormone generation (GO:0006590)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thyroxine 5'-deiodinase activity (GO:0004800)|thyroxine 5-deiodinase activity (GO:0033798)	p.V165I(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)|skin(1)	22		all_neural(303;0.185)				CCAGCGCGACGTCGACTTCCT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	14											51	57	55					14																	102028404		2102	4202	6304	101098157	SO:0001583	missense	1735			S79854	CCDS41992.1, CCDS41992.2	14q32	2012-10-08			ENSG00000197406	ENSG00000197406			2885	protein-coding gene	gene with protein product		601038		TXDI3		9787088, 7593630	Standard	NM_001362		Approved		uc021sdx.1	P55073	OTTHUMG00000160681	ENST00000510508.4:c.571G>A	14.37:g.102028404G>A	ENSP00000427336:p.Val191Ile		101098157	G3XAM0|Q8WVN5	Missense_Mutation	SNP	ENST00000510508.4	37	CCDS41992.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243441	0.79912	.	.	ENSG00000197406;ENSG00000258865	ENST00000359323;ENST00000510508	T;T	0.49139	0.79;0.79	3.51	3.51	0.40186	Thioredoxin-like fold (1);	0.093065	0.40222	U	0.001146	T	0.36193	0.0958	N	0.19112	0.55	0.80722	D	1	D	0.59767	0.986	P	0.48114	0.567	T	0.25745	-1.0123	10	0.72032	D	0.01	.	8.2607	0.31783	0.1105:0.0:0.8895:0.0	.	165	P55073	IOD3_HUMAN	I	165;191	ENSP00000352273:V165I;ENSP00000427336:V191I	ENSP00000352273:V191I	V	+	1	0	DIO3;AL049836.1	101098157	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	7.685000	0.84117	1.799000	0.52666	0.462000	0.41574	GTC		0.622	DIO3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000361712.4	NM_001362		A	102028404	G	A	102028404	3	1	61	1	0	0	0	0	1	0	0	0	4537	1145	40	1	573	1	DIO3	14	102028404	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1180726	102028404	5321136	9129	17114										
PPP2R5C	5527	broad.mit.edu	37	chr14	102359423	102359423	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctttgcacaaagtgaaatCtctgagtgtctaccatcccc	6	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102359423C>A	ENST00000334743.5	+	7	824	c.776C>A	c.(775-777)tCt>tAt	p.S259Y	PPP2R5C_ENST00000557095.1_Missense_Mutation_p.S259Y|PPP2R5C_ENST00000328724.5_Missense_Mutation_p.S314Y|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.S290Y|PPP2R5C_ENST00000445439.3_Missense_Mutation_p.S259Y|PPP2R5C_ENST00000350249.3_Missense_Mutation_p.S259Y	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	259					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.S259Y(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AAAGTGAAATCTCTGAGTGTC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	14											86	79	82					14																	102359423		2203	4300	6503	101429176	SO:0001583	missense	5527			L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.776C>A	14.37:g.102359423C>A	ENSP00000333905:p.Ser259Tyr		101429176	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	37	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	34	5.296661	0.95574	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334756;ENST00000445439;ENST00000334743;ENST00000557095;ENST00000557716	T;T;T;T;T	0.51574	0.71;0.71;0.7;0.76;0.7	5.48	5.48	0.80851	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76835	0.4043	M	0.91510	3.215	0.80722	D	1	D;P;D;D;D;D	0.89917	0.998;0.936;1.0;1.0;0.962;1.0	P;B;D;D;P;D	0.85130	0.865;0.439;0.992;0.995;0.785;0.997	T	0.82039	-0.0655	10	0.72032	D	0.01	-18.1777	19.3508	0.94384	0.0:1.0:0.0:0.0	.	290;157;259;259;259;314	F5GWP3;E9PHN5;Q13362-3;Q13362;Q13362-2;Q6ZN33	.;.;.;2A5G_HUMAN;.;.	Y	290;314;288;259;157;259;259;259;55	ENSP00000412324:S290Y;ENSP00000329009:S314Y;ENSP00000450931:S288Y;ENSP00000262239:S259Y;ENSP00000333905:S259Y	ENSP00000329009:S314Y	S	+	2	0	PPP2R5C	101429176	1.000000	0.71417	0.965000	0.40720	0.992000	0.81027	7.776000	0.85560	2.567000	0.86603	0.591000	0.81541	TCT		0.413	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		A	102359423	C	A	102359423	3	1	61	1	0	0	0	0	1	0	0	0	12428	913	32	2	1171	2	PPP2R5C	14	102359423	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	331019	102359423	4990117	9130	17115										
DYNC1H1	1778	broad.mit.edu	37	chr14	102452477	102452477	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtaagatgagtcacgttCgtgacttgccccctgtgtca	10	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102452477C>T	ENST00000360184.4	+	8	2079	c.1915C>T	c.(1915-1917)Cgt>Tgt	p.R639C		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	639	Interaction with DYNC1I2. {ECO:0000250}.|Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.R639C(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGTCACGTTCGTGACTTGCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	14											73	62	66					14																	102452477		2203	4300	6503	101522230	SO:0001583	missense	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.1915C>T	14.37:g.102452477C>T	ENSP00000348965:p.Arg639Cys		101522230	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.331575	0.81690	.	.	ENSG00000197102	ENST00000360184	T	0.60040	0.22	5.85	5.85	0.93711	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	D	0.82559	0.5063	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.85939	0.1457	10	0.87932	D	0	.	20.155	0.98106	0.0:1.0:0.0:0.0	.	639	Q14204	DYHC1_HUMAN	C	639	ENSP00000348965:R639C	ENSP00000348965:R639C	R	+	1	0	DYNC1H1	101522230	1.000000	0.71417	0.798000	0.32154	0.702000	0.40608	7.484000	0.81180	2.760000	0.94817	0.655000	0.94253	CGT		0.537	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102452477	C	T	102452477	3	4	61	1	0	0	0	0	1	0	0	0	4852	884	31	1	1945	1	DYNC1H1	14	102452477	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93054	102452477	4897063	9131	17116										
DYNC1H1	1778	broad.mit.edu	37	chr14	102470912	102470912	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggaaacagcaagaatgtCgctaaattacagaaacactt	7	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102470912C>T	ENST00000360184.4	+	24	5105	c.4941C>T	c.(4939-4941)gtC>gtT	p.V1647V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1647	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.V1647V(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCAAGAATGTCGCTAAATTAC	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	14											92	87	89					14																	102470912		2203	4300	6503	101540665	SO:0001819	synonymous_variant	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.4941C>T	14.37:g.102470912C>T			101540665	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																				0.348	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102470912	C	T	102470912	2	4	61	1	0	0	0	0	0	0	0	1	4852	871	31	1		1	DYNC1H1	14	102470912	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18435	102470912	4878628	9132	17117										
DYNC1H1	1778	broad.mit.edu	37	chr14	102493853	102493853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattctggattcctggagcGaatgaatacccttctggcca	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102493853G>A	ENST00000360184.4	+	46	9184	c.9020G>A	c.(9019-9021)cGa>cAa	p.R3007Q		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3007	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.R3007Q(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TTCCTGGAGCGAATGAATACC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	14											126	118	121					14																	102493853		2203	4300	6503	101563606	SO:0001583	missense	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.9020G>A	14.37:g.102493853G>A	ENSP00000348965:p.Arg3007Gln		101563606	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	36	5.839281	0.97009	.	.	ENSG00000197102	ENST00000360184	T	0.41758	0.99	5.81	5.81	0.92471	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.73171	0.3553	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74213	-0.3738	10	0.31617	T	0.26	.	20.0707	0.97721	0.0:0.0:1.0:0.0	.	3007	Q14204	DYHC1_HUMAN	Q	3007	ENSP00000348965:R3007Q	ENSP00000348965:R3007Q	R	+	2	0	DYNC1H1	101563606	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.514000	0.98013	2.746000	0.94184	0.609000	0.83330	CGA		0.443	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102493853	G	A	102493853	3	1	61	1	0	0	0	0	1	0	0	0	4852	1058	37	1	9202	1	DYNC1H1	14	102493853	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22941	102493853	4855687	9133	17118										
HSP90AA1	3320	broad.mit.edu	37	chr14	102551263	102551263	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgactctttctcttctttttCtttttcttcttctttgtctt	2	11	8	0	rs3208445|rs557944512		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102551263C>A	ENST00000216281.8	-	5	941	c.736G>T	c.(736-738)Gaa>Taa	p.E246*	HSP90AA1_ENST00000441629.2_Nonsense_Mutation_p.E67*|HSP90AA1_ENST00000334701.7_Nonsense_Mutation_p.E368*	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	246					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.E368*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	tcttctttttctttttcttct	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											54	51	52					14																	102551263		2203	4300	6503	101621016	SO:0001587	stop_gained	3320			M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.736G>T	14.37:g.102551263C>A	ENSP00000216281:p.Glu246*		101621016	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Nonsense_Mutation	SNP	ENST00000216281.8	37	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	c	21.5	4.157654	0.78114	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	.	.	.	4.37	3.46	0.39613	.	0.373083	0.23187	U	0.050957	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-14.214	8.3772	0.32451	0.0:0.8186:0.0:0.1814	.	.	.	.	X	246;368;67	.	ENSP00000216281:E246X	E	-	1	0	HSP90AA1	101621016	1.000000	0.71417	0.630000	0.29268	0.849000	0.48306	5.824000	0.69279	2.152000	0.67230	0.591000	0.81541	GAA		0.373	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		A	102551263	C	A	102551263	4	1	61	1	0	0	0	0	0	1	0	0	7422	922	32	2	1490	2	HSP90AA1	14	102551263	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57410	102551263	4798277	9134	17119										
TECPR2	9895	broad.mit.edu	37	chr14	102900625	102900625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaatcgacaccctgctccGaatttcctggggacagtccc	10	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:102900625G>A	ENST00000359520.7	+	9	1697	c.1471G>A	c.(1471-1473)Gaa>Aaa	p.E491K	TECPR2_ENST00000558678.1_Missense_Mutation_p.E491K	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	491					autophagy (GO:0006914)|cell death (GO:0008219)			p.E491K(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						ACCCTGCTCCGAATTTCCTGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	14											54	52	53					14																	102900625		2203	4300	6503	101970378	SO:0001583	missense	9895			AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.1471G>A	14.37:g.102900625G>A	ENSP00000352510:p.Glu491Lys		101970378	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.621037	0.66787	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.17528	2.27	5.81	4.92	0.64577	.	0.361005	0.29260	N	0.012670	T	0.34164	0.0888	L	0.56769	1.78	0.31776	N	0.63154	D;D	0.76494	0.999;0.999	P;P	0.61533	0.89;0.89	T	0.44574	-0.9319	10	0.66056	D	0.02	.	13.12	0.59321	0.0736:0.0:0.9264:0.0	.	491;491	A5PKY3;O15040	.;TCPR2_HUMAN	K	491	ENSP00000352510:E491K	ENSP00000352510:E491K	E	+	1	0	TECPR2	101970378	1.000000	0.71417	0.233000	0.24025	0.345000	0.29048	4.808000	0.62583	1.467000	0.48044	0.650000	0.86243	GAA		0.498	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		A	102900625	G	A	102900625	3	1	61	1	0	0	0	0	1	0	0	0	15783	1059	37	1	1501	1	TECPR2	14	102900625	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	349362	102900625	4448915	9135	17120										
RCOR1	23186	broad.mit.edu	37	chr14	103188610	103188610	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtgaaaaacttttttgtaAattatcgacgccgcttcaac	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:103188610A>C	ENST00000570597.1	+	11	1267	c.1267A>C	c.(1267-1269)Aat>Cat	p.N423H	RCOR1_ENST00000262241.6_Missense_Mutation_p.N426H			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	423	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)	p.N423H(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CTTTTTTGTAAATTATCGACG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	14											93	98	97					14																	103188610		2203	4300	6503	102258363	SO:0001583	missense	23186			AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"REST corepressor"	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.1267A>C	14.37:g.103188610A>C	ENSP00000459789:p.Asn423His		102258363	Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	37		.	.	.	.	.	.	.	.	.	.	A	28.2	4.902556	0.92035	.	.	ENSG00000089902	ENST00000262241	.	.	.	5.74	5.74	0.90152	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.79741	0.4498	M	0.81802	2.56	0.80722	D	1	D	0.71674	0.998	D	0.71656	0.974	T	0.81577	-0.0869	9	0.52906	T	0.07	-33.5799	16.0499	0.80749	1.0:0.0:0.0:0.0	.	423	Q9UKL0	RCOR1_HUMAN	H	423	.	ENSP00000262241:N423H	N	+	1	0	RCOR1	102258363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.193000	0.70182	0.533000	0.62120	AAT		0.418	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		C	103188610	A	C	103188610	3	2	61	1	0	0	0	0	1	0	0	0	13219	14	1	4	1309	4	RCOR1	14	103188610	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	287985	103188610	4160930	9136	17121										
CDC42BPB	9578	broad.mit.edu	37	chr14	103436580	103436580	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggcctcagcaacagcatCatcaagctgagcttccagct	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:103436580C>A	ENST00000361246.2	-	14	2191	c.1903G>T	c.(1903-1905)Gat>Tat	p.D635Y		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)									p.D635Y(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCAACAGCATCATCAAGCTGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	14											58	49	52					14																	103436580		2203	4300	6503	102506333	SO:0001583	missense	9578			AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1903G>T	14.37:g.103436580C>A	ENSP00000355237:p.Asp635Tyr		102506333		Missense_Mutation	SNP	ENST00000361246.2	37	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957714	0.53400	.	.	ENSG00000198752	ENST00000361246	D	0.86627	-2.15	5.45	4.55	0.56014	.	0.135593	0.64402	D	0.000003	D	0.91590	0.7343	M	0.74258	2.255	0.80722	D	1	B	0.33583	0.418	P	0.49561	0.615	D	0.91712	0.5382	10	0.66056	D	0.02	.	15.5282	0.75928	0.1393:0.8607:0.0:0.0	.	635	Q9Y5S2	MRCKB_HUMAN	Y	635	ENSP00000355237:D635Y	ENSP00000355237:D635Y	D	-	1	0	CDC42BPB	102506333	1.000000	0.71417	0.023000	0.16930	0.232000	0.25224	7.610000	0.82949	1.261000	0.44149	0.655000	0.94253	GAT		0.527	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		A	103436580	C	A	103436580	3	1	61	1	0	0	0	0	1	0	0	0	3079	826	29	2	3328	2	CDC42BPB	14	103436580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	247970	103436580	3912960	9137	17122										
CDC42BPB	9578	broad.mit.edu	37	chr14	103438344	103438344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctcctcctccttgtctCgcagctgccgggacaccttc	7	19	2	0	rs369423884		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:103438344C>T	ENST00000361246.2	-	13	2084	c.1796G>A	c.(1795-1797)cGa>cAa	p.R599Q		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)									p.R599Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CTCCTTGTCTCGCAGCTGCCG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	GLN/ARG	0,4406		0,0,2203	125	101	109		1796	5.4	1	14		109	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDC42BPB	NM_006035.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	599/1712	103438344	1,13005	2203	4300	6503	102508097	SO:0001583	missense	9578			AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1796G>A	14.37:g.103438344C>T	ENSP00000355237:p.Arg599Gln		102508097		Missense_Mutation	SNP	ENST00000361246.2	37	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	C	36	5.919444	0.97105	0.0	1.16E-4	ENSG00000198752	ENST00000361246	D	0.82803	-1.65	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.85221	0.5647	M	0.83953	2.67	0.80722	D	1	P	0.39480	0.675	B	0.36608	0.229	D	0.87505	0.2436	10	0.66056	D	0.02	.	19.2513	0.93926	0.0:1.0:0.0:0.0	.	599	Q9Y5S2	MRCKB_HUMAN	Q	599	ENSP00000355237:R599Q	ENSP00000355237:R599Q	R	-	2	0	CDC42BPB	102508097	1.000000	0.71417	0.951000	0.38953	0.987000	0.75469	7.755000	0.85180	2.562000	0.86427	0.655000	0.94253	CGA		0.622	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103438344	C	T	103438344	3	4	61	1	0	0	0	0	1	0	0	0	3079	884	31	1	3439	1	CDC42BPB	14	103438344	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1764	103438344	3911196	9138	17123										
MARK3	4140	broad.mit.edu	37	chr14	103969545	103969545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatattgcttccaaaattgCcaatgagctaaagctgtaac	6	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:103969545C>T	ENST00000429436.2	+	18	2753	c.2243C>T	c.(2242-2244)gCc>gTc	p.A748V	MARK3_ENST00000553942.1_Missense_Mutation_p.A739V|MARK3_ENST00000440884.3_Missense_Mutation_p.A654V|MARK3_ENST00000216288.7_Missense_Mutation_p.A708V|MARK3_ENST00000335102.5_Missense_Mutation_p.A771V|MARK3_ENST00000303622.9_Missense_Mutation_p.A724V|MARK3_ENST00000416682.2_Missense_Mutation_p.A747V	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	748	KA1. {ECO:0000255|PROSITE- ProRule:PRU00565}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A708V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			TCCAAAATTGCCAATGAGCTA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	14											56	56	56					14																	103969545		1934	4163	6097	103039298	SO:0001583	missense	4140			M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.2243C>T	14.37:g.103969545C>T	ENSP00000411397:p.Ala748Val		103039298	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.0|24.0	4.483051|4.483051	0.84747|0.84747	.|.	.|.	ENSG00000075413|ENSG00000075413	ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942;ENST00000556744|ENST00000554627	T;T;T;T;T;T;T;T|.	0.42513|.	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Kinase-associated KA1 (4);|.	0.046763|.	0.85682|.	D|.	0.000000|.	T|T	0.51856|0.51856	0.1699|0.1699	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	D;D;D;P;D;D;D;D;D|.	0.89917|.	0.998;0.999;1.0;0.941;0.996;0.997;0.977;1.0;0.996|.	D;D;D;P;D;D;P;D;D|.	0.79108|.	0.987;0.972;0.986;0.721;0.939;0.992;0.862;0.986;0.976|.	T|T	0.42327|0.42327	-0.9458|-0.9458	10|5	0.66056|.	D|.	0.02|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	755;326;747;457;708;748;654;739;724|.	P27448-7;A2SY06;P27448-2;B4DKN1;P27448-6;P27448;Q86TT8;P27448-4;P27448-3|.	.;.;.;.;.;MARK3_HUMAN;.;.;.|.	V|S	771;440;654;747;748;724;708;739;326|500	ENSP00000335347:A771V;ENSP00000402104:A654V;ENSP00000408092:A747V;ENSP00000411397:A748V;ENSP00000303698:A724V;ENSP00000216288:A708V;ENSP00000450772:A739V;ENSP00000451623:A326V|.	ENSP00000216288:A739V|.	A|P	+|+	2|1	0|0	MARK3|MARK3	103039298|103039298	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.403000|0.403000	0.30841|0.30841	7.770000|7.770000	0.85390|0.85390	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCC|CCA		0.393	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		T	103969545	C	T	103969545	3	4	61	1	0	0	0	0	1	0	0	0	9344	739	26	3	2313	3	MARK3	14	103969545	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	531201	103969545	3379995	9139	17124										
BAG5	9529	broad.mit.edu	37	chr14	104026187	104026187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattcatcagatttcaggtCgagatagctgagaatattct	8	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:104026187C>T	ENST00000445922.2	-	2	1561	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	BAG5_ENST00000299204.4_Missense_Mutation_p.D439N|BAG5_ENST00000337322.4_Missense_Mutation_p.D480N|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	439	BAG 5. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.D439N(2)		endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GATTTCAGGTCGAGATAGCTG	0.453																																					NSCLC(171;1832 2055 18950 31566 41632)											2	Substitution - Missense(2)	large_intestine(2)	14											125	122	123					14																	104026187		2203	4300	6503	103095940	SO:0001583	missense	9529			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.1315G>A	14.37:g.104026187C>T	ENSP00000391713:p.Asp439Asn		103095940	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	37	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	C	34	5.314606	0.95655	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.96104	-3.91;-3.91;-3.91	5.87	5.87	0.94306	BAG domain (3);	0.000000	0.85682	D	0.000000	D	0.97629	0.9223	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97641	1.0148	10	0.87932	D	0	-44.4964	20.5827	0.99408	0.0:1.0:0.0:0.0	.	439;480	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	N	439;439;480	ENSP00000299204:D439N;ENSP00000391713:D439N;ENSP00000338814:D480N	ENSP00000299204:D439N	D	-	1	0	BAG5	103095940	1.000000	0.71417	0.949000	0.38748	0.992000	0.81027	7.195000	0.77798	2.941000	0.99782	0.655000	0.94253	GAC		0.453	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			T	104026187	C	T	104026187	3	4	61	1	0	0	0	0	1	0	0	0	1291	884	31	1	32	1	BAG5	14	104026187	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56642	104026187	3323353	9140	17125										
BAG5	9529	broad.mit.edu	37	chr14	104026334	104026334	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtagttcttatcggttcGatttccatcaaatgaaagaa	8	6	2	2	rs182208325		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:104026334G>A	ENST00000445922.2	-	2	1414	c.1168C>T	c.(1168-1170)Cga>Tga	p.R390*	APOPT1_ENST00000409074.2_5'Flank|BAG5_ENST00000299204.4_Nonsense_Mutation_p.R390*|BAG5_ENST00000337322.4_Nonsense_Mutation_p.R431*|RP11-894P9.2_ENST00000556332.1_RNA|APOPT1_ENST00000556253.2_5'Flank|RP11-73M18.2_ENST00000472726.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	390	BAG 5. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.R390*(1)		endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			TTATCGGTTCGATTTCCATCA	0.512																																					NSCLC(171;1832 2055 18950 31566 41632)											1	Substitution - Nonsense(1)	large_intestine(1)	14											75	80	78					14																	104026334		2203	4300	6503	103096087	SO:0001587	stop_gained	9529			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.1168C>T	14.37:g.104026334G>A	ENSP00000391713:p.Arg390*		103096087	O94950|Q86W59	Nonsense_Mutation	SNP	ENST00000445922.2	37	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	G	35	5.565638	0.96540	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	.	.	.	5.85	3.8	0.43715	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.0107	13.6318	0.62200	0.0:0.0:0.5719:0.4281	.	.	.	.	X	390;390;431	.	ENSP00000299204:R390X	R	-	1	2	BAG5	103096087	0.943000	0.32029	0.020000	0.16555	0.688000	0.40055	1.363000	0.34159	1.435000	0.47434	0.563000	0.77884	CGA		0.512	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			A	104026334	G	A	104026334	4	1	61	1	0	0	0	0	0	1	0	0	1291	1066	37	1	179	1	BAG5	14	104026334	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	147	104026334	3323206	9141	17126										
PPP1R13B	23368	broad.mit.edu	37	chr14	104204146	104204146	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggcaccactctccaccagCtgtttgcagaggtgaacgct	11	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:104204146C>A	ENST00000202556.9	-	15	3198	c.2916G>T	c.(2914-2916)caG>caT	p.Q972H	PPP1R13B_ENST00000423488.2_Intron|PPP1R13B_ENST00000555391.1_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	972					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Q972H(1)		endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TCTCCACCAGCTGTTTGCAGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											55	58	57					14																	104204146		2150	4261	6411	103273899	SO:0001583	missense	23368			AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.2916G>T	14.37:g.104204146C>A	ENSP00000202556:p.Gln972His		103273899	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	37	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.108752	0.56291	.	.	ENSG00000088808	ENST00000202556	T	0.64803	-0.12	5.14	5.14	0.70334	Src homology-3 domain (1);Ankyrin repeat-containing domain (3);	0.189555	0.46758	D	0.000266	T	0.54983	0.1892	N	0.16656	0.425	0.80722	D	1	D	0.57257	0.979	P	0.55222	0.771	T	0.56025	-0.8047	10	0.48119	T	0.1	.	7.8954	0.29704	0.1641:0.7486:0.0:0.0873	.	972	Q96KQ4	ASPP1_HUMAN	H	972	ENSP00000202556:Q972H	ENSP00000202556:Q972H	Q	-	3	2	PPP1R13B	103273899	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.854000	0.27791	2.671000	0.90904	0.655000	0.94253	CAG		0.562	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		A	104204146	C	A	104204146	3	1	61	1	0	0	0	0	1	0	0	0	12391	796	28	2	368	2	PPP1R13B	14	104204146	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177812	104204146	3145394	9142	17127										
TDRD9	122402	broad.mit.edu	37	chr14	104481165	104481165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtatatatataagcagcGattcatcctacaggtgtgct	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:104481165G>A	ENST00000409874.4	+	21	2258	c.2210G>A	c.(2209-2211)cGa>cAa	p.R737Q	RN7SL634P_ENST00000485467.2_RNA|TDRD9_ENST00000339063.5_Missense_Mutation_p.R737Q	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	737					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.R737Q(1)|p.R452Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TATAAGCAGCGATTCATCCTA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	14											137	136	136					14																	104481165		2203	4300	6503	103550918	SO:0001583	missense	122402			AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.2210G>A	14.37:g.104481165G>A	ENSP00000387303:p.Arg737Gln		103550918	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	37	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	G	14.64	2.594738	0.46318	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	T;T	0.03413	3.94;3.95	4.94	4.94	0.65067	.	0.324112	0.25148	N	0.032775	T	0.06325	0.0163	L	0.54323	1.7	0.43103	D	0.994797	D;P	0.58620	0.983;0.931	B;B	0.43838	0.433;0.201	T	0.34403	-0.9830	10	0.42905	T	0.14	.	13.9138	0.63883	0.0764:0.0:0.9235:0.0	.	737;737	Q8NDG6-2;Q8NDG6	.;TDRD9_HUMAN	Q	737	ENSP00000387303:R737Q;ENSP00000343545:R737Q	ENSP00000343545:R737Q	R	+	2	0	TDRD9	103550918	0.989000	0.36119	0.994000	0.49952	0.719000	0.41307	2.047000	0.41269	2.447000	0.82792	0.563000	0.77884	CGA		0.398	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		A	104481165	G	A	104481165	3	1	61	1	0	0	0	0	1	0	0	0	15775	1058	37	1	2292	1	TDRD9	14	104481165	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	277019	104481165	2868375	9143	17128										
AHNAK2	113146	broad.mit.edu	37	chr14	105405983	105405983	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtcaagatcacaccttaGaatatctgtggatgatttgc	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105405983G>T	ENST00000333244.5	-	7	15924	c.15805C>A	c.(15805-15807)Cta>Ata	p.L5269I	AHNAK2_ENST00000557457.1_Missense_Mutation_p.L267I	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5269				L -> P (in Ref. 5; CAD98019). {ECO:0000305}.		costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.L5269I(1)|p.L239I(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			TCACACCTTAGAATATCTGTG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	14											130	136	134					14																	105405983		2044	4193	6237	104477028	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.15805C>A	14.37:g.105405983G>T	ENSP00000353114:p.Leu5269Ile		104477028	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.555942	0.45487	.	.	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.03524	3.9;5.38	5.18	1.13	0.20643	.	0.800496	0.10040	U	0.723637	T	0.02649	0.0080	L	0.27053	0.805	0.09310	N	1	P	0.43938	0.822	B	0.37387	0.248	T	0.46582	-0.9181	10	0.35671	T	0.21	.	4.9159	0.13846	0.2628:0.3045:0.4328:0.0	.	5269	Q8IVF2	AHNK2_HUMAN	I	267;5269	ENSP00000450998:L267I;ENSP00000353114:L5269I	ENSP00000353114:L5269I	L	-	1	2	AHNAK2	104477028	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.637000	0.24659	0.010000	0.14839	-0.258000	0.10820	CTA		0.517	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105405983	G	T	105405983	3	4	61	1	0	0	0	0	1	0	0	0	415	933	33	2	1586	2	AHNAK2	14	105405983	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	924818	105405983	1943557	9144	17129										
AHNAK2	113146	broad.mit.edu	37	chr14	105407446	105407446	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagggagagagaatagaaGattcaaagtgaggaccagtg	14	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105407446G>T	ENST00000333244.5	-	7	14461	c.14342C>A	c.(14341-14343)tCt>tAt	p.S4781Y	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4781						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.S4781Y(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GAGAATAGAAGATTCAAAGTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	14											93	98	96					14																	105407446		1940	4134	6074	104478491	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14342C>A	14.37:g.105407446G>T	ENSP00000353114:p.Ser4781Tyr		104478491	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217224	0.39201	.	.	ENSG00000185567	ENST00000333244	T	0.06294	3.32	3.65	-7.3	0.01446	.	.	.	.	.	T	0.02929	0.0087	N	0.22421	0.69	0.09310	N	1	B	0.34241	0.444	B	0.31101	0.124	T	0.39683	-0.9602	9	0.46703	T	0.11	.	2.0372	0.03542	0.3345:0.3283:0.2276:0.1096	.	4781	Q8IVF2	AHNK2_HUMAN	Y	4781	ENSP00000353114:S4781Y	ENSP00000353114:S4781Y	S	-	2	0	AHNAK2	104478491	.	.	0.000000	0.03702	0.016000	0.09150	.	.	-0.863000	0.04084	0.460000	0.39030	TCT		0.498	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105407446	G	T	105407446	3	4	61	1	0	0	0	0	1	0	0	0	415	942	33	2	3049	2	AHNAK2	14	105407446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1463	105407446	1942094	9145	17130										
AHNAK2	113146	broad.mit.edu	37	chr14	105409027	105409027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacacctccacgacggggGtcatcacatccgccttgggg	13	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105409027G>A	ENST00000333244.5	-	7	12880	c.12761C>T	c.(12760-12762)aCc>aTc	p.T4254I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4254						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.T4254I(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CACGACGGGGGTCATCACATC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	14											119	131	127					14																	105409027		1917	4124	6041	104480072	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12761C>T	14.37:g.105409027G>A	ENSP00000353114:p.Thr4254Ile		104480072	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	6.278	0.419360	0.11928	.	.	ENSG00000185567	ENST00000333244	T	0.00588	6.37	3.8	-2.81	0.05805	.	0.477164	0.14587	U	0.310494	T	0.00552	0.0018	L	0.48642	1.525	0.09310	N	1	B	0.31193	0.312	B	0.36922	0.236	T	0.45542	-0.9254	10	0.38643	T	0.18	-11.9676	1.3481	0.02167	0.3241:0.1474:0.3793:0.1493	.	4254	Q8IVF2	AHNK2_HUMAN	I	4254	ENSP00000353114:T4254I	ENSP00000353114:T4254I	T	-	2	0	AHNAK2	104480072	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.775000	0.01783	-0.171000	0.10797	-0.772000	0.03388	ACC		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409027	G	A	105409027	3	1	61	1	0	0	0	0	1	0	0	0	415	1261	44	3	4630	3	AHNAK2	14	105409027	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1581	105409027	1940513	9146	17131										
AHNAK2	113146	broad.mit.edu	37	chr14	105409382	105409382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggcatcttgaacttggGcattttgaacttgctgtctt	10	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105409382G>A	ENST00000333244.5	-	7	12525	c.12406C>T	c.(12406-12408)Ccc>Tcc	p.P4136S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4136						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.P4136S(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			TTGAACTTGGGCATTTTGAAC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	14											293	304	300					14																	105409382		2011	4138	6149	104480427	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12406C>T	14.37:g.105409382G>A	ENSP00000353114:p.Pro4136Ser		104480427	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	21.6	4.169196	0.78339	.	.	ENSG00000185567	ENST00000333244	T	0.03152	4.03	4.11	4.11	0.48088	.	.	.	.	.	T	0.28300	0.0699	H	0.95437	3.67	0.33110	D	0.540379	D	0.89917	1.0	D	0.91635	0.999	T	0.58929	-0.7549	9	0.54805	T	0.06	.	16.428	0.83831	0.0:0.0:1.0:0.0	.	4136	Q8IVF2	AHNK2_HUMAN	S	4136	ENSP00000353114:P4136S	ENSP00000353114:P4136S	P	-	1	0	AHNAK2	104480427	0.878000	0.30173	1.000000	0.80357	0.786000	0.44442	1.269000	0.33074	1.865000	0.54081	0.485000	0.47835	CCC		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409382	G	A	105409382	3	1	61	1	0	0	0	0	1	0	0	0	415	1203	42	3	4985	3	AHNAK2	14	105409382	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	355	105409382	1940158	9147	17132										
AHNAK2	113146	broad.mit.edu	37	chr14	105411170	105411170	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacggggccctccaggagttCcacatccacttggacagcct	10	16	0	0	rs200970518		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105411170C>A	ENST00000333244.5	-	7	10737	c.10618G>T	c.(10618-10620)Gaa>Taa	p.E3540*	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3540						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.E3540*(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			TCCAGGAGTTCCACATCCACT	0.632																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											93	100	98					14																	105411170		1910	4119	6029	104482215	SO:0001587	stop_gained	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10618G>T	14.37:g.105411170C>A	ENSP00000353114:p.Glu3540*		104482215	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Nonsense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	51	17.542485	0.99888	.	.	ENSG00000185567	ENST00000333244	.	.	.	3.76	-3.73	0.04398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	1.5586	0.02589	0.1319:0.2672:0.1349:0.466	.	.	.	.	X	3540	.	ENSP00000353114:E3540X	E	-	1	0	AHNAK2	104482215	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.097000	0.01348	-0.268000	0.09312	-1.451000	0.01035	GAA		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105411170	C	A	105411170	4	1	61	1	0	0	0	0	0	1	0	0	415	864	30	2	6773	2	AHNAK2	14	105411170	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1788	105411170	1938370	9148	17133										
AHNAK2	113146	broad.mit.edu	37	chr14	105411838	105411838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggggcagacgccctgtacGacggcatcttgaatttgggc	14	11	1	2	rs375227548		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105411838G>A	ENST00000333244.5	-	7	10069	c.9950C>T	c.(9949-9951)tCg>tTg	p.S3317L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3317						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.S3317L(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CGCCCTGTACGACGGCATCTT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	14						G	LEU/SER	0,4020		0,0,2010	193	192	193		9950	3.2	0.1	14		193	1,8323		0,1,4161	no	missense	AHNAK2	NM_138420.2	145	0,1,6171	AA,AG,GG		0.012,0.0,0.0081	probably-damaging	3317/5796	105411838	1,12343	2010	4162	6172	104482883	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9950C>T	14.37:g.105411838G>A	ENSP00000353114:p.Ser3317Leu		104482883	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	11.31	1.601818	0.28534	0.0	1.2E-4	ENSG00000185567	ENST00000333244	T	0.01902	4.57	4.23	3.25	0.37280	.	.	.	.	.	T	0.07503	0.0189	M	0.90542	3.125	0.09310	N	1	D	0.56746	0.977	P	0.48488	0.579	T	0.21759	-1.0236	9	0.27082	T	0.32	.	8.7959	0.34878	0.0:0.2575:0.5969:0.1456	.	3317	Q8IVF2	AHNK2_HUMAN	L	3317	ENSP00000353114:S3317L	ENSP00000353114:S3317L	S	-	2	0	AHNAK2	104482883	0.002000	0.14202	0.050000	0.19076	0.061000	0.15899	0.871000	0.28023	1.929000	0.55896	0.485000	0.47835	TCG		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105411838	G	A	105411838	3	1	61	1	0	0	0	0	1	0	0	0	415	1059	37	1	7441	1	AHNAK2	14	105411838	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	668	105411838	1937702	9149	17134										
AHNAK2	113146	broad.mit.edu	37	chr14	105412944	105412944	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttgctctcggggcctcGacgtccacctccacgctggg	12	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105412944G>A	ENST00000333244.5	-	7	8963	c.8844C>T	c.(8842-8844)gtC>gtT	p.V2948V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2948						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.V2948V(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			TCGGGGCCTCGACGTCCACCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	14											150	163	159					14																	105412944		1994	4168	6162	104483989	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8844C>T	14.37:g.105412944G>A			104483989	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105412944	G	A	105412944	2	1	61	1	0	0	0	0	0	0	0	1	415	1045	37	1		1	AHNAK2	14	105412944	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1106	105412944	1936596	9150	17135										
AHNAK2	113146	broad.mit.edu	37	chr14	105418521	105418521	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccactttgggcatcttGaaactgggcatctccacctt	10	12	2	1	rs142241633	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105418521G>T	ENST00000333244.5	-	7	3386	c.3267C>A	c.(3265-3267)ttC>ttA	p.F1089L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1089						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.F1089L(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			TGGGCATCTTGAAACTGGGCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	14											128	149	143					14																	105418521		1865	4104	5969	104489566	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3267C>A	14.37:g.105418521G>T	ENSP00000353114:p.Phe1089Leu		104489566	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.212693	0.00289	.	.	ENSG00000185567	ENST00000333244	T	0.00570	6.51	3.09	-0.189	0.13260	.	.	.	.	.	T	0.00468	0.0015	L	0.33668	1.02	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49031	-0.8981	9	0.02654	T	1	.	17.0326	0.86465	0.0:0.4545:0.5455:0.0	.	1089	Q8IVF2	AHNK2_HUMAN	L	1089	ENSP00000353114:F1089L	ENSP00000353114:F1089L	F	-	3	2	AHNAK2	104489566	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.199000	0.03032	-0.803000	0.04415	-3.858000	0.00018	TTC		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105418521	G	T	105418521	3	4	61	1	0	0	0	0	1	0	0	0	415	1281	45	2	14124	2	AHNAK2	14	105418521	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5577	105418521	1931019	9151	17136										
AHNAK2	113146	broad.mit.edu	37	chr14	105420682	105420682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcctgtggcagccccaGtctcctcgaggctatcaccc	10	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105420682G>A	ENST00000333244.5	-	7	1225	c.1106C>T	c.(1105-1107)aCt>aTt	p.T369I	AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	369						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.T369I(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GGCAGCCCCAGTCTCCTCGAG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	14											56	59	58					14																	105420682		1989	4159	6148	104491727	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.1106C>T	14.37:g.105420682G>A	ENSP00000353114:p.Thr369Ile		104491727	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	10.06	1.248088	0.22880	.	.	ENSG00000185567	ENST00000333244	T	0.03496	3.91	3.69	-0.951	0.10369	.	.	.	.	.	T	0.03095	0.0091	L	0.29908	0.895	0.09310	N	1	B	0.17268	0.021	B	0.16289	0.015	T	0.42982	-0.9419	9	0.35671	T	0.21	.	8.0447	0.30542	0.0947:0.4613:0.444:0.0	.	369	Q8IVF2	AHNK2_HUMAN	I	369	ENSP00000353114:T369I	ENSP00000353114:T369I	T	-	2	0	AHNAK2	104491727	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.953000	0.03877	-0.311000	0.08754	0.650000	0.86243	ACT		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105420682	G	A	105420682	3	1	61	1	0	0	0	0	1	0	0	0	415	1029	36	3	16285	3	AHNAK2	14	105420682	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2161	105420682	1928858	9152	17137										
GPR132	29933	broad.mit.edu	37	chr14	105517709	105517709	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaccaggtggtacggggcGaagcagactaggaagatgac	16	7	0	4	rs201367136	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr14:105517709G>A	ENST00000329797.3	-	4	1676	c.765C>T	c.(763-765)ttC>ttT	p.F255F	GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Silent_p.F246F|GPR132_ENST00000539291.2_Silent_p.F255F	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	255					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F255F(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GGTACGGGGCGAAGCAGACTA	0.567													G|||	3	0.000599042	0.0015	0	5008	,	,		21734	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14						G		2,4404	4.2+/-10.8	0,2,2201	113	112	113		765	-1.3	0.2	14		113	0,8600		0,0,4300	no	coding-synonymous	GPR132	NM_013345.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		255/381	105517709	2,13004	2203	4300	6503	104588754	SO:0001819	synonymous_variant	29933			AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.765C>T	14.37:g.105517709G>A			104588754	A8K7X7|B4E144|Q9BSU2	Silent	SNP	ENST00000329797.3	37	CCDS9997.1																																																																																				0.567	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		A	105517709	G	A	105517709	2	1	61	1	0	0	0	0	0	0	0	1	6662	1049	37	1		1	GPR132	14	105517709	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97027	105517709	1831831	9153	17138										
OR4M2	390538	broad.mit.edu	37	chr15	22368669	22368669	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtcctatttgttatatttCtatccttctatttgttcatc	3	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22368669C>A	ENST00000332663.2	+	1	192	c.94C>A	c.(94-96)Cta>Ata	p.L32I	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L32I(1)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TGTTATATTTCTATCCTTCTA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											317	283	294					15																	22368669		2203	4300	6503	19870033	SO:0001583	missense	390538			AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.94C>A	15.37:g.22368669C>A	ENSP00000329467:p.Leu32Ile		19870033	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	11.75	1.732852	0.30684	.	.	ENSG00000182974	ENST00000332663	T	0.01854	4.6	2.5	-0.257	0.12979	.	0.000000	0.37095	N	0.002251	T	0.06600	0.0169	M	0.85373	2.75	0.24507	N	0.994228	P	0.51449	0.945	P	0.53102	0.718	T	0.12142	-1.0559	10	0.40728	T	0.16	-5.4749	5.7331	0.18051	0.0:0.5982:0.0:0.4018	.	32	Q8NGB6	OR4M2_HUMAN	I	32	ENSP00000329467:L32I	ENSP00000329467:L32I	L	+	1	2	OR4M2	19870033	0.000000	0.05858	0.988000	0.46212	0.548000	0.35241	-1.158000	0.03153	-0.187000	0.10516	-0.406000	0.06334	CTA		0.403	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			A	22368669	C	A	22368669	3	1	61	1	0	0	0	0	1	0	0	0	11107	912	32	2	96	2	OR4M2	15	22368669	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		22368669	80162723	9154	17139										
OR4M2	390538	broad.mit.edu	37	chr15	22369079	22369079	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattgttcgacttcctttCtgtgggcccaatgagttaga	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22369079C>T	ENST00000332663.2	+	1	602	c.504C>T	c.(502-504)ttC>ttT	p.F168F	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F168F(1)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		GACTTCCTTTCTGTGGGCCCA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	15											310	256	274					15																	22369079		2203	4300	6503	19870443	SO:0001819	synonymous_variant	390538			AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.504C>T	15.37:g.22369079C>T			19870443	B9EH16|Q6IEY2	Silent	SNP	ENST00000332663.2	37	CCDS32172.1																																																																																				0.493	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			T	22369079	C	T	22369079	2	4	61	1	0	0	0	0	0	0	0	1	11107	912	32	3		3	OR4M2	15	22369079	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	410	22369079	80162313	9155	17140										
OR4N4	283694	broad.mit.edu	37	chr15	22383287	22383287	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagctgacaagatggtttCtctctttcacacagtgatct	7	11	4	3	rs376814938		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22383287C>A	ENST00000328795.4	+	1	906	c.815C>A	c.(814-816)tCt>tAt	p.S272Y	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S272Y(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		AAGATGGTTTCTCTCTTTCAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15						C	TYR/SER	1,4377		0,1,2188	197	176	183		815	3.2	1	15		183	0,8522		0,0,4261	no	missense	OR4N4	NM_001005241.2	144	0,1,6449	AA,AC,CC		0.0,0.0228,0.0078	probably-damaging	272/317	22383287	1,12899	2189	4261	6450	19884651	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.815C>A	15.37:g.22383287C>A	ENSP00000332500:p.Ser272Tyr		19884651	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	7.985	0.752023	0.15778	2.28E-4	0.0	ENSG00000183706	ENST00000328795	T	0.00274	8.35	3.2	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.153130	0.30979	N	0.008497	T	0.01029	0.0034	H	0.96633	3.855	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.11348	-1.0591	10	0.87932	D	0	-9.0549	12.2303	0.54484	0.0:1.0:0.0:0.0	.	272	Q8N0Y3	OR4N4_HUMAN	Y	272	ENSP00000332500:S272Y	ENSP00000332500:S272Y	S	+	2	0	OR4N4	19884651	0.000000	0.05858	0.997000	0.53966	0.038000	0.13279	0.779000	0.26746	1.784000	0.52394	0.404000	0.27445	TCT		0.418	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			A	22383287	C	A	22383287	3	1	61	1	0	0	0	0	1	0	0	0	11109	913	32	2	817	2	OR4N4	15	22383287	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14208	22383287	80148105	9156	17141										
TUBGCP5	114791	broad.mit.edu	37	chr15	22849045	22849045	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagaacctaccaggctttCatgtgggccctgtacaaata	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22849045C>A	ENST00000283645.4	+	10	1222	c.1092C>A	c.(1090-1092)ttC>ttA	p.F364L	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.F364L|TUBGCP5_ENST00000559846.1_3'UTR	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	364					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.F364L(1)		breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		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;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		ACCAGGCTTTCATGTGGGCCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	77	77					15																	22849045		2203	4300	6503	20400486	SO:0001583	missense	114791			AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.1092C>A	15.37:g.22849045C>A	ENSP00000283645:p.Phe364Leu		20400486	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	37	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	.	19.37	3.815163	0.70912	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.07216	3.21;3.21	5.42	3.52	0.40303	.	0.099785	0.64402	D	0.000001	T	0.19287	0.0463	M	0.61703	1.905	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.02596	-1.1136	10	0.39692	T	0.17	-15.5123	3.8968	0.09143	0.1715:0.5571:0.0:0.2714	.	364;364	Q96RT8;E9PB12	GCP5_HUMAN;.	L	364	ENSP00000283645:F364L;ENSP00000409217:F364L	ENSP00000283645:F364L	F	+	3	2	TUBGCP5	20400486	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	2.139000	0.42149	0.762000	0.33152	-0.216000	0.12614	TTC		0.408	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		A	22849045	C	A	22849045	3	1	61	1	0	0	0	0	1	0	0	0	16809	825	29	2	1130	2	TUBGCP5	15	22849045	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	465758	22849045	79682347	9157	17142										
TUBGCP5	114791	broad.mit.edu	37	chr15	22868879	22868879	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagtttcaacatcaagtCgaggaagccaaggatttaga	11	7	2	1	rs113414194		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22868879C>T	ENST00000283645.4	+	20	2881	c.2751C>T	c.(2749-2751)gtC>gtT	p.V917V	TUBGCP5_ENST00000453949.2_Silent_p.V917V	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	917					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.V917V(1)		breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		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;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		AACATCAAGTCGAGGAAGCCA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C	,	1,4405	2.1+/-5.4	0,1,2202	110	102	105		2751,2751	-10.5	0	15	dbSNP_132	105	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TUBGCP5	NM_001102610.1,NM_052903.4	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	917/1025,917/1025	22868879	1,13005	2203	4300	6503	20420320	SO:0001819	synonymous_variant	114791			AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.2751C>T	15.37:g.22868879C>T			20420320	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	37	CCDS10008.1																																																																																				0.418	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		T	22868879	C	T	22868879	2	4	61	1	0	0	0	0	0	0	0	1	16809	871	31	1		1	TUBGCP5	15	22868879	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19834	22868879	79662513	9158	17143										
CYFIP1	23191	broad.mit.edu	37	chr15	22963848	22963848	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactggcgattggacgatttGaaagtgaagatttgacctcc	11	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:22963848G>A	ENST00000313077.7	+	21	2487	c.2362G>A	c.(2362-2364)Gaa>Aaa	p.E788K	CYFIP1_ENST00000560848.1_Missense_Mutation_p.E788K|CYFIP1_ENST00000435939.2_Missense_Mutation_p.E357K	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1									p.E788K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		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)		TGGACGATTTGAAAGTGAAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											132	123	126					15																	22963848		2203	4300	6503	20515289	SO:0001583	missense	23191			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2362G>A	15.37:g.22963848G>A	ENSP00000324549:p.Glu788Lys		20515289		Missense_Mutation	SNP	ENST00000313077.7	37	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	G	37	6.056497	0.97241	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.26518	1.73;1.73	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000001	T	0.61652	0.2364	M	0.89904	3.07	0.80722	D	1	P;D;D	0.89917	0.822;1.0;0.992	B;D;D	0.79108	0.325;0.992;0.954	T	0.68754	-0.5325	10	0.87932	D	0	-26.7633	19.9036	0.96999	0.0:0.0:1.0:0.0	.	816;357;788	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	K	788;816;357	ENSP00000324549:E788K;ENSP00000405956:E357K	ENSP00000324549:E788K	E	+	1	0	CYFIP1	20515289	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.622000	0.98378	2.706000	0.92434	0.655000	0.94253	GAA		0.438	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		A	22963848	G	A	22963848	3	1	61	1	0	0	0	0	1	0	0	0	4143	1291	45	3	2821	3	CYFIP1	15	22963848	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94969	22963848	79567544	9159	17144										
MKRN3	7681	broad.mit.edu	37	chr15	23811120	23811120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccctgtagctccagtccCtgcccacctccgcagaggag	9	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:23811120C>T	ENST00000314520.3	+	1	667	c.191C>T	c.(190-192)cCt>cTt	p.P64L	MKRN3_ENST00000568252.1_Missense_Mutation_p.P64L|MKRN3_ENST00000564592.1_Missense_Mutation_p.P64L|RP11-73C9.1_ENST00000563044.1_RNA	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	64					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P64L(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		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)		GCTCCAGTCCCTGCCCACCTC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	15											30	31	31					15																	23811120		2203	4300	6503	21362213	SO:0001583	missense	7681			U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.191C>T	15.37:g.23811120C>T	ENSP00000313881:p.Pro64Leu		21362213		Missense_Mutation	SNP	ENST00000314520.3	37	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	c	10.30	1.311632	0.23821	.	.	ENSG00000179455	ENST00000314520	T	0.33865	1.39	2.31	1.35	0.21983	.	0.754756	0.10815	U	0.631117	T	0.31888	0.0811	N	0.08118	0	0.09310	N	1	D;P	0.59357	0.985;0.601	P;B	0.61003	0.882;0.291	T	0.17440	-1.0369	10	0.56958	D	0.05	.	6.8181	0.23843	0.0:0.7064:0.2936:0.0	.	64;64	Q6NSB6;Q13064	.;MKRN3_HUMAN	L	64	ENSP00000313881:P64L	ENSP00000313881:P64L	P	+	2	0	MKRN3	21362213	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.017000	0.12590	0.509000	0.28195	-0.300000	0.09419	CCT		0.667	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		T	23811120	C	T	23811120	3	4	61	1	0	0	0	0	1	0	0	0	9638	681	24	3	193	3	MKRN3	15	23811120	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	847272	23811120	78720272	9160	17145										
NDN	4692	broad.mit.edu	37	chr15	23931681	23931681	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagcttccgcacgtccccGaaggtggagtgcttcttcca	11	13	1	1	rs149718513		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:23931681G>A	ENST00000331837.4	-	1	769	c.684C>T	c.(682-684)ttC>ttT	p.F228F		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	228	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F228F(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		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;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GCACGTCCCCGAAGGTGGAGT	0.602									Prader-Willi syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	15						G		1,4401		0,1,2200	35	34	35		684	0.8	0.6	15	dbSNP_134	35	0,8592		0,0,4296	no	coding-synonymous	NDN	NM_002487.2		0,1,6496	AA,AG,GG		0.0,0.0227,0.0077		228/322	23931681	1,12993	2201	4296	6497	21482774	SO:0001819	synonymous_variant	4692	Familial Cancer Database	Prader-Labhart-Willi syndrome	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.684C>T	15.37:g.23931681G>A			21482774	B2R6Z5	Silent	SNP	ENST00000331837.4	37	CCDS10014.1																																																																																				0.602	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		A	23931681	G	A	23931681	2	1	61	1	0	0	0	0	0	0	0	1	10278	1049	37	1		1	NDN	15	23931681	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120561	23931681	78599711	9161	17146										
NDN	4692	broad.mit.edu	37	chr15	23932017	23932017	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggaaaccagatgatcatCttcttctggtccttgaccag	8	11	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:23932017C>A	ENST00000331837.4	-	1	433	c.348G>T	c.(346-348)aaG>aaT	p.K116N		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	116	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K116N(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		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;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGATGATCATCTTCTTCTGGT	0.642									Prader-Willi syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	15											89	82	84					15																	23932017		2203	4300	6503	21483110	SO:0001583	missense	4692	Familial Cancer Database	Prader-Labhart-Willi syndrome	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.348G>T	15.37:g.23932017C>A	ENSP00000332643:p.Lys116Asn		21483110	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	37	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436299	0.43224	.	.	ENSG00000182636	ENST00000331837	T	0.06608	3.28	3.7	-1.01	0.10169	.	0.184969	0.42821	D	0.000644	T	0.15046	0.0363	M	0.73217	2.22	0.33121	D	0.541792	D	0.54397	0.966	D	0.64877	0.93	T	0.09997	-1.0649	10	0.87932	D	0	.	4.4694	0.11704	0.0:0.419:0.3477:0.2333	.	116	Q99608	NECD_HUMAN	N	116	ENSP00000332643:K116N	ENSP00000332643:K116N	K	-	3	2	NDN	21483110	0.000000	0.05858	0.240000	0.24138	0.701000	0.40568	-0.679000	0.05203	-0.325000	0.08577	-0.175000	0.13238	AAG		0.642	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		A	23932017	C	A	23932017	3	1	61	1	0	0	0	0	1	0	0	0	10278	912	32	2	621	2	NDN	15	23932017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336	23932017	78599375	9162	17147										
C15orf2	23742	broad.mit.edu	37	chr15	24921209	24921209	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcagcagccagcatcttCgtcgcccctaagaggccgtg	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:24921209C>T	ENST00000329468.2	+	1	669	c.195C>T	c.(193-195)ttC>ttT	p.F65F		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	65					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.F65F(1)									CCAGCATCTTCGTCGCCCCTA	0.721																																																1	Substitution - coding silent(1)	large_intestine(1)	15											18	22	20					15																	24921209		2193	4278	6471	22472302	SO:0001819	synonymous_variant	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.195C>T	15.37:g.24921209C>T			22472302		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.721	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921209	C	T	24921209	2	4	61	1	0	0	0	0	0	0	0	1	1788	883	31	1		1	C15orf2	15	24921209	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	989192	24921209	77610183	9163	17148										
C15orf2	23742	broad.mit.edu	37	chr15	24921850	24921850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagaagttggctgcggAagtgctgaatgaagagccac	15	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:24921850A>G	ENST00000329468.2	+	1	1310	c.836A>G	c.(835-837)gAa>gGa	p.E279G		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	279					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E279G(1)									TTGGCTGCGGAAGTGCTGAAT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											40	41	41					15																	24921850		2203	4299	6502	22472943	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.836A>G	15.37:g.24921850A>G	ENSP00000333735:p.Glu279Gly		22472943		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	11.55	1.673062	0.29693	.	.	ENSG00000185823	ENST00000329468	T	0.12465	2.68	1.78	0.529	0.17095	.	0.767664	0.10766	N	0.636588	T	0.08492	0.0211	L	0.29908	0.895	0.09310	N	1	P	0.38370	0.628	B	0.36922	0.236	T	0.30416	-0.9979	10	0.30078	T	0.28	.	3.7849	0.08695	0.6668:0.0:0.0:0.3331	.	279	Q9NZP6	CO002_HUMAN	G	279	ENSP00000333735:E279G	ENSP00000333735:E279G	E	+	2	0	C15orf2	22472943	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.021000	0.13489	0.128000	0.18479	0.358000	0.22013	GAA		0.602	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		G	24921850	A	G	24921850	3	3	61	1	0	0	0	0	1	0	0	0	1788	246	9	4	838	4	C15orf2	15	24921850	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	641	24921850	77609542	9164	17149										
C15orf2	23742	broad.mit.edu	37	chr15	24921938	24921938	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcctgatgagaagcctttCtgtattcctccaaggagcgc	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:24921938C>A	ENST00000329468.2	+	1	1398	c.924C>A	c.(922-924)ttC>ttA	p.F308L		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	308	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.F308L(1)									AGAAGCCTTTCTGTATTCCTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											51	51	51					15																	24921938		2203	4300	6503	22473031	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.924C>A	15.37:g.24921938C>A	ENSP00000333735:p.Phe308Leu		22473031		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	9.453	1.091186	0.20471	.	.	ENSG00000185823	ENST00000329468	T	0.10573	2.86	1.69	-3.37	0.04898	.	3.158670	0.01402	N	0.013658	T	0.07503	0.0189	N	0.22421	0.69	0.09310	N	1	P	0.34934	0.476	B	0.36666	0.23	T	0.15321	-1.0441	10	0.28530	T	0.3	.	3.7762	0.08661	0.3419:0.4811:0.177:0.0	.	308	Q9NZP6	CO002_HUMAN	L	308	ENSP00000333735:F308L	ENSP00000333735:F308L	F	+	3	2	C15orf2	22473031	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.657000	0.05335	-0.963000	0.03600	0.205000	0.17691	TTC		0.582	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24921938	C	A	24921938	3	1	61	1	0	0	0	0	1	0	0	0	1788	912	32	2	926	2	C15orf2	15	24921938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88	24921938	77609454	9165	17150										
C15orf2	23742	broad.mit.edu	37	chr15	24923330	24923330	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggagccacccctcaaccCaaatttggggcccctgatgg	10	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:24923330C>A	ENST00000329468.2	+	1	2790	c.2316C>A	c.(2314-2316)ccC>ccA	p.P772P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	772					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P772P(1)									CCCCTCAACCCAAATTTGGGG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	15											111	130	123					15																	24923330		2203	4300	6503	22474423	SO:0001819	synonymous_variant	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2316C>A	15.37:g.24923330C>A			22474423		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.562	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923330	C	A	24923330	2	1	61	1	0	0	0	0	0	0	0	1	1788	581	21	2		2	C15orf2	15	24923330	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1392	24923330	77608062	9166	17151										
C15orf2	23742	broad.mit.edu	37	chr15	24923760	24923760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctgacagttcttttattCtggggaatccagcaacccca	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:24923760C>A	ENST00000329468.2	+	1	3220	c.2746C>A	c.(2746-2748)Ctg>Atg	p.L916M		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	916					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L916M(1)									TTCTTTTATTCTGGGGAATCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	15											108	115	112					15																	24923760		2203	4300	6503	22474853	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2746C>A	15.37:g.24923760C>A	ENSP00000333735:p.Leu916Met		22474853		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	14.42	2.530368	0.45073	.	.	ENSG00000185823	ENST00000329468	T	0.11277	2.79	2.04	-3.7	0.04437	.	2.261340	0.02424	N	0.082851	T	0.15652	0.0377	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.17868	-1.0355	10	0.41790	T	0.15	.	4.2521	0.10700	0.0:0.4821:0.2146:0.3033	.	916	Q9NZP6	CO002_HUMAN	M	916	ENSP00000333735:L916M	ENSP00000333735:L916M	L	+	1	2	C15orf2	22474853	0.000000	0.05858	0.000000	0.03702	0.732000	0.41865	-2.866000	0.00723	-1.044000	0.03254	0.313000	0.20887	CTG		0.483	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923760	C	A	24923760	3	1	61	1	0	0	0	0	1	0	0	0	1788	912	32	2	2748	2	C15orf2	15	24923760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	430	24923760	77607632	9167	17152										
UBE3A	7337	broad.mit.edu	37	chr15	25599562	25599562	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtttcttctagtgcttgGaaatctagattctgcaaatt	8	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25599562G>T	ENST00000397954.2	-	9	2300	c.2301C>A	c.(2299-2301)ttC>ttA	p.F767L	UBE3A_ENST00000566215.1_Missense_Mutation_p.F744L|UBE3A_ENST00000232165.3_Missense_Mutation_p.F764L|UBE3A_ENST00000438097.1_Missense_Mutation_p.F744L|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.F744L			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	767					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.F767L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CTAGTGCTTGGAAATCTAGAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											149	128	135					15																	25599562		2203	4300	6503	23150655	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.2301C>A	15.37:g.25599562G>T	ENSP00000381045:p.Phe767Leu		23150655	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783402	0.70222	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.56	4.65	0.58169	HECT (4);	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	L	0.39514	1.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.976	T	0.59925	-0.7362	10	0.46703	T	0.11	.	9.247	0.37532	0.2075:0.0:0.7925:0.0	.	764;767	Q05086-3;Q05086	.;UBE3A_HUMAN	L	764;764;767;744;744	ENSP00000232165:F764L;ENSP00000381045:F767L;ENSP00000411258:F744L;ENSP00000401265:F744L	ENSP00000232165:F764L	F	-	3	2	UBE3A	23150655	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.565000	0.36386	1.352000	0.45808	0.591000	0.81541	TTC		0.358	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		T	25599562	G	T	25599562	3	4	61	1	0	0	0	0	1	0	0	0	16919	1165	41	2	338	2	UBE3A	15	25599562	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	675802	25599562	76931830	9168	17153										
UBE3A	7337	broad.mit.edu	37	chr15	25601861	25601861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagagtctcccaagtcacGaaaagttccttttttcccca	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25601861G>A	ENST00000397954.2	-	6	1944	c.1945C>T	c.(1945-1947)Cgt>Tgt	p.R649C	UBE3A_ENST00000566215.1_Missense_Mutation_p.R626C|UBE3A_ENST00000232165.3_Missense_Mutation_p.R646C|UBE3A_ENST00000438097.1_Missense_Mutation_p.R626C|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.R626C			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	649				TFR -> LFV (in Ref. 7; AAA35542). {ECO:0000305}.	androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.R649C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CCCAAGTCACGAAAAGTTCCT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	15											130	141	137					15																	25601861		2203	4300	6503	23152954	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1945C>T	15.37:g.25601861G>A	ENSP00000381045:p.Arg649Cys		23152954	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094282	0.36952	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	5.72	4.79	0.61399	HECT (4);	0.099783	0.64402	N	0.000001	T	0.51975	0.1706	L	0.42632	1.34	0.80722	D	1	D;B	0.58620	0.983;0.055	B;B	0.42653	0.394;0.009	T	0.57306	-0.7834	10	0.56958	D	0.05	.	15.0885	0.72174	0.0688:0.0:0.9312:0.0	.	646;649	Q05086-3;Q05086	.;UBE3A_HUMAN	C	646;646;649;626;626	ENSP00000232165:R646C;ENSP00000381045:R649C;ENSP00000411258:R626C;ENSP00000401265:R626C	ENSP00000232165:R646C	R	-	1	0	UBE3A	23152954	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	3.704000	0.54815	1.401000	0.46761	0.655000	0.94253	CGT		0.333	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25601861	G	A	25601861	3	1	61	1	0	0	0	0	1	0	0	0	16919	1058	37	1	706	1	UBE3A	15	25601861	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2299	25601861	76929531	9169	17154										
UBE3A	7337	broad.mit.edu	37	chr15	25615813	25615813	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgtagagaacagtgattCttcgttcactgtacatgcga	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25615813C>A	ENST00000397954.2	-	4	1516	c.1517G>T	c.(1516-1518)aGa>aTa	p.R506I	UBE3A_ENST00000566215.1_Missense_Mutation_p.R483I|UBE3A_ENST00000232165.3_Missense_Mutation_p.R503I|UBE3A_ENST00000438097.1_Missense_Mutation_p.R483I|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.R483I			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	506	Interaction with HCV core protein.				androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.R506I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		AACAGTGATTCTTCGTTCACT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											101	92	95					15																	25615813		2203	4297	6500	23166906	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1517G>T	15.37:g.25615813C>A	ENSP00000381045:p.Arg506Ile		23166906	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.375328	0.82682	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.93527	0.7934	M	0.92367	3.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.986	D	0.94734	0.7912	10	0.87932	D	0	.	19.2105	0.93753	0.0:1.0:0.0:0.0	.	503;506	Q05086-3;Q05086	.;UBE3A_HUMAN	I	503;503;506;483;483	ENSP00000232165:R503I;ENSP00000381045:R506I;ENSP00000411258:R483I;ENSP00000401265:R483I	ENSP00000232165:R503I	R	-	2	0	UBE3A	23166906	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.553000	0.86117	0.591000	0.81541	AGA		0.363	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25615813	C	A	25615813	3	1	61	1	0	0	0	0	1	0	0	0	16919	913	32	2	1142	2	UBE3A	15	25615813	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13952	25615813	76915579	9170	17155										
UBE3A	7337	broad.mit.edu	37	chr15	25615914	25615914	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcataaaagagaatttgttCtctgtttctactttgaaaaa	6	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25615914C>A	ENST00000397954.2	-	4	1415	c.1416G>T	c.(1414-1416)gaG>gaT	p.E472D	UBE3A_ENST00000566215.1_Missense_Mutation_p.E449D|UBE3A_ENST00000232165.3_Missense_Mutation_p.E469D|UBE3A_ENST00000438097.1_Missense_Mutation_p.E449D|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.E449D			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	472	Interaction with HCV core protein.				androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.E472D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		AGAATTTGTTCTCTGTTTCTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	15											40	40	40					15																	25615914		2203	4299	6502	23167007	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1416G>T	15.37:g.25615914C>A	ENSP00000381045:p.Glu472Asp		23167007	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	C	8.033	0.762109	0.15914	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.25	3.22	0.36961	.	0.000000	0.85682	D	0.000000	T	0.54822	0.1882	N	0.21097	0.63	0.51482	D	0.999923	B;B	0.16802	0.019;0.002	B;B	0.21360	0.034;0.005	T	0.33701	-0.9858	10	0.15499	T	0.54	.	6.4922	0.22121	0.0:0.4471:0.0:0.5529	.	469;472	Q05086-3;Q05086	.;UBE3A_HUMAN	D	469;469;472;449;449	ENSP00000232165:E469D;ENSP00000381045:E472D;ENSP00000411258:E449D;ENSP00000401265:E449D	ENSP00000232165:E469D	E	-	3	2	UBE3A	23167007	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	0.446000	0.21694	0.509000	0.28195	-0.373000	0.07131	GAG		0.313	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25615914	C	A	25615914	3	1	61	1	0	0	0	0	1	0	0	0	16919	912	32	2	1243	2	UBE3A	15	25615914	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101	25615914	76915478	9171	17156										
UBE3A	7337	broad.mit.edu	37	chr15	25616254	25616254	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatcattcactagatttCgactgttaaattcattgctt	4	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25616254C>T	ENST00000397954.2	-	4	1075	c.1076G>A	c.(1075-1077)cGa>cAa	p.R359Q	UBE3A_ENST00000566215.1_Missense_Mutation_p.R336Q|UBE3A_ENST00000232165.3_Missense_Mutation_p.R356Q|UBE3A_ENST00000438097.1_Missense_Mutation_p.R336Q|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.R336Q			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	359				R -> RNLVNEFNSR (in Ref. 7; AA sequence). {ECO:0000305}.	androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.R359Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CACTAGATTTCGACTGTTAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											111	107	108					15																	25616254		2203	4300	6503	23167347	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1076G>A	15.37:g.25616254C>T	ENSP00000381045:p.Arg359Gln		23167347	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.663848	0.29515	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.17691	2.26;2.26;2.27;2.27	5.73	5.73	0.89815	.	0.120739	0.56097	D	0.000031	T	0.11281	0.0275	N	0.22421	0.69	0.58432	D	0.999995	P;B	0.46020	0.871;0.226	B;B	0.34180	0.177;0.048	T	0.18713	-1.0328	10	0.12103	T	0.63	.	19.907	0.97012	0.0:1.0:0.0:0.0	.	356;359	Q05086-3;Q05086	.;UBE3A_HUMAN	Q	356;356;359;336;336	ENSP00000232165:R356Q;ENSP00000381045:R359Q;ENSP00000411258:R336Q;ENSP00000401265:R336Q	ENSP00000232165:R356Q	R	-	2	0	UBE3A	23167347	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.956000	0.70315	2.718000	0.92993	0.585000	0.79938	CGA		0.383	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		T	25616254	C	T	25616254	3	4	61	1	0	0	0	0	1	0	0	0	16919	884	31	1	1583	1	UBE3A	15	25616254	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	340	25616254	76915138	9172	17157										
ATP10A	57194	broad.mit.edu	37	chr15	25940213	25940213	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctcatgctcactttgccCttggtcttctcaggggctct	8	14	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25940213C>A	ENST00000356865.6	-	14	2952	c.2841G>T	c.(2839-2841)aaG>aaT	p.K947N		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	947					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.K947N(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCACTTTGCCCTTGGTCTTCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	117	121					15																	25940213		2203	4300	6503	23491306	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2841G>T	15.37:g.25940213C>A	ENSP00000349325:p.Lys947Asn		23491306	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	3.371	-0.128420	0.06753	.	.	ENSG00000206190	ENST00000356865	D	0.82711	-1.64	4.91	-9.81	0.00487	HAD-like domain (1);	1.886200	0.02280	N	0.069288	T	0.58133	0.2101	N	0.11673	0.155	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.56541	-0.7962	10	0.17832	T	0.49	0.4798	0.5771	0.00706	0.2843:0.0855:0.2509:0.3793	.	947	O60312	AT10A_HUMAN	N	947	ENSP00000349325:K947N	ENSP00000349325:K947N	K	-	3	2	ATP10A	23491306	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.487000	0.06505	-3.638000	0.00128	-1.141000	0.01876	AAG		0.612	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25940213	C	A	25940213	3	1	61	1	0	0	0	0	1	0	0	0	1117	680	24	2	1690	2	ATP10A	15	25940213	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323959	25940213	76591179	9173	17158										
ATP10A	57194	broad.mit.edu	37	chr15	25961940	25961940	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatggtgagtgcgatgaaGaaatcaaagacgtcagacag	13	6	2	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:25961940G>T	ENST00000356865.6	-	9	1824	c.1713C>A	c.(1711-1713)ttC>ttA	p.F571L		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	571					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.F571L(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GTGCGATGAAGAAATCAAAGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	15											167	140	149					15																	25961940		2203	4300	6503	23513033	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1713C>A	15.37:g.25961940G>T	ENSP00000349325:p.Phe571Leu		23513033	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021256	0.75275	.	.	ENSG00000206190	ENST00000356865	D	0.89270	-2.49	5.39	4.48	0.54585	HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.93294	0.7863	M	0.81802	2.56	0.51482	D	0.999923	D	0.89917	1.0	D	0.91635	0.999	D	0.92430	0.5953	10	0.48119	T	0.1	-38.7619	8.6453	0.34003	0.2284:0.0:0.7716:0.0	.	571	O60312	AT10A_HUMAN	L	571	ENSP00000349325:F571L	ENSP00000349325:F571L	F	-	3	2	ATP10A	23513033	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	3.304000	0.51866	1.276000	0.44395	0.655000	0.94253	TTC		0.572	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25961940	G	T	25961940	3	4	61	1	0	0	0	0	1	0	0	0	1117	933	33	2	2838	2	ATP10A	15	25961940	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21727	25961940	76569452	9174	17159										
ATP10A	57194	broad.mit.edu	37	chr15	26026172	26026172	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgggtcacttacaagctcCgagaagccgcggaccacctg	12	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:26026172C>T	ENST00000356865.6	-	2	759	c.648G>A	c.(646-648)tcG>tcA	p.S216S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	216					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.S216S(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTACAAGCTCCGAGAAGCCGC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	15											57	61	60					15																	26026172		2203	4300	6503	23577265	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.648G>A	15.37:g.26026172C>T			23577265	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.607	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	26026172	C	T	26026172	2	4	61	1	0	0	0	0	0	0	0	1	1117	639	23	1		1	ATP10A	15	26026172	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64232	26026172	76505220	9175	17160										
GABRB3	2562	broad.mit.edu	37	chr15	26792957	26792957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactcagttaacatagtacaGccagtaaactaagttgaaaa	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:26792957G>A	ENST00000311550.5	-	9	1516	c.1405C>T	c.(1405-1407)Ctg>Ttg	p.L469L	GABRB3_ENST00000541819.2_Silent_p.L525L|GABRB3_ENST00000545868.1_Silent_p.L384L|GABRB3_ENST00000299267.4_Silent_p.L469L|GABRB3_ENST00000400188.3_Silent_p.L398L	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	469					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.L469L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACATAGTACAGCCAGTAAACT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	15											89	75	80					15																	26792957		2203	4300	6503	24344050	SO:0001819	synonymous_variant	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1405C>T	15.37:g.26792957G>A			24344050	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																				0.353	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26792957	G	A	26792957	2	1	61	1	0	0	0	0	0	0	0	1	6187	962	34	3		3	GABRB3	15	26792957	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	766785	26792957	75738435	9176	17161										
GABRB3	2562	broad.mit.edu	37	chr15	26793032	26793032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtctatggcattcacatCggttagatcaggtattttaa	8	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:26793032C>T	ENST00000311550.5	-	9	1441	c.1330G>A	c.(1330-1332)Gat>Aat	p.D444N	GABRB3_ENST00000541819.2_Missense_Mutation_p.D500N|GABRB3_ENST00000545868.1_Missense_Mutation_p.D359N|GABRB3_ENST00000299267.4_Missense_Mutation_p.D444N|GABRB3_ENST00000400188.3_Missense_Mutation_p.D373N	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	444					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.D444N(4)|p.D500N(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCATTCACATCGGTTAGATCA	0.458																																																5	Substitution - Missense(5)	cervix(3)|large_intestine(2)	15											121	100	107					15																	26793032		2203	4300	6503	24344125	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1330G>A	15.37:g.26793032C>T	ENSP00000308725:p.Asp444Asn		24344125	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997911	0.54147	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03	6.03	6.03	0.97812	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.84723	0.5535	L	0.48260	1.515	0.80722	D	1	P;P;P	0.50443	0.893;0.92;0.935	B;B;P	0.46362	0.296;0.267;0.514	T	0.82329	-0.0511	10	0.30078	T	0.28	.	19.545	0.95291	0.0:1.0:0.0:0.0	.	500;444;444	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	N	444;500;444;373;359	ENSP00000308725:D444N;ENSP00000442408:D500N;ENSP00000299267:D444N;ENSP00000383049:D373N;ENSP00000439169:D359N	ENSP00000299267:D444N	D	-	1	0	GABRB3	24344125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.984000	0.70548	2.861000	0.98227	0.655000	0.94253	GAT		0.458	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			T	26793032	C	T	26793032	3	4	61	1	0	0	0	0	1	0	0	0	6187	884	31	1	95	1	GABRB3	15	26793032	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75	26793032	75738360	9177	17162										
GABRB3	2562	broad.mit.edu	37	chr15	26866642	26866642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaataggcgagccttttatCtctccaatattgttgaaaat	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:26866642C>A	ENST00000311550.5	-	4	391	c.280G>T	c.(280-282)Gat>Tat	p.D94Y	GABRB3_ENST00000541819.2_Missense_Mutation_p.D150Y|GABRB3_ENST00000545868.1_Missense_Mutation_p.D9Y|GABRB3_ENST00000299267.4_Missense_Mutation_p.D94Y|GABRB3_ENST00000400188.3_Missense_Mutation_p.D23Y	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	94					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.D94Y(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGCCTTTTATCTCTCCAATAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	83	83					15																	26866642		2203	4300	6503	24417735	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.280G>T	15.37:g.26866642C>A	ENSP00000308725:p.Asp94Tyr		24417735	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849486	0.91277	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868;ENST00000555094	D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	5.81	5.81	0.92471	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.98298	0.9436	H	0.98542	4.26	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.99320	1.0906	10	0.87932	D	0	.	19.0679	0.93119	0.0:1.0:0.0:0.0	.	150;94;94	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	Y	94;150;94;23;9;9	ENSP00000308725:D94Y;ENSP00000442408:D150Y;ENSP00000299267:D94Y;ENSP00000383049:D23Y;ENSP00000439169:D9Y;ENSP00000452272:D9Y	ENSP00000299267:D94Y	D	-	1	0	GABRB3	24417735	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.665000	0.83852	2.752000	0.94435	0.467000	0.42956	GAT		0.433	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26866642	C	A	26866642	3	1	61	1	0	0	0	0	1	0	0	0	6187	913	32	2	1165	2	GABRB3	15	26866642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73610	26866642	75664750	9178	17163										
GABRA5	2558	broad.mit.edu	37	chr15	27126047	27126047	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaccaatgacaacatcacGatatttaccaggatcttgga	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:27126047G>A	ENST00000335625.5	+	4	1029	c.141G>A	c.(139-141)acG>acA	p.T47T	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Silent_p.T47T|GABRA5_ENST00000557449.1_3'UTR|GABRA5_ENST00000400081.3_Silent_p.T47T	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	47					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.T47T(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	ACAACATCACGATATTTACCA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	15											101	102	101					15																	27126047		1978	4154	6132	24677140	SO:0001819	synonymous_variant	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.141G>A	15.37:g.27126047G>A			24677140	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	37	CCDS45194.1																																																																																				0.463	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			A	27126047	G	A	27126047	2	1	61	1	0	0	0	0	0	0	0	1	6183	1045	37	1		1	GABRA5	15	27126047	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259405	27126047	75405345	9179	17164										
GABRA5	2558	broad.mit.edu	37	chr15	27128356	27128356	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatctacgtcaccagcttCggcccggtgtccgacacgga	11	15	2	0	rs367578626		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:27128356C>T	ENST00000335625.5	+	5	1140	c.252C>T	c.(250-252)ttC>ttT	p.F84F	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Silent_p.F84F|GABRA5_ENST00000557449.1_Intron|GABRA5_ENST00000400081.3_Silent_p.F84F	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	84					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.F84F(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	TCACCAGCTTCGGCCCGGTGT	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C	,	0,4198		0,0,2099	63	71	69		252,252	-3.2	1	15		69	1,8427		0,1,4213	no	coding-synonymous,coding-synonymous	GABRA5	NM_000810.3,NM_001165037.1	,	0,1,6312	TT,TC,CC		0.0119,0.0,0.0079	,	84/463,84/463	27128356	1,12625	2099	4214	6313	24679449	SO:0001819	synonymous_variant	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.252C>T	15.37:g.27128356C>T			24679449	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	37	CCDS45194.1																																																																																				0.662	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27128356	C	T	27128356	2	4	61	1	0	0	0	0	0	0	0	1	6183	883	31	1		1	GABRA5	15	27128356	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2309	27128356	75403036	9180	17165										
GABRA5	2558	broad.mit.edu	37	chr15	27193221	27193221	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtaaaaccctctgaagaGaagacttctgaaagcaaaaa	7	8	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:27193221G>T	ENST00000335625.5	+	11	2118	c.1230G>T	c.(1228-1230)gaG>gaT	p.E410D	GABRA5_ENST00000355395.5_Missense_Mutation_p.E410D|GABRA5_ENST00000400081.3_Missense_Mutation_p.E410D	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	410					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.E410D(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CCTCTGAAGAGAAGACTTCTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											48	45	46					15																	27193221		1850	4097	5947	24775967	SO:0001583	missense	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.1230G>T	15.37:g.27193221G>T	ENSP00000335592:p.Glu410Asp		24775967	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	G	2.629	-0.286750	0.05605	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	D;D;D	0.82711	-1.64;-1.64;-1.64	4.66	1.61	0.23674	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.284221	0.39475	N	0.001357	T	0.68081	0.2962	L	0.34521	1.04	0.31995	N	0.604105	B	0.06786	0.001	B	0.15052	0.012	T	0.57382	-0.7821	10	0.09084	T	0.74	.	7.5005	0.27516	0.1302:0.4789:0.3909:0.0	.	410	P31644	GBRA5_HUMAN	D	410	ENSP00000335592:E410D;ENSP00000347557:E410D;ENSP00000382953:E410D	ENSP00000335592:E410D	E	+	3	2	GABRA5	24775967	1.000000	0.71417	0.998000	0.56505	0.352000	0.29268	1.142000	0.31540	0.479000	0.27511	0.591000	0.81541	GAG		0.438	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27193221	G	T	27193221	3	4	61	1	0	0	0	0	1	0	0	0	6183	933	33	2	1264	2	GABRA5	15	27193221	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64865	27193221	75338171	9181	17166										
OCA2	4948	broad.mit.edu	37	chr15	28117044	28117044	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttgttctccaacatattCtattaagtggagatgtgcca	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28117044C>A	ENST00000354638.3	-	20	2259	c.2104G>T	c.(2104-2106)Gaa>Taa	p.E702*	OCA2_ENST00000353809.5_Nonsense_Mutation_p.E678*	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	702					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.E702*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CCAACATATTCTATTAAGTGG	0.318									Oculocutaneous Albinism																																							1	Substitution - Nonsense(1)	large_intestine(1)	15											109	114	113					15																	28117044		2203	4300	6503	25790639	SO:0001587	stop_gained	4948	Familial Cancer Database			CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2104G>T	15.37:g.28117044C>A	ENSP00000346659:p.Glu702*		25790639	Q15211|Q15212|Q96EN1|Q9UMI5	Nonsense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	C	41	8.548944	0.98859	.	.	ENSG00000104044	ENST00000354638;ENST00000353809	.	.	.	5.27	4.35	0.52113	.	0.101758	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-8.7188	11.5363	0.50639	0.0:0.9127:0.0:0.0873	.	.	.	.	X	702;678	.	ENSP00000261276:E678X	E	-	1	0	OCA2	25790639	1.000000	0.71417	0.963000	0.40424	0.985000	0.73830	6.152000	0.71812	1.220000	0.43490	0.655000	0.94253	GAA		0.318	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		A	28117044	C	A	28117044	4	1	61	1	0	0	0	0	0	1	0	0	10846	922	32	2	432	2	OCA2	15	28117044	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	923823	28117044	74414348	9182	17167										
HERC2	8924	broad.mit.edu	37	chr15	28375399	28375400	+	Nonsense_Mutation	DNP	GA	GA	AG													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggacctgccgaggccttcGaacatggtcatctgatccat							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28375399_28375400GA>AG	ENST00000261609.7	-	83	12819_12820	c.12711_12712TC>CT	c.(12709-12714)gtTCga>gtCTga	p.R4238*		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.V4237>?(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CGAGGCCTTCGAACATGGTCAT	0.554																																																1	Complex(1)	large_intestine(1)	15																																								26048995	SO:0001587	stop_gained	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.12711_12712delinsAG	15.37:g.28375399_28375400delinsAG	ENSP00000261609:p.Arg4238*		26048994		Nonsense_Mutation	DNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.554	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		AG	28375400	GA	AG	28375399	4	1	61	1	0	0	0	0	0	1	0	0	7079	1066	37	1	1836	1	HERC2	15	28375399	Nonsense_Mutation	DNP	GA	TCGA-AG-A002-01A-01W-A00K-09	258355	28375399	74155993	9183	17168										
HERC2	8924	broad.mit.edu	37	chr15	28420712	28420712	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccccgacagccacatgcacGatcttcttccctctcagccc	6	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28420712G>A	ENST00000261609.7	-	64	9885	c.9777C>T	c.(9775-9777)atC>atT	p.I3259I		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.I3259I(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CCACATGCACGATCTTCTTCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	15											66	52	57					15																	28420712		2203	4300	6503	26094307	SO:0001819	synonymous_variant	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9777C>T	15.37:g.28420712G>A			26094307		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.637	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28420712	G	A	28420712	2	1	61	1	0	0	0	0	0	0	0	1	7079	1048	37	1		1	HERC2	15	28420712	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45313	28420712	74110680	9184	17169										
HERC2	8924	broad.mit.edu	37	chr15	28460812	28460812	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggtgcgtgcccttccacGaccttcatgagcagcgtgat	12	12	1	2	rs201824814		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28460812G>A	ENST00000261609.7	-	39	6273	c.6165C>T	c.(6163-6165)gtC>gtT	p.V2055V		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.V2055V(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		GCCCTTCCACGACCTTCATGA	0.627													G|||	1	0.000199681	0	0	5008	,	,		15030	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	15											21	18	19					15																	28460812		2202	4297	6499	26134407	SO:0001819	synonymous_variant	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6165C>T	15.37:g.28460812G>A			26134407		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.627	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28460812	G	A	28460812	2	1	61	1	0	0	0	0	0	0	0	1	7079	1045	37	1		1	HERC2	15	28460812	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40100	28460812	74070580	9185	17170										
HERC2	8924	broad.mit.edu	37	chr15	28463812	28463812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgttcctttcagtttgttCggcttctaaaaaaaataatc	5	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28463812C>T	ENST00000261609.7	-	38	5959	c.5851G>A	c.(5851-5853)Gaa>Aaa	p.E1951K		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.E1951K(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		TCAGTTTGTTCGGCTTCTAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	15											38	48	44					15																	28463812		1351	2275	3626	26137407	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.5851G>A	15.37:g.28463812C>T	ENSP00000261609:p.Glu1951Lys		26137407		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.672233	0.67928	.	.	ENSG00000128731	ENST00000261609	T	0.39592	1.07	4.4	3.47	0.39725	.	0.128657	0.51477	D	0.000093	T	0.28928	0.0718	L	0.47716	1.5	0.80722	D	1	P	0.44006	0.824	B	0.27500	0.08	T	0.11470	-1.0586	10	0.26408	T	0.33	.	14.0559	0.64769	0.1521:0.8479:0.0:0.0	.	1951	O95714	HERC2_HUMAN	K	1951	ENSP00000261609:E1951K	ENSP00000261609:E1951K	E	-	1	0	HERC2	26137407	1.000000	0.71417	0.973000	0.42090	0.571000	0.35966	7.320000	0.79064	1.191000	0.43056	0.650000	0.86243	GAA		0.343	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28463812	C	T	28463812	3	4	61	1	0	0	0	0	1	0	0	0	7079	893	31	1	8877	1	HERC2	15	28463812	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3000	28463812	74067580	9186	17171										
HERC2	8924	broad.mit.edu	37	chr15	28467179	28467179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatctctgagtacctgatCgccccatttccagtccacac	5	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28467179C>T	ENST00000261609.7	-	36	5755	c.5647G>A	c.(5647-5649)Gat>Aat	p.D1883N		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.D1883N(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		AGTACCTGATCGCCCCATTTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											17	12	13					15																	28467179		1985	3797	5782	26140774	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.5647G>A	15.37:g.28467179C>T	ENSP00000261609:p.Asp1883Asn		26140774		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	33	5.242554	0.95272	.	.	ENSG00000128731	ENST00000261609	T	0.46451	0.87	4.38	4.38	0.52667	Mib-herc2 (2);	0.051853	0.64402	D	0.000001	T	0.57695	0.2071	L	0.45137	1.4	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.62300	-0.6883	10	0.87932	D	0	.	17.498	0.87724	0.0:1.0:0.0:0.0	.	1883	O95714	HERC2_HUMAN	N	1883	ENSP00000261609:D1883N	ENSP00000261609:D1883N	D	-	1	0	HERC2	26140774	1.000000	0.71417	0.953000	0.39169	0.987000	0.75469	7.278000	0.78587	2.423000	0.82170	0.650000	0.86243	GAT		0.473	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28467179	C	T	28467179	3	4	61	1	0	0	0	0	1	0	0	0	7079	884	31	1	9089	1	HERC2	15	28467179	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3367	28467179	74064213	9187	17172										
HERC2	8924	broad.mit.edu	37	chr15	28514475	28514475	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttctctgcacaggcaatCtgtgtgactcccaggttggc	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:28514475C>T	ENST00000261609.7	-	11	1473	c.1365G>A	c.(1363-1365)caG>caA	p.Q455Q		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.Q455Q(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CACAGGCAATCTGTGTGACTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15											139	107	118					15																	28514475		2203	4300	6503	26188070	SO:0001819	synonymous_variant	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.1365G>A	15.37:g.28514475C>T			26188070		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.517	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28514475	C	T	28514475	2	4	61	1	0	0	0	0	0	0	0	1	7079	912	32	3		3	HERC2	15	28514475	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47296	28514475	74016917	9188	17173										
APBA2	321	broad.mit.edu	37	chr15	29346430	29346430	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagctacctagagggcatgGactgcaacggggaggagtac	15	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:29346430G>T	ENST00000558402.1	+	5	942	c.343G>T	c.(343-345)Gac>Tac	p.D115Y	APBA2_ENST00000411764.1_Missense_Mutation_p.D115Y|APBA2_ENST00000561069.1_Missense_Mutation_p.D115Y|APBA2_ENST00000558259.1_Missense_Mutation_p.D115Y|APBA2_ENST00000558330.1_Missense_Mutation_p.D115Y			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	115					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.D115Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		AGAGGGCATGGACTGCAACGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	15											127	104	111					15																	29346430		2203	4300	6503	27133722	SO:0001583	missense	321			AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.343G>T	15.37:g.29346430G>T	ENSP00000453293:p.Asp115Tyr		27133722	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.360428	0.82353	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.55234	0.53	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.71745	0.3376	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.75255	-0.3382	10	0.87932	D	0	.	17.5474	0.87866	0.0:0.0:1.0:0.0	.	115;115;115	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	Y	115	ENSP00000409312:D115Y	ENSP00000219865:D115Y	D	+	1	0	APBA2	27133722	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.995000	0.93534	2.354000	0.79902	0.557000	0.71058	GAC		0.637	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29346430	G	T	29346430	3	4	61	1	0	0	0	0	1	0	0	0	757	1174	41	2	345	2	APBA2	15	29346430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	831955	29346430	73184962	9189	17174										
APBA2	321	broad.mit.edu	37	chr15	29386515	29386515	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctaagatcaagaaaaaagCggtgtgtagggccttgaggc	14	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:29386515C>T	ENST00000558402.1	+	9	1849	c.1250C>T	c.(1249-1251)gCg>gTg	p.A417V	APBA2_ENST00000411764.1_Intron|APBA2_ENST00000561069.1_Splice_Site_p.A417V|APBA2_ENST00000558259.1_Splice_Site_p.A417V|APBA2_ENST00000558330.1_Intron			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	417	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.A417V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		AAGAAAAAAGCGGTGTGTAGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											184	173	177					15																	29386515		2203	4300	6503	27173807	SO:0001630	splice_region_variant	321			AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1251+1C>T	15.37:g.29386515C>T			27173807	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159722	0.57368	.	.	ENSG00000034053	ENST00000219865	.	.	.	4.91	3.98	0.46160	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.309310	0.33477	N	0.004879	T	0.44932	0.1317	L	0.29908	0.895	0.80722	D	1	B	0.17268	0.021	B	0.12837	0.008	T	0.42682	-0.9437	9	0.46703	T	0.11	.	12.8934	0.58084	0.0:0.9146:0.0:0.0854	.	417	Q99767	APBA2_HUMAN	V	417	.	ENSP00000219865:A417V	A	+	2	0	APBA2	27173807	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.477000	0.45180	2.427000	0.82271	0.561000	0.74099	GCG		0.522	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	Missense_Mutation	T	29386515	C	T	29386515	5	4	61	1	0	0	0	0	0	0	1	0	757	782	27	1	1268	1	APBA2	15	29386515	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40085	29386515	73144877	9190	17175										
TJP1	7082	broad.mit.edu	37	chr15	30000919	30000919	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggagaagtgggagtttttGaagacaagtcaggtttatgt	14	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:30000919G>T	ENST00000346128.6	-	25	5168	c.4694C>A	c.(4693-4695)tCa>tAa	p.S1565*	TJP1_ENST00000356107.6_Nonsense_Mutation_p.S1565*|TJP1_ENST00000545208.2_Nonsense_Mutation_p.S1485*|TJP1_ENST00000400011.2_Nonsense_Mutation_p.S1489*	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1565					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.S1565*(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		GGGAGTTTTTGAAGACAAGTC	0.418																																					Melanoma(77;681 1843 6309 6570)											1	Substitution - Nonsense(1)	large_intestine(1)	15											215	198	203					15																	30000919		1877	4112	5989	27788211	SO:0001587	stop_gained	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.4694C>A	15.37:g.30000919G>T	ENSP00000281537:p.Ser1565*		27788211	B4E3K1|Q2NKP3|Q4ZGJ6	Nonsense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	45	11.283592	0.99541	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	.	.	.	5.55	4.64	0.57946	.	0.480353	0.22570	N	0.058352	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.798	0.69891	0.0686:0.0:0.9313:0.0	.	.	.	.	X	1565;1489;1565;1485;1485	.	ENSP00000281537:S1565X	S	-	2	0	TJP1	27788211	0.971000	0.33674	0.359000	0.25824	0.985000	0.73830	4.511000	0.60462	1.622000	0.50330	0.644000	0.83932	TCA		0.418	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		T	30000919	G	T	30000919	4	4	61	1	0	0	0	0	0	1	0	0	15968	1294	45	2	568	2	TJP1	15	30000919	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	614404	30000919	72530473	9191	17176										
TJP1	7082	broad.mit.edu	37	chr15	30024838	30024838	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagaaaataaactaccttCtcgaagaaccactctttcat	4	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:30024838C>A	ENST00000346128.6	-	14	2392	c.1918G>T	c.(1918-1920)Gaa>Taa	p.E640*	TJP1_ENST00000356107.6_Nonsense_Mutation_p.E640*|TJP1_ENST00000545208.2_Nonsense_Mutation_p.E640*|TJP1_ENST00000400011.2_Nonsense_Mutation_p.E644*	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	640	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.E640*(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		AAACTACCTTCTCGAAGAACC	0.363																																					Melanoma(77;681 1843 6309 6570)											1	Substitution - Nonsense(1)	large_intestine(1)	15											70	67	68					15																	30024838		1824	4090	5914	27812130	SO:0001587	stop_gained	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.1918G>T	15.37:g.30024838C>A	ENSP00000281537:p.Glu640*		27812130	B4E3K1|Q2NKP3|Q4ZGJ6	Nonsense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	39	7.822935	0.98510	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1092	0.97906	0.0:1.0:0.0:0.0	.	.	.	.	X	640;644;640;640;640	.	.	E	-	1	0	TJP1	27812130	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.745000	0.94114	0.655000	0.94253	GAA		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30024838	C	A	30024838	4	1	61	1	0	0	0	0	0	1	0	0	15968	922	32	2	3388	2	TJP1	15	30024838	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23919	30024838	72506554	9192	17177										
TJP1	7082	broad.mit.edu	37	chr15	30058590	30058590	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacttgcacttctatccctCggccaaatcttctcactcct	3	17	3	0	rs199932396		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:30058590C>T	ENST00000346128.6	-	5	942	c.468G>A	c.(466-468)ccG>ccA	p.P156P	TJP1_ENST00000495972.2_Silent_p.P156P|TJP1_ENST00000356107.6_Silent_p.P156P|TJP1_ENST00000545208.2_Silent_p.P156P|TJP1_ENST00000400011.2_Silent_p.P160P	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	156					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.P156P(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TTCTATCCCTCGGCCAAATCT	0.493													C|||	1	0.000199681	0	0	5008	,	,		17197	0		0.001	False		,,,				2504	0				Melanoma(77;681 1843 6309 6570)											1	Substitution - coding silent(1)	large_intestine(1)	15											147	149	148					15																	30058590		2008	4177	6185	27845882	SO:0001819	synonymous_variant	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.468G>A	15.37:g.30058590C>T			27845882	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																				0.493	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		T	30058590	C	T	30058590	2	4	61	1	0	0	0	0	0	0	0	1	15968	871	31	1		1	TJP1	15	30058590	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33752	30058590	72472802	9193	17178										
ARHGAP11B	89839	broad.mit.edu	37	chr15	30922926	30922926	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaaatatttggagtaccTtttaatgcactgccccattc	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:30922926T>A	ENST00000428041.2	+	2	295	c.150T>A	c.(148-150)ccT>ccA	p.P50P		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	50	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.P50P(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		TTGGAGTACCTTTTAATGCAC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	15											37	40	39					15																	30922926		2196	4280	6476	28710218	SO:0001819	synonymous_variant	89839			BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"Rho GTPase activating proteins"	15782	protein-coding gene	gene with protein product	"GAP (1-8)"		"family with sequence similarity 7, member B1"	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.150T>A	15.37:g.30922926T>A			28710218		Silent	SNP	ENST00000428041.2	37	CCDS32185.1																																																																																				0.368	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841		A	30922926	T	A	30922926	2	1	61	1	0	0	0	0	0	0	0	1	864	1596	56	5		5	ARHGAP11B	15	30922926	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	864336	30922926	71608466	9194	17179										
MTMR15	22909	broad.mit.edu	37	chr15	31197154	31197154	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagtgttaccttagaagaTgtaacacctaagaagtcacc	7	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:31197154T>C	ENST00000362065.4	+	2	579	c.288T>C	c.(286-288)gaT>gaC	p.D96D	FAN1_ENST00000565466.1_Silent_p.D96D|FAN1_ENST00000561607.1_Silent_p.D96D|FAN1_ENST00000561594.1_Silent_p.D96D	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	96					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)	p.D96D(1)		autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						CCTTAGAAGATGTAACACCTA	0.403								Direct reversal of damage																																								1	Substitution - coding silent(1)	large_intestine(1)	15											74	69	71					15																	31197154		2202	4300	6502	28984446	SO:0001819	synonymous_variant	22909				CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.288T>C	15.37:g.31197154T>C			28984446	A8K4M2|Q86WU8	Silent	SNP	ENST00000362065.4	37	CCDS32186.1																																																																																				0.403	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		C	31197154	T	C	31197154	2	2	61	1	0	0	0	0	0	0	0	1	9973	1461	51	4		4	MTMR15	15	31197154	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	274228	31197154	71334238	9195	17180										
TRPM1	4308	broad.mit.edu	37	chr15	31324929	31324929	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacgtatggccccagatacTtgttgacaccaaagatgtcc	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:31324929T>G	ENST00000256552.6	-	22	3062	c.2915A>C	c.(2914-2916)aAg>aCg	p.K972T	RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000397795.2_Missense_Mutation_p.K950T|TRPM1_ENST00000542188.1_Missense_Mutation_p.K989T|RP11-348B17.1_ENST00000561299.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1									p.K950T(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CCCCAGATACTTGTTGACACC	0.488																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	15											121	116	118					15																	31324929		2001	4184	6185	29112221	SO:0001583	missense	4308			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2915A>C	15.37:g.31324929T>G	ENSP00000256552:p.Lys972Thr		29112221		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557619	0.86231	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.73897	-0.79;-0.79;-0.79	5.43	5.43	0.79202	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.87688	0.6240	M	0.88640	2.97	0.58432	D	0.999996	D;D	0.71674	0.998;0.971	D;P	0.66979	0.948;0.9	D	0.90180	0.4242	10	0.87932	D	0	-35.2937	15.7723	0.78180	0.0:0.0:0.0:1.0	.	944;950	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	T	950;989;972;950	ENSP00000380897:K950T;ENSP00000437849:K989T;ENSP00000256552:K972T	ENSP00000256552:K972T	K	-	2	0	TRPM1	29112221	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.183000	0.69458	0.523000	0.50628	AAG		0.488	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		G	31324929	T	G	31324929	3	3	61	1	0	0	0	0	1	0	0	0	16625	1609	56	4	1990	4	TRPM1	15	31324929	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	127775	31324929	71206463	9196	17181										
OTUD7A	161725	broad.mit.edu	37	chr15	31796012	31796012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtacacggggtcctcagaGttgtccacactgtgaaacaa	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:31796012G>T	ENST00000307050.4	-	7	974	c.882C>A	c.(880-882)aaC>aaA	p.N294K	OTUD7A_ENST00000382902.1_Missense_Mutation_p.N301K	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	294	Catalytic. {ECO:0000250}.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding. {ECO:0000250}.				protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.N294K(1)		endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GGTCCTCAGAGTTGTCCACAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											78	74	75					15																	31796012		2202	4300	6502	29583304	SO:0001583	missense	161725			AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"OTU domain containing"	20718	protein-coding gene	gene with protein product		612024	"chromosome 15 open reading frame 16", "OTU domain containing 7", "OTU domain containing 7A"	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.882C>A	15.37:g.31796012G>T	ENSP00000305926:p.Asn294Lys		29583304	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.846758	0.51164	.	.	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.32023	1.48;1.47	4.67	1.21	0.21127	Ovarian tumour, otubain (2);	0.091150	0.64402	D	0.000001	T	0.42585	0.1209	L	0.59436	1.845	0.54753	D	0.999986	D;D	0.71674	0.998;0.998	D;D	0.69654	0.941;0.965	T	0.26608	-1.0098	10	0.62326	D	0.03	-39.3718	5.5081	0.16866	0.6176:0.0:0.3824:0.0	.	301;294	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	K	294;301	ENSP00000305926:N294K;ENSP00000372358:N301K	ENSP00000305926:N294K	N	-	3	2	OTUD7A	29583304	1.000000	0.71417	0.980000	0.43619	0.710000	0.40934	2.082000	0.41605	0.507000	0.28148	-0.136000	0.14681	AAC		0.502	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		T	31796012	G	T	31796012	3	4	61	1	0	0	0	0	1	0	0	0	11349	1020	36	2	1918	2	OTUD7A	15	31796012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	471083	31796012	70735380	9197	17182										
CHRNA7	1139	broad.mit.edu	37	chr15	32404082	32404082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccagatttggaaaccagAcattcttctctataacaggt	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:32404082A>G	ENST00000306901.3	+	4	429	c.332A>G	c.(331-333)gAc>gGc	p.D111G	CHRNA7_ENST00000455693.2_Intron|CHRNA7_ENST00000454250.3_Missense_Mutation_p.D140G	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	111					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)	p.D111G(2)		endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGGAAACCAGACATTCTTCTC	0.378																																					Esophageal Squamous(193;529 2900 40232 43193)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	15											157	149	152					15																	32404082		2201	4300	6501	30191374	SO:0001583	missense	1139			Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1960	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 7 (neuronal)"	118511	"cholinergic receptor, nicotinic, alpha polypeptide 7"			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.332A>G	15.37:g.32404082A>G	ENSP00000303727:p.Asp111Gly		30191374	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Missense_Mutation	SNP	ENST00000306901.3	37	CCDS10027.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018096	0.75275	.	.	ENSG00000175344	ENST00000454250;ENST00000306901;ENST00000449991	D;D	0.84800	-1.9;-1.9	4.79	4.79	0.61399	Neurotransmitter-gated ion-channel ligand-binding (3);	0.091237	0.85682	D	0.000000	D	0.95172	0.8435	H	0.98507	4.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	D	0.96415	0.9307	10	0.87932	D	0	.	12.617	0.56582	1.0:0.0:0.0:0.0	.	111;127;111	F5H8K5;B1N7F6;P36544	.;.;ACHA7_HUMAN	G	140;111;111	ENSP00000407546:D140G;ENSP00000303727:D111G	ENSP00000303727:D111G	D	+	2	0	CHRNA7	30191374	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.321000	0.79088	2.138000	0.66242	0.533000	0.62120	GAC		0.378	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2			G	32404082	A	G	32404082	3	3	61	1	0	0	0	0	1	0	0	0	3394	275	10	4	346	4	CHRNA7	15	32404082	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	608070	32404082	70127310	9198	17183										
ARHGAP11A	9824	broad.mit.edu	37	chr15	32917744	32917744	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgttgggtattgatggtCtctgtgctactccatcactg	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:32917744C>A	ENST00000361627.3	+	6	1494	c.772C>A	c.(772-774)Ctc>Atc	p.L258I	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.L69I|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.L258I|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.L69I|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.L258I	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	258					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.L258I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TATTGATGGTCTCTGTGCTAC	0.408																																					Colon(45;757 1134 30003 36652)											1	Substitution - Missense(1)	large_intestine(1)	15											142	145	144					15																	32917744		2201	4298	6499	30705036	SO:0001583	missense	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.772C>A	15.37:g.32917744C>A	ENSP00000355090:p.Leu258Ile		30705036	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	9.085	1.000364	0.19121	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.09817	2.94	4.86	1.88	0.25563	.	0.553798	0.16278	N	0.221467	T	0.06735	0.0172	N	0.22421	0.69	0.18873	N	0.999985	B;B	0.10296	0.0;0.003	B;B	0.09377	0.001;0.004	T	0.39292	-0.9621	10	0.21540	T	0.41	.	8.8036	0.34923	0.0:0.5998:0.0:0.4002	.	258;69	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	I	258;69	ENSP00000355090:L258I	ENSP00000355090:L258I	L	+	1	0	ARHGAP11A	30705036	0.994000	0.37717	0.998000	0.56505	0.991000	0.79684	1.161000	0.31773	0.562000	0.29204	0.655000	0.94253	CTC		0.408	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		A	32917744	C	A	32917744	3	1	61	1	0	0	0	0	1	0	0	0	863	913	32	2	794	2	ARHGAP11A	15	32917744	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	513662	32917744	69613648	9199	17184										
ARHGAP11A	9824	broad.mit.edu	37	chr15	32925187	32925187	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttatttttgtagttcacatCgatacaagctcagaagggtc	9	7	2	1	rs138524535		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:32925187C>T	ENST00000361627.3	+	9	1835	c.1113C>T	c.(1111-1113)atC>atT	p.I371I	ARHGAP11A_ENST00000543522.1_Silent_p.I182I|ARHGAP11A_ENST00000567348.1_Silent_p.I371I|ARHGAP11A_ENST00000565905.1_Silent_p.I182I|ARHGAP11A_ENST00000563864.1_Intron	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	371					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.I371I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TAGTTCACATCGATACAAGCT	0.363																																					Colon(45;757 1134 30003 36652)											1	Substitution - coding silent(1)	large_intestine(1)	15						C	,	2,4400		0,2,2199	155	148	151		1113,1113	-1.4	0.1	15	dbSNP_134	151	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGAP11A	NM_014783.3,NM_199357.1	,	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	,	371/1024,371/502	32925187	2,13000	2201	4300	6501	30712479	SO:0001819	synonymous_variant	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1113C>T	15.37:g.32925187C>T			30712479	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																				0.363	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32925187	C	T	32925187	2	4	61	1	0	0	0	0	0	0	0	1	863	874	31	1		1	ARHGAP11A	15	32925187	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7443	32925187	69606205	9200	17185										
GREM1	26585	broad.mit.edu	37	chr15	33023238	33023238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcgcaccatcatcaaccGcttctgttacggccagtgca	8	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:33023238G>A	ENST00000300177.4	+	2	536	c.347G>A	c.(346-348)cGc>cAc	p.R116H	GREM1_ENST00000560830.1_Missense_Mutation_p.R75H|GREM1_ENST00000560677.1_3'UTR|GREM1_ENST00000322805.4_Missense_Mutation_p.R75H	NM_001191322.1|NM_001191323.1|NM_013372.6	NP_001178251.1|NP_001178252.1|NP_037504.1	O60565	GREM1_HUMAN	gremlin 1, DAN family BMP antagonist	116	CTCK.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell morphogenesis (GO:0000902)|collagen fibril organization (GO:0030199)|determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone mineralization (GO:0030502)|negative regulation of bone mineralization involved in bone maturation (GO:1900158)|negative regulation of bone remodeling (GO:0046851)|negative regulation of bone trabecula formation (GO:1900155)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of receptor activity (GO:2000273)|positive regulation of receptor internalization (GO:0002092)|positive regulation of telomerase activity (GO:0051973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|regulation of epithelial to mesenchymal transition (GO:0010717)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|receptor agonist activity (GO:0048018)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R116H(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)	10		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)		ATCATCAACCGCTTCTGTTAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											95	74	81					15																	33023238		2201	4300	6501	30810530	SO:0001583	missense	26585				CCDS10029.1, CCDS53927.1	15q13.3	2014-02-07	2013-02-26	2004-05-07	ENSG00000166923	ENSG00000166923			2001	protein-coding gene	gene with protein product		603054	"cysteine knot superfamily 1, BMP antagonist 1", "gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis)", "gremlin 1", "colorectal adenoma and carcinoma 1"	CKTSF1B1, CRAC1		9660951, 10026205, 22561515	Standard	NM_013372		Approved	DRM, gremlin, DAND2, HMPS	uc001zhe.2	O60565	OTTHUMG00000129319	ENST00000300177.4:c.347G>A	15.37:g.33023238G>A	ENSP00000300177:p.Arg116His		30810530	Q52LV3|Q8N914|Q8N936	Missense_Mutation	SNP	ENST00000300177.4	37	CCDS10029.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.006976	0.93287	.	.	ENSG00000166923	ENST00000300177;ENST00000322805	T;T	0.34072	1.38;1.38	5.57	4.65	0.58169	DAN (1);Cystine knot, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57814	0.2079	M	0.73430	2.235	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.992	D;D;P	0.77557	0.92;0.99;0.893	T	0.55224	-0.8174	10	0.35671	T	0.21	-17.9568	13.8474	0.63477	0.0729:0.0:0.9271:0.0	.	75;116;46	O60565-2;O60565;B3KTR9	.;GREM1_HUMAN;.	H	116;75	ENSP00000300177:R116H;ENSP00000323101:R75H	ENSP00000300177:R116H	R	+	2	0	GREM1	30810530	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.022000	0.88759	2.640000	0.89533	0.655000	0.94253	CGC		0.542	GREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251455.2	NM_013372		A	33023238	G	A	33023238	3	1	61	1	0	0	0	0	1	0	0	0	6782	1087	38	1	349	1	GREM1	15	33023238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98051	33023238	69508154	9201	17186										
FMN1	342184	broad.mit.edu	37	chr15	33358755	33358755	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgctggcttagaattggacCgttcaaacacagctcttagc	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:33358755C>T	ENST00000559047.1	-	3	2043				FMN1_ENST00000561249.1_Intron|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000334528.9_Missense_Mutation_p.R444Q|FMN1_ENST00000558197.1_Missense_Mutation_p.R444Q			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R444Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		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)		AGAATTGGACCGTTCAAACAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	15											53	52	52					15																	33358755		1934	4150	6084	31146047	SO:0001627	intron_variant	342184			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-1480G>A	15.37:g.33358755C>T			31146047	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	C	16.58	3.162235	0.57368	.	.	ENSG00000248905	ENST00000334528	T	0.59224	0.28	5.96	5.96	0.96718	.	0.106928	0.64402	D	0.000009	T	0.72070	0.3415	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.928	T	0.71784	-0.4488	8	0.29301	T	0.29	.	13.5937	0.61975	0.0:0.9296:0.0:0.0704	.	444;444	Q68DA7-3;Q68DA7-5	.;.	Q	444	ENSP00000333950:R444Q	ENSP00000333950:R444Q	R	-	2	0	FMN1	31146047	1.000000	0.71417	0.968000	0.41197	0.744000	0.42396	4.985000	0.63845	2.832000	0.97577	0.655000	0.94253	CGG		0.478	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		T	33358755	C	T	33358755	1	4	61	0	1	0	0	0	0	0	0	0	5968	652	23	1		1	FMN1	15	33358755	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	335517	33358755	69172637	9202	17187										
RYR3	6263	broad.mit.edu	37	chr15	33916104	33916104	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttacttccaaaagagaaGatgagattggagcctgtcaa	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:33916104G>T	ENST00000389232.4	+	20	2524	c.2454G>T	c.(2452-2454)aaG>aaT	p.K818N	RYR3_ENST00000415757.3_Missense_Mutation_p.K818N	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	818					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.K818N(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAAAAGAGAAGATGAGATTGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	15											147	144	145					15																	33916104		1898	4124	6022	31703396	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2454G>T	15.37:g.33916104G>T	ENSP00000373884:p.Lys818Asn		31703396	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.411225	0.42817	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96856	-4.15;-4.15	4.86	3.95	0.45737	.	0.064498	0.64402	D	0.000009	D	0.97059	0.9039	L	0.54323	1.7	0.51767	D	0.999933	D;B	0.67145	0.996;0.314	D;B	0.77557	0.99;0.134	D	0.97087	0.9788	10	0.59425	D	0.04	.	13.2041	0.59785	0.0772:0.0:0.9228:0.0	.	818;818	Q15413-2;Q15413	.;RYR3_HUMAN	N	818	ENSP00000373884:K818N;ENSP00000399610:K818N	ENSP00000354735:K818N	K	+	3	2	RYR3	31703396	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.211000	0.51137	1.277000	0.44412	-0.253000	0.11424	AAG		0.478	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33916104	G	T	33916104	3	4	61	1	0	0	0	0	1	0	0	0	13807	933	33	2	2532	2	RYR3	15	33916104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	557349	33916104	68615288	9203	17188										
RYR3	6263	broad.mit.edu	37	chr15	33954539	33954539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacctccccggcctccttcGatctggtttctatgacctgc	8	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:33954539G>A	ENST00000389232.4	+	35	4878	c.4808G>A	c.(4807-4809)cGa>cAa	p.R1603Q	RYR3_ENST00000415757.3_Missense_Mutation_p.R1603Q	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1603	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.R1603Q(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GGCCTCCTTCGATCTGGTTTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	15											77	73	74					15																	33954539		1996	4163	6159	31741831	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.4808G>A	15.37:g.33954539G>A	ENSP00000373884:p.Arg1603Gln		31741831	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	32	5.192200	0.94960	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.73789	-0.78;-0.78	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	D	0.88273	0.6392	M	0.86953	2.85	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.90294	0.4325	10	0.87932	D	0	.	18.3307	0.90268	0.0:0.0:1.0:0.0	.	1603;1603	Q15413-2;Q15413	.;RYR3_HUMAN	Q	1603	ENSP00000373884:R1603Q;ENSP00000399610:R1603Q	ENSP00000354735:R1603Q	R	+	2	0	RYR3	31741831	1.000000	0.71417	0.253000	0.24343	0.971000	0.66376	9.601000	0.98297	2.563000	0.86464	0.650000	0.86243	CGA		0.577	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	33954539	G	A	33954539	3	1	61	1	0	0	0	0	1	0	0	0	13807	1058	37	1	4946	1	RYR3	15	33954539	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38435	33954539	68576853	9204	17189										
RYR3	6263	broad.mit.edu	37	chr15	33954987	33954987	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctcctcctgattgatccCtctgtgtttggggagcatag	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:33954987C>T	ENST00000389232.4	+	35	5326	c.5256C>T	c.(5254-5256)ccC>ccT	p.P1752P	RYR3_ENST00000415757.3_Silent_p.P1752P	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1752	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.P1752P(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGATTGATCCCTCTGTGTTTG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	15											135	144	141					15																	33954987		2094	4233	6327	31742279	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5256C>T	15.37:g.33954987C>T			31742279	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.557	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33954987	C	T	33954987	2	4	61	1	0	0	0	0	0	0	0	1	13807	668	24	3		3	RYR3	15	33954987	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	448	33954987	68576405	9205	17190										
RYR3	6263	broad.mit.edu	37	chr15	34040439	34040439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgggaaaatgagaagcttcGaagtgtgtcccaggccaacc	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34040439G>A	ENST00000389232.4	+	54	8184	c.8114G>A	c.(8113-8115)cGa>cAa	p.R2705Q	RYR3_ENST00000415757.3_Missense_Mutation_p.R2705Q	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2705	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.R2705Q(2)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GAGAAGCTTCGAAGTGTGTCC	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	15											62	67	66					15																	34040439		1954	4150	6104	31827731	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.8114G>A	15.37:g.34040439G>A	ENSP00000373884:p.Arg2705Gln		31827731	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.144145	0.77888	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96619	-4.07;-4.07	5.18	5.18	0.71444	.	0.071281	0.56097	D	0.000040	D	0.93148	0.7818	L	0.41492	1.28	0.52099	D	0.999941	B;B	0.27951	0.195;0.019	B;B	0.15870	0.014;0.005	D	0.90695	0.4616	10	0.20519	T	0.43	.	18.8778	0.92345	0.0:0.0:1.0:0.0	.	2705;2705	Q15413-2;Q15413	.;RYR3_HUMAN	Q	2705	ENSP00000373884:R2705Q;ENSP00000399610:R2705Q	ENSP00000354735:R2705Q	R	+	2	0	RYR3	31827731	1.000000	0.71417	0.991000	0.47740	0.897000	0.52465	7.158000	0.77470	2.679000	0.91253	0.655000	0.94253	CGA		0.577	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34040439	G	A	34040439	3	1	61	1	0	0	0	0	1	0	0	0	13807	1058	37	1	8328	1	RYR3	15	34040439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	85452	34040439	68490953	9206	17191										
RYR3	6263	broad.mit.edu	37	chr15	34047326	34047326	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaggtttgcctataagttCttgaagaagatcctgaaata	9	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34047326C>T	ENST00000389232.4	+	58	8530	c.8460C>T	c.(8458-8460)ttC>ttT	p.F2820F	RYR3_ENST00000415757.3_Silent_p.F2820F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2820	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.F2820F(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCTATAAGTTCTTGAAGAAGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	15											94	96	95					15																	34047326		1896	4121	6017	31834618	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.8460C>T	15.37:g.34047326C>T			31834618	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34047326	C	T	34047326	2	4	61	1	0	0	0	0	0	0	0	1	13807	912	32	3		3	RYR3	15	34047326	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6887	34047326	68484066	9207	17192										
RYR3	6263	broad.mit.edu	37	chr15	34072491	34072491	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctggagcccacccttaatCgctacaatccactctcggtc	6	17	1	0	rs368231214		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34072491C>T	ENST00000389232.4	+	65	9287	c.9217C>T	c.(9217-9219)Cgc>Tgc	p.R3073C	RYR3_ENST00000415757.3_Missense_Mutation_p.R3073C	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3073					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.R3073C(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CACCCTTAATCGCTACAATCC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15						C	CYS/ARG	1,3849		0,1,1924	72	70	70		9217	0.2	1	15		70	0,8290		0,0,4145	no	missense	RYR3	NM_001036.3	180	0,1,6069	TT,TC,CC		0.0,0.026,0.0082	possibly-damaging	3073/4871	34072491	1,12139	1925	4145	6070	31859783	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.9217C>T	15.37:g.34072491C>T	ENSP00000373884:p.Arg3073Cys		31859783	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	10.41	1.342739	0.24339	2.6E-4	0.0	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.89123	-2.47;-2.47	5.52	0.191	0.15130	.	0.731440	0.13757	N	0.364885	T	0.77718	0.4172	N	0.14661	0.345	0.30853	N	0.734401	B;P	0.49961	0.002;0.93	B;B	0.42522	0.001;0.39	T	0.75071	-0.3447	10	0.66056	D	0.02	.	6.9632	0.24610	0.0:0.5314:0.1154:0.3531	.	3073;3073	Q15413-2;Q15413	.;RYR3_HUMAN	C	3073	ENSP00000373884:R3073C;ENSP00000399610:R3073C	ENSP00000354735:R3073C	R	+	1	0	RYR3	31859783	0.086000	0.21541	0.998000	0.56505	0.213000	0.24496	0.079000	0.14782	0.157000	0.19338	0.650000	0.86243	CGC		0.532	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34072491	C	T	34072491	3	4	61	1	0	0	0	0	1	0	0	0	13807	884	31	1	9475	1	RYR3	15	34072491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25165	34072491	68458901	9208	17193										
RYR3	6263	broad.mit.edu	37	chr15	34109101	34109101	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctccatggctatcagaGattttggatagaaacagagg	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34109101G>T	ENST00000389232.4	+	75	10611	c.10541G>T	c.(10540-10542)aGa>aTa	p.R3514I	RYR3_ENST00000415757.3_Missense_Mutation_p.R3509I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3514					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.R3513I(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GGCTATCAGAGATTTTGGATA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	15											74	69	71					15																	34109101		1865	4102	5967	31896393	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10541G>T	15.37:g.34109101G>T	ENSP00000373884:p.Arg3514Ile		31896393	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220454	0.58560	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.96745	-4.11	5.11	5.11	0.69529	.	0.111235	0.64402	D	0.000008	D	0.93546	0.7940	L	0.58101	1.795	0.58432	D	0.999997	P;P	0.41569	0.755;0.74	B;B	0.39590	0.26;0.304	D	0.92167	0.5740	10	0.62326	D	0.03	.	6.0933	0.20007	0.2174:0.0:0.7826:0.0	.	3509;3514	Q15413-2;Q15413	.;RYR3_HUMAN	I	3514;3513;3509	ENSP00000373884:R3514I	ENSP00000354735:R3509I	R	+	2	0	RYR3	31896393	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.281000	0.72632	2.650000	0.89964	0.655000	0.94253	AGA		0.468	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34109101	G	T	34109101	3	4	61	1	0	0	0	0	1	0	0	0	13807	942	33	2	10839	2	RYR3	15	34109101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36610	34109101	68422291	9209	17194										
RYR3	6263	broad.mit.edu	37	chr15	34110880	34110880	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccgcaacgctctcacggaGaggaggtcagaaccaccagc	12	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34110880G>T	ENST00000389232.4	+	76	10771	c.10701G>T	c.(10699-10701)gaG>gaT	p.E3567D	RYR3_ENST00000415757.3_Missense_Mutation_p.E3562D	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3567					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.E3566D(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTCTCACGGAGAGGAGGTCAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											81	86	84					15																	34110880		2065	4202	6267	31898172	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10701G>T	15.37:g.34110880G>T	ENSP00000373884:p.Glu3567Asp		31898172	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.031569	0.75504	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.97328	-4.34	4.99	3.11	0.35812	.	0.000000	0.85682	D	0.000000	D	0.97773	0.9269	M	0.77616	2.38	0.41148	D	0.986004	D;B	0.67145	0.996;0.33	D;B	0.65874	0.939;0.084	D	0.97308	0.9935	10	0.54805	T	0.06	.	11.1027	0.48184	0.1496:0.0:0.8504:0.0	.	3562;3567	Q15413-2;Q15413	.;RYR3_HUMAN	D	3567;3566;3562	ENSP00000373884:E3567D	ENSP00000354735:E3562D	E	+	3	2	RYR3	31898172	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	2.319000	0.43788	0.698000	0.31739	-0.136000	0.14681	GAG		0.522	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34110880	G	T	34110880	3	4	61	1	0	0	0	0	1	0	0	0	13807	933	33	2	11003	2	RYR3	15	34110880	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1779	34110880	68420512	9210	17195										
RYR3	6263	broad.mit.edu	37	chr15	34123273	34123273	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaagcagattttcaattCtcttacagaatacatccagg	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34123273C>A	ENST00000389232.4	+	86	11514	c.11444C>A	c.(11443-11445)tCt>tAt	p.S3815Y	RYR3_ENST00000415757.3_Missense_Mutation_p.S3810Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3815					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.S3814Y(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ATTTTCAATTCTCTTACAGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											80	73	75					15																	34123273		1875	4102	5977	31910565	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.11444C>A	15.37:g.34123273C>A	ENSP00000373884:p.Ser3815Tyr		31910565	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246525	0.80024	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T	0.68479	-0.33	5.65	5.65	0.86999	RyR/IP3R Homology associated domain (1);	0.000000	0.85682	D	0.000000	T	0.82240	0.4994	M	0.81802	2.56	0.53688	D	0.99997	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.99	D	0.83701	0.0182	10	0.87932	D	0	.	15.3988	0.74818	0.0:0.8616:0.1384:0.0	.	3810;3815	Q15413-2;Q15413	.;RYR3_HUMAN	Y	3815;3814;3811	ENSP00000373884:S3815Y	ENSP00000354735:S3811Y	S	+	2	0	RYR3	31910565	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.763000	0.68818	2.941000	0.99782	0.655000	0.94253	TCT		0.378	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34123273	C	A	34123273	3	1	61	1	0	0	0	0	1	0	0	0	13807	913	32	2	11786	2	RYR3	15	34123273	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12393	34123273	68408119	9211	17196										
RYR3	6263	broad.mit.edu	37	chr15	34134138	34134138	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtggacagaagtgacaAaaaagaagaagcggcggtgt	14	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34134138A>C	ENST00000389232.4	+	91	13181	c.13111A>C	c.(13111-13113)Aaa>Caa	p.K4371Q	RYR3_ENST00000415757.3_Missense_Mutation_p.K4366Q	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4371					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.K4370Q(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGAAGTGACAAAAAAGAAGAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	15											68	77	74					15																	34134138		1893	4116	6009	31921430	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13111A>C	15.37:g.34134138A>C	ENSP00000373884:p.Lys4371Gln		31921430	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	4.778	0.144727	0.09134	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.93906	-3.31	5.55	4.43	0.53597	Ryanodine Receptor TM 4-6 (1);	0.498586	0.20269	N	0.095714	D	0.83709	0.5313	N	0.14661	0.345	0.21697	N	0.999583	B;B	0.17667	0.023;0.001	B;B	0.21151	0.033;0.016	T	0.68032	-0.5516	10	0.10902	T	0.67	.	6.915	0.24355	0.7731:0.1507:0.0763:0.0	.	4366;4371	Q15413-2;Q15413	.;RYR3_HUMAN	Q	4371;4367	ENSP00000373884:K4371Q	ENSP00000354735:K4367Q	K	+	1	0	RYR3	31921430	0.877000	0.30153	0.062000	0.19696	0.072000	0.16883	2.777000	0.47717	1.137000	0.42214	0.533000	0.62120	AAA		0.468	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	34134138	A	C	34134138	3	2	61	1	0	0	0	0	1	0	0	0	13807	15	1	4	13473	4	RYR3	15	34134138	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	10865	34134138	68397254	9212	17197										
RYR3	6263	broad.mit.edu	37	chr15	34134200	34134200	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagctttcacagccaatttCtttaaagggctggaaatcta	8	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34134200C>A	ENST00000389232.4	+	91	13243	c.13173C>A	c.(13171-13173)ttC>ttA	p.F4391L	RYR3_ENST00000415757.3_Missense_Mutation_p.F4386L	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4391					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.F4390L(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAGCCAATTTCTTTAAAGGGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											41	50	47					15																	34134200		1901	4106	6007	31921492	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13173C>A	15.37:g.34134200C>A	ENSP00000373884:p.Phe4391Leu		31921492	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222091	0.58560	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.93133	-3.17	5.18	3.28	0.37604	Ryanodine Receptor TM 4-6 (1);	0.118422	0.64402	D	0.000020	D	0.88119	0.6351	L	0.35644	1.08	0.46044	D	0.998835	B;B	0.28850	0.225;0.019	B;B	0.26864	0.07;0.074	D	0.84121	0.0406	10	0.52906	T	0.07	.	9.8172	0.40860	0.0:0.7781:0.0:0.2219	.	4386;4391	Q15413-2;Q15413	.;RYR3_HUMAN	L	4391;4387	ENSP00000373884:F4391L	ENSP00000354735:F4387L	F	+	3	2	RYR3	31921492	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	0.726000	0.25984	0.748000	0.32831	0.655000	0.94253	TTC		0.502	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34134200	C	A	34134200	3	1	61	1	0	0	0	0	1	0	0	0	13807	912	32	2	13535	2	RYR3	15	34134200	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62	34134200	68397192	9213	17198										
AVEN	57099	broad.mit.edu	37	chr15	34295319	34295319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttcaatatcttgatatCgatcccagttagagacaatc	5	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34295319C>T	ENST00000306730.3	-	2	488	c.359G>A	c.(358-360)cGa>cAa	p.R120Q	CHRM5_ENST00000383263.5_Intron	NM_020371.2	NP_065104.1	Q9NQS1	AVEN_HUMAN	apoptosis, caspase activation inhibitor	120					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	intracellular (GO:0005622)|membrane (GO:0016020)		p.R120Q(1)		cervix(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	7		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)		ATCTTGATATCGATCCCAGTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											152	131	138					15																	34295319		2201	4298	6499	32082611	SO:0001583	missense	57099			AF283508	CCDS10030.1	15q13.1	2011-10-19		2008-07-07	ENSG00000169857	ENSG00000169857			13509	protein-coding gene	gene with protein product	"cell death regulator aven", "programmed cell death 12"	605265				10949025	Standard	XM_005254563		Approved	PDCD12	uc001zhj.3	Q9NQS1	OTTHUMG00000129371	ENST00000306730.3:c.359G>A	15.37:g.34295319C>T	ENSP00000306822:p.Arg120Gln		32082611		Missense_Mutation	SNP	ENST00000306730.3	37	CCDS10030.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607775	0.87258	.	.	ENSG00000169857	ENST00000306730	T	0.59502	0.26	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.77197	-0.2676	10	0.72032	D	0.01	-7.548	17.1238	0.86709	0.0:1.0:0.0:0.0	.	120	Q9NQS1	AVEN_HUMAN	Q	120	ENSP00000306822:R120Q	ENSP00000306822:R120Q	R	-	2	0	AVEN	32082611	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.373000	0.66162	2.357000	0.79964	0.591000	0.81541	CGA		0.403	AVEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251523.2	NM_020371		T	34295319	C	T	34295319	3	4	61	1	0	0	0	0	1	0	0	0	1227	884	31	1	749	1	AVEN	15	34295319	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161119	34295319	68236073	9214	17199										
CHRM5	1133	broad.mit.edu	37	chr15	34356255	34356255	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagcccagacactgagtgCcattctcctggccttcatca	8	15	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34356255C>A	ENST00000383263.5	+	3	2007	c.1337C>A	c.(1336-1338)gCc>gAc	p.A446D	CHRM5_ENST00000557872.1_Missense_Mutation_p.A446D	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	446					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.A446D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	ACACTGAGTGCCATTCTCCTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											183	139	154					15																	34356255		2201	4298	6499	32143547	SO:0001583	missense	1133				CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.1337C>A	15.37:g.34356255C>A	ENSP00000372750:p.Ala446Asp		32143547	Q96RG7	Missense_Mutation	SNP	ENST00000383263.5	37	CCDS10031.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.251026	0.80135	.	.	ENSG00000184984	ENST00000383263	T	0.40225	1.04	5.45	5.45	0.79879	GPCR, rhodopsin-like superfamily (1);	0.051706	0.85682	D	0.000000	T	0.71230	0.3315	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75599	-0.3262	10	0.87932	D	0	-26.0051	19.4929	0.95059	0.0:1.0:0.0:0.0	.	446	P08912	ACM5_HUMAN	D	446	ENSP00000372750:A446D	ENSP00000372750:A446D	A	+	2	0	CHRM5	32143547	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.651000	0.83577	2.835000	0.97688	0.650000	0.86243	GCC		0.512	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			A	34356255	C	A	34356255	3	1	61	1	0	0	0	0	1	0	0	0	3386	739	26	2	1339	2	CHRM5	15	34356255	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60936	34356255	68175137	9215	17200										
PGBD4	161779	broad.mit.edu	37	chr15	34396425	34396425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgcgctatttttgtgccGaatgtgatgttccgctttgt	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34396425G>A	ENST00000397766.2	+	1	2152	c.1693G>A	c.(1693-1695)Gaa>Aaa	p.E565K	EMC7_ENST00000532113.1_5'Flank|EMC7_ENST00000256545.4_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	565								p.E565K(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		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)		TTTTTGTGCCGAATGTGATGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											162	134	143					15																	34396425		2201	4298	6499	32183717	SO:0001583	missense	161779			AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.1693G>A	15.37:g.34396425G>A	ENSP00000380872:p.Glu565Lys		32183717	A1L487|A8K0C6|Q8N9E8	Missense_Mutation	SNP	ENST00000397766.2	37	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	g	0.031	-1.333396	0.01298	.	.	ENSG00000182405	ENST00000397766	T	0.15372	2.43	1.16	-1.48	0.08745	.	1.289640	0.06898	U	0.805460	T	0.04952	0.0133	N	0.04508	-0.205	0.09310	N	1	B	0.27951	0.195	B	0.20767	0.031	T	0.28808	-1.0032	10	0.02654	T	1	.	2.6291	0.04939	0.3986:0.2637:0.3377:0.0	.	565	Q96DM1	PGBD4_HUMAN	K	565	ENSP00000380872:E565K	ENSP00000380872:E565K	E	+	1	0	PGBD4	32183717	0.876000	0.30132	0.000000	0.03702	0.210000	0.24377	0.003000	0.13083	-0.415000	0.07484	0.306000	0.20318	GAA		0.418	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			A	34396425	G	A	34396425	3	1	61	1	0	0	0	0	1	0	0	0	11814	1059	37	1	1695	1	PGBD4	15	34396425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40170	34396425	68134967	9216	17201										
C15orf29	79768	broad.mit.edu	37	chr15	34455820	34455820	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaggaagatcaatgaaatGatcctcaatcttattacaaa	5	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34455820G>T	ENST00000256544.3	-	2	200	c.58C>A	c.(58-60)Cat>Aat	p.H20N		NM_024713.2	NP_078989.1	Q9H079	KTBL1_HUMAN	katanin p80 subunit B-like 1	20						nucleolus (GO:0005730)		p.H20N(1)									TCAATGAAATGATCCTCAATC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	15											62	63	63					15																	34455820		2199	4284	6483	32243112	SO:0001583	missense	79768			AL136908	CCDS10034.1	15q13.2	2012-09-27	2012-09-27	2012-09-27	ENSG00000134152	ENSG00000134152			26199	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 29"	C15orf29		11230166	Standard	NM_024713		Approved	FLJ22557	uc001zhp.3	Q9H079	OTTHUMG00000129368	ENST00000256544.3:c.58C>A	15.37:g.34455820G>T	ENSP00000256544:p.His20Asn		32243112	A8KAF6|Q2TAC0|Q9H670	Missense_Mutation	SNP	ENST00000256544.3	37	CCDS10034.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.243263	0.39697	.	.	ENSG00000134152	ENST00000256544	.	.	.	4.12	4.12	0.48240	.	0.328559	0.30519	N	0.009454	T	0.26231	0.0640	L	0.27053	0.805	0.22989	N	0.998462	B	0.12013	0.005	B	0.09377	0.004	T	0.10428	-1.0630	9	0.14252	T	0.57	.	10.2457	0.43339	0.0934:0.0:0.9066:0.0	.	20	Q9H079	CO029_HUMAN	N	20	.	ENSP00000256544:H20N	H	-	1	0	C15orf29	32243112	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	2.479000	0.45197	2.299000	0.77371	0.557000	0.71058	CAT		0.279	KATNBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251520.1	NM_024713		T	34455820	G	T	34455820	3	4	61	1	0	0	0	0	1	0	0	0	1793	1290	45	2	892	2	C15orf29	15	34455820	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59395	34455820	68075572	9217	17202										
SLC12A6	9990	broad.mit.edu	37	chr15	34530594	34530594	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggcagcagttgtcactcGaactgtgcctagggagaaaa	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34530594G>A	ENST00000354181.3	-	21	3133	c.2641C>T	c.(2641-2643)Cga>Tga	p.R881*	SLC12A6_ENST00000458406.2_Nonsense_Mutation_p.R822*|SLC12A6_ENST00000560164.1_Nonsense_Mutation_p.R693*|SLC12A6_ENST00000560611.1_Nonsense_Mutation_p.R881*|SLC12A6_ENST00000290209.5_Nonsense_Mutation_p.R830*|SLC12A6_ENST00000397707.2_Nonsense_Mutation_p.R866*|SLC12A6_ENST00000451844.2_Nonsense_Mutation_p.R693*|SLC12A6_ENST00000397702.2_Nonsense_Mutation_p.R822*|SLC12A6_ENST00000558589.1_Nonsense_Mutation_p.R872*|SLC12A6_ENST00000558667.1_Nonsense_Mutation_p.R881*			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	881					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)	p.R830*(1)		central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GTTGTCACTCGAACTGTGCCT	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											90	80	83					15																	34530594		2201	4298	6499	32317886	SO:0001587	stop_gained	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.2641C>T	15.37:g.34530594G>A	ENSP00000346112:p.Arg881*		32317886	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Nonsense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	G	43	10.319784	0.99382	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	.	.	.	5.01	5.01	0.66863	.	0.132353	0.51477	D	0.000085	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.2625	0.87073	0.0:0.0:1.0:0.0	.	.	.	.	X	830;866;872;822;822;693	.	ENSP00000290209:R830X	R	-	1	2	SLC12A6	32317886	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.383000	0.73172	2.586000	0.87340	0.655000	0.94253	CGA		0.458	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		A	34530594	G	A	34530594	4	1	61	1	0	0	0	0	0	1	0	0	14424	1066	37	1	835	1	SLC12A6	15	34530594	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74774	34530594	68000798	9218	17203										
C15orf55	256646	broad.mit.edu	37	chr15	34649003	34649003	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatagaacctgtcaacataCtagatgttaaagatgactgt	7	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:34649003C>A	ENST00000333756.4	+	7	2865	c.2710C>A	c.(2710-2712)Cta>Ata	p.L904I	NUTM1_ENST00000438749.3_Missense_Mutation_p.L922I|NUTM1_ENST00000537011.1_Missense_Mutation_p.L932I	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	904						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L904I(1)									TGTCAACATACTAGATGTTAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											59	56	57					15																	34649003		2201	4298	6499	32436295	SO:0001583	missense	256646			AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.2710C>A	15.37:g.34649003C>A	ENSP00000329448:p.Leu904Ile		32436295	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.588706	0.46110	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.12465	2.69;2.68;2.7	5.08	1.01	0.19927	.	0.491345	0.17250	N	0.181212	T	0.14960	0.0361	M	0.64997	1.995	0.09310	N	1	P;P;P	0.45957	0.793;0.869;0.793	B;B;B	0.43680	0.245;0.427;0.245	T	0.11155	-1.0599	10	0.66056	D	0.02	.	5.3013	0.15780	0.0:0.5027:0.3198:0.1775	.	922;932;904	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	I	932;922;904	ENSP00000444896:L932I;ENSP00000407031:L922I;ENSP00000329448:L904I	ENSP00000329448:L904I	L	+	1	2	C15orf55	32436295	0.014000	0.17966	0.015000	0.15790	0.004000	0.04260	0.398000	0.20899	0.040000	0.15660	-0.909000	0.02823	CTA		0.512	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34649003	C	A	34649003	3	1	61	1	0	0	0	0	1	0	0	0	1807	564	20	2	2736	2	C15orf55	15	34649003	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118409	34649003	67882389	9219	17204										
AQR	9716	broad.mit.edu	37	chr15	35152273	35152273	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgtgtagtctgtatcaaAtgcatgtacatgttgtatac	9	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:35152273A>G	ENST00000156471.5	-	34	4338	c.4113T>C	c.(4111-4113)caT>caC	p.H1371H		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1371					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.H1371H(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCTGTATCAAATGCATGTACA	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	15											167	151	156					15																	35152273		1809	4067	5876	32939565	SO:0001819	synonymous_variant	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.4113T>C	15.37:g.35152273A>G			32939565	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	37	CCDS42013.1																																																																																				0.303	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35152273	A	G	35152273	2	3	61	1	0	0	0	0	0	0	0	1	835	98	4	4		4	AQR	15	35152273	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	503270	35152273	67379119	9220	17205										
AQR	9716	broad.mit.edu	37	chr15	35174815	35174815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatctgtccagtccacttCgaagcaattcagaggctctg	9	11	3	2	rs370660482		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:35174815C>T	ENST00000156471.5	-	27	3278	c.3053G>A	c.(3052-3054)cGa>cAa	p.R1018Q		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1018					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1018Q(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		CAGTCCACTTCGAAGCAATTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	15						C	GLN/ARG	2,3668		0,2,1833	96	91	93		3053	5.7	1	15		93	0,8194		0,0,4097	no	missense	AQR	NM_014691.2	43	0,2,5930	TT,TC,CC		0.0,0.0545,0.0169	probably-damaging	1018/1486	35174815	2,11862	1835	4097	5932	32962107	SO:0001583	missense	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3053G>A	15.37:g.35174815C>T	ENSP00000156471:p.Arg1018Gln		32962107	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	37	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.876509	0.97055	5.45E-4	0.0	ENSG00000021776	ENST00000156471;ENST00000543879	T	0.81247	-1.47	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.91088	0.7195	M	0.85859	2.78	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.90977	0.4824	10	0.52906	T	0.07	-9.374	19.9019	0.96988	0.0:1.0:0.0:0.0	.	1018	O60306	AQR_HUMAN	Q	1018	ENSP00000156471:R1018Q	ENSP00000156471:R1018Q	R	-	2	0	AQR	32962107	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.090000	0.71397	2.698000	0.92095	0.591000	0.81541	CGA		0.393	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		T	35174815	C	T	35174815	3	4	61	1	0	0	0	0	1	0	0	0	835	884	31	1	1440	1	AQR	15	35174815	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22542	35174815	67356577	9221	17206										
AQR	9716	broad.mit.edu	37	chr15	35192958	35192958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatctgattgggcattttcGaataatgtgcactacttggg	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:35192958G>A	ENST00000156471.5	-	20	2333	c.2108C>T	c.(2107-2109)tCg>tTg	p.S703L		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	703					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S703L(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GGGCATTTTCGAATAATGTGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											141	129	133					15																	35192958		1922	4137	6059	32980250	SO:0001583	missense	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2108C>T	15.37:g.35192958G>A	ENSP00000156471:p.Ser703Leu		32980250	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	37	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723226	0.68959	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.93953	-3.32	5.78	5.78	0.91487	.	0.057776	0.64402	D	0.000001	D	0.93370	0.7886	M	0.78223	2.4	0.80722	D	1	P	0.43826	0.818	B	0.39738	0.308	D	0.92195	0.5763	10	0.32370	T	0.25	-15.9881	20.3754	0.98918	0.0:0.0:1.0:0.0	.	703	O60306	AQR_HUMAN	L	703	ENSP00000156471:S703L	ENSP00000156471:S703L	S	-	2	0	AQR	32980250	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.378000	0.97191	2.894000	0.99253	0.591000	0.81541	TCG		0.413	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		A	35192958	G	A	35192958	3	1	61	1	0	0	0	0	1	0	0	0	835	1059	37	1	2413	1	AQR	15	35192958	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18143	35192958	67338434	9222	17207										
AQR	9716	broad.mit.edu	37	chr15	35240485	35240485	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccatgcaggcacgttttCtctaaacttctcattcacca	4	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:35240485C>A	ENST00000156471.5	-	5	535	c.310G>T	c.(310-312)Gaa>Taa	p.E104*		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	104					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E104*(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GGCACGTTTTCTCTAAACTTC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											159	152	154					15																	35240485		1883	4113	5996	33027777	SO:0001587	stop_gained	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.310G>T	15.37:g.35240485C>A	ENSP00000156471:p.Glu104*		33027777	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Nonsense_Mutation	SNP	ENST00000156471.5	37	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.557972	0.86231	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-20.6404	20.4192	0.99033	0.0:1.0:0.0:0.0	.	.	.	.	X	104	.	ENSP00000156471:E104X	E	-	1	0	AQR	33027777	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.745000	0.85046	2.831000	0.97527	0.650000	0.86243	GAA		0.378	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		A	35240485	C	A	35240485	4	1	61	1	0	0	0	0	0	1	0	0	835	922	32	2	4271	2	AQR	15	35240485	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47527	35240485	67290907	9223	17208										
ATPBD4	89978	broad.mit.edu	37	chr15	35814428	35814428	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcaaatgcatgtgaaaatCttggagattcagagcatcat	8	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:35814428C>T	ENST00000256538.4	-	3	339				DPH6_ENST00000440392.2_Missense_Mutation_p.D122N	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6						peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)	p.D122N(1)									ATGTGAAAATCTTGGAGATTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											83	72	75					15																	35814428		1566	3580	5146	33601720	SO:0001627	intron_variant	89978				CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"diphthine--ammonia ligase"		"ATP binding domain 4", "DPH6 homolog (S. cerevisiae)"	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.312+16046G>A	15.37:g.35814428C>T			33601720	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	37	CCDS10043.1	.	.	.	.	.	.	.	.	.	.	C	0.650	-0.809843	0.02798	.	.	ENSG00000134146	ENST00000440392	T	0.44083	0.93	5.33	3.44	0.39384	.	.	.	.	.	T	0.17280	0.0415	.	.	.	0.20926	N	0.99982	B	0.02656	0.0	B	0.08055	0.003	T	0.29397	-1.0013	8	0.02654	T	1	.	7.0823	0.25237	0.139:0.714:0.0:0.1469	.	122	B3KWG1	.	N	122	ENSP00000406976:D122N	ENSP00000406976:D122N	D	-	1	0	ATPBD4	33601720	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.969000	0.40510	0.806000	0.34183	0.655000	0.94253	GAT		0.428	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650		T	35814428	C	T	35814428	1	4	61	0	1	0	0	0	0	0	0	0	1203	913	32	3		3	ATPBD4	15	35814428	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	573943	35814428	66716964	9224	17209										
MEIS2	4212	broad.mit.edu	37	chr15	37188835	37188835	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttggaacttgcctgctcGatttgactggtcaatcatgg	10	9	2	1	rs367563077		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:37188835G>A	ENST00000561208.1	-	10	1448	c.1030C>T	c.(1030-1032)Cga>Tga	p.R344*	MEIS2_ENST00000397624.3_Nonsense_Mutation_p.R256*|MEIS2_ENST00000397620.2_Nonsense_Mutation_p.R256*|MEIS2_ENST00000382766.2_Nonsense_Mutation_p.R344*|MEIS2_ENST00000219869.9_Nonsense_Mutation_p.R198*|MEIS2_ENST00000340545.5_Nonsense_Mutation_p.R331*|MEIS2_ENST00000559408.1_5'UTR|MEIS2_ENST00000559085.1_Nonsense_Mutation_p.R331*|MEIS2_ENST00000424352.2_Nonsense_Mutation_p.R344*|MEIS2_ENST00000338564.5_Nonsense_Mutation_p.R344*|MEIS2_ENST00000557796.2_Nonsense_Mutation_p.R331*|MEIS2_ENST00000559561.1_Nonsense_Mutation_p.R344*|MEIS2_ENST00000444725.1_Nonsense_Mutation_p.R344*			O14770	MEIS2_HUMAN	Meis homeobox 2	344	Transcriptional activation domain.				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R344*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TTGCCTGCTCGATTTGACTGG	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	15											179	154	163					15																	37188835		2201	4297	6498	34976127	SO:0001587	stop_gained	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.1030C>T	15.37:g.37188835G>A	ENSP00000453793:p.Arg344*		34976127	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Nonsense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	G	40	8.199426	0.98701	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.3478	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	X	344;344;344;344;344;331;331;256;198	.	ENSP00000219869:R198X	R	-	1	2	MEIS2	34976127	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.807000	0.99171	2.937000	0.99478	0.650000	0.86243	CGA		0.398	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		A	37188835	G	A	37188835	4	1	61	1	0	0	0	0	0	1	0	0	9498	1066	37	1	478	1	MEIS2	15	37188835	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1374407	37188835	65342557	9225	17210										
MEIS2	4212	broad.mit.edu	37	chr15	37390245	37390245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccggcatgacattggggtgCggggcgtgcgcgccgtagtg	20	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:37390245C>T	ENST00000561208.1	-	2	586	c.168G>A	c.(166-168)ccG>ccA	p.P56P	MEIS2_ENST00000397624.3_5'UTR|MEIS2_ENST00000397620.2_5'UTR|MEIS2_ENST00000382766.2_Silent_p.P56P|MEIS2_ENST00000219869.9_5'UTR|MEIS2_ENST00000340545.5_Silent_p.P43P|RP11-128A17.1_ENST00000559509.1_RNA|MEIS2_ENST00000559085.1_Silent_p.P43P|MEIS2_ENST00000424352.2_Silent_p.P56P|MEIS2_ENST00000338564.5_Silent_p.P56P|MEIS2_ENST00000557796.2_Silent_p.P43P|MEIS2_ENST00000559561.1_Silent_p.P56P|MEIS2_ENST00000444725.1_Silent_p.P56P			O14770	MEIS2_HUMAN	Meis homeobox 2	56					eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.P56P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		CATTGGGGTGCGGGGCGTGCG	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	15											59	60	59					15																	37390245		2201	4297	6498	35177537	SO:0001819	synonymous_variant	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.168G>A	15.37:g.37390245C>T			35177537	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Silent	SNP	ENST00000561208.1	37	CCDS10044.1																																																																																				0.677	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		T	37390245	C	T	37390245	2	4	61	1	0	0	0	0	0	0	0	1	9498	755	27	1		1	MEIS2	15	37390245	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201410	37390245	65141147	9226	17211										
MEIS2	4212	broad.mit.edu	37	chr15	37391659	37391659	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagatttaaacctaccctTtgcgccatcagtctgcgctc	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:37391659T>C	ENST00000561208.1	-	1	427	c.9A>G	c.(7-9)caA>caG	p.Q3Q	MEIS2_ENST00000397624.3_5'Flank|MEIS2_ENST00000397620.2_5'Flank|MEIS2_ENST00000382766.2_Silent_p.Q3Q|MEIS2_ENST00000219869.9_5'UTR|MEIS2_ENST00000340545.5_Intron|RP11-128A17.1_ENST00000559509.1_RNA|MEIS2_ENST00000559085.1_5'Flank|MEIS2_ENST00000424352.2_Silent_p.Q3Q|MEIS2_ENST00000338564.5_Silent_p.Q3Q|MEIS2_ENST00000557796.2_5'Flank|MEIS2_ENST00000559561.1_Silent_p.Q3Q|MEIS2_ENST00000444725.1_Silent_p.Q3Q			O14770	MEIS2_HUMAN	Meis homeobox 2	3					eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.Q3Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		AACCTACCCTTTGCGCCATCA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	15											126	134	131					15																	37391659		2200	4297	6497	35178951	SO:0001819	synonymous_variant	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.9A>G	15.37:g.37391659T>C			35178951	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Silent	SNP	ENST00000561208.1	37	CCDS10044.1																																																																																				0.458	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		C	37391659	T	C	37391659	2	2	61	1	0	0	0	0	0	0	0	1	9498	1838	64	4		4	MEIS2	15	37391659	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1414	37391659	65139733	9227	17212										
SPRED1	161742	broad.mit.edu	37	chr15	38591612	38591612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgagctgtggtgatgacccGagatgactcaagtggtggat	16	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:38591612G>A	ENST00000299084.4	+	2	931	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	SPRED1_ENST00000561205.1_3'UTR	NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	24	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.R24P(1)|p.R24Q(1)		kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		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)		GTGATGACCCGAGATGACTCA	0.458									Legius syndrome																												Melanoma(196;2146 2959 7698 16532)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	15											125	115	118					15																	38591612		2200	4297	6497	36378904	SO:0001583	missense	161742	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 147"	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.71G>A	15.37:g.38591612G>A	ENSP00000299084:p.Arg24Gln		36378904	B2RPJ8|Q05D53|Q8N256	Missense_Mutation	SNP	ENST00000299084.4	37	CCDS32193.1	.	.	.	.	.	.	.	.	.	.	G	36	5.727502	0.96847	.	.	ENSG00000166068	ENST00000299084	D	0.86366	-2.11	5.72	5.72	0.89469	EVH1 (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.93953	0.8064	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93226	0.6613	10	0.48119	T	0.1	-10.0701	19.8868	0.96915	0.0:0.0:1.0:0.0	.	24	Q7Z699	SPRE1_HUMAN	Q	24	ENSP00000299084:R24Q	ENSP00000299084:R24Q	R	+	2	0	SPRED1	36378904	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.864000	0.99589	2.709000	0.92574	0.655000	0.94253	CGA		0.458	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1			A	38591612	G	A	38591612	3	1	61	1	0	0	0	0	1	0	0	0	15131	1058	37	1	77	1	SPRED1	15	38591612	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1199953	38591612	63939780	9228	17213										
FAM98B	283742	broad.mit.edu	37	chr15	38762474	38762474	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagatattacagaacaaGaaacataaaaattctcaatt	3	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:38762474G>T	ENST00000491535.1	+	4	407	c.399G>T	c.(397-399)aaG>aaT	p.K133N	FAM98B_ENST00000397609.2_Missense_Mutation_p.K133N	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	133						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)	p.K133N(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		TACAGAACAAGAAACATAAAA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	15											26	27	27					15																	38762474		2194	4287	6481	36549766	SO:0001583	missense	283742				CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.399G>T	15.37:g.38762474G>T	ENSP00000453166:p.Lys133Asn		36549766	A8MUW5|Q8N935	Missense_Mutation	SNP	ENST00000491535.1	37	CCDS42015.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509846	0.64522	.	.	ENSG00000171262	ENST00000397609;ENST00000305752	T	0.50001	0.76	4.78	3.84	0.44239	.	0.325783	0.36101	N	0.002790	T	0.59636	0.2208	L	0.49640	1.575	0.53005	D	0.999968	D;P	0.76494	0.999;0.941	D;P	0.72625	0.978;0.676	T	0.56080	-0.8038	10	0.27082	T	0.32	-16.6284	13.8186	0.63308	0.0756:0.0:0.9244:0.0	.	133;133	A8MUW5;Q52LJ0	.;FA98B_HUMAN	N	133	ENSP00000380734:K133N	ENSP00000303412:K133N	K	+	3	2	FAM98B	36549766	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.590000	0.46154	1.346000	0.45694	0.585000	0.79938	AAG		0.274	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		T	38762474	G	T	38762474	3	4	61	1	0	0	0	0	1	0	0	0	5676	933	33	2	413	2	FAM98B	15	38762474	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170862	38762474	63768918	9229	17214										
RASGRP1	10125	broad.mit.edu	37	chr15	38803830	38803830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatttcatgtgggacatgcGaacttgtctccttgagcctc	10	10	2	2	rs369326621		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:38803830G>A	ENST00000310803.5	-	8	1118	c.941C>T	c.(940-942)tCg>tTg	p.S314L	RASGRP1_ENST00000450598.2_Missense_Mutation_p.S314L|RASGRP1_ENST00000539159.1_Missense_Mutation_p.S266L|RASGRP1_ENST00000561180.1_Missense_Mutation_p.S365L|RASGRP1_ENST00000558164.1_Missense_Mutation_p.S314L|RASGRP1_ENST00000559830.1_Missense_Mutation_p.S314L	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	314	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.S314L(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TGGGACATGCGAACTTGTCTC	0.493													G|||	1	0.000199681	0	0	5008	,	,		22735	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	15						G	LEU/SER,LEU/SER	0,4002		0,0,2001	121	121	121		941,941	5.4	1	15		121	1,8347		0,1,4173	no	missense,missense	RASGRP1	NM_001128602.1,NM_005739.3	145,145	0,1,6174	AA,AG,GG		0.012,0.0,0.0081	possibly-damaging,possibly-damaging	314/763,314/798	38803830	1,12349	2001	4174	6175	36591122	SO:0001583	missense	10125			AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.941C>T	15.37:g.38803830G>A	ENSP00000310244:p.Ser314Leu		36591122	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	37	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	G	34	5.335762	0.95758	0.0	1.2E-4	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.38	5.38	0.77491	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.220979	0.40640	N	0.001060	T	0.42177	0.1191	M	0.69358	2.11	0.80722	D	1	D;P;P;P	0.53462	0.96;0.782;0.782;0.859	P;P;B;B	0.46110	0.504;0.473;0.393;0.342	T	0.44003	-0.9356	10	0.72032	D	0.01	-9.966	19.3333	0.94303	0.0:0.0:1.0:0.0	.	314;314;314;314	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	L	314;314;314;314;266;314;314	ENSP00000310244:S314L;ENSP00000388540:S314L;ENSP00000444762:S266L;ENSP00000413105:S314L	ENSP00000310244:S314L	S	-	2	0	RASGRP1	36591122	1.000000	0.71417	0.967000	0.41034	0.994000	0.84299	9.657000	0.98554	2.793000	0.96121	0.655000	0.94253	TCG		0.493	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		A	38803830	G	A	38803830	3	1	61	1	0	0	0	0	1	0	0	0	13111	1059	37	1	1492	1	RASGRP1	15	38803830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41356	38803830	63727562	9230	17215										
THBS1	7057	broad.mit.edu	37	chr15	39874568	39874568	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccaagacctggtggatgCtgtgcgggcagaaaagggtt	16	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:39874568C>A	ENST00000260356.5	+	3	407	c.242C>A	c.(241-243)gCt>gAt	p.A81D		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	81	Heparin-binding.|Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.A81D(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CTGGTGGATGCTGTGCGGGCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	15											64	60	62					15																	39874568		2200	4297	6497	37661860	SO:0001583	missense	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.242C>A	15.37:g.39874568C>A	ENSP00000260356:p.Ala81Asp		37661860	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049261	0.55218	.	.	ENSG00000137801	ENST00000260356;ENST00000397591	T;T	0.02177	4.41;4.41	5.28	5.28	0.74379	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.35903	N	0.002903	T	0.02848	0.0085	L	0.47716	1.5	0.52501	D	0.999957	P	0.41597	0.756	B	0.34180	0.177	T	0.52268	-0.8598	10	0.62326	D	0.03	-21.8482	13.4254	0.61022	0.0:0.9223:0.0:0.0777	.	81	P07996	TSP1_HUMAN	D	81	ENSP00000260356:A81D;ENSP00000380720:A81D	ENSP00000260356:A81D	A	+	2	0	THBS1	37661860	1.000000	0.71417	0.927000	0.36925	0.660000	0.38997	4.510000	0.60455	2.741000	0.93983	0.563000	0.77884	GCT		0.617	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39874568	C	A	39874568	3	1	61	1	0	0	0	0	1	0	0	0	15892	797	28	2	248	2	THBS1	15	39874568	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1070738	39874568	62656824	9231	17216										
THBS1	7057	broad.mit.edu	37	chr15	39882794	39882794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgatgcctgtgatgatgaCgatgacaatgataaaattcc	11	6	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:39882794C>T	ENST00000260356.5	+	14	2388	c.2223C>T	c.(2221-2223)gaC>gaT	p.D741D	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	741					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.D741D(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GTGATGATGACGATGACAATG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	15											160	149	153					15																	39882794		2200	4297	6497	37670086	SO:0001819	synonymous_variant	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2223C>T	15.37:g.39882794C>T			37670086	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																				0.403	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39882794	C	T	39882794	2	4	61	1	0	0	0	0	0	0	0	1	15892	535	19	1		1	THBS1	15	39882794	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8226	39882794	62648598	9232	17217										
FSIP1	161835	broad.mit.edu	37	chr15	39910236	39910236	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctcaagcatatctgcatCttctacctcagttttctgga	5	12	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:39910236C>A	ENST00000350221.3	-	11	1608	c.1399G>T	c.(1399-1401)Gat>Tat	p.D467Y		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	467								p.D467Y(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ATATCTGCATCTTCTACCTCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	15											150	142	145					15																	39910236		2200	4297	6497	37697528	SO:0001583	missense	161835			BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1399G>T	15.37:g.39910236C>A	ENSP00000280236:p.Asp467Tyr		37697528	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	C	8.436	0.849790	0.17034	.	.	ENSG00000150667	ENST00000350221	T	0.19938	2.11	4.94	3.06	0.35304	.	0.137395	0.33572	N	0.004779	T	0.27169	0.0666	L	0.32530	0.975	0.09310	N	1	D	0.67145	0.996	D	0.65874	0.939	T	0.02464	-1.1155	9	.	.	.	-3.5571	6.9048	0.24303	0.0:0.6893:0.1475:0.1632	.	467	Q8NA03	FSIP1_HUMAN	Y	467	ENSP00000280236:D467Y	.	D	-	1	0	FSIP1	37697528	0.648000	0.27313	0.007000	0.13788	0.002000	0.02628	1.858000	0.39408	1.450000	0.47717	-0.136000	0.14681	GAT		0.423	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		A	39910236	C	A	39910236	3	1	61	1	0	0	0	0	1	0	0	0	6093	913	32	2	354	2	FSIP1	15	39910236	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27442	39910236	62621156	9233	17218										
FSIP1	161835	broad.mit.edu	37	chr15	40030386	40030386	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaccataaccactgggtttCttgattccttggccaactac	6	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40030386C>A	ENST00000350221.3	-	8	1006	c.797G>T	c.(796-798)aGa>aTa	p.R266I	FSIP1_ENST00000559692.1_5'Flank	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	266								p.R266I(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		CACTGGGTTTCTTGATTCCTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	15											111	116	114					15																	40030386		2203	4300	6503	37817678	SO:0001583	missense	161835			BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.797G>T	15.37:g.40030386C>A	ENSP00000280236:p.Arg266Ile		37817678	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630058	0.67015	.	.	ENSG00000150667	ENST00000350221	T	0.24350	1.86	6.17	5.08	0.68730	.	0.252307	0.34986	N	0.003529	T	0.32164	0.0820	L	0.44542	1.39	0.31627	N	0.649594	D	0.59767	0.986	P	0.54100	0.742	T	0.16217	-1.0410	9	.	.	.	-16.3769	11.3007	0.49304	0.0:0.9068:0.0:0.0932	.	266	Q8NA03	FSIP1_HUMAN	I	266	ENSP00000280236:R266I	.	R	-	2	0	FSIP1	37817678	0.967000	0.33354	0.866000	0.34008	0.918000	0.54935	1.682000	0.37628	2.941000	0.99782	0.655000	0.94253	AGA		0.393	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		A	40030386	C	A	40030386	3	1	61	1	0	0	0	0	1	0	0	0	6093	913	32	2	968	2	FSIP1	15	40030386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120150	40030386	62501006	9234	17219										
EIF2AK4	440275	broad.mit.edu	37	chr15	40265918	40265918	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttgaagaattacaacttCttggtaaaggagcttttgga	10	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40265918C>A	ENST00000263791.5	+	11	1829	c.1786C>A	c.(1786-1788)Ctt>Att	p.L596I	EIF2AK4_ENST00000559624.1_Missense_Mutation_p.L596I|EIF2AK4_ENST00000382727.2_Missense_Mutation_p.L596I	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	596	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)	p.L596I(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATTACAACTTCTTGGTAAAGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15											131	121	124					15																	40265918		1886	4111	5997	38053210	SO:0001583	missense	440275			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1786C>A	15.37:g.40265918C>A	ENSP00000263791:p.Leu596Ile		38053210	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	C	31	5.080573	0.94050	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.30981	1.51;1.51	5.7	5.7	0.88788	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.44244	0.1284	N	0.17872	0.535	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.41770	-0.9490	10	0.54805	T	0.06	-16.6238	19.8894	0.96925	0.0:1.0:0.0:0.0	.	596;596	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	I	596	ENSP00000263791:L596I;ENSP00000372174:L596I	ENSP00000263791:L596I	L	+	1	0	EIF2AK4	38053210	1.000000	0.71417	0.968000	0.41197	0.982000	0.71751	5.858000	0.69532	2.704000	0.92352	0.586000	0.80456	CTT		0.448	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			A	40265918	C	A	40265918	3	1	61	1	0	0	0	0	1	0	0	0	5010	913	32	2	1828	2	EIF2AK4	15	40265918	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235532	40265918	62265474	9235	17220										
EIF2AK4	440275	broad.mit.edu	37	chr15	40318189	40318189	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttaaggttaagtctttCgagaaggaaaggcagacaga	11	5	1	3	rs200983505		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40318189C>T	ENST00000263791.5	+	33	4444	c.4401C>T	c.(4399-4401)ttC>ttT	p.F1467F	EIF2AK4_ENST00000382727.2_Silent_p.F1439F	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1467	Histidyl-tRNA synthetase-like.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)	p.F1467F(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TTAAGTCTTTCGAGAAGGAAA	0.428													C|||	1	0.000199681	0	0	5008	,	,		19403	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											82	77	78					15																	40318189		1938	4141	6079	38105481	SO:0001819	synonymous_variant	440275			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4401C>T	15.37:g.40318189C>T			38105481	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	37	CCDS42016.1																																																																																				0.428	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			T	40318189	C	T	40318189	2	4	61	1	0	0	0	0	0	0	0	1	5010	883	31	1		1	EIF2AK4	15	40318189	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52271	40318189	62213203	9236	17221										
BUB1B	701	broad.mit.edu	37	chr15	40504802	40504802	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagctgttatcaatatcaaGatggctgtattgtttggcac	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40504802G>T	ENST00000287598.6	+	19	2683	c.2488G>T	c.(2488-2490)Gat>Tat	p.D830Y	BUB1B_ENST00000412359.3_Missense_Mutation_p.D844Y	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	830	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D830Y(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		TCAATATCAAGATGGCTGTAT	0.343			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																													yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	1	Substitution - Missense(1)	large_intestine(1)	15											113	109	110					15																	40504802		2203	4300	6503	38292094	SO:0001583	missense	701	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"budding uninhibited by benzimidazoles 1 (yeast homolog), beta", "budding uninhibited by benzimidazoles 1 homolog beta (yeast)"			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.2488G>T	15.37:g.40504802G>T	ENSP00000287598:p.Asp830Tyr		38292094	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.325042	0.60634	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.22539	1.95;1.95	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);	0.083241	0.49916	D	0.000128	T	0.44746	0.1308	M	0.77406	2.37	0.41792	D	0.989872	D	0.89917	1.0	D	0.83275	0.996	T	0.46048	-0.9219	10	0.87932	D	0	-18.0252	9.3176	0.37943	0.1584:0.0:0.8416:0.0	.	830	O60566	BUB1B_HUMAN	Y	830;844;713	ENSP00000287598:D830Y;ENSP00000398470:D844Y	ENSP00000287598:D830Y	D	+	1	0	BUB1B	38292094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.217000	0.51184	2.368000	0.80403	0.655000	0.94253	GAT		0.343	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			T	40504802	G	T	40504802	3	4	61	1	0	0	0	0	1	0	0	0	1574	942	33	2	2562	2	BUB1B	15	40504802	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186613	40504802	62026590	9237	17222										
BUB1B	701	broad.mit.edu	37	chr15	40512795	40512795	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgaattgtggaataaattCtttgtgcggattctgaatgc	12	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40512795C>A	ENST00000287598.6	+	23	3183	c.2988C>A	c.(2986-2988)ttC>ttA	p.F996L	RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000441369.1_Intron|PAK6_ENST00000453867.1_Intron|BUB1B_ENST00000412359.3_Missense_Mutation_p.F1010L	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	996	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F996L(2)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GGAATAAATTCTTTGTGCGGA	0.358			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																													yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	2	Substitution - Missense(2)	large_intestine(2)	15											109	111	111					15																	40512795		2203	4300	6503	38300087	SO:0001583	missense	701	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"budding uninhibited by benzimidazoles 1 (yeast homolog), beta", "budding uninhibited by benzimidazoles 1 homolog beta (yeast)"			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.2988C>A	15.37:g.40512795C>A	ENSP00000287598:p.Phe996Leu		38300087	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.301630	0.60195	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.14144	2.54;2.53	5.96	5.04	0.67666	.	0.063133	0.64402	N	0.000003	T	0.09598	0.0236	L	0.41824	1.3	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.08680	-1.0710	10	0.02654	T	1	-8.1168	9.8247	0.40905	0.0:0.8582:0.0:0.1418	.	996	O60566	BUB1B_HUMAN	L	996;1010;879	ENSP00000287598:F996L;ENSP00000398470:F1010L	ENSP00000287598:F996L	F	+	3	2	BUB1B	38300087	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.467000	0.35321	2.832000	0.97577	0.655000	0.94253	TTC		0.358	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			A	40512795	C	A	40512795	3	1	61	1	0	0	0	0	1	0	0	0	1574	912	32	2	3078	2	BUB1B	15	40512795	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7993	40512795	62018597	9238	17223										
DISP2	85455	broad.mit.edu	37	chr15	40661141	40661141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggcacctccaggcctccGccgtggttggttcactagcc	11	16	1	0	rs150424497		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40661141G>A	ENST00000267889.3	+	8	2915	c.2828G>A	c.(2827-2829)cGc>cAc	p.R943H	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	943					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.R943H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCAGGCCTCCGCCGTGGTTGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	69	72	71		2828	1.9	0	15	dbSNP_134	71	0,8600		0,0,4300	no	missense	DISP2	NM_033510.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	943/1402	40661141	1,13005	2203	4300	6503	38448433	SO:0001583	missense	85455			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2828G>A	15.37:g.40661141G>A	ENSP00000267889:p.Arg943His		38448433	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	G	6.619	0.482712	0.12581	2.27E-4	0.0	ENSG00000140323	ENST00000267889	D	0.91996	-2.95	4.85	1.85	0.25348	.	0.439260	0.24808	N	0.035425	D	0.87807	0.6270	L	0.57536	1.79	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.77493	-0.2567	10	0.44086	T	0.13	-8.3888	6.9909	0.24755	0.5791:0.0:0.4209:0.0	.	943	A7MBM2	DISP2_HUMAN	H	943	ENSP00000267889:R943H	ENSP00000267889:R943H	R	+	2	0	DISP2	38448433	0.002000	0.14202	0.049000	0.19019	0.596000	0.36781	1.657000	0.37366	0.223000	0.20920	0.555000	0.69702	CGC		0.612	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		A	40661141	G	A	40661141	3	1	61	1	0	0	0	0	1	0	0	0	4551	1087	38	1	2858	1	DISP2	15	40661141	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148346	40661141	61870251	9239	17224										
C15orf23	90417	broad.mit.edu	37	chr15	40683721	40683721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgagaccctggcatcacGacaagaatccactactgatc	8	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40683721G>A	ENST00000249776.8	+	7	828	c.713G>A	c.(712-714)cGa>cAa	p.R238Q	KNSTRN_ENST00000416151.2_Missense_Mutation_p.R238Q|KNSTRN_ENST00000448395.2_Intron|KNSTRN_ENST00000608100.1_Missense_Mutation_p.R160Q	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein									p.R238Q(1)									CTGGCATCACGACAAGAATCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											123	115	118					15																	40683721		2025	4188	6213	38471013	SO:0001583	missense	90417			AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.713G>A	15.37:g.40683721G>A	ENSP00000249776:p.Arg238Gln		38471013		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	G	2.375	-0.343359	0.05243	.	.	ENSG00000128944	ENST00000249776;ENST00000416151	T;T	0.20463	2.07;2.07	5.18	-4.78	0.03209	.	1.782710	0.02546	N	0.095169	T	0.07683	0.0193	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42481	-0.9449	10	0.05436	T	0.98	-5.1946	11.7381	0.51778	0.5953:0.0:0.4047:0.0	.	238;238	Q9Y448-2;Q9Y448	.;T4AF1_HUMAN	Q	238	ENSP00000249776:R238Q;ENSP00000391233:R238Q	ENSP00000249776:R238Q	R	+	2	0	C15orf23	38471013	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.158000	0.16422	-1.164000	0.02790	-1.655000	0.00754	CGA		0.473	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		A	40683721	G	A	40683721	3	1	61	1	0	0	0	0	1	0	0	0	1789	1058	37	1	739	1	C15orf23	15	40683721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22580	40683721	61847671	9240	17225										
CASC5	57082	broad.mit.edu	37	chr15	40915715	40915715	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagagaatcataaaaatGatatggatattacccagagt	7	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40915715G>T	ENST00000346991.5	+	11	3721	c.3331G>T	c.(3331-3333)Gat>Tat	p.D1111Y	CASC5_ENST00000399668.2_Missense_Mutation_p.D1085Y			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1111	2 X 104 AA approximate repeats.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.D1111Y(2)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TCATAAAAATGATATGGATAT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	15											49	46	47					15																	40915715		1813	4070	5883	38703007	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.3331G>T	15.37:g.40915715G>T	ENSP00000335463:p.Asp1111Tyr		38703007	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	9.328	1.059899	0.19987	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.18174	2.23;2.23	5.35	1.28	0.21552	.	0.570461	0.16621	N	0.206461	T	0.14013	0.0339	L	0.49350	1.555	0.09310	N	1	P;B;P	0.42518	0.583;0.352;0.782	B;B;B	0.37650	0.14;0.099;0.255	T	0.12066	-1.0562	10	0.72032	D	0.01	.	6.6517	0.22965	0.2094:0.0:0.6661:0.1245	.	1085;1111;1085	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	Y	1111;1085;1085	ENSP00000335463:D1111Y;ENSP00000382576:D1085Y	ENSP00000260369:D1085Y	D	+	1	0	CASC5	38703007	0.034000	0.19679	0.084000	0.20598	0.131000	0.20780	0.737000	0.26144	0.244000	0.21351	-0.145000	0.13849	GAT		0.358	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40915715	G	T	40915715	3	4	61	1	0	0	0	0	1	0	0	0	2669	1290	45	2	3369	2	CASC5	15	40915715	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231994	40915715	61615677	9241	17226										
CASC5	57082	broad.mit.edu	37	chr15	40939244	40939244	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaaatacttaagaagatCgataactgcctcactgagat	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:40939244C>T	ENST00000346991.5	+	18	6534	c.6144C>T	c.(6142-6144)atC>atT	p.I2048I	CTD-2339L15.3_ENST00000559841.1_RNA|CASC5_ENST00000399668.2_Silent_p.I2022I			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	2048	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.I2048I(2)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TTAAGAAGATCGATAACTGCC	0.294																																																2	Substitution - coding silent(2)	large_intestine(2)	15											89	90	90					15																	40939244		1804	4059	5863	38726536	SO:0001819	synonymous_variant	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.6144C>T	15.37:g.40939244C>T			38726536	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	37	CCDS42023.1																																																																																				0.294	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40939244	C	T	40939244	2	4	61	1	0	0	0	0	0	0	0	1	2669	874	31	1		1	CASC5	15	40939244	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23529	40939244	61592148	9242	17227										
PPP1R14D	54866	broad.mit.edu	37	chr15	41120789	41120789	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaccttcttacatgggttCtccccatctgggctgggaga	12	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41120789C>A	ENST00000299174.5	-	1	118	c.51G>T	c.(49-51)gaG>gaT	p.E17D	PPP1R14D_ENST00000427255.2_Missense_Mutation_p.E17D	NM_017726.7	NP_060196.1	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14D	17					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)	p.E17D(1)		breast(1)|large_intestine(2)|lung(2)|skin(1)	6		all_cancers(109;6.29e-14)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		TACATGGGTTCTCCCCATCTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	87	92					15																	41120789		2203	4300	6503	38908081	SO:0001583	missense	54866			AK000258	CCDS10066.1, CCDS45230.1	15q11.2-q14	2012-04-17			ENSG00000166143	ENSG00000166143		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14953	protein-coding gene	gene with protein product	"gut and brain phosphatase inhibitor 1", "PKC-dependent PP1 inhibitory protein"	613256				11948623	Standard	NM_017726		Approved	CPI17-like, FLJ20251, GBPI-1, MGC119014, MGC119016	uc001zmz.3	Q9NXH3	OTTHUMG00000130064	ENST00000299174.5:c.51G>T	15.37:g.41120789C>A	ENSP00000299174:p.Glu17Asp		38908081	Q4V773	Missense_Mutation	SNP	ENST00000299174.5	37	CCDS10066.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.700523	0.30142	.	.	ENSG00000166143	ENST00000299174;ENST00000427255	.	.	.	5.67	3.57	0.40892	.	0.263564	0.30076	N	0.010475	T	0.24198	0.0586	N	0.14661	0.345	0.22317	N	0.999201	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.12941	-1.0528	9	0.16896	T	0.51	-10.2342	12.2654	0.54674	0.0:0.5621:0.4378:0.0	.	17;17	E9PAT1;Q9NXH3	.;PP14D_HUMAN	D	17	.	ENSP00000299174:E17D	E	-	3	2	PPP1R14D	38908081	0.996000	0.38824	0.984000	0.44739	0.402000	0.30811	1.320000	0.33666	1.279000	0.44446	0.650000	0.86243	GAG		0.557	PPP1R14D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252355.2	NM_017726		A	41120789	C	A	41120789	3	1	61	1	0	0	0	0	1	0	0	0	12396	912	32	2	571	2	PPP1R14D	15	41120789	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	181545	41120789	61410603	9243	17228										
INO80	54617	broad.mit.edu	37	chr15	41342203	41342203	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgttgggtagagcccataGaagactgcaataaatcctca	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41342203G>T	ENST00000361937.3	-	20	2796	c.2372C>A	c.(2371-2373)tCt>tAt	p.S791Y	INO80_ENST00000401393.3_Missense_Mutation_p.S791Y			Q9ULG1	INO80_HUMAN	INO80 complex subunit	791	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.S791Y(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						AGAGCCCATAGAAGACTGCAA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	15											154	144	147					15																	41342203		2203	4300	6503	39129495	SO:0001583	missense	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2372C>A	15.37:g.41342203G>T	ENSP00000355205:p.Ser791Tyr		39129495	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.925077	0.92319	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	T;T	0.75938	-0.98;-0.98	5.14	5.14	0.70334	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.87533	0.6201	M	0.84326	2.69	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.89283	0.3613	10	0.72032	D	0.01	.	18.6026	0.91255	0.0:0.0:1.0:0.0	.	791	Q9ULG1	INO80_HUMAN	Y	791	ENSP00000355205:S791Y;ENSP00000384686:S791Y	ENSP00000355205:S791Y	S	-	2	0	INO80	39129495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.852000	0.99516	2.398000	0.81561	0.455000	0.32223	TCT		0.433	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		T	41342203	G	T	41342203	3	4	61	1	0	0	0	0	1	0	0	0	7767	942	33	2	2366	2	INO80	15	41342203	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	221414	41342203	61189189	9244	17229										
INO80	54617	broad.mit.edu	37	chr15	41347469	41347469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaatagcagatttgttttCggcatggctctcaatgtcct	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41347469C>T	ENST00000361937.3	-	18	2588	c.2164G>A	c.(2164-2166)Gaa>Aaa	p.E722K	INO80_ENST00000401393.3_Missense_Mutation_p.E722K			Q9ULG1	INO80_HUMAN	INO80 complex subunit	722	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.E722K(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GATTTGTTTTCGGCATGGCTC	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	15											144	127	133					15																	41347469		2203	4300	6503	39134761	SO:0001583	missense	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2164G>A	15.37:g.41347469C>T	ENSP00000355205:p.Glu722Lys		39134761	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	33	5.266948	0.95399	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.93659	-3.26;-3.26	4.71	4.71	0.59529	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.95185	0.8439	L	0.45051	1.395	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.95987	0.8982	10	0.87932	D	0	.	17.6488	0.88157	0.0:1.0:0.0:0.0	.	722	Q9ULG1	INO80_HUMAN	K	722	ENSP00000355205:E722K;ENSP00000384686:E722K	ENSP00000355205:E722K	E	-	1	0	INO80	39134761	1.000000	0.71417	0.994000	0.49952	0.867000	0.49689	7.805000	0.86005	2.179000	0.69175	0.305000	0.20034	GAA		0.373	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		T	41347469	C	T	41347469	3	4	61	1	0	0	0	0	1	0	0	0	7767	893	31	1	2582	1	INO80	15	41347469	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5266	41347469	61183923	9245	17230										
INO80	54617	broad.mit.edu	37	chr15	41384277	41384277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttcttatatttgtgtagtCgaagcatgttgtgaagttct	10	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41384277C>T	ENST00000361937.3	-	5	909	c.485G>A	c.(484-486)cGa>cAa	p.R162Q	INO80_ENST00000401393.3_Missense_Mutation_p.R162Q			Q9ULG1	INO80_HUMAN	INO80 complex subunit	162	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.R162Q(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TTTGTGTAGTCGAAGCATGTT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	15											187	179	182					15																	41384277		2203	4300	6503	39171569	SO:0001583	missense	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.485G>A	15.37:g.41384277C>T	ENSP00000355205:p.Arg162Gln		39171569	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	34	5.297118	0.95574	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.92495	-3.05;-3.05	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.95050	0.8397	M	0.65975	2.015	0.80722	D	1	D	0.64830	0.994	P	0.61201	0.885	D	0.94583	0.7781	10	0.51188	T	0.08	.	19.0939	0.93242	0.0:1.0:0.0:0.0	.	162	Q9ULG1	INO80_HUMAN	Q	162	ENSP00000355205:R162Q;ENSP00000384686:R162Q	ENSP00000355205:R162Q	R	-	2	0	INO80	39171569	1.000000	0.71417	0.990000	0.47175	0.962000	0.63368	6.847000	0.75404	2.753000	0.94483	0.455000	0.32223	CGA		0.388	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		T	41384277	C	T	41384277	3	4	61	1	0	0	0	0	1	0	0	0	7767	884	31	1	4313	1	INO80	15	41384277	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36808	41384277	61147115	9246	17231										
EXD1	161829	broad.mit.edu	37	chr15	41488143	41488143	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacttaccttcaaaattctCttgtcttctagtatcatctg	3	10	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41488143C>A	ENST00000314992.5	-	6	643	c.453G>T	c.(451-453)aaG>aaT	p.K151N	EXD1_ENST00000458580.2_Missense_Mutation_p.K209N	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	151							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)	p.K151N(1)		large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						TCAAAATTCTCTTGTCTTCTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											101	101	101					15																	41488143		2203	4300	6503	39275435	SO:0001583	missense	161829			BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"exonuclease 3'-5' domain-like 1"	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.453G>T	15.37:g.41488143C>A	ENSP00000321029:p.Lys151Asn		39275435	A8K909|B7Z839|Q6ZW94	Missense_Mutation	SNP	ENST00000314992.5	37	CCDS10072.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142758	0.57044	.	.	ENSG00000178997	ENST00000314992;ENST00000458580	T;T	0.63255	-0.03;-0.03	5.65	-0.0268	0.13929	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.186437	0.45361	D	0.000375	T	0.60287	0.2257	N	0.22421	0.69	0.29340	N	0.866067	D;D	0.65815	0.991;0.995	D;D	0.68039	0.92;0.955	T	0.58451	-0.7634	10	0.42905	T	0.14	-4.4404	9.8561	0.41086	0.0:0.5133:0.0:0.4867	.	209;151	B7Z839;Q8NHP7	.;EXD1_HUMAN	N	151;209	ENSP00000321029:K151N;ENSP00000415056:K209N	ENSP00000321029:K151N	K	-	3	2	EXD1	39275435	0.977000	0.34250	0.998000	0.56505	0.967000	0.64934	0.046000	0.14035	-0.024000	0.13941	0.462000	0.41574	AAG		0.378	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		A	41488143	C	A	41488143	3	1	61	1	0	0	0	0	1	0	0	0	5310	912	32	2	1111	2	EXD1	15	41488143	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103866	41488143	61043249	9247	17232										
NDUFAF1	51103	broad.mit.edu	37	chr15	41689207	41689207	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcagaagttggcttagaGaattttctgagaaaataagt	11	3	1	3	rs570752499		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41689207G>A	ENST00000260361.4	-	2	432	c.51C>T	c.(49-51)ttC>ttT	p.F17F		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	17					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)	p.F17F(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		TTGGCTTAGAGAATTTTCTGA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	15											39	40	40					15																	41689207		2202	4300	6502	39476499	SO:0001819	synonymous_variant	51103			AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.51C>T	15.37:g.41689207G>A			39476499	Q9BVZ5	Silent	SNP	ENST00000260361.4	37	CCDS10075.1																																																																																				0.428	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		A	41689207	G	A	41689207	2	1	61	1	0	0	0	0	0	0	0	1	10305	933	33	3		3	NDUFAF1	15	41689207	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	201064	41689207	60842185	9248	17233										
RTF1	23168	broad.mit.edu	37	chr15	41758426	41758426	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggagctaaaagcagagCgagaaaaacgaaagaacaga	13	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41758426C>T	ENST00000389629.4	+	6	877	c.865C>T	c.(865-867)Cga>Tga	p.R289*		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	289	Glu-rich.|Lys-rich.				DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)	p.R164*(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		AAAAGCAGAGCGAGAAAAACG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											118	112	114					15																	41758426		2203	4299	6502	39545718	SO:0001587	stop_gained	23168			D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.865C>T	15.37:g.41758426C>T	ENSP00000374280:p.Arg289*		39545718	Q96BX6	Nonsense_Mutation	SNP	ENST00000389629.4	37	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742898	0.89573	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.2	2.01	0.26516	.	0.056732	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4381	13.091	0.59167	0.6621:0.3379:0.0:0.0	.	.	.	.	X	289	.	ENSP00000374280:R289X	R	+	1	2	RTF1	39545718	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.109000	0.31135	0.732000	0.32470	0.655000	0.94253	CGA		0.438	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138		T	41758426	C	T	41758426	4	4	61	1	0	0	0	0	0	1	0	0	13758	760	27	1	887	1	RTF1	15	41758426	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69219	41758426	60772966	9249	17234										
RPAP1	26015	broad.mit.edu	37	chr15	41819230	41819230	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggtgggcaagaactctcGaactatagtctctatcagcc	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41819230G>A	ENST00000304330.4	-	14	1899	c.1783C>T	c.(1783-1785)Cga>Tga	p.R595*	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Nonsense_Mutation_p.R595*	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	595						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.R595*(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		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)		AAGAACTCTCGAACTATAGTC	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											75	76	76					15																	41819230		2203	4300	6503	39606522	SO:0001587	stop_gained	26015			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1783C>T	15.37:g.41819230G>A	ENSP00000306123:p.Arg595*		39606522	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Nonsense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	G	39	7.312888	0.98203	.	.	ENSG00000103932	ENST00000304330	.	.	.	5.1	4.18	0.49190	.	0.596334	0.17381	N	0.176305	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.6546	10.3736	0.44068	0.0:0.1268:0.681:0.1922	.	.	.	.	X	595	.	ENSP00000306123:R595X	R	-	1	2	RPAP1	39606522	0.944000	0.32072	0.962000	0.40283	0.976000	0.68499	3.630000	0.54273	1.262000	0.44165	-0.300000	0.09419	CGA		0.552	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		A	41819230	G	A	41819230	4	1	61	1	0	0	0	0	0	1	0	0	13578	1066	37	1	2446	1	RPAP1	15	41819230	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60804	41819230	60712162	9250	17235										
TYRO3	7301	broad.mit.edu	37	chr15	41853455	41853455	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggggctgtggtccagaaCttggaccagttgtacatccc	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41853455C>A	ENST00000263798.3	+	2	479	c.255C>A	c.(253-255)aaC>aaA	p.N85K	TYRO3_ENST00000559066.1_Missense_Mutation_p.N40K	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	85	Ig-like C2-type 1.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N85K(1)|p.N77K(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGGTCCAGAACTTGGACCAGT	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	15											78	73	74					15																	41853455		2203	4300	6503	39640747	SO:0001583	missense	7301			D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.255C>A	15.37:g.41853455C>A	ENSP00000263798:p.Asn85Lys		39640747	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	C	3.149	-0.174525	0.06421	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.66099	-0.19	4.65	-2.89	0.05665	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.832337	0.10281	N	0.693561	T	0.48241	0.1489	L	0.31926	0.97	0.25265	N	0.989566	B;B	0.24092	0.041;0.097	B;B	0.24701	0.031;0.055	T	0.31668	-0.9935	10	0.29301	T	0.29	-0.7554	12.6631	0.56826	0.0:0.542:0.0:0.458	.	85;146	Q06418;Q59FM9	TYRO3_HUMAN;.	K	17;85	ENSP00000263798:N85K	ENSP00000263798:N85K	N	+	3	2	TYRO3	39640747	0.992000	0.36948	0.000000	0.03702	0.826000	0.46750	0.374000	0.20501	-0.793000	0.04475	-0.404000	0.06349	AAC		0.627	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			A	41853455	C	A	41853455	3	1	61	1	0	0	0	0	1	0	0	0	16854	564	20	2	261	2	TYRO3	15	41853455	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34225	41853455	60677937	9251	17236										
MGA	23269	broad.mit.edu	37	chr15	41991274	41991274	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgtaggttacagagcaaGaatttcccagttggaaaagg	14	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:41991274G>T	ENST00000570161.1	+	4	2105	c.2105G>T	c.(2104-2106)aGa>aTa	p.R702I	MGA_ENST00000219905.7_Missense_Mutation_p.R702I|MGA_ENST00000545763.1_Missense_Mutation_p.R702I|MGA_ENST00000566586.1_Missense_Mutation_p.R702I|MGA_ENST00000389936.4_Missense_Mutation_p.R702I			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R702I(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TACAGAGCAAGAATTTCCCAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	72	73					15																	41991274		1829	4083	5912	39778566	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.2105G>T	15.37:g.41991274G>T	ENSP00000457035:p.Arg702Ile		39778566	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.418626	0.42918	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.48201	0.82;0.82;0.82	4.97	4.97	0.65823	.	3.548680	0.00559	N	0.000272	T	0.42653	0.1212	L	0.27053	0.805	0.42050	D	0.991111	P;B	0.34864	0.473;0.005	B;B	0.31751	0.135;0.005	T	0.25950	-1.0117	10	0.87932	D	0	.	12.4016	0.55416	0.0:0.0:0.8323:0.1677	.	702;702	F5H7K2;E7ENI0	.;.	I	702	ENSP00000219905:R702I;ENSP00000374586:R702I;ENSP00000442467:R702I	ENSP00000219905:R702I	R	+	2	0	MGA	39778566	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	3.831000	0.55776	2.323000	0.78572	0.561000	0.74099	AGA		0.388	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	41991274	G	T	41991274	3	4	61	1	0	0	0	0	1	0	0	0	9570	942	33	2	2119	2	MGA	15	41991274	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137819	41991274	60540118	9252	17237										
MGA	23269	broad.mit.edu	37	chr15	42021428	42021428	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgacttgtgctcgagttCgagtatatgagcgaaaaaaa	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42021428C>T	ENST00000570161.1	+	10	3724	c.3724C>T	c.(3724-3726)Cga>Tga	p.R1242*	MGA_ENST00000219905.7_Nonsense_Mutation_p.R1242*|MGA_ENST00000545763.1_Nonsense_Mutation_p.R1242*|MGA_ENST00000566586.1_Nonsense_Mutation_p.R1242*|MGA_ENST00000389936.4_Nonsense_Mutation_p.R1242*			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R1242*(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGCTCGAGTTCGAGTATATGA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											97	98	98					15																	42021428		1908	4126	6034	39808720	SO:0001587	stop_gained	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3724C>T	15.37:g.42021428C>T	ENSP00000457035:p.Arg1242*		39808720	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	C	43	10.435664	0.99404	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	.	.	.	5.65	5.65	0.86999	.	0.308803	0.26757	N	0.022652	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.869	0.70441	0.1436:0.8564:0.0:0.0	.	.	.	.	X	1242	.	ENSP00000219905:R1242X	R	+	1	2	MGA	39808720	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	1.727000	0.38095	2.817000	0.96982	0.563000	0.77884	CGA		0.413	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42021428	C	T	42021428	4	4	61	1	0	0	0	0	0	1	0	0	9570	876	31	1	3762	1	MGA	15	42021428	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30154	42021428	60509964	9253	17238										
MGA	23269	broad.mit.edu	37	chr15	42052641	42052641	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagcggcggcggcgtggtGaaatgagggatctctttgag	18	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42052641G>T	ENST00000570161.1	+	19	7312	c.7312G>T	c.(7312-7314)Gaa>Taa	p.E2438*	MGA_ENST00000219905.7_Nonsense_Mutation_p.E2438*|MGA_ENST00000545763.1_Nonsense_Mutation_p.E2229*|MGA_ENST00000566586.1_Nonsense_Mutation_p.E2229*|MGA_ENST00000389936.4_Nonsense_Mutation_p.E2399*			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.E2487*(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCGGCGTGGTGAAATGAGGGA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											112	112	112					15																	42052641		1887	4104	5991	39839933	SO:0001587	stop_gained	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7312G>T	15.37:g.42052641G>T	ENSP00000457035:p.Glu2438*		39839933	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	41	8.820003	0.98966	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	.	.	.	5.53	5.53	0.82687	.	0.000000	0.53938	D	0.000047	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.4485	0.94857	0.0:0.0:1.0:0.0	.	.	.	.	X	2438;2399;2229	.	ENSP00000219905:E2438X	E	+	1	0	MGA	39839933	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.159000	0.77483	2.583000	0.87209	0.655000	0.94253	GAA		0.443	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42052641	G	T	42052641	4	4	61	1	0	0	0	0	0	1	0	0	9570	1291	45	2	7386	2	MGA	15	42052641	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31213	42052641	60478751	9254	17239										
MGA	23269	broad.mit.edu	37	chr15	42058229	42058229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgacttatttatgatgccacGaattgttaatgtgacatcat	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42058229G>A	ENST00000570161.1	+	23	7949	c.7949G>A	c.(7948-7950)cGa>cAa	p.R2650Q	MGA_ENST00000219905.7_Missense_Mutation_p.R2650Q|MGA_ENST00000545763.1_Missense_Mutation_p.R2441Q|MGA_ENST00000566586.1_Missense_Mutation_p.R2441Q|MGA_ENST00000389936.4_Missense_Mutation_p.R2611Q			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R2699Q(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATGATGCCACGAATTGTTAAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											88	82	84					15																	42058229		1838	4095	5933	39845521	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7949G>A	15.37:g.42058229G>A	ENSP00000457035:p.Arg2650Gln		39845521	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038823	0.75617	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.85702	-1.99;-2.01;-2.02	5.08	5.08	0.68730	.	1.089600	0.07268	N	0.868563	D	0.85630	0.5741	N	0.19112	0.55	0.24205	N	0.995491	D;D	0.76494	0.999;0.998	P;P	0.61940	0.896;0.789	T	0.74636	-0.3599	10	0.87932	D	0	.	9.2136	0.37333	0.1625:0.0:0.8375:0.0	.	2441;2650	F5H7K2;E7ENI0	.;.	Q	2650;2611;2441	ENSP00000219905:R2650Q;ENSP00000374586:R2611Q;ENSP00000442467:R2441Q	ENSP00000219905:R2650Q	R	+	2	0	MGA	39845521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.563000	0.53784	2.793000	0.96121	0.655000	0.94253	CGA		0.363	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42058229	G	A	42058229	3	1	61	1	0	0	0	0	1	0	0	0	9570	1058	37	1	8039	1	MGA	15	42058229	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5588	42058229	60473163	9255	17240										
SPTBN5	51332	broad.mit.edu	37	chr15	42144838	42144838	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcagtcgtcacctctgtCttttgcatttgggcaaactt	10	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42144838C>A	ENST00000320955.6	-	61	10670	c.10443G>T	c.(10441-10443)aaG>aaT	p.K3481N	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3481					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.K3481N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TCACCTCTGTCTTTTGCATTT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	15											139	157	151					15																	42144838		2136	4225	6361	39932130	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.10443G>T	15.37:g.42144838C>A	ENSP00000317790:p.Lys3481Asn		39932130		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	12.47	1.946771	0.34377	.	.	ENSG00000137877	ENST00000320955	T	0.67345	-0.26	4.21	2.28	0.28536	.	0.767535	0.11766	N	0.531614	T	0.61261	0.2333	L	0.47716	1.5	0.20975	N	0.999815	B	0.32010	0.351	B	0.37780	0.258	T	0.54050	-0.8351	10	0.51188	T	0.08	.	8.3117	0.32075	0.0:0.7534:0.1573:0.0893	.	3481	Q9NRC6	SPTN5_HUMAN	N	3481	ENSP00000317790:K3481N	ENSP00000317790:K3481N	K	-	3	2	SPTBN5	39932130	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.041000	0.12084	0.396000	0.25283	0.655000	0.94253	AAG		0.587	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42144838	C	A	42144838	3	1	61	1	0	0	0	0	1	0	0	0	15161	912	32	2	613	2	SPTBN5	15	42144838	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86609	42144838	60386554	9256	17241										
SPTBN5	51332	broad.mit.edu	37	chr15	42155977	42155977	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaggccccttcgagctgCtgctggtaccggagcaagtt	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42155977C>A	ENST00000320955.6	-	41	7301	c.7074G>T	c.(7072-7074)caG>caT	p.Q2358H	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2358					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.Q2358H(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTTCGAGCTGCTGCTGGTACC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											92	102	99					15																	42155977		2115	4216	6331	39943269	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.7074G>T	15.37:g.42155977C>A	ENSP00000317790:p.Gln2358His		39943269		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	12.52	1.961191	0.34565	.	.	ENSG00000137877	ENST00000320955	T	0.52983	0.64	4.75	3.57	0.40892	.	0.444925	0.20269	N	0.095702	T	0.53932	0.1827	M	0.62723	1.935	0.23834	N	0.996716	P	0.48998	0.918	P	0.57548	0.823	T	0.47971	-0.9075	10	0.56958	D	0.05	.	4.1529	0.10247	0.0:0.67:0.0:0.3299	.	2358	Q9NRC6	SPTN5_HUMAN	H	2358	ENSP00000317790:Q2358H	ENSP00000317790:Q2358H	Q	-	3	2	SPTBN5	39943269	0.680000	0.27605	0.999000	0.59377	0.155000	0.21991	0.865000	0.27940	2.362000	0.80069	0.561000	0.74099	CAG		0.602	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42155977	C	A	42155977	3	1	61	1	0	0	0	0	1	0	0	0	15161	796	28	2	4062	2	SPTBN5	15	42155977	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11139	42155977	60375415	9257	17242										
EHD4	30844	broad.mit.edu	37	chr15	42192924	42192924	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcagctcgtagccgtcGagcttgatcttgatgaggtg	15	9	1	3	rs141440763		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42192924G>A	ENST00000220325.4	-	6	1628	c.1545C>T	c.(1543-1545)ctC>ctT	p.L515L	RP11-23P13.6_ENST00000564432.2_RNA	NM_139265.3	NP_644670.1	Q9H223	EHD4_HUMAN	EH-domain containing 4	515	EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				cellular response to growth factor stimulus (GO:0071363)|endocytic recycling (GO:0032456)|pinocytosis (GO:0006907)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein homooligomerization (GO:0051260)|regulation of endocytosis (GO:0030100)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.L515L(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(7)|ovary(2)|stomach(1)|urinary_tract(1)	20		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)		CGTAGCCGTCGAGCTTGATCT	0.662													G|||	1	0.000199681	0	0	5008	,	,		16017	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											44	40	41					15																	42192924		2203	4299	6502	39980216	SO:0001819	synonymous_variant	30844			AF181265	CCDS10081.1	15q11.1	2013-01-10			ENSG00000103966	ENSG00000103966		"EF-hand domain containing"	3245	protein-coding gene	gene with protein product		605892		PAST4		10673336, 11533061	Standard	NM_139265		Approved		uc001zot.3	Q9H223	OTTHUMG00000130370	ENST00000220325.4:c.1545C>T	15.37:g.42192924G>A			39980216	Q9HAR1|Q9NZN2	Silent	SNP	ENST00000220325.4	37	CCDS10081.1																																																																																				0.662	EHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252737.2	NM_139265		A	42192924	G	A	42192924	2	1	61	1	0	0	0	0	0	0	0	1	4991	1045	37	1		1	EHD4	15	42192924	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36947	42192924	60338468	9258	17243										
PLA2G4E	123745	broad.mit.edu	37	chr15	42281633	42281633	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagcatgtagcagattcgaGactccgggatcctcttcacc	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42281633G>T	ENST00000399518.3	-	15	2189	c.1703C>A	c.(1702-1704)tCt>tAt	p.S568Y	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Missense_Mutation_p.S539Y	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	556	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.S539Y(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		GCAGATTCGAGACTCCGGGAT	0.617											OREG0023079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											44	51	49					15																	42281633		2192	4296	6488	40068925	SO:0001583	missense	123745				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1703C>A	15.37:g.42281633G>T	ENSP00000382434:p.Ser568Tyr	907	40068925	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	37	CCDS55962.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609796	0.87258	.	.	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.11277	2.79;2.79	5.76	5.76	0.90799	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.296718	0.33092	N	0.005297	T	0.33962	0.0881	M	0.69463	2.115	0.32085	N	0.592646	P;D	0.76494	0.868;0.999	P;D	0.76071	0.755;0.987	T	0.19976	-1.0289	10	0.87932	D	0	-4.1611	18.733	0.91742	0.0:0.0:1.0:0.0	.	539;556	C9JK77;Q3MJ16	.;PA24E_HUMAN	Y	568;539	ENSP00000382434:S568Y;ENSP00000413897:S539Y	ENSP00000382434:S568Y	S	-	2	0	PLA2G4E	40068925	1.000000	0.71417	0.934000	0.37439	0.946000	0.59487	5.322000	0.65852	2.724000	0.93272	0.561000	0.74099	TCT		0.617	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		T	42281633	G	T	42281633	3	4	61	1	0	0	0	0	1	0	0	0	12036	942	33	2	927	2	PLA2G4E	15	42281633	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	88709	42281633	60249759	9259	17244										
PLA2G4E	123745	broad.mit.edu	37	chr15	42282432	42282432	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacagtttgcattcatttCtctgtggggaaacaaaatgg	10	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42282432C>A	ENST00000399518.3	-	14	1958	c.1472G>T	c.(1471-1473)aGa>aTa	p.R491I	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Splice_Site_p.R462I	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	479	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.R462I(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		GCATTCATTTCTCTGTGGGGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											130	137	135					15																	42282432		2051	4208	6259	40069724	SO:0001630	splice_region_variant	123745				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1471-1G>T	15.37:g.42282432C>A			40069724	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	37	CCDS55962.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.455858	0.43634	.	.	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.12361	2.69;2.69	5.42	-1.2	0.09554	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.258918	0.36167	N	0.002746	T	0.10208	0.0250	L	0.35341	1.055	0.80722	D	1	B;B	0.30605	0.287;0.04	B;B	0.33121	0.158;0.158	T	0.14172	-1.0482	10	0.51188	T	0.08	-0.5052	10.3662	0.44026	0.0:0.3036:0.0:0.6964	.	462;479	C9JK77;Q3MJ16	.;PA24E_HUMAN	I	491;462	ENSP00000382434:R491I;ENSP00000413897:R462I	ENSP00000382434:R491I	R	-	2	0	PLA2G4E	40069724	0.030000	0.19436	0.979000	0.43373	0.710000	0.40934	-0.130000	0.10498	-0.021000	0.14009	0.655000	0.94253	AGA		0.522	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	Missense_Mutation	A	42282432	C	A	42282432	5	1	61	1	0	0	0	0	0	0	1	0	12036	927	32	2	1162	2	PLA2G4E	15	42282432	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	799	42282432	60248960	9260	17245										
PLA2G4E	123745	broad.mit.edu	37	chr15	42293407	42293407	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatgaacctccaggcaggaGacttgtcgagactgtaaaaa	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42293407G>T	ENST00000399518.3	-	7	1107	c.621C>A	c.(619-621)gtC>gtA	p.V207V	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.V178V	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	198					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.V178V(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CCAGGCAGGAGACTTGTCGAG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	15											77	83	81					15																	42293407		1954	4161	6115	40080699	SO:0001819	synonymous_variant	123745				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.621C>A	15.37:g.42293407G>T			40080699	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																				0.552	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		T	42293407	G	T	42293407	2	4	61	1	0	0	0	0	0	0	0	1	12036	929	33	2		2	PLA2G4E	15	42293407	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10975	42293407	60237985	9261	17246										
PLA2G4F	255189	broad.mit.edu	37	chr15	42437840	42437840	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagccggcggtctttaggaaGatctcatccaggctggtggc	15	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42437840G>T	ENST00000382396.4	-	16	1799	c.1713C>A	c.(1711-1713)atC>atA	p.I571I	PLA2G4F_ENST00000397272.3_Silent_p.I573I			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	571	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)	p.I571I(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		TCTTTAGGAAGATCTCATCCA	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	15											82	88	86					15																	42437840		2203	4299	6502	40225132	SO:0001819	synonymous_variant	255189				CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1713C>A	15.37:g.42437840G>T			40225132	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																				0.652	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		T	42437840	G	T	42437840	2	4	61	1	0	0	0	0	0	0	0	1	12037	932	33	2		2	PLA2G4F	15	42437840	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144433	42437840	60093552	9262	17247										
GANC	2595	broad.mit.edu	37	chr15	42598779	42598779	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcctgtgggaagagaaAtttggaaaatttgtggatat	14	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42598779A>C	ENST00000318010.8	+	7	834	c.594A>C	c.(592-594)aaA>aaC	p.K198N	GANC_ENST00000566442.1_Missense_Mutation_p.K198N	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	198					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)	p.K198N(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GGGAAGAGAAATTTGGAAAAT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	15											86	87	87					15																	42598779		2203	4299	6502	40386071	SO:0001583	missense	2595			AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.594A>C	15.37:g.42598779A>C	ENSP00000326227:p.Lys198Asn		40386071	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	.	.	.	.	.	.	.	.	.	.	A	12.46	1.943936	0.34283	.	.	ENSG00000214013	ENST00000318010	T	0.18016	2.24	5.51	4.39	0.52855	Glycoside hydrolase-type carbohydrate-binding (1);	0.209202	0.44285	D	0.000463	T	0.10508	0.0257	L	0.27053	0.805	0.34023	D	0.652846	B;B	0.21753	0.002;0.06	B;B	0.25987	0.01;0.065	T	0.18524	-1.0334	10	0.13853	T	0.58	-18.4478	6.9638	0.24611	0.7739:0.1507:0.0754:0.0	.	198;198	Q8TET4;Q2M2A3	GANC_HUMAN;.	N	198	ENSP00000326227:K198N	ENSP00000326227:K198N	K	+	3	2	GANC	40386071	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.913000	0.39956	2.097000	0.63578	0.523000	0.50628	AAA		0.318	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141		C	42598779	A	C	42598779	3	2	61	1	0	0	0	0	1	0	0	0	6254	98	4	4	620	4	GANC	15	42598779	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	160939	42598779	59932613	9263	17248										
CAPN3	825	broad.mit.edu	37	chr15	42682159	42682159	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgggcctcaggatggcacGaacatgacctatggaacctc	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42682159G>A	ENST00000397163.3	+	6	1029	c.810G>A	c.(808-810)acG>acA	p.T270T	CAPN3_ENST00000318023.7_Silent_p.T270T|CAPN3_ENST00000356316.3_Silent_p.T183T|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000357568.3_Silent_p.T270T|CAPN3_ENST00000349748.3_Intron	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	270	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.T270T(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGGATGGCACGAACATGACCT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	15											114	90	98					15																	42682159		2203	4299	6502	40469451	SO:0001819	synonymous_variant	825			X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.810G>A	15.37:g.42682159G>A			40469451	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																				0.512	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			A	42682159	G	A	42682159	2	1	61	1	0	0	0	0	0	0	0	1	2634	1045	37	1		1	CAPN3	15	42682159	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83380	42682159	59849233	9264	17249										
ZFP106	64397	broad.mit.edu	37	chr15	42717043	42717043	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtacttgccttcatgcaaaGaatggttttgctatggccct	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42717043G>T	ENST00000263805.4	-	13	5436	c.5110C>A	c.(5110-5112)Ctt>Att	p.L1704I	ZNF106_ENST00000565380.1_Missense_Mutation_p.L932I|ZNF106_ENST00000565611.1_Missense_Mutation_p.L889I|ZNF106_ENST00000565660.1_5'Flank|RNU6-188P_ENST00000364207.1_RNA	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1704					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.L1704I(1)									TTCATGCAAAGAATGGTTTTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											71	58	62					15																	42717043		2203	4299	6502	40504335	SO:0001583	missense	64397			AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.5110C>A	15.37:g.42717043G>T	ENSP00000263805:p.Leu1704Ile		40504335	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.595564	0.66219	.	.	ENSG00000103994	ENST00000263805;ENST00000434903	T	0.60797	0.16	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76011	0.3928	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.991;0.998;0.998	T	0.76929	-0.2777	10	0.72032	D	0.01	-14.4556	19.4586	0.94906	0.0:0.0:1.0:0.0	.	932;1704;932	E9PE29;Q9H2Y7;B4DZ40	.;ZF106_HUMAN;.	I	1704;932	ENSP00000263805:L1704I	ENSP00000263805:L1704I	L	-	1	0	ZFP106	40504335	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.446000	0.80609	2.828000	0.97474	0.655000	0.94253	CTT		0.517	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		T	42717043	G	T	42717043	3	4	61	1	0	0	0	0	1	0	0	0	17676	942	33	2	569	2	ZFP106	15	42717043	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34884	42717043	59814349	9265	17250										
ZFP106	64397	broad.mit.edu	37	chr15	42742459	42742459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taattcagattctttctggcGaactatgggattacatgggg	11	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:42742459G>A	ENST00000263805.4	-	2	2268	c.1942C>T	c.(1942-1944)Cgc>Tgc	p.R648C	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	648					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R648C(1)									TCTTTCTGGCGAACTATGGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	15											168	175	173					15																	42742459		2203	4299	6502	40529751	SO:0001583	missense	64397			AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1942C>T	15.37:g.42742459G>A	ENSP00000263805:p.Arg648Cys		40529751	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	1.942	-0.443244	0.04604	.	.	ENSG00000103994	ENST00000263805	T	0.25085	1.82	5.14	3.25	0.37280	.	1.202190	0.05760	N	0.604768	T	0.16085	0.0387	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25641	-1.0126	10	0.37606	T	0.19	0.8339	10.5049	0.44828	0.0748:0.3078:0.6174:0.0	.	431;648	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	C	648	ENSP00000263805:R648C	ENSP00000263805:R648C	R	-	1	0	ZFP106	40529751	0.000000	0.05858	0.003000	0.11579	0.189000	0.23516	0.044000	0.13992	0.856000	0.35383	-0.850000	0.03035	CGC		0.463	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		A	42742459	G	A	42742459	3	1	61	1	0	0	0	0	1	0	0	0	17676	1058	37	1	3781	1	ZFP106	15	42742459	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25416	42742459	59788933	9266	17251										
CDAN1	146059	broad.mit.edu	37	chr15	43028262	43028262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggagttgggttgatcctgCgagaaggcttcgtcctgctg	15	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43028262C>T	ENST00000356231.3	-	3	607	c.584G>A	c.(583-585)cGc>cAc	p.R195H		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	195	Interaction with ASF1A/B.				chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R195H(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GTTGATCCTGCGAGAAGGCTT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	94	90					15																	43028262		2203	4299	6502	40815554	SO:0001583	missense	146059			AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.584G>A	15.37:g.43028262C>T	ENSP00000348564:p.Arg195His		40815554	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	C	36	5.624963	0.96660	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.94417	-3.42	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.96747	0.8938	L	0.61218	1.895	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	D	0.97038	0.9755	10	0.66056	D	0.02	-14.8053	18.6674	0.91495	0.0:1.0:0.0:0.0	.	195	Q8IWY9	CDAN1_HUMAN	H	195;226	ENSP00000348564:R195H	ENSP00000267892:R226H	R	-	2	0	CDAN1	40815554	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.292000	0.78731	2.579000	0.87056	0.462000	0.41574	CGC		0.552	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43028262	C	T	43028262	3	4	61	1	0	0	0	0	1	0	0	0	3060	768	27	1	3203	1	CDAN1	15	43028262	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	285803	43028262	59503130	9267	17252										
TTBK2	146057	broad.mit.edu	37	chr15	43044954	43044954	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatttggcaccacactaaaAgtctgtgtttttgtcacatc	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43044954A>C	ENST00000267890.6	-	14	2598	c.2490T>G	c.(2488-2490)acT>acG	p.T830T		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	830					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T830T(1)		NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CCACACTAAAAGTCTGTGTTT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	15											113	101	105					15																	43044954		1849	4095	5944	40832246	SO:0001819	synonymous_variant	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.2490T>G	15.37:g.43044954A>C			40832246	O94932|Q6ZN52|Q8IVV1	Silent	SNP	ENST00000267890.6	37	CCDS42029.1																																																																																				0.393	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		C	43044954	A	C	43044954	2	2	61	1	0	0	0	0	0	0	0	1	16717	59	3	4		4	TTBK2	15	43044954	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16692	43044954	59486438	9268	17253										
TTBK2	146057	broad.mit.edu	37	chr15	43045124	43045124	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcttcagtttccccagGgagattttcaaattctctca	5	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43045124G>T	ENST00000267890.6	-	14	2428	c.2320C>A	c.(2320-2322)Cct>Act	p.P774T		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	774					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P774T(1)		NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GTTTCCCCAGGGAGATTTTCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											181	167	171					15																	43045124		1840	4080	5920	40832416	SO:0001583	missense	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.2320C>A	15.37:g.43045124G>T	ENSP00000267890:p.Pro774Thr		40832416	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845477	0.51164	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.40756	1.02	5.73	5.73	0.89815	.	0.293677	0.33834	N	0.004503	T	0.54983	0.1892	L	0.59436	1.845	0.80722	D	1	D;D	0.61080	0.989;0.981	P;P	0.58266	0.836;0.69	T	0.57004	-0.7885	10	0.87932	D	0	.	12.408	0.55451	0.0769:0.0:0.9231:0.0	.	705;774	Q6IQ55-2;Q6IQ55	.;TTBK2_HUMAN	T	774;704;1179	ENSP00000267890:P774T	ENSP00000263802:P1179T	P	-	1	0	TTBK2	40832416	1.000000	0.71417	0.978000	0.43139	0.796000	0.44982	1.759000	0.38420	2.698000	0.92095	0.655000	0.94253	CCT		0.403	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		T	43045124	G	T	43045124	3	4	61	1	0	0	0	0	1	0	0	0	16717	1232	43	2	1422	2	TTBK2	15	43045124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	170	43045124	59486268	9269	17254										
TTBK2	146057	broad.mit.edu	37	chr15	43067514	43067514	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccttctttaaatgatcaTtttctgcccaaggacctaac	4	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43067514T>G	ENST00000267890.6	-	13	1925	c.1817A>C	c.(1816-1818)aAt>aCt	p.N606T		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	606					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.N606T(1)		NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		TAAATGATCATTTTCTGCCCA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	15											120	115	116					15																	43067514		1878	4105	5983	40854806	SO:0001583	missense	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.1817A>C	15.37:g.43067514T>G	ENSP00000267890:p.Asn606Thr		40854806	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358831	0.41801	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.38887	1.11	5.77	2.24	0.28232	.	0.327328	0.31949	N	0.006819	T	0.34919	0.0914	L	0.50333	1.59	0.49483	D	0.99979	B;B	0.18741	0.021;0.03	B;B	0.21151	0.033;0.022	T	0.19224	-1.0312	10	0.72032	D	0.01	.	8.2601	0.31779	0.0:0.2369:0.0:0.7631	.	537;606	Q6IQ55-2;Q6IQ55	.;TTBK2_HUMAN	T	606;536;1011	ENSP00000267890:N606T	ENSP00000263802:N1011T	N	-	2	0	TTBK2	40854806	0.992000	0.36948	0.958000	0.39756	0.994000	0.84299	2.287000	0.43505	0.451000	0.26802	0.528000	0.53228	AAT		0.458	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		G	43067514	T	G	43067514	3	3	61	1	0	0	0	0	1	0	0	0	16717	1493	52	4	1929	4	TTBK2	15	43067514	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22390	43067514	59463878	9270	17255										
UBR1	197131	broad.mit.edu	37	chr15	43309362	43309362	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagatttttctcttaatcgCttcactgtgtcaaacatctg	5	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43309362C>T	ENST00000290650.4	-	28	3036	c.2958G>A	c.(2956-2958)aaG>aaA	p.K986K	UBR1_ENST00000568782.1_5'Flank|UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	986					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K986K(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		CTCTTAATCGCTTCACTGTGT	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	15											136	119	124					15																	43309362		2202	4299	6501	41096654	SO:0001819	synonymous_variant	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.2958G>A	15.37:g.43309362C>T			41096654	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Silent	SNP	ENST00000290650.4	37	CCDS10091.1																																																																																				0.348	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43309362	C	T	43309362	2	4	61	1	0	0	0	0	0	0	0	1	16941	796	28	3		3	UBR1	15	43309362	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241848	43309362	59222030	9271	17256										
UBR1	197131	broad.mit.edu	37	chr15	43339398	43339398	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaacatgagtaaaatattCttcaattgcatctgtatagc	7	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43339398C>A	ENST00000290650.4	-	14	1707	c.1629G>T	c.(1627-1629)aaG>aaT	p.K543N	UBR1_ENST00000382177.2_Missense_Mutation_p.K543N	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	543					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K543N(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GTAAAATATTCTTCAATTGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											222	206	211					15																	43339398		2203	4299	6502	41126690	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.1629G>T	15.37:g.43339398C>A	ENSP00000290650:p.Lys543Asn		41126690	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.579240	0.46006	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.49432	0.78;0.78	4.61	1.61	0.23674	.	0.061083	0.64402	D	0.000007	T	0.35219	0.0924	L	0.53249	1.67	0.45515	D	0.998477	B;P	0.38922	0.286;0.651	B;B	0.35550	0.042;0.205	T	0.08310	-1.0728	10	0.19590	T	0.45	-8.1849	8.3246	0.32149	0.0:0.6619:0.0:0.3381	.	543;543	B4DYL2;Q8IWV7	.;UBR1_HUMAN	N	543	ENSP00000290650:K543N;ENSP00000371612:K543N	ENSP00000290650:K543N	K	-	3	2	UBR1	41126690	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.774000	0.26675	0.629000	0.30376	0.557000	0.71058	AAG		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		A	43339398	C	A	43339398	3	1	61	1	0	0	0	0	1	0	0	0	16941	912	32	2	3756	2	UBR1	15	43339398	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30036	43339398	59191994	9272	17257										
UBR1	197131	broad.mit.edu	37	chr15	43339471	43339471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgttgcccaacctgtcttCggatttcttccattccctgc	7	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43339471C>A	ENST00000290650.4	-	14	1634	c.1556G>T	c.(1555-1557)cGa>cTa	p.R519L	UBR1_ENST00000382177.2_Missense_Mutation_p.R519L	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	519					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R519L(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AACCTGTCTTCGGATTTCTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											246	223	231					15																	43339471		2203	4299	6502	41126763	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.1556G>T	15.37:g.43339471C>A	ENSP00000290650:p.Arg519Leu		41126763	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.000610	0.35320	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.45276	0.9;0.9	4.61	3.68	0.42216	.	0.171941	0.51477	D	0.000085	T	0.21267	0.0512	N	0.12961	0.28	0.33822	D	0.629138	B;B	0.31318	0.014;0.319	B;B	0.26094	0.007;0.066	T	0.21075	-1.0256	10	0.32370	T	0.25	-4.193	7.5155	0.27598	0.0:0.8181:0.0:0.1819	.	519;519	B4DYL2;Q8IWV7	.;UBR1_HUMAN	L	519	ENSP00000290650:R519L;ENSP00000371612:R519L	ENSP00000290650:R519L	R	-	2	0	UBR1	41126763	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.691000	0.54720	2.557000	0.86248	0.557000	0.71058	CGA		0.428	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		A	43339471	C	A	43339471	3	1	61	1	0	0	0	0	1	0	0	0	16941	884	31	2	3829	2	UBR1	15	43339471	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73	43339471	59191921	9273	17258										
UBR1	197131	broad.mit.edu	37	chr15	43340621	43340621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagaatcttcaaaaaagatCgaaaaccttcaaggaactgc	6	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43340621C>T	ENST00000290650.4	-	13	1586	c.1508G>A	c.(1507-1509)cGa>cAa	p.R503Q	UBR1_ENST00000382177.2_Missense_Mutation_p.R503Q	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	503					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R503Q(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		CAAAAAAGATCGAAAACCTTC	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	15											63	61	62					15																	43340621		2202	4294	6496	41127913	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.1508G>A	15.37:g.43340621C>T	ENSP00000290650:p.Arg503Gln		41127913	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.765577	0.31228	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.48836	0.8;0.8	5.02	5.02	0.67125	.	0.321395	0.27294	N	0.020028	T	0.29126	0.0724	L	0.42686	1.345	0.33215	D	0.553939	B;P	0.40066	0.023;0.701	B;B	0.27887	0.007;0.084	T	0.34675	-0.9819	10	0.13470	T	0.59	-19.5094	8.0336	0.30480	0.1705:0.7473:0.0:0.0822	.	503;503	B4DYL2;Q8IWV7	.;UBR1_HUMAN	Q	503	ENSP00000290650:R503Q;ENSP00000371612:R503Q	ENSP00000290650:R503Q	R	-	2	0	UBR1	41127913	0.957000	0.32711	1.000000	0.80357	0.996000	0.88848	1.082000	0.30803	2.608000	0.88229	0.462000	0.41574	CGA		0.303	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43340621	C	T	43340621	3	4	61	1	0	0	0	0	1	0	0	0	16941	884	31	1	3881	1	UBR1	15	43340621	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1150	43340621	59190771	9274	17259										
CCNDBP1	23582	broad.mit.edu	37	chr15	43482296	43482296	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggggcgccaccctggacatCgtggatggcatggctcagct	15	13	1	0	rs200360244		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43482296C>T	ENST00000300213.4	+	5	617	c.375C>T	c.(373-375)atC>atT	p.I125I	CCNDBP1_ENST00000356633.5_Intron|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	125	Interaction with RPLP0.|Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.I125I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-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;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		CCCTGGACATCGTGGATGGCA	0.522													C|||	1	0.000199681	0	0	5008	,	,		20081	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											89	78	82					15																	43482296		2203	4299	6502	41269588	SO:0001819	synonymous_variant	23582			AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.375C>T	15.37:g.43482296C>T			41269588	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Silent	SNP	ENST00000300213.4	37	CCDS10092.1																																																																																				0.522	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142		T	43482296	C	T	43482296	2	4	61	1	0	0	0	0	0	0	0	1	2925	874	31	1		1	CCNDBP1	15	43482296	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	141675	43482296	59049096	9275	17260										
CCNDBP1	23582	broad.mit.edu	37	chr15	43483788	43483788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctgcctgaagaaaattCggatgttagtggcagagaat	12	6	0	3	rs200466580	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43483788C>T	ENST00000300213.4	+	8	1017	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W	CCNDBP1_ENST00000356633.5_Missense_Mutation_p.R98W|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	259	Interaction with RPLP0.|Interaction with TCF3.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R259W(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-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;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		GAAGAAAATTCGGATGTTAGT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	15											92	84	86					15																	43483788		2203	4299	6502	41271080	SO:0001583	missense	23582			AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.775C>T	15.37:g.43483788C>T	ENSP00000300213:p.Arg259Trp		41271080	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	37	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.702778	0.48307	.	.	ENSG00000166946	ENST00000300213;ENST00000356633;ENST00000444658	T;T	0.45668	0.89;0.89	5.35	3.31	0.37934	.	0.290713	0.29551	N	0.011825	T	0.58850	0.2151	M	0.65975	2.015	0.38720	D	0.95342	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.64127	-0.6480	10	0.62326	D	0.03	-29.9893	10.1209	0.42621	0.3882:0.6118:0.0:0.0	.	259;259;131	O95273-2;O95273;O95273-4	.;CCDB1_HUMAN;.	W	259;98;131	ENSP00000300213:R259W;ENSP00000349047:R98W	ENSP00000300213:R259W	R	+	1	2	CCNDBP1	41271080	0.992000	0.36948	0.991000	0.47740	0.971000	0.66376	1.009000	0.29886	1.467000	0.48044	0.555000	0.69702	CGG		0.498	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142		T	43483788	C	T	43483788	3	4	61	1	0	0	0	0	1	0	0	0	2925	875	31	1	805	1	CCNDBP1	15	43483788	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1492	43483788	59047604	9276	17261										
CCNDBP1	23582	broad.mit.edu	37	chr15	43484994	43484994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgtgtcacctgaccgtgcGaatcaatgtaagtactggct	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43484994G>A	ENST00000300213.4	+	9	1156	c.914G>A	c.(913-915)cGa>cAa	p.R305Q	CCNDBP1_ENST00000356633.5_Missense_Mutation_p.R144Q|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	305	Interaction with RPLP0.|Interaction with TCF3.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R305Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-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;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		CTGACCGTGCGAATCAATGTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											191	163	172					15																	43484994		2203	4299	6502	41272286	SO:0001583	missense	23582			AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.914G>A	15.37:g.43484994G>A	ENSP00000300213:p.Arg305Gln		41272286	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	37	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759364	0.89932	.	.	ENSG00000166946	ENST00000300213;ENST00000356633;ENST00000444658	T;T	0.49432	0.78;0.78	5.42	5.42	0.78866	.	0.270197	0.32328	N	0.006259	T	0.67154	0.2863	M	0.72894	2.215	0.46376	D	0.999019	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.995	T	0.67118	-0.5751	10	0.52906	T	0.07	-16.9662	14.5872	0.68335	0.0:0.0:1.0:0.0	.	305;305;177	O95273-2;O95273;O95273-4	.;CCDB1_HUMAN;.	Q	305;144;177	ENSP00000300213:R305Q;ENSP00000349047:R144Q	ENSP00000300213:R305Q	R	+	2	0	CCNDBP1	41272286	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.222000	0.65277	2.820000	0.97059	0.650000	0.86243	CGA		0.388	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142		A	43484994	G	A	43484994	3	1	61	1	0	0	0	0	1	0	0	0	2925	1058	37	1	948	1	CCNDBP1	15	43484994	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1206	43484994	59046398	9277	17262										
TGM5	9333	broad.mit.edu	37	chr15	43527765	43527765	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcactcaggttcactttgAggtccttgaactgggaggac	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43527765A>G	ENST00000220420.5	-	10	1623	c.1616T>C	c.(1615-1617)cTc>cCc	p.L539P	TGM5_ENST00000349114.4_Missense_Mutation_p.L457P	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	539					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.L539P(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	GTTCACTTTGAGGTCCTTGAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	67	75					15																	43527765		2203	4299	6502	41315057	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1616T>C	15.37:g.43527765A>G	ENSP00000220420:p.Leu539Pro		41315057	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.882739	0.72410	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69435	-0.4;-0.4	5.05	5.05	0.67936	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.224065	0.37012	N	0.002283	T	0.79896	0.4525	M	0.71036	2.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.82214	-0.0568	10	0.87932	D	0	-26.4775	12.7913	0.57534	1.0:0.0:0.0:0.0	.	457;539	O43548-2;O43548	.;TGM5_HUMAN	P	539;457;538	ENSP00000220420:L539P;ENSP00000220419:L457P	ENSP00000220420:L539P	L	-	2	0	TGM5	41315057	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.831000	0.69330	2.126000	0.65437	0.533000	0.62120	CTC		0.552	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		G	43527765	A	G	43527765	3	3	61	1	0	0	0	0	1	0	0	0	15872	304	11	4	562	4	TGM5	15	43527765	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	42771	43527765	59003627	9278	17263										
TGM5	9333	broad.mit.edu	37	chr15	43531034	43531034	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcttcatacttgtagttCtctgtgatgtcatcccgctc	6	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43531034C>A	ENST00000220420.5	-	9	1333	c.1326G>T	c.(1324-1326)gaG>gaT	p.E442D	TGM5_ENST00000349114.4_Missense_Mutation_p.E360D	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	442					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.E442D(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	ACTTGTAGTTCTCTGTGATGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	15											156	126	136					15																	43531034		2203	4299	6502	41318326	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1326G>T	15.37:g.43531034C>A	ENSP00000220420:p.Glu442Asp		41318326	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	0.693	-0.793903	0.02862	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.21932	1.98;1.98	5.66	3.76	0.43208	.	0.348813	0.30686	N	0.009084	T	0.09598	0.0236	N	0.17922	0.545	0.22975	N	0.998481	B;P	0.38395	0.014;0.629	B;B	0.36134	0.032;0.218	T	0.19386	-1.0307	10	0.07644	T	0.81	-31.1267	5.1419	0.14963	0.1631:0.6603:0.0:0.1766	.	360;442	O43548-2;O43548	.;TGM5_HUMAN	D	442;360;441	ENSP00000220420:E442D;ENSP00000220419:E360D	ENSP00000220420:E442D	E	-	3	2	TGM5	41318326	0.000000	0.05858	0.998000	0.56505	0.695000	0.40330	-0.499000	0.06413	0.724000	0.32296	0.467000	0.42956	GAG		0.537	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		A	43531034	C	A	43531034	3	1	61	1	0	0	0	0	1	0	0	0	15872	912	32	2	856	2	TGM5	15	43531034	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3269	43531034	59000358	9279	17264										
TGM5	9333	broad.mit.edu	37	chr15	43552322	43552322	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagacccctggaaggagtCgatgtggattttcaagaggt	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43552322C>T	ENST00000220420.5	-	3	371	c.364G>A	c.(364-366)Gac>Aac	p.D122N	TGM5_ENST00000349114.4_Intron	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	122					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.D122N(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	TGGAAGGAGTCGATGTGGATT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	15											67	76	73					15																	43552322		2202	4299	6501	41339614	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.364G>A	15.37:g.43552322C>T	ENSP00000220420:p.Asp122Asn		41339614	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409546	0.42715	.	.	ENSG00000104055	ENST00000220420;ENST00000396996	D	0.88741	-2.42	5.33	1.18	0.20946	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.676625	0.13501	N	0.383269	T	0.82033	0.4949	L	0.40543	1.245	0.09310	N	0.999994	B	0.11235	0.004	B	0.09377	0.004	T	0.68318	-0.5440	10	0.40728	T	0.16	-10.9998	7.8005	0.29172	0.0:0.5493:0.0:0.4507	.	122	O43548	TGM5_HUMAN	N	122;121	ENSP00000220420:D122N	ENSP00000220420:D122N	D	-	1	0	TGM5	41339614	0.000000	0.05858	0.039000	0.18376	0.927000	0.56198	0.721000	0.25911	0.025000	0.15241	0.655000	0.94253	GAC		0.622	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43552322	C	T	43552322	3	4	61	1	0	0	0	0	1	0	0	0	15872	884	31	1	1842	1	TGM5	15	43552322	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21288	43552322	58979070	9280	17265										
TGM7	116179	broad.mit.edu	37	chr15	43569159	43569159	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgagggtgacatggactCtcagcgccttgcccacctca	12	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43569159C>A	ENST00000452443.2	-	12	1878	c.1874G>T	c.(1873-1875)aGa>aTa	p.R625I		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	625					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R625I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GACATGGACTCTCAGCGCCTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15											131	112	118					15																	43569159		2202	4299	6501	41356451	SO:0001583	missense	116179			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1874G>T	15.37:g.43569159C>A	ENSP00000389466:p.Arg625Ile		41356451		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	C	8.717	0.913479	0.17907	.	.	ENSG00000159495	ENST00000452443	T	0.68479	-0.33	4.73	-0.261	0.12963	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.871572	0.10165	N	0.707802	T	0.46678	0.1405	N	0.24115	0.695	0.09310	N	1	P	0.35821	0.523	B	0.35859	0.212	T	0.33111	-0.9881	10	0.41790	T	0.15	0.0626	3.9871	0.09521	0.1737:0.3255:0.0:0.5008	.	625	Q96PF1	TGM7_HUMAN	I	625	ENSP00000389466:R625I	ENSP00000389466:R625I	R	-	2	0	TGM7	41356451	0.000000	0.05858	0.009000	0.14445	0.487000	0.33371	-1.272000	0.02826	-0.088000	0.12506	0.585000	0.79938	AGA		0.567	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		A	43569159	C	A	43569159	3	1	61	1	0	0	0	0	1	0	0	0	15874	913	32	2	266	2	TGM7	15	43569159	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16837	43569159	58962233	9281	17266										
TGM7	116179	broad.mit.edu	37	chr15	43571406	43571406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccgcgatgccagacacgCggatgagcttttcgtccgtt	11	14	0	2	rs199638924	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43571406C>T	ENST00000452443.2	-	11	1752	c.1748G>A	c.(1747-1749)cGc>cAc	p.R583H		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	583					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R583H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GCCAGACACGCGGATGAGCTT	0.512													C|||	3	0.000599042	0.0015	0	5008	,	,		20405	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15						C	HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	96	81	86		1748	4.5	0.9	15	dbSNP_134	86	0,8598		0,0,4299	yes	missense	TGM7	NM_052955.2	29	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	583/711	43571406	1,13001	2202	4299	6501	41358698	SO:0001583	missense	116179			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1748G>A	15.37:g.43571406C>T	ENSP00000389466:p.Arg583His		41358698		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	15.90	2.969130	0.53614	2.27E-4	0.0	ENSG00000159495	ENST00000452443	T	0.34072	1.38	5.42	4.49	0.54785	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.180300	0.49916	N	0.000139	T	0.29491	0.0735	L	0.47716	1.5	0.32470	N	0.54287	B	0.27068	0.167	B	0.17098	0.017	T	0.35798	-0.9774	10	0.38643	T	0.18	-2.9555	10.5236	0.44934	0.0:0.9098:0.0:0.0902	.	583	Q96PF1	TGM7_HUMAN	H	583	ENSP00000389466:R583H	ENSP00000389466:R583H	R	-	2	0	TGM7	41358698	0.601000	0.26907	0.894000	0.35097	0.919000	0.55068	0.849000	0.27723	1.256000	0.44068	0.655000	0.94253	CGC		0.512	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43571406	C	T	43571406	3	4	61	1	0	0	0	0	1	0	0	0	15874	768	27	1	396	1	TGM7	15	43571406	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2247	43571406	58959986	9282	17267										
ZSCAN29	146050	broad.mit.edu	37	chr15	43653653	43653653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctcctgtgtggattCtcctatgggtgatgaaattt	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43653653C>A	ENST00000396976.2	-	5	2311	c.2177G>T	c.(2176-2178)aGa>aTa	p.R726I	ZSCAN29_ENST00000396972.1_Missense_Mutation_p.R337I|ZSCAN29_ENST00000562072.1_3'UTR|ZSCAN29_ENST00000568898.1_Missense_Mutation_p.R336I	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	726					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R726I(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TGTGTGGATTCTCCTATGGGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											74	72	73					15																	43653653		2201	4299	6500	41440945	SO:0001583	missense	146050			AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.2177G>T	15.37:g.43653653C>A	ENSP00000380174:p.Arg726Ile		41440945	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	C	20.1	3.938353	0.73557	.	.	ENSG00000140265	ENST00000396976;ENST00000396972	T;T	0.02446	4.29;4.29	5.17	5.17	0.71159	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000004	T	0.17152	0.0412	M	0.82716	2.605	0.58432	D	0.999996	D;D	0.76494	0.999;0.999	D;D	0.83275	0.969;0.996	T	0.00069	-1.2136	10	0.59425	D	0.04	-14.8354	16.2243	0.82283	0.0:1.0:0.0:0.0	.	337;726	Q8IWY8-4;Q8IWY8	.;ZSC29_HUMAN	I	726;337	ENSP00000380174:R726I;ENSP00000380170:R337I	ENSP00000380170:R337I	R	-	2	0	ZSCAN29	41440945	0.029000	0.19370	1.000000	0.80357	0.998000	0.95712	3.012000	0.49575	2.683000	0.91414	0.655000	0.94253	AGA		0.433	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		A	43653653	C	A	43653653	3	1	61	1	0	0	0	0	1	0	0	0	18275	913	32	2	385	2	ZSCAN29	15	43653653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82247	43653653	58877739	9283	17268										
ZSCAN29	146050	broad.mit.edu	37	chr15	43656386	43656386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggccattcttaactttccGatagctggtttgcaggcttt	9	10	1	0	rs369750925		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43656386G>A	ENST00000396976.2	-	4	1551	c.1417C>T	c.(1417-1419)Cgg>Tgg	p.R473W	ZSCAN29_ENST00000396972.1_Intron|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.R472W|ZSCAN29_ENST00000568898.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	473					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R473W(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TTAACTTTCCGATAGCTGGTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	TRP/ARG	0,4402		0,0,2201	101	97	98		1417	5.2	1	15		98	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZSCAN29	NM_152455.3	101	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	473/853	43656386	1,12999	2201	4299	6500	41443678	SO:0001583	missense	146050			AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1417C>T	15.37:g.43656386G>A	ENSP00000380174:p.Arg473Trp		41443678	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252058	0.59212	0.0	1.16E-4	ENSG00000140265	ENST00000396976	T	0.51574	0.7	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000011	T	0.67468	0.2896	M	0.66939	2.045	0.80722	D	1	P;D	0.89917	0.928;1.0	P;D	0.87578	0.565;0.998	T	0.69847	-0.5034	10	0.87932	D	0	-12.0277	16.3111	0.82872	0.0:0.0:1.0:0.0	.	472;473	C9K0J8;Q8IWY8	.;ZSC29_HUMAN	W	473	ENSP00000380174:R473W	ENSP00000380174:R473W	R	-	1	2	ZSCAN29	41443678	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.047000	0.41269	2.715000	0.92844	0.655000	0.94253	CGG		0.517	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		A	43656386	G	A	43656386	3	1	61	1	0	0	0	0	1	0	0	0	18275	1057	37	1	1149	1	ZSCAN29	15	43656386	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2733	43656386	58875006	9284	17269										
TP53BP1	7158	broad.mit.edu	37	chr15	43701248	43701248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggaagtacttccgggttCgacaatgctgatccgcaatt	10	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43701248C>T	ENST00000263801.3	-	26	5684	c.5432G>A	c.(5431-5433)cGa>cAa	p.R1811Q	TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1814Q|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1766Q|TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1816Q	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1811	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.R1811Q(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		CTTCCGGGTTCGACAATGCTG	0.498								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	15											147	111	123					15																	43701248		2201	4298	6499	41488540	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.5432G>A	15.37:g.43701248C>T	ENSP00000263801:p.Arg1811Gln		41488540	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.633542|5.633542	0.96682|0.96682	.|.	.|.	ENSG00000067369|ENSG00000067369	ENST00000434595|ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	.|D;D;D;D	.|0.91351	.|-2.83;-2.83;-2.83;-2.83	5.35|5.35	5.35|5.35	0.76521|0.76521	.|BRCT (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96259|0.96259	0.8780|0.8780	M|M	0.88450|0.88450	2.955|2.955	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.997;1.0	.|D;D;D	.|0.85130	.|0.994;0.949;0.997	D|D	0.96645|0.96645	0.9477|0.9477	5|10	.|0.87932	.|D	.|0	-6.8155|-6.8155	19.425|19.425	0.94737|0.94737	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1811;1816;1814	.|Q12888;Q12888-2;F8VY86	.|TP53B_HUMAN;.;.	K|Q	136|1811;1816;1766;1814	.|ENSP00000263801:R1811Q;ENSP00000371475:R1816Q;ENSP00000371470:R1766Q;ENSP00000393497:R1814Q	.|ENSP00000263801:R1811Q	E|R	-|-	1|2	0|0	TP53BP1|TP53BP1	41488540|41488540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.515000|5.515000	0.67049|0.67049	2.664000|2.664000	0.90586|0.90586	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.498	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			T	43701248	C	T	43701248	3	4	61	1	0	0	0	0	1	0	0	0	16423	884	31	1	498	1	TP53BP1	15	43701248	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44862	43701248	58830144	9285	17270										
TP53BP1	7158	broad.mit.edu	37	chr15	43712818	43712818	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagcaccagcacccacatCtgttcgtctggtggagtctg	10	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43712818C>A	ENST00000263801.3	-	21	4603	c.4351G>T	c.(4351-4353)Gat>Tat	p.D1451Y	TP53BP1_ENST00000450115.2_Missense_Mutation_p.D1456Y|TP53BP1_ENST00000382039.3_Missense_Mutation_p.D1406Y|TP53BP1_ENST00000382044.4_Missense_Mutation_p.D1456Y	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1451					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.D1451Y(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		GCACCCACATCTGTTCGTCTG	0.542								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	15											68	66	67					15																	43712818		2201	4298	6499	41500110	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.4351G>T	15.37:g.43712818C>A	ENSP00000263801:p.Asp1451Tyr		41500110	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.971211	0.53614	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.05199	3.48;3.48;3.52;3.48	5.45	5.45	0.79879	.	0.187490	0.46758	D	0.000275	T	0.15089	0.0364	L	0.27053	0.805	0.23210	N	0.998112	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.996;0.998;0.998	T	0.03413	-1.1039	10	0.72032	D	0.01	-8.9113	14.9844	0.71336	0.0:0.847:0.153:0.0	.	1456;1451;1456;1456	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	Y	1451;1456;1406;1456	ENSP00000263801:D1451Y;ENSP00000371475:D1456Y;ENSP00000371470:D1406Y;ENSP00000393497:D1456Y	ENSP00000263801:D1451Y	D	-	1	0	TP53BP1	41500110	0.192000	0.23301	0.315000	0.25238	0.976000	0.68499	2.176000	0.42500	2.717000	0.92951	0.585000	0.79938	GAT		0.542	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43712818	C	A	43712818	3	1	61	1	0	0	0	0	1	0	0	0	16423	913	32	2	1599	2	TP53BP1	15	43712818	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11570	43712818	58818574	9286	17271										
TP53BP1	7158	broad.mit.edu	37	chr15	43720305	43720305	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgtacttcccggattgttCtcatgtgacgatgtaagaca	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43720305C>A	ENST00000263801.3	-	18	3974	c.3722G>T	c.(3721-3723)aGa>aTa	p.R1241I	TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1246I|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1246I|TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1246I	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1241					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.R1241I(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		CCGGATTGTTCTCATGTGACG	0.423								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	15											240	209	219					15																	43720305		2201	4298	6499	41507597	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3722G>T	15.37:g.43720305C>A	ENSP00000263801:p.Arg1241Ile		41507597	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	35	5.519226	0.96416	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.10573	3.02;3.02;2.86;3.01	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.26048	0.0635	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;1.0	D;D;D;D	0.91635	0.991;0.997;0.999;0.999	T	0.00630	-1.1636	10	0.62326	D	0.03	-13.8849	19.7689	0.96353	0.0:1.0:0.0:0.0	.	1246;1241;1246;1246	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	I	1241;1246;1246;1246	ENSP00000263801:R1241I;ENSP00000371475:R1246I;ENSP00000371470:R1246I;ENSP00000393497:R1246I	ENSP00000263801:R1241I	R	-	2	0	TP53BP1	41507597	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.395000	0.79876	2.747000	0.94245	0.650000	0.86243	AGA		0.423	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43720305	C	A	43720305	3	1	61	1	0	0	0	0	1	0	0	0	16423	913	32	2	2240	2	TP53BP1	15	43720305	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7487	43720305	58811087	9287	17272										
TP53BP1	7158	broad.mit.edu	37	chr15	43748491	43748491	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcacaagaaacatcaactCtgggagatggctctttcaca	8	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43748491C>A	ENST00000263801.3	-	12	2552	c.2300G>T	c.(2299-2301)aGa>aTa	p.R767I	TP53BP1_ENST00000450115.2_Missense_Mutation_p.R772I|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R772I|TP53BP1_ENST00000605155.1_5'Flank|TP53BP1_ENST00000382044.4_Missense_Mutation_p.R772I	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	767					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.R767I(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		AACATCAACTCTGGGAGATGG	0.453								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	15											75	75	75					15																	43748491		2201	4298	6499	41535783	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2300G>T	15.37:g.43748491C>A	ENSP00000263801:p.Arg767Ile		41535783	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288621	0.59976	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.15718	3.52;3.52;3.51;3.52;2.4	5.25	2.95	0.34219	.	0.380604	0.27060	N	0.021126	T	0.19525	0.0469	N	0.19112	0.55	0.41229	D	0.986562	D;D;D;D	0.76494	0.998;0.998;0.999;0.999	D;D;D;D	0.83275	0.991;0.991;0.996;0.996	T	0.11227	-1.0596	10	0.40728	T	0.16	-6.4401	3.0708	0.06230	0.267:0.5646:0.0:0.1684	.	772;767;772;772	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	I	767;772;772;772;772	ENSP00000263801:R767I;ENSP00000371475:R772I;ENSP00000371470:R772I;ENSP00000393497:R772I;ENSP00000388028:R772I	ENSP00000263801:R767I	R	-	2	0	TP53BP1	41535783	0.337000	0.24766	0.986000	0.45419	0.905000	0.53344	1.891000	0.39738	1.328000	0.45358	0.563000	0.77884	AGA		0.453	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43748491	C	A	43748491	3	1	61	1	0	0	0	0	1	0	0	0	16423	913	32	2	3686	2	TP53BP1	15	43748491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28186	43748491	58782901	9288	17273										
TP53BP1	7158	broad.mit.edu	37	chr15	43748582	43748582	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttccttatgttccaattCttggtcaagtattgccaact	6	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43748582C>A	ENST00000263801.3	-	12	2461	c.2209G>T	c.(2209-2211)Gaa>Taa	p.E737*	TP53BP1_ENST00000450115.2_Nonsense_Mutation_p.E742*|TP53BP1_ENST00000382039.3_Nonsense_Mutation_p.E742*|TP53BP1_ENST00000605155.1_5'Flank|TP53BP1_ENST00000382044.4_Nonsense_Mutation_p.E742*	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	737					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.E737*(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		TGTTCCAATTCTTGGTCAAGT	0.408								Other conserved DNA damage response genes																																								1	Substitution - Nonsense(1)	large_intestine(1)	15											97	99	99					15																	43748582		2201	4298	6499	41535874	SO:0001587	stop_gained	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2209G>T	15.37:g.43748582C>A	ENSP00000263801:p.Glu737*		41535874	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Nonsense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	41	8.788858	0.98954	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	.	.	.	5.03	4.11	0.48088	.	0.072060	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-13.7247	12.6432	0.56720	0.1653:0.8347:0.0:0.0	.	.	.	.	X	737;742;742;742;742	.	ENSP00000263801:E737X	E	-	1	0	TP53BP1	41535874	0.998000	0.40836	1.000000	0.80357	0.964000	0.63967	4.413000	0.59795	1.228000	0.43614	0.563000	0.77884	GAA		0.408	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43748582	C	A	43748582	4	1	61	1	0	0	0	0	0	1	0	0	16423	922	32	2	3777	2	TP53BP1	15	43748582	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91	43748582	58782810	9289	17274										
TP53BP1	7158	broad.mit.edu	37	chr15	43771698	43771698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgctatggggatatcttCgttggactgttcttcatgct	10	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43771698C>T	ENST00000263801.3	-	7	922	c.670G>A	c.(670-672)Gaa>Aaa	p.E224K	TP53BP1_ENST00000450115.2_Missense_Mutation_p.E229K|TP53BP1_ENST00000382039.3_Missense_Mutation_p.E229K|TP53BP1_ENST00000382044.4_Missense_Mutation_p.E229K	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	224					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.E224K(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		GGGATATCTTCGTTGGACTGT	0.403								Other conserved DNA damage response genes																																								1	Substitution - Missense(1)	large_intestine(1)	15											255	200	219					15																	43771698		2201	4298	6499	41558990	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.670G>A	15.37:g.43771698C>T	ENSP00000263801:p.Glu224Lys		41558990	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028722	0.54790	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.11277	3.64;3.63;3.63;3.63;2.79	4.95	4.95	0.65309	.	0.324271	0.29040	N	0.013338	T	0.13157	0.0319	M	0.62723	1.935	0.26400	N	0.97643	D;P;P;P	0.56521	0.976;0.923;0.954;0.954	B;B;B;B	0.41299	0.353;0.114;0.229;0.229	T	0.23013	-1.0200	10	0.31617	T	0.26	-4.2886	13.5588	0.61777	0.0:1.0:0.0:0.0	.	229;224;229;229	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	K	224;229;229;229;229	ENSP00000263801:E224K;ENSP00000371475:E229K;ENSP00000371470:E229K;ENSP00000393497:E229K;ENSP00000388028:E229K	ENSP00000263801:E224K	E	-	1	0	TP53BP1	41558990	0.806000	0.28996	0.168000	0.22838	0.187000	0.23431	3.347000	0.52200	2.579000	0.87056	0.585000	0.79938	GAA		0.403	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			T	43771698	C	T	43771698	3	4	61	1	0	0	0	0	1	0	0	0	16423	893	31	1	5336	1	TP53BP1	15	43771698	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23116	43771698	58759694	9290	17275										
MAP1A	4130	broad.mit.edu	37	chr15	43813692	43813692	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggacggcgtggctgagttCtccgagtatgtctctgagac	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43813692C>A	ENST00000300231.5	+	4	471	c.21C>A	c.(19-21)ttC>ttA	p.F7L	MAP1A_ENST00000382031.1_Missense_Mutation_p.F245L|MAP1A_ENST00000399453.1_Missense_Mutation_p.F7L			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	7					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.F7L(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TGGCTGAGTTCTCCGAGTATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	15											77	81	80					15																	43813692		2070	4205	6275	41600984	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.21C>A	15.37:g.43813692C>A	ENSP00000300231:p.Phe7Leu		41600984	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640462	0.29157	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.34859	1.34;1.34;1.34	5.22	2.3	0.28687	.	0.000000	0.35585	N	0.003115	T	0.55049	0.1896	M	0.73598	2.24	0.58432	D	0.99999	D	0.89917	1.0	D	0.85130	0.997	T	0.56505	-0.7968	10	0.87932	D	0	-12.376	8.7331	0.34512	0.0:0.6216:0.0:0.3784	.	7	P78559	MAP1A_HUMAN	L	245;7;7;7	ENSP00000371462:F245L;ENSP00000382380:F7L;ENSP00000300231:F7L	ENSP00000300231:F7L	F	+	3	2	MAP1A	41600984	0.998000	0.40836	1.000000	0.80357	0.932000	0.56968	0.626000	0.24492	0.794000	0.33899	-0.254000	0.11334	TTC		0.587	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43813692	C	A	43813692	3	1	61	1	0	0	0	0	1	0	0	0	9257	912	32	2	23	2	MAP1A	15	43813692	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41994	43813692	58717700	9291	17276										
MAP1A	4130	broad.mit.edu	37	chr15	43814259	43814259	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacaaaatgggtgtgggCcggctggacatgtatgtcct	13	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43814259C>T	ENST00000300231.5	+	4	1038	c.588C>T	c.(586-588)ggC>ggT	p.G196G	MAP1A_ENST00000382031.1_Silent_p.G434G|MAP1A_ENST00000399453.1_Silent_p.G196G			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	196					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.G196G(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TGGGTGTGGGCCGGCTGGACA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	15											63	63	63					15																	43814259		2037	4173	6210	41601551	SO:0001819	synonymous_variant	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.588C>T	15.37:g.43814259C>T			41601551	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																				0.532	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43814259	C	T	43814259	2	4	61	1	0	0	0	0	0	0	0	1	9257	726	26	3		3	MAP1A	15	43814259	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	567	43814259	58717133	9292	17277										
MAP1A	4130	broad.mit.edu	37	chr15	43818291	43818291	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaggcccaggaacaaaaGgataaagtctcagaaaagaa	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43818291G>T	ENST00000300231.5	+	4	5070	c.4620G>T	c.(4618-4620)aaG>aaT	p.K1540N	MAP1A_ENST00000382031.1_Missense_Mutation_p.K1778N|MAP1A_ENST00000399453.1_Missense_Mutation_p.K1540N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1540					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.K1540N(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AGGAACAAAAGGATAAAGTCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	15											59	66	64					15																	43818291		1863	4089	5952	41605583	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4620G>T	15.37:g.43818291G>T	ENSP00000300231:p.Lys1540Asn		41605583	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747984	0.30955	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.02944	4.1;4.1;4.1	4.08	0.948	0.19561	.	.	.	.	.	T	0.04227	0.0117	M	0.64404	1.975	0.09310	N	1	B	0.26195	0.144	B	0.30782	0.12	T	0.42378	-0.9455	9	0.23302	T	0.38	-2.1826	7.752	0.28903	0.308:0.0:0.692:0.0	.	1540	P78559	MAP1A_HUMAN	N	1778;1540;1540	ENSP00000371462:K1778N;ENSP00000382380:K1540N;ENSP00000300231:K1540N	ENSP00000300231:K1540N	K	+	3	2	MAP1A	41605583	0.000000	0.05858	0.349000	0.25694	0.495000	0.33615	-0.033000	0.12246	0.097000	0.17492	0.563000	0.77884	AAG		0.478	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43818291	G	T	43818291	3	4	61	1	0	0	0	0	1	0	0	0	9257	991	35	2	4622	2	MAP1A	15	43818291	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4032	43818291	58713101	9293	17278										
MAP1A	4130	broad.mit.edu	37	chr15	43818616	43818616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggcaggatgtggtccagGagtggcaagaaacatctcct	16	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43818616G>A	ENST00000300231.5	+	4	5395	c.4945G>A	c.(4945-4947)Gag>Aag	p.E1649K	MAP1A_ENST00000382031.1_Missense_Mutation_p.E1887K|MAP1A_ENST00000399453.1_Missense_Mutation_p.E1649K			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1649					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.E1649K(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TGTGGTCCAGGAGTGGCAAGA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	15											44	57	52					15																	43818616		1969	4139	6108	41605908	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4945G>A	15.37:g.43818616G>A	ENSP00000300231:p.Glu1649Lys		41605908	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	9.805	1.181648	0.21787	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01495	4.83;4.83;4.83	4.05	4.05	0.47172	.	.	.	.	.	T	0.01592	0.0051	N	0.20986	0.625	0.23515	N	0.997512	B	0.02656	0.0	B	0.08055	0.003	T	0.43015	-0.9417	9	0.06625	T	0.88	-5.2156	13.7819	0.63087	0.0:0.0:1.0:0.0	.	1649	P78559	MAP1A_HUMAN	K	1887;1649;1649	ENSP00000371462:E1887K;ENSP00000382380:E1649K;ENSP00000300231:E1649K	ENSP00000300231:E1649K	E	+	1	0	MAP1A	41605908	0.820000	0.29190	1.000000	0.80357	0.665000	0.39181	3.422000	0.52749	2.095000	0.63458	0.563000	0.77884	GAG		0.577	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43818616	G	A	43818616	3	1	61	1	0	0	0	0	1	0	0	0	9257	1175	41	3	4947	3	MAP1A	15	43818616	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325	43818616	58712776	9294	17279										
STRC	161497	broad.mit.edu	37	chr15	43900122	43900122	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccctacagttgtccattCtggttctggcattgccatcc	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43900122C>T	ENST00000450892.2	-	18	3810	c.3733G>A	c.(3733-3735)Gaa>Aaa	p.E1245K	STRC_ENST00000541030.1_Missense_Mutation_p.E472K	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1245					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)		p.E1245K(1)		skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GTTGTCCATTCTGGTTCTGGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											57	64	62					15																	43900122		2167	4289	6456	41687414	SO:0001583	missense	161497			BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.3733G>A	15.37:g.43900122C>T	ENSP00000401513:p.Glu1245Lys		41687414		Missense_Mutation	SNP	ENST00000450892.2	37	CCDS10098.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188345	0.78789	.	.	ENSG00000242866	ENST00000450892;ENST00000299992;ENST00000541030	T;T	0.80214	-1.35;-1.3	5.6	5.6	0.85130	.	0.126932	0.35936	N	0.002890	T	0.79857	0.4518	N	0.19112	0.55	0.39423	D	0.966942	D;P	0.64830	0.994;0.718	P;B	0.60789	0.879;0.295	T	0.75912	-0.3150	10	0.15066	T	0.55	-14.2032	17.102	0.86652	0.0:1.0:0.0:0.0	.	472;1245	F5GXA4;Q7RTU9	.;STRC_HUMAN	K	1245;1245;472	ENSP00000401513:E1245K;ENSP00000440413:E472K	ENSP00000299992:E1245K	E	-	1	0	STRC	41687414	0.999000	0.42202	1.000000	0.80357	0.431000	0.31685	2.585000	0.46111	2.640000	0.89533	0.457000	0.33378	GAA		0.542	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700		T	43900122	C	T	43900122	3	4	61	1	0	0	0	0	1	0	0	0	15367	922	32	3	1642	3	STRC	15	43900122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81506	43900122	58631270	9295	17280										
CATSPER2	117155	broad.mit.edu	37	chr15	43924921	43924921	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcttcggctcaccaatagAttcagaaaatctggattcag	8	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43924921A>C	ENST00000321596.5	-	11	1589	c.1390T>G	c.(1390-1392)Tct>Gct	p.S464A	CATSPER2_ENST00000354127.4_Missense_Mutation_p.S462A|CATSPER2_ENST00000355438.2_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.S468A|CATSPER2_ENST00000396879.1_Missense_Mutation_p.S462A|STRC_ENST00000541030.1_Intron			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	464	Ser-rich.				calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.S462A(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TCACCAATAGATTCAGAAAAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											51	54	53					15																	43924921		2199	4294	6493	41712213	SO:0001583	missense	117155			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.1390T>G	15.37:g.43924921A>C	ENSP00000321463:p.Ser464Ala		41712213	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.647319	0.00792	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127	D;D;D;D	0.95980	-3.85;-3.86;-3.87;-3.85	2.79	-5.58	0.02512	.	0.390690	0.11065	U	0.603552	D	0.86826	0.6026	L	0.34521	1.04	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.74034	-0.3794	10	0.13108	T	0.6	.	1.3932	0.02255	0.1477:0.2724:0.3369:0.243	.	468;464	F8W9H2;Q96P56	.;CTSR2_HUMAN	A	462;464;468;464;462	ENSP00000380088:S462A;ENSP00000371180:S468A;ENSP00000321463:S464A;ENSP00000339137:S462A	ENSP00000299989:S464A	S	-	1	0	CATSPER2	41712213	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.621000	0.00878	-2.720000	0.00389	-0.268000	0.10319	TCT		0.388	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		C	43924921	A	C	43924921	3	2	61	1	0	0	0	0	1	0	0	0	2694	333	12	4	214	4	CATSPER2	15	43924921	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24799	43924921	58606471	9296	17281										
CATSPER2	117155	broad.mit.edu	37	chr15	43925015	43925015	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctcttttttgacaaggtCtcttctgtttttgatgcaga	7	8	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:43925015C>T	ENST00000321596.5	-	11	1495	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E	CATSPER2_ENST00000354127.4_Silent_p.E430E|CATSPER2_ENST00000355438.2_Intron|CATSPER2_ENST00000381761.1_Silent_p.E436E|CATSPER2_ENST00000396879.1_Silent_p.E430E|STRC_ENST00000541030.1_Intron			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	432	Ser-rich.				calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.E430E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TTGACAAGGTCTCTTCTGTTT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	15											119	113	115					15																	43925015		2199	4296	6495	41712307	SO:0001819	synonymous_variant	117155			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.1296G>A	15.37:g.43925015C>T			41712307	Q8NHT9|Q96P54|Q96P55	Silent	SNP	ENST00000321596.5	37	CCDS10099.1																																																																																				0.393	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		T	43925015	C	T	43925015	2	4	61	1	0	0	0	0	0	0	0	1	2694	912	32	3		3	CATSPER2	15	43925015	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94	43925015	58606377	9297	17282										
SERINC4	619189	broad.mit.edu	37	chr15	44087294	44087294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtggggggccaacagagTggtgccagtaacagccccag	17	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44087294T>C	ENST00000319327.6	-	12	1695	c.1461A>G	c.(1459-1461)ccA>ccG	p.P487P	SERF2_ENST00000409291.1_Intron|MIR1282_ENST00000408865.1_RNA|HYPK_ENST00000406925.1_5'Flank|SERF2_ENST00000409646.1_Intron|RP11-296A16.1_ENST00000417761.2_Intron|SERINC4_ENST00000249714.3_Silent_p.P243P|SERINC4_ENST00000299969.6_Missense_Mutation_p.H413R|SERF2_ENST00000594896.1_Intron	NM_001258031.1	NP_001244960.1	A6NH21	SERC4_HUMAN	serine incorporator 4	487					phospholipid biosynthetic process (GO:0008654)	integral component of membrane (GO:0016021)		p.P243P(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	6		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;7.81e-07)		GCCAACAGAGTGGTGCCAGTA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	15											65	73	70					15																	44087294		2198	4298	6496	41874586	SO:0001819	synonymous_variant	619189			DQ103711	CCDS58360.1	15q15.3	2013-09-25			ENSG00000184716	ENSG00000184716			32237	protein-coding gene	gene with protein product		614550					Standard	NM_001258031		Approved	FLJ40363	uc031qrp.1	A6NH21	OTTHUMG00000060144	ENST00000319327.6:c.1461A>G	15.37:g.44087294T>C			41874586	B2RN41|Q3YL75	Silent	SNP	ENST00000319327.6	37	CCDS58360.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.601327	0.28534	.	.	ENSG00000184716	ENST00000299969	T	0.26957	1.7	5.27	1.67	0.24075	.	.	.	.	.	T	0.16727	0.0402	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17018	-1.0383	8	0.87932	D	0	-7.6376	1.3299	0.02132	0.1373:0.2177:0.1423:0.5027	.	413	A6NM42	.	R	413	ENSP00000299969:H413R	ENSP00000299969:H413R	H	-	2	0	SERINC4	41874586	0.001000	0.12720	0.997000	0.53966	0.720000	0.41350	-1.197000	0.03038	0.316000	0.23135	0.528000	0.53228	CAC		0.572	SERINC4-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133485.2			C	44087294	T	C	44087294	2	2	61	1	0	0	0	0	0	0	0	1	14119	1683	59	4		4	SERINC4	15	44087294	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	162279	44087294	58444098	9298	17283										
CASC4	113201	broad.mit.edu	37	chr15	44620947	44620947	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttcaggactataggaaGaacaatacttaccttgtgaa	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44620947G>A	ENST00000345795.2	+	3	717	c.447G>A	c.(445-447)aaG>aaA	p.K149K	CASC4_ENST00000360824.3_Silent_p.K149K|CASC4_ENST00000299957.6_Silent_p.K149K	NM_177974.2	NP_816929.1	Q6P4E1	CASC4_HUMAN	cancer susceptibility candidate 4	149						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K149K(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(2)	17		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)		ACTATAGGAAGAACAATACTT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	15											93	85	88					15																	44620947		2198	4298	6496	42408239	SO:0001819	synonymous_variant	113201			AF103804	CCDS10108.1, CCDS10109.1	15q15.1	2010-11-24			ENSG00000166734	ENSG00000166734			24892	protein-coding gene	gene with protein product						10497265	Standard	NM_138423		Approved	H63, DKFZp459F1927	uc001ztp.3	Q6P4E1	OTTHUMG00000131133	ENST00000345795.2:c.447G>A	15.37:g.44620947G>A			42408239	B4DPZ6|G5E934|Q6UY45|Q96EM1	Silent	SNP	ENST00000345795.2	37	CCDS10109.1																																																																																				0.378	CASC4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253816.1	NM_138423		A	44620947	G	A	44620947	2	1	61	1	0	0	0	0	0	0	0	1	2668	933	33	3		3	CASC4	15	44620947	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	533653	44620947	57910445	9299	17284										
CTDSPL2	51496	broad.mit.edu	37	chr15	44813513	44813513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatttattgttttagctttCtaatggaatccctatagaaa	5	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44813513C>A	ENST00000260327.4	+	12	1807	c.1244C>A	c.(1243-1245)tCt>tAt	p.S415Y	CTDSPL2_ENST00000558373.1_Missense_Mutation_p.S343Y|CTDSPL2_ENST00000396780.1_Missense_Mutation_p.S343Y|CTDSPL2_ENST00000558966.1_Missense_Mutation_p.S415Y	NM_016396.2	NP_057480.2	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	415	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.						phosphoprotein phosphatase activity (GO:0004721)	p.S415Y(1)|p.S415C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	13		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		TTTTAGCTTTCTAATGGAATC	0.269																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	15											51	53	52					15																	44813513		2196	4296	6492	42600805	SO:0001583	missense	51496			AF161478	CCDS10110.1	15q15.3-q21.1	2010-06-21			ENSG00000137770	ENSG00000137770		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	26936	protein-coding gene	gene with protein product							Standard	NM_016396		Approved	HSPC129, FLJ10523	uc001ztr.3	Q05D32	OTTHUMG00000131159	ENST00000260327.4:c.1244C>A	15.37:g.44813513C>A	ENSP00000260327:p.Ser415Tyr		42600805	Q3ZTU1|Q6AI06|Q8IYI9|Q9NVT2|Q9NZX8|Q9P030	Missense_Mutation	SNP	ENST00000260327.4	37	CCDS10110.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960424	0.92791	.	.	ENSG00000137770	ENST00000260327;ENST00000396780	T;T	0.18338	2.22;2.22	5.51	5.51	0.81932	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.29458	0.0734	L	0.33710	1.025	0.80722	D	1	D;P	0.56968	0.978;0.942	P;P	0.57324	0.761;0.818	T	0.01330	-1.1383	10	0.72032	D	0.01	-9.61	19.4177	0.94708	0.0:1.0:0.0:0.0	.	343;415	Q05D32-2;Q05D32	.;CTSL2_HUMAN	Y	415;343	ENSP00000260327:S415Y;ENSP00000380000:S343Y	ENSP00000260327:S415Y	S	+	2	0	CTDSPL2	42600805	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.793000	0.85851	2.575000	0.86900	0.484000	0.47621	TCT		0.269	CTDSPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253851.1	NM_016396		A	44813513	C	A	44813513	3	1	61	1	0	0	0	0	1	0	0	0	4012	913	32	2	1286	2	CTDSPL2	15	44813513	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192566	44813513	57717879	9300	17285										
EIF3J	8669	broad.mit.edu	37	chr15	44843088	44843088	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttaggataactgggatgaCgatgatgatgaaaaaaaaga	11	3	0	5	rs146638481		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44843088C>T	ENST00000535391.1	+	3	174	c.162C>T	c.(160-162)gaC>gaT	p.D54D	EIF3J_ENST00000424492.3_Intron|EIF3J_ENST00000261868.5_Silent_p.D54D					eukaryotic translation initiation factor 3, subunit J									p.D54D(1)		endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		ACTGGGATGACGATGATGATG	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C		0,4396		0,0,2198	96	109	105		162	-1.8	1	15	dbSNP_134	105	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	EIF3J	NM_003758.2		0,1,6495	TT,TC,CC		0.0116,0.0,0.0077		54/259	44843088	1,12991	2198	4298	6496	42630380	SO:0001819	synonymous_variant	8669			U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000535391.1:c.162C>T	15.37:g.44843088C>T			42630380		Silent	SNP	ENST00000535391.1	37																																																																																					0.373	EIF3J-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396804.1	NM_003758		T	44843088	C	T	44843088	2	4	61	1	0	0	0	0	0	0	0	1	5033	535	19	1		1	EIF3J	15	44843088	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29575	44843088	57688304	9301	17286										
EIF3J	8669	broad.mit.edu	37	chr15	44849713	44849713	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatgcagtttatggaataGatgctatgaacccatcttca	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44849713G>T	ENST00000261868.5	+	6	574	c.436G>T	c.(436-438)Gat>Tat	p.D146Y	EIF3J_ENST00000424492.3_Missense_Mutation_p.D97Y|EIF3J_ENST00000535391.1_Intron|RP11-151N17.1_ENST00000558006.1_RNA	NM_003758.2	NP_003749.2			eukaryotic translation initiation factor 3, subunit J									p.D146Y(1)		endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		TTATGGAATAGATGCTATGAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	15											73	79	77					15																	44849713		2198	4297	6495	42637005	SO:0001583	missense	8669			U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000261868.5:c.436G>T	15.37:g.44849713G>T	ENSP00000261868:p.Asp146Tyr		42637005		Missense_Mutation	SNP	ENST00000261868.5	37	CCDS10111.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.7|26.7	4.763728|4.763728	0.89932|0.89932	.|.	.|.	ENSG00000104131|ENSG00000104131	ENST00000261868;ENST00000424492|ENST00000536248	T;T|.	0.51574|.	0.7;0.7|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Eukaryotic translation initiation factor 3-like domain (1);|.	0.139020|.	0.64402|.	D|.	0.000005|.	T|T	0.77011|0.77011	0.4068|0.4068	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.76575|.	0.988;0.983|.	T|T	0.74899|0.74899	-0.3507|-0.3507	10|5	0.87932|.	D|.	0|.	.|.	19.9883|19.9883	0.97356|0.97356	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	97;146|.	F5H425;O75822|.	.;EIF3J_HUMAN|.	Y|I	146;97|24	ENSP00000261868:D146Y;ENSP00000414548:D97Y|.	ENSP00000261868:D146Y|.	D|R	+|+	1|2	0|0	EIF3J|EIF3J	42637005|42637005	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.476000|9.476000	0.97823|0.97823	2.722000|2.722000	0.93159|0.93159	0.555000|0.555000	0.69702|0.69702	GAT|AGA		0.313	EIF3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253850.1	NM_003758		T	44849713	G	T	44849713	3	4	61	1	0	0	0	0	1	0	0	0	5033	942	33	2	458	2	EIF3J	15	44849713	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6625	44849713	57681679	9302	17287										
SPG11	80208	broad.mit.edu	37	chr15	44941171	44941171	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtctgtttaaaaactcttCttgagtcaaaccaaacaaaa	5	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44941171C>A	ENST00000261866.7	-	7	1511	c.1495G>T	c.(1495-1497)Gaa>Taa	p.E499*	SPG11_ENST00000535302.2_Nonsense_Mutation_p.E499*|SPG11_ENST00000558319.1_Nonsense_Mutation_p.E499*|SPG11_ENST00000427534.2_Nonsense_Mutation_p.E499*|SPG11_ENST00000559193.1_Nonsense_Mutation_p.E499*	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	499					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.E499*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		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)		AAAAACTCTTCTTGAGTCAAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											90	88	89					15																	44941171		2198	4298	6496	42728463	SO:0001587	stop_gained	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1495G>T	15.37:g.44941171C>A	ENSP00000261866:p.Glu499*		42728463	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Nonsense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	C	37	6.591487	0.97688	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	.	.	.	5.85	5.85	0.93711	.	0.063724	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.7539	0.96283	0.0:1.0:0.0:0.0	.	.	.	.	X	499	.	ENSP00000261866:E499X	E	-	1	0	SPG11	42728463	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	6.101000	0.71479	2.770000	0.95276	0.563000	0.77884	GAA		0.373	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			A	44941171	C	A	44941171	4	1	61	1	0	0	0	0	0	1	0	0	15080	922	32	2	5972	2	SPG11	15	44941171	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91458	44941171	57590221	9303	17288										
SPG11	80208	broad.mit.edu	37	chr15	44944095	44944095	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacctccagtttggagttCtttattgtttcattcaatga	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:44944095C>A	ENST00000261866.7	-	6	1066	c.1050G>T	c.(1048-1050)aaG>aaT	p.K350N	SPG11_ENST00000535302.2_Missense_Mutation_p.K350N|SPG11_ENST00000558319.1_Missense_Mutation_p.K350N|SPG11_ENST00000427534.2_Missense_Mutation_p.K350N|SPG11_ENST00000559193.1_Missense_Mutation_p.K350N	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	350					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.K350N(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		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)		GTTTGGAGTTCTTTATTGTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											52	45	47					15																	44944095		2198	4298	6496	42731387	SO:0001583	missense	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1050G>T	15.37:g.44944095C>A	ENSP00000261866:p.Lys350Asn		42731387	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.721282	0.48728	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.78481	-1.18;-0.92;-0.92	5.96	4.04	0.47022	.	0.547075	0.18061	N	0.152925	T	0.76428	0.3986	L	0.59436	1.845	0.25180	N	0.99021	P;P;P;P	0.43352	0.804;0.804;0.763;0.804	B;B;P;B	0.44897	0.36;0.36;0.463;0.36	T	0.68606	-0.5364	10	0.72032	D	0.01	.	9.9807	0.41811	0.0:0.7885:0.1382:0.0734	.	350;350;350;350	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	N	350	ENSP00000261866:K350N;ENSP00000445278:K350N;ENSP00000396110:K350N	ENSP00000261866:K350N	K	-	3	2	SPG11	42731387	0.881000	0.30235	0.535000	0.28026	0.978000	0.69477	1.183000	0.32041	0.815000	0.34398	0.655000	0.94253	AAG		0.403	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			A	44944095	C	A	44944095	3	1	61	1	0	0	0	0	1	0	0	0	15080	912	32	2	6421	2	SPG11	15	44944095	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2924	44944095	57587297	9304	17289										
TRIM69	140691	broad.mit.edu	37	chr15	45047124	45047124	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaacccctcctccaacatCgatccaggcgactatgttga	6	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45047124C>T	ENST00000559390.1	+	3	961	c.33C>T	c.(31-33)atC>atT	p.I11I	TRIM69_ENST00000338264.4_Intron|TRIM69_ENST00000560442.1_Intron|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000329464.4_Silent_p.I11I|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000558329.1_Intron			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	11	Necessary for nuclear localization. {ECO:0000250}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I11I(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		CCTCCAACATCGATCCAGGCG	0.433																																					Pancreas(84;519 1450 1802 20427 34706)											1	Substitution - coding silent(1)	large_intestine(1)	15											130	122	125					15																	45047124		2198	4298	6496	42834416	SO:0001819	synonymous_variant	140691			AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.33C>T	15.37:g.45047124C>T			42834416	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Silent	SNP	ENST00000559390.1	37	CCDS32220.1																																																																																				0.433	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1			T	45047124	C	T	45047124	2	4	61	1	0	0	0	0	0	0	0	1	16582	874	31	1		1	TRIM69	15	45047124	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103029	45047124	57484268	9305	17290										
TRIM69	140691	broad.mit.edu	37	chr15	45059523	45059523	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcatggtgacattaagaaGataatgcctgatgatcctga	11	6	0	6	rs142877382		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45059523G>T	ENST00000559390.1	+	8	1984	c.1056G>T	c.(1054-1056)aaG>aaT	p.K352N	TRIM69_ENST00000338264.4_Missense_Mutation_p.K193N|TRIM69_ENST00000560442.1_Missense_Mutation_p.K148N|TRIM69_ENST00000558173.1_Missense_Mutation_p.K148N|TRIM69_ENST00000329464.4_Missense_Mutation_p.K352N|TRIM69_ENST00000561043.1_Missense_Mutation_p.K115N|TRIM69_ENST00000558329.1_Missense_Mutation_p.K131N			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	352	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K352N(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		ACATTAAGAAGATAATGCCTG	0.488																																					Pancreas(84;519 1450 1802 20427 34706)											1	Substitution - Missense(1)	large_intestine(1)	15											143	143	143					15																	45059523		2198	4298	6496	42846815	SO:0001583	missense	140691			AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.1056G>T	15.37:g.45059523G>T	ENSP00000453177:p.Lys352Asn		42846815	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.448719	0.26074	.	.	ENSG00000185880	ENST00000329464;ENST00000338264	T;T	0.10860	2.83;2.83	5.5	4.58	0.56647	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.189124	0.36555	N	0.002536	T	0.07954	0.0199	L	0.38175	1.15	0.28664	N	0.90599	B;B;B	0.32753	0.21;0.27;0.383	B;B;B	0.29942	0.109;0.062;0.079	T	0.15521	-1.0434	10	0.25106	T	0.35	.	8.3174	0.32108	0.0854:0.1556:0.759:0.0	.	131;193;352	Q86WT6-4;Q86WT6-2;Q86WT6	.;.;TRI69_HUMAN	N	352;193	ENSP00000332284:K352N;ENSP00000342922:K193N	ENSP00000332284:K352N	K	+	3	2	TRIM69	42846815	0.826000	0.29277	0.972000	0.41901	0.099000	0.18886	1.192000	0.32150	2.589000	0.87451	0.650000	0.86243	AAG		0.488	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1			T	45059523	G	T	45059523	3	4	61	1	0	0	0	0	1	0	0	0	16582	933	33	2	1082	2	TRIM69	15	45059523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12399	45059523	57471869	9306	17291										
SORD	6652	broad.mit.edu	37	chr15	45353372	45353372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctgtgccacgccccccGatgacgggaacctctgccgg	11	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45353372G>A	ENST00000267814.9	+	4	553	c.373G>A	c.(373-375)Gat>Aat	p.D125N	RP11-109D20.1_ENST00000560324.1_RNA|SORD_ENST00000558580.1_Missense_Mutation_p.D104N	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	125					fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)	p.D125N(1)		endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		CACGCCCCCCGATGACGGGAA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	15											113	96	102					15																	45353372		2198	4298	6496	43140664	SO:0001583	missense	6652				CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.373G>A	15.37:g.45353372G>A	ENSP00000267814:p.Asp125Asn		43140664	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	37	CCDS10116.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.358679	0.41801	.	.	ENSG00000140263	ENST00000267814	T	0.04502	3.61	4.23	4.23	0.50019	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.04137	0.0115	N	0.16743	0.435	0.80722	D	1	B;B	0.20368	0.044;0.02	B;B	0.17433	0.012;0.018	T	0.50591	-0.8810	10	0.29301	T	0.29	-17.3182	15.7782	0.78240	0.0:0.0:1.0:0.0	.	46;125	B4DKI2;Q00796	.;DHSO_HUMAN	N	125	ENSP00000267814:D125N	ENSP00000267814:D125N	D	+	1	0	SORD	43140664	1.000000	0.71417	0.942000	0.38095	0.464000	0.32679	9.494000	0.97962	2.184000	0.69523	0.563000	0.77884	GAT		0.527	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3			A	45353372	G	A	45353372	3	1	61	1	0	0	0	0	1	0	0	0	14970	1058	37	1	387	1	SORD	15	45353372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293849	45353372	57178020	9307	17292										
DUOXA1	90527	broad.mit.edu	37	chr15	45411419	45411419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcagccatggaccggtagCgggggctcaggagtccacct	15	12	2	0	rs199559225		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45411419C>T	ENST00000560572.1	-	6	922	c.917G>A	c.(916-918)cGc>cAc	p.R306H	DUOXA1_ENST00000558422.1_Missense_Mutation_p.R261H|DUOXA1_ENST00000267803.4_Missense_Mutation_p.R306H|DUOXA1_ENST00000558996.1_Missense_Mutation_p.R261H|DUOXA1_ENST00000430224.2_Missense_Mutation_p.R261H|DUOXA1_ENST00000559014.1_Missense_Mutation_p.R306H	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	306					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R306H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		GGACCGGTAGCGGGGGCTCAG	0.577													C|||	1	0.000199681	0	0	5008	,	,		18446	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											83	83	83					15																	45411419		2198	4298	6496	43198711	SO:0001583	missense	90527			BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.917G>A	15.37:g.45411419C>T	ENSP00000454084:p.Arg306His		43198711	Q8N6K9|Q96MI4	Missense_Mutation	SNP	ENST00000560572.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.69	2.012245	0.35511	.	.	ENSG00000140254	ENST00000267803;ENST00000430224	T;T	0.61392	0.56;0.11	5.31	2.42	0.29668	.	0.362455	0.24167	N	0.040932	T	0.36413	0.0966	N	0.24115	0.695	0.24271	N	0.995248	B;B;B;B	0.19935	0.032;0.004;0.008;0.04	B;B;B;B	0.14023	0.01;0.002;0.002;0.006	T	0.19844	-1.0293	10	0.48119	T	0.1	-12.1969	3.6237	0.08105	0.1737:0.5497:0.0:0.2766	.	261;261;306;306	B5M0C0;B5M0B8;Q1HG43;A8K9Q6	.;.;DOXA1_HUMAN;.	H	306;261	ENSP00000267803:R306H;ENSP00000415512:R261H	ENSP00000267803:R306H	R	-	2	0	DUOXA1	43198711	0.048000	0.20356	0.992000	0.48379	0.574000	0.36063	0.430000	0.21428	0.373000	0.24621	-0.140000	0.14226	CGC		0.577	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565		T	45411419	C	T	45411419	3	4	61	1	0	0	0	0	1	0	0	0	4813	768	27	1	546	1	DUOXA1	15	45411419	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58047	45411419	57119973	9308	17293										
DUOX1	53905	broad.mit.edu	37	chr15	45436370	45436370	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccacagaaggtcaacttCgtcctgtccagcaaccgtgg	9	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45436370C>T	ENST00000321429.4	+	18	2480	c.2073C>T	c.(2071-2073)ttC>ttT	p.F691F	DUOX1_ENST00000561166.1_Silent_p.F337F|DUOX1_ENST00000389037.3_Silent_p.F691F	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	691					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.F691F(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		AGGTCAACTTCGTCCTGTCCA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	15											89	74	79					15																	45436370		2198	4298	6496	43223662	SO:0001819	synonymous_variant	53905			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2073C>T	15.37:g.45436370C>T			43223662	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																				0.612	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45436370	C	T	45436370	2	4	61	1	0	0	0	0	0	0	0	1	4811	883	31	1		1	DUOX1	15	45436370	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24951	45436370	57095022	9309	17294										
DUOX1	53905	broad.mit.edu	37	chr15	45455738	45455738	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtccccagatctacttCatctgggtgacgcggaccca	10	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45455738C>A	ENST00000321429.4	+	33	4664	c.4257C>A	c.(4255-4257)ttC>ttA	p.F1419L	DUOX1_ENST00000561166.1_Missense_Mutation_p.F1065L|DUOX1_ENST00000389037.3_Missense_Mutation_p.F1419L|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1419					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.F1419L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		AGATCTACTTCATCTGGGTGA	0.557											OREG0023103	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											95	86	89					15																	45455738		2198	4298	6496	43243030	SO:0001583	missense	53905			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.4257C>A	15.37:g.45455738C>A	ENSP00000317997:p.Phe1419Leu	931	43243030	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133369	0.77662	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.94046	-3.34;-3.34	4.36	3.44	0.39384	Ferric reductase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.93546	0.7940	M	0.74258	2.255	0.80722	D	1	P	0.45011	0.848	P	0.50825	0.651	D	0.92459	0.5976	10	0.87932	D	0	-24.7355	6.5588	0.22476	0.0:0.7863:0.0:0.2137	.	1419	Q9NRD9	DUOX1_HUMAN	L	1419	ENSP00000317997:F1419L;ENSP00000373689:F1419L	ENSP00000317997:F1419L	F	+	3	2	DUOX1	43243030	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.997000	0.49457	1.033000	0.39918	0.491000	0.48974	TTC		0.557	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		A	45455738	C	A	45455738	3	1	61	1	0	0	0	0	1	0	0	0	4811	825	29	2	4379	2	DUOX1	15	45455738	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19368	45455738	57075654	9310	17295										
C15orf48	84419	broad.mit.edu	37	chr15	45724330	45724330	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctactgtacctcaaaaGgtattgttaaattaaaaaca	5	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45724330G>T	ENST00000344300.3	+	3	373	c.183G>T	c.(181-183)aaG>aaT	p.K61N	RP11-519G16.5_ENST00000559553.1_RNA|MIR147B_ENST00000390185.1_RNA|C15orf48_ENST00000396650.2_Splice_Site_p.K61N	NM_032413.3	NP_115789.1	Q9C002	NMES1_HUMAN	chromosome 15 open reading frame 48	61						mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.K61N(1)		large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.67e-16)|GBM - Glioblastoma multiforme(94;1.71e-06)		TACCTCAAAAGGTATTGTTAA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	74	75					15																	45724330		2198	4298	6496	43511622	SO:0001630	splice_region_variant	84419				CCDS10124.1	15q21.1	2014-05-29			ENSG00000166920	ENSG00000166920			29898	protein-coding gene	gene with protein product	"normal mucosa of esophagus specific 1"	608409				12209954	Standard	NM_032413		Approved	NMES1	uc001zvh.4	Q9C002	OTTHUMG00000131424	ENST00000344300.3:c.183+1G>T	15.37:g.45724330G>T			43511622		Missense_Mutation	SNP	ENST00000344300.3	37	CCDS10124.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086275	0.55861	.	.	ENSG00000166920	ENST00000396650;ENST00000344300	D;D	0.82255	-1.59;-1.59	5.14	4.21	0.49690	.	0.000000	0.85682	D	0.000000	D	0.90445	0.7008	.	.	.	0.50313	D	0.999863	D	0.89917	1.0	D	0.91635	0.999	D	0.91317	0.5079	9	0.87932	D	0	-14.8573	12.3403	0.55091	0.0:0.0:0.8307:0.1693	.	61	Q9C002	NMES1_HUMAN	N	61	ENSP00000379887:K61N;ENSP00000341610:K61N	ENSP00000341610:K61N	K	+	3	2	C15orf48	43511622	1.000000	0.71417	0.978000	0.43139	0.416000	0.31233	7.884000	0.87274	1.286000	0.44565	0.563000	0.77884	AAG		0.318	C15orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254217.2	NM_032413	Missense_Mutation	T	45724330	G	T	45724330	5	4	61	1	0	0	0	0	0	0	1	0	1803	1014	35	2	193	2	C15orf48	15	45724330	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	268592	45724330	56807062	9311	17296										
SLC30A4	7782	broad.mit.edu	37	chr15	45779760	45779760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactgtatcccatatgattCgaaatgttgtaaaagccaca	6	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:45779760C>T	ENST00000261867.4	-	6	1279	c.965G>A	c.(964-966)cGa>cAa	p.R322Q	RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	322					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)	p.R322Q(2)		endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		CCATATGATTCGAAATGTTGT	0.348																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	15											124	130	128					15																	45779760		2198	4297	6495	43567052	SO:0001583	missense	7782				CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.965G>A	15.37:g.45779760C>T	ENSP00000261867:p.Arg322Gln		43567052	Q8TC39	Missense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300857	0.60195	.	.	ENSG00000104154	ENST00000261867	T	0.64618	-0.11	6.03	5.11	0.69529	.	0.051596	0.85682	D	0.000000	T	0.48677	0.1513	L	0.45137	1.4	0.52099	D	0.999941	P	0.43094	0.799	B	0.34180	0.177	T	0.46289	-0.9202	10	0.14252	T	0.57	-3.3258	14.091	0.64990	0.0:0.9276:0.0:0.0724	.	322	O14863	ZNT4_HUMAN	Q	322	ENSP00000261867:R322Q	ENSP00000261867:R322Q	R	-	2	0	SLC30A4	43567052	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.450000	0.60041	1.563000	0.49615	-0.140000	0.14226	CGA		0.348	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			T	45779760	C	T	45779760	3	4	61	1	0	0	0	0	1	0	0	0	14594	884	31	1	336	1	SLC30A4	15	45779760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55430	45779760	56751632	9312	17297										
SEMA6D	80031	broad.mit.edu	37	chr15	48052553	48052553	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcaggcaatgaatcgcaGcacaggctggactttcagct	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48052553G>T	ENST00000316364.5	+	3	601	c.162G>T	c.(160-162)caG>caT	p.Q54H	SEMA6D_ENST00000389432.2_Missense_Mutation_p.Q54H|SEMA6D_ENST00000389433.2_Missense_Mutation_p.Q54H|SEMA6D_ENST00000389428.3_Missense_Mutation_p.Q54H|SEMA6D_ENST00000354744.4_Missense_Mutation_p.Q54H|SEMA6D_ENST00000355997.3_Missense_Mutation_p.Q54H|SEMA6D_ENST00000358066.4_Missense_Mutation_p.Q54H|SEMA6D_ENST00000537942.1_Missense_Mutation_p.Q54H|SEMA6D_ENST00000558014.1_Missense_Mutation_p.Q54H|SEMA6D_ENST00000536845.2_Missense_Mutation_p.Q54H|SEMA6D_ENST00000558816.1_Missense_Mutation_p.Q54H|SEMA6D_ENST00000389425.3_Missense_Mutation_p.Q54H	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	54	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.Q54H(1)		biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ATGAATCGCAGCACAGGCTGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	97	99					15																	48052553		2198	4297	6495	45839845	SO:0001583	missense	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.162G>T	15.37:g.48052553G>T	ENSP00000324857:p.Gln54His		45839845	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681499	0.68042	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.000000	0.85682	D	0.000000	T	0.32071	0.0817	L	0.33485	1.01	0.80722	D	1	D;D;D;B;D	0.64830	0.994;0.98;0.994;0.249;0.994	D;P;D;B;D	0.63597	0.916;0.629;0.916;0.118;0.916	T	0.00802	-1.1560	10	0.31617	T	0.26	.	14.1691	0.65497	0.0712:0.0:0.9288:0.0	.	54;54;54;54;54	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	H	54	ENSP00000442040:Q54H;ENSP00000446152:Q54H;ENSP00000324857:Q54H;ENSP00000374084:Q54H;ENSP00000374083:Q54H;ENSP00000346786:Q54H;ENSP00000350770:Q54H;ENSP00000374079:Q54H;ENSP00000348276:Q54H;ENSP00000374076:Q54H	ENSP00000324857:Q54H	Q	+	3	2	SEMA6D	45839845	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.309000	0.59135	2.726000	0.93360	0.655000	0.94253	CAG		0.398	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48052553	G	T	48052553	3	4	61	1	0	0	0	0	1	0	0	0	14079	962	34	2	168	2	SEMA6D	15	48052553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2272793	48052553	54478839	9313	17298										
SEMA6D	80031	broad.mit.edu	37	chr15	48055275	48055275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcttctttcgagaaatcGctgtcgaacataataattta	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48055275G>A	ENST00000316364.5	+	9	1160	c.721G>A	c.(721-723)Gct>Act	p.A241T	SEMA6D_ENST00000389432.2_Missense_Mutation_p.A241T|SEMA6D_ENST00000389433.2_Missense_Mutation_p.A241T|SEMA6D_ENST00000389428.3_Missense_Mutation_p.A241T|SEMA6D_ENST00000354744.4_Missense_Mutation_p.A241T|SEMA6D_ENST00000355997.3_Missense_Mutation_p.A241T|SEMA6D_ENST00000358066.4_Missense_Mutation_p.A241T|SEMA6D_ENST00000537942.1_Missense_Mutation_p.A241T|SEMA6D_ENST00000558014.1_Missense_Mutation_p.A241T|SEMA6D_ENST00000536845.2_Missense_Mutation_p.A241T|SEMA6D_ENST00000558816.1_Missense_Mutation_p.A241T|SEMA6D_ENST00000389425.3_Missense_Mutation_p.A241T	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	241	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.A241T(1)		biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TCGAGAAATCGCTGTCGAACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											86	82	83					15																	48055275		2198	4296	6494	45842567	SO:0001583	missense	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.721G>A	15.37:g.48055275G>A	ENSP00000324857:p.Ala241Thr		45842567	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	35	5.466457	0.96257	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59;2.59;2.59;2.59;2.59;2.59	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	M	0.87456	2.885	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.996;0.999;1.0;1.0	D;P;D;D;D	0.91635	0.961;0.885;0.961;0.999;0.961	T	0.50906	-0.8772	10	0.87932	D	0	.	20.0706	0.97721	0.0:0.0:1.0:0.0	.	241;241;241;241;241	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	T	241	ENSP00000442040:A241T;ENSP00000446152:A241T;ENSP00000324857:A241T;ENSP00000374084:A241T;ENSP00000374083:A241T;ENSP00000346786:A241T;ENSP00000350770:A241T;ENSP00000374079:A241T;ENSP00000348276:A241T;ENSP00000374076:A241T	ENSP00000324857:A241T	A	+	1	0	SEMA6D	45842567	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	9.476000	0.97823	2.744000	0.94065	0.655000	0.94253	GCT		0.358	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48055275	G	A	48055275	3	1	61	1	0	0	0	0	1	0	0	0	14079	1087	38	1	751	1	SEMA6D	15	48055275	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2722	48055275	54476117	9314	17299										
SEMA6D	80031	broad.mit.edu	37	chr15	48056168	48056168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttctgtccctggagattCgtttttctactttgatgttc	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48056168C>T	ENST00000316364.5	+	10	1308	c.869C>T	c.(868-870)tCg>tTg	p.S290L	SEMA6D_ENST00000389432.2_Missense_Mutation_p.S290L|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S290L|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S290L|SEMA6D_ENST00000354744.4_Missense_Mutation_p.S290L|SEMA6D_ENST00000355997.3_Missense_Mutation_p.S290L|SEMA6D_ENST00000358066.4_Missense_Mutation_p.S290L|SEMA6D_ENST00000537942.1_Missense_Mutation_p.S290L|SEMA6D_ENST00000558014.1_Missense_Mutation_p.S290L|SEMA6D_ENST00000536845.2_Missense_Mutation_p.S290L|SEMA6D_ENST00000558816.1_Missense_Mutation_p.S290L|SEMA6D_ENST00000389425.3_Missense_Mutation_p.S290L	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	290	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.S290L(1)		biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CCTGGAGATTCGTTTTTCTAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	15											142	125	131					15																	48056168		2198	4297	6495	45843460	SO:0001583	missense	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.869C>T	15.37:g.48056168C>T	ENSP00000324857:p.Ser290Leu		45843460	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	36	5.664858	0.96745	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05	5.87	5.87	0.94306	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	M	0.68317	2.08	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.929;0.943;0.929;0.999;0.991	T	0.41342	-0.9514	10	0.87932	D	0	.	20.206	0.98277	0.0:1.0:0.0:0.0	.	290;290;290;290;290	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	L	290	ENSP00000442040:S290L;ENSP00000446152:S290L;ENSP00000324857:S290L;ENSP00000374084:S290L;ENSP00000374083:S290L;ENSP00000346786:S290L;ENSP00000350770:S290L;ENSP00000374079:S290L;ENSP00000348276:S290L;ENSP00000374076:S290L	ENSP00000324857:S290L	S	+	2	0	SEMA6D	45843460	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	7.818000	0.86416	2.785000	0.95823	0.655000	0.94253	TCG		0.468	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48056168	C	T	48056168	3	4	61	1	0	0	0	0	1	0	0	0	14079	893	31	1	903	1	SEMA6D	15	48056168	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	893	48056168	54475224	9315	17300										
SLC12A1	6557	broad.mit.edu	37	chr15	48513123	48513123	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttctatccacaggtaagAtgcatgctgaacatctgggg	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48513123A>G	ENST00000558405.1	+	3	572	c.558A>G	c.(556-558)agA>agG	p.R186R	SLC12A1_ENST00000561031.1_Silent_p.R186R|SLC12A1_ENST00000396577.3_Silent_p.R186R|SLC12A1_ENST00000330289.6_Silent_p.R186R|SLC12A1_ENST00000380993.3_Silent_p.R186R			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	186					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.R186R(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CACAGGTAAGATGCATGCTGA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	15											122	116	118					15																	48513123		2198	4297	6495	46300415	SO:0001819	synonymous_variant	6557				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.558A>G	15.37:g.48513123A>G			46300415	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	37	CCDS10129.2																																																																																				0.468	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			G	48513123	A	G	48513123	2	3	61	1	0	0	0	0	0	0	0	1	14419	330	12	4		4	SLC12A1	15	48513123	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	456955	48513123	54018269	9316	17301										
SLC12A1	6557	broad.mit.edu	37	chr15	48518675	48518675	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttcattgctaacaggtCttggagttctcataattctt	6	8	5	0	rs183594799		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48518675C>A	ENST00000558405.1	+	4	645	c.631C>A	c.(631-633)Ctt>Att	p.L211I	SLC12A1_ENST00000396577.3_Intron|SLC12A1_ENST00000559723.1_Intron|SLC12A1_ENST00000330289.6_Missense_Mutation_p.L211I|SLC12A1_ENST00000380993.3_Missense_Mutation_p.L211I			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	211					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.L211I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GCTAACAGGTCTTGGAGTTCT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											122	117	119					15																	48518675		1852	4095	5947	46305967	SO:0001583	missense	6557				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.631C>A	15.37:g.48518675C>A	ENSP00000453409:p.Leu211Ile		46305967	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657417	0.88154	.	.	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000330289	D;D	0.98835	-5.17;-5.17	5.82	5.82	0.92795	Amino acid permease domain (1);	.	.	.	.	D	0.99211	0.9726	M	0.85630	2.765	0.80722	D	1	P;D	0.65815	0.943;0.995	P;D	0.70487	0.826;0.969	D	0.99486	1.0949	9	0.59425	D	0.04	.	20.0956	0.97842	0.0:1.0:0.0:0.0	.	211;211	Q8IUN5;Q13621	.;S12A1_HUMAN	I	24;211;211	ENSP00000370381:L211I;ENSP00000331550:L211I	ENSP00000331550:L211I	L	+	1	0	SLC12A1	46305967	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.249000	0.65427	2.746000	0.94184	0.650000	0.86243	CTT		0.378	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48518675	C	A	48518675	3	1	61	1	0	0	0	0	1	0	0	0	14419	913	32	2	645	2	SLC12A1	15	48518675	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5552	48518675	54012717	9317	17302										
SLC12A1	6557	broad.mit.edu	37	chr15	48524968	48524968	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctaattgctattgcaaaCttcttcattggaactgtcat	5	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48524968C>A	ENST00000558405.1	+	7	1034	c.1020C>A	c.(1018-1020)aaC>aaA	p.N340K	SLC12A1_ENST00000396577.3_Missense_Mutation_p.N340K|SLC12A1_ENST00000559723.1_3'UTR|SLC12A1_ENST00000330289.6_Missense_Mutation_p.N340K|SLC12A1_ENST00000380993.3_Missense_Mutation_p.N340K			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	340					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.N340K(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CTATTGCAAACTTCTTCATTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	15											152	159	157					15																	48524968		2198	4297	6495	46312260	SO:0001583	missense	6557				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1020C>A	15.37:g.48524968C>A	ENSP00000453409:p.Asn340Lys		46312260	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791861	0.70452	.	.	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.98701	-5.08;-5.08;-5.08	5.74	3.73	0.42828	Amino acid permease domain (1);	0.043047	0.85682	D	0.000000	D	0.99001	0.9659	M	0.90425	3.115	0.50039	D	0.999841	D;D;D	0.76494	0.971;0.995;0.999	P;D;D	0.73708	0.9;0.936;0.981	D	0.99698	1.1003	10	0.87932	D	0	.	7.6569	0.28381	0.0:0.6476:0.0:0.3524	.	340;340;340	Q8IUN5;E9PDW4;Q13621	.;.;S12A1_HUMAN	K	153;340;340;340	ENSP00000370381:N340K;ENSP00000379822:N340K;ENSP00000331550:N340K	ENSP00000331550:N340K	N	+	3	2	SLC12A1	46312260	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	0.365000	0.20348	1.344000	0.45657	0.563000	0.77884	AAC		0.333	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48524968	C	A	48524968	3	1	61	1	0	0	0	0	1	0	0	0	14419	564	20	2	1146	2	SLC12A1	15	48524968	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6293	48524968	54006424	9318	17303										
SLC12A1	6557	broad.mit.edu	37	chr15	48527104	48527104	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagaaaactttgggccacGcttcacaaagggtgaaggct	12	9	1	2	rs150258541		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48527104G>A	ENST00000558405.1	+	8	1132	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	SLC12A1_ENST00000396577.3_Missense_Mutation_p.R373H|SLC12A1_ENST00000559723.1_3'UTR|SLC12A1_ENST00000330289.6_Missense_Mutation_p.R373H|SLC12A1_ENST00000380993.3_Missense_Mutation_p.R373H			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	373					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.R373H(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TTTGGGCCACGCTTCACAAAG	0.393													G|||	1	0.000199681	0	0	5008	,	,		17317	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	97	100	99		1118,1118	3.2	1	15	dbSNP_134	99	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense	SLC12A1	NM_000338.2,NM_001184832.1	29,29	0,4,6491	AA,AG,GG		0.0465,0.0,0.0308	benign,benign	373/1100,373/1100	48527104	4,12986	2198	4297	6495	46314396	SO:0001583	missense	6557				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1118G>A	15.37:g.48527104G>A	ENSP00000453409:p.Arg373His		46314396	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.66	2.899566	0.52227	0.0	4.65E-4	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.98747	-5.11;-5.11;-5.11	5.06	3.16	0.36331	Amino acid permease domain (1);	0.150320	0.56097	D	0.000021	D	0.92489	0.7615	N	0.02674	-0.535	0.24190	N	0.995552	B;B;B	0.29085	0.02;0.232;0.126	B;B;B	0.29598	0.029;0.104;0.099	D	0.88249	0.2915	10	0.87932	D	0	.	5.3133	0.15843	0.4013:0.0:0.5987:0.0	.	373;373;373	Q8IUN5;E9PDW4;Q13621	.;.;S12A1_HUMAN	H	186;373;373;373	ENSP00000370381:R373H;ENSP00000379822:R373H;ENSP00000331550:R373H	ENSP00000331550:R373H	R	+	2	0	SLC12A1	46314396	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.706000	0.47135	1.270000	0.44297	0.467000	0.42956	CGC		0.393	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48527104	G	A	48527104	3	1	61	1	0	0	0	0	1	0	0	0	14419	1087	38	1	1248	1	SLC12A1	15	48527104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2136	48527104	54004288	9319	17304										
SLC12A1	6557	broad.mit.edu	37	chr15	48559893	48559893	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatggtgtccgaagtcttCttcaggtaaggctgcattga	14	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48559893C>A	ENST00000558405.1	+	17	2304	c.2290C>A	c.(2290-2292)Ctt>Att	p.L764I	SLC12A1_ENST00000396577.3_Missense_Mutation_p.L764I|SLC12A1_ENST00000380993.3_Missense_Mutation_p.L764I			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	764					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.L764I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CCGAAGTCTTCTTCAGGTAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	15											125	128	127					15																	48559893		2198	4297	6495	46347185	SO:0001583	missense	6557				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.2290C>A	15.37:g.48559893C>A	ENSP00000453409:p.Leu764Ile		46347185	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.193389|4.193389	0.78902|0.78902	.|.	.|.	ENSG00000074803|ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000546071|ENST00000428362	D;D|.	0.94793|.	-3.52;-3.52|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.061993|.	0.64402|.	D|.	0.000003|.	T|T	0.69691|0.69691	0.3139|0.3139	L|L	0.37897|0.37897	1.145|1.145	0.80722|0.80722	D|D	1|1	D;D|.	0.61080|.	0.989;0.978|.	P;P|.	0.62649|.	0.804;0.905|.	T|T	0.69946|0.69946	-0.5007|-0.5007	10|6	0.56958|0.87932	D|D	0.05|0	.|.	20.5407|20.5407	0.99260|0.99260	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	764;764|.	E9PDW4;Q13621|.	.;S12A1_HUMAN|.	I|Y	764;764;158|576	ENSP00000370381:L764I;ENSP00000379822:L764I|.	ENSP00000370381:L764I|ENSP00000410367:S576Y	L|S	+|+	1|2	0|0	SLC12A1|SLC12A1	46347185|46347185	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.859000|0.859000	0.49053|0.49053	6.672000|6.672000	0.74477|0.74477	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	CTT|TCT		0.468	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48559893	C	A	48559893	3	1	61	1	0	0	0	0	1	0	0	0	14419	913	32	2	2456	2	SLC12A1	15	48559893	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32789	48559893	53971499	9320	17305										
FBN1	2200	broad.mit.edu	37	chr15	48703453	48703453	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgattcgtcagagttgtaaGagctggaaggagttctagga	15	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48703453G>T	ENST00000316623.5	-	66	8805	c.8350C>A	c.(8350-8352)Ctt>Att	p.L2784I	FBN1_ENST00000561429.1_5'UTR	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2784					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.L2784I(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGAGTTGTAAGAGCTGGAAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											158	151	154					15																	48703453		2198	4297	6495	46490745	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.8350C>A	15.37:g.48703453G>T	ENSP00000325527:p.Leu2784Ile		46490745	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215720	0.39102	.	.	ENSG00000166147	ENST00000316623	D	0.81908	-1.55	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.86732	0.6003	L	0.41415	1.275	0.50171	D	0.999855	D	0.63880	0.993	D	0.70016	0.967	T	0.82926	-0.0215	10	0.21540	T	0.41	.	18.2948	0.90141	0.0:0.0:1.0:0.0	.	2784	P35555	FBN1_HUMAN	I	2784	ENSP00000325527:L2784I	ENSP00000325527:L2784I	L	-	1	0	FBN1	46490745	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	6.061000	0.71148	2.727000	0.93392	0.650000	0.86243	CTT		0.418	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48703453	G	T	48703453	3	4	61	1	0	0	0	0	1	0	0	0	5721	942	33	2	269	2	FBN1	15	48703453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143560	48703453	53827939	9321	17306										
FBN1	2200	broad.mit.edu	37	chr15	48707951	48707951	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcagatgtgagcgctgagGcattcgttttcatctgcagg	13	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48707951G>A	ENST00000316623.5	-	64	8288	c.7833C>T	c.(7831-7833)tgC>tgT	p.C2611C	FBN1_ENST00000561429.1_5'UTR	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2611	EGF-like 46; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.C2611C(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GAGCGCTGAGGCATTCGTTTT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	15											68	64	66					15																	48707951		2198	4296	6494	46495243	SO:0001819	synonymous_variant	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.7833C>T	15.37:g.48707951G>A			46495243	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																				0.552	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48707951	G	A	48707951	2	1	61	1	0	0	0	0	0	0	0	1	5721	1195	42	3		3	FBN1	15	48707951	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4498	48707951	53823441	9322	17307										
FBN1	2200	broad.mit.edu	37	chr15	48729218	48729218	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcagcgataggaaccatCtgtattgatgcactgtccat	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48729218C>A	ENST00000316623.5	-	53	6891	c.6436G>T	c.(6436-6438)Gat>Tat	p.D2146Y		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2146	EGF-like 36; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.D2146Y(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TAGGAACCATCTGTATTGATG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											120	115	117					15																	48729218		2198	4296	6494	46516510	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6436G>T	15.37:g.48729218C>A	ENSP00000325527:p.Asp2146Tyr		46516510	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966343	0.92855	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92348	-3.02	5.77	5.77	0.91146	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.95098	0.8412	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94588	0.7785	10	0.56958	D	0.05	.	19.9576	0.97228	0.0:1.0:0.0:0.0	.	2146	P35555	FBN1_HUMAN	Y	2146;714;1036	ENSP00000325527:D2146Y	ENSP00000325527:D2146Y	D	-	1	0	FBN1	46516510	1.000000	0.71417	0.708000	0.30435	0.874000	0.50279	7.776000	0.85560	2.885000	0.99019	0.655000	0.94253	GAT		0.358	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48729218	C	A	48729218	3	1	61	1	0	0	0	0	1	0	0	0	5721	913	32	2	2235	2	FBN1	15	48729218	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21267	48729218	53802174	9323	17308										
FBN1	2200	broad.mit.edu	37	chr15	48729989	48729989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttccgtggggcagagctCgcaggggtctccccagcctt	15	13	1	1	rs397515831		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48729989C>T	ENST00000316623.5	-	51	6744	c.6289G>A	c.(6289-6291)Gag>Aag	p.E2097K		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2097	TB 8.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.E2097K(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GGGCAGAGCTCGCAGGGGTCT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											84	74	78					15																	48729989		2198	4296	6494	46517281	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6289G>A	15.37:g.48729989C>T	ENSP00000325527:p.Glu2097Lys		46517281	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.656063	0.96724	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.95885	-3.84	5.65	4.73	0.59995	Matrix fibril-associated (3);TGF-beta binding (1);	0.132156	0.64402	N	0.000002	D	0.95207	0.8446	M	0.84511	2.7	0.80722	D	1	B	0.23990	0.095	B	0.24006	0.05	D	0.93784	0.7086	10	0.40728	T	0.16	.	14.5447	0.68020	0.0:0.9296:0.0:0.0704	.	2097	P35555	FBN1_HUMAN	K	2097;665;987	ENSP00000325527:E2097K	ENSP00000325527:E2097K	E	-	1	0	FBN1	46517281	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	7.651000	0.83577	1.626000	0.50381	0.655000	0.94253	GAG		0.532	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48729989	C	T	48729989	3	4	61	1	0	0	0	0	1	0	0	0	5721	893	31	1	2390	1	FBN1	15	48729989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	771	48729989	53801403	9324	17309										
FBN1	2200	broad.mit.edu	37	chr15	48748865	48748865	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacttgtcattatagaaGaatcccactggacattcaca	5	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48748865G>T	ENST00000316623.5	-	44	5846	c.5391C>A	c.(5389-5391)ttC>ttA	p.F1797L		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1797	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.F1797L(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CATTATAGAAGAATCCCACTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											159	144	149					15																	48748865		2198	4296	6494	46536157	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5391C>A	15.37:g.48748865G>T	ENSP00000325527:p.Phe1797Leu		46536157	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.794695	0.90453	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.93488	-3.23	5.8	2.95	0.34219	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.90937	0.7151	M	0.65320	2	0.80722	D	1	P	0.34462	0.454	B	0.34931	0.192	D	0.87147	0.2206	10	0.49607	T	0.09	.	11.1164	0.48262	0.1919:0.0:0.8081:0.0	.	1797	P35555	FBN1_HUMAN	L	1797;365;687	ENSP00000325527:F1797L	ENSP00000325527:F1797L	F	-	3	2	FBN1	46536157	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.142000	0.58044	0.382000	0.24878	0.655000	0.94253	TTC		0.433	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48748865	G	T	48748865	3	4	61	1	0	0	0	0	1	0	0	0	5721	933	33	2	3316	2	FBN1	15	48748865	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18876	48748865	53782527	9325	17310										
FBN1	2200	broad.mit.edu	37	chr15	48764844	48764844	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactggccattgccacagaGattcaggttctcagagcact	10	12	2	2	rs376840416		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48764844G>T	ENST00000316623.5	-	35	4695	c.4240C>A	c.(4240-4242)Ctc>Atc	p.L1414I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1414	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.L1414I(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTGCCACAGAGATTCAGGTTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											120	112	115					15																	48764844		2198	4296	6494	46552136	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4240C>A	15.37:g.48764844G>T	ENSP00000325527:p.Leu1414Ile		46552136	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225663	0.79576	.	.	ENSG00000166147	ENST00000316623;ENST00000544030	D	0.92965	-3.14	5.81	3.83	0.44106	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.90981	0.7164	N	0.13043	0.29	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.90379	0.4386	10	0.54805	T	0.06	.	11.0483	0.47872	0.1605:0.0:0.8395:0.0	.	1414	P35555	FBN1_HUMAN	I	1414;304	ENSP00000325527:L1414I	ENSP00000325527:L1414I	L	-	1	0	FBN1	46552136	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.965000	0.56788	0.703000	0.31848	0.650000	0.86243	CTC		0.512	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48764844	G	T	48764844	3	4	61	1	0	0	0	0	1	0	0	0	5721	942	33	2	4503	2	FBN1	15	48764844	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15979	48764844	53766548	9326	17311										
FBN1	2200	broad.mit.edu	37	chr15	48776109	48776109	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcactgaccaccatcacaGatattgggattatcttcaca	7	11	3	2	rs201786043		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48776109G>T	ENST00000316623.5	-	31	4199	c.3744C>A	c.(3742-3744)atC>atA	p.I1248I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1248	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.I1248I(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACCATCACAGATATTGGGAT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	15											144	113	123					15																	48776109		2198	4296	6494	46563401	SO:0001819	synonymous_variant	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.3744C>A	15.37:g.48776109G>T			46563401	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																				0.408	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48776109	G	T	48776109	2	4	61	1	0	0	0	0	0	0	0	1	5721	932	33	2		2	FBN1	15	48776109	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11265	48776109	53755283	9327	17312										
FBN1	2200	broad.mit.edu	37	chr15	48797303	48797303	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcagtgttgacgcaacGcccattcatgcagatcccag	9	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:48797303G>A	ENST00000316623.5	-	16	2334	c.1879C>T	c.(1879-1881)Cgt>Tgt	p.R627C		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	627	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		R -> C (in MFS; enhances proteolytic degradation). {ECO:0000269|PubMed:16220557, ECO:0000269|PubMed:8004112, ECO:0000269|PubMed:9338581}.		extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R627C(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTGACGCAACGCCCATTCATG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15	GRCh37	CM940760	FBN1	M							156	144	148					15																	48797303		2197	4296	6493	46584595	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1879C>T	15.37:g.48797303G>A	ENSP00000325527:p.Arg627Cys		46584595	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852113	0.91355	.	.	ENSG00000166147	ENST00000316623	T	0.72725	-0.68	5.67	5.67	0.87782	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.099514	0.64402	D	0.000001	D	0.83912	0.5357	M	0.90870	3.155	0.80722	D	1	D	0.69078	0.997	P	0.53146	0.719	D	0.85961	0.1470	10	0.44086	T	0.13	.	18.3401	0.90302	0.0:0.0:1.0:0.0	.	627	P35555	FBN1_HUMAN	C	627	ENSP00000325527:R627C	ENSP00000325527:R627C	R	-	1	0	FBN1	46584595	1.000000	0.71417	0.735000	0.30896	0.656000	0.38851	9.869000	0.99810	2.684000	0.91462	0.650000	0.86243	CGT		0.448	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48797303	G	A	48797303	3	1	61	1	0	0	0	0	1	0	0	0	5721	1087	38	1	6940	1	FBN1	15	48797303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21194	48797303	53734089	9328	17313										
CEP152	22995	broad.mit.edu	37	chr15	49030779	49030779	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaacagattcacttggtatTtccaaagttccttgtggcct	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49030779T>C	ENST00000380950.2	-	27	4987	c.4800A>G	c.(4798-4800)gaA>gaG	p.E1600E	CEP152_ENST00000399334.3_Silent_p.E1544E	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1600					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E1544E(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CACTTGGTATTTCCAAAGTTC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	15											98	98	98					15																	49030779		1892	4123	6015	46818071	SO:0001819	synonymous_variant	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4800A>G	15.37:g.49030779T>C			46818071	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	37	CCDS58361.1																																																																																				0.413	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		C	49030779	T	C	49030779	2	2	61	1	0	0	0	0	0	0	0	1	3254	1838	64	4		4	CEP152	15	49030779	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	233476	49030779	53500613	9329	17314										
CEP152	22995	broad.mit.edu	37	chr15	49037157	49037157	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcatgtcgttgttttcttCtattaattcttcaacaactt	3	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49037157C>A	ENST00000380950.2	-	23	3854	c.3667G>T	c.(3667-3669)Gaa>Taa	p.E1223*	CEP152_ENST00000325747.5_Nonsense_Mutation_p.E1130*|CEP152_ENST00000399334.3_Nonsense_Mutation_p.E1167*	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1223					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E1167*(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTGTTTTCTTCTATTAATTCT	0.259																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											75	69	71					15																	49037157		1770	4031	5801	46824449	SO:0001587	stop_gained	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.3667G>T	15.37:g.49037157C>A	ENSP00000370337:p.Glu1223*		46824449	E7ER66|Q17RV1|Q6NTA0	Nonsense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	C	42	9.416093	0.99164	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	.	.	.	5.14	3.25	0.37280	.	0.224802	0.38217	N	0.001780	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-9.3148	8.9304	0.35666	0.0:0.7718:0.1488:0.0794	.	.	.	.	X	1223;1130;1167	.	ENSP00000321000:E1130X	E	-	1	0	CEP152	46824449	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.975000	0.49281	0.752000	0.32923	-0.515000	0.04445	GAA		0.259	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49037157	C	A	49037157	4	1	61	1	0	0	0	0	0	1	0	0	3254	922	32	2	1485	2	CEP152	15	49037157	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6378	49037157	53494235	9330	17315										
CEP152	22995	broad.mit.edu	37	chr15	49054632	49054632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgagttccaattcaatttCgagtttcttcatagccccct	5	11	3	1	rs544161048	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49054632C>T	ENST00000380950.2	-	18	2705	c.2518G>A	c.(2518-2520)Gaa>Aaa	p.E840K	CEP152_ENST00000325747.5_Missense_Mutation_p.E747K|CEP152_ENST00000399334.3_Missense_Mutation_p.E840K	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	840					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E840K(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AATTCAATTTCGAGTTTCTTC	0.358													C|||	12	0.00239617	0	0	5008	,	,		19086	0		0	False		,,,				2504	0.0123															1	Substitution - Missense(1)	large_intestine(1)	15											156	139	144					15																	49054632		1824	4081	5905	46841924	SO:0001583	missense	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2518G>A	15.37:g.49054632C>T	ENSP00000370337:p.Glu840Lys		46841924	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507606	0.44558	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.58652	0.32;0.38;0.38	5.18	4.26	0.50523	.	0.122489	0.56097	D	0.000035	T	0.71567	0.3355	L	0.59436	1.845	0.26981	N	0.965359	D;D;D	0.89917	1.0;0.991;1.0	D;P;D	0.85130	0.992;0.847;0.997	T	0.66073	-0.6014	10	0.66056	D	0.02	-19.0376	14.1312	0.65255	0.0:0.8497:0.1503:0.0	.	747;840;840	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	K	840;747;840	ENSP00000370337:E840K;ENSP00000321000:E747K;ENSP00000382271:E840K	ENSP00000321000:E747K	E	-	1	0	CEP152	46841924	0.921000	0.31238	0.048000	0.18961	0.114000	0.19823	1.897000	0.39799	1.534000	0.49203	0.650000	0.86243	GAA		0.358	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49054632	C	T	49054632	3	4	61	1	0	0	0	0	1	0	0	0	3254	893	31	1	2482	1	CEP152	15	49054632	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17475	49054632	53476760	9331	17316										
CEP152	22995	broad.mit.edu	37	chr15	49089912	49089912	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagctcatctccaattgCtcaggatgatgtggtctcga	9	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49089912C>T	ENST00000380950.2	-	4	394	c.207G>A	c.(205-207)gaG>gaA	p.E69E	CEP152_ENST00000325747.5_Silent_p.E69E|CEP152_ENST00000399334.3_Silent_p.E69E	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	69					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E69E(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TCTCCAATTGCTCAGGATGAT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	15											170	154	159					15																	49089912		1939	4136	6075	46877204	SO:0001819	synonymous_variant	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.207G>A	15.37:g.49089912C>T			46877204	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	37	CCDS58361.1																																																																																				0.388	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49089912	C	T	49089912	2	4	61	1	0	0	0	0	0	0	0	1	3254	796	28	3		3	CEP152	15	49089912	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35280	49089912	53441480	9332	17317										
CEP152	22995	broad.mit.edu	37	chr15	49097786	49097786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctttcatagtcctcttCgtcatactcttcatcttcat	2	14	8	0	rs187563127	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49097786C>T	ENST00000380950.2	-	2	248	c.61G>A	c.(61-63)Gaa>Aaa	p.E21K	CEP152_ENST00000325747.5_Missense_Mutation_p.E21K|CEP152_ENST00000399334.3_Missense_Mutation_p.E21K	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	21					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.E21K(2)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TAGTCCTCTTCGTCATACTCT	0.363													T|||	5	0.000998403	0.003	0.0014	5008	,	,		15074	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	15						T	LYS/GLU,LYS/GLU	18,3654		2,14,1820	174	149	157		61,61	1.3	1	15		157	0,8172		0,0,4086	yes	missense,missense	CEP152	NM_001194998.1,NM_014985.3	56,56	2,14,5906	TT,TC,CC		0.0,0.4902,0.152	benign,benign	21/1711,21/1655	49097786	18,11826	1836	4086	5922	46885078	SO:0001583	missense	22995			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.61G>A	15.37:g.49097786C>T	ENSP00000370337:p.Glu21Lys		46885078	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	0.957	-0.704547	0.03255	0.004902	0.0	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334;ENST00000541880	T;T;T	0.47528	2.07;0.84;2.07	5.03	1.32	0.21799	.	0.294591	0.37857	N	0.001920	T	0.07007	0.0178	N	0.00246	-1.78	0.21325	N	0.999726	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.04013	0.001;0.0;0.001	T	0.38351	-0.9665	10	0.02654	T	1	-2.7725	6.9884	0.24741	0.0:0.1583:0.3308:0.5109	.	21;21;21	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	K	21	ENSP00000370337:E21K;ENSP00000321000:E21K;ENSP00000382271:E21K	ENSP00000321000:E21K	E	-	1	0	CEP152	46885078	1.000000	0.71417	0.999000	0.59377	0.449000	0.32228	1.177000	0.31969	0.078000	0.16900	-1.301000	0.01330	GAA		0.363	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49097786	C	T	49097786	3	4	61	1	0	0	0	0	1	0	0	0	3254	893	31	1	5003	1	CEP152	15	49097786	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7874	49097786	53433606	9333	17318										
SECISBP2L	9728	broad.mit.edu	37	chr15	49288645	49288645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgctgcagagggattccGagaatgtcccatgtggtgtg	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49288645G>A	ENST00000559471.1	-	17	2805	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.R803W|Y_RNA_ENST00000384377.1_RNA	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	848							poly(A) RNA binding (GO:0044822)	p.R803W(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						GAGGGATTCCGAGAATGTCCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											236	216	223					15																	49288645		2197	4295	6492	47075937	SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2542C>T	15.37:g.49288645G>A	ENSP00000453854:p.Arg848Trp		47075937	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578486	0.86645	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.93189	-3.18	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.94509	0.8232	L	0.29908	0.895	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.79108	0.981;0.992	D	0.95400	0.8489	10	0.87932	D	0	.	18.3573	0.90362	0.0:0.0:1.0:0.0	.	848;803	Q93073;Q93073-2	SBP2L_HUMAN;.	W	803;848	ENSP00000261847:R803W	ENSP00000261847:R803W	R	-	1	2	SECISBP2L	47075937	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.276000	0.78559	2.569000	0.86673	0.650000	0.86243	CGG		0.418	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		A	49288645	G	A	49288645	3	1	61	1	0	0	0	0	1	0	0	0	14044	1057	37	1	771	1	SECISBP2L	15	49288645	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190859	49288645	53242747	9334	17319										
SECISBP2L	9728	broad.mit.edu	37	chr15	49301541	49301541	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttctgacttgctggagaGagtgaagtatcactgggcat	14	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49301541G>A	ENST00000559471.1	-	14	2162	c.1899C>T	c.(1897-1899)ctC>ctT	p.L633L	SECISBP2L_ENST00000261847.3_Silent_p.L588L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	633							poly(A) RNA binding (GO:0044822)	p.L588L(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTGCTGGAGAGAGTGAAGTAT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	15											166	150	156					15																	49301541		2197	4295	6492	47088833	SO:0001819	synonymous_variant	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1899C>T	15.37:g.49301541G>A			47088833	Q8N767	Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																				0.428	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		A	49301541	G	A	49301541	2	1	61	1	0	0	0	0	0	0	0	1	14044	929	33	3		3	SECISBP2L	15	49301541	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12896	49301541	53229851	9335	17320										
SECISBP2L	9728	broad.mit.edu	37	chr15	49303970	49303970	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaagtcatcaataaaatCtaagtgcatttctgttggtt	8	6	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49303970C>A	ENST00000559471.1	-	13	2085	c.1822G>T	c.(1822-1824)Gat>Tat	p.D608Y	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.D563Y	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	608							poly(A) RNA binding (GO:0044822)	p.D563Y(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TCAATAAAATCTAAGTGCATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											124	124	124					15																	49303970		2197	4295	6492	47091262	SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1822G>T	15.37:g.49303970C>A	ENSP00000453854:p.Asp608Tyr		47091262	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830183	0.50845	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.73363	-0.74	5.29	5.29	0.74685	.	0.222920	0.47093	D	0.000246	T	0.62282	0.2415	L	0.43152	1.355	0.38497	D	0.948133	B;P	0.40834	0.055;0.73	B;B	0.36845	0.03;0.234	T	0.67795	-0.5578	10	0.59425	D	0.04	.	6.3555	0.21398	0.0:0.79:0.0:0.21	.	608;563	Q93073;Q93073-2	SBP2L_HUMAN;.	Y	563;608	ENSP00000261847:D563Y	ENSP00000261847:D563Y	D	-	1	0	SECISBP2L	47091262	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.754000	0.47532	2.760000	0.94817	0.557000	0.71058	GAT		0.403	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		A	49303970	C	A	49303970	3	1	61	1	0	0	0	0	1	0	0	0	14044	913	32	2	1507	2	SECISBP2L	15	49303970	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2429	49303970	53227422	9336	17321										
SECISBP2L	9728	broad.mit.edu	37	chr15	49327568	49327568	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgttactgtttctgcttCgatggctggacaatgggaag	12	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49327568C>T	ENST00000559471.1	-	3	754	c.491G>A	c.(490-492)cGa>cAa	p.R164Q	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.R164Q	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	164							poly(A) RNA binding (GO:0044822)	p.R164Q(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						GTTTCTGCTTCGATGGCTGGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											138	131	133					15																	49327568		2197	4295	6492	47114860	SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.491G>A	15.37:g.49327568C>T	ENSP00000453854:p.Arg164Gln		47114860	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605993	0.87157	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.88896	-2.44	5.57	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.90903	0.7141	L	0.34521	1.04	0.43693	D	0.996141	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.91155	0.4956	10	0.51188	T	0.08	.	14.4083	0.67099	0.0:0.929:0.0:0.071	.	164;164	Q93073;Q93073-2	SBP2L_HUMAN;.	Q	164	ENSP00000261847:R164Q	ENSP00000261847:R164Q	R	-	2	0	SECISBP2L	47114860	1.000000	0.71417	0.859000	0.33776	0.745000	0.42441	5.257000	0.65473	1.354000	0.45846	0.655000	0.94253	CGA		0.413	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		T	49327568	C	T	49327568	3	4	61	1	0	0	0	0	1	0	0	0	14044	884	31	1	2739	1	SECISBP2L	15	49327568	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23598	49327568	53203824	9337	17322										
GALK2	2585	broad.mit.edu	37	chr15	49528114	49528114	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttgtggcacaactatttCttatgtggacttaaaggaat	8	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49528114C>A	ENST00000560031.1	+	4	640	c.333C>A	c.(331-333)ttC>ttA	p.F111L	GALK2_ENST00000327171.3_Missense_Mutation_p.F100L|GALK2_ENST00000544523.1_Missense_Mutation_p.F87L|GALK2_ENST00000543495.1_5'UTR|GALK2_ENST00000396509.2_Missense_Mutation_p.F87L|GALK2_ENST00000559454.1_Missense_Mutation_p.F87L			Q01415	GALK2_HUMAN	galactokinase 2	111					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.F100L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		ACAACTATTTCTTATGTGGAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	15											166	172	170					15																	49528114		2196	4295	6491	47315406	SO:0001583	missense	2585				CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.333C>A	15.37:g.49528114C>A	ENSP00000453129:p.Phe111Leu		47315406	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482307	0.84747	.	.	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000544523	D;D	0.82893	-1.66;-1.66	5.7	5.7	0.88788	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.90584	0.7048	M	0.90977	3.165	0.80722	D	1	D;P	0.62365	0.991;0.938	P;B	0.55615	0.78;0.428	D	0.92095	0.5683	10	0.72032	D	0.01	-20.5779	13.0794	0.59104	0.0:0.9269:0.0:0.0731	.	111;100	Q01415;Q7Z4Q4	GALK2_HUMAN;.	L	100;111;87	ENSP00000316632:F100L;ENSP00000440312:F87L	ENSP00000316632:F100L	F	+	3	2	GALK2	47315406	0.998000	0.40836	0.991000	0.47740	0.983000	0.72400	2.146000	0.42216	2.697000	0.92050	0.557000	0.71058	TTC		0.333	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1			A	49528114	C	A	49528114	3	1	61	1	0	0	0	0	1	0	0	0	6224	912	32	2	371	2	GALK2	15	49528114	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200546	49528114	53003278	9338	17323										
C15orf33	196951	broad.mit.edu	37	chr15	49869034	49869034	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgctttgaatcctgtgaaGctgcaaccctagaaagagga	10	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49869034G>A	ENST00000299338.6	-	7	753	c.450C>T	c.(448-450)agC>agT	p.S150S	FAM227B_ENST00000560246.1_3'UTR|FAM227B_ENST00000561064.1_Silent_p.S150S|FAM227B_ENST00000558594.1_3'UTR	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	150								p.S150S(2)									ATCCTGTGAAGCTGCAACCCT	0.323																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	15											37	40	39					15																	49869034		2196	4295	6491	47656326	SO:0001819	synonymous_variant	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.450C>T	15.37:g.49869034G>A			47656326	Q86WS2	Silent	SNP	ENST00000299338.6	37	CCDS32237.1																																																																																				0.323	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		A	49869034	G	A	49869034	2	1	61	1	0	0	0	0	0	0	0	1	1795	962	34	3		3	C15orf33	15	49869034	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	340920	49869034	52662358	9339	17324										
C15orf33	196951	broad.mit.edu	37	chr15	49903463	49903463	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttggaggttcttgcatTttctaataaagtaatatcaa	6	6	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49903463T>A	ENST00000299338.6	-	3	357	c.54A>T	c.(52-54)aaA>aaT	p.K18N	FAM227B_ENST00000560246.1_Missense_Mutation_p.K18N|FAM227B_ENST00000558862.1_5'UTR|FAM227B_ENST00000561064.1_Missense_Mutation_p.K18N|FAM227B_ENST00000558594.1_Missense_Mutation_p.K18N	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	18								p.K18N(1)									GTTCTTGCATTTTCTAATAAA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	15											55	57	56					15																	49903463		2193	4282	6475	47690755	SO:0001583	missense	196951				CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.54A>T	15.37:g.49903463T>A	ENSP00000299338:p.Lys18Asn		47690755	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	37	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.506724	0.26949	.	.	ENSG00000166262	ENST00000299338;ENST00000354658	.	.	.	4.63	4.63	0.57726	.	0.790089	0.11307	N	0.577538	T	0.57169	0.2035	L	0.54323	1.7	0.80722	D	1	P;P	0.44429	0.665;0.835	B;B	0.43728	0.429;0.429	T	0.58880	-0.7558	9	0.62326	D	0.03	6.5123	10.6289	0.45523	0.0:0.0:0.0:1.0	.	18;18	Q96M60-2;Q96M60	.;CO033_HUMAN	N	18	.	ENSP00000299338:K18N	K	-	3	2	C15orf33	47690755	0.701000	0.27806	0.486000	0.27416	0.072000	0.16883	2.098000	0.41757	2.073000	0.62155	0.533000	0.62120	AAA		0.254	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		A	49903463	T	A	49903463	3	1	61	1	0	0	0	0	1	0	0	0	1795	1838	64	5	1528	5	C15orf33	15	49903463	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34429	49903463	52627929	9340	17325										
DTWD1	56986	broad.mit.edu	37	chr15	49926782	49926782	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctcaataaaagatatttCttttcatctgcaaaaaagga	4	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:49926782C>A	ENST00000251250.6	+	5	665	c.458C>A	c.(457-459)tCt>tAt	p.S153Y	DTWD1_ENST00000403028.3_Missense_Mutation_p.S153Y|DTWD1_ENST00000415425.1_Missense_Mutation_p.S66Y|DTWD1_ENST00000559223.1_3'UTR|DTWD1_ENST00000558653.1_Missense_Mutation_p.S153Y	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	153								p.S153Y(1)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		AAAGATATTTCTTTTCATCTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	15											42	46	45					15																	49926782		2196	4293	6489	47714074	SO:0001583	missense	56986			BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.458C>A	15.37:g.49926782C>A	ENSP00000251250:p.Ser153Tyr		47714074	Q567Q3|Q8WVG9|Q9NRU6	Missense_Mutation	SNP	ENST00000251250.6	37	CCDS10132.1	.	.	.	.	.	.	.	.	.	.	C	8.941	0.965739	0.18583	.	.	ENSG00000104047	ENST00000403028;ENST00000251250;ENST00000415425	T;T	0.23950	1.88;1.88	4.95	4.95	0.65309	DTW (1);	0.532611	0.21854	N	0.068131	T	0.37785	0.1016	M	0.61703	1.905	0.80722	D	1	P;P	0.47034	0.834;0.889	B;P	0.48982	0.311;0.597	T	0.09207	-1.0685	9	.	.	.	-13.0043	16.7372	0.85449	0.0:1.0:0.0:0.0	.	66;153	Q8N5C7-2;Q8N5C7	.;DTWD1_HUMAN	Y	153;153;66	ENSP00000385399:S153Y;ENSP00000251250:S153Y	.	S	+	2	0	DTWD1	47714074	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.179000	0.31993	2.455000	0.83008	0.655000	0.94253	TCT		0.338	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234		A	49926782	C	A	49926782	3	1	61	1	0	0	0	0	1	0	0	0	4802	913	32	2	468	2	DTWD1	15	49926782	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23319	49926782	52604610	9341	17326										
ATP8B4	79895	broad.mit.edu	37	chr15	50154525	50154525	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagccactgttgttaagaGaattacaagccagatgcact	9	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50154525G>T	ENST00000284509.6	-	27	3355	c.3214C>A	c.(3214-3216)Ctc>Atc	p.L1072I	ATP8B4_ENST00000559829.1_Missense_Mutation_p.L1072I	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	1072						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.L1072I(1)		breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		GTTGTTAAGAGAATTACAAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	15											91	83	86					15																	50154525		2196	4295	6491	47941817	SO:0001583	missense	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.3214C>A	15.37:g.50154525G>T	ENSP00000284509:p.Leu1072Ile		47941817	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	3.159	-0.172483	0.06421	.	.	ENSG00000104043	ENST00000284509	T	0.63096	-0.02	5.36	2.13	0.27403	.	0.452476	0.21862	N	0.068005	T	0.34571	0.0902	N	0.21583	0.68	0.27725	N	0.945007	P;B	0.40553	0.721;0.017	B;B	0.34652	0.187;0.013	T	0.09930	-1.0652	10	0.16420	T	0.52	.	2.186	0.03887	0.1655:0.1598:0.51:0.1646	.	150;1072	Q6PG43;Q8TF62	.;AT8B4_HUMAN	I	1072	ENSP00000284509:L1072I	ENSP00000284509:L1072I	L	-	1	0	ATP8B4	47941817	1.000000	0.71417	0.999000	0.59377	0.483000	0.33249	0.954000	0.29175	1.215000	0.43411	0.563000	0.77884	CTC		0.408	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		T	50154525	G	T	50154525	3	4	61	1	0	0	0	0	1	0	0	0	1198	942	33	2	372	2	ATP8B4	15	50154525	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	227743	50154525	52376867	9342	17327										
ATP8B4	79895	broad.mit.edu	37	chr15	50264787	50264787	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttctcttaccatagattCtcccattaatggaacatctt	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50264787C>A	ENST00000284509.6	-	13	1376	c.1235G>T	c.(1234-1236)aGa>aTa	p.R412I	ATP8B4_ENST00000559829.1_Missense_Mutation_p.R412I	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	412						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R412I(1)		breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		ACCATAGATTCTCCCATTAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	71	75					15																	50264787		2196	4295	6491	48052079	SO:0001583	missense	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1235G>T	15.37:g.50264787C>A	ENSP00000284509:p.Arg412Ile		48052079	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298249	0.40694	.	.	ENSG00000104043	ENST00000284509	T	0.62639	0.01	5.08	-0.109	0.13584	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.726076	0.13544	N	0.379999	T	0.36441	0.0967	N	0.10629	0.01	0.23156	N	0.998203	B	0.14438	0.01	B	0.21546	0.035	T	0.24548	-1.0157	10	0.17369	T	0.5	.	8.7319	0.34505	0.0:0.4908:0.0:0.5092	.	412	Q8TF62	AT8B4_HUMAN	I	412	ENSP00000284509:R412I	ENSP00000284509:R412I	R	-	2	0	ATP8B4	48052079	0.000000	0.05858	0.980000	0.43619	0.969000	0.65631	-0.552000	0.06020	-0.043000	0.13513	0.650000	0.86243	AGA		0.348	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		A	50264787	C	A	50264787	3	1	61	1	0	0	0	0	1	0	0	0	1198	913	32	2	2407	2	ATP8B4	15	50264787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110262	50264787	52266605	9343	17328										
HDC	3067	broad.mit.edu	37	chr15	50544660	50544660	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacgcctgagttggcatgCctgaggtagatgggattcac	14	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50544660C>T	ENST00000267845.3	-	9	1410	c.1008G>A	c.(1006-1008)agG>agA	p.R336R	HDC_ENST00000543581.1_Silent_p.R336R	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.R336R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGTTGGCATGCCTGAGGTAGA	0.597																																					GBM(95;1627 1936 6910 9570)											1	Substitution - coding silent(1)	large_intestine(1)	15											178	143	155					15																	50544660		2196	4295	6491	48331952	SO:0001819	synonymous_variant	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1008G>A	15.37:g.50544660C>T			48331952		Silent	SNP	ENST00000267845.3	37	CCDS10134.1																																																																																				0.597	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			T	50544660	C	T	50544660	2	4	61	1	0	0	0	0	0	0	0	1	7036	738	26	3		3	HDC	15	50544660	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279873	50544660	51986732	9344	17329										
HDC	3067	broad.mit.edu	37	chr15	50550644	50550644	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcatcagccagcatgtctCctagcagggagggccaagag	14	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50550644C>A	ENST00000267845.3	-	3	677	c.275G>T	c.(274-276)gGa>gTa	p.G92V	HDC_ENST00000543581.1_Missense_Mutation_p.G92V	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0	Ala/Gly-rich.				respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.G92V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		CAGCATGTCTCCTAGCAGGGA	0.577																																					GBM(95;1627 1936 6910 9570)											1	Substitution - Missense(1)	large_intestine(1)	15											89	76	80					15																	50550644		2196	4295	6491	48337936	SO:0001583	missense	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.275G>T	15.37:g.50550644C>A	ENSP00000267845:p.Gly92Val		48337936		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	31	5.099930	0.94197	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.52526	0.66;0.66	5.69	5.69	0.88448	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.80352	0.4607	H	0.96489	3.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.86162	0.1594	10	0.87932	D	0	-15.4907	19.8006	0.96506	0.0:1.0:0.0:0.0	.	92;92	B7ZM01;P19113	.;DCHS_HUMAN	V	92	ENSP00000267845:G92V;ENSP00000440252:G92V	ENSP00000267845:G92V	G	-	2	0	HDC	48337936	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.975000	0.70475	2.687000	0.91594	0.462000	0.41574	GGA		0.577	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50550644	C	A	50550644	3	1	61	1	0	0	0	0	1	0	0	0	7036	855	30	2	1753	2	HDC	15	50550644	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5984	50550644	51980748	9345	17330										
GABPB1	2553	broad.mit.edu	37	chr15	50570923	50570923	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctttaggagctgctgtCgatatttttgtgcttctcga	9	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50570923C>T	ENST00000220429.8	-	9	1262	c.1094G>A	c.(1093-1095)cGa>cAa	p.R365Q	GABPB1_ENST00000380877.3_Missense_Mutation_p.R353Q|GABPB1_ENST00000543881.1_Missense_Mutation_p.R289Q			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	365					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R365Q(1)		cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						GAGCTGCTGTCGATATTTTTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											153	137	143					15																	50570923		2196	4295	6491	48358215	SO:0001583	missense	2553			D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.1094G>A	15.37:g.50570923C>T	ENSP00000220429:p.Arg365Gln		48358215	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Missense_Mutation	SNP	ENST00000220429.8	37	CCDS32239.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.697959	0.68386	.	.	ENSG00000104064	ENST00000220429;ENST00000380877;ENST00000543881	T	0.61859	0.07	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000010	T	0.70237	0.3201	L	0.39147	1.195	0.80722	D	1	D;D	0.69078	0.997;0.988	D;B	0.67725	0.953;0.382	T	0.71017	-0.4714	10	0.87932	D	0	-2.9041	20.3172	0.98658	0.0:1.0:0.0:0.0	.	365;353	Q06547;Q06547-2	GABP1_HUMAN;.	Q	353;365;289	ENSP00000442500:R289Q	ENSP00000220429:R353Q	R	-	2	0	GABPB1	48358215	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.792000	0.75125	2.801000	0.96364	0.650000	0.86243	CGA		0.368	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			T	50570923	C	T	50570923	3	4	61	1	0	0	0	0	1	0	0	0	6177	884	31	1	97	1	GABPB1	15	50570923	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20279	50570923	51960469	9346	17331										
GABPB1	2553	broad.mit.edu	37	chr15	50578348	50578348	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcacttataacagtttCttcagcaatgtctgttgctg	6	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50578348C>A	ENST00000220429.8	-	8	1120	c.952G>T	c.(952-954)Gaa>Taa	p.E318*	GABPB1_ENST00000429662.2_Nonsense_Mutation_p.E318*|GABPB1_ENST00000380877.3_Nonsense_Mutation_p.E306*|GABPB1_ENST00000396464.3_Nonsense_Mutation_p.E306*|GABPB1_ENST00000560825.1_Nonsense_Mutation_p.E305*|GABPB1_ENST00000359031.4_Nonsense_Mutation_p.E306*|GABPB1_ENST00000543881.1_Nonsense_Mutation_p.E242*			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	318	Transcription activation and HCFC1 interaction.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E318*(1)		cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						ATAACAGTTTCTTCAGCAATG	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											86	86	86					15																	50578348		2196	4295	6491	48365640	SO:0001587	stop_gained	2553			D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.952G>T	15.37:g.50578348C>A	ENSP00000220429:p.Glu318*		48365640	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Nonsense_Mutation	SNP	ENST00000220429.8	37	CCDS32239.1	.	.	.	.	.	.	.	.	.	.	C	37	6.540495	0.97650	.	.	ENSG00000104064	ENST00000220429;ENST00000380877;ENST00000543881;ENST00000396464;ENST00000429662;ENST00000359031	.	.	.	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-16.4616	19.9379	0.97147	0.0:1.0:0.0:0.0	.	.	.	.	X	306;318;242;306;318;306	.	ENSP00000220429:E306X	E	-	1	0	GABPB1	48365640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.710000	0.92621	0.555000	0.69702	GAA		0.313	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			A	50578348	C	A	50578348	4	1	61	1	0	0	0	0	0	1	0	0	6177	922	32	2	291	2	GABPB1	15	50578348	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7425	50578348	51953044	9347	17332										
USP8	9101	broad.mit.edu	37	chr15	50773953	50773953	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaactgaggaaggaagaAcaagaacaaaaagccaaaaa	10	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50773953A>G	ENST00000396444.3	+	11	1832	c.1494A>G	c.(1492-1494)gaA>gaG	p.E498E	USP8_ENST00000425032.3_Silent_p.E421E|USP8_ENST00000307179.4_Silent_p.E498E|USP8_ENST00000433963.1_Silent_p.E498E	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	498					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.E498E(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		ggaaggaagaacaagaacaaa	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	15											50	58	55					15																	50773953		2195	4293	6488	48561245	SO:0001819	synonymous_variant	9101			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.1494A>G	15.37:g.50773953A>G			48561245	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Silent	SNP	ENST00000396444.3	37	CCDS10137.1																																																																																				0.353	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		G	50773953	A	G	50773953	2	3	61	1	0	0	0	0	0	0	0	1	17129	40	2	4		4	USP8	15	50773953	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	195605	50773953	51757439	9348	17333										
USP8	9101	broad.mit.edu	37	chr15	50786372	50786372	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagtccaaaggactttaaAatcaccattgggaagatcaa	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50786372A>C	ENST00000396444.3	+	16	2891	c.2553A>C	c.(2551-2553)aaA>aaC	p.K851N	USP8_ENST00000425032.3_Missense_Mutation_p.K745N|RP11-562A8.5_ENST00000560159.1_lincRNA|USP8_ENST00000307179.4_Missense_Mutation_p.K851N|USP8_ENST00000433963.1_Missense_Mutation_p.K851N	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	851	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.K851N(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGGACTTTAAAATCACCATTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											133	127	129					15																	50786372		2196	4294	6490	48573664	SO:0001583	missense	9101			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2553A>C	15.37:g.50786372A>C	ENSP00000379721:p.Lys851Asn		48573664	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	19.28	3.798212	0.70567	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032;ENST00000419830;ENST00000396440	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.18	1.62	0.23740	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.53481	0.1799	M	0.74258	2.255	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.71656	0.951;0.974	T	0.53041	-0.8494	10	0.72032	D	0.01	-26.408	8.4213	0.32703	0.617:0.0:0.383:0.0	.	745;851	B4DKA8;P40818	.;UBP8_HUMAN	N	851;851;851;745;76;71	ENSP00000379721:K851N;ENSP00000405537:K851N;ENSP00000302239:K851N;ENSP00000412682:K745N	ENSP00000302239:K851N	K	+	3	2	USP8	48573664	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.995000	0.40767	0.390000	0.25115	-0.263000	0.10527	AAA		0.398	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		C	50786372	A	C	50786372	3	2	61	1	0	0	0	0	1	0	0	0	17129	11	1	4	2611	4	USP8	15	50786372	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12419	50786372	51745020	9349	17334										
USP50	373509	broad.mit.edu	37	chr15	50831000	50831000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaaaggagcagtgaatttCgttgttccaggtcagtgcgt	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50831000C>T	ENST00000532404.1	-	5	882	c.709G>A	c.(709-711)Gaa>Aaa	p.E237K	USP50_ENST00000530218.1_5'UTR	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	242	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.E242K(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		CAGTGAATTTCGTTGTTCCAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											91	85	87					15																	50831000		1866	4092	5958	48618292	SO:0001583	missense	373509			AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.709G>A	15.37:g.50831000C>T	ENSP00000434676:p.Glu237Lys		48618292	E9PP86	Missense_Mutation	SNP	ENST00000532404.1	37	CCDS53944.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.453378	0.26161	.	.	ENSG00000170236	ENST00000532404	T	0.25085	1.82	5.41	4.5	0.54988	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.212594	0.40302	N	0.001137	T	0.10165	0.0249	N	0.01277	-0.915	0.23762	N	0.996915	B	0.24092	0.097	B	0.14023	0.01	T	0.20773	-1.0265	10	0.56958	D	0.05	-3.8294	13.4742	0.61299	0.0:0.159:0.841:0.0	.	242	Q70EL3	UBP50_HUMAN	K	237	ENSP00000434676:E237K	ENSP00000434014:E12K	E	-	1	0	USP50	48618292	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	4.048000	0.57390	1.303000	0.44873	-0.182000	0.12963	GAA		0.403	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			T	50831000	C	T	50831000	3	4	61	1	0	0	0	0	1	0	0	0	17122	893	31	1	307	1	USP50	15	50831000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44628	50831000	51700392	9350	17335										
USP50	373509	broad.mit.edu	37	chr15	50835867	50835867	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatcttgttgcatctttttCgtaaatgctgggtagaggtt	11	6	2	1	rs548734276		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50835867C>T	ENST00000532404.1	-	3	545	c.372G>A	c.(370-372)acG>acA	p.T124T	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	129	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.T129T(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		GCATCTTTTTCGTAAATGCTG	0.408													c|||	1	0.000199681	0	0	5008	,	,		20117	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											65	60	61					15																	50835867		1861	4110	5971	48623159	SO:0001819	synonymous_variant	373509			AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.372G>A	15.37:g.50835867C>T			48623159	E9PP86	Silent	SNP	ENST00000532404.1	37	CCDS53944.1																																																																																				0.408	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			T	50835867	C	T	50835867	2	4	61	1	0	0	0	0	0	0	0	1	17122	871	31	1		1	USP50	15	50835867	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4867	50835867	51695525	9351	17336										
TRPM7	54822	broad.mit.edu	37	chr15	50853889	50853889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaatattataacatcagacGaacagaattagttgattctg	6	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50853889G>A	ENST00000313478.7	-	39	5865	c.5584C>T	c.(5584-5586)Cgt>Tgt	p.R1862C	RP11-120K9.2_ENST00000558237.1_RNA|TRPM7_ENST00000561443.1_5'UTR|TRPM7_ENST00000560955.1_Missense_Mutation_p.R1861C	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1862					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R1861C(2)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AACATCAGACGAACAGAATTA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	15											51	51	51					15																	50853889		1841	4092	5933	48641181	SO:0001583	missense	54822			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.5584C>T	15.37:g.50853889G>A	ENSP00000320239:p.Arg1862Cys		48641181	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605475	0.66445	.	.	ENSG00000092439	ENST00000313478	T	0.57436	0.4	4.77	4.77	0.60923	.	0.093884	0.42172	D	0.000751	T	0.59851	0.2224	M	0.66939	2.045	0.58432	D	0.999997	D	0.67145	0.996	P	0.47528	0.549	T	0.68116	-0.5494	10	0.87932	D	0	-13.6287	17.9592	0.89079	0.0:0.0:1.0:0.0	.	1862	Q96QT4	TRPM7_HUMAN	C	1862	ENSP00000320239:R1862C	ENSP00000320239:R1862C	R	-	1	0	TRPM7	48641181	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.492000	0.73654	2.470000	0.83445	0.585000	0.79938	CGT		0.363	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50853889	G	A	50853889	3	1	61	1	0	0	0	0	1	0	0	0	16631	1058	37	1	17	1	TRPM7	15	50853889	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18022	50853889	51677503	9352	17337										
TRPM7	54822	broad.mit.edu	37	chr15	50901830	50901830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaaaggcataaaactttCgcgtaattggaagctttttt	8	5	0	0	rs377252016		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50901830C>T	ENST00000313478.7	-	19	2809	c.2528G>A	c.(2527-2529)cGa>cAa	p.R843Q	TRPM7_ENST00000560955.1_Missense_Mutation_p.R843Q	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	843					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R843Q(2)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		ATAAAACTTTCGCGTAATTGG	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	15						C	GLN/ARG	1,3651		0,1,1825	177	165	169		2528	5.6	1	15		169	0,8140		0,0,4070	no	missense	TRPM7	NM_017672.4	43	0,1,5895	TT,TC,CC		0.0,0.0274,0.0085	benign	843/1866	50901830	1,11791	1826	4070	5896	48689122	SO:0001583	missense	54822			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.2528G>A	15.37:g.50901830C>T	ENSP00000320239:p.Arg843Gln		48689122	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.259084	0.59321	2.74E-4	0.0	ENSG00000092439	ENST00000313478	D	0.83914	-1.78	5.59	5.59	0.84812	.	0.060945	0.64402	D	0.000005	T	0.75004	0.3791	L	0.41710	1.295	0.42123	D	0.991433	B	0.21071	0.051	B	0.09377	0.004	T	0.71490	-0.4577	10	0.51188	T	0.08	-10.1931	9.8132	0.40835	0.0:0.8419:0.0:0.1581	.	843	Q96QT4	TRPM7_HUMAN	Q	843	ENSP00000320239:R843Q	ENSP00000320239:R843Q	R	-	2	0	TRPM7	48689122	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.738000	0.62073	2.645000	0.89757	0.467000	0.42956	CGA		0.299	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		T	50901830	C	T	50901830	3	4	61	1	0	0	0	0	1	0	0	0	16631	884	31	1	3153	1	TRPM7	15	50901830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47941	50901830	51629562	9353	17338										
TRPM7	54822	broad.mit.edu	37	chr15	50929630	50929630	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacttactagcatgaattCtttgctgattaatagttttt	5	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50929630C>A	ENST00000313478.7	-	7	1102	c.821G>T	c.(820-822)aGa>aTa	p.R274I	TRPM7_ENST00000560955.1_Missense_Mutation_p.R274I	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	274					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R274I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AGCATGAATTCTTTGCTGATT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											83	79	80					15																	50929630		1849	4088	5937	48716922	SO:0001583	missense	54822			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.821G>T	15.37:g.50929630C>A	ENSP00000320239:p.Arg274Ile		48716922	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202032	0.58234	.	.	ENSG00000092439	ENST00000313478	T	0.61040	0.14	5.36	5.36	0.76844	.	0.047465	0.85682	D	0.000000	T	0.54398	0.1856	L	0.49126	1.545	0.58432	D	0.999998	P	0.47841	0.901	B	0.38616	0.277	T	0.63024	-0.6729	10	0.87932	D	0	-17.3852	19.3357	0.94316	0.0:1.0:0.0:0.0	.	274	Q96QT4	TRPM7_HUMAN	I	274	ENSP00000320239:R274I	ENSP00000320239:R274I	R	-	2	0	TRPM7	48716922	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.192000	0.50989	2.805000	0.96524	0.650000	0.86243	AGA		0.363	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50929630	C	A	50929630	3	1	61	1	0	0	0	0	1	0	0	0	16631	913	32	2	4908	2	TRPM7	15	50929630	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27800	50929630	51601762	9354	17339										
TRPM7	54822	broad.mit.edu	37	chr15	50949997	50949997	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgacgagttgctgacaaaTttgacatcctggaaggcatc	10	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:50949997T>A	ENST00000313478.7	-	3	384	c.103A>T	c.(103-105)Att>Ttt	p.I35F	TRPM7_ENST00000560955.1_Missense_Mutation_p.I35F	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	35					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.I35F(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TGCTGACAAATTTGACATCCT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	15											58	52	54					15																	50949997		1791	4066	5857	48737289	SO:0001583	missense	54822			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.103A>T	15.37:g.50949997T>A	ENSP00000320239:p.Ile35Phe		48737289	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.992734	0.74703	.	.	ENSG00000092439	ENST00000313478	T	0.61980	0.06	4.92	4.92	0.64577	.	0.586820	0.15891	N	0.239543	T	0.54143	0.1840	N	0.20685	0.6	0.50467	D	0.999879	P	0.52316	0.952	P	0.46585	0.521	T	0.58239	-0.7671	10	0.52906	T	0.07	-14.4261	14.5931	0.68383	0.0:0.0:0.0:1.0	.	35	Q96QT4	TRPM7_HUMAN	F	35	ENSP00000320239:I35F	ENSP00000320239:I35F	I	-	1	0	TRPM7	48737289	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.704000	0.68347	1.863000	0.54032	0.528000	0.53228	ATT		0.274	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50949997	T	A	50949997	3	1	61	1	0	0	0	0	1	0	0	0	16631	1493	52	5	5642	5	TRPM7	15	50949997	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20367	50949997	51581395	9355	17340										
SPPL2A	84888	broad.mit.edu	37	chr15	51040897	51040897	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacttactaggacactgttAttgacaactaacattgcttc	5	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51040897A>G	ENST00000261854.5	-	3	622	c.348T>C	c.(346-348)aaT>aaC	p.N116N	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	116	PA.				membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.N116N(2)		endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		GGACACTGTTATTGACAACTA	0.358																																					Melanoma(50;790 1209 4069 22965 33125)											2	Substitution - coding silent(2)	large_intestine(2)	15											149	151	151					15																	51040897		2196	4294	6490	48828189	SO:0001819	synonymous_variant	84888				CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"intramembrane protease 3", "presenilin-like protein 2"	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.348T>C	15.37:g.51040897A>G			48828189	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																				0.358	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		G	51040897	A	G	51040897	2	3	61	1	0	0	0	0	0	0	0	1	15127	446	16	4		4	SPPL2A	15	51040897	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	90900	51040897	51490495	9356	17341										
AP4E1	23431	broad.mit.edu	37	chr15	51217364	51217364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagccagattttcccctgcGaaatgattccagctgttctt	7	11	1	2	rs556357549		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51217364G>A	ENST00000261842.5	+	5	596	c.490G>A	c.(490-492)Gaa>Aaa	p.E164K	AP4E1_ENST00000560508.1_Missense_Mutation_p.E89K	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	164					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.E164K(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		TTTCCCCTGCGAAATGATTCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											123	109	114					15																	51217364		2196	4294	6490	49004656	SO:0001583	missense	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.490G>A	15.37:g.51217364G>A	ENSP00000261842:p.Glu164Lys		49004656	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.024927	0.93518	.	.	ENSG00000081014	ENST00000261842	T	0.16897	2.31	5.53	5.53	0.82687	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.052250	0.85682	D	0.000000	T	0.45597	0.1350	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	0.971;1.0	P;D	0.74023	0.593;0.982	T	0.44050	-0.9353	10	0.87932	D	0	-20.3531	18.4414	0.90667	0.0:0.0:1.0:0.0	.	164;164	B4DM48;Q9UPM8	.;AP4E1_HUMAN	K	164	ENSP00000261842:E164K	ENSP00000261842:E164K	E	+	1	0	AP4E1	49004656	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	9.444000	0.97578	2.597000	0.87782	0.460000	0.39030	GAA		0.368	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			A	51217364	G	A	51217364	3	1	61	1	0	0	0	0	1	0	0	0	752	1059	37	1	508	1	AP4E1	15	51217364	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176467	51217364	51314028	9357	17342										
AP4E1	23431	broad.mit.edu	37	chr15	51223004	51223004	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgcggggggatgtaggaGaattcatctggatataaaga	14	3	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51223004G>T	ENST00000261842.5	+	7	811	c.705G>T	c.(703-705)gaG>gaT	p.E235D	AP4E1_ENST00000560508.1_Missense_Mutation_p.E160D	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	235					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.E235D(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GGATGTAGGAGAATTCATCTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	85	84					15																	51223004		2196	4294	6490	49010296	SO:0001583	missense	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.705G>T	15.37:g.51223004G>T	ENSP00000261842:p.Glu235Asp		49010296	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559131	0.27827	.	.	ENSG00000081014	ENST00000261842	T	0.25912	1.77	6.02	5.1	0.69264	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.161074	0.56097	D	0.000039	T	0.16128	0.0388	L	0.31294	0.92	0.53688	D	0.999979	B;B	0.18013	0.025;0.004	B;B	0.20184	0.028;0.014	T	0.12041	-1.0563	10	0.20519	T	0.43	-10.8666	5.7776	0.18287	0.1754:0.1617:0.6629:0.0	.	235;235	B4DM48;Q9UPM8	.;AP4E1_HUMAN	D	235	ENSP00000261842:E235D	ENSP00000261842:E235D	E	+	3	2	AP4E1	49010296	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	3.562000	0.53777	1.533000	0.49186	0.655000	0.94253	GAG		0.348	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51223004	G	T	51223004	3	4	61	1	0	0	0	0	1	0	0	0	752	933	33	2	731	2	AP4E1	15	51223004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5640	51223004	51308388	9358	17343										
AP4E1	23431	broad.mit.edu	37	chr15	51289577	51289577	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggaaatcaaaagtcaaaGaagctaaaagtggcgaaaca	10	5	2	1	rs556450190		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51289577G>T	ENST00000261842.5	+	18	2507	c.2401G>T	c.(2401-2403)Gaa>Taa	p.E801*	AP4E1_ENST00000560508.1_Nonsense_Mutation_p.E726*	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	801					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.E801*(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AAAAGTCAAAGAAGCTAAAAG	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											100	96	98					15																	51289577		2196	4294	6490	49076869	SO:0001587	stop_gained	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2401G>T	15.37:g.51289577G>T	ENSP00000261842:p.Glu801*		49076869	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Nonsense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	35	5.493681	0.96339	.	.	ENSG00000081014	ENST00000261842	.	.	.	5.19	4.27	0.50696	.	0.610687	0.17659	N	0.166417	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-6.1057	10.7309	0.46096	0.1488:0.0:0.8512:0.0	.	.	.	.	X	801	.	ENSP00000261842:E801X	E	+	1	0	AP4E1	49076869	1.000000	0.71417	0.888000	0.34837	0.191000	0.23601	3.963000	0.56773	2.417000	0.82017	0.467000	0.42956	GAA		0.323	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51289577	G	T	51289577	4	4	61	1	0	0	0	0	0	1	0	0	752	943	33	2	2471	2	AP4E1	15	51289577	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66573	51289577	51241815	9359	17344										
AP4E1	23431	broad.mit.edu	37	chr15	51289708	51289708	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggagacaaggaattaaaGaaattttctctcacttcaga	7	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51289708G>T	ENST00000261842.5	+	18	2638	c.2532G>T	c.(2530-2532)aaG>aaT	p.K844N	AP4E1_ENST00000560508.1_Missense_Mutation_p.K769N	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	844					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.K844N(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AGGAATTAAAGAAATTTTCTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	15											122	120	121					15																	51289708		2196	4294	6490	49077000	SO:0001583	missense	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2532G>T	15.37:g.51289708G>T	ENSP00000261842:p.Lys844Asn		49077000	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	1.321	-0.599473	0.03744	.	.	ENSG00000081014	ENST00000261842	T	0.18338	2.22	5.1	3.17	0.36434	.	1.211720	0.05759	N	0.604546	T	0.09642	0.0237	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.17369	T	0.5	0.3992	8.4729	0.32997	0.0747:0.0:0.6415:0.2838	.	844	Q9UPM8	AP4E1_HUMAN	N	844	ENSP00000261842:K844N	ENSP00000261842:K844N	K	+	3	2	AP4E1	49077000	0.879000	0.30193	0.568000	0.28447	0.105000	0.19272	0.318000	0.19504	0.489000	0.27749	0.467000	0.42956	AAG		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51289708	G	T	51289708	3	4	61	1	0	0	0	0	1	0	0	0	752	933	33	2	2602	2	AP4E1	15	51289708	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131	51289708	51241684	9360	17345										
TNFAIP8L3	388121	broad.mit.edu	37	chr15	51350201	51350201	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcggcaaagtggttaaaGacgtggttgatgcgcccgtg	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51350201G>T	ENST00000327536.5	-	3	855	c.756C>A	c.(754-756)gtC>gtA	p.V252V	RP11-108K3.1_ENST00000559909.1_lincRNA	NM_207381.2	NP_997264.2	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 3	252								p.V252V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	11				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		AGTGGTTAAAGACGTGGTTGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	15											78	67	71					15																	51350201		2196	4293	6489	49137493	SO:0001819	synonymous_variant	388121			AK123281	CCDS32241.1	15q21.2	2005-08-09				ENSG00000183578			20620	protein-coding gene	gene with protein product							Standard	XM_005254367		Approved	FLJ41287	uc001zyy.3	Q5GJ75		ENST00000327536.5:c.756C>A	15.37:g.51350201G>T			49137493	Q6ZWD1	Silent	SNP	ENST00000327536.5	37	CCDS32241.1																																																																																				0.542	TNFAIP8L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418661.1	NM_207381		T	51350201	G	T	51350201	2	4	61	1	0	0	0	0	0	0	0	1	16318	929	33	2		2	TNFAIP8L3	15	51350201	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60493	51350201	51181191	9361	17346										
CYP19A1	1588	broad.mit.edu	37	chr15	51503240	51503240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagccaaatggctgaaagTacctataaggaacctatgaa	8	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51503240T>C	ENST00000396402.1	-	10	1430	c.1277A>G	c.(1276-1278)tAc>tGc	p.Y426C	CYP19A1_ENST00000559878.1_Missense_Mutation_p.Y426C|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000260433.2_Missense_Mutation_p.Y426C|CYP19A1_ENST00000396404.4_Missense_Mutation_p.Y426C	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	426					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.Y426C(1)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	TGGCTGAAAGTACCTATAAGG	0.448																																					Melanoma(142;1016 1807 39614 48966 51721)											1	Substitution - Missense(1)	large_intestine(1)	15											71	60	63					15																	51503240		2196	4293	6489	49290532	SO:0001583	missense	1588			D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"Cytochrome P450s"	2594	protein-coding gene	gene with protein product		107910	"cytochrome P450, subfamily XIX (aromatization of androgens)"	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.1277A>G	15.37:g.51503240T>C	ENSP00000379683:p.Tyr426Cys		49290532	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	37	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	T	19.19	3.779028	0.70107	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000396404	T;T;T	0.69926	-0.44;-0.44;-0.44	5.37	5.37	0.77165	.	0.109295	0.64402	D	0.000004	D	0.82403	0.5029	M	0.83312	2.635	0.58432	D	0.999999	D	0.76494	0.999	D	0.68353	0.957	D	0.85501	0.1191	10	0.87932	D	0	-15.5739	15.6507	0.77091	0.0:0.0:0.0:1.0	.	426	P11511	CP19A_HUMAN	C	426	ENSP00000379683:Y426C;ENSP00000260433:Y426C;ENSP00000379685:Y426C	ENSP00000260433:Y426C	Y	-	2	0	CYP19A1	49290532	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.548000	0.60718	2.163000	0.67991	0.482000	0.46254	TAC		0.448	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1			C	51503240	T	C	51503240	3	2	61	1	0	0	0	0	1	0	0	0	4154	1638	57	4	238	4	CYP19A1	15	51503240	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	153039	51503240	51028152	9362	17347										
DMXL2	23312	broad.mit.edu	37	chr15	51791231	51791231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccacttacactaatagttCgagagagatgtcgcttagtt	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51791231C>T	ENST00000251076.5	-	18	4477	c.4190G>A	c.(4189-4191)cGa>cAa	p.R1397Q	DMXL2_ENST00000543779.2_Missense_Mutation_p.R1397Q|DMXL2_ENST00000449909.3_Intron|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1397						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.R1397Q(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ACTAATAGTTCGAGAGAGATG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											238	222	227					15																	51791231		2195	4293	6488	49578523	SO:0001583	missense	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.4190G>A	15.37:g.51791231C>T	ENSP00000251076:p.Arg1397Gln		49578523	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689686	0.88735	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.23348	1.91;1.91	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.84683	2.71	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.74674	0.976;0.984	T	0.59984	-0.7351	10	0.49607	T	0.09	.	19.736	0.96205	0.0:1.0:0.0:0.0	.	1397;1397	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	Q	1397	ENSP00000251076:R1397Q;ENSP00000441858:R1397Q	ENSP00000251076:R1397Q	R	-	2	0	DMXL2	49578523	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.427000	0.80284	2.669000	0.90835	0.591000	0.81541	CGA		0.413	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51791231	C	T	51791231	3	4	61	1	0	0	0	0	1	0	0	0	4606	884	31	1	5027	1	DMXL2	15	51791231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	287991	51791231	50740161	9363	17348										
DMXL2	23312	broad.mit.edu	37	chr15	51806663	51806663	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatggctgaaaaaatatttCtgtttcctttttctccatat	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51806663C>A	ENST00000251076.5	-	15	2907	c.2620G>T	c.(2620-2622)Gaa>Taa	p.E874*	DMXL2_ENST00000543779.2_Nonsense_Mutation_p.E874*|DMXL2_ENST00000449909.3_Nonsense_Mutation_p.E874*	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	874						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.E874*(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AAAAATATTTCTGTTTCCTTT	0.318																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											204	195	198					15																	51806663		2195	4292	6487	49593955	SO:0001587	stop_gained	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2620G>T	15.37:g.51806663C>A	ENSP00000251076:p.Glu874*		49593955	B2RTR3|B7ZMH3|F5GWF1|O94938	Nonsense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	40	8.035752	0.98621	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	4.97	4.97	0.65823	.	0.368200	0.32970	N	0.005427	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	18.5956	0.91228	0.0:1.0:0.0:0.0	.	.	.	.	X	874	.	ENSP00000251076:E874X	E	-	1	0	DMXL2	49593955	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.980000	0.70516	2.472000	0.83506	0.591000	0.81541	GAA		0.318	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51806663	C	A	51806663	4	1	61	1	0	0	0	0	0	1	0	0	4606	922	32	2	6609	2	DMXL2	15	51806663	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15432	51806663	50724729	9364	17349										
DMXL2	23312	broad.mit.edu	37	chr15	51828668	51828668	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcaatagagcattatgaTgagaggatgtcaataacagt	11	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51828668T>G	ENST00000251076.5	-	12	2296	c.2009A>C	c.(2008-2010)cAt>cCt	p.H670P	DMXL2_ENST00000543779.2_Missense_Mutation_p.H670P|DMXL2_ENST00000449909.3_Missense_Mutation_p.H670P	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	670						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.H670P(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AGCATTATGATGAGAGGATGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											95	94	94					15																	51828668		2195	4293	6488	49615960	SO:0001583	missense	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2009A>C	15.37:g.51828668T>G	ENSP00000251076:p.His670Pro		49615960	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.438309	0.62955	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.11277	2.79;2.79;2.79	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	M	0.84433	2.695	0.38944	D	0.958201	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.91635	0.999;0.994;0.994	T	0.47275	-0.9130	10	0.87932	D	0	.	15.14	0.72604	0.0:0.0:0.0:1.0	.	670;670;670	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	P	670	ENSP00000251076:H670P;ENSP00000441858:H670P;ENSP00000400855:H670P	ENSP00000251076:H670P	H	-	2	0	DMXL2	49615960	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	1.966000	0.57179	0.533000	0.62120	CAT		0.368	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		G	51828668	T	G	51828668	3	3	61	1	0	0	0	0	1	0	0	0	4606	1464	51	4	7232	4	DMXL2	15	51828668	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22005	51828668	50702724	9365	17350										
SCG3	29106	broad.mit.edu	37	chr15	51974734	51974734	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaatctctacataatagaGaattaagtgcagaaagacct	6	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:51974734G>A	ENST00000220478.3	+	2	506	c.103G>A	c.(103-105)Gaa>Aaa	p.E35K	SCG3_ENST00000542355.2_Intron	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III	35					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)	p.E35K(1)		breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		ACATAATAGAGAATTAAGTGC	0.239																																																1	Substitution - Missense(1)	large_intestine(1)	15											42	48	46					15																	51974734		2190	4268	6458	49762026	SO:0001583	missense	29106			AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.103G>A	15.37:g.51974734G>A	ENSP00000220478:p.Glu35Lys		49762026	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	Missense_Mutation	SNP	ENST00000220478.3	37	CCDS10142.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707155	0.89018	.	.	ENSG00000104112	ENST00000220478	T	0.26810	1.71	5.68	5.68	0.88126	.	0.164901	0.52532	D	0.000072	T	0.31765	0.0807	L	0.29908	0.895	0.80722	D	1	D	0.57571	0.98	P	0.52514	0.701	T	0.02444	-1.1158	10	0.72032	D	0.01	.	16.2945	0.82763	0.0:0.1411:0.8589:0.0	.	35	Q8WXD2	SCG3_HUMAN	K	35	ENSP00000220478:E35K	ENSP00000220478:E35K	E	+	1	0	SCG3	49762026	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.306000	0.51881	2.677000	0.91161	0.491000	0.48974	GAA		0.239	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254670.2	NM_013243		A	51974734	G	A	51974734	3	1	61	1	0	0	0	0	1	0	0	0	13929	943	33	3	109	3	SCG3	15	51974734	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146066	51974734	50556658	9366	17351										
MAPK6	5597	broad.mit.edu	37	chr15	52356227	52356227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtacaagttgatccccGaaaatatttggatggagatc	10	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52356227G>A	ENST00000261845.5	+	6	2003	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	399					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.R399Q(1)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		GTTGATCCCCGAAAATATTTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	83	85					15																	52356227		2195	4293	6488	50143519	SO:0001583	missense	5597			L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.1196G>A	15.37:g.52356227G>A	ENSP00000261845:p.Arg399Gln		50143519	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	G	33	5.276927	0.95459	.	.	ENSG00000069956	ENST00000261845	T	0.45668	0.89	5.26	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.40372	0.1114	L	0.59436	1.845	0.80722	D	1	B	0.24533	0.105	B	0.12156	0.007	T	0.43893	-0.9363	10	0.87932	D	0	-6.9633	14.2942	0.66300	0.0731:0.0:0.9269:0.0	.	399	Q16659	MK06_HUMAN	Q	399	ENSP00000261845:R399Q	ENSP00000261845:R399Q	R	+	2	0	MAPK6	50143519	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.211000	0.95120	2.501000	0.84356	0.644000	0.83932	CGA		0.408	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		A	52356227	G	A	52356227	3	1	61	1	0	0	0	0	1	0	0	0	9311	1058	37	1	1214	1	MAPK6	15	52356227	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	381493	52356227	50175165	9367	17352										
MYO5C	55930	broad.mit.edu	37	chr15	52531991	52531991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagctgaatattaagcacgAatcgtcggatactctggaat	9	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52531991A>G	ENST00000261839.7	-	21	2803	c.2642T>C	c.(2641-2643)tTc>tCc	p.F881S	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	881	IQ 5. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.F881S(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATTAAGCACGAATCGTCGGAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	15											80	76	77					15																	52531991		1962	4157	6119	50319283	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2642T>C	15.37:g.52531991A>G	ENSP00000261839:p.Phe881Ser		50319283	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.850672	0.51270	.	.	ENSG00000128833	ENST00000261839	T	0.70045	-0.45	5.43	5.43	0.79202	.	0.123891	0.56097	D	0.000031	T	0.44414	0.1292	N	0.05078	-0.115	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.40289	-0.9571	10	0.12430	T	0.62	.	15.1608	0.72782	1.0:0.0:0.0:0.0	.	881	Q9NQX4	MYO5C_HUMAN	S	881	ENSP00000261839:F881S	ENSP00000261839:F881S	F	-	2	0	MYO5C	50319283	1.000000	0.71417	0.813000	0.32504	0.992000	0.81027	8.962000	0.93254	2.058000	0.61347	0.528000	0.53228	TTC		0.438	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52531991	A	G	52531991	3	3	61	1	0	0	0	0	1	0	0	0	10110	246	9	4	2670	4	MYO5C	15	52531991	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	175764	52531991	49999401	9368	17353										
MYO5C	55930	broad.mit.edu	37	chr15	52553238	52553238	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgtctcagagcttgtgacGattttgcgattgcacagcca	10	11	1	2	rs199783351	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52553238G>A	ENST00000261839.7	-	10	1295	c.1134C>T	c.(1132-1134)atC>atT	p.I378I	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Silent_p.I321I	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	378	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.I378I(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		AGCTTGTGACGATTTTGCGAT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	15											91	93	92					15																	52553238		2034	4194	6228	50340530	SO:0001819	synonymous_variant	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1134C>T	15.37:g.52553238G>A			50340530	Q6P1W8	Silent	SNP	ENST00000261839.7	37	CCDS42036.1																																																																																				0.532	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52553238	G	A	52553238	2	1	61	1	0	0	0	0	0	0	0	1	10110	1048	37	1		1	MYO5C	15	52553238	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21247	52553238	49978154	9369	17354										
MYO5C	55930	broad.mit.edu	37	chr15	52567856	52567856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcatggcatagcgagccGacactgtctttccagcacct	8	15	2	0	rs201485345		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52567856G>A	ENST00000261839.7	-	5	670	c.509C>T	c.(508-510)tCg>tTg	p.S170L	MYO5C_ENST00000541028.1_5'UTR|MIR1266_ENST00000408125.1_RNA|MYO5C_ENST00000443683.2_Missense_Mutation_p.S113L	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	170	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S170L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATAGCGAGCCGACACTGTCTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	LEU/SER	0,4226		0,0,2113	127	129	128		509	5.3	1	15		128	2,8434		0,2,4216	yes	missense	MYO5C	NM_018728.3	145	0,2,6329	AA,AG,GG		0.0237,0.0,0.0158	probably-damaging	170/1743	52567856	2,12660	2113	4218	6331	50355148	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.509C>T	15.37:g.52567856G>A	ENSP00000261839:p.Ser170Leu		50355148	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	33	5.204513	0.95033	0.0	2.37E-4	ENSG00000128833	ENST00000261839;ENST00000443683;ENST00000541028	D;D	0.87887	-2.31;-2.31	5.32	5.32	0.75619	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.95947	0.8680	H	0.96547	3.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97213	0.9872	10	0.87932	D	0	.	19.0034	0.92842	0.0:0.0:1.0:0.0	.	133;170	F5H231;Q9NQX4	.;MYO5C_HUMAN	L	170;113;133	ENSP00000261839:S170L;ENSP00000410582:S113L	ENSP00000261839:S170L	S	-	2	0	MYO5C	50355148	1.000000	0.71417	0.960000	0.40013	0.768000	0.43524	9.869000	0.99810	2.484000	0.83849	0.467000	0.42956	TCG		0.473	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52567856	G	A	52567856	3	1	61	1	0	0	0	0	1	0	0	0	10110	1059	37	1	4867	1	MYO5C	15	52567856	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14618	52567856	49963536	9370	17355										
MYO5A	4644	broad.mit.edu	37	chr15	52662575	52662575	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagttgtatattccttccaGattggttagtttctccacaa	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52662575G>T	ENST00000399231.3	-	22	3100	c.2857C>A	c.(2857-2859)Ctg>Atg	p.L953M	MYO5A_ENST00000356338.6_Missense_Mutation_p.L953M|MYO5A_ENST00000553916.1_Missense_Mutation_p.L953M|MYO5A_ENST00000399233.2_Missense_Mutation_p.L953M|MYO5A_ENST00000358212.6_Missense_Mutation_p.L953M	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	953					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)	p.L953M(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATTCCTTCCAGATTGGTTAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											58	57	57					15																	52662575		1853	4077	5930	50449867	SO:0001583	missense	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.2857C>A	15.37:g.52662575G>T	ENSP00000382177:p.Leu953Met		50449867	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601490	0.46423	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	5.69	3.74	0.42951	.	0.000000	0.64402	D	0.000001	T	0.16685	0.0401	L	0.43152	1.355	0.53005	D	0.999966	B;P	0.34462	0.439;0.454	B;B	0.25614	0.062;0.047	T	0.05370	-1.0889	10	0.59425	D	0.04	.	11.9996	0.53222	0.1435:0.0:0.8565:0.0	.	953;953	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	M	953;487;953;953;953;583;953	ENSP00000382177:L953M;ENSP00000382179:L953M;ENSP00000348693:L953M;ENSP00000350945:L953M;ENSP00000451109:L953M	ENSP00000348693:L953M	L	-	1	2	MYO5A	50449867	0.977000	0.34250	0.997000	0.53966	0.973000	0.67179	1.696000	0.37773	1.340000	0.45581	0.655000	0.94253	CTG		0.368	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		T	52662575	G	T	52662575	3	4	61	1	0	0	0	0	1	0	0	0	10108	933	33	2	2790	2	MYO5A	15	52662575	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94719	52662575	49868817	9371	17356										
KIAA1370	56204	broad.mit.edu	37	chr15	52876985	52876985	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccgttcttctgtgtgtcGgatgttctctttattaacac	7	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52876985G>A	ENST00000261844.7	-	12	3186	c.3034C>T	c.(3034-3036)Cga>Tga	p.R1012*	RP11-23N2.4_ENST00000562062.1_RNA|RP11-23N2.4_ENST00000566344.1_RNA|FAM214A_ENST00000546305.2_Nonsense_Mutation_p.R1019*	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	1012								p.R1012*(1)									TCTGTGTGTCGGATGTTCTCT	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											169	166	167					15																	52876985		1862	4101	5963	50664277	SO:0001587	stop_gained	56204			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.3034C>T	15.37:g.52876985G>A	ENSP00000261844:p.Arg1012*		50664277	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Nonsense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215373	0.79352	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000546305	.	.	.	5.3	5.3	0.74995	.	0.858652	0.10383	N	0.681335	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3121	0.94192	0.0:0.0:1.0:0.0	.	.	.	.	X	1012;1012;1019	.	ENSP00000261844:R1012X	R	-	1	2	KIAA1370	50664277	0.998000	0.40836	0.938000	0.37757	0.977000	0.68977	2.771000	0.47670	2.636000	0.89361	0.467000	0.42956	CGA		0.343	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		A	52876985	G	A	52876985	4	1	61	1	0	0	0	0	0	1	0	0	8247	1124	39	1	204	1	KIAA1370	15	52876985	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214410	52876985	49654407	9372	17357										
KIAA1370	56204	broad.mit.edu	37	chr15	52897412	52897412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaatgaaaattatgttttCgccacacatttgaatgtttc	7	6	0	2	rs556851664		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52897412C>T	ENST00000261844.7	-	7	2530	c.2378G>A	c.(2377-2379)cGa>cAa	p.R793Q	FAM214A_ENST00000546305.2_Missense_Mutation_p.R800Q	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	793								p.R793Q(1)									ATTATGTTTTCGCCACACATT	0.333													C|||	1	0.000199681	8e-04	0	5008	,	,		15749	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											157	157	157					15																	52897412		1839	4095	5934	50684704	SO:0001583	missense	56204			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2378G>A	15.37:g.52897412C>T	ENSP00000261844:p.Arg793Gln		50684704	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.240354	0.22711	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.32753	1.44;1.44	5.06	-0.609	0.11608	.	0.342225	0.30752	N	0.008951	T	0.13372	0.0324	N	0.11427	0.14	0.29139	N	0.879132	B;B	0.17268	0.021;0.012	B;B	0.08055	0.003;0.001	T	0.23154	-1.0196	10	0.20046	T	0.44	.	10.2715	0.43485	0.0:0.4698:0.0:0.5302	.	800;793	F5H8G0;Q32MH5	.;K1370_HUMAN	Q	793;793;792;800	ENSP00000261844:R793Q;ENSP00000443598:R800Q	ENSP00000261844:R793Q	R	-	2	0	KIAA1370	50684704	0.001000	0.12720	0.690000	0.30148	0.995000	0.86356	-0.898000	0.04105	-0.294000	0.08973	0.650000	0.86243	CGA		0.333	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		T	52897412	C	T	52897412	3	4	61	1	0	0	0	0	1	0	0	0	8247	884	31	1	880	1	KIAA1370	15	52897412	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20427	52897412	49633980	9373	17358										
KIAA1370	56204	broad.mit.edu	37	chr15	52902223	52902223	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggatatagtttgatattTttgacagctgcagtatattc	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:52902223T>G	ENST00000261844.7	-	6	1040	c.888A>C	c.(886-888)aaA>aaC	p.K296N	FAM214A_ENST00000546305.2_Missense_Mutation_p.K303N	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	296								p.K296N(1)									GTTTGATATTTTTGACAGCTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											88	72	77					15																	52902223		1862	4091	5953	50689515	SO:0001583	missense	56204			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.888A>C	15.37:g.52902223T>G	ENSP00000261844:p.Lys296Asn		50689515	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.586120	0.28268	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.37411	1.2;1.2	5.19	2.89	0.33648	.	0.369554	0.34046	N	0.004319	T	0.38665	0.1049	L	0.60455	1.87	0.27422	N	0.954252	P;P	0.47545	0.897;0.835	P;B	0.49853	0.624;0.42	T	0.16748	-1.0392	10	0.21014	T	0.42	.	9.0295	0.36249	0.0:0.1493:0.0:0.8507	.	303;296	F5H8G0;Q32MH5	.;K1370_HUMAN	N	296;296;295;303	ENSP00000261844:K296N;ENSP00000443598:K303N	ENSP00000261844:K296N	K	-	3	2	KIAA1370	50689515	1.000000	0.71417	0.997000	0.53966	0.355000	0.29361	2.661000	0.46758	0.925000	0.37094	0.533000	0.62120	AAA		0.418	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		G	52902223	T	G	52902223	3	3	61	1	0	0	0	0	1	0	0	0	8247	1838	64	4	2374	4	KIAA1370	15	52902223	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4811	52902223	49629169	9374	17359										
WDR72	256764	broad.mit.edu	37	chr15	53809937	53809937	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctttgctatccatgaatGatgccttggctcacctagga	9	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:53809937G>T	ENST00000396328.1	-	20	3507	c.3268C>A	c.(3268-3270)Cat>Aat	p.H1090N	WDR72_ENST00000559418.1_Missense_Mutation_p.H1100N|WDR72_ENST00000557913.1_Missense_Mutation_p.H1087N|WDR72_ENST00000360509.5_Missense_Mutation_p.H1090N|WDR72_ENST00000567224.1_5'UTR	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1090								p.H1090N(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		ATCCATGAATGATGCCTTGGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											141	134	137					15																	53809937		2194	4293	6487	51597229	SO:0001583	missense	256764			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.3268C>A	15.37:g.53809937G>T	ENSP00000379619:p.His1090Asn		51597229	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535336	0.45176	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.35789	1.29;1.29	5.85	5.85	0.93711	.	0.225469	0.31438	N	0.007657	T	0.26011	0.0634	N	0.22421	0.69	0.23464	N	0.997621	B	0.21071	0.051	B	0.14578	0.011	T	0.11108	-1.0601	10	0.31617	T	0.26	.	14.0439	0.64693	0.0:0.0:0.8493:0.1507	.	1090	Q3MJ13	WDR72_HUMAN	N	1090	ENSP00000379619:H1090N;ENSP00000353699:H1090N	ENSP00000353699:H1090N	H	-	1	0	WDR72	51597229	1.000000	0.71417	0.963000	0.40424	0.933000	0.57130	4.393000	0.59665	2.773000	0.95371	0.585000	0.79938	CAT		0.413	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		T	53809937	G	T	53809937	3	4	61	1	0	0	0	0	1	0	0	0	17362	1290	45	2	44	2	WDR72	15	53809937	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	907714	53809937	48721455	9375	17360										
WDR72	256764	broad.mit.edu	37	chr15	53815457	53815457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcacatctgtcaggcatgtCctccacgtcttggaagtttg	11	11	3	0	rs148695841	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:53815457C>T	ENST00000396328.1	-	19	3450	c.3211G>A	c.(3211-3213)Gac>Aac	p.D1071N	WDR72_ENST00000559418.1_Missense_Mutation_p.D1081N|WDR72_ENST00000557913.1_Missense_Mutation_p.D1068N|WDR72_ENST00000360509.5_Missense_Mutation_p.D1071N|WDR72_ENST00000567224.1_5'UTR	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1071								p.D1071N(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		TCAGGCATGTCCTCCACGTCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15											193	185	188					15																	53815457		2194	4293	6487	51602749	SO:0001583	missense	256764			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.3211G>A	15.37:g.53815457C>T	ENSP00000379619:p.Asp1071Asn		51602749	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.269843	0.40095	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.50813	0.73;0.73	6.17	4.3	0.51218	.	0.097447	0.46442	D	0.000290	T	0.38957	0.1060	L	0.51422	1.61	0.30349	N	0.784954	B	0.18461	0.028	B	0.17433	0.018	T	0.33675	-0.9859	10	0.13108	T	0.6	.	11.8513	0.52413	0.0:0.8607:0.0:0.1393	.	1071	Q3MJ13	WDR72_HUMAN	N	1071	ENSP00000379619:D1071N;ENSP00000353699:D1071N	ENSP00000353699:D1071N	D	-	1	0	WDR72	51602749	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	2.204000	0.42761	1.625000	0.50366	0.655000	0.94253	GAC		0.448	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		T	53815457	C	T	53815457	3	4	61	1	0	0	0	0	1	0	0	0	17362	855	30	3	105	3	WDR72	15	53815457	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5520	53815457	48715935	9376	17361										
WDR72	256764	broad.mit.edu	37	chr15	53907722	53907722	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtatctgactctcgcaaaGaatcacaattattttccaat	4	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:53907722G>T	ENST00000396328.1	-	15	2920	c.2681C>A	c.(2680-2682)tCt>tAt	p.S894Y	WDR72_ENST00000559418.1_Missense_Mutation_p.S904Y|WDR72_ENST00000557913.1_Missense_Mutation_p.S891Y|WDR72_ENST00000360509.5_Missense_Mutation_p.S894Y	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	894								p.S894Y(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CTCTCGCAAAGAATCACAATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	15											48	49	49					15																	53907722		2194	4293	6487	51695014	SO:0001583	missense	256764			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.2681C>A	15.37:g.53907722G>T	ENSP00000379619:p.Ser894Tyr		51695014	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	6.922	0.539728	0.13250	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.36878	1.23;1.23	5.72	3.82	0.43975	.	0.665843	0.14679	N	0.304862	T	0.25827	0.0629	L	0.32530	0.975	0.09310	N	1	B	0.20550	0.046	B	0.21151	0.033	T	0.22800	-1.0206	10	0.59425	D	0.04	.	5.2007	0.15262	0.0757:0.2828:0.5104:0.1312	.	894	Q3MJ13	WDR72_HUMAN	Y	894	ENSP00000379619:S894Y;ENSP00000353699:S894Y	ENSP00000353699:S894Y	S	-	2	0	WDR72	51695014	0.002000	0.14202	0.929000	0.37066	0.474000	0.32979	1.126000	0.31344	0.747000	0.32809	-0.137000	0.14449	TCT		0.338	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		T	53907722	G	T	53907722	3	4	61	1	0	0	0	0	1	0	0	0	17362	942	33	2	651	2	WDR72	15	53907722	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92265	53907722	48623670	9377	17362										
WDR72	256764	broad.mit.edu	37	chr15	53957939	53957939	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaataattcgtgctctttCtcctgtctcatgtctttcca	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:53957939C>A	ENST00000396328.1	-	14	2031	c.1792G>T	c.(1792-1794)Gaa>Taa	p.E598*	WDR72_ENST00000559418.1_Nonsense_Mutation_p.E608*|WDR72_ENST00000557913.1_Nonsense_Mutation_p.E595*|WDR72_ENST00000360509.5_Nonsense_Mutation_p.E598*	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	598								p.E598*(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CGTGCTCTTTCTCCTGTCTCA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											116	104	108					15																	53957939		2194	4293	6487	51745231	SO:0001587	stop_gained	256764			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1792G>T	15.37:g.53957939C>A	ENSP00000379619:p.Glu598*		51745231	Q7Z3I3|Q8N8X2	Nonsense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	39	7.397981	0.98258	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	.	.	.	5.57	4.65	0.58169	.	0.482624	0.22591	N	0.058097	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	13.3893	0.60813	0.0:0.9243:0.0:0.0757	.	.	.	.	X	598	.	ENSP00000353699:E598X	E	-	1	0	WDR72	51745231	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.791000	0.55469	1.348000	0.45733	0.563000	0.77884	GAA		0.373	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		A	53957939	C	A	53957939	4	1	61	1	0	0	0	0	0	1	0	0	17362	922	32	2	1544	2	WDR72	15	53957939	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50217	53957939	48573453	9378	17363										
WDR72	256764	broad.mit.edu	37	chr15	53997398	53997398	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatgcttatcaaaattatCttgaagagtccaggtggcag	9	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:53997398C>A	ENST00000396328.1	-	11	1374	c.1135G>T	c.(1135-1137)Gat>Tat	p.D379Y	WDR72_ENST00000559418.1_Missense_Mutation_p.D389Y|WDR72_ENST00000557913.1_Missense_Mutation_p.D376Y|WDR72_ENST00000360509.5_Missense_Mutation_p.D379Y	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	379								p.D379Y(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		TCAAAATTATCTTGAAGAGTC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	15											75	75	75					15																	53997398		2194	4293	6487	51784690	SO:0001583	missense	256764			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1135G>T	15.37:g.53997398C>A	ENSP00000379619:p.Asp379Tyr		51784690	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.565029	0.65651	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.61392	0.11;0.11	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.063984	0.64402	D	0.000005	T	0.75583	0.3869	M	0.68317	2.08	0.43126	D	0.994852	D	0.89917	1.0	D	0.73380	0.98	T	0.77230	-0.2664	10	0.87932	D	0	.	18.9451	0.92620	0.0:1.0:0.0:0.0	.	379	Q3MJ13	WDR72_HUMAN	Y	379	ENSP00000379619:D379Y;ENSP00000353699:D379Y	ENSP00000353699:D379Y	D	-	1	0	WDR72	51784690	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.975000	0.56859	2.729000	0.93468	0.460000	0.39030	GAT		0.343	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		A	53997398	C	A	53997398	3	1	61	1	0	0	0	0	1	0	0	0	17362	913	32	2	2213	2	WDR72	15	53997398	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39459	53997398	48533994	9379	17364										
UNC13C	440279	broad.mit.edu	37	chr15	54306334	54306334	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacagatattctaactcatGacatcagagaaagaaaagag	7	7	3	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:54306334G>T	ENST00000260323.11	+	1	1234	c.1234G>T	c.(1234-1236)Gac>Tac	p.D412Y	UNC13C_ENST00000545554.1_Missense_Mutation_p.D412Y|UNC13C_ENST00000537900.1_Missense_Mutation_p.D412Y	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	412					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.D412Y(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCTAACTCATGACATCAGAGA	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	15											98	92	94					15																	54306334		1842	4090	5932	52093626	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1234G>T	15.37:g.54306334G>T	ENSP00000260323:p.Asp412Tyr		52093626	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562550	0.65538	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.83250	-1.7;-1.7;-1.7	5.64	5.64	0.86602	.	.	.	.	.	D	0.85630	0.5741	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	P	0.60789	0.879	D	0.87177	0.2225	9	0.87932	D	0	.	18.6946	0.91596	0.0:0.0:1.0:0.0	.	412	Q8NB66	UN13C_HUMAN	Y	412	ENSP00000260323:D412Y;ENSP00000438156:D412Y;ENSP00000442569:D412Y	ENSP00000260323:D412Y	D	+	1	0	UNC13C	52093626	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.392000	0.97252	2.665000	0.90641	0.655000	0.94253	GAC		0.378	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54306334	G	T	54306334	3	4	61	1	0	0	0	0	1	0	0	0	17026	1290	45	2	1236	2	UNC13C	15	54306334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	308936	54306334	48225058	9380	17365										
UNC13C	440279	broad.mit.edu	37	chr15	54307015	54307015	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatggtgtgtgcatctggaGaccggagtcattacagtgat	14	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:54307015G>A	ENST00000260323.11	+	1	1915	c.1915G>A	c.(1915-1917)Gac>Aac	p.D639N	UNC13C_ENST00000545554.1_Missense_Mutation_p.D639N|UNC13C_ENST00000537900.1_Missense_Mutation_p.D639N	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	639					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.D639N(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TGCATCTGGAGACCGGAGTCA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	15											153	151	151					15																	54307015		2073	4211	6284	52094307	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1915G>A	15.37:g.54307015G>A	ENSP00000260323:p.Asp639Asn		52094307	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165868	0.57476	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.85088	-1.94;-1.94;-1.94	5.16	4.24	0.50183	.	.	.	.	.	T	0.73830	0.3637	N	0.24115	0.695	0.37351	D	0.910817	P	0.43094	0.799	B	0.35039	0.194	T	0.79514	-0.1772	9	0.66056	D	0.02	.	12.6166	0.56580	0.0794:0.0:0.9206:0.0	.	639	Q8NB66	UN13C_HUMAN	N	639	ENSP00000260323:D639N;ENSP00000438156:D639N;ENSP00000442569:D639N	ENSP00000260323:D639N	D	+	1	0	UNC13C	52094307	1.000000	0.71417	0.156000	0.22583	0.859000	0.49053	7.448000	0.80631	1.396000	0.46663	0.650000	0.86243	GAC		0.448	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54307015	G	A	54307015	3	1	61	1	0	0	0	0	1	0	0	0	17026	942	33	3	1917	3	UNC13C	15	54307015	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681	54307015	48224377	9381	17366										
PIGB	9488	broad.mit.edu	37	chr15	55647027	55647027	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccacttcccatgagatttCtccagtgcccgccagacctg	8	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:55647027C>A	ENST00000164305.5	+	11	1660	c.1369C>A	c.(1369-1371)Ctc>Atc	p.L457I	DYX1C1-CCPG1_ENST00000565113.1_RNA|PIGB_ENST00000539642.1_Missense_Mutation_p.L262I	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	457					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)	p.L457I(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		CATGAGATTTCTCCAGTGCCC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											66	61	62					15																	55647027		1864	4103	5967	53434319	SO:0001583	missense	9488			D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	8959	protein-coding gene	gene with protein product	"GPI mannosyltransferase 3", "dol-P-Man dependent GPI mannosyltransferase"	604122	"phosphatidylinositol glycan, class B"			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.1369C>A	15.37:g.55647027C>A	ENSP00000164305:p.Leu457Ile		53434319	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.086815	0.76642	.	.	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.75704	-0.63;-0.96	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.87055	0.6082	M	0.83852	2.665	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	D	0.84014	0.0350	10	0.25751	T	0.34	-20.5319	19.2028	0.93717	0.0:1.0:0.0:0.0	.	457	Q92521	PIGB_HUMAN	I	457;262	ENSP00000164305:L457I;ENSP00000438963:L262I	ENSP00000164305:L457I	L	+	1	0	PIGB	53434319	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.395000	0.79876	2.785000	0.95823	0.591000	0.81541	CTC		0.358	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855		A	55647027	C	A	55647027	3	1	61	1	0	0	0	0	1	0	0	0	11916	913	32	2	1411	2	PIGB	15	55647027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1340012	55647027	46884365	9382	17367										
PYGO1	26108	broad.mit.edu	37	chr15	55841114	55841114	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtcagtttacctgtgtAtttgccttgcgctttttctt	7	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:55841114A>G	ENST00000302000.6	-	2	223	c.129T>C	c.(127-129)aaT>aaC	p.N43N	PYGO1_ENST00000563719.1_Silent_p.N43N	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	43					hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.N43N(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		TTACCTGTGTATTTGCCTTGC	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	15											152	147	148					15																	55841114		2193	4292	6485	53628406	SO:0001819	synonymous_variant	26108			AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"Zinc fingers, PHD-type"	30256	protein-coding gene	gene with protein product		606902	"pygopus homolog 1 (Drosophila)"			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.129T>C	15.37:g.55841114A>G			53628406	A7Y2D6	Silent	SNP	ENST00000302000.6	37	CCDS10155.1																																																																																				0.368	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		G	55841114	A	G	55841114	2	3	61	1	0	0	0	0	0	0	0	1	12900	446	16	4		4	PYGO1	15	55841114	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	194087	55841114	46690278	9383	17368										
NEDD4	4734	broad.mit.edu	37	chr15	56122106	56122106	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgtaatctaatcaactcCatcaaagccctgggtgtttt	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56122106C>A	ENST00000508342.1	-	25	4248	c.3949G>T	c.(3949-3951)Gga>Tga	p.G1317*	NEDD4_ENST00000338963.2_Nonsense_Mutation_p.G1245*|NEDD4_ENST00000506154.1_Nonsense_Mutation_p.G1301*|NEDD4_ENST00000435532.3_Nonsense_Mutation_p.G898*	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	1317	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.G1245*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TAATCAACTCCATCAAAGCCC	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											87	80	83					15																	56122106		2193	4292	6485	53909398	SO:0001587	stop_gained	4734			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.3949G>T	15.37:g.56122106C>A	ENSP00000424827:p.Gly1317*		53909398	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Nonsense_Mutation	SNP	ENST00000508342.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.324086|7.324086	0.98210|0.98210	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154|ENST00000508871	.|.	.|.	.|.	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.104630|.	0.64402|.	D|.	0.000004|.	.|T	.|0.76593	.|0.4009	.|.	.|.	.|.	0.43471|0.43471	D|D	0.995688|0.995688	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73392	.|-0.3997	.|4	0.87932|.	D|.	0|.	.|.	19.6603|19.6603	0.95864|0.95864	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	1317;898;1245;1301|907	.|.	ENSP00000345530:G1245X|.	G|M	-|-	1|3	0|0	NEDD4|NEDD4	53909398|53909398	1.000000|1.000000	0.71417|0.71417	0.980000|0.980000	0.43619|0.43619	0.774000|0.774000	0.43823|0.43823	7.625000|7.625000	0.83145|0.83145	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GGA|ATG		0.338	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56122106	C	A	56122106	4	1	61	1	0	0	0	0	0	1	0	0	10341	603	21	2	14	2	NEDD4	15	56122106	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	280992	56122106	46409286	9384	17369										
NEDD4	4734	broad.mit.edu	37	chr15	56144725	56144725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaacctggtggtaatccaGatgaagtaggcaaaagctaa	10	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56144725G>T	ENST00000508342.1	-	9	2599	c.2300C>A	c.(2299-2301)tCt>tAt	p.S767Y	NEDD4_ENST00000338963.2_Missense_Mutation_p.S695Y|NEDD4_ENST00000506154.1_Missense_Mutation_p.S751Y|NEDD4_ENST00000435532.3_Missense_Mutation_p.S348Y	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	767	Mediates interaction with TNIK. {ECO:0000250}.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.S695Y(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TGGTAATCCAGATGAAGTAGG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	109	116					15																	56144725		2193	4292	6485	53932017	SO:0001583	missense	4734			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.2300C>A	15.37:g.56144725G>T	ENSP00000424827:p.Ser767Tyr		53932017	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.1|23.1	4.379935|4.379935	0.82682|0.82682	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	.|T;T;T;T	.|0.21361	.|2.01;2.08;2.02;2.02	5.4|5.4	5.4|5.4	0.78164|0.78164	.|WW/Rsp5/WWP (3);	.|0.265686	.|0.44097	.|D	.|0.000490	T|T	0.48840|0.48840	0.1522|0.1522	M|M	0.77616|0.77616	2.38|2.38	0.58432|0.58432	D|D	0.99999|0.99999	.|D;D;D;D	.|0.76494	.|0.999;0.98;0.994;0.997	.|D;P;P;P	.|0.67548	.|0.952;0.782;0.837;0.888	T|T	0.52177|0.52177	-0.8610|-0.8610	5|10	.|0.87932	.|D	.|0	.|.	18.1866|18.1866	0.89795|0.89795	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|751;348;767;695	.|P46934-2;P46934-4;P46934;P46934-3	.|.;.;NEDD4_HUMAN;.	M|Y	358|767;348;695;751	.|ENSP00000424827:S767Y;ENSP00000410613:S348Y;ENSP00000345530:S695Y;ENSP00000422705:S751Y	.|ENSP00000345530:S695Y	L|S	-|-	1|2	2|0	NEDD4|NEDD4	53932017|53932017	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.594000|7.594000	0.82698|0.82698	2.529000|2.529000	0.85273|0.85273	0.555000|0.555000	0.69702|0.69702	CTG|TCT		0.383	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		T	56144725	G	T	56144725	3	4	61	1	0	0	0	0	1	0	0	0	10341	942	33	2	1727	2	NEDD4	15	56144725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22619	56144725	46386667	9385	17370										
NEDD4	4734	broad.mit.edu	37	chr15	56161868	56161868	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcagataacctttaactCttgatttgtgactgtagaaa	7	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56161868C>A	ENST00000508342.1	-	4	1972	c.1673G>T	c.(1672-1674)aGa>aTa	p.R558I	NEDD4_ENST00000338963.2_Intron|NEDD4_ENST00000506154.1_Missense_Mutation_p.R558I|NEDD4_ENST00000435532.3_Missense_Mutation_p.R139I	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	558					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.R139I(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		ACCTTTAACTCTTGATTTGTG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	15											61	52	55					15																	56161868		1782	4054	5836	53949160	SO:0001583	missense	4734			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.1673G>T	15.37:g.56161868C>A	ENSP00000424827:p.Arg558Ile		53949160	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.2|23.2	4.384564|4.384564	0.82792|0.82792	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000506154	.|D;D;T	.|0.89746	.|-2.56;-2.56;-0.57	5.68|5.68	4.74|4.74	0.60224|0.60224	.|.	.|.	.|.	.|.	.|.	.|D	.|0.93706	.|0.7989	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	.|D;B;D	.|0.67145	.|0.996;0.282;0.984	.|D;B;P	.|0.64410	.|0.925;0.083;0.707	.|D	.|0.94034	.|0.7303	.|9	.|0.87932	.|D	.|0	.|.	14.6731|14.6731	0.68958|0.68958	0.0:0.9265:0.0:0.0735|0.0:0.9265:0.0:0.0735	.|.	.|558;139;558	.|P46934-2;P46934-4;P46934	.|.;.;NEDD4_HUMAN	X|I	149|558;139;558	.|ENSP00000424827:R558I;ENSP00000410613:R139I;ENSP00000422705:R558I	.|ENSP00000410613:R139I	E|R	-|-	1|2	0|0	NEDD4|NEDD4	53949160|53949160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.346000|4.346000	0.59367|0.59367	2.843000|2.843000	0.97960|0.97960	0.585000|0.585000	0.79938|0.79938	GAG|AGA		0.323	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56161868	C	A	56161868	3	1	61	1	0	0	0	0	1	0	0	0	10341	913	32	2	2374	2	NEDD4	15	56161868	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17143	56161868	46369524	9386	17371										
NEDD4	4734	broad.mit.edu	37	chr15	56207960	56207960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtctgggagtattattcGaaagaacaattttcttctgt	8	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56207960G>A	ENST00000508342.1	-	1	1369	c.1070C>T	c.(1069-1071)tCg>tTg	p.S357L	NEDD4_ENST00000338963.2_Missense_Mutation_p.S357L|NEDD4_ENST00000506154.1_Missense_Mutation_p.S357L|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	357					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.S357L(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		AGTATTATTCGAAAGAACAAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											50	51	50					15																	56207960		2191	4291	6482	53995252	SO:0001583	missense	4734			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.1070C>T	15.37:g.56207960G>A	ENSP00000424827:p.Ser357Leu		53995252	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.	.	.	.	.	.	.	.	.	.	G	6.599	0.478867	0.12581	.	.	ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154	T;T;T	0.39229	1.09;1.09;1.09	5.46	4.55	0.56014	.	11.057000	0.00424	N	0.000062	T	0.37156	0.0993	L	0.38175	1.15	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.003	B;B;B	0.04013	0.001;0.0;0.001	T	0.22208	-1.0223	10	0.22109	T	0.4	.	8.247	0.31695	0.1862:0.0:0.8138:0.0	.	357;357;357	P46934-2;P46934;P46934-3	.;NEDD4_HUMAN;.	L	357	ENSP00000424827:S357L;ENSP00000345530:S357L;ENSP00000422705:S357L	ENSP00000345530:S357L	S	-	2	0	NEDD4	53995252	0.007000	0.16637	0.007000	0.13788	0.038000	0.13279	1.406000	0.34646	1.331000	0.45412	-0.378000	0.06908	TCG		0.418	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56207960	G	A	56207960	3	1	61	1	0	0	0	0	1	0	0	0	10341	1059	37	1	2989	1	NEDD4	15	56207960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46092	56207960	46323432	9387	17372										
RFX7	64864	broad.mit.edu	37	chr15	56385786	56385786	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaacctgatatcgctagaGaaatcagatgcagtattagt	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56385786G>T	ENST00000559447.2	-	9	4120	c.3849C>A	c.(3847-3849)ttC>ttA	p.F1283L	RFX7_ENST00000422057.1_Intron|RFX7_ENST00000317318.6_Intron|RFX7_ENST00000423270.1_Missense_Mutation_p.F1380L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	1283					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F1380L(1)|p.F1283L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TATCGCTAGAGAAATCAGATG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	15											76	71	72					15																	56385786		1944	4142	6086	54173078	SO:0001583	missense	64864					15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.3849C>A	15.37:g.56385786G>T	ENSP00000453281:p.Phe1283Leu		54173078	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	G	14.35	2.509853	0.44660	.	.	ENSG00000181827	ENST00000423270	T	0.61742	0.08	5.87	3.96	0.45880	.	0.000000	0.52532	U	0.000066	T	0.42988	0.1227	L	0.29908	0.895	0.58432	D	0.999995	B	0.10296	0.003	B	0.09377	0.004	T	0.35101	-0.9802	10	0.87932	D	0	-8.0012	7.9181	0.29829	0.1526:0.1347:0.7127:0.0	.	1283	Q2KHR2	RFX7_HUMAN	L	1380	ENSP00000397644:F1380L	ENSP00000397644:F1380L	F	-	3	2	RFX7	54173078	1.000000	0.71417	0.991000	0.47740	0.939000	0.58152	1.507000	0.35758	0.905000	0.36596	0.655000	0.94253	TTC		0.463	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		T	56385786	G	T	56385786	3	4	61	1	0	0	0	0	1	0	0	0	13305	933	33	2	246	2	RFX7	15	56385786	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	177826	56385786	46145606	9388	17373										
MNS1	55329	broad.mit.edu	37	chr15	56726546	56726546	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggccatttgttcttcaaaAtcttgcttcatctctttttg	5	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56726546A>C	ENST00000260453.3	-	8	1223	c.1059T>G	c.(1057-1059)gaT>gaG	p.D353E	TEX9_ENST00000537232.1_Intron|MNS1_ENST00000566386.1_5'Flank|TEX9_ENST00000352903.2_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	353	Glu-rich.				cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)	p.D353E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		GTTCTTCAAAATCTTGCTTCA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											179	163	168					15																	56726546		2192	4292	6484	54513838	SO:0001583	missense	55329			AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"spermatogenesis associated 40"	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.1059T>G	15.37:g.56726546A>C	ENSP00000260453:p.Asp353Glu		54513838	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031689	0.35797	.	.	ENSG00000138587	ENST00000260453	T	0.09445	2.98	5.41	1.73	0.24493	.	0.677347	0.14269	N	0.330274	T	0.07683	0.0193	L	0.56769	1.78	0.22787	N	0.998734	B	0.23185	0.081	B	0.25506	0.061	T	0.44620	-0.9316	10	0.02654	T	1	-4.8245	0.5302	0.00627	0.3436:0.1278:0.1637:0.3649	.	353	Q8NEH6	MNS1_HUMAN	E	353	ENSP00000260453:D353E	ENSP00000260453:D353E	D	-	3	2	MNS1	54513838	0.739000	0.28196	0.981000	0.43875	0.970000	0.65996	-0.086000	0.11233	0.099000	0.17552	0.460000	0.39030	GAT		0.348	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		C	56726546	A	C	56726546	3	2	61	1	0	0	0	0	1	0	0	0	9707	98	4	4	440	4	MNS1	15	56726546	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	340760	56726546	45804846	9389	17374										
ZNF280D	54816	broad.mit.edu	37	chr15	56968943	56968943	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaacgggcatagcaagttCttagtgttttcatgggatgt	11	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:56968943C>A	ENST00000267807.7	-	13	1551	c.1335G>T	c.(1333-1335)aaG>aaT	p.K445N	ZNF280D_ENST00000559000.1_Missense_Mutation_p.K432N|ZNF280D_ENST00000396245.1_Missense_Mutation_p.K149N|ZNF280D_ENST00000559237.1_Missense_Mutation_p.K432N	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K445N(1)		endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		ATAGCAAGTTCTTAGTGTTTT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	15											137	137	137					15																	56968943		2192	4292	6484	54756235	SO:0001583	missense	54816			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1335G>T	15.37:g.56968943C>A	ENSP00000267807:p.Lys445Asn		54756235	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.36|16.36	3.101991|3.101991	0.56183|0.56183	.|.	.|.	ENSG00000137871|ENSG00000137871	ENST00000260435|ENST00000267807;ENST00000455329;ENST00000260435;ENST00000396245	.|T;T	.|0.05996	.|3.36;3.9	5.73|5.73	4.79|4.79	0.61399|0.61399	.|Zinc finger, C2H2 (1);	.|10.453700	.|0.00166	.|N	.|0.000002	.|T	.|0.21718	.|0.0523	L|L	0.51422|0.51422	1.61|1.61	0.37976|0.37976	D|D	0.933435|0.933435	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	.|T	.|0.01162	.|-1.1432	.|10	.|0.40728	.|T	.|0.16	.|-14.2268	7.0676|7.0676	0.25161|0.25161	0.0:0.723:0.0:0.277|0.0:0.723:0.0:0.277	.|.	.|508;445	.|B4DHL1;Q6N043	.|.;Z280D_HUMAN	.|N	-1|445;432;281;149	.|ENSP00000267807:K445N;ENSP00000379545:K149N	.|ENSP00000260435:K281N	.|K	-|-	.|3	.|2	ZNF280D|ZNF280D	54756235|54756235	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.794000|0.794000	0.44872|0.44872	1.346000|1.346000	0.33964|0.33964	1.374000|1.374000	0.46228|0.46228	0.650000|0.650000	0.86243|0.86243	.|AAG		0.313	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		A	56968943	C	A	56968943	3	1	61	1	0	0	0	0	1	0	0	0	17856	912	32	2	1644	2	ZNF280D	15	56968943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	242397	56968943	45562449	9390	17375										
TCF12	6938	broad.mit.edu	37	chr15	57524979	57524979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaatgtccagctttcatCgcggcagtaccagcagttca	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:57524979C>T	ENST00000267811.5	+	11	1199	c.895C>T	c.(895-897)Cgc>Tgc	p.R299C	TCF12_ENST00000557843.1_Missense_Mutation_p.R299C|TCF12_ENST00000452095.2_Missense_Mutation_p.R295C|TCF12_ENST00000543579.1_Missense_Mutation_p.R129C|TCF12_ENST00000333725.5_Missense_Mutation_p.R299C|TCF12_ENST00000438423.2_Missense_Mutation_p.R299C|TCF12_ENST00000537840.1_Missense_Mutation_p.R63C|TCF12_ENST00000343827.3_Missense_Mutation_p.R129C|TCF12_ENST00000560764.1_3'UTR	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	299					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.R295C(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CAGCTTTCATCGCGGCAGTAC	0.443			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	1	Substitution - Missense(1)	large_intestine(1)	15											162	121	135					15																	57524979		2192	4292	6484	55312271	SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.895C>T	15.37:g.57524979C>T	ENSP00000267811:p.Arg299Cys		55312271	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789072	0.90367	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827	T;T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.87692	0.6241	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.972;0.991;0.99;0.999;0.994;0.928;0.994	D	0.87366	0.2347	10	0.54805	T	0.06	-13.1826	19.6555	0.95837	0.0:1.0:0.0:0.0	.	63;295;351;129;129;299;299	B4E1W1;E9PGY0;F5H6Z6;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;HTF4_HUMAN;.	C	351;299;299;295;299;129;63;129	ENSP00000267811:R299C;ENSP00000388940:R299C;ENSP00000396881:R295C;ENSP00000331057:R299C;ENSP00000440017:R129C;ENSP00000444696:R63C;ENSP00000342459:R129C	ENSP00000267811:R299C	R	+	1	0	TCF12	55312271	1.000000	0.71417	0.507000	0.27676	0.825000	0.46686	4.776000	0.62354	2.653000	0.90120	0.557000	0.71058	CGC		0.443	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		T	57524979	C	T	57524979	3	4	61	1	0	0	0	0	1	0	0	0	15726	884	31	1	1006	1	TCF12	15	57524979	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	556036	57524979	45006413	9391	17376										
TCF12	6938	broad.mit.edu	37	chr15	57565325	57565325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagagaacgcttacgcgtgCgggatattaatgaagcattc	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:57565325C>T	ENST00000267811.5	+	18	2075	c.1771C>T	c.(1771-1773)Cgg>Tgg	p.R591W	TCF12_ENST00000557843.1_Missense_Mutation_p.R591W|TCF12_ENST00000452095.2_Missense_Mutation_p.R611W|TCF12_ENST00000543579.1_Missense_Mutation_p.R445W|TCF12_ENST00000333725.5_Missense_Mutation_p.R615W|TCF12_ENST00000559710.1_Missense_Mutation_p.R225W|TCF12_ENST00000438423.2_Missense_Mutation_p.R615W|TCF12_ENST00000537840.1_Missense_Mutation_p.R355W|TCF12_ENST00000343827.3_Missense_Mutation_p.R421W|TCF12_ENST00000559703.1_Missense_Mutation_p.R248W	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	591	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.R611W(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CTTACGCGTGCGGGATATTAA	0.443			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	1	Substitution - Missense(1)	large_intestine(1)	15											97	103	101					15																	57565325		2192	4292	6484	55352617	SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1771C>T	15.37:g.57565325C>T	ENSP00000267811:p.Arg591Trp		55352617	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190964	0.78789	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827;ENST00000543417	D;D;D;D;D;D;D	0.98075	-4.7;-4.7;-4.7;-4.7;-4.7;-4.7;-4.7	4.72	2.73	0.32206	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	M	0.87097	2.86	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.995;0.999;0.999;0.992;0.999;0.998;0.996;0.996;0.994	D	0.98888	1.0772	10	0.87932	D	0	-5.321	12.4683	0.55773	0.4397:0.5603:0.0:0.0	.	611;225;445;355;611;643;445;421;591;615	B4DGI9;B4DZP2;B4DH96;B4E1W1;E9PGY0;F5H6Z6;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;.;.;.;HTF4_HUMAN;.	W	643;591;615;611;615;445;355;421;203	ENSP00000267811:R591W;ENSP00000388940:R615W;ENSP00000396881:R611W;ENSP00000331057:R615W;ENSP00000440017:R445W;ENSP00000444696:R355W;ENSP00000342459:R421W	ENSP00000267811:R591W	R	+	1	2	TCF12	55352617	0.998000	0.40836	0.912000	0.35992	0.948000	0.59901	2.397000	0.44477	0.464000	0.27142	0.655000	0.94253	CGG		0.443	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		T	57565325	C	T	57565325	3	4	61	1	0	0	0	0	1	0	0	0	15726	759	27	1	1986	1	TCF12	15	57565325	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40346	57565325	44966067	9392	17377										
TCF12	6938	broad.mit.edu	37	chr15	57574699	57574699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagggaagaagaaaaagttTctgccgtatcggcagagccg	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:57574699T>C	ENST00000267811.5	+	19	2267	c.1963T>C	c.(1963-1965)Tct>Cct	p.S655P	TCF12_ENST00000557843.1_Missense_Mutation_p.S655P|TCF12_ENST00000452095.2_Missense_Mutation_p.S675P|TCF12_ENST00000543579.1_Missense_Mutation_p.S509P|TCF12_ENST00000333725.5_Missense_Mutation_p.S679P|TCF12_ENST00000559710.1_Missense_Mutation_p.S289P|TCF12_ENST00000438423.2_Missense_Mutation_p.S679P|TCF12_ENST00000537840.1_Missense_Mutation_p.S419P|TCF12_ENST00000343827.3_Missense_Mutation_p.S485P|TCF12_ENST00000559703.1_Missense_Mutation_p.S312P	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	655	Class A specific domain.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.S675P(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AGAAAAAGTTTCTGCCGTATC	0.458			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	1	Substitution - Missense(1)	large_intestine(1)	15											118	115	116					15																	57574699		2192	4292	6484	55361991	SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1963T>C	15.37:g.57574699T>C	ENSP00000267811:p.Ser655Pro		55361991	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.105200	0.77096	.	.	ENSG00000140262	ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827;ENST00000543417	T;T;T;T;T;T;T	0.27890	2.24;2.22;2.22;2.22;1.97;1.64;2.01	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.68317	2.08	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.995;0.998;0.996;0.987;0.999;0.997;0.995;0.997	D;D;D;D;D;D;D;D	0.83275	0.979;0.99;0.933;0.958;0.996;0.991;0.979;0.991	T	0.57894	-0.7732	10	0.72032	D	0.01	-30.1344	16.1966	0.82029	0.0:0.0:0.0:1.0	.	289;509;419;675;509;485;655;679	B4DZP2;B4DH96;B4E1W1;E9PGY0;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;.;HTF4_HUMAN;.	P	655;679;675;679;509;419;485;267	ENSP00000267811:S655P;ENSP00000388940:S679P;ENSP00000396881:S675P;ENSP00000331057:S679P;ENSP00000440017:S509P;ENSP00000444696:S419P;ENSP00000342459:S485P	ENSP00000267811:S655P	S	+	1	0	TCF12	55361991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.768000	0.85345	2.232000	0.73038	0.528000	0.53228	TCT		0.458	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		C	57574699	T	C	57574699	3	2	61	1	0	0	0	0	1	0	0	0	15726	1783	62	4	2182	4	TCF12	15	57574699	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9374	57574699	44956693	9393	17378										
CGNL1	84952	broad.mit.edu	37	chr15	57730585	57730585	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgagggcaagaatggagttCtagatcgcaaagacgggtct	14	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:57730585C>A	ENST00000281282.5	+	2	466	c.388C>A	c.(388-390)Cta>Ata	p.L130I		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	130	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.L130I(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GAATGGAGTTCTAGATCGCAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											51	51	51					15																	57730585		2192	4292	6484	55517877	SO:0001583	missense	84952			AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.388C>A	15.37:g.57730585C>A	ENSP00000281282:p.Leu130Ile		55517877	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	8.782	0.928523	0.18131	.	.	ENSG00000128849	ENST00000281282	T	0.06933	3.24	4.87	3.93	0.45458	.	0.213470	0.23629	N	0.046141	T	0.09512	0.0234	L	0.60455	1.87	0.09310	N	1	B	0.20052	0.041	B	0.14023	0.01	T	0.17167	-1.0378	10	0.40728	T	0.16	-3.7354	8.6737	0.34165	0.0:0.7255:0.1518:0.1227	.	130	Q0VF96	CGNL1_HUMAN	I	130	ENSP00000281282:L130I	ENSP00000281282:L130I	L	+	1	2	CGNL1	55517877	0.000000	0.05858	0.062000	0.19696	0.865000	0.49528	-0.082000	0.11304	1.215000	0.43411	0.650000	0.86243	CTA		0.488	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		A	57730585	C	A	57730585	3	1	61	1	0	0	0	0	1	0	0	0	3310	912	32	2	390	2	CGNL1	15	57730585	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	155886	57730585	44800807	9394	17379										
CGNL1	84952	broad.mit.edu	37	chr15	57730905	57730905	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacctcagtgtgtgtaaaCgttcagagctgcaccaagga	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:57730905C>A	ENST00000281282.5	+	2	786	c.708C>A	c.(706-708)aaC>aaA	p.N236K		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	236	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.N236K(1)|p.N236N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TGTGTGTAAACGTTCAGAGCT	0.567																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	15											90	94	93					15																	57730905		2192	4292	6484	55518197	SO:0001583	missense	84952			AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.708C>A	15.37:g.57730905C>A	ENSP00000281282:p.Asn236Lys		55518197	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	9.468	1.094909	0.20471	.	.	ENSG00000128849	ENST00000281282	T	0.76578	-1.03	5.26	-1.09	0.09904	.	0.119070	0.38058	N	0.001835	T	0.67202	0.2868	L	0.51422	1.61	0.09310	N	1	B	0.31026	0.304	B	0.26416	0.069	T	0.59118	-0.7514	10	0.66056	D	0.02	-31.1636	10.6292	0.45525	0.0:0.3994:0.0:0.6006	.	236	Q0VF96	CGNL1_HUMAN	K	236	ENSP00000281282:N236K	ENSP00000281282:N236K	N	+	3	2	CGNL1	55518197	0.580000	0.26733	0.030000	0.17652	0.608000	0.37181	-0.233000	0.09041	-0.394000	0.07727	-0.143000	0.13931	AAC		0.567	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		A	57730905	C	A	57730905	3	1	61	1	0	0	0	0	1	0	0	0	3310	535	19	2	710	2	CGNL1	15	57730905	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	320	57730905	44800487	9395	17380										
LIPC	3990	broad.mit.edu	37	chr15	58838003	58838003	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaatcgtctttctccagatGatgccaattttgtggatgcc	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:58838003G>T	ENST00000356113.6	+	7	1252	c.637G>T	c.(637-639)Gat>Tat	p.D213Y	LIPC_ENST00000414170.3_Missense_Mutation_p.D213Y|LIPC_ENST00000299022.5_Missense_Mutation_p.D213Y|LIPC_ENST00000433326.2_Missense_Mutation_p.D152Y			P11150	LIPC_HUMAN	lipase, hepatic	213					cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)	p.D213Y(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		TTCTCCAGATGATGCCAATTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	96	98					15																	58838003		2192	4292	6484	56625295	SO:0001583	missense	3990				CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.637G>T	15.37:g.58838003G>T	ENSP00000348425:p.Asp213Tyr		56625295	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	37	CCDS10166.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126425	0.77549	.	.	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	5.44	5.44	0.79542	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98698	0.9563	H	0.99336	4.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.99577	1.0972	10	0.87932	D	0	.	19.2665	0.93988	0.0:0.0:1.0:0.0	.	152;213	E7EUK6;P11150	.;LIPC_HUMAN	Y	213;213;213;152	ENSP00000348425:D213Y;ENSP00000395569:D213Y;ENSP00000299022:D213Y;ENSP00000395002:D152Y	ENSP00000299022:D213Y	D	+	1	0	LIPC	56625295	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	9.843000	0.99491	2.548000	0.85928	0.563000	0.77884	GAT		0.532	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1			T	58838003	G	T	58838003	3	4	61	1	0	0	0	0	1	0	0	0	8844	1290	45	2	655	2	LIPC	15	58838003	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1107098	58838003	43693389	9396	17381										
LIPC	3990	broad.mit.edu	37	chr15	58855764	58855764	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacgctggatgtggatatCggcgagctgatcatgatcaa	12	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:58855764C>T	ENST00000356113.6	+	10	1845	c.1230C>T	c.(1228-1230)atC>atT	p.I410I	LIPC_ENST00000414170.3_Silent_p.I410I|LIPC_ENST00000433326.2_Silent_p.I349I|LIPC_ENST00000299022.5_Silent_p.I410I			P11150	LIPC_HUMAN	lipase, hepatic	410	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)	p.I410I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		ATGTGGATATCGGCGAGCTGA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	15											135	111	119					15																	58855764		2192	4292	6484	56643056	SO:0001819	synonymous_variant	3990				CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.1230C>T	15.37:g.58855764C>T			56643056	A2RUB4|A8K9B6|O43571|P78529|Q99465	Silent	SNP	ENST00000356113.6	37	CCDS10166.1																																																																																				0.468	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1			T	58855764	C	T	58855764	2	4	61	1	0	0	0	0	0	0	0	1	8844	874	31	1		1	LIPC	15	58855764	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17761	58855764	43675628	9397	17382										
ADAM10	102	broad.mit.edu	37	chr15	58925524	58925524	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcttaccatctgaataGagtttacttttttcacatat	3	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:58925524G>T	ENST00000260408.3	-	9	1490	c.1047C>A	c.(1045-1047)ctC>ctA	p.L349L	ADAM10_ENST00000396140.2_Silent_p.L48L|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Silent_p.L48L	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	349	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.L349L(1)		breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		CATCTGAATAGAGTTTACTTT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	15											102	101	101					15																	58925524		2192	4292	6484	56712816	SO:0001819	synonymous_variant	102			AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1047C>A	15.37:g.58925524G>T			56712816	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	37	CCDS10167.1																																																																																				0.368	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		T	58925524	G	T	58925524	2	4	61	1	0	0	0	0	0	0	0	1	234	929	33	2		2	ADAM10	15	58925524	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69760	58925524	43605868	9398	17383										
FAM63B	54629	broad.mit.edu	37	chr15	59064158	59064158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcattcttttcccagtagCtgcgagttcaatagtgagga	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59064158C>A	ENST00000559228.1	+	1	646	c.564C>A	c.(562-564)agC>agA	p.S188R	RP11-30K9.6_ENST00000500929.2_lincRNA|FAM63B_ENST00000450403.2_Missense_Mutation_p.S188R			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	188								p.S188R(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						TTCCCAGTAGCTGCGAGTTCA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	15											30	32	31					15																	59064158		1902	4120	6022	56851450	SO:0001583	missense	54629			AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.564C>A	15.37:g.59064158C>A	ENSP00000452885:p.Ser188Arg		56851450	B2RTT8|Q9ULQ6	Missense_Mutation	SNP	ENST00000559228.1	37	CCDS42046.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061564	0.76187	.	.	ENSG00000128923	ENST00000316848;ENST00000450403	T	0.60797	0.16	3.89	3.89	0.44902	.	0.195941	0.36555	N	0.002538	T	0.59676	0.2211	N	0.24115	0.695	0.43467	D	0.995677	D;D	0.63880	0.988;0.993	P;P	0.59424	0.723;0.857	T	0.64647	-0.6358	10	0.51188	T	0.08	-23.1997	16.0667	0.80887	0.0:1.0:0.0:0.0	.	188;188	Q8NBR6;Q8NBR6-2	FA63B_HUMAN;.	R	188	ENSP00000393231:S188R	ENSP00000326194:S188R	S	+	3	2	FAM63B	56851450	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.526000	0.67116	1.998000	0.58463	0.543000	0.68304	AGC		0.627	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092		A	59064158	C	A	59064158	3	1	61	1	0	0	0	0	1	0	0	0	5616	796	28	2	566	2	FAM63B	15	59064158	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138634	59064158	43467234	9399	17384										
SLTM	79811	broad.mit.edu	37	chr15	59182619	59182619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcacgaattattctaatgCgttctcgctctcgacgctct	7	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59182619C>T	ENST00000380516.2	-	15	2027	c.1940G>A	c.(1939-1941)cGc>cAc	p.R647H	SLTM_ENST00000536328.1_Missense_Mutation_p.R216H|AC025918.2_ENST00000452467.1_RNA	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	647	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R647H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TATTCTAATGCGTTCTCGCTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											104	101	102					15																	59182619		2192	4292	6484	56969911	SO:0001583	missense	79811			BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.1940G>A	15.37:g.59182619C>T	ENSP00000369887:p.Arg647His		56969911	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	37	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731832	0.69189	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.16743	2.32	5.86	4.94	0.65067	.	0.000000	0.56097	D	0.000021	T	0.20495	0.0493	L	0.57536	1.79	0.51767	D	0.999939	B;B	0.19817	0.039;0.027	B;B	0.14578	0.007;0.011	T	0.01795	-1.1272	10	0.51188	T	0.08	.	14.8308	0.70146	0.0:0.9312:0.0:0.0688	.	647;216	Q9NWH9;A8K5V8	SLTM_HUMAN;.	H	647;213;216	ENSP00000369887:R647H	ENSP00000369887:R647H	R	-	2	0	SLTM	56969911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.083000	0.76859	1.486000	0.48398	0.655000	0.94253	CGC		0.413	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		T	59182619	C	T	59182619	3	4	61	1	0	0	0	0	1	0	0	0	14791	768	27	1	1192	1	SLTM	15	59182619	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118461	59182619	43348773	9400	17385										
SLTM	79811	broad.mit.edu	37	chr15	59191829	59191829	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctttatggttcgcattCatctcataatccttgctttc	4	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59191829C>A	ENST00000380516.2	-	7	984	c.897G>T	c.(895-897)atG>atT	p.M299I	SLTM_ENST00000536328.1_Intron|SLTM_ENST00000557950.1_5'Flank	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	299					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M299I(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGTTCGCATTCATCTCATAAT	0.448																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	15											157	150	153					15																	59191829		2192	4292	6484	56979121	SO:0001583	missense	79811			BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.897G>T	15.37:g.59191829C>A	ENSP00000369887:p.Met299Ile		56979121	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	37	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	C	9.700	1.154151	0.21371	.	.	ENSG00000137776	ENST00000380516;ENST00000249736	D;D	0.88741	-2.42;-2.42	5.78	5.78	0.91487	Nucleotide-binding, alpha-beta plait (1);	0.080592	0.52532	D	0.000063	D	0.87509	0.6195	L	0.50333	1.59	0.80722	D	1	B;B	0.13145	0.006;0.007	B;B	0.14023	0.01;0.003	T	0.81961	-0.0693	10	0.42905	T	0.14	.	20.0114	0.97452	0.0:1.0:0.0:0.0	.	281;299	C9IZZ3;Q9NWH9	.;SLTM_HUMAN	I	299;281	ENSP00000369887:M299I;ENSP00000249736:M281I	ENSP00000249736:M281I	M	-	3	0	SLTM	56979121	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.851000	0.48302	2.732000	0.93576	0.591000	0.81541	ATG		0.448	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		A	59191829	C	A	59191829	3	1	61	1	0	0	0	0	1	0	0	0	14791	826	29	2	2267	2	SLTM	15	59191829	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9210	59191829	43339563	9401	17386										
RNF111	54778	broad.mit.edu	37	chr15	59344611	59344611	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtgaagtggagattgtaAcagttggagaaagctatcgg	14	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59344611A>C	ENST00000557998.1	+	3	1275	c.988A>C	c.(988-990)Aca>Cca	p.T330P	RNF111_ENST00000559209.1_Missense_Mutation_p.T330P|RNF111_ENST00000348370.4_Missense_Mutation_p.T330P|RNF111_ENST00000434298.1_Missense_Mutation_p.T330P|RNF111_ENST00000561186.1_Missense_Mutation_p.T330P	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	330	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T330P(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		GGAGATTGTAACAGTTGGAGA	0.338																																					NSCLC(72;983 1365 10746 34387 47081)											1	Substitution - Missense(1)	large_intestine(1)	15											116	104	108					15																	59344611		2192	4291	6483	57131903	SO:0001583	missense	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.988A>C	15.37:g.59344611A>C	ENSP00000452732:p.Thr330Pro		57131903	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.127968	0.77549	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.20200	2.09;2.1	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.39784	0.1091	L	0.44542	1.39	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.996;0.998	T	0.16897	-1.0387	10	0.62326	D	0.03	-8.8528	15.5466	0.76108	1.0:0.0:0.0:0.0	.	330;330;330	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	P	330	ENSP00000288199:T330P;ENSP00000393641:T330P	ENSP00000288199:T330P	T	+	1	0	RNF111	57131903	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	8.117000	0.89575	2.065000	0.61736	0.421000	0.28195	ACA		0.338	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		C	59344611	A	C	59344611	3	2	61	1	0	0	0	0	1	0	0	0	13462	43	2	4	994	4	RNF111	15	59344611	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	152782	59344611	43186781	9402	17387										
MYO1E	4643	broad.mit.edu	37	chr15	59480399	59480399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttcagacccaaatattCgacttgatgctttaccctgt	5	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59480399C>T	ENST00000288235.4	-	18	2221	c.1822G>A	c.(1822-1824)Gaa>Aaa	p.E608K		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	608	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.E608K(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CCCAAATATTCGACTTGATGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											141	134	136					15																	59480399		2191	4291	6482	57267691	SO:0001583	missense	4643			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1822G>A	15.37:g.59480399C>T	ENSP00000288235:p.Glu608Lys		57267691	Q14778	Missense_Mutation	SNP	ENST00000288235.4	37	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.202630	0.79127	.	.	ENSG00000157483	ENST00000288235	D	0.86164	-2.08	4.82	4.82	0.62117	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.82116	0.4967	N	0.13272	0.32	0.80722	D	1	D	0.61697	0.99	P	0.54174	0.744	T	0.78219	-0.2289	10	0.02654	T	1	.	17.7194	0.88347	0.0:1.0:0.0:0.0	.	608	Q12965	MYO1E_HUMAN	K	608	ENSP00000288235:E608K	ENSP00000288235:E608K	E	-	1	0	MYO1E	57267691	1.000000	0.71417	0.775000	0.31657	0.936000	0.57629	7.556000	0.82233	2.503000	0.84419	0.655000	0.94253	GAA		0.473	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		T	59480399	C	T	59480399	3	4	61	1	0	0	0	0	1	0	0	0	10102	893	31	1	1548	1	MYO1E	15	59480399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135788	59480399	43050993	9403	17388										
MYO1E	4643	broad.mit.edu	37	chr15	59487694	59487694	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctgggcttcttggtttCgtttggcttgatgcagcgaa	13	8	2	1	rs11539755		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59487694C>T	ENST00000288235.4	-	17	2170	c.1771G>A	c.(1771-1773)Gaa>Aaa	p.E591K		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	591	Actin-binding. {ECO:0000255}.|Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.E591K(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TTCTTGGTTTCGTTTGGCTTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											197	185	189					15																	59487694		2191	4291	6482	57274986	SO:0001583	missense	4643			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1771G>A	15.37:g.59487694C>T	ENSP00000288235:p.Glu591Lys		57274986	Q14778	Missense_Mutation	SNP	ENST00000288235.4	37	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	36	5.818314	0.96982	.	.	ENSG00000157483	ENST00000288235	D	0.88354	-2.37	5.46	5.46	0.80206	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.95837	0.8645	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.96265	0.9194	10	0.72032	D	0.01	.	18.2528	0.90009	0.0:1.0:0.0:0.0	rs11539755	591	Q12965	MYO1E_HUMAN	K	591	ENSP00000288235:E591K	ENSP00000288235:E591K	E	-	1	0	MYO1E	57274986	1.000000	0.71417	0.980000	0.43619	0.954000	0.61252	7.301000	0.78850	2.840000	0.97914	0.655000	0.94253	GAA		0.517	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		T	59487694	C	T	59487694	3	4	61	1	0	0	0	0	1	0	0	0	10102	893	31	1	1603	1	MYO1E	15	59487694	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7295	59487694	43043698	9404	17389										
LDHAL6B	92483	broad.mit.edu	37	chr15	59500085	59500085	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaagtattttgaagaatCttaggagaatacatccagtt	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59500085C>A	ENST00000307144.4	+	1	1044	c.946C>A	c.(946-948)Ctt>Att	p.L316I	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	316					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)	p.L316I(1)		endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						TTTGAAGAATCTTAGGAGAAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	81	79					15																	59500085		2191	4289	6480	57287377	SO:0001583	missense	92483			AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"lactate dehydrogenase A-like 6"	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.946C>A	15.37:g.59500085C>A	ENSP00000302393:p.Leu316Ile		57287377	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908509	0.52333	.	.	ENSG00000171989	ENST00000307144	T	0.63580	-0.05	1.47	1.47	0.22746	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.254509	0.24640	U	0.036802	T	0.70815	0.3267	M	0.93375	3.41	0.28751	N	0.90142	B	0.22346	0.068	B	0.38225	0.268	T	0.67345	-0.5694	10	0.46703	T	0.11	.	4.9066	0.13802	0.3566:0.6434:0.0:0.0	.	316	Q9BYZ2	LDH6B_HUMAN	I	316	ENSP00000302393:L316I	ENSP00000302393:L316I	L	+	1	0	LDHAL6B	57287377	0.906000	0.30813	0.111000	0.21465	0.739000	0.42172	-0.051000	0.11885	0.784000	0.33661	0.305000	0.20034	CTT		0.388	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195		A	59500085	C	A	59500085	3	1	61	1	0	0	0	0	1	0	0	0	8722	913	32	2	948	2	LDHAL6B	15	59500085	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12391	59500085	43031307	9405	17390										
GCNT3	9245	broad.mit.edu	37	chr15	59911370	59911370	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtccaacatgttttgaaGaaccctaaatcccaacaact	4	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:59911370G>T	ENST00000396065.1	+	3	1381	c.933G>T	c.(931-933)aaG>aaT	p.K311N	GCNT3_ENST00000560585.1_Missense_Mutation_p.K311N	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	311					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.K311N(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATGTTTTGAAGAACCCTAAAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	15											153	154	153					15																	59911370		2190	4290	6480	57698662	SO:0001583	missense	9245			AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.933G>T	15.37:g.59911370G>T	ENSP00000379377:p.Lys311Asn		57698662		Missense_Mutation	SNP	ENST00000396065.1	37	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	G	2.438	-0.329369	0.05314	.	.	ENSG00000140297	ENST00000396065	T	0.11712	2.75	5.41	4.44	0.53790	.	0.728089	0.13642	N	0.372915	T	0.03136	0.0092	N	0.01789	-0.72	0.20764	N	0.99986	B	0.02656	0.0	B	0.04013	0.001	T	0.43766	-0.9371	10	0.06365	T	0.9	-7.0432	4.6986	0.12816	0.0791:0.1271:0.6007:0.1932	.	311	O95395	GCNT3_HUMAN	N	311	ENSP00000379377:K311N	ENSP00000379377:K311N	K	+	3	2	GCNT3	57698662	0.076000	0.21285	0.959000	0.39883	0.860000	0.49131	0.068000	0.14531	1.114000	0.41781	0.655000	0.94253	AAG		0.458	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		T	59911370	G	T	59911370	3	4	61	1	0	0	0	0	1	0	0	0	6322	933	33	2	935	2	GCNT3	15	59911370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	411285	59911370	42620022	9406	17391										
VPS13C	54832	broad.mit.edu	37	chr15	62169234	62169234	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcttgtagaactgatatcGaatttcataataagcaagtc	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62169234G>A	ENST00000261517.5	-	75	10235	c.10162C>T	c.(10162-10164)Cga>Tga	p.R3388*	VPS13C_ENST00000395896.4_Nonsense_Mutation_p.R3388*|VPS13C_ENST00000249837.3_Nonsense_Mutation_p.R3345*|VPS13C_ENST00000558919.1_5'UTR|VPS13C_ENST00000395898.3_Nonsense_Mutation_p.R3345*	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.R3388*(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AACTGATATCGAATTTCATAA	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											91	99	96					15																	62169234		2203	4295	6498	59956526	SO:0001587	stop_gained	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10162C>T	15.37:g.62169234G>A	ENSP00000261517:p.Arg3388*		59956526		Nonsense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	50	17.180658	0.99881	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	.	.	.	5.06	4.14	0.48551	.	0.247444	0.38272	N	0.001742	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6843	0.51476	0.0:0.0:0.6055:0.3945	.	.	.	.	X	3345;3388;3388;3388	.	ENSP00000249837:R3345X	R	-	1	2	VPS13C	59956526	0.874000	0.30092	0.553000	0.28255	0.499000	0.33736	4.013000	0.57138	1.247000	0.43917	0.585000	0.79938	CGA		0.299	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62169234	G	A	62169234	4	1	61	1	0	0	0	0	0	1	0	0	17231	1066	37	1	1171	1	VPS13C	15	62169234	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2257864	62169234	40362158	9407	17392										
VPS13C	54832	broad.mit.edu	37	chr15	62214690	62214690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaataataaaggtacagttCgatgtccaaggccacattct	7	10	1	0	rs560778934		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62214690C>T	ENST00000261517.5	-	54	6954	c.6881G>A	c.(6880-6882)cGa>cAa	p.R2294Q	VPS13C_ENST00000395896.4_Missense_Mutation_p.R2294Q|VPS13C_ENST00000249837.3_Missense_Mutation_p.R2251Q|VPS13C_ENST00000395898.3_Missense_Mutation_p.R2251Q	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.R2294Q(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AGGTACAGTTCGATGTCCAAG	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		17275	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											154	149	151					15																	62214690		2203	4300	6503	60001982	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6881G>A	15.37:g.62214690C>T	ENSP00000261517:p.Arg2294Gln		60001982		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.121726	0.77436	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.44482	0.92;0.92;0.92	5.31	5.31	0.75309	.	0.062798	0.64402	D	0.000005	T	0.54062	0.1835	M	0.81802	2.56	0.80722	D	1	B;B;B;B	0.27416	0.024;0.178;0.054;0.052	B;B;B;B	0.34242	0.049;0.178;0.077;0.055	T	0.57522	-0.7797	10	0.59425	D	0.04	.	19.3523	0.94393	0.0:1.0:0.0:0.0	.	2251;2294;2251;2294	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	Q	2251;2294;2294;2294	ENSP00000249837:R2251Q;ENSP00000261517:R2294Q;ENSP00000379233:R2294Q	ENSP00000249837:R2251Q	R	-	2	0	VPS13C	60001982	0.996000	0.38824	0.998000	0.56505	0.928000	0.56348	3.409000	0.52657	2.635000	0.89317	0.650000	0.86243	CGA		0.393	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62214690	C	T	62214690	3	4	61	1	0	0	0	0	1	0	0	0	17231	884	31	1	4536	1	VPS13C	15	62214690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45456	62214690	40316702	9408	17393										
VPS13C	54832	broad.mit.edu	37	chr15	62219469	62219469	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctggcaacaaataccacttCtggatctgtgatcatggcct	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62219469C>A	ENST00000261517.5	-	52	6410	c.6337G>T	c.(6337-6339)Gaa>Taa	p.E2113*	VPS13C_ENST00000395896.4_Nonsense_Mutation_p.E2113*|VPS13C_ENST00000249837.3_Nonsense_Mutation_p.E2070*|VPS13C_ENST00000395898.3_Nonsense_Mutation_p.E2070*	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.E2113*(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AATACCACTTCTGGATCTGTG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											155	155	155					15																	62219469		2203	4300	6503	60006761	SO:0001587	stop_gained	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6337G>T	15.37:g.62219469C>A	ENSP00000261517:p.Glu2113*		60006761		Nonsense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	47	13.479736	0.99744	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1595	0.93525	0.0:1.0:0.0:0.0	.	.	.	.	X	2070;2113;2113;2113	.	ENSP00000249837:E2070X	E	-	1	0	VPS13C	60006761	1.000000	0.71417	0.983000	0.44433	0.776000	0.43924	7.238000	0.78173	2.585000	0.87301	0.655000	0.94253	GAA		0.428	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62219469	C	A	62219469	4	1	61	1	0	0	0	0	0	1	0	0	17231	922	32	2	5088	2	VPS13C	15	62219469	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4779	62219469	40311923	9409	17394										
VPS13C	54832	broad.mit.edu	37	chr15	62223291	62223291	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactcagagctgacaaacctCgatgttgctctctcaattcc	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62223291C>T	ENST00000261517.5	-	50	6109	c.6036G>A	c.(6034-6036)tcG>tcA	p.S2012S	VPS13C_ENST00000395896.4_Silent_p.S2012S|VPS13C_ENST00000249837.3_Silent_p.S1969S|VPS13C_ENST00000395898.3_Silent_p.S1969S	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.S2012S(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TGACAAACCTCGATGTTGCTC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	15											125	107	113					15																	62223291		2203	4300	6503	60010583	SO:0001819	synonymous_variant	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6036G>A	15.37:g.62223291C>T			60010583		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																				0.438	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62223291	C	T	62223291	2	4	61	1	0	0	0	0	0	0	0	1	17231	871	31	1		1	VPS13C	15	62223291	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3822	62223291	40308101	9410	17395										
VPS13C	54832	broad.mit.edu	37	chr15	62256049	62256049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaccttgaatcttgatttCggcgatattgttcttttcgt	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62256049C>T	ENST00000261517.5	-	32	3389	c.3316G>A	c.(3316-3318)Gaa>Aaa	p.E1106K	VPS13C_ENST00000395896.4_Missense_Mutation_p.E1106K|VPS13C_ENST00000249837.3_Missense_Mutation_p.E1063K|VPS13C_ENST00000395898.3_Missense_Mutation_p.E1063K	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.E1106K(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATCTTGATTTCGGCGATATTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	15											117	106	110					15																	62256049		2202	4300	6502	60043341	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3316G>A	15.37:g.62256049C>T	ENSP00000261517:p.Glu1106Lys		60043341		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233612	0.79688	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.45276	0.9;0.9;0.9	5.66	5.66	0.87406	.	0.058966	0.64402	D	0.000003	T	0.45577	0.1349	L	0.49126	1.545	0.58432	D	0.999997	D;D;D;D	0.63880	0.991;0.98;0.993;0.976	P;P;P;B	0.47864	0.477;0.559;0.559;0.427	T	0.22977	-1.0201	10	0.13108	T	0.6	.	19.7559	0.96291	0.0:1.0:0.0:0.0	.	1063;1106;1063;1106	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	K	1063;1106;1106;1106	ENSP00000249837:E1063K;ENSP00000261517:E1106K;ENSP00000379233:E1106K	ENSP00000249837:E1063K	E	-	1	0	VPS13C	60043341	1.000000	0.71417	1.000000	0.80357	0.420000	0.31355	6.902000	0.75699	2.656000	0.90262	0.655000	0.94253	GAA		0.353	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62256049	C	T	62256049	3	4	61	1	0	0	0	0	1	0	0	0	17231	893	31	1	8189	1	VPS13C	15	62256049	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32758	62256049	40275343	9411	17396										
VPS13C	54832	broad.mit.edu	37	chr15	62269297	62269297	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctggccattctaatgtCtttttctaccatggccttag	6	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62269297C>A	ENST00000261517.5	-	24	2465	c.2392G>T	c.(2392-2394)Gac>Tac	p.D798Y	VPS13C_ENST00000395896.4_Missense_Mutation_p.D798Y|VPS13C_ENST00000249837.3_Missense_Mutation_p.D755Y|VPS13C_ENST00000395898.3_Missense_Mutation_p.D755Y	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.D798Y(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATTCTAATGTCTTTTTCTACC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	15											87	81	83					15																	62269297		2203	4300	6503	60056589	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.2392G>T	15.37:g.62269297C>A	ENSP00000261517:p.Asp798Tyr		60056589		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275515	0.80580	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.55588	0.51;0.51;0.51	5.02	5.02	0.67125	.	0.051050	0.85682	D	0.000000	T	0.74604	0.3738	M	0.81497	2.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.992;0.999	T	0.73936	-0.3825	10	0.38643	T	0.18	.	19.2184	0.93786	0.0:1.0:0.0:0.0	.	755;798;755;798	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	Y	755;798;798;798	ENSP00000249837:D755Y;ENSP00000261517:D798Y;ENSP00000379233:D798Y	ENSP00000249837:D755Y	D	-	1	0	VPS13C	60056589	1.000000	0.71417	0.992000	0.48379	0.958000	0.62258	6.869000	0.75521	2.704000	0.92352	0.591000	0.81541	GAC		0.358	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62269297	C	A	62269297	3	1	61	1	0	0	0	0	1	0	0	0	17231	913	32	2	9145	2	VPS13C	15	62269297	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13248	62269297	40262095	9412	17397										
VPS13C	54832	broad.mit.edu	37	chr15	62305244	62305244	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacattaatattaccaaaatCtgttcccttgatctctggta	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62305244C>A	ENST00000261517.5	-	11	892	c.819G>T	c.(817-819)caG>caT	p.Q273H	VPS13C_ENST00000395896.4_Missense_Mutation_p.Q273H|VPS13C_ENST00000249837.3_Missense_Mutation_p.Q230H|VPS13C_ENST00000395898.3_Missense_Mutation_p.Q230H	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.Q273H(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTACCAAAATCTGTTCCCTTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											80	73	75					15																	62305244		2203	4299	6502	60092536	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.819G>T	15.37:g.62305244C>A	ENSP00000261517:p.Gln273His		60092536		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.758512	0.31137	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46819	0.87;0.86;1.04	5.83	2.89	0.33648	.	0.568411	0.17787	N	0.162030	T	0.37812	0.1017	L	0.45137	1.4	0.27060	N	0.96357	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.12156	0.002;0.003;0.007;0.002	T	0.31392	-0.9945	10	0.54805	T	0.06	.	8.0047	0.30319	0.0:0.4724:0.3827:0.1449	.	230;273;230;273	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	H	230;273;273;273	ENSP00000249837:Q230H;ENSP00000261517:Q273H;ENSP00000379233:Q273H	ENSP00000249837:Q230H	Q	-	3	2	VPS13C	60092536	0.952000	0.32445	1.000000	0.80357	0.988000	0.76386	-0.043000	0.12043	0.363000	0.24346	-0.145000	0.13849	CAG		0.373	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62305244	C	A	62305244	3	1	61	1	0	0	0	0	1	0	0	0	17231	912	32	2	10770	2	VPS13C	15	62305244	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35947	62305244	40226148	9413	17398										
VPS13C	54832	broad.mit.edu	37	chr15	62306149	62306149	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccttgtatataattttgtCtgcttcatttaatatgcatg	5	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:62306149C>A	ENST00000261517.5	-	10	800	c.727G>T	c.(727-729)Gac>Tac	p.D243Y	VPS13C_ENST00000395896.4_Missense_Mutation_p.D243Y|VPS13C_ENST00000249837.3_Missense_Mutation_p.D200Y|VPS13C_ENST00000395898.3_Missense_Mutation_p.D200Y	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.D243Y(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATAATTTTGTCTGCTTCATTT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	15											85	87	86					15																	62306149		2203	4299	6502	60093441	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.727G>T	15.37:g.62306149C>A	ENSP00000261517:p.Asp243Tyr		60093441		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491975	0.44352	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.47869	0.83;0.84;1.0	5.24	5.24	0.73138	.	0.444110	0.22924	N	0.053989	T	0.36580	0.0972	N	0.14661	0.345	0.26837	N	0.96845	P;P;B;P	0.42296	0.775;0.775;0.315;0.667	P;P;B;B	0.45343	0.477;0.477;0.284;0.285	T	0.31861	-0.9928	10	0.66056	D	0.02	.	10.8091	0.46535	0.0:0.8524:0.0:0.1476	.	200;243;200;243	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	Y	200;243;243;243	ENSP00000249837:D200Y;ENSP00000261517:D243Y;ENSP00000379233:D243Y	ENSP00000249837:D200Y	D	-	1	0	VPS13C	60093441	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.671000	0.54576	2.605000	0.88082	0.585000	0.79938	GAC		0.323	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62306149	C	A	62306149	3	1	61	1	0	0	0	0	1	0	0	0	17231	913	32	2	10866	2	VPS13C	15	62306149	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	905	62306149	40225243	9414	17399										
TLN2	83660	broad.mit.edu	37	chr15	63032911	63032911	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctgttagctgccaagtCtctctctgtagatccaggag	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63032911C>A	ENST00000561311.1	+	31	4198	c.3968C>A	c.(3967-3969)tCt>tAt	p.S1323Y	TLN2_ENST00000306829.6_Missense_Mutation_p.S1323Y			Q9Y4G6	TLN2_HUMAN	talin 2	1323					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.S1323Y(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GCTGCCAAGTCTCTCTCTGTA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	15											84	75	78					15																	63032911		2203	4300	6503	60820203	SO:0001583	missense	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3968C>A	15.37:g.63032911C>A	ENSP00000453508:p.Ser1323Tyr		60820203	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.274694	0.59649	.	.	ENSG00000171914	ENST00000306829	T	0.15017	2.46	5.87	5.87	0.94306	.	0.094038	0.85682	D	0.000000	T	0.26846	0.0657	L	0.61218	1.895	0.80722	D	1	B	0.33135	0.399	B	0.38156	0.266	T	0.01099	-1.1452	10	0.29301	T	0.29	-13.3132	20.5827	0.99408	0.0:1.0:0.0:0.0	.	1323	Q9Y4G6	TLN2_HUMAN	Y	1323	ENSP00000303476:S1323Y	ENSP00000303476:S1323Y	S	+	2	0	TLN2	60820203	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.002000	0.70693	2.941000	0.99782	0.655000	0.94253	TCT		0.493	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63032911	C	A	63032911	3	1	61	1	0	0	0	0	1	0	0	0	15987	913	32	2	4082	2	TLN2	15	63032911	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	726762	63032911	39498481	9415	17400										
TLN2	83660	broad.mit.edu	37	chr15	63040640	63040640	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataatgccctgcgggagctCgaggtaggtccctgggaagg	17	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63040640C>T	ENST00000561311.1	+	32	4346	c.4116C>T	c.(4114-4116)ctC>ctT	p.L1372L	TLN2_ENST00000306829.6_Silent_p.L1372L			Q9Y4G6	TLN2_HUMAN	talin 2	1372					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.L1372L(2)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TGCGGGAGCTCGAGGTAGGTC	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	15											84	81	82					15																	63040640		2203	4300	6503	60827932	SO:0001819	synonymous_variant	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.4116C>T	15.37:g.63040640C>T			60827932	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																				0.532	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63040640	C	T	63040640	2	4	61	1	0	0	0	0	0	0	0	1	15987	871	31	1		1	TLN2	15	63040640	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7729	63040640	39490752	9416	17401										
TLN2	83660	broad.mit.edu	37	chr15	63044599	63044599	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggattgcatccaaggctctCtgtgggctgacagaggctgc	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63044599C>A	ENST00000561311.1	+	34	4535	c.4305C>A	c.(4303-4305)ctC>ctA	p.L1435L	TLN2_ENST00000306829.6_Silent_p.L1435L			Q9Y4G6	TLN2_HUMAN	talin 2	1435					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.L1435L(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCAAGGCTCTCTGTGGGCTGA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	15											111	104	106					15																	63044599		2203	4300	6503	60831891	SO:0001819	synonymous_variant	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.4305C>A	15.37:g.63044599C>A			60831891	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																				0.597	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63044599	C	A	63044599	2	1	61	1	0	0	0	0	0	0	0	1	15987	900	32	2		2	TLN2	15	63044599	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3959	63044599	39486793	9417	17402										
TLN2	83660	broad.mit.edu	37	chr15	63058571	63058571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaaatcggacaccttatcGatcccatcgccacagcggct	9	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63058571G>A	ENST00000561311.1	+	40	5376	c.5146G>A	c.(5146-5148)Gat>Aat	p.D1716N	TLN2_ENST00000306829.6_Missense_Mutation_p.D1716N|TLN2_ENST00000472902.1_Missense_Mutation_p.D109N			Q9Y4G6	TLN2_HUMAN	talin 2	1716					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.D1716N(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						ACACCTTATCGATCCCATCGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15											65	53	57					15																	63058571		2203	4300	6503	60845863	SO:0001583	missense	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.5146G>A	15.37:g.63058571G>A	ENSP00000453508:p.Asp1716Asn		60845863	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691064	0.88735	.	.	ENSG00000171914	ENST00000306829	T	0.13089	2.62	5.58	5.58	0.84498	.	0.043287	0.85682	D	0.000000	T	0.28300	0.0699	L	0.54323	1.7	0.80722	D	1	D;D	0.58620	0.983;0.972	P;P	0.55222	0.771;0.684	T	0.00230	-1.1897	10	0.33141	T	0.24	-20.3654	19.568	0.95403	0.0:0.0:1.0:0.0	.	760;1716	G1UI21;Q9Y4G6	.;TLN2_HUMAN	N	1716	ENSP00000303476:D1716N	ENSP00000303476:D1716N	D	+	1	0	TLN2	60845863	1.000000	0.71417	0.965000	0.40720	0.918000	0.54935	9.700000	0.98707	2.626000	0.88956	0.655000	0.94253	GAT		0.567	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63058571	G	A	63058571	3	1	61	1	0	0	0	0	1	0	0	0	15987	1058	37	1	5296	1	TLN2	15	63058571	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13972	63058571	39472821	9418	17403										
TLN2	83660	broad.mit.edu	37	chr15	63084842	63084842	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcttgcctctgcagatCggattccagattcgcactcg	11	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63084842C>T	ENST00000561311.1	+	45	5969	c.5739C>T	c.(5737-5739)atC>atT	p.I1913I	TLN2_ENST00000306829.6_Silent_p.I1913I			Q9Y4G6	TLN2_HUMAN	talin 2	1913					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.I1913I(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CTCTGCAGATCGGATTCCAGA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	15											70	59	63					15																	63084842		2203	4299	6502	60871895	SO:0001819	synonymous_variant	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.5739C>T	15.37:g.63084842C>T			60871895	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																				0.587	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63084842	C	T	63084842	2	4	61	1	0	0	0	0	0	0	0	1	15987	874	31	1		1	TLN2	15	63084842	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26271	63084842	39446550	9419	17404										
TLN2	83660	broad.mit.edu	37	chr15	63132761	63132761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactggcccaaatccgccaGcagcagtataagtttttacc	7	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63132761G>T	ENST00000561311.1	+	58	7811	c.7581G>T	c.(7579-7581)caG>caT	p.Q2527H	TLN2_ENST00000306829.6_Missense_Mutation_p.Q2527H|RP11-1069G10.1_ENST00000560963.1_RNA|RP11-1069G10.1_ENST00000558404.1_RNA|RP11-1069G10.1_ENST00000557994.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2527	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.Q2527H(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AAATCCGCCAGCAGCAGTATA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											60	65	63					15																	63132761		2203	4300	6503	60919814	SO:0001583	missense	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7581G>T	15.37:g.63132761G>T	ENSP00000453508:p.Gln2527His		60919814	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127800	0.56721	.	.	ENSG00000171914	ENST00000306829	T	0.44482	0.92	5.59	3.64	0.41730	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.44787	0.1310	N	0.17474	0.49	0.49299	D	0.999774	D;D	0.76494	0.999;0.998	D;D	0.91635	0.979;0.999	T	0.35076	-0.9803	10	0.46703	T	0.11	-15.4165	9.7769	0.40626	0.2789:0.0:0.7211:0.0	.	143;2527	B4DGF3;Q9Y4G6	.;TLN2_HUMAN	H	2527	ENSP00000303476:Q2527H	ENSP00000303476:Q2527H	Q	+	3	2	TLN2	60919814	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.902000	0.48703	0.617000	0.30160	0.655000	0.94253	CAG		0.532	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63132761	G	T	63132761	3	4	61	1	0	0	0	0	1	0	0	0	15987	962	34	2	7803	2	TLN2	15	63132761	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47919	63132761	39398631	9420	17405										
RAB8B	51762	broad.mit.edu	37	chr15	63547774	63547774	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaaaaattggatcagaaaCattgaagaggtatgtgtgga	11	2	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63547774C>A	ENST00000321437.4	+	4	471	c.315C>A	c.(313-315)aaC>aaA	p.N105K	RAB8B_ENST00000448330.2_Missense_Mutation_p.N105K	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	105					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)	p.N105K(1)		kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						GGATCAGAAACATTGAAGAGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											58	62	61					15																	63547774		2203	4300	6503	61334827	SO:0001583	missense	51762			AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"RAB, member RAS oncogene"	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.315C>A	15.37:g.63547774C>A	ENSP00000312734:p.Asn105Lys		61334827	Q5JPC4|Q9P293	Missense_Mutation	SNP	ENST00000321437.4	37	CCDS10183.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867171	0.72065	.	.	ENSG00000166128	ENST00000321437;ENST00000448330	T;T	0.75821	-0.97;-0.97	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.76471	0.3992	N	0.25647	0.755	0.54753	D	0.99998	D;D	0.54047	0.957;0.964	P;P	0.55345	0.513;0.774	T	0.78448	-0.2200	10	0.72032	D	0.01	.	19.3123	0.94195	0.0:1.0:0.0:0.0	.	105;105	F5GY21;Q92930	.;RAB8B_HUMAN	K	105	ENSP00000312734:N105K;ENSP00000405463:N105K	ENSP00000312734:N105K	N	+	3	2	RAB8B	61334827	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.579000	0.36536	2.811000	0.96726	0.555000	0.69702	AAC		0.398	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1	NM_016530		A	63547774	C	A	63547774	3	1	61	1	0	0	0	0	1	0	0	0	12994	477	17	2	329	2	RAB8B	15	63547774	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	415013	63547774	38983618	9421	17406										
APH1B	83464	broad.mit.edu	37	chr15	63571366	63571366	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgtatttttcagagctttCttctggttggtgtctctact	8	10	4	1	rs11554840		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63571366C>A	ENST00000261879.5	+	2	190	c.120C>A	c.(118-120)ttC>ttA	p.F40L	APH1B_ENST00000380343.4_Missense_Mutation_p.F40L	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	40					apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.F40L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						TCAGAGCTTTCTTCTGGTTGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											179	164	169					15																	63571366		2203	4300	6503	61358419	SO:0001583	missense	83464			AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"anterior pharynx defective 1 homolog B (C. elegans)"			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.120C>A	15.37:g.63571366C>A	ENSP00000261879:p.Phe40Leu		61358419	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.91|14.91	2.676325|2.676325	0.47886|0.47886	.|.	.|.	ENSG00000138613|ENSG00000138613	ENST00000380343;ENST00000261879|ENST00000380340	T;T|.	0.54479|.	0.57;0.57|.	4.64|4.64	0.419|0.419	0.16438|0.16438	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72431|0.72431	0.3459|0.3459	M|M	0.85373|0.85373	2.75|2.75	0.58432|0.58432	D|D	0.999997|0.999997	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.79108|.	0.992;0.992|.	T|T	0.72010|0.72010	-0.4419|-0.4419	10|6	0.35671|0.87932	T|D	0.21|0	-17.8101|-17.8101	7.593|7.593	0.28031|0.28031	0.0:0.5953:0.0:0.4047|0.0:0.5953:0.0:0.4047	rs11554840|rs11554840	40;40|.	Q564N3;Q8WW43|.	.;APH1B_HUMAN|.	L|I	40|62	ENSP00000369700:F40L;ENSP00000261879:F40L|.	ENSP00000261879:F40L|ENSP00000369697:L62I	F|L	+|+	3|1	2|0	APH1B|APH1B	61358419|61358419	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	0.582000|0.582000	0.23834|0.23834	0.118000|0.118000	0.18165|0.18165	0.462000|0.462000	0.41574|0.41574	TTC|CTT		0.363	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301		A	63571366	C	A	63571366	3	1	61	1	0	0	0	0	1	0	0	0	772	912	32	2	126	2	APH1B	15	63571366	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23592	63571366	38960026	9422	17407										
HERC1	8925	broad.mit.edu	37	chr15	63943477	63943477	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgccagatattcaccatCttttccaaagcgcctgctag	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63943477C>A	ENST00000443617.2	-	53	10608	c.10521G>T	c.(10519-10521)aaG>aaT	p.K3507N		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3507					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.K3507N(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TATTCACCATCTTTTCCAAAG	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	15											114	108	110					15																	63943477		1826	4087	5913	61730530	SO:0001583	missense	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.10521G>T	15.37:g.63943477C>A	ENSP00000390158:p.Lys3507Asn		61730530	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.398031	0.62177	.	.	ENSG00000103657	ENST00000443617	T	0.62364	0.03	5.43	5.43	0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.64649	0.2617	N	0.12746	0.255	0.58432	D	0.999998	D	0.71674	0.998	D	0.76071	0.987	T	0.63220	-0.6686	10	0.21540	T	0.41	.	19.258	0.93955	0.0:1.0:0.0:0.0	.	3507	Q15751	HERC1_HUMAN	N	3507	ENSP00000390158:K3507N	ENSP00000390158:K3507N	K	-	3	2	HERC1	61730530	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.206000	0.42779	2.554000	0.86153	0.655000	0.94253	AAG		0.423	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63943477	C	A	63943477	3	1	61	1	0	0	0	0	1	0	0	0	7078	912	32	2	4168	2	HERC1	15	63943477	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	372111	63943477	38587915	9423	17408										
HERC1	8925	broad.mit.edu	37	chr15	63955346	63955346	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctgggtcttgctgcaaaGatattccttctctccgactt	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63955346G>T	ENST00000443617.2	-	44	8825	c.8738C>A	c.(8737-8739)tCt>tAt	p.S2913Y		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2913					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S2913Y(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTGCTGCAAAGATATTCCTTC	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	15											171	173	172					15																	63955346		1919	4117	6036	61742399	SO:0001583	missense	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.8738C>A	15.37:g.63955346G>T	ENSP00000390158:p.Ser2913Tyr		61742399	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.089990	0.55968	.	.	ENSG00000103657	ENST00000443617	T	0.24723	1.84	5.77	5.77	0.91146	.	0.074067	0.53938	U	0.000047	T	0.23572	0.0570	N	0.22421	0.69	0.49687	D	0.999813	P	0.47350	0.894	B	0.41723	0.365	T	0.02358	-1.1171	10	0.87932	D	0	.	20.0615	0.97676	0.0:0.0:1.0:0.0	.	2913	Q15751	HERC1_HUMAN	Y	2913	ENSP00000390158:S2913Y	ENSP00000390158:S2913Y	S	-	2	0	HERC1	61742399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.445000	0.73456	2.748000	0.94277	0.549000	0.68633	TCT		0.418	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63955346	G	T	63955346	3	4	61	1	0	0	0	0	1	0	0	0	7078	942	33	2	5987	2	HERC1	15	63955346	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11869	63955346	38576046	9424	17409										
HERC1	8925	broad.mit.edu	37	chr15	63966843	63966843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcactaagtgacttcataGcaccgaggtaaagataggac	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63966843G>A	ENST00000443617.2	-	38	7631	c.7544C>T	c.(7543-7545)gCt>gTt	p.A2515V	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2515					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.A2515V(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TGACTTCATAGCACCGAGGTA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	15											59	58	58					15																	63966843		1973	4161	6134	61753896	SO:0001583	missense	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.7544C>T	15.37:g.63966843G>A	ENSP00000390158:p.Ala2515Val		61753896	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082602	0.94050	.	.	ENSG00000103657	ENST00000443617	T	0.39592	1.07	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.57198	0.2037	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	T	0.57911	-0.7729	10	0.87932	D	0	.	20.1991	0.98252	0.0:0.0:1.0:0.0	.	2515	Q15751	HERC1_HUMAN	V	2515	ENSP00000390158:A2515V	ENSP00000390158:A2515V	A	-	2	0	HERC1	61753896	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.775000	0.95449	0.650000	0.86243	GCT		0.438	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63966843	G	A	63966843	3	1	61	1	0	0	0	0	1	0	0	0	7078	971	34	3	7205	3	HERC1	15	63966843	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11497	63966843	38564549	9425	17410										
HERC1	8925	broad.mit.edu	37	chr15	63984706	63984706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgaagatacaactctgcGaagaaaaactaaaaaatccc	5	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:63984706G>A	ENST00000443617.2	-	31	5821	c.5734C>T	c.(5734-5736)Cgc>Tgc	p.R1912C	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1912					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1912C(4)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACAACTCTGCGAAGAAAAACT	0.403																																																4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	15											69	65	66					15																	63984706		1817	4084	5901	61771759	SO:0001583	missense	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.5734C>T	15.37:g.63984706G>A	ENSP00000390158:p.Arg1912Cys		61771759	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115422	0.77323	.	.	ENSG00000103657	ENST00000443617	T	0.42131	0.98	5.64	4.69	0.59074	.	0.000000	0.64402	U	0.000001	T	0.53818	0.1820	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.55976	-0.8055	10	0.87932	D	0	.	14.3837	0.66929	0.0:0.0:0.7359:0.2641	.	1912	Q15751	HERC1_HUMAN	C	1912	ENSP00000390158:R1912C	ENSP00000390158:R1912C	R	-	1	0	HERC1	61771759	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.224000	0.51238	2.652000	0.90054	0.650000	0.86243	CGC		0.403	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63984706	G	A	63984706	3	1	61	1	0	0	0	0	1	0	0	0	7078	1058	37	1	9043	1	HERC1	15	63984706	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17863	63984706	38546686	9426	17411										
HERC1	8925	broad.mit.edu	37	chr15	64025343	64025343	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgatatccagttgcattCtctaaagaacaataaaatag	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:64025343C>A	ENST00000443617.2	-	14	2735	c.2648G>T	c.(2647-2649)aGa>aTa	p.R883I		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	883					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R883I(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CAGTTGCATTCTCTAAAGAAC	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	15											105	101	102					15																	64025343		1893	4113	6006	61812396	SO:0001630	splice_region_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.2647-1G>T	15.37:g.64025343C>A			61812396	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	33	5.259865	0.95368	.	.	ENSG00000103657	ENST00000443617	T	0.30714	1.52	5.73	5.73	0.89815	.	0.000000	0.85682	U	0.000000	T	0.55289	0.1911	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	T	0.54616	-0.8267	10	0.87932	D	0	.	19.9059	0.97007	0.0:1.0:0.0:0.0	.	883	Q15751	HERC1_HUMAN	I	883	ENSP00000390158:R883I	ENSP00000390158:R883I	R	-	2	0	HERC1	61812396	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.709000	0.84645	2.693000	0.91896	0.655000	0.94253	AGA		0.388	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	Missense_Mutation	A	64025343	C	A	64025343	5	1	61	1	0	0	0	0	0	0	1	0	7078	927	32	2	12197	2	HERC1	15	64025343	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40637	64025343	38506049	9427	17412										
SNX1	6642	broad.mit.edu	37	chr15	64420005	64420005	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttcttggaaaaagaagaGgttagtattcagtgcaaact	11	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:64420005G>T	ENST00000559844.1	+	8	821	c.807G>T	c.(805-807)gaG>gaT	p.E269D	SNX1_ENST00000353874.4_Splice_Site_p.E269D|SNX1_ENST00000561026.1_Splice_Site_p.E204D|SNX1_ENST00000261889.5_Splice_Site_p.E269D|SNX1_ENST00000560829.1_Splice_Site_p.E51D			Q13596	SNX1_HUMAN	sorting nexin 1	269	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.E269D(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						AAAAAGAAGAGGTTAGTATTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	86	87					15																	64420005		2203	4300	6503	62207058	SO:0001630	splice_region_variant	6642			BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.807+1G>T	15.37:g.64420005G>T			62207058	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Missense_Mutation	SNP	ENST00000559844.1	37	CCDS32266.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.430205	0.43122	.	.	ENSG00000028528	ENST00000380285;ENST00000353874;ENST00000261889	T	0.36157	1.27	4.64	3.72	0.42706	Phox homologous domain (2);	0.103824	0.64402	D	0.000004	T	0.26122	0.0637	L	0.34521	1.04	0.80722	D	1	B;B;B;B;B;B	0.11235	0.001;0.0;0.004;0.001;0.0;0.001	B;B;B;B;B;B	0.19946	0.01;0.003;0.027;0.012;0.001;0.01	T	0.05099	-1.0906	10	0.13853	T	0.58	-33.4654	12.2507	0.54597	0.083:0.0:0.917:0.0	.	269;179;269;204;269;269	Q6ZRJ8;Q59GU6;Q53GY8;Q13596-2;A6NKH4;Q13596	.;.;.;.;.;SNX1_HUMAN	D	269;269;204	ENSP00000326668:E269D	ENSP00000261889:E204D	E	+	3	2	SNX1	62207058	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.674000	0.54598	1.299000	0.44798	-0.258000	0.10820	GAG		0.378	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099	Missense_Mutation	T	64420005	G	T	64420005	5	4	61	1	0	0	0	0	0	0	1	0	14917	1014	35	2	837	2	SNX1	15	64420005	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	394662	64420005	38111387	9428	17413										
SNX1	6642	broad.mit.edu	37	chr15	64428564	64428564	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaatatgaaagggacttCgagaggatttcaacagtggt	11	6	2	2	rs76908230	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:64428564C>T	ENST00000559844.1	+	13	1415	c.1401C>T	c.(1399-1401)ttC>ttT	p.F467F	SNX1_ENST00000353874.4_Silent_p.F419F|SNX1_ENST00000561026.1_Silent_p.F402F|SNX1_ENST00000261889.5_Silent_p.F467F|SNX1_ENST00000560829.1_Silent_p.F249F			Q13596	SNX1_HUMAN	sorting nexin 1	467	BAR.				early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.F467F(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						AAAGGGACTTCGAGAGGATTT	0.428													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		23089	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15						C	,	51,4355	52.3+/-87.9	1,49,2153	144	137	140		1401,1206	2.4	1	15	dbSNP_131	140	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SNX1	NM_003099.4,NM_148955.3	,	1,49,6453	TT,TC,CC		0.0,1.1575,0.3921	,	467/523,402/458	64428564	51,12955	2203	4300	6503	62215617	SO:0001819	synonymous_variant	6642			BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.1401C>T	15.37:g.64428564C>T			62215617	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Silent	SNP	ENST00000559844.1	37	CCDS32266.1																																																																																				0.428	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		T	64428564	C	T	64428564	2	4	61	1	0	0	0	0	0	0	0	1	14917	883	31	1		1	SNX1	15	64428564	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8559	64428564	38102828	9429	17414										
ZNF609	23060	broad.mit.edu	37	chr15	64791682	64791682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacccggttgagacatacGacagtggggatgaatgggac	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:64791682G>A	ENST00000326648.3	+	1	192	c.64G>A	c.(64-66)Gac>Aac	p.D22N	ZNF609_ENST00000416172.1_Missense_Mutation_p.D22N	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	22						nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.D22N(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGAGACATACGACAGTGGGGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											166	147	154					15																	64791682		2203	4300	6503	62578735	SO:0001583	missense	23060			BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.64G>A	15.37:g.64791682G>A	ENSP00000316527:p.Asp22Asn		62578735	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	37	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	.	26.0	4.697412	0.88830	.	.	ENSG00000180357	ENST00000416172;ENST00000326648	T	0.60171	0.21	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.78130	-0.2324	10	0.72032	D	0.01	-18.7935	19.7418	0.96234	0.0:0.0:1.0:0.0	.	22;22	E7ERY8;O15014	.;ZN609_HUMAN	N	22	ENSP00000316527:D22N	ENSP00000316527:D22N	D	+	1	0	ZNF609	62578735	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.799000	0.99117	2.742000	0.94016	0.645000	0.84053	GAC		0.512	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		A	64791682	G	A	64791682	3	1	61	1	0	0	0	0	1	0	0	0	18074	1058	37	1	66	1	ZNF609	15	64791682	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	363118	64791682	37739710	9430	17415										
OAZ2	4947	broad.mit.edu	37	chr15	64982667	64982667	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagaagagaccttcacctCggtgacctcatactggaagt	9	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:64982667C>T	ENST00000326005.6	-	4	491	c.259G>A	c.(259-261)Gag>Aag	p.E87K	OAZ2_ENST00000559753.1_5'UTR|OAZ2_ENST00000560258.2_Missense_Mutation_p.E87K|OAZ2_ENST00000560837.1_5'UTR			O95190	OAZ2_HUMAN	ornithine decarboxylase antizyme 2	87					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|polyamine biosynthetic process (GO:0006596)|polyamine metabolic process (GO:0006595)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein catabolic process (GO:0045732)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ornithine decarboxylase inhibitor activity (GO:0008073)									L-Ornithine(DB00129)	ACCTTCACCTCGGTGACCTCA	0.517																																																0			15											162	156	158					15																	64982667		1944	4143	6087	62769720	SO:0001583	missense	4947			AF057297	CCDS58372.1	15q22.31	2006-05-11				ENSG00000180304			8096	protein-coding gene	gene with protein product		604152				9782076, 10352227	Standard	NM_002537		Approved		uc002ano.2	O95190		ENST00000326005.6:c.259G>A	15.37:g.64982667C>T	ENSP00000463013:p.Glu87Lys		62769720		Missense_Mutation	SNP	ENST00000326005.6	37	CCDS58372.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.750170	0.69533	.	.	ENSG00000180304	ENST00000326005;ENST00000403937	.	.	.	5.84	5.84	0.93424	Acyl-CoA N-acyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.83631	0.5296	M	0.79926	2.475	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	D	0.83865	0.0270	9	0.56958	D	0.05	.	20.1434	0.98067	0.0:1.0:0.0:0.0	.	87	O95190	OAZ2_HUMAN	K	85	.	ENSP00000316264:E85K	E	-	1	0	OAZ2	62769720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.788000	0.55446	2.769000	0.95229	0.563000	0.77884	GAG		0.517	OAZ2-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418707.2	NM_002537		T	64982667	C	T	64982667	3	4	61	1	0	0	0	0	1	0	0	0	10836	893	31	1	322	1	OAZ2	15	64982667	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	190985	64982667	37548725	9431	17416										
ANKDD1A	348094	broad.mit.edu	37	chr15	65239797	65239797	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcacatgtcgacgccatCgagcaacagtggacaggtac	13	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:65239797C>T	ENST00000380230.3	+	13	1364	c.1335C>T	c.(1333-1335)atC>atT	p.I445I	ANKDD1A_ENST00000357698.3_Silent_p.I413I|ANKDD1A_ENST00000395723.1_Silent_p.I322I|ANKDD1A_ENST00000395720.1_Silent_p.I445I	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	445	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)			p.I445I(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TCGACGCCATCGAGCAACAGT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	15											70	46	54					15																	65239797		2202	4299	6501	63026850	SO:0001819	synonymous_variant	348094				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1335C>T	15.37:g.65239797C>T			63026850	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	37	CCDS10197.2																																																																																				0.582	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65239797	C	T	65239797	2	4	61	1	0	0	0	0	0	0	0	1	624	874	31	1		1	ANKDD1A	15	65239797	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	257130	65239797	37291595	9432	17417										
ANKDD1A	348094	broad.mit.edu	37	chr15	65242156	65242156	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccccagcaaagcgctgttCgagggcctcgtggccattgg	13	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:65242156C>T	ENST00000380230.3	+	14	1475	c.1446C>T	c.(1444-1446)ttC>ttT	p.F482F	ANKDD1A_ENST00000357698.3_Silent_p.F450F|ANKDD1A_ENST00000395723.1_Silent_p.F359F|ANKDD1A_ENST00000395720.1_Silent_p.F482F	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	482	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)			p.F482F(2)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						AAGCGCTGTTCGAGGGCCTCG	0.632																																																2	Substitution - coding silent(2)	large_intestine(2)	15											85	84	84					15																	65242156		2202	4299	6501	63029209	SO:0001819	synonymous_variant	348094				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1446C>T	15.37:g.65242156C>T			63029209	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	37	CCDS10197.2																																																																																				0.632	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65242156	C	T	65242156	2	4	61	1	0	0	0	0	0	0	0	1	624	883	31	1		1	ANKDD1A	15	65242156	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2359	65242156	37289236	9433	17418										
MTFMT	123263	broad.mit.edu	37	chr15	65295559	65295559	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtagctgttagtgatttCttgagcatcactgatcgaac	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:65295559C>A	ENST00000220058.4	-	9	1024	c.1011G>T	c.(1009-1011)aaG>aaT	p.K337N		NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	337						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)	p.K337N(2)		endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	TTAGTGATTTCTTGAGCATCA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	15											90	79	83					15																	65295559		1869	4108	5977	63082612	SO:0001583	missense	123263			AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.1011G>T	15.37:g.65295559C>A	ENSP00000220058:p.Lys337Asn		63082612	B7Z734	Missense_Mutation	SNP	ENST00000220058.4	37	CCDS45280.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.320146	0.60634	.	.	ENSG00000103707	ENST00000220058	T	0.56776	0.44	5.23	5.23	0.72850	Formyl transferase, C-terminal-like (1);Formyl transferase, C-terminal (2);	0.050432	0.85682	D	0.000000	T	0.71273	0.3320	M	0.80847	2.515	0.45899	D	0.998743	P	0.51537	0.946	P	0.59889	0.865	T	0.75665	-0.3239	10	0.87932	D	0	-17.8582	16.0551	0.80798	0.0:1.0:0.0:0.0	.	337	Q96DP5	FMT_HUMAN	N	337	ENSP00000220058:K337N	ENSP00000220058:K337N	K	-	3	2	MTFMT	63082612	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	1.814000	0.38972	2.581000	0.87130	0.591000	0.81541	AAG		0.408	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242		A	65295559	C	A	65295559	3	1	61	1	0	0	0	0	1	0	0	0	9954	912	32	2	162	2	MTFMT	15	65295559	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53403	65295559	37235833	9434	17419										
CILP	8483	broad.mit.edu	37	chr15	65490080	65490080	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagatagggctgagggacGccaattgcatttgggttgaa	15	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:65490080G>A	ENST00000261883.4	-	9	2710	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	848					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.G848G(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						GCTGAGGGACGCCAATTGCAT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	15											123	104	111					15																	65490080		2200	4297	6497	63277133	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.2544C>T	15.37:g.65490080G>A			63277133	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.522	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65490080	G	A	65490080	2	1	61	1	0	0	0	0	0	0	0	1	3435	1074	38	1		1	CILP	15	65490080	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194521	65490080	37041312	9435	17420										
IGDCC3	9543	broad.mit.edu	37	chr15	65624345	65624345	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccatttttcagccacgtgAcatgaggcggtggctcaccc	11	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:65624345A>G	ENST00000327987.4	-	7	1333	c.1082T>C	c.(1081-1083)gTc>gCc	p.V361A	IGDCC3_ENST00000559231.1_5'UTR	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	361	Ig-like C2-type 4.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)		p.V361A(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGCCACGTGACATGAGGCGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											98	82	87					15																	65624345		2201	4299	6500	63411398	SO:0001583	missense	9543			AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1082T>C	15.37:g.65624345A>G	ENSP00000332773:p.Val361Ala		63411398	O95215	Missense_Mutation	SNP	ENST00000327987.4	37	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673884	0.47781	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.76578	-1.03	4.42	4.42	0.53409	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.161524	0.45126	D	0.000396	D	0.82444	0.5038	M	0.70903	2.155	0.47214	D	0.999354	P	0.43287	0.802	P	0.50192	0.634	D	0.85137	0.0978	10	0.87932	D	0	-24.5864	13.9773	0.64282	1.0:0.0:0.0:0.0	.	361	Q8IVU1	IGDC3_HUMAN	A	361;224	ENSP00000332773:V361A	ENSP00000332773:V361A	V	-	2	0	IGDCC3	63411398	1.000000	0.71417	0.565000	0.28409	0.007000	0.05969	9.283000	0.95860	1.741000	0.51731	0.533000	0.62120	GTC		0.602	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		G	65624345	A	G	65624345	3	3	61	1	0	0	0	0	1	0	0	0	7589	275	10	4	1394	4	IGDCC3	15	65624345	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	134265	65624345	36907047	9436	17421										
DENND4A	10260	broad.mit.edu	37	chr15	66025127	66025127	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctgaggagatggaaaaGgaactttatgcataaaatga	11	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66025127G>T	ENST00000431932.2	-	8	1278	c.1070C>A	c.(1069-1071)cCt>cAt	p.P357H	DENND4A_ENST00000443035.3_Missense_Mutation_p.P357H	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	357	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.P357H(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGATGGAAAAGGAACTTTATG	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	15											75	67	70					15																	66025127		1839	4079	5918	63812181	SO:0001583	missense	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.1070C>A	15.37:g.66025127G>T	ENSP00000396830:p.Pro357His		63812181	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.894842	0.91962	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.13778	2.56;2.56	5.33	5.33	0.75918	DENN (3);	0.000000	0.85682	D	0.000000	T	0.47911	0.1471	M	0.89658	3.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;1.0	T	0.58561	-0.7615	10	0.87932	D	0	.	19.0016	0.92836	0.0:0.0:1.0:0.0	.	357;357;357	B7Z5Y3;E7EPL3;Q7Z401	.;.;MYCPP_HUMAN	H	357	ENSP00000391167:P357H;ENSP00000396830:P357H	ENSP00000396830:P357H	P	-	2	0	DENND4A	63812181	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.539000	0.98076	2.492000	0.84095	0.484000	0.47621	CCT		0.353	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	66025127	G	T	66025127	3	4	61	1	0	0	0	0	1	0	0	0	4444	1000	35	2	4754	2	DENND4A	15	66025127	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	400782	66025127	36506265	9437	17422										
DENND4A	10260	broad.mit.edu	37	chr15	66044917	66044917	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcccatagggagtactctGaataatttcacaaccctgtt	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66044917G>T	ENST00000431932.2	-	4	569	c.361C>A	c.(361-363)Cag>Aag	p.Q121K	DENND4A_ENST00000443035.3_Missense_Mutation_p.Q121K	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	121	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.Q121K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GGAGTACTCTGAATAATTTCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	15											43	38	40					15																	66044917		1805	4059	5864	63831971	SO:0001583	missense	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.361C>A	15.37:g.66044917G>T	ENSP00000396830:p.Gln121Lys		63831971	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369363	0.42003	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.24908	1.83;1.83	5.1	4.17	0.49024	MABP domain (1);	0.000000	0.85682	D	0.000000	T	0.41213	0.1149	L	0.46947	1.48	0.80722	D	1	B;D;D	0.61080	0.002;0.989;0.987	B;D;P	0.64776	0.01;0.929;0.902	T	0.13737	-1.0498	10	0.35671	T	0.21	.	15.0581	0.71930	0.0:0.0:0.8568:0.1432	.	121;121;121	B7Z5Y3;E7EPL3;Q7Z401	.;.;MYCPP_HUMAN	K	121	ENSP00000391167:Q121K;ENSP00000396830:Q121K	ENSP00000396830:Q121K	Q	-	1	0	DENND4A	63831971	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	5.537000	0.67186	1.220000	0.43490	0.563000	0.77884	CAG		0.333	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	66044917	G	T	66044917	3	4	61	1	0	0	0	0	1	0	0	0	4444	1299	45	2	5479	2	DENND4A	15	66044917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19790	66044917	36486475	9438	17423										
RAB11A	8766	broad.mit.edu	37	chr15	66169727	66169727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcctgtctcgatttactcGaaatgagtttaatctggaaa	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66169727G>A	ENST00000261890.2	+	2	226	c.98G>A	c.(97-99)cGa>cAa	p.R33Q	RAB11A_ENST00000569896.1_Missense_Mutation_p.R33Q|RAB11A_ENST00000435304.2_Missense_Mutation_p.R33Q|RAB11A_ENST00000565075.1_Missense_Mutation_p.R33Q|RAB11A_ENST00000564910.1_Intron	NM_001206836.1|NM_004663.4	NP_001193765.1|NP_004654.1	P62491	RB11A_HUMAN	RAB11A, member RAS oncogene family	33					cytokinesis (GO:0000910)|establishment of protein localization to membrane (GO:0090150)|exosomal secretion (GO:1990182)|GTP catabolic process (GO:0006184)|melanosome transport (GO:0032402)|multivesicular body assembly (GO:0036258)|neuron projection development (GO:0031175)|plasma membrane to endosome transport (GO:0048227)|positive regulation of axon extension (GO:0045773)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of multivesicular body size (GO:0010796)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	axon (GO:0030424)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|syntaxin binding (GO:0019905)	p.R33Q(1)		kidney(1)|large_intestine(2)|lung(1)|prostate(1)	5						CGATTTACTCGAAATGAGTTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											90	81	84					15																	66169727		2201	4299	6500	63956781	SO:0001583	missense	8766			X56740	CCDS10212.1, CCDS58373.1	15q22.31	2008-05-14			ENSG00000103769	ENSG00000103769		"RAB, member RAS oncogene"	9760	protein-coding gene	gene with protein product		605570				1704119, 9662449	Standard	NM_004663		Approved	YL8	uc002apk.3	P62491	OTTHUMG00000133162	ENST00000261890.2:c.98G>A	15.37:g.66169727G>A	ENSP00000261890:p.Arg33Gln		63956781	B2R4B6|B4DT13|P24410|Q5TZN9|Q9JLX1	Missense_Mutation	SNP	ENST00000261890.2	37	CCDS10212.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664992	0.88251	.	.	ENSG00000103769	ENST00000261890;ENST00000435304	T;T	0.76186	-1.0;-1.0	5.42	5.42	0.78866	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.57021	0.2025	N	0.12663	0.25	0.80722	D	1	P;B	0.38642	0.641;0.222	B;B	0.26310	0.065;0.068	T	0.66031	-0.6024	10	0.87932	D	0	.	19.2309	0.93839	0.0:0.0:1.0:0.0	.	33;33	B4DT13;P62491	.;RB11A_HUMAN	Q	33	ENSP00000261890:R33Q;ENSP00000405767:R33Q	ENSP00000261890:R33Q	R	+	2	0	RAB11A	63956781	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.976000	0.88070	2.536000	0.85505	0.655000	0.94253	CGA		0.398	RAB11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256864.1			A	66169727	G	A	66169727	3	1	61	1	0	0	0	0	1	0	0	0	12928	1058	37	1	104	1	RAB11A	15	66169727	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	124810	66169727	36361665	9439	17424										
MEGF11	84465	broad.mit.edu	37	chr15	66210410	66210410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagctgggcacagtcctgCccaaagtatcctccagcaca	9	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66210410C>T	ENST00000409699.2	-	16	2152	c.1980G>A	c.(1978-1980)ggG>ggA	p.G660G	MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000422354.1_Silent_p.G660G|MEGF11_ENST00000395625.2_Silent_p.G585G|MEGF11_ENST00000360698.4_Silent_p.G660G|MEGF11_ENST00000288745.3_Silent_p.G585G			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	660	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G585G(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						CACAGTCCTGCCCAAAGTATC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	15											93	69	77					15																	66210410		2201	4299	6500	63997464	SO:0001819	synonymous_variant	84465			AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.1980G>A	15.37:g.66210410C>T			63997464	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Silent	SNP	ENST00000409699.2	37	CCDS10213.2																																																																																				0.602	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		T	66210410	C	T	66210410	2	4	61	1	0	0	0	0	0	0	0	1	9491	726	26	3		3	MEGF11	15	66210410	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40683	66210410	36320982	9440	17425										
DIS3L	115752	broad.mit.edu	37	chr15	66625388	66625388	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgccattctgatacaatcaGacttgaaataattagtaaca	5	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66625388G>A	ENST00000319212.4	+	17	2953	c.2903G>A	c.(2902-2904)aGa>aAa	p.R968K	DIS3L_ENST00000319194.5_Missense_Mutation_p.R885K|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	968					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)	p.R968K(1)|p.R885K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GATACAATCAGACTTGAAATA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	15											56	59	58					15																	66625388		2201	4299	6500	64412442	SO:0001583	missense	115752				CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"DIS3 mitotic control homolog (S. cerevisiae)-like"			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.2903G>A	15.37:g.66625388G>A	ENSP00000321711:p.Arg968Lys		64412442	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	37	CCDS45286.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.964959	0.34659	.	.	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.21543	2.0;2.0	5.79	5.79	0.91817	.	0.559608	0.21143	N	0.079445	T	0.11537	0.0281	N	0.16307	0.4	0.80722	D	1	B	0.11235	0.004	B	0.09377	0.004	T	0.06661	-1.0814	10	0.05525	T	0.97	-13.4496	12.2704	0.54702	0.085:0.0:0.915:0.0	.	968	Q8TF46	DI3L1_HUMAN	K	885;968	ENSP00000321583:R885K;ENSP00000321711:R968K	ENSP00000321583:R885K	R	+	2	0	DIS3L	64412442	1.000000	0.71417	0.951000	0.38953	0.770000	0.43624	4.502000	0.60400	2.734000	0.93682	0.655000	0.94253	AGA		0.333	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		A	66625388	G	A	66625388	3	1	61	1	0	0	0	0	1	0	0	0	4547	942	33	3	2969	3	DIS3L	15	66625388	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	414978	66625388	35906004	9441	17426										
MAP2K1	5604	broad.mit.edu	37	chr15	66781590	66781590	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggagtgttcagtctggAatttcaagattttgtgaata	11	4	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:66781590A>C	ENST00000307102.5	+	9	1529	c.998A>C	c.(997-999)gAa>gCa	p.E333A	CTD-3185P2.2_ENST00000602360.1_RNA|CTD-3185P2.1_ENST00000565387.1_RNA|MAP2K1_ENST00000566326.1_Missense_Mutation_p.E157A	NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	333	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.E333A(2)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	TTCAGTCTGGAATTTCAAGAT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	15											116	105	109					15																	66781590		2201	4299	6500	64568644	SO:0001583	missense	5604			L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.998A>C	15.37:g.66781590A>C	ENSP00000302486:p.Glu333Ala		64568644		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.361082	0.61403	.	.	ENSG00000169032	ENST00000307102	T	0.68181	-0.31	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.57080	0.2029	L	0.28115	0.83	0.80722	D	1	B;P	0.38535	0.045;0.635	B;B	0.39935	0.057;0.314	T	0.59820	-0.7382	10	0.44086	T	0.13	-24.4487	14.694	0.69107	1.0:0.0:0.0:0.0	.	311;333	B4DFY5;Q02750	.;MP2K1_HUMAN	A	333	ENSP00000302486:E333A	ENSP00000302486:E333A	E	+	2	0	MAP2K1	64568644	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.003000	0.93577	2.145000	0.66743	0.533000	0.62120	GAA		0.483	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4			C	66781590	A	C	66781590	3	2	61	1	0	0	0	0	1	0	0	0	9266	246	9	4	1032	4	MAP2K1	15	66781590	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	156202	66781590	35749802	9442	17427										
SMAD3	4088	broad.mit.edu	37	chr15	67459118	67459118	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccttctgattcccagaGaccccaccccctggctacct	5	20	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:67459118G>T	ENST00000327367.4	+	4	844	c.534G>T	c.(532-534)gaG>gaT	p.E178D	SMAD3_ENST00000439724.3_Splice_Site_p.E134D|SMAD3_ENST00000537194.2_5'UTR|SMAD3_ENST00000540846.2_Splice_Site_p.E73D	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	178	Linker.			E -> EVGTWAAQAGL (in Ref. 3; BAA22032). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E178D(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GATTCCCAGAGACCCCACCCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											86	67	73					15																	67459118		2200	4298	6498	65246172	SO:0001630	splice_region_variant	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.533-1G>T	15.37:g.67459118G>T			65246172	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	G	7.830	0.719633	0.15372	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724	D;D;D	0.97256	-4.31;-4.31;-4.31	5.03	-1.05	0.10036	SMAD/FHA domain (1);	0.110401	0.64402	D	0.000009	D	0.90689	0.7079	N	0.20530	0.585	0.48762	D	0.999706	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.78768	-0.2075	10	0.12766	T	0.61	.	10.4892	0.44741	0.499:0.0:0.5009:0.0	.	134;178	B7Z4Z5;P84022	.;SMAD3_HUMAN	D	178;178;73;134	ENSP00000332973:E178D;ENSP00000437757:E73D;ENSP00000401133:E134D	ENSP00000332973:E178D	E	+	3	2	SMAD3	65246172	1.000000	0.71417	0.997000	0.53966	0.887000	0.51463	0.855000	0.27805	-0.158000	0.11040	-0.266000	0.10368	GAG		0.517	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	Missense_Mutation	T	67459118	G	T	67459118	5	4	61	1	0	0	0	0	0	0	1	0	14796	956	33	2	626	2	SMAD3	15	67459118	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	677528	67459118	35072274	9443	17428										
IQCH	64799	broad.mit.edu	37	chr15	67664702	67664702	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtttgagctgacgaataAacttaccagatatgaccttc	8	8	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:67664702A>T	ENST00000335894.4	+	9	1073	c.1007A>T	c.(1006-1008)aAa>aTa	p.K336I	IQCH_ENST00000358767.3_Missense_Mutation_p.K163I|IQCH_ENST00000546225.1_Missense_Mutation_p.K84I|IQCH_ENST00000360277.4_Missense_Mutation_p.K88I	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	336								p.K336I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		CTGACGAATAAACTTACCAGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											109	117	114					15																	67664702		2201	4299	6500	65451756	SO:0001583	missense	64799			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1007A>T	15.37:g.67664702A>T	ENSP00000336861:p.Lys336Ile		65451756	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	.	.	.	.	.	.	.	.	.	.	A	11.18	1.562749	0.27915	.	.	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.47177	0.85;0.86;0.86;0.85	5.53	-3.06	0.05379	.	0.554109	0.21244	N	0.077770	T	0.39733	0.1089	L	0.54323	1.7	0.09310	N	1	P;B;B;B;P	0.44380	0.834;0.178;0.178;0.006;0.727	B;B;B;B;B	0.43103	0.178;0.075;0.075;0.026;0.408	T	0.42032	-0.9475	10	0.40728	T	0.16	-5.4639	10.3943	0.44192	0.3348:0.1135:0.5517:0.0	.	163;84;88;336;163	F8WAL8;Q86VS3-2;Q86VS3-4;Q86VS3;Q86VS3-3	.;.;.;IQCH_HUMAN;.	I	163;84;336;88	ENSP00000351617:K163I;ENSP00000444118:K84I;ENSP00000336861:K336I;ENSP00000353419:K88I	ENSP00000336861:K336I	K	+	2	0	IQCH	65451756	0.001000	0.12720	0.000000	0.03702	0.713000	0.41058	-0.015000	0.12634	-0.376000	0.07943	0.482000	0.46254	AAA		0.433	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		T	67664702	A	T	67664702	3	4	61	1	0	0	0	0	1	0	0	0	7832	14	1	5	1169	5	IQCH	15	67664702	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	205584	67664702	34866690	9444	17429										
IQCH	64799	broad.mit.edu	37	chr15	67713870	67713870	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtggttggttacttttcGatagatctggtgacttttat	11	4	1	2	rs369243986		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:67713870G>A	ENST00000335894.4	+	16	2526	c.2460G>A	c.(2458-2460)tcG>tcA	p.S820S	IQCH_ENST00000358767.3_Silent_p.S556S|IQCH_ENST00000546225.1_Silent_p.S477S|IQCH_ENST00000360277.4_Silent_p.S481S|IQCH-AS1_ENST00000559298.1_lincRNA	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	820								p.S820S(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		GTTACTTTTCGATAGATCTGG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	15						G		1,4401	2.1+/-5.4	0,1,2200	100	91	94		2460	-9.5	0	15		94	0,8598		0,0,4299	no	coding-synonymous	IQCH	NM_001031715.2		0,1,6499	AA,AG,GG		0.0,0.0227,0.0077		820/1028	67713870	1,12999	2201	4299	6500	65500924	SO:0001819	synonymous_variant	64799			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.2460G>A	15.37:g.67713870G>A			65500924	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Silent	SNP	ENST00000335894.4	37	CCDS32273.1																																																																																				0.443	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		A	67713870	G	A	67713870	2	1	61	1	0	0	0	0	0	0	0	1	7832	1045	37	1		1	IQCH	15	67713870	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49168	67713870	34817522	9445	17430										
MAP2K5	5607	broad.mit.edu	37	chr15	67985905	67985905	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaacaaatgcttatatggCggtaagtaaacttatgcaaa	9	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:67985905C>T	ENST00000178640.5	+	15	1598	c.971C>T	c.(970-972)gCg>gTg	p.A324V	MAP2K5_ENST00000395476.2_Splice_Site_p.A324V|MAP2K5_ENST00000354498.5_Splice_Site_p.A288V|MAP2K5_ENST00000340972.4_Splice_Site_p.A134V	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.A324V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						GCTTATATGGCGGTAAGTAAA	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	15											132	126	128					15																	67985905		2200	4296	6496	65772959	SO:0001630	splice_region_variant	5607			U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.972+1C>T	15.37:g.67985905C>T			65772959	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	37	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.024210	0.75390	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70290	0.3207	H	0.98276	4.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.82896	-0.0230	10	0.87932	D	0	-16.1519	19.5552	0.95342	0.0:1.0:0.0:0.0	.	134;324;324	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	V	324;324;324;288;134	ENSP00000378859:A324V;ENSP00000178640:A324V;ENSP00000346493:A288V;ENSP00000342101:A134V	ENSP00000178640:A324V	A	+	2	0	MAP2K5	65772959	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.102000	0.77005	2.630000	0.89119	0.585000	0.79938	GCG		0.303	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162	Missense_Mutation	T	67985905	C	T	67985905	5	4	61	1	0	0	0	0	0	0	1	0	9270	782	27	1	1029	1	MAP2K5	15	67985905	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	272035	67985905	34545487	9446	17431										
LBXCOR1	390598	broad.mit.edu	37	chr15	68118796	68118796	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgccaagtgcatcaagtgCggctactgcagcatgtactt	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:68118796C>T	ENST00000380035.2	+	2	688	c.630C>T	c.(628-630)tgC>tgT	p.C210C	SKOR1_ENST00000389002.1_Silent_p.C201C|SKOR1_ENST00000554054.1_Silent_p.C182C|SKOR1_ENST00000554240.1_Silent_p.C171C|SKOR1_ENST00000341418.5_Silent_p.C396C			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	210					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)	p.C201C(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GCATCAAGTGCGGCTACTGCA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	15											108	94	99					15																	68118796		2200	4298	6498	65905850	SO:0001819	synonymous_variant	390598				CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"SKI transcriptional corepressors"	21326	protein-coding gene	gene with protein product	"transcriptional corepressor CORL1", "functional smad suppressing element 15", "corepressor for LBX1"	611273	"Lbxcor1 homolog (mouse)"	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.630C>T	15.37:g.68118796C>T			65905850	A6NIP4|A6NJY0|Q2VWA5	Silent	SNP	ENST00000380035.2	37																																																																																					0.582	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807		T	68118796	C	T	68118796	2	4	61	1	0	0	0	0	0	0	0	1	8677	776	27	1		1	LBXCOR1	15	68118796	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132891	68118796	34412596	9447	17432										
CALML4	91860	broad.mit.edu	37	chr15	68489887	68489887	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaacatggctagaagaatTtctttctttgggtcttcttg	8	7	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:68489887T>G	ENST00000467889.1	-	4	568	c.384A>C	c.(382-384)gaA>gaC	p.E128D	CALML4_ENST00000540479.1_Missense_Mutation_p.E52D|CALML4_ENST00000395465.3_Intron|RP11-315D16.2_ENST00000562767.1_Missense_Mutation_p.N55H|CALML4_ENST00000448060.2_Missense_Mutation_p.E81D	NM_033429.2	NP_219501.2	Q96GE6	CALL4_HUMAN	calmodulin-like 4	128	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.E128D(1)		large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						CTAGAAGAATTTCTTTCTTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											147	135	139					15																	68489887		1876	4102	5978	66276941	SO:0001583	missense	91860			AF308287	CCDS10226.2, CCDS42052.1, CCDS66808.1	15q22.31	2013-01-10			ENSG00000129007	ENSG00000129007		"EF-hand domain containing"	18445	protein-coding gene	gene with protein product							Standard	NM_033429		Approved	MGC4809, NY-BR-20	uc002arb.3	Q96GE6	OTTHUMG00000133287	ENST00000467889.1:c.384A>C	15.37:g.68489887T>G	ENSP00000419081:p.Glu128Asp		66276941	B4DL15|F8W6Y4|Q6MZY3|Q6N048|Q9H286	Missense_Mutation	SNP	ENST00000467889.1	37	CCDS10226.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192156	0.78902	.	.	ENSG00000129007	ENST00000478113;ENST00000448060;ENST00000395463;ENST00000540479;ENST00000467889	T;T;T	0.79845	-1.31;1.12;1.12	4.88	-3.33	0.04958	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.86053	0.5841	M	0.64260	1.97	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.84602	0.0673	10	0.72032	D	0.01	-32.2506	16.1666	0.81759	0.0:0.7165:0.0:0.2835	.	81;128	F8W6Y4;Q96GE6	.;CALL4_HUMAN	D	13;81;13;52;128	ENSP00000400755:E81D;ENSP00000438177:E52D;ENSP00000419081:E128D	ENSP00000435285:E13D	E	-	3	2	CALML4	66276941	0.769000	0.28531	0.717000	0.30585	0.985000	0.73830	-0.129000	0.10515	-0.894000	0.03925	0.402000	0.26972	GAA		0.473	CALML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257067.3	NM_033429		G	68489887	T	G	68489887	3	3	61	1	0	0	0	0	1	0	0	0	2594	1838	64	4	214	4	CALML4	15	68489887	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	371091	68489887	34041505	9448	17433										
ITGA11	22801	broad.mit.edu	37	chr15	68612698	68612698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgcggagcagtcctgcGcaggcttcctcagcaccctc	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:68612698G>A	ENST00000315757.7	-	20	2527	c.2441C>T	c.(2440-2442)gCg>gTg	p.A814V	ITGA11_ENST00000423218.2_Missense_Mutation_p.A814V	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	814					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)	p.A814V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GCAGTCCTGCGCAGGCTTCCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	15											35	37	36					15																	68612698		2075	4222	6297	66399752	SO:0001583	missense	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.2441C>T	15.37:g.68612698G>A	ENSP00000327290:p.Ala814Val		66399752	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	g	6.056	0.378620	0.11466	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.60040	0.22;0.22	5.62	-6.55	0.01854	Integrin alpha-2 (1);	1.192530	0.05483	N	0.555229	T	0.41650	0.1168	L	0.36672	1.1	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.09377	0.004;0.002	T	0.27706	-1.0066	10	0.28530	T	0.3	.	8.8121	0.34974	0.4943:0.0:0.3833:0.1225	.	814;814	A8K8T0;Q9UKX5	.;ITA11_HUMAN	V	814;814;449	ENSP00000327290:A814V;ENSP00000403392:A814V	ENSP00000327290:A814V	A	-	2	0	ITGA11	66399752	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.108000	0.03313	-0.907000	0.03862	-0.974000	0.02594	GCG		0.592	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		A	68612698	G	A	68612698	3	1	61	1	0	0	0	0	1	0	0	0	7895	1087	38	1	1169	1	ITGA11	15	68612698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122811	68612698	33918694	9449	17434										
NOX5	79400	broad.mit.edu	37	chr15	69341382	69341382	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactggagatggaccaggcCgaggaggctcaatacggtaa	14	8	1	1	rs143553877	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:69341382C>T	ENST00000388866.3	+	14	2024	c.1983C>T	c.(1981-1983)gcC>gcT	p.A661A	NOX5_ENST00000530406.2_Silent_p.A633A|NOX5_ENST00000455873.3_Silent_p.A626A|NOX5_ENST00000525163.1_3'UTR|NOX5_ENST00000448182.3_Silent_p.A615A|NOX5_ENST00000260364.5_Silent_p.A643A	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	661					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.A643A(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						TGGACCAGGCCGAGGAGGCTC	0.502													C|||	3	0.000599042	0.0023	0	5008	,	,		17061	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15						C	,,	9,4391	16.8+/-37.8	0,9,2191	52	47	49		1899,1878,1983	-3.3	0.1	15	dbSNP_134	49	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX5	NM_001184779.1,NM_001184780.1,NM_024505.3	,,	0,10,6488	TT,TC,CC		0.0116,0.2045,0.0769	,,	633/738,626/731,661/766	69341382	10,12986	2200	4298	6498	67128436	SO:0001819	synonymous_variant	79400			AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1983C>T	15.37:g.69341382C>T			67128436	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Silent	SNP	ENST00000388866.3	37	CCDS32276.2																																																																																				0.502	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		T	69341382	C	T	69341382	2	4	61	1	0	0	0	0	0	0	0	1	10590	639	23	1		1	NOX5	15	69341382	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	728684	69341382	33190010	9450	17435										
GLCE	26035	broad.mit.edu	37	chr15	69548197	69548197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactttgattattatctgcGcactcttcactttggtcaca	6	10	4	2	rs138637994		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:69548197G>A	ENST00000261858.2	+	3	280	c.52G>A	c.(52-54)Gca>Aca	p.A18T	GLCE_ENST00000559420.2_5'UTR	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	18					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)	p.A18T(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						TATTATCTGCGCACTCTTCAC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											147	136	140					15																	69548197		2200	4298	6498	67335251	SO:0001583	missense	26035			AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.52G>A	15.37:g.69548197G>A	ENSP00000261858:p.Ala18Thr		67335251	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	37	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023355	0.54683	.	.	ENSG00000138604	ENST00000261858	T	0.36699	1.24	5.65	4.71	0.59529	.	0.101202	0.64402	N	0.000002	T	0.23572	0.0570	L	0.35288	1.05	0.50632	D	0.999884	B	0.27264	0.173	B	0.13407	0.009	T	0.06789	-1.0807	10	0.28530	T	0.3	2.4587	7.9826	0.30192	0.0842:0.0:0.7596:0.1562	.	18	O94923	GLCE_HUMAN	T	18	ENSP00000261858:A18T	ENSP00000261858:A18T	A	+	1	0	GLCE	67335251	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.093000	0.41710	1.460000	0.47911	0.655000	0.94253	GCA		0.433	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		A	69548197	G	A	69548197	3	1	61	1	0	0	0	0	1	0	0	0	6452	1087	38	1	54	1	GLCE	15	69548197	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206815	69548197	32983195	9451	17436										
GLCE	26035	broad.mit.edu	37	chr15	69548607	69548607	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctatgatcggtttgaattCtctcatagctattccaaagt	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:69548607C>A	ENST00000261858.2	+	3	690	c.462C>A	c.(460-462)ttC>ttA	p.F154L	GLCE_ENST00000559420.2_Missense_Mutation_p.F90L	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	154					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)	p.F154L(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						GGTTTGAATTCTCTCATAGCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											248	241	244					15																	69548607		2200	4298	6498	67335661	SO:0001583	missense	26035			AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.462C>A	15.37:g.69548607C>A	ENSP00000261858:p.Phe154Leu		67335661	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	37	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833184	0.71258	.	.	ENSG00000138604	ENST00000261858	T	0.33216	1.42	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.31513	0.0799	L	0.42581	1.335	0.58432	D	0.999999	P	0.47762	0.9	P	0.46237	0.508	T	0.03008	-1.1083	10	0.52906	T	0.07	-18.1976	11.2039	0.48758	0.0:0.9147:0.0:0.0853	.	154	O94923	GLCE_HUMAN	L	154	ENSP00000261858:F154L	ENSP00000261858:F154L	F	+	3	2	GLCE	67335661	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.917000	0.56424	2.578000	0.87016	0.655000	0.94253	TTC		0.433	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		A	69548607	C	A	69548607	3	1	61	1	0	0	0	0	1	0	0	0	6452	912	32	2	464	2	GLCE	15	69548607	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	410	69548607	32982785	9452	17437										
GLCE	26035	broad.mit.edu	37	chr15	69561167	69561167	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacagccccttataagtttCtatctgagcagcatggagtt	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:69561167C>A	ENST00000261858.2	+	5	1666	c.1438C>A	c.(1438-1440)Cta>Ata	p.L480I	GLCE_ENST00000559420.2_Missense_Mutation_p.L416I	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	480					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)	p.L480I(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						TTATAAGTTTCTATCTGAGCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											57	64	61					15																	69561167		2200	4298	6498	67348221	SO:0001583	missense	26035			AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1438C>A	15.37:g.69561167C>A	ENSP00000261858:p.Leu480Ile		67348221	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	37	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	C	3.896	-0.023012	0.07634	.	.	ENSG00000138604	ENST00000261858	T	0.42513	0.97	5.01	4.07	0.47477	.	0.294208	0.37483	N	0.002061	T	0.25005	0.0607	N	0.14661	0.345	0.22648	N	0.998895	B	0.32010	0.351	B	0.31495	0.131	T	0.12915	-1.0529	10	0.22109	T	0.4	-27.6428	13.0708	0.59059	0.0:0.9155:0.0:0.0845	.	480	O94923	GLCE_HUMAN	I	480	ENSP00000261858:L480I	ENSP00000261858:L480I	L	+	1	2	GLCE	67348221	0.961000	0.32948	0.841000	0.33234	0.218000	0.24690	2.130000	0.42064	2.479000	0.83701	0.557000	0.71058	CTA		0.383	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		A	69561167	C	A	69561167	3	1	61	1	0	0	0	0	1	0	0	0	6452	912	32	2	1448	2	GLCE	15	69561167	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12560	69561167	32970225	9453	17438										
KIF23	9493	broad.mit.edu	37	chr15	69718484	69718484	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtacagaagttgaagtGaaatctactgaggaggcttt	13	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:69718484G>T	ENST00000260363.4	+	8	927	c.810G>T	c.(808-810)gtG>gtT	p.V270V	KIF23_ENST00000558585.1_Silent_p.V87V|KIF23_ENST00000352331.4_Silent_p.V270V|KIF23_ENST00000395392.2_Silent_p.V270V|KIF23_ENST00000559279.1_Silent_p.V270V|KIF23_ENST00000537891.1_Silent_p.V87V	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	270	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)	p.V270V(1)		central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						AAGTTGAAGTGAAATCTACTG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	15											81	83	82					15																	69718484		2199	4298	6497	67505538	SO:0001819	synonymous_variant	9493			X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"Kinesins"	6392	protein-coding gene	gene with protein product		605064	"kinesin-like 5 (mitotic kinesin-like protein 1)"	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.810G>T	15.37:g.69718484G>T			67505538	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																				0.358	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	69718484	G	T	69718484	2	4	61	1	0	0	0	0	0	0	0	1	8312	1277	45	2		2	KIF23	15	69718484	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157317	69718484	32812908	9454	17439										
UACA	55075	broad.mit.edu	37	chr15	70959098	70959098	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctatttgtttagcagattCttgtattcttctttgtaact	5	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:70959098C>A	ENST00000322954.6	-	16	4110	c.3925G>T	c.(3925-3927)Gaa>Taa	p.E1309*	UACA_ENST00000379983.2_Nonsense_Mutation_p.E1296*|UACA_ENST00000539319.1_Nonsense_Mutation_p.E1200*|UACA_ENST00000560441.1_Nonsense_Mutation_p.E1294*	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1309					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.E1296*(2)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTAGCAGATTCTTGTATTCTT	0.383																																																2	Substitution - Nonsense(2)	large_intestine(2)	15											163	130	141					15																	70959098		2199	4298	6497	68746152	SO:0001587	stop_gained	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3925G>T	15.37:g.70959098C>A	ENSP00000314556:p.Glu1309*		68746152	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Nonsense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	C	40	8.242055	0.98722	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	.	.	.	5.85	5.85	0.93711	.	0.182125	0.38326	N	0.001730	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-19.8524	14.9374	0.70967	0.1429:0.8571:0.0:0.0	.	.	.	.	X	1309;1296;1200	.	ENSP00000314556:E1309X	E	-	1	0	UACA	68746152	1.000000	0.71417	0.992000	0.48379	0.804000	0.45430	2.690000	0.47001	2.767000	0.95098	0.655000	0.94253	GAA		0.383	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			A	70959098	C	A	70959098	4	1	61	1	0	0	0	0	0	1	0	0	16864	922	32	2	341	2	UACA	15	70959098	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1240614	70959098	31572294	9455	17440										
UACA	55075	broad.mit.edu	37	chr15	70960820	70960820	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcatttcaattgttaagtTatgtgcttgctccttgagga	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:70960820T>G	ENST00000322954.6	-	16	2388	c.2203A>C	c.(2203-2205)Aac>Cac	p.N735H	UACA_ENST00000379983.2_Missense_Mutation_p.N722H|UACA_ENST00000539319.1_Missense_Mutation_p.N626H|UACA_ENST00000560441.1_Missense_Mutation_p.N720H	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	735					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.N722H(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						ATTGTTAAGTTATGTGCTTGC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	83	82					15																	70960820		2198	4294	6492	68747874	SO:0001583	missense	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.2203A>C	15.37:g.70960820T>G	ENSP00000314556:p.Asn735His		68747874	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	14.36	2.511563	0.44660	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.34472	1.36;1.37;1.85	5.6	4.48	0.54585	.	0.396999	0.24359	N	0.039218	T	0.41949	0.1181	L	0.44542	1.39	0.09310	N	1	D;P;D;D	0.58620	0.98;0.938;0.964;0.983	P;P;P;P	0.56823	0.735;0.547;0.547;0.807	T	0.18745	-1.0327	10	0.35671	T	0.21	-15.7137	8.5125	0.33226	0.0:0.2158:0.0:0.7842	.	626;735;735;722	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	H	735;722;626	ENSP00000314556:N735H;ENSP00000369319:N722H;ENSP00000438667:N626H	ENSP00000314556:N735H	N	-	1	0	UACA	68747874	0.014000	0.17966	0.002000	0.10522	0.982000	0.71751	2.154000	0.42291	0.963000	0.38082	0.459000	0.35465	AAC		0.299	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			G	70960820	T	G	70960820	3	3	61	1	0	0	0	0	1	0	0	0	16864	1754	61	4	2063	4	UACA	15	70960820	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1722	70960820	31570572	9456	17441										
UACA	55075	broad.mit.edu	37	chr15	70972014	70972014	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgcatgtgtgtcaaatttCgctttggtaaaacataagaa	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:70972014C>T	ENST00000322954.6	-	10	1009	c.824G>A	c.(823-825)cGa>cAa	p.R275Q	UACA_ENST00000379983.2_Splice_Site_p.R262Q|UACA_ENST00000539319.1_Splice_Site_p.R166Q|UACA_ENST00000559183.1_5'Flank|UACA_ENST00000560441.1_Splice_Site_p.R262Q	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	275					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.R262Q(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TGTCAAATTTCGCTTTGGTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	15											109	97	101					15																	70972014		2199	4297	6496	68759068	SO:0001630	splice_region_variant	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.823-1G>A	15.37:g.70972014C>T			68759068	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.655924	0.88056	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	T;T;T	0.70516	1.33;1.33;-0.49	5.94	5.94	0.96194	.	0.134487	0.34133	N	0.004222	T	0.79953	0.4535	L	0.60455	1.87	0.41483	D	0.988177	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;P;D	0.66196	0.942;0.876;0.876;0.921	T	0.74487	-0.3649	10	0.20046	T	0.44	-13.5456	17.0928	0.86627	0.0:1.0:0.0:0.0	.	166;275;275;262	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	Q	275;262;262;166	ENSP00000314556:R275Q;ENSP00000369319:R262Q;ENSP00000438667:R166Q	ENSP00000314556:R275Q	R	-	2	0	UACA	68759068	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	3.838000	0.55828	2.820000	0.97059	0.650000	0.86243	CGA		0.338	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		Missense_Mutation	T	70972014	C	T	70972014	5	4	61	1	0	0	0	0	0	0	1	0	16864	898	31	1	3466	1	UACA	15	70972014	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11194	70972014	31559378	9457	17442										
LARP6	55323	broad.mit.edu	37	chr15	71124895	71124895	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatgtactgaagctcctcGactctcttgttcagggactt	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:71124895G>A	ENST00000299213.8	-	3	1042	c.972C>T	c.(970-972)gtC>gtT	p.V324V	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	324					regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.V324V(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						GAAGCTCCTCGACTCTCTTGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	15											152	143	146					15																	71124895		2199	4297	6496	68911949	SO:0001819	synonymous_variant	55323			BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"La ribonucleoprotein domain containing"	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.972C>T	15.37:g.71124895G>A			68911949	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																				0.557	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		A	71124895	G	A	71124895	2	1	61	1	0	0	0	0	0	0	0	1	8654	1045	37	1		1	LARP6	15	71124895	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152881	71124895	31406497	9458	17443										
LARP6	55323	broad.mit.edu	37	chr15	71125078	71125078	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggctgcttccacctcctcGaactccacgatggcgcactc	8	17	0	0	rs371562863		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:71125078G>A	ENST00000299213.8	-	3	859	c.789C>T	c.(787-789)ttC>ttT	p.F263F	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	263	RRM.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.F263F(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						CCACCTCCTCGAACTCCACGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	15						G		0,4398		0,0,2199	78	70	73		789	-3.5	1	15		73	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	LARP6	NM_018357.2		0,1,6495	AA,AG,GG		0.0116,0.0,0.0077		263/492	71125078	1,12991	2199	4297	6496	68912132	SO:0001819	synonymous_variant	55323			BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"La ribonucleoprotein domain containing"	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.789C>T	15.37:g.71125078G>A			68912132	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																				0.562	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		A	71125078	G	A	71125078	2	1	61	1	0	0	0	0	0	0	0	1	8654	1049	37	1		1	LARP6	15	71125078	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	183	71125078	31406314	9459	17444										
THSD4	79875	broad.mit.edu	37	chr15	71952907	71952907	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttaggctccgacaaagtCgtggacaaatgtggggtgtg	14	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:71952907C>T	ENST00000355327.3	+	8	1325	c.1191C>T	c.(1189-1191)gtC>gtT	p.V397V	THSD4_ENST00000261862.6_Silent_p.V397V|THSD4_ENST00000567838.1_3'UTR|THSD4_ENST00000357769.4_Silent_p.V37V			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	397					elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)	p.V397V(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CCGACAAAGTCGTGGACAAAT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	15											176	179	178					15																	71952907		1985	4173	6158	69739961	SO:0001819	synonymous_variant	79875			AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1191C>T	15.37:g.71952907C>T			69739961	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	37	CCDS10238.2																																																																																				0.522	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		T	71952907	C	T	71952907	2	4	61	1	0	0	0	0	0	0	0	1	15917	871	31	1		1	THSD4	15	71952907	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	827829	71952907	30578485	9460	17445										
MYO9A	4649	broad.mit.edu	37	chr15	72191239	72191239	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcctctatggcttttattCtgttgtcaaaagaacaatcc	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72191239C>A	ENST00000356056.5	-	25	4077	c.3605G>T	c.(3604-3606)aGa>aTa	p.R1202I	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Missense_Mutation_p.R822I|MYO9A_ENST00000424560.1_Missense_Mutation_p.R1202I|MYO9A_ENST00000444904.1_Missense_Mutation_p.R1183I|MYO9A_ENST00000564571.1_Missense_Mutation_p.R1202I	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1202	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.R1202I(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GGCTTTTATTCTGTTGTCAAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											155	153	154					15																	72191239		2199	4297	6496	69978293	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3605G>T	15.37:g.72191239C>A	ENSP00000348349:p.Arg1202Ile		69978293	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.693840	0.68386	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.85861	-2.04;-2.03;-2.03	4.91	4.91	0.64330	.	.	.	.	.	D	0.83769	0.5326	N	0.24115	0.695	0.54753	D	0.999988	D;B	0.62365	0.991;0.028	P;B	0.54706	0.759;0.007	D	0.84299	0.0504	9	0.39692	T	0.17	.	16.3	0.82806	0.0:1.0:0.0:0.0	.	1183;1202	B2RTY4-2;B2RTY4	.;MYO9A_HUMAN	I	1202;1202;1183	ENSP00000348349:R1202I;ENSP00000399162:R1202I;ENSP00000398250:R1183I	ENSP00000348349:R1202I	R	-	2	0	MYO9A	69978293	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.696000	0.54757	2.277000	0.76020	0.585000	0.79938	AGA		0.413	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72191239	C	A	72191239	3	1	61	1	0	0	0	0	1	0	0	0	10114	913	32	2	4113	2	MYO9A	15	72191239	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	238332	72191239	30340153	9461	17446										
MYO9A	4649	broad.mit.edu	37	chr15	72195370	72195370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggatggaataatatttCggggaagaagtacatggaag	13	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72195370C>T	ENST00000356056.5	-	22	3384	c.2912G>A	c.(2911-2913)cGa>cAa	p.R971Q	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Missense_Mutation_p.R591Q|MYO9A_ENST00000424560.1_Missense_Mutation_p.R971Q|MYO9A_ENST00000444904.1_Missense_Mutation_p.R952Q|MYO9A_ENST00000564571.1_Missense_Mutation_p.R971Q	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	971	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.R971Q(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AATAATATTTCGGGGAAGAAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	15											46	52	50					15																	72195370		2194	4282	6476	69982424	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2912G>A	15.37:g.72195370C>T	ENSP00000348349:p.Arg971Gln		69982424	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017915	0.35606	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.86865	-2.18;-2.18;-2.18	5.8	2.77	0.32553	Myosin head, motor domain (2);	.	.	.	.	T	0.77054	0.4074	N	0.20986	0.625	0.21675	N	0.999599	B;B;B	0.15473	0.008;0.013;0.006	B;B;B	0.13407	0.007;0.009;0.009	T	0.62353	-0.6872	9	0.34782	T	0.22	.	7.6036	0.28089	0.0:0.4937:0.0:0.5063	.	952;952;971	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	Q	971;971;952;952	ENSP00000348349:R971Q;ENSP00000399162:R971Q;ENSP00000398250:R952Q	ENSP00000261864:R952Q	R	-	2	0	MYO9A	69982424	0.881000	0.30235	1.000000	0.80357	0.736000	0.42039	0.531000	0.23052	0.306000	0.22856	-0.345000	0.07892	CGA		0.279	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72195370	C	T	72195370	3	4	61	1	0	0	0	0	1	0	0	0	10114	884	31	1	4818	1	MYO9A	15	72195370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4131	72195370	30336022	9462	17447										
MYO9A	4649	broad.mit.edu	37	chr15	72227743	72227743	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaattagcaaatattccatCtttatcaagcaaggaggtgc	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72227743C>A	ENST00000356056.5	-	17	2933	c.2461G>T	c.(2461-2463)Gat>Tat	p.D821Y	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Missense_Mutation_p.D441Y|MYO9A_ENST00000424560.1_Missense_Mutation_p.D821Y|MYO9A_ENST00000444904.1_Missense_Mutation_p.D802Y|MYO9A_ENST00000564571.1_Missense_Mutation_p.D821Y	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	821	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.D821Y(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AATATTCCATCTTTATCAAGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											97	98	98					15																	72227743		2199	4297	6496	70014797	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2461G>T	15.37:g.72227743C>A	ENSP00000348349:p.Asp821Tyr		70014797	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.913023	0.72983	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.86097	-2.07;-2.05;-2.06	4.39	4.39	0.52855	Myosin head, motor domain (1);	.	.	.	.	D	0.87613	0.6221	L	0.36672	1.1	0.48632	D	0.999687	D;D;D	0.89917	1.0;0.969;0.997	D;P;D	0.74348	0.983;0.66;0.979	D	0.86646	0.1895	9	0.38643	T	0.18	.	13.9907	0.64364	0.0:1.0:0.0:0.0	.	802;802;821	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	Y	821;821;802;802	ENSP00000348349:D821Y;ENSP00000399162:D821Y;ENSP00000398250:D802Y	ENSP00000261864:D802Y	D	-	1	0	MYO9A	70014797	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.640000	0.67875	2.281000	0.76405	0.585000	0.79938	GAT		0.373	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72227743	C	A	72227743	3	1	61	1	0	0	0	0	1	0	0	0	10114	913	32	2	5289	2	MYO9A	15	72227743	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32373	72227743	30303649	9463	17448										
MYO9A	4649	broad.mit.edu	37	chr15	72231198	72231198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaacacacttactgttgGtttttttcatttagagcatt	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72231198G>T	ENST00000356056.5	-	16	2845	c.2373C>A	c.(2371-2373)aaC>aaA	p.N791K	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Missense_Mutation_p.N411K|MYO9A_ENST00000424560.1_Missense_Mutation_p.N791K|MYO9A_ENST00000444904.1_Missense_Mutation_p.N772K|MYO9A_ENST00000564571.1_Missense_Mutation_p.N791K	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	791	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.N791K(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTTACTGTTGGTTTTTTTCAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	15											70	71	71					15																	72231198		2199	4296	6495	70018252	SO:0001583	missense	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2373C>A	15.37:g.72231198G>T	ENSP00000348349:p.Asn791Lys		70018252	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204506	0.38905	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.83837	-1.77;-1.76;-1.76	5.1	2.5	0.30297	Myosin head, motor domain (1);	.	.	.	.	T	0.68201	0.2975	L	0.40543	1.245	0.30382	N	0.781887	P;B;B	0.35226	0.491;0.003;0.013	B;B;B	0.29862	0.108;0.004;0.017	T	0.59705	-0.7404	9	0.06625	T	0.88	.	6.7375	0.23417	0.2879:0.0:0.7121:0.0	.	772;772;791	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	K	791;791;772;772	ENSP00000348349:N791K;ENSP00000399162:N791K;ENSP00000398250:N772K	ENSP00000261864:N772K	N	-	3	2	MYO9A	70018252	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.550000	0.23345	0.255000	0.21593	0.484000	0.47621	AAC		0.308	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72231198	G	T	72231198	3	4	61	1	0	0	0	0	1	0	0	0	10114	1252	44	2	5381	2	MYO9A	15	72231198	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3455	72231198	30300194	9464	17449										
GRAMD2	196996	broad.mit.edu	37	chr15	72461298	72461298	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccttctcggccacacttCtttatctcttcacccttcaa	2	18	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72461298C>A	ENST00000309731.7	-	3	187	c.174G>T	c.(172-174)aaG>aaT	p.K58N	GRAMD2_ENST00000564184.1_5'Flank	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	58						integral component of membrane (GO:0016021)		p.K58N(1)		cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						GGCCACACTTCTTTATCTCTT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	15											151	124	133					15																	72461298		2199	4297	6496	70248352	SO:0001583	missense	196996			AK002016	CCDS32283.1	15q23	2006-11-29	2005-11-03	2005-11-03					27287	protein-coding gene	gene with protein product						12477932	Standard	NM_001012642		Approved		uc002atq.3	Q8IUY3		ENST00000309731.7:c.174G>T	15.37:g.72461298C>A	ENSP00000311657:p.Lys58Asn		70248352	B3KT68	Missense_Mutation	SNP	ENST00000309731.7	37	CCDS32283.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509472	0.64522	.	.	ENSG00000175318	ENST00000309731	T	0.37058	1.22	5.41	4.49	0.54785	.	0.126753	0.51477	D	0.000087	T	0.55178	0.1904	M	0.70275	2.135	0.42256	D	0.991994	D	0.89917	1.0	D	0.87578	0.998	T	0.53585	-0.8418	10	0.26408	T	0.33	.	11.2951	0.49274	0.0:0.9137:0.0:0.0863	.	58	Q8IUY3	GRAM2_HUMAN	N	58	ENSP00000311657:K58N	ENSP00000311657:K58N	K	-	3	2	GRAMD2	70248352	1.000000	0.71417	0.999000	0.59377	0.663000	0.39108	2.481000	0.45215	1.276000	0.44395	0.561000	0.74099	AAG		0.537	GRAMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420040.1	NM_001012642		A	72461298	C	A	72461298	3	1	61	1	0	0	0	0	1	0	0	0	6771	912	32	2	930	2	GRAMD2	15	72461298	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	230100	72461298	30070094	9465	17450										
PKM2	5315	broad.mit.edu	37	chr15	72500985	72500985	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaccccctcatgattctcGattttgctgataatcttgat	6	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72500985G>A	ENST00000335181.5	-	6	916	c.813C>T	c.(811-813)atC>atT	p.I271I	PKM_ENST00000449901.2_Silent_p.I256I|PKM_ENST00000319622.6_Silent_p.I271I|PKM_ENST00000568883.1_Silent_p.I106I|PKM_ENST00000565184.1_Silent_p.I271I|PKM_ENST00000568459.1_Silent_p.I271I|PKM_ENST00000389093.3_Silent_p.I271I|PKM_ENST00000565154.1_Silent_p.I271I	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	271					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.I271I(1)		endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	CATGATTCTCGATTTTGCTGA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	15											181	155	164					15																	72500985		2199	4297	6496	70288039	SO:0001819	synonymous_variant	5315			M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.813C>T	15.37:g.72500985G>A			70288039	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																				0.512	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1			A	72500985	G	A	72500985	2	1	61	1	0	0	0	0	0	0	0	1	12008	1048	37	1		1	PKM2	15	72500985	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39687	72500985	30030407	9466	17451										
TMEM202	338949	broad.mit.edu	37	chr15	72699485	72699485	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggttcactggcatactagGgatgccatggagtcagatct	12	9	3	1	rs113026067		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72699485G>A	ENST00000341689.3	+	4	600	c.546G>A	c.(544-546)agG>agA	p.R182R	TMEM202_ENST00000567679.1_Intron	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	182						integral component of membrane (GO:0016021)		p.R182R(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						GGCATACTAGGGATGCCATGG	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	15											202	169	180					15																	72699485		2199	4297	6496	70486539	SO:0001819	synonymous_variant	338949				CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.546G>A	15.37:g.72699485G>A			70486539		Silent	SNP	ENST00000341689.3	37	CCDS32287.1																																																																																				0.483	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		A	72699485	G	A	72699485	2	1	61	1	0	0	0	0	0	0	0	1	16166	1223	43	3		3	TMEM202	15	72699485	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198500	72699485	29831907	9467	17452										
ARIH1	25820	broad.mit.edu	37	chr15	72847642	72847642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttgaatgtggacataagTtttgtatgcagtgctggagt	13	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72847642T>C	ENST00000379887.4	+	4	933	c.619T>C	c.(619-621)Ttt>Ctt	p.F207L		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	207	Interaction with UBE2L3.				cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F207L(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TGGACATAAGTTTTGTATGCA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	15											138	132	134					15																	72847642		2198	4297	6495	70634696	SO:0001583	missense	25820			AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.619T>C	15.37:g.72847642T>C	ENSP00000369217:p.Phe207Leu		70634696	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	37	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	T	32	5.184411	0.94885	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.85484	-1.99	5.36	5.36	0.76844	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.93380	0.7889	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.94438	0.7656	10	0.62326	D	0.03	.	15.3032	0.73972	0.0:0.0:0.0:1.0	.	207	Q9Y4X5	ARI1_HUMAN	L	207;177	ENSP00000369217:F207L	ENSP00000299305:F177L	F	+	1	0	ARIH1	70634696	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.555000	0.82223	2.154000	0.67381	0.477000	0.44152	TTT		0.328	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		C	72847642	T	C	72847642	3	2	61	1	0	0	0	0	1	0	0	0	923	1725	60	4	633	4	ARIH1	15	72847642	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	148157	72847642	29683750	9468	17453										
ARIH1	25820	broad.mit.edu	37	chr15	72853877	72853877	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcagcatttaataacaaAtagctttgtagaggtaagtg	9	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:72853877A>C	ENST00000379887.4	+	6	1105	c.791A>C	c.(790-792)aAt>aCt	p.N264T		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	264					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N264T(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TTAATAACAAATAGCTTTGTA	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	15											38	42	41					15																	72853877		2195	4290	6485	70640931	SO:0001583	missense	25820			AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.791A>C	15.37:g.72853877A>C	ENSP00000369217:p.Asn264Thr		70640931	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	37	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.377685	0.82682	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	T	0.81247	-1.47	5.52	5.52	0.82312	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.89674	0.6783	M	0.82056	2.57	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.90875	0.4749	10	0.66056	D	0.02	.	15.624	0.76833	1.0:0.0:0.0:0.0	.	264	Q9Y4X5	ARI1_HUMAN	T	264;234	ENSP00000369217:N264T	ENSP00000299305:N234T	N	+	2	0	ARIH1	70640931	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.908000	0.92640	2.232000	0.73038	0.528000	0.53228	AAT		0.264	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		C	72853877	A	C	72853877	3	2	61	1	0	0	0	0	1	0	0	0	923	101	4	4	813	4	ARIH1	15	72853877	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	6235	72853877	29677515	9469	17454										
NEO1	4756	broad.mit.edu	37	chr15	73542048	73542048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaccagatgttgctgttcGaacattgtcagatggtgagt	11	8	1	3	rs368526754		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:73542048G>A	ENST00000339362.5	+	12	2327	c.1880G>A	c.(1879-1881)cGa>cAa	p.R627Q	NEO1_ENST00000261908.6_Missense_Mutation_p.R627Q|NEO1_ENST00000558964.1_Missense_Mutation_p.R627Q|NEO1_ENST00000560262.1_Missense_Mutation_p.R627Q			Q92859	NEO1_HUMAN	neogenin 1	627	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R627Q(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						GTTGCTGTTCGAACATTGTCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	GLN/ARG,GLN/ARG,GLN/ARG	0,4396		0,0,2198	178	163	168		1880,1880,1880	3.8	0.9	15		168	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense,missense	NEO1	NM_001172623.1,NM_001172624.1,NM_002499.3	43,43,43	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	627/1409,627/1451,627/1462	73542048	1,12989	2198	4297	6495	71329101	SO:0001583	missense	4756			U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1880G>A	15.37:g.73542048G>A	ENSP00000341198:p.Arg627Gln		71329101	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226281	0.79576	0.0	1.16E-4	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.55588	0.51;0.51	5.79	3.85	0.44370	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.113255	0.64402	N	0.000011	T	0.69296	0.3095	M	0.78285	2.405	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.965;0.999	D;D;P;D	0.81914	0.995;0.965;0.466;0.936	T	0.67118	-0.5751	10	0.32370	T	0.25	-2.1478	11.3043	0.49325	0.1549:0.0:0.8451:0.0	.	627;627;365;627	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	Q	627;365;627	ENSP00000341198:R627Q;ENSP00000261908:R627Q	ENSP00000261908:R627Q	R	+	2	0	NEO1	71329101	0.999000	0.42202	0.943000	0.38184	0.773000	0.43773	3.250000	0.51445	0.720000	0.32209	-0.345000	0.07892	CGA		0.418	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		A	73542048	G	A	73542048	3	1	61	1	0	0	0	0	1	0	0	0	10367	1058	37	1	1922	1	NEO1	15	73542048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	688171	73542048	28989344	9470	17455										
NEO1	4756	broad.mit.edu	37	chr15	73547130	73547130	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaagagtgatgtcactgaGaccttggtaagcgggacaca	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:73547130G>T	ENST00000339362.5	+	14	2499	c.2052G>T	c.(2050-2052)gaG>gaT	p.E684D	NEO1_ENST00000261908.6_Missense_Mutation_p.E684D|NEO1_ENST00000558964.1_Missense_Mutation_p.E684D|NEO1_ENST00000560262.1_Missense_Mutation_p.E684D|RP11-272D12.2_ENST00000560337.1_RNA			Q92859	NEO1_HUMAN	neogenin 1	684	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.E684D(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						ATGTCACTGAGACCTTGGTAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											134	126	129					15																	73547130		2198	4297	6495	71334183	SO:0001583	missense	4756			U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2052G>T	15.37:g.73547130G>T	ENSP00000341198:p.Glu684Asp		71334183	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	g	14.42	2.530950	0.45073	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.60171	0.21;0.21	5.23	2.13	0.27403	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.154925	0.56097	D	0.000035	T	0.47192	0.1432	L	0.53561	1.675	0.43907	D	0.996544	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.002;0.002;0.001;0.004	T	0.27262	-1.0079	10	0.20519	T	0.43	-16.7301	9.3996	0.38424	0.2483:0.0:0.7517:0.0	.	684;684;422;684	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	D	684;422;684	ENSP00000341198:E684D;ENSP00000261908:E684D	ENSP00000261908:E684D	E	+	3	2	NEO1	71334183	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	2.531000	0.45650	0.145000	0.18977	-0.140000	0.14226	GAG		0.488	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		T	73547130	G	T	73547130	3	4	61	1	0	0	0	0	1	0	0	0	10367	933	33	2	2102	2	NEO1	15	73547130	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5082	73547130	28984262	9471	17456										
HCN4	10021	broad.mit.edu	37	chr15	73616567	73616567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggccctcacgctggctgtgCgccggccccgggtcagcagg	16	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:73616567C>T	ENST00000261917.3	-	7	2999	c.2006G>A	c.(2005-2007)cGc>cAc	p.R669H		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	669					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.R669H(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GCTGGCTGTGCGCCGGCCCCG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	15											55	46	49					15																	73616567		2198	4297	6495	71403620	SO:0001583	missense	10021			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.2006G>A	15.37:g.73616567C>T	ENSP00000261917:p.Arg669His		71403620	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.876729	0.51801	.	.	ENSG00000138622	ENST00000261917	D	0.97994	-4.65	3.46	3.46	0.39613	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	.	.	.	.	D	0.98905	0.9629	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99544	1.0964	9	0.87932	D	0	.	15.125	0.72475	0.0:1.0:0.0:0.0	.	669	Q9Y3Q4	HCN4_HUMAN	H	669	ENSP00000261917:R669H	ENSP00000261917:R669H	R	-	2	0	HCN4	71403620	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	7.109000	0.77062	1.761000	0.52028	0.313000	0.20887	CGC		0.652	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73616567	C	T	73616567	3	4	61	1	0	0	0	0	1	0	0	0	7020	768	27	1	1613	1	HCN4	15	73616567	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69437	73616567	28914825	9472	17457										
HCN4	10021	broad.mit.edu	37	chr15	73617477	73617477	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacgtcacgaagttggggtcCgcattggcaaacagtggcat	14	9	1	0	rs371484779		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:73617477C>T	ENST00000261917.3	-	6	2790	c.1797G>A	c.(1795-1797)gcG>gcA	p.A599A		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	599					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.A599A(2)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AGTTGGGGTCCGCATTGGCAA	0.567																																																2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	15						C		0,4396		0,0,2198	138	122	128		1797	-5.8	0.9	15		128	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	HCN4	NM_005477.2		0,1,6494	TT,TC,CC		0.0116,0.0,0.0077		599/1204	73617477	1,12989	2198	4297	6495	71404530	SO:0001819	synonymous_variant	10021			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1797G>A	15.37:g.73617477C>T			71404530	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																				0.567	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73617477	C	T	73617477	2	4	61	1	0	0	0	0	0	0	0	1	7020	639	23	1		1	HCN4	15	73617477	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	910	73617477	28913915	9473	17458										
ARID3B	10620	broad.mit.edu	37	chr15	74884147	74884147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccatgaagatcaggatcaAcggcaggggtgagccaggct	14	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:74884147A>G	ENST00000346246.5	+	7	1643	c.1412A>G	c.(1411-1413)aAc>aGc	p.N471S		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	471	REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)	p.N471S(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						ATCAGGATCAACGGCAGGGGT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	15											43	45	44					15																	74884147		2196	4296	6492	72671200	SO:0001583	missense	10620				CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"-"	14350	protein-coding gene	gene with protein product		612457	"AT rich interactive domain 3B (BRIGHT- like)"				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.1412A>G	15.37:g.74884147A>G	ENSP00000343126:p.Asn471Ser		72671200	O95443|Q59HC9|Q6P9C9	Missense_Mutation	SNP	ENST00000346246.5	37	CCDS10264.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.579787	0.65992	.	.	ENSG00000179361	ENST00000346246	T	0.46819	0.86	5.31	4.16	0.48862	REKLES domain (1);	0.865322	0.10510	N	0.666291	T	0.48572	0.1507	L	0.54323	1.7	0.48571	D	0.99967	P;P	0.48294	0.908;0.808	B;B	0.43990	0.368;0.438	T	0.31392	-0.9945	10	0.44086	T	0.13	-18.0906	12.335	0.55062	0.8585:0.1415:0.0:0.0	.	471;471	Q8IVW6;Q8IVW6-4	ARI3B_HUMAN;.	S	471	ENSP00000343126:N471S	ENSP00000343126:N471S	N	+	2	0	ARID3B	72671200	0.535000	0.26370	0.923000	0.36655	0.937000	0.57800	1.331000	0.33793	0.833000	0.34828	0.533000	0.62120	AAC		0.647	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465		G	74884147	A	G	74884147	3	3	61	1	0	0	0	0	1	0	0	0	917	43	2	4	1434	4	ARID3B	15	74884147	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1266670	74884147	27647245	9474	17459										
CPLX3	594855	broad.mit.edu	37	chr15	75122677	75122677	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctcaagcaatcagctgaGaagtgtcacgtcatgtgacc	10	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75122677G>T	ENST00000395018.4	+	3	616	c.459G>T	c.(457-459)gaG>gaT	p.E153D	RP11-414J4.2_ENST00000564823.1_RNA	NM_001030005.2	NP_001025176.1	Q8WVH0	CPLX3_HUMAN	complexin 3	153					insulin secretion (GO:0030073)|regulation of neurotransmitter secretion (GO:0046928)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)	neurotransmitter transporter activity (GO:0005326)	p.E153D(1)		large_intestine(2)|lung(2)	4						AATCAGCTGAGAAGTGTCACG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	15											57	44	48					15																	75122677		2197	4295	6492	72909730	SO:0001583	missense	594855			BC018026	CCDS32294.1	15q24.1	2005-08-09			ENSG00000213578	ENSG00000213578			27652	protein-coding gene	gene with protein product		609585				15911881	Standard	NM_001030005		Approved	CPX-III	uc002ayu.1	Q8WVH0	OTTHUMG00000142816	ENST00000395018.4:c.459G>T	15.37:g.75122677G>T	ENSP00000378464:p.Glu153Asp		72909730	D3DW66|Q8TEM6|Q9H818	Missense_Mutation	SNP	ENST00000395018.4	37	CCDS32294.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.595819	0.66332	.	.	ENSG00000213578	ENST00000395018	.	.	.	5.38	0.748	0.18376	.	0.000000	0.64402	U	0.000001	T	0.49064	0.1535	M	0.73217	2.22	0.38509	D	0.948414	P	0.38473	0.633	B	0.32805	0.153	T	0.52457	-0.8573	9	0.62326	D	0.03	-23.0994	8.3794	0.32461	0.2243:0.1168:0.6589:0.0	.	153	Q8WVH0	CPLX3_HUMAN	D	153	.	ENSP00000378464:E153D	E	+	3	2	CPLX3	72909730	0.998000	0.40836	1.000000	0.80357	0.830000	0.47004	0.376000	0.20535	0.253000	0.21552	-0.150000	0.13652	GAG		0.592	CPLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286402.2	NM_001030005		T	75122677	G	T	75122677	3	4	61	1	0	0	0	0	1	0	0	0	3812	933	33	2	469	2	CPLX3	15	75122677	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	238530	75122677	27408715	9475	17460										
C15orf39	56905	broad.mit.edu	37	chr15	75499573	75499573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagcatcccctgggcttgGagggacaccaccttcccaga	12	14	0	1	rs375288255		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75499573G>A	ENST00000360639.2	+	2	1504	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	C15orf39_ENST00000394987.4_Missense_Mutation_p.G395E|C15orf39_ENST00000567617.1_Missense_Mutation_p.G395E			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	395						cytoplasm (GO:0005737)		p.G395E(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CCTGGGCTTGGAGGGACACCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	15											84	88	87					15																	75499573		2197	4295	6492	73286626	SO:0001583	missense	56905			AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1184G>A	15.37:g.75499573G>A	ENSP00000353854:p.Gly395Glu		73286626	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.833603	0.32421	.	.	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.71341	-0.56;-0.56	4.57	2.5	0.30297	.	0.385458	0.22518	N	0.059005	T	0.65554	0.2702	M	0.62723	1.935	0.09310	N	1	P	0.51351	0.944	P	0.47470	0.548	T	0.58736	-0.7584	10	0.05833	T	0.94	-1.5525	10.3087	0.43695	0.0:0.4402:0.5598:0.0	.	395	Q6ZRI6	CO039_HUMAN	E	395	ENSP00000353854:G395E;ENSP00000378438:G395E	ENSP00000353854:G395E	G	+	2	0	C15orf39	73286626	0.725000	0.28048	0.082000	0.20525	0.970000	0.65996	1.118000	0.31246	0.893000	0.36288	0.462000	0.41574	GGA		0.612	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		A	75499573	G	A	75499573	3	1	61	1	0	0	0	0	1	0	0	0	1797	1174	41	3	1186	3	C15orf39	15	75499573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	376896	75499573	27031819	9476	17461										
SIN3A	25942	broad.mit.edu	37	chr15	75664549	75664549	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgcttacacgctcatggGactgcaaaacagaaaaaaaa	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75664549G>A	ENST00000394947.3	-	21	3907	c.3593C>T	c.(3592-3594)tCc>tTc	p.S1198F	RP11-817O13.8_ENST00000563278.1_lincRNA|SIN3A_ENST00000360439.4_Splice_Site_p.S1198F|SIN3A_ENST00000394949.4_Splice_Site_p.S1198F	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.S1198F(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ACGCTCATGGGACTGCAAAAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	15											80	79	79					15																	75664549		2197	4294	6491	73451602	SO:0001630	splice_region_variant	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3592-1C>T	15.37:g.75664549G>A			73451602		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880913	0.72294	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.49139	0.79;0.79;0.79	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	M	0.78049	2.395	0.80722	D	1	D	0.59357	0.985	D	0.64237	0.923	T	0.72308	-0.4332	10	0.59425	D	0.04	-12.776	17.6425	0.88140	0.0:0.0:1.0:0.0	.	1198	Q96ST3	SIN3A_HUMAN	F	1198	ENSP00000378402:S1198F;ENSP00000378403:S1198F;ENSP00000353622:S1198F	ENSP00000353622:S1198F	S	-	2	0	SIN3A	73451602	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.768000	0.98965	2.415000	0.81967	0.484000	0.47621	TCC		0.423	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	Missense_Mutation	A	75664549	G	A	75664549	5	1	61	1	0	0	0	0	0	0	1	0	14362	1188	41	3	232	3	SIN3A	15	75664549	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164976	75664549	26866843	9477	17462										
SIN3A	25942	broad.mit.edu	37	chr15	75685053	75685053	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcttcacatggtggataAtcagagcagcagcatcttcc	9	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75685053A>C	ENST00000394947.3	-	15	2695	c.2381T>G	c.(2380-2382)aTt>aGt	p.I794S	SIN3A_ENST00000360439.4_Missense_Mutation_p.I794S|SIN3A_ENST00000394949.4_Missense_Mutation_p.I794S	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.I794S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATGGTGGATAATCAGAGCAGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	15											159	147	151					15																	75685053		2197	4294	6491	73472106	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.2381T>G	15.37:g.75685053A>C	ENSP00000378402:p.Ile794Ser		73472106		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.532861	0.85812	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.52526	0.66;0.66;0.66	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.67942	0.2947	M	0.78285	2.405	0.80722	D	1	D	0.67145	0.996	D	0.65233	0.933	T	0.71328	-0.4626	10	0.56958	D	0.05	-17.571	15.3114	0.74035	1.0:0.0:0.0:0.0	.	794	Q96ST3	SIN3A_HUMAN	S	794	ENSP00000378402:I794S;ENSP00000378403:I794S;ENSP00000353622:I794S	ENSP00000353622:I794S	I	-	2	0	SIN3A	73472106	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	9.302000	0.96175	2.218000	0.71995	0.533000	0.62120	ATT		0.443	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		C	75685053	A	C	75685053	3	2	61	1	0	0	0	0	1	0	0	0	14362	101	4	4	1468	4	SIN3A	15	75685053	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	20504	75685053	26846339	9478	17463										
SIN3A	25942	broad.mit.edu	37	chr15	75693169	75693169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtttacaagaagcataatCtatctccatagcaatgccct	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75693169C>A	ENST00000394947.3	-	11	1953	c.1639G>T	c.(1639-1641)Gat>Tat	p.D547Y	SIN3A_ENST00000360439.4_Missense_Mutation_p.D547Y|SIN3A_ENST00000394949.4_Missense_Mutation_p.D547Y	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.D547Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GAAGCATAATCTATCTCCATA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	15											121	106	111					15																	75693169		2197	4294	6491	73480222	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1639G>T	15.37:g.75693169C>A	ENSP00000378402:p.Asp547Tyr		73480222		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.969278	0.92855	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.57436	0.4;0.4;0.4	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85820	0.1385	10	0.87932	D	0	-27.1386	19.2838	0.94063	0.0:1.0:0.0:0.0	.	547	Q96ST3	SIN3A_HUMAN	Y	547	ENSP00000378402:D547Y;ENSP00000378403:D547Y;ENSP00000353622:D547Y	ENSP00000353622:D547Y	D	-	1	0	SIN3A	73480222	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.817000	0.86213	2.805000	0.96524	0.460000	0.39030	GAT		0.448	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75693169	C	A	75693169	3	1	61	1	0	0	0	0	1	0	0	0	14362	913	32	2	2226	2	SIN3A	15	75693169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8116	75693169	26838223	9479	17464										
SIN3A	25942	broad.mit.edu	37	chr15	75699483	75699483	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattgagcagtttgggtttCttctgcaaaagaaagataca	10	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75699483C>A	ENST00000394947.3	-	9	1634	c.1320G>T	c.(1318-1320)aaG>aaT	p.K440N	SIN3A_ENST00000360439.4_Missense_Mutation_p.K440N|SIN3A_ENST00000394949.4_Missense_Mutation_p.K440N	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.K440N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GTTTGGGTTTCTTCTGCAAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											96	89	91					15																	75699483		2197	4294	6491	73486536	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1320G>T	15.37:g.75699483C>A	ENSP00000378402:p.Lys440Asn		73486536		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.179049	0.78564	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.51071	0.72;0.72;0.72	5.29	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.66954	0.2842	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.68637	-0.5356	10	0.48119	T	0.1	-25.5475	12.0593	0.53555	0.0:0.9164:0.0:0.0836	.	440	Q96ST3	SIN3A_HUMAN	N	440	ENSP00000378402:K440N;ENSP00000378403:K440N;ENSP00000353622:K440N	ENSP00000353622:K440N	K	-	3	2	SIN3A	73486536	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.448000	0.44926	1.205000	0.43262	0.563000	0.77884	AAG		0.373	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75699483	C	A	75699483	3	1	61	1	0	0	0	0	1	0	0	0	14362	912	32	2	2553	2	SIN3A	15	75699483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6314	75699483	26831909	9480	17465										
SIN3A	25942	broad.mit.edu	37	chr15	75703963	75703963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgttctgcaaggatgggGccgttcccaacgagattgtc	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75703963G>A	ENST00000394947.3	-	6	1192	c.878C>T	c.(877-879)gCc>gTc	p.A293V	SIN3A_ENST00000360439.4_Missense_Mutation_p.A293V|SIN3A_ENST00000394949.4_Missense_Mutation_p.A293V	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.A293V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CAAGGATGGGGCCGTTCCCAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											207	194	198					15																	75703963		2197	4294	6491	73491016	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.878C>T	15.37:g.75703963G>A	ENSP00000378402:p.Ala293Val		73491016		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300594	0.60195	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.49139	0.79;0.79;0.79	6.06	5.13	0.70059	.	0.293955	0.37623	N	0.002003	T	0.33469	0.0864	N	0.17474	0.49	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.06285	-1.0835	10	0.24483	T	0.36	-16.0968	16.371	0.83361	0.0:0.1318:0.8682:0.0	.	293	Q96ST3	SIN3A_HUMAN	V	293	ENSP00000378402:A293V;ENSP00000378403:A293V;ENSP00000353622:A293V	ENSP00000353622:A293V	A	-	2	0	SIN3A	73491016	1.000000	0.71417	0.997000	0.53966	0.939000	0.58152	5.470000	0.66756	1.517000	0.48917	0.655000	0.94253	GCC		0.512	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75703963	G	A	75703963	3	1	61	1	0	0	0	0	1	0	0	0	14362	1203	42	3	3007	3	SIN3A	15	75703963	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4480	75703963	26827429	9481	17466										
SIN3A	25942	broad.mit.edu	37	chr15	75706569	75706569	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatttaaattccttcatGatgtcaaggaaatcattgta	7	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75706569G>T	ENST00000394947.3	-	4	764	c.450C>A	c.(448-450)atC>atA	p.I150I	SIN3A_ENST00000360439.4_Silent_p.I150I|SIN3A_ENST00000394949.4_Silent_p.I150I	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.I150I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATTCCTTCATGATGTCAAGGA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	15											110	93	99					15																	75706569		2197	4294	6491	73493622	SO:0001819	synonymous_variant	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.450C>A	15.37:g.75706569G>T			73493622		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																				0.398	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		T	75706569	G	T	75706569	2	4	61	1	0	0	0	0	0	0	0	1	14362	1280	45	2		2	SIN3A	15	75706569	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2606	75706569	26824823	9482	17467										
SIN3A	25942	broad.mit.edu	37	chr15	75715110	75715110	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtgatgatggctgctatGaactgctgctatagcgggcc	15	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75715110G>T	ENST00000394947.3	-	3	558	c.244C>A	c.(244-246)Cat>Aat	p.H82N	SIN3A_ENST00000567289.1_Missense_Mutation_p.H82N|SIN3A_ENST00000360439.4_Missense_Mutation_p.H82N|SIN3A_ENST00000394949.4_Missense_Mutation_p.H82N	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.H82N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						TGGCTGCTATGAACTGCTGCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	97	99					15																	75715110		2197	4294	6491	73502163	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.244C>A	15.37:g.75715110G>T	ENSP00000378402:p.His82Asn		73502163		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.090380	0.55968	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.43688	0.94;0.94;0.94	5.2	5.2	0.72013	.	0.089556	0.85682	D	0.000000	T	0.39384	0.1076	L	0.50333	1.59	0.80722	D	1	B	0.17667	0.023	B	0.14023	0.01	T	0.14282	-1.0478	10	0.22109	T	0.4	-24.5746	17.4692	0.87641	0.0:0.0:1.0:0.0	.	82	Q96ST3	SIN3A_HUMAN	N	82	ENSP00000378402:H82N;ENSP00000378403:H82N;ENSP00000353622:H82N	ENSP00000353622:H82N	H	-	1	0	SIN3A	73502163	1.000000	0.71417	0.964000	0.40570	0.994000	0.84299	9.065000	0.93941	2.706000	0.92434	0.467000	0.42956	CAT		0.567	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		T	75715110	G	T	75715110	3	4	61	1	0	0	0	0	1	0	0	0	14362	1290	45	2	3653	2	SIN3A	15	75715110	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8541	75715110	26816282	9483	17468										
PTPN9	5780	broad.mit.edu	37	chr15	75798053	75798053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaacagggttctcacgacGaatgtcttcatattcctcat	7	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75798053G>A	ENST00000306726.2	-	7	1443	c.931C>T	c.(931-933)Cgt>Tgt	p.R311C	PTPN9_ENST00000564970.1_5'UTR	NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	311	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)	p.R311C(1)		central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTCTCACGACGAATGTCTTCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											156	140	146					15																	75798053		2197	4294	6491	73585108	SO:0001583	missense	5780				CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.931C>T	15.37:g.75798053G>A	ENSP00000303554:p.Arg311Cys		73585108	Q53XR9	Missense_Mutation	SNP	ENST00000306726.2	37	CCDS10280.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.950099	0.53186	.	.	ENSG00000169410	ENST00000306726;ENST00000544966	T	0.14022	2.54	5.61	4.7	0.59300	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.107752	0.64402	N	0.000007	T	0.14874	0.0359	M	0.78456	2.415	0.80722	D	1	P	0.36587	0.559	B	0.25759	0.063	T	0.02966	-1.1088	10	0.54805	T	0.06	.	8.5169	0.33250	0.0767:0.0:0.7712:0.1521	.	311	P43378	PTN9_HUMAN	C	311;301	ENSP00000303554:R311C	ENSP00000303554:R311C	R	-	1	0	PTPN9	73585108	1.000000	0.71417	0.671000	0.29857	0.971000	0.66376	4.866000	0.63005	1.400000	0.46741	0.650000	0.86243	CGT		0.473	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			A	75798053	G	A	75798053	3	1	61	1	0	0	0	0	1	0	0	0	12831	1058	37	1	878	1	PTPN9	15	75798053	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82943	75798053	26733339	9484	17469										
SNUPN	10073	broad.mit.edu	37	chr15	75893520	75893520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcacatcacacaggctttCgggagtgcaagggaagttct	12	9	2	0	rs142962123		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:75893520C>T	ENST00000564644.1	-	9	1296	c.718G>A	c.(718-720)Gaa>Aaa	p.E240K	SNUPN_ENST00000308588.5_Missense_Mutation_p.E240K|CTD-2323K18.1_ENST00000568707.1_RNA|SNUPN_ENST00000564675.1_Missense_Mutation_p.E240K|SNUPN_ENST00000567134.1_Missense_Mutation_p.E240K|SNUPN_ENST00000371091.5_Missense_Mutation_p.E282K			O95149	SPN1_HUMAN	snurportin 1	240	Necessary for binding to the m3G-cap structure.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein import into nucleus (GO:0006606)|RNA metabolic process (GO:0016070)|snRNA import into nucleus (GO:0061015)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear pore (GO:0005643)	protein transporter activity (GO:0008565)|RNA cap binding (GO:0000339)	p.E240K(1)		endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)	8						CACAGGCTTTCGGGAGTGCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	15						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4394		0,0,2197	137	122	127		718,718,718	4.8	1	15	dbSNP_134	127	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense,missense	SNUPN	NM_001042581.1,NM_001042588.1,NM_005701.3	56,56,56	0,1,6490	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	240/361,240/361,240/361	75893520	1,12981	2197	4294	6491	73680575	SO:0001583	missense	10073			AF039029	CCDS10281.1	15q24.2	2008-02-05	2006-07-14	2006-07-14	ENSG00000169371	ENSG00000169371			14245	protein-coding gene	gene with protein product		607902	"RNA, U transporter 1"	RNUT1		9670026	Standard	NM_005701		Approved	SNURPORTIN-1, Snurportin1	uc002bas.3	O95149	OTTHUMG00000142833	ENST00000564644.1:c.718G>A	15.37:g.75893520C>T	ENSP00000454852:p.Glu240Lys		73680575	A6NE34|A8K0B0|D3DW76	Missense_Mutation	SNP	ENST00000564644.1	37	CCDS10281.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561446	0.45590	0.0	1.16E-4	ENSG00000169371	ENST00000308588;ENST00000371091	.	.	.	5.68	4.77	0.60923	.	0.100752	0.64402	N	0.000002	T	0.58764	0.2145	M	0.73962	2.25	0.58432	D	0.999992	B;B	0.19583	0.037;0.012	B;B	0.15870	0.014;0.004	T	0.56092	-0.8036	9	0.31617	T	0.26	-25.8184	9.0403	0.36314	0.1455:0.7806:0.0:0.0738	.	282;240	C9K0X5;O95149	.;SPN1_HUMAN	K	240;282	.	ENSP00000309831:E240K	E	-	1	0	SNUPN	73680575	0.995000	0.38212	0.983000	0.44433	0.682000	0.39822	2.555000	0.45854	1.433000	0.47394	-0.232000	0.12228	GAA		0.393	SNUPN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420332.1	NM_005701		T	75893520	C	T	75893520	3	4	61	1	0	0	0	0	1	0	0	0	14914	893	31	1	372	1	SNUPN	15	75893520	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	95467	75893520	26637872	9485	17470										
FBXO22	26263	broad.mit.edu	37	chr15	76206460	76206460	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttttacagcaaggaaaaGaactagtatggaaacagcac	8	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:76206460G>T	ENST00000308275.3	+	4	482	c.377G>T	c.(376-378)aGa>aTa	p.R126I	FBXO22_ENST00000540507.1_Missense_Mutation_p.R22I|FBXO22_ENST00000453211.2_Missense_Mutation_p.R126I	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	126					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.R126I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCAAGGAAAAGAACTAGTATG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	92	95					15																	76206460		2197	4294	6491	73993515	SO:0001583	missense	26263			AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"F-boxes /  "other""	13593	protein-coding gene	gene with protein product	"FIST domain containing 1"	609096	"F-box only protein 22"			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.377G>T	15.37:g.76206460G>T	ENSP00000307833:p.Arg126Ile		73993515	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215152	0.79352	.	.	ENSG00000167196	ENST00000308275;ENST00000453211;ENST00000540507	.	.	.	5.44	4.52	0.55395	.	0.163210	0.53938	D	0.000041	T	0.54615	0.1869	L	0.29908	0.895	0.80722	D	1	D;D	0.60160	0.987;0.971	P;P	0.58454	0.809;0.839	T	0.58002	-0.7713	9	0.72032	D	0.01	-17.2245	11.0456	0.47857	0.0868:0.0:0.9132:0.0	.	126;126	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	I	126;126;22	.	ENSP00000307833:R126I	R	+	2	0	FBXO22	73993515	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.264000	0.43302	1.289000	0.44618	0.650000	0.86243	AGA		0.348	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		T	76206460	G	T	76206460	3	4	61	1	0	0	0	0	1	0	0	0	5753	942	33	2	391	2	FBXO22	15	76206460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	312940	76206460	26324932	9486	17471										
ETFA	2108	broad.mit.edu	37	chr15	76518260	76518260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctgggtctttattaattGccacaattgtctgtgaaata	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:76518260G>A	ENST00000557943.1	-	11	973	c.893C>T	c.(892-894)gCa>gTa	p.A298V	ETFA_ENST00000433983.2_Missense_Mutation_p.A249V|ETFA_ENST00000559602.1_Missense_Mutation_p.A194V|ETFA_ENST00000560726.1_Missense_Mutation_p.A38V	NM_000126.3	NP_000117.1	P13804	ETFA_HUMAN	electron-transfer-flavoprotein, alpha polypeptide	298	Domain II. {ECO:0000269|PubMed:8962055}.				cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity (GO:0016491)	p.A298V(1)		endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9						TTTATTAATTGCCACAATTGT	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	15											94	105	101					15																	76518260		2197	4294	6491	74305315	SO:0001583	missense	2108			J04058	CCDS32299.1, CCDS45311.1	15q23-q25	2012-04-04	2008-08-01		ENSG00000140374	ENSG00000140374			3481	protein-coding gene	gene with protein product	"glutaric aciduria II"	608053					Standard	NM_000126		Approved	GA2, EMA, MADD	uc002bbt.2	P13804	OTTHUMG00000172586	ENST00000557943.1:c.893C>T	15.37:g.76518260G>A	ENSP00000452762:p.Ala298Val		74305315	B4DT43|Q53XN3	Missense_Mutation	SNP	ENST00000557943.1	37	CCDS32299.1	.	.	.	.	.	.	.	.	.	.	G	33	5.253545	0.95336	.	.	ENSG00000140374	ENST00000433983;ENST00000267950	D	0.94966	-3.57	5.56	5.56	0.83823	Electron transfer flavoprotein, alpha subunit, C-terminal, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97396	0.9148	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67382	0.944;0.951	D	0.97924	1.0316	10	0.87932	D	0	-14.5431	18.5116	0.90918	0.0:0.0:1.0:0.0	.	249;298	B4DT43;P13804	.;ETFA_HUMAN	V	249;298	ENSP00000399273:A249V	ENSP00000267950:A298V	A	-	2	0	ETFA	74305315	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.631000	0.90991	2.602000	0.87976	0.563000	0.77884	GCA		0.313	ETFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419302.2	NM_000126		A	76518260	G	A	76518260	3	1	61	1	0	0	0	0	1	0	0	0	5282	1319	46	3	116	3	ETFA	15	76518260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	311800	76518260	26013132	9487	17472										
SCAPER	49855	broad.mit.edu	37	chr15	76643614	76643614	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggttttccgcttgacctgGagtctgtgccaaatcctgta	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:76643614G>T	ENST00000563290.1	-	31	4158	c.4063C>A	c.(4063-4065)Cca>Aca	p.P1355T	SCAPER_ENST00000324767.7_Missense_Mutation_p.P1355T|SCAPER_ENST00000538941.2_Missense_Mutation_p.P1109T			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1355						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P1355T(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GCTTGACCTGGAGTCTGTGCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											108	101	103					15																	76643614		1844	4084	5928	74430669	SO:0001583	missense	49855			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.4063C>A	15.37:g.76643614G>T	ENSP00000454973:p.Pro1355Thr		74430669	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	G	9.079	0.998787	0.19121	.	.	ENSG00000140386	ENST00000324767;ENST00000538941	T;T	0.21543	2.01;2.0	5.76	1.73	0.24493	.	0.636831	0.17075	N	0.188039	T	0.14184	0.0343	L	0.40543	1.245	0.20074	N	0.999937	B;B	0.18166	0.025;0.026	B;B	0.17722	0.008;0.019	T	0.27502	-1.0072	10	0.25106	T	0.35	.	5.3293	0.15924	0.3156:0.1373:0.5472:0.0	.	1354;1109	Q9BY12;F5H7X8	SCAPE_HUMAN;.	T	1355;1109	ENSP00000326924:P1355T;ENSP00000442190:P1109T	ENSP00000326924:P1355T	P	-	1	0	SCAPER	74430669	0.904000	0.30761	0.139000	0.22197	0.854000	0.48673	1.233000	0.32648	0.140000	0.18849	0.655000	0.94253	CCA		0.373	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	76643614	G	T	76643614	3	4	61	1	0	0	0	0	1	0	0	0	13915	1174	41	2	147	2	SCAPER	15	76643614	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125354	76643614	25887778	9488	17473										
RCN2	5955	broad.mit.edu	37	chr15	77241413	77241413	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttttattttgaaggcGcttcatctaattgatgaaat	7	4	2	3	rs17849874|rs58665121	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:77241413G>A	ENST00000394885.3	+	7	1027	c.804G>A	c.(802-804)gcG>gcA	p.A268A	RCN2_ENST00000394883.3_Silent_p.A167A|RCN2_ENST00000320963.5_Silent_p.A286A	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	268	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)	p.A268A(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TTTTGAAGGCGCTTCATCTAA	0.358													G|||	18	0.00359425	0.0136	0	5008	,	,		18485	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15						G		39,4353	40.8+/-73.8	1,37,2158	107	120	115		804	1	1	15	dbSNP_129	115	0,8588		0,0,4294	no	coding-synonymous	RCN2	NM_002902.2		1,37,6452	AA,AG,GG		0.0,0.888,0.3005		268/318	77241413	39,12941	2196	4294	6490	75028468	SO:0001819	synonymous_variant	5955			X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.804G>A	15.37:g.77241413G>A			75028468	A8MTG6|F8WCY5|Q53XN8	Silent	SNP	ENST00000394885.3	37	CCDS10291.1																																																																																				0.358	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		A	77241413	G	A	77241413	2	1	61	1	0	0	0	0	0	0	0	1	13217	1074	38	1		1	RCN2	15	77241413	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	597799	77241413	25289979	9489	17474										
TSPAN3	10099	broad.mit.edu	37	chr15	77345214	77345214	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacactctggtttttggtttCtttgaaccaatctgtatttt	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:77345214C>A	ENST00000267970.4	-	5	763	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	TSPAN3_ENST00000561277.1_5'UTR|TSPAN3_ENST00000424443.3_Nonsense_Mutation_p.E100*|TSPAN3_ENST00000558394.1_5'Flank|TSPAN3_ENST00000346495.2_Nonsense_Mutation_p.E139*|TSPAN3_ENST00000559494.1_Nonsense_Mutation_p.E75*|TSPAN3_ENST00000558745.1_5'UTR	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	164						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.E164*(1)		kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		TTTTTGGTTTCTTTGAACCAA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											109	87	94					15																	77345214		2196	4294	6490	75132269	SO:0001587	stop_gained	10099				CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"Tetraspanins"	17752	protein-coding gene	gene with protein product		613134	"transmembrane 4 superfamily member 8"	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.490G>T	15.37:g.77345214C>A	ENSP00000267970:p.Glu164*		75132269	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	Nonsense_Mutation	SNP	ENST00000267970.4	37	CCDS10292.1	.	.	.	.	.	.	.	.	.	.	C	37	6.093732	0.97276	.	.	ENSG00000140391	ENST00000267970;ENST00000424443;ENST00000423920;ENST00000346495	.	.	.	6.16	5.24	0.73138	.	0.045131	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	13.3349	0.60512	0.1195:0.752:0.1285:0.0	.	.	.	.	X	164;100;126;139	.	ENSP00000267970:E164X	E	-	1	0	TSPAN3	75132269	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.192000	0.42649	1.606000	0.50161	0.650000	0.86243	GAA		0.443	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724		A	77345214	C	A	77345214	4	1	61	1	0	0	0	0	0	1	0	0	16685	922	32	2	283	2	TSPAN3	15	77345214	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103801	77345214	25186178	9490	17475										
SGK269	79834	broad.mit.edu	37	chr15	77472838	77472838	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggctgctgacacatccacGacagtatatggcttgcacaa	9	11	0	1	rs374860881	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:77472838G>A	ENST00000560626.2	-	4	1906	c.1431C>T	c.(1429-1431)gtC>gtT	p.V477V	PEAK1_ENST00000312493.4_Silent_p.V477V|PEAK1_ENST00000558305.1_Silent_p.V477V			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	477					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.V477V(2)									ACACATCCACGACAGTATATG	0.507													g|||	2	0.000399361	0.0015	0	5008	,	,		19225	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	15						A		0,4056		0,0,2028	127	125	126		1431	-11.1	0	15		126	3,8379		0,3,4188	no	coding-synonymous	PEAK1	NM_024776.3		0,3,6216	AA,AG,GG		0.0358,0.0,0.0241		477/1747	77472838	3,12435	2028	4191	6219	75259893	SO:0001819	synonymous_variant	79834				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.1431C>T	15.37:g.77472838G>A			75259893	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																				0.507	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77472838	G	A	77472838	2	1	61	1	0	0	0	0	0	0	0	1	14248	1045	37	1		1	SGK269	15	77472838	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127624	77472838	25058554	9491	17476										
SGK269	79834	broad.mit.edu	37	chr15	77473361	77473361	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagtccacagcacagattCtctgcagagacttgtttcgc	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:77473361C>A	ENST00000560626.2	-	4	1383	c.908G>T	c.(907-909)aGa>aTa	p.R303I	PEAK1_ENST00000312493.4_Missense_Mutation_p.R303I|PEAK1_ENST00000558305.1_Missense_Mutation_p.R303I			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	303					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R303I(2)									AGCACAGATTCTCTGCAGAGA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	15											85	79	81					15																	77473361		1925	4127	6052	75260416	SO:0001583	missense	79834				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.908G>T	15.37:g.77473361C>A	ENSP00000452796:p.Arg303Ile		75260416	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305119	0.81247	.	.	ENSG00000173517	ENST00000312493	T	0.79554	-1.28	5.3	5.3	0.74995	.	0.000000	0.33327	U	0.005025	D	0.85699	0.5757	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87381	0.2357	10	0.87932	D	0	-8.7377	18.9555	0.92657	0.0:1.0:0.0:0.0	.	303	Q9H792	PEAK1_HUMAN	I	303	ENSP00000309230:R303I	ENSP00000309230:R303I	R	-	2	0	AC087465.1	75260416	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.666000	0.83877	2.469000	0.83416	0.557000	0.71058	AGA		0.438	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77473361	C	A	77473361	3	1	61	1	0	0	0	0	1	0	0	0	14248	913	32	2	4348	2	SGK269	15	77473361	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	523	77473361	25058031	9492	17477										
LINGO1	84894	broad.mit.edu	37	chr15	77907976	77907976	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggtgcgggaagctggcGaactcgtcctggttgagcgt	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:77907976G>A	ENST00000355300.6	-	2	447	c.273C>T	c.(271-273)ttC>ttT	p.F91F	LINGO1_ENST00000561030.1_Silent_p.F85F	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	91					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F85F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						GGAAGCTGGCGAACTCGTCCT	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	15											32	36	35					15																	77907976		2115	4224	6339	75695031	SO:0001819	synonymous_variant	84894			AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.273C>T	15.37:g.77907976G>A			75695031	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																				0.637	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		A	77907976	G	A	77907976	2	1	61	1	0	0	0	0	0	0	0	1	8838	1049	37	1		1	LINGO1	15	77907976	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	434615	77907976	24623416	9493	17478										
TBC1D2B	23102	broad.mit.edu	37	chr15	78322512	78322512	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaaagaagacatcgaattCctgttgggaaaaacaatatg	10	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78322512C>T	ENST00000300584.3	-	4	683	c.684G>A	c.(682-684)aaG>aaA	p.K228K	TBC1D2B_ENST00000409931.3_Splice_Site_p.K228K	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	228							Rab GTPase activator activity (GO:0005097)	p.K228K(2)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						ACATCGAATTCCTGTTGGGAA	0.343																																																2	Substitution - coding silent(2)	large_intestine(2)	15											46	41	42					15																	78322512		2196	4293	6489	76109567	SO:0001630	splice_region_variant	23102			AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.684-1G>A	15.37:g.78322512C>T			76109567	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	C	6.486	0.457769	0.12342	.	.	ENSG00000167202	ENST00000418039	.	.	.	5.07	0.0326	0.14176	.	.	.	.	.	T	0.57272	0.2042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49862	-0.8894	4	.	.	.	.	9.8614	0.41116	0.0:0.3955:0.0:0.6045	.	.	.	.	K	110	.	.	R	-	2	0	TBC1D2B	76109567	0.992000	0.36948	0.929000	0.37066	0.445000	0.32107	0.097000	0.15168	-0.246000	0.09611	-0.483000	0.04790	AGA		0.343	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	Silent	T	78322512	C	T	78322512	5	4	61	1	0	0	0	0	0	0	1	0	15658	869	30	3	2247	3	TBC1D2B	15	78322512	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	414536	78322512	24208880	9494	17479										
IDH3A	3419	broad.mit.edu	37	chr15	78455867	78455867	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcggatgtcagatgggctTtttctacaaaaatgcaggga	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78455867T>G	ENST00000299518.2	+	7	713	c.630T>G	c.(628-630)ctT>ctG	p.L210L	IDH3A_ENST00000559205.1_Intron|IDH3A_ENST00000561366.1_5'Flank|IDH3A_ENST00000558554.1_Silent_p.L175L|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000441490.2_Silent_p.L101L	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	210					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.L210L(1)		endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CAGATGGGCTTTTTCTACAAA	0.299																																																1	Substitution - coding silent(1)	large_intestine(1)	15											85	90	88					15																	78455867		2196	4293	6489	76242922	SO:0001819	synonymous_variant	3419				CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"H-IDH alpha", "isocitric dehydrogenase", "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "NAD+-specific ICDH", "NAD(H)-specific isocitrate dehydrogenase alpha subunit", "isocitrate dehydrogenase (NAD+) alpha chain"	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.630T>G	15.37:g.78455867T>G			76242922	D3DW83|Q9H3X0	Silent	SNP	ENST00000299518.2	37	CCDS10297.1																																																																																				0.299	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		G	78455867	T	G	78455867	2	3	61	1	0	0	0	0	0	0	0	1	7517	1828	64	4		4	IDH3A	15	78455867	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	133355	78455867	24075525	9495	17480										
IDH3A	3419	broad.mit.edu	37	chr15	78461336	78461336	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatctgtcgccgagtaaaaGatttagattaacacttctac	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78461336G>T	ENST00000299518.2	+	11	1173	c.1090G>T	c.(1090-1092)Gat>Tat	p.D364Y	IDH3A_ENST00000559205.1_Missense_Mutation_p.D85Y|IDH3A_ENST00000558554.1_Missense_Mutation_p.D329Y|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000441490.2_Missense_Mutation_p.D255Y|ACSBG1_ENST00000258873.4_3'UTR	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	364					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.D364Y(1)		endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CCGAGTAAAAGATTTAGATTA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	15											134	132	133					15																	78461336		2196	4293	6489	76248391	SO:0001583	missense	3419				CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"H-IDH alpha", "isocitric dehydrogenase", "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "NAD+-specific ICDH", "NAD(H)-specific isocitrate dehydrogenase alpha subunit", "isocitrate dehydrogenase (NAD+) alpha chain"	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.1090G>T	15.37:g.78461336G>T	ENSP00000299518:p.Asp364Tyr		76248391	D3DW83|Q9H3X0	Missense_Mutation	SNP	ENST00000299518.2	37	CCDS10297.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.597550	0.87055	.	.	ENSG00000166411	ENST00000299518;ENST00000441490	T;T	0.56611	0.45;0.47	6.17	6.17	0.99709	Isopropylmalate dehydrogenase-like domain (1);	0.085998	0.85682	D	0.000000	T	0.64929	0.2643	M	0.65975	2.015	0.80722	D	1	D;P;D	0.55385	0.965;0.938;0.971	P;B;P	0.50617	0.541;0.423;0.646	T	0.66260	-0.5968	10	0.72032	D	0.01	-28.6373	19.8676	0.96824	0.0:0.0:1.0:0.0	.	329;314;364	B4DSY4;B4DJB4;P50213	.;.;IDH3A_HUMAN	Y	364;255	ENSP00000299518:D364Y;ENSP00000387506:D255Y	ENSP00000299518:D364Y	D	+	1	0	IDH3A	76248391	1.000000	0.71417	0.341000	0.25589	0.914000	0.54420	7.146000	0.77373	2.941000	0.99782	0.655000	0.94253	GAT		0.373	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		T	78461336	G	T	78461336	3	4	61	1	0	0	0	0	1	0	0	0	7517	942	33	2	1132	2	IDH3A	15	78461336	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5469	78461336	24070056	9496	17481										
IREB2	3658	broad.mit.edu	37	chr15	78764188	78764188	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtggtttttgaagaaaaaGacctcctcttcccagacagt	9	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78764188G>T	ENST00000258886.8	+	7	954	c.805G>T	c.(805-807)Gac>Tac	p.D269Y	IREB2_ENST00000560440.1_Missense_Mutation_p.D269Y	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	269					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)	p.D269Y(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TGAAGAAAAAGACCTCCTCTT	0.398																																					NSCLC(200;764 2208 35157 49871 50830)											1	Substitution - Missense(1)	large_intestine(1)	15											57	58	58					15																	78764188		2196	4293	6489	76551243	SO:0001583	missense	3658			M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.805G>T	15.37:g.78764188G>T	ENSP00000258886:p.Asp269Tyr		76551243	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.693656	0.68386	.	.	ENSG00000136381	ENST00000258886	T	0.17691	2.26	5.59	1.5	0.22942	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.306181	0.40469	N	0.001092	T	0.19967	0.0480	L	0.54323	1.7	0.34830	D	0.739601	P;P	0.43938	0.822;0.809	B;P	0.45558	0.446;0.485	T	0.22382	-1.0218	10	0.66056	D	0.02	-9.126	9.7826	0.40658	0.2849:0.0:0.7151:0.0	.	269;269	P48200;Q8WVK6	IREB2_HUMAN;.	Y	269	ENSP00000258886:D269Y	ENSP00000258886:D269Y	D	+	1	0	IREB2	76551243	1.000000	0.71417	0.003000	0.11579	0.887000	0.51463	3.116000	0.50399	0.085000	0.17107	0.585000	0.79938	GAC		0.398	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		T	78764188	G	T	78764188	3	4	61	1	0	0	0	0	1	0	0	0	7847	942	33	2	831	2	IREB2	15	78764188	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	302852	78764188	23767204	9497	17482										
IREB2	3658	broad.mit.edu	37	chr15	78770699	78770699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagctgtgaaattgtttcGaaatgaccagaattcttcag	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78770699G>A	ENST00000258886.8	+	10	1405	c.1256G>A	c.(1255-1257)cGa>cAa	p.R419Q	RP11-650L12.1_ENST00000560094.1_RNA	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	419					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)	p.R419Q(3)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		AAATTGTTTCGAAATGACCAG	0.393																																					NSCLC(200;764 2208 35157 49871 50830)											3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	15											92	90	90					15																	78770699		2196	4293	6489	76557754	SO:0001583	missense	3658			M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.1256G>A	15.37:g.78770699G>A	ENSP00000258886:p.Arg419Gln		76557754	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135347	0.94517	.	.	ENSG00000136381	ENST00000258886	T	0.17854	2.25	5.37	4.38	0.52667	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.101689	0.64402	N	0.000004	T	0.35480	0.0933	M	0.81497	2.545	0.80722	D	1	D	0.59767	0.986	P	0.55577	0.779	T	0.24835	-1.0149	10	0.72032	D	0.01	-15.4669	11.2102	0.48793	0.0954:0.0:0.9046:0.0	.	419	P48200	IREB2_HUMAN	Q	419	ENSP00000258886:R419Q	ENSP00000258886:R419Q	R	+	2	0	IREB2	76557754	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	5.168000	0.64978	1.249000	0.43950	0.591000	0.81541	CGA		0.393	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		A	78770699	G	A	78770699	3	1	61	1	0	0	0	0	1	0	0	0	7847	1058	37	1	1294	1	IREB2	15	78770699	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6511	78770699	23760693	9498	17483										
IREB2	3658	broad.mit.edu	37	chr15	78789594	78789594	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgggcctctccggtagaGaaacattttctttaacattt	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78789594G>T	ENST00000258886.8	+	21	2871	c.2722G>T	c.(2722-2724)Gaa>Taa	p.E908*		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	908					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)	p.E908*(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		CTCCGGTAGAGAAACATTTTC	0.343																																					NSCLC(200;764 2208 35157 49871 50830)											1	Substitution - Nonsense(1)	large_intestine(1)	15											73	72	72					15																	78789594		2196	4293	6489	76576649	SO:0001587	stop_gained	3658			M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.2722G>T	15.37:g.78789594G>T	ENSP00000258886:p.Glu908*		76576649	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Nonsense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	G	41	9.151234	0.99082	.	.	ENSG00000136381	ENST00000258886	.	.	.	5.87	5.87	0.94306	.	0.088500	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	X	908	.	ENSP00000258886:E908X	E	+	1	0	IREB2	76576649	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.945000	0.92985	2.941000	0.99782	0.655000	0.94253	GAA		0.343	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		T	78789594	G	T	78789594	4	4	61	1	0	0	0	0	0	1	0	0	7847	943	33	2	2804	2	IREB2	15	78789594	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18895	78789594	23741798	9499	17484										
CHRNA5	1138	broad.mit.edu	37	chr15	78882935	78882935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgcgctcgattctattcGctacattacaagacacatca	6	12	2	1	rs141180754	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:78882935G>A	ENST00000299565.5	+	5	1402	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	RP11-650L12.2_ENST00000567141.1_RNA|CHRNA5_ENST00000559554.1_Intron	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	401					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)	p.R401H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	GATTCTATTCGCTACATTACA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG	3,4389	6.2+/-15.9	0,3,2193	65	63	64		1202	4.8	0.5	15	dbSNP_134	64	0,8586		0,0,4293	no	missense	CHRNA5	NM_000745.3	29	0,3,6486	AA,AG,GG		0.0,0.0683,0.0231	benign	401/469	78882935	3,12975	2196	4293	6489	76669990	SO:0001583	missense	1138				CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1959	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 5 (neuronal)"	118505	"cholinergic receptor, nicotinic, alpha polypeptide 5"			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1202G>A	15.37:g.78882935G>A	ENSP00000299565:p.Arg401His		76669990	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.144789	0.37825	6.83E-4	0.0	ENSG00000169684	ENST00000299565	D	0.85773	-2.03	4.79	4.79	0.61399	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.167902	0.52532	D	0.000061	D	0.85008	0.5599	M	0.72576	2.205	0.80722	D	1	B	0.23185	0.081	B	0.19946	0.027	T	0.82764	-0.0296	10	0.42905	T	0.14	.	18.2639	0.90046	0.0:0.0:1.0:0.0	.	401	P30532	ACHA5_HUMAN	H	401	ENSP00000299565:R401H	ENSP00000299565:R401H	R	+	2	0	CHRNA5	76669990	1.000000	0.71417	0.533000	0.28001	0.184000	0.23303	7.991000	0.88244	2.382000	0.81193	0.558000	0.71614	CGC		0.398	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1			A	78882935	G	A	78882935	3	1	61	1	0	0	0	0	1	0	0	0	3392	1087	38	1	1220	1	CHRNA5	15	78882935	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93341	78882935	23648457	9500	17485										
RASGRF1	5923	broad.mit.edu	37	chr15	79264252	79264252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagtttgttgaaactggcGaatctctcggataatatggg	13	6	1	1	rs561370237		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:79264252G>A	ENST00000419573.3	-	27	3959	c.3685C>T	c.(3685-3687)Cgc>Tgc	p.R1229C	RASGRF1_ENST00000558480.2_Missense_Mutation_p.R1213C|RASGRF1_ENST00000394745.3_Missense_Mutation_p.R445C	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1229	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1229C(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGAAACTGGCGAATCTCTCGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	15											292	242	259					15																	79264252		2196	4293	6489	77051307	SO:0001583	missense	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3685C>T	15.37:g.79264252G>A	ENSP00000405963:p.Arg1229Cys		77051307	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.528966	0.64860	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.32515	1.45;1.45	4.23	4.23	0.50019	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.55337	0.1914	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.72625	0.889;0.978	T	0.62186	-0.6907	10	0.87932	D	0	.	14.1673	0.65486	0.0:0.0:1.0:0.0	.	1231;1213	Q13972;F8VPA5	RGRF1_HUMAN;.	C	1229;1213;445	ENSP00000405963:R1229C;ENSP00000378228:R445C	ENSP00000378224:R1213C	R	-	1	0	RASGRF1	77051307	0.997000	0.39634	0.999000	0.59377	0.774000	0.43823	1.860000	0.39428	2.169000	0.68431	0.561000	0.74099	CGC		0.483	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79264252	G	A	79264252	3	1	61	1	0	0	0	0	1	0	0	0	13109	1058	37	1	144	1	RASGRF1	15	79264252	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	381317	79264252	23267140	9501	17486										
RASGRF1	5923	broad.mit.edu	37	chr15	79284111	79284111	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagggctgagtggttttcaAagggctcagccttcacgcct	12	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:79284111A>C	ENST00000419573.3	-	22	3375	c.3101T>G	c.(3100-3102)tTt>tGt	p.F1034C	RASGRF1_ENST00000558480.2_Missense_Mutation_p.F1018C|RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000394745.3_Missense_Mutation_p.F250C	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1034					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F1034C(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTGGTTTTCAAAGGGCTCAGC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	15											106	94	98					15																	79284111		2196	4293	6489	77071166	SO:0001583	missense	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3101T>G	15.37:g.79284111A>C	ENSP00000405963:p.Phe1034Cys		77071166	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097519	0.56075	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.35973	1.28;1.28	4.13	4.13	0.48395	Guanine-nucleotide dissociation stimulator CDC25 (1);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.51584	0.1683	L	0.52573	1.65	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.998	D;D;D;D	0.85130	0.997;0.994;0.997;0.967	T	0.54173	-0.8333	10	0.87932	D	0	.	11.149	0.48447	1.0:0.0:0.0:0.0	.	430;1018;1036;1018	B7Z6Z6;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	C	1034;1018;250	ENSP00000405963:F1034C;ENSP00000378228:F250C	ENSP00000378224:F1018C	F	-	2	0	RASGRF1	77071166	1.000000	0.71417	1.000000	0.80357	0.314000	0.28054	8.880000	0.92407	1.726000	0.51525	0.528000	0.53228	TTT		0.547	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		C	79284111	A	C	79284111	3	2	61	1	0	0	0	0	1	0	0	0	13109	14	1	4	748	4	RASGRF1	15	79284111	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	19859	79284111	23247281	9502	17487										
TMED3	23423	broad.mit.edu	37	chr15	79606168	79606168	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggaacaccatctacagaGaaacgaagaagcagtacgac	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:79606168G>T	ENST00000299705.5	+	2	426	c.238G>T	c.(238-240)Gaa>Taa	p.E80*	TMED3_ENST00000424155.2_Nonsense_Mutation_p.E80*|TMED3_ENST00000536821.1_Nonsense_Mutation_p.E80*	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	80	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.E80*(1)		large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						CATCTACAGAGAAACGAAGAA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											155	135	142					15																	79606168		2196	4293	6489	77393223	SO:0001587	stop_gained	23423			BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 22", "transmembrane emp24 domain containing 3"	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.238G>T	15.37:g.79606168G>T	ENSP00000299705:p.Glu80*		77393223	A8K069|B4DN05|Q2T9F8	Nonsense_Mutation	SNP	ENST00000299705.5	37	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	G	37	6.448522	0.97577	.	.	ENSG00000166557	ENST00000299705;ENST00000424155;ENST00000536821;ENST00000543455	.	.	.	4.7	4.7	0.59300	.	0.060301	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-5.0442	15.505	0.75731	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000299705:E80X	E	+	1	0	TMED3	77393223	1.000000	0.71417	0.881000	0.34555	0.955000	0.61496	9.130000	0.94437	2.578000	0.87016	0.655000	0.94253	GAA		0.468	TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364		T	79606168	G	T	79606168	4	4	61	1	0	0	0	0	0	1	0	0	16044	943	33	2	244	2	TMED3	15	79606168	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	322057	79606168	22925224	9503	17488										
KIAA1024	23251	broad.mit.edu	37	chr15	79749341	79749341	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcaaagcagagaatgaGcacagggaaccccagagtcg	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:79749341G>A	ENST00000305428.3	+	2	927	c.852G>A	c.(850-852)gaG>gaA	p.E284E		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	284						integral component of membrane (GO:0016021)		p.E284E(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						CAGAGAATGAGCACAGGGAAC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	15											113	128	123					15																	79749341		2196	4293	6489	77536396	SO:0001819	synonymous_variant	23251			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.852G>A	15.37:g.79749341G>A			77536396	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																				0.478	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		A	79749341	G	A	79749341	2	1	61	1	0	0	0	0	0	0	0	1	8226	962	34	3		3	KIAA1024	15	79749341	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143173	79749341	22782051	9504	17489										
KIAA1024	23251	broad.mit.edu	37	chr15	79750667	79750667	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtccaaaattgccagcatCtccaactcgcccagagactg	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:79750667C>A	ENST00000305428.3	+	2	2253	c.2178C>A	c.(2176-2178)atC>atA	p.I726I		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	726						integral component of membrane (GO:0016021)		p.I726I(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						TTGCCAGCATCTCCAACTCGC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15											85	80	82					15																	79750667		2196	4293	6489	77537722	SO:0001819	synonymous_variant	23251			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.2178C>A	15.37:g.79750667C>A			77537722	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																				0.517	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		A	79750667	C	A	79750667	2	1	61	1	0	0	0	0	0	0	0	1	8226	903	32	2		2	KIAA1024	15	79750667	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1326	79750667	22780725	9505	17490										
FAH	2184	broad.mit.edu	37	chr15	80465480	80465480	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctttgctgtgcccaacccGaagcaggtaagcacattctc	8	15	1	0	rs372980573		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:80465480G>A	ENST00000407106.1	+	10	986	c.831G>A	c.(829-831)ccG>ccA	p.P277P	FAH_ENST00000558627.1_3'UTR|FAH_ENST00000561421.1_Silent_p.P277P|FAH_ENST00000261755.5_Silent_p.P277P|FAH_ENST00000539156.1_Silent_p.P207P			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	277					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)	p.P277P(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGCCCAACCCGAAGCAGGTAA	0.587									Tyrosinemia, type 1		OREG0023354	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	15						G		1,4405	2.1+/-5.4	0,1,2202	173	142	153		831	-7.7	0.1	15		153	0,8600		0,0,4300	no	coding-synonymous	FAH	NM_000137.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		277/420	80465480	1,13005	2203	4300	6503	78252535	SO:0001819	synonymous_variant	2184	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.831G>A	15.37:g.80465480G>A		1198	78252535	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																				0.587	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2			A	80465480	G	A	80465480	2	1	61	1	0	0	0	0	0	0	0	1	5387	1045	37	1		1	FAH	15	80465480	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	714813	80465480	22065912	9506	17491										
ARNT2	9915	broad.mit.edu	37	chr15	80762585	80762585	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatagtgaaatcgaaaggcGcagacggaacaagatgactc	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:80762585G>A	ENST00000303329.4	+	4	386	c.221G>A	c.(220-222)cGc>cAc	p.R74H	ARNT2_ENST00000531595.3_3'UTR|ARNT2_ENST00000533983.1_Missense_Mutation_p.R63H|ARNT2_ENST00000527771.1_Missense_Mutation_p.R63H	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	74	Poly-Arg.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.R74H(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			ATCGAAAGGCGCAGACGGAAC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											76	66	69					15																	80762585		2203	4300	6503	78549640	SO:0001583	missense	9915			AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"Basic helix-loop-helix proteins"	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.221G>A	15.37:g.80762585G>A	ENSP00000307479:p.Arg74His		78549640	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.496821	0.85069	.	.	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	D	0.98493	-4.96	5.0	5.0	0.66597	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99269	0.9745	H	0.94886	3.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.984;0.993	D	0.98959	1.0797	10	0.87932	D	0	.	18.4737	0.90783	0.0:0.0:1.0:0.0	.	74;74	Q9HBZ2;Q86TN1	ARNT2_HUMAN;.	H	63;74;74	ENSP00000307479:R74H	ENSP00000307479:R74H	R	+	2	0	ARNT2	78549640	1.000000	0.71417	1.000000	0.80357	0.429000	0.31625	9.186000	0.94906	2.597000	0.87782	0.650000	0.86243	CGC		0.502	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			A	80762585	G	A	80762585	3	1	61	1	0	0	0	0	1	0	0	0	967	1087	38	1	235	1	ARNT2	15	80762585	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297105	80762585	21768807	9507	17492										
KIAA1199	57214	broad.mit.edu	37	chr15	81173325	81173325	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgctcttgagttgcatggAcagaaaaagctctcctggac	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81173325A>G	ENST00000394685.3	+	6	884	c.465A>G	c.(463-465)ggA>ggG	p.G155G	KIAA1199_ENST00000220244.3_Silent_p.G155G|KIAA1199_ENST00000356249.5_Silent_p.G155G			Q8WUJ3	CEMIP_HUMAN		155	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.G155G(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						AGTTGCATGGACAGAAAAAGC	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	15											131	128	129					15																	81173325		2203	4300	6503	78960380	SO:0001819	synonymous_variant	57214																														ENST00000394685.3:c.465A>G	15.37:g.81173325A>G			78960380	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																				0.502	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			G	81173325	A	G	81173325	2	3	61	1	0	0	0	0	0	0	0	1	8234	262	10	4		4	KIAA1199	15	81173325	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	410740	81173325	21358067	9508	17493										
MESDC2	23184	broad.mit.edu	37	chr15	81271764	81271764	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagtccttgatctcccaGgcgtagctcccatcgcgaag	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81271764G>T	ENST00000261758.4	-	3	587	c.501C>A	c.(499-501)gcC>gcA	p.A167A	MESDC2_ENST00000560244.1_5'Flank	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	167	Escort domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)		p.A167A(1)		cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						TGATCTCCCAGGCGTAGCTCC	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	15											75	70	72					15																	81271764		2203	4300	6503	79058819	SO:0001819	synonymous_variant	23184			D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.501C>A	15.37:g.81271764G>T			79058819	B4DW84|D3DW96|Q969U1	Silent	SNP	ENST00000261758.4	37	CCDS32308.1																																																																																				0.527	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		T	81271764	G	T	81271764	2	4	61	1	0	0	0	0	0	0	0	1	9511	987	35	2		2	MESDC2	15	81271764	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98439	81271764	21259628	9509	17494										
C15orf26	161502	broad.mit.edu	37	chr15	81428868	81428868	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattgtagatgcaactttcCgtaactgaagatggctatat	8	6	0	3	rs373978881		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81428868C>T	ENST00000286732.4	+	3	254	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_173528.2	NP_775799.2	Q6P656	CO026_HUMAN	chromosome 15 open reading frame 26	57								p.S57S(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(6)|skin(1)	17						TGCAACTTTCCGTAACTGAAG	0.408													C|||	1	0.000199681	0	0	5008	,	,		21246	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	15						C		1,4061		0,1,2030	111	109	110		171	-3.9	0	15		110	2,8362		0,2,4180	no	coding-synonymous	C15orf26	NM_173528.2		0,3,6210	TT,TC,CC		0.0239,0.0246,0.0241		57/302	81428868	3,12423	2031	4182	6213	79215923	SO:0001819	synonymous_variant	161502			AK095934	CCDS42068.1	15q25.1	2012-09-10			ENSG00000156206	ENSG00000156206			26782	protein-coding gene	gene with protein product						14702039	Standard	NM_173528		Approved	FLJ38615	uc002bgb.3	Q6P656	OTTHUMG00000172263	ENST00000286732.4:c.171C>T	15.37:g.81428868C>T			79215923	Q8N906	Silent	SNP	ENST00000286732.4	37	CCDS42068.1																																																																																				0.408	C15orf26-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417587.1	NM_173528		T	81428868	C	T	81428868	2	4	61	1	0	0	0	0	0	0	0	1	1791	639	23	1		1	C15orf26	15	81428868	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	157104	81428868	21102524	9510	17495										
C15orf26	161502	broad.mit.edu	37	chr15	81436094	81436094	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagatgaggtctcccatgTgaactgctggcaggctgcct	12	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81436094T>C	ENST00000286732.4	+	5	652	c.569T>C	c.(568-570)gTg>gCg	p.V190A		NM_173528.2	NP_775799.2	Q6P656	CO026_HUMAN	chromosome 15 open reading frame 26	190								p.V190A(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(6)|skin(1)	17						GTCTCCCATGTGAACTGCTGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											148	146	147					15																	81436094		2013	4163	6176	79223149	SO:0001583	missense	161502			AK095934	CCDS42068.1	15q25.1	2012-09-10			ENSG00000156206	ENSG00000156206			26782	protein-coding gene	gene with protein product						14702039	Standard	NM_173528		Approved	FLJ38615	uc002bgb.3	Q6P656	OTTHUMG00000172263	ENST00000286732.4:c.569T>C	15.37:g.81436094T>C	ENSP00000286732:p.Val190Ala		79223149	Q8N906	Missense_Mutation	SNP	ENST00000286732.4	37	CCDS42068.1	.	.	.	.	.	.	.	.	.	.	T	7.460	0.644407	0.14451	.	.	ENSG00000156206	ENST00000286732;ENST00000398681	T	0.39997	1.05	4.98	2.62	0.31277	.	0.345440	0.27012	N	0.021376	T	0.17704	0.0425	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.26883	-1.0090	10	0.09590	T	0.72	-22.206	6.7872	0.23679	0.1401:0.0:0.3254:0.5344	.	190	Q6P656	CO026_HUMAN	A	190;165	ENSP00000286732:V190A	ENSP00000286732:V190A	V	+	2	0	C15orf26	79223149	0.844000	0.29557	0.863000	0.33907	0.023000	0.10783	1.427000	0.34881	0.230000	0.21059	-0.331000	0.08364	GTG		0.532	C15orf26-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417587.1	NM_173528		C	81436094	T	C	81436094	3	2	61	1	0	0	0	0	1	0	0	0	1791	1696	59	4	587	4	C15orf26	15	81436094	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	7226	81436094	21095298	9511	17496										
IL16	3603	broad.mit.edu	37	chr15	81558046	81558046	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgattttccaatgaccaaGaaatctgcagcgcccacgga	8	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81558046G>T	ENST00000302987.4	+	3	468	c.468G>T	c.(466-468)aaG>aaT	p.K156N	IL16_ENST00000394660.2_Missense_Mutation_p.K156N			Q14005	IL16_HUMAN	interleukin 16	156					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K156N(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CAATGACCAAGAAATCTGCAG	0.448											OREG0023362	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											69	64	66					15																	81558046		1911	4129	6040	79345101	SO:0001583	missense	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.468G>T	15.37:g.81558046G>T	ENSP00000302935:p.Lys156Asn	1207	79345101	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965403	0.34659	.	.	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000302987	T;T	0.11821	2.74;2.74	4.45	2.4	0.29515	.	0.314453	0.22608	N	0.057861	T	0.14056	0.0340	M	0.63428	1.95	0.80722	D	1	P;P	0.38504	0.501;0.634	B;B	0.39465	0.157;0.3	T	0.04870	-1.0921	10	0.27785	T	0.31	.	7.1703	0.25715	0.2827:0.0:0.7173:0.0	.	156;156	Q14005;Q14005-2	IL16_HUMAN;.	N	156	ENSP00000378155:K156N;ENSP00000302935:K156N	ENSP00000302935:K156N	K	+	3	2	IL16	79345101	1.000000	0.71417	0.034000	0.17996	0.026000	0.11368	2.537000	0.45702	1.083000	0.41159	0.650000	0.86243	AAG		0.448	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81558046	G	T	81558046	3	4	61	1	0	0	0	0	1	0	0	0	7654	933	33	2	478	2	IL16	15	81558046	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121952	81558046	20973346	9512	17497										
IL16	3603	broad.mit.edu	37	chr15	81575048	81575048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcatctctggcattttcGtccacacgctgtcaccagga	8	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81575048G>A	ENST00000302987.4	+	8	1150	c.1150G>A	c.(1150-1152)Gtc>Atc	p.V384I	IL16_ENST00000394660.2_Missense_Mutation_p.V384I			Q14005	IL16_HUMAN	interleukin 16	384	Interaction with GRIN2A.|PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V384I(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TGGCATTTTCGTCCACACGCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	15											171	180	177					15																	81575048		2148	4250	6398	79362103	SO:0001583	missense	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1150G>A	15.37:g.81575048G>A	ENSP00000302935:p.Val384Ile		79362103	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	1.405	-0.576966	0.03854	.	.	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000355368;ENST00000302987	T;T	0.18960	2.18;2.18	5.46	2.13	0.27403	PDZ/DHR/GLGF (3);	0.372399	0.19498	N	0.112817	T	0.05181	0.0138	N	0.01482	-0.84	0.80722	D	1	B;B	0.16396	0.01;0.017	B;B	0.10450	0.002;0.005	T	0.33394	-0.9870	10	0.02654	T	1	.	5.5128	0.16890	0.5631:0.0:0.4369:0.0	.	384;384	Q14005;Q14005-2	IL16_HUMAN;.	I	384;384;216;384	ENSP00000378155:V384I;ENSP00000302935:V384I	ENSP00000302935:V384I	V	+	1	0	IL16	79362103	1.000000	0.71417	0.042000	0.18584	0.412000	0.31113	2.464000	0.45067	0.652000	0.30806	0.591000	0.81541	GTC		0.597	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		A	81575048	G	A	81575048	3	1	61	1	0	0	0	0	1	0	0	0	7654	1145	40	1	1180	1	IL16	15	81575048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17002	81575048	20956344	9513	17498										
IL16	3603	broad.mit.edu	37	chr15	81589321	81589321	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggaagacacagcagggaGaagccctagtgcctctgccg	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81589321G>T	ENST00000302987.4	+	12	1955	c.1955G>T	c.(1954-1956)aGa>aTa	p.R652I	IL16_ENST00000394660.2_Missense_Mutation_p.R652I|IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_5'UTR			Q14005	IL16_HUMAN	interleukin 16	652					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R606I(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						ACAGCAGGGAGAAGCCCTAGT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	15											36	41	39					15																	81589321		1969	4161	6130	79376376	SO:0001583	missense	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1955G>T	15.37:g.81589321G>T	ENSP00000302935:p.Arg652Ile		79376376	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.241850	0.22796	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653	T;T	0.11821	2.74;2.74	4.7	-0.657	0.11432	.	0.468638	0.18179	N	0.149184	T	0.12561	0.0305	M	0.65975	2.015	0.21105	N	0.999786	P;B;B;B;B	0.39964	0.697;0.001;0.002;0.379;0.231	B;B;B;B;B	0.36030	0.216;0.001;0.002;0.157;0.146	T	0.12192	-1.0557	10	0.51188	T	0.08	.	7.0608	0.25125	0.0:0.3762:0.3247:0.2991	.	146;189;42;652;652	Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;IL16_HUMAN;.	I	652;484;652;189;42	ENSP00000378155:R652I;ENSP00000302935:R652I	ENSP00000302935:R652I	R	+	2	0	IL16	79376376	0.977000	0.34250	0.032000	0.17829	0.005000	0.04900	1.661000	0.37408	0.104000	0.17725	-0.165000	0.13383	AGA		0.607	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81589321	G	T	81589321	3	4	61	1	0	0	0	0	1	0	0	0	7654	942	33	2	2001	2	IL16	15	81589321	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14273	81589321	20942071	9514	17499										
IL16	3603	broad.mit.edu	37	chr15	81592202	81592202	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaggcagagaatcagctcCtttgaaacctttggctcctc	8	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81592202C>A	ENST00000302987.4	+	13	2535	c.2535C>A	c.(2533-2535)tcC>tcA	p.S845S	IL16_ENST00000394660.2_Silent_p.S845S|IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_Silent_p.S144S			Q14005	IL16_HUMAN	interleukin 16	845					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S799S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GAATCAGCTCCTTTGAAACCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	15											28	28	28					15																	81592202		2203	4299	6502	79379257	SO:0001819	synonymous_variant	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2535C>A	15.37:g.81592202C>A			79379257	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																				0.592	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		A	81592202	C	A	81592202	2	1	61	1	0	0	0	0	0	0	0	1	7654	668	24	2		2	IL16	15	81592202	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2881	81592202	20939190	9515	17500										
IL16	3603	broad.mit.edu	37	chr15	81598384	81598384	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccatcctccgccaagctCgagagcccaggcaagctgtg	12	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:81598384C>T	ENST00000302987.4	+	16	3556	c.3556C>T	c.(3556-3558)Cga>Tga	p.R1186*	RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Nonsense_Mutation_p.R1186*|IL16_ENST00000394652.2_Nonsense_Mutation_p.R485*			Q14005	IL16_HUMAN	interleukin 16	1186	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1140*(2)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CCGCCAAGCTCGAGAGCCCAG	0.577																																																2	Substitution - Nonsense(2)	large_intestine(1)|breast(1)	15											132	134	133					15																	81598384		2203	4300	6503	79385439	SO:0001587	stop_gained	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3556C>T	15.37:g.81598384C>T	ENSP00000302935:p.Arg1186*		79385439	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Nonsense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945330	0.73672	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000394653;ENST00000394652;ENST00000394656	.	.	.	4.64	2.62	0.31277	.	0.000000	0.41938	D	0.000800	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3392	0.60535	0.2862:0.7138:0.0:0.0	.	.	.	.	X	1186;1018;1186;576;485;485	.	ENSP00000302935:R1186X	R	+	1	2	IL16	79385439	1.000000	0.71417	0.688000	0.30117	0.000000	0.00434	2.594000	0.46189	1.136000	0.42199	-0.182000	0.12963	CGA		0.577	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81598384	C	T	81598384	4	4	61	1	0	0	0	0	0	1	0	0	7654	876	31	1	3618	1	IL16	15	81598384	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6182	81598384	20933008	9516	17501										
MEX3B	84206	broad.mit.edu	37	chr15	82335531	82335531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcggatggcctgagtgacCgcggtgtggcagaccgggca	18	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:82335531C>T	ENST00000329713.4	-	2	2115	c.1680G>A	c.(1678-1680)gcG>gcA	p.A560A	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	560					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A560A(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CCTGAGTGACCGCGGTGTGGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	15											39	41	40					15																	82335531		2203	4300	6503	80122586	SO:0001819	synonymous_variant	84206			AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.1680G>A	15.37:g.82335531C>T			80122586	Q4G0W1|Q8IVG2|Q9H0J0	Silent	SNP	ENST00000329713.4	37	CCDS10319.1																																																																																				0.647	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		T	82335531	C	T	82335531	2	4	61	1	0	0	0	0	0	0	0	1	9540	639	23	1		1	MEX3B	15	82335531	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	737147	82335531	20195861	9517	17502										
MEX3B	84206	broad.mit.edu	37	chr15	82336595	82336595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctggcatgccggtcacctCgaacaccggctccttatccc	8	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:82336595C>T	ENST00000329713.4	-	2	1051	c.616G>A	c.(616-618)Gag>Aag	p.E206K	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	206	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E206K(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CCGGTCACCTCGAACACCGGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	15											134	126	129					15																	82336595		2203	4300	6503	80123650	SO:0001583	missense	84206			AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.616G>A	15.37:g.82336595C>T	ENSP00000329918:p.Glu206Lys		80123650	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	37	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	C	35	5.561935	0.96527	.	.	ENSG00000183496	ENST00000329713	T	0.32272	1.46	4.88	4.88	0.63580	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.56978	0.2022	M	0.77616	2.38	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.61441	-0.7062	10	0.62326	D	0.03	-31.6479	16.946	0.86230	0.0:1.0:0.0:0.0	.	206	Q6ZN04	MEX3B_HUMAN	K	206	ENSP00000329918:E206K	ENSP00000329918:E206K	E	-	1	0	MEX3B	80123650	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.355000	0.79434	2.526000	0.85167	0.655000	0.94253	GAG		0.622	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		T	82336595	C	T	82336595	3	4	61	1	0	0	0	0	1	0	0	0	9540	893	31	1	1097	1	MEX3B	15	82336595	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1064	82336595	20194797	9518	17503										
FAM154B	283726	broad.mit.edu	37	chr15	82564057	82564057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaaacgggatttgaattCgtataaagtgcagcctgtgg	11	7	0	1	rs138112776	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:82564057C>T	ENST00000339465.5	+	2	236	c.167C>T	c.(166-168)tCg>tTg	p.S56L	FAM154B_ENST00000565432.1_Missense_Mutation_p.S69L|FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Missense_Mutation_p.S41L	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	56								p.S56L(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						GATTTGAATTCGTATAAAGTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15						C	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	91	82	85		167	4	0.5	15	dbSNP_134	85	0,8600		0,0,4300	yes	missense	FAM154B	NM_001008226.1	145	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign	56/399	82564057	5,13001	2203	4300	6503	80351112	SO:0001583	missense	283726			AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.167C>T	15.37:g.82564057C>T	ENSP00000340445:p.Ser56Leu		80351112	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.230547	0.39399	0.001135	0.0	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.18657	2.2;2.2	4.98	4.04	0.47022	.	0.504726	0.18593	N	0.136673	T	0.20941	0.0504	M	0.61703	1.905	0.21841	N	0.99951	B;B	0.34255	0.445;0.08	B;B	0.28709	0.093;0.036	T	0.11275	-1.0594	10	0.27082	T	0.32	-0.8298	13.9161	0.63899	0.0:0.9205:0.0:0.0795	.	41;56	B4E2M2;Q658L1	.;F154B_HUMAN	L	56;41	ENSP00000340445:S56L;ENSP00000403743:S41L	ENSP00000340445:S56L	S	+	2	0	FAM154B	80351112	0.934000	0.31675	0.526000	0.27913	0.287000	0.27160	1.814000	0.38972	2.481000	0.83766	0.591000	0.81541	TCG		0.403	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		T	82564057	C	T	82564057	3	4	61	1	0	0	0	0	1	0	0	0	5480	893	31	1	173	1	FAM154B	15	82564057	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	227462	82564057	19967335	9519	17504										
CPEB1	64506	broad.mit.edu	37	chr15	83215979	83215979	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggttattgaaagtcacacGaccagaacctaggacaacag	9	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83215979G>T	ENST00000562019.1	-	10	1739	c.1423C>A	c.(1423-1425)Cgt>Agt	p.R475S	CPEB1_ENST00000398592.2_Missense_Mutation_p.R244S|CPEB1_ENST00000423133.2_Missense_Mutation_p.R395S|CPEB1_ENST00000564522.1_Missense_Mutation_p.R395S|CPEB1_ENST00000568128.1_Missense_Mutation_p.R470S|CPEB1_ENST00000450751.2_Missense_Mutation_p.R395S|CPEB1_ENST00000563800.1_Missense_Mutation_p.R497S|RP11-152F13.10_ENST00000562833.1_Silent_p.V204V|RP11-379H8.1_ENST00000568285.1_Intron|CPEB1_ENST00000568757.1_Missense_Mutation_p.R395S|CPEB1_ENST00000261723.6_Missense_Mutation_p.R473S|CPEB1_ENST00000398591.2_Missense_Mutation_p.R400S			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	475	Necessary for stress granule assembly and correct localization in dcp1 bodies.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.R400S(1)		breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			AAAGTCACACGACCAGAACCT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	15											69	66	67					15																	83215979		1897	4133	6030	81013034	SO:0001583	missense	64506			AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.1423C>A	15.37:g.83215979G>T	ENSP00000457836:p.Arg475Ser		81013034	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Missense_Mutation	SNP	ENST00000562019.1	37		.	.	.	.	.	.	.	.	.	.	g	24.9	4.585796	0.86748	.	.	ENSG00000214575	ENST00000450751;ENST00000398593;ENST00000423133;ENST00000398591;ENST00000261723;ENST00000398592	T;T;T;T	0.05855	3.38;3.38;3.38;3.38	5.18	4.2	0.49525	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	U	0.000000	T	0.31857	0.0810	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.995;0.998	T	0.32241	-0.9914	10	0.87932	D	0	-8.6322	14.7937	0.69863	0.0:0.0:0.8552:0.1448	.	473;470;475;470	B7Z237;Q9BZB8-3;Q9BZB8;E7ET70	.;.;CPEB1_HUMAN;.	S	470;470;395;400;473;244	ENSP00000397526:R395S;ENSP00000381591:R400S;ENSP00000261723:R473S;ENSP00000381592:R244S	ENSP00000261723:R473S	R	-	1	0	CPEB1	81013034	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.240000	0.72363	2.569000	0.86673	0.591000	0.81541	CGT		0.413	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594		T	83215979	G	T	83215979	3	4	61	1	0	0	0	0	1	0	0	0	3806	1058	37	2	289	2	CPEB1	15	83215979	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	651922	83215979	19315413	9520	17505										
CPEB1	64506	broad.mit.edu	37	chr15	83224787	83224787	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgctcttggtccatccgaGaccctacccccatctttaaa	5	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83224787G>T	ENST00000562019.1	-	5	1008	c.692C>A	c.(691-693)tCt>tAt	p.S231Y	CPEB1_ENST00000398592.2_Missense_Mutation_p.S5Y|CPEB1_ENST00000423133.2_Missense_Mutation_p.S156Y|CPEB1_ENST00000564522.1_Missense_Mutation_p.S156Y|CPEB1_ENST00000568128.1_Missense_Mutation_p.S231Y|CPEB1_ENST00000450751.2_Missense_Mutation_p.S156Y|CPEB1_ENST00000563800.1_Missense_Mutation_p.S258Y|RP11-152F13.10_ENST00000562833.1_5'Flank|RP11-379H8.1_ENST00000568285.1_Intron|CPEB1_ENST00000568757.1_Missense_Mutation_p.S156Y|CPEB1_ENST00000261723.6_Missense_Mutation_p.S234Y|CPEB1_ENST00000398591.2_Missense_Mutation_p.S156Y			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	231					cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.S156Y(1)		breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			GTCCATCCGAGACCCTACCCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	15											38	38	38					15																	83224787		1919	4126	6045	81021842	SO:0001583	missense	64506			AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.692C>A	15.37:g.83224787G>T	ENSP00000457836:p.Ser231Tyr		81021842	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Missense_Mutation	SNP	ENST00000562019.1	37		.	.	.	.	.	.	.	.	.	.	G	26.5	4.742988	0.89573	.	.	ENSG00000214575	ENST00000450751;ENST00000398593;ENST00000423133;ENST00000398591;ENST00000261723;ENST00000398592	T;T;T	0.10288	2.89;2.89;2.89	5.81	5.81	0.92471	.	0.144107	0.48286	U	0.000190	T	0.26048	0.0635	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.993;0.998	D;D;P;D	0.67548	0.93;0.952;0.884;0.93	T	0.00229	-1.1898	10	0.66056	D	0.02	-14.5838	20.0736	0.97735	0.0:0.0:1.0:0.0	.	234;231;231;231	B7Z237;Q9BZB8-3;Q9BZB8;E7ET70	.;.;CPEB1_HUMAN;.	Y	231;231;156;156;234;5	ENSP00000397526:S156Y;ENSP00000381591:S156Y;ENSP00000261723:S234Y	ENSP00000261723:S234Y	S	-	2	0	CPEB1	81021842	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.155000	0.77445	2.748000	0.94277	0.655000	0.94253	TCT		0.572	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594		T	83224787	G	T	83224787	3	4	61	1	0	0	0	0	1	0	0	0	3806	942	33	2	1040	2	CPEB1	15	83224787	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8808	83224787	19306605	9521	17506										
CPEB1	64506	broad.mit.edu	37	chr15	83240163	83240163	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtcggtcccagcctgtcaGactgagggactgcaggccaa	15	12	1	2	rs373592605		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83240163G>T	ENST00000562019.1	-	3	626	c.310C>A	c.(310-312)Ctg>Atg	p.L104M	CPEB1_ENST00000261723.6_Missense_Mutation_p.L107M|CPEB1_ENST00000568128.1_Missense_Mutation_p.L104M|CPEB1_ENST00000564522.1_Missense_Mutation_p.L29M|CPEB1_ENST00000568757.1_Missense_Mutation_p.L29M|CPEB1_ENST00000450751.2_Missense_Mutation_p.L29M|CPEB1_ENST00000398592.2_De_novo_Start_OutOfFrame|CPEB1_ENST00000563800.1_Missense_Mutation_p.L131M|CPEB1_ENST00000398591.2_Missense_Mutation_p.L29M|CPEB1_ENST00000423133.2_Missense_Mutation_p.L29M			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	104					cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.L29M(1)		breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			CAGCCTGTCAGACTGAGGGAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	15											113	116	115					15																	83240163		1989	4179	6168	81037218	SO:0001583	missense	64506			AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.310C>A	15.37:g.83240163G>T	ENSP00000457836:p.Leu104Met		81037218	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Missense_Mutation	SNP	ENST00000562019.1	37		.	.	.	.	.	.	.	.	.	.	G	19.07	3.756682	0.69648	.	.	ENSG00000214575	ENST00000450751;ENST00000398593;ENST00000423133;ENST00000398591;ENST00000261723	.	.	.	5.71	4.61	0.57282	.	0.000000	0.64402	U	0.000003	T	0.65801	0.2726	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.998;0.998	T	0.69206	-0.5206	9	0.87932	D	0	-8.2695	15.583	0.76459	0.0769:0.0:0.9231:0.0	.	107;104;104;104	B7Z237;Q9BZB8-3;Q9BZB8;E7ET70	.;.;CPEB1_HUMAN;.	M	104;104;29;29;107	.	ENSP00000261723:L107M	L	-	1	2	CPEB1	81037218	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.233000	0.65337	2.694000	0.91930	0.557000	0.71058	CTG		0.572	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594		T	83240163	G	T	83240163	3	4	61	1	0	0	0	0	1	0	0	0	3806	933	33	2	1430	2	CPEB1	15	83240163	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15376	83240163	19291229	9522	17507										
FSD2	123722	broad.mit.edu	37	chr15	83455609	83455609	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttacaagtgacacagaaGacatcagcagcttcttcttc	7	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83455609G>T	ENST00000334574.8	-	2	715	c.534C>A	c.(532-534)gtC>gtA	p.V178V	FSD2_ENST00000541889.1_Silent_p.V178V			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	178								p.V178V(1)		breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TGACACAGAAGACATCAGCAG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	15											141	141	141					15																	83455609		2016	4174	6190	81252663	SO:0001819	synonymous_variant	123722			AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.534C>A	15.37:g.83455609G>T			81252663	B3KVG1|B7ZM02	Silent	SNP	ENST00000334574.8	37	CCDS45332.1																																																																																				0.468	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		T	83455609	G	T	83455609	2	4	61	1	0	0	0	0	0	0	0	1	6090	929	33	2		2	FSD2	15	83455609	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215446	83455609	19075783	9523	17508										
BNC1	646	broad.mit.edu	37	chr15	83932029	83932029	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggttccatcccaggtgtGaagtagtgttcatggccacc	13	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83932029G>T	ENST00000345382.2	-	4	2059	c.1974C>A	c.(1972-1974)ttC>ttA	p.F658L	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.F651L	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	658					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F658L(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						TCCCAGGTGTGAAGTAGTGTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	15											102	102	102					15																	83932029		2203	4300	6503	81723033	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1974C>A	15.37:g.83932029G>T	ENSP00000307041:p.Phe658Leu		81723033	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182777	0.01620	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.38887	1.11	4.79	0.0832	0.14432	.	0.582709	0.17372	N	0.176656	T	0.10035	0.0246	N	0.01109	-1.01	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25467	-1.0131	10	0.09590	T	0.72	-18.2689	1.8353	0.03138	0.2731:0.1095:0.4469:0.1705	.	651;658	F5GY04;Q01954	.;BNC1_HUMAN	L	658;651	ENSP00000307041:F658L	ENSP00000307041:F658L	F	-	3	2	BNC1	81723033	0.004000	0.15560	0.036000	0.18154	0.197000	0.23852	0.239000	0.18023	0.174000	0.19809	-0.345000	0.07892	TTC		0.547	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		T	83932029	G	T	83932029	3	4	61	1	0	0	0	0	1	0	0	0	1475	1281	45	2	1018	2	BNC1	15	83932029	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	476420	83932029	18599363	9524	17509										
BNC1	646	broad.mit.edu	37	chr15	83932836	83932836	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaccatgttacacccttcGatggtgcacttatgcttgat	7	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:83932836G>A	ENST00000345382.2	-	4	1252	c.1167C>T	c.(1165-1167)atC>atT	p.I389I	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Silent_p.I382I	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	389					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I389I(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						TACACCCTTCGATGGTGCACT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15											143	129	134					15																	83932836		2203	4300	6503	81723840	SO:0001819	synonymous_variant	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1167C>T	15.37:g.83932836G>A			81723840	Q15840	Silent	SNP	ENST00000345382.2	37	CCDS10324.1																																																																																				0.517	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83932836	G	A	83932836	2	1	61	1	0	0	0	0	0	0	0	1	1475	1048	37	1		1	BNC1	15	83932836	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	807	83932836	18598556	9525	17510										
SH3GL3	6457	broad.mit.edu	37	chr15	84241376	84241376	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgaggtgaaagactctCttgatattaatgtaaagcaa	10	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:84241376C>A	ENST00000427482.2	+	5	697	c.391C>A	c.(391-393)Ctt>Att	p.L131I	SH3GL3_ENST00000434347.1_Missense_Mutation_p.L139I|SH3GL3_ENST00000324537.5_Missense_Mutation_p.L139I|SH3GL3_ENST00000535412.1_Missense_Mutation_p.L131I	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	131	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.L139I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						GAAAGACTCTCTTGATATTAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	15											113	100	105					15																	84241376		2203	4300	6503	82032380	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.391C>A	15.37:g.84241376C>A	ENSP00000391372:p.Leu131Ile		82032380	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.272910	0.80580	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.45	4.53	0.55603	BAR (3);	0.136528	0.51477	D	0.000089	D	0.83963	0.5368	M	0.89601	3.045	0.58432	D	0.999999	D;D;D	0.69078	0.98;0.997;0.981	D;D;D	0.79108	0.918;0.992;0.977	D	0.87255	0.2275	10	0.72032	D	0.01	-2.8088	13.6159	0.62108	0.0:0.9251:0.0:0.0749	.	131;131;139	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	I	131;131;139;139	ENSP00000391372:L131I;ENSP00000439239:L131I;ENSP00000320092:L139I;ENSP00000397871:L139I	ENSP00000320092:L139I	L	+	1	0	SH3GL3	82032380	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.471000	0.60182	1.433000	0.47394	0.585000	0.79938	CTT		0.338	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		A	84241376	C	A	84241376	3	1	61	1	0	0	0	0	1	0	0	0	14289	913	32	2	409	2	SH3GL3	15	84241376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308540	84241376	18290016	9526	17511										
SH3GL3	6457	broad.mit.edu	37	chr15	84286958	84286958	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaatcaaatagatgaaaaCtggtatgaaggaatgataca	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:84286958C>A	ENST00000427482.2	+	9	1269	c.963C>A	c.(961-963)aaC>aaA	p.N321K	SH3GL3_ENST00000564054.1_3'UTR|AC087738.1_ENST00000411248.1_RNA|SH3GL3_ENST00000434347.1_Missense_Mutation_p.N329K|SH3GL3_ENST00000324537.5_Missense_Mutation_p.N329K|SH3GL3_ENST00000535412.1_3'UTR	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	321	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.N329K(1)		central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						TAGATGAAAACTGGTATGAAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											114	106	109					15																	84286958		2203	4300	6503	82077962	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.963C>A	15.37:g.84286958C>A	ENSP00000391372:p.Asn321Lys		82077962	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	C	19.02	3.745372	0.69418	.	.	ENSG00000140600	ENST00000427482;ENST00000324537;ENST00000434347	T;T;T	0.31510	1.49;1.49;1.49	5.54	1.58	0.23477	Src homology-3 domain (5);	0.170294	0.64402	N	0.000007	T	0.50905	0.1643	M	0.92784	3.345	0.58432	D	0.999996	P;P	0.50066	0.868;0.931	P;B	0.52758	0.708;0.396	T	0.56402	-0.7985	10	0.87932	D	0	-37.5799	8.2432	0.31673	0.0:0.5914:0.0:0.4086	.	321;329	Q99963;Q99963-3	SH3G3_HUMAN;.	K	321;329;329	ENSP00000391372:N321K;ENSP00000320092:N329K;ENSP00000397871:N329K	ENSP00000320092:N329K	N	+	3	2	SH3GL3	82077962	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.501000	0.22578	0.300000	0.22699	0.563000	0.77884	AAC		0.403	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		A	84286958	C	A	84286958	3	1	61	1	0	0	0	0	1	0	0	0	14289	564	20	2	997	2	SH3GL3	15	84286958	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45582	84286958	18244434	9527	17512										
ADAMTSL3	57188	broad.mit.edu	37	chr15	84539657	84539657	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaatttcagaggggctcCgagaggcaaacttttaagat	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:84539657C>T	ENST00000286744.5	+	9	1130	c.906C>T	c.(904-906)tcC>tcT	p.S302S	ADAMTSL3_ENST00000567476.1_Silent_p.S302S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	302						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S302S(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGAGGGGCTCCGAGAGGCAAA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	15											75	81	79					15																	84539657		2203	4300	6503	82330661	SO:0001819	synonymous_variant	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.906C>T	15.37:g.84539657C>T			82330661	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																				0.438	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84539657	C	T	84539657	2	4	61	1	0	0	0	0	0	0	0	1	276	639	23	1		1	ADAMTSL3	15	84539657	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252699	84539657	17991735	9528	17513										
ADAMTSL3	57188	broad.mit.edu	37	chr15	84651189	84651189	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattattaagtgccccgtgCgacgattccagaaatctctg	9	10	1	2	rs370313572		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:84651189C>T	ENST00000286744.5	+	21	3033	c.2809C>T	c.(2809-2811)Cga>Tga	p.R937*	ADAMTSL3_ENST00000567476.1_Nonsense_Mutation_p.R937*	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	937	Ig-like C2-type 1.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R937*(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GTGCCCCGTGCGACGATTCCA	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	15						C	stop/ARG	0,4406		0,0,2203	145	135	138		2809	2.9	0.9	15		138	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	ADAMTSL3	NM_207517.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		937/1692	84651189	1,13005	2203	4300	6503	82442193	SO:0001587	stop_gained	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2809C>T	15.37:g.84651189C>T	ENSP00000286744:p.Arg937*		82442193	A1A566|A1A567|Q9ULI7	Nonsense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	40	8.117786	0.98662	0.0	1.16E-4	ENSG00000156218	ENST00000286744	.	.	.	5.05	2.87	0.33458	.	0.000000	0.36066	N	0.002814	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9764	0.71277	0.2712:0.7288:0.0:0.0	.	.	.	.	X	937	.	ENSP00000286744:R937X	R	+	1	2	ADAMTSL3	82442193	0.503000	0.26115	0.918000	0.36340	0.971000	0.66376	0.578000	0.23773	1.073000	0.40885	0.563000	0.77884	CGA		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84651189	C	T	84651189	4	4	61	1	0	0	0	0	0	1	0	0	276	760	27	1	2887	1	ADAMTSL3	15	84651189	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111532	84651189	17880203	9529	17514										
ZSCAN2	54993	broad.mit.edu	37	chr15	85165259	85165259	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagaactcacatgaaagaGaaactttattgaagtggcaa	9	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85165259G>T	ENST00000448803.2	+	3	2125	c.1833G>T	c.(1831-1833)gaG>gaT	p.E611D	ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000327179.6_Missense_Mutation_p.E610D|ZSCAN2_ENST00000358472.3_Missense_Mutation_p.E461D|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000546148.1_Missense_Mutation_p.E611D|ZSCAN2_ENST00000485222.2_Intron	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	611					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E611D(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		ACATGAAAGAGAAACTTTATT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											51	56	55					15																	85165259		2203	4299	6502	82966263	SO:0001583	missense	54993			BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"-", "Zinc fingers, C2H2-type"	20994	protein-coding gene	gene with protein product			"zinc finger protein 29"	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1833G>T	15.37:g.85165259G>T	ENSP00000410198:p.Glu611Asp		82966263	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	37	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030999	0.35797	.	.	ENSG00000176371	ENST00000448803;ENST00000546148;ENST00000358472;ENST00000327179;ENST00000379353	T;T;T;T	0.07114	3.23;3.23;3.22;3.22	5.04	1.9	0.25705	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.390352	0.22115	N	0.064432	T	0.14056	0.0340	M	0.77486	2.375	0.80722	D	1	P;B	0.45396	0.857;0.0	P;B	0.46076	0.503;0.0	T	0.02385	-1.1167	9	.	.	.	-16.5951	8.0913	0.30803	0.0871:0.3024:0.6105:0.0	.	611;611	A8K5A9;Q7Z7L9	.;ZSCA2_HUMAN	D	611;611;461;610;592	ENSP00000410198:E611D;ENSP00000445451:E611D;ENSP00000351257:E461D;ENSP00000325123:E610D	.	E	+	3	2	ZSCAN2	82966263	0.768000	0.28519	0.997000	0.53966	0.976000	0.68499	0.030000	0.13688	0.512000	0.28257	0.655000	0.94253	GAG		0.488	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		T	85165259	G	T	85165259	3	4	61	1	0	0	0	0	1	0	0	0	18270	933	33	2	1929	2	ZSCAN2	15	85165259	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	514070	85165259	17366133	9530	17515										
ZNF592	9640	broad.mit.edu	37	chr15	85326329	85326329	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacccaccttcaaccagttCagtccaatctccagcccaga	4	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85326329C>A	ENST00000560079.2	+	4	711	c.423C>A	c.(421-423)ttC>ttA	p.F141L	ZNF592_ENST00000299927.3_Missense_Mutation_p.F141L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	141					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F141L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TCAACCAGTTCAGTCCAATCT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	15											110	117	115					15																	85326329		2203	4299	6502	83127333	SO:0001583	missense	9640			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.423C>A	15.37:g.85326329C>A	ENSP00000452877:p.Phe141Leu		83127333	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181095	0.57800	.	.	ENSG00000166716	ENST00000299927	T	0.00882	5.58	6.06	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.03348	0.0097	L	0.52573	1.65	0.46798	D	0.999207	D	0.89917	1.0	D	0.85130	0.997	T	0.50642	-0.8804	10	0.87932	D	0	-23.9264	9.8941	0.41306	0.0:0.8271:0.0:0.1729	.	141	Q92610	ZN592_HUMAN	L	141	ENSP00000299927:F141L	ENSP00000299927:F141L	F	+	3	2	ZNF592	83127333	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.706000	0.25690	0.837000	0.34925	-0.140000	0.14226	TTC		0.483	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		A	85326329	C	A	85326329	3	1	61	1	0	0	0	0	1	0	0	0	18061	825	29	2	425	2	ZNF592	15	85326329	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161070	85326329	17205063	9531	17516										
ZNF592	9640	broad.mit.edu	37	chr15	85328041	85328041	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcatccggtactcaatcaAgtgtcttgaatgtcacaagc	8	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85328041A>C	ENST00000560079.2	+	4	2423	c.2135A>C	c.(2134-2136)aAg>aCg	p.K712T	ZNF592_ENST00000299927.3_Missense_Mutation_p.K712T	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	712					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K712T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TACTCAATCAAGTGTCTTGAA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15											83	77	79					15																	85328041		2203	4299	6502	83129045	SO:0001583	missense	9640			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2135A>C	15.37:g.85328041A>C	ENSP00000452877:p.Lys712Thr		83129045	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946764	0.73672	.	.	ENSG00000166716	ENST00000299927	T	0.36340	1.26	6.07	6.07	0.98685	Zinc finger, C2H2-like (1);	0.275847	0.41097	D	0.000952	T	0.37705	0.1013	L	0.41415	1.275	0.40625	D	0.981803	P	0.41188	0.741	B	0.43658	0.426	T	0.30650	-0.9971	10	0.87932	D	0	-17.8611	14.5927	0.68378	1.0:0.0:0.0:0.0	.	712	Q92610	ZN592_HUMAN	T	712	ENSP00000299927:K712T	ENSP00000299927:K712T	K	+	2	0	ZNF592	83129045	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.714000	0.61902	2.326000	0.78906	0.533000	0.62120	AAG		0.567	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		C	85328041	A	C	85328041	3	2	61	1	0	0	0	0	1	0	0	0	18061	72	3	4	2137	4	ZNF592	15	85328041	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1712	85328041	17203351	9532	17517										
ALPK3	57538	broad.mit.edu	37	chr15	85382262	85382262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgatacggagctggaccGctactgtggcttgccaaaat	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85382262G>A	ENST00000258888.5	+	4	1129	c.962G>A	c.(961-963)cGc>cAc	p.R321H		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	321	Ig-like 1.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R321H(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GAGCTGGACCGCTACTGTGGC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											61	51	54					15																	85382262		2203	4299	6502	83183266	SO:0001583	missense	57538			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.962G>A	15.37:g.85382262G>A	ENSP00000258888:p.Arg321His		83183266	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.858119	0.91433	.	.	ENSG00000136383	ENST00000258888	T	0.67345	-0.26	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	L	0.54323	1.7	0.48185	D	0.999607	D	0.89917	1.0	D	0.97110	1.0	T	0.80289	-0.1445	10	0.66056	D	0.02	-15.8636	15.5548	0.76184	0.0:0.0:1.0:0.0	.	321	Q96L96	ALPK3_HUMAN	H	321	ENSP00000258888:R321H	ENSP00000258888:R321H	R	+	2	0	ALPK3	83183266	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.332000	0.96446	2.266000	0.75297	0.491000	0.48974	CGC		0.532	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85382262	G	A	85382262	3	1	61	1	0	0	0	0	1	0	0	0	546	1087	38	1	976	1	ALPK3	15	85382262	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54221	85382262	17149130	9533	17518										
ALPK3	57538	broad.mit.edu	37	chr15	85384009	85384009	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgacagcaagcccatttCttctctgagtcaagctccag	7	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85384009C>A	ENST00000258888.5	+	5	2272	c.2105C>A	c.(2104-2106)tCt>tAt	p.S702Y		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	702					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S702Y(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AAGCCCATTTCTTCTCTGAGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											47	47	47					15																	85384009		2203	4299	6502	83185013	SO:0001583	missense	57538			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.2105C>A	15.37:g.85384009C>A	ENSP00000258888:p.Ser702Tyr		83185013	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835415	0.50951	.	.	ENSG00000136383	ENST00000258888	T	0.61158	0.13	5.23	4.31	0.51392	.	1.817510	0.03327	U	0.192825	T	0.61813	0.2377	N	0.24115	0.695	0.09310	N	1	D	0.58970	0.984	P	0.57371	0.819	T	0.55256	-0.8169	10	0.51188	T	0.08	-7.8859	10.1274	0.42658	0.0:0.9052:0.0:0.0948	.	702	Q96L96	ALPK3_HUMAN	Y	702	ENSP00000258888:S702Y	ENSP00000258888:S702Y	S	+	2	0	ALPK3	83185013	0.001000	0.12720	0.008000	0.14137	0.017000	0.09413	1.304000	0.33482	2.444000	0.82710	0.557000	0.71058	TCT		0.602	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85384009	C	A	85384009	3	1	61	1	0	0	0	0	1	0	0	0	546	913	32	2	2123	2	ALPK3	15	85384009	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1747	85384009	17147383	9534	17519										
SLC28A1	9154	broad.mit.edu	37	chr15	85433735	85433735	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagcacatgcagctgtttCgatggatcggcacaggcctg	15	10	0	0	rs564042221		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:85433735C>T	ENST00000286749.3	+	4	337	c.247C>T	c.(247-249)Cga>Tga	p.R83*	SLC28A1_ENST00000537624.1_Nonsense_Mutation_p.R83*|SLC28A1_ENST00000538177.1_Nonsense_Mutation_p.R83*|SLC28A1_ENST00000537216.1_Nonsense_Mutation_p.R83*|SLC28A1_ENST00000537703.1_Nonsense_Mutation_p.R5*|SLC28A1_ENST00000338602.2_Nonsense_Mutation_p.R83*|SLC28A1_ENST00000394573.1_Nonsense_Mutation_p.R83*			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	83					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.R83*(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GCAGCTGTTTCGATGGATCGG	0.602																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											59	48	52					15																	85433735		2203	4299	6502	83234739	SO:0001587	stop_gained	9154			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.247C>T	15.37:g.85433735C>T	ENSP00000286749:p.Arg83*		83234739	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Nonsense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	C	36	5.922442	0.97105	.	.	ENSG00000156222	ENST00000338602;ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	.	.	.	4.29	1.1	0.20463	.	0.548689	0.18135	N	0.150601	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-5.7617	6.1816	0.20474	0.3669:0.4389:0.1942:0.0	.	.	.	.	X	83;83;83;83;83;83;5	.	ENSP00000286749:R83X	R	+	1	2	SLC28A1	83234739	0.000000	0.05858	0.003000	0.11579	0.153000	0.21895	0.083000	0.14871	0.054000	0.16065	0.563000	0.77884	CGA		0.602	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85433735	C	T	85433735	4	4	61	1	0	0	0	0	0	1	0	0	14568	876	31	1	257	1	SLC28A1	15	85433735	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49726	85433735	17097657	9535	17520										
AKAP13	11214	broad.mit.edu	37	chr15	86236540	86236540	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaagataagattaaggaGaaggagaaagattctaaaga	11	1	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:86236540G>T	ENST00000394518.2	+	17	5417	c.5322G>T	c.(5320-5322)gaG>gaT	p.E1774D	AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Missense_Mutation_p.E19D|AKAP13_ENST00000361243.2_Missense_Mutation_p.E1778D	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1774					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.E1778D(1)		NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						agattaaggagaaggagaaag	0.423																																					Melanoma(94;603 1453 3280 32295 32951)											1	Substitution - Missense(1)	large_intestine(1)	15											100	104	103					15																	86236540		2202	4299	6501	84037544	SO:0001583	missense	11214			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.5322G>T	15.37:g.86236540G>T	ENSP00000378026:p.Glu1774Asp		84037544	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.785498	0.49997	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.26373	2.81;2.82;1.74	5.65	3.77	0.43336	.	.	.	.	.	T	0.31606	0.0802	N	0.21194	0.64	0.32464	N	0.543764	D;D;D	0.76494	0.99;0.999;0.999	D;D;D	0.80764	0.98;0.987;0.994	T	0.28776	-1.0033	9	0.30854	T	0.27	.	8.1046	0.30879	0.2495:0.0:0.7505:0.0	.	1756;1774;1778	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	D	1778;1774;1777;1755;19	ENSP00000354718:E1778D;ENSP00000378026:E1774D;ENSP00000378018:E19D	ENSP00000354718:E1778D	E	+	3	2	AKAP13	84037544	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.258000	0.32944	0.723000	0.32274	0.655000	0.94253	GAG		0.423	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86236540	G	T	86236540	3	4	61	1	0	0	0	0	1	0	0	0	449	933	33	2	5454	2	AKAP13	15	86236540	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	802805	86236540	16294852	9536	17521										
AKAP13	11214	broad.mit.edu	37	chr15	86270342	86270342	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagaagctgattgtgagaGaagtggcacatgaggagaaa	14	3	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:86270342G>T	ENST00000394518.2	+	28	6963	c.6868G>T	c.(6868-6870)Gaa>Taa	p.E2290*	AKAP13_ENST00000560579.1_3'UTR|RP11-158M2.2_ENST00000561417.1_RNA|AKAP13_ENST00000394510.2_Nonsense_Mutation_p.E535*|AKAP13_ENST00000361243.2_Nonsense_Mutation_p.E2294*	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2290	Interaction with ESR1.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.E370*(1)|p.E2294*(1)		NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GATTGTGAGAGAAGTGGCACA	0.423																																					Melanoma(94;603 1453 3280 32295 32951)											2	Substitution - Nonsense(2)	large_intestine(2)	15											109	102	105					15																	86270342		2202	4299	6501	84071346	SO:0001587	stop_gained	11214			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.6868G>T	15.37:g.86270342G>T	ENSP00000378026:p.Glu2290*		84071346	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Nonsense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	49	15.228620	0.99827	.	.	ENSG00000170776	ENST00000426424;ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6094	0.91279	0.0:0.0:1.0:0.0	.	.	.	.	X	370;2294;2290;2293;2269;535	.	ENSP00000354718:E2294X	E	+	1	0	AKAP13	84071346	1.000000	0.71417	0.966000	0.40874	0.958000	0.62258	9.476000	0.97823	2.636000	0.89361	0.557000	0.71058	GAA		0.423	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86270342	G	T	86270342	4	4	61	1	0	0	0	0	0	1	0	0	449	943	33	2	7044	2	AKAP13	15	86270342	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33802	86270342	16261050	9537	17522										
AGBL1	123624	broad.mit.edu	37	chr15	86940623	86940623	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccatatcaggtgatcactGctcgagttcatccaggagag	11	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:86940623G>A	ENST00000441037.2	+	17	2358	c.2263G>A	c.(2263-2265)Gct>Act	p.A755T	AGBL1_ENST00000389298.3_Missense_Mutation_p.A486T|AGBL1_ENST00000421325.2_Missense_Mutation_p.A755T	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	755					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.A755T(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GGTGATCACTGCTCGAGTTCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	15											118	112	114					15																	86940623		1951	4137	6088	84741627	SO:0001583	missense	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2263G>A	15.37:g.86940623G>A	ENSP00000413001:p.Ala755Thr		84741627	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335541	0.81801	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.18016	2.24;2.24	5.49	5.49	0.81192	Peptidase M14, carboxypeptidase A (1);	0.079753	0.49916	D	0.000133	T	0.49406	0.1555	M	0.91090	3.175	0.36848	D	0.887766	D	0.76494	0.999	D	0.73380	0.98	T	0.64495	-0.6394	10	0.87932	D	0	-19.2008	13.6716	0.62430	0.0:0.0:0.8457:0.1543	.	755	Q96MI9	CBPC4_HUMAN	T	784;755;486	ENSP00000397173:A755T;ENSP00000373949:A486T	ENSP00000373949:A486T	A	+	1	0	AGBL1	84741627	1.000000	0.71417	0.965000	0.40720	0.949000	0.60115	6.470000	0.73558	2.733000	0.93635	0.655000	0.94253	GCT		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	86940623	G	A	86940623	3	1	61	1	0	0	0	0	1	0	0	0	375	1319	46	3	2325	3	AGBL1	15	86940623	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	670281	86940623	15590769	9538	17523										
AGBL1	123624	broad.mit.edu	37	chr15	87531274	87531274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgcttaccacttttttgCcattacaaactttttcaaga	4	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:87531274C>T	ENST00000441037.2	+	23	3235	c.3140C>T	c.(3139-3141)gCc>gTc	p.A1047V	RP11-133L19.1_ENST00000558587.1_RNA|AGBL1_ENST00000389298.3_Missense_Mutation_p.A778V|AGBL1_ENST00000421325.2_Missense_Mutation_p.A1047V	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1047			Missing (in FECD8; enriched in the nucleus, decreased TCF4-binding). {ECO:0000269|PubMed:24094747}.		C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.A1047V(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						cacttttttgccattacaaac	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	15											276	258	264					15																	87531274		1858	4084	5942	85332278	SO:0001583	missense	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.3140C>T	15.37:g.87531274C>T	ENSP00000413001:p.Ala1047Val		85332278	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	C	6.507	0.461826	0.12342	.	.	ENSG00000166748	ENST00000421325;ENST00000389298	T;T	0.10668	2.88;2.85	1.78	1.78	0.24846	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	B	0.28378	0.209	B	0.14578	0.011	T	0.38178	-0.9673	9	0.30078	T	0.28	.	7.0229	0.24924	0.0:1.0:0.0:0.0	.	1047	Q96MI9	CBPC4_HUMAN	V	1047;778	ENSP00000397173:A1047V;ENSP00000373949:A778V	ENSP00000373949:A778V	A	+	2	0	AGBL1	85332278	0.000000	0.05858	0.001000	0.08648	0.158000	0.22134	-0.680000	0.05197	1.281000	0.44480	0.514000	0.50259	GCC		0.388	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	87531274	C	T	87531274	3	4	61	1	0	0	0	0	1	0	0	0	375	739	26	3	3226	3	AGBL1	15	87531274	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	590651	87531274	15000118	9539	17524										
NTRK3	4916	broad.mit.edu	37	chr15	88524540	88524540	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatgggactagatgatctCtattgtccttcaagtttaat	8	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:88524540C>A	ENST00000360948.2	-	14	1747				NTRK3_ENST00000317501.3_Missense_Mutation_p.R546I|NTRK3_ENST00000558676.1_Intron|NTRK3_ENST00000542733.2_Intron|NTRK3_ENST00000394480.2_Intron|NTRK3_ENST00000557856.1_Intron|NTRK3_ENST00000355254.2_Intron|NTRK3_ENST00000558306.1_Intron|NTRK3_ENST00000357724.2_Intron|NTRK3_ENST00000540489.2_Missense_Mutation_p.R546I	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3						activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R546I(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			tagatgatctctattgtcctt	0.438			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	15											126	112	117					15																	88524540		2201	4299	6500	86325544	SO:0001627	intron_variant	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1586-40556G>T	15.37:g.88524540C>A			86325544	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691356	0.48097	.	.	ENSG00000140538	ENST00000543429;ENST00000540489;ENST00000317501	T;T	0.63417	-0.04;-0.04	3.83	3.83	0.44106	.	.	.	.	.	T	0.52338	0.1728	N	0.08118	0	0.41448	D	0.987967	P	0.45531	0.86	P	0.52309	0.695	T	0.60454	-0.7260	9	0.87932	D	0	.	11.5631	0.50790	0.0:1.0:0.0:0.0	.	546	Q96CY4	.	I	17;546;546	ENSP00000444673:R546I;ENSP00000318328:R546I	ENSP00000318328:R546I	R	-	2	0	NTRK3	86325544	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.827000	0.48112	2.419000	0.82065	0.655000	0.94253	AGA		0.438	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88524540	C	A	88524540	1	1	61	0	1	0	0	0	0	0	0	0	10739	913	32	2		2	NTRK3	15	88524540	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	993266	88524540	14006852	9540	17525										
NTRK3	4916	broad.mit.edu	37	chr15	88576190	88576190	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagtgtcgggcccggcatCcagtgacgagggcgtggtga	17	11	0	2	rs112443158		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:88576190C>A	ENST00000360948.2	-	13	1644	c.1483G>T	c.(1483-1485)Gat>Tat	p.D495Y	NTRK3_ENST00000317501.3_Missense_Mutation_p.D495Y|NTRK3_ENST00000558676.1_Missense_Mutation_p.D487Y|NTRK3_ENST00000542733.2_Missense_Mutation_p.D397Y|NTRK3_ENST00000394480.2_Missense_Mutation_p.D495Y|NTRK3_ENST00000557856.1_Missense_Mutation_p.D487Y|NTRK3_ENST00000355254.2_Missense_Mutation_p.D495Y|NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000357724.2_Missense_Mutation_p.D487Y|NTRK3_ENST00000540489.2_Missense_Mutation_p.D495Y	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	495					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D495Y(3)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGCCCGGCATCCAGTGACGAG	0.607			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	3	Substitution - Missense(3)	large_intestine(3)	15											99	64	76					15																	88576190		2201	4299	6500	86377194	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1483G>T	15.37:g.88576190C>A	ENSP00000354207:p.Asp495Tyr		86377194	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676714	0.47886	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74209	-0.82;-0.78;-0.78;-0.82;-0.71;-0.09;-0.09	4.91	3.96	0.45880	.	0.047454	0.85682	D	0.000000	T	0.81187	0.4770	L	0.50333	1.59	0.80722	D	1	D;D;B;D;D;B	0.89917	1.0;1.0;0.37;0.999;1.0;0.37	D;D;B;D;D;B	0.91635	0.997;0.997;0.152;0.915;0.999;0.248	T	0.82114	-0.0617	10	0.87932	D	0	.	11.0307	0.47772	0.0:0.9055:0.0:0.0945	.	397;487;487;495;495;495	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	Y	495;495;487;495;397;495;495	ENSP00000377990:D495Y;ENSP00000354207:D495Y;ENSP00000350356:D487Y;ENSP00000347397:D495Y;ENSP00000437773:D397Y;ENSP00000444673:D495Y;ENSP00000318328:D495Y	ENSP00000318328:D495Y	D	-	1	0	NTRK3	86377194	1.000000	0.71417	0.581000	0.28614	0.193000	0.23685	5.575000	0.67430	1.209000	0.43321	0.650000	0.86243	GAT		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88576190	C	A	88576190	3	1	61	1	0	0	0	0	1	0	0	0	10739	855	30	2	1326	2	NTRK3	15	88576190	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51650	88576190	13955202	9541	17526										
ACAN	176	broad.mit.edu	37	chr15	89398459	89398459	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtttcaggacaccttgaCttcagtgggcagctgtcagg	13	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89398459C>A	ENST00000561243.1	+	11	2643	c.2643C>A	c.(2641-2643)gaC>gaA	p.D881E	ACAN_ENST00000439576.2_Missense_Mutation_p.D881E|ACAN_ENST00000352105.7_Missense_Mutation_p.D881E|ACAN_ENST00000559004.1_Missense_Mutation_p.D881E			P16112	PGCA_HUMAN	aggrecan	880	CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.D881E(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GACACCTTGACTTCAGTGGGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	15											60	67	65					15																	89398459		2012	4187	6199	87199463	SO:0001583	missense	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2643C>A	15.37:g.89398459C>A	ENSP00000453342:p.Asp881Glu		87199463	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241015	0.39598	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.01787	4.82;4.64	5.51	-1.3	0.09259	.	0.000000	0.34507	N	0.003916	T	0.02494	0.0076	L	0.48642	1.525	0.09310	N	1	D;D	0.65815	0.992;0.995	P;D	0.63033	0.779;0.91	T	0.37407	-0.9707	10	0.02654	T	1	-14.971	1.0257	0.01527	0.1711:0.3572:0.1977:0.274	.	881;881	E7ENV9;E7EX88	.;.	E	881	ENSP00000387356:D881E;ENSP00000341615:D881E	ENSP00000268134:D881E	D	+	3	2	ACAN	87199463	0.000000	0.05858	0.000000	0.03702	0.925000	0.55904	-0.316000	0.08071	0.081000	0.16988	0.655000	0.94253	GAC		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89398459	C	A	89398459	3	1	61	1	0	0	0	0	1	0	0	0	117	564	20	2	2685	2	ACAN	15	89398459	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	822269	89398459	13132933	9542	17527										
ACAN	176	broad.mit.edu	37	chr15	89400441	89400441	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatttctgcctctggatTtggggacctcagtggacttc	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89400441T>G	ENST00000561243.1	+	11	4625	c.4625T>G	c.(4624-4626)tTt>tGt	p.F1542C	ACAN_ENST00000439576.2_Missense_Mutation_p.F1542C|ACAN_ENST00000352105.7_Missense_Mutation_p.F1542C|ACAN_ENST00000559004.1_Missense_Mutation_p.F1542C			P16112	PGCA_HUMAN	aggrecan	1574	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.F1428C(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCCTCTGGATTTGGGGACCTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											43	45	44					15																	89400441		1828	4081	5909	87201445	SO:0001583	missense	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4625T>G	15.37:g.89400441T>G	ENSP00000453342:p.Phe1542Cys		87201445	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.247837	0.22880	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.94758	-3.51;-3.51	4.27	-0.823	0.10815	.	.	.	.	.	D	0.90851	0.7126	N	0.22421	0.69	0.09310	N	1	D;D	0.61697	0.99;0.963	P;P	0.57776	0.827;0.719	T	0.81906	-0.0718	9	0.44086	T	0.13	0.3036	1.2111	0.01905	0.1713:0.3588:0.1762:0.2938	.	1542;1542	E7ENV9;E7EX88	.;.	C	1542;1542;1428	ENSP00000387356:F1542C;ENSP00000341615:F1542C	ENSP00000268134:F1428C	F	+	2	0	ACAN	87201445	0.004000	0.15560	0.000000	0.03702	0.017000	0.09413	-0.727000	0.04931	-0.032000	0.13758	0.260000	0.18958	TTT		0.532	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89400441	T	G	89400441	3	3	61	1	0	0	0	0	1	0	0	0	117	1841	64	4	4667	4	ACAN	15	89400441	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1982	89400441	13130951	9543	17528										
ACAN	176	broad.mit.edu	37	chr15	89400807	89400807	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgtttccctagtggattCtacattggtggaagtggtca	11	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89400807C>T	ENST00000561243.1	+	11	4991	c.4991C>T	c.(4990-4992)tCt>tTt	p.S1664F	ACAN_ENST00000439576.2_Missense_Mutation_p.S1664F|ACAN_ENST00000352105.7_Missense_Mutation_p.S1664F|ACAN_ENST00000559004.1_Missense_Mutation_p.S1664F			P16112	PGCA_HUMAN	aggrecan	1719	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.S1550F(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CTAGTGGATTCTACATTGGTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	15											140	141	141					15																	89400807		1969	4137	6106	87201811	SO:0001583	missense	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4991C>T	15.37:g.89400807C>T	ENSP00000453342:p.Ser1664Phe		87201811	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225731	0.58668	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02812	4.39;4.15	5.86	4.92	0.64577	.	0.518738	0.14513	N	0.315003	T	0.08179	0.0204	L	0.27053	0.805	0.20975	N	0.999818	D;D	0.69078	0.994;0.997	P;D	0.64042	0.885;0.921	T	0.31668	-0.9935	10	0.72032	D	0.01	-2.5622	15.6936	0.77477	0.0:0.8582:0.1418:0.0	.	1664;1664	E7ENV9;E7EX88	.;.	F	1664;1664;1550	ENSP00000387356:S1664F;ENSP00000341615:S1664F	ENSP00000268134:S1550F	S	+	2	0	ACAN	87201811	0.164000	0.22935	0.191000	0.23289	0.989000	0.77384	1.721000	0.38032	1.439000	0.47511	0.655000	0.94253	TCT		0.542	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89400807	C	T	89400807	3	4	61	1	0	0	0	0	1	0	0	0	117	913	32	3	5033	3	ACAN	15	89400807	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	366	89400807	13130585	9544	17529										
MFGE8	4240	broad.mit.edu	37	chr15	89442929	89442929	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctggtactcagtccagttCgcactgtcattactgtaggc	9	12	2	0	rs369704324		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89442929C>T	ENST00000566497.1	-	7	1045	c.984G>A	c.(982-984)gcG>gcA	p.A328A	MFGE8_ENST00000539437.1_Silent_p.A320A|MFGE8_ENST00000268150.8_Silent_p.A328A|MFGE8_ENST00000542878.1_Silent_p.A284A|MFGE8_ENST00000268151.7_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	328	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.A328A(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CAGTCCAGTTCGCACTGTCAT	0.562																																																2	Substitution - coding silent(2)	large_intestine(1)|stomach(1)	15						C	,	0,4400		0,0,2200	106	89	95		,984	3.1	0	15		95	1,8597	1.2+/-3.3	0,1,4298	no	intron,coding-synonymous	MFGE8	NM_001114614.1,NM_005928.2	,	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	,	,328/388	89442929	1,12997	2200	4299	6499	87243933	SO:0001819	synonymous_variant	4240			U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.984G>A	15.37:g.89442929C>T			87243933	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	37	CCDS10347.1																																																																																				0.562	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		T	89442929	C	T	89442929	2	4	61	1	0	0	0	0	0	0	0	1	9550	871	31	1		1	MFGE8	15	89442929	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42122	89442929	13088463	9545	17530										
ABHD2	11057	broad.mit.edu	37	chr15	89695047	89695047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggagccacttctacattcGacctcttcgagcccttggct	8	14	2	0	rs373748122		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89695047G>A	ENST00000352732.5	+	4	854	c.334G>A	c.(334-336)Gac>Aac	p.D112N	ABHD2_ENST00000565973.1_Missense_Mutation_p.D112N|ABHD2_ENST00000355100.3_Missense_Mutation_p.D112N	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	112					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.D112N(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					TTCTACATTCGACCTCTTCGA	0.522																																					Colon(11;252 417 24570 33239 41878)											1	Substitution - Missense(1)	large_intestine(1)	15						G	ASN/ASP,ASN/ASP	0,4400		0,0,2200	229	192	204		334,334	5.7	1	15		204	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	ABHD2	NM_007011.7,NM_152924.4	23,23	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	112/426,112/426	89695047	1,12997	2200	4299	6499	87496051	SO:0001583	missense	11057			X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"Abhydrolase domain containing"	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.334G>A	15.37:g.89695047G>A	ENSP00000268129:p.Asp112Asn		87496051	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	G	36	5.932554	0.97116	0.0	1.16E-4	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.41400	1.0;1.0	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.67998	0.2953	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.70561	-0.4838	10	0.72032	D	0.01	-0.2168	19.7219	0.96145	0.0:0.0:1.0:0.0	.	112	P08910	ABHD2_HUMAN	N	112	ENSP00000268129:D112N;ENSP00000347217:D112N	ENSP00000268129:D112N	D	+	1	0	ABHD2	87496051	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	9.502000	0.97981	2.648000	0.89879	0.655000	0.94253	GAC		0.522	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			A	89695047	G	A	89695047	3	1	61	1	0	0	0	0	1	0	0	0	82	1058	37	1	340	1	ABHD2	15	89695047	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252118	89695047	12836345	9546	17531										
RLBP1	6017	broad.mit.edu	37	chr15	89753629	89753629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagggcaggatgttctcatCgatctcctggtagaaaccag	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89753629C>T	ENST00000268125.5	-	9	1280	c.841G>A	c.(841-843)Gat>Aat	p.D281N		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	281	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.D281N(2)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	ATGTTCTCATCGATCTCCTGG	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	15											77	73	74					15																	89753629		2200	4299	6499	87554633	SO:0001583	missense	6017			BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.841G>A	15.37:g.89753629C>T	ENSP00000268125:p.Asp281Asn		87554633	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.519086	0.27211	.	.	ENSG00000140522	ENST00000268125	D	0.86030	-2.06	5.21	4.29	0.51040	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	T	0.78886	0.4354	L	0.52126	1.63	0.80722	D	1	P	0.35208	0.49	B	0.26094	0.066	T	0.76030	-0.3108	10	0.30854	T	0.27	-5.3024	14.0021	0.64439	0.0:0.9267:0.0:0.0733	.	281	P12271	RLBP1_HUMAN	N	281	ENSP00000268125:D281N	ENSP00000268125:D281N	D	-	1	0	RLBP1	87554633	1.000000	0.71417	0.042000	0.18584	0.921000	0.55340	5.751000	0.68720	1.204000	0.43247	0.555000	0.69702	GAT		0.577	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		T	89753629	C	T	89753629	3	4	61	1	0	0	0	0	1	0	0	0	13425	884	31	1	116	1	RLBP1	15	89753629	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58582	89753629	12777763	9547	17532										
RLBP1	6017	broad.mit.edu	37	chr15	89758460	89758460	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggtactgcagccggaaaTtcacatagcctggaggaagg	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89758460T>G	ENST00000268125.5	-	6	795	c.356A>C	c.(355-357)aAt>aCt	p.N119T		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	119					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.N119T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	CAGCCGGAAATTCACATAGCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											72	66	68					15																	89758460		2200	4299	6499	87559464	SO:0001583	missense	6017			BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.356A>C	15.37:g.89758460T>G	ENSP00000268125:p.Asn119Thr		87559464	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.861544	0.32884	.	.	ENSG00000140522	ENST00000268125	D	0.87412	-2.25	4.65	4.65	0.58169	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.255320	0.45867	D	0.000325	T	0.76069	0.3936	N	0.25286	0.73	0.47621	D	0.999478	B	0.06786	0.001	B	0.06405	0.002	T	0.69281	-0.5186	10	0.05351	T	0.99	-15.3256	14.3736	0.66857	0.0:0.0:0.0:1.0	.	119	P12271	RLBP1_HUMAN	T	119	ENSP00000268125:N119T	ENSP00000268125:N119T	N	-	2	0	RLBP1	87559464	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	2.121000	0.41977	1.874000	0.54306	0.459000	0.35465	AAT		0.602	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		G	89758460	T	G	89758460	3	3	61	1	0	0	0	0	1	0	0	0	13425	1493	52	4	613	4	RLBP1	15	89758460	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4831	89758460	12772932	9548	17533										
FANCI	55215	broad.mit.edu	37	chr15	89817416	89817416	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtgcttgatcttttaaaGacttcggttgtaaagagctt	10	5	1	3	rs146916445		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89817416G>T	ENST00000310775.7	+	12	1079	c.993G>T	c.(991-993)aaG>aaT	p.K331N	FANCI_ENST00000300027.8_Missense_Mutation_p.K331N	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	331					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)	p.K331N(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					ATCTTTTAAAGACTTCGGTTG	0.294								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	15											39	35	36					15																	89817416		2182	4274	6456	87618420	SO:0001583	missense	55215	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.993G>T	15.37:g.89817416G>T	ENSP00000310842:p.Lys331Asn		87618420	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.862093	0.32884	.	.	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.74106	-0.8;-0.81;-0.08	5.26	-0.304	0.12788	.	0.000000	0.85682	D	0.000000	D	0.82710	0.5096	M	0.77103	2.36	0.48040	D	0.999577	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.995;0.996;0.996	T	0.81134	-0.1071	10	0.72032	D	0.01	-15.0388	9.3998	0.38426	0.6151:0.0:0.3849:0.0	.	331;331;331	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	N	331	ENSP00000300027:K331N;ENSP00000310842:K331N;ENSP00000413249:K331N	ENSP00000300027:K331N	K	+	3	2	FANCI	87618420	1.000000	0.71417	0.251000	0.24312	0.360000	0.29518	1.225000	0.32551	-0.002000	0.14469	-0.253000	0.11424	AAG		0.294	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		T	89817416	G	T	89817416	3	4	61	1	0	0	0	0	1	0	0	0	5688	933	33	2	1035	2	FANCI	15	89817416	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58956	89817416	12713976	9549	17534										
FANCI	55215	broad.mit.edu	37	chr15	89834855	89834855	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatacacagttaaaacagttCtatgagccaaaacctgatct	5	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:89834855C>A	ENST00000310775.7	+	20	1988	c.1902C>A	c.(1900-1902)ttC>ttA	p.F634L	FANCI_ENST00000300027.8_Missense_Mutation_p.F634L	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	634					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)	p.F634L(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					TAAAACAGTTCTATGAGCCAA	0.358								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	large_intestine(1)	15											125	132	130					15																	89834855		2200	4299	6499	87635859	SO:0001583	missense	55215	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.1902C>A	15.37:g.89834855C>A	ENSP00000310842:p.Phe634Leu		87635859	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.382377	0.42207	.	.	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.51071	0.72;0.72;0.72	5.7	1.03	0.20045	.	0.207947	0.52532	D	0.000071	T	0.45094	0.1325	L	0.47716	1.5	0.80722	D	1	P;B;B	0.41232	0.743;0.164;0.259	P;B;B	0.47430	0.547;0.047;0.047	T	0.23655	-1.0182	10	0.33141	T	0.24	-4.2718	10.0583	0.42259	0.0:0.4873:0.0:0.5127	.	634;634;634	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	L	634	ENSP00000300027:F634L;ENSP00000310842:F634L;ENSP00000413249:F634L	ENSP00000300027:F634L	F	+	3	2	FANCI	87635859	1.000000	0.71417	0.965000	0.40720	0.988000	0.76386	0.569000	0.23638	0.295000	0.22570	0.655000	0.94253	TTC		0.358	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		A	89834855	C	A	89834855	3	1	61	1	0	0	0	0	1	0	0	0	5688	912	32	2	1976	2	FANCI	15	89834855	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17439	89834855	12696537	9550	17535										
C15orf42	90381	broad.mit.edu	37	chr15	90135404	90135404	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccgatttgatggagtcatTtgggtaaaacgtttttatat	9	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90135404T>G	ENST00000268138.7	+	5	1643	c.1538T>G	c.(1537-1539)tTt>tGt	p.F513C	RP11-429B14.1_ENST00000559041.1_RNA|TICRR_ENST00000560985.1_Missense_Mutation_p.F512C			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	513					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.F513C(1)									ATGGAGTCATTTGGGTAAAAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											125	116	119					15																	90135404		1928	4141	6069	87936408	SO:0001583	missense	90381			AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1538T>G	15.37:g.90135404T>G	ENSP00000268138:p.Phe513Cys		87936408	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	T	21.4	4.148277	0.78001	.	.	ENSG00000140534	ENST00000268138	T	0.31769	1.48	5.25	5.25	0.73442	.	0.212508	0.48286	D	0.000185	T	0.54382	0.1855	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.58674	-0.7595	10	0.87932	D	0	-18.1487	15.1574	0.72755	0.0:0.0:0.0:1.0	.	513	Q7Z2Z1	TICRR_HUMAN	C	513	ENSP00000268138:F513C	ENSP00000268138:F513C	F	+	2	0	C15orf42	87936408	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	6.979000	0.76154	1.993000	0.58246	0.402000	0.26972	TTT		0.398	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		G	90135404	T	G	90135404	3	3	61	1	0	0	0	0	1	0	0	0	1800	1841	64	4	1556	4	C15orf42	15	90135404	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	300549	90135404	12395988	9551	17536										
KIF7	374654	broad.mit.edu	37	chr15	90172756	90172756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagctgcatctccagttCcgagaaggcaatctgctgct	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90172756C>T	ENST00000394412.3	-	17	3443	c.3367G>A	c.(3367-3369)Gaa>Aaa	p.E1123K	KIF7_ENST00000558928.1_5'Flank	NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	1123					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E610K(1)|p.E1123K(1)		central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			ATCTCCAGTTCCGAGAAGGCA	0.637																																																2	Substitution - Missense(2)	large_intestine(2)	15											77	73	74					15																	90172756		2200	4299	6499	87973760	SO:0001583	missense	374654			AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.3367G>A	15.37:g.90172756C>T	ENSP00000377934:p.Glu1123Lys		87973760	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	C	31	5.090630	0.94149	.	.	ENSG00000166813	ENST00000394412	T	0.75367	-0.93	5.06	4.13	0.48395	.	0.000000	0.85682	D	0.000000	D	0.83876	0.5349	M	0.64997	1.995	0.80722	D	1	D;D	0.76494	0.999;0.983	D;P	0.81914	0.995;0.723	D	0.85916	0.1443	10	0.72032	D	0.01	.	15.4947	0.75641	0.0:0.8609:0.1391:0.0	.	609;1123	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	K	1123	ENSP00000377934:E1123K	ENSP00000377934:E1123K	E	-	1	0	KIF7	87973760	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.548000	0.82154	1.330000	0.45394	0.462000	0.41574	GAA		0.637	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		T	90172756	C	T	90172756	3	4	61	1	0	0	0	0	1	0	0	0	8330	864	30	3	676	3	KIF7	15	90172756	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37352	90172756	12358636	9552	17537										
KIF7	374654	broad.mit.edu	37	chr15	90177036	90177036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgagctgcacgttccgctCgagctcctgcagtcgcttct	10	15	1	1	rs558861570		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90177036C>T	ENST00000394412.3	-	12	2549	c.2473G>A	c.(2473-2475)Gag>Aag	p.E825K		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	825					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E825K(1)|p.E312K(1)		central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			ACGTTCCGCTCGAGCTCCTGC	0.632																																																2	Substitution - Missense(2)	large_intestine(2)	15											51	48	49					15																	90177036		2200	4299	6499	87978040	SO:0001583	missense	374654			AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.2473G>A	15.37:g.90177036C>T	ENSP00000377934:p.Glu825Lys		87978040	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	C	34	5.340223	0.95783	.	.	ENSG00000166813	ENST00000394412	T	0.52526	0.66	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.70570	0.3239	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	T	0.72520	-0.4268	10	0.48119	T	0.1	.	18.5338	0.91001	0.0:1.0:0.0:0.0	.	311;825	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	K	825	ENSP00000377934:E825K	ENSP00000377934:E825K	E	-	1	0	KIF7	87978040	1.000000	0.71417	0.998000	0.56505	0.839000	0.47603	7.712000	0.84684	2.378000	0.81104	0.491000	0.48974	GAG		0.632	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		T	90177036	C	T	90177036	3	4	61	1	0	0	0	0	1	0	0	0	8330	893	31	1	1590	1	KIF7	15	90177036	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4280	90177036	12354356	9553	17538										
PLIN1	5346	broad.mit.edu	37	chr15	90213334	90213334	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagcaaattccgcagtgtCtctggccaccccccaggcaa	10	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90213334C>A	ENST00000300055.5	-	5	640	c.475G>T	c.(475-477)Gac>Tac	p.D159Y	PLIN1_ENST00000430628.2_Missense_Mutation_p.D159Y	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	159					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)	p.D159Y(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						TCCGCAGTGTCTCTGGCCACC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	15											35	36	36					15																	90213334		2200	4299	6499	88014338	SO:0001583	missense	5346			AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.475G>T	15.37:g.90213334C>A	ENSP00000300055:p.Asp159Tyr		88014338	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	37	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253256	0.59212	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.05925	3.37;3.37	5.21	5.21	0.72293	.	0.438855	0.22814	N	0.055307	T	0.19765	0.0475	M	0.63428	1.95	0.28391	N	0.919086	D	0.67145	0.996	D	0.67900	0.954	T	0.01496	-1.1340	10	0.66056	D	0.02	-30.1	11.8385	0.52340	0.0:0.9139:0.0:0.0861	.	159	O60240	PLIN1_HUMAN	Y	159	ENSP00000300055:D159Y;ENSP00000402167:D159Y	ENSP00000300055:D159Y	D	-	1	0	PLIN1	88014338	0.833000	0.29383	0.989000	0.46669	0.673000	0.39480	1.861000	0.39438	2.439000	0.82584	0.305000	0.20034	GAC		0.627	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		A	90213334	C	A	90213334	3	1	61	1	0	0	0	0	1	0	0	0	12120	913	32	2	1113	2	PLIN1	15	90213334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36298	90213334	12318058	9554	17539										
PEX11A	8800	broad.mit.edu	37	chr15	90226610	90226610	+	Nonstop_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagcctaaaaacaccctAacgggtcttcagcttcatct	5	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90226610A>C	ENST00000300056.3	-	3	891	c.742T>G	c.(742-744)Tag>Gag	p.*248E	PEX11A_ENST00000561257.1_Nonstop_Mutation_p.*217E|PEX11A_ENST00000561224.1_Intron|PEX11A_ENST00000557982.1_Intron|PEX11A_ENST00000559170.1_3'UTR	NM_001271573.1	NP_001258502.1	O75192	PX11A_HUMAN	peroxisomal biogenesis factor 11 alpha	0					brown fat cell differentiation (GO:0050873)|cellular lipid metabolic process (GO:0044255)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|regulation of peroxisome size (GO:0044375)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	protein homodimerization activity (GO:0042803)	p.*248E(1)		endometrium(2)|large_intestine(2)|lung(3)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AAAACACCCTAACGGGTCTTC	0.443																																																1	Nonstop extension(1)	large_intestine(1)	15											185	194	191					15																	90226610		2200	4299	6499	88027614	SO:0001578	stop_lost	8800			AF093668	CCDS10354.1, CCDS61751.1	15q	2008-08-26	2008-08-26		ENSG00000166821	ENSG00000166821			8852	protein-coding gene	gene with protein product		603866	"peroxisomal biogenesis factor 11A"			9792670	Standard	NM_003847		Approved	PEX11-ALPHA, MGC119947, MGC138534	uc002boi.4	O75192	OTTHUMG00000149809	ENST00000300056.3:c.742T>G	15.37:g.90226610A>C	ENSP00000300056:p.*248Glnext*38		88027614	B4DV88	Nonstop_Mutation	SNP	ENST00000300056.3	37	CCDS10354.1	.	.	.	.	.	.	.	.	.	.	A	6.530	0.466068	0.12402	.	.	ENSG00000166821	ENST00000300056	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.26692	N	0.971334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4119	0.49931	1.0:0.0:0.0:0.0	.	.	.	.	E	248	.	.	X	-	1	0	PEX11A	88027614	0.210000	0.23517	0.024000	0.17045	0.210000	0.24377	2.162000	0.42367	2.188000	0.69820	0.533000	0.62120	TAG		0.443	PEX11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313420.1	NM_003847		C	90226610	A	C	90226610	4	2	61	1	0	0	0	0	0	0	0	0	11768	375	13	4	5	4	PEX11A	15	90226610	Nonstop_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13276	90226610	12304782	9555	17540										
WDR93	56964	broad.mit.edu	37	chr15	90255298	90255298	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtataaagatggagatCtctcaaggaggggactttgc	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90255298C>A	ENST00000268130.7	+	5	704	c.603C>A	c.(601-603)atC>atA	p.I201I	RNU6-132P_ENST00000383863.1_RNA|WDR93_ENST00000560294.1_Silent_p.I201I	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	201					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.I201I(1)		NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AGATGGAGATCTCTCAAGGAG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	15											86	86	86					15																	90255298		2200	4299	6499	88056302	SO:0001819	synonymous_variant	56964				CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.603C>A	15.37:g.90255298C>A			88056302	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																				0.403	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		A	90255298	C	A	90255298	2	1	61	1	0	0	0	0	0	0	0	1	17380	903	32	2		2	WDR93	15	90255298	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28688	90255298	12276094	9556	17541										
WDR93	56964	broad.mit.edu	37	chr15	90286527	90286527	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtgtggccctcagctatCggaagctggagaagaaccca	13	10	1	2	rs189442055		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90286527C>T	ENST00000268130.7	+	17	2067	c.1966C>T	c.(1966-1968)Cgg>Tgg	p.R656W	WDR93_ENST00000444934.2_Missense_Mutation_p.R373W|WDR93_ENST00000560294.1_Missense_Mutation_p.R628W	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	656					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.R656W(1)		NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CCTCAGCTATCGGAAGCTGGA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											61	67	65					15																	90286527		2200	4299	6499	88087531	SO:0001583	missense	56964				CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1966C>T	15.37:g.90286527C>T	ENSP00000268130:p.Arg656Trp		88087531	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.732567	0.48939	.	.	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.46819	1.86;0.86	3.71	2.76	0.32466	.	0.564637	0.15966	N	0.236031	T	0.37598	0.1009	N	0.22421	0.69	0.09310	N	1	D;D	0.67145	0.996;0.987	P;B	0.47573	0.55;0.319	T	0.16100	-1.0414	10	0.66056	D	0.02	-8.0276	9.2617	0.37616	0.0:0.7796:0.2204:0.0	.	628;656	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	W	656;373	ENSP00000268130:R656W;ENSP00000403871:R373W	ENSP00000268130:R656W	R	+	1	2	WDR93	88087531	0.116000	0.22171	0.267000	0.24556	0.010000	0.07245	0.223000	0.17719	1.125000	0.41998	0.456000	0.33151	CGG		0.582	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		T	90286527	C	T	90286527	3	4	61	1	0	0	0	0	1	0	0	0	17380	875	31	1	2028	1	WDR93	15	90286527	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31229	90286527	12244865	9557	17542										
ANPEP	290	broad.mit.edu	37	chr15	90342704	90342704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcttcctccagttctcttCgtcgtagttcacccggtaat	6	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90342704C>T	ENST00000300060.6	-	13	2219	c.1906G>A	c.(1906-1908)Gaa>Aaa	p.E636K	ANPEP_ENST00000558177.1_5'UTR	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	636	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.E636K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CAGTTCTCTTCGTCGTAGTTC	0.587																																					NSCLC(30;827 977 2459 19669 26125)											1	Substitution - Missense(1)	large_intestine(1)	15											138	123	128					15																	90342704		2200	4299	6499	88143708	SO:0001583	missense	290			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1906G>A	15.37:g.90342704C>T	ENSP00000300060:p.Glu636Lys		88143708	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	C	7.241	0.601234	0.13939	.	.	ENSG00000166825	ENST00000300060	T	0.62788	-0.0	5.15	-0.669	0.11388	.	0.447569	0.21672	N	0.070849	T	0.46600	0.1401	L	0.56769	1.78	0.09310	N	1	P	0.36712	0.566	B	0.36666	0.23	T	0.43015	-0.9417	10	0.07482	T	0.82	.	5.7834	0.18320	0.1308:0.2962:0.4915:0.0815	.	636	P15144	AMPN_HUMAN	K	636	ENSP00000300060:E636K	ENSP00000300060:E636K	E	-	1	0	ANPEP	88143708	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-3.000000	0.00653	-0.073000	0.12842	-0.302000	0.09304	GAA		0.587	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90342704	C	T	90342704	3	4	61	1	0	0	0	0	1	0	0	0	710	893	31	1	1033	1	ANPEP	15	90342704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56177	90342704	12188688	9558	17543										
C15orf38	348110	broad.mit.edu	37	chr15	90447101	90447101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgactcgggcatccagaacGccactgtgtggtcgggggtg	16	11	0	2	rs201638212		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90447101G>A	ENST00000357484.5	-	4	536	c.416C>T	c.(415-417)gCg>gTg	p.A139V	C15orf38-AP3S2_ENST00000560224.1_5'Flank|C15orf38_ENST00000460685.1_Missense_Mutation_p.A43V|C15orf38-AP3S2_ENST00000398333.3_Missense_Mutation_p.A139V	NM_001282380.1|NM_182616.2	NP_001269309.1|NP_872422.1	Q7Z6K5	ARPIN_HUMAN		139					directional locomotion (GO:0033058)|negative regulation of actin nucleation (GO:0051126)|negative regulation of cell migration (GO:0030336)|negative regulation of lamellipodium morphogenesis (GO:2000393)	lamellipodium (GO:0030027)		p.A139V(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	10	Melanoma(11;0.0171)|Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			CATCCAGAACGCCACTGTGTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	VAL/ALA,VAL/ALA	0,4246		0,0,2123	63	71	69		416,416	5.5	1	15		69	2,8498		0,2,4248	yes	missense,missense	C15orf38,C15orf38-AP3S2	NM_001199058.1,NM_182616.2	64,64	0,2,6371	AA,AG,GG		0.0235,0.0,0.0157	probably-damaging,probably-damaging	139/395,139/227	90447101	2,12744	2123	4250	6373	88248105	SO:0001583	missense	10239																														ENST00000357484.5:c.416C>T	15.37:g.90447101G>A	ENSP00000350075:p.Ala139Val		88248105	E2QRD5	Missense_Mutation	SNP	ENST00000357484.5	37	CCDS42080.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.510876	0.85389	0.0	2.35E-4	ENSG00000250021;ENSG00000242498	ENST00000398333;ENST00000357484	T	0.48522	0.81	5.49	5.49	0.81192	.	0.000000	0.64402	U	0.000001	T	0.67906	0.2943	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.70146	-0.4952	10	0.72032	D	0.01	-2.0036	16.865	0.86027	0.0:0.0:1.0:0.0	.	139;139	Q7Z6K5;E2QRD5	CO038_HUMAN;.	V	139	ENSP00000381377:A139V	ENSP00000381377:A139V	A	-	2	0	C15orf38-AP3S2;C15orf38	88248105	1.000000	0.71417	0.954000	0.39281	0.396000	0.30629	6.293000	0.72731	2.583000	0.87209	0.579000	0.79373	GCG		0.652	C15orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335629.1			A	90447101	G	A	90447101	3	1	61	1	0	0	0	0	1	0	0	0	1796	1087	38	1	276	1	C15orf38	15	90447101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104397	90447101	12084291	9559	17544										
ZNF710	374655	broad.mit.edu	37	chr15	90611795	90611795	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatggagttcagccagattCaccacctcaagcagcactcc	8	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90611795C>A	ENST00000268154.4	+	2	1677	c.1426C>A	c.(1426-1428)Cac>Aac	p.H476N		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H476N(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			CAGCCAGATTCACCACCTCAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	15											199	182	188					15																	90611795		2200	4298	6498	88412799	SO:0001583	missense	374655			AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"Zinc fingers, C2H2-type"	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.1426C>A	15.37:g.90611795C>A	ENSP00000268154:p.His476Asn		88412799	A0AVS3|Q6ZMK9|Q8NDU0	Missense_Mutation	SNP	ENST00000268154.4	37	CCDS10358.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.403763	0.42613	.	.	ENSG00000140548	ENST00000268154	T	0.14766	2.48	5.46	5.46	0.80206	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000009	T	0.22437	0.0541	N	0.16098	0.37	0.58432	D	0.999999	D	0.63880	0.993	D	0.74674	0.984	T	0.05084	-1.0907	10	0.38643	T	0.18	-42.1978	18.0678	0.89396	0.0:1.0:0.0:0.0	.	476	Q8N1W2	ZN710_HUMAN	N	476	ENSP00000268154:H476N	ENSP00000268154:H476N	H	+	1	0	ZNF710	88412799	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.635000	0.83286	2.840000	0.97914	0.655000	0.94253	CAC		0.577	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526		A	90611795	C	A	90611795	3	1	61	1	0	0	0	0	1	0	0	0	18154	826	29	2	1428	2	ZNF710	15	90611795	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	164694	90611795	11919597	9560	17545										
TTLL13	440307	broad.mit.edu	37	chr15	90801366	90801366	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatcatcaaaaccatcatCtcagcccattctgttctacg	3	14	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90801366C>A	ENST00000339615.5	+	9	1322	c.1032C>A	c.(1030-1032)atC>atA	p.I344I	RP11-697E2.6_ENST00000561573.1_Intron|TTLL13_ENST00000438251.1_Silent_p.I344I	NM_001029964.2	NP_001025135.2			tubulin tyrosine ligase-like family, member 13									p.I344I(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	16	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			AAACCATCATCTCAGCCCATT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	15											284	243	257					15																	90801366		2199	4298	6497	88602370	SO:0001819	synonymous_variant	440307			BC036668		15q26.1	2013-02-14				ENSG00000213471		"Tubulin tyrosine ligase-like family"	32484	protein-coding gene	gene with protein product						15890843	Standard	NR_104604		Approved	FLJ46079, MGC33417	uc002bpd.1	A6NNM8		ENST00000339615.5:c.1032C>A	15.37:g.90801366C>A			88602370		Silent	SNP	ENST00000339615.5	37	CCDS32328.1																																																																																				0.493	TTLL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435854.1	NM_001029964		A	90801366	C	A	90801366	2	1	61	1	0	0	0	0	0	0	0	1	16766	903	32	2		2	TTLL13	15	90801366	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	189571	90801366	11730026	9561	17546										
ZNF774	342132	broad.mit.edu	37	chr15	90904163	90904163	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatttggtcacgcaccaaaGaacacacacaggtgagagac	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90904163G>T	ENST00000354377.3	+	4	1286	c.1100G>T	c.(1099-1101)aGa>aTa	p.R367I	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R367I(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ACGCACCAAAGAACACACACA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	15											88	86	87					15																	90904163		2199	4298	6497	88705167	SO:0001583	missense	342132			BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"Zinc fingers, C2H2-type"	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.1100G>T	15.37:g.90904163G>T	ENSP00000346348:p.Arg367Ile		88705167	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765385	0.69878	.	.	ENSG00000196391	ENST00000354377	T	0.02446	4.29	5.22	4.3	0.51218	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39146	N	0.001454	T	0.08714	0.0216	L	0.58101	1.795	0.80722	D	1	D	0.56968	0.978	P	0.56474	0.799	T	0.02358	-1.1171	10	0.72032	D	0.01	.	11.319	0.49410	0.0893:0.0:0.9107:0.0	.	367	Q6NX45	ZN774_HUMAN	I	367	ENSP00000346348:R367I	ENSP00000346348:R367I	R	+	2	0	ZNF774	88705167	0.909000	0.30893	0.949000	0.38748	0.595000	0.36748	4.539000	0.60657	1.199000	0.43173	0.561000	0.74099	AGA		0.498	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309		T	90904163	G	T	90904163	3	4	61	1	0	0	0	0	1	0	0	0	18186	942	33	2	1110	2	ZNF774	15	90904163	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102797	90904163	11627229	9562	17547										
ZNF774	342132	broad.mit.edu	37	chr15	90904331	90904331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactttattacccatcagcGaatccacttaggagacaggc	7	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90904331G>A	ENST00000354377.3	+	4	1454	c.1268G>A	c.(1267-1269)cGa>cAa	p.R423Q	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R423Q(2)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ACCCATCAGCGAATCCACTTA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	15											76	71	72					15																	90904331		2199	4298	6497	88705335	SO:0001583	missense	342132			BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"Zinc fingers, C2H2-type"	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.1268G>A	15.37:g.90904331G>A	ENSP00000346348:p.Arg423Gln		88705335	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199969	0.58126	.	.	ENSG00000196391	ENST00000354377	T	0.24723	1.84	5.31	4.08	0.47627	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31472	N	0.007586	T	0.41834	0.1176	L	0.51422	1.61	0.42084	D	0.991265	D	0.89917	1.0	D	0.79108	0.992	T	0.25950	-1.0117	10	0.72032	D	0.01	.	9.6798	0.40063	0.1405:0.0:0.8595:0.0	.	423	Q6NX45	ZN774_HUMAN	Q	423	ENSP00000346348:R423Q	ENSP00000346348:R423Q	R	+	2	0	ZNF774	88705335	0.029000	0.19370	0.001000	0.08648	0.576000	0.36127	2.048000	0.41278	0.861000	0.35504	0.655000	0.94253	CGA		0.493	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309		A	90904331	G	A	90904331	3	1	61	1	0	0	0	0	1	0	0	0	18186	1058	37	1	1278	1	ZNF774	15	90904331	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	90904331	11627061	9563	17548										
IQGAP1	8826	broad.mit.edu	37	chr15	90977000	90977000	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatcgaaagaacatgccaaGatgtatctactgtatccatg	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90977000G>T	ENST00000268182.5	+	5	564	c.440G>T	c.(439-441)aGa>aTa	p.R147I	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	147	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)	p.R147I(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AACATGCCAAGATGTATCTAC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	15											122	121	121					15																	90977000		2198	4298	6496	88778004	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.440G>T	15.37:g.90977000G>T	ENSP00000268182:p.Arg147Ile		88778004	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379766	0.82682	.	.	ENSG00000140575	ENST00000268182	D	0.95001	-3.58	5.28	5.28	0.74379	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97561	0.9201	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98087	1.0407	10	0.87932	D	0	-17.9682	18.0822	0.89444	0.0:0.0:1.0:0.0	.	147	P46940	IQGA1_HUMAN	I	147	ENSP00000268182:R147I	ENSP00000268182:R147I	R	+	2	0	IQGAP1	88778004	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.503000	0.66962	2.744000	0.94065	0.655000	0.94253	AGA		0.328	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	90977000	G	T	90977000	3	4	61	1	0	0	0	0	1	0	0	0	7835	942	33	2	458	2	IQGAP1	15	90977000	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72669	90977000	11554392	9564	17549										
IQGAP1	8826	broad.mit.edu	37	chr15	90996012	90996012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttttttacacaggattgGcagcagtagcactgattaat	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:90996012G>A	ENST00000268182.5	+	12	1292	c.1168G>A	c.(1168-1170)Gca>Aca	p.A390T	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	390					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)	p.A390T(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			CACAGGATTGGCAGCAGTAGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											71	71	71					15																	90996012		2198	4298	6496	88797016	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.1168G>A	15.37:g.90996012G>A	ENSP00000268182:p.Ala390Thr		88797016	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	4.631	0.117309	0.08881	.	.	ENSG00000140575	ENST00000268182	T	0.06768	3.26	5.17	3.3	0.37823	.	0.414323	0.26923	N	0.021812	T	0.07593	0.0191	L	0.47016	1.485	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.21861	-1.0233	10	0.16896	T	0.51	-3.491	8.5999	0.33738	0.2338:0.0:0.7662:0.0	.	390	P46940	IQGA1_HUMAN	T	390	ENSP00000268182:A390T	ENSP00000268182:A390T	A	+	1	0	IQGAP1	88797016	1.000000	0.71417	0.626000	0.29213	0.083000	0.17756	2.288000	0.43514	0.756000	0.33013	0.655000	0.94253	GCA		0.488	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		A	90996012	G	A	90996012	3	1	61	1	0	0	0	0	1	0	0	0	7835	1203	42	3	1214	3	IQGAP1	15	90996012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19012	90996012	11535380	9565	17550										
IQGAP1	8826	broad.mit.edu	37	chr15	91035934	91035934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcttggataacttagccaGcaagggcaagtgagtatttt	11	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91035934G>T	ENST00000268182.5	+	35	4743	c.4619G>T	c.(4618-4620)aGc>aTc	p.S1540I	IQGAP1_ENST00000560738.1_Missense_Mutation_p.S968I	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1540	C2.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)	p.S1540I(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AACTTAGCCAGCAAGGGCAAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											51	51	51					15																	91035934		2198	4298	6496	88836938	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.4619G>T	15.37:g.91035934G>T	ENSP00000268182:p.Ser1540Ile		88836938	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.997572	0.54147	.	.	ENSG00000140575	ENST00000268182	T	0.48201	0.82	5.84	5.84	0.93424	RasGAP protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.44808	0.1311	L	0.39147	1.195	0.80722	D	1	B;B	0.18166	0.002;0.026	B;B	0.21708	0.01;0.036	T	0.21177	-1.0253	10	0.42905	T	0.14	-20.7874	19.1245	0.93376	0.0:0.0:1.0:0.0	.	161;1540	B4DNP4;P46940	.;IQGA1_HUMAN	I	1540	ENSP00000268182:S1540I	ENSP00000268182:S1540I	S	+	2	0	IQGAP1	88836938	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.606000	0.67641	2.774000	0.95407	0.484000	0.47621	AGC		0.383	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	91035934	G	T	91035934	3	4	61	1	0	0	0	0	1	0	0	0	7835	971	34	2	4757	2	IQGAP1	15	91035934	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39922	91035934	11495458	9566	17551										
CRTC3	64784	broad.mit.edu	37	chr15	91181802	91181802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctgcagcagccccgcgCccctgaggcccctgcccagc	10	23	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91181802C>T	ENST00000268184.6	+	12	1395	c.1391C>T	c.(1390-1392)gCc>gTc	p.A464V	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Missense_Mutation_p.A464V			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	464					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.A464V(1)	CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CAGCCCCGCGCCCCTGAGGCC	0.672			T	MAML2	salivary gland mucoepidermoid																																		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	1	Substitution - Missense(1)	large_intestine(1)	15											40	46	44					15																	91181802		2198	4298	6496	88982806	SO:0001583	missense	64784				CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.1391C>T	15.37:g.91181802C>T	ENSP00000268184:p.Ala464Val		88982806	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	37	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	C	8.875	0.950229	0.18431	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.11821	2.74;2.74	5.3	4.35	0.52113	.	0.822425	0.11580	N	0.549856	T	0.13457	0.0326	L	0.51422	1.61	0.09310	N	1	B;B	0.22414	0.041;0.069	B;B	0.21917	0.016;0.037	T	0.06935	-1.0799	10	0.35671	T	0.21	0.2464	7.466	0.27322	0.0:0.7436:0.1684:0.088	.	464;464	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	V	428;464;464	ENSP00000268184:A464V;ENSP00000416573:A464V	ENSP00000268184:A464V	A	+	2	0	CRTC3	88982806	0.290000	0.24343	0.687000	0.30102	0.026000	0.11368	0.693000	0.25497	2.775000	0.95449	0.650000	0.86243	GCC		0.672	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		T	91181802	C	T	91181802	3	4	61	1	0	0	0	0	1	0	0	0	3907	739	26	3	1437	3	CRTC3	15	91181802	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	145868	91181802	11349590	9567	17552										
BLM	641	broad.mit.edu	37	chr15	91292938	91292938	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttagttcttcaccagattCtttaagtaccatcaatgatt	4	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91292938C>A	ENST00000355112.3	+	3	558	c.440C>A	c.(439-441)tCt>tAt	p.S147Y	BLM_ENST00000560509.1_Missense_Mutation_p.S147Y	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	147					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)	p.S147Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TCACCAGATTCTTTAAGTACC	0.378			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																													yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	15											69	68	68					15																	91292938		2198	4298	6496	89093942	SO:0001583	missense	641	Familial Cancer Database		U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.440C>A	15.37:g.91292938C>A	ENSP00000347232:p.Ser147Tyr		89093942	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.565339	0.65651	.	.	ENSG00000197299	ENST00000355112	T	0.52754	0.65	5.54	5.54	0.83059	.	0.167618	0.45606	D	0.000348	T	0.67069	0.2854	M	0.73598	2.24	0.37988	D	0.933812	D;D	0.76494	0.999;0.999	D;D	0.64595	0.927;0.927	T	0.73113	-0.4085	10	0.87932	D	0	-16.7652	15.3668	0.74529	0.0:1.0:0.0:0.0	.	147;147	B2RAN0;P54132	.;BLM_HUMAN	Y	147	ENSP00000347232:S147Y	ENSP00000347232:S147Y	S	+	2	0	BLM	89093942	0.800000	0.28916	0.934000	0.37439	0.610000	0.37248	2.578000	0.46051	2.774000	0.95407	0.650000	0.86243	TCT		0.378	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			A	91292938	C	A	91292938	3	1	61	1	0	0	0	0	1	0	0	0	1446	913	32	2	446	2	BLM	15	91292938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111136	91292938	11238454	9568	17553										
RCCD1	91433	broad.mit.edu	37	chr15	91503594	91503594	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatggttctcaggtgaagaGaacgggtggggctgaggatg	19	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91503594G>T	ENST00000394258.2	+	6	1017	c.815G>T	c.(814-816)aGa>aTa	p.R272I	RCCD1_ENST00000555155.1_Missense_Mutation_p.R270I|RCCD1_ENST00000556618.1_Missense_Mutation_p.R272I	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	272						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.R272I(1)		breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			CAGGTGAAGAGAACGGGTGGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											73	75	74					15																	91503594		2198	4298	6496	89304598	SO:0001583	missense	91433				CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.815G>T	15.37:g.91503594G>T	ENSP00000377801:p.Arg272Ile		89304598	B2RTP9|Q29RX6	Missense_Mutation	SNP	ENST00000394258.2	37	CCDS32333.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629592	0.28978	.	.	ENSG00000166965	ENST00000394258;ENST00000555155;ENST00000556618;ENST00000556333	T;T;T	0.38240	1.15;1.18;1.15	4.82	-0.511	0.11970	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	1.403040	0.03833	N	0.269310	T	0.31702	0.0805	M	0.62723	1.935	0.09310	N	1	B;B	0.25667	0.131;0.08	B;B	0.22152	0.038;0.017	T	0.11616	-1.0580	10	0.22706	T	0.39	.	2.91	0.05733	0.1254:0.2712:0.4491:0.1543	.	270;272	G3V2I3;A6NED2	.;RCCD1_HUMAN	I	272;270;272;61	ENSP00000377801:R272I;ENSP00000450678:R270I;ENSP00000451963:R272I	ENSP00000377801:R272I	R	+	2	0	RCCD1	89304598	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.038000	0.12144	0.085000	0.17107	0.555000	0.69702	AGA		0.517	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		T	91503594	G	T	91503594	3	4	61	1	0	0	0	0	1	0	0	0	13212	942	33	2	833	2	RCCD1	15	91503594	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210656	91503594	11027798	9569	17554										
PRC1	9055	broad.mit.edu	37	chr15	91513657	91513657	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccagaaggaggaagtcGagacacgggggagtggtaga	19	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91513657G>A	ENST00000361188.5	-	12	2760	c.1549C>T	c.(1549-1551)Cga>Tga	p.R517*	PRC1_ENST00000361919.3_Nonsense_Mutation_p.R517*|PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000394249.3_Nonsense_Mutation_p.R517*|PRC1-AS1_ENST00000556200.1_RNA|PRC1_ENST00000442656.2_Nonsense_Mutation_p.R476*					protein regulator of cytokinesis 1									p.R517*(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					GGAGGAAGTCGAGACACGGGG	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											274	219	238					15																	91513657		2198	4298	6496	89314661	SO:0001587	stop_gained	9055			AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1549C>T	15.37:g.91513657G>A	ENSP00000354679:p.Arg517*		89314661		Nonsense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	G	48	14.279862	0.99788	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000555455;ENST00000442656	.	.	.	6.16	3.27	0.37495	.	0.281465	0.33457	N	0.004886	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1994	0.25873	0.1463:0.0:0.7143:0.1393	.	.	.	.	X	517;517;517;120;476	.	ENSP00000354679:R517X	R	-	1	2	PRC1	89314661	1.000000	0.71417	0.964000	0.40570	0.123000	0.20343	3.805000	0.55575	0.465000	0.27167	-0.145000	0.13849	CGA		0.542	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		A	91513657	G	A	91513657	4	1	61	1	0	0	0	0	0	1	0	0	12480	1066	37	1	329	1	PRC1	15	91513657	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10063	91513657	11017735	9570	17555										
SV2B	9899	broad.mit.edu	37	chr15	91795666	91795666	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctcgggagaagcgaggaGaacacctcagttggctgggc	16	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:91795666G>A	ENST00000394232.1	+	4	1170	c.700G>A	c.(700-702)Gaa>Aaa	p.E234K	SV2B_ENST00000330276.4_Missense_Mutation_p.E234K|SV2B_ENST00000545111.2_Missense_Mutation_p.E83K	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	234					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.E234K(1)		NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GAAGCGAGGAGAACACCTCAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	15											113	103	107					15																	91795666		2198	4298	6496	89596670	SO:0001583	missense	9899			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.700G>A	15.37:g.91795666G>A	ENSP00000377779:p.Glu234Lys		89596670	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	G	35	5.506632	0.96386	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.56611	0.45;0.45;0.45	5.36	5.36	0.76844	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.60457	0.2270	L	0.31476	0.935	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.51919	-0.8644	10	0.16420	T	0.52	-23.8897	18.0217	0.89257	0.0:0.0:1.0:0.0	.	234	Q7L1I2	SV2B_HUMAN	K	83;234;234	ENSP00000443243:E83K;ENSP00000377779:E234K;ENSP00000332818:E234K	ENSP00000332818:E234K	E	+	1	0	SV2B	89596670	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	9.528000	0.98046	2.665000	0.90641	0.563000	0.77884	GAA		0.502	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91795666	G	A	91795666	3	1	61	1	0	0	0	0	1	0	0	0	15457	943	33	3	710	3	SV2B	15	91795666	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	282009	91795666	10735726	9571	17556										
CHD2	1106	broad.mit.edu	37	chr15	93547887	93547887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcgagtaaatcaaagcGatctcagggtcctgtccata	8	10	3	0	rs374157769		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:93547887G>A	ENST00000394196.4	+	34	5387	c.4319G>A	c.(4318-4320)cGa>cAa	p.R1440Q	CHD2_ENST00000557381.1_Missense_Mutation_p.R1440Q	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1440					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.R1440Q(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			AAATCAAAGCGATCTCAGGGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	15											170	154	159					15																	93547887		2197	4298	6495	91348891	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4319G>A	15.37:g.93547887G>A	ENSP00000377747:p.Arg1440Gln		91348891	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107375	0.56291	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;D	0.89875	4.34;-2.58	5.34	4.42	0.53409	.	0.000000	0.32015	U	0.006716	T	0.81721	0.4882	L	0.34521	1.04	0.80722	D	1	B;B	0.23490	0.052;0.086	B;B	0.12837	0.003;0.008	T	0.75470	-0.3306	10	0.13853	T	0.58	-5.4645	14.1743	0.65529	0.0726:0.0:0.9274:0.0	.	1440;1440	O14647;O14647-2	CHD2_HUMAN;.	Q	1440	ENSP00000377747:R1440Q;ENSP00000451366:R1440Q	ENSP00000377747:R1440Q	R	+	2	0	CHD2	91348891	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	1.240000	0.43803	0.655000	0.94253	CGA		0.433	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		A	93547887	G	A	93547887	3	1	61	1	0	0	0	0	1	0	0	0	3331	1058	37	1	4453	1	CHD2	15	93547887	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1752221	93547887	8983505	9572	17557										
CHD2	1106	broad.mit.edu	37	chr15	93563317	93563317	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccatggggaagcgacaGgcaccatcagtatgagcagc	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:93563317G>T	ENST00000394196.4	+	38	6050	c.4982G>T	c.(4981-4983)aGg>aTg	p.R1661M	CHD2_ENST00000557381.1_Missense_Mutation_p.R1661M	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1661					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.R1661M(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GGAAGCGACAGGCACCATCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	101	111					15																	93563317		2197	4298	6495	91364321	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4982G>T	15.37:g.93563317G>T	ENSP00000377747:p.Arg1661Met		91364321	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	33	5.239393	0.95240	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.92199	-2.99;-2.93	5.61	5.61	0.85477	.	0.000000	0.30547	U	0.009393	D	0.94003	0.8079	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.99;0.995	D	0.94307	0.7542	10	0.59425	D	0.04	-23.896	19.6303	0.95699	0.0:0.0:1.0:0.0	.	1661;1661	O14647;O14647-2	CHD2_HUMAN;.	M	1661	ENSP00000377747:R1661M;ENSP00000451366:R1661M	ENSP00000377747:R1661M	R	+	2	0	CHD2	91364321	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.148000	0.94652	2.641000	0.89580	0.655000	0.94253	AGG		0.517	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		T	93563317	G	T	93563317	3	4	61	1	0	0	0	0	1	0	0	0	3331	1000	35	2	5132	2	CHD2	15	93563317	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15430	93563317	8968075	9573	17558										
MCTP2	55784	broad.mit.edu	37	chr15	94882589	94882589	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagtaaagtcatatataaGaacttgaacccagtatggga	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:94882589G>T	ENST00000357742.4	+	4	708	c.708G>T	c.(706-708)aaG>aaT	p.K236N	MCTP2_ENST00000451018.3_Missense_Mutation_p.K236N|MCTP2_ENST00000543482.1_Missense_Mutation_p.K236N|MCTP2_ENST00000331706.4_5'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	236	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.K236N(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TCATATATAAGAACTTGAACC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											111	115	114					15																	94882589		2197	4298	6495	92683593	SO:0001583	missense	55784			AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.708G>T	15.37:g.94882589G>T	ENSP00000350377:p.Lys236Asn		92683593	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199258	0.79015	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.09723	2.95;2.95;2.95	6.03	5.11	0.69529	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.26521	0.0648	L	0.46157	1.445	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.953;1.0;1.0;1.0	D;P;D;D;D	0.97110	0.999;0.867;1.0;1.0;0.999	T	0.00108	-1.2050	10	0.87932	D	0	.	14.4118	0.67119	0.0708:0.0:0.9292:0.0	.	236;236;236;236;236	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	N	236	ENSP00000438521:K236N;ENSP00000395109:K236N;ENSP00000350377:K236N	ENSP00000350377:K236N	K	+	3	2	MCTP2	92683593	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.742000	0.55097	2.861000	0.98227	0.655000	0.94253	AAG		0.363	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94882589	G	T	94882589	3	4	61	1	0	0	0	0	1	0	0	0	9431	933	33	2	722	2	MCTP2	15	94882589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1319272	94882589	7648803	9574	17559										
IGF1R	3480	broad.mit.edu	37	chr15	99440115	99440115	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcaagggcaatttgctCattaacatccgacgggggag	11	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99440115C>A	ENST00000268035.6	+	4	1694	c.1083C>A	c.(1081-1083)ctC>ctA	p.L361L	IGF1R_ENST00000558762.1_Silent_p.L361L|IGF1R_ENST00000560432.1_3'UTR	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	361					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.L361L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCAATTTGCTCATTAACATCC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	15											120	103	109					15																	99440115		2197	4297	6494	97257638	SO:0001819	synonymous_variant	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1083C>A	15.37:g.99440115C>A			97257638	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																				0.463	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99440115	C	A	99440115	2	1	61	1	0	0	0	0	0	0	0	1	7592	813	29	2		2	IGF1R	15	99440115	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4557526	99440115	3091277	9575	17560										
IGF1R	3480	broad.mit.edu	37	chr15	99482585	99482585	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagatttcacagtcaaaatCggaggtgtgtccttagcttt	10	7	2	1	rs375579623		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99482585C>T	ENST00000268035.6	+	18	4064	c.3453C>T	c.(3451-3453)atC>atT	p.I1151I	IGF1R_ENST00000558762.1_Silent_p.I1150I	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.I1151I(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CAGTCAAAATCGGAGGTGTGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C		0,4394		0,0,2197	139	129	133		3453	-8.9	0.4	15		133	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	IGF1R	NM_000875.3		0,1,6493	TT,TC,CC		0.0116,0.0,0.0077		1151/1368	99482585	1,12987	2197	4297	6494	97300108	SO:0001819	synonymous_variant	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3453C>T	15.37:g.99482585C>T			97300108	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																				0.493	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		T	99482585	C	T	99482585	2	4	61	1	0	0	0	0	0	0	0	1	7592	874	31	1		1	IGF1R	15	99482585	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42470	99482585	3048807	9576	17561										
PGPEP1L	145814	broad.mit.edu	37	chr15	99512682	99512682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcgggaaaagatcacgtCgacaccctccacagctacgc	8	15	2	1	rs577639159		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99512682C>T	ENST00000378919.6	-	4	548	c.343G>A	c.(343-345)Gac>Aac	p.D115N	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Missense_Mutation_p.D61N	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	115							cysteine-type peptidase activity (GO:0008234)	p.D115N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						AAGATCACGTCGACACCCTCC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	15											119	121	121					15																	99512682		2190	4294	6484	97330205	SO:0001583	missense	145814				CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.343G>A	15.37:g.99512682C>T	ENSP00000368199:p.Asp115Asn		97330205	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.909249	0.33721	.	.	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.41400	1.0	4.37	2.35	0.29111	.	0.642985	0.14346	N	0.325435	T	0.39384	0.1076	L	0.42686	1.345	0.09310	N	1	B	0.19583	0.037	B	0.24701	0.055	T	0.45963	-0.9225	10	0.66056	D	0.02	-12.2741	15.6029	0.76639	0.0:0.723:0.277:0.0	.	115	A6NFU8	PGPIL_HUMAN	N	115;108	ENSP00000368199:D115N	ENSP00000368199:D115N	D	-	1	0	PGPEP1L	97330205	0.055000	0.20627	0.003000	0.11579	0.002000	0.02628	2.088000	0.41663	1.035000	0.39972	0.655000	0.94253	GAC		0.632	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2		T	99512682	C	T	99512682	3	4	61	1	0	0	0	0	1	0	0	0	11835	884	31	1	255	1	PGPEP1L	15	99512682	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30097	99512682	3018710	9577	17562										
SYNM	23336	broad.mit.edu	37	chr15	99671320	99671320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcggtgaatttcatgccGaacccacagtcattgaaaaa	9	9	2	2	rs376246829		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99671320G>A	ENST00000560674.1	+	4	2366	c.1897G>A	c.(1897-1899)Gaa>Aaa	p.E633K	SYNM_ENST00000328642.7_Missense_Mutation_p.E918K|RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000336292.6_Missense_Mutation_p.E918K|SYNM_ENST00000561323.1_3'UTR			O15061	SYNEM_HUMAN	synemin, intermediate filament protein	919	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)	p.E918K(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						ATTTCATGCCGAACCCACAGT	0.537																																					Pancreas(125;1071 1762 21750 40003 40381)											1	Substitution - Missense(1)	large_intestine(1)	15						G	LYS/GLU,LYS/GLU	1,3813		0,1,1906	33	34	34		2754,2754	4.8	0	15		34	0,8232		0,0,4116	no	missense,missense	SYNM	NM_145728.2,NM_015286.5	56,56	0,1,6022	AA,AG,GG		0.0,0.0262,0.0083	benign,benign	919/1566,919/1254	99671320	1,12045	1907	4116	6023	97488843	SO:0001583	missense	23336			AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000560674.1:c.1897G>A	15.37:g.99671320G>A	ENSP00000453040:p.Glu633Lys		97488843	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000560674.1	37		.	.	.	.	.	.	.	.	.	.	G	14.86	2.661171	0.47572	2.62E-4	0.0	ENSG00000182253	ENST00000336292;ENST00000328642	D;D	0.85702	-1.95;-2.02	5.76	4.85	0.62838	.	.	.	.	.	T	0.77691	0.4168	.	.	.	0.09310	N	1	B;B	0.34255	0.225;0.445	B;B	0.23150	0.032;0.044	T	0.68996	-0.5262	8	0.52906	T	0.07	.	13.9218	0.63937	0.0725:0.0:0.9275:0.0	.	919;918	O15061;C9JIE4	SYNEM_HUMAN;.	K	918	ENSP00000336775:E918K;ENSP00000330469:E918K	ENSP00000330469:E918K	E	+	1	0	SYNM	97488843	1.000000	0.71417	0.004000	0.12327	0.868000	0.49771	5.490000	0.66881	1.439000	0.47511	0.655000	0.94253	GAA		0.537	SYNM-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000415698.2	NM_145728		A	99671320	G	A	99671320	3	1	61	1	0	0	0	0	1	0	0	0	15494	1059	37	1	2768	1	SYNM	15	99671320	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	158638	99671320	2860072	9578	17563										
SYNM	23336	broad.mit.edu	37	chr15	99672721	99672721	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccccaggaggatagtgcaGaggacacatcaggggcagaa	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99672721G>T	ENST00000336292.6	+	5	4273	c.4153G>T	c.(4153-4155)Gag>Tag	p.E1385*	SYNM_ENST00000328642.7_Intron|SYNM_ENST00000560674.1_Intron|RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000561323.1_3'UTR	NM_145728.2	NP_663780.2	O15061	SYNEM_HUMAN	synemin, intermediate filament protein	1386	Interaction with DMD and UTRN.|Interaction with TLN1 and VCL.|Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)	p.E1385*(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						GGATAGTGCAGAGGACACATC	0.493																																					Pancreas(125;1071 1762 21750 40003 40381)											1	Substitution - Nonsense(1)	large_intestine(1)	15											194	188	190					15																	99672721		1978	4166	6144	97490244	SO:0001587	stop_gained	23336			AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000336292.6:c.4153G>T	15.37:g.99672721G>T	ENSP00000336775:p.Glu1385*		97490244	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Nonsense_Mutation	SNP	ENST00000336292.6	37		.	.	.	.	.	.	.	.	.	.	G	42	9.200560	0.99098	.	.	ENSG00000182253	ENST00000336292	.	.	.	5.42	3.49	0.39957	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	6.9753	0.24672	0.1585:0.1427:0.6988:0.0	.	.	.	.	X	1385	.	ENSP00000336775:E1385X	E	+	1	0	SYNM	97490244	0.053000	0.20554	0.001000	0.08648	0.005000	0.04900	1.269000	0.33074	0.606000	0.29965	0.655000	0.94253	GAG		0.493	SYNM-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_145728		T	99672721	G	T	99672721	4	4	61	1	0	0	0	0	0	1	0	0	15494	943	33	2	4169	2	SYNM	15	99672721	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1401	99672721	2858671	9579	17564										
LRRC28	123355	broad.mit.edu	37	chr15	99926274	99926274	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcttactgctgctccacCcagtgtctgcagacttttga	10	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:99926274C>T	ENST00000301981.3	+	10	1311	c.1071C>T	c.(1069-1071)acC>acT	p.T357T	LRRC28_ENST00000558879.1_3'UTR|LRRC28_ENST00000331450.5_Silent_p.T83T|LRRC28_ENST00000422500.2_Silent_p.T288T|LRRC28_ENST00000447360.2_Missense_Mutation_p.P304L	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	357								p.T357T(1)		endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			GCTGCTCCACCCAGTGTCTGC	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	15											321	324	323					15																	99926274		2197	4297	6494	97743797	SO:0001819	synonymous_variant	123355			AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.1071C>T	15.37:g.99926274C>T			97743797	A8KA22|Q6UY49|Q6ZSS6	Silent	SNP	ENST00000301981.3	37	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.367177	0.41902	.	.	ENSG00000168904	ENST00000447360	T	0.40476	1.03	5.6	1.54	0.23209	.	.	.	.	.	T	0.25901	0.0631	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05370	-1.0889	8	0.25106	T	0.35	.	6.2868	0.21037	0.1303:0.659:0.0:0.2107	.	304	Q86X40-2	.	L	304	ENSP00000404520:P304L	ENSP00000404520:P304L	P	+	2	0	LRRC28	97743797	1.000000	0.71417	0.998000	0.56505	1.000000	0.99986	1.237000	0.32695	0.032000	0.15435	0.655000	0.94253	CCC		0.488	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		T	99926274	C	T	99926274	2	4	61	1	0	0	0	0	0	0	0	1	9011	610	22	3		3	LRRC28	15	99926274	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253553	99926274	2605118	9580	17565										
MEF2A	4205	broad.mit.edu	37	chr15	100230589	100230589	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtaggaaaccagatcttCgagttgtcatccccccttca	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:100230589C>T	ENST00000557785.1	+	8	1163	c.814C>T	c.(814-816)Cga>Tga	p.R272*	MEF2A_ENST00000338042.6_Nonsense_Mutation_p.R272*|MEF2A_ENST00000453228.2_Nonsense_Mutation_p.R272*|MEF2A_ENST00000558812.1_Nonsense_Mutation_p.R204*|MEF2A_ENST00000354410.5_Nonsense_Mutation_p.R274*|MEF2A_ENST00000449277.2_Nonsense_Mutation_p.R204*|MEF2A_ENST00000557942.1_Nonsense_Mutation_p.R272*	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	274	Required for interaction with MAPKs.				apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)	p.R274*(2)|p.R272*(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			ACCAGATCTTCGAGTTGTCAT	0.433																																																3	Substitution - Nonsense(3)	large_intestine(3)	15											61	59	60					15																	100230589		1898	4116	6014	98048112	SO:0001587	stop_gained	4205				CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.814C>T	15.37:g.100230589C>T	ENSP00000453441:p.Arg272*		98048112	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Nonsense_Mutation	SNP	ENST00000557785.1	37	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	C	39	7.331825	0.98217	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	.	.	.	5.85	4.93	0.64822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2928	16.3198	0.82945	0.1335:0.8665:0.0:0.0	.	.	.	.	X	272;274;272;204	.	ENSP00000337202:R272X	R	+	1	2	MEF2A	98048112	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.721000	0.54941	1.458000	0.47871	-0.188000	0.12872	CGA		0.433	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			T	100230589	C	T	100230589	4	4	61	1	0	0	0	0	0	1	0	0	9485	876	31	1	978	1	MEF2A	15	100230589	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	304315	100230589	2300803	9581	17566										
LYSMD4	145748	broad.mit.edu	37	chr15	100269604	100269604	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaccatccataggcgtcttCggaggtgccgggagcagtgg	16	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:100269604C>T	ENST00000409796.1	-	3	677	c.615G>A	c.(613-615)ccG>ccA	p.P205P	LYSMD4_ENST00000545021.1_Silent_p.P79P|LYSMD4_ENST00000332728.4_Silent_p.P205P|LYSMD4_ENST00000604213.1_Intron|LYSMD4_ENST00000344791.2_Silent_p.P206P	NM_001284417.1|NM_001284418.1|NM_001284420.1	NP_001271346.1|NP_001271347.1|NP_001271349.1	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain containing 4	205						integral component of membrane (GO:0016021)		p.P206P(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)	10	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			TAGGCGTCTTCGGAGGTGCCG	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	15											125	120	122					15																	100269604		2203	4300	6503	98087127	SO:0001819	synonymous_variant	145748			BC041097	CCDS10381.1, CCDS66876.1, CCDS66877.1, CCDS73788.1	15q26.3	2005-10-24			ENSG00000183060	ENSG00000183060			26571	protein-coding gene	gene with protein product						12477932	Standard	NM_001284418		Approved	FLJ33008	uc002bvl.3	Q5XG99	OTTHUMG00000149853	ENST00000409796.1:c.615G>A	15.37:g.100269604C>T			98087127	A6NII6|A8K2N1|Q96LY7	Silent	SNP	ENST00000409796.1	37																																																																																					0.483	LYSMD4-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335634.1	NM_152449		T	100269604	C	T	100269604	2	4	61	1	0	0	0	0	0	0	0	1	9157	871	31	1		1	LYSMD4	15	100269604	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39015	100269604	2261788	9582	17567										
ADAMTS17	170691	broad.mit.edu	37	chr15	100739575	100739575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaattgagaccattgtcttCggcaagcacacacttcctct	6	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:100739575C>T	ENST00000268070.4	-	8	1234	c.1129G>A	c.(1129-1131)Gaa>Aaa	p.E377K	ADAMTS17_ENST00000559976.1_5'UTR	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	377	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E377K(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	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)		CCATTGTCTTCGGCAAGCACA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											305	245	265					15																	100739575		2203	4300	6503	98557098	SO:0001583	missense	170691			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1129G>A	15.37:g.100739575C>T	ENSP00000268070:p.Glu377Lys		98557098	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	C	35	5.503884	0.96371	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	D	0.87571	-2.27	5.55	5.55	0.83447	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.92835	0.7721	M	0.62209	1.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.92873	0.6316	10	0.62326	D	0.03	.	19.5283	0.95215	0.0:1.0:0.0:0.0	.	134;377	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	K	377;134	ENSP00000268070:E377K	ENSP00000268070:E377K	E	-	1	0	ADAMTS17	98557098	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.918000	0.75788	2.596000	0.87737	0.655000	0.94253	GAA		0.488	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		T	100739575	C	T	100739575	3	4	61	1	0	0	0	0	1	0	0	0	262	893	31	1	2218	1	ADAMTS17	15	100739575	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	469971	100739575	1791817	9583	17568										
ADAMTS17	170691	broad.mit.edu	37	chr15	100794378	100794378	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatccttgtgtacacagaaAtctgtcctaaaaaataaaaa	4	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:100794378A>T	ENST00000268070.4	-	7	1143	c.1038T>A	c.(1036-1038)gaT>gaA	p.D346E	ADAMTS17_ENST00000559976.1_5'UTR	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	346	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D346E(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	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)		GTACACAGAAATCTGTCCTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											98	94	96					15																	100794378		2203	4300	6503	98611901	SO:0001583	missense	170691			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1038T>A	15.37:g.100794378A>T	ENSP00000268070:p.Asp346Glu		98611901	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.025228	0.75390	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	D	0.90004	-2.6	5.47	1.43	0.22495	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (1);	0.060803	0.64402	N	0.000008	D	0.93324	0.7872	M	0.83692	2.655	0.41919	D	0.990502	D;D	0.89917	1.0;0.997	D;D	0.80764	0.978;0.994	D	0.92402	0.5930	10	0.72032	D	0.01	.	10.0935	0.42460	0.7681:0.0:0.2319:0.0	.	103;346	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	E	346;103	ENSP00000268070:D346E	ENSP00000268070:D346E	D	-	3	2	ADAMTS17	98611901	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.016000	0.49607	0.370000	0.24538	0.528000	0.53228	GAT		0.398	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		T	100794378	A	T	100794378	3	4	61	1	0	0	0	0	1	0	0	0	262	98	4	5	2313	5	ADAMTS17	15	100794378	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	54803	100794378	1737014	9584	17569										
LASS3	204219	broad.mit.edu	37	chr15	101031058	101031058	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaatgtttgaaaaaattCtctaagacagtatttggtgt	10	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101031058C>A	ENST00000394113.1	-	6	942	c.252G>T	c.(250-252)gaG>gaT	p.E84D	CERS3_ENST00000560944.1_Intron|CERS3_ENST00000538112.2_Missense_Mutation_p.E84D|CERS3_ENST00000284382.4_Missense_Mutation_p.E84D			Q8IU89	CERS3_HUMAN	ceramide synthase 3	84					ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.E84D(2)									TGAAAAAATTCTCTAAGACAG	0.303																																																2	Substitution - Missense(2)	large_intestine(2)	15											111	110	110					15																	101031058		2203	4299	6502	98848581	SO:0001583	missense	204219				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.252G>T	15.37:g.101031058C>A	ENSP00000377672:p.Glu84Asp		98848581	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620296	0.87460	.	.	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	D;D	0.97791	-4.54;-4.54	5.53	5.53	0.82687	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98874	0.9619	M	0.89658	3.05	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.99425	1.0934	10	0.87932	D	0	-22.871	15.3311	0.74212	0.0:1.0:0.0:0.0	.	84	Q8IU89	CERS3_HUMAN	D	84;95;84	ENSP00000284382:E84D;ENSP00000437640:E84D	ENSP00000284382:E84D	E	-	3	2	CERS3	98848581	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.111000	0.50360	2.763000	0.94921	0.563000	0.77884	GAG		0.303	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		A	101031058	C	A	101031058	3	1	61	1	0	0	0	0	1	0	0	0	8662	912	32	2	935	2	LASS3	15	101031058	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	236680	101031058	1500334	9585	17570										
LINS1	55180	broad.mit.edu	37	chr15	101110321	101110321	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctttcagtggcttcacatcCtctgaaaatgaagataatgg	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101110321C>A	ENST00000314742.8	-	7	1618	c.1396G>T	c.(1396-1398)Gga>Tga	p.G466*	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	466								p.G466*(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						GCTTCACATCCTCTGAAAATG	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											52	52	52					15																	101110321		2200	4297	6497	98927844	SO:0001630	splice_region_variant	55180			AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1395-1G>T	15.37:g.101110321C>A			98927844	Q96FW2|Q9NVQ3	Nonsense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.835246	0.91117	.	.	ENSG00000140471	ENST00000314742	.	.	.	5.39	1.14	0.20703	.	1.168720	0.06059	N	0.657987	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-0.7971	1.5991	0.02670	0.2372:0.4572:0.133:0.1726	.	.	.	.	X	466	.	ENSP00000318423:G466X	G	-	1	0	LINS	98927844	0.007000	0.16637	0.299000	0.25016	0.236000	0.25371	0.385000	0.20685	0.254000	0.21573	-0.140000	0.14226	GGA		0.333	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	Nonsense_Mutation	A	101110321	C	A	101110321	5	1	61	1	0	0	0	0	0	0	1	0	8842	695	24	2	881	2	LINS1	15	101110321	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79263	101110321	1421071	9586	17571										
LINS1	55180	broad.mit.edu	37	chr15	101114187	101114187	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaggaatatgatgaccttCcttttaacaaaagcctgaat	7	7	0	4	rs377158396		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101114187C>T	ENST00000314742.8	-	5	1113	c.891G>A	c.(889-891)agG>agA	p.R297R	LINS_ENST00000560133.1_Silent_p.R178R|LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_Silent_p.R297R	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	297								p.R297R(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						TGATGACCTTCCTTTTAACAA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	15						C		0,4406		0,0,2203	83	79	80		891	0	0.8	15		80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LINS	NM_001040616.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		297/758	101114187	1,13005	2203	4300	6503	98931710	SO:0001819	synonymous_variant	55180			AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.891G>A	15.37:g.101114187C>T			98931710	Q96FW2|Q9NVQ3	Silent	SNP	ENST00000314742.8	37	CCDS10385.1																																																																																				0.428	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		T	101114187	C	T	101114187	2	4	61	1	0	0	0	0	0	0	0	1	8842	854	30	3		3	LINS1	15	101114187	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3866	101114187	1417205	9587	17572										
ASB7	140460	broad.mit.edu	37	chr15	101169898	101169898	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaccacaccgcttcagctCgccattatccgagagaggtc	10	14	1	1	rs549056141		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101169898C>T	ENST00000332783.7	+	5	1253	c.468C>T	c.(466-468)ctC>ctT	p.L156L	ASB7_ENST00000558747.1_Intron|ASB7_ENST00000343276.4_Silent_p.L156L	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	156					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.L156L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	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)			CGCTTCAGCTCGCCATTATCC	0.532													C|||	1	0.000199681	0	0	5008	,	,		20237	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15											88	71	77					15																	101169898		2203	4300	6503	98987421	SO:0001819	synonymous_variant	140460				CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"Ankyrin repeat domain containing"	17182	protein-coding gene	gene with protein product		615052	"ankyrin repeat and SOCS box-containing 7"				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.468C>T	15.37:g.101169898C>T			98987421	A8K1E5|Q6GSJ6|Q7Z4S3	Silent	SNP	ENST00000332783.7	37	CCDS10387.1																																																																																				0.532	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708		T	101169898	C	T	101169898	2	4	61	1	0	0	0	0	0	0	0	1	1029	871	31	1		1	ASB7	15	101169898	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55711	101169898	1361494	9588	17573										
ALDH1A3	220	broad.mit.edu	37	chr15	101440960	101440960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcaaaacagaacaggggcCtcaggtaatccccctggtgt	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101440960C>T	ENST00000329841.5	+	9	1596	c.1064C>T	c.(1063-1065)cCt>cTt	p.P355L	ALDH1A3_ENST00000346623.6_Missense_Mutation_p.P248L|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	355					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)	p.P355L(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	GAACAGGGGCCTCAGGTAATC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											37	39	38					15																	101440960		2203	4300	6503	99258483	SO:0001583	missense	220			U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"Aldehyde dehydrogenases"	409	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 3"	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.1064C>T	15.37:g.101440960C>T	ENSP00000332256:p.Pro355Leu		99258483	Q6NT64	Missense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477523	0.63849	.	.	ENSG00000184254	ENST00000329841;ENST00000346623	D	0.87029	-2.2	5.7	4.79	0.61399	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.96920	0.8994	H	0.99890	4.9	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.976	D	0.98327	1.0531	10	0.87932	D	0	.	14.6588	0.68852	0.0:0.9304:0.0:0.0696	.	259;355	Q7Z3A2;P47895	.;AL1A3_HUMAN	L	355;259	ENSP00000332256:P355L	ENSP00000332256:P355L	P	+	2	0	ALDH1A3	99258483	1.000000	0.71417	0.896000	0.35187	0.094000	0.18550	7.380000	0.79704	1.401000	0.46761	0.655000	0.94253	CCT		0.582	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2			T	101440960	C	T	101440960	3	4	61	1	0	0	0	0	1	0	0	0	492	681	24	3	1098	3	ALDH1A3	15	101440960	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271062	101440960	1090432	9589	17574										
ALDH1A3	220	broad.mit.edu	37	chr15	101448683	101448683	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtcaggaaatggcagaGaactgtaagtgtttccatca	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101448683G>T	ENST00000329841.5	+	12	1994	c.1462G>T	c.(1462-1464)Gaa>Taa	p.E488*	ALDH1A3_ENST00000346623.6_Nonsense_Mutation_p.E381*|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	488					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)	p.E488*(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	AAATGGCAGAGAACTGTAAGT	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											125	109	114					15																	101448683		2203	4300	6503	99266206	SO:0001587	stop_gained	220			U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"Aldehyde dehydrogenases"	409	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 3"	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.1462G>T	15.37:g.101448683G>T	ENSP00000332256:p.Glu488*		99266206	Q6NT64	Nonsense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	G	38	7.051507	0.98029	.	.	ENSG00000184254	ENST00000329841;ENST00000346623	.	.	.	5.22	5.22	0.72569	.	0.047335	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.8097	0.92053	0.0:0.0:1.0:0.0	.	.	.	.	X	488;392	.	ENSP00000332256:E488X	E	+	1	0	ALDH1A3	99266206	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.711000	0.98735	2.430000	0.82344	0.643000	0.83706	GAA		0.488	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2			T	101448683	G	T	101448683	4	4	61	1	0	0	0	0	0	1	0	0	492	943	33	2	1508	2	ALDH1A3	15	101448683	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7723	101448683	1082709	9590	17575										
LRRK1	79705	broad.mit.edu	37	chr15	101588776	101588776	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacaggaaaccagagaaaTcgctgtagcacattcagagt	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101588776T>G	ENST00000388948.3	+	22	3572	c.3213T>G	c.(3211-3213)aaT>aaG	p.N1071K	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.N1068K|RP11-505E24.3_ENST00000558979.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.N1071K(1)|p.N1083K(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	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)			ACCAGAGAAATCGCTGTAGCA	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	15											129	128	128					15																	101588776		1880	4124	6004	99406299	SO:0001583	missense	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3213T>G	15.37:g.101588776T>G	ENSP00000373600:p.Asn1071Lys		99406299		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.670022	0.67814	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.72835	-0.64;-0.69	5.1	-2.54	0.06307	.	0.000000	0.85682	D	0.000000	T	0.55832	0.1945	L	0.51422	1.61	0.40217	D	0.977697	B	0.31077	0.307	B	0.29440	0.102	T	0.55592	-0.8117	10	0.05833	T	0.94	.	14.8455	0.70257	0.0:0.757:0.0:0.243	.	1071	Q38SD2	LRRK1_HUMAN	K	1071;1068	ENSP00000373600:N1071K;ENSP00000284395:N1068K	ENSP00000284395:N1068K	N	+	3	2	LRRK1	99406299	0.023000	0.18921	0.995000	0.50966	0.999000	0.98932	-0.799000	0.04560	-0.333000	0.08476	0.528000	0.53228	AAT		0.433	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		G	101588776	T	G	101588776	3	3	61	1	0	0	0	0	1	0	0	0	9061	1432	50	4	3295	4	LRRK1	15	101588776	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	140093	101588776	942616	9591	17576										
PCSK6	5046	broad.mit.edu	37	chr15	101933603	101933603	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattcccagatgcccagacGaaaatggagcccaggccctg	10	15	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:101933603G>A	ENST00000348070.1	-	9	1019	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	PCSK6_ENST00000358417.3_Silent_p.F340F|PCSK6_ENST00000398181.2_Silent_p.F340F|PCSK6_ENST00000331826.7_Silent_p.F175F|PCSK6_ENST00000344273.2_Silent_p.F340F|PCSK6_ENST00000561177.1_5'UTR	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	341	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)	p.F340F(3)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ATGCCCAGACGAAAATGGAGC	0.627																																																3	Substitution - coding silent(3)	large_intestine(3)	15											42	50	47					15																	101933603		2193	4299	6492	99751126	SO:0001819	synonymous_variant	5046				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"subtilisin-like protease", "subtilisin-like proprotein convertase 4", "subtilisin/kexin-like protease PACE4"	167405	"paired basic amino acid cleaving system 4"	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.1020C>T	15.37:g.101933603G>A			99751126	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Silent	SNP	ENST00000348070.1	37																																																																																					0.627	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570		A	101933603	G	A	101933603	2	1	61	1	0	0	0	0	0	0	0	1	11635	1049	37	1		1	PCSK6	15	101933603	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	344827	101933603	597789	9592	17577										
OR4F15	390649	broad.mit.edu	37	chr15	102358483	102358483	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctactttttgttttctctTtgttgttctactttgcgagc	6	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:102358483T>G	ENST00000332238.4	+	1	118	c.94T>G	c.(94-96)Ttg>Gtg	p.L32V		NM_001001674.1	NP_001001674.1	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F, member 15	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L32V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(10)	19	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TGTTTTCTCTTTGTTGTTCTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	15											218	193	202					15																	102358483		2203	4300	6503	100176006	SO:0001583	missense	390649			BK004405	CCDS32342.1	15q26.3	2012-08-09				ENSG00000182854		"GPCR / Class A : Olfactory receptors"	15078	protein-coding gene	gene with protein product							Standard	NM_001001674		Approved		uc010uts.2	Q8NGB8		ENST00000332238.4:c.94T>G	15.37:g.102358483T>G	ENSP00000333184:p.Leu32Val		100176006	B2RNQ5|Q6IF57|Q96R70	Missense_Mutation	SNP	ENST00000332238.4	37	CCDS32342.1	.	.	.	.	.	.	.	.	.	.	.	1.890	-0.455626	0.04540	.	.	ENSG00000182854	ENST00000332238	T	0.01902	4.57	5.24	1.44	0.22558	.	1.002720	0.08038	N	0.994635	T	0.03871	0.0109	M	0.81239	2.535	0.09310	N	1	B	0.16603	0.018	B	0.17098	0.017	T	0.47824	-0.9087	9	.	.	.	.	1.3908	0.02250	0.3096:0.0838:0.1611:0.4455	.	32	Q8NGB8	O4F15_HUMAN	V	32	ENSP00000333184:L32V	.	L	+	1	2	OR4F15	100176006	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.530000	0.06179	0.064000	0.16427	0.528000	0.53228	TTG		0.423	OR4F15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417594.1	NM_001001674		G	102358483	T	G	102358483	3	3	61	1	0	0	0	0	1	0	0	0	11092	1838	64	4	96	4	OR4F15	15	102358483	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	424880	102358483	172909	9593	17578										
OR4F15	390649	broad.mit.edu	37	chr15	102358716	102358716	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagccatgctcttgggggCactgagatggtgctgctcat	13	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr15:102358716C>A	ENST00000332238.4	+	1	351	c.327C>A	c.(325-327)ggC>ggA	p.G109G		NM_001001674.1	NP_001001674.1	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F, member 15	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G109G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(10)	19	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			CTCTTGGGGGCACTGAGATGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	15											138	126	130					15																	102358716		2203	4300	6503	100176239	SO:0001819	synonymous_variant	390649			BK004405	CCDS32342.1	15q26.3	2012-08-09				ENSG00000182854		"GPCR / Class A : Olfactory receptors"	15078	protein-coding gene	gene with protein product							Standard	NM_001001674		Approved		uc010uts.2	Q8NGB8		ENST00000332238.4:c.327C>A	15.37:g.102358716C>A			100176239	B2RNQ5|Q6IF57|Q96R70	Silent	SNP	ENST00000332238.4	37	CCDS32342.1																																																																																				0.458	OR4F15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417594.1	NM_001001674		A	102358716	C	A	102358716	2	1	61	1	0	0	0	0	0	0	0	1	11092	697	25	2		2	OR4F15	15	102358716	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	233	102358716	172676	9594	17579										
POLR3K	51728	broad.mit.edu	37	chr16	97554	97554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgttcgcatttgggacacGactctggcaatgagaaaaaa	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:97554G>A	ENST00000293860.5	-	3	244	c.203C>T	c.(202-204)tCg>tTg	p.S68L		NM_016310.3	NP_057394.2	Q9Y2Y1	RPC10_HUMAN	polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa	68					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.S68L(1)		central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				TTTGGGACACGACTCTGGCAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	16											69	60	63					16																	97554		2203	4300	6503	37554	SO:0001583	missense	51728			AF051316	CCDS10395.1	16p13.3	2013-01-21	2002-08-29		ENSG00000161980	ENSG00000161980		"RNA polymerase subunits"	14121	protein-coding gene	gene with protein product		606007	"polymerase (RNA) III (DNA directed) polypeptide K (12.3 kDa)"			9869639, 10079944	Standard	NM_016310		Approved	RPC11	uc002cfi.2	Q9Y2Y1	OTTHUMG00000060722	ENST00000293860.5:c.203C>T	16.37:g.97554G>A	ENSP00000293860:p.Ser68Leu		37554	Q1W6H4|Q96S35	Missense_Mutation	SNP	ENST00000293860.5	37	CCDS10395.1	.	.	.	.	.	.	.	.	.	.	.	9.290	1.050376	0.19827	.	.	ENSG00000161980	ENST00000293860	T	0.43688	0.94	4.59	2.6	0.31112	Zinc finger, TFIIS-type (3);	0.211582	0.49916	D	0.000132	T	0.22322	0.0538	N	0.10972	0.075	0.23391	N	0.997775	B	0.15473	0.013	B	0.15484	0.013	T	0.16041	-1.0416	10	0.30078	T	0.28	-3.7294	10.3436	0.43893	0.162:0.0:0.838:0.0	.	68	Q9Y2Y1	RPC10_HUMAN	L	68	ENSP00000293860:S68L	ENSP00000293860:S68L	S	-	2	0	POLR3K	37554	1.000000	0.71417	0.433000	0.26760	0.204000	0.24138	4.293000	0.59037	0.502000	0.28037	0.449000	0.29647	TCG		0.468	POLR3K-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134192.1	NM_016310		A	97554	G	A	97554	3	1	61	1	0	0	0	0	1	0	0	0	12268	1059	37	1	127	1	POLR3K	16	97554	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		97554	90257199	9595	17580										
NPRL3	8131	broad.mit.edu	37	chr16	167326	167326	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaacaccacattaaaaaGaatcatagtaggtgcttccc	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:167326G>T	ENST00000399953.3	-	4	769	c.367C>A	c.(367-369)Ctt>Att	p.L123I	NPRL3_ENST00000399951.3_Intron|NPRL3_ENST00000405960.3_5'UTR	NM_001077350.2|NM_001243247.1|NM_001243248.1|NM_001243249.1	NP_001070818.1|NP_001230176.1|NP_001230177.1|NP_001230178.1	Q12980	NPRL3_HUMAN	nitrogen permease regulator-like 3 (S. cerevisiae)	123					aorta morphogenesis (GO:0035909)|cardiac muscle tissue development (GO:0048738)|palate development (GO:0060021)|ventricular septum development (GO:0003281)		GTPase activator activity (GO:0005096)	p.L123I(2)		endometrium(1)|large_intestine(3)|ovary(2)	6						ACATTAAAAAGAATCATAGTA	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	16											66	63	64					16																	167326		1870	4092	5962	107326	SO:0001583	missense	8131				CCDS73794.1, CCDS73795.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000103148	ENSG00000103148			14124	protein-coding gene	gene with protein product	"conserved gene telomeric to alpha globin cluster"	600928	"chromosome 16 open reading frame 35"	C16orf35		8575760	Standard	NM_001243247		Approved	CGTHBA, RMD11, NPR3, MARE, HS-40	uc002cfr.3	Q12980	OTTHUMG00000047792	ENST00000399953.3:c.367C>A	16.37:g.167326G>T	ENSP00000382834:p.Leu123Ile		107326	D3DU40|Q1W6H0|Q4TT56|Q92469	Missense_Mutation	SNP	ENST00000399953.3	37		.	.	.	.	.	.	.	.	.	.	G	29.7	5.028632	0.93518	.	.	ENSG00000103148	ENST00000399953;ENST00000419636	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.79269	0.4417	.	.	.	0.80722	D	1	P;D	0.76494	0.817;0.999	B;D	0.80764	0.284;0.994	T	0.78331	-0.2245	8	0.42905	T	0.14	0.0277	18.4759	0.90792	0.0:0.0:1.0:0.0	.	45;123	B7Z220;Q12980	.;NPRL3_HUMAN	I	123;136	.	ENSP00000382834:L123I	L	-	1	0	NPRL3	107326	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.575000	0.74018	2.673000	0.90976	0.655000	0.94253	CTT		0.413	NPRL3-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039476		T	167326	G	T	167326	3	4	61	1	0	0	0	0	1	0	0	0	10629	942	33	2	1381	2	NPRL3	16	167326	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69772	167326	90187427	9596	17581										
UBE2I	7329	broad.mit.edu	37	chr16	1370198	1370198	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattcgaaccaccattatttCacccgaatgtgtacccttcg	5	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:1370198C>A	ENST00000355803.4	+	5	798	c.247C>A	c.(247-249)Cac>Aac	p.H83N	UBE2I_ENST00000403747.2_Missense_Mutation_p.H83N|UBE2I_ENST00000406620.1_Missense_Mutation_p.H83N|UBE2I_ENST00000325437.5_Missense_Mutation_p.H83N|UBE2I_ENST00000397515.2_Missense_Mutation_p.H83N|LA16c-358B7.3_ENST00000567829.1_RNA|UBE2I_ENST00000397514.3_Missense_Mutation_p.H83N|LA16c-358B7.3_ENST00000568106.1_RNA|UBE2I_ENST00000566587.1_Missense_Mutation_p.H83N|UBE2I_ENST00000402301.1_Missense_Mutation_p.H83N	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	83					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.H83N(1)		breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				ACCATTATTTCACCCGAATGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											87	78	81					16																	1370198		2199	4300	6499	1310199	SO:0001583	missense	7329			D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"Ubiquitin-conjugating enzymes E2"	12485	protein-coding gene	gene with protein product		601661	"ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)", "ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.247C>A	16.37:g.1370198C>A	ENSP00000348056:p.His83Asn		1310199	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Missense_Mutation	SNP	ENST00000355803.4	37	CCDS10433.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672629	0.88348	.	.	ENSG00000103275	ENST00000325437;ENST00000355803;ENST00000397514;ENST00000397515;ENST00000406620;ENST00000403747;ENST00000402301	T;T;T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33;0.33;0.33	5.13	5.13	0.70059	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	D	0.86818	0.6024	H	0.99740	4.74	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.74348	0.983;0.97	D	0.92434	0.5956	10	0.87932	D	0	.	16.1129	0.81275	0.0:1.0:0.0:0.0	.	83;83	B0QYN7;P63279	.;UBC9_HUMAN	N	83	ENSP00000324897:H83N;ENSP00000348056:H83N;ENSP00000380649:H83N;ENSP00000380650:H83N;ENSP00000384568:H83N;ENSP00000385009:H83N;ENSP00000384361:H83N	ENSP00000324897:H83N	H	+	1	0	UBE2I	1310199	1.000000	0.71417	0.943000	0.38184	0.832000	0.47134	7.606000	0.82863	2.679000	0.91253	0.561000	0.74099	CAC		0.542	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345		A	1370198	C	A	1370198	3	1	61	1	0	0	0	0	1	0	0	0	16899	826	29	2	261	2	UBE2I	16	1370198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1202872	1370198	88984555	9597	17582										
IFT140	9742	broad.mit.edu	37	chr16	1633319	1633319	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgaaaagaacccacctgcActccgtatcgcggctccaga	10	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:1633319A>G	ENST00000426508.2	-	12	1791	c.1428T>C	c.(1426-1428)agT>agC	p.S476S	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	476					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.S476S(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ACCCACCTGCACTCCGTATCG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	16											83	66	72					16																	1633319		2199	4300	6499	1573320	SO:0001819	synonymous_variant	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1428T>C	16.37:g.1633319A>G			1573320	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				0.572	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		G	1633319	A	G	1633319	2	3	61	1	0	0	0	0	0	0	0	1	7577	156	6	4		4	IFT140	16	1633319	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	263121	1633319	88721434	9598	17583										
RPL3L	6123	broad.mit.edu	37	chr16	1995893	1995893	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaacccttcagcatgacGaagtcgttgttcacttcccc	6	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:1995893G>A	ENST00000268661.7	-	8	1084	c.990C>T	c.(988-990)ttC>ttT	p.F330F	MSRB1_ENST00000564908.1_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000399753.2_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	330					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.F330F(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						TCAGCATGACGAAGTCGTTGT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	16											153	129	137					16																	1995893		2199	4300	6499	1935894	SO:0001819	synonymous_variant	6123			U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"L ribosomal proteins"	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.990C>T	16.37:g.1995893G>A			1935894		Silent	SNP	ENST00000268661.7	37	CCDS10450.1																																																																																				0.602	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		A	1995893	G	A	1995893	2	1	61	1	0	0	0	0	0	0	0	1	13631	1049	37	1		1	RPL3L	16	1995893	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	362574	1995893	88358860	9599	17584										
GFER	2671	broad.mit.edu	37	chr16	2035969	2035969	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgggcaagcctgacttCgactgctcaaaagtggatga	12	9	1	2	rs142220504	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2035969C>T	ENST00000248114.6	+	3	564	c.558C>T	c.(556-558)ttC>ttT	p.F186F	AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000567719.1_Silent_p.F111F|GFER_ENST00000569451.1_3'UTR	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	186	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)	p.F186F(1)		endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	AGCCTGACTTCGACTGCTCAA	0.607													C|||	2	0.000399361	0	0.0029	5008	,	,		21734	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											92	86	88					16																	2035969		2198	4300	6498	1975970	SO:0001819	synonymous_variant	2671			BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.558C>T	16.37:g.2035969C>T			1975970	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Silent	SNP	ENST00000248114.6	37	CCDS32368.1																																																																																				0.607	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		T	2035969	C	T	2035969	2	4	61	1	0	0	0	0	0	0	0	1	6358	883	31	1		1	GFER	16	2035969	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40076	2035969	88318784	9600	17585										
MLST8	64223	broad.mit.edu	37	chr16	2256574	2256574	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctacgacggcgtcaacaaGaacatcgcgtctgtgggctt	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2256574G>T	ENST00000569417.1	+	4	612	c.258G>T	c.(256-258)aaG>aaT	p.K86N	AC009065.3_ENST00000517149.1_RNA|MLST8_ENST00000382450.4_Missense_Mutation_p.K85N|MLST8_ENST00000564088.1_Missense_Mutation_p.K86N|MLST8_ENST00000301725.7_Missense_Mutation_p.K105N|MLST8_ENST00000565250.1_Missense_Mutation_p.K86N|MLST8_ENST00000561651.1_3'UTR|MLST8_ENST00000397124.1_Missense_Mutation_p.K86N|MLST8_ENST00000301724.10_Missense_Mutation_p.K86N	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	86					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.K86N(3)		large_intestine(3)|lung(2)|skin(1)	6						GCGTCAACAAGAACATCGCGT	0.582																																																3	Substitution - Missense(3)	large_intestine(3)	16											180	183	182					16																	2256574		2092	4213	6305	2196575	SO:0001583	missense	64223				CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.258G>T	16.37:g.2256574G>T	ENSP00000456405:p.Lys86Asn		2196575	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Missense_Mutation	SNP	ENST00000569417.1	37	CCDS10462.2	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663049	0.67700	.	.	ENSG00000167965	ENST00000382450;ENST00000301724;ENST00000397124;ENST00000301725	T;T;T	0.59906	0.23;0.23;0.23	4.33	3.37	0.38596	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	N	0.21282	0.65	0.80722	D	1	D;D;D;D	0.76494	0.999;0.989;0.999;0.981	D;D;D;P	0.85130	0.997;0.978;0.974;0.772	T	0.50285	-0.8846	10	0.15066	T	0.55	-44.8314	10.5966	0.45341	0.0953:0.0:0.9047:0.0	.	86;105;20;86	B4E2R3;Q9BVC4-4;Q9BVC4-3;Q9BVC4	.;.;.;LST8_HUMAN	N	86;86;86;105	ENSP00000301724:K86N;ENSP00000380313:K86N;ENSP00000301725:K105N	ENSP00000301724:K86N	K	+	3	2	MLST8	2196575	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	4.556000	0.60775	1.038000	0.40049	0.561000	0.74099	AAG		0.582	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372		T	2256574	G	T	2256574	3	4	61	1	0	0	0	0	1	0	0	0	9664	933	33	2	268	2	MLST8	16	2256574	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	220605	2256574	88098179	9601	17586										
ABCA3	21	broad.mit.edu	37	chr16	2336751	2336751	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggggctgggggaagttggaGaccacaatggaggcgtgagg	21	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2336751G>T	ENST00000301732.5	-	22	3922	c.3222C>A	c.(3220-3222)gtC>gtA	p.V1074V	ABCA3_ENST00000382381.3_Silent_p.V1016V	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1074					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.V1074V(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GGAAGTTGGAGACCACAATGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	16											106	108	107					16																	2336751		2198	4300	6498	2276752	SO:0001819	synonymous_variant	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.3222C>A	16.37:g.2336751G>T			2276752	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																				0.632	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		T	2336751	G	T	2336751	2	4	61	1	0	0	0	0	0	0	0	1	33	929	33	2		2	ABCA3	16	2336751	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80177	2336751	88018002	9602	17587										
ABCA3	21	broad.mit.edu	37	chr16	2358456	2358456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcaaacactcacctttcGcctcaaatttcccaatgagc	5	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2358456G>A	ENST00000301732.5	-	11	1980	c.1280C>T	c.(1279-1281)gCg>gTg	p.A427V	ABCA3_ENST00000382381.3_Intron	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	427					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.A427V(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CTCACCTTTCGCCTCAAATTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	16											103	86	92					16																	2358456		2198	4300	6498	2298457	SO:0001583	missense	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1280C>T	16.37:g.2358456G>A	ENSP00000301732:p.Ala427Val		2298457	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	7.921	0.738516	0.15574	.	.	ENSG00000167972	ENST00000301732	T	0.74632	-0.86	5.65	3.59	0.41128	.	.	.	.	.	T	0.61850	0.2380	L	0.53780	1.695	0.80722	D	1	B;B	0.32829	0.386;0.386	B;B	0.22753	0.041;0.041	T	0.56625	-0.7948	9	0.20046	T	0.44	.	8.2688	0.31831	0.0863:0.2912:0.6225:0.0	.	427;427	A7MBM9;Q99758	.;ABCA3_HUMAN	V	427	ENSP00000301732:A427V	ENSP00000301732:A427V	A	-	2	0	ABCA3	2298457	1.000000	0.71417	0.042000	0.18584	0.005000	0.04900	6.126000	0.71635	1.389000	0.46526	0.650000	0.86243	GCG		0.557	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2358456	G	A	2358456	3	1	61	1	0	0	0	0	1	0	0	0	33	1087	38	1	3926	1	ABCA3	16	2358456	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21705	2358456	87996297	9603	17588										
ABCA3	21	broad.mit.edu	37	chr16	2369687	2369687	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctggtactggatggccacGaggaaggggtctgcgatgaa	17	7	1	1	rs138445429	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2369687G>A	ENST00000301732.5	-	8	1468	c.768C>T	c.(766-768)ctC>ctT	p.L256L	ABCA3_ENST00000382381.3_Silent_p.L256L	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	256					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.L256L(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GGATGGCCACGAGGAAGGGGT	0.622													G|||	2	0.000399361	0	0.0014	5008	,	,		18019	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16						G		1,4395	2.1+/-5.4	0,1,2197	117	99	105		768	-9.9	0	16	dbSNP_134	105	0,8600		0,0,4300	no	coding-synonymous	ABCA3	NM_001089.2		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		256/1705	2369687	1,12995	2198	4300	6498	2309688	SO:0001819	synonymous_variant	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.768C>T	16.37:g.2369687G>A			2309688	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																				0.622	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2369687	G	A	2369687	2	1	61	1	0	0	0	0	0	0	0	1	33	1045	37	1		1	ABCA3	16	2369687	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11231	2369687	87985066	9604	17589										
SRRM2	23524	broad.mit.edu	37	chr16	2813312	2813312	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataatatcaccaagacaaaGaagccattctggctcctctt	5	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2813312G>T	ENST00000301740.8	+	11	3332	c.2783G>T	c.(2782-2784)aGa>aTa	p.R928I		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	928	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.R928I(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CCAAGACAAAGAAGCCATTCT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	75	77					16																	2813312		2198	4300	6498	2753313	SO:0001583	missense	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2783G>T	16.37:g.2813312G>T	ENSP00000301740:p.Arg928Ile		2753313	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.467932	0.01053	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.27256	1.68	2.19	1.22	0.21188	.	0.780174	0.10772	N	0.635909	T	0.19127	0.0459	L	0.48642	1.525	0.09310	N	1	B	0.18968	0.032	B	0.04013	0.001	T	0.28808	-1.0032	10	0.54805	T	0.06	0.7523	2.7353	0.05238	0.1652:0.0:0.5557:0.2791	.	928	Q9UQ35	SRRM2_HUMAN	I	928;928;180;893	ENSP00000301740:R928I	ENSP00000301740:R928I	R	+	2	0	SRRM2	2753313	0.002000	0.14202	0.053000	0.19242	0.129000	0.20672	0.046000	0.14035	0.486000	0.27676	0.655000	0.94253	AGA		0.498	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2813312	G	T	2813312	3	4	61	1	0	0	0	0	1	0	0	0	15208	942	33	2	2821	2	SRRM2	16	2813312	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	443625	2813312	87541441	9605	17590										
SRRM2	23524	broad.mit.edu	37	chr16	2813979	2813979	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatatcctacagtggactcGaattctctcttggggcagag	10	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2813979G>A	ENST00000301740.8	+	11	3999	c.3450G>A	c.(3448-3450)tcG>tcA	p.S1150S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1150	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.S1150S(2)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CAGTGGACTCGAATTCTCTCT	0.478																																																2	Substitution - coding silent(2)	urinary_tract(1)|large_intestine(1)	16											88	93	91					16																	2813979		2198	4300	6498	2753980	SO:0001819	synonymous_variant	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3450G>A	16.37:g.2813979G>A			2753980	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																				0.478	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2813979	G	A	2813979	2	1	61	1	0	0	0	0	0	0	0	1	15208	1045	37	1		1	SRRM2	16	2813979	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	667	2813979	87540774	9606	17591										
SRRM2	23524	broad.mit.edu	37	chr16	2814964	2814964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccatctagagggagaagcGaatgtgattcttccccagaa	11	10	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2814964G>A	ENST00000301740.8	+	11	4984	c.4435G>A	c.(4435-4437)Gaa>Aaa	p.E1479K		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1479	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.E1479K(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AGGGAGAAGCGAATGTGATTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											99	100	100					16																	2814964		2198	4300	6498	2754965	SO:0001583	missense	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.4435G>A	16.37:g.2814964G>A	ENSP00000301740:p.Glu1479Lys		2754965	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.381486	0.42207	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.26957	1.7	6.06	6.06	0.98353	.	0.092720	0.47455	D	0.000222	T	0.14570	0.0352	N	0.22421	0.69	0.34454	D	0.701004	P	0.47545	0.897	B	0.32864	0.154	T	0.20706	-1.0267	10	0.15952	T	0.53	-13.4045	16.1209	0.81357	0.0:0.0:1.0:0.0	.	1479	Q9UQ35	SRRM2_HUMAN	K	1479;1479;731	ENSP00000301740:E1479K	ENSP00000301740:E1479K	E	+	1	0	SRRM2	2754965	0.995000	0.38212	1.000000	0.80357	0.891000	0.51852	2.528000	0.45624	2.882000	0.98803	0.655000	0.94253	GAA		0.532	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2814964	G	A	2814964	3	1	61	1	0	0	0	0	1	0	0	0	15208	1059	37	1	4473	1	SRRM2	16	2814964	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	985	2814964	87539789	9607	17592										
SRRM2	23524	broad.mit.edu	37	chr16	2816536	2816536	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcacatctccagtaactCgaagaaggtcccgctctcga	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2816536C>T	ENST00000301740.8	+	11	6556	c.6007C>T	c.(6007-6009)Cga>Tga	p.R2003*		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2003	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.R2003*(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCCAGTAACTCGAAGAAGGTC	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											74	78	76					16																	2816536		2198	4300	6498	2756537	SO:0001587	stop_gained	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.6007C>T	16.37:g.2816536C>T	ENSP00000301740:p.Arg2003*		2756537	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Nonsense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	47	13.450001	0.99743	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	.	.	.	5.46	4.48	0.54585	.	0.000000	0.46145	D	0.000319	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0401	6.8786	0.24160	0.1759:0.7362:0.0:0.0879	.	.	.	.	X	2003;2003;1255	.	ENSP00000301740:R2003X	R	+	1	2	SRRM2	2756537	0.662000	0.27439	0.893000	0.35052	0.998000	0.95712	1.700000	0.37815	1.265000	0.44215	0.650000	0.86243	CGA		0.567	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2816536	C	T	2816536	4	4	61	1	0	0	0	0	0	1	0	0	15208	876	31	1	6045	1	SRRM2	16	2816536	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1572	2816536	87538217	9608	17593										
SRRM2	23524	broad.mit.edu	37	chr16	2817975	2817975	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctggggcagtggcaacGaccacgtcctctgctggtga	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2817975G>A	ENST00000301740.8	+	11	7995	c.7446G>A	c.(7444-7446)acG>acA	p.T2482T	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2482	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.T2482T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CAGTGGCAACGACCACGTCCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	16											116	97	104					16																	2817975		2198	4300	6498	2757976	SO:0001819	synonymous_variant	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7446G>A	16.37:g.2817975G>A			2757976	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																				0.607	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2817975	G	A	2817975	2	1	61	1	0	0	0	0	0	0	0	1	15208	1045	37	1		1	SRRM2	16	2817975	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1439	2817975	87536778	9609	17594										
PRSS21	10942	broad.mit.edu	37	chr16	2868816	2868816	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagccctcgctacctgggGaattcaccctatgacattgc	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2868816G>A	ENST00000005995.3	+	4	438	c.396G>A	c.(394-396)ggG>ggA	p.G132G	PRSS21_ENST00000450020.3_Silent_p.G132G|PRSS21_ENST00000455114.1_Silent_p.G130G			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G132G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						GCTACCTGGGGAATTCACCCT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	16											212	172	185					16																	2868816		2198	4300	6498	2808817	SO:0001819	synonymous_variant	10942			AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.396G>A	16.37:g.2868816G>A			2808817	Q9NS34|Q9P2V6	Silent	SNP	ENST00000005995.3	37	CCDS10478.1																																																																																				0.517	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		A	2868816	G	A	2868816	2	1	61	1	0	0	0	0	0	0	0	1	12652	1161	41	3		3	PRSS21	16	2868816	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50841	2868816	87485937	9610	17595										
PRSS22	64063	broad.mit.edu	37	chr16	2903914	2903914	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagccggcacacagcatgtcCtcagtgatgggtccctgtcc	11	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:2903914C>A	ENST00000161006.3	-	5	734	c.669G>T	c.(667-669)gaG>gaT	p.E223D	PRSS22_ENST00000574768.1_5'Flank|PRSS22_ENST00000571228.1_Missense_Mutation_p.E113D	NM_022119.3	NP_071402.1	Q9GZN4	BSSP4_HUMAN	protease, serine, 22	223	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.E223D(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|skin(2)	10						ACAGCATGTCCTCAGTGATGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	16											82	76	78					16																	2903914		2198	4300	6498	2843915	SO:0001583	missense	64063			AF321182	CCDS10481.1	16p13.3	2010-05-07			ENSG00000005001	ENSG00000005001		"Serine peptidases / Serine peptidases"	14368	protein-coding gene	gene with protein product	"brain-specific serine protease 4"	609343				11602603, 15701722	Standard	XM_005255473		Approved	hBSSP-4, BSSP-4, SP001LA	uc002cry.1	Q9GZN4	OTTHUMG00000128961	ENST00000161006.3:c.669G>T	16.37:g.2903914C>A	ENSP00000161006:p.Glu223Asp		2843915	O43342|Q6UXE0	Missense_Mutation	SNP	ENST00000161006.3	37	CCDS10481.1	.	.	.	.	.	.	.	.	.	.	c	9.359	1.067566	0.20067	.	.	ENSG00000005001	ENST00000161006	T	0.80994	-1.44	4.24	0.409	0.16382	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.542430	0.16703	N	0.203030	T	0.53802	0.1819	N	0.02960	-0.455	0.24648	N	0.993533	P	0.43024	0.798	P	0.47044	0.535	T	0.58994	-0.7537	10	0.02654	T	1	.	2.962	0.05895	0.0:0.452:0.2346:0.3134	.	223	Q9GZN4	BSSP4_HUMAN	D	223	ENSP00000161006:E223D	ENSP00000161006:E223D	E	-	3	2	PRSS22	2843915	0.498000	0.26075	0.997000	0.53966	0.599000	0.36880	0.037000	0.13840	0.336000	0.23639	0.306000	0.20318	GAG		0.642	PRSS22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250943.1	NM_022119		A	2903914	C	A	2903914	3	1	61	1	0	0	0	0	1	0	0	0	12653	680	24	2	292	2	PRSS22	16	2903914	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35098	2903914	87450839	9611	17596										
ZNF205	7755	broad.mit.edu	37	chr16	3165383	3165383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgtggacatcctcatcagGaaatgccttctaagctgggg	11	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3165383G>A	ENST00000382192.3	+	3	290	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205-AS1_ENST00000572691.1_RNA|ZNF205_ENST00000219091.4_Missense_Mutation_p.E29K|ZNF205-AS1_ENST00000576943.1_RNA|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	29					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E29K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						TCCTCATCAGGAAATGCCTTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											82	80	80					16																	3165383		2197	4300	6497	3105384	SO:0001583	missense	7755			AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"Zinc fingers, C2H2-type", "-"	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.85G>A	16.37:g.3165383G>A	ENSP00000371627:p.Glu29Lys		3105384	A8MZK0|D3DUB4|Q9BU95	Missense_Mutation	SNP	ENST00000382192.3	37	CCDS10494.2	.	.	.	.	.	.	.	.	.	.	G	14.54	2.565653	0.45694	.	.	ENSG00000122386	ENST00000382192;ENST00000219091;ENST00000444510;ENST00000414351	T;T;T;T	0.51325	3.2;3.2;0.71;3.06	4.85	2.79	0.32731	.	0.361650	0.20185	N	0.097429	T	0.40498	0.1119	L	0.57536	1.79	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.37911	-0.9685	10	0.62326	D	0.03	-8.271	7.2187	0.25975	0.0906:0.3342:0.5752:0.0	.	29	O95201	ZN205_HUMAN	K	29	ENSP00000371627:E29K;ENSP00000219091:E29K;ENSP00000394360:E29K;ENSP00000403306:E29K	ENSP00000219091:E29K	E	+	1	0	ZNF205	3105384	0.001000	0.12720	0.176000	0.23000	0.062000	0.15995	0.771000	0.26633	0.531000	0.28639	0.491000	0.48974	GAA		0.592	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456		A	3165383	G	A	3165383	3	1	61	1	0	0	0	0	1	0	0	0	17803	1175	41	3	91	3	ZNF205	16	3165383	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	261469	3165383	87189370	9612	17597										
MEFV	4210	broad.mit.edu	37	chr16	3293324	3293324	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccaactctgtagtccacGaagatgcccacacgcttggg	9	14	1	1	rs11466047	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3293324G>A	ENST00000219596.1	-	10	2202	c.2163C>T	c.(2161-2163)ttC>ttT	p.F721F	MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000536379.1_Silent_p.F510F|MEFV_ENST00000339854.4_Silent_p.F541F	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	721	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.F721F(1)		NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						TGTAGTCCACGAAGATGCCCA	0.522													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		19435	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16						G	,	82,4312	70.9+/-108.8	0,82,2115	109	106	107		2163,	-3.8	0	16	dbSNP_120	107	0,8600		0,0,4300	no	coding-synonymous,utr-3	MEFV	NM_000243.2,NM_001198536.1	,	0,82,6415	AA,AG,GG		0.0,1.8662,0.6311	,	721/782,	3293324	82,12912	2197	4300	6497	3233325	SO:0001819	synonymous_variant	4210			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.2163C>T	16.37:g.3293324G>A			3233325	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																				0.522	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		A	3293324	G	A	3293324	2	1	61	1	0	0	0	0	0	0	0	1	9489	1049	37	1		1	MEFV	16	3293324	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127941	3293324	87061429	9613	17598										
MEFV	4210	broad.mit.edu	37	chr16	3297076	3297076	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttccccaatcagcgcatcGagcagggcgatgtcctggga	13	12	1	0	rs571832030		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3297076G>A	ENST00000219596.1	-	5	1566	c.1527C>T	c.(1525-1527)ctC>ctT	p.L509L	MEFV_ENST00000541159.1_Silent_p.L298L|MEFV_ENST00000536379.1_Silent_p.L298L|MEFV_ENST00000339854.4_Silent_p.L329L	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	509	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.L509L(1)		NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						TCAGCGCATCGAGCAGGGCGA	0.597													G|||	1	0.000199681	0	0	5008	,	,		20443	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16											152	130	137					16																	3297076		2197	4300	6497	3237077	SO:0001819	synonymous_variant	4210			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1527C>T	16.37:g.3297076G>A			3237077	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																				0.597	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		A	3297076	G	A	3297076	2	1	61	1	0	0	0	0	0	0	0	1	9489	1045	37	1		1	MEFV	16	3297076	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3752	3297076	87057677	9614	17599										
ZNF263	10127	broad.mit.edu	37	chr16	3334055	3334055	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatgcgcacgaaggagcaGatcttggagctgctggtgtt	16	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3334055G>T	ENST00000219069.5	+	1	1113	c.237G>T	c.(235-237)caG>caT	p.Q79H	ZNF263_ENST00000574253.1_Missense_Mutation_p.Q79H|ZNF263_ENST00000538765.1_Intron|ZNF263_ENST00000573578.1_Missense_Mutation_p.Q79H	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	79	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q79H(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CGAAGGAGCAGATCTTGGAGC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	16											73	75	74					16																	3334055		2197	4300	6497	3274056	SO:0001583	missense	10127			AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.237G>T	16.37:g.3334055G>T	ENSP00000219069:p.Gln79His		3274056	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.913179	0.52439	.	.	ENSG00000006194	ENST00000219069	T	0.09255	3.0	5.06	4.11	0.48088	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.50627	D	0.000103	T	0.41143	0.1146	H	0.94658	3.565	0.37624	D	0.921413	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.57365	-0.7824	10	0.87932	D	0	.	9.7263	0.40333	0.0942:0.0:0.9058:0.0	.	79;79	O14978;D3DUC1	ZN263_HUMAN;.	H	79	ENSP00000219069:Q79H	ENSP00000219069:Q79H	Q	+	3	2	ZNF263	3274056	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	2.200000	0.42724	1.496000	0.48567	0.655000	0.94253	CAG		0.632	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			T	3334055	G	T	3334055	3	4	61	1	0	0	0	0	1	0	0	0	17842	933	33	2	239	2	ZNF263	16	3334055	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36979	3334055	87020698	9615	17600										
ZNF263	10127	broad.mit.edu	37	chr16	3340035	3340035	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacctccttcggcaccagaGaattcacactggagagcgac	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3340035G>T	ENST00000219069.5	+	6	2405	c.1529G>T	c.(1528-1530)aGa>aTa	p.R510I	ZNF263_ENST00000538765.1_Missense_Mutation_p.R158I	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	510					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R510I(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CGGCACCAGAGAATTCACACT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	16											57	56	56					16																	3340035		2197	4300	6497	3280036	SO:0001583	missense	10127			AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1529G>T	16.37:g.3340035G>T	ENSP00000219069:p.Arg510Ile		3280036	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.422687	0.83559	.	.	ENSG00000006194	ENST00000538765;ENST00000219069	T;T	0.24908	1.83;1.83	5.85	5.85	0.93711	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000007	T	0.47154	0.1430	M	0.76838	2.35	0.80722	D	1	D	0.58620	0.983	P	0.58577	0.841	T	0.45454	-0.9260	10	0.87932	D	0	.	12.9191	0.58222	0.0:0.0:0.8379:0.1621	.	510	O14978	ZN263_HUMAN	I	158;510	ENSP00000444497:R158I;ENSP00000219069:R510I	ENSP00000219069:R510I	R	+	2	0	ZNF263	3280036	0.960000	0.32886	1.000000	0.80357	0.997000	0.91878	2.892000	0.48625	2.941000	0.99782	0.655000	0.94253	AGA		0.527	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			T	3340035	G	T	3340035	3	4	61	1	0	0	0	0	1	0	0	0	17842	942	33	2	1551	2	ZNF263	16	3340035	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5980	3340035	87014718	9616	17601										
ZNF263	10127	broad.mit.edu	37	chr16	3340115	3340115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcacacctcgtcattcacGaaagaactcatgagagagag	9	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3340115G>A	ENST00000219069.5	+	6	2485	c.1609G>A	c.(1609-1611)Gaa>Aaa	p.E537K	ZNF263_ENST00000538765.1_Missense_Mutation_p.E185K	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	537					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E537K(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CGTCATTCACGAAAGAACTCA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											43	41	42					16																	3340115		2197	4300	6497	3280116	SO:0001583	missense	10127			AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1609G>A	16.37:g.3340115G>A	ENSP00000219069:p.Glu537Lys		3280116	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819009	0.50633	.	.	ENSG00000006194	ENST00000538765;ENST00000219069	T;T	0.60424	0.19;0.19	5.85	5.85	0.93711	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000016	T	0.47857	0.1468	N	0.26042	0.785	0.80722	D	1	D	0.63046	0.992	P	0.45343	0.477	T	0.38824	-0.9643	10	0.33141	T	0.24	.	13.604	0.62037	0.0:0.1553:0.8446:0.0	.	537	O14978	ZN263_HUMAN	K	185;537	ENSP00000444497:E185K;ENSP00000219069:E537K	ENSP00000219069:E537K	E	+	1	0	ZNF263	3280116	0.040000	0.19996	0.995000	0.50966	0.944000	0.59088	0.630000	0.24553	2.941000	0.99782	0.655000	0.94253	GAA		0.507	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			A	3340115	G	A	3340115	3	1	61	1	0	0	0	0	1	0	0	0	17842	1059	37	1	1631	1	ZNF263	16	3340115	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80	3340115	87014638	9617	17602										
ZNF263	10127	broad.mit.edu	37	chr16	3340260	3340260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttgtgggaaaagcttccGgcagggcatgcacctcacca	12	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3340260G>A	ENST00000219069.5	+	6	2630	c.1754G>A	c.(1753-1755)cGg>cAg	p.R585Q	ZNF263_ENST00000538765.1_Missense_Mutation_p.R233Q	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	585					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R585Q(2)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						AAAAGCTTCCGGCAGGGCATG	0.473																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	16											68	64	65					16																	3340260		2197	4300	6497	3280261	SO:0001583	missense	10127			AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1754G>A	16.37:g.3340260G>A	ENSP00000219069:p.Arg585Gln		3280261	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634988	0.47049	.	.	ENSG00000006194	ENST00000538765;ENST00000219069	T;T	0.00966	5.49;5.49	5.2	4.25	0.50352	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.126184	0.35615	N	0.003081	T	0.01592	0.0051	M	0.75777	2.31	0.80722	D	1	B	0.19583	0.037	B	0.10450	0.005	T	0.49351	-0.8949	10	0.51188	T	0.08	.	7.0759	0.25203	0.086:0.0:0.7453:0.1687	.	585	O14978	ZN263_HUMAN	Q	233;585	ENSP00000444497:R233Q;ENSP00000219069:R585Q	ENSP00000219069:R585Q	R	+	2	0	ZNF263	3280261	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.055000	0.14229	1.580000	0.49851	0.655000	0.94253	CGG		0.473	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			A	3340260	G	A	3340260	3	1	61	1	0	0	0	0	1	0	0	0	17842	1116	39	1	1776	1	ZNF263	16	3340260	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	145	3340260	87014493	9618	17603										
CLUAP1	23059	broad.mit.edu	37	chr16	3556343	3556343	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatagatatgagccccaGactgacatcccgcctgacgt	9	13	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3556343G>T	ENST00000576634.1	+	3	291	c.147G>T	c.(145-147)caG>caT	p.Q49H	CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000571025.1_Missense_Mutation_p.Q49H|CLUAP1_ENST00000341633.5_Missense_Mutation_p.Q49H|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	49					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)		p.Q49H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATGAGCCCCAGACTGACATCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											141	125	131					16																	3556343		2197	4300	6497	3496344	SO:0001583	missense	23059			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.147G>T	16.37:g.3556343G>T	ENSP00000460850:p.Gln49His		3496344	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	.	.	.	.	.	.	.	.	.	.	G	5.889	0.348083	0.11126	.	.	ENSG00000103351	ENST00000341633	T	0.44881	0.91	5.24	-0.697	0.11284	.	0.452091	0.27415	N	0.019472	T	0.18593	0.0446	N	0.12746	0.255	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.03394	-1.1041	10	0.52906	T	0.07	-9.5948	3.0332	0.06113	0.1591:0.3905:0.3172:0.1332	.	49	Q96AJ1	CLUA1_HUMAN	H	49	ENSP00000344392:Q49H	ENSP00000344392:Q49H	Q	+	3	2	CLUAP1	3496344	1.000000	0.71417	0.996000	0.52242	0.060000	0.15804	0.862000	0.27899	0.037000	0.15575	0.557000	0.71058	CAG		0.478	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		T	3556343	G	T	3556343	3	4	61	1	0	0	0	0	1	0	0	0	3575	933	33	2	157	2	CLUAP1	16	3556343	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216083	3556343	86798410	9619	17604										
CLUAP1	23059	broad.mit.edu	37	chr16	3569974	3569974	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaatttagaagccaaaatCgaaaagagaaaattagaact	7	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3569974C>T	ENST00000576634.1	+	7	795	c.651C>T	c.(649-651)atC>atT	p.I217I	CLUAP1_ENST00000572600.1_Silent_p.I51I|CLUAP1_ENST00000445795.2_5'UTR|CLUAP1_ENST00000417763.2_Silent_p.I51I|CLUAP1_ENST00000571025.1_Silent_p.I217I|CLUAP1_ENST00000341633.5_Silent_p.I217I	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	217					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)		p.I217I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						AAGCCAAAATCGAAAAGAGAA	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	16											102	104	103					16																	3569974		2197	4300	6497	3509975	SO:0001819	synonymous_variant	23059			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.651C>T	16.37:g.3569974C>T			3509975	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																				0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		T	3569974	C	T	3569974	2	4	61	1	0	0	0	0	0	0	0	1	3575	874	31	1		1	CLUAP1	16	3569974	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13631	3569974	86784779	9620	17605										
BTBD12	84464	broad.mit.edu	37	chr16	3640008	3640008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgctgcagcacagcttCgcttcttggtgggctctggg	13	13	2	0	rs202032197		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3640008C>T	ENST00000294008.3	-	12	4271	c.3631G>A	c.(3631-3633)Gaa>Aaa	p.E1211K		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1211	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.E1211K(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AGCACAGCTTCGCTTCTTGGT	0.557								Direct reversal of damage					C|||	1	0.000199681	0	0	5008	,	,		17175	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											60	63	62					16																	3640008		2197	4300	6497	3580009	SO:0001583	missense	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3631G>A	16.37:g.3640008C>T	ENSP00000294008:p.Glu1211Lys		3580009	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.52	1.662284	0.29515	.	.	ENSG00000188827	ENST00000294008	T	0.19394	2.15	6.07	4.12	0.48240	.	1.069720	0.07172	N	0.852525	T	0.17450	0.0419	L	0.56769	1.78	0.09310	N	1	P	0.50710	0.938	B	0.35607	0.206	T	0.16482	-1.0401	10	0.15499	T	0.54	.	6.2413	0.20793	0.0:0.6805:0.154:0.1655	.	1211	Q8IY92	SLX4_HUMAN	K	1211	ENSP00000294008:E1211K	ENSP00000294008:E1211K	E	-	1	0	SLX4	3580009	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	0.730000	0.26043	0.893000	0.36288	0.655000	0.94253	GAA		0.557	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3640008	C	T	3640008	3	4	61	1	0	0	0	0	1	0	0	0	1543	893	31	1	1889	1	BTBD12	16	3640008	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70034	3640008	86714745	9621	17606										
BTBD12	84464	broad.mit.edu	37	chr16	3640612	3640612	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccccctttccctgacagcGccactttgttcctcgggctc	8	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3640612G>A	ENST00000294008.3	-	12	3667	c.3027C>T	c.(3025-3027)ggC>ggT	p.G1009G		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1009	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.G1009G(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CCCTGACAGCGCCACTTTGTT	0.597								Direct reversal of damage																																								1	Substitution - coding silent(1)	large_intestine(1)	16											66	67	66					16																	3640612		2197	4300	6497	3580613	SO:0001819	synonymous_variant	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3027C>T	16.37:g.3640612G>A			3580613	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																				0.597	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3640612	G	A	3640612	2	1	61	1	0	0	0	0	0	0	0	1	1543	1074	38	1		1	BTBD12	16	3640612	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	604	3640612	86714141	9622	17607										
BTBD12	84464	broad.mit.edu	37	chr16	3641293	3641293	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgttcgcacaggtgaacGagctcactcacgccaaacct	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3641293G>A	ENST00000294008.3	-	12	2986	c.2346C>T	c.(2344-2346)ctC>ctT	p.L782L		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	782	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.L782L(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						ACAGGTGAACGAGCTCACTCA	0.592								Direct reversal of damage			OREG0032061	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																																				1	Substitution - coding silent(1)	large_intestine(1)	16											71	70	70					16																	3641293		2197	4300	6497	3581294	SO:0001819	synonymous_variant	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2346C>T	16.37:g.3641293G>A		612	3581294	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																				0.592	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3641293	G	A	3641293	2	1	61	1	0	0	0	0	0	0	0	1	1543	1045	37	1		1	BTBD12	16	3641293	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681	3641293	86713460	9623	17608										
BTBD12	84464	broad.mit.edu	37	chr16	3652140	3652140	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcacatgctgttcccttCgggtcacgttcatggctgag	11	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3652140C>T	ENST00000294008.3	-	4	1569	c.929G>A	c.(928-930)cGa>cAa	p.R310Q		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	310	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.R310Q(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTGTTCCCTTCGGGTCACGTT	0.567								Direct reversal of damage																																								1	Substitution - Missense(1)	large_intestine(1)	16											114	98	103					16																	3652140		2197	4300	6497	3592141	SO:0001583	missense	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.929G>A	16.37:g.3652140C>T	ENSP00000294008:p.Arg310Gln		3592141	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	19.55	3.849093	0.71603	.	.	ENSG00000188827	ENST00000294008	T	0.01854	4.6	5.83	5.83	0.93111	.	0.152155	0.45361	D	0.000367	T	0.09862	0.0242	L	0.58810	1.83	0.28740	N	0.902041	D	0.89917	1.0	D	0.81914	0.995	T	0.01071	-1.1461	10	0.56958	D	0.05	.	13.6264	0.62168	0.1549:0.8451:0.0:0.0	.	310	Q8IY92	SLX4_HUMAN	Q	310	ENSP00000294008:R310Q	ENSP00000294008:R310Q	R	-	2	0	SLX4	3592141	0.997000	0.39634	0.199000	0.23439	0.368000	0.29767	4.305000	0.59110	2.769000	0.95229	0.655000	0.94253	CGA		0.567	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3652140	C	T	3652140	3	4	61	1	0	0	0	0	1	0	0	0	1543	884	31	1	4623	1	BTBD12	16	3652140	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10847	3652140	86702613	9624	17609										
TRAP1	10131	broad.mit.edu	37	chr16	3725373	3725373	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtacaaggggaagctgacGaagttgctgtacttcgttac	12	7	0	1	rs377042927		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3725373G>A	ENST00000246957.5	-	8	928	c.840C>T	c.(838-840)ttC>ttT	p.F280F	TRAP1_ENST00000575671.1_Silent_p.F71F|TRAP1_ENST00000538171.1_Silent_p.F227F|TRAP1_ENST00000573872.1_5'UTR	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	280					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)	p.F280F(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				GGAAGCTGACGAAGTTGCTGT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G		0,4394		0,0,2197	164	121	136		840	-10.5	0.4	16		136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAP1	NM_016292.2		0,1,6496	AA,AG,GG		0.0116,0.0,0.0077		280/705	3725373	1,12993	2197	4300	6497	3665374	SO:0001819	synonymous_variant	10131			AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.840C>T	16.37:g.3725373G>A			3665374	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	37	CCDS10508.1																																																																																				0.488	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		A	3725373	G	A	3725373	2	1	61	1	0	0	0	0	0	0	0	1	16495	1049	37	1		1	TRAP1	16	3725373	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73233	3725373	86629380	9625	17610										
CREBBP	1387	broad.mit.edu	37	chr16	3779578	3779578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgtggtagcagcagagggCgatgagctgcttgcacaccg	17	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3779578C>T	ENST00000262367.5	-	31	6279	c.5470G>A	c.(5470-5472)Gcc>Acc	p.A1824T	CREBBP_ENST00000382070.3_Missense_Mutation_p.A1786T	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1824	Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A1824T(2)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CAGCAGAGGGCGATGAGCTGC	0.602			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	16											149	128	135					16																	3779578		2197	4300	6497	3719579	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.5470G>A	16.37:g.3779578C>T	ENSP00000262367:p.Ala1824Thr		3719579	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	14.62	2.590345	0.46214	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.82433	-1.61;-1.61	5.35	5.35	0.76521	Zinc finger, TAZ-type (5);	0.000000	0.85682	D	0.000000	D	0.89511	0.6736	L	0.56280	1.765	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.89065	0.3465	10	0.48119	T	0.1	-18.0228	19.0688	0.93123	0.0:1.0:0.0:0.0	.	1854;1824	Q4LE28;Q92793	.;CBP_HUMAN	T	1824;1854;1786;359	ENSP00000262367:A1824T;ENSP00000371502:A1786T	ENSP00000262367:A1824T	A	-	1	0	CREBBP	3719579	1.000000	0.71417	0.988000	0.46212	0.993000	0.82548	7.755000	0.85180	2.513000	0.84729	0.591000	0.81541	GCC		0.602	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3779578	C	T	3779578	3	4	61	1	0	0	0	0	1	0	0	0	3867	768	27	1	1862	1	CREBBP	16	3779578	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54205	3779578	86575175	9626	17611										
CREBBP	1387	broad.mit.edu	37	chr16	3900775	3900775	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggccatgttagcactgttCggctgcccttgagcctggcc	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3900775C>T	ENST00000262367.5	-	2	1130	c.321G>A	c.(319-321)ccG>ccA	p.P107P	CREBBP_ENST00000382070.3_Silent_p.P107P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	107					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.P107P(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TAGCACTGTTCGGCTGCCCTT	0.622			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - coding silent(1)	large_intestine(1)	16											43	42	42					16																	3900775		2197	4300	6497	3840776	SO:0001819	synonymous_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.321G>A	16.37:g.3900775C>T			3840776	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.622	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3900775	C	T	3900775	2	4	61	1	0	0	0	0	0	0	0	1	3867	871	31	1		1	CREBBP	16	3900775	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121197	3900775	86453978	9627	17612										
CREBBP	1387	broad.mit.edu	37	chr16	3900860	3900860	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgggttgatactagagCcgctgcctcctcgtagaagc	11	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:3900860C>A	ENST00000262367.5	-	2	1045	c.236G>T	c.(235-237)gGc>gTc	p.G79V	CREBBP_ENST00000382070.3_Missense_Mutation_p.G79V	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	79					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G79V(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GATACTAGAGCCGCTGCCTCC	0.547			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - Missense(1)	large_intestine(1)	16	GRCh37	CD052984	CREBBP	D							64	62	62					16																	3900860		2197	4300	6497	3840861	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.236G>T	16.37:g.3900860C>A	ENSP00000262367:p.Gly79Val		3840861	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.369903	0.42003	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.83755	-1.69;-1.76	5.87	5.87	0.94306	.	0.266513	0.33401	N	0.004941	D	0.85031	0.5604	L	0.40543	1.245	0.80722	D	1	D;D	0.59357	0.962;0.985	P;P	0.58130	0.833;0.715	T	0.81313	-0.0989	10	0.22706	T	0.39	-9.1577	17.3643	0.87359	0.0:1.0:0.0:0.0	.	147;79	Q4LE28;Q92793	.;CBP_HUMAN	V	79;147;79	ENSP00000262367:G79V;ENSP00000371502:G79V	ENSP00000262367:G79V	G	-	2	0	CREBBP	3840861	0.996000	0.38824	0.973000	0.42090	0.639000	0.38242	3.313000	0.51935	2.774000	0.95407	0.650000	0.86243	GGC		0.547	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3900860	C	A	3900860	3	1	61	1	0	0	0	0	1	0	0	0	3867	739	26	2	7212	2	CREBBP	16	3900860	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85	3900860	86453893	9628	17613										
ADCY9	115	broad.mit.edu	37	chr16	4164270	4164270	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaaataaaatactgacttCttcgatctgctgcatcttaa	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4164270C>A	ENST00000294016.3	-	2	1712	c.1174G>T	c.(1174-1176)Gaa>Taa	p.E392*		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	392					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.E392*(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ATACTGACTTCTTCGATCTGC	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											92	92	92					16																	4164270		2197	4300	6497	4104271	SO:0001587	stop_gained	115			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1174G>T	16.37:g.4164270C>A	ENSP00000294016:p.Glu392*		4104271	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Nonsense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	44	10.642474	0.99443	.	.	ENSG00000162104	ENST00000294016	.	.	.	5.57	3.47	0.39725	.	0.119503	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	10.2862	0.43568	0.0:0.6603:0.2523:0.0874	.	.	.	.	X	392	.	ENSP00000294016:E392X	E	-	1	0	ADCY9	4104271	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	4.080000	0.57620	1.379000	0.46325	0.555000	0.69702	GAA		0.502	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4164270	C	A	4164270	4	1	61	1	0	0	0	0	0	1	0	0	301	922	32	2	2927	2	ADCY9	16	4164270	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	263410	4164270	86190483	9629	17614										
ADCY9	115	broad.mit.edu	37	chr16	4164759	4164759	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagcaaaaagagcacttCgatgcacatggagaagctcc	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4164759C>T	ENST00000294016.3	-	2	1223	c.685G>A	c.(685-687)Gaa>Aaa	p.E229K		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	229					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.E229K(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AAGAGCACTTCGATGCACATG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											72	58	63					16																	4164759		2197	4300	6497	4104760	SO:0001583	missense	115			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.685G>A	16.37:g.4164759C>T	ENSP00000294016:p.Glu229Lys		4104760	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980616	0.74474	.	.	ENSG00000162104	ENST00000294016	T	0.27557	1.66	5.41	4.43	0.53597	.	0.053889	0.64402	D	0.000001	T	0.32912	0.0845	M	0.81802	2.56	0.58432	D	0.999996	P	0.46578	0.88	B	0.32342	0.144	T	0.42378	-0.9455	10	0.41790	T	0.15	.	16.0341	0.80608	0.0:0.8653:0.1347:0.0	.	229	O60503	ADCY9_HUMAN	K	229	ENSP00000294016:E229K	ENSP00000294016:E229K	E	-	1	0	ADCY9	4104760	1.000000	0.71417	0.987000	0.45799	0.979000	0.70002	6.059000	0.71133	1.267000	0.44247	0.549000	0.68633	GAA		0.542	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			T	4164759	C	T	4164759	3	4	61	1	0	0	0	0	1	0	0	0	301	893	31	1	3416	1	ADCY9	16	4164759	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	489	4164759	86189994	9630	17615										
DNAJA3	9093	broad.mit.edu	37	chr16	4491408	4491408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtgaagaggaagcagtaCgatgcctacggctctgcagg	16	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4491408C>T	ENST00000262375.6	+	4	539	c.462C>T	c.(460-462)taC>taT	p.Y154Y	DNAJA3_ENST00000431375.2_Intron|DNAJA3_ENST00000572139.1_3'UTR|DNAJA3_ENST00000355296.4_Silent_p.Y154Y	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	154	J.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)	p.Y154Y(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						GGAAGCAGTACGATGCCTACG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	16											84	78	80					16																	4491408		2197	4300	6497	4431409	SO:0001819	synonymous_variant	9093			AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"Heat shock proteins / DNAJ (HSP40)"	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.462C>T	16.37:g.4491408C>T			4431409	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Silent	SNP	ENST00000262375.6	37	CCDS10515.1																																																																																				0.582	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1			T	4491408	C	T	4491408	2	4	61	1	0	0	0	0	0	0	0	1	4624	547	19	1		1	DNAJA3	16	4491408	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	326649	4491408	85863345	9631	17616										
HMOX2	3163	broad.mit.edu	37	chr16	4555581	4555581	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagtcagaaaaaaagaactCtggggccctagaaaaggaga	12	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4555581C>T	ENST00000570646.1	+	2	661	c.56C>T	c.(55-57)tCt>tTt	p.S19F	HMOX2_ENST00000398595.3_Missense_Mutation_p.S19F|HMOX2_ENST00000458134.3_Missense_Mutation_p.S19F|HMOX2_ENST00000414777.1_Missense_Mutation_p.S19F|HMOX2_ENST00000219700.6_Missense_Mutation_p.S19F|HMOX2_ENST00000406590.2_Missense_Mutation_p.S19F|HMOX2_ENST00000575120.1_Intron	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	19					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)	p.S19F(1)		endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						AAAAAGAACTCTGGGGCCCTA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	16											79	74	76					16																	4555581		2196	4296	6492	4495582	SO:0001583	missense	3163				CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.56C>T	16.37:g.4555581C>T	ENSP00000459214:p.Ser19Phe		4495582	A8MT35|D3DUD5|I3L430|O60605	Missense_Mutation	SNP	ENST00000570646.1	37	CCDS10517.1	.	.	.	.	.	.	.	.	.	.	C	0.042	-1.281309	0.01398	.	.	ENSG00000103415	ENST00000406590;ENST00000458134;ENST00000219700;ENST00000414777;ENST00000398595	T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89	5.75	1.15	0.20763	.	0.962152	0.08693	N	0.907573	T	0.15003	0.0362	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35748	-0.9776	10	0.11182	T	0.66	0.0225	5.2127	0.15327	0.2272:0.6048:0.0:0.168	.	19;19	B3KSE0;P30519	.;HMOX2_HUMAN	F	19	ENSP00000385100:S19F;ENSP00000394103:S19F;ENSP00000219700:S19F;ENSP00000391637:S19F;ENSP00000381595:S19F	ENSP00000219700:S19F	S	+	2	0	HMOX2	4495582	0.000000	0.05858	0.009000	0.14445	0.047000	0.14425	0.843000	0.27640	0.765000	0.33221	0.655000	0.94253	TCT		0.567	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			T	4555581	C	T	4555581	3	4	61	1	0	0	0	0	1	0	0	0	7265	913	32	3	58	3	HMOX2	16	4555581	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64173	4555581	85799172	9632	17617										
HMOX2	3163	broad.mit.edu	37	chr16	4557857	4557857	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaggacatggagtatttCtttggtgaaaactgggagga	13	5	1	1	rs8045851		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4557857C>A	ENST00000570646.1	+	4	953	c.348C>A	c.(346-348)ttC>ttA	p.F116L	HMOX2_ENST00000398595.3_Missense_Mutation_p.F116L|HMOX2_ENST00000458134.3_Missense_Mutation_p.F116L|HMOX2_ENST00000414777.1_Missense_Mutation_p.F116L|HMOX2_ENST00000219700.6_Missense_Mutation_p.F116L|HMOX2_ENST00000406590.2_Missense_Mutation_p.F116L|HMOX2_ENST00000575120.1_Missense_Mutation_p.F87L	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	116					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)	p.F116L(1)		endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						TGGAGTATTTCTTTGGTGAAA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											67	60	62					16																	4557857		2197	4300	6497	4497858	SO:0001583	missense	3163				CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.348C>A	16.37:g.4557857C>A	ENSP00000459214:p.Phe116Leu		4497858	A8MT35|D3DUD5|I3L430|O60605	Missense_Mutation	SNP	ENST00000570646.1	37	CCDS10517.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411975	0.62511	.	.	ENSG00000103415	ENST00000406590;ENST00000458134;ENST00000219700;ENST00000414777;ENST00000398595	T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04	5.62	4.67	0.58626	Haem oxygenase-like, multi-helical (2);	0.041945	0.85682	N	0.000000	T	0.20129	0.0484	L	0.33137	0.985	0.80722	D	1	B;B	0.29085	0.232;0.232	B;B	0.34536	0.185;0.185	T	0.04522	-1.0945	10	0.62326	D	0.03	-8.0547	13.1213	0.59327	0.0:0.9222:0.0:0.0778	.	116;116	B3KSE0;P30519	.;HMOX2_HUMAN	L	116	ENSP00000385100:F116L;ENSP00000394103:F116L;ENSP00000219700:F116L;ENSP00000391637:F116L;ENSP00000381595:F116L	ENSP00000219700:F116L	F	+	3	2	HMOX2	4497858	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	2.573000	0.46007	1.379000	0.46325	0.561000	0.74099	TTC		0.572	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			A	4557857	C	A	4557857	3	1	61	1	0	0	0	0	1	0	0	0	7265	912	32	2	358	2	HMOX2	16	4557857	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2276	4557857	85796896	9633	17618										
MGRN1	23295	broad.mit.edu	37	chr16	4707316	4707316	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggggtgagccagcagttCtccctgccctccttcaagat	11	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4707316C>A	ENST00000399577.5	+	5	606	c.513C>A	c.(511-513)ttC>ttA	p.F171L	MGRN1_ENST00000262370.7_Missense_Mutation_p.F171L|MGRN1_ENST00000415496.1_Missense_Mutation_p.F171L|MGRN1_ENST00000586183.1_Missense_Mutation_p.F171L|MGRN1_ENST00000588994.1_Missense_Mutation_p.F171L	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	171					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F171L(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						GCCAGCAGTTCTCCCTGCCCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											84	89	87					16																	4707316		2043	4177	6220	4647317	SO:0001583	missense	23295			AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.513C>A	16.37:g.4707316C>A	ENSP00000382487:p.Phe171Leu		4647317	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	37	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.605937	0.66445	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.22	4.27	0.50696	.	0.045491	0.85682	D	0.000000	T	0.46190	0.1380	M	0.88775	2.98	0.80722	D	1	B;P;B;B;P;B	0.48998	0.056;0.907;0.025;0.12;0.918;0.033	B;B;B;B;P;B	0.45971	0.135;0.382;0.033;0.153;0.499;0.064	T	0.58053	-0.7704	10	0.66056	D	0.02	-34.4473	12.682	0.56926	0.0:0.919:0.0:0.081	.	171;171;171;171;171;171	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	L	171	ENSP00000262370:F171L;ENSP00000382487:F171L;ENSP00000393311:F171L;ENSP00000443810:F171L	ENSP00000262370:F171L	F	+	3	2	MGRN1	4647317	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.969000	0.56816	1.196000	0.43129	0.561000	0.74099	TTC		0.592	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			A	4707316	C	A	4707316	3	1	61	1	0	0	0	0	1	0	0	0	9589	912	32	2	531	2	MGRN1	16	4707316	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149459	4707316	85647437	9634	17619										
MGRN1	23295	broad.mit.edu	37	chr16	4723613	4723613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctctgtacctcctgcgccGacacgctgcgctaccaggcc	10	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:4723613G>A	ENST00000399577.5	+	10	1003	c.910G>A	c.(910-912)Gac>Aac	p.D304N	MGRN1_ENST00000262370.7_Missense_Mutation_p.D304N|MGRN1_ENST00000415496.1_Missense_Mutation_p.D305N|MGRN1_ENST00000586183.1_Missense_Mutation_p.D304N|MGRN1_ENST00000588994.1_Missense_Mutation_p.D304N|MGRN1_ENST00000588015.1_3'UTR	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	304					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D304N(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						CTCCTGCGCCGACACGCTGCG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	16											66	75	72					16																	4723613		2197	4299	6496	4663614	SO:0001583	missense	23295			AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.910G>A	16.37:g.4723613G>A	ENSP00000382487:p.Asp304Asn		4663614	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	37	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	G	32	5.185317	0.94885	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-0.2	4.8	4.8	0.61643	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	T	0.81341	0.4802	L	0.33753	1.03	0.80722	D	1	P;D;D;D;B;D	0.71674	0.796;0.992;0.998;0.998;0.056;0.987	B;P;P;D;B;P	0.64687	0.34;0.844;0.904;0.928;0.027;0.853	T	0.82214	-0.0568	10	0.46703	T	0.11	-39.8457	16.4203	0.83755	0.0:0.0:1.0:0.0	.	304;304;304;305;304;304	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	N	304;304;305;304	ENSP00000262370:D304N;ENSP00000382487:D304N;ENSP00000393311:D305N;ENSP00000443810:D304N	ENSP00000262370:D304N	D	+	1	0	MGRN1	4663614	1.000000	0.71417	0.938000	0.37757	0.865000	0.49528	9.770000	0.98971	2.215000	0.71742	0.436000	0.28706	GAC		0.637	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			A	4723613	G	A	4723613	3	1	61	1	0	0	0	0	1	0	0	0	9589	1058	37	1	951	1	MGRN1	16	4723613	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16297	4723613	85631140	9635	17620										
SEC14L5	9717	broad.mit.edu	37	chr16	5040860	5040860	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaaaatgccttggagaaGatcgccatgaagcagtacac	10	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:5040860G>T	ENST00000251170.7	+	5	618	c.438G>T	c.(436-438)aaG>aaT	p.K146N		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	146	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)	p.K146N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						CCTTGGAGAAGATCGCCATGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	16											51	53	52					16																	5040860		2089	4214	6303	4980861	SO:0001583	missense	9717			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.438G>T	16.37:g.5040860G>T	ENSP00000251170:p.Lys146Asn		4980861		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495570	0.64186	.	.	ENSG00000103184	ENST00000251170	T	0.20332	2.08	4.37	2.2	0.27929	PRELI/MSF1 (2);	0.000000	0.64402	D	0.000006	T	0.47875	0.1469	M	0.88842	2.985	0.54753	D	0.999989	D	0.89917	1.0	D	0.91635	0.999	T	0.53472	-0.8434	10	0.87932	D	0	-21.9817	9.1924	0.37207	0.2623:0.0:0.7377:0.0	.	146	O43304	S14L5_HUMAN	N	146	ENSP00000251170:K146N	ENSP00000251170:K146N	K	+	3	2	SEC14L5	4980861	1.000000	0.71417	0.963000	0.40424	0.989000	0.77384	1.560000	0.36331	1.025000	0.39708	0.555000	0.69702	AAG		0.522	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5040860	G	T	5040860	3	4	61	1	0	0	0	0	1	0	0	0	14022	933	33	2	452	2	SEC14L5	16	5040860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	317247	5040860	85313893	9636	17621										
C16orf89	146556	broad.mit.edu	37	chr16	5105344	5105344	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaagccgcccattccacaGaacatgactggaagtaaaga	10	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:5105344G>T	ENST00000315997.5	-	6	972	c.771C>A	c.(769-771)ttC>ttA	p.F257L	C16orf89_ENST00000350219.4_Missense_Mutation_p.F295L|C16orf89_ENST00000422873.1_Missense_Mutation_p.F295L|C16orf89_ENST00000474471.3_Missense_Mutation_p.F289L|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Missense_Mutation_p.F257L	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	257						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)	p.F295L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						CCATTCCACAGAACATGACTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	16											22	23	22					16																	5105344		1931	4128	6059	5045345	SO:0001583	missense	146556				CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.771C>A	16.37:g.5105344G>T	ENSP00000324672:p.Phe257Leu		5045345	B4DUM5|Q8N2I3|Q8N4T1	Missense_Mutation	SNP	ENST00000315997.5	37	CCDS42116.2	.	.	.	.	.	.	.	.	.	.	G	13.47	2.245794	0.39697	.	.	ENSG00000153446	ENST00000474471;ENST00000472572;ENST00000477550;ENST00000422873;ENST00000350219;ENST00000315997	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.49	3.53	0.40419	.	0.270714	0.35585	N	0.003102	T	0.18718	0.0449	L	0.29908	0.895	0.31249	N	0.694221	B;B	0.24186	0.06;0.099	B;B	0.22753	0.018;0.041	T	0.14172	-1.0482	10	0.19147	T	0.46	-15.8073	7.45	0.27234	0.1897:0.0:0.8103:0.0	.	257;295	Q6UX73;G3V0F0	CP089_HUMAN;.	L	289;257;257;295;295;289	ENSP00000417158:F289L;ENSP00000420566:F257L;ENSP00000390402:F295L;ENSP00000283478:F295L	ENSP00000324672:F289L	F	-	3	2	C16orf89	5045345	0.988000	0.35896	0.997000	0.53966	0.995000	0.86356	0.012000	0.13287	1.310000	0.45006	0.557000	0.71058	TTC		0.637	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459		T	5105344	G	T	5105344	3	4	61	1	0	0	0	0	1	0	0	0	1846	933	33	2	584	2	C16orf89	16	5105344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64484	5105344	85249409	9637	17622										
A2BP1	54715	broad.mit.edu	37	chr16	7743326	7743326	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcttccagaaatcagttCgtcttcgttgcagcagatga	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:7743326C>T	ENST00000550418.1	+	15	1983				RBFOX1_ENST00000355637.4_Silent_p.F356F|RBFOX1_ENST00000552089.1_Silent_p.F352F|RBFOX1_ENST00000553186.1_Intron|RBFOX1_ENST00000535565.2_Silent_p.F292F|RBFOX1_ENST00000311745.5_Intron|RBFOX1_ENST00000547372.1_Silent_p.F378F|RBFOX1_ENST00000340209.4_Intron|RBFOX1_ENST00000436368.2_Intron|RBFOX1_ENST00000422070.4_Intron|RBFOX1_ENST00000547338.1_Intron	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1						mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.F356F(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						GAAATCAGTTCGTCTTCGTTG	0.433																																					Ovarian(157;934 2567 15163 39509)											1	Substitution - coding silent(1)	large_intestine(1)	16											160	141	147					16																	7743326		2197	4300	6497	7683327	SO:0001627	intron_variant	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.996-15732C>T	16.37:g.7743326C>T			7683327	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	37	CCDS55983.1																																																																																				0.433	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7743326	C	T	7743326	1	4	61	0	1	0	0	0	0	0	0	0	3	883	31	1		1	A2BP1	16	7743326	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2637982	7743326	82611427	9638	17623										
USP7	7874	broad.mit.edu	37	chr16	9000373	9000373	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcatgaagaatataattTgcagggtccttaggatctgt	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9000373T>C	ENST00000344836.4	-	13	1536	c.1338A>G	c.(1336-1338)gcA>gcG	p.A446A	USP7_ENST00000381886.4_Silent_p.A430A|USP7_ENST00000535863.1_Silent_p.A347A	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	446	USP.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A446A(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						GAATATAATTTGCAGGGTCCT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	16											92	92	92					16																	9000373		2197	4300	6497	8907874	SO:0001819	synonymous_variant	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.1338A>G	16.37:g.9000373T>C			8907874	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																				0.363	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			C	9000373	T	C	9000373	2	2	61	1	0	0	0	0	0	0	0	1	17128	1799	63	4		4	USP7	16	9000373	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1257047	9000373	81354380	9639	17624										
USP7	7874	broad.mit.edu	37	chr16	9015052	9015052	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaatccccaatcattttCtttatggaagaacaaatgac	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9015052C>A	ENST00000344836.4	-	4	682	c.484G>T	c.(484-486)Gaa>Taa	p.E162*	USP7_ENST00000381886.4_Nonsense_Mutation_p.E146*|USP7_ENST00000535863.1_Nonsense_Mutation_p.E63*|USP7_ENST00000566224.1_5'Flank	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	162	Interaction with TSPYL5.|Interaction with p53/TP53, MDM2 and EBNA1.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Necessary for nuclear localization.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E162*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CAATCATTTTCTTTATGGAAG	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											78	73	75					16																	9015052		2197	4300	6497	8922553	SO:0001587	stop_gained	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.484G>T	16.37:g.9015052C>A	ENSP00000343535:p.Glu162*		8922553	A6NMY8|B7Z815|H0Y3G8	Nonsense_Mutation	SNP	ENST00000344836.4	37	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	C	36	5.927121	0.97110	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	.	.	.	5.47	5.47	0.80525	.	0.042931	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.7874	0.96444	0.0:1.0:0.0:0.0	.	.	.	.	X	162;170;63;63;104	.	ENSP00000343535:E162X	E	-	1	0	USP7	8922553	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.779000	0.68948	2.761000	0.94854	0.552000	0.68991	GAA		0.373	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			A	9015052	C	A	9015052	4	1	61	1	0	0	0	0	0	1	0	0	17128	922	32	2	2936	2	USP7	16	9015052	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14679	9015052	81339701	9640	17625										
GRIN2A	2903	broad.mit.edu	37	chr16	9857197	9857197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttgacctcaaggacgaccGaagatagctgtcattcaccg	10	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9857197G>A	ENST00000396573.2	-	14	4513	c.4204C>T	c.(4204-4206)Cgg>Tgg	p.R1402W	GRIN2A_ENST00000562109.1_3'UTR|GRIN2A_ENST00000535259.1_3'UTR|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R1402W|GRIN2A_ENST00000396575.2_Missense_Mutation_p.R1402W|GRIN2A_ENST00000404927.2_3'UTR	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1402					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.R1402W(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAGGACGACCGAAGATAGCTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	16											118	102	107					16																	9857197		2197	4300	6497	9764698	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.4204C>T	16.37:g.9857197G>A	ENSP00000379818:p.Arg1402Trp		9764698	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193835	0.58017	.	.	ENSG00000183454	ENST00000396573;ENST00000330684;ENST00000396575	T;T;T	0.13538	2.58;2.58;2.58	5.79	4.76	0.60689	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.109289	0.56097	D	0.000025	T	0.30792	0.0776	M	0.69823	2.125	0.80722	D	1	D	0.71674	0.998	P	0.59643	0.861	T	0.00697	-1.1605	9	.	.	.	.	13.3416	0.60549	0.0:0.0:0.7547:0.2453	.	1402	Q12879	NMDE1_HUMAN	W	1402	ENSP00000379818:R1402W;ENSP00000332549:R1402W;ENSP00000379820:R1402W	.	R	-	1	2	GRIN2A	9764698	1.000000	0.71417	0.847000	0.33407	0.965000	0.64279	3.029000	0.49712	2.733000	0.93635	0.655000	0.94253	CGG		0.522	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9857197	G	A	9857197	3	1	61	1	0	0	0	0	1	0	0	0	6800	1057	37	1	194	1	GRIN2A	16	9857197	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	842145	9857197	80497556	9641	17626										
GRIN2A	2903	broad.mit.edu	37	chr16	9858098	9858098	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttcaggtaggtgcgctcGacctcactacagtccttggg	12	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9858098G>A	ENST00000396573.2	-	14	3612	c.3303C>T	c.(3301-3303)gtC>gtT	p.V1101V	GRIN2A_ENST00000562109.1_Silent_p.V1101V|GRIN2A_ENST00000535259.1_Silent_p.V944V|GRIN2A_ENST00000330684.3_Silent_p.V1101V|GRIN2A_ENST00000396575.2_Silent_p.V1101V|GRIN2A_ENST00000404927.2_Silent_p.V1101V	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1101					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.V1101V(2)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGGTGCGCTCGACCTCACTAC	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	16											155	144	148					16																	9858098		2197	4300	6497	9765599	SO:0001819	synonymous_variant	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3303C>T	16.37:g.9858098G>A			9765599	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.493	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9858098	G	A	9858098	2	1	61	1	0	0	0	0	0	0	0	1	6800	1045	37	1		1	GRIN2A	16	9858098	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	901	9858098	80496655	9642	17627										
GRIN2A	2903	broad.mit.edu	37	chr16	9858394	9858394	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctagagttcgctttggattCtgtgctcacggccacctcca	9	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9858394C>A	ENST00000396573.2	-	14	3316	c.3007G>T	c.(3007-3009)Gaa>Taa	p.E1003*	GRIN2A_ENST00000562109.1_Nonsense_Mutation_p.E1003*|GRIN2A_ENST00000535259.1_Nonsense_Mutation_p.E846*|GRIN2A_ENST00000330684.3_Nonsense_Mutation_p.E1003*|GRIN2A_ENST00000396575.2_Nonsense_Mutation_p.E1003*|GRIN2A_ENST00000404927.2_Nonsense_Mutation_p.E1003*	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1003					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.E1003*(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTTTGGATTCTGTGCTCACG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											96	93	94					16																	9858394		2197	4300	6497	9765895	SO:0001587	stop_gained	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3007G>T	16.37:g.9858394C>A	ENSP00000379818:p.Glu1003*		9765895	O00669|Q17RZ6	Nonsense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	39	7.555392	0.98355	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	.	.	.	5.33	5.33	0.75918	.	0.267510	0.42682	D	0.000677	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0263	0.89270	0.0:1.0:0.0:0.0	.	.	.	.	X	1003;1003;846;1003;1003	.	.	E	-	1	0	GRIN2A	9765895	1.000000	0.71417	0.943000	0.38184	0.948000	0.59901	5.474000	0.66781	2.491000	0.84063	0.655000	0.94253	GAA		0.512	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9858394	C	A	9858394	4	1	61	1	0	0	0	0	0	1	0	0	6800	922	32	2	1391	2	GRIN2A	16	9858394	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296	9858394	80496359	9643	17628										
GRIN2A	2903	broad.mit.edu	37	chr16	9916248	9916248	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaggcactgtcccaaatcGaaaaggtggggaatagtcat	11	7	1	0	rs397518472		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9916248G>A	ENST00000396573.2	-	11	2350	c.2041C>T	c.(2041-2043)Cga>Tga	p.R681*	GRIN2A_ENST00000562109.1_Nonsense_Mutation_p.R681*|GRIN2A_ENST00000535259.1_Nonsense_Mutation_p.R524*|GRIN2A_ENST00000330684.3_Nonsense_Mutation_p.R681*|GRIN2A_ENST00000396575.2_Nonsense_Mutation_p.R681*|GRIN2A_ENST00000404927.2_Nonsense_Mutation_p.R681*	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	681					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.R681*(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTCCCAAATCGAAAAGGTGGG	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											106	91	96					16																	9916248		2197	4300	6497	9823749	SO:0001587	stop_gained	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2041C>T	16.37:g.9916248G>A	ENSP00000379818:p.Arg681*		9823749	O00669|Q17RZ6	Nonsense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	44	10.827836	0.99474	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7287	0.91726	0.0:0.0:1.0:0.0	.	.	.	.	X	681;681;524;681;681	.	.	R	-	1	2	GRIN2A	9823749	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.695000	0.98691	2.655000	0.90218	0.655000	0.94253	CGA		0.448	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9916248	G	A	9916248	4	1	61	1	0	0	0	0	0	1	0	0	6800	1066	37	1	2369	1	GRIN2A	16	9916248	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57854	9916248	80438505	9644	17629										
GRIN2A	2903	broad.mit.edu	37	chr16	9934931	9934931	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaccccttgcagcatttCttcacattcatcccctcatt	3	16	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:9934931C>A	ENST00000396573.2	-	7	1668	c.1359G>T	c.(1357-1359)aaG>aaT	p.K453N	GRIN2A_ENST00000562109.1_Missense_Mutation_p.K453N|GRIN2A_ENST00000535259.1_Missense_Mutation_p.K296N|GRIN2A_ENST00000330684.3_Missense_Mutation_p.K453N|GRIN2A_ENST00000396575.2_Missense_Mutation_p.K453N|GRIN2A_ENST00000404927.2_Missense_Mutation_p.K453N	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	453					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.K453N(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCAGCATTTCTTCACATTCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	16											95	84	88					16																	9934931		2197	4300	6497	9842432	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1359G>T	16.37:g.9934931C>A	ENSP00000379818:p.Lys453Asn		9842432	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.706312	0.68615	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	5.63	-0.153	0.13403	Glutamate receptor, L-glutamate/glycine-binding (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	L	0.43923	1.385	0.50632	D	0.999882	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.976;0.982;0.997	T	0.45862	-0.9232	9	.	.	.	.	9.8985	0.41334	0.0:0.5841:0.0:0.4159	.	296;453;453	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	N	453;453;296;453;453	ENSP00000379818:K453N;ENSP00000385872:K453N;ENSP00000441572:K296N;ENSP00000332549:K453N;ENSP00000379820:K453N	.	K	-	3	2	GRIN2A	9842432	0.682000	0.27624	0.995000	0.50966	0.986000	0.74619	-0.143000	0.10296	-0.004000	0.14419	-0.302000	0.09304	AAG		0.423	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9934931	C	A	9934931	3	1	61	1	0	0	0	0	1	0	0	0	6800	912	32	2	3067	2	GRIN2A	16	9934931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18683	9934931	80419822	9645	17630										
ATF7IP2	80063	broad.mit.edu	37	chr16	10524750	10524750	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagagaaaagtaaagtattCtctcagaattgcataaaacc	6	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:10524750C>A	ENST00000396560.2	+	3	500	c.273C>A	c.(271-273)ttC>ttA	p.F91L	ATF7IP2_ENST00000396559.1_Missense_Mutation_p.F91L|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.F91L|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.F91L	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	91					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.F91L(1)		large_intestine(3)	3						GTAAAGTATTCTCTCAGAATT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	16											39	43	42					16																	10524750		2197	4300	6497	10432251	SO:0001583	missense	80063			AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.273C>A	16.37:g.10524750C>A	ENSP00000379808:p.Phe91Leu		10432251	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	C	8.255	0.809907	0.16537	.	.	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	4.97	-1.48	0.08745	.	1.109350	0.07074	N	0.835976	T	0.32793	0.0841	L	0.47716	1.5	0.09310	N	1	B;B	0.17038	0.017;0.02	B;B	0.15484	0.011;0.013	T	0.35051	-0.9804	10	0.49607	T	0.09	0.7943	5.1768	0.15139	0.0:0.3367:0.1566:0.5067	.	91;91	Q5U623-2;Q5U623	.;MCAF2_HUMAN	L	91	ENSP00000379807:F91L;ENSP00000379808:F91L;ENSP00000440791:F91L;ENSP00000348799:F91L;ENSP00000322811:F91L	ENSP00000322811:F91L	F	+	3	2	ATF7IP2	10432251	0.000000	0.05858	0.001000	0.08648	0.587000	0.36485	-0.311000	0.08124	-0.147000	0.11254	0.467000	0.42956	TTC		0.333	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		A	10524750	C	A	10524750	3	1	61	1	0	0	0	0	1	0	0	0	1089	912	32	2	275	2	ATF7IP2	16	10524750	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	589819	10524750	79830003	9646	17631										
EMP2	2013	broad.mit.edu	37	chr16	10631921	10631921	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcctggaccgcctgcagCgtggagtactctgcgggaaa	16	11	1	0	rs61731468	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:10631921C>T	ENST00000359543.3	-	4	389	c.180G>A	c.(178-180)acG>acA	p.T60T	EMP2_ENST00000536829.1_Silent_p.T60T	NM_001424.4	NP_001415.1	P54851	EMP2_HUMAN	epithelial membrane protein 2	60					cell proliferation (GO:0008283)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|regulation of glomerular filtration (GO:0003093)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	integrin binding (GO:0005178)	p.T60T(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6						CCGCCTGCAGCGTGGAGTACT	0.622													C|||	4	0.000798722	0	0	5008	,	,		17777	0.004		0	False		,,,				2504	0				GBM(158;2021 2691 14714 39478)											1	Substitution - coding silent(1)	large_intestine(1)	16						C		1,4393	2.1+/-5.4	0,1,2196	125	114	117		180	-6.2	0	16	dbSNP_129	117	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	EMP2	NM_001424.4		0,9,6488	TT,TC,CC		0.093,0.0228,0.0693		60/168	10631921	9,12985	2197	4300	6497	10539422	SO:0001819	synonymous_variant	2013			U52100	CCDS10541.1	16p13.2	2008-08-01			ENSG00000213853	ENSG00000213853			3334	protein-coding gene	gene with protein product		602334				8996089, 10331954, 16216233	Standard	NM_001424		Approved	XMP	uc002czx.3	P54851	OTTHUMG00000129752	ENST00000359543.3:c.180G>A	16.37:g.10631921C>T			10539422	B2R7V6|D3DUF8	Silent	SNP	ENST00000359543.3	37	CCDS10541.1																																																																																				0.622	EMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251965.1	NM_001424		T	10631921	C	T	10631921	2	4	61	1	0	0	0	0	0	0	0	1	5115	755	27	1		1	EMP2	16	10631921	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107171	10631921	79722832	9647	17632										
TEKT5	146279	broad.mit.edu	37	chr16	10775927	10775927	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttaaagcacttctcatcGatacactgggccgagctttt	9	10	1	0	rs148685770		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:10775927G>A	ENST00000283025.2	-	4	857	c.786C>T	c.(784-786)atC>atT	p.I262I		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	262						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.I262I(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						ACTTCTCATCGATACACTGGG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G		0,4394		0,0,2197	284	218	240		786	-8.2	0	16	dbSNP_134	240	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	TEKT5	NM_144674.1		0,4,6493	AA,AG,GG		0.0465,0.0,0.0308		262/486	10775927	4,12990	2197	4300	6497	10683428	SO:0001819	synonymous_variant	146279				CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.786C>T	16.37:g.10775927G>A			10683428	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																				0.537	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		A	10775927	G	A	10775927	2	1	61	1	0	0	0	0	0	0	0	1	15795	1048	37	1		1	TEKT5	16	10775927	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144006	10775927	79578826	9648	17633										
TEKT5	146279	broad.mit.edu	37	chr16	10788442	10788442	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcacctgcagctggttggActggtcccagtcgtgggggc	16	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:10788442A>G	ENST00000283025.2	-	1	360	c.289T>C	c.(289-291)Tcc>Ccc	p.S97P	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	97						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.S97P(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						AGCTGGTTGGACTGGTCCCAG	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	16											64	75	71					16																	10788442		2197	4300	6497	10695943	SO:0001583	missense	146279				CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.289T>C	16.37:g.10788442A>G	ENSP00000283025:p.Ser97Pro		10695943	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	.	14.05	2.419827	0.42918	.	.	ENSG00000153060	ENST00000283025	T	0.02787	4.16	5.4	0.278	0.15673	.	0.563722	0.17280	N	0.180022	T	0.10594	0.0259	M	0.80616	2.505	0.41313	D	0.987123	P	0.40602	0.723	P	0.53988	0.739	T	0.01323	-1.1385	10	0.66056	D	0.02	-17.92	9.982	0.41819	0.3776:0.5095:0.0:0.1128	.	97	Q96M29	TEKT5_HUMAN	P	97	ENSP00000283025:S97P	ENSP00000283025:S97P	S	-	1	0	TEKT5	10695943	0.855000	0.29742	0.083000	0.20561	0.092000	0.18411	1.801000	0.38843	-0.165000	0.10908	0.528000	0.53228	TCC		0.677	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		G	10788442	A	G	10788442	3	3	61	1	0	0	0	0	1	0	0	0	15795	275	10	4	1196	4	TEKT5	16	10788442	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12515	10788442	79566311	9649	17634										
CIITA	4261	broad.mit.edu	37	chr16	11001566	11001566	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccgcagtacctagcattGaccccaaggaagaagaggcc	10	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11001566G>T	ENST00000324288.8	+	11	2350	c.2217G>T	c.(2215-2217)ttG>ttT	p.L739F	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	739					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.L739F(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						ACCTAGCATTGACCCCAAGGA	0.632			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	1	Substitution - Missense(1)	large_intestine(1)	16											74	79	77					16																	11001566		2197	4300	6497	10909067	SO:0001583	missense	4261			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2217G>T	16.37:g.11001566G>T	ENSP00000316328:p.Leu739Phe		10909067	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202306	0.38905	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.77750	-1.12	5.15	4.17	0.49024	.	0.000000	0.42964	D	0.000627	D	0.83658	0.5302	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.76494	0.973;0.998;0.984;0.999	P;P;P;D	0.87578	0.685;0.882;0.881;0.998	T	0.81897	-0.0722	10	0.38643	T	0.18	.	10.1775	0.42948	0.0:0.1482:0.6985:0.1533	.	739;739;691;739	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	F	739;691	ENSP00000316328:L739F	ENSP00000316328:L739F	L	+	3	2	CIITA	10909067	1.000000	0.71417	0.976000	0.42696	0.326000	0.28443	1.682000	0.37628	1.119000	0.41883	0.655000	0.94253	TTG		0.632	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		T	11001566	G	T	11001566	3	4	61	1	0	0	0	0	1	0	0	0	3434	1281	45	2	2259	2	CIITA	16	11001566	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213124	11001566	79353187	9650	17635										
CLEC16A	23274	broad.mit.edu	37	chr16	11118741	11118741	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgattaccatgccctgttCgtgctctgcctcctctatgc	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11118741C>T	ENST00000409790.1	+	13	1730	c.1500C>T	c.(1498-1500)ttC>ttT	p.F500F	CLEC16A_ENST00000409552.3_Silent_p.F482F|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.F500F(1)|p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ATGCCCTGTTCGTGCTCTGCC	0.552																																																2	Whole gene deletion(1)|Substitution - coding silent(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											96	98	97					16																	11118741		2133	4239	6372	11026242	SO:0001819	synonymous_variant	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1500C>T	16.37:g.11118741C>T			11026242		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																				0.552	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11118741	C	T	11118741	2	4	61	1	0	0	0	0	0	0	0	1	3506	883	31	1		1	CLEC16A	16	11118741	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117175	11118741	79236012	9651	17636										
CLEC16A	23274	broad.mit.edu	37	chr16	11141179	11141179	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttggacatgtttgaaGatgagtataggagcatgaca	11	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11141179G>T	ENST00000409790.1	+	17	2076	c.1846G>T	c.(1846-1848)Gat>Tat	p.D616Y	CLEC16A_ENST00000409552.3_Missense_Mutation_p.D598Y|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)|p.D616Y(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CATGTTTGAAGATGAGTATAG	0.463																																																2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											68	67	67					16																	11141179		1910	4120	6030	11048680	SO:0001583	missense	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1846G>T	16.37:g.11141179G>T	ENSP00000387122:p.Asp616Tyr		11048680		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902019	0.92035	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.53640	0.61	5.39	5.39	0.77823	.	0.091594	0.64402	D	0.000001	T	0.67887	0.2941	M	0.79693	2.465	0.80722	D	1	D;D	0.69078	0.997;0.986	P;P	0.59948	0.866;0.814	T	0.73030	-0.4111	10	0.87932	D	0	-20.6323	16.7323	0.85438	0.0:0.0:1.0:0.0	.	616;598	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	Y	616;616;598	ENSP00000387122:D616Y	ENSP00000386495:D598Y	D	+	1	0	CLEC16A	11048680	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.773000	0.91762	2.543000	0.85770	0.650000	0.86243	GAT		0.463	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11141179	G	T	11141179	3	4	61	1	0	0	0	0	1	0	0	0	3506	942	33	2	1908	2	CLEC16A	16	11141179	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22438	11141179	79213574	9652	17637										
CLEC16A	23274	broad.mit.edu	37	chr16	11272334	11272334	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagcctgtcccccagcctCgtccctgcccggcagcccac	9	23	0	0	rs201719789		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11272334C>T	ENST00000409790.1	+	24	3179	c.2949C>T	c.(2947-2949)ctC>ctT	p.L983L	CLEC16A_ENST00000381822.2_Silent_p.L70L	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.L983L(1)|p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCCCCAGCCTCGTCCCTGCCC	0.632																																																2	Whole gene deletion(1)|Substitution - coding silent(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											62	75	71					16																	11272334		2154	4251	6405	11179835	SO:0001819	synonymous_variant	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2949C>T	16.37:g.11272334C>T			11179835		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																				0.632	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11272334	C	T	11272334	2	4	61	1	0	0	0	0	0	0	0	1	3506	871	31	1		1	CLEC16A	16	11272334	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131155	11272334	79082419	9653	17638										
TNP2	7142	broad.mit.edu	37	chr16	11362879	11362879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcatagtctttttgtggcGctttggtggtggactagtgt	14	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11362879G>A	ENST00000312693.3	-	1	310	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	81					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)|p.R81C(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						TTTTTGTGGCGCTTTGGTGGT	0.602																																																2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											142	150	148					16																	11362879		2087	4219	6306	11270380	SO:0001583	missense	7142				CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.241C>T	16.37:g.11362879G>A	ENSP00000325738:p.Arg81Cys		11270380	Q9NZB0	Missense_Mutation	SNP	ENST00000312693.3	37	CCDS45410.1	.	.	.	.	.	.	.	.	.	.	G	8.195	0.796775	0.16327	.	.	ENSG00000178279	ENST00000312693	T	0.51574	0.7	3.2	2.23	0.28157	.	0.214824	0.23666	N	0.045773	T	0.41811	0.1175	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	P	0.51777	0.679	T	0.22452	-1.0216	10	0.87932	D	0	-6.5072	7.8219	0.29292	0.0:0.0:0.7526:0.2474	.	81	Q05952	STP2_HUMAN	C	81	ENSP00000325738:R81C	ENSP00000325738:R81C	R	-	1	0	TNP2	11270380	0.018000	0.18449	0.005000	0.12908	0.006000	0.05464	0.537000	0.23144	0.908000	0.36671	-0.277000	0.10078	CGC		0.602	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425		A	11362879	G	A	11362879	3	1	61	1	0	0	0	0	1	0	0	0	16373	1087	38	1	183	1	TNP2	16	11362879	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90545	11362879	78991874	9654	17639										
PRM2	5620	broad.mit.edu	37	chr16	11370104	11370104	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggtcctctcgtagacctCgacgtgctccgggctcagcc	12	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11370104C>T	ENST00000241808.4	-	1	233	c.124G>A	c.(124-126)Gag>Aag	p.E42K	PRM2_ENST00000435245.2_Missense_Mutation_p.E42K|PRM3_ENST00000327157.2_5'Flank|RMI2_ENST00000572173.1_Intron|SNORA48_ENST00000390926.1_RNA	NM_002762.2	NP_002753.2	P04554	PRM2_HUMAN	protamine 2	42					cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)|p.E42K(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)	7						TCGTAGACCTCGACGTGCTCC	0.632																																																2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											87	93	91					16																	11370104		2173	4275	6448	11277605	SO:0001583	missense	5620				CCDS42118.1, CCDS66944.1	16p13.13	2013-10-17			ENSG00000122304	ENSG00000122304			9448	protein-coding gene	gene with protein product	"cancer/testis antigen family 94, member 2"	182890				16632464	Standard	NM_001286356		Approved	CT94.2	uc002dau.1	P04554	OTTHUMG00000172317	ENST00000241808.4:c.124G>A	16.37:g.11370104C>T	ENSP00000241808:p.Glu42Lys		11277605	Q6ZMM0	Missense_Mutation	SNP	ENST00000241808.4	37	CCDS42118.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948593	0.53186	.	.	ENSG00000122304	ENST00000241808;ENST00000435245	.	.	.	3.35	1.34	0.21922	.	0.881969	0.09257	N	0.827100	T	0.26846	0.0657	L	0.29908	0.895	0.09310	N	1	P;P	0.49696	0.927;0.816	B;B	0.40009	0.316;0.209	T	0.16364	-1.0405	9	0.87932	D	0	-0.1281	10.0648	0.42297	0.0:0.6974:0.3026:0.0	.	42;42	Q6ZMM0;P04554	.;PRM2_HUMAN	K	42	.	ENSP00000241808:E42K	E	-	1	0	PRM2	11277605	0.002000	0.14202	0.001000	0.08648	0.020000	0.10135	1.053000	0.30442	0.427000	0.26145	0.491000	0.48974	GAG		0.632	PRM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417808.1			T	11370104	C	T	11370104	3	4	61	1	0	0	0	0	1	0	0	0	12567	893	31	1	192	1	PRM2	16	11370104	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7225	11370104	78984649	9655	17640										
TXNDC11	51061	broad.mit.edu	37	chr16	11773668	11773668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggtgatggggacgtcttCggggtatttcacacttaggt	15	6	2	1	rs151125071		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11773668C>T	ENST00000356957.3	-	13	2448	c.2341G>A	c.(2341-2343)Gaa>Aaa	p.E781K	TXNDC11_ENST00000283033.5_Missense_Mutation_p.E754K|TXNDC11_ENST00000570917.1_5'UTR			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	781	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.E754K(1)		endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GGGACGTCTTCGGGGTATTTC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	LYS/GLU	0,4394		0,0,2197	57	46	50		2260	4.9	0.8	16	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	missense	TXNDC11	NM_015914.5	56	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	754/959	11773668	1,12993	2197	4300	6497	11681169	SO:0001583	missense	51061			BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"EF-hand binding protein 1"					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.2341G>A	16.37:g.11773668C>T	ENSP00000349439:p.Glu781Lys		11681169	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Missense_Mutation	SNP	ENST00000356957.3	37		.	.	.	.	.	.	.	.	.	.	C	15.55	2.866775	0.51588	0.0	1.16E-4	ENSG00000153066	ENST00000356957;ENST00000283033	T;T	0.15718	2.63;2.4	5.9	4.94	0.65067	Thioredoxin-like fold (2);	0.155864	0.56097	D	0.000027	T	0.16257	0.0391	L	0.38175	1.15	0.47374	D	0.999403	B;D	0.53312	0.402;0.959	B;B	0.42882	0.146;0.401	T	0.02797	-1.1109	10	0.27082	T	0.32	-15.5921	15.5817	0.76448	0.1387:0.8613:0.0:0.0	.	781;754	Q6PKC3;Q6PKC3-2	TXD11_HUMAN;.	K	781;754	ENSP00000349439:E781K;ENSP00000283033:E754K	ENSP00000283033:E754K	E	-	1	0	TXNDC11	11681169	1.000000	0.71417	0.847000	0.33407	0.670000	0.39368	5.372000	0.66156	1.482000	0.48325	0.650000	0.86243	GAA		0.507	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914		T	11773668	C	T	11773668	3	4	61	1	0	0	0	0	1	0	0	0	16832	893	31	1	620	1	TXNDC11	16	11773668	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	403564	11773668	78581085	9656	17641										
ZC3H7A	29066	broad.mit.edu	37	chr16	11855829	11855829	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaatgacttgaccgtttCtcagacactgggcgcacaca	9	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:11855829C>A	ENST00000396516.2	-	17	2347	c.2150G>T	c.(2149-2151)aGa>aTa	p.R717I	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.R717I|ZC3H7A_ENST00000575984.1_5'Flank			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	717						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R717I(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						TTGACCGTTTCTCAGACACTG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	16											128	112	117					16																	11855829		2196	4299	6495	11763330	SO:0001583	missense	29066			AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.2150G>T	16.37:g.11855829C>A	ENSP00000379773:p.Arg717Ile		11763330	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	37	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677684	0.88445	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.12255	2.7;2.7	5.52	3.56	0.40772	.	0.042016	0.85682	D	0.000000	T	0.33818	0.0876	M	0.76574	2.34	0.80722	D	1	D;P	0.60160	0.987;0.796	D;P	0.70016	0.967;0.786	T	0.09684	-1.0663	10	0.72032	D	0.01	.	10.7837	0.46393	0.0:0.8474:0.0:0.1526	.	438;717	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	I	717	ENSP00000347999:R717I;ENSP00000379773:R717I	ENSP00000347999:R717I	R	-	2	0	ZC3H7A	11763330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.222000	0.51223	1.320000	0.45209	0.591000	0.81541	AGA		0.328	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		A	11855829	C	A	11855829	3	1	61	1	0	0	0	0	1	0	0	0	17611	913	32	2	789	2	ZC3H7A	16	11855829	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82161	11855829	78498924	9657	17642										
RUNDC2A	92017	broad.mit.edu	37	chr16	12140254	12140254	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcagcactttttatgaaGactggtcttttgtgatggat	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:12140254G>T	ENST00000566228.1	+	6	511	c.442G>T	c.(442-444)Gac>Tac	p.D148Y	SNX29_ENST00000568359.1_3'UTR	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	148	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.D148Y(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						TTTTTATGAAGACTGGTCTTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	16											188	168	175					16																	12140254		2197	4300	6497	12047755	SO:0001583	missense	84127			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.442G>T	16.37:g.12140254G>T	ENSP00000456480:p.Asp148Tyr		12047755	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557645	0.86231	.	.	ENSG00000140660	ENST00000268271	.	.	.	5.63	5.63	0.86233	.	0.061993	0.64402	D	0.000009	T	0.71643	0.3364	L	0.50333	1.59	0.80722	D	1	.	.	.	.	.	.	T	0.72811	-0.4180	7	0.66056	D	0.02	-9.1272	18.2552	0.90017	0.0:0.0:1.0:0.0	.	.	.	.	Y	148	.	ENSP00000268271:D148Y	D	+	1	0	RUNDC2A	12047755	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.654000	0.98509	2.644000	0.89710	0.563000	0.77884	GAC		0.483	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12140254	G	T	12140254	3	4	61	1	0	0	0	0	1	0	0	0	13780	942	33	2	464	2	RUNDC2A	16	12140254	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	284425	12140254	78214499	9658	17643										
SNX29	92017	broad.mit.edu	37	chr16	12492312	12492312	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatggtaggtgcctggaGatttgagtcaaacgtccgaa	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:12492312G>T	ENST00000566228.1	+	17	1978	c.1909G>T	c.(1909-1911)Gat>Tat	p.D637Y	SNX29_ENST00000306030.3_Missense_Mutation_p.D252Y|SNX29_ENST00000323433.4_Missense_Mutation_p.D252Y	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	637						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.D252Y(2)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GGTGCCTGGAGATTTGAGTCA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	16											128	125	126					16																	12492312		1859	4109	5968	12399813	SO:0001583	missense	92017			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1909G>T	16.37:g.12492312G>T	ENSP00000456480:p.Asp637Tyr		12399813	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.121556	0.77436	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.68933	0.3055	L	0.58810	1.83	0.33957	D	0.6452	.	.	.	.	.	.	T	0.78393	-0.2221	7	0.87932	D	0	-26.0635	17.1552	0.86790	0.0:0.0:1.0:0.0	.	.	.	.	Y	252	.	ENSP00000306940:D252Y	D	+	1	0	SNX29	12399813	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.835000	0.75344	2.633000	0.89246	0.655000	0.94253	GAT		0.458	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12492312	G	T	12492312	3	4	61	1	0	0	0	0	1	0	0	0	14935	942	33	2	788	2	SNX29	16	12492312	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	352058	12492312	77862441	9659	17644										
ERCC4	2072	broad.mit.edu	37	chr16	14024596	14024596	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattatctggatcctttgtgGcaccagcttggagccaagac	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:14024596G>A	ENST00000311895.7	+	5	831	c.822G>A	c.(820-822)tgG>tgA	p.W274*	CTD-2135D7.2_ENST00000570663.1_RNA|ERCC4_ENST00000574781.1_3'UTR|CTD-2135D7.2_ENST00000575137.1_RNA|ERCC4_ENST00000575156.1_Nonsense_Mutation_p.W274*	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	274	Helicase-like.|Leucine-zipper 2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.W274*(2)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						ATCCTTTGTGGCACCAGCTTG	0.333			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	16											85	77	80					16																	14024596		2197	4300	6497	13932097	SO:0001587	stop_gained	2072	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.822G>A	16.37:g.14024596G>A	ENSP00000310520:p.Trp274*		13932097	A5PKV6|A8K111|O00140|Q8TD83	Nonsense_Mutation	SNP	ENST00000311895.7	37	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	G	35	5.552125	0.96501	.	.	ENSG00000175595	ENST00000311895;ENST00000439007;ENST00000389138	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0634	19.0512	0.93046	0.0:0.0:1.0:0.0	.	.	.	.	X	274;263;263	.	ENSP00000310520:W274X	W	+	3	0	ERCC4	13932097	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.471000	0.97696	2.741000	0.93983	0.650000	0.86243	TGG		0.333	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		A	14024596	G	A	14024596	4	1	61	1	0	0	0	0	0	1	0	0	5228	1212	42	3	840	3	ERCC4	16	14024596	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1532284	14024596	76330157	9660	17645										
MKL2	57496	broad.mit.edu	37	chr16	14307415	14307415	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaagactgaaaacttttTgaaacacaagattcggagtc	7	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:14307415T>C	ENST00000341243.5	+	4	257	c.257T>C	c.(256-258)tTg>tCg	p.L86S	MKL2_ENST00000318282.5_Missense_Mutation_p.L97S|MKL2_ENST00000574045.1_Missense_Mutation_p.L97S|MKL2_ENST00000573051.1_Missense_Mutation_p.L46S|MKL2_ENST00000572567.1_Missense_Mutation_p.L86S|MKL2_ENST00000571589.1_Missense_Mutation_p.L97S			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	86					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.L97S(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GAAAACTTTTTGAAACACAAG	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	16											67	67	67					16																	14307415		2197	4300	6497	14214916	SO:0001583	missense	57496			AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.257T>C	16.37:g.14307415T>C	ENSP00000345841:p.Leu86Ser		14214916	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	37		.	.	.	.	.	.	.	.	.	.	t	20.9	4.067778	0.76301	.	.	ENSG00000186260	ENST00000318282;ENST00000389126;ENST00000341243	D;D	0.99823	-6.95;-6.95	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.99846	0.9929	M	0.89715	3.055	0.50632	D	0.999889	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96721	0.9532	10	0.66056	D	0.02	-10.7747	15.4318	0.75105	0.0:0.0:0.0:1.0	.	46;97;86;97	Q9ULH7-2;B4DGT8;Q9ULH7;Q9ULH7-4	.;.;MKL2_HUMAN;.	S	97;86;86	ENSP00000339086:L97S;ENSP00000345841:L86S	ENSP00000339086:L97S	L	+	2	0	MKL2	14214916	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.161000	0.71868	2.237000	0.73441	0.528000	0.53228	TTG		0.279	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		C	14307415	T	C	14307415	3	2	61	1	0	0	0	0	1	0	0	0	9632	1821	63	4	304	4	MKL2	16	14307415	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	282819	14307415	76047338	9661	17646										
MKL2	57496	broad.mit.edu	37	chr16	14340348	14340348	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtatcagaactgaagacaGaactgaagttaaggggtctg	13	5	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:14340348G>T	ENST00000341243.5	+	10	1198	c.1198G>T	c.(1198-1200)Gaa>Taa	p.E400*	MKL2_ENST00000318282.5_Nonsense_Mutation_p.E411*|MKL2_ENST00000574045.1_Nonsense_Mutation_p.E411*|MKL2_ENST00000571589.1_Nonsense_Mutation_p.E411*			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	400	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.E411*(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACTGAAGACAGAACTGAAGTT	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											49	45	47					16																	14340348		2197	4300	6497	14247849	SO:0001587	stop_gained	57496			AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1198G>T	16.37:g.14340348G>T	ENSP00000345841:p.Glu400*		14247849	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Nonsense_Mutation	SNP	ENST00000341243.5	37		.	.	.	.	.	.	.	.	.	.	G	41	8.620078	0.98888	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-21.6687	19.2512	0.93926	0.0:0.0:1.0:0.0	.	.	.	.	X	411;400	.	ENSP00000339086:E411X	E	+	1	0	MKL2	14247849	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.807000	0.99171	2.788000	0.95919	0.655000	0.94253	GAA		0.488	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		T	14340348	G	T	14340348	4	4	61	1	0	0	0	0	0	1	0	0	9632	943	33	2	1269	2	MKL2	16	14340348	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32933	14340348	76014405	9662	17647										
MKL2	57496	broad.mit.edu	37	chr16	14340860	14340860	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggagaaagagaagcaaatCgaagagctgaagaggaaact	13	5	0	5	rs148779363	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:14340860C>T	ENST00000341243.5	+	10	1710	c.1710C>T	c.(1708-1710)atC>atT	p.I570I	MKL2_ENST00000318282.5_Silent_p.I581I|MKL2_ENST00000574045.1_Silent_p.I581I|MKL2_ENST00000571589.1_Silent_p.I581I			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	570	Required for interaction with itself and with MKL1.				blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.I581I(3)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGAAGCAAATCGAAGAGCTGA	0.507																																																3	Substitution - coding silent(3)	large_intestine(2)|lung(1)	16						C		0,4394		0,0,2197	37	39	38		1743	-5.9	0.8	16	dbSNP_134	38	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	MKL2	NM_014048.3		0,3,6494	TT,TC,CC		0.0349,0.0,0.0231		581/1050	14340860	3,12991	2197	4300	6497	14248361	SO:0001819	synonymous_variant	57496			AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1710C>T	16.37:g.14340860C>T			14248361	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	37																																																																																					0.507	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		T	14340860	C	T	14340860	2	4	61	1	0	0	0	0	0	0	0	1	9632	874	31	1		1	MKL2	16	14340860	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	512	14340860	76013893	9663	17648										
PDXDC1	23042	broad.mit.edu	37	chr16	15102664	15102664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccttcccctgcttgtgccGtgtaccctgtaacactgtgt	9	15	0	0	rs371802617		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15102664G>A	ENST00000396410.4	+	7	705	c.608G>A	c.(607-609)cGt>cAt	p.R203H	PDXDC1_ENST00000325823.7_Missense_Mutation_p.R188H|PDXDC1_ENST00000569715.1_Missense_Mutation_p.R176H|PDXDC1_ENST00000455313.2_Intron|MIR1972-1_ENST00000459337.1_RNA|PDXDC1_ENST00000535621.2_Missense_Mutation_p.R203H|PDXDC1_ENST00000563679.1_Missense_Mutation_p.R221H|PDXDC1_ENST00000450288.2_Missense_Mutation_p.R175H|PDXDC1_ENST00000447912.2_Missense_Mutation_p.R112H	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	203					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)	p.R203H(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGCTTGTGCCGTGTACCCTGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	16						G	HIS/ARG	1,4393	2.1+/-5.4	0,1,2196	367	317	334		608	3.8	1	16		334	0,8600		0,0,4300	no	missense	PDXDC1	NM_015027.2	29	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	benign	203/789	15102664	1,12993	2197	4300	6497	15010165	SO:0001583	missense	23042			AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.608G>A	16.37:g.15102664G>A	ENSP00000379691:p.Arg203His		15010165	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157176	0.57259	2.28E-4	0.0	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	5.8	3.75	0.43078	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.322125	0.37530	N	0.002041	T	0.32194	0.0821	L	0.52573	1.65	0.42382	D	0.992494	B;B;B;B;B;B	0.23185	0.02;0.081;0.036;0.028;0.02;0.02	B;B;B;B;B;B	0.16722	0.01;0.01;0.016;0.01;0.01;0.01	T	0.06023	-1.0850	10	0.13108	T	0.6	-17.5596	10.4865	0.44724	0.0729:0.1352:0.7919:0.0	.	175;112;188;203;175;203	E7EPL4;E7EMH5;B4DHL7;Q86XE2;B4DR55;Q6P996	.;.;.;.;.;PDXD1_HUMAN	H	188;112;203;203;175	ENSP00000322807:R188H;ENSP00000400310:R112H;ENSP00000437835:R203H;ENSP00000379691:R203H;ENSP00000391147:R175H	ENSP00000322807:R188H	R	+	2	0	PDXDC1	15010165	0.961000	0.32948	1.000000	0.80357	0.985000	0.73830	1.439000	0.35013	2.752000	0.94435	0.650000	0.86243	CGT		0.458	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15102664	G	A	15102664	3	1	61	1	0	0	0	0	1	0	0	0	11727	1145	40	1	634	1	PDXDC1	16	15102664	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	761804	15102664	75252089	9664	17649										
MPV17L	255027	broad.mit.edu	37	chr16	15501853	15501853	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgctggagtctgtggttttCtctgggccaccttcatctgt	11	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15501853C>A	ENST00000396385.3	+	4	594	c.475C>A	c.(475-477)Ctc>Atc	p.L159I	MPV17L_ENST00000287594.7_Missense_Mutation_p.S135Y|RP11-1021N1.1_ENST00000568222.1_Intron	NM_001128423.1	NP_001121895.1	Q2QL34	MP17L_HUMAN	MPV17 mitochondrial membrane protein-like	159					negative regulation of hydrogen peroxide biosynthetic process (GO:0010730)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|reactive oxygen species metabolic process (GO:0072593)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	receptor binding (GO:0005102)	p.S135Y(1)		kidney(2)|large_intestine(1)|skin(1)	4						CTGTGGTTTTCTCTGGGCCAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											65	57	60					16																	15501853		2197	4300	6497	15409354	SO:0001583	missense	255027			DQ004255	CCDS10560.1, CCDS45421.1	16p13.11	2009-04-06			ENSG00000156968	ENSG00000156968			26827	protein-coding gene	gene with protein product						16631601	Standard	NM_001128423		Approved	FLJ39599, MLPH1, MLPH2, MPV17L1	uc002ddn.2	Q2QL34	OTTHUMG00000129882	ENST00000396385.3:c.475C>A	16.37:g.15501853C>A	ENSP00000379669:p.Leu159Ile		15409354	B4DDY1|Q6P7T6|Q8N8E9	Missense_Mutation	SNP	ENST00000396385.3	37	CCDS45421.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.151|0.151	-1.091409|-1.091409	0.01858|0.01858	.|.	.|.	ENSG00000156968|ENSG00000156968	ENST00000396385|ENST00000287594	D|D	0.85773|0.92911	-2.03|-3.13	5.29|5.29	3.32|3.32	0.38043|0.38043	.|.	0.435897|.	0.19479|.	U|.	0.113245|.	D|D	0.87533|0.87533	0.6201|0.6201	.|.	.|.	.|.	0.29779|0.29779	N|N	0.834183|0.834183	B|P	0.31256|0.45078	0.316|0.85	B|B	0.27608|0.40285	0.081|0.325	D|D	0.83983|0.83983	0.0333|0.0333	9|8	0.07813|0.72032	T|D	0.8|0.01	-9.8577|-9.8577	5.9653|5.9653	0.19322|0.19322	0.0:0.6692:0.1561:0.1747|0.0:0.6692:0.1561:0.1747	.|.	159|135	Q2QL34|Q2QL34-2	MP17L_HUMAN|.	I|Y	159|135	ENSP00000379669:L159I|ENSP00000287594:S135Y	ENSP00000379669:L159I|ENSP00000287594:S135Y	L|S	+|+	1|2	0|0	MPV17L|MPV17L	15409354|15409354	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.079000|0.079000	0.17450|0.17450	0.434000|0.434000	0.21494|0.21494	1.240000|1.240000	0.43803|0.43803	0.471000|0.471000	0.43371|0.43371	CTC|TCT		0.498	MPV17L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422450.1	NM_173803		A	15501853	C	A	15501853	3	1	61	1	0	0	0	0	1	0	0	0	9776	913	32	2	489	2	MPV17L	16	15501853	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	399189	15501853	74852900	9665	17650										
C16orf45	89927	broad.mit.edu	37	chr16	15675086	15675086	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttccagaaaaagaaaaaaCcaaactgcagaagcagagag	8	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15675086C>A	ENST00000300006.4	+	4	676	c.317C>A	c.(316-318)aCc>aAc	p.T106N	C16orf45_ENST00000565913.1_3'UTR|C16orf45_ENST00000561692.1_Missense_Mutation_p.T58N|C16orf45_ENST00000452191.2_Missense_Mutation_p.T89N|C16orf45_ENST00000566490.1_Missense_Mutation_p.T106N	NM_033201.2	NP_149978.1	Q96MC5	CP045_HUMAN	chromosome 16 open reading frame 45	106								p.T106N(3)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)	11						AAAGAAAAAACCAAACTGCAG	0.493																																																3	Substitution - Missense(3)	large_intestine(3)	16											69	62	64					16																	15675086		2197	4300	6497	15582587	SO:0001583	missense	89927			AK057180	CCDS10561.1, CCDS45422.1	16p13.2	2012-10-09			ENSG00000166780	ENSG00000166780			19213	protein-coding gene	gene with protein product							Standard	NM_033201		Approved	FLJ32618	uc002ddo.3	Q96MC5	OTTHUMG00000129883	ENST00000300006.4:c.317C>A	16.37:g.15675086C>A	ENSP00000300006:p.Thr106Asn		15582587	O00223|O75769|Q8IZ36|Q96H25	Missense_Mutation	SNP	ENST00000300006.4	37	CCDS10561.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086918	0.55861	.	.	ENSG00000166780	ENST00000300006;ENST00000452191	T;T	0.55760	0.5;0.5	5.33	5.33	0.75918	Domain of unknown function DUF3585 (1);	0.141685	0.64402	D	0.000005	T	0.52041	0.1710	L	0.58428	1.81	0.47905	D	0.999544	B;B	0.29552	0.248;0.01	B;B	0.25884	0.064;0.01	T	0.53774	-0.8391	10	0.54805	T	0.06	-4.0795	18.5994	0.91242	0.0:1.0:0.0:0.0	.	50;106	B4DE25;Q96MC5	.;CP045_HUMAN	N	106;89	ENSP00000300006:T106N;ENSP00000408976:T89N	ENSP00000300006:T106N	T	+	2	0	C16orf45	15582587	0.989000	0.36119	0.998000	0.56505	0.995000	0.86356	2.631000	0.46502	2.499000	0.84300	0.655000	0.94253	ACC		0.493	C16orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252130.2	NM_033201		A	15675086	C	A	15675086	3	1	61	1	0	0	0	0	1	0	0	0	1818	507	18	2	390	2	C16orf45	16	15675086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173233	15675086	74679667	9666	17651										
MYH11	4629	broad.mit.edu	37	chr16	15829295	15829295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagggcctccagctcctcgCcgaggtctcgcttctgcttt	10	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15829295C>T	ENST00000300036.5	-	26	3543	c.3434G>A	c.(3433-3435)gGc>gAc	p.G1145D	MYH11_ENST00000452625.2_Missense_Mutation_p.G1152D|MYH11_ENST00000396324.3_Missense_Mutation_p.G1152D|AF001548.5_ENST00000574212.1_RNA|MYH11_ENST00000576790.2_Missense_Mutation_p.G1145D	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1145					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.G1145D(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CAGCTCCTCGCCGAGGTCTCG	0.612			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - Missense(1)	large_intestine(1)	16											152	131	138					16																	15829295		2197	4300	6497	15736796	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3434G>A	16.37:g.15829295C>T	ENSP00000300036:p.Gly1145Asp		15736796	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390972	0.82902	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	5.19	5.19	0.71726	Myosin tail (1);	0.061906	0.64402	D	0.000004	D	0.87301	0.6143	L	0.48642	1.525	0.58432	D	0.999998	P;P;P;P;P	0.42357	0.777;0.71;0.578;0.71;0.71	P;P;P;P;P	0.56216	0.673;0.794;0.72;0.794;0.794	D	0.88415	0.3024	10	0.87932	D	0	.	17.73	0.88375	0.0:1.0:0.0:0.0	.	1152;1145;1152;1145;1152	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	D	1145;1145;1152;1152;1152	ENSP00000300036:G1145D;ENSP00000345136:G1145D;ENSP00000379616:G1152D;ENSP00000407821:G1152D	ENSP00000300036:G1145D	G	-	2	0	MYH11	15736796	0.994000	0.37717	1.000000	0.80357	0.845000	0.48019	5.942000	0.70203	2.420000	0.82092	0.442000	0.29010	GGC		0.612	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15829295	C	T	15829295	3	4	61	1	0	0	0	0	1	0	0	0	10061	739	26	3	2583	3	MYH11	16	15829295	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154209	15829295	74525458	9667	17652										
MYH11	4629	broad.mit.edu	37	chr16	15832474	15832474	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcagcttggtaagattCttggccttttcttcctcttc	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15832474C>A	ENST00000300036.5	-	24	3178	c.3069G>T	c.(3067-3069)aaG>aaT	p.K1023N	MYH11_ENST00000452625.2_Missense_Mutation_p.K1030N|MYH11_ENST00000396324.3_Missense_Mutation_p.K1030N|AF001548.6_ENST00000577048.1_RNA|MYH11_ENST00000576790.2_Missense_Mutation_p.K1023N	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1023					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.K1023N(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGGTAAGATTCTTGGCCTTTT	0.343			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - Missense(1)	large_intestine(1)	16											162	153	156					16																	15832474		2197	4300	6497	15739975	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3069G>T	16.37:g.15832474C>A	ENSP00000300036:p.Lys1023Asn		15739975	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185130	0.38609	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	4.16	1.03	0.20045	.	0.118986	0.56097	D	0.000034	D	0.84853	0.5564	L	0.31926	0.97	0.80722	D	1	P;P;P;P;P	0.45594	0.862;0.633;0.633;0.633;0.633	P;P;P;P;P	0.57468	0.821;0.659;0.732;0.585;0.732	T	0.80058	-0.1541	10	0.02654	T	1	.	7.1112	0.25390	0.0:0.5918:0.0:0.4082	.	1030;1023;1030;1023;1030	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	N	1023;1023;1030;1030;1030	ENSP00000300036:K1023N;ENSP00000345136:K1023N;ENSP00000379616:K1030N;ENSP00000407821:K1030N	ENSP00000300036:K1023N	K	-	3	2	MYH11	15739975	0.991000	0.36638	0.999000	0.59377	0.994000	0.84299	0.340000	0.19892	0.329000	0.23460	0.555000	0.69702	AAG		0.343	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15832474	C	A	15832474	3	1	61	1	0	0	0	0	1	0	0	0	10061	912	32	2	2956	2	MYH11	16	15832474	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3179	15832474	74522279	9668	17653										
MYH11	4629	broad.mit.edu	37	chr16	15869975	15869975	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcaatcatgtagtaaaaGatgtggaatgtcctctcgtc	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15869975G>T	ENST00000300036.5	-	8	958	c.849C>A	c.(847-849)atC>atA	p.I283I	MYH11_ENST00000452625.2_Silent_p.I290I|MYH11_ENST00000396324.3_Silent_p.I290I|MYH11_ENST00000576790.2_Silent_p.I283I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	283	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.I283I(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGTAGTAAAAGATGTGGAATG	0.478			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - coding silent(1)	large_intestine(1)	16											332	295	307					16																	15869975		2197	4300	6497	15777476	SO:0001819	synonymous_variant	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.849C>A	16.37:g.15869975G>T			15777476	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																				0.478	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15869975	G	T	15869975	2	4	61	1	0	0	0	0	0	0	0	1	10061	932	33	2		2	MYH11	16	15869975	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37501	15869975	74484778	9669	17654										
MYH11	4629	broad.mit.edu	37	chr16	15878555	15878555	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacactctcagttactcacGtaggcaaaagatgggccttg	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15878555G>A	ENST00000300036.5	-	5	743				MYH11_ENST00000452625.2_Splice_Site_p.Y218Y|MYH11_ENST00000396324.3_Splice_Site_p.Y218Y|MYH11_ENST00000576790.2_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle						axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.Y218Y(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						AGTTACTCACGTAGGCAAAAG	0.483			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	1	Substitution - coding silent(1)	large_intestine(1)	16											107	108	107					16																	15878555		2058	4200	6258	15786056	SO:0001627	intron_variant	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.633+1931C>T	16.37:g.15878555G>A			15786056	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																				0.483	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15878555	G	A	15878555	1	1	61	0	1	0	0	0	0	0	0	0	10061	1159	40	1		1	MYH11	16	15878555	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8580	15878555	74476198	9670	17655										
MYH11	4629	broad.mit.edu	37	chr16	15917266	15917266	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgcagaagaggccagagtaCgtctgcagacagagaaccca	12	11	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15917266C>T	ENST00000300036.5	-	3	457	c.348G>A	c.(346-348)acG>acA	p.T116T	MYH11_ENST00000452625.2_Silent_p.T116T|MYH11_ENST00000396324.3_Silent_p.T116T|MYH11_ENST00000576790.2_Silent_p.T116T	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	116	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.T116T(2)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GGCCAGAGTACGTCTGCAGAC	0.512			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	2	Substitution - coding silent(2)	large_intestine(2)	16											146	117	127					16																	15917266		2197	4300	6497	15824767	SO:0001819	synonymous_variant	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.348G>A	16.37:g.15917266C>T			15824767	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																				0.512	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15917266	C	T	15917266	2	4	61	1	0	0	0	0	0	0	0	1	10061	523	19	1		1	MYH11	16	15917266	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38711	15917266	74437487	9671	17656										
MYH11	4629	broad.mit.edu	37	chr16	15932105	15932105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgagttggcccttctgcGccatggtgccttgttggtcc	12	13	1	1	rs587781072|rs150600829		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:15932105G>A	ENST00000300036.5	-	2	114	c.5C>T	c.(4-6)gCg>gTg	p.A2V	MYH11_ENST00000452625.2_Missense_Mutation_p.A2V|MYH11_ENST00000396324.3_Missense_Mutation_p.A2V|MYH11_ENST00000576790.2_Missense_Mutation_p.A2V	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	2					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.A2V(2)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCCTTCTGCGCCATGGTGCC	0.552			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	2	Substitution - Missense(2)	large_intestine(2)	16						G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4394		0,0,2197	49	48	48		5,5,5,5	5.8	1	16	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	64,64,64,64	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	2/1946,2/1980,2/1973,2/1939	15932105	1,12993	2197	4300	6497	15839606	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5C>T	16.37:g.15932105G>A	ENSP00000300036:p.Ala2Val		15839606	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247472	0.80024	0.0	1.16E-4	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.82	5.82	0.92795	.	0.195281	0.44097	D	0.000495	T	0.74756	0.3758	N	0.14661	0.345	0.47153	D	0.99933	P;P;P;P;P	0.35411	0.5;0.5;0.5;0.5;0.5	B;B;B;B;B	0.26416	0.069;0.069;0.069;0.069;0.069	T	0.77146	-0.2695	10	0.66056	D	0.02	.	19.0811	0.93182	0.0:0.0:1.0:0.0	.	2;2;2;2;2	Q4G140;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	V	2	ENSP00000300036:A2V;ENSP00000345136:A2V;ENSP00000379616:A2V;ENSP00000407821:A2V	ENSP00000300036:A2V	A	-	2	0	MYH11	15839606	1.000000	0.71417	0.973000	0.42090	0.963000	0.63663	6.031000	0.70911	2.756000	0.94617	0.561000	0.74099	GCG		0.552	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15932105	G	A	15932105	3	1	61	1	0	0	0	0	1	0	0	0	10061	1087	38	1	6133	1	MYH11	16	15932105	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14839	15932105	74422648	9672	17657										
ABCC1	4363	broad.mit.edu	37	chr16	16208886	16208886	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgctggccacgcccatcGccgccatcatcatcccgccc	7	22	2	0	rs371062976		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:16208886G>A	ENST00000399410.3	+	23	3518	c.3343G>A	c.(3343-3345)Gcc>Acc	p.A1115T	ABCC1_ENST00000351154.5_Missense_Mutation_p.A1056T|ABCC1_ENST00000346370.5_Missense_Mutation_p.A1059T|ABCC1_ENST00000345148.5_Missense_Mutation_p.A1115T|ABCC1_ENST00000349029.5_Missense_Mutation_p.A1000T|ABCC1_ENST00000399408.2_Missense_Mutation_p.A1125T	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1115	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.A1115T(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CACGCCCATCGCCGCCATCAT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4276		0,0,2138	60	65	63		3343,3166,3175,2998,3343	5.2	0	16		63	1,8505		0,1,4252	no	missense,missense,missense,missense,missense	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	58,58,58,58,58	0,1,6390	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1115/1532,1056/1473,1059/1476,1000/1417,1115/1467	16208886	1,12781	2138	4253	6391	16116387	SO:0001583	missense	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.3343G>A	16.37:g.16208886G>A	ENSP00000382342:p.Ala1115Thr		16116387	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.243284	0.39697	0.0	1.18E-4	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.18	5.18	0.71444	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.113544	0.64402	D	0.000008	D	0.89798	0.6819	L	0.33485	1.01	0.30349	N	0.784928	B;P;D;D;D;D	0.61080	0.194;0.909;0.971;0.989;0.976;0.971	B;B;P;P;P;P	0.56700	0.092;0.373;0.642;0.656;0.804;0.704	D	0.88435	0.3038	10	0.66056	D	0.02	-16.586	17.6861	0.88256	0.0:0.0:1.0:0.0	.	1000;1115;1059;1056;1115;1125	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	T	1115;1125;1059;1056;1115;1000;799	ENSP00000382342:A1115T;ENSP00000382340:A1125T;ENSP00000263019:A1059T;ENSP00000263017:A1056T;ENSP00000263014:A1115T;ENSP00000263016:A1000T	ENSP00000263014:A1115T	A	+	1	0	ABCC1	16116387	1.000000	0.71417	0.027000	0.17364	0.052000	0.14988	5.509000	0.67012	2.417000	0.82017	0.655000	0.94253	GCC		0.552	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16208886	G	A	16208886	3	1	61	1	0	0	0	0	1	0	0	0	49	1087	38	1	3433	1	ABCC1	16	16208886	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	276781	16208886	74145867	9673	17658										
ABCC1	4363	broad.mit.edu	37	chr16	16228264	16228264	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgaccctgggcttatttCggatcaacgagtctgccgaa	10	13	2	1	rs201020041		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:16228264C>T	ENST00000399410.3	+	28	4199	c.4024C>T	c.(4024-4026)Cgg>Tgg	p.R1342W	ABCC1_ENST00000351154.5_Missense_Mutation_p.R1283W|ABCC1_ENST00000346370.5_Missense_Mutation_p.R1286W|ABCC1_ENST00000345148.5_Missense_Mutation_p.R1342W|ABCC1_ENST00000349029.5_Missense_Mutation_p.R1227W|ABCC1_ENST00000399408.2_Missense_Mutation_p.R1352W	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1342	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.R1342W(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GGGCTTATTTCGGATCAACGA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4258		0,0,2129	74	81	79		4024,3847,3856,3679,4024	5.8	1	16		79	1,8453		0,1,4226	no	missense,missense,missense,missense,missense	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	101,101,101,101,101	0,1,6355	TT,TC,CC		0.0118,0.0,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1342/1532,1283/1473,1286/1476,1227/1417,1342/1467	16228264	1,12711	2129	4227	6356	16135765	SO:0001583	missense	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4024C>T	16.37:g.16228264C>T	ENSP00000382342:p.Arg1342Trp		16135765	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	C	31	5.061670	0.93846	0.0	1.18E-4	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03;-3.03;-3.03	5.84	5.84	0.93424	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.053119	0.85682	N	0.000000	D	0.97876	0.9302	H	0.98068	4.14	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;1.0;0.998;0.995;0.999;0.998	D	0.98858	1.0761	10	0.87932	D	0	-31.3675	19.1415	0.93448	0.0:1.0:0.0:0.0	.	1227;1342;1286;1283;1342;1352	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	W	1342;1352;1286;1283;1342;1227;1026	ENSP00000382342:R1342W;ENSP00000382340:R1352W;ENSP00000263019:R1286W;ENSP00000263017:R1283W;ENSP00000263014:R1342W;ENSP00000263016:R1227W	ENSP00000263014:R1342W	R	+	1	2	ABCC1	16135765	0.998000	0.40836	1.000000	0.80357	0.468000	0.32798	3.316000	0.51960	2.758000	0.94735	0.655000	0.94253	CGG		0.597	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16228264	C	T	16228264	3	4	61	1	0	0	0	0	1	0	0	0	49	875	31	1	4134	1	ABCC1	16	16228264	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19378	16228264	74126489	9674	17659										
XYLT1	64131	broad.mit.edu	37	chr16	17211541	17211541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcgagaaggtcagaggcGcaacgaggaatttggtctct	14	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:17211541G>A	ENST00000261381.6	-	11	2603	c.2519C>T	c.(2518-2520)gCg>gTg	p.A840V		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	840					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.A840E(1)|p.A840V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGTCAGAGGCGCAACGAGGAA	0.542																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	16											73	69	71					16																	17211541		2197	4300	6497	17119042	SO:0001583	missense	64131			AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2519C>T	16.37:g.17211541G>A	ENSP00000261381:p.Ala840Val		17119042	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.138951	0.21123	.	.	ENSG00000103489	ENST00000261381	T	0.04119	3.7	5.11	5.11	0.69529	.	0.097576	0.64402	D	0.000001	T	0.06600	0.0169	L	0.38175	1.15	0.58432	D	0.999996	D	0.64830	0.994	P	0.48270	0.572	T	0.21690	-1.0238	10	0.02654	T	1	-14.7591	17.8959	0.88888	0.0:0.0:1.0:0.0	.	840	Q86Y38	XYLT1_HUMAN	V	840	ENSP00000261381:A840V	ENSP00000261381:A840V	A	-	2	0	XYLT1	17119042	0.998000	0.40836	0.243000	0.24186	0.887000	0.51463	4.874000	0.63064	2.515000	0.84797	0.563000	0.77884	GCG		0.542	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17211541	G	A	17211541	3	1	61	1	0	0	0	0	1	0	0	0	17503	1087	38	1	368	1	XYLT1	16	17211541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	983277	17211541	73143212	9675	17660										
XYLT1	64131	broad.mit.edu	37	chr16	17235156	17235156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgccctctgggatccgccGatctcccaggcgccacatgt	10	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:17235156G>A	ENST00000261381.6	-	7	1525	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	481			R -> W (in DBQD2; loss of predominance of Golgi localization in mutant cells; DCN in cell culture supernatant demonstrates glycosylation differences between patient and control cells). {ECO:0000269|PubMed:23982343}.		cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.R481W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGGATCCGCCGATCTCCCAGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											79	82	81					16																	17235156		2197	4300	6497	17142657	SO:0001583	missense	64131			AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1441C>T	16.37:g.17235156G>A	ENSP00000261381:p.Arg481Trp		17142657	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156166	0.78114	.	.	ENSG00000103489	ENST00000261381	T	0.08807	3.05	5.92	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.38188	0.1031	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55418	-0.8144	10	0.87932	D	0	-45.3942	14.2396	0.65948	0.0:0.0:0.5185:0.4815	.	481	Q86Y38	XYLT1_HUMAN	W	481	ENSP00000261381:R481W	ENSP00000261381:R481W	R	-	1	2	XYLT1	17142657	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	2.523000	0.45580	1.451000	0.47736	0.555000	0.69702	CGG		0.597	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17235156	G	A	17235156	3	1	61	1	0	0	0	0	1	0	0	0	17503	1057	37	1	1462	1	XYLT1	16	17235156	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23615	17235156	73119597	9676	17661										
NOMO2	283820	broad.mit.edu	37	chr16	18532101	18532101	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttaccgcgcccagtaagaGaaatcatacgagaaggggcc	12	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18532101G>T	ENST00000381474.3	-	19	2324	c.2259C>A	c.(2257-2259)ttC>ttA	p.F753L	NOMO2_ENST00000543392.1_Missense_Mutation_p.F586L|NOMO2_ENST00000330537.6_Missense_Mutation_p.F753L	NM_001004060.1	NP_001004060.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	753						endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.F753L(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						CCCAGTAAGAGAAATCATACG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											22	22	22					16																	18532101		1543	3265	4808	18439602	SO:0001583	missense	283820			AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164			22652	protein-coding gene	gene with protein product		609158				15257293	Standard	NM_001004060		Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000381474.3:c.2259C>A	16.37:g.18532101G>T	ENSP00000370883:p.Phe753Leu		18439602	Q4G177	Missense_Mutation	SNP	ENST00000381474.3	37	CCDS32394.1	.	.	.	.	.	.	.	.	.	.	.	11.92	1.782391	0.31502	.	.	ENSG00000185164	ENST00000330537;ENST00000381474;ENST00000543392	T;T;T	0.04454	3.65;3.64;3.62	3.37	1.35	0.21983	.	0.000000	0.85682	D	0.000000	T	0.11153	0.0272	M	0.66939	2.045	0.58432	D	0.999996	D;D	0.62365	0.988;0.991	P;P	0.56514	0.755;0.8	T	0.02781	-1.1111	10	0.48119	T	0.1	-27.9097	6.9528	0.24554	0.3487:0.0:0.6513:0.0	.	586;753	Q4G177;Q5JPE7	.;NOMO2_HUMAN	L	753;753;586	ENSP00000331851:F753L;ENSP00000370883:F753L;ENSP00000439970:F586L	ENSP00000331851:F753L	F	-	3	2	NOMO2	18439602	1.000000	0.71417	0.995000	0.50966	0.092000	0.18411	1.873000	0.39558	0.230000	0.21059	0.455000	0.32223	TTC		0.478	NOMO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435858.1	NM_001004060		T	18532101	G	T	18532101	3	4	61	1	0	0	0	0	1	0	0	0	10563	933	33	2	1604	2	NOMO2	16	18532101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1296945	18532101	71822652	9677	17662										
RPS15A	6210	broad.mit.edu	37	chr16	18796086	18796086	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcgggatggaagcagattAttctgccatttttccaggtc	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18796086A>C	ENST00000565420.1	-	4	641	c.273T>G	c.(271-273)aaT>aaG	p.N91K	RPS15A_ENST00000563390.1_Missense_Mutation_p.N91K|RPS15A_ENST00000569083.1_Missense_Mutation_p.N91K|RPS15A_ENST00000576436.1_3'UTR|RPS15A_ENST00000322989.4_Missense_Mutation_p.N91K|RPS15A_ENST00000575669.1_5'UTR			P62244	RS15A_HUMAN	ribosomal protein S15a	91					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|response to virus (GO:0009615)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.N91K(1)		endometrium(1)|large_intestine(1)	2						GAAGCAGATTATTCTGCCATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	16											121	126	124					16																	18796086		2197	4300	6497	18703587	SO:0001583	missense	6210			AB007154	CCDS10571.1	16p12.3	2011-04-05			ENSG00000134419	ENSG00000134419		"S ribosomal proteins"	10389	protein-coding gene	gene with protein product		603674				9582194	Standard	NM_001019		Approved	S15A	uc002dfi.1	P62244	OTTHUMG00000131365	ENST00000565420.1:c.273T>G	16.37:g.18796086A>C	ENSP00000458115:p.Asn91Lys		18703587	P39027|P39031|Q3MHD9|Q8C023|Q9BV24	Missense_Mutation	SNP	ENST00000565420.1	37	CCDS10571.1	.	.	.	.	.	.	.	.	.	.	a	20.4	3.987824	0.74589	.	.	ENSG00000134419	ENST00000322989	.	.	.	4.69	-0.349	0.12609	.	0.000000	0.85682	U	0.000000	T	0.38348	0.1037	L	0.29908	0.895	0.80722	D	1	B	0.02656	0.0	B	0.14023	0.01	T	0.10405	-1.0631	9	0.17832	T	0.49	.	9.6955	0.40154	0.4584:0.0:0.5416:0.0	.	91	P62244	RS15A_HUMAN	K	91	.	ENSP00000318646:N91K	N	-	3	2	RPS15A	18703587	1.000000	0.71417	0.987000	0.45799	0.972000	0.66771	1.648000	0.37271	-0.032000	0.13758	0.460000	0.39030	AAT		0.388	RPS15A-005	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435778.1	NM_001019		C	18796086	A	C	18796086	3	2	61	1	0	0	0	0	1	0	0	0	13663	446	16	4	127	4	RPS15A	16	18796086	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	263985	18796086	71558667	9678	17663										
ARL6IP1	23204	broad.mit.edu	37	chr16	18804691	18804691	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagcaatagtaaggaagtCacttaaaataaaaaaaaacc	7	5	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18804691C>A	ENST00000304414.7	-	6	706	c.495G>T	c.(493-495)gtG>gtT	p.V165V	RPS15A_ENST00000563390.1_5'Flank|ARL6IP1_ENST00000546206.2_Splice_Site_p.V136V|ARL6IP1_ENST00000562819.1_Splice_Site_p.V50V|RP11-1035H13.3_ENST00000567078.2_Intron	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	165					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)		p.V165V(1)		breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						GTAAGGAAGTCACTTAAAATA	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	16											51	49	50					16																	18804691		2197	4300	6497	18712192	SO:0001630	splice_region_variant	23204			BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.494-1G>T	16.37:g.18804691C>A			18712192		Silent	SNP	ENST00000304414.7	37	CCDS10572.1																																																																																				0.318	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161	Silent	A	18804691	C	A	18804691	5	1	61	1	0	0	0	0	0	0	1	0	943	840	29	2	120	2	ARL6IP1	16	18804691	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8605	18804691	71550062	9679	17664										
SMG1	23049	broad.mit.edu	37	chr16	18828749	18828749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttctgcagttcttgttCgtaaactttcaaaatgaatg	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18828749C>T	ENST00000446231.2	-	57	10350	c.9938G>A	c.(9937-9939)cGa>cAa	p.R3313Q	SMG1_ENST00000389467.3_Missense_Mutation_p.R3314Q			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3313					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R3309Q(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AGTTCTTGTTCGTAAACTTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											67	59	61					16																	18828749		1864	4111	5975	18736250	SO:0001583	missense	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9938G>A	16.37:g.18828749C>T	ENSP00000402515:p.Arg3313Gln		18736250	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036621	0.93630	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.02944	4.1;4.1	5.8	5.8	0.92144	.	0.000000	0.51477	D	0.000095	T	0.10337	0.0253	L	0.34521	1.04	0.50313	D	0.999869	D	0.69078	0.997	D	0.70227	0.968	T	0.03608	-1.1020	10	0.66056	D	0.02	.	20.0618	0.97678	0.0:1.0:0.0:0.0	.	3313	Q96Q15	SMG1_HUMAN	Q	3313;3314	ENSP00000402515:R3313Q;ENSP00000374118:R3314Q	ENSP00000374118:R3314Q	R	-	2	0	SMG1	18736250	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.259000	0.78381	2.730000	0.93505	0.650000	0.86243	CGA		0.428	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18828749	C	T	18828749	3	4	61	1	0	0	0	0	1	0	0	0	14832	884	31	1	1075	1	SMG1	16	18828749	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24058	18828749	71526004	9680	17665										
SMG1	23049	broad.mit.edu	37	chr16	18859302	18859302	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattcagaaaccagcaattCttctccttgaatattgccaa	4	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18859302C>A	ENST00000446231.2	-	37	6089	c.5677G>T	c.(5677-5679)Gaa>Taa	p.E1893*	SMG1_ENST00000389467.3_Nonsense_Mutation_p.E1893*			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1893	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1889*(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACCAGCAATTCTTCTCCTTGA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											108	100	103					16																	18859302		1851	4095	5946	18766803	SO:0001587	stop_gained	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5677G>T	16.37:g.18859302C>A	ENSP00000402515:p.Glu1893*		18766803	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Nonsense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	48	14.525903	0.99799	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	.	.	.	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	19.8622	0.96787	0.0:1.0:0.0:0.0	.	.	.	.	X	1893	.	ENSP00000374118:E1893X	E	-	1	0	SMG1	18766803	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.498000	0.66931	2.695000	0.91970	0.491000	0.48974	GAA		0.373	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18859302	C	A	18859302	4	1	61	1	0	0	0	0	0	1	0	0	14832	922	32	2	5416	2	SMG1	16	18859302	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30553	18859302	71495451	9681	17666										
SMG1	23049	broad.mit.edu	37	chr16	18881209	18881209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcccatacaaaataaaaCtaataacatcagagaaatct	3	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:18881209C>T	ENST00000446231.2	-	19	3012	c.2600G>A	c.(2599-2601)aGt>aAt	p.S867N	snoU13_ENST00000459248.1_RNA|SMG1_ENST00000389467.3_Missense_Mutation_p.S867N			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	867	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S863N(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CAAAATAAAACTAATAACATC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	16											18	19	18					16																	18881209		1607	3582	5189	18788710	SO:0001583	missense	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2600G>A	16.37:g.18881209C>T	ENSP00000402515:p.Ser867Asn		18788710	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671354	0.67814	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.64991	-0.13;-0.13	5.67	5.67	0.87782	Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.48677	0.1513	N	0.16903	0.455	0.35451	D	0.79567	P	0.37781	0.608	B	0.35413	0.202	T	0.55952	-0.8059	10	0.29301	T	0.29	.	19.7756	0.96391	0.0:1.0:0.0:0.0	.	867	Q96Q15	SMG1_HUMAN	N	867	ENSP00000402515:S867N;ENSP00000374118:S867N	ENSP00000374118:S867N	S	-	2	0	SMG1	18788710	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.760000	0.68793	2.694000	0.91930	0.555000	0.69702	AGT		0.323	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18881209	C	T	18881209	3	4	61	1	0	0	0	0	1	0	0	0	14832	565	20	3	8565	3	SMG1	16	18881209	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21907	18881209	71473544	9682	17667										
SYT17	51760	broad.mit.edu	37	chr16	19236089	19236089	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaaggggcacaattgatcCtttctacaatgaatccttca	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:19236089C>A	ENST00000355377.2	+	7	1555	c.1157C>A	c.(1156-1158)cCt>cAt	p.P386H	SYT17_ENST00000568115.1_Missense_Mutation_p.P325H|SYT17_ENST00000568433.1_Missense_Mutation_p.P80H|SYT17_ENST00000562711.2_Missense_Mutation_p.P382H|SYT17_ENST00000562034.1_Missense_Mutation_p.P325H	NM_016524.2	NP_057608.2	Q9BSW7	SYT17_HUMAN	synaptotagmin XVII	386	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)	membrane (GO:0016020)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)	p.P386H(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	17						ACAATTGATCCTTTCTACAAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											130	127	128					16																	19236089		2197	4300	6497	19143590	SO:0001583	missense	51760				CCDS10575.1	16p12.3	2013-01-21			ENSG00000103528	ENSG00000103528		"Synaptotagmins"	24119	protein-coding gene	gene with protein product	"B/K protein"					10493829	Standard	NM_016524		Approved		uc002dfw.3	Q9BSW7	OTTHUMG00000131461	ENST00000355377.2:c.1157C>A	16.37:g.19236089C>A	ENSP00000347538:p.Pro386His		19143590	O43330|Q9NZ18	Missense_Mutation	SNP	ENST00000355377.2	37	CCDS10575.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089074	0.94100	.	.	ENSG00000103528	ENST00000355377	D	0.91407	-2.84	5.29	5.29	0.74685	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000008	D	0.97517	0.9187	H	0.98466	4.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99184	1.0868	10	0.87932	D	0	.	18.9333	0.92576	0.0:1.0:0.0:0.0	.	386;325	Q9BSW7;B4DJB2	SYT17_HUMAN;.	H	386	ENSP00000347538:P386H	ENSP00000347538:P386H	P	+	2	0	SYT17	19143590	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.642000	0.74329	2.472000	0.83506	0.561000	0.74099	CCT		0.428	SYT17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254286.2	NM_016524		A	19236089	C	A	19236089	3	1	61	1	0	0	0	0	1	0	0	0	15512	681	24	2	1183	2	SYT17	16	19236089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	354880	19236089	71118664	9683	17668										
TMC5	79838	broad.mit.edu	37	chr16	19475304	19475304	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtttaccgtggccaaaaaGaacaccctccagttcactgg	8	13	1	1	rs373261054		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:19475304G>T	ENST00000396229.2	+	8	2192	c.1443G>T	c.(1441-1443)aaG>aaT	p.K481N	TMC5_ENST00000541464.1_Missense_Mutation_p.K481N|TMC5_ENST00000561503.1_Missense_Mutation_p.K122N|TMC5_ENST00000381414.4_Missense_Mutation_p.K481N|TMC5_ENST00000542583.2_Missense_Mutation_p.K481N|TMC5_ENST00000564959.1_Missense_Mutation_p.K164N|TMC5_ENST00000219821.5_Missense_Mutation_p.K235N	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	481					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K481N(1)|p.K235N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TGGCCAAAAAGAACACCCTCC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	16											97	89	92					16																	19475304		2197	4300	6497	19382805	SO:0001583	missense	79838			AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1443G>T	16.37:g.19475304G>T	ENSP00000379531:p.Lys481Asn		19382805	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	8.077	0.771450	0.16051	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	5.67	3.48	0.39840	.	0.411906	0.28409	N	0.015446	T	0.32406	0.0828	N	0.24115	0.695	0.35872	D	0.828277	B;B;B;B;B;B	0.13145	0.007;0.0;0.007;0.004;0.004;0.007	B;B;B;B;B;B	0.15484	0.013;0.001;0.009;0.004;0.006;0.009	T	0.24368	-1.0162	10	0.20046	T	0.44	-14.3048	6.3579	0.21412	0.1249:0.3609:0.5141:0.0	.	481;164;235;235;481;481	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	N	481;481;481;481;235;164	ENSP00000441227:K481N;ENSP00000370822:K481N;ENSP00000379531:K481N;ENSP00000446274:K481N;ENSP00000219821:K235N	ENSP00000219821:K235N	K	+	3	2	TMC5	19382805	0.998000	0.40836	0.908000	0.35775	0.214000	0.24535	1.505000	0.35736	1.371000	0.46172	0.637000	0.83480	AAG		0.478	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		T	19475304	G	T	19475304	3	4	61	1	0	0	0	0	1	0	0	0	16027	933	33	2	1779	2	TMC5	16	19475304	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239215	19475304	70879449	9684	17669										
CP110	9738	broad.mit.edu	37	chr16	19548162	19548162	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgtgtcatatacttataAataacccaataaatgcctgt	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:19548162A>C	ENST00000381396.5	+	4	1418	c.1171A>C	c.(1171-1173)Aat>Cat	p.N391H	CCP110_ENST00000396208.2_Missense_Mutation_p.N391H|CCP110_ENST00000396212.2_Missense_Mutation_p.N391H	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	391	Interaction with CEP76.				cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)		p.N391H(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						TATACTTATAAATAACCCAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	16											53	54	53					16																	19548162		2195	4299	6494	19455663	SO:0001583	missense	9738			AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1171A>C	16.37:g.19548162A>C	ENSP00000370803:p.Asn391His		19455663	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.907233	0.72868	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.18810	2.19;2.19;2.19	6.07	6.07	0.98685	.	0.122835	0.56097	D	0.000023	T	0.44705	0.1306	L	0.58101	1.795	0.39705	D	0.971247	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	T	0.40289	-0.9571	10	0.72032	D	0.01	-2.9911	16.6406	0.85098	1.0:0.0:0.0:0.0	.	391;391	O43303;O43303-2	CP110_HUMAN;.	H	391	ENSP00000379515:N391H;ENSP00000370803:N391H;ENSP00000379511:N391H	ENSP00000370803:N391H	N	+	1	0	CCP110	19455663	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.778000	0.75043	2.326000	0.78906	0.533000	0.62120	AAT		0.383	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		C	19548162	A	C	19548162	3	2	61	1	0	0	0	0	1	0	0	0	3794	14	1	4	1181	4	CP110	16	19548162	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72858	19548162	70806591	9685	17670										
C16orf62	57020	broad.mit.edu	37	chr16	19628082	19628082	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttacctccccttgtacccGcctgccatggactggatctt	7	16	2	0	rs200120905		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:19628082G>A	ENST00000251143.5	+	14	1188	c.1176G>A	c.(1174-1176)ccG>ccA	p.P392P	C16orf62_ENST00000438132.3_Silent_p.P481P|C16orf62_ENST00000417362.2_Intron|C16orf62_ENST00000448695.1_Silent_p.P242P|C16orf62_ENST00000542263.1_Intron|C16orf62_ENST00000543152.1_Silent_p.P141P			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	392						integral component of membrane (GO:0016021)		p.P392P(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						CCTTGTACCCGCCTGCCATGG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	16											119	94	102					16																	19628082		2197	4300	6497	19535583	SO:0001819	synonymous_variant	57020				CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.1176G>A	16.37:g.19628082G>A			19535583	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																					0.567	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		A	19628082	G	A	19628082	2	1	61	1	0	0	0	0	0	0	0	1	1829	1074	38	1		1	C16orf62	16	19628082	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79920	19628082	70726671	9686	17671										
IQCK	124152	broad.mit.edu	37	chr16	19838450	19838450	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattttctgggccaagcaaGaacaaaaaggtaagttgctg	10	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:19838450G>T	ENST00000320394.6	+	9	1492	c.793G>T	c.(793-795)Gaa>Taa	p.E265*	IQCK_ENST00000562762.1_3'UTR|IQCK_ENST00000564186.1_Nonsense_Mutation_p.E265*|IQCK_ENST00000541926.1_Missense_Mutation_p.K236N|IQCK_ENST00000433597.2_Nonsense_Mutation_p.E177*	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	265								p.E265*(1)		kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						GGCCAAGCAAGAACAAAAAGG	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											89	85	86					16																	19838450		2197	4300	6497	19745951	SO:0001587	stop_gained	124152			AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.793G>T	16.37:g.19838450G>T	ENSP00000324901:p.Glu265*		19745951	B2RDU0|O43327|Q8NFF4	Nonsense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.258790|10.258790	0.99370|0.99370	.|.	.|.	ENSG00000174628|ENSG00000174628	ENST00000320394;ENST00000433597|ENST00000541926	.|.	.|.	.|.	5.73|5.73	4.78|4.78	0.61160|0.61160	.|.	0.109437|.	0.41097|.	D|.	0.000958|.	.|T	.|0.67268	.|0.2875	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999995|0.999995	.|D	.|0.61080	.|0.989	.|P	.|0.55923	.|0.787	.|T	.|0.68644	.|-0.5354	.|6	.|.	.|.	.|.	-16.744|-16.744	12.7109|12.7109	0.57089|0.57089	0.0797:0.0:0.9203:0.0|0.0797:0.0:0.9203:0.0	.|.	.|236	.|B4DXE1	.|.	X|N	265;177|236	.|.	.|.	E|K	+|+	1|3	0|2	IQCK|IQCK	19745951|19745951	1.000000|1.000000	0.71417|0.71417	0.714000|0.714000	0.30535|0.30535	0.893000|0.893000	0.52053|0.52053	4.663000|4.663000	0.61532|0.61532	1.558000|1.558000	0.49541|0.49541	0.655000|0.655000	0.94253|0.94253	GAA|AAG		0.453	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208		T	19838450	G	T	19838450	4	4	61	1	0	0	0	0	0	1	0	0	7834	943	33	2	823	2	IQCK	16	19838450	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210368	19838450	70516303	9687	17672										
GP2	2813	broad.mit.edu	37	chr16	20327320	20327320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctagaacccgggctaggtCgatggccggtacttcactgc	12	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20327320C>T	ENST00000381362.4	-	10	1544	c.1468G>A	c.(1468-1470)Gac>Aac	p.D490N	GP2_ENST00000341642.5_Missense_Mutation_p.D340N|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000302555.5_Missense_Mutation_p.D487N|GP2_ENST00000381360.5_Missense_Mutation_p.D343N	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	490					antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)	p.D487N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						CGGGCTAGGTCGATGGCCGGT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	16											116	108	111					16																	20327320		2203	4300	6503	20234821	SO:0001583	missense	2813			U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1468G>A	16.37:g.20327320C>T	ENSP00000370767:p.Asp490Asn		20234821	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.252332	0.22880	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;T;D	0.90844	-2.73;-2.74;-1.49;-1.5	5.37	1.56	0.23342	.	.	.	.	.	T	0.80819	0.4696	N	0.20574	0.59	0.09310	N	1	B;B;B;B	0.28880	0.02;0.226;0.083;0.012	B;B;B;B	0.23150	0.018;0.044;0.025;0.012	T	0.68036	-0.5515	9	0.36615	T	0.2	-6.7779	8.0272	0.30444	0.0:0.6901:0.0:0.3099	.	340;468;487;490	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	N	487;490;343;340;468	ENSP00000304044:D487N;ENSP00000370767:D490N;ENSP00000370765:D343N;ENSP00000343861:D340N	ENSP00000304044:D487N	D	-	1	0	GP2	20234821	0.002000	0.14202	0.001000	0.08648	0.059000	0.15707	0.113000	0.15499	0.470000	0.27294	0.655000	0.94253	GAC		0.468	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295		T	20327320	C	T	20327320	3	4	61	1	0	0	0	0	1	0	0	0	6602	884	31	1	157	1	GP2	16	20327320	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	488870	20327320	70027433	9688	17673										
PDILT	204474	broad.mit.edu	37	chr16	20371908	20371908	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcatcctcatcctcaatCttagttttgatgtggctttc	5	12	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20371908C>A	ENST00000302451.4	-	11	1736	c.1488G>T	c.(1486-1488)aaG>aaT	p.K496N		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	496					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.K496N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						CATCCTCAATCTTAGTTTTGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	16											240	217	225					16																	20371908		2203	4300	6503	20279409	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1488G>T	16.37:g.20371908C>A	ENSP00000305465:p.Lys496Asn		20279409	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	C	7.971	0.749118	0.15710	.	.	ENSG00000169340	ENST00000302451	T	0.18810	2.19	4.58	-0.751	0.11076	Thioredoxin-like fold (1);	0.459264	0.24463	N	0.038311	T	0.07773	0.0195	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.24368	-1.0162	10	0.29301	T	0.29	.	4.5146	0.11928	0.0:0.4271:0.3088:0.2641	.	496	Q8N807	PDILT_HUMAN	N	496	ENSP00000305465:K496N	ENSP00000305465:K496N	K	-	3	2	PDILT	20279409	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.146000	0.10250	-0.063000	0.13065	-0.756000	0.03474	AAG		0.448	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		A	20371908	C	A	20371908	3	1	61	1	0	0	0	0	1	0	0	0	11705	912	32	2	274	2	PDILT	16	20371908	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44588	20371908	69982845	9689	17674										
PDILT	204474	broad.mit.edu	37	chr16	20380861	20380861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaaatttcttgaggctttCgtaggttatgtcatctgaag	10	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20380861C>T	ENST00000302451.4	-	8	1317	c.1069G>A	c.(1069-1071)Gaa>Aaa	p.E357K		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	357					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.E357K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TTGAGGCTTTCGTAGGTTATG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	16											174	174	174					16																	20380861		2203	4300	6503	20288362	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1069G>A	16.37:g.20380861C>T	ENSP00000305465:p.Glu357Lys		20288362	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	C	6.518	0.463807	0.12402	.	.	ENSG00000169340	ENST00000302451	T	0.16743	2.32	4.89	-6.73	0.01749	Thioredoxin-like fold (1);	0.737812	0.13608	N	0.375360	T	0.07188	0.0182	L	0.28400	0.85	0.09310	N	1	B	0.26876	0.162	B	0.20955	0.032	T	0.21177	-1.0253	10	0.27785	T	0.31	.	2.4392	0.04490	0.1003:0.3331:0.1996:0.367	.	357	Q8N807	PDILT_HUMAN	K	357	ENSP00000305465:E357K	ENSP00000305465:E357K	E	-	1	0	PDILT	20288362	0.028000	0.19301	0.000000	0.03702	0.006000	0.05464	0.081000	0.14823	-1.390000	0.02087	-0.271000	0.10264	GAA		0.448	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20380861	C	T	20380861	3	4	61	1	0	0	0	0	1	0	0	0	11705	893	31	1	705	1	PDILT	16	20380861	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8953	20380861	69973892	9690	17675										
PDILT	204474	broad.mit.edu	37	chr16	20380984	20380984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacgtccatttctgggttCgtctgcatccacaaggatga	10	11	2	1	rs373943417		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20380984C>T	ENST00000302451.4	-	8	1194	c.946G>A	c.(946-948)Gaa>Aaa	p.E316K		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	316					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.E316K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TTTCTGGGTTCGTCTGCATCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	LYS/GLU	0,4406		0,0,2203	120	117	118		946	3.9	0.6	16		118	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDILT	NM_174924.1	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	316/585	20380984	1,13005	2203	4300	6503	20288485	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.946G>A	16.37:g.20380984C>T	ENSP00000305465:p.Glu316Lys		20288485	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354199	0.41700	0.0	1.16E-4	ENSG00000169340	ENST00000302451	T	0.14266	2.52	4.9	3.94	0.45596	Thioredoxin-like fold (1);	0.150565	0.64402	D	0.000019	T	0.24812	0.0602	M	0.72894	2.215	0.19575	N	0.999969	D	0.58970	0.984	P	0.53912	0.737	T	0.13926	-1.0491	10	0.14656	T	0.56	.	12.9358	0.58313	0.0:0.8355:0.1645:0.0	.	316	Q8N807	PDILT_HUMAN	K	316	ENSP00000305465:E316K	ENSP00000305465:E316K	E	-	1	0	PDILT	20288485	1.000000	0.71417	0.554000	0.28268	0.031000	0.12232	3.002000	0.49496	1.258000	0.44101	0.563000	0.77884	GAA		0.473	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20380984	C	T	20380984	3	4	61	1	0	0	0	0	1	0	0	0	11705	893	31	1	828	1	PDILT	16	20380984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	123	20380984	69973769	9691	17676										
PDILT	204474	broad.mit.edu	37	chr16	20384349	20384349	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacctcagtgttgtattcGatcacaaaatctgtaaggtg	9	8	3	1	rs145263436		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20384349G>T	ENST00000302451.4	-	6	1025	c.777C>A	c.(775-777)atC>atA	p.I259I		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	259					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.I259I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TGTTGTATTCGATCACAAAAT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	16											201	190	194					16																	20384349		2203	4300	6503	20291850	SO:0001819	synonymous_variant	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.777C>A	16.37:g.20384349G>T			20291850	Q8IVQ5	Silent	SNP	ENST00000302451.4	37	CCDS10584.1																																																																																				0.443	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20384349	G	T	20384349	2	4	61	1	0	0	0	0	0	0	0	1	11705	1048	37	2		2	PDILT	16	20384349	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3365	20384349	69970404	9692	17677										
ACSM5	54988	broad.mit.edu	37	chr16	20448432	20448432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttacatcacaggggaccGagctcgcatggacaaggatg	12	10	1	0	rs369151501		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20448432G>A	ENST00000331849.4	+	11	1514	c.1367G>A	c.(1366-1368)cGa>cAa	p.R456Q		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	456					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.R456Q(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						ACAGGGGACCGAGCTCGCATG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	16						G	GLN/ARG	0,4406		0,0,2203	174	161	165		1367	3.2	1	16		165	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACSM5	NM_017888.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	456/580	20448432	1,13005	2203	4300	6503	20355933	SO:0001583	missense	54988				CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"Acyl-CoA synthetase family"	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1367G>A	16.37:g.20448432G>A	ENSP00000327916:p.Arg456Gln		20355933	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.516257	0.64634	0.0	1.16E-4	ENSG00000183549	ENST00000331849	T	0.41758	0.99	5.15	3.19	0.36642	AMP-dependent synthetase/ligase (1);	0.274583	0.25509	N	0.030197	T	0.36771	0.0979	L	0.61387	1.9	0.32960	D	0.52096	P	0.48589	0.912	B	0.37508	0.252	T	0.55704	-0.8099	10	0.62326	D	0.03	-4.7894	10.8795	0.46929	0.156:0.0:0.844:0.0	.	456	Q6NUN0	ACSM5_HUMAN	Q	456	ENSP00000327916:R456Q	ENSP00000327916:R456Q	R	+	2	0	ACSM5	20355933	1.000000	0.71417	0.966000	0.40874	0.950000	0.60333	4.238000	0.58688	0.682000	0.31407	0.650000	0.86243	CGA		0.483	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888		A	20448432	G	A	20448432	3	1	61	1	0	0	0	0	1	0	0	0	187	1058	37	1	1405	1	ACSM5	16	20448432	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64083	20448432	69906321	9693	17678										
ACSM1	116285	broad.mit.edu	37	chr16	20682957	20682957	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaccattgggtccaaggtCtttgacttaacacaggtgtg	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20682957C>A	ENST00000307493.4	-	4	715	c.648G>T	c.(646-648)aaG>aaT	p.K216N	ACSM1_ENST00000219151.4_5'UTR|ACSM1_ENST00000520010.1_Missense_Mutation_p.K216N	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	216					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.K216N(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						GGTCCAAGGTCTTTGACTTAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	16											136	115	122					16																	20682957		2201	4300	6501	20590458	SO:0001583	missense	116285			AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.648G>T	16.37:g.20682957C>A	ENSP00000301956:p.Lys216Asn		20590458	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	37	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.447597	0.43429	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.48836	0.8;0.8	5.19	3.08	0.35506	AMP-dependent synthetase/ligase (1);	0.000000	0.52532	D	0.000076	T	0.55593	0.1930	L	0.45422	1.42	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.55036	-0.8203	10	0.51188	T	0.08	.	9.2215	0.37379	0.0:0.8074:0.0:0.1926	.	216	Q08AH1	ACSM1_HUMAN	N	216	ENSP00000301956:K216N;ENSP00000428047:K216N	ENSP00000301956:K216N	K	-	3	2	ACSM1	20590458	0.818000	0.29161	0.908000	0.35775	0.639000	0.38242	0.590000	0.23954	1.378000	0.46305	0.603000	0.83216	AAG		0.483	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		A	20682957	C	A	20682957	3	1	61	1	0	0	0	0	1	0	0	0	182	912	32	2	1125	2	ACSM1	16	20682957	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	234525	20682957	69671796	9694	17679										
ACSM1	116285	broad.mit.edu	37	chr16	20702428	20702428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attctgataaagaccggcagCgcagctgtgaaggggcaggg	16	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20702428C>T	ENST00000307493.4	-	1	150	c.83G>A	c.(82-84)cGc>cAc	p.R28H	ACSM1_ENST00000219151.4_5'UTR|ACSM1_ENST00000520010.1_Missense_Mutation_p.R28H	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	28					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.R28H(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						AGACCGGCAGCGCAGCTGTGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	16											137	146	143					16																	20702428		2201	4300	6501	20609929	SO:0001583	missense	116285			AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.83G>A	16.37:g.20702428C>T	ENSP00000301956:p.Arg28His		20609929	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	37	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	c	7.668	0.686318	0.14973	.	.	ENSG00000166743	ENST00000307493;ENST00000520010;ENST00000523065	T;T;T	0.44083	0.93;0.93;1.5	4.69	-9.38	0.00623	.	1.924530	0.02462	N	0.086648	T	0.14657	0.0354	N	0.02011	-0.69	0.21984	N	0.999439	B	0.09022	0.002	B	0.04013	0.001	T	0.16571	-1.0398	10	0.33940	T	0.23	.	6.3504	0.21373	0.3663:0.1401:0.0:0.4936	.	28	Q08AH1	ACSM1_HUMAN	H	28	ENSP00000301956:R28H;ENSP00000428047:R28H;ENSP00000428830:R28H	ENSP00000301956:R28H	R	-	2	0	ACSM1	20609929	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.891000	0.01611	-1.660000	0.01486	0.502000	0.49764	CGC		0.502	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		T	20702428	C	T	20702428	3	4	61	1	0	0	0	0	1	0	0	0	182	768	27	1	1702	1	ACSM1	16	20702428	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19471	20702428	69652325	9695	17680										
ACSM3	6296	broad.mit.edu	37	chr16	20792297	20792297	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactctttgttttcccaggTtctggctagatttgacaccc	7	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20792297T>C	ENST00000289416.5	+	6	1259	c.784T>C	c.(784-786)Ttc>Ctc	p.F262L	ACSM3_ENST00000440284.2_Splice_Site_p.F262L|ERI2_ENST00000300005.3_Intron|ACSM3_ENST00000450120.2_Splice_Site_p.F254L	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	262					cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)	p.F262L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						TTTTCCCAGGTTCTGGCTAGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	16											147	146	146					16																	20792297		2201	4300	6501	20699798	SO:0001630	splice_region_variant	6296			D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.783-1T>C	16.37:g.20792297T>C			20699798	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Missense_Mutation	SNP	ENST00000289416.5	37	CCDS10589.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845898	0.71603	.	.	ENSG00000005187	ENST00000289416;ENST00000440284;ENST00000450120	T;T;T	0.41065	1.01;1.01;1.01	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.131156	0.52532	D	0.000068	T	0.30198	0.0757	N	0.13003	0.285	0.80722	D	1	B;B;B	0.11235	0.001;0.001;0.004	B;B;B	0.11329	0.004;0.004;0.006	T	0.05257	-1.0896	10	0.45353	T	0.12	-13.7894	16.2108	0.82158	0.0:0.0:0.0:1.0	.	254;262;262	E7ETR5;Q53FZ2;Q53FZ2-2	.;ACSM3_HUMAN;.	L	262;262;254	ENSP00000289416:F262L;ENSP00000394565:F262L;ENSP00000395297:F254L	ENSP00000289416:F262L	F	+	1	0	ACSM3	20699798	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.454000	0.73493	2.232000	0.73038	0.533000	0.62120	TTC		0.433	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	Missense_Mutation	C	20792297	T	C	20792297	5	2	61	1	0	0	0	0	0	0	1	0	185	1739	60	4	802	4	ACSM3	16	20792297	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	89869	20792297	69562456	9696	17681										
DNAH3	55567	broad.mit.edu	37	chr16	20975762	20975762	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtactcaactccttgctgTttgaatgttgccttgagcaa	8	9	1	2	rs373572000		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20975762T>C	ENST00000261383.3	-	53	9443	c.9444A>G	c.(9442-9444)aaA>aaG	p.K3148K	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3148	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.K3148K(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCCTTGCTGTTTGAATGTTG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	16						T		0,4402		0,0,2201	179	173	175		9444	-0.5	1	16		175	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH3	NM_017539.1		0,1,6500	CC,CT,TT		0.0116,0.0,0.0077		3148/4117	20975762	1,13001	2201	4300	6501	20883263	SO:0001819	synonymous_variant	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.9444A>G	16.37:g.20975762T>C			20883263	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																				0.433	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		C	20975762	T	C	20975762	2	2	61	1	0	0	0	0	0	0	0	1	4614	1722	60	4		4	DNAH3	16	20975762	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	183465	20975762	69378991	9697	17682										
DNAH3	55567	broad.mit.edu	37	chr16	20999096	20999096	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaagacgtaatgtgacttCgagggagttggcaagaagtt	13	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:20999096C>T	ENST00000261383.3	-	46	6800	c.6801G>A	c.(6799-6801)tcG>tcA	p.S2267S	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2267	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.S2267S(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AATGTGACTTCGAGGGAGTTG	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	16											127	106	113					16																	20999096		2201	4300	6501	20906597	SO:0001819	synonymous_variant	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.6801G>A	16.37:g.20999096C>T			20906597	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																				0.493	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	20999096	C	T	20999096	2	4	61	1	0	0	0	0	0	0	0	1	4614	871	31	1		1	DNAH3	16	20999096	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23334	20999096	69355657	9698	17683										
DNAH3	55567	broad.mit.edu	37	chr16	21031063	21031063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttctttctgctgtctgCgttgatggtgccagccacgg	11	10	3	1	rs142809716	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21031063C>T	ENST00000261383.3	-	41	5904	c.5905G>A	c.(5905-5907)Gca>Aca	p.A1969T	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1969					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.A1969T(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTGCTGTCTGCGTTGATGGTG	0.468													C|||	4	0.000798722	0	0	5008	,	,		19204	0.004		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	16											151	135	140					16																	21031063		2201	4300	6501	20938564	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.5905G>A	16.37:g.21031063C>T	ENSP00000261383:p.Ala1969Thr		20938564	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	5.774	0.327208	0.10900	.	.	ENSG00000158486	ENST00000261383	T	0.25749	1.78	5.73	-2.03	0.07365	.	0.930262	0.09054	N	0.855342	T	0.09598	0.0236	N	0.13198	0.31	0.09310	N	1	B	0.30511	0.282	B	0.12156	0.007	T	0.32745	-0.9895	10	0.12103	T	0.63	.	4.3564	0.11181	0.419:0.3017:0.0:0.2793	.	1969	Q8TD57	DYH3_HUMAN	T	1969	ENSP00000261383:A1969T	ENSP00000261383:A1969T	A	-	1	0	DNAH3	20938564	0.000000	0.05858	0.000000	0.03702	0.698000	0.40448	0.852000	0.27764	-0.342000	0.08363	-0.318000	0.08688	GCA		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21031063	C	T	21031063	3	4	61	1	0	0	0	0	1	0	0	0	4614	768	27	1	6532	1	DNAH3	16	21031063	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31967	21031063	69323690	9699	17684										
DNAH3	55567	broad.mit.edu	37	chr16	21080894	21080894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccaaattgtcttgtatgcGaattagcttttcttcccatt	5	9	2	0	rs541368919	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21080894G>A	ENST00000261383.3	-	23	3222	c.3223C>T	c.(3223-3225)Cgc>Tgc	p.R1075C	DNAH3_ENST00000415178.1_Missense_Mutation_p.R1075C	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1075	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R1075C(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TCTTGTATGCGAATTAGCTTT	0.458													G|||	2	0.000399361	0	0	5008	,	,		19096	0		0	False		,,,				2504	0.002															2	Substitution - Missense(2)	large_intestine(2)	16											168	126	140					16																	21080894		2201	4300	6501	20988395	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3223C>T	16.37:g.21080894G>A	ENSP00000261383:p.Arg1075Cys		20988395	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521152	0.27211	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.62232	0.04;0.04	5.4	4.38	0.52667	Dynein heavy chain, domain-2 (1);	0.726956	0.12981	N	0.423277	T	0.67571	0.2907	M	0.61703	1.905	0.09310	N	0.999999	D	0.71674	0.998	P	0.56916	0.809	T	0.59920	-0.7363	10	0.49607	T	0.09	.	5.2981	0.15764	0.0831:0.1449:0.6224:0.1496	.	1075	Q8TD57	DYH3_HUMAN	C	1075	ENSP00000261383:R1075C;ENSP00000394245:R1075C	ENSP00000261383:R1075C	R	-	1	0	DNAH3	20988395	0.019000	0.18553	0.931000	0.37212	0.665000	0.39181	1.662000	0.37418	2.696000	0.92011	0.655000	0.94253	CGC		0.458	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21080894	G	A	21080894	3	1	61	1	0	0	0	0	1	0	0	0	4614	1058	37	1	9286	1	DNAH3	16	21080894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49831	21080894	69273859	9700	17685										
DNAH3	55567	broad.mit.edu	37	chr16	21086837	21086837	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattctatccaagtttttCtccagagagtattccttgct	5	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21086837C>A	ENST00000261383.3	-	21	3014	c.3015G>T	c.(3013-3015)gaG>gaT	p.E1005D	DNAH3_ENST00000415178.1_Missense_Mutation_p.E1005D	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1005	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.E1005D(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCAAGTTTTTCTCCAGAGAGT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	16											114	101	106					16																	21086837		2201	4300	6501	20994338	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3015G>T	16.37:g.21086837C>A	ENSP00000261383:p.Glu1005Asp		20994338	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	33	5.275851	0.95459	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.67865	-0.29;-0.29	5.93	5.93	0.95920	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.87912	0.6297	H	0.94183	3.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90201	0.4257	10	0.87932	D	0	.	20.3324	0.98724	0.0:1.0:0.0:0.0	.	1005	Q8TD57	DYH3_HUMAN	D	1005	ENSP00000261383:E1005D;ENSP00000394245:E1005D	ENSP00000261383:E1005D	E	-	3	2	DNAH3	20994338	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.838000	0.55828	2.799000	0.96334	0.650000	0.86243	GAG		0.478	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21086837	C	A	21086837	3	1	61	1	0	0	0	0	1	0	0	0	4614	912	32	2	9502	2	DNAH3	16	21086837	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5943	21086837	69267916	9701	17686										
DNAH3	55567	broad.mit.edu	37	chr16	21128594	21128594	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatcagaaacaagtttttCttctgcgttaacagttccaa	5	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21128594C>A	ENST00000261383.3	-	12	1743	c.1744G>T	c.(1744-1746)Gaa>Taa	p.E582*	DNAH3_ENST00000415178.1_Nonsense_Mutation_p.E582*	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	582	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.E582*(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ACAAGTTTTTCTTCTGCGTTA	0.368																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											74	71	72					16																	21128594		2200	4299	6499	21036095	SO:0001587	stop_gained	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1744G>T	16.37:g.21128594C>A	ENSP00000261383:p.Glu582*		21036095	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Nonsense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.820759	0.90873	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	17.9245	0.88979	0.0:1.0:0.0:0.0	.	.	.	.	X	582;582;522	.	ENSP00000261383:E582X	E	-	1	0	DNAH3	21036095	1.000000	0.71417	0.992000	0.48379	0.138000	0.21146	5.322000	0.65852	2.512000	0.84698	0.655000	0.94253	GAA		0.368	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21128594	C	A	21128594	4	1	61	1	0	0	0	0	0	1	0	0	4614	922	32	2	10809	2	DNAH3	16	21128594	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41757	21128594	69226159	9702	17687										
ZP2	7783	broad.mit.edu	37	chr16	21210907	21210907	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctcgcctgtgcctagaGgacacagggcaggtcacaga	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21210907G>T	ENST00000574002.1	-	17	2393	c.1911C>A	c.(1909-1911)tcC>tcA	p.S637S	ZP2_ENST00000219593.4_Silent_p.S637S|ZP2_ENST00000574091.1_Silent_p.S628S|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	637	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)	p.S637S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TGTGCCTAGAGGACACAGGGC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	16											105	103	103					16																	21210907		2200	4300	6500	21118408	SO:0001819	synonymous_variant	7783			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1911C>A	16.37:g.21210907G>T			21118408	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Silent	SNP	ENST00000574002.1	37	CCDS10596.1																																																																																				0.443	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			T	21210907	G	T	21210907	2	4	61	1	0	0	0	0	0	0	0	1	18255	987	35	2		2	ZP2	16	21210907	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82313	21210907	69143846	9703	17688										
OTOA	146183	broad.mit.edu	37	chr16	21716511	21716511	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggggctgctggtttgtttCtacaatgacctggaattgct	12	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:21716511C>A	ENST00000286149.4	+	11	1045	c.1044C>A	c.(1042-1044)ttC>ttA	p.F348L	OTOA_ENST00000388956.4_Missense_Mutation_p.F255L|OTOA_ENST00000388957.3_Missense_Mutation_p.F10L|OTOA_ENST00000569064.1_3'UTR|OTOA_ENST00000388958.3_Missense_Mutation_p.F334L			Q7RTW8	OTOAN_HUMAN	otoancorin	348					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)		p.F334L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		TGGTTTGTTTCTACAATGACC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	16											102	96	98					16																	21716511		2199	4300	6499	21624012	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1044C>A	16.37:g.21716511C>A	ENSP00000286149:p.Phe348Leu		21624012	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	C	22.5	4.293481	0.80914	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957	T;T;T;T	0.77750	3.61;-1.12;3.61;-1.12	5.3	4.35	0.52113	.	0.057100	0.64402	D	0.000001	D	0.83848	0.5343	M	0.66939	2.045	0.45239	D	0.998243	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.995;0.998;0.995	D	0.83441	0.0043	10	0.52906	T	0.07	-24.9819	7.1459	0.25583	0.0:0.8155:0.0:0.1845	.	255;10;334	B3KWU3;Q7RTW8-2;E9PF51	.;.;.	L	334;348;255;10	ENSP00000373610:F334L;ENSP00000286149:F348L;ENSP00000373608:F255L;ENSP00000373609:F10L	ENSP00000286149:F348L	F	+	3	2	OTOA	21624012	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	2.359000	0.44142	2.480000	0.83734	0.561000	0.74099	TTC		0.522	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			A	21716511	C	A	21716511	3	1	61	1	0	0	0	0	1	0	0	0	11333	912	32	2	1090	2	OTOA	16	21716511	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	505604	21716511	68638242	9704	17689										
VWA3A	146177	broad.mit.edu	37	chr16	22152970	22152970	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaagtcaagggaagcagaGacatctcttttactgttcta	8	9	3	1	rs377058854		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:22152970G>T	ENST00000389398.5	+	24	2547	c.2451G>T	c.(2449-2451)gaG>gaT	p.E817D	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	817						extracellular region (GO:0005576)		p.E817D(1)|p.E13D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GGGAAGCAGAGACATCTCTTT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	16											81	88	86					16																	22152970		2009	4176	6185	22060471	SO:0001583	missense	146177			AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2451G>T	16.37:g.22152970G>T	ENSP00000374049:p.Glu817Asp		22060471	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.128583	0.37533	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.12569	2.67	5.32	2.08	0.27032	.	0.743246	0.12943	N	0.426431	T	0.12944	0.0314	L	0.56769	1.78	0.09310	N	0.999994	B	0.06786	0.001	B	0.04013	0.001	T	0.28618	-1.0038	10	0.33141	T	0.24	.	5.651	0.17616	0.1829:0.2182:0.599:0.0	.	817	A6NCI4	VWA3A_HUMAN	D	817;440	ENSP00000374049:E817D	ENSP00000299840:E440D	E	+	3	2	VWA3A	22060471	0.978000	0.34361	0.001000	0.08648	0.275000	0.26752	1.885000	0.39678	0.237000	0.21200	0.655000	0.94253	GAG		0.532	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			T	22152970	G	T	22152970	3	4	61	1	0	0	0	0	1	0	0	0	17280	933	33	2	2545	2	VWA3A	16	22152970	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436459	22152970	68201783	9705	17690										
EEF2K	29904	broad.mit.edu	37	chr16	22277769	22277769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccacctgccgagggcttCggccgtggccctggaagtgc	14	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:22277769C>T	ENST00000263026.5	+	14	1973	c.1499C>T	c.(1498-1500)tCg>tTg	p.S500L		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	500					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)	p.S500L(1)		breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CCGAGGGCTTCGGCCGTGGCC	0.572																																					NSCLC(195;1411 2157 20319 27471 51856)											1	Substitution - Missense(1)	large_intestine(1)	16											122	130	127					16																	22277769		2197	4300	6497	22185270	SO:0001583	missense	29904			U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.1499C>T	16.37:g.22277769C>T	ENSP00000263026:p.Ser500Leu		22185270	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	35	5.431753	0.96150	.	.	ENSG00000103319	ENST00000263026	T	0.11277	2.79	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.25901	0.0631	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.69479	0.964	T	0.00231	-1.1896	10	0.87932	D	0	-11.1176	20.5568	0.99304	0.0:1.0:0.0:0.0	.	500	O00418	EF2K_HUMAN	L	500	ENSP00000263026:S500L	ENSP00000263026:S500L	S	+	2	0	EEF2K	22185270	1.000000	0.71417	0.949000	0.38748	0.990000	0.78478	6.715000	0.74697	2.861000	0.98227	0.655000	0.94253	TCG		0.572	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22277769	C	T	22277769	3	4	61	1	0	0	0	0	1	0	0	0	4941	893	31	1	1549	1	EEF2K	16	22277769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124799	22277769	68076984	9706	17691										
CDR2	1039	broad.mit.edu	37	chr16	22358682	22358682	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcctcgtggcccttcacGatgtcactccctgccaagct	8	17	3	0	rs201108991	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:22358682G>A	ENST00000268383.2	-	5	1276	c.969C>T	c.(967-969)atC>atT	p.I323I		NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	323						cytoplasm (GO:0005737)		p.I323I(1)		endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GGCCCTTCACGATGTCACTCC	0.577													G|||	9	0.00179712	0	0	5008	,	,		21096	0.0069		0.001	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16											74	56	62					16																	22358682		2197	4300	6497	22266183	SO:0001819	synonymous_variant	1039			M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.969C>T	16.37:g.22358682G>A			22266183	A8K8A8|Q13977	Silent	SNP	ENST00000268383.2	37	CCDS32404.1																																																																																				0.577	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			A	22358682	G	A	22358682	2	1	61	1	0	0	0	0	0	0	0	1	3178	1048	37	1		1	CDR2	16	22358682	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80913	22358682	67996071	9707	17692										
CDR2	1039	broad.mit.edu	37	chr16	22376229	22376229	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaagtgaattacctcaatTtcctgtaactgctcctgatt	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:22376229T>G	ENST00000268383.2	-	2	493	c.186A>C	c.(184-186)gaA>gaC	p.E62D	RP11-21M24.3_ENST00000566764.1_RNA|CDR2_ENST00000569045.1_5'Flank	NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	62						cytoplasm (GO:0005737)		p.E62D(1)		endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		TTACCTCAATTTCCTGTAACT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	16											165	130	142					16																	22376229		2197	4300	6497	22283730	SO:0001583	missense	1039			M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.186A>C	16.37:g.22376229T>G	ENSP00000268383:p.Glu62Asp		22283730	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	37	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.458510	0.84317	.	.	ENSG00000140743	ENST00000268383	T	0.30182	1.54	5.78	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.55465	0.1922	M	0.83774	2.66	0.51482	D	0.999926	D	0.89917	1.0	D	0.83275	0.996	T	0.59043	-0.7528	10	0.52906	T	0.07	-14.7143	10.315	0.43732	0.0:0.1308:0.0:0.8692	.	62	Q01850	CDR2_HUMAN	D	62	ENSP00000268383:E62D	ENSP00000268383:E62D	E	-	3	2	CDR2	22283730	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	0.909000	0.28558	2.212000	0.71576	0.260000	0.18958	GAA		0.423	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			G	22376229	T	G	22376229	3	3	61	1	0	0	0	0	1	0	0	0	3178	1838	64	4	1194	4	CDR2	16	22376229	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	17547	22376229	67978524	9708	17693										
HS3ST2	9956	broad.mit.edu	37	chr16	22926878	22926878	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggcaggacttcaggtggGaataagcccacgaaaggaaa	14	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:22926878G>T	ENST00000261374.3	+	2	1533	c.1099G>T	c.(1099-1101)Gaa>Taa	p.E367*		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	367					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)	p.E367*(1)		breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		CTTCAGGTGGGAATAAGCCCA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											83	94	90					16																	22926878		2193	4298	6491	22834379	SO:0001587	stop_gained	9956			AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.1099G>T	16.37:g.22926878G>T	ENSP00000261374:p.Glu367*		22834379	Q52LZ1	Nonsense_Mutation	SNP	ENST00000261374.3	37	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	39	7.319073	0.98210	.	.	ENSG00000122254	ENST00000261374	.	.	.	5.2	5.2	0.72013	.	0.052749	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.7604	0.88463	0.0:0.0:1.0:0.0	.	.	.	.	X	367	.	ENSP00000261374:E367X	E	+	1	0	HS3ST2	22834379	1.000000	0.71417	0.995000	0.50966	0.598000	0.36846	9.869000	0.99810	2.423000	0.82170	0.561000	0.74099	GAA		0.468	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		T	22926878	G	T	22926878	4	4	61	1	0	0	0	0	0	1	0	0	7385	1175	41	2	1105	2	HS3ST2	16	22926878	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	550649	22926878	67427875	9709	17694										
USP31	57478	broad.mit.edu	37	chr16	23079661	23079661	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagacttaacagagctcccAccagcctttttagagagcaa	7	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23079661A>C	ENST00000219689.7	-	16	3764	c.3765T>G	c.(3763-3765)ggT>ggG	p.G1255G	USP31_ENST00000567975.1_Silent_p.G548G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.G1255G(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CAGAGCTCCCACCAGCCTTTT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	16											155	162	160					16																	23079661		2197	4300	6497	22987162	SO:0001819	synonymous_variant	57478			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.3765T>G	16.37:g.23079661A>C			22987162	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	37	CCDS10607.1																																																																																				0.552	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		C	23079661	A	C	23079661	2	2	61	1	0	0	0	0	0	0	0	1	17102	146	6	4		4	USP31	16	23079661	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	152783	23079661	67275092	9710	17695										
USP31	57478	broad.mit.edu	37	chr16	23085117	23085117	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggatgtatgctgtctgcGtgcagacctcatcttctgac	11	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23085117G>A	ENST00000219689.7	-	14	2260	c.2261C>T	c.(2260-2262)aCg>aTg	p.T754M	USP31_ENST00000567975.1_5'Flank	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	410	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.T754M(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TGCTGTCTGCGTGCAGACCTC	0.567																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	16											95	80	85					16																	23085117		2197	4300	6497	22992618	SO:0001583	missense	57478			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2261C>T	16.37:g.23085117G>A	ENSP00000219689:p.Thr754Met		22992618	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520350	0.85495	.	.	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.32515	1.45	5.91	4.9	0.64082	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.287517	0.32204	N	0.006428	T	0.48077	0.1480	M	0.69248	2.105	0.80722	D	1	D;D	0.69078	0.997;0.996	P;P	0.58620	0.754;0.842	T	0.48198	-0.9056	10	0.87932	D	0	-13.1122	13.5546	0.61751	0.0:0.0:0.7889:0.2111	.	57;754	Q70CQ4-2;Q70CQ4	.;UBP31_HUMAN	M	754;57	ENSP00000219689:T754M	ENSP00000219689:T754M	T	-	2	0	USP31	22992618	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.329000	0.65892	2.793000	0.96121	0.655000	0.94253	ACG		0.567	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		A	23085117	G	A	23085117	3	1	61	1	0	0	0	0	1	0	0	0	17102	1145	40	1	1809	1	USP31	16	23085117	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5456	23085117	67269636	9711	17696										
SCNN1G	6340	broad.mit.edu	37	chr16	23226541	23226541	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcccgccgccagtggcaGaaagccaaggagtggtgggc	16	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23226541G>T	ENST00000300061.2	+	13	1844	c.1701G>T	c.(1699-1701)caG>caT	p.Q567H	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	567					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)	p.Q567H(1)		NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GCCAGTGGCAGAAAGCCAAGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											90	86	88					16																	23226541		2197	4300	6497	23134042	SO:0001583	missense	6340			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1701G>T	16.37:g.23226541G>T	ENSP00000300061:p.Gln567His		23134042	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	37	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	G	7.869	0.727631	0.15439	.	.	ENSG00000166828	ENST00000300061	T	0.71934	-0.61	5.22	2.09	0.27110	.	0.360247	0.27720	N	0.018121	T	0.49064	0.1535	N	0.08118	0	0.31361	N	0.681329	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	10	0.15066	T	0.55	-13.64	16.3143	0.82909	0.0:0.5454:0.4546:0.0	.	567	P51170	SCNNG_HUMAN	H	567	ENSP00000300061:Q567H	ENSP00000300061:Q567H	Q	+	3	2	SCNN1G	23134042	0.998000	0.40836	1.000000	0.80357	0.931000	0.56810	0.272000	0.18644	0.172000	0.19760	0.561000	0.74099	CAG		0.572	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		T	23226541	G	T	23226541	3	4	61	1	0	0	0	0	1	0	0	0	13967	933	33	2	1747	2	SCNN1G	16	23226541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141424	23226541	67128212	9712	17697										
SCNN1B	6338	broad.mit.edu	37	chr16	23364139	23364139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtattccaaaatcaagcAtttgctgaaggacctggatg	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23364139A>G	ENST00000343070.2	+	3	505	c.329A>G	c.(328-330)cAt>cGt	p.H110R	SCNN1B_ENST00000568085.1_Missense_Mutation_p.H110R|SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000568923.1_Missense_Mutation_p.H110R|SCNN1B_ENST00000307331.5_Missense_Mutation_p.H155R	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	110					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)	p.H110R(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	AAAATCAAGCATTTGCTGAAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											91	86	88					16																	23364139		2197	4300	6497	23271640	SO:0001583	missense	6338			X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.329A>G	16.37:g.23364139A>G	ENSP00000345751:p.His110Arg		23271640	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729789	0.48833	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.61274	0.12;0.12	4.86	1.03	0.20045	.	1.090280	0.07247	N	0.865273	T	0.65312	0.2679	L	0.56769	1.78	0.25039	N	0.991216	P	0.50819	0.939	P	0.52386	0.697	T	0.57717	-0.7763	10	0.23891	T	0.37	-13.0357	14.6534	0.68814	0.3097:0.6903:0.0:0.0	.	110	P51168	SCNNB_HUMAN	R	110;155	ENSP00000345751:H110R;ENSP00000302874:H155R	ENSP00000302874:H155R	H	+	2	0	SCNN1B	23271640	0.037000	0.19845	0.190000	0.23270	0.978000	0.69477	0.237000	0.17985	-0.119000	0.11830	0.379000	0.24179	CAT		0.507	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			G	23364139	A	G	23364139	3	3	61	1	0	0	0	0	1	0	0	0	13965	217	8	4	335	4	SCNN1B	16	23364139	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	137598	23364139	66990614	9713	17698										
COG7	91949	broad.mit.edu	37	chr16	23415069	23415069	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgcgcaggaacacggaatcGaaagccagctggtgggcctg	15	10	0	0	rs370272896		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23415069G>A	ENST00000307149.5	-	13	1934	c.1749C>T	c.(1747-1749)ttC>ttT	p.F583F		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	583					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.F583F(1)		breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		ACACGGAATCGAAAGCCAGCT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G		1,4393	2.1+/-5.4	0,1,2196	91	81	84		1749	-2.4	0.8	16		84	0,8600		0,0,4300	no	coding-synonymous	COG7	NM_153603.3		0,1,6496	AA,AG,GG		0.0,0.0228,0.0077		583/771	23415069	1,12993	2197	4300	6497	23322570	SO:0001819	synonymous_variant	91949			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1749C>T	16.37:g.23415069G>A			23322570	Q6UWU7	Silent	SNP	ENST00000307149.5	37	CCDS10610.1																																																																																				0.522	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			A	23415069	G	A	23415069	2	1	61	1	0	0	0	0	0	0	0	1	3669	1049	37	1		1	COG7	16	23415069	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50930	23415069	66939684	9714	17699										
COG7	91949	broad.mit.edu	37	chr16	23417447	23417447	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatattcagcagggttatCtttctggaggtaattatatt	10	5	3	0	rs34221967		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23417447C>A	ENST00000307149.5	-	12	1797	c.1612G>T	c.(1612-1614)Gat>Tat	p.D538Y		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	538					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.D538Y(1)		breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GCAGGGTTATCTTTCTGGAGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	16											126	131	129					16																	23417447		2197	4300	6497	23324948	SO:0001583	missense	91949			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1612G>T	16.37:g.23417447C>A	ENSP00000305442:p.Asp538Tyr		23324948	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.503740	0.85176	.	.	ENSG00000168434	ENST00000307149	T	0.44083	0.93	5.7	5.7	0.88788	.	0.318953	0.38720	N	0.001586	T	0.40815	0.1132	N	0.08118	0	0.53005	D	0.999961	P	0.38110	0.618	P	0.49999	0.628	T	0.49031	-0.8981	10	0.62326	D	0.03	-5.0329	18.8293	0.92132	0.0:1.0:0.0:0.0	.	538	P83436	COG7_HUMAN	Y	538	ENSP00000305442:D538Y	ENSP00000305442:D538Y	D	-	1	0	COG7	23324948	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	4.761000	0.62243	2.683000	0.91414	0.655000	0.94253	GAT		0.433	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			A	23417447	C	A	23417447	3	1	61	1	0	0	0	0	1	0	0	0	3669	913	32	2	724	2	COG7	16	23417447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2378	23417447	66937306	9715	17700										
PALB2	79728	broad.mit.edu	37	chr16	23641217	23641217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggggtgtgcagcaagttCgtccagcaacttctgtagat	13	8	1	1	rs587778586		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23641217C>T	ENST00000261584.4	-	5	2410	c.2258G>A	c.(2257-2259)cGa>cAa	p.R753Q		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	753					DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R753Q(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		GCAGCAAGTTCGTCCAGCAAC	0.478			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	1	Substitution - Missense(1)	large_intestine(1)	16											133	117	123					16																	23641217		2197	4300	6497	23548718	SO:0001583	missense	79728				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.2258G>A	16.37:g.23641217C>T	ENSP00000261584:p.Arg753Gln		23548718	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450621	0.26074	.	.	ENSG00000083093	ENST00000261584	T	0.13538	2.58	5.96	-10.8	0.00216	.	1.369690	0.04520	N	0.384426	T	0.03827	0.0108	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31024	-0.9958	10	0.22109	T	0.4	10.777	4.6724	0.12696	0.0793:0.3386:0.3719:0.2103	.	753	Q86YC2	PALB2_HUMAN	Q	753	ENSP00000261584:R753Q	ENSP00000261584:R753Q	R	-	2	0	PALB2	23548718	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.683000	0.01934	-2.391000	0.00586	-1.851000	0.00568	CGA		0.478	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		T	23641217	C	T	23641217	3	4	61	1	0	0	0	0	1	0	0	0	11437	884	31	1	1338	1	PALB2	16	23641217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	223770	23641217	66713536	9716	17701										
PALB2	79728	broad.mit.edu	37	chr16	23647326	23647326	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatttttgctactgatttCttcctgttcctttagtcttt	6	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23647326C>A	ENST00000261584.4	-	4	693	c.541G>T	c.(541-543)Gaa>Taa	p.E181*		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	181	DNA-binding (with the preference D loop > dsDNA > ssDNA).|Interaction with BRCA1.|Interaction with RAD51.				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E181*(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		CTACTGATTTCTTCCTGTTCC	0.393			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	1	Substitution - Nonsense(1)	large_intestine(1)	16											170	169	169					16																	23647326		2197	4300	6497	23554827	SO:0001587	stop_gained	79728				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.541G>T	16.37:g.23647326C>A	ENSP00000261584:p.Glu181*		23554827	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Nonsense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.598508	0.28445	.	.	ENSG00000083093	ENST00000261584	.	.	.	6.08	-4.98	0.03019	.	1.767130	0.02504	N	0.090832	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	0.0245	0.4083	0.00437	0.2763:0.1912:0.1468:0.3856	.	.	.	.	X	181	.	ENSP00000261584:E181X	E	-	1	0	PALB2	23554827	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.883000	0.04170	-0.580000	0.05944	0.591000	0.81541	GAA		0.393	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		A	23647326	C	A	23647326	4	1	61	1	0	0	0	0	0	1	0	0	11437	922	32	2	3059	2	PALB2	16	23647326	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6109	23647326	66707427	9717	17702										
PALB2	79728	broad.mit.edu	37	chr16	23649442	23649442	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcaagaatgctaatttCtcctttaactggaagaagaa	6	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23649442C>A	ENST00000261584.4	-	2	209	c.57G>T	c.(55-57)gaG>gaT	p.E19D		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	19	DNA-binding (with the preference D loop > dsDNA > ssDNA).|Interaction with BRCA1.|Interaction with RAD51.|Required for its oligomerization and is important for its focal concentration at DNA damage sites.				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E19D(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		ATGCTAATTTCTCCTTTAACT	0.433			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	1	Substitution - Missense(1)	large_intestine(1)	16											126	118	121					16																	23649442		2197	4300	6497	23556943	SO:0001583	missense	79728				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.57G>T	16.37:g.23649442C>A	ENSP00000261584:p.Glu19Asp		23556943	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	C	33	5.247518	0.95305	.	.	ENSG00000083093	ENST00000261584	T	0.19806	2.12	5.5	2.02	0.26589	.	0.086631	0.49916	D	0.000123	T	0.36826	0.0981	M	0.72118	2.19	0.29525	N	0.853171	D	0.64830	0.994	P	0.61800	0.894	T	0.27571	-1.0070	10	0.87932	D	0	-16.086	7.8399	0.29393	0.0:0.2589:0.0:0.7411	.	19	Q86YC2	PALB2_HUMAN	D	19	ENSP00000261584:E19D	ENSP00000261584:E19D	E	-	3	2	PALB2	23556943	0.997000	0.39634	0.999000	0.59377	0.979000	0.70002	0.282000	0.18829	0.072000	0.16694	-0.302000	0.09304	GAG		0.433	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		A	23649442	C	A	23649442	3	1	61	1	0	0	0	0	1	0	0	0	11437	912	32	2	3551	2	PALB2	16	23649442	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2116	23649442	66705311	9718	17703										
PLK1	5347	broad.mit.edu	37	chr16	23691502	23691502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggctgccagtacctgcaccGaaaccgagttattcatcgag	10	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23691502G>A	ENST00000300093.4	+	2	617	c.506G>A	c.(505-507)cGa>cAa	p.R169Q	PLK1_ENST00000564202.1_3'UTR	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	169	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.R169Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		TACCTGCACCGAAACCGAGTT	0.537																																					Colon(12;240 564 27038 33155)											1	Substitution - Missense(1)	large_intestine(1)	16											129	111	117					16																	23691502		2197	4300	6497	23599003	SO:0001583	missense	5347				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.506G>A	16.37:g.23691502G>A	ENSP00000300093:p.Arg169Gln		23599003	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	G	6.642	0.486961	0.12641	.	.	ENSG00000166851	ENST00000300093;ENST00000425844;ENST00000330792	T	0.24350	1.86	5.51	2.05	0.26809	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.364346	0.32161	N	0.006485	T	0.13243	0.0321	N	0.20357	0.565	0.23762	N	0.996917	B	0.09022	0.002	B	0.06405	0.002	T	0.30534	-0.9975	10	0.10902	T	0.67	-1.3396	9.8284	0.40925	0.2694:0.0:0.7306:0.0	.	169	P53350	PLK1_HUMAN	Q	169;72;169	ENSP00000300093:R169Q	ENSP00000300093:R169Q	R	+	2	0	PLK1	23599003	0.098000	0.21812	0.799000	0.32177	0.929000	0.56500	1.182000	0.32029	0.705000	0.31890	-0.263000	0.10527	CGA		0.537	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		A	23691502	G	A	23691502	3	1	61	1	0	0	0	0	1	0	0	0	12125	1058	37	1	512	1	PLK1	16	23691502	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42060	23691502	66663251	9719	17704										
PLK1	5347	broad.mit.edu	37	chr16	23695351	23695351	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccattccaccaaggttttCgattgctcccagcagcctgg	9	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:23695351C>T	ENST00000300093.4	+	5	1088	c.977C>T	c.(976-978)tCg>tTg	p.S326L		NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	326					activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.S326L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		CCAAGGTTTTCGATTGCTCCC	0.547																																					Colon(12;240 564 27038 33155)											1	Substitution - Missense(1)	large_intestine(1)	16											133	137	136					16																	23695351		2197	4300	6497	23602852	SO:0001583	missense	5347				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.977C>T	16.37:g.23695351C>T	ENSP00000300093:p.Ser326Leu		23602852	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.947513	0.73672	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.22539	1.95	5.28	5.28	0.74379	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.23133	0.0559	M	0.70595	2.14	0.80722	D	1	P	0.39520	0.676	B	0.27170	0.077	T	0.08086	-1.0739	10	0.48119	T	0.1	-9.6738	16.7603	0.85510	0.0:1.0:0.0:0.0	.	326	P53350	PLK1_HUMAN	L	326;229	ENSP00000300093:S326L	ENSP00000300093:S326L	S	+	2	0	PLK1	23602852	1.000000	0.71417	0.919000	0.36401	0.898000	0.52572	7.169000	0.77578	2.620000	0.88729	0.655000	0.94253	TCG		0.547	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		T	23695351	C	T	23695351	3	4	61	1	0	0	0	0	1	0	0	0	12125	893	31	1	995	1	PLK1	16	23695351	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3849	23695351	66659402	9720	17705										
PRKCB	5579	broad.mit.edu	37	chr16	24135258	24135258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaccggatgaaactgaccGattttaacttcctaatggtg	10	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24135258G>A	ENST00000321728.7	+	9	1196	c.1021G>A	c.(1021-1023)Gat>Aat	p.D341N	PRKCB_ENST00000303531.7_Missense_Mutation_p.D341N	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	341					apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.D341N(6)		central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	GAAACTGACCGATTTTAACTT	0.483																																																6	Substitution - Missense(6)	liver(4)|large_intestine(2)	16											194	185	188					16																	24135258		2197	4300	6497	24042759	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1021G>A	16.37:g.24135258G>A	ENSP00000318315:p.Asp341Asn		24042759	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681390	0.88542	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.25414	1.8;1.8	4.92	4.92	0.64577	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.50854	0.1640	M	0.81942	2.565	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.61800	0.894;0.839	T	0.53662	-0.8407	10	0.48119	T	0.1	.	17.2875	0.87146	0.0:0.0:1.0:0.0	.	341;341	P05771-2;P05771	.;KPCB_HUMAN	N	341	ENSP00000318315:D341N;ENSP00000305355:D341N	ENSP00000305355:D341N	D	+	1	0	PRKCB	24042759	1.000000	0.71417	0.821000	0.32701	0.912000	0.54170	9.040000	0.93783	2.562000	0.86427	0.563000	0.77884	GAT		0.483	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		A	24135258	G	A	24135258	3	1	61	1	0	0	0	0	1	0	0	0	12542	1058	37	1	1055	1	PRKCB	16	24135258	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	439907	24135258	66219495	9721	17706										
CACNG3	10368	broad.mit.edu	37	chr16	24268258	24268258	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaagtaatgacccattcGgggctgtggaggacctgctg	15	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24268258G>T	ENST00000005284.3	+	1	1385	c.183G>T	c.(181-183)tcG>tcT	p.S61S		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	61					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.S61S(1)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		TGACCCATTCGGGGCTGTGGA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	16											96	91	93					16																	24268258		2197	4300	6497	24175759	SO:0001819	synonymous_variant	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.183G>T	16.37:g.24268258G>T			24175759		Silent	SNP	ENST00000005284.3	37	CCDS10620.1																																																																																				0.448	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24268258	G	T	24268258	2	4	61	1	0	0	0	0	0	0	0	1	2564	1103	39	2		2	CACNG3	16	24268258	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133000	24268258	66086495	9722	17707										
CACNG3	10368	broad.mit.edu	37	chr16	24372887	24372887	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccactcggagttcctgaaGaaatctacttttgcccgcct	7	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24372887G>T	ENST00000005284.3	+	4	1853	c.651G>T	c.(649-651)aaG>aaT	p.K217N		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	217					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.K217N(1)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		AGTTCCTGAAGAAATCTACTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	16											104	97	99					16																	24372887		2197	4300	6497	24280388	SO:0001583	missense	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.651G>T	16.37:g.24372887G>T	ENSP00000005284:p.Lys217Asn		24280388		Missense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534618	0.64972	.	.	ENSG00000006116	ENST00000005284	T	0.60299	0.2	4.82	4.82	0.62117	.	0.051997	0.85682	D	0.000000	T	0.55909	0.1950	M	0.66939	2.045	0.51012	D	0.999904	P	0.44627	0.839	B	0.36134	0.218	T	0.66452	-0.5920	10	0.66056	D	0.02	-17.4537	17.5421	0.87851	0.0:0.0:1.0:0.0	.	217	O60359	CCG3_HUMAN	N	217	ENSP00000005284:K217N	ENSP00000005284:K217N	K	+	3	2	CACNG3	24280388	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.442000	0.97566	2.204000	0.70986	0.561000	0.74099	AAG		0.517	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24372887	G	T	24372887	3	4	61	1	0	0	0	0	1	0	0	0	2564	933	33	2	665	2	CACNG3	16	24372887	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104629	24372887	65981866	9723	17708										
RBBP6	5930	broad.mit.edu	37	chr16	24578481	24578481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaagtataaaccgtgggcGacaccacagcgaaagatcac	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24578481G>A	ENST00000319715.4	+	15	2039	c.1607G>A	c.(1606-1608)cGa>cAa	p.R536Q	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Missense_Mutation_p.R536Q	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	536					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R536Q(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AACCGTGGGCGACACCACAGC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	16											126	121	123					16																	24578481		2197	4300	6497	24485982	SO:0001583	missense	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.1607G>A	16.37:g.24578481G>A	ENSP00000317872:p.Arg536Gln		24485982	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.333866	0.60853	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.16597	2.33;2.41	5.8	5.8	0.92144	.	0.000000	0.46145	D	0.000313	T	0.31358	0.0794	L	0.27053	0.805	0.47308	D	0.999384	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.988	T	0.01452	-1.1351	10	0.32370	T	0.25	-9.2581	20.0522	0.97631	0.0:0.0:1.0:0.0	.	536;536	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	Q	536	ENSP00000317872:R536Q;ENSP00000316291:R536Q	ENSP00000317872:R536Q	R	+	2	0	RBBP6	24485982	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.066000	0.71185	2.737000	0.93849	0.563000	0.77884	CGA		0.438	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		A	24578481	G	A	24578481	3	1	61	1	0	0	0	0	1	0	0	0	13140	1058	37	1	1719	1	RBBP6	16	24578481	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205594	24578481	65776272	9724	17709										
RBBP6	5930	broad.mit.edu	37	chr16	24578770	24578770	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataccatcccaacaacacaAgcaccacctttgtccaggga	5	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24578770A>T	ENST00000319715.4	+	15	2328	c.1896A>T	c.(1894-1896)caA>caT	p.Q632H	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Missense_Mutation_p.Q632H	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	632					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q632H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		CAACAACACAAGCACCACCTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	16											150	153	152					16																	24578770		2197	4300	6497	24486271	SO:0001583	missense	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.1896A>T	16.37:g.24578770A>T	ENSP00000317872:p.Gln632His		24486271	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	11.77	1.737959	0.30774	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.16324	2.39;2.35	5.74	4.64	0.57946	.	0.200483	0.35615	N	0.003097	T	0.19604	0.0471	N	0.19112	0.55	0.30121	N	0.805728	D;D	0.65815	0.995;0.991	P;P	0.58172	0.834;0.687	T	0.04090	-1.0978	10	0.56958	D	0.05	-22.1074	8.1759	0.31281	0.7846:0.0:0.2154:0.0	.	632;632	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	H	632	ENSP00000317872:Q632H;ENSP00000316291:Q632H	ENSP00000317872:Q632H	Q	+	3	2	RBBP6	24486271	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.065000	0.30592	0.989000	0.38761	0.460000	0.39030	CAA		0.413	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24578770	A	T	24578770	3	4	61	1	0	0	0	0	1	0	0	0	13140	69	3	5	2008	5	RBBP6	16	24578770	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	289	24578770	65775983	9725	17710										
RBBP6	5930	broad.mit.edu	37	chr16	24581196	24581196	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacctccaattaaaaaagCcaaagaggagactccgaaga	8	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24581196C>T	ENST00000319715.4	+	17	3617	c.3185C>T	c.(3184-3186)gCc>gTc	p.A1062V	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Missense_Mutation_p.A1028V	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1062	Interaction with RB1. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A1062V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ATTAAAAAAGCCAAAGAGGAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	16											52	53	53					16																	24581196		2195	4300	6495	24488697	SO:0001583	missense	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3185C>T	16.37:g.24581196C>T	ENSP00000317872:p.Ala1062Val		24488697	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.533236	0.45073	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.12879	2.64;2.67	5.49	5.49	0.81192	.	0.000000	0.56097	D	0.000021	T	0.07773	0.0195	N	0.12182	0.205	0.30443	N	0.776004	B;B	0.13594	0.008;0.005	B;B	0.17722	0.019;0.008	T	0.12502	-1.0545	10	0.26408	T	0.33	-9.7983	9.34	0.38074	0.0:0.7999:0.0:0.2001	.	1028;1062	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	V	1062;1028	ENSP00000317872:A1062V;ENSP00000316291:A1028V	ENSP00000317872:A1062V	A	+	2	0	RBBP6	24488697	0.312000	0.24545	1.000000	0.80357	0.999000	0.98932	0.424000	0.21330	2.578000	0.87016	0.655000	0.94253	GCC		0.393	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24581196	C	T	24581196	3	4	61	1	0	0	0	0	1	0	0	0	13140	739	26	3	3305	3	RBBP6	16	24581196	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2426	24581196	65773557	9726	17711										
RBBP6	5930	broad.mit.edu	37	chr16	24582702	24582702	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgtctgaatgaacaaggaAattttaaaagtctgtctcaa	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24582702A>C	ENST00000319715.4	+	18	4747	c.4315A>C	c.(4315-4317)Aat>Cat	p.N1439H	RBBP6_ENST00000381039.3_Missense_Mutation_p.N599H|RBBP6_ENST00000348022.2_Missense_Mutation_p.N1405H	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1439	Interaction with p53. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N1439H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGAACAAGGAAATTTTAAAAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	16											75	73	74					16																	24582702		2197	4300	6497	24490203	SO:0001583	missense	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4315A>C	16.37:g.24582702A>C	ENSP00000317872:p.Asn1439His		24490203	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	6.711	0.499959	0.12762	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.19394	2.15;2.42;2.42	5.52	3.23	0.37069	.	0.269330	0.31624	N	0.007332	T	0.10895	0.0266	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.001	T	0.30149	-0.9988	10	0.23302	T	0.38	-3.1263	8.4113	0.32644	0.7938:0.1368:0.0694:0.0	.	599;1405;1439	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	H	599;1439;1405	ENSP00000370427:N599H;ENSP00000317872:N1439H;ENSP00000316291:N1405H	ENSP00000317872:N1439H	N	+	1	0	RBBP6	24490203	0.979000	0.34478	0.189000	0.23252	0.961000	0.63080	2.523000	0.45580	0.451000	0.26802	0.460000	0.39030	AAT		0.403	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24582702	A	C	24582702	3	2	61	1	0	0	0	0	1	0	0	0	13140	14	1	4	4439	4	RBBP6	16	24582702	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1506	24582702	65772051	9727	17712										
TNRC6A	27327	broad.mit.edu	37	chr16	24788388	24788388	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagccacagcagcagcagCaacagcagcagccgcagcag	12	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24788388C>A	ENST00000395799.3	+	5	427	c.298C>A	c.(298-300)Caa>Aaa	p.Q100K	TNRC6A_ENST00000315183.7_Missense_Mutation_p.Q100K	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	100	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Q100K(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		gcagcagcagcaacagcagca	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											21	30	27					16																	24788388		2113	4201	6314	24695889	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.298C>A	16.37:g.24788388C>A	ENSP00000379144:p.Gln100Lys		24695889	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	8.150	0.787114	0.16189	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.13778	2.58;2.56	3.27	3.27	0.37495	.	0.000000	0.44902	D	0.000404	T	0.07999	0.0200	N	0.14661	0.345	0.49483	D	0.999792	B	0.06786	0.001	B	0.06405	0.002	T	0.17077	-1.0381	10	0.41790	T	0.15	0.6279	10.304	0.43670	0.0:1.0:0.0:0.0	.	100	Q8NDV7	TNR6A_HUMAN	K	100	ENSP00000326900:Q100K;ENSP00000379144:Q100K	ENSP00000326900:Q100K	Q	+	1	0	TNRC6A	24695889	0.971000	0.33674	0.192000	0.23308	0.364000	0.29643	0.878000	0.28126	2.137000	0.66172	0.591000	0.81541	CAA		0.597	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24788388	C	A	24788388	3	1	61	1	0	0	0	0	1	0	0	0	16379	711	25	2	316	2	TNRC6A	16	24788388	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205686	24788388	65566365	9728	17713										
TNRC6A	27327	broad.mit.edu	37	chr16	24820776	24820776	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcatttctgtgaacacatCtttggatcaaaactccagca	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24820776C>A	ENST00000395799.3	+	18	4775	c.4646C>A	c.(4645-4647)tCt>tAt	p.S1549Y	TNRC6A_ENST00000315183.7_Missense_Mutation_p.S1500Y|CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Missense_Mutation_p.S27Y	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1549					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S1549Y(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GTGAACACATCTTTGGATCAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	16											88	88	88					16																	24820776		2197	4300	6497	24728277	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4646C>A	16.37:g.24820776C>A	ENSP00000379144:p.Ser1549Tyr		24728277	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753176	0.89753	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.13420	2.6;2.59	5.39	5.39	0.77823	.	0.131903	0.53938	D	0.000056	T	0.27866	0.0686	L	0.61218	1.895	0.46396	D	0.999025	D;P;D;D	0.67145	0.983;0.932;0.994;0.996	P;P;P;P	0.57776	0.804;0.61;0.827;0.804	T	0.05886	-1.0858	10	0.06891	T	0.86	-7.6618	19.164	0.93546	0.0:1.0:0.0:0.0	.	216;688;1500;1549	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7	.;.;.;TNR6A_HUMAN	Y	1500;1549;27	ENSP00000326900:S1500Y;ENSP00000379144:S1549Y	ENSP00000326900:S1500Y	S	+	2	0	TNRC6A	24728277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.721000	0.68477	2.528000	0.85240	0.591000	0.81541	TCT		0.353	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24820776	C	A	24820776	3	1	61	1	0	0	0	0	1	0	0	0	16379	913	32	2	4716	2	TNRC6A	16	24820776	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32388	24820776	65533977	9729	17714										
TNRC6A	27327	broad.mit.edu	37	chr16	24831490	24831490	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattccaaattgacatggtCtcctggttcagttacaaaca	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24831490C>T	ENST00000395799.3	+	22	5240	c.5111C>T	c.(5110-5112)tCt>tTt	p.S1704F	TNRC6A_ENST00000315183.7_Missense_Mutation_p.S1655F|CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Missense_Mutation_p.S182F	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1704	Sufficient for interaction with AGO2.			S -> F (in Ref. 8; BAA91899). {ECO:0000305}.	cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S1704F(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TTGACATGGTCTCCTGGTTCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	16											110	104	106					16																	24831490		2197	4300	6497	24738991	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5111C>T	16.37:g.24831490C>T	ENSP00000379144:p.Ser1704Phe		24738991	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	29.6	5.015907	0.93404	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.22336	1.97;1.96	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.50650	0.1628	M	0.75615	2.305	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.986	T	0.49952	-0.8884	10	0.87932	D	0	-7.7175	20.04	0.97581	0.0:1.0:0.0:0.0	.	1655;1704	Q8NDV7-6;Q8NDV7	.;TNR6A_HUMAN	F	1655;1704;182	ENSP00000326900:S1655F;ENSP00000379144:S1704F	ENSP00000326900:S1655F	S	+	2	0	TNRC6A	24738991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.770000	0.85390	2.733000	0.93635	0.655000	0.94253	TCT		0.463	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		T	24831490	C	T	24831490	3	4	61	1	0	0	0	0	1	0	0	0	16379	913	32	3	5197	3	TNRC6A	16	24831490	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10714	24831490	65523263	9730	17715										
TNRC6A	27327	broad.mit.edu	37	chr16	24835001	24835001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcacttcactctgggggaCcccgcattattccacaagcc	9	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24835001C>T	ENST00000395799.3	+	25	5891	c.5762C>T	c.(5761-5763)aCc>aTc	p.T1921I	TNRC6A_ENST00000315183.7_Missense_Mutation_p.T1872I|TNRC6A_ENST00000432286.2_Missense_Mutation_p.T399I	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1921	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T1921I(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CTCTGGGGGACCCCGCATTAT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	16											80	85	84					16																	24835001		2197	4300	6497	24742502	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5762C>T	16.37:g.24835001C>T	ENSP00000379144:p.Thr1921Ile		24742502	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	c	9.497	1.102316	0.20632	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.12039	2.73;2.72	5.64	5.64	0.86602	.	0.091008	0.47852	D	0.000205	T	0.10723	0.0262	N	0.22421	0.69	0.34408	D	0.696044	B;B	0.30763	0.078;0.294	B;B	0.24974	0.04;0.057	T	0.14643	-1.0465	10	0.45353	T	0.12	-5.3831	15.5283	0.75928	0.0:0.8231:0.1769:0.0	.	1872;1921	Q8NDV7-6;Q8NDV7	.;TNR6A_HUMAN	I	1872;1921;399	ENSP00000326900:T1872I;ENSP00000379144:T1921I	ENSP00000326900:T1872I	T	+	2	0	TNRC6A	24742502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.777000	0.47717	2.638000	0.89438	0.651000	0.88453	ACC		0.567	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		T	24835001	C	T	24835001	3	4	61	1	0	0	0	0	1	0	0	0	16379	507	18	3	5860	3	TNRC6A	16	24835001	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3511	24835001	65519752	9731	17716										
SLC5A11	115584	broad.mit.edu	37	chr16	24918051	24918051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggctgttcggacatcgcGtatcccaaactcgtgctgga	11	12	1	0	rs540504136	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24918051G>A	ENST00000569071.1	+	9	947	c.682G>A	c.(682-684)Gta>Ata	p.V228I	SLC5A11_ENST00000424767.2_Silent_p.A325A|SLC5A11_ENST00000565769.1_Silent_p.A296A|SLC5A11_ENST00000449109.2_Missense_Mutation_p.V228I|SLC5A11_ENST00000347898.3_Silent_p.A360A|SLC5A11_ENST00000567758.1_Silent_p.A325A|SLC5A11_ENST00000545376.1_Silent_p.A290A|SLC5A11_ENST00000568579.1_Silent_p.A290A|SLC5A11_ENST00000539472.1_Silent_p.A296A					solute carrier family 5 (sodium/inositol cotransporter), member 11									p.A360A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		CGGACATCGCGTATCCCAAAC	0.557											OREG0023688	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	8e-04	0	5008	,	,		18590	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	16											100	82	88					16																	24918051		2197	4300	6497	24825552	SO:0001583	missense	115584			AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"Solute carriers"	23091	protein-coding gene	gene with protein product		610238	"solute carrier family 5 (sodium/glucose cotransporter), member 11"			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000569071.1:c.682G>A	16.37:g.24918051G>A	ENSP00000456376:p.Val228Ile	775	24825552		Silent	SNP	ENST00000569071.1	37	CCDS58440.1	.	.	.	.	.	.	.	.	.	.	G	6.871	0.530144	0.13127	.	.	ENSG00000158865	ENST00000449109	D	0.83837	-1.77	5.73	-11.5	0.00074	.	.	.	.	.	T	0.68256	0.2981	.	.	.	0.80722	D	1	B	0.11235	0.004	B	0.08055	0.003	T	0.52902	-0.8513	8	0.72032	D	0.01	.	5.1958	0.15236	0.5403:0.2625:0.1222:0.075	.	228	Q05BF1	.	I	228	ENSP00000389606:V228I	ENSP00000389606:V228I	V	+	1	0	SLC5A11	24825552	0.000000	0.05858	0.006000	0.13384	0.950000	0.60333	-4.503000	0.00224	-3.768000	0.00109	-1.087000	0.02190	GTA		0.557	SLC5A11-006	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435852.1	NM_052944		A	24918051	G	A	24918051	3	1	61	1	0	0	0	0	1	0	0	0	14700	1132	40	1	1118	1	SLC5A11	16	24918051	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83050	24918051	65436702	9732	17717										
ARHGAP17	55114	broad.mit.edu	37	chr16	24950862	24950862	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcgggggatatgtgctttCtatttagagtgccaccccgc	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:24950862C>A	ENST00000289968.6	-	17	1616	c.1547G>T	c.(1546-1548)aGa>aTa	p.R516I	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Intron	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	516					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)	p.R516I(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		TATGTGCTTTCTATTTAGAGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											26	27	27					16																	24950862		2195	4299	6494	24858363	SO:0001583	missense	55114			AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1547G>T	16.37:g.24950862C>A	ENSP00000289968:p.Arg516Ile		24858363	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	37	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.054396	0.75960	.	.	ENSG00000140750	ENST00000289968;ENST00000455311	T	0.26067	1.76	5.0	5.0	0.66597	.	0.000000	0.48767	D	0.000175	T	0.47875	0.1469	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.91635	0.862;0.999	T	0.43278	-0.9401	10	0.62326	D	0.03	.	15.8573	0.78989	0.0:1.0:0.0:0.0	.	516;49	Q68EM7;Q68EM7-7	RHG17_HUMAN;.	I	516	ENSP00000289968:R516I	ENSP00000289968:R516I	R	-	2	0	ARHGAP17	24858363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.623000	0.61247	2.595000	0.87683	0.655000	0.94253	AGA		0.597	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		A	24950862	C	A	24950862	3	1	61	1	0	0	0	0	1	0	0	0	867	913	32	2	1114	2	ARHGAP17	16	24950862	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32811	24950862	65403891	9733	17718										
AQP8	343	broad.mit.edu	37	chr16	25232799	25232799	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggacacttcaaccctgcGgtgtccctggcagccatgct	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:25232799G>A	ENST00000219660.5	+	3	407	c.282G>A	c.(280-282)gcG>gcA	p.A94A	AQP8_ENST00000566125.1_Silent_p.A88A	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	94					canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)	p.A94A(2)		NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		TCAACCCTGCGGTGTCCCTGG	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	16											112	93	99					16																	25232799		2197	4300	6497	25140300	SO:0001819	synonymous_variant	343			BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"Ion channels / Aquaporins"	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.282G>A	16.37:g.25232799G>A			25140300	Q8IUU3|Q9UIA4	Silent	SNP	ENST00000219660.5	37	CCDS10626.1																																																																																				0.622	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169		A	25232799	G	A	25232799	2	1	61	1	0	0	0	0	0	0	0	1	832	1103	39	1		1	AQP8	16	25232799	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281937	25232799	65121954	9734	17719										
HS3ST4	9951	broad.mit.edu	37	chr16	26146948	26146948	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctagaaatgtgatgcccaaGactttggatgggcaaataac	10	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:26146948G>T	ENST00000331351.5	+	2	1142	c.750G>T	c.(748-750)aaG>aaT	p.K250N	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	250					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.K250N(1)		breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		TGATGCCCAAGACTTTGGATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	16											66	61	63					16																	26146948		1568	3582	5150	26054449	SO:0001583	missense	9951			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.750G>T	16.37:g.26146948G>T	ENSP00000330606:p.Lys250Asn		26054449	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	G	9.587	1.125234	0.20959	.	.	ENSG00000182601	ENST00000331351	T	0.81415	-1.49	5.32	4.36	0.52297	Sulfotransferase domain (1);	0.278391	0.27901	U	0.017386	T	0.78515	0.4295	L	0.37697	1.125	0.37125	D	0.900971	P	0.51653	0.947	P	0.51101	0.659	T	0.79783	-0.1658	10	0.34782	T	0.22	.	12.9595	0.58449	0.0786:0.0:0.9214:0.0	.	250	Q9Y661	HS3S4_HUMAN	N	250	ENSP00000330606:K250N	ENSP00000330606:K250N	K	+	3	2	HS3ST4	26054449	1.000000	0.71417	0.998000	0.56505	0.770000	0.43624	1.507000	0.35758	1.233000	0.43693	0.561000	0.74099	AAG		0.423	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		T	26146948	G	T	26146948	3	4	61	1	0	0	0	0	1	0	0	0	7388	933	33	2	756	2	HS3ST4	16	26146948	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	914149	26146948	64207805	9735	17720										
NSMCE1	197370	broad.mit.edu	37	chr16	27236549	27236549	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccctctccttctcagggtCgaagacttctgtagacagaa	8	13	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27236549C>T	ENST00000361439.4	-	8	829	c.730G>A	c.(730-732)Gac>Aac	p.D244N	NSMCE1_ENST00000565384.1_5'UTR	NM_145080.3	NP_659547.2	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog (S. cerevisiae)	244					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|intracellular signal transduction (GO:0035556)|positive regulation of response to DNA damage stimulus (GO:2001022)|protein ubiquitination (GO:0016567)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D244N(1)		endometrium(2)|large_intestine(2)|lung(3)	7						TTCTCAGGGTCGAAGACTTCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											43	46	45					16																	27236549		1968	4171	6139	27144050	SO:0001583	missense	197370			AF161451	CCDS10628.2	16p12.1	2010-03-23	2006-07-05		ENSG00000169189	ENSG00000169189			29897	protein-coding gene	gene with protein product						11927594	Standard	XM_005255163		Approved	NSE1	uc002doi.1	Q8WV22	OTTHUMG00000131674	ENST00000361439.4:c.730G>A	16.37:g.27236549C>T	ENSP00000355077:p.Asp244Asn		27144050	D3DWF6|Q9P045|Q9P049	Missense_Mutation	SNP	ENST00000361439.4	37	CCDS10628.2	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505221	0.26949	.	.	ENSG00000169189	ENST00000361439	D	0.81579	-1.51	3.98	-0.66	0.11421	.	0.737404	0.13513	N	0.382376	T	0.63165	0.2488	L	0.27053	0.805	0.22591	N	0.998959	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	10	0.18710	T	0.47	.	6.8149	0.23824	0.0:0.5232:0.0:0.4768	.	244	Q8WV22	NSE1_HUMAN	N	244	ENSP00000355077:D244N	ENSP00000355077:D244N	D	-	1	0	NSMCE1	27144050	0.950000	0.32346	0.996000	0.52242	0.833000	0.47200	-0.258000	0.08733	-0.063000	0.13065	-0.258000	0.10820	GAC		0.582	NSMCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254577.3	NM_145080		T	27236549	C	T	27236549	3	4	61	1	0	0	0	0	1	0	0	0	10706	884	31	1	74	1	NSMCE1	16	27236549	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1089601	27236549	63118204	9736	17721										
IL21R	50615	broad.mit.edu	37	chr16	27460002	27460002	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggagctacaagaaccagcaGagctggtggagtctgacggt	15	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27460002G>A	ENST00000337929.3	+	9	1488	c.1015G>A	c.(1015-1017)Gag>Aag	p.E339K	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395755.1_Missense_Mutation_p.E339K|IL21R_ENST00000395754.4_Missense_Mutation_p.E339K|IL21R_ENST00000564089.1_Missense_Mutation_p.E339K	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	339					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)	p.E339K(1)		breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						AGAACCAGCAGAGCTGGTGGA	0.652			T	BCL6	NHL																																		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	1	Substitution - Missense(1)	large_intestine(1)	16											33	34	34					16																	27460002		2197	4299	6496	27367503	SO:0001583	missense	50615			AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1015G>A	16.37:g.27460002G>A	ENSP00000338010:p.Glu339Lys		27367503	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.309665	0.23821	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.32753	1.44;1.44;1.44	5.24	4.29	0.51040	.	2.544920	0.01112	N	0.005587	T	0.26085	0.0636	L	0.29908	0.895	0.09310	N	1	B	0.21225	0.053	B	0.20955	0.032	T	0.31280	-0.9949	10	0.11182	T	0.66	-7.3687	9.5641	0.39387	0.0961:0.0:0.9039:0.0	.	339	Q9HBE5	IL21R_HUMAN	K	339	ENSP00000338010:E339K;ENSP00000379104:E339K;ENSP00000379103:E339K	ENSP00000338010:E339K	E	+	1	0	IL21R	27367503	0.003000	0.15002	0.002000	0.10522	0.037000	0.13140	1.292000	0.33342	1.210000	0.43336	0.561000	0.74099	GAG		0.652	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		A	27460002	G	A	27460002	3	1	61	1	0	0	0	0	1	0	0	0	7692	943	33	3	1045	3	IL21R	16	27460002	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223453	27460002	62894751	9737	17722										
GTF3C1	2975	broad.mit.edu	37	chr16	27476025	27476025	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtctggcctgggggtcttCtctctggatgtcggcgtctt	16	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27476025C>A	ENST00000356183.4	-	34	5503	c.5488G>T	c.(5488-5490)Gaa>Taa	p.E1830*	GTF3C1_ENST00000561623.1_Nonsense_Mutation_p.E1830*	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1830					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.E1830*(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TGGGGGTCTTCTCTCTGGATG	0.677																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											24	30	28					16																	27476025		2109	4157	6266	27383526	SO:0001587	stop_gained	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.5488G>T	16.37:g.27476025C>A	ENSP00000348510:p.Glu1830*		27383526	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Nonsense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	43	10.351171	0.99389	.	.	ENSG00000077235	ENST00000356183	.	.	.	4.78	3.82	0.43975	.	0.683858	0.13798	N	0.362020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-29.1553	11.5907	0.50943	0.179:0.821:0.0:0.0	.	.	.	.	X	1830	.	ENSP00000348510:E1830X	E	-	1	0	GTF3C1	27383526	0.003000	0.15002	0.023000	0.16930	0.076000	0.17211	1.193000	0.32162	1.013000	0.39391	0.561000	0.74099	GAA		0.677	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		A	27476025	C	A	27476025	4	1	61	1	0	0	0	0	0	1	0	0	6893	922	32	2	857	2	GTF3C1	16	27476025	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16023	27476025	62878728	9738	17723										
KIAA0556	23247	broad.mit.edu	37	chr16	27760973	27760973	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaggagcacacacttcacGagtcatggagctccctcagt	10	13	3	0	rs376515834		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27760973G>A	ENST00000261588.4	+	16	2711	c.2692G>A	c.(2692-2694)Gag>Aag	p.E898K		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	898						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E898K(2)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CACACTTCACGAGTCATGGAG	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	16						G	LYS/GLU	0,4394		0,0,2197	90	85	86		2692	4.7	0.6	16		86	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA0556	NM_015202.2	56	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	898/1619	27760973	1,12993	2197	4300	6497	27668474	SO:0001583	missense	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2692G>A	16.37:g.27760973G>A	ENSP00000261588:p.Glu898Lys		27668474	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	G	34	5.396253	0.96009	0.0	1.16E-4	ENSG00000047578	ENST00000261588	T	0.13420	2.59	4.7	4.7	0.59300	.	0.057872	0.64402	D	0.000003	T	0.27384	0.0672	L	0.58101	1.795	0.43435	D	0.995605	D	0.61080	0.989	P	0.53490	0.727	T	0.01889	-1.1253	10	0.54805	T	0.06	0.0125	17.6464	0.88149	0.0:0.0:1.0:0.0	.	898	O60303	K0556_HUMAN	K	898	ENSP00000261588:E898K	ENSP00000261588:E898K	E	+	1	0	KIAA0556	27668474	1.000000	0.71417	0.603000	0.28903	0.961000	0.63080	7.057000	0.76669	2.320000	0.78422	0.655000	0.94253	GAG		0.617	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27760973	G	A	27760973	3	1	61	1	0	0	0	0	1	0	0	0	8204	1059	37	1	2754	1	KIAA0556	16	27760973	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	284948	27760973	62593780	9739	17724										
KIAA0556	23247	broad.mit.edu	37	chr16	27761525	27761525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggaactacaataaatctCggatacattccttccgaggc	7	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27761525C>T	ENST00000261588.4	+	16	3263	c.3244C>T	c.(3244-3246)Cgg>Tgg	p.R1082W		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1082						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1082W(4)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CAATAAATCTCGGATACATTC	0.542																																																4	Substitution - Missense(4)	large_intestine(4)	16											96	92	94					16																	27761525		2197	4300	6497	27669026	SO:0001583	missense	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3244C>T	16.37:g.27761525C>T	ENSP00000261588:p.Arg1082Trp		27669026	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737340	0.69304	.	.	ENSG00000047578	ENST00000261588	T	0.13420	2.59	5.32	3.3	0.37823	.	0.000000	0.85682	D	0.000000	T	0.42449	0.1203	M	0.89353	3.025	0.51233	D	0.999911	D	0.89917	1.0	D	0.97110	1.0	T	0.50617	-0.8807	10	0.87932	D	0	-11.4923	13.1792	0.59645	0.4185:0.5815:0.0:0.0	.	1082	O60303	K0556_HUMAN	W	1082	ENSP00000261588:R1082W	ENSP00000261588:R1082W	R	+	1	2	KIAA0556	27669026	0.990000	0.36364	0.369000	0.25952	0.961000	0.63080	2.889000	0.48601	0.678000	0.31325	0.655000	0.94253	CGG		0.542	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27761525	C	T	27761525	3	4	61	1	0	0	0	0	1	0	0	0	8204	875	31	1	3306	1	KIAA0556	16	27761525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	552	27761525	62593228	9740	17725										
KIAA0556	23247	broad.mit.edu	37	chr16	27788279	27788279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttatgtgattttcgatctgCctaccaccgtgtcaatgatc	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27788279C>T	ENST00000261588.4	+	25	4499	c.4480C>T	c.(4480-4482)Cct>Tct	p.P1494S		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1494						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P1494S(2)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TTTCGATCTGCCTACCACCGT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	16											228	222	224					16																	27788279		2197	4300	6497	27695780	SO:0001583	missense	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.4480C>T	16.37:g.27788279C>T	ENSP00000261588:p.Pro1494Ser		27695780	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.975559	0.92919	.	.	ENSG00000047578	ENST00000261588	T	0.24908	1.83	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.58864	0.2152	M	0.89715	3.055	0.58432	D	0.999999	D	0.69078	0.997	D	0.66847	0.947	T	0.67369	-0.5688	10	0.54805	T	0.06	-7.1154	18.3127	0.90206	0.0:1.0:0.0:0.0	.	1494	O60303	K0556_HUMAN	S	1494	ENSP00000261588:P1494S	ENSP00000261588:P1494S	P	+	1	0	KIAA0556	27695780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.505000	0.81655	2.409000	0.81822	0.561000	0.74099	CCT		0.483	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27788279	C	T	27788279	3	4	61	1	0	0	0	0	1	0	0	0	8204	739	26	3	4578	3	KIAA0556	16	27788279	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26754	27788279	62566474	9741	17726										
KIAA0556	23247	broad.mit.edu	37	chr16	27789942	27789942	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggagacgagacgacggCgctgctgactggtgaaggag	18	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27789942C>T	ENST00000261588.4	+	28	4868	c.4849C>T	c.(4849-4851)Cgc>Tgc	p.R1617C		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1617	Poly-Arg.					extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1617C(2)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GAGACGACGGCGCTGCTGACT	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	16											123	108	113					16																	27789942		2197	4300	6497	27697443	SO:0001583	missense	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.4849C>T	16.37:g.27789942C>T	ENSP00000261588:p.Arg1617Cys		27697443	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.060028	0.55325	.	.	ENSG00000047578	ENST00000261588	T	0.12879	2.64	4.6	2.37	0.29283	.	0.000000	0.64402	D	0.000009	T	0.24275	0.0588	L	0.54323	1.7	0.36202	D	0.850823	D	0.76494	0.999	P	0.61003	0.882	T	0.16482	-1.0401	10	0.87932	D	0	-21.286	8.1658	0.31226	0.1668:0.7365:0.0:0.0967	.	1617	O60303	K0556_HUMAN	C	1617	ENSP00000261588:R1617C	ENSP00000261588:R1617C	R	+	1	0	KIAA0556	27697443	1.000000	0.71417	0.999000	0.59377	0.632000	0.37999	0.559000	0.23485	0.934000	0.37316	0.561000	0.74099	CGC		0.597	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27789942	C	T	27789942	3	4	61	1	0	0	0	0	1	0	0	0	8204	768	27	1	4959	1	KIAA0556	16	27789942	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1663	27789942	62564811	9742	17727										
GSG1L	146395	broad.mit.edu	37	chr16	27974513	27974513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccaggtcaatgaagctgcGacatttttcacctttgaaaa	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:27974513G>A	ENST00000447459.2	-	2	445	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	GSG1L_ENST00000395724.3_Missense_Mutation_p.R121C|GSG1L_ENST00000380898.2_5'UTR	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	121					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R121C(1)		endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						ATGAAGCTGCGACATTTTTCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	87	85					16																	27974513		2005	4167	6172	27882014	SO:0001583	missense	146395			AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.361C>T	16.37:g.27974513G>A	ENSP00000394954:p.Arg121Cys		27882014	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	37	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885478	0.72410	.	.	ENSG00000169181	ENST00000447459;ENST00000395724	T;T	0.35789	1.29;1.29	4.68	4.68	0.58851	.	0.073618	0.52532	U	0.000069	T	0.59307	0.2184	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.64032	-0.6502	10	0.87932	D	0	-18.3836	13.4559	0.61199	0.0:0.0:1.0:0.0	.	121;121	Q6UXU4-3;Q6UXU4	.;GSG1L_HUMAN	C	121	ENSP00000394954:R121C;ENSP00000379074:R121C	ENSP00000379074:R121C	R	-	1	0	GSG1L	27882014	1.000000	0.71417	0.995000	0.50966	0.948000	0.59901	5.504000	0.66968	2.312000	0.78011	0.460000	0.39030	CGC		0.547	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		A	27974513	G	A	27974513	3	1	61	1	0	0	0	0	1	0	0	0	6842	1058	37	1	658	1	GSG1L	16	27974513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	184571	27974513	62380240	9743	17728										
XPO6	23214	broad.mit.edu	37	chr16	28123308	28123308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagatgttagagagggctCggcacaccaacacctgggcc	13	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28123308C>T	ENST00000304658.5	-	17	2671	c.2171G>A	c.(2170-2172)cGa>cAa	p.R724Q	XPO6_ENST00000565698.1_Missense_Mutation_p.R710Q	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	724					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.R724Q(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						AGAGAGGGCTCGGCACACCAA	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	16											44	48	46					16																	28123308		2072	4199	6271	28030809	SO:0001583	missense	23214			AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.2171G>A	16.37:g.28123308C>T	ENSP00000302790:p.Arg724Gln		28030809	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	37	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	C	36	5.862241	0.97036	.	.	ENSG00000169180	ENST00000304658	T	0.67865	-0.29	5.77	5.77	0.91146	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76948	0.4059	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.58970	0.683;0.849	T	0.74497	-0.3646	10	0.36615	T	0.2	-4.418	17.4866	0.87691	0.0:1.0:0.0:0.0	.	724;724	B7ZM10;Q96QU8	.;XPO6_HUMAN	Q	724	ENSP00000302790:R724Q	ENSP00000302790:R724Q	R	-	2	0	XPO6	28030809	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.607000	0.82883	2.745000	0.94114	0.650000	0.86243	CGA		0.592	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		T	28123308	C	T	28123308	3	4	61	1	0	0	0	0	1	0	0	0	17488	884	31	1	1238	1	XPO6	16	28123308	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	148795	28123308	62231445	9744	17729										
NUPR1	26471	broad.mit.edu	37	chr16	28549402	28549402	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggtcaccagtttcctctCgtgcccgccagggctggggc	13	15	2	0	rs371618392		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28549402C>T	ENST00000324873.6	-	2	453	c.187G>A	c.(187-189)Gag>Aag	p.E63K	NUPR1_ENST00000395641.2_Missense_Mutation_p.E81K	NM_001042483.1|NM_012385.2	NP_001035948.1|NP_036517.1	O60356	NUPR1_HUMAN	nuclear protein, transcriptional regulator, 1	63					acute inflammatory response (GO:0002526)|cell growth (GO:0016049)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male gonad development (GO:0008584)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein modification process (GO:0031401)|protein acetylation (GO:0006473)|protein complex assembly (GO:0006461)|regulation of female gonad development (GO:2000194)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E63K(1)		breast(1)|large_intestine(1)|lung(1)	3						AGTTTCCTCTCGTGCCCGCCA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	LYS/GLU,LYS/GLU	0,4394		0,0,2197	124	141	135		241,187	5.5	1	16		135	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NUPR1	NM_001042483.1,NM_012385.2	56,56	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	81/101,63/83	28549402	1,12993	2197	4300	6497	28456903	SO:0001583	missense	26471			AF069073	CCDS10634.1, CCDS42137.1	16p11.2	2012-07-04	2012-07-04		ENSG00000176046	ENSG00000176046			29990	protein-coding gene	gene with protein product	"candidate of metastasis 1"	614812				9405444, 10493524, 10092851	Standard	NM_012385		Approved	COM1, p8	uc002dqd.1	O60356	OTTHUMG00000131764	ENST00000324873.6:c.187G>A	16.37:g.28549402C>T	ENSP00000315559:p.Glu63Lys		28456903	B2R5C4|O60357|Q6FGG3	Missense_Mutation	SNP	ENST00000324873.6	37	CCDS10634.1	.	.	.	.	.	.	.	.	.	.	C	36	5.936202	0.97122	0.0	1.16E-4	ENSG00000176046	ENST00000324873;ENST00000395641	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.79323	0.4426	.	.	.	0.52501	D	0.999951	D	0.89917	1.0	D	0.91635	0.999	T	0.80876	-0.1186	8	0.66056	D	0.02	-24.4866	15.2482	0.73523	0.0:1.0:0.0:0.0	.	63	O60356	NUPR1_HUMAN	K	63;81	.	ENSP00000315559:E63K	E	-	1	0	NUPR1	28456903	0.998000	0.40836	0.998000	0.56505	0.989000	0.77384	4.683000	0.61679	2.748000	0.94277	0.655000	0.94253	GAG		0.622	NUPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254692.2	NM_012385		T	28549402	C	T	28549402	3	4	61	1	0	0	0	0	1	0	0	0	10807	893	31	1	65	1	NUPR1	16	28549402	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426094	28549402	61805351	9745	17730										
ATXN2L	11273	broad.mit.edu	37	chr16	28841213	28841213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacaactcagaagagtttCgtcagcgagagctgcgtgcg	14	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28841213C>T	ENST00000336783.4	+	8	1035	c.868C>T	c.(868-870)Cgt>Tgt	p.R290C	ATXN2L_ENST00000564304.1_Missense_Mutation_p.R290C|ATXN2L_ENST00000395547.2_Missense_Mutation_p.R290C|ATXN2L_ENST00000570200.1_Missense_Mutation_p.R290C|ATXN2L_ENST00000382686.4_Missense_Mutation_p.R290C|ATXN2L_ENST00000340394.8_Missense_Mutation_p.R290C|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000325215.6_Missense_Mutation_p.R290C	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	290					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)	p.R290C(2)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGAAGAGTTTCGTCAGCGAGA	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	16											69	67	68					16																	28841213		2197	4300	6497	28748714	SO:0001583	missense	11273				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.868C>T	16.37:g.28841213C>T	ENSP00000338718:p.Arg290Cys		28748714	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Missense_Mutation	SNP	ENST00000336783.4	37	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	24.3	4.516411	0.85495	.	.	ENSG00000168488	ENST00000340394;ENST00000395547;ENST00000336783;ENST00000359153;ENST00000382686;ENST00000325215	T;T;T;T;T	0.52057	0.7;0.68;0.7;0.7;0.7	5.85	5.85	0.93711	LsmAD domain (1);	0.000000	0.64402	D	0.000002	T	0.67363	0.2885	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.997;0.994;0.998;0.998;0.997;0.997;0.998;0.997	T	0.69075	-0.5241	10	0.72032	D	0.01	-10.5407	13.8453	0.63463	0.1531:0.8469:0.0:0.0	.	290;290;290;290;290;290;290;290	Q8WWM7-6;Q8WWM7-5;Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3	.;.;.;ATX2L_HUMAN;.;.;.;.	C	290	ENSP00000341459:R290C;ENSP00000378917:R290C;ENSP00000338718:R290C;ENSP00000372133:R290C;ENSP00000315650:R290C	ENSP00000315650:R290C	R	+	1	0	ATXN2L	28748714	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	2.595000	0.46197	2.779000	0.95612	0.491000	0.48974	CGT		0.557	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		T	28841213	C	T	28841213	3	4	61	1	0	0	0	0	1	0	0	0	1213	884	31	1	898	1	ATXN2L	16	28841213	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	291811	28841213	61513540	9746	17731										
ATXN2L	11273	broad.mit.edu	37	chr16	28845850	28845850	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccttcctccgcagcgctcgGaccaacaccagccagcctca	7	21	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28845850G>A	ENST00000336783.4	+	18	2436	c.2269G>A	c.(2269-2271)Gac>Aac	p.D757N	ATXN2L_ENST00000564304.1_Missense_Mutation_p.D763N|ATXN2L_ENST00000395547.2_Missense_Mutation_p.D757N|ATXN2L_ENST00000570200.1_Missense_Mutation_p.D757N|ATXN2L_ENST00000382686.4_Missense_Mutation_p.D757N|ATXN2L_ENST00000340394.8_Missense_Mutation_p.D757N|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000565845.1_3'UTR|ATXN2L_ENST00000325215.6_Missense_Mutation_p.D757N	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	757					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)	p.D757N(2)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						GCAGCGCTCGGACCAACACCA	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	16											47	55	53					16																	28845850		2197	4299	6496	28753351	SO:0001583	missense	11273				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2269G>A	16.37:g.28845850G>A	ENSP00000338718:p.Asp757Asn		28753351	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Missense_Mutation	SNP	ENST00000336783.4	37	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	35	5.514359	0.96402	.	.	ENSG00000168488	ENST00000340394;ENST00000395547;ENST00000336783;ENST00000382686;ENST00000325215	T;T;T;T;T	0.68025	-0.17;-0.3;-0.26;-0.18;-0.19	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.78660	0.4318	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D;D	0.71674	0.998;0.997;0.997;0.998;0.998;0.997;0.998	D;D;D;D;D;D;D	0.74023	0.982;0.96;0.96;0.982;0.982;0.96;0.982	T	0.75175	-0.3410	10	0.34782	T	0.22	-16.0056	18.6431	0.91401	0.0:0.0:1.0:0.0	.	757;757;757;757;757;757;757	Q8WWM7-6;Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3	.;.;ATX2L_HUMAN;.;.;.;.	N	757	ENSP00000341459:D757N;ENSP00000378917:D757N;ENSP00000338718:D757N;ENSP00000372133:D757N;ENSP00000315650:D757N	ENSP00000315650:D757N	D	+	1	0	ATXN2L	28753351	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.075000	0.89502	2.704000	0.92352	0.563000	0.77884	GAC		0.687	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		A	28845850	G	A	28845850	3	1	61	1	0	0	0	0	1	0	0	0	1213	1174	41	3	2339	3	ATXN2L	16	28845850	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4637	28845850	61508903	9747	17732										
RABEP2	79874	broad.mit.edu	37	chr16	28917055	28917055	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgctgcacccgctccatCtctgtcctcaggctgcacag	8	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28917055C>T	ENST00000358201.4	-	11	2049	c.1461G>A	c.(1459-1461)gaG>gaA	p.E487E	RABEP2_ENST00000357573.6_Silent_p.E451E|RABEP2_ENST00000544477.1_Silent_p.E416E	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	487					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.E487E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						CCCGCTCCATCTCTGTCCTCA	0.677																																					Pancreas(66;639 1284 10093 31061 49099)											1	Substitution - coding silent(1)	large_intestine(1)	16											41	47	45					16																	28917055		2050	4188	6238	28824556	SO:0001819	synonymous_variant	79874			AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.1461G>A	16.37:g.28917055C>T			28824556		Silent	SNP	ENST00000358201.4	37	CCDS42140.1																																																																																				0.677	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		T	28917055	C	T	28917055	2	4	61	1	0	0	0	0	0	0	0	1	12999	912	32	3		3	RABEP2	16	28917055	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71205	28917055	61437698	9748	17733										
RABEP2	79874	broad.mit.edu	37	chr16	28931122	28931122	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaccttttccatctgcttCtccagggagtccagggggta	10	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:28931122C>A	ENST00000358201.4	-	3	1005	c.417G>T	c.(415-417)gaG>gaT	p.E139D	RABEP2_ENST00000357573.6_Missense_Mutation_p.E139D|RABEP2_ENST00000544477.1_Missense_Mutation_p.E68D|RABEP2_ENST00000561803.1_5'UTR	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	139					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.E139D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						CCATCTGCTTCTCCAGGGAGT	0.607																																					Pancreas(66;639 1284 10093 31061 49099)											1	Substitution - Missense(1)	large_intestine(1)	16											65	69	67					16																	28931122		1957	4152	6109	28838623	SO:0001583	missense	79874			AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.417G>T	16.37:g.28931122C>A	ENSP00000350934:p.Glu139Asp		28838623		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908280	0.92107	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.55588	0.51;0.53;0.55	4.75	4.75	0.60458	Rabaptin coiled-coil domain (1);	0.226096	0.35378	N	0.003244	T	0.67896	0.2942	L	0.52011	1.625	0.43313	D	0.99532	D;D;D;D	0.89917	0.997;0.986;1.0;0.973	D;P;D;P	0.87578	0.992;0.718;0.998;0.815	T	0.70757	-0.4785	10	0.66056	D	0.02	-24.669	17.0026	0.86384	0.0:1.0:0.0:0.0	.	68;139;139;139	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	D	139;139;68	ENSP00000350934:E139D;ENSP00000350186:E139D;ENSP00000442798:E68D	ENSP00000350186:E139D	E	-	3	2	RABEP2	28838623	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.981000	0.56902	2.395000	0.81488	0.650000	0.86243	GAG		0.607	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		A	28931122	C	A	28931122	3	1	61	1	0	0	0	0	1	0	0	0	12999	912	32	2	1336	2	RABEP2	16	28931122	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14067	28931122	61423631	9749	17734										
FAM57B	83723	broad.mit.edu	37	chr16	30037088	30037088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagacgaagggcgtgctgaCctctgccatcaacatgcaac	11	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30037088C>T	ENST00000380495.4	-	4	1230	c.499G>A	c.(499-501)Gtc>Atc	p.V167I	FAM57B_ENST00000564806.1_Missense_Mutation_p.V117I|FAM57B_ENST00000279389.4_Missense_Mutation_p.V117I	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	167	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)	p.V167I(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						GGCGTGCTGACCTCTGCCATC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	16											182	169	173					16																	30037088		2197	4300	6497	29944589	SO:0001583	missense	83723			AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.499G>A	16.37:g.30037088C>T	ENSP00000369863:p.Val167Ile		29944589	Q9H0J1	Missense_Mutation	SNP	ENST00000380495.4	37	CCDS10667.2	.	.	.	.	.	.	.	.	.	.	C	22.6	4.312623	0.81358	.	.	ENSG00000149926	ENST00000380495	D	0.84800	-1.9	5.17	5.17	0.71159	TRAM/LAG1/CLN8 homology domain (3);	0.067269	0.64402	D	0.000009	D	0.83562	0.5281	L	0.40543	1.245	0.38789	D	0.954934	P;P	0.48503	0.911;0.789	P;P	0.51516	0.672;0.525	T	0.82954	-0.0201	10	0.32370	T	0.25	-14.4485	11.0197	0.47711	0.0:0.9127:0.0:0.0873	.	167;167	F1T0F5;Q71RH2	.;FA57B_HUMAN	I	167	ENSP00000369863:V167I	ENSP00000369863:V167I	V	-	1	0	FAM57B	29944589	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.699000	0.54778	2.408000	0.81797	0.561000	0.74099	GTC		0.612	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255142.2	NM_031478		T	30037088	C	T	30037088	3	4	61	1	0	0	0	0	1	0	0	0	5608	507	18	3	333	3	FAM57B	16	30037088	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1105966	30037088	60317665	9750	17735										
MYLPF	1731	broad.mit.edu	37	chr16	30387745	30387745	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccccaaccccctccaggCcgcctcaatgtgaagaatga	7	17	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30387745C>T	ENST00000571393.1	-	0	1589				MYLPF_ENST00000322861.7_Splice_Site_p.G58G			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.G58G(2)		breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CCCCTCCAGGCCGCCTCAATG	0.577																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	16											85	90	88					16																	30387745		2197	4300	6497	30295246	SO:0001628	intergenic_variant	29895			AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"Septins"	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984		16.37:g.30387745C>T			30295246	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Silent	SNP	ENST00000571393.1	37																																																																																					0.577	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838		T	30387745	C	T	30387745	1	4	61	0	1	0	0	0	0	0	0	0	10090	753	26	3		3	MYLPF	16	30387745	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	350657	30387745	59967008	9751	17736										
ITGAL	3683	broad.mit.edu	37	chr16	30490684	30490684	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaacgtagacctggtatttCtgtttgatggttcgatgagc	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30490684C>A	ENST00000356798.6	+	6	658	c.478C>A	c.(478-480)Ctg>Atg	p.L160M	RP11-297C4.3_ENST00000562525.1_RNA|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000358164.5_Intron|ITGAL_ENST00000454514.2_Intron|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	160	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.L160M(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CCTGGTATTTCTGTTTGATGG	0.473																																					NSCLC(110;1462 1641 3311 33990 49495)											1	Substitution - Missense(1)	large_intestine(1)	16											117	105	109					16																	30490684		2197	4300	6497	30398185	SO:0001583	missense	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.478C>A	16.37:g.30490684C>A	ENSP00000349252:p.Leu160Met		30398185	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.645657	0.67358	.	.	ENSG00000005844	ENST00000356798	D	0.87103	-2.21	5.85	3.58	0.41010	von Willebrand factor, type A (3);	0.000000	0.41097	D	0.000958	D	0.92368	0.7578	M	0.84683	2.71	0.80722	D	1	D	0.55385	0.971	P	0.62560	0.904	D	0.92993	0.6416	10	0.87932	D	0	.	11.032	0.47779	0.0:0.8257:0.0:0.1743	.	160	P20701	ITAL_HUMAN	M	160	ENSP00000349252:L160M	ENSP00000349252:L160M	L	+	1	2	ITGAL	30398185	1.000000	0.71417	0.999000	0.59377	0.832000	0.47134	2.594000	0.46189	1.482000	0.48325	0.411000	0.27672	CTG		0.473	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			A	30490684	C	A	30490684	3	1	61	1	0	0	0	0	1	0	0	0	7907	912	32	2	500	2	ITGAL	16	30490684	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102939	30490684	59864069	9752	17737										
ITGAL	3683	broad.mit.edu	37	chr16	30507763	30507763	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttgctctcagcggataGaagggacccaagtgctctca	10	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30507763G>T	ENST00000356798.6	+	15	1888	c.1708G>T	c.(1708-1710)Gaa>Taa	p.E570*	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000358164.5_Nonsense_Mutation_p.E487*|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	570					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.E570*(1)|p.E570K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	TCAGCGGATAGAAGGGACCCA	0.587																																					NSCLC(110;1462 1641 3311 33990 49495)											2	Substitution - Missense(1)|Substitution - Nonsense(1)	upper_aerodigestive_tract(1)|large_intestine(1)	16											138	128	131					16																	30507763		2197	4300	6497	30415264	SO:0001587	stop_gained	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1708G>T	16.37:g.30507763G>T	ENSP00000349252:p.Glu570*		30415264	O43746|Q45H73|Q96HB1|Q9UBC8	Nonsense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	G	38	7.062727	0.98036	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	.	.	.	5.94	2.8	0.32819	.	0.693431	0.13567	N	0.378334	.	.	.	.	.	.	0.23483	N	0.997581	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	4.437	0.11555	0.2895:0.1725:0.538:0.0	.	.	.	.	X	570;487	.	ENSP00000349252:E570X	E	+	1	0	ITGAL	30415264	0.000000	0.05858	0.408000	0.26446	0.957000	0.61999	0.405000	0.21015	0.336000	0.23639	0.563000	0.77884	GAA		0.587	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30507763	G	T	30507763	4	4	61	1	0	0	0	0	0	1	0	0	7907	943	33	2	1766	2	ITGAL	16	30507763	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17079	30507763	59846990	9753	17738										
ITGAL	3683	broad.mit.edu	37	chr16	30507879	30507879	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggctgagagccagatgatCgtgctgaggtgagatgggtc	19	6	0	5	rs147713219		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30507879C>T	ENST00000356798.6	+	15	2004	c.1824C>T	c.(1822-1824)atC>atT	p.I608I	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000358164.5_Silent_p.I525I|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	608					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.I608I(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GCCAGATGATCGTGCTGAGGT	0.463																																					NSCLC(110;1462 1641 3311 33990 49495)											1	Substitution - coding silent(1)	large_intestine(1)	16						C	,	1,4393	2.1+/-5.4	0,1,2196	91	77	82		1575,1824	-0.5	0.9	16	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	,	525/1087,608/1171	30507879	1,12993	2197	4300	6497	30415380	SO:0001819	synonymous_variant	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1824C>T	16.37:g.30507879C>T			30415380	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.463	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30507879	C	T	30507879	2	4	61	1	0	0	0	0	0	0	0	1	7907	874	31	1		1	ITGAL	16	30507879	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116	30507879	59846874	9754	17739										
ITGAL	3683	broad.mit.edu	37	chr16	30515508	30515508	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctcaggtatgtgttcaaGacctcatctcccccatcaat	5	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30515508G>T	ENST00000356798.6	+	18	2338	c.2158G>T	c.(2158-2160)Gac>Tac	p.D720Y	MIR4518_ENST00000580665.1_RNA|ITGAL_ENST00000358164.5_Missense_Mutation_p.D637Y|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	720					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.D720Y(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	ATGTGTTCAAGACCTCATCTC	0.458																																					NSCLC(110;1462 1641 3311 33990 49495)											1	Substitution - Missense(1)	large_intestine(1)	16											157	140	146					16																	30515508		2197	4300	6497	30423009	SO:0001583	missense	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.2158G>T	16.37:g.30515508G>T	ENSP00000349252:p.Asp720Tyr		30423009	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028256	0.75390	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.79033	-1.23;-1.23	5.34	5.34	0.76211	Integrin alpha-2 (1);	0.000000	0.64402	D	0.000009	D	0.86867	0.6036	M	0.76002	2.32	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.974	D	0.87778	0.2610	10	0.87932	D	0	.	14.4791	0.67567	0.0:0.0:1.0:0.0	.	637;720	Q96HB1;P20701	.;ITAL_HUMAN	Y	720;637	ENSP00000349252:D720Y;ENSP00000350886:D637Y	ENSP00000349252:D720Y	D	+	1	0	ITGAL	30423009	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.606000	0.61126	2.799000	0.96334	0.505000	0.49811	GAC		0.458	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30515508	G	T	30515508	3	4	61	1	0	0	0	0	1	0	0	0	7907	942	33	2	2228	2	ITGAL	16	30515508	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7629	30515508	59839245	9755	17740										
ZNF764	92595	broad.mit.edu	37	chr16	30569163	30569163	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagctggcttgttgcctccGattcctagggaagaagaacg	13	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30569163G>A	ENST00000252797.2	-	2	281	c.201C>T	c.(199-201)atC>atT	p.I67I	AC002310.13_ENST00000568114.1_Intron|ZNF764_ENST00000395091.2_Silent_p.I67I	NM_001172679.1|NM_033410.3	NP_001166150.1|NP_219363.2	Q96H86	ZN764_HUMAN	zinc finger protein 764	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I67I(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7						TGTTGCCTCCGATTCCTAGGG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	16											30	27	28					16																	30569163		2197	4300	6497	30476664	SO:0001819	synonymous_variant	92595			BC008821	CCDS10683.1, CCDS54001.1	16p11.2	2013-01-08			ENSG00000169951	ENSG00000169951		"Zinc fingers, C2H2-type", "-"	28200	protein-coding gene	gene with protein product						12477932	Standard	NM_033410		Approved	MGC13138	uc002dyq.3	Q96H86	OTTHUMG00000132406	ENST00000252797.2:c.201C>T	16.37:g.30569163G>A			30476664	A8MZF4|B3KSN2|H9KV99|Q9BWS1	Silent	SNP	ENST00000252797.2	37	CCDS10683.1																																																																																				0.667	ZNF764-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255541.1	NM_033410		A	30569163	G	A	30569163	2	1	61	1	0	0	0	0	0	0	0	1	18177	1048	37	1		1	ZNF764	16	30569163	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53655	30569163	59785590	9756	17741										
SRCAP	10847	broad.mit.edu	37	chr16	30735667	30735667	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgtctactccaggaacctCtttagcctcagcttcaccgg	7	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30735667C>A	ENST00000262518.4	+	25	5307	c.4922C>A	c.(4921-4923)tCt>tAt	p.S1641Y	SRCAP_ENST00000344771.4_Missense_Mutation_p.S1483Y|SRCAP_ENST00000395059.2_Missense_Mutation_p.S1579Y	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1641	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.S1641Y(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CCAGGAACCTCTTTAGCCTCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											100	99	99					16																	30735667		2197	4300	6497	30643168	SO:0001583	missense	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4922C>A	16.37:g.30735667C>A	ENSP00000262518:p.Ser1641Tyr		30643168	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	9.754	1.168353	0.21621	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91407	-2.82;-2.84;-2.79	5.68	5.68	0.88126	.	0.282010	0.25941	N	0.027303	T	0.81875	0.4915	N	0.08118	0	0.20873	N	0.999839	B;P;B	0.34546	0.188;0.456;0.118	B;B;B	0.30401	0.081;0.115;0.054	T	0.77440	-0.2587	10	0.72032	D	0.01	-4.5578	17.2829	0.87133	0.0:1.0:0.0:0.0	.	1483;1579;1641	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	Y	1641;1579;1483	ENSP00000262518:S1641Y;ENSP00000378499:S1579Y;ENSP00000343042:S1483Y	ENSP00000262518:S1641Y	S	+	2	0	SRCAP	30643168	0.025000	0.19082	0.997000	0.53966	0.968000	0.65278	0.028000	0.13644	2.672000	0.90937	0.557000	0.71058	TCT		0.582	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30735667	C	A	30735667	3	1	61	1	0	0	0	0	1	0	0	0	15174	913	32	2	5012	2	SRCAP	16	30735667	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	166504	30735667	59619086	9757	17742										
SETD1A	9739	broad.mit.edu	37	chr16	30983010	30983010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccagtcacacccctgcccGaacaggaggcgtctccagca	9	19	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:30983010G>A	ENST00000262519.8	+	13	4014	c.3328G>A	c.(3328-3330)Gaa>Aaa	p.E1110K		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1110	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.E1110K(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ACCCCTGCCCGAACAGGAGGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	16											31	31	31					16																	30983010		2191	4287	6478	30890511	SO:0001583	missense	9739			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.3328G>A	16.37:g.30983010G>A	ENSP00000262519:p.Glu1110Lys		30890511	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.599346	0.28534	.	.	ENSG00000099381	ENST00000262519	D	0.94576	-3.46	5.66	5.66	0.87406	.	0.191986	0.43579	D	0.000543	D	0.95752	0.8618	M	0.61703	1.905	0.38503	D	0.94828	D	0.63046	0.992	D	0.65443	0.935	D	0.93963	0.7242	10	0.12430	T	0.62	.	15.2572	0.73593	0.0:0.0:1.0:0.0	.	1110	O15047	SET1A_HUMAN	K	1110	ENSP00000262519:E1110K	ENSP00000262519:E1110K	E	+	1	0	SETD1A	30890511	0.998000	0.40836	0.785000	0.31869	0.011000	0.07611	4.746000	0.62133	2.672000	0.90937	0.467000	0.42956	GAA		0.637	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30983010	G	A	30983010	3	1	61	1	0	0	0	0	1	0	0	0	14167	1059	37	1	3374	1	SETD1A	16	30983010	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	247343	30983010	59371743	9758	17743										
STX1B	112755	broad.mit.edu	37	chr16	31004728	31004728	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagctcgcggatgctggtCtccagcttgatgatctcatt	11	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31004728C>A	ENST00000215095.5	-	8	846	c.615G>T	c.(613-615)gaG>gaT	p.E205D	STX1B_ENST00000565419.1_Missense_Mutation_p.E205D	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	205	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)	p.E205D(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						GGATGCTGGTCTCCAGCTTGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16											191	147	162					16																	31004728		2197	4300	6497	30912229	SO:0001583	missense	112755			AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"syntaxin 1B1", "syntaxin 1B2"	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.615G>T	16.37:g.31004728C>A	ENSP00000215095:p.Glu205Asp		30912229	Q15531|Q2VPS2	Missense_Mutation	SNP	ENST00000215095.5	37	CCDS10699.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691083	0.68271	.	.	ENSG00000099365	ENST00000215095	T	0.35789	1.29	5.0	1.39	0.22231	t-SNARE (1);Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.122518	0.53938	D	0.000060	T	0.65026	0.2652	H	0.97440	4.005	0.58432	D	0.999999	P;D	0.55605	0.944;0.972	P;P	0.60949	0.881;0.811	T	0.67432	-0.5672	10	0.66056	D	0.02	.	7.4429	0.27194	0.0:0.4773:0.0:0.5227	.	205;205	Q2VPS2;P61266	.;STX1B_HUMAN	D	205	ENSP00000215095:E205D	ENSP00000215095:E205D	E	-	3	2	STX1B	30912229	0.820000	0.29190	1.000000	0.80357	0.932000	0.56968	-0.076000	0.11412	0.277000	0.22141	-0.367000	0.07326	GAG		0.552	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2			A	31004728	C	A	31004728	3	1	61	1	0	0	0	0	1	0	0	0	15383	912	32	2	263	2	STX1B	16	31004728	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21718	31004728	59350025	9759	17744										
PRSS36	146547	broad.mit.edu	37	chr16	31153162	31153162	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcacatggctgatccatggGccatgagtctgcagagggaa	14	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31153162G>A	ENST00000268281.4	-	11	1699	c.1641C>T	c.(1639-1641)ggC>ggT	p.G547G	PRSS36_ENST00000569305.1_Silent_p.G542G|PRSS36_ENST00000418068.2_Silent_p.G547G	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	547	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)	p.G547G(1)		kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						TGATCCATGGGCCATGAGTCT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	16											87	75	79					16																	31153162		2197	4300	6497	31060663	SO:0001819	synonymous_variant	146547			AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.1641C>T	16.37:g.31153162G>A			31060663	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Silent	SNP	ENST00000268281.4	37	CCDS32436.1																																																																																				0.597	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		A	31153162	G	A	31153162	2	1	61	1	0	0	0	0	0	0	0	1	12659	1190	42	3		3	PRSS36	16	31153162	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	148434	31153162	59201591	9760	17745										
ITGAM	3684	broad.mit.edu	37	chr16	31287004	31287004	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaccagcttcgggagaaGatctttgcgatcgagggtga	14	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31287004G>T	ENST00000287497.8	+	9	1068	c.993G>T	c.(991-993)aaG>aaT	p.K331N	ITGAM_ENST00000544665.3_Missense_Mutation_p.K331N			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	331					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.K331N(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TTCGGGAGAAGATCTTTGCGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											66	67	67					16																	31287004		2011	4172	6183	31194505	SO:0001583	missense	3684			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.993G>T	16.37:g.31287004G>T	ENSP00000287497:p.Lys331Asn		31194505	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.373769	0.61624	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.70869	-0.52;-0.52	4.51	4.51	0.55191	von Willebrand factor, type A (1);	.	.	.	.	D	0.82802	0.5116	M	0.82132	2.575	0.34893	D	0.745716	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	D	0.87867	0.2668	9	0.87932	D	0	.	10.7431	0.46164	0.0928:0.0:0.9072:0.0	.	331;331	Q4VAK1;P11215	.;ITAM_HUMAN	N	331	ENSP00000441691:K331N;ENSP00000287497:K331N	ENSP00000287497:K331N	K	+	3	2	ITGAM	31194505	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.586000	0.36611	2.464000	0.83262	0.561000	0.74099	AAG		0.532	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31287004	G	T	31287004	3	4	61	1	0	0	0	0	1	0	0	0	7908	933	33	2	1027	2	ITGAM	16	31287004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133842	31287004	59067749	9761	17746										
ITGAM	3684	broad.mit.edu	37	chr16	31308849	31308849	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagatcggcgcctacttCggggcctccctctgctccgt	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31308849C>T	ENST00000287497.8	+	13	1446	c.1371C>T	c.(1369-1371)ttC>ttT	p.F457F	ITGAM_ENST00000544665.3_Silent_p.F457F			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	457					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.F457F(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GCGCCTACTTCGGGGCCTCCC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	16											117	128	124					16																	31308849		2190	4293	6483	31216350	SO:0001819	synonymous_variant	3684			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1371C>T	16.37:g.31308849C>T			31216350	Q4VAK0|Q4VAK1|Q4VAK2	Silent	SNP	ENST00000287497.8	37	CCDS45470.1																																																																																				0.587	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31308849	C	T	31308849	2	4	61	1	0	0	0	0	0	0	0	1	7908	883	31	1		1	ITGAM	16	31308849	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21845	31308849	59045904	9762	17747										
ITGAX	3687	broad.mit.edu	37	chr16	31372406	31372406	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggattagcttttcaaaacaGaaattcttggaaagaattaa	7	4	2	2	rs150242454		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31372406G>T	ENST00000268296.4	+	9	1005	c.884G>T	c.(883-885)aGa>aTa	p.R295I	ITGAX_ENST00000562522.1_Missense_Mutation_p.R295I	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	295	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.R295I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TTTCAAAACAGAAATTCTTGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	16											103	113	110					16																	31372406		2197	4300	6497	31279907	SO:0001583	missense	3687			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.884G>T	16.37:g.31372406G>T	ENSP00000268296:p.Arg295Ile		31279907	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	1.156	-0.645253	0.03531	.	.	ENSG00000140678	ENST00000268296	D	0.83419	-1.72	5.07	-10.1	0.00402	von Willebrand factor, type A (3);	.	.	.	.	T	0.65460	0.2693	L	0.40543	1.245	0.09310	N	1	B	0.18013	0.025	B	0.17722	0.019	T	0.52071	-0.8624	9	0.21540	T	0.41	.	1.0748	0.01629	0.2614:0.1106:0.2684:0.3596	.	295	P20702	ITAX_HUMAN	I	295	ENSP00000268296:R295I	ENSP00000268296:R295I	R	+	2	0	ITGAX	31279907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-13.824000	0.00000	-6.284000	0.00005	-2.202000	0.00303	AGA		0.373	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		T	31372406	G	T	31372406	3	4	61	1	0	0	0	0	1	0	0	0	7910	942	33	2	918	2	ITGAX	16	31372406	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63557	31372406	58982347	9763	17748										
ITGAD	3681	broad.mit.edu	37	chr16	31434506	31434506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaaagaggctgagcatcGataccgtgtgagagtctagg	14	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31434506G>A	ENST00000389202.2	+	24	2901	c.2852G>A	c.(2851-2853)cGa>cAa	p.R951Q		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	951					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.R951Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCTGAGCATCGATACCGTGTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											78	67	71					16																	31434506		2197	4300	6497	31342007	SO:0001583	missense	3681			U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2852G>A	16.37:g.31434506G>A	ENSP00000373854:p.Arg951Gln		31342007	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331575	0.24167	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.44482	0.92	5.59	1.43	0.22495	Integrin alpha-2 (1);	.	.	.	.	T	0.20251	0.0487	L	0.28400	0.85	0.09310	N	1	P;P	0.47034	0.889;0.889	B;B	0.28638	0.092;0.092	T	0.09443	-1.0674	9	0.20046	T	0.44	.	7.3842	0.26872	0.3411:0.0:0.6589:0.0	.	967;951	Q59H14;Q13349	.;ITAD_HUMAN	Q	967;951	ENSP00000373854:R951Q	ENSP00000373854:R951Q	R	+	2	0	ITGAD	31342007	0.000000	0.05858	0.003000	0.11579	0.453000	0.32348	-0.053000	0.11846	0.704000	0.31869	0.650000	0.86243	CGA		0.498	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31434506	G	A	31434506	3	1	61	1	0	0	0	0	1	0	0	0	7905	1058	37	1	2946	1	ITGAD	16	31434506	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62100	31434506	58920247	9764	17749										
ZNF267	10308	broad.mit.edu	37	chr16	31926823	31926823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgtggcaaagcctttcGctgtagttcataccttacta	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:31926823G>A	ENST00000300870.10	+	4	1462	c.1253G>A	c.(1252-1254)cGc>cAc	p.R418H		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	418					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R418H(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAAGCCTTTCGCTGTAGTTCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	16											43	48	46					16																	31926823		2197	4297	6494	31834324	SO:0001583	missense	10308			X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1253G>A	16.37:g.31926823G>A	ENSP00000300870:p.Arg418His		31834324	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	37	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	4.243	0.044049	0.08196	.	.	ENSG00000185947	ENST00000300870	T	0.01005	5.45	0.458	-0.616	0.11583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	L	0.35723	1.085	0.09310	N	1	P	0.43542	0.81	B	0.29862	0.108	T	0.50101	-0.8867	9	0.35671	T	0.21	.	3.7552	0.08582	0.6257:0.0:0.3743:0.0	.	418	Q14586	ZN267_HUMAN	H	418	ENSP00000300870:R418H	ENSP00000300870:R418H	R	+	2	0	ZNF267	31834324	0.000000	0.05858	0.026000	0.17262	0.025000	0.11179	-2.107000	0.01337	-0.354000	0.08212	-0.350000	0.07774	CGC		0.363	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		A	31926823	G	A	31926823	3	1	61	1	0	0	0	0	1	0	0	0	17845	1087	38	1	1267	1	ZNF267	16	31926823	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	492317	31926823	58427930	9765	17750										
MYLK3	91807	broad.mit.edu	37	chr16	46766411	46766411	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccttcaggggtctgttCtccgggctcagtcccagggg	15	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:46766411C>A	ENST00000394809.4	-	4	1286	c.1171G>T	c.(1171-1173)Gaa>Taa	p.E391*	MYLK3_ENST00000536476.1_Nonsense_Mutation_p.E50*	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	391					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.E470*(1)|p.E391*(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GGGGTCTGTTCTCCGGGCTCA	0.701																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											26	29	28					16																	46766411		2203	4299	6502	45323912	SO:0001587	stop_gained	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1171G>T	16.37:g.46766411C>A	ENSP00000378288:p.Glu391*		45323912	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Nonsense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	36	5.677979	0.96764	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	.	.	.	5.51	2.23	0.28157	.	1.290410	0.06019	N	0.650942	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	6.4777	0.22045	0.179:0.7003:0.0:0.1207	.	.	.	.	X	391;50	.	ENSP00000378288:E391X	E	-	1	0	MYLK3	45323912	0.000000	0.05858	0.001000	0.08648	0.349000	0.29174	-0.192000	0.09587	0.576000	0.29452	0.655000	0.94253	GAA		0.701	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		A	46766411	C	A	46766411	4	1	61	1	0	0	0	0	0	1	0	0	10088	922	32	2	1328	2	MYLK3	16	46766411	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14839588	46766411	43588342	9766	17751										
C16orf87	388272	broad.mit.edu	37	chr16	46836877	46836877	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagtatcagagaataagtCtttgattgataatttttcta	6	4	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:46836877C>A	ENST00000285697.4	-	4	713	c.452G>T	c.(451-453)aGa>aTa	p.R151I	C16orf87_ENST00000394806.2_Missense_Mutation_p.R90I|C16orf87_ENST00000564250.1_5'Flank	NM_001001436.2	NP_001001436.1	Q6PH81	CP087_HUMAN	chromosome 16 open reading frame 87	151								p.R151I(2)		large_intestine(4)|urinary_tract(1)	5						GAGAATAAGTCTTTGATTGAT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	16											81	80	81					16																	46836877		2203	4298	6501	45394378	SO:0001583	missense	388272				CCDS10724.1	16q11.2	2008-08-08			ENSG00000155330	ENSG00000155330			33754	protein-coding gene	gene with protein product							Standard	NM_001001436		Approved		uc002eek.1	Q6PH81	OTTHUMG00000132538	ENST00000285697.4:c.452G>T	16.37:g.46836877C>A	ENSP00000285697:p.Arg151Ile		45394378	Q63HN9	Missense_Mutation	SNP	ENST00000285697.4	37	CCDS10724.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.248337	0.80024	.	.	ENSG00000155330	ENST00000285697;ENST00000394806	.	.	.	5.8	5.8	0.92144	.	0.042064	0.85682	D	0.000000	T	0.49372	0.1553	N	0.19112	0.55	0.80722	D	1	D	0.59357	0.985	P	0.47827	0.558	T	0.54931	-0.8219	9	0.87932	D	0	.	20.051	0.97627	0.0:1.0:0.0:0.0	.	151	Q6PH81	CP087_HUMAN	I	151;90	.	ENSP00000285697:R151I	R	-	2	0	C16orf87	45394378	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.506000	0.66993	2.740000	0.93945	0.650000	0.86243	AGA		0.368	C16orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255738.2	NM_001001436		A	46836877	C	A	46836877	3	1	61	1	0	0	0	0	1	0	0	0	1844	913	32	2	16	2	C16orf87	16	46836877	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70466	46836877	43517876	9767	17752										
C16orf87	388272	broad.mit.edu	37	chr16	46843615	46843615	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgagacctctttctgttTtctaaatctttatttactgt	4	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:46843615T>G	ENST00000285697.4	-	3	507	c.246A>C	c.(244-246)gaA>gaC	p.E82D	C16orf87_ENST00000394806.2_Intron|C16orf87_ENST00000564250.1_5'UTR	NM_001001436.2	NP_001001436.1	Q6PH81	CP087_HUMAN	chromosome 16 open reading frame 87	82								p.E82D(1)		large_intestine(4)|urinary_tract(1)	5						TCTTTCTGTTTTCTAAATCTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	16											251	226	234					16																	46843615		2203	4300	6503	45401116	SO:0001583	missense	388272				CCDS10724.1	16q11.2	2008-08-08			ENSG00000155330	ENSG00000155330			33754	protein-coding gene	gene with protein product							Standard	NM_001001436		Approved		uc002eek.1	Q6PH81	OTTHUMG00000132538	ENST00000285697.4:c.246A>C	16.37:g.46843615T>G	ENSP00000285697:p.Glu82Asp		45401116	Q63HN9	Missense_Mutation	SNP	ENST00000285697.4	37	CCDS10724.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245504	0.80024	.	.	ENSG00000155330	ENST00000285697	.	.	.	6.06	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.52224	0.1721	N	0.24115	0.695	0.50467	D	0.999872	D	0.58970	0.984	D	0.65443	0.935	T	0.47774	-0.9091	9	0.49607	T	0.09	.	9.3393	0.38069	0.0:0.3341:0.0:0.6659	.	82	Q6PH81	CP087_HUMAN	D	82	.	ENSP00000285697:E82D	E	-	3	2	C16orf87	45401116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.180000	0.32005	0.178000	0.19917	0.528000	0.53228	GAA		0.388	C16orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255738.2	NM_001001436		G	46843615	T	G	46843615	3	3	61	1	0	0	0	0	1	0	0	0	1844	1838	64	4	226	4	C16orf87	16	46843615	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	6738	46843615	43511138	9768	17753										
DNAJA2	10294	broad.mit.edu	37	chr16	46998608	46998608	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccccagtgaatgtaattCtctgtccatgtttcatgcct	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:46998608C>A	ENST00000317089.5	-	6	904	c.689G>T	c.(688-690)aGa>aTa	p.R230I		NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	230					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.R230I(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				GAATGTAATTCTCTGTCCATG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	16											207	193	198					16																	46998608		2203	4300	6503	45556109	SO:0001583	missense	10294			AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"Heat shock proteins / DNAJ (HSP40)"	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.689G>T	16.37:g.46998608C>A	ENSP00000314030:p.Arg230Ile		45556109	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	37	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076893	0.76415	.	.	ENSG00000069345	ENST00000317089	T	0.44482	0.92	6.17	5.13	0.70059	HSP40/DnaJ peptide-binding (1);	0.081748	0.85682	D	0.000000	T	0.53642	0.1809	M	0.85462	2.755	0.80722	D	1	P	0.48998	0.918	P	0.44561	0.453	T	0.64829	-0.6315	10	0.87932	D	0	-18.4225	15.1437	0.72630	0.0:0.9283:0.0:0.0717	.	230	O60884	DNJA2_HUMAN	I	230	ENSP00000314030:R230I	ENSP00000314030:R230I	R	-	2	0	DNAJA2	45556109	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.401000	0.59716	1.463000	0.47967	0.655000	0.94253	AGA		0.423	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2			A	46998608	C	A	46998608	3	1	61	1	0	0	0	0	1	0	0	0	4623	913	32	2	565	2	DNAJA2	16	46998608	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154993	46998608	43356145	9769	17754										
PHKB	5257	broad.mit.edu	37	chr16	47683049	47683049	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagactgtggtttgttacccGattattttcgacctaagtga	9	7	0	2	rs201607512		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:47683049G>A	ENST00000323584.5	+	18	1755	c.1731G>A	c.(1729-1731)ccG>ccA	p.P577P	PHKB_ENST00000455779.1_Silent_p.P570P|PHKB_ENST00000566044.1_Silent_p.P570P|PHKB_ENST00000299167.8_Silent_p.P577P	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	577					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.P577P(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTTGTTACCCGATTATTTTCG	0.363													G|||	1	0.000199681	0	0	5008	,	,		18938	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	16						G	,	0,4402		0,0,2201	180	166	171		1731,1710	1.4	1	16		171	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PHKB	NM_000293.2,NM_001031835.2	,	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,	577/1094,570/1087	47683049	1,13001	2201	4300	6501	46240550	SO:0001819	synonymous_variant	5257				CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1731G>A	16.37:g.47683049G>A			46240550	Q8N4T5	Silent	SNP	ENST00000323584.5	37	CCDS10729.1																																																																																				0.363	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47683049	G	A	47683049	2	1	61	1	0	0	0	0	0	0	0	1	11876	1045	37	1		1	PHKB	16	47683049	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	684441	47683049	42671704	9770	17755										
ABCC12	94160	broad.mit.edu	37	chr16	48122519	48122519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgttcaagttcaggctgtCgagaacaaggggggtgttgt	15	5	2	1	rs372800149		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:48122519C>T	ENST00000311303.3	-	24	3757	c.3412G>A	c.(3412-3414)Gac>Aac	p.D1138N	ABCC12_ENST00000532355.1_5'Flank|ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1138	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.D1138N(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				TTCAGGCTGTCGAGAACAAGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	ASN/ASP	0,4402		0,0,2201	121	106	111		3412	-5.2	0	16		111	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCC12	NM_033226.2	23	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	1138/1360	48122519	1,13001	2201	4300	6501	46680020	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3412G>A	16.37:g.48122519C>T	ENSP00000311030:p.Asp1138Asn		46680020	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	C	2.256	-0.370310	0.05069	0.0	1.16E-4	ENSG00000140798	ENST00000311303	D	0.93953	-3.32	5.73	-5.16	0.02857	ABC transporter-like (1);	0.705245	0.14265	N	0.330553	T	0.82006	0.4943	N	0.12961	0.28	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.68311	-0.5442	10	0.30078	T	0.28	.	7.8666	0.29541	0.0:0.1481:0.3272:0.5247	.	1138	Q96J65	MRP9_HUMAN	N	1138	ENSP00000311030:D1138N	ENSP00000311030:D1138N	D	-	1	0	ABCC12	46680020	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-0.721000	0.04963	-0.744000	0.04778	0.655000	0.94253	GAC		0.517	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48122519	C	T	48122519	3	4	61	1	0	0	0	0	1	0	0	0	52	884	31	1	691	1	ABCC12	16	48122519	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	439470	48122519	42232234	9771	17756										
ABCC12	94160	broad.mit.edu	37	chr16	48145777	48145777	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggttcccttttcacaaatCtctccatcttctaataaaat	3	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:48145777C>A	ENST00000311303.3	-	14	2379	c.2034G>T	c.(2032-2034)gaG>gaT	p.E678D	ABCC12_ENST00000448542.1_Missense_Mutation_p.E678D|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	678	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.E678D(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				TTTCACAAATCTCTCCATCTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	16											110	105	107					16																	48145777		2201	4300	6501	46703278	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2034G>T	16.37:g.48145777C>A	ENSP00000311030:p.Glu678Asp		46703278	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	C	6.329	0.428751	0.11987	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	D;D	0.88277	-2.36;-2.36	5.56	2.44	0.29823	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.176539	0.48286	D	0.000186	T	0.80934	0.4719	L	0.46567	1.45	0.80722	D	1	B	0.20164	0.042	B	0.24394	0.053	T	0.65952	-0.6043	10	0.20046	T	0.44	.	2.8777	0.05636	0.1322:0.4294:0.2871:0.1513	.	678	Q96J65	MRP9_HUMAN	D	678;678;620	ENSP00000311030:E678D;ENSP00000401855:E678D	ENSP00000311030:E678D	E	-	3	2	ABCC12	46703278	0.919000	0.31177	0.995000	0.50966	0.073000	0.16967	0.266000	0.18534	0.259000	0.21709	-0.268000	0.10319	GAG		0.438	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		A	48145777	C	A	48145777	3	1	61	1	0	0	0	0	1	0	0	0	52	912	32	2	2109	2	ABCC12	16	48145777	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23258	48145777	42208976	9772	17757										
ABCC12	94160	broad.mit.edu	37	chr16	48174610	48174610	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcttacctcgccaacagaGatgtgggtcaatgtcttgaa	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:48174610G>T	ENST00000311303.3	-	4	990	c.645C>A	c.(643-645)atC>atA	p.I215I	ABCC12_ENST00000448542.1_Silent_p.I215I|ABCC12_ENST00000416054.1_Silent_p.I215I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	215	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.I215I(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CGCCAACAGAGATGTGGGTCA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	16											120	123	122					16																	48174610		2201	4300	6501	46732111	SO:0001819	synonymous_variant	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.645C>A	16.37:g.48174610G>T			46732111	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																				0.522	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48174610	G	T	48174610	2	4	61	1	0	0	0	0	0	0	0	1	52	932	33	2		2	ABCC12	16	48174610	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28833	48174610	42180143	9773	17758										
ABCC11	85320	broad.mit.edu	37	chr16	48226448	48226448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccttgttgaagagcttgtTgtgcagggccgtggatgcct	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:48226448T>C	ENST00000394747.1	-	19	3038	c.2689A>G	c.(2689-2691)Aac>Gac	p.N897D	ABCC11_ENST00000394748.1_Missense_Mutation_p.N897D|ABCC11_ENST00000537808.1_3'UTR|ABCC11_ENST00000356608.2_Missense_Mutation_p.N897D|ABCC11_ENST00000353782.5_Missense_Mutation_p.N897D	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	897	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)	p.N897D(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	AAGAGCTTGTTGTGCAGGGCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	77	78					16																	48226448		2201	4300	6501	46783949	SO:0001583	missense	85320			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2689A>G	16.37:g.48226448T>C	ENSP00000378230:p.Asn897Asp		46783949	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	T	6.229	0.410301	0.11812	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747	D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5	5.07	0.268	0.15626	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.511393	0.22217	N	0.063007	T	0.77857	0.4193	N	0.25647	0.755	0.80722	D	1	B;B	0.28880	0.009;0.226	B;B	0.34038	0.016;0.174	T	0.62784	-0.6781	10	0.07990	T	0.79	-12.7562	7.6859	0.28540	0.0:0.3373:0.0:0.6627	.	897;897	Q96J66-2;Q96J66	.;ABCCB_HUMAN	D	897	ENSP00000311326:N897D;ENSP00000349017:N897D;ENSP00000378231:N897D;ENSP00000378230:N897D	ENSP00000311326:N897D	N	-	1	0	ABCC11	46783949	0.125000	0.22332	0.252000	0.24328	0.305000	0.27757	-0.606000	0.05654	0.106000	0.17784	0.460000	0.39030	AAC		0.527	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		C	48226448	T	C	48226448	3	2	61	1	0	0	0	0	1	0	0	0	51	1812	63	4	1503	4	ABCC11	16	48226448	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	51838	48226448	42128305	9774	17759										
SIAH1	6477	broad.mit.edu	37	chr16	48396298	48396298	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgggatggtggacacttCgaggtaccggtaggtaatgc	15	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:48396298C>T	ENST00000380006.2	-	1	1495	c.42G>A	c.(40-42)tcG>tcA	p.S14S	SIAH1_ENST00000356721.3_Silent_p.S45S|SIAH1_ENST00000573005.1_5'Flank|SIAH1_ENST00000394725.2_Silent_p.S14S			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	14					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S14S(1)		endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				GTGGACACTTCGAGGTACCGG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	16											84	77	80					16																	48396298		2200	4300	6500	46953799	SO:0001819	synonymous_variant	6477			U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.42G>A	16.37:g.48396298C>T			46953799	A0FKF3|O43269|Q49A58|Q92880	Silent	SNP	ENST00000380006.2	37	CCDS10735.1																																																																																				0.453	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			T	48396298	C	T	48396298	2	4	61	1	0	0	0	0	0	0	0	1	14336	871	31	1		1	SIAH1	16	48396298	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	169850	48396298	41958455	9775	17760										
C16orf78	123970	broad.mit.edu	37	chr16	49430394	49430394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggccaaacccattccgtcGacaaagcattgtcttagatc	8	13	1	1	rs16947350	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49430394G>A	ENST00000299191.3	+	4	572	c.455G>A	c.(454-456)cGa>cAa	p.R152Q		NM_144602.2	NP_653203.1	Q8WTQ4	CP078_HUMAN	chromosome 16 open reading frame 78	152			R -> Q (in dbSNP:rs16947350).			nucleus (GO:0005634)		p.R152Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(1)	22						CCATTCCGTCGACAAAGCATT	0.498													G|||	196	0.0391374	0.143	0.0072	5008	,	,		20913	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16						G	GLN/ARG	562,3836	252.7+/-259.0	31,500,1668	103	94	97		455	2.1	0	16	dbSNP_123	97	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C16orf78	NM_144602.2	43	31,502,5966	AA,AG,GG		0.0233,12.7785,4.3391	probably-damaging	152/266	49430394	564,12434	2199	4300	6499	47987895	SO:0001583	missense	123970			BC021181	CCDS10738.1	16q12.1	2008-02-05			ENSG00000166152	ENSG00000166152			28479	protein-coding gene	gene with protein product						12477932	Standard	NM_144602		Approved	MGC33367	uc002efr.3	Q8WTQ4	OTTHUMG00000133149	ENST00000299191.3:c.455G>A	16.37:g.49430394G>A	ENSP00000299191:p.Arg152Gln		47987895		Missense_Mutation	SNP	ENST00000299191.3	37	CCDS10738.1	58	0.026556776556776556	54	0.10975609756097561	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	18.49	3.636061	0.67130	0.127785	2.33E-4	ENSG00000166152	ENST00000299191	T	0.60171	0.21	5.38	2.14	0.27477	.	0.417296	0.17889	N	0.158593	T	0.00695	0.0023	M	0.67953	2.075	0.09310	N	1	P	0.51057	0.941	B	0.43082	0.407	T	0.00883	-1.1528	9	.	.	.	-19.9266	5.2188	0.15358	0.1843:0.1693:0.6465:0.0	rs16947350;rs52836340;rs57356274;rs16947350	152	Q8WTQ4	CP078_HUMAN	Q	152	ENSP00000299191:R152Q	.	R	+	2	0	C16orf78	47987895	0.000000	0.05858	0.009000	0.14445	0.017000	0.09413	0.249000	0.18216	0.739000	0.32628	0.655000	0.94253	CGA		0.498	C16orf78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256846.1	NM_144602		A	49430394	G	A	49430394	3	1	61	1	0	0	0	0	1	0	0	0	1839	1058	37	1	469	1	C16orf78	16	49430394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1034096	49430394	40924359	9776	17761										
ZNF423	23090	broad.mit.edu	37	chr16	49559343	49559343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctcaatgaggtgacagaGgagcttggccggggagtcga	18	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49559343G>T	ENST00000561648.1	-	6	3693	c.3640C>A	c.(3640-3642)Ctc>Atc	p.L1214I	ZNF423_ENST00000563137.2_Missense_Mutation_p.L1154I|ZNF423_ENST00000562871.1_Missense_Mutation_p.L1154I|ZNF423_ENST00000567169.1_Missense_Mutation_p.L1097I|ZNF423_ENST00000262383.2_Missense_Mutation_p.L1214I|ZNF423_ENST00000535559.1_Missense_Mutation_p.L1097I|ZNF423_ENST00000562520.1_Missense_Mutation_p.L1154I	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	1214					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L1214I(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AGGTGACAGAGGAGCTTGGCC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	16											116	95	102					16																	49559343		2199	4300	6499	48116844	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.3640C>A	16.37:g.49559343G>T	ENSP00000455426:p.Leu1214Ile		48116844	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	18.06	3.539862	0.65085	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.28454	1.61;1.61	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000008	T	0.30916	0.0780	N	0.17082	0.46	0.37885	D	0.930527	D	0.55800	0.973	P	0.55824	0.785	T	0.10590	-1.0623	9	.	.	.	-27.4849	12.4816	0.55847	0.0765:0.0:0.9235:0.0	.	1214	Q2M1K9	ZN423_HUMAN	I	1214;1097	ENSP00000262383:L1214I;ENSP00000442321:L1097I	.	L	-	1	0	ZNF423	48116844	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.491000	0.73649	2.521000	0.84997	0.462000	0.41574	CTC		0.572	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49559343	G	T	49559343	3	4	61	1	0	0	0	0	1	0	0	0	17937	1000	35	2	226	2	ZNF423	16	49559343	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128949	49559343	40795410	9777	17762										
ZNF423	23090	broad.mit.edu	37	chr16	49670461	49670461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctcatggctgttaggtgCctcagggttcttaagcagca	13	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49670461C>T	ENST00000561648.1	-	4	2655	c.2602G>A	c.(2602-2604)Gca>Aca	p.A868T	ZNF423_ENST00000563137.2_Missense_Mutation_p.A808T|ZNF423_ENST00000562871.1_Missense_Mutation_p.A808T|ZNF423_ENST00000567169.1_Missense_Mutation_p.A751T|ZNF423_ENST00000262383.2_Missense_Mutation_p.A868T|ZNF423_ENST00000535559.1_Missense_Mutation_p.A751T|ZNF423_ENST00000562520.1_Missense_Mutation_p.A808T	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	868					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A868T(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				CTGTTAGGTGCCTCAGGGTTC	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	16											76	67	70					16																	49670461		2198	4300	6498	48227962	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2602G>A	16.37:g.49670461C>T	ENSP00000455426:p.Ala868Thr		48227962	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	5.400	0.259046	0.10239	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08546	3.08;3.12	4.66	4.66	0.58398	.	0.348047	0.33290	N	0.005066	T	0.05090	0.0136	N	0.17082	0.46	0.30328	N	0.786939	B	0.02656	0.0	B	0.04013	0.001	T	0.19614	-1.0300	9	.	.	.	-22.0685	9.0893	0.36601	0.0:0.8605:0.0:0.1395	.	868	Q2M1K9	ZN423_HUMAN	T	868;751	ENSP00000262383:A868T;ENSP00000442321:A751T	.	A	-	1	0	ZNF423	48227962	0.129000	0.22400	0.984000	0.44739	0.189000	0.23516	0.115000	0.15540	2.153000	0.67306	0.561000	0.74099	GCA		0.622	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49670461	C	T	49670461	3	4	61	1	0	0	0	0	1	0	0	0	17937	739	26	3	1272	3	ZNF423	16	49670461	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111118	49670461	40684292	9778	17763										
ZNF423	23090	broad.mit.edu	37	chr16	49670971	49670971	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgaggaaaattgcttgtCgcagctctcgcacacatagt	9	12	1	0	rs148732968		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49670971C>T	ENST00000561648.1	-	4	2145	c.2092G>A	c.(2092-2094)Gac>Aac	p.D698N	ZNF423_ENST00000563137.2_Missense_Mutation_p.D638N|ZNF423_ENST00000562871.1_Missense_Mutation_p.D638N|ZNF423_ENST00000567169.1_Missense_Mutation_p.D581N|ZNF423_ENST00000262383.2_Missense_Mutation_p.D698N|ZNF423_ENST00000535559.1_Missense_Mutation_p.D581N|ZNF423_ENST00000562520.1_Missense_Mutation_p.D638N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	698					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D698N(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AATTGCTTGTCGCAGCTCTCG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	16						C	ASN/ASP	0,4396		0,0,2198	95	94	94		2092	4.8	1	16	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF423	NM_015069.2	23	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	698/1285	49670971	1,12995	2198	4300	6498	48228472	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2092G>A	16.37:g.49670971C>T	ENSP00000455426:p.Asp698Asn		48228472	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.138002	0.37728	0.0	1.16E-4	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.52057	0.68;0.68	4.79	4.79	0.61399	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	N	0.21583	0.68	0.53005	D	0.99996	D	0.89917	1.0	D	0.85130	0.997	T	0.54510	-0.8283	9	.	.	.	.	17.8561	0.88764	0.0:1.0:0.0:0.0	.	698	Q2M1K9	ZN423_HUMAN	N	698;581	ENSP00000262383:D698N;ENSP00000442321:D581N	.	D	-	1	0	ZNF423	48228472	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.089000	0.71384	2.212000	0.71576	0.561000	0.74099	GAC		0.557	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49670971	C	T	49670971	3	4	61	1	0	0	0	0	1	0	0	0	17937	884	31	1	1782	1	ZNF423	16	49670971	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	510	49670971	40683782	9779	17764										
ZNF423	23090	broad.mit.edu	37	chr16	49671592	49671592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgcaggctattgatgtCggcgaacatctcggggcagt	13	11	1	1	rs138661785		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49671592C>T	ENST00000561648.1	-	4	1524	c.1471G>A	c.(1471-1473)Gac>Aac	p.D491N	ZNF423_ENST00000563137.2_Missense_Mutation_p.D431N|ZNF423_ENST00000562871.1_Missense_Mutation_p.D431N|ZNF423_ENST00000567169.1_Missense_Mutation_p.D374N|ZNF423_ENST00000262383.2_Missense_Mutation_p.D491N|ZNF423_ENST00000535559.1_Missense_Mutation_p.D374N|ZNF423_ENST00000562520.1_Missense_Mutation_p.D431N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	491					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D491N(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				CTATTGATGTCGGCGAACATC	0.562													C|||	1	0.000199681	0	0	5008	,	,		21693	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	16						C	ASN/ASP	2,4394	2.1+/-5.4	0,2,2196	105	90	95		1471	4.8	0.9	16	dbSNP_134	95	0,8600		0,0,4300	no	missense	ZNF423	NM_015069.2	23	0,2,6496	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	491/1285	49671592	2,12994	2198	4300	6498	48229093	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1471G>A	16.37:g.49671592C>T	ENSP00000455426:p.Asp491Asn		48229093	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.26	2.779441	0.49891	4.55E-4	0.0	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.27720	1.65;1.65	4.81	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.41396	0.1157	L	0.28694	0.88	0.46901	D	0.999247	D	0.65815	0.995	P	0.62382	0.901	T	0.16660	-1.0395	9	.	.	.	.	17.895	0.88885	0.0:1.0:0.0:0.0	.	491	Q2M1K9	ZN423_HUMAN	N	491;374	ENSP00000262383:D491N;ENSP00000442321:D374N	.	D	-	1	0	ZNF423	48229093	1.000000	0.71417	0.929000	0.37066	0.980000	0.70556	7.818000	0.86416	2.216000	0.71823	0.561000	0.74099	GAC		0.562	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671592	C	T	49671592	3	4	61	1	0	0	0	0	1	0	0	0	17937	884	31	1	2403	1	ZNF423	16	49671592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	621	49671592	40683161	9780	17765										
ZNF423	23090	broad.mit.edu	37	chr16	49672433	49672433	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgggtcttcaggtggatCttgaggtggtcgctgcggga	18	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:49672433C>A	ENST00000561648.1	-	4	683	c.630G>T	c.(628-630)aaG>aaT	p.K210N	ZNF423_ENST00000563137.2_Missense_Mutation_p.K150N|ZNF423_ENST00000562871.1_Missense_Mutation_p.K150N|ZNF423_ENST00000567169.1_Missense_Mutation_p.K93N|ZNF423_ENST00000262383.2_Missense_Mutation_p.K210N|ZNF423_ENST00000535559.1_Missense_Mutation_p.K93N|ZNF423_ENST00000562520.1_Missense_Mutation_p.K150N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	210					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K210N(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TCAGGTGGATCTTGAGGTGGT	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	16											68	49	55					16																	49672433		2198	4300	6498	48229934	SO:0001583	missense	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.630G>T	16.37:g.49672433C>A	ENSP00000455426:p.Lys210Asn		48229934	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.611925	0.46631	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08102	3.13;3.13	5.0	5.0	0.66597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.12178	0.0296	N	0.13140	0.3	0.39736	D	0.971674	D	0.89917	1.0	D	0.91635	0.999	T	0.26710	-1.0095	9	.	.	.	.	8.8727	0.35325	0.0:0.8268:0.0:0.1732	.	210	Q2M1K9	ZN423_HUMAN	N	210;93	ENSP00000262383:K210N;ENSP00000442321:K93N	.	K	-	3	2	ZNF423	48229934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.111000	0.50360	2.331000	0.79229	0.561000	0.74099	AAG		0.612	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49672433	C	A	49672433	3	1	61	1	0	0	0	0	1	0	0	0	17937	912	32	2	3244	2	ZNF423	16	49672433	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	841	49672433	40682320	9781	17766										
HEATR3	55027	broad.mit.edu	37	chr16	50136224	50136224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatccttcccttgtggtaGcaggagaagctttggatgcc	12	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50136224G>A	ENST00000299192.7	+	14	1989	c.1798G>A	c.(1798-1800)Gca>Aca	p.A600T	HEATR3_ENST00000285767.4_Missense_Mutation_p.A514T|RP11-429P3.5_ENST00000566770.1_RNA	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	600								p.A600T(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CCTTGTGGTAGCAGGAGAAGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	16											187	167	174					16																	50136224		2198	4300	6498	48693725	SO:0001583	missense	55027			BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1798G>A	16.37:g.50136224G>A	ENSP00000299192:p.Ala600Thr		48693725	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Missense_Mutation	SNP	ENST00000299192.7	37	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842589	0.32606	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	T;T	0.64618	-0.11;-0.11	5.49	3.48	0.39840	Armadillo-type fold (1);	0.425256	0.28766	N	0.014210	T	0.36358	0.0964	N	0.11560	0.145	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.11329	0.006;0.001	T	0.13791	-1.0496	10	0.16420	T	0.52	.	7.1747	0.25738	0.1438:0.0:0.7178:0.1383	.	514;600	B7WNW7;Q7Z4Q2	.;HEAT3_HUMAN	T	514;600	ENSP00000285767:A514T;ENSP00000299192:A600T	ENSP00000285767:A514T	A	+	1	0	HEATR3	48693725	0.894000	0.30519	0.875000	0.34327	0.998000	0.95712	2.176000	0.42500	1.427000	0.47276	0.650000	0.86243	GCA		0.398	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		A	50136224	G	A	50136224	3	1	61	1	0	0	0	0	1	0	0	0	7050	971	34	3	1852	3	HEATR3	16	50136224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	463791	50136224	40218529	9782	17767										
HEATR3	55027	broad.mit.edu	37	chr16	50136320	50136320	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattattatctgctctgaaaGaattccagccggtctttaaa	6	8	3	2	rs149086832		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50136320G>T	ENST00000299192.7	+	14	2085	c.1894G>T	c.(1894-1896)Gaa>Taa	p.E632*	HEATR3_ENST00000285767.4_Nonsense_Mutation_p.E546*|RP11-429P3.5_ENST00000566770.1_RNA	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	632								p.E632*(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGCTCTGAAAGAATTCCAGCC	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											65	70	69					16																	50136320		2198	4300	6498	48693821	SO:0001587	stop_gained	55027			BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1894G>T	16.37:g.50136320G>T	ENSP00000299192:p.Glu632*		48693821	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Nonsense_Mutation	SNP	ENST00000299192.7	37	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	39	7.734084	0.98459	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	5.39	5.39	0.77823	.	0.210292	0.49916	D	0.000131	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	12.8304	0.57742	0.0751:0.0:0.9249:0.0	.	.	.	.	X	546;632	.	ENSP00000285767:E546X	E	+	1	0	HEATR3	48693821	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.446000	0.73460	2.697000	0.92050	0.650000	0.86243	GAA		0.398	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		T	50136320	G	T	50136320	4	4	61	1	0	0	0	0	0	1	0	0	7050	943	33	2	1948	2	HEATR3	16	50136320	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96	50136320	40218433	9783	17768										
ADCY7	113	broad.mit.edu	37	chr16	50343497	50343497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttccagagctgcctgttggCaatgagacaggcctactggc	13	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50343497C>T	ENST00000394697.2	+	18	2440	c.2100C>T	c.(2098-2100)ggC>ggT	p.G700G	ADCY7_ENST00000537579.1_3'UTR|ADCY7_ENST00000538642.1_Silent_p.G700G|ADCY7_ENST00000254235.3_Silent_p.G700G|ADCY7_ENST00000566433.2_Silent_p.G700G			P51828	ADCY7_HUMAN	adenylate cyclase 7	700					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.G700G(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TGCCTGTTGGCAATGAGACAG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	16											55	53	54					16																	50343497		2198	4300	6498	48900998	SO:0001819	synonymous_variant	113			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2100C>T	16.37:g.50343497C>T			48900998	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																				0.622	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50343497	C	T	50343497	2	4	61	1	0	0	0	0	0	0	0	1	299	697	25	3		3	ADCY7	16	50343497	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	207177	50343497	40011256	9784	17769										
ADCY7	113	broad.mit.edu	37	chr16	50346004	50346004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagttcaagaaggagcacGaggagtttgagaccatggag	15	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50346004G>A	ENST00000394697.2	+	21	2846	c.2506G>A	c.(2506-2508)Gag>Aag	p.E836K	ADCY7_ENST00000254235.3_Missense_Mutation_p.E836K			P51828	ADCY7_HUMAN	adenylate cyclase 7	836					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.E836K(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		GAAGGAGCACGAGGAGTTTGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											113	105	107					16																	50346004		2198	4300	6498	48903505	SO:0001583	missense	113			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2506G>A	16.37:g.50346004G>A	ENSP00000378187:p.Glu836Lys		48903505	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	37	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	G	34	5.399310	0.96030	.	.	ENSG00000121281	ENST00000394697;ENST00000254235	D;D	0.83755	-1.76;-1.76	4.77	4.77	0.60923	.	0.000000	0.44688	U	0.000440	D	0.90328	0.6974	M	0.74389	2.26	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.89808	0.3980	10	0.40728	T	0.16	.	17.9745	0.89123	0.0:0.0:1.0:0.0	.	836	P51828	ADCY7_HUMAN	K	836	ENSP00000378187:E836K;ENSP00000254235:E836K	ENSP00000254235:E836K	E	+	1	0	ADCY7	48903505	1.000000	0.71417	0.976000	0.42696	0.993000	0.82548	9.657000	0.98554	2.470000	0.83445	0.462000	0.41574	GAG		0.532	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			A	50346004	G	A	50346004	3	1	61	1	0	0	0	0	1	0	0	0	299	1059	37	1	2584	1	ADCY7	16	50346004	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2507	50346004	40008749	9785	17770										
NKD1	85407	broad.mit.edu	37	chr16	50666240	50666240	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggctgctaccaccattgCgtagatgagaacatcgagag	11	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50666240C>T	ENST00000268459.3	+	9	968	c.744C>T	c.(742-744)tgC>tgT	p.C248C		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	248					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C248C(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		ACCACCATTGCGTAGATGAGA	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	16											90	72	78					16																	50666240		2198	4300	6498	49223741	SO:0001819	synonymous_variant	85407			AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"EF-hand domain containing"	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.744C>T	16.37:g.50666240C>T			49223741	B2RC39|Q8WZ08	Silent	SNP	ENST00000268459.3	37	CCDS10743.1																																																																																				0.567	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			T	50666240	C	T	50666240	2	4	61	1	0	0	0	0	0	0	0	1	10472	776	27	1		1	NKD1	16	50666240	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	320236	50666240	39688513	9786	17771										
NOD2	64127	broad.mit.edu	37	chr16	50746277	50746277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgccttggtgtctgcaagGctctgtagtgagtgttactg	13	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50746277G>A	ENST00000300589.2	+	4	2560	c.2455G>A	c.(2455-2457)Gct>Act	p.A819T	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	819					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.A819T(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TGTCTGCAAGGCTCTGTAGTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	113	111					16																	50746277		2198	4300	6498	49303778	SO:0001583	missense	64127			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2455G>A	16.37:g.50746277G>A	ENSP00000300589:p.Ala819Thr		49303778	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.59|19.59	3.856089|3.856089	0.71834|0.71834	.|.	.|.	ENSG00000167207|ENSG00000167207	ENST00000526417;ENST00000300589|ENST00000534057	T|.	0.49139|.	0.79|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.074217|.	0.53938|.	D|.	0.000049|.	T|T	0.56381|0.56381	0.1981|0.1981	L|L	0.31752|0.31752	0.955|0.955	0.38611|0.38611	D|D	0.950907|0.950907	D;D;D|.	0.89917|.	1.0;0.991;1.0|.	D;P;D|.	0.87578|.	0.997;0.853;0.998|.	T|T	0.55829|0.55829	-0.8079|-0.8079	10|5	0.21540|.	T|.	0.41|.	.|.	16.4535|16.4535	0.84003|0.84003	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	603;792;819|.	D6CHF9;Q9HC29-2;Q9HC29|.	.;.;NOD2_HUMAN|.	T|D	792;819|58	ENSP00000300589:A819T|.	ENSP00000300589:A819T|.	A|G	+|+	1|2	0|0	NOD2|NOD2	49303778|49303778	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	4.117000|4.117000	0.57877|0.57877	2.480000|2.480000	0.83734|0.83734	0.561000|0.561000	0.74099|0.74099	GCT|GGC		0.612	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50746277	G	A	50746277	3	1	61	1	0	0	0	0	1	0	0	0	10548	1203	42	3	2469	3	NOD2	16	50746277	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80037	50746277	39608476	9787	17772										
NOD2	64127	broad.mit.edu	37	chr16	50750503	50750503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttgtctctttagtttgcGcgataacaatatctcagacc	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50750503G>A	ENST00000300589.2	+	5	2573	c.2468G>A	c.(2467-2469)cGc>cAc	p.R823H		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	823					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.R823H(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TTTAGTTTGCGCGATAACAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	16											70	64	66					16																	50750503		2198	4300	6498	49308004	SO:0001583	missense	64127			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2468G>A	16.37:g.50750503G>A	ENSP00000300589:p.Arg823His		49308004	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495269	0.85069	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.54479	0.57	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000003	T	0.73505	0.3595	M	0.80746	2.51	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.73652	-0.3915	10	0.44086	T	0.13	.	15.4789	0.75508	0.0:0.0:1.0:0.0	.	796;823	Q9HC29-2;Q9HC29	.;NOD2_HUMAN	H	796;823	ENSP00000300589:R823H	ENSP00000300589:R823H	R	+	2	0	NOD2	49308004	1.000000	0.71417	0.980000	0.43619	0.747000	0.42532	5.080000	0.64437	2.719000	0.93026	0.555000	0.69702	CGC		0.408	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50750503	G	A	50750503	3	1	61	1	0	0	0	0	1	0	0	0	10548	1087	38	1	2486	1	NOD2	16	50750503	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4226	50750503	39604250	9788	17773										
CYLD	1540	broad.mit.edu	37	chr16	50783748	50783748	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtaccgaagggaagtataGgacagtatattcaagatcgt	11	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50783748G>T	ENST00000427738.3	+	2	344	c.139G>T	c.(139-141)Gga>Tga	p.G47*	CYLD_ENST00000540145.1_Nonsense_Mutation_p.G47*|CYLD_ENST00000569418.1_Nonsense_Mutation_p.G47*|CYLD_ENST00000566206.1_Nonsense_Mutation_p.G47*|CYLD_ENST00000564326.1_Nonsense_Mutation_p.G47*|CYLD_ENST00000568704.2_Nonsense_Mutation_p.G47*|CYLD_ENST00000398568.2_Nonsense_Mutation_p.G47*|CYLD_ENST00000311559.9_Nonsense_Mutation_p.G47*			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	47					cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.G47*(1)		central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				GGGAAGTATAGGACAGTATAT	0.403			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	1	Substitution - Nonsense(1)	large_intestine(1)	16											107	102	104					16																	50783748		1855	4094	5949	49341249	SO:0001587	stop_gained	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.139G>T	16.37:g.50783748G>T	ENSP00000392025:p.Gly47*		49341249	O94934|Q7L3N6|Q96EH0|Q9NZX9	Nonsense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474069	0.63737	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	.	.	.	5.87	5.87	0.94306	.	0.052737	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.5314	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	X	47	.	ENSP00000308928:G47X	G	+	1	0	CYLD	49341249	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	7.262000	0.78410	2.941000	0.99782	0.655000	0.94253	GGA		0.403	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			T	50783748	G	T	50783748	4	4	61	1	0	0	0	0	0	1	0	0	4149	1001	35	2	141	2	CYLD	16	50783748	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33245	50783748	39571005	9789	17774										
CYLD	1540	broad.mit.edu	37	chr16	50828330	50828330	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctttgacagcatggccGatcgggatggtactgaaaac	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:50828330G>A	ENST00000427738.3	+	17	2882	c.2677G>A	c.(2677-2679)Gat>Aat	p.D893N	CYLD_ENST00000540145.1_Missense_Mutation_p.D893N|CYLD_ENST00000569418.1_Missense_Mutation_p.D890N|CYLD_ENST00000566206.1_Missense_Mutation_p.D890N|CYLD_ENST00000564326.1_Missense_Mutation_p.D890N|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000568704.2_Missense_Mutation_p.D708N|CYLD_ENST00000398568.2_Missense_Mutation_p.D890N|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000311559.9_Missense_Mutation_p.D893N			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	893	USP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.D893N(1)		central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CAGCATGGCCGATCGGGATGG	0.473			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	1	Substitution - Missense(1)	large_intestine(1)	16											160	155	157					16																	50828330		1969	4172	6141	49385831	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.2677G>A	16.37:g.50828330G>A	ENSP00000392025:p.Asp893Asn		49385831	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227095	0.95173	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.37915	1.17;1.17;1.17	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.64735	0.2625	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.66520	-0.5903	10	0.87932	D	0	-24.8294	20.1615	0.98135	0.0:0.0:1.0:0.0	.	890;890	A8KAB0;Q9NQC7-2	.;.	N	893;893;890;890	ENSP00000445447:D893N;ENSP00000308928:D893N;ENSP00000381574:D890N	ENSP00000308928:D893N	D	+	1	0	CYLD	49385831	1.000000	0.71417	0.507000	0.27676	0.912000	0.54170	9.361000	0.97122	2.835000	0.97688	0.650000	0.86243	GAT		0.473	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			A	50828330	G	A	50828330	3	1	61	1	0	0	0	0	1	0	0	0	4149	1058	37	1	2739	1	CYLD	16	50828330	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44582	50828330	39526423	9790	17775										
SALL1	6299	broad.mit.edu	37	chr16	51173681	51173681	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagttgtctaggtcatcaaAatttttctcatcaaaggaac	7	7	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:51173681A>C	ENST00000251020.4	-	2	2485	c.2452T>G	c.(2452-2454)Ttt>Gtt	p.F818V	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.F721V|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	818					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F818V(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AGGTCATCAAAATTTTTCTCA	0.502																																					GBM(103;1352 1446 1855 4775 8890)											1	Substitution - Missense(1)	large_intestine(1)	16											130	138	135					16																	51173681		2198	4300	6498	49731182	SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2452T>G	16.37:g.51173681A>C	ENSP00000251020:p.Phe818Val		49731182	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.782621	0.00079	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.06608	3.28;3.28	5.2	5.2	0.72013	.	0.148969	0.64402	D	0.000009	T	0.05640	0.0148	L	0.36672	1.1	0.49389	D	0.999786	B	0.13594	0.008	B	0.08055	0.003	T	0.35968	-0.9767	10	0.14656	T	0.56	.	10.3705	0.44051	0.8537:0.0:0.0:0.1463	.	818	Q9NSC2	SALL1_HUMAN	V	818;721;782	ENSP00000251020:F818V;ENSP00000407914:F721V	ENSP00000251020:F818V	F	-	1	0	SALL1	49731182	1.000000	0.71417	0.979000	0.43373	0.077000	0.17291	2.768000	0.47645	1.976000	0.57569	0.248000	0.18094	TTT		0.502	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51173681	A	C	51173681	3	2	61	1	0	0	0	0	1	0	0	0	13847	14	1	4	1530	4	SALL1	16	51173681	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	345351	51173681	39181072	9791	17776										
SALL1	6299	broad.mit.edu	37	chr16	51175392	51175392	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggtgacgaatctgttcGatcaattgcagctggtggat	12	6	2	1	rs372297077		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:51175392G>A	ENST00000251020.4	-	2	774	c.741C>T	c.(739-741)atC>atT	p.I247I	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.I150I|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	247					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I247I(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAATCTGTTCGATCAATTGCA	0.542																																					GBM(103;1352 1446 1855 4775 8890)											1	Substitution - coding silent(1)	large_intestine(1)	16						G	,	1,4395	2.1+/-5.4	0,1,2197	83	86	85		450,741	1.9	1	16		85	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	150/1228,247/1325	51175392	1,12995	2198	4300	6498	49732893	SO:0001819	synonymous_variant	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.741C>T	16.37:g.51175392G>A			49732893	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																				0.542	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51175392	G	A	51175392	2	1	61	1	0	0	0	0	0	0	0	1	13847	1048	37	1		1	SALL1	16	51175392	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1711	51175392	39179361	9792	17777										
CHD9	80205	broad.mit.edu	37	chr16	53260363	53260363	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagaagaggttaaaggttCtatgaaaataaaaaagaatt	9	1	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53260363C>A	ENST00000398510.3	+	4	2069	c.1982C>A	c.(1981-1983)tCt>tAt	p.S661Y	CHD9_ENST00000566029.1_Missense_Mutation_p.S661Y|CHD9_ENST00000447540.1_Missense_Mutation_p.S661Y|CHD9_ENST00000564845.1_Missense_Mutation_p.S661Y			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	661	Lys-rich.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.S661Y(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GTTAAAGGTTCTATGAAAATA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	16											101	101	101					16																	53260363		1806	4068	5874	51817864	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.1982C>A	16.37:g.53260363C>A	ENSP00000381522:p.Ser661Tyr		51817864	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	C	14.76	2.631924	0.46944	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	T;T	0.65549	-0.16;-0.16	5.39	4.42	0.53409	.	0.220254	0.32055	N	0.006652	T	0.60470	0.2271	L	0.44542	1.39	0.09310	N	1	B;D;P;P	0.53312	0.186;0.959;0.79;0.867	B;P;B;B	0.49561	0.141;0.615;0.202;0.367	T	0.56007	-0.8050	10	0.62326	D	0.03	-4.6184	10.732	0.46102	0.1439:0.7083:0.1478:0.0	.	187;661;661;661	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	Y	661;661;187	ENSP00000396345:S661Y;ENSP00000381522:S661Y	ENSP00000219084:S187Y	S	+	2	0	CHD9	51817864	0.940000	0.31905	0.153000	0.22517	0.688000	0.40055	1.829000	0.39121	1.234000	0.43709	0.655000	0.94253	TCT		0.318	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53260363	C	A	53260363	3	1	61	1	0	0	0	0	1	0	0	0	3338	913	32	2	1996	2	CHD9	16	53260363	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2084971	53260363	37094390	9793	17778										
CHD9	80205	broad.mit.edu	37	chr16	53342703	53342703	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagtacctcactcggcttCgagagcttcaaagtgcatca	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53342703C>T	ENST00000398510.3	+	33	7246	c.7159C>T	c.(7159-7161)Cga>Tga	p.R2387*	CHD9_ENST00000566029.1_Nonsense_Mutation_p.R2371*|CHD9_ENST00000447540.1_Nonsense_Mutation_p.R2372*|CHD9_ENST00000564845.1_Nonsense_Mutation_p.R2371*			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2387	Binds A/T-rich DNA.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R2388*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CACTCGGCTTCGAGAGCTTCA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											68	69	69					16																	53342703		1938	4154	6092	51900204	SO:0001587	stop_gained	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.7159C>T	16.37:g.53342703C>T	ENSP00000381522:p.Arg2387*		51900204	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Nonsense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	C	49	15.469321	0.99835	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	.	.	.	5.6	5.6	0.85130	.	0.000000	0.52532	D	0.000068	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.25	19.6229	0.95667	0.0:1.0:0.0:0.0	.	.	.	.	X	2372;2371;453	.	ENSP00000381522:R2371X	R	+	1	2	CHD9	51900204	1.000000	0.71417	0.992000	0.48379	0.818000	0.46254	7.415000	0.80131	2.648000	0.89879	0.561000	0.74099	CGA		0.443	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		T	53342703	C	T	53342703	4	4	61	1	0	0	0	0	0	1	0	0	3338	876	31	1	7241	1	CHD9	16	53342703	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82340	53342703	37012050	9794	17779										
CHD9	80205	broad.mit.edu	37	chr16	53358659	53358659	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagaagaagattccagaaTtaaagatcaggaagacaaag	9	4	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53358659T>G	ENST00000398510.3	+	38	8633	c.8546T>G	c.(8545-8547)aTt>aGt	p.I2849S	CHD9_ENST00000566029.1_Missense_Mutation_p.I2833S|CHD9_ENST00000447540.1_Missense_Mutation_p.I2834S|CHD9_ENST00000564845.1_Missense_Mutation_p.I2833S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2849					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.I2850T(1)|p.I2850S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GATTCCAGAATTAAAGATCAG	0.393																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	16											50	45	46					16																	53358659		1843	4086	5929	51916160	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8546T>G	16.37:g.53358659T>G	ENSP00000381522:p.Ile2849Ser		51916160	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	T	0.175	-1.068176	0.01934	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.84944	-1.92	5.16	-1.88	0.07713	.	0.803304	0.10604	N	0.655262	T	0.67627	0.2913	N	0.08118	0	0.23174	N	0.998171	P;B;P;B	0.49447	0.495;0.003;0.924;0.003	B;B;B;B	0.43809	0.09;0.006;0.432;0.006	T	0.61584	-0.7033	10	0.16420	T	0.52	0.2066	7.9714	0.30130	0.0:0.1292:0.4786:0.3922	.	915;2834;2849;2833	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	S	2834;2833;915	ENSP00000396345:I2834S	ENSP00000381522:I2833S	I	+	2	0	CHD9	51916160	0.987000	0.35691	0.914000	0.36105	0.945000	0.59286	0.277000	0.18734	-0.593000	0.05844	-0.256000	0.11100	ATT		0.393	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53358659	T	G	53358659	3	3	61	1	0	0	0	0	1	0	0	0	3338	1493	52	4	8648	4	CHD9	16	53358659	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	15956	53358659	36996094	9795	17780										
AKTIP	64400	broad.mit.edu	37	chr16	53528084	53528087	+	Frame_Shift_Del	DEL	CAAA	CAAA	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttctattttaggttggtCaaacaaacgagcagtgcaca							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CAAA	CAAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53528084_53528087delCAAA	ENST00000394657.7	-	8	847_850	c.673_676delTTTG	c.(673-678)tttgacfs	p.FD225fs	AKTIP_ENST00000300245.4_Frame_Shift_Del_p.FD225fs|AKTIP_ENST00000570004.1_Frame_Shift_Del_p.FD225fs	NM_001012398.1|NM_022476.2	NP_001012398.1|NP_071921.1	Q9H8T0	AKTIP_HUMAN	AKT interacting protein	225					apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031)	FHF complex (GO:0070695)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)	p.F225fs*5(1)		large_intestine(1)|lung(2)|prostate(2)	5		all_cancers(37;0.14)				TTAGGTTGGTCAAACAAACGAGCA	0.387																																																1	Deletion - Frameshift(1)	large_intestine(1)	16																																								52085588	SO:0001589	frameshift_variant	64400			AK023320	CCDS10749.1	16q12.2	2010-01-14	2007-01-16	2007-01-16	ENSG00000166971	ENSG00000166971		"Ubiquitin-conjugating enzymes E2"	16710	protein-coding gene	gene with protein product		608483	"fused toes (mouse) homolog", "fused toes homolog (mouse)"	FTS		7818539, 8626685	Standard	XM_005256094		Approved	FLJ13258	uc002ehl.3	Q9H8T0	OTTHUMG00000133199	ENST00000394657.7:c.673_676delTTTG	16.37:g.53528088_53528091delCAAA	ENSP00000378152:p.Phe225fs		52085585	Q503B1|Q53H38	Frame_Shift_Del	DEL	ENST00000394657.7	37	CCDS10749.1																																																																																				0.387	AKTIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256909.4	NM_022476		-	53528087	CAAA	-	53528084	7	5	61	1	0	1	0	1	0	0	0	0	482	826	29	0	214	0	AKTIP	16	53528084	Frame_Shift_Del	DEL	CAAA	TCGA-AG-A002-01A-01W-A00K-09	169425	53528084	36826669	9796	17781										
RPGRIP1L	23322	broad.mit.edu	37	chr16	53639521	53639521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcactgaccacggtgaagCgaaggctggtaaggcagaga	16	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53639521C>T	ENST00000379925.3	-	26	3757	c.3707G>A	c.(3706-3708)cGc>cAc	p.R1236H	RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.R1190H|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.R1202H|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.R1156H	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1236			R -> C (in MKS5; dbSNP:rs151332923). {ECO:0000269|PubMed:19430481}.		camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.R1236H(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CACGGTGAAGCGAAGGCTGGT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	16											88	72	78					16																	53639521		2198	4300	6498	52197022	SO:0001583	missense	23322				CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3707G>A	16.37:g.53639521C>T	ENSP00000369257:p.Arg1236His		52197022	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972987	0.74246	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.70749	-0.51;-0.51	5.81	5.81	0.92471	.	0.069655	0.64402	D	0.000018	T	0.75591	0.3870	L	0.43152	1.355	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.999	D;D;P;P	0.65874	0.939;0.939;0.794;0.899	T	0.76785	-0.2831	10	0.72032	D	0.01	-6.6825	9.0708	0.36491	0.1481:0.7774:0.0:0.0745	.	1190;1190;1236;1156	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	H	1236;1156	ENSP00000369257:R1236H;ENSP00000262135:R1156H	ENSP00000262135:R1156H	R	-	2	0	RPGRIP1L	52197022	0.998000	0.40836	1.000000	0.80357	0.755000	0.42902	1.631000	0.37092	2.752000	0.94435	0.557000	0.71058	CGC		0.522	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		T	53639521	C	T	53639521	3	4	61	1	0	0	0	0	1	0	0	0	13587	768	27	1	248	1	RPGRIP1L	16	53639521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111437	53639521	36715232	9797	17782										
RPGRIP1L	23322	broad.mit.edu	37	chr16	53674994	53674994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagataccttcttatctacaGgtgttaaacgttgtcttggt	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53674994G>T	ENST00000379925.3	-	19	2959	c.2909C>A	c.(2908-2910)cCt>cAt	p.P970H	RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.P970H|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.P970H|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.P970H|RPGRIP1L_ENST00000568009.1_5'Flank	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	970					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.P970H(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CTTATCTACAGGTGTTAAACG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	16											121	99	107					16																	53674994		2198	4300	6498	52232495	SO:0001583	missense	23322				CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.2909C>A	16.37:g.53674994G>T	ENSP00000369257:p.Pro970His		52232495	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	G	3.605	-0.080840	0.07141	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.77098	-0.85;-1.07	5.16	1.78	0.24846	.	0.791890	0.11807	N	0.527560	T	0.56202	0.1969	N	0.12182	0.205	0.09310	N	1	B;B;B;B	0.09022	0.0;0.001;0.002;0.001	B;B;B;B	0.11329	0.003;0.002;0.003;0.006	T	0.43228	-0.9404	10	0.37606	T	0.19	-0.317	3.8791	0.09071	0.0874:0.1366:0.5287:0.2473	.	970;970;970;970	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	H	970	ENSP00000369257:P970H;ENSP00000262135:P970H	ENSP00000262135:P970H	P	-	2	0	RPGRIP1L	52232495	0.002000	0.14202	0.010000	0.14722	0.956000	0.61745	0.875000	0.28079	0.606000	0.29965	0.591000	0.81541	CCT		0.353	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		T	53674994	G	T	53674994	3	4	61	1	0	0	0	0	1	0	0	0	13587	1000	35	2	1074	2	RPGRIP1L	16	53674994	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35473	53674994	36679759	9798	17783										
RPGRIP1L	23322	broad.mit.edu	37	chr16	53682950	53682950	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccctttctcgataaagtcGaattgcttgatccatgggaa	9	9	1	1	rs267604575		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53682950G>A	ENST00000379925.3	-	16	2280	c.2230C>T	c.(2230-2232)Cga>Tga	p.R744*	RPGRIP1L_ENST00000564374.1_Nonsense_Mutation_p.R744*|RPGRIP1L_ENST00000563746.1_Nonsense_Mutation_p.R744*|RPGRIP1L_ENST00000262135.4_Nonsense_Mutation_p.R744*	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	744			R -> Q (in dbSNP:rs2302677).		camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.R744*(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CGATAAAGTCGAATTGCTTGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											127	116	120					16																	53682950		2198	4300	6498	52240451	SO:0001587	stop_gained	23322				CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.2230C>T	16.37:g.53682950G>A	ENSP00000369257:p.Arg744*		52240451	A0PJ88|Q9Y2K8	Nonsense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	G	39	7.454208	0.98296	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	.	.	.	6.08	4.0	0.46444	.	0.179987	0.33916	N	0.004430	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.1324	12.0768	0.53649	0.0:0.1007:0.6343:0.265	.	.	.	.	X	744	.	ENSP00000262135:R744X	R	-	1	2	RPGRIP1L	52240451	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.651000	0.24873	1.566000	0.49654	-0.282000	0.10007	CGA		0.418	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53682950	G	A	53682950	4	1	61	1	0	0	0	0	0	1	0	0	13587	1066	37	1	1765	1	RPGRIP1L	16	53682950	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7956	53682950	36671803	9799	17784										
FTO	79068	broad.mit.edu	37	chr16	53860037	53860037	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctaatataaaacacaccGaggctgaaatagccgctgct	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:53860037G>A	ENST00000471389.1	+	3	607	c.385G>A	c.(385-387)Gag>Aag	p.E129K	FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	129	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)	p.E129K(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						AAAACACACCGAGGCTGAAAT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	16											58	54	55					16																	53860037		2198	4300	6498	52417538	SO:0001583	missense	79068			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"Alkylation repair homologs"	24678	protein-coding gene	gene with protein product	"AlkB homolog 9", "alpha-ketoglutarate-dependent dioxygenase"	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.385G>A	16.37:g.53860037G>A	ENSP00000418823:p.Glu129Lys		52417538	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316870	0.23908	.	.	ENSG00000140718	ENST00000471389	T	0.77098	-1.07	5.46	2.36	0.29203	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	0.660516	0.17198	N	0.183235	T	0.58652	0.2137	L	0.27053	0.805	0.09310	N	0.999998	B	0.24533	0.105	B	0.17433	0.018	T	0.38045	-0.9679	10	0.20046	T	0.44	-0.994	4.9694	0.14108	0.286:0.2787:0.4353:0.0	.	129	Q9C0B1	FTO_HUMAN	K	129	ENSP00000418823:E129K	ENSP00000418823:E129K	E	+	1	0	FTO	52417538	0.754000	0.28360	0.003000	0.11579	0.382000	0.30200	2.184000	0.42575	0.650000	0.30769	0.650000	0.86243	GAG		0.493	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432		A	53860037	G	A	53860037	3	1	61	1	0	0	0	0	1	0	0	0	6105	1059	37	1	395	1	FTO	16	53860037	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	177087	53860037	36494716	9800	17785										
IRX3	79191	broad.mit.edu	37	chr16	54318969	54318969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctaggtcgccatccctgCgcgccgccccagccagggac	13	19	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:54318969C>T	ENST00000329734.3	-	2	1536	c.824G>A	c.(823-825)cGc>cAc	p.R275H		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	275					mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R275H(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						GCCATCCCTGCGCGCCGCCCC	0.642																																					GBM(143;1830 1866 4487 4646 37383)											1	Substitution - Missense(1)	large_intestine(1)	16											30	27	28					16																	54318969		2198	4297	6495	52876470	SO:0001583	missense	79191			U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"Homeoboxes / TALE class"	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.824G>A	16.37:g.54318969C>T	ENSP00000331608:p.Arg275His		52876470	Q7Z4A4|Q7Z4A5|Q8IVC6	Missense_Mutation	SNP	ENST00000329734.3	37	CCDS10750.1	.	.	.	.	.	.	.	.	.	.	C	6.688	0.495505	0.12762	.	.	ENSG00000177508	ENST00000329734	T	0.52983	0.64	4.8	-2.51	0.06365	.	0.552403	0.18875	N	0.128721	T	0.19167	0.0460	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14643	-1.0465	10	0.19147	T	0.46	-1.1342	5.4358	0.16480	0.133:0.4738:0.0:0.3932	.	275	P78415	IRX3_HUMAN	H	275	ENSP00000331608:R275H	ENSP00000331608:R275H	R	-	2	0	IRX3	52876470	0.995000	0.38212	0.000000	0.03702	0.320000	0.28249	0.878000	0.28126	-0.683000	0.05190	-0.286000	0.09958	CGC		0.642	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2			T	54318969	C	T	54318969	3	4	61	1	0	0	0	0	1	0	0	0	7866	768	27	1	693	1	IRX3	16	54318969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	458932	54318969	36035784	9801	17786										
IRX5	10265	broad.mit.edu	37	chr16	54966652	54966652	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccaggtgtccacctggttCgccaacgcgcgccggcgcct	12	18	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:54966652C>T	ENST00000394636.4	+	2	829	c.492C>T	c.(490-492)ttC>ttT	p.F164F	IRX5_ENST00000558597.1_Silent_p.F98F|IRX5_ENST00000320990.5_Silent_p.F164F|IRX5_ENST00000560154.1_Intron|CTD-3032H12.2_ENST00000560487.1_lincRNA			P78411	IRX5_HUMAN	iroquois homeobox 5	164					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)	p.F164F(1)		kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CCACCTGGTTCGCCAACGCGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	16											108	100	103					16																	54966652		2198	4300	6498	53524153	SO:0001819	synonymous_variant	10265			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"Homeoboxes / TALE class"	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.492C>T	16.37:g.54966652C>T			53524153	H0YMS7|P78416|Q7Z2E1	Silent	SNP	ENST00000394636.4	37	CCDS10751.1																																																																																				0.597	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			T	54966652	C	T	54966652	2	4	61	1	0	0	0	0	0	0	0	1	7868	883	31	1		1	IRX5	16	54966652	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	647683	54966652	35388101	9802	17787										
MMP2	4313	broad.mit.edu	37	chr16	55517016	55517016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacttcttccctcgcaagCccaagtgggacaagaaccag	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:55517016C>T	ENST00000219070.4	+	2	858	c.349C>T	c.(349-351)Ccc>Tcc	p.P117S	MMP2_ENST00000543485.1_Missense_Mutation_p.P41S|MMP2_ENST00000437642.2_Missense_Mutation_p.P67S|MMP2_ENST00000570308.1_Missense_Mutation_p.P41S	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	117	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.P117S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	CCCTCGCAAGCCCAAGTGGGA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											84	76	79					16																	55517016		2198	4300	6498	54074517	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.349C>T	16.37:g.55517016C>T	ENSP00000219070:p.Pro117Ser		54074517	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.516327	0.27123	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.80480	-1.38;-1.38;-1.38	4.79	4.79	0.61399	Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.353444	0.33959	N	0.004382	T	0.73536	0.3599	L	0.51422	1.61	0.80722	D	1	B;P	0.40534	0.267;0.72	B;B	0.36534	0.045;0.227	T	0.72616	-0.4239	10	0.07482	T	0.82	.	18.1835	0.89786	0.0:1.0:0.0:0.0	.	67;117	E9PE45;P08253	.;MMP2_HUMAN	S	117;41;67	ENSP00000219070:P117S;ENSP00000444143:P41S;ENSP00000394237:P67S	ENSP00000219070:P117S	P	+	1	0	MMP2	54074517	1.000000	0.71417	1.000000	0.80357	0.519000	0.34347	5.959000	0.70339	2.366000	0.80165	0.557000	0.71058	CCC		0.597	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			T	55517016	C	T	55517016	3	4	61	1	0	0	0	0	1	0	0	0	9688	739	26	3	362	3	MMP2	16	55517016	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	550364	55517016	34837737	9803	17788										
MMP2	4313	broad.mit.edu	37	chr16	55518029	55518029	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccccactgcggttttctcGaatccatgatggagaggcag	12	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:55518029G>A	ENST00000219070.4	+	3	991	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	MMP2_ENST00000543485.1_Missense_Mutation_p.R85Q|MMP2_ENST00000437642.2_Missense_Mutation_p.R111Q|MMP2_ENST00000570308.1_Missense_Mutation_p.R85Q	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	161	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.R161Q(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	CGGTTTTCTCGAATCCATGAT	0.547																																																2	Substitution - Missense(2)	large_intestine(1)|NS(1)	16											136	110	118					16																	55518029		2198	4300	6498	54075530	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.482G>A	16.37:g.55518029G>A	ENSP00000219070:p.Arg161Gln		54075530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	G	35	5.483909	0.96307	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.21191	2.02;2.02;2.02	4.72	4.72	0.59763	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.22859	0.0552	N	0.25957	0.775	0.80722	D	1	D;D	0.63880	0.993;0.987	P;B	0.47744	0.556;0.335	T	0.02560	-1.1141	10	0.54805	T	0.06	.	18.0532	0.89356	0.0:0.0:1.0:0.0	.	111;161	E9PE45;P08253	.;MMP2_HUMAN	Q	161;85;111	ENSP00000219070:R161Q;ENSP00000444143:R85Q;ENSP00000394237:R111Q	ENSP00000219070:R161Q	R	+	2	0	MMP2	54075530	1.000000	0.71417	0.974000	0.42286	0.969000	0.65631	7.919000	0.87513	2.346000	0.79739	0.455000	0.32223	CGA		0.547	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			A	55518029	G	A	55518029	3	1	61	1	0	0	0	0	1	0	0	0	9688	1058	37	1	499	1	MMP2	16	55518029	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1013	55518029	34836724	9804	17789										
SLC6A2	6530	broad.mit.edu	37	chr16	55690765	55690765	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgccccgcgacggcgacgcGcagccccgggagacctgggg	18	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:55690765G>A	ENST00000379906.2	+	1	414	c.159G>A	c.(157-159)gcG>gcA	p.A53A	SLC6A2_ENST00000566163.1_Silent_p.A53A|SLC6A2_ENST00000561820.1_Silent_p.A53A|SLC6A2_ENST00000568943.1_Silent_p.A53A|SLC6A2_ENST00000414754.3_Silent_p.A53A|SLC6A2_ENST00000219833.8_Silent_p.A53A	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	53					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)	p.A53A(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	ACGGCGACGCGCAGCCCCGGG	0.682																																																2	Substitution - coding silent(2)	large_intestine(2)	16											46	49	48					16																	55690765		2198	4300	6498	54248266	SO:0001819	synonymous_variant	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.159G>A	16.37:g.55690765G>A			54248266	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	37	CCDS10754.1																																																																																				0.682	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			A	55690765	G	A	55690765	2	1	61	1	0	0	0	0	0	0	0	1	14720	1074	38	1		1	SLC6A2	16	55690765	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172736	55690765	34663988	9805	17790										
SLC6A2	6530	broad.mit.edu	37	chr16	55731916	55731916	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttcagcactttccttctCgccctgttctgcataaccaa	4	16	3	0	rs140641227	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:55731916C>A	ENST00000379906.2	+	9	1623	c.1368C>A	c.(1366-1368)ctC>ctA	p.L456L	SLC6A2_ENST00000566163.1_Silent_p.L411L|SLC6A2_ENST00000561820.1_Silent_p.L456L|SLC6A2_ENST00000568943.1_Silent_p.L456L|SLC6A2_ENST00000414754.3_Silent_p.L456L|SLC6A2_ENST00000219833.8_Silent_p.L456L|SLC6A2_ENST00000567238.1_Silent_p.L351L	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	456					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)	p.L456L(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTTTCCTTCTCGCCCTGTTCT	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	16											139	124	129					16																	55731916		2198	4300	6498	54289417	SO:0001819	synonymous_variant	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.1368C>A	16.37:g.55731916C>A			54289417	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	37	CCDS10754.1																																																																																				0.552	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			A	55731916	C	A	55731916	2	1	61	1	0	0	0	0	0	0	0	1	14720	871	31	2		2	SLC6A2	16	55731916	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41151	55731916	34622837	9806	17791										
CES7	221223	broad.mit.edu	37	chr16	55883537	55883537	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtggccagtcccttaccGaacataacaatgtccccctt	7	14	0	0	rs369099039		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:55883537G>A	ENST00000290567.9	-	11	1543	c.1422C>T	c.(1420-1422)ttC>ttT	p.F474F	CES5A_ENST00000518005.1_Splice_Site_p.F368F|CES5A_ENST00000319165.9_Intron|CES5A_ENST00000521992.1_Splice_Site_p.F503F|CES5A_ENST00000520435.1_Splice_Site_p.F444F|CES5A_ENST00000541580.1_5'UTR	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	474						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)	p.F503F(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						GTCCCTTACCGAACATAACAA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G	,,	2,3134		0,2,1566	175	152	159		1422,1509,	-3.2	0.9	16		159	0,7164		0,0,3582	no	coding-synonymous-near-splice,coding-synonymous-near-splice,intron	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	,,	0,2,5148	AA,AG,GG		0.0,0.0638,0.0194	,,	474/576,503/605,	55883537	2,10298	1568	3582	5150	54441038	SO:0001630	splice_region_variant	221223			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1423+1C>T	16.37:g.55883537G>A			54441038	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Silent	SNP	ENST00000290567.9	37	CCDS45490.1																																																																																				0.537	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	Silent	A	55883537	G	A	55883537	5	1	61	1	0	0	0	0	0	0	1	0	3278	1072	37	1	317	1	CES7	16	55883537	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151621	55883537	34471216	9807	17792										
AMFR	267	broad.mit.edu	37	chr16	56443491	56443491	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaaattccaaaatttgtCtttgagatgctaaaaaagaa	5	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:56443491C>A	ENST00000290649.5	-	3	568	c.358G>T	c.(358-360)Gac>Tac	p.D120Y	RP11-413H22.2_ENST00000563090.1_RNA	NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	120					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D120Y(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						CAAAATTTGTCTTTGAGATGC	0.398																																					Pancreas(2;144 323 39528)											1	Substitution - Missense(1)	large_intestine(1)	16											60	63	62					16																	56443491		2198	4300	6498	55000992	SO:0001583	missense	267			L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.358G>T	16.37:g.56443491C>A	ENSP00000290649:p.Asp120Tyr		55000992	P26442|Q8IZ70	Missense_Mutation	SNP	ENST00000290649.5	37	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798451	0.90538	.	.	ENSG00000159461	ENST00000290649	T	0.20069	2.1	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.50531	0.1621	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.48581	-0.9023	10	0.87932	D	0	-31.9093	20.2618	0.98447	0.0:1.0:0.0:0.0	.	120	Q9UKV5	AMFR2_HUMAN	Y	120	ENSP00000290649:D120Y	ENSP00000290649:D120Y	D	-	1	0	AMFR	55000992	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.681000	0.84073	2.793000	0.96121	0.655000	0.94253	GAC		0.398	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			A	56443491	C	A	56443491	3	1	61	1	0	0	0	0	1	0	0	0	571	913	32	2	1621	2	AMFR	16	56443491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	559954	56443491	33911262	9808	17793										
BBS2	583	broad.mit.edu	37	chr16	56519562	56519562	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaggtttcccaacagctCtgtgtgattgttacagcgaa	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:56519562C>A	ENST00000245157.5	-	16	2419	c.1999G>T	c.(1999-2001)Gag>Tag	p.E667*	BBS2_ENST00000568104.1_Nonsense_Mutation_p.E621*	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	667					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.E667*(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CCCAACAGCTCTGTGTGATTG	0.388									Bardet-Biedl syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	16											215	209	211					16																	56519562		2198	4300	6498	55077063	SO:0001587	stop_gained	583	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1999G>T	16.37:g.56519562C>A	ENSP00000245157:p.Glu667*		55077063	Q96CM0|Q96SN9	Nonsense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	C	43	10.393551	0.99397	.	.	ENSG00000125124	ENST00000245157	.	.	.	5.64	5.64	0.86602	.	0.046925	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-19.3584	19.6921	0.96007	0.0:1.0:0.0:0.0	.	.	.	.	X	667	.	ENSP00000245157:E667X	E	-	1	0	BBS2	55077063	1.000000	0.71417	0.979000	0.43373	0.993000	0.82548	7.278000	0.78587	2.655000	0.90218	0.585000	0.79938	GAG		0.388	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56519562	C	A	56519562	4	1	61	1	0	0	0	0	0	1	0	0	1339	922	32	2	174	2	BBS2	16	56519562	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76071	56519562	33835191	9809	17794										
BBS2	583	broad.mit.edu	37	chr16	56553721	56553721	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtagcgccctatggccacCattcgggggctgattttgtg	13	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:56553721C>A	ENST00000245157.5	-	1	474	c.54G>T	c.(52-54)atG>atT	p.M18I	BBS2_ENST00000568104.1_Missense_Mutation_p.M18I	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	18					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.M18I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CTATGGCCACCATTCGGGGGC	0.677									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	16											51	45	47					16																	56553721		2198	4300	6498	55111222	SO:0001583	missense	583	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.54G>T	16.37:g.56553721C>A	ENSP00000245157:p.Met18Ile		55111222	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.798173	0.70567	.	.	ENSG00000125124	ENST00000245157	T	0.63580	-0.05	4.82	4.82	0.62117	WD40 repeat-like-containing domain (1);	0.106237	0.85682	D	0.000000	T	0.56920	0.2018	L	0.42245	1.32	0.80722	D	1	B;B	0.23806	0.091;0.091	B;B	0.23716	0.048;0.048	T	0.52961	-0.8505	10	0.33141	T	0.24	-22.9357	18.4483	0.90693	0.0:1.0:0.0:0.0	.	18;18	A8K0N9;Q9BXC9	.;BBS2_HUMAN	I	18	ENSP00000245157:M18I	ENSP00000245157:M18I	M	-	3	0	BBS2	55111222	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.004000	0.76317	2.665000	0.90641	0.462000	0.41574	ATG		0.677	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56553721	C	A	56553721	3	1	61	1	0	0	0	0	1	0	0	0	1339	594	21	2	2179	2	BBS2	16	56553721	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34159	56553721	33801032	9810	17795										
NUP93	9688	broad.mit.edu	37	chr16	56852629	56852629	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaagctctctggataacatCgagatggcctatgcgcggca	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:56852629C>T	ENST00000308159.5	+	6	664	c.543C>T	c.(541-543)atC>atT	p.I181I	NUP93_ENST00000542526.1_Silent_p.I58I|NUP93_ENST00000569842.1_Silent_p.I181I|NUP93_ENST00000564887.1_Silent_p.I58I	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	181					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.I181I(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TGGATAACATCGAGATGGCCT	0.453																																					Colon(33;610 796 1305 1705 38917)											1	Substitution - coding silent(1)	large_intestine(1)	16											130	124	126					16																	56852629		2198	4300	6498	55410130	SO:0001819	synonymous_variant	9688			D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.543C>T	16.37:g.56852629C>T			55410130	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	37	CCDS10769.1																																																																																				0.453	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		T	56852629	C	T	56852629	2	4	61	1	0	0	0	0	0	0	0	1	10803	874	31	1		1	NUP93	16	56852629	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298908	56852629	33502124	9811	17796										
NUP93	9688	broad.mit.edu	37	chr16	56866228	56866228	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaccaagtgtgttttgacGacgatggcaccagctcccca	10	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:56866228G>A	ENST00000308159.5	+	12	1394	c.1273G>A	c.(1273-1275)Gac>Aac	p.D425N	NUP93_ENST00000542526.1_Missense_Mutation_p.D302N|NUP93_ENST00000569842.1_Missense_Mutation_p.D425N|NUP93_ENST00000564887.1_Missense_Mutation_p.D302N	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	425					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.D425N(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GTGTTTTGACGACGATGGCAC	0.478																																					Colon(33;610 796 1305 1705 38917)											1	Substitution - Missense(1)	large_intestine(1)	16											185	167	173					16																	56866228		2198	4300	6498	55423729	SO:0001583	missense	9688			D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1273G>A	16.37:g.56866228G>A	ENSP00000310668:p.Asp425Asn		55423729	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	37	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605819	0.66445	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.46451	0.87;0.87	6.03	6.03	0.97812	.	0.042884	0.85682	D	0.000000	T	0.37210	0.0995	L	0.41415	1.275	0.80722	D	1	B	0.24368	0.102	B	0.15052	0.012	T	0.13282	-1.0515	10	0.16896	T	0.51	-19.2659	20.5568	0.99304	0.0:0.0:1.0:0.0	.	425	Q8N1F7	NUP93_HUMAN	N	425;302	ENSP00000310668:D425N;ENSP00000440235:D302N	ENSP00000310668:D425N	D	+	1	0	NUP93	55423729	1.000000	0.71417	0.978000	0.43139	0.521000	0.34408	9.687000	0.98667	2.861000	0.98227	0.655000	0.94253	GAC		0.478	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		A	56866228	G	A	56866228	3	1	61	1	0	0	0	0	1	0	0	0	10803	1058	37	1	1315	1	NUP93	16	56866228	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13599	56866228	33488525	9812	17797										
CPNE2	221184	broad.mit.edu	37	chr16	57171082	57171082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggatggtattgcccaggCgtactcagcttgcctgcccc	12	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57171082C>T	ENST00000535318.2	+	15	1551	c.1190C>T	c.(1189-1191)gCg>gTg	p.A397V	CPNE2_ENST00000290776.8_Missense_Mutation_p.A397V|CPNE2_ENST00000537605.1_Missense_Mutation_p.A295V|CPNE2_ENST00000565951.1_Intron|CPNE2_ENST00000565874.1_Missense_Mutation_p.A397V			Q96FN4	CPNE2_HUMAN	copine II	397	VWFA.					extracellular vesicular exosome (GO:0070062)		p.A397V(1)		central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				ATTGCCCAGGCGTACTCAGCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	16											133	75	95					16																	57171082		2198	4300	6498	55728583	SO:0001583	missense	221184				CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.1190C>T	16.37:g.57171082C>T	ENSP00000439018:p.Ala397Val		55728583	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	32	5.170127	0.94768	.	.	ENSG00000140848	ENST00000290776;ENST00000537605;ENST00000535318	T;T;T	0.23147	1.92;1.92;1.92	5.88	5.88	0.94601	von Willebrand factor, type A (1);Copine (1);	0.000000	0.85682	D	0.000000	T	0.54854	0.1884	M	0.85859	2.78	0.58432	D	0.999998	D;D	0.69078	0.997;0.989	P;P	0.59643	0.812;0.861	T	0.58814	-0.7570	10	0.62326	D	0.03	-10.8515	20.2422	0.98381	0.0:1.0:0.0:0.0	.	397;397	A8K8A4;Q96FN4	.;CPNE2_HUMAN	V	397;295;397	ENSP00000290776:A397V;ENSP00000445468:A295V;ENSP00000439018:A397V	ENSP00000290776:A397V	A	+	2	0	CPNE2	55728583	1.000000	0.71417	0.993000	0.49108	0.877000	0.50540	7.788000	0.85771	2.782000	0.95742	0.655000	0.94253	GCG		0.587	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		T	57171082	C	T	57171082	3	4	61	1	0	0	0	0	1	0	0	0	3818	768	27	1	1240	1	CPNE2	16	57171082	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	304854	57171082	33183671	9813	17798										
RSPRY1	89970	broad.mit.edu	37	chr16	57255282	57255282	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtggtcacttctggcgtCatgcagattggctgggccac	13	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57255282C>A	ENST00000537866.1	+	10	1989	c.1116C>A	c.(1114-1116)gtC>gtA	p.V372V	RSPRY1_ENST00000394420.4_Silent_p.V372V			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	372	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)	p.V372V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						CTTCTGGCGTCATGCAGATTG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	16											171	154	160					16																	57255282		2198	4300	6498	55812783	SO:0001819	synonymous_variant	89970			AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1116C>A	16.37:g.57255282C>A			55812783	Q6UX21|Q8ND53	Silent	SNP	ENST00000537866.1	37	CCDS10775.1																																																																																				0.502	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		A	57255282	C	A	57255282	2	1	61	1	0	0	0	0	0	0	0	1	13750	813	29	2		2	RSPRY1	16	57255282	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84200	57255282	33099471	9814	17799										
RSPRY1	89970	broad.mit.edu	37	chr16	57265111	57265111	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcagctagtttcatgtCatatcaacaatgtgagttca	8	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57265111C>A	ENST00000537866.1	+	13	2282	c.1409C>A	c.(1408-1410)tCa>tAa	p.S470*	RSPRY1_ENST00000394420.4_Nonsense_Mutation_p.S470*|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	470	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)	p.S470*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						AGTTTCATGTCATATCAACAA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											103	100	101					16																	57265111		2198	4300	6498	55822612	SO:0001587	stop_gained	89970			AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1409C>A	16.37:g.57265111C>A	ENSP00000443176:p.Ser470*		55822612	Q6UX21|Q8ND53	Nonsense_Mutation	SNP	ENST00000537866.1	37	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	C	47	13.193280	0.99726	.	.	ENSG00000159579	ENST00000394420;ENST00000537866	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0175	0.97485	0.0:1.0:0.0:0.0	rs35236945	.	.	.	X	470	.	ENSP00000377942:S470X	S	+	2	0	RSPRY1	55822612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.730000	0.93505	0.650000	0.86243	TCA		0.323	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		A	57265111	C	A	57265111	4	1	61	1	0	0	0	0	0	1	0	0	13750	838	29	2	1455	2	RSPRY1	16	57265111	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9829	57265111	33089642	9815	17800										
ARL2BP	23568	broad.mit.edu	37	chr16	57286102	57286102	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaaggccgaggactggacTtaagcagtggcttagtggtg	16	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57286102T>G	ENST00000219204.3	+	6	685	c.415T>G	c.(415-417)Tta>Gta	p.L139V	RP11-407G23.3_ENST00000564376.1_RNA|ARL2BP_ENST00000562023.1_Missense_Mutation_p.L99V	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	139					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)	p.L139V(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						AGGACTGGACTTAAGCAGTGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	16											115	96	102					16																	57286102		2198	4300	6498	55843603	SO:0001583	missense	23568			AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"binder of Arl2"	615407	"retinitis pigmentosa 66 (autosomal recessive)"	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.415T>G	16.37:g.57286102T>G	ENSP00000219204:p.Leu139Val		55843603	B3KQJ5|Q504R0	Missense_Mutation	SNP	ENST00000219204.3	37	CCDS10776.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203537	0.79127	.	.	ENSG00000102931	ENST00000219204	T	0.55930	0.49	6.02	3.79	0.43588	.	0.000000	0.53938	U	0.000049	T	0.50650	0.1628	M	0.70842	2.15	0.53688	D	0.999972	P	0.36599	0.56	B	0.36186	0.219	T	0.50833	-0.8781	10	0.66056	D	0.02	-7.0897	9.7865	0.40679	0.0:0.1387:0.0:0.8613	.	139	Q9Y2Y0	AR2BP_HUMAN	V	139	ENSP00000219204:L139V	ENSP00000219204:L139V	L	+	1	2	ARL2BP	55843603	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	3.014000	0.49590	0.539000	0.28788	0.528000	0.53228	TTA		0.488	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106		G	57286102	T	G	57286102	3	3	61	1	0	0	0	0	1	0	0	0	935	1606	56	4	437	4	ARL2BP	16	57286102	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	20991	57286102	33068651	9816	17801										
CCL22	6367	broad.mit.edu	37	chr16	57397476	57397476	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtgccctgggtgaagatGattctcaataagctgagcca	12	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57397476G>T	ENST00000219235.4	+	3	303	c.258G>T	c.(256-258)atG>atT	p.M86I		NM_002990.4	NP_002981.2	O00626	CCL22_HUMAN	chemokine (C-C motif) ligand 22	86					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)	p.M86I(1)		large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						GGGTGAAGATGATTCTCAATA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											114	96	102					16																	57397476		2198	4300	6498	55954977	SO:0001583	missense	6367			U83171	CCDS10778.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000102962	ENSG00000102962		"Chemokine ligands", "Endogenous ligands"	10621	protein-coding gene	gene with protein product		602957	"small inducible cytokine subfamily A (Cys-Cys), member 22"	SCYA22		9151897, 9691168	Standard	NM_002990		Approved	MDC, STCP-1, ABCD-1, DC/B-CK, A-152E5.1, MGC34554	uc002elh.3	O00626	OTTHUMG00000133454	ENST00000219235.4:c.258G>T	16.37:g.57397476G>T	ENSP00000219235:p.Met86Ile		55954977	A0N0Q6|B2R4W2	Missense_Mutation	SNP	ENST00000219235.4	37	CCDS10778.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884492	0.33255	.	.	ENSG00000102962	ENST00000219235	T	0.04551	3.6	4.47	1.18	0.20946	Chemokine interleukin-8-like domain (3);	0.544621	0.19056	N	0.123920	T	0.04588	0.0125	.	.	.	0.09310	N	1	B	0.31209	0.313	B	0.36922	0.236	T	0.34229	-0.9837	9	0.54805	T	0.06	-8.89	3.5563	0.07865	0.2119:0.0:0.5912:0.1969	.	86	O00626	CCL22_HUMAN	I	86	ENSP00000219235:M86I	ENSP00000219235:M86I	M	+	3	0	CCL22	55954977	0.018000	0.18449	0.129000	0.21949	0.019000	0.09904	0.725000	0.25970	0.625000	0.30304	0.462000	0.41574	ATG		0.532	CCL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257328.1	NM_002990		T	57397476	G	T	57397476	3	4	61	1	0	0	0	0	1	0	0	0	2900	1290	45	2	268	2	CCL22	16	57397476	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111374	57397476	32957277	9817	17802										
CX3CL1	6376	broad.mit.edu	37	chr16	57416442	57416442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccacccaggcctccactgCgtcctccccagccccagagg	8	22	0	1	rs529786529		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57416442C>T	ENST00000006053.6	+	3	803	c.692C>T	c.(691-693)gCg>gTg	p.A231V	CX3CL1_ENST00000563383.1_Missense_Mutation_p.A237V|CX3CL1_ENST00000565912.1_Missense_Mutation_p.A193V	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	231	Mucin-like stalk.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)	p.A231V(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GCCTCCACTGCGTCCTCCCCA	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	16											34	38	36					16																	57416442		2198	4299	6497	55973943	SO:0001583	missense	6376			U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"Endogenous ligands"	10647	protein-coding gene	gene with protein product		601880	"small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.692C>T	16.37:g.57416442C>T	ENSP00000006053:p.Ala231Val		55973943	O00672	Missense_Mutation	SNP	ENST00000006053.6	37	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.310321	0.23821	.	.	ENSG00000006210	ENST00000006053	T	0.04234	3.67	4.86	-5.81	0.02340	.	13.360600	0.00919	U	0.002577	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	10	0.87932	D	0	-24.1521	1.3009	0.02079	0.1249:0.2728:0.2506:0.3517	.	231	P78423	X3CL1_HUMAN	V	231	ENSP00000006053:A231V	ENSP00000006053:A231V	A	+	2	0	CX3CL1	55973943	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.444000	0.01012	-0.967000	0.03582	-0.885000	0.02943	GCG		0.672	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		T	57416442	C	T	57416442	3	4	61	1	0	0	0	0	1	0	0	0	4080	768	27	1	702	1	CX3CL1	16	57416442	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18966	57416442	32938311	9818	17803										
COQ9	57017	broad.mit.edu	37	chr16	57485105	57485105	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacctgatccagagtcttCtcattcaccccccaggtagg	7	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57485105C>T	ENST00000262507.6	+	2	296	c.227C>T	c.(226-228)tCt>tTt	p.S76F	COQ9_ENST00000567933.1_Missense_Mutation_p.S76F|COQ9_ENST00000567384.1_3'UTR|COQ9_ENST00000567072.1_Missense_Mutation_p.S76F	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	76					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)		p.S76F(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CCAGAGTCTTCTCATTCACCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	83	82					16																	57485105		2198	4300	6498	56042606	SO:0001583	missense	57017			BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"chromosome 16 open reading frame 49", "coenzyme Q9 homolog (yeast)", "coenzyme Q9 homolog (S. cerevisiae)"	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.227C>T	16.37:g.57485105C>T	ENSP00000262507:p.Ser76Phe		56042606	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Missense_Mutation	SNP	ENST00000262507.6	37	CCDS32459.1	.	.	.	.	.	.	.	.	.	.	C	9.445	1.089170	0.20390	.	.	ENSG00000088682	ENST00000262507	.	.	.	5.16	4.21	0.49690	.	1.000800	0.08061	N	0.998128	T	0.27098	0.0664	L	0.40543	1.245	0.09310	N	1	B;B;B;B;P	0.40107	0.228;0.009;0.004;0.001;0.703	B;B;B;B;B	0.34385	0.082;0.011;0.005;0.002;0.181	T	0.26503	-1.0101	9	0.59425	D	0.04	1.0309	4.3737	0.11260	0.1584:0.603:0.1532:0.0854	.	76;76;76;76;76	B4E0U3;B4DIV2;B4DEE3;O75208;O75208-2	.;.;.;COQ9_HUMAN;.	F	76	.	ENSP00000262507:S76F	S	+	2	0	COQ9	56042606	0.000000	0.05858	0.010000	0.14722	0.733000	0.41908	0.420000	0.21263	1.178000	0.42870	0.655000	0.94253	TCT		0.507	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312		T	57485105	C	T	57485105	3	4	61	1	0	0	0	0	1	0	0	0	3757	913	32	3	233	3	COQ9	16	57485105	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68663	57485105	32869648	9819	17804										
GPR56	9289	broad.mit.edu	37	chr16	57689793	57689793	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccatgtatctaggacaaGaattccagccaagtcctggg	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57689793G>T	ENST00000388812.4	+	7	1346	c.906G>T	c.(904-906)aaG>aaT	p.K302N	GPR56_ENST00000568908.1_Missense_Mutation_p.K302N|GPR56_ENST00000562631.1_Missense_Mutation_p.K302N|GPR56_ENST00000540164.2_Missense_Mutation_p.K302N|GPR56_ENST00000388813.5_Missense_Mutation_p.K302N|GPR56_ENST00000544297.1_Missense_Mutation_p.K127N|GPR56_ENST00000567835.1_Missense_Mutation_p.K302N|GPR56_ENST00000379694.4_Missense_Mutation_p.K132N|GPR56_ENST00000562558.1_Missense_Mutation_p.K302N|GPR56_ENST00000568909.1_Missense_Mutation_p.K302N|GPR56_ENST00000456916.1_Missense_Mutation_p.K302N|GPR56_ENST00000538815.1_Missense_Mutation_p.K302N|GPR56_ENST00000379696.3_Missense_Mutation_p.K302N			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	302					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)	p.K302N(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						TCTAGGACAAGAATTCCAGCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											115	114	114					16																	57689793		2198	4300	6498	56247294	SO:0001583	missense	9289			AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"-", "GPCR / Class B : Orphans"	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.906G>T	16.37:g.57689793G>T	ENSP00000373464:p.Lys302Asn		56247294	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650091	0.29336	.	.	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.44881	0.92;0.91;0.92;0.91;0.92;1.78;1.17;0.91	5.59	3.3	0.37823	.	0.086211	0.49916	D	0.000122	T	0.39655	0.1086	M	0.65975	2.015	0.28050	N	0.933413	P;P;B;P;P	0.35433	0.493;0.501;0.046;0.501;0.501	B;B;B;B;B	0.35607	0.206;0.143;0.041;0.143;0.203	T	0.34950	-0.9808	10	0.39692	T	0.17	.	10.0019	0.41933	0.2372:0.0:0.7628:0.0	.	127;307;302;302;132	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	N	302;302;302;302;302;127;132;302	ENSP00000373465:K302N;ENSP00000373464:K302N;ENSP00000444415:K302N;ENSP00000398034:K302N;ENSP00000444911:K302N;ENSP00000438006:K127N;ENSP00000369016:K132N;ENSP00000369018:K302N	ENSP00000369016:K132N	K	+	3	2	GPR56	56247294	1.000000	0.71417	1.000000	0.80357	0.469000	0.32828	1.025000	0.30090	1.358000	0.45922	0.655000	0.94253	AAG		0.542	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3			T	57689793	G	T	57689793	3	4	61	1	0	0	0	0	1	0	0	0	6720	933	33	2	943	2	GPR56	16	57689793	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	204688	57689793	32664960	9820	17805										
KIFC3	3801	broad.mit.edu	37	chr16	57805499	57805499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacctgctggctttgtgcGcagctcttgcagctcggcct	14	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:57805499G>A	ENST00000379655.4	-	5	738	c.481C>T	c.(481-483)Cgc>Tgc	p.R161C	KIFC3_ENST00000539578.1_Missense_Mutation_p.R103C|KIFC3_ENST00000541240.1_Missense_Mutation_p.R183C|KIFC3_ENST00000566975.1_5'Flank|KIFC3_ENST00000421376.2_Missense_Mutation_p.R22C|KIFC3_ENST00000540079.2_Missense_Mutation_p.R59C|KIFC3_ENST00000562903.1_Missense_Mutation_p.R22C|KIFC3_ENST00000465878.2_Missense_Mutation_p.R22C|KIFC3_ENST00000543930.1_Missense_Mutation_p.R22C|KIFC3_ENST00000445690.2_Missense_Mutation_p.R161C	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	161					ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R161C(1)		breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				GGCTTTGTGCGCAGCTCTTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	16											76	53	60					16																	57805499		2198	4300	6498	56363000	SO:0001583	missense	3801			BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.481C>T	16.37:g.57805499G>A	ENSP00000368976:p.Arg161Cys		56363000	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	G	2.131	-0.399017	0.04865	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.75260	-0.84;-0.84;-0.83;-0.85;-0.84;-0.92;-0.85	5.09	1.69	0.24217	.	0.448245	0.22090	N	0.064771	T	0.61578	0.2358	L	0.36672	1.1	0.19300	N	0.999978	B;B;B;B;B;B	0.16396	0.01;0.017;0.004;0.007;0.004;0.002	B;B;B;B;B;B	0.10450	0.001;0.005;0.001;0.002;0.001;0.001	T	0.56739	-0.7929	10	0.72032	D	0.01	.	8.506	0.33188	0.0:0.1258:0.5291:0.3451	.	183;103;22;59;161;22	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	C	161;161;22;183;59;22;103	ENSP00000368976:R161C;ENSP00000401696:R161C;ENSP00000396399:R22C;ENSP00000442008:R183C;ENSP00000438805:R59C;ENSP00000444012:R22C;ENSP00000444884:R103C	ENSP00000368976:R161C	R	-	1	0	KIFC3	56363000	0.614000	0.27017	0.031000	0.17742	0.081000	0.17604	0.492000	0.22435	0.530000	0.28619	0.655000	0.94253	CGC		0.657	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		A	57805499	G	A	57805499	3	1	61	1	0	0	0	0	1	0	0	0	8335	1087	38	1	2089	1	KIFC3	16	57805499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115706	57805499	32549254	9821	17806										
TEPP	374739	broad.mit.edu	37	chr16	58011868	58011868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acccagccctgcccaccctgCgccacatggacagggacacc	9	20	0	0	rs573261072		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58011868C>T	ENST00000441824.2	+	2	350	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	TEPP_ENST00000290871.5_Missense_Mutation_p.R105C|TEPP_ENST00000569996.1_Intron	NM_199456.2	NP_955535.2	Q6URK8	TEPP_HUMAN	testis, prostate and placenta expressed	105						extracellular region (GO:0005576)		p.R105C(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	8						GCCCACCCTGCGCCACATGGA	0.642													C|||	1	0.000199681	0	0	5008	,	,		16738	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16											58	46	50					16																	58011868		2198	4300	6498	56569369	SO:0001583	missense	374739			BC104458	CCDS10790.1, CCDS45496.1	16q13	2009-04-20			ENSG00000159648	ENSG00000159648			33745	protein-coding gene	gene with protein product		610264				14652002	Standard	NM_199456		Approved		uc002emv.4	Q6URK8	OTTHUMG00000133463	ENST00000441824.2:c.313C>T	16.37:g.58011868C>T	ENSP00000401917:p.Arg105Cys		56569369	Q6URK7	Missense_Mutation	SNP	ENST00000441824.2	37	CCDS45496.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.741800	0.69304	.	.	ENSG00000159648	ENST00000290871;ENST00000441824	T;T	0.67345	-0.26;-0.26	4.36	3.25	0.37280	.	0.000000	0.53938	D	0.000044	T	0.80904	0.4713	M	0.86343	2.81	0.46654	D	0.99914	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82524	-0.0414	10	0.87932	D	0	-7.588	8.2742	0.31862	0.3012:0.6988:0.0:0.0	.	105;105	Q6URK8;Q6URK8-2	TEPP_HUMAN;.	C	105	ENSP00000290871:R105C;ENSP00000401917:R105C	ENSP00000290871:R105C	R	+	1	0	TEPP	56569369	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.093000	0.30939	2.121000	0.65114	0.423000	0.28283	CGC		0.642	TEPP-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000431966.1	NM_199456		T	58011868	C	T	58011868	3	4	61	1	0	0	0	0	1	0	0	0	15799	768	27	1	319	1	TEPP	16	58011868	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	206369	58011868	32342885	9822	17807										
MMP15	4324	broad.mit.edu	37	chr16	58074569	58074569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaacttcaagctgcccGaggacgatctccgtggcatc	10	13	2	1	rs148331048	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58074569G>A	ENST00000219271.3	+	5	1662	c.877G>A	c.(877-879)Gag>Aag	p.E293K		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	293					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E293K(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CAAGCTGCCCGAGGACGATCT	0.627													G|||	2	0.000399361	0.0015	0	5008	,	,		20617	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16						G	LYS/GLU	7,4389	12.9+/-30.5	0,7,2191	122	99	107		877	5.2	1	16	dbSNP_134	107	0,8600		0,0,4300	yes	missense	MMP15	NM_002428.2	56	0,7,6491	AA,AG,GG		0.0,0.1592,0.0539	benign	293/670	58074569	7,12989	2198	4300	6498	56632070	SO:0001583	missense	4324			Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.877G>A	16.37:g.58074569G>A	ENSP00000219271:p.Glu293Lys		56632070	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.731912	0.48939	0.001592	0.0	ENSG00000102996	ENST00000219271	T	0.20463	2.07	5.17	5.17	0.71159	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.104740	0.64402	D	0.000005	T	0.30759	0.0775	L	0.36672	1.1	0.80722	D	1	D	0.63880	0.993	P	0.55391	0.775	T	0.01087	-1.1456	10	0.32370	T	0.25	.	17.6579	0.88183	0.0:0.0:1.0:0.0	.	293	P51511	MMP15_HUMAN	K	293	ENSP00000219271:E293K	ENSP00000219271:E293K	E	+	1	0	MMP15	56632070	1.000000	0.71417	0.993000	0.49108	0.576000	0.36127	5.662000	0.68032	2.421000	0.82119	0.563000	0.77884	GAG		0.627	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		A	58074569	G	A	58074569	3	1	61	1	0	0	0	0	1	0	0	0	9684	1059	37	1	895	1	MMP15	16	58074569	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62701	58074569	32280184	9823	17808										
CCDC113	29070	broad.mit.edu	37	chr16	58313629	58313629	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcgtaaggcttggaatcGaatgaaaataaccaatgagc	9	8	0	2	rs146122026		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58313629G>A	ENST00000219299.4	+	9	1161	c.1082G>A	c.(1081-1083)cGa>cAa	p.R361Q	CCDC113_ENST00000443128.2_Missense_Mutation_p.R307Q	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	361						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.R361Q(1)		large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						GCTTGGAATCGAATGAAAATA	0.413													G|||	1	0.000199681	0	0	5008	,	,		18966	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16						G	GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	71	69	70		920,1082	-0.7	0.9	16	dbSNP_134	70	0,8600		0,0,4300	yes	missense,missense	CCDC113	NM_001142302.1,NM_014157.3	43,43	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	307/324,361/378	58313629	1,12995	2198	4300	6498	56871130	SO:0001583	missense	29070			AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	ENST00000219299.4:c.1082G>A	16.37:g.58313629G>A	ENSP00000219299:p.Arg361Gln		56871130	B2RAQ7|B4DR20|Q9NZX2	Missense_Mutation	SNP	ENST00000219299.4	37	CCDS10795.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.942	0.543584	0.13250	2.27E-4	0.0	ENSG00000103021	ENST00000443128;ENST00000219299	T;T	0.29917	1.55;1.63	6.03	-0.697	0.11284	.	0.472014	0.24050	N	0.042015	T	0.09818	0.0241	N	0.08118	0	0.20074	N	0.999933	B;B	0.20887	0.049;0.014	B;B	0.11329	0.006;0.002	T	0.34675	-0.9819	10	0.02654	T	1	-7.7531	5.7642	0.18217	0.5139:0.1387:0.3474:0.0	.	307;361	B4DR20;Q9H0I3	.;CC113_HUMAN	Q	307;361	ENSP00000402588:R307Q;ENSP00000219299:R361Q	ENSP00000219299:R361Q	R	+	2	0	CCDC113	56871130	0.754000	0.28360	0.868000	0.34077	0.072000	0.16883	0.674000	0.25218	-0.111000	0.12001	-0.302000	0.09304	CGA		0.413	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		A	58313629	G	A	58313629	3	1	61	1	0	0	0	0	1	0	0	0	2756	1058	37	1	1116	1	CCDC113	16	58313629	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239060	58313629	32041124	9824	17809										
GINS3	64785	broad.mit.edu	37	chr16	58426556	58426556	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgcgctggggcctgaggaGaactttctttctttggacga	15	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58426556G>T	ENST00000318129.5	+	1	259	c.51G>T	c.(49-51)gaG>gaT	p.E17D	GINS3_ENST00000328514.7_Missense_Mutation_p.E17D|GINS3_ENST00000426538.2_Missense_Mutation_p.E17D	NM_022770.3	NP_073607.2	Q9BRX5	PSF3_HUMAN	GINS complex subunit 3 (Psf3 homolog)	17					DNA replication (GO:0006260)	nucleus (GO:0005634)		p.E17D(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	7						GGCCTGAGGAGAACTTTCTTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	16											81	83	82					16																	58426556		2198	4300	6498	56984057	SO:0001583	missense	64785			BC005879	CCDS10796.1, CCDS45498.1, CCDS45499.1	16q21	2008-02-05			ENSG00000181938	ENSG00000181938			25851	protein-coding gene	gene with protein product		610610				12477932	Standard	NM_022770		Approved	FLJ13912, PSF3	uc010cdj.3	Q9BRX5	OTTHUMG00000133486	ENST00000318129.5:c.51G>T	16.37:g.58426556G>T	ENSP00000318196:p.Glu17Asp		56984057	B2RDP3|E9PB21|Q9H870	Missense_Mutation	SNP	ENST00000318129.5	37	CCDS10796.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217059	0.79352	.	.	ENSG00000181938	ENST00000426538;ENST00000328514;ENST00000318129	T	0.17370	2.28	5.71	1.5	0.22942	.	0.000000	0.85682	D	0.000000	T	0.30727	0.0774	M	0.65498	2.005	0.42070	D	0.991209	D;D;B	0.71674	0.998;0.99;0.028	D;D;B	0.74674	0.984;0.971;0.043	T	0.11446	-1.0587	10	0.18710	T	0.47	-1.648	7.7558	0.28923	0.3511:0.0:0.6489:0.0	.	17;17;17	E9PB21;Q9BRX5-2;Q9BRX5	.;.;PSF3_HUMAN	D	17	ENSP00000318196:E17D	ENSP00000318196:E17D	E	+	3	2	GINS3	56984057	1.000000	0.71417	1.000000	0.80357	0.563000	0.35712	2.067000	0.41461	0.313000	0.23062	0.591000	0.81541	GAG		0.607	GINS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257384.2	NM_022770		T	58426556	G	T	58426556	3	4	61	1	0	0	0	0	1	0	0	0	6409	933	33	2	53	2	GINS3	16	58426556	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112927	58426556	31928197	9825	17810										
CNOT1	23019	broad.mit.edu	37	chr16	58573745	58573745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaacctccaagagacttCgaagagcctgagcttgaggg	11	11	0	4	rs181822641		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58573745C>T	ENST00000317147.5	-	35	5251	c.4919G>A	c.(4918-4920)cGa>cAa	p.R1640Q	CNOT1_ENST00000569240.1_Missense_Mutation_p.R1635Q|CNOT1_ENST00000245138.4_Missense_Mutation_p.R491Q	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1640					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.R1640Q(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CAAGAGACTTCGAAGAGCCTG	0.433													C|||	1	0.000199681	0	0	5008	,	,		18022	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											130	113	119					16																	58573745		2198	4300	6498	57131246	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4919G>A	16.37:g.58573745C>T	ENSP00000320949:p.Arg1640Gln		57131246	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.22	3.334835	0.60853	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200	T;T	0.16743	2.32;2.32	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.09730	0.0239	N	0.04508	-0.205	0.80722	D	1	B;B;B	0.24651	0.041;0.032;0.108	B;B;B	0.20577	0.008;0.014;0.03	T	0.31613	-0.9937	10	0.13108	T	0.6	-13.0679	20.1338	0.98010	0.0:1.0:0.0:0.0	.	491;1640;1635	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	Q	1640;491;1635	ENSP00000320949:R1640Q;ENSP00000245138:R491Q	ENSP00000245138:R491Q	R	-	2	0	CNOT1	57131246	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.089000	0.71384	2.770000	0.95276	0.655000	0.94253	CGA		0.433	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		T	58573745	C	T	58573745	3	4	61	1	0	0	0	0	1	0	0	0	3623	884	31	1	2271	1	CNOT1	16	58573745	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147189	58573745	31781008	9826	17811										
CNOT1	23019	broad.mit.edu	37	chr16	58577650	58577650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgcattcgagattcctccGaatccagggcaaaatccttc	7	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58577650G>A	ENST00000317147.5	-	31	4627	c.4295C>T	c.(4294-4296)tCg>tTg	p.S1432L	CNOT1_ENST00000569240.1_Missense_Mutation_p.S1427L|CNOT1_ENST00000245138.4_Missense_Mutation_p.S283L|CNOT1_ENST00000441024.2_Missense_Mutation_p.S1432L	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1432	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.S1432L(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AGATTCCTCCGAATCCAGGGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											121	94	103					16																	58577650		2198	4300	6498	57135151	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4295C>T	16.37:g.58577650G>A	ENSP00000320949:p.Ser1432Leu		57135151	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.727005	0.89390	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.46063	0.89;0.88	5.3	5.3	0.74995	CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 (1);	0.000000	0.85682	D	0.000000	T	0.38532	0.1044	L	0.39245	1.2	0.80722	D	1	P;D;P;P	0.53151	0.843;0.958;0.867;0.839	B;B;B;B	0.40534	0.083;0.332;0.24;0.228	T	0.40308	-0.9570	10	0.62326	D	0.03	.	18.9405	0.92604	0.0:0.0:1.0:0.0	.	283;1432;1432;1427	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	L	1432;283;1427;1432	ENSP00000320949:S1432L;ENSP00000413113:S1432L	ENSP00000245138:S283L	S	-	2	0	CNOT1	57135151	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.835000	0.99442	2.461000	0.83175	0.585000	0.79938	TCG		0.478	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58577650	G	A	58577650	3	1	61	1	0	0	0	0	1	0	0	0	3623	1059	37	1	3133	1	CNOT1	16	58577650	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3905	58577650	31777103	9827	17812										
CNOT1	23019	broad.mit.edu	37	chr16	58583674	58583674	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttgttaaattcaggattCttcagcgtgtcaaggaagtt	9	6	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58583674C>A	ENST00000317147.5	-	25	3803	c.3471G>T	c.(3469-3471)aaG>aaT	p.K1157N	CNOT1_ENST00000569732.1_5'Flank|CNOT1_ENST00000569240.1_Missense_Mutation_p.K1152N|CNOT1_ENST00000245138.4_Missense_Mutation_p.K47N|CNOT1_ENST00000441024.2_Missense_Mutation_p.K1157N|SNORA46_ENST00000384762.1_RNA	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1157	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.K1157N(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		ATTCAGGATTCTTCAGCGTGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	16											144	142	143					16																	58583674		2198	4300	6498	57141175	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3471G>T	16.37:g.58583674C>A	ENSP00000320949:p.Lys1157Asn		57141175	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.201960	0.38905	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.18338	2.22;2.22	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.26268	0.0641	L	0.31294	0.92	0.80722	D	1	B;D;B;B	0.61080	0.091;0.989;0.067;0.162	B;D;B;B	0.75020	0.039;0.985;0.012;0.039	T	0.02431	-1.1160	10	0.13853	T	0.58	.	13.4785	0.61322	0.0:0.9246:0.0:0.0754	.	47;1157;1157;1152	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	N	1157;586;47;1152;1157	ENSP00000320949:K1157N;ENSP00000413113:K1157N	ENSP00000245138:K47N	K	-	3	2	CNOT1	57141175	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.351000	0.34022	2.536000	0.85505	0.491000	0.48974	AAG		0.343	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58583674	C	A	58583674	3	1	61	1	0	0	0	0	1	0	0	0	3623	912	32	2	3981	2	CNOT1	16	58583674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6024	58583674	31771079	9828	17813										
CNOT1	23019	broad.mit.edu	37	chr16	58616711	58616711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaccagttctttaagaaCgtcaatcaagacttctacat	4	11	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:58616711C>T	ENST00000317147.5	-	10	1362	c.1030G>A	c.(1030-1032)Gtt>Att	p.V344I	CNOT1_ENST00000569240.1_Missense_Mutation_p.V344I|CNOT1_ENST00000441024.2_Missense_Mutation_p.V344I	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	344					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.V344I(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TCTTTAAGAACGTCAATCAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	16											170	161	164					16																	58616711		2198	4300	6498	57174212	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.1030G>A	16.37:g.58616711C>T	ENSP00000320949:p.Val344Ile		57174212	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.000180	0.54147	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.43688	0.94;0.94	5.88	5.88	0.94601	.	0.111469	0.64402	D	0.000012	T	0.36358	0.0964	L	0.31926	0.97	0.80722	D	1	B;B;B	0.13145	0.006;0.002;0.007	B;B;B	0.12837	0.008;0.0;0.002	T	0.09975	-1.0650	9	.	.	.	-16.0532	20.2422	0.98381	0.0:1.0:0.0:0.0	.	344;344;344	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	I	344	ENSP00000320949:V344I;ENSP00000413113:V344I	.	V	-	1	0	CNOT1	57174212	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.763000	0.62257	2.788000	0.95919	0.650000	0.86243	GTT		0.378	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		T	58616711	C	T	58616711	3	4	61	1	0	0	0	0	1	0	0	0	3623	536	19	1	6482	1	CNOT1	16	58616711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33037	58616711	31738042	9829	17814										
CDH8	1006	broad.mit.edu	37	chr16	61823376	61823376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccaggtcagtgtgccggtCgatggaaaacctacaaaaca	10	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:61823376C>T	ENST00000577390.1	-	8	2242	c.1288G>A	c.(1288-1290)Gac>Aac	p.D430N	CDH8_ENST00000584337.1_Missense_Mutation_p.D430N|CDH8_ENST00000577730.1_Missense_Mutation_p.D430N|CDH8_ENST00000299345.6_Missense_Mutation_p.D430N	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	430	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.D430N(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GTGTGCCGGTCGATGGAAAAC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											174	147	156					16																	61823376		2203	4299	6502	60380877	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1288G>A	16.37:g.61823376C>T	ENSP00000462701:p.Asp430Asn		60380877	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	33	5.268405	0.95429	.	.	ENSG00000150394	ENST00000299345	T	0.01725	4.67	5.3	5.3	0.74995	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.08582	0.0213	L	0.51853	1.615	0.80722	D	1	D;D	0.89917	0.982;1.0	P;D	0.77557	0.853;0.99	T	0.05468	-1.0883	10	0.59425	D	0.04	.	19.305	0.94157	0.0:1.0:0.0:0.0	.	246;430	Q3LID3;P55286	.;CADH8_HUMAN	N	430	ENSP00000299345:D430N	ENSP00000299345:D430N	D	-	1	0	CDH8	60380877	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.323000	0.79105	2.629000	0.89072	0.491000	0.48974	GAC		0.428	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61823376	C	T	61823376	3	4	61	1	0	0	0	0	1	0	0	0	3122	884	31	1	1131	1	CDH8	16	61823376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3206665	61823376	28531377	9830	17815										
CDH11	1009	broad.mit.edu	37	chr16	65038750	65038750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggcacaccagggcggctTgtaaacagtagttctccttc	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:65038750T>C	ENST00000268603.4	-	3	638	c.23A>G	c.(22-24)cAa>cGa	p.Q8R	CDH11_ENST00000394156.3_Missense_Mutation_p.Q8R|CDH11_ENST00000566827.1_Intron|CDH11_ENST00000569624.1_5'UTR	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	8					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q8R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CAGGGCGGCTTGTAAACAGTA	0.597			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																													Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	1	Substitution - Missense(1)	large_intestine(1)	16											19	26	23					16																	65038750		2187	4286	6473	63596251	SO:0001583	missense	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.23A>G	16.37:g.65038750T>C	ENSP00000268603:p.Gln8Arg		63596251	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984030	0.35036	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000536902	T;T	0.54866	0.55;0.55	5.47	5.47	0.80525	.	0.187525	0.45867	D	0.000321	T	0.33440	0.0863	N	0.08118	0	0.80722	D	1	B;B	0.22146	0.065;0.009	B;B	0.22601	0.04;0.005	T	0.15263	-1.0443	10	0.23891	T	0.37	.	14.7371	0.69424	0.0:0.0:0.0:1.0	.	8;8	P55287-2;P55287	.;CAD11_HUMAN	R	8	ENSP00000268603:Q8R;ENSP00000377711:Q8R	ENSP00000268603:Q8R	Q	-	2	0	CDH11	63596251	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.335000	0.43929	2.081000	0.62600	0.482000	0.46254	CAA		0.597	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		C	65038750	T	C	65038750	3	2	61	1	0	0	0	0	1	0	0	0	3103	1812	63	4	2411	4	CDH11	16	65038750	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3215374	65038750	25316003	9831	17816										
TK2	7084	broad.mit.edu	37	chr16	66551054	66551054	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaccagcggaatgaccttCtcctcttccctgcatctctt	5	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66551054C>A	ENST00000451102.2	-	8	953	c.603G>T	c.(601-603)gaG>gaT	p.E201D	TK2_ENST00000417693.3_Missense_Mutation_p.E183D|TK2_ENST00000299697.7_Missense_Mutation_p.E243D|TK2_ENST00000545043.2_Missense_Mutation_p.E176D|TK2_ENST00000563369.2_Missense_Mutation_p.E104D|TK2_ENST00000527284.1_Missense_Mutation_p.E170D|TK2_ENST00000544898.1_Missense_Mutation_p.E152D|RP11-403P17.5_ENST00000561728.1_Nonsense_Mutation_p.E18*|TK2_ENST00000527800.1_Missense_Mutation_p.E104D|TK2_ENST00000525974.1_Missense_Mutation_p.E104D|TK2_ENST00000564917.1_Missense_Mutation_p.E201D			O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	201					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|DNA replication (GO:0006260)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|thymidine kinase activity (GO:0004797)	p.E243D(1)		large_intestine(1)|lung(2)|urinary_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		GAATGACCTTCTCCTCTTCCC	0.512											OREG0032067	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																																				1	Substitution - Missense(1)	large_intestine(1)	16											269	267	267					16																	66551054		2201	4300	6501	65108555	SO:0001583	missense	7084				CCDS10805.1, CCDS10805.2, CCDS54016.1, CCDS54017.1, CCDS54018.1, CCDS61955.1	16q22-q23.1	2012-10-02			ENSG00000166548	ENSG00000166548	2.7.1.21		11831	protein-coding gene	gene with protein product		188250					Standard	NM_004614		Approved		uc002eos.3	O00142	OTTHUMG00000137499	ENST00000451102.2:c.603G>T	16.37:g.66551054C>A	ENSP00000414334:p.Glu201Asp	1092	65108555	B4DGJ7|B4DZK7|B7ZAB1|E9PH08|O15238	Missense_Mutation	SNP	ENST00000451102.2	37	CCDS10805.2	.	.	.	.	.	.	.	.	.	.	C	23.6	4.438493	0.83885	.	.	ENSG00000166548	ENST00000299697;ENST00000417693;ENST00000545043;ENST00000451102;ENST00000527800;ENST00000527284;ENST00000544898;ENST00000525974	D;D;D;D;D;D;D;D	0.99158	-5.5;-5.5;-5.5;-5.5;-5.5;-5.5;-5.5;-5.5	5.6	3.3	0.37823	.	0.000000	0.85682	D	0.000000	D	0.99321	0.9762	M	0.92077	3.27	0.53688	D	0.999976	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.989;0.999;0.984	D	0.99066	1.0832	10	0.87932	D	0	-29.5938	10.9992	0.47596	0.0:0.8197:0.0:0.1803	.	243;201;152;243;170	Q8IZR3;O00142;F5GYK4;E5KNQ5;O00142-2	.;KITM_HUMAN;.;.;.	D	243;183;176;201;104;170;152;104	ENSP00000299697:E243D;ENSP00000407469:E183D;ENSP00000438143:E176D;ENSP00000414334:E201D;ENSP00000433770:E104D;ENSP00000435312:E170D;ENSP00000440898:E152D;ENSP00000434594:E104D	ENSP00000299697:E243D	E	-	3	2	TK2	65108555	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.760000	0.38430	1.371000	0.46172	0.655000	0.94253	GAG		0.512	TK2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268806.4			A	66551054	C	A	66551054	3	1	61	1	0	0	0	0	1	0	0	0	15972	912	32	2	206	2	TK2	16	66551054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1512304	66551054	23803699	9832	17817										
CMTM2	146225	broad.mit.edu	37	chr16	66620981	66620981	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtcggcgatccatgaatCtccactacttacttgctgtg	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66620981C>A	ENST00000268595.2	+	3	677	c.526C>A	c.(526-528)Ctc>Atc	p.L176I	CMTM2_ENST00000379486.2_Missense_Mutation_p.L123I	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	176	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.L176I(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		ATCCATGAATCTCCACTACTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											243	184	204					16																	66620981		2201	4300	6501	65178482	SO:0001583	missense	146225			BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"chemokine-like factor super family 2", "chemokine-like factor superfamily 2"	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.526C>A	16.37:g.66620981C>A	ENSP00000268595:p.Leu176Ile		65178482	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.849490	0.00563	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.44083	0.93;1.39	4.05	-8.1	0.01086	Marvel (1);	2.644000	0.01368	N	0.012462	T	0.19805	0.0476	N	0.08118	0	0.09310	N	1	B;B	0.17268	0.021;0.021	B;B	0.12837	0.008;0.005	T	0.21793	-1.0235	10	0.49607	T	0.09	5.7066	2.8266	0.05487	0.1447:0.3818:0.25:0.2235	.	123;176	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	I	123;176	ENSP00000368800:L123I;ENSP00000268595:L176I	ENSP00000268595:L176I	L	+	1	0	CMTM2	65178482	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.580000	0.00019	-5.251000	0.00018	-1.431000	0.01090	CTC		0.498	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			A	66620981	C	A	66620981	3	1	61	1	0	0	0	0	1	0	0	0	3589	913	32	2	536	2	CMTM2	16	66620981	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69927	66620981	23733772	9833	17818										
DYNC1LI2	1783	broad.mit.edu	37	chr16	66776562	66776562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaatccacacgttgcagCgcgtgtgatctgagaaaaca	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66776562C>T	ENST00000258198.2	-	4	514	c.308G>A	c.(307-309)cGc>cAc	p.R103H	DYNC1LI2_ENST00000440564.2_Missense_Mutation_p.R64H|DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.R103H|DYNC1LI2_ENST00000443351.2_Intron	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	103					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R103H(1)		central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		CACGTTGCAGCGCGTGTGATC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	16											57	50	53					16																	66776562		2200	4300	6500	65334063	SO:0001583	missense	1783			AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"Cytoplasmic dyneins"	2966	protein-coding gene	gene with protein product		611406	"dynein, cytoplasmic, light intermediate polypeptide 2"	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.308G>A	16.37:g.66776562C>T	ENSP00000258198:p.Arg103His		65334063	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	37	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	C	34	5.307687	0.95629	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000440564	T;T;T	0.32515	1.45;1.45;1.45	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.57154	0.2034	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	1.0;0.969;1.0	D;P;D	0.87578	0.998;0.614;0.998	T	0.57929	-0.7726	10	0.59425	D	0.04	-18.3496	19.0071	0.92856	0.0:1.0:0.0:0.0	.	64;103;103	B4E2E0;B4DHD8;O43237	.;.;DC1L2_HUMAN	H	103;103;64	ENSP00000258198:R103H;ENSP00000368795:R103H;ENSP00000408566:R64H	ENSP00000258198:R103H	R	-	2	0	DYNC1LI2	65334063	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.562000	0.82300	2.793000	0.96121	0.563000	0.77884	CGC		0.463	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		T	66776562	C	T	66776562	3	4	61	1	0	0	0	0	1	0	0	0	4856	768	27	1	1210	1	DYNC1LI2	16	66776562	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	155581	66776562	23578191	9834	17819										
NAE1	8883	broad.mit.edu	37	chr16	66857470	66857470	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagacatcgctatttaattCttgtaagaattccatggcag	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66857470C>A	ENST00000290810.3	-	5	380	c.283G>T	c.(283-285)Gaa>Taa	p.E95*	NAE1_ENST00000379463.2_Nonsense_Mutation_p.E89*|NAE1_ENST00000394074.2_Nonsense_Mutation_p.E6*|NAE1_ENST00000564040.2_5'UTR|NAE1_ENST00000359087.4_Nonsense_Mutation_p.E98*			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	95					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)	p.E95*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	CTATTTAATTCTTGTAAGAAT	0.308																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											70	68	68					16																	66857470		2200	4299	6499	65414971	SO:0001587	stop_gained	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.283G>T	16.37:g.66857470C>A	ENSP00000290810:p.Glu95*		65414971	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Nonsense_Mutation	SNP	ENST00000290810.3	37	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	C	35	5.456917	0.96223	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463;ENST00000394074	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-18.1961	19.6512	0.95812	0.0:1.0:0.0:0.0	.	.	.	.	X	98;95;89;6	.	ENSP00000290810:E95X	E	-	1	0	NAE1	65414971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.264000	0.78432	2.712000	0.92718	0.591000	0.81541	GAA		0.308	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905		A	66857470	C	A	66857470	4	1	61	1	0	0	0	0	0	1	0	0	10169	922	32	2	1385	2	NAE1	16	66857470	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80908	66857470	23497283	9835	17820										
CA7	766	broad.mit.edu	37	chr16	66886692	66886692	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactactggacctacccgggCtctctgacgactcccccact	7	19	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66886692C>T	ENST00000338437.2	+	6	703	c.594C>T	c.(592-594)ggC>ggT	p.G198G	CA7_ENST00000394069.3_Silent_p.G142G|RP11-61A14.1_ENST00000551187.1_RNA	NM_005182.2	NP_005173.1	P43166	CAH7_HUMAN	carbonic anhydrase VII	198					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of chloride transport (GO:2001225)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.G198G(1)		kidney(1)|large_intestine(1)|lung(4)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)	Acetazolamide(DB00819)|Diclofenamide(DB01144)|Methazolamide(DB00703)|Zonisamide(DB00909)	CCTACCCGGGCTCTCTGACGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	16											60	56	57					16																	66886692		2200	4300	6500	65444193	SO:0001819	synonymous_variant	766				CCDS10821.1, CCDS42173.1	16q22.1	2008-02-05			ENSG00000168748	ENSG00000168748	4.2.1.1	"Carbonic anhydrases"	1381	protein-coding gene	gene with protein product		114770				1783392	Standard	XM_005256135		Approved		uc002eqi.3	P43166	OTTHUMG00000137524	ENST00000338437.2:c.594C>T	16.37:g.66886692C>T			65444193	Q541F0|Q86YU0	Silent	SNP	ENST00000338437.2	37	CCDS10821.1																																																																																				0.607	CA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268847.1			T	66886692	C	T	66886692	2	4	61	1	0	0	0	0	0	0	0	1	2528	784	28	3		3	CA7	16	66886692	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29222	66886692	23468061	9836	17821										
PDP2	57546	broad.mit.edu	37	chr16	66918608	66918608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgatgtttggcatcttcGatggacatggtggtcatgca	13	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66918608G>A	ENST00000311765.2	+	2	755	c.421G>A	c.(421-423)Gat>Aat	p.D141N	PDP2_ENST00000568720.1_Intron	NM_020786.2	NP_065837.1	Q9P2J9	PDP2_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 2	141					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|magnesium-dependent protein serine/threonine phosphatase activity (GO:0004724)|metal ion binding (GO:0046872)	p.D141N(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		TGGCATCTTCGATGGACATGG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	80	89					16																	66918608		2200	4300	6500	65476109	SO:0001583	missense	57546			AB037769	CCDS10822.1	16q22.1	2012-04-17			ENSG00000172840	ENSG00000172840		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	30263	protein-coding gene	gene with protein product	"protein phosphatase 2C, magnesium-dependent, catalytic subunit 2"	615499				9651365	Standard	NM_020786		Approved	KIAA1348, PPM2C2	uc002eqk.2	Q9P2J9	OTTHUMG00000137512	ENST00000311765.2:c.421G>A	16.37:g.66918608G>A	ENSP00000309548:p.Asp141Asn		65476109	A8K924	Missense_Mutation	SNP	ENST00000311765.2	37	CCDS10822.1	.	.	.	.	.	.	.	.	.	.	G	31	5.092565	0.94149	.	.	ENSG00000172840	ENST00000311765	T	0.55413	0.52	5.86	5.86	0.93980	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.80336	0.4604	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83164	-0.0097	10	0.87932	D	0	-17.1119	20.5632	0.99335	0.0:0.0:1.0:0.0	.	141	Q9P2J9	PDP2_HUMAN	N	141	ENSP00000309548:D141N	ENSP00000309548:D141N	D	+	1	0	PDP2	65476109	1.000000	0.71417	0.992000	0.48379	0.974000	0.67602	9.813000	0.99286	2.937000	0.99478	0.650000	0.86243	GAT		0.572	PDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268831.2	NM_020786		A	66918608	G	A	66918608	3	1	61	1	0	0	0	0	1	0	0	0	11717	1058	37	1	423	1	PDP2	16	66918608	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31916	66918608	23436145	9837	17822										
CDH16	1014	broad.mit.edu	37	chr16	66942343	66942343	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctggttgatccgggtcCttcttccttgacatggtcca	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:66942343C>A	ENST00000299752.4	-	18	2635	c.2442G>T	c.(2440-2442)aaG>aaT	p.K814N	CDH16_ENST00000568632.1_Missense_Mutation_p.K717N|CDH16_ENST00000570262.1_Missense_Mutation_p.K734N|CDH16_ENST00000394055.3_Missense_Mutation_p.K792N|CDH16_ENST00000565796.1_Missense_Mutation_p.K775N	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	814					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.K814N(1)		endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GATCCGGGTCCTTCTTCCTTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											110	105	107					16																	66942343		2200	4300	6500	65499844	SO:0001583	missense	1014			AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"Cadherins / Major cadherins"	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.2442G>T	16.37:g.66942343C>A	ENSP00000299752:p.Lys814Asn		65499844	B4DPA8|H3BPD3|Q6UW93	Missense_Mutation	SNP	ENST00000299752.4	37	CCDS10823.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307922	0.40895	.	.	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	T;T	0.60548	0.18;0.2	5.11	2.93	0.34026	.	0.165860	0.37219	N	0.002181	T	0.54727	0.1876	N	0.14661	0.345	0.39008	D	0.95948	D;D;P	0.76494	0.999;0.999;0.787	D;D;B	0.80764	0.943;0.994;0.219	T	0.59579	-0.7428	10	0.72032	D	0.01	-26.4532	6.8821	0.24179	0.1863:0.7129:0.0:0.1007	.	792;814;814	O75309-2;B2R7S8;O75309	.;.;CAD16_HUMAN	N	792;814;778	ENSP00000377619:K792N;ENSP00000299752:K814N	ENSP00000299752:K814N	K	-	3	2	CDH16	65499844	1.000000	0.71417	0.994000	0.49952	0.217000	0.24651	0.291000	0.18994	1.142000	0.42291	0.655000	0.94253	AAG		0.582	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062		A	66942343	C	A	66942343	3	1	61	1	0	0	0	0	1	0	0	0	3107	680	24	2	51	2	CDH16	16	66942343	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23735	66942343	23412410	9838	17823										
SLC9A5	6553	broad.mit.edu	37	chr16	67290591	67290591	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctgttcttccgagccctCggtattgctggcaccctctg	9	15	2	0	rs528679277		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67290591C>T	ENST00000299798.11	+	6	1196	c.1131C>T	c.(1129-1131)ctC>ctT	p.L377L		NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	377					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.L377L(1)		breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		TCCGAGCCCTCGGTATTGCTG	0.567													C|||	1	0.000199681	8e-04	0	5008	,	,		19476	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											153	152	153					16																	67290591		2098	4210	6308	65848092	SO:0001630	splice_region_variant	6553				CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"Solute carriers"	11078	protein-coding gene	gene with protein product		600477	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 5", "solute carrier family 9 (sodium/hydrogen exchanger), member 5"			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.1132+1C>T	16.37:g.67290591C>T			65848092	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																				0.567	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		Silent	T	67290591	C	T	67290591	5	4	61	1	0	0	0	0	0	0	1	0	14754	898	31	1	1153	1	SLC9A5	16	67290591	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	348248	67290591	23064162	9839	17824										
PLEKHG4	25894	broad.mit.edu	37	chr16	67315038	67315038	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagtgctagttgatgcccGaatttgtgctccaagttctt	10	9	1	1	rs145862477		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67315038G>A	ENST00000360461.5	+	4	3299	c.764G>A	c.(763-765)cGa>cAa	p.R255Q	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.R255Q|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.R255Q|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.R174Q	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	255							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R255Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		GTTGATGCCCGAATTTGTGCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	16											127	114	119					16																	67315038		2198	4300	6498	65872539	SO:0001583	missense	25894			AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.764G>A	16.37:g.67315038G>A	ENSP00000353646:p.Arg255Gln		65872539	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555108	0.65425	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.71	2.75	0.32379	.	0.677970	0.11391	N	0.568776	T	0.50120	0.1597	M	0.71871	2.18	0.23249	N	0.998044	B;P;B	0.39326	0.014;0.668;0.015	B;B;B	0.28011	0.006;0.085;0.008	T	0.42430	-0.9452	10	0.66056	D	0.02	.	7.9755	0.30153	0.2521:0.0:0.7479:0.0	.	174;62;255	Q58EX7-2;B4E3H4;Q58EX7	.;.;PKHG4_HUMAN	Q	255;255;255;174	ENSP00000353646:R255Q;ENSP00000401118:R255Q;ENSP00000368649:R255Q;ENSP00000398030:R174Q	ENSP00000353646:R255Q	R	+	2	0	PLEKHG4	65872539	0.948000	0.32251	0.365000	0.25901	0.762000	0.43233	1.403000	0.34612	0.366000	0.24427	-0.216000	0.12614	CGA		0.493	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		A	67315038	G	A	67315038	3	1	61	1	0	0	0	0	1	0	0	0	12102	1058	37	1	778	1	PLEKHG4	16	67315038	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24447	67315038	23039715	9840	17825										
PLEKHG4	25894	broad.mit.edu	37	chr16	67318747	67318747	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctgcccacttccgaaaGatgtgggctctggccacggg	12	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67318747G>T	ENST00000360461.5	+	12	4359	c.1824G>T	c.(1822-1824)aaG>aaT	p.K608N	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.K608N|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.K608N|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.K527N	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	608							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K608N(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		ACTTCCGAAAGATGTGGGCTC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	16											19	22	21					16																	67318747		2198	4300	6498	65876248	SO:0001583	missense	25894			AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1824G>T	16.37:g.67318747G>T	ENSP00000353646:p.Lys608Asn		65876248	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286992	0.80803	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.10005	2.92;2.92;2.92;2.95	4.5	2.36	0.29203	.	.	.	.	.	T	0.11367	0.0277	L	0.32530	0.975	0.30926	N	0.727429	P;P	0.47409	0.879;0.895	P;P	0.48677	0.586;0.535	T	0.13335	-1.0513	9	0.33141	T	0.24	.	7.2992	0.26411	0.2572:0.0:0.7427:0.0	.	527;608	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	N	608;608;608;527	ENSP00000353646:K608N;ENSP00000401118:K608N;ENSP00000368649:K608N;ENSP00000398030:K527N	ENSP00000353646:K608N	K	+	3	2	PLEKHG4	65876248	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.291000	0.51764	0.214000	0.20742	0.585000	0.79938	AAG		0.677	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		T	67318747	G	T	67318747	3	4	61	1	0	0	0	0	1	0	0	0	12102	933	33	2	1870	2	PLEKHG4	16	67318747	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3709	67318747	23036006	9841	17826										
KCTD19	146212	broad.mit.edu	37	chr16	67335782	67335782	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaatacatcaatgttggaGaaattatccggtagtaaaat	7	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67335782G>T	ENST00000304372.5	-	5	742	c.687C>A	c.(685-687)ttC>ttA	p.F229L	KCTD19_ENST00000562860.1_5'UTR	NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	229					protein homooligomerization (GO:0051260)			p.F229L(1)		endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		CAATGTTGGAGAAATTATCCG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	16											120	121	120					16																	67335782		1841	4090	5931	65893283	SO:0001583	missense	146212			AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.687C>A	16.37:g.67335782G>T	ENSP00000305702:p.Phe229Leu		65893283	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335256	0.81801	.	.	ENSG00000168676	ENST00000304372	T	0.75477	-0.94	6.17	5.04	0.67666	BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.76564	0.4005	N	0.24115	0.695	0.33614	D	0.603905	D	0.67145	0.996	D	0.70227	0.968	T	0.81982	-0.0683	10	0.87932	D	0	-24.1373	13.271	0.60161	0.0857:0.0:0.9143:0.0	.	229	Q17RG1	KCD19_HUMAN	L	229	ENSP00000305702:F229L	ENSP00000305702:F229L	F	-	3	2	KCTD19	65893283	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.075000	0.30716	2.941000	0.99782	0.655000	0.94253	TTC		0.418	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		T	67335782	G	T	67335782	3	4	61	1	0	0	0	0	1	0	0	0	8127	933	33	2	2141	2	KCTD19	16	67335782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17035	67335782	23018971	9842	17827										
LRRC36	55282	broad.mit.edu	37	chr16	67410754	67410754	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaactgaaggaggctgcGcagctggtccctaatgacat	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67410754G>A	ENST00000329956.6	+	11	1804	c.1785G>A	c.(1783-1785)gcG>gcA	p.A595A	LRRC36_ENST00000541146.1_Intron|LRRC36_ENST00000563189.1_Silent_p.A474A|LRRC36_ENST00000290940.7_Intron|LRRC36_ENST00000435835.3_Intron	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	595								p.A595A(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		AGGAGGCTGCGCAGCTGGTCC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	16											120	114	116					16																	67410754		2198	4300	6498	65968255	SO:0001819	synonymous_variant	55282			BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.1785G>A	16.37:g.67410754G>A			65968255	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Silent	SNP	ENST00000329956.6	37	CCDS32467.1																																																																																				0.517	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		A	67410754	G	A	67410754	2	1	61	1	0	0	0	0	0	0	0	1	9019	1074	38	1		1	LRRC36	16	67410754	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74972	67410754	22943999	9843	17828										
ATP6V0D1	9114	broad.mit.edu	37	chr16	67478507	67478507	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacggcctccatctgctcGaagctgcctagtgggtggca	12	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67478507G>A	ENST00000290949.3	-	3	555	c.405C>T	c.(403-405)ttC>ttT	p.F135F	ATP6V0D1_ENST00000540149.1_Silent_p.F176F|ATP6V0D1_ENST00000602876.1_Silent_p.F58F	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	135					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)	p.F135F(1)		large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		CCATCTGCTCGAAGCTGCCTA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	16											118	80	92					16																	67478507		2198	4300	6498	66036008	SO:0001819	synonymous_variant	9114			X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"ATPases / V-type"	13724	protein-coding gene	gene with protein product		607028	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.405C>T	16.37:g.67478507G>A			66036008	P12953|Q02547	Silent	SNP	ENST00000290949.3	37	CCDS10838.1																																																																																				0.582	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691		A	67478507	G	A	67478507	2	1	61	1	0	0	0	0	0	0	0	1	1174	1049	37	1		1	ATP6V0D1	16	67478507	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67753	67478507	22876246	9844	17829										
FAM65A	79567	broad.mit.edu	37	chr16	67578324	67578324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacctgtaccactgcagtcGcctcctgctggtgaggctga	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67578324G>A	ENST00000379312.3	+	15	2856	c.2735G>A	c.(2734-2736)cGc>cAc	p.R912H	FAM65A_ENST00000540839.3_Missense_Mutation_p.R927H|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R922H|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000042381.4_Missense_Mutation_p.R908H|FAM65A_ENST00000422602.2_Missense_Mutation_p.R928H	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	912						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.R908H(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CACTGCAGTCGCCTCCTGCTG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	16											90	82	85					16																	67578324		2198	4300	6498	66135825	SO:0001583	missense	79567			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2735G>A	16.37:g.67578324G>A	ENSP00000368614:p.Arg912His		66135825	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654243	0.29425	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.76448	-1.02;-1.02;-1.02	5.55	0.947	0.19555	.	0.690542	0.14688	N	0.304307	T	0.53706	0.1813	N	0.04090	-0.28	0.09310	N	1	B;B;B	0.19445	0.015;0.036;0.005	B;B;B	0.04013	0.001;0.001;0.001	T	0.37314	-0.9711	10	0.23891	T	0.37	-0.573	11.6031	0.51015	0.3702:0.0:0.6298:0.0	.	922;928;912	B4DIM2;E9PBS3;Q6ZS17	.;.;FA65A_HUMAN	H	912;908;928;922	ENSP00000368614:R912H;ENSP00000042381:R908H;ENSP00000400099:R928H	ENSP00000042381:R908H	R	+	2	0	FAM65A	66135825	0.000000	0.05858	0.979000	0.43373	0.997000	0.91878	-0.053000	0.11846	0.321000	0.23259	0.655000	0.94253	CGC		0.627	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67578324	G	A	67578324	3	1	61	1	0	0	0	0	1	0	0	0	5618	1087	38	1	2777	1	FAM65A	16	67578324	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99817	67578324	22776429	9845	17830										
CTCF	10664	broad.mit.edu	37	chr16	67650710	67650710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaccagtggagaattggttCggcatcgtcgttacaaacac	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67650710C>T	ENST00000264010.4	+	5	1459	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	AC009095.4_ENST00000388909.4_RNA|CTCF_ENST00000401394.1_Missense_Mutation_p.R11W	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	339			R -> W (in a Wilms' tumor). {ECO:0000269|PubMed:11782357}.		chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R339W(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		AGAATTGGTTCGGCATCGTCG	0.483																																					Colon(175;1200 1966 6945 23069 27405)											1	Substitution - Missense(1)	large_intestine(1)	16											327	269	288					16																	67650710		2198	4300	6498	66208211	SO:0001583	missense	10664			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.1015C>T	16.37:g.67650710C>T	ENSP00000264010:p.Arg339Trp		66208211	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	37	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534257	0.85812	.	.	ENSG00000102974	ENST00000264010;ENST00000401394	T;T	0.26660	1.72;1.72	4.89	4.89	0.63831	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.199220	0.33346	N	0.005003	T	0.54143	0.1840	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.59836	-0.7379	10	0.66056	D	0.02	.	13.3046	0.60345	0.1581:0.8419:0.0:0.0	.	339	P49711	CTCF_HUMAN	W	339;11	ENSP00000264010:R339W;ENSP00000384707:R11W	ENSP00000264010:R339W	R	+	1	2	CTCF	66208211	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.529000	0.53532	2.553000	0.86117	0.558000	0.71614	CGG		0.483	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		T	67650710	C	T	67650710	3	4	61	1	0	0	0	0	1	0	0	0	4006	875	31	1	1025	1	CTCF	16	67650710	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72386	67650710	22704043	9846	17831										
GFOD2	81577	broad.mit.edu	37	chr16	67709826	67709826	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagctgtttcatgcgcacGaaggcaggcaggaagcgcag	14	10	2	0	rs142530623		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67709826G>A	ENST00000268797.7	-	3	735	c.390C>T	c.(388-390)ttC>ttT	p.F130F	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	130					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)	p.F130F(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		TCATGCGCACGAAGGCAGGCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	16											103	83	89					16																	67709826		2198	4300	6498	66267327	SO:0001819	synonymous_variant	81577			AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.390C>T	16.37:g.67709826G>A			66267327	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Silent	SNP	ENST00000268797.7	37	CCDS10845.1																																																																																				0.592	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819		A	67709826	G	A	67709826	2	1	61	1	0	0	0	0	0	0	0	1	6364	1049	37	1		1	GFOD2	16	67709826	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59116	67709826	22644927	9847	17832										
TSNAXIP1	80152	broad.mit.edu	37	chr16	67859647	67859647	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgacccgcacgcagatgGaactcaacaacatgaaggcc	9	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67859647G>A	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.E298K|TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.E244K|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.E229K	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E244K(1)		NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CACGCAGATGGAACTCAACAA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											104	112	109					16																	67859647		2103	4250	6353	66417148	SO:0001628	intergenic_variant	55815			AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			16.37:g.67859647G>A			66417148	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	37	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341761	0.61073	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.7	5.7	0.88788	.	0.083367	0.47852	D	0.000220	T	0.43743	0.1261	L	0.41824	1.3	0.37050	D	0.897563	P;P;P;P	0.40970	0.734;0.734;0.487;0.487	B;B;B;B	0.39503	0.301;0.301;0.301;0.301	T	0.47560	-0.9108	9	0.27785	T	0.31	-17.6965	12.3218	0.54989	0.0796:0.0:0.9204:0.0	.	229;298;34;244	E7ENJ7;B4DXD0;B4DY78;Q2TAA8	.;.;.;TXIP1_HUMAN	K	229;244;34	.	ENSP00000373485:E244K	E	+	1	0	TSNAXIP1	66417148	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.884000	0.63135	2.679000	0.91253	0.655000	0.94253	GAA		0.572	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67859647	G	A	67859647	1	1	61	0	1	0	0	0	0	0	0	0	16672	1175	41	3		3	TSNAXIP1	16	67859647	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149821	67859647	22495106	9848	17833										
TSNAXIP1	80152	broad.mit.edu	37	chr16	67861792	67861792	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgccagaggagggtgacGagaaggaagaagccgtggtg	18	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:67861792G>A	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.E679K|TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.E625K|CENPT_ENST00000562947.1_5'Flank|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.E610K	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E625K(1)		NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		GGAGGGTGACGAGAAGGAAGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	16											80	89	86					16																	67861792		2198	4300	6498	66419293	SO:0001628	intergenic_variant	55815			AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			16.37:g.67861792G>A			66419293	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	37	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.573368	0.65765	.	.	ENSG00000102904	ENST00000415766;ENST00000388833	.	.	.	6.04	2.79	0.32731	.	0.132626	0.48286	D	0.000183	T	0.27524	0.0676	L	0.56769	1.78	0.09310	N	1	P;P;P;P	0.44260	0.83;0.83;0.655;0.733	B;B;B;B	0.34652	0.131;0.187;0.093;0.187	T	0.22034	-1.0228	9	0.40728	T	0.16	-16.5044	8.4095	0.32636	0.0844:0.2264:0.6893:0.0	.	610;679;333;625	E7ENJ7;B4DXD0;Q2TAA8-2;Q2TAA8	.;.;.;TXIP1_HUMAN	K	610;625	.	ENSP00000373485:E625K	E	+	1	0	TSNAXIP1	66419293	0.686000	0.27661	0.003000	0.11579	0.047000	0.14425	1.336000	0.33850	1.572000	0.49736	0.561000	0.74099	GAG		0.592	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67861792	G	A	67861792	1	1	61	0	1	0	0	0	0	0	0	0	16672	1059	37	1		1	TSNAXIP1	16	67861792	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2145	67861792	22492961	9849	17834										
DPEP3	64180	broad.mit.edu	37	chr16	68012447	68012447	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagtaggaggcacacatgCggtgaatgaggtcaatctgc	14	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68012447C>T	ENST00000268793.4	-	3	945	c.572G>A	c.(571-573)cGc>cAc	p.R191H	DPEP3_ENST00000574342.1_5'Flank	NM_001129758.1|NM_022357.3	NP_001123230.1|NP_071752.3	Q9H4B8	DPEP3_HUMAN	dipeptidase 3	166					male meiosis (GO:0007140)	anchored component of membrane (GO:0031225)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)	p.R191H(1)		breast(4)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0117)|Epithelial(162;0.0481)|all cancers(182;0.236)		GGCACACATGCGGTGAATGAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											182	161	168					16																	68012447		2198	4300	6498	66569948	SO:0001583	missense	64180			AJ291679	CCDS10856.1	16q22.1	2011-07-22			ENSG00000141096	ENSG00000141096	3.4.13.19		23029	protein-coding gene	gene with protein product		609926					Standard	NM_022357		Approved		uc002evc.4	Q9H4B8	OTTHUMG00000137544	ENST00000268793.4:c.572G>A	16.37:g.68012447C>T	ENSP00000268793:p.Arg191His		66569948	B3KQ48|Q6PEZ5|Q6UXE4	Missense_Mutation	SNP	ENST00000268793.4	37	CCDS10856.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906318	0.92107	.	.	ENSG00000141096	ENST00000268793	T	0.26373	1.74	4.88	4.88	0.63580	.	0.056597	0.64402	D	0.000001	T	0.51568	0.1682	M	0.94021	3.485	0.58432	D	0.999999	D	0.63880	0.993	P	0.51055	0.657	T	0.68269	-0.5453	10	0.87932	D	0	-0.1135	15.5407	0.76043	0.0:1.0:0.0:0.0	.	166	Q9H4B8	DPEP3_HUMAN	H	191	ENSP00000268793:R191H	ENSP00000268793:R191H	R	-	2	0	DPEP3	66569948	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	6.920000	0.75799	2.269000	0.75478	0.561000	0.74099	CGC		0.582	DPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268875.3	NM_022357		T	68012447	C	T	68012447	3	4	61	1	0	0	0	0	1	0	0	0	4726	768	27	1	1001	1	DPEP3	16	68012447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150655	68012447	22342306	9850	17835										
DDX28	55794	broad.mit.edu	37	chr16	68055913	68055913	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagaacaccagaacagttCctgagggaccagtcctttct	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68055913C>A	ENST00000332395.5	-	1	1857	c.1193G>T	c.(1192-1194)gGa>gTa	p.G398V	DUS2_ENST00000432752.1_5'Flank|DUS2_ENST00000565263.1_5'Flank|DUS2_ENST00000358896.6_5'Flank	NM_018380.3	NP_060850.2	Q9NUL7	DDX28_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	398	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.G398V(1)		central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0116)|Epithelial(162;0.0474)|all cancers(182;0.233)		CAGAACAGTTCCTGAGGGACC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											116	99	104					16																	68055913		2198	4300	6498	66613414	SO:0001583	missense	55794			AF329821	CCDS10858.1	16q22.1-q22.3	2008-02-05	2003-06-13		ENSG00000182810	ENSG00000182810		"DEAD-boxes"	17330	protein-coding gene	gene with protein product		607618	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 28"			10493829, 11350955	Standard	NM_018380		Approved	MDDX28, FLJ11282	uc002evh.2	Q9NUL7	OTTHUMG00000137549	ENST00000332395.5:c.1193G>T	16.37:g.68055913C>A	ENSP00000332340:p.Gly398Val		66613414		Missense_Mutation	SNP	ENST00000332395.5	37	CCDS10858.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.803214	0.31869	.	.	ENSG00000182810	ENST00000332395	T	0.73575	-0.76	6.01	5.06	0.68205	Helicase, C-terminal (1);	0.248378	0.40728	N	0.001036	T	0.67832	0.2935	L	0.42008	1.315	0.80722	D	1	P	0.37824	0.609	B	0.33690	0.168	T	0.71580	-0.4550	10	0.72032	D	0.01	-14.4507	16.4253	0.83813	0.1326:0.8674:0.0:0.0	.	398	Q9NUL7	DDX28_HUMAN	V	398	ENSP00000332340:G398V	ENSP00000332340:G398V	G	-	2	0	DDX28	66613414	1.000000	0.71417	0.110000	0.21437	0.178000	0.23041	5.649000	0.67936	1.546000	0.49388	-0.175000	0.13238	GGA		0.498	DDX28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268883.1	NM_018380		A	68055913	C	A	68055913	3	1	61	1	0	0	0	0	1	0	0	0	4361	855	30	2	433	2	DDX28	16	68055913	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43466	68055913	22298840	9851	17836										
ZFP90	146198	broad.mit.edu	37	chr16	68591974	68591974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgtcgaccctgctcagaGgagcttatacagggatgtga	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68591974G>T	ENST00000570495.1	+	3	399	c.107G>T	c.(106-108)aGg>aTg	p.R36M	ZFP90_ENST00000563169.2_Missense_Mutation_p.R36M|ZFP90_ENST00000570884.1_3'UTR|ZFP90_ENST00000564323.1_Missense_Mutation_p.R36M|ZFP90_ENST00000398253.2_Missense_Mutation_p.R36M			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R36M(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CCTGCTCAGAGGAGCTTATAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	16											139	139	139					16																	68591974		2197	4300	6497	67149475	SO:0001583	missense	146198			AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.107G>T	16.37:g.68591974G>T	ENSP00000460547:p.Arg36Met		67149475	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.767702	0.69878	.	.	ENSG00000184939	ENST00000398253	T	0.03035	4.07	5.61	4.46	0.54185	Krueppel-associated box (4);	.	.	.	.	T	0.19248	0.0462	M	0.85542	2.76	0.27949	N	0.93721	D	0.76494	0.999	D	0.70487	0.969	T	0.01349	-1.1378	9	0.56958	D	0.05	-9.4217	12.6715	0.56870	0.094:0.0:0.906:0.0	.	36	Q8TF47	ZFP90_HUMAN	M	36	ENSP00000381304:R36M	ENSP00000381304:R36M	R	+	2	0	ZFP90	67149475	0.915000	0.31059	0.998000	0.56505	0.995000	0.86356	1.421000	0.34815	2.651000	0.90000	0.591000	0.81541	AGG		0.473	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		T	68591974	G	T	68591974	3	4	61	1	0	0	0	0	1	0	0	0	17693	1000	35	2	113	2	ZFP90	16	68591974	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	536061	68591974	21762779	9852	17837										
ZFP90	146198	broad.mit.edu	37	chr16	68597679	68597679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccttgttcaacaccagcGaattcacactggagagaaac	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68597679G>A	ENST00000570495.1	+	5	1281	c.989G>A	c.(988-990)cGa>cAa	p.R330Q	ZFP90_ENST00000563169.2_Missense_Mutation_p.R330Q|ZFP90_ENST00000398253.2_Missense_Mutation_p.R330Q			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	330					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R330Q(2)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CAACACCAGCGAATTCACACT	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	16											63	70	68					16																	68597679		2172	4295	6467	67155180	SO:0001583	missense	146198			AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.989G>A	16.37:g.68597679G>A	ENSP00000460547:p.Arg330Gln		67155180	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893355	0.91889	.	.	ENSG00000184939	ENST00000398253	T	0.24723	1.84	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49270	0.1547	L	0.52823	1.66	0.41641	D	0.989072	D	0.89917	1.0	D	0.97110	1.0	T	0.36335	-0.9752	9	0.72032	D	0.01	-18.6122	18.3732	0.90420	0.0:0.0:1.0:0.0	.	330	Q8TF47	ZFP90_HUMAN	Q	330	ENSP00000381304:R330Q	ENSP00000381304:R330Q	R	+	2	0	ZFP90	67155180	0.127000	0.22367	1.000000	0.80357	0.996000	0.88848	2.361000	0.44160	2.941000	0.99782	0.655000	0.94253	CGA		0.512	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		A	68597679	G	A	68597679	3	1	61	1	0	0	0	0	1	0	0	0	17693	1058	37	1	1003	1	ZFP90	16	68597679	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5705	68597679	21757074	9853	17838										
ZFP90	146198	broad.mit.edu	37	chr16	68598026	68598026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatgaaagcactcttaccGaagtgaaatcctaccattgt	7	9	1	3	rs199604310		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68598026G>A	ENST00000570495.1	+	5	1628	c.1336G>A	c.(1336-1338)Gaa>Aaa	p.E446K	ZFP90_ENST00000563169.2_Missense_Mutation_p.E446K|ZFP90_ENST00000398253.2_Missense_Mutation_p.E446K			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	446					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.E446K(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CACTCTTACCGAAGTGAAATC	0.418													G|||	1	0.000199681	8e-04	0	5008	,	,		22880	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											104	100	101					16																	68598026		1993	4183	6176	67155527	SO:0001583	missense	146198			AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1336G>A	16.37:g.68598026G>A	ENSP00000460547:p.Glu446Lys		67155527	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.12	1.842870	0.32606	.	.	ENSG00000184939	ENST00000398253	T	0.15256	2.44	5.66	4.7	0.59300	.	.	.	.	.	T	0.12774	0.0310	N	0.17312	0.475	0.33789	D	0.625237	B	0.24426	0.103	B	0.17098	0.017	T	0.10291	-1.0636	9	0.87932	D	0	-6.3161	14.8898	0.70600	0.0:0.1439:0.8561:0.0	.	446	Q8TF47	ZFP90_HUMAN	K	446	ENSP00000381304:E446K	ENSP00000381304:E446K	E	+	1	0	ZFP90	67155527	0.978000	0.34361	0.844000	0.33320	0.438000	0.31896	4.032000	0.57274	1.532000	0.49169	0.655000	0.94253	GAA		0.418	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		A	68598026	G	A	68598026	3	1	61	1	0	0	0	0	1	0	0	0	17693	1059	37	1	1350	1	ZFP90	16	68598026	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	347	68598026	21756727	9854	17839										
ZFP90	146198	broad.mit.edu	37	chr16	68598240	68598240	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtttcatagagcatcacaGaattcatactggagagaaac	8	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68598240G>T	ENST00000570495.1	+	5	1842	c.1550G>T	c.(1549-1551)aGa>aTa	p.R517I	ZFP90_ENST00000563169.2_Missense_Mutation_p.R517I|ZFP90_ENST00000398253.2_Missense_Mutation_p.R517I			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	517					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R517I(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		GAGCATCACAGAATTCATACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	16											62	68	66					16																	68598240		2192	4299	6491	67155741	SO:0001583	missense	146198			AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1550G>T	16.37:g.68598240G>T	ENSP00000460547:p.Arg517Ile		67155741	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.684744	0.68157	.	.	ENSG00000184939	ENST00000398253	T	0.24908	1.83	5.76	5.76	0.90799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47414	0.1444	M	0.68317	2.08	0.52099	D	0.999948	D	0.69078	0.997	P	0.59889	0.865	T	0.37150	-0.9718	9	0.66056	D	0.02	-16.3368	17.8359	0.88697	0.0:0.0:1.0:0.0	.	517	Q8TF47	ZFP90_HUMAN	I	517	ENSP00000381304:R517I	ENSP00000381304:R517I	R	+	2	0	ZFP90	67155741	0.040000	0.19996	1.000000	0.80357	0.977000	0.68977	1.811000	0.38942	2.891000	0.99171	0.655000	0.94253	AGA		0.418	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		T	68598240	G	T	68598240	3	4	61	1	0	0	0	0	1	0	0	0	17693	942	33	2	1564	2	ZFP90	16	68598240	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214	68598240	21756513	9855	17840										
ZFP90	146198	broad.mit.edu	37	chr16	68598576	68598576	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcttactaaacaccagaGaattcatactcgaaataaac	4	10	2	1	rs184859531		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68598576G>T	ENST00000570495.1	+	5	2178	c.1886G>T	c.(1885-1887)aGa>aTa	p.R629I	ZFP90_ENST00000563169.2_Missense_Mutation_p.R629I|ZFP90_ENST00000398253.2_Missense_Mutation_p.R629I			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	629					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.R629I(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		AAACACCAGAGAATTCATACT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	16											64	68	66					16																	68598576		1999	4200	6199	67156077	SO:0001583	missense	146198			AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1886G>T	16.37:g.68598576G>T	ENSP00000460547:p.Arg629Ile		67156077	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.05|15.05	2.717657|2.717657	0.48622|0.48622	.|.	.|.	ENSG00000184939|ENSG00000184939	ENST00000327567|ENST00000398253	.|T	.|0.10005	.|2.92	5.02|5.02	4.0|4.0	0.46444|0.46444	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.06872	.|0.0175	L|L	0.29908|0.29908	0.895|0.895	0.42923|0.42923	D|D	0.994296|0.994296	.|P	.|0.35745	.|0.518	.|B	.|0.29663	.|0.105	.|T	.|0.12400	.|-1.0549	.|9	0.19147|0.87932	T|D	0.46|0	-15.0054|-15.0054	5.9365|5.9365	0.19169|0.19169	0.0948:0.0:0.7163:0.1889|0.0948:0.0:0.7163:0.1889	.|.	.|629	.|Q8TF47	.|ZFP90_HUMAN	X|I	102|629	.|ENSP00000381304:R629I	ENSP00000329859:E102X|ENSP00000381304:R629I	E|R	+|+	1|2	0|0	ZFP90|ZFP90	67156077|67156077	0.690000|0.690000	0.27699|0.27699	1.000000|1.000000	0.80357|0.80357	0.883000|0.883000	0.51084|0.51084	2.477000|2.477000	0.45180|0.45180	2.786000|2.786000	0.95864|0.95864	0.484000|0.484000	0.47621|0.47621	GAA|AGA		0.373	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		T	68598576	G	T	68598576	3	4	61	1	0	0	0	0	1	0	0	0	17693	942	33	2	1900	2	ZFP90	16	68598576	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	336	68598576	21756177	9856	17841										
CDH3	1001	broad.mit.edu	37	chr16	68729808	68729808	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagccaacccagatgaaatCggcaactttataattgaggt	8	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68729808C>T	ENST00000264012.4	+	15	2806	c.2262C>T	c.(2260-2262)atC>atT	p.I754I	CDH3_ENST00000581171.1_Silent_p.I699I|CDH3_ENST00000429102.2_Silent_p.I754I	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	754					adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I754I(2)|p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		CAGATGAAATCGGCAACTTTA	0.592																																																4	Unknown(2)|Substitution - coding silent(2)	large_intestine(2)|breast(2)	16											69	50	56					16																	68729808		2198	4300	6498	67287309	SO:0001819	synonymous_variant	1001			X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"Cadherins / Major cadherins"	1762	protein-coding gene	gene with protein product		114021	"cadherin 3, P-cadherin (placental)"			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.2262C>T	16.37:g.68729808C>T			67287309	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																				0.592	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		T	68729808	C	T	68729808	2	4	61	1	0	0	0	0	0	0	0	1	3117	874	31	1		1	CDH3	16	68729808	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131232	68729808	21624945	9857	17842										
TMCO7	79613	broad.mit.edu	37	chr16	68894270	68894270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcccccgatgcaactcGaagactgtacaccagctgca	9	15	0	1	rs77249067	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68894270G>A	ENST00000261778.1	+	2	590	c.578G>A	c.(577-579)cGa>cAa	p.R193Q		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	193						integral component of membrane (GO:0016021)		p.R193Q(1)									GATGCAACTCGAAGACTGTAC	0.512													G|||	3	0.000599042	0.0023	0	5008	,	,		19620	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16						G	GLN/ARG	8,4048		0,8,2020	201	194	196		578	1.4	1	16	dbSNP_133	196	0,8412		0,0,4206	yes	missense	TMCO7	NM_024562.1	43	0,8,6226	AA,AG,GG		0.0,0.1972,0.0642	probably-damaging	193/1095	68894270	8,12460	2028	4206	6234	67451771	SO:0001583	missense	79613				CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.578G>A	16.37:g.68894270G>A	ENSP00000261778:p.Arg193Gln		67451771	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	37	CCDS45516.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	14.63	2.593424	0.46214	0.001972	0.0	ENSG00000103047	ENST00000261778	T	0.67698	-0.28	5.01	1.44	0.22558	.	.	.	.	.	T	0.63129	0.2485	M	0.72894	2.215	0.25321	N	0.989113	B;B	0.23735	0.09;0.037	B;B	0.10450	0.005;0.005	T	0.56360	-0.7992	9	0.46703	T	0.11	-4.2864	10.9965	0.47580	0.2567:0.0:0.7433:0.0	.	193;32	Q9C0B7;B3KTB6	TMCO7_HUMAN;.	Q	193	ENSP00000261778:R193Q	ENSP00000261778:R193Q	R	+	2	0	TMCO7	67451771	0.212000	0.23540	0.996000	0.52242	0.883000	0.51084	0.554000	0.23407	0.519000	0.28406	0.561000	0.74099	CGA		0.512	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		A	68894270	G	A	68894270	3	1	61	1	0	0	0	0	1	0	0	0	16040	1058	37	1	584	1	TMCO7	16	68894270	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164462	68894270	21460483	9858	17843										
TMCO7	79613	broad.mit.edu	37	chr16	68901033	68901033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgggccccagcttggcttCggcgtctatgtggacagctg	15	12	1	0	rs556600020		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:68901033C>T	ENST00000261778.1	+	4	916	c.904C>T	c.(904-906)Cgg>Tgg	p.R302W		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	302						integral component of membrane (GO:0016021)		p.R302W(1)									AGCTTGGCTTCGGCGTCTATG	0.473													C|||	1	0.000199681	0	0	5008	,	,		14981	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											124	124	124					16																	68901033		1934	4123	6057	67458534	SO:0001583	missense	79613				CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.904C>T	16.37:g.68901033C>T	ENSP00000261778:p.Arg302Trp		67458534	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	37	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718583	0.89205	.	.	ENSG00000103047	ENST00000261778	T	0.70986	-0.53	5.83	5.83	0.93111	.	.	.	.	.	D	0.85635	0.5742	M	0.80982	2.52	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86678	0.1915	9	0.87932	D	0	-7.5079	18.8787	0.92349	0.0:1.0:0.0:0.0	.	302;141	Q9C0B7;B3KTB6	TMCO7_HUMAN;.	W	302	ENSP00000261778:R302W	ENSP00000261778:R302W	R	+	1	2	TMCO7	67458534	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.703000	0.61824	2.755000	0.94549	0.650000	0.86243	CGG		0.473	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68901033	C	T	68901033	3	4	61	1	0	0	0	0	1	0	0	0	16040	875	31	1	918	1	TMCO7	16	68901033	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6763	68901033	21453720	9859	17844										
CIRH1A	84916	broad.mit.edu	37	chr16	69199408	69199408	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccatgatgcctacatgttCtgcatcattgacaagtcatt	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:69199408C>A	ENST00000314423.7	+	15	1989	c.1812C>A	c.(1810-1812)ttC>ttA	p.F604L	CIRH1A_ENST00000352319.4_Missense_Mutation_p.F489L|CIRH1A_ENST00000563094.1_Missense_Mutation_p.F604L			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	604					maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)	p.F604L(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		CCTACATGTTCTGCATCATTG	0.423																																					Melanoma(69;1156 1278 4951 8715 52012)											1	Substitution - Missense(1)	large_intestine(1)	16											176	133	147					16																	69199408		2198	4300	6498	67756909	SO:0001583	missense	84916			AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"WD repeat domain containing"	1983	protein-coding gene	gene with protein product	"UTP4, small subunit (SSU) processome component, homolog (yeast)"	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.1812C>A	16.37:g.69199408C>A	ENSP00000327179:p.Phe604Leu		67756909	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	37	CCDS10872.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939570	0.52972	.	.	ENSG00000141076	ENST00000314423;ENST00000352319	T;T	0.36699	1.79;1.24	6.17	3.14	0.36123	.	0.140435	0.64402	N	0.000003	T	0.22360	0.0539	L	0.37561	1.115	0.45899	D	0.998742	B;B	0.24043	0.015;0.096	B;B	0.25614	0.004;0.062	T	0.06826	-1.0805	10	0.06099	T	0.92	.	7.7315	0.28789	0.1249:0.6892:0.1202:0.0656	.	604;604	Q969X6;Q969X6-3	CIR1A_HUMAN;.	L	604;489	ENSP00000327179:F604L;ENSP00000339164:F489L	ENSP00000327179:F604L	F	+	3	2	CIRH1A	67756909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.179000	0.50887	0.465000	0.27167	0.655000	0.94253	TTC		0.423	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830		A	69199408	C	A	69199408	3	1	61	1	0	0	0	0	1	0	0	0	3440	912	32	2	1866	2	CIRH1A	16	69199408	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	298375	69199408	21155345	9860	17845										
VPS4A	27183	broad.mit.edu	37	chr16	69354176	69354176	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaggatcaaaacggagttCttggtccagatgcagggtgt	15	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:69354176C>A	ENST00000254950.11	+	7	909	c.753C>A	c.(751-753)ttC>ttA	p.F251L	COG8_ENST00000564419.1_5'UTR|RP11-343C2.11_ENST00000570054.2_Missense_Mutation_p.F275L	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)									p.F251L(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				AAACGGAGTTCTTGGTCCAGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											53	63	60					16																	69354176		1891	4102	5993	67911677	SO:0001583	missense	27183			AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"ATPases / AAA-type"	13488	protein-coding gene	gene with protein product		609982	"vacuolar protein sorting 4A (yeast homolog)", "vacuolar protein sorting 4A (yeast)"			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.753C>A	16.37:g.69354176C>A	ENSP00000254950:p.Phe251Leu		67911677		Missense_Mutation	SNP	ENST00000254950.11	37	CCDS45517.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.777682	0.49786	.	.	ENSG00000132612	ENST00000254950	D	0.86865	-2.18	6.07	4.09	0.47781	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.044361	0.85682	D	0.000000	T	0.75443	0.3850	N	0.02708	-0.52	0.80722	D	1	B	0.32338	0.365	B	0.42798	0.398	T	0.68398	-0.5419	10	0.14656	T	0.56	-30.9348	12.139	0.53986	0.0:0.856:0.0:0.144	.	251	Q9UN37	VPS4A_HUMAN	L	251	ENSP00000254950:F251L	ENSP00000254950:F251L	F	+	3	2	VPS4A	67911677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.187000	0.42602	0.853000	0.35312	-0.137000	0.14449	TTC		0.572	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245		A	69354176	C	A	69354176	3	1	61	1	0	0	0	0	1	0	0	0	17252	912	32	2	779	2	VPS4A	16	69354176	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154768	69354176	21000577	9861	17846										
TERF2	7014	broad.mit.edu	37	chr16	69404525	69404525	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatattcaggagatcatttCtcagcttctacacaatggac	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:69404525C>A	ENST00000254942.3	-	5	717	c.701G>T	c.(700-702)aGa>aTa	p.R234I	TERF2_ENST00000567296.2_Missense_Mutation_p.R234I|TERF2_ENST00000603068.1_Missense_Mutation_p.R192I|TERF2_ENST00000569611.2_5'UTR	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	234	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)	p.R192I(1)		NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				GAGATCATTTCTCAGCTTCTA	0.403																																					Ovarian(13;63 524 30420 31710 34037)											1	Substitution - Missense(1)	large_intestine(1)	16											125	121	122					16																	69404525		2198	4300	6498	67962026	SO:0001583	missense	7014				CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.701G>T	16.37:g.69404525C>A	ENSP00000254942:p.Arg234Ile		67962026		Missense_Mutation	SNP	ENST00000254942.3	37		.	.	.	.	.	.	.	.	.	.	C	17.32	3.359202	0.61403	.	.	ENSG00000132604	ENST00000254942	.	.	.	5.28	4.31	0.51392	Telomere repeat-binding factor, dimerisation domain (4);	0.150674	0.64402	D	0.000014	T	0.51568	0.1682	L	0.27053	0.805	0.80722	D	1	D;P	0.57571	0.98;0.85	P;P	0.55923	0.787;0.543	T	0.55088	-0.8195	9	0.87932	D	0	-9.3693	10.153	0.42805	0.0:0.9063:0.0:0.0937	.	192;192	Q15554-2;Q15554	.;TERF2_HUMAN	I	192	.	ENSP00000254942:R192I	R	-	2	0	TERF2	67962026	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.606000	0.24194	1.207000	0.43291	0.555000	0.69702	AGA		0.403	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2			A	69404525	C	A	69404525	3	1	61	1	0	0	0	0	1	0	0	0	15801	913	32	2	951	2	TERF2	16	69404525	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50349	69404525	20950228	9862	17847										
NQO1	1728	broad.mit.edu	37	chr16	69752152	69752152	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttcgcagggtccttcagTttacctgcagagaagaaaaa	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:69752152T>C	ENST00000320623.5	-	3	688	c.177A>G	c.(175-177)aaA>aaG	p.K59K	NQO1_ENST00000379046.2_Silent_p.K59K|NQO1_ENST00000564043.1_Silent_p.K38K|NQO1_ENST00000561500.1_Silent_p.K59K|NQO1_ENST00000439109.2_Silent_p.K59K|NQO1_ENST00000379047.3_Silent_p.K59K	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	59					aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)	p.K59K(1)		autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	GGTCCTTCAGTTTACCTGCAG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	16											73	80	77					16																	69752152		2198	4300	6498	68309653	SO:0001819	synonymous_variant	1728			M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.177A>G	16.37:g.69752152T>C			68309653	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Silent	SNP	ENST00000320623.5	37	CCDS10883.1																																																																																				0.512	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2			C	69752152	T	C	69752152	2	2	61	1	0	0	0	0	0	0	0	1	10642	1722	60	4		4	NQO1	16	69752152	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	347627	69752152	20602601	9863	17848										
WWP2	11060	broad.mit.edu	37	chr16	69965465	69965465	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttccaggcagacgcttttCgaagattccttccaacaggt	9	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:69965465C>T	ENST00000359154.2	+	15	1676	c.1575C>T	c.(1573-1575)ttC>ttT	p.F525F	MIR140_ENST00000385282.1_RNA|WWP2_ENST00000542271.1_Silent_p.F409F|WWP2_ENST00000568684.1_Silent_p.F86F|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.F525F|WWP2_ENST00000356003.2_Silent_p.F525F	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	525					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.F525F(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGACGCTTTTCGAAGATTCCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	16											87	77	80					16																	69965465		2198	4300	6498	68522966	SO:0001819	synonymous_variant	11060			BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1575C>T	16.37:g.69965465C>T			68522966	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																				0.502	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		T	69965465	C	T	69965465	2	4	61	1	0	0	0	0	0	0	0	1	17456	883	31	1		1	WWP2	16	69965465	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	213313	69965465	20389288	9864	17849										
AARS	16	broad.mit.edu	37	chr16	70302242	70302242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattgagcttttcatgggCgtatcggacagctcggcgga	15	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70302242C>T	ENST00000261772.8	-	8	1146	c.1003G>A	c.(1003-1005)Gcc>Acc	p.A335T		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase									p.A335T(1)		breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		TTTTCATGGGCGTATCGGACA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											114	100	104					16																	70302242		2198	4300	6498	68859743	SO:0001583	missense	16			D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.1003G>A	16.37:g.70302242C>T	ENSP00000261772:p.Ala335Thr		68859743		Missense_Mutation	SNP	ENST00000261772.8	37	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.884537	0.72410	.	.	ENSG00000090861	ENST00000261772	T	0.73575	-0.76	5.77	4.68	0.58851	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.203421	0.53938	D	0.000052	D	0.85741	0.5767	M	0.93854	3.465	0.39068	D	0.960652	P;P	0.43788	0.817;0.809	B;P	0.52823	0.442;0.71	D	0.88183	0.2872	10	0.87932	D	0	-7.6595	10.3972	0.44207	0.666:0.334:0.0:0.0	.	343;335	E7ETK8;P49588	.;SYAC_HUMAN	T	335	ENSP00000261772:A335T	ENSP00000261772:A335T	A	-	1	0	AARS	68859743	1.000000	0.71417	0.998000	0.56505	0.823000	0.46562	3.334000	0.52097	1.026000	0.39733	-0.271000	0.10264	GCC		0.507	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		T	70302242	C	T	70302242	3	4	61	1	0	0	0	0	1	0	0	0	19	768	27	1	1959	1	AARS	16	70302242	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336777	70302242	20052511	9865	17850										
DDX19A	55308	broad.mit.edu	37	chr16	70399022	70399022	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagcttgcctatgccgttCgaggcaataaatgtgagtac	11	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70399022C>T	ENST00000302243.7	+	7	755	c.592C>T	c.(592-594)Cga>Tga	p.R198*	RP11-529K1.3_ENST00000567706.1_Intron|DDX19A_ENST00000443119.2_Nonsense_Mutation_p.R108*|DDX19A_ENST00000417604.2_Nonsense_Mutation_p.R167*	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	198	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|N-terminal lobe. {ECO:0000250}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.R198*(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				CTATGCCGTTCGAGGCAATAA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											97	86	89					16																	70399022		2198	4300	6498	68956523	SO:0001587	stop_gained	55308			AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"DEAD-boxes"	25628	protein-coding gene	gene with protein product			"DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.592C>T	16.37:g.70399022C>T	ENSP00000306117:p.Arg198*		68956523	B2RPL0|B4DRZ7|Q53FM0	Nonsense_Mutation	SNP	ENST00000302243.7	37	CCDS10889.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093155	0.76756	.	.	ENSG00000168872	ENST00000302243;ENST00000302227;ENST00000417604;ENST00000443119	.	.	.	5.42	3.48	0.39840	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0623	0.42282	0.0:0.8416:0.0:0.1584	.	.	.	.	X	198;90;167;108	.	ENSP00000306209:R90X	R	+	1	2	DDX19A	68956523	0.998000	0.40836	0.999000	0.59377	0.705000	0.40729	2.814000	0.48010	0.670000	0.31165	0.655000	0.94253	CGA		0.483	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332		T	70399022	C	T	70399022	4	4	61	1	0	0	0	0	0	1	0	0	4352	876	31	1	618	1	DDX19A	16	70399022	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96780	70399022	19955731	9866	17851										
SF3B3	23450	broad.mit.edu	37	chr16	70602203	70602203	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcatattgccaattatatCtctgggatccagactatcgg	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70602203C>A	ENST00000302516.5	+	22	3181	c.2970C>A	c.(2968-2970)atC>atA	p.I990I		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	990					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.I990I(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CCAATTATATCTCTGGGATCC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	16											117	114	115					16																	70602203		2198	4300	6498	69159704	SO:0001819	synonymous_variant	23450			AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2970C>A	16.37:g.70602203C>A			69159704	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																				0.418	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		A	70602203	C	A	70602203	2	1	61	1	0	0	0	0	0	0	0	1	14189	903	32	2		2	SF3B3	16	70602203	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203181	70602203	19752550	9867	17852										
VAC14	55697	broad.mit.edu	37	chr16	70765509	70765509	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatggtgggagttgaaggaGaacattctaagcctttggta	13	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70765509G>T	ENST00000261776.5	-	14	1810	c.1550C>A	c.(1549-1551)tCt>tAt	p.S517Y		NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	517					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)	p.S517Y(1)		breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				AGTTGAAGGAGAACATTCTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	16											135	137	137					16																	70765509		2198	4300	6498	69323010	SO:0001583	missense	55697			AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"Tax1 (human T-cell leukemia virus type I) binding protein 2"	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.1550C>A	16.37:g.70765509G>T	ENSP00000261776:p.Ser517Tyr		69323010	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Missense_Mutation	SNP	ENST00000261776.5	37	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	G	31	5.084951	0.94100	.	.	ENSG00000103043	ENST00000261776	.	.	.	5.43	5.43	0.79202	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69833	0.3155	M	0.67953	2.075	0.80722	D	1	D	0.55605	0.972	P	0.48227	0.571	T	0.74487	-0.3649	9	0.87932	D	0	-10.7973	19.6058	0.95582	0.0:0.0:1.0:0.0	.	517	Q08AM6	VAC14_HUMAN	Y	517	.	ENSP00000261776:S517Y	S	-	2	0	VAC14	69323010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.250000	0.95477	2.722000	0.93159	0.655000	0.94253	TCT		0.433	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052		T	70765509	G	T	70765509	3	4	61	1	0	0	0	0	1	0	0	0	17151	942	33	2	822	2	VAC14	16	70765509	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163306	70765509	19589244	9868	17853										
HYDIN	54768	broad.mit.edu	37	chr16	70852466	70852466	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatttgtcacctcgtttcGgaagatcacctgcattcacg	7	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70852466G>A	ENST00000393567.2	-	84	14587	c.14437C>T	c.(14437-14439)Cga>Tga	p.R4813*		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4813					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R4764*(1)|p.R4812*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ACCTCGTTTCGGAAGATCACC	0.512																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											11	9	10					16																	70852466		1744	3957	5701	69409967	SO:0001587	stop_gained	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14437C>T	16.37:g.70852466G>A	ENSP00000377197:p.Arg4813*		69409967	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Nonsense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	56	25.720040	0.99966	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	.	.	.	5.84	3.85	0.44370	.	0.376195	0.15072	U	0.282154	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9321	0.70923	0.0:0.0:0.7384:0.2616	.	.	.	.	X	4813;4812	.	ENSP00000313052:R4812X	R	-	1	2	HYDIN	69409967	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	2.669000	0.46825	0.779000	0.33543	0.609000	0.83330	CGA		0.512	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70852466	G	A	70852466	4	1	61	1	0	0	0	0	0	1	0	0	7488	1124	39	1	940	1	HYDIN	16	70852466	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86957	70852466	19502287	9869	17854										
HYDIN	54768	broad.mit.edu	37	chr16	70884495	70884495	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggactttcttttccacattGcagatcaaattaaagttcac	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70884495G>A	ENST00000393567.2	-	74	12657	c.12507C>T	c.(12505-12507)tgC>tgT	p.C4169C	RNU6ATAC25P_ENST00000408798.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4169					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.C4168C(1)|p.C4120C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TTTCCACATTGCAGATCAAAT	0.443																																																2	Substitution - coding silent(2)	large_intestine(2)	16											58	51	53					16																	70884495		1845	4095	5940	69441996	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12507C>T	16.37:g.70884495G>A			69441996	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.443	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70884495	G	A	70884495	2	1	61	1	0	0	0	0	0	0	0	1	7488	1311	46	3		3	HYDIN	16	70884495	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32029	70884495	19470258	9870	17855										
HYDIN	54768	broad.mit.edu	37	chr16	70908454	70908454	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatcaaattcagctgtatCtccaggagaaacaaccaagg	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70908454C>A	ENST00000393567.2	-	64	10852	c.10702G>T	c.(10702-10704)Gat>Tat	p.D3568Y	AC027281.1_ENST00000411384.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3568					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.D3567Y(1)|p.D3519Y(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCAGCTGTATCTCCAGGAGAA	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	16											4	3	3					16																	70908454		1601	3684	5285	69465955	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.10702G>T	16.37:g.70908454C>A	ENSP00000377197:p.Asp3568Tyr		69465955	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.897574	0.33535	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00922	5.54	4.71	1.53	0.23141	.	0.798432	0.09936	U	0.736629	T	0.01905	0.0060	L	0.44542	1.39	0.80722	D	1	P	0.49696	0.927	P	0.50440	0.641	T	0.64127	-0.6480	10	0.72032	D	0.01	.	8.9188	0.35599	0.0:0.7403:0.0:0.2597	.	3567	F8WD23	.	Y	3568;3567	ENSP00000377197:D3568Y	ENSP00000313052:D3567Y	D	-	1	0	HYDIN	69465955	0.906000	0.30813	0.837000	0.33122	0.273000	0.26683	0.209000	0.17435	0.029000	0.15352	-0.424000	0.05967	GAT		0.418	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70908454	C	A	70908454	3	1	61	1	0	0	0	0	1	0	0	0	7488	913	32	2	4755	2	HYDIN	16	70908454	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23959	70908454	19446299	9871	17856										
HYDIN	54768	broad.mit.edu	37	chr16	70925549	70925549	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtaaatatttgtcttacGctttcttttgatgaatgggg	9	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70925549G>A	ENST00000393567.2	-	57	9806	c.9656C>T	c.(9655-9657)gCa>gTa	p.A3219V		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3219					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.A3218V(1)|p.A3170V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TTTGTCTTACGCTTTCTTTTG	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	16											1	1	1					16																	70925549		129	267	396	69483050	SO:0001630	splice_region_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.9656+1C>T	16.37:g.70925549G>A			69483050	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.587434	0.28268	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00932	5.53	5.2	-10.4	0.00318	.	2.391630	0.02819	N	0.125359	T	0.00580	0.0019	N	0.04043	-0.29	0.58432	D	0.999998	B	0.21071	0.051	B	0.15870	0.014	T	0.50642	-0.8804	9	.	.	.	.	14.0573	0.64776	0.1296:0.5461:0.3243:0.0	.	3218	F8WD23	.	V	3219;3218	ENSP00000377197:A3219V	.	A	-	2	0	HYDIN	69483050	0.000000	0.05858	0.036000	0.18154	0.342000	0.28953	-3.480000	0.00457	-3.282000	0.00197	-0.430000	0.05897	GCA		0.358	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		Missense_Mutation	A	70925549	G	A	70925549	5	1	61	1	0	0	0	0	0	0	1	0	7488	1101	38	1	5829	1	HYDIN	16	70925549	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17095	70925549	19429204	9872	17857										
HYDIN	54768	broad.mit.edu	37	chr16	70937662	70937662	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacaatgctgtcttcaaaGacaccaactgaagtagggta	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70937662G>T	ENST00000393567.2	-	52	8865	c.8715C>A	c.(8713-8715)gtC>gtA	p.V2905V		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2905					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.V2856V(1)|p.V462V(1)|p.V2904V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGTCTTCAAAGACACCAACTG	0.468																																																3	Substitution - coding silent(3)	large_intestine(3)	16											1	1	1					16																	70937662		214	591	805	69495163	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8715C>A	16.37:g.70937662G>T			69495163	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.468	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70937662	G	T	70937662	2	4	61	1	0	0	0	0	0	0	0	1	7488	929	33	2		2	HYDIN	16	70937662	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12113	70937662	19417091	9873	17858										
HYDIN	54768	broad.mit.edu	37	chr16	70937921	70937921	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccattaaggaagtgttcaGgattgttagcgtctccatgt	10	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70937921G>T	ENST00000393567.2	-	51	8713	c.8563C>A	c.(8563-8565)Ctg>Atg	p.L2855M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2855					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.L412M(1)|p.L2854M(1)|p.L2806M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GAAGTGTTCAGGATTGTTAGC	0.458																																																3	Substitution - Missense(3)	large_intestine(3)	16											16	18	17					16																	70937921		1689	4068	5757	69495422	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8563C>A	16.37:g.70937921G>T	ENSP00000377197:p.Leu2855Met		69495422	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	8.410	0.843977	0.16963	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00949	5.51	4.6	2.65	0.31530	.	0.000000	0.27871	U	0.017514	T	0.00967	0.0032	L	0.32530	0.975	0.80722	D	1	B	0.26002	0.139	B	0.28305	0.088	T	0.64601	-0.6369	10	0.27785	T	0.31	.	8.38	0.32466	0.2349:0.0:0.7651:0.0	.	2854	F8WD23	.	M	2855;2854	ENSP00000377197:L2855M	ENSP00000313052:L2854M	L	-	1	2	HYDIN	69495422	1.000000	0.71417	0.998000	0.56505	0.257000	0.26127	4.454000	0.60068	0.557000	0.29117	-0.507000	0.04495	CTG		0.458	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70937921	G	T	70937921	3	4	61	1	0	0	0	0	1	0	0	0	7488	991	35	2	6946	2	HYDIN	16	70937921	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259	70937921	19416832	9874	17859										
HYDIN	54768	broad.mit.edu	37	chr16	70942262	70942262	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtttggtcaaagttcccGaactcatcagaagagaagtg	11	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70942262G>A	ENST00000393567.2	-	49	8439	c.8289C>T	c.(8287-8289)ttC>ttT	p.F2763F		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2763					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.F2714F(1)|p.F2762F(1)|p.F320F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CAAAGTTCCCGAACTCATCAG	0.488																																																3	Substitution - coding silent(3)	large_intestine(3)	16											10	9	10					16																	70942262		1775	4013	5788	69499763	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8289C>T	16.37:g.70942262G>A			69499763	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.488	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70942262	G	A	70942262	2	1	61	1	0	0	0	0	0	0	0	1	7488	1049	37	1		1	HYDIN	16	70942262	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4341	70942262	19412491	9875	17860										
HYDIN	54768	broad.mit.edu	37	chr16	70942693	70942693	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcttgtctttctgaatctcGaagacttggtctatcttttc	7	10	5	2	rs183164278		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70942693G>A	ENST00000393567.2	-	48	8226	c.8076C>T	c.(8074-8076)ttC>ttT	p.F2692F		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2692					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.F249F(1)|p.F2691F(1)|p.F249L(1)|p.F2691L(1)|p.F2643L(1)|p.F2643F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCTGAATCTCGAAGACTTGGT	0.458													G|||	1	0.000199681	8e-04	0	5008	,	,		23324	0		0	False		,,,				2504	0															6	Substitution - Missense(3)|Substitution - coding silent(3)	large_intestine(3)|kidney(3)	16											155	133	140					16																	70942693		1873	4100	5973	69500194	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8076C>T	16.37:g.70942693G>A			69500194	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.458	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70942693	G	A	70942693	2	1	61	1	0	0	0	0	0	0	0	1	7488	1049	37	1		1	HYDIN	16	70942693	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	431	70942693	19412060	9876	17861										
HYDIN	54768	broad.mit.edu	37	chr16	70972530	70972530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgacctcttcttccgctCgcggagcgcctgctgaatcc	9	18	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70972530C>T	ENST00000393567.2	-	44	7132	c.6982G>A	c.(6982-6984)Gag>Aag	p.E2328K		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2328					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.E2279K(1)|p.E2327K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TTCTTCCGCTCGCGGAGCGCC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	16											20	18	19					16																	70972530		1777	4029	5806	69530031	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6982G>A	16.37:g.70972530C>T	ENSP00000377197:p.Glu2328Lys		69530031	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.396503	0.62177	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00940	5.52	5.6	5.6	0.85130	.	0.000000	0.33253	U	0.005119	T	0.03348	0.0097	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.69157	-0.5219	10	0.34782	T	0.22	.	19.2678	0.93997	0.0:1.0:0.0:0.0	.	2327	F8WD23	.	K	2328;2327	ENSP00000377197:E2328K	ENSP00000313052:E2327K	E	-	1	0	HYDIN	69530031	0.991000	0.36638	0.966000	0.40874	0.017000	0.09413	2.933000	0.48948	2.660000	0.90430	0.603000	0.83216	GAG		0.602	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70972530	C	T	70972530	3	4	61	1	0	0	0	0	1	0	0	0	7488	893	31	1	8555	1	HYDIN	16	70972530	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29837	70972530	19382223	9877	17862										
HYDIN	54768	broad.mit.edu	37	chr16	70986461	70986461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggccaccagagtcatctCggaggctaacttgcccaagg	13	12	2	1	rs373417090		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:70986461C>T	ENST00000393567.2	-	41	6544	c.6394G>A	c.(6394-6396)Gag>Aag	p.E2132K		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2132					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.E2083K(2)|p.E2131K(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AGAGTCATCTCGGAGGCTAAC	0.537																																																4	Substitution - Missense(4)	large_intestine(2)|skin(2)	16						C	LYS/GLU	1,4003		0,1,2001	55	55	55		6391	3.9	0	16		55	0,8362		0,0,4181	no	missense	HYDIN	NM_032821.2	56	0,1,6182	TT,TC,CC		0.0,0.025,0.0081	probably-damaging	2131/5121	70986461	1,12365	2002	4181	6183	69543962	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6394G>A	16.37:g.70986461C>T	ENSP00000377197:p.Glu2132Lys		69543962	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.796776	0.50208	2.5E-4	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00902	5.56	3.91	3.91	0.45181	.	0.227862	0.21098	U	0.080205	T	0.01523	0.0049	M	0.62723	1.935	0.80722	D	1	D	0.54047	0.964	B	0.41510	0.359	T	0.73017	-0.4115	10	0.27785	T	0.31	.	13.2619	0.60111	0.0:1.0:0.0:0.0	.	2131	F8WD23	.	K	2132;2131	ENSP00000377197:E2132K	ENSP00000313052:E2131K	E	-	1	0	HYDIN	69543962	0.823000	0.29233	0.026000	0.17262	0.094000	0.18550	3.689000	0.54706	2.178000	0.69098	0.195000	0.17529	GAG		0.537	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70986461	C	T	70986461	3	4	61	1	0	0	0	0	1	0	0	0	7488	893	31	1	9155	1	HYDIN	16	70986461	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13931	70986461	19368292	9878	17863										
HYDIN	54768	broad.mit.edu	37	chr16	71009119	71009119	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgttttctgatgttctagGacatagctttggactataag	10	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71009119G>A	ENST00000393567.2	-	31	4842	c.4692C>T	c.(4690-4692)gtC>gtT	p.V1564V		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1564					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.V1515V(1)|p.V1563V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GATGTTCTAGGACATAGCTTT	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	16											1	1	1					16																	71009119		1077	2308	3385	69566620	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4692C>T	16.37:g.71009119G>A			69566620	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.478	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71009119	G	A	71009119	2	1	61	1	0	0	0	0	0	0	0	1	7488	1161	41	3		3	HYDIN	16	71009119	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22658	71009119	19345634	9879	17864										
HYDIN	54768	broad.mit.edu	37	chr16	71052117	71052117	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggtgatggtaacgtagcGaatgagctcagtatcgttca	13	6	2	2	rs199955766		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71052117G>A	ENST00000393567.2	-	23	3709	c.3559C>T	c.(3559-3561)Cgc>Tgc	p.R1187C	HYDIN_ENST00000448089.2_Missense_Mutation_p.R1139C	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1187					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R1139C(2)|p.R1187C(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GTAACGTAGCGAATGAGCTCA	0.502																																																4	Substitution - Missense(4)	large_intestine(4)	16											1	1	1					16																	71052117		261	618	879	69609618	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.3559C>T	16.37:g.71052117G>A	ENSP00000377197:p.Arg1187Cys		69609618	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484496	0.63962	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089	T;T	0.04809	5.43;3.55	5.37	5.37	0.77165	.	0.000000	0.32563	U	0.005922	T	0.21307	0.0513	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	P	0.62014	0.897	T	0.00232	-1.1895	10	0.52906	T	0.07	.	18.6874	0.91570	0.0:0.0:1.0:0.0	.	1187	F8WD23	.	C	1187;1187;1139	ENSP00000377197:R1187C;ENSP00000398544:R1139C	ENSP00000313052:R1187C	R	-	1	0	HYDIN	69609618	0.873000	0.30073	0.803000	0.32268	0.496000	0.33645	4.341000	0.59335	2.536000	0.85505	0.505000	0.49811	CGC		0.502	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71052117	G	A	71052117	3	1	61	1	0	0	0	0	1	0	0	0	7488	1058	37	1	12059	1	HYDIN	16	71052117	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42998	71052117	19302636	9880	17865										
HYDIN	54768	broad.mit.edu	37	chr16	71059336	71059336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagagctggatgagaggtgCgacgaactcacaggtgatgt	17	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71059336C>T	ENST00000393567.2	-	21	3286	c.3136G>A	c.(3136-3138)Gca>Aca	p.A1046T	HYDIN_ENST00000448089.2_Intron	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1046					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.A1046T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATGAGAGGTGCGACGAACTCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											1	1	1					16																	71059336		98	257	355	69616837	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.3136G>A	16.37:g.71059336C>T	ENSP00000377197:p.Ala1046Thr		69616837	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.970948	0.53614	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.06449	3.3	5.14	4.18	0.49190	.	0.265749	0.18349	U	0.143928	T	0.11110	0.0271	L	0.53249	1.67	0.80722	D	1	D	0.57899	0.981	P	0.48334	0.574	T	0.23691	-1.0181	10	0.21014	T	0.42	.	14.6256	0.68618	0.1473:0.8527:0.0:0.0	.	1046	F8WD23	.	T	1046	ENSP00000377197:A1046T	ENSP00000313052:A1046T	A	-	1	0	HYDIN	69616837	0.967000	0.33354	0.007000	0.13788	0.104000	0.19210	3.357000	0.52277	1.170000	0.42753	0.400000	0.26472	GCA		0.572	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	71059336	C	T	71059336	3	4	61	1	0	0	0	0	1	0	0	0	7488	768	27	1	12490	1	HYDIN	16	71059336	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7219	71059336	19295417	9881	17866										
HYDIN	54768	broad.mit.edu	37	chr16	71061732	71061732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagaacaactgttggatccGacgtcccttgttgatcaact	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71061732G>A	ENST00000393567.2	-	20	2965	c.2815C>T	c.(2815-2817)Cgg>Tgg	p.R939W	HYDIN_ENST00000321489.5_Missense_Mutation_p.R939W|HYDIN_ENST00000448089.2_Missense_Mutation_p.R939W|HYDIN_ENST00000448691.1_Missense_Mutation_p.R939W	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	939					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R939W(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGTTGGATCCGACGTCCCTTG	0.493																																																3	Substitution - Missense(3)	large_intestine(3)	16											4	3	3					16																	71061732		1554	3177	4731	69619233	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2815C>T	16.37:g.71061732G>A	ENSP00000377197:p.Arg939Trp		69619233	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004076	0.93287	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489	T;T;T;T	0.07908	3.15;3.15;3.15;3.15	5.07	5.07	0.68467	.	0.000000	0.31020	U	0.008406	T	0.33962	0.0881	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.11036	-1.0604	10	0.38643	T	0.18	.	18.0946	0.89485	0.0:0.0:1.0:0.0	.	939;939	Q4G0P3-5;F8WD23	.;.	W	939	ENSP00000377197:R939W;ENSP00000398544:R939W;ENSP00000394826:R939W;ENSP00000314736:R939W	ENSP00000313052:R939W	R	-	1	2	HYDIN	69619233	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	5.070000	0.64376	2.400000	0.81607	0.499000	0.49734	CGG		0.493	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71061732	G	A	71061732	3	1	61	1	0	0	0	0	1	0	0	0	7488	1057	37	1	12827	1	HYDIN	16	71061732	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2396	71061732	19293021	9882	17867										
HYDIN	54768	broad.mit.edu	37	chr16	71212878	71212878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttcatagacttcacaggGagtgtagttctgaaatataa	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71212878G>A	ENST00000393567.2	-	4	484	c.334C>T	c.(334-336)Ccc>Tcc	p.P112S	HYDIN_ENST00000321489.5_Missense_Mutation_p.P112S|HYDIN_ENST00000448089.2_Missense_Mutation_p.P112S|HYDIN_ENST00000538248.1_Missense_Mutation_p.P139S|HYDIN_ENST00000288168.10_Missense_Mutation_p.P129S|HYDIN_ENST00000541601.1_Missense_Mutation_p.P129S|HYDIN_ENST00000448691.1_Missense_Mutation_p.P112S|HYDIN_ENST00000393550.2_Missense_Mutation_p.P112S	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	112					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.P112S(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ACTTCACAGGGAGTGTAGTTC	0.388																																																3	Substitution - Missense(3)	large_intestine(3)	16											109	112	111					16																	71212878		2198	4300	6498	69770379	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.334C>T	16.37:g.71212878G>A	ENSP00000377197:p.Pro112Ser		69770379	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631081	0.67015	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550	T;T;T;T;T;T;T;T	0.19938	5.23;3.34;3.35;3.35;3.32;3.33;2.98;2.11	5.43	4.42	0.53409	.	0.000000	0.31323	U	0.007852	T	0.35740	0.0942	M	0.69185	2.1	0.34158	D	0.668316	D;D;D;D;D	0.64830	0.969;0.969;0.987;0.987;0.994	P;P;P;P;P	0.58721	0.662;0.527;0.797;0.728;0.844	T	0.34129	-0.9841	10	0.07482	T	0.82	.	16.586	0.84727	0.0:0.2288:0.7712:0.0	.	139;129;129;112;112	B4DRN4;F5H6V3;F8WD03;Q4G0P3-5;F8WD23	.;.;.;.;.	S	112;112;112;112;112;139;129;129;112	ENSP00000377197:P112S;ENSP00000398544:P112S;ENSP00000394826:P112S;ENSP00000314736:P112S;ENSP00000444970:P139S;ENSP00000437341:P129S;ENSP00000288168:P129S;ENSP00000377181:P112S	ENSP00000288168:P129S	P	-	1	0	HYDIN	69770379	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	4.038000	0.57318	2.547000	0.85894	0.462000	0.41574	CCC		0.388	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71212878	G	A	71212878	3	1	61	1	0	0	0	0	1	0	0	0	7488	1174	41	3	15372	3	HYDIN	16	71212878	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151146	71212878	19141875	9883	17868										
HYDIN	54768	broad.mit.edu	37	chr16	71220669	71220669	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccggatacattaccattcGgtttacttcttcttctgtaa	5	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71220669G>A	ENST00000393567.2	-	2	280	c.130C>T	c.(130-132)Cga>Tga	p.R44*	HYDIN_ENST00000321489.5_Nonsense_Mutation_p.R44*|HYDIN_ENST00000448089.2_Nonsense_Mutation_p.R44*|HYDIN_ENST00000538248.1_Nonsense_Mutation_p.R71*|HYDIN_ENST00000288168.10_Nonsense_Mutation_p.R61*|HYDIN_ENST00000541601.1_Nonsense_Mutation_p.R61*|HYDIN_ENST00000448691.1_Nonsense_Mutation_p.R44*|HYDIN_ENST00000393550.2_Nonsense_Mutation_p.R44*	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	44					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R44*(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATTACCATTCGGTTTACTTCT	0.408																																																3	Substitution - Nonsense(3)	large_intestine(3)	16											140	127	131					16																	71220669		2198	4300	6498	69778170	SO:0001587	stop_gained	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.130C>T	16.37:g.71220669G>A	ENSP00000377197:p.Arg44*		69778170	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Nonsense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.074945	0.55646	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550	.	.	.	5.37	1.92	0.25849	.	0.905027	0.08776	U	0.895473	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8473	0.63474	0.0:0.0:0.6017:0.3983	.	.	.	.	X	44;44;44;44;44;71;61;61;44	.	ENSP00000288168:R61X	R	-	1	2	HYDIN	69778170	0.370000	0.25047	0.701000	0.30321	0.733000	0.41908	0.890000	0.28295	0.619000	0.30197	0.650000	0.86243	CGA		0.408	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71220669	G	A	71220669	4	1	61	1	0	0	0	0	0	1	0	0	7488	1124	39	1	15584	1	HYDIN	16	71220669	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7791	71220669	19134084	9884	17869										
FTSJD1	55783	broad.mit.edu	37	chr16	71317988	71317988	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccatcatgaagcaatgaAcagctaaaagttgtgagttc	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71317988A>G	ENST00000338099.5	-	3	2172	c.1836T>C	c.(1834-1836)tgT>tgC	p.C612C	CMTR2_ENST00000434935.2_Silent_p.C612C			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	612					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.C612C(1)									GAAGCAATGAACAGCTAAAAG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	16											54	53	53					16																	71317988		2198	4300	6498	69875489	SO:0001819	synonymous_variant	55783			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1836T>C	16.37:g.71317988A>G			69875489	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	37	CCDS10898.1																																																																																				0.428	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		G	71317988	A	G	71317988	2	3	61	1	0	0	0	0	0	0	0	1	6109	41	2	4		4	FTSJD1	16	71317988	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	97319	71317988	19036765	9885	17870										
FTSJD1	55783	broad.mit.edu	37	chr16	71318604	71318604	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagatgtttcagttgaaatTtttgcataaaatattgtata	6	2	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71318604T>G	ENST00000338099.5	-	3	1556	c.1220A>C	c.(1219-1221)aAa>aCa	p.K407T	CMTR2_ENST00000434935.2_Missense_Mutation_p.K407T			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	407					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.K407T(1)									CAGTTGAAATTTTTGCATAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	16											26	28	27					16																	71318604		2196	4282	6478	69876105	SO:0001583	missense	55783			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1220A>C	16.37:g.71318604T>G	ENSP00000337512:p.Lys407Thr		69876105	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	10.46	1.356163	0.24598	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15017	2.46;2.46	5.95	5.95	0.96441	.	0.177661	0.47455	D	0.000237	T	0.15219	0.0367	L	0.54323	1.7	0.31422	N	0.674152	B	0.32245	0.361	B	0.26416	0.069	T	0.19811	-1.0294	10	0.56958	D	0.05	-9.7465	6.7077	0.23260	0.1367:0.0731:0.0:0.7902	.	407	Q8IYT2	FTSJ1_HUMAN	T	407	ENSP00000337512:K407T;ENSP00000411148:K407T	ENSP00000337512:K407T	K	-	2	0	FTSJD1	69876105	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.649000	0.37281	2.279000	0.76181	0.402000	0.26972	AAA		0.313	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		G	71318604	T	G	71318604	3	3	61	1	0	0	0	0	1	0	0	0	6109	1841	64	4	1096	4	FTSJD1	16	71318604	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	616	71318604	19036149	9886	17871										
FTSJD1	55783	broad.mit.edu	37	chr16	71319623	71319623	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacttcatttagggagttCttcaaatcaagaaatgcatt	6	6	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71319623C>A	ENST00000338099.5	-	3	537	c.201G>T	c.(199-201)aaG>aaT	p.K67N	CMTR2_ENST00000434935.2_Missense_Mutation_p.K67N			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	67					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.K67N(1)									TTAGGGAGTTCTTCAAATCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	16											98	97	97					16																	71319623		2198	4300	6498	69877124	SO:0001583	missense	55783			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.201G>T	16.37:g.71319623C>A	ENSP00000337512:p.Lys67Asn		69877124	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.915983	0.52546	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.28895	1.59;1.59	5.7	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.54870	0.1885	M	0.81497	2.545	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	T	0.58918	-0.7551	10	0.66056	D	0.02	-22.3545	9.9368	0.41556	0.0:0.8469:0.0:0.1531	.	67	Q8IYT2	FTSJ1_HUMAN	N	67	ENSP00000337512:K67N;ENSP00000411148:K67N	ENSP00000337512:K67N	K	-	3	2	FTSJD1	69877124	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.171000	0.42453	1.401000	0.46761	0.655000	0.94253	AAG		0.393	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		A	71319623	C	A	71319623	3	1	61	1	0	0	0	0	1	0	0	0	6109	912	32	2	2115	2	FTSJD1	16	71319623	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1019	71319623	19035130	9887	17872										
ZNF23	7571	broad.mit.edu	37	chr16	71482685	71482685	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatagggtttctcgcctgTgtgaattctctggtgttgga	12	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71482685T>G	ENST00000393539.2	-	6	2056	c.1243A>C	c.(1243-1245)Aca>Cca	p.T415P	ZNF23_ENST00000428724.2_Missense_Mutation_p.T357P|ZNF23_ENST00000417828.1_Missense_Mutation_p.T415P|ZNF23_ENST00000358700.2_3'UTR|ZNF23_ENST00000539742.1_5'UTR|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000564528.1_Missense_Mutation_p.T357P|ZNF23_ENST00000357254.4_Missense_Mutation_p.T415P	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T415P(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TTCTCGCCTGTGTGAATTCTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	16											59	54	55					16																	71482685		2198	4300	6498	70040186	SO:0001583	missense	7571			X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.1243A>C	16.37:g.71482685T>G	ENSP00000377171:p.Thr415Pro		70040186	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.576247	0.65878	.	.	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	4.14	4.14	0.48551	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000343	T	0.47728	0.1461	M	0.78456	2.415	0.48288	D	0.999626	D;D	0.65815	0.987;0.995	D;D	0.63597	0.916;0.916	T	0.52866	-0.8518	10	0.87932	D	0	-15.6216	11.7765	0.51989	0.0:0.0:0.0:1.0	.	415;415	B3KR55;P17027	.;ZNF23_HUMAN	P	415;415;415;357;357	ENSP00000377171:T415P;ENSP00000349796:T415P;ENSP00000395712:T415P;ENSP00000387673:T357P	ENSP00000349796:T415P	T	-	1	0	ZNF23	70040186	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	4.016000	0.57159	2.097000	0.63578	0.454000	0.30748	ACA		0.463	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		G	71482685	T	G	71482685	3	3	61	1	0	0	0	0	1	0	0	0	17822	1696	59	4	692	4	ZNF23	16	71482685	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	163062	71482685	18872068	9888	17873										
ZNF19	7567	broad.mit.edu	37	chr16	71509404	71509404	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctcctcactgtgaattCtctggtgccgagttagtttt	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71509404C>A	ENST00000288177.5	-	6	1301	c.1046G>T	c.(1045-1047)aGa>aTa	p.R349I	ZNF19_ENST00000565100.2_Missense_Mutation_p.R279I|ZNF19_ENST00000565637.1_Missense_Mutation_p.R307I|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000564230.1_Missense_Mutation_p.R349I	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	349					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R349I(2)		NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		ACTGTGAATTCTCTGGTGCCG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	16											76	76	76					16																	71509404		2198	4300	6498	70066905	SO:0001583	missense	7567			X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"Zinc fingers, C2H2-type", "-"	12981	protein-coding gene	gene with protein product		194525	"zinc finger protein 19 (KOX 12)"			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.1046G>T	16.37:g.71509404C>A	ENSP00000288177:p.Arg349Ile		70066905	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	ENST00000288177.5	37	CCDS10901.1	.	.	.	.	.	.	.	.	.	.	C	6.119	0.390278	0.11581	.	.	ENSG00000157429	ENST00000288177	T	0.24908	1.83	3.25	1.22	0.21188	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.471713	0.15920	N	0.238177	T	0.32823	0.0842	M	0.66560	2.04	0.29154	N	0.878198	P	0.40107	0.703	P	0.46885	0.53	T	0.24012	-1.0172	10	0.87932	D	0	.	7.7848	0.29085	0.0:0.7775:0.0:0.2225	.	349	P17023	ZNF19_HUMAN	I	349	ENSP00000288177:R349I	ENSP00000288177:R349I	R	-	2	0	ZNF19	70066905	0.000000	0.05858	0.331000	0.25455	0.102000	0.19082	-0.085000	0.11250	0.376000	0.24707	-0.150000	0.13652	AGA		0.413	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961		A	71509404	C	A	71509404	3	1	61	1	0	0	0	0	1	0	0	0	17794	913	32	2	334	2	ZNF19	16	71509404	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26719	71509404	18845349	9889	17874										
CHST4	10164	broad.mit.edu	37	chr16	71571256	71571256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatctcatgattgacagtCgcattgtgatggggcagcat	13	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71571256C>T	ENST00000338482.5	+	3	1019	c.676C>T	c.(676-678)Cgc>Tgc	p.R226C	CHST4_ENST00000572450.1_Missense_Mutation_p.R226C|CHST4_ENST00000539698.3_Missense_Mutation_p.R226C|RP11-510M2.5_ENST00000568523.1_RNA|ZNF19_ENST00000568446.1_Intron			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	226					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.R226C(1)		cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						GATTGACAGTCGCATTGTGAT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16											75	66	69					16																	71571256		2198	4300	6498	70128757	SO:0001583	missense	10164			AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"Sulfotransferases, membrane-bound"	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.676C>T	16.37:g.71571256C>T	ENSP00000341206:p.Arg226Cys		70128757	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181946	0.57800	.	.	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.96651	-4.08;-4.08	6.02	6.02	0.97574	Sulfotransferase domain (1);	0.776024	0.12498	N	0.463611	D	0.97461	0.9169	M	0.73217	2.22	0.29716	N	0.839052	D	0.71674	0.998	P	0.61658	0.892	D	0.94604	0.7798	10	0.54805	T	0.06	-8.9872	13.5981	0.62002	0.0:0.8447:0.1553:0.0	.	226	Q8NCG5	CHST4_HUMAN	C	226	ENSP00000341206:R226C;ENSP00000441204:R226C	ENSP00000341206:R226C	R	+	1	0	CHST4	70128757	0.030000	0.19436	0.924000	0.36721	0.732000	0.41865	0.262000	0.18460	2.865000	0.98341	0.655000	0.94253	CGC		0.552	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769		T	71571256	C	T	71571256	3	4	61	1	0	0	0	0	1	0	0	0	3412	884	31	1	678	1	CHST4	16	71571256	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61852	71571256	18783497	9890	17875										
TAT	6898	broad.mit.edu	37	chr16	71602685	71602685	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccacatcgttctcaaattCtgggaaatgttccatctcaa	5	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71602685C>T	ENST00000355962.4	-	11	1286	c.1153G>A	c.(1153-1155)Gaa>Aaa	p.E385K	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	385					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)	p.E385K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TTCTCAAATTCTGGGAAATGT	0.507																																					Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)											1	Substitution - Missense(1)	large_intestine(1)	16											78	66	70					16																	71602685		2198	4300	6498	70160186	SO:0001583	missense	6898				CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1153G>A	16.37:g.71602685C>T	ENSP00000348234:p.Glu385Lys		70160186	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510213	0.85282	.	.	ENSG00000198650	ENST00000355962	D	0.87729	-2.29	5.93	5.93	0.95920	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.138311	0.64402	D	0.000004	D	0.84379	0.5459	L	0.42686	1.345	0.80722	D	1	B	0.33103	0.397	B	0.35182	0.197	T	0.79897	-0.1609	10	0.16420	T	0.52	-14.4812	20.3539	0.98825	0.0:1.0:0.0:0.0	.	385	P17735	ATTY_HUMAN	K	385	ENSP00000348234:E385K	ENSP00000348234:E385K	E	-	1	0	TAT	70160186	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.780000	0.68956	2.826000	0.97356	0.655000	0.94253	GAA		0.507	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			T	71602685	C	T	71602685	3	4	61	1	0	0	0	0	1	0	0	0	15629	922	32	3	219	3	TAT	16	71602685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31429	71602685	18752068	9891	17876										
TAT	6898	broad.mit.edu	37	chr16	71609927	71609927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttccaaacacagtagggtCccctttttatgggaggaaaa	10	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71609927C>T	ENST00000355962.4	-	3	371	c.238G>A	c.(238-240)Gac>Aac	p.D80N	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	80					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)	p.D80N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	ACAGTAGGGTCCCCTTTTTAT	0.498																																					Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)											1	Substitution - Missense(1)	large_intestine(1)	16											90	91	90					16																	71609927		2198	4300	6498	70167428	SO:0001583	missense	6898				CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.238G>A	16.37:g.71609927C>T	ENSP00000348234:p.Asp80Asn		70167428	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	C	34	5.351065	0.95830	.	.	ENSG00000198650	ENST00000355962	D	0.90620	-2.7	5.75	5.75	0.90469	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.95478	0.8531	M	0.90542	3.125	0.80722	D	1	P;D	0.63046	0.901;0.992	P;D	0.66602	0.829;0.945	D	0.93190	0.6582	10	0.07325	T	0.83	-31.2724	19.9361	0.97143	0.0:1.0:0.0:0.0	.	80;80	A1L4G7;P17735	.;ATTY_HUMAN	N	80	ENSP00000348234:D80N	ENSP00000348234:D80N	D	-	1	0	TAT	70167428	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.487000	0.81328	2.716000	0.92895	0.655000	0.94253	GAC		0.498	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			T	71609927	C	T	71609927	3	4	61	1	0	0	0	0	1	0	0	0	15629	855	30	3	1166	3	TAT	16	71609927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7242	71609927	18744826	9892	17877										
MARVELD3	91862	broad.mit.edu	37	chr16	71663281	71663281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttatagtgaacccccttCggagagatatctgccctcga	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71663281C>T	ENST00000268485.3	+	2	523	c.479C>T	c.(478-480)tCg>tTg	p.S160L	RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000567566.1_Missense_Mutation_p.S160L|MARVELD3_ENST00000567501.1_5'UTR|MARVELD3_ENST00000565261.1_Missense_Mutation_p.R106W|MARVELD3_ENST00000299952.4_Missense_Mutation_p.S160L	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	160	Pro-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)		p.S160L(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GAACCCCCTTCGGAGAGATAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	16											88	83	85					16																	71663281		2198	4300	6498	70220782	SO:0001583	missense	91862			BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.479C>T	16.37:g.71663281C>T	ENSP00000268485:p.Ser160Leu		70220782	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247190	0.22796	.	.	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.52983	0.67;0.64	5.57	3.52	0.40303	.	0.481200	0.22276	N	0.062182	T	0.43567	0.1253	M	0.67953	2.075	0.20307	N	0.999917	B;B;D	0.55800	0.14;0.14;0.973	B;B;B	0.43052	0.039;0.039;0.406	T	0.43147	-0.9409	10	0.49607	T	0.09	-29.7778	6.5685	0.22525	0.1767:0.7335:0.0:0.0898	.	160;160;183	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	L	160	ENSP00000268485:S160L;ENSP00000299952:S160L	ENSP00000268485:S160L	S	+	2	0	MARVELD3	70220782	0.003000	0.15002	0.010000	0.14722	0.038000	0.13279	0.786000	0.26844	1.362000	0.46000	-0.215000	0.12644	TCG		0.512	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858		T	71663281	C	T	71663281	3	4	61	1	0	0	0	0	1	0	0	0	9349	893	31	1	485	1	MARVELD3	16	71663281	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53354	71663281	18691472	9893	17878										
AP1G1	164	broad.mit.edu	37	chr16	71779455	71779455	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctccatttgtctgcacaAtctcagtagggccatttgtg	8	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71779455A>T	ENST00000299980.4	-	18	2234	c.1793T>A	c.(1792-1794)aTt>aAt	p.I598N	AP1G1_ENST00000393512.3_Missense_Mutation_p.I601N|AP1G1_ENST00000569748.1_Missense_Mutation_p.I598N|AP1G1_ENST00000433195.2_Missense_Mutation_p.I621N|AP1G1_ENST00000564155.1_Missense_Mutation_p.I23N|AP1G1_ENST00000423132.2_Missense_Mutation_p.I601N	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	598					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)	p.I598N(1)		breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TGTCTGCACAATCTCAGTAGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	16											205	191	196					16																	71779455		2198	4300	6498	70336956	SO:0001583	missense	164			Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1793T>A	16.37:g.71779455A>T	ENSP00000299980:p.Ile598Asn		70336956	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	37	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018969	0.35606	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	5.71	5.71	0.89125	Armadillo-type fold (1);	0.120160	0.64402	D	0.000004	T	0.11367	0.0277	L	0.29908	0.895	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.004;0.002	T	0.14783	-1.0460	10	0.14252	T	0.57	-2.1634	15.9895	0.80193	1.0:0.0:0.0:0.0	.	598;621;601	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	N	598;601;601;621	ENSP00000299980:I598N;ENSP00000377148:I601N;ENSP00000409153:I601N;ENSP00000403259:I621N	ENSP00000299980:I598N	I	-	2	0	AP1G1	70336956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.906000	0.92626	2.183000	0.69458	0.459000	0.35465	ATT		0.502	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			T	71779455	A	T	71779455	3	4	61	1	0	0	0	0	1	0	0	0	732	101	4	5	699	5	AP1G1	16	71779455	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116174	71779455	18575298	9894	17879										
AP1G1	164	broad.mit.edu	37	chr16	71807247	71807247	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaacccctgtacgaattgCgtgctatgattaagatcact	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71807247C>T	ENST00000299980.4	-	4	786	c.345G>A	c.(343-345)acG>acA	p.T115T	AP1G1_ENST00000393512.3_Silent_p.T115T|AP1G1_ENST00000569748.1_Silent_p.T115T|AP1G1_ENST00000433195.2_Silent_p.T138T|AP1G1_ENST00000423132.2_Silent_p.T115T	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	115					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)	p.T115T(1)		breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				GTACGAATTGCGTGCTATGAT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	16											86	83	84					16																	71807247		2198	4300	6498	70364748	SO:0001819	synonymous_variant	164			Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.345G>A	16.37:g.71807247C>T			70364748	O75709|O75842|Q9UG09|Q9Y3U4	Silent	SNP	ENST00000299980.4	37	CCDS32480.1																																																																																				0.478	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			T	71807247	C	T	71807247	2	4	61	1	0	0	0	0	0	0	0	1	732	755	27	1		1	AP1G1	16	71807247	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27792	71807247	18547506	9895	17880										
ZNF821	55565	broad.mit.edu	37	chr16	71894352	71894352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgttccagccgctgcagccGtacttccaaaggctcattct	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:71894352G>A	ENST00000565601.1	-	7	1215	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W	ZNF821_ENST00000313565.6_Missense_Mutation_p.R228W|ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000425432.1_Missense_Mutation_p.R270W|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000446827.2_Missense_Mutation_p.R228W	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R228W(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						CGCTGCAGCCGTACTTCCAAA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	16											70	64	66					16																	71894352		2198	4300	6498	70451853	SO:0001583	missense	55565			AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"Zinc fingers, C2H2-type"	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.808C>T	16.37:g.71894352G>A	ENSP00000455648:p.Arg270Trp		70451853	A6NK48|B4DKK4|D3DWS3	Missense_Mutation	SNP	ENST00000565601.1	37	CCDS56006.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.043009	0.55003	.	.	ENSG00000102984	ENST00000425432;ENST00000313565;ENST00000446827	T;T;T	0.02197	5.92;4.4;4.4	5.63	-0.28	0.12886	.	0.000000	0.85682	D	0.000000	T	0.09291	0.0229	L	0.57536	1.79	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.99;0.994;0.99	T	0.00690	-1.1608	10	0.87932	D	0	-12.582	16.7375	0.85451	0.0:0.0:0.3091:0.6909	.	270;228;270	B4DKK4;O75541-2;O75541	.;.;ZN821_HUMAN	W	270;228;228	ENSP00000398089:R270W;ENSP00000313822:R228W;ENSP00000405908:R228W	ENSP00000313822:R228W	R	-	1	2	ZNF821	70451853	0.778000	0.28640	0.220000	0.23810	0.792000	0.44763	1.081000	0.30791	0.014000	0.14944	-0.152000	0.13540	CGG		0.612	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530		A	71894352	G	A	71894352	3	1	61	1	0	0	0	0	1	0	0	0	18217	1144	40	1	434	1	ZNF821	16	71894352	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87105	71894352	18460401	9896	17881										
HP	3240	broad.mit.edu	37	chr16	72094027	72094027	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtatgtgggaagcccaaGaatccggcaaacccagtgca	11	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:72094027G>T	ENST00000355906.5	+	7	517	c.459G>T	c.(457-459)aaG>aaT	p.K153N	HP_ENST00000357763.4_Missense_Mutation_p.K189N|HP_ENST00000570083.1_Missense_Mutation_p.K94N|HP_ENST00000565574.1_Missense_Mutation_p.K94N|HP_ENST00000562526.1_Intron|HPR_ENST00000356967.5_Intron|HP_ENST00000398131.2_Missense_Mutation_p.K94N	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	153					acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)	p.K153N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		GGAAGCCCAAGAATCCGGCAA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											16	16	16					16																	72094027		1817	4049	5866	70651528	SO:0001583	missense	3240				CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.459G>T	16.37:g.72094027G>T	ENSP00000348170:p.Lys153Asn		70651528	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Missense_Mutation	SNP	ENST00000355906.5	37	CCDS45524.1	.	.	.	.	.	.	.	.	.	.	G	5.182	0.219145	0.09863	.	.	ENSG00000257017	ENST00000355906;ENST00000398131;ENST00000357763	T;T	0.48836	0.8;0.8	4.91	3.95	0.45737	Peptidase cysteine/serine, trypsin-like (1);Complement control module (1);	0.524360	0.20088	N	0.099506	T	0.52805	0.1757	M	0.78637	2.42	0.23168	N	0.998185	P;B	0.51653	0.947;0.291	P;B	0.49047	0.599;0.157	T	0.47005	-0.9150	10	0.32370	T	0.25	.	8.0733	0.30701	0.0861:0.1601:0.7538:0.0	.	94;153	Q0VAC5;P00738	.;HPT_HUMAN	N	153;94;129	ENSP00000348170:K153N;ENSP00000381199:K94N	ENSP00000348170:K153N	K	+	3	2	HP	70651528	0.542000	0.26426	0.017000	0.16124	0.561000	0.35649	1.633000	0.37113	1.432000	0.47375	0.591000	0.81541	AAG		0.542	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143		T	72094027	G	T	72094027	3	4	61	1	0	0	0	0	1	0	0	0	7348	933	33	2	485	2	HP	16	72094027	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199675	72094027	18260726	9897	17882										
DHX38	9785	broad.mit.edu	37	chr16	72130868	72130868	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaggattggaagaaggaGaaatcgcgggatcgagacta	15	4	0	3	rs375554088		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:72130868G>A	ENST00000268482.3	+	3	980	c.471G>A	c.(469-471)gaG>gaA	p.E157E	DHX38_ENST00000536867.1_Intron|TXNL4B_ENST00000426362.2_5'Flank	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	157					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.E157E(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				GGAAGAAGGAGAAATCGCGGG	0.502																																					Melanoma(97;711 1442 7855 13832 28836)											1	Substitution - coding silent(1)	large_intestine(1)	16						G		1,4395	2.1+/-5.4	0,1,2197	113	109	110		471	2	1	16		110	0,8600		0,0,4300	no	coding-synonymous	DHX38	NM_014003.3		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		157/1228	72130868	1,12995	2198	4300	6498	70688369	SO:0001819	synonymous_variant	9785			AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.471G>A	16.37:g.72130868G>A			70688369	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																				0.502	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72130868	G	A	72130868	2	1	61	1	0	0	0	0	0	0	0	1	4522	933	33	3		3	DHX38	16	72130868	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36841	72130868	18223885	9898	17883										
PMFBP1	83449	broad.mit.edu	37	chr16	72162690	72162690	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactttctggaattctcttTcaactgttccctcattaaag	4	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:72162690T>G	ENST00000237353.10	-	14	2215	c.1954A>C	c.(1954-1956)Aaa>Caa	p.K652Q	PMFBP1_ENST00000537465.1_Missense_Mutation_p.K657Q|PMFBP1_ENST00000355636.6_Missense_Mutation_p.K507Q	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	657						cytoplasm (GO:0005737)		p.K652Q(1)		NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				GAATTCTCTTTCAACTGTTCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											124	113	117					16																	72162690		2198	4300	6498	70720191	SO:0001583	missense	83449			AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.1954A>C	16.37:g.72162690T>G	ENSP00000237353:p.Lys652Gln		70720191	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.135065	0.56828	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.13778	2.56;2.57;2.56	5.41	5.41	0.78517	.	0.371366	0.23295	N	0.049750	T	0.16599	0.0399	L	0.32530	0.975	0.09310	N	1	P;P;P	0.51351	0.944;0.944;0.944	P;P;P	0.52957	0.714;0.714;0.714	T	0.13282	-1.0515	10	0.14656	T	0.56	-17.3902	11.754	0.51866	0.0:0.0:0.0:1.0	.	657;652;657	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	Q	657;652;507	ENSP00000443817:K657Q;ENSP00000237353:K652Q;ENSP00000347854:K507Q	ENSP00000237353:K652Q	K	-	1	0	PMFBP1	70720191	0.084000	0.21492	0.011000	0.14972	0.098000	0.18820	3.301000	0.51842	2.265000	0.75225	0.533000	0.62120	AAA		0.428	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		G	72162690	T	G	72162690	3	3	61	1	0	0	0	0	1	0	0	0	12165	1792	62	4	1161	4	PMFBP1	16	72162690	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	31822	72162690	18192063	9899	17884										
ZFHX3	463	broad.mit.edu	37	chr16	72830969	72830969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcttttcggggtgctggCttggctgaaggagggcagag	17	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:72830969C>T	ENST00000268489.5	-	9	6284	c.5612G>A	c.(5611-5613)aGc>aAc	p.S1871N	ZFHX3_ENST00000397992.5_Missense_Mutation_p.S957N	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1871					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S1871N(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GGGGTGCTGGCTTGGCTGAAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16											103	108	106					16																	72830969		2198	4300	6498	71388470	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5612G>A	16.37:g.72830969C>T	ENSP00000268489:p.Ser1871Asn		71388470	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412258	0.25465	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74002	-0.8;-0.78	5.85	5.85	0.93711	.	0.245586	0.28901	N	0.013765	T	0.59418	0.2192	N	0.08118	0	0.33086	D	0.537329	B	0.27559	0.181	B	0.29353	0.101	T	0.63603	-0.6600	10	0.31617	T	0.26	.	18.3455	0.90321	0.0:1.0:0.0:0.0	.	1871	Q15911	ZFHX3_HUMAN	N	1871;957	ENSP00000268489:S1871N;ENSP00000438926:S957N	ENSP00000268489:S1871N	S	-	2	0	ZFHX3	71388470	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.507000	0.60434	2.753000	0.94483	0.655000	0.94253	AGC		0.552	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72830969	C	T	72830969	3	4	61	1	0	0	0	0	1	0	0	0	17673	797	28	3	5507	3	ZFHX3	16	72830969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	668279	72830969	17523784	9900	17885										
MLKL	197259	broad.mit.edu	37	chr16	74708907	74708907	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcccggcactcatcaatGatctcccgcagctctgaagg	11	14	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:74708907G>T	ENST00000308807.7	-	10	1795	c.1332C>A	c.(1330-1332)atC>atA	p.I444I	MLKL_ENST00000306247.7_Silent_p.I236I	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like									p.I444I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTCATCAATGATCTCCCGCA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	16											59	60	60					16																	74708907		2198	4300	6498	73266408	SO:0001819	synonymous_variant	197259			AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.1332C>A	16.37:g.74708907G>T			73266408		Silent	SNP	ENST00000308807.7	37	CCDS32487.1																																																																																				0.552	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		T	74708907	G	T	74708907	2	4	61	1	0	0	0	0	0	0	0	1	9649	1280	45	2		2	MLKL	16	74708907	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1877938	74708907	15645846	9901	17886										
MLKL	197259	broad.mit.edu	37	chr16	74729391	74729391	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtcctggcttgctgttaGaaacctgcagatattggatc	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:74729391G>T	ENST00000308807.7	-	2	728	c.265C>A	c.(265-267)Cta>Ata	p.L89I	MLKL_ENST00000306247.7_Missense_Mutation_p.L89I	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like									p.L89I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CTTGCTGTTAGAAACCTGCAG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											173	163	167					16																	74729391		2198	4300	6498	73286892	SO:0001583	missense	197259			AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.265C>A	16.37:g.74729391G>T	ENSP00000308351:p.Leu89Ile		73286892		Missense_Mutation	SNP	ENST00000308807.7	37	CCDS32487.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847641	0.32606	.	.	ENSG00000168404	ENST00000308807;ENST00000306247	T;T	0.79554	-1.28;2.48	4.63	-0.0351	0.13894	.	0.826496	0.10758	N	0.637525	T	0.68302	0.2986	L	0.32530	0.975	0.09310	N	1	P;P	0.45715	0.865;0.835	B;B	0.43478	0.421;0.195	T	0.57579	-0.7787	10	0.38643	T	0.18	-0.077	3.4376	0.07452	0.0959:0.3296:0.4166:0.158	.	89;89	Q8NB16-2;Q8NB16	.;MLKL_HUMAN	I	89	ENSP00000308351:L89I;ENSP00000303118:L89I	ENSP00000303118:L89I	L	-	1	2	MLKL	73286892	0.057000	0.20700	0.001000	0.08648	0.010000	0.07245	-0.176000	0.09811	-0.048000	0.13401	0.650000	0.86243	CTA		0.478	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		T	74729391	G	T	74729391	3	4	61	1	0	0	0	0	1	0	0	0	9649	933	33	2	1221	2	MLKL	16	74729391	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20484	74729391	15625362	9902	17887										
LDHD	197257	broad.mit.edu	37	chr16	75148027	75148027	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgtcccctcggagcccacGaagagccccgtgaggttgta	13	14	0	2	rs141944225	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:75148027G>A	ENST00000450168.2	-	6	716	c.666C>T	c.(664-666)ttC>ttT	p.F222F	LDHD_ENST00000300051.4_Silent_p.F245F	NM_194436.2	NP_919417.1			lactate dehydrogenase D									p.F245F(1)		endometrium(1)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	16						CGGAGCCCACGAAGAGCCCCG	0.652													G|||	3	0.000599042	0.0023	0	5008	,	,		16918	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16						G	,	15,4381	21.2+/-45.6	0,15,2183	80	80	80		735,666	1.1	1	16	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LDHD	NM_153486.3,NM_194436.2	,	0,15,6483	AA,AG,GG		0.0,0.3412,0.1154	,	245/508,222/485	75148027	15,12981	2198	4300	6498	73705528	SO:0001819	synonymous_variant	197257			AY092767	CCDS10913.1, CCDS45529.1	16q22.3	2011-01-27			ENSG00000166816	ENSG00000166816			19708	protein-coding gene	gene with protein product		607490				12127981	Standard	NM_153486		Approved		uc002fdm.3	Q86WU2	OTTHUMG00000137605	ENST00000450168.2:c.666C>T	16.37:g.75148027G>A			73705528		Silent	SNP	ENST00000450168.2	37	CCDS45529.1																																																																																				0.652	LDHD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434651.1	NM_153486		A	75148027	G	A	75148027	2	1	61	1	0	0	0	0	0	0	0	1	8725	1049	37	1		1	LDHD	16	75148027	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	418636	75148027	15206726	9903	17888										
CFDP1	10428	broad.mit.edu	37	chr16	75448521	75448521	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttcccttgggttttcTgtgtctgctcttcaccatcc	6	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:75448521T>A	ENST00000283882.3	-	2	269	c.137A>T	c.(136-138)cAg>cTg	p.Q46L	CFDP1_ENST00000564286.1_5'UTR|RP11-77K12.1_ENST00000561887.1_Intron|RP11-77K12.1_ENST00000567194.1_Missense_Mutation_p.Q103L	NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	46	Glu-rich.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)			p.Q46L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						TTGGGTTTTCTGTGTCTGCTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	16											200	181	188					16																	75448521		2198	4300	6498	74006022	SO:0001583	missense	10428			AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.137A>T	16.37:g.75448521T>A	ENSP00000283882:p.Gln46Leu		74006022	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Missense_Mutation	SNP	ENST00000283882.3	37	CCDS10916.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.424165	0.62733	.	.	ENSG00000153774	ENST00000283882	T	0.45276	0.9	5.64	5.64	0.86602	.	0.524252	0.20948	N	0.082802	T	0.37489	0.1005	L	0.53249	1.67	0.26966	N	0.965694	B	0.26672	0.156	B	0.16722	0.016	T	0.24835	-1.0149	10	0.33141	T	0.24	-11.2314	12.2601	0.54645	0.0:0.0:0.0:1.0	.	46	Q9UEE9	CFDP1_HUMAN	L	46	ENSP00000283882:Q46L	ENSP00000283882:Q46L	Q	-	2	0	CFDP1	74006022	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.527000	0.45615	2.148000	0.66965	0.533000	0.62120	CAG		0.453	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324		A	75448521	T	A	75448521	3	1	61	1	0	0	0	0	1	0	0	0	3288	1580	55	5	786	5	CFDP1	16	75448521	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	300494	75448521	14906232	9904	17889										
TMEM231	79583	broad.mit.edu	37	chr16	75574039	75574039	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacatactgcacccaggcGaactttaccatctcccagaa	6	15	1	2	rs149118721	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:75574039G>A	ENST00000258173.6	-	7	880	c.804C>T	c.(802-804)ttC>ttT	p.F268F	TMEM231_ENST00000568377.1_Silent_p.F297F|RP11-77K12.7_ENST00000460606.1_Intron|TMEM231_ENST00000565067.1_Silent_p.F220F|TMEM231_ENST00000569294.1_5'UTR|RP11-77K12.8_ENST00000564489.1_RNA	NM_001077418.1	NP_001070886.1	Q9H6L2	TM231_HUMAN	transmembrane protein 231	268					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.F297F(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						GCACCCAGGCGAACTTTACCA	0.448													G|||	6	0.00119808	0.0045	0	5008	,	,		22688	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16						G	,,	11,3859		0,11,1924	61	55	57		891,804,456	-5.9	1	16	dbSNP_134	57	1,8261		0,1,4130	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM231	NM_001077416.1,NM_001077418.1,NM_001077419.1	,,	0,12,6054	AA,AG,GG		0.0121,0.2842,0.0989	,,	297/346,268/317,152/201	75574039	12,12120	1935	4131	6066	74131540	SO:0001819	synonymous_variant	79583				CCDS45530.1	16q23.1	2014-01-28			ENSG00000205084	ENSG00000205084			37234	protein-coding gene	gene with protein product		614949				23012439	Standard	NM_001077416		Approved	FLJ22167, ALYE870, PRO1886, JBTS20, MKS11	uc002fek.4	Q9H6L2		ENST00000258173.6:c.804C>T	16.37:g.75574039G>A			74131540	A0JLU1|A6NDZ6|B3KU85|G5E9E3|Q6P450|Q6UWW5	Silent	SNP	ENST00000258173.6	37	CCDS45530.1																																																																																				0.448	TMEM231-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435481.2	NM_001077416		A	75574039	G	A	75574039	2	1	61	1	0	0	0	0	0	0	0	1	16188	1049	37	1		1	TMEM231	16	75574039	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125518	75574039	14780714	9905	17890										
CNTNAP4	85445	broad.mit.edu	37	chr16	76555988	76555988	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaatgggccttttgaaatCtcagtgcagtcacccaccca	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:76555988C>A	ENST00000476707.1	+	16	2737	c.2598C>A	c.(2596-2598)atC>atA	p.I866I	CNTNAP4_ENST00000377504.4_Silent_p.I814I|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Silent_p.I790I|CNTNAP4_ENST00000307431.8_Silent_p.I862I			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	863	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.I862I(1)|p.I790I(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						CTTTTGAAATCTCAGTGCAGT	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	16											191	186	187					16																	76555988		2007	4207	6214	75113489	SO:0001819	synonymous_variant	85445			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.2598C>A	16.37:g.76555988C>A			75113489	E9PFZ6|Q86YZ7	Silent	SNP	ENST00000476707.1	37																																																																																					0.468	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		A	76555988	C	A	76555988	2	1	61	1	0	0	0	0	0	0	0	1	3655	903	32	2		2	CNTNAP4	16	76555988	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	981949	76555988	13798765	9906	17891										
CNTNAP4	85445	broad.mit.edu	37	chr16	76556132	76556132	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgggcatgtcctgttacaGctcaacagtcagctcttcgt	10	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:76556132G>T	ENST00000476707.1	+	16	2881	c.2742G>T	c.(2740-2742)caG>caT	p.Q914H	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.Q862H|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.Q838H|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.Q910H			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	911	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.Q910H(1)|p.Q838H(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TCCTGTTACAGCTCAACAGTC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	16											65	67	66					16																	76556132		2003	4197	6200	75113633	SO:0001583	missense	85445			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.2742G>T	16.37:g.76556132G>T	ENSP00000417628:p.Gln914His		75113633	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	G	17.22	3.334220	0.60853	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.87	3.91	0.45181	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.39544	N	0.001326	T	0.58278	0.2111	.	.	.	0.46499	D	0.999071	P;P;D	0.89917	0.732;0.932;1.0	P;P;D	0.79108	0.856;0.695;0.992	T	0.58132	-0.7690	9	0.45353	T	0.12	.	8.2984	0.31999	0.2253:0.0:0.7747:0.0	.	838;914;911	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	H	910;862;838;914	ENSP00000306893:Q910H;ENSP00000439733:Q862H;ENSP00000418741:Q838H;ENSP00000417628:Q914H	ENSP00000306893:Q910H	Q	+	3	2	CNTNAP4	75113633	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	3.204000	0.51082	1.410000	0.46936	-0.136000	0.14681	CAG		0.448	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		T	76556132	G	T	76556132	3	4	61	1	0	0	0	0	1	0	0	0	3655	962	34	2	2812	2	CNTNAP4	16	76556132	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144	76556132	13798621	9907	17892										
NUDT7	283927	broad.mit.edu	37	chr16	77775652	77775652	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgttttattaatcatatCtttgagtacacaaaccctga	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:77775652C>A	ENST00000268533.5	+	4	591	c.522C>A	c.(520-522)atC>atA	p.I174I	NUDT7_ENST00000564031.1_3'UTR|NUDT7_ENST00000564085.1_3'UTR|NUDT7_ENST00000437314.3_Silent_p.I121I|RP11-264M12.2_ENST00000563690.1_RNA|NUDT7_ENST00000563839.1_3'UTR	NM_001105663.2	NP_001099133.1	P0C024	NUDT7_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 7	174					acetyl-CoA catabolic process (GO:0046356)|brown fat cell differentiation (GO:0050873)|coenzyme A catabolic process (GO:0015938)|nucleoside diphosphate metabolic process (GO:0009132)	peroxisome (GO:0005777)	acetyl-CoA hydrolase activity (GO:0003986)|hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides (GO:0016818)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|receptor binding (GO:0005102)|snoRNA binding (GO:0030515)	p.I174I(1)		breast(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|skin(1)	18						TTAATCATATCTTTGAGTACA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	16											102	95	97					16																	77775652		1930	4144	6074	76333153	SO:0001819	synonymous_variant	283927			AA227330	CCDS42195.1, CCDS58480.1, CCDS58479.1, CCDS73916.1	16q23.1	2007-06-15				ENSG00000140876		"Nudix motif containing"	8054	protein-coding gene	gene with protein product		609231				11415433	Standard	NM_001105663		Approved		uc010chd.3	P0C024		ENST00000268533.5:c.522C>A	16.37:g.77775652C>A			76333153	B4DLE5|H3BUB8	Silent	SNP	ENST00000268533.5	37	CCDS42195.1																																																																																				0.443	NUDT7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433873.1			A	77775652	C	A	77775652	2	1	61	1	0	0	0	0	0	0	0	1	10775	903	32	2		2	NUDT7	16	77775652	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1219520	77775652	12579101	9908	17893										
VAT1L	57687	broad.mit.edu	37	chr16	77859262	77859262	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctccgaggctgctgcattCcccatgaacttcgtcacagc	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:77859262C>T	ENST00000302536.2	+	3	636	c.483C>T	c.(481-483)ttC>ttT	p.F161F		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	161							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.F161F(2)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						CTGCTGCATTCCCCATGAACT	0.537																																																2	Substitution - coding silent(2)	urinary_tract(1)|large_intestine(1)	16											124	98	107					16																	77859262		2198	4300	6498	76416763	SO:0001819	synonymous_variant	57687			AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.483C>T	16.37:g.77859262C>T			76416763	Q8IYW8	Silent	SNP	ENST00000302536.2	37	CCDS32492.1																																																																																				0.537	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		T	77859262	C	T	77859262	2	4	61	1	0	0	0	0	0	0	0	1	17170	854	30	3		3	VAT1L	16	77859262	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83610	77859262	12495491	9909	17894										
VAT1L	57687	broad.mit.edu	37	chr16	78005801	78005801	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacattggcaagttaattCtggatgtagaaaagacccca	10	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:78005801C>A	ENST00000302536.2	+	8	1285	c.1132C>A	c.(1132-1134)Ctg>Atg	p.L378M		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	378							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.L378M(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						CAAGTTAATTCTGGATGTAGA	0.522											OREG0023950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	16											205	211	209					16																	78005801		2198	4300	6498	76563302	SO:0001583	missense	57687			AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.1132C>A	16.37:g.78005801C>A	ENSP00000303129:p.Leu378Met	1180	76563302	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	37	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488056	0.84854	.	.	ENSG00000171724	ENST00000302536	T	0.12984	2.63	5.44	4.47	0.54385	.	0.131843	0.52532	D	0.000064	T	0.42223	0.1193	M	0.86864	2.845	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.45011	-0.9290	10	0.66056	D	0.02	-0.4033	14.9144	0.70785	0.0:0.9263:0.0:0.0737	.	378	Q9HCJ6	VAT1L_HUMAN	M	378	ENSP00000303129:L378M	ENSP00000303129:L378M	L	+	1	2	VAT1L	76563302	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.557000	0.67313	2.724000	0.93272	0.462000	0.41574	CTG		0.522	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		A	78005801	C	A	78005801	3	1	61	1	0	0	0	0	1	0	0	0	17170	912	32	2	1162	2	VAT1L	16	78005801	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146539	78005801	12348952	9910	17895										
WWOX	51741	broad.mit.edu	37	chr16	78312539	78312539	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccagaaaagtgcagaataAaaattttccactagcaaaag	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:78312539A>C	ENST00000566780.1	+	6	882				WWOX_ENST00000355860.3_Missense_Mutation_p.K186Q|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000408984.3_Intron|WWOX_ENST00000539474.2_Intron|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase						cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)	p.K186Q(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		GTGCAGAATAAAAATTTTCCA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	16											33	30	31					16																	78312539		1805	4061	5866	76870040	SO:0001627	intron_variant	51741			AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	12799	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 41C, member 1"	605131	"WW domain-containing oxidoreductase"			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.517-108218A>C	16.37:g.78312539A>C			76870040	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.160354	0.57368	.	.	ENSG00000186153	ENST00000355860	T	0.80909	-1.43	5.02	5.02	0.67125	.	.	.	.	.	T	0.75817	0.3901	.	.	.	0.46774	D	0.999193	B	0.19445	0.036	B	0.25291	0.059	T	0.74659	-0.3591	8	0.87932	D	0	.	11.7033	0.51583	1.0:0.0:0.0:0.0	.	186	Q9NZC7-3	.	Q	186	ENSP00000348119:K186Q	ENSP00000348119:K186Q	K	+	1	0	WWOX	76870040	0.027000	0.19231	0.007000	0.13788	0.088000	0.18126	1.677000	0.37576	2.193000	0.70182	0.533000	0.62120	AAA		0.318	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			C	78312539	A	C	78312539	1	2	61	0	1	0	0	0	0	0	0	0	17454	15	1	4		4	WWOX	16	78312539	Intron	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	306738	78312539	12042214	9911	17896										
DYNLRB2	83657	broad.mit.edu	37	chr16	80577224	80577224	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtcataaaggggttattGgaactatggttgtaaatgca	12	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:80577224G>T	ENST00000305904.6	+	2	175	c.55G>T	c.(55-57)Gga>Tga	p.G19*	RP11-525K10.3_ENST00000568776.1_RNA|DYNLRB2_ENST00000568035.1_Nonsense_Mutation_p.G19*|RP11-525K10.3_ENST00000565050.1_RNA|DYNLRB2_ENST00000562982.1_Nonsense_Mutation_p.G48*|RP11-525K10.3_ENST00000568819.1_RNA|RP11-525K10.3_ENST00000563267.1_RNA|RP11-525K10.3_ENST00000568552.1_RNA|RP11-525K10.3_ENST00000564411.1_RNA	NM_130897.1	NP_570967.1	Q8TF09	DLRB2_HUMAN	dynein, light chain, roadblock-type 2	19					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	cytoplasmic dynein complex (GO:0005868)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.G19*(1)		large_intestine(1)|lung(4)|prostate(1)	6						AGGGGTTATTGGAACTATGGT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											146	143	144					16																	80577224		2203	4300	6503	79134725	SO:0001587	stop_gained	83657			AF125108	CCDS10929.1	16q23.3	2008-02-05	2005-11-25	2005-11-25	ENSG00000168589	ENSG00000168589		"Cytoplasmic dyneins"	15467	protein-coding gene	gene with protein product	"roadblock domain containing 2"	607168	"dynein, cytoplasmic, light polypeptide 2B"	DNCL2B		11750132, 16260502	Standard	NM_130897		Approved	DNLC2B, ROBLD2	uc002ffo.3	Q8TF09	OTTHUMG00000137622	ENST00000305904.6:c.55G>T	16.37:g.80577224G>T	ENSP00000302936:p.Gly19*		79134725		Nonsense_Mutation	SNP	ENST00000305904.6	37	CCDS10929.1	.	.	.	.	.	.	.	.	.	.	G	37	6.371925	0.97515	.	.	ENSG00000168589	ENST00000305904;ENST00000338542	.	.	.	5.85	5.85	0.93711	.	0.064446	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-3.4154	18.7169	0.91679	0.0:0.0:1.0:0.0	.	.	.	.	X	19	.	ENSP00000302936:G19X	G	+	1	0	DYNLRB2	79134725	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.321000	0.96353	2.767000	0.95098	0.655000	0.94253	GGA		0.438	DYNLRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269043.1	NM_130897		T	80577224	G	T	80577224	4	4	61	1	0	0	0	0	0	1	0	0	4862	1349	47	2	61	2	DYNLRB2	16	80577224	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2264685	80577224	9777529	9912	17897										
CDYL2	124359	broad.mit.edu	37	chr16	80718994	80718994	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatactcccattttcctttCttgttcttcctcttgtctac	3	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:80718994C>A	ENST00000570137.2	-	2	212	c.57G>T	c.(55-57)aaG>aaT	p.K19N	CDYL2_ENST00000562812.1_Missense_Mutation_p.K19N|CDYL2_ENST00000563890.1_Missense_Mutation_p.K19N|CDYL2_ENST00000566173.1_Missense_Mutation_p.K19N|CDYL2_ENST00000562753.1_5'UTR	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	19	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.					nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.K19N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						ATTTTCCTTTCTTGTTCTTCC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	16											127	109	115					16																	80718994		2203	4299	6502	79276495	SO:0001583	missense	124359			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"chromodomain Y-like protein 2"			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.57G>T	16.37:g.80718994C>A	ENSP00000476295:p.Lys19Asn		79276495	Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359127	0.82353	.	.	ENSG00000166446	ENST00000299564	T	0.76316	-1.01	5.08	5.08	0.68730	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.159946	0.56097	N	0.000036	T	0.82254	0.4997	L	0.52011	1.625	0.49915	D	0.999833	D	0.54397	0.966	P	0.62089	0.898	T	0.83275	-0.0041	10	0.87932	D	0	.	11.1187	0.48275	0.0:0.9168:0.0:0.0832	.	19	Q8N8U2	CDYL2_HUMAN	N	19	ENSP00000299564:K19N	ENSP00000299564:K19N	K	-	3	2	CDYL2	79276495	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.406000	0.34646	2.636000	0.89361	0.655000	0.94253	AAG		0.488	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		A	80718994	C	A	80718994	3	1	61	1	0	0	0	0	1	0	0	0	3192	912	32	2	1487	2	CDYL2	16	80718994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	141770	80718994	9635759	9913	17898										
CENPN	55839	broad.mit.edu	37	chr16	81053751	81053751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaatgcagtctggattcGaattgcctggggaacacagt	14	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81053751G>A	ENST00000305850.5	+	6	1191	c.401G>A	c.(400-402)cGa>cAa	p.R134Q	CENPN_ENST00000299572.5_Missense_Mutation_p.R134Q|CENPN_ENST00000439957.3_Missense_Mutation_p.R114Q|CENPN_ENST00000569461.1_3'UTR|CENPN_ENST00000428963.2_Missense_Mutation_p.R134Q|CMC2_ENST00000565914.1_Intron|CENPN_ENST00000393335.3_Missense_Mutation_p.R134Q|RP11-303E16.3_ENST00000562315.1_RNA	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N	134					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R114Q(1)|p.R134Q(1)		breast(1)|large_intestine(5)|lung(4)	10						GTCTGGATTCGAATTGCCTGG	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	16											129	100	110					16																	81053751		2202	4300	6502	79611252	SO:0001583	missense	55839			AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"chromosome 16 open reading frame 60"	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.401G>A	16.37:g.81053751G>A	ENSP00000305608:p.Arg134Gln		79611252	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000305850.5	37	CCDS42200.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.636819	0.87760	.	.	ENSG00000166451	ENST00000305850;ENST00000299572;ENST00000439957;ENST00000393335;ENST00000428963	T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.88164	0.6363	M	0.75264	2.295	0.54753	D	0.999981	D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.997	P;P;P;P;P	0.57720	0.812;0.826;0.826;0.826;0.733	D	0.87992	0.2750	10	0.51188	T	0.08	-12.6125	19.7192	0.96135	0.0:0.0:1.0:0.0	.	114;134;134;134;134	E7ETS3;E7ES30;A8MZE6;Q96H22;Q96H22-2	.;.;.;CENPN_HUMAN;.	Q	134;134;114;134;134	ENSP00000305608:R134Q;ENSP00000299572:R134Q;ENSP00000395235:R114Q;ENSP00000377007:R134Q;ENSP00000393991:R134Q	ENSP00000299572:R134Q	R	+	2	0	CENPN	79611252	1.000000	0.71417	0.995000	0.50966	0.338000	0.28826	6.671000	0.74472	2.656000	0.90262	0.655000	0.94253	CGA		0.433	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269051.1	NM_018455		A	81053751	G	A	81053751	3	1	61	1	0	0	0	0	1	0	0	0	3244	1058	37	1	419	1	CENPN	16	81053751	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334757	81053751	9301002	9914	17899										
ATMIN	23300	broad.mit.edu	37	chr16	81077783	81077783	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttaaatcaagatattgaGaaatctgcaccaattataaa	4	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81077783G>T	ENST00000299575.4	+	4	1704	c.1680G>T	c.(1678-1680)gaG>gaT	p.E560D	ATMIN_ENST00000566488.1_Missense_Mutation_p.E404D|ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000564241.1_Missense_Mutation_p.E404D	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	560					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)	p.E560D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						AAGATATTGAGAAATCTGCAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	16											42	42	42					16																	81077783		2202	4299	6501	79635284	SO:0001583	missense	23300			BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.1680G>T	16.37:g.81077783G>T	ENSP00000299575:p.Glu560Asp		79635284	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	37	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	G	9.397	1.076899	0.20227	.	.	ENSG00000166454	ENST00000299575;ENST00000539819	T	0.31247	1.5	6.17	1.57	0.23409	.	0.251483	0.34932	N	0.003572	T	0.20251	0.0487	L	0.46741	1.465	0.30281	N	0.791287	B	0.17852	0.024	B	0.10450	0.005	T	0.20806	-1.0264	10	0.12766	T	0.61	-17.1769	6.0699	0.19883	0.3166:0.0:0.5556:0.1279	.	560	O43313	ATMIN_HUMAN	D	560;331	ENSP00000299575:E560D	ENSP00000299575:E560D	E	+	3	2	ATMIN	79635284	0.893000	0.30496	0.988000	0.46212	0.838000	0.47535	-0.083000	0.11286	0.480000	0.27534	0.655000	0.94253	GAG		0.338	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		T	81077783	G	T	81077783	3	4	61	1	0	0	0	0	1	0	0	0	1111	933	33	2	1694	2	ATMIN	16	81077783	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24032	81077783	9276970	9915	17900										
ATMIN	23300	broad.mit.edu	37	chr16	81078236	81078236	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacagacttaaactttttCttagacagtagccctcatct	5	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81078236C>A	ENST00000299575.4	+	4	2157	c.2133C>A	c.(2131-2133)ttC>ttA	p.F711L	ATMIN_ENST00000566488.1_Missense_Mutation_p.F555L|ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000564241.1_Missense_Mutation_p.F555L	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	711					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)	p.F711L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						TAAACTTTTTCTTAGACAGTA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	16											125	131	129					16																	81078236		2202	4300	6502	79635737	SO:0001583	missense	23300			BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.2133C>A	16.37:g.81078236C>A	ENSP00000299575:p.Phe711Leu		79635737	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	37	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851654	0.32699	.	.	ENSG00000166454	ENST00000299575;ENST00000539819	T	0.28255	1.62	6.02	-3.0	0.05480	.	0.051357	0.85682	D	0.000000	T	0.25901	0.0631	L	0.58101	1.795	0.41837	D	0.990104	B	0.27765	0.188	B	0.24974	0.057	T	0.10894	-1.0610	10	0.32370	T	0.25	-13.6138	13.9083	0.63850	0.0:0.5654:0.0:0.4346	.	711	O43313	ATMIN_HUMAN	L	711;482	ENSP00000299575:F711L	ENSP00000299575:F711L	F	+	3	2	ATMIN	79635737	0.053000	0.20554	0.948000	0.38648	0.977000	0.68977	-0.866000	0.04245	-0.401000	0.07644	-0.345000	0.07892	TTC		0.453	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		A	81078236	C	A	81078236	3	1	61	1	0	0	0	0	1	0	0	0	1111	912	32	2	2147	2	ATMIN	16	81078236	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	453	81078236	9276517	9916	17901										
ATMIN	23300	broad.mit.edu	37	chr16	81078453	81078453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgttcttcaccagcaacGaaactcagacagcaatggat	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81078453G>A	ENST00000299575.4	+	4	2374	c.2350G>A	c.(2350-2352)Gaa>Aaa	p.E784K	ATMIN_ENST00000566488.1_Missense_Mutation_p.E628K|ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000564241.1_Missense_Mutation_p.E628K	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	784					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)	p.E784K(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						CACCAGCAACGAAACTCAGAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											79	78	78					16																	81078453		2202	4300	6502	79635954	SO:0001583	missense	23300			BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.2350G>A	16.37:g.81078453G>A	ENSP00000299575:p.Glu784Lys		79635954	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	37	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	G	35	5.450742	0.96205	.	.	ENSG00000166454	ENST00000299575;ENST00000539819	T	0.42513	0.97	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.68458	0.3003	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70769	-0.4782	10	0.87932	D	0	-25.4572	19.9598	0.97242	0.0:0.0:1.0:0.0	.	784	O43313	ATMIN_HUMAN	K	784;555	ENSP00000299575:E784K	ENSP00000299575:E784K	E	+	1	0	ATMIN	79635954	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.742000	0.98846	2.716000	0.92895	0.655000	0.94253	GAA		0.478	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		A	81078453	G	A	81078453	3	1	61	1	0	0	0	0	1	0	0	0	1111	1059	37	1	2364	1	ATMIN	16	81078453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	217	81078453	9276300	9917	17902										
PKD1L2	114780	broad.mit.edu	37	chr16	81180945	81180945	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgagtgttacagggtcctCtctctttttggcttcctccc	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81180945C>A	ENST00000525539.1	-	0	5145				PKD1L2_ENST00000533478.1_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.E1716*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ACAGGGTCCTCTCTCTTTTTG	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											175	179	178					16																	81180945		1926	4121	6047	79738446			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81180945C>A			79738446	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000525539.1	37																																																																																					0.507	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			A	81180945	C	A	81180945	1	1	61	0	1	0	0	0	0	0	0	0	11996	922	32	2		2	PKD1L2	16	81180945	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102492	81180945	9173808	9918	17903										
PKD1L2	114780	broad.mit.edu	37	chr16	81209291	81209291	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcagcacaaagtcattgttCtcctctccaagtggcagata	8	11	4	1	rs377130552		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81209291C>A	ENST00000527937.1	-	0	383				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.E834D(2)|p.E149D(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGTCATTGTTCTCCTCTCCAA	0.552																																																3	Substitution - Missense(3)	large_intestine(3)	16											108	108	108					16																	81209291		2058	4204	6262	79766792			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81209291C>A			79766792	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.65|15.65	2.895423|2.895423	0.52121|0.52121	.|.	.|.	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.28454|.	1.61;1.61;1.61|.	4.82|4.82	-0.0387|-0.0387	0.13878|0.13878	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);|.	0.353856|0.353856	0.28583|0.28583	N|N	0.014833|0.014833	T|.	0.15955|.	0.0384|.	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999991|0.999991	B;P;P|.	0.50272|.	0.053;0.933;0.912|.	B;P;P|.	0.48982|.	0.046;0.597;0.596|.	T|.	0.22556|.	-1.0213|.	9|.	0.54805|0.12766	T|T	0.06|0.61	-3.7447|-3.7447	4.4919|4.4919	0.11817|0.11817	0.0:0.3961:0.1894:0.4145|0.0:0.3961:0.1894:0.4145	.|.	90;834;834|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	D|X	149;834;90|362	ENSP00000436309:E149D;ENSP00000337397:E834D;ENSP00000432818:E90D|.	ENSP00000337397:E834D|ENSP00000436389:E362X	E|E	-|-	3|1	2|0	PKD1L2|PKD1L2	79766792|79766792	0.998000|0.998000	0.40836|0.40836	0.840000|0.840000	0.33206|0.33206	0.772000|0.772000	0.43724|0.43724	0.919000|0.919000	0.28692|0.28692	-0.058000|-0.058000	0.13177|0.13177	-0.391000|-0.391000	0.06502|0.06502	GAG|GAA		0.552	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			A	81209291	C	A	81209291	1	1	61	0	1	0	0	0	0	0	0	0	11996	912	32	2		2	PKD1L2	16	81209291	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28346	81209291	9145462	9919	17904										
PKD1L2	114780	broad.mit.edu	37	chr16	81211489	81211489	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatggcaaagctcgtcagaAcggtgccctcctctggggca	13	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81211489A>G	ENST00000527937.1	-	0	319				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.V787A(2)|p.V102A(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCTCGTCAGAACGGTGCCCTC	0.597																																																3	Substitution - Missense(3)	large_intestine(3)	16											82	84	84					16																	81211489		2046	4189	6235	79768990			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81211489A>G			79768990	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		.	.	.	.	.	.	.	.	.	.	A	10.51	1.369740	0.24771	.	.	ENSG00000166473	ENST00000531391;ENST00000337114	T;T	0.68331	-0.32;-0.32	4.89	4.89	0.63831	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.518619	0.18782	N	0.131303	T	0.54549	0.1865	.	.	.	0.09310	N	1	P;B	0.41524	0.753;0.254	B;B	0.37091	0.241;0.146	T	0.50065	-0.8871	9	0.35671	T	0.21	-3.4902	12.1197	0.53885	1.0:0.0:0.0:0.0	.	787;787	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	102;787	ENSP00000436309:V102A;ENSP00000337397:V787A	ENSP00000337397:V787A	V	-	2	0	PKD1L2	79768990	0.083000	0.21467	0.042000	0.18584	0.052000	0.14988	4.659000	0.61504	1.858000	0.53909	0.449000	0.29647	GTT		0.597	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			G	81211489	A	G	81211489	1	3	61	0	1	0	0	0	0	0	0	0	11996	43	2	4		4	PKD1L2	16	81211489	RNA	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2198	81211489	9143264	9920	17905										
PKD1L2	114780	broad.mit.edu	37	chr16	81222591	81222591	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggatgtacacctccatatCgcctttatctttctgcaaaa	5	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81222591C>T	ENST00000525539.1	-	0	1683				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.D562N(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ACCTCCATATCGCCTTTATCT	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	16											135	132	133					16																	81222591		1977	4161	6138	79780092			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81222591C>T			79780092	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.423|6.423	0.446249|0.446249	0.12164|0.12164	.|.	.|.	ENSG00000166473|ENSG00000166473	ENST00000337114|ENST00000526632	T|.	0.01252|.	5.1|.	4.97|4.97	-9.95|-9.95	0.00446|0.00446	Egg jelly receptor, REJ-like (1);|.	2.070470|.	0.02116|.	N|.	0.055189|.	T|T	0.15176|0.15176	0.0366|0.0366	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	P;B|.	0.40250|.	0.709;0.005|.	B;B|.	0.30251|.	0.113;0.002|.	T|T	0.13019|0.13019	-1.0525|-1.0525	9|4	0.44086|.	T|.	0.13|.	0.8558|0.8558	2.6334|2.6334	0.04951|0.04951	0.1934:0.1039:0.1937:0.509|0.1934:0.1039:0.1937:0.509	.|.	562;562|.	Q7Z442-3;Q7Z442|.	.;PK1L2_HUMAN|.	N|Q	562|89	ENSP00000337397:D562N|.	ENSP00000337397:D562N|.	D|R	-|-	1|2	0|0	PKD1L2|PKD1L2	79780092|79780092	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.399000|-1.399000	0.02506|0.02506	-2.129000|-2.129000	0.00817|0.00817	-1.527000|-1.527000	0.00925|0.00925	GAT|CGA		0.512	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81222591	C	T	81222591	1	4	61	0	1	0	0	0	0	0	0	0	11996	884	31	1		1	PKD1L2	16	81222591	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11102	81222591	9132162	9921	17906										
PKD1L2	114780	broad.mit.edu	37	chr16	81232498	81232498	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactgtaatgtttctggagaTtgtagaggtggtggtgttgc	16	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81232498T>G	ENST00000525539.1	-	0	1311				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.I438L(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TTTCTGGAGATTGTAGAGGTG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	16											187	189	188					16																	81232498		1978	4140	6118	79789999			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232498T>G			79789999	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		.	.	.	.	.	.	.	.	.	.	T	0.264	-0.997761	0.02145	.	.	ENSG00000166473	ENST00000337114	T	0.01209	5.17	4.98	1.76	0.24704	Egg jelly receptor, REJ-like (1);	1.471950	0.03845	N	0.271320	T	0.00815	0.0027	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46091	-0.9216	9	0.11794	T	0.64	-0.3769	4.4296	0.11520	0.0776:0.1142:0.44:0.3682	.	438;438	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	L	438	ENSP00000337397:I438L	ENSP00000337397:I438L	I	-	1	0	PKD1L2	79789999	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.259000	0.18405	0.523000	0.28482	-0.264000	0.10439	ATC		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			G	81232498	T	G	81232498	1	3	61	0	1	0	0	0	0	0	0	0	11996	1493	52	4		4	PKD1L2	16	81232498	RNA	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	9907	81232498	9122255	9922	17907										
GAN	8139	broad.mit.edu	37	chr16	81388123	81388123	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggctgcattgctgctgaGaactgtattggtatccgtga	13	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81388123G>A	ENST00000568107.2	+	3	558	c.396G>A	c.(394-396)gaG>gaA	p.E132E		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	132					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E132E(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				TTGCTGCTGAGAACTGTATTG	0.473																																					GBM(106;1239 1507 7582 9741 33976)											1	Substitution - coding silent(1)	large_intestine(1)	16											231	208	216					16																	81388123		2202	4300	6502	79945624	SO:0001819	synonymous_variant	8139			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.396G>A	16.37:g.81388123G>A			79945624		Silent	SNP	ENST00000568107.2	37	CCDS10935.1																																																																																				0.473	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			A	81388123	G	A	81388123	2	1	61	1	0	0	0	0	0	0	0	1	6252	933	33	3		3	GAN	16	81388123	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155625	81388123	8966630	9923	17908										
GAN	8139	broad.mit.edu	37	chr16	81388328	81388328	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtctttgaagcagtaattCgatggatagcacatgataca	9	6	1	2	rs119485090		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81388328C>T	ENST00000568107.2	+	3	763	c.601C>T	c.(601-603)Cga>Tga	p.R201*		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	201	BACK.				cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R201*(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				AGCAGTAATTCGATGGATAGC	0.313																																					GBM(106;1239 1507 7582 9741 33976)											1	Substitution - Nonsense(1)	large_intestine(1)	16	GRCh37	CM020938	GAN	M	rs119485090						63	62	62					16																	81388328		2202	4300	6502	79945829	SO:0001587	stop_gained	8139			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.601C>T	16.37:g.81388328C>T	ENSP00000476795:p.Arg201*		79945829		Nonsense_Mutation	SNP	ENST00000568107.2	37	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	C	39	7.290336	0.98189	.	.	ENSG00000127688	ENST00000248272	.	.	.	5.8	5.8	0.92144	.	0.054743	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	15.7284	0.77780	0.1447:0.8552:0.0:0.0	.	.	.	.	X	201	.	ENSP00000248272:R201X	R	+	1	2	GAN	79945829	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	3.643000	0.54374	2.751000	0.94390	0.650000	0.86243	CGA		0.313	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81388328	C	T	81388328	4	4	61	1	0	0	0	0	0	1	0	0	6252	876	31	1	611	1	GAN	16	81388328	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205	81388328	8966425	9924	17909										
GAN	8139	broad.mit.edu	37	chr16	81391484	81391484	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaacaggcagctttggatCgaactggcccctttaagcat	9	12	0	0	rs368910322		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81391484C>T	ENST00000568107.2	+	5	1083	c.921C>T	c.(919-921)atC>atT	p.I307I		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	307					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.I307I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				AGCTTTGGATCGAACTGGCCC	0.458																																					GBM(106;1239 1507 7582 9741 33976)											1	Substitution - coding silent(1)	large_intestine(1)	16											167	140	149					16																	81391484		2202	4300	6502	79948985	SO:0001819	synonymous_variant	8139			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.921C>T	16.37:g.81391484C>T			79948985		Silent	SNP	ENST00000568107.2	37	CCDS10935.1																																																																																				0.458	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81391484	C	T	81391484	2	4	61	1	0	0	0	0	0	0	0	1	6252	874	31	1		1	GAN	16	81391484	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3156	81391484	8963269	9925	17910										
CMIP	80790	broad.mit.edu	37	chr16	81735298	81735298	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggaatacaacatcatcGacaacaacgacacccaactg	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81735298G>A	ENST00000537098.3	+	16	1861	c.1789G>A	c.(1789-1791)Gac>Aac	p.D597N	CMIP_ENST00000398040.4_Missense_Mutation_p.D444N|CMIP_ENST00000539778.2_Missense_Mutation_p.D503N|CMIP_ENST00000566513.1_3'UTR	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	597						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.D502N(1)		endometrium(5)|kidney(1)|lung(7)	13						CAACATCATCGACAACAACGA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	16											218	228	225					16																	81735298		2166	4269	6435	80292799	SO:0001583	missense	80790			AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.1789G>A	16.37:g.81735298G>A	ENSP00000446100:p.Asp597Asn		80292799	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556632	0.45487	.	.	ENSG00000153815	ENST00000537098;ENST00000539778;ENST00000398040;ENST00000542097	T;T	0.08807	3.05;3.05	4.83	4.83	0.62350	.	0.052057	0.85682	D	0.000000	T	0.05318	0.0141	N	0.14661	0.345	0.51482	D	0.999928	P;P;B	0.46327	0.876;0.876;0.118	B;B;B	0.35859	0.117;0.212;0.015	T	0.50988	-0.8762	10	0.33141	T	0.24	.	16.1162	0.81306	0.0:0.0:1.0:0.0	.	444;503;597	Q8IY22-3;Q8IY22-2;Q8IY22	.;.;CMIP_HUMAN	N	597;503;503;410	ENSP00000446100:D597N;ENSP00000440401:D503N	ENSP00000381120:D503N	D	+	1	0	CMIP	80292799	1.000000	0.71417	0.999000	0.59377	0.249000	0.25844	9.821000	0.99360	2.233000	0.73108	0.313000	0.20887	GAC		0.577	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		A	81735298	G	A	81735298	3	1	61	1	0	0	0	0	1	0	0	0	3584	1058	37	1	1873	1	CMIP	16	81735298	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	343814	81735298	8619455	9926	17911										
PLCG2	5336	broad.mit.edu	37	chr16	81941355	81941355	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagtgatgacattgaacaGactatggaggaggaagtgcc	13	6	1	4	rs151013036	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81941355G>T	ENST00000359376.3	+	16	1747	c.1533G>T	c.(1531-1533)caG>caT	p.Q511H		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	511					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.Q511H(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ACATTGAACAGACTATGGAGG	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	16											61	61	61					16																	81941355		1970	4167	6137	80498856	SO:0001583	missense	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1533G>T	16.37:g.81941355G>T	ENSP00000352336:p.Gln511His		80498856	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039505	0.55003	.	.	ENSG00000197943	ENST00000359376	T	0.67523	-0.27	5.3	4.34	0.51931	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.188549	0.37955	N	0.001868	T	0.61763	0.2373	L	0.40543	1.245	0.58432	D	0.999998	B;D	0.62365	0.011;0.991	B;P	0.47744	0.014;0.556	T	0.62946	-0.6746	10	0.49607	T	0.09	.	10.873	0.46894	0.1507:0.0:0.8493:0.0	.	378;511	B4E3H3;P16885	.;PLCG2_HUMAN	H	511	ENSP00000352336:Q511H	ENSP00000352336:Q511H	Q	+	3	2	PLCG2	80498856	0.999000	0.42202	0.914000	0.36105	0.658000	0.38924	2.379000	0.44318	1.248000	0.43934	0.655000	0.94253	CAG		0.572	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81941355	G	T	81941355	3	4	61	1	0	0	0	0	1	0	0	0	12067	933	33	2	1591	2	PLCG2	16	81941355	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	206057	81941355	8413398	9927	17912										
PLCG2	5336	broad.mit.edu	37	chr16	81942036	81942036	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaggatataccccctacaGaactacattttggggagaaa	8	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81942036G>T	ENST00000359376.3	+	17	1787	c.1573G>T	c.(1573-1575)Gaa>Taa	p.E525*		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	525					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.E525*(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ACCCCCTACAGAACTACATTT	0.537																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											58	58	58					16																	81942036		1908	4119	6027	80499537	SO:0001587	stop_gained	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1573G>T	16.37:g.81942036G>T	ENSP00000352336:p.Glu525*		80499537	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Nonsense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	40	7.998070	0.98602	.	.	ENSG00000197943	ENST00000359376	.	.	.	4.85	4.85	0.62838	.	0.265926	0.42294	D	0.000730	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.982	0.89144	0.0:0.0:1.0:0.0	.	.	.	.	X	525	.	ENSP00000352336:E525X	E	+	1	0	PLCG2	80499537	1.000000	0.71417	0.993000	0.49108	0.676000	0.39594	9.261000	0.95576	2.249000	0.74217	0.655000	0.94253	GAA		0.537	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81942036	G	T	81942036	4	4	61	1	0	0	0	0	0	1	0	0	12067	943	33	2	1635	2	PLCG2	16	81942036	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	681	81942036	8412717	9928	17913										
PLCG2	5336	broad.mit.edu	37	chr16	81969848	81969848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcagacagaagcccgtcGacctcctgaagtacaatcaa	7	13	3	3	rs568724894		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:81969848G>A	ENST00000359376.3	+	27	3131	c.2917G>A	c.(2917-2919)Gac>Aac	p.D973N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	973	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.D973N(4)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GAAGCCCGTCGACCTCCTGAA	0.527																																																4	Substitution - Missense(4)	large_intestine(4)	16											73	76	75					16																	81969848		1954	4151	6105	80527349	SO:0001583	missense	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.2917G>A	16.37:g.81969848G>A	ENSP00000352336:p.Asp973Asn		80527349	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228364	0.39399	.	.	ENSG00000197943	ENST00000359376	T	0.54279	0.58	4.79	4.79	0.61399	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.154254	0.56097	D	0.000024	T	0.44953	0.1318	L	0.35249	1.045	0.54753	D	0.999985	D	0.53885	0.963	B	0.43990	0.438	T	0.32025	-0.9922	10	0.15952	T	0.53	.	17.8393	0.88710	0.0:0.0:1.0:0.0	.	973	P16885	PLCG2_HUMAN	N	973	ENSP00000352336:D973N	ENSP00000352336:D973N	D	+	1	0	PLCG2	80527349	1.000000	0.71417	0.123000	0.21794	0.042000	0.13812	4.847000	0.62867	2.208000	0.71279	0.561000	0.74099	GAC		0.527	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			A	81969848	G	A	81969848	3	1	61	1	0	0	0	0	1	0	0	0	12067	1058	37	1	3019	1	PLCG2	16	81969848	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27812	81969848	8384905	9929	17914										
HSD17B2	3294	broad.mit.edu	37	chr16	82069065	82069065	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggacacagcatggatctgCctggctgtccccacagtact	10	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:82069065C>T	ENST00000199936.4	+	1	229	c.36C>T	c.(34-36)tgC>tgT	p.C12C		NM_002153.2	NP_002144.1	P37059	DHB2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 2	12					in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|response to retinoic acid (GO:0032526)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.C12C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	10						CATGGATCTGCCTGGCTGTCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	16											74	63	67					16																	82069065		2201	4300	6501	80626566	SO:0001819	synonymous_variant	3294				CCDS10936.1	16q24.1-q24.2	2011-09-14			ENSG00000086696	ENSG00000086696	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5211	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 2"	109685				7759109, 19027726	Standard	NM_002153		Approved	HSD17, SDR9C2	uc002fgv.3	P37059	OTTHUMG00000137631	ENST00000199936.4:c.36C>T	16.37:g.82069065C>T			80626566	B2R7T4	Silent	SNP	ENST00000199936.4	37	CCDS10936.1																																																																																				0.552	HSD17B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269057.2	NM_002153		T	82069065	C	T	82069065	2	4	61	1	0	0	0	0	0	0	0	1	7405	747	26	3		3	HSD17B2	16	82069065	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99217	82069065	8285688	9930	17915										
HSD17B2	3294	broad.mit.edu	37	chr16	82069255	82069255	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacttacttatctggccaaGaattgttacctgtggatcag	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:82069255G>T	ENST00000199936.4	+	1	419	c.226G>T	c.(226-228)Gaa>Taa	p.E76*		NM_002153.2	NP_002144.1	P37059	DHB2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 2	76					in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|response to retinoic acid (GO:0032526)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.E76*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	10						ATCTGGCCAAGAATTGTTACC	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											149	119	129					16																	82069255		2201	4300	6501	80626756	SO:0001587	stop_gained	3294				CCDS10936.1	16q24.1-q24.2	2011-09-14			ENSG00000086696	ENSG00000086696	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5211	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 2"	109685				7759109, 19027726	Standard	NM_002153		Approved	HSD17, SDR9C2	uc002fgv.3	P37059	OTTHUMG00000137631	ENST00000199936.4:c.226G>T	16.37:g.82069255G>T	ENSP00000199936:p.Glu76*		80626756	B2R7T4	Nonsense_Mutation	SNP	ENST00000199936.4	37	CCDS10936.1	.	.	.	.	.	.	.	.	.	.	G	37	6.569049	0.97671	.	.	ENSG00000086696	ENST00000199936	.	.	.	5.31	4.36	0.52297	.	4.645640	0.00610	N	0.000418	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	10.2035	0.43099	0.0926:0.0:0.9074:0.0	.	.	.	.	X	76	.	ENSP00000199936:E76X	E	+	1	0	HSD17B2	80626756	0.875000	0.30112	0.219000	0.23793	0.985000	0.73830	2.417000	0.44653	1.381000	0.46364	0.591000	0.81541	GAA		0.488	HSD17B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269057.2	NM_002153		T	82069255	G	T	82069255	4	4	61	1	0	0	0	0	0	1	0	0	7405	943	33	2	228	2	HSD17B2	16	82069255	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	190	82069255	8285498	9931	17916										
CDH13	1012	broad.mit.edu	37	chr16	83813768	83813768	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgaaatccacaaacaagCtgttcctgataaagtctgga	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:83813768C>A	ENST00000566620.1	+	12	2167	c.1877C>A	c.(1876-1878)gCt>gAt	p.A626D	CDH13_ENST00000428848.3_Missense_Mutation_p.A587D|CDH13_ENST00000268613.10_Missense_Mutation_p.A673D	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	626	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)	p.A626D(1)		large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CACAAACAAGCTGTTCCTGAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	16											38	35	36					16																	83813768		1856	4102	5958	82371269	SO:0001583	missense	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1877C>A	16.37:g.83813768C>A	ENSP00000454435:p.Ala626Asp		82371269	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025343	0.35701	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000539548;ENST00000540531	T	0.52526	0.66	5.52	4.55	0.56014	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.40909	0.1136	L	0.39514	1.22	0.80722	D	1	B;B;P	0.38677	0.249;0.004;0.642	B;B;B	0.35770	0.21;0.027;0.131	T	0.42413	-0.9453	9	0.72032	D	0.01	.	15.3096	0.74019	0.0:0.8596:0.1404:0.0	.	587;673;626	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	D	673;626;587;328;185;316	ENSP00000268613:A673D	ENSP00000268613:A673D	A	+	2	0	CDH13	82371269	0.068000	0.21057	0.130000	0.21974	0.536000	0.34869	2.635000	0.46537	1.269000	0.44280	0.655000	0.94253	GCT		0.393	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		A	83813768	C	A	83813768	3	1	61	1	0	0	0	0	1	0	0	0	3105	797	28	2	1923	2	CDH13	16	83813768	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1744513	83813768	6540985	9932	17917										
CDH13	1012	broad.mit.edu	37	chr16	83828630	83828630	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaccctctctattcaggtCtgtgagaactcctgacgtct	8	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:83828630C>A	ENST00000566620.1	+	14	2427	c.2137C>A	c.(2137-2139)Ctg>Atg	p.L713M	RP11-483P21.3_ENST00000567109.1_lincRNA|CDH13_ENST00000428848.3_Missense_Mutation_p.L674M|CDH13_ENST00000268613.10_Missense_Mutation_p.L760M|RP11-483P21.2_ENST00000567342.1_RNA|RP11-483P21.2_ENST00000565714.1_RNA	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	713					adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)	p.L713M(1)		large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CTATTCAGGTCTGTGAGAACT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	16											87	77	80					16																	83828630		1842	4092	5934	82386131	SO:0001583	missense	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.2137C>A	16.37:g.83828630C>A	ENSP00000454435:p.Leu713Met		82386131	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524311	0.44866	.	.	ENSG00000140945	ENST00000540531	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	T	0.67258	0.2874	L	0.27053	0.805	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.83275	0.994;0.996;0.994	T	0.69461	-0.5139	8	0.62326	D	0.03	.	18.885	0.92372	0.0:1.0:0.0:0.0	.	674;760;713	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	M	403	.	ENSP00000445918:L403M	L	+	1	2	CDH13	82386131	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.897000	0.63231	2.691000	0.91804	0.655000	0.94253	CTG		0.383	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		A	83828630	C	A	83828630	3	1	61	1	0	0	0	0	1	0	0	0	3105	912	32	2	2191	2	CDH13	16	83828630	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14862	83828630	6526123	9933	17918										
SLC38A8	146167	broad.mit.edu	37	chr16	84067037	84067037	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtctgcgtaccacggctgCggggcgggcggggtgccaga	20	11	1	1	rs201965163		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84067037C>T	ENST00000299709.3	-	3	425	c.426G>A	c.(424-426)ccG>ccA	p.P142P		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	142					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.P142P(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACCACGGCTGCGGGGCGGGCG	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	16											37	43	41					16																	84067037		2199	4299	6498	82624538	SO:0001819	synonymous_variant	146167				CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"Solute carriers"	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.426G>A	16.37:g.84067037C>T			82624538		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																				0.657	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		T	84067037	C	T	84067037	2	4	61	1	0	0	0	0	0	0	0	1	14647	755	27	1		1	SLC38A8	16	84067037	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	238407	84067037	6287716	9934	17919										
MBTPS1	8720	broad.mit.edu	37	chr16	84103570	84103570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagagaactctcttgcttCgcgggggagtaggaattatc	12	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84103570C>T	ENST00000343411.3	-	14	2351	c.1856G>A	c.(1855-1857)cGa>cAa	p.R619Q	MBTPS1_ENST00000569770.1_5'Flank	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	619					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.R619Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTCTTGCTTCGCGGGGGAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	16											145	152	150					16																	84103570		2200	4300	6500	82661071	SO:0001583	missense	8720			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1856G>A	16.37:g.84103570C>T	ENSP00000344223:p.Arg619Gln		82661071	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	C	36	5.817519	0.96982	.	.	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.23754	1.89	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.58380	0.2118	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.63528	-0.6617	10	0.87932	D	0	-19.9132	19.8383	0.96670	0.0:1.0:0.0:0.0	.	619	Q14703	MBTP1_HUMAN	Q	619;64	ENSP00000344223:R619Q	ENSP00000344223:R619Q	R	-	2	0	MBTPS1	82661071	1.000000	0.71417	0.965000	0.40720	0.889000	0.51656	7.818000	0.86416	2.683000	0.91414	0.650000	0.86243	CGA		0.423	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		T	84103570	C	T	84103570	3	4	61	1	0	0	0	0	1	0	0	0	9391	884	31	1	1342	1	MBTPS1	16	84103570	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36533	84103570	6251183	9935	17920										
MBTPS1	8720	broad.mit.edu	37	chr16	84132690	84132690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagggaacgaaagacttttCgttggggcgtgacccgtttg	15	7	0	3	rs148577579		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84132690C>T	ENST00000343411.3	-	3	884	c.389G>A	c.(388-390)cGa>cAa	p.R130Q		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	130					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.R130Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AAAGACTTTTCGTTGGGGCGT	0.413													C|||	1	0.000199681	0	0	5008	,	,		17865	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16						C	GLN/ARG	0,4400		0,0,2200	172	162	165		389	5.6	1	16	dbSNP_134	165	10,8590	8.4+/-32.0	0,10,4290	yes	missense	MBTPS1	NM_003791.2	43	0,10,6490	TT,TC,CC		0.1163,0.0,0.0769	possibly-damaging	130/1053	84132690	10,12990	2200	4300	6500	82690191	SO:0001583	missense	8720			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.389G>A	16.37:g.84132690C>T	ENSP00000344223:p.Arg130Gln		82690191	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	C	32	5.144017	0.94603	0.0	0.001163	ENSG00000140943	ENST00000343411	T	0.43294	0.95	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	M	0.66939	2.045	0.80722	D	1	D	0.56035	0.974	B	0.38428	0.273	T	0.54529	-0.8280	10	0.62326	D	0.03	-29.8791	19.6277	0.95684	0.0:1.0:0.0:0.0	.	130	Q14703	MBTP1_HUMAN	Q	130	ENSP00000344223:R130Q	ENSP00000344223:R130Q	R	-	2	0	MBTPS1	82690191	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	5.668000	0.68074	2.648000	0.89879	0.650000	0.86243	CGA		0.413	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		T	84132690	C	T	84132690	3	4	61	1	0	0	0	0	1	0	0	0	9391	884	31	1	2853	1	MBTPS1	16	84132690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29120	84132690	6222063	9936	17921										
MBTPS1	8720	broad.mit.edu	37	chr16	84135308	84135308	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggccttttcaaaagatttCttttccagtctgtcgcccag	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84135308C>A	ENST00000343411.3	-	2	576	c.81G>T	c.(79-81)aaG>aaT	p.K27N		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	27					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.K27N(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CAAAAGATTTCTTTTCCAGTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	16											110	108	109					16																	84135308		2200	4300	6500	82692809	SO:0001583	missense	8720			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.81G>T	16.37:g.84135308C>A	ENSP00000344223:p.Lys27Asn		82692809	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512218	0.27036	.	.	ENSG00000140943	ENST00000343411	T	0.30448	1.53	6.17	2.78	0.32641	.	0.342284	0.33057	N	0.005328	T	0.11495	0.0280	N	0.03608	-0.345	0.21386	N	0.999702	B	0.02656	0.0	B	0.01281	0.0	T	0.27331	-1.0077	10	0.14656	T	0.56	-13.7457	8.7011	0.34327	0.4887:0.331:0.1803:0.0	.	27	Q14703	MBTP1_HUMAN	N	27	ENSP00000344223:K27N	ENSP00000344223:K27N	K	-	3	2	MBTPS1	82692809	0.894000	0.30519	0.940000	0.37924	0.997000	0.91878	1.094000	0.30951	1.575000	0.49775	0.655000	0.94253	AAG		0.453	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		A	84135308	C	A	84135308	3	1	61	1	0	0	0	0	1	0	0	0	9391	912	32	2	3165	2	MBTPS1	16	84135308	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2618	84135308	6219445	9937	17922										
WFDC1	58189	broad.mit.edu	37	chr16	84358040	84358040	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagatgggcgaatcctacGacacaaactttacaaagaat	7	10	0	2	rs370380475		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84358040G>A	ENST00000219454.5	+	5	904	c.578G>A	c.(577-579)cGa>cAa	p.R193Q	WFDC1_ENST00000568638.1_Missense_Mutation_p.R193Q	NM_001282466.1|NM_001282467.1	NP_001269395.1|NP_001269396.1	Q9HC57	WFDC1_HUMAN	WAP four-disulfide core domain 1	193					negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|response to drug (GO:0042493)|response to estradiol (GO:0032355)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R193Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)	9						CGAATCCTACGACACAAACTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	16											105	103	104					16																	84358040		2200	4300	6500	82915541	SO:0001583	missense	58189			AF302109	CCDS10946.1	16q24.1	2013-01-21			ENSG00000103175	ENSG00000103175		"WAP four-disulfide core domain containing"	15466	protein-coding gene	gene with protein product		605322				10967136	Standard	NM_021197		Approved	PS20	uc002fhw.3	Q9HC57	OTTHUMG00000137641	ENST00000219454.5:c.578G>A	16.37:g.84358040G>A	ENSP00000219454:p.Arg193Gln		82915541	D3DUL7|Q8NC27|Q9HAU1	Missense_Mutation	SNP	ENST00000219454.5	37	CCDS10946.1	.	.	.	.	.	.	.	.	.	.	G	10.64	1.405679	0.25378	.	.	ENSG00000103175	ENST00000219454	T	0.37752	1.18	4.55	3.59	0.41128	.	0.125962	0.50627	N	0.000102	T	0.26085	0.0636	L	0.34521	1.04	0.53005	D	0.999962	B	0.28470	0.213	B	0.15052	0.012	T	0.11717	-1.0576	10	0.72032	D	0.01	-2.5874	11.638	0.51215	0.0877:0.0:0.9123:0.0	.	193	Q9HC57	WFDC1_HUMAN	Q	193	ENSP00000219454:R193Q	ENSP00000219454:R193Q	R	+	2	0	WFDC1	82915541	0.264000	0.24093	0.018000	0.16275	0.018000	0.09664	1.376000	0.34306	1.266000	0.44231	0.650000	0.86243	CGA		0.358	WFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269083.2			A	84358040	G	A	84358040	3	1	61	1	0	0	0	0	1	0	0	0	17386	1058	37	1	596	1	WFDC1	16	84358040	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	222732	84358040	5996713	9938	17923										
KIAA1609	57707	broad.mit.edu	37	chr16	84531579	84531579	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatttggatgagacattCgggctgtttttatctgatga	12	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84531579C>T	ENST00000343629.6	-	2	296	c.114G>A	c.(112-114)ccG>ccA	p.P38P	TLDC1_ENST00000535580.1_5'UTR|RP11-517C16.4_ENST00000568771.1_RNA|TLDC1_ENST00000561807.1_5'UTR	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	38						lysosomal membrane (GO:0005765)		p.P38P(1)									ATGAGACATTCGGGCTGTTTT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	16											173	167	169					16																	84531579		2199	4300	6499	83089080	SO:0001819	synonymous_variant	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.114G>A	16.37:g.84531579C>T			83089080	Q8IZ64|Q9HCG3|Q9NTE8	Silent	SNP	ENST00000343629.6	37	CCDS32498.1																																																																																				0.478	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		T	84531579	C	T	84531579	2	4	61	1	0	0	0	0	0	0	0	1	8268	871	31	1		1	KIAA1609	16	84531579	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173539	84531579	5823174	9939	17924										
COTL1	23406	broad.mit.edu	37	chr16	84600556	84600556	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatcacaaactccttagcGaaattctgcaagaacaaagg	7	10	2	2	rs577103781		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84600556G>A	ENST00000262428.4	-	4	486	c.324C>T	c.(322-324)ttC>ttT	p.F108F	COTL1_ENST00000564057.1_Silent_p.F39F|COTL1_ENST00000567278.1_5'UTR	NM_021149.2	NP_066972.1	Q14019	COTL1_HUMAN	coactosin-like F-actin binding protein 1	108	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				defense response to fungus (GO:0050832)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)	p.F108F(1)		endometrium(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	6						ACTCCTTAGCGAAATTCTGCA	0.512													G|||	1	0.000199681	8e-04	0	5008	,	,		19671	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											80	79	79					16																	84600556		2199	4300	6499	83158057	SO:0001819	synonymous_variant	23406			L54057	CCDS10947.1	16q24.1	2014-03-05	2014-03-05	2002-08-01	ENSG00000103187	ENSG00000103187			18304	protein-coding gene	gene with protein product		606748	"coactosin-like 1 (Dictyostelium)"			10051563, 9326934, 16924104	Standard	NM_021149		Approved	CLP	uc002fid.3	Q14019	OTTHUMG00000137634	ENST00000262428.4:c.324C>T	16.37:g.84600556G>A			83158057	B2RDU3|D3DUL9|Q86XM5	Silent	SNP	ENST00000262428.4	37	CCDS10947.1																																																																																				0.512	COTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269075.1	NM_021149		A	84600556	G	A	84600556	2	1	61	1	0	0	0	0	0	0	0	1	3767	1049	37	1		1	COTL1	16	84600556	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68977	84600556	5754197	9940	17925										
USP10	9100	broad.mit.edu	37	chr16	84778270	84778270	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagaattgagtttggtgtCgatgaagtcattgaacccag	12	6	1	4	rs537583328		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84778270C>T	ENST00000219473.7	+	4	296	c.183C>T	c.(181-183)gtC>gtT	p.V61V	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.V65V	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	61	Interaction with p53/TP53.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.V61V(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AGTTTGGTGTCGATGAAGTCA	0.408													C|||	1	0.000199681	0	0	5008	,	,		16222	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											49	46	47					16																	84778270		1849	4088	5937	83335771	SO:0001819	synonymous_variant	9100			D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"Ubiquitin-specific peptidases"	12608	protein-coding gene	gene with protein product		609818	"ubiquitin specific protease 10"			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.183C>T	16.37:g.84778270C>T			83335771	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.051753	0.36181	.	.	ENSG00000103194	ENST00000540269	.	.	.	5.06	-3.52	0.04682	.	.	.	.	.	T	0.46249	0.1383	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50550	-0.8815	5	0.72032	D	0.01	-9.3282	0.9847	0.01443	0.138:0.239:0.2676:0.3554	.	.	.	.	L	41	.	ENSP00000445589:S41L	S	+	2	0	USP10	83335771	0.990000	0.36364	0.045000	0.18777	0.683000	0.39861	0.062000	0.14389	-1.144000	0.02862	-0.339000	0.08088	TCG		0.408	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			T	84778270	C	T	84778270	2	4	61	1	0	0	0	0	0	0	0	1	17081	871	31	1		1	USP10	16	84778270	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177714	84778270	5576483	9941	17926										
CRISPLD2	83716	broad.mit.edu	37	chr16	84900571	84900571	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacggctcccattcctgaaGaaaaccatgtttggctccaa	7	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84900571G>T	ENST00000262424.5	+	7	1002	c.778G>T	c.(778-780)Gaa>Taa	p.E260*	CRISPLD2_ENST00000564567.1_Nonsense_Mutation_p.E260*|CRISPLD2_ENST00000567845.1_Nonsense_Mutation_p.E259*	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	260					extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)	p.E260*(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						CATTCCTGAAGAAAACCATGT	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											123	104	111					16																	84900571		2199	4300	6499	83458072	SO:0001587	stop_gained	83716			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"LCCL domain containing cysteine-rich secretory protein 2"	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.778G>T	16.37:g.84900571G>T	ENSP00000262424:p.Glu260*		83458072	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Nonsense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.409246	0.42715	.	.	ENSG00000103196	ENST00000262424	.	.	.	5.66	3.72	0.42706	.	0.638733	0.16615	N	0.206743	.	.	.	.	.	.	0.22240	N	0.999263	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	10.3	0.43646	0.1599:0.0:0.8401:0.0	.	.	.	.	X	260	.	ENSP00000262424:E260X	E	+	1	0	CRISPLD2	83458072	0.999000	0.42202	0.001000	0.08648	0.041000	0.13682	3.249000	0.51437	0.761000	0.33130	-0.136000	0.14681	GAA		0.498	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		T	84900571	G	T	84900571	4	4	61	1	0	0	0	0	0	1	0	0	3889	943	33	2	800	2	CRISPLD2	16	84900571	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122301	84900571	5454182	9942	17927										
CRISPLD2	83716	broad.mit.edu	37	chr16	84902504	84902504	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaggacaggtgcaaagggTccacgtgtaacaggtgagcc	15	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:84902504T>C	ENST00000262424.5	+	8	1125	c.901T>C	c.(901-903)Tcc>Ccc	p.S301P	CRISPLD2_ENST00000564567.1_Missense_Mutation_p.S301P|CRISPLD2_ENST00000567845.1_Missense_Mutation_p.S300P	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	301	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)	p.S301P(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						GTGCAAAGGGTCCACGTGTAA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											182	134	150					16																	84902504		2199	4300	6499	83460005	SO:0001583	missense	83716			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"LCCL domain containing cysteine-rich secretory protein 2"	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.901T>C	16.37:g.84902504T>C	ENSP00000262424:p.Ser301Pro		83460005	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688938	0.68271	.	.	ENSG00000103196	ENST00000262424	D	0.89617	-2.54	5.37	5.37	0.77165	LCCL (5);	0.212625	0.42964	D	0.000637	D	0.92721	0.7686	L	0.61387	1.9	0.80722	D	1	D;D;D	0.71674	0.998;0.991;0.997	D;P;D	0.69479	0.964;0.865;0.949	D	0.93225	0.6612	10	0.66056	D	0.02	.	13.323	0.60444	0.0:0.0:0.0:1.0	.	301;301;301	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	P	301	ENSP00000262424:S301P	ENSP00000262424:S301P	S	+	1	0	CRISPLD2	83460005	0.998000	0.40836	0.935000	0.37517	0.741000	0.42261	3.028000	0.49705	2.031000	0.59945	0.533000	0.62120	TCC		0.572	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		C	84902504	T	C	84902504	3	2	61	1	0	0	0	0	1	0	0	0	3889	1667	58	4	927	4	CRISPLD2	16	84902504	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1933	84902504	5452249	9943	17928										
KIAA0513	9764	broad.mit.edu	37	chr16	85116194	85116194	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctggagaggaggaggaGaagaggtgtgtgtgtccacg	20	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:85116194G>T	ENST00000566428.1	+	10	1636	c.1005G>T	c.(1003-1005)gaG>gaT	p.E335D	KIAA0513_ENST00000258180.3_Missense_Mutation_p.E335D|KIAA0513_ENST00000538274.1_Intron			O60268	K0513_HUMAN	KIAA0513	335						cytoplasm (GO:0005737)		p.E335D(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		AGGAGGAGGAGAAGAGGTGTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	16											190	168	176					16																	85116194		2198	4300	6498	83673695	SO:0001583	missense	9764			AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.1005G>T	16.37:g.85116194G>T	ENSP00000457408:p.Glu335Asp		83673695	B4DSS5|D3DUM2|Q8N6G0	Missense_Mutation	SNP	ENST00000566428.1	37	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.607239	0.28623	.	.	ENSG00000135709	ENST00000258180	T	0.46063	0.88	4.51	3.43	0.39272	.	0.277450	0.33382	N	0.004962	T	0.15176	0.0366	N	0.02011	-0.69	0.30950	N	0.724831	B	0.02656	0.0	B	0.08055	0.003	T	0.14699	-1.0463	10	0.13108	T	0.6	-15.8923	9.5479	0.39293	0.152:0.0:0.848:0.0	.	335	O60268	K0513_HUMAN	D	335	ENSP00000258180:E335D	ENSP00000258180:E335D	E	+	3	2	KIAA0513	83673695	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.660000	0.25009	2.072000	0.62099	0.561000	0.74099	GAG		0.532	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732		T	85116194	G	T	85116194	3	4	61	1	0	0	0	0	1	0	0	0	8202	933	33	2	1039	2	KIAA0513	16	85116194	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213690	85116194	5238559	9944	17929										
FAM92B	339145	broad.mit.edu	37	chr16	85132796	85132796	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttaccctacgtcgttagaGagaatgtcctggaagcatga	10	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:85132796G>T	ENST00000539556.1	-	9	1065	c.910C>A	c.(910-912)Ctc>Atc	p.L304I		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	304								p.L304I(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						CGTCGTTAGAGAGAATGTCCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	16											104	94	97					16																	85132796		2198	4300	6498	83690297	SO:0001583	missense	339145				CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.910C>A	16.37:g.85132796G>T	ENSP00000443411:p.Leu304Ile		83690297		Missense_Mutation	SNP	ENST00000539556.1	37	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	G	9.855	1.194802	0.22037	.	.	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.36520	1.25	1.06	1.06	0.20224	.	.	.	.	.	T	0.28101	0.0693	N	0.08118	0	0.09310	N	1	D	0.57571	0.98	P	0.56216	0.794	T	0.10291	-1.0636	9	0.87932	D	0	.	5.458	0.16602	0.0:0.0:1.0:0.0	.	304	Q6ZTR7	FA92B_HUMAN	I	304	ENSP00000443411:L304I	ENSP00000376937:L304I	L	-	1	0	FAM92B	83690297	0.014000	0.17966	0.021000	0.16686	0.013000	0.08279	0.430000	0.21428	0.900000	0.36469	0.313000	0.20887	CTC		0.478	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491		T	85132796	G	T	85132796	3	4	61	1	0	0	0	0	1	0	0	0	5672	942	33	2	8	2	FAM92B	16	85132796	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16602	85132796	5221957	9945	17930										
GINS2	51659	broad.mit.edu	37	chr16	85715220	85715220	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcgtaagttccatgtaGtaagggctgggcattggggt	15	6	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:85715220G>T	ENST00000253462.3	-	3	373	c.273C>A	c.(271-273)taC>taA	p.Y91*		NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	91					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)		p.Y91*(1)		endometrium(2)|large_intestine(2)|lung(2)	6						GTTCCATGTAGTAAGGGCTGG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											190	171	178					16																	85715220		2198	4300	6498	84272721	SO:0001587	stop_gained	51659			BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.273C>A	16.37:g.85715220G>T	ENSP00000253462:p.Tyr91*		84272721	D3DUM5|Q6IAG9	Nonsense_Mutation	SNP	ENST00000253462.3	37	CCDS10953.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059195	0.93846	.	.	ENSG00000131153	ENST00000253462	.	.	.	4.98	0.77	0.18497	.	0.118916	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-16.5331	5.5596	0.17135	0.3732:0.132:0.4948:0.0	.	.	.	.	X	91	.	ENSP00000253462:Y91X	Y	-	3	2	GINS2	84272721	1.000000	0.71417	0.946000	0.38457	0.969000	0.65631	1.253000	0.32886	-0.067000	0.12976	0.561000	0.74099	TAC		0.438	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095		T	85715220	G	T	85715220	4	4	61	1	0	0	0	0	0	1	0	0	6408	1024	36	2	296	2	GINS2	16	85715220	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	582424	85715220	4639533	9946	17931										
FOXF1	2294	broad.mit.edu	37	chr16	86544587	86544587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcgaggagggctcctttCggcggcggccgcgcggcttc	17	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:86544587C>T	ENST00000262426.4	+	1	455	c.412C>T	c.(412-414)Cgg>Tgg	p.R138W	FENDRR_ENST00000595886.1_lincRNA	NM_001451.2	NP_001442.2	Q12946	FOXF1_HUMAN	forkhead box F1	138					blood vessel development (GO:0001568)|branching involved in open tracheal system development (GO:0060446)|cardiac left ventricle morphogenesis (GO:0003214)|cellular response to cytokine stimulus (GO:0071345)|cellular response to organic cyclic compound (GO:0071407)|detection of wounding (GO:0014822)|determination of left/right symmetry (GO:0007368)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic ectodermal digestive tract morphogenesis (GO:0048613)|embryonic foregut morphogenesis (GO:0048617)|endocardial cushion development (GO:0003197)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lateral mesodermal cell differentiation (GO:0048371)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mesenchyme migration (GO:0090131)|midgut development (GO:0007494)|morphogenesis of a branching structure (GO:0001763)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|respiratory tube development (GO:0030323)|right lung morphogenesis (GO:0060461)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|smoothened signaling pathway (GO:0007224)|somitogenesis (GO:0001756)|trachea development (GO:0060438)|ureter development (GO:0072189)|vasculogenesis (GO:0001570)|venous blood vessel development (GO:0060841)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)	p.R113W(2)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	12						GGGCTCCTTTCGGCGGCGGCC	0.647																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	16											53	67	62					16																	86544587		2197	4299	6496	85102088	SO:0001583	missense	2294			U13219	CCDS10957.2	16q24	2008-02-05			ENSG00000103241	ENSG00000103241		"Forkhead boxes"	3809	protein-coding gene	gene with protein product		601089		FKHL5		8825632, 7957066	Standard	NM_001451		Approved	FREAC1	uc002fjl.3	Q12946	OTTHUMG00000137651	ENST00000262426.4:c.412C>T	16.37:g.86544587C>T	ENSP00000262426:p.Arg138Trp		85102088	B2RAF4|Q5FWE5	Missense_Mutation	SNP	ENST00000262426.4	37	CCDS10957.2	.	.	.	.	.	.	.	.	.	.	C	19.11	3.763771	0.69878	.	.	ENSG00000103241	ENST00000262426	T	0.39787	1.06	4.51	4.51	0.55191	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (2);	0.000000	0.85682	D	0.000000	T	0.68458	0.3003	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75199	-0.3402	10	0.87932	D	0	.	11.4517	0.50156	0.1801:0.8199:0.0:0.0	.	138	Q12946	FOXF1_HUMAN	W	138	ENSP00000262426:R138W	ENSP00000262426:R138W	R	+	1	2	FOXF1	85102088	0.953000	0.32496	0.992000	0.48379	0.805000	0.45488	2.134000	0.42102	2.052000	0.61016	0.650000	0.86243	CGG		0.647	FOXF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000269103.2	NM_001451		T	86544587	C	T	86544587	3	4	61	1	0	0	0	0	1	0	0	0	6024	875	31	1	414	1	FOXF1	16	86544587	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	829367	86544587	3810166	9947	17932										
MTHFSD	64779	broad.mit.edu	37	chr16	86582089	86582089	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgagaggtggcacattttCtcaagatgtctttagttgcc	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:86582089C>A	ENST00000360900.6	-	4	357	c.332G>T	c.(331-333)aGa>aTa	p.R111I	MTHFSD_ENST00000543303.2_Missense_Mutation_p.R110I|MTHFSD_ENST00000568037.1_5'UTR|MTHFSD_ENST00000546093.1_5'UTR|MTHFSD_ENST00000381214.5_Missense_Mutation_p.R111I|MTHFSD_ENST00000322911.6_Missense_Mutation_p.R110I	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	111							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R111I(1)|p.R110I(1)		endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						GGCACATTTTCTCAAGATGTC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	16											145	139	141					16																	86582089		1892	4110	6002	85139590	SO:0001583	missense	64779			AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"RNA binding motif (RRM) containing"	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.332G>T	16.37:g.86582089C>A	ENSP00000354152:p.Arg111Ile		85139590	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178744	0.78564	.	.	ENSG00000103248	ENST00000543303;ENST00000381214;ENST00000360900;ENST00000322911	T;T;T	0.41758	0.99;0.99;0.99	5.3	5.3	0.74995	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	0.048670	0.85682	D	0.000000	T	0.68815	0.3042	M	0.83953	2.67	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.996	T	0.73726	-0.3892	10	0.72032	D	0.01	-6.8512	17.9576	0.89074	0.0:1.0:0.0:0.0	.	111;110;111;110	E9PAM1;B7ZLC0;Q2M296;Q2M296-2	.;.;MTHSD_HUMAN;.	I	109;111;111;110	ENSP00000370612:R111I;ENSP00000354152:R111I;ENSP00000326777:R110I	ENSP00000326777:R110I	R	-	2	0	MTHFSD	85139590	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	5.124000	0.64709	2.485000	0.83878	0.655000	0.94253	AGA		0.448	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		A	86582089	C	A	86582089	3	1	61	1	0	0	0	0	1	0	0	0	9963	913	32	2	839	2	MTHFSD	16	86582089	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37502	86582089	3772664	9948	17933										
CA5A	763	broad.mit.edu	37	chr16	87936104	87936104	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaattttggtatttcacaGaattccagtgaactaaatgc	7	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:87936104G>T	ENST00000309893.2	-	4	547	c.482C>A	c.(481-483)tCt>tAt	p.S161Y		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	161					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.S161Y(1)		large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	GTATTTCACAGAATTCCAGTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	16											56	53	54					16																	87936104		2198	4297	6495	86493605	SO:0001583	missense	763			L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"Carbonic anhydrases"	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.482C>A	16.37:g.87936104G>T	ENSP00000309649:p.Ser161Tyr		86493605	B2RPF2	Missense_Mutation	SNP	ENST00000309893.2	37	CCDS10965.1	.	.	.	.	.	.	.	.	.	.	g	14.73	2.621740	0.46840	.	.	ENSG00000174990	ENST00000309893	T	0.70399	-0.48	4.82	3.84	0.44239	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.332212	0.32328	N	0.006247	D	0.84656	0.5520	M	0.88450	2.955	0.09310	N	1	D	0.71674	0.998	D	0.72338	0.977	T	0.77397	-0.2603	10	0.87932	D	0	-3.7513	11.4998	0.50430	0.0:0.3506:0.6494:0.0	.	161	P35218	CAH5A_HUMAN	Y	161	ENSP00000309649:S161Y	ENSP00000309649:S161Y	S	-	2	0	CA5A	86493605	0.680000	0.27605	0.021000	0.16686	0.950000	0.60333	4.989000	0.63870	0.982000	0.38575	0.484000	0.47621	TCT		0.408	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739		T	87936104	G	T	87936104	3	4	61	1	0	0	0	0	1	0	0	0	2525	942	33	2	451	2	CA5A	16	87936104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1354015	87936104	2418649	9949	17934										
BANP	54971	broad.mit.edu	37	chr16	88014704	88014704	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgaaacgccagcgactaGaaatcaattgccaggatcca	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:88014704G>T	ENST00000393207.1	+	3	354	c.133G>T	c.(133-135)Gaa>Taa	p.E45*	BANP_ENST00000355022.4_Nonsense_Mutation_p.E45*|BANP_ENST00000286122.7_Nonsense_Mutation_p.E45*|BANP_ENST00000393208.2_Nonsense_Mutation_p.E45*|BANP_ENST00000355163.5_Nonsense_Mutation_p.E51*|BANP_ENST00000479780.2_Nonsense_Mutation_p.E45*|BANP_ENST00000538234.1_Nonsense_Mutation_p.E45*	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	45					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E45*(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CCAGCGACTAGAAATCAATTG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											106	97	100					16																	88014704		2198	4300	6498	86572205	SO:0001587	stop_gained	54971			AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.133G>T	16.37:g.88014704G>T	ENSP00000376902:p.Glu45*		86572205	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Nonsense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723635	0.89298	.	.	ENSG00000172530	ENST00000439677;ENST00000286122;ENST00000355163;ENST00000289484;ENST00000454563;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000412691;ENST00000355022;ENST00000436970;ENST00000538234;ENST00000436274;ENST00000456902;ENST00000393207	.	.	.	4.56	4.56	0.56223	.	0.230651	0.41194	D	0.000940	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.6775	0.85283	0.0:0.0:1.0:0.0	.	.	.	.	X	51;45;51;45;56;45;45;45;45;45;45;45;45;45;45	.	ENSP00000286122:E45X	E	+	1	0	BANP	86572205	1.000000	0.71417	0.973000	0.42090	0.403000	0.30841	6.927000	0.75840	2.255000	0.74692	0.455000	0.32223	GAA		0.393	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		T	88014704	G	T	88014704	4	4	61	1	0	0	0	0	0	1	0	0	1311	943	33	2	157	2	BANP	16	88014704	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78600	88014704	2340049	9950	17935										
BANP	54971	broad.mit.edu	37	chr16	88066718	88066718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgttgcccccacagagcCgatgatgagcaccccacctc	8	18	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:88066718C>T	ENST00000393207.1	+	9	1264	c.1043C>T	c.(1042-1044)cCg>cTg	p.P348L	BANP_ENST00000355022.4_Missense_Mutation_p.P317L|BANP_ENST00000286122.7_Missense_Mutation_p.P348L|BANP_ENST00000393208.2_Missense_Mutation_p.P317L|BANP_ENST00000355163.5_Missense_Mutation_p.P323L|BANP_ENST00000479780.2_Missense_Mutation_p.P317L|BANP_ENST00000538234.1_Missense_Mutation_p.P356L	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	348	DNA-binding. {ECO:0000250}.|Necessary and sufficient for TP53 activation. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P317L(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CCCACAGAGCCGATGATGAGC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	16																																								86624219	SO:0001583	missense	54971			AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1043C>T	16.37:g.88066718C>T	ENSP00000376902:p.Pro348Leu		86624219	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	C	8.127	0.782177	0.16189	.	.	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	.	.	.	3.75	1.52	0.23074	.	0.536094	0.20729	N	0.086754	T	0.22085	0.0532	N	0.14661	0.345	0.31187	N	0.7014	B;B;B;B;B;B	0.26577	0.103;0.054;0.0;0.081;0.0;0.153	B;B;B;B;B;B	0.20767	0.011;0.014;0.0;0.014;0.0;0.031	T	0.17471	-1.0368	9	0.28530	T	0.3	.	9.594	0.39563	0.0:0.5132:0.4867:0.0	.	356;323;317;348;317;317	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	L	348;323;313;317;317;317;317;356;348	.	ENSP00000286122:P348L	P	+	2	0	BANP	86624219	0.997000	0.39634	0.997000	0.53966	0.169000	0.22640	1.442000	0.35046	0.883000	0.36040	0.305000	0.20034	CCG		0.652	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		T	88066718	C	T	88066718	3	4	61	1	0	0	0	0	1	0	0	0	1311	652	23	1	1115	1	BANP	16	88066718	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52014	88066718	2288035	9951	17936										
ZNF778	197320	broad.mit.edu	37	chr16	89294186	89294186	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctgactgagcacgcgaGaatccataccggagagaaac	11	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:89294186G>T	ENST00000433976.2	+	6	1738	c.1406G>T	c.(1405-1407)aGa>aTa	p.R469I	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Missense_Mutation_p.R427I	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	469					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R469I(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GAGCACGCGAGAATCCATACC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	16											74	77	76					16																	89294186		2186	4297	6483	87821687	SO:0001583	missense	197320			AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1406G>T	16.37:g.89294186G>T	ENSP00000405289:p.Arg469Ile		87821687	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	37	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806956	0.70797	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.24908	1.83;1.83	1.13	1.13	0.20643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46405	0.1391	M	0.77820	2.39	0.40603	D	0.981609	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.49133	-0.8971	9	0.62326	D	0.03	.	8.1979	0.31407	0.0:0.0:1.0:0.0	.	427;469	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	I	469;427	ENSP00000405289:R469I;ENSP00000305203:R427I	ENSP00000305203:R427I	R	+	2	0	ZNF778	87821687	0.000000	0.05858	0.213000	0.23690	0.318000	0.28184	0.597000	0.24059	0.927000	0.37143	0.558000	0.71614	AGA		0.498	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		T	89294186	G	T	89294186	3	4	61	1	0	0	0	0	1	0	0	0	18190	942	33	2	1424	2	ZNF778	16	89294186	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1227468	89294186	1060567	9952	17937										
ANKRD11	29123	broad.mit.edu	37	chr16	89341336	89341336	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcagtgaacccgcagaatCtcctgctcacaggatacgat	10	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:89341336C>A	ENST00000301030.4	-	11	8059	c.7599G>T	c.(7597-7599)gaG>gaT	p.E2533D	ANKRD11_ENST00000378330.2_Missense_Mutation_p.E2533D	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2533					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E2533D(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CCCGCAGAATCTCCTGCTCAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	16											57	54	55					16																	89341336		2198	4300	6498	87868837	SO:0001583	missense	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7599G>T	16.37:g.89341336C>A	ENSP00000301030:p.Glu2533Asp		87868837	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802278	0.70682	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.54479	0.57;0.57	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000002	T	0.76435	0.3987	M	0.84585	2.705	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.80415	-0.1392	10	0.72032	D	0.01	.	18.6113	0.91286	0.0:1.0:0.0:0.0	.	2533	Q6UB99	ANR11_HUMAN	D	2533	ENSP00000301030:E2533D;ENSP00000367581:E2533D	ENSP00000301030:E2533D	E	-	3	2	ANKRD11	87868837	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.083000	0.50136	2.569000	0.86673	0.655000	0.94253	GAG		0.612	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89341336	C	A	89341336	3	1	61	1	0	0	0	0	1	0	0	0	639	912	32	2	404	2	ANKRD11	16	89341336	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47150	89341336	1013417	9953	17938										
ANKRD11	29123	broad.mit.edu	37	chr16	89348605	89348605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgttgatggcactagatcCataaggctttagttcctttt	9	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:89348605C>T	ENST00000301030.4	-	9	4805	c.4345G>A	c.(4345-4347)Gga>Aga	p.G1449R	ANKRD11_ENST00000378330.2_Missense_Mutation_p.G1449R	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1449	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G1449R(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GCACTAGATCCATAAGGCTTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	16											112	91	98					16																	89348605		2198	4300	6498	87876106	SO:0001583	missense	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4345G>A	16.37:g.89348605C>T	ENSP00000301030:p.Gly1449Arg		87876106	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	9.287	1.049517	0.19827	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.38077	1.16;1.16	5.11	5.11	0.69529	.	0.215320	0.32002	N	0.006730	T	0.36220	0.0959	L	0.54323	1.7	0.20196	N	0.999922	P	0.44877	0.845	P	0.45037	0.467	T	0.29518	-1.0009	10	0.33940	T	0.23	.	9.3991	0.38422	0.0:0.8382:0.0:0.1618	.	1449	Q6UB99	ANR11_HUMAN	R	1449	ENSP00000301030:G1449R;ENSP00000367581:G1449R	ENSP00000301030:G1449R	G	-	1	0	ANKRD11	87876106	0.000000	0.05858	0.146000	0.22360	0.011000	0.07611	0.486000	0.22340	2.530000	0.85305	0.563000	0.77884	GGA		0.413	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89348605	C	T	89348605	3	4	61	1	0	0	0	0	1	0	0	0	639	603	21	3	3666	3	ANKRD11	16	89348605	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7269	89348605	1006148	9954	17939										
ANKRD11	29123	broad.mit.edu	37	chr16	89348773	89348773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctccaggaagtccttttCgtactggccggagtccttcc	10	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:89348773C>T	ENST00000301030.4	-	9	4637	c.4177G>A	c.(4177-4179)Gaa>Aaa	p.E1393K	ANKRD11_ENST00000378330.2_Missense_Mutation_p.E1393K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1393	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E1393K(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		AAGTCCTTTTCGTACTGGCCG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	16											117	107	111					16																	89348773		2198	4300	6498	87876274	SO:0001583	missense	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4177G>A	16.37:g.89348773C>T	ENSP00000301030:p.Glu1393Lys		87876274	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867079	0.72065	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.52526	0.66;0.66	5.11	5.11	0.69529	.	0.265410	0.35870	N	0.002929	T	0.49012	0.1532	L	0.51422	1.61	0.80722	D	1	D	0.62365	0.991	P	0.44597	0.454	T	0.56529	-0.7964	10	0.72032	D	0.01	.	18.4974	0.90870	0.0:1.0:0.0:0.0	.	1393	Q6UB99	ANR11_HUMAN	K	1393	ENSP00000301030:E1393K;ENSP00000367581:E1393K	ENSP00000301030:E1393K	E	-	1	0	ANKRD11	87876274	1.000000	0.71417	0.500000	0.27589	0.067000	0.16453	7.189000	0.77747	2.530000	0.85305	0.563000	0.77884	GAA		0.493	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89348773	C	T	89348773	3	4	61	1	0	0	0	0	1	0	0	0	639	893	31	1	3834	1	ANKRD11	16	89348773	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168	89348773	1005980	9955	17940										
FANCA	2175	broad.mit.edu	37	chr16	89882338	89882338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcaggaggcgcacagctgAttcctttaatttctgtgccc	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:89882338A>G	ENST00000389301.3	-	2	166	c.136T>C	c.(136-138)Tca>Cca	p.S46P	FANCA_ENST00000389302.3_Missense_Mutation_p.S46P|FANCA_ENST00000543736.1_Missense_Mutation_p.S46P|FANCA_ENST00000568369.1_Missense_Mutation_p.S46P|FANCA_ENST00000534992.1_Missense_Mutation_p.S46P|FANCA_ENST00000563673.1_Missense_Mutation_p.S46P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	46					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S46P(1)		breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CGCACAGCTGATTCCTTTAAT	0.507			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	1	Substitution - Missense(1)	large_intestine(1)	16											141	129	133					16																	89882338		2198	4300	6498	88409839	SO:0001583	missense	2175	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.136T>C	16.37:g.89882338A>G	ENSP00000373952:p.Ser46Pro		88409839	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.648754	0.67358	.	.	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.47	2.05	0.26809	.	0.345964	0.20236	N	0.096391	T	0.56202	0.1969	M	0.62723	1.935	0.09310	N	1	P;D;D;D;D;P	0.61697	0.93;0.982;0.99;0.99;0.99;0.93	P;P;P;P;P;P	0.62382	0.462;0.802;0.901;0.901;0.901;0.462	T	0.51965	-0.8638	10	0.59425	D	0.04	-8.3811	12.6013	0.56499	0.2869:0.7131:0.0:0.0	.	46;46;46;46;46;46	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	P	46	ENSP00000373952:S46P;ENSP00000373953:S46P;ENSP00000443675:S46P;ENSP00000443409:S46P	ENSP00000373952:S46P	S	-	1	0	FANCA	88409839	0.057000	0.20700	0.002000	0.10522	0.092000	0.18411	0.595000	0.24029	0.062000	0.16340	0.525000	0.51046	TCA		0.507	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			G	89882338	A	G	89882338	3	3	61	1	0	0	0	0	1	0	0	0	5681	333	12	4	4404	4	FANCA	16	89882338	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	533565	89882338	472415	9956	17941										
PRDM7	11105	broad.mit.edu	37	chr16	90126764	90126764	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacctctccctgccatgaGctctttcttccacttgctgc	5	18	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr16:90126764G>A	ENST00000449207.2	-	9	1237	c.1218C>T	c.(1216-1218)agC>agT	p.S406S	PRDM7_ENST00000325921.6_Intron|PRDM7_ENST00000407825.1_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	406					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)	p.S406S(1)		lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CCTGCCATGAGCTCTTTCTTC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	16											94	98	97					16																	90126764		1903	4105	6008	88654265	SO:0001819	synonymous_variant	11105			AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1218C>T	16.37:g.90126764G>A			88654265	A4Q9G8|Q08EM4|Q9NQW4	Silent	SNP	ENST00000449207.2	37	CCDS45557.1																																																																																				0.463	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			A	90126764	G	A	90126764	2	1	61	1	0	0	0	0	0	0	0	1	12495	962	34	3		3	PRDM7	16	90126764	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244426	90126764	227989	9957	17942										
VPS53	55275	broad.mit.edu	37	chr17	531401	531401	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttttgatgatttcctgtTtgatcctgggatctagaata	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:531401T>G	ENST00000571805.1	-	9	894	c.758A>C	c.(757-759)aAa>aCa	p.K253T	VPS53_ENST00000401468.3_Intron|VPS53_ENST00000437048.2_Missense_Mutation_p.K253T|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.K224T|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000446250.2_Missense_Mutation_p.K55T			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	253					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)		p.K224T(1)		breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GATTTCCTGTTTGATCCTGGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	17											138	130	133					17																	531401		2203	4300	6503	478151	SO:0001583	missense	55275				CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.758A>C	17.37:g.531401T>G	ENSP00000459312:p.Lys253Thr		478151	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		.	.	.	.	.	.	.	.	.	.	T	25.8	4.670703	0.88348	.	.	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074	T;T;T	0.36157	1.27;1.27;1.27	5.93	5.93	0.95920	Vps53-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65995	0.2745	M	0.89414	3.03	0.80722	D	1	D;D;D;D	0.61080	0.989;0.981;0.985;0.981	D;D;D;D	0.68621	0.932;0.959;0.958;0.947	T	0.73116	-0.4084	10	0.87932	D	0	-23.9418	15.5567	0.76200	0.0:0.0:0.0:1.0	.	253;55;253;224	Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	T	253;55;224	ENSP00000401435:K253T;ENSP00000394386:K55T;ENSP00000291074:K224T	ENSP00000291074:K224T	K	-	2	0	VPS53	478151	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.803000	0.62546	2.270000	0.75569	0.460000	0.39030	AAA		0.373	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		G	531401	T	G	531401	3	3	61	1	0	0	0	0	1	0	0	0	17255	1841	64	4	1811	4	VPS53	17	531401	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09		531401	80663809	9958	17943										
GLOD4	51031	broad.mit.edu	37	chr17	680205	680205	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccaaatcccaccattgttTtactccatttcccatcataa	2	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:680205T>G	ENST00000301328.5	-	4	232	c.209A>C	c.(208-210)aAa>aCa	p.K70T	GLOD4_ENST00000301329.6_Missense_Mutation_p.K55T|GLOD4_ENST00000536578.1_Missense_Mutation_p.K46T			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	70						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)		p.K55T(1)		endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CACCATTGTTTTACTCCATTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	17											147	125	132					17																	680205		2203	4300	6503	626955	SO:0001583	missense	51031			AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 25"	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38		ENST00000301328.5:c.209A>C	17.37:g.680205T>G	ENSP00000301328:p.Lys70Thr		626955	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		.	.	.	.	.	.	.	.	.	.	T	27.4	4.823548	0.90873	.	.	ENSG00000167699	ENST00000301329;ENST00000397393;ENST00000301328;ENST00000536578	T;T;T	0.61742	0.08;0.08;0.08	5.45	5.45	0.79879	.	0.045726	0.85682	D	0.000000	T	0.79575	0.4469	M	0.88031	2.925	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.83602	0.0129	10	0.66056	D	0.02	-14.9622	14.6781	0.68996	0.0:0.0:0.0:1.0	.	46;70;55	B7Z403;Q9HC38;Q9HC38-2	.;GLOD4_HUMAN;.	T	55;258;70;46	ENSP00000301329:K55T;ENSP00000301328:K70T;ENSP00000444315:K46T	ENSP00000301328:K70T	K	-	2	0	GLOD4	626955	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.736000	0.84948	2.060000	0.61445	0.533000	0.62120	AAA		0.448	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080		G	680205	T	G	680205	3	3	61	1	0	0	0	0	1	0	0	0	6470	1841	64	4	760	4	GLOD4	17	680205	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	148804	680205	80515005	9959	17944										
NXN	64359	broad.mit.edu	37	chr17	707013	707013	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatcggctgaatcagctgcTtggccgcctcggactctccg	11	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:707013T>G	ENST00000336868.3	-	7	1125	c.1034A>C	c.(1033-1035)aAg>aCg	p.K345T	NXN_ENST00000537628.2_Missense_Mutation_p.K96T|NXN_ENST00000575801.1_Missense_Mutation_p.K237T|NXN_ENST00000538650.1_Missense_Mutation_p.K36T	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	345					cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)	p.K345T(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		AATCAGCTGCTTGGCCGCCTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	100	101					17																	707013		2203	4300	6503	653763	SO:0001583	missense	64359				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.1034A>C	17.37:g.707013T>G	ENSP00000337443:p.Lys345Thr		653763	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Missense_Mutation	SNP	ENST00000336868.3	37	CCDS10998.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327421	0.81690	.	.	ENSG00000167693	ENST00000336868;ENST00000538650;ENST00000537628	T;T	0.33216	1.42;2.52	5.26	5.26	0.73747	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	L	0.47716	1.5	0.80722	D	1	D;D;D	0.76494	0.999;0.989;0.992	D;D;P	0.81914	0.995;0.969;0.908	T	0.25745	-1.0123	10	0.27785	T	0.31	-26.0884	14.3143	0.66437	0.0:0.0:0.0:1.0	.	237;36;345	B4DXQ0;B4DNN6;Q6DKJ4	.;.;NXN_HUMAN	T	345;36;237	ENSP00000337443:K345T;ENSP00000445087:K36T	ENSP00000337443:K345T	K	-	2	0	NXN	653763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.032000	0.70918	2.129000	0.65627	0.533000	0.62120	AAG		0.547	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1			G	707013	T	G	707013	3	3	61	1	0	0	0	0	1	0	0	0	10818	1609	56	4	281	4	NXN	17	707013	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	26808	707013	80488197	9960	17945										
TUSC5	286753	broad.mit.edu	37	chr17	1198789	1198789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgctctctccgcagtctcGaagcagcatgcaacagggca	11	13	2	0	rs200319809	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:1198789G>A	ENST00000333813.3	+	2	731	c.392G>A	c.(391-393)cGa>cAa	p.R131Q		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	131					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)		p.R131Q(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCGCAGTCTCGAAGCAGCATG	0.652													G|||	3	0.000599042	0.0015	0	5008	,	,		17834	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											104	118	113					17																	1198789		2057	4203	6260	1145539	SO:0001583	missense	286753			AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"located at seventeen p thirteen point three 1", "interferon induced transmembrane protein domain containing 3"	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.392G>A	17.37:g.1198789G>A	ENSP00000329548:p.Arg131Gln		1145539	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	37	CCDS42225.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269189	0.80469	.	.	ENSG00000184811	ENST00000333813	D	0.87029	-2.2	5.56	5.56	0.83823	.	0.000000	0.64402	U	0.000003	D	0.93497	0.7925	M	0.80028	2.48	0.48571	D	0.999678	D	0.89917	1.0	D	0.91635	0.999	D	0.93627	0.6953	10	0.56958	D	0.05	-5.4651	16.2486	0.82467	0.0:0.0:1.0:0.0	.	131	Q8IXB3	TUSC5_HUMAN	Q	131	ENSP00000329548:R131Q	ENSP00000329548:R131Q	R	+	2	0	TUSC5	1145539	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	7.527000	0.81931	2.629000	0.89072	0.609000	0.83330	CGA		0.652	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367		A	1198789	G	A	1198789	3	1	61	1	0	0	0	0	1	0	0	0	16819	1058	37	1	398	1	TUSC5	17	1198789	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	491776	1198789	79996421	9961	17946										
INPP5K	51763	broad.mit.edu	37	chr17	1401248	1401248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctccaagtcgaacgtgccGgagacaggcttgtggtcgct	13	12	0	1	rs370433971	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:1401248G>A	ENST00000421807.2	-	8	1333	c.945C>T	c.(943-945)tcC>tcT	p.S315S	INPP5K_ENST00000542125.1_Silent_p.S219S|INPP5K_ENST00000406424.4_Silent_p.S239S|INPP5K_ENST00000320345.6_Silent_p.S239S|INPP5K_ENST00000397335.3_Silent_p.S223S	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	315	Catalytic. {ECO:0000255}.		S -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)	p.S315S(1)|p.S239S(1)		endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CGAACGTGCCGGAGACAGGCT	0.592													G|||	3	0.000599042	0	0	5008	,	,		19573	0		0	False		,,,				2504	0.0031															2	Substitution - coding silent(2)	large_intestine(2)	17						G	,,	1,4405	2.1+/-5.4	0,1,2202	153	134	141		717,945,717	-6.3	0.3	17		141	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	INPP5K	NM_001135642.1,NM_016532.3,NM_130766.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	239/373,315/449,239/373	1401248	1,13005	2203	4300	6503	1347998	SO:0001819	synonymous_variant	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.945C>T	17.37:g.1401248G>A			1347998	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																				0.592	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			A	1401248	G	A	1401248	2	1	61	1	0	0	0	0	0	0	0	1	7781	1103	39	1		1	INPP5K	17	1401248	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202459	1401248	79793962	9962	17947										
SLC43A2	124935	broad.mit.edu	37	chr17	1520008	1520008	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagccgttcatccagctCacctcctcgtgccccggctc	8	20	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:1520008C>A	ENST00000301335.5	-	3	304	c.216G>T	c.(214-216)gtG>gtT	p.V72V	snoU13_ENST00000459614.1_RNA|SLC43A2_ENST00000571650.1_Silent_p.V72V|SLC43A2_ENST00000382147.4_Silent_p.V72V	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	72					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)	p.V72V(1)		endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		TCATCCAGCTCACCTCCTCGT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	17											88	70	76					17																	1520008		2203	4300	6503	1466758	SO:0001819	synonymous_variant	124935			BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"Solute carriers"	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.216G>T	17.37:g.1520008C>A			1466758	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																				0.602	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		A	1520008	C	A	1520008	2	1	61	1	0	0	0	0	0	0	0	1	14670	813	29	2		2	SLC43A2	17	1520008	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118760	1520008	79675202	9963	17948										
PRPF8	10594	broad.mit.edu	37	chr17	1585217	1585217	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctccagtggctcaacatCtaggatgttgtcagcatagt	11	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:1585217C>A	ENST00000572621.1	-	4	815	c.550G>T	c.(550-552)Gat>Tat	p.D184Y	PRPF8_ENST00000304992.6_Missense_Mutation_p.D184Y			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	184				D -> N (in Ref. 2; BAA22563). {ECO:0000305}.	gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.D184Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGCTCAACATCTAGGATGTTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											93	95	94					17																	1585217		2203	4300	6503	1531967	SO:0001583	missense	10594			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.550G>T	17.37:g.1585217C>A	ENSP00000460348:p.Asp184Tyr		1531967	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735697	0.89482	.	.	ENSG00000174231	ENST00000304992	T	0.54071	0.59	5.47	5.47	0.80525	Pre-mRNA-processing-splicing factor 8 (2);	0.000000	0.85682	D	0.000000	T	0.79137	0.4395	M	0.91561	3.22	0.80722	D	1	D	0.64830	0.994	D	0.69479	0.964	D	0.83825	0.0249	10	0.87932	D	0	.	19.3655	0.94460	0.0:1.0:0.0:0.0	.	184	Q6P2Q9	PRP8_HUMAN	Y	184	ENSP00000304350:D184Y	ENSP00000304350:D184Y	D	-	1	0	PRPF8	1531967	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.789000	0.85783	2.580000	0.87095	0.550000	0.68814	GAT		0.542	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			A	1585217	C	A	1585217	3	1	61	1	0	0	0	0	1	0	0	0	12609	913	32	2	6613	2	PRPF8	17	1585217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65209	1585217	79609993	9964	17949										
SERPINF1	5176	broad.mit.edu	37	chr17	1675263	1675263	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgcttggacctgcaagaGatcaacaactgggtgcaggc	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:1675263G>T	ENST00000254722.4	+	5	700	c.537G>T	c.(535-537)gaG>gaT	p.E179D		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	179					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E179D(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						ACCTGCAAGAGATCAACAACT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											87	81	83					17																	1675263		2203	4300	6503	1622013	SO:0001583	missense	5176			M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.537G>T	17.37:g.1675263G>T	ENSP00000254722:p.Glu179Asp		1622013	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Missense_Mutation	SNP	ENST00000254722.4	37	CCDS11012.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571467	0.45798	.	.	ENSG00000132386	ENST00000254722	D	0.85013	-1.93	5.79	2.72	0.32119	Serpin domain (3);	0.096077	0.64402	D	0.000001	D	0.84982	0.5593	L	0.43152	1.355	0.80722	D	1	D	0.61697	0.99	D	0.63877	0.919	T	0.80259	-0.1457	10	0.17369	T	0.5	.	8.3724	0.32423	0.3393:0.0:0.6607:0.0	.	179	P36955	PEDF_HUMAN	D	179	ENSP00000254722:E179D	ENSP00000254722:E179D	E	+	3	2	SERPINF1	1622013	0.747000	0.28283	0.989000	0.46669	0.024000	0.10985	0.151000	0.16283	1.444000	0.47605	0.561000	0.74099	GAG		0.552	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		T	1675263	G	T	1675263	3	4	61	1	0	0	0	0	1	0	0	0	14151	933	33	2	551	2	SERPINF1	17	1675263	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90046	1675263	79519947	9965	17950										
TSR1	55720	broad.mit.edu	37	chr17	2227493	2227493	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatctctttgaatccattaCtccatgcccccttgaggcac	6	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2227493C>A	ENST00000301364.5	-	15	3491	c.2412G>T	c.(2410-2412)gaG>gaT	p.E804D	SRR_ENST00000344595.5_3'UTR	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	804					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E804D(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						GAATCCATTACTCCATGCCCC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	17											156	148	151					17																	2227493		2203	4300	6503	2174243	SO:0001583	missense	55720			AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.2412G>T	17.37:g.2227493C>A	ENSP00000301364:p.Glu804Asp		2174243	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	C	3.299	-0.143284	0.06669	.	.	ENSG00000167721	ENST00000301364	T	0.11604	2.76	4.92	-1.41	0.08941	.	0.148138	0.64402	D	0.000016	T	0.04588	0.0125	N	0.08118	0	0.33046	D	0.532069	B	0.29531	0.247	B	0.28553	0.091	T	0.29549	-1.0008	10	0.38643	T	0.18	-21.6177	8.9792	0.35955	0.0:0.4374:0.0:0.5626	.	804	Q2NL82	TSR1_HUMAN	D	804	ENSP00000301364:E804D	ENSP00000301364:E804D	E	-	3	2	TSR1	2174243	1.000000	0.71417	0.214000	0.23707	0.045000	0.14185	0.342000	0.19926	-0.088000	0.12506	0.655000	0.94253	GAG		0.463	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		A	2227493	C	A	2227493	3	1	61	1	0	0	0	0	1	0	0	0	16704	564	20	2	6	2	TSR1	17	2227493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	552230	2227493	78967717	9966	17951										
TSR1	55720	broad.mit.edu	37	chr17	2236935	2236935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctctgcttgcaaggattCctgtctaccagggtctgcct	9	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2236935C>T	ENST00000301364.5	-	6	2136	c.1057G>A	c.(1057-1059)Gaa>Aaa	p.E353K	TSR1_ENST00000576112.2_Missense_Mutation_p.E337K	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	353					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E353K(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TGCAAGGATTCCTGTCTACCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											175	154	161					17																	2236935		2203	4300	6503	2183685	SO:0001583	missense	55720			AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.1057G>A	17.37:g.2236935C>T	ENSP00000301364:p.Glu353Lys		2183685	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	C	36	5.975933	0.97162	.	.	ENSG00000167721	ENST00000301364	T	0.13420	2.59	5.98	5.98	0.97165	.	0.042967	0.85682	D	0.000000	T	0.38585	0.1046	M	0.79123	2.44	0.80722	D	1	D	0.67145	0.996	P	0.61201	0.885	T	0.02917	-1.1094	10	0.49607	T	0.09	-23.6603	19.4434	0.94836	0.0:1.0:0.0:0.0	.	353	Q2NL82	TSR1_HUMAN	K	353	ENSP00000301364:E353K	ENSP00000301364:E353K	E	-	1	0	TSR1	2183685	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.403000	0.66338	2.839000	0.97877	0.650000	0.86243	GAA		0.483	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		T	2236935	C	T	2236935	3	4	61	1	0	0	0	0	1	0	0	0	16704	864	30	3	1397	3	TSR1	17	2236935	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9442	2236935	78958275	9967	17952										
METT10D	79066	broad.mit.edu	37	chr17	2367631	2367631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggaggtcttcgaggatttCgtgagtttactccctgaaaa	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2367631C>T	ENST00000263092.6	-	6	726	c.599G>A	c.(598-600)cGa>cAa	p.R200Q	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	200							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.R200Q(4)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						TCGAGGATTTCGTGAGTTTAC	0.393																																																4	Substitution - Missense(4)	large_intestine(4)	17											112	99	103					17																	2367631		1841	4083	5924	2314381	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.599G>A	17.37:g.2367631C>T	ENSP00000263092:p.Arg200Gln		2314381	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.624875	0.96660	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.50277	0.75	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.80764	0.964;0.994	T	0.79135	-0.1928	10	0.87932	D	0	.	17.3068	0.87197	0.0:1.0:0.0:0.0	.	200;200	Q86W50-2;Q86W50	.;MET16_HUMAN	Q	200	ENSP00000263092:R200Q	ENSP00000263092:R200Q	R	-	2	0	METTL16	2314381	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.770000	0.85390	2.683000	0.91414	0.591000	0.81541	CGA		0.393	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		T	2367631	C	T	2367631	3	4	61	1	0	0	0	0	1	0	0	0	9520	884	31	1	1109	1	METT10D	17	2367631	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130696	2367631	78827579	9968	17953										
METT10D	79066	broad.mit.edu	37	chr17	2381121	2381121	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaatagaaagtccaaaatCttcccttaggagagtacacg	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2381121C>A	ENST00000263092.6	-	3	314	c.187G>T	c.(187-189)Gat>Tat	p.D63Y	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	63							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.D63Y(2)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						AGTCCAAAATCTTCCCTTAGG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	17											135	130	131					17																	2381121		1839	4076	5915	2327871	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.187G>T	17.37:g.2381121C>A	ENSP00000263092:p.Asp63Tyr		2327871	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.855472	0.91355	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.19806	2.12	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	L	0.46567	1.45	0.80722	D	1	P;D	0.71674	0.826;0.998	P;D	0.73380	0.519;0.98	T	0.01508	-1.1337	10	0.44086	T	0.13	-2.1597	18.1377	0.89624	0.0:1.0:0.0:0.0	.	63;63	Q86W50-2;Q86W50	.;MET16_HUMAN	Y	63	ENSP00000263092:D63Y	ENSP00000263092:D63Y	D	-	1	0	METTL16	2327871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.695000	0.84257	2.890000	0.99128	0.650000	0.86243	GAT		0.398	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		A	2381121	C	A	2381121	3	1	61	1	0	0	0	0	1	0	0	0	9520	913	32	2	1533	2	METT10D	17	2381121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13490	2381121	78814089	9969	17954										
RAP1GAP2	23108	broad.mit.edu	37	chr17	2867315	2867315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacatttggctacaagctcGagtgcaagggtgaagccagg	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2867315G>A	ENST00000254695.8	+	7	535	c.445G>A	c.(445-447)Gag>Aag	p.E149K	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.E134K|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.E149K|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.E130K|CTD-3060P21.1_ENST00000574885.1_RNA	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	149					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.E149K(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CTACAAGCTCGAGTGCAAGGG	0.647																																																2	Substitution - Missense(2)	large_intestine(2)	17											59	63	62					17																	2867315		2090	4215	6305	2814065	SO:0001583	missense	23108			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.445G>A	17.37:g.2867315G>A	ENSP00000254695:p.Glu149Lys		2814065	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	g	33	5.244175	0.95272	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.94807	0.8323	M	0.82630	2.6	0.80722	D	1	D;D	0.61697	0.99;0.983	P;B	0.46452	0.517;0.339	D	0.95477	0.8557	10	0.87932	D	0	-2.2685	18.6341	0.91371	0.0:0.0:1.0:0.0	.	134;149	Q684P5-2;Q684P5	.;RPGP2_HUMAN	K	149;134;130;149	ENSP00000254695:E149K;ENSP00000389824:E134K;ENSP00000439688:E130K;ENSP00000444890:E149K	ENSP00000254695:E149K	E	+	1	0	RAP1GAP2	2814065	1.000000	0.71417	0.961000	0.40146	0.784000	0.44337	9.168000	0.94781	2.661000	0.90470	0.645000	0.84053	GAG		0.647	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			A	2867315	G	A	2867315	3	1	61	1	0	0	0	0	1	0	0	0	13075	1059	37	1	471	1	RAP1GAP2	17	2867315	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	486194	2867315	78327895	9970	17955										
RAP1GAP2	23108	broad.mit.edu	37	chr17	2883593	2883593	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgcaggtccaaactgaaGacggtacatgagcggatccc	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2883593G>T	ENST00000254695.8	+	9	699	c.609G>T	c.(607-609)aaG>aaT	p.K203N	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.K188N|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.K203N|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.K184N	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	203					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.K203N(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CCAAACTGAAGACGGTACATG	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	17											90	87	88					17																	2883593		1997	4166	6163	2830343	SO:0001583	missense	23108			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.609G>T	17.37:g.2883593G>T	ENSP00000254695:p.Lys203Asn		2830343	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085975	0.36758	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	4.99	1.55	0.23275	.	0.095500	0.64402	D	0.000001	D	0.90981	0.7164	M	0.70595	2.14	0.40839	D	0.983652	P;P	0.51449	0.892;0.945	P;B	0.46629	0.522;0.439	D	0.86203	0.1620	10	0.27785	T	0.31	-19.955	5.1153	0.14831	0.4338:0.0:0.5662:0.0	.	188;203	Q684P5-2;Q684P5	.;RPGP2_HUMAN	N	203;188;184;203	ENSP00000254695:K203N;ENSP00000389824:K188N;ENSP00000439688:K184N;ENSP00000444890:K203N	ENSP00000254695:K203N	K	+	3	2	RAP1GAP2	2830343	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.633000	0.37113	0.527000	0.28560	0.555000	0.69702	AAG		0.542	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			T	2883593	G	T	2883593	3	4	61	1	0	0	0	0	1	0	0	0	13075	933	33	2	643	2	RAP1GAP2	17	2883593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16278	2883593	78311617	9971	17956										
OR1D2	4991	broad.mit.edu	37	chr17	2995871	2995871	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaaaggagtaagatacaGagcttagggctcatggctgt	14	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:2995871G>T	ENST00000331459.1	-	1	419	c.420C>A	c.(418-420)ctC>ctA	p.L140L		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	140					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L140L(1)		kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						GTAAGATACAGAGCTTAGGGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	17											83	89	87					17																	2995871		2203	4300	6503	2942621	SO:0001819	synonymous_variant	4991			U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"GPCR / Class A : Olfactory receptors"	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.420C>A	17.37:g.2995871G>T			2942621	Q6IFL8|Q96RA4|Q9UM78	Silent	SNP	ENST00000331459.1	37	CCDS11019.1																																																																																				0.542	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548		T	2995871	G	T	2995871	2	4	61	1	0	0	0	0	0	0	0	1	10984	929	33	2		2	OR1D2	17	2995871	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	112278	2995871	78199339	9972	17957										
OR1E1	8387	broad.mit.edu	37	chr17	3300895	3300895	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatagccatgacagtgtcCtttagagtagaactattagc	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3300895C>A	ENST00000322608.2	-	1	809	c.810G>T	c.(808-810)aaG>aaT	p.K270N		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K270N(1)		endometrium(3)|large_intestine(2)|lung(5)	10						TGACAGTGTCCTTTAGAGTAG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	17											105	97	100					17																	3300895		2203	4300	6503	3247645	SO:0001583	missense	8387			U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"GPCR / Class A : Olfactory receptors"	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.810G>T	17.37:g.3300895C>A	ENSP00000313384:p.Lys270Asn		3247645	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Missense_Mutation	SNP	ENST00000322608.2	37	CCDS11024.1	.	.	.	.	.	.	.	.	.	.	C	8.451	0.853052	0.17106	.	.	ENSG00000180016	ENST00000322608	T	0.00107	8.72	4.69	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.088454	0.49916	D	0.000136	T	0.00241	0.0007	M	0.77313	2.365	0.29456	N	0.858114	B	0.27625	0.183	B	0.37387	0.248	T	0.02661	-1.1127	10	0.52906	T	0.07	.	7.6329	0.28249	0.0:0.6473:0.0:0.3527	.	270	P30953	OR1E1_HUMAN	N	270	ENSP00000313384:K270N	ENSP00000313384:K270N	K	-	3	2	OR1E1	3247645	0.000000	0.05858	0.997000	0.53966	0.038000	0.13279	-0.020000	0.12525	0.602000	0.29896	0.591000	0.81541	AAG		0.493	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553		A	3300895	C	A	3300895	3	1	61	1	0	0	0	0	1	0	0	0	10985	680	24	2	138	2	OR1E1	17	3300895	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	305024	3300895	77894315	9973	17958										
ASPA	443	broad.mit.edu	37	chr17	3385003	3385003	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctatgacattatttttgacCttcacaacaccacctctaac	2	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3385003C>A	ENST00000263080.2	+	2	501	c.343C>A	c.(343-345)Ctt>Att	p.L115I	ASPA_ENST00000456349.2_Missense_Mutation_p.L115I|SPATA22_ENST00000541913.1_Intron	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	115					aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)	p.L115I(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	TATTTTTGACCTTCACAACAC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											83	77	79					17																	3385003		2203	4300	6503	3331753	SO:0001583	missense	443			S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"aminoacylase 2", "Canavan disease"	608034	"aspartoacylase (aminoacylase 2, Canavan disease)"			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.343C>A	17.37:g.3385003C>A	ENSP00000263080:p.Leu115Ile		3331753		Missense_Mutation	SNP	ENST00000263080.2	37	CCDS11028.1	.	.	.	.	.	.	.	.	.	.	c	22.1	4.249553	0.80024	.	.	ENSG00000108381	ENST00000456349;ENST00000263080	D;D	0.99494	-6.01;-6.01	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.99468	0.9811	M	0.74881	2.28	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.99218	1.0878	10	0.48119	T	0.1	-24.7928	19.0107	0.92871	0.0:1.0:0.0:0.0	.	115	P45381	ACY2_HUMAN	I	115	ENSP00000409976:L115I;ENSP00000263080:L115I	ENSP00000263080:L115I	L	+	1	0	ASPA	3331753	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.742000	0.68646	2.812000	0.96745	0.557000	0.71058	CTT		0.338	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049		A	3385003	C	A	3385003	3	1	61	1	0	0	0	0	1	0	0	0	1051	681	24	2	349	2	ASPA	17	3385003	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84108	3385003	77810207	9974	17959										
ASPA	443	broad.mit.edu	37	chr17	3402365	3402365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctcaatgcaaaaagtattCgctgctgtttacattagaaa	7	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3402365C>T	ENST00000263080.2	+	6	1083	c.925C>T	c.(925-927)Cgc>Tgc	p.R309C	ASPA_ENST00000456349.2_Missense_Mutation_p.R309C|SPATA22_ENST00000541913.1_Intron	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	309					aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)	p.R309C(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	AAAAAGTATTCGCTGCTGTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											92	78	83					17																	3402365		2203	4300	6503	3349115	SO:0001583	missense	443			S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"aminoacylase 2", "Canavan disease"	608034	"aspartoacylase (aminoacylase 2, Canavan disease)"			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.925C>T	17.37:g.3402365C>T	ENSP00000263080:p.Arg309Cys		3349115		Missense_Mutation	SNP	ENST00000263080.2	37	CCDS11028.1	.	.	.	.	.	.	.	.	.	.	c	11.49	1.655737	0.29425	.	.	ENSG00000108381	ENST00000456349;ENST00000263080	D;D	0.95788	-3.81;-3.81	5.76	-1.88	0.07713	.	0.453783	0.26096	N	0.026367	D	0.85234	0.5650	N	0.08118	0	0.41628	D	0.989003	B	0.09022	0.002	B	0.01281	0.0	T	0.71258	-0.4646	10	0.72032	D	0.01	3.0086	4.7804	0.13199	0.215:0.4162:0.0:0.3689	.	309	P45381	ACY2_HUMAN	C	309	ENSP00000409976:R309C;ENSP00000263080:R309C	ENSP00000263080:R309C	R	+	1	0	ASPA	3349115	0.807000	0.29009	0.814000	0.32528	0.289000	0.27227	0.647000	0.24812	-0.028000	0.13850	-0.229000	0.12294	CGC		0.408	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049		T	3402365	C	T	3402365	3	4	61	1	0	0	0	0	1	0	0	0	1051	884	31	1	947	1	ASPA	17	3402365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17362	3402365	77792845	9975	17960										
TRPV1	7442	broad.mit.edu	37	chr17	3475529	3475529	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctcttctccgtgtccagGatggtgatggctctctgcag	12	11	3	1	rs548898102	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3475529G>A	ENST00000571088.1	-	14	2331	c.2118C>T	c.(2116-2118)atC>atT	p.I706I	TRPV1_ENST00000310522.5_Silent_p.I646I|TRPV1_ENST00000399759.3_Silent_p.I706I|SHPK_ENST00000572705.1_Silent_p.I706I|TRPV1_ENST00000576351.1_Silent_p.I696I|TRPV1_ENST00000174621.6_Silent_p.I704I|TRPV1_ENST00000399756.4_Silent_p.I706I|TRPV1_ENST00000425167.2_Silent_p.I717I	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	706	AD. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)	p.I717I(1)|p.I706I(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	CCGTGTCCAGGATGGTGATGG	0.617																																					Melanoma(38;962 1762 15789)											2	Substitution - coding silent(2)	large_intestine(2)	17											51	54	53					17																	3475529		2092	4232	6324	3422279	SO:0001819	synonymous_variant	7442			AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.2118C>T	17.37:g.3475529G>A			3422279	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																				0.617	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		A	3475529	G	A	3475529	2	1	61	1	0	0	0	0	0	0	0	1	16635	1164	41	3		3	TRPV1	17	3475529	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73164	3475529	77719681	9976	17961										
P2RX5	5026	broad.mit.edu	37	chr17	3592888	3592888	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggccaaagtggcatgatttCaggaaagatctgtccttgac	12	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3592888C>T	ENST00000225328.5	-	7	1049	c.651G>A	c.(649-651)ctG>ctA	p.L217L	P2RX5_ENST00000345901.3_Silent_p.L193L|P2RX5_ENST00000550772.1_Intron|P2RX5-TAX1BP3_ENST00000550383.1_Silent_p.L217L|P2RX5_ENST00000552050.1_Silent_p.L157L|P2RX5_ENST00000435558.1_Silent_p.L217L|P2RX5_ENST00000551178.1_Silent_p.L192L|P2RX5_ENST00000547178.1_Silent_p.L216L|P2RX5_ENST00000552276.1_Silent_p.L216L	NM_001204519.1|NM_002561.3	NP_001191448.1|NP_002552.2	Q93086	P2RX5_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 5	217					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transport (GO:0006810)	integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|ion channel activity (GO:0005216)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)	p.L217L(1)		endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						GGCATGATTTCAGGAAAGATC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	17											240	185	204					17																	3592888		2203	4300	6503	3539637	SO:0001819	synonymous_variant	5026			AF016709	CCDS11034.1, CCDS11035.1, CCDS56014.1, CCDS56015.1	17p13.3	2012-01-17			ENSG00000083454	ENSG00000083454		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8536	protein-coding gene	gene with protein product		602836				9414125	Standard	NM_002561		Approved	P2X5	uc002fwi.3	Q93086	OTTHUMG00000090700	ENST00000225328.5:c.651G>A	17.37:g.3592888C>T			3539637	G5E981|O43450|O75540|Q308M5|Q59F38|Q8IXW4|Q93087|Q9NZV0	Silent	SNP	ENST00000225328.5	37	CCDS11034.1																																																																																				0.572	P2RX5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207388.3	NM_002561, NM_175080, NM_175081		T	3592888	C	T	3592888	2	4	61	1	0	0	0	0	0	0	0	1	11374	813	29	3		3	P2RX5	17	3592888	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117359	3592888	77602322	9977	17962										
ITGAE	3682	broad.mit.edu	37	chr17	3631413	3631413	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttacatggaagaggaattCtttgtggtgagaaagcccct	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3631413C>A	ENST00000263087.4	-	25	3060	c.2962G>T	c.(2962-2964)Gaa>Taa	p.E988*	ITGAE_ENST00000571185.1_5'UTR|CTD-3195I5.4_ENST00000575043.1_RNA	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	988					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.E988*(1)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		AAGAGGAATTCTTTGTGGTGA	0.423																																					NSCLC(182;635 2928 8995 38788)											1	Substitution - Nonsense(1)	large_intestine(1)	17											134	130	132					17																	3631413		2203	4300	6503	3578162	SO:0001587	stop_gained	3682			L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.2962G>T	17.37:g.3631413C>A	ENSP00000263087:p.Glu988*		3578162	Q17RS6|Q9NZU9	Nonsense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	c	37	5.986375	0.97173	.	.	ENSG00000083457	ENST00000263087	.	.	.	5.45	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	13.8388	0.63426	0.0:0.8466:0.1534:0.0	.	.	.	.	X	988	.	ENSP00000263087:E988X	E	-	1	0	ITGAE	3578162	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	2.773000	0.47686	1.464000	0.47987	-0.121000	0.15023	GAA		0.423	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		A	3631413	C	A	3631413	4	1	61	1	0	0	0	0	0	1	0	0	7906	922	32	2	605	2	ITGAE	17	3631413	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38525	3631413	77563797	9978	17963										
ITGAE	3682	broad.mit.edu	37	chr17	3649210	3649210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgtgaagttgagaagtgCctcgcggaggcctgggaatg	17	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3649210C>T	ENST00000263087.4	-	18	2265	c.2167G>A	c.(2167-2169)Gca>Aca	p.A723T		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	723					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.A723T(1)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		TTGAGAAGTGCCTCGCGGAGG	0.612																																					NSCLC(182;635 2928 8995 38788)											1	Substitution - Missense(1)	large_intestine(1)	17											116	97	104					17																	3649210		2203	4300	6503	3595959	SO:0001583	missense	3682			L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.2167G>A	17.37:g.3649210C>T	ENSP00000263087:p.Ala723Thr		3595959	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	C	2.926	-0.222220	0.06061	.	.	ENSG00000083457	ENST00000263087	T	0.45276	0.9	4.33	0.703	0.18116	Integrin alpha-2 (1);	.	.	.	.	T	0.08670	0.0215	N	0.00368	-1.59	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.32745	-0.9895	9	0.06099	T	0.92	.	3.1304	0.06421	0.1774:0.2106:0.0:0.612	.	723	P38570	ITAE_HUMAN	T	723	ENSP00000263087:A723T	ENSP00000263087:A723T	A	-	1	0	ITGAE	3595959	0.002000	0.14202	0.000000	0.03702	0.063000	0.16089	1.226000	0.32563	-0.017000	0.14103	-0.499000	0.04595	GCA		0.612	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3649210	C	T	3649210	3	4	61	1	0	0	0	0	1	0	0	0	7906	739	26	3	1428	3	ITGAE	17	3649210	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17797	3649210	77546000	9979	17964										
ATP2A3	489	broad.mit.edu	37	chr17	3844927	3844927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggactgagctacagcgctCgatcacactctcaggagccc	11	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3844927C>T	ENST00000352011.3	-	13	1621	c.1567G>A	c.(1567-1569)Gag>Aag	p.E523K	ATP2A3_ENST00000397041.3_Missense_Mutation_p.E523K|ATP2A3_ENST00000397035.3_Missense_Mutation_p.E523K|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Missense_Mutation_p.E523K|ATP2A3_ENST00000397043.3_Missense_Mutation_p.E523K|ATP2A3_ENST00000359983.3_Missense_Mutation_p.E523K			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	523					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.E523K(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CTACAGCGCTCGATCACACTC	0.622																																					GBM(32;29 774 15719 37967)											1	Substitution - Missense(1)	large_intestine(1)	17											31	35	34					17																	3844927		2203	4300	6503	3791676	SO:0001583	missense	489				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"ATPases / P-type"	813	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 3", "calcium pump 3"	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1567G>A	17.37:g.3844927C>T	ENSP00000301387:p.Glu523Lys		3791676	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	37	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946679	0.53186	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	3.8	3.8	0.43715	ATPase, cation-transporting, domain N (1);ATPase, P-type, cytoplasmic domain N (1);	0.061459	0.64402	D	0.000004	T	0.79040	0.4379	L	0.28740	0.885	0.80722	D	1	D;P;B;P;P;P	0.59767	0.986;0.526;0.381;0.719;0.533;0.719	P;B;B;B;B;B	0.47705	0.555;0.091;0.103;0.131;0.131;0.131	T	0.82080	-0.0634	10	0.54805	T	0.06	.	15.9154	0.79512	0.0:1.0:0.0:0.0	.	523;523;523;523;523;523	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	K	523	ENSP00000380236:E523K;ENSP00000301387:E523K;ENSP00000353072:E523K;ENSP00000380234:E523K;ENSP00000312577:E523K;ENSP00000380229:E523K	ENSP00000312577:E523K	E	-	1	0	ATP2A3	3791676	1.000000	0.71417	0.969000	0.41365	0.171000	0.22731	7.604000	0.82830	2.413000	0.81919	0.561000	0.74099	GAG		0.622	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		T	3844927	C	T	3844927	3	4	61	1	0	0	0	0	1	0	0	0	1139	893	31	1	1679	1	ATP2A3	17	3844927	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	195717	3844927	77350283	9980	17965										
ATP2A3	489	broad.mit.edu	37	chr17	3846739	3846739	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcctgcaggtcggtgtcGaacacgttcatcttctccac	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3846739G>A	ENST00000352011.3	-	11	1419	c.1365C>T	c.(1363-1365)ttC>ttT	p.F455F	ATP2A3_ENST00000397041.3_Silent_p.F455F|ATP2A3_ENST00000397035.3_Silent_p.F455F|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Silent_p.F455F|ATP2A3_ENST00000397043.3_Silent_p.F455F|ATP2A3_ENST00000359983.3_Silent_p.F455F			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	455					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.F455F(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GGTCGGTGTCGAACACGTTCA	0.647																																					GBM(32;29 774 15719 37967)											1	Substitution - coding silent(1)	large_intestine(1)	17											154	140	144					17																	3846739		2203	4300	6503	3793488	SO:0001819	synonymous_variant	489				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"ATPases / P-type"	813	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 3", "calcium pump 3"	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1365C>T	17.37:g.3846739G>A			3793488	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																				0.647	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		A	3846739	G	A	3846739	2	1	61	1	0	0	0	0	0	0	0	1	1139	1049	37	1		1	ATP2A3	17	3846739	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1812	3846739	77348471	9981	17966										
ZZEF1	23140	broad.mit.edu	37	chr17	3923012	3923012	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctttttcatctgcagttCgtatatggcccggagaatgt	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3923012C>T	ENST00000381638.2	-	46	7580	c.7456G>A	c.(7456-7458)Gaa>Aaa	p.E2486K		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2486							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.E2486K(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ATCTGCAGTTCGTATATGGCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											126	111	116					17																	3923012		2203	4300	6503	3869761	SO:0001583	missense	23140			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.7456G>A	17.37:g.3923012C>T	ENSP00000371051:p.Glu2486Lys		3869761	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	36	5.773854	0.96922	.	.	ENSG00000074755	ENST00000381638	T	0.47177	0.85	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.60444	0.2269	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.63157	-0.6700	10	0.87932	D	0	-18.8227	19.7617	0.96321	0.0:1.0:0.0:0.0	.	2486	O43149	ZZEF1_HUMAN	K	2486	ENSP00000371051:E2486K	ENSP00000371051:E2486K	E	-	1	0	ZZEF1	3869761	1.000000	0.71417	0.905000	0.35620	0.977000	0.68977	7.290000	0.78711	2.671000	0.90904	0.655000	0.94253	GAA		0.502	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3923012	C	T	3923012	3	4	61	1	0	0	0	0	1	0	0	0	18294	893	31	1	1469	1	ZZEF1	17	3923012	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76273	3923012	77272198	9982	17967										
ZZEF1	23140	broad.mit.edu	37	chr17	3977452	3977452	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgcacttacggcgcacaGacttgagcgccatgcactgg	12	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:3977452G>T	ENST00000381638.2	-	24	3801	c.3677C>A	c.(3676-3678)tCt>tAt	p.S1226Y	ZZEF1_ENST00000574474.1_5'Flank	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1226							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.S1226Y(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ACGGCGCACAGACTTGAGCGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	100	101					17																	3977452		2203	4300	6503	3924201	SO:0001583	missense	23140			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.3677C>A	17.37:g.3977452G>T	ENSP00000371051:p.Ser1226Tyr		3924201	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495699	0.64186	.	.	ENSG00000074755	ENST00000381638	T	0.25579	1.79	5.87	4.87	0.63330	.	0.105578	0.64402	D	0.000002	T	0.31670	0.0804	L	0.57536	1.79	0.45621	D	0.998554	D	0.53462	0.96	P	0.47376	0.545	T	0.04693	-1.0933	10	0.87932	D	0	-12.973	11.2221	0.48862	0.0:0.1367:0.7214:0.1419	.	1226	O43149	ZZEF1_HUMAN	Y	1226	ENSP00000371051:S1226Y	ENSP00000371051:S1226Y	S	-	2	0	ZZEF1	3924201	1.000000	0.71417	0.957000	0.39632	0.386000	0.30323	8.699000	0.91316	2.780000	0.95670	0.655000	0.94253	TCT		0.587	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3977452	G	T	3977452	3	4	61	1	0	0	0	0	1	0	0	0	18294	942	33	2	5336	2	ZZEF1	17	3977452	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54440	3977452	77217758	9983	17968										
ANKFY1	51479	broad.mit.edu	37	chr17	4088314	4088314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggttggccaggccatgccGacacgctgtgtgcaacgggg	17	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4088314G>A	ENST00000341657.4	-	12	1533	c.1498C>T	c.(1498-1500)Cgg>Tgg	p.R500W	ANKFY1_ENST00000574367.1_Missense_Mutation_p.R500W|CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000570535.1_Missense_Mutation_p.R542W|ANKFY1_ENST00000573722.1_5'UTR|Y_RNA_ENST00000516003.1_RNA	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	500					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.R500W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						AGGCCATGCCGACACGCTGTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											40	45	44					17																	4088314		2131	4252	6383	4035063	SO:0001583	missense	51479			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1498C>T	17.37:g.4088314G>A	ENSP00000343362:p.Arg500Trp		4035063	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	26.0	4.694601	0.88830	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	T	0.67345	-0.26	5.86	4.88	0.63580	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.71617	0.3361	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69142	0.95;0.962;0.957;0.941	T	0.74604	-0.3610	10	0.62326	D	0.03	-24.8339	13.8192	0.63309	0.0:0.0:0.7073:0.2927	.	441;500;500;542	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	W	500;441	ENSP00000343362:R500W	ENSP00000343362:R500W	R	-	1	2	ANKFY1	4035063	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.735000	0.62051	1.452000	0.47756	0.655000	0.94253	CGG		0.582	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		A	4088314	G	A	4088314	3	1	61	1	0	0	0	0	1	0	0	0	626	1057	37	1	2070	1	ANKFY1	17	4088314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110862	4088314	77106896	9984	17969										
ANKFY1	51479	broad.mit.edu	37	chr17	4139184	4139184	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaacctttatcttcagatCgctgatgaagaaaaagatcc	6	11	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4139184C>T	ENST00000341657.4	-	3	240	c.205G>A	c.(205-207)Gat>Aat	p.D69N	ANKFY1_ENST00000574367.1_Splice_Site_p.D69N|ANKFY1_ENST00000570535.1_Splice_Site_p.D111N|ANKFY1_ENST00000433651.1_Splice_Site_p.D69N	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	69	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.D69N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						ATCTTCAGATCGCTGATGAAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											116	113	114					17																	4139184		1887	4111	5998	4085933	SO:0001630	splice_region_variant	51479			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.204-1G>A	17.37:g.4139184C>T			4085933	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	C	29.6	5.018104	0.93404	.	.	ENSG00000185722	ENST00000341657;ENST00000433651	T;T	0.69175	-0.38;-0.38	5.19	5.19	0.71726	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.88254	0.6387	H	0.96861	3.895	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.999;0.997;0.997	D	0.92164	0.5738	10	0.72032	D	0.01	-22.1226	17.7846	0.88533	0.0:1.0:0.0:0.0	.	69;69;69;69;111	B4DZ21;Q9P2R3-3;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;.;ANFY1_HUMAN;.;.	N	69	ENSP00000343362:D69N;ENSP00000416005:D69N	ENSP00000343362:D69N	D	-	1	0	ANKFY1	4085933	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	5.857000	0.69525	2.431000	0.82371	0.558000	0.71614	GAT		0.418	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	Missense_Mutation	T	4139184	C	T	4139184	5	4	61	1	0	0	0	0	0	0	1	0	626	898	31	1	3491	1	ANKFY1	17	4139184	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50870	4139184	77056026	9985	17970										
ARRB2	409	broad.mit.edu	37	chr17	4621594	4621594	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctcaatgtaaatgtccaCgtcaccaacaactccaccaa	3	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4621594C>T	ENST00000269260.2	+	9	893	c.660C>T	c.(658-660)caC>caT	p.H220H	ARRB2_ENST00000381488.6_Silent_p.H205H|ARRB2_ENST00000572457.1_Silent_p.H28H|ARRB2_ENST00000575877.1_Silent_p.H220H|ARRB2_ENST00000574954.1_Silent_p.H28H|ARRB2_ENST00000571206.1_Silent_p.H28H|ARRB2_ENST00000412477.3_Silent_p.H241H|ARRB2_ENST00000346341.2_Silent_p.H205H	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN	arrestin, beta 2	220					adult walking behavior (GO:0007628)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell chemotaxis (GO:0060326)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|Notch signaling pathway (GO:0007219)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|receptor internalization (GO:0031623)|regulation of androgen receptor signaling pathway (GO:0060765)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	angiotensin receptor binding (GO:0031701)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|ubiquitin protein ligase binding (GO:0031625)	p.H220H(1)		large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						TAAATGTCCACGTCACCAACA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	17											97	91	93					17																	4621594		2203	4300	6503	4568343	SO:0001819	synonymous_variant	409				CCDS11050.1, CCDS11051.1, CCDS58504.1, CCDS58505.1, CCDS59276.1	17p13	2008-12-11			ENSG00000141480	ENSG00000141480			712	protein-coding gene	gene with protein product	"arrestin 3"	107941		ARR2		7695743	Standard	NM_001257329		Approved	BARR2, DKFZp686L0365	uc002fyl.3	P32121	OTTHUMG00000090759	ENST00000269260.2:c.660C>T	17.37:g.4621594C>T			4568343	B4DLW0|B5B0C0|B7WPL3|D3DTK2|H0Y688|Q0Z8D3|Q2PP19|Q6ICT3|Q8N7Y2|Q9UEQ6	Silent	SNP	ENST00000269260.2	37	CCDS11050.1																																																																																				0.532	ARRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439552.1	NM_004313		T	4621594	C	T	4621594	2	4	61	1	0	0	0	0	0	0	0	1	982	535	19	1		1	ARRB2	17	4621594	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	482410	4621594	76573616	9986	17971										
CXCL16	84225	broad.mit.edu	37	chr17	4642635	4642635	+	5'Flank	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccgcaagtcccgtcccatCtcggggctccgcggactctg	13	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4642635C>A	ENST00000433935.1	+	0	0				ZMYND15_ENST00000269289.6_5'Flank|ZMYND15_ENST00000592813.1_5'Flank|CXCL16_ENST00000574412.1_Missense_Mutation_p.E19D|ZMYND15_ENST00000573751.2_5'Flank|CXCL16_ENST00000576153.1_5'Flank|CXCL16_ENST00000293778.6_Missense_Mutation_p.E19D	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15						negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.E19D(2)		endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						CCCGTCCCATCTCGGGGCTCC	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	17											23	28	26					17																	4642635		2203	4299	6502	4589384	SO:0001631	upstream_gene_variant	58191			AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"Zinc fingers, MYND-type"	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760		17.37:g.4642635C>A	Exception_encountered		4589384	B4DXY5|I3L296	Missense_Mutation	SNP	ENST00000433935.1	37	CCDS45584.1	.	.	.	.	.	.	.	.	.	.	C	9.309	1.055175	0.19907	.	.	ENSG00000161921	ENST00000293778	T	0.32023	1.47	3.69	1.65	0.23941	.	1.590230	0.04483	U	0.378049	T	0.27697	0.0681	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.38286	-0.9668	7	0.22706	T	0.39	-0.3861	12.188	0.54250	0.0:0.6721:0.3279:0.0	.	.	.	.	D	19	ENSP00000293778:E19D	ENSP00000293778:E19D	E	-	3	2	CXCL16	4589384	0.124000	0.22315	0.225000	0.23894	0.007000	0.05969	0.031000	0.13710	0.164000	0.19529	-1.358000	0.01219	GAG		0.687	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		A	4642635	C	A	4642635	1	1	61	0	1	0	0	0	0	0	0	0	4089	912	32	2		2	CXCL16	17	4642635	5'Flank	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21041	4642635	76552575	9987	17972										
ZMYND15	84225	broad.mit.edu	37	chr17	4644894	4644894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaggctgcccccctgcacGtttcctgtctcttacttgtg	9	15	1	1	rs200227685		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4644894G>A	ENST00000433935.1	+	3	667	c.610G>A	c.(610-612)Gtt>Att	p.V204I	ZMYND15_ENST00000269289.6_Missense_Mutation_p.V204I|ZMYND15_ENST00000592813.1_Missense_Mutation_p.V204I|CXCL16_ENST00000574412.1_5'Flank|ZMYND15_ENST00000573751.2_Missense_Mutation_p.V204I|CXCL16_ENST00000293778.6_5'Flank	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	204					negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.V204I(1)		endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						CCCCCTGCACGTTTCCTGTCT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	157	165	162		610,610	3.2	1	17		162	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ZMYND15	NM_001136046.1,NM_032265.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	204/743,204/704	4644894	1,13005	2203	4300	6503	4591643	SO:0001583	missense	84225			AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"Zinc fingers, MYND-type"	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760	ENST00000433935.1:c.610G>A	17.37:g.4644894G>A	ENSP00000391742:p.Val204Ile		4591643	B4DXY5|I3L296	Missense_Mutation	SNP	ENST00000433935.1	37	CCDS45584.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846815	0.32606	0.0	1.16E-4	ENSG00000141497	ENST00000433935;ENST00000269289	T;T	0.50001	0.78;0.76	5.15	3.17	0.36434	.	0.384446	0.21929	N	0.067049	T	0.28001	0.0690	N	0.14661	0.345	0.18873	N	0.999983	B;B	0.21753	0.06;0.013	B;B	0.13407	0.009;0.001	T	0.20638	-1.0269	10	0.72032	D	0.01	-7.5379	7.5	0.27511	0.0:0.5915:0.3223:0.0862	.	204;204	B4DXY5;Q9H091	.;ZMY15_HUMAN	I	204	ENSP00000391742:V204I;ENSP00000269289:V204I	ENSP00000269289:V204I	V	+	1	0	ZMYND15	4591643	0.982000	0.34865	1.000000	0.80357	0.897000	0.52465	0.656000	0.24948	0.763000	0.33175	-0.226000	0.12346	GTT		0.562	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		A	4644894	G	A	4644894	3	1	61	1	0	0	0	0	1	0	0	0	17747	1145	40	1	616	1	ZMYND15	17	4644894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2259	4644894	76550316	9988	17973										
CHRNE	1145	broad.mit.edu	37	chr17	4806026	4806026	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgaagagatggtgataaaGacgcagttcctcgttcttcc	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4806026G>T	ENST00000293780.4	-	2	89	c.79C>A	c.(79-81)Ctt>Att	p.L27I	CHRNE_ENST00000575637.1_5'Flank|C17orf107_ENST00000381365.3_3'UTR	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	27					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)	p.L27I(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	TGGTGATAAAGACGCAGTTCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											146	150	148					17																	4806026		2203	4300	6503	4746805	SO:0001583	missense	1145			X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1966	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, epsilon (muscle)"	100725	"cholinergic receptor, nicotinic, epsilon"			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.79C>A	17.37:g.4806026G>T	ENSP00000293780:p.Leu27Ile		4746805	D3DTK6	Missense_Mutation	SNP	ENST00000293780.4	37	CCDS11058.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.755321	0.69648	.	.	ENSG00000108556	ENST00000293780	D	0.83506	-1.73	5.11	5.11	0.69529	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.64402	D	0.000001	D	0.92773	0.7702	M	0.92459	3.31	0.80722	D	1	D	0.55800	0.973	D	0.91635	0.999	D	0.93916	0.7201	10	0.87932	D	0	.	13.9116	0.63871	0.0:0.0:1.0:0.0	.	27	Q04844	ACHE_HUMAN	I	27	ENSP00000293780:L27I	ENSP00000293780:L27I	L	-	1	0	CHRNE	4746805	0.666000	0.27475	0.388000	0.26195	0.619000	0.37552	1.071000	0.30666	2.652000	0.90054	0.655000	0.94253	CTT		0.567	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3			T	4806026	G	T	4806026	3	4	61	1	0	0	0	0	1	0	0	0	3401	942	33	2	1446	2	CHRNE	17	4806026	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161132	4806026	76389184	9989	17974										
ENO3	2027	broad.mit.edu	37	chr17	4856137	4856137	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcttccacgggtatctatGaggctctggaactaagagac	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4856137G>T	ENST00000323997.6	+	3	265	c.133G>T	c.(133-135)Gag>Tag	p.E45*	ENO3_ENST00000519584.1_Nonsense_Mutation_p.E45*|ENO3_ENST00000518175.1_Nonsense_Mutation_p.E45*	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	45					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)	p.E45*(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						GGGTATCTATGAGGCTCTGGA	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											31	32	32					17																	4856137		2203	4300	6503	4796883	SO:0001587	stop_gained	2027			X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"enolase 3, (beta, muscle)"				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.133G>T	17.37:g.4856137G>T	ENSP00000324105:p.Glu45*		4796883	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Nonsense_Mutation	SNP	ENST00000323997.6	37	CCDS11062.1	.	.	.	.	.	.	.	.	.	.	G	33	5.234619	0.95207	.	.	ENSG00000108515	ENST00000522798;ENST00000519602;ENST00000323997;ENST00000522249;ENST00000519584;ENST00000518175	.	.	.	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.8053	15.2036	0.73159	0.0:0.0:1.0:0.0	.	.	.	.	X	45	.	ENSP00000324105:E45X	E	+	1	0	ENO3	4796883	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.223000	0.95203	2.460000	0.83146	0.655000	0.94253	GAG		0.607	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2			T	4856137	G	T	4856137	4	4	61	1	0	0	0	0	0	1	0	0	5136	1291	45	2	139	2	ENO3	17	4856137	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50111	4856137	76339073	9990	17975										
ZFP3	124961	broad.mit.edu	37	chr17	4995232	4995232	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagcctcatacatgtaaaGaatgtgggaaagcctttaat	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:4995232G>T	ENST00000318833.3	+	2	769	c.433G>T	c.(433-435)Gaa>Taa	p.E145*		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E145*(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						TACATGTAAAGAATGTGGGAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											57	59	58					17																	4995232		2203	4300	6503	4935956	SO:0001587	stop_gained	124961			BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"Zinc fingers, C2H2-type"	12861	protein-coding gene	gene with protein product		194480	"zinc finger protein homologous to Zfp-3 in mouse", "zinc finger protein 3 homolog (mouse)"				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.433G>T	17.37:g.4995232G>T	ENSP00000320347:p.Glu145*		4935956	A5PLL4	Nonsense_Mutation	SNP	ENST00000318833.3	37	CCDS11067.1	.	.	.	.	.	.	.	.	.	.	G	36	5.767061	0.96914	.	.	ENSG00000180787	ENST00000318833	.	.	.	4.07	4.07	0.47477	.	0.000000	0.33813	N	0.004540	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.9202	14.6278	0.68635	0.0:0.0:1.0:0.0	.	.	.	.	X	145	.	ENSP00000320347:E145X	E	+	1	0	ZFP3	4935956	0.202000	0.23423	1.000000	0.80357	0.956000	0.61745	1.387000	0.34430	2.586000	0.87340	0.551000	0.68910	GAA		0.378	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018		T	4995232	G	T	4995232	4	4	61	1	0	0	0	0	0	1	0	0	17682	943	33	2	435	2	ZFP3	17	4995232	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139095	4995232	76199978	9991	17976										
USP6	9098	broad.mit.edu	37	chr17	5033955	5033955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgttggaatcaacagcaGcattgatcgttttggcattt	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5033955G>A	ENST00000574788.1	+	11	2361	c.131G>A	c.(130-132)aGc>aAc	p.S44N	USP6_ENST00000250066.6_Missense_Mutation_p.S44N|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000332776.4_Missense_Mutation_p.S44N|USP6_ENST00000572429.1_Intron			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	44					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.S44N(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ATCAACAGCAGCATTGATCGT	0.552			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	2	Substitution - Missense(2)	large_intestine(2)	17											173	188	183					17																	5033955		2203	4300	6503	4974679	SO:0001583	missense	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.131G>A	17.37:g.5033955G>A	ENSP00000460380:p.Ser44Asn		4974679	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.187|3.187	-0.166597|-0.166597	0.06461|0.06461	.|.	.|.	ENSG00000129204|ENSG00000129204	ENST00000396805|ENST00000332776;ENST00000250066	.|T;T	.|0.27256	.|1.68;1.68	0.0465|0.0465	0.0465|0.0465	0.14256|0.14256	.|.	.|0.058261	.|0.64402	.|D	.|0.000002	T|T	0.04137|0.04137	0.0115|0.0115	N|N	0.00823|0.00823	-1.155|-1.155	0.80722|0.80722	D|D	1|1	.|P;B	.|0.38110	.|0.618;0.347	.|B;B	.|0.23018	.|0.043;0.03	T|T	0.45862|0.45862	-0.9232|-0.9232	5|9	0.66056|0.02654	D|T	0.02|1	.|.	.|.	.|.	.|.	.|.	.|44;44	.|B9A6N0;P35125	.|.;UBP6_HUMAN	T|N	43|44	.|ENSP00000328010:S44N;ENSP00000250066:S44N	ENSP00000380022:A43T|ENSP00000250066:S44N	A|S	+|+	1|2	0|0	USP6|USP6	4974679|4974679	0.965000|0.965000	0.33210|0.33210	0.015000|0.015000	0.15790|0.15790	0.015000|0.015000	0.08874|0.08874	-0.093000|-0.093000	0.11111|0.11111	0.132000|0.132000	0.18615|0.18615	0.134000|0.134000	0.15878|0.15878	GCA|AGC		0.552	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		A	5033955	G	A	5033955	3	1	61	1	0	0	0	0	1	0	0	0	17126	971	34	3	137	3	USP6	17	5033955	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38723	5033955	76161255	9992	17977										
USP6	9098	broad.mit.edu	37	chr17	5041528	5041528	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcatcttagggcctctacGaagaaactaacaaggaagca	9	9	2	1	rs148093961		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5041528G>A	ENST00000574788.1	+	21	3268	c.1038G>A	c.(1036-1038)acG>acA	p.T346T	USP6_ENST00000250066.6_Silent_p.T346T|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000332776.4_Silent_p.T346T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	346					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.T346T(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GGGCCTCTACGAAGAAACTAA	0.587			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	2	Substitution - coding silent(2)	large_intestine(2)	17						G		0,4406		0,0,2203	127	130	129		1038	0.9	0.5	17	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	USP6	NM_004505.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		346/1407	5041528	1,13005	2203	4300	6503	4982252	SO:0001819	synonymous_variant	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1038G>A	17.37:g.5041528G>A			4982252	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																				0.587	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		A	5041528	G	A	5041528	2	1	61	1	0	0	0	0	0	0	0	1	17126	1045	37	1		1	USP6	17	5041528	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7573	5041528	76153682	9993	17978										
USP6	9098	broad.mit.edu	37	chr17	5073800	5073800	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcttcatcaagaaaaagtGgaaccagctgtccctccagc	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5073800G>T	ENST00000574788.1	+	36	5774	c.3544G>T	c.(3544-3546)Gga>Tga	p.G1182*	USP6_ENST00000250066.6_Nonsense_Mutation_p.G1182*|USP6_ENST00000304328.5_Nonsense_Mutation_p.G865*|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1182	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.G1182*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AAGAAAAAGTGGAACCAGCTG	0.512			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	1	Substitution - Nonsense(1)	large_intestine(1)	17											16	19	18					17																	5073800		2082	4180	6262	5014524	SO:0001587	stop_gained	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3544G>T	17.37:g.5073800G>T	ENSP00000460380:p.Gly1182*		5014524	Q15634|Q86WP6|Q8IWT4	Nonsense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	G	50	17.028295	0.99877	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	.	.	.	2.35	1.34	0.21922	.	0.394655	0.29760	N	0.011264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	4.7744	0.13171	0.3212:0.0:0.6788:0.0	.	.	.	.	X	1182;865	.	ENSP00000250066:G1182X	G	+	1	0	USP6	5014524	1.000000	0.71417	1.000000	0.80357	0.175000	0.22909	2.191000	0.42640	0.323000	0.23307	-1.207000	0.01640	GGA		0.512	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5073800	G	T	5073800	4	4	61	1	0	0	0	0	0	1	0	0	17126	1349	47	2	3650	2	USP6	17	5073800	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32272	5073800	76121410	9994	17979										
USP6	9098	broad.mit.edu	37	chr17	5073936	5073936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtaagaagaacttggatgCcagcaaagagaatggggctg	14	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5073936C>T	ENST00000574788.1	+	36	5910	c.3680C>T	c.(3679-3681)gCc>gTc	p.A1227V	USP6_ENST00000250066.6_Missense_Mutation_p.A1227V|USP6_ENST00000304328.5_Missense_Mutation_p.A910V|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1227	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.A1227V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AACTTGGATGCCAGCAAAGAG	0.582			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	1	Substitution - Missense(1)	large_intestine(1)	17											29	29	29					17																	5073936		2203	4300	6503	5014660	SO:0001583	missense	9098			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3680C>T	17.37:g.5073936C>T	ENSP00000460380:p.Ala1227Val		5014660	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348850	0.24426	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.15139	2.86;2.45	2.35	2.35	0.29111	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.390787	0.30293	N	0.009950	T	0.13841	0.0335	L	0.29908	0.895	0.24293	N	0.995156	B;P	0.36944	0.274;0.574	B;B	0.42462	0.173;0.388	T	0.09357	-1.0678	10	0.62326	D	0.03	.	6.3704	0.21479	0.2929:0.7071:0.0:0.0	.	910;1227	P35125-2;P35125	.;UBP6_HUMAN	V	1227;910	ENSP00000250066:A1227V;ENSP00000305473:A910V	ENSP00000250066:A1227V	A	+	2	0	USP6	5014660	0.988000	0.35896	1.000000	0.80357	0.227000	0.25037	0.593000	0.23999	1.313000	0.45069	0.184000	0.17185	GCC		0.582	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5073936	C	T	5073936	3	4	61	1	0	0	0	0	1	0	0	0	17126	739	26	3	3786	3	USP6	17	5073936	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136	5073936	76121274	9995	17980										
ZNF594	84622	broad.mit.edu	37	chr17	5086290	5086290	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgtgaattctatgatgtCtcagaaggtctgagctctga	10	8	4	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5086290C>A	ENST00000399604.4	-	1	1402	c.1262G>T	c.(1261-1263)aGa>aTa	p.R421I	ZNF594_ENST00000575779.1_Missense_Mutation_p.R421I			Q96JF6	ZN594_HUMAN	zinc finger protein 594	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R421I(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TCTATGATGTCTCAGAAGGTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	17											154	155	155					17																	5086290		2024	4220	6244	5027014	SO:0001583	missense	84622			AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1262G>T	17.37:g.5086290C>A	ENSP00000382513:p.Arg421Ile		5027014	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	8.415	0.844997	0.16963	.	.	ENSG00000180626	ENST00000399604;ENST00000389222	T	0.26223	1.75	1.97	-3.95	0.04118	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14356	0.0347	L	0.31926	0.97	0.09310	N	1	B	0.31625	0.332	B	0.32149	0.141	T	0.26849	-1.0091	9	0.21014	T	0.42	.	4.8977	0.13759	0.0:0.4567:0.3659:0.1774	.	421	Q96JF6	ZN594_HUMAN	I	421;16	ENSP00000382513:R421I	ENSP00000373874:R16I	R	-	2	0	ZNF594	5027014	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.357000	0.00128	-1.339000	0.02230	-0.499000	0.04595	AGA		0.403	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		A	5086290	C	A	5086290	3	1	61	1	0	0	0	0	1	0	0	0	18063	913	32	2	1165	2	ZNF594	17	5086290	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12354	5086290	76108920	9996	17981										
NUP88	4927	broad.mit.edu	37	chr17	5302881	5302881	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaaactcacctgatccaaGaaatttgtgaagtttatgaa	7	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5302881G>T	ENST00000573584.1	-	8	1791	c.1282C>A	c.(1282-1284)Ctt>Att	p.L428I		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	428					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.L428I(1)		endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CCTGATCCAAGAAATTTGTGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	17											74	70	71					17																	5302881		2203	4300	6503	5243605	SO:0001583	missense	4927			Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1282C>A	17.37:g.5302881G>T	ENSP00000458954:p.Leu428Ile		5243605	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022303	0.54683	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.75591	0.3870	L	0.59436	1.845	0.58432	D	0.999993	P;B;D	0.69078	0.476;0.288;0.997	B;B;D	0.85130	0.159;0.069;0.997	T	0.74420	-0.3671	9	0.39692	T	0.17	-0.711	16.987	0.86342	0.0:0.0:1.0:0.0	.	428;297;428	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	I	428;297	.	ENSP00000225696:L428I	L	-	1	0	NUP88	5243605	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.784000	0.75084	2.580000	0.87095	0.460000	0.39030	CTT		0.343	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		T	5302881	G	T	5302881	3	4	61	1	0	0	0	0	1	0	0	0	10802	942	33	2	983	2	NUP88	17	5302881	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216591	5302881	75892329	9997	17982										
RPAIN	84268	broad.mit.edu	37	chr17	5331502	5331502	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcactggaggaacagaaGaaaagtccagtcttctcatg	10	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5331502G>T	ENST00000381209.3	+	6	1171	c.601G>T	c.(601-603)Gaa>Taa	p.E201*	RPAIN_ENST00000381208.5_Intron|RPAIN_ENST00000327154.6_Intron|RPAIN_ENST00000405578.4_Nonsense_Mutation_p.E201*|CTC-524C5.2_ENST00000575890.1_RNA|RPAIN_ENST00000574003.1_3'UTR|RPAIN_ENST00000536255.2_Intron	NM_001033002.3	NP_001028174.2	Q86UA6	RIP_HUMAN	RPA interacting protein	201					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|protein import into nucleus (GO:0006606)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)	metal ion binding (GO:0046872)|protein complex binding (GO:0032403)	p.E201*(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)	6						AGGAACAGAAGAAAAGTCCAG	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											110	106	108					17																	5331502		2203	4300	6503	5272226	SO:0001587	stop_gained	84268			AY775314	CCDS32536.1, CCDS54075.1, CCDS54076.1, CCDS54077.1, CCDS54079.1	17p13.2	2014-02-12	2006-05-08			ENSG00000129197			28641	protein-coding gene	gene with protein product						16135809, 16008515	Standard	NM_001033002		Approved	MGC4189, RIP, hRIP	uc010vsz.1	Q86UA6		ENST00000381209.3:c.601G>T	17.37:g.5331502G>T	ENSP00000370606:p.Glu201*		5272226	B4DI36|B4DTX7|E9PES3|J3KNH8|Q4G2Y0|Q4G2Y5|Q4G2Y8|Q6B4V9|Q6B4W0|Q6B4W1|Q6B4W4|Q86X49|Q9BT00	Nonsense_Mutation	SNP	ENST00000381209.3	37	CCDS32536.1	.	.	.	.	.	.	.	.	.	.	G	39	7.750864	0.98468	.	.	ENSG00000129197	ENST00000381209;ENST00000405578	.	.	.	4.96	3.99	0.46301	.	0.514246	0.23332	N	0.049331	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-34.3684	12.5083	0.55993	0.0804:0.0:0.9196:0.0	.	.	.	.	X	201	.	ENSP00000370606:E201X	E	+	1	0	RPAIN	5272226	1.000000	0.71417	0.065000	0.19835	0.986000	0.74619	4.119000	0.57891	1.316000	0.45131	0.563000	0.77884	GAA		0.483	RPAIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439373.1	NM_001033002		T	5331502	G	T	5331502	4	4	61	1	0	0	0	0	0	1	0	0	13577	943	33	2	623	2	RPAIN	17	5331502	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28621	5331502	75863708	9998	17983										
DHX33	56919	broad.mit.edu	37	chr17	5352201	5352201	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgctgttgacaaaattCtctttgcaccaatcctgaat	5	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5352201C>A	ENST00000225296.3	-	11	1943	c.1743G>T	c.(1741-1743)gaG>gaT	p.E581D	DHX33_ENST00000433302.3_Missense_Mutation_p.E357D	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	581					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)	p.E581D(1)		breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGACAAAATTCTCTTTGCACC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	17											132	109	117					17																	5352201		2203	4300	6503	5292925	SO:0001583	missense	56919			AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"DEAH-boxes"	16718	protein-coding gene	gene with protein product		614405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1743G>T	17.37:g.5352201C>A	ENSP00000225296:p.Glu581Asp		5292925	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.225838	0.39300	.	.	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02579	4.24;4.24	5.18	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.03178	0.0093	L	0.45698	1.435	0.58432	D	0.999999	B;B	0.31193	0.312;0.004	B;B	0.26693	0.072;0.005	T	0.52571	-0.8558	10	0.33940	T	0.23	.	9.2742	0.37690	0.0:0.8381:0.0:0.1619	.	357;581	Q05BE5;Q9H6R0	.;DHX33_HUMAN	D	581;357	ENSP00000225296:E581D;ENSP00000413779:E357D	ENSP00000225296:E581D	E	-	3	2	DHX33	5292925	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.715000	0.37971	1.430000	0.47334	0.563000	0.77884	GAG		0.458	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		A	5352201	C	A	5352201	3	1	61	1	0	0	0	0	1	0	0	0	4517	912	32	2	388	2	DHX33	17	5352201	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20699	5352201	75843009	9999	17984										
WSCD1	23302	broad.mit.edu	37	chr17	5991352	5991352	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacgatggccacgagaggaCtctgaaaggagctgtgtttt	14	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:5991352C>T	ENST00000574946.1	+	3	860	c.470C>T	c.(469-471)aCt>aTt	p.T157I	WSCD1_ENST00000574232.1_Missense_Mutation_p.T157I|WSCD1_ENST00000539421.1_Missense_Mutation_p.T157I|WSCD1_ENST00000573634.1_Missense_Mutation_p.T41I|WSCD1_ENST00000317744.5_Missense_Mutation_p.T157I			Q658N2	WSCD1_HUMAN	WSC domain containing 1	157	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.T157I(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						CACGAGAGGACTCTGAAAGGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											172	145	154					17																	5991352		2203	4300	6503	5932076	SO:0001583	missense	23302				CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.470C>T	17.37:g.5991352C>T	ENSP00000460825:p.Thr157Ile		5932076	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477138	0.84640	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	T;T	0.55588	0.51;0.51	5.97	4.95	0.65309	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.174158	0.50627	D	0.000116	T	0.54711	0.1875	L	0.45137	1.4	0.38279	D	0.942371	D	0.54397	0.966	P	0.52856	0.711	T	0.52586	-0.8556	10	0.30854	T	0.27	-20.5437	13.7135	0.62682	0.1547:0.8453:0.0:0.0	.	157	Q658N2	WSCD1_HUMAN	I	157	ENSP00000323087:T157I;ENSP00000446032:T157I	ENSP00000323087:T157I	T	+	2	0	WSCD1	5932076	0.989000	0.36119	0.328000	0.25416	0.978000	0.69477	3.109000	0.50345	2.836000	0.97738	0.655000	0.94253	ACT		0.542	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		T	5991352	C	T	5991352	3	4	61	1	0	0	0	0	1	0	0	0	17446	565	20	3	476	3	WSCD1	17	5991352	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	639151	5991352	75203858	10000	17985										
WSCD1	23302	broad.mit.edu	37	chr17	6012996	6012996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaccccccggttcaacctgCgggatgccatggacagctca	10	16	2	0	rs138096430		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:6012996C>T	ENST00000574946.1	+	6	1309	c.919C>T	c.(919-921)Cgg>Tgg	p.R307W	WSCD1_ENST00000574232.1_Missense_Mutation_p.R307W|WSCD1_ENST00000539421.1_Missense_Mutation_p.R307W|WSCD1_ENST00000573634.1_Missense_Mutation_p.R191W|WSCD1_ENST00000317744.5_Missense_Mutation_p.R307W			Q658N2	WSCD1_HUMAN	WSC domain containing 1	307	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.R307W(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						GTTCAACCTGCGGGATGCCAT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	175	161	165		919	5.6	1	17	dbSNP_134	165	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WSCD1	NM_015253.1	101	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	307/576	6012996	3,13003	2203	4300	6503	5953720	SO:0001583	missense	23302				CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.919C>T	17.37:g.6012996C>T	ENSP00000460825:p.Arg307Trp		5953720	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.963379	0.53507	2.27E-4	2.33E-4	ENSG00000179314	ENST00000317744;ENST00000539421	T;T	0.56103	0.48;0.48	5.64	5.64	0.86602	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.549871	0.19528	N	0.112105	T	0.52757	0.1754	L	0.43152	1.355	0.38246	D	0.941463	D	0.59767	0.986	P	0.50537	0.643	T	0.57814	-0.7746	10	0.54805	T	0.06	-15.2864	10.6102	0.45417	0.0:0.9129:0.0:0.0871	.	307	Q658N2	WSCD1_HUMAN	W	307	ENSP00000323087:R307W;ENSP00000446032:R307W	ENSP00000323087:R307W	R	+	1	2	WSCD1	5953720	0.989000	0.36119	0.983000	0.44433	0.295000	0.27426	5.507000	0.66999	2.644000	0.89710	0.557000	0.71058	CGG		0.577	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		T	6012996	C	T	6012996	3	4	61	1	0	0	0	0	1	0	0	0	17446	759	27	1	937	1	WSCD1	17	6012996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21644	6012996	75182214	10001	17986										
KIAA0753	9851	broad.mit.edu	37	chr17	6515343	6515343	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccacggctaacacctcgtCtttgaagcttgcactttggt	9	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:6515343C>A	ENST00000361413.3	-	8	1799	c.1441G>T	c.(1441-1443)Gac>Tac	p.D481Y	KIAA0753_ENST00000589033.1_Intron|KIAA0753_ENST00000542606.1_Missense_Mutation_p.D182Y|KIAA0753_ENST00000572370.1_Missense_Mutation_p.D182Y	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	481						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.D481Y(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AACACCTCGTCTTTGAAGCTT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	17											192	188	189					17																	6515343		1882	4108	5990	6456067	SO:0001583	missense	9851				CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1441G>T	17.37:g.6515343C>A	ENSP00000355250:p.Asp481Tyr		6456067	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.866116	0.51588	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.09817	2.94;2.94	4.52	3.55	0.40652	.	0.952579	0.08861	N	0.883066	T	0.15609	0.0376	L	0.47716	1.5	0.20873	N	0.999839	P	0.50528	0.936	P	0.48141	0.568	T	0.16424	-1.0403	10	0.59425	D	0.04	-4.0747	8.5921	0.33693	0.0:0.8973:0.0:0.1027	.	481	Q2KHM9	K0753_HUMAN	Y	481;182	ENSP00000355250:D481Y;ENSP00000444634:D182Y	ENSP00000355250:D481Y	D	-	1	0	KIAA0753	6456067	0.004000	0.15560	0.007000	0.13788	0.270000	0.26580	1.525000	0.35953	1.510000	0.48803	0.655000	0.94253	GAC		0.463	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		A	6515343	C	A	6515343	3	1	61	1	0	0	0	0	1	0	0	0	8212	913	32	2	1510	2	KIAA0753	17	6515343	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	502347	6515343	74679867	10002	17987										
KIAA0753	9851	broad.mit.edu	37	chr17	6524137	6524137	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgctttgctacagaaggtCgacttgtttcctgtgggaat	12	8	0	1	rs199555049		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:6524137C>T	ENST00000361413.3	-	7	1644	c.1286G>A	c.(1285-1287)cGa>cAa	p.R429Q	KIAA0753_ENST00000589033.1_5'UTR|KIAA0753_ENST00000542606.1_Missense_Mutation_p.R130Q|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R130Q	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	429						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R429Q(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TACAGAAGGTCGACTTGTTTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	17											181	171	174					17																	6524137		1928	4121	6049	6464861	SO:0001583	missense	9851				CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1286G>A	17.37:g.6524137C>T	ENSP00000355250:p.Arg429Gln		6464861	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	C	8.942	0.965974	0.18659	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.09073	3.02;3.02	4.92	-9.83	0.00482	.	1.314050	0.05243	N	0.512636	T	0.03263	0.0095	N	0.11201	0.11	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.36792	-0.9733	10	0.30854	T	0.27	6.0978	4.3736	0.11260	0.0845:0.4978:0.1682:0.2496	.	429	Q2KHM9	K0753_HUMAN	Q	429;130	ENSP00000355250:R429Q;ENSP00000444634:R130Q	ENSP00000355250:R429Q	R	-	2	0	KIAA0753	6464861	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.223000	0.02962	-2.796000	0.00354	-1.641000	0.00772	CGA		0.448	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		T	6524137	C	T	6524137	3	4	61	1	0	0	0	0	1	0	0	0	8212	884	31	1	1669	1	KIAA0753	17	6524137	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8794	6524137	74671073	10003	17988										
XAF1	54739	broad.mit.edu	37	chr17	6659425	6659425	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacttctcggtgtgcaggAactggtaagaaagtgctttc	13	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:6659425A>T	ENST00000361842.3	+	1	267	c.28A>T	c.(28-30)Aac>Tac	p.N10Y	XAF1_ENST00000441631.1_Missense_Mutation_p.N10Y|XAF1_ENST00000346752.4_Missense_Mutation_p.N10Y|XAF1_ENST00000576459.1_3'UTR|XAF1_ENST00000438512.1_Missense_Mutation_p.N10Y	NM_017523.3	NP_059993.2	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1	10					apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|negative regulation of protein complex assembly (GO:0031333)|response to interferon-beta (GO:0035456)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.N10Y(1)		large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	6						GGTGTGCAGGAACTGGTAAGA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	17											104	102	103					17																	6659425		2203	4300	6503	6600149	SO:0001583	missense	54739			X99699	CCDS11080.1, CCDS11081.1	17p13.2	2010-03-19			ENSG00000132530	ENSG00000132530			30932	protein-coding gene	gene with protein product		606717				12029096, 11175744	Standard	NM_199139		Approved	BIRC4BP, XIAPAF1, HSXIAPAF1	uc002gdn.3	Q6GPH4		ENST00000361842.3:c.28A>T	17.37:g.6659425A>T	ENSP00000354822:p.Asn10Tyr		6600149	A2T931|A2T932|A8K2L1|A8K9Y3|D3DTM6|Q6MZE8|Q8N557|Q99982	Missense_Mutation	SNP	ENST00000361842.3	37	CCDS11080.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042225	0.55003	.	.	ENSG00000132530	ENST00000361842;ENST00000441631;ENST00000346752;ENST00000438512	T;T;T;T	0.29917	1.55;1.65;1.65;1.65	4.52	0.851	0.18989	.	0.183917	0.37483	N	0.002071	T	0.50769	0.1635	M	0.89287	3.02	0.20821	N	0.999848	D;D;D	0.63880	0.993;0.98;0.969	D;P;P	0.63381	0.914;0.828;0.724	T	0.40739	-0.9547	10	0.56958	D	0.05	-3.2178	5.553	0.17101	0.541:0.3619:0.0971:0.0	.	10;10;10	C9J7Z8;Q6GPH4-2;Q6GPH4	.;.;XAF1_HUMAN	Y	10	ENSP00000354822:N10Y;ENSP00000413199:N10Y;ENSP00000341029:N10Y;ENSP00000406233:N10Y	ENSP00000341029:N10Y	N	+	1	0	XAF1	6600149	0.156000	0.22821	0.073000	0.20177	0.080000	0.17528	0.453000	0.21811	0.001000	0.14605	0.533000	0.62120	AAC		0.517	XAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439643.5	NM_017523		T	6659425	A	T	6659425	3	4	61	1	0	0	0	0	1	0	0	0	17459	246	9	5	30	5	XAF1	17	6659425	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	135288	6659425	74535785	10004	17989										
ASGR2	433	broad.mit.edu	37	chr17	7005464	7005465	+	Missense_Mutation	DNP	CC	CC	AT													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaagagccatcactgtCcgtgagacctatccaggtat					rs199645896	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7005464_7005465CC>AT	ENST00000380952.2	-	8	978_979	c.714_715GG>AT	c.(712-717)acGGac>acATac	p.D239Y	ASGR2_ENST00000355035.5_Missense_Mutation_p.D239Y|ASGR2_ENST00000254850.7_Missense_Mutation_p.D215Y|ASGR2_ENST00000446679.2_Missense_Mutation_p.D220Y	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	239	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.T238>?(1)|p.T238T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	CCATCACTGTCCGTGAGACCTA	0.46																																																2	Complex(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	17																																								6946189	SO:0001583	missense	433			M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"C-type lectin domain containing"	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.714_715delinsAT	17.37:g.7005464_7005465delinsAT	ENSP00000370339:p.Asp239Tyr		6946188	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	DNP	ENST00000380952.2	37	CCDS32544.1																																																																																				0.46	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914		AT	7005465	CC	AT	7005464	3	1	61	1	0	0	0	0	1	0	0	0	1041	855	30	2	228	2	ASGR2	17	7005464	Missense_Mutation	DNP	CC	TCGA-AG-A002-01A-01W-A00K-09	346039	7005464	74189746	10005	17990										
DLG4	1742	broad.mit.edu	37	chr17	7096856	7096856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagagaagatcatcgttggCgcggtccttggtgggcccaa	16	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7096856C>T	ENST00000399506.2	-	16	1830	c.1639G>A	c.(1639-1641)Gcc>Acc	p.A547T	DLG4_ENST00000399510.2_Missense_Mutation_p.A590T|DLG4_ENST00000302955.6_Missense_Mutation_p.A544T			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	547	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)	p.A590T(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	TCATCGTTGGCGCGGTCCTTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											73	77	75					17																	7096856		2035	4176	6211	7037580	SO:0001583	missense	1742			U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1639G>A	17.37:g.7096856C>T	ENSP00000382425:p.Ala547Thr		7037580	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	37		.	.	.	.	.	.	.	.	.	.	C	18.29	3.591700	0.66219	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.17213	2.29;2.29;2.29	5.08	4.11	0.48088	Src homology-3 domain (1);Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	.	.	.	.	T	0.14614	0.0353	L	0.38175	1.15	0.29130	N	0.879686	B;P;B;B	0.38370	0.441;0.628;0.318;0.394	B;B;B;B	0.34824	0.137;0.19;0.073;0.114	T	0.06844	-1.0804	9	0.87932	D	0	.	11.5164	0.50524	0.0:0.9132:0.0:0.0868	.	587;547;544;590	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	T	547;544;590;590;487;590	ENSP00000382425:A547T;ENSP00000307471:A544T;ENSP00000382428:A590T	ENSP00000293813:A590T	A	-	1	0	DLG4	7037580	0.837000	0.29446	0.848000	0.33437	0.989000	0.77384	1.503000	0.35715	1.379000	0.46325	0.655000	0.94253	GCC		0.612	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		T	7096856	C	T	7096856	3	4	61	1	0	0	0	0	1	0	0	0	4568	768	27	1	555	1	DLG4	17	7096856	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91392	7096856	74098354	10006	17991										
DVL2	1856	broad.mit.edu	37	chr17	7130748	7130748	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcattagggatggtgatCttgagccacatgcggtcccg	14	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7130748C>A	ENST00000005340.5	-	12	1620	c.1338G>T	c.(1336-1338)aaG>aaT	p.K446N	DVL2_ENST00000574642.1_5'Flank|DVL2_ENST00000575458.1_Missense_Mutation_p.K440N	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	446	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)	p.K446N(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GGATGGTGATCTTGAGCCACA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											75	78	77					17																	7130748		2203	4300	6503	7071472	SO:0001583	missense	1856			BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1338G>T	17.37:g.7130748C>A	ENSP00000005340:p.Lys446Asn		7071472	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	37	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511208	0.64522	.	.	ENSG00000004975	ENST00000005340	T	0.22945	1.93	4.66	2.69	0.31865	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.93678	3.445	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.56751	-0.7927	10	0.87932	D	0	-25.1514	6.4036	0.21652	0.0:0.7012:0.0:0.2988	.	440;446	B4DLQ0;O14641	.;DVL2_HUMAN	N	446	ENSP00000005340:K446N	ENSP00000005340:K446N	K	-	3	2	DVL2	7071472	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.547000	0.36190	0.599000	0.29845	-0.218000	0.12543	AAG		0.607	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		A	7130748	C	A	7130748	3	1	61	1	0	0	0	0	1	0	0	0	4847	912	32	2	888	2	DVL2	17	7130748	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33892	7130748	74064462	10007	17992										
DULLARD	23399	broad.mit.edu	37	chr17	7149674	7149674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtaaacaccaccagctCgtaccactggctcacctgaa	7	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7149674C>T	ENST00000573600.1	-	6	797	c.376G>A	c.(376-378)Gag>Aag	p.E126K	CTDNEP1_ENST00000318988.6_Missense_Mutation_p.E126K|CTDNEP1_ENST00000572043.1_5'UTR|CTDNEP1_ENST00000574322.1_Missense_Mutation_p.E126K|CTD-2545G14.7_ENST00000570760.2_5'Flank			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	126	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)	p.E126K(2)		central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						ACCACCAGCTCGTACCACTGG	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	17											84	80	81					17																	7149674		2203	4300	6503	7090398	SO:0001583	missense	23399			AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	19085	protein-coding gene	gene with protein product	"C-terminal domain nuclear envelope phosphatase 1"	610684	"dullard homolog (Xenopus laevis)"	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.376G>A	17.37:g.7149674C>T	ENSP00000461749:p.Glu126Lys		7090398	D3DTN7|Q96GQ9	Missense_Mutation	SNP	ENST00000573600.1	37	CCDS11093.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.912363	0.72983	.	.	ENSG00000175826	ENST00000318988	T	0.22539	1.95	4.86	4.86	0.63082	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	M	0.89095	3.005	0.80722	D	1	D	0.55800	0.973	P	0.52598	0.703	T	0.51911	-0.8645	10	0.46703	T	0.11	-16.5804	15.5281	0.75928	0.0:1.0:0.0:0.0	.	126	O95476	CNEP1_HUMAN	K	126	ENSP00000321732:E126K	ENSP00000321732:E126K	E	-	1	0	CTDNEP1	7090398	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.476000	0.73587	2.522000	0.85027	0.655000	0.94253	GAG		0.453	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343		T	7149674	C	T	7149674	3	4	61	1	0	0	0	0	1	0	0	0	4810	893	31	1	374	1	DULLARD	17	7149674	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18926	7149674	74045536	10008	17993										
SLC2A4	6517	broad.mit.edu	37	chr17	7188168	7188168	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctaggttttctattattcGaccagcatcttcgagacagc	7	11	3	1	rs541494158		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7188168G>A	ENST00000317370.8	+	8	1198	c.930G>A	c.(928-930)tcG>tcA	p.S310S	SLC2A4_ENST00000424875.2_Silent_p.S300S|RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Silent_p.S310S	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	310					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)	p.S310S(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						TCTATTATTCGACCAGCATCT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	17											150	151	151					17																	7188168		2203	4300	6503	7128892	SO:0001819	synonymous_variant	6517			M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.930G>A	17.37:g.7188168G>A			7128892	Q05BQ3|Q14CX2	Silent	SNP	ENST00000317370.8	37	CCDS11097.1																																																																																				0.552	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			A	7188168	G	A	7188168	2	1	61	1	0	0	0	0	0	0	0	1	14583	1045	37	1		1	SLC2A4	17	7188168	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38494	7188168	74007042	10009	17994										
SLC2A4	6517	broad.mit.edu	37	chr17	7189116	7189116	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggccccattccttggttCatcgtggccgagctcttcag	10	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7189116C>A	ENST00000317370.8	+	10	1483	c.1215C>A	c.(1213-1215)ttC>ttA	p.F405L	SLC2A4_ENST00000424875.2_Missense_Mutation_p.F395L|RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Missense_Mutation_p.F405L	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	405					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)	p.F405L(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						TTCCTTGGTTCATCGTGGCCG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	94	97					17																	7189116		2203	4300	6503	7129840	SO:0001583	missense	6517			M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1215C>A	17.37:g.7189116C>A	ENSP00000320935:p.Phe405Leu		7129840	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524979	0.85600	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.73681	-0.77;-0.77	5.09	4.12	0.48240	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.72415	0.3457	N	0.20483	0.58	0.52501	D	0.999957	D;P	0.63880	0.993;0.699	D;B	0.63381	0.914;0.209	T	0.71024	-0.4712	10	0.34782	T	0.22	.	10.9068	0.47084	0.0:0.9101:0.0:0.0898	.	405;395	P14672;F5H081	GTR4_HUMAN;.	L	405;395	ENSP00000320935:F405L;ENSP00000396887:F395L	ENSP00000320935:F405L	F	+	3	2	SLC2A4	7129840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.903000	0.39858	1.375000	0.46248	0.563000	0.77884	TTC		0.582	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			A	7189116	C	A	7189116	3	1	61	1	0	0	0	0	1	0	0	0	14583	825	29	2	1253	2	SLC2A4	17	7189116	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	948	7189116	74006094	10010	17995										
ACAP1	9744	broad.mit.edu	37	chr17	7250451	7250451	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcacgtggtggcccaggtCcagagtgtggatggcaatgc	18	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7250451C>T	ENST00000158762.3	+	14	1439	c.1233C>T	c.(1231-1233)gtC>gtT	p.V411V		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	411	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.|Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.V411V(1)		NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						TGGCCCAGGTCCAGAGTGTGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	17											56	62	60					17																	7250451		2203	4300	6503	7191175	SO:0001819	synonymous_variant	9744			D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1233C>T	17.37:g.7250451C>T			7191175	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																				0.662	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7250451	C	T	7250451	2	4	61	1	0	0	0	0	0	0	0	1	118	842	30	3		3	ACAP1	17	7250451	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61335	7250451	73944759	10011	17996										
ACAP1	9744	broad.mit.edu	37	chr17	7251307	7251307	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatgggagccagaactagtGaaggtaacttagcgtattgt	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7251307G>T	ENST00000158762.3	+	15	1616	c.1410G>T	c.(1408-1410)gtG>gtT	p.V470V	ACAP1_ENST00000575415.1_5'Flank|ACAP1_ENST00000570504.1_5'Flank|ACAP1_ENST00000571471.1_5'Flank|ACAP1_ENST00000574499.1_5'Flank	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	470	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.|Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.V470V(1)		NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						CAGAACTAGTGAAGGTAACTT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											85	78	80					17																	7251307		2203	4300	6503	7192031	SO:0001819	synonymous_variant	9744			D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1410G>T	17.37:g.7251307G>T			7192031	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																				0.592	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7251307	G	T	7251307	2	4	61	1	0	0	0	0	0	0	0	1	118	1277	45	2		2	ACAP1	17	7251307	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	856	7251307	73943903	10012	17997										
ACAP1	9744	broad.mit.edu	37	chr17	7252364	7252364	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctggggccctactgtttCgagcgtctgggcatcctcca	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7252364C>T	ENST00000158762.3	+	18	1935	c.1729C>T	c.(1729-1731)Cga>Tga	p.R577*	ACAP1_ENST00000575415.1_5'Flank|KCTD11_ENST00000333751.3_5'Flank|ACAP1_ENST00000570504.1_5'Flank|ACAP1_ENST00000571471.1_5'Flank|ACAP1_ENST00000574499.1_5'Flank	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	577	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R577*(1)		NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						CCTACTGTTTCGAGCGTCTGG	0.602																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											104	101	102					17																	7252364		2203	4300	6503	7193088	SO:0001587	stop_gained	9744			D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1729C>T	17.37:g.7252364C>T	ENSP00000158762:p.Arg577*		7193088	Q53XN9	Nonsense_Mutation	SNP	ENST00000158762.3	37	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	C	36	5.764855	0.96906	.	.	ENSG00000072818	ENST00000158762	.	.	.	5.13	2.96	0.34315	.	0.275542	0.32563	N	0.005937	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1326	0.25510	0.1751:0.7265:0.0:0.0984	.	.	.	.	X	577	.	ENSP00000158762:R577X	R	+	1	2	ACAP1	7193088	0.997000	0.39634	1.000000	0.80357	0.185000	0.23345	0.810000	0.27183	1.347000	0.45714	0.655000	0.94253	CGA		0.602	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7252364	C	T	7252364	4	4	61	1	0	0	0	0	0	1	0	0	118	876	31	1	1799	1	ACAP1	17	7252364	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1057	7252364	73942846	10013	17998										
TNK1	8711	broad.mit.edu	37	chr17	7286624	7286624	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgttctgggcctaagtctaaGaactgggtctacaaggtgtg	13	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7286624G>T	ENST00000576812.1	+	3	588	c.219G>T	c.(217-219)aaG>aaT	p.K73N	TNK1_ENST00000570896.1_Missense_Mutation_p.K73N|TNK1_ENST00000311668.2_Missense_Mutation_p.K73N	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1									p.K73N(1)		central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CTAAGTCTAAGAACTGGGTCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											80	89	86					17																	7286624		2008	4166	6174	7227348	SO:0001583	missense	8711			U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.219G>T	17.37:g.7286624G>T	ENSP00000459799:p.Lys73Asn		7227348		Missense_Mutation	SNP	ENST00000576812.1	37	CCDS58510.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560340	0.65538	.	.	ENSG00000174292	ENST00000311668	T	0.38240	1.15	4.29	4.29	0.51040	.	0.000000	0.52532	D	0.000073	T	0.44456	0.1294	M	0.68317	2.08	0.34070	D	0.658298	P;P	0.44260	0.83;0.739	P;B	0.47645	0.553;0.351	T	0.61491	-0.7052	10	0.59425	D	0.04	.	12.5556	0.56252	0.0:0.0:1.0:0.0	.	73;73	Q13470-2;Q13470	.;TNK1_HUMAN	N	73	ENSP00000312309:K73N	ENSP00000312309:K73N	K	+	3	2	TNK1	7227348	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.116000	0.50399	2.675000	0.91044	0.637000	0.83480	AAG		0.617	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985		T	7286624	G	T	7286624	3	4	61	1	0	0	0	0	1	0	0	0	16356	933	33	2	225	2	TNK1	17	7286624	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34260	7286624	73908586	10014	17999										
PLSCR3	100529211	broad.mit.edu	37	chr17	7296934	7296934	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacctgcaccaggaattCgaggccagaaggcacccctg	10	15	1	1	rs199962387		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7296934C>T	ENST00000576362.1	-	2	386	c.229G>A	c.(229-231)Gaa>Aaa	p.E77K	TMEM256-PLSCR3_ENST00000324822.11_Missense_Mutation_p.E77K|TMEM256-PLSCR3_ENST00000574401.1_Missense_Mutation_p.E77K|TMEM256-PLSCR3_ENST00000535512.1_Missense_Mutation_p.E77K|TMEM256-PLSCR3_ENST00000576201.1_Missense_Mutation_p.E77K|C17orf61-PLSCR3_ENST00000573331.1_3'UTR					TMEM256-PLSCR3 readthrough (NMD candidate)									p.E77K(2)									ACCAGGAATTCGAGGCCAGAA	0.682																																																2	Substitution - Missense(2)	large_intestine(2)	17											23	27	26					17																	7296934		2024	4160	6184	7237658	SO:0001583	missense	57048					17p13.1	2013-09-25			ENSG00000187838	ENSG00000187838			49186	other	readthrough							Standard	NR_037719		Approved				OTTHUMG00000178150	ENST00000576362.1:c.229G>A	17.37:g.7296934C>T	ENSP00000460800:p.Glu77Lys		7237658		Missense_Mutation	SNP	ENST00000576362.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.286657	0.80803	.	.	ENSG00000187838	ENST00000535512;ENST00000324822;ENST00000380658	T;T	0.25250	1.81;1.81	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.54598	0.1868	M	0.83012	2.62	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.59521	-0.7439	10	0.72032	D	0.01	-13.4048	14.8178	0.70048	0.0:1.0:0.0:0.0	.	77;132	Q9NRY6;D3DTP7	PLS3_HUMAN;.	K	77	ENSP00000438547:E77K;ENSP00000316021:E77K	ENSP00000316021:E77K	E	-	1	0	PLSCR3	7237658	0.993000	0.37304	0.996000	0.52242	0.949000	0.60115	2.885000	0.48570	2.584000	0.87258	0.462000	0.41574	GAA		0.682	TMEM256-PLSCR3-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000440808.1			T	7296934	C	T	7296934	3	4	61	1	0	0	0	0	1	0	0	0	12142	893	31	1	682	1	PLSCR3	17	7296934	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10310	7296934	73898276	10015	18000										
C17orf74	201243	broad.mit.edu	37	chr17	7329356	7329356	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagacaagatgattgattgGgctactcagaaaagtaagtg	11	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7329356G>A	ENST00000333870.3	+	2	257	c.183G>A	c.(181-183)tgG>tgA	p.W61*	C17orf74_ENST00000574034.1_Nonsense_Mutation_p.W61*|RP11-104H15.7_ENST00000575310.1_RNA	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	61						integral component of membrane (GO:0016021)		p.W61*(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				TGATTGATTGGGCTACTCAGA	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											76	79	78					17																	7329356		1999	4151	6150	7270080	SO:0001587	stop_gained	201243			BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.183G>A	17.37:g.7329356G>A	ENSP00000328061:p.Trp61*		7270080		Nonsense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122132	0.37436	.	.	ENSG00000184560	ENST00000333870	.	.	.	3.58	-0.134	0.13481	.	1.773300	0.03723	U	0.252217	.	.	.	.	.	.	0.52501	D	0.999959	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-9.0138	10.6903	0.45867	0.0:0.5989:0.4011:0.0	.	.	.	.	X	61	.	ENSP00000328061:W61X	W	+	3	0	C17orf74	7270080	0.869000	0.29996	0.018000	0.16275	0.084000	0.17831	0.792000	0.26929	0.254000	0.21573	-0.512000	0.04463	TGG		0.597	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		A	7329356	G	A	7329356	4	1	61	1	0	0	0	0	0	1	0	0	1884	1241	43	3	189	3	C17orf74	17	7329356	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32422	7329356	73865854	10016	18001										
C17orf74	201243	broad.mit.edu	37	chr17	7329798	7329798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcttccgtaacccacatcGcagccaaaagatgtcacaac	6	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7329798G>A	ENST00000333870.3	+	3	562	c.488G>A	c.(487-489)cGc>cAc	p.R163H	C17orf74_ENST00000574034.1_Intron|RP11-104H15.7_ENST00000575310.1_RNA	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	163						integral component of membrane (GO:0016021)		p.R163H(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				AACCCACATCGCAGCCAAAAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											121	128	126					17																	7329798		2030	4175	6205	7270522	SO:0001583	missense	201243			BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.488G>A	17.37:g.7329798G>A	ENSP00000328061:p.Arg163His		7270522		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	.	.	.	.	.	.	.	.	.	.	G	3.766	-0.048532	0.07407	.	.	ENSG00000184560	ENST00000333870	T	0.42131	0.98	4.0	-7.18	0.01505	.	0.927198	0.08987	N	0.864961	T	0.16727	0.0402	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28744	-1.0034	10	0.17832	T	0.49	-14.8655	8.1818	0.31315	0.77:0.1089:0.1212:0.0	.	163	Q0P670	CQ074_HUMAN	H	163	ENSP00000328061:R163H	ENSP00000328061:R163H	R	+	2	0	C17orf74	7270522	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.127000	0.03251	-1.585000	0.01634	-0.339000	0.08088	CGC		0.587	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		A	7329798	G	A	7329798	3	1	61	1	0	0	0	0	1	0	0	0	1884	1087	38	1	498	1	C17orf74	17	7329798	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	442	7329798	73865412	10017	18002										
FGF11	2256	broad.mit.edu	37	chr17	7345197	7345197	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagggactgctctacagttCggtgagacaatgaggctgag	15	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7345197C>T	ENST00000293829.4	+	3	1001	c.407C>T	c.(406-408)tCg>tTg	p.S136L	FGF11_ENST00000575235.1_Splice_Site_p.S12L|FGF11_ENST00000575398.1_Splice_Site_p.S12L|FGF11_ENST00000572907.1_Splice_Site_p.S12L|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|FGF11_ENST00000575082.1_Splice_Site_p.S12L|RP11-104H15.7_ENST00000575310.1_RNA	NM_004112.2	NP_004103.1	Q92914	FGF11_HUMAN	fibroblast growth factor 11	136					cell-cell signaling (GO:0007267)|nervous system development (GO:0007399)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	growth factor activity (GO:0008083)	p.S136L(1)		central_nervous_system(1)|large_intestine(3)|ovary(1)|prostate(1)	6		Prostate(122;0.157)				CTCTACAGTTCGGTGAGACAA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											102	83	89					17																	7345197		2203	4300	6503	7285921	SO:0001630	splice_region_variant	2256				CCDS11105.1	17p13.1	2008-07-18			ENSG00000161958	ENSG00000161958			3667	protein-coding gene	gene with protein product	"fibroblast growth factor homologous factor 3"	601514				8790420	Standard	NM_004112		Approved	FHF3, FLJ16061, MGC45269, MGC102953	uc002ggz.3	Q92914	OTTHUMG00000108136	ENST00000293829.4:c.408+1C>T	17.37:g.7345197C>T			7285921	Q2YDX8	Missense_Mutation	SNP	ENST00000293829.4	37	CCDS11105.1	.	.	.	.	.	.	.	.	.	.	C	34	5.330574	0.95733	.	.	ENSG00000161958	ENST00000293829	D	0.83419	-1.72	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.91865	0.7425	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.957;0.99	D	0.93067	0.6479	10	0.87932	D	0	.	15.7855	0.78300	0.0:1.0:0.0:0.0	.	77;136	B7Z1C3;Q92914	.;FGF11_HUMAN	L	136	ENSP00000293829:S136L	ENSP00000293829:S136L	S	+	2	0	FGF11	7285921	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.993000	0.76245	2.605000	0.88082	0.555000	0.69702	TCG		0.537	FGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226939.3	NM_004112	Missense_Mutation	T	7345197	C	T	7345197	5	4	61	1	0	0	0	0	0	0	1	0	5859	898	31	1	417	1	FGF11	17	7345197	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15399	7345197	73850013	10018	18003										
POLR2A	5430	broad.mit.edu	37	chr17	7399887	7399887	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagatggacaacaagttCggtgtggaacaacctgaggg	16	6	0	2	rs368365915		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7399887C>T	ENST00000322644.6	+	4	891	c.492C>T	c.(490-492)ttC>ttT	p.F164F	POLR2A_ENST00000572844.1_Silent_p.F164F	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	164					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)	p.F164F(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ACAACAAGTTCGGTGTGGAAC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		0,4406		0,0,2203	139	144	142		492	-8.9	0.5	17		142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	POLR2A	NM_000937.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		164/1971	7399887	1,13005	2203	4300	6503	7340611	SO:0001819	synonymous_variant	5430					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.492C>T	17.37:g.7399887C>T			7340611	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																				0.562	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7399887	C	T	7399887	2	4	61	1	0	0	0	0	0	0	0	1	12245	883	31	1		1	POLR2A	17	7399887	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54690	7399887	73795323	10019	18004										
SHBG	6462	broad.mit.edu	37	chr17	7534935	7534935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccctggatggctgcctgcGccgggattcctggctggaca	15	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7534935G>A	ENST00000380450.4	+	5	615	c.584G>A	c.(583-585)cGc>cAc	p.R195H	SHBG_ENST00000574539.1_Missense_Mutation_p.R137H|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000441599.2_Missense_Mutation_p.R195H|SHBG_ENST00000576478.1_Missense_Mutation_p.R83H|SHBG_ENST00000575314.1_Missense_Mutation_p.R137H|SHBG_ENST00000340624.5_Missense_Mutation_p.R137H|SHBG_ENST00000576728.1_Missense_Mutation_p.R83H|SHBG_ENST00000570547.1_Missense_Mutation_p.R137H|SHBG_ENST00000572262.1_Missense_Mutation_p.R83H|SHBG_ENST00000416273.3_Missense_Mutation_p.R195H|SHBG_ENST00000575903.1_Intron	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	195	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.R195H(1)|p.0?(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	GGCTGCCTGCGCCGGGATTCC	0.572																																																3	Substitution - Missense(1)|Unknown(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)	17											109	113	111					17																	7534935		2203	4300	6503	7475660	SO:0001583	missense	6462				CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.584G>A	17.37:g.7534935G>A	ENSP00000369816:p.Arg195His		7475660	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952555	0.34471	.	.	ENSG00000129214	ENST00000340624;ENST00000441599;ENST00000416273;ENST00000441313;ENST00000380450	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	4.84	1.6	0.23607	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.87406	0.6169	M	0.89601	3.045	0.09310	N	0.999994	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;P;P;D;P;D;D;D	0.85130	0.926;0.902;0.877;0.938;0.877;0.997;0.956;0.914	T	0.77362	-0.2616	10	0.87932	D	0	-1.1151	7.2317	0.26046	0.0839:0.0:0.6217:0.2944	.	195;114;141;195;114;168;195;137	F5H5Z8;B0FWH6;E9PH59;E9PGW1;B0FWH5;B0FWH4;P04278;B4DYU0	.;.;.;.;.;.;SHBG_HUMAN;.	H	137;195;195;141;195	ENSP00000345675:R137H;ENSP00000393426:R195H;ENSP00000388867:R195H;ENSP00000369816:R195H	ENSP00000345675:R137H	R	+	2	0	SHBG	7475660	0.222000	0.23652	0.001000	0.08648	0.119000	0.20118	1.513000	0.35823	0.429000	0.26202	0.563000	0.77884	CGC		0.572	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		A	7534935	G	A	7534935	3	1	61	1	0	0	0	0	1	0	0	0	14306	1087	38	1	602	1	SHBG	17	7534935	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	135048	7534935	73660275	10020	18005										
ATP1B2	482	broad.mit.edu	37	chr17	7557256	7557256	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagaagctcaacaagttCttggagcgtgagtgtgggcc	14	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7557256C>A	ENST00000250111.4	+	3	746	c.339C>A	c.(337-339)ttC>ttA	p.F113L		NM_001678.3	NP_001669.3	P14415	AT1B2_HUMAN	ATPase, Na+/K+ transporting, beta 2 polypeptide	113					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.0?(2)|p.F113L(1)|p.?(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|pancreas(1)	10		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)		TCAACAAGTTCTTGGAGCGTG	0.522																																																4	Whole gene deletion(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|bone(1)	17											136	112	120					17																	7557256		2203	4300	6503	7497981	SO:0001583	missense	482			U45945	CCDS32550.1	17p13.1	2012-10-22			ENSG00000129244	ENSG00000129244	3.6.3.9	"ATPases / P-type"	805	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-2", "sodium pump subunit beta-2", "sodium-potassium ATPase subunit beta 2 (non-catalytic)"	182331				1699290	Standard	NM_001678		Approved	AMOG	uc002gif.1	P14415		ENST00000250111.4:c.339C>A	17.37:g.7557256C>A	ENSP00000250111:p.Phe113Leu		7497981	A0AV17|A8K278|D3DTQ2|O60444	Missense_Mutation	SNP	ENST00000250111.4	37	CCDS32550.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996852	0.54147	.	.	ENSG00000129244	ENST00000250111	T	0.35605	1.3	5.18	3.19	0.36642	.	0.102585	0.64402	D	0.000002	T	0.30198	0.0757	L	0.55213	1.73	0.52501	D	0.999951	B	0.22541	0.071	B	0.22152	0.038	T	0.10636	-1.0621	10	0.54805	T	0.06	-1.5665	5.6594	0.17660	0.0:0.6612:0.161:0.1779	.	113	P14415	AT1B2_HUMAN	L	113	ENSP00000250111:F113L	ENSP00000250111:F113L	F	+	3	2	ATP1B2	7497981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.428000	0.52792	0.575000	0.29434	0.561000	0.74099	TTC		0.522	ATP1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440234.1	NM_001678		A	7557256	C	A	7557256	3	1	61	1	0	0	0	0	1	0	0	0	1134	912	32	2	349	2	ATP1B2	17	7557256	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22321	7557256	73637954	10021	18006										
ATP1B2	482	broad.mit.edu	37	chr17	7558934	7558934	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttcccctactatggcaaAaagttccacgtaagtcccag	6	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7558934A>C	ENST00000250111.4	+	6	1106	c.699A>C	c.(697-699)aaA>aaC	p.K233N		NM_001678.3	NP_001669.3	P14415	AT1B2_HUMAN	ATPase, Na+/K+ transporting, beta 2 polypeptide	233	immunoglobulin-like.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.0?(2)|p.K233N(1)|p.?(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|pancreas(1)	10		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)		ACTATGGCAAAAAGTTCCACG	0.602																																																4	Whole gene deletion(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|bone(1)	17											117	91	100					17																	7558934		2203	4300	6503	7499659	SO:0001583	missense	482			U45945	CCDS32550.1	17p13.1	2012-10-22			ENSG00000129244	ENSG00000129244	3.6.3.9	"ATPases / P-type"	805	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-2", "sodium pump subunit beta-2", "sodium-potassium ATPase subunit beta 2 (non-catalytic)"	182331				1699290	Standard	NM_001678		Approved	AMOG	uc002gif.1	P14415		ENST00000250111.4:c.699A>C	17.37:g.7558934A>C	ENSP00000250111:p.Lys233Asn		7499659	A0AV17|A8K278|D3DTQ2|O60444	Missense_Mutation	SNP	ENST00000250111.4	37	CCDS32550.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.957653	0.34565	.	.	ENSG00000129244	ENST00000250111	T	0.36520	1.25	4.32	-0.762	0.11034	.	0.052242	0.85682	D	0.000000	T	0.28366	0.0701	M	0.62723	1.935	0.44719	D	0.997711	P	0.42785	0.79	B	0.37833	0.259	T	0.03630	-1.1018	10	0.56958	D	0.05	-0.0175	6.1051	0.20069	0.4454:0.1448:0.4098:0.0	.	233	P14415	AT1B2_HUMAN	N	233	ENSP00000250111:K233N	ENSP00000250111:K233N	K	+	3	2	ATP1B2	7499659	1.000000	0.71417	0.989000	0.46669	0.539000	0.34962	1.219000	0.32479	-0.366000	0.08064	-1.843000	0.00578	AAA		0.602	ATP1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440234.1	NM_001678		C	7558934	A	C	7558934	3	2	61	1	0	0	0	0	1	0	0	0	1134	11	1	4	721	4	ATP1B2	17	7558934	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1678	7558934	73636276	10022	18007										
WRAP53	55135	broad.mit.edu	37	chr17	7606153	7606153	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaatcagcgcatctacttCgatctggacccgtgagtggc	10	13	3	1	rs140635900		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7606153C>T	ENST00000316024.5	+	8	3605	c.1257C>T	c.(1255-1257)ttC>ttT	p.F419F	EFNB3_ENST00000226091.2_5'Flank|WRAP53_ENST00000534050.1_Silent_p.F386F|WRAP53_ENST00000431639.2_Silent_p.F419F|WRAP53_ENST00000396463.2_Silent_p.F419F|WRAP53_ENST00000457584.2_Silent_p.F419F			Q9BUR4	WAP53_HUMAN	WD repeat containing, antisense to TP53	419					positive regulation of telomerase activity (GO:0051973)|telomere formation via telomerase (GO:0032203)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	RNA binding (GO:0003723)	p.F419F(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(2)	18						GCATCTACTTCGATCTGGACC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C	,,,	1,4405	2.1+/-5.4	0,1,2202	91	78	82		1257,1257,1257,1257	-3.4	0.9	17	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WRAP53	NM_001143990.1,NM_001143991.1,NM_001143992.1,NM_018081.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	419/549,419/549,419/549,419/549	7606153	1,13005	2203	4300	6503	7546878	SO:0001819	synonymous_variant	55135			AK001247, DQ431240	CCDS11119.1	17p13.1	2014-09-17	2009-02-16	2009-02-16	ENSG00000141499	ENSG00000141499		"WD repeat domain containing"	25522	protein-coding gene	gene with protein product	"telomerase cajal body protein 1", "WD-encoding RNA antisense to p53"	612661	"WD repeat domain 79"	WDR79		19179534, 19250907, 19571673, 19342896, 20494116, 21441950	Standard	NM_018081		Approved	FLJ10385, TCAB1	uc010vuh.2	Q9BUR4	OTTHUMG00000134323	ENST00000316024.5:c.1257C>T	17.37:g.7606153C>T			7546878	B3KPR9|D3DTQ4|Q08ET9|Q9NW09	Silent	SNP	ENST00000316024.5	37	CCDS11119.1																																																																																				0.597	WRAP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259385.2	NM_018081		T	7606153	C	T	7606153	2	4	61	1	0	0	0	0	0	0	0	1	17440	883	31	1		1	WRAP53	17	7606153	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47219	7606153	73589057	10023	18008										
DNAH2	146754	broad.mit.edu	37	chr17	7626992	7626992	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagtgaagaatcagtggaGcccgaggcagatgtggtagg	17	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7626992G>A	ENST00000572933.1	+	3	1673	c.213G>A	c.(211-213)gaG>gaA	p.E71E	DNAH2_ENST00000082259.3_Silent_p.E71E|DNAH2_ENST00000570791.1_Silent_p.E71E|DNAH2_ENST00000389173.2_Silent_p.E71E			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	71	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E71E(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AATCAGTGGAGCCCGAGGCAG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	17											140	121	127					17																	7626992		2203	4300	6503	7567717	SO:0001819	synonymous_variant	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.213G>A	17.37:g.7626992G>A			7567717	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																				0.478	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7626992	G	A	7626992	2	1	61	1	0	0	0	0	0	0	0	1	4613	962	34	3		3	DNAH2	17	7626992	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20839	7626992	73568218	10024	18009										
DNAH2	146754	broad.mit.edu	37	chr17	7662299	7662299	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctggtacgcattagtggcAaacgggtatacagggacctg	14	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7662299A>G	ENST00000572933.1	+	15	3765	c.2305A>G	c.(2305-2307)Aaa>Gaa	p.K769E	DNAH2_ENST00000389173.2_Missense_Mutation_p.K769E			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	769	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K769E(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CATTAGTGGCAAACGGGTATA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											99	88	92					17																	7662299		2203	4300	6503	7603024	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.2305A>G	17.37:g.7662299A>G	ENSP00000458355:p.Lys769Glu		7603024	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282696	0.80692	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.24908	1.83	5.42	5.42	0.78866	.	0.192518	0.41097	D	0.000960	T	0.43144	0.1234	M	0.75264	2.295	0.80722	D	1	P	0.51537	0.946	P	0.57620	0.824	T	0.35226	-0.9797	10	0.12430	T	0.62	.	14.4448	0.67342	1.0:0.0:0.0:0.0	.	769	Q9P225	DYH2_HUMAN	E	769	ENSP00000373825:K769E	ENSP00000353818:K769E	K	+	1	0	DNAH2	7603024	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.717000	0.68446	2.051000	0.60960	0.454000	0.30748	AAA		0.507	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7662299	A	G	7662299	3	3	61	1	0	0	0	0	1	0	0	0	4613	131	5	4	2359	4	DNAH2	17	7662299	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	35307	7662299	73532911	10025	18010										
DNAH2	146754	broad.mit.edu	37	chr17	7696462	7696462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacccctggagctgatccGcctctggattgactatggct	11	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7696462G>A	ENST00000572933.1	+	48	8968	c.7508G>A	c.(7507-7509)cGc>cAc	p.R2503H	DNAH2_ENST00000389173.2_Missense_Mutation_p.R2503H			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2503	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2503H(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GAGCTGATCCGCCTCTGGATT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											97	87	91					17																	7696462		2203	4300	6503	7637187	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.7508G>A	17.37:g.7696462G>A	ENSP00000458355:p.Arg2503His		7637187	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186123	0.78789	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.51071	0.72	4.39	4.39	0.52855	ATPase, AAA+ type, core (1);	0.301950	0.32015	N	0.006705	T	0.72326	0.3446	H	0.97783	4.075	0.80722	D	1	B	0.31680	0.335	B	0.42138	0.377	T	0.80957	-0.1150	10	0.72032	D	0.01	.	15.9412	0.79756	0.0:0.0:1.0:0.0	.	2503	Q9P225	DYH2_HUMAN	H	2503	ENSP00000373825:R2503H	ENSP00000353818:R2503H	R	+	2	0	DNAH2	7637187	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.328000	0.79160	2.295000	0.77249	0.632000	0.83419	CGC		0.522	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7696462	G	A	7696462	3	1	61	1	0	0	0	0	1	0	0	0	4613	1087	38	1	7694	1	DNAH2	17	7696462	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34163	7696462	73498748	10026	18011										
DNAH2	146754	broad.mit.edu	37	chr17	7700784	7700784	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggcatcataagcgacaaGctcggctccttctttgacct	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7700784G>T	ENST00000572933.1	+	52	9476	c.8016G>T	c.(8014-8016)aaG>aaT	p.K2672N	DNAH2_ENST00000389173.2_Missense_Mutation_p.K2672N			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2672					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K2672N(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TAAGCGACAAGCTCGGCTCCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											134	134	134					17																	7700784		2203	4300	6503	7641509	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.8016G>T	17.37:g.7700784G>T	ENSP00000458355:p.Lys2672Asn		7641509	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	7.531	0.658778	0.14645	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.23754	1.89	5.08	-1.44	0.08856	.	0.053932	0.64402	D	0.000001	T	0.19927	0.0479	M	0.76002	2.32	0.80722	D	1	P	0.38582	0.638	B	0.28553	0.091	T	0.30446	-0.9978	10	0.12766	T	0.61	.	11.9181	0.52778	0.4302:0.0:0.5698:0.0	.	2672	Q9P225	DYH2_HUMAN	N	2672	ENSP00000373825:K2672N	ENSP00000353818:K2672N	K	+	3	2	DNAH2	7641509	0.998000	0.40836	0.982000	0.44146	0.214000	0.24535	0.462000	0.21956	-0.435000	0.07264	-0.300000	0.09419	AAG		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7700784	G	T	7700784	3	4	61	1	0	0	0	0	1	0	0	0	4613	962	34	2	8218	2	DNAH2	17	7700784	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4322	7700784	73494426	10027	18012										
DNAH2	146754	broad.mit.edu	37	chr17	7708654	7708654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggagatagtgatgcagGcagttatgattcttcgaggc	14	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7708654G>A	ENST00000572933.1	+	61	10845	c.9385G>A	c.(9385-9387)Gca>Aca	p.A3129T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3129T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3129	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A3129T(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AGTGATGCAGGCAGTTATGAT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											107	102	104					17																	7708654		2203	4300	6503	7649379	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.9385G>A	17.37:g.7708654G>A	ENSP00000458355:p.Ala3129Thr		7649379	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018675	0.93404	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.80214	-1.35	5.62	4.63	0.57726	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	D	0.91253	0.7243	M	0.90759	3.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.93075	0.6486	10	0.87932	D	0	.	15.3655	0.74519	0.0:0.1405:0.8595:0.0	.	3090;3129	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3090;3129	ENSP00000373825:A3129T	ENSP00000353818:A3090T	A	+	1	0	DNAH2	7649379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.593000	0.90832	1.355000	0.45865	0.655000	0.94253	GCA		0.522	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7708654	G	A	7708654	3	1	61	1	0	0	0	0	1	0	0	0	4613	1203	42	3	9623	3	DNAH2	17	7708654	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7870	7708654	73486556	10028	18013										
DNAH2	146754	broad.mit.edu	37	chr17	7721733	7721733	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacccccactacagcccagaGacctcagccaagaccaccat	5	19	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7721733G>T	ENST00000572933.1	+	69	11951	c.10491G>T	c.(10489-10491)gaG>gaT	p.E3497D	DNAH2_ENST00000389173.2_Missense_Mutation_p.E3497D			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3497	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E3497D(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				ACAGCCCAGAGACCTCAGCCA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											227	218	221					17																	7721733		2203	4300	6503	7662458	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10491G>T	17.37:g.7721733G>T	ENSP00000458355:p.Glu3497Asp		7662458	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710137	0.68730	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.30448	1.53	4.99	1.98	0.26296	.	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.49224	-0.8962	10	0.87932	D	0	.	8.1821	0.31317	0.3297:0.0:0.6703:0.0	.	3458;3497	Q9P225-2;Q9P225	.;DYH2_HUMAN	D	3458;3497	ENSP00000373825:E3497D	ENSP00000353818:E3458D	E	+	3	2	DNAH2	7662458	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.409000	0.52657	0.314000	0.23086	0.655000	0.94253	GAG		0.507	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7721733	G	T	7721733	3	4	61	1	0	0	0	0	1	0	0	0	4613	933	33	2	10761	2	DNAH2	17	7721733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13079	7721733	73473477	10029	18014										
CHD3	1107	broad.mit.edu	37	chr17	7804220	7804220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgaggccttgaattcacGaggtggtgggaaccaggtgt	15	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7804220G>A	ENST00000330494.7	+	19	3179	c.3029G>A	c.(3028-3030)cGa>cAa	p.R1010Q	CHD3_ENST00000380358.4_Missense_Mutation_p.R1069Q|CHD3_ENST00000358181.4_Missense_Mutation_p.R1010Q	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1010					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R1010Q(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TTGAATTCACGAGGTGGTGGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											108	101	103					17																	7804220		2203	4300	6503	7744945	SO:0001583	missense	1107			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.3029G>A	17.37:g.7804220G>A	ENSP00000332628:p.Arg1010Gln		7744945	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.624353	0.46840	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	T;T;T	0.75154	-0.91;-0.91;-0.91	4.95	4.95	0.65309	SNF2-related (1);	0.000000	0.37955	N	0.001879	T	0.63022	0.2476	L	0.28400	0.85	0.42650	D	0.993445	P;P;D	0.53151	0.876;0.898;0.958	B;B;B	0.41299	0.131;0.207;0.353	T	0.69537	-0.5119	10	0.72032	D	0.01	-6.6537	12.5678	0.56320	0.0873:0.0:0.9127:0.0	.	1010;1010;1069	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	Q	1069;1010;1010	ENSP00000369716:R1069Q;ENSP00000350907:R1010Q;ENSP00000332628:R1010Q	ENSP00000332628:R1010Q	R	+	2	0	CHD3	7744945	0.027000	0.19231	1.000000	0.80357	0.988000	0.76386	1.875000	0.39578	2.744000	0.94065	0.561000	0.74099	CGA		0.418	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		A	7804220	G	A	7804220	3	1	61	1	0	0	0	0	1	0	0	0	3332	1058	37	1	3384	1	CHD3	17	7804220	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82487	7804220	73390990	10030	18015										
CHD3	1107	broad.mit.edu	37	chr17	7811765	7811765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacgggcagctatttcctCggggaaactcaatgagatct	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7811765C>T	ENST00000330494.7	+	35	5348	c.5198C>T	c.(5197-5199)tCg>tTg	p.S1733L	CHD3_ENST00000380358.4_Missense_Mutation_p.S1792L|CHD3_ENST00000358181.4_Missense_Mutation_p.S1699L|SCARNA21_ENST00000517026.1_RNA	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1733	Required for interaction with PCNT.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S1733L(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GCTATTTCCTCGGGGAAACTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											89	80	83					17																	7811765		2203	4300	6503	7752490	SO:0001583	missense	1107			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.5198C>T	17.37:g.7811765C>T	ENSP00000332628:p.Ser1733Leu		7752490	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.704859	0.68615	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494;ENST00000439235;ENST00000449744	D;D;D	0.90844	-2.74;-2.71;-2.68	4.45	4.45	0.53987	.	0.000000	0.41294	D	0.000920	D	0.93446	0.7909	L	0.46157	1.445	0.80722	D	1	D;D;P;D	0.89917	1.0;0.982;0.833;0.991	D;P;B;P	0.76575	0.988;0.689;0.256;0.874	D	0.94263	0.7504	10	0.72032	D	0.01	-9.7893	17.2758	0.87114	0.0:1.0:0.0:0.0	.	310;1699;1733;1792	B3KWV4;Q12873-2;Q12873;E9PG89	.;.;CHD3_HUMAN;.	L	1792;1699;1733;61;25	ENSP00000369716:S1792L;ENSP00000350907:S1699L;ENSP00000332628:S1733L	ENSP00000332628:S1733L	S	+	2	0	CHD3	7752490	1.000000	0.71417	0.992000	0.48379	0.743000	0.42351	7.651000	0.83577	2.311000	0.77944	0.561000	0.74099	TCG		0.483	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		T	7811765	C	T	7811765	3	4	61	1	0	0	0	0	1	0	0	0	3332	893	31	1	5617	1	CHD3	17	7811765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7545	7811765	73383445	10031	18016										
GUCY2D	3000	broad.mit.edu	37	chr17	7907334	7907334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggaggccttggccgcactcGccaacagctcccagcttcgc	11	18	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7907334G>A	ENST00000254854.4	+	3	1036	c.886G>A	c.(886-888)Gcc>Acc	p.A296T		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	296					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.A296T(1)		skin(1)	1		Prostate(122;0.157)				GGCCGCACTCGCCAACAGCTC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	17											91	94	93					17																	7907334		2203	4300	6503	7848059	SO:0001583	missense	3000			L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.886G>A	17.37:g.7907334G>A	ENSP00000254854:p.Ala296Thr		7848059	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	1.301	-0.604947	0.03717	.	.	ENSG00000132518	ENST00000254854	D	0.82984	-1.67	4.53	1.19	0.21007	Extracellular ligand-binding receptor (1);	0.493342	0.17155	N	0.184900	T	0.61937	0.2387	N	0.16602	0.42	0.09310	N	1	B	0.16166	0.016	B	0.09377	0.004	T	0.41161	-0.9524	10	0.10377	T	0.69	.	4.1705	0.10327	0.2775:0.0:0.5482:0.1743	.	296	Q02846	GUC2D_HUMAN	T	296	ENSP00000254854:A296T	ENSP00000254854:A296T	A	+	1	0	GUCY2D	7848059	0.013000	0.17824	0.410000	0.26471	0.123000	0.20343	1.113000	0.31184	0.526000	0.28541	-0.314000	0.08810	GCC		0.682	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7907334	G	A	7907334	3	1	61	1	0	0	0	0	1	0	0	0	6918	1087	38	1	892	1	GUCY2D	17	7907334	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95569	7907334	73287876	10032	18017										
ALOX12B	242	broad.mit.edu	37	chr17	7983557	7983557	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgccccattccataccggaGacgacagatttcttgccagg	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:7983557G>T	ENST00000319144.4	-	6	1010	c.750C>A	c.(748-750)gtC>gtA	p.V250V	AC129492.6_ENST00000399413.3_Missense_Mutation_p.D80Y|ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	250	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.V250V(1)		endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						CCATACCGGAGACGACAGATT	0.612										Multiple Myeloma(8;0.094)	OREG0024153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	17											80	94	89					17																	7983557		2203	4300	6503	7924282	SO:0001819	synonymous_variant	242			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.750C>A	17.37:g.7983557G>T		645	7924282		Silent	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.511165	0.27036	.	.	ENSG00000214999	ENST00000399413	.	.	.	4.85	3.88	0.44766	.	.	.	.	.	T	0.61800	0.2376	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63616	-0.6597	5	0.87932	D	0	-9.4964	6.422	0.21748	0.0949:0.0:0.7252:0.1799	.	.	.	.	Y	80	.	ENSP00000382345:D80Y	D	+	1	0	AC129492.6	7924282	1.000000	0.71417	0.895000	0.35142	0.191000	0.23601	2.413000	0.44618	1.178000	0.42870	0.555000	0.69702	GAC		0.612	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			T	7983557	G	T	7983557	2	4	61	1	0	0	0	0	0	0	0	1	537	929	33	2		2	ALOX12B	17	7983557	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76223	7983557	73211653	10033	18018										
ALOXE3	59344	broad.mit.edu	37	chr17	8015449	8015449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaccagaagatgttctgcAtgtcatccagcttcttccag	9	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8015449A>G	ENST00000448843.2	-	7	1086	c.746T>C	c.(745-747)aTg>aCg	p.M249T	ALOXE3_ENST00000318227.3_Missense_Mutation_p.M381T|ALOXE3_ENST00000380149.1_Missense_Mutation_p.M405T	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	249	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.M249T(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						GATGTTCTGCATGTCATCCAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											209	174	186					17																	8015449		2203	4300	6503	7956174	SO:0001583	missense	59344			AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"Arachidonate lipoxygenases"	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.746T>C	17.37:g.8015449A>G	ENSP00000400581:p.Met249Thr		7956174	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	37	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.813369	0.32053	.	.	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	D;D;D	0.89875	-2.58;-2.58;-2.58	5.87	5.87	0.94306	Lipoxygenase, C-terminal (2);	0.453231	0.27275	N	0.020103	D	0.90154	0.6923	M	0.67953	2.075	0.33032	D	0.530294	B;B;B	0.29671	0.031;0.254;0.254	B;B;B	0.38880	0.071;0.191;0.284	D	0.92906	0.6343	10	0.72032	D	0.01	-4.0561	15.5573	0.76208	1.0:0.0:0.0:0.0	.	381;249;249	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	T	405;381;249	ENSP00000369494:M405T;ENSP00000314879:M381T;ENSP00000400581:M249T	ENSP00000314879:M381T	M	-	2	0	ALOXE3	7956174	1.000000	0.71417	0.295000	0.24960	0.103000	0.19146	7.287000	0.78681	2.371000	0.80710	0.533000	0.62120	ATG		0.537	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1			G	8015449	A	G	8015449	3	3	61	1	0	0	0	0	1	0	0	0	542	217	8	4	1429	4	ALOXE3	17	8015449	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	31892	8015449	73179761	10034	18019										
ARHGEF15	22899	broad.mit.edu	37	chr17	8218583	8218583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctcagcccccaggagagGcgcatgcaggaggtgggagc	16	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8218583G>A	ENST00000361926.3	+	6	1358	c.1248G>A	c.(1246-1248)agG>agA	p.R416R	AC135178.7_ENST00000458568.1_RNA|ARHGEF15_ENST00000421050.1_Silent_p.R416R	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	416					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R416R(1)		breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CCCAGGAGAGGCGCATGCAGG	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	17											20	22	21					17																	8218583		2202	4300	6502	8159308	SO:0001819	synonymous_variant	22899			AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.1248G>A	17.37:g.8218583G>A			8159308	A8K6G1|Q8N449|Q9H8B4	Silent	SNP	ENST00000361926.3	37	CCDS11139.1																																																																																				0.677	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		A	8218583	G	A	8218583	2	1	61	1	0	0	0	0	0	0	0	1	898	1194	42	3		3	ARHGEF15	17	8218583	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203134	8218583	72976627	10035	18020										
KRBA2	124751	broad.mit.edu	37	chr17	8272583	8272583	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcctgcctgatccaaaGgctattttctagctgttctt	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8272583G>T	ENST00000331336.2	-	2	1353	c.1348C>A	c.(1348-1350)Ctt>Att	p.L450I	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Missense_Mutation_p.L368I|RP11-849F2.5_ENST00000580537.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	450					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.L450I(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						CTGATCCAAAGGCTATTTTCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											146	140	142					17																	8272583		2203	4300	6503	8213308	SO:0001583	missense	124751			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"-"	26989	protein-coding gene	gene with protein product			"KRAB A domain containing 2"			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.1348C>A	17.37:g.8272583G>T	ENSP00000328017:p.Leu450Ile		8213308	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	g	6.986	0.552088	0.13374	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.26223	1.76;1.75	2.78	-0.421	0.12332	.	.	.	.	.	T	0.13500	0.0327	L	0.34521	1.04	0.20764	N	0.999851	P	0.39809	0.689	B	0.30716	0.119	T	0.16958	-1.0385	9	0.87932	D	0	.	3.3176	0.07039	0.2658:0.2207:0.5135:0.0	.	450	Q6ZNG9	KRBA2_HUMAN	I	368;450	ENSP00000379565:L368I;ENSP00000328017:L450I	ENSP00000328017:L450I	L	-	1	0	KRBA2	8213308	0.550000	0.26489	0.975000	0.42487	0.513000	0.34164	-0.147000	0.10234	-0.039000	0.13602	-0.145000	0.13849	CTT		0.468	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		T	8272583	G	T	8272583	3	4	61	1	0	0	0	0	1	0	0	0	8461	1000	35	2	134	2	KRBA2	17	8272583	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54000	8272583	72922627	10036	18021										
KRBA2	124751	broad.mit.edu	37	chr17	8273384	8273384	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtacataataccgtattcGatcacgttctccatgagtag	7	9	2	1	rs202118881	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8273384G>A	ENST00000331336.2	-	2	552	c.547C>T	c.(547-549)Cga>Tga	p.R183*	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Nonsense_Mutation_p.R101*|RP11-849F2.5_ENST00000580537.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	183					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.R183*(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						TACCGTATTCGATCACGTTCT	0.438													G|||	8	0.00159744	0	0	5008	,	,		20956	0.0079		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	17											206	186	192					17																	8273384		2203	4300	6503	8214109	SO:0001587	stop_gained	124751			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"-"	26989	protein-coding gene	gene with protein product			"KRAB A domain containing 2"			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.547C>T	17.37:g.8273384G>A	ENSP00000328017:p.Arg183*		8214109	Q8IYY0	Nonsense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	G	12.75	2.031138	0.35797	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	.	.	.	2.42	1.44	0.22558	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	5.1214	0.14862	0.167:0.0:0.833:0.0	.	.	.	.	X	101;183	.	ENSP00000328017:R183X	R	-	1	2	KRBA2	8214109	0.000000	0.05858	0.012000	0.15200	0.581000	0.36288	-0.317000	0.08060	0.602000	0.29896	0.555000	0.69702	CGA		0.438	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		A	8273384	G	A	8273384	4	1	61	1	0	0	0	0	0	1	0	0	8461	1066	37	1	935	1	KRBA2	17	8273384	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	801	8273384	72921826	10037	18022										
KRBA2	124751	broad.mit.edu	37	chr17	8274823	8274823	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagcaggactggggaagaGacaagagagggcaccaggaa	16	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8274823G>T	ENST00000331336.2	-	1	35	c.30C>A	c.(28-30)gtC>gtA	p.V10V	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Intron|RP11-849F2.5_ENST00000580537.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	10					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.V10V(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						CTGGGGAAGAGACAAGAGAGG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	17											61	65	63					17																	8274823		2203	4300	6503	8215548	SO:0001819	synonymous_variant	124751			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"-"	26989	protein-coding gene	gene with protein product			"KRAB A domain containing 2"			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.30C>A	17.37:g.8274823G>T			8215548	Q8IYY0	Silent	SNP	ENST00000331336.2	37	CCDS11141.1																																																																																				0.478	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		T	8274823	G	T	8274823	2	4	61	1	0	0	0	0	0	0	0	1	8461	929	33	2		2	KRBA2	17	8274823	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1439	8274823	72920387	10038	18023										
NDEL1	81565	broad.mit.edu	37	chr17	8354128	8354128	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaactagcagttcgggaaaGacaacaggaagtaactagaa	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8354128G>T	ENST00000334527.7	+	6	754	c.557G>T	c.(556-558)aGa>aTa	p.R186I	NDEL1_ENST00000402554.3_Missense_Mutation_p.R186I|NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Missense_Mutation_p.R186I|NDEL1_ENST00000299734.7_Missense_Mutation_p.R186I	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	186	Interaction with CENPF.|Interaction with KATNB1. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)	p.R186I(1)		large_intestine(6)|lung(4)|skin(3)	13						GTTCGGGAAAGACAACAGGAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											67	59	62					17																	8354128		2203	4300	6503	8294853	SO:0001583	missense	81565			AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.557G>T	17.37:g.8354128G>T	ENSP00000333982:p.Arg186Ile		8294853	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	37	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500577	0.85176	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	4.98	4.98	0.66077	NUDE protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72676	0.3490	M	0.62723	1.935	0.80722	D	1	P;P	0.44380	0.589;0.834	P;P	0.52598	0.589;0.703	T	0.74996	-0.3473	9	0.66056	D	0.02	-3.1886	18.8054	0.92035	0.0:0.0:1.0:0.0	.	186;186	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	I	186;186;241;186	.	ENSP00000299734:R186I	R	+	2	0	NDEL1	8294853	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.081000	0.76844	2.744000	0.94065	0.655000	0.94253	AGA		0.443	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		T	8354128	G	T	8354128	3	4	61	1	0	0	0	0	1	0	0	0	10275	942	33	2	575	2	NDEL1	17	8354128	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79305	8354128	72841082	10039	18024										
NDEL1	81565	broad.mit.edu	37	chr17	8363345	8363345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctttagaatccaaattaGcagcttgcaggaattttgca	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8363345G>A	ENST00000334527.7	+	8	1008	c.811G>A	c.(811-813)Gca>Aca	p.A271T	NDEL1_ENST00000402554.3_Missense_Mutation_p.A271T|NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Intron|NDEL1_ENST00000299734.7_Missense_Mutation_p.A271T	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	271	Interaction with CENPF.|Interaction with DISC1.|Interaction with NEFL. {ECO:0000250}.|Required for localization to the centrosome and interaction with dynein, dynactin, tubulin gamma, PCM1 and PCNT.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)	p.A271T(2)		large_intestine(6)|lung(4)|skin(3)	13						ATCCAAATTAGCAGCTTGCAG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	17											118	115	116					17																	8363345		2203	4300	6503	8304070	SO:0001583	missense	81565			AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.811G>A	17.37:g.8363345G>A	ENSP00000333982:p.Ala271Thr		8304070	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	37	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483614	0.84854	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	5.0	4.04	0.47022	NUDE protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76969	0.4062	M	0.80982	2.52	0.80722	D	1	P;D	0.54397	0.886;0.966	P;D	0.64237	0.788;0.923	T	0.78046	-0.2357	9	0.38643	T	0.18	-4.2125	13.8772	0.63660	0.0739:0.0:0.9261:0.0	.	271;271	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	T	271;271;326;271	.	ENSP00000299734:A271T	A	+	1	0	NDEL1	8304070	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.344000	0.90055	1.480000	0.48289	0.491000	0.48974	GCA		0.378	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		A	8363345	G	A	8363345	3	1	61	1	0	0	0	0	1	0	0	0	10275	971	34	3	837	3	NDEL1	17	8363345	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9217	8363345	72831865	10040	18025										
MYH10	4628	broad.mit.edu	37	chr17	8390796	8390796	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcatcccgagctttgttCgcagcctcgatttgggcttc	9	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8390796C>T	ENST00000269243.4	-	34	5046	c.4908G>A	c.(4906-4908)gcG>gcA	p.A1636A	MYH10_ENST00000360416.3_Silent_p.A1667A|MYH10_ENST00000396239.1_Silent_p.A1657A|MYH10_ENST00000379980.4_Silent_p.A1652A	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1636					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.A1636A(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GAGCTTTGTTCGCAGCCTCGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	17											247	220	230					17																	8390796		2203	4300	6503	8331521	SO:0001819	synonymous_variant	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4908G>A	17.37:g.8390796C>T			8331521	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																				0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8390796	C	T	8390796	2	4	61	1	0	0	0	0	0	0	0	1	10060	871	31	1		1	MYH10	17	8390796	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27451	8390796	72804414	10041	18026										
MYH10	4628	broad.mit.edu	37	chr17	8409737	8409737	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctggtcctgcaggtcggtCgtctccccgtcgagttttct	11	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8409737C>T	ENST00000269243.4	-	25	3330	c.3192G>A	c.(3190-3192)acG>acA	p.T1064T	MYH10_ENST00000379980.4_Silent_p.T1080T|MYH10_ENST00000396239.1_Silent_p.T1085T|MYH10_ENST00000360416.3_Silent_p.T1095T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1064					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T1064T(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GCAGGTCGGTCGTCTCCCCGT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	17											136	116	123					17																	8409737		2203	4300	6503	8350462	SO:0001819	synonymous_variant	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.3192G>A	17.37:g.8409737C>T			8350462	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																				0.527	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8409737	C	T	8409737	2	4	61	1	0	0	0	0	0	0	0	1	10060	871	31	1		1	MYH10	17	8409737	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18941	8409737	72785473	10042	18027										
MYH10	4628	broad.mit.edu	37	chr17	8411935	8411935	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccaagtttttcgccttttCttcctcttcagccagctgag	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8411935C>A	ENST00000269243.4	-	24	3196	c.3058G>T	c.(3058-3060)Gaa>Taa	p.E1020*	MYH10_ENST00000379980.4_Nonsense_Mutation_p.E1036*|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000396239.1_Nonsense_Mutation_p.E1041*|MYH10_ENST00000360416.3_Nonsense_Mutation_p.E1051*	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1020					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E1020*(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TTCGCCTTTTCTTCCTCTTCA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											213	190	198					17																	8411935		2203	4300	6503	8352660	SO:0001587	stop_gained	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.3058G>T	17.37:g.8411935C>A	ENSP00000269243:p.Glu1020*		8352660	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Nonsense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	C	42	9.813042	0.99270	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	.	.	.	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.5061	0.90898	0.0:1.0:0.0:0.0	.	.	.	.	X	1020;1051;1041;1036	.	ENSP00000269243:E1020X	E	-	1	0	MYH10	8352660	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.645000	0.83430	2.587000	0.87381	0.563000	0.77884	GAA		0.428	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			A	8411935	C	A	8411935	4	1	61	1	0	0	0	0	0	1	0	0	10060	922	32	2	2944	2	MYH10	17	8411935	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2198	8411935	72783275	10043	18028										
MYH10	4628	broad.mit.edu	37	chr17	8455404	8455404	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagataacaactggtaaaaGatatgaaaagtacgttcatc	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8455404G>T	ENST00000269243.4	-	8	987	c.849C>A	c.(847-849)atC>atA	p.I283I	MYH10_ENST00000379980.4_Silent_p.I299I|MYH10_ENST00000396239.1_Silent_p.I283I|MYH10_ENST00000360416.3_Silent_p.I293I	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	283	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.I283I(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ACTGGTAAAAGATATGAAAAG	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	17											48	49	49					17																	8455404		2203	4300	6503	8396129	SO:0001819	synonymous_variant	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.849C>A	17.37:g.8455404G>T			8396129	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																				0.303	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8455404	G	T	8455404	2	4	61	1	0	0	0	0	0	0	0	1	10060	932	33	2		2	MYH10	17	8455404	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43469	8455404	72739806	10044	18029										
CCDC42	146849	broad.mit.edu	37	chr17	8638451	8638451	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgtcctccagtgccaccTcagtcacctccttcaggtgc	10	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8638451T>A	ENST00000293845.3	-	6	1062	c.836A>T	c.(835-837)gAg>gTg	p.E279V	CCDC42_ENST00000539522.2_Missense_Mutation_p.E205V	NM_144681.2	NP_653282.2	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42	279								p.E279V(1)		kidney(1)|large_intestine(4)|lung(3)|ovary(1)	9						CAGTGCCACCTCAGTCACCTC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											108	90	96					17																	8638451		2203	4300	6503	8579176	SO:0001583	missense	146849			AK057296	CCDS11145.1, CCDS54088.1	17p13.1	2012-05-28			ENSG00000161973	ENSG00000161973			26528	protein-coding gene	gene with protein product							Standard	NM_144681		Approved	FLJ32734, CCDC42A	uc002gln.3	Q96M95		ENST00000293845.3:c.836A>T	17.37:g.8638451T>A	ENSP00000293845:p.Glu279Val		8579176	Q8N6Q0	Missense_Mutation	SNP	ENST00000293845.3	37	CCDS11145.1	.	.	.	.	.	.	.	.	.	.	T	1.140	-0.649952	0.03506	.	.	ENSG00000161973	ENST00000293845;ENST00000539522	T;T	0.24908	1.83;1.85	5.11	-10.2	0.00374	.	3.909620	0.00575	N	0.000317	T	0.09379	0.0231	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.18713	-1.0328	10	0.30854	T	0.27	2.4966	1.4548	0.02383	0.176:0.3008:0.2736:0.2496	.	279	Q96M95	CCD42_HUMAN	V	279;205	ENSP00000293845:E279V;ENSP00000444359:E205V	ENSP00000293845:E279V	E	-	2	0	CCDC42	8579176	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.023000	0.01438	-2.660000	0.00419	-1.276000	0.01395	GAG		0.617	CCDC42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442491.1	NM_144681		A	8638451	T	A	8638451	3	1	61	1	0	0	0	0	1	0	0	0	2820	1551	54	5	122	5	CCDC42	17	8638451	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	183047	8638451	72556759	10045	18030										
CCDC42	146849	broad.mit.edu	37	chr17	8647476	8647476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagatggatggggactccGacgccccctcaacattgggg	14	13	1	1	rs536001412		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8647476G>A	ENST00000293845.3	-	2	336	c.110C>T	c.(109-111)tCg>tTg	p.S37L	CCDC42_ENST00000539522.2_Missense_Mutation_p.S37L	NM_144681.2	NP_653282.2	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42	37								p.S37L(1)		kidney(1)|large_intestine(4)|lung(3)|ovary(1)	9						TGGGGACTCCGACGCCCCCTC	0.542													G|||	1	0.000199681	8e-04	0	5008	,	,		18272	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											120	102	109					17																	8647476		2203	4300	6503	8588201	SO:0001583	missense	146849			AK057296	CCDS11145.1, CCDS54088.1	17p13.1	2012-05-28			ENSG00000161973	ENSG00000161973			26528	protein-coding gene	gene with protein product							Standard	NM_144681		Approved	FLJ32734, CCDC42A	uc002gln.3	Q96M95		ENST00000293845.3:c.110C>T	17.37:g.8647476G>A	ENSP00000293845:p.Ser37Leu		8588201	Q8N6Q0	Missense_Mutation	SNP	ENST00000293845.3	37	CCDS11145.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.445989	0.01089	.	.	ENSG00000161973	ENST00000293845;ENST00000539522	T;T	0.26067	1.76;1.82	4.35	1.26	0.21427	.	0.255507	0.28067	N	0.016728	T	0.10508	0.0257	N	0.12182	0.205	0.09310	N	0.999994	B	0.13594	0.008	B	0.06405	0.002	T	0.35126	-0.9801	10	0.10111	T	0.7	-0.619	6.8614	0.24069	0.3788:0.0:0.6212:0.0	.	37	Q96M95	CCD42_HUMAN	L	37	ENSP00000293845:S37L;ENSP00000444359:S37L	ENSP00000293845:S37L	S	-	2	0	CCDC42	8588201	0.033000	0.19621	0.080000	0.20451	0.003000	0.03518	0.755000	0.26405	0.220000	0.20860	-0.149000	0.13747	TCG		0.542	CCDC42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442491.1	NM_144681		A	8647476	G	A	8647476	3	1	61	1	0	0	0	0	1	0	0	0	2820	1059	37	1	864	1	CCDC42	17	8647476	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9025	8647476	72547734	10046	18031										
MFSD6L	162387	broad.mit.edu	37	chr17	8701224	8701224	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaagctgagggcgaccgaGaaacccatgaccagctcgcc	12	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8701224G>A	ENST00000329805.4	-	1	1443	c.1215C>T	c.(1213-1215)ttC>ttT	p.F405F		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	405						integral component of membrane (GO:0016021)		p.F405F(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						GGGCGACCGAGAAACCCATGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	17											83	97	92					17																	8701224		2203	4300	6503	8641949	SO:0001819	synonymous_variant	162387			AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1215C>T	17.37:g.8701224G>A			8641949	Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																				0.562	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599		A	8701224	G	A	8701224	2	1	61	1	0	0	0	0	0	0	0	1	9566	933	33	3		3	MFSD6L	17	8701224	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53748	8701224	72493986	10047	18032										
PIK3R6	146850	broad.mit.edu	37	chr17	8725231	8725231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaggaaacggtgacctctCggggccggtggctaagcaag	16	11	1	1	rs199606703		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8725231C>T	ENST00000311434.9	-	17	2050	c.1811G>A	c.(1810-1812)cGa>cAa	p.R604Q	PIK3R6_ENST00000434064.2_5'UTR	NM_001010855.2	NP_001010855.1	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	604					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										GGTGACCTCTCGGGGCCGGTG	0.592																																																0			17						T	GLN/ARG	0,3956		0,0,1978	28	30	30		1811	-8	0	17		30	1,8337		0,1,4168	yes	missense	PIK3R6	NM_001010855.2	43	0,1,6146	TT,TC,CC		0.012,0.0,0.0081	benign	604/755	8725231	1,12293	1978	4169	6147	8665956	SO:0001583	missense	146850			AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000311434.9:c.1811G>A	17.37:g.8725231C>T	ENSP00000475670:p.Arg604Gln		8665956	Q658R3	Missense_Mutation	SNP	ENST00000311434.9	37																																																																																					0.592	PIK3R6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001010855		T	8725231	C	T	8725231	3	4	61	1	0	0	0	0	1	0	0	0	11954	884	31	1	468	1	PIK3R6	17	8725231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24007	8725231	72469979	10048	18033										
PIK3R6	146850	broad.mit.edu	37	chr17	8739899	8739899	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacagctcattcgtcaagttCtgttcggcaatgaccatcct	7	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8739899C>A	ENST00000311434.9	-	7	665	c.426G>T	c.(424-426)caG>caT	p.Q142H	PIK3R6_ENST00000434064.2_5'UTR	NM_001010855.2	NP_001010855.1	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	142					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										TCGTCAAGTTCTGTTCGGCAA	0.507																																																0			17											132	130	131					17																	8739899		2056	4194	6250	8680624	SO:0001583	missense	146850			AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000311434.9:c.426G>T	17.37:g.8739899C>A	ENSP00000475670:p.Gln142His		8680624	Q658R3	Missense_Mutation	SNP	ENST00000311434.9	37																																																																																					0.507	PIK3R6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001010855		A	8739899	C	A	8739899	3	1	61	1	0	0	0	0	1	0	0	0	11954	912	32	2	1893	2	PIK3R6	17	8739899	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14668	8739899	72455311	10049	18034										
PIK3R6	146850	broad.mit.edu	37	chr17	8740140	8740140	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccgttttcagccttatcGcgcagtccaaggcgactgtg	10	13	2	0	rs577072208		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:8740140G>A	ENST00000311434.9	-	6	598	c.359C>T	c.(358-360)gCg>gTg	p.A120V	PIK3R6_ENST00000434064.2_5'UTR	NM_001010855.2	NP_001010855.1	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	120					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										CAGCCTTATCGCGCAGTCCAA	0.537													G|||	1	0.000199681	0	0	5008	,	,		17729	0		0	False		,,,				2504	0.001															0			17											81	85	84					17																	8740140		2040	4199	6239	8680865	SO:0001583	missense	146850			AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000311434.9:c.359C>T	17.37:g.8740140G>A	ENSP00000475670:p.Ala120Val		8680865	Q658R3	Missense_Mutation	SNP	ENST00000311434.9	37																																																																																					0.537	PIK3R6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001010855		A	8740140	G	A	8740140	3	1	61	1	0	0	0	0	1	0	0	0	11954	1087	38	1	1964	1	PIK3R6	17	8740140	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241	8740140	72455070	10050	18035										
STX8	9482	broad.mit.edu	37	chr17	9281939	9281939	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaagtttttcatctgtgttCtccactaggttggcaaggtc	10	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:9281939C>A	ENST00000306357.4	-	7	1000	c.573G>T	c.(571-573)gaG>gaT	p.E191D	STX8_ENST00000574431.1_Missense_Mutation_p.E80D	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	191	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.E191D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						CATCTGTGTTCTCCACTAGGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	17											248	235	240					17																	9281939		2203	4300	6503	9222664	SO:0001583	missense	9482			AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310			11443	protein-coding gene	gene with protein product		604203				9852078, 10198254	Standard	NM_004853		Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.573G>T	17.37:g.9281939C>A	ENSP00000305255:p.Glu191Asp		9222664	O60712|Q53XT8	Missense_Mutation	SNP	ENST00000306357.4	37	CCDS32565.1	.	.	.	.	.	.	.	.	.	.	C	9.385	1.073967	0.20147	.	.	ENSG00000170310	ENST00000306357	.	.	.	6.01	3.98	0.46160	Target SNARE coiled-coil domain (3);	0.100614	0.64402	N	0.000002	T	0.15869	0.0382	N	0.02158	-0.66	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.17561	-1.0365	9	0.02654	T	1	-21.1028	5.8456	0.18663	0.1557:0.6868:0.0:0.1575	.	191	Q9UNK0	STX8_HUMAN	D	191	.	ENSP00000305255:E191D	E	-	3	2	STX8	9222664	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.757000	0.26433	0.832000	0.34804	0.650000	0.86243	GAG		0.433	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439206.3	NM_004853		A	9281939	C	A	9281939	3	1	61	1	0	0	0	0	1	0	0	0	15390	912	32	2	145	2	STX8	17	9281939	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	541799	9281939	71913271	10051	18036										
USP43	124739	broad.mit.edu	37	chr17	9631794	9631794	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggagggccagaaggccatGaactggaaggagagcttcca	15	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:9631794G>T	ENST00000285199.7	+	15	2955	c.2859G>T	c.(2857-2859)atG>atT	p.M953I	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.M948I	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	953					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.M954I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						AGAAGGCCATGAACTGGAAGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	17											33	35	35					17																	9631794		1966	4145	6111	9572519	SO:0001583	missense	124739			AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"Ubiquitin-specific peptidases"	20072	protein-coding gene	gene with protein product			"ubiquitin specific protease 43"			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.2859G>T	17.37:g.9631794G>T	ENSP00000285199:p.Met953Ile		9572519	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331813	0.41297	.	.	ENSG00000154914	ENST00000285199	T	0.08546	3.08	5.5	-10.3	0.00346	.	5.100030	0.00983	N	0.003404	T	0.04092	0.0114	N	0.08118	0	0.09310	N	1	B;B;B;B	0.16802	0.011;0.019;0.011;0.019	B;B;B;B	0.18871	0.006;0.023;0.006;0.023	T	0.29792	-1.0000	10	0.39692	T	0.17	3.1239	9.3618	0.38201	0.5165:0.3619:0.1216:0.0	.	948;642;953;465	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	I	953	ENSP00000285199:M953I	ENSP00000285199:M953I	M	+	3	0	USP43	9572519	0.000000	0.05858	0.000000	0.03702	0.195000	0.23768	-2.881000	0.00715	-1.851000	0.01168	0.655000	0.94253	ATG		0.557	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		T	9631794	G	T	9631794	3	4	61	1	0	0	0	0	1	0	0	0	17114	1290	45	2	2917	2	USP43	17	9631794	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	349855	9631794	71563416	10052	18037										
GLP2R	9340	broad.mit.edu	37	chr17	9745901	9745901	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatttggcaggatgactccGaatgctccgagaaccacagc	10	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:9745901G>A	ENST00000262441.5	+	4	985	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	GLP2R_ENST00000574745.1_5'UTR	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	158					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)	p.E158K(1)		endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GGATGACTCCGAATGCTCCGA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											130	104	113					17																	9745901		2203	4300	6503	9686626	SO:0001583	missense	9340			AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.472G>A	17.37:g.9745901G>A	ENSP00000262441:p.Glu158Lys		9686626	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	37	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	G	35	5.538263	0.96460	.	.	ENSG00000065325	ENST00000396206;ENST00000304773;ENST00000262441	T	0.37915	1.17	5.06	5.06	0.68205	GPCR, family 2, extracellular hormone receptor domain (1);	0.000000	0.39341	N	0.001387	T	0.54711	0.1875	M	0.74258	2.255	0.53688	D	0.999978	P	0.50156	0.932	P	0.54026	0.74	T	0.59621	-0.7420	10	0.72032	D	0.01	.	17.3704	0.87376	0.0:0.0:1.0:0.0	.	158	O95838	GLP2R_HUMAN	K	158;133;158	ENSP00000262441:E158K	ENSP00000262441:E158K	E	+	1	0	GLP2R	9686626	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	6.102000	0.71486	2.643000	0.89663	0.655000	0.94253	GAA		0.547	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9745901	G	A	9745901	3	1	61	1	0	0	0	0	1	0	0	0	6473	1059	37	1	486	1	GLP2R	17	9745901	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114107	9745901	71449309	10053	18038										
GLP2R	9340	broad.mit.edu	37	chr17	9792803	9792803	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaaatgtcccaagaagctCtcggaaggagatggcgctga	14	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:9792803C>T	ENST00000262441.5	+	13	1956	c.1443C>T	c.(1441-1443)ctC>ctT	p.L481L	GLP2R_ENST00000574745.1_Silent_p.L301L	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	481					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)	p.L481L(1)		endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	CCAAGAAGCTCTCGGAAGGAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											58	58	58					17																	9792803		2203	4300	6503	9733528	SO:0001819	synonymous_variant	9340			AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1443C>T	17.37:g.9792803C>T			9733528	Q4VAT3	Silent	SNP	ENST00000262441.5	37	CCDS11150.1																																																																																				0.592	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			T	9792803	C	T	9792803	2	4	61	1	0	0	0	0	0	0	0	1	6473	900	32	3		3	GLP2R	17	9792803	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46902	9792803	71402407	10054	18039										
MYH13	8735	broad.mit.edu	37	chr17	10219309	10219309	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatttcactaaattgatCttctaccgtccggcacgttc	6	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10219309C>A	ENST00000418404.3	-	27	3935	c.3772G>T	c.(3772-3774)Gat>Tat	p.D1258Y	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.D1258Y			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1258					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.D1258Y(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CTAAATTGATCTTCTACCGTC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	17											184	175	178					17																	10219309		1964	4149	6113	10160034	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3772G>T	17.37:g.10219309C>A	ENSP00000404570:p.Asp1258Tyr		10160034	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951541	0.73787	.	.	ENSG00000006788	ENST00000252172	D	0.83992	-1.79	4.36	4.36	0.52297	Myosin tail (1);	.	.	.	.	D	0.93259	0.7852	M	0.93241	3.395	0.51767	D	0.999939	D	0.89917	1.0	D	0.81914	0.995	D	0.95298	0.8401	9	0.87932	D	0	.	17.2531	0.87048	0.0:1.0:0.0:0.0	.	1258	Q9UKX3	MYH13_HUMAN	Y	1258	ENSP00000252172:D1258Y	ENSP00000252172:D1258Y	D	-	1	0	MYH13	10160034	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	7.682000	0.84083	2.124000	0.65301	0.551000	0.68910	GAT		0.423	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		A	10219309	C	A	10219309	3	1	61	1	0	0	0	0	1	0	0	0	10062	913	32	2	2100	2	MYH13	17	10219309	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426506	10219309	70975901	10055	18040										
MYH13	8735	broad.mit.edu	37	chr17	10222241	10222241	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaagctcggccacactatCtgcttgcttcttcctcaggg	8	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10222241C>A	ENST00000418404.3	-	26	3767	c.3604G>T	c.(3604-3606)Gat>Tat	p.D1202Y	RP11-401O9.3_ENST00000577743.1_RNA|RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.D1202Y			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1202					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.D1202Y(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCCACACTATCTGCTTGCTTC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	17											120	114	116					17																	10222241		2203	4300	6503	10162966	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3604G>T	17.37:g.10222241C>A	ENSP00000404570:p.Asp1202Tyr		10162966	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.228504	0.58777	.	.	ENSG00000006788	ENST00000252172	T	0.80738	-1.41	4.05	4.05	0.47172	Myosin tail (1);	.	.	.	.	D	0.93314	0.7869	H	0.97587	4.035	0.53005	D	0.99996	D	0.89917	1.0	D	0.91635	0.999	D	0.95885	0.8902	9	0.87932	D	0	.	16.7633	0.85517	0.0:1.0:0.0:0.0	.	1202	Q9UKX3	MYH13_HUMAN	Y	1202	ENSP00000252172:D1202Y	ENSP00000252172:D1202Y	D	-	1	0	MYH13	10162966	1.000000	0.71417	0.996000	0.52242	0.272000	0.26649	5.865000	0.69583	2.236000	0.73375	0.591000	0.81541	GAT		0.572	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		A	10222241	C	A	10222241	3	1	61	1	0	0	0	0	1	0	0	0	10062	913	32	2	2272	2	MYH13	17	10222241	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2932	10222241	70972969	10056	18041										
MYH13	8735	broad.mit.edu	37	chr17	10231268	10231268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttccggcgagcctcagatCgggccagttcttccttggtc	11	15	2	1	rs147387198	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10231268C>T	ENST00000418404.3	-	21	2769	c.2606G>A	c.(2605-2607)cGa>cAa	p.R869Q	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.R869Q			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	869					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R869Q(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						AGCCTCAGATCGGGCCAGTTC	0.532											OREG0024177	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	8	0.00159744	0.0015	0.0086	5008	,	,		19217	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	17						C	GLN/ARG	0,4386		0,0,2193	73	76	75		2606	0.9	1	17	dbSNP_134	75	5,8591	4.3+/-15.6	0,5,4293	yes	missense	MYH13	NM_003802.2	43	0,5,6486	TT,TC,CC		0.0582,0.0,0.0385	benign	869/1939	10231268	5,12977	2193	4298	6491	10171993	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2606G>A	17.37:g.10231268C>T	ENSP00000404570:p.Arg869Gln	663	10171993	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	5	0.0022893772893772895	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	0	0.0	C	11.95	1.792893	0.31685	0.0	5.82E-4	ENSG00000006788	ENST00000252172;ENST00000418404	D	0.82803	-1.65	4.01	0.889	0.19212	.	.	.	.	.	T	0.65852	0.2731	L	0.41632	1.29	0.26565	N	0.973663	B	0.17465	0.022	B	0.20577	0.03	T	0.61903	-0.6967	9	0.72032	D	0.01	.	2.8434	0.05536	0.0:0.3634:0.2358:0.4008	.	869	Q9UKX3	MYH13_HUMAN	Q	869;544	ENSP00000252172:R869Q	ENSP00000252172:R869Q	R	-	2	0	MYH13	10171993	0.558000	0.26554	0.983000	0.44433	0.272000	0.26649	0.987000	0.29603	0.461000	0.27071	0.563000	0.77884	CGA		0.532	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10231268	C	T	10231268	3	4	61	1	0	0	0	0	1	0	0	0	10062	884	31	1	3290	1	MYH13	17	10231268	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9027	10231268	70963942	10057	18042										
MYH13	8735	broad.mit.edu	37	chr17	10243705	10243705	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcccgcccttcttgctTcctccggagtcgcctggaga	9	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10243705T>C	ENST00000418404.3	-	16	2071	c.1908A>G	c.(1906-1908)ggA>ggG	p.G636G	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.G636G			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	636	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.G636G(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCTTCTTGCTTCCTCCGGAGT	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	17											57	63	61					17																	10243705		2013	4181	6194	10184430	SO:0001819	synonymous_variant	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.1908A>G	17.37:g.10243705T>C			10184430	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																				0.562	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		C	10243705	T	C	10243705	2	2	61	1	0	0	0	0	0	0	0	1	10062	1770	62	4		4	MYH13	17	10243705	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12437	10243705	70951505	10058	18043										
MYH13	8735	broad.mit.edu	37	chr17	10258071	10258071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggctcacgaaggggaagtCgaaggggttggtggagatca	18	5	2	1	rs371327620		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10258071C>T	ENST00000418404.3	-	10	1094	c.931G>A	c.(931-933)Gac>Aac	p.D311N	MYH13_ENST00000252172.4_Missense_Mutation_p.D311N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	311	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.D311N(4)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						AAGGGGAAGTCGAAGGGGTTG	0.458																																																4	Substitution - Missense(4)	large_intestine(4)	17						C	ASN/ASP	2,3890		0,2,1944	107	108	108		931	3.7	1	17		108	0,8278		0,0,4139	no	missense	MYH13	NM_003802.2	23	0,2,6083	TT,TC,CC		0.0,0.0514,0.0164	probably-damaging	311/1939	10258071	2,12168	1946	4139	6085	10198796	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.931G>A	17.37:g.10258071C>T	ENSP00000404570:p.Asp311Asn		10198796	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	31	5.060602	0.93846	5.14E-4	0.0	ENSG00000006788	ENST00000252172	D	0.87412	-2.25	3.72	3.72	0.42706	Myosin head, motor domain (2);	.	.	.	.	D	0.93419	0.7901	M	0.84219	2.685	0.48632	D	0.999683	D	0.89917	1.0	D	0.79784	0.993	D	0.94690	0.7873	9	0.87932	D	0	.	16.0467	0.80725	0.0:1.0:0.0:0.0	.	311	Q9UKX3	MYH13_HUMAN	N	311	ENSP00000252172:D311N	ENSP00000252172:D311N	D	-	1	0	MYH13	10198796	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.492000	0.81482	2.080000	0.62538	0.655000	0.94253	GAC		0.458	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10258071	C	T	10258071	3	4	61	1	0	0	0	0	1	0	0	0	10062	884	31	1	5009	1	MYH13	17	10258071	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14366	10258071	70937139	10059	18044										
MYH8	4626	broad.mit.edu	37	chr17	10298701	10298701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatcaacttcagacttgaCttggtttaactcaagctgga	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10298701C>A	ENST00000403437.2	-	34	4805	c.4711G>T	c.(4711-4713)Gtc>Ttc	p.V1571F	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1571					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.V1571F(1)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TCAGACTTGACTTGGTTTAAC	0.408									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							1	Substitution - Missense(1)	large_intestine(1)	17											113	97	103					17																	10298701		2203	4300	6503	10239426	SO:0001583	missense	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.4711G>T	17.37:g.10298701C>A	ENSP00000384330:p.Val1571Phe		10239426	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957384	0.53400	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.79141	-1.24	4.85	4.85	0.62838	Myosin tail (1);	0.000000	0.37577	U	0.002025	T	0.75613	0.3873	L	0.48362	1.52	0.50039	D	0.999849	B	0.15141	0.012	B	0.26693	0.072	T	0.73962	-0.3817	10	0.87932	D	0	.	18.168	0.89734	0.0:1.0:0.0:0.0	.	1571	P13535	MYH8_HUMAN	F	1571	ENSP00000384330:V1571F	ENSP00000252173:V1571F	V	-	1	0	MYH8	10239426	0.222000	0.23652	1.000000	0.80357	0.980000	0.70556	0.178000	0.16820	2.521000	0.84997	0.650000	0.86243	GTC		0.408	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10298701	C	A	10298701	3	1	61	1	0	0	0	0	1	0	0	0	10071	565	20	2	1130	2	MYH8	17	10298701	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40630	10298701	70896509	10060	18045										
MYH8	4626	broad.mit.edu	37	chr17	10304365	10304365	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctaaaaggctcctacttTtcaagcttttcatcaagttg	5	9	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10304365T>G	ENST00000403437.2	-	25	3346	c.3252A>C	c.(3250-3252)gaA>gaC	p.E1084D	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1084					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.E1084D(1)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GCTCCTACTTTTCAAGCTTTT	0.363									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							1	Substitution - Missense(1)	large_intestine(1)	17											128	123	125					17																	10304365		2202	4300	6502	10245090	SO:0001583	missense	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3252A>C	17.37:g.10304365T>G	ENSP00000384330:p.Glu1084Asp		10245090	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.125459	0.37533	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.83163	-1.69	5.49	4.42	0.53409	Myosin tail (1);	0.152818	0.29480	U	0.012026	T	0.65678	0.2714	N	0.08118	0	0.22213	N	0.999281	B	0.09022	0.002	B	0.08055	0.003	T	0.58679	-0.7594	10	0.87932	D	0	.	7.4734	0.27361	0.0:0.2054:0.0:0.7946	.	1084	P13535	MYH8_HUMAN	D	1084	ENSP00000384330:E1084D	ENSP00000252173:E1084D	E	-	3	2	MYH8	10245090	0.847000	0.29606	1.000000	0.80357	0.993000	0.82548	-0.079000	0.11357	1.098000	0.41479	0.533000	0.62120	GAA		0.363	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		G	10304365	T	G	10304365	3	3	61	1	0	0	0	0	1	0	0	0	10071	1838	64	4	2625	4	MYH8	17	10304365	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5664	10304365	70890845	10061	18046										
MYH8	4626	broad.mit.edu	37	chr17	10304474	10304474	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctctttctagatccattCgaagcttcttttcttgttcc	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10304474C>T	ENST00000403437.2	-	25	3237	c.3143G>A	c.(3142-3144)cGa>cAa	p.R1048Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1048					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.R1048Q(3)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TAGATCCATTCGAAGCTTCTT	0.348									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							3	Substitution - Missense(3)	large_intestine(3)	17											117	103	108					17																	10304474		2203	4300	6503	10245199	SO:0001583	missense	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3143G>A	17.37:g.10304474C>T	ENSP00000384330:p.Arg1048Gln		10245199	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987772	0.93106	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.95756	-3.8	5.48	5.48	0.80851	.	0.000000	0.38381	U	0.001703	D	0.98356	0.9454	H	0.97918	4.105	0.58432	D	0.999998	D	0.53885	0.963	P	0.54401	0.751	D	0.99357	1.0916	10	0.87932	D	0	.	19.5559	0.95347	0.0:1.0:0.0:0.0	.	1048	P13535	MYH8_HUMAN	Q	1048	ENSP00000384330:R1048Q	ENSP00000252173:R1048Q	R	-	2	0	MYH8	10245199	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	7.447000	0.80620	2.861000	0.98227	0.650000	0.86243	CGA		0.348	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10304474	C	T	10304474	3	4	61	1	0	0	0	0	1	0	0	0	10071	884	31	1	2734	1	MYH8	17	10304474	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109	10304474	70890736	10062	18047										
MYH4	4622	broad.mit.edu	37	chr17	10357937	10357937	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccatcttttcttctagttCtttcctttttgcctctgtct	3	13	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10357937C>A	ENST00000255381.2	-	22	2736	c.2626G>T	c.(2626-2628)Gaa>Taa	p.E876*	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	876					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)	p.E876*(1)		NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCTTCTAGTTCTTTCCTTTTT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											204	175	184					17																	10357937		2203	4300	6503	10298662	SO:0001587	stop_gained	4622				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.2626G>T	17.37:g.10357937C>A	ENSP00000255381:p.Glu876*		10298662		Nonsense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	39	7.620305	0.98393	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.3	5.3	0.74995	.	0.000000	0.37906	U	0.001896	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.3106	0.94186	0.0:1.0:0.0:0.0	.	.	.	.	X	876	.	ENSP00000255381:E876X	E	-	1	0	MYH4	10298662	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	7.689000	0.84165	2.631000	0.89168	0.563000	0.77884	GAA		0.408	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		A	10357937	C	A	10357937	4	1	61	1	0	0	0	0	0	1	0	0	10067	922	32	2	3269	2	MYH4	17	10357937	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53463	10357937	70837273	10063	18048										
MYH1	4619	broad.mit.edu	37	chr17	10398524	10398524	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacatcagtgatggccttCttggccttctcttctgcatt	7	13	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10398524C>A	ENST00000226207.5	-	36	5374	c.5280G>T	c.(5278-5280)aaG>aaT	p.K1760N	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1760					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K1760N(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TGATGGCCTTCTTGGCCTTCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17											282	237	252					17																	10398524		2203	4300	6503	10339249	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.5280G>T	17.37:g.10398524C>A	ENSP00000226207:p.Lys1760Asn		10339249	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166914	0.78339	.	.	ENSG00000109061	ENST00000226207	T	0.77489	-1.1	5.28	5.28	0.74379	Myosin tail (1);	0.000000	0.45361	U	0.000378	D	0.90106	0.6909	M	0.93720	3.45	0.54753	D	0.999982	D	0.76494	0.999	D	0.73708	0.981	D	0.91853	0.5493	10	0.72032	D	0.01	.	12.6206	0.56601	0.0:0.9234:0.0:0.0766	.	1760	P12882	MYH1_HUMAN	N	1760	ENSP00000226207:K1760N	ENSP00000226207:K1760N	K	-	3	2	MYH1	10339249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.930000	0.56522	2.618000	0.88619	0.561000	0.74099	AAG		0.453	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10398524	C	A	10398524	3	1	61	1	0	0	0	0	1	0	0	0	10059	912	32	2	559	2	MYH1	17	10398524	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40587	10398524	70796686	10064	18049										
MYH1	4619	broad.mit.edu	37	chr17	10404709	10404709	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccggcttcttccagcctCtcgctgatctcctccagctc	6	20	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10404709C>A	ENST00000226207.5	-	27	3550	c.3456G>T	c.(3454-3456)gaG>gaT	p.E1152D	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1152					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E1152D(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTTCCAGCCTCTCGCTGATCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											67	77	73					17																	10404709		2203	4300	6503	10345434	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3456G>T	17.37:g.10404709C>A	ENSP00000226207:p.Glu1152Asp		10345434	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826667	0.90955	.	.	ENSG00000109061	ENST00000226207	T	0.80566	-1.39	5.51	4.54	0.55810	Myosin tail (1);	0.000000	0.43579	U	0.000542	T	0.81992	0.4940	M	0.77712	2.385	0.54753	D	0.999983	B	0.21309	0.054	B	0.29176	0.099	T	0.80400	-0.1398	10	0.51188	T	0.08	.	14.4907	0.67649	0.0:0.9294:0.0:0.0706	.	1152	P12882	MYH1_HUMAN	D	1152	ENSP00000226207:E1152D	ENSP00000226207:E1152D	E	-	3	2	MYH1	10345434	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	5.937000	0.70162	1.464000	0.47987	0.650000	0.86243	GAG		0.617	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10404709	C	A	10404709	3	1	61	1	0	0	0	0	1	0	0	0	10059	912	32	2	2419	2	MYH1	17	10404709	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6185	10404709	70790501	10065	18050										
MYH1	4619	broad.mit.edu	37	chr17	10406139	10406139	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgcaggtcatccagggtCtgctggtgggcctcctggag	16	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10406139C>A	ENST00000226207.5	-	24	3121	c.3027G>T	c.(3025-3027)caG>caT	p.Q1009H	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1009					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Q1009H(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CATCCAGGGTCTGCTGGTGGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											122	120	120					17																	10406139		2203	4297	6500	10346864	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3027G>T	17.37:g.10406139C>A	ENSP00000226207:p.Gln1009His		10346864	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.286176	0.80803	.	.	ENSG00000109061	ENST00000226207	D	0.89552	-2.53	5.37	5.37	0.77165	.	0.000000	0.41194	U	0.000936	D	0.95367	0.8496	H	0.95294	3.65	0.44012	D	0.996728	P	0.52316	0.952	P	0.53954	0.738	D	0.96450	0.9333	10	0.87932	D	0	.	19.4761	0.94989	0.0:1.0:0.0:0.0	.	1009	P12882	MYH1_HUMAN	H	1009	ENSP00000226207:Q1009H	ENSP00000226207:Q1009H	Q	-	3	2	MYH1	10346864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.110000	0.31147	2.689000	0.91719	0.650000	0.86243	CAG		0.483	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10406139	C	A	10406139	3	1	61	1	0	0	0	0	1	0	0	0	10059	912	32	2	2860	2	MYH1	17	10406139	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1430	10406139	70789071	10066	18051										
MYH1	4619	broad.mit.edu	37	chr17	10406392	10406392	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaggtcatcaatgtctttCttgagttctgaacattcatc	6	9	7	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10406392C>A	ENST00000226207.5	-	23	2959	c.2865G>T	c.(2863-2865)aaG>aaT	p.K955N	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	955					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K955N(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CAATGTCTTTCTTGAGTTCTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											98	96	97					17																	10406392		2202	4281	6483	10347117	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2865G>T	17.37:g.10406392C>A	ENSP00000226207:p.Lys955Asn		10347117	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.268080	0.80469	.	.	ENSG00000109061	ENST00000226207	D	0.84730	-1.89	5.34	5.34	0.76211	.	0.000000	0.45361	U	0.000378	D	0.94785	0.8316	H	0.95816	3.725	0.53688	D	0.999978	D	0.71674	0.998	D	0.67382	0.951	D	0.95937	0.8943	10	0.87932	D	0	.	19.4116	0.94675	0.0:1.0:0.0:0.0	.	955	P12882	MYH1_HUMAN	N	955	ENSP00000226207:K955N	ENSP00000226207:K955N	K	-	3	2	MYH1	10347117	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.977000	0.70492	2.676000	0.91093	0.557000	0.71058	AAG		0.428	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10406392	C	A	10406392	3	1	61	1	0	0	0	0	1	0	0	0	10059	912	32	2	3026	2	MYH1	17	10406392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	253	10406392	70788818	10067	18052										
MYH1	4619	broad.mit.edu	37	chr17	10418205	10418205	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatcaagatagactgattCtcccgatctagaagaaaaac	8	8	3	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10418205C>A	ENST00000226207.5	-	6	607	c.513G>T	c.(511-513)gaG>gaT	p.E171D	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	171	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E171D(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TAGACTGATTCTCCCGATCTA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	17											116	121	119					17																	10418205		2203	4297	6500	10358930	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.513G>T	17.37:g.10418205C>A	ENSP00000226207:p.Glu171Asp		10358930	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.598590	0.46318	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	D	0.89746	-2.56	5.36	3.32	0.38043	Myosin head, motor domain (2);	0.000000	0.43416	U	0.000577	D	0.88962	0.6580	M	0.82323	2.585	0.43355	D	0.995424	B	0.11235	0.004	B	0.25291	0.059	D	0.85069	0.0939	10	0.51188	T	0.08	.	10.5026	0.44815	0.0:0.8366:0.0:0.1634	.	171	P12882	MYH1_HUMAN	D	171	ENSP00000226207:E171D	ENSP00000226207:E171D	E	-	3	2	MYH1	10358930	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.687000	0.25407	0.678000	0.31325	0.655000	0.94253	GAG		0.323	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10418205	C	A	10418205	3	1	61	1	0	0	0	0	1	0	0	0	10059	912	32	2	5446	2	MYH1	17	10418205	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11813	10418205	70777005	10068	18053										
MYH1	4619	broad.mit.edu	37	chr17	10419767	10419767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttactcacagctccagcttCggtcttagctgtcaccttcc	6	15	3	0	rs544824288		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10419767C>T	ENST00000226207.5	-	3	287	c.193G>A	c.(193-195)Gaa>Aaa	p.E65K	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	65					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E65K(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GCTCCAGCTTCGGTCTTAGCT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											227	209	215					17																	10419767		2203	4300	6503	10360492	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.193G>A	17.37:g.10419767C>T	ENSP00000226207:p.Glu65Lys		10360492	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.494808	0.44352	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	T	0.81163	-1.46	5.5	5.5	0.81552	Myosin, N-terminal, SH3-like (1);	0.000000	0.44483	U	0.000453	T	0.79076	0.4385	M	0.64260	1.97	0.46542	D	0.999097	B	0.14438	0.01	B	0.21546	0.035	T	0.72988	-0.4124	10	0.12103	T	0.63	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	65	P12882	MYH1_HUMAN	K	65	ENSP00000226207:E65K	ENSP00000226207:E65K	E	-	1	0	MYH1	10360492	0.213000	0.23551	0.944000	0.38274	0.770000	0.43624	1.567000	0.36407	2.861000	0.98227	0.655000	0.94253	GAA		0.473	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10419767	C	T	10419767	3	4	61	1	0	0	0	0	1	0	0	0	10059	893	31	1	5778	1	MYH1	17	10419767	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1562	10419767	70775443	10069	18054										
MYH2	4620	broad.mit.edu	37	chr17	10427102	10427102	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggccttcttggccttttCttctgcattgcgggcttcct	10	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10427102C>A	ENST00000245503.5	-	36	5659	c.5275G>T	c.(5275-5277)Gaa>Taa	p.E1759*	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Nonsense_Mutation_p.E1759*	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1759					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E1759*(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TTGGCCTTTTCTTCTGCATTG	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											192	170	177					17																	10427102		2203	4300	6503	10367827	SO:0001587	stop_gained	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.5275G>T	17.37:g.10427102C>A	ENSP00000245503:p.Glu1759*		10367827	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Nonsense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	47	13.319394	0.99734	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	.	.	.	5.4	5.4	0.78164	.	0.000000	0.39687	U	0.001291	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.3641	0.94454	0.0:1.0:0.0:0.0	.	.	.	.	X	1759	.	ENSP00000245503:E1759X	E	-	1	0	MYH2	10367827	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.638000	0.83328	2.805000	0.96524	0.609000	0.83330	GAA		0.458	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10427102	C	A	10427102	4	1	61	1	0	0	0	0	0	1	0	0	10065	922	32	2	570	2	MYH2	17	10427102	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7335	10427102	70768108	10070	18055										
MYH2	4620	broad.mit.edu	37	chr17	10432764	10432764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagccctttctaggtccatgCgaagtttcttttcttgctcc	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10432764C>T	ENST00000245503.5	-	25	3536	c.3152G>A	c.(3151-3153)cGc>cAc	p.R1051H	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.R1051H	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1051					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R1051H(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TAGGTCCATGCGAAGTTTCTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	117	120					17																	10432764		2203	4300	6503	10373489	SO:0001583	missense	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.3152G>A	17.37:g.10432764C>T	ENSP00000245503:p.Arg1051His		10373489	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448449	0.84101	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	D;D	0.95853	-3.83;-3.83	5.24	5.24	0.73138	.	0.000000	0.40144	U	0.001162	D	0.98273	0.9428	H	0.97265	3.97	0.80722	D	1	D	0.64830	0.994	P	0.55087	0.768	D	0.99544	1.0964	10	0.87932	D	0	.	19.0151	0.92890	0.0:1.0:0.0:0.0	.	1051	Q9UKX2	MYH2_HUMAN	H	1051	ENSP00000245503:R1051H;ENSP00000380367:R1051H	ENSP00000245503:R1051H	R	-	2	0	MYH2	10373489	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.346000	0.79347	2.718000	0.92993	0.591000	0.81541	CGC		0.383	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		T	10432764	C	T	10432764	3	4	61	1	0	0	0	0	1	0	0	0	10065	768	27	1	2737	1	MYH2	17	10432764	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5662	10432764	70762446	10071	18056										
MYH2	4620	broad.mit.edu	37	chr17	10440987	10440987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcaaaaccaaccttctCgatgagctcgatgcaggcag	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10440987C>T	ENST00000245503.5	-	15	1966	c.1582G>A	c.(1582-1584)Gag>Aag	p.E528K	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Missense_Mutation_p.E528K|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.E528K	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	528	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E528K(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCAACCTTCTCGATGAGCTCG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	17											170	150	157					17																	10440987		2203	4300	6503	10381712	SO:0001583	missense	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.1582G>A	17.37:g.10440987C>T	ENSP00000245503:p.Glu528Lys		10381712	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.382959|5.382959	0.95967|0.95967	.|.	.|.	ENSG00000125414|ENSG00000214970	ENST00000532183;ENST00000245503;ENST00000397183|ENST00000399342	D;D;D|.	0.90385|.	-2.66;-2.66;-2.66|.	5.71|5.71	5.71|5.71	0.89125|0.89125	Myosin head, motor domain (3);|.	0.000000|.	0.39475|.	U|.	0.001356|.	D|D	0.91280|0.91280	0.7251|0.7251	H|H	0.98769|0.98769	4.325|4.325	0.80722|0.80722	D|D	1|1	D;P|.	0.76494|.	0.999;0.79|.	D;P|.	0.83275|.	0.996;0.736|.	D|D	0.94411|0.94411	0.7632|0.7632	10|6	0.87932|0.87932	D|D	0|0	.|.	18.8558|18.8558	0.92251|0.92251	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	528;528|.	Q567P6;Q9UKX2|.	.;MYH2_HUMAN|.	K|L	528|20	ENSP00000433944:E528K;ENSP00000245503:E528K;ENSP00000380367:E528K|.	ENSP00000245503:E528K|ENSP00000382280:S20L	E|S	-|+	1|2	0|0	MYH2|AC005323.1	10381712|10381712	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.580000|0.580000	0.36256|0.36256	6.048000|6.048000	0.71046|0.71046	2.709000|2.709000	0.92574|0.92574	0.655000|0.655000	0.94253|0.94253	GAG|TCG		0.433	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		T	10440987	C	T	10440987	3	4	61	1	0	0	0	0	1	0	0	0	10065	893	31	1	4347	1	MYH2	17	10440987	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8223	10440987	70754223	10072	18057										
MYH2	4620	broad.mit.edu	37	chr17	10443342	10443342	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgtgagcttgtaaatggaGaccttttcttcattagtaaa	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10443342G>T	ENST00000245503.5	-	12	1434	c.1050C>A	c.(1048-1050)gtC>gtA	p.V350V	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Silent_p.V350V|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Silent_p.V350V	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	350	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.V350V(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TGTAAATGGAGACCTTTTCTT	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	17											157	148	151					17																	10443342		2203	4300	6503	10384067	SO:0001819	synonymous_variant	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.1050C>A	17.37:g.10443342G>T			10384067	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																				0.418	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		T	10443342	G	T	10443342	2	4	61	1	0	0	0	0	0	0	0	1	10065	929	33	2		2	MYH2	17	10443342	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2355	10443342	70751868	10073	18058										
MYH3	4621	broad.mit.edu	37	chr17	10537376	10537376	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcacagtttcaagttgatCtaaggcttcctcgtaggcat	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10537376C>A	ENST00000583535.1	-	32	4567	c.4480G>T	c.(4480-4482)Gat>Tat	p.D1494Y	MYH3_ENST00000226209.7_Missense_Mutation_p.D1494Y	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1494					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.D1494Y(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCAAGTTGATCTAAGGCTTCC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											168	149	155					17																	10537376		2203	4300	6503	10478101	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4480G>T	17.37:g.10537376C>A	ENSP00000464317:p.Asp1494Tyr		10478101	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.807369	0.90623	.	.	ENSG00000109063	ENST00000226209	D	0.84070	-1.8	5.31	5.31	0.75309	Myosin tail (1);	.	.	.	.	D	0.93893	0.8046	H	0.94886	3.595	0.58432	D	0.999994	D	0.89917	1.0	D	0.76575	0.988	D	0.95228	0.8340	9	0.87932	D	0	.	19.3282	0.94273	0.0:1.0:0.0:0.0	.	1494	P11055	MYH3_HUMAN	Y	1494	ENSP00000226209:D1494Y	ENSP00000226209:D1494Y	D	-	1	0	MYH3	10478101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.003000	0.70701	2.623000	0.88846	0.655000	0.94253	GAT		0.483	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10537376	C	A	10537376	3	1	61	1	0	0	0	0	1	0	0	0	10066	913	32	2	1382	2	MYH3	17	10537376	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	94034	10537376	70657834	10074	18059										
MYH3	4621	broad.mit.edu	37	chr17	10541530	10541530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcgcggccaccatggcttCgtgctgcagtgtggcctcct	13	15	0	0	rs557068462		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10541530C>T	ENST00000583535.1	-	27	3646	c.3559G>A	c.(3559-3561)Gaa>Aaa	p.E1187K	MYH3_ENST00000226209.7_Missense_Mutation_p.E1187K	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1187					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.E1187K(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						ACCATGGCTTCGTGCTGCAGT	0.622													C|||	1	0.000199681	0	0.0014	5008	,	,		17076	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											84	70	75					17																	10541530		2203	4300	6503	10482255	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.3559G>A	17.37:g.10541530C>T	ENSP00000464317:p.Glu1187Lys		10482255	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	36	5.702529	0.96812	.	.	ENSG00000109063	ENST00000226209	D	0.86297	-2.1	5.45	5.45	0.79879	Myosin tail (1);	.	.	.	.	D	0.96309	0.8796	H	0.98178	4.165	0.53005	D	0.999962	D	0.89917	1.0	D	0.71414	0.973	D	0.97546	1.0089	9	0.87932	D	0	.	19.661	0.95871	0.0:1.0:0.0:0.0	.	1187	P11055	MYH3_HUMAN	K	1187	ENSP00000226209:E1187K	ENSP00000226209:E1187K	E	-	1	0	MYH3	10482255	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.776000	0.85560	2.714000	0.92807	0.563000	0.77884	GAA		0.622	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10541530	C	T	10541530	3	4	61	1	0	0	0	0	1	0	0	0	10066	893	31	1	2323	1	MYH3	17	10541530	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4154	10541530	70653680	10075	18060										
MYH3	4621	broad.mit.edu	37	chr17	10543750	10543750	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcggtcatcccgcatctCttccagggttcccagcaagc	10	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10543750C>A	ENST00000583535.1	-	21	2413	c.2326G>T	c.(2326-2328)Gag>Tag	p.E776*	MYH3_ENST00000226209.7_Nonsense_Mutation_p.E776*	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	776	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.E776*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCCCGCATCTCTTCCAGGGTT	0.537																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											105	103	104					17																	10543750		2203	4300	6503	10484475	SO:0001587	stop_gained	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2326G>T	17.37:g.10543750C>A	ENSP00000464317:p.Glu776*		10484475	Q15492	Nonsense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	40	8.139053	0.98672	.	.	ENSG00000109063	ENST00000226209	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.5451	0.95291	0.0:1.0:0.0:0.0	.	.	.	.	X	776	.	ENSP00000226209:E776X	E	-	1	0	MYH3	10484475	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	7.772000	0.85439	2.685000	0.91497	0.561000	0.74099	GAG		0.537	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10543750	C	A	10543750	4	1	61	1	0	0	0	0	0	1	0	0	10066	922	32	2	3580	2	MYH3	17	10543750	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2220	10543750	70651460	10076	18061										
MYH3	4621	broad.mit.edu	37	chr17	10550730	10550730	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggttccaaaatggattCggatgaacttgccctgtatg	11	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10550730C>T	ENST00000583535.1	-	9	836	c.749G>A	c.(748-750)cGa>cAa	p.R250Q	MYH3_ENST00000226209.7_Missense_Mutation_p.R250Q	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	250	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.R250Q(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AAAATGGATTCGGATGAACTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											66	68	67					17																	10550730		2203	4300	6503	10491455	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.749G>A	17.37:g.10550730C>T	ENSP00000464317:p.Arg250Gln		10491455	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	36	5.749879	0.96890	.	.	ENSG00000109063	ENST00000226209	T	0.71222	-0.55	5.34	5.34	0.76211	Myosin head, motor domain (3);	.	.	.	.	D	0.84497	0.5485	M	0.74258	2.255	0.44880	D	0.997894	D	0.89917	1.0	D	0.81914	0.995	D	0.85651	0.1282	9	0.87932	D	0	.	19.2333	0.93849	0.0:1.0:0.0:0.0	.	250	P11055	MYH3_HUMAN	Q	250	ENSP00000226209:R250Q	ENSP00000226209:R250Q	R	-	2	0	MYH3	10491455	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.560000	0.82277	2.787000	0.95880	0.555000	0.69702	CGA		0.483	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10550730	C	T	10550730	3	4	61	1	0	0	0	0	1	0	0	0	10066	884	31	1	5205	1	MYH3	17	10550730	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6980	10550730	70644480	10077	18062										
SCO1	6341	broad.mit.edu	37	chr17	10595205	10595205	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctttcacataatttgcGatggcttcttttgtgtccct	6	10	2	0	rs144621417		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10595205G>A	ENST00000255390.5	-	4	699	c.639C>T	c.(637-639)atC>atT	p.I213I	SCO1_ENST00000577427.1_Silent_p.I182I|SCO1_ENST00000582053.1_5'Flank	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	213					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)	p.I213I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						CATAATTTGCGATGGCTTCTT	0.353													G|||	1	0.000199681	0	0	5008	,	,		20995	0		0.001	False		,,,				2504	0				Melanoma(128;591 1731 19711 31891 44645)											1	Substitution - coding silent(1)	large_intestine(1)	17											97	93	94					17																	10595205		2203	4300	6503	10535930	SO:0001819	synonymous_variant	6341			AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"Mitochondrial respiratory chain complex assembly factors"	10603	protein-coding gene	gene with protein product		603644	"SCO (cytochrome oxidase deficient, yeast) homolog 1", "SCO cytochrome oxidase deficient homolog 1 (yeast)"	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.639C>T	17.37:g.10595205G>A			10535930	B2RDM0	Silent	SNP	ENST00000255390.5	37	CCDS11158.1																																																																																				0.353	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589		A	10595205	G	A	10595205	2	1	61	1	0	0	0	0	0	0	0	1	13968	1048	37	1		1	SCO1	17	10595205	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44475	10595205	70600005	10078	18063										
PIRT	644139	broad.mit.edu	37	chr17	10728777	10728777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgaaaagcaggatggcaccGcccactgacatgataacgat	10	12	0	2	rs555559126		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:10728777G>A	ENST00000580256.2	-	2	824	c.186C>T	c.(184-186)ggC>ggT	p.G62G		NM_001101387.1	NP_001094857.1	P0C851	PIRT_HUMAN	phosphoinositide-interacting regulator of transient receptor potential channels	62						integral component of membrane (GO:0016021)		p.G62G(2)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)	8						GGATGGCACCGCCCACTGACA	0.567													G|||	1	0.000199681	0	0	5008	,	,		19700	0.001		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	17											72	75	74					17																	10728777		2107	4215	6322	10669502	SO:0001819	synonymous_variant	644139			AK021549	CCDS45614.1	17p12	2010-06-04			ENSG00000233670	ENSG00000233670			37239	protein-coding gene	gene with protein product	"phosphoinositide-interacting regulator of TRPV1"	612068				18455988	Standard	NM_001101387		Approved		uc010col.3	P0C851		ENST00000580256.2:c.186C>T	17.37:g.10728777G>A			10669502	B7Z648	Silent	SNP	ENST00000580256.2	37	CCDS45614.1																																																																																				0.567	PIRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441078.2	NM_001101387		A	10728777	G	A	10728777	2	1	61	1	0	0	0	0	0	0	0	1	11976	1074	38	1		1	PIRT	17	10728777	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133572	10728777	70466433	10079	18064										
DNAH9	1770	broad.mit.edu	37	chr17	11535946	11535946	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttaaccagaaagtagaaGatcttgaccgaagattgggg	11	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:11535946G>T	ENST00000262442.4	+	8	1629	c.1561G>T	c.(1561-1563)Gat>Tat	p.D521Y	DNAH9_ENST00000454412.2_Missense_Mutation_p.D521Y	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	521	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.D521Y(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		GAAAGTAGAAGATCTTGACCG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											108	108	108					17																	11535946		2203	4300	6503	11476671	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.1561G>T	17.37:g.11535946G>T	ENSP00000262442:p.Asp521Tyr		11476671	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406777	0.62399	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.58358	0.34;0.34	5.18	5.18	0.71444	Dynein heavy chain, domain-1 (1);	1.438580	0.04258	N	0.339838	T	0.79656	0.4483	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65236	-0.6217	10	0.62326	D	0.03	.	15.6299	0.76899	0.0:0.0:1.0:0.0	.	521	Q9NYC9	DYH9_HUMAN	Y	521	ENSP00000262442:D521Y;ENSP00000414874:D521Y	ENSP00000262442:D521Y	D	+	1	0	DNAH9	11476671	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	7.402000	0.79972	2.427000	0.82271	0.650000	0.86243	GAT		0.408	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11535946	G	T	11535946	3	4	61	1	0	0	0	0	1	0	0	0	4619	942	33	2	1591	2	DNAH9	17	11535946	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	807169	11535946	69659264	10080	18065										
DNAH9	1770	broad.mit.edu	37	chr17	11597209	11597209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaaaggtttgaaggcatcGacattgactttaaagagcta	9	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:11597209G>A	ENST00000262442.4	+	21	4707	c.4639G>A	c.(4639-4641)Gac>Aac	p.D1547N	DNAH9_ENST00000454412.2_Missense_Mutation_p.D1547N	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1547	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.D1547N(2)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		TGAAGGCATCGACATTGACTT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	17											116	111	112					17																	11597209		2203	4300	6503	11537934	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.4639G>A	17.37:g.11597209G>A	ENSP00000262442:p.Asp1547Asn		11537934	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291731	0.59976	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.64991	-0.13;-0.13	4.72	4.72	0.59763	Dynein heavy chain, domain-2 (1);	0.125210	0.52532	D	0.000062	T	0.74627	0.3741	M	0.78344	2.41	0.80722	D	1	P	0.41498	0.752	P	0.51385	0.668	T	0.75557	-0.3276	10	0.44086	T	0.13	.	17.8424	0.88719	0.0:0.0:1.0:0.0	.	1547	Q9NYC9	DYH9_HUMAN	N	1547;1547;129	ENSP00000262442:D1547N;ENSP00000414874:D1547N	ENSP00000262442:D1547N	D	+	1	0	DNAH9	11537934	1.000000	0.71417	0.701000	0.30321	0.152000	0.21847	7.176000	0.77643	2.627000	0.88993	0.655000	0.94253	GAC		0.428	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11597209	G	A	11597209	3	1	61	1	0	0	0	0	1	0	0	0	4619	1058	37	1	4721	1	DNAH9	17	11597209	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61263	11597209	69598001	10081	18066										
DNAH9	1770	broad.mit.edu	37	chr17	11648245	11648245	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggatttcaacatccccaaGattgtgactgatgacatgcc	9	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:11648245G>T	ENST00000262442.4	+	31	6311	c.6243G>T	c.(6241-6243)aaG>aaT	p.K2081N	DNAH9_ENST00000454412.2_Missense_Mutation_p.K2081N	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2081					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.K2081N(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		ACATCCCCAAGATTGTGACTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											67	64	65					17																	11648245		2203	4300	6503	11588970	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6243G>T	17.37:g.11648245G>T	ENSP00000262442:p.Lys2081Asn		11588970	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.837841	0.71373	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.46451	0.87;0.87	5.46	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.73513	0.3596	H	0.99740	4.74	0.80722	D	1	D	0.60160	0.987	P	0.56648	0.803	T	0.81938	-0.0704	10	0.87932	D	0	.	9.6114	0.39665	0.2763:0.0:0.7237:0.0	.	2081	Q9NYC9	DYH9_HUMAN	N	2081;2081;663	ENSP00000262442:K2081N;ENSP00000414874:K2081N	ENSP00000262442:K2081N	K	+	3	2	DNAH9	11588970	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.932000	0.40143	1.311000	0.45024	-0.145000	0.13849	AAG		0.597	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11648245	G	T	11648245	3	4	61	1	0	0	0	0	1	0	0	0	4619	933	33	2	6365	2	DNAH9	17	11648245	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51036	11648245	69546965	10082	18067										
DNAH9	1770	broad.mit.edu	37	chr17	11725349	11725349	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagagaactgttggaagttCtttatagatcggatccggcg	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:11725349C>A	ENST00000262442.4	+	46	8888	c.8820C>A	c.(8818-8820)ttC>ttA	p.F2940L	DNAH9_ENST00000454412.2_Missense_Mutation_p.F2940L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2940	AAA 4. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.F2940L(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		GTTGGAAGTTCTTTATAGATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17											71	67	68					17																	11725349		2203	4300	6503	11666074	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.8820C>A	17.37:g.11725349C>A	ENSP00000262442:p.Phe2940Leu		11666074	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374206	0.61735	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.54071	0.59;0.59	4.2	3.22	0.36961	Dynein heavy chain, P-loop containing D4 domain (1);	0.986339	0.08252	N	0.974374	T	0.60869	0.2302	M	0.81942	2.565	0.80722	D	1	B	0.21452	0.056	B	0.33750	0.169	T	0.57418	-0.7815	10	0.87932	D	0	.	9.1209	0.36786	0.0:0.7565:0.0:0.2435	.	2940	Q9NYC9	DYH9_HUMAN	L	2940;2940;1522	ENSP00000262442:F2940L;ENSP00000414874:F2940L	ENSP00000262442:F2940L	F	+	3	2	DNAH9	11666074	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	0.911000	0.28584	0.763000	0.33175	0.460000	0.39030	TTC		0.453	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11725349	C	A	11725349	3	1	61	1	0	0	0	0	1	0	0	0	4619	912	32	2	9002	2	DNAH9	17	11725349	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77104	11725349	69469861	10083	18068										
ZNF18	7566	broad.mit.edu	37	chr17	11881496	11881496	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtggtggcgcaatcctgaGaagtcactaaagcctttccc	10	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:11881496G>T	ENST00000322748.3	-	9	2032	c.1428C>A	c.(1426-1428)ttC>ttA	p.F476L	RP11-1096G20.5_ENST00000580270.1_RNA|ZNF18_ENST00000454073.3_Missense_Mutation_p.F475L|ZNF18_ENST00000580306.2_Missense_Mutation_p.F476L	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	476					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.F476L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		GCAATCCTGAGAAGTCACTAA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	17											93	95	94					17																	11881496		2203	4300	6503	11822221	SO:0001583	missense	7566			X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"Zinc fingers, C2H2-type", "-", "-", "-"	12969	protein-coding gene	gene with protein product		194524	"zinc finger protein 18 (KOX 11)"			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.1428C>A	17.37:g.11881496G>T	ENSP00000315664:p.Phe476Leu		11822221	Q5QHQ3|Q8IYC4|Q8NAH6	Missense_Mutation	SNP	ENST00000322748.3	37	CCDS32568.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495708	0.26774	.	.	ENSG00000154957	ENST00000454073;ENST00000322748	T	0.13901	2.55	5.62	3.59	0.41128	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.110713	0.41194	N	0.000935	T	0.05502	0.0145	N	0.04162	-0.26	0.09310	N	0.999998	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.36212	-0.9757	10	0.27785	T	0.31	-11.3736	6.128	0.20189	0.1675:0.1704:0.662:0.0	.	475;476	P17022-2;P17022	.;ZNF18_HUMAN	L	476	ENSP00000315664:F476L	ENSP00000315664:F476L	F	-	3	2	ZNF18	11822221	0.210000	0.23517	0.998000	0.56505	0.991000	0.79684	0.385000	0.20685	0.702000	0.31825	0.557000	0.71058	TTC		0.433	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596		T	11881496	G	T	11881496	3	4	61	1	0	0	0	0	1	0	0	0	17786	933	33	2	225	2	ZNF18	17	11881496	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	156147	11881496	69313714	10084	18069										
MAP2K4	6416	broad.mit.edu	37	chr17	12032524	12032524	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatcaactaacacaagtCgtgaaaggagatcctccgca	8	10	1	3	rs368291515		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12032524C>T	ENST00000353533.5	+	9	1023	c.960C>T	c.(958-960)gtC>gtT	p.V320V	MAP2K4_ENST00000415385.3_Silent_p.V331V	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	320	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.V320V(1)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TAACACAAGTCGTGAAAGGAG	0.413			"D, Mis, N"		"pancreatic, breast, colorectal"																																		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	12	Whole gene deletion(10)|Substitution - coding silent(1)|Unknown(1)	breast(4)|ovary(4)|biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	17						C		0,4406		0,0,2203	95	87	90		960	-4.1	1	17		90	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	MAP2K4	NM_003010.2		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		320/400	12032524	1,13003	2203	4299	6502	11973249	SO:0001819	synonymous_variant	6416			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.960C>T	17.37:g.12032524C>T			11973249	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Silent	SNP	ENST00000353533.5	37	CCDS11162.1																																																																																				0.413	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	12032524	C	T	12032524	2	4	61	1	0	0	0	0	0	0	0	1	9269	871	31	1		1	MAP2K4	17	12032524	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151028	12032524	69162686	10085	18070										
MYOCD	93649	broad.mit.edu	37	chr17	12626293	12626293	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggaaaaaaacattcttcCtgtggattctgctgtgaaag	11	6	2	1	rs373364614		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12626293C>A	ENST00000343344.4	+	5	383	c.383C>A	c.(382-384)cCt>cAt	p.P128H	MYOCD_ENST00000395988.1_3'UTR|MYOCD_ENST00000425538.1_Missense_Mutation_p.P128H|AC005358.1_ENST00000609971.1_Missense_Mutation_p.P32H			Q8IZQ8	MYCD_HUMAN	myocardin	128					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.P128H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AACATTCTTCCTGTGGATTCT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											124	126	125					17																	12626293		2203	4300	6503	12567018	SO:0001583	missense	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.383C>A	17.37:g.12626293C>A	ENSP00000341835:p.Pro128His		12567018	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	37	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.287328	0.80803	.	.	ENSG00000141052	ENST00000425538;ENST00000343344;ENST00000395988	T	0.52526	0.66	5.33	4.36	0.52297	.	0.180485	0.48286	D	0.000185	T	0.59636	0.2208	L	0.48642	1.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.99	D;D;P	0.78314	0.991;0.964;0.794	T	0.58239	-0.7671	10	0.39692	T	0.17	-23.0492	12.9033	0.58137	0.0:0.9208:0.0:0.0792	.	32;128;128	Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;MYCD_HUMAN	H	128;128;32	ENSP00000341835:P128H	ENSP00000341835:P128H	P	+	2	0	MYOCD	12567018	1.000000	0.71417	0.759000	0.31340	0.993000	0.82548	7.574000	0.82434	1.470000	0.48102	0.561000	0.74099	CCT		0.488	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		A	12626293	C	A	12626293	3	1	61	1	0	0	0	0	1	0	0	0	10117	681	24	2	401	2	MYOCD	17	12626293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	593769	12626293	68568917	10086	18071										
MYOCD	93649	broad.mit.edu	37	chr17	12666502	12666502	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccctcggcttcctttgaAcaagcctcttcaggcagcca	8	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12666502A>G	ENST00000343344.4	+	13	2358	c.2358A>G	c.(2356-2358)gaA>gaG	p.E786E	RP11-1090M7.1_ENST00000584772.1_RNA|MYOCD_ENST00000425538.1_Silent_p.E834E			Q8IZQ8	MYCD_HUMAN	myocardin	786					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.E786E(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		CTTCCTTTGAACAAGCCTCTT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	17											100	97	98					17																	12666502		2203	4300	6503	12607227	SO:0001819	synonymous_variant	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2358A>G	17.37:g.12666502A>G			12607227	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																				0.498	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		G	12666502	A	G	12666502	2	3	61	1	0	0	0	0	0	0	0	1	10117	40	2	4		4	MYOCD	17	12666502	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	40209	12666502	68528708	10087	18072										
MYOCD	93649	broad.mit.edu	37	chr17	12666860	12666860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccacaccaggctttagcGccctcaccaccagcagcccc	6	20	1	0	rs370289662		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12666860G>A	ENST00000343344.4	+	13	2716	c.2716G>A	c.(2716-2718)Gcc>Acc	p.A906T	RP11-1090M7.1_ENST00000584772.1_RNA|MYOCD_ENST00000425538.1_Missense_Mutation_p.A954T			Q8IZQ8	MYCD_HUMAN	myocardin	906					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.A906T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AGGCTTTAGCGCCCTCACCAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	THR/ALA,THR/ALA	0,4406		0,0,2203	62	56	58		2716,2860	2.6	0.5	17		58	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	MYOCD	NM_153604.2,NM_001146312.1	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	906/939,954/987	12666860	1,13005	2203	4300	6503	12607585	SO:0001583	missense	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2716G>A	17.37:g.12666860G>A	ENSP00000341835:p.Ala906Thr		12607585	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	37	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	G	6.641	0.486760	0.12641	0.0	1.16E-4	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000443061	T;T	0.43688	0.94;0.95	6.08	2.59	0.31030	.	0.687575	0.15464	N	0.260979	T	0.20455	0.0492	N	0.08118	0	0.23076	N	0.998331	B;B;B	0.29341	0.242;0.194;0.003	B;B;B	0.20767	0.008;0.031;0.004	T	0.12682	-1.0538	10	0.56958	D	0.05	-13.4936	7.6075	0.28110	0.2468:0.0:0.1263:0.6269	.	630;954;906	E9PEP9;Q8IZQ8-3;Q8IZQ8	.;.;MYCD_HUMAN	T	630;954;906;616	ENSP00000341835:A906T;ENSP00000400148:A616T	ENSP00000341835:A906T	A	+	1	0	MYOCD	12607585	0.944000	0.32072	0.460000	0.27093	0.011000	0.07611	1.111000	0.31159	0.160000	0.19432	-1.061000	0.02294	GCC		0.517	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		A	12666860	G	A	12666860	3	1	61	1	0	0	0	0	1	0	0	0	10117	1087	38	1	2926	1	MYOCD	17	12666860	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	358	12666860	68528350	10088	18073										
RICH2	9912	broad.mit.edu	37	chr17	12819294	12819294	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgagttgcaagtagagaGagacgtgattgagcccctgt	13	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12819294G>T	ENST00000379672.5	+	5	653	c.353G>T	c.(352-354)aGa>aTa	p.R118I	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.R118I|MIR1269B_ENST00000580405.1_RNA|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.R118I	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	118	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)	p.R118I(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CAAGTAGAGAGAGACGTGATT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											99	98	98					17																	12819294		2075	4207	6282	12760019	SO:0001583	missense	9912				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.353G>T	17.37:g.12819294G>T	ENSP00000368994:p.Arg118Ile		12760019	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819767	0.50633	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	T;T	0.64618	-0.11;-0.11	5.92	5.92	0.95590	BAR (3);	0.000000	0.85682	D	0.000000	T	0.73877	0.3643	M	0.63843	1.955	0.80722	D	1	D;D	0.57257	0.966;0.979	P;D	0.65573	0.837;0.936	T	0.75534	-0.3284	10	0.87932	D	0	.	11.135	0.48368	0.0831:0.0:0.9169:0.0	.	118;118	A6NCP5;Q17R89	.;RHG44_HUMAN	I	118	ENSP00000368994:R118I;ENSP00000342566:R118I	ENSP00000342566:R118I	R	+	2	0	ARHGAP44	12760019	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.491000	0.90468	2.818000	0.97014	0.655000	0.94253	AGA		0.522	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		T	12819294	G	T	12819294	3	4	61	1	0	0	0	0	1	0	0	0	13394	942	33	2	371	2	RICH2	17	12819294	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152434	12819294	68375916	10089	18074										
RICH2	9912	broad.mit.edu	37	chr17	12860001	12860001	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatgatgaccacagtgtCgctgcaaattgttgggatca	12	7	1	3	rs372255404		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:12860001C>A	ENST00000379672.5	+	15	1580	c.1280C>A	c.(1279-1281)tCg>tAg	p.S427*	ARHGAP44_ENST00000340825.3_Nonsense_Mutation_p.S427*|ARHGAP44_ENST00000262444.9_Nonsense_Mutation_p.S427*	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	427	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)	p.S427*(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						ACCACAGTGTCGCTGCAAATT	0.537																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											89	89	89					17																	12860001		2104	4248	6352	12800726	SO:0001587	stop_gained	9912				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.1280C>A	17.37:g.12860001C>A	ENSP00000368994:p.Ser427*		12800726	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Nonsense_Mutation	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	C	37	6.474956	0.97598	.	.	ENSG00000006740	ENST00000379672;ENST00000544416;ENST00000340825	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6601	0.88191	0.0:1.0:0.0:0.0	.	.	.	.	X	427;89;427	.	ENSP00000342566:S427X	S	+	2	0	ARHGAP44	12800726	1.000000	0.71417	0.195000	0.23364	0.469000	0.32828	7.445000	0.80570	2.773000	0.95371	0.585000	0.79938	TCG		0.537	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12860001	C	A	12860001	4	1	61	1	0	0	0	0	0	1	0	0	13394	893	31	2	1338	2	RICH2	17	12860001	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40707	12860001	68335209	10090	18075										
CDRT1	374286	broad.mit.edu	37	chr17	15492480	15492480	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagctgtagcacttggttCgattccattccatcccacgt	8	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15492480C>A	ENST00000395906.3	-	12	2067	c.2068G>T	c.(2068-2070)Gaa>Taa	p.E690*	CDRT1_ENST00000583965.1_3'UTR|CDRT1_ENST00000354433.3_Nonsense_Mutation_p.E190*|RP11-385D13.1_ENST00000455584.2_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	690								p.E190*(2)|p.E690*(2)|p.E190K(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GCACTTGGTTCGATTCCATTC	0.507																																																5	Substitution - Nonsense(4)|Substitution - Missense(1)	large_intestine(5)	17											105	112	109					17																	15492480		2199	4299	6498	15433205	SO:0001587	stop_gained	374286			U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"F-boxes / WD-40 domains", "WD repeat domain containing"	14379	protein-coding gene	gene with protein product		604596	"F-box and WD repeat domain containing 10 pseudogene 1", "F-box and WD-40 domain protein 10 pseudogene 1"	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.2068G>T	17.37:g.15492480C>A	ENSP00000379242:p.Glu690*		15433205	O43848|O95611	Nonsense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.302280	0.60195	.	.	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	.	.	.	1.38	0.0901	0.14462	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8388	0.18623	0.4061:0.5939:0.0:0.0	.	.	.	.	X	190;720;690	.	ENSP00000346416:E190X	E	-	1	0	CDRT1;RP11-385D13.1	15433205	0.851000	0.29673	0.000000	0.03702	0.000000	0.00434	-0.129000	0.10515	-0.389000	0.07786	0.000000	0.15137	GAA		0.507	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		A	15492480	C	A	15492480	4	1	61	1	0	0	0	0	0	1	0	0	3180	893	31	2	194	2	CDRT1	17	15492480	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2632479	15492480	65702730	10091	18076										
ZNF286A	57335	broad.mit.edu	37	chr17	15609790	15609790	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagggatgtgatgctggaGaactataggaacctagtctc	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15609790G>T	ENST00000464847.2	+	3	769	c.216G>T	c.(214-216)gaG>gaT	p.E72D	ZNF286A_ENST00000395893.2_Missense_Mutation_p.E72D|ZNF286A_ENST00000583566.1_Missense_Mutation_p.E72D|ZNF286A_ENST00000472486.1_Missense_Mutation_p.E62D|ZNF286A_ENST00000421016.1_Missense_Mutation_p.E72D|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000580259.1_Intron|ZNF286A_ENST00000413242.2_Missense_Mutation_p.E72D|ZNF286A_ENST00000593105.1_Missense_Mutation_p.E62D|ZNF286A_ENST00000395894.2_Missense_Mutation_p.E72D|ZNF286A_ENST00000581529.1_Intron|ZNF286A_ENST00000585194.1_Missense_Mutation_p.E72D			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E72D(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TGATGCTGGAGAACTATAGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											129	123	125					17																	15609790		2203	4300	6503	15550515	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.216G>T	17.37:g.15609790G>T	ENSP00000464218:p.Glu72Asp		15550515	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	g	15.61	2.883519	0.51908	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.03920	3.76;3.76;3.76;3.76	4.67	3.71	0.42584	Krueppel-associated box (4);	0.270756	0.20384	N	0.093385	T	0.19485	0.0468	M	0.87456	2.885	0.29467	N	0.857352	D	0.65815	0.995	D	0.65140	0.932	T	0.04255	-1.0965	10	0.66056	D	0.02	-13.2156	7.2734	0.26271	0.1958:0.0:0.8042:0.0	.	72	Q9HBT8	Z286A_HUMAN	D	72;62;72;72	ENSP00000397163:E72D;ENSP00000408168:E62D;ENSP00000379231:E72D;ENSP00000379230:E72D	ENSP00000435872:E72D	E	+	3	2	ZNF286A	15550515	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.195000	0.51013	1.319000	0.45190	-0.136000	0.14681	GAG		0.408	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15609790	G	T	15609790	3	4	61	1	0	0	0	0	1	0	0	0	17862	933	33	2	226	2	ZNF286A	17	15609790	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117310	15609790	65585420	10092	18077										
ZNF286A	57335	broad.mit.edu	37	chr17	15619742	15619742	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacttaatgaaaaagcagaGaacttataaagagaaaaaac	6	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15619742G>T	ENST00000464847.2	+	5	1257	c.704G>T	c.(703-705)aGa>aTa	p.R235I	ZNF286A_ENST00000583566.1_Missense_Mutation_p.R235I|ZNF286A_ENST00000472486.1_3'UTR|ZNF286A_ENST00000421016.1_Missense_Mutation_p.R235I|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Missense_Mutation_p.R235I|ZNF286A_ENST00000593105.1_Missense_Mutation_p.R225I|ZNF286A_ENST00000395894.2_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R235I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		AAAAAGCAGAGAACTTATAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											25	25	25					17																	15619742		2197	4287	6484	15560467	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.704G>T	17.37:g.15619742G>T	ENSP00000464218:p.Arg235Ile		15560467	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	g	7.447	0.641818	0.14451	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.02446	4.29;4.29	4.06	3.07	0.35406	.	0.152839	0.30879	N	0.008699	T	0.06508	0.0167	M	0.78223	2.4	0.28209	N	0.927025	D	0.56746	0.977	P	0.46389	0.515	T	0.12091	-1.0561	10	0.59425	D	0.04	-18.5274	8.4342	0.32778	0.0954:0.156:0.7486:0.0	.	235	Q9HBT8	Z286A_HUMAN	I	235;225;235	ENSP00000397163:R235I;ENSP00000408168:R225I	ENSP00000435872:R235I	R	+	2	0	ZNF286A	15560467	0.983000	0.35010	0.993000	0.49108	0.612000	0.37316	2.040000	0.41203	0.482000	0.27582	-0.813000	0.03139	AGA		0.368	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15619742	G	T	15619742	3	4	61	1	0	0	0	0	1	0	0	0	17862	942	33	2	722	2	ZNF286A	17	15619742	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9952	15619742	65575468	10093	18078										
ZNF286A	57335	broad.mit.edu	37	chr17	15619910	15619910	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttaactaaacaccagaGaactcatactagaattctct	3	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15619910G>T	ENST00000464847.2	+	5	1425	c.872G>T	c.(871-873)aGa>aTa	p.R291I	ZNF286A_ENST00000583566.1_Missense_Mutation_p.R291I|ZNF286A_ENST00000421016.1_Missense_Mutation_p.R291I|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Missense_Mutation_p.R291I|ZNF286A_ENST00000593105.1_Missense_Mutation_p.R281I|ZNF286A_ENST00000395894.2_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R291I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		AAACACCAGAGAACTCATACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											50	52	51					17																	15619910		2203	4299	6502	15560635	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.872G>T	17.37:g.15619910G>T	ENSP00000464218:p.Arg291Ile		15560635	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	g	16.81	3.224815	0.58668	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.18502	2.21;2.21	4.53	4.53	0.55603	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43919	D	0.000505	T	0.40322	0.1112	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.25606	-1.0127	10	0.56958	D	0.05	-26.3126	14.8057	0.69952	0.0:0.0:1.0:0.0	.	291	Q9HBT8	Z286A_HUMAN	I	291;281;291	ENSP00000397163:R291I;ENSP00000408168:R281I	ENSP00000435872:R291I	R	+	2	0	ZNF286A	15560635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.993000	0.49425	2.335000	0.79485	0.650000	0.86243	AGA		0.408	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15619910	G	T	15619910	3	4	61	1	0	0	0	0	1	0	0	0	17862	942	33	2	890	2	ZNF286A	17	15619910	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	15619910	65575300	10094	18079										
ZNF286A	57335	broad.mit.edu	37	chr17	15620327	15620327	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcttgttcaacatcagaGaattcacactggagagaaac	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15620327G>T	ENST00000464847.2	+	5	1842	c.1289G>T	c.(1288-1290)aGa>aTa	p.R430I	ZNF286A_ENST00000583566.1_Missense_Mutation_p.R430I|ZNF286A_ENST00000421016.1_Missense_Mutation_p.R430I|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Missense_Mutation_p.R430I|ZNF286A_ENST00000593105.1_Missense_Mutation_p.R420I|ZNF286A_ENST00000395894.2_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R430I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		CAACATCAGAGAATTCACACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											35	42	39					17																	15620327		2203	4297	6500	15561052	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.1289G>T	17.37:g.15620327G>T	ENSP00000464218:p.Arg430Ile		15561052	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	g	18.46	3.628598	0.67015	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.24908	1.83;1.83	4.02	4.02	0.46733	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43579	D	0.000548	T	0.38188	0.1031	L	0.42487	1.325	0.58432	D	0.999991	D	0.89917	1.0	D	0.85130	0.997	T	0.13495	-1.0507	10	0.66056	D	0.02	-23.8783	7.794	0.29138	0.1131:0.0:0.8869:0.0	.	430	Q9HBT8	Z286A_HUMAN	I	430;420;430	ENSP00000397163:R430I;ENSP00000408168:R420I	ENSP00000435872:R430I	R	+	2	0	ZNF286A	15561052	0.960000	0.32886	1.000000	0.80357	0.988000	0.76386	3.160000	0.50739	2.248000	0.74166	0.585000	0.79938	AGA		0.388	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15620327	G	T	15620327	3	4	61	1	0	0	0	0	1	0	0	0	17862	942	33	2	1307	2	ZNF286A	17	15620327	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	417	15620327	65574883	10095	18080										
TBC1D26	353149	broad.mit.edu	37	chr17	15641598	15641598	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcttctgtctgtagctgtCtcaaagagtatacaaagtca	8	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15641598C>A	ENST00000437605.2	+	7	534	c.284C>A	c.(283-285)tCt>tAt	p.S95Y	AC005324.6_ENST00000580194.1_RNA|TBC1D26_ENST00000579428.1_Missense_Mutation_p.S95Y|AC005324.6_ENST00000433873.1_RNA|AC005324.6_ENST00000434017.1_RNA|ZNF286A_ENST00000413242.2_3'UTR	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	95							Rab GTPase activator activity (GO:0005097)	p.S95Y(1)		endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		CTGTAGCTGTCTCAAAGAGTA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	84	86					17																	15641598		1967	4147	6114	15582323	SO:0001583	missense	353149				CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.284C>A	17.37:g.15641598C>A	ENSP00000410111:p.Ser95Tyr		15582323	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	c	0.004	-2.288901	0.00248	.	.	ENSG00000214946	ENST00000437605	T	0.30182	1.54	1.44	-2.89	0.05665	Rab-GAP/TBC domain (1);	4.902450	0.00916	U	0.002533	T	0.20251	0.0487	N	0.25647	0.755	0.09310	N	1	B;B	0.30455	0.28;0.022	B;B	0.28916	0.096;0.056	T	0.10109	-1.0644	10	0.31617	T	0.26	.	5.2392	0.15462	0.5207:0.4793:0.0:0.0	.	95;95	Q86UD7;Q86UD7-2	TBC26_HUMAN;.	Y	95	ENSP00000410111:S95Y	ENSP00000410111:S95Y	S	+	2	0	TBC1D26	15582323	0.001000	0.12720	0.000000	0.03702	0.015000	0.08874	-0.621000	0.05559	-0.585000	0.05905	0.411000	0.27672	TCT		0.537	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571		A	15641598	C	A	15641598	3	1	61	1	0	0	0	0	1	0	0	0	15655	913	32	2	302	2	TBC1D26	17	15641598	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21271	15641598	65553612	10096	18081										
NCOR1	9611	broad.mit.edu	37	chr17	15965425	15965425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaagagactgacatgattCgtagctgagcagttggatcc	11	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15965425C>T	ENST00000268712.3	-	36	5638	c.5381G>A	c.(5380-5382)cGa>cAa	p.R1794Q	NCOR1_ENST00000395851.1_Missense_Mutation_p.R1810Q|NCOR1_ENST00000395857.3_Missense_Mutation_p.R378Q	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1794	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.R1794Q(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TGACATGATTCGTAGCTGAGC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											147	129	135					17																	15965425		2203	4300	6503	15906150	SO:0001583	missense	9611			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5381G>A	17.37:g.15965425C>T	ENSP00000268712:p.Arg1794Gln		15906150	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.042255	0.75732	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.46819	0.86;0.86;0.86	5.74	5.74	0.90152	.	0.136830	0.48767	D	0.000161	T	0.62551	0.2437	L	0.40543	1.245	0.48135	D	0.99959	D;D;D;D;D	0.89917	0.999;1.0;0.997;0.998;0.999	D;D;D;D;P	0.80764	0.994;0.988;0.968;0.986;0.885	T	0.61860	-0.6976	10	0.56958	D	0.05	-6.8779	18.9133	0.92494	0.0:1.0:0.0:0.0	.	604;1698;1794;1810;314	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1	.;.;NCOR1_HUMAN;.;.	Q	1794;1810;1698;378	ENSP00000268712:R1794Q;ENSP00000379192:R1810Q;ENSP00000379198:R378Q	ENSP00000268712:R1794Q	R	-	2	0	NCOR1	15906150	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	5.950000	0.70265	2.715000	0.92844	0.650000	0.86243	CGA		0.383	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15965425	C	T	15965425	3	4	61	1	0	0	0	0	1	0	0	0	10266	884	31	1	1985	1	NCOR1	17	15965425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323827	15965425	65229785	10097	18082										
NCOR1	9611	broad.mit.edu	37	chr17	15983784	15983784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggttgtgagttttggcttCggggagaaaattcttcctgc	13	7	1	2	rs150513105	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15983784C>T	ENST00000268712.3	-	25	3595	c.3338G>A	c.(3337-3339)cGa>cAa	p.R1113Q	NCOR1_ENST00000395851.1_Missense_Mutation_p.R1129Q|NCOR1_ENST00000395857.3_5'Flank	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1113	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.R1113Q(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GTTTTGGCTTCGGGGAGAAAA	0.438													C|||	12	0.00239617	0	0	5008	,	,		15189	0.0119		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											100	105	104					17																	15983784		2203	4300	6503	15924509	SO:0001583	missense	9611			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.3338G>A	17.37:g.15983784C>T	ENSP00000268712:p.Arg1113Gln		15924509	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	6	0.0027472527472527475	0	0.0	0	0.0	6	0.01048951048951049	0	0.0	C	32	5.154039	0.94645	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849	D;D	0.82803	-1.65;-1.65	6.07	5.11	0.69529	.	0.210251	0.41294	D	0.000902	D	0.83667	0.5304	M	0.64170	1.965	0.80722	D	1	D;B;B	0.69078	0.997;0.083;0.135	P;B;B	0.56788	0.806;0.004;0.01	D	0.86213	0.1626	10	0.56958	D	0.05	-7.4873	14.4647	0.67475	0.0:0.9301:0.0:0.0699	.	1020;1113;1129	E7EVK1;O75376;O75376-2	.;NCOR1_HUMAN;.	Q	1113;1129;1020	ENSP00000268712:R1113Q;ENSP00000379192:R1129Q	ENSP00000268712:R1113Q	R	-	2	0	NCOR1	15924509	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.006000	0.70724	1.587000	0.49959	-0.136000	0.14681	CGA		0.438	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15983784	C	T	15983784	3	4	61	1	0	0	0	0	1	0	0	0	10266	884	31	1	4072	1	NCOR1	17	15983784	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18359	15983784	65211426	10098	18083										
NCOR1	9611	broad.mit.edu	37	chr17	15983934	15983934	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactgacctgatttggcagaTtcctgttgccgtggcagtcc	11	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:15983934T>G	ENST00000268712.3	-	24	3542	c.3285A>C	c.(3283-3285)gaA>gaC	p.E1095D	NCOR1_ENST00000395851.1_Missense_Mutation_p.E1111D|NCOR1_ENST00000395857.3_5'Flank	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1095	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.E1095D(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATTTGGCAGATTCCTGTTGCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	17											182	161	169					17																	15983934		2203	4300	6503	15924659	SO:0001583	missense	9611			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.3285A>C	17.37:g.15983934T>G	ENSP00000268712:p.Glu1095Asp		15924659	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	4.240	0.043408	0.08196	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849	D;D	0.82526	-1.62;-1.62	6.07	-7.9	0.01169	.	0.042794	0.85682	D	0.000000	T	0.64068	0.2565	N	0.16233	0.39	0.80722	D	1	B;B	0.23442	0.051;0.085	B;B	0.21360	0.015;0.034	T	0.53107	-0.8485	10	0.02654	T	1	-12.9723	21.5777	0.99957	0.0:0.6833:0.0:0.3167	.	1095;1111	O75376;O75376-2	NCOR1_HUMAN;.	D	1095;1111;1002	ENSP00000268712:E1095D;ENSP00000379192:E1111D	ENSP00000268712:E1095D	E	-	3	2	NCOR1	15924659	0.036000	0.19791	0.001000	0.08648	0.975000	0.68041	-0.624000	0.05540	-1.643000	0.01519	-0.256000	0.11100	GAA		0.438	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15983934	T	G	15983934	3	3	61	1	0	0	0	0	1	0	0	0	10266	1490	52	4	4129	4	NCOR1	17	15983934	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	150	15983934	65211276	10099	18084										
NCOR1	9611	broad.mit.edu	37	chr17	16042492	16042492	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagagctgccgcatttgtttCtcattattctggaaaaaaaa	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16042492C>A	ENST00000268712.3	-	12	1439	c.1182G>T	c.(1180-1182)gaG>gaT	p.E394D	NCOR1_ENST00000395851.1_Missense_Mutation_p.E394D|NCOR1_ENST00000395848.1_Missense_Mutation_p.E285D|RNU6-862P_ENST00000362804.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	394					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.E394D(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GCATTTGTTTCTCATTATTCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											43	42	42					17																	16042492		2203	4300	6503	15983217	SO:0001583	missense	9611			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.1182G>T	17.37:g.16042492C>A	ENSP00000268712:p.Glu394Asp		15983217	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	C	11.21	1.570352	0.28003	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000458113;ENST00000395848;ENST00000411510;ENST00000436828	T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24	5.38	3.19	0.36642	.	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	N	0.11560	0.145	0.80722	D	1	P;P;P;B;P;D	0.71674	0.855;0.855;0.855;0.034;0.731;0.998	B;B;B;B;B;D	0.77557	0.348;0.348;0.348;0.076;0.437;0.99	T	0.22800	-1.0206	10	0.56958	D	0.05	-10.668	6.823	0.23866	0.0:0.6327:0.0:0.3673	.	403;394;394;285;394;394	E7EU93;E7EV02;E7EW50;E9PGV6;O75376;O75376-2	.;.;.;.;NCOR1_HUMAN;.	D	394;394;285;403;285;394;403	ENSP00000268712:E394D;ENSP00000379192:E394D;ENSP00000379189:E285D;ENSP00000407998:E394D;ENSP00000387727:E403D	ENSP00000268712:E394D	E	-	3	2	NCOR1	15983217	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.852000	0.27764	1.267000	0.44247	-0.150000	0.13652	GAG		0.363	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16042492	C	A	16042492	3	1	61	1	0	0	0	0	1	0	0	0	10266	912	32	2	6280	2	NCOR1	17	16042492	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58558	16042492	65152718	10100	18085										
TRPV2	51393	broad.mit.edu	37	chr17	16323446	16323446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtcagccggatccaaaccGatttgaccgagatcggctct	10	13	2	2	rs569542610		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16323446G>A	ENST00000338560.7	+	3	617	c.218G>A	c.(217-219)cGa>cAa	p.R73Q	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	73	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.R73Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GATCCAAACCGATTTGACCGA	0.582													G|||	1	0.000199681	0	0	5008	,	,		19193	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	17											84	76	78					17																	16323446		2203	4300	6503	16264171	SO:0001583	missense	51393			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.218G>A	17.37:g.16323446G>A	ENSP00000342222:p.Arg73Gln		16264171	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	37	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719863	0.48728	.	.	ENSG00000187688	ENST00000338560	D	0.87729	-2.29	5.41	3.43	0.39272	Ankyrin repeat-containing domain (1);	0.509456	0.23086	N	0.052096	T	0.78534	0.4298	M	0.62723	1.935	0.80722	D	1	D	0.56035	0.974	B	0.31101	0.124	T	0.73541	-0.3950	10	0.22109	T	0.4	-28.7212	9.2141	0.37337	0.1681:0.0:0.8319:0.0	.	73	Q9Y5S1	TRPV2_HUMAN	Q	73	ENSP00000342222:R73Q	ENSP00000342222:R73Q	R	+	2	0	TRPV2	16264171	0.998000	0.40836	0.926000	0.36857	0.610000	0.37248	1.904000	0.39868	0.666000	0.31087	0.655000	0.94253	CGA		0.582	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		A	16323446	G	A	16323446	3	1	61	1	0	0	0	0	1	0	0	0	16636	1058	37	1	224	1	TRPV2	17	16323446	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	280954	16323446	64871764	10101	18086										
ZNF287	57336	broad.mit.edu	37	chr17	16456563	16456563	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catattcttgtgaaaggactGacttcaaactgaaacctctt	6	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16456563G>T	ENST00000395824.1	-	6	1510	c.893C>A	c.(892-894)tCa>tAa	p.S298*	ZNF287_ENST00000395825.3_Nonsense_Mutation_p.S298*			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	291					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S291*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		TGAAAGGACTGACTTCAAACT	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											101	105	103					17																	16456563		2203	4299	6502	16397288	SO:0001587	stop_gained	57336			AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"Zinc fingers, C2H2-type", "-", "-", "-"	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.893C>A	17.37:g.16456563G>T	ENSP00000379168:p.Ser298*		16397288	Q6IAG1	Nonsense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	G	37	6.376096	0.97515	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	.	.	.	4.88	4.88	0.63580	.	0.000000	0.41294	D	0.000913	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9346	0.79691	0.0:0.0:1.0:0.0	.	.	.	.	X	298	.	ENSP00000379168:S298X	S	-	2	0	ZNF287	16397288	0.001000	0.12720	0.413000	0.26509	0.484000	0.33280	0.998000	0.29744	2.714000	0.92807	0.585000	0.79938	TCA		0.328	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			T	16456563	G	T	16456563	4	4	61	1	0	0	0	0	0	1	0	0	17864	1294	45	2	1396	2	ZNF287	17	16456563	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133117	16456563	64738647	10102	18087										
ZNF624	57547	broad.mit.edu	37	chr17	16525763	16525763	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttctgaaggcttttccacAttcttcacatttatagggcc	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16525763A>C	ENST00000311331.7	-	6	2528	c.2437T>G	c.(2437-2439)Tgt>Ggt	p.C813G		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	813					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C813G(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GCTTTTCCACATTCTTCACAT	0.403																																					NSCLC(186;1023 2134 13330 38202 39800)											1	Substitution - Missense(1)	large_intestine(1)	17											122	120	121					17																	16525763		2203	4300	6503	16466488	SO:0001583	missense	57547			AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"Zinc fingers, C2H2-type", "-"	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.2437T>G	17.37:g.16525763A>C	ENSP00000310472:p.Cys813Gly		16466488	Q3SY62|Q3SY63|Q6ZN27	Missense_Mutation	SNP	ENST00000311331.7	37	CCDS11180.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.415901	0.42817	.	.	ENSG00000197566	ENST00000311331	D	0.85861	-2.04	3.34	2.26	0.28386	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94542	0.8242	H	0.99336	4.52	0.36568	D	0.872812	D	0.69078	0.997	D	0.74023	0.982	D	0.93446	0.6798	9	0.87932	D	0	.	6.8261	0.23885	0.8832:0.0:0.1168:0.0	.	813	Q9P2J8	ZN624_HUMAN	G	813	ENSP00000310472:C813G	ENSP00000310472:C813G	C	-	1	0	ZNF624	16466488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.590000	0.67530	0.674000	0.31244	0.533000	0.62120	TGT		0.403	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617		C	16525763	A	C	16525763	3	2	61	1	0	0	0	0	1	0	0	0	18087	217	8	4	164	4	ZNF624	17	16525763	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	69200	16525763	64669447	10103	18088										
CCDC144A	9720	broad.mit.edu	37	chr17	16615032	16615032	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacagaagtaatagcacaGaattatcaggaaccctaact	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16615032G>T	ENST00000360524.8	+	6	1694	c.1618G>T	c.(1618-1620)Gaa>Taa	p.E540*	CCDC144A_ENST00000443444.2_Nonsense_Mutation_p.E540*|CCDC144A_ENST00000399273.1_Nonsense_Mutation_p.E540*|CCDC144A_ENST00000340621.5_Nonsense_Mutation_p.E539*|CCDC144A_ENST00000456009.1_Nonsense_Mutation_p.E260*|RN7SL620P_ENST00000580704.1_RNA|RP11-219A15.1_ENST00000448331.3_Nonsense_Mutation_p.E540*	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	540								p.E540*(1)									TAATAGCACAGAATTATCAGG	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											1	1	1					17																	16615032		803	1892	2695	16555757	SO:0001587	stop_gained	9720			BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.1618G>T	17.37:g.16615032G>T	ENSP00000353717:p.Glu540*		16555757	O60311|Q6ZU57	Nonsense_Mutation	SNP	ENST00000360524.8	37	CCDS45621.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	27.7|27.7	4.852969|4.852969	0.91355|0.91355	.|.	.|.	ENSG00000170160|ENSG00000170160	ENST00000340621;ENST00000399273;ENST00000443444;ENST00000448331;ENST00000360524;ENST00000456009;ENST00000360495|ENST00000328495	.|.	.|.	.|.	1.84|1.84	1.84|1.84	0.25277|0.25277	.|.	.|.	.|.	.|.	.|.	.|T	.|0.41026	.|0.1141	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.49437	.|-0.8940	.|3	0.24483|.	T|.	0.36|.	.|.	7.1379|7.1379	0.25539|0.25539	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|H	539;540;540;540;540;260;540|23	.|.	ENSP00000344740:E539X|.	E|Q	+|+	1|3	0|2	CCDC144A|CCDC144A	16555757|16555757	0.002000|0.002000	0.14202|0.14202	0.012000|0.012000	0.15200|0.15200	0.005000|0.005000	0.04900|0.04900	-0.018000|-0.018000	0.12568|0.12568	1.025000|1.025000	0.39708|0.39708	0.418000|0.418000	0.28097|0.28097	GAA|CAG		0.378	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			T	16615032	G	T	16615032	4	4	61	1	0	0	0	0	0	1	0	0	2783	943	33	2	1640	2	CCDC144A	17	16615032	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89269	16615032	64580178	10104	18089										
CCDC144A	9720	broad.mit.edu	37	chr17	16638085	16638085	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattgccttgctgagactgGaaatagatacaataaaaaat	7	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:16638085G>T	ENST00000360524.8	+	12	2576	c.2500G>T	c.(2500-2502)Gaa>Taa	p.E834*	CCDC144A_ENST00000443444.2_Nonsense_Mutation_p.E834*|CCDC144A_ENST00000399273.1_Nonsense_Mutation_p.E834*|CCDC144A_ENST00000456009.1_Nonsense_Mutation_p.E554*|RP11-219A15.1_ENST00000448331.3_Nonsense_Mutation_p.E834*	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	834								p.E834*(1)									GCTGAGACTGGAAATAGATAC	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											11	11	11					17																	16638085		1806	4050	5856	16578810	SO:0001587	stop_gained	9720			BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.2500G>T	17.37:g.16638085G>T	ENSP00000353717:p.Glu834*		16578810	O60311|Q6ZU57	Nonsense_Mutation	SNP	ENST00000360524.8	37	CCDS45621.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	36|36	5.864837|5.864837	0.97043|0.97043	.|.	.|.	ENSG00000170160|ENSG00000170160	ENST00000399273;ENST00000443444;ENST00000360524;ENST00000456009|ENST00000328495	.|.	.|.	.|.	2.08|2.08	2.08|2.08	0.27032|0.27032	.|.	.|.	.|.	.|.	.|.	.|T	.|0.50667	.|0.1629	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.59847	.|-0.7377	.|3	0.87932|.	D|.	0|.	.|.	9.8235|9.8235	0.40896|0.40896	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|C	834;834;834;554|317	.|.	ENSP00000353717:E834X|.	E|W	+|+	1|3	0|0	CCDC144A|CCDC144A	16578810|16578810	1.000000|1.000000	0.71417|0.71417	0.515000|0.515000	0.27774|0.27774	0.107000|0.107000	0.19398|0.19398	4.112000|4.112000	0.57845|0.57845	1.153000|1.153000	0.42468|0.42468	0.393000|0.393000	0.25936|0.25936	GAA|TGG		0.323	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			T	16638085	G	T	16638085	4	4	61	1	0	0	0	0	0	1	0	0	2783	1175	41	2	2546	2	CCDC144A	17	16638085	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23053	16638085	64557125	10105	18090										
COPS3	8533	broad.mit.edu	37	chr17	17168149	17168149	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagagagctctttcaaagttCttcagcccagtatagatcat	7	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:17168149C>A	ENST00000268717.5	-	6	694	c.588G>T	c.(586-588)aaG>aaT	p.K196N	COPS3_ENST00000439936.2_Missense_Mutation_p.K176N|COPS3_ENST00000539941.2_Missense_Mutation_p.K176N	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	196	PCI.				cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.K196N(1)		NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TTTCAAAGTTCTTCAGCCCAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											89	87	88					17																	17168149		2203	4300	6503	17108874	SO:0001583	missense	8533			AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3", "COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.588G>T	17.37:g.17168149C>A	ENSP00000268717:p.Lys196Asn		17108874	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	37	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504659	0.85176	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352;ENST00000439936	T;T;T	0.62788	0.0;0.0;0.0	5.76	5.76	0.90799	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.83820	0.5337	M	0.91561	3.22	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.85229	0.1031	10	0.46703	T	0.11	-25.4661	18.9546	0.92654	0.0:1.0:0.0:0.0	.	196	Q9UNS2	CSN3_HUMAN	N	196;176;196;220	ENSP00000268717:K196N;ENSP00000437606:K176N;ENSP00000409028:K196N	ENSP00000268717:K196N	K	-	3	2	COPS3	17108874	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.644000	0.61397	2.718000	0.92993	0.655000	0.94253	AAG		0.363	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			A	17168149	C	A	17168149	3	1	61	1	0	0	0	0	1	0	0	0	3740	912	32	2	711	2	COPS3	17	17168149	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	530064	17168149	64027061	10106	18091										
COPS3	8533	broad.mit.edu	37	chr17	17171262	17171262	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgcatcttgtctatggcTtgcttaaggatgccaattcc	8	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:17171262T>G	ENST00000268717.5	-	5	484	c.378A>C	c.(376-378)caA>caC	p.Q126H	COPS3_ENST00000439936.2_Missense_Mutation_p.Q106H|COPS3_ENST00000539941.2_Missense_Mutation_p.Q106H	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	126					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.Q126H(1)		NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TGTCTATGGCTTGCTTAAGGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	17											266	195	219					17																	17171262		2203	4300	6503	17111987	SO:0001583	missense	8533			AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3", "COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.378A>C	17.37:g.17171262T>G	ENSP00000268717:p.Gln126His		17111987	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	37	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.189544	0.38707	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352;ENST00000439936	T;T;T	0.64991	-0.13;-0.13;-0.13	5.48	3.23	0.37069	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.33731	0.0873	N	0.02539	-0.55	0.58432	D	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.05649	-1.0872	10	0.39692	T	0.17	-12.8513	9.3387	0.38067	0.0:0.1475:0.0:0.8525	.	126	Q9UNS2	CSN3_HUMAN	H	126;106;126;150	ENSP00000268717:Q126H;ENSP00000437606:Q106H;ENSP00000409028:Q126H	ENSP00000268717:Q126H	Q	-	3	2	COPS3	17111987	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.055000	0.49916	0.361000	0.24292	0.528000	0.53228	CAA		0.438	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			G	17171262	T	G	17171262	3	3	61	1	0	0	0	0	1	0	0	0	3740	1606	56	4	925	4	COPS3	17	17171262	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3113	17171262	64023948	10107	18092										
PEMT	10400	broad.mit.edu	37	chr17	17412849	17412849	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcctccttgaggatcccGaagtaatcacctgtggatga	10	12	1	2	rs564981683		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:17412849G>A	ENST00000395783.1	-	5	545	c.366C>T	c.(364-366)ttC>ttT	p.F122F	PEMT_ENST00000484838.2_5'UTR|PEMT_ENST00000435340.2_Silent_p.F137F|PEMT_ENST00000255389.5_Silent_p.F159F|RP11-524F11.1_ENST00000582325.1_RNA|PEMT_ENST00000395782.1_Silent_p.F122F|PEMT_ENST00000395781.2_Silent_p.F159F	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	122					cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)	p.F159F(1)		endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		TGAGGATCCCGAAGTAATCAC	0.607													G|||	0	0	0	0	5008	,	,		21545	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											145	111	123					17																	17412849		2203	4300	6503	17353574	SO:0001819	synonymous_variant	10400			AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.366C>T	17.37:g.17412849G>A			17353574	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Silent	SNP	ENST00000395783.1	37	CCDS11187.1																																																																																				0.607	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169		A	17412849	G	A	17412849	2	1	61	1	0	0	0	0	0	0	0	1	11757	1049	37	1		1	PEMT	17	17412849	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241587	17412849	63782361	10108	18093										
RAI1	10743	broad.mit.edu	37	chr17	17698007	17698007	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacggcagtctgccgctcgAcagcttctccaagttcgtgg	11	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:17698007A>C	ENST00000353383.1	+	3	2214	c.1745A>C	c.(1744-1746)gAc>gCc	p.D582A	RAI1_ENST00000261641.6_Missense_Mutation_p.D582A	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	582					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.D582A(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CTGCCGCTCGACAGCTTCTCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											77	77	77					17																	17698007		2203	4296	6499	17638732	SO:0001583	missense	10743			AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1745A>C	17.37:g.17698007A>C	ENSP00000323074:p.Asp582Ala		17638732	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	A	16.17	3.048348	0.55110	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.70282	-0.47;2.27;0.13	5.18	5.18	0.71444	.	0.067257	0.64402	D	0.000010	T	0.75295	0.3830	L	0.60455	1.87	0.43879	D	0.996493	D	0.60575	0.988	P	0.54759	0.76	T	0.72357	-0.4318	10	0.20046	T	0.44	.	15.0197	0.71621	1.0:0.0:0.0:0.0	.	582	Q7Z5J4	RAI1_HUMAN	A	582;582;582;582;582;534	ENSP00000323074:D582A;ENSP00000379120:D582A;ENSP00000261641:D582A	ENSP00000261641:D582A	D	+	2	0	RAI1	17638732	1.000000	0.71417	0.998000	0.56505	0.757000	0.42996	5.089000	0.64492	1.960000	0.56953	0.459000	0.35465	GAC		0.637	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		C	17698007	A	C	17698007	3	2	61	1	0	0	0	0	1	0	0	0	13044	275	10	4	1747	4	RAI1	17	17698007	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	285158	17698007	63497203	10109	18094										
MYO15A	51168	broad.mit.edu	37	chr17	18034585	18034585	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacccctcttggagtccttCggtaatgccaaaaccgtcag	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18034585C>T	ENST00000205890.5	+	9	4409	c.4071C>T	c.(4069-4071)ttC>ttT	p.F1357F		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1357	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.F1357F(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TGGAGTCCTTCGGTAATGCCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	17											64	66	65					17																	18034585		1955	4181	6136	17975310	SO:0001819	synonymous_variant	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.4071C>T	17.37:g.18034585C>T			17975310	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.572	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18034585	C	T	18034585	2	4	61	1	0	0	0	0	0	0	0	1	10093	883	31	1		1	MYO15A	17	18034585	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336578	18034585	63160625	10110	18095										
MYO15A	51168	broad.mit.edu	37	chr17	18039745	18039745	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctaggagacaatgcgagaGaagatcttcacgcccctaac	9	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18039745G>T	ENST00000205890.5	+	14	4949	c.4611G>T	c.(4609-4611)gaG>gaT	p.E1537D		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1537	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E1537D(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAATGCGAGAGAAGATCTTCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	17											68	76	73					17																	18039745		2186	4291	6477	17980470	SO:0001583	missense	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.4611G>T	17.37:g.18039745G>T	ENSP00000205890:p.Glu1537Asp		17980470	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460364	0.63401	.	.	ENSG00000091536	ENST00000205890	D	0.95980	-3.87	5.57	4.61	0.57282	Myosin head, motor domain (2);	.	.	.	.	D	0.94843	0.8334	M	0.61387	1.9	0.80722	D	1	P	0.41978	0.767	P	0.45138	0.471	D	0.94404	0.7625	9	0.56958	D	0.05	.	13.4963	0.61428	0.0746:0.0:0.9254:0.0	.	1537	Q9UKN7	MYO15_HUMAN	D	1537	ENSP00000205890:E1537D	ENSP00000205890:E1537D	E	+	3	2	MYO15A	17980470	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.570000	0.45981	1.371000	0.46172	-0.136000	0.14681	GAG		0.642	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18039745	G	T	18039745	3	4	61	1	0	0	0	0	1	0	0	0	10093	933	33	2	4657	2	MYO15A	17	18039745	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5160	18039745	63155465	10111	18096										
MYO15A	51168	broad.mit.edu	37	chr17	18045511	18045511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcattaagcggcgattccGctctctgcgccacaagatca	8	14	3	1	rs571036199		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18045511G>A	ENST00000205890.5	+	24	6106	c.5768G>A	c.(5767-5769)cGc>cAc	p.R1923H		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1923	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1923H(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CGGCGATTCCGCTCTCTGCGC	0.577													G|||	1	0.000199681	0	0	5008	,	,		19696	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	17											41	44	43					17																	18045511		2176	4283	6459	17986236	SO:0001583	missense	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.5768G>A	17.37:g.18045511G>A	ENSP00000205890:p.Arg1923His		17986236	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.229806	0.58777	.	.	ENSG00000091536	ENST00000205890	D	0.95821	-3.82	5.69	5.69	0.88448	.	.	.	.	.	D	0.90297	0.6965	L	0.49699	1.58	0.80722	D	1	P	0.36282	0.546	B	0.19666	0.026	D	0.87163	0.2216	9	0.14656	T	0.56	.	10.2718	0.43487	0.147:0.0:0.853:0.0	.	1923	Q9UKN7	MYO15_HUMAN	H	1923	ENSP00000205890:R1923H	ENSP00000205890:R1923H	R	+	2	0	MYO15A	17986236	0.995000	0.38212	1.000000	0.80357	0.889000	0.51656	1.528000	0.35985	2.690000	0.91761	0.655000	0.94253	CGC		0.577	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18045511	G	A	18045511	3	1	61	1	0	0	0	0	1	0	0	0	10093	1087	38	1	5854	1	MYO15A	17	18045511	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5766	18045511	63149699	10112	18097										
MYO15A	51168	broad.mit.edu	37	chr17	18054450	18054450	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcaccagaggcacagccGacgtctgtaggcaccggtcc	12	16	1	1	rs371622693		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18054450G>A	ENST00000205890.5	+	39	7838	c.7500G>A	c.(7498-7500)ccG>ccA	p.P2500P	MYO15A_ENST00000418233.3_5'Flank|MYO15A_ENST00000585180.1_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2500	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.P2500P(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AGGCACAGCCGACGTCTGTAG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	17						G		0,4004		0,0,2002	119	134	129		7500	-4.7	0.1	17		129	1,8319		0,1,4159	no	coding-synonymous	MYO15A	NM_016239.3		0,1,6161	AA,AG,GG		0.012,0.0,0.0081		2500/3531	18054450	1,12323	2002	4160	6162	17995175	SO:0001819	synonymous_variant	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7500G>A	17.37:g.18054450G>A			17995175	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.647	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18054450	G	A	18054450	2	1	61	1	0	0	0	0	0	0	0	1	10093	1045	37	1		1	MYO15A	17	18054450	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8939	18054450	63140760	10113	18098										
FLII	2314	broad.mit.edu	37	chr17	18155057	18155057	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagcacctgcttggcctgGtcatcctgggctgaatcctt	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18155057G>C	ENST00000327031.4	-	12	1545	c.1320C>G	c.(1318-1320)gaC>gaG	p.D440E	FLII_ENST00000545457.2_Missense_Mutation_p.D385E|FLII_ENST00000578558.1_Missense_Mutation_p.D439E|FLII_ENST00000379450.4_Missense_Mutation_p.D354E|FLII_ENST00000584444.1_5'Flank|FLII_ENST00000579294.1_Missense_Mutation_p.D429E	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	440					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.D440E(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					GCTTGGCCTGGTCATCCTGGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											143	131	135					17																	18155057		2203	4300	6503	18095782	SO:0001583	missense	2314			U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.1320C>G	17.37:g.18155057G>C	ENSP00000324573:p.Asp440Glu		18095782	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.324473	0.41197	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.35236	1.32;1.4	5.78	4.79	0.61399	.	0.043989	0.85682	D	0.000000	T	0.53481	0.1799	M	0.65975	2.015	0.51233	D	0.999913	P;P;B;B;D	0.64830	0.702;0.702;0.42;0.232;0.994	B;B;B;B;D	0.72625	0.217;0.217;0.061;0.186;0.978	T	0.53330	-0.8454	10	0.07990	T	0.79	-29.7797	15.2029	0.73153	0.0683:0.0:0.9317:0.0	.	354;354;440;440;409	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	E	440;440;354	ENSP00000324573:D440E;ENSP00000368763:D354E	ENSP00000324573:D440E	D	-	3	2	FLII	18095782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.870000	0.48451	1.420000	0.47138	0.561000	0.74099	GAC		0.612	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18155057	G	C	18155057	3	2	61	1	0	0	0	0	1	0	0	0	5944	1252	44	5	2565	5	FLII	17	18155057	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100607	18155057	63040153	10114	18099										
LGALS9C	654346	broad.mit.edu	37	chr17	18396139	18396139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggagcgaagtctgccccGaaaaatgcccttcgtccgag	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18396139G>A	ENST00000328114.6	+	10	971	c.890G>A	c.(889-891)cGa>cAa	p.R297Q	LGALS9C_ENST00000581545.1_Intron|LGALS9C_ENST00000584941.1_Intron|LGALS9C_ENST00000583322.1_Missense_Mutation_p.R264Q|LGALS9C_ENST00000412421.2_Missense_Mutation_p.R209Q	NM_001040078.2	NP_001035167.2	Q6DKI2	LEG9C_HUMAN	lectin, galactoside-binding, soluble, 9C	297	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)	p.R297Q(1)		NS(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	7						AGTCTGCCCCGAAAAATGCCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											27	18	21					17																	18396139		2181	4023	6204	18336864	SO:0001583	missense	654346				CCDS32587.1	17p11.2	2011-08-04			ENSG00000171916	ENSG00000171916		"Lectins, galactoside-binding"	33874	protein-coding gene	gene with protein product							Standard	NM_001040078		Approved		uc002gtw.3	Q6DKI2	OTTHUMG00000059251	ENST00000328114.6:c.890G>A	17.37:g.18396139G>A	ENSP00000329932:p.Arg297Gln		18336864	B0AZM7	Missense_Mutation	SNP	ENST00000328114.6	37	CCDS32587.1	.	.	.	.	.	.	.	.	.	.	g	12.98	2.099580	0.37048	.	.	ENSG00000171916	ENST00000412421;ENST00000328114	T;T	0.05513	3.43;3.43	2.26	1.21	0.21127	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.993975	0.08161	N	0.988449	T	0.04497	0.0123	N	0.20986	0.625	0.09310	N	1	B	0.27882	0.192	B	0.14023	0.01	T	0.44112	-0.9349	10	0.29301	T	0.29	.	7.9733	0.30140	0.0:0.0:0.7544:0.2456	.	297	Q6DKI2	LEG9C_HUMAN	Q	209;297	ENSP00000390286:R209Q;ENSP00000329932:R297Q	ENSP00000329932:R297Q	R	+	2	0	LGALS9C	18336864	0.033000	0.19621	0.000000	0.03702	0.712000	0.41017	2.325000	0.43840	0.464000	0.27142	0.184000	0.17185	CGA		0.582	LGALS9C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000131456.2	NM_001040078		A	18396139	G	A	18396139	3	1	61	1	0	0	0	0	1	0	0	0	8773	1058	37	1	928	1	LGALS9C	17	18396139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241082	18396139	62799071	10115	18100										
CCDC144B	348254	broad.mit.edu	37	chr17	18486811	18486811	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacatatcggcatttcttttCtcccattttcttgttttaag	4	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18486811C>T								CTD-2303H24.2 (41577 upstream) : CCDC144B (4781 downstream)																							CATTTCTTTTCTCCCATTTTC	0.303																																																0			17											119	103	108					17																	18486811		1810	4068	5878	18427536	SO:0001628	intergenic_variant	284047																															17.37:g.18486811C>T			18427536		Missense_Mutation	SNP		37																																																																																				0	0.303									T	18486811	C	T	18486811	1	4	61	0	1	0	0	0	0	0	0	0	2784	913	32	3		3	CCDC144B	17	18486811	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90672	18486811	62708399	10116	18101										
CCDC144B	348254	broad.mit.edu	37	chr17	18528713	18528713	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcgtagactgccagcttCggagacccctcagcccctcc	11	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18528713C>T								CCDC144B (19009 upstream) : TBC1D28 (9605 downstream)																							CTGCCAGCTTCGGAGACCCCT	0.647																																																0			17											24	29	27					17																	18528713		2202	4300	6502	18469438	SO:0001628	intergenic_variant	284047																															17.37:g.18528713C>T			18469438		Silent	SNP		37																																																																																				0	0.647									T	18528713	C	T	18528713	1	4	61	0	1	0	0	0	0	0	0	0	2784	871	31	1		1	CCDC144B	17	18528713	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41902	18528713	62666497	10117	18102										
FAM18B	51030	broad.mit.edu	37	chr17	18700945	18700945	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtggaatcacattgatgaAgatggaaagagccattgggt	14	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:18700945A>G	ENST00000307767.8	+	4	593	c.294A>G	c.(292-294)gaA>gaG	p.E98E	TVP23B_ENST00000581733.1_Silent_p.E34E|TVP23B_ENST00000574226.1_Silent_p.E98E|TVP23B_ENST00000476139.1_Silent_p.E34E	NM_016078.4	NP_057162.4	Q9NYZ1	TV23B_HUMAN	trans-golgi network vesicle protein 23 homolog B (S. cerevisiae)	98						integral component of membrane (GO:0016021)		p.E98E(1)									ACATTGATGAAGATGGAAAGA	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	17											59	59	59					17																	18700945		2188	4264	6452	18641670	SO:0001819	synonymous_variant	51030			AF151906	CCDS42274.1	17p11.2	2012-11-29	2012-11-29	2012-11-29	ENSG00000171928	ENSG00000171928			20399	protein-coding gene	gene with protein product			"family with sequence similarity 18, member B", "family with sequence similarity 18, member B1"	FAM18B, FAM18B1		10810093	Standard	NM_016078		Approved	CGI-148, YDR084C	uc002gum.2	Q9NYZ1	OTTHUMG00000059052	ENST00000307767.8:c.294A>G	17.37:g.18700945A>G			18641670	A8K448|Q96HK5|Q9Y3E6	Silent	SNP	ENST00000307767.8	37	CCDS42274.1																																																																																				0.313	TVP23B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130667.2	NM_016078		G	18700945	A	G	18700945	2	3	61	1	0	0	0	0	0	0	0	1	5535	69	3	4		4	FAM18B	17	18700945	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	172232	18700945	62494265	10118	18103										
MAPK7	5598	broad.mit.edu	37	chr17	19283132	19283132	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagatccctaatgctttCgatgtggtgaccaatgccaa	9	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:19283132C>T	ENST00000308406.5	+	3	656	c.270C>T	c.(268-270)ttC>ttT	p.F90F	MAPK7_ENST00000571657.1_Intron|B9D1_ENST00000477478.2_5'Flank|B9D1_ENST00000575403.1_5'Flank|MAPK7_ENST00000395604.3_Silent_p.F90F|MAPK7_ENST00000299612.7_Intron|B9D1_ENST00000468679.3_5'Flank|MAPK7_ENST00000395602.4_Silent_p.F90F	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	90	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for binding to MAP2K5. {ECO:0000250}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)	p.F90F(1)		autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CTAATGCTTTCGATGTGGTGA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	17											114	107	109					17																	19283132		2203	4300	6503	19223725	SO:0001819	synonymous_variant	5598			U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.270C>T	17.37:g.19283132C>T			19223725	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	37	CCDS11206.1																																																																																				0.527	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		T	19283132	C	T	19283132	2	4	61	1	0	0	0	0	0	0	0	1	9312	883	31	1		1	MAPK7	17	19283132	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	582187	19283132	61912078	10119	18104										
SLC47A1	55244	broad.mit.edu	37	chr17	19480789	19480789	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaacagctggtgctgcggCgagggcttctgctcctgggg	18	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:19480789C>T	ENST00000270570.4	+	17	1722	c.1636C>T	c.(1636-1638)Cga>Tga	p.R546*	SLC47A1_ENST00000395585.1_Nonsense_Mutation_p.R546*|RP11-1113L8.1_ENST00000574267.1_RNA|SLC47A1_ENST00000457293.1_Nonsense_Mutation_p.R546*|SLC47A1_ENST00000571335.1_Nonsense_Mutation_p.R292*|SLC47A1_ENST00000436810.2_3'UTR|SLC47A1_ENST00000575023.1_Nonsense_Mutation_p.R244*|AC025627.7_ENST00000420951.1_RNA	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	546					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)	p.R546*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	GGTGCTGCGGCGAGGGCTTCT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											137	145	142					17																	19480789		2203	4300	6503	19421381	SO:0001587	stop_gained	55244				CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1636C>T	17.37:g.19480789C>T	ENSP00000270570:p.Arg546*		19421381	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Nonsense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.649845	0.47362	.	.	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000395585;ENST00000455670;ENST00000424755	.	.	.	5.16	-0.0541	0.13815	.	0.072725	0.50627	D	0.000106	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.8214	7.3471	0.26670	0.4232:0.4907:0.0:0.0861	.	.	.	.	X	546;546;546;221;258	.	ENSP00000270570:R546X	R	+	1	2	SLC47A1	19421381	0.953000	0.32496	0.013000	0.15412	0.279000	0.26890	0.245000	0.18142	0.162000	0.19483	0.462000	0.41574	CGA		0.522	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19480789	C	T	19480789	4	4	61	1	0	0	0	0	0	1	0	0	14684	760	27	1	1702	1	SLC47A1	17	19480789	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	197657	19480789	61714421	10120	18105										
SLC47A2	146802	broad.mit.edu	37	chr17	19609977	19609977	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacccatgaggaagctcccGatctcataggcccaccactc	8	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:19609977G>A	ENST00000325411.5	-	9	983	c.933C>T	c.(931-933)atC>atT	p.I311I	SLC47A2_ENST00000350657.5_Silent_p.I275I|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	311					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)	p.I311I(1)|p.I275I(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GGAAGCTCCCGATCTCATAGG	0.647																																																2	Substitution - coding silent(2)	large_intestine(2)	17											101	87	92					17																	19609977		2203	4300	6503	19550569	SO:0001819	synonymous_variant	146802			AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"Solute carriers"	26439	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 2"	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.933C>T	17.37:g.19609977G>A			19550569	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																				0.647	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908		A	19609977	G	A	19609977	2	1	61	1	0	0	0	0	0	0	0	1	14685	1048	37	1		1	SLC47A2	17	19609977	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129188	19609977	61585233	10121	18106										
AKAP10	11216	broad.mit.edu	37	chr17	19861512	19861512	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcaagtgattctgagtgCtgttagttctattattcagg	11	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:19861512C>A	ENST00000225737.6	-	4	849	c.692G>T	c.(691-693)aGc>aTc	p.S231I	AKAP10_ENST00000395536.3_Missense_Mutation_p.S231I|AKAP10_ENST00000572155.1_5'Flank	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	231	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)		p.S231I(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					ATTCTGAGTGCTGTTAGTTCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											112	107	108					17																	19861512		2203	4300	6503	19802104	SO:0001583	missense	11216			AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.692G>T	17.37:g.19861512C>A	ENSP00000225737:p.Ser231Ile		19802104	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	.	.	.	.	.	.	.	.	.	.	C	8.621	0.891304	0.17613	.	.	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.19394	2.15	6.08	-0.265	0.12946	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.271854	0.41097	N	0.000954	T	0.10895	0.0266	N	0.22421	0.69	0.09310	N	1	B;B;B	0.28971	0.0;0.229;0.162	B;B;B	0.27887	0.001;0.054;0.084	T	0.22452	-1.0216	10	0.30854	T	0.27	-1.3796	6.6987	0.23213	0.1261:0.4029:0.0:0.471	.	231;231;231	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	I	231	ENSP00000225737:S231I	ENSP00000225737:S231I	S	-	2	0	AKAP10	19802104	0.374000	0.25081	0.058000	0.19502	0.711000	0.40976	0.030000	0.13688	-0.295000	0.08960	-0.964000	0.02622	AGC		0.428	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		A	19861512	C	A	19861512	3	1	61	1	0	0	0	0	1	0	0	0	446	797	28	2	1344	2	AKAP10	17	19861512	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	251535	19861512	61333698	10122	18107										
CYTSB	92521	broad.mit.edu	37	chr17	20107938	20107938	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttcgaagtgaactaaaGaaatacaaagagaaaaggac	10	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:20107938G>T	ENST00000261503.5	+	4	627	c.576G>T	c.(574-576)aaG>aaT	p.K192N	SPECC1_ENST00000395527.4_Missense_Mutation_p.K192N|SPECC1_ENST00000395529.3_Missense_Mutation_p.K192N|SPECC1_ENST00000584527.1_5'Flank|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395525.3_Missense_Mutation_p.K111N|SPECC1_ENST00000395522.2_Missense_Mutation_p.K111N|SPECC1_ENST00000395530.2_Missense_Mutation_p.K111N	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	192					cell adhesion (GO:0007155)	nucleus (GO:0005634)		p.K192N(1)		breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		GTGAACTAAAGAAATACAAAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											111	126	121					17																	20107938		2203	4300	6503	20048530	SO:0001583	missense	92521			AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.576G>T	17.37:g.20107938G>T	ENSP00000261503:p.Lys192Asn		20048530	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434098	0.43224	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.67698	-0.28;2.81;2.81;2.81	4.82	3.84	0.44239	.	0.140928	0.64402	D	0.000003	T	0.67552	0.2905	L	0.53249	1.67	0.80722	D	1	P;P;P;P	0.52061	0.95;0.95;0.95;0.749	P;P;P;B	0.52554	0.702;0.702;0.702;0.269	T	0.68957	-0.5272	10	0.66056	D	0.02	-37.6827	7.3299	0.26575	0.2086:0.0:0.7914:0.0	.	111;111;192;192	Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;CYTSB_HUMAN	N	192;192;192;111;111;111	ENSP00000261503:K192N;ENSP00000378900:K192N;ENSP00000378893:K111N;ENSP00000378896:K111N	ENSP00000261503:K192N	K	+	3	2	SPECC1	20048530	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	2.478000	0.45189	1.314000	0.45095	0.655000	0.94253	AAG		0.468	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		T	20107938	G	T	20107938	3	4	61	1	0	0	0	0	1	0	0	0	4216	933	33	2	630	2	CYTSB	17	20107938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246426	20107938	61087272	10123	18108										
CCDC144NL	339184	broad.mit.edu	37	chr17	20799146	20799146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaaggcgccctcaccgtgcTtgctctcgctgccgacgctg	11	17	2	0	rs199662233		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:20799146T>C	ENST00000327925.5	-	1	307	c.188A>G	c.(187-189)aAg>aGg	p.K63R	RP11-344E13.3_ENST00000583962.1_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000582324.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA|RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	63								p.K63R(1)		large_intestine(3)|lung(3)|skin(1)	7						CTCACCGTGCTTGCTCTCGCT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											76	85	82					17																	20799146		2203	4300	6503	20739738	SO:0001583	missense	339184				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.188A>G	17.37:g.20799146T>C	ENSP00000328054:p.Lys63Arg		20739738		Missense_Mutation	SNP	ENST00000327925.5	37	CCDS32591.1	.	.	.	.	.	.	.	.	.	.	t	8.405	0.842886	0.16963	.	.	ENSG00000205212	ENST00000327925	T	0.20332	2.08	0.63	0.63	0.17693	.	.	.	.	.	T	0.08044	0.0201	N	0.08118	0	0.09310	N	1	P	0.39424	0.673	B	0.28916	0.096	T	0.21415	-1.0246	8	0.52906	T	0.07	.	.	.	.	.	63	Q6NUI1	C144L_HUMAN	R	63	ENSP00000328054:K63R	ENSP00000328054:K63R	K	-	2	0	CCDC144NL	20739738	0.023000	0.18921	0.001000	0.08648	0.016000	0.09150	0.163000	0.16520	0.526000	0.28541	0.130000	0.15844	AAG		0.652	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306		C	20799146	T	C	20799146	3	2	61	1	0	0	0	0	1	0	0	0	2785	1609	56	4	493	4	CCDC144NL	17	20799146	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	691208	20799146	60396064	10124	18109										
TMEM11	8834	broad.mit.edu	37	chr17	21101654	21101654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcatacggcatagagttCgtaaatcttctttacacagt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:21101654C>T	ENST00000317635.5	-	2	1033	c.562G>A	c.(562-564)Gaa>Aaa	p.E188K	TMEM11_ENST00000584432.1_5'UTR	NM_003876.2	NP_003867.1	P17152	TMM11_HUMAN	transmembrane protein 11	188					mitochondrion organization (GO:0007005)	integral component of mitochondrial inner membrane (GO:0031305)|integral component of plasma membrane (GO:0005887)		p.E188K(1)		endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						GCATAGAGTTCGTAAATCTTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											162	146	151					17																	21101654		2203	4300	6503	21042246	SO:0001583	missense	8834			BC002819	CCDS11216.1	17p11.1	2011-08-12	2005-09-08	2005-09-08		ENSG00000178307			16823	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 35"	C17orf35		2110658, 21274005	Standard	NM_003876		Approved	PMI, PM1	uc002gyp.2	P17152		ENST00000317635.5:c.562G>A	17.37:g.21101654C>T	ENSP00000319992:p.Glu188Lys		21042246	Q53YB2	Missense_Mutation	SNP	ENST00000317635.5	37	CCDS11216.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.014873	0.54468	.	.	ENSG00000178307	ENST00000317635	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.53674	0.1811	N	0.25647	0.755	0.80722	D	1	B	0.19073	0.033	B	0.13407	0.009	T	0.45220	-0.9276	9	0.44086	T	0.13	-25.6636	20.0067	0.97435	0.0:1.0:0.0:0.0	.	188	P17152	TMM11_HUMAN	K	188	.	ENSP00000319992:E188K	E	-	1	0	TMEM11	21042246	1.000000	0.71417	0.977000	0.42913	0.668000	0.39293	7.345000	0.79337	2.731000	0.93534	0.650000	0.86243	GAA		0.532	TMEM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444150.2	NM_003876		T	21101654	C	T	21101654	3	4	61	1	0	0	0	0	1	0	0	0	16065	893	31	1	20	1	TMEM11	17	21101654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	302508	21101654	60093556	10125	18110										
MAP2K3	5606	broad.mit.edu	37	chr17	21215553	21215553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtccccccagctcccagccGaccgtttctcccccgagttt	7	21	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:21215553G>A	ENST00000342679.4	+	10	1123	c.874G>A	c.(874-876)Gac>Aac	p.D292N	MAP2K3_ENST00000316920.6_Missense_Mutation_p.D263N|MAP2K3_ENST00000361818.5_Missense_Mutation_p.D263N	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	292	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.D296N(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GCTCCCAGCCGACCGTTTCTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											66	60	62					17																	21215553		2203	4300	6503	21156146	SO:0001583	missense	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.874G>A	17.37:g.21215553G>A	ENSP00000345083:p.Asp292Asn		21156146	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.716609	0.68844	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.66815	-0.23;-0.23	5.93	5.93	0.95920	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.154346	0.41605	D	0.000854	T	0.57533	0.2060	L	0.28344	0.845	0.58432	D	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.48281	-0.9049	10	0.28530	T	0.3	-36.02	20.3507	0.98813	0.0:0.0:1.0:0.0	.	292	P46734	MP2K3_HUMAN	N	292;263;263;296	ENSP00000345083:D292N;ENSP00000355081:D263N	ENSP00000319139:D296N	D	+	1	0	MAP2K3	21156146	1.000000	0.71417	0.790000	0.31976	0.793000	0.44817	7.783000	0.85696	2.808000	0.96608	0.655000	0.94253	GAC		0.647	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		A	21215553	G	A	21215553	3	1	61	1	0	0	0	0	1	0	0	0	9268	1058	37	1	912	1	MAP2K3	17	21215553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113899	21215553	59979657	10126	18111										
NOS2	4843	broad.mit.edu	37	chr17	26100226	26100226	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatctctcttctcttgggtCtccgcttctcgtcctgccag	8	15	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26100226C>A	ENST00000313735.6	-	13	1753	c.1520G>T	c.(1519-1521)aGa>aTa	p.R507I		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	507					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.R507I(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	TCTCTTGGGTCTCCGCTTCTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	17											334	288	304					17																	26100226		2203	4300	6503	23124353	SO:0001583	missense	4843			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1520G>T	17.37:g.26100226C>A	ENSP00000327251:p.Arg507Ile		23124353	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959961	0.53400	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.01804	4.63	5.41	3.42	0.39159	.	0.268407	0.37261	N	0.002180	T	0.03434	0.0099	M	0.74258	2.255	0.51767	D	0.999935	B;P	0.34587	0.257;0.458	B;B	0.36885	0.142;0.235	T	0.37619	-0.9698	10	0.66056	D	0.02	.	8.0979	0.30840	0.0:0.7511:0.0:0.2489	.	507;507	F8WEM3;P35228	.;NOS2_HUMAN	I	507;468;507	ENSP00000327251:R507I	ENSP00000305638:R507I	R	-	2	0	NOS2	23124353	0.795000	0.28851	0.365000	0.25901	0.643000	0.38383	1.845000	0.39279	0.659000	0.30945	0.561000	0.74099	AGA		0.527	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26100226	C	A	26100226	3	1	61	1	0	0	0	0	1	0	0	0	10574	913	32	2	2001	2	NOS2	17	26100226	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4884673	26100226	55094984	10127	18112										
NOS2	4843	broad.mit.edu	37	chr17	26109101	26109101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgtgttcaaacatttccCgggcagtggaacagctgcgg	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26109101C>T	ENST00000313735.6	-	7	895	c.662G>A	c.(661-663)cGg>cAg	p.R221Q		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	221			R -> W (in dbSNP:rs3730017). {ECO:0000269|Ref.10}.		arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.R221Q(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AAACATTTCCCGGGCAGTGGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											158	111	127					17																	26109101		2203	4300	6503	23133228	SO:0001583	missense	4843			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.662G>A	17.37:g.26109101C>T	ENSP00000327251:p.Arg221Gln		23133228	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	2.933	-0.220631	0.06061	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.21734	1.99	5.38	1.58	0.23477	Nitric oxide synthase, oxygenase domain (3);	0.705400	0.13460	N	0.386223	T	0.08537	0.0212	N	0.05487	-0.04	0.24640	N	0.993578	B;B	0.12630	0.005;0.006	B;B	0.04013	0.001;0.001	T	0.40021	-0.9585	10	0.15952	T	0.53	.	5.4132	0.16360	0.0:0.1794:0.1436:0.6769	.	221;221	F8WEM3;P35228	.;NOS2_HUMAN	Q	221	ENSP00000327251:R221Q	ENSP00000305638:R221Q	R	-	2	0	NOS2	23133228	1.000000	0.71417	0.848000	0.33437	0.463000	0.32649	2.305000	0.43664	-0.027000	0.13873	0.484000	0.47621	CGG		0.552	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		T	26109101	C	T	26109101	3	4	61	1	0	0	0	0	1	0	0	0	10574	652	23	1	2883	1	NOS2	17	26109101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8875	26109101	55086109	10128	18113										
NLK	51701	broad.mit.edu	37	chr17	26449740	26449740	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggaattgaagatgttgtgTttttttaagcatgataatgt	11	2	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26449740T>C	ENST00000407008.3	+	2	1288	c.570T>C	c.(568-570)tgT>tgC	p.C190C		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	190	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for interaction with TAB2. {ECO:0000250}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.C190C(2)|p.C178C(2)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		AGATGTTGTGTTTTTTTAAGC	0.388																																																4	Substitution - coding silent(4)	large_intestine(2)|kidney(2)	17											143	142	142					17																	26449740		2203	4300	6503	23473867	SO:0001819	synonymous_variant	51701			AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.570T>C	17.37:g.26449740T>C			23473867	B2RCX1|Q2PNI9|Q6P2A3	Silent	SNP	ENST00000407008.3	37	CCDS11224.2																																																																																				0.388	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231		C	26449740	T	C	26449740	2	2	61	1	0	0	0	0	0	0	0	1	10497	1731	60	4		4	NLK	17	26449740	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	340639	26449740	54745470	10129	18114										
TNFAIP1	7126	broad.mit.edu	37	chr17	26669303	26669303	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccacctgctgaaaaacatCgagctgtttgacaagctctc	8	12	1	2	rs560731179		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26669303C>T	ENST00000226225.2	+	6	816	c.549C>T	c.(547-549)atC>atT	p.I183I	TNFAIP1_ENST00000544907.2_Silent_p.I79I|TNFAIP1_ENST00000583213.1_3'UTR	NM_021137.4	NP_066960.1	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1 (endothelial)	183					apoptotic process (GO:0006915)|cell migration (GO:0016477)|DNA replication (GO:0006260)|embryo development (GO:0009790)|immune response (GO:0006955)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleolus (GO:0005730)	GTP-Rho binding (GO:0017049)	p.I183I(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	12	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TGAAAAACATCGAGCTGTTTG	0.542													C|||	1	0.000199681	8e-04	0	5008	,	,		20396	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											101	83	89					17																	26669303		2203	4300	6503	23693430	SO:0001819	synonymous_variant	7126				CCDS11227.1	17q22-q23	2013-01-09			ENSG00000109079	ENSG00000109079		"BTB/POZ domain containing"	11894	protein-coding gene	gene with protein product		191161		EDP1		2406243, 2233719	Standard	NM_021137		Approved	B61, B12, MGC2317, BTBD34	uc002hay.3	Q13829	OTTHUMG00000132501	ENST00000226225.2:c.549C>T	17.37:g.26669303C>T			23693430	B7Z6M4|Q5TZQ1	Silent	SNP	ENST00000226225.2	37	CCDS11227.1																																																																																				0.542	TNFAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255681.2	NM_021137		T	26669303	C	T	26669303	2	4	61	1	0	0	0	0	0	0	0	1	16311	874	31	1		1	TNFAIP1	17	26669303	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219563	26669303	54525907	10130	18115										
POLDIP2	26073	broad.mit.edu	37	chr17	26680800	26680800	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacctccttggagccatggCcagcagggttctctgctcta	10	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26680800C>T	ENST00000540200.1	-	5	355	c.356G>A	c.(355-357)gGc>gAc	p.G119D	POLDIP2_ENST00000003607.4_5'UTR	NM_015584.3	NP_056399.1	Q9Y2S7	PDIP2_HUMAN	polymerase (DNA-directed), delta interacting protein 2	120					mitochondrion morphogenesis (GO:0070584)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)					all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		GGAGCCATGGCCAGCAGGGTT	0.532																																																0			17											184	176	178					17																	26680800		1990	4176	6166	23704927	SO:0001583	missense	26073			AF077203	CCDS74018.1	17q11.2	2008-02-05			ENSG00000004142	ENSG00000004142			23781	protein-coding gene	gene with protein product		611519				12522211	Standard	NM_015584		Approved	PDIP38, DKFZP586F1524	uc002haz.3	Q9Y2S7	OTTHUMG00000132065	ENST00000540200.1:c.356G>A	17.37:g.26680800C>T	ENSP00000475924:p.Gly119Asp		23704927	B2R846|Q96JE4	Missense_Mutation	SNP	ENST00000540200.1	37																																																																																					0.532	POLDIP2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015584		T	26680800	C	T	26680800	3	4	61	1	0	0	0	0	1	0	0	0	12225	739	26	3	779	3	POLDIP2	17	26680800	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11497	26680800	54514410	10131	18116										
VTN	7448	broad.mit.edu	37	chr17	26696573	26696573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgaggtcggtgaaggcgtCgaagggcttcccactgcaca	14	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26696573C>T	ENST00000226218.4	-	3	1102	c.484G>A	c.(484-486)Gac>Aac	p.D162N	TMEM199_ENST00000509083.1_Intron|CTB-96E2.2_ENST00000555059.2_5'Flank|SARM1_ENST00000457710.3_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000438614.1_5'Flank|VTN_ENST00000536498.1_5'UTR|SARM1_ENST00000379061.4_Intron	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	162					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.D162N(1)		kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GTGAAGGCGTCGAAGGGCTTC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											56	55	55					17																	26696573		2203	4300	6503	23720700	SO:0001583	missense	7448			BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"Endogenous ligands"	12724	protein-coding gene	gene with protein product	"serum spreading factor", "somatomedin B", "complement S-protein"	193190	"vitronectin (serum spreading factor, somatomedin B, complement S-protein)"			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.484G>A	17.37:g.26696573C>T	ENSP00000226218:p.Asp162Asn		23720700	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000113	0.93227	.	.	ENSG00000255604	ENST00000226218	T	0.08282	3.11	5.92	5.92	0.95590	Hemopexin/matrixin (2);	0.042797	0.85682	D	0.000000	T	0.25717	0.0626	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	P	0.61874	0.895	T	0.00047	-1.2208	10	0.46703	T	0.11	-33.8933	15.4562	0.75314	0.0:0.9321:0.0:0.0679	.	162	P04004	VTNC_HUMAN	N	162	ENSP00000226218:D162N	ENSP00000226218:D162N	D	-	1	0	AC002094.1	23720700	1.000000	0.71417	0.993000	0.49108	0.736000	0.42039	3.545000	0.53648	2.804000	0.96469	0.655000	0.94253	GAC		0.627	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638		T	26696573	C	T	26696573	3	4	61	1	0	0	0	0	1	0	0	0	17277	884	31	1	976	1	VTN	17	26696573	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15773	26696573	54498637	10132	18117										
SLC13A2	9058	broad.mit.edu	37	chr17	26817510	26817510	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggactccaacctcctgttCttcggggggctgctggtggc	14	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26817510C>A	ENST00000314669.5	+	3	690	c.270C>A	c.(268-270)ttC>ttA	p.F90L	SLC13A2_ENST00000545060.1_Missense_Mutation_p.F47L|SLC13A2_ENST00000537681.1_Missense_Mutation_p.F19L|SLC13A2_ENST00000444914.3_Missense_Mutation_p.F139L	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	90					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.F90L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	ACCTCCTGTTCTTCGGGGGGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	113	117					17																	26817510		2203	4300	6503	23841637	SO:0001583	missense	9058			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.270C>A	17.37:g.26817510C>A	ENSP00000316202:p.Phe90Leu		23841637	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857497	0.32791	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.02737	4.18;4.18;4.18;4.18	5.58	1.03	0.20045	.	0.089365	0.85682	D	0.000000	T	0.10035	0.0246	M	0.77486	2.375	0.52501	D	0.999957	D;P;P;D;P	0.71674	0.964;0.932;0.828;0.998;0.698	P;P;P;D;P	0.67725	0.797;0.777;0.654;0.953;0.777	T	0.03413	-1.1039	10	0.40728	T	0.16	-4.1499	6.1602	0.20360	0.1184:0.5854:0.0:0.2962	.	47;139;46;19;90	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	L	90;139;47;46;19	ENSP00000316202:F90L;ENSP00000392411:F139L;ENSP00000441935:F47L;ENSP00000440802:F19L	ENSP00000316202:F90L	F	+	3	2	SLC13A2	23841637	0.017000	0.18338	0.083000	0.20561	0.056000	0.15407	0.321000	0.19558	-0.013000	0.14199	-1.000000	0.02509	TTC		0.642	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		A	26817510	C	A	26817510	3	1	61	1	0	0	0	0	1	0	0	0	14429	912	32	2	427	2	SLC13A2	17	26817510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120937	26817510	54377700	10133	18118										
SLC13A2	9058	broad.mit.edu	37	chr17	26820598	26820598	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcctgcagcttccggaaGaactttggcattggggaaaa	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26820598G>T	ENST00000314669.5	+	7	1308	c.888G>T	c.(886-888)aaG>aaT	p.K296N	SLC13A2_ENST00000545060.1_Missense_Mutation_p.K253N|SLC13A2_ENST00000537681.1_Missense_Mutation_p.K225N|SLC13A2_ENST00000444914.3_Missense_Mutation_p.K345N	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	296					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.K296N(2)|p.K345N(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	GCTTCCGGAAGAACTTTGGCA	0.617																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	17											37	35	36					17																	26820598		2203	4300	6503	23844725	SO:0001583	missense	9058			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.888G>T	17.37:g.26820598G>T	ENSP00000316202:p.Lys296Asn		23844725	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585584	0.86748	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.03094	4.05;4.05;4.05;4.05	4.7	3.72	0.42706	.	0.138901	0.64402	D	0.000004	T	0.12220	0.0297	L	0.59912	1.85	0.53688	D	0.999976	D;P;D;D;D	0.76494	0.999;0.795;0.98;0.995;0.993	D;P;P;D;P	0.70935	0.971;0.596;0.876;0.92;0.899	T	0.14504	-1.0470	10	0.22109	T	0.4	-6.5767	13.0744	0.59079	0.0789:0.0:0.9211:0.0	.	253;345;252;225;296	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	N	296;345;253;252;225	ENSP00000316202:K296N;ENSP00000392411:K345N;ENSP00000441935:K253N;ENSP00000440802:K225N	ENSP00000316202:K296N	K	+	3	2	SLC13A2	23844725	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	4.180000	0.58296	1.106000	0.41623	0.449000	0.29647	AAG		0.617	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		T	26820598	G	T	26820598	3	4	61	1	0	0	0	0	1	0	0	0	14429	933	33	2	1061	2	SLC13A2	17	26820598	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3088	26820598	54374612	10134	18119										
SLC13A2	9058	broad.mit.edu	37	chr17	26820713	26820713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaaggccatcagcatcCtattcgtcatcctggtgctg	9	12	2	1	rs377179409		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26820713C>A	ENST00000314669.5	+	7	1423	c.1003C>A	c.(1003-1005)Cta>Ata	p.L335I	SLC13A2_ENST00000545060.1_Missense_Mutation_p.L292I|SLC13A2_ENST00000537681.1_Missense_Mutation_p.L264I|SLC13A2_ENST00000444914.3_Missense_Mutation_p.L384I	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	335					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.L335I(2)|p.L384I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CATCAGCATCCTATTCGTCAT	0.572																																																3	Substitution - Missense(3)	breast(2)|large_intestine(1)	17											71	68	69					17																	26820713		2203	4300	6503	23844840	SO:0001583	missense	9058			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1003C>A	17.37:g.26820713C>A	ENSP00000316202:p.Leu335Ile		23844840	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	C	6.296	0.422770	0.11928	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.03553	3.89;3.89;3.89;3.89	4.5	-0.308	0.12773	.	0.360682	0.31847	N	0.006962	T	0.01905	0.0060	N	0.11341	0.13	0.36982	D	0.894324	B;B;B;B;B	0.28233	0.204;0.087;0.005;0.065;0.022	B;B;B;B;B	0.30572	0.084;0.117;0.057;0.05;0.057	T	0.54899	-0.8224	10	0.24483	T	0.36	-0.9846	5.8809	0.18854	0.1328:0.64:0.0:0.2272	.	292;384;291;264;335	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	I	335;384;292;291;264	ENSP00000316202:L335I;ENSP00000392411:L384I;ENSP00000441935:L292I;ENSP00000440802:L264I	ENSP00000316202:L335I	L	+	1	2	SLC13A2	23844840	0.020000	0.18652	0.030000	0.17652	0.001000	0.01503	0.288000	0.18939	0.103000	0.17682	-0.391000	0.06502	CTA		0.572	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		A	26820713	C	A	26820713	3	1	61	1	0	0	0	0	1	0	0	0	14429	680	24	2	1176	2	SLC13A2	17	26820713	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115	26820713	54374497	10135	18120										
ALDOC	230	broad.mit.edu	37	chr17	26901108	26901108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagctgggggcacagtgCgacgcagggcagtgacagtt	18	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26901108C>T	ENST00000226253.4	-	7	1251	c.776G>A	c.(775-777)cGc>cAc	p.R259H	ALDOC_ENST00000395319.3_Missense_Mutation_p.R231H|ALDOC_ENST00000395321.2_Missense_Mutation_p.R259H|PIGS_ENST00000543734.1_5'Flank|PIGS_ENST00000395346.2_5'Flank|RP11-192H23.5_ENST00000585189.1_RNA|PIGS_ENST00000308360.7_5'Flank	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	259					aging (GO:0007568)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|organ regeneration (GO:0031100)|protein heterotetramerization (GO:0051290)|protein homotetramerization (GO:0051289)|response to hypoxia (GO:0001666)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	cytoskeletal protein binding (GO:0008092)|fructose-bisphosphate aldolase activity (GO:0004332)	p.R259H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Lung NSC(42;0.00431)					GGGCACAGTGCGACGCAGGGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											127	128	128					17																	26901108		2203	4300	6503	23925235	SO:0001583	missense	230			AF054987	CCDS11236.1	17q11.2	2013-09-20			ENSG00000109107	ENSG00000109107	4.1.2.13		418	protein-coding gene	gene with protein product		103870					Standard	XM_005257947		Approved		uc002hbp.3	P09972	OTTHUMG00000132605	ENST00000226253.4:c.776G>A	17.37:g.26901108C>T	ENSP00000226253:p.Arg259His		23925235	B2R5R3|Q3SYL3|Q6FH94|Q6P0L5	Missense_Mutation	SNP	ENST00000226253.4	37	CCDS11236.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.707263	0.68615	.	.	ENSG00000109107	ENST00000395319;ENST00000226253;ENST00000395321	D;D;D	0.89681	-2.55;-2.55;-2.55	5.28	5.28	0.74379	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.89458	0.6721	M	0.65320	2	0.80722	D	1	B;D	0.54964	0.208;0.969	B;P	0.45428	0.11;0.48	D	0.91018	0.4855	10	0.87932	D	0	-8.4487	18.0486	0.89341	0.0:1.0:0.0:0.0	.	231;259	A8MVZ9;P09972	.;ALDOC_HUMAN	H	231;259;259	ENSP00000378729:R231H;ENSP00000226253:R259H;ENSP00000378731:R259H	ENSP00000226253:R259H	R	-	2	0	ALDOC	23925235	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.810000	0.86072	2.637000	0.89404	0.555000	0.69702	CGC		0.607	ALDOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255839.4			T	26901108	C	T	26901108	3	4	61	1	0	0	0	0	1	0	0	0	509	768	27	1	330	1	ALDOC	17	26901108	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80395	26901108	54294102	10136	18121										
SPAG5	10615	broad.mit.edu	37	chr17	26912340	26912340	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtcccaaatactcacatcCagttgcatggacctccagtc	7	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26912340C>A	ENST00000321765.5	-	9	2282	c.1950G>T	c.(1948-1950)ctG>ctT	p.L650L		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	650	Gln-rich.|Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)		p.L650L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TACTCACATCCAGTTGCATGG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	17											120	106	111					17																	26912340		2203	4300	6503	23936467	SO:0001819	synonymous_variant	10615			AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.1950G>T	17.37:g.26912340C>A			23936467	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																				0.468	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		A	26912340	C	A	26912340	2	1	61	1	0	0	0	0	0	0	0	1	15020	581	21	2		2	SPAG5	17	26912340	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11232	26912340	54282870	10137	18122										
KIAA0100	9703	broad.mit.edu	37	chr17	26947571	26947571	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcaggttgttgacaatgtCcaggatcatggcatactgag	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26947571C>A	ENST00000528896.2	-	29	5394	c.5320G>T	c.(5320-5322)Gac>Tac	p.D1774Y	KIAA0100_ENST00000389003.3_Missense_Mutation_p.D1631Y|KIAA0100_ENST00000544884.1_Missense_Mutation_p.D1631Y|KIAA0100_ENST00000579924.2_5'Flank	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1774						extracellular region (GO:0005576)		p.D1774Y(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TTGACAATGTCCAGGATCATG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	17											161	134	143					17																	26947571		2203	4300	6503	23971698	SO:0001583	missense	9703			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5320G>T	17.37:g.26947571C>A	ENSP00000436773:p.Asp1774Tyr		23971698	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078774	0.76528	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.48522	0.81;0.81	5.53	5.53	0.82687	FMP27,  C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67239	0.2872	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61739	-0.7001	10	0.09843	T	0.71	.	19.0648	0.93106	0.0:1.0:0.0:0.0	.	1774	Q14667	K0100_HUMAN	Y	1774;1744;1774;1631	ENSP00000436773:D1774Y;ENSP00000446443:D1631Y	ENSP00000005905:D1774Y	D	-	1	0	KIAA0100	23971698	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.374000	0.79633	2.611000	0.88343	0.462000	0.41574	GAC		0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26947571	C	A	26947571	3	1	61	1	0	0	0	0	1	0	0	0	8175	855	30	2	1431	2	KIAA0100	17	26947571	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35231	26947571	54247639	10138	18123										
KIAA0100	9703	broad.mit.edu	37	chr17	26958596	26958596	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagacagtgatcagcattCtcttcagtgggtgaggccat	11	9	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26958596C>A	ENST00000528896.2	-	23	4274	c.4200G>T	c.(4198-4200)gaG>gaT	p.E1400D	RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.E1257D|KIAA0100_ENST00000544884.1_Missense_Mutation_p.E1257D|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1400						extracellular region (GO:0005576)		p.E1400D(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GATCAGCATTCTCTTCAGTGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											112	77	89					17																	26958596		2203	4300	6503	23982723	SO:0001583	missense	9703			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.4200G>T	17.37:g.26958596C>A	ENSP00000436773:p.Glu1400Asp		23982723	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.302425	0.60195	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24538	1.86;1.85	5.81	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.42449	0.1203	L	0.57536	1.79	0.58432	D	0.999999	D	0.63880	0.993	D	0.70016	0.967	T	0.18903	-1.0322	10	0.23891	T	0.37	.	11.1395	0.48394	0.0:0.8589:0.0:0.1411	.	1400	Q14667	K0100_HUMAN	D	1400;1370;1400;1257	ENSP00000436773:E1400D;ENSP00000446443:E1257D	ENSP00000005905:E1400D	E	-	3	2	KIAA0100	23982723	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.973000	0.40550	1.449000	0.47699	0.650000	0.86243	GAG		0.537	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26958596	C	A	26958596	3	1	61	1	0	0	0	0	1	0	0	0	8175	912	32	2	2575	2	KIAA0100	17	26958596	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11025	26958596	54236614	10139	18124										
KIAA0100	9703	broad.mit.edu	37	chr17	26961566	26961566	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacattgcacttgagcatTcgacaccactgaatgacaag	8	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:26961566T>C	ENST00000528896.2	-	16	3113	c.3039A>G	c.(3037-3039)cgA>cgG	p.R1013R	RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Silent_p.R870R|KIAA0100_ENST00000544884.1_Silent_p.R870R|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1013						extracellular region (GO:0005576)		p.R1013R(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					ACTTGAGCATTCGACACCACT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	17											89	84	86					17																	26961566		2203	4300	6503	23985693	SO:0001819	synonymous_variant	9703			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.3039A>G	17.37:g.26961566T>C			23985693	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Silent	SNP	ENST00000528896.2	37	CCDS32595.1																																																																																				0.502	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26961566	T	C	26961566	2	2	61	1	0	0	0	0	0	0	0	1	8175	1770	62	4		4	KIAA0100	17	26961566	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2970	26961566	54233644	10140	18125										
SUPT6H	6830	broad.mit.edu	37	chr17	27002084	27002084	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagaagctattgcggaaGaaatcttccaggatggggaa	12	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27002084G>T	ENST00000314616.6	+	5	725	c.442G>T	c.(442-444)Gaa>Taa	p.E148*	AC010761.13_ENST00000578819.1_RNA|SUPT6H_ENST00000347486.4_Nonsense_Mutation_p.E148*	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	148	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E148*(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TATTGCGGAAGAAATCTTCCA	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											81	76	78					17																	27002084		2203	4300	6503	24026211	SO:0001587	stop_gained	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.442G>T	17.37:g.27002084G>T	ENSP00000319104:p.Glu148*		24026211	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Nonsense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	37	6.171950	0.97348	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-19.3607	15.69	0.77442	0.0:0.0:0.8619:0.138	.	.	.	.	X	148	.	ENSP00000319104:E148X	E	+	1	0	SUPT6H	24026211	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.010000	0.93611	1.345000	0.45676	0.655000	0.94253	GAA		0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27002084	G	T	27002084	4	4	61	1	0	0	0	0	0	1	0	0	15439	943	33	2	456	2	SUPT6H	17	27002084	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40518	27002084	54193126	10141	18126										
NEK8	284086	broad.mit.edu	37	chr17	27061086	27061086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagatgaccaaggaagagCggcaggcagcccagaatgag	14	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27061086C>T	ENST00000268766.6	+	2	167	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W	AC010761.6_ENST00000584779.1_RNA|NEK8_ENST00000593261.1_3'UTR	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	45	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R45W(1)		breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					CAAGGAAGAGCGGCAGGCAGC	0.527																																					NSCLC(6;19 293 14866 25253 49845)											1	Substitution - Missense(1)	large_intestine(1)	17											108	96	100					17																	27061086		2203	4300	6503	24085213	SO:0001583	missense	284086			AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.133C>T	17.37:g.27061086C>T	ENSP00000268766:p.Arg45Trp		24085213	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	37	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236905	0.79800	.	.	ENSG00000160602	ENST00000543014;ENST00000268766	T;T	0.67171	-0.25;-0.25	4.92	-0.0942	0.13646	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81721	0.4882	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83942	0.0312	10	0.87932	D	0	.	13.7296	0.62779	0.5733:0.4267:0.0:0.0	.	45	Q86SG6	NEK8_HUMAN	W	45	ENSP00000465859:R45W;ENSP00000268766:R45W	ENSP00000268766:R45W	R	+	1	2	NEK8	24085213	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	1.511000	0.35801	0.050000	0.15949	0.313000	0.20887	CGG		0.527	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			T	27061086	C	T	27061086	3	4	61	1	0	0	0	0	1	0	0	0	10361	759	27	1	139	1	NEK8	17	27061086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59002	27061086	54134124	10142	18127										
SEZ6	124925	broad.mit.edu	37	chr17	27284490	27284490	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattgcacggtggcccccacGggaaacttggggctggatat	14	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27284490G>A	ENST00000317338.12	-	12	2798	c.2370C>T	c.(2368-2370)ccC>ccT	p.P790P	SEZ6_ENST00000335960.6_Intron|SEZ6_ENST00000360295.9_Silent_p.P790P|SEZ6_ENST00000442608.3_Silent_p.P790P|PIPOX_ENST00000583215.1_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	790	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.P790P(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TGGCCCCCACGGGAAACTTGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	17											52	60	58					17																	27284490		1950	4135	6085	24308616	SO:0001819	synonymous_variant	124925			AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"seizure related gene 6 (mouse) homolog"			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.2370C>T	17.37:g.27284490G>A			24308616	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Silent	SNP	ENST00000317338.12	37	CCDS45639.1																																																																																				0.597	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3			A	27284490	G	A	27284490	2	1	61	1	0	0	0	0	0	0	0	1	14179	1103	39	1		1	SEZ6	17	27284490	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223404	27284490	53910720	10143	18128										
SEZ6	124925	broad.mit.edu	37	chr17	27287584	27287584	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtactgagctcaacaaaGaagtgtttgccagagctgag	11	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27287584G>T	ENST00000317338.12	-	7	1943	c.1515C>A	c.(1513-1515)ttC>ttA	p.F505L	SEZ6_ENST00000335960.6_Intron|SEZ6_ENST00000360295.9_Missense_Mutation_p.F505L|SEZ6_ENST00000442608.3_Missense_Mutation_p.F505L|PIPOX_ENST00000583215.1_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	505	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.F505L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			GCTCAACAAAGAAGTGTTTGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											36	39	38					17																	27287584		2007	4144	6151	24311710	SO:0001583	missense	124925			AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"seizure related gene 6 (mouse) homolog"			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.1515C>A	17.37:g.27287584G>T	ENSP00000312942:p.Phe505Leu		24311710	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.155|6.155	0.396725|0.396725	0.11638|0.11638	.|.	.|.	ENSG00000063015|ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381|ENST00000539265	T;T|.	0.13196|.	2.61;2.61|.	4.15|4.15	4.15|4.15	0.48705|0.48705	CUB (5);|.	0.072277|.	0.64402|.	D|.	0.000019|.	T|T	0.07999|0.07999	0.0200|0.0200	N|N	0.00030|0.00030	-2.61|-2.61	0.80722|0.80722	D|D	1|1	B;B|.	0.27625|.	0.183;0.029|.	B;B|.	0.26416|.	0.069;0.037|.	T|T	0.36939|0.36939	-0.9727|-0.9727	10|5	0.02654|.	T|.	1|.	.|.	14.3201|14.3201	0.66479|0.66479	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	505;505|.	Q53EL9-3;Q53EL9|.	.;SEZ6_HUMAN|.	L|Y	505;505;380;505|92	ENSP00000403784:F505L;ENSP00000353440:F505L|.	ENSP00000312942:F380L|.	F|S	-|-	3|2	2|0	SEZ6|SEZ6	24311710|24311710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	3.498000|3.498000	0.53302|0.53302	2.331000|2.331000	0.79229|0.79229	0.305000|0.305000	0.20034|0.20034	TTC|TCT		0.602	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3			T	27287584	G	T	27287584	3	4	61	1	0	0	0	0	1	0	0	0	14179	933	33	2	1526	2	SEZ6	17	27287584	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3094	27287584	53907626	10144	18129										
MYO18A	399687	broad.mit.edu	37	chr17	27422017	27422017	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttctcccgctgcagcttCtcccgctgcagcttctcccg	7	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27422017C>A	ENST00000527372.1	-	29	4626	c.4446G>T	c.(4444-4446)gaG>gaT	p.E1482D	MYO18A_ENST00000354329.4_Missense_Mutation_p.E1482D|MYO18A_ENST00000533112.1_Missense_Mutation_p.E1482D|MYO18A_ENST00000531253.1_Missense_Mutation_p.E1482D	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1482					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)	p.E1482D(1)		NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GCTGCAGCTTCTCCCGCTGCA	0.637																																					Esophageal Squamous(182;472 2015 7001 15270 22562)											1	Substitution - Missense(1)	large_intestine(1)	17											20	23	22					17																	27422017		2086	4221	6307	24446143	SO:0001583	missense	399687			D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4446G>T	17.37:g.27422017C>A	ENSP00000437073:p.Glu1482Asp		24446143	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.074318	0.76415	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	T;T;T;T	0.77229	-1.08;1.21;-1.08;-1.08	5.8	5.8	0.92144	Myosin tail (1);	0.000000	0.85682	D	0.000000	T	0.79805	0.4509	L	0.56199	1.76	0.47905	D	0.999546	B;B;B;B;B	0.26258	0.145;0.037;0.096;0.096;0.145	B;B;B;B;B	0.35550	0.205;0.024;0.038;0.038;0.086	T	0.76924	-0.2779	10	0.72032	D	0.01	.	20.0609	0.97674	0.0:1.0:0.0:0.0	.	1151;1094;1482;1482;1482	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	D	1482;1482;1482;1482;1482;378;378;1094	ENSP00000346291:E1482D;ENSP00000435932:E1482D;ENSP00000434228:E1482D;ENSP00000437073:E1482D	ENSP00000346291:E1482D	E	-	3	2	MYO18A	24446143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.393000	0.52544	2.755000	0.94549	0.655000	0.94253	GAG		0.637	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		A	27422017	C	A	27422017	3	1	61	1	0	0	0	0	1	0	0	0	10095	912	32	2	1774	2	MYO18A	17	27422017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	134433	27422017	53773193	10145	18130										
CRYBA1	1411	broad.mit.edu	37	chr17	27579133	27579133	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcaacagtttatcctggaGagaggagaataccctcgctg	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27579133G>A	ENST00000225387.3	+	4	268	c.267G>A	c.(265-267)gaG>gaA	p.E89E		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	89	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)	p.E89E(1)		breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			TTATCCTGGAGAGAGGAGAAT	0.502											OREG0024293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	17											166	144	152					17																	27579133		2203	4300	6503	24603259	SO:0001819	synonymous_variant	1411				CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"eye lens structural protein"	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.267G>A	17.37:g.27579133G>A		795	24603259	Q13633|Q14CM9	Silent	SNP	ENST00000225387.3	37	CCDS11249.1																																																																																				0.502	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208		A	27579133	G	A	27579133	2	1	61	1	0	0	0	0	0	0	0	1	3913	933	33	3		3	CRYBA1	17	27579133	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	157116	27579133	53616077	10146	18131										
NUFIP2	57532	broad.mit.edu	37	chr17	27613024	27613024	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttacctttagtgtgatatAcaatagcagccctcaggtca	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27613024A>G	ENST00000225388.4	-	2	2046	c.1988T>C	c.(1987-1989)gTa>gCa	p.V663A	NUFIP2_ENST00000579665.1_Intron	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	663						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.V663A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			AGTGTGATATACAATAGCAGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	17											66	66	66					17																	27613024		2203	4300	6503	24637150	SO:0001583	missense	57532			AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.1988T>C	17.37:g.27613024A>G	ENSP00000225388:p.Val663Ala		24637150	A1L3A6|Q9P2M5	Missense_Mutation	SNP	ENST00000225388.4	37	CCDS32600.1	.	.	.	.	.	.	.	.	.	.	A	6.935	0.542302	0.13250	.	.	ENSG00000108256	ENST00000225388	.	.	.	5.93	5.93	0.95920	.	0.169377	0.40640	N	0.001056	T	0.37571	0.1008	N	0.11560	0.145	0.80722	D	1	B	0.17268	0.021	B	0.15484	0.013	T	0.25152	-1.0140	9	0.23891	T	0.37	-5.6967	12.5988	0.56485	0.876:0.0:0.0:0.124	.	663	Q7Z417	NUFP2_HUMAN	A	663	.	ENSP00000225388:V663A	V	-	2	0	NUFIP2	24637150	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.737000	0.62066	2.273000	0.75805	0.482000	0.46254	GTA		0.358	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		G	27613024	A	G	27613024	3	3	61	1	0	0	0	0	1	0	0	0	10780	391	14	4	111	4	NUFIP2	17	27613024	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33891	27613024	53582186	10147	18132										
NUFIP2	57532	broad.mit.edu	37	chr17	27614111	27614111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttactatctgagcttttccGaagcatatcacccacagcag	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27614111G>A	ENST00000225388.4	-	2	959	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	NUFIP2_ENST00000579665.1_Intron	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	301						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R301W(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			GAGCTTTTCCGAAGCATATCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	17											100	105	103					17																	27614111		2203	4300	6503	24638237	SO:0001583	missense	57532			AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.901C>T	17.37:g.27614111G>A	ENSP00000225388:p.Arg301Trp		24638237	A1L3A6|Q9P2M5	Missense_Mutation	SNP	ENST00000225388.4	37	CCDS32600.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529011	0.44969	.	.	ENSG00000108256	ENST00000225388	.	.	.	6.17	3.11	0.35812	.	0.000000	0.64402	D	0.000001	T	0.45617	0.1351	L	0.36672	1.1	0.80722	D	1	B	0.27910	0.193	B	0.23574	0.047	T	0.41016	-0.9532	9	0.87932	D	0	0.1132	10.7938	0.46449	0.0622:0.0:0.5181:0.4197	.	301	Q7Z417	NUFP2_HUMAN	W	301	.	ENSP00000225388:R301W	R	-	1	2	NUFIP2	24638237	0.569000	0.26643	0.993000	0.49108	0.843000	0.47879	0.456000	0.21859	0.473000	0.27368	0.655000	0.94253	CGG		0.478	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		A	27614111	G	A	27614111	3	1	61	1	0	0	0	0	1	0	0	0	10780	1057	37	1	1198	1	NUFIP2	17	27614111	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1087	27614111	53581099	10148	18133										
GIT1	28964	broad.mit.edu	37	chr17	27906004	27906004	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacatgcacttttgccgaGatctaagtccagaggaaggc	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:27906004G>T	ENST00000225394.3	-	8	1010				GIT1_ENST00000394869.3_Missense_Mutation_p.S255Y|GIT1_ENST00000579937.1_Intron|RP11-68I3.2_ENST00000581474.1_RNA|GIT1_ENST00000581348.1_Missense_Mutation_p.S255Y	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1						regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.S255Y(1)		large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		CTTTTGCCGAGATCTAAGTCC	0.607																																					Colon(81;41 1719 20078 35068)											1	Substitution - Missense(1)	large_intestine(1)	17											93	106	102					17																	27906004		2185	4281	6466	24930130	SO:0001627	intron_variant	28964			AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4272	protein-coding gene	gene with protein product		608434	"G protein-coupled receptor kinase interactor 1"			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.762-207C>A	17.37:g.27906004G>T			24930130	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Missense_Mutation	SNP	ENST00000225394.3	37	CCDS11250.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.937425	0.52972	.	.	ENSG00000108262	ENST00000394869	T	0.70749	-0.51	5.36	5.36	0.76844	.	0.643282	0.12950	U	0.425846	T	0.53077	0.1774	N	0.08118	0	0.80722	D	1	B;B	0.20887	0.007;0.049	B;B	0.19946	0.001;0.027	T	0.51172	-0.8739	10	0.56958	D	0.05	.	12.4609	0.55731	0.082:0.0:0.918:0.0	.	259;255	Q59FC3;B4DGU9	.;.	Y	255	ENSP00000378338:S255Y	ENSP00000378338:S255Y	S	-	2	0	GIT1	24930130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.716000	0.61916	2.692000	0.91855	0.561000	0.74099	TCT		0.607	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030		T	27906004	G	T	27906004	1	4	61	0	1	0	0	0	0	0	0	0	6416	942	33	2		2	GIT1	17	27906004	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	291893	27906004	53289206	10149	18134										
EFCAB5	374786	broad.mit.edu	37	chr17	28361332	28361332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccactctgcagatgaatttCgggaggtcataaaagctgac	11	9	2	3	rs370396201		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28361332C>T	ENST00000394835.3	+	8	1321	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	EFCAB5_ENST00000536908.2_Missense_Mutation_p.R321W|EFCAB5_ENST00000541045.1_Missense_Mutation_p.R34W|EFCAB5_ENST00000394832.2_Missense_Mutation_p.R377W|EFCAB5_ENST00000378738.3_Missense_Mutation_p.R377W|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R377W	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	377							calcium ion binding (GO:0005509)	p.R377W(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						AGATGAATTTCGGGAGGTCAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	TRP/ARG,TRP/ARG	1,3863		0,1,1931	71	70	70		961,1129	-1.5	0.9	17		70	0,8260		0,0,4130	no	missense,missense	EFCAB5	NM_001145053.1,NM_198529.3	101,101	0,1,6061	TT,TC,CC		0.0,0.0259,0.0082	probably-damaging,probably-damaging	321/857,377/1504	28361332	1,12123	1932	4130	6062	25385458	SO:0001583	missense	374786			AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.1129C>T	17.37:g.28361332C>T	ENSP00000378312:p.Arg377Trp		25385458	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621440	0.66787	2.59E-4	0.0	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66;0.66	5.2	-1.5	0.08691	.	0.444772	0.18541	N	0.138181	T	0.57975	0.2090	M	0.70275	2.135	0.24481	N	0.99435	D;D;D;D;P;D	0.89917	1.0;1.0;1.0;1.0;0.917;1.0	D;D;D;D;B;D	0.91635	0.999;0.999;0.966;0.966;0.291;0.966	T	0.48007	-0.9072	10	0.66056	D	0.02	-5.7019	4.2597	0.10735	0.3953:0.4101:0.1084:0.0862	.	321;321;377;377;377;377	B4DS75;F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;.;EFCB5_HUMAN	W	321;120;34;377;377;377;377;321;183	ENSP00000440619:R321W;ENSP00000445575:R34W;ENSP00000378312:R377W;ENSP00000322003:R377W;ENSP00000378309:R377W;ENSP00000368012:R377W;ENSP00000417009:R183W	ENSP00000322003:R377W	R	+	1	2	EFCAB5	25385458	1.000000	0.71417	0.878000	0.34440	0.881000	0.50899	0.779000	0.26746	-0.110000	0.12022	0.561000	0.74099	CGG		0.413	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		T	28361332	C	T	28361332	3	4	61	1	0	0	0	0	1	0	0	0	4949	875	31	1	1159	1	EFCAB5	17	28361332	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	455328	28361332	52833878	10150	18135										
EFCAB5	374786	broad.mit.edu	37	chr17	28378183	28378183	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggccctgctggaattgttCtatgaccatagttcacaaat	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28378183C>A	ENST00000394835.3	+	9	1440	c.1248C>A	c.(1246-1248)ttC>ttA	p.F416L	EFCAB5_ENST00000536908.2_Missense_Mutation_p.F360L|EFCAB5_ENST00000541045.1_Missense_Mutation_p.F73L|EFCAB5_ENST00000394832.2_Missense_Mutation_p.F416L|EFCAB5_ENST00000378738.3_Missense_Mutation_p.F416L|EFCAB5_ENST00000320856.5_Missense_Mutation_p.F416L	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	416							calcium ion binding (GO:0005509)	p.F416L(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TGGAATTGTTCTATGACCATA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	17											118	105	109					17																	28378183		1912	4123	6035	25402309	SO:0001583	missense	374786			AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.1248C>A	17.37:g.28378183C>A	ENSP00000378312:p.Phe416Leu		25402309	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883060	0.72410	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.48	3.5	0.40072	.	0.113538	0.39083	N	0.001465	T	0.65312	0.2679	M	0.75264	2.295	0.37476	D	0.915817	D;D;D;D;D;D	0.89917	0.997;0.998;1.0;0.998;0.997;0.998	D;D;D;D;D;D	0.85130	0.985;0.994;0.997;0.994;0.957;0.994	T	0.69577	-0.5108	10	0.59425	D	0.04	-16.0395	10.2458	0.43341	0.0:0.8496:0.0:0.1504	.	360;360;416;416;416;416	B4DS75;F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;.;EFCB5_HUMAN	L	360;159;73;416;416;416;416;360;222	ENSP00000440619:F360L;ENSP00000445575:F73L;ENSP00000378312:F416L;ENSP00000322003:F416L;ENSP00000378309:F416L;ENSP00000368012:F416L;ENSP00000417009:F222L	ENSP00000322003:F416L	F	+	3	2	EFCAB5	25402309	1.000000	0.71417	0.985000	0.45067	0.697000	0.40408	1.233000	0.32648	0.677000	0.31305	0.655000	0.94253	TTC		0.433	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28378183	C	A	28378183	3	1	61	1	0	0	0	0	1	0	0	0	4949	912	32	2	1282	2	EFCAB5	17	28378183	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16851	28378183	52817027	10151	18136										
CCDC55	84081	broad.mit.edu	37	chr17	28511765	28511765	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagatgcagacagtgacttCgatgctaagagcagtgcgga	13	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28511765C>T	ENST00000247026.5	+	7	813	c.750C>T	c.(748-750)ttC>ttT	p.F250F	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	250					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.F250F(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						ACAGTGACTTCGATGCTAAGA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	17											75	70	72					17																	28511765		2203	4300	6503	25535891	SO:0001819	synonymous_variant	84081			AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.750C>T	17.37:g.28511765C>T			25535891	Q6FI71	Silent	SNP	ENST00000247026.5	37	CCDS11255.1																																																																																				0.413	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		T	28511765	C	T	28511765	2	4	61	1	0	0	0	0	0	0	0	1	2831	883	31	1		1	CCDC55	17	28511765	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133582	28511765	52683445	10152	18137										
BLMH	642	broad.mit.edu	37	chr17	28599588	28599588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcactcacagattcatgTcactgaggcccagcttgcta	8	14	3	2	rs184963100		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28599588T>C	ENST00000261714.6	-	9	1193	c.1019A>G	c.(1018-1020)gAc>gGc	p.D340G	BLMH_ENST00000582669.1_5'Flank|BLMH_ENST00000394819.3_Missense_Mutation_p.D253G	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	340					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)	p.D340G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	CAGATTCATGTCACTGAGGCC	0.433													T|||	1	0.000199681	0	0	5008	,	,		19503	0.001		0	False		,,,				2504	0				Pancreas(127;628 1772 12912 33293 36203)											1	Substitution - Missense(1)	large_intestine(1)	17											227	227	227					17																	28599588		2203	4300	6503	25623714	SO:0001583	missense	642			X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.1019A>G	17.37:g.28599588T>C	ENSP00000261714:p.Asp340Gly		25623714	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	24.9	4.581462	0.86748	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.54279	0.58;0.58	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.79137	0.4395	M	0.92555	3.32	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.993;0.996	D	0.83966	0.0324	10	0.62326	D	0.03	-23.1189	15.5295	0.75942	0.0:0.0:0.0:1.0	.	253;340	E7EMN3;Q13867	.;BLMH_HUMAN	G	340;253	ENSP00000261714:D340G;ENSP00000378296:D253G	ENSP00000261714:D340G	D	-	2	0	BLMH	25623714	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.254000	0.74563	0.533000	0.62120	GAC		0.433	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		C	28599588	T	C	28599588	3	2	61	1	0	0	0	0	1	0	0	0	1447	1667	58	4	364	4	BLMH	17	28599588	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	87823	28599588	52595622	10153	18138										
TMIGD1	388364	broad.mit.edu	37	chr17	28652112	28652112	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccacttaggagaggaggaActgcaagactcaagcattta	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28652112A>G	ENST00000328886.4	-	4	434	c.362T>C	c.(361-363)tTt>tCt	p.F121S	TMIGD1_ENST00000538566.2_Splice_Site_p.F121S	NM_206832.1	NP_996663.1	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain containing 1	121						integral component of membrane (GO:0016021)		p.F121S(1)		breast(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	12						GAGAGGAGGAACTGCAAGACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											90	84	86					17																	28652112		2203	4300	6503	25676238	SO:0001630	splice_region_variant	388364			AY358153	CCDS32605.1	17q11.2	2013-01-29	2006-07-05	2006-07-05		ENSG00000182271		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32431	protein-coding gene	gene with protein product				TMIGD		12975309	Standard	NM_206832		Approved	UNQ9372	uc002hfa.1	Q6UXZ0		ENST00000328886.4:c.362-1T>C	17.37:g.28652112A>G			25676238	A8K2K1|Q6ZMC6	Missense_Mutation	SNP	ENST00000328886.4	37	CCDS32605.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.589407	0.66105	.	.	ENSG00000182271	ENST00000328886;ENST00000538566	T;T	0.13657	2.57;2.57	5.79	1.85	0.25348	Immunoglobulin-like fold (1);	0.290241	0.39985	N	0.001208	T	0.32255	0.0823	M	0.69823	2.125	0.44042	D	0.996773	D;D	0.76494	0.996;0.999	P;D	0.69824	0.885;0.966	T	0.05131	-1.0904	10	0.87932	D	0	.	11.4223	0.49989	0.6454:0.0:0.0:0.3546	.	121;121	Q6UXZ0-2;Q6UXZ0	.;TMIG1_HUMAN	S	121	ENSP00000332404:F121S;ENSP00000446118:F121S	ENSP00000332404:F121S	F	-	2	0	TMIGD1	25676238	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.258000	0.51507	0.421000	0.25980	0.533000	0.62120	TTT		0.408	TMIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447955.1	NM_206832	Missense_Mutation	G	28652112	A	G	28652112	5	3	61	1	0	0	0	0	0	0	1	0	16269	57	2	4	442	4	TMIGD1	17	28652112	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	52524	28652112	52543098	10154	18139										
CPD	1362	broad.mit.edu	37	chr17	28750684	28750684	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaccttatgccatccatGaatcctgatgggtatgaaaa	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28750684G>T	ENST00000225719.4	+	6	1894	c.1818G>T	c.(1816-1818)atG>atT	p.M606I	CPD_ENST00000543464.2_Missense_Mutation_p.M359I	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	606	Carboxypeptidase-like 2.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)	p.M606I(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						TGCCATCCATGAATCCTGATG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	17											108	103	105					17																	28750684		2203	4300	6503	25774810	SO:0001583	missense	1362			U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.1818G>T	17.37:g.28750684G>T	ENSP00000225719:p.Met606Ile		25774810	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Missense_Mutation	SNP	ENST00000225719.4	37	CCDS11257.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031687	0.93575	.	.	ENSG00000108582	ENST00000225719;ENST00000543464	T;T	0.10763	2.84;2.84	5.75	5.75	0.90469	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.31918	0.0812	L	0.58810	1.83	0.80722	D	1	D;D	0.64830	0.994;0.993	D;D	0.72338	0.961;0.977	T	0.00366	-1.1786	10	0.66056	D	0.02	.	18.948	0.92628	0.0:0.0:1.0:0.0	.	359;606	F5GZH6;O75976	.;CBPD_HUMAN	I	606;359	ENSP00000225719:M606I;ENSP00000444443:M359I	ENSP00000225719:M606I	M	+	3	0	CPD	25774810	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.555000	0.82223	2.716000	0.92895	0.655000	0.94253	ATG		0.353	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		T	28750684	G	T	28750684	3	4	61	1	0	0	0	0	1	0	0	0	3804	1290	45	2	1840	2	CPD	17	28750684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	98572	28750684	52444526	10155	18140										
GOSR1	9527	broad.mit.edu	37	chr17	28817228	28817228	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgggatcagtacgaaaaGatattgagtaagttactttt	9	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:28817228G>T	ENST00000225724.5	+	5	505	c.433G>T	c.(433-435)Gat>Tat	p.D145Y	GOSR1_ENST00000451249.2_Missense_Mutation_p.D143Y|GOSR1_ENST00000467337.2_Missense_Mutation_p.D80Y|GOSR1_ENST00000581721.1_Missense_Mutation_p.D145Y	NM_001007024.1|NM_001007025.1|NM_004871.2	NP_001007025.1|NP_001007026.1|NP_004862.1	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1	145					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.D145Y(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	12						AGTACGAAAAGATATTGAGTA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	17											70	66	67					17																	28817228		2203	4299	6502	25841354	SO:0001583	missense	9527			AF047438	CCDS11258.1, CCDS45643.1, CCDS45644.1	17q11	2011-04-15			ENSG00000108587	ENSG00000108587			4430	protein-coding gene	gene with protein product	"golgi integral membrane protein 2"	604026				8638159, 9653160, 15004235	Standard	XM_005258072		Approved	GOS28, P28, GS28, GOS-28, GOLIM2	uc002hfe.3	O95249	OTTHUMG00000132796	ENST00000225724.5:c.433G>T	17.37:g.28817228G>T	ENSP00000225724:p.Asp145Tyr		25841354	J3KST5|O75392	Missense_Mutation	SNP	ENST00000225724.5	37	CCDS11258.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737246	0.89482	.	.	ENSG00000108587	ENST00000225724;ENST00000451249;ENST00000414833;ENST00000427274	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.83917	0.5358	M	0.88979	2.995	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.63033	0.91;0.91	D	0.86771	0.1973	9	0.87932	D	0	-17.4657	18.2606	0.90034	0.0:0.0:1.0:0.0	.	145;143	O95249;E9PCW1	GOSR1_HUMAN;.	Y	145;143;80;143	.	ENSP00000225724:D145Y	D	+	1	0	GOSR1	25841354	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.247000	0.95444	2.658000	0.90341	0.563000	0.77884	GAT		0.318	GOSR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256208.2			T	28817228	G	T	28817228	3	4	61	1	0	0	0	0	1	0	0	0	6597	942	33	2	451	2	GOSR1	17	28817228	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66544	28817228	52377982	10156	18141										
CRLF3	51379	broad.mit.edu	37	chr17	29111438	29111438	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtaactgatttgtcatttCttttccattgacaaaaactg	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29111438C>A	ENST00000324238.6	-	8	1220	c.1096G>T	c.(1096-1098)Gaa>Taa	p.E366*	CRLF3_ENST00000544695.1_Nonsense_Mutation_p.E250*|CTD-2349P21.10_ENST00000585212.1_RNA|CRLF3_ENST00000577725.1_5'Flank	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	366					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)		p.E366*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				TTTGTCATTTCTTTTCCATTG	0.383																																					Pancreas(30;346 881 29244 33464 41299)											1	Substitution - Nonsense(1)	large_intestine(1)	17											71	70	70					17																	29111438		2203	4300	6503	26135564	SO:0001587	stop_gained	51379			AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.1096G>T	17.37:g.29111438C>A	ENSP00000318804:p.Glu366*		26135564	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Nonsense_Mutation	SNP	ENST00000324238.6	37	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	C	38	6.750499	0.97809	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-27.6146	18.7014	0.91621	0.0:1.0:0.0:0.0	.	.	.	.	X	366;250	.	ENSP00000318804:E366X	E	-	1	0	CRLF3	26135564	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.393000	0.79851	2.492000	0.84095	0.460000	0.39030	GAA		0.383	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			A	29111438	C	A	29111438	4	1	61	1	0	0	0	0	0	1	0	0	3894	922	32	2	236	2	CRLF3	17	29111438	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	294210	29111438	52083772	10157	18142										
CRLF3	51379	broad.mit.edu	37	chr17	29120666	29120666	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaaactggagcctgtaatCttgggctgtaaagtcatcat	10	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29120666C>A	ENST00000324238.6	-	5	752	c.628G>T	c.(628-630)Gat>Tat	p.D210Y	CRLF3_ENST00000544695.1_Missense_Mutation_p.D94Y|CTD-2349P21.9_ENST00000580085.1_lincRNA|CRLF3_ENST00000577725.1_Intron	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	210	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)		p.D210Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				AGCCTGTAATCTTGGGCTGTA	0.363																																					Pancreas(30;346 881 29244 33464 41299)											1	Substitution - Missense(1)	large_intestine(1)	17											72	68	69					17																	29120666		2203	4300	6503	26144792	SO:0001583	missense	51379			AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.628G>T	17.37:g.29120666C>A	ENSP00000318804:p.Asp210Tyr		26144792	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	37	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.293926	0.81025	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.26518	1.73;1.73	5.64	5.64	0.86602	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.089034	0.85682	D	0.000000	T	0.35653	0.0939	L	0.55481	1.735	0.80722	D	1	D	0.53462	0.96	P	0.49276	0.605	T	0.07121	-1.0789	10	0.66056	D	0.02	-23.895	15.9871	0.80168	0.0:0.8652:0.1348:0.0	.	210	Q8IUI8	CRLF3_HUMAN	Y	210;94	ENSP00000318804:D210Y;ENSP00000444188:D94Y	ENSP00000318804:D210Y	D	-	1	0	CRLF3	26144792	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.665000	0.68052	2.663000	0.90544	0.591000	0.81541	GAT		0.363	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			A	29120666	C	A	29120666	3	1	61	1	0	0	0	0	1	0	0	0	3894	913	32	2	716	2	CRLF3	17	29120666	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9228	29120666	52074544	10158	18143										
ATAD5	79915	broad.mit.edu	37	chr17	29161662	29161662	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgacctccctgcaaaattCtaaaaaagtaaatcctaaac	3	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29161662C>A	ENST00000321990.4	+	2	941	c.563C>A	c.(562-564)tCt>tAt	p.S188Y	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	188					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.S188Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CTGCAAAATTCTAAAAAAGTA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											64	72	69					17																	29161662		2202	4296	6498	26185788	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.563C>A	17.37:g.29161662C>A	ENSP00000313171:p.Ser188Tyr		26185788	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	C	3.215	-0.160696	0.06502	.	.	ENSG00000176208	ENST00000321990	T	0.17854	2.25	5.69	-0.511	0.11970	.	1.732580	0.02736	N	0.115697	T	0.29158	0.0725	L	0.56769	1.78	0.09310	N	1	D;P	0.54964	0.969;0.947	P;P	0.54100	0.742;0.453	T	0.20940	-1.0260	10	0.59425	D	0.04	.	6.056	0.19812	0.2962:0.4685:0.1728:0.0624	.	188;188	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	Y	188	ENSP00000313171:S188Y	ENSP00000313171:S188Y	S	+	2	0	ATAD5	26185788	0.000000	0.05858	0.004000	0.12327	0.660000	0.38997	-0.369000	0.07533	0.080000	0.16959	0.655000	0.94253	TCT		0.338	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29161662	C	A	29161662	3	1	61	1	0	0	0	0	1	0	0	0	1077	913	32	2	569	2	ATAD5	17	29161662	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40996	29161662	52033548	10159	18144										
ATAD5	79915	broad.mit.edu	37	chr17	29161837	29161837	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatactacaagccatgcAaactctagagataacgtaac	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29161837A>G	ENST00000321990.4	+	2	1116	c.738A>G	c.(736-738)gcA>gcG	p.A246A	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	246					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.A246A(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CAAGCCATGCAAACTCTAGAG	0.338																																																1	Substitution - coding silent(1)	large_intestine(1)	17											80	84	83					17																	29161837		2202	4300	6502	26185963	SO:0001819	synonymous_variant	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.738A>G	17.37:g.29161837A>G			26185963	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																				0.338	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29161837	A	G	29161837	2	3	61	1	0	0	0	0	0	0	0	1	1077	117	5	4		4	ATAD5	17	29161837	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	175	29161837	52033373	10160	18145										
ATAD5	79915	broad.mit.edu	37	chr17	29195361	29195361	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtggcagttggttgaaaGactggaaaagaagagctgaa	14	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29195361G>T	ENST00000321990.4	+	12	3622	c.3244G>T	c.(3244-3246)Gac>Tac	p.D1082Y		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1082					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.D1082Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TTGGTTGAAAGACTGGAAAAG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	17											85	89	87					17																	29195361		2203	4300	6503	26219487	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3244G>T	17.37:g.29195361G>T	ENSP00000313171:p.Asp1082Tyr		26219487	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384383	0.42308	.	.	ENSG00000176208	ENST00000321990	T	0.05925	3.37	5.42	5.42	0.78866	.	0.054544	0.64402	D	0.000001	T	0.30479	0.0766	M	0.88450	2.955	0.49299	D	0.999772	D;D	0.64830	0.994;0.994	P;P	0.62089	0.879;0.898	T	0.16335	-1.0406	10	0.87932	D	0	.	18.8334	0.92150	0.0:0.0:1.0:0.0	.	1082;1082	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	Y	1082	ENSP00000313171:D1082Y	ENSP00000313171:D1082Y	D	+	1	0	ATAD5	26219487	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.724000	0.61972	2.525000	0.85131	0.655000	0.94253	GAC		0.328	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29195361	G	T	29195361	3	4	61	1	0	0	0	0	1	0	0	0	1077	942	33	2	3290	2	ATAD5	17	29195361	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33524	29195361	51999849	10161	18146										
ATAD5	79915	broad.mit.edu	37	chr17	29196559	29196559	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgcagtggtagacaaattCtatctcagttgaaggaagct	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29196559C>A	ENST00000321990.4	+	14	3880	c.3502C>A	c.(3502-3504)Cta>Ata	p.L1168I		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1168					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.L1168I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TAGACAAATTCTATCTCAGTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											115	114	114					17																	29196559		2203	4300	6503	26220685	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3502C>A	17.37:g.29196559C>A	ENSP00000313171:p.Leu1168Ile		26220685	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.638904	0.29157	.	.	ENSG00000176208	ENST00000321990	T	0.10288	2.89	5.62	2.49	0.30216	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.169997	0.40144	N	0.001170	T	0.22589	0.0545	L	0.55743	1.74	0.41169	D	0.986154	P;D	0.59357	0.936;0.985	P;D	0.69654	0.802;0.965	T	0.00420	-1.1750	10	0.52906	T	0.07	.	8.0761	0.30718	0.0:0.6727:0.0:0.3273	.	1168;1168	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	I	1168	ENSP00000313171:L1168I	ENSP00000313171:L1168I	L	+	1	2	ATAD5	26220685	0.998000	0.40836	0.997000	0.53966	0.615000	0.37417	1.470000	0.35354	0.272000	0.22027	0.655000	0.94253	CTA		0.363	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29196559	C	A	29196559	3	1	61	1	0	0	0	0	1	0	0	0	1077	912	32	2	3556	2	ATAD5	17	29196559	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1198	29196559	51998651	10162	18147										
ATAD5	79915	broad.mit.edu	37	chr17	29220384	29220384	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattccaaatgcggaatgtaGattttttatatagtaatctt	6	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29220384G>T	ENST00000321990.4	+	21	4891	c.4513G>T	c.(4513-4515)Gat>Tat	p.D1505Y		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1505					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.D1505Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GCGGAATGTAGATTTTTTATA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											79	95	90					17																	29220384		2194	4295	6489	26244510	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4513G>T	17.37:g.29220384G>T	ENSP00000313171:p.Asp1505Tyr		26244510	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892532	0.52121	.	.	ENSG00000176208	ENST00000321990	T	0.11385	2.78	5.68	5.68	0.88126	.	0.197265	0.53938	D	0.000060	T	0.27866	0.0686	L	0.52364	1.645	0.48185	D	0.999605	D	0.89917	1.0	D	0.85130	0.997	T	0.00064	-1.2151	10	0.56958	D	0.05	.	14.9239	0.70862	0.0:0.0:0.8569:0.1431	.	1505	Q96QE3	ATAD5_HUMAN	Y	1505	ENSP00000313171:D1505Y	ENSP00000313171:D1505Y	D	+	1	0	ATAD5	26244510	1.000000	0.71417	0.962000	0.40283	0.339000	0.28857	3.825000	0.55730	2.837000	0.97791	0.591000	0.81541	GAT		0.338	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29220384	G	T	29220384	3	4	61	1	0	0	0	0	1	0	0	0	1077	942	33	2	4595	2	ATAD5	17	29220384	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23825	29220384	51974826	10163	18148										
ATAD5	79915	broad.mit.edu	37	chr17	29221100	29221100	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaggaagagatccaaccaaCgatcttactttttatgtttc	6	8	1	1	rs548420328		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29221100C>T	ENST00000321990.4	+	21	5607	c.5229C>T	c.(5227-5229)aaC>aaT	p.N1743N		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1743					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.N1743N(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ATCCAACCAACGATCTTACTT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	17											44	45	45					17																	29221100		2202	4299	6501	26245226	SO:0001819	synonymous_variant	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.5229C>T	17.37:g.29221100C>T			26245226	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																				0.333	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29221100	C	T	29221100	2	4	61	1	0	0	0	0	0	0	0	1	1077	535	19	1		1	ATAD5	17	29221100	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	716	29221100	51974110	10164	18149										
NF1	4763	broad.mit.edu	37	chr17	29533315	29533316	+	Nonsense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtcactcggttgaacttCgaaatatgtttggtgaaaca							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29533315_29533316CG>TA	ENST00000358273.4	+	12	1701_1702	c.1318_1319CG>TA	c.(1318-1320)CGa>TAa	p.R440*	NF1_ENST00000431387.4_Nonsense_Mutation_p.R440*|NF1_ENST00000356175.3_Nonsense_Mutation_p.R440*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	440					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.R440*(3)|p.R440>?(2)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GGTTGAACTTCGAAATATGTTT	0.396			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	19	Whole gene deletion(8)|Unknown(6)|Substitution - Nonsense(3)|Complex(2)	soft_tissue(9)|central_nervous_system(4)|autonomic_ganglia(3)|large_intestine(2)|lung(1)	17	GRCh37	CM950845	NF1	M																																				26557442	SO:0001587	stop_gained	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	Exception_encountered	17.37:g.29533315_29533316delinsTA	ENSP00000351015:p.Arg440*		26557441	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	DNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.396	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		TA	29533316	CG	TA	29533315	4	4	61	1	0	0	0	0	0	1	0	0	10387	876	31	1	1364	1	NF1	17	29533315	Nonsense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	312215	29533315	51661895	10165	18150										
NF1	4763	broad.mit.edu	37	chr17	29588740	29588740	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatctagggatcataaagCtgttggaagacgaccttttg	11	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29588740C>A	ENST00000358273.4	+	35	4972	c.4589C>A	c.(4588-4590)gCt>gAt	p.A1530D	NF1_ENST00000356175.3_Missense_Mutation_p.A1509D	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1530					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.A1530D(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GATCATAAAGCTGTTGGAAGA	0.408			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(4)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)|large_intestine(1)	17											120	105	110					17																	29588740		2203	4300	6503	26612866	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4589C>A	17.37:g.29588740C>A	ENSP00000351015:p.Ala1530Asp		26612866	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717355	0.89205	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.81499	-1.5;-1.5;-1.5	5.44	5.44	0.79542	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (1);	0.000000	0.85682	D	0.000000	D	0.86502	0.5948	L	0.52364	1.645	0.80722	D	1	B;D;B	0.76494	0.094;0.999;0.028	B;D;B	0.80764	0.048;0.994;0.024	T	0.82859	-0.0249	10	0.21540	T	0.41	.	18.2551	0.90017	0.0:1.0:0.0:0.0	.	559;1509;1530	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	D	1530;1509;1175	ENSP00000351015:A1530D;ENSP00000348498:A1509D;ENSP00000389907:A1175D	ENSP00000348498:A1509D	A	+	2	0	NF1	26612866	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.266000	0.78452	2.565000	0.86533	0.650000	0.86243	GCT		0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29588740	C	A	29588740	3	1	61	1	0	0	0	0	1	0	0	0	10387	797	28	2	4788	2	NF1	17	29588740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55425	29588740	51606470	10166	18151										
NF1	4763	broad.mit.edu	37	chr17	29592343	29592343	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgggaatcctattttttaTtatgttgcacggaggtaaga	11	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:29592343T>G	ENST00000358273.4	+	36	5204	c.4821T>G	c.(4819-4821)taT>taG	p.Y1607*	NF1_ENST00000356175.3_Nonsense_Mutation_p.Y1586*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1607	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.Y1607*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CTATTTTTTATTATGTTGCAC	0.343			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(4)|Substitution - Nonsense(1)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)|large_intestine(1)	17											56	57	56					17																	29592343		2201	4298	6499	26616469	SO:0001587	stop_gained	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4821T>G	17.37:g.29592343T>G	ENSP00000351015:p.Tyr1607*		26616469	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	42	9.378353	0.99153	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	6.16	3.75	0.43078	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5954	0.28046	0.0:0.4206:0.0:0.5794	.	.	.	.	X	1607;1586;1252	.	ENSP00000348498:Y1586X	Y	+	3	2	NF1	26616469	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.315000	0.43752	0.463000	0.27118	0.528000	0.53228	TAT		0.343	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29592343	T	G	29592343	4	3	61	1	0	0	0	0	0	1	0	0	10387	1500	52	4	5024	4	NF1	17	29592343	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3603	29592343	51602867	10167	18152										
UTP6	55813	broad.mit.edu	37	chr17	30192430	30192430	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagctctctcataatattCtcttatgttcgccatattgc	4	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30192430C>A	ENST00000261708.4	-	18	1728	c.1591G>T	c.(1591-1593)Gaa>Taa	p.E531*		NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	531					rRNA processing (GO:0006364)	nucleolus (GO:0005730)		p.E531*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				TCATAATATTCTCTTATGTTC	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											113	110	111					17																	30192430		2203	4300	6503	27216543	SO:0001587	stop_gained	55813			AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.1591G>T	17.37:g.30192430C>A	ENSP00000261708:p.Glu531*		27216543	Q8IX96|Q96BL2|Q9NQ91	Nonsense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	c	39	7.744167	0.98465	.	.	ENSG00000108651	ENST00000261708	.	.	.	5.17	5.17	0.71159	.	0.157212	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-3.5748	18.2619	0.90038	0.0:1.0:0.0:0.0	.	.	.	.	X	531	.	ENSP00000261708:E531X	E	-	1	0	UTP6	27216543	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	6.296000	0.72751	2.401000	0.81631	0.558000	0.71614	GAA		0.353	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		A	30192430	C	A	30192430	4	1	61	1	0	0	0	0	0	1	0	0	17142	922	32	2	210	2	UTP6	17	30192430	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	600087	30192430	51002780	10168	18153										
UTP6	55813	broad.mit.edu	37	chr17	30213078	30213078	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcagaataatcaggattCtcctaaagagtgttatatca	6	7	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30213078C>T	ENST00000261708.4	-	9	761	c.624G>A	c.(622-624)gaG>gaA	p.E208E	CTC-542B22.2_ENST00000583236.1_lincRNA|UTP6_ENST00000490218.2_5'UTR	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	208					rRNA processing (GO:0006364)	nucleolus (GO:0005730)		p.E208E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				AATCAGGATTCTCCTAAAGAG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	17											87	90	89					17																	30213078		2203	4300	6503	27237191	SO:0001819	synonymous_variant	55813			AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.624G>A	17.37:g.30213078C>T			27237191	Q8IX96|Q96BL2|Q9NQ91	Silent	SNP	ENST00000261708.4	37	CCDS11269.1																																																																																				0.358	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		T	30213078	C	T	30213078	2	4	61	1	0	0	0	0	0	0	0	1	17142	912	32	3		3	UTP6	17	30213078	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20648	30213078	50982132	10169	18154										
UTP6	55813	broad.mit.edu	37	chr17	30221999	30221999	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctacttactgttcttcttCtctggatcagctccaaaaga	5	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30221999C>A	ENST00000261708.4	-	3	346	c.209G>T	c.(208-210)aGa>aTa	p.R70I	UTP6_ENST00000490218.2_5'UTR	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	70					rRNA processing (GO:0006364)	nucleolus (GO:0005730)		p.R70I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				TGTTCTTCTTCTCTGGATCAG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	17											76	62	67					17																	30221999		2200	4296	6496	27246112	SO:0001583	missense	55813			AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.209G>T	17.37:g.30221999C>A	ENSP00000261708:p.Arg70Ile		27246112	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.654594	0.29425	.	.	ENSG00000108651	ENST00000261708	T	0.30182	1.54	5.31	0.512	0.16994	U3 small nucleolar RNA-associated protein 6 (1);	0.249022	0.46145	D	0.000312	T	0.11665	0.0284	N	0.04297	-0.235	0.44539	D	0.997497	B;B	0.26902	0.046;0.163	B;B	0.23716	0.029;0.048	T	0.09250	-1.0683	10	0.37606	T	0.19	-4.9754	6.4188	0.21732	0.0:0.4565:0.0:0.5435	.	70;70	B4DSL9;Q9NYH9	.;UTP6_HUMAN	I	70	ENSP00000261708:R70I	ENSP00000261708:R70I	R	-	2	0	UTP6	27246112	1.000000	0.71417	0.994000	0.49952	0.560000	0.35617	3.528000	0.53524	0.323000	0.23307	-0.793000	0.03317	AGA		0.313	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		A	30221999	C	A	30221999	3	1	61	1	0	0	0	0	1	0	0	0	17142	913	32	2	1652	2	UTP6	17	30221999	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8921	30221999	50973211	10170	18155										
LRRC37B	114659	broad.mit.edu	37	chr17	30374820	30374820	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccagaaggagcgttcatGaagatgttacaagcccggaa	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30374820G>T	ENST00000341671.7	+	9	2288	c.2283G>T	c.(2281-2283)atG>atT	p.M761I	LRRC37B_ENST00000543378.2_Missense_Mutation_p.M679I|LRRC37B_ENST00000394713.3_Missense_Mutation_p.M710I|LRRC37B_ENST00000584368.1_Missense_Mutation_p.M722I|LRRC37B_ENST00000327564.7_Missense_Mutation_p.M788I	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	761						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.M761I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				GAGCGTTCATGAAGATGTTAC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											118	122	121					17																	30374820		2203	4300	6503	27398933	SO:0001583	missense	114659			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.2283G>T	17.37:g.30374820G>T	ENSP00000340519:p.Met761Ile		27398933	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	4.260	0.047223	0.08243	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.68025	-0.2;-0.3;0.9;-0.29	1.9	0.895	0.19247	.	.	.	.	.	T	0.58424	0.2121	M	0.62723	1.935	0.09310	N	1	B;B	0.31599	0.33;0.228	B;B	0.31547	0.132;0.026	T	0.54583	-0.8272	9	0.66056	D	0.02	.	4.2992	0.10916	0.2126:0.0:0.7874:0.0	.	710;761	Q17RC9;Q96QE4	.;LR37B_HUMAN	I	679;788;710;761	ENSP00000443345:M679I;ENSP00000332536:M788I;ENSP00000378202:M710I;ENSP00000340519:M761I	ENSP00000332536:M788I	M	+	3	0	LRRC37B	27398933	1.000000	0.71417	0.231000	0.23993	0.037000	0.13140	1.008000	0.29872	0.358000	0.24211	0.440000	0.28878	ATG		0.473	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		T	30374820	G	T	30374820	3	4	61	1	0	0	0	0	1	0	0	0	9023	1290	45	2	2317	2	LRRC37B	17	30374820	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	152821	30374820	50820390	10171	18156										
RHOT1	55288	broad.mit.edu	37	chr17	30529799	30529800	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttttagtgacaagagatINSaaaaagatagacctgcagaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30529799_30529800insA	ENST00000333942.6	+	15	1451_1452	c.1212_1213insA	c.(1213-1215)aaafs	p.K405fs	RHOT1_ENST00000358365.3_Frame_Shift_Ins_p.K405fs|RHOT1_ENST00000354266.3_Frame_Shift_Ins_p.K384fs|RHOT1_ENST00000581094.1_Frame_Shift_Ins_p.K405fs|RHOT1_ENST00000583994.1_Frame_Shift_Ins_p.K278fs|RHOT1_ENST00000394692.2_Frame_Shift_Ins_p.K405fs|RHOT1_ENST00000545287.2_Frame_Shift_Ins_p.K405fs	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	405					cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.I407fs*16(1)		NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				TGACAAGAGATAAAAAGATAGA	0.342																																																1	Insertion - Frameshift(1)	large_intestine(1)	17																																								27553913	SO:0001589	frameshift_variant	55288			AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"EF-hand domain containing"	21168	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 1"	613888	"ras homolog gene family, member T1"	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1217dupA	17.37:g.30529804_30529804dupA	ENSP00000334724:p.Lys405fs		27553912	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Frame_Shift_Ins	INS	ENST00000333942.6	37	CCDS32612.1																																																																																				0.342	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		A	30529800	-	A	30529799	7	5	61	1	0	1	1	0	0	0	0	0	13380	1403	49	0	1270	0	RHOT1	17	30529799	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	154979	30529799	50665411	10172	18157										
RHBDL3	162494	broad.mit.edu	37	chr17	30625188	30625188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggtgcatggagccacccGaattgggcttgtctacgtgg	15	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30625188G>A	ENST00000269051.4	+	6	760	c.746G>A	c.(745-747)cGa>cAa	p.R249Q	RHBDL3_ENST00000536287.1_Missense_Mutation_p.R151Q|RHBDL3_ENST00000538145.1_Missense_Mutation_p.R241Q	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	249						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.R249Q(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				GGAGCCACCCGAATTGGGCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	17											150	125	134					17																	30625188		2203	4300	6503	27649301	SO:0001583	missense	162494			AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.746G>A	17.37:g.30625188G>A	ENSP00000269051:p.Arg249Gln		27649301	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	37	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	G	36	5.665718	0.96745	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145;ENST00000536287	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.72	5.72	0.89469	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.51024	0.1650	M	0.87180	2.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.997	T	0.56768	-0.7924	10	0.87932	D	0	-6.4293	19.8863	0.96913	0.0:0.0:1.0:0.0	.	249;241;249	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	Q	249;249;241;151	ENSP00000394849:R249Q;ENSP00000269051:R249Q;ENSP00000442092:R241Q;ENSP00000466508:R151Q	ENSP00000269051:R249Q	R	+	2	0	RHBDL3	27649301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.102000	0.94226	2.706000	0.92434	0.561000	0.74099	CGA		0.622	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		A	30625188	G	A	30625188	3	1	61	1	0	0	0	0	1	0	0	0	13360	1058	37	1	768	1	RHBDL3	17	30625188	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95389	30625188	50570022	10173	18158										
RHBDL3	162494	broad.mit.edu	37	chr17	30643287	30643287	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgccagttcaagctgctgCggatggctgtggcccttatc	13	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:30643287C>T	ENST00000269051.4	+	8	933	c.919C>T	c.(919-921)Cgg>Tgg	p.R307W	RHBDL3_ENST00000536287.1_Missense_Mutation_p.R209W|RHBDL3_ENST00000538145.1_Missense_Mutation_p.R299W	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	307						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.R307W(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				CAAGCTGCTGCGGATGGCTGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											158	159	158					17																	30643287		2203	4300	6503	27667400	SO:0001583	missense	162494			AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.919C>T	17.37:g.30643287C>T	ENSP00000269051:p.Arg307Trp		27667400	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	37	CCDS32613.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.2|23.2	4.381660|4.381660	0.82792|0.82792	.|.	.|.	ENSG00000141314|ENSG00000141314	ENST00000431505|ENST00000269051;ENST00000538145;ENST00000536287	T|T;T;T	0.67523|0.11385	-0.27|2.78;2.78;2.78	5.56|5.56	3.43|3.43	0.39272|0.39272	.|Peptidase S54, rhomboid domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.36166|0.36166	0.0957|0.0957	M|M	0.82517|0.82517	2.595|2.595	0.80722|0.80722	D|D	1|1	P|D;D	0.37997|0.89917	0.614|1.0;1.0	B|D;D	0.25614|0.91635	0.062|0.999;0.999	T|T	0.45775|0.45775	-0.9238|-0.9238	9|10	0.87932|0.87932	D|D	0|0	.|.	15.6414|15.6414	0.77006|0.77006	0.288:0.712:0.0:0.0|0.288:0.712:0.0:0.0	.|.	273|299;307	E9PD28|Q495Y5;P58872	.|.;RHBL3_HUMAN	V|W	273|307;299;209	ENSP00000394849:A273V|ENSP00000269051:R307W;ENSP00000442092:R299W;ENSP00000466508:R209W	ENSP00000394849:A273V|ENSP00000269051:R307W	A|R	+|+	2|1	0|2	RHBDL3|RHBDL3	27667400|27667400	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	2.195000|2.195000	0.42677|0.42677	1.329000|1.329000	0.45376|0.45376	0.563000|0.563000	0.77884|0.77884	GCG|CGG		0.547	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		T	30643287	C	T	30643287	3	4	61	1	0	0	0	0	1	0	0	0	13360	759	27	1	949	1	RHBDL3	17	30643287	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18099	30643287	50551923	10174	18159										
MYO1D	4642	broad.mit.edu	37	chr17	31094749	31094749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcaacaactctgaattCggcagcatcattgatagaag	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:31094749C>T	ENST00000318217.5	-	7	1040	c.736G>A	c.(736-738)Gaa>Aaa	p.E246K	MYO1D_ENST00000579584.1_Missense_Mutation_p.E246K|MYO1D_ENST00000394649.4_Missense_Mutation_p.E158K|MYO1D_ENST00000583621.1_Missense_Mutation_p.E246K	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	246	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E246K(2)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ACTCTGAATTCGGCAGCATCA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	17											88	77	81					17																	31094749		2203	4300	6503	28118862	SO:0001583	missense	4642			AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.736G>A	17.37:g.31094749C>T	ENSP00000324527:p.Glu246Lys		28118862	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571597	0.65765	.	.	ENSG00000176658	ENST00000318217	T	0.72835	-0.69	6.0	5.01	0.66863	Myosin head, motor domain (2);	0.187967	0.25099	U	0.033151	T	0.70064	0.3181	M	0.62723	1.935	0.50467	D	0.999873	B;B	0.22080	0.064;0.064	B;B	0.26202	0.067;0.067	T	0.68534	-0.5383	10	0.56958	D	0.05	.	14.8407	0.70220	0.0:0.8553:0.1447:0.0	.	157;246	Q7Z3N6;O94832	.;MYO1D_HUMAN	K	246	ENSP00000324527:E246K	ENSP00000324527:E246K	E	-	1	0	MYO1D	28118862	1.000000	0.71417	0.942000	0.38095	0.967000	0.64934	7.487000	0.81328	1.505000	0.48720	0.655000	0.94253	GAA		0.363	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			T	31094749	C	T	31094749	3	4	61	1	0	0	0	0	1	0	0	0	10101	893	31	1	2348	1	MYO1D	17	31094749	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	451462	31094749	50100461	10175	18160										
SPACA3	124912	broad.mit.edu	37	chr17	31322667	31322667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggccaagctctacggtcGttgtgaactggccagagtgc	14	10	1	3	rs368023924		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:31322667G>A	ENST00000269053.3	+	2	345	c.275G>A	c.(274-276)cGt>cAt	p.R92H	SPACA3_ENST00000394638.1_Intron|SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Missense_Mutation_p.R23H	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	92					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)	p.R92H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			CTCTACGGTCGTTGTGAACTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	HIS/ARG	0,4406		0,0,2203	106	70	82		275	3.7	1	17		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	SPACA3	NM_173847.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	92/216	31322667	1,13005	2203	4300	6503	28346780	SO:0001583	missense	124912			AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"cancer/testis antigen 54", "sperm lyzozyme-like acrosomal protein 1"	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.275G>A	17.37:g.31322667G>A	ENSP00000269053:p.Arg92His		28346780	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	37	CCDS11275.1	.	.	.	.	.	.	.	.	.	.	g	15.44	2.832902	0.50951	0.0	1.16E-4	ENSG00000141316	ENST00000269053;ENST00000394637	T	0.73681	-0.77	3.67	3.67	0.42095	Lysozyme-like domain (1);	0.158649	0.35708	N	0.003025	D	0.85835	0.5789	M	0.91249	3.19	0.80722	D	1	D	0.64830	0.994	P	0.59056	0.851	D	0.86669	0.1909	10	0.87932	D	0	-1.3152	11.1864	0.48660	0.0:0.0:1.0:0.0	.	92	Q8IXA5	SACA3_HUMAN	H	92;93	ENSP00000269053:R92H	ENSP00000269053:R92H	R	+	2	0	SPACA3	28346780	0.994000	0.37717	0.990000	0.47175	0.101000	0.19017	3.292000	0.51772	0.455000	0.26910	-0.411000	0.06167	CGT		0.617	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847		A	31322667	G	A	31322667	3	1	61	1	0	0	0	0	1	0	0	0	15010	1145	40	1	281	1	SPACA3	17	31322667	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	227918	31322667	49872543	10176	18161										
C17orf102	400591	broad.mit.edu	37	chr17	32904630	32904630	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgatgttggagatatgCaccatactactgtgaaaggg	12	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:32904630C>T	ENST00000357754.1	-	2	508	c.420G>A	c.(418-420)gtG>gtA	p.V140V		NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	140								p.V140V(1)		central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						TGGAGATATGCACCATACTAC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	17											117	112	113					17																	32904630		2026	4197	6223	29928743	SO:0001819	synonymous_variant	400591				CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.420G>A	17.37:g.32904630C>T			29928743	A5PKX0|Q6ZTB3	Silent	SNP	ENST00000357754.1	37	CCDS42297.1																																																																																				0.493	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454		T	32904630	C	T	32904630	2	4	61	1	0	0	0	0	0	0	0	1	1853	697	25	3		3	C17orf102	17	32904630	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1581963	32904630	48290580	10177	18162										
TMEM132E	124842	broad.mit.edu	37	chr17	32956184	32956184	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtcactgagctgacggtCattcagcgggatgtgcaagc	14	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:32956184C>A	ENST00000321639.5	+	5	1357	c.1029C>A	c.(1027-1029)gtC>gtA	p.V343V		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	343						integral component of membrane (GO:0016021)		p.V343V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		AGCTGACGGTCATTCAGCGGG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	17											64	52	56					17																	32956184		2203	4300	6503	29980297	SO:0001819	synonymous_variant	124842			BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1029C>A	17.37:g.32956184C>A			29980297	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	37	CCDS11283.1																																																																																				0.607	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32956184	C	A	32956184	2	1	61	1	0	0	0	0	0	0	0	1	16087	813	29	2		2	TMEM132E	17	32956184	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51554	32956184	48239026	10178	18163										
CCT6B	10693	broad.mit.edu	37	chr17	33288348	33288348	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgggcggcgcatatattgAcagccaaagctgcccgggcc	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33288348A>C	ENST00000314144.5	-	1	180	c.65T>G	c.(64-66)gTc>gGc	p.V22G	CCT6B_ENST00000421975.3_Missense_Mutation_p.V22G|CCT6B_ENST00000436961.3_Missense_Mutation_p.V22G|ZNF830_ENST00000361952.3_5'Flank	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	22				AALAVNICAARGL -> QLWLSIYAPPRV (in Ref. 1; BAA11347). {ECO:0000305}.	chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)	p.V22G(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				GCATATATTGACAGCCAAAGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											35	38	37					17																	33288348		2203	4299	6502	30312461	SO:0001583	missense	10693			D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.65T>G	17.37:g.33288348A>C	ENSP00000327191:p.Val22Gly		30312461	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.641408	0.67244	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.11821	2.74;2.74;2.74	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.19366	0.0465	L	0.39020	1.185	0.80722	D	1	P;P;D	0.57899	0.913;0.956;0.981	P;P;P	0.52881	0.477;0.655;0.712	T	0.00601	-1.1650	10	0.41790	T	0.15	-7.7987	13.3897	0.60816	1.0:0.0:0.0:0.0	.	22;22;22	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	G	22	ENSP00000398044:V22G;ENSP00000327191:V22G;ENSP00000400917:V22G	ENSP00000327191:V22G	V	-	2	0	CCT6B	30312461	1.000000	0.71417	0.917000	0.36280	0.073000	0.16967	8.004000	0.88535	2.324000	0.78689	0.533000	0.62120	GTC		0.567	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		C	33288348	A	C	33288348	3	2	61	1	0	0	0	0	1	0	0	0	2964	275	10	4	1583	4	CCT6B	17	33288348	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	332164	33288348	47906862	10179	18164										
LIG3	3980	broad.mit.edu	37	chr17	33310406	33310406	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtggtgcccaatcccttcTcagagtctgggggtgatatg	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33310406T>A	ENST00000378526.4	+	2	515	c.382T>A	c.(382-384)Tca>Aca	p.S128T	LIG3_ENST00000586407.1_Intron|LIG3_ENST00000262327.5_Missense_Mutation_p.S128T	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	128					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)	p.S41T(1)|p.S128T(1)		endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	CAATCCCTTCTCAGAGTCTGG	0.498								Other BER factors																																								2	Substitution - Missense(2)	large_intestine(2)	17											68	64	65					17																	33310406		2203	4300	6503	30334519	SO:0001583	missense	3980				CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.382T>A	17.37:g.33310406T>A	ENSP00000367787:p.Ser128Thr		30334519	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	37	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	T	15.06	2.721952	0.48728	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.29655	1.56;1.56	5.93	5.93	0.95920	Zinc finger, PARP-type (4);	0.175245	0.45361	D	0.000377	T	0.31575	0.0801	L	0.39397	1.21	0.38879	D	0.956875	B;B;B;P	0.35628	0.007;0.007;0.001;0.513	B;B;B;B	0.43052	0.025;0.025;0.023;0.406	T	0.22730	-1.0208	10	0.51188	T	0.08	-6.8261	9.5503	0.39306	0.2456:0.0:0.0:0.7544	.	128;128;128;128	E5KLB5;P49916;E5KLB6;Q96DF0	.;DNLI3_HUMAN;.;.	T	128	ENSP00000367787:S128T;ENSP00000262327:S128T	ENSP00000262327:S128T	S	+	1	0	LIG3	30334519	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.594000	0.61041	2.281000	0.76405	0.533000	0.62120	TCA		0.498	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		A	33310406	T	A	33310406	3	1	61	1	0	0	0	0	1	0	0	0	8805	1551	54	5	384	5	LIG3	17	33310406	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22058	33310406	47884804	10180	18165										
LIG3	3980	broad.mit.edu	37	chr17	33310495	33310495	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggccaccacaaaaaaaatCgaggacctcacagagctgga	10	12	1	1	rs61749869		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33310495C>T	ENST00000378526.4	+	2	604	c.471C>T	c.(469-471)atC>atT	p.I157I	LIG3_ENST00000586407.1_Intron|LIG3_ENST00000262327.5_Silent_p.I157I	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	157					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)	p.I70I(1)|p.I157I(1)		endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	CAAAAAAAATCGAGGACCTCA	0.483								Other BER factors																																								2	Substitution - coding silent(2)	large_intestine(2)	17											34	38	36					17																	33310495		2198	4299	6497	30334608	SO:0001819	synonymous_variant	3980				CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.471C>T	17.37:g.33310495C>T			30334608	Q16714|Q6NVK3	Silent	SNP	ENST00000378526.4	37	CCDS11284.2																																																																																				0.483	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		T	33310495	C	T	33310495	2	4	61	1	0	0	0	0	0	0	0	1	8805	874	31	1		1	LIG3	17	33310495	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89	33310495	47884715	10181	18166										
RAD51L3	5892	broad.mit.edu	37	chr17	33428365	33428365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcccgctgtccctgtctCgagttatgtggttggtcacc	11	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33428365C>T	ENST00000345365.6	-	9	1013	c.758G>A	c.(757-759)cGa>cAa	p.R253Q	RAD51L3-RFFL_ENST00000593039.1_Missense_Mutation_p.R94Q|RAD51D_ENST00000460118.2_Missense_Mutation_p.R134Q|RAD51D_ENST00000335858.7_Missense_Mutation_p.R141Q|RAD51D_ENST00000590380.1_5'UTR|RAD51D_ENST00000590016.1_Missense_Mutation_p.R273Q|RAD51D_ENST00000394589.4_Missense_Mutation_p.R253Q|RAD51D_ENST00000360276.3_Missense_Mutation_p.R208Q	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	253					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)	p.R141Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GTCCCTGTCTCGAGTTATGTG	0.532								Direct reversal of damage																																								1	Substitution - Missense(1)	large_intestine(1)	17											96	87	90					17																	33428365		2203	4300	6503	30452478	SO:0001583	missense	5892			AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"recombination repair protein", "DNA repair protein RAD51 homolog 4"	602954	"RAD51 (S. cerevisiae)-like 3", "RAD51-like 3 (S. cerevisiae)", "RAD51 homolog D (S. cerevisiae)"	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.758G>A	17.37:g.33428365C>T	ENSP00000338790:p.Arg253Gln		30452478	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	37	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109373	0.37242	.	.	ENSG00000185379	ENST00000345365;ENST00000394589;ENST00000335858;ENST00000360276;ENST00000345766	T;T	0.68765	1.12;-0.35	4.86	2.84	0.33178	ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.214060	0.47455	N	0.000235	T	0.80763	0.4685	M	0.91196	3.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.978;0.971	D;D;P;P	0.70935	0.971;0.947;0.668;0.611	T	0.78732	-0.2089	10	0.62326	D	0.03	-0.9502	4.443	0.11584	0.1798:0.6378:0.0:0.1825	.	273;141;253;253	B4DJU7;O75771-3;O75771;F8W8E6	.;.;RA51D_HUMAN;.	Q	253;273;253;208;141	ENSP00000338790:R253Q;ENSP00000353417:R208Q	ENSP00000338408:R253Q	R	-	2	0	RAD51D	30452478	1.000000	0.71417	0.956000	0.39512	0.856000	0.48823	2.397000	0.44477	0.746000	0.32786	0.655000	0.94253	CGA		0.532	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878		T	33428365	C	T	33428365	3	4	61	1	0	0	0	0	1	0	0	0	13027	884	31	1	236	1	RAD51L3	17	33428365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117870	33428365	47766845	10182	18167										
SLFN11	91607	broad.mit.edu	37	chr17	33679510	33679510	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctcctttccaggcctgaGaatcgccgaacactgtccaa	8	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33679510G>T	ENST00000394566.1	-	7	2843	c.2571C>A	c.(2569-2571)ttC>ttA	p.F857L	SLFN11_ENST00000308377.4_Missense_Mutation_p.F857L	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	857					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.F857L(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCAGGCCTGAGAATCGCCGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											259	227	238					17																	33679510		2203	4300	6503	30703623	SO:0001583	missense	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2571C>A	17.37:g.33679510G>T	ENSP00000378067:p.Phe857Leu		30703623	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	g	17.46	3.394722	0.62066	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.84070	-1.8;-1.8	4.0	0.506	0.16961	.	0.000000	0.48767	D	0.000171	D	0.88570	0.6472	M	0.83384	2.64	0.27046	N	0.963894	D	0.89917	1.0	D	0.78314	0.991	T	0.79843	-0.1632	10	0.87932	D	0	.	5.8649	0.18768	0.4276:0.0:0.5724:0.0	.	857	Q7Z7L1	SLN11_HUMAN	L	857	ENSP00000312402:F857L;ENSP00000378067:F857L	ENSP00000312402:F857L	F	-	3	2	SLFN11	30703623	0.723000	0.28027	0.924000	0.36721	0.845000	0.48019	-0.428000	0.06991	0.010000	0.14839	-0.140000	0.14226	TTC		0.488	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		T	33679510	G	T	33679510	3	4	61	1	0	0	0	0	1	0	0	0	14770	933	33	2	138	2	SLFN11	17	33679510	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	251145	33679510	47515700	10183	18168										
SLFN11	91607	broad.mit.edu	37	chr17	33679887	33679887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctattggatctgcattgcGaactattctggtgagctctt	11	8	3	1	rs200734680		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33679887G>A	ENST00000394566.1	-	7	2466	c.2194C>T	c.(2194-2196)Cgc>Tgc	p.R732C	SLFN11_ENST00000308377.4_Missense_Mutation_p.R732C	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	732					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R732C(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCTGCATTGCGAACTATTCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											141	139	140					17																	33679887		2203	4300	6503	30704000	SO:0001583	missense	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2194C>T	17.37:g.33679887G>A	ENSP00000378067:p.Arg732Cys		30704000	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	g	9.725	1.160599	0.21454	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.98105	-4.72;-4.72	3.85	2.88	0.33553	.	0.000000	0.48767	D	0.000176	D	0.95850	0.8649	M	0.79926	2.475	0.25052	N	0.991124	D	0.54397	0.966	B	0.39094	0.29	D	0.91658	0.5340	10	0.87932	D	0	.	7.3942	0.26927	0.1209:0.0:0.8791:0.0	.	732	Q7Z7L1	SLN11_HUMAN	C	732	ENSP00000312402:R732C;ENSP00000378067:R732C	ENSP00000312402:R732C	R	-	1	0	SLFN11	30704000	0.115000	0.22152	0.016000	0.15963	0.130000	0.20726	2.299000	0.43611	0.953000	0.37825	0.655000	0.94253	CGC		0.443	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33679887	G	A	33679887	3	1	61	1	0	0	0	0	1	0	0	0	14770	1058	37	1	515	1	SLFN11	17	33679887	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	377	33679887	47515323	10184	18169										
SLFN11	91607	broad.mit.edu	37	chr17	33690347	33690347	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaaggtccttcttccaaGatttttggcttccttttggt	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33690347G>T	ENST00000394566.1	-	4	752	c.480C>A	c.(478-480)atC>atA	p.I160I	SLFN11_ENST00000308377.4_Silent_p.I160I	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	160					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.I160I(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTCTTCCAAGATTTTTGGCT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	17											96	99	98					17																	33690347		2203	4300	6503	30714460	SO:0001819	synonymous_variant	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.480C>A	17.37:g.33690347G>T			30714460	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																				0.458	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		T	33690347	G	T	33690347	2	4	61	1	0	0	0	0	0	0	0	1	14770	932	33	2		2	SLFN11	17	33690347	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10460	33690347	47504863	10185	18170										
SLFN11	91607	broad.mit.edu	37	chr17	33690785	33690785	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattgatgaccaggtctggGtaagatggttccacaaccag	11	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33690785G>A	ENST00000394566.1	-	4	314	c.42C>T	c.(40-42)taC>taT	p.Y14Y	SLFN11_ENST00000308377.4_Silent_p.Y14Y	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	14					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.Y14Y(2)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCAGGTCTGGGTAAGATGGTT	0.423																																																2	Substitution - coding silent(2)	large_intestine(1)|skin(1)	17											65	70	68					17																	33690785		2202	4300	6502	30714898	SO:0001819	synonymous_variant	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.42C>T	17.37:g.33690785G>A			30714898	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																				0.423	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33690785	G	A	33690785	2	1	61	1	0	0	0	0	0	0	0	1	14770	1256	44	3		3	SLFN11	17	33690785	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	438	33690785	47504425	10186	18171										
SLFN12	55106	broad.mit.edu	37	chr17	33749255	33749255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcttcctaatggacttttCgatttctctttctaagtcat	4	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33749255C>T	ENST00000394562.1	-	4	1316	c.793G>A	c.(793-795)Gaa>Aaa	p.E265K	SLFN12_ENST00000304905.5_Missense_Mutation_p.E265K|SLFN12_ENST00000460530.1_5'Flank|SLFN12_ENST00000452764.3_Missense_Mutation_p.E265K			Q8IYM2	SLN12_HUMAN	schlafen family member 12	265							ATP binding (GO:0005524)	p.E265K(1)		breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATGGACTTTTCGATTTCTCTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	17											81	84	83					17																	33749255		2203	4300	6503	30773368	SO:0001583	missense	55106			AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.793G>A	17.37:g.33749255C>T	ENSP00000378063:p.Glu265Lys		30773368	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	C	8.465	0.856150	0.17106	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.64618	-0.11;-0.11;-0.11	3.49	-1.62	0.08372	.	.	.	.	.	T	0.37128	0.0992	L	0.35854	1.095	0.09310	N	1	P	0.36647	0.563	B	0.25140	0.058	T	0.19257	-1.0311	9	0.14656	T	0.56	.	3.5778	0.07941	0.0:0.433:0.1951:0.3719	.	265	Q8IYM2	SLN12_HUMAN	K	265	ENSP00000378063:E265K;ENSP00000302077:E265K;ENSP00000394903:E265K	ENSP00000302077:E265K	E	-	1	0	SLFN12	30773368	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.127000	0.10547	-0.031000	0.13781	-0.436000	0.05848	GAA		0.343	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		T	33749255	C	T	33749255	3	4	61	1	0	0	0	0	1	0	0	0	14771	893	31	1	955	1	SLFN12	17	33749255	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58470	33749255	47445955	10187	18172										
SLFN13	146857	broad.mit.edu	37	chr17	33768653	33768653	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcacagtgaaacacattCctgatcttctccatgatctt	5	13	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33768653C>T	ENST00000285013.6	-	5	2126	c.1851G>A	c.(1849-1851)agG>agA	p.R617R	SLFN13_ENST00000542635.1_Silent_p.R617R|SLFN13_ENST00000360502.2_Silent_p.R299R|SLFN13_ENST00000526861.1_Silent_p.R617R|SLFN13_ENST00000533791.1_Silent_p.R617R|SLFN13_ENST00000534689.1_Silent_p.R299R	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	617						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.R617R(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GAAACACATTCCTGATCTTCT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	17											38	41	40					17																	33768653		2191	4278	6469	30792766	SO:0001819	synonymous_variant	146857			AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1851G>A	17.37:g.33768653C>T			30792766	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																				0.458	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33768653	C	T	33768653	2	4	61	1	0	0	0	0	0	0	0	1	14773	854	30	3		3	SLFN13	17	33768653	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19398	33768653	47426557	10188	18173										
PEX12	5193	broad.mit.edu	37	chr17	33904198	33904198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcttttcctaggatgtatCgaagttgttgtacaagaaac	10	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33904198C>T	ENST00000225873.4	-	2	1146	c.539G>A	c.(538-540)cGa>cAa	p.R180Q	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	180					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.R180Q(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TAGGATGTATCGAAGTTGTTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											94	88	90					17																	33904198		2203	4300	6503	30928311	SO:0001583	missense	5193			U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.539G>A	17.37:g.33904198C>T	ENSP00000225873:p.Arg180Gln		30928311	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	37	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.646452	0.29246	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.82803	-1.65	5.63	-3.86	0.04230	Pex, N-terminal (1);	0.707462	0.14200	N	0.334744	T	0.70552	0.3237	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.52518	-0.8565	10	0.33940	T	0.23	0.5578	11.8245	0.52259	0.0:0.4505:0.0:0.5495	.	180	O00623	PEX12_HUMAN	Q	180	ENSP00000225873:R180Q	ENSP00000225873:R180Q	R	-	2	0	PEX12	30928311	0.000000	0.05858	0.332000	0.25469	0.897000	0.52465	-0.369000	0.07533	-0.943000	0.03691	-0.300000	0.09419	CGA		0.507	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		T	33904198	C	T	33904198	3	4	61	1	0	0	0	0	1	0	0	0	11771	884	31	1	548	1	PEX12	17	33904198	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135545	33904198	47291012	10189	18174										
PEX12	5193	broad.mit.edu	37	chr17	33904465	33904465	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgtcccccattacaattCtctttaagccgtaaaagttt	6	10	1	0	rs61752100		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33904465C>A	ENST00000225873.4	-	2	879	c.272G>T	c.(271-273)aGa>aTa	p.R91I	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	91					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.R91I(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CATTACAATTCTCTTTAAGCC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	17											151	170	163					17																	33904465		2203	4300	6503	30928578	SO:0001583	missense	5193			U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.272G>T	17.37:g.33904465C>A	ENSP00000225873:p.Arg91Ile		30928578	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	37	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063198	0.93898	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.85955	-2.05	5.46	5.46	0.80206	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93510	0.7929	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94316	0.7549	10	0.87932	D	0	-16.826	18.3052	0.90177	0.0:1.0:0.0:0.0	.	91	O00623	PEX12_HUMAN	I	91	ENSP00000225873:R91I	ENSP00000225873:R91I	R	-	2	0	PEX12	30928578	1.000000	0.71417	0.891000	0.34965	0.936000	0.57629	7.104000	0.77024	2.568000	0.86640	0.650000	0.86243	AGA		0.423	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		A	33904465	C	A	33904465	3	1	61	1	0	0	0	0	1	0	0	0	11771	913	32	2	815	2	PEX12	17	33904465	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	267	33904465	47290745	10190	18175										
AP2B1	163	broad.mit.edu	37	chr17	33954701	33954701	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtggatgttgactttgttCgaaaagctgtgcgggccatt	14	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:33954701C>T	ENST00000262325.7	+	9	1664	c.1111C>T	c.(1111-1113)Cga>Tga	p.R371*	AP2B1_ENST00000592545.1_Nonsense_Mutation_p.R333*|AP2B1_ENST00000537622.2_Nonsense_Mutation_p.R371*|AP2B1_ENST00000538556.1_Nonsense_Mutation_p.R314*|AP2B1_ENST00000589344.1_Nonsense_Mutation_p.R371*|AP2B1_ENST00000312678.8_Nonsense_Mutation_p.R371*|AP2B1_ENST00000545922.2_3'UTR	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	371					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)	p.R371*(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TGACTTTGTTCGAAAAGCTGT	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											123	115	117					17																	33954701		2203	4300	6503	30978814	SO:0001587	stop_gained	163			M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1111C>T	17.37:g.33954701C>T	ENSP00000262325:p.Arg371*		30978814	A6NJP3|P21851|Q7Z451|Q96J19	Nonsense_Mutation	SNP	ENST00000262325.7	37	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	C	40	8.032689	0.98619	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.9073	13.8298	0.63373	0.1528:0.8472:0.0:0.0	.	.	.	.	X	371;371;314;371;108	.	ENSP00000262325:R371X	R	+	1	2	AP2B1	30978814	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.663000	0.61532	2.712000	0.92718	0.650000	0.86243	CGA		0.443	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			T	33954701	C	T	33954701	4	4	61	1	0	0	0	0	0	1	0	0	741	876	31	1	1141	1	AP2B1	17	33954701	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50236	33954701	47240509	10191	18176										
GAS2L2	246176	broad.mit.edu	37	chr17	34073225	34073225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggtggggttcccggcgtCggttccccagctgtctgttt	16	11	1	0	rs202100272		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34073225C>T	ENST00000254466.6	-	6	1318	c.1291G>A	c.(1291-1293)Gac>Aac	p.D431N	GAS2L2_ENST00000587565.1_Missense_Mutation_p.D415N	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	431					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)	p.D431N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTCCCGGCGTCGGTTCCCCAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											124	137	132					17																	34073225		2203	4300	6503	31097338	SO:0001583	missense	246176			AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1291G>A	17.37:g.34073225C>T	ENSP00000254466:p.Asp431Asn		31097338	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	1.393	-0.580225	0.03854	.	.	ENSG00000132139	ENST00000254466	T	0.18174	2.23	5.3	-1.62	0.08372	.	0.711655	0.13119	N	0.412336	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	B	0.26318	0.146	B	0.17098	0.017	T	0.35375	-0.9791	10	0.22109	T	0.4	-0.1391	1.8601	0.03187	0.2387:0.3534:0.2814:0.1265	.	431	Q8NHY3	GA2L2_HUMAN	N	431	ENSP00000254466:D431N	ENSP00000254466:D431N	D	-	1	0	GAS2L2	31097338	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.002000	0.13061	0.109000	0.17891	-1.131000	0.01979	GAC		0.582	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34073225	C	T	34073225	3	4	61	1	0	0	0	0	1	0	0	0	6267	884	31	1	1355	1	GAS2L2	17	34073225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118524	34073225	47121985	10192	18177										
C17orf66	256957	broad.mit.edu	37	chr17	34191513	34191513	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctcacctgtgctgcataGaactgctcatcctctctggg	8	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34191513G>T	ENST00000311880.2	-	5	646	c.498C>A	c.(496-498)ttC>ttA	p.F166L	C17orf66_ENST00000592980.1_Missense_Mutation_p.F126L|C17orf66_ENST00000587585.1_5'Flank	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		166					hematopoietic progenitor cell differentiation (GO:0002244)			p.F166L(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		GTGCTGCATAGAACTGCTCAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											128	119	122					17																	34191513		2203	4300	6503	31215626	SO:0001583	missense	256957																														ENST00000311880.2:c.498C>A	17.37:g.34191513G>T	ENSP00000309560:p.Phe166Leu		31215626	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Missense_Mutation	SNP	ENST00000311880.2	37	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	G	2.405	-0.336644	0.05278	.	.	ENSG00000172653	ENST00000311880	T	0.42513	0.97	5.17	1.98	0.26296	Armadillo-like helical (1);Armadillo-type fold (1);	2.038100	0.02015	N	0.047308	T	0.21468	0.0517	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.19224	-1.0312	10	0.09084	T	0.74	.	3.574	0.07927	0.0921:0.1836:0.5623:0.162	.	132;126;166	A2RTY3-4;A2RTY3-3;A2RTY3	.;.;CQ066_HUMAN	L	166	ENSP00000309560:F166L	ENSP00000309560:F166L	F	-	3	2	C17orf66	31215626	0.912000	0.30974	0.006000	0.13384	0.974000	0.67602	1.257000	0.32932	0.294000	0.22547	0.655000	0.94253	TTC		0.483	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			T	34191513	G	T	34191513	3	4	61	1	0	0	0	0	1	0	0	0	1879	933	33	2	1258	2	C17orf66	17	34191513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118288	34191513	47003697	10193	18178										
MYO19	80179	broad.mit.edu	37	chr17	34869523	34869523	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaaggcagctccctcagGaaggtgccactggagcctct	14	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34869523G>A	ENST00000431794.3	-	10	1288	c.766C>T	c.(766-768)Cct>Tct	p.P256S	MYO19_ENST00000544606.1_Missense_Mutation_p.P122S|MYO19_ENST00000586007.1_Missense_Mutation_p.P256S|MYO19_ENST00000268852.9_Missense_Mutation_p.P256S	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	256	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.P256S(2)		endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GCTCCCTCAGGAAGGTGCCAC	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	17											65	70	69					17																	34869523		2064	4200	6264	31943636	SO:0001583	missense	80179			BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.766C>T	17.37:g.34869523G>A	ENSP00000409936:p.Pro256Ser		31943636	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354611	0.61293	.	.	ENSG00000141140	ENST00000431794;ENST00000268852;ENST00000544606	D;D;D	0.86366	-2.11;-2.11;-2.11	5.55	5.55	0.83447	Myosin head, motor domain (2);	0.000000	0.42294	D	0.000739	T	0.81384	0.4811	N	0.25286	0.73	0.45883	D	0.998731	B;P;B;P	0.49635	0.242;0.926;0.059;0.811	B;P;B;B	0.44772	0.101;0.46;0.039;0.383	T	0.79647	-0.1716	10	0.23302	T	0.38	.	16.2213	0.82258	0.0:0.0:1.0:0.0	.	122;256;256;256	B4DSL5;Q96H55;Q96H55-2;Q96H55-4	.;MYO19_HUMAN;.;.	S	256;256;122	ENSP00000409936:P256S;ENSP00000268852:P256S;ENSP00000438365:P122S	ENSP00000268852:P256S	P	-	1	0	MYO19	31943636	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	4.518000	0.60510	2.622000	0.88805	0.655000	0.94253	CCT		0.617	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		A	34869523	G	A	34869523	3	1	61	1	0	0	0	0	1	0	0	0	10097	1174	41	3	2274	3	MYO19	17	34869523	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	678010	34869523	46325687	10194	18179										
GGNBP2	79893	broad.mit.edu	37	chr17	34923534	34923534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtatgggaactaatgtCgcaggaatgcagggatgaag	16	4	0	1	rs201874238		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34923534C>T	ENST00000304718.4	+	6	876	c.560C>T	c.(559-561)tCg>tTg	p.S187L		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	187					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.S187L(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GAACTAATGTCGCAGGAATGC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	17											175	163	167					17																	34923534		2203	4300	6503	31997647	SO:0001583	missense	79893			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.560C>T	17.37:g.34923534C>T	ENSP00000307617:p.Ser187Leu		31997647	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	37	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764020	0.89932	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.48	5.48	0.80851	.	0.053487	0.85682	D	0.000000	T	0.75686	0.3883	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.994	D;P	0.65987	0.94;0.736	T	0.76471	-0.2947	9	0.59425	D	0.04	-5.1991	19.4017	0.94632	0.0:1.0:0.0:0.0	.	187;187	Q9H3C7;Q9H3C7-3	GGNB2_HUMAN;.	L	187	.	ENSP00000307617:S187L	S	+	2	0	GGNBP2	31997647	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.191000	0.77763	2.577000	0.86979	0.558000	0.71614	TCG		0.358	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34923534	C	T	34923534	3	4	61	1	0	0	0	0	1	0	0	0	6379	893	31	1	578	1	GGNBP2	17	34923534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	54011	34923534	46271676	10195	18180										
GGNBP2	79893	broad.mit.edu	37	chr17	34935715	34935715	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacaatagatatagctcaaGaagaagttctgacctgcttg	9	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34935715G>T	ENST00000304718.4	+	8	1202	c.886G>T	c.(886-888)Gaa>Taa	p.E296*		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	296					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.E296*(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TATAGCTCAAGAAGAAGTTCT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											165	168	167					17																	34935715		2203	4300	6503	32009828	SO:0001587	stop_gained	79893			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.886G>T	17.37:g.34935715G>T	ENSP00000307617:p.Glu296*		32009828	B2RPK7|Q96T90|Q9GZR8|Q9H767	Nonsense_Mutation	SNP	ENST00000304718.4	37	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	G	40	7.929888	0.98565	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.3002	19.5755	0.95441	0.0:0.0:1.0:0.0	.	.	.	.	X	296	.	ENSP00000307617:E296X	E	+	1	0	GGNBP2	32009828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.026000	0.93700	2.700000	0.92200	0.585000	0.79938	GAA		0.398	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34935715	G	T	34935715	4	4	61	1	0	0	0	0	0	1	0	0	6379	943	33	2	912	2	GGNBP2	17	34935715	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12181	34935715	46259495	10196	18181										
GGNBP2	79893	broad.mit.edu	37	chr17	34941781	34941781	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctgtggcagcactgaaGatggtaatacttgtgtagaa	12	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:34941781G>A	ENST00000304718.4	+	10	1583	c.1267G>A	c.(1267-1269)Gat>Aat	p.D423N		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	423					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.D423N(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CAGCACTGAAGATGGTAATAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	17											104	107	106					17																	34941781		2203	4300	6503	32015894	SO:0001583	missense	79893			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1267G>A	17.37:g.34941781G>A	ENSP00000307617:p.Asp423Asn		32015894	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	37	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.291464	0.80914	.	.	ENSG00000005955	ENST00000304718	.	.	.	6.17	6.17	0.99709	.	0.090226	0.85682	D	0.000000	T	0.38719	0.1051	N	0.14661	0.345	0.80722	D	1	P;B;B	0.39480	0.675;0.241;0.13	B;B;B	0.35550	0.205;0.094;0.071	T	0.29427	-1.0012	9	0.44086	T	0.13	-23.2201	19.0599	0.93085	0.0:0.0:1.0:0.0	.	423;423;423	A8K3S2;Q9H3C7;Q9H3C7-3	.;GGNB2_HUMAN;.	N	423	.	ENSP00000307617:D423N	D	+	1	0	GGNBP2	32015894	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.383000	0.79741	2.941000	0.99782	0.655000	0.94253	GAT		0.393	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		A	34941781	G	A	34941781	3	1	61	1	0	0	0	0	1	0	0	0	6379	942	33	3	1301	3	GGNBP2	17	34941781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6066	34941781	46253429	10197	18182										
ACACA	31	broad.mit.edu	37	chr17	35518742	35518742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccacatgaaacatatggcGaatttcttctgccagtccga	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:35518742G>A	ENST00000394406.2	-	42	5381	c.5191C>T	c.(5191-5193)Cgc>Tgc	p.R1731C	ACACA_ENST00000353139.5_Missense_Mutation_p.R1768C|ACACA_ENST00000360679.3_Missense_Mutation_p.R1673C|ACACA_ENST00000335166.5_Missense_Mutation_p.R1653C|ACACA_ENST00000361253.5_5'UTR	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1731	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.R1673C(2)|p.R1768C(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AACATATGGCGAATTTCTTCT	0.448																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											3	Substitution - Missense(3)	large_intestine(3)	17											184	146	159					17																	35518742		2203	4300	6503	32592855	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5191C>T	17.37:g.35518742G>A	ENSP00000377928:p.Arg1731Cys		32592855	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141556	0.77775	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330	D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42	5.01	5.01	0.66863	Carboxyl transferase (1);Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98105	0.9375	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.995;0.994	D;D;P;P	0.66847	0.921;0.947;0.892;0.827	D	0.98839	1.0754	10	0.62326	D	0.03	-8.6175	18.692	0.91586	0.0:0.0:1.0:0.0	.	430;1768;1731;1673	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	C	1768;1673;1731;1755;1653;430	ENSP00000344789:R1768C;ENSP00000353898:R1673C;ENSP00000377928:R1731C;ENSP00000335323:R1653C	ENSP00000335323:R1653C	R	-	1	0	ACACA	32592855	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.447000	0.52936	2.488000	0.83962	0.467000	0.42956	CGC		0.448	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35518742	G	A	35518742	3	1	61	1	0	0	0	0	1	0	0	0	106	1058	37	1	1909	1	ACACA	17	35518742	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	576961	35518742	45676468	10198	18183										
ACACA	31	broad.mit.edu	37	chr17	35581989	35581989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagactctacttggttatggCgaagctcatatgatggcaaa	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:35581989C>T	ENST00000394406.2	-	27	3477	c.3287G>A	c.(3286-3288)cGc>cAc	p.R1096H	ACACA_ENST00000353139.5_Missense_Mutation_p.R1133H|ACACA_ENST00000360679.3_Missense_Mutation_p.R1038H|ACACA_ENST00000335166.5_Missense_Mutation_p.R1018H	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1096					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.R1038H(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTGGTTATGGCGAAGCTCATA	0.368																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											1	Substitution - Missense(1)	large_intestine(1)	17											106	97	100					17																	35581989		2203	4300	6503	32656102	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3287G>A	17.37:g.35581989C>T	ENSP00000377928:p.Arg1096His		32656102	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678160	0.88542	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.95	5.95	0.96441	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	D	0.93625	0.7964	M	0.92604	3.325	0.80722	D	1	D;D;D	0.89917	0.986;0.999;1.0	D;D;D	0.73380	0.919;0.973;0.98	D	0.94193	0.7443	10	0.87932	D	0	-2.0597	20.3932	0.98965	0.0:1.0:0.0:0.0	.	1133;1096;1038	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	H	1133;1038;1096;1120;1018	ENSP00000344789:R1133H;ENSP00000353898:R1038H;ENSP00000377928:R1096H;ENSP00000335323:R1018H	ENSP00000335323:R1018H	R	-	2	0	ACACA	32656102	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.770000	0.85390	2.824000	0.97209	0.655000	0.94253	CGC		0.368	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35581989	C	T	35581989	3	4	61	1	0	0	0	0	1	0	0	0	106	768	27	1	3873	1	ACACA	17	35581989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63247	35581989	45613221	10199	18184										
DDX52	11056	broad.mit.edu	37	chr17	35984404	35984404	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatacctttttaacaagttCtctcatggccagaagttttc	5	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:35984404C>A	ENST00000349699.2	-	9	1256	c.1213G>T	c.(1213-1215)Gaa>Taa	p.E405*	DDX52_ENST00000394367.3_Nonsense_Mutation_p.E297*	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	405	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.E405*(1)		biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				TTAACAAGTTCTCTCATGGCC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											99	98	98					17																	35984404		2203	4300	6503	33058517	SO:0001587	stop_gained	11056			AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"DEAD-boxes"	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.1213G>T	17.37:g.35984404C>A	ENSP00000268854:p.Glu405*		33058517	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Nonsense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	C	41	8.677848	0.98912	.	.	ENSG00000141141	ENST00000349699;ENST00000394367	.	.	.	5.8	3.78	0.43462	.	0.321948	0.36703	N	0.002458	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-17.8479	10.7204	0.46036	0.0:0.7966:0.1324:0.071	.	.	.	.	X	405;297	.	ENSP00000268854:E405X	E	-	1	0	DDX52	33058517	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.000000	0.63940	0.770000	0.33336	0.650000	0.86243	GAA		0.378	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		A	35984404	C	A	35984404	4	1	61	1	0	0	0	0	0	1	0	0	4376	922	32	2	614	2	DDX52	17	35984404	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402415	35984404	45210806	10200	18185										
HNF1B	6928	broad.mit.edu	37	chr17	36064986	36064986	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttttgagattgctggggaTtatggtgggagaggctgtgg	20	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36064986T>G	ENST00000225893.4	-	6	1638	c.1277A>C	c.(1276-1278)aAt>aCt	p.N426T	HNF1B_ENST00000561193.1_Missense_Mutation_p.N400T|HNF1B_ENST00000560016.1_Missense_Mutation_p.N426T|HNF1B_ENST00000427275.2_Missense_Mutation_p.N400T	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	426					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.N426T(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			TTGCTGGGGATTATGGTGGGA	0.478																																					Colon(71;102 1179 9001 27917 43397)											1	Substitution - Missense(1)	large_intestine(1)	17											189	180	183					17																	36064986		2203	4300	6503	33139099	SO:0001583	missense	6928			BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1277A>C	17.37:g.36064986T>G	ENSP00000225893:p.Asn426Thr		33139099	B4DKM3|E0YMJ9	Missense_Mutation	SNP	ENST00000225893.4	37	CCDS11324.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.64|11.64	1.697789|1.697789	0.30142|0.30142	.|.	.|.	ENSG00000108753|ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000539087|ENST00000544593	D;D|.	0.97041|.	-4.22;-4.22|.	5.6|5.6	5.6|5.6	0.85130|0.85130	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);|.	0.196474|.	0.53938|.	D|.	0.000051|.	T|.	0.63616|.	0.2526|.	L|L	0.51422|0.51422	1.61|1.61	0.37002|0.37002	D|D	0.895322|0.895322	B;B|.	0.28178|.	0.146;0.202|.	B;B|.	0.36766|.	0.232;0.183|.	T|.	0.66960|.	-0.5791|.	10|.	0.24483|.	T|.	0.36|.	-10.5811|-10.5811	14.969|14.969	0.71217|0.71217	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	400;426|.	E0YMJ6;P35680|.	.;HNF1B_HUMAN|.	T|Y	426;400;314|426	ENSP00000225893:N426T;ENSP00000412212:N400T|.	ENSP00000225893:N426T|.	N|X	-|-	2|3	0|2	HNF1B|HNF1B	33139099|33139099	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.986000|0.986000	0.74619|0.74619	2.659000|2.659000	0.46741|0.46741	2.133000|2.133000	0.65898|0.65898	0.533000|0.533000	0.62120|0.62120	AAT|TAA		0.478	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		G	36064986	T	G	36064986	3	3	61	1	0	0	0	0	1	0	0	0	7273	1493	52	4	412	4	HNF1B	17	36064986	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	80582	36064986	45130224	10201	18186										
MRPL45	84311	broad.mit.edu	37	chr17	36454459	36454460	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatagttccagtaagaactINSaaaaaacgtttcacacctcc							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36454459_36454460insA	ENST00000312513.5	+	2	272_273	c.111_112insA	c.(112-114)aaafs	p.K38fs		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	38						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)	p.R40fs*10(1)		breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAGTAAGAACTAAAAAACGTTT	0.381																																																1	Insertion - Frameshift(1)	large_intestine(1)	17																																								33707979	SO:0001589	frameshift_variant	84311			BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"Mitochondrial ribosomal proteins / large subunits"	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.117dupA	17.37:g.36454465_36454465dupA	ENSP00000308901:p.Lys38fs		33707978	A1L436|Q6ZMJ5	Frame_Shift_Ins	INS	ENST00000312513.5	37	CCDS11326.1																																																																																				0.381	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351		A	36454460	-	A	36454459	7	5	61	1	0	1	1	0	0	0	0	0	9839	1509	53	0	47	0	MRPL45	17	36454459	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	389473	36454459	44740751	10202	18187										
GPR179	440435	broad.mit.edu	37	chr17	36482770	36482770	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttatttccttctggatCtgtgatttcccattggcaca	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36482770C>A	ENST00000342292.4	-	11	6702	c.6682G>T	c.(6682-6684)Gat>Tat	p.D2228Y	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2228					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D2228Y(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CCTTCTGGATCTGTGATTTCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											104	102	103					17																	36482770		1980	4166	6146	33736296	SO:0001583	missense	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.6682G>T	17.37:g.36482770C>A	ENSP00000345060:p.Asp2228Tyr		33736296		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120025	0.77323	.	.	ENSG00000188888	ENST00000342292	T	0.61158	0.13	4.85	4.85	0.62838	.	0.000000	0.39475	N	0.001357	T	0.72203	0.3431	L	0.57536	1.79	0.49130	D	0.999758	D	0.89917	1.0	D	0.68192	0.956	T	0.75342	-0.3351	10	0.87932	D	0	-16.0563	16.9087	0.86135	0.0:1.0:0.0:0.0	.	2228	Q6PRD1	GP179_HUMAN	Y	2228	ENSP00000345060:D2228Y	ENSP00000345060:D2228Y	D	-	1	0	GPR179	33736296	0.046000	0.20272	1.000000	0.80357	0.990000	0.78478	1.569000	0.36428	2.516000	0.84829	0.460000	0.39030	GAT		0.542	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36482770	C	A	36482770	3	1	61	1	0	0	0	0	1	0	0	0	6694	913	32	2	425	2	GPR179	17	36482770	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28311	36482770	44712440	10203	18188										
GPR179	440435	broad.mit.edu	37	chr17	36483702	36483702	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacctgtctttgggtcttgtCtcaggtcccccttctctgtt	8	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36483702C>A	ENST00000342292.4	-	11	5770	c.5750G>T	c.(5749-5751)aGa>aTa	p.R1917I	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1917					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1917I(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TGGGTCTTGTCTCAGGTCCCC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											78	77	77					17																	36483702		1929	4148	6077	33737228	SO:0001583	missense	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.5750G>T	17.37:g.36483702C>A	ENSP00000345060:p.Arg1917Ile		33737228		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768656	0.49680	.	.	ENSG00000188888	ENST00000342292	T	0.52295	0.67	4.9	-0.548	0.11833	.	0.775586	0.11371	N	0.570869	T	0.30603	0.0770	L	0.36672	1.1	0.09310	N	0.999999	B	0.14805	0.011	B	0.08055	0.003	T	0.26395	-1.0104	10	0.54805	T	0.06	-1.0916	1.5965	0.02665	0.1295:0.2716:0.1654:0.4336	.	1917	Q6PRD1	GP179_HUMAN	I	1917	ENSP00000345060:R1917I	ENSP00000345060:R1917I	R	-	2	0	GPR179	33737228	0.000000	0.05858	0.926000	0.36857	0.612000	0.37316	-1.366000	0.02585	-0.198000	0.10333	0.561000	0.74099	AGA		0.507	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36483702	C	A	36483702	3	1	61	1	0	0	0	0	1	0	0	0	6694	913	32	2	1357	2	GPR179	17	36483702	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	932	36483702	44711508	10204	18189										
GPR179	440435	broad.mit.edu	37	chr17	36484436	36484436	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgacatctggagaagggtTtggggtctctctgtgtcttg	14	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36484436T>G	ENST00000342292.4	-	11	5036	c.5016A>C	c.(5014-5016)caA>caC	p.Q1672H	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1672					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Q1672H(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGAGAAGGGTTTGGGGTCTCT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	113	113					17																	36484436		1944	4148	6092	33737962	SO:0001583	missense	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.5016A>C	17.37:g.36484436T>G	ENSP00000345060:p.Gln1672His		33737962		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.411532	0.42817	.	.	ENSG00000188888	ENST00000342292	T	0.52526	0.66	4.92	2.62	0.31277	.	1.264610	0.05442	N	0.547844	T	0.41373	0.1156	L	0.34521	1.04	0.09310	N	1	P	0.46706	0.883	P	0.44811	0.461	T	0.30909	-0.9962	10	0.54805	T	0.06	-1.7208	5.2746	0.15643	0.1566:0.0874:0.0:0.756	.	1672	Q6PRD1	GP179_HUMAN	H	1672	ENSP00000345060:Q1672H	ENSP00000345060:Q1672H	Q	-	3	2	GPR179	33737962	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.296000	0.08287	0.874000	0.35823	-0.336000	0.08194	CAA		0.562	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			G	36484436	T	G	36484436	3	3	61	1	0	0	0	0	1	0	0	0	6694	1838	64	4	2091	4	GPR179	17	36484436	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	734	36484436	44710774	10205	18190										
GPR179	440435	broad.mit.edu	37	chr17	36485720	36485720	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcagtgacctcccagggGcatacctctgccaccctgtg	10	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36485720G>A	ENST00000342292.4	-	11	3752	c.3732C>T	c.(3730-3732)tgC>tgT	p.C1244C	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1244					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.C1244C(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CCTCCCAGGGGCATACCTCTG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	17											71	76	75					17																	36485720		1947	4156	6103	33739246	SO:0001819	synonymous_variant	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3732C>T	17.37:g.36485720G>A			33739246		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																				0.602	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36485720	G	A	36485720	2	1	61	1	0	0	0	0	0	0	0	1	6694	1195	42	3		3	GPR179	17	36485720	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1284	36485720	44709490	10206	18191										
GPR179	440435	broad.mit.edu	37	chr17	36486506	36486506	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaagttggggctttgtggGgatactgggactggtgccag	18	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36486506G>A	ENST00000342292.4	-	11	2966	c.2946C>T	c.(2944-2946)tcC>tcT	p.S982S	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	982					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S982S(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGCTTTGTGGGGATActggga	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	17											40	43	42					17																	36486506		1980	4162	6142	33740032	SO:0001819	synonymous_variant	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2946C>T	17.37:g.36486506G>A			33740032		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																				0.612	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36486506	G	A	36486506	2	1	61	1	0	0	0	0	0	0	0	1	6694	1219	43	3		3	GPR179	17	36486506	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	786	36486506	44708704	10207	18192										
GPR179	440435	broad.mit.edu	37	chr17	36493059	36493059	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctgccttctgggaacccGaattgcccggtagtctggaa	12	11	3	0	rs149830172	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36493059G>A	ENST00000342292.4	-	4	1049	c.1029C>T	c.(1027-1029)ttC>ttT	p.F343F		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	343					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F343F(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTGGGAACCCGAATTGCCCGG	0.577													G|||	8	0.00159744	0.0061	0	5008	,	,		19139	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17						G		18,4000		0,18,1991	35	37	36		1029	-9	0	17	dbSNP_134	36	0,8342		0,0,4171	no	coding-synonymous	GPR179	NM_001004334.2		0,18,6162	AA,AG,GG		0.0,0.448,0.1456		343/2368	36493059	18,12342	2009	4171	6180	33746585	SO:0001819	synonymous_variant	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.1029C>T	17.37:g.36493059G>A			33746585		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																				0.577	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36493059	G	A	36493059	2	1	61	1	0	0	0	0	0	0	0	1	6694	1049	37	1		1	GPR179	17	36493059	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6553	36493059	44702151	10208	18193										
PSMB3	5691	broad.mit.edu	37	chr17	36909450	36909450	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcatggccatgaaggggaaGaactgtgtggccatcgctgc	15	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:36909450G>T	ENST00000225426.4	+	2	142	c.51G>T	c.(49-51)aaG>aaT	p.K17N	RNU6-866P_ENST00000516469.1_RNA	NM_002795.2	NP_002786.2	P49720	PSB3_HUMAN	proteasome (prosome, macropain) subunit, beta type, 3	17					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)	p.K17N(1)		endometrium(2)|large_intestine(1)|lung(1)	4						TGAAGGGGAAGAACTGTGTGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											48	43	44					17																	36909450		2203	4300	6503	34162976	SO:0001583	missense	5691			BC013008	CCDS11328.1	17q12	2014-05-06			ENSG00000108294	ENSG00000277791		"Proteasome (prosome, macropain) subunits"	9540	protein-coding gene	gene with protein product		602176				7918633	Standard	NM_002795		Approved	HC10-II, MGC4147	uc002hqr.3	P49720	OTTHUMG00000188503	ENST00000225426.4:c.51G>T	17.37:g.36909450G>T	ENSP00000225426:p.Lys17Asn		34162976	P31147|Q0P6J7|Q96E27	Missense_Mutation	SNP	ENST00000225426.4	37	CCDS11328.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775496	0.49786	.	.	ENSG00000108294	ENST00000225426	T	0.49720	0.77	5.63	3.65	0.41850	Proteasome, beta-type subunit, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.50922	0.1644	M	0.79926	2.475	0.80722	D	1	B	0.20368	0.044	B	0.25987	0.065	T	0.51188	-0.8737	10	0.52906	T	0.07	.	11.08	0.48053	0.1513:0.0:0.8487:0.0	.	17	P49720	PSB3_HUMAN	N	17	ENSP00000225426:K17N	ENSP00000225426:K17N	K	+	3	2	PSMB3	34162976	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.161000	0.50747	0.747000	0.32809	-0.291000	0.09656	AAG		0.597	PSMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256810.2	NM_002795		T	36909450	G	T	36909450	3	4	61	1	0	0	0	0	1	0	0	0	12712	933	33	2	57	2	PSMB3	17	36909450	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	416391	36909450	44285760	10209	18194										
FBXO47	494188	broad.mit.edu	37	chr17	37118236	37118236	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgcttcctgatgaggttgaGatataattaataatgtgttg	10	3	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:37118236G>T	ENST00000378079.2	-	3	445	c.246C>A	c.(244-246)atC>atA	p.I82I		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	82	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.							p.I82I(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						ATGAGGTTGAGATATAATTAA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	17											182	176	178					17																	37118236		2203	4300	6503	34371762	SO:0001819	synonymous_variant	494188				CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.246C>A	17.37:g.37118236G>T			34371762	B2RTZ4	Silent	SNP	ENST00000378079.2	37	CCDS32639.1																																																																																				0.388	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		T	37118236	G	T	37118236	2	4	61	1	0	0	0	0	0	0	0	1	5775	932	33	2		2	FBXO47	17	37118236	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208786	37118236	44076974	10210	18195										
ERBB2	2064	broad.mit.edu	37	chr17	37866082	37866082	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggccacccctgttctccGatgtgtaagggctcccgctg	11	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:37866082G>A	ENST00000269571.5	+	5	750	c.591G>A	c.(589-591)ccG>ccA	p.P197P	ERBB2_ENST00000584450.1_Silent_p.P197P|ERBB2_ENST00000540147.1_Silent_p.P167P|ERBB2_ENST00000578199.1_Silent_p.P167P|ERBB2_ENST00000406381.2_Silent_p.P167P|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000541774.1_Silent_p.P182P|ERBB2_ENST00000540042.1_Silent_p.P167P|ERBB2_ENST00000584601.1_Silent_p.P167P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	197					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.P197P(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CCTGTTCTCCGATGTGTAAGG	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	1	Substitution - coding silent(1)	large_intestine(1)	17											84	75	78					17																	37866082		2203	4300	6503	35119608	SO:0001819	synonymous_variant	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.591G>A	17.37:g.37866082G>A			35119608	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																				0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37866082	G	A	37866082	2	1	61	1	0	0	0	0	0	0	0	1	5219	1045	37	1		1	ERBB2	17	37866082	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	747846	37866082	43329128	10211	18196										
ERBB2	2064	broad.mit.edu	37	chr17	37881410	37881410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacagacttcgggctggctCggctgctggacattgacgag	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:37881410C>T	ENST00000269571.5	+	21	2761	c.2602C>T	c.(2602-2604)Cgg>Tgg	p.R868W	ERBB2_ENST00000584450.1_Missense_Mutation_p.R868W|ERBB2_ENST00000540147.1_Missense_Mutation_p.R838W|ERBB2_ENST00000406381.2_Missense_Mutation_p.R838W|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000445658.2_Missense_Mutation_p.R592W|ERBB2_ENST00000541774.1_Missense_Mutation_p.R853W|ERBB2_ENST00000584601.1_Missense_Mutation_p.R838W			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	868	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.R868W(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CGGGCTGGCTCGGCTGCTGGA	0.582		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	1	Substitution - Missense(1)	large_intestine(1)	17											69	70	70					17																	37881410		2203	4300	6503	35134936	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2602C>T	17.37:g.37881410C>T	ENSP00000269571:p.Arg868Trp		35134936	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	12.75	2.031576	0.35797	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99	5.09	4.07	0.47477	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.95037	0.8393	H	0.97465	4.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.96432	0.9320	9	0.87932	D	0	.	15.8469	0.78899	0.1447:0.8553:0.0:0.0	.	592;853;868	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	W	838;853;592;868;838	ENSP00000385185:R838W;ENSP00000446466:R853W;ENSP00000404047:R592W;ENSP00000269571:R868W;ENSP00000443562:R838W	ENSP00000269571:R868W	R	+	1	2	ERBB2	35134936	0.016000	0.18221	1.000000	0.80357	0.979000	0.70002	0.296000	0.19083	2.651000	0.90000	0.563000	0.77884	CGG		0.582	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37881410	C	T	37881410	3	4	61	1	0	0	0	0	1	0	0	0	5219	875	31	1	2684	1	ERBB2	17	37881410	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15328	37881410	43313800	10212	18197										
GSDMB	55876	broad.mit.edu	37	chr17	38062192	38062192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgcttaggagaggcttgTctgggtcctccatgtgtagc	15	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38062192T>C	ENST00000394179.1	-	8	1050	c.920A>G	c.(919-921)gAc>gGc	p.D307G	GSDMB_ENST00000309481.7_Missense_Mutation_p.D299G|GSDMB_ENST00000418519.1_Missense_Mutation_p.D312G|GSDMB_ENST00000520542.1_Missense_Mutation_p.D303G|GSDMB_ENST00000360317.3_Missense_Mutation_p.D312G|GSDMB_ENST00000394175.2_Missense_Mutation_p.D290G			Q8TAX9	GSDMB_HUMAN	gasdermin B	307						cytoplasm (GO:0005737)		p.D290G(1)|p.D312G(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						GAGAGGCTTGTCTGGGTCCTC	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	17											70	69	69					17																	38062192		2203	4300	6503	35315718	SO:0001583	missense	55876			AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"gasdermin-like"	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.920A>G	17.37:g.38062192T>C	ENSP00000377733:p.Asp307Gly		35315718	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Missense_Mutation	SNP	ENST00000394179.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.981|6.981	0.551067|0.551067	0.13374|0.13374	.|.	.|.	ENSG00000073605|ENSG00000073605	ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179|ENST00000420491	T;T;T;T;T|.	0.22539|.	1.95;1.95;1.95;1.95;1.95|.	3.9|3.9	-2.39|-2.39	0.06602|0.06602	.|.	2.160190|.	0.02370|.	N|.	0.077800|.	T|T	0.09512|0.09512	0.0234|0.0234	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.25441|.	0.017;0.002;0.126;0.002;0.002|.	B;B;B;B;B|.	0.28916|.	0.026;0.007;0.096;0.004;0.007|.	T|T	0.30909|0.30909	-0.9962|-0.9962	10|5	0.10377|.	T|.	0.69|.	.|.	3.5981|3.5981	0.08014|0.08014	0.2129:0.0:0.2785:0.5086|0.2129:0.0:0.2785:0.5086	.|.	303;312;307;299;290|.	B4DKK7;Q8TAX9-4;Q8TAX9;Q8TAX9-3;Q8TAX9-2|.	.;.;GSDMB_HUMAN;.;.|.	G|A	307;290;299;303;312;307|244	ENSP00000377729:D290G;ENSP00000312584:D299G;ENSP00000430157:D303G;ENSP00000415049:D312G;ENSP00000377733:D307G|.	ENSP00000312584:D299G|.	D|T	-|-	2|1	0|0	GSDMB|GSDMB	35315718|35315718	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.604000|-1.604000	0.02076|0.02076	-0.158000|-0.158000	0.11040|0.11040	-1.016000|-1.016000	0.02456|0.02456	GAC|ACA		0.537	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530		C	38062192	T	C	38062192	3	2	61	1	0	0	0	0	1	0	0	0	6838	1667	58	4	327	4	GSDMB	17	38062192	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	180782	38062192	43133018	10213	18198										
GSDMA	284110	broad.mit.edu	37	chr17	38130558	38130558	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcttcaggacactaaaaGaagaagttcagagagagacc	11	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38130558G>T	ENST00000301659.4	+	9	902	c.784G>T	c.(784-786)Gaa>Taa	p.E262*		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	262					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)		p.E262*(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						GACACTAAAAGAAGAAGTTCA	0.532																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											45	44	44					17																	38130558		1912	4120	6032	35384084	SO:0001587	stop_gained	284110			AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"gasdermin", "gasdermin 1"	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.784G>T	17.37:g.38130558G>T	ENSP00000301659:p.Glu262*		35384084	Q32MC5|Q86VE7|Q8N1M6	Nonsense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866810	0.91511	.	.	ENSG00000167914	ENST00000301659	.	.	.	5.66	3.33	0.38152	.	0.088358	0.48767	D	0.000179	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-14.9412	8.9799	0.35959	0.1947:0.0:0.8053:0.0	.	.	.	.	X	262	.	ENSP00000301659:E262X	E	+	1	0	GSDMA	35384084	1.000000	0.71417	0.983000	0.44433	0.792000	0.44763	1.996000	0.40776	1.400000	0.46741	0.561000	0.74099	GAA		0.532	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		T	38130558	G	T	38130558	4	4	61	1	0	0	0	0	0	1	0	0	6837	943	33	2	814	2	GSDMA	17	38130558	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68366	38130558	43064652	10214	18199										
MED24	9862	broad.mit.edu	37	chr17	38189706	38189706	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctcgatggcagtccaaGaagctggcagagggaaggaa	15	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38189706G>T	ENST00000394128.2	-	7	644	c.563C>A	c.(562-564)tCt>tAt	p.S188Y	MED24_ENST00000479829.1_5'Flank|MED24_ENST00000394126.1_Missense_Mutation_p.S213Y|MED24_ENST00000356271.3_Missense_Mutation_p.S175Y|MED24_ENST00000501516.3_Missense_Mutation_p.S207Y|MED24_ENST00000394127.2_Missense_Mutation_p.S175Y	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	188					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.S188Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GGCAGTCCAAGAAGCTGGCAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											27	23	25					17																	38189706		2203	4300	6503	35443232	SO:0001583	missense	9862			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.563C>A	17.37:g.38189706G>T	ENSP00000377686:p.Ser188Tyr		35443232	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	9.439	1.087521	0.20390	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000535508;ENST00000431269;ENST00000428757	T;T;T;T	0.47528	0.84;0.84;0.84;0.85	5.6	3.58	0.41010	Mediator complex, subunit Med24, N-terminal (1);	0.109442	0.64402	D	0.000005	T	0.59662	0.2210	L	0.54323	1.7	0.49687	D	0.999811	D;P;P;D;P;B;P;P;P	0.64830	0.994;0.921;0.912;0.984;0.763;0.207;0.471;0.527;0.892	D;P;P;D;P;B;B;P;P	0.65874	0.939;0.671;0.757;0.921;0.549;0.074;0.421;0.557;0.518	T	0.59573	-0.7429	10	0.59425	D	0.04	-15.783	11.2392	0.48960	0.0685:0.1278:0.8037:0.0	.	162;175;138;117;138;98;175;188;130	B9TX63;B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;.;MED24_HUMAN;.	Y	188;188;188;138;175;130;162;162;98;207	ENSP00000377686:S188Y;ENSP00000443344:S138Y;ENSP00000377685:S175Y;ENSP00000392276:S207Y	ENSP00000348610:S188Y	S	-	2	0	MED24	35443232	1.000000	0.71417	1.000000	0.80357	0.453000	0.32348	4.723000	0.61965	0.710000	0.31997	0.609000	0.83330	TCT		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38189706	G	T	38189706	3	4	61	1	0	0	0	0	1	0	0	0	9472	942	33	2	2486	2	MED24	17	38189706	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59148	38189706	43005504	10215	18200										
CASC3	22794	broad.mit.edu	37	chr17	38297832	38297832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttatttcagctgttctctCggattatgaaagtgcagaag	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38297832C>T	ENST00000264645.7	+	3	495	c.269C>T	c.(268-270)tCg>tTg	p.S90L		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3	90					gene expression (GO:0010467)|intracellular mRNA localization (GO:0008298)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)	p.S90L(1)		endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	16						GCTGTTCTCTCGGATTATGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	17											191	195	194					17																	38297832		2203	4300	6503	35551358	SO:0001583	missense	22794			X80199	CCDS11362.1	17q21.1	2012-09-20			ENSG00000108349	ENSG00000108349			17040	protein-coding gene	gene with protein product		606504				7490069, 18332872	Standard	NM_007359		Approved	MLN51, BTZ	uc002hue.3	O15234	OTTHUMG00000133323	ENST00000264645.7:c.269C>T	17.37:g.38297832C>T	ENSP00000264645:p.Ser90Leu		35551358	A8K8R0	Missense_Mutation	SNP	ENST00000264645.7	37	CCDS11362.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682075	0.88542	.	.	ENSG00000108349	ENST00000264645;ENST00000418132;ENST00000394114	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	L	0.34521	1.04	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.70227	0.968;0.968	T	0.69041	-0.5250	9	0.87932	D	0	-7.3945	15.5918	0.76537	0.0:1.0:0.0:0.0	.	90;90	B4DKR6;O15234	.;CASC3_HUMAN	L	90	.	ENSP00000264645:S90L	S	+	2	0	CASC3	35551358	0.996000	0.38824	0.992000	0.48379	0.997000	0.91878	4.409000	0.59768	2.660000	0.90430	0.555000	0.69702	TCG		0.353	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359		T	38297832	C	T	38297832	3	4	61	1	0	0	0	0	1	0	0	0	2667	893	31	1	279	1	CASC3	17	38297832	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108126	38297832	42897378	10216	18201										
CDC6	990	broad.mit.edu	37	chr17	38457234	38457234	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatcttggtttgctctttGatgctcttgatcaggcagtt	10	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38457234G>T	ENST00000209728.4	+	10	1875	c.1404G>T	c.(1402-1404)ttG>ttT	p.L468F	CTD-2267D19.6_ENST00000602403.1_lincRNA	NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	468					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)	p.L468F(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						TTTGCTCTTTGATGCTCTTGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											184	153	163					17																	38457234		2203	4300	6503	35710760	SO:0001583	missense	990			U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.1404G>T	17.37:g.38457234G>T	ENSP00000209728:p.Leu468Phe		35710760	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735606	0.69189	.	.	ENSG00000094804	ENST00000209728	T	0.54071	0.59	5.96	1.47	0.22746	Winged helix-turn-helix transcription repressor DNA-binding (1);CDC6, C-terminal (1);	0.070428	0.56097	N	0.000022	T	0.68467	0.3004	M	0.82823	2.61	0.49213	D	0.999765	D	0.89917	1.0	D	0.87578	0.998	T	0.67070	-0.5763	10	0.87932	D	0	-3.8087	6.3112	0.21166	0.0663:0.1157:0.5976:0.2205	.	468	Q99741	CDC6_HUMAN	F	468	ENSP00000209728:L468F	ENSP00000209728:L468F	L	+	3	2	CDC6	35710760	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.975000	0.40569	0.385000	0.24970	0.655000	0.94253	TTG		0.468	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			T	38457234	G	T	38457234	3	4	61	1	0	0	0	0	1	0	0	0	3089	1281	45	2	1438	2	CDC6	17	38457234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	159402	38457234	42737976	10217	18202										
TOP2A	7153	broad.mit.edu	37	chr17	38556217	38556217	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcattcctaggagccattCttttcttaatccataatatt	4	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38556217C>A	ENST00000423485.1	-	24	3261	c.3103G>T	c.(3103-3105)Gaa>Taa	p.E1035*		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1035					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)	p.E1035*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	AGGAGCCATTCTTTTCTTAAT	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											60	58	59					17																	38556217		1824	4062	5886	35809743	SO:0001587	stop_gained	7153				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3103G>T	17.37:g.38556217C>A	ENSP00000411532:p.Glu1035*		35809743	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Nonsense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	C	43	9.875152	0.99285	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	.	.	.	5.41	5.41	0.78517	.	0.092236	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	19.561	0.95373	0.0:1.0:0.0:0.0	.	.	.	.	X	1035;1115;1058;1071	.	ENSP00000269577:E1115X	E	-	1	0	TOP2A	35809743	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.715000	0.84713	2.696000	0.92011	0.655000	0.94253	GAA		0.348	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38556217	C	A	38556217	4	1	61	1	0	0	0	0	0	1	0	0	16405	922	32	2	1540	2	TOP2A	17	38556217	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98983	38556217	42638993	10218	18203										
TOP2A	7153	broad.mit.edu	37	chr17	38569031	38569031	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcagtttatttccattaaGaaagactttgacatctttgg	8	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38569031G>A	ENST00000423485.1	-	7	927	c.769C>T	c.(769-771)Ctt>Ttt	p.L257F		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	257					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)	p.L257F(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TTTCCATTAAGAAAGACTTTG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	17											73	66	68					17																	38569031		1844	4098	5942	35822557	SO:0001583	missense	7153				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.769C>T	17.37:g.38569031G>A	ENSP00000411532:p.Leu257Phe		35822557	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756000	0.49362	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.28255	1.62	5.75	5.75	0.90469	Ribosomal protein S5 domain 2-type fold (1);ATPase-like, ATP-binding domain (2);DNA topoisomerase, type IIA, subunit B/N-terminal (1);	0.056397	0.64402	D	0.000001	T	0.40423	0.1116	M	0.85197	2.74	0.80722	D	1	B	0.23442	0.085	B	0.21360	0.034	T	0.29941	-0.9995	10	0.46703	T	0.11	.	14.1342	0.65276	0.0716:0.0:0.9284:0.0	.	257	P11388	TOP2A_HUMAN	F	257;256;256;259	ENSP00000411532:L257F	ENSP00000269577:L256F	L	-	1	0	TOP2A	35822557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.111000	0.57838	2.707000	0.92482	0.591000	0.81541	CTT		0.353	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38569031	G	A	38569031	3	1	61	1	0	0	0	0	1	0	0	0	16405	942	33	3	3942	3	TOP2A	17	38569031	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12814	38569031	42626179	10219	18204										
CCR7	1236	broad.mit.edu	37	chr17	38711994	38711994	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtccttcttggagcacaaaGactcgaacaaagtgtagtcc	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38711994G>T	ENST00000246657.2	-	3	199	c.137C>A	c.(136-138)tCt>tAt	p.S46Y	CCR7_ENST00000579344.1_Missense_Mutation_p.S40Y	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	46					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)	p.S46Y(1)		breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				GGAGCACAAAGACTCGAACAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											111	93	99					17																	38711994		2203	4300	6503	35965520	SO:0001583	missense	1236				CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.137C>A	17.37:g.38711994G>T	ENSP00000246657:p.Ser46Tyr		35965520		Missense_Mutation	SNP	ENST00000246657.2	37	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.024702	0.00041	.	.	ENSG00000126353	ENST00000246657	T	0.37235	1.21	4.74	3.75	0.43078	.	0.750410	0.12132	N	0.496655	T	0.23410	0.0566	L	0.37850	1.14	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.33163	-0.9879	10	0.02654	T	1	.	8.3128	0.32082	0.0765:0.0:0.6282:0.2952	.	46	P32248	CCR7_HUMAN	Y	46	ENSP00000246657:S46Y	ENSP00000246657:S46Y	S	-	2	0	CCR7	35965520	0.000000	0.05858	0.085000	0.20634	0.118000	0.20060	0.620000	0.24403	1.281000	0.44480	0.561000	0.74099	TCT		0.502	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			T	38711994	G	T	38711994	3	4	61	1	0	0	0	0	1	0	0	0	2952	942	33	2	1003	2	CCR7	17	38711994	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142963	38711994	42483216	10220	18205										
KRT222	125113	broad.mit.edu	37	chr17	38816309	38816309	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagcctcatcttcgtgttgaGaagcatctcgtgctcttgaa	9	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38816309G>T	ENST00000476049.1	-	3	417	c.376C>A	c.(376-378)Ctc>Atc	p.L126I	KRT222_ENST00000394052.3_Missense_Mutation_p.L126I			Q8N1A0	KT222_HUMAN	keratin 222	126						intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.L126I(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1)	15						TTCGTGTTGAGAAGCATCTCG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											281	238	252					17																	38816309		2203	4300	6503	36069835	SO:0001583	missense	125113			AK092967	CCDS11371.1	17q21.2	2013-06-25	2009-08-25	2009-08-25	ENSG00000213424	ENSG00000213424		"-"	28695	protein-coding gene	gene with protein product			"keratin 222 pseudogene"	KRT222P		16831889	Standard	NM_152349		Approved	KA21, MGC45562	uc002hvc.2	Q8N1A0	OTTHUMG00000133374	ENST00000476049.1:c.376C>A	17.37:g.38816309G>T	ENSP00000463483:p.Leu126Ile		36069835	Q7Z368	Missense_Mutation	SNP	ENST00000476049.1	37	CCDS11371.1	.	.	.	.	.	.	.	.	.	.	G	34	5.371441	0.95923	.	.	ENSG00000213424	ENST00000394049;ENST00000394052	D	0.92858	-3.12	5.82	5.82	0.92795	Filament (1);	0.000000	0.64402	U	0.000019	D	0.97263	0.9105	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.97575	1.0107	10	0.87932	D	0	-7.1904	20.1086	0.97902	0.0:0.0:1.0:0.0	.	86;126	Q8N1A0-2;Q8N1A0	.;KT222_HUMAN	I	86;126	ENSP00000377616:L126I	ENSP00000377613:L86I	L	-	1	0	KRT222	36069835	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	9.476000	0.97823	2.756000	0.94617	0.563000	0.77884	CTC		0.443	KRT222-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000447539.1	NM_152349		T	38816309	G	T	38816309	3	4	61	1	0	0	0	0	1	0	0	0	8480	942	33	2	527	2	KRT222	17	38816309	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104315	38816309	42378901	10221	18206										
KRT24	192666	broad.mit.edu	37	chr17	38855782	38855782	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaattgcttgtactctgcGttctggcatttagtctcacc	8	11	3	0	rs139679856		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38855782G>A	ENST00000264651.2	-	6	1331	c.1275C>T	c.(1273-1275)aaC>aaT	p.N425N		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	425	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)	p.N425N(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				TGTACTCTGCGTTCTGGCATT	0.547																																					GBM(61;380 1051 14702 23642 31441)											2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	17						G		1,4405	2.1+/-5.4	0,1,2202	175	170	172		1275	-11.2	0	17	dbSNP_134	172	0,8600		0,0,4300	no	coding-synonymous	KRT24	NM_019016.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		425/526	38855782	1,13005	2203	4300	6503	36109308	SO:0001819	synonymous_variant	192666				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.1275C>T	17.37:g.38855782G>A			36109308	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																				0.547	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		A	38855782	G	A	38855782	2	1	61	1	0	0	0	0	0	0	0	1	8482	1136	40	1		1	KRT24	17	38855782	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39473	38855782	42339428	10222	18207										
KRT24	192666	broad.mit.edu	37	chr17	38857449	38857449	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaactctcaatctgcatCtccaggtcagagcgggtcat	10	11	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38857449C>A	ENST00000264651.2	-	3	854	c.798G>T	c.(796-798)gaG>gaT	p.E266D		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	266	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)	p.E266D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CAATCTGCATCTCCAGGTCAG	0.512																																					GBM(61;380 1051 14702 23642 31441)											1	Substitution - Missense(1)	large_intestine(1)	17											132	114	120					17																	38857449		2203	4300	6503	36110975	SO:0001583	missense	192666				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.798G>T	17.37:g.38857449C>A	ENSP00000264651:p.Glu266Asp		36110975	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.358581	0.41801	.	.	ENSG00000167916	ENST00000264651	D	0.91894	-2.93	5.82	4.85	0.62838	Prefoldin (1);Filament (1);	.	.	.	.	D	0.92100	0.7496	M	0.84326	2.69	0.38771	D	0.954545	B	0.29162	0.235	B	0.32465	0.146	D	0.91930	0.5554	9	0.87932	D	0	.	10.5599	0.45140	0.1345:0.7973:0.0:0.0682	.	266	Q2M2I5	K1C24_HUMAN	D	266	ENSP00000264651:E266D	ENSP00000264651:E266D	E	-	3	2	KRT24	36110975	0.194000	0.23325	1.000000	0.80357	0.380000	0.30137	0.214000	0.17541	1.458000	0.47871	-0.320000	0.08662	GAG		0.512	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		A	38857449	C	A	38857449	3	1	61	1	0	0	0	0	1	0	0	0	8482	912	32	2	803	2	KRT24	17	38857449	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1667	38857449	42337761	10223	18208										
KRT24	192666	broad.mit.edu	37	chr17	38859543	38859543	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttcccctccagagaaaaGccccccatcgccaacaccac	4	20	0	1	rs200550767		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38859543G>T	ENST00000264651.2	-	1	459	c.403C>A	c.(403-405)Ctt>Att	p.L135I		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	135	Gly-rich.|Head.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)	p.L135I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CCAGAGAAAAGCCCCCCATCG	0.532																																					GBM(61;380 1051 14702 23642 31441)											1	Substitution - Missense(1)	large_intestine(1)	17											191	206	201					17																	38859543		2203	4300	6503	36113069	SO:0001583	missense	192666				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.403C>A	17.37:g.38859543G>T	ENSP00000264651:p.Leu135Ile		36113069	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308362	0.60305	.	.	ENSG00000167916	ENST00000264651	D	0.83914	-1.78	5.6	5.6	0.85130	.	.	.	.	.	D	0.82609	0.5074	L	0.52759	1.655	0.33648	D	0.608114	P	0.52577	0.954	P	0.47206	0.541	D	0.87381	0.2357	9	0.52906	T	0.07	.	14.5638	0.68159	0.0:0.1459:0.8541:0.0	.	135	Q2M2I5	K1C24_HUMAN	I	135	ENSP00000264651:L135I	ENSP00000264651:L135I	L	-	1	0	KRT24	36113069	0.991000	0.36638	0.978000	0.43139	0.758000	0.43043	2.927000	0.48900	2.800000	0.96347	0.655000	0.94253	CTT		0.532	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		T	38859543	G	T	38859543	3	4	61	1	0	0	0	0	1	0	0	0	8482	971	34	2	1206	2	KRT24	17	38859543	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2094	38859543	42335667	10224	18209										
KRT27	342574	broad.mit.edu	37	chr17	38938638	38938638	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccaatgcctggcacaccGcatgtgtttccagccccaaa	7	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38938638G>A	ENST00000301656.3	-	1	148	c.108C>T	c.(106-108)tgC>tgT	p.C36C		NM_181537.3	NP_853515.2			keratin 27									p.C36C(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CTGGCACACCGCATGTGTTTC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	17											63	59	60					17																	38938638		2203	4300	6503	36192164	SO:0001819	synonymous_variant	342574			AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.108C>T	17.37:g.38938638G>A			36192164		Silent	SNP	ENST00000301656.3	37	CCDS11375.1																																																																																				0.602	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		A	38938638	G	A	38938638	2	1	61	1	0	0	0	0	0	0	0	1	8485	1079	38	1		1	KRT27	17	38938638	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79095	38938638	42256572	10225	18210										
KRT27	342574	broad.mit.edu	37	chr17	38938741	38938741	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtagaagaaaagcgcacaGacatggtgtccggaggctgg	16	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38938741G>A	ENST00000301656.3	-	1	45	c.5C>T	c.(4-6)tCt>tTt	p.S2F		NM_181537.3	NP_853515.2			keratin 27									p.S2F(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				AAAGCGCACAGACATGGTGTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											28	28	28					17																	38938741		2196	4290	6486	36192267	SO:0001583	missense	342574			AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.5C>T	17.37:g.38938741G>A	ENSP00000301656:p.Ser2Phe		36192267		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.636512	0.67130	.	.	ENSG00000171446	ENST00000301656	D	0.84800	-1.9	5.59	4.61	0.57282	.	0.217541	0.33092	N	0.005295	D	0.93077	0.7796	M	0.88031	2.925	0.45066	D	0.998084	D	0.76494	0.999	D	0.69824	0.966	D	0.94433	0.7651	10	0.87932	D	0	.	15.5062	0.75743	0.0:0.1391:0.8609:0.0	.	2	Q7Z3Y8	K1C27_HUMAN	F	2	ENSP00000301656:S2F	ENSP00000301656:S2F	S	-	2	0	KRT27	36192267	0.998000	0.40836	0.905000	0.35620	0.559000	0.35586	2.647000	0.46639	1.474000	0.48178	0.655000	0.94253	TCT		0.532	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		A	38938741	G	A	38938741	3	1	61	1	0	0	0	0	1	0	0	0	8485	942	33	3	1406	3	KRT27	17	38938741	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103	38938741	42256469	10226	18211										
KRT10	3858	broad.mit.edu	37	chr17	38978478	38978478	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccgcctccaccaaagccGcctccaccaaagctgccccc	6	22	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:38978478G>A	ENST00000269576.5	-	1	369	c.360C>T	c.(358-360)ggC>ggT	p.G120G	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	120	Gly-rich.|Head.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)	p.G120G(1)		NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				caCCAAAGCCGCCTCCACCAA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	17											53	47	49					17																	38978478		2203	4300	6503	36232004	SO:0001819	synonymous_variant	3858			J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.360C>T	17.37:g.38978478G>A			36232004	Q14664|Q8N175	Silent	SNP	ENST00000269576.5	37	CCDS11377.1																																																																																				0.542	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		A	38978478	G	A	38978478	2	1	61	1	0	0	0	0	0	0	0	1	8469	1074	38	1		1	KRT10	17	38978478	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	39737	38978478	42216732	10227	18212										
KRT12	3859	broad.mit.edu	37	chr17	39019473	39019473	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtggtccacgttctggcgCtctgcgtccgcgcgcacctg	14	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39019473C>A	ENST00000251643.4	-	6	1241	c.1218G>T	c.(1216-1218)gaG>gaT	p.E406D	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	406	Coil 2.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.E406D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	CGTTCTGGCGCTCTGCGTCCG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	17											25	23	24					17																	39019473		2200	4292	6492	36272999	SO:0001583	missense	3859				CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"-", "Intermediate filaments type I, keratins (acidic)"	6414	protein-coding gene	gene with protein product	"Meesmann corneal dystrophy"	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.1218G>T	17.37:g.39019473C>A	ENSP00000251643:p.Glu406Asp		36272999	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367067	0.61513	.	.	ENSG00000187242	ENST00000251643	D	0.89939	-2.59	5.05	4.09	0.47781	Filament (1);	0.000000	0.51477	D	0.000086	D	0.94703	0.8291	M	0.92317	3.295	0.41466	D	0.988079	D	0.89917	1.0	D	0.73708	0.981	D	0.94660	0.7847	10	0.87932	D	0	.	8.4926	0.33108	0.0:0.7682:0.0:0.2318	.	406	Q99456	K1C12_HUMAN	D	406	ENSP00000251643:E406D	ENSP00000251643:E406D	E	-	3	2	KRT12	36272999	0.942000	0.31987	1.000000	0.80357	0.500000	0.33767	0.869000	0.27996	1.381000	0.46364	-0.333000	0.08304	GAG		0.672	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		A	39019473	C	A	39019473	3	1	61	1	0	0	0	0	1	0	0	0	8470	796	28	2	278	2	KRT12	17	39019473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40995	39019473	42175737	10228	18213										
KRT20	54474	broad.mit.edu	37	chr17	39041055	39041055	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcatctctcacctgacttCgcagctcttcaatttgtctg	5	14	6	1	rs201355464		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39041055C>T	ENST00000167588.3	-	1	424	c.383G>A	c.(382-384)cGa>cAa	p.R128Q		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	128	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.R128Q(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				CACCTGACTTCGCAGCTCTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	17											87	85	86					17																	39041055		2203	4300	6503	36294581	SO:0001583	missense	54474			BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.383G>A	17.37:g.39041055C>T	ENSP00000167588:p.Arg128Gln		36294581	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	C	6.952	0.545479	0.13312	.	.	ENSG00000171431	ENST00000167588	D	0.92595	-3.07	5.5	-2.14	0.07123	Filament (1);	0.360696	0.23393	N	0.048673	T	0.80116	0.4564	N	0.13299	0.325	0.09310	N	0.999995	B	0.17465	0.022	B	0.11329	0.006	T	0.62835	-0.6770	10	0.02654	T	1	.	14.3822	0.66919	0.0:0.5352:0.0:0.4648	.	128	P35900	K1C20_HUMAN	Q	128	ENSP00000167588:R128Q	ENSP00000167588:R128Q	R	-	2	0	KRT20	36294581	0.000000	0.05858	0.034000	0.17996	0.049000	0.14656	-0.815000	0.04481	-0.436000	0.07254	-0.302000	0.09304	CGA		0.438	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			T	39041055	C	T	39041055	3	4	61	1	0	0	0	0	1	0	0	0	8479	884	31	1	923	1	KRT20	17	39041055	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21582	39041055	42154155	10229	18214										
KRT33B	3884	broad.mit.edu	37	chr17	39525698	39525698	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgaagtaggactggtagCtggggcacagcaagggctcc	15	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39525698C>A	ENST00000251646.3	-	1	354	c.305G>T	c.(304-306)aGc>aTc	p.S102I		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	102	Linker 1.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.S102I(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GGACTGGTAGCTGGGGCACAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											70	69	69					17																	39525698		2192	4300	6492	36779224	SO:0001583	missense	3884			X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"-", "Intermediate filaments type I, keratins (acidic)"	6451	protein-coding gene	gene with protein product	"hard keratin type I 3II"	602762	"keratin, hair, acidic, 3B"	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.305G>T	17.37:g.39525698C>A	ENSP00000251646:p.Ser102Ile		36779224	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	10.69	1.422208	0.25639	.	.	ENSG00000131738	ENST00000251646	D	0.87491	-2.26	4.41	-5.8	0.02347	Filament (1);	0.912119	0.09416	N	0.805060	T	0.71660	0.3366	N	0.04018	-0.295	0.19775	N	0.999954	B	0.26041	0.14	B	0.35073	0.195	T	0.64313	-0.6437	10	0.87932	D	0	.	7.5342	0.27700	0.0:0.5556:0.1544:0.29	.	102	Q14525	KT33B_HUMAN	I	102	ENSP00000251646:S102I	ENSP00000251646:S102I	S	-	2	0	KRT33B	36779224	0.987000	0.35691	0.023000	0.16930	0.211000	0.24417	2.075000	0.41538	-0.986000	0.03498	-0.355000	0.07637	AGC		0.562	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		A	39525698	C	A	39525698	3	1	61	1	0	0	0	0	1	0	0	0	8491	797	28	2	937	2	KRT33B	17	39525698	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	484643	39525698	41669512	10230	18215										
KRT31	3881	broad.mit.edu	37	chr17	39553543	39553543	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccggatgaggttctccagCtccgcgttgtcccgctccag	11	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39553543C>T	ENST00000251645.2	-	1	301	c.249G>A	c.(247-249)gaG>gaA	p.E83E		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	83	Coil 1A.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.E83E(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				GGTTCTCCAGCTCCGCGTTGT	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	17											73	70	71					17																	39553543		2203	4299	6502	36807069	SO:0001819	synonymous_variant	3881			X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"-", "Intermediate filaments type I, keratins (acidic)"	6448	protein-coding gene	gene with protein product	"hard keratin type I 1"	601077	"keratin, hair, acidic, 1"	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.249G>A	17.37:g.39553543C>T			36807069	Q9UE12	Silent	SNP	ENST00000251645.2	37	CCDS11391.1																																																																																				0.582	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		T	39553543	C	T	39553543	2	4	61	1	0	0	0	0	0	0	0	1	8488	796	28	3		3	KRT31	17	39553543	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27845	39553543	41641667	10231	18216										
KRT37	8688	broad.mit.edu	37	chr17	39577188	39577188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccggtgacagggccacagCttggacaagaagtacaggag	14	10	0	2	rs138529350	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39577188C>T	ENST00000225550.3	-	7	1291	c.1292G>A	c.(1291-1293)aGc>aAc	p.S431N	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	431	Tail.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.S431N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				AGGGCCACAGCTTGGACAAGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											70	72	71					17																	39577188		2203	4300	6503	36830714	SO:0001583	missense	8688			Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.1292G>A	17.37:g.39577188C>T	ENSP00000225550:p.Ser431Asn		36830714		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040958	0.35989	.	.	ENSG00000108417	ENST00000225550	D	0.82619	-1.63	5.38	2.2	0.27929	.	0.733893	0.12169	N	0.493188	T	0.64940	0.2644	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.56062	-0.8041	10	0.59425	D	0.04	.	5.975	0.19373	0.0:0.6693:0.1551:0.1756	.	431	O76014	KRT37_HUMAN	N	431	ENSP00000225550:S431N	ENSP00000225550:S431N	S	-	2	0	KRT37	36830714	0.001000	0.12720	0.003000	0.11579	0.037000	0.13140	0.095000	0.15127	0.626000	0.30322	0.655000	0.94253	AGC		0.542	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39577188	C	T	39577188	3	4	61	1	0	0	0	0	1	0	0	0	8495	797	28	3	61	3	KRT37	17	39577188	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23645	39577188	41618022	10232	18217										
KRT35	3886	broad.mit.edu	37	chr17	39635611	39635611	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctcacctcctcatggttCttcttcaggcagagcagctc	8	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39635611C>A	ENST00000393989.1	-	3	741	c.699G>T	c.(697-699)aaG>aaT	p.K233N	KRT35_ENST00000246639.2_Missense_Mutation_p.K203N	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	233	Coil 1B.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.K233N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				ccTCATGGTTCTTCTTCAGGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											95	91	93					17																	39635611		2203	4300	6503	36889137	SO:0001583	missense	3886			X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.699G>T	17.37:g.39635611C>A	ENSP00000377558:p.Lys233Asn		36889137	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049501	0.36181	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.89617	-2.54;-2.54	4.47	3.5	0.40072	Filament (1);	0.110120	0.40728	N	0.001021	D	0.86896	0.6043	M	0.66378	2.025	0.44092	D	0.996851	B	0.26935	0.164	B	0.30716	0.119	D	0.85181	0.1004	10	0.66056	D	0.02	.	9.3103	0.37900	0.0:0.7721:0.1453:0.0826	.	233	Q92764	KRT35_HUMAN	N	203;233	ENSP00000246639:K203N;ENSP00000377558:K233N	ENSP00000246639:K203N	K	-	3	2	KRT35	36889137	1.000000	0.71417	1.000000	0.80357	0.047000	0.14425	1.258000	0.32944	1.220000	0.43490	-0.140000	0.14226	AAG		0.597	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		A	39635611	C	A	39635611	3	1	61	1	0	0	0	0	1	0	0	0	8493	912	32	2	688	2	KRT35	17	39635611	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58423	39635611	41559599	10233	18218										
KRT14	3861	broad.mit.edu	37	chr17	39742613	39742613	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagggactgtagtctttgatCtcagcaggccgctgcctctg	12	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39742613C>A	ENST00000167586.6	-	1	560	c.474G>T	c.(472-474)gaG>gaT	p.E158D		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	158	Linker 1.|Rod.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)	p.E158D(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				AGTCTTTGATCTCAGCAGGCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											167	159	162					17																	39742613		2203	4300	6503	36996139	SO:0001583	missense	3861			BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"-", "Intermediate filaments type I, keratins (acidic)"	6416	protein-coding gene	gene with protein product	"epidermolysis bullosa simplex, Dowling-Meara, Koebner"	148066	"keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.474G>T	17.37:g.39742613C>A	ENSP00000167586:p.Glu158Asp		36996139	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	.	.	.	.	.	.	.	.	.	.	C	3.758	-0.050198	0.07407	.	.	ENSG00000186847	ENST00000167586	D	0.92397	-3.03	4.95	0.316	0.15857	Filament (1);	0.000000	0.53938	D	0.000044	D	0.84442	0.5473	N	0.17800	0.525	0.09310	N	1	P	0.36048	0.534	P	0.47376	0.545	T	0.73023	-0.4113	10	0.15066	T	0.55	.	1.446	0.02365	0.1452:0.3347:0.1259:0.3942	.	158	P02533	K1C14_HUMAN	D	158	ENSP00000167586:E158D	ENSP00000167586:E158D	E	-	3	2	KRT14	36996139	0.000000	0.05858	0.089000	0.20774	0.014000	0.08584	-1.989000	0.01480	0.226000	0.20979	-0.275000	0.10095	GAG		0.582	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526		A	39742613	C	A	39742613	3	1	61	1	0	0	0	0	1	0	0	0	8472	912	32	2	976	2	KRT14	17	39742613	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	107002	39742613	41452597	10234	18219										
KRT14	3861	broad.mit.edu	37	chr17	39742717	39742717	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtaggaggccaggcggtCattgaggttctgcatggtca	16	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39742717C>T	ENST00000167586.6	-	1	456	c.370G>A	c.(370-372)Gac>Aac	p.D124N		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	124	Coil 1A.|Rod.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)	p.D124N(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				GCCAGGCGGTCATTGAGGTTC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											140	147	145					17																	39742717		2203	4297	6500	36996243	SO:0001583	missense	3861			BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"-", "Intermediate filaments type I, keratins (acidic)"	6416	protein-coding gene	gene with protein product	"epidermolysis bullosa simplex, Dowling-Meara, Koebner"	148066	"keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.370G>A	17.37:g.39742717C>T	ENSP00000167586:p.Asp124Asn		36996243	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970226	0.92855	.	.	ENSG00000186847	ENST00000167586	D	0.91945	-2.94	5.11	5.11	0.69529	Filament (1);	0.000000	0.56097	D	0.000024	D	0.95554	0.8555	M	0.74389	2.26	0.52501	D	0.999959	D	0.59357	0.985	D	0.63381	0.914	D	0.95755	0.8795	10	0.66056	D	0.02	.	18.9	0.92439	0.0:1.0:0.0:0.0	.	124	P02533	K1C14_HUMAN	N	124	ENSP00000167586:D124N	ENSP00000167586:D124N	D	-	1	0	KRT14	36996243	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	6.017000	0.70805	2.541000	0.85698	0.549000	0.68633	GAC		0.617	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526		T	39742717	C	T	39742717	3	4	61	1	0	0	0	0	1	0	0	0	8472	826	29	3	1080	3	KRT14	17	39742717	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104	39742717	41452493	10235	18220										
SC65	10609	broad.mit.edu	37	chr17	39967251	39967251	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgctgctgcggaaatccccGctgttgtagagcttcacagc	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:39967251G>A	ENST00000355468.3	-	4	1117	c.651C>T	c.(649-651)agC>agT	p.S217S	LEPREL4_ENST00000393928.1_Silent_p.S217S|FKBP10_ENST00000321562.4_5'Flank			Q92791	SC65_HUMAN	leprecan-like 4	217					synaptonemal complex assembly (GO:0007130)	condensed nuclear chromosome (GO:0000794)|nucleolus (GO:0005730)|synaptonemal complex (GO:0000795)		p.S217S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						GGAAATCCCCGCTGTTGTAGA	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	17											46	46	46					17																	39967251		2203	4300	6503	37220777	SO:0001819	synonymous_variant	10609			BC001047	CCDS11408.1	17q12	2013-05-03	2002-08-29		ENSG00000141696	ENSG00000141696			16946	protein-coding gene	gene with protein product			"nucleolar autoantigen (55kD)", "rat synaptonemal complex protein"			8862517	Standard	NM_006455		Approved	SC65, NO55	uc002hxt.3	Q92791	OTTHUMG00000133501	ENST00000355468.3:c.651C>T	17.37:g.39967251G>A			37220777	Q53GI6|Q9H4F6	Silent	SNP	ENST00000355468.3	37	CCDS11408.1																																																																																				0.662	LEPREL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257439.2			A	39967251	G	A	39967251	2	1	61	1	0	0	0	0	0	0	0	1	13904	1078	38	1		1	SC65	17	39967251	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	224534	39967251	41227959	10236	18221										
KLHL10	317719	broad.mit.edu	37	chr17	40001553	40001553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacccactcaccagaccacGcttgccctatgccatcctct	4	20	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40001553G>A	ENST00000293303.4	+	3	1013	c.860G>A	c.(859-861)cGc>cAc	p.R287H		NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	287					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)		p.R287H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				ACCAGACCACGCTTGCCCTAT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											139	129	133					17																	40001553		2020	4170	6190	37255079	SO:0001583	missense	317719			AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.860G>A	17.37:g.40001553G>A	ENSP00000293303:p.Arg287His		37255079	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	37	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077421	0.94000	.	.	ENSG00000161594	ENST00000293303	T	0.73897	-0.79	6.17	6.17	0.99709	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.88314	0.6403	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.87747	0.2589	9	.	.	.	.	19.4432	0.94831	0.0:0.0:1.0:0.0	.	281;287	B4DXV2;Q6JEL2	.;KLH10_HUMAN	H	287	ENSP00000293303:R287H	.	R	+	2	0	KLHL10	37255079	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.901000	0.92560	2.941000	0.99782	0.655000	0.94253	CGC		0.507	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		A	40001553	G	A	40001553	3	1	61	1	0	0	0	0	1	0	0	0	8387	1087	38	1	870	1	KLHL10	17	40001553	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34302	40001553	41193657	10237	18222										
TTC25	1267	broad.mit.edu	37	chr17	40117342	40117342	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccttcgggagaattagaGcaaagactctcaggagaatt	12	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40117342G>T	ENST00000393892.3	+	0	0				CNP_ENST00000472031.1_5'Flank|CNP_ENST00000393888.1_5'Flank|TTC25_ENST00000591658.1_RNA|CNP_ENST00000591072.1_5'Flank	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase						adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)	p.E620D(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		GAGAATTAGAGCAAAGACTCT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											51	49	50					17																	40117342		1838	4085	5923	37370868	SO:0001631	upstream_gene_variant	83538				CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502		17.37:g.40117342G>T	Exception_encountered		37370868		Missense_Mutation	SNP	ENST00000393892.3	37	CCDS11414.2																																																																																				0.443	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2			T	40117342	G	T	40117342	1	4	61	0	1	0	0	0	0	0	0	0	16733	962	34	2		2	TTC25	17	40117342	5'Flank	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115789	40117342	41077868	10238	18223										
DNAJC7	7266	broad.mit.edu	37	chr17	40141444	40141444	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaggcaatgcaggccttcTcgtggtcaggagccatcctg	13	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40141444T>C	ENST00000457167.4	-	7	967	c.731A>G	c.(730-732)gAg>gGg	p.E244G	DNAJC7_ENST00000316603.7_Missense_Mutation_p.E188G|DNAJC7_ENST00000426588.3_Missense_Mutation_p.E188G	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	244					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)	p.E234G(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				GCAGGCCTTCTCGTGGTCAGG	0.463																																					Colon(63;618 1117 8600 10857 19751)											1	Substitution - Missense(1)	large_intestine(1)	17											130	122	125					17																	40141444		1901	4127	6028	37394970	SO:0001583	missense	7266			U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"Heat shock proteins / DNAJ (HSP40)", "Tetratricopeptide (TTC) repeat domain containing"	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.731A>G	17.37:g.40141444T>C	ENSP00000406463:p.Glu244Gly		37394970	Q7Z784	Missense_Mutation	SNP	ENST00000457167.4	37	CCDS45677.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.502972	0.64298	.	.	ENSG00000168259	ENST00000457167;ENST00000426588;ENST00000316603	T;T;T	0.75589	-0.79;-0.95;-0.95	5.57	5.57	0.84162	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.162995	0.56097	D	0.000029	T	0.63640	0.2528	N	0.25286	0.73	0.80722	D	1	B;B;B	0.23591	0.002;0.016;0.088	B;B;B	0.20184	0.004;0.01;0.028	T	0.61753	-0.6998	10	0.52906	T	0.07	-2.9185	15.7362	0.77846	0.0:0.0:0.0:1.0	.	233;188;244	Q59EH7;Q7Z784;Q99615	.;.;DNJC7_HUMAN	G	244;188;188	ENSP00000406463:E244G;ENSP00000394327:E188G;ENSP00000313311:E188G	ENSP00000313311:E188G	E	-	2	0	DNAJC7	37394970	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	7.698000	0.84413	2.135000	0.66039	0.379000	0.24179	GAG		0.463	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2			C	40141444	T	C	40141444	3	2	61	1	0	0	0	0	1	0	0	0	4665	1551	54	4	785	4	DNAJC7	17	40141444	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24102	40141444	41053766	10239	18224										
DNAJC7	7266	broad.mit.edu	37	chr17	40152539	40152539	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attataagcttcattgtaatCtttcttggcatagtatgcat	6	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40152539C>A	ENST00000457167.4	-	2	363	c.127G>T	c.(127-129)Gat>Tat	p.D43Y	DNAJC7_ENST00000589547.1_5'Flank|DNAJC7_ENST00000316603.7_Intron|DNAJC7_ENST00000426588.3_5'UTR	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	43					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)	p.D33Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				TCATTGTAATCTTTCTTGGCA	0.318																																					Colon(63;618 1117 8600 10857 19751)											1	Substitution - Missense(1)	large_intestine(1)	17											163	156	158					17																	40152539		1828	4089	5917	37406065	SO:0001583	missense	7266			U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"Heat shock proteins / DNAJ (HSP40)", "Tetratricopeptide (TTC) repeat domain containing"	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.127G>T	17.37:g.40152539C>A	ENSP00000406463:p.Asp43Tyr		37406065	Q7Z784	Missense_Mutation	SNP	ENST00000457167.4	37	CCDS45677.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.793539	0.90453	.	.	ENSG00000168259	ENST00000457167	T	0.62639	0.01	5.28	5.28	0.74379	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.79839	0.4515	M	0.83483	2.645	0.80722	D	1	P	0.48407	0.91	P	0.60345	0.873	T	0.80897	-0.1177	10	0.51188	T	0.08	-0.9045	18.8546	0.92246	0.0:1.0:0.0:0.0	.	43	Q99615	DNJC7_HUMAN	Y	43	ENSP00000406463:D43Y	ENSP00000406463:D43Y	D	-	1	0	DNAJC7	37406065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.429000	0.66495	2.628000	0.89032	0.650000	0.86243	GAT		0.318	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2			A	40152539	C	A	40152539	3	1	61	1	0	0	0	0	1	0	0	0	4665	913	32	2	1409	2	DNAJC7	17	40152539	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11095	40152539	41042671	10240	18225										
GHDC	84514	broad.mit.edu	37	chr17	40344535	40344535	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagaaaacatccagaagttCgacagccgtcccagcctcca	7	15	0	2	rs148046976		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40344535C>T	ENST00000301671.8	-	4	1054	c.613G>A	c.(613-615)Gaa>Aaa	p.E205K	GHDC_ENST00000593209.1_Missense_Mutation_p.E205K|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000587427.1_Missense_Mutation_p.E205K|GHDC_ENST00000428494.2_Missense_Mutation_p.E166K|GHDC_ENST00000436923.2_Missense_Mutation_p.E205K|GHDC_ENST00000414034.3_Missense_Mutation_p.E205K			Q8N2G8	GHDC_HUMAN	GH3 domain containing	205						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E205K(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		TCCAGAAGTTCGACAGCCGTC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4404		0,0,2202	68	79	75		496,613,613	4.5	0.9	17	dbSNP_134	75	1,8591		0,1,4295	no	missense,missense,missense	GHDC	NM_001142622.1,NM_001142623.1,NM_032484.4	56,56,56	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	166/492,205/475,205/531	40344535	1,12995	2202	4296	6498	37598061	SO:0001583	missense	84514			AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.613G>A	17.37:g.40344535C>T	ENSP00000301671:p.Glu205Lys		37598061	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	37	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.427469	0.43122	0.0	1.16E-4	ENSG00000167925	ENST00000393854;ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.52	4.52	0.55395	.	0.190342	0.34777	N	0.003686	T	0.58581	0.2132	M	0.63428	1.95	0.31209	N	0.698871	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.83275	0.967;0.9;0.996	T	0.55321	-0.8159	9	0.06757	T	0.87	-11.8629	11.497	0.50415	0.1786:0.8213:0.0:0.0	.	166;205;205	E9PDB5;Q8N2G8-2;Q8N2G8	.;.;GHDC_HUMAN	K	149;166;205;205;205	.	ENSP00000301671:E205K	E	-	1	0	GHDC	37598061	0.993000	0.37304	0.886000	0.34754	0.302000	0.27658	4.376000	0.59556	2.352000	0.79861	0.561000	0.74099	GAA		0.657	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		T	40344535	C	T	40344535	3	4	61	1	0	0	0	0	1	0	0	0	6389	893	31	1	1092	1	GHDC	17	40344535	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191996	40344535	40850675	10241	18226										
STAT5B	6777	broad.mit.edu	37	chr17	40354360	40354360	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaagaatgccacctacttCtgtgggtacatgttatagtg	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40354360C>A	ENST00000293328.3	-	18	2403	c.2235G>T	c.(2233-2235)caG>caT	p.Q745H		NM_012448.3	NP_036580.2	P51692	STA5B_HUMAN	signal transducer and activator of transcription 5B	745					2-oxoglutarate metabolic process (GO:0006103)|acute-phase response (GO:0006953)|allantoin metabolic process (GO:0000255)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|liver development (GO:0001889)|luteinization (GO:0001553)|natural killer cell differentiation (GO:0001779)|negative regulation of apoptotic process (GO:0043066)|negative regulation of erythrocyte differentiation (GO:0045647)|oxaloacetate metabolic process (GO:0006107)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cellular component movement (GO:0051272)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone metabolic process (GO:0042448)|prolactin signaling pathway (GO:0038161)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription from RNA polymerase II promoter (GO:0006366)|valine metabolic process (GO:0006573)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|glucocorticoid receptor binding (GO:0035259)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.Q745H(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	CCACCTACTTCTGTGGGTACA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											45	41	42					17																	40354360		2203	4300	6503	37607886	SO:0001583	missense	6777			BC065227	CCDS11423.1	17q11.2	2014-09-17			ENSG00000173757	ENSG00000173757		"SH2 domain containing"	11367	protein-coding gene	gene with protein product		604260				8631883	Standard	NM_012448		Approved		uc002hzh.3	P51692	OTTHUMG00000150724	ENST00000293328.3:c.2235G>T	17.37:g.40354360C>A	ENSP00000293328:p.Gln745His		37607886	Q8WWS8	Missense_Mutation	SNP	ENST00000293328.3	37	CCDS11423.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568023	0.28003	.	.	ENSG00000173757	ENST00000293328	D	0.88046	-2.33	4.76	2.74	0.32292	.	0.182510	0.49916	D	0.000128	D	0.83031	0.5166	L	0.51422	1.61	0.31199	N	0.700026	P	0.38767	0.646	B	0.41813	0.367	T	0.78460	-0.2195	10	0.23302	T	0.38	-1.0E-4	10.3257	0.43792	0.0:0.7904:0.1351:0.0745	.	745	P51692	STA5B_HUMAN	H	745	ENSP00000293328:Q745H	ENSP00000293328:Q745H	Q	-	3	2	STAT5B	37607886	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	0.779000	0.26746	0.605000	0.29947	-0.140000	0.14226	CAG		0.637	STAT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319797.1	NM_012448		A	40354360	C	A	40354360	3	1	61	1	0	0	0	0	1	0	0	0	15308	912	32	2	136	2	STAT5B	17	40354360	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9825	40354360	40840850	10242	18227										
ATP6V0A1	535	broad.mit.edu	37	chr17	40622172	40622172	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccaggaagctctgaagaGaaacttcctggaactgaccg	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40622172G>T	ENST00000343619.4	+	5	482	c.359G>T	c.(358-360)aGa>aTa	p.R120I	ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.R120I|ATP6V0A1_ENST00000537728.1_Intron|ATP6V0A1_ENST00000585525.1_Intron|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.R120I|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.R120I|ATP6V0A1_ENST00000544137.1_Intron	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	120					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.R120I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		GCTCTGAAGAGAAACTTCCTG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											30	32	31					17																	40622172		2203	4299	6502	37875698	SO:0001583	missense	535			U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.359G>T	17.37:g.40622172G>T	ENSP00000342951:p.Arg120Ile		37875698	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725397	0.89298	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	6.07	5.09	0.68999	.	0.086330	0.85682	D	0.000000	D	0.90594	0.7051	M	0.67517	2.055	0.80722	D	1	B;D;B;P	0.53462	0.146;0.96;0.257;0.537	B;P;B;B	0.55011	0.207;0.766;0.185;0.419	D	0.91127	0.4934	10	0.72032	D	0.01	-15.0799	15.6717	0.77283	0.0662:0.0:0.9338:0.0	.	120;120;120;120	B7Z3B7;Q93050;Q93050-1;F5H569	.;VPP1_HUMAN;.;.	I	120	ENSP00000342951:R120I;ENSP00000444676:R120I;ENSP00000377415:R120I;ENSP00000264649:R120I	ENSP00000264649:R120I	R	+	2	0	ATP6V0A1	37875698	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.154000	0.64894	2.890000	0.99128	0.650000	0.86243	AGA		0.338	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		T	40622172	G	T	40622172	3	4	61	1	0	0	0	0	1	0	0	0	1169	942	33	2	373	2	ATP6V0A1	17	40622172	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	267812	40622172	40573038	10243	18228										
NAGLU	4669	broad.mit.edu	37	chr17	40693095	40693095	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgggagcctcttcctgcgaGagctgatcaaagagtttggc	13	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40693095G>T	ENST00000225927.2	+	5	993	c.892G>T	c.(892-894)Gag>Tag	p.E298*	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	298					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)	p.E298*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CTTCCTGCGAGAGCTGATCAA	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											132	125	128					17																	40693095		2203	4300	6503	37946621	SO:0001587	stop_gained	4669				CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.892G>T	17.37:g.40693095G>T	ENSP00000225927:p.Glu298*		37946621		Nonsense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	37	6.333569	0.97480	.	.	ENSG00000108784	ENST00000225927	.	.	.	5.03	5.03	0.67393	.	0.118375	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-17.8096	12.9497	0.58391	0.0:0.1631:0.8369:0.0	.	.	.	.	X	298	.	ENSP00000225927:E298X	E	+	1	0	NAGLU	37946621	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	4.518000	0.60510	2.636000	0.89361	0.555000	0.69702	GAG		0.562	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		T	40693095	G	T	40693095	4	4	61	1	0	0	0	0	0	1	0	0	10173	943	33	2	910	2	NAGLU	17	40693095	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70923	40693095	40502115	10244	18229										
COASY	80347	broad.mit.edu	37	chr17	40714708	40714708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccctagcccctcgcctggCctccatcctgacctcggcgg	9	21	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40714708C>T	ENST00000393818.2	+	1	524	c.68C>T	c.(67-69)gCc>gTc	p.A23V	COASY_ENST00000449624.1_Intron|COASY_ENST00000421097.2_Missense_Mutation_p.A23V|COASY_ENST00000420359.1_Missense_Mutation_p.A23V|COASY_ENST00000590958.1_Missense_Mutation_p.A52V|RP11-400F19.8_ENST00000585572.1_RNA	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	23					cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)	p.A23V(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCTCGCCTGGCCTCCATCCTG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	17											32	37	35					17																	40714708		2202	4296	6498	37968234	SO:0001583	missense	80347			AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"Coenzyme A synthase"			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.68C>T	17.37:g.40714708C>T	ENSP00000377406:p.Ala23Val		37968234	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Missense_Mutation	SNP	ENST00000393818.2	37	CCDS11429.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.766457	0.49574	.	.	ENSG00000068120	ENST00000421097;ENST00000420359;ENST00000393818;ENST00000426807	T;T	0.32023	1.47;1.47	5.71	1.28	0.21552	.	0.232083	0.42964	N	0.000636	T	0.18635	0.0447	L	0.29908	0.895	0.80722	D	1	B;B	0.14805	0.011;0.011	B;B	0.13407	0.009;0.004	T	0.05321	-1.0892	10	0.44086	T	0.13	-0.9973	5.788	0.18345	0.1315:0.5418:0.2544:0.0724	.	52;23	Q13057-2;Q13057	.;COASY_HUMAN	V	52;23;23;23	ENSP00000413338:A23V;ENSP00000377406:A23V	ENSP00000377406:A23V	A	+	2	0	COASY	37968234	0.917000	0.31117	0.749000	0.31150	0.795000	0.44927	1.835000	0.39181	0.041000	0.15688	-0.502000	0.04539	GCC		0.687	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233		T	40714708	C	T	40714708	3	4	61	1	0	0	0	0	1	0	0	0	3658	739	26	3	161	3	COASY	17	40714708	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21613	40714708	40480502	10245	18230										
CNTNAP1	8506	broad.mit.edu	37	chr17	40847574	40847574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagccgggcacctggatgCgctataacctacagtcagcg	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40847574C>T	ENST00000264638.4	+	19	3245	c.3028C>T	c.(3028-3030)Cgc>Tgc	p.R1010C	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	1010					axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.R1010C(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		CACCTGGATGCGCTATAACCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17											65	67	66					17																	40847574		2203	4300	6503	38101100	SO:0001583	missense	8506			U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"neurexin 4"	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.3028C>T	17.37:g.40847574C>T	ENSP00000264638:p.Arg1010Cys		38101100		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.592927	0.66219	.	.	ENSG00000108797	ENST00000264638	T	0.79845	-1.31	4.86	4.86	0.63082	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.64402	D	0.000002	D	0.84817	0.5556	L	0.39898	1.24	0.58432	D	0.999998	D	0.89917	1.0	D	0.69654	0.965	D	0.85850	0.1403	10	0.59425	D	0.04	.	15.5399	0.76035	0.0:1.0:0.0:0.0	.	1010	P78357	CNTP1_HUMAN	C	1010	ENSP00000264638:R1010C	ENSP00000264638:R1010C	R	+	1	0	CNTNAP1	38101100	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.599000	0.46231	2.508000	0.84585	0.563000	0.77884	CGC		0.582	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		T	40847574	C	T	40847574	3	4	61	1	0	0	0	0	1	0	0	0	3652	768	27	1	3102	1	CNTNAP1	17	40847574	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132866	40847574	40347636	10246	18231										
EZH1	2145	broad.mit.edu	37	chr17	40864381	40864381	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggtgccatggaagactcGaaaaagagattcttcagccc	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40864381G>A	ENST00000428826.2	-	12	1448	c.1327C>T	c.(1327-1329)Cga>Tga	p.R443*	EZH1_ENST00000585893.1_Nonsense_Mutation_p.R403*|EZH1_ENST00000590783.1_5'Flank|EZH1_ENST00000592743.1_Nonsense_Mutation_p.R443*|EZH1_ENST00000435174.1_Nonsense_Mutation_p.R304*|EZH1_ENST00000590078.1_Nonsense_Mutation_p.R373*|EZH1_ENST00000415827.2_Nonsense_Mutation_p.R434*			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	443					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)	p.R443*(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TGGAAGACTCGAAAAAGAGAT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											139	129	132					17																	40864381		2203	4300	6503	38117907	SO:0001587	stop_gained	2145				CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1327C>T	17.37:g.40864381G>A	ENSP00000404658:p.Arg443*		38117907	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Nonsense_Mutation	SNP	ENST00000428826.2	37	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	G	38	7.004609	0.97994	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	.	.	.	5.23	3.07	0.35406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1313	0.65255	0.0:0.0:0.6378:0.3622	.	.	.	.	X	446;443;403;304	.	ENSP00000264646:R446X	R	-	1	2	EZH1	38117907	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.574000	0.46016	1.393000	0.46605	0.655000	0.94253	CGA		0.522	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		A	40864381	G	A	40864381	4	1	61	1	0	0	0	0	0	1	0	0	5346	1066	37	1	956	1	EZH1	17	40864381	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16807	40864381	40330829	10247	18232										
BECN1	8678	broad.mit.edu	37	chr17	40968062	40968062	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtttaaattcactgtattCtctctgatacctgtgagcag	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:40968062C>A	ENST00000361523.4	-	8	826	c.694G>T	c.(694-696)Gaa>Taa	p.E232*	BECN1_ENST00000438274.3_Nonsense_Mutation_p.E156*|BECN1_ENST00000590099.1_Nonsense_Mutation_p.E232*	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	232					autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032)	dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)		p.E232*(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TCACTGTATTCTCTCTGATAC	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											120	104	109					17																	40968062		2203	4300	6503	38221588	SO:0001587	stop_gained	8678			AF077301	CCDS11441.1	17q21	2014-02-12	2008-01-14		ENSG00000126581	ENSG00000126581			1034	protein-coding gene	gene with protein product	"ATG6 autophagy related 6 homolog (S. cerevisiae)"	604378	"beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)"			9765397	Standard	NM_003766		Approved	ATG6, VPS30	uc002ibn.2	Q14457		ENST00000361523.4:c.694G>T	17.37:g.40968062C>A	ENSP00000355231:p.Glu232*		38221588	B2R6N7|O75595|Q9UNA8	Nonsense_Mutation	SNP	ENST00000361523.4	37	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	C	38	6.637174	0.97726	.	.	ENSG00000126581	ENST00000361523;ENST00000438274;ENST00000543382	.	.	.	5.94	4.97	0.65823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	17.1621	0.86806	0.0:0.8736:0.1264:0.0	.	.	.	.	X	232;156;145	.	ENSP00000355231:E232X	E	-	1	0	BECN1	38221588	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	7.578000	0.82498	1.505000	0.48720	-0.181000	0.13052	GAA		0.473	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	NM_003766		A	40968062	C	A	40968062	4	1	61	1	0	0	0	0	0	1	0	0	1397	922	32	2	678	2	BECN1	17	40968062	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103681	40968062	40227148	10248	18233										
AOC3	8639	broad.mit.edu	37	chr17	41004494	41004494	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggtggaaattccccagcAgcaatgacgacccgctatgt	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:41004494A>G	ENST00000308423.2	+	1	1294	c.1134A>G	c.(1132-1134)gcA>gcG	p.A378A	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	378					amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)	p.A378A(1)		breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	ATTCCCCAGCAGCAATGACGA	0.562																																					NSCLC(3;192 220 10664 11501 16477)											1	Substitution - coding silent(1)	large_intestine(1)	17											84	74	77					17																	41004494		2203	4300	6503	38258020	SO:0001819	synonymous_variant	8639			AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1134A>G	17.37:g.41004494A>G			38258020	B2RCI5|K7ESB3|L0L8N9|Q45F94	Silent	SNP	ENST00000308423.2	37	CCDS11444.1																																																																																				0.562	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		G	41004494	A	G	41004494	2	3	61	1	0	0	0	0	0	0	0	1	728	175	7	4		4	AOC3	17	41004494	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	36432	41004494	40190716	10249	18234										
AOC3	8639	broad.mit.edu	37	chr17	41004707	41004707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccactcagatctctactcGcactactttgggggtcttgc	8	14	3	1	rs115107156	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:41004707G>A	ENST00000308423.2	+	1	1507	c.1347G>A	c.(1345-1347)tcG>tcA	p.S449S	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	449					amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)	p.S449S(2)		breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	ATCTCTACTCGCACTACTTTG	0.542													G|||	4	0.000798722	0.003	0	5008	,	,		19486	0		0	False		,,,				2504	0				NSCLC(3;192 220 10664 11501 16477)											2	Substitution - coding silent(2)	large_intestine(2)	17						G		11,4395	17.9+/-39.9	0,11,2192	124	110	114		1347	-4.8	0	17	dbSNP_132	114	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AOC3	NM_003734.2		0,12,6491	AA,AG,GG		0.0116,0.2497,0.0923		449/764	41004707	12,12994	2203	4300	6503	38258233	SO:0001819	synonymous_variant	8639			AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1347G>A	17.37:g.41004707G>A			38258233	B2RCI5|K7ESB3|L0L8N9|Q45F94	Silent	SNP	ENST00000308423.2	37	CCDS11444.1																																																																																				0.542	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		A	41004707	G	A	41004707	2	1	61	1	0	0	0	0	0	0	0	1	728	1074	38	1		1	AOC3	17	41004707	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213	41004707	40190503	10250	18235										
G6PC	2538	broad.mit.edu	37	chr17	41063104	41063104	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaagcccagaggtggtgCgagcagccagaatgggtcca	16	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:41063104C>T	ENST00000253801.2	+	5	814	c.735C>T	c.(733-735)tgC>tgT	p.C245C	G6PC_ENST00000585489.1_3'UTR|G6PC_ENST00000592383.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	245					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.C245C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGAGGTGGTGCGAGCAGCCAG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	17	GRCh37	CP952395	G6PC	X							94	80	85					17																	41063104		2203	4300	6503	38316630	SO:0001819	synonymous_variant	2538			U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.735C>T	17.37:g.41063104C>T			38316630	A1L4C0|B4E1C3|K7EL82	Silent	SNP	ENST00000253801.2	37	CCDS11446.1																																																																																				0.567	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		T	41063104	C	T	41063104	2	4	61	1	0	0	0	0	0	0	0	1	6162	776	27	1		1	G6PC	17	41063104	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58397	41063104	40132106	10251	18236										
BRCA1	672	broad.mit.edu	37	chr17	41246189	41246189	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttgtcttcaatattactCtctactgatttggagtgaac	6	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:41246189C>A	ENST00000357654.3	-	10	1477	c.1359G>T	c.(1357-1359)gaG>gaT	p.E453D	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.E406D|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.E453D|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.E157D|BRCA1_ENST00000346315.3_Missense_Mutation_p.E453D|BRCA1_ENST00000354071.3_Missense_Mutation_p.E453D|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000491747.2_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	453					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E453D(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CAATATTACTCTCTACTGATT	0.363			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	1	Substitution - Missense(1)	large_intestine(1)	17											100	97	98					17																	41246189		2203	4300	6503	38499715	SO:0001583	missense	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.1359G>T	17.37:g.41246189C>A	ENSP00000350283:p.Glu453Asp		38499715	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.605|8.605	0.887856|0.887856	0.17540|0.17540	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152;ENST00000497488;ENST00000494123|ENST00000473961	D;D;D;D;D;D;D;D;D;D|.	0.92348|.	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02|.	4.57|4.57	1.09|1.09	0.20402|0.20402	.|.	0.345070|.	0.25022|.	N|.	0.033749|.	T|T	0.65698|0.65698	0.2716|0.2716	H|H	0.94222|0.94222	3.51|3.51	0.09310|0.09310	N|N	1|1	P;P;P;B;P;P|.	0.48294|.	0.872;0.872;0.549;0.368;0.908;0.833|.	P;P;B;P;P;P|.	0.58391|.	0.5;0.5;0.329;0.474;0.838;0.637|.	T|T	0.58668|0.58668	-0.7596|-0.7596	10|5	0.87932|.	D|.	0|.	-1.1763|-1.1763	4.4836|4.4836	0.11780|0.11780	0.0:0.3491:0.1682:0.4827|0.0:0.3491:0.1682:0.4827	.|.	453;412;453;453;453;453|.	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2|.	.;.;.;.;BRCA1_HUMAN;.|.	D|I	453;453;453;453;157;453;406;453;427;157;453|319	ENSP00000350283:E453D;ENSP00000326002:E453D;ENSP00000246907:E453D;ENSP00000310938:E157D;ENSP00000418960:E453D;ENSP00000418775:E406D;ENSP00000419274:E453D;ENSP00000419988:E427D;ENSP00000418986:E157D;ENSP00000419103:E453D|.	ENSP00000310938:E157D|.	E|R	-|-	3|2	2|0	BRCA1|BRCA1	38499715|38499715	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.012000|0.012000	0.07955|0.07955	-0.063000|-0.063000	0.11655|0.11655	0.133000|0.133000	0.18654|0.18654	0.561000|0.561000	0.74099|0.74099	GAG|AGA		0.363	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		A	41246189	C	A	41246189	3	1	61	1	0	0	0	0	1	0	0	0	1501	912	32	2	4358	2	BRCA1	17	41246189	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	183085	41246189	39949021	10252	18237										
PPY	5539	broad.mit.edu	37	chr17	42018852	42018852	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggcctggtcagcatgttGatgtatctacggagatcagc	12	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42018852G>T	ENST00000591228.1	-	2	258	c.171C>A	c.(169-171)atC>atA	p.I57I	PPY_ENST00000587006.1_Silent_p.I57I|PPY_ENST00000225992.3_Silent_p.I57I			P01298	PAHO_HUMAN	pancreatic polypeptide	57					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.I57I(1)		large_intestine(2)|lung(1)|skin(1)	4		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TCAGCATGTTGATGTATCTAC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	17											150	139	143					17																	42018852		2203	4300	6503	39374378	SO:0001819	synonymous_variant	5539				CCDS11472.1	17q21.31	2013-02-28			ENSG00000108849	ENSG00000108849		"Endogenous ligands"	9327	protein-coding gene	gene with protein product	"pancreatic polypeptide Y", "prepro-PP (prepropancreatic polypeptide)"	167780				3753985	Standard	NM_002722		Approved	PNP	uc002iep.3	P01298		ENST00000591228.1:c.171C>A	17.37:g.42018852G>T			39374378		Silent	SNP	ENST00000591228.1	37	CCDS11472.1																																																																																				0.617	PPY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457656.1	NM_002722		T	42018852	G	T	42018852	2	4	61	1	0	0	0	0	0	0	0	1	12449	1280	45	2		2	PPY	17	42018852	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	772663	42018852	39176358	10253	18238										
HDAC5	10014	broad.mit.edu	37	chr17	42156199	42156199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctctagcgtggccactgCgttgatgttgggcttttgct	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42156199C>T	ENST00000393622.2	-	25	3458	c.3127G>A	c.(3127-3129)Gca>Aca	p.A1043T	HDAC5_ENST00000225983.6_Missense_Mutation_p.A1044T|HDAC5_ENST00000336057.5_Missense_Mutation_p.A958T|HDAC5_ENST00000586802.1_Missense_Mutation_p.A1043T	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	1043					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A1043T(2)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		GTGGCCACTGCGTTGATGTTG	0.592																																																2	Substitution - Missense(2)	large_intestine(2)	17											167	148	155					17																	42156199		2203	4300	6503	39511725	SO:0001583	missense	10014			AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.3127G>A	17.37:g.42156199C>T	ENSP00000377244:p.Ala1043Thr		39511725	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480576	0.63849	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.56941	0.43;0.43;0.69	4.88	3.92	0.45320	Histone deacetylase domain (1);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.81614	2.55	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.927;0.999;0.997	T	0.75505	-0.3294	10	0.66056	D	0.02	-8.8397	12.1613	0.54105	0.0:0.9159:0.0:0.0841	.	958;1044;1043	Q9UQL6-2;Q9UQL6-3;Q9UQL6	.;.;HDAC5_HUMAN	T	1044;1043;958	ENSP00000225983:A1044T;ENSP00000377244:A1043T;ENSP00000337290:A958T	ENSP00000225983:A1044T	A	-	1	0	HDAC5	39511725	1.000000	0.71417	0.759000	0.31340	0.070000	0.16714	7.552000	0.82192	1.287000	0.44583	-0.136000	0.14681	GCA		0.592	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		T	42156199	C	T	42156199	3	4	61	1	0	0	0	0	1	0	0	0	7031	768	27	1	253	1	HDAC5	17	42156199	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137347	42156199	39039011	10254	18239										
UBTF	7343	broad.mit.edu	37	chr17	42288694	42288694	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctccacctcgtaatctttCtttttctgggaaagtgagtg	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42288694C>A	ENST00000302904.4	-	11	1545	c.1053G>T	c.(1051-1053)aaG>aaT	p.K351N	UBTF_ENST00000533177.1_Missense_Mutation_p.K314N|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000527034.1_Missense_Mutation_p.K314N|UBTF_ENST00000436088.1_Missense_Mutation_p.K351N|UBTF_ENST00000529383.1_Missense_Mutation_p.K351N|UBTF_ENST00000343638.5_Missense_Mutation_p.K314N|UBTF_ENST00000393606.3_Missense_Mutation_p.K314N|UBTF_ENST00000526094.1_Missense_Mutation_p.K314N			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	351					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.K351N(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CGTAATCTTTCTTTTTCTGGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											70	62	64					17																	42288694		2203	4300	6503	39644220	SO:0001583	missense	7343			BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.1053G>T	17.37:g.42288694C>A	ENSP00000302640:p.Lys351Asn		39644220	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	c	20.8	4.051183	0.75960	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383	T;T;T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72;1.72;1.72	4.34	3.36	0.38483	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	T	0.46580	0.1400	M	0.70842	2.15	0.48762	D	0.999705	D;P;D	0.89917	1.0;0.589;1.0	D;B;D	0.87578	0.998;0.437;0.997	T	0.39761	-0.9598	10	0.45353	T	0.12	-30.0218	11.7069	0.51601	0.0:0.9064:0.0:0.0936	.	314;314;351	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	N	314;351;314;314;351;314;314;351	ENSP00000345297:K314N;ENSP00000302640:K351N;ENSP00000431539:K314N;ENSP00000437180:K314N;ENSP00000390669:K351N;ENSP00000377231:K314N;ENSP00000432925:K314N;ENSP00000435708:K351N	ENSP00000302640:K351N	K	-	3	2	UBTF	39644220	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.517000	0.53443	2.408000	0.81797	0.491000	0.48974	AAG		0.577	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		A	42288694	C	A	42288694	3	1	61	1	0	0	0	0	1	0	0	0	16949	912	32	2	1285	2	UBTF	17	42288694	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132495	42288694	38906516	10255	18240										
UBTF	7343	broad.mit.edu	37	chr17	42293103	42293103	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatctcagggtggagtttCgcatacttggcccgcttctc	10	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42293103C>T	ENST00000302904.4	-	5	885	c.393G>A	c.(391-393)gcG>gcA	p.A131A	UBTF_ENST00000533177.1_Silent_p.A131A|UBTF_ENST00000537550.1_5'UTR|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000527034.1_Silent_p.A131A|UBTF_ENST00000436088.1_Silent_p.A131A|UBTF_ENST00000529383.1_Silent_p.A131A|UBTF_ENST00000343638.5_Silent_p.A131A|UBTF_ENST00000393606.3_Silent_p.A131A|UBTF_ENST00000526094.1_Silent_p.A131A			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	131					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.A131A(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GGTGGAGTTTCGCATACTTGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	17											108	111	110					17																	42293103		2203	4300	6503	39648629	SO:0001819	synonymous_variant	7343			BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.393G>A	17.37:g.42293103C>T			39648629	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1																																																																																				0.507	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		T	42293103	C	T	42293103	2	4	61	1	0	0	0	0	0	0	0	1	16949	871	31	1		1	UBTF	17	42293103	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4409	42293103	38902107	10256	18241										
ITGA2B	3674	broad.mit.edu	37	chr17	42462328	42462328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgttaccccagtagccgtCgaagtactctgggttgctgg	14	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42462328C>T	ENST00000262407.5	-	7	818	c.787G>A	c.(787-789)Gac>Aac	p.D263N	ITGA2B_ENST00000377068.3_Intron|ITGA2B_ENST00000353281.4_Missense_Mutation_p.D263N	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	263					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.D263N(1)		biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CAGTAGCCGTCGAAGTACTCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											82	93	90					17																	42462328		2203	4300	6503	39817854	SO:0001583	missense	3674				CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.787G>A	17.37:g.42462328C>T	ENSP00000262407:p.Asp263Asn		39817854	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	37	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.042786	0.93685	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.71817	-0.6;-0.6	5.47	3.43	0.39272	.	2.946000	0.02429	N	0.083386	T	0.80065	0.4555	M	0.62088	1.915	0.80722	D	1	D	0.67145	0.996	P	0.53006	0.715	T	0.63659	-0.6587	10	0.87932	D	0	.	12.5903	0.56439	0.0:0.6815:0.3185:0.0	.	263	P08514	ITA2B_HUMAN	N	263	ENSP00000262407:D263N;ENSP00000340536:D263N	ENSP00000262407:D263N	D	-	1	0	ITGA2B	39817854	0.254000	0.23992	0.821000	0.32701	0.376000	0.30014	0.971000	0.29396	0.637000	0.30526	-0.416000	0.06073	GAC		0.607	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42462328	C	T	42462328	3	4	61	1	0	0	0	0	1	0	0	0	7897	884	31	1	2428	1	ITGA2B	17	42462328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	169225	42462328	38732882	10257	18242										
C17orf104	284071	broad.mit.edu	37	chr17	42743947	42743947	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacaaaaaatagatgaacTtcatcatggatttactggtt	6	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42743947T>G	ENST00000409122.2	+	5	810	c.668T>G	c.(667-669)cTt>cGt	p.L223R	C17orf104_ENST00000359945.3_Missense_Mutation_p.L223R|C17orf104_ENST00000409464.1_Missense_Mutation_p.L57R	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	223								p.L223R(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						ATAGATGAACTTCATCATGGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											100	87	92					17																	42743947		2203	4299	6502	40099473	SO:0001583	missense	284071				CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.668T>G	17.37:g.42743947T>G	ENSP00000386452:p.Leu223Arg		40099473	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050871	0.36181	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T	0.38401	1.19;1.19;1.14;1.28	5.54	5.54	0.83059	.	0.509407	0.19428	N	0.114518	T	0.39655	0.1086	L	0.34521	1.04	0.28445	N	0.916631	D;D;D	0.57571	0.963;0.98;0.963	P;P;P	0.56700	0.735;0.804;0.735	T	0.36311	-0.9753	10	0.66056	D	0.02	-16.3624	7.3468	0.26668	0.0:0.0757:0.1571:0.7672	.	223;223;57	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	R	223;223;57;57;57	ENSP00000353028:L223R;ENSP00000386452:L223R;ENSP00000399809:L57R;ENSP00000386586:L57R	ENSP00000353028:L223R	L	+	2	0	C17orf104	40099473	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.318000	0.43779	2.220000	0.72140	0.482000	0.46254	CTT		0.368	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		G	42743947	T	G	42743947	3	3	61	1	0	0	0	0	1	0	0	0	1855	1609	56	4	686	4	C17orf104	17	42743947	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	281619	42743947	38451263	10258	18243										
C17orf104	284071	broad.mit.edu	37	chr17	42744952	42744952	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgcagaaagaatccaatCtgtcaatcacatagaaggac	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42744952C>T	ENST00000409122.2	+	5	1815	c.1673C>T	c.(1672-1674)tCt>tTt	p.S558F	C17orf104_ENST00000359945.3_Missense_Mutation_p.S558F|C17orf104_ENST00000409464.1_Missense_Mutation_p.S392F	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	558								p.S558F(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						AGAATCCAATCTGTCAATCAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	17											32	34	34					17																	42744952		2195	4299	6494	40100478	SO:0001583	missense	284071				CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.1673C>T	17.37:g.42744952C>T	ENSP00000386452:p.Ser558Phe		40100478	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563125	0.45694	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000409464	T;T;T	0.36157	1.27;1.27;1.29	5.66	5.66	0.87406	.	0.548825	0.19270	N	0.118457	T	0.46347	0.1388	L	0.34521	1.04	0.35458	D	0.796273	D;D;D	0.60575	0.988;0.986;0.974	P;P;P	0.57152	0.804;0.814;0.748	T	0.54569	-0.8274	10	0.59425	D	0.04	-14.3048	17.913	0.88940	0.0:1.0:0.0:0.0	.	558;558;392	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	F	558;558;392	ENSP00000353028:S558F;ENSP00000386452:S558F;ENSP00000386586:S392F	ENSP00000353028:S558F	S	+	2	0	C17orf104	40100478	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.038000	0.64177	2.663000	0.90544	0.655000	0.94253	TCT		0.333	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42744952	C	T	42744952	3	4	61	1	0	0	0	0	1	0	0	0	1855	913	32	3	1691	3	C17orf104	17	42744952	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1005	42744952	38450258	10259	18244										
EFTUD2	9343	broad.mit.edu	37	chr17	42929857	42929857	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctcaaagccaaaagagtCgatggccgggataaaagctt	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42929857C>T	ENST00000426333.2	-	26	2932	c.2635G>A	c.(2635-2637)Gac>Aac	p.D879N	EFTUD2_ENST00000402521.3_Missense_Mutation_p.D844N|EFTUD2_ENST00000592576.1_Missense_Mutation_p.D869N|EFTUD2_ENST00000591382.1_Missense_Mutation_p.D879N	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	879					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.D879N(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				CCAAAAGAGTCGATGGCCGGG	0.542																																					Ovarian(10;65 485 10258 29980 30707)											1	Substitution - Missense(1)	large_intestine(1)	17											97	84	88					17																	42929857		2203	4300	6503	40285383	SO:0001583	missense	9343			D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.2635G>A	17.37:g.42929857C>T	ENSP00000392094:p.Asp879Asn		40285383	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	37	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	C	36	5.745690	0.96882	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.62788	-0.0;-0.0	6.06	6.06	0.98353	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81235	0.4780	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68483	0.958;0.958	T	0.82063	-0.0643	10	0.87932	D	0	-29.4381	20.2194	0.98323	0.0:1.0:0.0:0.0	.	869;879	B4DMC0;Q15029	.;U5S1_HUMAN	N	879;869;844	ENSP00000392094:D879N;ENSP00000385873:D844N	ENSP00000262414:D869N	D	-	1	0	EFTUD2	40285383	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.794000	0.85869	2.879000	0.98667	0.650000	0.86243	GAC		0.542	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		T	42929857	C	T	42929857	3	4	61	1	0	0	0	0	1	0	0	0	4972	884	31	1	295	1	EFTUD2	17	42929857	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	184905	42929857	38265353	10260	18245										
CCDC103	388389	broad.mit.edu	37	chr17	42979014	42979014	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggatgtggccactgaaatCtccccggtaggtgaggccct	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42979014C>A	ENST00000417826.2	+	3	365	c.270C>A	c.(268-270)atC>atA	p.I90I	EFTUD2_ENST00000402521.3_5'Flank|EFTUD2_ENST00000592576.1_5'Flank|EFTUD2_ENST00000591382.1_5'Flank|FAM187A_ENST00000412523.2_Intron|CCDC103_ENST00000410006.2_Silent_p.I90I|AC015936.3_ENST00000441312.1_RNA|CCDC103_ENST00000410027.1_Silent_p.I90I|EFTUD2_ENST00000426333.2_5'Flank|FAM187A_ENST00000331733.4_5'UTR	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	Q8IW40	CC103_HUMAN	coiled-coil domain containing 103	90					axonemal dynein complex assembly (GO:0070286)|cell projection organization (GO:0030030)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|outer dynein arm assembly (GO:0036158)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein homodimerization activity (GO:0042803)	p.I90I(1)		endometrium(1)|kidney(1)|large_intestine(3)|prostate(1)|skin(1)	7		Prostate(33;0.109)				CCACTGAAATCTCCCCGGTAG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	17											99	84	89					17																	42979014		2203	4300	6503	40334540	SO:0001819	synonymous_variant	388389			AK023156	CCDS11490.1, CCDS58554.1	17q21.31	2013-02-22			ENSG00000167131	ENSG00000167131			32700	protein-coding gene	gene with protein product		614677				22581229	Standard	NM_213607		Approved	FLJ13094, FLJ34211, PR46b, CILD17	uc031ray.1	Q8IW40	OTTHUMG00000154264	ENST00000417826.2:c.270C>A	17.37:g.42979014C>A			40334540	A8K145|B8ZZU0	Silent	SNP	ENST00000417826.2	37	CCDS11490.1																																																																																				0.478	CCDC103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334578.1	NM_213607		A	42979014	C	A	42979014	2	1	61	1	0	0	0	0	0	0	0	1	2744	903	32	2		2	CCDC103	17	42979014	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49157	42979014	38216196	10261	18246										
GFAP	2670	broad.mit.edu	37	chr17	42990657	42990657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggagcggtaccactcttCggcttcatgcatgttgctgg	12	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:42990657C>T	ENST00000253408.5	-	4	825	c.760G>A	c.(760-762)Gaa>Aaa	p.E254K	GFAP_ENST00000586793.1_Missense_Mutation_p.E254K|GFAP_ENST00000435360.2_Missense_Mutation_p.E254K|GFAP_ENST00000591327.1_5'Flank|GFAP_ENST00000588735.1_Intron	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	254	Linker 2.|Rod.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)	p.E254K(3)		endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				TACCACTCTTCGGCTTCATGC	0.607																																																3	Substitution - Missense(3)	kidney(2)|large_intestine(1)	17											154	128	137					17																	42990657		2203	4300	6503	40346183	SO:0001583	missense	2670			S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"Intermediate filaments type III"	4235	protein-coding gene	gene with protein product	"intermediate filament protein"	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.760G>A	17.37:g.42990657C>T	ENSP00000253408:p.Glu254Lys		40346183	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283867	0.80803	.	.	ENSG00000131095	ENST00000253408;ENST00000421021;ENST00000435360	D;D	0.93763	-3.28;-3.28	5.08	5.08	0.68730	Filament (1);	0.000000	0.85682	D	0.000000	D	0.97037	0.9032	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.954	D	0.97337	0.9954	10	0.87932	D	0	.	18.6455	0.91409	0.0:1.0:0.0:0.0	.	254;254	E9PAX3;P14136	.;GFAP_HUMAN	K	254;229;254	ENSP00000253408:E254K;ENSP00000403962:E254K	ENSP00000253408:E254K	E	-	1	0	GFAP	40346183	1.000000	0.71417	0.911000	0.35937	0.102000	0.19082	5.937000	0.70162	2.826000	0.97356	0.655000	0.94253	GAA		0.607	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		T	42990657	C	T	42990657	3	4	61	1	0	0	0	0	1	0	0	0	6357	893	31	1	691	1	GFAP	17	42990657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11643	42990657	38204553	10262	18247										
HEXIM2	124790	broad.mit.edu	37	chr17	43246603	43246603	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaccgtcggcggccatcGaagcgcaaaaggcactggcg	13	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:43246603G>A	ENST00000307275.3	+	4	724	c.288G>A	c.(286-288)tcG>tcA	p.S96S	HEXIM2_ENST00000591576.1_Silent_p.S96S|HEXIM2_ENST00000592695.1_Silent_p.S96S|RP13-890H12.2_ENST00000589796.1_RNA|RP13-890H12.2_ENST00000589451.1_RNA	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	96					negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)	p.S96S(1)		endometrium(1)|large_intestine(3)|lung(1)	5						GGCGGCCATCGAAGCGCAAAA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	17											30	34	33					17																	43246603		2203	4300	6503	40602386	SO:0001819	synonymous_variant	124790			AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.288G>A	17.37:g.43246603G>A			40602386	D3DX66	Silent	SNP	ENST00000307275.3	37	CCDS11496.1																																																																																				0.672	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608		A	43246603	G	A	43246603	2	1	61	1	0	0	0	0	0	0	0	1	7098	1045	37	1		1	HEXIM2	17	43246603	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	255946	43246603	37948607	10263	18248										
FMNL1	752	broad.mit.edu	37	chr17	43315997	43315997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatgaggacagcaacatcGacttcatggtgagctcagga	13	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:43315997G>A	ENST00000331495.3	+	10	1297	c.961G>A	c.(961-963)Gac>Aac	p.D321N	FMNL1_ENST00000592006.1_3'UTR|FMNL1_ENST00000328118.3_Missense_Mutation_p.D321N|CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000587489.1_5'Flank|CTD-2020K17.3_ENST00000393507.2_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	321	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)	p.D321N(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CAGCAACATCGACTTCATGGT	0.602																																					GBM(164;1247 1997 8702 11086 51972)											1	Substitution - Missense(1)	large_intestine(1)	17											82	78	79					17																	43315997		2203	4300	6503	40671780	SO:0001583	missense	752			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.961G>A	17.37:g.43315997G>A	ENSP00000329219:p.Asp321Asn		40671780	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	37	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133763	0.77662	.	.	ENSG00000184922	ENST00000328118;ENST00000331495;ENST00000539884	D;D	0.83914	-1.78;-1.78	4.04	4.04	0.47022	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.103621	0.64402	D	0.000006	D	0.87212	0.6121	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84949	0.0870	10	0.26408	T	0.33	.	15.7259	0.77761	0.0:0.0:1.0:0.0	.	321	O95466	FMNL_HUMAN	N	321;321;39	ENSP00000327442:D321N;ENSP00000329219:D321N	ENSP00000327442:D321N	D	+	1	0	FMNL1	40671780	1.000000	0.71417	0.997000	0.53966	0.969000	0.65631	9.619000	0.98369	2.243000	0.73865	0.400000	0.26472	GAC		0.602	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		A	43315997	G	A	43315997	3	1	61	1	0	0	0	0	1	0	0	0	5970	1058	37	1	999	1	FMNL1	17	43315997	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69394	43315997	37879213	10264	18249										
ARHGAP27	201176	broad.mit.edu	37	chr17	43481984	43481984	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctggggcagctcccatcGaacagaggagtcctctggat	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:43481984G>A	ENST00000428638.1	-	4	1311	c.1312C>T	c.(1312-1314)Cga>Tga	p.R438*	ARHGAP27_ENST00000376922.2_Nonsense_Mutation_p.R97*|ARHGAP27_ENST00000532891.2_Nonsense_Mutation_p.R438*|ARHGAP27_ENST00000455881.1_Nonsense_Mutation_p.R97*|ARHGAP27_ENST00000528384.1_Intron|ARHGAP27_ENST00000582826.1_5'Flank|ARHGAP27_ENST00000532038.1_Nonsense_Mutation_p.R238*|ARHGAP27_ENST00000442348.1_Intron			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	438	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)	p.R97*(1)		endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					AGCTCCCATCGAACAGAGGAG	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											44	45	45					17																	43481984		2203	4300	6503	40837767	SO:0001587	stop_gained	201176			AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	31813	protein-coding gene	gene with protein product		610591	"SH3 domain containing 20"	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.1312C>T	17.37:g.43481984G>A	ENSP00000403323:p.Arg438*		40837767	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Nonsense_Mutation	SNP	ENST00000428638.1	37		.	.	.	.	.	.	.	.	.	.	G	33	5.250219	0.95305	.	.	ENSG00000159314	ENST00000532038;ENST00000376922;ENST00000532891;ENST00000428638;ENST00000455881;ENST00000528677	.	.	.	5.76	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	9.0714	0.36495	0.0774:0.0:0.7754:0.1472	.	.	.	.	X	238;97;438;438;97;181	.	ENSP00000366121:R97X	R	-	1	2	ARHGAP27	40837767	0.015000	0.18098	0.010000	0.14722	0.734000	0.41952	1.594000	0.36697	0.773000	0.33404	-0.229000	0.12294	CGA		0.597	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282		A	43481984	G	A	43481984	4	1	61	1	0	0	0	0	0	1	0	0	876	1066	37	1	1413	1	ARHGAP27	17	43481984	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165987	43481984	37713226	10265	18250										
CRHR1	1394	broad.mit.edu	37	chr17	43884432	43884432	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctccaggaccagcactgCgagagcctgtccctggccag	11	17	0	1	rs543785844		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:43884432C>T	ENST00000398285.3	+	2	90	c.90C>T	c.(88-90)tgC>tgT	p.C30C	CRHR1_ENST00000293493.7_5'UTR|CRHR1_ENST00000314537.5_Silent_p.C30C|CRHR1_ENST00000339069.5_5'UTR|CRHR1_ENST00000577353.1_Silent_p.C30C|CRHR1_ENST00000352855.5_Silent_p.C30C|RP11-105N13.4_ENST00000587305.1_RNA	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	30					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)	p.C30C(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		ACCAGCACTGCGAGAGCCTGT	0.622													C|||	1	0.000199681	0	0	5008	,	,		18731	0.001		0	False		,,,				2504	0				Ovarian(110;57 1568 10207 38216 49865)											1	Substitution - coding silent(1)	large_intestine(1)	17											58	64	62					17																	43884432		2075	4196	6271	41240212	SO:0001819	synonymous_variant	1394			L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.90C>T	17.37:g.43884432C>T			41240212	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																				0.622	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			T	43884432	C	T	43884432	2	4	61	1	0	0	0	0	0	0	0	1	3877	776	27	1		1	CRHR1	17	43884432	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402448	43884432	37310778	10266	18251										
CRHR1	1394	broad.mit.edu	37	chr17	43912093	43912093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccacctccccaacccgtgTcagctttcacagcatcaagc	5	20	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:43912093T>C	ENST00000398285.3	+	14	1298	c.1298T>C	c.(1297-1299)gTc>gCc	p.V433A	CRHR1_ENST00000352855.5_Missense_Mutation_p.V364A|CRHR1_ENST00000577353.1_Missense_Mutation_p.V390A|CRHR1_ENST00000293493.7_Missense_Mutation_p.V229A|CRHR1_ENST00000314537.5_Missense_Mutation_p.V404A|CRHR1_ENST00000339069.5_Missense_Mutation_p.S258P	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	433					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)	p.V404A(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCAACCCGTGTCAGCTTTCAC	0.642																																					Ovarian(110;57 1568 10207 38216 49865)											1	Substitution - Missense(1)	large_intestine(1)	17											68	81	77					17																	43912093		2191	4292	6483	41267874	SO:0001583	missense	1394			L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.1298T>C	17.37:g.43912093T>C	ENSP00000381333:p.Val433Ala		41267874	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	37	CCDS45712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.945456|3.945456	0.73672|0.73672	.|.	.|.	ENSG00000120088|ENSG00000120088	ENST00000339069|ENST00000293493;ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855	T|T;T;T;T	0.48836|0.45668	0.8|1.52;1.06;0.89;1.06	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	.|0.237278	.|0.42420	.|D	.|0.000708	T|T	0.33933|0.33933	0.0880|0.0880	N|N	0.21373|0.21373	0.66|0.66	0.54753|0.54753	D|D	0.999981|0.999981	D|P;P;B;P;P	0.61080|0.45474	0.989|0.68;0.859;0.271;0.68;0.68	P|P;P;B;B;P	0.50314|0.45660	0.637|0.458;0.489;0.066;0.356;0.458	T|T	0.06303|0.06303	-1.0834|-1.0834	9|10	0.87932|0.24483	D|T	0|0.36	.|.	13.1022|13.1022	0.59226|0.59226	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	258|390;433;303;364;404	B4DMR5|P34998-4;P34998;B3TIK8;P34998-3;P34998-2	.|.;CRFR1_HUMAN;.;.;.	P|A	258|229;433;404;390;364	ENSP00000340522:S258P|ENSP00000293493:V229A;ENSP00000381333:V433A;ENSP00000326060:V404A;ENSP00000344068:V364A	ENSP00000340522:S258P|ENSP00000293493:V229A	S|V	+|+	1|2	0|0	CRHR1|CRHR1	41267874|41267874	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	8.019000|8.019000	0.88732|0.88732	1.985000|1.985000	0.57927|0.57927	0.454000|0.454000	0.30748|0.30748	TCA|GTC		0.642	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			C	43912093	T	C	43912093	3	2	61	1	0	0	0	0	1	0	0	0	3877	1667	58	4	1352	4	CRHR1	17	43912093	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	27661	43912093	37283117	10267	18252										
MAPT	4137	broad.mit.edu	37	chr17	44049280	44049280	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaaccgggctctgaaacCtctgatgctaagagcactcc	11	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:44049280C>A	ENST00000571987.1	+	2	189	c.189C>A	c.(187-189)acC>acA	p.T63T	MAPT_ENST00000431008.3_Silent_p.T63T|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000347967.5_5'UTR|MAPT_ENST00000574436.1_Silent_p.T63T|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000415613.2_Silent_p.T63T|MAPT_ENST00000344290.5_Silent_p.T63T|MAPT_ENST00000351559.5_Silent_p.T63T|MAPT_ENST00000262410.5_Silent_p.T63T|MAPT_ENST00000340799.5_Silent_p.T63T|MAPT_ENST00000535772.1_Silent_p.T63T|MAPT_ENST00000576518.1_5'Flank|MAPT_ENST00000420682.2_Silent_p.T63T			P10636	TAU_HUMAN	microtubule-associated protein tau	63					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.T63T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCTCTGAAACCTCTGATGCTA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	17											71	63	66					17																	44049280		2203	4300	6503	41405116	SO:0001819	synonymous_variant	4137			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.189C>A	17.37:g.44049280C>A			41405116	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																				0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		A	44049280	C	A	44049280	2	1	61	1	0	0	0	0	0	0	0	1	9327	668	24	2		2	MAPT	17	44049280	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137187	44049280	37145930	10268	18253										
MAPT	4137	broad.mit.edu	37	chr17	44064408	44064408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattttatattttatcagctCgcatggtcagtaaaagcaaa	6	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:44064408C>T	ENST00000571987.1	+	6	1129	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	MAPT_ENST00000431008.3_Missense_Mutation_p.R126C|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000334239.8_Missense_Mutation_p.R68C|MAPT_ENST00000347967.5_Missense_Mutation_p.R32C|MAPT_ENST00000574436.1_Missense_Mutation_p.R126C|MAPT_ENST00000446361.3_Missense_Mutation_p.R68C|MAPT_ENST00000415613.2_Missense_Mutation_p.R377C|MAPT_ENST00000344290.5_Missense_Mutation_p.R377C|MAPT_ENST00000351559.5_Missense_Mutation_p.R126C|MAPT_ENST00000262410.5_Missense_Mutation_p.R377C|MAPT_ENST00000340799.5_Missense_Mutation_p.R97C|MAPT_ENST00000535772.1_Missense_Mutation_p.R126C|MAPT_ENST00000576518.1_Missense_Mutation_p.R57C|MAPT_ENST00000420682.2_Missense_Mutation_p.R97C			P10636	TAU_HUMAN	microtubule-associated protein tau	377					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.R377C(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TTTATCAGCTCGCATGGTCAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	89	89					17																	44064408		2203	4300	6503	41420245	SO:0001583	missense	4137			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1129C>T	17.37:g.44064408C>T	ENSP00000458742:p.Arg377Cys		41420245	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794454	0.90453	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000340799;ENST00000535772;ENST00000347967;ENST00000354326;ENST00000446361;ENST00000334239;ENST00000420682;ENST00000415613	T;T;T;T;T;T;T;T;T;T	0.32753	1.48;1.48;2.19;1.44;2.44;2.19;2.2;2.46;1.44;1.48	5.58	5.58	0.84498	.	0.000000	0.44483	D	0.000447	T	0.53012	0.1770	L	0.56769	1.78	0.31212	N	0.698512	D;D;D;D;D;D;D	0.89917	0.999;0.989;1.0;0.994;0.989;0.996;1.0	P;P;D;P;P;D;P	0.85130	0.736;0.711;0.997;0.711;0.711;0.924;0.759	T	0.56202	-0.8018	10	0.62326	D	0.03	-10.0913	16.6747	0.85275	0.0:1.0:0.0:0.0	.	377;97;75;68;68;126;377	P10636-9;P10636-7;F8WAB2;P10636-2;P10636-6;P10636-8;P10636	.;.;.;.;.;.;TAU_HUMAN	C	377;377;126;97;126;32;75;68;68;97;377	ENSP00000340820:R377C;ENSP00000262410:R377C;ENSP00000303214:R126C;ENSP00000340438:R97C;ENSP00000443028:R126C;ENSP00000302706:R32C;ENSP00000408975:R68C;ENSP00000334886:R68C;ENSP00000413056:R97C;ENSP00000410838:R377C	ENSP00000262410:R377C	R	+	1	0	MAPT	41420245	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.531000	0.60602	2.797000	0.96272	0.561000	0.74099	CGC		0.453	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		T	44064408	C	T	44064408	3	4	61	1	0	0	0	0	1	0	0	0	9327	884	31	1	1151	1	MAPT	17	44064408	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15128	44064408	37130802	10269	18254										
MAPT	4137	broad.mit.edu	37	chr17	44067363	44067363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccctgctgtgtgcccagaGccaccttcctctcctaaata	7	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:44067363G>A	ENST00000571987.1	+	7	1302	c.1302G>A	c.(1300-1302)gaG>gaA	p.E434E	MAPT_ENST00000431008.3_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000415613.2_Silent_p.E434E|MAPT_ENST00000344290.5_Silent_p.E434E|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000262410.5_Silent_p.E434E|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000420682.2_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	434					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.E434E(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TGTGCCCAGAGCCACCTTCCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	17											193	195	194					17																	44067363		2203	4300	6503	41423200	SO:0001819	synonymous_variant	4137			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1302G>A	17.37:g.44067363G>A			41423200	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																				0.507	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		A	44067363	G	A	44067363	2	1	61	1	0	0	0	0	0	0	0	1	9327	962	34	3		3	MAPT	17	44067363	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2955	44067363	37127847	10270	18255										
KIAA1267	284058	broad.mit.edu	37	chr17	44115905	44115905	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccacacaggtacttaccGatgtgctggctgtaacctgt	9	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:44115905G>A	ENST00000262419.6	-	10	3010	c.2540C>T	c.(2539-2541)tCg>tTg	p.S847L	KANSL1_ENST00000393476.3_Splice_Site_p.S141L|KANSL1_ENST00000575318.1_Splice_Site_p.S784L|KANSL1_ENST00000574590.1_Splice_Site_p.S847L|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000572904.1_Splice_Site_p.S847L|KANSL1_ENST00000432791.1_Splice_Site_p.S847L	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	847					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S847L(1)									GGTACTTACCGATGTGCTGGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											82	74	77					17																	44115905		2203	4300	6503	41471752	SO:0001630	splice_region_variant	284058			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2541+1C>T	17.37:g.44115905G>A			41471752	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.037030	0.54896	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.24723	2.67;2.67;1.84	6.03	6.03	0.97812	.	0.231874	0.46145	D	0.000304	T	0.23926	0.0579	L	0.43152	1.355	0.44247	D	0.997094	B;B;P;P	0.46327	0.229;0.104;0.876;0.876	B;B;B;B	0.37091	0.077;0.053;0.241;0.241	T	0.01532	-1.1331	10	0.49607	T	0.09	-7.8817	17.2897	0.87152	0.0:0.0:1.0:0.0	.	115;178;847;847	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	L	847;847;141	ENSP00000262419:S847L;ENSP00000387393:S847L;ENSP00000377117:S141L	ENSP00000262419:S847L	S	-	2	0	KIAA1267	41471752	1.000000	0.71417	0.993000	0.49108	0.331000	0.28603	5.873000	0.69644	2.861000	0.98227	0.655000	0.94253	TCG		0.597	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	Missense_Mutation	A	44115905	G	A	44115905	5	1	61	1	0	0	0	0	0	0	1	0	8240	1072	37	1	801	1	KIAA1267	17	44115905	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48542	44115905	37079305	10271	18256										
WNT9B	7484	broad.mit.edu	37	chr17	44953981	44953981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggggctatgacacccagaGccgcctggtggccttctcct	13	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:44953981G>A	ENST00000290015.2	+	4	1024	c.971G>A	c.(970-972)aGc>aAc	p.S324N	WNT9B_ENST00000393461.2_Intron	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	324					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.S324N(1)		large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GACACCCAGAGCCGCCTGGTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											30	32	31					17																	44953981		2203	4300	6503	42308980	SO:0001583	missense	7484			AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"Wingless-type MMTV integration sites"	12779	protein-coding gene	gene with protein product		602864	"wingless-type MMTV integration site family, member 15"	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.971G>A	17.37:g.44953981G>A	ENSP00000290015:p.Ser324Asn		42308980	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765218	0.49574	.	.	ENSG00000158955	ENST00000376843;ENST00000290015	T	0.75938	-0.98	5.39	3.28	0.37604	.	0.288709	0.42821	N	0.000645	T	0.59972	0.2233	L	0.41824	1.3	0.80722	D	1	B	0.14438	0.01	B	0.17433	0.018	T	0.52697	-0.8541	10	0.26408	T	0.33	.	5.3307	0.15930	0.0749:0.2469:0.5465:0.1317	.	324	O14905	WNT9B_HUMAN	N	318;324	ENSP00000290015:S324N	ENSP00000290015:S324N	S	+	2	0	WNT9B	42308980	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.434000	0.44802	1.274000	0.44362	0.561000	0.74099	AGC		0.652	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		A	44953981	G	A	44953981	3	1	61	1	0	0	0	0	1	0	0	0	17439	971	34	3	985	3	WNT9B	17	44953981	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	838076	44953981	36241229	10272	18257										
GOSR2	9570	broad.mit.edu	37	chr17	45008526	45008526	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccgtctagaacgtctggaGattttgtccagcaaggagcc	12	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45008526G>T	ENST00000393456.2	+	3	213	c.156G>T	c.(154-156)gaG>gaT	p.E52D	GOSR2_ENST00000439730.2_Missense_Mutation_p.E52D|GOSR2_ENST00000415811.2_Missense_Mutation_p.E52D|RP11-156P1.2_ENST00000571841.1_Missense_Mutation_p.E52D|GOSR2_ENST00000575949.1_Missense_Mutation_p.E52D|GOSR2_ENST00000225567.4_Missense_Mutation_p.E52D|GOSR2_ENST00000576910.2_Missense_Mutation_p.E52D	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2	52					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.E52D(2)		kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			AACGTCTGGAGATTTTGTCCA	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	17											73	77	76					17																	45008526		2203	4300	6503	42363525	SO:0001583	missense	9570			AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.156G>T	17.37:g.45008526G>T	ENSP00000377101:p.Glu52Asp		42363525	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	37	CCDS42355.1	.	.	.	.	.	.	.	.	.	.	G	6.695	0.496819	0.12762	.	.	ENSG00000108433	ENST00000225567;ENST00000393456;ENST00000415811;ENST00000439730	T;T;T;T	0.43688	0.94;0.94;0.94;1.89	5.87	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.17492	0.0420	N	0.04880	-0.145	0.58432	D	0.999991	B;B;B;B	0.18166	0.007;0.023;0.013;0.026	B;B;B;B	0.22386	0.013;0.009;0.029;0.039	T	0.13335	-1.0513	10	0.02654	T	1	-32.7259	7.2494	0.26140	0.2783:0.0:0.7217:0.0	.	52;52;52;52	E7EQ34;O14653;O14653-2;Q8N4B8	.;GOSR2_HUMAN;.;.	D	52	ENSP00000225567:E52D;ENSP00000377101:E52D;ENSP00000394559:E52D;ENSP00000390577:E52D	ENSP00000225567:E52D	E	+	3	2	GOSR2	42363525	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.686000	0.61700	1.627000	0.50400	0.655000	0.94253	GAG		0.443	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1			T	45008526	G	T	45008526	3	4	61	1	0	0	0	0	1	0	0	0	6598	933	33	2	166	2	GOSR2	17	45008526	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54545	45008526	36186684	10273	18258										
CDC27	996	broad.mit.edu	37	chr17	45201281	45201281	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagaagtaaacgagggattCtttgggaacaatttgtttca	10	4	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45201281C>A	ENST00000066544.3	-	17	2299	c.2206G>T	c.(2206-2208)Gaa>Taa	p.E736*	CDC27_ENST00000531206.1_Nonsense_Mutation_p.E742*|CDC27_ENST00000446365.2_Nonsense_Mutation_p.E675*|CDC27_ENST00000527547.1_Nonsense_Mutation_p.E735*	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	736					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.E736*(2)|p.E742*(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						ACGAGGGATTCTTTGGGAACA	0.318																																																3	Substitution - Nonsense(3)	large_intestine(3)	17											61	63	62					17																	45201281		2203	4300	6503	42556280	SO:0001587	stop_gained	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.2206G>T	17.37:g.45201281C>A	ENSP00000066544:p.Glu736*		42556280	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	41	9.133443	0.99077	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	2.1357	16.524	0.84326	0.0:1.0:0.0:0.0	.	.	.	.	X	736;742;675;735	.	ENSP00000066544:E736X	E	-	1	0	CDC27	42556280	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.551000	0.82182	2.497000	0.84241	0.557000	0.71058	GAA		0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			A	45201281	C	A	45201281	4	1	61	1	0	0	0	0	0	1	0	0	3072	922	32	2	280	2	CDC27	17	45201281	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192755	45201281	35993929	10274	18259										
CDC27	996	broad.mit.edu	37	chr17	45206868	45206868	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatccaaagccttctctgatTttttcagtgcatgttgaacc	6	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45206868T>G	ENST00000066544.3	-	16	2144	c.2051A>C	c.(2050-2052)aAa>aCa	p.K684T	CDC27_ENST00000531206.1_Missense_Mutation_p.K690T|CDC27_ENST00000446365.2_Missense_Mutation_p.K623T|CDC27_ENST00000527547.1_Missense_Mutation_p.K683T	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	684					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.K684T(1)|p.K690T(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTTCTCTGATTTTTTCAGTGC	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	17											86	87	87					17																	45206868		2203	4300	6503	42561867	SO:0001583	missense	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.2051A>C	17.37:g.45206868T>G	ENSP00000066544:p.Lys684Thr		42561867	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	19.91	3.914925	0.72983	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.68	5.68	0.88126	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.81945	0.4930	M	0.81942	2.565	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.79784	0.993;0.973;0.989;0.99	D	0.84581	0.0661	10	0.87932	D	0	-1.0996	13.8853	0.63704	0.0:0.0:0.0:1.0	.	623;683;690;684	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	T	684;690;623;683	ENSP00000066544:K684T;ENSP00000434614:K690T;ENSP00000392802:K623T;ENSP00000437339:K683T	ENSP00000066544:K684T	K	-	2	0	CDC27	42561867	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	8.032000	0.88838	2.156000	0.67533	0.460000	0.39030	AAA		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			G	45206868	T	G	45206868	3	3	61	1	0	0	0	0	1	0	0	0	3072	1841	64	4	439	4	CDC27	17	45206868	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	5587	45206868	35988342	10275	18260										
CDC27	996	broad.mit.edu	37	chr17	45214664	45214664	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttggatagctctctggaaGaatttaattgcaatatcatg	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45214664G>T	ENST00000066544.3	-	14	1860	c.1767C>A	c.(1765-1767)ttC>ttA	p.F589L	CDC27_ENST00000531206.1_Missense_Mutation_p.F595L|CDC27_ENST00000446365.2_Missense_Mutation_p.F528L|CDC27_ENST00000527547.1_Missense_Mutation_p.F588L	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	589					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.F595L(1)|p.F589L(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTCTCTGGAAGAATTTAATTG	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	17											58	61	60					17																	45214664		2203	4300	6503	42569663	SO:0001583	missense	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1767C>A	17.37:g.45214664G>T	ENSP00000066544:p.Phe589Leu		42569663	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	31	5.104404	0.94245	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.62788	1.32;1.32;-0.0;1.32	5.6	3.55	0.40652	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.75391	0.3843	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.77557	0.99;0.99;0.99;0.986	T	0.73404	-0.3993	10	0.22109	T	0.4	-21.6483	8.5484	0.33435	0.1966:0.0:0.8034:0.0	.	528;588;595;589	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	L	589;595;528;588	ENSP00000066544:F589L;ENSP00000434614:F595L;ENSP00000392802:F528L;ENSP00000437339:F588L	ENSP00000066544:F589L	F	-	3	2	CDC27	42569663	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.738000	0.74822	1.296000	0.44742	0.585000	0.79938	TTC		0.378	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			T	45214664	G	T	45214664	3	4	61	1	0	0	0	0	1	0	0	0	3072	933	33	2	731	2	CDC27	17	45214664	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7796	45214664	35980546	10276	18261										
ITGB3	3690	broad.mit.edu	37	chr17	45360758	45360758	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcgctgtgacctgaaggaGaatctgctgaaggataactg	12	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45360758G>T	ENST00000559488.1	+	3	220	c.204G>T	c.(202-204)gaG>gaT	p.E68D	ITGB3_ENST00000560629.1_Nonsense_Mutation_p.E57*|ITGB3_ENST00000435993.2_Missense_Mutation_p.E21D|ITGB3_ENST00000571680.1_Missense_Mutation_p.E68D	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	68					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.E68D(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	ACCTGAAGGAGAATCTGCTGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	79	82					17																	45360758		2203	4300	6503	42715757	SO:0001583	missense	3690				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.204G>T	17.37:g.45360758G>T	ENSP00000452786:p.Glu68Asp		42715757	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.567717	0.45798	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.92911	-3.13	5.88	1.54	0.23209	Integrin beta subunit, N-terminal (2);	0.485095	0.23180	N	0.051036	D	0.83110	0.5183	L	0.33093	0.98	0.22926	N	0.998551	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.69277	-0.5187	10	0.39692	T	0.17	.	1.9112	0.03287	0.1533:0.1367:0.4285:0.2814	.	68;68	P05106;Q2YFE1	ITB3_HUMAN;.	D	68;21	ENSP00000407801:E21D	ENSP00000262017:E68D	E	+	3	2	C17orf57	42715757	0.078000	0.21339	0.998000	0.56505	0.997000	0.91878	0.186000	0.16978	0.078000	0.16900	0.655000	0.94253	GAG		0.572	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45360758	G	T	45360758	3	4	61	1	0	0	0	0	1	0	0	0	7916	933	33	2	214	2	ITGB3	17	45360758	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146094	45360758	35834452	10277	18262										
C17orf57	124989	broad.mit.edu	37	chr17	45425209	45425209	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaaatttttagtaaaattCgaagtggtaagatttatgtg	9	1	0	1	rs201299500	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45425209C>T	ENST00000331493.2	+	9	964	c.553C>T	c.(553-555)Cga>Tga	p.R185*	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	185						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R185*(1)									TAGTAAAATTCGAAGTGGTAA	0.323													C|||	3	0.000599042	0.0023	0	5008	,	,		17103	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	17						C	,stop/ARG	4,4398	8.1+/-20.4	0,4,2197	71	70	70		,553	2.5	0.8	17		70	0,8588		0,0,4294	yes	intron,stop-gained	C17orf57	NM_001195192.1,NM_152347.4	,	0,4,6491	TT,TC,CC		0.0,0.0909,0.0308	,	,185/974	45425209	4,12986	2201	4294	6495	42780208	SO:0001587	stop_gained	124989			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.553C>T	17.37:g.45425209C>T	ENSP00000332111:p.Arg185*		42780208	G3V128|Q49AG9	Nonsense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	39	7.388548	0.98252	9.09E-4	0.0	ENSG00000178852	ENST00000331493	.	.	.	4.57	2.55	0.30701	.	0.364949	0.15838	N	0.242166	.	.	.	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4187	5.6423	0.17571	0.1936:0.7034:0.0:0.103	.	.	.	.	X	185	.	ENSP00000332111:R185X	R	+	1	2	C17orf57	42780208	0.912000	0.30974	0.776000	0.31678	0.994000	0.84299	2.057000	0.41365	0.358000	0.24211	0.650000	0.86243	CGA		0.323	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		T	45425209	C	T	45425209	4	4	61	1	0	0	0	0	0	1	0	0	1870	876	31	1	575	1	C17orf57	17	45425209	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64451	45425209	35770001	10278	18263										
NPEPPS	9520	broad.mit.edu	37	chr17	45660192	45660192	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcattggttgttcctaaaGacagagtagctttatcaaac	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45660192G>A	ENST00000322157.4	+	5	862	c.625G>A	c.(625-627)Gac>Aac	p.D209N	NPEPPS_ENST00000544660.1_Intron|NPEPPS_ENST00000530173.1_Missense_Mutation_p.D205N|NPEPPS_ENST00000525037.1_3'UTR	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	209					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D209N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						TGTTCCTAAAGACAGAGTAGC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	17											10	8	8					17																	45660192		1748	3953	5701	43015191	SO:0001583	missense	9520			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.625G>A	17.37:g.45660192G>A	ENSP00000320324:p.Asp209Asn		43015191	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205632	0.79127	.	.	ENSG00000141279	ENST00000525007;ENST00000530173;ENST00000322157;ENST00000539572	T;T;T	0.04502	3.61;3.61;3.61	5.66	5.66	0.87406	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.045285	0.85682	D	0.000000	T	0.05593	0.0147	N	0.25485	0.75	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.18871	0.023;0.023	T	0.49322	-0.8952	10	0.21014	T	0.42	.	19.7302	0.96179	0.0:0.0:1.0:0.0	.	205;209	E9PLK3;P55786	.;PSA_HUMAN	N	196;205;209;196	ENSP00000437019:D196N;ENSP00000433287:D205N;ENSP00000320324:D209N	ENSP00000320324:D209N	D	+	1	0	NPEPPS	43015191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.857000	0.99534	2.669000	0.90835	0.585000	0.79938	GAC		0.348	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		A	45660192	G	A	45660192	3	1	61	1	0	0	0	0	1	0	0	0	10606	942	33	3	643	3	NPEPPS	17	45660192	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	234983	45660192	35535018	10279	18264										
TBX21	30009	broad.mit.edu	37	chr17	45822325	45822325	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctatgaggctgagtttcgaGcagtcagcatgaagcctgca	13	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45822325G>T	ENST00000177694.1	+	6	1412	c.1201G>T	c.(1201-1203)Gca>Tca	p.A401S		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	401					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.A401S(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGAGTTTCGAGCAGTCAGCAT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											52	52	52					17																	45822325		2203	4300	6503	43177324	SO:0001583	missense	30009			AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1201G>T	17.37:g.45822325G>T	ENSP00000177694:p.Ala401Ser		43177324		Missense_Mutation	SNP	ENST00000177694.1	37	CCDS11514.1	.	.	.	.	.	.	.	.	.	.	G	0.070	-1.205108	0.01568	.	.	ENSG00000073861	ENST00000177694	D	0.84146	-1.81	5.2	2.83	0.33086	.	0.660669	0.15314	N	0.268881	T	0.71508	0.3348	L	0.33245	0.995	0.09310	N	1	B	0.22800	0.075	B	0.16289	0.015	T	0.54483	-0.8287	10	0.02654	T	1	.	8.3109	0.32071	0.2106:0.0:0.7894:0.0	.	401	Q9UL17	TBX21_HUMAN	S	401	ENSP00000177694:A401S	ENSP00000177694:A401S	A	+	1	0	TBX21	43177324	0.342000	0.24809	0.411000	0.26484	0.681000	0.39784	1.580000	0.36547	1.173000	0.42796	0.655000	0.94253	GCA		0.647	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		T	45822325	G	T	45822325	3	4	61	1	0	0	0	0	1	0	0	0	15696	971	34	2	1223	2	TBX21	17	45822325	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	162133	45822325	35372885	10280	18265										
OSBPL7	114881	broad.mit.edu	37	chr17	45891086	45891086	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaccttggacaggtctTtgccgatgttgttgcgcaga	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:45891086T>G	ENST00000007414.3	-	15	1657	c.1466A>C	c.(1465-1467)aAa>aCa	p.K489T	OSBPL7_ENST00000392507.3_Missense_Mutation_p.K489T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	489					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.K489T(1)		autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGACAGGTCTTTGCCGATGTT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											67	62	64					17																	45891086		2203	4300	6503	43246085	SO:0001583	missense	114881			AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1466A>C	17.37:g.45891086T>G	ENSP00000007414:p.Lys489Thr		43246085	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	37	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.699865	0.88924	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.36699	1.24;1.24	4.82	4.82	0.62117	.	0.053128	0.64402	D	0.000001	T	0.68513	0.3009	M	0.93283	3.4	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.77803	-0.2451	10	0.87932	D	0	-17.1426	13.3618	0.60661	0.0:0.0:0.0:1.0	.	489	Q9BZF2	OSBL7_HUMAN	T	489	ENSP00000007414:K489T;ENSP00000376295:K489T	ENSP00000007414:K489T	K	-	2	0	OSBPL7	43246085	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.884000	0.87274	1.777000	0.52277	0.383000	0.25322	AAA		0.657	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		G	45891086	T	G	45891086	3	3	61	1	0	0	0	0	1	0	0	0	11313	1841	64	4	1098	4	OSBPL7	17	45891086	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	68761	45891086	35304124	10281	18266										
CDK5RAP3	80279	broad.mit.edu	37	chr17	46052898	46052898	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggcgaaaatgtccgaggaGaactgctggccctggtgaag	16	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46052898G>T	ENST00000338399.4	+	7	638	c.532G>T	c.(532-534)Gaa>Taa	p.E178*	RP11-6N17.9_ENST00000582262.1_RNA|CDK5RAP3_ENST00000536708.2_Nonsense_Mutation_p.E203*	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	178					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)	p.E178*(1)		NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						TGTCCGAGGAGAACTGCTGGC	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											63	68	66					17																	46052898		2084	4233	6317	43407897	SO:0001587	stop_gained	80279			AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.532G>T	17.37:g.46052898G>T	ENSP00000344683:p.Glu178*		43407897	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Nonsense_Mutation	SNP	ENST00000338399.4	37	CCDS42356.1	.	.	.	.	.	.	.	.	.	.	G	36	5.749816	0.96890	.	.	ENSG00000108465	ENST00000536708;ENST00000338399	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-1.1652	17.9577	0.89074	0.0:0.0:1.0:0.0	.	.	.	.	X	203;178	.	ENSP00000344683:E178X	E	+	1	0	CDK5RAP3	43407897	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.930000	0.92872	2.547000	0.85894	0.655000	0.94253	GAA		0.562	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096		T	46052898	G	T	46052898	4	4	61	1	0	0	0	0	0	1	0	0	3153	943	33	2	558	2	CDK5RAP3	17	46052898	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161812	46052898	35142312	10282	18267										
SNX11	29916	broad.mit.edu	37	chr17	46196102	46196102	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgggaagtcaaccttcttCggcacctcagatgagttcat	9	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46196102C>T	ENST00000393405.2	+	6	621	c.267C>T	c.(265-267)ttC>ttT	p.F89F	SNX11_ENST00000580219.1_Silent_p.F81F|SNX11_ENST00000578861.1_3'UTR|SNX11_ENST00000452859.2_5'UTR|SNX11_ENST00000359238.2_Silent_p.F89F|SNX11_ENST00000439357.2_Silent_p.F28F|SNX11_ENST00000582104.1_Silent_p.F81F	NM_152244.1	NP_689450.1	Q9Y5W9	SNX11_HUMAN	sorting nexin 11	89	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|vesicle organization (GO:0016050)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol phosphate binding (GO:1901981)	p.F89F(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	14						CAACCTTCTTCGGCACCTCAG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	17											90	82	85					17																	46196102		2203	4300	6503	43551101	SO:0001819	synonymous_variant	29916			AF121861	CCDS11526.1	17q21.32	2011-05-03			ENSG00000002919	ENSG00000002919		"Sorting nexins"	14975	protein-coding gene	gene with protein product		614906					Standard	NM_013323		Approved		uc002ing.1	Q9Y5W9		ENST00000393405.2:c.267C>T	17.37:g.46196102C>T			43551101	B3KRL6|B4DPY5|D3DTV0|Q53YC0|Q9H885	Silent	SNP	ENST00000393405.2	37	CCDS11526.1																																																																																				0.507	SNX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443423.1			T	46196102	C	T	46196102	2	4	61	1	0	0	0	0	0	0	0	1	14919	883	31	1		1	SNX11	17	46196102	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	143204	46196102	34999108	10283	18268										
SNX11	29916	broad.mit.edu	37	chr17	46198699	46198699	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccagttgttgactctgaGgttccttccttggaaagtcc	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46198699G>T	ENST00000393405.2	+	8	996	c.642G>T	c.(640-642)gaG>gaT	p.E214D	SNX11_ENST00000580219.1_Missense_Mutation_p.E206D|SNX11_ENST00000452859.2_Missense_Mutation_p.E70D|SNX11_ENST00000359238.2_Missense_Mutation_p.E214D|SNX11_ENST00000439357.2_Missense_Mutation_p.E153D|SNX11_ENST00000582104.1_Missense_Mutation_p.E206D	NM_152244.1	NP_689450.1	Q9Y5W9	SNX11_HUMAN	sorting nexin 11	214					intracellular protein transport (GO:0006886)|vesicle organization (GO:0016050)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol phosphate binding (GO:1901981)	p.E214D(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	14						TTGACTCTGAGGTTCCTTCCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											157	144	148					17																	46198699		2203	4300	6503	43553698	SO:0001583	missense	29916			AF121861	CCDS11526.1	17q21.32	2011-05-03			ENSG00000002919	ENSG00000002919		"Sorting nexins"	14975	protein-coding gene	gene with protein product		614906					Standard	NM_013323		Approved		uc002ing.1	Q9Y5W9		ENST00000393405.2:c.642G>T	17.37:g.46198699G>T	ENSP00000377059:p.Glu214Asp		43553698	B3KRL6|B4DPY5|D3DTV0|Q53YC0|Q9H885	Missense_Mutation	SNP	ENST00000393405.2	37	CCDS11526.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194856	0.58017	.	.	ENSG00000002919	ENST00000452859;ENST00000393405;ENST00000439357;ENST00000359238	T;T	0.66099	-0.19;-0.19	6.16	2.95	0.34219	.	0.450333	0.22920	N	0.054021	T	0.48277	0.1491	L	0.44542	1.39	0.31401	N	0.676688	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.45702	-0.9243	10	0.34782	T	0.22	-10.4643	5.6897	0.17823	0.1691:0.0:0.6772:0.1536	.	153;206;214	B4DKH7;B4DPY5;Q9Y5W9	.;.;SNX11_HUMAN	D	70;214;153;214	ENSP00000377059:E214D;ENSP00000352175:E214D	ENSP00000352175:E214D	E	+	3	2	SNX11	43553698	0.990000	0.36364	0.985000	0.45067	0.997000	0.91878	0.607000	0.24209	0.393000	0.25203	0.650000	0.86243	GAG		0.522	SNX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443423.1			T	46198699	G	T	46198699	3	4	61	1	0	0	0	0	1	0	0	0	14919	991	35	2	664	2	SNX11	17	46198699	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2597	46198699	34996511	10284	18269										
HOXB1	3211	broad.mit.edu	37	chr17	46607954	46607954	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatagcctccgtctccttCtgattgacccagagggtagt	9	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46607954C>A	ENST00000239174.6	-	1	405	c.313G>T	c.(313-315)Gaa>Taa	p.E105*	HOXB1_ENST00000577092.1_Nonsense_Mutation_p.E105*	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	105					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.E105*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCGTCTCCTTCTGATTGACCC	0.662																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											64	66	65					17																	46607954		2203	4300	6503	43962953	SO:0001587	stop_gained	3211				CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"Homeoboxes / ANTP class : HOXL subclass"	5111	protein-coding gene	gene with protein product		142968	"homeo box B1"	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.313G>T	17.37:g.46607954C>A	ENSP00000355140:p.Glu105*		43962953	Q4VB03	Nonsense_Mutation	SNP	ENST00000239174.6	37	CCDS32675.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381889	0.82792	.	.	ENSG00000120094	ENST00000239174	.	.	.	4.37	4.37	0.52481	.	0.152027	0.30791	N	0.008876	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	16.7235	0.85416	0.0:1.0:0.0:0.0	.	.	.	.	X	105	.	ENSP00000355140:E105X	E	-	1	0	HOXB1	43962953	1.000000	0.71417	0.926000	0.36857	0.701000	0.40568	6.968000	0.76086	2.266000	0.75297	0.643000	0.83706	GAA		0.662	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3			A	46607954	C	A	46607954	4	1	61	1	0	0	0	0	0	1	0	0	7320	922	32	2	600	2	HOXB1	17	46607954	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	409255	46607954	34587256	10285	18270										
HOXB3	3213	broad.mit.edu	37	chr17	46629594	46629594	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggcggggccgacaggggCtcgggggccagacccggcct	19	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46629594C>A	ENST00000470495.1	-	1	1690	c.243G>T	c.(241-243)gaG>gaT	p.E81D	HOXB-AS1_ENST00000435312.1_RNA|HOXB3_ENST00000490677.1_Intron|HOXB-AS1_ENST00000502764.2_RNA|HOXB3_ENST00000498678.1_Missense_Mutation_p.E81D|HOXB3_ENST00000485909.2_Intron|HOXB3_ENST00000311626.4_Missense_Mutation_p.E81D|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000476342.1_Missense_Mutation_p.E81D|HOXB3_ENST00000472863.1_Missense_Mutation_p.E8D|HOXB3_ENST00000489475.1_Missense_Mutation_p.E8D|HOXB-AS1_ENST00000508688.1_RNA			P14651	HXB3_HUMAN	homeobox B3	81					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|face development (GO:0060324)|glossopharyngeal nerve morphogenesis (GO:0021615)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neurogenesis (GO:0050767)|rhombomere development (GO:0021546)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E81D(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(16)|prostate(4)|upper_aerodigestive_tract(1)	30						CCGACAGGGGCTCGGGGGCCA	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	17											29	39	36					17																	46629594		2200	4297	6497	43984593	SO:0001583	missense	3213				CCDS11528.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120093	ENSG00000120093		"Homeoboxes / ANTP class : HOXL subclass"	5114	protein-coding gene	gene with protein product		142966	"homeo box B3"	HOX2, HOX2G		1973146, 1358459	Standard	XM_006721854		Approved		uc002ino.3	P14651	OTTHUMG00000159922	ENST00000470495.1:c.243G>T	17.37:g.46629594C>A	ENSP00000417207:p.Glu81Asp		43984593	A8K567|B7Z5N8|B7Z5P8|B7ZAD0|D3DTV3|O95615|P17484	Missense_Mutation	SNP	ENST00000470495.1	37	CCDS11528.1	.	.	.	.	.	.	.	.	.	.	C	5.076	0.199735	0.09652	.	.	ENSG00000120093	ENST00000470495;ENST00000472863;ENST00000311626;ENST00000498678;ENST00000489475;ENST00000476342;ENST00000471459	D;D;D;D;D;D;T	0.91351	-2.81;-2.83;-2.81;-2.81;-2.83;-2.81;1.38	3.96	2.96	0.34315	.	0.371166	0.25820	N	0.028092	D	0.86397	0.5923	L	0.52905	1.665	0.80722	D	1	B	0.22080	0.064	B	0.17979	0.02	T	0.80484	-0.1362	10	0.19147	T	0.46	.	12.7074	0.57067	0.1665:0.8335:0.0:0.0	.	81	P14651	HXB3_HUMAN	D	81;8;81;81;8;81;8	ENSP00000417207:E81D;ENSP00000419676:E8D;ENSP00000308252:E81D;ENSP00000420595:E81D;ENSP00000418729:E8D;ENSP00000418892:E81D;ENSP00000417400:E8D	ENSP00000308252:E81D	E	-	3	2	HOXB3	43984593	0.971000	0.33674	0.995000	0.50966	0.008000	0.06430	0.127000	0.15790	0.976000	0.38417	-0.500000	0.04577	GAG		0.687	HOXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358261.1			A	46629594	C	A	46629594	3	1	61	1	0	0	0	0	1	0	0	0	7323	796	28	2	1060	2	HOXB3	17	46629594	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21640	46629594	34565616	10286	18271										
HOXB4	3214	broad.mit.edu	37	chr17	46654195	46654195	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtggtcttttttccacttCatgcgccggttctggaacca	9	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46654195C>A	ENST00000332503.5	-	2	2436	c.645G>T	c.(643-645)atG>atT	p.M215I	HOXB3_ENST00000490677.1_5'Flank|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000311626.4_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000476342.1_Intron|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000489475.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	215					anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M215I(1)		central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						TTTTCCACTTCATGCGCCGGT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											84	90	88					17																	46654195		2203	4300	6503	44009194	SO:0001583	missense	3214				CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.645G>T	17.37:g.46654195C>A	ENSP00000328928:p.Met215Ile		44009194	Q9NTA0	Missense_Mutation	SNP	ENST00000332503.5	37	CCDS11529.1	.	.	.	.	.	.	.	.	.	.	C	34	5.296951	0.95574	.	.	ENSG00000182742	ENST00000332503	D	0.96136	-3.92	5.78	5.78	0.91487	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	M	0.73372	2.23	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.97925	1.0317	10	0.87932	D	0	.	19.6218	0.95660	0.0:1.0:0.0:0.0	.	215	P17483	HXB4_HUMAN	I	215	ENSP00000328928:M215I	ENSP00000328928:M215I	M	-	3	0	HOXB4	44009194	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.801000	0.85960	2.724000	0.93272	0.555000	0.69702	ATG		0.652	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			A	46654195	C	A	46654195	3	1	61	1	0	0	0	0	1	0	0	0	7324	826	29	2	114	2	HOXB4	17	46654195	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24601	46654195	34541015	10287	18272										
HOXB8	3218	broad.mit.edu	37	chr17	46690633	46690633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccgctccagcttctgtttCtccagctcctcctgctcgca	7	19	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:46690633C>A	ENST00000239144.4	-	2	897	c.663G>T	c.(661-663)gaG>gaT	p.E221D	HOXB7_ENST00000567101.2_Intron|HOXB7_ENST00000239165.7_5'Flank|HOXB8_ENST00000576562.1_Missense_Mutation_p.E220D	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	221					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E221D(1)		large_intestine(1)|lung(8)|urinary_tract(2)	11						GCTTCTGTTTCTCCAGCTCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	89	88					17																	46690633		2203	4300	6503	44045632	SO:0001583	missense	3218				CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"Homeoboxes / ANTP class : HOXL subclass"	5119	protein-coding gene	gene with protein product		142963	"homeo box B8"	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.663G>T	17.37:g.46690633C>A	ENSP00000239144:p.Glu221Asp		44045632	Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	37	CCDS11533.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.765940	0.49574	.	.	ENSG00000120068	ENST00000239144	D	0.90133	-2.62	3.04	1.01	0.19927	.	0.000000	0.42682	U	0.000676	T	0.79639	0.4480	N	0.19112	0.55	0.44175	D	0.996982	B	0.19200	0.034	B	0.12156	0.007	T	0.67632	-0.5621	10	0.23891	T	0.37	.	8.0044	0.30317	0.0:0.6888:0.0:0.3112	.	221	P17481	HXB8_HUMAN	D	221	ENSP00000239144:E221D	ENSP00000239144:E221D	E	-	3	2	HOXB8	44045632	0.953000	0.32496	1.000000	0.80357	0.995000	0.86356	0.242000	0.18087	0.639000	0.30564	0.479000	0.44913	GAG		0.597	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3			A	46690633	C	A	46690633	3	1	61	1	0	0	0	0	1	0	0	0	7328	912	32	2	72	2	HOXB8	17	46690633	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36438	46690633	34504577	10288	18273										
IGF2BP1	10642	broad.mit.edu	37	chr17	47115563	47115563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaatggccaccagttggaGaaccatgccctgaaggtctc	11	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47115563G>T	ENST00000290341.3	+	6	769	c.435G>T	c.(433-435)gaG>gaT	p.E145D	RNU6-826P_ENST00000516827.1_RNA|IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	145	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)	p.E145D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						ACCAGTTGGAGAACCATGCCC	0.577																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)											1	Substitution - Missense(1)	large_intestine(1)	17											86	89	88					17																	47115563		2203	4300	6503	44470562	SO:0001583	missense	10642			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.435G>T	17.37:g.47115563G>T	ENSP00000290341:p.Glu145Asp		44470562	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184037	0.38609	.	.	ENSG00000159217	ENST00000290341	T	0.15834	2.39	5.42	3.44	0.39384	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.055845	0.64402	D	0.000001	T	0.12433	0.0302	N	0.25201	0.72	0.80722	D	1	B	0.16802	0.019	B	0.30782	0.12	T	0.10590	-1.0623	10	0.37606	T	0.19	-32.6098	8.1065	0.30890	0.311:0.0:0.689:0.0	.	145	Q9NZI8	IF2B1_HUMAN	D	145	ENSP00000290341:E145D	ENSP00000290341:E145D	E	+	3	2	IGF2BP1	44470562	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.990000	0.29642	0.653000	0.30826	-0.251000	0.11542	GAG		0.577	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		T	47115563	G	T	47115563	3	4	61	1	0	0	0	0	1	0	0	0	7594	933	33	2	457	2	IGF2BP1	17	47115563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	424930	47115563	34079647	10289	18274										
IGF2BP1	10642	broad.mit.edu	37	chr17	47117344	47117344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtgcataggaaggagaacGcaggtgcagctgaaaaagcc	14	8	0	2	rs375360274		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47117344G>A	ENST00000290341.3	+	7	1043	c.709G>A	c.(709-711)Gca>Aca	p.A237T	IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	237	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with ELAVL4 and binding to TAU mRNA. {ECO:0000250}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)	p.A237T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						GAAGGAGAACGCAGGTGCAGC	0.542																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)											1	Substitution - Missense(1)	large_intestine(1)	17						G	,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	139	127	131		,709	4.6	0.7	17		131	0,8600		0,0,4300	no	intron,missense	IGF2BP1	NM_001160423.1,NM_006546.3	,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,benign	,237/578	47117344	1,13005	2203	4300	6503	44472343	SO:0001583	missense	10642			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.709G>A	17.37:g.47117344G>A	ENSP00000290341:p.Ala237Thr		44472343	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036777	0.54896	2.27E-4	0.0	ENSG00000159217	ENST00000290341	T	0.42131	0.98	5.65	4.63	0.57726	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.056676	0.64402	D	0.000001	T	0.40815	0.1132	L	0.59436	1.845	0.80722	D	1	B	0.27910	0.193	B	0.28139	0.086	T	0.28170	-1.0052	10	0.37606	T	0.19	-15.9972	14.3287	0.66537	0.0:0.0:0.851:0.149	.	237	Q9NZI8	IF2B1_HUMAN	T	237	ENSP00000290341:A237T	ENSP00000290341:A237T	A	+	1	0	IGF2BP1	44472343	1.000000	0.71417	0.654000	0.29608	0.654000	0.38779	7.885000	0.87282	2.655000	0.90218	0.655000	0.94253	GCA		0.542	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		A	47117344	G	A	47117344	3	1	61	1	0	0	0	0	1	0	0	0	7594	1087	38	1	735	1	IGF2BP1	17	47117344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1781	47117344	34077866	10290	18275										
IGF2BP1	10642	broad.mit.edu	37	chr17	47119662	47119662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactgtgaagggggccatcGagaattgttgcagggccgag	16	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47119662G>A	ENST00000290341.3	+	9	1334	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	IGF2BP1_ENST00000431824.2_Missense_Mutation_p.E195K	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	334	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with ELAVL4 and binding to TAU mRNA. {ECO:0000250}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)	p.E334K(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						GGGGGCCATCGAGAATTGTTG	0.527																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)											1	Substitution - Missense(1)	large_intestine(1)	17											116	115	115					17																	47119662		2203	4300	6503	44474661	SO:0001583	missense	10642			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.1000G>A	17.37:g.47119662G>A	ENSP00000290341:p.Glu334Lys		44474661	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.662202	0.88251	.	.	ENSG00000159217	ENST00000290341;ENST00000431824	T;T	0.35973	1.28;1.28	5.59	5.59	0.84812	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.051943	0.85682	D	0.000000	T	0.56247	0.1972	L	0.55213	1.73	0.80722	D	1	D;P	0.54772	0.968;0.523	D;B	0.65010	0.931;0.344	T	0.50988	-0.8762	10	0.48119	T	0.1	-27.4242	19.5457	0.95295	0.0:0.0:1.0:0.0	.	195;334	C9JT33;Q9NZI8	.;IF2B1_HUMAN	K	334;195	ENSP00000290341:E334K;ENSP00000389135:E195K	ENSP00000290341:E334K	E	+	1	0	IGF2BP1	44474661	1.000000	0.71417	0.995000	0.50966	0.974000	0.67602	9.696000	0.98695	2.763000	0.94921	0.655000	0.94253	GAG		0.527	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		A	47119662	G	A	47119662	3	1	61	1	0	0	0	0	1	0	0	0	7594	1059	37	1	1034	1	IGF2BP1	17	47119662	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2318	47119662	34075548	10291	18276										
B4GALNT2	124872	broad.mit.edu	37	chr17	47241548	47241548	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattcgagagtattacccaGacttgaccgtaatagtggct	10	8	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47241548G>T	ENST00000300404.2	+	8	1104	c.1045G>T	c.(1045-1047)Gac>Tac	p.D349Y	B4GALNT2_ENST00000504681.1_Missense_Mutation_p.D263Y|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.D289Y	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	349					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)	p.D349Y(1)		endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			GTATTACCCAGACTTGACCGT	0.488																																					GBM(124;244 1635 8663 18097 33175)											1	Substitution - Missense(1)	large_intestine(1)	17											165	165	165					17																	47241548		2203	4300	6503	44596547	SO:0001583	missense	124872			AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	24136	protein-coding gene	gene with protein product		111730	"UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1045G>T	17.37:g.47241548G>T	ENSP00000300404:p.Asp349Tyr		44596547	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.229802	0.58777	.	.	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.79554	-1.28;-1.28;-1.28	5.58	5.58	0.84498	Glycosyl transferase, family 2 (1);	0.128081	0.51477	D	0.000086	D	0.86213	0.5879	L	0.54323	1.7	0.39191	D	0.962959	D;D	0.89917	1.0;0.999	D;D	0.79108	0.991;0.992	D	0.87363	0.2345	10	0.62326	D	0.03	-31.9085	11.772	0.51965	0.0822:0.0:0.9178:0.0	.	289;349	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	Y	263;289;349	ENSP00000425510:D263Y;ENSP00000377022:D289Y;ENSP00000300404:D349Y	ENSP00000300404:D349Y	D	+	1	0	B4GALNT2	44596547	0.980000	0.34600	1.000000	0.80357	0.737000	0.42083	3.724000	0.54962	2.621000	0.88768	0.555000	0.69702	GAC		0.488	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		T	47241548	G	T	47241548	3	4	61	1	0	0	0	0	1	0	0	0	1268	942	33	2	1093	2	B4GALNT2	17	47241548	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121886	47241548	33953662	10292	18277										
B4GALNT2	124872	broad.mit.edu	37	chr17	47246102	47246102	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttgctggaacagagtgaGaatggggcctgccttcacaa	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47246102G>T	ENST00000300404.2	+	10	1394	c.1335G>T	c.(1333-1335)gaG>gaT	p.E445D	B4GALNT2_ENST00000504681.1_Missense_Mutation_p.E359D|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.E385D	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	445					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)	p.E445D(1)		endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			AACAGAGTGAGAATGGGGCCT	0.542																																					GBM(124;244 1635 8663 18097 33175)											1	Substitution - Missense(1)	large_intestine(1)	17											101	77	85					17																	47246102		2203	4300	6503	44601101	SO:0001583	missense	124872			AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	24136	protein-coding gene	gene with protein product		111730	"UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1335G>T	17.37:g.47246102G>T	ENSP00000300404:p.Glu445Asp		44601101	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	.	.	.	.	.	.	.	.	.	.	G	9.259	1.042633	0.19748	.	.	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.27104	1.69;1.69;1.69	5.7	2.67	0.31697	.	0.614190	0.15418	N	0.263392	T	0.12008	0.0292	N	0.16130	0.375	0.09310	N	1	B;B	0.30068	0.003;0.267	B;B	0.27608	0.011;0.081	T	0.26815	-1.0092	10	0.18710	T	0.47	-12.1329	6.0636	0.19852	0.2175:0.1464:0.6361:0.0	.	385;445	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	D	359;385;445	ENSP00000425510:E359D;ENSP00000377022:E385D;ENSP00000300404:E445D	ENSP00000300404:E445D	E	+	3	2	B4GALNT2	44601101	0.995000	0.38212	0.009000	0.14445	0.759000	0.43091	0.511000	0.22739	0.769000	0.33313	-0.225000	0.12378	GAG		0.542	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		T	47246102	G	T	47246102	3	4	61	1	0	0	0	0	1	0	0	0	1268	933	33	2	1391	2	B4GALNT2	17	47246102	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4554	47246102	33949108	10293	18278										
ZNF652	22834	broad.mit.edu	37	chr17	47375855	47375855	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcctctatgatttaaagGctcactcttaaagagagctg	9	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47375855G>T	ENST00000362063.2	-	6	2059	c.1741C>A	c.(1741-1743)Cct>Act	p.P581T	ZNF652_ENST00000430262.2_Missense_Mutation_p.P581T	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	581	Mediates interaction with CBFA2T3.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P581S(1)|p.P581T(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			TGATTTAAAGGCTCACTCTTA	0.542																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	17											79	78	79					17																	47375855		2203	4300	6503	44730854	SO:0001583	missense	22834			AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"Zinc fingers, C2H2-type"	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.1741C>A	17.37:g.47375855G>T	ENSP00000354686:p.Pro581Thr		44730854	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796681	0.70567	.	.	ENSG00000198740	ENST00000362063;ENST00000430262	T;T	0.78481	-1.18;-1.18	4.51	4.51	0.55191	.	0.055059	0.85682	D	0.000000	T	0.66944	0.2841	L	0.36672	1.1	0.53688	D	0.999973	P	0.37781	0.608	B	0.32465	0.146	T	0.72211	-0.4359	10	0.62326	D	0.03	-10.0371	13.1798	0.59647	0.0:0.1604:0.8396:0.0	.	581	Q9Y2D9	ZN652_HUMAN	T	581	ENSP00000354686:P581T;ENSP00000416305:P581T	ENSP00000354686:P581T	P	-	1	0	ZNF652	44730854	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.927000	0.70080	2.506000	0.84524	0.591000	0.81541	CCT		0.542	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		T	47375855	G	T	47375855	3	4	61	1	0	0	0	0	1	0	0	0	18104	1203	42	2	83	2	ZNF652	17	47375855	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129753	47375855	33819355	10294	18279										
ZNF652	22834	broad.mit.edu	37	chr17	47390127	47390127	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatttcacaggaaaatttCttttctgcatatccatggac	5	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47390127C>A	ENST00000362063.2	-	3	1299	c.981G>T	c.(979-981)aaG>aaT	p.K327N	ZNF652_ENST00000430262.2_Missense_Mutation_p.K327N	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K327N(2)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			AGGAAAATTTCTTTTCTGCAT	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	17											78	79	79					17																	47390127		2203	4300	6503	44745126	SO:0001583	missense	22834			AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"Zinc fingers, C2H2-type"	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.981G>T	17.37:g.47390127C>A	ENSP00000354686:p.Lys327Asn		44745126	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698319	0.68386	.	.	ENSG00000198740	ENST00000362063;ENST00000430262	T;T	0.35048	1.33;1.33	5.67	4.7	0.59300	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	M	0.76938	2.355	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.61357	-0.7079	10	0.87932	D	0	-21.4443	10.6194	0.45470	0.0:0.8424:0.0:0.1576	.	327	Q9Y2D9	ZN652_HUMAN	N	327	ENSP00000354686:K327N;ENSP00000416305:K327N	ENSP00000354686:K327N	K	-	3	2	ZNF652	44745126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.936000	0.56568	1.377000	0.46286	0.591000	0.81541	AAG		0.363	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		A	47390127	C	A	47390127	3	1	61	1	0	0	0	0	1	0	0	0	18104	912	32	2	855	2	ZNF652	17	47390127	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14272	47390127	33805083	10295	18280										
PHB	5245	broad.mit.edu	37	chr17	47482547	47482547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcagcagagatgatggccGcctttttctgttgctcagcc	10	13	3	2	rs377541756		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47482547G>A	ENST00000300408.3	-	7	698	c.626C>T	c.(625-627)gCg>gTg	p.A209V	RP11-81K2.1_ENST00000576461.1_Intron|RP11-1079K10.4_ENST00000506504.3_RNA|PHB_ENST00000508009.1_5'Flank|PHB_ENST00000511832.1_Intron	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	209					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)	p.A209V(1)		endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			GATGATGGCCGCCTTTTTCTG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	VAL/ALA	0,4406		0,0,2203	25	24	25		626	5.1	1	17		25	1,8595		0,1,4297	no	missense	PHB	NM_002634.2	64	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	209/273	47482547	1,13001	2203	4298	6501	44837546	SO:0001583	missense	5245				CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.626C>T	17.37:g.47482547G>A	ENSP00000300408:p.Ala209Val		44837546	B4DY47|Q4VBQ0	Missense_Mutation	SNP	ENST00000300408.3	37	CCDS11548.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070160	0.76301	0.0	1.16E-4	ENSG00000167085	ENST00000300408;ENST00000419140;ENST00000504124	.	.	.	5.14	5.14	0.70334	.	0.102691	0.64402	D	0.000003	T	0.76147	0.3947	M	0.86651	2.83	0.80722	D	1	P	0.35527	0.507	B	0.40375	0.327	T	0.79581	-0.1744	9	0.56958	D	0.05	.	18.3887	0.90474	0.0:0.0:1.0:0.0	.	209	P35232	PHB_HUMAN	V	209	.	ENSP00000300408:A209V	A	-	2	0	PHB	44837546	1.000000	0.71417	0.976000	0.42696	0.644000	0.38419	9.620000	0.98373	2.661000	0.90470	0.655000	0.94253	GCG		0.552	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		A	47482547	G	A	47482547	3	1	61	1	0	0	0	0	1	0	0	0	11845	1087	38	1	196	1	PHB	17	47482547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	92420	47482547	33712663	10296	18281										
NGFR	4804	broad.mit.edu	37	chr17	47590207	47590207	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaccagcccgagcacataGactcctttacccatgaggcc	8	16	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47590207G>T	ENST00000172229.3	+	6	1245	c.1120G>T	c.(1120-1122)Gac>Tac	p.D374Y	NGFR_ENST00000504201.1_Missense_Mutation_p.D280Y|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	374	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.D374Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					CGAGCACATAGACTCCTTTAC	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	17											40	45	44					17																	47590207		2203	4299	6502	44945206	SO:0001583	missense	4804			M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.1120G>T	17.37:g.47590207G>T	ENSP00000172229:p.Asp374Tyr		44945206	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263637	0.80358	.	.	ENSG00000064300	ENST00000172229;ENST00000504201	D;D	0.86769	-2.17;-2.17	4.85	4.85	0.62838	Death (3);DEATH-like (2);	0.261083	0.35407	N	0.003222	D	0.91415	0.7291	L	0.55481	1.735	0.45366	D	0.998355	D	0.67145	0.996	D	0.67382	0.951	D	0.92513	0.6018	10	0.87932	D	0	-37.4687	16.7461	0.85471	0.0:0.0:1.0:0.0	.	374	P08138	TNR16_HUMAN	Y	374;280	ENSP00000172229:D374Y;ENSP00000421731:D280Y	ENSP00000172229:D374Y	D	+	1	0	NGFR	44945206	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.455000	0.73497	2.233000	0.73108	0.561000	0.74099	GAC		0.701	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			T	47590207	G	T	47590207	3	4	61	1	0	0	0	0	1	0	0	0	10427	942	33	2	1142	2	NGFR	17	47590207	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107660	47590207	33605003	10297	18282										
FAM117A	81558	broad.mit.edu	37	chr17	47788670	47788670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttctgatggtggggtgcGctgccatggctcgaatggca	15	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47788670G>A	ENST00000240364.2	-	8	1388	c.1309C>T	c.(1309-1311)Cgc>Tgc	p.R437C	RP11-613C6.2_ENST00000512720.1_RNA|FAM117A_ENST00000513602.1_Missense_Mutation_p.R165C	NM_030802.3	NP_110429.1	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	437	Pro-rich.							p.R437C(1)		haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	17						GGTGGGGTGCGCTGCCATGGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											25	27	26					17																	47788670		2203	4299	6502	45143669	SO:0001583	missense	81558			BC037572	CCDS11553.1	17q21.33	2006-04-26				ENSG00000121104			24179	protein-coding gene	gene with protein product	"C/EBP induced protein"					12477932	Standard	NM_030802		Approved		uc002ipk.3	Q9C073		ENST00000240364.2:c.1309C>T	17.37:g.47788670G>A	ENSP00000240364:p.Arg437Cys		45143669	B7Z7Q3	Missense_Mutation	SNP	ENST00000240364.2	37	CCDS11553.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406769	0.62399	.	.	ENSG00000121104	ENST00000240364	.	.	.	5.23	4.24	0.50183	.	0.186093	0.31020	N	0.008407	T	0.33731	0.0873	N	0.08118	0	0.42444	D	0.992725	D	0.59767	0.986	P	0.47015	0.534	T	0.41928	-0.9481	9	0.87932	D	0	-12.0034	13.0687	0.59048	0.0:0.0:0.839:0.161	.	437	Q9C073	F117A_HUMAN	C	437	.	ENSP00000240364:R437C	R	-	1	0	FAM117A	45143669	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	3.295000	0.51794	1.393000	0.46605	0.557000	0.71058	CGC		0.637	FAM117A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365736.1	NM_030802		A	47788670	G	A	47788670	3	1	61	1	0	0	0	0	1	0	0	0	5425	1087	38	1	56	1	FAM117A	17	47788670	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	198463	47788670	33406540	10298	18283										
MYST2	11143	broad.mit.edu	37	chr17	47874243	47874243	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctcttcggcagactcgtTcatctggttcagaaactgag	9	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:47874243T>G	ENST00000259021.4	+	3	575	c.295T>G	c.(295-297)Tca>Gca	p.S99A	KAT7_ENST00000454930.2_Intron|KAT7_ENST00000509773.1_Missense_Mutation_p.S99A|KAT7_ENST00000424009.2_Missense_Mutation_p.S99A|KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000510819.1_Intron	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	99					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S99A(1)									GCAGACTCGTTCATCTGGTTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	17											156	157	156					17																	47874243		2203	4300	6503	45229242	SO:0001583	missense	11143			AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.295T>G	17.37:g.47874243T>G	ENSP00000259021:p.Ser99Ala		45229242	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.789957	0.90367	.	.	ENSG00000136504	ENST00000259021;ENST00000509773;ENST00000424009	.	.	.	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000001	T	0.66674	0.2813	L	0.47716	1.5	0.80722	D	1	P;P;P	0.47910	0.841;0.841;0.902	P;P;P	0.57283	0.661;0.661;0.817	T	0.64236	-0.6455	9	0.37606	T	0.19	-7.9955	16.0444	0.80711	0.0:0.0:0.0:1.0	.	99;99;99	B4DFB4;O95251;G5E9K7	.;KAT7_HUMAN;.	A	99	.	ENSP00000259021:S99A	S	+	1	0	KAT7	45229242	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	7.206000	0.77891	2.271000	0.75665	0.459000	0.35465	TCA		0.478	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		G	47874243	T	G	47874243	3	3	61	1	0	0	0	0	1	0	0	0	10133	1783	62	4	305	4	MYST2	17	47874243	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	85573	47874243	33320967	10299	18284										
PDK2	5164	broad.mit.edu	37	chr17	48186759	48186759	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccgatgctgtcatctatCtcaaggtgagggcccttccc	11	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48186759C>A	ENST00000503176.1	+	10	1239	c.1078C>A	c.(1078-1080)Ctc>Atc	p.L360I	PDK2_ENST00000007708.3_Missense_Mutation_p.L296I	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	360	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.L360I(1)		central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						TGTCATCTATCTCAAGGTGAG	0.587									Autosomal Dominant Polycystic Kidney Disease																																							1	Substitution - Missense(1)	large_intestine(1)	17											68	57	61					17																	48186759		2203	4300	6503	45541758	SO:0001583	missense	5164	Familial Cancer Database	ADPKD	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"pyruvate dehydrogenase kinase, isoenzyme 2"			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.1078C>A	17.37:g.48186759C>A	ENSP00000420927:p.Leu360Ile		45541758	A8K3A7|B3KNW0|Q6P515|Q9BS05	Missense_Mutation	SNP	ENST00000503176.1	37	CCDS11559.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548678	0.65311	.	.	ENSG00000005882	ENST00000007708;ENST00000503176	T;T	0.60548	0.18;0.18	4.85	4.85	0.62838	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.64402	D	0.000006	T	0.68714	0.3031	M	0.72479	2.2	0.80722	D	1	P	0.43973	0.823	P	0.60068	0.868	T	0.67741	-0.5592	10	0.38643	T	0.18	-29.2355	7.825	0.29309	0.0:0.8203:0.0:0.1797	.	360	Q15119	PDK2_HUMAN	I	296;360	ENSP00000007708:L296I;ENSP00000420927:L360I	ENSP00000007708:L296I	L	+	1	0	PDK2	45541758	0.973000	0.33851	1.000000	0.80357	0.972000	0.66771	0.172000	0.16704	2.401000	0.81631	0.462000	0.41574	CTC		0.587	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611		A	48186759	C	A	48186759	3	1	61	1	0	0	0	0	1	0	0	0	11707	913	32	2	1116	2	PDK2	17	48186759	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	312516	48186759	33008451	10300	18285										
SAMD14	201191	broad.mit.edu	37	chr17	48202316	48202316	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggttctcggagctttgaaGaagccatgactcaagagagc	13	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48202316G>T	ENST00000330175.4	-	2	325	c.8C>A	c.(7-9)tCt>tAt	p.S3Y	SAMD14_ENST00000503131.1_Missense_Mutation_p.S3Y|SAMD14_ENST00000503734.1_5'Flank	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	3								p.S3Y(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						GAGCTTTGAAGAAGCCATGAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	111	112					17																	48202316		2203	4300	6503	45557315	SO:0001583	missense	201191				CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.8C>A	17.37:g.48202316G>T	ENSP00000329144:p.Ser3Tyr		45557315	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	37	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971623	0.34754	.	.	ENSG00000167100	ENST00000330175;ENST00000503131;ENST00000511964	.	.	.	5.11	5.11	0.69529	.	0.000000	0.40469	U	0.001100	T	0.60676	0.2287	N	0.14661	0.345	0.44085	D	0.996844	D;D	0.58620	0.972;0.983	D;P	0.69142	0.962;0.837	T	0.67665	-0.5612	9	0.87932	D	0	-1.3489	15.4499	0.75265	0.0:0.0:1.0:0.0	.	3;3	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	Y	3	.	ENSP00000329144:S3Y	S	-	2	0	SAMD14	45557315	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.004000	0.63966	2.375000	0.81037	0.655000	0.94253	TCT		0.498	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		T	48202316	G	T	48202316	3	4	61	1	0	0	0	0	1	0	0	0	13856	942	33	2	1369	2	SAMD14	17	48202316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15557	48202316	32992894	10301	18286										
COL1A1	1277	broad.mit.edu	37	chr17	48262896	48262896	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagggccaacgtcgaagccGaattcctggtctggggcacc	13	13	1	0	rs72656352		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48262896G>A	ENST00000225964.5	-	51	4480	c.4362C>T	c.(4360-4362)ttC>ttT	p.F1454F		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1454	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.F1454F(1)	COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	CGTCGAAGCCGAATTCCTGGT	0.582			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																																Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	1	Substitution - coding silent(1)	large_intestine(1)	17											108	96	100					17																	48262896		2203	4300	6503	45617895	SO:0001819	synonymous_variant	1277			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.4362C>T	17.37:g.48262896G>A			45617895	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																				0.582	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48262896	G	A	48262896	2	1	61	1	0	0	0	0	0	0	0	1	3683	1049	37	1		1	COL1A1	17	48262896	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60580	48262896	32932314	10302	18287										
CHAD	1101	broad.mit.edu	37	chr17	48542777	48542777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcacaggtggcatctgggCgggaggccttggcttccagc	17	11	1	0	rs34405131	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48542777C>T	ENST00000508540.1	-	3	1114	c.962G>A	c.(961-963)cGc>cAc	p.R321H	ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000427954.2_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.R321H|ACSF2_ENST00000300441.4_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	321	LRRCT.				bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)		p.R321H(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGCATCTGGGCGGGAGGCCTT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											47	41	43					17																	48542777		2203	4300	6503	45897776	SO:0001583	missense	1101			U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1909	protein-coding gene	gene with protein product	"chondroadherin proteoglycan"	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.962G>A	17.37:g.48542777C>T	ENSP00000423812:p.Arg321His		45897776	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.163498|5.163498	0.94727|0.94727	.|.	.|.	ENSG00000136457|ENSG00000136457	ENST00000506187|ENST00000508540;ENST00000258969	.|T;T	.|0.56611	.|0.45;0.45	5.12|5.12	5.12|5.12	0.69794|0.69794	.|Cysteine-rich flanking region, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71813|0.71813	0.3384|0.3384	M|M	0.69358|0.69358	2.11|2.11	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.78314	.|0.991	T|T	0.74219|0.74219	-0.3736|-0.3736	5|10	.|0.59425	.|D	.|0.04	.|.	18.5806|18.5806	0.91170|0.91170	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|321	.|O15335	.|CHAD_HUMAN	T|H	4|321	.|ENSP00000423812:R321H;ENSP00000258969:R321H	.|ENSP00000258969:R321H	A|R	-|-	1|2	0|0	CHAD|CHAD	45897776|45897776	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.244000|5.244000	0.65400|0.65400	2.380000|2.380000	0.81148|0.81148	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.627	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		T	48542777	C	T	48542777	3	4	61	1	0	0	0	0	1	0	0	0	3316	768	27	1	121	1	CHAD	17	48542777	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279881	48542777	32652433	10303	18288										
MYCBPAP	84073	broad.mit.edu	37	chr17	48595005	48595005	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatcctgccccaccacatCttggggagtctccaggattt	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48595005C>A	ENST00000323776.5	+	4	705	c.543C>A	c.(541-543)atC>atA	p.I181I	MYCBPAP_ENST00000436259.2_Silent_p.I144I	NM_032133.4	NP_115509.4			MYCBP associated protein									p.I144I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			CCCACCACATCTTGGGGAGTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	17											69	67	68					17																	48595005		2203	4300	6503	45950004	SO:0001819	synonymous_variant	84073			BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.543C>A	17.37:g.48595005C>A			45950004		Silent	SNP	ENST00000323776.5	37	CCDS32680.2																																																																																				0.517	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		A	48595005	C	A	48595005	2	1	61	1	0	0	0	0	0	0	0	1	10049	903	32	2		2	MYCBPAP	17	48595005	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52228	48595005	32600205	10304	18289										
CACNA1G	8913	broad.mit.edu	37	chr17	48693689	48693689	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcttcactgtcatctttgtCttggagtcagttttcaaact	6	9	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48693689C>A	ENST00000359106.5	+	28	4965	c.4965C>A	c.(4963-4965)gtC>gtA	p.V1655V	CACNA1G_ENST00000354983.4_Silent_p.V1621V|CACNA1G_ENST00000352832.5_Silent_p.V1621V|CACNA1G_ENST00000515411.1_Silent_p.V1637V|CACNA1G_ENST00000514181.1_Silent_p.V1637V|CACNA1G_ENST00000429973.2_Silent_p.V1637V|CACNA1G_ENST00000515165.1_Silent_p.V1655V|CACNA1G_ENST00000515765.1_Silent_p.V1644V|CACNA1G_ENST00000505165.1_Silent_p.V1655V|CACNA1G_ENST00000503485.1_Silent_p.V1621V|CACNA1G_ENST00000442258.2_Silent_p.V1614V|CACNA1G_ENST00000507510.2_Silent_p.V1655V|CACNA1G_ENST00000507336.1_Silent_p.V1644V|CACNA1G_ENST00000513689.2_Silent_p.V1610V|CACNA1G_ENST00000358244.5_Silent_p.V1621V|CACNA1G_ENST00000514717.1_Silent_p.V1598V|CACNA1G_ENST00000510366.1_Silent_p.V1603V|CACNA1G_ENST00000510115.1_Silent_p.V1621V|CACNA1G_ENST00000514079.1_Silent_p.V1662V|CACNA1G_ENST00000513964.1_Silent_p.V1610V|CACNA1G_ENST00000512389.1_Silent_p.V1644V|CACNA1G_ENST00000507609.1_Silent_p.V1655V|CACNA1G_ENST00000502264.1_Silent_p.V1632V|CACNA1G_ENST00000507896.1_Silent_p.V1644V|CACNA1G_ENST00000360761.4_Silent_p.V1632V	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1655					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.V1621V(1)|p.V1655V(1)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TCATCTTTGTCTTGGAGTCAG	0.517																																																2	Substitution - coding silent(2)	large_intestine(2)	17											123	120	121					17																	48693689		1911	4120	6031	46048688	SO:0001819	synonymous_variant	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4965C>A	17.37:g.48693689C>A			46048688	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																				0.517	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48693689	C	A	48693689	2	1	61	1	0	0	0	0	0	0	0	1	2550	900	32	2		2	CACNA1G	17	48693689	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98684	48693689	32501521	10305	18290										
LUC7L3	51747	broad.mit.edu	37	chr17	48821170	48821170	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgctaaggtccacaacgtCggtgagtaaaccttatttca	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48821170C>T	ENST00000505658.1	+	6	719	c.530C>T	c.(529-531)tCg>tTg	p.S177L	LUC7L3_ENST00000393227.2_Splice_Site_p.S177L|LUC7L3_ENST00000544170.1_Splice_Site_p.S101L|LUC7L3_ENST00000240304.1_Splice_Site_p.S177L			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	177					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.S177L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						TCCACAACGTCGGTGAGTAAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											83	84	84					17																	48821170		2203	4300	6503	46176169	SO:0001630	splice_region_variant	51747				CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.531+1C>T	17.37:g.48821170C>T			46176169	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	37	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.067365	0.55539	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000544170	T;T;T;T	0.64085	1.38;-0.08;1.38;1.54	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.74635	0.3742	L	0.47716	1.5	0.80722	D	1	B;D;D	0.71674	0.295;0.997;0.998	B;D;D	0.76575	0.258;0.968;0.988	T	0.70714	-0.4796	10	0.34782	T	0.22	-3.3888	19.7073	0.96079	0.0:1.0:0.0:0.0	.	101;177;177	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	L	177;177;177;177;101	ENSP00000425092:S177L;ENSP00000376919:S177L;ENSP00000240304:S177L;ENSP00000444253:S101L	ENSP00000240304:S177L	S	+	2	0	LUC7L3	46176169	1.000000	0.71417	0.993000	0.49108	0.016000	0.09150	7.776000	0.85560	2.722000	0.93159	0.557000	0.71058	TCG		0.368	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424	Missense_Mutation	T	48821170	C	T	48821170	5	4	61	1	0	0	0	0	0	0	1	0	9113	898	31	1	552	1	LUC7L3	17	48821170	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127481	48821170	32374040	10306	18291										
TOB1	10140	broad.mit.edu	37	chr17	48941288	48941288	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaagaagtctttcaagttCttcaccaaaaatgttgacac	5	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:48941288C>A	ENST00000268957.3	-	3	519	c.91G>T	c.(91-93)Gaa>Taa	p.E31*	TOB1-AS1_ENST00000416263.3_RNA|TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Nonsense_Mutation_p.E31*|TOB1-AS1_ENST00000523470.1_RNA	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	31					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)	p.R22fs*5(1)|p.E31*(1)		breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			CTTTCAAGTTCTTCACCAAAA	0.383																																					NSCLC(144;643 1919 24513 29423 40686)											2	Substitution - Nonsense(1)|Deletion - Frameshift(1)	large_intestine(1)|liver(1)	17											100	103	102					17																	48941288		2203	4300	6503	46296287	SO:0001587	stop_gained	10140			D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.91G>T	17.37:g.48941288C>A	ENSP00000268957:p.Glu31*		46296287	B2R9T0|D3DTY3|Q4KMQ0	Nonsense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	C	37	6.600296	0.97697	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	19.7503	0.96265	0.0:1.0:0.0:0.0	.	.	.	.	X	31	.	ENSP00000268957:E31X	E	-	1	0	TOB1	46296287	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.717000	0.68446	2.648000	0.89879	0.655000	0.94253	GAA		0.383	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			A	48941288	C	A	48941288	4	1	61	1	0	0	0	0	0	1	0	0	16386	922	32	2	950	2	TOB1	17	48941288	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120118	48941288	32253922	10307	18292										
SPAG9	9043	broad.mit.edu	37	chr17	49067097	49067097	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcccaaaggatctgtaaaGacatgctctgtgtagacgcc	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:49067097G>T	ENST00000262013.7	-	21	2962	c.2754C>A	c.(2752-2754)gtC>gtA	p.V918V	SPAG9_ENST00000510283.1_Silent_p.V761V|SPAG9_ENST00000357122.4_Silent_p.V904V|SPAG9_ENST00000505279.1_Silent_p.V908V	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	918					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.V904V(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GATCTGTAAAGACATGCTCTG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	17											147	119	129					17																	49067097		2203	4300	6503	46422096	SO:0001819	synonymous_variant	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2754C>A	17.37:g.49067097G>T			46422096	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316781	0.23908	.	.	ENSG00000008294	ENST00000513906	.	.	.	5.77	-1.31	0.09230	.	.	.	.	.	T	0.39911	0.1096	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23868	-1.0176	4	.	.	.	-13.2053	1.5637	0.02600	0.345:0.2325:0.3088:0.1136	.	.	.	.	Y	162	.	.	S	-	2	0	SPAG9	46422096	0.995000	0.38212	0.981000	0.43875	0.997000	0.91878	0.261000	0.18442	-0.434000	0.07275	0.650000	0.86243	TCT		0.488	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		T	49067097	G	T	49067097	2	4	61	1	0	0	0	0	0	0	0	1	15024	929	33	2		2	SPAG9	17	49067097	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125809	49067097	32128113	10308	18293										
SPAG9	9043	broad.mit.edu	37	chr17	49079095	49079095	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgaatcatctctgtccatcGaacagcttcctgaagctcca	6	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:49079095G>A	ENST00000262013.7	-	13	1796	c.1588C>T	c.(1588-1590)Cga>Tga	p.R530*	SPAG9_ENST00000510283.1_Nonsense_Mutation_p.R373*|SPAG9_ENST00000357122.4_Nonsense_Mutation_p.R516*|SPAG9_ENST00000505279.1_Nonsense_Mutation_p.R516*	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	530					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.R516*(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TCTGTCCATCGAACAGCTTCC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											143	129	134					17																	49079095		2203	4300	6503	46434094	SO:0001587	stop_gained	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.1588C>T	17.37:g.49079095G>A	ENSP00000262013:p.Arg530*		46434094	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Nonsense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	40	8.332554	0.98764	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.	.	.	5.68	5.68	0.88126	.	0.056956	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8475	14.9304	0.70911	0.0:0.0:0.8569:0.1431	.	.	.	.	X	530;286;272;373;516;516;128	.	ENSP00000262013:R530X	R	-	1	2	SPAG9	46434094	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.122000	0.50446	2.838000	0.97847	0.655000	0.94253	CGA		0.423	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49079095	G	A	49079095	4	1	61	1	0	0	0	0	0	1	0	0	15024	1066	37	1	2449	1	SPAG9	17	49079095	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11998	49079095	32116115	10309	18294										
SPAG9	9043	broad.mit.edu	37	chr17	49082620	49082620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatcttcagcttctgcccGagctctagtggggaaaaaac	10	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:49082620G>A	ENST00000262013.7	-	12	1637	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	SPAG9_ENST00000510283.1_Missense_Mutation_p.R320W|SPAG9_ENST00000357122.4_Missense_Mutation_p.R463W|SPAG9_ENST00000505279.1_Missense_Mutation_p.R463W	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	477					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.R463W(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GCTTCTGCCCGAGCTCTAGTG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	17											130	102	111					17																	49082620		2203	4300	6503	46437619	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.1429C>T	17.37:g.49082620G>A	ENSP00000262013:p.Arg477Trp		46437619	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.330783	0.81690	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445;ENST00000511795	D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.93752	0.8003	M	0.71581	2.175	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999;0.999	D;D;D;D;P;D	0.80764	0.976;0.994;0.977;0.991;0.901;0.91	D	0.93795	0.7096	10	0.87932	D	0	-13.3482	15.3096	0.74019	0.0:0.0:0.8601:0.1398	.	463;477;463;477;463;320	O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.;.;.;JIP4_HUMAN;.;.	W	477;233;219;320;463;463;75;156	ENSP00000262013:R477W;ENSP00000423165:R320W;ENSP00000426900:R463W;ENSP00000349636:R463W	ENSP00000262013:R477W	R	-	1	2	SPAG9	46437619	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.383000	0.59600	2.868000	0.98415	0.557000	0.71058	CGG		0.343	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49082620	G	A	49082620	3	1	61	1	0	0	0	0	1	0	0	0	15024	1057	37	1	2612	1	SPAG9	17	49082620	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3525	49082620	32112590	10310	18295										
SPAG9	9043	broad.mit.edu	37	chr17	49091664	49091664	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacagttcttcaaagagaGattctgtattgcgatcaaaa	8	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:49091664G>A	ENST00000262013.7	-	9	1350	c.1142C>T	c.(1141-1143)tCt>tTt	p.S381F	SPAG9_ENST00000510283.1_Missense_Mutation_p.S224F|SPAG9_ENST00000357122.4_Missense_Mutation_p.S367F|SPAG9_ENST00000505279.1_Missense_Mutation_p.S367F	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	381					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.S367F(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TTCAAAGAGAGATTCTGTATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	17											141	125	130					17																	49091664		2203	4300	6503	46446663	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.1142C>T	17.37:g.49091664G>A	ENSP00000262013:p.Ser381Phe		46446663	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	32	5.175573	0.94807	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000511795	T;T;T;T	0.38560	1.2;1.13;1.18;1.19	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.65923	0.2738	M	0.67397	2.05	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;0.997	D;D;D;D;D;D	0.97110	0.999;1.0;0.993;0.993;0.991;0.976	T	0.66705	-0.5856	10	0.87932	D	0	-12.3124	20.0529	0.97634	0.0:0.0:1.0:0.0	.	367;381;367;381;367;224	O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.;.;.;JIP4_HUMAN;.;.	F	381;137;123;123;224;367;367;51	ENSP00000262013:S381F;ENSP00000423165:S224F;ENSP00000426900:S367F;ENSP00000349636:S367F	ENSP00000262013:S381F	S	-	2	0	SPAG9	46446663	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.717000	0.98755	2.814000	0.96858	0.591000	0.81541	TCT		0.388	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49091664	G	A	49091664	3	1	61	1	0	0	0	0	1	0	0	0	15024	942	33	3	2911	3	SPAG9	17	49091664	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9044	49091664	32103546	10311	18296										
CA10	56934	broad.mit.edu	37	chr17	49731052	49731052	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttggactctttgcagcttCtgtgacattcgtatatagct	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:49731052C>A	ENST00000285273.4	-	6	1622	c.511G>T	c.(511-513)Gaa>Taa	p.E171*	CA10_ENST00000570565.1_Nonsense_Mutation_p.E96*|CA10_ENST00000442502.2_Nonsense_Mutation_p.E171*|CA10_ENST00000340813.6_Nonsense_Mutation_p.E177*|CA10_ENST00000571918.1_5'UTR|CA10_ENST00000451037.2_Nonsense_Mutation_p.E171*	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	171					brain development (GO:0007420)			p.E171*(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TTTGCAGCTTCTGTGACATTC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											111	104	106					17																	49731052		2203	4300	6503	47086051	SO:0001587	stop_gained	56934			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.511G>T	17.37:g.49731052C>A	ENSP00000285273:p.Glu171*		47086051	B2R7J0|B4DGL6	Nonsense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	C	47	13.670923	0.99756	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	.	.	.	5.55	5.55	0.83447	.	0.046988	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.856	0.92252	0.0:1.0:0.0:0.0	.	.	.	.	X	171;171;171;177	.	.	E	-	1	0	CA10	47086051	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.356000	0.79445	2.753000	0.94483	0.655000	0.94253	GAA		0.393	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		A	49731052	C	A	49731052	4	1	61	1	0	0	0	0	0	1	0	0	2517	922	32	2	495	2	CA10	17	49731052	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	639388	49731052	31464158	10312	18297										
KIF2B	84643	broad.mit.edu	37	chr17	51901733	51901733	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcaagttttccctcgttGatttagctgggaatgaaaga	11	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:51901733G>T	ENST00000268919.4	+	1	1495	c.1339G>T	c.(1339-1341)Gat>Tat	p.D447Y		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	447	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D447Y(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TTCCCTCGTTGATTTAGCTGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											58	52	54					17																	51901733		2203	4300	6503	49256732	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1339G>T	17.37:g.51901733G>T	ENSP00000268919:p.Asp447Tyr		49256732	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921413	0.73213	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	D	0.93189	-3.18	5.73	5.73	0.89815	Kinesin, motor domain (5);Kinesin, motor region, conserved site (1);	0.000000	0.47093	D	0.000250	D	0.98501	0.9500	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99301	1.0901	10	0.87932	D	0	.	19.2577	0.93952	0.0:0.0:1.0:0.0	.	447	Q8N4N8	KIF2B_HUMAN	Y	447;335	ENSP00000268919:D447Y	ENSP00000268919:D447Y	D	+	1	0	KIF2B	49256732	1.000000	0.71417	0.959000	0.39883	0.770000	0.43624	9.813000	0.99286	2.854000	0.98071	0.655000	0.94253	GAT		0.502	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901733	G	T	51901733	3	4	61	1	0	0	0	0	1	0	0	0	8319	1290	45	2	1341	2	KIF2B	17	51901733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2170681	51901733	29293477	10313	18298										
STXBP4	252983	broad.mit.edu	37	chr17	53120674	53120674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgatgccttgaaagaagtAaatacacttaaggtaacctc	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:53120674A>G	ENST00000376352.2	+	11	1140	c.933A>G	c.(931-933)gtA>gtG	p.V311V	STXBP4_ENST00000299341.4_Silent_p.V236V|STXBP4_ENST00000434978.2_Silent_p.V311V|STXBP4_ENST00000405898.1_Silent_p.V311V|STXBP4_ENST00000398391.2_Silent_p.V236V	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	311					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.V311V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						TGAAAGAAGTAAATACACTTA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	17											70	67	68					17																	53120674		2203	4296	6499	50475673	SO:0001819	synonymous_variant	252983			BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.933A>G	17.37:g.53120674A>G			50475673	Q8IVZ5	Silent	SNP	ENST00000376352.2	37	CCDS11584.2																																																																																				0.323	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		G	53120674	A	G	53120674	2	3	61	1	0	0	0	0	0	0	0	1	15394	349	13	4		4	STXBP4	17	53120674	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1218941	53120674	28074536	10314	18299										
HLF	3131	broad.mit.edu	37	chr17	53392736	53392736	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccctcgcaaacgcaagttCtctgaggaagaactgaagcc	10	12	1	3	rs371745405		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:53392736C>A	ENST00000226067.5	+	3	1073	c.600C>A	c.(598-600)ttC>ttA	p.F200L	HLF_ENST00000430986.2_Missense_Mutation_p.F115L|HLF_ENST00000573945.1_Missense_Mutation_p.F115L|HLF_ENST00000575345.1_Missense_Mutation_p.F115L	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	200	Pro-rich (proline/acidic region (PAR)).				multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F200L(1)		large_intestine(1)|ovary(2)	3						AACGCAAGTTCTCTGAGGAAG	0.502			T	TCF3	ALL																																		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	1	Substitution - Missense(1)	large_intestine(1)	17											98	91	94					17																	53392736		2203	4300	6503	50747735	SO:0001583	missense	3131				CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.600C>A	17.37:g.53392736C>A	ENSP00000226067:p.Phe200Leu		50747735	A8K1X8|Q6FHS9	Missense_Mutation	SNP	ENST00000226067.5	37	CCDS11585.1	.	.	.	.	.	.	.	.	.	.	C	35	5.537319	0.96460	.	.	ENSG00000108924	ENST00000226067;ENST00000430986	.	.	.	5.6	5.6	0.85130	.	0.054481	0.64402	D	0.000001	D	0.83959	0.5367	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.97	D	0.84014	0.0350	9	0.42905	T	0.14	.	18.6178	0.91310	0.0:1.0:0.0:0.0	.	148;200	B4DIQ5;Q16534	.;HLF_HUMAN	L	200;115	.	ENSP00000226067:F200L	F	+	3	2	HLF	50747735	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.070000	0.71220	2.644000	0.89710	0.655000	0.94253	TTC		0.502	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126		A	53392736	C	A	53392736	3	1	61	1	0	0	0	0	1	0	0	0	7235	912	32	2	610	2	HLF	17	53392736	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	272062	53392736	27802474	10315	18300										
TMEM100	55273	broad.mit.edu	37	chr17	53798079	53798079	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctgtttgactctcccgtCtcttggctttcttgctcctt	8	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:53798079C>A	ENST00000575734.1	-	4	1161	c.353G>T	c.(352-354)aGa>aTa	p.R118I	TMEM100_ENST00000570586.1_5'Flank|TMEM100_ENST00000424486.2_Missense_Mutation_p.R118I	NM_001099640.1	NP_001093110.1	Q9NV29	TM100_HUMAN	transmembrane protein 100	118					angiogenesis (GO:0001525)|arterial endothelial cell differentiation (GO:0060842)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|in utero embryonic development (GO:0001701)|Notch signaling pathway (GO:0007219)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of vasculogenesis (GO:2001214)|protein kinase B signaling (GO:0043491)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)		p.R118I(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	11						ACTCTCCCGTCTCTTGGCTTT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											115	112	113					17																	53798079		2203	4300	6503	51153078	SO:0001583	missense	55273			AK001832	CCDS11587.1	17q23.1	2005-12-16				ENSG00000166292			25607	protein-coding gene	gene with protein product							Standard	NM_018286		Approved	FLJ10970, FLJ37856	uc002iuj.4	Q9NV29		ENST00000575734.1:c.353G>T	17.37:g.53798079C>A	ENSP00000465638:p.Arg118Ile		51153078	D3DTY7|I3L214|Q96FZ0	Missense_Mutation	SNP	ENST00000575734.1	37	CCDS11587.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055807	0.93793	.	.	ENSG00000166292	ENST00000299377;ENST00000424486	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.79446	0.4447	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81158	-0.1060	9	0.87932	D	0	-9.6555	18.4525	0.90709	0.0:1.0:0.0:0.0	.	118	Q9NV29	TM100_HUMAN	I	118	.	ENSP00000299377:R118I	R	-	2	0	TMEM100	51153078	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.462000	0.80851	2.593000	0.87608	0.655000	0.94253	AGA		0.483	TMEM100-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439266.2	NM_018286		A	53798079	C	A	53798079	3	1	61	1	0	0	0	0	1	0	0	0	16054	913	32	2	55	2	TMEM100	17	53798079	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	405343	53798079	27397131	10316	18301										
PCTP	58488	broad.mit.edu	37	chr17	53844698	53844698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgttctgtttttatagaaGactggactttatgagtataa	8	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:53844698G>T	ENST00000268896.5	+	2	269	c.144G>T	c.(142-144)aaG>aaT	p.K48N	PCTP_ENST00000573500.1_Missense_Mutation_p.K48N|PCTP_ENST00000325214.6_5'UTR|PCTP_ENST00000576183.1_Missense_Mutation_p.K48N	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	48	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)	p.K48N(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			TTTTATAGAAGACTGGACTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	17											96	93	94					17																	53844698		2203	4300	6503	51199697	SO:0001583	missense	58488			AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"StAR-related lipid transfer (START) domain containing"	8752	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 2"	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.144G>T	17.37:g.53844698G>T	ENSP00000268896:p.Lys48Asn		51199697	Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	.	.	.	.	.	.	.	.	.	.	G	9.251	1.040686	0.19669	.	.	ENSG00000141179	ENST00000268896;ENST00000325214	T	0.39592	1.07	5.64	-8.13	0.01073	Lipid-binding START (3);START-like domain (1);	0.800074	0.11559	N	0.551862	T	0.11623	0.0283	N	0.03608	-0.345	0.24460	N	0.994448	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.007	T	0.21348	-1.0248	10	0.15066	T	0.55	-18.1108	2.4531	0.04523	0.3584:0.2864:0.2588:0.0964	.	48;48	Q549N3;Q9UKL6	.;PPCT_HUMAN	N	48;27	ENSP00000268896:K48N	ENSP00000268896:K48N	K	+	3	2	PCTP	51199697	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.364000	0.07583	-1.327000	0.02264	-0.145000	0.13849	AAG		0.393	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213		T	53844698	G	T	53844698	3	4	61	1	0	0	0	0	1	0	0	0	11638	933	33	2	150	2	PCTP	17	53844698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46619	53844698	27350512	10317	18302										
ANKFN1	162282	broad.mit.edu	37	chr17	54428134	54428134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcttcttaggaattgtCgtgtgaaaatgacgcaacaa	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:54428134C>T	ENST00000318698.2	+	4	240	c.205C>T	c.(205-207)Cgt>Tgt	p.R69C	ANKFN1_ENST00000566473.2_Missense_Mutation_p.R69C	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	69								p.R69C(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TAGGAATTGTCGTGTGAAAAT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											89	89	89					17																	54428134		2203	4300	6503	51783133	SO:0001583	missense	162282			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.205C>T	17.37:g.54428134C>T	ENSP00000321627:p.Arg69Cys		51783133		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	c	7.864	0.726604	0.15439	.	.	ENSG00000153930	ENST00000318698	T	0.23348	1.91	5.57	-6.12	0.02124	.	1.490830	0.03541	N	0.223895	T	0.19644	0.0472	L	0.29908	0.895	0.27876	N	0.939853	B	0.02656	0.0	B	0.01281	0.0	T	0.20042	-1.0287	10	0.46703	T	0.11	.	12.1817	0.54216	0.0:0.3146:0.0821:0.6034	.	69	Q8N957	ANKF1_HUMAN	C	69	ENSP00000321627:R69C	ENSP00000321627:R69C	R	+	1	0	ANKFN1	51783133	0.000000	0.05858	0.002000	0.10522	0.547000	0.35210	-1.502000	0.02279	-2.206000	0.00741	-1.739000	0.00688	CGT		0.383	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54428134	C	T	54428134	3	4	61	1	0	0	0	0	1	0	0	0	625	884	31	1	219	1	ANKFN1	17	54428134	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	583436	54428134	26767076	10318	18303										
ANKFN1	162282	broad.mit.edu	37	chr17	54554941	54554941	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagctctgtggatcaaatCaaagttcttgttacccaaaa	7	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:54554941C>A	ENST00000318698.2	+	15	1910	c.1875C>A	c.(1873-1875)atC>atA	p.I625I	ANKFN1_ENST00000566473.2_Silent_p.I625I	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	625								p.I625I(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TGGATCAAATCAAAGTTCTTG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	17											140	135	137					17																	54554941		2203	4300	6503	51909940	SO:0001819	synonymous_variant	162282			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.1875C>A	17.37:g.54554941C>A			51909940		Silent	SNP	ENST00000318698.2	37	CCDS32686.1																																																																																				0.398	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		A	54554941	C	A	54554941	2	1	61	1	0	0	0	0	0	0	0	1	625	816	29	2		2	ANKFN1	17	54554941	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	126807	54554941	26640269	10319	18304										
DGKE	8526	broad.mit.edu	37	chr17	54933967	54933967	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggcaccatctctgttttCtagcagaattcttaataagg	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:54933967C>A	ENST00000284061.3	+	8	1373	c.1193C>A	c.(1192-1194)tCt>tAt	p.S398Y		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	398					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.S398Y(1)		breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					TCTCTGTTTTCTAGCAGAATT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											112	100	104					17																	54933967		2203	4300	6503	52288966	SO:0001583	missense	8526			U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1193C>A	17.37:g.54933967C>A	ENSP00000284061:p.Ser398Tyr		52288966	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.649624	0.87958	.	.	ENSG00000153933	ENST00000284061	T	0.30981	1.51	5.69	5.69	0.88448	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.49932	0.1586	L	0.59436	1.845	0.80722	D	1	P;P	0.38167	0.621;0.621	P;P	0.52031	0.688;0.688	T	0.36212	-0.9757	10	0.51188	T	0.08	.	19.8959	0.96958	0.0:1.0:0.0:0.0	.	398;398	A1L4Q0;P52429	.;DGKE_HUMAN	Y	398	ENSP00000284061:S398Y	ENSP00000284061:S398Y	S	+	2	0	DGKE	52288966	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.297000	0.59061	2.695000	0.91970	0.632000	0.83419	TCT		0.363	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		A	54933967	C	A	54933967	3	1	61	1	0	0	0	0	1	0	0	0	4479	913	32	2	1219	2	DGKE	17	54933967	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	379026	54933967	26261243	10320	18305										
DGKE	8526	broad.mit.edu	37	chr17	54939586	54939586	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaactggctaatccttttCgaataggacaggcacataca	7	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:54939586C>T	ENST00000284061.3	+	11	1678	c.1498C>T	c.(1498-1500)Cga>Tga	p.R500*		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	500					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R500*(1)		breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					TAATCCTTTTCGAATAGGACA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											85	77	80					17																	54939586		2203	4300	6503	52294585	SO:0001587	stop_gained	8526			U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1498C>T	17.37:g.54939586C>T	ENSP00000284061:p.Arg500*		52294585	Q8TBM4|Q9UKQ3	Nonsense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	C	36	5.660062	0.96734	.	.	ENSG00000153933	ENST00000284061	.	.	.	5.36	5.36	0.76844	.	0.056928	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3648	0.66799	0.148:0.852:0.0:0.0	.	.	.	.	X	500	.	ENSP00000284061:R500X	R	+	1	2	DGKE	52294585	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	3.445000	0.52921	2.661000	0.90470	0.650000	0.86243	CGA		0.393	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		T	54939586	C	T	54939586	4	4	61	1	0	0	0	0	0	1	0	0	4479	876	31	1	1536	1	DGKE	17	54939586	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5619	54939586	26255624	10321	18306										
MSI2	124540	broad.mit.edu	37	chr17	55339540	55339540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagttgcatttcctcgtcGagcgcaacccaaggtaagta	9	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:55339540G>A	ENST00000284073.2	+	5	508	c.299G>A	c.(298-300)cGa>cAa	p.R100Q	MSI2_ENST00000416426.2_Missense_Mutation_p.R78Q|MSI2_ENST00000322684.3_Missense_Mutation_p.R96Q	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	100	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)	p.R96Q(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		TTTCCTCGTCGAGCGCAACCC	0.363			T	HOXA9	CML																																		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	1	Substitution - Missense(1)	large_intestine(1)	17											105	99	101					17																	55339540		2203	4300	6503	52694539	SO:0001583	missense	124540			BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	18585	protein-coding gene	gene with protein product		607897	"musashi homolog 2 (Drosophila)"			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.299G>A	17.37:g.55339540G>A	ENSP00000284073:p.Arg100Gln		52694539	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.617229	0.66672	.	.	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000322684	D;D;D	0.85484	-1.99;-1.99;-1.99	5.95	5.95	0.96441	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.178825	0.34725	N	0.003737	D	0.87783	0.6264	N	0.20445	0.575	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.945;0.999;0.957	D	0.88057	0.2791	10	0.49607	T	0.09	.	19.3906	0.94581	0.0:0.0:1.0:0.0	.	78;96;100	B4DHE8;Q96DH6-2;Q96DH6	.;.;MSI2H_HUMAN	Q	78;100;96	ENSP00000414671:R78Q;ENSP00000284073:R100Q;ENSP00000313616:R96Q	ENSP00000284073:R100Q	R	+	2	0	MSI2	52694539	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.454000	0.90352	2.827000	0.97445	0.650000	0.86243	CGA		0.363	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			A	55339540	G	A	55339540	3	1	61	1	0	0	0	0	1	0	0	0	9906	1058	37	1	367	1	MSI2	17	55339540	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	399954	55339540	25855670	10322	18307										
OR4D1	26689	broad.mit.edu	37	chr17	56232578	56232578	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagggttttcacagacccaaGagctccagaaattcctgttc	8	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56232578G>T	ENST00000268912.5	+	1	85	c.64G>T	c.(64-66)Gag>Tag	p.E22*		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	22					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E22*(1)		kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						ACAGACCCAAGAGCTCCAGAA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											127	126	126					17																	56232578		1943	4157	6100	53587577	SO:0001587	stop_gained	26689			X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"GPCR / Class A : Olfactory receptors"	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.64G>T	17.37:g.56232578G>T	ENSP00000365451:p.Glu22*		53587577	B2RN14|Q8NGB1|Q96R76	Nonsense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	g	22.3	4.269336	0.80469	.	.	ENSG00000141194	ENST00000268912	.	.	.	5.63	5.63	0.86233	.	0.000000	0.41500	U	0.000877	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-5.2368	10.5911	0.45310	0.0871:0.0:0.9129:0.0	.	.	.	.	X	22	.	ENSP00000365451:E22X	E	+	1	0	OR4D1	53587577	0.000000	0.05858	0.017000	0.16124	0.836000	0.47400	0.189000	0.17037	2.652000	0.90054	0.543000	0.68304	GAG		0.463	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			T	56232578	G	T	56232578	4	4	61	1	0	0	0	0	0	1	0	0	11084	943	33	2	66	2	OR4D1	17	56232578	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	893038	56232578	24962632	10323	18308										
MKS1	54903	broad.mit.edu	37	chr17	56283520	56283520	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcatgcggcgccgggctcGacggaaggcctctgtaagga	16	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56283520G>A	ENST00000393119.2	-	18	1674	c.1600C>T	c.(1600-1602)Cga>Tga	p.R534*	MKS1_ENST00000313863.6_3'UTR|MKS1_ENST00000337050.7_Intron|MKS1_ENST00000537529.2_Nonsense_Mutation_p.R524*|MKS1_ENST00000546108.1_Nonsense_Mutation_p.R331*	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	534					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)		p.R534*(1)		endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGCCGGGCTCGACGGAAGGCC	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											30	34	33					17																	56283520		1900	4112	6012	53638519	SO:0001587	stop_gained	54903			DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"POC12 centriolar protein homolog (Chlamydomonas)"	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.1600C>T	17.37:g.56283520G>A	ENSP00000376827:p.Arg534*		53638519	B7WNX4|F5H885|Q284T0|Q96G13	Nonsense_Mutation	SNP	ENST00000393119.2	37	CCDS11603.2	.	.	.	.	.	.	.	.	.	.	G	37	6.307110	0.97462	.	.	ENSG00000011143	ENST00000537529;ENST00000393119;ENST00000546108	.	.	.	5.35	4.36	0.52297	.	0.055041	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-36.1465	11.9451	0.52924	0.0:0.0:0.6848:0.3152	.	.	.	.	X	524;534;331	.	ENSP00000376827:R534X	R	-	1	2	MKS1	53638519	1.000000	0.71417	0.858000	0.33744	0.847000	0.48162	2.386000	0.44380	1.430000	0.47334	0.555000	0.69702	CGA		0.607	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777		A	56283520	G	A	56283520	4	1	61	1	0	0	0	0	0	1	0	0	9639	1066	37	1	83	1	MKS1	17	56283520	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50942	56283520	24911690	10324	18309										
MKS1	54903	broad.mit.edu	37	chr17	56291699	56291699	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggttgttcctgacaaactCttctgagggctcccaggtga	12	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56291699C>A	ENST00000393119.2	-	6	639	c.565G>T	c.(565-567)Gag>Tag	p.E189*	MKS1_ENST00000313863.6_Nonsense_Mutation_p.E189*|MKS1_ENST00000337050.7_Nonsense_Mutation_p.E189*|MKS1_ENST00000537529.2_Nonsense_Mutation_p.E179*|MKS1_ENST00000546108.1_5'UTR	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	189					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)		p.E189*(2)		endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CTGACAAACTCTTCTGAGGGC	0.557																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											114	118	117					17																	56291699		1998	4156	6154	53646698	SO:0001587	stop_gained	54903			DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"POC12 centriolar protein homolog (Chlamydomonas)"	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.565G>T	17.37:g.56291699C>A	ENSP00000376827:p.Glu189*		53646698	B7WNX4|F5H885|Q284T0|Q96G13	Nonsense_Mutation	SNP	ENST00000393119.2	37	CCDS11603.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.114794|5.114794	0.94339|0.94339	.|.	.|.	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050|ENST00000313863	.|.	.|.	.|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.187376|.	0.56097|.	D|.	0.000029|.	.|T	.|0.74619	.|0.3740	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72779	.|-0.4190	.|4	0.66056|.	D|.	0.02|.	-33.2773|-33.2773	18.1989|18.1989	0.89831|0.89831	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	179;189;189;189|189	.|.	ENSP00000338407:E189X|.	E|K	-|-	1|3	0|2	MKS1|MKS1	53646698|53646698	1.000000|1.000000	0.71417|0.71417	0.895000|0.895000	0.35142|0.35142	0.324000|0.324000	0.28378|0.28378	7.216000|7.216000	0.77974|0.77974	2.634000|2.634000	0.89283|0.89283	0.549000|0.549000	0.68633|0.68633	GAG|AAG		0.557	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777		A	56291699	C	A	56291699	4	1	61	1	0	0	0	0	0	1	0	0	9639	922	32	2	1166	2	MKS1	17	56291699	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8179	56291699	24903511	10325	18310										
LPO	4025	broad.mit.edu	37	chr17	56332201	56332201	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcctcagagcatattctgCtggccacatcccacaccctc	7	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56332201C>T	ENST00000262290.4	+	9	1451	c.1135C>T	c.(1135-1137)Ctg>Ttg	p.L379L	LPO_ENST00000582328.1_Silent_p.L296L|LPO_ENST00000543544.1_Silent_p.L320L|LPO_ENST00000421678.2_Silent_p.L296L	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	379					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)	p.L379L(1)		breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						GCATATTCTGCTGGCCACATC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	17											86	85	85					17																	56332201		2203	4300	6503	53687200	SO:0001819	synonymous_variant	4025			M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1135C>T	17.37:g.56332201C>T			53687200	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Silent	SNP	ENST00000262290.4	37	CCDS32689.1																																																																																				0.537	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			T	56332201	C	T	56332201	2	4	61	1	0	0	0	0	0	0	0	1	8951	796	28	3		3	LPO	17	56332201	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40502	56332201	24863009	10326	18311										
LPO	4025	broad.mit.edu	37	chr17	56343597	56343597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgatgactggagagctgCgcaacaagcttttccagcca	10	10	0	3	rs372987674		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56343597C>T	ENST00000262290.4	+	11	1919	c.1603C>T	c.(1603-1605)Cgc>Tgc	p.R535C	LPO_ENST00000582328.1_Missense_Mutation_p.R452C|LPO_ENST00000543544.1_Missense_Mutation_p.R476C|LPO_ENST00000421678.2_Missense_Mutation_p.R452C	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	535					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)	p.R535C(1)		breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TGGAGAGCTGCGCAACAAGCT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											65	57	60					17																	56343597		2203	4300	6503	53698596	SO:0001583	missense	4025			M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1603C>T	17.37:g.56343597C>T	ENSP00000262290:p.Arg535Cys		53698596	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	37	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247312	0.80024	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.71461	-0.57;-0.57;-0.57	6.06	4.02	0.46733	.	0.212137	0.46442	D	0.000298	D	0.86707	0.5997	H	0.95079	3.62	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.88063	0.2795	10	0.72032	D	0.01	-18.0602	8.4282	0.32742	0.2712:0.6587:0.0:0.07	.	452;535	E7EMJ3;P22079	.;PERL_HUMAN	C	535;452;476;280	ENSP00000262290:R535C;ENSP00000400245:R452C;ENSP00000445344:R476C	ENSP00000262290:R535C	R	+	1	0	LPO	53698596	1.000000	0.71417	0.937000	0.37676	0.996000	0.88848	2.974000	0.49272	1.572000	0.49736	0.655000	0.94253	CGC		0.542	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			T	56343597	C	T	56343597	3	4	61	1	0	0	0	0	1	0	0	0	8951	768	27	1	1641	1	LPO	17	56343597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11396	56343597	24851613	10327	18312										
MPO	4353	broad.mit.edu	37	chr17	56355217	56355217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaggggatgcgcgctgagCggttggtgaggagacagggg	22	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56355217C>T	ENST00000225275.3	-	7	1351	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	MPO_ENST00000578493.1_5'UTR|MPO_ENST00000340482.3_Missense_Mutation_p.R424H	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	392					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R392H(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	GCGCGCTGAGCGGTTGGTGAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											62	63	62					17																	56355217		2203	4300	6503	53710216	SO:0001583	missense	4353				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1175G>A	17.37:g.56355217C>T	ENSP00000225275:p.Arg392His		53710216	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365591	0.41902	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.72942	-0.7;-0.7	4.8	3.83	0.44106	.	0.217487	0.38111	N	0.001813	T	0.61110	0.2321	M	0.69823	2.125	0.41243	D	0.98665	P	0.37636	0.603	B	0.22880	0.042	T	0.63752	-0.6566	10	0.46703	T	0.11	-17.1754	8.7245	0.34460	0.0:0.8293:0.0:0.1707	.	392	P05164	PERM_HUMAN	H	424;392	ENSP00000344419:R424H;ENSP00000225275:R392H	ENSP00000225275:R392H	R	-	2	0	MPO	53710216	0.188000	0.23250	0.960000	0.40013	0.676000	0.39594	0.691000	0.25467	1.276000	0.44395	0.561000	0.74099	CGC		0.627	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56355217	C	T	56355217	3	4	61	1	0	0	0	0	1	0	0	0	9762	768	27	1	1086	1	MPO	17	56355217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11620	56355217	24839993	10328	18313										
BZRAP1	9256	broad.mit.edu	37	chr17	56385076	56385076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagccacaaagatcctgaCgggtaggtgctggtaagcca	13	10	0	3	rs199511069	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56385076C>T	ENST00000343736.4	-	24	5042	c.4879G>A	c.(4879-4881)Gtc>Atc	p.V1627I	BZRAP1_ENST00000268893.6_Missense_Mutation_p.V1567I|BZRAP1_ENST00000355701.3_Missense_Mutation_p.V1627I			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1627	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.V1627I(4)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGATCCTGACGGGTAGGTGC	0.587													C|||	3	0.000599042	8e-04	0	5008	,	,		21619	0		0.001	False		,,,				2504	0.001															4	Substitution - Missense(4)	large_intestine(4)	17											137	108	118					17																	56385076		2203	4300	6503	53740075	SO:0001583	missense	9256			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4879G>A	17.37:g.56385076C>T	ENSP00000345824:p.Val1627Ile		53740075	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	16.57	3.159670	0.57368	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.29917	1.55;1.55;1.55	5.27	1.08	0.20341	Src homology-3 domain (2);	0.403453	0.26731	N	0.022788	T	0.19725	0.0474	L	0.43152	1.355	0.09310	N	1	B;P;P	0.49358	0.07;0.923;0.85	B;B;B	0.40565	0.005;0.333;0.123	T	0.14364	-1.0475	10	0.27785	T	0.31	.	5.0521	0.14514	0.1369:0.5504:0.0:0.3127	.	1627;1567;1627	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	I	1627;1627;1567	ENSP00000347929:V1627I;ENSP00000345824:V1627I;ENSP00000268893:V1567I	ENSP00000268893:V1567I	V	-	1	0	BZRAP1	53740075	0.014000	0.17966	0.074000	0.20217	0.951000	0.60555	0.506000	0.22658	0.093000	0.17368	0.655000	0.94253	GTC		0.587	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56385076	C	T	56385076	3	4	61	1	0	0	0	0	1	0	0	0	1580	536	19	1	726	1	BZRAP1	17	56385076	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29859	56385076	24810134	10329	18314										
BZRAP1	9256	broad.mit.edu	37	chr17	56386595	56386595	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacagcctgcccctgacttCtcctcctcctcgtcctcctc	5	21	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56386595C>A	ENST00000343736.4	-	22	4201	c.4038G>T	c.(4036-4038)gaG>gaT	p.E1346D	BZRAP1_ENST00000268893.6_Missense_Mutation_p.E1286D|BZRAP1_ENST00000355701.3_Missense_Mutation_p.E1346D			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1346	Poly-Glu.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.E1346D(2)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCCCTGActtctcctcctcct	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	17											73	74	74					17																	56386595		2203	4300	6503	53741594	SO:0001583	missense	9256			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4038G>T	17.37:g.56386595C>A	ENSP00000345824:p.Glu1346Asp		53741594	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	c	5.860	0.342819	0.11069	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	D;D;D	0.87729	-2.29;-2.29;-2.29	5.48	4.5	0.54988	.	1.302720	0.04976	N	0.464706	T	0.79534	0.4462	L	0.29908	0.895	0.09310	N	1	B;P;P	0.37663	0.18;0.604;0.469	B;B;B	0.33454	0.06;0.164;0.079	T	0.66822	-0.5826	10	0.19147	T	0.46	.	8.7841	0.34809	0.1466:0.776:0.0:0.0774	.	1346;1286;1346	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	D	1346;1346;1286	ENSP00000347929:E1346D;ENSP00000345824:E1346D;ENSP00000268893:E1286D	ENSP00000268893:E1286D	E	-	3	2	BZRAP1	53741594	0.463000	0.25799	0.247000	0.24249	0.227000	0.25037	0.664000	0.25068	2.557000	0.86248	0.558000	0.71614	GAG		0.617	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		A	56386595	C	A	56386595	3	1	61	1	0	0	0	0	1	0	0	0	1580	912	32	2	1575	2	BZRAP1	17	56386595	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1519	56386595	24808615	10330	18315										
RNF43	54894	broad.mit.edu	37	chr17	56492694	56492694	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttatacttgcctgcattAattttccttctgctggagtt	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56492694A>G	ENST00000584437.1	-	1	2200	c.245T>C	c.(244-246)tTa>tCa	p.L82S	BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.L82S|RNF43_ENST00000407977.2_Missense_Mutation_p.L82S|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000581868.1_Intron|RNF43_ENST00000583753.1_Missense_Mutation_p.L82S|RNF43_ENST00000500597.2_Missense_Mutation_p.L82S			Q68DV7	RNF43_HUMAN	ring finger protein 43	82					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L82S(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCCTGCATTAATTTTCCTTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	17											59	59	59					17																	56492694		2203	4300	6503	53847693	SO:0001583	missense	54894				CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.245T>C	17.37:g.56492694A>G	ENSP00000463069:p.Leu82Ser		53847693	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392979	0.83011	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.13196	2.66;2.61	5.27	5.27	0.74061	.	0.146689	0.31041	N	0.008365	T	0.23806	0.0576	N	0.19112	0.55	0.40156	D	0.977007	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.07616	-1.0763	10	0.87932	D	0	-14.0466	14.669	0.68929	1.0:0.0:0.0:0.0	.	82;82	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	S	82	ENSP00000385328:L82S;ENSP00000441969:L82S	ENSP00000385328:L82S	L	-	2	0	RNF43	53847693	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.322000	0.90000	2.115000	0.64714	0.533000	0.62120	TTA		0.383	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		G	56492694	A	G	56492694	3	3	61	1	0	0	0	0	1	0	0	0	13532	372	13	4	2142	4	RNF43	17	56492694	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	106099	56492694	24702516	10331	18316										
SEPT4	5414	broad.mit.edu	37	chr17	56598193	56598193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtcggtaccactttcccGagtcagtttgctaaagggag	12	9	1	0	rs147468433		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56598193G>A	ENST00000317268.3	-	11	1464	c.1288C>T	c.(1288-1290)Cgg>Tgg	p.R430W	SEPT4_ENST00000393086.1_Missense_Mutation_p.R411W|SEPT4_ENST00000579371.1_Intron|SEPT4_ENST00000580844.1_Missense_Mutation_p.R331W|SEPT4_ENST00000583114.1_Missense_Mutation_p.R283W|SEPT4_ENST00000457347.2_Missense_Mutation_p.R445W|MTMR4_ENST00000579925.1_5'Flank|SEPT4_ENST00000317256.6_Missense_Mutation_p.R411W|SEPT4_ENST00000412945.3_Missense_Mutation_p.R422W|MTMR4_ENST00000323456.5_5'Flank|SEPT4_ENST00000426861.1_3'UTR|RP11-112H10.4_ENST00000580589.1_RNA	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	430					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.R430W(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCACTTTCCCGAGTCAGTTTG	0.527											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	17						G	TRP/ARG,TRP/ARG,,TRP/ARG	0,4406		0,0,2203	126	124	124		1264,1288,,1231	4.6	1	17	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,utr-3,missense	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	101,101,,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,probably-damaging	422/471,430/479,,411/460	56598193	1,13005	2203	4300	6503	53953192	SO:0001583	missense	5414			AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.1288C>T	17.37:g.56598193G>A	ENSP00000321674:p.Arg430Trp	1016	53953192	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	.	.	.	.	.	.	.	.	.	.	G	8.196	0.796982	0.16327	0.0	1.16E-4	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086	T;T;T;T	0.54675	0.56;0.57;0.56;0.57	5.62	4.62	0.57501	.	0.463918	0.21864	N	0.067998	T	0.68550	0.3013	M	0.75615	2.305	0.49915	D	0.999832	D;D;D;D;D	0.89917	0.992;0.999;0.992;1.0;0.986	P;P;P;D;P	0.64042	0.663;0.855;0.54;0.921;0.453	T	0.72174	-0.4370	10	0.87932	D	0	.	11.537	0.50643	0.0:0.0:0.6634:0.3366	.	422;445;411;283;430	O43236-3;O43236-4;O43236-2;O43236-5;O43236	.;.;.;.;SEPT4_HUMAN	W	422;444;411;430;411	ENSP00000414779:R422W;ENSP00000321071:R411W;ENSP00000321674:R430W;ENSP00000376801:R411W	ENSP00000321071:R411W	R	-	1	2	SEPT4	53953192	0.982000	0.34865	1.000000	0.80357	0.996000	0.88848	1.672000	0.37523	1.438000	0.47492	0.655000	0.94253	CGG		0.527	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		A	56598193	G	A	56598193	3	1	61	1	0	0	0	0	1	0	0	0	14103	1057	37	1	156	1	SEPT4	17	56598193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	105499	56598193	24597017	10332	18317										
SEPT4	5414	broad.mit.edu	37	chr17	56599412	56599412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttcaggccactctcgtctCggaaatactgctcaaactgc	9	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56599412C>T	ENST00000317268.3	-	6	889	c.713G>A	c.(712-714)cGa>cAa	p.R238Q	SEPT4_ENST00000393086.1_Missense_Mutation_p.R219Q|SEPT4_ENST00000579371.1_Missense_Mutation_p.R139Q|SEPT4_ENST00000580844.1_Missense_Mutation_p.R139Q|SEPT4_ENST00000583114.1_Missense_Mutation_p.R91Q|SEPT4_ENST00000457347.2_Missense_Mutation_p.R253Q|SEPT4_ENST00000580809.1_Missense_Mutation_p.R120Q|SEPT4_ENST00000317256.6_Missense_Mutation_p.R219Q|SEPT4_ENST00000412945.3_Missense_Mutation_p.R230Q|SEPT4_ENST00000426861.1_Missense_Mutation_p.R219Q|RP11-112H10.4_ENST00000580589.1_RNA	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	238	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.R238Q(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTCTCGTCTCGGAAATACTG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	17											164	136	146					17																	56599412		2203	4300	6503	53954411	SO:0001583	missense	5414			AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.713G>A	17.37:g.56599412C>T	ENSP00000321674:p.Arg238Gln		53954411	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027098	0.54683	.	.	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086;ENST00000426861	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.59810	0.2221	L	0.37561	1.115	0.80722	D	1	D;D;P;P;D;B;D	0.89917	1.0;0.999;0.642;0.582;1.0;0.284;1.0	D;D;B;B;D;B;D	0.91635	0.999;0.99;0.107;0.18;0.999;0.175;0.999	T	0.51348	-0.8717	10	0.27785	T	0.31	.	17.7759	0.88508	0.0:1.0:0.0:0.0	.	230;253;91;219;219;91;238	O43236-3;O43236-4;B3KR63;O43236-6;O43236-2;O43236-5;O43236	.;.;.;.;.;.;SEPT4_HUMAN	Q	230;252;219;238;219;219	ENSP00000414779:R230Q;ENSP00000321071:R219Q;ENSP00000321674:R238Q;ENSP00000376801:R219Q;ENSP00000402348:R219Q	ENSP00000321071:R219Q	R	-	2	0	SEPT4	53954411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.786000	0.95864	0.563000	0.77884	CGA		0.537	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		T	56599412	C	T	56599412	3	4	61	1	0	0	0	0	1	0	0	0	14103	884	31	1	836	1	SEPT4	17	56599412	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1219	56599412	24595798	10333	18318										
SEPT4	5414	broad.mit.edu	37	chr17	56604121	56604121	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagaggggctggggcacaGaagtactgctggttgtcaga	17	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56604121G>T	ENST00000317268.3	-	2	455	c.279C>A	c.(277-279)ttC>ttA	p.F93L	SEPT4_ENST00000393086.1_Missense_Mutation_p.F74L|SEPT4_ENST00000579371.1_Intron|SEPT4_ENST00000580844.1_Intron|SEPT4_ENST00000583114.1_De_novo_Start_OutOfFrame|RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000457347.2_Missense_Mutation_p.F108L|SEPT4_ENST00000580809.1_Intron|SEPT4_ENST00000317256.6_Missense_Mutation_p.F74L|SEPT4_ENST00000580791.1_5'UTR|SEPT4_ENST00000412945.3_Missense_Mutation_p.F85L|SEPT4_ENST00000426861.1_Missense_Mutation_p.F74L|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	93					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.F93L(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGGGGCACAGAAGTACTGCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											43	53	50					17																	56604121		2203	4300	6503	53959120	SO:0001583	missense	5414			AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.279C>A	17.37:g.56604121G>T	ENSP00000321674:p.Phe93Leu		53959120	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920681	0.33908	.	.	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086;ENST00000426861	T;T;T;T;T	0.62639	0.79;0.8;0.79;0.8;0.01	5.01	5.01	0.66863	.	1.717000	0.02704	N	0.112060	T	0.51805	0.1696	N	0.24115	0.695	0.40320	D	0.978811	B;B;P;B;B	0.34462	0.102;0.002;0.454;0.002;0.068	B;B;B;B;B	0.27715	0.033;0.002;0.082;0.002;0.014	T	0.14896	-1.0456	10	0.27082	T	0.32	.	13.8143	0.63281	0.0:0.0:1.0:0.0	.	85;108;74;74;93	O43236-3;O43236-4;O43236-6;O43236-2;O43236	.;.;.;.;SEPT4_HUMAN	L	85;107;74;93;74;74	ENSP00000414779:F85L;ENSP00000321071:F74L;ENSP00000321674:F93L;ENSP00000376801:F74L;ENSP00000402348:F74L	ENSP00000321071:F74L	F	-	3	2	SEPT4	53959120	0.993000	0.37304	1.000000	0.80357	0.997000	0.91878	3.732000	0.55021	2.339000	0.79563	0.561000	0.74099	TTC		0.637	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		T	56604121	G	T	56604121	3	4	61	1	0	0	0	0	1	0	0	0	14103	933	33	2	1286	2	SEPT4	17	56604121	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4709	56604121	24591089	10334	18319										
C17orf47	284083	broad.mit.edu	37	chr17	56621430	56621430	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagggagactgcagcacttcGatggcttgaggcaagaacgt	14	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56621430G>A	ENST00000321691.3	-	1	299	c.118C>T	c.(118-120)Cga>Tga	p.R40*	RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	40								p.R40*(2)		NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCAGCACTTCGATGGCTTGAG	0.557																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											167	132	144					17																	56621430		2203	4300	6503	53976429	SO:0001587	stop_gained	284083				CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.118C>T	17.37:g.56621430G>A	ENSP00000354874:p.Arg40*		53976429	Q8N821	Nonsense_Mutation	SNP	ENST00000321691.3	37	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422539	0.62622	.	.	ENSG00000181013	ENST00000321691	.	.	.	5.41	3.24	0.37175	.	1.170850	0.06312	N	0.702804	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.121	11.2029	0.48751	0.0:0.0:0.6725:0.3275	.	.	.	.	X	40	.	ENSP00000354874:R40X	R	-	1	2	C17orf47	53976429	0.001000	0.12720	0.050000	0.19076	0.014000	0.08584	0.643000	0.24750	1.363000	0.46019	0.655000	0.94253	CGA		0.557	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		A	56621430	G	A	56621430	4	1	61	1	0	0	0	0	0	1	0	0	1863	1066	37	1	1602	1	C17orf47	17	56621430	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17309	56621430	24573780	10335	18320										
TEX14	56155	broad.mit.edu	37	chr17	56638903	56638903	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagagcccttgggaaggtCttgtagctccacgctctcct	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56638903C>A	ENST00000240361.8	-	30	4358	c.4273G>T	c.(4273-4275)Gac>Tac	p.D1425Y	TEX14_ENST00000584699.1_5'UTR|TEX14_ENST00000389934.3_Missense_Mutation_p.D1419Y|TEX14_ENST00000349033.5_Missense_Mutation_p.D1379Y			Q8IWB6	TEX14_HUMAN	testis expressed 14	1425					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.D1425Y(1)|p.D1379Y(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGGGAAGGTCTTGTAGCTCC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	17											146	143	144					17																	56638903		2203	4300	6503	53993902	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.4273G>T	17.37:g.56638903C>A	ENSP00000240361:p.Asp1425Tyr		53993902	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.231158	0.22626	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.24350	1.86;1.86;1.86	5.09	4.11	0.48088	.	0.320085	0.26723	N	0.022840	T	0.41719	0.1171	L	0.59436	1.845	0.09310	N	1	D;D;D	0.65815	0.991;0.993;0.995	P;P;D	0.63877	0.832;0.891;0.919	T	0.18335	-1.0340	10	0.87932	D	0	-3.7796	9.7028	0.40198	0.0:0.9055:0.0:0.0945	.	1425;1379;1419	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	Y	1425;1419;1379	ENSP00000240361:D1425Y;ENSP00000374584:D1419Y;ENSP00000268910:D1379Y	ENSP00000240361:D1425Y	D	-	1	0	TEX14	53993902	0.898000	0.30612	0.017000	0.16124	0.093000	0.18481	1.697000	0.37784	1.365000	0.46057	0.655000	0.94253	GAC		0.478	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			A	56638903	C	A	56638903	3	1	61	1	0	0	0	0	1	0	0	0	15817	913	32	2	236	2	TEX14	17	56638903	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17473	56638903	24556307	10336	18321										
TEX14	56155	broad.mit.edu	37	chr17	56665319	56665319	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccggtggcttgacagagtGaagagtgcactattaaactg	13	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56665319G>T	ENST00000240361.8	-	16	2743	c.2658C>A	c.(2656-2658)ttC>ttA	p.F886L	TEX14_ENST00000389934.3_Missense_Mutation_p.F880L|TEX14_ENST00000349033.5_Missense_Mutation_p.F880L			Q8IWB6	TEX14_HUMAN	testis expressed 14	886					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.F886L(1)|p.F880L(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGACAGAGTGAAGAGTGcac	0.522											OREG0024616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	17											139	119	126					17																	56665319		2203	4300	6503	54020318	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2658C>A	17.37:g.56665319G>T	ENSP00000240361:p.Phe886Leu	1017	54020318	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299354	0.23650	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.79141	-1.24;-1.24;-1.18	4.22	-2.03	0.07365	.	0.541545	0.19359	N	0.116199	T	0.41926	0.1180	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.42310	-0.9459	10	0.02654	T	1	-0.1717	3.8156	0.08814	0.0982:0.4499:0.2877:0.1642	.	886;880;880	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	L	886;880;880	ENSP00000240361:F886L;ENSP00000374584:F880L;ENSP00000268910:F880L	ENSP00000240361:F886L	F	-	3	2	TEX14	54020318	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.408000	0.07169	-0.265000	0.09352	0.557000	0.71058	TTC		0.522	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56665319	G	T	56665319	3	4	61	1	0	0	0	0	1	0	0	0	15817	1281	45	2	1907	2	TEX14	17	56665319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26416	56665319	24529891	10337	18322										
TEX14	56155	broad.mit.edu	37	chr17	56676845	56676845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtagatctcgttgatttCgaaactgcagaggcttggct	12	7	1	4	rs201938572		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56676845C>T	ENST00000240361.8	-	14	1964	c.1879G>A	c.(1879-1881)Gaa>Aaa	p.E627K	TEX14_ENST00000389934.3_Missense_Mutation_p.E621K|TEX14_ENST00000349033.5_Missense_Mutation_p.E621K			Q8IWB6	TEX14_HUMAN	testis expressed 14	627					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.E621K(1)|p.E627K(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCGTTGATTTCGAAACTGCAG	0.532													C|||	1	0.000199681	0	0	5008	,	,		15295	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	17						C	LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	70	70	70		1879,1861,1861	4.8	0.9	17		70	3,8597	3.0+/-9.4	1,1,4298	yes	missense,missense,missense	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	56,56,56	1,2,6500	TT,TC,CC		0.0349,0.0227,0.0308	probably-damaging,probably-damaging,probably-damaging	627/1498,621/1452,621/1492	56676845	4,13002	2203	4300	6503	54031844	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1879G>A	17.37:g.56676845C>T	ENSP00000240361:p.Glu627Lys		54031844	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049726	0.55218	2.27E-4	3.49E-4	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	D;D;D	0.82893	-1.66;-1.65;-1.55	5.75	4.79	0.61399	.	0.163209	0.43416	D	0.000575	D	0.89234	0.6657	M	0.67953	2.075	0.35260	D	0.779497	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.92724	0.6194	10	0.72032	D	0.01	-11.2081	12.0797	0.53663	0.0:0.9204:0.0:0.0796	.	627;621;621	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	K	627;621;621	ENSP00000240361:E627K;ENSP00000374584:E621K;ENSP00000268910:E621K	ENSP00000240361:E627K	E	-	1	0	TEX14	54031844	0.981000	0.34729	0.896000	0.35187	0.046000	0.14306	2.282000	0.43461	1.458000	0.47871	-0.119000	0.15052	GAA		0.532	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56676845	C	T	56676845	3	4	61	1	0	0	0	0	1	0	0	0	15817	893	31	1	2694	1	TEX14	17	56676845	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11526	56676845	24518365	10338	18323										
TEX14	56155	broad.mit.edu	37	chr17	56679251	56679251	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagatagacattgacatcggGatggagtccgtatctctgca	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56679251G>T	ENST00000240361.8	-	13	1697	c.1612C>A	c.(1612-1614)Ccc>Acc	p.P538T	TEX14_ENST00000389934.3_Missense_Mutation_p.P532T|TEX14_ENST00000349033.5_Missense_Mutation_p.P532T			Q8IWB6	TEX14_HUMAN	testis expressed 14	538					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.P538T(1)|p.P532T(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGACATCGGGATGGAGTCCG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	17											185	172	176					17																	56679251		2203	4300	6503	54034250	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1612C>A	17.37:g.56679251G>T	ENSP00000240361:p.Pro538Thr		54034250	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652236	0.67472	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.80123	-1.34;-1.34;-1.25	6.04	6.04	0.98038	.	0.093367	0.47852	D	0.000202	D	0.83501	0.5268	L	0.34521	1.04	0.36433	D	0.865029	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71414	0.94;0.973;0.973	D	0.84875	0.0827	10	0.41790	T	0.15	-9.9265	13.6935	0.62562	0.0:0.1542:0.8458:0.0	.	538;532;532	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	T	538;532;532	ENSP00000240361:P538T;ENSP00000374584:P532T;ENSP00000268910:P532T	ENSP00000240361:P538T	P	-	1	0	TEX14	54034250	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	0.964000	0.29306	2.873000	0.98535	0.563000	0.77884	CCC		0.458	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56679251	G	T	56679251	3	4	61	1	0	0	0	0	1	0	0	0	15817	1174	41	2	2965	2	TEX14	17	56679251	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2406	56679251	24515959	10339	18324										
TEX14	56155	broad.mit.edu	37	chr17	56693569	56693569	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaggggccgctgaagaaaGagaaggtgggctcatcatca	15	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56693569G>T	ENST00000240361.8	-	7	837	c.752C>A	c.(751-753)tCt>tAt	p.S251Y	TEX14_ENST00000389934.3_Missense_Mutation_p.S245Y|TEX14_ENST00000349033.5_Missense_Mutation_p.S245Y			Q8IWB6	TEX14_HUMAN	testis expressed 14	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.S245Y(1)|p.S251Y(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCTGAAGAAAGAGAAGGTGGG	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	17											95	84	88					17																	56693569		2203	4300	6503	54048568	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.752C>A	17.37:g.56693569G>T	ENSP00000240361:p.Ser251Tyr		54048568	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468729	0.84533	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.81078	-1.45;-1.44;-1.37	5.46	5.46	0.80206	Protein kinase, catalytic domain (1);	0.092187	0.48286	D	0.000181	D	0.88081	0.6341	L	0.56769	1.78	0.48395	D	0.999641	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.962;0.977;0.983	D	0.88917	0.3363	10	0.87932	D	0	-18.0308	17.8819	0.88843	0.0:0.0:1.0:0.0	.	251;245;245	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	Y	251;245;245	ENSP00000240361:S251Y;ENSP00000374584:S245Y;ENSP00000268910:S245Y	ENSP00000240361:S251Y	S	-	2	0	TEX14	54048568	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.847000	0.75404	2.566000	0.86566	0.655000	0.94253	TCT		0.502	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56693569	G	T	56693569	3	4	61	1	0	0	0	0	1	0	0	0	15817	942	33	2	3849	2	TEX14	17	56693569	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14318	56693569	24501641	10340	18325										
TEX14	56155	broad.mit.edu	37	chr17	56693650	56693650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagataggccatctgtgtcGccccagtaagataaaactga	9	10	1	3	rs201712949		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56693650G>A	ENST00000240361.8	-	7	756	c.671C>T	c.(670-672)gCg>gTg	p.A224V	TEX14_ENST00000389934.3_Missense_Mutation_p.A218V|TEX14_ENST00000349033.5_Missense_Mutation_p.A218V			Q8IWB6	TEX14_HUMAN	testis expressed 14	224					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.A218V(1)|p.A224V(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CATCTGTGTCGCCCCAGTAAG	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	17						G	VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	81	74	76		671,653,653	2.4	0	17		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	64,64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	224/1498,218/1452,218/1492	56693650	1,13005	2203	4300	6503	54048649	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.671C>T	17.37:g.56693650G>A	ENSP00000240361:p.Ala224Val		54048649	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417409	0.11870	0.0	1.16E-4	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.79352	-1.25;-1.26;-1.22	5.65	2.43	0.29744	.	0.369495	0.26282	N	0.025274	T	0.52996	0.1769	N	0.14661	0.345	0.09310	N	1	B;B;B	0.27951	0.0;0.195;0.0	B;B;B	0.20577	0.001;0.03;0.001	T	0.31138	-0.9954	10	0.18710	T	0.47	-6.2861	5.0674	0.14589	0.1393:0.4948:0.2903:0.0756	.	224;218;218	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	V	224;218;218	ENSP00000240361:A224V;ENSP00000374584:A218V;ENSP00000268910:A218V	ENSP00000240361:A224V	A	-	2	0	TEX14	54048649	0.000000	0.05858	0.008000	0.14137	0.015000	0.08874	-0.135000	0.10420	0.761000	0.33130	-0.821000	0.03111	GCG		0.468	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			A	56693650	G	A	56693650	3	1	61	1	0	0	0	0	1	0	0	0	15817	1087	38	1	3930	1	TEX14	17	56693650	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81	56693650	24501560	10341	18326										
TEX14	56155	broad.mit.edu	37	chr17	56729236	56729236	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtgcttacctttcttaaGaattttcttcactttcacat	4	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:56729236G>T	ENST00000240361.8	-	2	212	c.127C>A	c.(127-129)Ctt>Att	p.L43I	TEX14_ENST00000389934.3_Missense_Mutation_p.L43I|TEX14_ENST00000349033.5_Missense_Mutation_p.L43I			Q8IWB6	TEX14_HUMAN	testis expressed 14	43					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.L43I(2)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCTTTCTTAAGAATTTTCTTC	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	17											131	120	124					17																	56729236		2203	4300	6503	54084235	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.127C>A	17.37:g.56729236G>T	ENSP00000240361:p.Leu43Ile		54084235	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316494	0.81469	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.69685	-0.42;-0.42;-0.42	5.31	5.31	0.75309	Ankyrin repeat-containing domain (4);	0.000000	0.52532	D	0.000063	T	0.73079	0.3541	L	0.31157	0.91	0.33671	D	0.610873	D;D;D	0.89917	1.0;0.999;0.997	D;D;D	0.83275	0.996;0.993;0.979	T	0.80420	-0.1390	10	0.87932	D	0	-2.6529	14.8872	0.70579	0.0:0.0:1.0:0.0	.	43;43;43	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	I	43	ENSP00000240361:L43I;ENSP00000374584:L43I;ENSP00000268910:L43I	ENSP00000240361:L43I	L	-	1	0	TEX14	54084235	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.714000	0.54889	2.652000	0.90054	0.638000	0.83543	CTT		0.413	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56729236	G	T	56729236	3	4	61	1	0	0	0	0	1	0	0	0	15817	942	33	2	4476	2	TEX14	17	56729236	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35586	56729236	24465974	10342	18327										
PPM1E	22843	broad.mit.edu	37	chr17	57033094	57033094	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctttctgcacattatatCccaaaggaaacggatggcac	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57033094C>A	ENST00000308249.2	+	2	678	c.549C>A	c.(547-549)atC>atA	p.I183I		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)	p.I183I(1)		biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			CACATTATATCCCAAAGGAAA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	17											119	108	112					17																	57033094		2203	4300	6503	54387876	SO:0001819	synonymous_variant	22843			AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.549C>A	17.37:g.57033094C>A			54387876	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	37	CCDS11613.1																																																																																				0.403	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	57033094	C	A	57033094	2	1	61	1	0	0	0	0	0	0	0	1	12372	845	30	2		2	PPM1E	17	57033094	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	303858	57033094	24162116	10343	18328										
TRIM37	4591	broad.mit.edu	37	chr17	57105781	57105781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacatattacttacagtttCgtatgtaacaattggcaact	6	7	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57105781C>T	ENST00000262294.7	-	19	2511	c.2252G>A	c.(2251-2253)cGa>cAa	p.R751Q	TRIM37_ENST00000393066.3_Missense_Mutation_p.R751Q|TRIM37_ENST00000376149.3_Missense_Mutation_p.R629Q|TRIM37_ENST00000393065.2_Missense_Mutation_p.R717Q	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	751					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R751Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CTTACAGTTTCGTATGTAACA	0.398									Mulibrey Nanism																																							1	Substitution - Missense(1)	large_intestine(1)	17											42	39	40					17																	57105781		2203	4300	6503	54460563	SO:0001583	missense	4591	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.2252G>A	17.37:g.57105781C>T	ENSP00000262294:p.Arg751Gln		54460563	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.579728	0.86645	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.61	4.64	0.57946	.	0.000000	0.64402	D	0.000004	T	0.44561	0.1299	L	0.32530	0.975	0.48975	D	0.999733	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77557	0.99;0.99;0.978	T	0.44832	-0.9302	10	0.87932	D	0	-7.7252	14.3698	0.66830	0.0:0.9286:0.0:0.0714	.	717;629;751	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	Q	751;751;629;717	ENSP00000376785:R751Q;ENSP00000262294:R751Q;ENSP00000365319:R629Q;ENSP00000376784:R717Q	ENSP00000262294:R751Q	R	-	2	0	TRIM37	54460563	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.552000	0.36244	1.371000	0.46172	0.585000	0.79938	CGA		0.398	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		T	57105781	C	T	57105781	3	4	61	1	0	0	0	0	1	0	0	0	16551	884	31	1	674	1	TRIM37	17	57105781	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72687	57105781	24089429	10344	18329										
SKA2	348235	broad.mit.edu	37	chr17	57196832	57196832	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactttatcactgacaattCctttaagagtgtaactggat	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57196832C>A	ENST00000330137.7	-	3	250	c.145G>T	c.(145-147)Gaa>Taa	p.E49*	SKA2_ENST00000580541.1_Intron|SKA2_ENST00000437036.2_Intron|AC099850.1_ENST00000451775.1_RNA|SKA2_ENST00000583927.1_Intron|SKA2_ENST00000578105.1_Nonsense_Mutation_p.E20*|SKA2_ENST00000581068.1_Intron|SKA2_ENST00000583380.1_Nonsense_Mutation_p.E49*	NM_182620.3	NP_872426.1	Q8WVK7	SKA2_HUMAN	spindle and kinetochore associated complex subunit 2	49					cell division (GO:0051301)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|spindle microtubule (GO:0005876)	microtubule binding (GO:0008017)	p.E39*(1)		lung(4)	4						ACTGACAATTCCTTTAAGAGT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											126	118	120					17																	57196832		1810	4077	5887	54551614	SO:0001587	stop_gained	348235			BC017873	CCDS45747.1, CCDS45748.1	17q23.2	2013-01-17	2009-08-19	2009-08-19	ENSG00000182628	ENSG00000182628			28006	protein-coding gene	gene with protein product			"family with sequence similarity 33, member A"	FAM33A		17093495, 19289083, 18583474	Standard	NM_182620		Approved	FLJ12758	uc010dde.1	Q8WVK7		ENST00000330137.7:c.145G>T	17.37:g.57196832C>A	ENSP00000333433:p.Glu49*		54551614	A6NIL3|B3KPL3|E9PCB8	Nonsense_Mutation	SNP	ENST00000330137.7	37	CCDS45747.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332538	0.41297	.	.	ENSG00000182628	ENST00000330137	.	.	.	5.25	5.25	0.73442	.	0.156556	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	12.1582	0.54089	0.0:0.8275:0.1725:0.0	.	.	.	.	X	49	.	ENSP00000333433:E49X	E	-	1	0	SKA2	54551614	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.451000	0.35145	2.435000	0.82474	0.467000	0.42956	GAA		0.323	SKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445939.1	NM_182620		A	57196832	C	A	57196832	4	1	61	1	0	0	0	0	0	1	0	0	14390	864	30	2	228	2	SKA2	17	57196832	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91051	57196832	23998378	10345	18330										
C17orf71	55181	broad.mit.edu	37	chr17	57288676	57288676	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagcatgtggagctagttCtaagcaagaaaggtttcgat	13	6	1	1	rs147742546		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57288676C>A	ENST00000543872.2	+	2	1528	c.1264C>A	c.(1264-1266)Cta>Ata	p.L422I	SMG8_ENST00000580498.1_Intron|SMG8_ENST00000578922.1_Missense_Mutation_p.L422I|SMG8_ENST00000300917.5_Missense_Mutation_p.L422I|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	422					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.L422I(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						GGAGCTAGTTCTAAGCAAGAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	17											85	80	82					17																	57288676		2203	4300	6503	54643458	SO:0001583	missense	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.1264C>A	17.37:g.57288676C>A	ENSP00000438748:p.Leu422Ile		54643458	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.796785	0.50208	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.61627	0.09;0.09	6.06	2.67	0.31697	.	0.062472	0.64402	D	0.000004	T	0.58680	0.2139	L	0.45581	1.43	0.46542	D	0.999095	D	0.62365	0.991	P	0.54401	0.751	T	0.54009	-0.8357	10	0.40728	T	0.16	-11.3003	9.8086	0.40808	0.0:0.7544:0.0:0.2456	.	422	Q8ND04	SMG8_HUMAN	I	422	ENSP00000300917:L422I;ENSP00000438748:L422I	ENSP00000300917:L422I	L	+	1	2	SMG8	54643458	0.971000	0.33674	0.941000	0.38009	0.875000	0.50365	2.225000	0.42954	0.307000	0.22880	-0.136000	0.14681	CTA		0.463	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		A	57288676	C	A	57288676	3	1	61	1	0	0	0	0	1	0	0	0	1883	912	32	2	1266	2	C17orf71	17	57288676	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91844	57288676	23906534	10346	18331										
C17orf71	55181	broad.mit.edu	37	chr17	57289009	57289009	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcttgcccaggctcttCgagtgtacagtcaacatgct	9	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57289009C>T	ENST00000543872.2	+	2	1861	c.1597C>T	c.(1597-1599)Cga>Tga	p.R533*	SMG8_ENST00000580498.1_Intron|SMG8_ENST00000578922.1_Nonsense_Mutation_p.R533*|SMG8_ENST00000300917.5_Nonsense_Mutation_p.R533*|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	533					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.R533*(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CCAGGCTCTTCGAGTGTACAG	0.458																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											86	78	80					17																	57289009		2203	4300	6503	54643791	SO:0001587	stop_gained	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.1597C>T	17.37:g.57289009C>T	ENSP00000438748:p.Arg533*		54643791	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Nonsense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	39	7.555064	0.98355	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3897	18.9389	0.92597	0.0:1.0:0.0:0.0	.	.	.	.	X	533	.	ENSP00000300917:R533X	R	+	1	2	SMG8	54643791	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.205000	0.51090	2.705000	0.92388	0.655000	0.94253	CGA		0.458	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		T	57289009	C	T	57289009	4	4	61	1	0	0	0	0	0	1	0	0	1883	876	31	1	1599	1	C17orf71	17	57289009	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	333	57289009	23906201	10347	18332										
C17orf71	55181	broad.mit.edu	37	chr17	57290205	57290205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcctgctcctccagattCggatgctgataaacttaaag	7	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57290205C>T	ENST00000543872.2	+	4	2285	c.2021C>T	c.(2020-2022)tCg>tTg	p.S674L	SMG8_ENST00000580498.1_3'UTR|SMG8_ENST00000300917.5_Missense_Mutation_p.S674L|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	674					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.S674L(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CCTCCAGATTCGGATGCTGAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											122	136	131					17																	57290205		2203	4300	6503	54644987	SO:0001583	missense	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2021C>T	17.37:g.57290205C>T	ENSP00000438748:p.Ser674Leu		54644987	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.140724	0.37825	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.43294	0.95;0.95	5.82	3.72	0.42706	.	0.467148	0.23664	N	0.045795	T	0.24774	0.0601	N	0.19112	0.55	0.29324	N	0.867136	B	0.18166	0.026	B	0.17433	0.018	T	0.09640	-1.0665	10	0.40728	T	0.16	-1.4329	6.0656	0.19862	0.0:0.5921:0.2403:0.1676	.	674	Q8ND04	SMG8_HUMAN	L	674	ENSP00000300917:S674L;ENSP00000438748:S674L	ENSP00000300917:S674L	S	+	2	0	SMG8	54644987	0.993000	0.37304	0.987000	0.45799	0.924000	0.55760	2.914000	0.48797	1.458000	0.47871	0.655000	0.94253	TCG		0.428	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		T	57290205	C	T	57290205	3	4	61	1	0	0	0	0	1	0	0	0	1883	893	31	1	2031	1	C17orf71	17	57290205	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1196	57290205	23905005	10348	18333										
CLTC	1213	broad.mit.edu	37	chr17	57743514	57743514	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcagcagtgtactgcattCttgcttgatgctctgaagaa	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57743514C>A	ENST00000269122.3	+	11	1969	c.1695C>A	c.(1693-1695)ttC>ttA	p.F565L	CLTC_ENST00000393043.1_Missense_Mutation_p.F565L|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	565	Distal segment.|Heavy chain arm.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)	p.F565L(1)	CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GTACTGCATTCTTGCTTGATG	0.353			T	"ALK, TFE3"	"ALCL, renal "																																		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	1	Substitution - Missense(1)	large_intestine(1)	17											130	113	119					17																	57743514		2203	4300	6503	55098296	SO:0001583	missense	1213			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.1695C>A	17.37:g.57743514C>A	ENSP00000269122:p.Phe565Leu		55098296	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307478	0.81247	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.17528	2.27;2.27	5.53	1.26	0.21427	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.40743	0.1129	M	0.84326	2.69	0.80722	D	1	D;B	0.53619	0.961;0.265	D;B	0.74023	0.982;0.427	T	0.30416	-0.9979	10	0.46703	T	0.11	.	11.7152	0.51647	0.0:0.765:0.0:0.235	.	565;565	Q00610;Q00610-2	CLH1_HUMAN;.	L	565	ENSP00000269122:F565L;ENSP00000376763:F565L	ENSP00000269122:F565L	F	+	3	2	CLTC	55098296	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.354000	0.34056	0.386000	0.24997	0.650000	0.86243	TTC		0.353	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		A	57743514	C	A	57743514	3	1	61	1	0	0	0	0	1	0	0	0	3572	912	32	2	1737	2	CLTC	17	57743514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	453309	57743514	23451696	10349	18334										
CLTC	1213	broad.mit.edu	37	chr17	57758369	57758369	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accttcctaatgaactcattGaactgctggagaaaattgtc	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57758369G>T	ENST00000269122.3	+	19	3290	c.3016G>T	c.(3016-3018)Gaa>Taa	p.E1006*	CLTC_ENST00000393043.1_Nonsense_Mutation_p.E1006*|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1006	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)	p.E1006*(1)	CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TGAACTCATTGAACTGCTGGA	0.398			T	"ALK, TFE3"	"ALCL, renal "																																		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	1	Substitution - Nonsense(1)	large_intestine(1)	17											144	140	141					17																	57758369		2203	4300	6503	55113151	SO:0001587	stop_gained	1213			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.3016G>T	17.37:g.57758369G>T	ENSP00000269122:p.Glu1006*		55113151	D3DU00|Q6N0A0|Q86TF2	Nonsense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	43	10.284934	0.99376	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	.	.	.	5.31	5.31	0.75309	.	0.111416	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	18.9844	0.92764	0.0:0.0:1.0:0.0	.	.	.	.	X	1006	.	ENSP00000269122:E1006X	E	+	1	0	CLTC	55113151	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.869000	0.99810	2.492000	0.84095	0.650000	0.86243	GAA		0.398	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57758369	G	T	57758369	4	4	61	1	0	0	0	0	0	1	0	0	3572	1291	45	2	3090	2	CLTC	17	57758369	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14855	57758369	23436841	10350	18335										
TUBD1	51174	broad.mit.edu	37	chr17	57952010	57952010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacatgtgaggaatgttaCgaacactcagcatcttgaat	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:57952010C>T	ENST00000592426.1	-	5	824	c.824G>A	c.(823-825)cGt>cAt	p.R275H	TUBD1_ENST00000340993.6_Intron|TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000394239.3_Missense_Mutation_p.R275H|TUBD1_ENST00000539018.1_Missense_Mutation_p.R59H|TUBD1_ENST00000376094.4_Intron|TUBD1_ENST00000325752.3_Missense_Mutation_p.R275H			Q9UJT1	TBD_HUMAN	tubulin, delta 1	275					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R275H(1)		NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	AGGAATGTTACGAACACTCAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											188	175	180					17																	57952010		2203	4300	6503	55306792	SO:0001583	missense	51174			AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"Tubulins"	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.824G>A	17.37:g.57952010C>T	ENSP00000468518:p.Arg275His		55306792	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	37	CCDS11620.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599450	0.46318	.	.	ENSG00000108423	ENST00000325752;ENST00000394239;ENST00000539018	T;T	0.78595	-1.19;-0.85	5.62	5.62	0.85841	Tubulin/FtsZ, C-terminal (1);	0.142969	0.64402	D	0.000004	D	0.87759	0.6258	M	0.73962	2.25	0.42692	D	0.993583	D;D	0.76494	0.999;0.96	D;B	0.64595	0.927;0.223	D	0.88626	0.3166	10	0.72032	D	0.01	-15.3713	19.6572	0.95847	0.0:1.0:0.0:0.0	.	275;275	E9PCA7;Q9UJT1	.;TBD_HUMAN	H	275;275;59	ENSP00000320797:R275H;ENSP00000377785:R275H	ENSP00000320797:R275H	R	-	2	0	TUBD1	55306792	1.000000	0.71417	1.000000	0.80357	0.118000	0.20060	4.513000	0.60476	2.651000	0.90000	0.563000	0.77884	CGT		0.368	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261		T	57952010	C	T	57952010	3	4	61	1	0	0	0	0	1	0	0	0	16802	536	19	1	553	1	TUBD1	17	57952010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	193641	57952010	23243200	10351	18336										
USP32	84669	broad.mit.edu	37	chr17	58275693	58275693	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatacttgaatccaaaccGcatcatataggtctttcttc	7	10	3	1	rs202121527		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:58275693G>A	ENST00000300896.4	-	27	3556	c.3362C>T	c.(3361-3363)gCg>gTg	p.A1121V	USP32_ENST00000592339.1_Missense_Mutation_p.A791V	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1121	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A1121V(1)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATCCAAACCGCATCATATAG	0.488													G|||	1	0.000199681	0	0	5008	,	,		19421	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											176	157	163					17																	58275693		2203	4300	6503	55630475	SO:0001583	missense	84669			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.3362C>T	17.37:g.58275693G>A	ENSP00000300896:p.Ala1121Val		55630475	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	27.3	4.817706	0.90790	.	.	ENSG00000170832	ENST00000300896	T	0.47177	0.85	5.15	5.15	0.70609	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.52468	0.1736	L	0.31926	0.97	0.80722	D	1	D	0.63046	0.992	P	0.55965	0.788	T	0.44159	-0.9346	10	0.26408	T	0.33	.	18.6199	0.91317	0.0:0.0:1.0:0.0	.	1121	Q8NFA0	UBP32_HUMAN	V	1121	ENSP00000300896:A1121V	ENSP00000300896:A1121V	A	-	2	0	USP32	55630475	1.000000	0.71417	0.992000	0.48379	0.970000	0.65996	7.963000	0.87922	2.381000	0.81170	0.561000	0.74099	GCG		0.488	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		A	58275693	G	A	58275693	3	1	61	1	0	0	0	0	1	0	0	0	17103	1087	38	1	1484	1	USP32	17	58275693	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	323683	58275693	22919517	10352	18337										
USP32	84669	broad.mit.edu	37	chr17	58372050	58372050	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttaactatacctctgaGaaacacttcctgagtgtatc	5	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:58372050G>T	ENST00000300896.4	-	4	599	c.405C>A	c.(403-405)ttC>ttA	p.F135L	USP32_ENST00000393003.3_Missense_Mutation_p.F135L	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	135					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.F135L(1)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ATACCTCTGAGAAACACTTCC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											77	73	74					17																	58372050		2203	4300	6503	55726832	SO:0001583	missense	84669			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.405C>A	17.37:g.58372050G>T	ENSP00000300896:p.Phe135Leu		55726832	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.136060	0.56936	.	.	ENSG00000170832	ENST00000300896;ENST00000393003	T;T	0.47869	0.83;0.83	5.6	3.18	0.36537	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.62392	0.2424	M	0.74881	2.28	0.58432	D	0.99999	D;B	0.54964	0.969;0.258	D;B	0.63381	0.914;0.089	T	0.64474	-0.6399	10	0.54805	T	0.06	.	9.9339	0.41539	0.2565:0.0:0.7435:0.0	.	135;135	Q7Z5T3;Q8NFA0	.;UBP32_HUMAN	L	135	ENSP00000300896:F135L;ENSP00000376727:F135L	ENSP00000300896:F135L	F	-	3	2	USP32	55726832	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.218000	0.51192	1.286000	0.44565	0.591000	0.81541	TTC		0.338	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		T	58372050	G	T	58372050	3	4	61	1	0	0	0	0	1	0	0	0	17103	933	33	2	4533	2	USP32	17	58372050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96357	58372050	22823160	10353	18338										
APPBP2	10513	broad.mit.edu	37	chr17	58539195	58539195	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaattgcaacagactgacaGatattatctacattgagtaa	6	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:58539195G>T	ENST00000083182.3	-	8	1199	c.912C>A	c.(910-912)atC>atA	p.I304I	APPBP2_ENST00000592995.1_5'UTR	NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	304					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)	p.I304I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			CAGACTGACAGATATTATCTA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	17											101	110	107					17																	58539195		2203	4299	6502	55893977	SO:0001819	synonymous_variant	10513			AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"protein interacting with APP tail 1"	605324	"amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.912C>A	17.37:g.58539195G>T			55893977	A8K862|O95095|Q8WVC9	Silent	SNP	ENST00000083182.3	37	CCDS32699.1																																																																																				0.333	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		T	58539195	G	T	58539195	2	4	61	1	0	0	0	0	0	0	0	1	816	932	33	2		2	APPBP2	17	58539195	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167145	58539195	22656015	10354	18339										
BCAS3	54828	broad.mit.edu	37	chr17	58979988	58979988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttttctcagttgattcGatgtcatcagtcccgtggtg	9	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:58979988G>A	ENST00000390652.5	+	11	777	c.746G>A	c.(745-747)cGa>cAa	p.R249Q	BCAS3_ENST00000588874.1_Missense_Mutation_p.R20Q|BCAS3_ENST00000585744.1_Missense_Mutation_p.R20Q|BCAS3_ENST00000588462.1_Missense_Mutation_p.R249Q|RN7SL448P_ENST00000475566.2_RNA|BCAS3_ENST00000407086.3_Missense_Mutation_p.R249Q|BCAS3_ENST00000408905.3_Missense_Mutation_p.R249Q|BCAS3_ENST00000589222.1_Missense_Mutation_p.R249Q	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.R249Q(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			CAGTTGATTCGATGTCATCAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											201	189	193					17																	58979988		1929	4158	6087	56334770	SO:0001583	missense	54828			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.746G>A	17.37:g.58979988G>A	ENSP00000375067:p.Arg249Gln		56334770		Missense_Mutation	SNP	ENST00000390652.5	37	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.218681	0.58560	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000405070;ENST00000408905;ENST00000405217	T;T;T	0.30714	1.53;1.52;1.52	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.49695	0.1572	L	0.45581	1.43	0.53005	D	0.999967	B;D;D;D	0.69078	0.288;0.997;0.994;0.991	B;D;D;P	0.69479	0.026;0.964;0.921;0.563	T	0.14309	-1.0477	10	0.28530	T	0.3	.	20.1518	0.98089	0.0:0.0:1.0:0.0	.	54;249;249;249	Q70WD9;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;BCAS3_HUMAN;.	Q	249;249;249;249;54	ENSP00000375067:R249Q;ENSP00000385323:R249Q;ENSP00000386173:R249Q	ENSP00000375067:R249Q	R	+	2	0	BCAS3	56334770	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.452000	0.97615	2.769000	0.95229	0.491000	0.48974	CGA		0.428	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		A	58979988	G	A	58979988	3	1	61	1	0	0	0	0	1	0	0	0	1353	1058	37	1	784	1	BCAS3	17	58979988	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	440793	58979988	22215222	10355	18340										
BCAS3	54828	broad.mit.edu	37	chr17	59112099	59112099	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgtgtggctgctatcttCggaacatccaggtcatggtt	11	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:59112099C>T	ENST00000390652.5	+	18	1786	c.1755C>T	c.(1753-1755)ttC>ttT	p.F585F	BCAS3_ENST00000588874.1_Silent_p.F341F|BCAS3_ENST00000585744.1_Silent_p.F356F|BCAS3_ENST00000588462.1_Silent_p.F585F|BCAS3_ENST00000407086.3_Silent_p.F570F|RP11-264B14.1_ENST00000588604.1_RNA|BCAS3_ENST00000408905.3_Silent_p.F570F|BCAS3_ENST00000589222.1_Silent_p.F570F	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.F585F(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			CTGCTATCTTCGGAACATCCA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	17											96	91	92					17																	59112099		1804	4083	5887	56466881	SO:0001819	synonymous_variant	54828			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.1755C>T	17.37:g.59112099C>T			56466881		Silent	SNP	ENST00000390652.5	37	CCDS45749.1																																																																																				0.343	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		T	59112099	C	T	59112099	2	4	61	1	0	0	0	0	0	0	0	1	1353	883	31	1		1	BCAS3	17	59112099	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132111	59112099	22083111	10356	18341										
TBX4	9496	broad.mit.edu	37	chr17	59556059	59556059	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgatgagaacaatgctttCggctccaaaaacactgcttt	8	10	0	2	rs150224277	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:59556059C>T	ENST00000240335.1	+	5	666	c.621C>T	c.(619-621)ttC>ttT	p.F207F	TBX4_ENST00000393853.4_Silent_p.F207F|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	207					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F207F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						ACAATGCTTTCGGCTCCAAAA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		1,4405	2.1+/-5.4	0,1,2202	219	179	193		621	0	1	17	dbSNP_134	193	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TBX4	NM_018488.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		207/546	59556059	3,13003	2203	4300	6503	56910841	SO:0001819	synonymous_variant	9496			AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.621C>T	17.37:g.59556059C>T			56910841	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																				0.522	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		T	59556059	C	T	59556059	2	4	61	1	0	0	0	0	0	0	0	1	15699	883	31	1		1	TBX4	17	59556059	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	443960	59556059	21639151	10357	18342										
BRIP1	83990	broad.mit.edu	37	chr17	59763253	59763253	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaatttttggtaataattTtaggacactgtagttcctgg	10	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:59763253T>G	ENST00000259008.2	-	19	3116	c.2849A>C	c.(2848-2850)aAa>aCa	p.K950T	BRIP1_ENST00000577598.1_Missense_Mutation_p.K950T	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	950	Interaction with BRCA1.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K950T(1)		NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						GGTAATAATTTTAGGACACTG	0.363			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	17											154	166	162					17																	59763253		2203	4300	6503	57118035	SO:0001583	missense	83990			AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.2849A>C	17.37:g.59763253T>G	ENSP00000259008:p.Lys950Thr		57118035	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	T	0.041	-1.284667	0.01398	.	.	ENSG00000136492	ENST00000259008	T	0.74002	-0.8	5.38	0.0837	0.14434	.	2.676840	0.01346	N	0.011755	T	0.53997	0.1831	N	0.04880	-0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43245	-0.9403	9	.	.	.	0.2073	8.3939	0.32544	0.118:0.0:0.462:0.42	.	950;950	C9JGZ0;Q9BX63	.;FANCJ_HUMAN	T	950	ENSP00000259008:K950T	.	K	-	2	0	BRIP1	57118035	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.019000	0.12546	0.305000	0.22832	0.533000	0.62120	AAA		0.363	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		G	59763253	T	G	59763253	3	3	61	1	0	0	0	0	1	0	0	0	1517	1841	64	4	908	4	BRIP1	17	59763253	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	207194	59763253	21431957	10358	18343										
INTS2	57508	broad.mit.edu	37	chr17	59968949	59968949	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggcttctggattagatttCgacgcaggagtaagtataga	13	5	1	2	rs578079823		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:59968949C>T	ENST00000444766.3	-	14	1899	c.1824G>A	c.(1822-1824)tcG>tcA	p.S608S	INTS2_ENST00000251334.6_Silent_p.S600S	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	608					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)		p.S608S(1)		NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						GATTAGATTTCGACGCAGGAG	0.373													C|||	1	0.000199681	0	0	5008	,	,		14210	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											133	133	133					17																	59968949		1873	4098	5971	57323731	SO:0001819	synonymous_variant	57508			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1824G>A	17.37:g.59968949C>T			57323731	Q9ULD3	Silent	SNP	ENST00000444766.3	37	CCDS45750.1																																																																																				0.373	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		T	59968949	C	T	59968949	2	4	61	1	0	0	0	0	0	0	0	1	7799	871	31	1		1	INTS2	17	59968949	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	205696	59968949	21226261	10359	18344										
INTS2	57508	broad.mit.edu	37	chr17	59984936	59984936	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggaagaatgcccatcaaCtccagaagaagctgccttct	10	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:59984936C>T	ENST00000444766.3	-	8	1113	c.1038G>A	c.(1036-1038)gaG>gaA	p.E346E	INTS2_ENST00000251334.6_Silent_p.E338E	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	346					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)		p.E346E(1)		NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						TGCCCATCAACTCCAGAAGAA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	17											65	60	62					17																	59984936		1917	4123	6040	57339718	SO:0001819	synonymous_variant	57508			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1038G>A	17.37:g.59984936C>T			57339718	Q9ULD3	Silent	SNP	ENST00000444766.3	37	CCDS45750.1																																																																																				0.458	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		T	59984936	C	T	59984936	2	4	61	1	0	0	0	0	0	0	0	1	7799	564	20	3		3	INTS2	17	59984936	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15987	59984936	21210274	10360	18345										
MED13	9969	broad.mit.edu	37	chr17	60042387	60042387	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcagacacatcaggatgCggctgagtgggaagtgaaga	14	7	2	4	rs372390031		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60042387C>T	ENST00000397786.2	-	20	4900	c.4824G>A	c.(4822-4824)ccG>ccA	p.P1608P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1608					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.P1608P(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CATCAGGATGCGGCTGAGTGG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		1,3799		0,1,1899	70	67	68		4824	-0.2	1	17		68	0,8270		0,0,4135	no	coding-synonymous	MED13	NM_005121.2		0,1,6034	TT,TC,CC		0.0,0.0263,0.0083		1608/2175	60042387	1,12069	1900	4135	6035	57397169	SO:0001819	synonymous_variant	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4824G>A	17.37:g.60042387C>T			57397169	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																				0.403	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		T	60042387	C	T	60042387	2	4	61	1	0	0	0	0	0	0	0	1	9460	755	27	1		1	MED13	17	60042387	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57451	60042387	21152823	10361	18346										
MED13	9969	broad.mit.edu	37	chr17	60045430	60045430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagatctctaaaaaagcttTttgctccatttaacaaggct	5	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60045430T>C	ENST00000397786.2	-	18	4233	c.4157A>G	c.(4156-4158)aAa>aGa	p.K1386R		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1386					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.K1386R(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AAAAAAGCTTTTTGCTCCATT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	17											141	128	132					17																	60045430		1839	4095	5934	57400212	SO:0001583	missense	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4157A>G	17.37:g.60045430T>C	ENSP00000380888:p.Lys1386Arg		57400212	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.295515	0.40594	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.58060	0.36	5.44	4.36	0.52297	.	0.043957	0.85682	N	0.000000	T	0.42154	0.1190	L	0.39147	1.195	0.53688	D	0.999973	B	0.06786	0.001	B	0.08055	0.003	T	0.20706	-1.0267	10	0.35671	T	0.21	-3.6672	10.4773	0.44672	0.0:0.0777:0.0:0.9223	.	1386	Q9UHV7	MED13_HUMAN	R	1386;1385	ENSP00000380888:K1386R	ENSP00000262436:K1385R	K	-	2	0	MED13	57400212	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.951000	0.70273	0.903000	0.36546	0.533000	0.62120	AAA		0.348	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60045430	T	C	60045430	3	2	61	1	0	0	0	0	1	0	0	0	9460	1841	64	4	2419	4	MED13	17	60045430	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3043	60045430	21149780	10362	18347										
MED13	9969	broad.mit.edu	37	chr17	60061597	60061597	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattttccaacagtccaactCtgacggtaaatacactcttc	4	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60061597C>A	ENST00000397786.2	-	15	2899	c.2823G>T	c.(2821-2823)caG>caT	p.Q941H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	941					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.Q941H(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CAGTCCAACTCTGACGGTAAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	113	117					17																	60061597		1841	4089	5930	57416379	SO:0001583	missense	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.2823G>T	17.37:g.60061597C>A	ENSP00000380888:p.Gln941His		57416379	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307254	0.60305	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74315	-0.83	5.83	3.47	0.39725	.	0.048773	0.85682	D	0.000000	T	0.69672	0.3137	N	0.22421	0.69	0.37208	D	0.904674	D	0.61697	0.99	P	0.53593	0.73	T	0.76876	-0.2797	10	0.87932	D	0	-1.7706	11.2907	0.49247	0.0:0.7818:0.0:0.2182	.	941	Q9UHV7	MED13_HUMAN	H	941;940	ENSP00000380888:Q941H	ENSP00000262436:Q940H	Q	-	3	2	MED13	57416379	0.996000	0.38824	1.000000	0.80357	0.998000	0.95712	0.351000	0.20096	1.448000	0.47680	0.655000	0.94253	CAG		0.408	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60061597	C	A	60061597	3	1	61	1	0	0	0	0	1	0	0	0	9460	912	32	2	3765	2	MED13	17	60061597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16167	60061597	21133613	10363	18348										
MED13	9969	broad.mit.edu	37	chr17	60129924	60129924	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttataggtttttcatctttTtcataaggctttacaaacca	4	7	3	0	rs375630135		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60129924T>G	ENST00000397786.2	-	3	520	c.444A>C	c.(442-444)gaA>gaC	p.E148D		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	148					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.E148D(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTCATCTTTTTCATAAGGCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											121	117	118					17																	60129924		1806	4078	5884	57484706	SO:0001583	missense	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.444A>C	17.37:g.60129924T>G	ENSP00000380888:p.Glu148Asp		57484706	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.780229	0.49891	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.76186	-1.0	5.53	4.45	0.53987	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.85682	D	0.000000	T	0.77363	0.4119	L	0.56280	1.765	0.51767	D	0.999934	D	0.60160	0.987	P	0.61592	0.891	T	0.74259	-0.3723	10	0.33141	T	0.24	1.6054	6.1318	0.20209	0.0:0.317:0.0:0.683	.	148	Q9UHV7	MED13_HUMAN	D	148;147	ENSP00000380888:E148D	ENSP00000262436:E147D	E	-	3	2	MED13	57484706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.178000	0.42519	1.050000	0.40346	0.533000	0.62120	GAA		0.338	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60129924	T	G	60129924	3	3	61	1	0	0	0	0	1	0	0	0	9460	1838	64	4	6192	4	MED13	17	60129924	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	68327	60129924	21065286	10364	18349										
EFCAB3	146779	broad.mit.edu	37	chr17	60491173	60491173	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcaaatgctcaagaaaaaGcagacttgtacagtggccga	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60491173G>T	ENST00000305286.3	+	9	1026	c.948G>T	c.(946-948)aaG>aaT	p.K316N	EFCAB3_ENST00000450662.2_Missense_Mutation_p.K368N	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	316							calcium ion binding (GO:0005509)	p.K316N(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			TCAAGAAAAAGCAGACTTGTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											100	102	101					17																	60491173		2203	4300	6503	57844905	SO:0001583	missense	146779			AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.948G>T	17.37:g.60491173G>T	ENSP00000302649:p.Lys316Asn		57844905	J3KQM8	Missense_Mutation	SNP	ENST00000305286.3	37	CCDS11632.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.251023	0.39797	.	.	ENSG00000172421	ENST00000450662;ENST00000305286	T;T	0.61510	0.1;0.13	5.05	5.05	0.67936	.	0.231875	0.32190	N	0.006442	T	0.70509	0.3232	M	0.62723	1.935	0.36553	D	0.871956	D	0.76494	0.999	D	0.64144	0.922	T	0.77539	-0.2550	10	0.72032	D	0.01	.	13.767	0.63002	0.0:0.0:1.0:0.0	.	316	Q8N7B9	EFCB3_HUMAN	N	368;316	ENSP00000403932:K368N;ENSP00000302649:K316N	ENSP00000302649:K316N	K	+	3	2	EFCAB3	57844905	0.998000	0.40836	0.473000	0.27253	0.016000	0.09150	4.157000	0.58144	2.625000	0.88918	0.557000	0.71058	AAG		0.363	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		T	60491173	G	T	60491173	3	4	61	1	0	0	0	0	1	0	0	0	4946	962	34	2	1146	2	EFCAB3	17	60491173	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	361249	60491173	20704037	10365	18350										
TLK2	11011	broad.mit.edu	37	chr17	60631068	60631068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgcactagaaaacagtaaGaattctgacttagagaagaa	8	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60631068G>T	ENST00000326270.9	+	9	940	c.672G>T	c.(670-672)aaG>aaT	p.K224N	TLK2_ENST00000346027.5_Missense_Mutation_p.K224N|TLK2_ENST00000343388.7_Missense_Mutation_p.K192N|TLK2_ENST00000542523.1_Missense_Mutation_p.K192N|TLK2_ENST00000582809.1_Missense_Mutation_p.K75N|RP11-464D20.6_ENST00000583426.1_RNA	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	224					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K223N(1)|p.K224N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						AAAACAGTAAGAATTCTGACT	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	17											54	62	59					17																	60631068		2202	4296	6498	57984800	SO:0001583	missense	11011			AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.672G>T	17.37:g.60631068G>T	ENSP00000316512:p.Lys224Asn		57984800	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	G	10.91	1.483343	0.26598	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	4.24	3.27	0.37495	.	0.000000	0.85682	D	0.000000	T	0.55924	0.1951	L	0.46741	1.465	0.58432	D	0.999998	D;B;P;P	0.89917	1.0;0.34;0.544;0.609	D;B;B;B	0.87578	0.998;0.112;0.316;0.168	T	0.51560	-0.8690	10	0.36615	T	0.2	.	7.8339	0.29360	0.1901:0.0:0.8099:0.0	.	224;192;224;224	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	N	224;192;224;192	ENSP00000275780:K224N;ENSP00000340800:K192N;ENSP00000316512:K224N;ENSP00000442311:K192N	ENSP00000316512:K224N	K	+	3	2	TLK2	57984800	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.531000	0.45650	1.005000	0.39183	0.460000	0.39030	AAG		0.299	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		T	60631068	G	T	60631068	3	4	61	1	0	0	0	0	1	0	0	0	15983	933	33	2	702	2	TLK2	17	60631068	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139895	60631068	20564142	10366	18351										
TLK2	11011	broad.mit.edu	37	chr17	60678097	60678097	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgtcggagaaagaggccCggtccattatcatgcagatt	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60678097C>T	ENST00000326270.9	+	19	1970	c.1702C>T	c.(1702-1704)Cgg>Tgg	p.R568W	TLK2_ENST00000346027.5_Missense_Mutation_p.R546W|TLK2_ENST00000343388.7_Missense_Mutation_p.R514W|TLK2_ENST00000542523.1_Missense_Mutation_p.R514W|TLK2_ENST00000582809.1_Missense_Mutation_p.R397W	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	568	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R568W(1)|p.R545W(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						GAAAGAGGCCCGGTCCATTAT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	17											83	76	78					17																	60678097		2203	4300	6503	58031829	SO:0001583	missense	11011			AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1702C>T	17.37:g.60678097C>T	ENSP00000316512:p.Arg568Trp		58031829	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	C	14.93	2.682774	0.47991	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.6	4.59	0.56863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.23094	0.0558	L	0.53249	1.67	0.80722	D	1	B;P;P;B	0.43431	0.208;0.807;0.683;0.143	B;B;B;B	0.38655	0.075;0.278;0.218;0.083	T	0.06463	-1.0825	10	0.87932	D	0	.	15.6804	0.77364	0.0:0.8635:0.1365:0.0	.	568;514;546;546	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	W	546;514;568;514	ENSP00000275780:R546W;ENSP00000340800:R514W;ENSP00000316512:R568W;ENSP00000442311:R514W	ENSP00000316512:R568W	R	+	1	2	TLK2	58031829	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.041000	0.70988	2.636000	0.89361	0.467000	0.42956	CGG		0.358	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		T	60678097	C	T	60678097	3	4	61	1	0	0	0	0	1	0	0	0	15983	643	23	1	1702	1	TLK2	17	60678097	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47029	60678097	20517113	10367	18352										
MARCH10	162333	broad.mit.edu	37	chr17	60865909	60865909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgcccccaaaactgatCgcgtttcttctcatttgggt	7	13	3	1	rs371345442		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:60865909C>T	ENST00000311269.5	-	3	416	c.142G>A	c.(142-144)Gat>Aat	p.D48N	MARCH10_ENST00000456609.2_Missense_Mutation_p.D48N|MARCH10_ENST00000544856.2_Missense_Mutation_p.D48N|MARCH10_ENST00000583600.1_Missense_Mutation_p.D48N	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	48					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D48N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						CAAAACTGATCGCGTTTCTTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	142	120	128		142,142	4.2	0	17		128	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	MARCH10	NM_001100875.1,NM_152598.2	23,23	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	48/809,48/809	60865909	2,13004	2203	4300	6503	58219641	SO:0001583	missense	162333			AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.142G>A	17.37:g.60865909C>T	ENSP00000311496:p.Asp48Asn		58219641	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.400175	0.25291	0.0	2.33E-4	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.25912	1.77;1.77;1.77	5.2	4.21	0.49690	.	0.342522	0.21152	N	0.079309	T	0.26231	0.0640	M	0.63428	1.95	0.20873	N	0.999835	B;P;B	0.35774	0.384;0.519;0.384	B;B;B	0.33339	0.078;0.162;0.078	T	0.19257	-1.0311	10	0.72032	D	0.01	-5.3846	10.6303	0.45532	0.2113:0.7887:0.0:0.0	.	48;48;48	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	N	48	ENSP00000416177:D48N;ENSP00000311496:D48N;ENSP00000443746:D48N	ENSP00000311496:D48N	D	-	1	0	MARCH10	58219641	0.961000	0.32948	0.030000	0.17652	0.560000	0.35617	2.298000	0.43602	1.116000	0.41820	0.561000	0.74099	GAT		0.443	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		T	60865909	C	T	60865909	3	4	61	1	0	0	0	0	1	0	0	0	9329	884	31	1	2320	1	MARCH10	17	60865909	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187812	60865909	20329301	10368	18353										
TANC2	26115	broad.mit.edu	37	chr17	61492995	61492995	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccgggaactaaaggtgtCtctcctcctcaacctctctc	6	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61492995C>A	ENST00000424789.2	+	23	3879	c.3875C>A	c.(3874-3876)tCt>tAt	p.S1292Y	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.S1302Y|AC015923.1_ENST00000431604.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1292					in utero embryonic development (GO:0001701)			p.S1302Y(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CTAAAGGTGTCTCTCCTCCTC	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	17											90	88	88					17																	61492995		1927	4144	6071	58846727	SO:0001583	missense	26115			AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.3875C>A	17.37:g.61492995C>A	ENSP00000387593:p.Ser1292Tyr		58846727	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	37	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165426	0.94768	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.74106	-0.81;-0.81	5.76	5.76	0.90799	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.88503	0.6454	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.85130	0.976;0.997	D	0.89417	0.3707	10	0.87932	D	0	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	1302;1292	Q9HCD6-2;Q9HCD6	.;TANC2_HUMAN	Y	1302;1292	ENSP00000374171:S1302Y;ENSP00000387593:S1292Y	ENSP00000374171:S1302Y	S	+	2	0	TANC2	58846727	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.713000	0.92767	0.655000	0.94253	TCT		0.507	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			A	61492995	C	A	61492995	3	1	61	1	0	0	0	0	1	0	0	0	15584	913	32	2	3965	2	TANC2	17	61492995	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	627086	61492995	19702215	10369	18354										
KCNH6	81033	broad.mit.edu	37	chr17	61623144	61623144	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatcccctggaagtacaaGgactcatctgtggtccctgc	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61623144G>T	ENST00000583023.1	+	14	2877	c.2866G>T	c.(2866-2868)Gga>Tga	p.G956*	KCNH6_ENST00000581784.1_Nonsense_Mutation_p.G867*|KCNH6_ENST00000456941.2_Nonsense_Mutation_p.G867*|KCNH6_ENST00000314672.5_Nonsense_Mutation_p.G920*	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	956					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.G956*(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GGAAGTACAAGGACTCATCTG	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											129	118	122					17																	61623144		2203	4300	6503	58976876	SO:0001587	stop_gained	81033			AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2866G>T	17.37:g.61623144G>T	ENSP00000463533:p.Gly956*		58976876	Q9BRD7	Nonsense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	33	5.246651	0.95305	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	.	.	.	4.57	3.57	0.40892	.	1.303990	0.05727	U	0.598830	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	9.2402	0.37491	0.0819:0.1473:0.7708:0.0	.	.	.	.	X	956;867	.	ENSP00000318212:G956X	G	+	1	0	KCNH6	58976876	1.000000	0.71417	0.972000	0.41901	0.069000	0.16628	4.268000	0.58883	2.228000	0.72767	0.563000	0.77884	GGA		0.567	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61623144	G	T	61623144	4	4	61	1	0	0	0	0	0	1	0	0	8057	1001	35	2	2920	2	KCNH6	17	61623144	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	130149	61623144	19572066	10370	18355										
KCNH6	81033	broad.mit.edu	37	chr17	61623220	61623220	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcagctggacttccagaGacatggctcagatcctggat	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61623220G>T	ENST00000583023.1	+	14	2953	c.2942G>T	c.(2941-2943)aGa>aTa	p.R981I	KCNH6_ENST00000581784.1_Missense_Mutation_p.R892I|KCNH6_ENST00000456941.2_Missense_Mutation_p.R892I|KCNH6_ENST00000314672.5_Missense_Mutation_p.R945I	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	981					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.R981I(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GACTTCCAGAGACATGGCTCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	84	85					17																	61623220		2203	4300	6503	58976952	SO:0001583	missense	81033			AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2942G>T	17.37:g.61623220G>T	ENSP00000463533:p.Arg981Ile		58976952	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420845	0.83559	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99885	-7.5	4.57	3.57	0.40892	.	0.167307	0.37219	U	0.002194	D	0.99782	0.9909	L	0.55481	1.735	0.58432	D	0.999999	B;D;D;D	0.76494	0.067;0.998;0.993;0.999	B;D;P;D	0.83275	0.015;0.991;0.823;0.996	D	0.95936	0.8942	10	0.87932	D	0	.	13.4601	0.61223	0.0805:0.0:0.9195:0.0	.	822;945;892;981	B4DPJ3;B4DKC0;Q9H252-2;Q9H252	.;.;.;KCNH6_HUMAN	I	981;892	ENSP00000396900:R892I	ENSP00000318212:R981I	R	+	2	0	KCNH6	58976952	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.782000	0.75073	2.228000	0.72767	0.563000	0.77884	AGA		0.542	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61623220	G	T	61623220	3	4	61	1	0	0	0	0	1	0	0	0	8057	942	33	2	2996	2	KCNH6	17	61623220	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76	61623220	19571990	10371	18356										
CCDC47	57003	broad.mit.edu	37	chr17	61831816	61831816	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcataatttttggaccagaGaactggtctgaaaaatgaac	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61831816G>T	ENST00000225726.5	-	9	1393	c.1011C>A	c.(1009-1011)ttC>ttA	p.F337L	CCDC47_ENST00000403162.3_Missense_Mutation_p.F337L|RP11-51F16.8_ENST00000580553.1_5'Flank|CCDC47_ENST00000582252.1_Missense_Mutation_p.F337L	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	337					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.F337L(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						TTGGACCAGAGAACTGGTCTG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	17											46	48	48					17																	61831816		2203	4300	6503	59185548	SO:0001583	missense	57003			AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1011C>A	17.37:g.61831816G>T	ENSP00000225726:p.Phe337Leu		59185548	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Missense_Mutation	SNP	ENST00000225726.5	37	CCDS11643.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.264734	0.40095	.	.	ENSG00000108588	ENST00000225726;ENST00000403162	.	.	.	5.95	4.98	0.66077	.	0.042517	0.85682	D	0.000000	T	0.53786	0.1818	L	0.47716	1.5	0.80722	D	1	B;P	0.41420	0.206;0.749	B;B	0.42462	0.164;0.388	T	0.45629	-0.9248	9	0.11485	T	0.65	-9.2168	17.387	0.87418	0.066:0.0:0.934:0.0	.	337;337	Q96A33-2;Q96A33	.;CCD47_HUMAN	L	337	.	ENSP00000225726:F337L	F	-	3	2	CCDC47	59185548	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.331000	0.52075	0.870000	0.35726	-1.119000	0.02030	TTC		0.318	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198		T	61831816	G	T	61831816	3	4	61	1	0	0	0	0	1	0	0	0	2824	933	33	2	460	2	CCDC47	17	61831816	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	208596	61831816	19363394	10372	18357										
PSMC5	5705	broad.mit.edu	37	chr17	61907214	61907214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtctgtttgccatctagttCgcctattgcgggaggagcta	12	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61907214C>T	ENST00000310144.6	+	4	477	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C	PSMC5_ENST00000580864.1_Missense_Mutation_p.R49C|PSMC5_ENST00000375812.4_Missense_Mutation_p.R49C|PSMC5_ENST00000581882.1_Missense_Mutation_p.R49C|FTSJ3_ENST00000427159.2_5'Flank|FTSJ3_ENST00000580295.1_5'UTR	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	57					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.R57C(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						CCATCTAGTTCGCCTATTGCG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											65	65	65					17																	61907214		2203	4300	6503	59260946	SO:0001583	missense	5705			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.169C>T	17.37:g.61907214C>T	ENSP00000310572:p.Arg57Cys		59260946	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689538	0.88735	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	T;T	0.42900	0.96;0.96	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	M	0.89840	3.065	0.80722	D	1	D;D	0.76494	0.996;0.999	P;P	0.59643	0.781;0.861	T	0.71836	-0.4472	10	0.87932	D	0	.	11.0663	0.47976	0.1848:0.8152:0.0:0.0	.	49;57	A8K3Z3;P62195	.;PRS8_HUMAN	C	57;49	ENSP00000310572:R57C;ENSP00000364970:R49C	ENSP00000310572:R57C	R	+	1	0	PSMC5	59260946	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.588000	0.60999	2.661000	0.90470	0.655000	0.94253	CGC		0.507	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61907214	C	T	61907214	3	4	61	1	0	0	0	0	1	0	0	0	12724	884	31	1	183	1	PSMC5	17	61907214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75398	61907214	19287996	10373	18358										
PSMC5	5705	broad.mit.edu	37	chr17	61907721	61907721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagacccattagtgtcactgAtgatggtggagaaagtacca	11	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61907721A>G	ENST00000310144.6	+	6	720	c.412A>G	c.(412-414)Atg>Gtg	p.M138V	PSMC5_ENST00000580864.1_Missense_Mutation_p.M130V|PSMC5_ENST00000375812.4_Missense_Mutation_p.M130V|PSMC5_ENST00000581882.1_Missense_Mutation_p.M130V|FTSJ3_ENST00000427159.2_5'Flank|FTSJ3_ENST00000580295.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	138					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.M138V(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						AGTGTCACTGATGATGGTGGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	17											124	114	117					17																	61907721		2203	4300	6503	59261453	SO:0001583	missense	5705			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.412A>G	17.37:g.61907721A>G	ENSP00000310572:p.Met138Val		59261453	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824693	0.71143	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.94497	-3.44;-3.42	5.3	5.3	0.74995	.	0.169485	0.64402	D	0.000009	D	0.95953	0.8682	M	0.92122	3.275	0.80722	D	1	P;P	0.50943	0.94;0.94	B;P	0.45856	0.391;0.495	D	0.96567	0.9420	10	0.87932	D	0	.	13.2525	0.60060	1.0:0.0:0.0:0.0	.	130;138	A8K3Z3;P62195	.;PRS8_HUMAN	V	138;130	ENSP00000310572:M138V;ENSP00000364970:M130V	ENSP00000310572:M138V	M	+	1	0	PSMC5	59261453	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	9.070000	0.93974	2.235000	0.73313	0.533000	0.62120	ATG		0.478	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		G	61907721	A	G	61907721	3	3	61	1	0	0	0	0	1	0	0	0	12724	333	12	4	434	4	PSMC5	17	61907721	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	507	61907721	19287489	10374	18359										
PSMC5	5705	broad.mit.edu	37	chr17	61908504	61908504	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgcggctggaggggggttCtggaggggacagtgaagtgc	21	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61908504C>A	ENST00000310144.6	+	8	1096	c.788C>A	c.(787-789)tCt>tAt	p.S263Y	PSMC5_ENST00000580864.1_Missense_Mutation_p.S255Y|PSMC5_ENST00000375812.4_Missense_Mutation_p.S255Y|PSMC5_ENST00000581882.1_Missense_Mutation_p.S255Y|FTSJ3_ENST00000580295.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	263	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.S263Y(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GAGGGGGGTTCTGGAGGGGAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											79	85	83					17																	61908504		2203	4300	6503	59262236	SO:0001583	missense	5705			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.788C>A	17.37:g.61908504C>A	ENSP00000310572:p.Ser263Tyr		59262236	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313069	0.81358	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.93426	-3.22;-3.22	5.64	5.64	0.86602	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.94192	0.8136	L	0.52206	1.635	0.80722	D	1	B;P	0.36909	0.142;0.573	P;P	0.48921	0.467;0.595	D	0.93897	0.7185	10	0.72032	D	0.01	.	17.243	0.87019	0.0:1.0:0.0:0.0	.	255;263	A8K3Z3;P62195	.;PRS8_HUMAN	Y	263;255	ENSP00000310572:S263Y;ENSP00000364970:S255Y	ENSP00000310572:S263Y	S	+	2	0	PSMC5	59262236	1.000000	0.71417	0.948000	0.38648	0.817000	0.46193	5.871000	0.69628	2.937000	0.99478	0.650000	0.86243	TCT		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		A	61908504	C	A	61908504	3	1	61	1	0	0	0	0	1	0	0	0	12724	913	32	2	818	2	PSMC5	17	61908504	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	783	61908504	19286706	10375	18360										
CSH2	1443	broad.mit.edu	37	chr17	61949543	61949543	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatgcgcaggaatgtctcGaccttgtccatgtccttcct	8	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61949543G>A	ENST00000392886.2	-	5	748	c.597C>T	c.(595-597)gtC>gtT	p.V199V	CSH2_ENST00000560142.1_Silent_p.V142V|CSH2_ENST00000336844.5_3'UTR|CSH2_ENST00000345366.7_Silent_p.V104V	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	199						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.V199V(1)		endometrium(2)|large_intestine(1)|lung(3)	6						GGAATGTCTCGACCTTGTCCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	17											137	117	124					17																	61949543		2203	4300	6503	59303275	SO:0001819	synonymous_variant	2689			V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"placental lactogen", "chorionic somatomammotropin B"	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.597C>T	17.37:g.61949543G>A			59303275	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000392886.2	37	CCDS42369.1																																																																																				0.572	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417657.1	NM_020991		A	61949543	G	A	61949543	2	1	61	1	0	0	0	0	0	0	0	1	3947	1045	37	1		1	CSH2	17	61949543	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41039	61949543	19245667	10376	18361										
GH2	2689	broad.mit.edu	37	chr17	61958464	61958464	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagggaggtctgggggttCtgcaggaatgaatacttctg	16	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61958464C>A	ENST00000423893.2	-	3	277	c.216G>T	c.(214-216)caG>caT	p.Q72H	GH2_ENST00000332800.7_Missense_Mutation_p.Q72H|GH2_ENST00000456543.2_Missense_Mutation_p.Q72H|GH2_ENST00000449787.2_Splice_Site			P01242	SOM2_HUMAN	growth hormone 2	72					JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.Q72H(2)		breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						TCTGGGGGTTCTGCAGGAATG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	17											198	210	206					17																	61958464		2203	4300	6503	59312196	SO:0001583	missense	2689			J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"Endogenous ligands"	4262	protein-coding gene	gene with protein product	"placental-specific growth hormone", "placenta-specific growth hormone"	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.216G>T	17.37:g.61958464C>A	ENSP00000409294:p.Gln72His		59312196	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|c	0.181|0.181	-1.062320|-1.062320	0.01950|0.01950	.|.	.|.	ENSG00000136487|ENSG00000136487	ENST00000449787|ENST00000332800;ENST00000456543;ENST00000423893	.|D;D;D	.|0.89050	.|-2.46;-2.46;-2.46	3.1|3.1	-0.415|-0.415	0.12355|0.12355	.|Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.|0.164006	.|0.51477	.|D	.|0.000091	.|D	.|0.83036	.|0.5167	N|N	0.17345|0.17345	0.48|0.48	0.28213|0.28213	N|N	0.926848|0.926848	.|B;B;D;B	.|0.76494	.|0.067;0.127;0.999;0.067	.|B;B;D;B	.|0.67548	.|0.07;0.016;0.952;0.07	.|T	.|0.74771	.|-0.3552	.|10	.|0.13853	.|T	.|0.58	.|.	2.888|2.888	0.05667|0.05667	0.1817:0.5303:0.1771:0.1109|0.1817:0.5303:0.1771:0.1109	.|.	.|72;72;72;72	.|P01242;O14644;B1A4H7;B1A4H5	.|SOM2_HUMAN;.;.;.	.|H	-1|72	.|ENSP00000333157:Q72H;ENSP00000394122:Q72H;ENSP00000409294:Q72H	.|ENSP00000333157:Q72H	.|Q	-|-	.|3	.|2	GH2|GH2	59312196|59312196	0.994000|0.994000	0.37717|0.37717	0.143000|0.143000	0.22291|0.22291	0.003000|0.003000	0.03518|0.03518	0.903000|0.903000	0.28475|0.28475	-0.144000|-0.144000	0.11314|0.11314	-0.471000|-0.471000	0.05019|0.05019	.|CAG		0.517	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		A	61958464	C	A	61958464	3	1	61	1	0	0	0	0	1	0	0	0	6388	927	32	2	786	2	GH2	17	61958464	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8921	61958464	19236746	10377	18362										
CSH1	1442	broad.mit.edu	37	chr17	61973867	61973867	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaggggcgcttacctggaGccattgccactaggtgagct	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:61973867G>T	ENST00000316193.8	-	1	146	c.5C>A	c.(4-6)gCt>gAt	p.A2D	CSH1_ENST00000453363.3_Missense_Mutation_p.A2D|CSH1_ENST00000329882.8_Missense_Mutation_p.A2D	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)	2						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.A2D(1)		central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CTTACCTGGAGCCATTGCCAC	0.597									Russell-Silver syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	17											106	102	103					17																	61973867		2201	4300	6501	59327599	SO:0001583	missense	1442	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.5C>A	17.37:g.61973867G>T	ENSP00000316416:p.Ala2Asp		59327599	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000316193.8	37	CCDS11649.1	.	.	.	.	.	.	.	.	.	.	g	11.73	1.726853	0.30593	.	.	ENSG00000136488	ENST00000329882;ENST00000316193;ENST00000453363	D;D;D	0.91740	-2.53;-2.48;-2.9	1.9	1.9	0.25705	.	2.137290	0.01794	N	0.032492	D	0.96106	0.8731	M	0.84585	2.705	0.80722	D	1	D;P;P;P	0.64830	0.994;0.726;0.825;0.747	D;B;B;B	0.67725	0.953;0.279;0.367;0.17	D	0.88642	0.3176	10	0.87932	D	0	.	7.3004	0.26418	0.0:0.0:1.0:0.0	.	2;2;2;2	B1A4H2;A6NFB4;Q6PF11;P01243	.;.;.;CSH_HUMAN	D	2	ENSP00000333268:A2D;ENSP00000316416:A2D;ENSP00000402517:A2D	ENSP00000316416:A2D	A	-	2	0	CSH1	59327599	1.000000	0.71417	0.995000	0.50966	0.042000	0.13812	1.815000	0.38981	1.360000	0.45960	0.313000	0.20887	GCT		0.597	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		T	61973867	G	T	61973867	3	4	61	1	0	0	0	0	1	0	0	0	3946	971	34	2	917	2	CSH1	17	61973867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15403	61973867	19221343	10378	18363										
SCN4A	6329	broad.mit.edu	37	chr17	62020211	62020211	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggacaggatgacgaccacGaagtcaaagatgttccagcc	11	10	1	2	rs267604989		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62020211G>A	ENST00000435607.1	-	23	4339	c.4263C>T	c.(4261-4263)ttC>ttT	p.F1421F	SCN4A_ENST00000578147.1_Silent_p.F1421F	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1421					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.F1421F(2)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGACGACCACGAAGTCAAAGA	0.582																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	17											115	113	114					17																	62020211		2198	4295	6493	59373943	SO:0001819	synonymous_variant	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4263C>T	17.37:g.62020211G>A			59373943	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																				0.582	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62020211	G	A	62020211	2	1	61	1	0	0	0	0	0	0	0	1	13957	1049	37	1		1	SCN4A	17	62020211	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46344	62020211	19174999	10379	18364										
SCN4A	6329	broad.mit.edu	37	chr17	62025384	62025384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatattctaggatggtgcGaatgactcgccgctgctcaa	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62025384G>A	ENST00000435607.1	-	17	3260	c.3184C>T	c.(3184-3186)Cgc>Tgc	p.R1062C	SCN4A_ENST00000578147.1_Missense_Mutation_p.R1062C	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1062					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R1062C(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGATGGTGCGAATGACTCGC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	17											98	98	98					17																	62025384		2150	4277	6427	59379116	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3184C>T	17.37:g.62025384G>A	ENSP00000396320:p.Arg1062Cys		59379116	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012287	0.75046	.	.	ENSG00000007314	ENST00000435607	D	0.97529	-4.42	4.49	3.44	0.39384	.	0.190189	0.41712	D	0.000830	D	0.94666	0.8280	L	0.50993	1.605	0.37781	D	0.927001	D	0.55605	0.972	B	0.42386	0.386	D	0.95375	0.8468	10	0.87932	D	0	.	11.802	0.52133	0.0:0.0:0.7267:0.2733	.	1062	P35499	SCN4A_HUMAN	C	1062	ENSP00000396320:R1062C	ENSP00000396320:R1062C	R	-	1	0	SCN4A	59379116	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.624000	0.67764	2.503000	0.84419	0.455000	0.32223	CGC		0.572	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62025384	G	A	62025384	3	1	61	1	0	0	0	0	1	0	0	0	13957	1058	37	1	2358	1	SCN4A	17	62025384	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5173	62025384	19169826	10380	18365										
SCN4A	6329	broad.mit.edu	37	chr17	62026016	62026016	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagacaatgaaggtctcGaaccagttgtgctcgacaat	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62026016G>A	ENST00000435607.1	-	16	3175	c.3099C>T	c.(3097-3099)ttC>ttT	p.F1033F	SCN4A_ENST00000578147.1_Silent_p.F1033F	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1033					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.F1033F(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAAGGTCTCGAACCAGTTGT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	17											50	53	52					17																	62026016		2202	4300	6502	59379748	SO:0001819	synonymous_variant	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3099C>T	17.37:g.62026016G>A			59379748	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																				0.627	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62026016	G	A	62026016	2	1	61	1	0	0	0	0	0	0	0	1	13957	1049	37	1		1	SCN4A	17	62026016	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	632	62026016	19169194	10381	18366										
SCN4A	6329	broad.mit.edu	37	chr17	62034710	62034710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccaaggcaatcttgcacaCgcactccttgtagctcttgc	8	14	2	0	rs113462659		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62034710C>T	ENST00000435607.1	-	13	2264	c.2188G>A	c.(2188-2190)Gtg>Atg	p.V730M	SCN4A_ENST00000578147.1_Missense_Mutation_p.V730M	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	730					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V730M(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATCTTGCACACGCACTCCTTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	100	107	104		2188	3.9	1	17	dbSNP_132	104	8,8592	6.4+/-24.3	0,8,4292	yes	missense	SCN4A	NM_000334.4	21	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	probably-damaging	730/1837	62034710	9,12997	2203	4300	6503	59388442	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2188G>A	17.37:g.62034710C>T	ENSP00000396320:p.Val730Met		59388442	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742290	0.69418	2.27E-4	9.3E-4	ENSG00000007314	ENST00000435607	D	0.98550	-4.99	3.91	3.91	0.45181	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98463	0.9488	M	0.64260	1.97	0.41346	D	0.987338	D	0.76494	0.999	D	0.73380	0.98	D	0.99585	1.0974	10	0.87932	D	0	.	15.018	0.71600	0.0:1.0:0.0:0.0	.	730	P35499	SCN4A_HUMAN	M	730	ENSP00000396320:V730M	ENSP00000396320:V730M	V	-	1	0	SCN4A	59388442	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.811000	0.62606	2.180000	0.69256	0.561000	0.74099	GTG		0.577	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62034710	C	T	62034710	3	4	61	1	0	0	0	0	1	0	0	0	13957	536	19	1	3370	1	SCN4A	17	62034710	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8694	62034710	19160500	10382	18367										
SCN4A	6329	broad.mit.edu	37	chr17	62034853	62034853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatgttcagcgttggccacGacttggccagcttgaagacc	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62034853G>A	ENST00000435607.1	-	13	2121	c.2045C>T	c.(2044-2046)tCg>tTg	p.S682L	SCN4A_ENST00000578147.1_Missense_Mutation_p.S682L	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	682					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.S682L(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CGTTGGCCACGACTTGGCCAG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17											66	73	71					17																	62034853		2145	4254	6399	59388585	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2045C>T	17.37:g.62034853G>A	ENSP00000396320:p.Ser682Leu		59388585	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606257	0.87157	.	.	ENSG00000007314	ENST00000435607	D	0.98221	-4.8	3.66	3.66	0.41972	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99017	0.9664	M	0.91090	3.175	0.58432	D	0.999999	D	0.76494	0.999	D	0.70016	0.967	D	0.99143	1.0856	10	0.72032	D	0.01	.	14.9158	0.70795	0.0:0.0:1.0:0.0	.	682	P35499	SCN4A_HUMAN	L	682	ENSP00000396320:S682L	ENSP00000396320:S682L	S	-	2	0	SCN4A	59388585	1.000000	0.71417	0.943000	0.38184	0.878000	0.50629	9.601000	0.98297	2.062000	0.61559	0.561000	0.74099	TCG		0.592	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62034853	G	A	62034853	3	1	61	1	0	0	0	0	1	0	0	0	13957	1059	37	1	3513	1	SCN4A	17	62034853	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143	62034853	19160357	10383	18368										
CCDC45	90799	broad.mit.edu	37	chr17	62522265	62522265	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagagattaacagaacaaGaattacatgatgtatcagaa	8	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62522265G>T	ENST00000556440.2	+	10	1609	c.1099G>T	c.(1099-1101)Gaa>Taa	p.E367*	CEP95_ENST00000553412.1_Nonsense_Mutation_p.E203*|CEP95_ENST00000577476.1_3'UTR	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	367						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)		p.E367*(2)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						AACAGAACAAGAATTACATGA	0.393																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											118	112	114					17																	62522265		1827	4087	5914	59952727	SO:0001587	stop_gained	90799			AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.1099G>T	17.37:g.62522265G>T	ENSP00000450461:p.Glu367*		59952727	B4DMD2|Q96M81	Nonsense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	G	39	7.420089	0.98272	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	.	.	.	5.54	4.57	0.56435	.	0.236995	0.42682	D	0.000676	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-10.5227	11.8528	0.52422	0.0808:0.0:0.9192:0.0	.	.	.	.	X	302;367;203	.	ENSP00000438458:E302X	E	+	1	0	CEP95	59952727	1.000000	0.71417	0.958000	0.39756	0.053000	0.15095	4.731000	0.62022	1.467000	0.48044	0.655000	0.94253	GAA		0.393	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		T	62522265	G	T	62522265	4	4	61	1	0	0	0	0	0	1	0	0	2822	943	33	2	1137	2	CCDC45	17	62522265	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	487412	62522265	18672945	10384	18369										
CCDC45	90799	broad.mit.edu	37	chr17	62533816	62533816	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatgatgatgatgttttCttccgggaactggaagctga	12	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62533816C>A	ENST00000556440.2	+	20	2895	c.2385C>A	c.(2383-2385)ttC>ttA	p.F795L	CEP95_ENST00000553412.1_Missense_Mutation_p.F631L	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	795						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)		p.F795L(2)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						ATGATGTTTTCTTCCGGGAAC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	17											64	64	64					17																	62533816		1945	4141	6086	59964278	SO:0001583	missense	90799			AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2385C>A	17.37:g.62533816C>A	ENSP00000450461:p.Phe795Leu		59964278	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410075	0.83340	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.50813	0.73;0.77	5.82	4.85	0.62838	.	0.334756	0.36200	N	0.002733	T	0.63105	0.2483	M	0.70595	2.14	0.38191	D	0.939909	D	0.76494	0.999	D	0.69142	0.962	T	0.66995	-0.5782	10	0.44086	T	0.13	-11.3735	9.582	0.39493	0.0:0.8005:0.0:0.1995	.	795	Q96GE4	CEP95_HUMAN	L	730;795;631	ENSP00000450461:F795L;ENSP00000450906:F631L	ENSP00000438458:F730L	F	+	3	2	CEP95	59964278	0.990000	0.36364	1.000000	0.80357	0.982000	0.71751	0.308000	0.19314	1.472000	0.48140	0.462000	0.41574	TTC		0.453	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		A	62533816	C	A	62533816	3	1	61	1	0	0	0	0	1	0	0	0	2822	912	32	2	2463	2	CCDC45	17	62533816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11551	62533816	18661394	10385	18370										
LRRC37A3	374819	broad.mit.edu	37	chr17	62855948	62855948	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccattttgtctcagtttgtTtaacagttggccctaagttg	8	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:62855948T>G	ENST00000584306.1	-	11	4846	c.4316A>C	c.(4315-4317)aAa>aCa	p.K1439T	LRRC37A3_ENST00000334962.5_Missense_Mutation_p.K416T|LRRC37A3_ENST00000339474.5_Missense_Mutation_p.K557T|LRRC37A3_ENST00000400877.3_Missense_Mutation_p.K477T|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.K1439T	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1439						integral component of membrane (GO:0016021)		p.K1439T(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CTCAGTTTGTTTAACAGTTGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											28	31	30					17																	62855948		2173	4259	6432	60286410	SO:0001583	missense	374819			AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.4316A>C	17.37:g.62855948T>G	ENSP00000464535:p.Lys1439Thr		60286410	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	4.442	0.081865	0.08533	.	.	ENSG00000176809	ENST00000339474;ENST00000400877;ENST00000334962;ENST00000319651	T;T;T	0.60424	1.4;1.4;0.19	1.86	-0.812	0.10853	.	.	.	.	.	T	0.46190	0.1380	L	0.59436	1.845	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.12156	0.007;0.002	T	0.44159	-0.9346	9	0.52906	T	0.07	.	1.7916	0.03053	0.2772:0.1863:0.0:0.5365	.	557;1439	B4DG20;O60309	.;L37A3_HUMAN	T	520;477;416;1439	ENSP00000383674:K477T;ENSP00000335617:K416T;ENSP00000325713:K1439T	ENSP00000325713:K1439T	K	-	2	0	LRRC37A3	60286410	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.095000	0.15127	-0.228000	0.09869	0.155000	0.16302	AAA		0.483	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		G	62855948	T	G	62855948	3	3	61	1	0	0	0	0	1	0	0	0	9022	1841	64	4	604	4	LRRC37A3	17	62855948	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	322132	62855948	18339262	10386	18371										
RGS9	8787	broad.mit.edu	37	chr17	63223393	63223393	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcctcttgcacctgaagCtttttccagatcaaaatgga	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:63223393C>A	ENST00000262406.9	+	19	1960	c.1893C>A	c.(1891-1893)aaC>aaA	p.N631K	RGS9_ENST00000449996.3_Splice_Site_p.N628K	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	631					dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.N631K(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						GCACCTGAAGCTTTTTCCAGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											83	86	85					17																	63223393		1985	4165	6150	60653855	SO:0001630	splice_region_variant	8787			AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"Regulators of G-protein signaling"	10004	protein-coding gene	gene with protein product	"regulator of G protein signalling 9", "regulator of G protein signalling 9L", "regulator of G-protein signaling 9L"	604067	"regulator of G-protein signalling 9"			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1893-1C>A	17.37:g.63223393C>A			60653855	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952419	0.53293	.	.	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.35789	1.31;1.29	4.81	3.83	0.44106	.	0.111128	0.64402	D	0.000008	T	0.33818	0.0876	L	0.59436	1.845	0.39223	D	0.963537	P;P	0.46142	0.799;0.873	B;B	0.42361	0.214;0.385	T	0.15723	-1.0427	9	.	.	.	.	9.3764	0.38286	0.0:0.8354:0.0:0.1646	.	631;628	O75916;O75916-5	RGS9_HUMAN;.	K	631;628	ENSP00000262406:N631K;ENSP00000396329:N628K	.	N	+	3	2	RGS9	60653855	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.713000	0.37951	2.590000	0.87494	0.561000	0.74099	AAC		0.552	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835	Missense_Mutation	A	63223393	C	A	63223393	5	1	61	1	0	0	0	0	0	0	1	0	13350	811	28	2	2022	2	RGS9	17	63223393	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	367445	63223393	17971817	10387	18372										
AXIN2	8313	broad.mit.edu	37	chr17	63554176	63554176	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcagaagtcaaaaacatcTggtaggcattttcctccatc	6	10	3	1	rs149000772		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:63554176T>G	ENST00000375702.5	-	1	671	c.563A>C	c.(562-564)cAg>cCg	p.Q188P	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Missense_Mutation_p.Q188P			Q9Y2T1	AXIN2_HUMAN	axin 2	188	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.Q188P(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CAAAAACATCTGGTAGGCATT	0.473									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	17											122	105	111					17																	63554176		2203	4300	6503	60984638	SO:0001583	missense	8313	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.563A>C	17.37:g.63554176T>G	ENSP00000364854:p.Gln188Pro		60984638	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		.	.	.	.	.	.	.	.	.	.	T	7.456	0.643635	0.14451	.	.	ENSG00000168646	ENST00000307078;ENST00000375702	T;T	0.16897	2.31;2.31	5.07	5.07	0.68467	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.055177	0.85682	D	0.000000	T	0.07908	0.0198	N	0.00335	-1.625	0.58432	D	0.999999	D;B;D	0.76494	0.999;0.0;0.999	D;B;P	0.69307	0.963;0.003;0.869	T	0.49652	-0.8917	10	0.02654	T	1	-28.1659	7.6379	0.28277	0.0:0.1608:0.0:0.8392	.	188;188;188	B7ZKL5;Q9Y2T1;E7ES00	.;AXIN2_HUMAN;.	P	188	ENSP00000302625:Q188P;ENSP00000364854:Q188P	ENSP00000302625:Q188P	Q	-	2	0	AXIN2	60984638	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.992000	0.56980	1.895000	0.54865	0.374000	0.22700	CAG		0.473	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		G	63554176	T	G	63554176	3	3	61	1	0	0	0	0	1	0	0	0	1238	1580	55	4	2008	4	AXIN2	17	63554176	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	330783	63554176	17641034	10388	18373										
CCDC46	201134	broad.mit.edu	37	chr17	64025368	64025368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctttatgcagtgtgttaCgcctaaaaacaagagaataa	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:64025368C>T	ENST00000392769.2	-	14	1594	c.1376G>A	c.(1375-1377)cGt>cAt	p.R459H	CEP112_ENST00000541355.1_Missense_Mutation_p.R94H|CEP112_ENST00000535342.2_Missense_Mutation_p.R459H|CEP112_ENST00000537949.1_Missense_Mutation_p.R417H	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	459					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)		p.R459H(2)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						CAGTGTGTTACGCCTAAAAAC	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	17											158	148	151					17																	64025368		2202	4297	6499	61455830	SO:0001583	missense	201134			AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"coiled-coil domain containing 46"	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1376G>A	17.37:g.64025368C>T	ENSP00000376522:p.Arg459His		61455830	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.805616	0.31961	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000541355;ENST00000537949	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.55	0.0613	0.14340	.	0.732994	0.13710	N	0.368190	T	0.11024	0.0269	N	0.16478	0.41	0.27426	N	0.954141	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.08055	0.003;0.002;0.003	T	0.35992	-0.9766	10	0.15066	T	0.55	0.5283	10.3727	0.44064	0.0:0.5771:0.0:0.4229	.	417;417;459	F5GYE8;A2RRR7;Q8N8E3	.;.;CE112_HUMAN	H	459;459;94;417	ENSP00000442784:R459H;ENSP00000376522:R459H;ENSP00000443711:R94H;ENSP00000440775:R417H	ENSP00000376522:R459H	R	-	2	0	CEP112	61455830	0.000000	0.05858	0.804000	0.32291	0.686000	0.39977	-0.100000	0.10990	0.102000	0.17638	0.655000	0.94253	CGT		0.279	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036		T	64025368	C	T	64025368	3	4	61	1	0	0	0	0	1	0	0	0	2823	536	19	1	1713	1	CCDC46	17	64025368	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	471192	64025368	17169842	10389	18374										
APOH	350	broad.mit.edu	37	chr17	64208284	64208284	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcggatgcatcagttttCcaaaaagccagagaactgtg	9	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:64208284C>T	ENST00000205948.6	-	8	1042	c.1005G>A	c.(1003-1005)tgG>tgA	p.W335*		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	335	Sushi-like.		W -> S (in allele APOH*3W; loss of phosphatidylserine-binding; dbSNP:rs1801690). {ECO:0000269|PubMed:9063752, ECO:0000269|Ref.8}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)	p.W335*(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			CATCAGTTTTCCAAAAAGCCA	0.368																																					Melanoma(155;624 1882 16869 48804 51309)											1	Substitution - Nonsense(1)	large_intestine(1)	17											97	98	97					17																	64208284		2203	4300	6503	61638746	SO:0001587	stop_gained	350				CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.1005G>A	17.37:g.64208284C>T	ENSP00000205948:p.Trp335*		61638746	B2R9M3|Q9UCN7	Nonsense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	c	22.9	4.345512	0.82022	.	.	ENSG00000091583	ENST00000205948	.	.	.	5.7	5.7	0.88788	.	0.362482	0.30151	N	0.010297	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	15.3453	0.74330	0.0:1.0:0.0:0.0	.	.	.	.	X	335	.	ENSP00000205948:W335X	W	-	3	0	APOH	61638746	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	3.506000	0.53364	2.679000	0.91253	0.555000	0.69702	TGG		0.368	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		T	64208284	C	T	64208284	4	4	61	1	0	0	0	0	0	1	0	0	804	856	30	3	36	3	APOH	17	64208284	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	182916	64208284	16986926	10390	18375										
APOH	350	broad.mit.edu	37	chr17	64216739	64216739	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtatcatttccaaacatCgcatgttgtggcaaacattc	6	9	1	0	rs367862167		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:64216739C>T	ENST00000205948.6	-	5	574	c.537G>A	c.(535-537)gcG>gcA	p.A179A		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	179	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)	p.A179A(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TTCCAAACATCGCATGTTGTG	0.418																																					Melanoma(155;624 1882 16869 48804 51309)											1	Substitution - coding silent(1)	large_intestine(1)	17						C		1,4405	2.1+/-5.4	0,1,2202	173	157	163		537	-10.7	0	17		163	0,8600		0,0,4300	no	coding-synonymous	APOH	NM_000042.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		179/346	64216739	1,13005	2203	4300	6503	61647201	SO:0001819	synonymous_variant	350				CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.537G>A	17.37:g.64216739C>T			61647201	B2R9M3|Q9UCN7	Silent	SNP	ENST00000205948.6	37	CCDS11663.1																																																																																				0.418	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		T	64216739	C	T	64216739	2	4	61	1	0	0	0	0	0	0	0	1	804	871	31	1		1	APOH	17	64216739	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8455	64216739	16978471	10391	18376										
PRKCA	5578	broad.mit.edu	37	chr17	64637530	64637530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggaagccccaccttctgcGatcactgtgggtcactgctc	10	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:64637530G>A	ENST00000413366.3	+	4	372	c.346G>A	c.(346-348)Gat>Aat	p.D116N	RNA5SP445_ENST00000515889.1_RNA	NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	116					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)	p.D116N(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	CACCTTCTGCGATCACTGTGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											208	173	185					17																	64637530		2203	4300	6503	62067992	SO:0001583	missense	5578				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.346G>A	17.37:g.64637530G>A	ENSP00000408695:p.Asp116Asn		62067992	B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	37	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	G	36	5.647691	0.96714	.	.	ENSG00000154229	ENST00000413366;ENST00000284384	D	0.92965	-3.14	6.04	6.04	0.98038	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.000000	0.85682	D	0.000000	D	0.96087	0.8725	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	D	0.95726	0.8770	10	0.72032	D	0.01	.	20.1896	0.98226	0.0:0.0:1.0:0.0	.	116	P17252	KPCA_HUMAN	N	116;23	ENSP00000408695:D116N	ENSP00000284384:D23N	D	+	1	0	PRKCA	62067992	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	9.333000	0.96459	2.873000	0.98535	0.561000	0.74099	GAT		0.468	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1			A	64637530	G	A	64637530	3	1	61	1	0	0	0	0	1	0	0	0	12541	1058	37	1	360	1	PRKCA	17	64637530	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420791	64637530	16557680	10392	18377										
HELZ	9931	broad.mit.edu	37	chr17	65116685	65116685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcctgatgtgtaataattCgaggatcaactgcaaaccta	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65116685C>T	ENST00000358691.5	-	27	3840	c.3674G>A	c.(3673-3675)cGa>cAa	p.R1225Q	HELZ_ENST00000580168.1_Missense_Mutation_p.R1226Q	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1225						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1225Q(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TGTAATAATTCGAGGATCAAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											171	156	161					17																	65116685		1937	4128	6065	62547147	SO:0001583	missense	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.3674G>A	17.37:g.65116685C>T	ENSP00000351524:p.Arg1225Gln		62547147	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663453	0.67700	.	.	ENSG00000198265	ENST00000358691	D	0.86432	-2.12	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.91771	0.7397	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.978	D	0.91686	0.5362	10	0.62326	D	0.03	-12.0924	20.0203	0.97492	0.0:1.0:0.0:0.0	.	1226;1225	B7ZLW2;P42694	.;HELZ_HUMAN	Q	1225	ENSP00000351524:R1225Q	ENSP00000351524:R1225Q	R	-	2	0	HELZ	62547147	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.298000	0.78815	2.730000	0.93505	0.655000	0.94253	CGA		0.408	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65116685	C	T	65116685	3	4	61	1	0	0	0	0	1	0	0	0	7070	884	31	1	2182	1	HELZ	17	65116685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	479155	65116685	16078525	10393	18378										
HELZ	9931	broad.mit.edu	37	chr17	65119168	65119168	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccagtgtgaggatctattCtttgaacagggcttggagat	12	7	2	3	rs372453784		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65119168C>A	ENST00000358691.5	-	26	3714	c.3548G>T	c.(3547-3549)aGa>aTa	p.R1183I	HELZ_ENST00000580168.1_Missense_Mutation_p.R1184I	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1183						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1183I(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AGGATCTATTCTTTGAACAGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	108	110					17																	65119168		1855	4085	5940	62549630	SO:0001583	missense	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.3548G>T	17.37:g.65119168C>A	ENSP00000351524:p.Arg1183Ile		62549630	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.235343	0.58886	.	.	ENSG00000198265	ENST00000358691	D	0.84298	-1.83	5.5	5.5	0.81552	.	0.091790	0.85682	D	0.000000	D	0.90497	0.7023	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.991	D	0.90804	0.4696	10	0.72032	D	0.01	-3.376	19.7595	0.96308	0.0:1.0:0.0:0.0	.	1184;1183	B7ZLW2;P42694	.;HELZ_HUMAN	I	1183	ENSP00000351524:R1183I	ENSP00000351524:R1183I	R	-	2	0	HELZ	62549630	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.252000	0.78309	2.732000	0.93576	0.650000	0.86243	AGA		0.433	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65119168	C	A	65119168	3	1	61	1	0	0	0	0	1	0	0	0	7070	913	32	2	2312	2	HELZ	17	65119168	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2483	65119168	16076042	10394	18379										
HELZ	9931	broad.mit.edu	37	chr17	65132250	65132250	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttctttttaattggtgtCtgtttatgtttacaagtatg	7	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65132250C>A	ENST00000358691.5	-	23	3184	c.3018G>T	c.(3016-3018)caG>caT	p.Q1006H	HELZ_ENST00000580168.1_Missense_Mutation_p.Q1007H	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1006						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q1006H(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TAATTGGTGTCTGTTTATGTT	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	17											94	93	93					17																	65132250		1822	4084	5906	62562712	SO:0001583	missense	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.3018G>T	17.37:g.65132250C>A	ENSP00000351524:p.Gln1006His		62562712	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.324361	0.24080	.	.	ENSG00000198265	ENST00000358691	D	0.83755	-1.76	4.94	3.73	0.42828	.	0.000000	0.85682	D	0.000000	D	0.85177	0.5637	L	0.49778	1.585	0.58432	D	0.999996	D;D	0.67145	0.996;0.996	D;D	0.68765	0.96;0.941	D	0.84089	0.0389	10	0.52906	T	0.07	-10.8216	6.4683	0.21993	0.0:0.7777:0.0:0.2223	.	1007;1006	B7ZLW2;P42694	.;HELZ_HUMAN	H	1006	ENSP00000351524:Q1006H	ENSP00000351524:Q1006H	Q	-	3	2	HELZ	62562712	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.576000	0.23744	2.447000	0.82792	0.591000	0.81541	CAG		0.318	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65132250	C	A	65132250	3	1	61	1	0	0	0	0	1	0	0	0	7070	912	32	2	2854	2	HELZ	17	65132250	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13082	65132250	16062960	10395	18380										
HELZ	9931	broad.mit.edu	37	chr17	65163821	65163821	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaagcttaaagcgaccaaAaagttgtccattctgagcat	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65163821A>T	ENST00000358691.5	-	14	1688	c.1522T>A	c.(1522-1524)Ttt>Att	p.F508I	HELZ_ENST00000580168.1_Missense_Mutation_p.F508I	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	508						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F508I(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AAGCGACCAAAAAGTTGTCCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											110	98	102					17																	65163821		1871	4118	5989	62594283	SO:0001583	missense	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1522T>A	17.37:g.65163821A>T	ENSP00000351524:p.Phe508Ile		62594283	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.242010	0.58995	.	.	ENSG00000198265	ENST00000358691	D	0.89485	-2.52	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.92867	0.7731	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.997;0.998	P;D	0.65684	0.88;0.937	D	0.93595	0.6925	10	0.72032	D	0.01	-16.3775	15.2605	0.73617	1.0:0.0:0.0:0.0	.	508;508	B7ZLW2;P42694	.;HELZ_HUMAN	I	508	ENSP00000351524:F508I	ENSP00000351524:F508I	F	-	1	0	HELZ	62594283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.692000	0.91284	2.008000	0.58898	0.533000	0.62120	TTT		0.418	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65163821	A	T	65163821	3	4	61	1	0	0	0	0	1	0	0	0	7070	14	1	5	4386	5	HELZ	17	65163821	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	31571	65163821	16031389	10396	18381										
PSMD12	5718	broad.mit.edu	37	chr17	65343510	65343510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgctgatgatttgtgttCgaatgtaatccttcacagct	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65343510C>T	ENST00000356126.3	-	6	709	c.602G>A	c.(601-603)cGa>cAa	p.R201Q	PSMD12_ENST00000581618.1_5'Flank|PSMD12_ENST00000357146.4_Missense_Mutation_p.R181Q	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	201					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.R201Q(2)		breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					GATTTGTGTTCGAATGTAATC	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	17											106	99	102					17																	65343510		2203	4300	6503	62773972	SO:0001583	missense	5718			AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.602G>A	17.37:g.65343510C>T	ENSP00000348442:p.Arg201Gln		62773972	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	37	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733484	0.69189	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.05925	3.37;3.37	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.49256	1.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.982;0.987	T	0.03166	-1.1065	10	0.14656	T	0.56	-12.0908	20.3151	0.98650	0.0:1.0:0.0:0.0	.	181;201	A6NP15;O00232	.;PSD12_HUMAN	Q	201;181	ENSP00000348442:R201Q;ENSP00000349667:R181Q	ENSP00000348442:R201Q	R	-	2	0	PSMD12	62773972	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	7.470000	0.80973	2.809000	0.96659	0.467000	0.42956	CGA		0.388	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		T	65343510	C	T	65343510	3	4	61	1	0	0	0	0	1	0	0	0	12729	884	31	1	792	1	PSMD12	17	65343510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179689	65343510	15851700	10397	18382										
PSMD12	5718	broad.mit.edu	37	chr17	65353481	65353481	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcattaagtaaatcccattCtttagcctcatagcacatct	3	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65353481C>A	ENST00000356126.3	-	3	342	c.235G>T	c.(235-237)Gaa>Taa	p.E79*	PSMD12_ENST00000581618.1_5'UTR|PSMD12_ENST00000357146.4_Nonsense_Mutation_p.E59*	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	79					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.E79*(1)		breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					AAATCCCATTCTTTAGCCTCA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											83	83	83					17																	65353481		2203	4300	6503	62783943	SO:0001587	stop_gained	5718			AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.235G>T	17.37:g.65353481C>A	ENSP00000348442:p.Glu79*		62783943	A6NP15|Q53HA2|Q6P053	Nonsense_Mutation	SNP	ENST00000356126.3	37	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	C	36	5.623521	0.96660	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	.	.	.	5.29	5.29	0.74685	.	0.137701	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-14.2275	18.9241	0.92537	0.0:1.0:0.0:0.0	.	.	.	.	X	79;59	.	ENSP00000348442:E79X	E	-	1	0	PSMD12	62783943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.356000	0.79445	2.477000	0.83638	0.591000	0.81541	GAA		0.368	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		A	65353481	C	A	65353481	4	1	61	1	0	0	0	0	0	1	0	0	12729	922	32	2	1171	2	PSMD12	17	65353481	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9971	65353481	15841729	10398	18383										
BPTF	2186	broad.mit.edu	37	chr17	65871774	65871774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtccctctgaagggaggaGccctgtggggtgtctctcag	15	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65871774G>A	ENST00000321892.4	+	5	2028	c.1967G>A	c.(1966-1968)aGc>aAc	p.S656N	BPTF_ENST00000335221.5_Missense_Mutation_p.S656N|BPTF_ENST00000306378.6_Intron|BPTF_ENST00000424123.3_Missense_Mutation_p.S517N			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	656	Interaction with KEAP1.				anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.S656N(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GAAGGGAGGAGCCCTGTGGGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											71	67	68					17																	65871774		2203	4300	6503	63302236	SO:0001583	missense	2186			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1967G>A	17.37:g.65871774G>A	ENSP00000315454:p.Ser656Asn		63302236	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	G	10.51	1.370805	0.24771	.	.	ENSG00000171634	ENST00000544491;ENST00000335221;ENST00000321892;ENST00000544778	T;T	0.62788	0.0;-0.0	5.47	5.47	0.80525	.	.	.	.	.	T	0.43077	0.1231	N	0.14661	0.345	0.29170	N	0.877227	B;B	0.20887	0.001;0.049	B;B	0.20184	0.003;0.028	T	0.25502	-1.0130	9	0.25751	T	0.34	.	8.7982	0.34892	0.1279:0.0:0.8721:0.0	.	656;656	Q12830;Q12830-4	BPTF_HUMAN;.	N	561;656;656;517	ENSP00000334351:S656N;ENSP00000315454:S656N	ENSP00000315454:S656N	S	+	2	0	BPTF	63302236	1.000000	0.71417	1.000000	0.80357	0.520000	0.34377	3.250000	0.51445	2.729000	0.93468	0.467000	0.42956	AGC		0.532	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		A	65871774	G	A	65871774	3	1	61	1	0	0	0	0	1	0	0	0	1498	971	34	3	1985	3	BPTF	17	65871774	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	518293	65871774	15323436	10399	18384										
BPTF	2186	broad.mit.edu	37	chr17	65890193	65890193	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgtgtagcaaacccagaGaatttgcattggctttagcc	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65890193G>T	ENST00000321892.4	+	9	2894	c.2833G>T	c.(2833-2835)Gaa>Taa	p.E945*	BPTF_ENST00000335221.5_Nonsense_Mutation_p.E945*|BPTF_ENST00000306378.6_Nonsense_Mutation_p.E819*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.E806*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	945					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E945*(1)|p.E819*(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAAACCCAGAGAATTTGCATT	0.378																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											144	136	139					17																	65890193		2203	4300	6503	63320655	SO:0001587	stop_gained	2186			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.2833G>T	17.37:g.65890193G>T	ENSP00000315454:p.Glu945*		63320655	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	G	39	7.493260	0.98319	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-18.1014	19.5998	0.95557	0.0:0.0:1.0:0.0	.	.	.	.	X	819;945;945;743	.	ENSP00000307208:E819X	E	+	1	0	BPTF	63320655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.734000	0.98822	2.717000	0.92951	0.655000	0.94253	GAA		0.378	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65890193	G	T	65890193	4	4	61	1	0	0	0	0	0	1	0	0	1498	943	33	2	2867	2	BPTF	17	65890193	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	18419	65890193	15305017	10400	18385										
BPTF	2186	broad.mit.edu	37	chr17	65907077	65907077	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgacatgaaaacagagtCacatgtaaattgtcaggaga	10	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65907077C>A	ENST00000321892.4	+	13	3516	c.3455C>A	c.(3454-3456)tCa>tAa	p.S1152*	BPTF_ENST00000335221.5_Nonsense_Mutation_p.S1152*|BPTF_ENST00000306378.6_Nonsense_Mutation_p.S1026*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.S1013*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1152					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.S1026*(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAACAGAGTCACATGTAAAT	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											90	87	88					17																	65907077		2203	4300	6503	63337539	SO:0001587	stop_gained	2186			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.3455C>A	17.37:g.65907077C>A	ENSP00000315454:p.Ser1152*		63337539	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	C	38	7.242543	0.98157	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0044	20.0769	0.97748	0.0:1.0:0.0:0.0	.	.	.	.	X	1026;1152;1152	.	ENSP00000307208:S1026X	S	+	2	0	BPTF	63337539	0.991000	0.36638	0.825000	0.32803	0.349000	0.29174	4.010000	0.57117	2.820000	0.97059	0.650000	0.86243	TCA		0.378	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		A	65907077	C	A	65907077	4	1	61	1	0	0	0	0	0	1	0	0	1498	838	29	2	3505	2	BPTF	17	65907077	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16884	65907077	15288133	10401	18386										
BPTF	2186	broad.mit.edu	37	chr17	65942230	65942230	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgccccagcaaatcaaacTccagttacctatccaaattc	4	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:65942230T>G	ENST00000321892.4	+	23	7845	c.7784T>G	c.(7783-7785)cTc>cGc	p.L2595R	BPTF_ENST00000335221.5_Intron|BPTF_ENST00000306378.6_Missense_Mutation_p.L2469R|BPTF_ENST00000424123.3_Intron			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2595					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.L2469R(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAAATCAAACTCCAGTTACCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											106	94	98					17																	65942230		2203	4300	6503	63372692	SO:0001583	missense	2186			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.7784T>G	17.37:g.65942230T>G	ENSP00000315454:p.Leu2595Arg		63372692	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	T	10.63	1.403125	0.25291	.	.	ENSG00000171634	ENST00000306378;ENST00000321892	T;T	0.10477	2.87;2.87	5.88	5.88	0.94601	.	.	.	.	.	T	0.28599	0.0708	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.10405	-1.0631	9	0.07990	T	0.79	-5.9941	16.2874	0.82727	0.0:0.0:0.0:1.0	.	2469	Q12830-2	.	R	2469;2595	ENSP00000307208:L2469R;ENSP00000315454:L2595R	ENSP00000307208:L2469R	L	+	2	0	BPTF	63372692	1.000000	0.71417	0.952000	0.39060	0.039000	0.13416	5.924000	0.70054	2.248000	0.74166	0.528000	0.53228	CTC		0.502	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65942230	T	G	65942230	3	3	61	1	0	0	0	0	1	0	0	0	1498	1551	54	4	7874	4	BPTF	17	65942230	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	35153	65942230	15252980	10402	18387										
SLC16A6	9120	broad.mit.edu	37	chr17	66267636	66267636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttcaagcatatactgcGcttctttccgattttcctgg	6	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66267636G>A	ENST00000327268.4	-	6	829	c.665C>T	c.(664-666)gCg>gTg	p.A222V	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.A222V	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	222					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.A222V(1)		large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CATATACTGCGCTTCTTTCCG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17											175	168	171					17																	66267636		2203	4300	6503	63779231	SO:0001583	missense	9120			U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.665C>T	17.37:g.66267636G>A	ENSP00000319991:p.Ala222Val		63779231	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	G	0.815	-0.750711	0.03041	.	.	ENSG00000108932	ENST00000327268	T	0.58358	0.34	4.59	0.771	0.18504	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	5.200610	0.00424	N	0.000075	T	0.31071	0.0785	N	0.03608	-0.345	0.23859	N	0.996646	B	0.06786	0.001	B	0.04013	0.001	T	0.20438	-1.0275	10	0.19590	T	0.45	.	9.3134	0.37919	0.3982:0.0:0.6018:0.0	.	222	O15403	MOT7_HUMAN	V	222	ENSP00000319991:A222V	ENSP00000319991:A222V	A	-	2	0	SLC16A6	63779231	0.026000	0.19158	0.950000	0.38849	0.047000	0.14425	1.249000	0.32839	-0.063000	0.13065	-0.350000	0.07774	GCG		0.428	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		A	66267636	G	A	66267636	3	1	61	1	0	0	0	0	1	0	0	0	14449	1087	38	1	914	1	SLC16A6	17	66267636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	325406	66267636	14927574	10403	18388										
SLC16A6	9120	broad.mit.edu	37	chr17	66268787	66268787	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagtccacctacctggtgcGaaagcaaacacagcgaaaca	9	12	0	0	rs143522620	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66268787G>A	ENST00000327268.4	-	5	662	c.498C>T	c.(496-498)ttC>ttT	p.F166F	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Silent_p.F166F	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	166					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.F166F(1)		large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TACCTGGTGCGAAAGCAAACA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	17						G	,,	1,4405	2.1+/-5.4	0,1,2202	173	146	155		498,498,	-0.4	1	17	dbSNP_134	155	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous,coding-synonymous,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	,,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	,,	166/524,166/524,	66268787	9,12997	2203	4300	6503	63780382	SO:0001819	synonymous_variant	9120			U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.498C>T	17.37:g.66268787G>A			63780382	Q6P1X3	Silent	SNP	ENST00000327268.4	37	CCDS11675.1																																																																																				0.443	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		A	66268787	G	A	66268787	2	1	61	1	0	0	0	0	0	0	0	1	14449	1049	37	1		1	SLC16A6	17	66268787	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1151	66268787	14926423	10404	18389										
ARSG	22901	broad.mit.edu	37	chr17	66366659	66366659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcactggattttggcaaactCgtcaaggtaaggggctcagc	12	9	3	0	rs144503106	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66366659C>T	ENST00000448504.2	+	8	1772	c.976C>T	c.(976-978)Cgt>Tgt	p.R326C	ARSG_ENST00000452479.2_Missense_Mutation_p.R162C|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	326					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.R326C(1)		NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTGGCAAACTCGTCAAGGTAA	0.552													C|||	2	0.000399361	0	0	5008	,	,		18113	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	17											99	82	87					17																	66366659		2203	4300	6503	63878254	SO:0001583	missense	22901			AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"Arylsulfatase family"	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.976C>T	17.37:g.66366659C>T	ENSP00000407193:p.Arg326Cys		63878254	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.996233	0.35226	.	.	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.0	3.97	0.46021	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.826360	0.11156	N	0.593620	T	0.28599	0.0708	N	0.22421	0.69	0.09310	N	1	P	0.40360	0.714	B	0.43575	0.424	T	0.08432	-1.0722	9	0.52906	T	0.07	.	7.5126	0.27583	0.1953:0.6383:0.1664:0.0	.	326	Q96EG1	ARSG_HUMAN	C	326;225	.	ENSP00000407193:R225C	R	+	1	0	ARSG	63878254	0.000000	0.05858	0.018000	0.16275	0.037000	0.13140	0.480000	0.22244	2.596000	0.87737	0.561000	0.74099	CGT		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		T	66366659	C	T	66366659	3	4	61	1	0	0	0	0	1	0	0	0	993	884	31	1	1002	1	ARSG	17	66366659	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97872	66366659	14828551	10405	18390										
WIPI1	55062	broad.mit.edu	37	chr17	66447016	66447016	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggagaagaggcgctccacGatgtagacgtccgggatttc	14	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66447016G>A	ENST00000262139.5	-	3	185	c.186C>T	c.(184-186)atC>atT	p.I62I	WIPI1_ENST00000546360.1_5'UTR|WIPI1_ENST00000589459.1_5'UTR	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	62					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)	p.I62I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						GGCGCTCCACGATGTAGACGT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	17											111	99	103					17																	66447016		2203	4300	6503	63958611	SO:0001819	synonymous_variant	55062				CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"WD repeat domain containing"	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.186C>T	17.37:g.66447016G>A			63958611	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																				0.527	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		A	66447016	G	A	66447016	2	1	61	1	0	0	0	0	0	0	0	1	17410	1048	37	1		1	WIPI1	17	66447016	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80357	66447016	14748194	10406	18391										
PRKAR1A	5573	broad.mit.edu	37	chr17	66519878	66519878	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctaggttataccaaaaGattacaagacaatggccgct	7	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66519878G>T	ENST00000589228.1	+	4	489	c.361G>T	c.(361-363)Gat>Tat	p.D121Y	PRKAR1A_ENST00000588188.2_Missense_Mutation_p.D121Y|PRKAR1A_ENST00000536854.2_Missense_Mutation_p.D121Y|PRKAR1A_ENST00000358598.2_Missense_Mutation_p.D121Y|PRKAR1A_ENST00000586397.1_Missense_Mutation_p.D121Y|PRKAR1A_ENST00000392711.1_Missense_Mutation_p.D121Y	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	121	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.D121Y(1)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					TATACCAAAAGATTACAAGAC	0.373			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	17											89	88	88					17																	66519878		2203	4300	6503	64031473	SO:0001583	missense	5573	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.361G>T	17.37:g.66519878G>T	ENSP00000464977:p.Asp121Tyr		64031473	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	G	33	5.269439	0.95429	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	D;D;D	0.84516	-1.86;-1.86;-1.86	6.08	6.08	0.98989	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.93125	0.7811	M	0.85859	2.78	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.63703	0.917;0.917	D	0.93017	0.6437	10	0.72032	D	0.01	-43.5625	20.6647	0.99678	0.0:0.0:1.0:0.0	.	121;121	B2R5T5;P10644	.;KAP0_HUMAN	Y	121	ENSP00000351410:D121Y;ENSP00000376475:D121Y;ENSP00000445625:D121Y	ENSP00000351410:D121Y	D	+	1	0	PRKAR1A	64031473	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.890000	0.99128	0.655000	0.94253	GAT		0.373	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			T	66519878	G	T	66519878	3	4	61	1	0	0	0	0	1	0	0	0	12537	942	33	2	371	2	PRKAR1A	17	66519878	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72862	66519878	14675332	10407	18392										
PRKAR1A	5573	broad.mit.edu	37	chr17	66526418	66526418	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatctttgctttctccagGtgaaattgcactactgatga	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66526418G>T	ENST00000589228.1	+	11	1102	c.974G>T	c.(973-975)gGt>gTt	p.G325V	PRKAR1A_ENST00000588188.2_Intron|PRKAR1A_ENST00000536854.2_Splice_Site_p.G325V|PRKAR1A_ENST00000358598.2_Splice_Site_p.G325V|PRKAR1A_ENST00000586397.1_Splice_Site_p.G325V|PRKAR1A_ENST00000392711.1_Splice_Site_p.G325V	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	325					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.G325V(1)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					CTTTCTCCAGGTGAAATTGCA	0.438			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	17											187	168	175					17																	66526418		2203	4300	6503	64038013	SO:0001630	splice_region_variant	5573	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.974-1G>T	17.37:g.66526418G>T			64038013	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227825	0.79576	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	D;D;D	0.98207	-4.79;-4.79;-4.79	5.9	5.9	0.94986	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.99197	4.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97860	1.0280	9	.	.	.	.	20.2704	0.98474	0.0:0.0:1.0:0.0	.	325	P10644	KAP0_HUMAN	V	325	ENSP00000351410:G325V;ENSP00000376475:G325V;ENSP00000445625:G325V	.	G	+	2	0	PRKAR1A	64038013	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	9.869000	0.99810	2.793000	0.96121	0.591000	0.81541	GGT		0.438	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1		Missense_Mutation	T	66526418	G	T	66526418	5	4	61	1	0	0	0	0	0	0	1	0	12537	1275	44	2	1012	2	PRKAR1A	17	66526418	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6540	66526418	14668792	10408	18393										
PRKAR1A	5573	broad.mit.edu	37	chr17	66526547	66526547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctcagacatcctcaaacGaaacatccagcagtacaaca	5	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66526547G>A	ENST00000589228.1	+	11	1231	c.1103G>A	c.(1102-1104)cGa>cAa	p.R368Q	PRKAR1A_ENST00000588188.2_Intron|PRKAR1A_ENST00000536854.2_Missense_Mutation_p.R368Q|PRKAR1A_ENST00000358598.2_Missense_Mutation_p.R368Q|PRKAR1A_ENST00000586397.1_Missense_Mutation_p.R368Q|PRKAR1A_ENST00000392711.1_Missense_Mutation_p.R368Q	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	368					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.R368Q(1)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					ATCCTCAAACGAAACATCCAG	0.512			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	17											213	167	183					17																	66526547		2203	4300	6503	64038142	SO:0001583	missense	5573	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.1103G>A	17.37:g.66526547G>A	ENSP00000464977:p.Arg368Gln		64038142	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	G	35	5.591461	0.96590	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	D;D;D	0.88586	-2.4;-2.4;-2.4	5.63	5.63	0.86233	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.137882	0.47093	D	0.000249	D	0.96015	0.8702	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.96549	0.9406	10	0.87932	D	0	-16.1203	19.6895	0.95993	0.0:0.0:1.0:0.0	.	368	P10644	KAP0_HUMAN	Q	368	ENSP00000351410:R368Q;ENSP00000376475:R368Q;ENSP00000445625:R368Q	ENSP00000351410:R368Q	R	+	2	0	PRKAR1A	64038142	1.000000	0.71417	0.933000	0.37362	0.992000	0.81027	9.825000	0.99386	2.644000	0.89710	0.591000	0.81541	CGA		0.512	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			A	66526547	G	A	66526547	3	1	61	1	0	0	0	0	1	0	0	0	12537	1058	37	1	1141	1	PRKAR1A	17	66526547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129	66526547	14668663	10409	18394										
ABCA8	10351	broad.mit.edu	37	chr17	66883513	66883513	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtaagtagcatgtcttcGaagtttgaaatgtagctcat	9	5	2	1	rs201100712	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66883513G>A	ENST00000269080.2	-	23	3296	c.3159C>T	c.(3157-3159)ttC>ttT	p.F1053F	ABCA8_ENST00000586539.1_Silent_p.F1093F|ABCA8_ENST00000430352.2_Silent_p.F1093F	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1053					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.F1053F(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GCATGTCTTCGAAGTTTGAAA	0.343													G|||	2	0.000399361	0	0	5008	,	,		18138	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											76	84	81					17																	66883513		2203	4300	6503	64395108	SO:0001819	synonymous_variant	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3159C>T	17.37:g.66883513G>A			64395108	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																				0.343	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66883513	G	A	66883513	2	1	61	1	0	0	0	0	0	0	0	1	38	1049	37	1		1	ABCA8	17	66883513	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356966	66883513	14311697	10410	18395										
ABCA8	10351	broad.mit.edu	37	chr17	66887690	66887690	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactcgatgttaaaaccagCcagaacatgatatatgccag	7	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66887690C>T	ENST00000269080.2	-	22	3101	c.2964G>A	c.(2962-2964)tgG>tgA	p.W988*	ABCA8_ENST00000586539.1_Nonsense_Mutation_p.W1028*|ABCA8_ENST00000430352.2_Nonsense_Mutation_p.W1028*	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	988					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.W988*(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TTAAAACCAGCCAGAACATGA	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											126	108	114					17																	66887690		2203	4300	6503	64399285	SO:0001587	stop_gained	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.2964G>A	17.37:g.66887690C>T	ENSP00000269080:p.Trp988*		64399285	A1L3U3|C9JQE6|Q86WW0	Nonsense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	38	7.082305	0.98051	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	.	.	.	4.66	3.69	0.42338	.	0.145894	0.32343	N	0.006228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	6.3484	0.21363	0.0:0.806:0.0:0.194	.	.	.	.	X	988;1028;967	.	ENSP00000269080:W988X	W	-	3	0	ABCA8	64399285	0.001000	0.12720	0.278000	0.24718	0.028000	0.11728	0.376000	0.20535	2.574000	0.86865	0.650000	0.86243	TGG		0.348	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66887690	C	T	66887690	4	4	61	1	0	0	0	0	0	1	0	0	38	740	26	3	1849	3	ABCA8	17	66887690	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4177	66887690	14307520	10411	18396										
ABCA8	10351	broad.mit.edu	37	chr17	66890330	66890330	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctccaaaaatgtacttCtttcagttcggatatgtact	5	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66890330C>A	ENST00000269080.2	-	21	3037	c.2900G>T	c.(2899-2901)aGa>aTa	p.R967I	ABCA8_ENST00000586539.1_Missense_Mutation_p.R1007I|ABCA8_ENST00000430352.2_Missense_Mutation_p.R1007I	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	967					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R967I(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					AAATGTACTTCTTTCAGTTCG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											62	60	60					17																	66890330		2202	4299	6501	64401925	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.2900G>T	17.37:g.66890330C>A	ENSP00000269080:p.Arg967Ile		64401925	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.790044	0.70337	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.87256	-2.23;-2.23	5.08	5.08	0.68730	.	0.384615	0.22878	N	0.054541	D	0.92886	0.7737	M	0.81942	2.565	0.36536	D	0.870999	D;D;D;P;D	0.61697	0.987;0.99;0.978;0.946;0.979	D;D;P;P;D	0.69142	0.921;0.962;0.864;0.847;0.936	D	0.94429	0.7648	10	0.56958	D	0.05	.	14.1648	0.65469	0.0:1.0:0.0:0.0	.	946;1007;1007;1007;967	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	I	967;1007;946	ENSP00000269080:R967I;ENSP00000402814:R1007I	ENSP00000269080:R967I	R	-	2	0	ABCA8	64401925	0.001000	0.12720	0.339000	0.25562	0.026000	0.11368	0.759000	0.26461	2.801000	0.96364	0.655000	0.94253	AGA		0.368	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66890330	C	A	66890330	3	1	61	1	0	0	0	0	1	0	0	0	38	913	32	2	1917	2	ABCA8	17	66890330	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2640	66890330	14304880	10412	18397										
ABCA8	10351	broad.mit.edu	37	chr17	66903886	66903886	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcatgcacattacctggaAatttatttgttctttctaag	6	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66903886A>C	ENST00000269080.2	-	16	2290	c.2153T>G	c.(2152-2154)tTt>tGt	p.F718C	ABCA8_ENST00000586539.1_Missense_Mutation_p.F758C|ABCA8_ENST00000430352.2_Missense_Mutation_p.F758C	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	718					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.F718C(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					ATTACCTGGAAATTTATTTGT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	17											123	117	119					17																	66903886		2202	4297	6499	64415481	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.2153T>G	17.37:g.66903886A>C	ENSP00000269080:p.Phe718Cys		64415481	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.769893	0.69992	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.90563	-2.69;-2.69	4.9	4.9	0.64082	.	0.000000	0.50627	D	0.000118	D	0.96950	0.9004	H	0.97291	3.975	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;1.0	D	0.98136	1.0433	10	0.87932	D	0	.	13.8531	0.63510	1.0:0.0:0.0:0.0	.	697;758;758;758;718	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	C	718;758;697	ENSP00000269080:F718C;ENSP00000402814:F758C	ENSP00000269080:F718C	F	-	2	0	ABCA8	64415481	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.731000	0.74785	2.057000	0.61298	0.533000	0.62120	TTT		0.294	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66903886	A	C	66903886	3	2	61	1	0	0	0	0	1	0	0	0	38	14	1	4	2684	4	ABCA8	17	66903886	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	13556	66903886	14291324	10413	18398										
ABCA8	10351	broad.mit.edu	37	chr17	66925340	66925340	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccggtgaggaaagatttCtttaccaagatgctcattaa	10	7	2	3	rs143207789		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66925340C>A	ENST00000269080.2	-	8	1112	c.975G>T	c.(973-975)aaG>aaT	p.K325N	ABCA8_ENST00000586539.1_Missense_Mutation_p.K325N|ABCA8_ENST00000430352.2_Missense_Mutation_p.K325N	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	325					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.K325N(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GGAAAGATTTCTTTACCAAGA	0.418													C|||	1	0.000199681	8e-04	0	5008	,	,		17482	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17						C	ASN/LYS	3,4403	6.2+/-15.9	0,3,2200	68	56	60		975	4.7	1	17	dbSNP_134	60	0,8600		0,0,4300	no	missense	ABCA8	NM_007168.2	94	0,3,6500	AA,AC,CC		0.0,0.0681,0.0231	probably-damaging	325/1582	66925340	3,13003	2203	4300	6503	64436935	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.975G>T	17.37:g.66925340C>A	ENSP00000269080:p.Lys325Asn		64436935	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.33	3.599315	0.66332	6.81E-4	0.0	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.84873	-1.91;-1.91	4.67	4.67	0.58626	.	0.229117	0.30492	N	0.009507	D	0.90553	0.7039	M	0.84082	2.675	0.33150	D	0.545507	D;D;B;D;D	0.67145	0.995;0.996;0.099;0.989;0.996	D;D;B;D;D	0.72625	0.962;0.965;0.098;0.972;0.978	D	0.89242	0.3584	10	0.13470	T	0.59	.	11.1047	0.48197	0.0:0.9093:0.0:0.0907	.	264;325;325;325;325	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	N	325;325;264	ENSP00000269080:K325N;ENSP00000402814:K325N	ENSP00000269080:K325N	K	-	3	2	ABCA8	64436935	1.000000	0.71417	0.998000	0.56505	0.710000	0.40934	0.843000	0.27640	2.592000	0.87571	0.655000	0.94253	AAG		0.418	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66925340	C	A	66925340	3	1	61	1	0	0	0	0	1	0	0	0	38	912	32	2	3894	2	ABCA8	17	66925340	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21454	66925340	14269870	10414	18399										
ABCA9	10350	broad.mit.edu	37	chr17	66978729	66978729	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaatttgaagaaagcctgtGataaaggtcgcacatcctca	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:66978729G>T	ENST00000340001.4	-	37	4905	c.4694C>A	c.(4693-4695)tCa>tAa	p.S1565*	ABCA9_ENST00000453985.2_Nonsense_Mutation_p.S1527*|ABCA9_ENST00000370732.2_3'UTR	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1565					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S1565*(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GAAAGCCTGTGATAAAGGTCG	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											138	133	134					17																	66978729		2203	4300	6503	64490324	SO:0001587	stop_gained	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4694C>A	17.37:g.66978729G>T	ENSP00000342216:p.Ser1565*		64490324	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Nonsense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	G	43	10.465212	0.99410	.	.	ENSG00000154258	ENST00000340001;ENST00000453985	.	.	.	4.9	4.9	0.64082	.	0.000000	0.39210	N	0.001439	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.0308	0.86460	0.0:0.0:1.0:0.0	.	.	.	.	X	1565;1510	.	ENSP00000342216:S1565X	S	-	2	0	ABCA9	64490324	1.000000	0.71417	0.437000	0.26809	0.992000	0.81027	8.313000	0.89978	2.418000	0.82041	0.609000	0.83330	TCA		0.423	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	66978729	G	T	66978729	4	4	61	1	0	0	0	0	0	1	0	0	39	1294	45	2	192	2	ABCA9	17	66978729	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53389	66978729	14216481	10415	18400										
ABCA9	10350	broad.mit.edu	37	chr17	67012444	67012444	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttctgacgaattaaaaaTtccaagtagtccattgctaa	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67012444T>G	ENST00000340001.4	-	22	3200	c.2989A>C	c.(2989-2991)Att>Ctt	p.I997L	ABCA9-AS1_ENST00000458677.1_RNA|ABCA9_ENST00000453985.2_Missense_Mutation_p.I997L|ABCA9_ENST00000370732.2_Missense_Mutation_p.I997L	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	997					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.I997L(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GAATTAAAAATTCCAAGTAGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	17											111	110	110					17																	67012444		2203	4300	6503	64524039	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2989A>C	17.37:g.67012444T>G	ENSP00000342216:p.Ile997Leu		64524039	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	T	1.797	-0.478065	0.04414	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	D;D	0.87887	-2.31;-2.31	5.1	1.68	0.24146	.	0.662303	0.12820	N	0.436515	T	0.77671	0.4165	L	0.41961	1.31	0.20074	N	0.999936	B;B	0.09022	0.002;0.001	B;B	0.09377	0.003;0.004	T	0.57027	-0.7881	10	0.05959	T	0.93	.	7.7292	0.28777	0.0:0.2584:0.0:0.7416	.	997;997	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	L	997;980;997;992	ENSP00000342216:I997L;ENSP00000359767:I997L	ENSP00000342216:I997L	I	-	1	0	ABCA9	64524039	0.000000	0.05858	0.751000	0.31187	0.044000	0.14063	0.387000	0.20718	0.009000	0.14813	0.482000	0.46254	ATT		0.338	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		G	67012444	T	G	67012444	3	3	61	1	0	0	0	0	1	0	0	0	39	1493	52	4	1957	4	ABCA9	17	67012444	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	33715	67012444	14182766	10416	18401										
ABCA9	10350	broad.mit.edu	37	chr17	67014669	67014669	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttctgatatgactcgtaGaatagatgttccaaaagttg	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67014669G>T	ENST00000340001.4	-	20	2863	c.2652C>A	c.(2650-2652)ttC>ttA	p.F884L	ABCA9-AS1_ENST00000458677.1_RNA|ABCA9_ENST00000453985.2_Missense_Mutation_p.F884L|ABCA9_ENST00000370732.2_Missense_Mutation_p.F884L	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	884					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.F884L(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					ATGACTCGTAGAATAGATGTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											212	220	217					17																	67014669		2203	4300	6503	64526264	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2652C>A	17.37:g.67014669G>T	ENSP00000342216:p.Phe884Leu		64526264	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	G	2.108	-0.404418	0.04832	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	T;T	0.75821	-0.97;-0.97	5.29	0.895	0.19247	.	0.850405	0.09751	U	0.760603	T	0.45558	0.1348	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.31943	-0.9925	10	0.10902	T	0.67	.	4.9442	0.13982	0.1577:0.125:0.6014:0.1158	.	884;884	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	L	884;867;884;879	ENSP00000342216:F884L;ENSP00000359767:F884L	ENSP00000342216:F884L	F	-	3	2	ABCA9	64526264	0.000000	0.05858	0.006000	0.13384	0.012000	0.07955	-1.141000	0.03207	0.624000	0.30286	-0.137000	0.14449	TTC		0.368	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	67014669	G	T	67014669	3	4	61	1	0	0	0	0	1	0	0	0	39	933	33	2	2302	2	ABCA9	17	67014669	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2225	67014669	14180541	10417	18402										
ABCA9	10350	broad.mit.edu	37	chr17	67045565	67045565	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacatttgaggagtgtcatGaacttgatgtaaattggaga	12	3	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67045565G>T	ENST00000340001.4	-	3	374	c.163C>A	c.(163-165)Cat>Aat	p.H55N	ABCA9_ENST00000495634.1_Missense_Mutation_p.H55N|ABCA9_ENST00000453985.2_Missense_Mutation_p.H55N|ABCA9_ENST00000370732.2_Missense_Mutation_p.H55N	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	55					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.H55N(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GGAGTGTCATGAACTTGATGT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	17											125	127	126					17																	67045565		2203	4300	6503	64557160	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.163C>A	17.37:g.67045565G>T	ENSP00000342216:p.His55Asn		64557160	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.160620	0.00321	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	D;D	0.86297	-2.0;-2.1	4.78	-2.36	0.06663	.	0.796800	0.10628	N	0.652517	T	0.60805	0.2297	N	0.01454	-0.855	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.52540	-0.8562	10	0.19147	T	0.46	.	3.7839	0.08692	0.1255:0.0871:0.49:0.2974	.	55;55	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	N	55;38;55;50	ENSP00000342216:H55N;ENSP00000359767:H55N	ENSP00000342216:H55N	H	-	1	0	ABCA9	64557160	0.003000	0.15002	0.026000	0.17262	0.001000	0.01503	-0.218000	0.09240	-0.540000	0.06265	-0.873000	0.02984	CAT		0.343	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	67045565	G	T	67045565	3	4	61	1	0	0	0	0	1	0	0	0	39	1290	45	2	4859	2	ABCA9	17	67045565	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30896	67045565	14149645	10418	18403										
ABCA6	23460	broad.mit.edu	37	chr17	67092428	67092428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgttttttctccttttgcGaaaaataaatgatatcatat	4	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67092428G>A	ENST00000284425.2	-	25	3535	c.3361C>T	c.(3361-3363)Cgc>Tgc	p.R1121C	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1121					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1121C(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					CTCCTTTTGCGAAAAATAAAT	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	17											24	28	26					17																	67092428		2178	4242	6420	64604023	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3361C>T	17.37:g.67092428G>A	ENSP00000284425:p.Arg1121Cys		64604023	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.728931	0.48833	.	.	ENSG00000154262	ENST00000284425	D	0.85955	-2.05	4.61	1.4	0.22301	.	0.275088	0.25887	N	0.027657	D	0.89815	0.6824	M	0.85630	2.765	0.54753	D	0.999984	D	0.76494	0.999	D	0.70487	0.969	D	0.86029	0.1512	10	0.72032	D	0.01	.	2.939	0.05824	0.1006:0.1882:0.5318:0.1795	.	1121	Q8N139	ABCA6_HUMAN	C	1121	ENSP00000284425:R1121C	ENSP00000284425:R1121C	R	-	1	0	ABCA6	64604023	0.998000	0.40836	0.702000	0.30337	0.691000	0.40173	0.549000	0.23329	0.245000	0.21373	0.650000	0.86243	CGC		0.269	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67092428	G	A	67092428	3	1	61	1	0	0	0	0	1	0	0	0	36	1058	37	1	1552	1	ABCA6	17	67092428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46863	67092428	14102782	10419	18404										
ABCA6	23460	broad.mit.edu	37	chr17	67094098	67094098	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccatggtgatataaggaGaaatgctacatagaaccaaa	9	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67094098G>T	ENST00000284425.2	-	23	3257	c.3083C>A	c.(3082-3084)tCt>tAt	p.S1028Y	ABCA6_ENST00000446604.2_5'UTR|MIR4524B_ENST00000581569.1_RNA	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1028					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S1028Y(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GATATAAGGAGAAATGCTACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	17											60	55	57					17																	67094098		2203	4300	6503	64605693	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3083C>A	17.37:g.67094098G>T	ENSP00000284425:p.Ser1028Tyr		64605693	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363504	0.41902	.	.	ENSG00000154262	ENST00000284425	D	0.86956	-2.19	4.92	4.92	0.64577	.	0.124126	0.36555	N	0.002531	D	0.92835	0.7721	M	0.81942	2.565	0.80722	D	1	D	0.65815	0.995	D	0.68943	0.961	D	0.93320	0.6692	10	0.87932	D	0	.	13.8152	0.63287	0.0:0.0:1.0:0.0	.	1028	Q8N139	ABCA6_HUMAN	Y	1028	ENSP00000284425:S1028Y	ENSP00000284425:S1028Y	S	-	2	0	ABCA6	64605693	0.781000	0.28676	0.589000	0.28718	0.176000	0.22953	3.043000	0.49823	2.717000	0.92951	0.557000	0.71058	TCT		0.368	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67094098	G	T	67094098	3	4	61	1	0	0	0	0	1	0	0	0	36	942	33	2	1838	2	ABCA6	17	67094098	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1670	67094098	14101112	10420	18405										
ABCA6	23460	broad.mit.edu	37	chr17	67108387	67108387	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaacctgcacacttcagtCtcccattggacatgatcact	6	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67108387C>A	ENST00000284425.2	-	16	2243	c.2069G>T	c.(2068-2070)aGa>aTa	p.R690I		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	690	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R690I(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					ACACTTCAGTCTCCCATTGGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	17											144	152	149					17																	67108387		2203	4300	6503	64619982	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.2069G>T	17.37:g.67108387C>A	ENSP00000284425:p.Arg690Ile		64619982	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.721940	0.30503	.	.	ENSG00000154262	ENST00000284425	T	0.68479	-0.33	4.65	-0.911	0.10507	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.867092	0.09945	N	0.735458	T	0.61060	0.2317	M	0.72894	2.215	0.09310	N	1	B	0.28933	0.228	B	0.28553	0.091	T	0.55698	-0.8100	10	0.56958	D	0.05	.	6.5959	0.22672	0.0:0.5741:0.1291:0.2968	.	690	Q8N139	ABCA6_HUMAN	I	690	ENSP00000284425:R690I	ENSP00000284425:R690I	R	-	2	0	ABCA6	64619982	0.000000	0.05858	0.000000	0.03702	0.834000	0.47266	-0.190000	0.09615	0.016000	0.14998	-0.150000	0.13652	AGA		0.378	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67108387	C	A	67108387	3	1	61	1	0	0	0	0	1	0	0	0	36	913	32	2	2880	2	ABCA6	17	67108387	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14289	67108387	14086823	10421	18406										
ABCA6	23460	broad.mit.edu	37	chr17	67119514	67119514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaagatgatgaattcaaGaaaaataaaggagaataatg	8	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67119514G>T	ENST00000284425.2	-	10	1476	c.1302C>A	c.(1300-1302)ttC>ttA	p.F434L		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	434					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.F434L(1)|p.F434F(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					ATGAATTCAAGAAAAATAAAG	0.363																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	17											95	92	93					17																	67119514		2203	4300	6503	64631109	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1302C>A	17.37:g.67119514G>T	ENSP00000284425:p.Phe434Leu		64631109	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.898920	0.52227	.	.	ENSG00000154262	ENST00000284425	D	0.91011	-2.77	4.91	1.85	0.25348	.	0.126991	0.35615	N	0.003097	D	0.90273	0.6958	M	0.69185	2.1	0.80722	D	1	B	0.33528	0.416	P	0.44518	0.452	D	0.88270	0.2929	10	0.66056	D	0.02	.	8.0306	0.30463	0.3233:0.0:0.6767:0.0	.	434	Q8N139	ABCA6_HUMAN	L	434	ENSP00000284425:F434L	ENSP00000284425:F434L	F	-	3	2	ABCA6	64631109	1.000000	0.71417	0.952000	0.39060	0.531000	0.34715	1.024000	0.30077	0.766000	0.33244	0.637000	0.83480	TTC		0.363	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67119514	G	T	67119514	3	4	61	1	0	0	0	0	1	0	0	0	36	933	33	2	3671	2	ABCA6	17	67119514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11127	67119514	14075696	10422	18407										
ABCA6	23460	broad.mit.edu	37	chr17	67129895	67129895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggagaaatgaagcaagaaGaataaaataaacatctcatt	9	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67129895G>T	ENST00000284425.2	-	6	852	c.678C>A	c.(676-678)ttC>ttA	p.F226L		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	226					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.F226L(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GAAGCAAGAAGAATAAAATAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	17											59	62	61					17																	67129895		2203	4296	6499	64641490	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.678C>A	17.37:g.67129895G>T	ENSP00000284425:p.Phe226Leu		64641490	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	6.764	0.509779	0.12883	.	.	ENSG00000154262	ENST00000284425	D	0.86297	-2.1	5.61	2.5	0.30297	.	1.291270	0.05323	N	0.526920	D	0.83714	0.5314	L	0.53561	1.675	0.09310	N	0.999992	B	0.11235	0.004	B	0.24974	0.057	T	0.63305	-0.6667	10	0.21014	T	0.42	.	5.4639	0.16632	0.168:0.0:0.6724:0.1596	.	226	Q8N139	ABCA6_HUMAN	L	226	ENSP00000284425:F226L	ENSP00000284425:F226L	F	-	3	2	ABCA6	64641490	0.001000	0.12720	0.061000	0.19648	0.002000	0.02628	0.768000	0.26590	0.388000	0.25054	0.655000	0.94253	TTC		0.323	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67129895	G	T	67129895	3	4	61	1	0	0	0	0	1	0	0	0	36	933	33	2	4311	2	ABCA6	17	67129895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10381	67129895	14065315	10423	18408										
ABCA10	10349	broad.mit.edu	37	chr17	67149612	67149612	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accccgagcctggcccatacCtttctctttattccctctga	5	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67149612C>A	ENST00000269081.4	-	34	4950	c.4041G>T	c.(4039-4041)aaG>aaT	p.K1347N	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1347	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.K1347N(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TGGCCCATACCTTTCTCTTTA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	17											115	123	120					17																	67149612		2203	4300	6503	64661207	SO:0001630	splice_region_variant	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.4041+1G>T	17.37:g.67149612C>A			64661207	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.554185	0.86231	.	.	ENSG00000154263	ENST00000269081	T	0.15718	2.4	3.58	3.58	0.41010	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.35320	U	0.003297	T	0.51890	0.1701	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.997	T	0.68700	-0.5339	9	.	.	.	.	15.3524	0.74399	0.0:1.0:0.0:0.0	.	339;1347	B4DPV2;Q8WWZ4	.;ABCAA_HUMAN	N	1347	ENSP00000269081:K1347N	.	K	-	3	2	ABCA10	64661207	1.000000	0.71417	0.994000	0.49952	0.240000	0.25518	4.837000	0.62796	1.817000	0.53016	0.563000	0.77884	AAG		0.507	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	Missense_Mutation	A	67149612	C	A	67149612	5	1	61	1	0	0	0	0	0	0	1	0	29	695	24	2	618	2	ABCA10	17	67149612	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19717	67149612	14045598	10424	18409										
ABCA10	10349	broad.mit.edu	37	chr17	67151176	67151176	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccttttttaacacaaaaGgaaacatttctgatggctat	5	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67151176G>T	ENST00000269081.4	-	31	4587	c.3678C>A	c.(3676-3678)tcC>tcA	p.S1226S	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1226	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S1226S(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TAACACAAAAGGAAACATTTC	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	17											56	55	55					17																	67151176		2202	4296	6498	64662771	SO:0001819	synonymous_variant	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3678C>A	17.37:g.67151176G>T			64662771	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																				0.289	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67151176	G	T	67151176	2	4	61	1	0	0	0	0	0	0	0	1	29	987	35	2		2	ABCA10	17	67151176	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1564	67151176	14044034	10425	18410										
ABCA10	10349	broad.mit.edu	37	chr17	67152063	67152063	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctactccgtggagaGattctacagaggaaataaaa	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67152063G>T	ENST00000269081.4	-	30	4368	c.3459C>A	c.(3457-3459)atC>atA	p.I1153I	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1153					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.I1153I(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TCCGTGGAGAGATTCTACAGA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	17											101	98	99					17																	67152063		2203	4300	6503	64663658	SO:0001819	synonymous_variant	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3459C>A	17.37:g.67152063G>T			64663658	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																				0.358	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67152063	G	T	67152063	2	4	61	1	0	0	0	0	0	0	0	1	29	932	33	2		2	ABCA10	17	67152063	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	887	67152063	14043147	10426	18411										
ABCA5	23461	broad.mit.edu	37	chr17	67248006	67248006	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcagttcgaattgctcGcctataaaacataaataaaa	5	7	0	0	rs143193092		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67248006G>A	ENST00000392676.3	-	35	4481	c.4417C>T	c.(4417-4419)Cga>Tga	p.R1473*	ABCA5_ENST00000392677.2_Splice_Site_p.R1474*|ABCA5_ENST00000588877.1_Splice_Site_p.R1473*			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1473	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1473*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CGAATTGCTCGCCTATAAAAC	0.358													G|||	1	0.000199681	0	0	5008	,	,		14755	0		0	False		,,,				2504	0.001															1	Substitution - Nonsense(1)	large_intestine(1)	17						G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	50	47	48		4417,4417	1.8	1	17	dbSNP_134	48	2,8598	2.2+/-6.3	0,2,4298	no	stop-gained-near-splice,stop-gained-near-splice	ABCA5	NM_018672.3,NM_172232.2	,	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,	1473/1643,1473/1643	67248006	3,13003	2203	4300	6503	64759601	SO:0001630	splice_region_variant	23461			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.4416-1C>T	17.37:g.67248006G>A			64759601	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Nonsense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	G	51	18.345737	0.99903	2.27E-4	2.33E-4	ENSG00000154265	ENST00000392677;ENST00000392676	.	.	.	5.44	1.79	0.24919	.	0.000000	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	14.7935	0.69860	0.0:0.0:0.431:0.5689	.	.	.	.	X	1474;1473	.	ENSP00000376443:R1473X	R	-	1	2	ABCA5	64759601	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.498000	0.35660	0.729000	0.32403	0.591000	0.81541	CGA		0.358	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	Nonsense_Mutation	A	67248006	G	A	67248006	5	1	61	1	0	0	0	0	0	0	1	0	35	1101	38	1	531	1	ABCA5	17	67248006	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95943	67248006	13947204	10427	18412										
ABCA5	23461	broad.mit.edu	37	chr17	67256534	67256534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataggtgtccacattttttCgtacattcttccaagaaatc	5	9	1	1	rs370220843		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67256534C>T	ENST00000392676.3	-	27	3648	c.3584G>A	c.(3583-3585)cGa>cAa	p.R1195Q	ABCA5_ENST00000392677.2_Missense_Mutation_p.R1196Q|ABCA5_ENST00000588877.1_Missense_Mutation_p.R1195Q			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1195					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1195Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CACATTTTTTCGTACATTCTT	0.284																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	GLN/ARG,GLN/ARG	0,4404		0,0,2202	77	70	73		3584,3584	-0.1	0	17		73	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	ABCA5	NM_172232.2,NM_018672.3	43,43	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1195/1643,1195/1643	67256534	1,12997	2202	4297	6499	64768129	SO:0001583	missense	23461			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.3584G>A	17.37:g.67256534C>T	ENSP00000376443:p.Arg1195Gln		64768129	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	C	2.656	-0.280907	0.05642	0.0	1.16E-4	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.82803	-1.65;-1.65	5.06	-0.134	0.13481	.	1.370600	0.05079	N	0.483135	T	0.61677	0.2366	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49351	-0.8949	9	.	.	.	.	5.6003	0.17349	0.0:0.1468:0.4254:0.4278	.	1195	Q8WWZ7	ABCA5_HUMAN	Q	1196;1195	ENSP00000376444:R1196Q;ENSP00000376443:R1195Q	.	R	-	2	0	ABCA5	64768129	0.000000	0.05858	0.001000	0.08648	0.505000	0.33919	-0.108000	0.10857	0.040000	0.15660	0.655000	0.94253	CGA		0.284	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		T	67256534	C	T	67256534	3	4	61	1	0	0	0	0	1	0	0	0	35	884	31	1	1396	1	ABCA5	17	67256534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8528	67256534	13938676	10428	18413										
MAP2K6	5608	broad.mit.edu	37	chr17	67513662	67513662	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgaggtgaaggcagatGacctggagcctataatggaa	13	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67513662G>T	ENST00000590474.1	+	4	441	c.154G>T	c.(154-156)Gac>Tac	p.D52Y	MAP2K6_ENST00000589647.1_5'UTR	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	52					activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.D52Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					GAAGGCAGATGACCTGGAGCC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											103	82	89					17																	67513662		2203	4300	6503	65025257	SO:0001583	missense	5608			U39064	CCDS11686.1	17q	2011-06-09						"Mitogen-activated protein kinase cascade / Kinase kinases"	6846	protein-coding gene	gene with protein product	"protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.154G>T	17.37:g.67513662G>T	ENSP00000468348:p.Asp52Tyr		65025257		Missense_Mutation	SNP	ENST00000590474.1	37	CCDS11686.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818859	0.90873	.	.	ENSG00000108984	ENST00000359094	T	0.34667	1.35	5.31	5.31	0.75309	Protein kinase-like domain (1);	0.051315	0.85682	D	0.000000	T	0.62392	0.2424	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.986;0.986	T	0.63166	-0.6698	9	.	.	.	-18.9456	17.8901	0.88869	0.0:0.0:1.0:0.0	.	82;52;52	Q6MZH7;P52564;A8K3Y2	.;MP2K6_HUMAN;.	Y	52	ENSP00000351997:D52Y	.	D	+	1	0	MAP2K6	65025257	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.715000	0.98748	2.634000	0.89283	0.585000	0.79938	GAC		0.488	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758		T	67513662	G	T	67513662	3	4	61	1	0	0	0	0	1	0	0	0	9271	1290	45	2	168	2	MAP2K6	17	67513662	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	257128	67513662	13681548	10429	18414										
MAP2K6	5608	broad.mit.edu	37	chr17	67516506	67516506	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagacaattccagaggacatCttagggaaaatagcagtttc	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:67516506C>A	ENST00000590474.1	+	6	749	c.462C>A	c.(460-462)atC>atA	p.I154I	MAP2K6_ENST00000589647.1_Silent_p.I98I	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	154	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.I154I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					CAGAGGACATCTTAGGGAAAA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	17											107	107	107					17																	67516506		2203	4300	6503	65028101	SO:0001819	synonymous_variant	5608			U39064	CCDS11686.1	17q	2011-06-09						"Mitogen-activated protein kinase cascade / Kinase kinases"	6846	protein-coding gene	gene with protein product	"protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.462C>A	17.37:g.67516506C>A			65028101		Silent	SNP	ENST00000590474.1	37	CCDS11686.1																																																																																				0.398	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758		A	67516506	C	A	67516506	2	1	61	1	0	0	0	0	0	0	0	1	9271	903	32	2		2	MAP2K6	17	67516506	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2844	67516506	13678704	10430	18415										
KCNJ16	3773	broad.mit.edu	37	chr17	68129008	68129008	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccatgaaattgaccatgaGagccctctgtatgcccttga	9	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:68129008G>A	ENST00000589377.1	+	2	943	c.780G>A	c.(778-780)gaG>gaA	p.E260E	KCNJ16_ENST00000283936.1_Silent_p.E260E|KCNJ16_ENST00000392670.1_Silent_p.E260E|KCNJ16_ENST00000585558.1_Silent_p.E295E|KCNJ16_ENST00000586462.1_Silent_p.E299E|KCNJ16_ENST00000392671.1_Silent_p.E260E	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	260					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.E260E(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					TTGACCATGAGAGCCCTCTGT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	17											137	129	132					17																	68129008		2203	4300	6503	65640603	SO:0001819	synonymous_variant	3773			AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.780G>A	17.37:g.68129008G>A			65640603		Silent	SNP	ENST00000589377.1	37	CCDS11687.1																																																																																				0.443	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68129008	G	A	68129008	2	1	61	1	0	0	0	0	0	0	0	1	8071	933	33	3		3	KCNJ16	17	68129008	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	612502	68129008	13066202	10431	18416										
SLC39A11	201266	broad.mit.edu	37	chr17	71027782	71027782	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagaaggcaaaggcaccGaagcccccagaggacgtggc	16	11	0	2	rs79360131	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:71027782G>A	ENST00000542342.2	-	4	307	c.219C>T	c.(217-219)ttC>ttT	p.F73F	SLC39A11_ENST00000579732.1_Silent_p.F73F|SLC39A11_ENST00000255559.3_Silent_p.F73F	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	73					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.F73F(1)		endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CAAAGGCACCGAAGCCCCCAG	0.542													G|||	48	0.00958466	0	0.0014	5008	,	,		18088	0.0456		0	False		,,,				2504	0.001				NSCLC(95;736 1527 12296 39625 41839)											1	Substitution - coding silent(1)	large_intestine(1)	17											121	109	113					17																	71027782		2203	4300	6503	68539377	SO:0001819	synonymous_variant	201266			AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"Solute carriers"	14463	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 26"	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.219C>T	17.37:g.71027782G>A			68539377	B2R8H7|Q8WZ81	Silent	SNP	ENST00000542342.2	37	CCDS54160.1																																																																																				0.542	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			A	71027782	G	A	71027782	2	1	61	1	0	0	0	0	0	0	0	1	14651	1049	37	1		1	SLC39A11	17	71027782	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2898774	71027782	10167428	10432	18417										
SSTR2	6752	broad.mit.edu	37	chr17	71165605	71165605	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgcagtcctcacattcatCtattttgtggtctgcatcat	6	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:71165605C>A	ENST00000357585.2	+	2	516	c.147C>A	c.(145-147)atC>atA	p.I49I	SSTR2_ENST00000315332.2_Silent_p.I49I|RP11-143K11.5_ENST00000580671.1_RNA	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	49					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)	p.I49I(1)		endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	TCACATTCATCTATTTTGTGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	17											266	187	214					17																	71165605		2203	4300	6503	68677200	SO:0001819	synonymous_variant	6752				CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"GPCR / Class A : Somatostatin receptors"	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.147C>A	17.37:g.71165605C>A			68677200	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Silent	SNP	ENST00000357585.2	37	CCDS11691.1																																																																																				0.458	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1			A	71165605	C	A	71165605	2	1	61	1	0	0	0	0	0	0	0	1	15237	903	32	2		2	SSTR2	17	71165605	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137823	71165605	10029605	10433	18418										
SSTR2	6752	broad.mit.edu	37	chr17	71166296	71166296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatattcaacgtttcttccGtctccatggccatcagcccc	5	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:71166296G>A	ENST00000357585.2	+	2	1207	c.838G>A	c.(838-840)Gtc>Atc	p.V280I	SSTR2_ENST00000315332.2_Missense_Mutation_p.V280I|RP11-143K11.5_ENST00000580671.1_RNA	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	280					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)	p.V280I(1)		endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CGTTTCTTCCGTCTCCATGGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	17											212	175	188					17																	71166296		2203	4300	6503	68677891	SO:0001583	missense	6752				CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"GPCR / Class A : Somatostatin receptors"	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.838G>A	17.37:g.71166296G>A	ENSP00000350198:p.Val280Ile		68677891	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	37	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.612484	0.66672	.	.	ENSG00000180616	ENST00000357585;ENST00000315332	T;T	0.37584	1.19;1.19	5.49	5.49	0.81192	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49098	0.1537	L	0.41906	1.305	0.80722	D	1	D	0.62365	0.991	P	0.58077	0.832	T	0.47560	-0.9108	10	0.66056	D	0.02	.	18.9738	0.92725	0.0:0.0:1.0:0.0	.	280	P30874	SSR2_HUMAN	I	280	ENSP00000350198:V280I;ENSP00000326616:V280I	ENSP00000326616:V280I	V	+	1	0	SSTR2	68677891	1.000000	0.71417	0.448000	0.26945	0.493000	0.33554	6.648000	0.74359	2.577000	0.86979	0.655000	0.94253	GTC		0.512	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1			A	71166296	G	A	71166296	3	1	61	1	0	0	0	0	1	0	0	0	15237	1145	40	1	840	1	SSTR2	17	71166296	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	691	71166296	10028914	10434	18419										
C17orf80	55028	broad.mit.edu	37	chr17	71231960	71231960	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcagataaagacatcaaGaatccaatccaaccatcctt	5	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:71231960G>T	ENST00000535032.2	+	2	452	c.339G>T	c.(337-339)aaG>aaT	p.K113N	C17orf80_ENST00000268942.8_Missense_Mutation_p.K113N|C17orf80_ENST00000359042.2_Missense_Mutation_p.K113N|C17orf80_ENST00000255557.4_Missense_Mutation_p.K113N|C17orf80_ENST00000426147.2_Missense_Mutation_p.K113N|C17orf80_ENST00000577615.1_Missense_Mutation_p.K113N|FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000582793.1_Intron			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	113						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K113N(1)		kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			AAGACATCAAGAATCCAATCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											72	69	70					17																	71231960		2203	4300	6503	68743555	SO:0001583	missense	55028			AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.339G>T	17.37:g.71231960G>T	ENSP00000440551:p.Lys113Asn		68743555	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Missense_Mutation	SNP	ENST00000535032.2	37	CCDS11694.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.419005	0.62622	.	.	ENSG00000141219	ENST00000255557;ENST00000359042;ENST00000268942;ENST00000426147;ENST00000535032	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	5.55	1.27	0.21489	.	0.578399	0.16691	N	0.203558	T	0.42223	0.1193	M	0.61703	1.905	0.09310	N	1	D;P;D;D	0.71674	0.992;0.952;0.992;0.998	P;P;P;P	0.62298	0.826;0.677;0.866;0.9	T	0.21895	-1.0232	10	0.72032	D	0.01	-5.3387	4.571	0.12210	0.2796:0.1788:0.5415:0.0	.	113;113;113;113	B7Z7E5;Q9BSJ5;Q9BSJ5-2;Q9BSJ5-3	.;CQ080_HUMAN;.;.	N	113	ENSP00000255557:K113N;ENSP00000351937:K113N;ENSP00000268942:K113N;ENSP00000396970:K113N;ENSP00000440551:K113N	ENSP00000255557:K113N	K	+	3	2	C17orf80	68743555	0.001000	0.12720	0.003000	0.11579	0.134000	0.20937	0.126000	0.15769	0.026000	0.15269	0.561000	0.74099	AAG		0.408	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		T	71231960	G	T	71231960	3	4	61	1	0	0	0	0	1	0	0	0	1890	933	33	2	341	2	C17orf80	17	71231960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65664	71231960	9963250	10435	18420										
SDK2	54549	broad.mit.edu	37	chr17	71346841	71346841	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccccggatgatgagcacGaagaccagaagcaggatgaa	14	9	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:71346841G>A	ENST00000392650.3	-	42	5847	c.5847C>T	c.(5845-5847)ttC>ttT	p.F1949F	SDK2_ENST00000388726.3_Silent_p.F1930F|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1949					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.F1949F(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						TGATGAGCACGAAGACCAGAA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	17											141	125	130					17																	71346841		2203	4300	6503	68858436	SO:0001819	synonymous_variant	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5847C>T	17.37:g.71346841G>A			68858436	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																				0.552	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71346841	G	A	71346841	2	1	61	1	0	0	0	0	0	0	0	1	14006	1049	37	1		1	SDK2	17	71346841	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114881	71346841	9848369	10436	18421										
TTYH2	94015	broad.mit.edu	37	chr17	72249394	72249394	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accatctccaacgcccctgtCtccgagtacatgtacggcct	7	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72249394C>A	ENST00000269346.4	+	12	1508	c.1434C>A	c.(1432-1434)gtC>gtA	p.V478V	TTYH2_ENST00000529107.1_Silent_p.V457V|TTYH2_ENST00000441391.2_Silent_p.V157V	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	478						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.V478V(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ACGCCCCTGTCTCCGAGTACA	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	17											54	55	55					17																	72249394		2203	4300	6503	69760989	SO:0001819	synonymous_variant	94015				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1434C>A	17.37:g.72249394C>A			69760989	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Silent	SNP	ENST00000269346.4	37	CCDS32717.1																																																																																				0.657	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			A	72249394	C	A	72249394	2	1	61	1	0	0	0	0	0	0	0	1	16780	900	32	2		2	TTYH2	17	72249394	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	902553	72249394	8945816	10437	18422										
KIF19	124602	broad.mit.edu	37	chr17	72338095	72338095	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggagaagtcctacctgttCgacgtggcctttgacttcac	11	12	1	2	rs149423393		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72338095C>T	ENST00000389916.4	+	3	339	c.201C>T	c.(199-201)ttC>ttT	p.F67F		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	67	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.F67F(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CCTACCTGTTCGACGTGGCCT	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		0,4406		0,0,2203	116	112	113		201	-3.1	0.9	17	dbSNP_134	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIF19	NM_153209.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		67/999	72338095	1,13005	2203	4300	6503	69849690	SO:0001819	synonymous_variant	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.201C>T	17.37:g.72338095C>T			69849690	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																				0.657	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72338095	C	T	72338095	2	4	61	1	0	0	0	0	0	0	0	1	8303	883	31	1		1	KIF19	17	72338095	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88701	72338095	8857115	10438	18423										
KIF19	124602	broad.mit.edu	37	chr17	72345364	72345364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctcctaccacatcgcccaGtacaccagcatcatcgctga	6	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72345364G>T	ENST00000389916.4	+	10	1227	c.1089G>T	c.(1087-1089)caG>caT	p.Q363H		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	363					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.Q363H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						ACATCGCCCAGTACACCAGCA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											83	70	75					17																	72345364		2203	4300	6503	69856959	SO:0001583	missense	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1089G>T	17.37:g.72345364G>T	ENSP00000374566:p.Gln363His		69856959	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805560	0.50315	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.73047	-0.71;-0.71	5.9	3.93	0.45458	.	.	.	.	.	D	0.82953	0.5149	M	0.81497	2.545	0.46631	D	0.999132	D;D;P;P	0.89917	0.999;1.0;0.86;0.679	D;D;B;B	0.80764	0.973;0.994;0.43;0.43	D	0.83505	0.0077	9	0.54805	T	0.06	.	12.013	0.53299	0.1423:0.0:0.8577:0.0	.	363;321;321;363	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	H	321;363	ENSP00000449134:Q321H;ENSP00000374566:Q363H	ENSP00000374566:Q363H	Q	+	3	2	KIF19	69856959	1.000000	0.71417	1.000000	0.80357	0.215000	0.24574	5.645000	0.67909	0.865000	0.35603	0.556000	0.70494	CAG		0.637	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72345364	G	T	72345364	3	4	61	1	0	0	0	0	1	0	0	0	8303	1020	36	2	1127	2	KIF19	17	72345364	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7269	72345364	8849846	10439	18424										
CD300A	11314	broad.mit.edu	37	chr17	72480259	72480259	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattacagtgtgataaggaaGacataggcttttgtcctgcc	11	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72480259G>T	ENST00000360141.3	+	7	1182	c.894G>T	c.(892-894)aaG>aaT	p.K298N	CD300A_ENST00000361933.3_Missense_Mutation_p.K102N|CD300A_ENST00000577511.1_Missense_Mutation_p.K168N|CD300A_ENST00000392625.3_Missense_Mutation_p.K149N|CD300A_ENST00000310828.5_Missense_Mutation_p.K185N	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	298					cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)	p.K298N(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						TGATAAGGAAGACATAGGCTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											110	105	107					17																	72480259		2203	4300	6503	69991854	SO:0001583	missense	11314			BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19319	protein-coding gene	gene with protein product		606790	"CD300a antigen"			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.894G>T	17.37:g.72480259G>T	ENSP00000353259:p.Lys298Asn		69991854	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Missense_Mutation	SNP	ENST00000360141.3	37	CCDS32720.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.751776	0.31046	.	.	ENSG00000167851	ENST00000361933;ENST00000360141;ENST00000392625;ENST00000310828	T;T	0.56611	3.83;0.45	3.16	2.16	0.27623	.	.	.	.	.	T	0.32496	0.0831	N	0.14661	0.345	0.09310	N	1	B;P;P;P	0.44816	0.385;0.844;0.728;0.759	B;B;B;B	0.39152	0.181;0.292;0.181;0.153	T	0.08806	-1.0704	9	0.48119	T	0.1	.	8.3457	0.32272	0.0:0.2427:0.7573:0.0	.	102;149;185;298	Q9UGN4-3;Q9UGN4-4;Q9UGN4-2;Q9UGN4	.;.;.;CLM8_HUMAN	N	102;298;149;185	ENSP00000353259:K298N;ENSP00000308188:K185N	ENSP00000308188:K185N	K	+	3	2	CD300A	69991854	0.541000	0.26417	0.108000	0.21378	0.091000	0.18340	1.264000	0.33015	0.893000	0.36288	0.555000	0.69702	AAG		0.547	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261		T	72480259	G	T	72480259	3	4	61	1	0	0	0	0	1	0	0	0	3002	933	33	2	920	2	CD300A	17	72480259	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134895	72480259	8714951	10440	18425										
CD300LB	124599	broad.mit.edu	37	chr17	72522125	72522125	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcaccaccacttaatgtaGgtctcccatccttgcttata	6	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72522125G>T	ENST00000392621.1	-	2	247	c.243C>A	c.(241-243)acC>acA	p.T81T	CD300LB_ENST00000314401.3_Silent_p.T81T	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	44	Ig-like V-type.				cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T81T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						ACTTAATGTAGGTCTCCCATC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	17											189	173	179					17																	72522125		2203	4300	6503	70033720	SO:0001819	synonymous_variant	124599			AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.243C>A	17.37:g.72522125G>T			70033720	Q1EG73|Q8IX40|Q8N6D1	Silent	SNP	ENST00000392621.1	37	CCDS11700.1																																																																																				0.552	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		T	72522125	G	T	72522125	2	4	61	1	0	0	0	0	0	0	0	1	3005	987	35	2		2	CD300LB	17	72522125	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41866	72522125	8673085	10441	18426										
TMEM104	54868	broad.mit.edu	37	chr17	72832754	72832754	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaccttctgggtgggcttCgtgctgctctgggctttctc	12	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72832754C>T	ENST00000335464.5	+	10	1581	c.1419C>T	c.(1417-1419)ttC>ttT	p.F473F	TMEM104_ENST00000582773.1_Intron|TMEM104_ENST00000417024.2_Intron|TMEM104_ENST00000582330.1_Silent_p.F473F	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	473						integral component of membrane (GO:0016021)		p.F473F(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					GGGTGGGCTTCGTGCTGCTCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											62	51	54					17																	72832754		2203	4300	6503	70344349	SO:0001819	synonymous_variant	54868			AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.1419C>T	17.37:g.72832754C>T			70344349	Q8TEU1|Q9NT56|Q9NXH1	Silent	SNP	ENST00000335464.5	37	CCDS32723.1																																																																																				0.592	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		T	72832754	C	T	72832754	2	4	61	1	0	0	0	0	0	0	0	1	16057	883	31	1		1	TMEM104	17	72832754	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	310629	72832754	8362456	10442	18427										
GRIN2C	2905	broad.mit.edu	37	chr17	72844010	72844010	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttgcctctggtgaggttCtggttgtagctgacagggct	14	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72844010C>A	ENST00000293190.5	-	8	1898	c.1752G>T	c.(1750-1752)caG>caT	p.Q584H	GRIN2C_ENST00000347612.4_Missense_Mutation_p.Q584H	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	584					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.Q584H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGGTGAGGTTCTGGTTGTAGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											104	82	89					17																	72844010		2203	4300	6503	70355605	SO:0001583	missense	2905				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1752G>T	17.37:g.72844010C>A	ENSP00000293190:p.Gln584His		70355605	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	C	8.061	0.768026	0.15983	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.54279	0.58	3.39	2.41	0.29592	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.513484	0.19683	N	0.108463	T	0.49218	0.1544	N	0.19112	0.55	0.33050	D	0.532571	P;D	0.54601	0.564;0.967	P;P	0.59115	0.663;0.852	T	0.60260	-0.7298	10	0.72032	D	0.01	.	8.1252	0.30995	0.0:0.8075:0.0:0.1925	.	618;584	Q8IW23;Q14957	.;NMDE3_HUMAN	H	584;618	ENSP00000293190:Q584H	ENSP00000293190:Q584H	Q	-	3	2	GRIN2C	70355605	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.698000	0.37794	0.987000	0.38709	0.561000	0.74099	CAG		0.602	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			A	72844010	C	A	72844010	3	1	61	1	0	0	0	0	1	0	0	0	6802	912	32	2	1973	2	GRIN2C	17	72844010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11256	72844010	8351200	10443	18428										
GRIN2C	2905	broad.mit.edu	37	chr17	72846458	72846458	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccagcttcttgaggatgtCgatgcagaatcccttacagc	11	11	1	2	rs201869035		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72846458C>T	ENST00000293190.5	-	6	1524	c.1378G>A	c.(1378-1380)Gac>Aac	p.D460N	GRIN2C_ENST00000347612.4_Missense_Mutation_p.D460N|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	460					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.D460N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TTGAGGATGTCGATGCAGAAT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											143	131	135					17																	72846458		2203	4300	6503	70358053	SO:0001583	missense	2905				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1378G>A	17.37:g.72846458C>T	ENSP00000293190:p.Asp460Asn		70358053	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.196915	0.58126	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.41065	1.01	4.65	3.65	0.41850	Extracellular solute-binding protein, family 3 (1);Glutamate receptor, L-glutamate/glycine-binding (1);Ionotropic glutamate receptor (1);	0.105548	0.64402	D	0.000007	T	0.73353	0.3576	H	0.95437	3.67	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82410	-0.0471	10	0.87932	D	0	.	13.9123	0.63876	0.1537:0.8463:0.0:0.0	.	494;460	Q8IW23;Q14957	.;NMDE3_HUMAN	N	460;494	ENSP00000293190:D460N	ENSP00000293190:D460N	D	-	1	0	GRIN2C	70358053	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.603000	0.82811	1.268000	0.44264	0.491000	0.48974	GAC		0.602	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			T	72846458	C	T	72846458	3	4	61	1	0	0	0	0	1	0	0	0	6802	884	31	1	2355	1	GRIN2C	17	72846458	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2448	72846458	8348752	10444	18429										
OTOP2	92736	broad.mit.edu	37	chr17	72923856	72923856	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccactcctacagcagttcTcacagcaacgccagccacgc	6	19	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:72923856T>G	ENST00000580223.1	+	4	636	c.606T>G	c.(604-606)tcT>tcG	p.S202S	OTOP2_ENST00000331427.4_Silent_p.S202S			Q7RTS6	OTOP2_HUMAN	otopetrin 2	202						integral component of membrane (GO:0016021)		p.S202S(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					ACAGCAGTTCTCACAGCAACG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	17											110	80	90					17																	72923856		2203	4300	6503	70435451	SO:0001819	synonymous_variant	92736			BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.606T>G	17.37:g.72923856T>G			70435451		Silent	SNP	ENST00000580223.1	37	CCDS11708.1																																																																																				0.572	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160		G	72923856	T	G	72923856	2	3	61	1	0	0	0	0	0	0	0	1	11337	1538	54	4		4	OTOP2	17	72923856	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	77398	72923856	8271354	10445	18430										
GGA3	23163	broad.mit.edu	37	chr17	73238487	73238487	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcatctcactgagcagtCtcacgttgttgttaacttcc	8	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73238487C>A	ENST00000245541.6	-	8	893	c.677G>T	c.(676-678)aGa>aTa	p.R226I	GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000351904.7_Missense_Mutation_p.R193I|GGA3_ENST00000582486.1_Missense_Mutation_p.R154I|GGA3_ENST00000537686.1_3'UTR|GGA3_ENST00000538886.1_Missense_Mutation_p.R104I|GGA3_ENST00000578348.1_Missense_Mutation_p.R104I|GGA3_ENST00000582717.1_Missense_Mutation_p.R154I	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	226	Binds to ARF1 (in long isoform).|GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.R226I(1)		breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			ACTGAGCAGTCTCACGTTGTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	17											348	282	305					17																	73238487		2203	4300	6503	70750082	SO:0001583	missense	23163			AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.677G>T	17.37:g.73238487C>A	ENSP00000245541:p.Arg226Ile		70750082	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094671	0.36952	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T;T	0.45668	0.89;0.89;0.89	4.83	3.76	0.43208	GAT (2);	0.097230	0.64402	D	0.000001	T	0.35219	0.0924	L	0.49778	1.585	0.80722	D	1	B;B;B	0.29590	0.213;0.061;0.25	B;B;B	0.34093	0.057;0.039;0.175	T	0.17715	-1.0360	10	0.46703	T	0.11	-16.9174	5.329	0.15922	0.1549:0.0842:0.0:0.7609	.	104;193;226	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	I	226;193;154;104	ENSP00000245541:R226I;ENSP00000326575:R193I;ENSP00000446421:R104I	ENSP00000245541:R226I	R	-	2	0	GGA3	70750082	1.000000	0.71417	0.919000	0.36401	0.905000	0.53344	4.014000	0.57145	0.893000	0.36288	-0.302000	0.09304	AGA		0.557	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		A	73238487	C	A	73238487	3	1	61	1	0	0	0	0	1	0	0	0	6374	913	32	2	1622	2	GGA3	17	73238487	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	314631	73238487	7956723	10446	18431										
MIF4GD	57409	broad.mit.edu	37	chr17	73266224	73266224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcttcagcagctgctggGtctctgcatcaaaggactgg	12	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73266224G>A	ENST00000325102.8	-	2	177	c.53C>T	c.(52-54)aCc>aTc	p.T18I	RP11-649A18.12_ENST00000585075.1_RNA|MIF4GD_ENST00000245551.5_Missense_Mutation_p.T18I|RP11-649A18.12_ENST00000582668.1_RNA|MIF4GD_ENST00000578305.1_Missense_Mutation_p.T18I|MIF4GD_ENST00000580571.1_Missense_Mutation_p.T18I|MIF4GD_ENST00000579119.1_Missense_Mutation_p.T18I|MIF4GD_ENST00000579297.1_Missense_Mutation_p.T18I|MIF4GD_ENST00000577542.1_Missense_Mutation_p.T18I	NM_001242501.1	NP_001229430.1	A9UHW6	MI4GD_HUMAN	MIF4G domain containing	18	MIF4G.				regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.T18I(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	10	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)			CAGCTGCTGGGTCTCTGCATC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17											192	192	192					17																	73266224		2203	4300	6503	70777819	SO:0001583	missense	57409			CR605810	CCDS11719.1, CCDS56044.1, CCDS58598.1	17q25.1	2005-12-15		2005-12-15					24030	protein-coding gene	gene with protein product		612072		MIFD			Standard	NM_001242498		Approved	AD023, MGC45027	uc002jnq.3	A9UHW6		ENST00000325102.8:c.53C>T	17.37:g.73266224G>A	ENSP00000321625:p.Thr18Ile		70777819	B4DUM7|Q8N4Q5|Q9HBL5	Missense_Mutation	SNP	ENST00000325102.8	37	CCDS56044.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.420439	0.42918	.	.	ENSG00000125457	ENST00000245551;ENST00000325102	T	0.15834	2.39	5.13	4.14	0.48551	MIF4G-like, type 3 (1);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.051770	0.85682	D	0.000000	T	0.18551	0.0445	L	0.57536	1.79	0.30045	N	0.812276	B;B;B	0.19200	0.023;0.033;0.034	B;B;B	0.28553	0.024;0.091;0.042	T	0.09207	-1.0685	10	0.33940	T	0.23	-4.6479	8.9238	0.35628	0.0785:0.0:0.7713:0.1502	.	18;18;18	A9UHW6;A9UHW6-2;B4DUM7	MI4GD_HUMAN;.;.	I	18	ENSP00000321625:T18I	ENSP00000245551:T18I	T	-	2	0	MIF4GD	70777819	1.000000	0.71417	0.974000	0.42286	0.961000	0.63080	5.392000	0.66272	1.108000	0.41662	0.455000	0.32223	ACC		0.592	MIF4GD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446671.1	NM_020679		A	73266224	G	A	73266224	3	1	61	1	0	0	0	0	1	0	0	0	9614	1261	44	3	741	3	MIF4GD	17	73266224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27737	73266224	7928986	10447	18432										
GRB2	2885	broad.mit.edu	37	chr17	73317828	73317828	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccaccagctcattcaaaGaattgaacttcaccacccag	4	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73317828G>T	ENST00000392562.1	-	5	1162	c.380C>A	c.(379-381)tCt>tAt	p.S127Y	GRB2_ENST00000316804.5_Missense_Mutation_p.S127Y|GRB2_ENST00000462266.1_5'UTR|GRB2_ENST00000316615.5_Missense_Mutation_p.S86Y|GRB2_ENST00000392564.1_Missense_Mutation_p.S127Y|GRB2_ENST00000578961.1_Intron|GRB2_ENST00000392563.1_Missense_Mutation_p.S86Y			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	127	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.S127Y(1)		breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	CTCATTCAAAGAATTGAACTT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											99	90	93					17																	73317828		2203	4300	6503	70829423	SO:0001583	missense	2885				CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885		"SH2 domain containing"	4566	protein-coding gene	gene with protein product		108355					Standard	NM_002086		Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000392562.1:c.380C>A	17.37:g.73317828G>T	ENSP00000376345:p.Ser127Tyr		70829423	P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	37	CCDS11721.1	.	.	.	.	.	.	.	.	.	.	G	35	5.445535	0.96187	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564;ENST00000392563;ENST00000316615	T;T;T;D;D	0.85861	1.32;1.32;1.32;-2.04;-2.04	5.95	5.95	0.96441	SH2 motif (5);	0.000000	0.85682	D	0.000000	D	0.95853	0.8650	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.96243	0.9177	10	0.54805	T	0.06	-23.2968	20.3931	0.98965	0.0:0.0:1.0:0.0	.	86;127	P62993-2;P62993	.;GRB2_HUMAN	Y	127;127;127;86;86	ENSP00000339007:S127Y;ENSP00000376345:S127Y;ENSP00000376347:S127Y;ENSP00000376346:S86Y;ENSP00000317360:S86Y	ENSP00000317360:S86Y	S	-	2	0	GRB2	70829423	1.000000	0.71417	0.947000	0.38551	0.996000	0.88848	7.912000	0.87465	2.824000	0.97209	0.655000	0.94253	TCT		0.502	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1			T	73317828	G	T	73317828	3	4	61	1	0	0	0	0	1	0	0	0	6779	942	33	2	281	2	GRB2	17	73317828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51604	73317828	7877382	10448	18433										
ITGB4	3691	broad.mit.edu	37	chr17	73732224	73732224	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcaatgccacctgcatcGacagcaatggggtaggcctg	12	12	1	0	rs139115559		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73732224G>T	ENST00000200181.3	+	14	1937	c.1750G>T	c.(1750-1752)Gac>Tac	p.D584Y	ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000449880.2_Missense_Mutation_p.D584Y|ITGB4_ENST00000450894.3_Missense_Mutation_p.D584Y|ITGB4_ENST00000339591.3_Missense_Mutation_p.D584Y|ITGB4_ENST00000579662.1_Missense_Mutation_p.D584Y	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	584	Cysteine-rich tandem repeats.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)	p.D584Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CACCTGCATCGACAGCAATGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											131	109	117					17																	73732224		2203	4300	6503	71243819	SO:0001583	missense	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1750G>T	17.37:g.73732224G>T	ENSP00000200181:p.Asp584Tyr		71243819	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.857089	0.32791	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.92699	-3.09;-3.09;-3.09	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.94013	0.8082	L	0.52364	1.645	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0	D;D;D;D;D	0.80764	0.971;0.985;0.994;0.99;0.99	D	0.94324	0.7556	10	0.87932	D	0	.	12.1397	0.53991	0.0837:0.0:0.9163:0.0	.	544;584;584;584;584	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	Y	500;584;584;584	ENSP00000200181:D584Y;ENSP00000344079:D584Y;ENSP00000400217:D584Y	ENSP00000200181:D584Y	D	+	1	0	ITGB4	71243819	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.396000	0.79891	2.133000	0.65898	0.456000	0.33151	GAC		0.602	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			T	73732224	G	T	73732224	3	4	61	1	0	0	0	0	1	0	0	0	7918	1058	37	2	1800	2	ITGB4	17	73732224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	414396	73732224	7462986	10449	18434										
UNK	85451	broad.mit.edu	37	chr17	73805934	73805934	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgcttccactggcacttCgtgaaccagcggcgccgccg	11	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73805934C>T	ENST00000589666.1	+	2	308	c.198C>T	c.(196-198)ttC>ttT	p.F66F	UNK_ENST00000293218.3_Silent_p.F142F	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	66							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.F66F(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACTGGCACTTCGTGAACCAGC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											32	38	36					17																	73805934		2173	4281	6454	71317529	SO:0001819	synonymous_variant	85451			AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.198C>T	17.37:g.73805934C>T			71317529		Silent	SNP	ENST00000589666.1	37	CCDS45778.2																																																																																				0.592	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		T	73805934	C	T	73805934	2	4	61	1	0	0	0	0	0	0	0	1	17040	883	31	1		1	UNK	17	73805934	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73710	73805934	7389276	10450	18435										
UNK	85451	broad.mit.edu	37	chr17	73813592	73813592	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggagccgagtacctgaaAaatttcaaatgccaggtaag	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73813592A>C	ENST00000589666.1	+	9	1400	c.1290A>C	c.(1288-1290)aaA>aaC	p.K430N	UNK_ENST00000293218.3_Missense_Mutation_p.K506N|RP11-552F3.4_ENST00000586808.1_RNA	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	430							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K430N(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGTACCTGAAAAATTTCAAAT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											40	44	42					17																	73813592		1958	4137	6095	71325187	SO:0001583	missense	85451			AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.1290A>C	17.37:g.73813592A>C	ENSP00000464893:p.Lys430Asn		71325187		Missense_Mutation	SNP	ENST00000589666.1	37	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610550	0.46527	.	.	ENSG00000132478	ENST00000293218	.	.	.	4.81	0.837	0.18896	.	0.192877	0.41605	D	0.000857	T	0.45657	0.1353	L	0.44542	1.39	0.40575	D	0.981334	D	0.58268	0.982	P	0.49421	0.61	T	0.33879	-0.9851	9	0.19147	T	0.46	-10.4875	9.1041	0.36687	0.5872:0.0:0.4128:0.0	.	430	Q9C0B0	UNK_HUMAN	N	506	.	ENSP00000293218:K506N	K	+	3	2	UNK	71325187	1.000000	0.71417	0.995000	0.50966	0.952000	0.60782	1.874000	0.39568	-0.040000	0.13580	-0.371000	0.07208	AAA		0.577	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		C	73813592	A	C	73813592	3	2	61	1	0	0	0	0	1	0	0	0	17040	11	1	4	1556	4	UNK	17	73813592	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7658	73813592	7381618	10451	18436										
FBF1	85302	broad.mit.edu	37	chr17	73929094	73929094	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgttctcgcctttgaaGaagggaacatctgagataca	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:73929094G>T	ENST00000586717.1	-	4	380	c.107C>A	c.(106-108)tCt>tAt	p.S36Y	FBF1_ENST00000389570.4_Missense_Mutation_p.S36Y|FBF1_ENST00000319129.5_Missense_Mutation_p.S36Y			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	36					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.S36Y(1)		large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CGCCTTTGAAGAAGGGAACAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	17											74	71	72					17																	73929094		1915	4138	6053	71440689	SO:0001583	missense	85302			AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.107C>A	17.37:g.73929094G>T	ENSP00000465132:p.Ser36Tyr		71440689	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		.	.	.	.	.	.	.	.	.	.	G	15.68	2.904023	0.52333	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.20738	2.05;2.05	3.74	3.74	0.42951	.	.	.	.	.	T	0.35480	0.0933	L	0.47716	1.5	0.09310	N	1	D;D;D	0.63880	0.993;0.989;0.993	D;P;P	0.63113	0.911;0.859;0.858	T	0.05550	-1.0878	9	0.87932	D	0	-1.4384	11.3559	0.49615	0.0:0.0:1.0:0.0	.	50;36;36	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	Y	36;36;36;49	ENSP00000374221:S36Y;ENSP00000324292:S36Y	ENSP00000324292:S36Y	S	-	2	0	FBF1	71440689	0.019000	0.18553	0.019000	0.16419	0.146000	0.21551	2.469000	0.45110	2.361000	0.80049	0.557000	0.71058	TCT		0.473	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		T	73929094	G	T	73929094	3	4	61	1	0	0	0	0	1	0	0	0	5714	942	33	2	3398	2	FBF1	17	73929094	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115502	73929094	7266116	10452	18437										
EVPL	2125	broad.mit.edu	37	chr17	74004869	74004869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccgtggacttctccaggtCcgggtccttctccagcttga	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:74004869C>A	ENST00000301607.3	-	22	4670	c.4417G>T	c.(4417-4419)Gac>Tac	p.D1473Y	EVPL_ENST00000586740.1_Missense_Mutation_p.D1495Y|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1473	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.D1473Y(1)		breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TTCTCCAGGTCCGGGTCCTTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											138	130	133					17																	74004869		2203	4300	6503	71516464	SO:0001583	missense	2125			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4417G>T	17.37:g.74004869C>A	ENSP00000301607:p.Asp1473Tyr		71516464	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	9.959	1.222260	0.22457	.	.	ENSG00000167880	ENST00000301607	T	0.45668	0.89	4.97	4.97	0.65823	.	0.586898	0.18019	N	0.154287	T	0.36413	0.0966	L	0.44542	1.39	0.09310	N	1	P;P	0.46220	0.874;0.845	B;B	0.37888	0.26;0.188	T	0.38243	-0.9670	10	0.59425	D	0.04	-13.4321	15.3858	0.74699	0.0:0.8606:0.1394:0.0	.	1495;1473	B7ZLH8;Q92817	.;EVPL_HUMAN	Y	1473	ENSP00000301607:D1473Y	ENSP00000301607:D1473Y	D	-	1	0	EVPL	71516464	0.200000	0.23398	0.091000	0.20842	0.883000	0.51084	2.970000	0.49240	2.306000	0.77630	0.561000	0.74099	GAC		0.607	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		A	74004869	C	A	74004869	3	1	61	1	0	0	0	0	1	0	0	0	5305	855	30	2	1688	2	EVPL	17	74004869	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75775	74004869	7190341	10453	18438										
SRP68	6730	broad.mit.edu	37	chr17	74063360	74063360	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttgtgtctgttacccatCttgaagttgagtgtttttcg	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:74063360C>A	ENST00000307877.2	-	3	464	c.303G>T	c.(301-303)aaG>aaT	p.K101N	SRP68_ENST00000539137.1_Intron|SRP68_ENST00000355113.5_5'UTR	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	101					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.K101N(1)		NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						TGTTACCCATCTTGAAGTTGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											246	213	225					17																	74063360		2203	4300	6503	71574955	SO:0001583	missense	6730			AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"signal recognition particle 68kD"			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.303G>T	17.37:g.74063360C>A	ENSP00000312066:p.Lys101Asn		71574955	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	.	.	.	.	.	.	.	.	.	.	c	15.22	2.768048	0.49680	.	.	ENSG00000167881	ENST00000540937;ENST00000307877;ENST00000304220	.	.	.	4.43	3.46	0.39613	.	0.100651	0.64402	D	0.000002	T	0.56455	0.1986	L	0.58101	1.795	0.80722	D	1	P	0.43701	0.815	P	0.48227	0.571	T	0.50906	-0.8772	9	0.21014	T	0.42	-28.3136	8.8951	0.35458	0.0:0.8292:0.0:0.1708	.	101	Q9UHB9	SRP68_HUMAN	N	101	.	ENSP00000307756:K101N	K	-	3	2	SRP68	71574955	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.912000	0.39946	1.099000	0.41499	0.580000	0.79431	AAG		0.418	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		A	74063360	C	A	74063360	3	1	61	1	0	0	0	0	1	0	0	0	15195	912	32	2	1636	2	SRP68	17	74063360	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58491	74063360	7131850	10454	18439										
PRPSAP1	5635	broad.mit.edu	37	chr17	74328351	74328351	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcgcacactcacctgctttCgccagcatggatgctagcag	10	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:74328351C>T	ENST00000446526.3	-	4	901	c.456G>A	c.(454-456)gcG>gcA	p.A152A	PRPSAP1_ENST00000324684.4_Silent_p.A49A	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	123					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)	p.A123A(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						CACCTGCTTTCGCCAGCATGG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	17											180	170	173					17																	74328351		2203	4300	6503	71839946	SO:0001819	synonymous_variant	5635			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.456G>A	17.37:g.74328351C>T			71839946	B2R6M4|Q96H06	Silent	SNP	ENST00000446526.3	37	CCDS11743.2																																																																																				0.537	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766		T	74328351	C	T	74328351	2	4	61	1	0	0	0	0	0	0	0	1	12615	871	31	1		1	PRPSAP1	17	74328351	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	264991	74328351	6866859	10455	18440										
SFRS2	6427	broad.mit.edu	37	chr17	74732349	74732349	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggaggactcctggaccgaGaccgggacctggaccgcgaa	17	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:74732349G>T	ENST00000392485.2	-	2	732	c.560C>A	c.(559-561)tCt>tAt	p.S187Y	MFSD11_ENST00000588460.1_5'Flank|MFSD11_ENST00000586622.1_5'UTR|SRSF2_ENST00000508921.3_Missense_Mutation_p.S175Y|MFSD11_ENST00000336509.4_5'Flank|MIR636_ENST00000384825.1_RNA|SRSF2_ENST00000359995.5_Missense_Mutation_p.S187Y|MFSD11_ENST00000590514.1_5'Flank|MFSD11_ENST00000591864.1_5'Flank|MFSD11_ENST00000355954.3_5'Flank|MFSD11_ENST00000593181.1_5'Flank|MFSD11_ENST00000590393.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	187	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)	p.S187Y(1)		haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						CCTGGACCGAGACCGGGACCT	0.607			Mis		"MDS, CLL"																																		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	1	Substitution - Missense(1)	large_intestine(1)	17											107	93	98					17																	74732349		2203	4300	6503	72243944	SO:0001583	missense	6427			M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10783	protein-coding gene	gene with protein product	"SR splicing factor 2"	600813	"splicing factor, arginine/serine-rich 2"	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.560C>A	17.37:g.74732349G>T	ENSP00000376276:p.Ser187Tyr		72243944	B3KWD5|B4DN89|H0YG49	Missense_Mutation	SNP	ENST00000392485.2	37	CCDS11749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.96|10.96	1.498079|1.498079	0.26861|0.26861	.|.	.|.	ENSG00000161547|ENSG00000161547	ENST00000452355|ENST00000392485;ENST00000508921;ENST00000358156;ENST00000359995	.|T	.|0.39787	.|1.06	5.29|5.29	4.32|4.32	0.51571|0.51571	.|.	.|0.174964	.|0.38326	.|N	.|0.001737	T|T	0.44052|0.44052	0.1275|0.1275	M|M	0.81112|0.81112	2.525|2.525	0.80722|0.80722	D|D	1|1	.|P;P	.|0.40875	.|0.731;0.731	.|B;B	.|0.33568	.|0.166;0.166	T|T	0.53272|0.53272	-0.8462|-0.8462	6|10	0.21540|0.56958	T|D	0.41|0.05	.|.	14.0835|14.0835	0.64939|0.64939	0.0732:0.0:0.9268:0.0|0.0732:0.0:0.9268:0.0	.|.	.|175;187	.|B4DN89;Q01130	.|.;SRSF2_HUMAN	I|Y	137|187;214;175;167	.|ENSP00000376276:S187Y	ENSP00000391278:L137I|ENSP00000350877:S175Y	L|S	-|-	1|2	0|0	SRSF2|SRSF2	72243944|72243944	1.000000|1.000000	0.71417|0.71417	0.051000|0.051000	0.19133|0.19133	0.038000|0.038000	0.13279|0.13279	7.389000|7.389000	0.79806|0.79806	1.210000|1.210000	0.43336|0.43336	0.655000|0.655000	0.94253|0.94253	CTC|TCT		0.607	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016		T	74732349	G	T	74732349	3	4	61	1	0	0	0	0	1	0	0	0	14212	942	33	2	109	2	SFRS2	17	74732349	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	403998	74732349	6462861	10456	18441										
MFSD11	79157	broad.mit.edu	37	chr17	74763499	74763499	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttatgtgtcaccaaggaGatgctccttcttagtattac	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:74763499G>T	ENST00000588460.1	+	9	2756	c.714G>T	c.(712-714)gaG>gaT	p.E238D	MFSD11_ENST00000586622.1_Missense_Mutation_p.E238D|MFSD11_ENST00000336509.4_Missense_Mutation_p.E238D|MFSD11_ENST00000590514.1_Missense_Mutation_p.E238D|MFSD11_ENST00000355954.3_Missense_Mutation_p.E186D|MFSD11_ENST00000593181.1_Missense_Mutation_p.E186D	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	238						integral component of membrane (GO:0016021)		p.E238D(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TCACCAAGGAGATGCTCCTTC	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	105	108					17																	74763499		2203	4300	6503	72275094	SO:0001583	missense	79157			BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.714G>T	17.37:g.74763499G>T	ENSP00000464932:p.Glu238Asp		72275094	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	37	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544338	0.45280	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.80738	-1.41;-1.41	5.11	3.92	0.45320	Major facilitator superfamily domain, general substrate transporter (1);	0.047189	0.85682	D	0.000000	T	0.75265	0.3826	L	0.37630	1.12	0.80722	D	1	P;B	0.48503	0.911;0.003	P;B	0.46975	0.533;0.009	T	0.72023	-0.4415	10	0.21014	T	0.42	-6.1626	14.441	0.67318	0.0846:0.0:0.9154:0.0	.	186;238	O43934-2;O43934	.;MFS11_HUMAN	D	238;186	ENSP00000337240:E238D;ENSP00000348225:E186D	ENSP00000337240:E238D	E	+	3	2	MFSD11	72275094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.715000	0.54897	2.383000	0.81215	0.591000	0.81541	GAG		0.303	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		T	74763499	G	T	74763499	3	4	61	1	0	0	0	0	1	0	0	0	9559	933	33	2	748	2	MFSD11	17	74763499	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31150	74763499	6431711	10457	18442										
SEC14L1	6397	broad.mit.edu	37	chr17	75189628	75189628	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatataccagcaacattaaAaaagtgagtgtatcttggga	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:75189628A>C	ENST00000413679.2	+	6	774	c.471A>C	c.(469-471)aaA>aaC	p.K157N	SEC14L1_ENST00000430767.4_Missense_Mutation_p.K157N|SEC14L1_ENST00000585618.1_Missense_Mutation_p.K157N|SEC14L1_ENST00000443798.4_Missense_Mutation_p.K157N|SEC14L1_ENST00000431431.2_Missense_Mutation_p.K123N|SEC14L1_ENST00000436233.4_Missense_Mutation_p.K157N|SEC14L1_ENST00000591437.1_Missense_Mutation_p.K123N|SEC14L1_ENST00000392476.2_Missense_Mutation_p.K157N	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	157	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.K157N(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						GCAACATTAAAAAAGTGAGTG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	17											61	63	62					17																	75189628		2202	4300	6502	72701223	SO:0001583	missense	6397			D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.471A>C	17.37:g.75189628A>C	ENSP00000394716:p.Lys157Asn		72701223	A8K4E8|B4DDI5|D5G3K1|Q99780	Missense_Mutation	SNP	ENST00000413679.2	37	CCDS11752.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.303445	0.60195	.	.	ENSG00000129657	ENST00000392476;ENST00000443798;ENST00000436233;ENST00000430767;ENST00000413679;ENST00000431431	T;T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24;2.24	5.18	4.1	0.47936	PRELI/MSF1 (2);	0.043773	0.85682	D	0.000000	T	0.38453	0.1041	M	0.83118	2.625	0.47476	D	0.999437	D;D	0.59357	0.981;0.985	P;P	0.61477	0.823;0.889	T	0.16719	-1.0393	10	0.39692	T	0.17	-28.9786	10.3808	0.44110	0.9223:0.0:0.0777:0.0	.	157;157	Q92503-2;Q92503	.;S14L1_HUMAN	N	157;157;157;157;157;123	ENSP00000376268:K157N;ENSP00000406030:K157N;ENSP00000390392:K157N;ENSP00000408169:K157N;ENSP00000394716:K157N;ENSP00000389838:K123N	ENSP00000376268:K157N	K	+	3	2	SEC14L1	72701223	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	2.459000	0.45023	0.915000	0.36847	-0.256000	0.11100	AAA		0.398	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003		C	75189628	A	C	75189628	3	2	61	1	0	0	0	0	1	0	0	0	14018	11	1	4	485	4	SEC14L1	17	75189628	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	426129	75189628	6005582	10458	18443										
TNRC6C	57690	broad.mit.edu	37	chr17	76045655	76045655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccacttctcagaatgtgtCtttcagcgcacaacctcaga	7	13	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:76045655C>A	ENST00000588061.1	+	5	1239	c.512C>A	c.(511-513)tCt>tAt	p.S171Y	TNRC6C_ENST00000301624.4_Missense_Mutation_p.S171Y|TNRC6C_ENST00000335749.4_Missense_Mutation_p.S171Y|TNRC6C_ENST00000588847.1_Missense_Mutation_p.S171Y|TNRC6C_ENST00000541771.1_Missense_Mutation_p.S171Y|TNRC6C_ENST00000544502.1_Missense_Mutation_p.S171Y			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	171	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.S171Y(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CAGAATGTGTCTTTCAGCGCA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	17											148	148	148					17																	76045655		2056	4195	6251	73557250	SO:0001583	missense	57690			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.512C>A	17.37:g.76045655C>A	ENSP00000468647:p.Ser171Tyr		73557250	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	37	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800548	0.70567	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.25749	1.78;1.83;1.83;1.78	5.36	5.36	0.76844	.	0.104145	0.64402	D	0.000002	T	0.51278	0.1665	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.996;0.996	T	0.50259	-0.8849	10	0.87932	D	0	-12.1055	19.277	0.94036	0.0:1.0:0.0:0.0	.	171;171;171	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	Y	171	ENSP00000336783:S171Y;ENSP00000301624:S171Y;ENSP00000440310:S171Y;ENSP00000442421:S171Y	ENSP00000301624:S171Y	S	+	2	0	TNRC6C	73557250	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.257000	0.78362	2.782000	0.95742	0.655000	0.94253	TCT		0.483	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76045655	C	A	76045655	3	1	61	1	0	0	0	0	1	0	0	0	16381	913	32	2	514	2	TNRC6C	17	76045655	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	856027	76045655	5149555	10459	18444										
CYTH1	9267	broad.mit.edu	37	chr17	76695047	76695047	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaggagaggacgtaacaaGtatctaaagatgagagaaaa	11	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:76695047G>T	ENST00000446868.3	-	8	624	c.554C>A	c.(553-555)aCt>aAt	p.T185N	CYTH1_ENST00000589297.1_Missense_Mutation_p.T126N|CYTH1_ENST00000591455.1_Missense_Mutation_p.T185N|CYTH1_ENST00000585509.1_Missense_Mutation_p.T126N|CYTH1_ENST00000589296.1_Intron|CYTH1_ENST00000361101.4_Missense_Mutation_p.T185N|RNU6-638P_ENST00000516582.1_RNA			Q15438	CYH1_HUMAN	cytohesin 1	185	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)	p.T185N(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						GACGTAACAAGTATCTAAAGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											177	174	175					17																	76695047		2203	4300	6503	74206642	SO:0001583	missense	9267			M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"Pleckstrin homology (PH) domain containing"	9501	protein-coding gene	gene with protein product		182115	"pleckstrin homology, Sec7 and coiled-coil domains 1"	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.554C>A	17.37:g.76695047G>T	ENSP00000389095:p.Thr185Asn		74206642	A6NFW7|B7Z1T4|Q9P123|Q9P124	Missense_Mutation	SNP	ENST00000446868.3	37		.	.	.	.	.	.	.	.	.	.	G	25.7	4.668372	0.88348	.	.	ENSG00000108669	ENST00000446868;ENST00000361101;ENST00000539525;ENST00000537048;ENST00000262763;ENST00000392453	T;T	0.56103	0.48;0.48	5.34	5.34	0.76211	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.81004	0.4733	M	0.94142	3.5	0.80722	D	1	D;D	0.67145	0.991;0.996	D;D	0.73708	0.981;0.979	D	0.86585	0.1856	10	0.87932	D	0	.	19.0542	0.93056	0.0:0.0:1.0:0.0	.	185;185	Q15438;Q15438-2	CYH1_HUMAN;.	N	185;185;126;126;185;22	ENSP00000389095:T185N;ENSP00000354398:T185N	ENSP00000262763:T185N	T	-	2	0	CYTH1	74206642	1.000000	0.71417	0.954000	0.39281	0.814000	0.46013	9.726000	0.98782	2.475000	0.83589	0.591000	0.81541	ACT		0.468	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1	NM_004762		T	76695047	G	T	76695047	3	4	61	1	0	0	0	0	1	0	0	0	4209	1029	36	2	666	2	CYTH1	17	76695047	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	649392	76695047	4500163	10460	18445										
ENPP7	339221	broad.mit.edu	37	chr17	77705001	77705001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggctcccagaacaagctgCtcctggtgtccttcgacggc	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:77705001C>T	ENST00000328313.5	+	1	321	c.100C>T	c.(100-102)Ctc>Ttc	p.L34F		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7									p.L34F(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GAACAAGCTGCTCCTGGTGTC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											41	37	39					17																	77705001		2203	4300	6503	75319596	SO:0001583	missense	339221			AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"alkaline sphingomyelinase"					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.100C>T	17.37:g.77705001C>T	ENSP00000332656:p.Leu34Phe		75319596		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411450	0.62399	.	.	ENSG00000182156	ENST00000328313	T	0.80123	-1.34	4.59	3.62	0.41486	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.64402	D	0.000001	D	0.89213	0.6651	M	0.86502	2.82	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.89341	0.3654	10	0.87932	D	0	-36.9301	9.036	0.36289	0.0:0.8285:0.0:0.1715	.	34	Q6UWV6	ENPP7_HUMAN	F	34	ENSP00000332656:L34F	ENSP00000332656:L34F	L	+	1	0	ENPP7	75319596	1.000000	0.71417	0.709000	0.30452	0.487000	0.33371	3.826000	0.55738	1.143000	0.42306	0.561000	0.74099	CTC		0.652	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77705001	C	T	77705001	3	4	61	1	0	0	0	0	1	0	0	0	5148	797	28	3	102	3	ENPP7	17	77705001	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1009954	77705001	3490209	10461	18446										
CCDC40	55036	broad.mit.edu	37	chr17	78023758	78023758	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactacctgaaccgacagatCgaaaagttgaagctggacct	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78023758C>T	ENST00000397545.4	+	6	936	c.909C>T	c.(907-909)atC>atT	p.I303I	CCDC40_ENST00000374876.4_Silent_p.I303I|CCDC40_ENST00000269318.5_Silent_p.I303I|CCDC40_ENST00000374877.3_Silent_p.I303I	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	303					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)		p.I303I(2)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			ACCGACAGATCGAAAAGTTGA	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	17											80	88	85					17																	78023758		2006	4160	6166	75638353	SO:0001819	synonymous_variant	55036			AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.909C>T	17.37:g.78023758C>T			75638353	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																				0.532	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78023758	C	T	78023758	2	4	61	1	0	0	0	0	0	0	0	1	2818	874	31	1		1	CCDC40	17	78023758	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	318757	78023758	3171452	10462	18447										
CCDC40	55036	broad.mit.edu	37	chr17	78032705	78032705	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcccagcaactggaagaaGacattgccctgtttgaggct	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78032705G>T	ENST00000397545.4	+	9	1393	c.1366G>T	c.(1366-1368)Gac>Tac	p.D456Y	CCDC40_ENST00000374876.4_Intron|CCDC40_ENST00000269318.5_Missense_Mutation_p.D456Y|CCDC40_ENST00000374877.3_Missense_Mutation_p.D456Y	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	456					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)		p.D456Y(2)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			ACTGGAAGAAGACATTGCCCT	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	17											102	107	106					17																	78032705		2090	4214	6304	75647300	SO:0001583	missense	55036			AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.1366G>T	17.37:g.78032705G>T	ENSP00000380679:p.Asp456Tyr		75647300	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	G	7.187	0.590674	0.13812	.	.	ENSG00000141519	ENST00000374877;ENST00000269318;ENST00000397545	T;D;T	0.86164	0.87;-2.08;0.89	4.7	-0.126	0.13515	.	.	.	.	.	T	0.81749	0.4888	L	0.34521	1.04	0.09310	N	1	D;D	0.56287	0.958;0.975	P;P	0.47346	0.456;0.544	T	0.71751	-0.4498	9	0.59425	D	0.04	-9.8833	8.2668	0.31819	0.3749:0.423:0.202:0.0	.	456;239	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	Y	456	ENSP00000364011:D456Y;ENSP00000269318:D456Y;ENSP00000380679:D456Y	ENSP00000269318:D456Y	D	+	1	0	CCDC40	75647300	0.154000	0.22792	0.000000	0.03702	0.001000	0.01503	1.023000	0.30065	-0.346000	0.08312	-0.768000	0.03414	GAC		0.572	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78032705	G	T	78032705	3	4	61	1	0	0	0	0	1	0	0	0	2818	942	33	2	1400	2	CCDC40	17	78032705	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8947	78032705	3162505	10463	18448										
SLC26A11	284129	broad.mit.edu	37	chr17	78201627	78201627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtccacagggtaggtgacGccgtcctggggctggtctgc	16	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78201627G>A	ENST00000361193.3	+	7	884	c.604G>A	c.(604-606)Gcc>Acc	p.A202T	SLC26A11_ENST00000411502.3_Missense_Mutation_p.A202T|SLC26A11_ENST00000572725.1_Missense_Mutation_p.A202T|SLC26A11_ENST00000546047.2_Missense_Mutation_p.A202T	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11									p.A202T(1)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GGTAGGTGACGCCGTCCTGGG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											113	98	103					17																	78201627		2203	4300	6503	75816222	SO:0001583	missense	284129				CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"Solute carriers"	14471	protein-coding gene	gene with protein product		610117	"solute carrier family 26, member 11"				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.604G>A	17.37:g.78201627G>A	ENSP00000355384:p.Ala202Thr		75816222		Missense_Mutation	SNP	ENST00000361193.3	37	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	G	3.134	-0.177757	0.06380	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.93426	-3.22;-3.22;-3.22	4.52	3.53	0.40419	Sulphate transporter (1);	0.269290	0.37053	N	0.002274	D	0.85822	0.5786	N	0.25992	0.78	0.21499	N	0.999666	B	0.27316	0.175	B	0.23275	0.045	T	0.72187	-0.4366	10	0.17369	T	0.5	-22.9221	10.764	0.46281	0.0928:0.0:0.9072:0.0	.	202	Q86WA9	S2611_HUMAN	T	202	ENSP00000403998:A202T;ENSP00000440724:A202T;ENSP00000355384:A202T	ENSP00000355384:A202T	A	+	1	0	SLC26A11	75816222	0.925000	0.31364	0.044000	0.18714	0.069000	0.16628	4.350000	0.59392	2.060000	0.61445	0.491000	0.48974	GCC		0.652	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			A	78201627	G	A	78201627	3	1	61	1	0	0	0	0	1	0	0	0	14553	1087	38	1	622	1	SLC26A11	17	78201627	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168922	78201627	2993583	10464	18449										
RNF213	57674	broad.mit.edu	37	chr17	78317012	78317012	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgcctctgaaaacaattCgactgatcgaccctcaggtg	9	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78317012C>T	ENST00000582970.1	+	27	6213	c.6070C>T	c.(6070-6072)Cga>Tga	p.R2024*	RNF213_ENST00000336301.6_Nonsense_Mutation_p.R97*|RNF213_ENST00000508628.2_Nonsense_Mutation_p.R2073*	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2024					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R97*(1)|p.R2073*(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GAAAACAATTCGACTGATCGA	0.488																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											83	74	77					17																	78317012		2203	4300	6503	75931607	SO:0001587	stop_gained	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.6070C>T	17.37:g.78317012C>T	ENSP00000464087:p.Arg2024*		75931607	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Nonsense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	48	14.336948	0.99790	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	.	.	.	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9964	0.71436	0.1758:0.8242:0.0:0.0	.	.	.	.	X	2024;2073;97	.	ENSP00000338218:R97X	R	+	1	2	RNF213	75931607	0.963000	0.33076	0.258000	0.24420	0.671000	0.39405	1.597000	0.36729	2.815000	0.96918	0.650000	0.86243	CGA		0.488	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78317012	C	T	78317012	4	4	61	1	0	0	0	0	0	1	0	0	13514	876	31	1	6491	1	RNF213	17	78317012	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115385	78317012	2878198	10465	18450										
RNF213	57674	broad.mit.edu	37	chr17	78337501	78337501	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgtggctacagttggtgaaGaatctttccatgccgctgga	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78337501G>T	ENST00000582970.1	+	41	11804	c.11661G>T	c.(11659-11661)aaG>aaT	p.K3887N	CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.K1960N|RNF213_ENST00000508628.2_Missense_Mutation_p.K3936N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3887					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K3936N(1)|p.K1960N(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGTTGGTGAAGAATCTTTCCA	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	17											85	57	67					17																	78337501		2202	4300	6502	75952096	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11661G>T	17.37:g.78337501G>T	ENSP00000464087:p.Lys3887Asn		75952096	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413857	0.42817	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.25085	1.82	4.9	0.62	0.17637	.	0.000000	0.85682	D	0.000000	T	0.46852	0.1414	M	0.79805	2.47	0.29104	N	0.881278	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.988	T	0.38607	-0.9653	10	0.72032	D	0.01	.	8.6113	0.33804	0.3769:0.0:0.6231:0.0	.	3936;1960	C9JCP4;Q63HN8	.;RN213_HUMAN	N	3887;3936;1960	ENSP00000338218:K1960N	ENSP00000338218:K1960N	K	+	3	2	RNF213	75952096	0.999000	0.42202	0.708000	0.30435	0.135000	0.20990	1.732000	0.38146	0.476000	0.27440	0.563000	0.77884	AAG		0.602	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78337501	G	T	78337501	3	4	61	1	0	0	0	0	1	0	0	0	13514	933	33	2	12138	2	RNF213	17	78337501	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20489	78337501	2857709	10466	18451										
RNF213	57674	broad.mit.edu	37	chr17	78356790	78356790	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgtagggcttttaaatTttgacacagaattgtcaact	7	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78356790T>G	ENST00000582970.1	+	58	14133	c.13990T>G	c.(13990-13992)Ttt>Gtt	p.F4664V	CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.F2737V|RNF213_ENST00000508628.2_Missense_Mutation_p.F4713V|RNF213_ENST00000427003.3_3'UTR	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4664					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F4713V(1)|p.F2737V(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCTTTTAAATTTTGACACAGA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	17											91	87	88					17																	78356790		2203	4300	6503	75971385	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13990T>G	17.37:g.78356790T>G	ENSP00000464087:p.Phe4664Val		75971385	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.953245	0.73902	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T;T	0.61392	1.38;0.11	5.5	5.5	0.81552	.	0.156358	0.46145	D	0.000309	T	0.71500	0.3347	M	0.78637	2.42	0.31469	N	0.668628	D	0.63880	0.993	P	0.58520	0.84	T	0.76629	-0.2889	10	0.41790	T	0.15	.	13.5839	0.61919	0.0:0.0:0.0:1.0	.	2737	Q63HN8	RN213_HUMAN	V	4664;4713;2737;14	ENSP00000425956:F4664V;ENSP00000338218:F2737V	ENSP00000338218:F2737V	F	+	1	0	RNF213	75971385	0.987000	0.35691	0.018000	0.16275	0.043000	0.13939	2.831000	0.48144	2.089000	0.63090	0.528000	0.53228	TTT		0.383	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78356790	T	G	78356790	3	3	61	1	0	0	0	0	1	0	0	0	13514	1841	64	4	14535	4	RNF213	17	78356790	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19289	78356790	2838420	10467	18452										
RNF213	57674	broad.mit.edu	37	chr17	78367182	78367182	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagttacatgcaaactaaaGaaagtgaaattcttcctgaa	6	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78367182G>T	ENST00000582970.1	+	68	15651	c.15508G>T	c.(15508-15510)Gaa>Taa	p.E5170*	CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Nonsense_Mutation_p.E3243*|RNF213_ENST00000508628.2_Nonsense_Mutation_p.E5219*|RNF213_ENST00000427003.3_3'UTR	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5170					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E5219*(1)|p.E3243*(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCAAACTAAAGAAAGTGAAAT	0.443																																																2	Substitution - Nonsense(2)	large_intestine(2)	17											94	87	90					17																	78367182		2203	4300	6503	75981777	SO:0001587	stop_gained	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.15508G>T	17.37:g.78367182G>T	ENSP00000464087:p.Glu5170*		75981777	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Nonsense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	49	16.022425	0.99852	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	.	.	.	4.46	3.46	0.39613	.	0.708972	0.13120	N	0.412242	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	13.7829	0.63093	0.0:0.0:0.8452:0.1548	.	.	.	.	X	5170;5219;3243;520	.	ENSP00000338218:E3243X	E	+	1	0	RNF213	75981777	1.000000	0.71417	0.236000	0.24074	0.392000	0.30506	4.433000	0.59929	0.963000	0.38082	0.563000	0.77884	GAA		0.443	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78367182	G	T	78367182	4	4	61	1	0	0	0	0	0	1	0	0	13514	943	33	2	16093	2	RNF213	17	78367182	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10392	78367182	2828028	10468	18453										
RPTOR	57521	broad.mit.edu	37	chr17	78866640	78866640	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccaggagcctcaacaaatCtttgcagaacctgagtttga	9	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:78866640C>A	ENST00000306801.3	+	19	2575	c.2213C>A	c.(2212-2214)tCt>tAt	p.S738Y	RPTOR_ENST00000544334.2_Missense_Mutation_p.S580Y|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	738					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.S738Y(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CTCAACAAATCTTTGCAGAAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	17											112	125	121					17																	78866640		2203	4300	6503	76481235	SO:0001583	missense	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.2213C>A	17.37:g.78866640C>A	ENSP00000307272:p.Ser738Tyr		76481235	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.007190	0.54361	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.54071	0.81;0.59	4.65	3.68	0.42216	Armadillo-type fold (1);	0.153836	0.45361	D	0.000377	T	0.58495	0.2126	L	0.38175	1.15	0.80722	D	1	D;P	0.64830	0.994;0.826	D;B	0.77004	0.989;0.196	T	0.51276	-0.8726	10	0.15952	T	0.53	.	12.5375	0.56150	0.0:0.9186:0.0:0.0814	.	580;738	F5H7J5;Q8N122	.;RPTOR_HUMAN	Y	738;580	ENSP00000307272:S738Y;ENSP00000442479:S580Y	ENSP00000307272:S738Y	S	+	2	0	RPTOR	76481235	1.000000	0.71417	0.073000	0.20177	0.596000	0.36781	4.879000	0.63100	0.958000	0.37956	0.650000	0.86243	TCT		0.498	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78866640	C	A	78866640	3	1	61	1	0	0	0	0	1	0	0	0	13702	913	32	2	2287	2	RPTOR	17	78866640	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	499458	78866640	2328570	10469	18454										
SLC38A10	124565	broad.mit.edu	37	chr17	79226320	79226320	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctgagtcgggcagaggCggcgccatctggccctggac	15	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:79226320C>T	ENST00000374759.3	-	13	2003	c.1620G>A	c.(1618-1620)ccG>ccA	p.P540P	SLC38A10_ENST00000288439.5_Silent_p.P540P	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	540					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.P540P(4)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CGGGCAGAGGCGGCGCCATCT	0.622																																																4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	17											50	52	51					17																	79226320		2203	4300	6503	76840915	SO:0001819	synonymous_variant	124565			BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1620G>A	17.37:g.79226320C>T			76840915	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																				0.622	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79226320	C	T	79226320	2	4	61	1	0	0	0	0	0	0	0	1	14639	755	27	1		1	SLC38A10	17	79226320	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	359680	79226320	1968890	10470	18455										
NPLOC4	55666	broad.mit.edu	37	chr17	79564278	79564278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctccacctcaccttatttCgactgtagcggacggtaccc	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:79564278C>T	ENST00000331134.6	-	10	1201	c.986G>A	c.(985-987)cGa>cAa	p.R329Q	NPLOC4_ENST00000374747.5_Missense_Mutation_p.R329Q|NPLOC4_ENST00000539314.1_Missense_Mutation_p.R168Q	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	329					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R329Q(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CACCTTATTTCGACTGTAGCG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											131	131	131					17																	79564278		2066	4193	6259	77174716	SO:0001583	missense	55666			AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.986G>A	17.37:g.79564278C>T	ENSP00000331487:p.Arg329Gln		77174716	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	37	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089099	0.94100	.	.	ENSG00000182446	ENST00000331134;ENST00000374747;ENST00000539314	.	.	.	5.54	5.54	0.83059	Nuclear pore localisation protein NPL4 (1);	0.000000	0.85682	D	0.000000	D	0.84902	0.5575	H	0.94771	3.58	0.80722	D	1	D;P;P	0.61080	0.989;0.919;0.785	P;B;P	0.55615	0.78;0.374;0.518	D	0.88903	0.3354	9	0.87932	D	0	-12.4761	19.9063	0.97008	0.0:1.0:0.0:0.0	.	168;329;329	B4DG89;Q8TAT6-2;Q8TAT6	.;.;NPL4_HUMAN	Q	329;328;168	.	ENSP00000331487:R329Q	R	-	2	0	NPLOC4	77174716	1.000000	0.71417	0.965000	0.40720	0.987000	0.75469	7.314000	0.78988	2.774000	0.95407	0.644000	0.83932	CGA		0.488	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1			T	79564278	C	T	79564278	3	4	61	1	0	0	0	0	1	0	0	0	10617	884	31	1	872	1	NPLOC4	17	79564278	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	337958	79564278	1630932	10471	18456										
CSNK1D	1453	broad.mit.edu	37	chr17	80209401	80209401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaggtatgtggcaaattCggctacaaaacaagaaactc	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80209401C>T	ENST00000314028.6	-	6	1088	c.739G>A	c.(739-741)Gaa>Aaa	p.E247K	CSNK1D_ENST00000392334.2_Missense_Mutation_p.E247K|CSNK1D_ENST00000578904.1_5'UTR|CSNK1D_ENST00000398519.5_Missense_Mutation_p.E247K	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.E247K(2)		breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			GTGGCAAATTCGGCTACAAAA	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	17											85	81	82					17																	80209401		2203	4300	6503	77802690	SO:0001583	missense	1453				CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551			2452	protein-coding gene	gene with protein product		600864				7797465	Standard	NM_001893		Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.739G>A	17.37:g.80209401C>T	ENSP00000324464:p.Glu247Lys		77802690	A2I2P2|Q96KZ6|Q9BTN5	Missense_Mutation	SNP	ENST00000314028.6	37	CCDS11805.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464810	0.63513	.	.	ENSG00000141551	ENST00000314028;ENST00000392334;ENST00000398519;ENST00000269361	T;T	0.06528	3.29;3.29	5.13	5.13	0.70059	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.38585	0.1046	H	0.95816	3.725	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.997;0.976;0.986	T	0.56245	-0.8011	10	0.87932	D	0	.	17.9504	0.89051	0.0:1.0:0.0:0.0	.	136;247;247;190	B4DIJ9;P48730;P48730-2;B4E0G1	.;KC1D_HUMAN;.;.	K	247;247;190;139	ENSP00000324464:E247K;ENSP00000376146:E247K	ENSP00000269361:E139K	E	-	1	0	CSNK1D	77802690	1.000000	0.71417	0.997000	0.53966	0.876000	0.50452	7.713000	0.84693	2.557000	0.86248	0.655000	0.94253	GAA		0.502	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442632.1	NM_139062		T	80209401	C	T	80209401	3	4	61	1	0	0	0	0	1	0	0	0	3958	893	31	1	561	1	CSNK1D	17	80209401	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	645123	80209401	985809	10472	18457										
NARF	26502	broad.mit.edu	37	chr17	80422268	80422268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtccaactttcccagcaaAatgccaaggacttcttccgc	7	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80422268A>C	ENST00000309794.11	+	3	412	c.214A>C	c.(214-216)Aat>Cat	p.N72H	NARF_ENST00000390006.4_Missense_Mutation_p.N13H|NARF_ENST00000412079.2_5'UTR|NARF_ENST00000345415.7_Intron|NARF_ENST00000581743.1_3'UTR|NARF_ENST00000457415.3_Missense_Mutation_p.N72H	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	72						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)	p.N72H(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			TTCCCAGCAAAATGCCAAGGA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	17											115	98	104					17																	80422268		2203	4300	6503	78015557	SO:0001583	missense	26502			BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.214A>C	17.37:g.80422268A>C	ENSP00000309899:p.Asn72His		78015557	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Missense_Mutation	SNP	ENST00000309794.11	37	CCDS32777.1	.	.	.	.	.	.	.	.	.	.	A	6.858	0.527697	0.13127	.	.	ENSG00000141562	ENST00000390006;ENST00000374611;ENST00000309794;ENST00000457415	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.41	4.34	0.51931	Iron hydrogenase (1);	0.111171	0.64402	D	0.000006	T	0.39989	0.1099	M	0.64170	1.965	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.998;0.989	D;D;P;P	0.68353	0.935;0.957;0.907;0.8	T	0.16335	-1.0406	10	0.66056	D	0.02	-20.4886	10.3735	0.44068	0.9232:0.0:0.0768:0.0	.	72;72;72;72	B4DND8;Q9UHQ1-2;E9PH27;Q9UHQ1	.;.;.;NARF_HUMAN	H	13;72;72;72	ENSP00000374656:N13H;ENSP00000363739:N72H;ENSP00000309899:N72H;ENSP00000414678:N72H	ENSP00000309899:N72H	N	+	1	0	NARF	78015557	1.000000	0.71417	0.684000	0.30055	0.006000	0.05464	5.567000	0.67378	0.908000	0.36671	0.459000	0.35465	AAT		0.512	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		C	80422268	A	C	80422268	3	2	61	1	0	0	0	0	1	0	0	0	10197	14	1	4	224	4	NARF	17	80422268	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	212867	80422268	772942	10473	18458										
NARF	26502	broad.mit.edu	37	chr17	80441626	80441626	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatggagcaaggtgacctCtcagtgagagatgctgccgt	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80441626C>A	ENST00000309794.11	+	8	1002	c.804C>A	c.(802-804)ctC>ctA	p.L268L	NARF_ENST00000390006.4_Silent_p.L209L|NARF-IT1_ENST00000584012.1_RNA|NARF_ENST00000412079.2_Silent_p.L140L|NARF_ENST00000345415.7_Silent_p.L220L|NARF_ENST00000457415.3_Silent_p.L314L	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	268						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)	p.L314L(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			AAGGTGACCTCTCAGTGAGAG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	17											126	112	117					17																	80441626		2203	4300	6503	78034915	SO:0001819	synonymous_variant	26502			BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.804C>A	17.37:g.80441626C>A			78034915	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Silent	SNP	ENST00000309794.11	37	CCDS32777.1																																																																																				0.547	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		A	80441626	C	A	80441626	2	1	61	1	0	0	0	0	0	0	0	1	10197	900	32	2		2	NARF	17	80441626	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19358	80441626	753584	10474	18459										
WDR45L	56270	broad.mit.edu	37	chr17	80574409	80574409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccactcaccaatgacggCgtttggctctgttccaaagg	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80574409C>T	ENST00000392325.4	-	9	1113	c.919G>A	c.(919-921)Gcc>Acc	p.A307T	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	307								p.A307T(1)									CCAATGACGGCGTTTGGCTCT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	17											133	133	133					17																	80574409		2203	4300	6503	78167698	SO:0001583	missense	56270			AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.919G>A	17.37:g.80574409C>T	ENSP00000376139:p.Ala307Thr		78167698	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294017	0.40594	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.76968	-1.06	5.11	5.11	0.69529	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.051815	0.85682	D	0.000000	T	0.41119	0.1145	N	0.00453	-1.485	0.80722	D	1	B	0.18863	0.031	B	0.08055	0.003	T	0.55792	-0.8085	10	0.02654	T	1	-13.6707	12.6028	0.56506	0.2896:0.7104:0.0:0.0	.	307	Q5MNZ6	WIPI3_HUMAN	T	307;279	ENSP00000376139:A307T	ENSP00000376139:A307T	A	-	1	0	WDR45L	78167698	0.996000	0.38824	0.644000	0.29465	0.491000	0.33493	3.414000	0.52693	2.540000	0.85666	0.563000	0.77884	GCC		0.547	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		T	80574409	C	T	80574409	3	4	61	1	0	0	0	0	1	0	0	0	17338	768	27	1	123	1	WDR45L	17	80574409	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132783	80574409	620801	10475	18460										
WDR45L	56270	broad.mit.edu	37	chr17	80583286	80583286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggggttatagcaggtttCgaagacgtgcaactgatggg	15	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80583286C>T	ENST00000392325.4	-	5	600	c.406G>A	c.(406-408)Gaa>Aaa	p.E136K	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	136								p.E136K(1)									TAGCAGGTTTCGAAGACGTGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											145	120	129					17																	80583286		2203	4300	6503	78176575	SO:0001583	missense	56270			AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.406G>A	17.37:g.80583286C>T	ENSP00000376139:p.Glu136Lys		78176575	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	-	17.11	3.305555	0.60305	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.62639	0.01	4.54	4.54	0.55810	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.047590	0.85682	D	0.000000	T	0.66177	0.2763	M	0.86953	2.85	0.80722	D	1	P	0.46859	0.885	B	0.36885	0.235	T	0.76924	-0.2779	10	0.54805	T	0.06	-43.4622	17.664	0.88199	0.0:1.0:0.0:0.0	.	136	Q5MNZ6	WIPI3_HUMAN	K	136;108	ENSP00000376139:E136K	ENSP00000376139:E136K	E	-	1	0	WDR45L	78176575	1.000000	0.71417	1.000000	0.80357	0.491000	0.33493	7.240000	0.78192	2.244000	0.73946	0.552000	0.68991	GAA		0.488	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		T	80583286	C	T	80583286	3	4	61	1	0	0	0	0	1	0	0	0	17338	893	31	1	652	1	WDR45L	17	80583286	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8877	80583286	611924	10476	18461										
ZNF750	79755	broad.mit.edu	37	chr17	80789200	80789200	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcaggaattggactttcGaactcgacgtgttttctgtt	10	9	2	0	rs371946502		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80789200G>A	ENST00000269394.3	-	2	1964	c.1131C>T	c.(1129-1131)ttC>ttT	p.F377F	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron|ZNF750_ENST00000572562.1_5'UTR	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	377					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.F377F(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	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)			TTGGACTTTCGAACTCGACGT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	17											88	95	93					17																	80789200		2203	4300	6503	78382489	SO:0001819	synonymous_variant	79755			AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1131C>T	17.37:g.80789200G>A			78382489	Q9H899	Silent	SNP	ENST00000269394.3	37	CCDS11819.1																																																																																				0.567	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		A	80789200	G	A	80789200	2	1	61	1	0	0	0	0	0	0	0	1	18171	1049	37	1		1	ZNF750	17	80789200	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205914	80789200	406010	10477	18462										
ZNF750	79755	broad.mit.edu	37	chr17	80789311	80789311	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagctctgatctcgggtgagGccagtgacaggtgggagtct	17	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr17:80789311G>A	ENST00000269394.3	-	2	1853	c.1020C>T	c.(1018-1020)ggC>ggT	p.G340G	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron|ZNF750_ENST00000572562.1_5'UTR	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	340					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.G340G(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	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)			CTCGGGTGAGGCCAGTGACAG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	17											127	137	134					17																	80789311		2203	4300	6503	78382600	SO:0001819	synonymous_variant	79755			AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1020C>T	17.37:g.80789311G>A			78382600	Q9H899	Silent	SNP	ENST00000269394.3	37	CCDS11819.1																																																																																				0.522	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		A	80789311	G	A	80789311	2	1	61	1	0	0	0	0	0	0	0	1	18171	1190	42	3		3	ZNF750	17	80789311	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111	80789311	405899	10478	18463										
THOC1	9984	broad.mit.edu	37	chr18	224148	224148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcgggtgctgttctcttccGaattattctcgtaggtttgg	11	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:224148G>A	ENST00000261600.6	-	16	1247	c.1240C>T	c.(1240-1242)Cgg>Tgg	p.R414W		NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	414					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.R414W(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GTTCTCTTCCGAATTATTCTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	18											103	95	98					18																	224148		1823	4083	5906	214148	SO:0001583	missense	9984			AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"THO complex subunits"	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.1240C>T	18.37:g.224148G>A	ENSP00000261600:p.Arg414Trp		214148	B2RBP6|Q15219|Q64I72|Q64I73	Missense_Mutation	SNP	ENST00000261600.6	37	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.375455	0.24857	.	.	ENSG00000079134	ENST00000261600	.	.	.	5.63	2.7	0.31948	.	0.044427	0.85682	D	0.000000	T	0.60444	0.2269	M	0.78049	2.395	0.53688	D	0.999977	B	0.33477	0.413	B	0.21151	0.033	T	0.66874	-0.5813	9	0.87932	D	0	-5.4386	15.6568	0.77144	0.0:0.0:0.4317:0.5683	.	414	Q96FV9	THOC1_HUMAN	W	414	.	ENSP00000261600:R414W	R	-	1	2	THOC1	214148	0.993000	0.37304	0.776000	0.31678	0.782000	0.44232	1.574000	0.36482	0.684000	0.31448	0.585000	0.79938	CGG		0.373	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		A	224148	G	A	224148	3	1	61	1	0	0	0	0	1	0	0	0	15903	1057	37	1	757	1	THOC1	18	224148	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		224148	77853100	10479	18464										
THOC1	9984	broad.mit.edu	37	chr18	247929	247929	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaagtgaccagaattttcGatacaggttgtaatcaattg	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:247929G>A	ENST00000261600.6	-	10	713	c.706C>T	c.(706-708)Cga>Tga	p.R236*	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	236					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.R236*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CAGAATTTTCGATACAGGTTG	0.303																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											103	96	98					18																	247929		1802	4064	5866	237929	SO:0001587	stop_gained	9984			AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"THO complex subunits"	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.706C>T	18.37:g.247929G>A	ENSP00000261600:p.Arg236*		237929	B2RBP6|Q15219|Q64I72|Q64I73	Nonsense_Mutation	SNP	ENST00000261600.6	37	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	G	36	5.634018	0.96682	.	.	ENSG00000079134	ENST00000261600	.	.	.	5.38	-1.79	0.07932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-3.0747	17.6998	0.88291	0.0:0.0:0.1488:0.8512	.	.	.	.	X	236	.	ENSP00000261600:R236X	R	-	1	2	THOC1	237929	1.000000	0.71417	0.945000	0.38365	0.986000	0.74619	2.230000	0.42999	-0.166000	0.10890	-0.188000	0.12872	CGA		0.303	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		A	247929	G	A	247929	4	1	61	1	0	0	0	0	0	1	0	0	15903	1066	37	1	1315	1	THOC1	18	247929	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23781	247929	77829319	10480	18465										
COLEC12	81035	broad.mit.edu	37	chr18	480712	480712	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgttaggactcaccaaacCgcttgtaaccgaaggattgc	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:480712C>A	ENST00000400256.3	-	2	260	c.53G>T	c.(52-54)cGg>cTg	p.R18L		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	18					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)	p.R18L(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CTCACCAAACCGCTTGTAACC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	18											222	138	166					18																	480712		2203	4300	6503	470712	SO:0001583	missense	81035			AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.53G>T	18.37:g.480712C>A	ENSP00000383115:p.Arg18Leu		470712	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.915801	0.73098	.	.	ENSG00000158270	ENST00000400256	D	0.89270	-2.49	5.77	5.77	0.91146	.	0.229198	0.39615	N	0.001318	T	0.79885	0.4523	N	0.19112	0.55	0.49915	D	0.999837	P	0.35401	0.499	B	0.21151	0.033	T	0.81686	-0.0820	10	0.66056	D	0.02	-11.7624	15.553	0.76167	0.0:1.0:0.0:0.0	.	18	Q5KU26	COL12_HUMAN	L	18	ENSP00000383115:R18L	ENSP00000383115:R18L	R	-	2	0	COLEC12	470712	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.106000	0.57804	2.733000	0.93635	0.650000	0.86243	CGG		0.547	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			A	480712	C	A	480712	3	1	61	1	0	0	0	0	1	0	0	0	3718	652	23	2	2211	2	COLEC12	18	480712	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	232783	480712	77596536	10481	18466										
CLUL1	27098	broad.mit.edu	37	chr18	627181	627181	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctccccatcagtgaaaagCtcattgaggaagatgcacaa	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:627181C>A	ENST00000400606.2	+	5	653	c.508C>A	c.(508-510)Ctc>Atc	p.L170I	CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000338387.7_Missense_Mutation_p.L170I|CLUL1_ENST00000540035.1_Missense_Mutation_p.L222I|CLUL1_ENST00000581619.1_Missense_Mutation_p.L195I|CLUL1_ENST00000579494.1_Missense_Mutation_p.L170I	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	170					cell death (GO:0008219)	extracellular region (GO:0005576)		p.L170I(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(5)|liver(2)|lung(7)|ovary(2)|skin(1)	24						CAGTGAAAAGCTCATTGAGGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	18											163	147	152					18																	627181		1890	4128	6018	617181	SO:0001583	missense	27098			D63813	CCDS42405.1, CCDS74187.1	18p11.32	2008-07-28				ENSG00000079101			2096	protein-coding gene	gene with protein product						10675623, 14507903	Standard	NM_199167		Approved		uc002kkq.3	Q15846		ENST00000400606.2:c.508C>A	18.37:g.627181C>A	ENSP00000383449:p.Leu170Ile		617181	A0FDN7	Missense_Mutation	SNP	ENST00000400606.2	37	CCDS42405.1	.	.	.	.	.	.	.	.	.	.	C	1.766	-0.485504	0.04352	.	.	ENSG00000079101	ENST00000400606;ENST00000540035;ENST00000338387	T;T;T	0.22945	1.93;1.93;1.93	4.77	-9.54	0.00572	Clusterin, N-terminal (1);	2.137260	0.01579	N	0.020964	T	0.16128	0.0388	L	0.34521	1.04	0.09310	N	1	B;B	0.30146	0.148;0.27	B;B	0.28011	0.032;0.085	T	0.03443	-1.1036	10	0.21014	T	0.42	10.0741	9.0774	0.36531	0.0:0.1391:0.3449:0.516	.	222;170	F5GWQ8;Q15846	.;CLUL1_HUMAN	I	170;222;170	ENSP00000383449:L170I;ENSP00000441726:L222I;ENSP00000341128:L170I	ENSP00000341128:L170I	L	+	1	0	CLUL1	617181	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.861000	0.04268	-2.744000	0.00378	-0.367000	0.07326	CTC		0.388	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1			A	627181	C	A	627181	3	1	61	1	0	0	0	0	1	0	0	0	3576	797	28	2	522	2	CLUL1	18	627181	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146469	627181	77450067	10482	18467										
TYMS	7298	broad.mit.edu	37	chr18	672902	672902	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccaaagctcaggattcttCgaaaagttgagaaaattgat	8	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:672902C>T	ENST00000323274.10	+	7	986	c.847C>T	c.(847-849)Cga>Tga	p.R283*	ENOSF1_ENST00000319815.6_3'UTR|TYMS_ENST00000323224.7_Nonsense_Mutation_p.R249*|ENOSF1_ENST00000583973.1_5'Flank|ENOSF1_ENST00000383578.3_3'UTR|TYMS_ENST00000581920.1_3'UTR|TYMS_ENST00000323250.5_Nonsense_Mutation_p.R200*	NM_001071.2	NP_001062.1	P04818	TYSY_HUMAN	thymidylate synthetase	283					aging (GO:0007568)|cartilage development (GO:0051216)|circadian rhythm (GO:0007623)|deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|developmental growth (GO:0048589)|dTMP biosynthetic process (GO:0006231)|dTTP biosynthetic process (GO:0006235)|dUMP metabolic process (GO:0046078)|G1/S transition of mitotic cell cycle (GO:0000082)|immortalization of host cell by virus (GO:0019088)|intestinal epithelial cell maturation (GO:0060574)|mitotic cell cycle (GO:0000278)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|organ regeneration (GO:0031100)|polysaccharide metabolic process (GO:0005976)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to organophosphorus (GO:0046683)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|response to vitamin A (GO:0033189)|small molecule metabolic process (GO:0044281)|tetrahydrofolate metabolic process (GO:0046653)|uracil metabolic process (GO:0019860)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cofactor binding (GO:0048037)|drug binding (GO:0008144)|folic acid binding (GO:0005542)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|thymidylate synthase activity (GO:0004799)	p.R283*(1)		endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(2)	8					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Raltitrexed(DB00293)|Trifluridine(DB00432)|Trimethoprim(DB00440)	CAGGATTCTTCGAAAAGTTGA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											94	101	98					18																	672902		2203	4300	6503	662902	SO:0001587	stop_gained	7298			X02308	CCDS11821.1	18p11.31-p11.21	2014-09-17			ENSG00000176890	ENSG00000176890	2.1.1.45		12441	protein-coding gene	gene with protein product		188350		TS			Standard	NM_001071		Approved	Tsase, TMS, HsT422	uc010dka.1	P04818	OTTHUMG00000131473	ENST00000323274.10:c.847C>T	18.37:g.672902C>T	ENSP00000315644:p.Arg283*		662902	Q8WYK3|Q8WYK4	Nonsense_Mutation	SNP	ENST00000323274.10	37	CCDS11821.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.973726	0.53720	.	.	ENSG00000176890	ENST00000323274;ENST00000323224;ENST00000323250	.	.	.	5.9	5.9	0.94986	.	0.111500	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7752	20.2576	0.98430	0.0:1.0:0.0:0.0	.	.	.	.	X	283;249;200	.	ENSP00000314727:R249X	R	+	1	2	TYMS	662902	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	4.770000	0.62309	2.785000	0.95823	0.650000	0.86243	CGA		0.393	TYMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254316.1	NM_001071		T	672902	C	T	672902	4	4	61	1	0	0	0	0	0	1	0	0	16852	876	31	1	873	1	TYMS	18	672902	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45721	672902	77404346	10483	18468										
SMCHD1	23347	broad.mit.edu	37	chr18	2666177	2666177	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacttggcatttcacctgaaGaaaaatttgttattacaaca	5	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2666177G>T	ENST00000320876.6	+	2	546	c.208G>T	c.(208-210)Gaa>Taa	p.E70*	SMCHD1_ENST00000261598.8_Nonsense_Mutation_p.E70*	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	70					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.E70*(3)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TTCACCTGAAGAAAAATTTGT	0.244																																																3	Substitution - Nonsense(3)	large_intestine(3)	18											38	36	37					18																	2666177		1786	4047	5833	2656177	SO:0001587	stop_gained	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.208G>T	18.37:g.2666177G>T	ENSP00000326603:p.Glu70*		2656177	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	40	8.527295	0.98850	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	.	.	.	5.46	5.46	0.80206	.	0.121159	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.6691	0.95903	0.0:0.0:1.0:0.0	.	.	.	.	X	70	.	ENSP00000261598:E70X	E	+	1	0	SMCHD1	2656177	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.075000	0.89502	2.721000	0.93114	0.591000	0.81541	GAA		0.244	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2666177	G	T	2666177	4	4	61	1	0	0	0	0	0	1	0	0	14825	943	33	2	214	2	SMCHD1	18	2666177	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1993275	2666177	75411071	10484	18469										
SMCHD1	23347	broad.mit.edu	37	chr18	2703718	2703718	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaaaattgacagagaatTtgctttgtggctgaaggact	11	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2703718T>G	ENST00000320876.6	+	13	2014	c.1676T>G	c.(1675-1677)tTt>tGt	p.F559C	SMCHD1_ENST00000261598.8_Missense_Mutation_p.F559C|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	559					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.F559C(2)|p.F7C(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GACAGAGAATTTGCTTTGTGG	0.303																																																3	Substitution - Missense(3)	large_intestine(3)	18											66	67	67					18																	2703718		1817	4084	5901	2693718	SO:0001583	missense	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.1676T>G	18.37:g.2703718T>G	ENSP00000326603:p.Phe559Cys		2693718	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.212258	0.39102	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.36699	1.24;1.25	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.57403	0.2051	L	0.58101	1.795	0.47276	D	0.99937	D	0.89917	1.0	D	0.83275	0.996	T	0.60611	-0.7229	10	0.87932	D	0	-16.5938	15.6552	0.77129	0.0:0.0:0.0:1.0	.	559	A6NHR9	SMHD1_HUMAN	C	559	ENSP00000326603:F559C;ENSP00000261598:F559C	ENSP00000261598:F559C	F	+	2	0	SMCHD1	2693718	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.311000	0.78958	2.088000	0.63022	0.460000	0.39030	TTT		0.303	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			G	2703718	T	G	2703718	3	3	61	1	0	0	0	0	1	0	0	0	14825	1841	64	4	1726	4	SMCHD1	18	2703718	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37541	2703718	75373530	10485	18470										
SMCHD1	23347	broad.mit.edu	37	chr18	2729394	2729394	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccagacgcttaaagcaaGaattgaaatacctgtaagtt	8	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2729394G>T	ENST00000320876.6	+	24	3373	c.3035G>T	c.(3034-3036)aGa>aTa	p.R1012I	SMCHD1_ENST00000261598.8_Missense_Mutation_p.R1012I|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1012					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.R1012I(2)|p.R460I(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						CTTAAAGCAAGAATTGAAATA	0.303																																																3	Substitution - Missense(3)	large_intestine(3)	18											39	37	37					18																	2729394		1791	4036	5827	2719394	SO:0001583	missense	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3035G>T	18.37:g.2729394G>T	ENSP00000326603:p.Arg1012Ile		2719394	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659344	0.47467	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.24538	1.85;1.85	5.69	3.47	0.39725	.	0.288695	0.38058	N	0.001839	T	0.15089	0.0364	N	0.22421	0.69	0.49389	D	0.999785	B	0.31009	0.303	B	0.28553	0.091	T	0.07083	-1.0791	10	0.87932	D	0	-15.3312	6.2936	0.21073	0.5735:0.0:0.4265:0.0	.	1012	A6NHR9	SMHD1_HUMAN	I	1012	ENSP00000326603:R1012I;ENSP00000261598:R1012I	ENSP00000261598:R1012I	R	+	2	0	SMCHD1	2719394	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.095000	0.30964	1.238000	0.43771	0.655000	0.94253	AGA		0.303	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2729394	G	T	2729394	3	4	61	1	0	0	0	0	1	0	0	0	14825	942	33	2	3129	2	SMCHD1	18	2729394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25676	2729394	75347854	10486	18471										
SMCHD1	23347	broad.mit.edu	37	chr18	2740755	2740755	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagcattttcaccaagttCtttatcttctttgtcaattg	4	9	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2740755C>A	ENST00000320876.6	+	28	3907	c.3569C>A	c.(3568-3570)tCt>tAt	p.S1190Y	SMCHD1_ENST00000261598.8_Missense_Mutation_p.S1190Y|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1190					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.S1190Y(2)|p.S638Y(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TCACCAAGTTCTTTATCTTCT	0.308																																																3	Substitution - Missense(3)	large_intestine(3)	18											126	124	125					18																	2740755		1805	4055	5860	2730755	SO:0001583	missense	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3569C>A	18.37:g.2740755C>A	ENSP00000326603:p.Ser1190Tyr		2730755	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.498549	0.44455	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.25579	1.79;1.79	5.33	2.12	0.27331	.	0.270105	0.42964	D	0.000632	T	0.19967	0.0480	L	0.29908	0.895	0.32214	N	0.576118	P	0.34462	0.454	B	0.37833	0.259	T	0.23368	-1.0190	10	0.62326	D	0.03	-5.7224	10.263	0.43438	0.1132:0.3447:0.5421:0.0	.	1190	A6NHR9	SMHD1_HUMAN	Y	1190	ENSP00000326603:S1190Y;ENSP00000261598:S1190Y	ENSP00000261598:S1190Y	S	+	2	0	SMCHD1	2730755	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	1.859000	0.39418	0.676000	0.31285	0.650000	0.86243	TCT		0.308	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2740755	C	A	2740755	3	1	61	1	0	0	0	0	1	0	0	0	14825	913	32	2	3679	2	SMCHD1	18	2740755	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11361	2740755	75336493	10487	18472										
SMCHD1	23347	broad.mit.edu	37	chr18	2743906	2743906	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctaaacttctccttataGactggccagaactaaaggag	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2743906G>T	ENST00000320876.6	+	29	4119	c.3781G>T	c.(3781-3783)Gac>Tac	p.D1261Y	SMCHD1_ENST00000261598.8_Missense_Mutation_p.D1261Y|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1261					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.D1261Y(2)|p.D709Y(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TCTCCTTATAGACTGGCCAGA	0.373																																																3	Substitution - Missense(3)	large_intestine(3)	18											74	66	69					18																	2743906		1825	4083	5908	2733906	SO:0001583	missense	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3781G>T	18.37:g.2743906G>T	ENSP00000326603:p.Asp1261Tyr		2733906	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.580204	0.46006	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.26957	1.7;1.71	5.26	4.19	0.49359	.	0.210441	0.48767	D	0.000162	T	0.31606	0.0802	L	0.56769	1.78	0.37464	D	0.915341	P	0.47350	0.894	P	0.45037	0.467	T	0.41016	-0.9532	10	0.72032	D	0.01	-11.6145	14.4521	0.67392	0.0857:0.0:0.9143:0.0	.	1261	A6NHR9	SMHD1_HUMAN	Y	1261	ENSP00000326603:D1261Y;ENSP00000261598:D1261Y	ENSP00000261598:D1261Y	D	+	1	0	SMCHD1	2733906	1.000000	0.71417	0.955000	0.39395	0.946000	0.59487	5.007000	0.63984	2.425000	0.82216	0.585000	0.79938	GAC		0.373	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2743906	G	T	2743906	3	4	61	1	0	0	0	0	1	0	0	0	14825	942	33	2	3895	2	SMCHD1	18	2743906	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3151	2743906	75333342	10488	18473										
SMCHD1	23347	broad.mit.edu	37	chr18	2772321	2772321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaaaaaacctagaagatCgtgtactcttccaaactata	6	8	1	3	rs151311806	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2772321C>T	ENST00000320876.6	+	41	5464	c.5126C>T	c.(5125-5127)tCg>tTg	p.S1709L	SMCHD1_ENST00000261598.8_Missense_Mutation_p.S1709L|RP11-703M24.5_ENST00000583546.1_RNA|snoU13_ENST00000459147.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1709					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.S1709L(2)|p.S1157L(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						CCTAGAAGATCGTGTACTCTT	0.323													C|||	2	0.000399361	0	0	5008	,	,		16917	0.002		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	18											93	88	90					18																	2772321		1827	4075	5902	2762321	SO:0001583	missense	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5126C>T	18.37:g.2772321C>T	ENSP00000326603:p.Ser1709Leu		2762321	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	C	11.39	1.625613	0.28889	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	D;D	0.84298	-1.83;-1.83	5.66	4.78	0.61160	SMCs flexible hinge (1);	0.582255	0.16598	N	0.207443	T	0.67961	0.2949	N	0.16478	0.41	0.27380	N	0.955433	B	0.14438	0.01	B	0.04013	0.001	T	0.58126	-0.7691	10	0.23891	T	0.37	-5.6632	13.7173	0.62705	0.0:0.9251:0.0:0.0749	.	1709	A6NHR9	SMHD1_HUMAN	L	1709	ENSP00000326603:S1709L;ENSP00000261598:S1709L	ENSP00000261598:S1709L	S	+	2	0	SMCHD1	2762321	0.991000	0.36638	1.000000	0.80357	0.987000	0.75469	1.644000	0.37228	1.372000	0.46190	0.563000	0.77884	TCG		0.323	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2772321	C	T	2772321	3	4	61	1	0	0	0	0	1	0	0	0	14825	893	31	1	5288	1	SMCHD1	18	2772321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28415	2772321	75304927	10489	18474										
SMCHD1	23347	broad.mit.edu	37	chr18	2784502	2784502	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagagatggagatcgaattCgaagtaatggaaagtttggg	14	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2784502C>T	ENST00000320876.6	+	45	5940	c.5602C>T	c.(5602-5604)Cga>Tga	p.R1868*	SMCHD1_ENST00000261598.8_Nonsense_Mutation_p.R1868*|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1868					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.R1868*(2)|p.R1316*(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AGATCGAATTCGAAGTAATGG	0.398																																																3	Substitution - Nonsense(3)	large_intestine(3)	18											47	45	46					18																	2784502		1818	4077	5895	2774502	SO:0001587	stop_gained	23347			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5602C>T	18.37:g.2784502C>T	ENSP00000326603:p.Arg1868*		2774502	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	47	13.206972	0.99727	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	.	.	.	5.29	3.37	0.38596	.	0.062950	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.969	13.9592	0.64168	0.284:0.716:0.0:0.0	.	.	.	.	X	1868	.	ENSP00000261598:R1868X	R	+	1	2	SMCHD1	2774502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.898000	0.39809	1.148000	0.42385	0.591000	0.81541	CGA		0.398	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2784502	C	T	2784502	4	4	61	1	0	0	0	0	0	1	0	0	14825	876	31	1	5780	1	SMCHD1	18	2784502	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12181	2784502	75292746	10490	18475										
EMILIN2	84034	broad.mit.edu	37	chr18	2891141	2891141	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catggacagaaagctggctgAcctgaaaaactcatgtgagt	11	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2891141A>T	ENST00000254528.3	+	4	1175	c.1016A>T	c.(1015-1017)gAc>gTc	p.D339V		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	339					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.D339V(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AAGCTGGCTGACCTGAAAAAC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	18											107	110	109					18																	2891141		2203	4300	6503	2881141	SO:0001583	missense	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1016A>T	18.37:g.2891141A>T	ENSP00000254528:p.Asp339Val		2881141	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.274571	0.80580	.	.	ENSG00000132205	ENST00000254528	T	0.37235	1.21	5.41	5.41	0.78517	.	0.140304	0.48286	D	0.000188	T	0.57021	0.2025	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.56595	-0.7953	10	0.40728	T	0.16	-35.5446	15.4491	0.75259	1.0:0.0:0.0:0.0	.	339	Q9BXX0	EMIL2_HUMAN	V	339	ENSP00000254528:D339V	ENSP00000254528:D339V	D	+	2	0	EMILIN2	2881141	1.000000	0.71417	0.907000	0.35723	0.973000	0.67179	8.957000	0.93082	2.039000	0.60335	0.455000	0.32223	GAC		0.527	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891141	A	T	2891141	3	4	61	1	0	0	0	0	1	0	0	0	5107	275	10	5	1030	5	EMILIN2	18	2891141	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	106639	2891141	75186107	10491	18476										
EMILIN2	84034	broad.mit.edu	37	chr18	2891316	2891316	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcccaggcaaattgctgCgacagtgaaaagaatggtga	12	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2891316C>T	ENST00000254528.3	+	4	1350	c.1191C>T	c.(1189-1191)tgC>tgT	p.C397C		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	397					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.C397C(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		CAAATTGCTGCGACAGTGAAA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	18											50	53	52					18																	2891316		2202	4299	6501	2881316	SO:0001819	synonymous_variant	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1191C>T	18.37:g.2891316C>T			2881316	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																				0.478	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891316	C	T	2891316	2	4	61	1	0	0	0	0	0	0	0	1	5107	776	27	1		1	EMILIN2	18	2891316	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	175	2891316	75185932	10492	18477										
EMILIN2	84034	broad.mit.edu	37	chr18	2891551	2891551	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacattgaggaaacccttCggggcgccattaatggagag	12	8	0	2	rs546388595	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2891551C>T	ENST00000254528.3	+	4	1585	c.1426C>T	c.(1426-1428)Cgg>Tgg	p.R476W		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	476					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.R476W(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGAAACCCTTCGGGGCGCCAT	0.463													C|||	3	0.000599042	0	0.0014	5008	,	,		21889	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	18											87	96	93					18																	2891551		2203	4300	6503	2881551	SO:0001583	missense	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1426C>T	18.37:g.2891551C>T	ENSP00000254528:p.Arg476Trp		2881551	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801904	0.50315	.	.	ENSG00000132205	ENST00000254528	T	0.03689	3.84	5.4	4.52	0.55395	.	0.000000	0.64402	D	0.000007	T	0.14614	0.0353	M	0.62723	1.935	0.21527	N	0.999655	D	0.89917	1.0	D	0.76575	0.988	T	0.01935	-1.1244	10	0.54805	T	0.06	-39.8923	13.2759	0.60188	0.2884:0.7116:0.0:0.0	.	476	Q9BXX0	EMIL2_HUMAN	W	476	ENSP00000254528:R476W	ENSP00000254528:R476W	R	+	1	2	EMILIN2	2881551	0.045000	0.20229	0.866000	0.34008	0.642000	0.38348	0.473000	0.22132	1.242000	0.43836	0.563000	0.77884	CGG		0.463	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891551	C	T	2891551	3	4	61	1	0	0	0	0	1	0	0	0	5107	875	31	1	1440	1	EMILIN2	18	2891551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235	2891551	75185697	10493	18478										
EMILIN2	84034	broad.mit.edu	37	chr18	2891956	2891956	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaacaggattttagttttCtttattctcaattaaaccac	3	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2891956C>A	ENST00000254528.3	+	4	1990	c.1831C>A	c.(1831-1833)Ctt>Att	p.L611I		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	611					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.L611I(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		TTTTAGTTTTCTTTATTCTCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	18											49	52	51					18																	2891956		2203	4300	6503	2881956	SO:0001583	missense	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1831C>A	18.37:g.2891956C>A	ENSP00000254528:p.Leu611Ile		2881956	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	C	3.270	-0.149246	0.06585	.	.	ENSG00000132205	ENST00000254528	T	0.21932	1.98	4.9	2.88	0.33553	.	0.512935	0.18951	N	0.126689	T	0.22244	0.0536	L	0.53729	1.69	0.09310	N	1	P	0.51351	0.944	P	0.48770	0.589	T	0.08207	-1.0733	10	0.38643	T	0.18	-17.1997	4.4021	0.11392	0.2338:0.5553:0.1282:0.0827	.	611	Q9BXX0	EMIL2_HUMAN	I	611	ENSP00000254528:L611I	ENSP00000254528:L611I	L	+	1	0	EMILIN2	2881956	0.013000	0.17824	0.047000	0.18901	0.229000	0.25112	0.239000	0.18023	2.268000	0.75426	0.462000	0.41574	CTT		0.408	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		A	2891956	C	A	2891956	3	1	61	1	0	0	0	0	1	0	0	0	5107	913	32	2	1845	2	EMILIN2	18	2891956	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	405	2891956	75185292	10494	18479										
LPIN2	9663	broad.mit.edu	37	chr18	2921588	2921588	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagacggggcaaacagattCttgatatcatttagacactc	8	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:2921588C>A	ENST00000261596.4	-	18	2623	c.2385G>T	c.(2383-2385)aaG>aaT	p.K795N	RP11-737O24.5_ENST00000608032.1_RNA	NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	795	C-LIP.				cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)	p.K795N(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		CAAACAGATTCTTGATATCAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											122	119	120					18																	2921588		2203	4300	6503	2911588	SO:0001583	missense	9663			D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.2385G>T	18.37:g.2921588C>A	ENSP00000261596:p.Lys795Asn		2911588	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562563	0.65538	.	.	ENSG00000101577	ENST00000261596	T	0.77620	-1.11	5.56	3.71	0.42584	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.044645	0.85682	D	0.000000	D	0.84474	0.5480	M	0.80616	2.505	0.58432	D	0.999997	D	0.63046	0.992	D	0.65773	0.938	D	0.83950	0.0316	10	0.59425	D	0.04	.	5.3671	0.16119	0.1434:0.6403:0.0:0.2163	.	795	Q92539	LPIN2_HUMAN	N	795	ENSP00000261596:K795N	ENSP00000261596:K795N	K	-	3	2	LPIN2	2911588	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.763000	0.55257	1.352000	0.45808	0.563000	0.77884	AAG		0.398	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		A	2921588	C	A	2921588	3	1	61	1	0	0	0	0	1	0	0	0	8948	912	32	2	317	2	LPIN2	18	2921588	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29632	2921588	75155660	10495	18480										
MYOM1	8736	broad.mit.edu	37	chr18	3075754	3075754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaattcagcataggcctcatCgtatgctttaaaagaaaaaa	7	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3075754C>T	ENST00000356443.4	-	35	4987	c.4654G>A	c.(4654-4656)Gat>Aat	p.D1552N	MYOM1_ENST00000400569.3_Missense_Mutation_p.D1552N|MYOM1_ENST00000261606.7_Missense_Mutation_p.D1456N	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1552					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.D1552N(2)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TAGGCCTCATCGTATGCTTTA	0.443																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	18											54	54	54					18																	3075754		1868	4102	5970	3065754	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4654G>A	18.37:g.3075754C>T	ENSP00000348821:p.Asp1552Asn		3065754	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.286894	0.59867	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.51071	0.85;0.87;0.72	6.06	6.06	0.98353	.	0.191207	0.56097	D	0.000039	T	0.52757	0.1754	M	0.69823	2.125	0.58432	D	0.999999	P;P	0.37914	0.611;0.477	B;B	0.37346	0.247;0.103	T	0.49351	-0.8949	10	0.33141	T	0.24	.	20.6227	0.99507	0.0:1.0:0.0:0.0	.	1456;1552	P52179-2;P52179	.;MYOM1_HUMAN	N	1552;1552;1456	ENSP00000348821:D1552N;ENSP00000383413:D1552N;ENSP00000261606:D1456N	ENSP00000261606:D1456N	D	-	1	0	MYOM1	3065754	1.000000	0.71417	0.877000	0.34402	0.098000	0.18820	7.577000	0.82486	2.885000	0.99019	0.643000	0.83706	GAT		0.443	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3075754	C	T	3075754	3	4	61	1	0	0	0	0	1	0	0	0	10121	884	31	1	419	1	MYOM1	18	3075754	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	154166	3075754	75001494	10496	18481										
MYOM1	8736	broad.mit.edu	37	chr18	3079256	3079256	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatacttccctttgtcattCggggtgggctcgttgatttg	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3079256C>T	ENST00000356443.4	-	34	4902	c.4569G>A	c.(4567-4569)ccG>ccA	p.P1523P	MYOM1_ENST00000400569.3_Silent_p.P1523P|MYOM1_ENST00000261606.7_Silent_p.P1427P	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1523					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.P1523P(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CTTTGTCATTCGGGGTGGGCT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	18											99	94	95					18																	3079256		1887	4108	5995	3069256	SO:0001819	synonymous_variant	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4569G>A	18.37:g.3079256C>T			3069256	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																				0.473	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3079256	C	T	3079256	2	4	61	1	0	0	0	0	0	0	0	1	10121	871	31	1		1	MYOM1	18	3079256	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3502	3079256	74997992	10497	18482										
MYOM1	8736	broad.mit.edu	37	chr18	3094231	3094231	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcattgccagacagtttCtcagcctgcatccaaaaccg	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3094231C>A	ENST00000356443.4	-	26	4134	c.3801G>T	c.(3799-3801)gaG>gaT	p.E1267D	MYOM1_ENST00000400569.3_Missense_Mutation_p.E1267D|RNU7-25P_ENST00000516544.1_RNA|MYOM1_ENST00000261606.7_Missense_Mutation_p.E1171D	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1267					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.E1267D(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CAGACAGTTTCTCAGCCTGCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	18											70	68	69					18																	3094231		1822	4076	5898	3084231	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3801G>T	18.37:g.3094231C>A	ENSP00000348821:p.Glu1267Asp		3084231	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436877	0.43224	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.04758	3.56;3.56;3.56	5.55	2.58	0.30949	Immunoglobulin-like fold (1);	0.139516	0.64402	D	0.000004	T	0.04998	0.0134	L	0.51914	1.62	0.33459	D	0.584705	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.004	T	0.13953	-1.0490	10	0.23891	T	0.37	.	7.6236	0.28200	0.0:0.6098:0.0:0.3902	.	1171;1267	P52179-2;P52179	.;MYOM1_HUMAN	D	1267;1267;1171	ENSP00000348821:E1267D;ENSP00000383413:E1267D;ENSP00000261606:E1171D	ENSP00000261606:E1171D	E	-	3	2	MYOM1	3084231	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	0.534000	0.23098	0.884000	0.36064	0.655000	0.94253	GAG		0.383	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3094231	C	A	3094231	3	1	61	1	0	0	0	0	1	0	0	0	10121	912	32	2	1308	2	MYOM1	18	3094231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14975	3094231	74983017	10498	18483										
MYOM1	8736	broad.mit.edu	37	chr18	3102540	3102540	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acataatctttggaccaggaGaactcggactttggagtcat	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3102540G>T	ENST00000356443.4	-	23	3840	c.3507C>A	c.(3505-3507)ttC>ttA	p.F1169L	MYOM1_ENST00000400569.3_Missense_Mutation_p.F1169L|MYOM1_ENST00000261606.7_Missense_Mutation_p.F1073L	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1169	Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.F1169L(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TGGACCAGGAGAACTCGGACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											196	191	193					18																	3102540		1899	4120	6019	3092540	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3507C>A	18.37:g.3102540G>T	ENSP00000348821:p.Phe1169Leu		3092540	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892747	0.52121	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.65549	-0.16;-0.16;-0.16	5.46	5.46	0.80206	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	M	0.84585	2.705	0.45108	D	0.998126	P;B	0.43973	0.823;0.19	B;B	0.39904	0.313;0.095	T	0.67225	-0.5724	10	0.31617	T	0.26	.	12.257	0.54629	0.1229:0.0:0.8771:0.0	.	1073;1169	P52179-2;P52179	.;MYOM1_HUMAN	L	1169;1169;1073	ENSP00000348821:F1169L;ENSP00000383413:F1169L;ENSP00000261606:F1073L	ENSP00000261606:F1073L	F	-	3	2	MYOM1	3092540	0.973000	0.33851	0.672000	0.29872	0.817000	0.46193	1.430000	0.34914	2.554000	0.86153	0.557000	0.71058	TTC		0.418	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3102540	G	T	3102540	3	4	61	1	0	0	0	0	1	0	0	0	10121	933	33	2	1614	2	MYOM1	18	3102540	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8309	3102540	74974708	10499	18484										
MYOM1	8736	broad.mit.edu	37	chr18	3126851	3126851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagaaccattgagtcacGaaaactttcaagacaggtga	8	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3126851G>A	ENST00000356443.4	-	19	3172	c.2839C>T	c.(2839-2841)Cgt>Tgt	p.R947C	MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000400569.3_Missense_Mutation_p.R947C|MYOM1_ENST00000261606.7_Missense_Mutation_p.R851C	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	947	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R947C(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ATTGAGTCACGAAAACTTTCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											64	57	59					18																	3126851		1919	4147	6066	3116851	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2839C>T	18.37:g.3126851G>A	ENSP00000348821:p.Arg947Cys		3116851	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359548	0.82353	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.57595	0.39;0.39;0.39	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.051201	0.85682	D	0.000000	T	0.71626	0.3362	M	0.61703	1.905	0.58432	D	0.999993	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.946	T	0.73260	-0.4039	10	0.66056	D	0.02	.	19.3015	0.94145	0.0:0.0:1.0:0.0	.	851;947	P52179-2;P52179	.;MYOM1_HUMAN	C	947;947;851	ENSP00000348821:R947C;ENSP00000383413:R947C;ENSP00000261606:R851C	ENSP00000261606:R851C	R	-	1	0	MYOM1	3116851	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.548000	0.82154	2.559000	0.86315	0.655000	0.94253	CGT		0.423	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3126851	G	A	3126851	3	1	61	1	0	0	0	0	1	0	0	0	10121	1058	37	1	2298	1	MYOM1	18	3126851	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24311	3126851	74950397	10500	18485										
MYL12A	10627	broad.mit.edu	37	chr18	3253332	3253332	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctatgtttgaccagtcacaGattcaggagttcaaagaggc	11	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3253332G>A	ENST00000217652.3	+	2	482	c.87G>A	c.(85-87)caG>caA	p.Q29Q	RP13-270P17.1_ENST00000581905.1_RNA|MYL12A_ENST00000580887.1_Silent_p.Q35Q|RP13-270P17.1_ENST00000578800.1_RNA|MYL12A_ENST00000536605.1_Silent_p.Q29Q|MYL12A_ENST00000578611.1_Silent_p.Q29Q|MYL12A_ENST00000579226.1_Silent_p.Q29Q	NM_006471.2	NP_006462.1	P19105	ML12A_HUMAN	myosin, light chain 12A, regulatory, non-sarcomeric	29	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				platelet aggregation (GO:0070527)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)	extracellular vesicular exosome (GO:0070062)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)	p.Q29Q(1)		NS(1)|kidney(2)|large_intestine(2)	5						ACCAGTCACAGATTCAGGAGT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	18											203	187	192					18																	3253332		2203	4299	6502	3243332	SO:0001819	synonymous_variant	10627			X54304	CCDS11830.1	18p11.31	2013-01-10	2002-08-29		ENSG00000101608	ENSG00000101608		"Myosins / Light chain", "EF-hand domain containing"	16701	protein-coding gene	gene with protein product	"myosin regulatory light chain 3"		"myosin, light polypeptide, regulatory, non-sarcomeric (20kD)"			2216787	Standard	NM_006471		Approved	MLCB, MYL2B, MRLC3, MRCL3	uc002klr.3	P19105	OTTHUMG00000131509	ENST00000217652.3:c.87G>A	18.37:g.3253332G>A			3243332	Q53X45	Silent	SNP	ENST00000217652.3	37	CCDS11830.1																																																																																				0.438	MYL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254364.2	NM_006471		A	3253332	G	A	3253332	2	1	61	1	0	0	0	0	0	0	0	1	10075	933	33	3		3	MYL12A	18	3253332	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	126481	3253332	74823916	10501	18486										
MYL12A	10627	broad.mit.edu	37	chr18	3255808	3255808	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggatcggtttacagatgaGgaagtggatgagctgtacag	17	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:3255808G>A	ENST00000217652.3	+	4	803	c.408G>A	c.(406-408)gaG>gaA	p.E136E	RP13-270P17.1_ENST00000581905.1_RNA|MYL12A_ENST00000580887.1_Silent_p.E142E|RP13-270P17.1_ENST00000578800.1_RNA|MYL12A_ENST00000536605.1_Silent_p.E136E|MYL12A_ENST00000578611.1_Silent_p.E136E|MYL12A_ENST00000579226.1_Silent_p.E136E	NM_006471.2	NP_006462.1	P19105	ML12A_HUMAN	myosin, light chain 12A, regulatory, non-sarcomeric	136	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				platelet aggregation (GO:0070527)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)	extracellular vesicular exosome (GO:0070062)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)	p.E136E(1)		NS(1)|kidney(2)|large_intestine(2)	5						TTACAGATGAGGAAGTGGATG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	18											81	73	76					18																	3255808		2203	4300	6503	3245808	SO:0001819	synonymous_variant	10627			X54304	CCDS11830.1	18p11.31	2013-01-10	2002-08-29		ENSG00000101608	ENSG00000101608		"Myosins / Light chain", "EF-hand domain containing"	16701	protein-coding gene	gene with protein product	"myosin regulatory light chain 3"		"myosin, light polypeptide, regulatory, non-sarcomeric (20kD)"			2216787	Standard	NM_006471		Approved	MLCB, MYL2B, MRLC3, MRCL3	uc002klr.3	P19105	OTTHUMG00000131509	ENST00000217652.3:c.408G>A	18.37:g.3255808G>A			3245808	Q53X45	Silent	SNP	ENST00000217652.3	37	CCDS11830.1																																																																																				0.433	MYL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254364.2	NM_006471		A	3255808	G	A	3255808	2	1	61	1	0	0	0	0	0	0	0	1	10075	991	35	3		3	MYL12A	18	3255808	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2476	3255808	74821440	10502	18487										
EPB41L3	23136	broad.mit.edu	37	chr18	5395673	5395673	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcgtctgtgcactcatcaGcacgcctggctccagatctg	10	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:5395673G>T	ENST00000341928.2	-	20	3347	c.3007C>A	c.(3007-3009)Ctg>Atg	p.L1003M	EPB41L3_ENST00000427684.2_Missense_Mutation_p.L300M|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.L781M|EPB41L3_ENST00000400111.3_Missense_Mutation_p.L781M|EPB41L3_ENST00000544123.1_Missense_Mutation_p.L834M|EPB41L3_ENST00000342933.3_Missense_Mutation_p.L1003M|EPB41L3_ENST00000542146.1_Missense_Mutation_p.L308M	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1003	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.L1003M(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GCACTCATCAGCACGCCTGGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	18											322	247	272					18																	5395673		2203	4300	6503	5385673	SO:0001583	missense	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.3007C>A	18.37:g.5395673G>T	ENSP00000343158:p.Leu1003Met		5385673	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601738	0.66445	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.95	4.98	0.66077	Band 4.1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89473	0.6725	M	0.78456	2.415	0.52501	D	0.999957	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.996;1.0;0.997;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.996;0.999;1.0;0.972;0.999;0.93;1.0;0.997	D	0.88917	0.3363	10	0.54805	T	0.06	.	9.5103	0.39074	0.2184:0.0:0.7816:0.0	.	834;300;308;395;672;781;1003;238	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	M	1003;672;834;672;300;308;1003;781	ENSP00000343158:L1003M;ENSP00000441174:L834M;ENSP00000392195:L300M;ENSP00000442233:L308M;ENSP00000341138:L1003M;ENSP00000382981:L781M	ENSP00000343158:L1003M	L	-	1	2	EPB41L3	5385673	0.933000	0.31639	1.000000	0.80357	0.949000	0.60115	0.823000	0.27366	2.824000	0.97209	0.655000	0.94253	CTG		0.527	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5395673	G	T	5395673	3	4	61	1	0	0	0	0	1	0	0	0	5167	962	34	2	268	2	EPB41L3	18	5395673	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2139865	5395673	72681575	10503	18488										
EPB41L3	23136	broad.mit.edu	37	chr18	5397241	5397241	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttccctttaatgcctgtgAatgcgggctgtgctgcagca	11	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:5397241A>C	ENST00000341928.2	-	18	2997	c.2657T>G	c.(2656-2658)tTc>tGc	p.F886C	EPB41L3_ENST00000427684.2_Missense_Mutation_p.F183C|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.F664C|EPB41L3_ENST00000400111.3_Missense_Mutation_p.F664C|EPB41L3_ENST00000544123.1_Missense_Mutation_p.F717C|EPB41L3_ENST00000342933.3_Missense_Mutation_p.F886C|EPB41L3_ENST00000542146.1_Missense_Mutation_p.F191C	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	886	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.F886C(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						AATGCCTGTGAATGCGGGCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	18											98	84	89					18																	5397241		2203	4300	6503	5387241	SO:0001583	missense	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2657T>G	18.37:g.5397241A>C	ENSP00000343158:p.Phe886Cys		5387241	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	A	4.368	0.067908	0.08436	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	4.65	3.77	0.43336	.	0.762699	0.12317	N	0.479605	T	0.30135	0.0755	N	0.14661	0.345	0.09310	N	1	P;P;P;B;B;B;B;B	0.47604	0.474;0.898;0.733;0.141;0.042;0.341;0.141;0.007	B;B;P;B;B;B;B;B	0.46110	0.313;0.428;0.504;0.17;0.054;0.319;0.212;0.002	T	0.05131	-1.0904	10	0.37606	T	0.19	.	8.6574	0.34071	0.1769:0.0:0.8231:0.0	.	717;183;191;278;555;664;886;121	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	C	886;555;717;555;183;191;886;664	ENSP00000343158:F886C;ENSP00000441174:F717C;ENSP00000392195:F183C;ENSP00000442233:F191C;ENSP00000341138:F886C;ENSP00000382981:F664C	ENSP00000343158:F886C	F	-	2	0	EPB41L3	5387241	0.220000	0.23631	0.001000	0.08648	0.000000	0.00434	3.315000	0.51951	1.164000	0.42652	-0.462000	0.05337	TTC		0.607	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5397241	A	C	5397241	3	2	61	1	0	0	0	0	1	0	0	0	5167	246	9	4	626	4	EPB41L3	18	5397241	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1568	5397241	72680007	10504	18489										
EPB41L3	23136	broad.mit.edu	37	chr18	5428395	5428395	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggcaaatctgtttattcGcagccggtcgcgatatatca	9	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:5428395G>A	ENST00000341928.2	-	9	1322	c.982C>T	c.(982-984)Cga>Tga	p.R328*	EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Nonsense_Mutation_p.R328*|EPB41L3_ENST00000400111.3_Nonsense_Mutation_p.R328*|EPB41L3_ENST00000544123.1_Nonsense_Mutation_p.R328*|EPB41L3_ENST00000342933.3_Nonsense_Mutation_p.R328*	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	328	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.R328*(2)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CTGTTTATTCGCAGCCGGTCG	0.418																																																2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	18											143	146	145					18																	5428395		2203	4300	6503	5418395	SO:0001587	stop_gained	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.982C>T	18.37:g.5428395G>A	ENSP00000343158:p.Arg328*		5418395	B7Z4I5|F5GX05|O95713|Q9BRP5	Nonsense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	40	8.478804	0.98829	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	.	.	.	5.31	3.44	0.39384	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8071	0.63238	0.0:0.0:0.5071:0.4929	.	.	.	.	X	328;219;328;219;328;328	.	ENSP00000343158:R328X	R	-	1	2	EPB41L3	5418395	1.000000	0.71417	0.796000	0.32109	0.981000	0.71138	2.898000	0.48672	0.529000	0.28599	0.655000	0.94253	CGA		0.418	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5428395	G	A	5428395	4	1	61	1	0	0	0	0	0	1	0	0	5167	1095	38	1	2337	1	EPB41L3	18	5428395	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31154	5428395	72648853	10505	18490										
EPB41L3	23136	broad.mit.edu	37	chr18	5478333	5478333	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttaatggagaccgagaGagtttactgctagatgattt	10	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:5478333G>T	ENST00000341928.2	-	3	628	c.288C>A	c.(286-288)ctC>ctA	p.L96L	RP11-286N3.1_ENST00000577527.1_RNA|EPB41L3_ENST00000540638.2_Silent_p.L96L|EPB41L3_ENST00000400111.3_Silent_p.L96L|EPB41L3_ENST00000544123.1_Silent_p.L96L|EPB41L3_ENST00000342933.3_Silent_p.L96L	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	96					apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.L96L(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GAGACCGAGAGAGTTTACTGC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	18											182	165	171					18																	5478333		2203	4300	6503	5468333	SO:0001819	synonymous_variant	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.288C>A	18.37:g.5478333G>T			5468333	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	CCDS11838.1																																																																																				0.413	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5478333	G	T	5478333	2	4	61	1	0	0	0	0	0	0	0	1	5167	929	33	2		2	EPB41L3	18	5478333	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49938	5478333	72598915	10506	18491										
L3MBTL4	91133	broad.mit.edu	37	chr18	6239789	6239789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacaatatctgctatggtcGccacacacaccaaggaaggg	9	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:6239789G>A	ENST00000284898.6	-	9	835	c.635C>T	c.(634-636)gCg>gTg	p.A212V	L3MBTL4_ENST00000535782.1_Missense_Mutation_p.A25V|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.A212V|L3MBTL4_ENST00000400104.3_Missense_Mutation_p.A212V|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.A212V	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	212					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A212V(2)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				TGCTATGGTCGCCACACACAC	0.438																																					Esophageal Squamous(41;748 902 17366 28959 43175)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	18											162	134	143					18																	6239789		2203	4300	6503	6229789	SO:0001583	missense	91133			BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.635C>T	18.37:g.6239789G>A	ENSP00000284898:p.Ala212Val		6229789	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	37	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	G	32	5.161770	0.94727	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000535782;ENST00000400104	T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57	5.35	4.47	0.54385	.	0.000000	0.64402	D	0.000006	D	0.88317	0.6404	H	0.96365	3.81	0.46609	D	0.999122	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.976	D	0.91193	0.4985	10	0.72032	D	0.01	.	13.1434	0.59448	0.0:0.0:0.8386:0.1614	.	212;212	Q8NA19;F8W9S8	LMBL4_HUMAN;.	V	212;212;212;25;212	ENSP00000382976:A212V;ENSP00000318543:A212V;ENSP00000284898:A212V;ENSP00000444774:A25V;ENSP00000382975:A212V	ENSP00000284898:A212V	A	-	2	0	L3MBTL4	6229789	1.000000	0.71417	0.961000	0.40146	0.991000	0.79684	4.264000	0.58859	1.245000	0.43885	0.591000	0.81541	GCG		0.438	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		A	6239789	G	A	6239789	3	1	61	1	0	0	0	0	1	0	0	0	8616	1087	38	1	1284	1	L3MBTL4	18	6239789	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	761456	6239789	71837459	10507	18492										
ARHGAP28	79822	broad.mit.edu	37	chr18	6882238	6882238	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttgaaagcgtttttcagaGaactacccacctctctcttc	6	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:6882238G>T	ENST00000383472.4	+	11	1497	c.1393G>T	c.(1393-1395)Gaa>Taa	p.E465*	ARHGAP28_ENST00000419673.2_Nonsense_Mutation_p.E306*|ARHGAP28_ENST00000532996.1_Nonsense_Mutation_p.E288*|ARHGAP28_ENST00000531294.1_Nonsense_Mutation_p.E301*|ARHGAP28_ENST00000314319.3_Nonsense_Mutation_p.E306*|ARHGAP28_ENST00000418986.1_Nonsense_Mutation_p.E306*|ARHGAP28_ENST00000400091.2_Nonsense_Mutation_p.E465*|ARHGAP28_ENST00000262227.3_Nonsense_Mutation_p.E413*			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	465	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.E465*(1)|p.E306*(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				GTTTTTCAGAGAACTACCCAC	0.383																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											197	184	188					18																	6882238		2203	4300	6503	6872238	SO:0001587	stop_gained	79822			BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"Rho GTPase activating proteins"	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1393G>T	18.37:g.6882238G>T	ENSP00000372964:p.Glu465*		6872238	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Nonsense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	G	37	6.615638	0.97709	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	.	.	.	5.79	5.79	0.91817	.	0.098833	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	20.0313	0.97540	0.0:0.0:1.0:0.0	.	.	.	.	X	465;413;306;301;306;306;297;288	.	ENSP00000262227:E413X	E	+	1	0	ARHGAP28	6872238	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.154000	0.89641	2.746000	0.94184	0.655000	0.94253	GAA		0.383	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		T	6882238	G	T	6882238	4	4	61	1	0	0	0	0	0	1	0	0	877	943	33	2	950	2	ARHGAP28	18	6882238	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	642449	6882238	71195010	10508	18493										
ARHGAP28	79822	broad.mit.edu	37	chr18	6887207	6887207	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacacctcatggtcatggCgctgcctgatgccaacagag	10	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:6887207C>T	ENST00000383472.4	+	12	1609	c.1505C>T	c.(1504-1506)gCg>gTg	p.A502V	ARHGAP28_ENST00000419673.2_Missense_Mutation_p.A343V|ARHGAP28_ENST00000532996.1_Missense_Mutation_p.A325V|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.A338V|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.A343V|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.A343V|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.A502V|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.A450V			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	502	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.A502V(1)|p.A343V(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				ATGGTCATGGCGCTGCCTGAT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	18											151	125	134					18																	6887207		2203	4300	6503	6877207	SO:0001583	missense	79822			BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"Rho GTPase activating proteins"	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1505C>T	18.37:g.6887207C>T	ENSP00000372964:p.Ala502Val		6877207	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	C	16.27	3.075886	0.55646	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17;2.26	5.56	4.57	0.56435	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.372190	0.26307	N	0.025133	T	0.09468	0.0233	N	0.08118	0	0.24613	N	0.993711	B;B;B;B	0.06786	0.001;0.0;0.001;0.001	B;B;B;B	0.10450	0.002;0.002;0.001;0.005	T	0.08513	-1.0718	10	0.46703	T	0.11	.	4.4251	0.11498	0.0:0.703:0.0:0.297	.	502;334;343;450	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	V	502;450;343;338;343;343;334;325	ENSP00000382963:A502V;ENSP00000262227:A450V;ENSP00000392660:A343V;ENSP00000437262:A338V;ENSP00000313506:A343V;ENSP00000406907:A343V;ENSP00000435990:A334V	ENSP00000262227:A450V	A	+	2	0	ARHGAP28	6877207	1.000000	0.71417	0.988000	0.46212	0.993000	0.82548	4.589000	0.61006	2.633000	0.89246	0.478000	0.44815	GCG		0.478	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		T	6887207	C	T	6887207	3	4	61	1	0	0	0	0	1	0	0	0	877	768	27	1	1066	1	ARHGAP28	18	6887207	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4969	6887207	71190041	10509	18494										
LAMA1	284217	broad.mit.edu	37	chr18	6943295	6943295	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgatacggtgtttgcttTtgttagcttgaagagtgtgc	14	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:6943295T>G	ENST00000389658.3	-	62	9044	c.8951A>C	c.(8950-8952)aAa>aCa	p.K2984T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2984	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.K2984T(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTGTTTGCTTTTGTTAGCTTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	18											311	251	271					18																	6943295		2203	4300	6503	6933295	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8951A>C	18.37:g.6943295T>G	ENSP00000374309:p.Lys2984Thr		6933295		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.970280	0.53614	.	.	ENSG00000101680	ENST00000389658	T	0.42131	0.98	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.201214	0.38897	N	0.001524	T	0.60971	0.2310	M	0.64567	1.98	0.40524	D	0.98086	D;D	0.89917	1.0;1.0	D;D	0.83275	0.982;0.996	T	0.63812	-0.6552	10	0.54805	T	0.06	.	13.0814	0.59115	0.0:0.0:0.1334:0.8665	.	2984;314	P25391;B3KSD8	LAMA1_HUMAN;.	T	2984	ENSP00000374309:K2984T	ENSP00000374309:K2984T	K	-	2	0	LAMA1	6933295	1.000000	0.71417	0.982000	0.44146	0.192000	0.23643	5.889000	0.69766	2.187000	0.69744	0.460000	0.39030	AAA		0.483	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6943295	T	G	6943295	3	3	61	1	0	0	0	0	1	0	0	0	8627	1841	64	4	284	4	LAMA1	18	6943295	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	56088	6943295	71133953	10510	18495										
LAMA1	284217	broad.mit.edu	37	chr18	6997744	6997744	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttccagtacctacctgGagatatttagttgtattttc	7	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:6997744G>A	ENST00000389658.3	-	33	4896	c.4803C>T	c.(4801-4803)ctC>ctT	p.L1601L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1601	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.L1601L(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TACCTACCTGGAGATATTTAG	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	18											144	132	136					18																	6997744		2203	4300	6503	6987744	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4803C>T	18.37:g.6997744G>A			6987744		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.423	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	6997744	G	A	6997744	2	1	61	1	0	0	0	0	0	0	0	1	8627	1161	41	3		3	LAMA1	18	6997744	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54449	6997744	71079504	10511	18496										
LAMA1	284217	broad.mit.edu	37	chr18	7014033	7014033	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatgatgagtcgaccccacGagactgcaattgcaggcctg	12	12	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:7014033G>A	ENST00000389658.3	-	23	3237	c.3144C>T	c.(3142-3144)ctC>ctT	p.L1048L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1048	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.L1048L(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TCGACCCCACGAGACTGCAAT	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	18											32	28	29					18																	7014033		2203	4300	6503	7004033	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3144C>T	18.37:g.7014033G>A			7004033		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.483	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7014033	G	A	7014033	2	1	61	1	0	0	0	0	0	0	0	1	8627	1045	37	1		1	LAMA1	18	7014033	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16289	7014033	71063215	10512	18497										
LAMA1	284217	broad.mit.edu	37	chr18	7017280	7017280	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcacatgcatcttaccaaGcactggtcacactgctgtcc	7	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:7017280G>T	ENST00000389658.3	-	20	2898	c.2805C>A	c.(2803-2805)tgC>tgA	p.C935*		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	935	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.C935*(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATCTTACCAAGCACTGGTCAC	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											162	117	132					18																	7017280		2203	4300	6503	7007280	SO:0001587	stop_gained	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2805C>A	18.37:g.7017280G>T	ENSP00000374309:p.Cys935*		7007280		Nonsense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	39	7.848561	0.98522	.	.	ENSG00000101680	ENST00000389658	.	.	.	5.44	1.59	0.23543	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.232	0.48918	0.3943:0.0:0.6057:0.0	.	.	.	.	X	935	.	ENSP00000374309:C935X	C	-	3	2	LAMA1	7007280	0.958000	0.32768	0.972000	0.41901	0.565000	0.35776	0.585000	0.23879	0.034000	0.15491	-0.847000	0.03039	TGC		0.493	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7017280	G	T	7017280	4	4	61	1	0	0	0	0	0	1	0	0	8627	963	34	2	6598	2	LAMA1	18	7017280	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3247	7017280	71059968	10513	18498										
LAMA1	284217	broad.mit.edu	37	chr18	7023203	7023203	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcgtccccatagaacccGtcagcacacctttcacagtg	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:7023203G>A	ENST00000389658.3	-	19	2754	c.2661C>T	c.(2659-2661)gaC>gaT	p.D887D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	887	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.D887D(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CATAGAACCCGTCAGCACACC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	18											94	71	79					18																	7023203		2203	4300	6503	7013203	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2661C>T	18.37:g.7023203G>A			7013203		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.587	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7023203	G	A	7023203	2	1	61	1	0	0	0	0	0	0	0	1	8627	1136	40	1		1	LAMA1	18	7023203	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5923	7023203	71054045	10514	18499										
PTPRM	5797	broad.mit.edu	37	chr18	8085745	8085745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaagagtttcaaagctggGaaatgaaacccattttctgt	10	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:8085745G>A	ENST00000332175.8	+	10	2665	c.1628G>A	c.(1627-1629)gGa>gAa	p.G543E	PTPRM_ENST00000400060.4_Missense_Mutation_p.G543E|PTPRM_ENST00000578571.1_3'UTR|PTPRM_ENST00000400053.4_Missense_Mutation_p.G481E|PTPRM_ENST00000580170.1_Missense_Mutation_p.G543E|PTPRM_ENST00000444013.1_Missense_Mutation_p.G330E	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	543	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G543E(2)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TCAAAGCTGGGAAATGAAACC	0.433																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	18											108	99	102					18																	8085745		2203	4299	6502	8075745	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1628G>A	18.37:g.8085745G>A	ENSP00000331418:p.Gly543Glu		8075745	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454608	0.43634	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.86	5.86	0.93980	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.052746	0.85682	D	0.000000	T	0.62282	0.2415	M	0.80422	2.495	0.54753	D	0.999986	P;P;P	0.49307	0.851;0.922;0.922	P;P;P	0.49085	0.584;0.6;0.6	T	0.62515	-0.6838	10	0.02654	T	1	.	20.1986	0.98248	0.0:0.0:1.0:0.0	.	330;543;543	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	E	543;543;481;330	ENSP00000331418:G543E;ENSP00000382933:G543E;ENSP00000382927:G481E;ENSP00000387608:G330E	ENSP00000331418:G543E	G	+	2	0	PTPRM	8075745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.503000	0.66962	2.781000	0.95711	0.650000	0.86243	GGA		0.433	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	8085745	G	A	8085745	3	1	61	1	0	0	0	0	1	0	0	0	12843	1174	41	3	1666	3	PTPRM	18	8085745	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1062542	8085745	69991503	10515	18500										
PTPRM	5797	broad.mit.edu	37	chr18	8253336	8253336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggcagctccaccccgccaTccgggtggcagacctccttc	11	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:8253336T>C	ENST00000332175.8	+	17	3676	c.2639T>C	c.(2638-2640)aTc>aCc	p.I880T	PTPRM_ENST00000400060.4_Missense_Mutation_p.I894T|PTPRM_ENST00000400053.4_Missense_Mutation_p.I818T|PTPRM_ENST00000580170.1_Missense_Mutation_p.I893T|PTPRM_ENST00000444013.1_Missense_Mutation_p.I667T	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	880					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.I880T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CACCCCGCCATCCGGGTGGCA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	18											42	32	36					18																	8253336		2203	4300	6503	8243336	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2639T>C	18.37:g.8253336T>C	ENSP00000331418:p.Ile880Thr		8243336	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.525484	0.64860	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.55588	0.83;0.84;0.66;0.51	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.73210	0.3558	M	0.77313	2.365	0.80722	D	1	D;D;D	0.69078	0.997;0.985;0.985	D;D;D	0.68765	0.933;0.96;0.96	T	0.76705	-0.2861	10	0.87932	D	0	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	667;893;880	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	T	880;894;818;667	ENSP00000331418:I880T;ENSP00000382933:I894T;ENSP00000382927:I818T;ENSP00000387608:I667T	ENSP00000331418:I880T	I	+	2	0	PTPRM	8243336	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.036000	0.88901	2.317000	0.78254	0.459000	0.35465	ATC		0.602	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			C	8253336	T	C	8253336	3	2	61	1	0	0	0	0	1	0	0	0	12843	1435	50	4	2752	4	PTPRM	18	8253336	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	167591	8253336	69823912	10516	18501										
KIAA0802	23255	broad.mit.edu	37	chr18	8813096	8813096	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagacagtcacagcctggtCatggacctgcgctggcagat	13	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:8813096C>A	ENST00000306329.11	+	10	3681	c.3681C>A	c.(3679-3681)gtC>gtA	p.V1227V	SOGA2_ENST00000306285.7_Silent_p.V261V|SOGA2_ENST00000518815.1_Silent_p.V261V|SOGA2_ENST00000359865.3_Silent_p.V908V|SOGA2_ENST00000517570.1_Silent_p.V867V|SOGA2_ENST00000400050.3_Silent_p.V867V														p.V908V(1)									ACAGCCTGGTCATGGACCTGC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	18											52	50	51					18																	8813096		2203	4300	6503	8803096	SO:0001819	synonymous_variant	23255																														ENST00000306329.11:c.3681C>A	18.37:g.8813096C>A			8803096		Silent	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	C	10.88	1.475881	0.26511	.	.	ENSG00000168502	ENST00000519823	.	.	.	4.96	-1.86	0.07760	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	-25.4183	8.5698	0.33563	0.0:0.3795:0.4009:0.2196	.	.	.	.	N	42	.	.	H	+	1	0	CCDC165	8803096	0.686000	0.27661	0.993000	0.49108	0.991000	0.79684	-0.153000	0.10144	-0.206000	0.10203	0.462000	0.41574	CAT		0.592	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			A	8813096	C	A	8813096	2	1	61	1	0	0	0	0	0	0	0	1	8215	813	29	2		2	KIAA0802	18	8813096	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	559760	8813096	69264152	10517	18502										
ANKRD12	23253	broad.mit.edu	37	chr18	9195585	9195585	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcctacagcaaaactccaAaaattgaacgaagtgatgtg	7	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9195585A>C	ENST00000262126.4	+	3	364	c.124A>C	c.(124-126)Aaa>Caa	p.K42Q	ANKRD12_ENST00000540578.2_3'UTR|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K42Q|ANKRD12_ENST00000383440.2_Missense_Mutation_p.K42Q	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	42						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K42Q(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CAAAACTCCAAAAATTGAACG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	18											67	61	63					18																	9195585		2203	4300	6503	9185585	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.124A>C	18.37:g.9195585A>C	ENSP00000262126:p.Lys42Gln		9185585	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.792671	0.70452	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000540578	T;T;T	0.48201	3.44;0.82;3.44	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.67748	0.2926	M	0.66939	2.045	0.58432	D	0.999999	D;D;D	0.89917	0.993;1.0;0.999	P;D;D	0.85130	0.796;0.997;0.991	T	0.71140	-0.4679	10	0.87932	D	0	-0.8258	15.9507	0.79835	1.0:0.0:0.0:0.0	.	42;42;42	Q6PG48;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	Q	42	ENSP00000372932:K42Q;ENSP00000441510:K42Q;ENSP00000262126:K42Q	ENSP00000262126:K42Q	K	+	1	0	ANKRD12	9185585	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.548000	0.90669	2.178000	0.69098	0.454000	0.30748	AAA		0.328	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9195585	A	C	9195585	3	2	61	1	0	0	0	0	1	0	0	0	640	15	1	4	130	4	ANKRD12	18	9195585	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	382489	9195585	68881663	10518	18503										
ANKRD12	23253	broad.mit.edu	37	chr18	9254422	9254422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattcttaggaaagaacaacGaaaagaaaatgaacctgaag	8	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9254422G>A	ENST00000262126.4	+	9	1397	c.1157G>A	c.(1156-1158)cGa>cAa	p.R386Q	ANKRD12_ENST00000400020.3_Missense_Mutation_p.R363Q|ANKRD12_ENST00000383440.2_Missense_Mutation_p.R363Q	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	386						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R386Q(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AAAGAACAACGAAAAGAAAAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	18											80	86	84					18																	9254422		2203	4300	6503	9244422	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1157G>A	18.37:g.9254422G>A	ENSP00000262126:p.Arg386Gln		9244422	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684659	0.47991	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000359158	T;T	0.05925	3.44;3.37	5.66	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.74881	2.28	0.45097	D	0.998119	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.79108	0.928;0.873;0.992	T	0.00491	-1.1708	10	0.87932	D	0	-7.6776	10.603	0.45377	0.146:0.0:0.854:0.0	.	13;363;386	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	Q	363;363;386;93	ENSP00000372932:R363Q;ENSP00000262126:R386Q	ENSP00000262126:R386Q	R	+	2	0	ANKRD12	9244422	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	4.462000	0.60121	1.397000	0.46682	0.650000	0.86243	CGA		0.323	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9254422	G	A	9254422	3	1	61	1	0	0	0	0	1	0	0	0	640	1058	37	1	1187	1	ANKRD12	18	9254422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58837	9254422	68822826	10519	18504										
ANKRD12	23253	broad.mit.edu	37	chr18	9255570	9255570	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagggaggaaaaaataaaaGatctaaaagaagagagagaa	11	1	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9255570G>A	ENST00000262126.4	+	9	2545	c.2305G>A	c.(2305-2307)Gat>Aat	p.D769N	ANKRD12_ENST00000400020.3_Missense_Mutation_p.D746N|ANKRD12_ENST00000383440.2_Missense_Mutation_p.D746N	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	769						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.D769N(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AAAAATAAAAGATCTAAAAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	18											60	64	63					18																	9255570		2197	4288	6485	9245570	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2305G>A	18.37:g.9255570G>A	ENSP00000262126:p.Asp769Asn		9245570	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.438966	0.63067	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.51071	0.72;0.72	4.9	4.9	0.64082	.	0.062535	0.64402	D	0.000006	T	0.66167	0.2762	M	0.62723	1.935	0.52099	D	0.999944	D;D;D	0.89917	1.0;0.992;0.999	D;P;D	0.74023	0.982;0.747;0.922	T	0.64597	-0.6370	10	0.37606	T	0.19	-26.3635	18.4348	0.90642	0.0:0.0:1.0:0.0	.	396;746;769	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	N	746;769	ENSP00000372932:D746N;ENSP00000262126:D769N	ENSP00000262126:D769N	D	+	1	0	ANKRD12	9245570	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.313000	0.78978	2.421000	0.82119	0.460000	0.39030	GAT		0.353	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9255570	G	A	9255570	3	1	61	1	0	0	0	0	1	0	0	0	640	942	33	3	2335	3	ANKRD12	18	9255570	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1148	9255570	68821678	10520	18505										
ANKRD12	23253	broad.mit.edu	37	chr18	9257187	9257187	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagacctaccatagaagttCgaagatgtagcatgccttct	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9257187C>T	ENST00000262126.4	+	9	4162	c.3922C>T	c.(3922-3924)Cga>Tga	p.R1308*	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Nonsense_Mutation_p.R1285*|ANKRD12_ENST00000383440.2_Nonsense_Mutation_p.R1285*	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1308						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R1308*(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CATAGAAGTTCGAAGATGTAG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											108	104	105					18																	9257187		2203	4300	6503	9247187	SO:0001587	stop_gained	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3922C>T	18.37:g.9257187C>T	ENSP00000262126:p.Arg1308*		9247187	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Nonsense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	43	9.962398	0.99305	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	.	.	.	5.75	2.84	0.33178	.	0.205194	0.33650	N	0.004690	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.661	11.3037	0.49323	0.2642:0.6153:0.1206:0.0	.	.	.	.	X	1285;1308	.	ENSP00000262126:R1308X	R	+	1	2	ANKRD12	9247187	0.996000	0.38824	0.971000	0.41717	0.945000	0.59286	1.105000	0.31086	0.275000	0.22094	0.655000	0.94253	CGA		0.393	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9257187	C	T	9257187	4	4	61	1	0	0	0	0	0	1	0	0	640	876	31	1	3952	1	ANKRD12	18	9257187	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1617	9257187	68820061	10521	18506										
ANKRD12	23253	broad.mit.edu	37	chr18	9258721	9258721	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctggcagccattgtagattCtctaaaactagatgagattc	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9258721C>T	ENST00000262126.4	+	9	5696	c.5456C>T	c.(5455-5457)tCt>tTt	p.S1819F	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.S1796F|ANKRD12_ENST00000383440.2_Missense_Mutation_p.S1796F	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1819						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S1819F(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ATTGTAGATTCTCTAAAACTA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	18											55	58	57					18																	9258721		2203	4299	6502	9248721	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5456C>T	18.37:g.9258721C>T	ENSP00000262126:p.Ser1819Phe		9248721	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556385	0.86231	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.57595	0.39;0.39	5.33	5.33	0.75918	.	0.181703	0.49916	D	0.000136	T	0.64907	0.2641	L	0.38175	1.15	0.80722	D	1	D;D	0.76494	0.999;0.996	D;P	0.67548	0.952;0.853	T	0.67425	-0.5674	10	0.87932	D	0	-8.9499	19.3868	0.94560	0.0:1.0:0.0:0.0	.	1796;1819	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	F	1796;1819	ENSP00000372932:S1796F;ENSP00000262126:S1819F	ENSP00000262126:S1819F	S	+	2	0	ANKRD12	9248721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.650000	0.89964	0.655000	0.94253	TCT		0.378	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9258721	C	T	9258721	3	4	61	1	0	0	0	0	1	0	0	0	640	913	32	3	5486	3	ANKRD12	18	9258721	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1534	9258721	68818527	10522	18507										
ANKRD12	23253	broad.mit.edu	37	chr18	9258888	9258888	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacatttaacggatcatatCtcctggatggaaacccctta	6	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9258888C>A	ENST00000262126.4	+	9	5863	c.5623C>A	c.(5623-5625)Ctc>Atc	p.L1875I	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.L1852I|ANKRD12_ENST00000383440.2_Missense_Mutation_p.L1852I	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1875						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L1875I(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CGGATCATATCTCCTGGATGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	18											100	97	98					18																	9258888		2201	4299	6500	9248888	SO:0001583	missense	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5623C>A	18.37:g.9258888C>A	ENSP00000262126:p.Leu1875Ile		9248888	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.455258	0.84209	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.70631	-0.5;-0.5	5.44	5.44	0.79542	.	0.072465	0.64402	D	0.000020	D	0.84302	0.5442	M	0.72894	2.215	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	D;D	0.83275	0.996;0.991	D	0.85196	0.1012	10	0.72032	D	0.01	-5.1253	19.6223	0.95663	0.0:1.0:0.0:0.0	.	1852;1875	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	I	1852;1875	ENSP00000372932:L1852I;ENSP00000262126:L1875I	ENSP00000262126:L1875I	L	+	1	0	ANKRD12	9248888	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.781000	0.62389	2.707000	0.92482	0.655000	0.94253	CTC		0.368	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9258888	C	A	9258888	3	1	61	1	0	0	0	0	1	0	0	0	640	913	32	2	5653	2	ANKRD12	18	9258888	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	167	9258888	68818360	10523	18508										
TWSG1	57045	broad.mit.edu	37	chr18	9396447	9396447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaactttcacatcatgaGaatctggtttcatttttaga	7	6	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:9396447G>T	ENST00000262120.5	+	4	584	c.393G>T	c.(391-393)gaG>gaT	p.E131D	TWSG1_ENST00000581641.1_Missense_Mutation_p.E131D	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	131					BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.E131E(1)|p.E131D(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						CACATCATGAGAATCTGGTTT	0.448																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	18											107	102	104					18																	9396447		2203	4300	6503	9386447	SO:0001583	missense	57045			AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"twisted gastrulation homolog 1 (Drosophila)"			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.393G>T	18.37:g.9396447G>T	ENSP00000262120:p.Glu131Asp		9386447	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	37	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903746	0.52333	.	.	ENSG00000128791	ENST00000262120	.	.	.	5.33	2.53	0.30540	.	0.045811	0.85682	D	0.000000	T	0.40815	0.1132	L	0.35414	1.06	0.51482	D	0.999925	P	0.43578	0.811	B	0.43575	0.424	T	0.10109	-1.0644	9	0.30854	T	0.27	-28.5239	8.7285	0.34485	0.2488:0.0:0.7512:0.0	.	131	Q9GZX9	TWSG1_HUMAN	D	131	.	ENSP00000262120:E131D	E	+	3	2	TWSG1	9386447	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.832000	0.39151	0.623000	0.30267	0.561000	0.74099	GAG		0.448	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2			T	9396447	G	T	9396447	3	4	61	1	0	0	0	0	1	0	0	0	16825	933	33	2	403	2	TWSG1	18	9396447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137559	9396447	68680801	10524	18509										
APCDD1	147495	broad.mit.edu	37	chr18	10471810	10471810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacatgcccgggcttcctcGcagacgggggtccctgggtg	16	14	0	1	rs115383241		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:10471810G>A	ENST00000355285.5	+	3	880	c.526G>A	c.(526-528)Gca>Aca	p.A176T	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1									p.A176T(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GGGCTTCCTCGCAGACGGGGG	0.632													G|||	1	0.000199681	0	0	5008	,	,		15713	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18						G	THR/ALA	0,4406		0,0,2203	75	79	78		526	3.4	0	18	dbSNP_132	78	1,8599	1.2+/-3.3	0,1,4299	no	missense	APCDD1	NM_153000.4	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	176/515	10471810	1,13005	2203	4300	6503	10461810	SO:0001583	missense	147495			AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.526G>A	18.37:g.10471810G>A	ENSP00000347433:p.Ala176Thr		10461810		Missense_Mutation	SNP	ENST00000355285.5	37	CCDS11849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.35	1.325441	0.24080	0.0	1.16E-4	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.16196	2.36	5.3	3.41	0.39046	.	0.443695	0.26474	N	0.024168	T	0.07098	0.0180	N	0.08118	0	0.18873	N	0.999984	B	0.21381	0.055	B	0.15052	0.012	T	0.23976	-1.0173	10	0.33141	T	0.24	-14.6555	4.5317	0.12008	0.1185:0.5571:0.2297:0.0947	.	176	Q8J025	APCD1_HUMAN	T	176;227	ENSP00000347433:A176T	ENSP00000347433:A176T	A	+	1	0	APCDD1	10461810	0.545000	0.26449	0.002000	0.10522	0.006000	0.05464	1.941000	0.40233	1.241000	0.43820	0.655000	0.94253	GCA		0.632	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10471810	G	A	10471810	3	1	61	1	0	0	0	0	1	0	0	0	765	1087	38	1	536	1	APCDD1	18	10471810	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1075363	10471810	67605438	10525	18510										
GNAL	2774	broad.mit.edu	37	chr18	11872310	11872310	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgttcttgaacaaacaaGatatgctggcagaaaaagtc	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:11872310G>T	ENST00000423027.3	+	10	1165	c.844G>T	c.(844-846)Gat>Tat	p.D282Y	GNAL_ENST00000535121.1_Missense_Mutation_p.D282Y|GNAL_ENST00000269162.5_Missense_Mutation_p.D282Y|GNAL_ENST00000334049.6_Missense_Mutation_p.D359Y|GNAL_ENST00000602628.1_Missense_Mutation_p.D75Y			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	282					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.D359Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						GAACAAACAAGATATGCTGGC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											111	115	113					18																	11872310		2203	4298	6501	11862310	SO:0001583	missense	2774			AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.844G>T	18.37:g.11872310G>T	ENSP00000408489:p.Asp282Tyr		11862310	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	37	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.563582	0.86335	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027;ENST00000535980	D;D;D;D	0.96856	-4.15;-4.15;-4.15;-4.15	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.99083	0.9685	H	0.98786	4.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.98956	1.0796	10	0.87932	D	0	.	19.5608	0.95371	0.0:0.0:1.0:0.0	.	282;359	P38405;Q86XU3	GNAL_HUMAN;.	Y	221;359;282;282;282;75	ENSP00000334051:D359Y;ENSP00000439023:D282Y;ENSP00000269162:D282Y;ENSP00000408489:D282Y	ENSP00000269162:D282Y	D	+	1	0	GNAL	11862310	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.420000	0.97426	2.698000	0.92095	0.561000	0.74099	GAT		0.338	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071		T	11872310	G	T	11872310	3	4	61	1	0	0	0	0	1	0	0	0	6527	942	33	2	1262	2	GNAL	18	11872310	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1400500	11872310	66204938	10526	18511										
SPIRE1	56907	broad.mit.edu	37	chr18	12449837	12449837	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccagtcctccatcaactCtttgggaaactggagttctt	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:12449837C>A	ENST00000409402.4	-	17	2338	c.2071G>T	c.(2071-2073)Gag>Tag	p.E691*	SPIRE1_ENST00000309836.5_Nonsense_Mutation_p.E480*|RP11-861E21.2_ENST00000589795.1_RNA|SPIRE1_ENST00000453447.2_Nonsense_Mutation_p.E557*|RP11-861E21.2_ENST00000588197.1_RNA|SPIRE1_ENST00000464481.1_5'UTR|SPIRE1_ENST00000410092.3_Nonsense_Mutation_p.E677*	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1									p.E518*(1)|p.E691*(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						TCCATCAACTCTTTGGGAAAC	0.458																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											97	93	95					18																	12449837		2203	4300	6503	12439837	SO:0001587	stop_gained	56907			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.2071G>T	18.37:g.12449837C>A	ENSP00000387266:p.Glu691*		12439837		Nonsense_Mutation	SNP	ENST00000409402.4	37	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	C	40	8.470239	0.98825	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836	.	.	.	5.72	5.72	0.89469	.	0.094583	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-6.0999	19.8965	0.96963	0.0:1.0:0.0:0.0	.	.	.	.	X	557;691;677;480	.	ENSP00000309661:E480X	E	-	1	0	SPIRE1	12439837	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.519000	0.67074	2.717000	0.92951	0.655000	0.94253	GAG		0.458	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		A	12449837	C	A	12449837	4	1	61	1	0	0	0	0	0	1	0	0	15110	922	32	2	203	2	SPIRE1	18	12449837	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	577527	12449837	65627411	10527	18512										
CEP76	79959	broad.mit.edu	37	chr18	12678336	12678336	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggttgacaatttcccagGaacatctgatggttgaaaac	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:12678336G>T	ENST00000262127.2	-	10	1620	c.1395C>A	c.(1393-1395)ttC>ttA	p.F465L	PSMG2_ENST00000585331.2_Intron|PSMG2_ENST00000589405.1_Intron|CEP76_ENST00000423709.2_Missense_Mutation_p.F390L	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	465					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)		p.F465L(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AATTTCCCAGGAACATCTGAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											181	172	175					18																	12678336		2203	4300	6503	12668336	SO:0001583	missense	79959			BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.1395C>A	18.37:g.12678336G>T	ENSP00000262127:p.Phe465Leu		12668336	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	37	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999047	0.74818	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	T;T	0.31510	1.49;1.49	5.6	2.41	0.29592	.	0.092545	0.85682	D	0.000000	T	0.50667	0.1629	M	0.82823	2.61	0.52099	D	0.999947	D;D	0.76494	0.976;0.999	P;D	0.69654	0.797;0.965	T	0.49995	-0.8879	10	0.22706	T	0.39	1.146	9.5958	0.39573	0.368:0.0:0.632:0.0	.	390;465	Q8TAP6-2;Q8TAP6	.;CEP76_HUMAN	L	465;390	ENSP00000262127:F465L;ENSP00000403074:F390L	ENSP00000262127:F465L	F	-	3	2	CEP76	12668336	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.454000	0.35178	0.731000	0.32448	0.561000	0.74099	TTC		0.418	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		T	12678336	G	T	12678336	3	4	61	1	0	0	0	0	1	0	0	0	3267	1165	41	2	596	2	CEP76	18	12678336	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	228499	12678336	65398912	10528	18513										
CEP76	79959	broad.mit.edu	37	chr18	12691450	12691450	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatatacaagaaataatcGctctttctctgcagttttct	5	9	3	1	rs202106348		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:12691450G>A	ENST00000262127.2	-	7	1066	c.841C>T	c.(841-843)Cga>Tga	p.R281*	PSMG2_ENST00000585331.2_Intron|CEP76_ENST00000423709.2_Nonsense_Mutation_p.R206*	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	281					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)		p.R281*(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AGAAATAATCGCTCTTTCTCT	0.323													G|||	1	0.000199681	8e-04	0	5008	,	,		15797	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	18											92	92	92					18																	12691450		2203	4300	6503	12681450	SO:0001587	stop_gained	79959			BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.841C>T	18.37:g.12691450G>A	ENSP00000262127:p.Arg281*		12681450	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Nonsense_Mutation	SNP	ENST00000262127.2	37	CCDS11861.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	38	6.869888	0.97901	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1647	14.6031	0.68456	0.0:0.0:0.8541:0.1459	.	.	.	.	X	281;206	.	ENSP00000262127:R281X	R	-	1	2	CEP76	12681450	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	2.938000	0.48987	2.749000	0.94314	0.460000	0.39030	CGA		0.323	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		A	12691450	G	A	12691450	4	1	61	1	0	0	0	0	0	1	0	0	3267	1095	38	1	1162	1	CEP76	18	12691450	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13114	12691450	65385798	10529	18514										
CEP76	79959	broad.mit.edu	37	chr18	12701061	12701061	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttgatcaggtgccaattCttcccgtatagtctcagcaa	8	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:12701061C>T	ENST00000262127.2	-	2	340	c.115G>A	c.(115-117)Gaa>Aaa	p.E39K	PSMG2_ENST00000585331.2_Intron|PSMG2_ENST00000317615.6_5'Flank|PSMG2_ENST00000590217.1_5'Flank|CEP76_ENST00000423709.2_Missense_Mutation_p.E39K|CEP76_ENST00000586887.1_5'UTR	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	39					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)		p.E39K(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTGCCAATTCTTCCCGTATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	18											141	126	131					18																	12701061		2203	4300	6503	12691061	SO:0001583	missense	79959			BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.115G>A	18.37:g.12701061C>T	ENSP00000262127:p.Glu39Lys		12691061	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	37	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166446	0.78339	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	T;D	0.81996	-1.3;-1.56	5.29	5.29	0.74685	.	0.150219	0.64402	D	0.000018	D	0.87716	0.6247	L	0.40543	1.245	0.35452	D	0.795769	D;P;P	0.67145	0.996;0.557;0.557	D;B;B	0.77557	0.99;0.366;0.124	D	0.88937	0.3377	10	0.35671	T	0.21	0.0015	18.923	0.92532	0.0:1.0:0.0:0.0	.	39;39;39	B4DP81;Q8TAP6-2;Q8TAP6	.;.;CEP76_HUMAN	K	39	ENSP00000262127:E39K;ENSP00000403074:E39K	ENSP00000262127:E39K	E	-	1	0	CEP76	12691061	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.484000	0.81180	2.456000	0.83038	0.557000	0.71058	GAA		0.358	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		T	12701061	C	T	12701061	3	4	61	1	0	0	0	0	1	0	0	0	3267	922	32	3	1908	3	CEP76	18	12701061	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9611	12701061	65376187	10530	18515										
PTPN2	5771	broad.mit.edu	37	chr18	12859247	12859247	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtcatgggactcatttcGaatttccttaaaataacaaa	5	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:12859247G>A	ENST00000309660.5	-	2	169	c.76C>T	c.(76-78)Cga>Tga	p.R26*	PTPN2_ENST00000589086.1_5'UTR|PTPN2_ENST00000353319.4_Nonsense_Mutation_p.R26*|PTPN2_ENST00000327283.3_Nonsense_Mutation_p.R26*|PTPN2_ENST00000591115.1_Nonsense_Mutation_p.R26*	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	26	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)	p.R26*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				GACTCATTTCGAATTTCCtta	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											88	73	78					18																	12859247		2203	4300	6503	12849247	SO:0001587	stop_gained	5771			M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.76C>T	18.37:g.12859247G>A	ENSP00000311857:p.Arg26*		12849247	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Nonsense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	.	.	.	.	.	.	.	.	.	.	G	36	5.771191	0.96922	.	.	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000309660	.	.	.	5.41	5.41	0.78517	.	0.000000	0.44902	D	0.000418	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1145	0.81295	0.0:0.0:1.0:0.0	.	.	.	.	X	26	.	ENSP00000311857:R26X	R	-	1	2	PTPN2	12849247	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.110000	0.57831	2.532000	0.85374	0.591000	0.81541	CGA		0.358	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423		A	12859247	G	A	12859247	4	1	61	1	0	0	0	0	0	1	0	0	12820	1066	37	1	1229	1	PTPN2	18	12859247	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	158186	12859247	65218001	10531	18516										
CEP192	55125	broad.mit.edu	37	chr18	13071155	13071155	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgcttagatattccatcGattttgtccaacaaacaatt	4	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13071155G>A	ENST00000325971.8	+	26	5097	c.3504G>A	c.(3502-3504)tcG>tcA	p.S1168S	CEP192_ENST00000430049.2_Silent_p.S1289S|CEP192_ENST00000506447.1_Silent_p.S1764S			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1168					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.S1168S(1)|p.S1764S(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ATATTCCATCGATTTTGTCCA	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	18											100	101	101					18																	13071155		2203	4300	6503	13061155	SO:0001819	synonymous_variant	55125			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3504G>A	18.37:g.13071155G>A			13061155	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																					0.418	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		A	13071155	G	A	13071155	2	1	61	1	0	0	0	0	0	0	0	1	3257	1045	37	1		1	CEP192	18	13071155	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211908	13071155	65006093	10532	18517										
C18orf19	125228	broad.mit.edu	37	chr18	13681703	13681703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctaaatgtcttcttgaatCgttgataaagactaatagat	7	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13681703C>T	ENST00000322247.3	-	3	761	c.374G>A	c.(373-375)cGa>cAa	p.R125Q	FAM210A_ENST00000588475.1_5'UTR|FAM210A_ENST00000402563.1_Missense_Mutation_p.R125Q	NM_001098801.1	NP_001092271.1	Q96ND0	F210A_HUMAN	family with sequence similarity 210, member A	125	DUF1279.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.R125Q(1)									CTTCTTGAATCGTTGATAAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	18											113	114	114					18																	13681703		2203	4300	6503	13671703	SO:0001583	missense	125228			AK055618	CCDS11866.1	18p11.21	2011-11-24	2011-11-24	2011-11-24	ENSG00000177150	ENSG00000177150			28346	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 19"	C18orf19		14702039	Standard	NM_152352		Approved	MGC24180, HsT2329	uc010dli.3	Q96ND0	OTTHUMG00000131719	ENST00000322247.3:c.374G>A	18.37:g.13681703C>T	ENSP00000323635:p.Arg125Gln		13671703	D3DUJ4	Missense_Mutation	SNP	ENST00000322247.3	37	CCDS11866.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.882033	0.91740	.	.	ENSG00000177150	ENST00000322247;ENST00000402563	T;T	0.34072	1.38;1.38	5.51	4.64	0.57946	Domain of unknown function DUF1279 (1);	0.000000	0.85682	D	0.000000	T	0.33030	0.0849	L	0.46741	1.465	0.58432	D	0.999999	P	0.51351	0.944	B	0.40825	0.341	T	0.11012	-1.0605	10	0.44086	T	0.13	-12.8084	14.4261	0.67218	0.0:0.9289:0.0:0.0711	.	125	Q96ND0	CR019_HUMAN	Q	125	ENSP00000323635:R125Q;ENSP00000386115:R125Q	ENSP00000323635:R125Q	R	-	2	0	C18orf19	13671703	1.000000	0.71417	0.980000	0.43619	0.939000	0.58152	7.702000	0.84576	1.316000	0.45131	0.655000	0.94253	CGA		0.393	FAM210A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254637.1	NM_152352		T	13681703	C	T	13681703	3	4	61	1	0	0	0	0	1	0	0	0	1902	884	31	1	456	1	C18orf19	18	13681703	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	610548	13681703	64395545	10533	18518										
MC2R	4158	broad.mit.edu	37	chr18	13884645	13884645	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccagtacctgctgcagaaGatcatctttttgaatgcgtc	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13884645G>T	ENST00000327606.3	-	2	1053	c.873C>A	c.(871-873)atC>atA	p.I291I		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	291					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.I291I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	TGCTGCAGAAGATCATCTTTT	0.478																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - coding silent(1)	large_intestine(1)	18											119	115	116					18																	13884645		2203	4300	6503	13874645	SO:0001819	synonymous_variant	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.873C>A	18.37:g.13884645G>T			13874645	A8K016|Q3MI45|Q504X6	Silent	SNP	ENST00000327606.3	37	CCDS11869.1																																																																																				0.478	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			T	13884645	G	T	13884645	2	4	61	1	0	0	0	0	0	0	0	1	9394	932	33	2		2	MC2R	18	13884645	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202942	13884645	64192603	10534	18519										
MC2R	4158	broad.mit.edu	37	chr18	13884719	13884719	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggtcaatgacggcattgcAcatgatcaacatgccgttca	11	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13884719A>G	ENST00000327606.3	-	2	979	c.799T>C	c.(799-801)Tgc>Cgc	p.C267R		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	267					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.C267R(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	ACGGCATTGCACATGATCAAC	0.507																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - Missense(1)	large_intestine(1)	18											116	106	109					18																	13884719		2203	4300	6503	13874719	SO:0001583	missense	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.799T>C	18.37:g.13884719A>G	ENSP00000333821:p.Cys267Arg		13874719	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	37	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097851	0.56075	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T	0.37584	1.19	5.06	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.048698	0.85682	D	0.000000	T	0.63283	0.2498	M	0.87381	2.88	0.80722	D	1	D	0.67145	0.996	D	0.64595	0.927	T	0.71629	-0.4535	10	0.87932	D	0	.	14.81	0.69989	1.0:0.0:0.0:0.0	.	267	Q01718	ACTHR_HUMAN	R	267	ENSP00000333821:C267R	ENSP00000333821:C267R	C	-	1	0	MC2R	13874719	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.363000	0.52321	1.904000	0.55121	0.533000	0.62120	TGC		0.507	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			G	13884719	A	G	13884719	3	3	61	1	0	0	0	0	1	0	0	0	9394	159	6	4	98	4	MC2R	18	13884719	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	74	13884719	64192529	10535	18520										
MC2R	4158	broad.mit.edu	37	chr18	13885140	13885140	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatggtgatgtagcggtcCgcagcaatcacagacaggct	13	9	1	3	rs145345722		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13885140C>T	ENST00000327606.3	-	2	558	c.378G>A	c.(376-378)gcG>gcA	p.A126A		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	126					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.A126A(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	TGTAGCGGTCCGCAGCAATCA	0.572																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - coding silent(1)	large_intestine(1)	18						G		1,4405		0,1,2202	111	79	90		378	-3.6	0	18	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous	MC2R	NM_000529.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		126/298	13885140	1,13005	2203	4300	6503	13875140	SO:0001819	synonymous_variant	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.378G>A	18.37:g.13885140C>T			13875140	A8K016|Q3MI45|Q504X6	Silent	SNP	ENST00000327606.3	37	CCDS11869.1																																																																																				0.572	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			T	13885140	C	T	13885140	2	4	61	1	0	0	0	0	0	0	0	1	9394	639	23	1		1	MC2R	18	13885140	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	421	13885140	64192108	10536	18521										
MC2R	4158	broad.mit.edu	37	chr18	13885386	13885386	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaacacagccagcaggacGatcagattctccaaaactcc	7	13	2	2	rs369691563		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13885386G>A	ENST00000327606.3	-	2	312	c.132C>T	c.(130-132)atC>atT	p.I44I		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	44					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.I44I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	CCAGCAGGACGATCAGATTCT	0.428																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - coding silent(1)	large_intestine(1)	18	GRCh37	CM950791	MC2R	M		G		0,4406		0,0,2203	104	94	97		132	-8.3	0.2	18		97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MC2R	NM_000529.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		44/298	13885386	1,13005	2203	4300	6503	13875386	SO:0001819	synonymous_variant	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.132C>T	18.37:g.13885386G>A			13875386	A8K016|Q3MI45|Q504X6	Silent	SNP	ENST00000327606.3	37	CCDS11869.1																																																																																				0.428	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			A	13885386	G	A	13885386	2	1	61	1	0	0	0	0	0	0	0	1	9394	1048	37	1		1	MC2R	18	13885386	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	246	13885386	64191862	10537	18522										
MC2R	4158	broad.mit.edu	37	chr18	13885451	13885451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctccggcaaaaccacacGaggacagtcggaattatttc	8	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:13885451G>A	ENST00000327606.3	-	2	247	c.67C>T	c.(67-69)Cgt>Tgt	p.R23C		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	23					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.R23C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	AAAACCACACGAGGACAGTCG	0.418																																					Colon(141;1584 1782 35999 48227 48692)											1	Substitution - Missense(1)	large_intestine(1)	18											194	163	174					18																	13885451		2203	4300	6503	13875451	SO:0001583	missense	4158				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.67C>T	18.37:g.13885451G>A	ENSP00000333821:p.Arg23Cys		13875451	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	37	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	G	9.788	1.177064	0.21787	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T;D	0.84660	0.29;-1.88	4.39	1.49	0.22878	.	1.694500	0.03073	N	0.157497	T	0.71316	0.3325	N	0.08118	0	0.09310	N	1	B	0.30281	0.275	B	0.30855	0.121	T	0.64360	-0.6426	10	0.87932	D	0	.	2.6099	0.04888	0.164:0.1471:0.5372:0.1517	.	23	Q01718	ACTHR_HUMAN	C	23	ENSP00000333821:R23C;ENSP00000382718:R23C	ENSP00000333821:R23C	R	-	1	0	MC2R	13875451	0.001000	0.12720	0.391000	0.26233	0.304000	0.27724	1.041000	0.30291	0.403000	0.25479	0.650000	0.86243	CGT		0.418	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			A	13885451	G	A	13885451	3	1	61	1	0	0	0	0	1	0	0	0	9394	1058	37	1	830	1	MC2R	18	13885451	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	65	13885451	64191797	10538	18523										
ZNF519	162655	broad.mit.edu	37	chr18	14105352	14105352	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgcattCtctgatgctgagtaacgtat	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:14105352C>A	ENST00000590202.1	-	3	1339	c.1187G>T	c.(1186-1188)aGa>aTa	p.R396I	ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	396					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R396I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AGTATGCATTCTCTGATGCTG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											105	106	106					18																	14105352		2203	4300	6503	14095352	SO:0001583	missense	162655			BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1187G>T	18.37:g.14105352C>A	ENSP00000464872:p.Arg396Ile		14095352		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.489918	0.26686	.	.	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39306	0.1073	L	0.52759	1.655	0.42764	D	0.993815	P	0.48162	0.906	B	0.39419	0.299	T	0.24870	-1.0148	8	0.30078	T	0.28	.	7.2226	0.25997	0.0:0.9999:0.0:1.0E-4	.	396	Q8TB69	ZN519_HUMAN	I	396	.	ENSP00000307908:R396I	R	-	2	0	ZNF519	14095352	0.000000	0.05858	0.768000	0.31515	0.513000	0.34164	-0.739000	0.04866	0.661000	0.30985	0.089000	0.15464	AGA		0.418	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		A	14105352	C	A	14105352	3	1	61	1	0	0	0	0	1	0	0	0	18003	913	32	2	439	2	ZNF519	18	14105352	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	219901	14105352	63971896	10539	18524										
ZNF519	162655	broad.mit.edu	37	chr18	14106001	14106002	+	Missense_Mutation	DNP	AG	AG	CT													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattcattacaattgtaatAgttttctagaaaatgagtac							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:14106001_14106002AG>CT	ENST00000590202.1	-	3	689_690	c.537_538CT>AG	c.(535-540)aaCTat>aaAGat	p.179_180NY>KD	ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	179					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N179>?(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						CAATTGTAATAGTTTTCTAGAA	0.243																																																1	Complex(1)	large_intestine(1)	18																																								14096002	SO:0001583	missense	162655			BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.537_538delinsCT	18.37:g.14106001_14106002delinsCT	ENSP00000464872:p.N179_Y180delinsKD		14096001		Missense_Mutation	DNP	ENST00000590202.1	37	CCDS32797.1																																																																																				0.243	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		CT	14106002	AG	CT	14106001	3	2	61	1	0	0	0	0	1	0	0	0	18003	420	15	4	1088	4	ZNF519	18	14106001	Missense_Mutation	DNP	AG	TCGA-AG-A002-01A-01W-A00K-09	649	14106001	63971247	10540	18525										
ROCK1	6093	broad.mit.edu	37	chr18	18547870	18547870	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcaattttaaaatcttttCgattcattatttctgccaat	2	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:18547870C>T	ENST00000399799.2	-	26	3975	c.3035G>A	c.(3034-3036)cGa>cAa	p.R1012Q		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1012					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R1012Q(2)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					AAAATCTTTTCGATTCATTAT	0.264																																																2	Substitution - Missense(2)	large_intestine(2)	18											65	63	64					18																	18547870		2203	4300	6503	16801868	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3035G>A	18.37:g.18547870C>T	ENSP00000382697:p.Arg1012Gln		16801868	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	32	5.181034	0.94846	.	.	ENSG00000067900	ENST00000399799	T	0.14022	2.54	5.29	4.42	0.53409	Rho Binding (2);	0.000000	0.85682	D	0.000000	T	0.40423	0.1116	M	0.82193	2.58	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.42649	-0.9439	10	0.72032	D	0.01	.	13.8132	0.63276	0.0:0.9263:0.0:0.0737	.	1012	Q13464	ROCK1_HUMAN	Q	1012	ENSP00000382697:R1012Q	ENSP00000382697:R1012Q	R	-	2	0	ROCK1	16801868	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	7.818000	0.86416	1.230000	0.43646	0.585000	0.79938	CGA		0.264	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		T	18547870	C	T	18547870	3	4	61	1	0	0	0	0	1	0	0	0	13554	884	31	1	1061	1	ROCK1	18	18547870	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4441869	18547870	59529378	10541	18526										
ROCK1	6093	broad.mit.edu	37	chr18	18550366	18550366	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatttcttgaagcagctttCttgctttcttgcgtcaattc	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:18550366C>A	ENST00000399799.2	-	23	3703	c.2763G>T	c.(2761-2763)aaG>aaT	p.K921N		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	921	Glu-rich.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K921N(2)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					AAGCAGCTTTCTTGCTTTCTT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	18											193	173	180					18																	18550366		2203	4300	6503	16804364	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.2763G>T	18.37:g.18550366C>A	ENSP00000382697:p.Lys921Asn		16804364	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911119	0.72983	.	.	ENSG00000067900	ENST00000399799	T	0.14144	2.53	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.19366	0.0465	M	0.75615	2.305	0.58432	D	0.999998	P	0.45986	0.87	B	0.43194	0.411	T	0.00766	-1.1575	10	0.66056	D	0.02	.	9.0101	0.36135	0.0:0.8339:0.0:0.1661	.	921	Q13464	ROCK1_HUMAN	N	921	ENSP00000382697:K921N	ENSP00000382697:K921N	K	-	3	2	ROCK1	16804364	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.399000	0.44495	2.663000	0.90544	0.563000	0.77884	AAG		0.378	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		A	18550366	C	A	18550366	3	1	61	1	0	0	0	0	1	0	0	0	13554	912	32	2	1345	2	ROCK1	18	18550366	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2496	18550366	59526882	10542	18527										
ROCK1	6093	broad.mit.edu	37	chr18	18571266	18571266	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaagtttgtagtttaaatCtatctctaaattattctttt	3	4	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:18571266C>A	ENST00000399799.2	-	18	2954	c.2014G>T	c.(2014-2016)Gat>Tat	p.D672Y		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	672	Glu-rich.|Interaction with FHOD1.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D672Y(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TAGTTTAAATCTATCTCTAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	18											158	147	151					18																	18571266		2202	4300	6502	16825264	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.2014G>T	18.37:g.18571266C>A	ENSP00000382697:p.Asp672Tyr		16825264	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366601	0.82463	.	.	ENSG00000067900	ENST00000399799	T	0.67171	-0.25	4.33	4.33	0.51752	.	0.000000	0.85682	D	0.000000	D	0.82518	0.5054	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85936	0.1455	10	0.87932	D	0	.	17.0053	0.86391	0.0:1.0:0.0:0.0	.	672	Q13464	ROCK1_HUMAN	Y	672	ENSP00000382697:D672Y	ENSP00000382697:D672Y	D	-	1	0	ROCK1	16825264	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.936000	0.75892	2.215000	0.71742	0.655000	0.94253	GAT		0.308	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		A	18571266	C	A	18571266	3	1	61	1	0	0	0	0	1	0	0	0	13554	913	32	2	2114	2	ROCK1	18	18571266	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20900	18571266	59505982	10543	18528										
ROCK1	6093	broad.mit.edu	37	chr18	18629180	18629180	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catataccttcctggtggatTtatgccttacctttaaaatt	5	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:18629180T>G	ENST00000399799.2	-	4	1227	c.287A>C	c.(286-288)aAa>aCa	p.K96T		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K96T(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					CCTGGTGGATTTATGCCTTAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	18											90	96	94					18																	18629180		2203	4300	6503	16883178	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.287A>C	18.37:g.18629180T>G	ENSP00000382697:p.Lys96Thr		16883178	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	31	5.071801	0.93950	.	.	ENSG00000067900	ENST00000399799	T	0.66995	-0.24	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76709	0.4025	L	0.57536	1.79	0.80722	D	1	P	0.48503	0.911	P	0.57057	0.812	T	0.78797	-0.2063	10	0.87932	D	0	.	16.3985	0.83631	0.0:0.0:0.0:1.0	.	96	Q13464	ROCK1_HUMAN	T	96	ENSP00000382697:K96T	ENSP00000382697:K96T	K	-	2	0	ROCK1	16883178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.236000	0.72339	2.274000	0.75844	0.519000	0.50382	AAA		0.333	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		G	18629180	T	G	18629180	3	3	61	1	0	0	0	0	1	0	0	0	13554	1841	64	4	3897	4	ROCK1	18	18629180	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	57914	18629180	59448068	10544	18529										
ESCO1	114799	broad.mit.edu	37	chr18	19147949	19147949	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagtattacctggaaatTtattctctcctgtatcaatt	4	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19147949T>G	ENST00000269214.5	-	5	2574	c.1637A>C	c.(1636-1638)aAa>aCa	p.K546T		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	546					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)	p.K546T(1)		breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						ACCTGGAAATTTATTCTCTCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	18											76	76	76					18																	19147949		2203	4300	6503	17401947	SO:0001583	missense	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.1637A>C	18.37:g.19147949T>G	ENSP00000269214:p.Lys546Thr		17401947	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.285876	0.40394	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.59772	0.24;1.78	5.6	1.58	0.23477	.	0.353834	0.27802	N	0.017788	T	0.41903	0.1179	L	0.33485	1.01	0.23620	N	0.997276	B	0.17852	0.024	B	0.15052	0.012	T	0.21075	-1.0256	10	0.16420	T	0.52	-13.4284	11.9577	0.52991	0.0:0.0:0.404:0.596	.	546	Q5FWF5	ESCO1_HUMAN	T	546	ENSP00000269214:K546T;ENSP00000372763:K546T	ENSP00000269214:K546T	K	-	2	0	ESCO1	17401947	1.000000	0.71417	0.935000	0.37517	0.939000	0.58152	1.517000	0.35867	0.085000	0.17107	0.528000	0.53228	AAA		0.343	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		G	19147949	T	G	19147949	3	3	61	1	0	0	0	0	1	0	0	0	5261	1841	64	4	917	4	ESCO1	18	19147949	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	518769	19147949	58929299	10545	18530										
ESCO1	114799	broad.mit.edu	37	chr18	19153906	19153906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagctggagaatactacctCgtttgctctttcctgcttgc	9	11	1	2	rs575811331		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19153906C>T	ENST00000269214.5	-	4	1836	c.899G>A	c.(898-900)cGa>cAa	p.R300Q		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	300					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)	p.R300Q(2)		breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						AATACTACCTCGTTTGCTCTT	0.403													C|||	1	0.000199681	0	0	5008	,	,		19454	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	18											87	86	86					18																	19153906		2202	4300	6502	17407904	SO:0001583	missense	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.899G>A	18.37:g.19153906C>T	ENSP00000269214:p.Arg300Gln		17407904	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.776322	0.70107	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.68765	-0.35;1.15	5.5	5.5	0.81552	.	0.000000	0.51477	D	0.000093	T	0.77425	0.4128	M	0.66939	2.045	0.40957	D	0.984595	D	0.89917	1.0	D	0.64506	0.926	T	0.79004	-0.1980	10	0.54805	T	0.06	-20.1383	11.9722	0.53069	0.0:0.9208:0.0:0.0792	.	300	Q5FWF5	ESCO1_HUMAN	Q	300	ENSP00000269214:R300Q;ENSP00000372763:R300Q	ENSP00000269214:R300Q	R	-	2	0	ESCO1	17407904	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	3.500000	0.53318	2.599000	0.87857	0.655000	0.94253	CGA		0.403	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		T	19153906	C	T	19153906	3	4	61	1	0	0	0	0	1	0	0	0	5261	884	31	1	1659	1	ESCO1	18	19153906	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5957	19153906	58923342	10546	18531										
ESCO1	114799	broad.mit.edu	37	chr18	19154706	19154706	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgatttttttgctagattCttttgagaatcctgaatttc	6	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19154706C>A	ENST00000269214.5	-	4	1036	c.99G>T	c.(97-99)aaG>aaT	p.K33N		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	33					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)	p.K33N(1)		breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TTGCTAGATTCTTTTGAGAAT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											132	130	131					18																	19154706		2203	4299	6502	17408704	SO:0001583	missense	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.99G>T	18.37:g.19154706C>A	ENSP00000269214:p.Lys33Asn		17408704	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.889903	0.00527	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.58940	0.3;1.86	5.1	-1.31	0.09230	.	0.935982	0.09004	N	0.862570	T	0.33177	0.0854	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16748	-1.0392	10	0.33940	T	0.23	-19.8152	0.1029	0.00050	0.296:0.1751:0.2469:0.2821	.	33	Q5FWF5	ESCO1_HUMAN	N	33	ENSP00000269214:K33N;ENSP00000372763:K33N	ENSP00000269214:K33N	K	-	3	2	ESCO1	17408704	0.000000	0.05858	0.394000	0.26270	0.982000	0.71751	-0.534000	0.06150	-0.385000	0.07833	0.655000	0.94253	AAG		0.338	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		A	19154706	C	A	19154706	3	1	61	1	0	0	0	0	1	0	0	0	5261	912	32	2	2459	2	ESCO1	18	19154706	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	800	19154706	58922542	10547	18532										
ABHD3	171586	broad.mit.edu	37	chr18	19231709	19231709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattaggattttgcttagcaGtttctattggaatagcttca	8	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19231709G>A	ENST00000289119.2	-	9	1212	c.1073C>T	c.(1072-1074)aCt>aTt	p.T358I	ABHD3_ENST00000580981.1_Missense_Mutation_p.T305I|ABHD3_ENST00000578270.1_Missense_Mutation_p.T163I	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	358						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.T358I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						TTGCTTAGCAGTTTCTATTGG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	18											63	59	60					18																	19231709		2203	4300	6503	17485707	SO:0001583	missense	171586			AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.1073C>T	18.37:g.19231709G>A	ENSP00000289119:p.Thr358Ile		17485707	B0YIV0|B7Z5C2|O43411	Missense_Mutation	SNP	ENST00000289119.2	37	CCDS32802.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853238	0.32699	.	.	ENSG00000158201	ENST00000289119	T	0.69685	-0.42	5.35	5.35	0.76521	.	0.048652	0.85682	D	0.000000	T	0.59905	0.2228	L	0.44542	1.39	0.50039	D	0.99984	B	0.12013	0.005	B	0.18263	0.021	T	0.58612	-0.7606	10	0.59425	D	0.04	-4.048	13.3697	0.60707	0.0755:0.0:0.9245:0.0	.	358	Q8WU67	ABHD3_HUMAN	I	358	ENSP00000289119:T358I	ENSP00000289119:T358I	T	-	2	0	ABHD3	17485707	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.402000	0.66332	2.515000	0.84797	0.585000	0.79938	ACT		0.368	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			A	19231709	G	A	19231709	3	1	61	1	0	0	0	0	1	0	0	0	83	1029	36	3	160	3	ABHD3	18	19231709	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77003	19231709	58845539	10548	18533										
ABHD3	171586	broad.mit.edu	37	chr18	19239217	19239217	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaatgactctgagcaagcGaaggtgttccaaccaacgga	10	11	1	2	rs151040212		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19239217G>A	ENST00000289119.2	-	6	895	c.756C>T	c.(754-756)ttC>ttT	p.F252F	RP11-13N13.5_ENST00000584148.1_RNA|ABHD3_ENST00000580981.1_Silent_p.F199F|ABHD3_ENST00000578270.1_Silent_p.F57F	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	252						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.F252F(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						CTGAGCAAGCGAAGGTGTTCC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	18						G		0,4406		0,0,2203	90	92	91		756	0.3	1	18	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ABHD3	NM_138340.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		252/410	19239217	2,13004	2203	4300	6503	17493215	SO:0001819	synonymous_variant	171586			AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.756C>T	18.37:g.19239217G>A			17493215	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	37	CCDS32802.1																																																																																				0.408	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			A	19239217	G	A	19239217	2	1	61	1	0	0	0	0	0	0	0	1	83	1049	37	1		1	ABHD3	18	19239217	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7508	19239217	58838031	10549	18534										
ABHD3	171586	broad.mit.edu	37	chr18	19282317	19282317	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatggatcatatgaaggaTatatgactccttgcttgttc	9	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19282317T>G	ENST00000289119.2	-	3	608	c.469A>C	c.(469-471)Atc>Ctc	p.I157L	ABHD3_ENST00000579875.1_5'UTR|ABHD3_ENST00000580981.1_Missense_Mutation_p.I157L|ABHD3_ENST00000578270.1_5'UTR	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	157						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.I157L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						ATATGAAGGATATATGACTCC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	18											90	88	89					18																	19282317		2203	4300	6503	17536315	SO:0001583	missense	171586			AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.469A>C	18.37:g.19282317T>G	ENSP00000289119:p.Ile157Leu		17536315	B0YIV0|B7Z5C2|O43411	Missense_Mutation	SNP	ENST00000289119.2	37	CCDS32802.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.095613	0.56075	.	.	ENSG00000158201	ENST00000289119	T	0.08546	3.08	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.14917	0.0360	L	0.46819	1.47	0.80722	D	1	P	0.41597	0.756	P	0.46885	0.53	T	0.00485	-1.1711	10	0.62326	D	0.03	-0.5954	15.7247	0.77747	0.0:0.0:0.0:1.0	.	157	Q8WU67	ABHD3_HUMAN	L	157	ENSP00000289119:I157L	ENSP00000289119:I157L	I	-	1	0	ABHD3	17536315	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.930000	0.70104	2.116000	0.64780	0.533000	0.62120	ATC		0.368	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			G	19282317	T	G	19282317	3	3	61	1	0	0	0	0	1	0	0	0	83	1406	49	4	788	4	ABHD3	18	19282317	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	43100	19282317	58794931	10550	18535										
MIB1	57534	broad.mit.edu	37	chr18	19359513	19359513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatatagatctcgacctcGaaattgtacagtctttgcag	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19359513G>A	ENST00000261537.6	+	6	1039	c.775G>A	c.(775-777)Gaa>Aaa	p.E259K	MIB1_ENST00000578646.1_3'UTR|AC091038.1_ENST00000582102.1_RNA	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	259					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E259K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			TCTCGACCTCGAAATTGTACA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											263	240	248					18																	19359513		2203	4300	6503	17613511	SO:0001583	missense	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.775G>A	18.37:g.19359513G>A	ENSP00000261537:p.Glu259Lys		17613511	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214185	0.58452	.	.	ENSG00000101752	ENST00000261537	T	0.39406	1.08	4.67	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.57799	0.2078	M	0.83012	2.62	0.80722	D	1	P	0.50272	0.933	P	0.52189	0.692	T	0.65923	-0.6050	10	0.72032	D	0.01	-19.1978	13.328	0.60471	0.0776:0.0:0.9224:0.0	.	259	Q86YT6	MIB1_HUMAN	K	259	ENSP00000261537:E259K	ENSP00000261537:E259K	E	+	1	0	MIB1	17613511	1.000000	0.71417	0.997000	0.53966	0.711000	0.40976	7.981000	0.88123	1.109000	0.41680	-0.704000	0.03662	GAA		0.423	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		A	19359513	G	A	19359513	3	1	61	1	0	0	0	0	1	0	0	0	9596	1059	37	1	797	1	MIB1	18	19359513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77196	19359513	58717735	10551	18536										
MIB1	57534	broad.mit.edu	37	chr18	19429285	19429285	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacatattgctacctgttCtttatgttctccacgtgtca	7	10	3	0	rs138079123		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:19429285C>A	ENST00000261537.6	+	17	2786	c.2522C>A	c.(2521-2523)tCt>tAt	p.S841Y	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	841					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S841Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GCTACCTGTTCTTTATGTTCT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	18											166	154	158					18																	19429285		2203	4300	6503	17683283	SO:0001583	missense	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.2522C>A	18.37:g.19429285C>A	ENSP00000261537:p.Ser841Tyr		17683283	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.642551	0.67244	.	.	ENSG00000101752	ENST00000261537	T	0.78816	-1.21	5.33	5.33	0.75918	Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.84325	0.5447	L	0.42529	1.33	0.80722	D	1	D	0.57257	0.979	D	0.70487	0.969	D	0.83484	0.0066	10	0.41790	T	0.15	-11.9712	19.0421	0.93004	0.0:1.0:0.0:0.0	.	841	Q86YT6	MIB1_HUMAN	Y	841	ENSP00000261537:S841Y	ENSP00000261537:S841Y	S	+	2	0	MIB1	17683283	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.494000	0.84150	0.585000	0.79938	TCT		0.343	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		A	19429285	C	A	19429285	3	1	61	1	0	0	0	0	1	0	0	0	9596	913	32	2	2588	2	MIB1	18	19429285	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	69772	19429285	58647963	10552	18537										
NPC1	4864	broad.mit.edu	37	chr18	21125098	21125098	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgggattcttgtagtttttCacaaaattaataaacctaaa	5	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21125098C>A	ENST00000269228.5	-	12	2327	c.1773G>T	c.(1771-1773)gtG>gtT	p.V591V	NPC1_ENST00000412552.2_Silent_p.V273V|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	591					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)	p.V591V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGTAGTTTTTCACAAAATTAA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	18											63	62	62					18																	21125098		2203	4300	6503	19379096	SO:0001819	synonymous_variant	4864			AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1773G>T	18.37:g.21125098C>A			19379096	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																				0.333	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		A	21125098	C	A	21125098	2	1	61	1	0	0	0	0	0	0	0	1	10601	813	29	2		2	NPC1	18	21125098	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1695813	21125098	56952150	10553	18538										
NPC1	4864	broad.mit.edu	37	chr18	21134924	21134924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataagaggcagtaatgttttCgatggctatttgtaagtcaa	10	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21134924C>T	ENST00000269228.5	-	9	1905	c.1351G>A	c.(1351-1353)Gaa>Aaa	p.E451K	NPC1_ENST00000412552.2_Missense_Mutation_p.E201K|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	451			E -> K (in NPC1). {ECO:0000269|PubMed:12401890}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)	p.E451K(2)		breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GTAATGTTTTCGATGGCTATT	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	18	GRCh37	CM024407	NPC1	M							110	83	92					18																	21134924		2203	4300	6503	19388922	SO:0001583	missense	4864			AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1351G>A	18.37:g.21134924C>T	ENSP00000269228:p.Glu451Lys		19388922	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108661	0.37242	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.88818	-2.43;-2.43	4.88	4.88	0.63580	.	0.103731	0.64402	D	0.000005	D	0.83801	0.5333	L	0.39147	1.195	0.43069	D	0.994702	B;B	0.21381	0.055;0.055	B;B	0.17098	0.011;0.017	T	0.79495	-0.1780	10	0.09338	T	0.73	-23.645	18.4005	0.90514	0.0:1.0:0.0:0.0	.	462;451	Q59GR1;O15118	.;NPC1_HUMAN	K	451;201;296	ENSP00000269228:E451K;ENSP00000408606:E201K	ENSP00000269228:E451K	E	-	1	0	NPC1	19388922	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	5.814000	0.69208	2.402000	0.81655	0.655000	0.94253	GAA		0.393	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21134924	C	T	21134924	3	4	61	1	0	0	0	0	1	0	0	0	10601	893	31	1	2553	1	NPC1	18	21134924	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9826	21134924	56942324	10554	18539										
LAMA3	3909	broad.mit.edu	37	chr18	21422438	21422438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttaccaagcagcgcaccCgacgtttcccgcgcaggtgt	10	14	0	0	rs369681836		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21422438C>T	ENST00000313654.9	+	28	3657	c.3416C>T	c.(3415-3417)cCg>cTg	p.P1139L	LAMA3_ENST00000399516.3_Missense_Mutation_p.P1139L	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1139	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.P1139L(1)|p.P1139Q(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					GCAGCGCACCCGACGTTTCCC	0.587																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	18						C	LEU/PRO,LEU/PRO	1,4077		0,1,2038	75	79	78		3416,3416	5.5	0.9	18		78	0,8332		0,0,4166	no	missense,missense	LAMA3	NM_001127717.1,NM_198129.1	98,98	0,1,6204	TT,TC,CC		0.0,0.0245,0.0081	probably-damaging,probably-damaging	1139/3278,1139/3334	21422438	1,12409	2039	4166	6205	19676436	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3416C>T	18.37:g.21422438C>T	ENSP00000324532:p.Pro1139Leu		19676436	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623411	0.87460	2.45E-4	0.0	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.19250	2.17;2.16	5.46	5.46	0.80206	.	.	.	.	.	T	0.53367	0.1792	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.87578	0.709;0.998	T	0.56147	-0.8027	9	0.48119	T	0.1	.	19.3195	0.94233	0.0:1.0:0.0:0.0	.	1139;1139	Q6VU67;Q16787	.;LAMA3_HUMAN	L	1139;1139;1137	ENSP00000324532:P1139L;ENSP00000382432:P1139L	ENSP00000324532:P1139L	P	+	2	0	LAMA3	19676436	0.982000	0.34865	0.853000	0.33588	0.024000	0.10985	3.889000	0.56212	2.582000	0.87167	0.655000	0.94253	CCG		0.587	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21422438	C	T	21422438	3	4	61	1	0	0	0	0	1	0	0	0	8629	652	23	1	3526	1	LAMA3	18	21422438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	287514	21422438	56654810	10555	18540										
LAMA3	3909	broad.mit.edu	37	chr18	21426288	21426288	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcctccagattctgtaaGaattccgccaggtccctggt	9	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21426288G>T	ENST00000313654.9	+	31	3988	c.3747G>T	c.(3745-3747)aaG>aaT	p.K1249N	LAMA3_ENST00000399516.3_Missense_Mutation_p.K1249N	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1249	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.K1249N(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					GATTCTGTAAGAATTCCGCCA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	18											112	117	115					18																	21426288		1972	4156	6128	19680286	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3747G>T	18.37:g.21426288G>T	ENSP00000324532:p.Lys1249Asn		19680286	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.776880	0.70107	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.20598	2.07;2.06	5.97	5.97	0.96955	.	.	.	.	.	T	0.33000	0.0848	M	0.77616	2.38	0.80722	D	1	P;P	0.51449	0.945;0.931	P;P	0.49226	0.603;0.522	T	0.03423	-1.1038	9	0.33141	T	0.24	.	10.7282	0.46081	0.1407:0.0:0.8593:0.0	.	1249;1249	Q6VU67;Q16787	.;LAMA3_HUMAN	N	1249;1249;1247	ENSP00000324532:K1249N;ENSP00000382432:K1249N	ENSP00000324532:K1249N	K	+	3	2	LAMA3	19680286	1.000000	0.71417	0.995000	0.50966	0.946000	0.59487	3.120000	0.50430	2.837000	0.97791	0.655000	0.94253	AAG		0.607	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21426288	G	T	21426288	3	4	61	1	0	0	0	0	1	0	0	0	8629	933	33	2	3869	2	LAMA3	18	21426288	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3850	21426288	56650960	10556	18541										
LAMA3	3909	broad.mit.edu	37	chr18	21481258	21481258	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcaaatggcttgaaccaaGaaaacgagagagctttggga	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21481258G>T	ENST00000313654.9	+	48	6413	c.6172G>T	c.(6172-6174)Gaa>Taa	p.E2058*	LAMA3_ENST00000399516.3_Nonsense_Mutation_p.E2002*|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Nonsense_Mutation_p.E449*|LAMA3_ENST00000587184.1_Nonsense_Mutation_p.E393*	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2058	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.E2058*(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					CTTGAACCAAGAAAACGAGAG	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											53	51	52					18																	21481258		2203	4300	6503	19735256	SO:0001587	stop_gained	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.6172G>T	18.37:g.21481258G>T	ENSP00000324532:p.Glu2058*		19735256	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Nonsense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	47	13.642777	0.99754	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	19.8686	0.96842	0.0:0.0:1.0:0.0	.	.	.	.	X	2058;2002;449	.	ENSP00000269217:E449X	E	+	1	0	LAMA3	19735256	0.977000	0.34250	0.099000	0.21106	0.946000	0.59487	5.012000	0.64017	2.768000	0.95171	0.655000	0.94253	GAA		0.463	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21481258	G	T	21481258	4	4	61	1	0	0	0	0	0	1	0	0	8629	943	33	2	6537	2	LAMA3	18	21481258	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54970	21481258	56595990	10557	18542										
LAMA3	3909	broad.mit.edu	37	chr18	21501518	21501518	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgatttcagcacatattatCtgggaggaattccaattgca	8	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21501518C>A	ENST00000313654.9	+	62	8387	c.8146C>A	c.(8146-8148)Ctg>Atg	p.L2716M	LAMA3_ENST00000399516.3_Missense_Mutation_p.L2660M|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.L1107M|LAMA3_ENST00000587184.1_Missense_Mutation_p.L1051M	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2716	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.L2716M(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					CACATATTATCTGGGAGGAAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	18											121	127	125					18																	21501518		2203	4300	6503	19755516	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8146C>A	18.37:g.21501518C>A	ENSP00000324532:p.Leu2716Met		19755516	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306318	0.60305	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	D;D;D	0.82711	-1.64;-1.64;-1.64	5.77	3.02	0.34903	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.85071	0.5613	M	0.66939	2.045	0.36539	D	0.871182	P;P;P;D	0.53619	0.918;0.918;0.934;0.961	P;P;P;P	0.53401	0.554;0.577;0.544;0.725	D	0.86042	0.1520	9	0.72032	D	0.01	.	9.2693	0.37661	0.0:0.7031:0.0:0.2969	.	1051;1107;2660;2716	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	M	2716;2660;1107	ENSP00000324532:L2716M;ENSP00000382432:L2660M;ENSP00000269217:L1107M	ENSP00000269217:L1107M	L	+	1	2	LAMA3	19755516	0.915000	0.31059	0.988000	0.46212	0.989000	0.77384	0.503000	0.22610	0.362000	0.24319	-0.140000	0.14226	CTG		0.328	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21501518	C	A	21501518	3	1	61	1	0	0	0	0	1	0	0	0	8629	912	32	2	8567	2	LAMA3	18	21501518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20260	21501518	56575730	10558	18543										
LAMA3	3909	broad.mit.edu	37	chr18	21529764	21529764	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctttgtgggatgcctgaaGaactttcagctggattcaaa	11	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21529764G>T	ENST00000313654.9	+	71	9628	c.9387G>T	c.(9385-9387)aaG>aaT	p.K3129N	LAMA3_ENST00000399516.3_Missense_Mutation_p.K3073N|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.K1520N|LAMA3_ENST00000587184.1_Missense_Mutation_p.K1464N	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3129	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.K3129N(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					GATGCCTGAAGAACTTTCAGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	18											80	81	80					18																	21529764		2203	4300	6503	19783762	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.9387G>T	18.37:g.21529764G>T	ENSP00000324532:p.Lys3129Asn		19783762	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043467	0.75732	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.79033	-1.23;-1.23;-1.23	5.55	4.67	0.58626	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.82421	0.5033	M	0.64404	1.975	0.29401	N	0.861954	P;P;P;P	0.49783	0.684;0.734;0.858;0.928	B;P;P;P	0.54401	0.419;0.501;0.685;0.751	T	0.78638	-0.2126	9	0.72032	D	0.01	.	11.8353	0.52321	0.1429:0.0:0.8571:0.0	.	1464;1520;3073;3129	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	N	3129;3073;1520	ENSP00000324532:K3129N;ENSP00000382432:K3073N;ENSP00000269217:K1520N	ENSP00000269217:K1520N	K	+	3	2	LAMA3	19783762	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	3.003000	0.49505	1.316000	0.45131	0.655000	0.94253	AAG		0.478	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21529764	G	T	21529764	3	4	61	1	0	0	0	0	1	0	0	0	8629	933	33	2	9844	2	LAMA3	18	21529764	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28246	21529764	56547484	10559	18544										
LAMA3	3909	broad.mit.edu	37	chr18	21530075	21530075	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgggatcctaatacacatCggaagtcagcccgggaagca	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21530075C>T	ENST00000313654.9	+	72	9835	c.9594C>T	c.(9592-9594)atC>atT	p.I3198I	LAMA3_ENST00000399516.3_Silent_p.I3142I|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.I1589I|LAMA3_ENST00000587184.1_Silent_p.I1533I	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3198	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.I3198I(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					TAATACACATCGGAAGTCAGC	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	18											115	112	113					18																	21530075		2203	4300	6503	19784073	SO:0001819	synonymous_variant	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.9594C>T	18.37:g.21530075C>T			19784073	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																				0.478	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21530075	C	T	21530075	2	4	61	1	0	0	0	0	0	0	0	1	8629	874	31	1		1	LAMA3	18	21530075	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	311	21530075	56547173	10560	18545										
TTC39C	125488	broad.mit.edu	37	chr18	21660836	21660836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgggttttcctggagacCgcctacaggggctttcttca	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:21660836C>T	ENST00000317571.3	+	5	984	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000304621.6_Missense_Mutation_p.R189C	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	250								p.R189C(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TCCTGGAGACCGCCTACAGGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											68	68	68					18																	21660836		2203	4300	6503	19914834	SO:0001583	missense	125488			AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.748C>T	18.37:g.21660836C>T	ENSP00000323645:p.Arg250Cys		19914834	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	c	29.6	5.018276	0.93404	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.61274	0.12;0.12	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80817	-0.1213	10	0.87932	D	0	-23.0351	20.0231	0.97510	0.0:1.0:0.0:0.0	.	250	Q8N584	TT39C_HUMAN	C	189;250	ENSP00000306598:R189C;ENSP00000323645:R250C	ENSP00000306598:R189C	R	+	1	0	TTC39C	19914834	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.485000	0.81204	2.733000	0.93635	0.552000	0.68991	CGC		0.473	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		T	21660836	C	T	21660836	3	4	61	1	0	0	0	0	1	0	0	0	16749	652	23	1	766	1	TTC39C	18	21660836	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130761	21660836	56416412	10561	18546										
HRH4	59340	broad.mit.edu	37	chr18	22057076	22057076	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagatctctttctgcatcGacagaagttcctgcatcctt	8	11	2	2	rs372177844		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:22057076G>A	ENST00000256906.4	+	3	823	c.723G>A	c.(721-723)tcG>tcA	p.S241S	HRH4_ENST00000426880.2_Silent_p.S153S	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	241					inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)	p.S241S(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	TTTCTGCATCGACAGAAGTTC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	18						G	,,	1,4405	2.1+/-5.4	0,1,2202	116	113	114		459,,723	-3.3	0	18		114	0,8600		0,0,4300	no	coding-synonymous,utr-3,coding-synonymous	HRH4	NM_001143828.1,NM_001160166.1,NM_021624.3	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	153/303,,241/391	22057076	1,13005	2203	4300	6503	20311074	SO:0001819	synonymous_variant	59340			AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"GPCR / Class A : Histamine receptors"	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.723G>A	18.37:g.22057076G>A			20311074	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Silent	SNP	ENST00000256906.4	37	CCDS11887.1																																																																																				0.443	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1			A	22057076	G	A	22057076	2	1	61	1	0	0	0	0	0	0	0	1	7379	1045	37	1		1	HRH4	18	22057076	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	396240	22057076	56020172	10562	18547										
ZNF521	25925	broad.mit.edu	37	chr18	22804990	22804990	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggagggaaaccgctctccGcaaatagggcacatgtagtg	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:22804990G>A	ENST00000361524.3	-	4	3040	c.2892C>T	c.(2890-2892)tgC>tgT	p.C964C	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Silent_p.C964C|ZNF521_ENST00000584787.1_Silent_p.C744C	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	964					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.C964C(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ACCGCTCTCCGCAAATAGGGC	0.498			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - coding silent(1)	large_intestine(1)	18											91	85	87					18																	22804990		2203	4300	6503	21058988	SO:0001819	synonymous_variant	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2892C>T	18.37:g.22804990G>A			21058988	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																				0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22804990	G	A	22804990	2	1	61	1	0	0	0	0	0	0	0	1	18004	1079	38	1		1	ZNF521	18	22804990	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	747914	22804990	55272258	10563	18548										
ZNF521	25925	broad.mit.edu	37	chr18	22805549	22805549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttatgcactttcccttggTtttccaggtggttgtgtttc	9	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:22805549T>C	ENST00000361524.3	-	4	2481	c.2333A>G	c.(2332-2334)aAc>aGc	p.N778S	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.N778S|ZNF521_ENST00000584787.1_Missense_Mutation_p.N558S	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	778					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.N778S(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TTTCCCTTGGTTTTCCAGGTG	0.483			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - Missense(1)	large_intestine(1)	18											128	111	117					18																	22805549		2203	4300	6503	21059547	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2333A>G	18.37:g.22805549T>C	ENSP00000354794:p.Asn778Ser		21059547	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.402033	0.25291	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.08546	3.08;3.1	6.17	6.17	0.99709	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.06508	0.0167	N	0.04018	-0.295	0.44214	D	0.997042	P	0.42409	0.779	B	0.42593	0.392	T	0.47522	-0.9111	10	0.52906	T	0.07	-41.4592	16.8222	0.85835	0.0:0.0:0.0:1.0	.	778	Q96K83	ZN521_HUMAN	S	778;812;778	ENSP00000354794:N778S;ENSP00000382352:N778S	ENSP00000354794:N778S	N	-	2	0	ZNF521	21059547	1.000000	0.71417	0.965000	0.40720	0.993000	0.82548	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	AAC		0.483	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		C	22805549	T	C	22805549	3	2	61	1	0	0	0	0	1	0	0	0	18004	1725	60	4	1622	4	ZNF521	18	22805549	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	559	22805549	55271699	10564	18549										
SS18	6760	broad.mit.edu	37	chr18	23615838	23615838	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatcctcataaggcctatcGtagccttgttcaggatacga	9	10	2	0	rs570531592		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:23615838G>A	ENST00000415083.2	-	8	985	c.930C>T	c.(928-930)taC>taT	p.Y310Y	SS18_ENST00000269137.7_Intron|SS18_ENST00000542743.1_Intron|SS18_ENST00000542420.2_Silent_p.Y287Y|SS18_ENST00000545952.1_Intron|SS18_ENST00000539849.1_Silent_p.Y228Y	NM_001007559.1|NM_005637.2	NP_001007560.1|NP_005628.2	Q15532	SSXT_HUMAN	synovial sarcoma translocation, chromosome 18	310	Gln-rich.				cell morphogenesis (GO:0000902)|ephrin receptor signaling pathway (GO:0048013)|intracellular signal transduction (GO:0035556)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.Y310Y(1)	SS18/SSX2(706)|SS18/SSX1(1169)|SS18/SSX4(12)	endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(1)	19	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)					AAGGCCTATCGTAGCCTTGTT	0.408			T	"SSX1,  SSX2"	synovial sarcoma								G|||	1	0.000199681	0	0	5008	,	,		15808	0		0	False		,,,				2504	0.001						Dom	yes		18	18q11.2	6760	"synovial sarcoma translocation, chromosome 18"		M	1	Substitution - coding silent(1)	large_intestine(1)	18											140	100	114					18																	23615838		2203	4300	6503	21869836	SO:0001819	synonymous_variant	6760			X79201	CCDS32807.1, CCDS54183.1	18q11.2	2008-07-28				ENSG00000141380			11340	protein-coding gene	gene with protein product		600192		SSXT		8152806, 7951320, 16484776	Standard	XM_005258334		Approved	SYT	uc002kvm.3	Q15532		ENST00000415083.2:c.930C>T	18.37:g.23615838G>A			21869836	B0YJ95|Q16404|Q4VAX1|Q9BXC6	Silent	SNP	ENST00000415083.2	37	CCDS32807.1																																																																																				0.408	SS18-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446226.1			A	23615838	G	A	23615838	2	1	61	1	0	0	0	0	0	0	0	1	15214	1140	40	1		1	SS18	18	23615838	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	810289	23615838	54461410	10565	18550										
PSMA8	143471	broad.mit.edu	37	chr18	23772351	23772351	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaggaagaagcagagaaGaaaaaatcaaagaaatctgt	10	3	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:23772351G>T	ENST00000308268.6	+	7	836	c.747G>T	c.(745-747)aaG>aaT	p.K249N	PSMA8_ENST00000343848.6_Missense_Mutation_p.K205N|PSMA8_ENST00000415576.2_Missense_Mutation_p.K243N	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	249					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.K249N(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			AAGCAGAGAAGAAAAAATCAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	18											64	70	68					18																	23772351		2202	4299	6501	22026349	SO:0001583	missense	143471			BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"Proteasome (prosome, macropain) subunits"	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.747G>T	18.37:g.23772351G>T	ENSP00000311121:p.Lys249Asn		22026349	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Missense_Mutation	SNP	ENST00000308268.6	37	CCDS32808.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.696482	0.48202	.	.	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000536423	T;T;T	0.33654	1.4;1.81;1.4	4.49	4.49	0.54785	.	0.258920	0.37483	N	0.002075	T	0.26340	0.0643	L	0.29908	0.895	0.58432	D	0.99999	B;B;B	0.21688	0.059;0.048;0.029	B;B;B	0.17722	0.014;0.016;0.019	T	0.04454	-1.0950	10	0.28530	T	0.3	-2.9449	12.9203	0.58228	0.0:0.0:1.0:0.0	.	249;243;205	Q8TAA3;Q8TAA3-5;Q8TAA3-2	PSA7L_HUMAN;.;.	N	249;243;205;205	ENSP00000311121:K249N;ENSP00000409284:K243N;ENSP00000345584:K205N	ENSP00000311121:K249N	K	+	3	2	PSMA8	22026349	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.914000	0.56401	2.518000	0.84900	0.650000	0.86243	AAG		0.299	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662		T	23772351	G	T	23772351	3	4	61	1	0	0	0	0	1	0	0	0	12707	933	33	2	773	2	PSMA8	18	23772351	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	156513	23772351	54304897	10566	18551										
TAF4B	6875	broad.mit.edu	37	chr18	23807038	23807038	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgggcgccgtgactaaGgctcctgtcagcgtctgcgt	14	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:23807038G>T	ENST00000269142.5	+	1	1139	c.141G>T	c.(139-141)aaG>aaT	p.K47N	TAF4B_ENST00000400466.2_Missense_Mutation_p.K47N|TAF4B_ENST00000578121.1_Missense_Mutation_p.K47N	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	47					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K47N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CCGTGACTAAGGCTCCTGTCA	0.741																																																1	Substitution - Missense(1)	large_intestine(1)	18											13	15	15					18																	23807038		1909	4112	6021	22061036	SO:0001583	missense	6875			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.141G>T	18.37:g.23807038G>T	ENSP00000269142:p.Lys47Asn		22061036	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126044	0.37533	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.26067	1.76;1.77;1.76	5.05	2.29	0.28610	.	0.561366	0.12408	U	0.471514	T	0.24586	0.0596	N	0.19112	0.55	0.25376	N	0.988655	D;D	0.62365	0.991;0.991	P;P	0.58013	0.831;0.831	T	0.14144	-1.0483	10	0.17832	T	0.49	-5.319	7.0444	0.25038	0.2886:0.0:0.7114:0.0	.	47;47	Q92750;A4PBF7	TAF4B_HUMAN;.	N	47	ENSP00000389365:K47N;ENSP00000269142:K47N;ENSP00000383314:K47N	ENSP00000269142:K47N	K	+	3	2	TAF4B	22061036	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	2.049000	0.41288	0.178000	0.19917	-0.258000	0.10820	AAG		0.741	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23807038	G	T	23807038	3	4	61	1	0	0	0	0	1	0	0	0	15566	991	35	2	143	2	TAF4B	18	23807038	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34687	23807038	54270210	10567	18552										
CHST9	83539	broad.mit.edu	37	chr18	24496768	24496768	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgggtatatatcccttttaGgtcaaagctatctagcttct	8	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:24496768G>T	ENST00000284224.8	-	6	1064	c.787C>A	c.(787-789)Cta>Ata	p.L263I	AQP4-AS1_ENST00000568797.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.L263I|AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	263					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.L178I(1)|p.L263I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					ATCCCTTTTAGGTCAAAGCTA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	18											143	131	135					18																	24496768		1871	4099	5970	22750766	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.787C>A	18.37:g.24496768G>T	ENSP00000284224:p.Leu263Ile		22750766	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	G	2.771	-0.255708	0.05829	.	.	ENSG00000154080	ENST00000284224	T	0.74002	-0.8	6.17	2.25	0.28309	.	0.000000	0.56097	D	0.000040	T	0.71143	0.3305	L	0.31371	0.925	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.65129	-0.6243	10	0.19590	T	0.45	-7.9029	4.0848	0.09942	0.5204:0.0:0.3311:0.1485	.	263	Q7L1S5	CHST9_HUMAN	I	263	ENSP00000284224:L263I	ENSP00000284224:L263I	L	-	1	2	CHST9	22750766	0.940000	0.31905	1.000000	0.80357	0.175000	0.22909	0.404000	0.20999	0.184000	0.20083	-1.311000	0.01308	CTA		0.403	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		T	24496768	G	T	24496768	3	4	61	1	0	0	0	0	1	0	0	0	3417	991	35	2	548	2	CHST9	18	24496768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	689730	24496768	53580480	10568	18553										
CHST9	83539	broad.mit.edu	37	chr18	24497154	24497154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttagctccttgacgttttTcaatcaacttctctgttggt	6	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:24497154T>C	ENST00000284224.8	-	6	678	c.401A>G	c.(400-402)gAa>gGa	p.E134G	AQP4-AS1_ENST00000568797.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.E134G|AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	134					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.E134G(1)|p.E49G(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					TTGACGTTTTTCAATCAACTT	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	18											286	261	269					18																	24497154		1883	4107	5990	22751152	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.401A>G	18.37:g.24497154T>C	ENSP00000284224:p.Glu134Gly		22751152	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237232	0.39498	.	.	ENSG00000154080	ENST00000284224	T	0.68765	-0.35	6.17	2.42	0.29668	.	21.575300	0.00166	N	0.000000	T	0.55130	0.1901	L	0.27053	0.805	0.41747	D	0.989649	B	0.28713	0.22	B	0.24541	0.054	T	0.15752	-1.0426	10	0.33141	T	0.24	-18.05	7.9114	0.29793	0.0:0.0655:0.2595:0.675	.	134	Q7L1S5	CHST9_HUMAN	G	134	ENSP00000284224:E134G	ENSP00000284224:E134G	E	-	2	0	CHST9	22751152	0.024000	0.19004	0.110000	0.21437	0.014000	0.08584	0.169000	0.16641	0.180000	0.19960	0.533000	0.62120	GAA		0.388	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		C	24497154	T	C	24497154	3	2	61	1	0	0	0	0	1	0	0	0	3417	1783	62	4	934	4	CHST9	18	24497154	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	386	24497154	53580094	10569	18554										
CDH2	1000	broad.mit.edu	37	chr18	25532153	25532153	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatacatgtcagcaagtttCttgaaccgtggcccccagtc	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:25532153C>A	ENST00000269141.3	-	16	3108	c.2685G>T	c.(2683-2685)aaG>aaT	p.K895N	CDH2_ENST00000399380.3_Missense_Mutation_p.K864N|AC015933.2_ENST00000423367.1_RNA	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	895					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.K895N(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CAGCAAGTTTCTTGAACCGTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											124	116	119					18																	25532153		2203	4300	6503	23786151	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2685G>T	18.37:g.25532153C>A	ENSP00000269141:p.Lys895Asn		23786151	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332784	0.41297	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.78246	-1.16;-1.16	5.43	5.43	0.79202	Cadherin, cytoplasmic domain (1);	0.047806	0.85682	D	0.000000	D	0.87426	0.6174	M	0.67397	2.05	0.47737	D	0.9995	D;P	0.67145	0.996;0.801	D;B	0.72625	0.978;0.412	D	0.88175	0.2867	10	0.72032	D	0.01	.	19.2485	0.93913	0.0:1.0:0.0:0.0	.	864;895	A8MWK3;P19022	.;CADH2_HUMAN	N	895;864	ENSP00000269141:K895N;ENSP00000382312:K864N	ENSP00000269141:K895N	K	-	3	2	CDH2	23786151	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.245000	0.43133	2.563000	0.86464	0.591000	0.81541	AAG		0.473	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		A	25532153	C	A	25532153	3	1	61	1	0	0	0	0	1	0	0	0	3111	912	32	2	39	2	CDH2	18	25532153	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1034999	25532153	52545095	10570	18555										
CDH2	1000	broad.mit.edu	37	chr18	25565681	25565681	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcattgtcattaatatcaaGtaaatagatctgcagcgttc	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:25565681G>T	ENST00000269141.3	-	12	2209	c.1786C>A	c.(1786-1788)Ctt>Att	p.L596I	CDH2_ENST00000399380.3_Missense_Mutation_p.L565I	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	596	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.L596I(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTAATATCAAGTAAATAGATC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	18											86	89	88					18																	25565681		2203	4300	6503	23819679	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1786C>A	18.37:g.25565681G>T	ENSP00000269141:p.Leu596Ile		23819679	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	G	10.13	1.264491	0.23136	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.61158	0.13;0.13	5.96	5.96	0.96718	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.064020	0.64402	D	0.000004	T	0.55577	0.1929	L	0.35249	1.045	0.58432	D	0.999995	B;B	0.29232	0.001;0.238	B;B	0.39299	0.009;0.296	T	0.45411	-0.9263	10	0.15952	T	0.53	.	20.394	0.98981	0.0:0.0:1.0:0.0	.	565;596	A8MWK3;P19022	.;CADH2_HUMAN	I	596;565	ENSP00000269141:L596I;ENSP00000382312:L565I	ENSP00000269141:L596I	L	-	1	0	CDH2	23819679	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.086000	0.64474	2.830000	0.97506	0.585000	0.79938	CTT		0.403	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25565681	G	T	25565681	3	4	61	1	0	0	0	0	1	0	0	0	3111	1029	36	2	954	2	CDH2	18	25565681	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33528	25565681	52511567	10571	18556										
CDH2	1000	broad.mit.edu	37	chr18	25572744	25572744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatggggttgatccttatCggtcacagttagattagcta	11	6	1	2	rs568089577		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:25572744C>T	ENST00000269141.3	-	9	1642	c.1219G>A	c.(1219-1221)Gat>Aat	p.D407N	CDH2_ENST00000399380.3_Missense_Mutation_p.D376N	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	407	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.D407N(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TGATCCTTATCGGTCACAGTT	0.502													C|||	1	0.000199681	8e-04	0	5008	,	,		18969	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											235	180	199					18																	25572744		2203	4300	6503	23826742	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1219G>A	18.37:g.25572744C>T	ENSP00000269141:p.Asp407Asn		23826742	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.217785	0.79352	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.78003	-1.14;-1.14	5.54	5.54	0.83059	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.93409	0.7898	H	0.98407	4.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.95481	0.8560	10	0.87932	D	0	.	19.8453	0.96705	0.0:1.0:0.0:0.0	.	376;407	A8MWK3;P19022	.;CADH2_HUMAN	N	407;376	ENSP00000269141:D407N;ENSP00000382312:D376N	ENSP00000269141:D407N	D	-	1	0	CDH2	23826742	1.000000	0.71417	0.749000	0.31150	0.119000	0.20118	7.772000	0.85439	2.754000	0.94517	0.655000	0.94253	GAT		0.502	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25572744	C	T	25572744	3	4	61	1	0	0	0	0	1	0	0	0	3111	884	31	1	1533	1	CDH2	18	25572744	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7063	25572744	52504504	10572	18557										
DSC3	1825	broad.mit.edu	37	chr18	28604320	28604320	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaagcagacttaccaggtCtactactttccaaaacttca	4	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28604320C>A	ENST00000360428.4	-	6	850	c.770G>T	c.(769-771)aGa>aTa	p.R257I	DSC3_ENST00000434452.1_Missense_Mutation_p.R257I	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	257	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.R257I(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			CTTACCAGGTCTACTACTTTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	18											56	61	59					18																	28604320		2203	4300	6503	26858318	SO:0001583	missense	1825			X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.770G>T	18.37:g.28604320C>A	ENSP00000353608:p.Arg257Ile		26858318	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595265	0.66219	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.54479	0.57;0.57	4.94	0.595	0.17490	Cadherin (4);Cadherin-like (1);	0.218372	0.23312	N	0.049557	T	0.58047	0.2095	M	0.62209	1.925	0.53688	D	0.999972	B;P	0.52577	0.421;0.954	P;P	0.54270	0.515;0.747	T	0.58891	-0.7556	10	0.87932	D	0	.	9.4522	0.38734	0.0:0.6264:0.0:0.3736	.	257;257	Q14574;Q14574-2	DSC3_HUMAN;.	I	257	ENSP00000353608:R257I;ENSP00000392068:R257I	ENSP00000353608:R257I	R	-	2	0	DSC3	26858318	0.109000	0.22037	0.982000	0.44146	0.854000	0.48673	-0.098000	0.11024	0.046000	0.15833	0.655000	0.94253	AGA		0.363	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		A	28604320	C	A	28604320	3	1	61	1	0	0	0	0	1	0	0	0	4778	913	32	2	1995	2	DSC3	18	28604320	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3031576	28604320	49472928	10573	18558										
DSG1	1828	broad.mit.edu	37	chr18	28906843	28906843	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgtcatttaaggtaagaGattataacactaaaaatggc	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28906843G>T	ENST00000257192.4	+	3	303	c.91G>T	c.(91-93)Gat>Tat	p.D31Y		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	31					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.D31Y(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TAAGGTAAGAGATTATAACAC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	18											65	68	67					18																	28906843		2203	4298	6501	27160841	SO:0001583	missense	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.91G>T	18.37:g.28906843G>T	ENSP00000257192:p.Asp31Tyr		27160841	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.756575	0.69648	.	.	ENSG00000134760	ENST00000257192	T	0.59364	0.27	5.53	5.53	0.82687	.	0.098320	0.44097	D	0.000483	T	0.58352	0.2116	L	0.57536	1.79	0.80722	D	1	B	0.33345	0.409	B	0.34489	0.184	T	0.57418	-0.7815	10	0.39692	T	0.17	.	19.4571	0.94897	0.0:0.0:1.0:0.0	.	31	Q02413	DSG1_HUMAN	Y	31	ENSP00000257192:D31Y	ENSP00000257192:D31Y	D	+	1	0	DSG1	27160841	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	6.473000	0.73572	2.597000	0.87782	0.557000	0.71058	GAT		0.353	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28906843	G	T	28906843	3	4	61	1	0	0	0	0	1	0	0	0	4787	942	33	2	101	2	DSG1	18	28906843	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	302523	28906843	49170405	10574	18559										
DSG1	1828	broad.mit.edu	37	chr18	28906914	28906914	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgtgaatggatcaagttCgcagcagcctgtcgtgaagg	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28906914C>T	ENST00000257192.4	+	3	374	c.162C>T	c.(160-162)ttC>ttT	p.F54F		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	54	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.F54F(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			GGATCAAGTTCGCAGCAGCCT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	18											121	116	118					18																	28906914		2203	4300	6503	27160912	SO:0001819	synonymous_variant	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.162C>T	18.37:g.28906914C>T			27160912	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																				0.393	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28906914	C	T	28906914	2	4	61	1	0	0	0	0	0	0	0	1	4787	883	31	1		1	DSG1	18	28906914	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71	28906914	49170334	10575	18560										
DSG1	1828	broad.mit.edu	37	chr18	28914134	28914134	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatagaaatgaatgaaaGaacaaatgtgggaattttaa	10	1	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28914134G>T	ENST00000257192.4	+	8	1186	c.974G>T	c.(973-975)aGa>aTa	p.R325I		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	325	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.R325I(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			ATGAATGAAAGAACAAATGTG	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	18											58	67	64					18																	28914134		2200	4292	6492	27168132	SO:0001583	missense	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.974G>T	18.37:g.28914134G>T	ENSP00000257192:p.Arg325Ile		27168132	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.568591	0.65651	.	.	ENSG00000134760	ENST00000257192	T	0.38401	1.14	5.67	3.79	0.43588	Cadherin (4);Cadherin-like (1);	0.261634	0.33631	N	0.004701	T	0.34395	0.0896	L	0.52573	1.65	0.80722	D	1	B	0.24721	0.11	B	0.32928	0.155	T	0.18650	-1.0330	10	0.44086	T	0.13	.	10.8657	0.46853	0.0:0.2851:0.6082:0.1067	.	325	Q02413	DSG1_HUMAN	I	325	ENSP00000257192:R325I	ENSP00000257192:R325I	R	+	2	0	DSG1	27168132	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.078000	0.30754	2.668000	0.90789	0.563000	0.77884	AGA		0.269	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28914134	G	T	28914134	3	4	61	1	0	0	0	0	1	0	0	0	4787	942	33	2	1004	2	DSG1	18	28914134	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7220	28914134	49163114	10576	18561										
DSG1	1828	broad.mit.edu	37	chr18	28934568	28934568	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccaatctccccacatttCggcactaccacagtaatttc	3	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28934568C>T	ENST00000257192.4	+	15	2621	c.2409C>T	c.(2407-2409)ttC>ttT	p.F803F	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG1_ENST00000462981.2_Silent_p.F162F	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	803					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.F803F(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CCCCACATTTCGGCACTACCA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	18											117	107	111					18																	28934568		2203	4300	6503	27188566	SO:0001819	synonymous_variant	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.2409C>T	18.37:g.28934568C>T			27188566	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																				0.512	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28934568	C	T	28934568	2	4	61	1	0	0	0	0	0	0	0	1	4787	883	31	1		1	DSG1	18	28934568	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20434	28934568	49142680	10577	18562										
DSG4	147409	broad.mit.edu	37	chr18	28968333	28968333	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctatttttcttatagattCgatcagactgcgaatcgaac	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28968333C>T	ENST00000308128.4	+	4	355	c.220C>T	c.(220-222)Cga>Tga	p.R74*	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Nonsense_Mutation_p.R74*	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	74	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R74*(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTTATAGATTCGATCAGACTG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											63	56	58					18																	28968333		2203	4299	6502	27222331	SO:0001587	stop_gained	147409			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.220C>T	18.37:g.28968333C>T	ENSP00000311859:p.Arg74*		27222331	A2RUI1|Q6Y9L9|Q8IXV4	Nonsense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	37	6.336440	0.97485	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	.	.	.	5.73	4.84	0.62591	.	0.000000	0.30101	N	0.010401	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	14.0555	0.64767	0.1557:0.8443:0.0:0.0	.	.	.	.	X	74	.	ENSP00000311859:R74X	R	+	1	2	DSG4	27222331	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.756000	0.55205	1.361000	0.45981	0.650000	0.86243	CGA		0.418	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28968333	C	T	28968333	4	4	61	1	0	0	0	0	0	1	0	0	4790	876	31	1	234	1	DSG4	18	28968333	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33765	28968333	49108915	10578	18563										
DSG4	147409	broad.mit.edu	37	chr18	28968937	28968937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgataacgctccagtcttttCgcaaagtgtatacacagcca	7	11	1	1	rs369555342		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28968937C>T	ENST00000308128.4	+	5	608	c.473C>T	c.(472-474)tCg>tTg	p.S158L	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.S158L	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	158	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S158L(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CCAGTCTTTTCGCAAAGTGTA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	18						C	LEU/SER,LEU/SER	0,4406		0,0,2203	104	100	101		473,473	6.1	0.8	18		101	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	DSG4	NM_001134453.1,NM_177986.3	145,145	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	158/1060,158/1041	28968937	1,13003	2203	4299	6502	27222935	SO:0001583	missense	147409			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.473C>T	18.37:g.28968937C>T	ENSP00000311859:p.Ser158Leu		27222935	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.263611	0.59431	0.0	1.16E-4	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.61040	0.14;0.14	6.11	6.11	0.99139	Cadherin (3);Cadherin-like (1);	0.242046	0.21442	N	0.074461	T	0.56108	0.1963	M	0.69463	2.115	0.32283	N	0.567384	P;P	0.43431	0.807;0.549	B;B	0.36244	0.22;0.158	T	0.64698	-0.6346	10	0.25106	T	0.35	.	18.9147	0.92501	0.0:1.0:0.0:0.0	.	158;158	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	L	158	ENSP00000311859:S158L;ENSP00000352785:S158L	ENSP00000311859:S158L	S	+	2	0	DSG4	27222935	1.000000	0.71417	0.836000	0.33094	0.845000	0.48019	6.096000	0.71446	2.906000	0.99361	0.655000	0.94253	TCG		0.413	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28968937	C	T	28968937	3	4	61	1	0	0	0	0	1	0	0	0	4790	893	31	1	491	1	DSG4	18	28968937	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	604	28968937	49108311	10579	18564										
DSG4	147409	broad.mit.edu	37	chr18	28972152	28972152	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagagaattgtttaagttCggaactgatacgattacaag	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:28972152C>T	ENST00000308128.4	+	8	989	c.854C>T	c.(853-855)tCg>tTg	p.S285L	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.S285L	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	285	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S285L(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TGTTTAAGTTCGGAACTGATA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											115	115	115					18																	28972152		2203	4300	6503	27226150	SO:0001583	missense	147409			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.854C>T	18.37:g.28972152C>T	ENSP00000311859:p.Ser285Leu		27226150	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508014	0.64410	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.53206	0.63;0.63	5.45	5.45	0.79879	Cadherin (3);Cadherin-like (1);	0.000000	0.29239	N	0.012727	T	0.66307	0.2776	M	0.86502	2.82	0.30830	N	0.736843	P;D	0.57571	0.797;0.98	P;P	0.55667	0.521;0.781	T	0.72475	-0.4282	10	0.51188	T	0.08	.	13.6419	0.62255	0.1543:0.8457:0.0:0.0	.	285;285	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	L	285	ENSP00000311859:S285L;ENSP00000352785:S285L	ENSP00000311859:S285L	S	+	2	0	DSG4	27226150	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.129000	0.50500	2.721000	0.93114	0.655000	0.94253	TCG		0.338	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28972152	C	T	28972152	3	4	61	1	0	0	0	0	1	0	0	0	4790	893	31	1	884	1	DSG4	18	28972152	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3215	28972152	49105096	10580	18565										
KIAA1012	22878	broad.mit.edu	37	chr18	29429636	29429636	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggcaagtgagcttgtgGttttttcaattcagaagata	10	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29429636G>T	ENST00000283351.4	-	25	3963	c.3628C>A	c.(3628-3630)Cca>Aca	p.P1210T	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.P1156T	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1210					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.P1210T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGAGCTTGTGGTTTTTTCAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											96	90	92					18																	29429636		2203	4300	6503	27683634	SO:0001583	missense	22878			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.3628C>A	18.37:g.29429636G>T	ENSP00000283351:p.Pro1210Thr		27683634	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	G	4.853	0.158513	0.09236	.	.	ENSG00000153339	ENST00000283351	T	0.16743	2.32	5.57	-2.57	0.06248	.	1.181700	0.05698	N	0.593509	T	0.05135	0.0137	N	0.01874	-0.695	0.36324	D	0.858422	B	0.02656	0.0	B	0.06405	0.002	T	0.47623	-0.9103	10	0.12766	T	0.61	.	4.4232	0.11490	0.1433:0.0869:0.1649:0.6049	.	1210	Q9Y2L5	TPPC8_HUMAN	T	1210	ENSP00000283351:P1210T	ENSP00000283351:P1210T	P	-	1	0	TRAPPC8	27683634	0.852000	0.29690	0.153000	0.22517	0.420000	0.31355	0.265000	0.18515	-0.016000	0.14127	-0.182000	0.12963	CCA		0.348	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		T	29429636	G	T	29429636	3	4	61	1	0	0	0	0	1	0	0	0	8225	1261	44	2	699	2	KIAA1012	18	29429636	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	457484	29429636	48647612	10581	18566										
KIAA1012	22878	broad.mit.edu	37	chr18	29488855	29488855	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attattccagtatttcctttCtttgtttcatgtaacgatga	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29488855C>A	ENST00000283351.4	-	7	1319	c.984G>T	c.(982-984)aaG>aaT	p.K328N	TRAPPC8_ENST00000582513.1_Missense_Mutation_p.K328N|TRAPPC8_ENST00000582539.1_Missense_Mutation_p.K274N	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	328					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.K328N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TATTTCCTTTCTTTGTTTCAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											100	88	92					18																	29488855		2203	4300	6503	27742853	SO:0001583	missense	22878			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.984G>T	18.37:g.29488855C>A	ENSP00000283351:p.Lys328Asn		27742853	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.881726	0.33255	.	.	ENSG00000153339	ENST00000283351	T	0.08370	3.1	5.83	2.67	0.31697	.	0.127642	0.51477	D	0.000092	T	0.05135	0.0137	N	0.14661	0.345	0.48087	D	0.999581	B;P	0.36282	0.009;0.546	B;B	0.36608	0.013;0.229	T	0.50474	-0.8824	10	0.17832	T	0.49	.	12.1679	0.54141	0.0:0.7835:0.0:0.2165	.	328;328	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	N	328	ENSP00000283351:K328N	ENSP00000283351:K328N	K	-	3	2	TRAPPC8	27742853	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.661000	0.25023	0.818000	0.34468	0.655000	0.94253	AAG		0.398	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		A	29488855	C	A	29488855	3	1	61	1	0	0	0	0	1	0	0	0	8225	912	32	2	3415	2	KIAA1012	18	29488855	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	59219	29488855	48588393	10582	18567										
FAM59A	64762	broad.mit.edu	37	chr18	29848074	29848074	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgccatggggaaccgtcGccacaggatctgggggccag	17	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29848074G>A	ENST00000269209.6	-	6	2394	c.2391C>T	c.(2389-2391)ggC>ggT	p.G797G	GAREM_ENST00000399218.4_Silent_p.G796G			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	797					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.G796G(2)									GGGAACCGTCGCCACAGGATC	0.517																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	18											36	34	35					18																	29848074		2203	4300	6503	28102072	SO:0001819	synonymous_variant	64762			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.2391C>T	18.37:g.29848074G>A			28102072	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																				0.517	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29848074	G	A	29848074	2	1	61	1	0	0	0	0	0	0	0	1	5611	1074	38	1		1	FAM59A	18	29848074	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	359219	29848074	48229174	10583	18568										
FAM59A	64762	broad.mit.edu	37	chr18	29867850	29867850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttttctccacaatgttgCggatggtgtgttcgccctct	11	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29867850C>T	ENST00000269209.6	-	4	713	c.710G>A	c.(709-711)cGc>cAc	p.R237H	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000399218.4_Missense_Mutation_p.R237H|GAREM_ENST00000578619.1_5'UTR			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	237	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.R237H(1)									CACAATGTTGCGGATGGTGTG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	18											173	144	154					18																	29867850		2203	4300	6503	28121848	SO:0001583	missense	64762			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.710G>A	18.37:g.29867850C>T	ENSP00000269209:p.Arg237His		28121848	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	C	31	5.096815	0.94197	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.15017	2.46;2.46	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.45216	0.1331	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.995	T	0.30966	-0.9960	10	0.87932	D	0	-27.9758	20.0679	0.97707	0.0:1.0:0.0:0.0	.	237;237	Q9H706;Q9H706-3	FA59A_HUMAN;.	H	237	ENSP00000382165:R237H;ENSP00000269209:R237H	ENSP00000269209:R237H	R	-	2	0	FAM59A	28121848	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.398000	0.79919	2.821000	0.97095	0.561000	0.74099	CGC		0.552	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		T	29867850	C	T	29867850	3	4	61	1	0	0	0	0	1	0	0	0	5611	768	27	1	1929	1	FAM59A	18	29867850	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19776	29867850	48209398	10584	18569										
FAM59A	64762	broad.mit.edu	37	chr18	29890253	29890253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatattgcactggctcctttAtatctcggtcttgttccagc	7	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29890253A>G	ENST00000269209.6	-	3	299	c.296T>C	c.(295-297)aTa>aCa	p.I99T	GAREM_ENST00000399218.4_Missense_Mutation_p.I99T|GAREM_ENST00000578619.1_5'UTR			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	99	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.I99T(1)									TGGCTCCTTTATATCTCGGTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	18											204	182	190					18																	29890253		2203	4300	6503	28144251	SO:0001583	missense	64762			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.296T>C	18.37:g.29890253A>G	ENSP00000269209:p.Ile99Thr		28144251	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593518	0.86953	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.15139	2.45;2.45	5.76	5.76	0.90799	.	0.044856	0.85682	D	0.000000	T	0.30230	0.0758	L	0.36672	1.1	0.58432	D	0.999999	D;P	0.56968	0.978;0.778	P;P	0.60236	0.871;0.501	T	0.01748	-1.1282	10	0.87932	D	0	-13.358	16.066	0.80870	1.0:0.0:0.0:0.0	.	99;99	Q9H706;Q9H706-3	FA59A_HUMAN;.	T	99	ENSP00000382165:I99T;ENSP00000269209:I99T	ENSP00000269209:I99T	I	-	2	0	FAM59A	28144251	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.878000	0.92393	2.200000	0.70718	0.533000	0.62120	ATA		0.443	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		G	29890253	A	G	29890253	3	3	61	1	0	0	0	0	1	0	0	0	5611	449	16	4	2347	4	FAM59A	18	29890253	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22403	29890253	48186995	10585	18570										
FAM59A	64762	broad.mit.edu	37	chr18	29972974	29972974	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatcagcagatagtcatttTcccgcagcccttctacgcac	7	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:29972974T>A	ENST00000269209.6	-	2	149	c.146A>T	c.(145-147)gAa>gTa	p.E49V	GAREM_ENST00000399218.4_Missense_Mutation_p.E49V			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	49	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.E49V(1)									ATAGTCATTTTCCCGCAGCCC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											126	109	114					18																	29972974		2203	4300	6503	28226972	SO:0001583	missense	64762			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.146A>T	18.37:g.29972974T>A	ENSP00000269209:p.Glu49Val		28226972	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.981692	0.93044	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.14391	2.51;2.51	5.94	5.94	0.96194	.	0.107642	0.64402	D	0.000009	T	0.32763	0.0840	L	0.60455	1.87	0.80722	D	1	D;P	0.62365	0.991;0.81	P;P	0.62089	0.898;0.635	T	0.01692	-1.1294	10	0.87932	D	0	-24.162	16.3871	0.83514	0.0:0.0:0.0:1.0	.	49;49	Q9H706;Q9H706-3	FA59A_HUMAN;.	V	49	ENSP00000382165:E49V;ENSP00000269209:E49V	ENSP00000269209:E49V	E	-	2	0	FAM59A	28226972	1.000000	0.71417	0.985000	0.45067	0.996000	0.88848	7.671000	0.83941	2.276000	0.75962	0.533000	0.62120	GAA		0.423	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29972974	T	A	29972974	3	1	61	1	0	0	0	0	1	0	0	0	5611	1783	62	5	2501	5	FAM59A	18	29972974	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	82721	29972974	48104274	10586	18571										
C18orf34	374864	broad.mit.edu	37	chr18	30554573	30554573	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggaagttggccagcctcaTctggctgaagaggaccacca	12	12	2	2	rs142622043		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:30554573T>C	ENST00000383096.3	-	22	2643	c.2461A>G	c.(2461-2463)Atg>Gtg	p.M821V	CCDC178_ENST00000402325.1_Missense_Mutation_p.M771V|CCDC178_ENST00000581852.1_Missense_Mutation_p.M26V|CCDC178_ENST00000403303.1_Missense_Mutation_p.M821V|CCDC178_ENST00000583930.1_Missense_Mutation_p.M845V|CCDC178_ENST00000406524.2_Missense_Mutation_p.M845V|CCDC178_ENST00000300227.8_Missense_Mutation_p.M783V|CCDC178_ENST00000579947.1_Missense_Mutation_p.M821V|CCDC178_ENST00000579916.1_Missense_Mutation_p.M141V			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	821								p.M783V(1)|p.M821V(1)									GCCAGCCTCATCTGGCTGAAG	0.493													T|||	1	0.000199681	0	0	5008	,	,		16369	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	18											66	61	63					18																	30554573		2203	4300	6503	28808571	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2461A>G	18.37:g.30554573T>C	ENSP00000372576:p.Met821Val		28808571	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	7.057	0.565649	0.13560	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.14266	2.57;2.57;2.58;2.52;2.57	5.5	0.498	0.16908	.	.	.	.	.	T	0.08891	0.0220	L	0.36672	1.1	0.21147	N	0.99977	B;B;B;B;B;B	0.21606	0.058;0.005;0.058;0.058;0.058;0.058	B;B;B;B;B;B	0.16289	0.015;0.004;0.015;0.015;0.009;0.009	T	0.34576	-0.9823	9	0.31617	T	0.26	-3.0837	3.3455	0.07133	0.1799:0.379:0.0:0.4411	.	845;821;771;821;783;821	F8W7A7;A1L4G8;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;.;CR034_HUMAN	V	821;821;783;845;771	ENSP00000385591:M821V;ENSP00000372576:M821V;ENSP00000300227:M783V;ENSP00000385867:M845V;ENSP00000385234:M771V	ENSP00000300227:M783V	M	-	1	0	C18orf34	28808571	0.602000	0.26916	0.166000	0.22797	0.988000	0.76386	1.884000	0.39668	0.358000	0.24211	0.460000	0.39030	ATG		0.493	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30554573	T	C	30554573	3	2	61	1	0	0	0	0	1	0	0	0	1908	1435	50	4	150	4	C18orf34	18	30554573	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	581599	30554573	47522675	10587	18572										
C18orf34	374864	broad.mit.edu	37	chr18	30803114	30803114	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttttcttccccttttttcGtaattttttctttacttttc	3	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:30803114G>A	ENST00000383096.3	-	18	2070	c.1888C>T	c.(1888-1890)Cga>Tga	p.R630*	CCDC178_ENST00000402325.1_Nonsense_Mutation_p.R630*|CCDC178_ENST00000403303.1_Nonsense_Mutation_p.R630*|CCDC178_ENST00000583930.1_Nonsense_Mutation_p.R630*|CCDC178_ENST00000406524.2_Nonsense_Mutation_p.R630*|CCDC178_ENST00000300227.8_Intron|CCDC178_ENST00000579947.1_Nonsense_Mutation_p.R630*|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	630								p.R630*(1)									CCCTTTTTTCGTAATTTTTTC	0.289																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											125	116	118					18																	30803114		1798	4064	5862	29057112	SO:0001587	stop_gained	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1888C>T	18.37:g.30803114G>A	ENSP00000372576:p.Arg630*		29057112	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Nonsense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	G	36	5.620644	0.96660	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000406524;ENST00000402325	.	.	.	4.87	-3.73	0.04398	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	1.9035	10.261	0.43427	0.0:0.2174:0.2274:0.5552	.	.	.	.	X	630	.	ENSP00000372576:R630X	R	-	1	2	C18orf34	29057112	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.220000	0.09215	-0.906000	0.03866	-1.036000	0.02392	CGA		0.289	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30803114	G	A	30803114	4	1	61	1	0	0	0	0	0	1	0	0	1908	1153	40	1	739	1	C18orf34	18	30803114	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248541	30803114	47274134	10588	18573										
C18orf34	374864	broad.mit.edu	37	chr18	30825366	30825366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtcaaatattttatttcaGattcgtattttgattttttc	4	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:30825366G>T	ENST00000383096.3	-	15	1618	c.1436C>A	c.(1435-1437)tCt>tAt	p.S479Y	CCDC178_ENST00000402325.1_Missense_Mutation_p.S479Y|CCDC178_ENST00000403303.1_Missense_Mutation_p.S479Y|CCDC178_ENST00000583930.1_Missense_Mutation_p.S479Y|CCDC178_ENST00000406524.2_Missense_Mutation_p.S479Y|CCDC178_ENST00000300227.8_Missense_Mutation_p.S479Y|CCDC178_ENST00000579947.1_Missense_Mutation_p.S479Y|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	479								p.S479Y(1)									TTTTATTTCAGATTCGTATTT	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	18											84	76	79					18																	30825366		2202	4297	6499	29079364	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1436C>A	18.37:g.30825366G>T	ENSP00000372576:p.Ser479Tyr		29079364	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	G	4.945	0.175491	0.09391	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.75	0.418	0.16429	.	.	.	.	.	T	0.35158	0.0922	L	0.48642	1.525	0.09310	N	1	D;D;D;D	0.60160	0.987;0.987;0.987;0.987	P;P;P;P	0.55303	0.773;0.773;0.773;0.773	T	0.15636	-1.0430	9	0.62326	D	0.03	0.6779	5.5916	0.17303	0.0981:0.0:0.3722:0.5297	.	479;479;479;479	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	Y	479	ENSP00000385591:S479Y;ENSP00000372576:S479Y;ENSP00000300227:S479Y;ENSP00000385867:S479Y;ENSP00000385234:S479Y	ENSP00000300227:S479Y	S	-	2	0	C18orf34	29079364	0.012000	0.17670	0.020000	0.16555	0.010000	0.07245	0.120000	0.15647	0.257000	0.21650	0.563000	0.77884	TCT		0.264	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		T	30825366	G	T	30825366	3	4	61	1	0	0	0	0	1	0	0	0	1908	942	33	2	1203	2	C18orf34	18	30825366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22252	30825366	47251882	10589	18574										
C18orf34	374864	broad.mit.edu	37	chr18	30873182	30873182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttcccttattgcttcagTcacttcctcttccttctcct	3	15	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:30873182T>C	ENST00000383096.3	-	12	1299	c.1117A>G	c.(1117-1119)Act>Gct	p.T373A	CCDC178_ENST00000402325.1_Missense_Mutation_p.T373A|CCDC178_ENST00000403303.1_Missense_Mutation_p.T373A|CCDC178_ENST00000583930.1_Missense_Mutation_p.T373A|CCDC178_ENST00000406524.2_Missense_Mutation_p.T373A|CCDC178_ENST00000300227.8_Missense_Mutation_p.T373A|CCDC178_ENST00000579947.1_Missense_Mutation_p.T373A|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	373								p.T373A(1)									ATTGCTTCAGTCACTTCCTCT	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	18											121	115	117					18																	30873182		2200	4296	6496	29127180	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1117A>G	18.37:g.30873182T>C	ENSP00000372576:p.Thr373Ala		29127180	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	5.834	0.338065	0.11013	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	3.59	2.4	0.29515	.	.	.	.	.	T	0.30008	0.0751	L	0.39898	1.24	0.09310	N	1	B;B;B;B	0.30634	0.229;0.288;0.288;0.288	B;B;B;B	0.30572	0.117;0.05;0.05;0.05	T	0.17806	-1.0357	9	0.22706	T	0.39	-1.3273	6.274	0.20971	0.2214:0.0:0.0:0.7786	.	373;373;373;373	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	A	373	ENSP00000385591:T373A;ENSP00000372576:T373A;ENSP00000300227:T373A;ENSP00000385867:T373A;ENSP00000385234:T373A	ENSP00000300227:T373A	T	-	1	0	C18orf34	29127180	0.001000	0.12720	0.009000	0.14445	0.060000	0.15804	0.564000	0.23563	0.712000	0.32039	-0.723000	0.03601	ACT		0.294	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30873182	T	C	30873182	3	2	61	1	0	0	0	0	1	0	0	0	1908	1667	58	4	1534	4	C18orf34	18	30873182	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	47816	30873182	47204066	10590	18575										
ASXL3	80816	broad.mit.edu	37	chr18	31318781	31318781	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccaggatgaaaatcataaGacaatacctgaattttctga	7	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31318781G>T	ENST00000269197.5	+	11	1413	c.1413G>T	c.(1411-1413)aaG>aaT	p.K471N		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K178N(1)|p.K471N(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAAATCATAAGACAATACCTG	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	18											54	55	55					18																	31318781		1860	4086	5946	29572779	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.1413G>T	18.37:g.31318781G>T	ENSP00000269197:p.Lys471Asn		29572779	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	g	10.78	1.445956	0.25987	.	.	ENSG00000141431	ENST00000269197	T	0.21361	2.01	5.2	2.38	0.29361	.	1.365760	0.04677	N	0.411675	T	0.20373	0.0490	M	0.61703	1.905	0.25752	N	0.985048	P	0.43477	0.808	B	0.33454	0.164	T	0.28299	-1.0048	10	0.34782	T	0.22	.	6.8378	0.23945	0.264:0.1222:0.6138:0.0	.	471	Q9C0F0	ASXL3_HUMAN	N	471	ENSP00000269197:K471N	ENSP00000269197:K471N	K	+	3	2	ASXL3	29572779	0.997000	0.39634	0.993000	0.49108	0.943000	0.58893	1.403000	0.34612	0.275000	0.22094	-0.349000	0.07799	AAG		0.398	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31318781	G	T	31318781	3	4	61	1	0	0	0	0	1	0	0	0	1069	933	33	2	1455	2	ASXL3	18	31318781	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	445599	31318781	46758467	10591	18576										
ASXL3	80816	broad.mit.edu	37	chr18	31319022	31319022	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccacttcatctatgactCatgtcagtgacacagaacat	5	12	4	3	rs200334892	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31319022C>A	ENST00000269197.5	+	11	1654	c.1654C>A	c.(1654-1656)Cat>Aat	p.H552N		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H552N(1)|p.H259N(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ATCTATGACTCATGTCAGTGA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	18											71	68	69					18																	31319022		1934	4148	6082	29573020	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.1654C>A	18.37:g.31319022C>A	ENSP00000269197:p.His552Asn		29573020	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.304963	0.23736	.	.	ENSG00000141431	ENST00000269197	T	0.13778	2.56	5.47	3.24	0.37175	.	1.046090	0.07418	N	0.893518	T	0.09949	0.0244	L	0.36672	1.1	0.25061	N	0.991062	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.22706	T	0.39	.	1.9948	0.03454	0.293:0.447:0.0:0.2601	.	552	Q9C0F0	ASXL3_HUMAN	N	552	ENSP00000269197:H552N	ENSP00000269197:H552N	H	+	1	0	ASXL3	29573020	0.987000	0.35691	0.965000	0.40720	0.919000	0.55068	2.027000	0.41078	1.393000	0.46605	0.467000	0.42956	CAT		0.423	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31319022	C	A	31319022	3	1	61	1	0	0	0	0	1	0	0	0	1069	826	29	2	1696	2	ASXL3	18	31319022	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	241	31319022	46758226	10592	18577										
ASXL3	80816	broad.mit.edu	37	chr18	31319778	31319778	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctcccagcagaagaatCtgtctaatactcccgaaccc	5	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31319778C>A	ENST00000269197.5	+	11	2410	c.2410C>A	c.(2410-2412)Ctg>Atg	p.L804M		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	804					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L804M(1)|p.L511M(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GCAGAAGAATCTGTCTAATAC	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	18											40	40	40					18																	31319778		1916	4120	6036	29573776	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2410C>A	18.37:g.31319778C>A	ENSP00000269197:p.Leu804Met		29573776	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	8.521	0.868719	0.17322	.	.	ENSG00000141431	ENST00000269197	T	0.15372	2.43	6.04	2.07	0.26955	.	1.053760	0.07466	N	0.901455	T	0.11965	0.0291	L	0.27053	0.805	0.09310	N	1	P	0.46395	0.877	B	0.41723	0.365	T	0.21348	-1.0248	10	0.33141	T	0.24	.	4.7008	0.12827	0.1262:0.6177:0.1219:0.1342	.	804	Q9C0F0	ASXL3_HUMAN	M	804	ENSP00000269197:L804M	ENSP00000269197:L804M	L	+	1	2	ASXL3	29573776	0.000000	0.05858	0.202000	0.23494	0.078000	0.17371	0.139000	0.16036	0.430000	0.26230	0.563000	0.77884	CTG		0.483	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31319778	C	A	31319778	3	1	61	1	0	0	0	0	1	0	0	0	1069	912	32	2	2452	2	ASXL3	18	31319778	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	756	31319778	46757470	10593	18578										
ASXL3	80816	broad.mit.edu	37	chr18	31325280	31325280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactccaaatgagaaagcGagaaaaccaccccaaaaaga	6	12	0	3	rs201071954		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31325280G>A	ENST00000269197.5	+	12	5468	c.5468G>A	c.(5467-5469)cGa>cAa	p.R1823Q		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1823					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1823Q(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ATGAGAAAGCGAGAAAACCAC	0.478													G|||	1	0.000199681	0	0.0014	5008	,	,		19881	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											142	143	143					18																	31325280		1927	4124	6051	29579278	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.5468G>A	18.37:g.31325280G>A	ENSP00000269197:p.Arg1823Gln		29579278	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.14	3.313996	0.60414	.	.	ENSG00000141431	ENST00000269197	T	0.18502	2.21	5.7	5.7	0.88788	.	.	.	.	.	T	0.32133	0.0819	L	0.27053	0.805	0.47009	D	0.999282	D	0.89917	1.0	D	0.79108	0.992	T	0.02417	-1.1162	9	0.49607	T	0.09	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	1823	Q9C0F0	ASXL3_HUMAN	Q	1823	ENSP00000269197:R1823Q	ENSP00000269197:R1823Q	R	+	2	0	ASXL3	29579278	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.444000	0.66587	2.698000	0.92095	0.655000	0.94253	CGA		0.478	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31325280	G	A	31325280	3	1	61	1	0	0	0	0	1	0	0	0	1069	1058	37	1	5514	1	ASXL3	18	31325280	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5502	31325280	46751968	10594	18579										
ASXL3	80816	broad.mit.edu	37	chr18	31326217	31326217	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagccacaaaagccttttacCcaattagctgctcagaaaat	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31326217C>A	ENST00000269197.5	+	12	6405	c.6405C>A	c.(6403-6405)acC>acA	p.T2135T		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T2135T(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AGCCTTTTACCCAATTAGCTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	18											84	90	88					18																	31326217		1893	4115	6008	29580215	SO:0001819	synonymous_variant	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6405C>A	18.37:g.31326217C>A			29580215	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	37	CCDS45847.1																																																																																				0.413	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31326217	C	A	31326217	2	1	61	1	0	0	0	0	0	0	0	1	1069	610	22	2		2	ASXL3	18	31326217	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	937	31326217	46751031	10595	18580										
NOL4	8715	broad.mit.edu	37	chr18	31432850	31432850	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagttcatctgcagatcGcaataaaaatgcagctgatt	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31432850G>A	ENST00000261592.5	-	11	2170	c.1873C>T	c.(1873-1875)Cga>Tga	p.R625*	NOL4_ENST00000535384.1_Nonsense_Mutation_p.R340*|NOL4_ENST00000589544.1_Nonsense_Mutation_p.R523*|NOL4_ENST00000535475.1_Nonsense_Mutation_p.R406*|NOL4_ENST00000538587.1_Nonsense_Mutation_p.R551*|NOL4_ENST00000269185.4_Nonsense_Mutation_p.R409*	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	625						nucleolus (GO:0005730)	RNA binding (GO:0003723)	p.R625*(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						TCTGCAGATCGCAATAAAAAT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											137	124	128					18																	31432850		2203	4300	6503	29686848	SO:0001587	stop_gained	8715			AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1873C>T	18.37:g.31432850G>A	ENSP00000261592:p.Arg625*		29686848	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Nonsense_Mutation	SNP	ENST00000261592.5	37	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	G	40	8.105680	0.98657	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.296	20.4082	0.99013	0.0:0.0:1.0:0.0	.	.	.	.	X	625;409;340;406;551	.	ENSP00000261592:R625X	R	-	1	2	NOL4	29686848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.320000	0.96346	2.814000	0.96858	0.655000	0.94253	CGA		0.438	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		A	31432850	G	A	31432850	4	1	61	1	0	0	0	0	0	1	0	0	10555	1095	38	1	47	1	NOL4	18	31432850	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	106633	31432850	46644398	10596	18581										
NOL4	8715	broad.mit.edu	37	chr18	31463348	31463348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgagtaagtggcctgggtcGcctctggtttacactgtttg	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:31463348G>A	ENST00000261592.5	-	10	1880	c.1583C>T	c.(1582-1584)gCg>gTg	p.A528V	NOL4_ENST00000535384.1_Missense_Mutation_p.A243V|NOL4_ENST00000589544.1_Missense_Mutation_p.A426V|NOL4_ENST00000535475.1_Missense_Mutation_p.A309V|NOL4_ENST00000538587.1_Missense_Mutation_p.A454V|NOL4_ENST00000269185.4_Missense_Mutation_p.A312V	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	528						nucleolus (GO:0005730)	RNA binding (GO:0003723)	p.A528V(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						GGCCTGGGTCGCCTCTGGTTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											137	114	122					18																	31463348		2203	4300	6503	29717346	SO:0001583	missense	8715			AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1583C>T	18.37:g.31463348G>A	ENSP00000261592:p.Ala528Val		29717346	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	37	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223682	0.39300	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.78	3.94	0.45596	.	0.599043	0.17048	N	0.189053	T	0.44540	0.1298	L	0.29908	0.895	0.28822	N	0.897628	B;B;B;B;D;B	0.67145	0.165;0.165;0.052;0.052;0.996;0.387	B;B;B;B;P;B	0.57009	0.023;0.023;0.023;0.023;0.811;0.075	T	0.31364	-0.9946	9	0.39692	T	0.17	-2.6946	11.9138	0.52753	0.0669:0.1213:0.8117:0.0	.	243;454;528;243;426;309	B7Z3Z7;B4DSQ0;O94818;F5H1E3;O94818-2;B3KRF4	.;.;NOL4_HUMAN;.;.;.	V	528;312;243;309;454	.	ENSP00000261592:A528V	A	-	2	0	NOL4	29717346	1.000000	0.71417	0.829000	0.32907	0.456000	0.32438	4.317000	0.59184	1.401000	0.46761	0.563000	0.77884	GCG		0.473	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		A	31463348	G	A	31463348	3	1	61	1	0	0	0	0	1	0	0	0	10555	1087	38	1	341	1	NOL4	18	31463348	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30498	31463348	46613900	10597	18582										
ZNF397	84307	broad.mit.edu	37	chr18	32822559	32822559	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaagcagaatgggagtaCtcaatcctgccaagaattgt	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:32822559C>A	ENST00000330501.7	+	2	278	c.125C>A	c.(124-126)aCt>aAt	p.T42N	ZNF397_ENST00000261333.6_Missense_Mutation_p.T42N|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000585800.1_Missense_Mutation_p.T42N|ZNF397_ENST00000355632.4_Missense_Mutation_p.T42N|ZNF397_ENST00000591206.1_Missense_Mutation_p.T42N|ZNF397_ENST00000592264.1_Missense_Mutation_p.T42N	NM_001135178.2	NP_001128650.1	Q8NF99	ZN397_HUMAN	zinc finger protein 397	42					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T42N(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						AATGGGAGTACTCAATCCTGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	18											55	61	59					18																	32822559		2203	4300	6503	31076557	SO:0001583	missense	84307			BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812		"-", "Zinc fingers, C2H2-type"	18818	protein-coding gene	gene with protein product		609601	"zinc finger protein 47"	ZNF47			Standard	NM_032347		Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000330501.7:c.125C>A	18.37:g.32822559C>A	ENSP00000331577:p.Thr42Asn		31076557	Q9BRM2	Missense_Mutation	SNP	ENST00000330501.7	37	CCDS45852.1	.	.	.	.	.	.	.	.	.	.	C	3.400	-0.122495	0.06795	.	.	ENSG00000186812	ENST00000261333;ENST00000330501;ENST00000355632	T;T;T	0.06218	4.41;3.33;4.35	4.19	-2.3	0.06785	Retrovirus capsid, C-terminal (1);	1.876600	0.03244	N	0.180904	T	0.02047	0.0064	N	0.01352	-0.895	0.09310	N	1	P;B;P;B	0.46512	0.808;0.0;0.879;0.001	B;B;P;B	0.45449	0.288;0.0;0.481;0.002	T	0.29305	-1.0016	10	0.05959	T	0.93	.	0.1498	0.00092	0.2903:0.2684:0.1581:0.2831	.	42;42;42;42	Q96K65;Q8NF99;Q8NF99-2;Q8NF99-3	.;ZN397_HUMAN;.;.	N	42	ENSP00000261333:T42N;ENSP00000331577:T42N;ENSP00000347850:T42N	ENSP00000261333:T42N	T	+	2	0	ZNF397	31076557	0.000000	0.05858	0.000000	0.03702	0.965000	0.64279	-1.047000	0.03521	-0.498000	0.06632	0.591000	0.81541	ACT		0.463	ZNF397-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442398.1	NM_032347		A	32822559	C	A	32822559	3	1	61	1	0	0	0	0	1	0	0	0	17922	565	20	2	127	2	ZNF397	18	32822559	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1359211	32822559	45254689	10598	18583										
ZNF397OS	100101467	broad.mit.edu	37	chr18	32833622	32833622	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgatgttcaataaggataGaactcctaccaaaagcctta	6	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:32833622G>T	ENST00000420878.3	-	5	1732	c.1277C>A	c.(1276-1278)tCt>tAt	p.S426Y	ZSCAN30_ENST00000333206.5_Missense_Mutation_p.S426Y|ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000592264.1_Intron	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	426					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S426Y(1)		large_intestine(5)|lung(3)|urinary_tract(1)	9						AATAAGGATAGAACTCCTACC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											107	103	104					18																	32833622		1568	3582	5150	31087620	SO:0001583	missense	100101467			AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"-", "Zinc fingers, C2H2-type"	33517	protein-coding gene	gene with protein product			"zinc finger protein 397 opposite strand", "ZNF397 opposite strand"	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.1277C>A	18.37:g.32833622G>T	ENSP00000392371:p.Ser426Tyr		31087620	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	.	.	.	.	.	.	.	.	.	.	G	9.409	1.079953	0.20309	.	.	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.37058	1.22;1.22	4.19	2.31	0.28768	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35838	N	0.002954	T	0.30198	0.0757	M	0.73430	2.235	0.09310	N	0.999999	B	0.30664	0.289	B	0.22753	0.041	T	0.37842	-0.9688	10	0.66056	D	0.02	.	2.4964	0.04622	0.1067:0.1817:0.5087:0.2029	.	426	Q86W11	ZSC30_HUMAN	Y	426;426;361	ENSP00000392371:S426Y;ENSP00000329738:S426Y	ENSP00000329738:S426Y	S	-	2	0	ZSCAN30	31087620	0.019000	0.18553	0.642000	0.29436	0.986000	0.74619	1.403000	0.34612	0.472000	0.27344	0.655000	0.94253	TCT		0.418	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		T	32833622	G	T	32833622	3	4	61	1	0	0	0	0	1	0	0	0	17923	942	33	2	211	2	ZNF397OS	18	32833622	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11063	32833622	45243626	10599	18584										
ZNF24	7572	broad.mit.edu	37	chr18	32917344	32917344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgatgattaataagccccGaattctggctaaaggctttc	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:32917344G>A	ENST00000261332.6	-	4	1138	c.959C>T	c.(958-960)tCg>tTg	p.S320L	ZNF24_ENST00000399061.3_Missense_Mutation_p.S320L|ZNF24_ENST00000589881.1_3'UTR	NM_006965.2	NP_008896.2	P17028	ZNF24_HUMAN	zinc finger protein 24	320					myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S320L(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						AATAAGCCCCGAATTCTGGCT	0.418																																					Colon(42;769 913 8916 19469 46270)											1	Substitution - Missense(1)	large_intestine(1)	18											108	110	110					18																	32917344		2203	4300	6503	31171342	SO:0001583	missense	7572			AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466		"-", "Zinc fingers, C2H2-type"	13032	protein-coding gene	gene with protein product		194534	"zinc finger protein 24 (KOX 17)"	ZNF191			Standard	NM_006965		Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000261332.6:c.959C>T	18.37:g.32917344G>A	ENSP00000261332:p.Ser320Leu		31171342	O14754|Q53YE4|Q6ICR5|Q8IZN4	Missense_Mutation	SNP	ENST00000261332.6	37	CCDS11912.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.664242	0.47572	.	.	ENSG00000172466	ENST00000261332;ENST00000399061	T;T	0.07444	3.19;3.19	5.14	5.14	0.70334	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.120219	0.38778	N	0.001569	T	0.15522	0.0374	M	0.81239	2.535	0.35279	D	0.781144	D	0.63880	0.993	P	0.44647	0.456	T	0.18713	-1.0328	10	0.87932	D	0	.	11.0868	0.48091	0.0:0.0:0.8155:0.1845	.	320	P17028	ZNF24_HUMAN	L	320	ENSP00000261332:S320L;ENSP00000382015:S320L	ENSP00000261332:S320L	S	-	2	0	ZNF24	31171342	0.262000	0.24073	1.000000	0.80357	0.991000	0.79684	2.273000	0.43381	2.679000	0.91253	0.655000	0.94253	TCG		0.418	ZNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255769.1	NM_006965		A	32917344	G	A	32917344	3	1	61	1	0	0	0	0	1	0	0	0	17831	1059	37	1	151	1	ZNF24	18	32917344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83722	32917344	45159904	10600	18585										
ZNF24	7572	broad.mit.edu	37	chr18	32919901	32919901	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcttgagataccatgtCttctactagtacttcccgtt	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:32919901C>A	ENST00000261332.6	-	3	639	c.460G>T	c.(460-462)Gac>Tac	p.D154Y	ZNF24_ENST00000399061.3_Missense_Mutation_p.D154Y|ZNF24_ENST00000589881.1_Missense_Mutation_p.D154Y	NM_006965.2	NP_008896.2	P17028	ZNF24_HUMAN	zinc finger protein 24	154					myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.D154Y(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						GATACCATGTCTTCTACTAGT	0.448																																					Colon(42;769 913 8916 19469 46270)											1	Substitution - Missense(1)	large_intestine(1)	18											112	104	107					18																	32919901		2203	4300	6503	31173899	SO:0001583	missense	7572			AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466		"-", "Zinc fingers, C2H2-type"	13032	protein-coding gene	gene with protein product		194534	"zinc finger protein 24 (KOX 17)"	ZNF191			Standard	NM_006965		Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000261332.6:c.460G>T	18.37:g.32919901C>A	ENSP00000261332:p.Asp154Tyr		31173899	O14754|Q53YE4|Q6ICR5|Q8IZN4	Missense_Mutation	SNP	ENST00000261332.6	37	CCDS11912.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461270	0.26248	.	.	ENSG00000172466	ENST00000261332;ENST00000399061	T;T	0.05258	3.47;3.47	5.58	3.78	0.43462	Transcription regulator SCAN (1);	0.105137	0.42420	D	0.000711	T	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B;B	0.25105	0.118;0.072	B;B	0.30943	0.122;0.008	T	0.35151	-0.9800	10	0.87932	D	0	.	8.2087	0.31471	0.0:0.8214:0.0:0.1786	.	154;154	P17028-2;P17028	.;ZNF24_HUMAN	Y	154	ENSP00000261332:D154Y;ENSP00000382015:D154Y	ENSP00000261332:D154Y	D	-	1	0	ZNF24	31173899	0.389000	0.25205	0.169000	0.22859	0.635000	0.38103	1.359000	0.34113	1.515000	0.48885	0.655000	0.94253	GAC		0.448	ZNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255769.1	NM_006965		A	32919901	C	A	32919901	3	1	61	1	0	0	0	0	1	0	0	0	17831	913	32	2	654	2	ZNF24	18	32919901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2557	32919901	45157347	10601	18586										
C18orf21	83608	broad.mit.edu	37	chr18	33558851	33558851	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctcaaagaacaccagcaAaacaaagaaacacttctctc	3	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:33558851A>C	ENST00000592875.1	+	5	1191	c.545A>C	c.(544-546)aAa>aCa	p.K182T	C18orf21_ENST00000333234.5_Missense_Mutation_p.K94T	NM_031446.4	NP_113634.3	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21	182								p.K182T(1)		endometrium(1)|kidney(1)|large_intestine(1)|skin(2)	5						AACACCAGCAAAACAAAGAAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	18											88	87	87					18																	33558851		2203	4300	6503	31812849	SO:0001583	missense	83608			BC025950	CCDS11916.2, CCDS56064.1, CCDS74212.1	18q12.2	2004-05-05			ENSG00000141428	ENSG00000141428			28802	protein-coding gene	gene with protein product						12477932	Standard	NM_031446		Approved	PNAS-131, PNAS-124, HsT3108	uc002kzc.3	Q32NC0	OTTHUMG00000128531	ENST00000592875.1:c.545A>C	18.37:g.33558851A>C	ENSP00000465517:p.Lys182Thr		31812849	Q6GW03|Q9BXV6|Q9BXW2	Missense_Mutation	SNP	ENST00000592875.1	37	CCDS11916.2	.	.	.	.	.	.	.	.	.	.	A	13.09	2.132380	0.37630	.	.	ENSG00000141428	ENST00000333234;ENST00000269194	T	0.51574	0.7	5.67	1.95	0.26073	.	0.550372	0.20840	N	0.084725	T	0.54415	0.1857	.	.	.	0.28545	N	0.91192	D	0.63046	0.992	P	0.59357	0.856	T	0.49799	-0.8901	9	0.59425	D	0.04	-2.5116	4.9075	0.13806	0.7086:0.0:0.1538:0.1376	.	182	Q32NC0	CR021_HUMAN	T	182;94	ENSP00000269194:K94T	ENSP00000269194:K94T	K	+	2	0	C18orf21	31812849	0.950000	0.32346	0.660000	0.29694	0.015000	0.08874	1.093000	0.30939	0.155000	0.19261	-0.336000	0.08194	AAA		0.358	C18orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250364.1	NM_031446		C	33558851	A	C	33558851	3	2	61	1	0	0	0	0	1	0	0	0	1903	14	1	4	563	4	C18orf21	18	33558851	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	638950	33558851	44518397	10602	18587										
RPRD1A	55197	broad.mit.edu	37	chr18	33573184	33573184	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgacattgggcaatcgaGataagtctggcaggctctgg	14	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:33573184G>T	ENST00000399022.4	-	7	1040	c.869C>A	c.(868-870)tCt>tAt	p.S290Y	RPRD1A_ENST00000590898.1_Missense_Mutation_p.S254Y|RPRD1A_ENST00000588737.1_Missense_Mutation_p.S254Y|RPRD1A_ENST00000337059.5_Missense_Mutation_p.S254Y|RPRD1A_ENST00000357384.4_Missense_Mutation_p.S290Y	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	290					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.S290Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						GGGCAATCGAGATAAGTCTGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	18											109	100	103					18																	33573184		2203	4300	6503	31827182	SO:0001583	missense	55197			AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425			25560	protein-coding gene	gene with protein product	"cyclin-dependent kinase 2B-inhibitor-related protein", "Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)"	610347				12470661, 22231121	Standard	NM_018170		Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.869C>A	18.37:g.33573184G>T	ENSP00000381984:p.Ser290Tyr		31827182	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	Missense_Mutation	SNP	ENST00000399022.4	37	CCDS11917.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044374	0.75732	.	.	ENSG00000141425	ENST00000399022;ENST00000357384;ENST00000337059	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.78091	0.4229	M	0.66939	2.045	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.74348	0.905;0.983	T	0.79075	-0.1952	9	0.72032	D	0.01	-10.0903	17.5252	0.87798	0.0:0.0:1.0:0.0	.	290;254	Q96P16;Q96P16-3	RPR1A_HUMAN;.	Y	290;290;254	.	ENSP00000337476:S254Y	S	-	2	0	RPRD1A	31827182	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.675000	0.98638	2.746000	0.94184	0.655000	0.94253	TCT		0.537	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255802.1	NM_018170		T	33573184	G	T	33573184	3	4	61	1	0	0	0	0	1	0	0	0	13652	942	33	2	73	2	RPRD1A	18	33573184	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14333	33573184	44504064	10603	18588										
ELP2	55250	broad.mit.edu	37	chr18	33739747	33739747	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggagctgttaactagtacTggttttgagtatcagcaggt	13	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:33739747T>G	ENST00000358232.6	+	15	1647	c.1584T>G	c.(1582-1584)acT>acG	p.T528T	ELP2_ENST00000542050.1_3'UTR|ELP2_ENST00000350494.6_Silent_p.T523T|ELP2_ENST00000542824.1_Silent_p.T458T|ELP2_ENST00000442325.2_Silent_p.T593T|ELP2_ENST00000351393.6_Silent_p.T502T|ELP2_ENST00000423854.2_Silent_p.T458T	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	528					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)		p.T528T(1)		NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						TAACTAGTACTGGTTTTGAGT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	18											144	143	143					18																	33739747		2203	4300	6503	31993745	SO:0001819	synonymous_variant	55250			AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"Elongator acetyltransferase complex subunits", "WD repeat domain containing"	18248	protein-coding gene	gene with protein product			"signal transducer and activator of transcription 3 interacting protein 1", "elongation protein 2 homolog (S. cerevisiae)"	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.1584T>G	18.37:g.33739747T>G			31993745	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Silent	SNP	ENST00000358232.6	37	CCDS11918.1																																																																																				0.373	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255		G	33739747	T	G	33739747	2	3	61	1	0	0	0	0	0	0	0	1	5093	1567	55	4		4	ELP2	18	33739747	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	166563	33739747	44337501	10604	18589										
MOCOS	55034	broad.mit.edu	37	chr18	33783112	33783112	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcattccttgatgttatCgcgctaaaacatggatttga	7	8	1	2	rs540275885		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:33783112C>T	ENST00000261326.5	+	5	999	c.978C>T	c.(976-978)atC>atT	p.I326I		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase									p.I326I(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TTGATGTTATCGCGCTAAAAC	0.478													C|||	1	0.000199681	0	0	5008	,	,		20533	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	18											236	188	205					18																	33783112		2203	4300	6503	32037110	SO:0001819	synonymous_variant	55034			AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.978C>T	18.37:g.33783112C>T			32037110		Silent	SNP	ENST00000261326.5	37	CCDS11919.1																																																																																				0.478	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			T	33783112	C	T	33783112	2	4	61	1	0	0	0	0	0	0	0	1	9719	874	31	1		1	MOCOS	18	33783112	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43365	33783112	44294136	10605	18590										
MOCOS	55034	broad.mit.edu	37	chr18	33846726	33846726	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccaggttttggggccttgTcacagatgccagatgatttg	13	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:33846726T>C	ENST00000261326.5	+	14	2445	c.2424T>C	c.(2422-2424)tgT>tgC	p.C808C	MOCOS_ENST00000588132.1_3'UTR	NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase									p.C808C(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TGGGGCCTTGTCACAGATGCC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	18											96	85	89					18																	33846726		2203	4300	6503	32100724	SO:0001819	synonymous_variant	55034			AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.2424T>C	18.37:g.33846726T>C			32100724		Silent	SNP	ENST00000261326.5	37	CCDS11919.1																																																																																				0.493	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			C	33846726	T	C	33846726	2	2	61	1	0	0	0	0	0	0	0	1	9719	1673	58	4		4	MOCOS	18	33846726	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	63614	33846726	44230522	10606	18591										
FHOD3	80206	broad.mit.edu	37	chr18	34174854	34174854	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgtcactgctgttgacacGaaaagaggtgagtagtccct	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34174854G>A	ENST00000359247.4	+	7	711	c.711G>A	c.(709-711)acG>acA	p.T237T	FHOD3_ENST00000590592.1_Silent_p.T237T|FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000445677.1_Silent_p.T237T|FHOD3_ENST00000257209.4_Silent_p.T237T	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	237	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.T237T(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CTGTTGACACGAAAAGAGGTG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	18											116	91	99					18																	34174854		2203	4300	6503	32428852	SO:0001819	synonymous_variant	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.711G>A	18.37:g.34174854G>A			32428852	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Silent	SNP	ENST00000359247.4	37																																																																																					0.498	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34174854	G	A	34174854	2	1	61	1	0	0	0	0	0	0	0	1	5902	1045	37	1		1	FHOD3	18	34174854	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	328128	34174854	43902394	10607	18592										
FHOD3	80206	broad.mit.edu	37	chr18	34205498	34205498	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctcaggcacgaggatggcGatgagaccacggagccaccc	14	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34205498G>A	ENST00000359247.4	+	10	982	c.982G>A	c.(982-984)Gat>Aat	p.D328N	FHOD3_ENST00000590592.1_Missense_Mutation_p.D328N|FHOD3_ENST00000591635.1_Silent_p.A2A|FHOD3_ENST00000445677.1_Missense_Mutation_p.D328N|FHOD3_ENST00000257209.4_Missense_Mutation_p.D328N	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	328	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.D328N(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CGAGGATGGCGATGAGACCAC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	18											48	50	50					18																	34205498		2203	4300	6503	32459496	SO:0001583	missense	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.982G>A	18.37:g.34205498G>A	ENSP00000352186:p.Asp328Asn		32459496	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.066333	0.76187	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.36878	1.23;1.23;1.23	5.75	5.75	0.90469	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);	0.102055	0.64402	D	0.000003	T	0.55465	0.1922	L	0.52126	1.63	0.48830	D	0.999719	P;D;D;P	0.89917	0.825;1.0;1.0;0.771	B;D;D;B	0.81914	0.414;0.995;0.966;0.353	T	0.53837	-0.8382	10	0.62326	D	0.03	.	16.6927	0.85326	0.0:0.0:1.0:0.0	.	328;328;328;328	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	N	328	ENSP00000257209:D328N;ENSP00000352186:D328N;ENSP00000411430:D328N	ENSP00000257209:D328N	D	+	1	0	FHOD3	32459496	1.000000	0.71417	0.318000	0.25279	0.215000	0.24574	8.297000	0.89942	2.716000	0.92895	0.655000	0.94253	GAT		0.652	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34205498	G	A	34205498	3	1	61	1	0	0	0	0	1	0	0	0	5902	1058	37	1	1020	1	FHOD3	18	34205498	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30644	34205498	43871750	10608	18593										
FHOD3	80206	broad.mit.edu	37	chr18	34205696	34205696	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttcaagcccaaccaagtgCgagatctgcgtgaaaagtaa	10	10	2	2	rs376015995		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34205696C>T	ENST00000359247.4	+	10	1180	c.1180C>T	c.(1180-1182)Cga>Tga	p.R394*	FHOD3_ENST00000590592.1_Nonsense_Mutation_p.R394*|FHOD3_ENST00000591635.1_Silent_p.C68C|FHOD3_ENST00000445677.1_Nonsense_Mutation_p.R394*|FHOD3_ENST00000257209.4_Nonsense_Mutation_p.R394*	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	394	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.R394*(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CAACCAAGTGCGAGATCTGCG	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											122	125	124					18																	34205696		2203	4300	6503	32459694	SO:0001587	stop_gained	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1180C>T	18.37:g.34205696C>T	ENSP00000352186:p.Arg394*		32459694	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Nonsense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.208796	0.79240	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	.	.	.	4.94	2.98	0.34508	.	0.845757	0.10652	N	0.649828	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	13.9914	0.64369	0.0:0.6911:0.3089:0.0	.	.	.	.	X	394	.	ENSP00000257209:R394X	R	+	1	2	FHOD3	32459694	0.078000	0.21339	0.588000	0.28705	0.221000	0.24807	0.628000	0.24522	1.056000	0.40484	0.655000	0.94253	CGA		0.597	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34205696	C	T	34205696	4	4	61	1	0	0	0	0	0	1	0	0	5902	760	27	1	1218	1	FHOD3	18	34205696	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	198	34205696	43871552	10609	18594										
FHOD3	80206	broad.mit.edu	37	chr18	34267095	34267095	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatatttccattagccgaGattatttagacaaaagagag	7	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34267095G>T	ENST00000359247.4	+	12	1445				FHOD3_ENST00000590592.1_Missense_Mutation_p.D659Y|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000445677.1_Missense_Mutation_p.D446Y|FHOD3_ENST00000257209.4_Missense_Mutation_p.D484Y	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.D484Y(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CATTAGCCGAGATTATTTAGA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	18											126	116	120					18																	34267095		2203	4300	6503	32521093	SO:0001627	intron_variant	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1445+5562G>T	18.37:g.34267095G>T			32521093	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	18.85	3.711406	0.68730	.	.	ENSG00000134775	ENST00000257209;ENST00000445677	T;T	0.35605	1.3;1.36	5.79	5.79	0.91817	.	0.204017	0.50627	D	0.000113	T	0.34890	0.0913	L	0.29908	0.895	0.53005	D	0.999961	P;B	0.38048	0.616;0.441	B;B	0.43478	0.421;0.421	T	0.12016	-1.0564	10	0.59425	D	0.04	.	14.244	0.65975	0.0:0.1491:0.8509:0.0	.	446;484	Q2V2M9-2;Q2V2M9-3	.;.	Y	484;446	ENSP00000257209:D484Y;ENSP00000411430:D446Y	ENSP00000257209:D484Y	D	+	1	0	FHOD3	32521093	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.032000	0.70918	2.735000	0.93741	0.655000	0.94253	GAT		0.318	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34267095	G	T	34267095	1	4	61	0	1	0	0	0	0	0	0	0	5902	942	33	2		2	FHOD3	18	34267095	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61399	34267095	43810153	10610	18595										
FHOD3	80206	broad.mit.edu	37	chr18	34324002	34324002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttgcaaaacaggccaaagCgtttgagttaagctacctcg	10	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34324002C>T	ENST00000359247.4	+	19	3311	c.3311C>T	c.(3310-3312)gCg>gTg	p.A1104V	FHOD3_ENST00000590592.1_Missense_Mutation_p.A1296V|FHOD3_ENST00000592128.1_Missense_Mutation_p.A100V|FHOD3_ENST00000591635.1_Missense_Mutation_p.A317V|FHOD3_ENST00000445677.1_Missense_Mutation_p.A1083V|FHOD3_ENST00000257209.4_Missense_Mutation_p.A1121V	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1104	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.A1121V(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CAGGCCAAAGCGTTTGAGTTA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	18											171	162	165					18																	34324002		2203	4300	6503	32578000	SO:0001583	missense	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3311C>T	18.37:g.34324002C>T	ENSP00000352186:p.Ala1104Val		32578000	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	C	24.2	4.508756	0.85282	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.65549	-0.16;-0.16;-0.16	5.22	5.22	0.72569	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.048367	0.85682	D	0.000000	T	0.74068	0.3668	L	0.52011	1.625	0.52501	D	0.999953	P;D;D;D	0.76494	0.94;0.999;0.999;0.995	P;P;D;P	0.65684	0.804;0.895;0.937;0.89	T	0.76785	-0.2831	10	0.87932	D	0	.	17.3602	0.87348	0.0:1.0:0.0:0.0	.	325;1083;1104;1121	E7ETX5;Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;.;FHOD3_HUMAN;.	V	1121;1104;1083	ENSP00000257209:A1121V;ENSP00000352186:A1104V;ENSP00000411430:A1083V	ENSP00000257209:A1121V	A	+	2	0	FHOD3	32578000	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	5.174000	0.65015	2.428000	0.82296	0.563000	0.77884	GCG		0.458	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34324002	C	T	34324002	3	4	61	1	0	0	0	0	1	0	0	0	5902	768	27	1	3440	1	FHOD3	18	34324002	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56907	34324002	43753246	10611	18596										
FHOD3	80206	broad.mit.edu	37	chr18	34349366	34349366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgccgagggagaggaaacGatcccgggccaaccggaaat	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:34349366G>A	ENST00000359247.4	+	23	4163	c.4163G>A	c.(4162-4164)cGa>cAa	p.R1388Q	FHOD3_ENST00000590592.1_Missense_Mutation_p.R1588Q|FHOD3_ENST00000592128.1_Missense_Mutation_p.R384Q|FHOD3_ENST00000591635.1_Missense_Mutation_p.R601Q|FHOD3_ENST00000445677.1_Missense_Mutation_p.R1367Q|FHOD3_ENST00000257209.4_Missense_Mutation_p.R1405Q	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1388	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.R1405Q(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GAGAGGAAACGATCCCGGGCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	18											82	63	69					18																	34349366		2203	4300	6503	32603364	SO:0001583	missense	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.4163G>A	18.37:g.34349366G>A	ENSP00000352186:p.Arg1388Gln		32603364	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	35	5.563502	0.96527	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.52295	0.68;0.67;0.67	5.43	5.43	0.79202	Diaphanous autoregulatory (1);	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	M	0.76838	2.35	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.992;0.991	T	0.73691	-0.3903	10	0.87932	D	0	.	15.991	0.80206	0.0:0.0:1.0:0.0	.	1367;1388;1405	Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;FHOD3_HUMAN;.	Q	1405;1388;1367	ENSP00000257209:R1405Q;ENSP00000352186:R1388Q;ENSP00000411430:R1367Q	ENSP00000257209:R1405Q	R	+	2	0	FHOD3	32603364	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	9.464000	0.97655	2.547000	0.85894	0.655000	0.94253	CGA		0.567	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34349366	G	A	34349366	3	1	61	1	0	0	0	0	1	0	0	0	5902	1058	37	1	4308	1	FHOD3	18	34349366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25364	34349366	43727882	10612	18597										
PIK3C3	5289	broad.mit.edu	37	chr18	39584334	39584334	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttaggccttgacaaaattCttgaaatgtgttaattggga	9	4	1	2	rs200744647		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:39584334C>A	ENST00000262039.4	+	10	1085	c.999C>A	c.(997-999)ttC>ttA	p.F333L	PIK3C3_ENST00000398870.3_Missense_Mutation_p.F270L	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	333	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.			FLKCVN -> ILTSVI (in Ref. 1; CAA87094). {ECO:0000305}.	autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.F333L(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						TGACAAAATTCTTGAAATGTG	0.413										TSP Lung(28;0.18)			C|||	1	0.000199681	0	0	5008	,	,		17310	0.001		0	False		,,,				2504	0				NSCLC(37;552 1060 2683 16430 37914)											1	Substitution - Missense(1)	large_intestine(1)	18											50	50	50					18																	39584334		2203	4300	6503	37838332	SO:0001583	missense	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.999C>A	18.37:g.39584334C>A	ENSP00000262039:p.Phe333Leu		37838332	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	18.58	3.655339	0.67586	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.58797	0.31;0.31	5.45	2.28	0.28536	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.096585	0.85682	D	0.000000	T	0.62588	0.2440	L	0.41961	1.31	0.80722	D	1	D;D	0.61697	0.99;0.986	P;D	0.64144	0.749;0.922	T	0.58752	-0.7581	9	.	.	.	.	10.7634	0.46279	0.0:0.7289:0.0:0.2711	.	270;333	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	L	333;270	ENSP00000262039:F333L;ENSP00000381845:F270L	.	F	+	3	2	PIK3C3	37838332	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.729000	0.47327	0.689000	0.31550	-0.150000	0.13652	TTC		0.413	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		A	39584334	C	A	39584334	3	1	61	1	0	0	0	0	1	0	0	0	11943	912	32	2	1037	2	PIK3C3	18	39584334	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5234968	39584334	38492914	10613	18598										
PIK3C3	5289	broad.mit.edu	37	chr18	39595447	39595447	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attactttttcagctcccaaAttataaccagcccccttcct	2	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:39595447A>C	ENST00000262039.4	+	12	1419	c.1333A>C	c.(1333-1335)Att>Ctt	p.I445L	PIK3C3_ENST00000398870.3_Missense_Mutation_p.I382L	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	445	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.I445L(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CAGCTCCCAAATTATAACCAG	0.383										TSP Lung(28;0.18)																											NSCLC(37;552 1060 2683 16430 37914)											1	Substitution - Missense(1)	large_intestine(1)	18											132	133	133					18																	39595447		2203	4300	6503	37849445	SO:0001583	missense	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.1333A>C	18.37:g.39595447A>C	ENSP00000262039:p.Ile445Leu		37849445	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	A	9.905	1.207828	0.22205	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.62788	-0.0;0.37	5.73	5.73	0.89815	Phosphoinositide 3-kinase, accessory (PIK) domain (2);Armadillo-type fold (1);	0.285141	0.29185	N	0.012884	T	0.36991	0.0987	N	0.02802	-0.49	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32052	-0.9921	9	.	.	.	.	14.5843	0.68312	1.0:0.0:0.0:0.0	.	382;445	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	L	445;382	ENSP00000262039:I445L;ENSP00000381845:I382L	.	I	+	1	0	PIK3C3	37849445	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.204000	0.65180	2.189000	0.69895	0.533000	0.62120	ATT		0.383	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		C	39595447	A	C	39595447	3	2	61	1	0	0	0	0	1	0	0	0	11943	101	4	4	1379	4	PIK3C3	18	39595447	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	11113	39595447	38481801	10614	18599										
SYT4	6860	broad.mit.edu	37	chr18	40853938	40853938	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaagagagttcccagcttCtcttgtttctcttctgaagt	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:40853938C>A	ENST00000255224.3	-	2	824	c.456G>T	c.(454-456)gaG>gaT	p.E152D	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.E134D	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	152	Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.E152D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						TTCCCAGCTTCTCTTGTTTCT	0.453																																					NSCLC(85;81 1419 2855 22820 35912)											1	Substitution - Missense(1)	large_intestine(1)	18											46	47	46					18																	40853938		2203	4299	6502	39107936	SO:0001583	missense	6860			BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.456G>T	18.37:g.40853938C>A	ENSP00000255224:p.Glu152Asp		39107936	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	37	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	6.772	0.511286	0.12944	.	.	ENSG00000132872	ENST00000255224	T	0.08370	3.1	5.87	4.0	0.46444	C2 calcium/lipid-binding domain, CaLB (1);	0.243384	0.47852	D	0.000204	T	0.02380	0.0073	N	0.02011	-0.69	0.27207	N	0.960006	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47535	-0.9110	10	0.15499	T	0.54	.	3.6862	0.08329	0.3095:0.4748:0.1351:0.0805	.	134;152	B4DEU3;Q9H2B2	.;SYT4_HUMAN	D	152	ENSP00000255224:E152D	ENSP00000255224:E152D	E	-	3	2	SYT4	39107936	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.889000	0.28282	2.941000	0.99782	0.655000	0.94253	GAG		0.453	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40853938	C	A	40853938	3	1	61	1	0	0	0	0	1	0	0	0	15515	912	32	2	833	2	SYT4	18	40853938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1258491	40853938	37223310	10615	18600										
SYT4	6860	broad.mit.edu	37	chr18	40854096	40854096	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaaattgccattgagatCtctcttttcaagatccagat	8	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:40854096C>A	ENST00000255224.3	-	2	666	c.298G>T	c.(298-300)Gat>Tat	p.D100Y	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.D82Y	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	100					exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.D100Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						CCATTGAGATCTCTCTTTTCA	0.403																																					NSCLC(85;81 1419 2855 22820 35912)											1	Substitution - Missense(1)	large_intestine(1)	18											151	149	150					18																	40854096		2203	4300	6503	39108094	SO:0001583	missense	6860			BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.298G>T	18.37:g.40854096C>A	ENSP00000255224:p.Asp100Tyr		39108094	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	37	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.933852	0.73442	.	.	ENSG00000132872	ENST00000255224	T	0.42131	0.98	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.64349	0.2590	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.61720	-0.7005	10	0.59425	D	0.04	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	82;100	B4DEU3;Q9H2B2	.;SYT4_HUMAN	Y	100	ENSP00000255224:D100Y	ENSP00000255224:D100Y	D	-	1	0	SYT4	39108094	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.205000	0.77881	2.937000	0.99478	0.650000	0.86243	GAT		0.403	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40854096	C	A	40854096	3	1	61	1	0	0	0	0	1	0	0	0	15515	913	32	2	991	2	SYT4	18	40854096	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	158	40854096	37223152	10616	18601										
SETBP1	26040	broad.mit.edu	37	chr18	42529971	42529971	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagaaccacatggactgGtccaccaactctgacagcgg	10	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:42529971G>A	ENST00000282030.5	+	4	962	c.666G>A	c.(664-666)tgG>tgA	p.W222*		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	222						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.W168*(1)|p.W222*(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		ACATGGACTGGTCCACCAACT	0.537									Schinzel-Giedion syndrome																																							2	Substitution - Nonsense(2)	large_intestine(2)	18											87	79	82					18																	42529971		2203	4300	6503	40783969	SO:0001587	stop_gained	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.666G>A	18.37:g.42529971G>A	ENSP00000282030:p.Trp222*		40783969	A6H8W5|Q6P6C3|Q9UEF3	Nonsense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	G	39	7.321045	0.98210	.	.	ENSG00000152217	ENST00000282030	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9997	0.97405	0.0:0.0:1.0:0.0	.	.	.	.	X	222	.	ENSP00000282030:W222X	W	+	3	0	SETBP1	40783969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.472000	0.80996	2.813000	0.96785	0.655000	0.94253	TGG		0.537	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42529971	G	A	42529971	4	1	61	1	0	0	0	0	0	1	0	0	14166	1270	44	3	869	3	SETBP1	18	42529971	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1675875	42529971	35547277	10617	18602										
SETBP1	26040	broad.mit.edu	37	chr18	42530598	42530598	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcggtggtggaaaagatCatgccagagaaagccttggc	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:42530598C>A	ENST00000282030.5	+	4	1589	c.1293C>A	c.(1291-1293)atC>atA	p.I431I		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	431						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I431I(1)|p.I377I(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGGAAAAGATCATGCCAGAGA	0.473									Schinzel-Giedion syndrome																																							2	Substitution - coding silent(2)	large_intestine(2)	18											83	85	84					18																	42530598		2203	4300	6503	40784596	SO:0001819	synonymous_variant	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.1293C>A	18.37:g.42530598C>A			40784596	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																				0.473	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42530598	C	A	42530598	2	1	61	1	0	0	0	0	0	0	0	1	14166	816	29	2		2	SETBP1	18	42530598	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	627	42530598	35546650	10618	18603										
SETBP1	26040	broad.mit.edu	37	chr18	42530748	42530748	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccctcagttggccttgaAactggtggaaatgctgagaa	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:42530748A>C	ENST00000282030.5	+	4	1739	c.1443A>C	c.(1441-1443)gaA>gaC	p.E481D		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	481						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E481D(1)|p.E427D(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TTGGCCTTGAAACTGGTGGAA	0.488									Schinzel-Giedion syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	18											80	84	82					18																	42530748		2203	4300	6503	40784746	SO:0001583	missense	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.1443A>C	18.37:g.42530748A>C	ENSP00000282030:p.Glu481Asp		40784746	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	6.935	0.542168	0.13250	.	.	ENSG00000152217	ENST00000282030	T	0.68624	-0.34	6.08	-2.36	0.06663	.	0.159786	0.56097	D	0.000035	T	0.42063	0.1186	N	0.17082	0.46	0.19300	N	0.999976	B	0.14012	0.009	B	0.16722	0.016	T	0.28933	-1.0028	10	0.12766	T	0.61	.	10.6596	0.45694	0.319:0.1484:0.5326:0.0	.	481	Q9Y6X0	SETBP_HUMAN	D	481	ENSP00000282030:E481D	ENSP00000282030:E481D	E	+	3	2	SETBP1	40784746	0.069000	0.21087	0.178000	0.23040	0.803000	0.45373	0.010000	0.13242	-0.648000	0.05437	0.533000	0.62120	GAA		0.488	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		C	42530748	A	C	42530748	3	2	61	1	0	0	0	0	1	0	0	0	14166	11	1	4	1646	4	SETBP1	18	42530748	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	150	42530748	35546500	10619	18604										
SETBP1	26040	broad.mit.edu	37	chr18	42532327	42532327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgacccgttgctctatcttCgtaggacttcagacttgaag	9	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:42532327C>T	ENST00000282030.5	+	4	3318	c.3022C>T	c.(3022-3024)Cgt>Tgt	p.R1008C		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1008						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R1008C(1)|p.R954C(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GCTCTATCTTCGTAGGACTTC	0.443									Schinzel-Giedion syndrome																																							2	Substitution - Missense(2)	large_intestine(2)	18											105	102	103					18																	42532327		2203	4300	6503	40786325	SO:0001583	missense	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3022C>T	18.37:g.42532327C>T	ENSP00000282030:p.Arg1008Cys		40786325	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	C	16.29	3.080988	0.55753	.	.	ENSG00000152217	ENST00000282030	D	0.93076	-3.16	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.94899	0.8351	L	0.29908	0.895	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.95365	0.8459	10	0.87932	D	0	.	20.0893	0.97812	0.0:1.0:0.0:0.0	.	1008	Q9Y6X0	SETBP_HUMAN	C	1008	ENSP00000282030:R1008C	ENSP00000282030:R1008C	R	+	1	0	SETBP1	40786325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.764000	0.85297	2.761000	0.94854	0.655000	0.94253	CGT		0.443	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		T	42532327	C	T	42532327	3	4	61	1	0	0	0	0	1	0	0	0	14166	884	31	1	3225	1	SETBP1	18	42532327	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1579	42532327	35544921	10620	18605										
SLC14A2	8170	broad.mit.edu	37	chr18	43205689	43205689	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagtcacattgtgaagatCgaaaagctcaatgaaaggag	11	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43205689C>T	ENST00000255226.6	+	3	1008	c.192C>T	c.(190-192)atC>atT	p.I64I	SLC14A2_ENST00000586448.1_Silent_p.I64I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	64					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.I64I(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTGTGAAGATCGAAAAGCTCA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	18											65	60	62					18																	43205689		2203	4300	6503	41459687	SO:0001819	synonymous_variant	8170			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.192C>T	18.37:g.43205689C>T			41459687	A8K8Q7|Q2TBD6|Q96PH5	Silent	SNP	ENST00000255226.6	37	CCDS11924.1																																																																																				0.488	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43205689	C	T	43205689	2	4	61	1	0	0	0	0	0	0	0	1	14434	874	31	1		1	SLC14A2	18	43205689	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673362	43205689	34871559	10621	18606										
KIAA1632	57724	broad.mit.edu	37	chr18	43447564	43447564	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacttcctttgccaataaAatcatcatgaaaaggaggca	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43447564A>C	ENST00000282041.5	-	37	6409	c.6375T>G	c.(6373-6375)atT>atG	p.I2125M	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2125					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.I2125M(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TTGCCAATAAAATCATCATGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	18											143	141	141					18																	43447564		1894	4122	6016	41701562	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.6375T>G	18.37:g.43447564A>C	ENSP00000282041:p.Ile2125Met		41701562	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854556	0.51376	.	.	ENSG00000152223	ENST00000282041;ENST00000540322;ENST00000308403	T	0.12672	2.66	5.68	3.05	0.35203	.	.	.	.	.	T	0.09642	0.0237	N	0.19112	0.55	0.31677	N	0.643576	B	0.32526	0.374	B	0.38616	0.277	T	0.16247	-1.0409	9	0.87932	D	0	-1.1225	2.9305	0.05797	0.4601:0.2399:0.3:0.0	.	2125	Q9HCE0	EPG5_HUMAN	M	2125;53;1000	ENSP00000282041:I2125M	ENSP00000282041:I2125M	I	-	3	3	EPG5	41701562	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.269000	0.33074	1.096000	0.41439	0.528000	0.53228	ATT		0.453	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43447564	A	C	43447564	3	2	61	1	0	0	0	0	1	0	0	0	8270	10	1	4	1396	4	KIAA1632	18	43447564	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	241875	43447564	34629684	10622	18607										
KIAA1632	57724	broad.mit.edu	37	chr18	43497773	43497773	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgggatgccttctgcacagAacttctcaatgctatggaaa	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43497773A>C	ENST00000282041.5	-	17	3144	c.3110T>G	c.(3109-3111)tTc>tGc	p.F1037C	EPG5_ENST00000585906.1_5'Flank	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1037					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.F1037C(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TTCTGCACAGAACTTCTCAAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	18											91	82	85					18																	43497773		1873	4111	5984	41751771	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3110T>G	18.37:g.43497773A>C	ENSP00000282041:p.Phe1037Cys		41751771	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125524	0.77436	.	.	ENSG00000152223	ENST00000282041	T	0.15487	2.42	5.7	5.7	0.88788	.	0.489620	0.22116	N	0.064402	T	0.40791	0.1131	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	T	0.18777	-1.0326	10	0.72032	D	0.01	-21.0305	15.9579	0.79902	1.0:0.0:0.0:0.0	.	1037;1037	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	C	1037	ENSP00000282041:F1037C	ENSP00000282041:F1037C	F	-	2	0	EPG5	41751771	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	8.315000	0.89983	2.178000	0.69098	0.533000	0.62120	TTC		0.408	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43497773	A	C	43497773	3	2	61	1	0	0	0	0	1	0	0	0	8270	246	9	4	4741	4	KIAA1632	18	43497773	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	50209	43497773	34579475	10623	18608										
KIAA1632	57724	broad.mit.edu	37	chr18	43532513	43532513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtgctcagatttggcatCgaatagcttctttagctcca	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43532513C>T	ENST00000282041.5	-	3	1139	c.1105G>A	c.(1105-1107)Gat>Aat	p.D369N		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	369					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.D369N(2)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GATTTGGCATCGAATAGCTTC	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	18											98	99	99					18																	43532513		1916	4131	6047	41786511	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1105G>A	18.37:g.43532513C>T	ENSP00000282041:p.Asp369Asn		41786511	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042318	0.35989	.	.	ENSG00000152223	ENST00000282041	T	0.80738	-1.41	5.59	5.59	0.84812	.	0.616477	0.18140	N	0.150451	T	0.71762	0.3378	L	0.36672	1.1	0.34753	D	0.731983	P;P	0.48230	0.907;0.907	B;B	0.34138	0.176;0.176	T	0.77509	-0.2561	10	0.30078	T	0.28	-12.7407	19.9595	0.97236	0.0:1.0:0.0:0.0	.	369;369	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	N	369	ENSP00000282041:D369N	ENSP00000282041:D369N	D	-	1	0	EPG5	41786511	1.000000	0.71417	1.000000	0.80357	0.151000	0.21798	4.351000	0.59398	2.797000	0.96272	0.563000	0.77884	GAT		0.438	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		T	43532513	C	T	43532513	3	4	61	1	0	0	0	0	1	0	0	0	8270	884	31	1	6802	1	KIAA1632	18	43532513	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34740	43532513	34544735	10624	18609										
KIAA1632	57724	broad.mit.edu	37	chr18	43534889	43534889	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctggctgagtataagaaAaattagattggggtgcactt	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43534889A>C	ENST00000282041.5	-	2	513	c.479T>G	c.(478-480)tTt>tGt	p.F160C		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	160					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.F160C(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AGTATAAGAAAAATTAGATTG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	18											77	72	74					18																	43534889		1846	4091	5937	41788887	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.479T>G	18.37:g.43534889A>C	ENSP00000282041:p.Phe160Cys		41788887	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	6.169	0.399304	0.11696	.	.	ENSG00000152223	ENST00000282041	T	0.10005	2.92	5.12	2.45	0.29901	.	0.807437	0.11309	N	0.577280	T	0.07503	0.0189	N	0.19112	0.55	0.09310	N	1	B;B	0.28584	0.216;0.216	B;B	0.34385	0.181;0.181	T	0.39461	-0.9613	10	0.36615	T	0.2	-2.2872	4.5346	0.12022	0.6515:0.0:0.3485:0.0	.	160;160	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	C	160	ENSP00000282041:F160C	ENSP00000282041:F160C	F	-	2	0	EPG5	41788887	0.903000	0.30736	0.013000	0.15412	0.019000	0.09904	2.859000	0.48364	0.888000	0.36160	0.421000	0.28195	TTT		0.403	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43534889	A	C	43534889	3	2	61	1	0	0	0	0	1	0	0	0	8270	14	1	4	7432	4	KIAA1632	18	43534889	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2376	43534889	34542359	10625	18610										
PSTPIP2	9050	broad.mit.edu	37	chr18	43568710	43568710	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgtagtcatcaaccaaaGagtaattgggatcatctgca	8	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43568710G>T	ENST00000409746.5	-	14	1042	c.971C>A	c.(970-972)tCt>tAt	p.S324Y	PSTPIP2_ENST00000588801.1_Intron|RN7SKP26_ENST00000410247.1_RNA|PSTPIP2_ENST00000589328.1_Missense_Mutation_p.L292I	NM_024430.3	NP_077748.3	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting protein 2	324						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.L292I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	17						ATCAACCAAAGAGTAATTGGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											100	95	96					18																	43568710		2203	4300	6503	41822708	SO:0001583	missense	9050				CCDS32820.2	18q12	2008-07-28			ENSG00000152229	ENSG00000152229			9581	protein-coding gene	gene with protein product						9804817	Standard	NM_024430		Approved		uc002lbp.4	Q9H939	OTTHUMG00000152674	ENST00000409746.5:c.971C>A	18.37:g.43568710G>T	ENSP00000387261:p.Ser324Tyr		41822708		Missense_Mutation	SNP	ENST00000409746.5	37	CCDS32820.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.64|12.64	2.000001|2.000001	0.35320|0.35320	.|.	.|.	ENSG00000152229|ENSG00000152229	ENST00000360076|ENST00000409746	.|T	.|0.39229	.|1.09	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.253409	.|0.40222	.|N	.|0.001142	T|T	0.52549|0.52549	0.1741|0.1741	M|M	0.64997|0.64997	1.995|1.995	0.21841|0.21841	N|N	0.999513|0.999513	P|P	0.50443|0.38223	0.935|0.623	P|P	0.49752|0.46718	0.621|0.525	T|T	0.53556|0.53556	-0.8422|-0.8422	8|10	0.62326|0.72032	D|D	0.03|0.01	-2.797|-2.797	15.4239|15.4239	0.75035|0.75035	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	292|324	Q9H939-2|Q9H939	.|PPIP2_HUMAN	I|Y	292|324	.|ENSP00000387261:S324Y	ENSP00000353189:L292I|ENSP00000387261:S324Y	L|S	-|-	1|2	0|0	PSTPIP2|PSTPIP2	41822708|41822708	0.981000|0.981000	0.34729|0.34729	0.105000|0.105000	0.21289|0.21289	0.001000|0.001000	0.01503|0.01503	5.238000|5.238000	0.65366|0.65366	2.712000|2.712000	0.92718|0.92718	0.650000|0.650000	0.86243|0.86243	CTT|TCT		0.348	PSTPIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327522.1			T	43568710	G	T	43568710	3	4	61	1	0	0	0	0	1	0	0	0	12756	942	33	2	37	2	PSTPIP2	18	43568710	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33821	43568710	34508538	10626	18611										
ATP5A1	498	broad.mit.edu	37	chr18	43669637	43669637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggttcccgcactgaaattCgaggaatgataccgggggct	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43669637C>T	ENST00000398752.6	-	5	666	c.545G>A	c.(544-546)cGa>cAa	p.R182Q	ATP5A1_ENST00000593152.2_Missense_Mutation_p.R132Q|ATP5A1_ENST00000282050.2_Missense_Mutation_p.R182Q|ATP5A1_ENST00000590665.1_Missense_Mutation_p.R160Q	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	182					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.R182Q(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CACTGAAATTCGAGGAATGAT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											64	62	62					18																	43669637		2203	4300	6503	41923635	SO:0001583	missense	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.545G>A	18.37:g.43669637C>T	ENSP00000381736:p.Arg182Gln		41923635	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728968	0.96856	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.84589	-1.87;-1.87	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.90359	0.6983	M	0.81942	2.565	0.80722	D	1	D	0.53312	0.959	P	0.52189	0.692	D	0.91834	0.5478	10	0.72032	D	0.01	-3.2668	18.6794	0.91541	0.0:1.0:0.0:0.0	.	182	P25705	ATPA_HUMAN	Q	182;182;132	ENSP00000282050:R182Q;ENSP00000381736:R182Q	ENSP00000282050:R182Q	R	-	2	0	ATP5A1	41923635	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.035000	0.70940	2.411000	0.81874	0.563000	0.77884	CGA		0.473	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		T	43669637	C	T	43669637	3	4	61	1	0	0	0	0	1	0	0	0	1148	884	31	1	1148	1	ATP5A1	18	43669637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	100927	43669637	34407611	10627	18612										
C18orf25	147339	broad.mit.edu	37	chr18	43796108	43796108	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggccgagtttatgagagtGactcctctaatcactgcatg	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:43796108G>T	ENST00000282059.6	+	2	636	c.262G>T	c.(262-264)Gac>Tac	p.D88Y	C18orf25_ENST00000321319.6_Missense_Mutation_p.D88Y	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	88								p.D88Y(1)		central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						TTATGAGAGTGACTCCTCTAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	18											129	129	129					18																	43796108		1987	4162	6149	42050106	SO:0001583	missense	147339			AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242			28172	protein-coding gene	gene with protein product	"ARKadia-like 1"					15722956	Standard	NM_001008239		Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.262G>T	18.37:g.43796108G>T	ENSP00000282059:p.Asp88Tyr		42050106	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	Missense_Mutation	SNP	ENST00000282059.6	37	CCDS42430.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860037	0.71834	.	.	ENSG00000152242	ENST00000282059;ENST00000321319	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.77791	0.4183	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.77699	-0.2490	9	0.87932	D	0	-12.1407	20.3967	0.98985	0.0:0.0:1.0:0.0	.	88;88	Q96B23-2;Q96B23	.;CR025_HUMAN	Y	88	.	ENSP00000282059:D88Y	D	+	1	0	C18orf25	42050106	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.375000	0.97178	2.829000	0.97493	0.655000	0.94253	GAC		0.493	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445242.1	NM_145055		T	43796108	G	T	43796108	3	4	61	1	0	0	0	0	1	0	0	0	1905	1290	45	2	264	2	C18orf25	18	43796108	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	126471	43796108	34281140	10628	18613										
RNF165	494470	broad.mit.edu	37	chr18	44027527	44027527	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaggctgtttccctgcaggGatctcagtgtggatgctggc	15	9	1	1	rs377189495		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44027527G>A	ENST00000269439.7	+	4	538	c.487G>A	c.(487-489)Gat>Aat	p.D163N	RNF165_ENST00000543885.1_5'UTR	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	163							zinc ion binding (GO:0008270)	p.D163N(1)		NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		TCCCTGCAGGGATCTCAGTGT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	18						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	175	151	159		487	5.7	1	18		159	0,8600		0,0,4300	no	missense-near-splice	RNF165	NM_152470.2	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	163/347	44027527	1,13005	2203	4300	6503	42281525	SO:0001630	splice_region_variant	494470			BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"RING-type (C3HC4) zinc fingers"	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.486-1G>A	18.37:g.44027527G>A			42281525	B3KVD1	Missense_Mutation	SNP	ENST00000269439.7	37	CCDS32823.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139784	0.77775	2.27E-4	0.0	ENSG00000141622	ENST00000269439	T	0.18810	2.19	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.35068	0.0919	L	0.31294	0.92	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.01520	-1.1334	10	0.33141	T	0.24	-3.9662	18.0995	0.89501	0.0:0.0:1.0:0.0	.	163	Q6ZSG1	RN165_HUMAN	N	163	ENSP00000269439:D163N	ENSP00000269439:D163N	D	+	1	0	RNF165	42281525	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.500000	0.81588	2.712000	0.92718	0.561000	0.74099	GAT		0.527	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470	Missense_Mutation	A	44027527	G	A	44027527	5	1	61	1	0	0	0	0	0	0	1	0	13493	1188	41	3	501	3	RNF165	18	44027527	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231419	44027527	34049721	10629	18614										
RNF165	494470	broad.mit.edu	37	chr18	44036015	44036015	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaatgcacaatttgtctgTctatgctggaagatggagaa	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44036015T>C	ENST00000269439.7	+	7	946	c.895T>C	c.(895-897)Tct>Cct	p.S299P	RNF165_ENST00000543885.1_Missense_Mutation_p.S107P	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	299							zinc ion binding (GO:0008270)	p.S299P(1)		NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		AATTTGTCTGTCTATGCTGGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	18											147	109	122					18																	44036015		2203	4300	6503	42290013	SO:0001583	missense	494470			BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"RING-type (C3HC4) zinc fingers"	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.895T>C	18.37:g.44036015T>C	ENSP00000269439:p.Ser299Pro		42290013	B3KVD1	Missense_Mutation	SNP	ENST00000269439.7	37	CCDS32823.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797754	0.90538	.	.	ENSG00000141622	ENST00000269439;ENST00000543885	T;T	0.45668	0.89;0.89	5.11	5.11	0.69529	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.073964	0.56097	D	0.000037	T	0.68943	0.3056	M	0.88640	2.97	0.80722	D	1	D	0.65815	0.995	D	0.72075	0.976	T	0.75039	-0.3458	10	0.54805	T	0.06	.	14.571	0.68210	0.0:0.0:0.0:1.0	.	299	Q6ZSG1	RN165_HUMAN	P	299;107	ENSP00000269439:S299P;ENSP00000444285:S107P	ENSP00000269439:S299P	S	+	1	0	RNF165	42290013	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.932000	0.55993	0.397000	0.26171	TCT		0.498	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		C	44036015	T	C	44036015	3	2	61	1	0	0	0	0	1	0	0	0	13493	1667	58	4	921	4	RNF165	18	44036015	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8488	44036015	34041233	10630	18615										
ST8SIA5	29906	broad.mit.edu	37	chr18	44284627	44284627	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcataaaattcaaagtaCctggggaccaacagagacag	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44284627C>A	ENST00000315087.7	-	2	792	c.132G>T	c.(130-132)agG>agT	p.R44S	ST8SIA5_ENST00000538168.1_Splice_Site_p.R80S|ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Intron	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	44					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)	p.R44S(1)		kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						ATTCAAAGTACCTGGGGACCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	18											85	85	85					18																	44284627		2203	4300	6503	42538625	SO:0001630	splice_region_variant	29906			U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.132-1G>T	18.37:g.44284627C>A			42538625	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	37	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.005904	0.54254	.	.	ENSG00000101638	ENST00000315087;ENST00000538168	T;T	0.54279	1.03;0.58	4.48	4.48	0.54585	.	0.106321	0.64402	D	0.000004	T	0.51432	0.1674	M	0.61703	1.905	0.80722	D	1	B;B	0.25390	0.125;0.023	B;B	0.23018	0.043;0.019	T	0.53099	-0.8486	10	0.41790	T	0.15	.	16.3392	0.83076	0.0:1.0:0.0:0.0	.	80;44	B7Z1K9;O15466	.;SIA8E_HUMAN	S	44;80	ENSP00000321343:R44S;ENSP00000445492:R80S	ENSP00000321343:R44S	R	-	3	2	ST8SIA5	42538625	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.519000	0.67074	2.222000	0.72286	0.561000	0.74099	AGG		0.498	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305	Missense_Mutation	A	44284627	C	A	44284627	5	1	61	1	0	0	0	0	0	0	1	0	15274	521	18	2	1022	2	ST8SIA5	18	44284627	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	248612	44284627	33792621	10631	18616										
ST8SIA5	29906	broad.mit.edu	37	chr18	44336408	44336408	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaggcaaaggcgcagatgaAgatgaagagcaaagttcggc	14	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44336408A>C	ENST00000315087.7	-	1	724	c.64T>G	c.(64-66)Ttc>Gtc	p.F22V	RP11-742D12.2_ENST00000602333.1_RNA|ST8SIA5_ENST00000538168.1_Missense_Mutation_p.F22V|RP11-742D12.2_ENST00000602329.1_RNA|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.F22V	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	22					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)	p.F22V(1)		kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						GCGCAGATGAAGATGAAGAGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	18											108	101	103					18																	44336408		2203	4300	6503	42590406	SO:0001583	missense	29906			U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.64T>G	18.37:g.44336408A>C	ENSP00000321343:p.Phe22Val		42590406	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	37	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.936072	0.92458	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.55234	0.53;0.53;0.53	4.97	4.97	0.65823	.	0.061472	0.64402	D	0.000002	T	0.61974	0.2390	L	0.32530	0.975	0.47183	D	0.999343	D;D;D;P	0.89917	1.0;1.0;0.999;0.518	D;D;D;B	0.85130	0.997;0.996;0.991;0.24	T	0.63620	-0.6596	10	0.49607	T	0.09	.	14.3085	0.66400	1.0:0.0:0.0:0.0	.	22;22;22;22	F5H8D1;B7Z1K9;B7Z5F7;O15466	.;.;.;SIA8E_HUMAN	V	22	ENSP00000321343:F22V;ENSP00000445492:F22V;ENSP00000443683:F22V	ENSP00000321343:F22V	F	-	1	0	ST8SIA5	42590406	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.200000	0.77838	1.866000	0.54105	0.379000	0.24179	TTC		0.607	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		C	44336408	A	C	44336408	3	2	61	1	0	0	0	0	1	0	0	0	15274	72	3	4	1094	4	ST8SIA5	18	44336408	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	51781	44336408	33740840	10632	18617										
PIAS2	9063	broad.mit.edu	37	chr18	44395301	44395301	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaactggaataagggaaaGaaaatccaaacctaaaacaa	6	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44395301G>T	ENST00000585916.1	-	13	1659	c.1660C>A	c.(1660-1662)Ctt>Att	p.L554I		NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	554					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.L554I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						ATAAGGGAAAGAAAATCCAAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	18											115	120	118					18																	44395301		2203	4299	6502	42649299	SO:0001583	missense	9063			AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1660C>A	18.37:g.44395301G>T	ENSP00000465676:p.Leu554Ile		42649299	O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	37	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017479	0.75161	.	.	ENSG00000078043	ENST00000398654;ENST00000262161	.	.	.	5.81	5.81	0.92471	.	0.051265	0.85682	D	0.000000	T	0.52289	0.1725	L	0.43152	1.355	0.80722	D	1	P	0.42248	0.774	B	0.38327	0.271	T	0.56238	-0.8012	9	0.54805	T	0.06	-16.2627	17.2393	0.87008	0.0:0.0:1.0:0.0	.	554	O75928	PIAS2_HUMAN	I	554	.	ENSP00000262161:L554I	L	-	1	0	PIAS2	42649299	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.153000	0.71819	2.756000	0.94617	0.655000	0.94253	CTT		0.308	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		T	44395301	G	T	44395301	3	4	61	1	0	0	0	0	1	0	0	0	11907	942	33	2	213	2	PIAS2	18	44395301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	58893	44395301	33681947	10633	18618										
TCEB3B	51224	broad.mit.edu	37	chr18	44559634	44559634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcttgatctccccattttCggggtcagcgtctcctgcag	11	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44559634C>T	ENST00000332567.4	-	1	2354	c.2002G>A	c.(2002-2004)Gaa>Aaa	p.E668K	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	668					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E668K(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TCCCCATTTTCGGGGTCAGCG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	18											74	79	77					18																	44559634		2203	4299	6502	42813632	SO:0001583	missense	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.2002G>A	18.37:g.44559634C>T	ENSP00000331302:p.Glu668Lys		42813632	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	C	8.296	0.818922	0.16607	.	.	ENSG00000206181	ENST00000332567	T	0.08370	3.1	1.26	0.355	0.16069	.	1.475580	0.05026	N	0.473715	T	0.07638	0.0192	L	0.54323	1.7	0.09310	N	1	B	0.32382	0.368	B	0.21151	0.033	T	0.37314	-0.9711	10	0.29301	T	0.29	0.1151	3.5803	0.07950	0.0:0.7358:0.0:0.2642	.	668	Q8IYF1	ELOA2_HUMAN	K	668	ENSP00000331302:E668K	ENSP00000331302:E668K	E	-	1	0	TCEB3B	42813632	0.007000	0.16637	0.000000	0.03702	0.000000	0.00434	0.145000	0.16157	0.102000	0.17638	-0.192000	0.12808	GAA		0.577	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44559634	C	T	44559634	3	4	61	1	0	0	0	0	1	0	0	0	15721	893	31	1	263	1	TCEB3B	18	44559634	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	164333	44559634	33517614	10634	18619										
TCEB3B	51224	broad.mit.edu	37	chr18	44561564	44561564	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatatttctctagctttttCggctccgtcttagtggccag	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44561564C>T	ENST00000332567.4	-	1	424	c.72G>A	c.(70-72)ccG>ccA	p.P24P	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	24	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P24P(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CTAGCTTTTTCGGCTCCGTCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	18											49	48	48					18																	44561564		2203	4298	6501	42815562	SO:0001819	synonymous_variant	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.72G>A	18.37:g.44561564C>T			42815562	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																				0.587	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44561564	C	T	44561564	2	4	61	1	0	0	0	0	0	0	0	1	15721	871	31	1		1	TCEB3B	18	44561564	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1930	44561564	33515684	10635	18620										
KATNAL2	83473	broad.mit.edu	37	chr18	44595969	44595969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggattcagaaaaactcgttCgggtaggaattcttaatttt	10	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:44595969C>T	ENST00000245121.5	+	10	984	c.790C>T	c.(790-792)Cgg>Tgg	p.R264W	KATNAL2_ENST00000356157.7_Missense_Mutation_p.R336W|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2									p.R264W(1)		central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						AAAACTCGTTCGGGTAGGAAT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	18											65	62	63					18																	44595969		2203	4300	6503	42849967	SO:0001583	missense	83473			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.790C>T	18.37:g.44595969C>T	ENSP00000245121:p.Arg264Trp		42849967		Missense_Mutation	SNP	ENST00000245121.5	37	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.291167	0.59976	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.94417	-3.42;-3.42	5.78	5.78	0.91487	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.98520	0.9506	H	0.98701	4.305	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99372	1.0920	10	0.87932	D	0	-11.2445	15.5906	0.76523	0.1382:0.8617:0.0:0.0	.	336	Q8IYT4	KATL2_HUMAN	W	336;264;104	ENSP00000348478:R336W;ENSP00000245121:R264W	ENSP00000245121:R264W	R	+	1	2	KATNAL2	42849967	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	2.362000	0.44169	2.738000	0.93877	0.655000	0.94253	CGG		0.368	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		T	44595969	C	T	44595969	3	4	61	1	0	0	0	0	1	0	0	0	8007	875	31	1	824	1	KATNAL2	18	44595969	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34405	44595969	33481279	10636	18621										
SMAD2	4087	broad.mit.edu	37	chr18	45374945	45374945	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgggtctgtaaagccatCtacagtgagtgagggctgtg	15	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:45374945C>T	ENST00000402690.2	-	8	1292	c.898G>A	c.(898-900)Gat>Aat	p.D300N	SMAD2_ENST00000262160.6_Missense_Mutation_p.D300N|SMAD2_ENST00000356825.4_Missense_Mutation_p.D270N|SMAD2_ENST00000591214.1_Missense_Mutation_p.D270N|SMAD2_ENST00000586040.1_Missense_Mutation_p.D270N	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	300	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		D -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.D300N(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						GTAAAGCCATCTACAGTGAGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											124	111	116					18																	45374945		2203	4300	6503	43628943	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.898G>A	18.37:g.45374945C>T	ENSP00000384449:p.Asp300Asn		43628943		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	C	36	5.673172	0.96754	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.98090	-4.71;-4.71;-4.71	5.81	5.81	0.92471	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.089852	0.85682	D	0.000000	D	0.99214	0.9727	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;1.0	D	0.99019	1.0817	10	0.87932	D	0	.	20.0912	0.97820	0.0:1.0:0.0:0.0	.	270;270;300	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	N	300;270;300	ENSP00000262160:D300N;ENSP00000349282:D270N;ENSP00000384449:D300N	ENSP00000262160:D300N	D	-	1	0	SMAD2	43628943	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.045000	0.71020	2.746000	0.94184	0.591000	0.81541	GAT		0.418	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		T	45374945	C	T	45374945	3	4	61	1	0	0	0	0	1	0	0	0	14795	913	32	3	521	3	SMAD2	18	45374945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	778976	45374945	32702303	10637	18622										
ZBTB7C	201501	broad.mit.edu	37	chr18	45567259	45567259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaagtcgatctcatagaCgtagggctggctggctaggg	15	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:45567259C>T	ENST00000588982.1	-	3	721	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.V74I|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.V74I|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.V74I|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.V74I			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	74	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.V74I(1)		endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						ATCTCATAGACGTAGGGCTGG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	18											66	63	64					18																	45567259		2203	4300	6503	43821257	SO:0001583	missense	201501			Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.220G>A	18.37:g.45567259C>T	ENSP00000468782:p.Val74Ile		43821257	O73453	Missense_Mutation	SNP	ENST00000588982.1	37	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.805829	0.31961	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.67523	-0.27;-0.27	5.04	4.16	0.48862	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.059752	0.64402	D	0.000003	T	0.54532	0.1864	L	0.45228	1.405	0.42202	D	0.991777	B;B;B	0.29716	0.071;0.255;0.255	B;B;B	0.23018	0.043;0.029;0.017	T	0.54583	-0.8272	10	0.48119	T	0.1	.	9.6616	0.39958	0.0:0.8389:0.0:0.1611	.	74;74;74	B4DKU0;B2RG49;A1YPR0	.;.;ZBT7C_HUMAN	I	74	ENSP00000439781:V74I;ENSP00000328732:V74I	ENSP00000328732:V74I	V	-	1	0	ZBTB7C	43821257	1.000000	0.71417	0.997000	0.53966	0.753000	0.42808	4.919000	0.63383	1.107000	0.41642	0.561000	0.74099	GTC		0.587	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		T	45567259	C	T	45567259	3	4	61	1	0	0	0	0	1	0	0	0	17594	536	19	1	1647	1	ZBTB7C	18	45567259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192314	45567259	32509989	10638	18623										
C18orf32	497661	broad.mit.edu	37	chr18	47009989	47009989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctttgtttgtatcattggAttcttgtattgctttcttag	8	6	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47009989A>G	ENST00000318240.3	-	2	341	c.130T>C	c.(130-132)Tcc>Ccc	p.S44P	RPL17-C18orf32_ENST00000584895.1_Silent_p.N220N|C18orf32_ENST00000582392.1_Missense_Mutation_p.S44P|RPL17-C18orf32_ENST00000332968.6_Silent_p.N182N|C18orf32_ENST00000579820.1_Missense_Mutation_p.S44P|RP11-110H1.4_ENST00000580150.1_RNA	NM_001035005.3	NP_001030177.1	Q8TCD1	CR032_HUMAN	chromosome 18 open reading frame 32	44					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)		signal transducer activity (GO:0004871)	p.S44P(1)		large_intestine(2)|lung(1)	3						GTATCATTGGATTCTTGTATT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	18											251	229	236					18																	47009989		2203	4300	6503	45263987	SO:0001583	missense	497661			AK027111	CCDS32831.1	18q21.1	2012-10-24			ENSG00000177576	ENSG00000177576			31690	protein-coding gene	gene with protein product							Standard	NM_001035005		Approved	FLJ23458	uc002ldl.3	Q8TCD1	OTTHUMG00000179688	ENST00000318240.3:c.130T>C	18.37:g.47009989A>G	ENSP00000323199:p.Ser44Pro		45263987		Silent	SNP	ENST00000318240.3	37	CCDS32831.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.642121	0.29157	.	.	ENSG00000177576	ENST00000318240	T	0.41758	0.99	5.63	-10.2	0.00374	.	0.419661	0.22054	U	0.065279	T	0.16769	0.0403	.	.	.	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.04041	-1.0982	9	0.45353	T	0.12	0.0757	2.5891	0.04838	0.1128:0.2225:0.1736:0.4911	.	44	Q8TCD1	CR032_HUMAN	P	44	ENSP00000323199:S44P	ENSP00000323199:S44P	S	-	1	0	C18orf32	45263987	0.002000	0.14202	0.005000	0.12908	0.374000	0.29953	-0.392000	0.07314	-0.928000	0.03761	-0.301000	0.09380	TCC		0.403	C18orf32-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447656.1	NM_001035005		G	47009989	A	G	47009989	3	3	61	1	0	0	0	0	1	0	0	0	1907	333	12	4	108	4	C18orf32	18	47009989	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1442730	47009989	31067259	10639	18624										
MYO5B	4645	broad.mit.edu	37	chr18	47352920	47352920	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagagaagatggattaaatGgaaacaaaacaggaaacatg	10	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47352920G>T	ENST00000285039.7	-	40	5767	c.5468C>A	c.(5467-5469)cCa>cAa	p.P1823Q	MYO5B_ENST00000324581.6_Missense_Mutation_p.P938Q|SCARNA17_ENST00000589499.1_RNA|RP11-886H22.1_ENST00000590532.2_Missense_Mutation_p.P146Q|MYO5B_ENST00000592688.1_Missense_Mutation_p.P393Q	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1823					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.P1823Q(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TGGATTAAATGGAAACAAAAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											129	117	121					18																	47352920		1910	4136	6046	45606918	SO:0001583	missense	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.5468C>A	18.37:g.47352920G>T	ENSP00000285039:p.Pro1823Gln		45606918	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724866	0.89298	.	.	ENSG00000167306	ENST00000285039;ENST00000356732;ENST00000324581	D;T	0.87729	-2.29;2.17	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.94005	0.7279	10	0.59425	D	0.04	.	18.9053	0.92458	0.0:0.0:1.0:0.0	.	1823;938	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	Q	1823;695;938	ENSP00000285039:P1823Q;ENSP00000315531:P938Q	ENSP00000285039:P1823Q	P	-	2	0	MYO5B	45606918	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.600000	0.90860	2.802000	0.96397	0.650000	0.86243	CCA		0.423	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47352920	G	T	47352920	3	4	61	1	0	0	0	0	1	0	0	0	10109	1348	47	2	82	2	MYO5B	18	47352920	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	342931	47352920	30724328	10640	18625										
MYO5B	4645	broad.mit.edu	37	chr18	47390703	47390703	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccacggctttcctcagctcAttcaggtcattcttcagctt	7	14	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47390703A>G	ENST00000285039.7	-	28	3950	c.3651T>C	c.(3649-3651)aaT>aaC	p.N1217N	MYO5B_ENST00000324581.6_Silent_p.N358N|MYO5B_ENST00000587895.1_5'UTR	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1217					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.N1217N(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCCTCAGCTCATTCAGGTCAT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	18											138	148	145					18																	47390703		2010	4174	6184	45644701	SO:0001819	synonymous_variant	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3651T>C	18.37:g.47390703A>G			45644701	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																				0.582	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			G	47390703	A	G	47390703	2	3	61	1	0	0	0	0	0	0	0	1	10109	214	8	4		4	MYO5B	18	47390703	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	37783	47390703	30686545	10641	18626										
MYO5B	4645	broad.mit.edu	37	chr18	47398567	47398567	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtaggccagatctgcattCgggtccaaatctatgtcagt	10	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47398567C>T	ENST00000285039.7	-	27	3872	c.3573G>A	c.(3571-3573)ccG>ccA	p.P1191P	Y_RNA_ENST00000364798.1_RNA|MYO5B_ENST00000324581.6_Silent_p.P332P|MYO5B_ENST00000587895.1_5'UTR	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1191					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.P1191P(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GATCTGCATTCGGGTCCAAAT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	18											356	343	347					18																	47398567		1953	4136	6089	45652565	SO:0001819	synonymous_variant	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3573G>A	18.37:g.47398567C>T			45652565	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																				0.507	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47398567	C	T	47398567	2	4	61	1	0	0	0	0	0	0	0	1	10109	871	31	1		1	MYO5B	18	47398567	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7864	47398567	30678681	10642	18627										
MYO5B	4645	broad.mit.edu	37	chr18	47406797	47406797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttctcatctttcaagagaGcattttcttgctccaggtct	6	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47406797G>A	ENST00000285039.7	-	23	3373	c.3074C>T	c.(3073-3075)gCt>gTt	p.A1025V	MYO5B_ENST00000324581.6_Missense_Mutation_p.A166V	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1025					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.A1025V(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TTTCAAGAGAGCATTTTCTTG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	18											213	219	217					18																	47406797		1859	4096	5955	45660795	SO:0001583	missense	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3074C>T	18.37:g.47406797G>A	ENSP00000285039:p.Ala1025Val		45660795	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.802711	0.50315	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.19394	2.15;2.15	5.39	5.39	0.77823	.	0.059053	0.64402	D	0.000002	T	0.21062	0.0507	L	0.55481	1.735	0.50813	D	0.999896	B;B	0.25563	0.01;0.129	B;B	0.22152	0.009;0.038	T	0.02042	-1.1224	10	0.31617	T	0.26	.	12.447	0.55657	0.0815:0.0:0.9185:0.0	.	1025;166	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	V	1025;166	ENSP00000285039:A1025V;ENSP00000315531:A166V	ENSP00000285039:A1025V	A	-	2	0	MYO5B	45660795	1.000000	0.71417	0.981000	0.43875	0.857000	0.48899	5.517000	0.67061	2.684000	0.91462	0.650000	0.86243	GCT		0.438	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47406797	G	A	47406797	3	1	61	1	0	0	0	0	1	0	0	0	10109	971	34	3	2544	3	MYO5B	18	47406797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8230	47406797	30670451	10643	18628										
MYO5B	4645	broad.mit.edu	37	chr18	47518664	47518664	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctcccactcacctggaaGaccactctggacttctccaa	5	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:47518664G>T	ENST00000285039.7	-	6	1049	c.750C>A	c.(748-750)gtC>gtA	p.V250V		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	250	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.V250V(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCACCTGGAAGACCACTCTGG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	18											206	196	199					18																	47518664		1952	4147	6099	45772662	SO:0001819	synonymous_variant	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.750C>A	18.37:g.47518664G>T			45772662	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																				0.502	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47518664	G	T	47518664	2	4	61	1	0	0	0	0	0	0	0	1	10109	929	33	2		2	MYO5B	18	47518664	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111867	47518664	30558584	10644	18629										
ELAC1	55520	broad.mit.edu	37	chr18	48510836	48510836	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaacaatttgttgtaaaAgcatttcgcctctttcacag	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:48510836A>C	ENST00000269466.3	+	3	635	c.528A>C	c.(526-528)aaA>aaC	p.K176N	ELAC1_ENST00000588577.1_Intron|SMAD4_ENST00000452201.2_Intron|ELAC1_ENST00000591429.1_Missense_Mutation_p.K176N|RP11-729L2.2_ENST00000588256.1_Intron|RP11-729L2.2_ENST00000590722.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	176					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)	p.K176N(1)		kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		TTGTTGTAAAAGCATTTCGCC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	18											64	63	63					18																	48510836		2203	4300	6503	46764834	SO:0001583	missense	55520			AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"tRNA Z (short form)", "RNaseZ(S)"	608079	"elaC (E. coli) homolog 1", "elaC homolog 1 (E. coli)"			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.528A>C	18.37:g.48510836A>C	ENSP00000269466:p.Lys176Asn		46764834	Q9NS99	Missense_Mutation	SNP	ENST00000269466.3	37	CCDS11949.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115562	0.37339	.	.	ENSG00000141642	ENST00000269466	T	0.76709	-1.04	5.95	3.58	0.41010	Beta-lactamase-like (1);	0.042326	0.85682	D	0.000000	T	0.66356	0.2781	L	0.46819	1.47	0.80722	D	1	P;B	0.38223	0.623;0.283	B;B	0.34180	0.177;0.177	T	0.58836	-0.7566	10	0.28530	T	0.3	.	8.4672	0.32964	0.7769:0.0:0.2231:0.0	.	176;176	Q53EY2;Q9H777	.;RNZ1_HUMAN	N	176	ENSP00000269466:K176N	ENSP00000269466:K176N	K	+	3	2	ELAC1	46764834	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.790000	0.38734	0.513000	0.28278	0.528000	0.53228	AAA		0.408	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			C	48510836	A	C	48510836	3	2	61	1	0	0	0	0	1	0	0	0	5059	69	3	4	534	4	ELAC1	18	48510836	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	992172	48510836	29566412	10645	18630										
DCC	1630	broad.mit.edu	37	chr18	50278472	50278472	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcttcctctcagaaccttCtgatgccgtcacaatgcggg	10	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:50278472C>A	ENST00000442544.2	+	2	756	c.140C>A	c.(139-141)tCt>tAt	p.S47Y	DCC_ENST00000412726.1_5'Flank	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	47	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.S47Y(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TCAGAACCTTCTGATGCCGTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											56	57	57					18																	50278472		2203	4300	6503	48532470	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.140C>A	18.37:g.50278472C>A	ENSP00000389140:p.Ser47Tyr		48532470		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.223683	0.79576	.	.	ENSG00000187323	ENST00000442544	T	0.13538	2.58	5.66	5.66	0.87406	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.255515	0.35349	N	0.003269	T	0.36413	0.0966	M	0.77712	2.385	0.80722	D	1	D	0.63880	0.993	P	0.58210	0.835	T	0.07558	-1.0766	10	0.62326	D	0.03	.	18.5252	0.90969	0.0:1.0:0.0:0.0	.	47	P43146	DCC_HUMAN	Y	47	ENSP00000389140:S47Y	ENSP00000389140:S47Y	S	+	2	0	DCC	48532470	0.009000	0.17119	0.995000	0.50966	0.992000	0.81027	1.861000	0.39438	2.676000	0.91093	0.655000	0.94253	TCT		0.473	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		A	50278472	C	A	50278472	3	1	61	1	0	0	0	0	1	0	0	0	4288	913	32	2	146	2	DCC	18	50278472	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1767636	50278472	27798776	10646	18631										
DCC	1630	broad.mit.edu	37	chr18	50589685	50589685	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctttgcagttccgccatgGtttttaaatcatccttccaa	6	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:50589685G>T	ENST00000442544.2	+	6	1612	c.996G>T	c.(994-996)tgG>tgT	p.W332C	DCC_ENST00000412726.1_Missense_Mutation_p.W180C|DCC_ENST00000581580.1_5'UTR|DCC_ENST00000580146.1_3'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	332	Ig-like C2-type 4.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.W332C(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TTCCGCCATGGTTTTTAAATC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	18											240	239	239					18																	50589685		2203	4300	6503	48843683	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.996G>T	18.37:g.50589685G>T	ENSP00000389140:p.Trp332Cys		48843683		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.400214	0.42613	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	D;D	0.81659	-1.52;-1.52	5.82	5.82	0.92795	Immunoglobulin-like (1);	0.157934	0.45361	D	0.000379	T	0.67373	0.2886	N	0.08118	0	0.80722	D	1	P;P	0.50156	0.932;0.871	B;B	0.40444	0.329;0.329	T	0.74203	-0.3741	10	0.54805	T	0.06	.	18.8681	0.92301	0.0:0.0:1.0:0.0	.	180;332	E7EQM8;P43146	.;DCC_HUMAN	C	332;265;180	ENSP00000389140:W332C;ENSP00000397322:W180C	ENSP00000304146:W265C	W	+	3	0	DCC	48843683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.996000	0.63914	2.753000	0.94483	0.557000	0.71058	TGG		0.433	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50589685	G	T	50589685	3	4	61	1	0	0	0	0	1	0	0	0	4288	1270	44	2	1018	2	DCC	18	50589685	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	311213	50589685	27487563	10647	18632										
POLI	11201	broad.mit.edu	37	chr18	51797787	51797787	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccagagtcatagtacatgTggatctggattgcttttatg	10	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:51797787T>A	ENST00000579534.1	+	2	316	c.173T>A	c.(172-174)gTg>gAg	p.V58E	POLI_ENST00000579434.1_Intron|POLI_ENST00000406285.3_Missense_Mutation_p.V58E|POLI_ENST00000217800.5_5'UTR	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	58	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.V33E(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		ATAGTACATGTGGATCTGGAT	0.348								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	18											112	103	106					18																	51797787		2203	4300	6503	50051785	SO:0001583	missense	11201				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.173T>A	18.37:g.51797787T>A	ENSP00000462664:p.Val58Glu		50051785	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	37	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344463	0.82022	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.79653	-1.29	5.14	5.14	0.70334	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.280184	0.35708	N	0.003028	D	0.90055	0.6894	M	0.85630	2.765	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.78314	0.972;0.991	D	0.91681	0.5358	10	0.87932	D	0	-2.5011	13.9687	0.64225	0.0:0.0:0.0:1.0	.	57;58	B7Z780;Q9UNA4	.;POLI_HUMAN	E	58	ENSP00000385196:V58E	ENSP00000217800:V58E	V	+	2	0	POLI	50051785	1.000000	0.71417	0.953000	0.39169	0.980000	0.70556	4.879000	0.63100	1.931000	0.55961	0.460000	0.39030	GTG		0.348	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		A	51797787	T	A	51797787	3	1	61	1	0	0	0	0	1	0	0	0	12234	1696	59	5	179	5	POLI	18	51797787	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1208102	51797787	26279461	10648	18633										
POLI	11201	broad.mit.edu	37	chr18	51820704	51820704	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaatagagagccagattCtgttgatgagaaaattactt	9	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:51820704C>A	ENST00000579534.1	+	10	2233	c.2090C>A	c.(2089-2091)tCt>tAt	p.S697Y	POLI_ENST00000579434.1_Missense_Mutation_p.S594Y|POLI_ENST00000406285.3_Missense_Mutation_p.S618Y|POLI_ENST00000217800.5_Missense_Mutation_p.S571Y	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	697					DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.S672Y(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		GAGCCAGATTCTGTTGATGAG	0.408								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	18											76	75	76					18																	51820704		2203	4300	6503	50074702	SO:0001583	missense	11201				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.2090C>A	18.37:g.51820704C>A	ENSP00000462664:p.Ser697Tyr		50074702	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	37	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	C	5.054	0.195621	0.09599	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.52983	0.64	5.5	2.76	0.32466	.	0.967076	0.08604	N	0.920982	T	0.44685	0.1305	M	0.70595	2.14	0.09310	N	1	P;P	0.38582	0.638;0.638	B;B	0.34242	0.178;0.178	T	0.33979	-0.9847	10	0.51188	T	0.08	-2.8454	6.7403	0.23433	0.0:0.6952:0.1461:0.1587	.	617;697	B7Z780;Q9UNA4	.;POLI_HUMAN	Y	618;697	ENSP00000385196:S618Y	ENSP00000217800:S697Y	S	+	2	0	POLI	50074702	0.000000	0.05858	0.002000	0.10522	0.733000	0.41908	-0.244000	0.08903	0.375000	0.24679	0.650000	0.86243	TCT		0.408	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		A	51820704	C	A	51820704	3	1	61	1	0	0	0	0	1	0	0	0	12234	913	32	2	2128	2	POLI	18	51820704	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22917	51820704	26256544	10649	18634										
TCF4	6925	broad.mit.edu	37	chr18	52928698	52928698	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtcaatatttcctcaccGaagcaagtgctttccccaga	6	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:52928698G>A	ENST00000356073.4	-	12	1600	c.989C>T	c.(988-990)tCg>tTg	p.S330L	TCF4_ENST00000537578.1_Splice_Site_p.S306L|TCF4_ENST00000543082.1_Splice_Site_p.S288L|TCF4_ENST00000564403.2_Splice_Site_p.S336L|TCF4_ENST00000570177.2_Splice_Site_p.S200L|TCF4_ENST00000565018.2_Splice_Site_p.S330L|TCF4_ENST00000568740.1_Splice_Site_p.S305L|TCF4_ENST00000398339.1_Splice_Site_p.S432L|TCF4_ENST00000570287.2_Splice_Site_p.S170L|TCF4_ENST00000540999.1_Splice_Site_p.S306L|TCF4_ENST00000544241.2_Splice_Site_p.S259L|TCF4_ENST00000566279.1_Splice_Site_p.S270L|TCF4_ENST00000561992.1_Splice_Site_p.S200L|TCF4_ENST00000564228.1_Splice_Site_p.S259L|TCF4_ENST00000568673.1_Splice_Site_p.S306L|TCF4_ENST00000567880.1_Splice_Site_p.S270L|TCF4_ENST00000354452.3_Splice_Site_p.S330L|TCF4_ENST00000537856.3_Splice_Site_p.S200L|TCF4_ENST00000564999.1_Splice_Site_p.S330L|TCF4_ENST00000566286.1_Splice_Site_p.S328L|TCF4_ENST00000561831.3_Splice_Site_p.S170L|TCF4_ENST00000457482.3_Splice_Site_p.S170L|TCF4_ENST00000563760.1_5'UTR	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	330					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)	p.S330L(1)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TTTCCTCACCGAAGCAAGTGC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	18											194	215	208					18																	52928698		2203	4300	6503	51079696	SO:0001630	splice_region_variant	6925			M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.990+1C>T	18.37:g.52928698G>A			51079696	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	37	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	33	5.288218	0.95517	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.74092	0.3671	M	0.86178	2.8	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.98;0.999;0.999;0.997;0.983;0.999;0.995;0.995;0.997	T	0.76822	-0.2817	10	0.87932	D	0	-5.892	19.2296	0.93833	0.0:0.0:1.0:0.0	.	306;330;170;432;330;288;259;170;328	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	L	330;170;330;288;306;306;259;200;432	ENSP00000346440:S330L;ENSP00000409447:S170L;ENSP00000348374:S330L;ENSP00000439656:S288L;ENSP00000445202:S306L;ENSP00000440731:S306L;ENSP00000441562:S259L;ENSP00000439827:S200L;ENSP00000381382:S432L	ENSP00000346440:S330L	S	-	2	0	TCF4	51079696	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.069000	0.93967	2.835000	0.97688	0.650000	0.86243	TCG		0.433	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	Missense_Mutation	A	52928698	G	A	52928698	5	1	61	1	0	0	0	0	0	0	1	0	15734	1072	37	1	1058	1	TCF4	18	52928698	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1107994	52928698	25148550	10650	18635										
WDR7	23335	broad.mit.edu	37	chr18	54358452	54358452	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcttccttgcaggtgttCgatgccggagactattcctt	9	11	1	1	rs562541697		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:54358452C>T	ENST00000254442.3	+	8	934	c.723C>T	c.(721-723)ttC>ttT	p.F241F	WDR7_ENST00000357574.3_Silent_p.F241F|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	241					hematopoietic progenitor cell differentiation (GO:0002244)			p.F241F(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGCAGGTGTTCGATGCCGGAG	0.398													C|||	1	0.000199681	0	0	5008	,	,		16671	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	18											119	128	125					18																	54358452		2203	4300	6503	52509450	SO:0001819	synonymous_variant	23335			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.723C>T	18.37:g.54358452C>T			52509450	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Silent	SNP	ENST00000254442.3	37	CCDS11962.1																																																																																				0.398	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			T	54358452	C	T	54358452	2	4	61	1	0	0	0	0	0	0	0	1	17360	883	31	1		1	WDR7	18	54358452	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1429754	54358452	23718796	10651	18636										
WDR7	23335	broad.mit.edu	37	chr18	54363551	54363551	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctcatcaggtctcagctcGgtatgatcaaagatacctga	8	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:54363551G>A	ENST00000254442.3	+	12	1647	c.1436G>A	c.(1435-1437)cGg>cAg	p.R479Q	WDR7_ENST00000357574.3_Missense_Mutation_p.R479Q|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	479					hematopoietic progenitor cell differentiation (GO:0002244)			p.R479Q(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		GTCTCAGCTCGGTATGATCAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											144	126	132					18																	54363551		2203	4300	6503	52514549	SO:0001583	missense	23335			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.1436G>A	18.37:g.54363551G>A	ENSP00000254442:p.Arg479Gln		52514549	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	37	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	G	36	5.655086	0.96724	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000398311	T;T	0.69685	-0.42;-0.4	5.73	5.73	0.89815	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.968;0.994	T	0.74945	-0.3491	10	0.42905	T	0.14	.	19.8551	0.96755	0.0:0.0:1.0:0.0	.	479;479	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	Q	479	ENSP00000254442:R479Q;ENSP00000350187:R479Q	ENSP00000254442:R479Q	R	+	2	0	WDR7	52514549	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.619000	0.98369	2.861000	0.98227	0.655000	0.94253	CGG		0.418	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			A	54363551	G	A	54363551	3	1	61	1	0	0	0	0	1	0	0	0	17360	1116	39	1	1478	1	WDR7	18	54363551	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5099	54363551	23713697	10652	18637										
WDR7	23335	broad.mit.edu	37	chr18	54385328	54385328	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaatcaaatggaggccttCtgatgattacctggtggtgg	13	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:54385328C>A	ENST00000254442.3	+	13	1923	c.1712C>A	c.(1711-1713)tCt>tAt	p.S571Y	WDR7_ENST00000357574.3_Missense_Mutation_p.S571Y|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	571					hematopoietic progenitor cell differentiation (GO:0002244)			p.S571Y(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGGAGGCCTTCTGATGATTAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											188	169	176					18																	54385328		2203	4300	6503	52536326	SO:0001583	missense	23335			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.1712C>A	18.37:g.54385328C>A	ENSP00000254442:p.Ser571Tyr		52536326	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	37	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	C	8.936	0.964605	0.18583	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000398311	T;T	0.05258	3.47;3.47	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.179185	0.49916	D	0.000135	T	0.09862	0.0242	N	0.08118	0	0.41136	D	0.985925	D;D	0.61080	0.965;0.989	P;P	0.60541	0.617;0.876	T	0.53236	-0.8467	10	0.22706	T	0.39	.	19.1709	0.93576	0.0:1.0:0.0:0.0	.	571;571	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	Y	571	ENSP00000254442:S571Y;ENSP00000350187:S571Y	ENSP00000254442:S571Y	S	+	2	0	WDR7	52536326	0.988000	0.35896	0.981000	0.43875	0.896000	0.52359	3.808000	0.55598	2.632000	0.89209	0.655000	0.94253	TCT		0.398	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			A	54385328	C	A	54385328	3	1	61	1	0	0	0	0	1	0	0	0	17360	913	32	2	1758	2	WDR7	18	54385328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21777	54385328	23691920	10653	18638										
ST8SIA3	51046	broad.mit.edu	37	chr18	55024316	55024316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacccattatgaacaagcatTataatatttgtgctgtggtt	7	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55024316T>C	ENST00000324000.3	+	3	2509	c.475T>C	c.(475-477)Tat>Cat	p.Y159H		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	159					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.Y159H(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GAACAAGCATTATAATATTTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	18											113	118	116					18																	55024316		2203	4300	6503	53175314	SO:0001583	missense	51046			AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.475T>C	18.37:g.55024316T>C	ENSP00000320431:p.Tyr159His		53175314	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.493718	0.44352	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.31247	1.5	5.96	5.96	0.96718	.	0.051843	0.85682	D	0.000000	T	0.32224	0.0822	L	0.45470	1.425	0.58432	D	0.999998	P	0.43788	0.817	B	0.41988	0.372	T	0.03231	-1.1058	10	0.37606	T	0.19	-18.1709	16.1099	0.81255	0.0:0.0:0.0:1.0	.	159	O43173	SIA8C_HUMAN	H	266;159	ENSP00000320431:Y159H	ENSP00000320431:Y159H	Y	+	1	0	ST8SIA3	53175314	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.677000	0.84024	2.285000	0.76669	0.533000	0.62120	TAT		0.383	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		C	55024316	T	C	55024316	3	2	61	1	0	0	0	0	1	0	0	0	15272	1754	61	4	485	4	ST8SIA3	18	55024316	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	638988	55024316	23052932	10654	18639										
ST8SIA3	51046	broad.mit.edu	37	chr18	55024402	55024402	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaatcagattttgttttCcgttgcaatttcgcccctac	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55024402C>T	ENST00000324000.3	+	3	2595	c.561C>T	c.(559-561)ttC>ttT	p.F187F		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	187					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.F187F(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		ATTTTGTTTTCCGTTGCAATT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	18											86	91	89					18																	55024402		2203	4300	6503	53175400	SO:0001819	synonymous_variant	51046			AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.561C>T	18.37:g.55024402C>T			53175400	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	37	CCDS32834.1																																																																																				0.403	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		T	55024402	C	T	55024402	2	4	61	1	0	0	0	0	0	0	0	1	15272	854	30	3		3	ST8SIA3	18	55024402	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86	55024402	23052846	10655	18640										
ST8SIA3	51046	broad.mit.edu	37	chr18	55027403	55027403	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaaaaaggaaccaaattTaccaccaagtggcaggagtc	9	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55027403T>G	ENST00000324000.3	+	4	3072	c.1038T>G	c.(1036-1038)ttT>ttG	p.F346L		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	346					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.F346L(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GAACCAAATTTACCACCAAGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	18											88	78	81					18																	55027403		2203	4300	6503	53178401	SO:0001583	missense	51046			AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.1038T>G	18.37:g.55027403T>G	ENSP00000320431:p.Phe346Leu		53178401	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885119	0.72410	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.28069	1.63	6.11	2.21	0.28008	.	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	L	0.31207	0.915	0.58432	D	0.999997	P	0.46784	0.884	P	0.54815	0.761	T	0.03287	-1.1052	10	0.13470	T	0.59	-3.2426	9.4409	0.38668	0.0:0.4069:0.0:0.5931	.	346	O43173	SIA8C_HUMAN	L	453;346	ENSP00000320431:F346L	ENSP00000320431:F346L	F	+	3	2	ST8SIA3	53178401	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.565000	0.23578	0.128000	0.18479	0.533000	0.62120	TTT		0.488	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		G	55027403	T	G	55027403	3	3	61	1	0	0	0	0	1	0	0	0	15272	1751	61	4	1052	4	ST8SIA3	18	55027403	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3001	55027403	23049845	10656	18641										
FECH	2235	broad.mit.edu	37	chr18	55238688	55238688	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctgcttggaagtccatatCttgatgggggatccgcctcc	11	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55238688C>A	ENST00000262093.5	-	4	550	c.399G>T	c.(397-399)aaG>aaT	p.K133N	FECH_ENST00000382873.3_Missense_Mutation_p.K139N|FECH_ENST00000585699.1_5'UTR	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	133					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)	p.K139N(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				AAGTCCATATCTTGATGGGGG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	18											127	111	116					18																	55238688		2203	4300	6503	53389686	SO:0001583	missense	2235			D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"protoporphyria"	612386	"ferrochelatase (protoporphyria)"			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.399G>T	18.37:g.55238688C>A	ENSP00000262093:p.Lys133Asn		53389686	A8KA72|Q8IXN1|Q8NAN0	Missense_Mutation	SNP	ENST00000262093.5	37	CCDS11964.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760728	0.69763	.	.	ENSG00000066926	ENST00000262093;ENST00000382873	D;D	0.96459	-4.02;-4.02	5.79	3.69	0.42338	.	0.089542	0.85682	D	0.000000	D	0.93946	0.8062	N	0.20574	0.59	0.42263	D	0.99202	D;D	0.56035	0.974;0.968	P;P	0.54026	0.74;0.622	D	0.93503	0.6846	10	0.51188	T	0.08	-28.1679	10.6364	0.45567	0.0:0.7696:0.0:0.2304	.	133;139	P22830;P22830-2	HEMH_HUMAN;.	N	133;139	ENSP00000262093:K133N;ENSP00000372326:K139N	ENSP00000262093:K133N	K	-	3	2	FECH	53389686	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.294000	0.33365	1.467000	0.48044	0.561000	0.74099	AAG		0.478	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1			A	55238688	C	A	55238688	3	1	61	1	0	0	0	0	1	0	0	0	5827	912	32	2	904	2	FECH	18	55238688	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211285	55238688	22838560	10657	18642										
NARS	4677	broad.mit.edu	37	chr18	55283076	55283076	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcccgggattcactcttCatttgttccctatgccacat	5	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55283076C>T	ENST00000256854.5	-	3	680	c.225G>A	c.(223-225)atG>atA	p.M75I	NARS_ENST00000423481.2_5'UTR	NM_004539.3	NP_004530.1	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase	75					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.M75I(1)		breast(1)|endometrium(5)|large_intestine(5)|lung(8)|skin(1)	20		Colorectal(73;0.227)			L-Asparagine(DB00174)	ATTCACTCTTCATTTGTTCCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	18											218	208	211					18																	55283076		2203	4300	6503	53434074	SO:0001583	missense	4677			D84273	CCDS32837.1	18q21.31	2014-05-06			ENSG00000134440	ENSG00000134440	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	7643	protein-coding gene	gene with protein product	"asparagine tRNA ligase 1, cytoplasmic"	108410				6836455, 9421509	Standard	NM_004539		Approved	NARS1	uc002lgs.2	O43776	OTTHUMG00000180125	ENST00000256854.5:c.225G>A	18.37:g.55283076C>T	ENSP00000256854:p.Met75Ile		53434074	B4DG16|Q53GU6	Missense_Mutation	SNP	ENST00000256854.5	37	CCDS32837.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.685951	0.29962	.	.	ENSG00000134440	ENST00000256854;ENST00000411676;ENST00000540592	T	0.78246	-1.16	5.49	4.62	0.57501	.	0.137629	0.64402	D	0.000004	T	0.76335	0.3973	M	0.64997	1.995	0.80722	D	1	B;B;B	0.19706	0.022;0.038;0.001	B;B;B	0.25405	0.017;0.06;0.01	T	0.74250	-0.3726	10	0.59425	D	0.04	-6.1716	14.3069	0.66391	0.0:0.927:0.0:0.073	.	75;42;75	B4DGT6;F5H015;O43776	.;.;SYNC_HUMAN	I	75;42;75	ENSP00000256854:M75I	ENSP00000256854:M75I	M	-	3	0	NARS	53434074	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.538000	0.45710	1.313000	0.45069	0.643000	0.83706	ATG		0.383	NARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449872.2	NM_004539		T	55283076	C	T	55283076	3	4	61	1	0	0	0	0	1	0	0	0	10200	826	29	3	1469	3	NARS	18	55283076	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44388	55283076	22794172	10658	18643										
ATP8B1	5205	broad.mit.edu	37	chr18	55317640	55317640	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggtcattgacaggaatcGaatggcaacgacgggtagta	14	6	1	1	rs369054652		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55317640G>A	ENST00000283684.4	-	26	3489	c.3490C>T	c.(3490-3492)Cga>Tga	p.R1164*	RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Nonsense_Mutation_p.R1164*|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	1164					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1164*(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				GACAGGAATCGAATGGCAACG	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	18	GRCh37	CM043833	ATP8B1	M		G	,stop/ARG	0,4406		0,0,2203	176	142	154		,3490	4.6	0	18		154	1,8599	1.2+/-3.3	0,1,4299	no	intron,stop-gained	ATP8B1,LOC100505549	NM_001242804.1,NM_005603.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	,1164/1252	55317640	1,13005	2203	4300	6503	53468638	SO:0001587	stop_gained	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.3490C>T	18.37:g.55317640G>A	ENSP00000283684:p.Arg1164*		53468638	Q9BTP8	Nonsense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	G	39	7.809527	0.98501	0.0	1.16E-4	ENSG00000081923	ENST00000283684;ENST00000536015	.	.	.	5.51	4.64	0.57946	.	0.053998	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5567	0.76200	0.0:0.0:0.8607:0.1393	.	.	.	.	X	1164	.	ENSP00000283684:R1164X	R	-	1	2	ATP8B1	53468638	1.000000	0.71417	0.045000	0.18777	0.535000	0.34838	5.089000	0.64492	1.342000	0.45619	-0.226000	0.12346	CGA		0.453	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		A	55317640	G	A	55317640	4	1	61	1	0	0	0	0	0	1	0	0	1195	1066	37	1	273	1	ATP8B1	18	55317640	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34564	55317640	22759608	10659	18644										
ATP8B1	5205	broad.mit.edu	37	chr18	55336712	55336712	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaagagtttcatttgcaaaGatctgttttatttaaaaaaa	5	4	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:55336712G>T	ENST00000283684.4	-	17	1934	c.1935C>A	c.(1933-1935)atC>atA	p.I645I	RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Silent_p.I645I|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	645			Missing (in PFIC1). {ECO:0000269|PubMed:9500542}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.I645I(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				CATTTGCAAAGATCTGTTTTA	0.289																																																1	Substitution - coding silent(1)	large_intestine(1)	18											30	30	30					18																	55336712		2203	4300	6503	53487710	SO:0001819	synonymous_variant	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.1935C>A	18.37:g.55336712G>T			53487710	Q9BTP8	Silent	SNP	ENST00000283684.4	37	CCDS11965.1																																																																																				0.289	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		T	55336712	G	T	55336712	2	4	61	1	0	0	0	0	0	0	0	1	1195	932	33	2		2	ATP8B1	18	55336712	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19072	55336712	22740536	10660	18645										
NEDD4L	23327	broad.mit.edu	37	chr18	56010290	56010290	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgaggatagcgccaaaCggccggcccttcttcattga	11	11	2	2	rs199582650	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56010290C>T	ENST00000400345.3	+	16	1813	c.1530C>T	c.(1528-1530)aaC>aaT	p.N510N	NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000356462.6_Silent_p.N446N|NEDD4L_ENST00000357895.5_Silent_p.N502N|NEDD4L_ENST00000431212.2_Silent_p.N389N|NEDD4L_ENST00000456173.2_Silent_p.N369N|NEDD4L_ENST00000586263.1_Silent_p.N482N|NEDD4L_ENST00000256830.9_Silent_p.N406N|NEDD4L_ENST00000435432.2_Silent_p.N369N|NEDD4L_ENST00000256832.7_Silent_p.N369N|NEDD4L_ENST00000382850.4_Silent_p.N490N|NEDD4L_ENST00000456986.1_Silent_p.N389N	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	510	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)	p.N490N(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TAGCGCCAAACGGCCGGCCCT	0.488													C|||	3	0.000599042	0	0	5008	,	,		17291	0.002		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	18						C	,,,,,,,,	0,3894		0,0,1947	80	85	84		1167,1167,1167,1530,1506,1446,1107,1107,1470	-0.5	0.9	18		84	1,8241		0,1,4120	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEDD4L	NM_001144964.1,NM_001144965.1,NM_001144966.2,NM_001144967.2,NM_001144968.1,NM_001144969.1,NM_001144970.2,NM_001144971.1,NM_015277.5	,,,,,,,,	0,1,6067	TT,TC,CC		0.0121,0.0,0.0082	,,,,,,,,	389/855,389/855,389/855,510/976,502/968,482/948,369/835,369/835,490/956	56010290	1,12135	1947	4121	6068	54161270	SO:0001819	synonymous_variant	23327			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1530C>T	18.37:g.56010290C>T			54161270	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	37	CCDS45872.1																																																																																				0.488	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	56010290	C	T	56010290	2	4	61	1	0	0	0	0	0	0	0	1	10342	535	19	1		1	NEDD4L	18	56010290	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	673578	56010290	22066958	10661	18646										
NEDD4L	23327	broad.mit.edu	37	chr18	56033273	56033273	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgaaacttcacagaaatAacatatttgaagagtcctat	5	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56033273A>C	ENST00000400345.3	+	21	2159	c.1876A>C	c.(1876-1878)Aac>Cac	p.N626H	NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000356462.6_Missense_Mutation_p.N562H|NEDD4L_ENST00000357895.5_Missense_Mutation_p.N618H|NEDD4L_ENST00000431212.2_Missense_Mutation_p.N505H|NEDD4L_ENST00000456173.2_Missense_Mutation_p.N485H|NEDD4L_ENST00000586263.1_Missense_Mutation_p.N598H|NEDD4L_ENST00000256830.9_Missense_Mutation_p.N522H|NEDD4L_ENST00000435432.2_Missense_Mutation_p.N485H|NEDD4L_ENST00000256832.7_Missense_Mutation_p.N486H|NEDD4L_ENST00000382850.4_Missense_Mutation_p.N606H|NEDD4L_ENST00000456986.1_Missense_Mutation_p.N505H	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	626					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)	p.N606H(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TCACAGAAATAACATATTTGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											91	84	86					18																	56033273		1829	4083	5912	54184253	SO:0001583	missense	23327			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1876A>C	18.37:g.56033273A>C	ENSP00000383199:p.Asn626His		54184253	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	37	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.892028	0.33442	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.76448	0.92;0.92;0.92;0.92;-1.02;-1.02;0.92;-1.02;-1.02;-1.02	5.54	5.54	0.83059	HECT (1);	0.000000	0.85682	D	0.000000	T	0.77011	0.4068	N	0.05383	-0.06	0.80722	D	1	P;B;D;D;D;P	0.76494	0.47;0.329;0.998;0.999;0.992;0.47	B;B;P;D;P;B	0.81914	0.167;0.089;0.899;0.995;0.77;0.167	T	0.80589	-0.1315	10	0.42905	T	0.14	.	15.9755	0.80060	1.0:0.0:0.0:0.0	.	598;618;485;562;626;606	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	H	626;606;562;522;486;505;618;485;485;505	ENSP00000383199:N626H;ENSP00000372301:N606H;ENSP00000348847:N562H;ENSP00000256830:N522H;ENSP00000256832:N486H;ENSP00000411947:N505H;ENSP00000350569:N618H;ENSP00000393395:N485H;ENSP00000405440:N485H;ENSP00000389406:N505H	ENSP00000256830:N522H	N	+	1	0	NEDD4L	54184253	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.256000	0.72473	2.219000	0.72066	0.528000	0.53228	AAC		0.348	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56033273	A	C	56033273	3	2	61	1	0	0	0	0	1	0	0	0	10342	362	13	4	1986	4	NEDD4L	18	56033273	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22983	56033273	22043975	10662	18647										
ALPK2	115701	broad.mit.edu	37	chr18	56149069	56149069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggacgttaggttttcttttCgcctggggtctcaggccctg	14	10	2	0	rs543965909		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56149069C>T	ENST00000361673.3	-	13	6712	c.6499G>A	c.(6499-6501)Gaa>Aaa	p.E2167K		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	2167						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E2167K(1)|p.E1528K(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GTTTTCTTTTCGCCTGGGGTC	0.478													C|||	1	0.000199681	0	0	5008	,	,		19788	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	18											153	142	146					18																	56149069		2203	4300	6503	54300049	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.6499G>A	18.37:g.56149069C>T	ENSP00000354991:p.Glu2167Lys		54300049	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695570	0.48202	.	.	ENSG00000198796	ENST00000361673	T	0.49432	0.78	5.82	4.04	0.47022	.	0.422063	0.22723	N	0.056422	T	0.43077	0.1231	M	0.64997	1.995	0.09310	N	1	P	0.47253	0.892	B	0.39660	0.306	T	0.43130	-0.9410	10	0.87932	D	0	-3.4178	8.9382	0.35713	0.0:0.7382:0.1249:0.1369	.	2167	Q86TB3	ALPK2_HUMAN	K	2167	ENSP00000354991:E2167K	ENSP00000354991:E2167K	E	-	1	0	ALPK2	54300049	0.003000	0.15002	0.001000	0.08648	0.047000	0.14425	1.193000	0.32162	0.818000	0.34468	0.655000	0.94253	GAA		0.478	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56149069	C	T	56149069	3	4	61	1	0	0	0	0	1	0	0	0	545	893	31	1	17	1	ALPK2	18	56149069	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115796	56149069	21928179	10663	18648										
ALPK2	115701	broad.mit.edu	37	chr18	56171304	56171304	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggaatacttcacaaattCtccaatcagctcctcctcca	4	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56171304C>A	ENST00000361673.3	-	11	6319	c.6106G>T	c.(6106-6108)Gaa>Taa	p.E2036*		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	2036	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E1397*(1)|p.E2036*(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TTCACAAATTCTCCAATCAGC	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											180	173	175					18																	56171304		2203	4300	6503	54322284	SO:0001587	stop_gained	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.6106G>T	18.37:g.56171304C>A	ENSP00000354991:p.Glu2036*		54322284	Q6ZUX0|Q8NAT5|Q96L95	Nonsense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	48	14.921304	0.99815	.	.	ENSG00000198796	ENST00000361673	.	.	.	5.63	5.63	0.86233	.	0.171607	0.37857	N	0.001908	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-22.8411	19.3517	0.94389	0.0:1.0:0.0:0.0	.	.	.	.	X	2036	.	ENSP00000354991:E2036X	E	-	1	0	ALPK2	54322284	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.659000	0.68010	2.680000	0.91292	0.644000	0.83932	GAA		0.453	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56171304	C	A	56171304	4	1	61	1	0	0	0	0	0	1	0	0	545	922	32	2	418	2	ALPK2	18	56171304	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22235	56171304	21905944	10664	18649										
ALPK2	115701	broad.mit.edu	37	chr18	56184373	56184373	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagctgtcatggaggaagtCttctttgaagatgagttggc	14	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56184373C>A	ENST00000361673.3	-	9	5920	c.5707G>T	c.(5707-5709)Gac>Tac	p.D1903Y		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1903	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D1903Y(1)|p.D1264Y(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGGAGGAAGTCTTCTTTGAAG	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	18											67	69	68					18																	56184373		2203	4300	6503	54335353	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5707G>T	18.37:g.56184373C>A	ENSP00000354991:p.Asp1903Tyr		54335353	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712053	0.89112	.	.	ENSG00000198796	ENST00000361673	T	0.07567	3.18	5.91	5.91	0.95273	MHCK/EF2 kinase (1);Protein kinase-like domain (1);	0.065306	0.64402	D	0.000017	T	0.27027	0.0662	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00054	-1.2181	10	0.72032	D	0.01	-28.8229	19.8936	0.96942	0.0:1.0:0.0:0.0	.	1903	Q86TB3	ALPK2_HUMAN	Y	1903	ENSP00000354991:D1903Y	ENSP00000354991:D1903Y	D	-	1	0	ALPK2	54335353	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	5.679000	0.68160	2.793000	0.96121	0.655000	0.94253	GAC		0.527	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56184373	C	A	56184373	3	1	61	1	0	0	0	0	1	0	0	0	545	913	32	2	825	2	ALPK2	18	56184373	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13069	56184373	21892875	10665	18650										
ALPK2	115701	broad.mit.edu	37	chr18	56204919	56204919	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtatctacagagcaaatttCttgaggcgaatatttatcaa	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56204919C>A	ENST00000361673.3	-	5	2713	c.2500G>T	c.(2500-2502)Gaa>Taa	p.E834*	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	834						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E200*(1)|p.E834*(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GAGCAAATTTCTTGAGGCGAA	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											76	75	76					18																	56204919		2203	4300	6503	54355899	SO:0001587	stop_gained	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2500G>T	18.37:g.56204919C>A	ENSP00000354991:p.Glu834*		54355899	Q6ZUX0|Q8NAT5|Q96L95	Nonsense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	39	7.862906	0.98531	.	.	ENSG00000198796	ENST00000361673	.	.	.	5.57	5.57	0.84162	.	0.889460	0.09841	N	0.748805	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.0859	15.0658	0.71992	0.0:1.0:0.0:0.0	.	.	.	.	X	834	.	ENSP00000354991:E834X	E	-	1	0	ALPK2	54355899	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	4.038000	0.57318	2.630000	0.89119	0.591000	0.81541	GAA		0.398	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56204919	C	A	56204919	4	1	61	1	0	0	0	0	0	1	0	0	545	922	32	2	4048	2	ALPK2	18	56204919	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20546	56204919	21872329	10666	18651										
ALPK2	115701	broad.mit.edu	37	chr18	56204957	56204957	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caactggtctcccaacaagaGaatctatggtatcaaaacac	6	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56204957G>T	ENST00000361673.3	-	5	2675	c.2462C>A	c.(2461-2463)tCt>tAt	p.S821Y	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	821						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S187Y(1)|p.S821Y(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCCAACAAGAGAATCTATGGT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	18											104	99	101					18																	56204957		2203	4300	6503	54355937	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2462C>A	18.37:g.56204957G>T	ENSP00000354991:p.Ser821Tyr		54355937	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	4.873	0.162338	0.09287	.	.	ENSG00000198796	ENST00000361673	T	0.46451	0.87	5.57	2.35	0.29111	.	1.534230	0.03313	N	0.190769	T	0.48822	0.1521	L	0.48642	1.525	0.09310	N	1	P;P	0.50066	0.931;0.766	P;B	0.50590	0.645;0.325	T	0.31724	-0.9933	10	0.59425	D	0.04	-0.3963	7.6593	0.28394	0.3148:0.0:0.6852:0.0	.	821;821	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	Y	821	ENSP00000354991:S821Y	ENSP00000354991:S821Y	S	-	2	0	ALPK2	54355937	0.003000	0.15002	0.008000	0.14137	0.011000	0.07611	1.314000	0.33597	0.711000	0.32018	0.591000	0.81541	TCT		0.423	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56204957	G	T	56204957	3	4	61	1	0	0	0	0	1	0	0	0	545	942	33	2	4086	2	ALPK2	18	56204957	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38	56204957	21872291	10667	18652										
ALPK2	115701	broad.mit.edu	37	chr18	56247439	56247439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttcctttaacacccaaaGgattttcagaactggacaca	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56247439G>T	ENST00000361673.3	-	4	782	c.569C>A	c.(568-570)cCt>cAt	p.P190H	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	190						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P190H(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						AACACCCAAAGGATTTTCAGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	18											169	175	173					18																	56247439		2103	4233	6336	54398419	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.569C>A	18.37:g.56247439G>T	ENSP00000354991:p.Pro190His		54398419	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890181	0.33348	.	.	ENSG00000198796	ENST00000361673	T	0.48836	0.8	5.9	1.58	0.23477	.	.	.	.	.	T	0.39517	0.1081	L	0.29908	0.895	0.09310	N	1	D	0.60575	0.988	P	0.50231	0.635	T	0.16276	-1.0408	9	0.45353	T	0.12	-0.7197	5.0122	0.14319	0.3531:0.0:0.4796:0.1673	.	190	Q86TB3	ALPK2_HUMAN	H	190	ENSP00000354991:P190H	ENSP00000354991:P190H	P	-	2	0	ALPK2	54398419	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.028000	0.13644	0.352000	0.24053	0.563000	0.77884	CCT		0.438	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56247439	G	T	56247439	3	4	61	1	0	0	0	0	1	0	0	0	545	1000	35	2	5983	2	ALPK2	18	56247439	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42482	56247439	21829809	10668	18653										
MALT1	10892	broad.mit.edu	37	chr18	56363706	56363706	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttcaatatcagtggttcaAaatgaataaagaggtaattt	8	3	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:56363706A>C	ENST00000348428.3	+	3	743	c.485A>C	c.(484-486)aAa>aCa	p.K162T	MALT1_ENST00000345724.3_Missense_Mutation_p.K162T|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	162	Ig-like C2-type 1.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)	p.K162T(1)		central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						CAGTGGTTCAAAATGAATAAA	0.338			T	BIRC3	MALT																																		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	1	Substitution - Missense(1)	large_intestine(1)	18											42	46	45					18																	56363706		2203	4300	6503	54514686	SO:0001583	missense	10892				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.485A>C	18.37:g.56363706A>C	ENSP00000319279:p.Lys162Thr		54514686	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	19.23	3.787814	0.70337	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.18810	2.19;2.19	5.34	5.34	0.76211	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.56587	0.1995	M	0.93420	3.415	0.46113	D	0.998876	D;D	0.89917	1.0;1.0	D;D	0.79108	0.985;0.992	T	0.67883	-0.5555	10	0.56958	D	0.05	.	14.6056	0.68475	1.0:0.0:0.0:0.0	.	162;162	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	T	162	ENSP00000319279:K162T;ENSP00000304161:K162T	ENSP00000304161:K162T	K	+	2	0	MALT1	54514686	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.034000	0.76511	2.147000	0.66899	0.455000	0.32223	AAA		0.338	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			C	56363706	A	C	56363706	3	2	61	1	0	0	0	0	1	0	0	0	9232	14	1	4	495	4	MALT1	18	56363706	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116267	56363706	21713542	10669	18654										
LMAN1	3998	broad.mit.edu	37	chr18	57006031	57006031	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcctgctcctcttttagaGatttcctctgttaaggaaga	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:57006031G>T	ENST00000251047.5	-	9	1827	c.1110C>A	c.(1108-1110)atC>atA	p.I370I		NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	370					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.I370I(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	CTCTTTTAGAGATTTCCTCTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	18											189	184	185					18																	57006031		2203	4300	6503	55157011	SO:0001819	synonymous_variant	3998			X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.1110C>A	18.37:g.57006031G>T			55157011	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Silent	SNP	ENST00000251047.5	37	CCDS11974.1																																																																																				0.448	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		T	57006031	G	T	57006031	2	4	61	1	0	0	0	0	0	0	0	1	8860	932	33	2		2	LMAN1	18	57006031	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	642325	57006031	21071217	10670	18655										
LMAN1	3998	broad.mit.edu	37	chr18	57022574	57022574	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgtcaaaagaatcaaaaaAtattccaacaccattccaca	2	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:57022574A>C	ENST00000251047.5	-	3	1165	c.448T>G	c.(448-450)Ttt>Gtt	p.F150V		NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	150	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.F150V(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	GAATCAAAAAATATTCCAACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	18											78	71	73					18																	57022574		2203	4300	6503	55173554	SO:0001583	missense	3998			X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.448T>G	18.37:g.57022574A>C	ENSP00000251047:p.Phe150Val		55173554	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.521592	0.85600	.	.	ENSG00000074695	ENST00000251047	T	0.64438	-0.1	5.63	5.63	0.86233	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.75606	0.3872	M	0.86573	2.825	0.80722	D	1	P;P	0.46578	0.88;0.647	P;P	0.53518	0.728;0.559	T	0.74976	-0.3480	10	0.15499	T	0.54	-15.6881	15.5314	0.75964	1.0:0.0:0.0:0.0	.	150;150	B4DVV0;P49257	.;LMAN1_HUMAN	V	150	ENSP00000251047:F150V	ENSP00000251047:F150V	F	-	1	0	LMAN1	55173554	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.691000	0.91279	2.145000	0.66743	0.533000	0.62120	TTT		0.363	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		C	57022574	A	C	57022574	3	2	61	1	0	0	0	0	1	0	0	0	8860	101	4	4	1128	4	LMAN1	18	57022574	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	16543	57022574	21054674	10671	18656										
CDH20	28316	broad.mit.edu	37	chr18	59166573	59166573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcccagtatactctaagggCtcaagccctagacaggcgga	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:59166573C>T	ENST00000262717.4	+	3	799	c.401C>T	c.(400-402)gCt>gTt	p.A134V	CDH20_ENST00000536675.2_Missense_Mutation_p.A134V|CDH20_ENST00000538374.1_Missense_Mutation_p.A134V			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	134	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A134V(2)		breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				ACTCTAAGGGCTCAAGCCCTA	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	18											52	47	49					18																	59166573		2203	4300	6503	57317553	SO:0001583	missense	28316			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.401C>T	18.37:g.59166573C>T	ENSP00000262717:p.Ala134Val		57317553	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996214	0.93167	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.48836	0.8;0.8;0.8	5.82	5.82	0.92795	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	L	0.38838	1.175	0.80722	D	1	D	0.71674	0.998	D	0.64144	0.922	T	0.61579	-0.7034	10	0.87932	D	0	.	20.0851	0.97797	0.0:1.0:0.0:0.0	.	134	Q9HBT6	CAD20_HUMAN	V	134	ENSP00000444767:A134V;ENSP00000442226:A134V;ENSP00000262717:A134V	ENSP00000262717:A134V	A	+	2	0	CDH20	57317553	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	7.487000	0.81328	2.758000	0.94735	0.650000	0.86243	GCT		0.537	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		T	59166573	C	T	59166573	3	4	61	1	0	0	0	0	1	0	0	0	3112	797	28	3	407	3	CDH20	18	59166573	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2143999	59166573	18910675	10672	18657										
CDH20	28316	broad.mit.edu	37	chr18	59217306	59217306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatagcagatagcgggcagCccgtgctgagcagcacaggc	15	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:59217306C>T	ENST00000262717.4	+	11	2142	c.1744C>T	c.(1744-1746)Ccc>Tcc	p.P582S	CDH20_ENST00000536675.2_Missense_Mutation_p.P582S|CDH20_ENST00000538374.1_Missense_Mutation_p.P582S			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	582	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P582S(1)		breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				TAGCGGGCAGCCCGTGCTGAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	18											56	46	49					18																	59217306		2203	4300	6503	57368286	SO:0001583	missense	28316			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1744C>T	18.37:g.59217306C>T	ENSP00000262717:p.Pro582Ser		57368286	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	33	5.204030	0.95033	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.56776	0.44;0.44;0.44	5.93	5.93	0.95920	Cadherin (4);Cadherin-like (1);	0.054814	0.64402	D	0.000001	T	0.81380	0.4810	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85069	0.0939	10	0.87932	D	0	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	582	Q9HBT6	CAD20_HUMAN	S	582	ENSP00000444767:P582S;ENSP00000442226:P582S;ENSP00000262717:P582S	ENSP00000262717:P582S	P	+	1	0	CDH20	57368286	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	4.917000	0.63369	2.826000	0.97356	0.655000	0.94253	CCC		0.572	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		T	59217306	C	T	59217306	3	4	61	1	0	0	0	0	1	0	0	0	3112	739	26	3	1782	3	CDH20	18	59217306	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50733	59217306	18859942	10673	18658										
PIGN	23556	broad.mit.edu	37	chr18	59824364	59824364	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatcagtgactcttacctTtggcaaacataggcaggata	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:59824364T>G	ENST00000357637.5	-	6	855	c.440A>C	c.(439-441)aAa>aCa	p.K147T	PIGN_ENST00000400334.3_Missense_Mutation_p.K147T	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	147					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.K147T(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				ACTCTTACCTTTGGCAAACAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	18											66	63	64					18																	59824364		1834	4099	5933	57975344	SO:0001583	missense	23556			AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.440A>C	18.37:g.59824364T>G	ENSP00000350263:p.Lys147Thr		57975344	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	37	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.782546	0.90282	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.28666	1.6;1.6	5.17	5.17	0.71159	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.049934	0.85682	D	0.000000	T	0.49830	0.1580	M	0.63208	1.945	0.80722	D	1	P;D	0.56035	0.945;0.974	P;P	0.62089	0.864;0.898	T	0.46091	-0.9216	9	.	.	.	-5.469	15.3002	0.73945	0.0:0.0:0.0:1.0	.	147;147	B2RCI8;O95427	.;PIGN_HUMAN	T	147	ENSP00000350263:K147T;ENSP00000383188:K147T	.	K	-	2	0	PIGN	57975344	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.881000	0.87252	2.065000	0.61736	0.459000	0.35465	AAA		0.348	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		G	59824364	T	G	59824364	3	3	61	1	0	0	0	0	1	0	0	0	11924	1841	64	4	2459	4	PIGN	18	59824364	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	607058	59824364	18252884	10674	18659										
TNFRSF11A	8792	broad.mit.edu	37	chr18	60017060	60017060	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaggaaagtacatgtcttCtaaatgcactactacctctg	6	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:60017060C>A	ENST00000586569.1	+	3	211	c.173C>A	c.(172-174)tCt>tAt	p.S58Y	TNFRSF11A_ENST00000269485.7_Missense_Mutation_p.S58Y	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	58					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)	p.S58Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				TACATGTCTTCTAAATGCACT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	18											160	154	156					18																	60017060		2203	4300	6503	58168040	SO:0001583	missense	8792			AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"Tumor necrosis factor receptor superfamily", "CD molecules"	11908	protein-coding gene	gene with protein product		603499	"tumor necrosis factor receptor superfamily, member 11a, activator of NFKB", "Paget disease of bone 2", "loss of heterozygosity, 18, chromosomal region 1"	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.173C>A	18.37:g.60017060C>A	ENSP00000465500:p.Ser58Tyr		58168040	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705333	0.68615	.	.	ENSG00000141655	ENST00000382790;ENST00000269485	D	0.92048	-2.96	5.81	4.91	0.64330	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.326738	0.32884	N	0.005526	D	0.94656	0.8277	M	0.71581	2.175	0.34849	D	0.741438	D;D	0.71674	0.998;0.998	D;D	0.64144	0.922;0.922	D	0.96176	0.9127	9	.	.	.	-17.9975	13.6017	0.62024	0.1544:0.8456:0.0:0.0	.	80;58	Q59EP9;Q9Y6Q6	.;TNR11_HUMAN	Y	80;58	ENSP00000269485:S58Y	.	S	+	2	0	TNFRSF11A	58168040	0.997000	0.39634	1.000000	0.80357	0.972000	0.66771	3.116000	0.50399	2.748000	0.94277	0.462000	0.41574	TCT		0.378	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			A	60017060	C	A	60017060	3	1	61	1	0	0	0	0	1	0	0	0	16323	913	32	2	183	2	TNFRSF11A	18	60017060	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192696	60017060	18060188	10675	18660										
ZCCHC2	54877	broad.mit.edu	37	chr18	60242545	60242545	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctttttttctgcctcaGactccatatgcaaatggact	5	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:60242545G>T	ENST00000269499.5	+	13	3649	c.3231G>T	c.(3229-3231)caG>caT	p.Q1077H	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.Q756H	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1077						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.Q1077H(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TTCTGCCTCAGACTCCATATG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	18											63	63	63					18																	60242545		1939	4161	6100	58393525	SO:0001583	missense	54877			AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.3231G>T	18.37:g.60242545G>T	ENSP00000269499:p.Gln1077His		58393525	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	ENST00000269499.5	37	CCDS45880.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860999	0.32884	.	.	ENSG00000141664	ENST00000269499	T	0.22134	1.97	5.56	5.56	0.83823	.	0.246151	0.35677	N	0.003047	T	0.20659	0.0497	N	0.20530	0.585	0.38468	D	0.947394	D	0.57899	0.981	P	0.51999	0.687	T	0.01386	-1.1368	10	0.06099	T	0.92	-6.3853	18.0709	0.89405	0.0:0.0:1.0:0.0	.	1077	Q9C0B9	ZCHC2_HUMAN	H	1077	ENSP00000269499:Q1077H	ENSP00000269499:Q1077H	Q	+	3	2	ZCCHC2	58393525	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.059000	0.49947	2.774000	0.95407	0.650000	0.86243	CAG		0.473	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		T	60242545	G	T	60242545	3	4	61	1	0	0	0	0	1	0	0	0	17626	933	33	2	3281	2	ZCCHC2	18	60242545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	225485	60242545	17834703	10676	18661										
PHLPP1	23239	broad.mit.edu	37	chr18	60642763	60642763	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgccaaacagttctctgtCgaaatggaaagccgctgcct	10	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:60642763C>T	ENST00000262719.5	+	16	4123	c.3889C>T	c.(3889-3891)Cga>Tga	p.R1297*	PHLPP1_ENST00000400316.4_Nonsense_Mutation_p.R785*			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1297	PP2C-like.				apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.R784*(1)		endometrium(2)|kidney(2)|lung(13)	17						AGTTCTCTGTCGAAATGGAAA	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											158	152	154					18																	60642763		2000	4179	6179	58793743	SO:0001587	stop_gained	23239			AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3889C>T	18.37:g.60642763C>T	ENSP00000262719:p.Arg1297*		58793743	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Nonsense_Mutation	SNP	ENST00000262719.5	37	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	C	53	20.198635	0.99928	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	.	.	.	4.91	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.675	12.4072	0.55447	0.3056:0.6944:0.0:0.0	.	.	.	.	X	785;1297	.	ENSP00000262719:R1297X	R	+	1	2	PHLPP1	58793743	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.744000	0.55112	1.245000	0.43885	0.555000	0.69702	CGA		0.493	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		T	60642763	C	T	60642763	4	4	61	1	0	0	0	0	0	1	0	0	11885	876	31	1	3951	1	PHLPP1	18	60642763	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	400218	60642763	17434485	10677	18662										
KDSR	2531	broad.mit.edu	37	chr18	61027001	61027001	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatagagtgcatttcaatttCtttctttgcctgcagcagct	7	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61027001C>A	ENST00000406396.3	-	3	614	c.223G>T	c.(223-225)Gaa>Taa	p.E75*	KDSR_ENST00000326575.5_Nonsense_Mutation_p.E75*	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	75					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)	p.E75*(1)		endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						ATTTCAATTTCTTTCTTTGCC	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											131	120	123					18																	61027001		2203	4299	6502	59177981	SO:0001587	stop_gained	2531				CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	4021	protein-coding gene	gene with protein product	"3-dehydrosphinganine reductase", "short chain dehydrogenase/reductase family 35C, member 1"	136440	"follicular lymphoma variant translocation 1"	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.223G>T	18.37:g.61027001C>A	ENSP00000385083:p.Glu75*		59177981	B2R5Y1|B4DMX0	Nonsense_Mutation	SNP	ENST00000406396.3	37	CCDS11982.1	.	.	.	.	.	.	.	.	.	.	C	41	9.063198	0.99053	.	.	ENSG00000119537	ENST00000406396;ENST00000326575	.	.	.	5.41	5.41	0.78517	.	0.048215	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	17.3697	0.87373	0.0:1.0:0.0:0.0	.	.	.	.	X	75	.	ENSP00000312939:E75X	E	-	1	0	KDSR	59177981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.157000	0.77461	2.534000	0.85438	0.591000	0.81541	GAA		0.358	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2			A	61027001	C	A	61027001	4	1	61	1	0	0	0	0	0	1	0	0	8161	922	32	2	807	2	KDSR	18	61027001	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	384238	61027001	17050247	10678	18663										
VPS4B	9525	broad.mit.edu	37	chr18	61060766	61060766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagatggttaggatcagctCgggaaggtccgcgaacctga	14	9	1	2	rs147130607	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61060766C>T	ENST00000238497.5	-	10	1312	c.1109G>A	c.(1108-1110)cGa>cAa	p.R370Q		NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	370					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)	p.R370Q(1)		breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						AGGATCAGCTCGGGAAGGTCC	0.398													C|||	4	0.000798722	0	0	5008	,	,		14318	0.004		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											94	91	92					18																	61060766		2203	4300	6503	59211746	SO:0001583	missense	9525			AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.1109G>A	18.37:g.61060766C>T	ENSP00000238497:p.Arg370Gln		59211746	Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	37	CCDS11983.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	10.75	1.438966	0.25900	.	.	ENSG00000119541	ENST00000238497	D	0.93488	-3.23	5.92	4.1	0.47936	.	0.483440	0.22378	N	0.060853	D	0.86447	0.5935	L	0.58101	1.795	0.21675	N	0.999595	P	0.37914	0.611	B	0.29267	0.1	T	0.74497	-0.3646	10	0.12103	T	0.63	-9.0051	3.6896	0.08340	0.173:0.4861:0.2555:0.0854	.	370	O75351	VPS4B_HUMAN	Q	370	ENSP00000238497:R370Q	ENSP00000238497:R370Q	R	-	2	0	VPS4B	59211746	0.001000	0.12720	0.585000	0.28666	0.972000	0.66771	0.718000	0.25866	1.512000	0.48834	0.543000	0.68304	CGA		0.398	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		T	61060766	C	T	61060766	3	4	61	1	0	0	0	0	1	0	0	0	17253	884	31	1	233	1	VPS4B	18	61060766	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33765	61060766	17016482	10679	18664										
SERPINB12	89777	broad.mit.edu	37	chr18	61228356	61228356	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcaattttaccacacgacGattgaaagtgttgatttcca	6	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61228356G>A	ENST00000269491.1	+	4	423	c.423G>A	c.(421-423)acG>acA	p.T141T	SERPINB12_ENST00000382768.1_Silent_p.T161T	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	141					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T141T(1)		kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						ACCACACGACGATTGAAAGTG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	18											116	112	113					18																	61228356		2203	4300	6503	59379336	SO:0001819	synonymous_variant	89777			AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"Serine (or cysteine) peptidase inhibitors"	14220	protein-coding gene	gene with protein product		615662	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.423G>A	18.37:g.61228356G>A			59379336	Q3SYB4	Silent	SNP	ENST00000269491.1	37	CCDS11984.1																																																																																				0.383	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		A	61228356	G	A	61228356	2	1	61	1	0	0	0	0	0	0	0	1	14136	1045	37	1		1	SERPINB12	18	61228356	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167590	61228356	16848892	10680	18665										
SERPINB13	5275	broad.mit.edu	37	chr18	61260167	61260167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgcagccgatgaaagtcGaaagaagattaattcctggg	11	6	0	3	rs187247060		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61260167G>A	ENST00000344731.5	+	5	536	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	SERPINB13_ENST00000269489.5_Missense_Mutation_p.R145Q	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	145					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R145L(1)|p.R145Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						GATGAAAGTCGAAAGAAGATT	0.328													G|||	1	0.000199681	0	0	5008	,	,		20281	0.001		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	18											105	115	111					18																	61260167		2203	4300	6503	59411147	SO:0001583	missense	5275			AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.434G>A	18.37:g.61260167G>A	ENSP00000341584:p.Arg145Gln		59411147	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	37	CCDS11985.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	22.1	4.242915	0.79912	.	.	ENSG00000197641	ENST00000269489;ENST00000344731	D;D	0.85629	-2.01;-2.01	5.57	4.69	0.59074	Serpin domain (3);	0.153174	0.30168	N	0.010242	D	0.90783	0.7106	M	0.65498	2.005	0.50813	D	0.99989	D;D	0.89917	0.995;1.0	P;D	0.87578	0.844;0.998	D	0.90428	0.4422	9	.	.	.	.	14.038	0.64658	0.0731:0.0:0.9269:0.0	.	154;145	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	Q	145	ENSP00000269489:R145Q;ENSP00000341584:R145Q	.	R	+	2	0	SERPINB13	59411147	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.891000	0.75639	1.485000	0.48380	0.555000	0.69702	CGA		0.328	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		A	61260167	G	A	61260167	3	1	61	1	0	0	0	0	1	0	0	0	14137	1058	37	1	448	1	SERPINB13	18	61260167	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31811	61260167	16817081	10681	18666										
SERPINB4	6318	broad.mit.edu	37	chr18	61305069	61305069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgaaggagatgataattCgactactactacagcggtgg	12	6	0	3	rs386804122		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61305069C>T	ENST00000341074.5	-	8	1172	c.1057G>A	c.(1057-1059)Gaa>Aaa	p.E353K	SERPINB4_ENST00000356424.6_Missense_Mutation_p.E301K	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	353				E -> K (in Ref. 4; BAF84901). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E353K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GATGATAATTCGACTACTACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	18											126	120	122					18																	61305069		2203	4300	6503	59456049	SO:0001583	missense	6318			X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"Serine (or cysteine) peptidase inhibitors"	10570	protein-coding gene	gene with protein product	"squamous cell carcinoma antigen 2"	600518	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.1057G>A	18.37:g.61305069C>T	ENSP00000343445:p.Glu353Lys		59456049	A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	CCDS11986.1	.	.	.	.	.	.	.	.	.	.	C	0.035	-1.311849	0.01342	.	.	ENSG00000206073	ENST00000341074;ENST00000356424	D;D	0.81908	-1.55;-1.55	2.27	-4.54	0.03452	Serpin domain (3);	7.091560	0.00166	N	0.000007	T	0.62196	0.2408	N	0.05351	-0.065	0.09310	N	1	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.11329	0.006;0.006;0.006	T	0.55341	-0.8156	10	0.13108	T	0.6	.	4.2253	0.10577	0.0:0.4447:0.2134:0.342	.	353;353;332	Q5K684;P48594;Q9BYF7	.;SPB4_HUMAN;.	K	353;301	ENSP00000343445:E353K;ENSP00000348795:E301K	ENSP00000343445:E353K	E	-	1	0	SERPINB4	59456049	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.859000	0.00094	-0.946000	0.03677	-0.320000	0.08662	GAA		0.463	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		T	61305069	C	T	61305069	3	4	61	1	0	0	0	0	1	0	0	0	14140	893	31	1	119	1	SERPINB4	18	61305069	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44902	61305069	16772179	10682	18667										
SERPINB11	89778	broad.mit.edu	37	chr18	61387255	61387255	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttatacaaggaaaagtcGcaaatctctttggaaagagc	8	6	1	1	rs369601900		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61387255G>A	ENST00000382749.5	+	0	729				SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A162T(1)		breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				AGGAAAAGTCGCAAATCTCTT	0.323																																					Ovarian(27;496 784 5942 8975 23930)											1	Substitution - Missense(1)	large_intestine(1)	18						G	THR/ALA	1,3591		0,1,1795	68	68	68		484	2.8	0	18		68	0,8124		0,0,4062	no	missense	SERPINB11	NM_080475.2	58	0,1,5857	AA,AG,GG		0.0,0.0278,0.0085	benign	162/393	61387255	1,11715	1796	4062	5858	59538235			89778					18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"Serine (or cysteine) peptidase inhibitors"	14221	protein-coding gene	gene with protein product		615682	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11", "serpin peptidase inhibitor, clade B (ovalbumin), member 11"			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61387255G>A			59538235	A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Missense_Mutation	SNP	ENST00000382749.5	37		.	.	.	.	.	.	.	.	.	.	g	10.79	1.449748	0.26074	2.78E-4	0.0	ENSG00000206072	ENST00000544088	D	0.84223	-1.82	5.4	2.84	0.33178	Serpin domain (3);	.	.	.	.	T	0.52709	0.1751	N	0.00179	-1.91	0.46416	D	0.999038	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49570	-0.8926	9	0.33940	T	0.23	.	7.4124	0.27025	0.7805:0.1425:0.0771:0.0	.	162;162	F5GYW9;Q96P15	.;SPB11_HUMAN	T	162	ENSP00000441497:A162T	ENSP00000421854:A162T	A	+	1	0	SERPINB11	59538235	0.001000	0.12720	0.045000	0.18777	0.436000	0.31835	0.587000	0.23909	0.981000	0.38548	-0.404000	0.06349	GCA		0.323	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		A	61387255	G	A	61387255	1	1	61	0	1	0	0	0	0	0	0	0	14135	1087	38	1		1	SERPINB11	18	61387255	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82186	61387255	16689993	10683	18668										
SERPINB11	89778	broad.mit.edu	37	chr18	61387357	61387357	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaataaatttcaagtaagaGagacagttaaaagtcctttt	6	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61387357G>T	ENST00000382749.5	+	0	831				SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E196*(1)		breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				TCAAGTAAGAGAGACAGTTAA	0.333																																					Ovarian(27;496 784 5942 8975 23930)											1	Substitution - Nonsense(1)	large_intestine(1)	18											58	59	59					18																	61387357		1816	4084	5900	59538337			89778					18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"Serine (or cysteine) peptidase inhibitors"	14221	protein-coding gene	gene with protein product		615682	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11", "serpin peptidase inhibitor, clade B (ovalbumin), member 11"			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61387357G>T			59538337	A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Nonsense_Mutation	SNP	ENST00000382749.5	37		.	.	.	.	.	.	.	.	.	.	G	18.16	3.561613	0.65538	.	.	ENSG00000206072	ENST00000544088;ENST00000536691	.	.	.	5.62	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	6.6077	0.22734	0.0747:0.3439:0.4762:0.1052	.	.	.	.	X	196;21	.	ENSP00000421854:E196X	E	+	1	0	SERPINB11	59538337	0.000000	0.05858	0.961000	0.40146	0.410000	0.31052	-0.837000	0.04377	0.813000	0.34350	0.655000	0.94253	GAG		0.333	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		T	61387357	G	T	61387357	1	4	61	0	1	0	0	0	0	0	0	0	14135	943	33	2		2	SERPINB11	18	61387357	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102	61387357	16689891	10684	18669										
SERPINB11	89778	broad.mit.edu	37	chr18	61390517	61390517	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagccactggggacagcatcGctgtaaaaagcctaccaatg	10	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61390517G>A	ENST00000382749.5	+	0	1308				SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000536691.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A355T(1)		breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				GGACAGCATCGCTGTAAAAAG	0.498																																					Ovarian(27;496 784 5942 8975 23930)											1	Substitution - Missense(1)	large_intestine(1)	18											90	87	88					18																	61390517		2199	4298	6497	59541497			89778					18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"Serine (or cysteine) peptidase inhibitors"	14221	protein-coding gene	gene with protein product		615682	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11", "serpin peptidase inhibitor, clade B (ovalbumin), member 11"			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61390517G>A			59541497	A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Missense_Mutation	SNP	ENST00000382749.5	37		.	.	.	.	.	.	.	.	.	.	G	1.906	-0.451834	0.04572	.	.	ENSG00000206072	ENST00000544088;ENST00000538847;ENST00000536691	D;T;D	0.82255	-1.59;2.82;-1.59	5.27	0.162	0.14981	Serpin domain (3);	1.059330	0.07414	N	0.892904	T	0.57621	0.2066	N	0.04043	-0.29	0.09310	N	1	B;B;B;B	0.25563	0.008;0.032;0.129;0.009	B;B;B;B	0.15484	0.004;0.005;0.012;0.013	T	0.48293	-0.9048	10	0.02654	T	1	.	6.3904	0.21583	0.1356:0.0:0.4857:0.3786	.	180;153;268;355	F5GWT8;F5GY69;Q96P15-2;Q96P15	.;.;.;SPB11_HUMAN	T	355;153;180	ENSP00000441497:A355T;ENSP00000440795:A153T;ENSP00000441708:A180T	ENSP00000421854:A355T	A	+	1	0	SERPINB11	59541497	0.015000	0.18098	0.000000	0.03702	0.501000	0.33797	1.220000	0.32491	-0.201000	0.10284	-0.169000	0.13324	GCT		0.498	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		A	61390517	G	A	61390517	1	1	61	0	1	0	0	0	0	0	0	0	14135	1087	38	1		1	SERPINB11	18	61390517	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3160	61390517	16686731	10685	18670										
SERPINB2	5055	broad.mit.edu	37	chr18	61569701	61569701	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaacattggatacatagaaGacctaaaggctcagattcta	7	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61569701G>T	ENST00000299502.4	+	7	822	c.742G>T	c.(742-744)Gac>Tac	p.D248Y	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Missense_Mutation_p.D248Y	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	248					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D248Y(1)		NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ATACATAGAAGACCTAAAGGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	18											134	119	124					18																	61569701		2203	4300	6503	59720681	SO:0001583	missense	5055			Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.742G>T	18.37:g.61569701G>T	ENSP00000299502:p.Asp248Tyr		59720681	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.21|11.21	1.570944|1.570944	0.28003|0.28003	.|.	.|.	ENSG00000197632|ENSG00000242550	ENST00000299502;ENST00000457692|ENST00000397996;ENST00000418725	T;T|.	0.13089|.	2.62;2.62|.	5.4|5.4	2.62|2.62	0.31277|0.31277	Serpin domain (3);|.	0.319686|.	0.37136|.	N|.	0.002236|.	T|T	0.76176|0.76176	0.3951|0.3951	M|M	0.88842|0.88842	2.985|2.985	0.80722|0.80722	D|D	1|1	B;D|.	0.54772|.	0.331;0.968|.	B;P|.	0.53450|.	0.394;0.726|.	T|T	0.75059|0.75059	-0.3451|-0.3451	10|5	0.72032|.	D|.	0.01|.	.|.	10.0236|10.0236	0.42057|0.42057	0.1916:0.1037:0.7048:0.0|0.1916:0.1037:0.7048:0.0	.|.	248;248|.	B2R7Y0;P05120|.	.;PAI2_HUMAN|.	Y|I	248|124	ENSP00000299502:D248Y;ENSP00000401645:D248Y|.	ENSP00000299502:D248Y|.	D|R	+|+	1|2	0|0	SERPINB2|SERPINB10	59720681|59720681	0.018000|0.018000	0.18449|0.18449	0.104000|0.104000	0.21259|0.21259	0.005000|0.005000	0.04900|0.04900	0.852000|0.852000	0.27764|0.27764	0.080000|0.080000	0.16959|0.16959	-1.847000|-1.847000	0.00572|0.00572	GAC|AGA		0.408	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		T	61569701	G	T	61569701	3	4	61	1	0	0	0	0	1	0	0	0	14138	942	33	2	764	2	SERPINB2	18	61569701	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	179184	61569701	16507547	10686	18671										
SERPINB10	5273	broad.mit.edu	37	chr18	61585303	61585303	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacttaaaacagccaatgcGatatatggagagaaaacgta	8	6	0	1	rs199625177		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61585303G>A	ENST00000238508.3	+	4	398	c.339G>A	c.(337-339)gcG>gcA	p.A113A		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	113					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A113A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CAGCCAATGCGATATATGGAG	0.363													g|||	1	0.000199681	0	0	5008	,	,		21391	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	18						A		0,4406		0,0,2203	102	93	96		339	3.1	0	18		96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SERPINB10	NM_005024.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		113/398	61585303	1,13005	2203	4300	6503	59736283	SO:0001819	synonymous_variant	5273			U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.339G>A	18.37:g.61585303G>A			59736283	Q4VAX4|Q4VAX7	Silent	SNP	ENST00000238508.3	37	CCDS11990.1																																																																																				0.363	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		A	61585303	G	A	61585303	2	1	61	1	0	0	0	0	0	0	0	1	14134	1045	37	1		1	SERPINB10	18	61585303	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15602	61585303	16491945	10687	18672										
SERPINB10	5273	broad.mit.edu	37	chr18	61600292	61600292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttttagactacaagcaAaccagtgcaaatgatgttta	6	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61600292A>G	ENST00000238508.3	+	7	703	c.644A>G	c.(643-645)aAa>aGa	p.K215R		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	215					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.K215R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				ACTACAAGCAAACCAGTGCAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	18											74	81	78					18																	61600292		2203	4300	6503	59751272	SO:0001583	missense	5273			U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.644A>G	18.37:g.61600292A>G	ENSP00000238508:p.Lys215Arg		59751272	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500052	0.64298	.	.	ENSG00000242550	ENST00000238508	D	0.83075	-1.68	5.95	5.95	0.96441	Serpin domain (3);	0.096594	0.64402	D	0.000001	D	0.86619	0.5976	M	0.75085	2.285	0.47698	D	0.999496	D	0.52996	0.957	P	0.53490	0.727	D	0.85494	0.1187	10	0.32370	T	0.25	.	11.4705	0.50266	0.9286:0.0:0.0714:0.0	.	215	P48595	SPB10_HUMAN	R	215	ENSP00000238508:K215R	ENSP00000238508:K215R	K	+	2	0	SERPINB10	59751272	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	1.997000	0.40786	2.282000	0.76494	0.533000	0.62120	AAA		0.363	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		G	61600292	A	G	61600292	3	3	61	1	0	0	0	0	1	0	0	0	14134	14	1	4	666	4	SERPINB10	18	61600292	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	14989	61600292	16476956	10688	18673										
SERPINB8	5271	broad.mit.edu	37	chr18	61650954	61650954	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctctttaaaaccaacgAggtagggaaagatttttcag	9	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:61650954A>T	ENST00000397985.2	+	5	822	c.566A>T	c.(565-567)gAg>gTg	p.E189V	SERPINB8_ENST00000353706.2_Splice_Site_p.E189V|SERPINB8_ENST00000542677.1_Splice_Site_p.E7V|SERPINB8_ENST00000397988.3_Splice_Site_p.E189V	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	189					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E189V(1)		breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				AAAACCAACGAGGTAGGGAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											98	96	96					18																	61650954		2203	4300	6503	59801934	SO:0001630	splice_region_variant	5271			L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.567+1A>T	18.37:g.61650954A>T			59801934	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.10|17.10	3.302601|3.302601	0.60195|0.60195	.|.	.|.	ENSG00000166401|ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677;ENST00000397988|ENST00000295211	D;D;D;D|.	0.84800|.	-1.77;-1.77;-1.9;-1.77|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serpin domain (3);|.	0.194339|.	0.53938|.	D|.	0.000053|.	T|T	0.57227|0.57227	0.2039|0.2039	L|L	0.35593|0.35593	1.075|1.075	0.80722|0.80722	D|D	1|1	P;P|.	0.34699|.	0.464;0.464|.	P;P|.	0.45138|.	0.471;0.471|.	T|T	0.53563|0.53563	-0.8421|-0.8421	10|5	0.87932|.	D|.	0|.	.|.	15.2098|15.2098	0.73214|0.73214	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	189;189|.	P50452;Q8N178|.	SPB8_HUMAN;.|.	V|W	189;189;7;189|131	ENSP00000381072:E189V;ENSP00000331368:E189V;ENSP00000438328:E7V;ENSP00000381075:E189V|.	ENSP00000331368:E189V|.	E|R	+|+	2|1	0|2	SERPINB8|SERPINB8	59801934|59801934	1.000000|1.000000	0.71417|0.71417	0.944000|0.944000	0.38274|0.38274	0.072000|0.072000	0.16883|0.16883	7.229000|7.229000	0.78088|0.78088	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAG|AGG		0.338	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	Missense_Mutation	T	61650954	A	T	61650954	5	4	61	1	0	0	0	0	0	0	1	0	14144	318	11	5	580	5	SERPINB8	18	61650954	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	50662	61650954	16426294	10689	18674										
CDH7	1005	broad.mit.edu	37	chr18	63547837	63547837	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccggagggatgtgactccaGaaattcaattcctgagtcga	11	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:63547837G>T	ENST00000397968.2	+	12	2491	c.2065G>T	c.(2065-2067)Gaa>Taa	p.E689*	CDH7_ENST00000323011.3_Nonsense_Mutation_p.E689*	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	689					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E689*(1)		NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				TGTGACTCCAGAAATTCAATT	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											82	86	85					18																	63547837		2203	4300	6503	61698817	SO:0001587	stop_gained	1005			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.2065G>T	18.37:g.63547837G>T	ENSP00000381058:p.Glu689*		61698817	Q9H157	Nonsense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	40	8.531593	0.98852	.	.	ENSG00000081138	ENST00000323011;ENST00000397966;ENST00000397968	.	.	.	5.37	5.37	0.77165	.	0.055638	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.1123	0.93321	0.0:0.0:1.0:0.0	.	.	.	.	X	689	.	ENSP00000319166:E689X	E	+	1	0	CDH7	61698817	1.000000	0.71417	0.659000	0.29680	0.769000	0.43574	7.540000	0.82074	2.515000	0.84797	0.655000	0.94253	GAA		0.483	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63547837	G	T	63547837	4	4	61	1	0	0	0	0	0	1	0	0	3121	943	33	2	2107	2	CDH7	18	63547837	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1896883	63547837	14529411	10690	18675										
CDH19	28513	broad.mit.edu	37	chr18	64197181	64197181	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgcacatacagtgggatCgaagagatctgttctatatt	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:64197181C>T	ENST00000540086.1	-	9	1605	c.1359G>A	c.(1357-1359)tcG>tcA	p.S453S	CDH19_ENST00000262150.2_Silent_p.S453S	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	561	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S453S(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				ACAGTGGGATCGAAGAGATCT	0.313																																																2	Substitution - coding silent(2)	large_intestine(2)	18											107	103	104					18																	64197181		2203	4300	6503	62348161	SO:0001819	synonymous_variant	28513			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.1359G>A	18.37:g.64197181C>T			62348161	O15098	Silent	SNP	ENST00000540086.1	37	CCDS59325.1																																																																																				0.313	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		T	64197181	C	T	64197181	2	4	61	1	0	0	0	0	0	0	0	1	3110	871	31	1		1	CDH19	18	64197181	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	649344	64197181	13880067	10691	18676										
DSEL	92126	broad.mit.edu	37	chr18	65179453	65179453	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatccatcgcattagttttCtaaaagaaaggtaaaaacgc	6	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:65179453C>A	ENST00000310045.7	-	2	3896	c.2423G>T	c.(2422-2424)aGa>aTa	p.R808I	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	798					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.R808I(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CATTAGTTTTCTAAAAGAAAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	18											52	53	53					18																	65179453		2203	4300	6503	63330433	SO:0001583	missense	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2423G>T	18.37:g.65179453C>A	ENSP00000310565:p.Arg808Ile		63330433	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867818	0.32977	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.18960	2.18	4.98	4.98	0.66077	.	0.181085	0.44483	U	0.000450	T	0.15912	0.0383	N	0.22421	0.69	0.47009	D	0.999286	B	0.33073	0.396	B	0.25884	0.064	T	0.05354	-1.0890	10	0.62326	D	0.03	.	17.8508	0.88747	0.0:1.0:0.0:0.0	.	798	Q8IZU8	DSEL_HUMAN	I	808;798	ENSP00000310565:R808I	ENSP00000310565:R808I	R	-	2	0	DSEL	63330433	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	2.607000	0.46300	2.309000	0.77851	0.455000	0.32223	AGA		0.338	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65179453	C	A	65179453	3	1	61	1	0	0	0	0	1	0	0	0	4786	913	32	2	1249	2	DSEL	18	65179453	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	982272	65179453	12897795	10692	18677										
DSEL	92126	broad.mit.edu	37	chr18	65181248	65181248	+	Frame_Shift_Del	DEL	T	T	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctcagtaataacccataTtttttccaggtatttttgtc							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:65181248delT	ENST00000310045.7	-	2	2101	c.628delA	c.(628-630)atafs	p.I210fs	CTD-2541J13.2_ENST00000581951.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	200					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.I210fs*30(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				ATAACCCATATTTTTTCCAGG	0.383																																																1	Deletion - Frameshift(1)	large_intestine(1)	18											64	63	63					18																	65181248		2203	4300	6503	63332228	SO:0001589	frameshift_variant	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.628delA	18.37:g.65181248delT	ENSP00000310565:p.Ile210fs		63332228	Q17RH1|Q6P5Z3	Frame_Shift_Del	DEL	ENST00000310045.7	37	CCDS11995.1																																																																																				0.383	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		-	65181248	T	-	65181248	7	5	61	1	0	1	0	1	0	0	0	0	4786	1493	52	0	3044	0	DSEL	18	65181248	Frame_Shift_Del	DEL	T	TCGA-AG-A002-01A-01W-A00K-09	1795	65181248	12896000	10693	18678										
TMX3	54495	broad.mit.edu	37	chr18	66378626	66378626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagccaaatgtcatcatttCgattttctttaaacctaaaa	3	9	3	0	rs552445199		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:66378626C>T	ENST00000299608.2	-	3	432	c.116G>A	c.(115-117)cGa>cAa	p.R39Q	TMX3_ENST00000443099.2_Missense_Mutation_p.R39Q|TMX3_ENST00000562706.1_Missense_Mutation_p.R39Q	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	39	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.R39Q(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						GTCATCATTTCGATTTTCTTT	0.289													C|||	1	0.000199681	0	0.0014	5008	,	,		17340	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18											88	95	93					18																	66378626		2202	4289	6491	64529606	SO:0001583	missense	54495			BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.116G>A	18.37:g.66378626C>T	ENSP00000299608:p.Arg39Gln		64529606	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	37	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524252	0.85600	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.03242	4.0;4.0;4.0	5.36	5.36	0.76844	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.08088	0.0202	N	0.16233	0.39	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.72338	0.962;0.875;0.977	T	0.56896	-0.7903	10	0.17832	T	0.49	.	16.5775	0.84705	0.0:1.0:0.0:0.0	.	39;39;39	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	Q	39	ENSP00000299608:R39Q;ENSP00000444954:R39Q;ENSP00000402605:R39Q	ENSP00000299608:R39Q	R	-	2	0	TMX3	64529606	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.291000	0.72719	2.525000	0.85131	0.650000	0.86243	CGA		0.289	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		T	66378626	C	T	66378626	3	4	61	1	0	0	0	0	1	0	0	0	16307	884	31	1	1304	1	TMX3	18	66378626	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1197378	66378626	11698622	10694	18679										
DOK6	220164	broad.mit.edu	37	chr18	67365722	67365722	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatcactcatgaaaatatCtatctctgggatatccacaa	5	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67365722C>A	ENST00000382713.5	+	5	682	c.492C>A	c.(490-492)atC>atA	p.I164I	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	164	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.							p.I164I(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				ATGAAAATATCTATCTCTGGG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	18											121	101	108					18																	67365722		2203	4300	6503	65516702	SO:0001819	synonymous_variant	220164			AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.492C>A	18.37:g.67365722C>A			65516702	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Silent	SNP	ENST00000382713.5	37	CCDS32841.1																																																																																				0.448	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		A	67365722	C	A	67365722	2	1	61	1	0	0	0	0	0	0	0	1	4712	903	32	2		2	DOK6	18	67365722	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	987096	67365722	10711526	10695	18680										
DOK6	220164	broad.mit.edu	37	chr18	67365805	67365805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatacggtcgggactcaaCgtggttcacgtttgagtcag	14	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67365805C>T	ENST00000382713.5	+	5	765	c.575C>T	c.(574-576)aCg>aTg	p.T192M	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	192	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.							p.T192M(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				CGGGACTCAACGTGGTTCACG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	18											76	65	69					18																	67365805		2203	4300	6503	65516785	SO:0001583	missense	220164			AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.575C>T	18.37:g.67365805C>T	ENSP00000372160:p.Thr192Met		65516785	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	37	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900015	0.33535	.	.	ENSG00000206052	ENST00000382713	D	0.82984	-1.67	5.72	5.72	0.89469	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.85682	D	0.000000	D	0.87928	0.6301	L	0.42245	1.32	0.80722	D	1	D	0.89917	1.0	D	0.69142	0.962	D	0.86393	0.1737	10	0.39692	T	0.17	.	18.8571	0.92257	0.0:1.0:0.0:0.0	.	192	Q6PKX4	DOK6_HUMAN	M	192	ENSP00000372160:T192M	ENSP00000372160:T192M	T	+	2	0	DOK6	65516785	1.000000	0.71417	0.110000	0.21437	0.356000	0.29392	7.706000	0.84615	2.709000	0.92574	0.591000	0.81541	ACG		0.468	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		T	67365805	C	T	67365805	3	4	61	1	0	0	0	0	1	0	0	0	4712	536	19	1	593	1	DOK6	18	67365805	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83	67365805	10711443	10696	18681										
CD226	10666	broad.mit.edu	37	chr18	67562970	67562970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatctcatcacgaaggtttCgttttctcctgcgctggcct	8	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67562970C>T	ENST00000280200.4	-	4	962	c.694G>A	c.(694-696)Gaa>Aaa	p.E232K	CD226_ENST00000582621.1_Missense_Mutation_p.E232K|CD226_ENST00000581982.1_Missense_Mutation_p.E77K|CD226_ENST00000577287.1_Missense_Mutation_p.E77K	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	232	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)	p.E232K(2)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				ACGAAGGTTTCGTTTTCTCCT	0.562																																					NSCLC(184;838 2130 8673 21498 50749)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	18											140	141	141					18																	67562970		2203	4300	6503	65713950	SO:0001583	missense	10666			U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	16961	protein-coding gene	gene with protein product		605397	"CD226 antigen"			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.694G>A	18.37:g.67562970C>T	ENSP00000280200:p.Glu232Lys		65713950	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041596	0.35989	.	.	ENSG00000150637	ENST00000280200	T	0.11712	2.75	4.82	3.0	0.34707	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.865498	0.10488	N	0.668752	T	0.09949	0.0244	L	0.42245	1.32	0.09310	N	1	P	0.38565	0.637	B	0.39339	0.297	T	0.29088	-1.0023	10	0.18276	T	0.48	.	6.5803	0.22589	0.0:0.7811:0.0:0.2189	.	232	Q15762	CD226_HUMAN	K	232	ENSP00000280200:E232K	ENSP00000280200:E232K	E	-	1	0	CD226	65713950	0.003000	0.15002	0.003000	0.11579	0.008000	0.06430	0.434000	0.21494	0.722000	0.32252	0.650000	0.86243	GAA		0.562	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566		T	67562970	C	T	67562970	3	4	61	1	0	0	0	0	1	0	0	0	2992	893	31	1	332	1	CD226	18	67562970	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	197165	67562970	10514278	10697	18682										
RTTN	25914	broad.mit.edu	37	chr18	67781784	67781784	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggatatcatctgtttcttCtcgtgcctgtgactctgtca	8	12	6	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67781784C>A	ENST00000255674.6	-	27	3866	c.3580G>T	c.(3580-3582)Gaa>Taa	p.E1194*	RTTN_ENST00000437017.1_Nonsense_Mutation_p.E1194*|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1194					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.E1194*(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				TCTGTTTCTTCTCGTGCCTGT	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											113	106	108					18																	67781784		1867	4113	5980	65932764	SO:0001587	stop_gained	25914			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.3580G>T	18.37:g.67781784C>A	ENSP00000255674:p.Glu1194*		65932764	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Nonsense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	45	11.600150	0.99581	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	.	.	.	5.66	5.66	0.87406	.	0.279309	0.35525	N	0.003157	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	13.0165	0.58759	0.0:0.9266:0.0:0.0734	.	.	.	.	X	1194	.	ENSP00000255674:E1194X	E	-	1	0	RTTN	65932764	0.502000	0.26107	0.117000	0.21633	0.929000	0.56500	2.152000	0.42272	2.662000	0.90505	0.557000	0.71058	GAA		0.368	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		A	67781784	C	A	67781784	4	1	61	1	0	0	0	0	0	1	0	0	13774	922	32	2	3192	2	RTTN	18	67781784	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	218814	67781784	10295464	10698	18683										
RTTN	25914	broad.mit.edu	37	chr18	67788809	67788809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatgtctaagaagtaattCgagaatccagtttagaagtt	8	5	1	3	rs189160799	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67788809C>T	ENST00000255674.6	-	26	3797	c.3511G>A	c.(3511-3513)Gaa>Aaa	p.E1171K	RTTN_ENST00000437017.1_Missense_Mutation_p.E1171K|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1171					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.E1171K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				AGAAGTAATTCGAGAATCCAG	0.259													C|||	7	0.00139776	0.0015	0	5008	,	,		16678	0		0	False		,,,				2504	0.0051															1	Substitution - Missense(1)	large_intestine(1)	18											58	59	59					18																	67788809		1790	4059	5849	65939789	SO:0001583	missense	25914			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.3511G>A	18.37:g.67788809C>T	ENSP00000255674:p.Glu1171Lys		65939789	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.71	2.913982	0.52546	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.67698	-0.28;-0.28	6.17	6.17	0.99709	.	0.164624	0.51477	D	0.000089	T	0.58119	0.2100	L	0.52364	1.645	0.80722	D	1	P	0.38677	0.642	B	0.29267	0.1	T	0.60964	-0.7158	10	0.46703	T	0.11	.	14.9585	0.71138	0.0:0.9307:0.0:0.0693	.	1171	Q86VV8	RTTN_HUMAN	K	1171	ENSP00000255674:E1171K;ENSP00000399520:E1171K	ENSP00000255674:E1171K	E	-	1	0	RTTN	65939789	0.998000	0.40836	1.000000	0.80357	0.932000	0.56968	2.690000	0.47001	2.941000	0.99782	0.655000	0.94253	GAA		0.259	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		T	67788809	C	T	67788809	3	4	61	1	0	0	0	0	1	0	0	0	13774	893	31	1	3265	1	RTTN	18	67788809	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7025	67788809	10288439	10699	18684										
SOCS6	9306	broad.mit.edu	37	chr18	67992744	67992744	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtcgccccagagatcttCgtggatcagtccgtgaatgg	13	10	2	2	rs41535447	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:67992744C>T	ENST00000397942.3	+	2	1156	c.840C>T	c.(838-840)ttC>ttT	p.F280F	SOCS6_ENST00000582322.1_Silent_p.F280F	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	280					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)		p.F280F(1)		NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				CAGAGATCTTCGTGGATCAGT	0.582													C|||	4	0.000798722	0.003	0	5008	,	,		19539	0		0	False		,,,				2504	0				Melanoma(84;1024 1361 24382 36583 42651)											1	Substitution - coding silent(1)	large_intestine(1)	18						C		10,4396	16.8+/-37.8	0,10,2193	166	148	154		840	-5.8	0.7	18	dbSNP_127	154	0,8600		0,0,4300	no	coding-synonymous	SOCS6	NM_004232.3		0,10,6493	TT,TC,CC		0.0,0.227,0.0769		280/536	67992744	10,12996	2203	4300	6503	66143724	SO:0001819	synonymous_variant	9306			AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.840C>T	18.37:g.67992744C>T			66143724	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																				0.582	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			T	67992744	C	T	67992744	2	4	61	1	0	0	0	0	0	0	0	1	14955	883	31	1		1	SOCS6	18	67992744	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203935	67992744	10084504	10700	18685										
NETO1	81832	broad.mit.edu	37	chr18	70417353	70417353	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtggtcggcacctcttcGatttcatctatgtcacaggc	10	12	4	0	rs201303366		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:70417353G>A	ENST00000327305.6	-	9	2142	c.1485C>T	c.(1483-1485)atC>atT	p.I495I	NETO1_ENST00000583169.1_Silent_p.I495I|RNA5SP460_ENST00000516789.1_RNA|NETO1_ENST00000299430.2_Silent_p.I494I	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	495					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.I495I(1)		NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GCACCTCTTCGATTTCATCTA	0.468													G|||	1	0.000199681	0	0	5008	,	,		18133	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	18											134	115	122					18																	70417353		2203	4300	6503	68568333	SO:0001819	synonymous_variant	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1485C>T	18.37:g.70417353G>A			68568333	Q86W85|Q8ND78|Q8TDF4	Silent	SNP	ENST00000327305.6	37	CCDS12000.1																																																																																				0.468	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		A	70417353	G	A	70417353	2	1	61	1	0	0	0	0	0	0	0	1	10370	1048	37	1		1	NETO1	18	70417353	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2424609	70417353	7659895	10701	18686										
NETO1	81832	broad.mit.edu	37	chr18	70461450	70461450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtatagactccacaattcCttcggaaccgcccatctcaa	5	14	1	1	rs138679154		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:70461450C>T	ENST00000327305.6	-	6	1198	c.541G>A	c.(541-543)Gga>Aga	p.G181R	NETO1_ENST00000583169.1_Missense_Mutation_p.G181R|NETO1_ENST00000299430.2_Missense_Mutation_p.G180R	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	181	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.G181R(2)|p.G181*(1)		NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		TCCACAATTCCTTCGGAACCG	0.428																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	large_intestine(1)|stomach(1)|skin(1)	18											113	106	109					18																	70461450		2203	4300	6503	68612430	SO:0001583	missense	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.541G>A	18.37:g.70461450C>T	ENSP00000313088:p.Gly181Arg		68612430	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.868564	0.91587	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.34667	1.35;1.35	5.29	5.29	0.74685	CUB (4);	0.000000	0.56097	D	0.000022	T	0.65678	0.2714	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71213	-0.4659	10	0.87932	D	0	-29.4775	18.9328	0.92572	0.0:1.0:0.0:0.0	.	180;181	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	R	181;180	ENSP00000313088:G181R;ENSP00000299430:G180R	ENSP00000299430:G180R	G	-	1	0	NETO1	68612430	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.487000	0.81328	2.462000	0.83206	0.655000	0.94253	GGA		0.428	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70461450	C	T	70461450	3	4	61	1	0	0	0	0	1	0	0	0	10370	690	24	3	1080	3	NETO1	18	70461450	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44097	70461450	7615798	10702	18687										
ZNF407	55628	broad.mit.edu	37	chr18	72343146	72343146	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggtttttcagaatcatcGaactctgatagtgttgttat	9	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72343146G>A	ENST00000299687.5	+	1	171	c.171G>A	c.(169-171)tcG>tcA	p.S57S	ZNF407_ENST00000582337.1_Silent_p.S57S|ZNF407_ENST00000577538.1_Silent_p.S57S|ZNF407_ENST00000309902.6_Silent_p.S57S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	57					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S57S(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CAGAATCATCGAACTCTGATA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	18											91	89	90					18																	72343146		1841	4084	5925	70472134	SO:0001819	synonymous_variant	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.171G>A	18.37:g.72343146G>A			70472134	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.413	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72343146	G	A	72343146	2	1	61	1	0	0	0	0	0	0	0	1	17926	1045	37	1		1	ZNF407	18	72343146	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1881696	72343146	5734102	10703	18688										
ZNF407	55628	broad.mit.edu	37	chr18	72343541	72343541	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatacagttctcaaatgcaGcatctgtgggcatttgtttt	9	7	2	1	rs370362692		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72343541G>T	ENST00000299687.5	+	1	566	c.566G>T	c.(565-567)aGc>aTc	p.S189I	ZNF407_ENST00000582337.1_Missense_Mutation_p.S189I|ZNF407_ENST00000577538.1_Missense_Mutation_p.S189I|ZNF407_ENST00000309902.6_Missense_Mutation_p.S189I	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S189I(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTCAAATGCAGCATCTGTGGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	18											152	154	153					18																	72343541		1962	4140	6102	70472529	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.566G>T	18.37:g.72343541G>T	ENSP00000299687:p.Ser189Ile		70472529	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921390	0.33908	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.10005	2.92;3.34	5.63	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	2.999750	0.03613	U	0.235091	T	0.19525	0.0469	M	0.69463	2.115	0.09310	N	1	P;P;B	0.40875	0.731;0.547;0.412	B;B;B	0.44224	0.444;0.347;0.188	T	0.25433	-1.0132	10	0.37606	T	0.19	.	8.2994	0.32006	0.3628:0.0:0.6372:0.0	.	189;189;189	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	I	189	ENSP00000299687:S189I;ENSP00000310359:S189I	ENSP00000299687:S189I	S	+	2	0	ZNF407	70472529	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	0.211000	0.17474	-0.206000	0.10203	0.655000	0.94253	AGC		0.438	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72343541	G	T	72343541	3	4	61	1	0	0	0	0	1	0	0	0	17926	971	34	2	568	2	ZNF407	18	72343541	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	395	72343541	5733707	10704	18689										
ZNF407	55628	broad.mit.edu	37	chr18	72345662	72345662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactaagggagatatggaacGtcattgtgccaccaagaaac	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72345662G>A	ENST00000299687.5	+	1	2687	c.2687G>A	c.(2686-2688)cGt>cAt	p.R896H	ZNF407_ENST00000582337.1_Missense_Mutation_p.R896H|ZNF407_ENST00000577538.1_Missense_Mutation_p.R896H|ZNF407_ENST00000309902.6_Missense_Mutation_p.R896H	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	896					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R896H(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GATATGGAACGTCATTGTGCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											100	97	98					18																	72345662		1930	4139	6069	70474650	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.2687G>A	18.37:g.72345662G>A	ENSP00000299687:p.Arg896His		70474650	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768943	0.90020	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.30981	1.51;1.51	5.84	5.84	0.93424	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);	0.074358	0.51477	D	0.000100	T	0.59514	0.2199	M	0.69523	2.12	0.35018	D	0.757517	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.67039	-0.5771	10	0.56958	D	0.05	.	20.1346	0.98019	0.0:0.0:1.0:0.0	.	896;896;896	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	H	896	ENSP00000299687:R896H;ENSP00000310359:R896H	ENSP00000299687:R896H	R	+	2	0	ZNF407	70474650	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	9.476000	0.97823	-0.117000	0.11872	0.455000	0.32223	CGT		0.398	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72345662	G	A	72345662	3	1	61	1	0	0	0	0	1	0	0	0	17926	1145	40	1	2689	1	ZNF407	18	72345662	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2121	72345662	5731586	10705	18690										
ZNF407	55628	broad.mit.edu	37	chr18	72347615	72347615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattgtgggaagatgtgtcGaagcagcaactcgatggcct	14	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72347615G>A	ENST00000299687.5	+	1	4640	c.4640G>A	c.(4639-4641)cGa>cAa	p.R1547Q	ZNF407_ENST00000582337.1_Missense_Mutation_p.R1547Q|ZNF407_ENST00000577538.1_Missense_Mutation_p.R1547Q|ZNF407_ENST00000309902.6_Missense_Mutation_p.R1547Q	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1547					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1547Q(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		AAGATGTGTCGAAGCAGCAAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	18											88	97	94					18																	72347615		2113	4228	6341	70476603	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4640G>A	18.37:g.72347615G>A	ENSP00000299687:p.Arg1547Gln		70476603	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474322	0.84640	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.76968	-1.06;3.21	5.22	5.22	0.72569	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.199932	0.33092	N	0.005291	T	0.76241	0.3960	N	0.08118	0	0.31137	N	0.707066	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.984;0.965	T	0.76645	-0.2883	10	0.59425	D	0.04	.	12.1634	0.54117	0.0786:0.0:0.9214:0.0	.	1547;1547;1547	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	Q	1547	ENSP00000299687:R1547Q;ENSP00000310359:R1547Q	ENSP00000299687:R1547Q	R	+	2	0	ZNF407	70476603	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	7.103000	0.77014	-0.407000	0.07576	0.477000	0.44152	CGA		0.512	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72347615	G	A	72347615	3	1	61	1	0	0	0	0	1	0	0	0	17926	1058	37	1	4642	1	ZNF407	18	72347615	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1953	72347615	5729633	10706	18691										
ZNF407	55628	broad.mit.edu	37	chr18	72632493	72632493	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaactgtgctgaaaatatccGcaaacacattctgcatactg	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72632493G>A	ENST00000299687.5	+	7	5273	c.5273G>A	c.(5272-5274)cGc>cAc	p.R1758H	ZNF407_ENST00000577538.1_Missense_Mutation_p.R1758H	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1758					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1758H(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAAAATATCCGCAAACACATT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											87	85	86					18																	72632493		1982	4181	6163	70761481	SO:0001583	missense	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.5273G>A	18.37:g.72632493G>A	ENSP00000299687:p.Arg1758His		70761481	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596014	0.86953	.	.	ENSG00000215421	ENST00000299687	T	0.44482	0.92	5.57	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000017	T	0.39462	0.1079	M	0.66297	2.02	0.80722	D	1	P;P	0.41710	0.76;0.647	B;B	0.34873	0.191;0.093	T	0.40627	-0.9553	10	0.49607	T	0.09	.	12.9471	0.58379	0.0751:0.0:0.9249:0.0	.	1758;1758	Q9C0G0-2;Q9C0G0	.;ZN407_HUMAN	H	1758	ENSP00000299687:R1758H	ENSP00000299687:R1758H	R	+	2	0	ZNF407	70761481	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.722000	0.98770	1.474000	0.48178	-0.176000	0.13171	CGC		0.398	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72632493	G	A	72632493	3	1	61	1	0	0	0	0	1	0	0	0	17926	1087	38	1	5409	1	ZNF407	18	72632493	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	284878	72632493	5444755	10707	18692										
ZADH2	284273	broad.mit.edu	37	chr18	72913443	72913443	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttcccatgtacatataAttgacagcacggaatatgga	7	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72913443A>C	ENST00000322342.3	-	2	1351	c.1062T>G	c.(1060-1062)aaT>aaG	p.N354K	ZADH2_ENST00000537114.2_Missense_Mutation_p.N231K	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	354						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.N354K(1)		endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TGTACATATAATTGACAGCAC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	18											78	78	78					18																	72913443		2203	4300	6503	71042431	SO:0001583	missense	284273			BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.1062T>G	18.37:g.72913443A>C	ENSP00000323678:p.Asn354Lys		71042431	A8KA15|B4DZ91	Missense_Mutation	SNP	ENST00000322342.3	37	CCDS12008.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204159	0.38905	.	.	ENSG00000180011	ENST00000322342;ENST00000537114	T;T	0.13196	3.49;2.61	5.61	-0.016	0.13974	.	0.176608	0.48286	D	0.000181	T	0.06005	0.0156	N	0.12961	0.28	0.33803	D	0.626894	B	0.13594	0.008	B	0.16289	0.015	T	0.34179	-0.9839	10	0.11182	T	0.66	-0.1122	8.6209	0.33859	0.6382:0.0:0.3618:0.0	.	354	Q8N4Q0	ZADH2_HUMAN	K	354;231	ENSP00000323678:N354K;ENSP00000440111:N231K	ENSP00000323678:N354K	N	-	3	2	ZADH2	71042431	0.999000	0.42202	0.933000	0.37362	0.837000	0.47467	0.753000	0.26376	1.074000	0.40909	-0.269000	0.10298	AAT		0.433	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907		C	72913443	A	C	72913443	3	2	61	1	0	0	0	0	1	0	0	0	17551	98	4	4	75	4	ZADH2	18	72913443	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	280950	72913443	5163805	10708	18693										
TSHZ1	10194	broad.mit.edu	37	chr18	72999016	72999016	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagggagggctggacattCtcaagtccctggagaatacc	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:72999016C>A	ENST00000580243.1	+	2	2002	c.1654C>A	c.(1654-1656)Ctc>Atc	p.L552I	TSHZ1_ENST00000322038.5_Missense_Mutation_p.L507I			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	552					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L507I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GCTGGACATTCTCAAGTCCCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	18											94	92	92					18																	72999016		2203	4300	6503	71128004	SO:0001583	missense	10194			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1654C>A	18.37:g.72999016C>A	ENSP00000464391:p.Leu552Ile		71128004	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	C	9.259	1.042764	0.19748	.	.	ENSG00000179981	ENST00000322038	T	0.52295	0.67	5.42	3.3	0.37823	.	0.070473	0.53938	D	0.000057	T	0.49236	0.1545	M	0.83483	2.645	0.39787	D	0.972384	P	0.48294	0.908	B	0.41860	0.368	T	0.61113	-0.7128	10	0.66056	D	0.02	-25.6923	8.8976	0.35474	0.0:0.7282:0.0:0.2718	.	552	Q6ZSZ6	TSH1_HUMAN	I	507	ENSP00000323584:L507I	ENSP00000323584:L507I	L	+	1	0	TSHZ1	71128004	1.000000	0.71417	0.993000	0.49108	0.981000	0.71138	2.946000	0.49050	2.052000	0.61016	0.459000	0.35465	CTC		0.592	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999016	C	A	72999016	3	1	61	1	0	0	0	0	1	0	0	0	16663	913	32	2	1521	2	TSHZ1	18	72999016	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85573	72999016	5078232	10709	18694										
TSHZ1	10194	broad.mit.edu	37	chr18	73000268	73000268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggacacagggcatcctgTtttcttttgcaacgattgtg	10	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:73000268T>C	ENST00000580243.1	+	2	3254	c.2906T>C	c.(2905-2907)gTt>gCt	p.V969A	TSHZ1_ENST00000322038.5_Missense_Mutation_p.V924A			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	969					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V924A(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GGGCATCCTGTTTTCTTTTGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	18											115	93	101					18																	73000268		2203	4300	6503	71129256	SO:0001583	missense	10194			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2906T>C	18.37:g.73000268T>C	ENSP00000464391:p.Val969Ala		71129256	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	T	10.45	1.354059	0.24512	.	.	ENSG00000179981	ENST00000322038	T	0.01572	4.76	5.1	5.1	0.69264	.	0.066792	0.64402	D	0.000013	T	0.03608	0.0103	L	0.31207	0.915	0.32123	N	0.587712	D	0.56746	0.977	P	0.50590	0.645	T	0.04413	-1.0953	10	0.87932	D	0	-21.504	15.1778	0.72927	0.0:0.0:0.0:1.0	.	969	Q6ZSZ6	TSH1_HUMAN	A	924	ENSP00000323584:V924A	ENSP00000323584:V924A	V	+	2	0	TSHZ1	71129256	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.655000	0.83696	-0.203000	0.10251	0.533000	0.62120	GTT		0.488	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		C	73000268	T	C	73000268	3	2	61	1	0	0	0	0	1	0	0	0	16663	1725	60	4	2773	4	TSHZ1	18	73000268	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1252	73000268	5076980	10710	18695										
C18orf62	284274	broad.mit.edu	37	chr18	73139426	73139426	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcagcaaattccccttGaatatccgtcccattcctgc	5	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:73139426G>T	ENST00000579022.1	-	1	232	c.93C>A	c.(91-93)ttC>ttA	p.F31L	SMIM21_ENST00000382638.3_Missense_Mutation_p.F31L|SMIM21_ENST00000584508.1_Missense_Mutation_p.F31L	NM_001037331.2	NP_001032408.1	Q3B7S5	SMI21_HUMAN	small integral membrane protein 21	31						integral component of membrane (GO:0016021)		p.F31F(1)|p.F31L(1)									AATTCCCCTTGAATATCCGTC	0.483																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|endometrium(1)	18											225	198	207					18																	73139426		2203	4300	6503	71268414	SO:0001583	missense	284274				CCDS32845.1	18q23	2013-03-11	2013-03-11	2013-03-11	ENSG00000206026	ENSG00000206026			27598	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 62"	C18orf62			Standard	NM_001037331		Approved		uc002lma.1	Q3B7S5	OTTHUMG00000179126	ENST00000579022.1:c.93C>A	18.37:g.73139426G>T	ENSP00000462106:p.Phe31Leu		71268414		Missense_Mutation	SNP	ENST00000579022.1	37	CCDS32845.1	.	.	.	.	.	.	.	.	.	.	G	5.411	0.261014	0.10239	.	.	ENSG00000206026	ENST00000382638	.	.	.	2.28	0.159	0.14968	.	.	.	.	.	T	0.17704	0.0425	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20075	-1.0286	8	0.87932	D	0	.	6.2952	0.21081	0.0:0.0:0.4674:0.5326	.	31	Q3B7S5	CR062_HUMAN	L	31	.	ENSP00000372083:F31L	F	-	3	2	C18orf62	71268414	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.288000	0.18939	-0.284000	0.09102	0.260000	0.18958	TTC		0.483	SMIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444917.1	NM_001037331		T	73139426	G	T	73139426	3	4	61	1	0	0	0	0	1	0	0	0	1912	1281	45	2	224	2	C18orf62	18	73139426	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139158	73139426	4937822	10711	18696										
ZNF516	9658	broad.mit.edu	37	chr18	74090831	74090831	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtgctccaacccagggcCgctgacaccccatccctggt	9	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:74090831C>T	ENST00000443185.2	-	5	3555	c.3238G>A	c.(3238-3240)Ggc>Agc	p.G1080S	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1080					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G1079S(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AACCCAGGGCCGCTGACACCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	18											28	32	30					18																	74090831		1995	4173	6168	72219819	SO:0001583	missense	9658			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3238G>A	18.37:g.74090831C>T	ENSP00000394757:p.Gly1080Ser		72219819		Missense_Mutation	SNP	ENST00000443185.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.727|0.727	-0.781440|-0.781440	0.02929|0.02929	.|.	.|.	ENSG00000101493|ENSG00000101493	ENST00000443185|ENST00000542818	T|.	0.08102|.	3.13|.	4.26|4.26	-2.68|-2.68	0.06041|0.06041	.|.	0.768945|.	0.12126|.	N|.	0.497275|.	T|T	0.26268|0.26268	0.0641|0.0641	N|N	0.16266|0.16266	0.395|0.395	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.27468|0.27468	-1.0073|-1.0073	10|5	0.02654|.	T|.	1|.	.|.	11.6302|11.6302	0.51168|0.51168	0.0:0.2074:0.0:0.7926|0.0:0.2074:0.0:0.7926	.|.	1080|.	Q92618|.	ZN516_HUMAN|.	S|Q	1080|13	ENSP00000394757:G1080S|.	ENSP00000394757:G1080S|.	G|R	-|-	1|2	0|0	ZNF516|ZNF516	72219819|72219819	0.725000|0.725000	0.28048|0.28048	0.009000|0.009000	0.14445|0.14445	0.861000|0.861000	0.49209|0.49209	0.939000|0.939000	0.28978|0.28978	-0.854000|-0.854000	0.04131|0.04131	-0.948000|-0.948000	0.02665|0.02665	GGC|CGG		0.622	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		T	74090831	C	T	74090831	3	4	61	1	0	0	0	0	1	0	0	0	17999	652	23	1	269	1	ZNF516	18	74090831	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	951405	74090831	3986417	10712	18697										
ZNF516	9658	broad.mit.edu	37	chr18	74092021	74092021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcaccagggacgggcacCtcctgcttggggtgaaatgc	13	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:74092021C>A	ENST00000443185.2	-	4	2366	c.2049G>T	c.(2047-2049)gaG>gaT	p.E683D	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	683					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E683D(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGACGGGCACCTCCTGCTTGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	18											61	65	64					18																	74092021		1963	4167	6130	72221009	SO:0001583	missense	9658			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2049G>T	18.37:g.74092021C>A	ENSP00000394757:p.Glu683Asp		72221009		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	9.903	1.207433	0.22205	.	.	ENSG00000101493	ENST00000443185	T	0.10477	2.87	4.22	1.37	0.22104	.	0.483211	0.19134	N	0.121863	T	0.05181	0.0138	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.39165	-0.9627	9	0.22706	T	0.39	-19.2348	2.625	0.04927	0.1515:0.5443:0.1474:0.1568	.	683	Q92618	ZN516_HUMAN	D	683	ENSP00000394757:E683D	ENSP00000394757:E683D	E	-	3	2	ZNF516	72221009	0.544000	0.26441	0.032000	0.17829	0.194000	0.23727	0.589000	0.23939	0.068000	0.16574	0.655000	0.94253	GAG		0.527	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		A	74092021	C	A	74092021	3	1	61	1	0	0	0	0	1	0	0	0	17999	680	24	2	1459	2	ZNF516	18	74092021	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1190	74092021	3985227	10713	18698										
ZNF236	7776	broad.mit.edu	37	chr18	74583767	74583767	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccagttaacgcgacacaTtaggatacacacaggtatga	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:74583767T>A	ENST00000253159.8	+	5	845	c.647T>A	c.(646-648)aTt>aAt	p.I216N	ZNF236_ENST00000583095.1_Intron|ZNF236_ENST00000320610.9_Missense_Mutation_p.I218N	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	216					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I216N(2)		NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		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)		ACGCGACACATTAGGATACAC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	18											127	115	119					18																	74583767		2045	4184	6229	72712755	SO:0001583	missense	7776			AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.647T>A	18.37:g.74583767T>A	ENSP00000253159:p.Ile216Asn		72712755	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.041537	0.55003	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.08458	3.09;3.09	5.41	5.41	0.78517	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.192597	0.43260	D	0.000598	T	0.22781	0.0550	M	0.63169	1.94	0.25759	N	0.984968	B;D	0.61697	0.19;0.99	B;D	0.64877	0.071;0.93	T	0.14309	-1.0477	10	0.18276	T	0.48	.	15.7353	0.77837	0.0:0.0:0.0:1.0	.	216;216	Q9NWI2;Q9UL36	.;ZN236_HUMAN	N	216	ENSP00000253159:I216N;ENSP00000444524:I216N	ENSP00000253159:I216N	I	+	2	0	ZNF236	72712755	1.000000	0.71417	0.001000	0.08648	0.863000	0.49368	7.506000	0.81665	2.178000	0.69098	0.533000	0.62120	ATT		0.468	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74583767	T	A	74583767	3	1	61	1	0	0	0	0	1	0	0	0	17828	1493	52	5	665	5	ZNF236	18	74583767	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	491746	74583767	3493481	10714	18699										
ZNF236	7776	broad.mit.edu	37	chr18	74620320	74620320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagcatcagcaggcagcctCgatagatgacagcactgtag	11	11	1	2	rs372076275		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:74620320C>T	ENST00000253159.8	+	14	2534	c.2336C>T	c.(2335-2337)tCg>tTg	p.S779L	ZNF236_ENST00000320610.9_Missense_Mutation_p.S781L	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	779					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S779L(2)		NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		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)		CAGGCAGCCTCGATAGATGAC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	18						C	LEU/SER	0,4166		0,0,2083	121	128	126		2336	5.2	0	18		126	1,8453		0,1,4226	no	missense	ZNF236	NM_007345.3	145	0,1,6309	TT,TC,CC		0.0118,0.0,0.0079	benign	779/1846	74620320	1,12619	2083	4227	6310	72749308	SO:0001583	missense	7776			AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.2336C>T	18.37:g.74620320C>T	ENSP00000253159:p.Ser779Leu		72749308	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132109	0.37630	0.0	1.18E-4	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.11385	2.78;2.95	5.23	5.23	0.72850	.	0.189286	0.40818	N	0.001019	T	0.14442	0.0349	M	0.65975	2.015	0.30642	N	0.756324	P	0.37997	0.614	B	0.28553	0.091	T	0.06463	-1.0825	10	0.52906	T	0.07	.	19.1458	0.93467	0.0:1.0:0.0:0.0	.	779	Q9UL36	ZN236_HUMAN	L	779	ENSP00000253159:S779L;ENSP00000444524:S779L	ENSP00000253159:S779L	S	+	2	0	ZNF236	72749308	0.208000	0.23494	0.000000	0.03702	0.019000	0.09904	3.211000	0.51137	2.600000	0.87896	0.563000	0.77884	TCG		0.527	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74620320	C	T	74620320	3	4	61	1	0	0	0	0	1	0	0	0	17828	893	31	1	2390	1	ZNF236	18	74620320	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36553	74620320	3456928	10715	18700										
GALR1	2587	broad.mit.edu	37	chr18	74980805	74980805	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacctgagtgatactaaaGaaagtaaaagtcgaatagac	8	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:74980805G>T	ENST00000299727.3	+	3	997	c.997G>T	c.(997-999)Gaa>Taa	p.E333*		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	333					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)	p.E333*(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		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)		TGATACTAAAGAAAGTAAAAG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	18											73	78	76					18																	74980805		2203	4300	6503	73109793	SO:0001587	stop_gained	2587			U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"GPCR / Class A : Galanin receptors"	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.997G>T	18.37:g.74980805G>T	ENSP00000299727:p.Glu333*		73109793	Q4VBL7	Nonsense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110102	0.77210	.	.	ENSG00000166573	ENST00000299727	.	.	.	4.86	4.86	0.63082	.	0.117930	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	17.6142	0.88064	0.0:0.0:1.0:0.0	.	.	.	.	X	333	.	ENSP00000299727:E333X	E	+	1	0	GALR1	73109793	1.000000	0.71417	0.027000	0.17364	0.292000	0.27327	9.109000	0.94291	2.257000	0.74773	0.460000	0.39030	GAA		0.368	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1			T	74980805	G	T	74980805	4	4	61	1	0	0	0	0	0	1	0	0	6247	943	33	2	1007	2	GALR1	18	74980805	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	360485	74980805	3096443	10716	18701										
SALL3	27164	broad.mit.edu	37	chr18	76757026	76757026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagaaggacctggcagctCgggcaatgaacgtcgacccc	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:76757026C>T	ENST00000537592.2	+	3	3607	c.3607C>T	c.(3607-3609)Cgg>Tgg	p.R1203W	SALL3_ENST00000575389.2_Missense_Mutation_p.R1131W|SALL3_ENST00000536229.3_Missense_Mutation_p.R998W	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1203					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1203W(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CCTGGCAGCTCGGGCAATGAA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	18											74	72	72					18																	76757026		2203	4300	6503	74858014	SO:0001583	missense	27164			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3607C>T	18.37:g.76757026C>T	ENSP00000441823:p.Arg1203Trp		74858014	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	8.606	0.887987	0.17540	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.54675	0.56	5.2	4.31	0.51392	.	0.000000	0.47455	D	0.000230	T	0.73179	0.3554	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.985;0.992	T	0.77978	-0.2384	10	0.87932	D	0	-17.689	14.8733	0.70474	0.1446:0.8554:0.0:0.0	.	863;1203	F5GXY4;Q9BXA9	.;SALL3_HUMAN	W	1203;1131;863	ENSP00000441823:R1203W	ENSP00000299466:R1203W	R	+	1	2	SALL3	74858014	1.000000	0.71417	0.044000	0.18714	0.286000	0.27126	4.764000	0.62264	1.145000	0.42336	0.561000	0.74099	CGG		0.582	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76757026	C	T	76757026	3	4	61	1	0	0	0	0	1	0	0	0	13849	875	31	1	3617	1	SALL3	18	76757026	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1776221	76757026	1320222	10717	18702										
ATP9B	374868	broad.mit.edu	37	chr18	76936828	76936828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaggttcgtgttttattcGaactgatcaactagatggtg	10	7	1	2	rs140291894		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:76936828G>A	ENST00000426216.2	+	8	811	c.794G>A	c.(793-795)cGa>cAa	p.R265Q	ATP9B_ENST00000307671.7_Missense_Mutation_p.R265Q	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	265					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R265Q(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		TGTTTTATTCGAACTGATCAA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	18						G	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	106	102	103		794	5.6	1	18	dbSNP_134	103	0,8600		0,0,4300	no	missense	ATP9B	NM_198531.3	43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	265/1148	76936828	2,13004	2203	4300	6503	75037816	SO:0001583	missense	374868			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.794G>A	18.37:g.76936828G>A	ENSP00000398076:p.Arg265Gln		75037816	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	G	35	5.504855	0.96371	4.54E-4	0.0	ENSG00000166377	ENST00000426216;ENST00000307671	D;D	0.90444	-2.67;-2.67	5.56	5.56	0.83823	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.95645	0.8584	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.985	D	0.95811	0.8841	10	0.87932	D	0	.	19.5243	0.95197	0.0:0.0:1.0:0.0	.	265;265	O43861;O43861-2	ATP9B_HUMAN;.	Q	265	ENSP00000398076:R265Q;ENSP00000304500:R265Q	ENSP00000304500:R265Q	R	+	2	0	ATP9B	75037816	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.857000	0.92250	2.605000	0.88082	0.655000	0.94253	CGA		0.448	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531		A	76936828	G	A	76936828	3	1	61	1	0	0	0	0	1	0	0	0	1200	1058	37	1	824	1	ATP9B	18	76936828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	179802	76936828	1140420	10718	18703										
NFATC1	4772	broad.mit.edu	37	chr18	77211016	77211016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaacttcggaaaggagagaCggacatcgggaggaagaaca	15	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:77211016C>T	ENST00000427363.2	+	5	1652	c.1652C>T	c.(1651-1653)aCg>aTg	p.T551M	NFATC1_ENST00000586434.1_Missense_Mutation_p.T538M|NFATC1_ENST00000587635.1_Missense_Mutation_p.T551M|NFATC1_ENST00000542384.1_Missense_Mutation_p.T551M|NFATC1_ENST00000253506.5_Missense_Mutation_p.T551M|NFATC1_ENST00000591814.1_Missense_Mutation_p.T551M|NFATC1_ENST00000592223.1_Missense_Mutation_p.T538M|NFATC1_ENST00000329101.4_Missense_Mutation_p.T538M|NFATC1_ENST00000318065.5_Missense_Mutation_p.T538M|NFATC1_ENST00000545796.1_Missense_Mutation_p.T79M|NFATC1_ENST00000397790.2_Missense_Mutation_p.T79M			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	551	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.T538M(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AAAGGAGAGACGGACATCGGG	0.572																																					GBM(151;1210 2593 28719 45011)											1	Substitution - Missense(1)	large_intestine(1)	18											126	129	128					18																	77211016		2203	4300	6503	75312004	SO:0001583	missense	4772			U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1652C>T	18.37:g.77211016C>T	ENSP00000389377:p.Thr551Met		75312004	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		.	.	.	.	.	.	.	.	.	.	C	16.54	3.152534	0.57259	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000397790;ENST00000542384;ENST00000329101;ENST00000545796;ENST00000427363;ENST00000397794	D;D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0;-2.0	4.65	4.65	0.58169	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.110995	0.64402	D	0.000010	D	0.93064	0.7792	M	0.86028	2.79	0.58432	D	0.999995	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.993;0.993;0.989;1.0	D	0.94400	0.7622	10	0.87932	D	0	-23.153	17.5435	0.87854	0.0:1.0:0.0:0.0	.	538;538;551;551;551;538;551	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	M	551;551;79;551;538;79;538;515	ENSP00000253506:T551M;ENSP00000380892:T79M;ENSP00000442435:T551M;ENSP00000327850:T538M;ENSP00000439992:T79M	ENSP00000253506:T551M	T	+	2	0	NFATC1	75312004	1.000000	0.71417	0.922000	0.36590	0.257000	0.26127	5.742000	0.68646	2.144000	0.66660	0.563000	0.77884	ACG		0.572	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		T	77211016	C	T	77211016	3	4	61	1	0	0	0	0	1	0	0	0	10392	536	19	1	1762	1	NFATC1	18	77211016	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274188	77211016	866232	10719	18704										
CTDP1	9150	broad.mit.edu	37	chr18	77470382	77470382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaagcttttttctcaccGaatattatcaagggatgaat	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:77470382G>A	ENST00000299543.7	+	6	956	c.809G>A	c.(808-810)cGa>cAa	p.R270Q	CTDP1_ENST00000075430.7_Missense_Mutation_p.R270Q	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	270	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.R270Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TTTTCTCACCGAATATTATCA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	18											166	184	178					18																	77470382		2203	4300	6503	75571370	SO:0001583	missense	9150			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.809G>A	18.37:g.77470382G>A	ENSP00000299543:p.Arg270Gln		75571370	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977628	0.92982	.	.	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.20881	2.04;2.04	4.42	4.42	0.53409	NLI interacting factor (3);FCP1-like phosphatase, phosphatase domain (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.62097	0.2400	H	0.96576	3.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78247	-0.2278	10	0.87932	D	0	-11.0565	17.3991	0.87454	0.0:0.0:1.0:0.0	.	151;270;270	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	Q	270	ENSP00000299543:R270Q;ENSP00000075430:R270Q	ENSP00000075430:R270Q	R	+	2	0	CTDP1	75571370	1.000000	0.71417	0.991000	0.47740	0.756000	0.42949	8.916000	0.92745	2.170000	0.68504	0.462000	0.41574	CGA		0.443	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		A	77470382	G	A	77470382	3	1	61	1	0	0	0	0	1	0	0	0	4008	1058	37	1	831	1	CTDP1	18	77470382	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259366	77470382	606866	10720	18705										
CTDP1	9150	broad.mit.edu	37	chr18	77472976	77472976	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcattttcacttgtagaaatCtctttccttgtggagactca	7	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:77472976C>A	ENST00000299543.7	+	7	1015	c.868C>A	c.(868-870)Ctc>Atc	p.L290I	CTDP1_ENST00000075430.7_Missense_Mutation_p.L290I	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	290	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.L290I(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TTGTAGAAATCTCTTTCCTTG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	18											74	75	75					18																	77472976		2203	4300	6503	75573964	SO:0001583	missense	9150			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.868C>A	18.37:g.77472976C>A	ENSP00000299543:p.Leu290Ile		75573964	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.899893	0.72754	.	.	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.21543	2.0;2.0	4.91	4.91	0.64330	NLI interacting factor (3);FCP1-like phosphatase, phosphatase domain (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.42177	0.1191	M	0.63428	1.95	0.80722	D	1	D;D;D	0.89917	0.99;1.0;1.0	D;D;D	0.91635	0.939;0.998;0.999	T	0.16719	-1.0393	10	0.48119	T	0.1	-33.8782	12.8805	0.58014	0.0:0.9208:0.0:0.0792	.	171;290;290	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	I	290	ENSP00000299543:L290I;ENSP00000075430:L290I	ENSP00000075430:L290I	L	+	1	0	CTDP1	75573964	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	4.033000	0.57282	2.399000	0.81585	0.655000	0.94253	CTC		0.333	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		A	77472976	C	A	77472976	3	1	61	1	0	0	0	0	1	0	0	0	4008	913	32	2	894	2	CTDP1	18	77472976	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2594	77472976	604272	10721	18706										
ADNP2	22850	broad.mit.edu	37	chr18	77893502	77893502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttttaacagagatatcGaacaaagccatactgttgtg	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:77893502G>A	ENST00000262198.4	+	4	661	c.206G>A	c.(205-207)cGa>cAa	p.R69Q		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	69					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R69Q(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		CAGAGATATCGAACAAAGCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	18																																								75994493	SO:0001583	missense	22850			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.206G>A	18.37:g.77893502G>A	ENSP00000262198:p.Arg69Gln		75994493	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	37	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738988	0.89573	.	.	ENSG00000101544	ENST00000262198	T	0.73897	-0.79	5.44	4.57	0.56435	.	0.000000	0.56097	D	0.000030	T	0.69788	0.3150	M	0.64404	1.975	0.34978	D	0.753838	P	0.50066	0.931	B	0.39119	0.291	T	0.79240	-0.1885	9	.	.	.	-11.6939	14.4299	0.67243	0.0703:0.0:0.9297:0.0	.	69	Q6IQ32	ADNP2_HUMAN	Q	69	ENSP00000262198:R69Q	.	R	+	2	0	ADNP2	75994493	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	8.036000	0.88901	1.536000	0.49237	0.655000	0.94253	CGA		0.368	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		A	77893502	G	A	77893502	3	1	61	1	0	0	0	0	1	0	0	0	324	1058	37	1	216	1	ADNP2	18	77893502	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420526	77893502	183746	10722	18707										
ADNP2	22850	broad.mit.edu	37	chr18	77896488	77896488	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttaaagattatttccataaGaaaccatatcctagtaaaaa	3	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr18:77896488G>T	ENST00000262198.4	+	4	3647	c.3192G>T	c.(3190-3192)aaG>aaT	p.K1064N		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	1064					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K1064N(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		ATTTCCATAAGAAACCATATC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	18											47	52	50					18																	77896488		2200	4293	6493	75997479	SO:0001583	missense	22850			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.3192G>T	18.37:g.77896488G>T	ENSP00000262198:p.Lys1064Asn		75997479	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	37	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193764	0.58017	.	.	ENSG00000101544	ENST00000262198	D	0.92149	-2.98	4.75	3.86	0.44501	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.365576	0.26163	N	0.025974	D	0.90232	0.6946	L	0.59436	1.845	0.30825	N	0.737331	P	0.45474	0.859	P	0.45712	0.491	D	0.88415	0.3024	9	.	.	.	-23.2388	9.7748	0.40612	0.1582:0.0:0.8418:0.0	.	1064	Q6IQ32	ADNP2_HUMAN	N	1064	ENSP00000262198:K1064N	.	K	+	3	2	ADNP2	75997479	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.283000	0.58977	2.482000	0.83794	0.561000	0.74099	AAG		0.328	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		T	77896488	G	T	77896488	3	4	61	1	0	0	0	0	1	0	0	0	324	933	33	2	3202	2	ADNP2	18	77896488	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2986	77896488	180760	10723	18708										
MIER2	54531	broad.mit.edu	37	chr19	308859	308859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtctgctgggcgaagtagtCgtagcgctccgacttcttcc	12	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:308859C>T	ENST00000264819.4	-	11	1061	c.1051G>A	c.(1051-1053)Gac>Aac	p.D351N	CTD-3113P16.5_ENST00000591533.1_RNA	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D351N(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)		GCGAAGTAGTCGTAGCGCTCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	59	61					19																	308859		2203	4300	6503	259859	SO:0001583	missense	54531			AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"KIAA1193"	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.1051G>A	19.37:g.308859C>T	ENSP00000264819:p.Asp351Asn		259859	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	C	32	5.143462	0.94603	.	.	ENSG00000105556	ENST00000264819	T	0.68765	-0.35	4.49	4.49	0.54785	Homeodomain-like (1);	0.000000	0.48767	D	0.000165	T	0.82250	0.4996	M	0.83312	2.635	0.41098	D	0.98564	D	0.89917	1.0	D	0.69479	0.964	D	0.86215	0.1627	10	0.87932	D	0	-31.5428	16.1739	0.81840	0.0:1.0:0.0:0.0	.	351	Q8N344	MIER2_HUMAN	N	351	ENSP00000264819:D351N	ENSP00000264819:D351N	D	-	1	0	MIER2	259859	0.998000	0.40836	0.993000	0.49108	0.945000	0.59286	3.861000	0.56002	2.038000	0.60285	0.457000	0.33378	GAC		0.662	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		T	308859	C	T	308859	3	4	61	1	0	0	0	0	1	0	0	0	9611	884	31	1	602	1	MIER2	19	308859	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		308859	58820124	10724	18709										
MIER2	54531	broad.mit.edu	37	chr19	326596	326596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttcatcagccaggaaacGagctttgggaaaacagaggc	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:326596G>A	ENST00000264819.4	-	6	506	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C	MIER2_ENST00000592722.1_5'Flank	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	166					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R166C(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)		GCCAGGAAACGAGCTTTGGGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											85	85	85					19																	326596		2203	4300	6503	277596	SO:0001583	missense	54531			AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"KIAA1193"	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.496C>T	19.37:g.326596G>A	ENSP00000264819:p.Arg166Cys		277596	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	G	5.827	0.336846	0.11013	.	.	ENSG00000105556	ENST00000264819	T	0.22134	1.97	4.65	1.26	0.21427	.	1.502620	0.04133	N	0.318310	T	0.10723	0.0262	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.26189	-1.0110	10	0.36615	T	0.2	-5.078	2.6524	0.05003	0.1723:0.1338:0.5392:0.1547	.	166	Q8N344	MIER2_HUMAN	C	166	ENSP00000264819:R166C	ENSP00000264819:R166C	R	-	1	0	MIER2	277596	0.882000	0.30256	0.559000	0.28332	0.359000	0.29487	0.204000	0.17335	0.176000	0.19873	0.650000	0.86243	CGT		0.562	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		A	326596	G	A	326596	3	1	61	1	0	0	0	0	1	0	0	0	9611	1058	37	1	1177	1	MIER2	19	326596	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17737	326596	58802387	10725	18710										
C19orf21	126353	broad.mit.edu	37	chr19	758401	758401	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacaaagcaagaggcatcGaagccccctcggggatgccc	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:758401G>A	ENST00000215582.6	+	2	1558	c.1455G>A	c.(1453-1455)tcG>tcA	p.S485S		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	485					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.S485S(1)									AAGAGGCATCGAAGCCCCCTC	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	19											46	45	46					19																	758401		2203	4300	6503	709401	SO:0001819	synonymous_variant	126353			BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1455G>A	19.37:g.758401G>A			709401		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																				0.642	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	758401	G	A	758401	2	1	61	1	0	0	0	0	0	0	0	1	1919	1045	37	1		1	C19orf21	19	758401	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	431805	758401	58370582	10726	18711										
CNN2	1265	broad.mit.edu	37	chr19	1036489	1036489	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcatctctatgaccccaaGaaccatatcctgccccccat	5	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:1036489G>T	ENST00000263097.4	+	6	945	c.582G>T	c.(580-582)aaG>aaT	p.K194N	CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000565096.2_Missense_Mutation_p.K183N|CNN2_ENST00000348419.3_Missense_Mutation_p.K155N|CNN2_ENST00000562958.2_Missense_Mutation_p.K215N|AC011558.5_ENST00000585757.1_RNA	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	194				RRHLYDPKNHILPPMD -> AGISMTPRTISCPPWT (in Ref. 6; BAA20887). {ECO:0000305}.	actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)	p.K194N(1)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		ATGACCCCAAGAACCATATCC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	71	72					19																	1036489		2203	4300	6503	987489	SO:0001583	missense	1265			D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.582G>T	19.37:g.1036489G>T	ENSP00000263097:p.Lys194Asn		987489	A5D8U8|A6NFI4|D6W5X9|Q92578	Missense_Mutation	SNP	ENST00000263097.4	37	CCDS12053.1	.	.	.	.	.	.	.	.	.	.	g	17.19	3.325885	0.60743	.	.	ENSG00000064666	ENST00000263097;ENST00000348419;ENST00000442531	T;T	0.59224	1.24;0.28	4.18	2.04	0.26737	.	0.000000	0.85682	U	0.000000	T	0.74306	0.3699	M	0.86343	2.81	0.35947	D	0.833658	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.998;1.0	P;D;D;D;D;D	0.72982	0.907;0.979;0.979;0.979;0.929;0.979	T	0.78770	-0.2074	10	0.87932	D	0	.	8.1562	0.31171	0.2021:0.0:0.7979:0.0	.	215;183;169;155;194;194	B4DUT8;B4DDF4;B4DHU5;A6NFI4;Q99439;Q6FHE4	.;.;.;.;CNN2_HUMAN;.	N	194;155;173	ENSP00000263097:K194N;ENSP00000340129:K155N	ENSP00000263097:K194N	K	+	3	2	CNN2	987489	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	0.647000	0.24812	0.428000	0.26173	0.556000	0.70494	AAG		0.632	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368		T	1036489	G	T	1036489	3	4	61	1	0	0	0	0	1	0	0	0	3616	933	33	2	604	2	CNN2	19	1036489	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	278088	1036489	58092494	10727	18712										
MKNK2	2872	broad.mit.edu	37	chr19	2041073	2041073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgctgcaggacttgggcgGcactcagcctctgcttggcg	16	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2041073G>A	ENST00000591601.1	-	11	1111	c.1076C>T	c.(1075-1077)gCc>gTc	p.A359V	MKNK2_ENST00000250896.3_Missense_Mutation_p.A359V|MKNK2_ENST00000588014.1_Missense_Mutation_p.A103V|MKNK2_ENST00000309340.7_Missense_Mutation_p.A359V|MKNK2_ENST00000591588.1_Missense_Mutation_p.A103V|MKNK2_ENST00000541165.1_Missense_Mutation_p.A228V|MKNK2_ENST00000591142.1_Missense_Mutation_p.A103V			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	359	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A359V(2)		breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|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)		GACTTGGGCGGCACTCAGCCT	0.662																																																2	Substitution - Missense(2)	large_intestine(2)	19											125	100	109					19																	2041073		2203	4300	6503	1992073	SO:0001583	missense	2872			AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"Putative map kinase interacting kinase"	605069	"G protein-coupled receptor kinase 7"	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.1076C>T	19.37:g.2041073G>A	ENSP00000467811:p.Ala359Val		1992073	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140434	0.77775	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.46063	0.88;0.88;0.88	3.94	3.94	0.45596	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117336	0.56097	D	0.000022	T	0.52933	0.1765	L	0.38531	1.155	0.80722	D	1	D;D;P;P	0.71674	0.988;0.998;0.939;0.868	D;D;P;P	0.71414	0.951;0.973;0.779;0.859	T	0.55848	-0.8076	10	0.52906	T	0.07	-6.964	15.1499	0.72689	0.0:0.0:1.0:0.0	.	164;359;359;261	Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28	.;MKNK2_HUMAN;.;.	V	359;359;228;299	ENSP00000309485:A359V;ENSP00000250896:A359V;ENSP00000438904:A228V	ENSP00000250896:A359V	A	-	2	0	MKNK2	1992073	1.000000	0.71417	0.540000	0.28089	0.417000	0.31264	9.343000	0.97047	2.046000	0.60703	0.555000	0.69702	GCC		0.662	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		A	2041073	G	A	2041073	3	1	61	1	0	0	0	0	1	0	0	0	9635	1203	42	3	428	3	MKNK2	19	2041073	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1004584	2041073	57087910	10728	18713										
ZNF554	115196	broad.mit.edu	37	chr19	2834264	2834264	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttgagcgaacatcaaaGaattcacacgggggagaaac	10	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2834264G>T	ENST00000317243.5	+	5	1229	c.1031G>T	c.(1030-1032)aGa>aTa	p.R344I		NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R344I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		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)		GAACATCAAAGAATTCACACG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											61	68	66					19																	2834264		2079	4243	6322	2785264	SO:0001583	missense	115196			AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"Zinc fingers, C2H2-type", "-"	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.1031G>T	19.37:g.2834264G>T	ENSP00000321132:p.Arg344Ile		2785264	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854366	0.32791	.	.	ENSG00000172006	ENST00000317243	T	0.24908	1.83	2.65	1.45	0.22620	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18215	0.0437	L	0.55103	1.725	0.80722	D	1	P	0.41710	0.76	B	0.29524	0.103	T	0.19484	-1.0304	9	0.87932	D	0	.	8.2963	0.31986	0.0:0.0:0.7655:0.2345	.	344	Q86TJ5	ZN554_HUMAN	I	344	ENSP00000321132:R344I	ENSP00000321132:R344I	R	+	2	0	ZNF554	2785264	0.000000	0.05858	0.641000	0.29422	0.749000	0.42624	0.640000	0.24705	1.498000	0.48600	0.573000	0.79308	AGA		0.527	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303		T	2834264	G	T	2834264	3	4	61	1	0	0	0	0	1	0	0	0	18024	942	33	2	1049	2	ZNF554	19	2834264	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	793191	2834264	56294719	10729	18714										
ZNF554	115196	broad.mit.edu	37	chr19	2834684	2834684	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcccttgtgaggcacgagaGaactcacactggagagaaac	11	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2834684G>T	ENST00000317243.5	+	5	1649	c.1451G>T	c.(1450-1452)aGa>aTa	p.R484I		NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R484I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		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)		AGGCACGAGAGAACTCACACT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											54	62	59					19																	2834684		2199	4299	6498	2785684	SO:0001583	missense	115196			AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"Zinc fingers, C2H2-type", "-"	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.1451G>T	19.37:g.2834684G>T	ENSP00000321132:p.Arg484Ile		2785684	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.636060	0.47049	.	.	ENSG00000172006	ENST00000317243	T	0.24908	1.83	2.86	2.86	0.33363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47414	0.1444	M	0.75615	2.305	0.80722	D	1	D	0.71674	0.998	D	0.71414	0.973	T	0.52975	-0.8503	9	0.87932	D	0	.	11.5211	0.50551	0.0:0.0:1.0:0.0	.	484	Q86TJ5	ZN554_HUMAN	I	484	ENSP00000321132:R484I	ENSP00000321132:R484I	R	+	2	0	ZNF554	2785684	0.015000	0.18098	0.989000	0.46669	0.836000	0.47400	0.878000	0.28126	1.615000	0.50252	0.643000	0.83706	AGA		0.542	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303		T	2834684	G	T	2834684	3	4	61	1	0	0	0	0	1	0	0	0	18024	942	33	2	1469	2	ZNF554	19	2834684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420	2834684	56294299	10730	18715										
ZNF555	148254	broad.mit.edu	37	chr19	2853045	2853045	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagttattcttcggcttttCgaagacacatgataacacac	6	10	2	2	rs147891673		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2853045C>T	ENST00000334241.4	+	4	1120	c.982C>T	c.(982-984)Cga>Tga	p.R328*	ZNF555_ENST00000591539.1_Nonsense_Mutation_p.R327*|AC006130.3_ENST00000589365.1_RNA	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	328					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R328*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		TTCGGCTTTTCGAAGACACAT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	19						C	stop/ARG,stop/ARG	0,4406		0,0,2203	65	65	65		979,982	-1	0	19	dbSNP_134	65	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	ZNF555	NM_001172775.1,NM_152791.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	327/628,328/629	2853045	1,13005	2203	4300	6503	2804045	SO:0001587	stop_gained	148254			AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"Zinc fingers, C2H2-type", "-"	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.982C>T	19.37:g.2853045C>T	ENSP00000334853:p.Arg328*		2804045	A8KA89|K7EQM2|Q8NA46|Q96MP1	Nonsense_Mutation	SNP	ENST00000334241.4	37	CCDS12096.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063361	0.93898	0.0	1.16E-4	ENSG00000186300	ENST00000334241;ENST00000382127	.	.	.	3.22	-1.03	0.10102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	9.4709	0.38842	0.5198:0.4801:0.0:0.0	.	.	.	.	X	328;327	.	ENSP00000334853:R328X	R	+	1	2	ZNF555	2804045	0.000000	0.05858	0.002000	0.10522	0.867000	0.49689	-0.228000	0.09114	0.132000	0.18615	0.561000	0.74099	CGA		0.403	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791		T	2853045	C	T	2853045	4	4	61	1	0	0	0	0	0	1	0	0	18025	876	31	1	996	1	ZNF555	19	2853045	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18361	2853045	56275938	10731	18716										
ZNF555	148254	broad.mit.edu	37	chr19	2853297	2853297	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtcacccctcctcctttCgaggacacatgagggtgcac	9	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2853297C>T	ENST00000334241.4	+	4	1372	c.1234C>T	c.(1234-1236)Cga>Tga	p.R412*	ZNF555_ENST00000591539.1_Nonsense_Mutation_p.R411*|AC006130.3_ENST00000589365.1_RNA	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R412*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		CTCCTCCTTTCGAGGACACAT	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											66	55	59					19																	2853297		2203	4300	6503	2804297	SO:0001587	stop_gained	148254			AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"Zinc fingers, C2H2-type", "-"	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.1234C>T	19.37:g.2853297C>T	ENSP00000334853:p.Arg412*		2804297	A8KA89|K7EQM2|Q8NA46|Q96MP1	Nonsense_Mutation	SNP	ENST00000334241.4	37	CCDS12096.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693948	0.88735	.	.	ENSG00000186300	ENST00000334241;ENST00000382127	.	.	.	3.22	-0.976	0.10286	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	9.424	0.38567	0.6966:0.3034:0.0:0.0	.	.	.	.	X	412;411	.	ENSP00000334853:R412X	R	+	1	2	ZNF555	2804297	0.000000	0.05858	0.001000	0.08648	0.540000	0.34992	-0.156000	0.10100	0.139000	0.18822	0.561000	0.74099	CGA		0.468	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791		T	2853297	C	T	2853297	4	4	61	1	0	0	0	0	0	1	0	0	18025	876	31	1	1248	1	ZNF555	19	2853297	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252	2853297	56275686	10732	18717										
ZNF556	80032	broad.mit.edu	37	chr19	2878237	2878237	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacagaagcccagtaaatgCgaaaaatgtgggaaagcttt	12	6	0	1	rs540339084		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2878237C>T	ENST00000307635.2	+	4	1368	c.1281C>T	c.(1279-1281)tgC>tgT	p.C427C	ZNF556_ENST00000586426.1_Silent_p.C426C	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	427					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C427C(4)		endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		CCAGTAAATGCGAAAAATGTG	0.448																																																4	Substitution - coding silent(4)	large_intestine(2)|prostate(1)|endometrium(1)	19											101	112	108					19																	2878237		2203	4300	6503	2829237	SO:0001819	synonymous_variant	80032			BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.1281C>T	19.37:g.2878237C>T			2829237	Q96GM3	Silent	SNP	ENST00000307635.2	37	CCDS12097.1																																																																																				0.448	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		T	2878237	C	T	2878237	2	4	61	1	0	0	0	0	0	0	0	1	18026	776	27	1		1	ZNF556	19	2878237	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24940	2878237	56250746	10733	18718										
ZNF57	126295	broad.mit.edu	37	chr19	2915584	2915584	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtgggctttgctggattCtgctcagagggacctctaca	14	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2915584C>A	ENST00000306908.5	+	2	216	c.68C>A	c.(67-69)tCt>tAt	p.S23Y	ZNF57_ENST00000523428.1_5'UTR|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S23Y(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGCTGGATTCTGCTCAGAGG	0.522																																					NSCLC(150;910 1964 4303 10464 26498)											1	Substitution - Missense(1)	large_intestine(1)	19											180	161	168					19																	2915584		2203	4298	6501	2866584	SO:0001583	missense	126295			M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"Zinc fingers, C2H2-type", "-"	13125	protein-coding gene	gene with protein product			"zinc finger protein 424"	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.68C>A	19.37:g.2915584C>A	ENSP00000303696:p.Ser23Tyr		2866584	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284205	0.40394	.	.	ENSG00000171970	ENST00000306908;ENST00000395204	T	0.01918	4.56	2.12	-0.482	0.12078	Krueppel-associated box (4);	.	.	.	.	T	0.03095	0.0091	M	0.81942	2.565	0.09310	N	0.999998	P	0.44195	0.828	B	0.35278	0.199	T	0.33701	-0.9858	9	0.49607	T	0.09	.	4.2291	0.10594	0.2652:0.4751:0.2597:0.0	.	23	Q68EA5	ZNF57_HUMAN	Y	23	ENSP00000303696:S23Y	ENSP00000303696:S23Y	S	+	2	0	ZNF57	2866584	0.000000	0.05858	0.009000	0.14445	0.985000	0.73830	-1.905000	0.01591	-0.181000	0.10619	0.407000	0.27541	TCT		0.522	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		A	2915584	C	A	2915584	3	1	61	1	0	0	0	0	1	0	0	0	18040	913	32	2	74	2	ZNF57	19	2915584	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37347	2915584	56213399	10734	18719										
ZNF77	58492	broad.mit.edu	37	chr19	2934713	2934713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcactcagagggtttagcttCggtagggtaactcttgtgca	13	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2934713C>T	ENST00000314531.4	-	4	504	c.412G>A	c.(412-414)Gaa>Aaa	p.E138K		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E138K(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTTTAGCTTCGGTAGGGTAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19											138	127	131					19																	2934713		2203	4300	6503	2885713	SO:0001583	missense	58492			X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"Zinc fingers, C2H2-type", "-"	13150	protein-coding gene	gene with protein product		194551	"zinc finger protein 77 (pT1)"			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.412G>A	19.37:g.2934713C>T	ENSP00000319053:p.Glu138Lys		2885713	Q86XJ3|Q9NPP0	Missense_Mutation	SNP	ENST00000314531.4	37	CCDS12099.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.898926	0.33535	.	.	ENSG00000175691	ENST00000341064;ENST00000314531	T	0.15139	2.45	2.77	1.72	0.24424	.	.	.	.	.	T	0.10766	0.0263	N	0.17723	0.515	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.26883	-1.0090	9	0.87932	D	0	.	7.135	0.25523	0.0:0.8569:0.0:0.1431	.	138	Q15935	ZNF77_HUMAN	K	30;138	ENSP00000319053:E138K	ENSP00000319053:E138K	E	-	1	0	ZNF77	2885713	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	1.786000	0.38694	0.505000	0.28104	0.491000	0.48974	GAA		0.512	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		T	2934713	C	T	2934713	3	4	61	1	0	0	0	0	1	0	0	0	18181	893	31	1	1229	1	ZNF77	19	2934713	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19129	2934713	56194270	10735	18720										
ZNF77	58492	broad.mit.edu	37	chr19	2936570	2936570	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctccagtgttatcaaatCtccaattttctccaaaaata	3	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2936570C>A	ENST00000314531.4	-	3	355	c.263G>T	c.(262-264)aGa>aTa	p.R88I	ZNF77_ENST00000588050.1_5'Flank	NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R88I(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		GTTATCAAATCTCCAATTTTC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											84	86	86					19																	2936570		2203	4300	6503	2887570	SO:0001583	missense	58492			X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"Zinc fingers, C2H2-type", "-"	13150	protein-coding gene	gene with protein product		194551	"zinc finger protein 77 (pT1)"			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.263G>T	19.37:g.2936570C>A	ENSP00000319053:p.Arg88Ile		2887570	Q86XJ3|Q9NPP0	Missense_Mutation	SNP	ENST00000314531.4	37	CCDS12099.1	.	.	.	.	.	.	.	.	.	.	C	9.821	1.185745	0.21870	.	.	ENSG00000175691	ENST00000314531	T	0.08193	3.12	2.52	-2.87	0.05700	Krueppel-associated box (1);	.	.	.	.	T	0.04227	0.0117	N	0.24115	0.695	0.09310	N	1	B	0.17465	0.022	B	0.12156	0.007	T	0.42599	-0.9442	9	0.36615	T	0.2	.	0.4987	0.00576	0.2765:0.2086:0.3168:0.1981	.	88	Q15935	ZNF77_HUMAN	I	88	ENSP00000319053:R88I	ENSP00000319053:R88I	R	-	2	0	ZNF77	2887570	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-1.060000	0.03475	-0.746000	0.04766	0.484000	0.47621	AGA		0.458	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		A	2936570	C	A	2936570	3	1	61	1	0	0	0	0	1	0	0	0	18181	913	32	2	1382	2	ZNF77	19	2936570	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1857	2936570	56192413	10736	18721										
TLE6	79816	broad.mit.edu	37	chr19	2987915	2987915	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccccaggccacctgaggcCtcctccagtccccctgaggg	11	20	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:2987915C>A	ENST00000246112.4	+	10	846	c.645C>A	c.(643-645)gcC>gcA	p.A215A	TLE6_ENST00000478073.2_3'UTR|TLE6_ENST00000452088.1_Silent_p.A92A	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	215					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.A92A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		CACCTGAGGCCTCCTCCAGTC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	19											30	30	30					19																	2987915		2203	4300	6503	2938915	SO:0001819	synonymous_variant	79816			AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"WD repeat domain containing"	30788	protein-coding gene	gene with protein product		612399	"transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.645C>A	19.37:g.2987915C>A			2938915	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1																																																																																				0.657	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760		A	2987915	C	A	2987915	2	1	61	1	0	0	0	0	0	0	0	1	15981	668	24	2		2	TLE6	19	2987915	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51345	2987915	56141068	10737	18722										
ATCAY	85300	broad.mit.edu	37	chr19	3910853	3910853	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccacccctcgtggttcattCggactgtgctggccatctct	9	15	2	0	rs376658701		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:3910853C>T	ENST00000450849.2	+	8	1299	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	ATCAY_ENST00000398448.3_Missense_Mutation_p.R284W|ATCAY_ENST00000600960.1_Missense_Mutation_p.R278W|ATCAY_ENST00000301260.6_Missense_Mutation_p.R278W	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.R278W(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		GTGGTTCATTCGGACTGTGCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	TRP/ARG	0,4270		0,0,2135	119	127	124		832	4.3	1	19		124	1,8483		0,1,4241	no	missense	ATCAY	NM_033064.4	101	0,1,6376	TT,TC,CC		0.0118,0.0,0.0078	probably-damaging	278/372	3910853	1,12753	2135	4242	6377	3861853	SO:0001583	missense	85300				CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.832C>T	19.37:g.3910853C>T	ENSP00000390941:p.Arg278Trp		3861853	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	37	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366995	0.82463	0.0	1.18E-4	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.67523	-0.27;-0.27;-0.27	4.35	4.35	0.52113	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.063315	0.64402	D	0.000008	D	0.84174	0.5414	M	0.91717	3.235	0.50813	D	0.999898	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87653	0.2529	10	0.87932	D	0	-2.6229	12.7004	0.57029	0.165:0.835:0.0:0.0	.	284;278;278	B4DS11;Q86WG3-3;Q86WG3	.;.;ATCAY_HUMAN	W	278;278;278;284;256	ENSP00000390941:R278W;ENSP00000301260:R278W;ENSP00000381466:R284W	ENSP00000301260:R278W	R	+	1	2	ATCAY	3861853	0.998000	0.40836	0.999000	0.59377	0.977000	0.68977	3.866000	0.56040	1.970000	0.57323	0.456000	0.33151	CGG		0.592	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			T	3910853	C	T	3910853	3	4	61	1	0	0	0	0	1	0	0	0	1078	875	31	1	858	1	ATCAY	19	3910853	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	922938	3910853	55218130	10738	18723										
CREB3L3	84699	broad.mit.edu	37	chr19	4171432	4171432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctccatcagcccttttgGccccaacaaaaccgagagcc	6	19	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4171432G>A	ENST00000078445.2	+	9	1175	c.1028G>A	c.(1027-1029)gGc>gAc	p.G343D	CREB3L3_ENST00000252587.3_Missense_Mutation_p.A232T|CREB3L3_ENST00000595923.1_Missense_Mutation_p.G342D|CREB3L3_ENST00000602257.1_Missense_Mutation_p.G341D|CREB3L3_ENST00000602147.1_Nonsense_Mutation_p.W307*	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	343					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	p.G343D(1)		breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCCCTTTTGGCCCCAACAAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	79	82					19																	4171432		2203	4300	6503	4122432	SO:0001583	missense	84699				CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1028G>A	19.37:g.4171432G>A	ENSP00000078445:p.Gly343Asp		4122432	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	37	CCDS12121.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.994|0.994	-0.693182|-0.693182	0.03303|0.03303	.|.	.|.	ENSG00000060566|ENSG00000060566	ENST00000252587|ENST00000078445;ENST00000381943	T|D	0.77750|0.82619	-1.12|-1.63	4.68|4.68	1.1|1.1	0.20463|0.20463	.|.	.|0.843447	.|0.11054	.|N	.|0.604698	T|T	0.69151|0.69151	0.3079|0.3079	L|L	0.31926|0.31926	0.97|0.97	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.06786	.|0.0;0.001;0.001	.|B;B;B	.|0.06405	.|0.0;0.002;0.001	T|T	0.51028|0.51028	-0.8757|-0.8757	7|10	0.87932|0.22706	D|T	0|0.39	-0.9737|-0.9737	3.4072|3.4072	0.07345|0.07345	0.1558:0.4306:0.3164:0.0972|0.1558:0.4306:0.3164:0.0972	.|.	.|341;342;343	.|B7ZL69;Q68CJ9-2;Q68CJ9	.|.;.;CR3L3_HUMAN	T|D	232|343;301	ENSP00000252587:A232T|ENSP00000078445:G343D	ENSP00000252587:A232T|ENSP00000078445:G343D	A|G	+|+	1|2	0|0	CREB3L3|CREB3L3	4122432|4122432	0.004000|0.004000	0.15560|0.15560	0.019000|0.019000	0.16419|0.16419	0.178000|0.178000	0.23041|0.23041	1.536000|1.536000	0.36072|0.36072	0.031000|0.031000	0.15407|0.15407	-0.270000|-0.270000	0.10280|0.10280	GCC|GGC		0.617	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		A	4171432	G	A	4171432	3	1	61	1	0	0	0	0	1	0	0	0	3864	1203	42	3	1062	3	CREB3L3	19	4171432	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	260579	4171432	54957551	10739	18724										
CREB3L3	84699	broad.mit.edu	37	chr19	4171821	4171821	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccgcgaacctgaccaattCgacggaggagctggacaacg	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4171821C>T	ENST00000078445.2	+	10	1388	c.1241C>T	c.(1240-1242)tCg>tTg	p.S414L	CREB3L3_ENST00000252587.3_3'UTR|CREB3L3_ENST00000595923.1_Missense_Mutation_p.S413L|CREB3L3_ENST00000602257.1_Missense_Mutation_p.S412L|CREB3L3_ENST00000602147.1_3'UTR	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	414					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	p.S414L(1)		breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGACCAATTCGACGGAGGAG	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	19											39	43	42					19																	4171821		2203	4296	6499	4122821	SO:0001583	missense	84699				CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1241C>T	19.37:g.4171821C>T	ENSP00000078445:p.Ser414Leu		4122821	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	37	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.352141	0.24512	.	.	ENSG00000060566	ENST00000078445;ENST00000381943	D	0.83837	-1.77	3.83	-3.12	0.05282	.	2.409610	0.01449	N	0.015394	T	0.64649	0.2617	N	0.11560	0.145	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.002	B;B;B	0.06405	0.001;0.002;0.001	T	0.52586	-0.8556	10	0.22706	T	0.39	-35.7196	4.1348	0.10166	0.0:0.3465:0.3335:0.3199	.	412;413;414	B7ZL69;Q68CJ9-2;Q68CJ9	.;.;CR3L3_HUMAN	L	414;372	ENSP00000078445:S414L	ENSP00000078445:S414L	S	+	2	0	CREB3L3	4122821	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.266000	0.08631	-0.188000	0.10499	0.561000	0.74099	TCG		0.677	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4171821	C	T	4171821	3	4	61	1	0	0	0	0	1	0	0	0	3864	893	31	1	1279	1	CREB3L3	19	4171821	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	389	4171821	54957162	10740	18725										
TMIGD2	126259	broad.mit.edu	37	chr19	4298048	4298048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaggaatctctacggccGcccagcacacgtacgccccg	9	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4298048G>A	ENST00000301272.2	-	2	386	c.341C>T	c.(340-342)gCg>gTg	p.A114V	TMIGD2_ENST00000600114.1_Intron|TMIGD2_ENST00000600349.1_Intron|TMIGD2_ENST00000595645.1_Missense_Mutation_p.A114V	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	114	Ig-like.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.A114V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCTACGGCCGCCCAGCACAC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	89	86					19																	4298048		2203	4300	6503	4249048	SO:0001583	missense	126259			BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.341C>T	19.37:g.4298048G>A	ENSP00000301272:p.Ala114Val		4249048	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	.	.	.	.	.	.	.	.	.	.	G	0.446	-0.896254	0.02472	.	.	ENSG00000167664	ENST00000301272	T	0.14893	2.47	4.09	-5.9	0.02275	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.06690	0.0171	N	0.08118	0	0.09310	N	1	B;B	0.17852	0.019;0.024	B;B	0.17433	0.011;0.018	T	0.46610	-0.9179	9	0.08837	T	0.75	.	11.3834	0.49771	0.7542:0.0:0.2458:0.0	.	114;114	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	V	114	ENSP00000301272:A114V	ENSP00000301272:A114V	A	-	2	0	TMIGD2	4249048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.101000	0.03336	-0.937000	0.03719	-0.678000	0.03780	GCG		0.662	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615		A	4298048	G	A	4298048	3	1	61	1	0	0	0	0	1	0	0	0	16270	1087	38	1	523	1	TMIGD2	19	4298048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	126227	4298048	54830935	10741	18726										
FSD1	79187	broad.mit.edu	37	chr19	4305965	4305965	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccctgaggaagatcatcaAaacactggctgtgaagaatg	12	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4305965A>C	ENST00000221856.6	+	2	185	c.38A>C	c.(37-39)aAa>aCa	p.K13T	FSD1_ENST00000597590.1_Missense_Mutation_p.K13T	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	13					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.K13T(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGATCATCAAAACACTGGCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											142	129	133					19																	4305965		2203	4300	6503	4256965	SO:0001583	missense	79187			AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.38A>C	19.37:g.4305965A>C	ENSP00000221856:p.Lys13Thr		4256965	B2RDT0|Q9BXN0|Q9HAG4	Missense_Mutation	SNP	ENST00000221856.6	37	CCDS12127.1	.	.	.	.	.	.	.	.	.	.	A	0.411	-0.913407	0.02415	.	.	ENSG00000105255	ENST00000221856	T	0.40476	1.03	4.22	3.18	0.36537	B-box, C-terminal (1);	0.218384	0.37348	N	0.002132	T	0.08980	0.0222	N	0.00146	-1.995	0.21652	N	0.999605	B	0.02656	0.0	B	0.01281	0.0	T	0.36456	-0.9747	10	0.02654	T	1	.	11.0699	0.47997	0.1894:0.8106:0.0:0.0	.	13	Q9BTV5	FSD1_HUMAN	T	13	ENSP00000221856:K13T	ENSP00000221856:K13T	K	+	2	0	FSD1	4256965	0.996000	0.38824	0.708000	0.30435	0.455000	0.32408	3.422000	0.52749	0.771000	0.33359	-0.369000	0.07265	AAA		0.527	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		C	4305965	A	C	4305965	3	2	61	1	0	0	0	0	1	0	0	0	6089	14	1	4	44	4	FSD1	19	4305965	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7917	4305965	54823018	10742	18727										
STAP2	55620	broad.mit.edu	37	chr19	4327184	4327184	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctttttggtatgcgacaCgaaatagttgaccacggcgt	11	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4327184C>T	ENST00000594605.1	-	8	823	c.700G>A	c.(700-702)Gtg>Atg	p.V234M	STAP2_ENST00000600324.1_Missense_Mutation_p.V234M|STAP2_ENST00000597593.1_5'UTR	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	234	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.V234M(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		GTATGCGACACGAAATAGTTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	77	79					19																	4327184		2203	4300	6503	4278184	SO:0001583	missense	55620			AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.700G>A	19.37:g.4327184C>T	ENSP00000471052:p.Val234Met		4278184	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.973309	0.53614	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	5.09	3.83	0.44106	SH2 motif (2);	0.062468	0.64402	D	0.000007	T	0.67608	0.2911	L	0.58810	1.83	0.38720	D	0.953427	D;D	0.76494	0.997;0.999	P;D	0.67900	0.905;0.954	T	0.72010	-0.4419	9	0.87932	D	0	-17.5017	9.4156	0.38519	0.0:0.8842:0.0:0.1158	.	234;234	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	M	234	.	ENSP00000317912:V234M	V	-	1	0	STAP2	4278184	0.995000	0.38212	0.991000	0.47740	0.418000	0.31294	3.064000	0.49986	2.377000	0.81083	0.555000	0.69702	GTG		0.612	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841		T	4327184	C	T	4327184	3	4	61	1	0	0	0	0	1	0	0	0	15292	536	19	1	673	1	STAP2	19	4327184	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21219	4327184	54801799	10743	18728										
CHAF1A	10036	broad.mit.edu	37	chr19	4409115	4409115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttttaagaaatagaatcGaaaccagtattggccagagc	8	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4409115G>A	ENST00000301280.5	+	3	420	c.319G>A	c.(319-321)Gaa>Aaa	p.E107K		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	107	Binds to CBX1 chromo shadow domain.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)	p.E107K(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAATAGAATCGAAACCAGTAT	0.423								Chromatin Structure																																								1	Substitution - Missense(1)	large_intestine(1)	19											97	105	103					19																	4409115		2203	4300	6503	4360115	SO:0001583	missense	10036			U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.319G>A	19.37:g.4409115G>A	ENSP00000301280:p.Glu107Lys		4360115	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	37	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	3.499	-0.102307	0.06967	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.44083	0.93	4.96	-4.16	0.03869	.	.	.	.	.	T	0.15522	0.0374	N	0.01742	-0.745	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21999	-1.0229	9	0.87932	D	0	-2.5556	6.9635	0.24610	0.3447:0.3763:0.279:0.0	.	107	Q13111	CAF1A_HUMAN	K	107	ENSP00000301280:E107K	ENSP00000301280:E107K	E	+	1	0	CHAF1A	4360115	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.465000	0.22004	-1.397000	0.02068	-0.258000	0.10820	GAA		0.423	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		A	4409115	G	A	4409115	3	1	61	1	0	0	0	0	1	0	0	0	3317	1059	37	1	329	1	CHAF1A	19	4409115	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81931	4409115	54719868	10744	18729										
CHAF1A	10036	broad.mit.edu	37	chr19	4432007	4432007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgaaggccaaggagtgggAcgagttcctggctaagggga	17	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4432007A>G	ENST00000301280.5	+	12	2107	c.2006A>G	c.(2005-2007)gAc>gGc	p.D669G	CTB-50L17.5_ENST00000590159.1_RNA|CHAF1A_ENST00000587368.1_3'UTR	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	669	Binds to p60.|Necessary for homodimerization and competence for chromatin assembly.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)	p.D669G(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGGAGTGGGACGAGTTCCTG	0.562								Chromatin Structure																																								1	Substitution - Missense(1)	large_intestine(1)	19											100	92	95					19																	4432007		2203	4300	6503	4383007	SO:0001583	missense	10036			U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2006A>G	19.37:g.4432007A>G	ENSP00000301280:p.Asp669Gly		4383007	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	37	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596462	0.66332	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.34072	1.38	4.71	4.71	0.59529	.	.	.	.	.	T	0.54334	0.1852	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	T	0.58335	-0.7654	9	0.87932	D	0	-50.152	13.7872	0.63117	1.0:0.0:0.0:0.0	.	669	Q13111	CAF1A_HUMAN	G	669	ENSP00000301280:D669G	ENSP00000301280:D669G	D	+	2	0	CHAF1A	4383007	1.000000	0.71417	0.987000	0.45799	0.281000	0.26958	8.859000	0.92264	2.094000	0.63399	0.459000	0.35465	GAC		0.562	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		G	4432007	A	G	4432007	3	3	61	1	0	0	0	0	1	0	0	0	3317	275	10	4	2052	4	CHAF1A	19	4432007	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22892	4432007	54696976	10745	18730										
SEMA6B	10501	broad.mit.edu	37	chr19	4556998	4556998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccgacacacgtttatgtCgctggggttagatctccagg	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4556998C>T	ENST00000586582.1	-	5	644	c.334G>A	c.(334-336)Gac>Aac	p.D112N	SEMA6B_ENST00000586965.1_Missense_Mutation_p.D112N|SEMA6B_ENST00000301293.3_Missense_Mutation_p.D112N	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	112	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.D112N(1)		breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTTTATGTCGCTGGGGTTA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	49	55					19																	4556998		2203	4299	6502	4507998	SO:0001583	missense	10501			AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"Semaphorins"	10739	protein-coding gene	gene with protein product	"Sema VIb", "semaphorin Z", "semaphorin VIB"	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.334G>A	19.37:g.4556998C>T	ENSP00000467290:p.Asp112Asn		4507998	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724017	0.68959	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.25912	1.77	3.7	2.62	0.31277	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.137472	0.49305	U	0.000158	T	0.46054	0.1373	M	0.67953	2.075	0.40699	D	0.982469	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.49000	-0.8984	10	0.87932	D	0	.	11.2484	0.49010	0.1848:0.8152:0.0:0.0	.	112;112	B4DT36;Q9H3T3	.;SEM6B_HUMAN	N	112	ENSP00000301293:D112N	ENSP00000301292:D112N	D	-	1	0	SEMA6B	4507998	1.000000	0.71417	0.989000	0.46669	0.329000	0.28539	7.016000	0.76393	0.864000	0.35578	0.313000	0.20887	GAC		0.642	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		T	4556998	C	T	4556998	3	4	61	1	0	0	0	0	1	0	0	0	14077	884	31	1	2384	1	SEMA6B	19	4556998	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124991	4556998	54571985	10746	18731										
FEM1A	55527	broad.mit.edu	37	chr19	4793084	4793084	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacgccgactcgggcaatttCgagcgctgcatccgcttgtg	12	13	0	0	rs377569506		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:4793084C>T	ENST00000269856.3	+	1	1357	c.1218C>T	c.(1216-1218)ttC>ttT	p.F406F	AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	406					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)	p.F406F(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		CGGGCAATTTCGAGCGCTGCA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		1,4405	2.1+/-5.4	0,1,2202	61	58	59		1218	-0.4	1	19		59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FEM1A	NM_018708.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		406/670	4793084	2,13004	2203	4300	6503	4744084	SO:0001819	synonymous_variant	55527			BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1218C>T	19.37:g.4793084C>T			4744084	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	37	CCDS12135.1																																																																																				0.622	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			T	4793084	C	T	4793084	2	4	61	1	0	0	0	0	0	0	0	1	5828	883	31	1		1	FEM1A	19	4793084	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	236086	4793084	54335899	10747	18732										
ZNRF4	148066	broad.mit.edu	37	chr19	5455803	5455803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccgcgcaggcagtggtaCgggccgtgctggaagacaac	16	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5455803C>T	ENST00000222033.4	+	1	378	c.301C>T	c.(301-303)Cgg>Tgg	p.R101W		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	101						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R101W(1)		NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GGCAGTGGTACGGGCCGTGCT	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	19											46	56	53					19																	5455803		2131	4226	6357	5406803	SO:0001583	missense	148066			AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"RING-type (C3HC4) zinc fingers"	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.301C>T	19.37:g.5455803C>T	ENSP00000222033:p.Arg101Trp		5406803	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640579	0.29157	.	.	ENSG00000105428	ENST00000222033	T	0.04917	3.53	3.63	3.63	0.41609	.	1.017090	0.07895	U	0.971786	T	0.21921	0.0528	M	0.66939	2.045	0.09310	N	0.999999	D	0.89917	1.0	D	0.65874	0.939	T	0.09975	-1.0650	10	0.54805	T	0.06	.	10.79	0.46428	0.0:1.0:0.0:0.0	.	101	Q8WWF5	ZNRF4_HUMAN	W	101	ENSP00000222033:R101W	ENSP00000222033:R101W	R	+	1	2	ZNRF4	5406803	0.851000	0.29673	0.045000	0.18777	0.010000	0.07245	1.822000	0.39052	1.576000	0.49790	0.313000	0.20887	CGG		0.692	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		T	5455803	C	T	5455803	3	4	61	1	0	0	0	0	1	0	0	0	18253	527	19	1	303	1	ZNRF4	19	5455803	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	662719	5455803	53673180	10748	18733										
SAFB2	9667	broad.mit.edu	37	chr19	5592762	5592762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacaagaccactgacctgtCgatggcgtggtcctggtact	13	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5592762C>T	ENST00000252542.4	-	16	2608	c.2344G>A	c.(2344-2346)Gac>Aac	p.D782N		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	782	Arg-rich.|Interacts with SAFB1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D782N(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		ACTGACCTGTCGATGGCGTGG	0.602																																					Ovarian(127;888 1728 23957 44128 52668)											1	Substitution - Missense(1)	large_intestine(1)	19											120	84	96					19																	5592762		2203	4300	6503	5543762	SO:0001583	missense	9667			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2344G>A	19.37:g.5592762C>T	ENSP00000252542:p.Asp782Asn		5543762	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.225013	0.39300	.	.	ENSG00000130254	ENST00000252542	T	0.11712	2.75	4.76	3.73	0.42828	.	0.207562	0.33290	N	0.005069	T	0.13798	0.0334	M	0.71036	2.16	0.47778	D	0.999517	B	0.28470	0.213	B	0.17433	0.018	T	0.02661	-1.1127	10	0.48119	T	0.1	.	12.8632	0.57926	0.0:0.9206:0.0:0.0794	.	782	Q14151	SAFB2_HUMAN	N	782	ENSP00000252542:D782N	ENSP00000252542:D782N	D	-	1	0	SAFB2	5543762	0.999000	0.42202	0.277000	0.24703	0.198000	0.23893	4.419000	0.59835	0.999000	0.39023	0.561000	0.74099	GAC		0.602	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		T	5592762	C	T	5592762	3	4	61	1	0	0	0	0	1	0	0	0	13844	884	31	1	541	1	SAFB2	19	5592762	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136959	5592762	53536221	10749	18734										
SAFB2	9667	broad.mit.edu	37	chr19	5604628	5604628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccacagaatgatgtctgtCgacactcgataatttttcct	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5604628C>T	ENST00000252542.4	-	11	1789	c.1525G>A	c.(1525-1527)Gac>Aac	p.D509N	SAFB2_ENST00000591310.1_5'UTR	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	509	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D509N(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TGATGTCTGTCGACACTCGAT	0.433																																					Ovarian(127;888 1728 23957 44128 52668)											1	Substitution - Missense(1)	large_intestine(1)	19											94	86	89					19																	5604628		2203	4300	6503	5555628	SO:0001583	missense	9667			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.1525G>A	19.37:g.5604628C>T	ENSP00000252542:p.Asp509Asn		5555628	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.535625	0.85812	.	.	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542	T	0.22336	1.96	5.05	5.05	0.67936	.	0.095453	0.45606	D	0.000351	T	0.23846	0.0577	L	0.43923	1.385	0.53688	D	0.999979	D	0.56746	0.977	B	0.43301	0.415	T	0.02263	-1.1186	10	0.56958	D	0.05	-35.5764	18.5985	0.91239	0.0:1.0:0.0:0.0	.	509	Q14151	SAFB2_HUMAN	N	405;260;509;509	ENSP00000252542:D509N	ENSP00000252542:D509N	D	-	1	0	SAFB2	5555628	1.000000	0.71417	0.868000	0.34077	0.498000	0.33706	5.365000	0.66116	2.621000	0.88768	0.555000	0.69702	GAC		0.433	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		T	5604628	C	T	5604628	3	4	61	1	0	0	0	0	1	0	0	0	13844	884	31	1	1380	1	SAFB2	19	5604628	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11866	5604628	53524355	10750	18735										
SAFB2	9667	broad.mit.edu	37	chr19	5613529	5613529	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaagtgttcttaaatccttCcccatccacctgaaaaacaa	3	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5613529C>A	ENST00000252542.4	-	5	817	c.553G>T	c.(553-555)Gaa>Taa	p.E185*	SAFB2_ENST00000591310.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	185					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E185*(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TTAAATCCTTCCCCATCCACC	0.438																																					Ovarian(127;888 1728 23957 44128 52668)											1	Substitution - Nonsense(1)	large_intestine(1)	19											125	106	112					19																	5613529		2203	4300	6503	5564529	SO:0001587	stop_gained	9667			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.553G>T	19.37:g.5613529C>A	ENSP00000252542:p.Glu185*		5564529	B4DKG3|Q8TB13	Nonsense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	36	5.643145	0.96704	.	.	ENSG00000130254	ENST00000252542;ENST00000536849	.	.	.	5.47	4.41	0.53225	.	0.358200	0.23494	N	0.047578	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-13.1277	13.1871	0.59688	0.0:0.8398:0.1602:0.0	.	.	.	.	X	185;164	.	ENSP00000252542:E185X	E	-	1	0	SAFB2	5564529	0.320000	0.24616	0.129000	0.21949	0.425000	0.31504	1.837000	0.39201	1.280000	0.44463	0.563000	0.77884	GAA		0.438	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		A	5613529	C	A	5613529	4	1	61	1	0	0	0	0	0	1	0	0	13844	864	30	2	2376	2	SAFB2	19	5613529	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8901	5613529	53515454	10751	18736										
TMEM146	257062	broad.mit.edu	37	chr19	5745965	5745965	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccccctcaaccggagtttCgggctgtcttttgactataa	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5745965C>T	ENST00000381624.3	+	9	760	c.699C>T	c.(697-699)ttC>ttT	p.F233F	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	233					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.F233F(3)									ACCGGAGTTTCGGGCTGTCTT	0.532																																																3	Substitution - coding silent(3)	large_intestine(3)	19											167	160	163					19																	5745965		1888	4121	6009	5696965	SO:0001819	synonymous_variant	257062			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.699C>T	19.37:g.5745965C>T			5696965	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																				0.532	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5745965	C	T	5745965	2	4	61	1	0	0	0	0	0	0	0	1	16099	883	31	1		1	TMEM146	19	5745965	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132436	5745965	53383018	10752	18737										
TMEM146	257062	broad.mit.edu	37	chr19	5754252	5754252	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaggcacatccctgattcCtctggtaagtacatcttaat	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5754252C>A	ENST00000381624.3	+	13	1335	c.1274C>A	c.(1273-1275)cCt>cAt	p.P425H	CATSPERD_ENST00000381614.2_Missense_Mutation_p.P83H|CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	425					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.P425H(1)									TCCCTGATTCCTCTGGTAAGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											117	119	118					19																	5754252		1985	4173	6158	5705252	SO:0001583	missense	257062			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1274C>A	19.37:g.5754252C>A	ENSP00000371037:p.Pro425His		5705252	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477732	0.44044	.	.	ENSG00000174898	ENST00000394548;ENST00000381624;ENST00000381614;ENST00000309164;ENST00000381613	T;T	0.25250	1.81;1.81	3.53	3.53	0.40419	.	0.000000	0.40554	N	0.001074	T	0.44953	0.1318	M	0.64997	1.995	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.982;1.0	T	0.15407	-1.0438	10	0.87932	D	0	-22.3753	10.7762	0.46350	0.0:1.0:0.0:0.0	.	351;425	B7WNK5;Q86XM0	.;TM146_HUMAN	H	351;425;83;96;94	ENSP00000371037:P425H;ENSP00000371027:P83H	ENSP00000310546:P96H	P	+	2	0	TMEM146	5705252	0.008000	0.16893	0.009000	0.14445	0.008000	0.06430	1.607000	0.36836	1.993000	0.58246	0.549000	0.68633	CCT		0.493	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		A	5754252	C	A	5754252	3	1	61	1	0	0	0	0	1	0	0	0	16099	681	24	2	1324	2	TMEM146	19	5754252	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8287	5754252	53374731	10753	18738										
TMEM146	257062	broad.mit.edu	37	chr19	5776306	5776306	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttatgtcttctacatttcGatcgtggatccgtactacag	7	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:5776306G>A	ENST00000381624.3	+	21	2137	c.2076G>A	c.(2074-2076)tcG>tcA	p.S692S	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	692					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.S692S(1)									TCTACATTTCGATCGTGGATC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											85	84	84					19																	5776306		1928	4129	6057	5727306	SO:0001819	synonymous_variant	257062			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2076G>A	19.37:g.5776306G>A			5727306	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																				0.587	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		A	5776306	G	A	5776306	2	1	61	1	0	0	0	0	0	0	0	1	16099	1045	37	1		1	TMEM146	19	5776306	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22054	5776306	53352677	10754	18739										
RFX2	5990	broad.mit.edu	37	chr19	6016224	6016224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggtagtggttgtaaagaGaacttctggggagactcaca	14	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6016224G>T	ENST00000303657.5	-	7	805	c.656C>A	c.(655-657)tCt>tAt	p.S219Y	CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000359161.3_Missense_Mutation_p.S219Y|RFX2_ENST00000592546.1_Missense_Mutation_p.S194Y	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	219					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S219Y(1)		breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GTTGTAAAGAGAACTTCTGGG	0.512																																					Colon(38;171 817 19800 47433 48051)											1	Substitution - Missense(1)	large_intestine(1)	19											96	90	92					19																	6016224		2203	4300	6503	5967224	SO:0001583	missense	5990				CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"trans-acting regulatory factor 2", "DNA binding protein RFX2", "HLA class II regulatory factor RFX2"	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.656C>A	19.37:g.6016224G>T	ENSP00000306335:p.Ser219Tyr		5967224	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151979	0.57151	.	.	ENSG00000087903	ENST00000303657;ENST00000359161	D	0.82803	-1.65	4.64	4.64	0.57946	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.84302	0.5442	N	0.24115	0.695	0.80722	D	1	D;D	0.59357	0.985;0.98	P;P	0.62649	0.905;0.871	D	0.87080	0.2165	10	0.87932	D	0	-13.228	16.4582	0.84029	0.0:0.0:1.0:0.0	.	194;219	P48378-2;P48378	.;RFX2_HUMAN	Y	219;194	ENSP00000306335:S219Y	ENSP00000306335:S219Y	S	-	2	0	RFX2	5967224	1.000000	0.71417	0.091000	0.20842	0.118000	0.20060	9.602000	0.98312	2.286000	0.76751	0.561000	0.74099	TCT		0.512	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		T	6016224	G	T	6016224	3	4	61	1	0	0	0	0	1	0	0	0	13300	942	33	2	1563	2	RFX2	19	6016224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	239918	6016224	53112759	10755	18740										
ACSBG2	81616	broad.mit.edu	37	chr19	6151751	6151751	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttccacggagttggtatcCtggggtttaactctgcagag	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6151751C>A	ENST00000586696.1	+	4	607	c.331C>A	c.(331-333)Ctg>Atg	p.L111M	ACSBG2_ENST00000252669.5_Missense_Mutation_p.L111M|ACSBG2_ENST00000588304.1_Missense_Mutation_p.L61M|ACSBG2_ENST00000588485.1_5'UTR|ACSBG2_ENST00000591403.1_Missense_Mutation_p.L111M			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	111					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.L111M(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTTGGTATCCTGGGGTTTAA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											160	126	138					19																	6151751		2203	4300	6503	6102751	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.331C>A	19.37:g.6151751C>A	ENSP00000465589:p.Leu111Met		6102751	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.140968	0.77775	.	.	ENSG00000130377	ENST00000252669	T	0.46063	0.88	4.67	3.62	0.41486	AMP-dependent synthetase/ligase (1);	0.000000	0.27622	N	0.018557	T	0.54647	0.1871	L	0.48218	1.51	0.58432	D	0.999996	P;D	0.65815	0.933;0.995	P;D	0.70016	0.897;0.967	T	0.55598	-0.8116	10	0.59425	D	0.04	-21.488	12.2343	0.54505	0.1715:0.8285:0.0:0.0	.	111;111	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	M	111	ENSP00000252669:L111M	ENSP00000252669:L111M	L	+	1	2	ACSBG2	6102751	0.998000	0.40836	1.000000	0.80357	0.967000	0.64934	0.847000	0.27696	1.074000	0.40909	0.455000	0.32223	CTG		0.458	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		A	6151751	C	A	6151751	3	1	61	1	0	0	0	0	1	0	0	0	174	680	24	2	341	2	ACSBG2	19	6151751	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	135527	6151751	52977232	10756	18741										
ACSBG2	81616	broad.mit.edu	37	chr19	6185583	6185583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaaactacagaggccatcGatgatgaaggctggctacac	11	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6185583G>A	ENST00000586696.1	+	11	1735	c.1459G>A	c.(1459-1461)Gat>Aat	p.D487N	ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000252669.5_Missense_Mutation_p.D487N|ACSBG2_ENST00000588304.1_Missense_Mutation_p.D437N|ACSBG2_ENST00000588485.1_Missense_Mutation_p.D300N|ACSBG2_ENST00000591403.1_Missense_Mutation_p.D487N			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	487					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.D487N(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGAGGCCATCGATGATGAAGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	19											160	147	151					19																	6185583		2203	4300	6503	6136583	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1459G>A	19.37:g.6185583G>A	ENSP00000465589:p.Asp487Asn		6136583	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016685	0.75161	.	.	ENSG00000130377	ENST00000252669	T	0.12465	2.68	4.53	3.49	0.39957	AMP-dependent synthetase/ligase (1);	0.318982	0.22583	N	0.058188	T	0.41650	0.1168	M	0.88181	2.935	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.986;0.999	T	0.45323	-0.9269	10	0.87932	D	0	-29.3308	11.4245	0.50003	0.0899:0.0:0.9101:0.0	.	487;487	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	N	487	ENSP00000252669:D487N	ENSP00000252669:D487N	D	+	1	0	ACSBG2	6136583	1.000000	0.71417	0.002000	0.10522	0.003000	0.03518	7.565000	0.82337	0.912000	0.36772	-0.300000	0.09419	GAT		0.552	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		A	6185583	G	A	6185583	3	1	61	1	0	0	0	0	1	0	0	0	174	1058	37	1	1497	1	ACSBG2	19	6185583	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33832	6185583	52943400	10757	18742										
ACSBG2	81616	broad.mit.edu	37	chr19	6187386	6187386	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcatcagtaacgccatgTtagtaggagataaactgaag	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6187386T>C	ENST00000586696.1	+	12	1909	c.1633T>C	c.(1633-1635)Tta>Cta	p.L545L	RFX2_ENST00000587700.1_5'Flank|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000252669.5_Silent_p.L545L|ACSBG2_ENST00000588304.1_Silent_p.L495L|ACSBG2_ENST00000588485.1_Silent_p.L358L|ACSBG2_ENST00000591403.1_Silent_p.L545L			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	545					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.L545L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TAACGCCATGTTAGTAGGAGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	19											130	117	121					19																	6187386		2203	4300	6503	6138386	SO:0001819	synonymous_variant	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1633T>C	19.37:g.6187386T>C			6138386	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Silent	SNP	ENST00000586696.1	37	CCDS12159.1																																																																																				0.478	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		C	6187386	T	C	6187386	2	2	61	1	0	0	0	0	0	0	0	1	174	1722	60	4		4	ACSBG2	19	6187386	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1803	6187386	52941597	10758	18743										
ACER1	125981	broad.mit.edu	37	chr19	6309769	6309769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgctgttgagggcgtaggCgttgaccgtgggccgcagga	18	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6309769C>T	ENST00000301452.4	-	4	504	c.427G>A	c.(427-429)Gcc>Acc	p.A143T		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	143					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)	p.A143T(1)		NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						AGGGCGTAGGCGTTGACCGTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											148	108	122					19																	6309769		2203	4300	6503	6260769	SO:0001583	missense	125981			AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.427G>A	19.37:g.6309769C>T	ENSP00000301452:p.Ala143Thr		6260769		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130218	0.77549	.	.	ENSG00000167769	ENST00000301452	T	0.46063	0.88	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.65913	0.2737	M	0.84511	2.7	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	T	0.72462	-0.4286	10	0.59425	D	0.04	-10.5348	14.6637	0.68891	0.0:1.0:0.0:0.0	.	143	Q8TDN7	ACER1_HUMAN	T	143	ENSP00000301452:A143T	ENSP00000301452:A143T	A	-	1	0	ACER1	6260769	1.000000	0.71417	0.382000	0.26119	0.618000	0.37518	5.029000	0.64121	2.059000	0.61396	0.542000	0.68232	GCC		0.607	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		T	6309769	C	T	6309769	3	4	61	1	0	0	0	0	1	0	0	0	138	768	27	1	379	1	ACER1	19	6309769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122383	6309769	52819214	10759	18744										
GTF2F1	2962	broad.mit.edu	37	chr19	6389607	6389607	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattcgggcatctcctcctcTtggtagattttcttgttgct	9	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6389607T>G	ENST00000394456.5	-	4	638	c.174A>C	c.(172-174)caA>caC	p.Q58H	GTF2F1_ENST00000429701.2_Missense_Mutation_p.Q30H|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	58					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.Q58H(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						TCTCCTCCTCTTGGTAGATTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											116	122	120					19																	6389607		2203	4300	6503	6340607	SO:0001583	missense	2962				CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"General transcription factors"	4652	protein-coding gene	gene with protein product		189968	"general transcription factor IIF, polypeptide 1 (74kD subunit)"			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.174A>C	19.37:g.6389607T>G	ENSP00000377969:p.Gln58His		6340607	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330518	0.60743	.	.	ENSG00000125651	ENST00000394456;ENST00000429701;ENST00000542045;ENST00000543921;ENST00000541263	T;T	0.47528	0.84;0.84	5.43	-4.78	0.03209	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.191058	0.45606	N	0.000343	T	0.48857	0.1523	L	0.53249	1.67	0.37098	D	0.899741	B;D	0.55605	0.051;0.972	B;P	0.54889	0.033;0.763	T	0.57277	-0.7839	10	0.49607	T	0.09	-33.901	12.1624	0.54110	0.113:0.751:0.0:0.136	.	30;58	E7EUG6;P35269	.;T2FA_HUMAN	H	58;30;118;31;58	ENSP00000377969:Q58H;ENSP00000392107:Q30H	ENSP00000377969:Q58H	Q	-	3	2	GTF2F1	6340607	0.446000	0.25665	0.966000	0.40874	0.737000	0.42083	-0.343000	0.07791	-0.839000	0.04212	0.533000	0.62120	CAA		0.607	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		G	6389607	T	G	6389607	3	3	61	1	0	0	0	0	1	0	0	0	6879	1606	56	4	1419	4	GTF2F1	19	6389607	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	79838	6389607	52739376	10760	18745										
SLC25A23	79085	broad.mit.edu	37	chr19	6457528	6457528	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacctgtgcaaaattttCtcagcctgctccagcgagat	7	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6457528C>T	ENST00000301454.4	-	3	463	c.357G>A	c.(355-357)gaG>gaA	p.E119E	SLC25A23_ENST00000334510.5_Silent_p.E119E|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	119	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)	p.E119E(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						GCAAAATTTTCTCAGCCTGCT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19											55	55	55					19																	6457528		2203	4300	6503	6408528	SO:0001819	synonymous_variant	79085			AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.357G>A	19.37:g.6457528C>T			6408528	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																				0.562	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		T	6457528	C	T	6457528	2	4	61	1	0	0	0	0	0	0	0	1	14523	912	32	3		3	SLC25A23	19	6457528	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67921	6457528	52671455	10761	18746										
DENND1C	79958	broad.mit.edu	37	chr19	6467766	6467766	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgggctttgtgggggccaGaatttgggggctttctggag	19	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6467766G>T	ENST00000381480.2	-	23	2267	c.2155C>A	c.(2155-2157)Ctg>Atg	p.L719M	DENND1C_ENST00000543576.1_Missense_Mutation_p.L675M	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	719					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.L719M(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GTGGGGGCCAGAATTTGGGGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											17	19	18					19																	6467766		1869	4100	5969	6418766	SO:0001583	missense	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.2155C>A	19.37:g.6467766G>T	ENSP00000370889:p.Leu719Met		6418766	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658376	0.67586	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.12255	2.87;2.7	3.76	3.76	0.43208	.	.	.	.	.	T	0.13415	0.0325	N	0.24115	0.695	0.09310	N	1	D	0.55385	0.971	P	0.49012	0.598	T	0.13255	-1.0516	9	0.30854	T	0.27	-1.2734	11.3301	0.49470	0.0:0.0:1.0:0.0	.	719	Q8IV53	DEN1C_HUMAN	M	719;675	ENSP00000370889:L719M;ENSP00000437805:L675M	ENSP00000370889:L719M	L	-	1	2	DENND1C	6418766	0.037000	0.19845	0.013000	0.15412	0.817000	0.46193	2.734000	0.47368	2.128000	0.65567	0.298000	0.19748	CTG		0.602	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		T	6467766	G	T	6467766	3	4	61	1	0	0	0	0	1	0	0	0	4439	933	33	2	254	2	DENND1C	19	6467766	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10238	6467766	52661217	10762	18747										
DENND1C	79958	broad.mit.edu	37	chr19	6475303	6475303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgggctgcagacgagtgcGtcgcggtaccccccgaagag	15	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6475303G>A	ENST00000381480.2	-	14	1147	c.1035C>T	c.(1033-1035)gaC>gaT	p.D345D	DENND1C_ENST00000591030.1_5'Flank|DENND1C_ENST00000543576.1_Silent_p.D301D	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	345	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.D345D(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						AGACGAGTGCGTCGCGGTACC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	19											23	29	27					19																	6475303		1993	4154	6147	6426303	SO:0001819	synonymous_variant	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1035C>T	19.37:g.6475303G>A			6426303	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Silent	SNP	ENST00000381480.2	37	CCDS45938.1																																																																																				0.652	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6475303	G	A	6475303	2	1	61	1	0	0	0	0	0	0	0	1	4439	1136	40	1		1	DENND1C	19	6475303	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7537	6475303	52653680	10763	18748										
DENND1C	79958	broad.mit.edu	37	chr19	6478850	6478850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcttgtaaaacacctcgaAccaaggcaggtggctgtgga	12	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6478850A>G	ENST00000381480.2	-	6	422	c.310T>C	c.(310-312)Ttc>Ctc	p.F104L	DENND1C_ENST00000591030.1_5'UTR|DENND1C_ENST00000543576.1_Missense_Mutation_p.F60L	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	104	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.F104L(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						AACACCTCGAACCAAGGCAGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	67	63					19																	6478850		2043	4181	6224	6429850	SO:0001583	missense	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.310T>C	19.37:g.6478850A>G	ENSP00000370889:p.Phe104Leu		6429850	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.428231	0.62844	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11712	2.75;2.75	4.98	4.98	0.66077	DENN (3);	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	M	0.79011	2.435	0.45307	D	0.998301	P	0.50943	0.94	P	0.62813	0.907	T	0.03957	-1.0989	10	0.72032	D	0.01	-13.9744	12.587	0.56423	1.0:0.0:0.0:0.0	.	104	Q8IV53	DEN1C_HUMAN	L	104;60	ENSP00000370889:F104L;ENSP00000437805:F60L	ENSP00000370889:F104L	F	-	1	0	DENND1C	6429850	1.000000	0.71417	0.997000	0.53966	0.201000	0.24016	6.007000	0.70731	1.873000	0.54277	0.260000	0.18958	TTC		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		G	6478850	A	G	6478850	3	3	61	1	0	0	0	0	1	0	0	0	4439	43	2	4	2167	4	DENND1C	19	6478850	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3547	6478850	52650133	10764	18749										
DENND1C	79958	broad.mit.edu	37	chr19	6479707	6479707	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcaaaagggaagcagaatTtaggcaccatctgcatagct	9	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6479707T>G	ENST00000381480.2	-	4	261	c.149A>C	c.(148-150)aAa>aCa	p.K50T	DENND1C_ENST00000591030.1_5'UTR|DENND1C_ENST00000543576.1_Missense_Mutation_p.K6T	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	50	UDENN.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.K50T(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GAAGCAGAATTTAGGCACCAT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											112	111	112					19																	6479707		1957	4142	6099	6430707	SO:0001583	missense	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.149A>C	19.37:g.6479707T>G	ENSP00000370889:p.Lys50Thr		6430707	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	t	18.40	3.616563	0.66672	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.41758	0.99;0.99	5.14	3.0	0.34707	uDENN (3);	0.164905	0.52532	N	0.000065	T	0.48943	0.1528	M	0.70595	2.14	0.25744	N	0.985127	P	0.41041	0.736	P	0.51297	0.665	T	0.43702	-0.9375	10	0.52906	T	0.07	-8.6976	4.1163	0.10083	0.0:0.1845:0.1787:0.6368	.	50	Q8IV53	DEN1C_HUMAN	T	50;6	ENSP00000370889:K50T;ENSP00000437805:K6T	ENSP00000370889:K50T	K	-	2	0	DENND1C	6430707	1.000000	0.71417	0.840000	0.33206	0.993000	0.82548	1.185000	0.32065	0.275000	0.22094	0.375000	0.23000	AAA		0.567	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		G	6479707	T	G	6479707	3	3	61	1	0	0	0	0	1	0	0	0	4439	1841	64	4	2336	4	DENND1C	19	6479707	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	857	6479707	52649276	10765	18750										
DENND1C	79958	broad.mit.edu	37	chr19	6480028	6480028	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggcagggcaggccgcttCgaagaaccaatcaaacacag	13	11	1	1	rs372498127		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6480028C>T	ENST00000381480.2	-	2	164	c.52G>A	c.(52-54)Gaa>Aaa	p.E18K	DENND1C_ENST00000591030.1_Intron|DENND1C_ENST00000543576.1_Intron	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	18					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.E18K(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CAGGCCGCTTCGAAGAACCAA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	LYS/GLU	0,3946		0,0,1973	37	43	41		52	3.9	1	19		41	1,8285		0,1,4142	no	missense	DENND1C	NM_024898.2	56	0,1,6115	TT,TC,CC		0.0121,0.0,0.0082	possibly-damaging	18/802	6480028	1,12231	1973	4143	6116	6431028	SO:0001583	missense	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.52G>A	19.37:g.6480028C>T	ENSP00000370889:p.Glu18Lys		6431028	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.086160	0.76642	0.0	1.21E-4	ENSG00000205744	ENST00000381480	T	0.12672	2.66	4.95	3.9	0.45041	uDENN (1);	0.000000	0.85682	D	0.000000	T	0.17874	0.0429	L	0.52759	1.655	0.80722	D	1	D	0.55385	0.971	P	0.51833	0.681	T	0.06267	-1.0836	10	0.10111	T	0.7	-16.5774	11.2578	0.49065	0.0:0.8147:0.1853:0.0	.	18	Q8IV53	DEN1C_HUMAN	K	18	ENSP00000370889:E18K	ENSP00000370889:E18K	E	-	1	0	DENND1C	6431028	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	3.389000	0.52516	1.055000	0.40461	0.558000	0.71614	GAA		0.612	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		T	6480028	C	T	6480028	3	4	61	1	0	0	0	0	1	0	0	0	4439	893	31	1	2441	1	DENND1C	19	6480028	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	321	6480028	52648955	10766	18751										
C3	718	broad.mit.edu	37	chr19	6712606	6712606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtcacgatggggatcccGctgcgctctgcctgcaccat	13	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6712606G>A	ENST00000245907.6	-	10	1124	c.1032C>T	c.(1030-1032)agC>agT	p.S344S		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	344					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.S344S(1)		breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGGGGATCCCGCTGCGCTCTG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											216	189	198					19																	6712606		2203	4300	6503	6663606	SO:0001819	synonymous_variant	718			J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1032C>T	19.37:g.6712606G>A			6663606	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																				0.587	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6712606	G	A	6712606	2	1	61	1	0	0	0	0	0	0	0	1	2210	1078	38	1		1	C3	19	6712606	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232578	6712606	52416377	10767	18752										
GPR108	56927	broad.mit.edu	37	chr19	6732521	6732521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacatgacggcaaggccttCgatggggtggccctggctgt	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6732521C>T	ENST00000264080.7	-	11	999	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K	GPR108_ENST00000430424.4_Missense_Mutation_p.E83K|GPR108_ENST00000598626.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	325						integral component of membrane (GO:0016021)		p.E325K(1)		breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						GCAAGGCCTTCGATGGGGTGG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	75	74					19																	6732521		2107	4207	6314	6683521	SO:0001583	missense	56927				CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"GPCR / Unclassified : 7TM orphan receptors"	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.973G>A	19.37:g.6732521C>T	ENSP00000264080:p.Glu325Lys		6683521	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065911	0.76187	.	.	ENSG00000125734	ENST00000264080;ENST00000430424	T	0.25414	1.8	4.02	2.98	0.34508	.	0.000000	0.64402	U	0.000009	T	0.45736	0.1357	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.41502	-0.9505	10	0.72032	D	0.01	-11.6071	7.7417	0.28845	0.0:0.8833:0.0:0.1167	.	325	Q9NPR9	GP108_HUMAN	K	325;83	ENSP00000264080:E325K	ENSP00000264080:E325K	E	-	1	0	GPR108	6683521	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	3.877000	0.56123	1.026000	0.39733	0.491000	0.48974	GAA		0.632	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2			T	6732521	C	T	6732521	3	4	61	1	0	0	0	0	1	0	0	0	6644	893	31	1	690	1	GPR108	19	6732521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19915	6732521	52396462	10768	18753										
GPR108	56927	broad.mit.edu	37	chr19	6734027	6734027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccgaaacctgaatcactgCgggtgttgacttgggcttgc	12	12	1	2	rs369806355		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6734027C>T	ENST00000264080.7	-	6	564	c.538G>A	c.(538-540)Gca>Aca	p.A180T	GPR108_ENST00000430424.4_5'UTR|GPR108_ENST00000598626.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	180						integral component of membrane (GO:0016021)		p.A180T(1)		breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TGAATCACTGCGGGTGTTGAC	0.602											OREG0025092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	19						C	THR/ALA	1,3899		0,1,1949	89	90	90		538	-5.1	0	19		90	0,8282		0,0,4141	no	missense	GPR108	NM_001080452.1	58	0,1,6090	TT,TC,CC		0.0,0.0256,0.0082	benign	180/544	6734027	1,12181	1950	4141	6091	6685027	SO:0001583	missense	56927				CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"GPCR / Unclassified : 7TM orphan receptors"	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.538G>A	19.37:g.6734027C>T	ENSP00000264080:p.Ala180Thr	636	6685027	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.862|4.862	0.160145|0.160145	0.09287|0.09287	2.56E-4|2.56E-4	0.0|0.0	ENSG00000125734|ENSG00000125734	ENST00000264080|ENST00000549846	T|.	0.22743|.	1.94|.	3.87|3.87	-5.09|-5.09	0.02920|0.02920	.|.	13.826000|.	0.00848|.	N|.	0.001811|.	T|T	0.14013|0.14013	0.0339|0.0339	N|N	0.08118|0.08118	0|0	0.18873|0.18873	N|N	0.999989|0.999989	B|.	0.17268|.	0.021|.	B|.	0.12156|.	0.007|.	T|T	0.30475|0.30475	-0.9977|-0.9977	10|5	0.12766|.	T|.	0.61|.	1.5358|1.5358	5.6126|5.6126	0.17414|0.17414	0.0:0.3756:0.1444:0.48|0.0:0.3756:0.1444:0.48	.|.	180|.	Q9NPR9|.	GP108_HUMAN|.	T|H	180|162	ENSP00000264080:A180T|.	ENSP00000264080:A180T|.	A|R	-|-	1|2	0|0	GPR108|GPR108	6685027|6685027	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-1.128000|-1.128000	0.03247|0.03247	-0.615000|-0.615000	0.05679|0.05679	-0.258000|-0.258000	0.10820|0.10820	GCA|CGC		0.602	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2			T	6734027	C	T	6734027	3	4	61	1	0	0	0	0	1	0	0	0	6644	768	27	1	1145	1	GPR108	19	6734027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1506	6734027	52394956	10769	18754										
TRIP10	9322	broad.mit.edu	37	chr19	6742999	6742999	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagccagcaacagtccttCgtacagattctccaggaggt	9	12	2	1	rs148560112	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6742999C>T	ENST00000313244.9	+	4	254	c.219C>T	c.(217-219)ttC>ttT	p.F73F	TRIP10_ENST00000600428.1_5'UTR|TRIP10_ENST00000596543.1_3'UTR|TRIP10_ENST00000313285.8_Silent_p.F73F|TRIP10_ENST00000596758.1_Silent_p.F73F			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	73	F-BAR domain.|Required for podosome formation and interaction with AKAP9 and microtubules.|Required for translocation to the plasma membrane in response to insulin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.F73F(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						AACAGTCCTTCGTACAGATTC	0.582													C|||	8	0.00159744	0.0061	0	5008	,	,		16995	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		40,4366	43.1+/-76.7	0,40,2163	89	89	89		219	-4.6	0.3	19	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRIP10	NM_004240.2		0,41,6462	TT,TC,CC		0.0116,0.9079,0.3152		73/546	6742999	41,12965	2203	4300	6503	6693999	SO:0001819	synonymous_variant	9322			AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.219C>T	19.37:g.6742999C>T			6693999	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Silent	SNP	ENST00000313244.9	37																																																																																					0.582	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			T	6742999	C	T	6742999	2	4	61	1	0	0	0	0	0	0	0	1	16594	883	31	1		1	TRIP10	19	6742999	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8972	6742999	52385984	10770	18755										
SH2D3A	10045	broad.mit.edu	37	chr19	6760665	6760665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacctgagaggctctatccGagctgggccatccatcaggg	13	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6760665G>A	ENST00000245908.6	-	3	672	c.403C>T	c.(403-405)Cgg>Tgg	p.R135W	SH2D3A_ENST00000437152.3_Intron|SH2D3A_ENST00000599563.1_5'UTR	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	135					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)	p.R135W(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GGCTCTATCCGAGCTGGGCCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											36	35	35					19																	6760665		2203	4300	6503	6711665	SO:0001583	missense	10045			AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.403C>T	19.37:g.6760665G>A	ENSP00000245908:p.Arg135Trp		6711665	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342216	0.24339	.	.	ENSG00000125731	ENST00000245908	T	0.13538	2.58	4.91	1.27	0.21489	.	1.632810	0.03997	N	0.295778	T	0.16981	0.0408	M	0.64404	1.975	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33929	-0.9849	10	0.72032	D	0.01	-0.035	5.2445	0.15488	0.1895:0.2317:0.5787:0.0	.	135	Q9BRG2	SH23A_HUMAN	W	135	ENSP00000245908:R135W	ENSP00000245908:R135W	R	-	1	2	SH2D3A	6711665	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	0.053000	0.14184	0.212000	0.20703	0.549000	0.68633	CGG		0.557	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		A	6760665	G	A	6760665	3	1	61	1	0	0	0	0	1	0	0	0	14270	1057	37	1	1359	1	SH2D3A	19	6760665	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17666	6760665	52368318	10771	18756										
VAV1	7409	broad.mit.edu	37	chr19	6829846	6829846	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatctgtaagcgcaggggaGactcctatgacctcaaggac	11	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6829846G>T	ENST00000602142.1	+	14	1397	c.1315G>T	c.(1315-1317)Gac>Tac	p.D439Y	VAV1_ENST00000539284.1_Missense_Mutation_p.D342Y|VAV1_ENST00000304076.2_Missense_Mutation_p.D439Y|VAV1_ENST00000596764.1_Missense_Mutation_p.D407Y|VAV1_ENST00000599806.1_Missense_Mutation_p.D384Y	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	439	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D439Y(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						GCGCAGGGGAGACTCCTATGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	19											160	130	140					19																	6829846		2203	4300	6503	6780846	SO:0001583	missense	7409				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1315G>T	19.37:g.6829846G>T	ENSP00000472929:p.Asp439Tyr		6780846	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282684	0.59867	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	D;D	0.88896	-2.44;-2.44	4.82	4.82	0.62117	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.056154	0.64402	D	0.000002	D	0.91492	0.7314	L	0.43923	1.385	0.80722	D	1	D;D;B;P	0.89917	1.0;1.0;0.082;0.784	D;D;B;P	0.71656	0.941;0.974;0.083;0.471	D	0.90740	0.4649	10	0.38643	T	0.18	.	15.7353	0.77837	0.0:0.0:1.0:0.0	.	342;439;384;439	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	Y	439;342	ENSP00000302269:D439Y;ENSP00000443242:D342Y	ENSP00000302269:D439Y	D	+	1	0	VAV1	6780846	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	4.732000	0.62029	2.385000	0.81259	0.655000	0.94253	GAC		0.532	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			T	6829846	G	T	6829846	3	4	61	1	0	0	0	0	1	0	0	0	17171	942	33	2	1369	2	VAV1	19	6829846	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69181	6829846	52299137	10772	18757										
VAV1	7409	broad.mit.edu	37	chr19	6857081	6857081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggttggctggttccctgCcaactacgtggaggaagatt	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6857081C>A	ENST00000602142.1	+	27	2583	c.2501C>A	c.(2500-2502)gCc>gAc	p.A834D	VAV1_ENST00000539284.1_Missense_Mutation_p.A737D|VAV1_ENST00000304076.2_Missense_Mutation_p.A812D|VAV1_ENST00000596764.1_Missense_Mutation_p.A802D|VAV1_ENST00000599806.1_Missense_Mutation_p.A779D	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	834	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A834D(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						TGGTTCCCTGCCAACTACGTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											210	147	169					19																	6857081		2203	4300	6503	6808081	SO:0001583	missense	7409				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.2501C>A	19.37:g.6857081C>A	ENSP00000472929:p.Ala834Asp		6808081	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	c	16.20	3.055750	0.55325	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T	0.53640	0.61	3.76	3.76	0.43208	Src homology-3 domain (4);	0.266470	0.29964	N	0.010741	T	0.51991	0.1707	L	0.47078	1.49	0.42735	D	0.993725	B;B;B;B	0.28971	0.229;0.228;0.004;0.096	B;B;B;B	0.43658	0.252;0.129;0.189;0.426	T	0.59904	-0.7366	10	0.72032	D	0.01	.	13.1412	0.59436	0.0:1.0:0.0:0.0	.	737;834;779;834	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	D	834;737	ENSP00000443242:A737D	ENSP00000302269:A834D	A	+	2	0	VAV1	6808081	0.988000	0.35896	0.998000	0.56505	0.869000	0.49853	6.281000	0.72632	1.958000	0.56883	0.542000	0.68232	GCC		0.592	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			A	6857081	C	A	6857081	3	1	61	1	0	0	0	0	1	0	0	0	17171	739	26	2	2607	2	VAV1	19	6857081	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27235	6857081	52271902	10773	18758										
EMR1	2015	broad.mit.edu	37	chr19	6890546	6890546	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagacccacacggaaaccaaAcacaaagggtaagttggcca	9	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6890546A>C	ENST00000312053.4	+	2	123	c.86A>C	c.(85-87)aAc>aCc	p.N29T	EMR1_ENST00000381404.4_Missense_Mutation_p.N29T|EMR1_ENST00000381407.5_Missense_Mutation_p.N29T|EMR1_ENST00000450315.3_Missense_Mutation_p.N29T|EMR1_ENST00000250572.8_Missense_Mutation_p.N29T	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	29					cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.N29T(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					CGGAAACCAAACACAAAGGGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	83	91					19																	6890546		2203	4300	6503	6841546	SO:0001583	missense	2015			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.86A>C	19.37:g.6890546A>C	ENSP00000311545:p.Asn29Thr		6841546	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.984757	0.00046	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.77358	-1.04;-1.09;-1.08;0.08;0.34	2.02	-4.04	0.04010	.	.	.	.	.	T	0.40932	0.1137	N	0.01874	-0.695	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.0	T	0.20706	-1.0267	9	0.02654	T	1	.	4.3123	0.10976	0.5112:0.1735:0.0:0.3153	.	29;29;29;29;29	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	T	29	ENSP00000311545:N29T;ENSP00000370811:N29T;ENSP00000250572:N29T;ENSP00000370814:N29T;ENSP00000405974:N29T	ENSP00000250572:N29T	N	+	2	0	EMR1	6841546	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.300000	0.00521	-3.064000	0.00255	-0.783000	0.03347	AAC		0.463	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			C	6890546	A	C	6890546	3	2	61	1	0	0	0	0	1	0	0	0	5117	43	2	4	92	4	EMR1	19	6890546	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33465	6890546	52238437	10774	18759										
EMR1	2015	broad.mit.edu	37	chr19	6897257	6897257	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagctgtttagatggtttCtcttctcccactggaaatga	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6897257C>A	ENST00000312053.4	+	4	373	c.336C>A	c.(334-336)ttC>ttA	p.F112L	EMR1_ENST00000381404.4_Intron|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000450315.3_Missense_Mutation_p.F112L|EMR1_ENST00000250572.8_Missense_Mutation_p.F112L|AC020895.1_ENST00000580648.1_RNA	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	112	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.F112L(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					TAGATGGTTTCTCTTCTCCCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	62	63					19																	6897257		2203	4300	6503	6848257	SO:0001583	missense	2015			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.336C>A	19.37:g.6897257C>A	ENSP00000311545:p.Phe112Leu		6848257	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.391809	0.62066	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000250572;ENST00000450315	D;D;D	0.93488	-3.23;-3.23;-3.23	3.88	1.64	0.23874	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.93128	0.7812	M	0.72576	2.205	0.31319	N	0.686284	P;P;B	0.45428	0.858;0.518;0.085	P;P;B	0.50082	0.63;0.464;0.033	D	0.90453	0.4440	9	0.72032	D	0.01	.	6.3723	0.21489	0.0:0.7601:0.0:0.2399	.	112;112;112	E7EPX9;Q14246-2;Q14246	.;.;EMR1_HUMAN	L	112	ENSP00000311545:F112L;ENSP00000250572:F112L;ENSP00000405974:F112L	ENSP00000250572:F112L	F	+	3	2	EMR1	6848257	0.917000	0.31117	0.970000	0.41538	0.758000	0.43043	2.185000	0.42584	0.843000	0.35070	0.563000	0.77884	TTC		0.498	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6897257	C	A	6897257	3	1	61	1	0	0	0	0	1	0	0	0	5117	912	32	2	350	2	EMR1	19	6897257	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6711	6897257	52231726	10775	18760										
EMR1	2015	broad.mit.edu	37	chr19	6919714	6919714	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatgactggagagaagaaaGacggcttctcagatccaatc	10	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:6919714G>A	ENST00000312053.4	+	13	1613	c.1576G>A	c.(1576-1578)Gac>Aac	p.D526N	EMR1_ENST00000381404.4_Missense_Mutation_p.D474N|EMR1_ENST00000381407.5_Missense_Mutation_p.D385N|EMR1_ENST00000450315.3_Missense_Mutation_p.D349N|EMR1_ENST00000250572.8_Missense_Mutation_p.D526N	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	526	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.D526N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					AGAGAAGAAAGACGGCTTCTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											106	96	99					19																	6919714		2203	4300	6503	6870714	SO:0001583	missense	2015			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1576G>A	19.37:g.6919714G>A	ENSP00000311545:p.Asp526Asn		6870714	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.645150	0.47258	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.78003	-1.09;-1.12;-1.14;0.06;0.37	3.99	2.95	0.34219	.	.	.	.	.	T	0.68274	0.2983	L	0.27053	0.805	0.09310	N	1	P;P;P;D;P	0.53619	0.835;0.835;0.873;0.961;0.799	B;B;P;P;B	0.49637	0.42;0.42;0.544;0.617;0.343	T	0.55114	-0.8191	9	0.17832	T	0.49	.	7.3129	0.26485	0.1218:0.0:0.8782:0.0	.	349;385;526;474;526	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	N	526;526;474;526;385;349	ENSP00000311545:D526N;ENSP00000370811:D474N;ENSP00000250572:D526N;ENSP00000370814:D385N;ENSP00000405974:D349N	ENSP00000250572:D526N	D	+	1	0	EMR1	6870714	0.117000	0.22190	0.043000	0.18650	0.044000	0.14063	1.713000	0.37951	1.021000	0.39600	0.491000	0.48974	GAC		0.483	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6919714	G	A	6919714	3	1	61	1	0	0	0	0	1	0	0	0	5117	942	33	3	1626	3	EMR1	19	6919714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22457	6919714	52209269	10776	18761										
ARHGEF18	23370	broad.mit.edu	37	chr19	7516049	7516049	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctagaaaattggcaacttCtccatcgtgcggcggcttgg	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7516049C>A	ENST00000359920.6	+	6	1441	c.1188C>A	c.(1186-1188)ttC>ttA	p.F396L	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.S354Y|ARHGEF18_ENST00000319670.9_Missense_Mutation_p.F238L	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	396	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.F238L(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TTGGCAACTTCTCCATCGTGC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											104	96	98					19																	7516049		2203	4300	6503	7422049	SO:0001583	missense	23370			AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1188C>A	19.37:g.7516049C>A	ENSP00000352995:p.Phe396Leu		7422049	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	C	5.130	0.209666	0.09757	.	.	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.61980	0.06;0.06	5.21	-7.14	0.01527	Dbl homology (DH) domain (5);	0.464806	0.19889	N	0.103763	T	0.21801	0.0525	N	0.01109	-1.01	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.26292	-1.0107	10	0.27082	T	0.32	-0.1102	7.8419	0.29403	0.0:0.4976:0.2071:0.2953	.	238;396	Q6ZSZ5-2;Q6ZSZ5	.;ARHGI_HUMAN	L	238;396	ENSP00000319200:F238L;ENSP00000352995:F396L	ENSP00000319200:F238L	F	+	3	2	ARHGEF18	7422049	0.000000	0.05858	0.010000	0.14722	0.014000	0.08584	-2.919000	0.00694	-1.323000	0.02275	-0.177000	0.13119	TTC		0.483	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		A	7516049	C	A	7516049	3	1	61	1	0	0	0	0	1	0	0	0	901	912	32	2	1210	2	ARHGEF18	19	7516049	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	596335	7516049	51612934	10777	18762										
ARHGEF18	23370	broad.mit.edu	37	chr19	7518468	7518468	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccagcgcctcagggagatCgcagggaagatggacctgaa	16	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7518468C>T	ENST00000359920.6	+	7	1660	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.S427L|ARHGEF18_ENST00000319670.9_Silent_p.I311I	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	469					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I311I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TCAGGGAGATCGCAGGGAAGA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	19											116	103	108					19																	7518468		2203	4300	6503	7424468	SO:0001819	synonymous_variant	23370			AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1407C>T	19.37:g.7518468C>T			7424468	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	37	CCDS45946.1																																																																																				0.557	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		T	7518468	C	T	7518468	2	4	61	1	0	0	0	0	0	0	0	1	901	874	31	1		1	ARHGEF18	19	7518468	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2419	7518468	51610515	10778	18763										
MCOLN1	57192	broad.mit.edu	37	chr19	7593485	7593485	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctgccctccccgcaggaGacaacagcttccggctcctg	10	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7593485G>T	ENST00000264079.6	+	8	1005	c.880G>T	c.(880-882)Gac>Tac	p.D294Y		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	294					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)	p.D294Y(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCCCGCAGGAGACAACAGCTT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											127	80	96					19																	7593485		2203	4300	6503	7499485	SO:0001583	missense	57192			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"Voltage-gated ion channels / Transient receptor potential cation channels"	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.880G>T	19.37:g.7593485G>T	ENSP00000264079:p.Asp294Tyr		7499485	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702460	0.68501	.	.	ENSG00000090674	ENST00000264079;ENST00000394321	T	0.75367	-0.93	5.32	5.32	0.75619	.	0.096084	0.64402	D	0.000001	T	0.72598	0.3480	M	0.71036	2.16	0.80722	D	1	B;P	0.39831	0.434;0.69	B;B	0.40636	0.242;0.335	T	0.70726	-0.4793	10	0.06757	T	0.87	.	16.4854	0.84183	0.0:0.0:1.0:0.0	.	259;294	Q9GZU1-2;Q9GZU1	.;MCLN1_HUMAN	Y	294;259	ENSP00000264079:D294Y	ENSP00000264079:D294Y	D	+	1	0	MCOLN1	7499485	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	5.025000	0.64097	2.492000	0.84095	0.563000	0.77884	GAC		0.647	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533		T	7593485	G	T	7593485	3	4	61	1	0	0	0	0	1	0	0	0	9425	942	33	2	910	2	MCOLN1	19	7593485	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75017	7593485	51535498	10779	18764										
PNPLA6	10908	broad.mit.edu	37	chr19	7615271	7615271	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtgcgccagatggacttCgccatcgactggactgcagt	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7615271C>T	ENST00000221249.6	+	18	2216	c.1785C>T	c.(1783-1785)ttC>ttT	p.F595F	PNPLA6_ENST00000545201.2_Silent_p.F569F|PNPLA6_ENST00000600737.1_Silent_p.F634F|PNPLA6_ENST00000450331.3_Silent_p.F595F|PNPLA6_ENST00000414982.3_Silent_p.F643F|PNPLA6_ENST00000594864.1_3'UTR	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	634					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)	p.F595F(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						AGATGGACTTCGCCATCGACT	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	19											43	42	42					19																	7615271		2199	4296	6495	7521271	SO:0001819	synonymous_variant	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1785C>T	19.37:g.7615271C>T			7521271	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																				0.687	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		T	7615271	C	T	7615271	2	4	61	1	0	0	0	0	0	0	0	1	12200	883	31	1		1	PNPLA6	19	7615271	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21786	7615271	51513712	10780	18765										
KIAA1543	57662	broad.mit.edu	37	chr19	7682455	7682455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtacaaagaacccagcGccaagtccaacaagttcatc	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7682455G>A	ENST00000160298.4	+	16	3453	c.3352G>A	c.(3352-3354)Gcc>Acc	p.A1118T	CAMSAP3_ENST00000446248.2_Missense_Mutation_p.A1145T	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	1118	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)	p.A1118T(1)		cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						AGAACCCAGCGCCAAGTCCAA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	93	92					19																	7682455		2102	4234	6336	7588455	SO:0001583	missense	57662			AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 80"	612685	"KIAA1543"	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.3352G>A	19.37:g.7682455G>A	ENSP00000160298:p.Ala1118Thr		7588455	Q8NDF1	Missense_Mutation	SNP	ENST00000160298.4	37	CCDS42489.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.535892	0.64972	.	.	ENSG00000076826	ENST00000446248;ENST00000160298	T;T	0.15139	2.45;2.45	5.27	2.02	0.26589	PRC-barrel-like (1);Microtubule-binding calmodulin-regulated spectrin-associated, C-terminal (2);	0.133504	0.50627	D	0.000118	T	0.22475	0.0542	L	0.28115	0.83	0.33117	D	0.541249	D;P;D	0.60160	0.987;0.534;0.984	P;B;P	0.62740	0.906;0.218;0.849	T	0.21042	-1.0257	10	0.62326	D	0.03	-25.4416	9.2717	0.37675	0.2382:0.0:0.7618:0.0	.	1129;1118;1145	D6W648;Q9P1Y5;Q9P1Y5-2	.;CAMP3_HUMAN;.	T	1145;1118	ENSP00000416797:A1145T;ENSP00000160298:A1118T	ENSP00000160298:A1118T	A	+	1	0	KIAA1543	7588455	0.996000	0.38824	0.511000	0.27724	0.544000	0.35116	2.553000	0.45837	0.242000	0.21303	0.462000	0.41574	GCC		0.602	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		A	7682455	G	A	7682455	3	1	61	1	0	0	0	0	1	0	0	0	8264	1087	38	1	3503	1	KIAA1543	19	7682455	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67184	7682455	51446528	10781	18766										
STXBP2	6813	broad.mit.edu	37	chr19	7705692	7705692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggcccatatcttcttcaccGacagtgagtgaggagagcct	11	12	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7705692G>A	ENST00000221283.5	+	5	353	c.322G>A	c.(322-324)Gac>Aac	p.D108N	STXBP2_ENST00000441779.2_Missense_Mutation_p.D119N|CTD-3214H19.4_ENST00000595866.1_3'UTR|STXBP2_ENST00000414284.2_Missense_Mutation_p.D105N	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	108					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)	p.D108N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						CTTCTTCACCGACAGTGAGTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	69	70					19																	7705692		2203	4300	6503	7611692	SO:0001583	missense	6813			U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.322G>A	19.37:g.7705692G>A	ENSP00000221283:p.Asp108Asn		7611692	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	37	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.100676	0.76983	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902;ENST00000320400	T;T;T	0.78816	-1.21;-1.21;-1.21	5.13	5.13	0.70059	.	0.110512	0.64402	D	0.000013	D	0.85687	0.5754	L	0.57536	1.79	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72982	0.979;0.964;0.979	D	0.87042	0.2141	10	0.72032	D	0.01	0.0937	16.0692	0.80911	0.0:0.0:1.0:0.0	.	119;105;108	E7EQD5;Q15833-2;Q15833	.;.;STXB2_HUMAN	N	108;105;119;108;298	ENSP00000221283:D108N;ENSP00000409471:D105N;ENSP00000413606:D119N	ENSP00000221283:D108N	D	+	1	0	STXBP2	7611692	1.000000	0.71417	0.978000	0.43139	0.179000	0.23085	9.540000	0.98080	2.368000	0.80403	0.655000	0.94253	GAC		0.617	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		A	7705692	G	A	7705692	3	1	61	1	0	0	0	0	1	0	0	0	15392	1058	37	1	340	1	STXBP2	19	7705692	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23237	7705692	51423291	10782	18767										
CLEC4G	339390	broad.mit.edu	37	chr19	7794348	7794348	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagcatcatgacacagttCtcgcgcccccaagcgtcatt	8	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7794348C>T	ENST00000328853.5	-	9	854	c.786G>A	c.(784-786)gaG>gaA	p.E262E	CLEC4G_ENST00000598081.1_5'Flank	NM_001244856.1|NM_198492.3	NP_001231785.1|NP_940894.1	Q6UXB4	CLC4G_HUMAN	C-type lectin domain family 4, member G	262	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.E262E(1)		breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(1)	6						TGACACAGTTCTCGCGCCCCC	0.602																																					Esophageal Squamous(146;540 1807 3349 19438 30853)											1	Substitution - coding silent(1)	large_intestine(1)	19											68	57	61					19																	7794348		2203	4300	6503	7700348	SO:0001819	synonymous_variant	339390			AY358431	CCDS12185.1	19p13.2	2010-04-27	2008-11-04			ENSG00000182566		"C-type lectin domain containing"	24591	protein-coding gene	gene with protein product			"C-type lectin superfamily 4, member G"			12975309	Standard	NM_198492		Approved	UNQ431, LSECtin	uc002mhp.4	Q6UXB4		ENST00000328853.5:c.786G>A	19.37:g.7794348C>T			7700348		Silent	SNP	ENST00000328853.5	37	CCDS12185.1																																																																																				0.602	CLEC4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461989.1	NM_198492		T	7794348	C	T	7794348	2	4	61	1	0	0	0	0	0	0	0	1	3523	912	32	3		3	CLEC4G	19	7794348	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88656	7794348	51334635	10783	18768										
CLEC4M	10332	broad.mit.edu	37	chr19	7831059	7831059	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtccaagcagcagcaaatCtatcaagaactgaccgattt	7	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:7831059C>A	ENST00000327325.5	+	4	868	c.750C>A	c.(748-750)atC>atA	p.I250I	CLEC4M_ENST00000248228.4_Silent_p.I228I|CLEC4M_ENST00000334806.5_Silent_p.I199I|CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000394122.2_Silent_p.I238I|CLEC4M_ENST00000357361.2_Silent_p.I250I|CLEC4M_ENST00000596363.1_Silent_p.I222I|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000596707.1_Intron	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	250	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.I250I(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						AGCAGCAAATCTATCAAGAAC	0.507																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	19											145	148	147					19																	7831059		2203	4300	6503	7737059	SO:0001819	synonymous_variant	10332			AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"C-type lectin domain containing", "CD molecules"	13523	protein-coding gene	gene with protein product		605872	"CD299 antigen"	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.750C>A	19.37:g.7831059C>A			7737059	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Silent	SNP	ENST00000327325.5	37	CCDS12187.1																																																																																				0.507	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257		A	7831059	C	A	7831059	2	1	61	1	0	0	0	0	0	0	0	1	3524	903	32	2		2	CLEC4M	19	7831059	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36711	7831059	51297924	10784	18769										
FBN3	84467	broad.mit.edu	37	chr19	8137014	8137014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcgtagcaggcttcagacGagagcagctcctctttgtcc	10	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8137014G>A	ENST00000600128.1	-	63	8420	c.8006C>T	c.(8005-8007)tCg>tTg	p.S2669L	FBN3_ENST00000601739.1_Missense_Mutation_p.S2669L|FBN3_ENST00000270509.2_Missense_Mutation_p.S2669L			Q75N90	FBN3_HUMAN	fibrillin 3	2669						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.S2669L(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GGCTTCAGACGAGAGCAGCTC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	19											146	144	144					19																	8137014		2203	4300	6503	8043014	SO:0001583	missense	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.8006C>T	19.37:g.8137014G>A	ENSP00000470498:p.Ser2669Leu		8043014	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486479	0.63962	.	.	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.89196	-2.48	4.75	3.71	0.42584	.	0.136830	0.50627	U	0.000113	D	0.85622	0.5739	M	0.76727	2.345	0.51767	D	0.999937	P;P	0.48503	0.873;0.911	B;B	0.33121	0.077;0.158	D	0.86155	0.1590	10	0.87932	D	0	.	12.6424	0.56716	0.0816:0.0:0.9184:0.0	.	2669;732	Q75N90;Q6ZNB8	FBN3_HUMAN;.	L	2669;732	ENSP00000270509:S2669L	ENSP00000270509:S2669L	S	-	2	0	FBN3	8043014	1.000000	0.71417	0.002000	0.10522	0.045000	0.14185	6.489000	0.73641	0.999000	0.39023	0.609000	0.83330	TCG		0.657	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8137014	G	A	8137014	3	1	61	1	0	0	0	0	1	0	0	0	5723	1059	37	1	431	1	FBN3	19	8137014	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	305955	8137014	50991969	10785	18770										
FBN3	84467	broad.mit.edu	37	chr19	8171113	8171113	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagctcttggcactcgtcGatgtctgtcaggaagtaagg	14	9	3	0	rs111927115		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8171113G>A	ENST00000600128.1	-	38	5106	c.4692C>T	c.(4690-4692)atC>atT	p.I1564I	FBN3_ENST00000601739.1_Silent_p.I1564I|FBN3_ENST00000270509.2_Silent_p.I1564I			Q75N90	FBN3_HUMAN	fibrillin 3	1564	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.I1564I(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GGCACTCGTCGATGTCTGTCA	0.587													G|||	1	0.000199681	0	0	5008	,	,		20175	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	82	65	71		4692	-0.9	1	19	dbSNP_132	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FBN3	NM_032447.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		1564/2810	8171113	2,13004	2203	4300	6503	8077113	SO:0001819	synonymous_variant	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4692C>T	19.37:g.8171113G>A			8077113	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																				0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8171113	G	A	8171113	2	1	61	1	0	0	0	0	0	0	0	1	5723	1048	37	1		1	FBN3	19	8171113	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34099	8171113	50957870	10786	18771										
CD320	51293	broad.mit.edu	37	chr19	8367692	8367692	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaccccataggcagttggGcttccagactggtctccggc	11	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8367692G>A	ENST00000301458.5	-	4	739	c.675C>T	c.(673-675)agC>agT	p.S225S	CD320_ENST00000537716.2_Silent_p.S183S|CD320_ENST00000596246.1_5'Flank	NM_016579.3	NP_057663.1	Q9NPF0	CD320_HUMAN	CD320 molecule	225					cobalamin metabolic process (GO:0009235)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.S225S(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)	6						AGGCAGTTGGGCTTCCAGACT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19											50	50	50					19																	8367692		2203	4300	6503	8273692	SO:0001819	synonymous_variant	51293			AF161254	CCDS12198.1, CCDS54210.1	19p13.3-p13.2	2008-02-05	2006-03-28			ENSG00000167775		"CD molecules"	16692	protein-coding gene	gene with protein product	"8D6 antigen"	606475	"CD320 antigen"			10727470	Standard	NM_016579		Approved	8D6, 8D6A	uc002mjj.2	Q9NPF0		ENST00000301458.5:c.675C>T	19.37:g.8367692G>A			8273692	B2RDS5|D6W668|F5H6D3|Q53HF7	Silent	SNP	ENST00000301458.5	37	CCDS12198.1	.	.	.	.	.	.	.	.	.	.	G	3.319	-0.139058	0.06669	.	.	ENSG00000167775	ENST00000323539	.	.	.	4.01	0.716	0.18191	.	.	.	.	.	T	0.23410	0.0566	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23297	-1.0192	4	.	.	.	-14.7966	3.6098	0.08055	0.2096:0.0:0.5948:0.1956	.	.	.	.	S	56	.	.	P	-	1	0	CD320	8273692	0.021000	0.18746	0.001000	0.08648	0.005000	0.04900	0.185000	0.16958	0.270000	0.21984	-0.152000	0.13540	CCC		0.617	CD320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461366.1	NM_016579		A	8367692	G	A	8367692	2	1	61	1	0	0	0	0	0	0	0	1	3010	1194	42	3		3	CD320	19	8367692	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196579	8367692	50761291	10787	18772										
ANGPTL4	51129	broad.mit.edu	37	chr19	8436306	8436306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgtggccggccagctgggCgccaccaccgtcccacccag	12	21	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8436306C>T	ENST00000301455.2	+	6	1110	c.939C>T	c.(937-939)ggC>ggT	p.G313G	RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA|RAB11B-AS1_ENST00000597407.1_RNA|ANGPTL4_ENST00000541807.1_Silent_p.G146G|ANGPTL4_ENST00000393962.2_Silent_p.G275G	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	313	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)	p.G313G(1)		large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						GCCAGCTGGGCGCCACCACCG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	19											40	36	37					19																	8436306		2203	4299	6502	8342306	SO:0001819	synonymous_variant	51129			AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"Fibrinogen C domain containing"	16039	protein-coding gene	gene with protein product	"fasting-induced adipose factor", "hepatic angiopoietin-related protein", "PPARG angiopoietin related protein", "hepatic fibrinogen/angiopoietin-related protein", "peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein", "angiopoietin-related protein 4"	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.939C>T	19.37:g.8436306C>T			8342306	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Silent	SNP	ENST00000301455.2	37	CCDS12200.1																																																																																				0.667	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		T	8436306	C	T	8436306	2	4	61	1	0	0	0	0	0	0	0	1	616	755	27	1		1	ANGPTL4	19	8436306	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68614	8436306	50692677	10788	18773										
HNRNPM	4670	broad.mit.edu	37	chr19	8553642	8553642	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgtggcgtggttaagttCgagtcgccagaggtggccga	19	7	0	1	rs201359498		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8553642C>T	ENST00000325495.4	+	16	2138	c.2097C>T	c.(2095-2097)ttC>ttT	p.F699F	HNRNPM_ENST00000348943.3_Silent_p.F660F|HNRNPM_ENST00000602219.1_3'UTR	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	699	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)	p.F699F(1)		endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						TGGTTAAGTTCGAGTCGCCAG	0.547													C|||	1	0.000199681	0	0	5008	,	,		16567	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C	,	1,4405	2.1+/-5.4	0,1,2202	138	121	127		2097,1980	-0.1	1	19		127	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HNRNPM	NM_005968.4,NM_031203.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	699/731,660/692	8553642	1,13005	2203	4300	6503	8459642	SO:0001819	synonymous_variant	4670			L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.2097C>T	19.37:g.8553642C>T			8459642	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Silent	SNP	ENST00000325495.4	37	CCDS12203.1																																																																																				0.547	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			T	8553642	C	T	8553642	2	4	61	1	0	0	0	0	0	0	0	1	7292	883	31	1		1	HNRNPM	19	8553642	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117336	8553642	50575341	10789	18774										
ADAMTS10	81794	broad.mit.edu	37	chr19	8661280	8661280	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcgcgctcacacattccGcccaccggggccaggcctgg	11	19	2	0	rs371217540		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8661280G>A	ENST00000597188.1	-	10	1371	c.1101C>T	c.(1099-1101)ggC>ggT	p.G367G	ADAMTS10_ENST00000270328.4_Silent_p.G367G|ADAMTS10_ENST00000596709.1_5'Flank	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	367	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G367G(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CACACATTCCGCCCACCGGGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		2,4404	2.1+/-5.4	0,2,2201	35	32	33		1101	-9.5	0.6	19		33	0,8600		0,0,4300	no	coding-synonymous	ADAMTS10	NM_030957.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		367/1104	8661280	2,13004	2203	4300	6503	8567280	SO:0001819	synonymous_variant	81794			AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.1101C>T	19.37:g.8661280G>A			8567280	M0QZE4	Silent	SNP	ENST00000597188.1	37	CCDS12206.1																																																																																				0.662	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		A	8661280	G	A	8661280	2	1	61	1	0	0	0	0	0	0	0	1	256	1074	38	1		1	ADAMTS10	19	8661280	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107638	8661280	50467703	10790	18775										
MBD3L1	85509	broad.mit.edu	37	chr19	8953598	8953598	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcttacagcagtgcaggaGaactttcaagcactttggat	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8953598G>A	ENST00000595891.1	+	3	475	c.244G>A	c.(244-246)Gaa>Aaa	p.E82K	MBD3L1_ENST00000305625.2_Missense_Mutation_p.E82K			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	82	Transcription repressor.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E82K(1)		NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						CAGTGCAGGAGAACTTTCAAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	19											96	89	91					19																	8953598		2203	4300	6503	8814598	SO:0001583	missense	85509			AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"methyl-CpG binding domain protein 3-like"	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.244G>A	19.37:g.8953598G>A	ENSP00000471575:p.Glu82Lys		8814598	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	37	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863782	0.51482	.	.	ENSG00000170948	ENST00000305625	T	0.51574	0.7	3.75	2.71	0.32032	.	0.000000	0.33457	N	0.004895	T	0.59998	0.2235	M	0.80422	2.495	0.20926	N	0.999821	D	0.57257	0.979	P	0.57679	0.825	T	0.52419	-0.8578	10	0.72032	D	0.01	-23.5876	7.4088	0.27006	0.119:0.0:0.881:0.0	.	82	Q8WWY6	MB3L1_HUMAN	K	82	ENSP00000304198:E82K	ENSP00000304198:E82K	E	+	1	0	MBD3L1	8814598	0.549000	0.26481	0.004000	0.12327	0.015000	0.08874	3.162000	0.50755	1.130000	0.42092	0.655000	0.94253	GAA		0.522	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208		A	8953598	G	A	8953598	3	1	61	1	0	0	0	0	1	0	0	0	9375	943	33	3	246	3	MBD3L1	19	8953598	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	292318	8953598	50175385	10791	18776										
MUC16	94025	broad.mit.edu	37	chr19	8987234	8987234	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgcatgacgttgtctgtGatgttgaacttgagggagcc	14	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:8987234G>A	ENST00000397910.4	-	68	42056	c.41853C>T	c.(41851-41853)atC>atT	p.I13951I	MUC16_ENST00000380951.5_Silent_p.I592I	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13976	SEA 13. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.I13951I(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGTTGTCTGTGATGTTGAACT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											112	113	112					19																	8987234		2127	4248	6375	8848234	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41853C>T	19.37:g.8987234G>A			8848234	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	G	0.498	-0.872269	0.02570	.	.	ENSG00000181143	ENST00000542240	.	.	.	3.61	2.58	0.30949	.	.	.	.	.	T	0.41903	0.1179	.	.	.	.	.	.	.	.	.	.	.	.	T	0.50841	-0.8780	3	.	.	.	.	7.3496	0.26682	0.1203:0.0:0.8797:0.0	.	.	.	.	L	791	.	.	S	-	2	0	MUC16	8848234	1.000000	0.71417	0.921000	0.36526	0.001000	0.01503	1.167000	0.31847	1.102000	0.41551	-0.203000	0.12734	TCA		0.612	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8987234	G	A	8987234	2	1	61	1	0	0	0	0	0	0	0	1	10003	1280	45	3		3	MUC16	19	8987234	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33636	8987234	50141749	10792	18777										
MUC16	94025	broad.mit.edu	37	chr19	9028332	9028332	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctgtccagtccgaggtCttcagggtcagggcgatgtg	14	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9028332C>A	ENST00000397910.4	-	11	36663	c.36460G>T	c.(36460-36462)Gac>Tac	p.D12154Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12156	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.D12154Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTCCGAGGTCTTCAGGGTCA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											169	172	171					19																	9028332		2104	4221	6325	8889332	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36460G>T	19.37:g.9028332C>A	ENSP00000381008:p.Asp12154Tyr		8889332	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	C	6.397	0.441343	0.12164	.	.	ENSG00000181143	ENST00000397910	T	0.29142	1.58	2.63	2.63	0.31362	.	.	.	.	.	T	0.13927	0.0337	N	0.08118	0	.	.	.	P	0.42620	0.785	B	0.34931	0.192	T	0.09773	-1.0659	8	0.87932	D	0	.	8.8909	0.35432	0.0:1.0:0.0:0.0	.	12154	B5ME49	.	Y	12154	ENSP00000381008:D12154Y	ENSP00000381008:D12154Y	D	-	1	0	MUC16	8889332	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.265000	0.08644	1.757000	0.51966	0.591000	0.81541	GAC		0.567	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9028332	C	A	9028332	3	1	61	1	0	0	0	0	1	0	0	0	10003	913	32	2	7359	2	MUC16	19	9028332	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41098	9028332	50100651	10793	18778										
MUC16	94025	broad.mit.edu	37	chr19	9038404	9038404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggcaggggtccagtaccGacggttataacctgcagata	14	9	0	1	rs369910554		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9038404G>A	ENST00000397910.4	-	7	36318	c.36115C>T	c.(36115-36117)Cgg>Tgg	p.R12039W		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12041	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.R12039W(1)|p.R7672W(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCCAGTACCGACGGTTATAA	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	19						G	TRP/ARG	0,3788		0,0,1894	118	113	115		36115	2.8	0	19		115	1,8235		0,1,4117	no	missense	MUC16	NM_024690.2	101	0,1,6011	AA,AG,GG		0.0121,0.0,0.0083	probably-damaging	12039/14508	9038404	1,12023	1894	4118	6012	8899404	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36115C>T	19.37:g.9038404G>A	ENSP00000381008:p.Arg12039Trp		8899404	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	G	6.355	0.433550	0.12045	0.0	1.21E-4	ENSG00000181143	ENST00000397910	T	0.02258	4.37	2.81	2.81	0.32909	.	.	.	.	.	T	0.03651	0.0104	N	0.08118	0	.	.	.	D	0.89917	1.0	D	0.67725	0.953	T	0.49113	-0.8973	8	0.87932	D	0	.	9.3034	0.37861	0.0:0.0:1.0:0.0	.	12039	B5ME49	.	W	12039	ENSP00000381008:R12039W	ENSP00000381008:R12039W	R	-	1	2	MUC16	8899404	0.009000	0.17119	0.003000	0.11579	0.030000	0.12068	2.079000	0.41577	1.884000	0.54569	0.411000	0.27672	CGG		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9038404	G	A	9038404	3	1	61	1	0	0	0	0	1	0	0	0	10003	1057	37	1	7720	1	MUC16	19	9038404	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10072	9038404	50090579	10794	18779										
MUC16	94025	broad.mit.edu	37	chr19	9046340	9046340	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtctctggcataccaggaGaatgagtcaaagttggaaca	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9046340G>A	ENST00000397910.4	-	5	35494	c.35291C>T	c.(35290-35292)tCt>tTt	p.S11764F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11766	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S11764F(1)|p.S7397F(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATACCAGGAGAATGAGTCAA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											132	126	128					19																	9046340		2018	4196	6214	8907340	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.35291C>T	19.37:g.9046340G>A	ENSP00000381008:p.Ser11764Phe		8907340	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.928	0.540898	0.13250	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	3.57	1.43	0.22495	.	.	.	.	.	T	0.03477	0.0100	L	0.55990	1.75	.	.	.	B	0.32573	0.376	B	0.31614	0.133	T	0.17930	-1.0353	8	0.87932	D	0	.	5.2108	0.15316	0.2717:0.0:0.7283:0.0	.	11764	B5ME49	.	F	11764	ENSP00000381008:S11764F	ENSP00000381008:S11764F	S	-	2	0	MUC16	8907340	0.012000	0.17670	0.005000	0.12908	0.084000	0.17831	0.856000	0.27818	0.484000	0.27630	0.556000	0.70494	TCT		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9046340	G	A	9046340	3	1	61	1	0	0	0	0	1	0	0	0	10003	942	33	3	8552	3	MUC16	19	9046340	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7936	9046340	50082643	10795	18780										
MUC16	94025	broad.mit.edu	37	chr19	9046491	9046491	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccattacaggtgtggcatCtggactactatgggaaaaac	12	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9046491C>A	ENST00000397910.4	-	5	35343	c.35140G>T	c.(35140-35142)Gat>Tat	p.D11714Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11716	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.D11714Y(1)|p.D7347N(1)|p.D7347Y(1)|p.D11714N(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTGTGGCATCTGGACTACTA	0.507																																																4	Substitution - Missense(4)	large_intestine(2)|lung(2)	19											131	125	127					19																	9046491		1986	4162	6148	8907491	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.35140G>T	19.37:g.9046491C>A	ENSP00000381008:p.Asp11714Tyr		8907491	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	4.300	0.054906	0.08291	.	.	ENSG00000181143	ENST00000397910	T	0.02158	4.42	3.03	-0.373	0.12516	.	.	.	.	.	T	0.01765	0.0056	L	0.32530	0.975	.	.	.	P	0.37101	0.582	B	0.31614	0.133	T	0.42699	-0.9436	8	0.87932	D	0	.	4.2445	0.10665	0.1818:0.598:0.0:0.2202	.	11714	B5ME49	.	Y	11714	ENSP00000381008:D11714Y	ENSP00000381008:D11714Y	D	-	1	0	MUC16	8907491	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.532000	0.06164	0.027000	0.15297	-0.265000	0.10407	GAT		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9046491	C	A	9046491	3	1	61	1	0	0	0	0	1	0	0	0	10003	913	32	2	8703	2	MUC16	19	9046491	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	151	9046491	50082492	10796	18781										
MUC16	94025	broad.mit.edu	37	chr19	9049838	9049838	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaggatggataacccatGaagctgttgtatctggctca	11	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9049838G>T	ENST00000397910.4	-	5	31996	c.31793C>A	c.(31792-31794)tCa>tAa	p.S10598*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10600	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S6231*(1)|p.S10598*(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GATAACCCATGAAGCTGTTGT	0.473																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											124	115	118					19																	9049838		1896	4112	6008	8910838	SO:0001587	stop_gained	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31793C>A	19.37:g.9049838G>T	ENSP00000381008:p.Ser10598*		8910838	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	60	49.125572	0.99987	.	.	ENSG00000181143	ENST00000397910	.	.	.	3.11	2.07	0.26955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.9186	0.19070	0.1439:0.0:0.8561:0.0	.	.	.	.	X	10598	.	ENSP00000381008:S10598X	S	-	2	0	MUC16	8910838	0.034000	0.19679	0.005000	0.12908	0.004000	0.04260	2.457000	0.45005	0.859000	0.35456	0.450000	0.29827	TCA		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9049838	G	T	9049838	4	4	61	1	0	0	0	0	0	1	0	0	10003	1294	45	2	12050	2	MUC16	19	9049838	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3347	9049838	50079145	10797	18782										
MUC16	94025	broad.mit.edu	37	chr19	9057863	9057863	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatcctcctagtctcagaGaaggcaggatttgatgtgaa	12	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9057863G>A	ENST00000397910.4	-	3	29786	c.29583C>T	c.(29581-29583)ttC>ttT	p.F9861F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9863	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.F9861F(1)|p.F5494F(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAGTCTCAGAGAAGGCAGGAT	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	19											136	128	131					19																	9057863		1983	4168	6151	8918863	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29583C>T	19.37:g.9057863G>A			8918863	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9057863	G	A	9057863	2	1	61	1	0	0	0	0	0	0	0	1	10003	933	33	3		3	MUC16	19	9057863	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8025	9057863	50071120	10798	18783										
MUC16	94025	broad.mit.edu	37	chr19	9058707	9058707	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctcagtccaggggtcagaGatgacattgactctatctca	9	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9058707G>T	ENST00000397910.4	-	3	28942	c.28739C>A	c.(28738-28740)tCt>tAt	p.S9580Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9582	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S9580Y(1)|p.S5213Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGGTCAGAGATGACATTGA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	19											91	85	87					19																	9058707		2004	4172	6176	8919707	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28739C>A	19.37:g.9058707G>T	ENSP00000381008:p.Ser9580Tyr		8919707	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.157	0.027589	0.08054	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	2.5	1.39	0.22231	.	.	.	.	.	T	0.05686	0.0149	L	0.29908	0.895	.	.	.	D	0.58268	0.982	D	0.64877	0.93	T	0.33292	-0.9874	8	0.87932	D	0	.	4.275	0.10804	0.2268:0.0:0.7732:0.0	.	9580	B5ME49	.	Y	9580	ENSP00000381008:S9580Y	ENSP00000381008:S9580Y	S	-	2	0	MUC16	8919707	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.078000	0.30754	0.545000	0.28902	0.305000	0.20034	TCT		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9058707	G	T	9058707	3	4	61	1	0	0	0	0	1	0	0	0	10003	942	33	2	15112	2	MUC16	19	9058707	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	844	9058707	50070276	10799	18784										
MUC16	94025	broad.mit.edu	37	chr19	9058850	9058850	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctggggaagaggaataGagttcctctgtagcactggt	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9058850G>T	ENST00000397910.4	-	3	28799	c.28596C>A	c.(28594-28596)ctC>ctA	p.L9532L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9534	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.L9532L(1)|p.L5165L(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAGAGGAATAGAGTTCCTCTG	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	19											118	117	118					19																	9058850		1965	4148	6113	8919850	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28596C>A	19.37:g.9058850G>T			8919850	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9058850	G	T	9058850	2	4	61	1	0	0	0	0	0	0	0	1	10003	929	33	2		2	MUC16	19	9058850	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	143	9058850	50070133	10800	18785										
MUC16	94025	broad.mit.edu	37	chr19	9059476	9059476	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgctagaagagatggcttCtgtcctggagacctcagtag	12	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9059476C>A	ENST00000397910.4	-	3	28173	c.27970G>T	c.(27970-27972)Gaa>Taa	p.E9324*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9326	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E4957*(1)|p.E9324*(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGATGGCTTCTGTCCTGGAG	0.507																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											160	155	156					19																	9059476		1994	4179	6173	8920476	SO:0001587	stop_gained	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27970G>T	19.37:g.9059476C>A	ENSP00000381008:p.Glu9324*		8920476	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	60	43.413986	0.99986	.	.	ENSG00000181143	ENST00000397910	.	.	.	2.43	0.128	0.14733	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.5254	0.07757	0.0:0.5709:0.2676:0.1615	.	.	.	.	X	9324	.	ENSP00000381008:E9324X	E	-	1	0	MUC16	8920476	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.273000	0.18662	0.110000	0.17919	0.461000	0.40582	GAA		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9059476	C	A	9059476	4	1	61	1	0	0	0	0	0	1	0	0	10003	922	32	2	15881	2	MUC16	19	9059476	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	626	9059476	50069507	10801	18786										
MUC16	94025	broad.mit.edu	37	chr19	9067212	9067212	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgtgccctgtgatgtaGagccaagaggaggacctgtt	13	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9067212G>T	ENST00000397910.4	-	3	20437	c.20234C>A	c.(20233-20235)tCt>tAt	p.S6745Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6747	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S6745Y(2)|p.S2378Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGTGATGTAGAGCCAAGAGG	0.498																																																3	Substitution - Missense(3)	large_intestine(3)	19											283	278	280					19																	9067212		2196	4287	6483	8928212	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20234C>A	19.37:g.9067212G>T	ENSP00000381008:p.Ser6745Tyr		8928212	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.246	-0.154253	0.06585	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	2.2	-1.7	0.08159	.	.	.	.	.	T	0.01695	0.0054	N	0.14661	0.345	.	.	.	D	0.53462	0.96	B	0.41332	0.354	T	0.45086	-0.9285	8	0.87932	D	0	.	2.8643	0.05596	0.327:0.2444:0.4287:0.0	.	6745	B5ME49	.	Y	6745	ENSP00000381008:S6745Y	ENSP00000381008:S6745Y	S	-	2	0	MUC16	8928212	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.344000	0.07780	-0.293000	0.08986	0.386000	0.25728	TCT		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9067212	G	T	9067212	3	4	61	1	0	0	0	0	1	0	0	0	10003	942	33	2	23617	2	MUC16	19	9067212	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7736	9067212	50061771	10802	18787										
MUC16	94025	broad.mit.edu	37	chr19	9068130	9068130	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatggtcctttcttcggatTttgtcaggccagcaaaagta	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9068130T>G	ENST00000397910.4	-	3	19519	c.19316A>C	c.(19315-19317)aAa>aCa	p.K6439T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6441	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.K6439T(2)|p.K2072T(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTTCGGATTTTGTCAGGCC	0.512																																																3	Substitution - Missense(3)	large_intestine(3)	19											268	261	263					19																	9068130		1994	4173	6167	8929130	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.19316A>C	19.37:g.9068130T>G	ENSP00000381008:p.Lys6439Thr		8929130	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.548	-0.092322	0.07053	.	.	ENSG00000181143	ENST00000397910	T	0.02763	4.17	2.05	-0.196	0.13232	.	.	.	.	.	T	0.01627	0.0052	N	0.08118	0	.	.	.	B	0.17667	0.023	B	0.10450	0.005	T	0.41034	-0.9531	8	0.87932	D	0	.	4.3892	0.11332	0.0:0.3668:0.0:0.6332	.	6439	B5ME49	.	T	6439	ENSP00000381008:K6439T	ENSP00000381008:K6439T	K	-	2	0	MUC16	8929130	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.295000	0.02764	-0.114000	0.11936	0.149000	0.16113	AAA		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9068130	T	G	9068130	3	3	61	1	0	0	0	0	1	0	0	0	10003	1841	64	4	24535	4	MUC16	19	9068130	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	918	9068130	50060853	10803	18788										
MUC16	94025	broad.mit.edu	37	chr19	9069155	9069155	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatccagggacacactggaGaaaacagtgtttgactctgt	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9069155G>T	ENST00000397910.4	-	3	18494	c.18291C>A	c.(18289-18291)ttC>ttA	p.F6097L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6099	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.F6097L(2)|p.F1730L(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACACACTGGAGAAAACAGTGT	0.493																																																3	Substitution - Missense(3)	large_intestine(3)	19											73	79	77					19																	9069155		2093	4231	6324	8930155	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18291C>A	19.37:g.9069155G>T	ENSP00000381008:p.Phe6097Leu		8930155	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.294	0.053763	0.08291	.	.	ENSG00000181143	ENST00000397910	T	0.02446	4.29	1.11	-0.031	0.13911	.	.	.	.	.	T	0.00936	0.0031	N	0.00583	-1.355	.	.	.	B	0.12630	0.006	B	0.04013	0.001	T	0.44997	-0.9291	8	0.87932	D	0	.	3.0074	0.06033	0.6935:0.0:0.3065:0.0	.	6097	B5ME49	.	L	6097	ENSP00000381008:F6097L	ENSP00000381008:F6097L	F	-	3	2	MUC16	8930155	0.000000	0.05858	0.001000	0.08648	0.095000	0.18619	0.243000	0.18106	-0.045000	0.13468	0.163000	0.16589	TTC		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9069155	G	T	9069155	3	4	61	1	0	0	0	0	1	0	0	0	10003	933	33	2	25560	2	MUC16	19	9069155	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1025	9069155	50059828	10804	18789										
MUC16	94025	broad.mit.edu	37	chr19	9070925	9070925	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgtgggcacataagaaaaGgcagtatttgtctctgttgt	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9070925G>T	ENST00000397910.4	-	3	16724	c.16521C>A	c.(16519-16521)gcC>gcA	p.A5507A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5509	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A5507A(2)|p.A1140A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATAAGAAAAGGCAGTATTTG	0.493																																																3	Substitution - coding silent(3)	large_intestine(3)	19											133	126	129					19																	9070925		2001	4176	6177	8931925	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16521C>A	19.37:g.9070925G>T			8931925	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9070925	G	T	9070925	2	4	61	1	0	0	0	0	0	0	0	1	10003	987	35	2		2	MUC16	19	9070925	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1770	9070925	50058058	10805	18790										
MUC16	94025	broad.mit.edu	37	chr19	9071670	9071670	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcagattttgtcttaataGaggaggtgaagaccctgggg	14	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9071670G>T	ENST00000397910.4	-	3	15979	c.15776C>A	c.(15775-15777)tCt>tAt	p.S5259Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5261	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S5259Y(2)|p.S892Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTCTTAATAGAGGAGGTGAA	0.502																																																3	Substitution - Missense(3)	large_intestine(3)	19											170	166	167					19																	9071670		2033	4184	6217	8932670	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15776C>A	19.37:g.9071670G>T	ENSP00000381008:p.Ser5259Tyr		8932670	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	1.659	-0.511943	0.04200	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.94	-3.35	0.04928	.	.	.	.	.	T	0.01489	0.0048	N	0.14661	0.345	.	.	.	D	0.53462	0.96	B	0.38156	0.266	T	0.43343	-0.9397	8	0.87932	D	0	.	3.3859	0.07272	0.452:0.2135:0.3345:0.0	.	5259	B5ME49	.	Y	5259	ENSP00000381008:S5259Y	ENSP00000381008:S5259Y	S	-	2	0	MUC16	8932670	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.103000	0.15292	-0.773000	0.04596	-1.278000	0.01390	TCT		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9071670	G	T	9071670	3	4	61	1	0	0	0	0	1	0	0	0	10003	942	33	2	28075	2	MUC16	19	9071670	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	745	9071670	50057313	10806	18791										
MUC16	94025	broad.mit.edu	37	chr19	9072316	9072316	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcattgcaggtgaggacaGaaaggaagagggggagctgg	20	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9072316G>T	ENST00000397910.4	-	3	15333	c.15130C>A	c.(15130-15132)Ctg>Atg	p.L5044M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5046	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.L5044M(2)|p.L677M(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTGAGGACAGAAAGGAAGAG	0.478																																																3	Substitution - Missense(3)	large_intestine(3)	19											83	80	81					19																	9072316		1955	4149	6104	8933316	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15130C>A	19.37:g.9072316G>T	ENSP00000381008:p.Leu5044Met		8933316	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.350	0.064355	0.08388	.	.	ENSG00000181143	ENST00000397910	T	0.26660	1.72	1.59	-1.1	0.09872	.	.	.	.	.	T	0.13713	0.0332	L	0.40543	1.245	.	.	.	D	0.53462	0.96	B	0.34452	0.183	T	0.21930	-1.0231	8	0.87932	D	0	.	3.5819	0.07957	0.2685:0.4275:0.304:0.0	.	5044	B5ME49	.	M	5044	ENSP00000381008:L5044M	ENSP00000381008:L5044M	L	-	1	2	MUC16	8933316	.	.	0.000000	0.03702	0.353000	0.29299	.	.	-0.145000	0.11294	0.282000	0.19409	CTG		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9072316	G	T	9072316	3	4	61	1	0	0	0	0	1	0	0	0	10003	933	33	2	28721	2	MUC16	19	9072316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	646	9072316	50056667	10807	18792										
MUC16	94025	broad.mit.edu	37	chr19	9073640	9073640	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtgctgttctcttttcgTccagcagtcagggaggatgt	14	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9073640T>C	ENST00000397910.4	-	3	14009	c.13806A>G	c.(13804-13806)ggA>ggG	p.G4602G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4604	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.G4602G(2)|p.G235G(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCTCTTTTCGTCCAGCAGTCA	0.498																																																3	Substitution - coding silent(3)	large_intestine(3)	19											93	88	90					19																	9073640		1998	4176	6174	8934640	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13806A>G	19.37:g.9073640T>C			8934640	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9073640	T	C	9073640	2	2	61	1	0	0	0	0	0	0	0	1	10003	1654	58	4		4	MUC16	19	9073640	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1324	9073640	50055343	10808	18793										
MUC16	94025	broad.mit.edu	37	chr19	9075788	9075788	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcttctgagacagaattCatcatctcagtgatccaagg	8	9	5	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9075788C>A	ENST00000397910.4	-	3	11861	c.11658G>T	c.(11656-11658)atG>atT	p.M3886I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3887	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.M3886I(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGACAGAATTCATCATCTCAG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	19											108	99	102					19																	9075788		1986	4176	6162	8936788	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11658G>T	19.37:g.9075788C>A	ENSP00000381008:p.Met3886Ile		8936788	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	7.636	0.679915	0.14907	.	.	ENSG00000181143	ENST00000397910	T	0.02085	4.46	1.52	0.106	0.14540	.	.	.	.	.	T	0.01320	0.0043	N	0.08118	0	.	.	.	B	0.09022	0.002	B	0.06405	0.002	T	0.43702	-0.9375	8	0.87932	D	0	.	3.3525	0.07158	0.0:0.4102:0.0:0.5898	.	3886	B5ME49	.	I	3886	ENSP00000381008:M3886I	ENSP00000381008:M3886I	M	-	3	0	MUC16	8936788	0.000000	0.05858	0.000000	0.03702	0.708000	0.40852	-2.134000	0.01307	-0.025000	0.13918	0.205000	0.17691	ATG		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9075788	C	A	9075788	3	1	61	1	0	0	0	0	1	0	0	0	10003	826	29	2	32193	2	MUC16	19	9075788	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2148	9075788	50053195	10809	18794										
MUC16	94025	broad.mit.edu	37	chr19	9083587	9083587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaaagtgccactgtgatcGaaccttcataggttgtattc	9	8	1	2	rs371402846		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9083587G>A	ENST00000397910.4	-	1	8431	c.8228C>T	c.(8227-8229)tCg>tTg	p.S2743L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2743	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S2743L(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CACTGTGATCGAACCTTCATA	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											125	118	120					19																	9083587		1919	4115	6034	8944587	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8228C>T	19.37:g.9083587G>A	ENSP00000381008:p.Ser2743Leu		8944587	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.595	-0.831363	0.02713	.	.	ENSG00000181143	ENST00000397910	T	0.02656	4.21	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01592	0.0051	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.44081	-0.9351	7	0.87932	D	0	.	.	.	.	.	2743	B5ME49	.	L	2743	ENSP00000381008:S2743L	ENSP00000381008:S2743L	S	-	2	0	MUC16	8944587	0.001000	0.12720	0.004000	0.12327	0.004000	0.04260	-1.465000	0.02357	-0.677000	0.05231	-0.671000	0.03813	TCG		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9083587	G	A	9083587	3	1	61	1	0	0	0	0	1	0	0	0	10003	1059	37	1	35631	1	MUC16	19	9083587	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7799	9083587	50045396	10810	18795										
MUC16	94025	broad.mit.edu	37	chr19	9083847	9083847	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagctaatgaacttgttggCtcagtggcagtgagagggat	15	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9083847C>A	ENST00000397910.4	-	1	8171	c.7968G>T	c.(7966-7968)gaG>gaT	p.E2656D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2656	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E2656D(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACTTGTTGGCTCAGTGGCAG	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	19											52	51	51					19																	9083847		2004	4174	6178	8944847	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7968G>T	19.37:g.9083847C>A	ENSP00000381008:p.Glu2656Asp		8944847	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	7.521	0.656682	0.14580	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	0.235	0.235	0.15431	.	.	.	.	.	T	0.03434	0.0099	N	0.08118	0	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.45862	-0.9232	7	0.87932	D	0	.	.	.	.	.	2656	B5ME49	.	D	2656	ENSP00000381008:E2656D	ENSP00000381008:E2656D	E	-	3	2	MUC16	8944847	0.003000	0.15002	0.519000	0.27824	0.522000	0.34438	-0.314000	0.08092	0.308000	0.22923	0.313000	0.20887	GAG		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9083847	C	A	9083847	3	1	61	1	0	0	0	0	1	0	0	0	10003	796	28	2	35891	2	MUC16	19	9083847	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	260	9083847	50045136	10811	18796										
MUC16	94025	broad.mit.edu	37	chr19	9083978	9083978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaagatggtatctgtgaCcaaaatctttgaggtaagtg	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9083978C>T	ENST00000397910.4	-	1	8040	c.7837G>A	c.(7837-7839)Gtc>Atc	p.V2613I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2613	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V2613I(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTATCTGTGACCAAAATCTTT	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	19											97	94	95					19																	9083978		1931	4138	6069	8944978	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7837G>A	19.37:g.9083978C>T	ENSP00000381008:p.Val2613Ile		8944978	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	1.869	-0.460825	0.04508	.	.	ENSG00000181143	ENST00000397910	T	0.02421	4.3	0.225	0.225	0.15325	.	.	.	.	.	T	0.02848	0.0085	N	0.08118	0	.	.	.	P	0.41597	0.756	P	0.49752	0.621	T	0.44574	-0.9319	7	0.87932	D	0	.	.	.	.	.	2613	B5ME49	.	I	2613	ENSP00000381008:V2613I	ENSP00000381008:V2613I	V	-	1	0	MUC16	8944978	0.006000	0.16342	0.011000	0.14972	0.011000	0.07611	-0.175000	0.09825	0.300000	0.22699	0.305000	0.20034	GTC		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9083978	C	T	9083978	3	4	61	1	0	0	0	0	1	0	0	0	10003	507	18	3	36022	3	MUC16	19	9083978	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	131	9083978	50045005	10812	18797										
MUC16	94025	broad.mit.edu	37	chr19	9084535	9084535	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttactggaaacagatggaGaggtggctgtatttgtctct	13	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9084535G>A	ENST00000397910.4	-	1	7483	c.7280C>T	c.(7279-7281)tCt>tTt	p.S2427F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2427	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S2427F(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACAGATGGAGAGGTGGCTGT	0.498																																																2	Substitution - Missense(2)	large_intestine(2)	19											80	83	82					19																	9084535		1984	4153	6137	8945535	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7280C>T	19.37:g.9084535G>A	ENSP00000381008:p.Ser2427Phe		8945535	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.868	-0.028513	0.07589	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.225	0.225	0.15325	.	.	.	.	.	T	0.04048	0.0113	N	0.08118	0	.	.	.	D	0.58970	0.984	D	0.63877	0.919	T	0.45279	-0.9272	7	0.87932	D	0	.	.	.	.	.	2427	B5ME49	.	F	2427	ENSP00000381008:S2427F	ENSP00000381008:S2427F	S	-	2	0	MUC16	8945535	0.036000	0.19791	0.433000	0.26760	0.437000	0.31866	0.926000	0.28804	0.300000	0.22699	0.305000	0.20034	TCT		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9084535	G	A	9084535	3	1	61	1	0	0	0	0	1	0	0	0	10003	942	33	3	36579	3	MUC16	19	9084535	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	557	9084535	50044448	10813	18798										
MUC16	94025	broad.mit.edu	37	chr19	9084646	9084646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatgctagtgggactgatgGaggctgttttagtgacatcc	14	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9084646G>A	ENST00000397910.4	-	1	7372	c.7169C>T	c.(7168-7170)tCc>tTc	p.S2390F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2390	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S2390F(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGACTGATGGAGGCTGTTTT	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	19											117	115	116					19																	9084646		1980	4172	6152	8945646	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7169C>T	19.37:g.9084646G>A	ENSP00000381008:p.Ser2390Phe		8945646	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	0.883	-0.728011	0.03135	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.225	0.225	0.15325	.	.	.	.	.	T	0.04048	0.0113	N	0.08118	0	.	.	.	D	0.58970	0.984	D	0.63877	0.919	T	0.45279	-0.9272	7	0.87932	D	0	.	.	.	.	.	2390	B5ME49	.	F	2390	ENSP00000381008:S2390F	ENSP00000381008:S2390F	S	-	2	0	MUC16	8945646	0.010000	0.17322	0.038000	0.18304	0.039000	0.13416	-0.056000	0.11787	0.300000	0.22699	0.305000	0.20034	TCC		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9084646	G	A	9084646	3	1	61	1	0	0	0	0	1	0	0	0	10003	1174	41	3	36690	3	MUC16	19	9084646	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111	9084646	50044337	10814	18799										
MUC16	94025	broad.mit.edu	37	chr19	9085065	9085065	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaggggagggggaaaaggaGacagtgggaatactctcagc	17	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9085065G>T	ENST00000397910.4	-	1	6953	c.6750C>A	c.(6748-6750)gtC>gtA	p.V2250V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2250	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V2250V(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGAAAAGGAGACAGTGGGAA	0.463																																																2	Substitution - coding silent(2)	large_intestine(2)	19											91	88	89					19																	9085065		1956	4157	6113	8946065	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6750C>A	19.37:g.9085065G>T			8946065	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9085065	G	T	9085065	2	4	61	1	0	0	0	0	0	0	0	1	10003	929	33	2		2	MUC16	19	9085065	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	419	9085065	50043918	10815	18800										
MUC16	94025	broad.mit.edu	37	chr19	9085146	9085146	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaagccaggtggacctgcGctgtttactgggatgcttgt	14	9	0	0	rs73495780	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9085146G>A	ENST00000397910.4	-	1	6872	c.6669C>T	c.(6667-6669)agC>agT	p.S2223S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2223	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S2223S(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGACCTGCGCTGTTTACTG	0.488																																																2	Substitution - coding silent(2)	large_intestine(2)	19											115	111	112					19																	9085146		1984	4167	6151	8946146	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6669C>T	19.37:g.9085146G>A			8946146	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9085146	G	A	9085146	2	1	61	1	0	0	0	0	0	0	0	1	10003	1078	38	1		1	MUC16	19	9085146	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81	9085146	50043837	10816	18801										
MUC16	94025	broad.mit.edu	37	chr19	9085583	9085583	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgggtttgaaaccccagAatggcctgaggacagtgcct	12	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9085583A>C	ENST00000397910.4	-	1	6435	c.6232T>G	c.(6232-6234)Tct>Gct	p.S2078A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2078	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S2078A(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAACCCCAGAATGGCCTGAG	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	19											159	152	154					19																	9085583		1915	4126	6041	8946583	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6232T>G	19.37:g.9085583A>C	ENSP00000381008:p.Ser2078Ala		8946583	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	0.160	-1.082329	0.01888	.	.	ENSG00000181143	ENST00000397910	T	0.02395	4.31	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	.	.	.	B	0.19935	0.04	B	0.15052	0.012	T	0.44636	-0.9315	7	0.87932	D	0	.	.	.	.	rs34220940	2078	B5ME49	.	A	2078	ENSP00000381008:S2078A	ENSP00000381008:S2078A	S	-	1	0	MUC16	8946583	0.001000	0.12720	0.007000	0.13788	0.007000	0.05969	-0.053000	0.11846	-0.738000	0.04817	-0.736000	0.03550	TCT		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9085583	A	C	9085583	3	2	61	1	0	0	0	0	1	0	0	0	10003	246	9	4	37627	4	MUC16	19	9085583	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	437	9085583	50043400	10817	18802										
MUC16	94025	broad.mit.edu	37	chr19	9086714	9086714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactcagaaaggacagaggAaactcttcctaatgactggc	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9086714A>G	ENST00000397910.4	-	1	5304	c.5101T>C	c.(5101-5103)Tcc>Ccc	p.S1701P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1701	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S1701P(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGACAGAGGAAACTCTTCCT	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	19											155	145	148					19																	9086714		1975	4168	6143	8947714	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5101T>C	19.37:g.9086714A>G	ENSP00000381008:p.Ser1701Pro		8947714	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	6.110	0.388576	0.11581	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.33	0.261	0.15592	.	.	.	.	.	T	0.02848	0.0085	N	0.08118	0	.	.	.	D	0.62365	0.991	P	0.56088	0.791	T	0.44817	-0.9303	8	0.87932	D	0	.	3.0639	0.06209	0.7269:0.0:0.2731:0.0	.	1701	B5ME49	.	P	1701	ENSP00000381008:S1701P	ENSP00000381008:S1701P	S	-	1	0	MUC16	8947714	0.000000	0.05858	0.000000	0.03702	0.502000	0.33828	-0.020000	0.12525	0.011000	0.14865	0.260000	0.18958	TCC		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9086714	A	G	9086714	3	3	61	1	0	0	0	0	1	0	0	0	10003	246	9	4	38758	4	MUC16	19	9086714	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1131	9086714	50042269	10818	18803										
MUC16	94025	broad.mit.edu	37	chr19	9087069	9087069	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcagtaagatgggaaggGgatgctgaggctggtataga	16	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9087069G>T	ENST00000397910.4	-	1	4949	c.4746C>A	c.(4744-4746)tcC>tcA	p.S1582S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1582	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S1582S(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GATGGGAAGGGGATGCTGAGG	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	19											343	329	333					19																	9087069		2036	4190	6226	8948069	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4746C>A	19.37:g.9087069G>T			8948069	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9087069	G	T	9087069	2	4	61	1	0	0	0	0	0	0	0	1	10003	1219	43	2		2	MUC16	19	9087069	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	355	9087069	50041914	10819	18804										
MUC16	94025	broad.mit.edu	37	chr19	9088600	9088600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacactttctttggccatgGtaaaatccatagatgtctca	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9088600G>A	ENST00000397910.4	-	1	3418	c.3215C>T	c.(3214-3216)aCc>aTc	p.T1072I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1072	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T1072I(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTGGCCATGGTAAAATCCAT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											89	86	87					19																	9088600		1985	4178	6163	8949600	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3215C>T	19.37:g.9088600G>A	ENSP00000381008:p.Thr1072Ile		8949600	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.144	0.394776	0.11638	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.51	1.51	0.23008	.	.	.	.	.	T	0.01523	0.0049	N	0.08118	0	.	.	.	P	0.50710	0.938	B	0.37451	0.25	T	0.45731	-0.9241	8	0.87932	D	0	.	6.4457	0.21875	0.0:0.0:1.0:0.0	.	1072	B5ME49	.	I	1072	ENSP00000381008:T1072I	ENSP00000381008:T1072I	T	-	2	0	MUC16	8949600	0.000000	0.05858	0.001000	0.08648	0.408000	0.30992	0.297000	0.19101	1.145000	0.42336	0.305000	0.20034	ACC		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9088600	G	A	9088600	3	1	61	1	0	0	0	0	1	0	0	0	10003	1261	44	3	40644	3	MUC16	19	9088600	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1531	9088600	50040383	10820	18805										
MUC16	94025	broad.mit.edu	37	chr19	9089541	9089541	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctttgtctttgttgagatTtcaggagtccctgtggtaat	12	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9089541T>C	ENST00000397910.4	-	1	2477	c.2274A>G	c.(2272-2274)gaA>gaG	p.E758E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	758	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E758E(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTGTTGAGATTTCAGGAGTCC	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	19											189	195	193					19																	9089541		2101	4237	6338	8950541	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2274A>G	19.37:g.9089541T>C			8950541	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9089541	T	C	9089541	2	2	61	1	0	0	0	0	0	0	0	1	10003	1838	64	4		4	MUC16	19	9089541	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	941	9089541	50039442	10821	18806										
MUC16	94025	broad.mit.edu	37	chr19	9089788	9089788	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtctcagggatgacagaaGaaaccattgtatatgatggc	11	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9089788G>T	ENST00000397910.4	-	1	2230	c.2027C>A	c.(2026-2028)tCt>tAt	p.S676Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	676	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S676Y(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GATGACAGAAGAAACCATTGT	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	19											118	117	117					19																	9089788		2041	4206	6247	8950788	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2027C>A	19.37:g.9089788G>T	ENSP00000381008:p.Ser676Tyr		8950788	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.258	-0.369886	0.05069	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.56	1.56	0.23342	.	.	.	.	.	T	0.03263	0.0095	N	0.08118	0	.	.	.	D	0.58268	0.982	P	0.56163	0.793	T	0.43829	-0.9367	8	0.87932	D	0	.	6.5643	0.22503	0.0:0.0:1.0:0.0	.	676	B5ME49	.	Y	676	ENSP00000381008:S676Y	ENSP00000381008:S676Y	S	-	2	0	MUC16	8950788	0.010000	0.17322	0.002000	0.10522	0.019000	0.09904	2.242000	0.43106	1.175000	0.42826	0.205000	0.17691	TCT		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9089788	G	T	9089788	3	4	61	1	0	0	0	0	1	0	0	0	10003	942	33	2	41832	2	MUC16	19	9089788	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	247	9089788	50039195	10822	18807										
OR1M1	125963	broad.mit.edu	37	chr19	9204844	9204844	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaagctggtcaacagaaaGatcacctcatcttcctgacc	8	12	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9204844G>T	ENST00000429566.3	+	1	990	c.924G>T	c.(922-924)aaG>aaT	p.K308N		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K308N(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TCAACAGAAAGATCACCTCAT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	19											31	30	30					19																	9204844		2203	4299	6502	9065844	SO:0001583	missense	125963				CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"GPCR / Class A : Olfactory receptors"	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.924G>T	19.37:g.9204844G>T	ENSP00000401966:p.Lys308Asn		9065844	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	37	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	g	8.686	0.906292	0.17760	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.39406	1.08	2.98	0.701	0.18104	.	0.253832	0.27841	N	0.017635	T	0.25865	0.0630	N	0.25825	0.765	0.09310	N	1	P	0.41313	0.745	B	0.41236	0.351	T	0.10042	-1.0647	10	0.36615	T	0.2	.	5.2215	0.15371	0.6248:0.0:0.3752:0.0	.	308	Q8NGA1	OR1M1_HUMAN	N	311;308	ENSP00000401966:K308N	ENSP00000303195:K311N	K	+	3	2	OR1M1	9065844	0.000000	0.05858	0.020000	0.16555	0.073000	0.16967	-0.570000	0.05895	0.014000	0.14944	0.580000	0.79431	AAG		0.498	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			T	9204844	G	T	9204844	3	4	61	1	0	0	0	0	1	0	0	0	10999	933	33	2	926	2	OR1M1	19	9204844	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115056	9204844	49924139	10823	18808										
OR7G2	390882	broad.mit.edu	37	chr19	9213278	9213278	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgagtgtaagacaaaatGattccagacagaggaacacc	9	8	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9213278G>T	ENST00000305456.2	-	1	704	c.705C>A	c.(703-705)atC>atA	p.I235I		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I235I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						AAGACAAAATGATTCCAGACA	0.453																																					Esophageal Squamous(67;143 1448 28637 40648)											1	Substitution - coding silent(1)	large_intestine(1)	19											119	107	111					19																	9213278		2203	4300	6503	9074278	SO:0001819	synonymous_variant	390882				CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"GPCR / Class A : Olfactory receptors"	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.705C>A	19.37:g.9213278G>T			9074278	Q6IFJ4|Q96RA0	Silent	SNP	ENST00000305456.2	37	CCDS32897.1																																																																																				0.453	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1			T	9213278	G	T	9213278	2	4	61	1	0	0	0	0	0	0	0	1	11254	1280	45	2		2	OR7G2	19	9213278	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8434	9213278	49915705	10824	18809										
OR7G2	390882	broad.mit.edu	37	chr19	9213680	9213680	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttggatgttcaccagcatCtttgggatcgtggttgtgct	13	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9213680C>A	ENST00000305456.2	-	1	302	c.303G>T	c.(301-303)aaG>aaT	p.K101N		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K101N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						TCACCAGCATCTTTGGGATCG	0.478																																					Esophageal Squamous(67;143 1448 28637 40648)											1	Substitution - Missense(1)	large_intestine(1)	19											154	144	147					19																	9213680		2203	4300	6503	9074680	SO:0001583	missense	390882				CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"GPCR / Class A : Olfactory receptors"	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.303G>T	19.37:g.9213680C>A	ENSP00000303822:p.Lys101Asn		9074680	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	.	.	.	.	.	.	.	.	.	.	c	4.843	0.156659	0.09236	.	.	ENSG00000170923	ENST00000305456	T	0.01359	4.98	3.2	2.16	0.27623	GPCR, rhodopsin-like superfamily (1);	0.195754	0.24422	N	0.038671	T	0.02193	0.0068	M	0.74467	2.265	0.24350	N	0.994924	B	0.27679	0.185	B	0.29942	0.109	T	0.37126	-0.9719	10	0.66056	D	0.02	.	2.9872	0.05972	0.2172:0.5486:0.0:0.2342	.	80	Q8NG99	OR7G2_HUMAN	N	101	ENSP00000303822:K101N	ENSP00000303822:K101N	K	-	3	2	OR7G2	9074680	0.000000	0.05858	0.999000	0.59377	0.027000	0.11550	0.043000	0.13971	0.959000	0.37980	0.494000	0.49563	AAG		0.478	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1			A	9213680	C	A	9213680	3	1	61	1	0	0	0	0	1	0	0	0	11254	912	32	2	736	2	OR7G2	19	9213680	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402	9213680	49915303	10825	18810										
OR7G1	125962	broad.mit.edu	37	chr19	9225532	9225532	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacagcctaccaataagtTtcctcaaagctttcttcatc	4	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9225532T>G	ENST00000541538.1	-	1	907	c.908A>C	c.(907-909)aAa>aCa	p.K303T	OR7G1_ENST00000293614.1_Missense_Mutation_p.K303T	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K303T(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						ACCAATAAGTTTCCTCAAAGC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	100	104					19																	9225532		2203	4300	6503	9086532	SO:0001583	missense	125962				CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.908A>C	19.37:g.9225532T>G	ENSP00000444134:p.Lys303Thr		9086532	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	t	9.174	1.021875	0.19433	.	.	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.42131	0.98;0.98	2.99	-2.96	0.05547	.	0.690561	0.11902	U	0.518527	T	0.39989	0.1099	M	0.85099	2.735	0.09310	N	1	B	0.31193	0.312	B	0.29524	0.103	T	0.38045	-0.9679	10	0.52906	T	0.07	.	5.0586	0.14546	0.0:0.3876:0.1569:0.4555	.	303	Q8NGA0	OR7G1_HUMAN	T	303	ENSP00000293614:K303T;ENSP00000444134:K303T	ENSP00000293614:K303T	K	-	2	0	OR7G1	9086532	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.276000	0.08514	-0.672000	0.05266	0.410000	0.27636	AAA		0.408	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			G	9225532	T	G	9225532	3	3	61	1	0	0	0	0	1	0	0	0	11253	1841	64	4	101	4	OR7G1	19	9225532	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	11852	9225532	49903451	10826	18811										
OR7G1	125962	broad.mit.edu	37	chr19	9225769	9225769	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgatggcattctcagaacaGaggtgactatttgagaataa	10	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9225769G>T	ENST00000541538.1	-	1	670	c.671C>A	c.(670-672)tCt>tAt	p.S224Y	OR7G1_ENST00000293614.1_Missense_Mutation_p.S224Y	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S224Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						TCTCAGAACAGAGGTGACTAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											78	81	80					19																	9225769		2203	4300	6503	9086769	SO:0001583	missense	125962				CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.671C>A	19.37:g.9225769G>T	ENSP00000444134:p.Ser224Tyr		9086769	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	g	12.87	2.066605	0.36470	.	.	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.00164	8.64;8.64	3.78	1.56	0.23342	GPCR, rhodopsin-like superfamily (1);	0.215464	0.23389	U	0.048701	T	0.00384	0.0012	H	0.97440	4.005	0.09310	N	1	P	0.40909	0.732	B	0.44163	0.443	T	0.12451	-1.0547	10	0.87932	D	0	.	8.924	0.35630	0.2012:0.0:0.7988:0.0	.	224	Q8NGA0	OR7G1_HUMAN	Y	224	ENSP00000293614:S224Y;ENSP00000444134:S224Y	ENSP00000293614:S224Y	S	-	2	0	OR7G1	9086769	0.000000	0.05858	0.017000	0.16124	0.100000	0.18952	0.290000	0.18975	0.890000	0.36211	0.501000	0.49751	TCT		0.408	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			T	9225769	G	T	9225769	3	4	61	1	0	0	0	0	1	0	0	0	11253	942	33	2	338	2	OR7G1	19	9225769	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	237	9225769	49903214	10827	18812										
OR7G3	390883	broad.mit.edu	37	chr19	9236889	9236889	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccataaaacaaggaaacaacGattaaatgtgacccgcagat	7	9	0	2	rs149297110		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9236889G>A	ENST00000305444.2	-	1	737	c.738C>T	c.(736-738)atC>atT	p.I246I		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I246I(1)		NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AGGAAACAACGATTAAATGTG	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	104	102	103		738	-7.4	0	19	dbSNP_134	103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR7G3	NM_001001958.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		246/313	9236889	1,13005	2203	4300	6503	9097889	SO:0001819	synonymous_variant	390883				CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"GPCR / Class A : Olfactory receptors"	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.738C>T	19.37:g.9236889G>A			9097889	Q6IFJ6|Q96R99	Silent	SNP	ENST00000305444.2	37	CCDS32899.1																																																																																				0.443	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			A	9236889	G	A	9236889	2	1	61	1	0	0	0	0	0	0	0	1	11255	1048	37	1		1	OR7G3	19	9236889	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11120	9236889	49892094	10828	18813										
ZNF317	57693	broad.mit.edu	37	chr19	9267967	9267967	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcggtgactttccaagatgtCgctgtggactttaccgagaa	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9267967C>T	ENST00000247956.6	+	4	491	c.186C>T	c.(184-186)gtC>gtT	p.V62V	ZNF317_ENST00000360385.3_Silent_p.V62V	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	62	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V62V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						TCCAAGATGTCGCTGTGGACT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	19											97	89	92					19																	9267967		2203	4300	6503	9128967	SO:0001819	synonymous_variant	57693			AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.186C>T	19.37:g.9267967C>T			9128967	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Silent	SNP	ENST00000247956.6	37	CCDS12210.1																																																																																				0.488	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		T	9267967	C	T	9267967	2	4	61	1	0	0	0	0	0	0	0	1	17874	871	31	1		1	ZNF317	19	9267967	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31078	9267967	49861016	10829	18814										
ZNF317	57693	broad.mit.edu	37	chr19	9271604	9271604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtgcgggaagaccttccGaaaccagtccatccttaaga	10	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9271604G>A	ENST00000247956.6	+	7	1588	c.1283G>A	c.(1282-1284)cGa>cAa	p.R428Q	ZNF317_ENST00000360385.3_Missense_Mutation_p.R396Q	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	428					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R428Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						AAGACCTTCCGAAACCAGTCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											76	76	76					19																	9271604		2203	4300	6503	9132604	SO:0001583	missense	57693			AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1283G>A	19.37:g.9271604G>A	ENSP00000247956:p.Arg428Gln		9132604	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	37	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.229953	0.39399	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.04275	3.66;3.66	2.92	2.92	0.33932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35615	N	0.003091	T	0.11367	0.0277	L	0.42581	1.335	0.09310	N	1	D;D	0.71674	0.991;0.998	P;D	0.79108	0.461;0.992	T	0.03910	-1.0993	10	0.40728	T	0.16	-28.3521	8.0713	0.30691	0.0:0.2519:0.7481:0.0	.	396;428	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	Q	428;396	ENSP00000247956:R428Q;ENSP00000353554:R396Q	ENSP00000247956:R428Q	R	+	2	0	ZNF317	9132604	0.000000	0.05858	0.068000	0.19968	0.844000	0.47949	-0.554000	0.06006	1.958000	0.56883	0.491000	0.48974	CGA		0.527	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		A	9271604	G	A	9271604	3	1	61	1	0	0	0	0	1	0	0	0	17874	1058	37	1	1305	1	ZNF317	19	9271604	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3637	9271604	49857379	10830	18815										
OR7D2	162998	broad.mit.edu	37	chr19	9296968	9296968	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatctaatcttctgtaaaGattttgaaattccacatttt	4	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9296968G>T	ENST00000344248.2	+	1	690	c.511G>T	c.(511-513)Gat>Tat	p.D171Y		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	171					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D171Y(1)		breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						CTTCTGTAAAGATTTTGAAAT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											165	159	161					19																	9296968		2203	4300	6503	9157968	SO:0001583	missense	162998			AK095468	CCDS32900.1	19p13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.511G>T	19.37:g.9296968G>T	ENSP00000345563:p.Asp171Tyr		9157968	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	37	CCDS32900.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735144	0.30774	.	.	ENSG00000188000	ENST00000344248	T	0.37411	1.2	2.21	2.21	0.28008	GPCR, rhodopsin-like superfamily (1);	0.798077	0.10526	U	0.664430	T	0.49508	0.1561	M	0.64260	1.97	0.09310	N	1	D	0.58970	0.984	P	0.59115	0.852	T	0.28170	-1.0052	10	0.59425	D	0.04	.	8.5696	0.33561	0.0:0.2403:0.7597:0.0	.	171	Q96RA2	OR7D2_HUMAN	Y	171	ENSP00000345563:D171Y	ENSP00000345563:D171Y	D	+	1	0	OR7D2	9157968	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-1.946000	0.01536	1.583000	0.49898	0.511000	0.50034	GAT		0.463	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1			T	9296968	G	T	9296968	3	4	61	1	0	0	0	0	1	0	0	0	11250	942	33	2	513	2	OR7D2	19	9296968	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25364	9296968	49832015	10831	18816										
OR7D2	162998	broad.mit.edu	37	chr19	9297079	9297079	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgacgggtgtgctgggcGtttttcccctccttgggatc	13	10	0	1	rs145118134	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9297079G>A	ENST00000344248.2	+	1	801	c.622G>A	c.(622-624)Gtt>Att	p.V208I		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	208					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V208I(1)		breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TGTGCTGGGCGTTTTTCCCCT	0.463													G|||	17	0.00339457	0	0	5008	,	,		19958	0.0159		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19						G	ILE/VAL	0,4406		0,0,2203	136	127	130		622	1.1	0	19	dbSNP_134	130	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR7D2	NM_175883.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	208/313	9297079	2,13004	2203	4300	6503	9158079	SO:0001583	missense	162998			AK095468	CCDS32900.1	19p13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.622G>A	19.37:g.9297079G>A	ENSP00000345563:p.Val208Ile		9158079	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	37	CCDS32900.1	13	0.005952380952380952	0	0.0	0	0.0	13	0.022727272727272728	0	0.0	G	2.104	-0.405443	0.04832	0.0	2.33E-4	ENSG00000188000	ENST00000344248	T	0.37411	1.2	2.2	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	0.227461	0.22128	U	0.064236	T	0.11750	0.0286	N	0.11698	0.16	0.09310	N	1	D	0.59767	0.986	P	0.57057	0.812	T	0.17198	-1.0377	10	0.05959	T	0.93	.	4.0199	0.09660	0.137:0.0:0.6258:0.2372	.	208	Q96RA2	OR7D2_HUMAN	I	208	ENSP00000345563:V208I	ENSP00000345563:V208I	V	+	1	0	OR7D2	9158079	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.894000	0.04123	0.486000	0.27676	0.505000	0.49811	GTT		0.463	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1			A	9297079	G	A	9297079	3	1	61	1	0	0	0	0	1	0	0	0	11250	1145	40	1	624	1	OR7D2	19	9297079	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111	9297079	49831904	10832	18817										
OR7D4	125958	broad.mit.edu	37	chr19	9325110	9325110	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagaggcaggggttcatgAtgaccgtgtagtgcagtggg	17	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9325110A>G	ENST00000308682.2	-	1	432	c.404T>C	c.(403-405)aTc>aCc	p.I135T		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I135T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						GGGGTTCATGATGACCGTGTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	80	81					19																	9325110		2203	4300	6503	9186110	SO:0001583	missense	125958				CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"GPCR / Class A : Olfactory receptors"	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.404T>C	19.37:g.9325110A>G	ENSP00000310488:p.Ile135Thr		9186110	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	37	CCDS32901.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389030	0.61956	.	.	ENSG00000174667	ENST00000308682	T	0.21191	2.02	4.0	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.206543	0.34435	N	0.003970	T	0.41003	0.1140	M	0.78223	2.4	0.40029	D	0.975509	D	0.62365	0.991	P	0.58620	0.842	T	0.46735	-0.9170	10	0.66056	D	0.02	.	12.1734	0.54172	1.0:0.0:0.0:0.0	.	135	Q8NG98	OR7D4_HUMAN	T	135	ENSP00000310488:I135T	ENSP00000310488:I135T	I	-	2	0	OR7D4	9186110	0.957000	0.32711	0.999000	0.59377	0.543000	0.35085	2.878000	0.48515	1.831000	0.53308	0.358000	0.22013	ATC		0.483	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1			G	9325110	A	G	9325110	3	3	61	1	0	0	0	0	1	0	0	0	11251	333	12	4	538	4	OR7D4	19	9325110	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	28031	9325110	49803873	10833	18818										
OR7E24	26648	broad.mit.edu	37	chr19	9362412	9362412	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtctccctatctcaggGatccttttctcttactataa	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9362412G>T	ENST00000456448.1	+	1	807	c.693G>T	c.(691-693)ggG>ggT	p.G231G		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G231G(1)		endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						CTATCTCAGGGATCCTTTTCT	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	19											34	35	35					19																	9362412		1902	4140	6042	9223412	SO:0001819	synonymous_variant	26648			Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.693G>T	19.37:g.9362412G>T			9223412	B9EJD9|Q9UPJ1	Silent	SNP	ENST00000456448.1	37	CCDS45955.1																																																																																				0.453	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			T	9362412	G	T	9362412	2	4	61	1	0	0	0	0	0	0	0	1	11252	1161	41	2		2	OR7E24	19	9362412	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37302	9362412	49766571	10834	18819										
ZNF699	374879	broad.mit.edu	37	chr19	9413107	9413107	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacatctctgtagaggtttCtctgagcaagatccagcaaa	8	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9413107C>A	ENST00000591998.1	-	3	350	c.122G>T	c.(121-123)aGa>aTa	p.R41I	ZNF699_ENST00000308650.3_Missense_Mutation_p.R41I|ZNF699_ENST00000588336.1_5'Flank			Q32M78	ZN699_HUMAN	zinc finger protein 699	41	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R41I(2)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GTAGAGGTTTCTCTGAGCAAG	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	19											112	114	113					19																	9413107		2203	4300	6503	9274107	SO:0001583	missense	374879			BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"Zinc fingers, C2H2-type", "-"	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.122G>T	19.37:g.9413107C>A	ENSP00000467723:p.Arg41Ile		9274107	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	37	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917214	0.52546	.	.	ENSG00000196110	ENST00000308650	T	0.03035	4.07	3.62	0.199	0.15175	Krueppel-associated box (4);	.	.	.	.	T	0.11239	0.0274	H	0.95504	3.68	0.26831	N	0.968588	P	0.38617	0.64	B	0.42214	0.38	T	0.11743	-1.0575	9	0.87932	D	0	.	3.1479	0.06478	0.2092:0.5589:0.0:0.2319	.	41	Q32M78	ZN699_HUMAN	I	41	ENSP00000311596:R41I	ENSP00000311596:R41I	R	-	2	0	ZNF699	9274107	0.002000	0.14202	0.264000	0.24511	0.904000	0.53231	-0.348000	0.07740	0.143000	0.18926	0.549000	0.68633	AGA		0.423	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		A	9413107	C	A	9413107	3	1	61	1	0	0	0	0	1	0	0	0	18140	913	32	2	1822	2	ZNF699	19	9413107	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	50695	9413107	49715876	10835	18820										
ZNF177	7730	broad.mit.edu	37	chr19	9492371	9492371	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaagccttataaatgtaTtcagtgtgaaaaagccttta	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9492371T>G	ENST00000589262.1	+	6	1430	c.1364T>G	c.(1363-1365)aTt>aGt	p.I455S	ZNF177_ENST00000541595.2_Missense_Mutation_p.I295S|ZNF177_ENST00000602738.1_Missense_Mutation_p.I295S|ZNF177_ENST00000590616.1_Intron|ZNF177_ENST00000434737.2_Missense_Mutation_p.I455S|ZNF177_ENST00000602856.1_3'UTR|ZNF177_ENST00000343499.4_Missense_Mutation_p.I295S|ZNF177_ENST00000446085.4_3'UTR	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	455			I -> F (in dbSNP:rs2230752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8661005}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I295S(1)|p.I455S(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						TATAAATGTATTCAGTGTGAA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	19											141	149	147					19																	9492371		2203	4300	6503	9353371	SO:0001583	missense	7730			U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type", "-"	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.1364T>G	19.37:g.9492371T>G	ENSP00000468531:p.Ile455Ser		9353371	B4DY57|E9PDG0|I3L0I4|Q96ER2	Missense_Mutation	SNP	ENST00000589262.1	37	CCDS54214.1	.	.	.	.	.	.	.	.	.	.	T	4.909	0.168980	0.09339	.	.	ENSG00000188629	ENST00000541595;ENST00000343499;ENST00000434737	T;T;T	0.07114	3.22;3.22;3.22	2.49	-3.74	0.04385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01765	0.0056	N	0.00413	-1.525	0.26531	N	0.974258	B	0.06786	0.001	B	0.06405	0.002	T	0.44787	-0.9305	8	0.26408	T	0.33	.	4.5891	0.12297	0.2676:0.4813:0.0:0.2511	.	295	Q13360	ZN177_HUMAN	S	295;295;455	ENSP00000445323:I295S;ENSP00000341497:I295S;ENSP00000415070:I455S	ENSP00000341497:I295S	I	+	2	0	ZNF177	9353371	0.000000	0.05858	0.004000	0.12327	0.994000	0.84299	-5.376000	0.00127	-1.161000	0.02800	0.460000	0.39030	ATT		0.423	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451		G	9492371	T	G	9492371	3	3	61	1	0	0	0	0	1	0	0	0	17785	1493	52	4	1382	4	ZNF177	19	9492371	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	79264	9492371	49636612	10836	18821										
ZNF266	10781	broad.mit.edu	37	chr19	9523994	9523994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgccttctttcatgatttCgaaaggaactggaagaactg	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9523994C>T	ENST00000592904.1	-	5	3683	c.1607G>A	c.(1606-1608)cGa>cAa	p.R536Q	ZNF266_ENST00000590306.1_Missense_Mutation_p.R536Q|ZNF266_ENST00000361451.2_Missense_Mutation_p.R536Q|ZNF266_ENST00000588221.1_Missense_Mutation_p.R536Q|ZNF266_ENST00000361151.1_Missense_Mutation_p.R536Q|ZNF266_ENST00000592292.1_Missense_Mutation_p.R536Q|ZNF266_ENST00000588933.1_Missense_Mutation_p.R536Q			Q14584	ZN266_HUMAN	zinc finger protein 266	536					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R536Q(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						TTCATGATTTCGAAAGGAACT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	81	83					19																	9523994		2203	4300	6503	9384994	SO:0001583	missense	10781			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1607G>A	19.37:g.9523994C>T	ENSP00000466714:p.Arg536Gln		9384994	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.244590	0.22796	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.35789	1.29;1.29	2.21	-4.43	0.03568	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14830	0.0358	N	0.11892	0.195	0.09310	N	1	B	0.19200	0.034	B	0.04013	0.001	T	0.11542	-1.0583	9	0.41790	T	0.15	.	1.5931	0.02658	0.1365:0.1502:0.2719:0.4414	.	536	Q14584	ZN266_HUMAN	Q	536	ENSP00000354680:R536Q;ENSP00000355047:R536Q	ENSP00000355047:R536Q	R	-	2	0	ZNF266	9384994	0.000000	0.05858	0.000000	0.03702	0.409000	0.31022	-0.584000	0.05800	-1.965000	0.01010	0.455000	0.32223	CGA		0.438	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			T	9523994	C	T	9523994	3	4	61	1	0	0	0	0	1	0	0	0	17844	884	31	1	46	1	ZNF266	19	9523994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31623	9523994	49604989	10837	18822										
ZNF266	10781	broad.mit.edu	37	chr19	9524066	9524066	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtgtgagttCgttcatgtaactgaaacgaa	9	8	2	2	rs146314378		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9524066C>T	ENST00000592904.1	-	5	3611	c.1535G>A	c.(1534-1536)cGa>cAa	p.R512Q	ZNF266_ENST00000590306.1_Missense_Mutation_p.R512Q|ZNF266_ENST00000361451.2_Missense_Mutation_p.R512Q|ZNF266_ENST00000588221.1_Missense_Mutation_p.R512Q|ZNF266_ENST00000361151.1_Missense_Mutation_p.R512Q|ZNF266_ENST00000592292.1_Missense_Mutation_p.R512Q|ZNF266_ENST00000588933.1_Missense_Mutation_p.R512Q			Q14584	ZN266_HUMAN	zinc finger protein 266	512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R512Q(2)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						AGTGTGAGTTCGTTCATGTAA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	19						C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	98	77	84		1535,1535	-1.2	0	19	dbSNP_134	84	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ZNF266	NM_006631.2,NM_198058.1	43,43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	512/550,512/550	9524066	2,13004	2203	4300	6503	9385066	SO:0001583	missense	10781			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1535G>A	19.37:g.9524066C>T	ENSP00000466714:p.Arg512Gln		9385066	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983888	0.74474	0.0	2.33E-4	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.24723	1.84;1.84	2.4	-1.18	0.09617	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45276	0.1334	M	0.77486	2.375	0.09310	N	1	D	0.89917	1.0	D	0.70016	0.967	T	0.29640	-1.0005	9	0.72032	D	0.01	.	7.6122	0.28137	0.0:0.7087:0.0:0.2913	.	512	Q14584	ZN266_HUMAN	Q	512	ENSP00000354680:R512Q;ENSP00000355047:R512Q	ENSP00000355047:R512Q	R	-	2	0	ZNF266	9385066	0.000000	0.05858	0.000000	0.03702	0.580000	0.36256	0.055000	0.14229	-0.155000	0.11098	0.455000	0.32223	CGA		0.438	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			T	9524066	C	T	9524066	3	4	61	1	0	0	0	0	1	0	0	0	17844	884	31	1	118	1	ZNF266	19	9524066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72	9524066	49604917	10838	18823										
ZNF266	10781	broad.mit.edu	37	chr19	9524612	9524612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaatttctaaaggattttCcacatatcttacattcaaag	5	7	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9524612C>T	ENST00000592904.1	-	5	3065	c.989G>A	c.(988-990)gGa>gAa	p.G330E	ZNF266_ENST00000590306.1_Missense_Mutation_p.G330E|ZNF266_ENST00000361451.2_Missense_Mutation_p.G330E|ZNF266_ENST00000588221.1_Missense_Mutation_p.G330E|ZNF266_ENST00000361151.1_Missense_Mutation_p.G330E|ZNF266_ENST00000592292.1_Missense_Mutation_p.G330E|ZNF266_ENST00000588933.1_Missense_Mutation_p.G330E			Q14584	ZN266_HUMAN	zinc finger protein 266	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G330E(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						AAAGGATTTTCCACATATCTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	88	87					19																	9524612		2203	4300	6503	9385612	SO:0001583	missense	10781			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.989G>A	19.37:g.9524612C>T	ENSP00000466714:p.Gly330Glu		9385612	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833669	0.71258	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.58210	0.35;0.35	2.53	2.53	0.30540	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.59088	0.2168	L	0.45698	1.435	0.27814	N	0.94203	D	0.65815	0.995	P	0.57776	0.827	T	0.51505	-0.8697	9	0.59425	D	0.04	.	11.1769	0.48606	0.0:1.0:0.0:0.0	.	330	Q14584	ZN266_HUMAN	E	330	ENSP00000354680:G330E;ENSP00000355047:G330E	ENSP00000355047:G330E	G	-	2	0	ZNF266	9385612	0.004000	0.15560	0.321000	0.25320	0.630000	0.37929	0.376000	0.20535	1.727000	0.51537	0.555000	0.69702	GGA		0.383	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			T	9524612	C	T	9524612	3	4	61	1	0	0	0	0	1	0	0	0	17844	855	30	3	664	3	ZNF266	19	9524612	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	546	9524612	49604371	10839	18824										
ZNF560	147741	broad.mit.edu	37	chr19	9577447	9577447	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgcacatgattagtaagatCtgaatgacaagtgaaggctt	10	6	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9577447C>A	ENST00000301480.4	-	10	2389	c.2176G>T	c.(2176-2178)Gat>Tat	p.D726Y		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	726					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D726Y(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TTAGTAAGATCTGAATGACAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											123	114	117					19																	9577447		2203	4300	6503	9438447	SO:0001583	missense	147741			AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.2176G>T	19.37:g.9577447C>A	ENSP00000301480:p.Asp726Tyr		9438447	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	1.394	-0.579934	0.03854	.	.	ENSG00000198028	ENST00000301480	T	0.19394	2.15	2.02	-4.03	0.04021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09598	0.0236	L	0.31157	0.91	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.39542	-0.9609	9	0.12103	T	0.63	.	0.7177	0.00935	0.2904:0.2584:0.2875:0.1637	.	726	Q96MR9	ZN560_HUMAN	Y	726	ENSP00000301480:D726Y	ENSP00000301480:D726Y	D	-	1	0	ZNF560	9438447	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.847000	0.00095	-2.094000	0.00854	-0.379000	0.06801	GAT		0.398	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		A	9577447	C	A	9577447	3	1	61	1	0	0	0	0	1	0	0	0	18030	913	32	2	200	2	ZNF560	19	9577447	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52835	9577447	49551536	10840	18825										
ZNF560	147741	broad.mit.edu	37	chr19	9577834	9577834	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacattcatatggcttctCtccactgtgtcttcgtaaat	5	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9577834C>A	ENST00000301480.4	-	10	2002	c.1789G>T	c.(1789-1791)Gag>Tag	p.E597*		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	597					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E597*(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TATGGCTTCTCTCCACTGTGT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											155	135	141					19																	9577834		2203	4300	6503	9438834	SO:0001587	stop_gained	147741			AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1789G>T	19.37:g.9577834C>A	ENSP00000301480:p.Glu597*		9438834	Q495S9|Q495T1	Nonsense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	38	6.878422	0.97904	.	.	ENSG00000198028	ENST00000301480	.	.	.	2.05	-0.156	0.13391	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.0644	0.19856	0.0:0.698:0.0:0.3019	.	.	.	.	X	597	.	ENSP00000301480:E597X	E	-	1	0	ZNF560	9438834	0.409000	0.25368	0.002000	0.10522	0.761000	0.43186	1.640000	0.37186	0.017000	0.15025	-0.424000	0.05967	GAG		0.413	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		A	9577834	C	A	9577834	4	1	61	1	0	0	0	0	0	1	0	0	18030	922	32	2	587	2	ZNF560	19	9577834	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	387	9577834	49551149	10841	18826										
ZNF426	79088	broad.mit.edu	37	chr19	9639964	9639964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcccataattcctccattCgtagagtttttctccattgt	6	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9639964C>T	ENST00000535489.1	-	6	1093	c.757G>A	c.(757-759)Gaa>Aaa	p.E253K	ZNF426_ENST00000253115.2_Missense_Mutation_p.E253K|ZNF426_ENST00000593003.1_Missense_Mutation_p.E215K			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E253K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						TTCCTCCATTCGTAGAGTTTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											159	159	159					19																	9639964		2203	4300	6503	9500964	SO:0001583	missense	79088			AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.757G>A	19.37:g.9639964C>T	ENSP00000439017:p.Glu253Lys		9500964	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	C	4.585	0.108709	0.08780	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.05513	3.43;3.43	1.42	-2.25	0.06888	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	L	0.27053	0.805	0.09310	N	1	B;B	0.20550	0.046;0.046	B;B	0.13407	0.009;0.009	T	0.46721	-0.9171	9	0.18710	T	0.47	.	2.788	0.05379	0.2194:0.271:0.0:0.5095	.	240;253	Q59EH4;Q9BUY5	.;ZN426_HUMAN	K	240;253;253	ENSP00000253115:E253K;ENSP00000439017:E253K	ENSP00000253115:E253K	E	-	1	0	ZNF426	9500964	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.992000	0.03724	-0.686000	0.05170	0.313000	0.20887	GAA		0.383	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		T	9639964	C	T	9639964	3	4	61	1	0	0	0	0	1	0	0	0	17939	893	31	1	911	1	ZNF426	19	9639964	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62130	9639964	49489019	10842	18827										
ZNF561	93134	broad.mit.edu	37	chr19	9721101	9721101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttctccactatgagttttCaaatgtttactacgacggga	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9721101C>A	ENST00000302851.3	-	6	1599	c.1236G>T	c.(1234-1236)ttG>ttT	p.L412F	ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000354661.4_Missense_Mutation_p.L276F|ZNF561_ENST00000424629.1_Missense_Mutation_p.L343F|ZNF561_ENST00000326044.5_3'UTR	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L343F(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TATGAGTTTTCAAATGTTTAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											133	129	130					19																	9721101		2203	4300	6503	9582101	SO:0001583	missense	93134			AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"Zinc fingers, C2H2-type", "-"	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.1236G>T	19.37:g.9721101C>A	ENSP00000303915:p.Leu412Phe		9582101	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	37	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	C	6.737	0.504763	0.12822	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000354661	T;T;T	0.36340	1.26;1.26;1.26	1.1	-1.49	0.08718	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43299	0.1241	L	0.41632	1.29	0.09310	N	1	D	0.69078	0.997	D	0.81914	0.995	T	0.31586	-0.9938	9	0.87932	D	0	.	5.0507	0.14507	0.0:0.382:0.0:0.618	.	412	Q8N587	ZN561_HUMAN	F	343;412;276	ENSP00000393074:L343F;ENSP00000303915:L412F;ENSP00000346687:L276F	ENSP00000303915:L412F	L	-	3	2	ZNF561	9582101	0.000000	0.05858	0.002000	0.10522	0.068000	0.16541	-1.462000	0.02364	-0.428000	0.07339	0.298000	0.19748	TTG		0.408	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9721101	C	A	9721101	3	1	61	1	0	0	0	0	1	0	0	0	18031	825	29	2	228	2	ZNF561	19	9721101	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81137	9721101	49407882	10843	18828										
ZNF561	93134	broad.mit.edu	37	chr19	9721569	9721569	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaaggatttcccacatttCttagtctttttggatttctt	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9721569C>A	ENST00000302851.3	-	6	1131	c.768G>T	c.(766-768)aaG>aaT	p.K256N	ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000354661.4_Missense_Mutation_p.K120N|ZNF561_ENST00000424629.1_Missense_Mutation_p.K187N|ZNF561_ENST00000326044.5_3'UTR	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K187N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TCCCACATTTCTTAGTCTTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	75	75					19																	9721569		2202	4300	6502	9582569	SO:0001583	missense	93134			AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"Zinc fingers, C2H2-type", "-"	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.768G>T	19.37:g.9721569C>A	ENSP00000303915:p.Lys256Asn		9582569	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	37	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	C	10.04	1.240245	0.22711	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000354661;ENST00000444611	T;T;T;T	0.14893	3.03;3.15;3.07;2.47	1.42	-2.84	0.05751	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05868	0.0153	N	0.12182	0.205	0.09310	N	1	P	0.34522	0.455	B	0.30105	0.111	T	0.36553	-0.9743	9	0.09590	T	0.72	.	4.4094	0.11425	0.3767:0.2514:0.3719:0.0	.	256	Q8N587	ZN561_HUMAN	N	187;256;120;262	ENSP00000393074:K187N;ENSP00000303915:K256N;ENSP00000346687:K120N;ENSP00000392013:K262N	ENSP00000303915:K256N	K	-	3	2	ZNF561	9582569	0.000000	0.05858	0.000000	0.03702	0.730000	0.41778	-5.944000	0.00089	-1.146000	0.02854	0.298000	0.19748	AAG		0.378	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9721569	C	A	9721569	3	1	61	1	0	0	0	0	1	0	0	0	18031	912	32	2	696	2	ZNF561	19	9721569	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	468	9721569	49407414	10844	18829										
ZNF562	54811	broad.mit.edu	37	chr19	9764066	9764066	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacttctctcctttatgagtTtttgcatgtgcagaaagttg	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9764066T>G	ENST00000448622.1	-	6	1002	c.840A>C	c.(838-840)aaA>aaC	p.K280N	ZNF562_ENST00000537617.1_Missense_Mutation_p.K164N|ZNF562_ENST00000590155.1_Missense_Mutation_p.K279N|ZNF562_ENST00000541032.1_Missense_Mutation_p.K243N|ZNF562_ENST00000293648.4_Missense_Mutation_p.K208N|ZNF562_ENST00000453792.2_Missense_Mutation_p.K211N|ZNF562_ENST00000453372.2_Missense_Mutation_p.K280N	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K208N(1)|p.K280N(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						CTTTATGAGTTTTTGCATGTG	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	19											83	83	83					19																	9764066		2203	4300	6503	9625066	SO:0001583	missense	54811			AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"Zinc fingers, C2H2-type", "-"	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.840A>C	19.37:g.9764066T>G	ENSP00000411784:p.Lys280Asn		9625066	Q32MN2|Q9NXS5	Missense_Mutation	SNP	ENST00000448622.1	37	CCDS45956.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.895110	0.33442	.	.	ENSG00000171466	ENST00000453372;ENST00000448622;ENST00000293648;ENST00000541032;ENST00000453792;ENST00000537617	T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84	1.76	0.673	0.17941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39172	0.1068	L	0.52126	1.63	0.09310	N	1	D;D;D;D;D	0.76494	0.989;0.991;0.999;0.999;0.999	D;D;D;D;D	0.83275	0.985;0.987;0.996;0.995;0.991	T	0.14144	-1.0483	9	0.87932	D	0	.	6.0421	0.19740	0.0:0.0:0.2932:0.7068	.	164;279;243;280;208	F5H1B4;B4DMG0;B4DZP9;Q6V9R5;Q6V9R5-2	.;.;.;ZN562_HUMAN;.	N	280;280;208;243;211;164	ENSP00000410734:K280N;ENSP00000411784:K280N;ENSP00000293648:K208N;ENSP00000442614:K243N;ENSP00000440451:K211N;ENSP00000445816:K164N	ENSP00000293648:K208N	K	-	3	2	ZNF562	9625066	0.000000	0.05858	0.001000	0.08648	0.130000	0.20726	-1.468000	0.02350	0.142000	0.18901	0.260000	0.18958	AAA		0.348	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656		G	9764066	T	G	9764066	3	3	61	1	0	0	0	0	1	0	0	0	18032	1838	64	4	444	4	ZNF562	19	9764066	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	42497	9764066	49364917	10845	18830										
ZNF846	162993	broad.mit.edu	37	chr19	9868260	9868260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttgctccagtgtgagttCgtgtgtgaacgttaaggtat	13	5	0	2	rs563965653		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9868260C>T	ENST00000397902.2	-	6	1906	c.1493G>A	c.(1492-1494)cGa>cAa	p.R498Q	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000588267.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R498Q(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AGTGTGAGTTCGTGTGTGAAC	0.403													N|||	1	0.000199681	0	0	5008	,	,		22005	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											125	134	131					19																	9868260		2139	4282	6421	9729260	SO:0001583	missense	162993			AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1493G>A	19.37:g.9868260C>T	ENSP00000380999:p.Arg498Gln		9729260	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	16.34	3.096601	0.56075	.	.	ENSG00000196605	ENST00000397902	T	0.24723	1.84	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42698	0.1214	M	0.67953	2.075	0.20563	N	0.999885	D	0.76494	0.999	P	0.62382	0.901	T	0.13335	-1.0513	9	0.72032	D	0.01	.	9.5782	0.39470	0.0:1.0:0.0:0.0	.	498	Q147U1	ZN846_HUMAN	Q	498	ENSP00000380999:R498Q	ENSP00000380999:R498Q	R	-	2	0	ZNF846	9729260	0.000000	0.05858	0.495000	0.27527	0.129000	0.20672	-0.091000	0.11146	1.304000	0.44892	0.456000	0.33151	CGA		0.403	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		T	9868260	C	T	9868260	3	4	61	1	0	0	0	0	1	0	0	0	18231	884	31	1	112	1	ZNF846	19	9868260	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104194	9868260	49260723	10846	18831										
ZNF846	162993	broad.mit.edu	37	chr19	9873997	9873997	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagttctccaacatcacatCtctgtagagatctctctggg	8	11	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9873997C>A	ENST00000397902.2	-	3	516	c.103G>T	c.(103-105)Gat>Tat	p.D35Y	ZNF846_ENST00000586293.1_Missense_Mutation_p.D35Y|ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000588267.1_5'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	35	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D35Y(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AACATCACATCTCTGTAGAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											124	130	128					19																	9873997		2203	4300	6503	9734997	SO:0001583	missense	162993			AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.103G>T	19.37:g.9873997C>A	ENSP00000380999:p.Asp35Tyr		9734997	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	14.10	2.434576	0.43224	.	.	ENSG00000196605	ENST00000397902	T	0.02863	4.13	2.17	-0.00709	0.14011	Krueppel-associated box (4);	.	.	.	.	T	0.16214	0.0390	H	0.95539	3.685	0.24250	N	0.995322	D	0.63880	0.993	D	0.64687	0.928	T	0.04825	-1.0924	8	.	.	.	.	4.3646	0.11218	0.0:0.6473:0.0:0.3527	.	35	Q147U1	ZN846_HUMAN	Y	35	ENSP00000380999:D35Y	.	D	-	1	0	ZNF846	9734997	0.819000	0.29175	0.998000	0.56505	0.982000	0.71751	0.563000	0.23547	0.068000	0.16574	-0.351000	0.07748	GAT		0.403	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		A	9873997	C	A	9873997	3	1	61	1	0	0	0	0	1	0	0	0	18231	913	32	2	1514	2	ZNF846	19	9873997	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5737	9873997	49254986	10847	18832										
FBXL12	54850	broad.mit.edu	37	chr19	9922118	9922118	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggcagcacggtggggtcCtgctgcttgtggagccaggc	19	10	0	0	rs375572016		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9922118C>A	ENST00000247977.4	-	3	676	c.435G>T	c.(433-435)caG>caT	p.Q145H	FBXL12_ENST00000591009.1_Missense_Mutation_p.Q92H|FBXL12_ENST00000592067.1_3'UTR|FBXL12_ENST00000586651.1_3'UTR|FBXL12_ENST00000589626.1_3'UTR|FBXL12_ENST00000585379.1_Missense_Mutation_p.Q92H|FBXL12_ENST00000588922.1_3'UTR	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12	145					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)		p.Q145H(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						CGGTGGGGTCCTGCTGCTTGT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											52	55	54					19																	9922118		2203	4300	6503	9783118	SO:0001583	missense	54850			AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"F-boxes / Leucine-rich repeats"	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8		ENST00000247977.4:c.435G>T	19.37:g.9922118C>A	ENSP00000247977:p.Gln145His		9783118	B3KSJ8|Q9H5K4	Missense_Mutation	SNP	ENST00000247977.4	37	CCDS12218.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609175	0.28623	.	.	ENSG00000127452	ENST00000247977	T	0.16897	2.31	4.76	2.47	0.30058	.	1.484910	0.03700	N	0.248388	T	0.09598	0.0236	N	0.08118	0	0.20307	N	0.999911	D	0.53462	0.96	B	0.40565	0.333	T	0.18209	-1.0344	9	.	.	.	-16.2639	6.7652	0.23562	0.206:0.596:0.198:0.0	.	145	Q9NXK8	FXL12_HUMAN	H	145	ENSP00000247977:Q145H	.	Q	-	3	2	FBXL12	9783118	0.883000	0.30277	0.854000	0.33618	0.869000	0.49853	0.450000	0.21762	1.214000	0.43395	0.655000	0.94253	CAG		0.672	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450265.1	NM_017703		A	9922118	C	A	9922118	3	1	61	1	0	0	0	0	1	0	0	0	5727	680	24	2	549	2	FBXL12	19	9922118	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48121	9922118	49206865	10848	18833										
OLFM2	93145	broad.mit.edu	37	chr19	9965083	9965083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccaggtgggagttggtcaCgtagagcacaccgcagatca	14	10	2	2	rs148943256		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:9965083C>T	ENST00000264833.4	-	6	1329	c.1144G>A	c.(1144-1146)Gtg>Atg	p.V382M	AC008752.3_ENST00000582439.1_RNA|OLFM2_ENST00000590841.1_Missense_Mutation_p.V304M	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	382	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)		p.V382M(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						GAGTTGGTCACGTAGAGCACA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	118	103	108		1144	4.4	1	19	dbSNP_134	108	0,8600		0,0,4300	no	missense	OLFM2	NM_058164.2	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	382/455	9965083	1,13005	2203	4300	6503	9826083	SO:0001583	missense	93145			AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.1144G>A	19.37:g.9965083C>T	ENSP00000264833:p.Val382Met		9826083	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502266	0.64298	2.27E-4	0.0	ENSG00000105088	ENST00000264833	D	0.90900	-2.75	4.36	4.36	0.52297	Olfactomedin-like (3);	0.000000	0.64402	D	0.000001	D	0.95614	0.8574	M	0.88640	2.97	0.54753	D	0.999988	D	0.89917	1.0	D	0.80764	0.994	D	0.96024	0.9011	9	.	.	.	.	14.4229	0.67196	0.0:1.0:0.0:0.0	.	382	O95897	NOE2_HUMAN	M	382	ENSP00000264833:V382M	.	V	-	1	0	OLFM2	9826083	1.000000	0.71417	0.994000	0.49952	0.782000	0.44232	4.660000	0.61511	2.239000	0.73571	0.561000	0.74099	GTG		0.612	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			T	9965083	C	T	9965083	3	4	61	1	0	0	0	0	1	0	0	0	10884	536	19	1	224	1	OLFM2	19	9965083	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42965	9965083	49163900	10849	18834										
COL5A3	50509	broad.mit.edu	37	chr19	10071203	10071203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctcgagaagagctgaattCgaaaagggtcttcgtctgtc	12	9	2	3	rs563109290		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10071203C>T	ENST00000264828.3	-	67	5207	c.5122G>A	c.(5122-5124)Gaa>Aaa	p.E1708K		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1708	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.E1708K(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GAGCTGAATTCGAAAAGGGTC	0.572													C|||	1	0.000199681	0	0.0014	5008	,	,		18201	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											93	102	99					19																	10071203		2203	4300	6503	9932203	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.5122G>A	19.37:g.10071203C>T	ENSP00000264828:p.Glu1708Lys		9932203	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622486	0.28889	.	.	ENSG00000080573	ENST00000264828	T	0.76316	-1.01	4.03	1.79	0.24919	Fibrillar collagen, C-terminal (4);	0.175070	0.38164	U	0.001800	D	0.82296	0.5006	M	0.92169	3.28	0.34133	D	0.66547	P	0.44429	0.835	B	0.43194	0.411	D	0.87058	0.2151	10	0.56958	D	0.05	.	11.6369	0.51209	0.0:0.655:0.345:0.0	.	1708	P25940	CO5A3_HUMAN	K	1708	ENSP00000264828:E1708K	ENSP00000264828:E1708K	E	-	1	0	COL5A3	9932203	0.977000	0.34250	0.116000	0.21606	0.174000	0.22865	2.489000	0.45285	0.336000	0.23639	0.462000	0.41574	GAA		0.572	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10071203	C	T	10071203	3	4	61	1	0	0	0	0	1	0	0	0	3704	893	31	1	119	1	COL5A3	19	10071203	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106120	10071203	49057780	10850	18835										
COL5A3	50509	broad.mit.edu	37	chr19	10081910	10081910	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtctcctgggggccctaGatctccgggcagccccgtgg	16	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10081910G>T	ENST00000264828.3	-	52	3884	c.3799C>A	c.(3799-3801)Cta>Ata	p.L1267I		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1267	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.L1267I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GGGGGCCCTAGATCTCCGGGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	19											18	22	21					19																	10081910		2203	4299	6502	9942910	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3799C>A	19.37:g.10081910G>T	ENSP00000264828:p.Leu1267Ile		9942910	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.136797	0.37728	.	.	ENSG00000080573	ENST00000264828	D	0.93547	-3.24	4.62	4.62	0.57501	.	0.574192	0.15856	N	0.241260	D	0.84106	0.5399	N	0.05124	-0.11	0.09310	N	1	P	0.35077	0.483	B	0.27887	0.084	T	0.77864	-0.2429	10	0.46703	T	0.11	.	15.0029	0.71489	0.0:0.0:1.0:0.0	.	1267	P25940	CO5A3_HUMAN	I	1267	ENSP00000264828:L1267I	ENSP00000264828:L1267I	L	-	1	2	COL5A3	9942910	1.000000	0.71417	0.360000	0.25837	0.915000	0.54546	3.791000	0.55469	2.389000	0.81357	0.462000	0.41574	CTA		0.522	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10081910	G	T	10081910	3	4	61	1	0	0	0	0	1	0	0	0	3704	933	33	2	1502	2	COL5A3	19	10081910	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10707	10081910	49047073	10851	18836										
COL5A3	50509	broad.mit.edu	37	chr19	10085048	10085048	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctttctgcccaaagaggcCtgggggtccccggcgcccct	12	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10085048C>A	ENST00000264828.3	-	46	3464	c.3379G>T	c.(3379-3381)Ggc>Tgc	p.G1127C		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1127	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.G1127C(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CCAAAGAGGCCTGGGGGTCCC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											45	49	48					19																	10085048		2203	4300	6503	9946048	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3379G>T	19.37:g.10085048C>A	ENSP00000264828:p.Gly1127Cys		9946048	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442540	0.83993	.	.	ENSG00000080573	ENST00000264828	D	0.99637	-6.29	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	D	0.99806	0.9916	H	0.98426	4.23	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96693	0.9512	10	0.87932	D	0	.	15.5331	0.75980	0.0:1.0:0.0:0.0	.	1127	P25940	CO5A3_HUMAN	C	1127	ENSP00000264828:G1127C	ENSP00000264828:G1127C	G	-	1	0	COL5A3	9946048	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.605000	0.74155	2.246000	0.74042	0.313000	0.20887	GGC		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10085048	C	A	10085048	3	1	61	1	0	0	0	0	1	0	0	0	3704	681	24	2	1946	2	COL5A3	19	10085048	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3138	10085048	49043935	10852	18837										
COL5A3	50509	broad.mit.edu	37	chr19	10112446	10112446	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccatccccatccaacctCtaggatcgtggcattgagtc	7	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10112446C>A	ENST00000264828.3	-	7	1046	c.961G>T	c.(961-963)Gag>Tag	p.E321*		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	321	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.E321*(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CATCCAACCTCTAGGATCGTG	0.547											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	19											119	112	115					19																	10112446		2203	4300	6503	9973446	SO:0001587	stop_gained	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.961G>T	19.37:g.10112446C>A	ENSP00000264828:p.Glu321*	662	9973446	Q9NZQ6	Nonsense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	37	6.456209	0.97581	.	.	ENSG00000080573	ENST00000264828	.	.	.	4.95	1.05	0.20165	.	1.489540	0.06765	U	0.782498	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	6.4713	0.22009	0.0:0.3913:0.4965:0.1122	.	.	.	.	X	321	.	ENSP00000264828:E321X	E	-	1	0	COL5A3	9973446	0.369000	0.25039	0.442000	0.26870	0.494000	0.33585	0.471000	0.22100	0.537000	0.28751	0.462000	0.41574	GAG		0.547	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10112446	C	A	10112446	4	1	61	1	0	0	0	0	0	1	0	0	3704	922	32	2	4520	2	COL5A3	19	10112446	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27398	10112446	49016537	10853	18838										
COL5A3	50509	broad.mit.edu	37	chr19	10114298	10114298	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatttccttgttctttttCctgcccttccccttgcgacc	4	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10114298C>A	ENST00000264828.3	-	6	877	c.792G>T	c.(790-792)agG>agT	p.R264S		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	264	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.R264S(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TGTTCTTTTTCCTGCCCTTCC	0.577											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	19											270	200	223					19																	10114298		2203	4300	6503	9975298	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.792G>T	19.37:g.10114298C>A	ENSP00000264828:p.Arg264Ser	662	9975298	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	7.611	0.674800	0.14841	.	.	ENSG00000080573	ENST00000264828	D	0.89939	-2.59	4.08	1.84	0.25277	.	1.742540	0.02981	U	0.145682	T	0.80248	0.4588	L	0.40543	1.245	0.27961	N	0.936766	P	0.37781	0.608	B	0.27500	0.08	T	0.67530	-0.5647	10	0.09590	T	0.72	.	5.2922	0.15733	0.0:0.7009:0.0:0.2991	.	264	P25940	CO5A3_HUMAN	S	264	ENSP00000264828:R264S	ENSP00000264828:R264S	R	-	3	2	COL5A3	9975298	0.998000	0.40836	1.000000	0.80357	0.725000	0.41563	0.194000	0.17135	0.402000	0.25451	0.456000	0.33151	AGG		0.577	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10114298	C	A	10114298	3	1	61	1	0	0	0	0	1	0	0	0	3704	854	30	2	4693	2	COL5A3	19	10114298	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1852	10114298	49014685	10854	18839										
RDH8	50700	broad.mit.edu	37	chr19	10127844	10127844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacgtgtgcagtgatgagtCggtggcccagtgtctcagct	16	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10127844C>T	ENST00000171214.1	+	2	464	c.215C>T	c.(214-216)tCg>tTg	p.S72L	RDH8_ENST00000591589.1_Missense_Mutation_p.S92L	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	72					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.S72L(1)		endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	AGTGATGAGTCGGTGGCCCAG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	70	74					19																	10127844		2203	4300	6503	9988844	SO:0001583	missense	50700			AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	14423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 28C, member 2"	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.215C>T	19.37:g.10127844C>T	ENSP00000171214:p.Ser72Leu		9988844	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		.	.	.	.	.	.	.	.	.	.	C	27.8	4.861661	0.91433	.	.	ENSG00000080511	ENST00000171214	D	0.94417	-3.42	4.77	4.77	0.60923	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97504	0.9183	M	0.88450	2.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98419	1.0576	10	0.87932	D	0	.	15.3068	0.73998	0.0:1.0:0.0:0.0	.	72	Q9NYR8	RDH8_HUMAN	L	72	ENSP00000171214:S72L	ENSP00000171214:S72L	S	+	2	0	RDH8	9988844	1.000000	0.71417	0.922000	0.36590	0.878000	0.50629	7.304000	0.78882	2.190000	0.69967	0.655000	0.94253	TCG		0.602	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	10127844	C	T	10127844	3	4	61	1	0	0	0	0	1	0	0	0	13233	893	31	1	221	1	RDH8	19	10127844	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13546	10127844	49001139	10855	18840										
DNMT1	1786	broad.mit.edu	37	chr19	10265724	10265724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatccatcagaatgtattCggcaaatgctggggtgaaca	13	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10265724C>T	ENST00000340748.4	-	19	1688	c.1453G>A	c.(1453-1455)Gaa>Aaa	p.E485K	DNMT1_ENST00000359526.4_Missense_Mutation_p.E501K|DNMT1_ENST00000540357.1_Missense_Mutation_p.E485K			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	485	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E485K(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	AGAATGTATTCGGCAAATGCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	79	79					19																	10265724		2203	4300	6503	10126724	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1453G>A	19.37:g.10265724C>T	ENSP00000345739:p.Glu485Lys		10126724	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.976226	0.74360	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.76968	-1.06;-1.06;-1.06	5.94	5.94	0.96194	DNA (cytosine-5)-methyltransferase 1, replication foci domain (1);	0.047098	0.85682	D	0.000000	D	0.87334	0.6151	M	0.72894	2.215	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.998	D;P;D	0.67382	0.918;0.871;0.951	D	0.86246	0.1646	10	0.48119	T	0.1	.	19.1347	0.93422	0.0:1.0:0.0:0.0	.	485;501;485	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	K	501;485;485;353	ENSP00000352516:E501K;ENSP00000440457:E485K;ENSP00000345739:E485K	ENSP00000345739:E485K	E	-	1	0	DNMT1	10126724	1.000000	0.71417	0.535000	0.28026	0.004000	0.04260	7.796000	0.85898	2.826000	0.97356	0.561000	0.74099	GAA		0.537	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		T	10265724	C	T	10265724	3	4	61	1	0	0	0	0	1	0	0	0	4686	893	31	1	3485	1	DNMT1	19	10265724	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	137880	10265724	48863259	10856	18841										
DNMT1	1786	broad.mit.edu	37	chr19	10283797	10283797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttcttccttttcagtgCgcgttcctgattttgctctt	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10283797C>T	ENST00000340748.4	-	8	924	c.689G>A	c.(688-690)cGc>cAc	p.R230H	DNMT1_ENST00000359526.4_Missense_Mutation_p.R246H|DNMT1_ENST00000540357.1_Missense_Mutation_p.R230H			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	230	Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R230H(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTTTTCAGTGCGCGTTCCTGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											179	144	156					19																	10283797		2203	4300	6503	10144797	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.689G>A	19.37:g.10283797C>T	ENSP00000345739:p.Arg230His		10144797	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	7.291	0.611106	0.14066	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.29142	1.91;1.58;1.58	4.17	0.79	0.18613	.	0.956050	0.08592	N	0.922803	T	0.09642	0.0237	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33979	-0.9847	10	0.15499	T	0.54	.	2.509	0.04652	0.2031:0.2374:0.0:0.5594	.	230;246;230	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	H	246;230;230;98	ENSP00000352516:R246H;ENSP00000440457:R230H;ENSP00000345739:R230H	ENSP00000345739:R230H	R	-	2	0	DNMT1	10144797	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.346000	0.07760	-0.032000	0.13758	-0.302000	0.09304	CGC		0.433	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		T	10283797	C	T	10283797	3	4	61	1	0	0	0	0	1	0	0	0	4686	768	27	1	4293	1	DNMT1	19	10283797	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18073	10283797	48845186	10857	18842										
ICAM4	3386	broad.mit.edu	37	chr19	10398694	10398694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcccacagctttggcctccGgttccatcgctgcccttgta	9	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10398694G>A	ENST00000380770.3	+	3	776	c.730G>A	c.(730-732)Ggt>Agt	p.G244S	ICAM5_ENST00000221980.4_5'Flank|CTD-2369P2.8_ENST00000589379.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA|ICAM4_ENST00000393717.2_3'UTR|ICAM4_ENST00000340992.4_Missense_Mutation_p.R218Q	NM_001544.4	NP_001535.1	Q14773	ICAM4_HUMAN	intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)	244					extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)	p.R218Q(1)		breast(1)|large_intestine(3)|lung(2)|pancreas(1)	7			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			TTTGGCCTCCGGTTCCATCGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	74	77					19																	10398694		2203	4300	6503	10259694	SO:0001583	missense	3386			X93093	CCDS12232.1, CCDS32904.1, CCDS42500.1	19p13.2	2014-07-19	2006-02-23		ENSG00000105371	ENSG00000105371		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5347	protein-coding gene	gene with protein product		614088	"intercellular adhesion molecule 4, Landsteiner-Wiener blood group", "Landsteiner-Wiener blood group", "intercellular adhesion molecule 4 (LW blood group)"	LW		8639917, 6431896	Standard	NM_001039132		Approved	CD242	uc002mnr.2	Q14773	OTTHUMG00000180405	ENST00000380770.3:c.730G>A	19.37:g.10398694G>A	ENSP00000370147:p.Gly244Ser		10259694	A0M8X2|Q14771|Q14772|Q16375|Q9BWR0	Missense_Mutation	SNP	ENST00000380770.3	37	CCDS12232.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	3.745|3.745	-0.052793|-0.052793	0.07362|0.07362	.|.	.|.	ENSG00000105371|ENSG00000105371	ENST00000380770|ENST00000340992	T|T	0.05382|0.24908	3.45|1.83	3.94|3.94	-0.832|-0.832	0.10785|0.10785	.|.	.|4.874250	.|0.01145	.|N	.|0.006290	T|T	0.16981|0.16981	0.0408|0.0408	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999986|0.999986	B|B	0.02656|0.16603	0.0|0.018	B|B	0.01281|0.06405	0.0|0.002	T|T	0.26815|0.26815	-1.0092|-1.0092	8|9	0.17832|0.87932	T|D	0.49|0	-5.2662|-5.2662	0.4903|0.4903	0.00563|0.00563	0.4335:0.1808:0.2106:0.1751|0.4335:0.1808:0.2106:0.1751	.|.	244|218	Q14773|Q9BWR0	ICAM4_HUMAN|.	S|Q	244|218	ENSP00000370147:G244S|ENSP00000342114:R218Q	ENSP00000370147:G244S|ENSP00000342114:R218Q	G|R	+|+	1|2	0|0	ICAM4|ICAM4	10259694|10259694	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.005000|0.005000	0.04900|0.04900	-0.933000|-0.933000	0.03959|0.03959	-0.249000|-0.249000	0.09569|0.09569	-1.286000|-1.286000	0.01371|0.01371	GGT|CGG		0.607	ICAM4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451214.1	NM_001544		A	10398694	G	A	10398694	3	1	61	1	0	0	0	0	1	0	0	0	7503	1116	39	1	757	1	ICAM4	19	10398694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114897	10398694	48730289	10858	18843										
ICAM5	7087	broad.mit.edu	37	chr19	10404499	10404499	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatctgcgtgcgctctggaGaactcggggccgtcatcgag	15	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10404499G>T	ENST00000221980.4	+	7	1654	c.1591G>T	c.(1591-1593)Gaa>Taa	p.E531*		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	531	Ig-like C2-type 6.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.E531*(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			GCGCTCTGGAGAACTCGGGGC	0.652																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											81	86	84					19																	10404499		2203	4300	6503	10265499	SO:0001587	stop_gained	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1591G>T	19.37:g.10404499G>T	ENSP00000221980:p.Glu531*		10265499	Q9Y6F3	Nonsense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.046284	0.75846	.	.	ENSG00000105376	ENST00000221980	.	.	.	4.85	1.49	0.22878	.	1.082640	0.07104	N	0.841035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-1.9535	4.4201	0.11476	0.2094:0.186:0.6047:0.0	.	.	.	.	X	531	.	ENSP00000221980:E531X	E	+	1	0	ICAM5	10265499	0.001000	0.12720	0.008000	0.14137	0.051000	0.14879	0.096000	0.15147	0.228000	0.21019	0.448000	0.29417	GAA		0.652	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		T	10404499	G	T	10404499	4	4	61	1	0	0	0	0	0	1	0	0	7504	943	33	2	1617	2	ICAM5	19	10404499	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5805	10404499	48724484	10859	18844										
ATG4D	84971	broad.mit.edu	37	chr19	10655657	10655657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacagcgtttccagcgggActttgtgtcccgcctgtggc	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10655657A>G	ENST00000309469.4	+	3	517	c.344A>G	c.(343-345)gAc>gGc	p.D115G	ATG4D_ENST00000540862.1_5'Flank	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	115					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)	p.D115G(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TTCCAGCGGGACTTTGTGTCC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	97	94					19																	10655657		2203	4300	6503	10516657	SO:0001583	missense	84971			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.344A>G	19.37:g.10655657A>G	ENSP00000311318:p.Asp115Gly		10516657	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006589	0.54361	.	.	ENSG00000130734	ENST00000309469	T	0.49720	0.77	5.06	5.06	0.68205	.	0.299176	0.35466	N	0.003190	T	0.74574	0.3734	M	0.93062	3.375	0.80722	D	1	D;D;D	0.76494	0.998;0.985;0.999	D;P;D	0.73380	0.968;0.703;0.98	T	0.81688	-0.0819	10	0.87932	D	0	3.1986	13.7664	0.62997	1.0:0.0:0.0:0.0	.	52;138;115	B4DGM8;B7ZAY9;Q86TL0	.;.;ATG4D_HUMAN	G	115	ENSP00000311318:D115G	ENSP00000311318:D115G	D	+	2	0	ATG4D	10516657	1.000000	0.71417	0.985000	0.45067	0.004000	0.04260	4.160000	0.58164	1.895000	0.54865	0.523000	0.50628	GAC		0.672	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		G	10655657	A	G	10655657	3	3	61	1	0	0	0	0	1	0	0	0	1100	275	10	4	354	4	ATG4D	19	10655657	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	251158	10655657	48473326	10860	18845										
ILF3	3609	broad.mit.edu	37	chr19	10799332	10799332	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcggaggttctgggggcggCtcctcataccaaggcaaaca	15	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10799332C>A	ENST00000590261.1	+	18	2529	c.2529C>A	c.(2527-2529)ggC>ggA	p.G843G	ILF3_ENST00000318511.3_Silent_p.G843G|ILF3_ENST00000588657.1_Silent_p.G847G|ILF3_ENST00000586544.1_3'UTR|ILF3_ENST00000449870.1_Silent_p.G847G			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	843	Interaction with PRMT1.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G843G(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			CTGGGGGCGGCTCCTCATACC	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	19											45	56	53					19																	10799332		2202	4298	6500	10660332	SO:0001819	synonymous_variant	3609			U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"M-phase phosphoprotein 4"	603182	"interleukin enhancer binding factor 3, 90kD"			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.2529C>A	19.37:g.10799332C>A			10660332	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Silent	SNP	ENST00000590261.1	37	CCDS12246.1																																																																																				0.672	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1			A	10799332	C	A	10799332	2	1	61	1	0	0	0	0	0	0	0	1	7733	784	28	2		2	ILF3	19	10799332	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	143675	10799332	48329651	10861	18846										
DNM2	1785	broad.mit.edu	37	chr19	10904493	10904493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgggggcgcccgaatcaatCgcatcttccacgagcggttc	12	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10904493C>T	ENST00000355667.6	+	8	1170	c.1090C>T	c.(1090-1092)Cgc>Tgc	p.R364C	DNM2_ENST00000359692.6_Missense_Mutation_p.R364C|DNM2_ENST00000389253.4_Missense_Mutation_p.R364C|DNM2_ENST00000585892.1_Missense_Mutation_p.R364C|DNM2_ENST00000408974.4_Missense_Mutation_p.R364C|DNM2_ENST00000314646.5_Missense_Mutation_p.R364C	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	364					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.R364C(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CCGAATCAATCGCATCTTCCA	0.617			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	1	Substitution - Missense(1)	large_intestine(1)	19											95	101	99					19																	10904493		2203	4300	6503	10765493	SO:0001583	missense	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1090C>T	19.37:g.10904493C>T	ENSP00000347890:p.Arg364Cys		10765493	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.591650	0.86953	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8	4.93	3.9	0.45041	Dynamin central domain (1);	0.000000	0.85682	D	0.000000	D	0.86130	0.5859	M	0.85197	2.74	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0	D;D;D;D;D	0.77004	0.989;0.953;0.944;0.954;0.954	D	0.87648	0.2526	10	0.87932	D	0	-1.1672	12.1648	0.54123	0.0:0.9156:0.0:0.0844	.	97;364;364;364;364	B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;DYN2_HUMAN;.	C	353;364;364;364;364;364	ENSP00000386192:R364C;ENSP00000347890:R364C;ENSP00000352721:R364C;ENSP00000373905:R364C;ENSP00000313164:R364C	ENSP00000313164:R364C	R	+	1	0	DNM2	10765493	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.818000	0.86416	1.072000	0.40860	0.655000	0.94253	CGC		0.617	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		T	10904493	C	T	10904493	3	4	61	1	0	0	0	0	1	0	0	0	4683	884	31	1	1120	1	DNM2	19	10904493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105161	10904493	48224490	10862	18847										
DNM2	1785	broad.mit.edu	37	chr19	10906768	10906768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccccggacttggcattcGaggccattgtgaaaaagcag	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10906768G>A	ENST00000355667.6	+	10	1308	c.1228G>A	c.(1228-1230)Gag>Aag	p.E410K	DNM2_ENST00000359692.6_Missense_Mutation_p.E410K|DNM2_ENST00000389253.4_Intron|DNM2_ENST00000585892.1_Missense_Mutation_p.E410K|DNM2_ENST00000408974.4_Intron|DNM2_ENST00000314646.5_Intron	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	410					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.E410K(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CTTGGCATTCGAGGCCATTGT	0.512			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	1	Substitution - Missense(1)	large_intestine(1)	19											141	135	137					19																	10906768		2203	4300	6503	10767768	SO:0001583	missense	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1228G>A	19.37:g.10906768G>A	ENSP00000347890:p.Glu410Lys		10767768	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	35	5.435774	0.96168	.	.	ENSG00000079805	ENST00000355667;ENST00000359692	T;T	0.76709	-1.04;-1.04	4.7	4.7	0.59300	Dynamin central domain (1);	.	.	.	.	D	0.92057	0.7483	H	0.96604	3.85	0.80722	D	1	D;D;D	0.89917	1.0;0.966;0.996	D;P;P	0.87578	0.998;0.771;0.905	D	0.94865	0.8025	9	0.87932	D	0	.	16.4349	0.83872	0.0:0.0:1.0:0.0	.	4;410;410	Q8N1K8;P50570-2;P50570	.;.;DYN2_HUMAN	K	410	ENSP00000347890:E410K;ENSP00000352721:E410K	ENSP00000347890:E410K	E	+	1	0	DNM2	10767768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	2.174000	0.68829	0.561000	0.74099	GAG		0.512	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		A	10906768	G	A	10906768	3	1	61	1	0	0	0	0	1	0	0	0	4683	1059	37	1	1266	1	DNM2	19	10906768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2275	10906768	48222215	10863	18848										
DNM2	1785	broad.mit.edu	37	chr19	10935751	10935751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagaaaacgaggatgggGcccaggagaacaccttctcc	13	11	1	2	rs587778236		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10935751G>A	ENST00000355667.6	+	18	1992	c.1912G>A	c.(1912-1914)Gcc>Acc	p.A638T	DNM2_ENST00000359692.6_Missense_Mutation_p.A634T|DNM2_ENST00000389253.4_Missense_Mutation_p.A638T|DNM2_ENST00000585892.1_Missense_Mutation_p.A638T|DNM2_ENST00000408974.4_Missense_Mutation_p.A634T|DNM2_ENST00000314646.5_Missense_Mutation_p.A638T	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	638					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.A634T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CGAGGATGGGGCCCAGGAGAA	0.587			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	1	Substitution - Missense(1)	large_intestine(1)	19											102	97	99					19																	10935751		2203	4300	6503	10796751	SO:0001583	missense	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1912G>A	19.37:g.10935751G>A	ENSP00000347890:p.Ala638Thr		10796751	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	5.805	0.332840	0.11013	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	D;D;D	0.92348	-3.02;-3.02;-3.02	5.27	4.24	0.50183	.	0.570822	0.18012	N	0.154535	T	0.77363	0.4119	N	0.02213	-0.635	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.002;0.001;0.001;0.003;0.001;0.001	T	0.63202	-0.6690	10	0.12766	T	0.61	-1.8566	9.0343	0.36277	0.1707:0.0:0.8293:0.0	.	232;367;634;634;638;638	Q8N1K8;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;DYN2_HUMAN;.	T	634;634;638;638;638;245	ENSP00000386192:A634T;ENSP00000373905:A638T;ENSP00000313164:A638T	ENSP00000313164:A638T	A	+	1	0	DNM2	10796751	0.126000	0.22350	0.005000	0.12908	0.006000	0.05464	1.566000	0.36396	1.226000	0.43582	0.563000	0.77884	GCC		0.587	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		A	10935751	G	A	10935751	3	1	61	1	0	0	0	0	1	0	0	0	4683	1203	42	3	2125	3	DNM2	19	10935751	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28983	10935751	48193232	10864	18849										
DNM2	1785	broad.mit.edu	37	chr19	10939861	10939861	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggaggcgctcaacatcatCggtgacatcagcaccagcac	10	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:10939861C>T	ENST00000355667.6	+	19	2288	c.2208C>T	c.(2206-2208)atC>atT	p.I736I	DNM2_ENST00000359692.6_Silent_p.I732I|DNM2_ENST00000389253.4_Silent_p.I736I|DNM2_ENST00000585892.1_Silent_p.I736I|DNM2_ENST00000408974.4_Silent_p.I732I|DNM2_ENST00000314646.5_Silent_p.I736I	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	736	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.I732I(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			TCAACATCATCGGTGACATCA	0.637			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	1	Substitution - coding silent(1)	large_intestine(1)	19											89	66	73					19																	10939861		2203	4300	6503	10800861	SO:0001819	synonymous_variant	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2208C>T	19.37:g.10939861C>T			10800861	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																				0.637	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		T	10939861	C	T	10939861	2	4	61	1	0	0	0	0	0	0	0	1	4683	874	31	1		1	DNM2	19	10939861	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4110	10939861	48189122	10865	18850										
SMARCA4	6597	broad.mit.edu	37	chr19	11152012	11152012	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggcacgctggaggagatCgaagaggaggtccggcagaa	19	7	0	3	rs577059244		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11152012C>T	ENST00000429416.3	+	31	4481	c.4200C>T	c.(4198-4200)atC>atT	p.I1400I	SMARCA4_ENST00000444061.3_Silent_p.I1367I|SMARCA4_ENST00000358026.2_Silent_p.I1432I|SMARCA4_ENST00000413806.3_Silent_p.I1370I|SMARCA4_ENST00000344626.4_Silent_p.I1400I|SMARCA4_ENST00000450717.3_Silent_p.I1370I|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000589677.1_Silent_p.I1370I|SMARCA4_ENST00000590574.1_Silent_p.I1367I|SMARCA4_ENST00000541122.2_Silent_p.I1370I	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1400					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.I1400I(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGGAGGAGATCGAAGAGGAGG	0.622			"F, N, Mis"		NSCLC																																		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	19											56	66	63					19																	11152012		2203	4299	6502	11013012	SO:0001819	synonymous_variant	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4200C>T	19.37:g.11152012C>T			11013012	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	9.854	1.194359	0.22037	.	.	ENSG00000127616	ENST00000538456	.	.	.	4.38	3.34	0.38264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-28.3815	5.8667	0.18779	0.0:0.6953:0.0:0.3047	.	.	.	.	X	172	.	.	R	+	1	2	SMARCA4	11013012	0.078000	0.21339	1.000000	0.80357	0.994000	0.84299	-0.670000	0.05256	1.061000	0.40601	0.467000	0.42956	CGA		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11152012	C	T	11152012	2	4	61	1	0	0	0	0	0	0	0	1	14807	874	31	1		1	SMARCA4	19	11152012	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	212151	11152012	47976971	10866	18851										
LDLR	3949	broad.mit.edu	37	chr19	11224281	11224281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagagacatccaggcccccGacgggctggctgtggactgg	16	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11224281G>A	ENST00000558518.1	+	10	1616	c.1429G>A	c.(1429-1431)Gac>Aac	p.D477N	LDLR_ENST00000455727.2_Missense_Mutation_p.D309N|LDLR_ENST00000535915.1_Missense_Mutation_p.D436N|LDLR_ENST00000545707.1_Missense_Mutation_p.D350N|LDLR_ENST00000557933.1_Missense_Mutation_p.D477N|LDLR_ENST00000558013.1_Missense_Mutation_p.D477N	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	477					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.D477N(1)|p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	CCAGGCCCCCGACGGGCTGGC	0.597																																					GBM(18;201 575 7820 21545)											2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|lung(1)	19	GRCh37	CM055369	LDLR	M							50	48	49					19																	11224281		2203	4299	6502	11085281	SO:0001583	missense	3949			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1429G>A	19.37:g.11224281G>A	ENSP00000454071:p.Asp477Asn		11085281	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	33	5.252249	0.95336	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.95656	-3.77;-3.77;-3.77	4.72	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000012	D	0.97766	0.9267	M	0.86420	2.815	0.58432	D	0.999999	D;P;D;D;D;D	0.64830	0.994;0.813;0.989;0.97;0.989;0.98	D;P;D;P;D;D	0.71414	0.973;0.839;0.947;0.881;0.961;0.947	D	0.98126	1.0428	10	0.49607	T	0.09	.	16.4495	0.83974	0.0:0.0:1.0:0.0	.	309;350;356;436;489;477	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	N	477;350;436;309	ENSP00000437639:D350N;ENSP00000440520:D436N;ENSP00000397829:D309N	ENSP00000252444:D477N	D	+	1	0	LDLR	11085281	1.000000	0.71417	0.989000	0.46669	0.934000	0.57294	6.083000	0.71326	2.186000	0.69663	0.555000	0.69702	GAC		0.597	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			A	11224281	G	A	11224281	3	1	61	1	0	0	0	0	1	0	0	0	8726	1058	37	1	1467	1	LDLR	19	11224281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72269	11224281	47904702	10867	18852										
ZNF653	115950	broad.mit.edu	37	chr19	11609150	11609150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggggacctgctcccaagGcttcctgcaacagaaagagg	12	11	0	2	rs200796254		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11609150G>A	ENST00000293771.5	-	2	440	c.304C>T	c.(304-306)Cct>Tct	p.P102S	CTC-398G3.6_ENST00000585656.1_Silent_p.S72S|ZNF653_ENST00000593191.1_5'UTR	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	102					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P102S(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						TGCTCCCAAGGCTTCCTGCAA	0.572																																					Pancreas(83;980 1446 4542 6441 43352)											1	Substitution - Missense(1)	large_intestine(1)	19											165	159	161					19																	11609150		2203	4300	6503	11470150	SO:0001583	missense	115950			AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.304C>T	19.37:g.11609150G>A	ENSP00000293771:p.Pro102Ser		11470150	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	g	19.74	3.884741	0.72410	.	.	ENSG00000161914	ENST00000293771	T	0.10382	2.88	4.7	4.7	0.59300	.	0.278447	0.32314	N	0.006263	T	0.10766	0.0263	L	0.27053	0.805	0.36924	D	0.891527	D	0.54207	0.965	B	0.43950	0.437	T	0.10800	-1.0614	10	0.87932	D	0	-6.0817	14.8961	0.70644	0.0:0.0:1.0:0.0	.	102	Q96CK0	ZN653_HUMAN	S	102	ENSP00000293771:P102S	ENSP00000293771:P102S	P	-	1	0	ZNF653	11470150	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.620000	0.54203	2.309000	0.77851	0.556000	0.70494	CCT		0.572	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		A	11609150	G	A	11609150	3	1	61	1	0	0	0	0	1	0	0	0	18105	1203	42	3	1575	3	ZNF653	19	11609150	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	384869	11609150	47519833	10868	18853										
ZNF627	199692	broad.mit.edu	37	chr19	11728118	11728118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagttgttccaagtacattcGaatccatgaacgaactcaca	6	11	1	1	rs377017181	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11728118G>A	ENST00000361113.5	+	4	1008	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R267Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						AAGTACATTCGAATCCATGAA	0.443													G|||	2	0.000399361	0	0	5008	,	,		22567	0		0	False		,,,				2504	0.002				Melanoma(112;173 1614 10731 17751 23322)											1	Substitution - Missense(1)	large_intestine(1)	19						G	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	53	56	55		800	-1.2	0	19		55	0,8600		0,0,4300	no	missense	ZNF627	NM_145295.3	43	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	267/462	11728118	1,13001	2201	4300	6501	11589118	SO:0001583	missense	199692			AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.800G>A	19.37:g.11728118G>A	ENSP00000354414:p.Arg267Gln		11589118	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	37	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	10.37	1.330411	0.24167	2.27E-4	0.0	ENSG00000198551	ENST00000361113	T	0.04275	3.66	1.36	-1.24	0.09435	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	N	0.13327	0.33	0.09310	N	1	P	0.52316	0.952	B	0.41917	0.37	T	0.33317	-0.9873	9	0.11485	T	0.65	.	2.0859	0.03645	0.3657:0.0:0.3838:0.2505	.	267	Q7L945	ZN627_HUMAN	Q	267	ENSP00000354414:R267Q	ENSP00000354414:R267Q	R	+	2	0	ZNF627	11589118	0.000000	0.05858	0.002000	0.10522	0.763000	0.43281	-2.384000	0.01063	-0.227000	0.09884	0.313000	0.20887	CGA		0.443	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		A	11728118	G	A	11728118	3	1	61	1	0	0	0	0	1	0	0	0	18090	1058	37	1	814	1	ZNF627	19	11728118	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	118968	11728118	47400865	10869	18854										
ZNF627	199692	broad.mit.edu	37	chr19	11728370	11728370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatttccccagttcatttcGaatccatgaaaggacccaca	6	12	1	2	rs72489416		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11728370G>A	ENST00000361113.5	+	4	1260	c.1052G>A	c.(1051-1053)cGa>cAa	p.R351Q	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R351Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						AGTTCATTTCGAATCCATGAA	0.413													G|||	1	0.000199681	0	0	5008	,	,		20915	0.001		0	False		,,,				2504	0				Melanoma(112;173 1614 10731 17751 23322)											1	Substitution - Missense(1)	large_intestine(1)	19											67	72	70					19																	11728370		2199	4299	6498	11589370	SO:0001583	missense	199692			AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.1052G>A	19.37:g.11728370G>A	ENSP00000354414:p.Arg351Gln		11589370	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	37	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	6.405	0.442901	0.12164	.	.	ENSG00000198551	ENST00000361113	T	0.04275	3.66	1.49	-1.27	0.09347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	1	P	0.43750	0.816	B	0.35813	0.211	T	0.30149	-0.9988	9	0.02654	T	1	.	5.212	0.15322	0.6002:0.0:0.3998:0.0	.	351	Q7L945	ZN627_HUMAN	Q	351	ENSP00000354414:R351Q	ENSP00000354414:R351Q	R	+	2	0	ZNF627	11589370	0.000000	0.05858	0.002000	0.10522	0.987000	0.75469	-1.229000	0.02945	-0.224000	0.09928	0.460000	0.39030	CGA		0.413	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		A	11728370	G	A	11728370	3	1	61	1	0	0	0	0	1	0	0	0	18090	1058	37	1	1066	1	ZNF627	19	11728370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252	11728370	47400613	10870	18855										
ZNF627	199692	broad.mit.edu	37	chr19	11728453	11728453	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagttgttccagttcgtttCgaaaacatgaaagaattcac	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11728453C>T	ENST00000361113.5	+	4	1343	c.1135C>T	c.(1135-1137)Cga>Tga	p.R379*	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R379*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						CAGTTCGTTTCGAAAACATGA	0.418																																					Melanoma(112;173 1614 10731 17751 23322)											1	Substitution - Nonsense(1)	large_intestine(1)	19											45	49	48					19																	11728453		2197	4298	6495	11589453	SO:0001587	stop_gained	199692			AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.1135C>T	19.37:g.11728453C>T	ENSP00000354414:p.Arg379*		11589453	O14846|Q4KMP9|Q6NT81|Q9BRG4	Nonsense_Mutation	SNP	ENST00000361113.5	37	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	c	37	6.009776	0.97200	.	.	ENSG00000198551	ENST00000361113	.	.	.	1.5	0.272	0.15645	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.6348	0.04955	0.0:0.4661:0.323:0.211	.	.	.	.	X	379	.	ENSP00000354414:R379X	R	+	1	2	ZNF627	11589453	0.000000	0.05858	0.000000	0.03702	0.937000	0.57800	-1.302000	0.02746	0.150000	0.19136	0.467000	0.42956	CGA		0.418	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		T	11728453	C	T	11728453	4	4	61	1	0	0	0	0	0	1	0	0	18090	876	31	1	1149	1	ZNF627	19	11728453	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83	11728453	47400530	10871	18856										
ZNF823	55552	broad.mit.edu	37	chr19	11833351	11833351	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcccacatatcttacatTtatgtggtccgtctccagtg	6	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11833351T>G	ENST00000341191.6	-	4	1151	c.998A>C	c.(997-999)aAa>aCa	p.K333T	ZNF823_ENST00000545749.1_Missense_Mutation_p.K151T	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K333T(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						TATCTTACATTTATGTGGTCC	0.423										HNSCC(68;0.2)																																						2	Substitution - Missense(2)	large_intestine(2)	19											144	138	140					19																	11833351		2203	4300	6503	11694351	SO:0001583	missense	55552			X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.998A>C	19.37:g.11833351T>G	ENSP00000340683:p.Lys333Thr		11694351	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	37	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	t	15.37	2.814940	0.50527	.	.	ENSG00000197933	ENST00000545749;ENST00000341191;ENST00000431998	T;T;T	0.08458	3.09;3.09;3.09	0.632	0.632	0.17705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09468	0.0233	N	0.05050	-0.12	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.29731	-1.0002	9	0.62326	D	0.03	.	4.5828	0.12267	0.0:0.0:0.3312:0.6688	.	333	P16415	ZN823_HUMAN	T	151;333;289	ENSP00000440162:K151T;ENSP00000340683:K333T;ENSP00000410654:K289T	ENSP00000340683:K333T	K	-	2	0	ZNF823	11694351	0.000000	0.05858	0.007000	0.13788	0.875000	0.50365	-0.535000	0.06142	0.519000	0.28406	0.248000	0.18094	AAA		0.423	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		G	11833351	T	G	11833351	3	3	61	1	0	0	0	0	1	0	0	0	18218	1841	64	4	838	4	ZNF823	19	11833351	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	104898	11833351	47295632	10872	18857										
ZNF823	55552	broad.mit.edu	37	chr19	11833825	11833825	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttcggaggtttccaagaGaactaaaggtttttgcacat	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11833825G>T	ENST00000341191.6	-	4	677	c.524C>A	c.(523-525)tCt>tAt	p.S175Y	ZNF823_ENST00000545749.1_5'UTR|CTC-499B15.6_ENST00000586983.1_RNA	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S175Y(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						GTTTCCAAGAGAACTAAAGGT	0.463										HNSCC(68;0.2)																																						2	Substitution - Missense(2)	large_intestine(2)	19											111	117	115					19																	11833825		2189	4289	6478	11694825	SO:0001583	missense	55552			X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.524C>A	19.37:g.11833825G>T	ENSP00000340683:p.Ser175Tyr		11694825	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	37	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	g	3.280	-0.147245	0.06627	.	.	ENSG00000197933	ENST00000341191;ENST00000431998	T;T	0.15372	2.43;2.43	0.633	0.633	0.17712	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19525	0.0469	L	0.35854	1.095	0.19300	N	0.999976	D	0.69078	0.997	P	0.60682	0.878	T	0.05767	-1.0865	9	0.02654	T	1	.	8.7985	0.34894	0.0:0.0:1.0:0.0	.	175	P16415	ZN823_HUMAN	Y	175;131	ENSP00000340683:S175Y;ENSP00000410654:S131Y	ENSP00000340683:S175Y	S	-	2	0	ZNF823	11694825	0.000000	0.05858	0.053000	0.19242	0.516000	0.34256	-7.293000	0.00039	0.627000	0.30340	0.298000	0.19748	TCT		0.463	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		T	11833825	G	T	11833825	3	4	61	1	0	0	0	0	1	0	0	0	18218	942	33	2	1312	2	ZNF823	19	11833825	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	474	11833825	47295158	10873	18858										
ZNF823	55552	broad.mit.edu	37	chr19	11834017	11834017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgttgcaattaagagacGaatgacccaagacgacttct	9	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11834017G>A	ENST00000341191.6	-	4	485	c.332C>T	c.(331-333)tCg>tTg	p.S111L	ZNF823_ENST00000545749.1_5'UTR|CTC-499B15.6_ENST00000586983.1_RNA|ZNF823_ENST00000440527.1_3'UTR	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	111					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S111L(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						ATTAAGAGACGAATGACCCAA	0.433										HNSCC(68;0.2)																																						2	Substitution - Missense(2)	large_intestine(2)	19											159	151	154					19																	11834017		2202	4300	6502	11695017	SO:0001583	missense	55552			X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.332C>T	19.37:g.11834017G>A	ENSP00000340683:p.Ser111Leu		11695017	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	37	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	g	7.936	0.741774	0.15642	.	.	ENSG00000197933	ENST00000341191;ENST00000431998	T;T	0.07444	4.09;3.19	0.632	0.632	0.17705	.	.	.	.	.	T	0.13114	0.0318	M	0.85542	2.76	0.09310	N	0.999992	B	0.19583	0.037	B	0.13407	0.009	T	0.19844	-1.0293	9	0.66056	D	0.02	.	7.1241	0.25461	1.0E-4:0.0:0.9999:0.0	.	111	P16415	ZN823_HUMAN	L	111;67	ENSP00000340683:S111L;ENSP00000410654:S67L	ENSP00000340683:S111L	S	-	2	0	ZNF823	11695017	0.000000	0.05858	0.009000	0.14445	0.043000	0.13939	-0.975000	0.03790	0.618000	0.30179	0.298000	0.19748	TCG		0.433	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		A	11834017	G	A	11834017	3	1	61	1	0	0	0	0	1	0	0	0	18218	1059	37	1	1504	1	ZNF823	19	11834017	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	192	11834017	47294966	10874	18859										
ZNF491	126069	broad.mit.edu	37	chr19	11917528	11917528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatatgggaaagcattatctCgccttataagctttcgaaga	8	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11917528C>T	ENST00000323169.5	+	3	1091	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	254					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R254C(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						AGCATTATCTCGCCTTATAAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											59	60	59					19																	11917528		2203	4300	6503	11778528	SO:0001583	missense	126069			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"Zinc fingers, C2H2-type"	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.760C>T	19.37:g.11917528C>T	ENSP00000313443:p.Arg254Cys		11778528	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	.	.	.	.	.	.	.	.	.	.	c	2.169	-0.390313	0.04932	.	.	ENSG00000177599	ENST00000323169;ENST00000455048	T	0.16196	2.36	0.981	-0.117	0.13551	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12433	0.0302	L	0.28776	0.89	0.09310	N	1	D	0.60160	0.987	P	0.46940	0.532	T	0.17319	-1.0373	9	0.36615	T	0.2	.	3.6526	0.08209	0.2298:0.599:0.0:0.1712	.	254	Q8N8L2	ZN491_HUMAN	C	254;226	ENSP00000313443:R254C	ENSP00000313443:R254C	R	+	1	0	ZNF491	11778528	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.840000	0.00179	-0.065000	0.13021	-0.687000	0.03738	CGC		0.413	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		T	11917528	C	T	11917528	3	4	61	1	0	0	0	0	1	0	0	0	17981	884	31	1	762	1	ZNF491	19	11917528	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83511	11917528	47211455	10875	18860										
ZNF491	126069	broad.mit.edu	37	chr19	11917796	11917796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatctgccaagtacattcGaatacatggaaggactcaca	8	10	2	1	rs368005368		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11917796G>A	ENST00000323169.5	+	3	1359	c.1028G>A	c.(1027-1029)cGa>cAa	p.R343Q	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R343Q(3)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						AAGTACATTCGAATACATGGA	0.433																																																3	Substitution - Missense(3)	large_intestine(3)	19											63	64	64					19																	11917796		2203	4300	6503	11778796	SO:0001583	missense	126069			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"Zinc fingers, C2H2-type"	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.1028G>A	19.37:g.11917796G>A	ENSP00000313443:p.Arg343Gln		11778796	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	.	.	.	.	.	.	.	.	.	.	g	0.012	-1.677593	0.00751	.	.	ENSG00000177599	ENST00000323169;ENST00000455048	T	0.15256	2.44	0.874	-1.75	0.08031	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07503	0.0189	N	0.16201	0.385	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.39272	-0.9622	9	0.17832	T	0.49	.	4.4157	0.11455	0.4713:0.2738:0.2549:0.0	.	343	Q8N8L2	ZN491_HUMAN	Q	343;315	ENSP00000313443:R343Q	ENSP00000313443:R343Q	R	+	2	0	ZNF491	11778796	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.432000	0.01022	-1.558000	0.01690	-1.386000	0.01163	CGA		0.433	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		A	11917796	G	A	11917796	3	1	61	1	0	0	0	0	1	0	0	0	17981	1058	37	1	1030	1	ZNF491	19	11917796	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	268	11917796	47211187	10876	18861										
ZNF491	126069	broad.mit.edu	37	chr19	11917883	11917883	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgtcagctcctttcataGacatgaaaggactcacgctg	9	10	3	2	rs568248545		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11917883G>T	ENST00000323169.5	+	3	1446	c.1115G>T	c.(1114-1116)aGa>aTa	p.R372I	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R372I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						TCCTTTCATAGACATGAAAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											54	57	56					19																	11917883		2203	4300	6503	11778883	SO:0001583	missense	126069			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"Zinc fingers, C2H2-type"	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.1115G>T	19.37:g.11917883G>T	ENSP00000313443:p.Arg372Ile		11778883	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.308499	0.00237	.	.	ENSG00000177599	ENST00000323169;ENST00000455048	T	0.26223	1.75	0.981	-1.96	0.07525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18299	0.0439	L	0.53249	1.67	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.34304	-0.9834	9	0.18276	T	0.48	.	3.0758	0.06246	0.1643:0.1397:0.5558:0.1402	.	372	Q8N8L2	ZN491_HUMAN	I	372;344	ENSP00000313443:R372I	ENSP00000313443:R372I	R	+	2	0	ZNF491	11778883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.939000	0.00330	-3.119000	0.00239	-1.358000	0.01219	AGA		0.393	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		T	11917883	G	T	11917883	3	4	61	1	0	0	0	0	1	0	0	0	17981	942	33	2	1117	2	ZNF491	19	11917883	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87	11917883	47211100	10877	18862										
ZNF440	126070	broad.mit.edu	37	chr19	11942750	11942750	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagaactcacactggagaAaagccttatgaatatcagga	8	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11942750A>C	ENST00000304060.5	+	4	923	c.759A>C	c.(757-759)gaA>gaC	p.E253D		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E253D(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						ACACTGGAGAAAAGCCTTATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	67	66					19																	11942750		2199	4298	6497	11803750	SO:0001583	missense	126070			AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"Zinc fingers, C2H2-type", "-"	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.759A>C	19.37:g.11942750A>C	ENSP00000305373:p.Glu253Asp		11803750	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	.	.	.	.	.	.	.	.	.	.	a	14.83	2.653917	0.47362	.	.	ENSG00000171295	ENST00000304060;ENST00000427505	T;T	0.26810	1.71;1.71	1.19	-1.35	0.09114	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25975	0.0633	L	0.57536	1.79	0.26414	N	0.976214	B	0.24368	0.102	B	0.34346	0.18	T	0.42258	-0.9462	9	0.54805	T	0.06	.	6.1863	0.20500	0.3334:0.0:0.6666:0.0	.	253	Q8IYI8	ZN440_HUMAN	D	253;256	ENSP00000305373:E253D;ENSP00000393489:E256D	ENSP00000305373:E253D	E	+	3	2	ZNF440	11803750	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-1.271000	0.02828	-0.350000	0.08262	0.172000	0.16884	GAA		0.388	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		C	11942750	A	C	11942750	3	2	61	1	0	0	0	0	1	0	0	0	17952	11	1	4	773	4	ZNF440	19	11942750	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	24867	11942750	47186233	10878	18863										
ZNF440	126070	broad.mit.edu	37	chr19	11943750	11943750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggatctgcccagaaccttcGaattcatgaaaggacacaaa	8	11	2	2	rs555345914		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11943750G>A	ENST00000304060.5	+	4	1923	c.1759G>A	c.(1759-1761)Gaa>Aaa	p.E587K		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	587					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E587K(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CAGAACCTTCGAATTCATGAA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											60	59	59					19																	11943750		2184	4287	6471	11804750	SO:0001583	missense	126070			AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"Zinc fingers, C2H2-type", "-"	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.1759G>A	19.37:g.11943750G>A	ENSP00000305373:p.Glu587Lys		11804750	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	.	.	.	.	.	.	.	.	.	.	g	2.736	-0.263412	0.05754	.	.	ENSG00000171295	ENST00000304060	T	0.05025	3.51	0.763	-1.2	0.09554	.	.	.	.	.	T	0.03263	0.0095	N	0.12920	0.275	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43196	-0.9406	9	0.39692	T	0.17	.	3.115	0.06371	0.312:0.2668:0.4212:0.0	.	587	Q8IYI8	ZN440_HUMAN	K	587	ENSP00000305373:E587K	ENSP00000305373:E587K	E	+	1	0	ZNF440	11804750	.	.	0.001000	0.08648	0.009000	0.06853	.	.	-0.186000	0.10533	-1.050000	0.02344	GAA		0.443	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		A	11943750	G	A	11943750	3	1	61	1	0	0	0	0	1	0	0	0	17952	1059	37	1	1773	1	ZNF440	19	11943750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1000	11943750	47185233	10879	18864										
ZNF439	90594	broad.mit.edu	37	chr19	11977403	11977403	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtaccaaaaccccaggaGaaacttcaggtaatttgcac	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11977403G>T	ENST00000304030.2	+	2	427	c.227G>T	c.(226-228)aGa>aTa	p.R76I	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_5'UTR	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	76	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R76I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AACCCCAGGAGAAACTTCAGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	89	88					19																	11977403		2202	4299	6501	11838403	SO:0001583	missense	90594			AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.227G>T	19.37:g.11977403G>T	ENSP00000305077:p.Arg76Ile		11838403	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	g	13.66	2.304099	0.40795	.	.	ENSG00000171291	ENST00000442091;ENST00000304030	T;T	0.08458	5.03;3.09	1.31	-2.1	0.07210	Krueppel-associated box (2);	.	.	.	.	T	0.14442	0.0349	M	0.71036	2.16	0.09310	N	1	P	0.47034	0.889	P	0.50617	0.646	T	0.09443	-1.0674	9	0.87932	D	0	.	5.3293	0.15924	0.5716:0.0:0.4284:0.0	.	76	Q8NDP4	ZN439_HUMAN	I	63;76	ENSP00000388234:R63I;ENSP00000305077:R76I	ENSP00000305077:R76I	R	+	2	0	ZNF439	11838403	0.006000	0.16342	0.001000	0.08648	0.423000	0.31445	-0.179000	0.09768	-0.725000	0.04901	0.194000	0.17425	AGA		0.323	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			T	11977403	G	T	11977403	3	4	61	1	0	0	0	0	1	0	0	0	17950	942	33	2	233	2	ZNF439	19	11977403	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33653	11977403	47151580	10880	18865										
ZNF439	90594	broad.mit.edu	37	chr19	11978387	11978387	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaacctaaaaaagccttcaGatatcacccctccttgagaa	4	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11978387G>A	ENST00000304030.2	+	3	703	c.503G>A	c.(502-504)aGa>aAa	p.R168K	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.R32K	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	168					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R168K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AAAGCCTTCAGATATCACCCC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											147	142	144					19																	11978387		2203	4300	6503	11839387	SO:0001583	missense	90594			AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.503G>A	19.37:g.11978387G>A	ENSP00000305077:p.Arg168Lys		11839387	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	g	4.748	0.139155	0.09083	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.20200	2.09;2.09	0.575	-1.15	0.09709	.	.	.	.	.	T	0.13200	0.0320	N	0.16862	0.45	0.09310	N	1	B	0.29270	0.24	B	0.36766	0.232	T	0.37430	-0.9706	9	0.42905	T	0.14	.	5.9344	0.19156	0.0:0.0:0.492:0.508	.	168	Q8NDP4	ZN439_HUMAN	K	32;168	ENSP00000395632:R32K;ENSP00000305077:R168K	ENSP00000305077:R168K	R	+	2	0	ZNF439	11839387	.	.	0.000000	0.03702	0.008000	0.06430	.	.	-0.470000	0.06901	0.194000	0.17425	AGA		0.398	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			A	11978387	G	A	11978387	3	1	61	1	0	0	0	0	1	0	0	0	17950	942	33	3	513	3	ZNF439	19	11978387	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	984	11978387	47150596	10881	18866										
ZNF439	90594	broad.mit.edu	37	chr19	11978601	11978601	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagaactcacactggagaGaaaccgtatgaatgtaaaca	9	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11978601G>T	ENST00000304030.2	+	3	917	c.717G>T	c.(715-717)gaG>gaT	p.E239D	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.E103D	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	239					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E239D(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						ACACTGGAGAGAAACCGTATG	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	19											86	85	85					19																	11978601		2203	4300	6503	11839601	SO:0001583	missense	90594			AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.717G>T	19.37:g.11978601G>T	ENSP00000305077:p.Glu239Asp		11839601	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	g	13.88	2.368691	0.42003	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.26810	1.71;1.71	0.575	-1.0	0.10196	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30665	0.0772	L	0.46670	1.46	0.27193	N	0.960361	P	0.46987	0.888	P	0.55871	0.786	T	0.21075	-1.0256	9	0.66056	D	0.02	.	3.5981	0.08014	0.2094:0.2546:0.536:0.0	.	239	Q8NDP4	ZN439_HUMAN	D	103;239	ENSP00000395632:E103D;ENSP00000305077:E239D	ENSP00000305077:E239D	E	+	3	2	ZNF439	11839601	0.971000	0.33674	0.052000	0.19188	0.293000	0.27360	0.303000	0.19210	-0.341000	0.08376	0.194000	0.17425	GAG		0.368	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			T	11978601	G	T	11978601	3	4	61	1	0	0	0	0	1	0	0	0	17950	933	33	2	727	2	ZNF439	19	11978601	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214	11978601	47150382	10882	18867										
ZNF439	90594	broad.mit.edu	37	chr19	11978669	11978669	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacccatcgaatacatgaaaGaactcacattggagaaaagc	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11978669G>T	ENST00000304030.2	+	3	985	c.785G>T	c.(784-786)aGa>aTa	p.R262I	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.R126I	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R262I(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						ATACATGAAAGAACTCACATT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	19											75	75	75					19																	11978669		2203	4300	6503	11839669	SO:0001583	missense	90594			AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.785G>T	19.37:g.11978669G>T	ENSP00000305077:p.Arg262Ile		11839669	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	g	12.38	1.920213	0.33908	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.24908	1.83;1.83	0.641	0.641	0.17759	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39572	0.1083	M	0.63428	1.95	0.36993	D	0.894892	D	0.89917	1.0	D	0.87578	0.998	T	0.42949	-0.9421	9	0.48119	T	0.1	.	4.4707	0.11712	0.2512:0.0:0.7487:0.0	.	262	Q8NDP4	ZN439_HUMAN	I	126;262	ENSP00000395632:R126I;ENSP00000305077:R262I	ENSP00000305077:R262I	R	+	2	0	ZNF439	11839669	0.000000	0.05858	0.206000	0.23566	0.142000	0.21351	-2.386000	0.01061	0.623000	0.30267	0.306000	0.20318	AGA		0.398	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			T	11978669	G	T	11978669	3	4	61	1	0	0	0	0	1	0	0	0	17950	942	33	2	795	2	ZNF439	19	11978669	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68	11978669	47150314	10883	18868										
ZNF439	90594	broad.mit.edu	37	chr19	11978921	11978921	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagttttcaaacacacataaGaatgcactctggagaaagac	7	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:11978921G>T	ENST00000304030.2	+	3	1237	c.1037G>T	c.(1036-1038)aGa>aTa	p.R346I	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.R210I	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R346I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						ACACACATAAGAATGCACTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											92	93	92					19																	11978921		2203	4300	6503	11839921	SO:0001583	missense	90594			AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1037G>T	19.37:g.11978921G>T	ENSP00000305077:p.Arg346Ile		11839921	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	g	9.673	1.147234	0.21288	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.24908	1.83;1.83	0.575	-1.15	0.09709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33265	0.0857	M	0.64170	1.965	0.09310	N	1	D	0.59767	0.986	P	0.54856	0.762	T	0.19257	-1.0311	9	0.38643	T	0.18	.	6.5091	0.22212	0.0:0.0:0.7127:0.2872	.	346	Q8NDP4	ZN439_HUMAN	I	210;346	ENSP00000395632:R210I;ENSP00000305077:R346I	ENSP00000305077:R346I	R	+	2	0	ZNF439	11839921	0.000000	0.05858	0.002000	0.10522	0.212000	0.24457	0.065000	0.14466	-0.365000	0.08076	0.194000	0.17425	AGA		0.383	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			T	11978921	G	T	11978921	3	4	61	1	0	0	0	0	1	0	0	0	17950	942	33	2	1047	2	ZNF439	19	11978921	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252	11978921	47150062	10884	18869										
ZNF700	90592	broad.mit.edu	37	chr19	12060000	12060000	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaactcacactggagaGaaacgctataaatgcaagca	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12060000G>T	ENST00000254321.5	+	4	1304	c.1161G>T	c.(1159-1161)gaG>gaT	p.E387D	ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Missense_Mutation_p.E369D|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E387D(1)	ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						ACACTGGAGAGAAACGCTATA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											52	55	54					19																	12060000		2203	4300	6503	11921000	SO:0001583	missense	90592			AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.1161G>T	19.37:g.12060000G>T	ENSP00000254321:p.Glu387Asp		11921000	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	g	10.48	1.361507	0.24684	.	.	ENSG00000196757	ENST00000254321	T	0.26810	1.71	0.672	0.672	0.17935	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20373	0.0490	L	0.41824	1.3	0.28969	N	0.88937	B	0.06786	0.001	B	0.13407	0.009	T	0.22836	-1.0205	9	0.59425	D	0.04	.	8.8188	0.35011	0.0:0.0:1.0:0.0	.	387	Q9H0M5	ZN700_HUMAN	D	387	ENSP00000254321:E387D	ENSP00000254321:E387D	E	+	3	2	ZNF700	11921000	0.457000	0.25752	0.466000	0.27168	0.220000	0.24768	0.147000	0.16202	0.623000	0.30267	0.305000	0.20034	GAG		0.378	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12060000	G	T	12060000	3	4	61	1	0	0	0	0	1	0	0	0	18143	933	33	2	1175	2	ZNF700	19	12060000	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81079	12060000	47068983	10885	18870										
ZNF433	163059	broad.mit.edu	37	chr19	12128714	12128714	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtttctccttagattttcGtactctacatatatgttctg	6	8	3	1	rs200983088		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12128714G>A	ENST00000344980.6	-	3	347	c.177C>T	c.(175-177)taC>taT	p.Y59Y	CTD-2006C1.10_ENST00000547473.1_3'UTR|ZNF433_ENST00000419886.2_Silent_p.Y24Y|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Y59Y(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						TTAGATTTTCGTACTCTACAT	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,3638		0,0,1819	117	107	110		177	0.8	0	19		110	1,8133		0,1,4066	no	coding-synonymous	ZNF433	NM_001080411.1		0,1,5885	AA,AG,GG		0.0123,0.0,0.0085		59/674	12128714	1,11771	1819	4067	5886	11989714	SO:0001819	synonymous_variant	163059			AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"Zinc fingers, C2H2-type", "-"	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.177C>T	19.37:g.12128714G>A			11989714	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																				0.294	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602		A	12128714	G	A	12128714	2	1	61	1	0	0	0	0	0	0	0	1	17946	1140	40	1		1	ZNF433	19	12128714	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68714	12128714	47000269	10886	18871										
ZNF20	7568	broad.mit.edu	37	chr19	12246324	12246324	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaaaattaccttagatttCtcctgggatttttgtactca	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12246324C>A	ENST00000334213.5	-	3	415	c.191G>T	c.(190-192)aGa>aTa	p.R64I	ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Missense_Mutation_p.R61I	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	64	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R64I(1)		endometrium(1)|kidney(1)|lung(6)	8						CCTTAGATTTCTCCTGGGATT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											142	129	133					19																	12246324		1857	4129	5986	12107324	SO:0001583	missense	7568			X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.191G>T	19.37:g.12246324C>A	ENSP00000335437:p.Arg64Ile		12107324	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	C	8.428	0.848005	0.17034	.	.	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.06371	3.31;6.62	1.14	-1.73	0.08081	Krueppel-associated box (1);	.	.	.	.	T	0.05777	0.0151	L	0.45051	1.395	0.09310	N	1	P	0.49358	0.923	B	0.44044	0.439	T	0.24584	-1.0156	9	0.48119	T	0.1	.	2.397	0.04392	0.0:0.4166:0.329:0.2543	.	64	P17024	ZNF20_HUMAN	I	64;64;61	ENSP00000335437:R64I;ENSP00000390115:R61I	ENSP00000292241:R64I	R	-	2	0	ZNF20	12107324	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	-0.927000	0.03984	-0.463000	0.06973	0.306000	0.20318	AGA		0.393	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		A	12246324	C	A	12246324	3	1	61	1	0	0	0	0	1	0	0	0	17800	913	32	2	1415	2	ZNF20	19	12246324	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117610	12246324	46882659	10887	18872										
ZNF625	90589	broad.mit.edu	37	chr19	12256140	12256140	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctcgccttggcctttcGaagtgttggagctacagggt	12	10	2	0	rs140651282		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12256140G>A	ENST00000355738.1	-	4	1242	c.893C>T	c.(892-894)tCg>tTg	p.S298L	ZNF625_ENST00000542938.1_Missense_Mutation_p.S298L|ZNF625-ZNF20_ENST00000430024.1_Intron|ZNF625_ENST00000455799.1_3'UTR|CTC-359D24.3_ENST00000472362.1_RNA|ZNF625_ENST00000439556.2_Missense_Mutation_p.S364L			Q96I27	ZN625_HUMAN	zinc finger protein 625	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S298L(1)		breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TTGGCCTTTCGAAGTGTTGGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	99	92	95		1091	-1.3	0	19	dbSNP_134	95	0,8600		0,0,4300	no	missense	ZNF625	NM_145233.3	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	364/373	12256140	1,13005	2203	4300	6503	12117140	SO:0001583	missense	90589			BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"Zinc fingers, C2H2-type", "-"	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.893C>T	19.37:g.12256140G>A	ENSP00000347977:p.Ser298Leu		12117140	A4FU45|I3L0E9	Missense_Mutation	SNP	ENST00000355738.1	37		.	.	.	.	.	.	.	.	.	.	G	0.001	-3.034954	0.00040	2.27E-4	0.0	ENSG00000257591	ENST00000542938;ENST00000355738;ENST00000439556	T;T;T	0.07688	3.17;3.17;3.32	0.646	-1.29	0.09288	.	.	.	.	.	T	0.03011	0.0089	N	0.16368	0.405	0.09310	N	1	D;B	0.57571	0.98;0.319	B;B	0.28991	0.097;0.018	T	0.36890	-0.9729	9	0.62326	D	0.03	.	3.5637	0.07892	0.2953:0.4874:0.2172:0.0	.	298;298	A8K8U0;Q96I27	.;ZN625_HUMAN	L	298;298;364	ENSP00000438436:S298L;ENSP00000347977:S298L;ENSP00000394380:S364L	ENSP00000347977:S298L	S	-	2	0	AC022415.5	12117140	.	.	0.003000	0.11579	0.003000	0.03518	.	.	-1.537000	0.01736	-1.947000	0.00488	TCG		0.423	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233		A	12256140	G	A	12256140	3	1	61	1	0	0	0	0	1	0	0	0	18088	1059	37	1	31	1	ZNF625	19	12256140	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9816	12256140	46872843	10888	18873										
ZNF625	90589	broad.mit.edu	37	chr19	12256527	12256527	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgagttctttcatgtattCgaaggctaccagaatgacta	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12256527C>T	ENST00000355738.1	-	4	855	c.506G>A	c.(505-507)cGa>cAa	p.R169Q	ZNF625_ENST00000542938.1_Missense_Mutation_p.R169Q|ZNF625-ZNF20_ENST00000430024.1_Intron|ZNF625_ENST00000455799.1_3'UTR|CTC-359D24.3_ENST00000472362.1_RNA|ZNF625_ENST00000439556.2_Missense_Mutation_p.R235Q			Q96I27	ZN625_HUMAN	zinc finger protein 625	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R169Q(2)		breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TTCATGTATTCGAAGGCTACC	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	19											134	122	126					19																	12256527		2203	4300	6503	12117527	SO:0001583	missense	90589			BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"Zinc fingers, C2H2-type", "-"	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.506G>A	19.37:g.12256527C>T	ENSP00000347977:p.Arg169Gln		12117527	A4FU45|I3L0E9	Missense_Mutation	SNP	ENST00000355738.1	37		.	.	.	.	.	.	.	.	.	.	C	7.205	0.594292	0.13875	.	.	ENSG00000257591	ENST00000542938;ENST00000355738;ENST00000439556	T;T;T	0.07444	3.19;3.19;3.19	0.856	-1.5	0.08691	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04092	0.0114	N	0.20986	0.625	0.09310	N	1	B;B	0.34329	0.192;0.449	B;B	0.26614	0.001;0.071	T	0.44112	-0.9349	9	0.20519	T	0.43	.	5.913	0.19039	0.0:0.6765:0.0:0.3235	.	169;169	A8K8U0;Q96I27	.;ZN625_HUMAN	Q	169;169;235	ENSP00000438436:R169Q;ENSP00000347977:R169Q;ENSP00000394380:R235Q	ENSP00000347977:R169Q	R	-	2	0	AC022415.5	12117527	0.000000	0.05858	0.017000	0.16124	0.828000	0.46876	-2.546000	0.00932	-0.603000	0.05767	0.313000	0.20887	CGA		0.408	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233		T	12256527	C	T	12256527	3	4	61	1	0	0	0	0	1	0	0	0	18088	884	31	1	418	1	ZNF625	19	12256527	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	387	12256527	46872456	10889	18874										
ZNF136	7695	broad.mit.edu	37	chr19	12297659	12297659	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagttctcaccactcctttCgaacacatgagataattcac	4	13	3	1	rs574301770		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12297659C>T	ENST00000343979.4	+	4	606	c.466C>T	c.(466-468)Cga>Tga	p.R156*	ZNF136_ENST00000398616.2_Nonsense_Mutation_p.R90*	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	156					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.R156*(1)		NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						CCACTCCTTTCGAACACATGA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											86	78	81					19																	12297659		2203	4300	6503	12158659	SO:0001587	stop_gained	7695			U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"Zinc fingers, C2H2-type", "-"	12920	protein-coding gene	gene with protein product		604078	"zinc finger protein 136 (clone pHZ-20)"			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.466C>T	19.37:g.12297659C>T	ENSP00000344162:p.Arg156*		12158659		Nonsense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034674	0.75617	.	.	ENSG00000196646	ENST00000343979;ENST00000398616	.	.	.	1.41	0.27	0.15635	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9384	0.29944	0.2478:0.7522:0.0:0.0	.	.	.	.	X	156;90	.	.	R	+	1	2	ZNF136	12158659	0.000000	0.05858	0.156000	0.22583	0.856000	0.48823	-0.789000	0.04609	0.135000	0.18707	0.655000	0.94253	CGA		0.398	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437		T	12297659	C	T	12297659	4	4	61	1	0	0	0	0	0	1	0	0	17765	876	31	1	480	1	ZNF136	19	12297659	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41132	12297659	46831324	10890	18875										
ZNF44	51710	broad.mit.edu	37	chr19	12383305	12383305	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccacattccttacattCatagggcttctctccagtgt	5	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12383305C>A	ENST00000356109.5	-	5	2027	c.1909G>T	c.(1909-1911)Gaa>Taa	p.E637*	ZNF44_ENST00000355684.5_Nonsense_Mutation_p.E589*	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	637					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		TCCTTACATTCATAGGGCTTC	0.413																																																0			19											51	54	53					19																	12383305		2203	4300	6503	12244305	SO:0001587	stop_gained	51710			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1909G>T	19.37:g.12383305C>A	ENSP00000348419:p.Glu637*		12244305	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Nonsense_Mutation	SNP	ENST00000356109.5	37	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	C	36	5.737135	0.96865	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	.	.	.	0.997	-0.0899	0.13667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	0.4033	0.00429	0.2432:0.3146:0.2422:0.2	.	.	.	.	X	637;637;589;589	.	ENSP00000347910:E589X	E	-	1	0	ZNF44	12244305	0.000000	0.05858	0.033000	0.17914	0.979000	0.70002	-7.503000	0.00035	0.015000	0.14971	0.305000	0.20034	GAA		0.413	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		A	12383305	C	A	12383305	4	1	61	1	0	0	0	0	0	1	0	0	17951	835	29	2	86	2	ZNF44	19	12383305	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	85646	12383305	46745678	10891	18876										
ZNF44	51710	broad.mit.edu	37	chr19	12383447	12383447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggaaagagggccaaaaGaatgctttcctgcattgctt	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12383447G>T	ENST00000356109.5	-	5	1885	c.1767C>A	c.(1765-1767)ttC>ttA	p.F589L	ZNF44_ENST00000355684.5_Missense_Mutation_p.F541L	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	589					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AGGGCCAAAAGAATGCTTTCC	0.423																																																0			19											51	55	54					19																	12383447		2191	4300	6491	12244447	SO:0001583	missense	51710			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1767C>A	19.37:g.12383447G>T	ENSP00000348419:p.Phe589Leu		12244447	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	37	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161396	0.38119	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.46063	0.88;0.88;0.88	1.1	-0.276	0.12902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36193	0.0958	M	0.66560	2.04	.	.	.	B;B	0.33549	0.417;0.037	B;B	0.32928	0.155;0.022	T	0.41662	-0.9496	8	0.72032	D	0.01	.	5.0403	0.14456	0.6864:0.0:0.3136:0.0	.	589;541	P15621;F8W7T7	ZNF44_HUMAN;.	L	589;589;541;541	ENSP00000377008:F589L;ENSP00000348419:F589L;ENSP00000347910:F541L	ENSP00000347910:F541L	F	-	3	2	ZNF44	12244447	0.000000	0.05858	0.000000	0.03702	0.909000	0.53808	-1.359000	0.02602	-0.041000	0.13558	0.305000	0.20034	TTC		0.423	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		T	12383447	G	T	12383447	3	4	61	1	0	0	0	0	1	0	0	0	17951	933	33	2	228	2	ZNF44	19	12383447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142	12383447	46745536	10892	18877										
ZNF563	147837	broad.mit.edu	37	chr19	12429921	12429921	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttacactcatagggtttCtctgcactgtgagtggtttc	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12429921C>A	ENST00000293725.5	-	4	1123	c.918G>T	c.(916-918)gaG>gaT	p.E306D		NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E306D(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CATAGGGTTTCTCTGCACTGT	0.428																																					GBM(39;623 795 5132 29510 31476)											1	Substitution - Missense(1)	large_intestine(1)	19											154	148	150					19																	12429921		2203	4300	6503	12290921	SO:0001583	missense	147837			BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"Zinc fingers, C2H2-type", "-"	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.918G>T	19.37:g.12429921C>A	ENSP00000293725:p.Glu306Asp		12290921	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819549	0.50633	.	.	ENSG00000188868	ENST00000293725	T	0.26810	1.71	1.0	-2.0	0.07433	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39517	0.1081	L	0.56199	1.76	0.27371	N	0.955699	D	0.76494	0.999	D	0.85130	0.997	T	0.28870	-1.0030	9	0.59425	D	0.04	.	7.5889	0.28008	0.4475:0.5525:0.0:0.0	.	306	Q8TA94	ZN563_HUMAN	D	306	ENSP00000293725:E306D	ENSP00000293725:E306D	E	-	3	2	ZNF563	12290921	0.081000	0.21417	0.016000	0.15963	0.471000	0.32888	-0.275000	0.08525	-0.567000	0.06046	-0.666000	0.03841	GAG		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		A	12429921	C	A	12429921	3	1	61	1	0	0	0	0	1	0	0	0	18033	912	32	2	516	2	ZNF563	19	12429921	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46474	12429921	46699062	10893	18878										
ZNF563	147837	broad.mit.edu	37	chr19	12433451	12433451	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcacatatctgtataaattCttctgtgatggacccagcaa	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12433451C>A	ENST00000293725.5	-	2	283	c.78G>T	c.(76-78)aaG>aaT	p.K26N	ZNF563_ENST00000595977.1_Missense_Mutation_p.K26N	NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K26N(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TGTATAAATTCTTCTGTGATG	0.428																																					GBM(39;623 795 5132 29510 31476)											2	Substitution - Missense(2)	large_intestine(2)	19											135	122	126					19																	12433451		2203	4300	6503	12294451	SO:0001583	missense	147837			BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"Zinc fingers, C2H2-type", "-"	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.78G>T	19.37:g.12433451C>A	ENSP00000293725:p.Lys26Asn		12294451	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972745	0.34848	.	.	ENSG00000188868	ENST00000293725;ENST00000318168	T	0.02944	4.1	1.27	0.0423	0.14217	Krueppel-associated box (4);	.	.	.	.	T	0.16300	0.0392	M	0.92219	3.285	0.22796	N	0.998726	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.03121	-1.1070	9	0.72032	D	0.01	.	6.2568	0.20877	0.2977:0.7023:0.0:0.0	.	26;26	Q8TA94-2;Q8TA94	.;ZN563_HUMAN	N	26	ENSP00000293725:K26N	ENSP00000293725:K26N	K	-	3	2	ZNF563	12294451	0.016000	0.18221	0.665000	0.29768	0.054000	0.15201	-0.040000	0.12104	-0.124000	0.11724	-0.692000	0.03713	AAG		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		A	12433451	C	A	12433451	3	1	61	1	0	0	0	0	1	0	0	0	18033	912	32	2	1364	2	ZNF563	19	12433451	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3530	12433451	46695532	10894	18879										
ZNF442	79973	broad.mit.edu	37	chr19	12461065	12461065	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtcttcgaagggaactaGaaatacggaaggctttacca	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12461065G>T	ENST00000242804.4	-	6	1916	c.1334C>A	c.(1333-1335)tCt>tAt	p.S445Y	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.S376Y	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S445Y(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						AAGGGAACTAGAAATACGGAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											76	80	79					19																	12461065		2203	4300	6503	12322065	SO:0001583	missense	79973			AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.1334C>A	19.37:g.12461065G>T	ENSP00000242804:p.Ser445Tyr		12322065	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271650	0.23221	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.01209	5.17;5.17	0.832	-0.474	0.12108	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01156	0.0038	L	0.58583	1.82	0.09310	N	1	P	0.42961	0.795	B	0.35278	0.199	T	0.47849	-0.9085	9	0.15499	T	0.54	.	5.5521	0.17095	0.0:0.0:0.6772:0.3228	.	445	Q9H7R0	ZN442_HUMAN	Y	445;376	ENSP00000242804:S445Y;ENSP00000388634:S376Y	ENSP00000242804:S445Y	S	-	2	0	ZNF442	12322065	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-3.737000	0.00379	-0.114000	0.11936	0.313000	0.20887	TCT		0.368	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		T	12461065	G	T	12461065	3	4	61	1	0	0	0	0	1	0	0	0	17954	942	33	2	553	2	ZNF442	19	12461065	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27614	12461065	46667918	10895	18880										
ZNF442	79973	broad.mit.edu	37	chr19	12461221	12461221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgcattatcatatgacttCgaaagcttgagtgatgagat	10	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12461221C>T	ENST00000242804.4	-	6	1760	c.1178G>A	c.(1177-1179)cGa>cAa	p.R393Q	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.R324Q	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R393Q(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						CATATGACTTCGAAAGCTTGA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											218	203	208					19																	12461221		2203	4300	6503	12322221	SO:0001583	missense	79973			AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.1178G>A	19.37:g.12461221C>T	ENSP00000242804:p.Arg393Gln		12322221	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	C	6.441	0.449442	0.12223	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.07444	3.19;3.19	0.832	-1.52	0.08637	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02688	0.0081	N	0.12961	0.28	0.09310	N	1	P	0.45044	0.849	B	0.30855	0.121	T	0.42916	-0.9423	9	0.10377	T	0.69	.	5.0856	0.14680	0.0:0.3651:0.0:0.6349	.	393	Q9H7R0	ZN442_HUMAN	Q	393;324	ENSP00000242804:R393Q;ENSP00000388634:R324Q	ENSP00000242804:R393Q	R	-	2	0	ZNF442	12322221	0.006000	0.16342	0.001000	0.08648	0.448000	0.32197	-0.022000	0.12480	-0.626000	0.05596	0.313000	0.20887	CGA		0.428	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		T	12461221	C	T	12461221	3	4	61	1	0	0	0	0	1	0	0	0	17954	884	31	1	709	1	ZNF442	19	12461221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156	12461221	46667762	10896	18881										
ZNF442	79973	broad.mit.edu	37	chr19	12461293	12461293	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtgtgagttCtttcatgactttgcagtgaa	9	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12461293C>A	ENST00000242804.4	-	6	1688	c.1106G>T	c.(1105-1107)aGa>aTa	p.R369I	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.R300I	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	369					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R369I(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						AGTGTGAGTTCTTTCATGACT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											190	184	186					19																	12461293		2203	4298	6501	12322293	SO:0001583	missense	79973			AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.1106G>T	19.37:g.12461293C>A	ENSP00000242804:p.Arg369Ile		12322293	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.492240	0.64074	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.24908	1.83;1.83	0.832	0.832	0.18867	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40040	0.1101	M	0.71296	2.17	0.43054	D	0.994663	D	0.61080	0.989	P	0.60068	0.868	T	0.35871	-0.9771	9	0.62326	D	0.03	.	7.4953	0.27485	0.0:1.0:0.0:0.0	.	369	Q9H7R0	ZN442_HUMAN	I	369;300	ENSP00000242804:R369I;ENSP00000388634:R300I	ENSP00000242804:R369I	R	-	2	0	ZNF442	12322293	0.000000	0.05858	0.661000	0.29709	0.975000	0.68041	-0.282000	0.08445	0.737000	0.32582	0.313000	0.20887	AGA		0.413	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		A	12461293	C	A	12461293	3	1	61	1	0	0	0	0	1	0	0	0	17954	913	32	2	781	2	ZNF442	19	12461293	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72	12461293	46667690	10897	18882										
ZNF442	79973	broad.mit.edu	37	chr19	12461473	12461473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgagttctttcatgtattCgaagggaactggaaacactg	11	6	2	1	rs371108711		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12461473C>T	ENST00000242804.4	-	6	1508	c.926G>A	c.(925-927)cGa>cAa	p.R309Q	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.R240Q	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R309Q(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TTCATGTATTCGAAGGGAACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	GLN/ARG	0,4406		0,0,2203	158	155	156		926	-1.7	0	19		156	3,8597	3.0+/-9.4	0,3,4297	no	missense	ZNF442	NM_030824.2	43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	309/628	12461473	3,13003	2203	4300	6503	12322473	SO:0001583	missense	79973			AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.926G>A	19.37:g.12461473C>T	ENSP00000242804:p.Arg309Gln		12322473	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	C	3.230	-0.157594	0.06544	0.0	3.49E-4	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.04275	3.66;3.66	0.832	-1.66	0.08265	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02380	0.0073	L	0.31120	0.905	0.09310	N	1	P	0.35908	0.527	B	0.18871	0.023	T	0.48222	-0.9054	9	0.10636	T	0.68	.	6.273	0.20965	0.0:0.3237:0.0:0.6763	.	309	Q9H7R0	ZN442_HUMAN	Q	309;240	ENSP00000242804:R309Q;ENSP00000388634:R240Q	ENSP00000242804:R309Q	R	-	2	0	ZNF442	12322473	0.000000	0.05858	0.000000	0.03702	0.488000	0.33401	0.028000	0.13644	-1.247000	0.02507	-0.671000	0.03813	CGA		0.408	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		T	12461473	C	T	12461473	3	4	61	1	0	0	0	0	1	0	0	0	17954	884	31	1	961	1	ZNF442	19	12461473	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180	12461473	46667510	10898	18883										
ZNF799	90576	broad.mit.edu	37	chr19	12501625	12501625	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttacattcatacggcttCtctccagagtgaattctttc	5	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12501625C>A	ENST00000430385.3	-	4	1787	c.1587G>T	c.(1585-1587)gaG>gaT	p.E529D	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.E497D	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	529					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E529D(1)|p.E316D(1)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CATACGGCTTCTCTCCAGAGT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	19											84	87	86					19																	12501625		2197	4296	6493	12362625	SO:0001583	missense	90576			BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1587G>T	19.37:g.12501625C>A	ENSP00000411084:p.Glu529Asp		12362625		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015673	0.54468	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.26810	1.71;1.71	1.14	1.14	0.20703	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43366	0.1244	M	0.61703	1.905	0.36589	D	0.873971	D	0.63880	0.993	D	0.77557	0.99	T	0.53358	-0.8450	9	0.66056	D	0.02	.	9.8115	0.40826	0.0:1.0:0.0:0.0	.	529	Q96GE5	ZN799_HUMAN	D	497;529	ENSP00000415278:E497D;ENSP00000411084:E529D	ENSP00000415278:E497D	E	-	3	2	ZNF799	12362625	0.035000	0.19736	0.389000	0.26208	0.156000	0.22039	-0.238000	0.08977	0.922000	0.37019	0.195000	0.17529	GAG		0.403	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		A	12501625	C	A	12501625	3	1	61	1	0	0	0	0	1	0	0	0	18205	912	32	2	348	2	ZNF799	19	12501625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40152	12501625	46627358	10899	18884										
ZNF443	10224	broad.mit.edu	37	chr19	12541048	12541048	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccttacattcatatgggttCtctccagtgtgagttttttt	7	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12541048C>A	ENST00000301547.5	-	4	2135	c.1938G>T	c.(1936-1938)gaG>gaT	p.E646D	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	646					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E646D(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CATATGGGTTCTCTCCAGTGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											126	128	127					19																	12541048		2203	4300	6503	12402048	SO:0001583	missense	10224			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1938G>T	19.37:g.12541048C>A	ENSP00000301547:p.Glu646Asp		12402048		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	8.142	0.785515	0.16189	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.26810	1.71	1.05	1.05	0.20165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19765	0.0475	L	0.37800	1.135	0.21627	N	0.999616	B	0.20368	0.044	B	0.15870	0.014	T	0.23297	-1.0192	9	0.52906	T	0.07	.	9.6731	0.40023	0.0:1.0:0.0:0.0	.	646	Q9Y2A4	ZN443_HUMAN	D	646;618	ENSP00000301547:E646D	ENSP00000301547:E646D	E	-	3	2	ZNF443	12402048	0.001000	0.12720	0.074000	0.20217	0.076000	0.17211	0.457000	0.21875	0.889000	0.36185	0.184000	0.17185	GAG		0.388	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		A	12541048	C	A	12541048	3	1	61	1	0	0	0	0	1	0	0	0	17955	912	32	2	81	2	ZNF443	19	12541048	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39423	12541048	46587935	10900	18885										
ZNF443	10224	broad.mit.edu	37	chr19	12541399	12541399	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttacactcataaggtttCtctcctgtgtgagtcctttt	7	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12541399C>A	ENST00000301547.5	-	4	1784	c.1587G>T	c.(1585-1587)gaG>gaT	p.E529D	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	529					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E529D(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CATAAGGTTTCTCTCCTGTGT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	102	104					19																	12541399		2203	4300	6503	12402399	SO:0001583	missense	10224			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1587G>T	19.37:g.12541399C>A	ENSP00000301547:p.Glu529Asp		12402399		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.573842	0.28092	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.26810	1.71	1.37	-0.935	0.10423	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18964	0.0455	L	0.37897	1.145	0.26020	N	0.981872	B	0.16603	0.018	B	0.25506	0.061	T	0.31280	-0.9949	9	0.56958	D	0.05	.	6.3439	0.21339	0.0:0.691:0.0:0.309	.	529	Q9Y2A4	ZN443_HUMAN	D	529	ENSP00000301547:E529D	ENSP00000301547:E529D	E	-	3	2	ZNF443	12402399	0.011000	0.17503	0.059000	0.19551	0.126000	0.20510	-0.353000	0.07691	-0.211000	0.10124	-0.384000	0.06662	GAG		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		A	12541399	C	A	12541399	3	1	61	1	0	0	0	0	1	0	0	0	17955	912	32	2	432	2	ZNF443	19	12541399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	351	12541399	46587584	10901	18886										
ZNF443	10224	broad.mit.edu	37	chr19	12541592	12541592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgagttgtttcatgccttCgaagggaactggaaatacgg	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12541592C>T	ENST00000301547.5	-	4	1591	c.1394G>A	c.(1393-1395)cGa>cAa	p.R465Q	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	465					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R465Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TTCATGCCTTCGAAGGGAACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											98	99	99					19																	12541592		2203	4300	6503	12402592	SO:0001583	missense	10224			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1394G>A	19.37:g.12541592C>T	ENSP00000301547:p.Arg465Gln		12402592		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	9.073	0.997485	0.19043	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07444	3.19	1.37	-0.0118	0.13991	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04543	0.0124	L	0.33137	0.985	0.09310	N	1	P	0.36110	0.537	B	0.33890	0.172	T	0.37150	-0.9718	9	0.11794	T	0.64	.	2.3043	0.04170	0.2362:0.2178:0.0:0.546	.	465	Q9Y2A4	ZN443_HUMAN	Q	465	ENSP00000301547:R465Q	ENSP00000301547:R465Q	R	-	2	0	ZNF443	12402592	0.000000	0.05858	0.012000	0.15200	0.530000	0.34684	-6.920000	0.00049	-0.035000	0.13691	0.461000	0.40582	CGA		0.393	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		T	12541592	C	T	12541592	3	4	61	1	0	0	0	0	1	0	0	0	17955	884	31	1	625	1	ZNF443	19	12541592	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	193	12541592	46587391	10902	18887										
ZNF443	10224	broad.mit.edu	37	chr19	12541806	12541806	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccacactgcttgcattCatagggtttctctccagtgt	7	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12541806C>A	ENST00000301547.5	-	4	1377	c.1180G>T	c.(1180-1182)Gaa>Taa	p.E394*	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	394					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E394*(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TGCTTGCATTCATAGGGTTTC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											179	166	170					19																	12541806		2203	4300	6503	12402806	SO:0001587	stop_gained	10224			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1180G>T	19.37:g.12541806C>A	ENSP00000301547:p.Glu394*		12402806		Nonsense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310030	0.60414	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	.	.	.	1.37	-1.3	0.09259	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	3.013	0.06051	0.0:0.2849:0.2404:0.4747	.	.	.	.	X	394	.	ENSP00000301547:E394X	E	-	1	0	ZNF443	12402806	0.000000	0.05858	0.001000	0.08648	0.109000	0.19521	-5.448000	0.00121	-0.259000	0.09432	0.461000	0.40582	GAA		0.418	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		A	12541806	C	A	12541806	4	1	61	1	0	0	0	0	0	1	0	0	17955	835	29	2	839	2	ZNF443	19	12541806	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	214	12541806	46587177	10903	18888										
ZNF443	10224	broad.mit.edu	37	chr19	12541984	12541984	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctgacatgcatagggtttCtctgcactgtgagtggtttc	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12541984C>A	ENST00000301547.5	-	4	1199	c.1002G>T	c.(1000-1002)gaG>gaT	p.E334D	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	334					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E334D(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CATAGGGTTTCTCTGCACTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											202	188	193					19																	12541984		2203	4299	6502	12402984	SO:0001583	missense	10224			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1002G>T	19.37:g.12541984C>A	ENSP00000301547:p.Glu334Asp		12402984		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520704	0.44866	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.26810	1.71	1.44	-2.54	0.06307	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22704	0.0548	L	0.56124	1.755	0.27671	N	0.946751	B	0.32051	0.354	B	0.34346	0.18	T	0.29088	-1.0023	9	0.72032	D	0.01	.	7.1342	0.25519	0.0:0.4806:0.0:0.5194	.	334	Q9Y2A4	ZN443_HUMAN	D	334	ENSP00000301547:E334D	ENSP00000301547:E334D	E	-	3	2	ZNF443	12402984	0.000000	0.05858	0.001000	0.08648	0.065000	0.16274	-0.129000	0.10515	-0.602000	0.05775	-0.384000	0.06662	GAG		0.438	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		A	12541984	C	A	12541984	3	1	61	1	0	0	0	0	1	0	0	0	17955	912	32	2	1017	2	ZNF443	19	12541984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178	12541984	46586999	10904	18889										
ZNF709	163051	broad.mit.edu	37	chr19	12575907	12575907	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacactgatagggtttttCcccagtgtgagtcctttcat	8	10	1	2	rs148352272		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12575907C>A	ENST00000397732.3	-	4	1000	c.829G>T	c.(829-831)Gaa>Taa	p.E277*	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Nonsense_Mutation_p.E277*	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	277					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E277*(1)		large_intestine(3)|upper_aerodigestive_tract(3)	6						TAGGGTTTTTCCCCAGTGTGA	0.383																																					GBM(33;565 669 12371 29134 51667)											1	Substitution - Nonsense(1)	large_intestine(1)	19											33	35	34					19																	12575907		2156	4278	6434	12436907	SO:0001587	stop_gained	163051			AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.829G>T	19.37:g.12575907C>A	ENSP00000380840:p.Glu277*		12436907	A8K4E6	Nonsense_Mutation	SNP	ENST00000397732.3	37	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	C	37	6.533429	0.97641	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	.	.	.	2.8	0.548	0.17208	.	0.000000	0.35903	N	0.002915	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	5.9719	0.19357	0.1894:0.6973:0.0:0.1133	.	.	.	.	X	277	.	ENSP00000404127:E277X	E	-	1	0	ZNF709;CTD-2192J16.17	12436907	0.766000	0.28496	0.244000	0.24202	0.990000	0.78478	2.043000	0.41231	0.234000	0.21139	0.467000	0.42956	GAA		0.383	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		A	12575907	C	A	12575907	4	1	61	1	0	0	0	0	0	1	0	0	18152	864	30	2	1100	2	ZNF709	19	12575907	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33923	12575907	46553076	10905	18890										
ZNF709	163051	broad.mit.edu	37	chr19	12577565	12577565	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccaagttaacaaaggtttCttgcatcacatctctgtaga	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12577565C>A	ENST00000397732.3	-	2	274	c.103G>T	c.(103-105)Gaa>Taa	p.E35*	CTD-3105H18.18_ENST00000598753.1_Nonsense_Mutation_p.E35*|ZNF709_ENST00000428311.1_Nonsense_Mutation_p.E35*	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	35	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E35*(1)		large_intestine(3)|upper_aerodigestive_tract(3)	6						ACAAAGGTTTCTTGCATCACA	0.448																																					GBM(33;565 669 12371 29134 51667)											1	Substitution - Nonsense(1)	large_intestine(1)	19											99	100	99					19																	12577565		2202	4300	6502	12438565	SO:0001587	stop_gained	163051			AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.103G>T	19.37:g.12577565C>A	ENSP00000380840:p.Glu35*		12438565	A8K4E6	Nonsense_Mutation	SNP	ENST00000397732.3	37	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742185	0.89573	.	.	ENSG00000242852;ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000455490;ENST00000428311	.	.	.	3.19	3.19	0.36642	.	0.000000	0.36591	N	0.002506	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.283	0.54776	0.0:1.0:0.0:0.0	.	.	.	.	X	35;64;35	.	ENSP00000404127:E35X	E	-	1	0	ZNF709;CTD-2192J16.17	12438565	0.145000	0.22656	0.991000	0.47740	0.970000	0.65996	0.467000	0.22035	2.099000	0.63709	0.491000	0.48974	GAA		0.448	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		A	12577565	C	A	12577565	4	1	61	1	0	0	0	0	0	1	0	0	18152	922	32	2	1834	2	ZNF709	19	12577565	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1658	12577565	46551418	10906	18891										
ZNF490	57474	broad.mit.edu	37	chr19	12691932	12691932	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcatgactccgtaagtaCgtgggacaactgaaggcttt	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12691932C>T	ENST00000311437.6	-	5	1079	c.957G>A	c.(955-957)acG>acA	p.T319T	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T319T(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TCCGTAAGTACGTGGGACAAC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	19											85	80	81					19																	12691932		2203	4300	6503	12552932	SO:0001819	synonymous_variant	57474			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"Zinc fingers, C2H2-type", "-"	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.957G>A	19.37:g.12691932C>T			12552932		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																				0.433	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		T	12691932	C	T	12691932	2	4	61	1	0	0	0	0	0	0	0	1	17980	523	19	1		1	ZNF490	19	12691932	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114367	12691932	46437051	10907	18892										
ZNF490	57474	broad.mit.edu	37	chr19	12694260	12694260	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacctatacaggccaggttCttgaaggttgcccgcatcac	9	12	2	1	rs373138394		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12694260C>A	ENST00000311437.6	-	3	395	c.273G>T	c.(271-273)aaG>aaT	p.K91N	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	91	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K91N(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						AGGCCAGGTTCTTGAAGGTTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	ASN/LYS	0,4406		0,0,2203	114	111	112		273	-1.8	0	19		112	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF490	NM_020714.2	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	91/530	12694260	1,13005	2203	4300	6503	12555260	SO:0001583	missense	57474			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"Zinc fingers, C2H2-type", "-"	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.273G>T	19.37:g.12694260C>A	ENSP00000311521:p.Lys91Asn		12555260		Missense_Mutation	SNP	ENST00000311437.6	37	CCDS12272.1	.	.	.	.	.	.	.	.	.	.	C	7.120	0.577745	0.13686	0.0	1.16E-4	ENSG00000188033	ENST00000311437;ENST00000440366	T;T	0.01854	4.6;4.6	1.32	-1.77	0.07982	Krueppel-associated box (4);	.	.	.	.	T	0.02047	0.0064	L	0.35593	1.075	0.09310	N	1	B	0.16603	0.018	B	0.14023	0.01	T	0.42849	-0.9427	9	0.62326	D	0.03	.	6.4803	0.22060	0.5045:0.4955:0.0:0.0	.	91	Q9ULM2	ZN490_HUMAN	N	91;38	ENSP00000311521:K91N;ENSP00000404112:K38N	ENSP00000311521:K91N	K	-	3	2	ZNF490	12555260	0.002000	0.14202	0.015000	0.15790	0.064000	0.16182	0.264000	0.18497	-0.358000	0.08162	-0.500000	0.04577	AAG		0.473	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		A	12694260	C	A	12694260	3	1	61	1	0	0	0	0	1	0	0	0	17980	912	32	2	1328	2	ZNF490	19	12694260	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2328	12694260	46434723	10908	18893										
MAN2B1	4125	broad.mit.edu	37	chr19	12758346	12758346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagcgcagcagcaccatttCggggccccagctggccagcg	13	16	0	0	rs139366493		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12758346C>T	ENST00000456935.2	-	22	2771	c.2731G>A	c.(2731-2733)Gaa>Aaa	p.E911K	MAN2B1_ENST00000221363.4_Missense_Mutation_p.E910K|CTD-2192J16.22_ENST00000597692.1_Missense_Mutation_p.R97Q	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	911					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.E911K(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AGCACCATTTCGGGGCCCCAG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	61	64	63		2731,2728	-4.8	0	19	dbSNP_134	63	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	56,56	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign	911/1012,910/1011	12758346	2,13004	2203	4300	6503	12619346	SO:0001583	missense	4125				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2731G>A	19.37:g.12758346C>T	ENSP00000395473:p.Glu911Lys		12619346	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	C	6.414	0.444472	0.12164	2.27E-4	1.16E-4	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.82893	-1.66;-1.66	5.84	-4.8	0.03190	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	2.942610	0.00757	N	0.001115	T	0.62962	0.2471	N	0.05177	-0.1	0.09310	N	1	B;B	0.17268	0.003;0.021	B;B	0.08055	0.002;0.003	T	0.56511	-0.7967	10	0.13470	T	0.59	-1.9592	8.4529	0.32882	0.0:0.4019:0.1042:0.494	.	910;911	G5E928;O00754	.;MA2B1_HUMAN	K	911;850;910	ENSP00000395473:E911K;ENSP00000221363:E910K	ENSP00000221363:E910K	E	-	1	0	MAN2B1	12619346	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	0.101000	0.15251	-0.561000	0.06094	0.561000	0.74099	GAA		0.657	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			T	12758346	C	T	12758346	3	4	61	1	0	0	0	0	1	0	0	0	9246	893	31	1	316	1	MAN2B1	19	12758346	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	64086	12758346	46370637	10909	18894										
RNASEH2A	10535	broad.mit.edu	37	chr19	12918087	12918087	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggaggacacggactttgtCggctgggcgctggatgtgct	17	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12918087C>T	ENST00000221486.4	+	3	361	c.267C>T	c.(265-267)gtC>gtT	p.V89V		NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A	89					DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)	p.V89V(1)		breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						CGGACTTTGTCGGCTGGGCGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	19											176	163	168					19																	12918087		2203	4300	6503	12779087	SO:0001819	synonymous_variant	10535			Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"ribonuclease H2, large subunit", "Aicardi-Goutieres syndrome 4"			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.267C>T	19.37:g.12918087C>T			12779087	B2RCY1|Q96F11	Silent	SNP	ENST00000221486.4	37	CCDS12282.1																																																																																				0.597	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397		T	12918087	C	T	12918087	2	4	61	1	0	0	0	0	0	0	0	1	13449	871	31	1		1	RNASEH2A	19	12918087	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159741	12918087	46210896	10910	18895										
MAST1	22983	broad.mit.edu	37	chr19	12958769	12958769	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcatccaccaccagatCatcgagctggcccgggactg	10	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:12958769C>A	ENST00000251472.4	+	7	711	c.672C>A	c.(670-672)atC>atA	p.I224I	MAST1_ENST00000591495.1_Silent_p.I220I	NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1									p.I224I(1)		NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						ACCACCAGATCATCGAGCTGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	19											60	47	51					19																	12958769		2203	4300	6503	12819769	SO:0001819	synonymous_variant	22983			AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.672C>A	19.37:g.12958769C>A			12819769		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																				0.597	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		A	12958769	C	A	12958769	2	1	61	1	0	0	0	0	0	0	0	1	9354	816	29	2		2	MAST1	19	12958769	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40682	12958769	46170214	10911	18896										
GCDH	2639	broad.mit.edu	37	chr19	13002653	13002653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccttcccagcctcgcgtCccgagtttgactggcaggac	10	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13002653C>T	ENST00000222214.5	+	4	347	c.136C>T	c.(136-138)Ccc>Tcc	p.P46S	GCDH_ENST00000591470.1_Missense_Mutation_p.P46S|GCDH_ENST00000422947.2_5'UTR|GCDH_ENST00000457854.1_Missense_Mutation_p.P46S			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	46					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)	p.P46S(1)		autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	AGCCTCGCGTCCCGAGTTTGA	0.617																																					GBM(123;875 1636 7726 16444 26754)											1	Substitution - Missense(1)	large_intestine(1)	19											50	46	47					19																	13002653		2203	4300	6503	12863653	SO:0001583	missense	2639			AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.136C>T	19.37:g.13002653C>T	ENSP00000222214:p.Pro46Ser		12863653	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	37	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.728682	0.48833	.	.	ENSG00000105607	ENST00000457854;ENST00000222214;ENST00000421816	D;D	0.97328	-4.28;-4.34	5.32	4.22	0.49857	Acyl-CoA dehydrogenase/oxidase (1);	0.195768	0.44902	D	0.000419	D	0.91734	0.7386	N	0.19112	0.55	0.80722	D	1	B;B;B	0.20780	0.007;0.048;0.035	B;B;B	0.17098	0.008;0.005;0.017	D	0.87687	0.2551	10	0.10902	T	0.67	.	12.4453	0.55647	0.1684:0.8316:0.0:0.0	.	34;46;46	B4DQF2;Q92947;Q92947-2	.;GCDH_HUMAN;.	S	46;46;34	ENSP00000394872:P46S;ENSP00000222214:P46S	ENSP00000222214:P46S	P	+	1	0	GCDH	12863653	0.031000	0.19500	0.529000	0.27951	0.019000	0.09904	0.626000	0.24492	2.500000	0.84329	0.462000	0.41574	CCC		0.617	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			T	13002653	C	T	13002653	3	4	61	1	0	0	0	0	1	0	0	0	6307	855	30	3	146	3	GCDH	19	13002653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43884	13002653	46126330	10912	18897										
GCDH	2639	broad.mit.edu	37	chr19	13004318	13004318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatggctgtgctggggtttCgtctgtggcctatgggctcc	15	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13004318C>T	ENST00000222214.5	+	6	567	c.356C>T	c.(355-357)tCg>tTg	p.S119L	GCDH_ENST00000591470.1_Missense_Mutation_p.S119L|GCDH_ENST00000422947.2_Missense_Mutation_p.S75L|GCDH_ENST00000457854.1_Missense_Mutation_p.S119L			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	119					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)	p.S119L(1)		autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	GCTGGGGTTTCGTCTGTGGCC	0.597																																					GBM(123;875 1636 7726 16444 26754)											1	Substitution - Missense(1)	large_intestine(1)	19	GRCh37	CM002258	GCDH	M							116	87	97					19																	13004318		2203	4300	6503	12865318	SO:0001583	missense	2639			AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.356C>T	19.37:g.13004318C>T	ENSP00000222214:p.Ser119Leu		12865318	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	37	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.444388	0.83993	.	.	ENSG00000105607	ENST00000457854;ENST00000222214;ENST00000421816;ENST00000422947	D;D;D	0.99113	-5.44;-5.44;-5.44	5.19	5.19	0.71726	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.120884	0.56097	D	0.000031	D	0.99612	0.9859	H	0.98965	4.385	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.70487	0.967;0.957;0.969;0.93	D	0.97572	1.0105	10	0.87932	D	0	.	16.567	0.84601	0.0:1.0:0.0:0.0	.	75;86;119;119	B4DK85;B4DQF2;Q92947;Q92947-2	.;.;GCDH_HUMAN;.	L	119;119;86;75	ENSP00000394872:S119L;ENSP00000222214:S119L;ENSP00000394821:S75L	ENSP00000222214:S119L	S	+	2	0	GCDH	12865318	1.000000	0.71417	0.909000	0.35828	0.841000	0.47740	5.533000	0.67160	2.584000	0.87258	0.563000	0.77884	TCG		0.597	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			T	13004318	C	T	13004318	3	4	61	1	0	0	0	0	1	0	0	0	6307	893	31	1	374	1	GCDH	19	13004318	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1665	13004318	46124665	10913	18898										
CACNA1A	773	broad.mit.edu	37	chr19	13339558	13339558	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgcctaagccgagaggGggagatattactcgtaataa	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13339558G>T	ENST00000573710.2	-	37	5861	c.5583C>A	c.(5581-5583)ccC>ccA	p.P1861P	CACNA1A_ENST00000574822.1_5'Flank|CACNA1A_ENST00000360228.5_Intron	NM_001127221.1	NP_001120693.1	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1861					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.P1861P(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCCGAGAGGGGGAGATATTA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	19											66	61	63					19																	13339558		1568	3582	5150	13200558	SO:0001819	synonymous_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000573710.2:c.5583C>A	19.37:g.13339558G>T			13200558	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000573710.2	37	CCDS45999.1																																																																																				0.473	CACNA1A-002	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439639.2	NM_000068		T	13339558	G	T	13339558	2	4	61	1	0	0	0	0	0	0	0	1	2544	1219	43	2		2	CACNA1A	19	13339558	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	335240	13339558	45789425	10914	18899										
CACNA1A	773	broad.mit.edu	37	chr19	13341002	13341002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaaagttgtccatgatgaCggcgacaaagagattcagca	10	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13341002C>T	ENST00000360228.5	-	36	5421	c.5422G>A	c.(5422-5424)Gtc>Atc	p.V1808I	CACNA1A_ENST00000574822.1_5'UTR|CACNA1A_ENST00000573710.2_Missense_Mutation_p.V1809I	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1809					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.V1809I(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCATGATGACGGCGACAAAG	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	19											89	97	94					19																	13341002		2093	4253	6346	13202002	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.5422G>A	19.37:g.13341002C>T	ENSP00000353362:p.Val1808Ile		13202002	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.918246	0.73098	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98926	-5.24	4.33	4.33	0.51752	Ion transport (1);	0.000000	0.64402	D	0.000006	D	0.98877	0.9620	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.994;0.999;0.989;0.999	D	0.99521	1.0958	10	0.52906	T	0.07	.	15.5941	0.76566	0.0:1.0:0.0:0.0	.	1809;1814;1808;1809	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	I	1808;1814;1809;1809	ENSP00000353362:V1808I	ENSP00000317661:V1809I	V	-	1	0	CACNA1A	13202002	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	7.736000	0.84948	1.968000	0.57251	0.549000	0.68633	GTC		0.577	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13341002	C	T	13341002	3	4	61	1	0	0	0	0	1	0	0	0	2544	536	19	1	2247	1	CACNA1A	19	13341002	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1444	13341002	45787981	10915	18900										
CACNA1A	773	broad.mit.edu	37	chr19	13342526	13342526	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtccacagactcaccaGaaacgagcagaggaagatga	11	10	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13342526G>T	ENST00000360228.5	-	35	5397	c.5398C>A	c.(5398-5400)Ctg>Atg	p.L1800M	CACNA1A_ENST00000574822.1_5'UTR|CACNA1A_ENST00000573710.2_Missense_Mutation_p.L1801M	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1801					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.L1801M(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	AGACTCACCAGAAACGAGCAG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	19											60	62	61					19																	13342526		2001	4179	6180	13203526	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.5398C>A	19.37:g.13342526G>T	ENSP00000353362:p.Leu1800Met		13203526	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651096	0.47362	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98926	-5.24	4.61	3.57	0.40892	Ion transport (1);	0.000000	0.64402	D	0.000020	D	0.98817	0.9601	M	0.75884	2.315	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.987;0.986;0.999;0.992	D	0.99395	1.0926	10	0.87932	D	0	.	11.685	0.51481	0.0885:0.0:0.9115:0.0	.	1801;1806;1800;1801	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	M	1800;1806;1801;1801	ENSP00000353362:L1800M	ENSP00000317661:L1801M	L	-	1	2	CACNA1A	13203526	1.000000	0.71417	0.953000	0.39169	0.982000	0.71751	4.706000	0.61845	0.929000	0.37192	0.555000	0.69702	CTG		0.507	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13342526	G	T	13342526	3	4	61	1	0	0	0	0	1	0	0	0	2544	933	33	2	2275	2	CACNA1A	19	13342526	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1524	13342526	45786457	10916	18901										
CACNA1A	773	broad.mit.edu	37	chr19	13345847	13345847	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgatgccaatgttaccaaAcacctgtggaattggagggt	12	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13345847A>C	ENST00000360228.5	-	34	5136	c.5137T>G	c.(5137-5139)Ttt>Gtt	p.F1713V	CACNA1A_ENST00000574822.1_5'UTR|CACNA1A_ENST00000573710.2_Missense_Mutation_p.F1714V	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1714					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.F1714V(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGTTACCAAACACCTGTGGA	0.537											OREG0025293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	19											125	126	126					19																	13345847		2055	4198	6253	13206847	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.5137T>G	19.37:g.13345847A>C	ENSP00000353362:p.Phe1713Val	686	13206847	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254631	0.59212	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.99129	-5.46	5.01	5.01	0.66863	Ion transport (1);	0.132589	0.52532	D	0.000071	D	0.99670	0.9877	H	0.99863	4.86	0.80722	D	1	D;D;D;D	0.89917	0.996;0.995;1.0;0.996	D;D;D;D	0.87578	0.976;0.94;0.998;0.964	D	0.97061	0.9771	10	0.87932	D	0	.	13.7544	0.62928	1.0:0.0:0.0:0.0	.	1714;1719;1713;1714	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	V	1713;1719;1714;1714	ENSP00000353362:F1713V	ENSP00000317661:F1714V	F	-	1	0	CACNA1A	13206847	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	9.042000	0.93793	1.894000	0.54839	0.451000	0.29950	TTT		0.537	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		C	13345847	A	C	13345847	3	2	61	1	0	0	0	0	1	0	0	0	2544	43	2	4	2540	4	CACNA1A	19	13345847	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	3321	13345847	45783136	10917	18902										
CACNA1A	773	broad.mit.edu	37	chr19	13365938	13365938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcacgatggtgttgagggCgatcatggccatgatcgtgt	15	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13365938C>T	ENST00000360228.5	-	29	4725	c.4726G>A	c.(4726-4728)Gcc>Acc	p.A1576T	CACNA1A_ENST00000574822.1_5'Flank|CACNA1A_ENST00000573710.2_Missense_Mutation_p.A1577T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1577					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.A1577T(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGTTGAGGGCGATCATGGCC	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	19											91	101	97					19																	13365938		2122	4238	6360	13226938	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.4726G>A	19.37:g.13365938C>T	ENSP00000353362:p.Ala1576Thr		13226938	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.338593	0.60963	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084;ENST00000445042	D	0.97505	-4.41	4.8	4.8	0.61643	.	0.140325	0.46758	D	0.000276	D	0.98036	0.9353	M	0.65677	2.01	0.80722	D	1	P;P;D;P	0.89917	0.598;0.845;1.0;0.598	B;B;D;B	0.83275	0.103;0.196;0.996;0.071	D	0.98766	1.0726	10	0.56958	D	0.05	.	16.7134	0.85391	0.0:1.0:0.0:0.0	.	1577;1580;1576;1577	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	T	1576;1580;1577;1577;193	ENSP00000353362:A1576T	ENSP00000317661:A1577T	A	-	1	0	CACNA1A	13226938	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.728000	0.84847	2.227000	0.72691	0.650000	0.86243	GCC		0.557	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13365938	C	T	13365938	3	4	61	1	0	0	0	0	1	0	0	0	2544	768	27	1	2972	1	CACNA1A	19	13365938	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20091	13365938	45763045	10918	18903										
CACNA1A	773	broad.mit.edu	37	chr19	13386702	13386702	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggccccactgaccactatGaagtcgagaatattccagag	10	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13386702G>T	ENST00000360228.5	-	24	3950	c.3951C>A	c.(3949-3951)ttC>ttA	p.F1317L	CACNA1A_ENST00000573710.2_Missense_Mutation_p.F1318L	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1318					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.F1318L(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGACCACTATGAAGTCGAGAA	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	19											75	79	78					19																	13386702		1968	4139	6107	13247702	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3951C>A	19.37:g.13386702G>T	ENSP00000353362:p.Phe1317Leu		13247702	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.064227	0.36373	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98849	-5.18	4.57	3.45	0.39498	Ion transport (1);	0.159223	0.45126	D	0.000387	D	0.98469	0.9490	L	0.58354	1.805	0.45733	D	0.998632	D;B;D	0.69078	0.973;0.208;0.997	D;B;D	0.77004	0.93;0.248;0.989	D	0.98141	1.0436	10	0.72032	D	0.01	.	9.7146	0.40268	0.1504:0.0:0.8496:0.0	.	1318;1321;1317	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	L	1317;1321;1318;1318	ENSP00000353362:F1317L	ENSP00000317661:F1318L	F	-	3	2	CACNA1A	13247702	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.424000	0.52764	2.089000	0.63090	0.591000	0.81541	TTC		0.582	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13386702	G	T	13386702	3	4	61	1	0	0	0	0	1	0	0	0	2544	1281	45	2	3767	2	CACNA1A	19	13386702	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20764	13386702	45742281	10919	18904										
CACNA1A	773	broad.mit.edu	37	chr19	13419321	13419321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgacagcccagatgacctCgaagatgctcccaatgataa	8	11	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13419321C>T	ENST00000360228.5	-	13	1689	c.1690G>A	c.(1690-1692)Gag>Aag	p.E564K	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E565K	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	565					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.E565K(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CAGATGACCTCGAAGATGCTC	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	19											62	58	59					19																	13419321		2022	4178	6200	13280321	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1690G>A	19.37:g.13419321C>T	ENSP00000353362:p.Glu564Lys		13280321	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227854	0.79576	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98602	-5.02	5.33	5.33	0.75918	Ion transport (1);	0.064364	0.64402	D	0.000013	D	0.99387	0.9784	H	0.97291	3.975	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.994;0.988	D	0.98483	1.0606	10	0.72032	D	0.01	.	17.7841	0.88532	0.0:1.0:0.0:0.0	.	565;565;564	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	K	564;565;565;565	ENSP00000353362:E564K	ENSP00000317661:E565K	E	-	1	0	CACNA1A	13280321	1.000000	0.71417	0.983000	0.44433	0.826000	0.46750	7.747000	0.85070	2.495000	0.84180	0.563000	0.77884	GAG		0.488	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13419321	C	T	13419321	3	4	61	1	0	0	0	0	1	0	0	0	2544	893	31	1	6081	1	CACNA1A	19	13419321	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	32619	13419321	45709662	10920	18905										
CACNA1A	773	broad.mit.edu	37	chr19	13423557	13423557	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacatttttataaacatttCggacataaagagtcctaaga	6	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13423557C>T	ENST00000360228.5	-	12	1593	c.1594G>A	c.(1594-1596)Gaa>Aaa	p.E532K	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E533K	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	533					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.E533K(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	ATAAACATTTCGGACATAAAG	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	19	GRCh37	CM065992	CACNA1A	M							75	72	73					19																	13423557		1850	4099	5949	13284557	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1594G>A	19.37:g.13423557C>T	ENSP00000353362:p.Glu532Lys		13284557	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349644	0.82132	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98822	-5.16	5.11	5.11	0.69529	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99576	0.9847	H	0.99273	4.495	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.994;0.988	D	0.97583	1.0112	10	0.87932	D	0	.	17.6776	0.88235	0.0:1.0:0.0:0.0	.	533;533;532	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	K	532;533;533;533	ENSP00000353362:E532K	ENSP00000317661:E533K	E	-	1	0	CACNA1A	13284557	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.529000	0.85273	0.650000	0.86243	GAA		0.458	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13423557	C	T	13423557	3	4	61	1	0	0	0	0	1	0	0	0	2544	893	31	1	6181	1	CACNA1A	19	13423557	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4236	13423557	45705426	10921	18906										
CACNA1A	773	broad.mit.edu	37	chr19	13470495	13470495	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcaaacaggatgttgtcGaactgagtgatcccgttgtt	11	8	0	2	rs17846910		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13470495G>A	ENST00000360228.5	-	6	902	c.903C>T	c.(901-903)ttC>ttT	p.F301F	CACNA1A_ENST00000573710.2_Silent_p.F301F	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	301					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.F301F(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GGATGTTGTCGAACTGAGTGA	0.552													G|||	1	0.000199681	0	0	5008	,	,		19936	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	19						G	,,,,	1,4143		0,1,2071	103	97	99		903,903,903,903,903	-0.4	1	19	dbSNP_123	99	0,8444		0,0,4222	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	0,1,6293	AA,AG,GG		0.0,0.0241,0.0079	,,,,	301/2267,301/2262,301/2507,301/2264,301/2513	13470495	1,12587	2072	4222	6294	13331495	SO:0001819	synonymous_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.903C>T	19.37:g.13470495G>A			13331495	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																				0.552	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13470495	G	A	13470495	2	1	61	1	0	0	0	0	0	0	0	1	2544	1049	37	1		1	CACNA1A	19	13470495	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46938	13470495	45658488	10922	18907										
CACNA1A	773	broad.mit.edu	37	chr19	13476147	13476147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacctgtcccctcttcaaaGcaggtggtatgaaattttcc	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13476147G>A	ENST00000360228.5	-	5	767	c.768C>T	c.(766-768)tgC>tgT	p.C256C	CACNA1A_ENST00000573710.2_Silent_p.C256C	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	256			C -> R (in EA2; dbSNP:rs121908231). {ECO:0000269|PubMed:15173248}.		adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.C256C(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTCTTCAAAGCAGGTGGTAT	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	19											99	100	100					19																	13476147		1882	4105	5987	13337147	SO:0001819	synonymous_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.768C>T	19.37:g.13476147G>A			13337147	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																				0.453	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13476147	G	A	13476147	2	1	61	1	0	0	0	0	0	0	0	1	2544	963	34	3		3	CACNA1A	19	13476147	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5652	13476147	45652836	10923	18908										
CACNA1A	773	broad.mit.edu	37	chr19	13476262	13476262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcatcgccttcatgatcGacttcaggacgacttgtaaa	9	10	3	1	rs121908225		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:13476262G>A	ENST00000360228.5	-	5	652	c.653C>T	c.(652-654)tCg>tTg	p.S218L	CACNA1A_ENST00000573710.2_Missense_Mutation_p.S218L	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	218			S -> L (in FHM1; dbSNP:rs121908225). {ECO:0000269|PubMed:11409427}.		adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.S218L(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTCATGATCGACTTCAGGAC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	19	GRCh37	CM016081	CACNA1A	M	rs121908225						54	53	54					19																	13476262		1917	4131	6048	13337262	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.653C>T	19.37:g.13476262G>A	ENSP00000353362:p.Ser218Leu		13337262	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157215	0.57259	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98701	-5.08	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98915	0.9632	M	0.64997	1.995	0.58432	A	0.999999	D;D	0.89917	0.999;1.0	D;D	0.87578	0.994;0.998	D	0.99906	1.1180	9	0.87932	D	0	.	18.2896	0.90124	0.0:0.0:1.0:0.0	.	218;218	O00555;Q9NS88	CAC1A_HUMAN;.	L	218	ENSP00000353362:S218L	ENSP00000317661:S218L	S	-	2	0	CACNA1A	13337262	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	9.564000	0.98151	2.603000	0.88011	0.655000	0.94253	TCG		0.493	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13476262	G	A	13476262	3	1	61	1	0	0	0	0	1	0	0	0	2544	1059	37	1	7153	1	CACNA1A	19	13476262	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	115	13476262	45652721	10924	18909										
CC2D1A	54862	broad.mit.edu	37	chr19	14037824	14037824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcaaactctgcatcaaccGcagccaccgtggcttccgaa	8	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14037824G>A	ENST00000318003.7	+	21	2400	c.2159G>A	c.(2158-2160)cGc>cAc	p.R720H	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R720H	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	720	C2.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)	p.R720H(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TGCATCAACCGCAGCCACCGT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											61	64	63					19																	14037824		2052	4200	6252	13898824	SO:0001583	missense	54862			AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2159G>A	19.37:g.14037824G>A	ENSP00000313601:p.Arg720His		13898824	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	g	27.7	4.858598	0.91433	.	.	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.30714	1.52	5.25	4.21	0.49690	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.60327	0.2260	M	0.86420	2.815	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	T	0.68700	-0.5339	10	0.87932	D	0	-12.9858	14.1653	0.65473	0.0:0.0:0.8486:0.1514	.	342;720;720	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	H	720;343	ENSP00000313601:R720H	ENSP00000254346:R343H	R	+	2	0	CC2D1A	13898824	1.000000	0.71417	0.911000	0.35937	0.997000	0.91878	8.640000	0.91028	1.193000	0.43086	0.491000	0.48974	CGC		0.582	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		A	14037824	G	A	14037824	3	1	61	1	0	0	0	0	1	0	0	0	2732	1087	38	1	2241	1	CC2D1A	19	14037824	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	561562	14037824	45091159	10925	18910										
CD97	976	broad.mit.edu	37	chr19	14508711	14508711	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccctacagatatgactttCtccacctggaccccgccccc	5	19	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14508711C>A	ENST00000242786.5	+	8	863	c.783C>A	c.(781-783)ttC>ttA	p.F261L	CD97_ENST00000357355.3_Missense_Mutation_p.F212L|CD97_ENST00000358600.3_Missense_Mutation_p.F168L	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	261					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.F261L(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ATATGACTTTCTCCACCTGGA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											8	13	12					19																	14508711		1767	3755	5522	14369711	SO:0001583	missense	976				CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.783C>A	19.37:g.14508711C>A	ENSP00000242786:p.Phe261Leu		14369711	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	37	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.617573	0.28801	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.70399	-0.48;-0.4;-0.07	4.18	0.546	0.17196	.	0.238170	0.21916	N	0.067225	T	0.69424	0.3109	M	0.81802	2.56	0.09310	N	1	B;B;B	0.31174	0.257;0.311;0.013	B;B;B	0.37480	0.162;0.251;0.024	T	0.63523	-0.6618	10	0.56958	D	0.05	.	6.109	0.20090	0.0:0.5256:0.3686:0.1058	.	168;212;261	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	L	261;212;168;211	ENSP00000242786:F261L;ENSP00000349918:F212L;ENSP00000351413:F168L	ENSP00000242786:F261L	F	+	3	2	CD97	14369711	0.007000	0.16637	0.003000	0.11579	0.001000	0.01503	0.306000	0.19279	0.115000	0.18071	-0.291000	0.09656	TTC		0.617	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		A	14508711	C	A	14508711	3	1	61	1	0	0	0	0	1	0	0	0	3055	912	32	2	813	2	CD97	19	14508711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	470887	14508711	44620272	10926	18911										
CD97	976	broad.mit.edu	37	chr19	14517769	14517769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaagaaattaaagaaggCgaggtgagaggagaggctgg	17	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14517769C>T	ENST00000242786.5	+	17	2284	c.2204C>T	c.(2203-2205)gCg>gTg	p.A735V	CD97_ENST00000357355.3_Missense_Mutation_p.A686V|DDX39A_ENST00000592927.1_5'Flank|CD97_ENST00000358600.3_Missense_Mutation_p.A642V|CTC-548K16.5_ENST00000590626.1_RNA	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	735					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.A735V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TTAAAGAAGGCGAGGTGAGAG	0.572											OREG0025312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	19											92	102	99					19																	14517769		2203	4300	6503	14378769	SO:0001583	missense	976				CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.2204C>T	19.37:g.14517769C>T	ENSP00000242786:p.Ala735Val	695	14378769	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	37	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.023339	0.35701	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.47869	0.83;0.83;0.83	4.87	4.87	0.63330	GPCR, family 2-like (1);	0.507106	0.14818	N	0.296669	T	0.37237	0.0996	L	0.39147	1.195	0.30475	N	0.772954	D;P;B	0.53619	0.961;0.93;0.069	B;B;B	0.41946	0.371;0.371;0.018	T	0.29822	-0.9999	10	0.27785	T	0.31	.	9.1921	0.37207	0.0:0.8994:0.0:0.1006	.	642;686;735	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	V	735;686;642;685	ENSP00000242786:A735V;ENSP00000349918:A686V;ENSP00000351413:A642V	ENSP00000242786:A735V	A	+	2	0	CD97	14378769	0.962000	0.33011	0.542000	0.28115	0.036000	0.12997	1.957000	0.40392	2.245000	0.73994	0.655000	0.94253	GCG		0.572	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14517769	C	T	14517769	3	4	61	1	0	0	0	0	1	0	0	0	3055	768	27	1	2270	1	CD97	19	14517769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9058	14517769	44611214	10927	18912										
PKN1	5585	broad.mit.edu	37	chr19	14580255	14580255	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccggagcacgtgtgcttCgtgatggagtactcggccgg	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14580255C>T	ENST00000242783.6	+	16	2244	c.2079C>T	c.(2077-2079)ttC>ttT	p.F693F	PKN1_ENST00000342216.4_Silent_p.F699F	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.F693L(1)|p.F693F(1)		breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						ACGTGTGCTTCGTGATGGAGT	0.627																																					NSCLC(185;2539 2965 10733 52867)											2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	19											104	117	113					19																	14580255		2128	4237	6365	14441255	SO:0001819	synonymous_variant	5585			S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"protein kinase C-like 1"	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.2079C>T	19.37:g.14580255C>T			14441255	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Silent	SNP	ENST00000242783.6	37	CCDS42513.1																																																																																				0.627	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		T	14580255	C	T	14580255	2	4	61	1	0	0	0	0	0	0	0	1	12010	883	31	1		1	PKN1	19	14580255	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62486	14580255	44548728	10928	18913										
CLEC17A	388512	broad.mit.edu	37	chr19	14706090	14706090	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccctttctcccagctgtGaatcttgagccttctccatt	5	16	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14706090G>T	ENST00000417570.1	+	8	446	c.408G>T	c.(406-408)gtG>gtT	p.V136V	CLEC17A_ENST00000397439.2_Silent_p.V119V|CLEC17A_ENST00000547437.1_Silent_p.V136V	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	136						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)	p.V136V(1)									TCCCAGCTGTGAATCTTGAGC	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	19											256	243	247					19																	14706090		1955	4139	6094	14567090	SO:0001819	synonymous_variant	388512			AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"C-type lectin domain containing"	34520	protein-coding gene	gene with protein product	"prolectin"					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.408G>T	19.37:g.14706090G>T			14567090	A8MX68|B2RTX0|B7ZMM4	Silent	SNP	ENST00000417570.1	37	CCDS56087.1																																																																																				0.483	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390		T	14706090	G	T	14706090	2	4	61	1	0	0	0	0	0	0	0	1	3507	1277	45	2		2	CLEC17A	19	14706090	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125835	14706090	44422893	10929	18914										
EMR3	84658	broad.mit.edu	37	chr19	14765944	14765944	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccataaagtctgattggtgaGaagtgactcaaatttgtcca	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14765944G>T	ENST00000253673.5	-	6	527	c.427C>A	c.(427-429)Ctc>Atc	p.L143I	EMR3_ENST00000344373.4_Missense_Mutation_p.L91I|EMR3_ENST00000443157.2_Intron|EMR3_ENST00000599900.1_Intron	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	143					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.L143I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						TGATTGGTGAGAAGTGACTCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											117	113	114					19																	14765944		2203	4300	6503	14626944	SO:0001583	missense	84658			AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.427C>A	19.37:g.14765944G>T	ENSP00000253673:p.Leu143Ile		14626944		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	G	6.968	0.548505	0.13312	.	.	ENSG00000131355	ENST00000253673;ENST00000344373	T;T	0.29917	1.55;1.55	3.65	0.226	0.15353	.	.	.	.	.	T	0.23532	0.0569	L	0.43152	1.355	0.09310	N	1	B;B	0.31503	0.326;0.079	B;B	0.36719	0.231;0.08	T	0.33420	-0.9869	9	0.52906	T	0.07	.	1.5517	0.02576	0.1309:0.2594:0.4109:0.1988	.	91;143	Q9BY15-2;Q9BY15	.;EMR3_HUMAN	I	143;91	ENSP00000253673:L143I;ENSP00000340758:L91I	ENSP00000253673:L143I	L	-	1	0	EMR3	14626944	0.001000	0.12720	0.023000	0.16930	0.010000	0.07245	0.124000	0.15728	0.298000	0.22638	-0.169000	0.13324	CTC		0.373	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		T	14765944	G	T	14765944	3	4	61	1	0	0	0	0	1	0	0	0	5119	942	33	2	1575	2	EMR3	19	14765944	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	59854	14765944	44363039	10930	18915										
ZNF333	84449	broad.mit.edu	37	chr19	14817559	14817559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgcctactctgggccaccGcaacccatgggtggccaggg	14	14	1	0	rs571042009		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14817559G>A	ENST00000292530.6	+	7	576	c.485G>A	c.(484-486)cGc>cAc	p.R162H	ZNF333_ENST00000536363.1_Missense_Mutation_p.R53H|ZNF333_ENST00000601134.1_Silent_p.P102P|ZNF333_ENST00000540689.2_Missense_Mutation_p.R162H	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R162H(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						CTGGGCCACCGCAACCCATGG	0.572													G|||	1	0.000199681	0	0	5008	,	,		18225	0		0.001	False		,,,				2504	0				NSCLC(60;75 1281 16985 25154 29885)											1	Substitution - Missense(1)	large_intestine(1)	19											85	79	81					19																	14817559		2203	4300	6503	14678559	SO:0001583	missense	84449				CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.485G>A	19.37:g.14817559G>A	ENSP00000292530:p.Arg162His		14678559	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	G	9.591	1.126210	0.20959	.	.	ENSG00000160961	ENST00000536363;ENST00000540689;ENST00000292530	T;T;T	0.06933	3.24;5.82;3.31	2.29	-4.58	0.03410	.	.	.	.	.	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	P	0.43287	0.802	B	0.32090	0.14	T	0.39961	-0.9588	9	0.41790	T	0.15	.	5.4512	0.16566	0.0:0.2483:0.506:0.2457	.	162	Q96JL9	ZN333_HUMAN	H	53;162;162	ENSP00000439749:R53H;ENSP00000438130:R162H;ENSP00000292530:R162H	ENSP00000292530:R162H	R	+	2	0	ZNF333	14678559	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.496000	0.06436	-1.048000	0.03238	-1.437000	0.01076	CGC		0.572	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		A	14817559	G	A	14817559	3	1	61	1	0	0	0	0	1	0	0	0	17889	1087	38	1	507	1	ZNF333	19	14817559	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51615	14817559	44311424	10931	18916										
ZNF333	84449	broad.mit.edu	37	chr19	14826244	14826244	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggacaaagtggaggaaGaagctatggctcctgggctg	17	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14826244G>T	ENST00000292530.6	+	8	653	c.562G>T	c.(562-564)Gaa>Taa	p.E188*	ZNF333_ENST00000536363.1_Nonsense_Mutation_p.E79*|ZNF333_ENST00000540689.2_Nonsense_Mutation_p.E188*	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E188*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						AGTGGAGGAAGAAGCTATGGC	0.557																																					NSCLC(60;75 1281 16985 25154 29885)											1	Substitution - Nonsense(1)	large_intestine(1)	19											92	68	76					19																	14826244		2203	4300	6503	14687244	SO:0001587	stop_gained	84449				CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.562G>T	19.37:g.14826244G>T	ENSP00000292530:p.Glu188*		14687244	Q6P2E6|Q86WS6|Q8TDL0	Nonsense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	G	40	7.991309	0.98599	.	.	ENSG00000160961	ENST00000536363;ENST00000540689;ENST00000292530	.	.	.	3.27	3.27	0.37495	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	10.2279	0.43236	0.0:0.0:1.0:0.0	.	.	.	.	X	79;188;188	.	ENSP00000292530:E188X	E	+	1	0	ZNF333	14687244	0.008000	0.16893	0.004000	0.12327	0.175000	0.22909	1.032000	0.30178	1.844000	0.53588	0.655000	0.94253	GAA		0.557	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		T	14826244	G	T	14826244	4	4	61	1	0	0	0	0	0	1	0	0	17889	943	33	2	588	2	ZNF333	19	14826244	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8685	14826244	44302739	10932	18917										
ZNF333	84449	broad.mit.edu	37	chr19	14829226	14829226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgagaaaatccgtagtgggGataaatcctatgcatgtaac	10	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14829226G>A	ENST00000292530.6	+	12	1178	c.1087G>A	c.(1087-1089)Gat>Aat	p.D363N	ZNF333_ENST00000536363.1_Missense_Mutation_p.D254N|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D363N(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						CCGTAGTGGGGATAAATCCTA	0.433																																					NSCLC(60;75 1281 16985 25154 29885)											1	Substitution - Missense(1)	large_intestine(1)	19											85	85	85					19																	14829226		2203	4300	6503	14690226	SO:0001583	missense	84449				CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1087G>A	19.37:g.14829226G>A	ENSP00000292530:p.Asp363Asn		14690226	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302572	0.81136	.	.	ENSG00000160961	ENST00000536363;ENST00000292530	T;T	0.06294	4.72;3.32	3.24	2.18	0.27775	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07188	0.0182	L	0.51853	1.615	0.32076	N	0.593751	B	0.24963	0.115	B	0.19666	0.026	T	0.04427	-1.0952	9	0.72032	D	0.01	.	8.3272	0.32165	0.1227:0.0:0.8773:0.0	.	363	Q96JL9	ZN333_HUMAN	N	254;363	ENSP00000439749:D254N;ENSP00000292530:D363N	ENSP00000292530:D363N	D	+	1	0	ZNF333	14690226	1.000000	0.71417	0.169000	0.22859	0.387000	0.30353	6.654000	0.74387	0.705000	0.31890	0.585000	0.79938	GAT		0.433	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		A	14829226	G	A	14829226	3	1	61	1	0	0	0	0	1	0	0	0	17889	1174	41	3	1129	3	ZNF333	19	14829226	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2982	14829226	44299757	10933	18918										
EMR2	30817	broad.mit.edu	37	chr19	14863176	14863176	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaattgccacgaggaagaGgaggtgggccaggaagaggc	17	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14863176G>T	ENST00000315576.3	-	15	2204	c.1753C>A	c.(1753-1755)Ctc>Atc	p.L585I	EMR2_ENST00000392964.3_3'UTR|EMR2_ENST00000353005.1_Missense_Mutation_p.L443I|EMR2_ENST00000594076.1_Missense_Mutation_p.L492I|EMR2_ENST00000392965.3_Missense_Mutation_p.L527I|EMR2_ENST00000594294.1_Missense_Mutation_p.L536I|EMR2_ENST00000596991.2_Missense_Mutation_p.L574I|EMR2_ENST00000392967.2_Missense_Mutation_p.L574I|EMR2_ENST00000353876.1_Missense_Mutation_p.L492I|EMR2_ENST00000346057.1_Missense_Mutation_p.L536I|EMR2_ENST00000595839.1_Missense_Mutation_p.L443I|EMR2_ENST00000601345.1_Missense_Mutation_p.L574I	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	585					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)	p.L585I(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						ACGAGGAAGAGGAGGTGGGCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											112	96	102					19																	14863176		2203	4300	6503	14724176	SO:0001583	missense	30817			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.1753C>A	19.37:g.14863176G>T	ENSP00000319883:p.Leu585Ile		14724176	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	G	6.865	0.528981	0.13127	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22	4.22	1.93	0.25924	GPCR, family 2-like (1);	.	.	.	.	T	0.46560	0.1399	L	0.49699	1.58	0.80722	D	1	D;P;D;P;D;D;D;P	0.89917	0.999;0.931;1.0;0.712;0.994;0.995;0.995;0.919	D;P;D;P;D;D;D;P	0.97110	0.986;0.832;1.0;0.451;0.966;0.98;0.98;0.668	T	0.32402	-0.9908	9	0.13470	T	0.59	.	10.1212	0.42621	0.0:0.0:0.4734:0.5266	.	527;492;585;443;536;585;585;574	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	I	585;574;536;492;443;527	ENSP00000319883:L585I;ENSP00000376694:L574I;ENSP00000263380:L536I;ENSP00000319454:L492I;ENSP00000319838:L443I;ENSP00000376692:L527I	ENSP00000319883:L585I	L	-	1	0	EMR2	14724176	0.000000	0.05858	0.675000	0.29917	0.570000	0.35934	-0.293000	0.08320	0.305000	0.22832	0.508000	0.49915	CTC		0.572	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			T	14863176	G	T	14863176	3	4	61	1	0	0	0	0	1	0	0	0	5118	1000	35	2	746	2	EMR2	19	14863176	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33950	14863176	44265807	10934	18919										
EMR2	30817	broad.mit.edu	37	chr19	14876372	14876372	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggcggggtccaggtggaGaaagtcatatctgtagggaa	19	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14876372G>T	ENST00000315576.3	-	9	1243	c.792C>A	c.(790-792)ttC>ttA	p.F264L	EMR2_ENST00000392964.3_Missense_Mutation_p.F3L|EMR2_ENST00000353005.1_Missense_Mutation_p.F122L|EMR2_ENST00000594076.1_Missense_Mutation_p.F171L|EMR2_ENST00000392965.3_Missense_Mutation_p.F264L|EMR2_ENST00000594294.1_Missense_Mutation_p.F215L|EMR2_ENST00000596991.2_Missense_Mutation_p.F264L|EMR2_ENST00000392967.2_Missense_Mutation_p.F264L|EMR2_ENST00000353876.1_Missense_Mutation_p.F171L|EMR2_ENST00000346057.1_Missense_Mutation_p.F215L|EMR2_ENST00000595839.1_Missense_Mutation_p.F122L|EMR2_ENST00000601345.1_Missense_Mutation_p.F264L	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	264					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)	p.F264L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						TCCAGGTGGAGAAAGTCATAT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19																																								14737372	SO:0001583	missense	30817			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.792C>A	19.37:g.14876372G>T	ENSP00000319883:p.Phe264Leu		14737372	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	g	15.90	2.969884	0.53614	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965;ENST00000392964;ENST00000392962	T;T;T;T;T;T;T;T	0.79033	-0.86;-1.01;-0.4;0.36;1.12;-1.23;0.93;-1.16	3.82	-1.16	0.09678	.	.	.	.	.	T	0.69717	0.3142	M	0.81802	2.56	0.09310	N	0.999997	B;B;P;B;B;B;B;B	0.37141	0.126;0.02;0.584;0.002;0.284;0.003;0.011;0.096	B;B;B;B;B;B;B;B	0.35114	0.015;0.009;0.196;0.004;0.076;0.005;0.017;0.099	T	0.55854	-0.8075	9	0.12103	T	0.63	.	4.112	0.10063	0.2304:0.3886:0.3809:0.0	.	264;171;264;122;215;264;264;264	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	L	264;264;215;171;122;264;3;215	ENSP00000319883:F264L;ENSP00000376694:F264L;ENSP00000263380:F215L;ENSP00000319454:F171L;ENSP00000319838:F122L;ENSP00000376692:F264L;ENSP00000376691:F3L;ENSP00000376689:F215L	ENSP00000319883:F264L	F	-	3	2	EMR2	14737372	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	0.002000	0.13061	0.033000	0.15463	0.382000	0.24955	TTC		0.622	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			T	14876372	G	T	14876372	3	4	61	1	0	0	0	0	1	0	0	0	5118	933	33	2	1731	2	EMR2	19	14876372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13196	14876372	44252611	10935	18920										
EMR2	30817	broad.mit.edu	37	chr19	14883285	14883285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttccgcatgacactttcGacagtgttgcacactcgttg	8	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:14883285G>A	ENST00000315576.3	-	5	675	c.224C>T	c.(223-225)tCg>tTg	p.S75L	EMR2_ENST00000392964.3_5'Flank|EMR2_ENST00000353005.1_Missense_Mutation_p.S75L|EMR2_ENST00000594076.1_Missense_Mutation_p.S75L|EMR2_ENST00000392965.3_Missense_Mutation_p.S75L|EMR2_ENST00000594294.1_Missense_Mutation_p.S75L|EMR2_ENST00000596991.2_Missense_Mutation_p.S75L|EMR2_ENST00000392967.2_Missense_Mutation_p.S75L|EMR2_ENST00000353876.1_Missense_Mutation_p.S75L|EMR2_ENST00000346057.1_Missense_Mutation_p.S75L|EMR2_ENST00000595839.1_Missense_Mutation_p.S75L|EMR2_ENST00000601345.1_Missense_Mutation_p.S75L|EMR2_ENST00000599423.1_5'UTR	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	75	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)	p.S75L(2)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						TGACACTTTCGACAGTGTTGC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	19											147	108	121					19																	14883285		2203	4300	6503	14744285	SO:0001583	missense	30817			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.224C>T	19.37:g.14883285G>A	ENSP00000319883:p.Ser75Leu		14744285	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	G	3.456	-0.110948	0.06924	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000360222;ENST00000392965;ENST00000392962	D;D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	3.95	-7.9	0.01169	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.79770	0.4503	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B;B;B	0.23490	0.002;0.018;0.003;0.086;0.01;0.037;0.03	B;B;B;B;B;B;B	0.18263	0.001;0.003;0.002;0.021;0.003;0.005;0.004	T	0.65985	-0.6035	9	0.21540	T	0.41	.	7.3734	0.26815	0.2045:0.3655:0.43:0.0	.	75;75;75;75;75;75;75	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;.;.;.;EMR2_HUMAN;.	L	75	ENSP00000319883:S75L;ENSP00000376694:S75L;ENSP00000263380:S75L;ENSP00000319454:S75L;ENSP00000319838:S75L;ENSP00000376692:S75L;ENSP00000376689:S75L	ENSP00000319883:S75L	S	-	2	0	EMR2	14744285	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.195000	0.00563	-2.497000	0.00513	-0.445000	0.05633	TCG		0.542	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			A	14883285	G	A	14883285	3	1	61	1	0	0	0	0	1	0	0	0	5118	1059	37	1	2315	1	EMR2	19	14883285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6913	14883285	44245698	10936	18921										
CASP14	23581	broad.mit.edu	37	chr19	15164395	15164395	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctctggaacacatgtttCggcagctgagattcgaaagc	11	9	1	1	rs61731993	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15164395C>T	ENST00000427043.3	+	3	438	c.130C>T	c.(130-132)Cgg>Tgg	p.R44W	CASP14_ENST00000221740.1_Missense_Mutation_p.R44W|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	44					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.R44W(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						ACACATGTTTCGGCAGCTGAG	0.532													C|||	6	0.00119808	8e-04	0	5008	,	,		18628	0		0	False		,,,				2504	0.0051															1	Substitution - Missense(1)	large_intestine(1)	19						C	TRP/ARG	0,4406		0,0,2203	97	93	95		130	-2.3	0.1	19	dbSNP_129	95	1,8599	1.2+/-3.3	0,1,4299	no	missense	CASP14	NM_012114.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	44/243	15164395	1,13005	2203	4300	6503	15025395	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.130C>T	19.37:g.15164395C>T	ENSP00000393417:p.Arg44Trp		15025395	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	.	.	.	.	.	.	.	.	.	.	c	10.29	1.309140	0.23821	0.0	1.16E-4	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.22539	1.95;1.95	4.91	-2.3	0.06785	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (2);Peptidase C14, ICE, catalytic subunit p20 (1);	0.740041	0.12562	N	0.458063	T	0.20780	0.0500	M	0.70275	2.135	0.09310	N	1	P	0.45531	0.86	B	0.40329	0.326	T	0.19192	-1.0313	10	0.52906	T	0.07	.	8.3181	0.32113	0.2579:0.3604:0.3817:0.0	rs61731993	44	P31944	CASPE_HUMAN	W	44	ENSP00000393417:R44W;ENSP00000221740:R44W	ENSP00000221740:R44W	R	+	1	2	CASP14	15025395	0.011000	0.17503	0.071000	0.20095	0.103000	0.19146	-0.012000	0.12699	0.058000	0.16222	0.306000	0.20318	CGG		0.532	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15164395	C	T	15164395	3	4	61	1	0	0	0	0	1	0	0	0	2676	875	31	1	136	1	CASP14	19	15164395	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	281110	15164395	43964588	10937	18922										
CASP14	23581	broad.mit.edu	37	chr19	15164711	15164711	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgaggccctgaacaacaaGaactgccaggccctgcgagc	11	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15164711G>T	ENST00000427043.3	+	4	653	c.345G>T	c.(343-345)aaG>aaT	p.K115N	CASP14_ENST00000221740.1_Missense_Mutation_p.K115N|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	115					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.K115N(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TGAACAACAAGAACTGCCAGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	84	86					19																	15164711		2203	4300	6503	15025711	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.345G>T	19.37:g.15164711G>T	ENSP00000393417:p.Lys115Asn		15025711	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	.	.	.	.	.	.	.	.	.	.	g	17.69	3.450899	0.63290	.	.	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.20738	2.05;2.05	5.27	1.98	0.26296	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.000000	0.56097	D	0.000025	T	0.26774	0.0655	L	0.33624	1.015	0.34616	D	0.718093	D	0.76494	0.999	D	0.87578	0.998	T	0.29701	-1.0003	10	0.15952	T	0.53	.	7.2116	0.25937	0.2814:0.0:0.7186:0.0	.	115	P31944	CASPE_HUMAN	N	115	ENSP00000393417:K115N;ENSP00000221740:K115N	ENSP00000221740:K115N	K	+	3	2	CASP14	15025711	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.643000	0.46604	0.229000	0.21039	0.306000	0.20318	AAG		0.552	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15164711	G	T	15164711	3	4	61	1	0	0	0	0	1	0	0	0	2676	933	33	2	355	2	CASP14	19	15164711	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	316	15164711	43964272	10938	18923										
OR1I1	126370	broad.mit.edu	37	chr19	15198262	15198262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgtggccattgtccaccCacagcgttacttggttctca	8	14	1	0	rs201426979		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15198262C>T	ENST00000209540.2	+	1	472	c.386C>T	c.(385-387)cCa>cTa	p.P129L		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P129L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						ATTGTCCACCCACAGCGTTAC	0.572													c|||	1	0.000199681	0	0.0014	5008	,	,		21456	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											83	69	73					19																	15198262		2203	4300	6503	15059262	SO:0001583	missense	126370			AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"GPCR / Class A : Olfactory receptors"	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.386C>T	19.37:g.15198262C>T	ENSP00000209540:p.Pro129Leu		15059262	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	c	12.84	2.058271	0.36277	.	.	ENSG00000094661	ENST00000209540	T	0.01902	4.57	4.8	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31760	U	0.007110	T	0.19685	0.0473	H	0.97783	4.075	0.48901	D	0.999727	D	0.89917	1.0	D	0.97110	1.0	T	0.03773	-1.1005	10	0.87932	D	0	.	9.4135	0.38507	0.0:0.8249:0.0:0.1751	.	129	O60431	OR1I1_HUMAN	L	129	ENSP00000209540:P129L	ENSP00000209540:P129L	P	+	2	0	OR1I1	15059262	0.903000	0.30736	0.273000	0.24645	0.000000	0.00434	3.036000	0.49767	0.651000	0.30788	-0.993000	0.02533	CCA		0.572	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1			T	15198262	C	T	15198262	3	4	61	1	0	0	0	0	1	0	0	0	10989	594	21	3	388	3	OR1I1	19	15198262	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33551	15198262	43930721	10939	18924										
OR1I1	126370	broad.mit.edu	37	chr19	15198473	15198473	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaccaacgagctggtgatCtttgcttttggcattgtcgt	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15198473C>T	ENST00000209540.2	+	1	683	c.597C>T	c.(595-597)atC>atT	p.I199I		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I199I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						AGCTGGTGATCTTTGCTTTTG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	19											146	118	128					19																	15198473		2203	4300	6503	15059473	SO:0001819	synonymous_variant	126370			AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"GPCR / Class A : Olfactory receptors"	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.597C>T	19.37:g.15198473C>T			15059473	Q96R92	Silent	SNP	ENST00000209540.2	37	CCDS32937.1																																																																																				0.542	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1			T	15198473	C	T	15198473	2	4	61	1	0	0	0	0	0	0	0	1	10989	903	32	3		3	OR1I1	19	15198473	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	211	15198473	43930510	10940	18925										
SYDE1	85360	broad.mit.edu	37	chr19	15224675	15224675	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgacttcgaagacgacttCgatgcgcccttcaacccgca	10	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15224675C>T	ENST00000342784.2	+	8	2140	c.2109C>T	c.(2107-2109)ttC>ttT	p.F703F	SYDE1_ENST00000600252.1_Silent_p.F360F|SYDE1_ENST00000600440.1_Silent_p.F636F	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	703					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)	p.F703F(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						AAGACGACTTCGATGCGCCCT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	19											138	147	144					19																	15224675		2203	4300	6503	15085675	SO:0001819	synonymous_variant	85360			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.2109C>T	19.37:g.15224675C>T			15085675	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	37	CCDS12324.1																																																																																				0.602	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15224675	C	T	15224675	2	4	61	1	0	0	0	0	0	0	0	1	15474	883	31	1		1	SYDE1	19	15224675	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26202	15224675	43904308	10941	18926										
BRD4	23476	broad.mit.edu	37	chr19	15355563	15355563	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccccttcttttttgacttCggagccatctctgcagagga	9	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15355563C>T	ENST00000263377.2	-	12	2390	c.2169G>A	c.(2167-2169)ccG>ccA	p.P723P		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	723					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)	p.P723P(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TTTTTGACTTCGGAGCCATCT	0.567			T	C15orf55	lethal midline carcinoma of young people																																		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	1	Substitution - coding silent(1)	large_intestine(1)	19											113	112	113					19																	15355563		2203	4300	6503	15216563	SO:0001819	synonymous_variant	23476			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.2169G>A	19.37:g.15355563C>T			15216563	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																				0.567	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		T	15355563	C	T	15355563	2	4	61	1	0	0	0	0	0	0	0	1	1507	871	31	1		1	BRD4	19	15355563	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130888	15355563	43773420	10942	18927										
PGLYRP2	114770	broad.mit.edu	37	chr19	15587015	15587015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaatggccacaacatctgGaaaggtatctccagtctccc	8	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15587015G>A	ENST00000340880.4	-	2	946	c.466C>T	c.(466-468)Cca>Tca	p.P156S	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.P156S	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	156					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.P156S(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						ACAACATCTGGAAAGGTATCT	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	19											77	73	75					19																	15587015		2203	4300	6503	15448015	SO:0001583	missense	114770			AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"peptidoglycan recognition protein L precursor", "peptidoglycan recognition protein-like", "N-acetylmuramoyl-L-alanine amidase"	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.466C>T	19.37:g.15587015G>A	ENSP00000345968:p.Pro156Ser		15448015	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	G	9.164	1.019467	0.19355	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.05925	3.44;3.37	3.56	-0.0382	0.13881	.	1.041250	0.07660	N	0.933440	T	0.06826	0.0174	M	0.63428	1.95	0.09310	N	1	B;B	0.31581	0.138;0.329	B;B	0.28849	0.055;0.095	T	0.43310	-0.9399	10	0.20046	T	0.44	-7.6565	4.3179	0.11002	0.2428:0.1944:0.5628:0.0	.	156;156	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	S	156	ENSP00000345968:P156S;ENSP00000292609:P156S	ENSP00000292609:P156S	P	-	1	0	PGLYRP2	15448015	0.010000	0.17322	0.016000	0.15963	0.037000	0.13140	0.494000	0.22467	0.146000	0.19002	0.467000	0.42956	CCA		0.587	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15587015	G	A	15587015	3	1	61	1	0	0	0	0	1	0	0	0	11825	1174	41	3	1280	3	PGLYRP2	19	15587015	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	231452	15587015	43541968	10943	18928										
PGLYRP2	114770	broad.mit.edu	37	chr19	15587160	15587160	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgccagcaccaccccataTtccttcccttctcgtacgtc	6	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15587160T>G	ENST00000340880.4	-	2	801	c.321A>C	c.(319-321)gaA>gaC	p.E107D	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.E107D	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	107					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.E107D(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCACCCCATATTCCTTCCCTT	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	19											171	123	139					19																	15587160		2203	4300	6503	15448160	SO:0001583	missense	114770			AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"peptidoglycan recognition protein L precursor", "peptidoglycan recognition protein-like", "N-acetylmuramoyl-L-alanine amidase"	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.321A>C	19.37:g.15587160T>G	ENSP00000345968:p.Glu107Asp		15448160	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487564	0.64074	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.28069	1.81;1.63	5.27	-1.39	0.08997	.	0.139042	0.44483	D	0.000453	T	0.52289	0.1725	M	0.83483	2.645	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.48875	-0.8996	10	0.87932	D	0	-8.2869	10.6311	0.45536	0.0:0.8085:0.0:0.1915	.	107;107	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	D	107	ENSP00000345968:E107D;ENSP00000292609:E107D	ENSP00000292609:E107D	E	-	3	2	PGLYRP2	15448160	0.334000	0.24739	0.000000	0.03702	0.004000	0.04260	0.405000	0.21015	-0.475000	0.06852	-0.376000	0.06991	GAA		0.612	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		G	15587160	T	G	15587160	3	3	61	1	0	0	0	0	1	0	0	0	11825	1490	52	4	1425	4	PGLYRP2	19	15587160	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	145	15587160	43541823	10944	18929										
CYP4F22	126410	broad.mit.edu	37	chr19	15640536	15640536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtaccttccaaatgaggCgggccttcaagatgagaaga	12	9	1	4	rs116743462		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15640536C>T	ENST00000269703.3	+	4	438	c.239C>T	c.(238-240)gCg>gTg	p.A80V	CYP4F22_ENST00000601005.2_Missense_Mutation_p.A80V	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	80						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.A80V(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						CCAAATGAGGCGGGCCTTCAA	0.557													C|||	1	0.000199681	8e-04	0	5008	,	,		18960	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											109	87	94					19																	15640536		2203	4300	6503	15501536	SO:0001583	missense	126410				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.239C>T	19.37:g.15640536C>T	ENSP00000269703:p.Ala80Val		15501536	Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.09	2.432811	0.43224	.	.	ENSG00000171954	ENST00000269703	D	0.88201	-2.35	5.5	-3.98	0.04082	.	1.652790	0.03063	N	0.156083	T	0.76535	0.4001	N	0.05414	-0.055	0.09310	N	1	B	0.12630	0.006	B	0.22880	0.042	T	0.64980	-0.6279	10	0.52906	T	0.07	.	5.1083	0.14796	0.513:0.1869:0.0:0.3001	.	80	Q6NT55	CP4FN_HUMAN	V	80	ENSP00000269703:A80V	ENSP00000269703:A80V	A	+	2	0	CYP4F22	15501536	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-1.005000	0.03674	-0.653000	0.05401	0.561000	0.74099	GCG		0.557	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		T	15640536	C	T	15640536	3	4	61	1	0	0	0	0	1	0	0	0	4195	768	27	1	245	1	CYP4F22	19	15640536	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53376	15640536	43488447	10945	18930										
OR10H1	26539	broad.mit.edu	37	chr19	15917911	15917911	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacatcattacatttttttCtgggtagagtttactgaaga	7	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:15917911C>A	ENST00000334920.2	-	1	1025	c.937G>T	c.(937-939)Gaa>Taa	p.E313*		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E313*(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						ACATTTTTTTCTGGGTAGAGT	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											85	83	84					19																	15917911		2203	4300	6503	15778911	SO:0001587	stop_gained	26539			AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.937G>T	19.37:g.15917911C>A	ENSP00000335596:p.Glu313*		15778911	Q6IFQ2|Q96R59	Nonsense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	.	.	.	.	.	.	.	.	.	.	.	13.99	2.401539	0.42613	.	.	ENSG00000186723	ENST00000334920	.	.	.	4.02	-2.79	0.05841	.	2.742250	0.02273	U	0.068657	.	.	.	.	.	.	0.23416	N	0.997722	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.0418	0.01560	0.1671:0.1801:0.1503:0.5026	.	.	.	.	X	313	.	ENSP00000335596:E313X	E	-	1	0	OR10H1	15778911	0.002000	0.14202	0.002000	0.10522	0.005000	0.04900	0.036000	0.13819	-0.206000	0.10203	-0.157000	0.13467	GAA		0.448	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			A	15917911	C	A	15917911	4	1	61	1	0	0	0	0	0	1	0	0	10936	922	32	2	23	2	OR10H1	19	15917911	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	277375	15917911	43211072	10946	18931										
OR10H4	126541	broad.mit.edu	37	chr19	16060764	16060764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaattctgtcctccaagttCctgagcgccagtttggtggt	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16060764C>T	ENST00000322107.1	+	1	947	c.947C>T	c.(946-948)tCc>tTc	p.S316F		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S316F(1)		breast(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						CCTCCAAGTTCCTGAGCGCCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											29	31	30					19																	16060764		2193	4293	6486	15921764	SO:0001583	missense	126541			AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"GPCR / Class A : Olfactory receptors"	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.947C>T	19.37:g.16060764C>T	ENSP00000318834:p.Ser316Phe		15921764	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412196	0.25465	.	.	ENSG00000176231	ENST00000322107	T	0.03496	3.91	1.38	0.285	0.15705	.	1.636630	0.04026	U	0.300632	T	0.04407	0.0121	N	0.08118	0	0.09310	N	1	D	0.61080	0.989	P	0.55087	0.768	T	0.36016	-0.9765	10	0.87932	D	0	.	3.2704	0.06879	0.0:0.4973:0.0:0.5027	.	316	Q8NGA5	O10H4_HUMAN	F	316	ENSP00000318834:S316F	ENSP00000318834:S316F	S	+	2	0	OR10H4	15921764	0.079000	0.21365	0.017000	0.16124	0.015000	0.08874	1.183000	0.32041	0.735000	0.32537	0.305000	0.20034	TCC		0.383	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1			T	16060764	C	T	16060764	3	4	61	1	0	0	0	0	1	0	0	0	10939	855	30	3	949	3	OR10H4	19	16060764	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	142853	16060764	43068219	10947	18932										
TPM4	7171	broad.mit.edu	37	chr19	16192751	16192751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgtggccgccctcaaccGacgcatccagctcgttgagg	12	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16192751G>A	ENST00000300933.4	+	2	421	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	TPM4_ENST00000538887.1_Missense_Mutation_p.R90Q|TPM4_ENST00000344824.6_Missense_Mutation_p.R90Q	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	54					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.R90Q(1)	TPM4/ALK(12)	breast(1)|large_intestine(3)	4						GCCCTCAACCGACGCATCCAG	0.612			T	ALK	ALCL																																		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	1	Substitution - Missense(1)	large_intestine(1)	19											47	48	48					19																	16192751		2203	4300	6503	16053751	SO:0001583	missense	7171				CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.161G>A	19.37:g.16192751G>A	ENSP00000300933:p.Arg54Gln		16053751	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Missense_Mutation	SNP	ENST00000300933.4	37	CCDS12338.1	.	.	.	.	.	.	.	.	.	.	G	35	5.469738	0.96274	.	.	ENSG00000167460	ENST00000344824;ENST00000538887;ENST00000300933	D;D;D	0.98807	-5.15;-5.15;-5.15	4.62	4.62	0.57501	.	0.000000	0.52532	U	0.000080	D	0.99483	0.9816	H	0.98068	4.14	0.58432	D	0.999996	D;D	0.76494	0.998;0.999	D;D	0.73708	0.94;0.981	D	0.97985	1.0351	10	0.87932	D	0	-2.1957	16.8417	0.85971	0.0:0.0:1.0:0.0	.	54;90	P67936;P67936-2	TPM4_HUMAN;.	Q	90;90;54	ENSP00000345230:R90Q;ENSP00000439135:R90Q;ENSP00000300933:R54Q	ENSP00000300933:R54Q	R	+	2	0	TPM4	16053751	1.000000	0.71417	0.914000	0.36105	0.939000	0.58152	9.484000	0.97940	2.265000	0.75225	0.591000	0.81541	CGA		0.612	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		A	16192751	G	A	16192751	3	1	61	1	0	0	0	0	1	0	0	0	16448	1058	37	1	415	1	TPM4	19	16192751	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131987	16192751	42936232	10948	18933										
EPS15L1	58513	broad.mit.edu	37	chr19	16472601	16472601	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacttacagaggtgaagtCtgcaaagcccgaggcagagg	13	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16472601C>A	ENST00000248070.6	-	23	2714	c.2575G>T	c.(2575-2577)Gac>Tac	p.D859Y	EPS15L1_ENST00000455140.2_Missense_Mutation_p.D859Y|EPS15L1_ENST00000535753.2_3'UTR	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	859					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D859Y(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						GAGGTGAAGTCTGCAAAGCCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											43	47	46					19																	16472601		2203	4300	6503	16333601	SO:0001583	missense	58513			AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2575G>T	19.37:g.16472601C>A	ENSP00000248070:p.Asp859Tyr		16333601	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	37	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472886	0.63737	.	.	ENSG00000127527	ENST00000455140;ENST00000248070	T;T	0.53206	0.63;0.63	4.96	4.96	0.65561	.	0.173311	0.49305	D	0.000153	T	0.54711	0.1875	L	0.44542	1.39	0.80722	D	1	D;P	0.76494	0.999;0.85	P;B	0.60173	0.87;0.325	T	0.57318	-0.7832	10	0.72032	D	0.01	.	10.7817	0.46382	0.0:0.9131:0.0:0.0869	.	859;859	Q9UBC2;G3V0H2	EP15R_HUMAN;.	Y	859	ENSP00000393313:D859Y;ENSP00000248070:D859Y	ENSP00000248070:D859Y	D	-	1	0	EPS15L1	16333601	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.848000	0.39309	2.318000	0.78349	0.561000	0.74099	GAC		0.537	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		A	16472601	C	A	16472601	3	1	61	1	0	0	0	0	1	0	0	0	5206	913	32	2	23	2	EPS15L1	19	16472601	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	279850	16472601	42656382	10949	18934										
EPS15L1	58513	broad.mit.edu	37	chr19	16513194	16513194	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaggttggccaggtcggTcaggctggcaccatgggctc	16	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16513194T>C	ENST00000248070.6	-	16	1868	c.1729A>G	c.(1729-1731)Acc>Gcc	p.T577A	EPS15L1_ENST00000602009.1_Missense_Mutation_p.T423A|EPS15L1_ENST00000455140.2_Missense_Mutation_p.T577A|EPS15L1_ENST00000597937.1_Missense_Mutation_p.T577A|EPS15L1_ENST00000535753.2_Missense_Mutation_p.T577A|EPS15L1_ENST00000594975.1_Missense_Mutation_p.T577A	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	577					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T577A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						GCCAGGTCGGTCAGGCTGGCA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19											97	88	91					19																	16513194		2203	4300	6503	16374194	SO:0001583	missense	58513			AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.1729A>G	19.37:g.16513194T>C	ENSP00000248070:p.Thr577Ala		16374194	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	37	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	T	7.019	0.558383	0.13436	.	.	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	T;T;T	0.30182	1.95;1.95;1.54	5.29	1.95	0.26073	.	0.237782	0.42053	N	0.000780	T	0.14313	0.0346	N	0.19112	0.55	0.22873	N	0.998628	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.18085	-1.0348	10	0.24483	T	0.36	.	2.3317	0.04237	0.1496:0.0858:0.1673:0.5972	.	577;577;576;577;577;577	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	A	577	ENSP00000393313:T577A;ENSP00000248070:T577A;ENSP00000440103:T577A	ENSP00000248070:T577A	T	-	1	0	EPS15L1	16374194	1.000000	0.71417	0.073000	0.20177	0.110000	0.19582	1.932000	0.40143	0.023000	0.15187	0.533000	0.62120	ACC		0.577	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		C	16513194	T	C	16513194	3	2	61	1	0	0	0	0	1	0	0	0	5206	1667	58	4	897	4	EPS15L1	19	16513194	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	40593	16513194	42615789	10950	18935										
C19orf44	84167	broad.mit.edu	37	chr19	16611755	16611756	+	Frame_Shift_Ins	INS	-	-	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtcatagcagatttctINSaaaaagaaaccaaactctag							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16611755_16611756insA	ENST00000221671.3	+	2	308_309	c.152_153insA	c.(151-156)ctaaaafs	p.LK51fs	C19orf44_ENST00000594035.1_Frame_Shift_Ins_p.LK51fs|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	51								p.R53fs*7(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						AGCAGATTTCTAAAAAGAAACC	0.436																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								16472756	SO:0001589	frameshift_variant	84167			AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.157dupA	19.37:g.16611760_16611760dupA	ENSP00000221671:p.Leu51fs		16472755	Q8N6Y7	Frame_Shift_Ins	INS	ENST00000221671.3	37	CCDS12345.1																																																																																				0.436	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		A	16611756	-	A	16611755	7	5	61	1	0	1	1	0	0	0	0	0	1933	1522	53	0	154	0	C19orf44	19	16611755	Frame_Shift_Ins	INS	-	TCGA-AG-A002-01A-01W-A00K-09	98561	16611755	42517228	10951	18936										
C19orf44	84167	broad.mit.edu	37	chr19	16612252	16612252	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagacagtgacgaagaaGaaatgaaagtattgctagga	11	6	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16612252G>T	ENST00000221671.3	+	2	805	c.649G>T	c.(649-651)Gaa>Taa	p.E217*	C19orf44_ENST00000594035.1_Nonsense_Mutation_p.E217*|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	217								p.E217*(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						TGACGAAGAAGAAATGAAAGT	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											77	81	80					19																	16612252		2203	4299	6502	16473252	SO:0001587	stop_gained	84167			AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.649G>T	19.37:g.16612252G>T	ENSP00000221671:p.Glu217*		16473252	Q8N6Y7	Nonsense_Mutation	SNP	ENST00000221671.3	37	CCDS12345.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425664	0.83667	.	.	ENSG00000105072	ENST00000221671	.	.	.	5.16	5.16	0.70880	.	0.142263	0.45361	D	0.000376	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-20.0791	12.0314	0.53399	0.0:0.1738:0.8262:0.0	.	.	.	.	X	217	.	ENSP00000221671:E217X	E	+	1	0	C19orf44	16473252	1.000000	0.71417	0.929000	0.37066	0.261000	0.26267	3.386000	0.52492	2.395000	0.81488	0.655000	0.94253	GAA		0.443	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		T	16612252	G	T	16612252	4	4	61	1	0	0	0	0	0	1	0	0	1933	943	33	2	651	2	C19orf44	19	16612252	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	497	16612252	42516731	10952	18937										
NWD1	284434	broad.mit.edu	37	chr19	16899834	16899834	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatttgccaaagggaccctcGccaactctgcttcaaaggat	8	12	2	0	rs112298174	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16899834G>A	ENST00000552788.1	+	11	2773	c.2773G>A	c.(2773-2775)Gcc>Acc	p.A925T	NWD1_ENST00000379808.3_Missense_Mutation_p.A925T|NWD1_ENST00000523826.1_Missense_Mutation_p.A719T|NWD1_ENST00000549814.1_Missense_Mutation_p.A925T|NWD1_ENST00000339803.6_Missense_Mutation_p.A790T|NWD1_ENST00000524140.2_Missense_Mutation_p.A925T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	925							ATP binding (GO:0005524)	p.A790T(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGGGACCCTCGCCAACTCTGC	0.493													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		19298	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						G	THR/ALA	72,4334	65.8+/-103.3	0,72,2131	118	114	115		2773	5.7	0.1	19	dbSNP_132	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense	NWD1	NM_001007525.3	58	0,75,6428	AA,AG,GG		0.0349,1.6341,0.5767	possibly-damaging	925/1433	16899834	75,12931	2203	4300	6503	16760834	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2773G>A	19.37:g.16899834G>A	ENSP00000447224:p.Ala925Thr		16760834	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	14.54	2.567166	0.45694	0.016341	3.49E-4	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.199793	0.44097	D	0.000498	T	0.50309	0.1608	L	0.60904	1.88	0.28380	N	0.919596	D;D;D	0.69078	0.963;0.997;0.992	P;P;P	0.54431	0.59;0.752;0.699	T	0.59177	-0.7503	10	0.49607	T	0.09	-19.0545	15.2049	0.73173	0.0:0.0:1.0:0.0	.	925;925;790	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	T	790;925;925;925;719;925;790	ENSP00000428579:A925T;ENSP00000447548:A925T;ENSP00000369136:A925T;ENSP00000428955:A719T;ENSP00000447224:A925T;ENSP00000340159:A790T	ENSP00000340159:A790T	A	+	1	0	NWD1	16760834	1.000000	0.71417	0.094000	0.20943	0.037000	0.13140	5.303000	0.65738	2.661000	0.90470	0.591000	0.81541	GCC		0.493	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16899834	G	A	16899834	3	1	61	1	0	0	0	0	1	0	0	0	10812	1087	38	1	2402	1	NWD1	19	16899834	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	287582	16899834	42229149	10953	18938										
NWD1	284434	broad.mit.edu	37	chr19	16899951	16899951	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaacctcagatctggaacCttcatgtggatgaggcacac	10	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:16899951C>A	ENST00000552788.1	+	11	2890	c.2890C>A	c.(2890-2892)Ctt>Att	p.L964I	NWD1_ENST00000379808.3_Missense_Mutation_p.L964I|NWD1_ENST00000523826.1_Missense_Mutation_p.L758I|NWD1_ENST00000549814.1_Missense_Mutation_p.L964I|NWD1_ENST00000339803.6_Missense_Mutation_p.L829I|NWD1_ENST00000524140.2_Missense_Mutation_p.L964I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	964							ATP binding (GO:0005524)	p.L829I(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GATCTGGAACCTTCATGTGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											93	85	88					19																	16899951		2203	4300	6503	16760951	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2890C>A	19.37:g.16899951C>A	ENSP00000447224:p.Leu964Ile		16760951	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	C	15.51	2.855200	0.51376	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.43688	1.44;0.94;1.44;3.47;3.47;3.47	5.35	4.3	0.51218	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.46908	0.1417	N	0.20986	0.625	0.09310	N	1	D;D;D	0.89917	0.976;1.0;0.997	P;D;D	0.83275	0.535;0.996;0.991	T	0.33343	-0.9872	10	0.29301	T	0.29	-18.2572	11.5617	0.50780	0.1792:0.8208:0.0:0.0	.	964;964;829	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	829;964;964;964;758;964;829	ENSP00000428579:L964I;ENSP00000447548:L964I;ENSP00000369136:L964I;ENSP00000428955:L758I;ENSP00000447224:L964I;ENSP00000340159:L829I	ENSP00000340159:L829I	L	+	1	0	NWD1	16760951	0.966000	0.33281	0.060000	0.19600	0.079000	0.17450	2.691000	0.47010	1.348000	0.45733	0.591000	0.81541	CTT		0.458	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16899951	C	A	16899951	3	1	61	1	0	0	0	0	1	0	0	0	10812	681	24	2	2519	2	NWD1	19	16899951	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117	16899951	42229032	10954	18939										
CPAMD8	27151	broad.mit.edu	37	chr19	17038831	17038831	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacgcaccgatgatggaggCggtggctcgctcagacccag	15	12	1	3	rs372897642		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17038831C>T	ENST00000443236.1	-	25	3530	c.3499G>A	c.(3499-3501)Gcc>Acc	p.A1167T		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1120						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A1167T(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ATGATGGAGGCGGTGGCTCGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	THR/ALA	0,4080		0,0,2040	43	51	48		3499	3	0	19		48	1,8367		0,1,4183	no	missense	CPAMD8	NM_015692.2	58	0,1,6223	TT,TC,CC		0.012,0.0,0.0080	probably-damaging	1167/1933	17038831	1,12447	2040	4184	6224	16899831	SO:0001583	missense	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3499G>A	19.37:g.17038831C>T	ENSP00000402505:p.Ala1167Thr		16899831	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.510497	0.44660	0.0	1.2E-4	ENSG00000160111	ENST00000291440	.	.	.	3.02	3.02	0.34903	.	0.240195	0.33309	N	0.005043	T	0.73426	0.3585	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.74581	-0.3618	9	0.45353	T	0.12	.	13.9882	0.64348	0.0:1.0:0.0:0.0	.	1120	Q8IZJ3	CPMD8_HUMAN	T	1167	.	ENSP00000291440:A1167T	A	-	1	0	CPAMD8	16899831	1.000000	0.71417	0.014000	0.15608	0.035000	0.12851	6.465000	0.73538	1.237000	0.43756	0.655000	0.94253	GCC		0.622	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17038831	C	T	17038831	3	4	61	1	0	0	0	0	1	0	0	0	3801	768	27	1	2371	1	CPAMD8	19	17038831	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138880	17038831	42090152	10955	18940										
CPAMD8	27151	broad.mit.edu	37	chr19	17040037	17040037	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatacttgttgggggtggaGatgtggactctctctggatg	15	6	3	1	rs375563538		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17040037G>T	ENST00000443236.1	-	24	3031	c.3000C>A	c.(2998-3000)atC>atA	p.I1000I		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	953						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.I1000I(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TGGGGGTGGAGATGTGGACTC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	19											49	55	53					19																	17040037		2078	4213	6291	16901037	SO:0001819	synonymous_variant	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3000C>A	19.37:g.17040037G>T			16901037	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	9.057	0.993596	0.19043	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.39	2.22	0.28083	.	.	.	.	.	T	0.44953	0.1318	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37220	-0.9715	4	.	.	.	.	3.1349	0.06436	0.6215:0.0:0.3785:0.0	.	.	.	.	Y	1011	.	.	S	-	2	0	CPAMD8	16901037	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.263000	0.43293	1.460000	0.47911	0.650000	0.86243	TCT		0.582	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17040037	G	T	17040037	2	4	61	1	0	0	0	0	0	0	0	1	3801	932	33	2		2	CPAMD8	19	17040037	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1206	17040037	42088946	10956	18941										
CPAMD8	27151	broad.mit.edu	37	chr19	17086913	17086913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagccctgatccgcaggtCgacaacctccccaggttggg	12	15	0	1	rs374113157		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17086913C>T	ENST00000443236.1	-	16	1979	c.1948G>A	c.(1948-1950)Gac>Aac	p.D650N	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	603						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D650N(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ATCCGCAGGTCGACAACCTCC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	ASN/ASP	1,4119		0,1,2059	42	46	45		1948	2.9	0	19		45	0,8412		0,0,4206	no	missense	CPAMD8	NM_015692.2	23	0,1,6265	TT,TC,CC		0.0,0.0243,0.0080	benign	650/1933	17086913	1,12531	2060	4206	6266	16947913	SO:0001583	missense	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1948G>A	19.37:g.17086913C>T	ENSP00000402505:p.Asp650Asn		16947913	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	C	0.241	-1.013373	0.02095	2.43E-4	0.0	ENSG00000160111	ENST00000291440	.	.	.	2.89	2.89	0.33648	Alpha-2-macroglobulin, N-terminal 2 (1);	0.274070	0.31020	N	0.008417	T	0.26122	0.0637	L	0.33485	1.01	0.19945	N	0.999946	B	0.19583	0.037	B	0.17979	0.02	T	0.16571	-1.0398	9	0.09590	T	0.72	.	8.8142	0.34985	0.0:0.8685:0.0:0.1315	.	603	Q8IZJ3	CPMD8_HUMAN	N	650	.	ENSP00000291440:D650N	D	-	1	0	CPAMD8	16947913	0.940000	0.31905	0.004000	0.12327	0.002000	0.02628	1.800000	0.38833	1.351000	0.45789	0.561000	0.74099	GAC		0.557	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17086913	C	T	17086913	3	4	61	1	0	0	0	0	1	0	0	0	3801	884	31	1	3958	1	CPAMD8	19	17086913	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46876	17086913	42042070	10957	18942										
CPAMD8	27151	broad.mit.edu	37	chr19	17091315	17091315	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccggctcacctgtctcaGaaaggtgtgttaaacgaatc	10	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17091315G>T	ENST00000443236.1	-	14	1749	c.1718C>A	c.(1717-1719)tCt>tAt	p.S573Y	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	526						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S573Y(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ACCTGTCTCAGAAAGGTGTGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											51	56	54					19																	17091315		1970	4147	6117	16952315	SO:0001583	missense	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1718C>A	19.37:g.17091315G>T	ENSP00000402505:p.Ser573Tyr		16952315	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.013991|4.013991	0.75161|0.75161	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	2.9|2.9	1.83|1.83	0.25207|0.25207	.|Alpha-2-macroglobulin, N-terminal 2 (1);	.|0.942978	.|0.08694	.|U	.|0.907511	T|T	0.49881|0.49881	0.1583|0.1583	L|L	0.40543|0.40543	1.245|1.245	0.54753|0.54753	D|D	0.999989|0.999989	.|P	.|0.50710	.|0.938	.|P	.|0.52109	.|0.69	T|T	0.40961|0.40961	-0.9535|-0.9535	5|9	.|0.12103	.|T	.|0.63	.|.	8.0621|8.0621	0.30640|0.30640	0.1203:0.0:0.8796:0.0|0.1203:0.0:0.8796:0.0	.|.	.|526	.|Q8IZJ3	.|CPMD8_HUMAN	M|Y	584|573	.|.	.|ENSP00000291440:S573Y	L|S	-|-	1|2	2|0	CPAMD8|CPAMD8	16952315|16952315	0.996000|0.996000	0.38824|0.38824	0.441000|0.441000	0.26858|0.26858	0.880000|0.880000	0.50808|0.50808	3.026000|3.026000	0.49689|0.49689	0.223000|0.223000	0.20920|0.20920	0.467000|0.467000	0.42956|0.42956	CTG|TCT		0.572	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17091315	G	T	17091315	3	4	61	1	0	0	0	0	1	0	0	0	3801	942	33	2	4196	2	CPAMD8	19	17091315	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4402	17091315	42037668	10958	18943										
HAUS8	93323	broad.mit.edu	37	chr19	17163678	17163678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccgtcacgtccttgagttCgctcagtaagtccagcacct	9	15	2	1	rs538139096	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17163678C>T	ENST00000253669.5	-	10	1076	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K	HAUS8_ENST00000448593.2_Missense_Mutation_p.E295K|HAUS8_ENST00000593360.1_Missense_Mutation_p.E235K|CTD-2528A14.3_ENST00000598893.1_RNA			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	296					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.E296K(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						TCCTTGAGTTCGCTCAGTAAG	0.532											OREG0025339	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	8e-04	0	5008	,	,		21088	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	19											194	164	174					19																	17163678		2203	4300	6503	17024678	SO:0001583	missense	93323			BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"HAUS augmin-like complex subunits"	30532	protein-coding gene	gene with protein product		613434	"HEC1/NDC80 interacting, centrosome associated 1"	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.886G>A	19.37:g.17163678C>T	ENSP00000253669:p.Glu296Lys	715	17024678	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Missense_Mutation	SNP	ENST00000253669.5	37	CCDS32948.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381752	0.82792	.	.	ENSG00000131351	ENST00000253669;ENST00000448593	T;T	0.75477	-0.94;-0.94	4.64	4.64	0.57946	.	0.086838	0.46145	D	0.000319	T	0.81004	0.4733	L	0.46157	1.445	0.26772	N	0.969785	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72625	0.968;0.978;0.978	T	0.74070	-0.3783	10	0.72032	D	0.01	-29.4659	13.0094	0.58724	0.0:1.0:0.0:0.0	.	235;295;296	Q9BT25-2;C9JBZ4;Q9BT25	.;.;HAUS8_HUMAN	K	296;295	ENSP00000253669:E296K;ENSP00000395298:E295K	ENSP00000253669:E296K	E	-	1	0	HAUS8	17024678	0.981000	0.34729	0.162000	0.22713	0.353000	0.29299	3.356000	0.52269	2.129000	0.65627	0.561000	0.74099	GAA		0.532	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699		T	17163678	C	T	17163678	3	4	61	1	0	0	0	0	1	0	0	0	6993	893	31	1	354	1	HAUS8	19	17163678	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72363	17163678	41965305	10959	18944										
NR2F6	2063	broad.mit.edu	37	chr19	17343227	17343227	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatgtctctgatcagtgtCtcaatgggcgtcttccccac	9	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17343227C>A	ENST00000291442.3	-	4	1868	c.1149G>T	c.(1147-1149)gaG>gaT	p.E383D		NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	383	Important for dimerization. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)	p.E383D(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						TGATCAGTGTCTCAATGGGCG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	66	69					19																	17343227		2203	4300	6503	17204227	SO:0001583	missense	2063			X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113		"Nuclear hormone receptors"	7977	protein-coding gene	gene with protein product		132880		ERBAL2		2905047	Standard	NM_005234		Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.1149G>T	19.37:g.17343227C>A	ENSP00000291442:p.Glu383Asp		17204227	B2RC68|Q5XGA0|Q6P586|Q9BUE8	Missense_Mutation	SNP	ENST00000291442.3	37	CCDS12352.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920612	0.52653	.	.	ENSG00000160113	ENST00000291442;ENST00000536940	T	0.47869	0.83	4.71	2.57	0.30868	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.38268	0.1034	N	0.12443	0.215	0.52099	D	0.99994	D	0.63046	0.992	D	0.77004	0.989	T	0.48725	-0.9010	10	0.02654	T	1	.	6.0882	0.19978	0.0:0.6974:0.0:0.3026	.	383	P10588	NR2F6_HUMAN	D	383;356	ENSP00000291442:E383D	ENSP00000291442:E383D	E	-	3	2	NR2F6	17204227	0.997000	0.39634	0.993000	0.49108	0.833000	0.47200	0.492000	0.22435	0.975000	0.38392	0.555000	0.69702	GAG		0.667	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463325.1			A	17343227	C	A	17343227	3	1	61	1	0	0	0	0	1	0	0	0	10660	912	32	2	69	2	NR2F6	19	17343227	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179549	17343227	41785756	10960	18945										
USHBP1	83878	broad.mit.edu	37	chr19	17366231	17366231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtccccgctgctgccacctCcgctgctatgtccgccactg	9	20	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17366231C>T	ENST00000252597.3	-	10	1828	c.1655G>A	c.(1654-1656)gGa>gAa	p.G552E	USHBP1_ENST00000431146.2_Missense_Mutation_p.G488E|AC010646.3_ENST00000594059.1_5'UTR	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.G552E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						GCTGCCACCTCCGCTGCTATG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											63	67	66					19																	17366231		2203	4300	6503	17227231	SO:0001583	missense	83878			AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1655G>A	19.37:g.17366231C>T	ENSP00000252597:p.Gly552Glu		17227231		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	C	9.465	1.094164	0.20471	.	.	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.18657	2.21;2.2	4.92	-2.84	0.05751	.	1.157650	0.06295	N	0.699923	T	0.09468	0.0233	L	0.31294	0.92	0.09310	N	0.999999	B;B	0.12013	0.005;0.005	B;B	0.06405	0.002;0.002	T	0.31943	-0.9925	10	0.02654	T	1	-3.4088	0.1965	0.00140	0.3028:0.2682:0.1486:0.2804	.	488;552	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	E	552;488	ENSP00000252597:G552E;ENSP00000407902:G488E	ENSP00000252597:G552E	G	-	2	0	USHBP1	17227231	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-0.547000	0.06055	-0.460000	0.07003	-0.181000	0.13052	GGA		0.622	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		T	17366231	C	T	17366231	3	4	61	1	0	0	0	0	1	0	0	0	17077	855	30	3	472	3	USHBP1	19	17366231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23004	17366231	41762752	10961	18946										
USHBP1	83878	broad.mit.edu	37	chr19	17370501	17370501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgggtgctggaatggctgCggaggcgccgaagcaggggg	21	8	1	0	rs147305519		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17370501C>T	ENST00000252597.3	-	6	982	c.809G>A	c.(808-810)cGc>cAc	p.R270H	USHBP1_ENST00000431146.2_Missense_Mutation_p.R206H|USHBP1_ENST00000598570.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.R270H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						GGAATGGCTGCGGAGGCGCCG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19						T	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	73	82	79		809	-8.9	0	19	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	yes	missense	USHBP1	NM_031941.3	29	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	benign	270/704	17370501	3,13003	2203	4300	6503	17231501	SO:0001583	missense	83878			AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.809G>A	19.37:g.17370501C>T	ENSP00000252597:p.Arg270His		17231501		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	c	4.605	0.112465	0.08831	4.54E-4	1.16E-4	ENSG00000130307	ENST00000252597;ENST00000431146;ENST00000324554	T;T	0.24151	1.87;1.87	5.12	-8.9	0.00782	.	0.917493	0.08960	N	0.868881	T	0.15349	0.0370	N	0.20986	0.625	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.004	B;B;B	0.04013	0.001;0.001;0.001	T	0.21621	-1.0240	10	0.39692	T	0.17	-2.5778	15.7192	0.77694	0.0:0.2727:0.0:0.7273	.	206;270;270	B4DUE8;Q8N8Y1;Q8N6Y0	.;.;USBP1_HUMAN	H	270;206;270	ENSP00000252597:R270H;ENSP00000407902:R206H	ENSP00000252597:R270H	R	-	2	0	USHBP1	17231501	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.346000	0.01096	-1.682000	0.01446	-3.330000	0.00044	CGC		0.577	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		T	17370501	C	T	17370501	3	4	61	1	0	0	0	0	1	0	0	0	17077	768	27	1	1334	1	USHBP1	19	17370501	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4270	17370501	41758482	10962	18947										
ANKLE1	126549	broad.mit.edu	37	chr19	17394193	17394193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacaaacatgggagctcggCgtcccctccagggcactggg	15	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17394193C>T	ENST00000394458.3	+	5	896	c.620C>T	c.(619-621)gCg>gTg	p.A207V	ANKLE1_ENST00000433424.2_Missense_Mutation_p.A261V|ANKLE1_ENST00000594072.1_Missense_Mutation_p.A196V|ANKLE1_ENST00000598347.1_Missense_Mutation_p.A207V|ANKLE1_ENST00000404085.1_Missense_Mutation_p.A229V	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	207								p.A193V(1)|p.A207V(1)		large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GGGAGCTCGGCGTCCCCTCCA	0.622																																																2	Substitution - Missense(2)	large_intestine(2)	19											75	86	82					19																	17394193		2202	4300	6502	17255193	SO:0001583	missense	126549			AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"Ankyrin repeat domain containing"	26812	protein-coding gene	gene with protein product	"LEM domain containing 6"		"ankyrin repeat domain 41"	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.620C>T	19.37:g.17394193C>T	ENSP00000377971:p.Ala207Val		17255193	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	.	.	.	.	.	.	.	.	.	.	C	13.46	2.244442	0.39697	.	.	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.72167	-0.49;-0.58;-0.63	3.3	-0.662	0.11413	.	5.126170	0.00597	N	0.000379	T	0.47619	0.1455	N	0.14661	0.345	0.09310	N	1	D;P;P;B	0.58268	0.982;0.871;0.604;0.029	B;B;B;B	0.38296	0.27;0.206;0.071;0.003	T	0.45991	-0.9223	10	0.15066	T	0.55	-46.7434	4.9624	0.14072	0.5963:0.2733:0.1303:0.0	.	207;193;207;196	E7ETZ9;Q8NAG6-1;Q8NAG6;A0JLW0	.;.;ANKL1_HUMAN;.	V	207;261;229;196;207	ENSP00000384753:A207V;ENSP00000394460:A261V;ENSP00000384008:A229V	ENSP00000377971:A196V	A	+	2	0	ANKLE1	17255193	0.000000	0.05858	0.000000	0.03702	0.367000	0.29736	-0.634000	0.05477	-0.271000	0.09272	0.313000	0.20887	GCG		0.622	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363		T	17394193	C	T	17394193	3	4	61	1	0	0	0	0	1	0	0	0	632	768	27	1	638	1	ANKLE1	19	17394193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23692	17394193	41734790	10963	18948										
PLVAP	83483	broad.mit.edu	37	chr19	17476358	17476358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcttccagcttctggcGttggaggtctgagttctcgc	14	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17476358G>A	ENST00000252590.4	-	3	977	c.916C>T	c.(916-918)Cgc>Tgc	p.R306C	CTD-2278I10.1_ENST00000597592.1_RNA	NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	306					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R306C(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AGCTTCTGGCGTTGGAGGTCT	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											35	32	33					19																	17476358		2203	4300	6503	17337358	SO:0001583	missense	83483			AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.916C>T	19.37:g.17476358G>A	ENSP00000252590:p.Arg306Cys		17337358	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Missense_Mutation	SNP	ENST00000252590.4	37	CCDS32952.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.590272	0.66105	.	.	ENSG00000130300	ENST00000252590	.	.	.	5.42	3.1	0.35709	.	0.538685	0.19998	N	0.101405	T	0.57051	0.2027	L	0.34521	1.04	0.39386	D	0.966335	D	0.89917	1.0	D	0.73380	0.98	T	0.59166	-0.7505	9	0.62326	D	0.03	-24.553	7.9928	0.30250	0.0:0.1766:0.6406:0.1828	.	306	Q9BX97	PLVAP_HUMAN	C	306	.	ENSP00000252590:R306C	R	-	1	0	PLVAP	17337358	0.986000	0.35501	0.936000	0.37596	0.755000	0.42902	1.365000	0.34182	1.249000	0.43950	0.462000	0.41574	CGC		0.662	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		A	17476358	G	A	17476358	3	1	61	1	0	0	0	0	1	0	0	0	12147	1145	40	1	428	1	PLVAP	19	17476358	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82165	17476358	41652625	10964	18949										
PLVAP	83483	broad.mit.edu	37	chr19	17476993	17476993	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatgtacctctgattgttCgtgtagatgacctgcccgga	11	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17476993C>T	ENST00000252590.4	-	2	442	c.381G>A	c.(379-381)acG>acA	p.T127T		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	127					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.T127T(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCTGATTGTTCGTGTAGATGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	19											203	177	186					19																	17476993		2203	4300	6503	17337993	SO:0001819	synonymous_variant	83483			AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.381G>A	19.37:g.17476993C>T			17337993	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Silent	SNP	ENST00000252590.4	37	CCDS32952.1																																																																																				0.542	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		T	17476993	C	T	17476993	2	4	61	1	0	0	0	0	0	0	0	1	12147	871	31	1		1	PLVAP	19	17476993	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	635	17476993	41651990	10965	18950										
BST2	684	broad.mit.edu	37	chr19	17514561	17514561	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagctggggcgccgcagcGgagctggagtcctgggagct	19	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17514561G>A	ENST00000252593.6	-	4	558	c.486C>T	c.(484-486)tcC>tcT	p.S162S	BST2_ENST00000527220.1_5'Flank|CTD-2521M24.9_ENST00000500836.2_lincRNA	NM_004335.2	NP_004326.1	Q10589	BST2_HUMAN	bone marrow stromal cell antigen 2	162					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of plasmacytoid dendritic cell cytokine production (GO:0002737)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of actin cytoskeleton organization (GO:0032956)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metalloendopeptidase inhibitor activity (GO:0008191)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.S162S(1)		endometrium(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(2)	9						GCGCCGCAGCGGAGCTGGAGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19											86	86	86					19																	17514561		2203	4300	6503	17375561	SO:0001819	synonymous_variant	684				CCDS12358.1	19p13.2	2009-10-30				ENSG00000130303		"CD molecules"	1119	protein-coding gene	gene with protein product		600534				7607676	Standard	NM_004335		Approved	CD317, tetherin	uc002ngl.3	Q10589		ENST00000252593.6:c.486C>T	19.37:g.17514561G>A			17375561	A8K4Y4|Q53G07	Silent	SNP	ENST00000252593.6	37	CCDS12358.1																																																																																				0.617	BST2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387346.1	NM_004335		A	17514561	G	A	17514561	2	1	61	1	0	0	0	0	0	0	0	1	1537	1103	39	1		1	BST2	19	17514561	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37568	17514561	41614422	10966	18951										
FAM125A	93343	broad.mit.edu	37	chr19	17534604	17534604	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccagcctctatggcatCtcaggtgagcacagagtggg	13	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17534604C>A	ENST00000317040.7	+	6	1691	c.636C>A	c.(634-636)atC>atA	p.I212I	MVB12A_ENST00000528515.1_Missense_Mutation_p.S170Y|MVB12A_ENST00000392702.2_Silent_p.I172I|CTD-2521M24.6_ENST00000593957.1_RNA|MVB12A_ENST00000529939.1_Silent_p.I212I|MVB12A_ENST00000543795.1_Silent_p.I212I			Q96EY5	MB12A_HUMAN	multivesicular body subunit 12A	212	Interaction with TSG101, VPS37B and VPS28.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|vesicle (GO:0031982)	lipid binding (GO:0008289)|ubiquitin binding (GO:0043130)	p.I212I(1)									TCTATGGCATCTCAGGTGAGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											37	34	35					19																	17534604		2203	4299	6502	17395604	SO:0001819	synonymous_variant	93343			BC011840	CCDS12359.1	19p13.11	2013-10-11	2012-12-03	2012-12-03	ENSG00000141971	ENSG00000141971			25153	protein-coding gene	gene with protein product			"family with sequence similarity 125, member A"	FAM125A		18005716, 20654576, 22232651	Standard	NM_138401		Approved	FLJ32495	uc002ngo.1	Q96EY5	OTTHUMG00000166252	ENST00000317040.7:c.636C>A	19.37:g.17534604C>A			17395604	Q96I18	Silent	SNP	ENST00000317040.7	37	CCDS12359.1	.	.	.	.	.	.	.	.	.	.	.	11.39	1.624533	0.28889	.	.	ENSG00000141971	ENST00000528515	.	.	.	5.31	3.16	0.36331	.	.	.	.	.	T	0.62478	0.2431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61695	-0.7010	5	0.72032	D	0.01	-19.61	6.5814	0.22596	0.1784:0.7291:0.0:0.0925	.	.	.	.	Y	170	.	ENSP00000433677:S170Y	S	+	2	0	FAM125A	17395604	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	0.612000	0.24283	0.602000	0.29896	0.558000	0.71614	TCT		0.587	MVB12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388723.2	NM_138401		A	17534604	C	A	17534604	2	1	61	1	0	0	0	0	0	0	0	1	5443	903	32	2		2	FAM125A	19	17534604	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20043	17534604	41594379	10967	18952										
NXNL1	115861	broad.mit.edu	37	chr19	17571367	17571367	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcacctcctcagatcatcCtcaaagggcaggaaaagcca	7	15	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17571367C>A	ENST00000301944.2	-	1	396	c.312G>T	c.(310-312)gaG>gaT	p.E104D	CTD-2521M24.10_ENST00000594663.1_Missense_Mutation_p.E11D	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	104	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E104D(1)		central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						TCAGATCATCCTCAAAGGGCA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	53	59					19																	17571367		2203	4300	6503	17432367	SO:0001583	missense	115861			BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"thioredoxin-like 6"	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.312G>T	19.37:g.17571367C>A	ENSP00000305631:p.Glu104Asp		17432367	Q0QD37	Missense_Mutation	SNP	ENST00000301944.2	37	CCDS12360.1	.	.	.	.	.	.	.	.	.	.	c	3.305	-0.142130	0.06669	.	.	ENSG00000171773	ENST00000301944	T	0.79141	-1.24	3.92	0.341	0.15991	Thioredoxin-like fold (3);	0.606668	0.17607	N	0.168214	T	0.52158	0.1717	N	0.16478	0.41	0.33014	D	0.527933	B	0.09022	0.002	B	0.12156	0.007	T	0.40079	-0.9582	10	0.09843	T	0.71	-13.7588	3.0451	0.06151	0.2032:0.4645:0.0:0.3324	.	104	Q96CM4	NXNL1_HUMAN	D	104	ENSP00000305631:E104D	ENSP00000305631:E104D	E	-	3	2	NXNL1	17432367	0.996000	0.38824	0.988000	0.46212	0.508000	0.34012	0.460000	0.21924	0.276000	0.22118	0.467000	0.42956	GAG		0.562	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454		A	17571367	C	A	17571367	3	1	61	1	0	0	0	0	1	0	0	0	10819	680	24	2	334	2	NXNL1	19	17571367	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36763	17571367	41557616	10968	18953										
SLC27A1	376497	broad.mit.edu	37	chr19	17615280	17615280	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataggcaccttcaagatccaGaagacgaggctgcagcgaga	12	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17615280G>A	ENST00000252595.7	+	12	1897	c.1800G>A	c.(1798-1800)caG>caA	p.Q600Q	SLC27A1_ENST00000598424.1_Silent_p.Q421Q|CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000598848.1_3'UTR|SLC27A1_ENST00000442725.1_Silent_p.Q600Q	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	600					adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.Q600Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TCAAGATCCAGAAGACGAGGC	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											86	74	78					19																	17615280		2203	4300	6503	17476280	SO:0001819	synonymous_variant	376497			BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1800G>A	19.37:g.17615280G>A			17476280	A6NIH2|B7Z662	Silent	SNP	ENST00000252595.7	37	CCDS32953.1																																																																																				0.587	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		A	17615280	G	A	17615280	2	1	61	1	0	0	0	0	0	0	0	1	14562	933	33	3		3	SLC27A1	19	17615280	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43913	17615280	41513703	10969	18954										
FAM129C	199786	broad.mit.edu	37	chr19	17643117	17643117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggacccctgacccagcttCggggccacccaccccggtgg	13	18	0	1	rs536652149		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17643117C>T	ENST00000335393.4	+	4	463	c.325C>T	c.(325-327)Cgg>Tgg	p.R109W	FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000300971.2_Missense_Mutation_p.R109W|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000600871.1_Missense_Mutation_p.R55W|FAM129C_ENST00000599164.1_Missense_Mutation_p.R78W|FAM129C_ENST00000332386.5_Missense_Mutation_p.R109W|FAM129C_ENST00000599124.1_Missense_Mutation_p.R78W|FAM129C_ENST00000352727.3_Missense_Mutation_p.R109W|FAM129C_ENST00000595684.1_Missense_Mutation_p.R109W|FAM129C_ENST00000601861.1_Missense_Mutation_p.R78W	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	109								p.R109W(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						GACCCAGCTTCGGGGCCACCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											61	60	60					19																	17643117		2203	4299	6502	17504117	SO:0001583	missense	199786			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.325C>T	19.37:g.17643117C>T	ENSP00000335040:p.Arg109Trp		17504117	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.595478	0.28445	.	.	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971;ENST00000435646	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.13	-0.563	0.11778	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	1.161840	0.06705	N	0.772089	T	0.09818	0.0241	N	0.16478	0.41	0.09310	N	0.999999	B;B	0.18013	0.025;0.025	B;B	0.14578	0.011;0.011	T	0.36432	-0.9748	10	0.49607	T	0.09	-6.3877	4.0478	0.09781	0.0:0.5378:0.1738:0.2884	.	109;109	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	W	109;109;109;109;55	ENSP00000335040:R109W;ENSP00000333447:R109W;ENSP00000341067:R109W;ENSP00000300971:R109W	ENSP00000300971:R109W	R	+	1	2	FAM129C	17504117	0.000000	0.05858	0.005000	0.12908	0.880000	0.50808	-0.914000	0.04038	-0.159000	0.11021	0.491000	0.48974	CGG		0.662	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		T	17643117	C	T	17643117	3	4	61	1	0	0	0	0	1	0	0	0	5454	875	31	1	339	1	FAM129C	19	17643117	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27837	17643117	41485866	10970	18955										
UNC13A	23025	broad.mit.edu	37	chr19	17746859	17746859	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcagggagtgtaggaattCttgtcttcctcaatgatgga	13	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17746859C>A	ENST00000519716.2	-	26	3188	c.3189G>T	c.(3187-3189)aaG>aaT	p.K1063N	UNC13A_ENST00000428389.2_Missense_Mutation_p.K1151N|UNC13A_ENST00000551649.1_Missense_Mutation_p.K1063N|UNC13A_ENST00000550896.1_Missense_Mutation_p.K1061N|UNC13A_ENST00000552293.1_Missense_Mutation_p.K1063N|UNC13A_ENST00000252773.7_Missense_Mutation_p.K1063N	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1063					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.K1063N(1)|p.K1151N(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TGTAGGAATTCTTGTCTTCCT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											79	76	77					19																	17746859		1976	4163	6139	17607859	SO:0001583	missense	23025			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3189G>T	19.37:g.17746859C>A	ENSP00000429562:p.Lys1063Asn		17607859	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	16.63	3.175384	0.57692	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.83419	-1.7;-1.72;-1.7;-1.56;-1.58;-1.71	3.52	1.37	0.22104	Calcium-dependent secretion activator (1);	0.000000	0.85682	U	0.000000	D	0.85124	0.5625	M	0.63843	1.955	0.44439	D	0.997363	P	0.46220	0.874	P	0.57620	0.824	T	0.82012	-0.0668	10	0.56958	D	0.05	-20.7874	7.2247	0.26007	0.0:0.7705:0.0:0.2295	.	1063	Q9UPW8	UN13A_HUMAN	N	1063;1151;1063;1063;1063;1061	ENSP00000429562:K1063N;ENSP00000400409:K1151N;ENSP00000252773:K1063N;ENSP00000447236:K1063N;ENSP00000447572:K1063N;ENSP00000446831:K1061N	ENSP00000252773:K1063N	K	-	3	2	UNC13A	17607859	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	0.871000	0.28023	0.213000	0.20722	0.305000	0.20034	AAG		0.468	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17746859	C	A	17746859	3	1	61	1	0	0	0	0	1	0	0	0	17024	912	32	2	1994	2	UNC13A	19	17746859	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103742	17746859	41382124	10971	18956										
UNC13A	23025	broad.mit.edu	37	chr19	17746965	17746965	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaacttcccccttcttgGcctgaaatggacagtggaga	12	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17746965G>A	ENST00000519716.2	-	26	3082	c.3083C>T	c.(3082-3084)gCc>gTc	p.A1028V	UNC13A_ENST00000428389.2_Splice_Site_p.A1116V|UNC13A_ENST00000551649.1_Splice_Site_p.A1028V|UNC13A_ENST00000550896.1_Splice_Site_p.A1026V|UNC13A_ENST00000552293.1_Splice_Site_p.A1028V|UNC13A_ENST00000252773.7_Splice_Site_p.A1028V	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1028					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.A1028V(1)|p.A1116V(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CCCCTTCTTGGCCTGAAATGG	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	19											54	51	52					19																	17746965		1892	4129	6021	17607965	SO:0001630	splice_region_variant	23025			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3082-1C>T	19.37:g.17746965G>A			17607965	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335058	0.24253	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;D;T;T;T;T	0.81499	-1.49;-1.5;-1.49;-1.35;-1.36;-1.48	3.34	3.34	0.38264	Calcium-dependent secretion activator (1);	0.487547	0.17814	U	0.161091	T	0.60932	0.2307	N	0.03608	-0.345	0.29502	N	0.854876	B	0.15719	0.014	B	0.16722	0.016	T	0.60115	-0.7326	10	0.48119	T	0.1	-12.6742	12.1977	0.54307	0.0:0.0:1.0:0.0	.	1028	Q9UPW8	UN13A_HUMAN	V	1028;1116;1028;1028;1028;1026	ENSP00000429562:A1028V;ENSP00000400409:A1116V;ENSP00000252773:A1028V;ENSP00000447236:A1028V;ENSP00000447572:A1028V;ENSP00000446831:A1026V	ENSP00000252773:A1028V	A	-	2	0	UNC13A	17607965	0.964000	0.33143	1.000000	0.80357	0.727000	0.41649	2.331000	0.43894	1.702000	0.51228	0.305000	0.20034	GCC		0.507	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	Missense_Mutation	A	17746965	G	A	17746965	5	1	61	1	0	0	0	0	0	0	1	0	17024	1217	42	3	2100	3	UNC13A	19	17746965	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	106	17746965	41382018	10972	18957										
UNC13A	23025	broad.mit.edu	37	chr19	17750661	17750661	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctacccggtacatggaGaggtcaatccgcagggagtt	12	11	1	1	rs573302812		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17750661G>T	ENST00000519716.2	-	23	2843	c.2844C>A	c.(2842-2844)ctC>ctA	p.L948L	UNC13A_ENST00000428389.2_Silent_p.L1036L|UNC13A_ENST00000551649.1_Silent_p.L948L|UNC13A_ENST00000550896.1_Silent_p.L946L|UNC13A_ENST00000552293.1_Silent_p.L948L|UNC13A_ENST00000252773.7_Silent_p.L948L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	948					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.L948L(1)|p.L1036L(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GGTACATGGAGAGGTCAATCC	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	19											94	92	93					19																	17750661		2091	4224	6315	17611661	SO:0001819	synonymous_variant	23025			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2844C>A	19.37:g.17750661G>T			17611661	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																				0.567	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17750661	G	T	17750661	2	4	61	1	0	0	0	0	0	0	0	1	17024	929	33	2		2	UNC13A	19	17750661	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3696	17750661	41378322	10973	18958										
UNC13A	23025	broad.mit.edu	37	chr19	17752351	17752351	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttctgcacgtcggtcacGaagtggaacaggttctgcca	12	10	3	0	rs375584692		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17752351G>A	ENST00000519716.2	-	21	2486	c.2487C>T	c.(2485-2487)ttC>ttT	p.F829F	UNC13A_ENST00000428389.2_Silent_p.F917F|UNC13A_ENST00000551649.1_Silent_p.F829F|UNC13A_ENST00000550896.1_Silent_p.F827F|UNC13A_ENST00000552293.1_Silent_p.F829F|UNC13A_ENST00000252773.7_Silent_p.F829F	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	829					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.F829F(1)|p.F917F(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CGTCGGTCACGAAGTGGAACA	0.572																																																2	Substitution - coding silent(2)	large_intestine(2)	19								1,4211		0,1,2105	93	91	92		2487	-3.5	0.4	19		92	1,8493		0,1,4246	no	coding-synonymous	UNC13A	NM_001080421.2		0,2,6351	AA,AG,GG		0.0118,0.0237,0.0157		829/1704	17752351	2,12704	2106	4247	6353	17613351	SO:0001819	synonymous_variant	23025			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2487C>T	19.37:g.17752351G>A			17613351	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																				0.572	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17752351	G	A	17752351	2	1	61	1	0	0	0	0	0	0	0	1	17024	1049	37	1		1	UNC13A	19	17752351	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1690	17752351	41376632	10974	18959										
MAP1S	55201	broad.mit.edu	37	chr19	17831830	17831830	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccgacactctgccaccttCtccagcattgtgaaaggtga	8	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17831830C>A	ENST00000324096.4	+	2	355	c.204C>A	c.(202-204)ttC>ttA	p.F68L	MAP1S_ENST00000544059.2_Missense_Mutation_p.F42L|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	68	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.F68L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTGCCACCTTCTCCAGCATTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											118	102	108					19																	17831830		2203	4300	6503	17692830	SO:0001583	missense	55201			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.204C>A	19.37:g.17831830C>A	ENSP00000325313:p.Phe68Leu		17692830	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	c	19.78	3.891257	0.72524	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.25912	1.77;1.77	3.87	2.81	0.32909	.	0.000000	0.50627	D	0.000113	T	0.26629	0.0651	L	0.59436	1.845	0.42869	D	0.994132	B;B;B	0.30455	0.234;0.28;0.172	B;B;B	0.33690	0.168;0.118;0.04	T	0.10132	-1.0643	10	0.72032	D	0.01	-31.8545	9.8241	0.40901	0.0:0.8917:0.0:0.1083	.	42;68;68	B4DH53;A8K940;Q66K74	.;.;MAP1S_HUMAN	L	68;42	ENSP00000325313:F68L;ENSP00000439243:F42L	ENSP00000325313:F68L	F	+	3	2	MAP1S	17692830	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.105000	0.31086	0.720000	0.32209	0.486000	0.48141	TTC		0.587	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		A	17831830	C	A	17831830	3	1	61	1	0	0	0	0	1	0	0	0	9264	912	32	2	210	2	MAP1S	19	17831830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79479	17831830	41297153	10975	18960										
B3GNT3	10331	broad.mit.edu	37	chr19	17922925	17922925	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcggcaatcagacacagatCtactgagtcagcatcagggt	11	10	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17922925C>T	ENST00000318683.6	+	3	1260	c.1113C>T	c.(1111-1113)atC>atT	p.I371I	B3GNT3_ENST00000595387.1_Silent_p.I371I	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	371					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)	p.I371I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						AGACACAGATCTACTGAGTCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	19											27	25	26					19																	17922925		2137	4189	6326	17783925	SO:0001819	synonymous_variant	10331			AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"Beta 3-glycosyltransferases"	13528	protein-coding gene	gene with protein product	"putative type II membrane protein", "beta-1,3-N-acetylglucosaminyltransferase bGnT-3", "transmembrane protein 3"	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.1113C>T	19.37:g.17922925C>T			17783925	B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Silent	SNP	ENST00000318683.6	37	CCDS12364.1																																																																																				0.577	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256		T	17922925	C	T	17922925	2	4	61	1	0	0	0	0	0	0	0	1	1259	903	32	3		3	B3GNT3	19	17922925	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91095	17922925	41206058	10976	18961										
SLC5A5	6528	broad.mit.edu	37	chr19	17991703	17991703	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctggtgctggacatcttCgaagatctgcctggagtccc	12	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17991703C>T	ENST00000222248.3	+	8	1346	c.999C>T	c.(997-999)ttC>ttT	p.F333F		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	333					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)	p.F333F(2)		NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TGGACATCTTCGAAGATCTGC	0.597																																					Melanoma(65;1008 1708 7910 46650)											2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	19											121	102	109					19																	17991703		2203	4300	6503	17852703	SO:0001819	synonymous_variant	6528				CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.999C>T	19.37:g.17991703C>T			17852703	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																				0.597	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17991703	C	T	17991703	2	4	61	1	0	0	0	0	0	0	0	1	14705	883	31	1		1	SLC5A5	19	17991703	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68778	17991703	41137280	10977	18962										
SLC5A5	6528	broad.mit.edu	37	chr19	17999152	17999152	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgcagctcaggaatggaCgccagccgacccgccttagc	11	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:17999152C>T	ENST00000222248.3	+	13	1886	c.1539C>T	c.(1537-1539)gaC>gaT	p.D513D		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	513					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)	p.D513D(1)		NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CAGGAATGGACGCCAGCCGAC	0.567																																					Melanoma(65;1008 1708 7910 46650)											1	Substitution - coding silent(1)	large_intestine(1)	19											112	94	100					19																	17999152		2203	4300	6503	17860152	SO:0001819	synonymous_variant	6528				CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1539C>T	19.37:g.17999152C>T			17860152	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																				0.567	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17999152	C	T	17999152	2	4	61	1	0	0	0	0	0	0	0	1	14705	535	19	1		1	SLC5A5	19	17999152	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	7449	17999152	41129831	10978	18963										
KIAA1683	80726	broad.mit.edu	37	chr19	18376994	18376994	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtgcatctggggtggggtCtttgccatcgcaggccccgg	18	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:18376994C>A	ENST00000600328.3	-	3	1549	c.1356G>T	c.(1354-1356)aaG>aaT	p.K452N	KIAA1683_ENST00000600359.3_Missense_Mutation_p.K406N|KIAA1683_ENST00000392413.4_Missense_Mutation_p.K452N			Q9H0B3	K1683_HUMAN	KIAA1683	452						mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.K452N(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGGGTGGGGTCTTTGCCATCG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	70	69					19																	18376994		2203	4300	6503	18237994	SO:0001583	missense	80726			AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1356G>T	19.37:g.18376994C>A	ENSP00000470780:p.Lys452Asn		18237994	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810503	0.50421	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.12774	2.74;2.68;2.65	4.48	2.34	0.29019	.	0.820986	0.10296	N	0.691675	T	0.13114	0.0318	L	0.47016	1.485	0.09310	N	1	P;P	0.41673	0.608;0.759	B;B	0.40565	0.142;0.333	T	0.19614	-1.0300	10	0.45353	T	0.12	-8.1874	5.9494	0.19237	0.0:0.7017:0.1937:0.1046	.	452;452	E9PDE0;Q9H0B3	.;K1683_HUMAN	N	452;452;406	ENSP00000376213:K452N;ENSP00000352774:K452N;ENSP00000404501:K406N	ENSP00000352774:K452N	K	-	3	2	KIAA1683	18237994	0.015000	0.18098	0.000000	0.03702	0.004000	0.04260	0.737000	0.26144	0.507000	0.28148	0.561000	0.74099	AAG		0.592	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			A	18376994	C	A	18376994	3	1	61	1	0	0	0	0	1	0	0	0	8272	912	32	2	2755	2	KIAA1683	19	18376994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	377842	18376994	40751989	10979	18964										
LRRC25	126364	broad.mit.edu	37	chr19	18507389	18507389	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctggccagagcagttgtCtcggcggatgtcgtgccagg	15	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:18507389C>A	ENST00000339007.3	-	1	1038	c.385G>T	c.(385-387)Gac>Tac	p.D129Y	LRRC25_ENST00000595840.1_Missense_Mutation_p.D129Y	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	129						integral component of membrane (GO:0016021)		p.D129Y(1)		endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						GAGCAGTTGTCTCGGCGGATG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											36	38	37					19																	18507389		2203	4300	6503	18368389	SO:0001583	missense	126364			AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.385G>T	19.37:g.18507389C>A	ENSP00000340983:p.Asp129Tyr		18368389	Q6IQ00|Q8N9A5	Missense_Mutation	SNP	ENST00000339007.3	37	CCDS12377.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.797743	0.50208	.	.	ENSG00000175489	ENST00000339007	T	0.32988	1.43	3.34	1.11	0.20524	.	0.635484	0.13682	N	0.370098	T	0.33469	0.0864	L	0.46157	1.445	0.09310	N	1	D	0.61697	0.99	P	0.53912	0.737	T	0.12760	-1.0535	10	0.62326	D	0.03	-8.7144	4.3488	0.11146	0.0:0.5802:0.0:0.4198	.	129	Q8N386	LRC25_HUMAN	Y	129	ENSP00000340983:D129Y	ENSP00000340983:D129Y	D	-	1	0	LRRC25	18368389	0.007000	0.16637	0.091000	0.20842	0.214000	0.24535	-0.178000	0.09782	0.320000	0.23234	0.491000	0.48974	GAC		0.662	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256		A	18507389	C	A	18507389	3	1	61	1	0	0	0	0	1	0	0	0	9009	913	32	2	540	2	LRRC25	19	18507389	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	130395	18507389	40621594	10980	18965										
ELL	8178	broad.mit.edu	37	chr19	18556072	18556072	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctgcaaaatctgccctcGagtagtctagaagaaaaaca	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:18556072G>A	ENST00000262809.4	-	11	1782	c.1711C>T	c.(1711-1713)Cga>Tga	p.R571*	ELL_ENST00000596124.3_Nonsense_Mutation_p.R438*|CTD-3137H5.1_ENST00000594590.2_RNA	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	571					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)	p.R571*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		ATCTGCCCTCGAGTAGTCTAG	0.488			T	MLL	AL																																		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	1	Substitution - Nonsense(1)	large_intestine(1)	19											171	182	178					19																	18556072		2203	4300	6503	18417072	SO:0001587	stop_gained	8178			U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23114	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 68"	600284	"chromosome 19 open reading frame 17"	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.1711C>T	19.37:g.18556072G>A	ENSP00000262809:p.Arg571*		18417072		Nonsense_Mutation	SNP	ENST00000262809.4	37	CCDS12380.1	.	.	.	.	.	.	.	.	.	.	G	39	7.631954	0.98399	.	.	ENSG00000105656	ENST00000262809	.	.	.	3.79	3.79	0.43588	.	0.143649	0.47455	U	0.000237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-7.2633	15.1944	0.73075	0.0:0.0:1.0:0.0	.	.	.	.	X	571	.	ENSP00000262809:R571X	R	-	1	2	ELL	18417072	1.000000	0.71417	0.102000	0.21198	0.901000	0.52897	5.135000	0.64777	2.133000	0.65898	0.282000	0.19409	CGA		0.488	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		A	18556072	G	A	18556072	4	1	61	1	0	0	0	0	0	1	0	0	5075	1066	37	1	162	1	ELL	19	18556072	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48683	18556072	40572911	10981	18966										
FKBP8	23770	broad.mit.edu	37	chr19	18650482	18650482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcccttgaccgggcggctcGaacctggcggccctgggacc	16	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:18650482G>A	ENST00000596558.2	-	3	450	c.341C>T	c.(340-342)tCg>tTg	p.S114L	FKBP8_ENST00000608443.1_Missense_Mutation_p.S114L|FKBP8_ENST00000597960.3_Missense_Mutation_p.S114L|FKBP8_ENST00000610101.1_Intron|FKBP8_ENST00000453489.2_Missense_Mutation_p.S143L|FKBP8_ENST00000222308.4_Missense_Mutation_p.S114L			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	114					apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.S114L(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						CGGGCGGCTCGAACCTGGCGG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											132	138	136					19																	18650482		2203	4300	6503	18511482	SO:0001583	missense	23770			L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"Tetratricopeptide (TTC) repeat domain containing"	3724	protein-coding gene	gene with protein product	"FK506-binding protein 8 (38kD)"	604840	"FK506-binding protein 8 (38kD)"			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.341C>T	19.37:g.18650482G>A	ENSP00000472302:p.Ser114Leu		18511482	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	37		.	.	.	.	.	.	.	.	.	.	G	12.88	2.070517	0.36566	.	.	ENSG00000105701	ENST00000222308;ENST00000453489	T;T	0.54479	0.57;0.57	3.5	3.5	0.40072	.	0.282502	0.31612	N	0.007353	T	0.57080	0.2029	L	0.49126	1.545	0.80722	D	1	D;D;D	0.89917	1.0;0.985;1.0	D;P;D	0.71656	0.974;0.591;0.939	T	0.56414	-0.7983	10	0.07482	T	0.82	-11.3653	8.5826	0.33637	0.0:0.0:0.6228:0.3772	.	143;114;114	B7Z6M0;Q14318;Q14318-2	.;FKBP8_HUMAN;.	L	114;143	ENSP00000222308:S114L;ENSP00000388891:S143L	ENSP00000222308:S114L	S	-	2	0	FKBP8	18511482	0.997000	0.39634	0.747000	0.31113	0.030000	0.12068	2.750000	0.47500	1.786000	0.52430	0.561000	0.74099	TCG		0.647	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		A	18650482	G	A	18650482	3	1	61	1	0	0	0	0	1	0	0	0	5933	1059	37	1	928	1	FKBP8	19	18650482	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94410	18650482	40478501	10982	18967										
UPF1	5976	broad.mit.edu	37	chr19	18974253	18974253	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcccttgttgcaggtatggCgtcatcattgtgggcaaccc	12	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:18974253C>T	ENST00000599848.1	+	19	2849	c.2640C>T	c.(2638-2640)ggC>ggT	p.G880G	UPF1_ENST00000262803.5_Silent_p.G869G			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	880					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.G869G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GCAGGTATGGCGTCATCATTG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											189	188	188					19																	18974253		2203	4300	6503	18835253	SO:0001819	synonymous_variant	5976			AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.2640C>T	19.37:g.18974253C>T			18835253	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																					0.587	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18974253	C	T	18974253	2	4	61	1	0	0	0	0	0	0	0	1	17043	755	27	1		1	UPF1	19	18974253	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	323771	18974253	40154730	10983	18968										
SFRS14	10147	broad.mit.edu	37	chr19	19135606	19135606	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaacaaagtggagtcttcGaagtttggaaacgcagcagg	12	8	1	0	rs570126557		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19135606G>A	ENST00000601879.1	-	3	1848	c.1551C>T	c.(1549-1551)ttC>ttT	p.F517F	SUGP2_ENST00000456085.2_Silent_p.F286F|SUGP2_ENST00000337018.6_Silent_p.F517F|SUGP2_ENST00000598202.1_5'Flank|SUGP2_ENST00000600377.1_Silent_p.F531F|SUGP2_ENST00000452918.2_Silent_p.F517F			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	517					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.F517F(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TGGAGTCTTCGAAGTTTGGAA	0.522													G|||	1	0.000199681	0	0.0014	5008	,	,		17896	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											106	108	107					19																	19135606		2203	4300	6503	18996606	SO:0001819	synonymous_variant	10147			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.1551C>T	19.37:g.19135606G>A			18996606	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	37	CCDS12392.1																																																																																				0.522	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		A	19135606	G	A	19135606	2	1	61	1	0	0	0	0	0	0	0	1	14207	1049	37	1		1	SFRS14	19	19135606	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161353	19135606	39993377	10984	18969										
SFRS14	10147	broad.mit.edu	37	chr19	19141819	19141819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactggcatccatgtgatatCgtttggctttttcttgtaat	8	8	1	1	rs201405749	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19141819C>T	ENST00000601879.1	-	2	359	c.62G>A	c.(61-63)cGa>cAa	p.R21Q	SUGP2_ENST00000456085.2_5'UTR|ARMC6_ENST00000392335.2_5'Flank|SUGP2_ENST00000337018.6_Missense_Mutation_p.R21Q|ARMC6_ENST00000535612.1_5'Flank|SUGP2_ENST00000598202.1_Intron|ARMC6_ENST00000269932.6_5'Flank|ARMC6_ENST00000546344.1_5'Flank|SUGP2_ENST00000600377.1_Missense_Mutation_p.R35Q|SUGP2_ENST00000452918.2_Missense_Mutation_p.R21Q			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	21					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R21Q(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CATGTGATATCGTTTGGCTTT	0.388													C|||	2	0.000399361	0	0.0029	5008	,	,		21141	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											279	253	262					19																	19141819		2203	4300	6503	19002819	SO:0001583	missense	10147			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.62G>A	19.37:g.19141819C>T	ENSP00000472286:p.Arg21Gln		19002819	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	16.42	3.118467	0.56505	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918	T;T;T	0.17691	2.26;2.26;2.26	5.28	5.28	0.74379	.	0.344244	0.23642	N	0.046013	T	0.26810	0.0656	L	0.27053	0.805	0.80722	D	1	P;D	0.89917	0.942;1.0	P;P	0.58331	0.489;0.837	T	0.02037	-1.1225	10	0.66056	D	0.02	-0.5393	17.4684	0.87639	0.0:1.0:0.0:0.0	.	21;21	A8K5G0;Q8IX01	.;SUGP2_HUMAN	Q	21	ENSP00000337926:R21Q;ENSP00000332373:R21Q;ENSP00000389380:R21Q	ENSP00000332373:R21Q	R	-	2	0	SUGP2	19002819	0.142000	0.22610	0.006000	0.13384	0.105000	0.19272	2.880000	0.48530	2.457000	0.83068	0.650000	0.86243	CGA		0.388	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		T	19141819	C	T	19141819	3	4	61	1	0	0	0	0	1	0	0	0	14207	884	31	1	3222	1	SFRS14	19	19141819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6213	19141819	39987164	10985	18970										
TMEM161A	54929	broad.mit.edu	37	chr19	19232453	19232453	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactgccagtcccacgcgGatagccagcttggccacagg	11	16	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19232453G>A	ENST00000162044.9	-	8	745	c.681C>T	c.(679-681)atC>atT	p.I227I	TMEM161A_ENST00000587583.2_Silent_p.I202I|TMEM161A_ENST00000450333.2_Silent_p.I124I	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	227					cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)		p.I227I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GTCCCACGCGGATAGCCAGCT	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	19											44	47	46					19																	19232453		2203	4300	6503	19093453	SO:0001819	synonymous_variant	54929			BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.681C>T	19.37:g.19232453G>A			19093453	B3KUE0|G5E9M6|Q7L2Y1	Silent	SNP	ENST00000162044.9	37	CCDS12393.1																																																																																				0.687	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814		A	19232453	G	A	19232453	2	1	61	1	0	0	0	0	0	0	0	1	16115	1164	41	3		3	TMEM161A	19	19232453	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	90634	19232453	39896530	10986	18971										
TM6SF2	53345	broad.mit.edu	37	chr19	19381886	19381886	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaagctgtagaccgccacGaaaagcagacccaggattag	11	11	0	2	rs371882936		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19381886G>A	ENST00000389363.4	-	2	216	c.144C>T	c.(142-144)ttC>ttT	p.F48F	TM6SF2_ENST00000586107.1_Intron|AC138430.4_ENST00000586064.2_RNA	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	48						integral component of membrane (GO:0016021)		p.F48F(1)		breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			AGACCGCCACGAAAAGCAGAC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4138		0,0,2069	98	100	100		144	-6.3	0	19		100	1,8413		0,1,4206	no	coding-synonymous	TM6SF2	NM_001001524.2		0,1,6275	AA,AG,GG		0.0119,0.0,0.0080		48/378	19381886	1,12551	2069	4207	6276	19242886	SO:0001819	synonymous_variant	53345			AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.144C>T	19.37:g.19381886G>A			19242886	Q0IJ64	Silent	SNP	ENST00000389363.4	37	CCDS42528.1																																																																																				0.602	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510		A	19381886	G	A	19381886	2	1	61	1	0	0	0	0	0	0	0	1	16012	1049	37	1		1	TM6SF2	19	19381886	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	149433	19381886	39747097	10987	18972										
ZNF101	94039	broad.mit.edu	37	chr19	19788768	19788768	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatctctacagagatgtgacGctggaaaccttcaggaacct	9	10	2	2	rs150949920	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19788768G>A	ENST00000592502.1	+	2	209	c.99G>A	c.(97-99)acG>acA	p.T33T	ZNF101_ENST00000415784.2_De_novo_Start_InFrame|ZNF101_ENST00000444249.2_Silent_p.T33T			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	33	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T33T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						GAGATGTGACGCTGGAAACCT	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		5,4401	9.9+/-24.2	0,5,2198	112	110	110		99	0.2	0.3	19	dbSNP_134	110	0,8600		0,0,4300	no	coding-synonymous	ZNF101	NM_033204.2		0,5,6498	AA,AG,GG		0.0,0.1135,0.0384		33/437	19788768	5,13001	2203	4300	6503	19649768	SO:0001819	synonymous_variant	94039			AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.99G>A	19.37:g.19788768G>A			19649768	C9JU83|Q0VDG9	Silent	SNP	ENST00000592502.1	37	CCDS32971.1																																																																																				0.502	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		A	19788768	G	A	19788768	2	1	61	1	0	0	0	0	0	0	0	1	17753	1074	38	1		1	ZNF101	19	19788768	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	406882	19788768	39340215	10988	18973										
ZNF101	94039	broad.mit.edu	37	chr19	19790292	19790292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgcacagtaacaccaactcGaaagagaccttatgaatgca	8	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19790292G>A	ENST00000592502.1	+	4	604	c.494G>A	c.(493-495)cGa>cAa	p.R165Q	ZNF101_ENST00000415784.2_Missense_Mutation_p.R45Q|ZNF101_ENST00000444249.2_3'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R165Q(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						ACACCAACTCGAAAGAGACCT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	19											96	99	98					19																	19790292		2203	4300	6503	19651292	SO:0001583	missense	94039			AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.494G>A	19.37:g.19790292G>A	ENSP00000468049:p.Arg165Gln		19651292	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	.	.	.	.	.	.	.	.	.	.	G	3.372	-0.128248	0.06753	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.08008	3.14;3.14	0.235	-0.47	0.12131	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.09310	N	0.999991	B	0.33044	0.395	B	0.18871	0.023	T	0.34725	-0.9817	9	0.72032	D	0.01	.	3.4864	0.07620	0.2367:0.2566:0.5067:0.0	.	165	Q8IZC7	ZN101_HUMAN	Q	165;165;45	ENSP00000319716:R165Q;ENSP00000400952:R45Q	ENSP00000319716:R165Q	R	+	2	0	ZNF101	19651292	0.000000	0.05858	0.110000	0.21437	0.111000	0.19643	-1.337000	0.02657	-2.173000	0.00773	-2.186000	0.00314	CGA		0.468	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		A	19790292	G	A	19790292	3	1	61	1	0	0	0	0	1	0	0	0	17753	1058	37	1	508	1	ZNF101	19	19790292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1524	19790292	39338691	10989	18974										
ZNF14	7561	broad.mit.edu	37	chr19	19822283	19822283	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgagacctttcatgaattcGaacagaacttgaaaatctga	8	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19822283G>A	ENST00000344099.3	-	4	1945	c.1807C>T	c.(1807-1809)Cga>Tga	p.R603*		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R603*(2)		breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TCATGAATTCGAACAGAACTT	0.408																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											74	73	73					19																	19822283		2203	4300	6503	19683283	SO:0001587	stop_gained	7561			AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.1807C>T	19.37:g.19822283G>A	ENSP00000340514:p.Arg603*		19683283	B9EGA4|Q9ULZ5	Nonsense_Mutation	SNP	ENST00000344099.3	37	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	G	37	6.163952	0.97338	.	.	ENSG00000105708	ENST00000344099	.	.	.	1.24	0.165	0.14995	.	.	.	.	.	.	.	.	.	.	.	0.49483	D	0.999792	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	5.2779	0.15659	0.2191:0.0:0.7809:0.0	.	.	.	.	X	603	.	ENSP00000340514:R603X	R	-	1	2	ZNF14	19683283	0.000000	0.05858	0.001000	0.08648	0.995000	0.86356	0.319000	0.19522	0.083000	0.17047	0.467000	0.42956	CGA		0.408	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		A	19822283	G	A	19822283	4	1	61	1	0	0	0	0	0	1	0	0	17767	1066	37	1	125	1	ZNF14	19	19822283	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31991	19822283	39306700	10990	18975										
ZNF14	7561	broad.mit.edu	37	chr19	19822535	19822535	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaattttttcatgttctcGaagggaacttgaaaaactga	9	5	2	3	rs146205130		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:19822535G>A	ENST00000344099.3	-	4	1693	c.1555C>T	c.(1555-1557)Cga>Tga	p.R519*		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	519					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R519*(1)		breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TCATGTTCTCGAAGGGAACTT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	19						G	stop/ARG	0,4406		0,0,2203	101	98	99		1555	-1.2	0	19	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	ZNF14	NM_021030.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		519/643	19822535	1,13005	2203	4300	6503	19683535	SO:0001587	stop_gained	7561			AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.1555C>T	19.37:g.19822535G>A	ENSP00000340514:p.Arg519*		19683535	B9EGA4|Q9ULZ5	Nonsense_Mutation	SNP	ENST00000344099.3	37	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	G	36	5.837333	0.97009	0.0	1.16E-4	ENSG00000105708	ENST00000344099	.	.	.	1.8	-1.2	0.09554	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.999977	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	2.6979	0.05140	0.3723:0.2562:0.3715:0.0	.	.	.	.	X	519	.	ENSP00000340514:R519X	R	-	1	2	ZNF14	19683535	0.000000	0.05858	0.001000	0.08648	0.967000	0.64934	-3.324000	0.00512	0.081000	0.16988	0.467000	0.42956	CGA		0.408	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		A	19822535	G	A	19822535	4	1	61	1	0	0	0	0	0	1	0	0	17767	1066	37	1	377	1	ZNF14	19	19822535	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252	19822535	39306448	10991	18976										
ZNF253	56242	broad.mit.edu	37	chr19	20002857	20002857	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggcaaagccttcaaccgAtccacagaccttactacaca	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:20002857A>C	ENST00000589717.1	+	4	893	c.801A>C	c.(799-801)cgA>cgC	p.R267R	ZNF253_ENST00000355650.4_Silent_p.R191R|AC011477.1_ENST00000578823.1_RNA|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	267				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R267R(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTTCAACCGATCCACAGACC	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	19											52	55	54					19																	20002857		2174	4283	6457	19863857	SO:0001819	synonymous_variant	56242			AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.801A>C	19.37:g.20002857A>C			19863857	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																				0.418	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		C	20002857	A	C	20002857	2	2	61	1	0	0	0	0	0	0	0	1	17836	320	12	4		4	ZNF253	19	20002857	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	180322	20002857	39126126	10992	18977										
ZNF93	81931	broad.mit.edu	37	chr19	20044592	20044592	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgacacttactaaacataaGaaaattcatactggagagaa	6	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:20044592G>T	ENST00000343769.5	+	4	856	c.828G>T	c.(826-828)aaG>aaT	p.K276N	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.K276N(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						CTAAACATAAGAAAATTCATA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											38	41	40					19																	20044592		2203	4298	6501	19905592	SO:0001583	missense	81931			M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"Zinc fingers, C2H2-type", "-"	13169	protein-coding gene	gene with protein product		603975	"zinc finger protein 505", "zinc finger protein 93 (HTF34)"	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.828G>T	19.37:g.20044592G>T	ENSP00000342002:p.Lys276Asn		19905592	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	.	.	.	.	.	.	.	.	.	.	g	11.48	1.651245	0.29336	.	.	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.07567	3.18	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15609	0.0376	L	0.48986	1.54	0.23003	N	0.998442	D	0.56035	0.974	P	0.57846	0.828	T	0.10965	-1.0607	9	0.66056	D	0.02	.	6.9971	0.24789	0.0:0.0:1.0:0.0	.	276	P35789	ZNF93_HUMAN	N	276	ENSP00000342002:K276N	ENSP00000342002:K276N	K	+	3	2	ZNF93	19905592	0.001000	0.12720	0.064000	0.19789	0.064000	0.16182	0.774000	0.26675	0.192000	0.20272	0.195000	0.17529	AAG		0.358	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044592	G	T	20044592	3	4	61	1	0	0	0	0	1	0	0	0	18241	933	33	2	842	2	ZNF93	19	20044592	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	41735	20044592	39084391	10993	18978										
ZNF486	90649	broad.mit.edu	37	chr19	20308252	20308252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaaatgtgaagaatgtggcAaagtctttaagtacttctct	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:20308252A>G	ENST00000335117.8	+	4	790	c.733A>G	c.(733-735)Aaa>Gaa	p.K245E	CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K239E(1)|p.K245E(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AGAATGTGGCAAAGTCTTTAA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	19											36	39	38					19																	20308252		2147	4271	6418	20169252	SO:0001583	missense	90649			BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"Zinc fingers, C2H2-type", "-"	20807	protein-coding gene	gene with protein product			"KRAB domain only 2"	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.733A>G	19.37:g.20308252A>G	ENSP00000335042:p.Lys245Glu		20169252	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	a	10.37	1.330175	0.24167	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.35973	1.28	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38401	0.1039	M	0.75884	2.315	0.26580	N	0.973395	B	0.22480	0.07	B	0.31686	0.134	T	0.46456	-0.9190	9	0.87932	D	0	.	5.4501	0.16560	1.0:0.0:0.0:0.0	.	245	Q96H40	ZN486_HUMAN	E	284;245	ENSP00000335042:K245E	ENSP00000335042:K245E	K	+	1	0	ZNF486	20169252	1.000000	0.71417	0.018000	0.16275	0.018000	0.09664	3.517000	0.53443	0.166000	0.19597	0.164000	0.16699	AAA		0.388	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		G	20308252	A	G	20308252	3	3	61	1	0	0	0	0	1	0	0	0	17978	131	5	4	747	4	ZNF486	19	20308252	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	263660	20308252	38820731	10994	18979										
ZNF626	199777	broad.mit.edu	37	chr19	20807349	20807349	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctctccagtatgaattCtcctatgtgtagtaaggatt	7	7	2	1	rs4809075	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:20807349C>A	ENST00000601440.1	-	4	1480	c.1334G>T	c.(1333-1335)aGa>aTa	p.R445I	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R445I(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						AGTATGAATTCTCCTATGTGT	0.378													c|||	3	0.000599042	0	0	5008	,	,		13761	0.002		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											64	57	59					19																	20807349		2109	4256	6365	20599189	SO:0001583	missense	199777			BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1334G>T	19.37:g.20807349C>A	ENSP00000469958:p.Arg445Ile		20599189	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	0.011	-1.710491	0.00712	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	0.832	-1.66	0.08265	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41534	0.1163	L	0.43598	1.365	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.32322	-0.9911	8	0.32370	T	0.25	.	4.2599	0.10735	0.215:0.5842:0.0:0.2008	rs4809075	445	Q68DY1	ZN626_HUMAN	I	445;369;445	.	ENSP00000445201:R445I	R	-	2	0	ZNF626	20599189	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.114000	0.10757	-3.249000	0.00205	-3.357000	0.00042	AGA		0.378	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		A	20807349	C	A	20807349	3	1	61	1	0	0	0	0	1	0	0	0	18089	913	32	2	256	2	ZNF626	19	20807349	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	499097	20807349	38321634	10995	18980										
ZNF85	7639	broad.mit.edu	37	chr19	21132661	21132661	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttactgaacataagaaaatTcatactggagagaaacccta	6	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21132661T>G	ENST00000328178.8	+	4	1454	c.1341T>G	c.(1339-1341)atT>atG	p.I447M	ZNF85_ENST00000601023.1_Missense_Mutation_p.I388M|ZNF85_ENST00000345030.6_Missense_Mutation_p.I414M	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	447					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.I447M(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						ATAAGAAAATTCATACTGGAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	19											20	22	22					19																	21132661		2197	4287	6484	20924501	SO:0001583	missense	7639			U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1341T>G	19.37:g.21132661T>G	ENSP00000329793:p.Ile447Met		20924501	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	3.852	-0.031637	0.07543	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.07800	3.16;3.16	1.35	0.13	0.14746	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.31371	0.925	0.80722	D	1	D;D;D	0.89917	0.999;0.991;1.0	D;D;D	0.91635	0.978;0.986;0.999	T	0.36456	-0.9747	9	0.72032	D	0.01	.	1.8702	0.03207	0.2747:0.347:0.0:0.3783	.	414;388;447	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	M	447;414;322	ENSP00000329793:I447M;ENSP00000342340:I414M	ENSP00000329793:I447M	I	+	3	3	ZNF85	20924501	0.014000	0.17966	0.026000	0.17262	0.031000	0.12232	-0.312000	0.08113	-0.289000	0.09038	-0.728000	0.03583	ATT		0.323	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		G	21132661	T	G	21132661	3	3	61	1	0	0	0	0	1	0	0	0	18232	1771	62	4	1355	4	ZNF85	19	21132661	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	325312	21132661	37996322	10996	18981										
ZNF430	80264	broad.mit.edu	37	chr19	21240265	21240265	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggcaaagctttttaccGattctcataccttactaaac	5	10	1	0	rs199515644	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21240265G>A	ENST00000261560.5	+	5	1332	c.1151G>A	c.(1150-1152)cGa>cAa	p.R384Q	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	384					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R384Q(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						GCTTTTTACCGATTCTCATAC	0.368													.|||	2	0.000399361	0.0015	0	5008	,	,		21260	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											30	34	32					19																	21240265		2190	4289	6479	21032105	SO:0001583	missense	80264			AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1151G>A	19.37:g.21240265G>A	ENSP00000261560:p.Arg384Gln		21032105	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	37	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.386331	0.00202	.	.	ENSG00000118620	ENST00000261560	T	0.35421	1.31	1.05	-2.11	0.07187	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09335	0.0230	N	0.05608	-0.01	0.09310	N	1	D;B	0.59767	0.986;0.146	B;B	0.31290	0.127;0.007	T	0.30268	-0.9984	9	0.02654	T	1	.	5.9345	0.19158	0.309:0.0:0.691:0.0	.	383;384	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	Q	384	ENSP00000261560:R384Q	ENSP00000261560:R384Q	R	+	2	0	ZNF430	21032105	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.205000	0.00274	-0.657000	0.05373	-0.672000	0.03802	CGA		0.368	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		A	21240265	G	A	21240265	3	1	61	1	0	0	0	0	1	0	0	0	17943	1058	37	1	1169	1	ZNF430	19	21240265	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	107604	21240265	37888718	10997	18982										
ZNF714	148206	broad.mit.edu	37	chr19	21300700	21300700	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttttaaccaatcctcaaaCcttaccaaacataagataat	2	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21300700C>A	ENST00000596143.1	+	5	1555	c.1230C>A	c.(1228-1230)aaC>aaA	p.N410K	ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N410K(1)		endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AATCCTCAAACCTTACCAAAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19																																								21092540	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1230C>A	19.37:g.21300700C>A	ENSP00000472368:p.Asn410Lys		21092540	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.010	-1.754315	0.00663	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17109	0.0411	N	0.25890	0.77	0.09310	N	1	B;P;P	0.44309	0.059;0.677;0.832	B;B;B	0.41946	0.02;0.157;0.371	T	0.10042	-1.0647	8	0.10902	T	0.67	.	4.5619	0.12165	0.0:0.7647:0.0:0.2353	.	411;410;411	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	K	410	.	ENSP00000291770:N410K	N	+	3	2	ZNF714	21092540	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-1.694000	0.01915	0.459000	0.27016	0.462000	0.41574	AAC		0.343	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21300700	C	A	21300700	3	1	61	1	0	0	0	0	1	0	0	0	18157	506	18	2	1240	2	ZNF714	19	21300700	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60435	21300700	37828283	10998	18983										
ZNF431	170959	broad.mit.edu	37	chr19	21349173	21349173	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggatgtggccatagaattCtctctggaggagtgggaatg	16	5	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21349173C>A	ENST00000311048.7	+	3	276	c.132C>A	c.(130-132)ttC>ttA	p.F44L	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000599296.1_Missense_Mutation_p.F44L|ZNF431_ENST00000600692.1_Missense_Mutation_p.F44L	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	44	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)	p.F44L(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						CCATAGAATTCTCTCTGGAGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											93	100	98					19																	21349173		2203	4300	6503	21141013	SO:0001583	missense	170959			AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"Zinc fingers, C2H2-type", "-"	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.132C>A	19.37:g.21349173C>A	ENSP00000308578:p.Phe44Leu		21141013	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	37	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	10.14	1.269083	0.23221	.	.	ENSG00000196705	ENST00000311048	T	0.12879	2.64	0.659	0.659	0.17861	Krueppel-associated box (4);	.	.	.	.	T	0.36082	0.0954	M	0.92738	3.34	0.19775	N	0.999953	P	0.46784	0.884	P	0.55011	0.766	T	0.12091	-1.0561	8	0.62326	D	0.03	.	.	.	.	.	44	Q8TF32	ZN431_HUMAN	L	44	ENSP00000308578:F44L	ENSP00000308578:F44L	F	+	3	2	ZNF431	21141013	0.569000	0.26643	0.420000	0.26596	0.177000	0.22998	0.848000	0.27710	0.608000	0.30000	0.455000	0.32223	TTC		0.398	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098		A	21349173	C	A	21349173	3	1	61	1	0	0	0	0	1	0	0	0	17944	912	32	2	142	2	ZNF431	19	21349173	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48473	21349173	37779810	10999	18984										
ZNF708	7562	broad.mit.edu	37	chr19	21477463	21477463	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatatccacattttccatatCttctcagtatcacttgttgg	5	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21477463C>T	ENST00000356929.3	-	4	502	c.305G>A	c.(304-306)aGa>aAa	p.R102K		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	38					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R102K(1)		breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TTTTCCATATCTTCTCAGTAT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											102	97	99					19																	21477463		2203	4300	6503	21269303	SO:0001583	missense	7562			X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"Zinc fingers, C2H2-type", "-"	12945	protein-coding gene	gene with protein product			"zinc finger protein 15-like 1 (KOX 8)", "zinc finger protein 708", "zinc finger protein 708 (KOX8)"	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.305G>A	19.37:g.21477463C>T	ENSP00000349401:p.Arg102Lys		21269303	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	4.934	0.173513	0.09391	.	.	ENSG00000182141	ENST00000356929	T	0.06294	3.32	0.449	0.449	0.16619	.	.	.	.	.	T	0.04952	0.0133	L	0.35341	1.055	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.42716	-0.9435	8	0.25751	T	0.34	.	.	.	.	.	102	P17019	ZN708_HUMAN	K	102	ENSP00000349401:R102K	ENSP00000349401:R102K	R	-	2	0	ZNF708	21269303	0.000000	0.05858	0.045000	0.18777	0.043000	0.13939	-0.122000	0.10627	0.475000	0.27415	0.478000	0.44815	AGA		0.373	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		T	21477463	C	T	21477463	3	4	61	1	0	0	0	0	1	0	0	0	18151	913	32	3	1390	3	ZNF708	19	21477463	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128290	21477463	37651520	11000	18985										
ZNF493	284443	broad.mit.edu	37	chr19	21606093	21606093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattagagagaattcttaccGatgtgaagaatgtggcaaag	11	4	1	4	rs145782852	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21606093G>A	ENST00000355504.4	+	2	514	c.248G>A	c.(247-249)cGa>cAa	p.R83Q	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.R211Q	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	83					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R83Q(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AATTCTTACCGATGTGAAGAA	0.353													.|||	2	0.000399361	0	0	5008	,	,		18444	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	19						G	GLN/ARG,GLN/ARG	0,4402		0,0,2201	53	59	57		632,248	-0.5	0.1	19	dbSNP_134	57	7,8587		0,7,4290	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	43,43	0,7,6491	AA,AG,GG		0.0815,0.0,0.0539	benign,benign	211/775,83/647	21606093	7,12989	2201	4297	6498	21397933	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.248G>A	19.37:g.21606093G>A	ENSP00000347691:p.Arg83Gln		21397933	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	6.628	0.484340	0.12641	0.0	8.15E-4	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.36878	1.23;1.23	1.05	-0.455	0.12193	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10337	0.0253	N	0.01188	-0.97	0.09310	N	1	B;B	0.23891	0.014;0.093	B;B	0.12156	0.007;0.005	T	0.21075	-1.0256	9	0.31617	T	0.26	.	2.6681	0.05058	0.5302:0.2697:0.2:0.0	.	83;211	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	Q	211;83	ENSP00000376110:R211Q;ENSP00000347691:R83Q	ENSP00000347691:R83Q	R	+	2	0	ZNF493	21397933	0.012000	0.17670	0.068000	0.19968	0.067000	0.16453	0.061000	0.14366	-0.488000	0.06726	-0.501000	0.04562	CGA		0.353	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		A	21606093	G	A	21606093	3	1	61	1	0	0	0	0	1	0	0	0	17983	1058	37	1	709	1	ZNF493	19	21606093	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128630	21606093	37522890	11001	18986										
ZNF493	284443	broad.mit.edu	37	chr19	21607573	21607573	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaaccttaatacgcataaGataattcatactggagagaa	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21607573G>T	ENST00000355504.4	+	2	1994	c.1728G>T	c.(1726-1728)aaG>aaT	p.K576N	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.K704N	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	576					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K576N(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						ATACGCATAAGATAATTCATA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	19											32	34	34					19																	21607573		2201	4299	6500	21399413	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1728G>T	19.37:g.21607573G>T	ENSP00000347691:p.Lys576Asn		21399413	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	11.71	1.718329	0.30503	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.18657	2.2;2.2	1.02	-0.84	0.10755	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18299	0.0439	L	0.49640	1.575	0.58432	D	0.999991	P;P	0.42039	0.769;0.722	B;B	0.42214	0.38;0.33	T	0.06991	-1.0796	9	0.72032	D	0.01	.	5.3138	0.15845	0.4001:0.0:0.5999:0.0	.	576;704	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	N	704;576	ENSP00000376110:K704N;ENSP00000347691:K576N	ENSP00000347691:K576N	K	+	3	2	ZNF493	21399413	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.334000	0.19787	-0.408000	0.07565	-0.396000	0.06452	AAG		0.338	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21607573	G	T	21607573	3	4	61	1	0	0	0	0	1	0	0	0	17983	933	33	2	2189	2	ZNF493	19	21607573	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1480	21607573	37521410	11002	18987										
ZNF429	353088	broad.mit.edu	37	chr19	21719238	21719238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgattgtaagctatacaaagGaggttataatggacttaacc	9	5	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21719238G>T	ENST00000358491.4	+	4	591	c.383G>T	c.(382-384)gGa>gTa	p.G128V	ZNF429_ENST00000594022.1_3'UTR|ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	128					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G128V(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						CTATACAAAGGAGGTTATAAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	76	74					19																	21719238		2148	4265	6413	21511078	SO:0001583	missense	353088			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.383G>T	19.37:g.21719238G>T	ENSP00000351280:p.Gly128Val		21511078	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	37	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	0.459	-0.890046	0.02511	.	.	ENSG00000197013	ENST00000358491	T	0.06371	3.31	0.614	-0.595	0.11660	.	.	.	.	.	T	0.06600	0.0169	M	0.71036	2.16	0.09310	N	0.999999	B	0.11235	0.004	B	0.08055	0.003	T	0.47328	-0.9126	9	0.13108	T	0.6	.	3.6947	0.08360	0.6282:0.0:0.3718:0.0	.	128	Q86V71	ZN429_HUMAN	V	128	ENSP00000351280:G128V	ENSP00000351280:G128V	G	+	2	0	ZNF429	21511078	0.000000	0.05858	0.018000	0.16275	0.028000	0.11728	-2.283000	0.01155	-0.242000	0.09667	0.298000	0.19748	GGA		0.328	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		T	21719238	G	T	21719238	3	4	61	1	0	0	0	0	1	0	0	0	17941	1174	41	2	397	2	ZNF429	19	21719238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111665	21719238	37409745	11003	18988										
ZNF429	353088	broad.mit.edu	37	chr19	21720012	21720012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagtcttcaagacttactcGacataaaaaaattcatactg	4	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21720012G>A	ENST00000358491.4	+	4	1365	c.1157G>A	c.(1156-1158)cGa>cAa	p.R386Q	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	386					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R386Q(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						AGACTTACTCGACATAAAAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	19											40	46	44					19																	21720012		2022	4220	6242	21511852	SO:0001583	missense	353088			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1157G>A	19.37:g.21720012G>A	ENSP00000351280:p.Arg386Gln		21511852	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	37	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	0.556	-0.847124	0.02651	.	.	ENSG00000197013	ENST00000358491	T	0.26223	1.75	0.185	0.185	0.15096	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10637	0.0260	N	0.16478	0.41	0.09310	N	1	B	0.25105	0.118	B	0.13407	0.009	T	0.34625	-0.9821	9	0.07482	T	0.82	.	4.7056	0.12848	0.0:0.0:0.64:0.3599	.	386	Q86V71	ZN429_HUMAN	Q	386	ENSP00000351280:R386Q	ENSP00000351280:R386Q	R	+	2	0	ZNF429	21511852	0.000000	0.05858	0.099000	0.21106	0.100000	0.18952	-10.014000	0.00008	0.293000	0.22520	0.298000	0.19748	CGA		0.353	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		A	21720012	G	A	21720012	3	1	61	1	0	0	0	0	1	0	0	0	17941	1058	37	1	1171	1	ZNF429	19	21720012	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	774	21720012	37408971	11004	18989										
ZNF43	7594	broad.mit.edu	37	chr19	21991570	21991570	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcacatttgtagggtttCtctccagtatgagttaactt	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:21991570C>A	ENST00000354959.4	-	4	1438	c.1269G>T	c.(1267-1269)gaG>gaT	p.E423D	ZNF43_ENST00000594012.1_Missense_Mutation_p.E417D|ZNF43_ENST00000598381.1_Missense_Mutation_p.E417D|ZNF43_ENST00000595461.1_Missense_Mutation_p.E417D	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E423D(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TGTAGGGTTTCTCTCCAGTAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	68	67					19																	21991570		2191	4291	6482	21783410	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.1269G>T	19.37:g.21991570C>A	ENSP00000347045:p.Glu423Asp		21783410	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745200	0.49151	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.26810	1.71	1.75	0.656	0.17844	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20007	0.0481	L	0.35644	1.08	0.26934	N	0.966396	B	0.12013	0.005	B	0.24541	0.054	T	0.30119	-0.9989	9	0.72032	D	0.01	.	7.4601	0.27289	0.0:0.8305:0.0:0.1695	.	423	P17038	ZNF43_HUMAN	D	422;423	ENSP00000347045:E423D	ENSP00000347045:E423D	E	-	3	2	ZNF43	21783410	0.023000	0.18921	0.013000	0.15412	0.090000	0.18270	0.185000	0.16958	0.972000	0.38314	0.298000	0.19748	GAG		0.378	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		A	21991570	C	A	21991570	3	1	61	1	0	0	0	0	1	0	0	0	17942	912	32	2	1164	2	ZNF43	19	21991570	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	271558	21991570	37137413	11005	18990										
ZNF208	7757	broad.mit.edu	37	chr19	22154422	22154422	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcacatttgtagggtttCtctccagtatgaattacctt	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22154422C>A	ENST00000397126.4	-	4	3562	c.3414G>T	c.(3412-3414)gaG>gaT	p.E1138D	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1010D(2)|p.E1138D(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TGTAGGGTTTCTCTCCAGTAT	0.368																																																3	Substitution - Missense(3)	large_intestine(3)	19											40	43	42					19																	22154422		2071	4203	6274	21946262	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.3414G>T	19.37:g.22154422C>A	ENSP00000380315:p.Glu1138Asp		21946262		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	9.262	1.043474	0.19748	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.26810	1.71	2.59	-1.48	0.08745	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17577	0.0422	.	.	.	0.21220	N	0.999752	B	0.16166	0.016	B	0.18871	0.023	T	0.25398	-1.0133	8	0.87932	D	0	.	5.0041	0.14279	0.0:0.6162:0.1689:0.2149	.	1010	O43345	ZN208_HUMAN	D	1138;1010	ENSP00000380315:E1138D	ENSP00000380315:E1138D	E	-	3	2	ZNF208	21946262	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.054000	0.11826	-0.834000	0.04239	-1.012000	0.02466	GAG		0.368	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22154422	C	A	22154422	3	1	61	1	0	0	0	0	1	0	0	0	17805	912	32	2	432	2	ZNF208	19	22154422	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162852	22154422	36974561	11006	18991										
ZNF208	7757	broad.mit.edu	37	chr19	22155026	22155026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttctctccagcatgagttTtcttatgtttactaaagact	5	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22155026T>C	ENST00000397126.4	-	4	2958	c.2810A>G	c.(2809-2811)aAa>aGa	p.K937R	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	937					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K837R(2)|p.K937R(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGCATGAGTTTTCTTATGTTT	0.373																																																3	Substitution - Missense(3)	large_intestine(3)	19											47	49	48					19																	22155026		2022	4198	6220	21946866	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2810A>G	19.37:g.22155026T>C	ENSP00000380315:p.Lys937Arg		21946866		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	0.025	-1.380034	0.01204	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.17213	2.29	2.84	-5.68	0.02436	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04952	0.0133	.	.	.	0.09310	N	1	B	0.24368	0.102	B	0.30401	0.115	T	0.34700	-0.9818	8	0.02654	T	1	.	1.7673	0.03004	0.1303:0.433:0.1296:0.3071	.	837	O43345	ZN208_HUMAN	R	937;837	ENSP00000380315:K937R	ENSP00000380315:K937R	K	-	2	0	ZNF208	21946866	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-5.802000	0.00097	-1.451000	0.01933	0.102000	0.15555	AAA		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22155026	T	C	22155026	3	2	61	1	0	0	0	0	1	0	0	0	17805	1841	64	4	1036	4	ZNF208	19	22155026	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	604	22155026	36973957	11007	18992										
ZNF208	7757	broad.mit.edu	37	chr19	22155357	22155357	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagggcttttctccagcatGaattgccttatgtgtagtaa	10	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22155357G>T	ENST00000397126.4	-	4	2627	c.2479C>A	c.(2479-2481)Cat>Aat	p.H827N	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	827					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.H727N(2)|p.H827N(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TCTCCAGCATGAATTGCCTTA	0.363																																																3	Substitution - Missense(3)	large_intestine(3)	19											64	70	68					19																	22155357		2089	4251	6340	21947197	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2479C>A	19.37:g.22155357G>T	ENSP00000380315:p.His827Asn		21947197		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829434	0.32329	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.67345	-0.26	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.80210	0.4581	.	.	.	0.34988	D	0.754744	D	0.64830	0.994	D	0.87578	0.998	D	0.85824	0.1387	8	0.87932	D	0	.	11.941	0.52901	0.0:0.0:1.0:0.0	.	727	O43345	ZN208_HUMAN	N	827;727	ENSP00000380315:H827N	ENSP00000380315:H827N	H	-	1	0	ZNF208	21947197	1.000000	0.71417	0.328000	0.25416	0.102000	0.19082	5.134000	0.64770	1.024000	0.39682	0.289000	0.19496	CAT		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155357	G	T	22155357	3	4	61	1	0	0	0	0	1	0	0	0	17805	1290	45	2	1367	2	ZNF208	19	22155357	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	331	22155357	36973626	11008	18993										
ZNF208	7757	broad.mit.edu	37	chr19	22155626	22155626	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaattaccttatgtttaGtaaggactgagaatgtacta	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22155626G>T	ENST00000397126.4	-	4	2358	c.2210C>A	c.(2209-2211)aCt>aAt	p.T737N	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	737					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.T637N(2)|p.T737N(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CTTATGTTTAGTAAGGACTGA	0.368																																																3	Substitution - Missense(3)	large_intestine(3)	19											53	57	56					19																	22155626		2101	4244	6345	21947466	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2210C>A	19.37:g.22155626G>T	ENSP00000380315:p.Thr737Asn		21947466		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	3.822	-0.037510	0.07497	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.35973	1.28	2.13	-1.83	0.07833	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40862	0.1134	.	.	.	0.09310	N	1	D	0.61080	0.989	D	0.69307	0.963	T	0.39820	-0.9595	8	0.15952	T	0.53	.	6.5937	0.22661	0.686:0.0:0.314:0.0	.	637	O43345	ZN208_HUMAN	N	737;637	ENSP00000380315:T737N	ENSP00000380315:T737N	T	-	2	0	ZNF208	21947466	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-4.383000	0.00243	-0.074000	0.12820	0.280000	0.19369	ACT		0.368	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155626	G	T	22155626	3	4	61	1	0	0	0	0	1	0	0	0	17805	1029	36	2	1636	2	ZNF208	19	22155626	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	269	22155626	36973357	11009	18994										
ZNF208	7757	broad.mit.edu	37	chr19	22155721	22155721	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgttccataaggtttgaGgaccagttgaaagctttgcc	10	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22155721G>T	ENST00000397126.4	-	4	2263	c.2115C>A	c.(2113-2115)tcC>tcA	p.S705S	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	705					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S605S(2)|p.S705S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TAAGGTTTGAGGACCAGTTGA	0.368																																																3	Substitution - coding silent(3)	large_intestine(3)	19											36	38	37					19																	22155721		2008	4197	6205	21947561	SO:0001819	synonymous_variant	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2115C>A	19.37:g.22155721G>T			21947561		Silent	SNP	ENST00000397126.4	37	CCDS54240.1																																																																																				0.368	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155721	G	T	22155721	2	4	61	1	0	0	0	0	0	0	0	1	17805	987	35	2		2	ZNF208	19	22155721	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95	22155721	36973262	11010	18995										
ZNF208	7757	broad.mit.edu	37	chr19	22157217	22157217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccagttaaaagctttgcCaccttcttcacatttgtagg	8	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22157217C>T	ENST00000397126.4	-	4	767	c.619G>A	c.(619-621)Ggc>Agc	p.G207S	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G207S(3)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AAAGCTTTGCCACCTTCTTCA	0.363																																																3	Substitution - Missense(3)	large_intestine(3)	19											61	65	63					19																	22157217		2036	4217	6253	21949057	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.619G>A	19.37:g.22157217C>T	ENSP00000380315:p.Gly207Ser		21949057		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980062	0.53827	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.21734	1.99	2.75	2.75	0.32379	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41673	0.1169	.	.	.	0.25960	N	0.982638	D	0.89917	1.0	D	0.79784	0.993	T	0.11036	-1.0604	8	0.54805	T	0.06	.	10.3396	0.43870	0.0:1.0:0.0:0.0	.	207	O43345	ZN208_HUMAN	S	207	ENSP00000380315:G207S	ENSP00000380315:G207S	G	-	1	0	ZNF208	21949057	0.176000	0.23096	0.008000	0.14137	0.028000	0.11728	2.392000	0.44433	1.079000	0.41038	0.306000	0.20318	GGC		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22157217	C	T	22157217	3	4	61	1	0	0	0	0	1	0	0	0	17805	594	21	3	3227	3	ZNF208	19	22157217	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1496	22157217	36971766	11011	18996										
ZNF257	113835	broad.mit.edu	37	chr19	22271314	22271314	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggtaattcatactagagaGaaaccctacaaatgtgaaga	8	6	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22271314G>T	ENST00000594947.1	+	4	906	c.762G>T	c.(760-762)gaG>gaT	p.E254D		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	254					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E254D(2)		haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATACTAGAGAGAAACCCTACA	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											38	41	40					19																	22271314		2115	4259	6374	22063154	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.762G>T	19.37:g.22271314G>T	ENSP00000470209:p.Glu254Asp		22063154	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.240801	0.22711	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	1.11	0.20524	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46795	0.1411	M	0.76170	2.325	0.25674	N	0.985869	B	0.16166	0.016	B	0.20955	0.032	T	0.47611	-0.9104	8	0.52906	T	0.07	.	9.0461	0.36347	0.0:0.0:1.0:0.0	.	254	Q9Y2Q1	ZN257_HUMAN	D	254;226	.	ENSP00000380312:E226D	E	+	3	2	ZNF257	22063154	0.790000	0.28787	0.015000	0.15790	0.084000	0.17831	0.442000	0.21628	0.518000	0.28383	0.313000	0.20887	GAG		0.388	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			T	22271314	G	T	22271314	3	4	61	1	0	0	0	0	1	0	0	0	17839	933	33	2	776	2	ZNF257	19	22271314	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114097	22271314	36857669	11012	18997										
ZNF257	113835	broad.mit.edu	37	chr19	22271517	22271517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacaaatgtgaagagtgtgGcaaagcctttaaccagtcct	9	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22271517G>A	ENST00000594947.1	+	4	1109	c.965G>A	c.(964-966)gGc>gAc	p.G322D		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G322D(1)		haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				GAAGAGTGTGGCAAAGCCTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	57	56					19																	22271517		2172	4290	6462	22063357	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.965G>A	19.37:g.22271517G>A	ENSP00000470209:p.Gly322Asp		22063357	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292409	0.40594	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	-2.23	0.06930	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25865	0.0630	L	0.48174	1.505	0.28825	N	0.897499	P	0.50156	0.932	B	0.40659	0.336	T	0.23904	-1.0175	8	0.59425	D	0.04	.	4.8081	0.13329	0.1849:0.2198:0.5953:0.0	.	322	Q9Y2Q1	ZN257_HUMAN	D	322;294	.	ENSP00000380312:G294D	G	+	2	0	ZNF257	22063357	0.796000	0.28864	0.014000	0.15608	0.011000	0.07611	0.450000	0.21762	-0.307000	0.08804	0.313000	0.20887	GGC		0.433	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			A	22271517	G	A	22271517	3	1	61	1	0	0	0	0	1	0	0	0	17839	1203	42	3	979	3	ZNF257	19	22271517	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	203	22271517	36857466	11013	18998										
ZNF257	113835	broad.mit.edu	37	chr19	22272156	22272156	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataccttaccgtacataagaGaattcatgctggagagaacc	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22272156G>T	ENST00000594947.1	+	4	1748	c.1604G>T	c.(1603-1605)aGa>aTa	p.R535I		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	535					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R535I(1)		haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				GTACATAAGAGAATTCATGCT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											30	33	32					19																	22272156		2117	4259	6376	22063996	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.1604G>T	19.37:g.22272156G>T	ENSP00000470209:p.Arg535Ile		22063996	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	5.292	0.239288	0.10023	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	1.11	0.20524	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40473	0.1118	L	0.33485	1.01	0.41315	D	0.987139	B	0.11235	0.004	B	0.12156	0.007	T	0.16867	-1.0388	8	0.32370	T	0.25	.	6.0631	0.19848	0.0:0.0:0.6989:0.301	.	535	Q9Y2Q1	ZN257_HUMAN	I	535;507	.	ENSP00000380312:R507I	R	+	2	0	ZNF257	22063996	0.000000	0.05858	0.045000	0.18777	0.076000	0.17211	-0.412000	0.07132	0.518000	0.28383	0.313000	0.20887	AGA		0.363	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			T	22272156	G	T	22272156	3	4	61	1	0	0	0	0	1	0	0	0	17839	942	33	2	1618	2	ZNF257	19	22272156	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	639	22272156	36856827	11014	18999										
ZNF676	163223	broad.mit.edu	37	chr19	22363078	22363078	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actaaagcctttgccacattCttcacatttgtaaggtttct	5	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22363078C>A	ENST00000397121.2	-	3	1758	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	481					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E481*(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTGCCACATTCTTCACATTTG	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											94	100	98					19																	22363078		2164	4274	6438	22154918	SO:0001587	stop_gained	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1441G>T	19.37:g.22363078C>A	ENSP00000380310:p.Glu481*		22154918	A8MVX5	Nonsense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	22.9	4.344025	0.82022	.	.	ENSG00000196109	ENST00000397121	.	.	.	0.81	-1.62	0.08372	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	7.3206	0.26526	0.0:0.7253:0.2747:0.0	.	.	.	.	X	481	.	ENSP00000380310:E481X	E	-	1	0	ZNF676	22154918	0.000000	0.05858	0.073000	0.20177	0.073000	0.16967	-0.958000	0.03857	0.181000	0.19994	0.184000	0.17185	GAA		0.393	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		A	22363078	C	A	22363078	4	1	61	1	0	0	0	0	0	1	0	0	18122	922	32	2	329	2	ZNF676	19	22363078	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	90922	22363078	36765905	11015	19000										
ZNF98	148198	broad.mit.edu	37	chr19	22574543	22574543	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgtgaggactggttaaaAgctttgccacattcttcaca	10	8	2	1	rs74169607		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22574543A>C	ENST00000357774.5	-	4	1615	c.1494T>G	c.(1492-1494)gcT>gcG	p.A498A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A498A(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				ACTGGTTAAAAGCTTTGCCAC	0.398																																																2	Substitution - coding silent(2)	large_intestine(2)	19											73	65	68					19																	22574543		2187	4283	6470	22366383	SO:0001819	synonymous_variant	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1494T>G	19.37:g.22574543A>C			22366383		Silent	SNP	ENST00000357774.5	37	CCDS46031.1																																																																																				0.398	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		C	22574543	A	C	22574543	2	2	61	1	0	0	0	0	0	0	0	1	18242	59	3	4		4	ZNF98	19	22574543	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	211465	22574543	36554440	11016	19001										
ZNF98	148198	broad.mit.edu	37	chr19	22585636	22585636	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcttcacattccaaggttCttttccttgctccagacagg	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22585636C>A	ENST00000357774.5	-	3	329	c.208G>T	c.(208-210)Gaa>Taa	p.E70*	ZNF98_ENST00000601553.1_Nonsense_Mutation_p.E70*	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	70	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E70*(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TTCCAAGGTTCTTTTCCTTGC	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											108	116	113					19																	22585636		2198	4300	6498	22377476	SO:0001587	stop_gained	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.208G>T	19.37:g.22585636C>A	ENSP00000350418:p.Glu70*		22377476		Nonsense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	21.4	4.143714	0.77888	.	.	ENSG00000197360	ENST00000357774	.	.	.	0.476	-0.698	0.11280	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	.	.	.	.	.	.	.	X	70	.	ENSP00000350418:E70X	E	-	1	0	ZNF98	22377476	0.000000	0.05858	0.044000	0.18714	0.873000	0.50193	-0.926000	0.03988	-0.295000	0.08960	0.298000	0.19748	GAA		0.423	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		A	22585636	C	A	22585636	4	1	61	1	0	0	0	0	0	1	0	0	18242	922	32	2	1518	2	ZNF98	19	22585636	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11093	22585636	36543347	11017	19002										
ZNF98	148198	broad.mit.edu	37	chr19	22586279	22586279	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgccactcctccagagaGaattctaaggccacatccct	6	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22586279G>A	ENST00000357774.5	-	2	187	c.66C>T	c.(64-66)ttC>ttT	p.F22F	ZNF98_ENST00000601553.1_Silent_p.F22F	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	22	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F22F(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				CCTCCAGAGAGAATTCTAAGG	0.403																																																2	Substitution - coding silent(2)	large_intestine(2)	19											94	100	98					19																	22586279		2203	4298	6501	22378119	SO:0001819	synonymous_variant	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.66C>T	19.37:g.22586279G>A			22378119		Silent	SNP	ENST00000357774.5	37	CCDS46031.1																																																																																				0.403	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		A	22586279	G	A	22586279	2	1	61	1	0	0	0	0	0	0	0	1	18242	933	33	3		3	ZNF98	19	22586279	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	643	22586279	36542704	11018	19003										
ZNF492	57615	broad.mit.edu	37	chr19	22847557	22847557	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagagaattcatgctggagaGaaattctacaaatgtgaagt	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22847557G>T	ENST00000456783.2	+	4	1330	c.1086G>T	c.(1084-1086)gaG>gaT	p.E362D	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E362D(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATGCTGGAGAGAAATTCTACA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											6	6	6					19																	22847557		1776	3957	5733	22639397	SO:0001583	missense	57615			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1086G>T	19.37:g.22847557G>T	ENSP00000413660:p.Glu362Asp		22639397	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	14.01	2.408655	0.42715	.	.	ENSG00000229676	ENST00000456783	T	0.26810	1.71	1.12	1.12	0.20585	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32466	0.0830	L	0.41710	1.295	0.27928	N	0.937977	P	0.50156	0.932	P	0.57502	0.822	T	0.14364	-1.0475	9	0.72032	D	0.01	.	7.4251	0.27094	0.0:0.0:1.0:0.0	.	362	Q9P255	ZN492_HUMAN	D	362	ENSP00000413660:E362D	ENSP00000413660:E362D	E	+	3	2	ZNF492	22639397	0.007000	0.16637	0.113000	0.21522	0.113000	0.19764	0.010000	0.13242	0.269000	0.21961	0.274000	0.19336	GAG		0.393	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		T	22847557	G	T	22847557	3	4	61	1	0	0	0	0	1	0	0	0	17982	933	33	2	1096	2	ZNF492	19	22847557	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	261278	22847557	36281426	11019	19004										
ZNF492	57615	broad.mit.edu	37	chr19	22847945	22847945	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttaacaactcctctattCttaacagacataagatgatt	3	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22847945C>T	ENST00000456783.2	+	4	1718	c.1474C>T	c.(1474-1476)Ctt>Ttt	p.L492F	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	492					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L492F(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				CTCCTCTATTCTTAACAGACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											15	21	19					19																	22847945		1883	4144	6027	22639785	SO:0001583	missense	57615			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1474C>T	19.37:g.22847945C>T	ENSP00000413660:p.Leu492Phe		22639785	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	4.648	0.120378	0.08881	.	.	ENSG00000229676	ENST00000456783	T	0.13657	2.57	1.06	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15219	0.0367	L	0.53249	1.67	0.09310	N	1	P	0.35155	0.487	B	0.39094	0.29	T	0.18808	-1.0325	9	0.56958	D	0.05	.	7.2565	0.26179	0.0:1.0:0.0:0.0	.	492	Q9P255	ZN492_HUMAN	F	492	ENSP00000413660:L492F	ENSP00000413660:L492F	L	+	1	0	ZNF492	22639785	0.004000	0.15560	0.682000	0.30024	0.702000	0.40608	0.147000	0.16202	0.149000	0.19098	0.152000	0.16155	CTT		0.363	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		T	22847945	C	T	22847945	3	4	61	1	0	0	0	0	1	0	0	0	17982	913	32	3	1484	3	ZNF492	19	22847945	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	388	22847945	36281038	11020	19005										
ZNF99	7652	broad.mit.edu	37	chr19	22939057	22939057	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttagtaagggctgaaaGatggttaaaagctttgccac	11	5	0	2	rs537379931	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22939057G>T	ENST00000596209.1	-	0	2686				ZNF99_ENST00000397104.3_Missense_Mutation_p.L1022I|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L1022I(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				AGGGCTGAAAGATGGTTAAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											52	73	66					19																	22939057		2001	4274	6275	22730897	SO:0001628	intergenic_variant	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4			19.37:g.22939057G>T			22730897	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.015	-1.547995	0.00926	.	.	ENSG00000213973	ENST00000397104	T	0.52754	0.65	1.04	-2.09	0.07232	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29190	0.0726	.	.	.	0.09310	N	1	B	0.14805	0.011	B	0.28385	0.089	T	0.27434	-1.0074	8	0.22706	T	0.39	.	3.5182	0.07732	0.1966:0.0:0.3963:0.4071	.	1021	A8MXY4	ZNF99_HUMAN	I	1022	ENSP00000380293:L1022I	ENSP00000380293:L1022I	L	-	1	0	ZNF99	22730897	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.571000	0.05889	-1.468000	0.01892	-0.606000	0.04082	CTT		0.363	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22939057	G	T	22939057	1	4	61	0	1	0	0	0	0	0	0	0	18243	942	33	2		2	ZNF99	19	22939057	IGR	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91112	22939057	36189926	11021	19006										
ZNF99	7652	broad.mit.edu	37	chr19	22942226	22942226	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtgtgtctaatcttatatCtatttgaatttgaatattta	5	3	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22942226C>A	ENST00000596209.1	-	4	575	c.485G>T	c.(484-486)aGa>aTa	p.R162I	ZNF99_ENST00000397104.3_Missense_Mutation_p.R183I	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R183I(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				AATCTTATATCTATTTGAATT	0.264																																																1	Substitution - Missense(1)	large_intestine(1)	19											28	27	27					19																	22942226		1847	4084	5931	22734066	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.485G>T	19.37:g.22942226C>A	ENSP00000472969:p.Arg162Ile		22734066	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	4.165	0.029047	0.08054	.	.	ENSG00000213973	ENST00000397104	T	0.26223	1.75	1.78	-3.56	0.04626	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15739	0.0379	L	0.45228	1.405	0.09310	N	1	P	0.41080	0.737	B	0.39771	0.309	T	0.07888	-1.0749	9	0.28530	T	0.3	.	1.486	0.02447	0.1892:0.406:0.2424:0.1623	.	183	A8MXY4	ZNF99_HUMAN	I	183	ENSP00000380293:R183I	ENSP00000380293:R183I	R	-	2	0	ZNF99	22734066	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.022000	0.12480	-1.431000	0.01982	0.395000	0.25975	AGA		0.264	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22942226	C	A	22942226	3	1	61	1	0	0	0	0	1	0	0	0	18243	913	32	2	2580	2	ZNF99	19	22942226	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3169	22942226	36186757	11022	19007										
ZNF99	7652	broad.mit.edu	37	chr19	22942370	22942370	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacactttcacaatcttttCttaatcgtaaattcttatgt	3	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:22942370C>A	ENST00000596209.1	-	4	431	c.341G>T	c.(340-342)aGa>aTa	p.R114I	ZNF99_ENST00000397104.3_Missense_Mutation_p.R135I	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R135I(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ACAATCTTTTCTTAATCGTAA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19											108	100	102					19																	22942370		1842	4096	5938	22734210	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.341G>T	19.37:g.22942370C>A	ENSP00000472969:p.Arg114Ile		22734210	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	2.913	-0.224954	0.06022	.	.	ENSG00000213973	ENST00000397104	T	0.06768	3.26	0.257	-0.514	0.11958	.	.	.	.	.	T	0.10423	0.0255	M	0.78456	2.415	0.09310	N	1	B	0.30211	0.273	B	0.32677	0.15	T	0.31779	-0.9931	9	0.42905	T	0.14	.	2.1933	0.03905	0.3262:0.3462:0.3275:0.0	.	135	A8MXY4	ZNF99_HUMAN	I	135	ENSP00000380293:R135I	ENSP00000380293:R135I	R	-	2	0	ZNF99	22734210	0.001000	0.12720	0.066000	0.19879	0.060000	0.15804	-0.265000	0.08644	-0.860000	0.04099	-0.882000	0.02950	AGA		0.333	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22942370	C	A	22942370	3	1	61	1	0	0	0	0	1	0	0	0	18243	913	32	2	2724	2	ZNF99	19	22942370	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	144	22942370	36186613	11023	19008										
ZNF91	7644	broad.mit.edu	37	chr19	23543125	23543125	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataaatgctttgtcacattCttcactcttggaaggtttct	7	8	5	0	rs370365358		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:23543125C>A	ENST00000300619.7	-	4	2861	c.2656G>T	c.(2656-2658)Gaa>Taa	p.E886*	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Nonsense_Mutation_p.E854*|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	886					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E886*(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTGTCACATTCTTCACTCTTG	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											75	82	79					19																	23543125		2169	4292	6461	23334965	SO:0001587	stop_gained	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2656G>T	19.37:g.23543125C>A	ENSP00000300619:p.Glu886*		23334965	A8K5E1|B7Z6G6	Nonsense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874267	0.72180	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	.	.	.	1.53	-3.05	0.05396	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	10.2649	0.43449	0.0:0.4645:0.5355:0.0	.	.	.	.	X	886;854	.	ENSP00000300619:E886X	E	-	1	0	ZNF91	23334965	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-2.250000	0.01187	-0.865000	0.04073	0.205000	0.17691	GAA		0.353	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23543125	C	A	23543125	4	1	61	1	0	0	0	0	0	1	0	0	18239	922	32	2	923	2	ZNF91	19	23543125	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	600755	23543125	35585858	11024	19009										
ZNF254	9534	broad.mit.edu	37	chr19	24289408	24289408	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacaagggaaagagccctgGaatatgaagcgacatgagat	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:24289408G>A	ENST00000357002.4	+	3	331	c.216G>A	c.(214-216)tgG>tgA	p.W72*	ZNF254_ENST00000342944.6_Intron|ZNF254_ENST00000339642.6_Nonsense_Mutation_p.W72*	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W72*(1)					all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AAGAGCCCTGGAATATGAAGC	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											130	140	136					19																	24289408		1511	2709	4220	24081248	SO:0001587	stop_gained	9534			AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.216G>A	19.37:g.24289408G>A	ENSP00000349494:p.Trp72*		24081248	A4QPC0|Q86XL7	Nonsense_Mutation	SNP	ENST00000357002.4	37	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	G	8.194	0.796586	0.16327	.	.	ENSG00000213096	ENST00000357002;ENST00000392281;ENST00000339642	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	72	.	ENSP00000341573:W72X	W	+	3	0	ZNF254	24081248	0.116000	0.22171	0.058000	0.19502	0.059000	0.15707	0.956000	0.29202	0.300000	0.22699	0.305000	0.20034	TGG		0.423	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		A	24289408	G	A	24289408	4	1	61	1	0	0	0	0	0	1	0	0	17837	1183	41	3	226	3	ZNF254	19	24289408	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	746283	24289408	34839575	11025	19010										
ZNF254	9534	broad.mit.edu	37	chr19	24310308	24310308	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcaaatcttttagccaatcCtcaacccttactacacataa	3	13	2	0	rs147490367	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:24310308C>A	ENST00000357002.4	+	4	1621	c.1506C>A	c.(1504-1506)tcC>tcA	p.S502S	ZNF254_ENST00000342944.6_Silent_p.S417S	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	502					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S502S(1)					all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TTAGCCAATCCTCAACCCTTA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	19											58	60	59					19																	24310308		2200	4296	6496	24102148	SO:0001819	synonymous_variant	9534			AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1506C>A	19.37:g.24310308C>A			24102148	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																				0.398	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		A	24310308	C	A	24310308	2	1	61	1	0	0	0	0	0	0	0	1	17837	668	24	2		2	ZNF254	19	24310308	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20900	24310308	34818675	11026	19011										
UQCRFS1	7386	broad.mit.edu	37	chr19	29698872	29698872	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcactcatgctggaaacGaactgggtgacggcattctt	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:29698872G>A	ENST00000304863.4	-	2	830	c.408C>T	c.(406-408)ttC>ttT	p.F136F		NM_006003.2	NP_005994.2	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	136					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)	p.F136F(1)		endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)			TGCTGGAAACGAACTGGGTGA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	19											26	25	25					19																	29698872		2201	4277	6478	34390712	SO:0001819	synonymous_variant	7386			BC010035	CCDS12415.1	19q12	2011-07-04			ENSG00000169021	ENSG00000169021	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12587	protein-coding gene	gene with protein product	"cytochrome b-c1 complex subunit 5"	191327				8088805	Standard	NM_006003		Approved	RIS1, RIP1, UQCR5, RISP	uc002nsd.2	P47985		ENST00000304863.4:c.408C>T	19.37:g.29698872G>A			34390712	A8K519|Q6NVX5|Q9UPH2	Silent	SNP	ENST00000304863.4	37	CCDS12415.1																																																																																				0.473	UQCRFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458563.1	NM_006003		A	29698872	G	A	29698872	2	1	61	1	0	0	0	0	0	0	0	1	17061	1049	37	1		1	UQCRFS1	19	29698872	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5388564	29698872	29430111	11027	19012										
CCNE1	898	broad.mit.edu	37	chr19	30311680	30311680	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctttgaccggtatatggcGacacaagaaaatgttgtaaa	9	6	1	2	rs368794196		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:30311680G>A	ENST00000262643.3	+	7	813	c.534G>A	c.(532-534)gcG>gcA	p.A178A	CCNE1_ENST00000444983.2_Silent_p.A163A|CCNE1_ENST00000357943.5_Intron	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	178					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)	p.A178A(2)		endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			GGTATATGGCGACACAAGAAA	0.328			A		serous ovarian																																		Dom	yes		19	19q12	898	cyclin E1		E	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	19						G		0,4406		0,0,2203	69	70	70		534	0.1	1	19		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CCNE1	NM_001238.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		178/411	30311680	1,13005	2203	4300	6503	35003520	SO:0001819	synonymous_variant	898			M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"cyclin Es", "cyclin Et"	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.534G>A	19.37:g.30311680G>A			35003520	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Silent	SNP	ENST00000262643.3	37	CCDS12419.1																																																																																				0.328	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238		A	30311680	G	A	30311680	2	1	61	1	0	0	0	0	0	0	0	1	2926	1045	37	1		1	CCNE1	19	30311680	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	612808	30311680	28817303	11028	19013										
C19orf2	8725	broad.mit.edu	37	chr19	30496605	30496605	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagaaattaaatgtgacttCgaatttaaaggtaagcagta	9	3	0	2	rs78325360	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:30496605C>T	ENST00000542441.2	+	6	804	c.507C>T	c.(505-507)ttC>ttT	p.F169F	URI1_ENST00000360605.4_Silent_p.F151F|URI1_ENST00000312051.6_Silent_p.F129F|URI1_ENST00000574176.1_3'UTR|URI1_ENST00000392271.1_Silent_p.F93F			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	169					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.F169F(2)									AATGTGACTTCGAATTTAAAG	0.318													C|||	3	0.000599042	8e-04	0	5008	,	,		17521	0.002		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	19											127	128	127					19																	30496605		2203	4300	6503	35188445	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.507C>T	19.37:g.30496605C>T			35188445	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.318	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		T	30496605	C	T	30496605	2	4	61	1	0	0	0	0	0	0	0	1	1917	883	31	1		1	C19orf2	19	30496605	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	184925	30496605	28632378	11029	19014										
C19orf2	8725	broad.mit.edu	37	chr19	30499948	30499948	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcaaatggagaagatacGacatcttctgaagaggaaaa	10	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:30499948G>A	ENST00000542441.2	+	8	1020	c.723G>A	c.(721-723)acG>acA	p.T241T	URI1_ENST00000360605.4_Silent_p.T223T|URI1_ENST00000312051.6_Silent_p.T201T|URI1_ENST00000392271.1_Silent_p.T165T			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	241					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.T241T(1)									GAGAAGATACGACATCTTCTG	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	19											84	74	77					19																	30499948		2203	4300	6503	35191788	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.723G>A	19.37:g.30499948G>A			35191788	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.343	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30499948	G	A	30499948	2	1	61	1	0	0	0	0	0	0	0	1	1917	1045	37	1		1	C19orf2	19	30499948	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3343	30499948	28629035	11030	19015										
C19orf2	8725	broad.mit.edu	37	chr19	30503251	30503251	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatccatcctgaagtctcGaagtagagagaatagtgtgt	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:30503251G>A	ENST00000542441.2	+	10	1535	c.1238G>A	c.(1237-1239)cGa>cAa	p.R413Q	URI1_ENST00000360605.4_Missense_Mutation_p.R395Q|URI1_ENST00000312051.6_Missense_Mutation_p.R373Q|URI1_ENST00000392271.1_Missense_Mutation_p.R337Q			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	413					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.R413Q(1)									CTGAAGTCTCGAAGTAGAGAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											168	152	157					19																	30503251		2203	4300	6503	35195091	SO:0001583	missense	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1238G>A	19.37:g.30503251G>A	ENSP00000442436:p.Arg413Gln		35195091	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.449580	0.63178	.	.	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T	0.52983	0.64	5.54	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.47691	0.1459	L	0.51422	1.61	0.58432	D	0.999991	D;D;D	0.57257	0.979;0.964;0.964	P;B;B	0.45610	0.487;0.293;0.217	T	0.53258	-0.8464	10	0.66056	D	0.02	-8.3824	14.2813	0.66213	0.0715:0.0:0.9285:0.0	.	373;413;410	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	Q	411;337;413;373	ENSP00000442436:R413Q	ENSP00000312530:R373Q	R	+	2	0	C19orf2	35195091	1.000000	0.71417	0.976000	0.42696	0.202000	0.24057	9.148000	0.94652	1.348000	0.45733	-0.225000	0.12378	CGA		0.433	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30503251	G	A	30503251	3	1	61	1	0	0	0	0	1	0	0	0	1917	1058	37	1	1276	1	C19orf2	19	30503251	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3303	30503251	28625732	11031	19016										
TSHZ3	57616	broad.mit.edu	37	chr19	31769277	31769277	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaccgctttctccttgtcGacttccttcttgacctccac	6	16	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:31769277G>A	ENST00000240587.4	-	2	1749	c.1422C>T	c.(1420-1422)gtC>gtT	p.V474V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	474					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V291V(2)|p.V474V(2)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TCTCCTTGTCGACTTCCTTCT	0.517																																																4	Substitution - coding silent(4)	large_intestine(2)|endometrium(2)	19											170	171	170					19																	31769277		2203	4300	6503	36461117	SO:0001819	synonymous_variant	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1422C>T	19.37:g.31769277G>A			36461117	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																				0.517	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31769277	G	A	31769277	2	1	61	1	0	0	0	0	0	0	0	1	16665	1045	37	1		1	TSHZ3	19	31769277	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1266026	31769277	27359706	11032	19017										
TSHZ3	57616	broad.mit.edu	37	chr19	31770405	31770405	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaccgtgacctccttggtCtcctcttcgttcttgatgga	11	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:31770405C>T	ENST00000240587.4	-	2	621	c.294G>A	c.(292-294)gaG>gaA	p.E98E		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	98					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E98E(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CCTCCTTGGTCTCCTCTTCGT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	19											113	111	112					19																	31770405		2106	4232	6338	36462245	SO:0001819	synonymous_variant	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.294G>A	19.37:g.31770405C>T			36462245	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																				0.532	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31770405	C	T	31770405	2	4	61	1	0	0	0	0	0	0	0	1	16665	912	32	3		3	TSHZ3	19	31770405	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1128	31770405	27358578	11033	19018										
PDCD5	9141	broad.mit.edu	37	chr19	33076768	33076768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaactaaagcagtagaGaattaccttatacagatggc	8	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33076768G>T	ENST00000590247.2	+	4	407	c.213G>T	c.(211-213)gaG>gaT	p.E71D	PDCD5_ENST00000586035.1_Missense_Mutation_p.E33D|PDCD5_ENST00000379316.3_Intron|PDCD5_ENST00000419343.3_Missense_Mutation_p.E71D|PDCD5_ENST00000592786.1_Intron	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	71					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E71D(1)		breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					AAGCAGTAGAGAATTACCTTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	113	111					19																	33076768		2203	4300	6503	37768608	SO:0001583	missense	9141			AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"TFAR19 novel apoptosis-related", "TF1 cell apoptosis-related gene 19"	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.213G>T	19.37:g.33076768G>T	ENSP00000466214:p.Glu71Asp		37768608	B4DE64|Q53YC9|Q6IB70	Missense_Mutation	SNP	ENST00000590247.2	37	CCDS12423.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.671483	0.47781	.	.	ENSG00000105185	ENST00000419343;ENST00000221784	.	.	.	5.45	2.03	0.26663	.	0.000000	0.85682	D	0.000000	D	0.85852	0.5793	H	0.97611	4.04	0.80722	D	1	D;D	0.89917	0.99;1.0	D;D	0.91635	0.989;0.999	D	0.86547	0.1832	9	0.87932	D	0	-7.7899	9.3482	0.38122	0.248:0.0:0.752:0.0	.	71;71	O14737;B4DE64	PDCD5_HUMAN;.	D	71	.	ENSP00000221784:E71D	E	+	3	2	PDCD5	37768608	0.992000	0.36948	1.000000	0.80357	0.154000	0.21943	0.195000	0.17155	0.594000	0.29761	0.557000	0.71058	GAG		0.328	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708		T	33076768	G	T	33076768	3	4	61	1	0	0	0	0	1	0	0	0	11653	933	33	2	227	2	PDCD5	19	33076768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1306363	33076768	26052215	11034	19019										
ANKRD27	84079	broad.mit.edu	37	chr19	33137443	33137443	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcattgtagaaagtttCttcaaagagaatgggcactg	9	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33137443C>A	ENST00000306065.4	-	4	450	c.292G>T	c.(292-294)Gaa>Taa	p.E98*	ANKRD27_ENST00000587352.1_Nonsense_Mutation_p.E98*	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	98					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.E98*(1)		breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TAGAAAGTTTCTTCAAAGAGA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											85	88	87					19																	33137443		2203	4300	6503	37829283	SO:0001587	stop_gained	84079			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.292G>T	19.37:g.33137443C>A	ENSP00000304292:p.Glu98*		37829283	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Nonsense_Mutation	SNP	ENST00000306065.4	37	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	C	38	6.851217	0.97885	.	.	ENSG00000105186	ENST00000306065	.	.	.	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-28.5218	18.8895	0.92392	0.0:1.0:0.0:0.0	.	.	.	.	X	98	.	ENSP00000304292:E98X	E	-	1	0	ANKRD27	37829283	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.657000	0.74402	2.467000	0.83353	0.545000	0.68477	GAA		0.403	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33137443	C	A	33137443	4	1	61	1	0	0	0	0	0	1	0	0	655	922	32	2	2964	2	ANKRD27	19	33137443	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60675	33137443	25991540	11035	19020										
SLC7A9	11136	broad.mit.edu	37	chr19	33353095	33353095	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagacagctgggcgccctcGaaagaattatcaaaattctt	8	10	2	2	rs372980958		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33353095G>A	ENST00000023064.4	-	6	824	c.633C>T	c.(631-633)ttC>ttT	p.F211F	RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Silent_p.F211F|SLC7A9_ENST00000590341.1_Silent_p.F211F	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	211					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)	p.F211F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	GGGCGCCCTCGAAAGAATTAT	0.517																																					GBM(181;1335 2108 9644 44178 46689)											1	Substitution - coding silent(1)	large_intestine(1)	19	GRCh37	CD010661	SLC7A9	D		G	,	0,4406		0,0,2203	68	67	68		633,633	-0.9	0.9	19		68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	211/488,211/488	33353095	1,13005	2203	4300	6503	38044935	SO:0001819	synonymous_variant	11136			AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.633C>T	19.37:g.33353095G>A			38044935	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																				0.517	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			A	33353095	G	A	33353095	2	1	61	1	0	0	0	0	0	0	0	1	14742	1049	37	1		1	SLC7A9	19	33353095	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	215652	33353095	25775888	11036	19021										
CCDC123	84902	broad.mit.edu	37	chr19	33406297	33406297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactgcgattttgccatccGagtgtgttttgagttcttgg	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33406297G>A	ENST00000305768.5	-	14	1599	c.1511C>T	c.(1510-1512)tCg>tTg	p.S504L		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	504					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.S504L(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TTTGCCATCCGAGTGTGTTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											121	109	113					19																	33406297		2203	4300	6503	38098137	SO:0001583	missense	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1511C>T	19.37:g.33406297G>A	ENSP00000306105:p.Ser504Leu		38098137	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.668305	0.00765	.	.	ENSG00000121289	ENST00000305768	D	0.87029	-2.2	5.6	4.58	0.56647	.	0.136085	0.51477	N	0.000098	T	0.63604	0.2525	N	0.00859	-1.14	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.01281	0.0;0.0	T	0.56944	-0.7895	10	0.14656	T	0.56	-5.2232	10.5525	0.45097	0.9218:0.0:0.0782:0.0	.	257;504	Q96ST8-2;Q96ST8	.;CEP89_HUMAN	L	504	ENSP00000306105:S504L	ENSP00000306105:S504L	S	-	2	0	CEP89	38098137	0.980000	0.34600	0.164000	0.22755	0.005000	0.04900	3.293000	0.51779	0.965000	0.38133	-0.469000	0.05056	TCG		0.393	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33406297	G	A	33406297	3	1	61	1	0	0	0	0	1	0	0	0	2765	1059	37	1	864	1	CCDC123	19	33406297	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53202	33406297	25722686	11037	19022										
RHPN2	85415	broad.mit.edu	37	chr19	33486950	33486950	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaacaacactgggggcgtCgatcaggttcagcaggtcat	12	11	3	0	rs148084786		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33486950C>T	ENST00000254260.3	-	11	1437	c.1402G>A	c.(1402-1404)Gac>Aac	p.D468N	RHPN2_ENST00000400226.4_Missense_Mutation_p.D317N	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	468					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.D468N(1)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					CTGGGGGCGTCGATCAGGTTC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	81	63	69		1402	0.2	0	19	dbSNP_134	69	0,8600		0,0,4300	no	missense	RHPN2	NM_033103.4	23	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	468/687	33486950	2,13004	2203	4300	6503	38178790	SO:0001583	missense	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1402G>A	19.37:g.33486950C>T	ENSP00000254260:p.Asp468Asn		38178790	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	c	10.42	1.346548	0.24426	4.54E-4	0.0	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.16597	2.33;2.33	4.86	0.203	0.15195	BRO1 domain (2);	0.923114	0.09501	N	0.793641	T	0.10252	0.0251	L	0.31664	0.95	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.37314	-0.9711	10	0.41790	T	0.15	2.122	1.1875	0.01858	0.262:0.2872:0.2856:0.1651	.	468	Q8IUC4	RHPN2_HUMAN	N	468;198;317	ENSP00000254260:D468N;ENSP00000402244:D317N	ENSP00000254260:D468N	D	-	1	0	RHPN2	38178790	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	0.591000	0.23969	0.113000	0.18004	-0.972000	0.02603	GAC		0.622	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33486950	C	T	33486950	3	4	61	1	0	0	0	0	1	0	0	0	13388	884	31	1	678	1	RHPN2	19	33486950	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80653	33486950	25642033	11038	19023										
GPATCH1	55094	broad.mit.edu	37	chr19	33584411	33584411	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccaccctccttgatgacctCataacgccagcaaagtgagc	8	15	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33584411C>A	ENST00000170564.2	+	4	755	c.441C>A	c.(439-441)ctC>ctA	p.L147L		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	147					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)	p.L147L(1)		breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					TTGATGACCTCATAACGCCAG	0.478																																					Pancreas(67;88 1713 4567 18227)											1	Substitution - coding silent(1)	large_intestine(1)	19											150	136	141					19																	33584411		2203	4300	6503	38276251	SO:0001819	synonymous_variant	55094			AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.441C>A	19.37:g.33584411C>A			38276251	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																				0.478	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		A	33584411	C	A	33584411	2	1	61	1	0	0	0	0	0	0	0	1	6610	813	29	2		2	GPATCH1	19	33584411	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97461	33584411	25544572	11039	19024										
WDR88	126248	broad.mit.edu	37	chr19	33639704	33639704	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcaggtatgataccttcatCgtctcctgtaagttttctcc	7	11	4	1	rs112724972	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33639704C>T	ENST00000355868.3	+	5	643	c.567C>T	c.(565-567)atC>atT	p.I189I	WDR88_ENST00000361680.2_Silent_p.I189I|WDR88_ENST00000592765.1_3'UTR	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	189								p.I189I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					ATACCTTCATCGTCTCCTGTA	0.463													C|||	2	0.000399361	0.0015	0	5008	,	,		23078	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	257	203	221		567	-0.6	0.1	19	dbSNP_132	221	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	WDR88	NM_173479.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		189/473	33639704	2,13004	2203	4300	6503	38331544	SO:0001819	synonymous_variant	126248			BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.567C>T	19.37:g.33639704C>T			38331544	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																				0.463	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		T	33639704	C	T	33639704	2	4	61	1	0	0	0	0	0	0	0	1	17375	874	31	1		1	WDR88	19	33639704	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55293	33639704	25489279	11040	19025										
PEPD	5184	broad.mit.edu	37	chr19	33968993	33968993	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatggtattgttgacttcGaacctgtagggcgaaaagaa	12	5	0	3	rs377714630		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:33968993G>A	ENST00000244137.7	-	7	540	c.507C>T	c.(505-507)ttC>ttT	p.F169F	PEPD_ENST00000436370.3_Silent_p.F105F|PEPD_ENST00000397032.4_Silent_p.F169F	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	169					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)	p.F169F(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					TGTTGACTTCGAACCTGTAGG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	19											85	86	86					19																	33968993		2023	4180	6203	38660833	SO:0001819	synonymous_variant	5184			BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"prolidase"	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.507C>T	19.37:g.33968993G>A			38660833	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Silent	SNP	ENST00000244137.7	37	CCDS42544.1																																																																																				0.478	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		A	33968993	G	A	33968993	2	1	61	1	0	0	0	0	0	0	0	1	11759	1049	37	1		1	PEPD	19	33968993	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	329289	33968993	25159990	11041	19026										
CHST8	64377	broad.mit.edu	37	chr19	34263720	34263720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctgcctcatcgactacGatttcgtaggcaagttcgag	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:34263720G>A	ENST00000262622.4	+	4	1785	c.1027G>A	c.(1027-1029)Gat>Aat	p.D343N	CHST8_ENST00000434302.1_Missense_Mutation_p.D343N|CHST8_ENST00000438847.3_Missense_Mutation_p.D343N	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	343					carbohydrate biosynthetic process (GO:0016051)|central nervous system development (GO:0007417)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.D343N(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(5)	27	Esophageal squamous(110;0.162)					CATCGACTACGATTTCGTAGG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	57	63					19																	34263720		2203	4299	6502	38955560	SO:0001583	missense	64377			AB047801	CCDS12433.1	19q13.1	2008-02-05				ENSG00000124302		"Sulfotransferases, membrane-bound"	15993	protein-coding gene	gene with protein product		610190				10988300, 11001942	Standard	NM_001127895		Approved	GALNAC-4-ST1	uc002nut.4	Q9H2A9		ENST00000262622.4:c.1027G>A	19.37:g.34263720G>A	ENSP00000262622:p.Asp343Asn		38955560	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	37	CCDS12433.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996255	0.74818	.	.	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.75589	-0.95;-0.95;-0.95	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.82935	0.5145	L	0.52364	1.645	0.53688	D	0.999975	D	0.89917	1.0	D	0.87578	0.998	T	0.82967	-0.0194	10	0.45353	T	0.12	-23.3678	17.2896	0.87152	0.0:0.0:1.0:0.0	.	343	Q9H2A9	CHST8_HUMAN	N	343	ENSP00000392604:D343N;ENSP00000393879:D343N;ENSP00000262622:D343N	ENSP00000262622:D343N	D	+	1	0	CHST8	38955560	1.000000	0.71417	0.994000	0.49952	0.557000	0.35523	7.988000	0.88194	2.331000	0.79229	0.297000	0.19635	GAT		0.622	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467		A	34263720	G	A	34263720	3	1	61	1	0	0	0	0	1	0	0	0	3416	1058	37	1	1037	1	CHST8	19	34263720	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	294727	34263720	24865263	11042	19027										
GPI	2821	broad.mit.edu	37	chr19	34890646	34890646	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtatgagcacaagatcttCgttcagggcatcatctggga	11	8	4	2	rs138799755	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:34890646C>T	ENST00000356487.5	+	17	1738	c.1497C>T	c.(1495-1497)ttC>ttT	p.F499F	GPI_ENST00000586425.1_Intron|RP11-618P17.4_ENST00000606020.1_5'Flank|GPI_ENST00000415930.3_Silent_p.F510F	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	499					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)	p.F499F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					ACAAGATCTTCGTTCAGGGCA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C	,	2,4404	4.2+/-10.8	0,2,2201	115	106	109		1497,1530	-1.6	1	19	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPI	NM_000175.3,NM_001184722.1	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	499/559,510/570	34890646	2,13004	2203	4300	6503	39582486	SO:0001819	synonymous_variant	2821			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"glucose phosphate isomerase"			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.1497C>T	19.37:g.34890646C>T			39582486	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Silent	SNP	ENST00000356487.5	37	CCDS12437.1																																																																																				0.547	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3			T	34890646	C	T	34890646	2	4	61	1	0	0	0	0	0	0	0	1	6631	883	31	1		1	GPI	19	34890646	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	626926	34890646	24238337	11043	19028										
SCGBL	284402	broad.mit.edu	37	chr19	35085230	35085230	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacacatcaaacacaacattCgcaagcagtttatcgatatc	5	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35085230C>T	ENST00000601241.1	-	3	2196	c.96G>A	c.(94-96)gcG>gcA	p.A32A	SCGB2B2_ENST00000379204.2_Silent_p.A32A|SCGB2B2_ENST00000595326.1_Intron			Q4G0G5	SC2B2_HUMAN	secretoglobin, family 2B, member 2	32						extracellular region (GO:0005576)		p.A32A(1)									ACACAACATTCGCAAGCAGTT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	19											122	106	111					19																	35085230		2203	4300	6503	39777070	SO:0001819	synonymous_variant	284402			AK093495	CCDS32989.1	19q13.12	2011-12-14	2011-12-14	2011-12-14	ENSG00000205209	ENSG00000205209		"Secretoglobins"	27616	protein-coding gene	gene with protein product		615063	"secretoglobin-like"	SCGBL		22155607	Standard	NM_001025591		Approved	SCGB4A2	uc002nvn.3	Q4G0G5		ENST00000601241.1:c.96G>A	19.37:g.35085230C>T			39777070		Silent	SNP	ENST00000601241.1	37	CCDS32989.1																																																																																				0.512	SCGB2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461457.2	NM_001025591		T	35085230	C	T	35085230	2	4	61	1	0	0	0	0	0	0	0	1	13939	871	31	1		1	SCGBL	19	35085230	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	194584	35085230	24043753	11044	19029										
ZNF599	148103	broad.mit.edu	37	chr19	35249976	35249976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttcgatggtgagtgaacGatgaactgtggctgaaggtc	14	6	1	4	rs375653236		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35249976G>A	ENST00000329285.8	-	4	2103	c.1730C>T	c.(1729-1731)tCg>tTg	p.S577L		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	577					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S577L(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GTGAGTGAACGATGAACTGTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	150	142	145		1730	2.4	0.9	19		145	0,8600		0,0,4300	no	missense	ZNF599	NM_001007248.2	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	577/589	35249976	1,13005	2203	4300	6503	39941816	SO:0001583	missense	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1730C>T	19.37:g.35249976G>A	ENSP00000333802:p.Ser577Leu		39941816	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	G	4.449	0.083213	0.08533	2.27E-4	0.0	ENSG00000153896	ENST00000392231;ENST00000329285	T	0.15834	2.39	2.43	2.43	0.29744	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13243	0.0321	L	0.53671	1.685	0.80722	D	1	P	0.35011	0.48	B	0.15484	0.013	T	0.12167	-1.0558	9	0.34782	T	0.22	.	10.9731	0.47450	0.0:0.0:1.0:0.0	.	577	Q96NL3	ZN599_HUMAN	L	576;577	ENSP00000333802:S577L	ENSP00000333802:S577L	S	-	2	0	ZNF599	39941816	0.000000	0.05858	0.864000	0.33941	0.691000	0.40173	0.026000	0.13599	1.676000	0.50930	0.491000	0.48974	TCG		0.408	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35249976	G	A	35249976	3	1	61	1	0	0	0	0	1	0	0	0	18068	1059	37	1	40	1	ZNF599	19	35249976	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	164746	35249976	23879007	11045	19030										
ZNF599	148103	broad.mit.edu	37	chr19	35250312	35250312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctattatgtcgaataaaaAcagagtggtgtgtaaaagcc	9	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35250312A>G	ENST00000329285.8	-	4	1767	c.1394T>C	c.(1393-1395)gTt>gCt	p.V465A		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V465A(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TCGAATAAAAACAGAGTGGTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											84	88	87					19																	35250312		2203	4300	6503	39942152	SO:0001583	missense	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1394T>C	19.37:g.35250312A>G	ENSP00000333802:p.Val465Ala		39942152	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	A	0.187	-1.056975	0.01965	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.10099	2.91	2.69	-2.56	0.06268	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	N	0.01464	-0.85	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.45396	-0.9264	9	0.11182	T	0.66	.	4.8787	0.13668	0.2479:0.0:0.1123:0.6398	.	465	Q96NL3	ZN599_HUMAN	A	464;465;239	ENSP00000333802:V465A	ENSP00000333802:V465A	V	-	2	0	ZNF599	39942152	0.000000	0.05858	0.000000	0.03702	0.710000	0.40934	-1.717000	0.01876	-0.773000	0.04596	0.402000	0.26972	GTT		0.413	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		G	35250312	A	G	35250312	3	3	61	1	0	0	0	0	1	0	0	0	18068	43	2	4	376	4	ZNF599	19	35250312	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	336	35250312	23878671	11046	19031										
ZNF599	148103	broad.mit.edu	37	chr19	35250485	35250485	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgtcggatgaaagtggaGcgatgagtaaaggcctttcc	13	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35250485G>A	ENST00000329285.8	-	4	1594	c.1221C>T	c.(1219-1221)cgC>cgT	p.R407R		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R407R(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TGAAAGTGGAGCGATGAGTAA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	19											66	64	65					19																	35250485		2203	4300	6503	39942325	SO:0001819	synonymous_variant	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1221C>T	19.37:g.35250485G>A			39942325	Q569K0|Q5PRG1	Silent	SNP	ENST00000329285.8	37	CCDS32991.1																																																																																				0.473	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35250485	G	A	35250485	2	1	61	1	0	0	0	0	0	0	0	1	18068	958	34	3		3	ZNF599	19	35250485	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173	35250485	23878498	11047	19032										
ZNF599	148103	broad.mit.edu	37	chr19	35251320	35251320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagttcccttcctgaattTttattagcttttcctcatct	3	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35251320T>G	ENST00000329285.8	-	4	759	c.386A>C	c.(385-387)aAa>aCa	p.K129T		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	129					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K129T(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTCCTGAATTTTTATTAGCTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	19											106	114	112					19																	35251320		2203	4300	6503	39943160	SO:0001583	missense	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.386A>C	19.37:g.35251320T>G	ENSP00000333802:p.Lys129Thr		39943160	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	T	2.326	-0.354424	0.05173	.	.	ENSG00000153896	ENST00000392231;ENST00000329285	T	0.22134	1.97	2.57	2.57	0.30868	.	.	.	.	.	T	0.08223	0.0205	N	0.03608	-0.345	0.20403	N	0.999909	B	0.02656	0.0	B	0.01281	0.0	T	0.23297	-1.0192	9	0.34782	T	0.22	.	4.3768	0.11274	0.0:0.1573:0.0:0.8427	.	129	Q96NL3	ZN599_HUMAN	T	128;129	ENSP00000333802:K129T	ENSP00000333802:K129T	K	-	2	0	ZNF599	39943160	0.000000	0.05858	0.134000	0.22075	0.058000	0.15608	-0.045000	0.12003	1.436000	0.47453	0.402000	0.26972	AAA		0.453	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		G	35251320	T	G	35251320	3	3	61	1	0	0	0	0	1	0	0	0	18068	1841	64	4	1384	4	ZNF599	19	35251320	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	835	35251320	23877663	11048	19033										
ZNF30	90075	broad.mit.edu	37	chr19	35422784	35422784	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatcacggatcagtgacatTtgaggatgtggccatagcct	12	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35422784T>A	ENST00000601142.1	+	3	284	c.47T>A	c.(46-48)tTt>tAt	p.F16Y	ZNF30_ENST00000426813.2_5'UTR|ZNF30_ENST00000439785.1_Missense_Mutation_p.F16Y|ZNF30_ENST00000601957.1_Missense_Mutation_p.F16Y|ZNF30_ENST00000303586.7_Missense_Mutation_p.F16Y			P17039	ZNF30_HUMAN	zinc finger protein 30	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F16Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		TCAGTGACATTTGAGGATGTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	87	86					19																	35422784		2138	4265	6403	40114624	SO:0001583	missense	90075			X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.47T>A	19.37:g.35422784T>A	ENSP00000469954:p.Phe16Tyr		40114624	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.711247	0.30322	.	.	ENSG00000168661	ENST00000439785;ENST00000303586	T;T	0.08370	3.1;3.1	1.55	1.55	0.23275	Krueppel-associated box (4);	.	.	.	.	T	0.22627	0.0546	M	0.93016	3.37	0.80722	D	1	P;D	0.54207	0.692;0.965	B;P	0.52598	0.073;0.703	T	0.03773	-1.1005	9	0.87932	D	0	.	5.2312	0.15422	0.0:0.0:0.0:1.0	.	16;16	P17039-2;P17039	.;ZNF30_HUMAN	Y	16	ENSP00000403441:F16Y;ENSP00000303889:F16Y	ENSP00000303889:F16Y	F	+	2	0	ZNF30	40114624	0.867000	0.29959	0.798000	0.32154	0.635000	0.38103	2.576000	0.46033	0.965000	0.38133	0.421000	0.28195	TTT		0.458	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		A	35422784	T	A	35422784	3	1	61	1	0	0	0	0	1	0	0	0	17869	1841	64	5	53	5	ZNF30	19	35422784	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	171464	35422784	23706199	11049	19034										
ZNF30	90075	broad.mit.edu	37	chr19	35434228	35434228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataagtagacagaaaccaCgtgaatgtcaggaatatgga	10	5	1	3	rs372094110		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35434228C>T	ENST00000601142.1	+	5	595	c.358C>T	c.(358-360)Cgt>Tgt	p.R120C	ZNF30_ENST00000595818.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.R39C|ZNF30_ENST00000439785.1_Missense_Mutation_p.R121C|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000303586.7_Missense_Mutation_p.R121C			P17039	ZNF30_HUMAN	zinc finger protein 30	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R121C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ACAGAAACCACGTGAATGTCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	CYS/ARG,CYS/ARG,CYS/ARG	0,3734		0,0,1867	82	78	79		361,361,358	-3.8	0	19		79	1,8209		0,1,4104	no	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	180,180,180	0,1,5971	TT,TC,CC		0.0122,0.0,0.0084	benign,benign,benign	121/625,121/625,120/624	35434228	1,11943	1867	4105	5972	40126068	SO:0001583	missense	90075			X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.358C>T	19.37:g.35434228C>T	ENSP00000469954:p.Arg120Cys		40126068	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	C	5.549	0.286110	0.10513	0.0	1.22E-4	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.27890	1.64;1.64	1.91	-3.82	0.04281	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12263	0.0298	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.04013	0.001;0.001	T	0.16512	-1.0400	9	0.52906	T	0.07	.	2.968	0.05913	0.2002:0.2196:0.0:0.5802	.	121;120	P17039-2;P17039	.;ZNF30_HUMAN	C	121;120;39	ENSP00000403441:R121C;ENSP00000416457:R39C	ENSP00000303889:R120C	R	+	1	0	ZNF30	40126068	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.183000	0.03079	-1.606000	0.01591	-1.257000	0.01473	CGT		0.383	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		T	35434228	C	T	35434228	3	4	61	1	0	0	0	0	1	0	0	0	17869	536	19	1	375	1	ZNF30	19	35434228	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11444	35434228	23694755	11050	19035										
ZNF792	126375	broad.mit.edu	37	chr19	35449072	35449072	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcccacattcgctgcattCgtaaggcctgtctggtttgt	9	11	1	0	rs139720825		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35449072C>T	ENST00000404801.1	-	4	2073	c.1687G>A	c.(1687-1689)Gaa>Aaa	p.E563K	ZNF792_ENST00000605484.1_Missense_Mutation_p.E496K	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E484K(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TCGCTGCATTCGTAAGGCCTG	0.522																																					GBM(1;7 183 21053 22581 22847)											1	Substitution - Missense(1)	large_intestine(1)	19						C	LYS/GLU	0,4406		0,0,2203	124	95	104		1687	-5.6	0	19	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF792	NM_175872.4	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	563/633	35449072	1,13005	2203	4300	6503	40140912	SO:0001583	missense	126375			AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1687G>A	19.37:g.35449072C>T	ENSP00000385099:p.Glu563Lys		40140912	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	37	CCDS12440.2	.	.	.	.	.	.	.	.	.	.	c	2.721	-0.266507	0.05754	0.0	1.16E-4	ENSG00000180884	ENST00000404801;ENST00000379189	T	0.19250	2.16	2.81	-5.62	0.02481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04452	0.0122	N	0.01284	-0.91	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31392	-0.9945	9	0.18276	T	0.48	.	1.0872	0.01655	0.2924:0.1302:0.1202:0.4572	.	563	Q3KQV3	ZN792_HUMAN	K	563;323	ENSP00000385099:E563K	ENSP00000368487:E323K	E	-	1	0	ZNF792	40140912	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-5.606000	0.00110	-1.710000	0.01397	-0.251000	0.11542	GAA		0.522	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		T	35449072	C	T	35449072	3	4	61	1	0	0	0	0	1	0	0	0	18203	893	31	1	215	1	ZNF792	19	35449072	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14844	35449072	23679911	11051	19036										
HPN	3249	broad.mit.edu	37	chr19	35551573	35551573	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcgagtgtttgccggtgcCgtggcccaggcctctcccca	14	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35551573C>T	ENST00000262626.2	+	9	1488	c.663C>T	c.(661-663)gcC>gcT	p.A221A	HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000392226.1_Silent_p.A221A|HPN_ENST00000597419.1_Silent_p.A63A	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	221	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.A221A(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	TTGCCGGTGCCGTGGCCCAGG	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	19											75	68	70					19																	35551573		2203	4299	6502	40243413	SO:0001819	synonymous_variant	3249				CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.663C>T	19.37:g.35551573C>T			40243413	B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																				0.677	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35551573	C	T	35551573	2	4	61	1	0	0	0	0	0	0	0	1	7357	639	23	1		1	HPN	19	35551573	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102501	35551573	23577410	11052	19037										
HAMP	57817	broad.mit.edu	37	chr19	35775856	35775856	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagcccatgttccagaggCgaaggaggcgagacacccac	12	14	0	2	rs104894695		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35775856C>T	ENST00000598398.1	+	4	462	c.166C>T	c.(166-168)Cga>Tga	p.R56*	HAMP_ENST00000222304.3_Nonsense_Mutation_p.R56*	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	56					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)		p.R56*(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTTCCAGAGGCGAAGGAGGCG	0.582																																																1	Substitution - Nonsense(1)	large_intestine(1)	19	GRCh37	CM030043	HAMP	M	rs104894695						160	148	152					19																	35775856		2203	4300	6503	40467696	SO:0001587	stop_gained	57817			AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.166C>T	19.37:g.35775856C>T	ENSP00000471894:p.Arg56*		40467696	Q1HE14|Q9BY68	Nonsense_Mutation	SNP	ENST00000598398.1	37	CCDS12454.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.549627	0.45383	.	.	ENSG00000105697	ENST00000222304	.	.	.	4.51	0.802	0.18686	.	1.709840	0.03749	N	0.256263	.	.	.	.	.	.	0.58432	A	0.999993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5064	9.9108	0.41403	0.5677:0.4323:0.0:0.0	.	.	.	.	X	56	.	ENSP00000222304:R56X	R	+	1	2	HAMP	40467696	0.001000	0.12720	0.000000	0.03702	0.079000	0.17450	0.850000	0.27737	0.492000	0.27815	0.561000	0.74099	CGA		0.582	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		T	35775856	C	T	35775856	4	4	61	1	0	0	0	0	0	1	0	0	6969	760	27	1	176	1	HAMP	19	35775856	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	224283	35775856	23353127	11053	19038										
MAG	4099	broad.mit.edu	37	chr19	35791235	35791235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggtgacccccgccgaaGacggcgtctatgcctgcctg	14	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35791235G>T	ENST00000392213.3	+	6	1057	c.898G>T	c.(898-900)Gac>Tac	p.D300Y	MAG_ENST00000537831.2_Missense_Mutation_p.D275Y|MAG_ENST00000361922.4_Missense_Mutation_p.D300Y	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	300	Ig-like C2-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.D300Y(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCCCGCCGAAGACGGCGTCTA	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	19											25	26	25					19																	35791235		2200	4299	6499	40483075	SO:0001583	missense	4099			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.898G>T	19.37:g.35791235G>T	ENSP00000376048:p.Asp300Tyr		40483075	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	37	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	g	16.45	3.125567	0.56721	.	.	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.67698	-0.28;-0.28;-0.28	4.03	4.03	0.46877	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.056361	0.64402	D	0.000002	T	0.74458	0.3719	L	0.46885	1.475	0.50813	D	0.999891	D;D;D	0.69078	0.995;0.997;0.997	D;D;D	0.67103	0.917;0.925;0.949	T	0.77032	-0.2738	10	0.62326	D	0.03	.	13.6985	0.62593	0.0:0.0:1.0:0.0	.	337;300;300	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	Y	337;300;300;275	ENSP00000355234:D300Y;ENSP00000376048:D300Y;ENSP00000440695:D275Y	ENSP00000262624:D337Y	D	+	1	0	MAG	40483075	1.000000	0.71417	0.994000	0.49952	0.209000	0.24338	6.261000	0.72509	2.077000	0.62373	0.298000	0.19748	GAC		0.687	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		T	35791235	G	T	35791235	3	4	61	1	0	0	0	0	1	0	0	0	9192	942	33	2	912	2	MAG	19	35791235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15379	35791235	23337748	11054	19039										
MAG	4099	broad.mit.edu	37	chr19	35801460	35801460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtcctcagatcgactgatGtgggccaagatcgggcctgt	13	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35801460G>A	ENST00000392213.3	+	9	1689	c.1530G>A	c.(1528-1530)atG>atA	p.M510I	MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Missense_Mutation_p.M485I|MAG_ENST00000361922.4_Missense_Mutation_p.M510I	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	510					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.M510I(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATCGACTGATGTGGGCCAAGA	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	19											85	76	79					19																	35801460		2203	4300	6503	40493300	SO:0001583	missense	4099			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1530G>A	19.37:g.35801460G>A	ENSP00000376048:p.Met510Ile		40493300	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	37	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143705	0.37825	.	.	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.63255	0.11;-0.03;0.04	4.92	4.92	0.64577	.	0.045499	0.85682	D	0.000000	T	0.48259	0.1490	L	0.34521	1.04	0.51233	D	0.999915	B;B;B	0.31581	0.047;0.329;0.329	B;B;B	0.28849	0.008;0.065;0.095	T	0.42716	-0.9435	10	0.16420	T	0.52	.	13.5969	0.61996	0.0:0.0:1.0:0.0	.	547;510;510	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	I	547;510;510;485	ENSP00000355234:M510I;ENSP00000376048:M510I;ENSP00000440695:M485I	ENSP00000262624:M547I	M	+	3	0	MAG	40493300	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	5.777000	0.68931	2.257000	0.74773	0.462000	0.41574	ATG		0.577	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		A	35801460	G	A	35801460	3	1	61	1	0	0	0	0	1	0	0	0	9192	1377	48	3	1556	3	MAG	19	35801460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10225	35801460	23327523	11055	19040										
MAG	4099	broad.mit.edu	37	chr19	35802896	35802896	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagcagcgacttccgcatCtctggggcaccagagaagta	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35802896C>T	ENST00000392213.3	+	10	1851	c.1692C>T	c.(1690-1692)atC>atT	p.I564I	MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Silent_p.I539I|MAG_ENST00000361922.4_Silent_p.I564I	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	564					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.I564I(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ACTTCCGCATCTCTGGGGCAC	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	19											43	34	37					19																	35802896		2203	4300	6503	40494736	SO:0001819	synonymous_variant	4099			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1692C>T	19.37:g.35802896C>T			40494736	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																				0.622	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		T	35802896	C	T	35802896	2	4	61	1	0	0	0	0	0	0	0	1	9192	903	32	3		3	MAG	19	35802896	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1436	35802896	23326087	11056	19041										
CD22	933	broad.mit.edu	37	chr19	35823509	35823509	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttgagcaccctgaaaccCtctacgcctgggagggggcc	12	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35823509C>A	ENST00000085219.5	+	3	160	c.94C>A	c.(94-96)Ctc>Atc	p.L32I	CD22_ENST00000270311.6_5'UTR|CD22_ENST00000341773.6_Missense_Mutation_p.L32I|CD22_ENST00000544992.2_Missense_Mutation_p.L32I|CD22_ENST00000595419.1_3'UTR|CD22_ENST00000536635.2_Missense_Mutation_p.L32I|CD22_ENST00000594250.1_Missense_Mutation_p.L32I|U62631.5_ENST00000597110.1_RNA|CD22_ENST00000419549.2_5'UTR	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	32	Ig-like V-type.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.L32I(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCCTGAAACCCTCTACGCCTG	0.502																																					Ovarian(42;1009 1133 23674 26041)											1	Substitution - Missense(1)	large_intestine(1)	19											50	55	53					19																	35823509		2203	4300	6503	40515349	SO:0001583	missense	933			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.94C>A	19.37:g.35823509C>A	ENSP00000085219:p.Leu32Ile		40515349	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	C	7.746	0.702333	0.15172	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.32	-1.1	0.09872	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.715070	0.12102	N	0.499385	T	0.17066	0.0410	L	0.39397	1.21	0.24354	N	0.994909	B;B;B;B	0.25351	0.02;0.124;0.002;0.004	B;B;B;B	0.24269	0.016;0.052;0.002;0.011	T	0.34675	-0.9819	10	0.07325	T	0.83	.	4.2407	0.10647	0.2455:0.442:0.2366:0.0759	.	32;32;32;32	F5GYU4;F5H7U3;P20273;P20273-2	.;.;CD22_HUMAN;.	I	32	ENSP00000085219:L32I;ENSP00000442279:L32I;ENSP00000339349:L32I;ENSP00000441237:L32I	ENSP00000085219:L32I	L	+	1	0	CD22	40515349	0.000000	0.05858	0.028000	0.17463	0.049000	0.14656	-0.769000	0.04710	-0.246000	0.09611	-3.118000	0.00062	CTC		0.502	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		A	35823509	C	A	35823509	3	1	61	1	0	0	0	0	1	0	0	0	2991	681	24	2	100	2	CD22	19	35823509	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20613	35823509	23305474	11057	19042										
CD22	933	broad.mit.edu	37	chr19	35827039	35827039	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcctgctatgggtatccGatccaattgcagtggctcct	9	12	1	0	rs534159105		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35827039G>A	ENST00000085219.5	+	4	579	c.513G>A	c.(511-513)ccG>ccA	p.P171P	CD22_ENST00000270311.6_Silent_p.P51P|CD22_ENST00000341773.6_Silent_p.P171P|CD22_ENST00000544992.2_Silent_p.P171P|CD22_ENST00000536635.2_Silent_p.P171P|CD22_ENST00000594250.1_Silent_p.P171P|CD22_ENST00000419549.2_Intron	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	171	Ig-like C2-type 1.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.P171P(2)		breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATGGGTATCCGATCCAATTGC	0.532													G|||	1	0.000199681	0	0	5008	,	,		19162	0		0	False		,,,				2504	0.001				Ovarian(42;1009 1133 23674 26041)											2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	19											94	98	96					19																	35827039		2203	4300	6503	40518879	SO:0001819	synonymous_variant	933			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.513G>A	19.37:g.35827039G>A			40518879	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																				0.532	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		A	35827039	G	A	35827039	2	1	61	1	0	0	0	0	0	0	0	1	2991	1045	37	1		1	CD22	19	35827039	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3530	35827039	23301944	11058	19043										
FFAR2	2867	broad.mit.edu	37	chr19	35940829	35940829	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagatcatcgaggctgcgtcGaacttccgctggtacctgcc	11	13	1	1	rs373797261		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35940829G>A	ENST00000599180.2	+	2	293	c.213G>A	c.(211-213)tcG>tcA	p.S71S	FFAR2_ENST00000246549.2_Silent_p.S71S|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2	71					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.S71S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	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)			AGGCTGCGTCGAACTTCCGCT	0.627																																					GBM(40;139 809 9833 23358 48736)											2	Substitution - coding silent(2)	large_intestine(2)	19						G		1,4405	2.1+/-5.4	0,1,2202	52	42	45		213	-11.2	0	19		45	0,8600		0,0,4300	no	coding-synonymous	FFAR2	NM_005306.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		71/331	35940829	1,13005	2203	4300	6503	40632669	SO:0001819	synonymous_variant	2867			AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.213G>A	19.37:g.35940829G>A			40632669	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	37	CCDS12461.1																																																																																				0.627	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		A	35940829	G	A	35940829	2	1	61	1	0	0	0	0	0	0	0	1	5847	1045	37	1		1	FFAR2	19	35940829	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113790	35940829	23188154	11059	19044										
FFAR2	2867	broad.mit.edu	37	chr19	35940982	35940982	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacaagctctcccgccgGcctctgtatggagtgattgc	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35940982G>A	ENST00000599180.2	+	2	446	c.366G>A	c.(364-366)cgG>cgA	p.R122R	FFAR2_ENST00000246549.2_Silent_p.R122R|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2	122					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R122R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	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)			TCTCCCGCCGGCCTCTGTATG	0.572																																					GBM(40;139 809 9833 23358 48736)											1	Substitution - coding silent(1)	large_intestine(1)	19											87	77	80					19																	35940982		2203	4300	6503	40632822	SO:0001819	synonymous_variant	2867			AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.366G>A	19.37:g.35940982G>A			40632822	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	37	CCDS12461.1																																																																																				0.572	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		A	35940982	G	A	35940982	2	1	61	1	0	0	0	0	0	0	0	1	5847	1190	42	3		3	FFAR2	19	35940982	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	153	35940982	23188001	11060	19045										
FFAR2	2867	broad.mit.edu	37	chr19	35941525	35941525	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccctgttgggacgcagaggCaaagacacagcagaggggac	15	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35941525C>G	ENST00000599180.2	+	2	989	c.909C>G	c.(907-909)ggC>ggG	p.G303G	FFAR2_ENST00000246549.2_Silent_p.G303G|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2	303					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.G303G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	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)			GACGCAGAGGCAAAGACACAG	0.567																																					GBM(40;139 809 9833 23358 48736)											1	Substitution - coding silent(1)	large_intestine(1)	19											71	72	71					19																	35941525		2203	4300	6503	40633365	SO:0001819	synonymous_variant	2867			AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.909C>G	19.37:g.35941525C>G			40633365	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	37	CCDS12461.1																																																																																				0.567	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		G	35941525	C	G	35941525	2	3	61	1	0	0	0	0	0	0	0	1	5847	697	25	5		5	FFAR2	19	35941525	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	543	35941525	23187458	11061	19046										
DMKN	93099	broad.mit.edu	37	chr19	35991440	35991440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacagagactcacctgatCgtctctgcctgcacgtttct	9	13	3	2	rs547354931		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:35991440C>T	ENST00000339686.3	-	12	1458	c.1282G>A	c.(1282-1284)Gat>Aat	p.D428N	DMKN_ENST00000414866.2_Missense_Mutation_p.D141N|DMKN_ENST00000467637.1_Missense_Mutation_p.D153N|DMKN_ENST00000436012.1_Missense_Mutation_p.D124N|DMKN_ENST00000462126.1_5'UTR|DMKN_ENST00000492341.2_Missense_Mutation_p.D75N|DMKN_ENST00000443640.1_Missense_Mutation_p.D191N|DMKN_ENST00000480502.1_Missense_Mutation_p.D122N|DMKN_ENST00000602781.1_Missense_Mutation_p.D141N|DMKN_ENST00000472252.2_Missense_Mutation_p.D75N|DMKN_ENST00000419602.1_Missense_Mutation_p.D417N|DMKN_ENST00000402589.2_Missense_Mutation_p.D141N|DMKN_ENST00000429837.1_Missense_Mutation_p.D387N|DMKN_ENST00000408915.2_Missense_Mutation_p.D42N	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	428						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.D428N(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	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)			CTCACCTGATCGTCTCTGCCT	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		19166	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											84	54	64					19																	35991440		2203	4300	6503	40683280	SO:0001583	missense	93099			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1282G>A	19.37:g.35991440C>T	ENSP00000342012:p.Asp428Asn		40683280	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.773|5.773	0.327002|0.327002	0.10900|0.10900	.|.	.|.	ENSG00000161249|ENSG00000161249	ENST00000408915;ENST00000402589;ENST00000339686;ENST00000436012;ENST00000414866;ENST00000429837;ENST00000419602;ENST00000443640|ENST00000434389	T;T;T;T;T;T;T;T|.	0.40756|.	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02|.	4.11|4.11	2.91|2.91	0.33838|0.33838	.|.	0.169711|.	0.27881|.	N|.	0.017472|.	T|T	0.31979|0.31979	0.0814|0.0814	L|L	0.29908|0.29908	0.895|0.895	0.18873|0.18873	N|N	0.999989|0.999989	B;B;P;B;P;P;D;B;B;B;B;B|.	0.63046|.	0.086;0.086;0.642;0.164;0.564;0.787;0.992;0.433;0.086;0.009;0.012;0.319|.	B;B;B;B;B;B;P;B;B;B;B;B|.	0.50791|.	0.008;0.008;0.062;0.042;0.061;0.14;0.65;0.049;0.008;0.003;0.003;0.018|.	T|T	0.18967|0.18967	-1.0320|-1.0320	10|5	0.36615|.	T|.	0.2|.	-2.8987|-2.8987	7.6162|7.6162	0.28158|0.28158	0.0:0.8677:0.0:0.1323|0.0:0.8677:0.0:0.1323	.|.	124;75;84;84;104;122;417;387;428;141;191;42|.	B4E3D1;B7ZB10;Q6E0U4-12;Q6E0U4-11;Q6E0U4-10;Q6E0U4-9;C9J4P6;Q6E0U4-4;Q6E0U4;Q6E0U4-8;C9IYI1;Q6E0U4-15|.	.;.;.;.;.;.;.;.;DMKN_HUMAN;.;.;.|.	N|Q	42;141;428;124;141;387;417;191|138	ENSP00000386225:D42N;ENSP00000384509:D141N;ENSP00000342012:D428N;ENSP00000412075:D124N;ENSP00000392222:D141N;ENSP00000405503:D387N;ENSP00000391036:D417N;ENSP00000406864:D191N|.	ENSP00000342012:D428N|.	D|R	-|-	1|2	0|0	DMKN|DMKN	40683280|40683280	0.000000|0.000000	0.05858|0.05858	0.050000|0.050000	0.19076|0.19076	0.208000|0.208000	0.24298|0.24298	-0.678000|-0.678000	0.05209|0.05209	0.910000|0.910000	0.36722|0.36722	0.436000|0.436000	0.28706|0.28706	GAT|CGA		0.607	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	35991440	C	T	35991440	3	4	61	1	0	0	0	0	1	0	0	0	4593	884	31	1	210	1	DMKN	19	35991440	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49915	35991440	23137543	11062	19047										
RBM42	79171	broad.mit.edu	37	chr19	36125221	36125221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaattgaaacggtgcattCgcacagcggcagggagcagc	14	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36125221C>T	ENST00000262633.4	+	8	1186	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	RBM42_ENST00000592202.1_Missense_Mutation_p.R307C|RBM42_ENST00000589559.1_Missense_Mutation_p.R332C|RBM42_ENST00000360475.4_Missense_Mutation_p.R332C|RBM42_ENST00000589871.1_Missense_Mutation_p.R339C|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000588161.1_Missense_Mutation_p.R331C	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	361	Necessary for interaction with HNRNPK. {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R361C(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ACGGTGCATTCGCACAGCGGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											54	49	50					19																	36125221		2203	4300	6503	40817061	SO:0001583	missense	79171			BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"RNA binding motif (RRM) containing"	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.1081C>T	19.37:g.36125221C>T	ENSP00000262633:p.Arg361Cys		40817061	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	37	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804923	0.70682	.	.	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.10005	2.92;2.99	5.91	5.91	0.95273	.	0.049334	0.85682	D	0.000000	T	0.31482	0.0798	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.992;0.999	D;P;P;P	0.64321	0.924;0.796;0.858;0.719	T	0.00363	-1.1788	10	0.87932	D	0	-4.6372	17.7902	0.88550	0.0:1.0:0.0:0.0	.	327;332;331;361	Q9BTD8-4;Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;.;RBM42_HUMAN	C	361;332	ENSP00000262633:R361C;ENSP00000353663:R332C	ENSP00000262633:R361C	R	+	1	0	RBM42	40817061	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	5.458000	0.66679	2.813000	0.96785	0.655000	0.94253	CGC		0.607	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		T	36125221	C	T	36125221	3	4	61	1	0	0	0	0	1	0	0	0	13173	884	31	1	1111	1	RBM42	19	36125221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	133781	36125221	23003762	11063	19048										
ZBTB32	27033	broad.mit.edu	37	chr19	36205935	36205935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagccagagaaaccctcaaGgaatcctgagagagaactgg	13	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36205935G>T	ENST00000392197.2	+	3	725	c.407G>T	c.(406-408)aGg>aTg	p.R136M	KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.R136M|KMT2B_ENST00000341701.1_5'Flank			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	136					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R136M(1)		large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AAACCCTCAAGGAATCCTGAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19											42	46	44					19																	36205935		2203	4300	6503	40897775	SO:0001583	missense	27033			AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.407G>T	19.37:g.36205935G>T	ENSP00000376035:p.Arg136Met		40897775	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	37	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.961634	0.34659	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09445	2.98;2.98	4.69	2.47	0.30058	.	0.275741	0.26387	N	0.024671	T	0.07143	0.0181	L	0.32530	0.975	0.09310	N	1	B	0.29378	0.243	B	0.20955	0.032	T	0.28332	-1.0047	10	0.54805	T	0.06	-3.6209	5.9941	0.19483	0.0994:0.0:0.7138:0.1868	.	136	Q9Y2Y4	ZBT32_HUMAN	M	136	ENSP00000262630:R136M;ENSP00000376035:R136M	ENSP00000262630:R136M	R	+	2	0	ZBTB32	40897775	0.001000	0.12720	0.004000	0.12327	0.382000	0.30200	0.451000	0.21779	0.482000	0.27582	0.655000	0.94253	AGG		0.547	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		T	36205935	G	T	36205935	3	4	61	1	0	0	0	0	1	0	0	0	17574	1000	35	2	409	2	ZBTB32	19	36205935	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80714	36205935	22923048	11064	19049										
MLL4	9757	broad.mit.edu	37	chr19	36227600	36227600	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgggaccaggtgaggcttCgagctctgaggaagagcctc	15	10	1	3	rs367682204		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36227600C>T	ENST00000222270.7	+	31	7169	c.7169C>T	c.(7168-7170)tCg>tTg	p.S2390L	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.S2390L	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2390					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S2392L(1)									GGTGAGGCTTCGAGCTCTGAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	LEU/SER	0,3972		0,0,1986	48	51	50		7169	5.8	1	19		50	1,8315		0,1,4157	no	missense	MLL4	NM_014727.1	145	0,1,6143	TT,TC,CC		0.012,0.0,0.0081	probably-damaging	2390/2716	36227600	1,12287	1986	4158	6144	40919440	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7169C>T	19.37:g.36227600C>T	ENSP00000222270:p.Ser2390Leu		40919440	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.031021	0.54790	0.0	1.2E-4	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.84298	-1.83;-1.83	5.84	5.84	0.93424	.	0.000000	0.35615	N	0.003096	D	0.84437	0.5472	L	0.46157	1.445	0.38496	D	0.948107	D	0.63046	0.992	P	0.45610	0.487	D	0.85958	0.1468	10	0.48119	T	0.1	.	18.9181	0.92515	0.0:1.0:0.0:0.0	.	2390	Q9UMN6	MLL4_HUMAN	L	2390	ENSP00000222270:S2390L;ENSP00000398837:S2390L	ENSP00000222270:S2390L	S	+	2	0	AD000671.1	40919440	0.995000	0.38212	0.990000	0.47175	0.980000	0.70556	3.422000	0.52749	2.755000	0.94549	0.655000	0.94253	TCG		0.587	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36227600	C	T	36227600	3	4	61	1	0	0	0	0	1	0	0	0	9653	893	31	1	7291	1	MLL4	19	36227600	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21665	36227600	22901383	11065	19050										
C19orf55	148137	broad.mit.edu	37	chr19	36255827	36255827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcagagctgccaggctgCtcaaacgcaggtgcccgcac	13	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36255827C>T	ENST00000544099.1	+	6	679	c.616C>T	c.(616-618)Ctc>Ttc	p.L206F	C19orf55_ENST00000396908.4_Missense_Mutation_p.L206F			Q2NL68	PRSR3_HUMAN		206								p.L206F(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	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)			TGCCAGGCTGCTCAAACGCAG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											50	61	57					19																	36255827		2117	4240	6357	40947667	SO:0001583	missense	148137																														ENST00000544099.1:c.616C>T	19.37:g.36255827C>T	ENSP00000467267:p.Leu206Phe		40947667	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	37		.	.	.	.	.	.	.	.	.	.	C	16.91	3.253841	0.59212	.	.	ENSG00000167595	ENST00000396908;ENST00000301165	T;T	0.52526	0.66;0.66	4.42	3.39	0.38822	.	0.000000	0.32671	N	0.005786	T	0.50188	0.1601	M	0.66939	2.045	0.09310	N	1	D	0.54047	0.964	P	0.48873	0.593	T	0.47275	-0.9130	10	0.66056	D	0.02	-21.4605	8.2684	0.31829	0.0:0.8908:0.0:0.1092	.	206	E5RFB9	.	F	206;205	ENSP00000380116:L206F;ENSP00000301165:L205F	ENSP00000301165:L205F	L	+	1	0	C19orf55	40947667	0.989000	0.36119	0.164000	0.22755	0.981000	0.71138	3.261000	0.51530	1.217000	0.43442	0.558000	0.71614	CTC		0.637	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2			T	36255827	C	T	36255827	3	4	61	1	0	0	0	0	1	0	0	0	1943	797	28	3	638	3	C19orf55	19	36255827	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28227	36255827	22873156	11066	19051										
NPHS1	4868	broad.mit.edu	37	chr19	36317520	36317520	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggatcctgatatgtgtCttcaggccagtggaggtccc	12	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36317520C>A	ENST00000378910.5	-	29	3621	c.3622G>T	c.(3622-3624)Gac>Tac	p.D1208Y	NPHS1_ENST00000353632.6_Missense_Mutation_p.D1168Y	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1208	Binds to NPHS2.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.D1208Y(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGATATGTGTCTTCAGGCCAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	77	79					19																	36317520		2203	4300	6503	41009360	SO:0001583	missense	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3622G>T	19.37:g.36317520C>A	ENSP00000368190:p.Asp1208Tyr		41009360	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	C	3.222	-0.159255	0.06544	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.74737	-0.74;-0.87	4.83	2.7	0.31948	.	1.066700	0.07199	N	0.857163	T	0.59649	0.2209	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.49799	-0.8901	10	0.51188	T	0.08	-4.4491	6.4056	0.21662	0.0:0.6995:0.2012:0.0993	.	1208	O60500	NPHN_HUMAN	Y	1208;1168	ENSP00000368190:D1208Y;ENSP00000343634:D1168Y	ENSP00000343634:D1168Y	D	-	1	0	NPHS1	41009360	0.001000	0.12720	0.010000	0.14722	0.005000	0.04900	0.120000	0.15647	0.668000	0.31126	0.644000	0.83932	GAC		0.537	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			A	36317520	C	A	36317520	3	1	61	1	0	0	0	0	1	0	0	0	10613	913	32	2	107	2	NPHS1	19	36317520	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61693	36317520	22811463	11067	19052										
NPHS1	4868	broad.mit.edu	37	chr19	36334418	36334418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggaggatgggattggcatCgacagtgcagactatgtcca	15	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36334418C>T	ENST00000378910.5	-	17	2289	c.2290G>A	c.(2290-2292)Gat>Aat	p.D764N	NPHS1_ENST00000353632.6_Missense_Mutation_p.D764N	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	764	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.D764N(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGATTGGCATCGACAGTGCAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											142	127	132					19																	36334418		2203	4300	6503	41026258	SO:0001583	missense	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2290G>A	19.37:g.36334418C>T	ENSP00000368190:p.Asp764Asn		41026258	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296626	0.81025	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.13307	2.6;2.6	5.04	5.04	0.67666	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051623	0.85682	D	0.000000	T	0.31638	0.0803	L	0.49256	1.55	0.50632	D	0.999882	D	0.89917	1.0	D	0.87578	0.998	T	0.01312	-1.1388	10	0.87932	D	0	-14.3377	14.3119	0.66422	0.0:1.0:0.0:0.0	.	764	O60500	NPHN_HUMAN	N	764	ENSP00000368190:D764N;ENSP00000343634:D764N	ENSP00000343634:D764N	D	-	1	0	NPHS1	41026258	0.998000	0.40836	0.791000	0.31998	0.612000	0.37316	5.194000	0.65125	2.532000	0.85374	0.456000	0.33151	GAT		0.582	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36334418	C	T	36334418	3	4	61	1	0	0	0	0	1	0	0	0	10613	884	31	1	1487	1	NPHS1	19	36334418	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16898	36334418	22794565	11068	19053										
TYROBP	7305	broad.mit.edu	37	chr19	36398646	36398646	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctaccgctctgggcctggGcctggacaggacggagacct	15	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36398646G>T	ENST00000262629.4	-	2	146	c.80C>A	c.(79-81)gCc>gAc	p.A27D	TYROBP_ENST00000544690.2_Intron|TYROBP_ENST00000585901.2_Missense_Mutation_p.A27D|TYROBP_ENST00000589517.1_Missense_Mutation_p.A27D|TYROBP_ENST00000424586.3_Intron	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	27					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)	p.A27D(1)		NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGGGCCTGGGCCTGGACAGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											47	47	47					19																	36398646		2203	4300	6503	41090486	SO:0001583	missense	7305			AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"killer activating receptor associated protein", "DNAX-activation protein 12"	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.80C>A	19.37:g.36398646G>T	ENSP00000262629:p.Ala27Asp		41090486	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Missense_Mutation	SNP	ENST00000262629.4	37	CCDS12482.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.279340	0.59758	.	.	ENSG00000011600	ENST00000262629;ENST00000424586	D	0.86297	-2.1	5.1	3.99	0.46301	.	0.418688	0.20067	N	0.099949	T	0.76962	0.4061	N	0.08118	0	0.80722	D	1	P;P	0.47762	0.9;0.9	P;P	0.44990	0.466;0.466	T	0.80551	-0.1332	10	0.87932	D	0	-21.8944	10.7109	0.45982	0.0:0.1932:0.8068:0.0	.	27;27	O43914-2;O43914	.;TYOBP_HUMAN	D	27	ENSP00000262629:A27D	ENSP00000262629:A27D	A	-	2	0	TYROBP	41090486	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.091000	0.64505	2.365000	0.80145	0.467000	0.42956	GCC		0.597	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1			T	36398646	G	T	36398646	3	4	61	1	0	0	0	0	1	0	0	0	16855	1203	42	2	277	2	TYROBP	19	36398646	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64228	36398646	22730337	11069	19054										
WDR62	284403	broad.mit.edu	37	chr19	36575580	36575580	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgagctgcacttcatggacGagctggtcaaggtggaggcc	15	10	2	0	rs147875659		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36575580G>A	ENST00000270301.7	+	12	1576	c.1576G>A	c.(1576-1578)Gag>Aag	p.E526K	WDR62_ENST00000401500.2_Missense_Mutation_p.E526K			O43379	WDR62_HUMAN	WD repeat domain 62	526			E -> K (in MCPH2). {ECO:0000269|PubMed:20729831}.		cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.E526K(1)		cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTTCATGGACGAGCTGGTCAA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	103	86	92		1576,1576	5.2	1	19	dbSNP_134	92	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	WDR62	NM_001083961.1,NM_173636.4	56,56	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	526/1524,526/1519	36575580	3,13003	2203	4300	6503	41267420	SO:0001583	missense	284403			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"WD repeat domain containing"	24502	protein-coding gene	gene with protein product		613583	"chromosome 19 open reading frame 14", "microcephaly, primary autosomal recessive 2"	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.1576G>A	19.37:g.36575580G>A	ENSP00000270301:p.Glu526Lys		41267420	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	.	.	.	.	.	.	.	.	.	.	G	31	5.073553	0.94000	2.27E-4	2.33E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.57436	1.04;0.4	5.15	5.15	0.70609	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71829	0.3386	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.986;0.999	T	0.68731	-0.5331	10	0.24483	T	0.36	-28.9554	16.4688	0.84094	0.0:0.0:1.0:0.0	.	526;526	O43379-4;O43379	.;WDR62_HUMAN	K	526	ENSP00000384792:E526K;ENSP00000270301:E526K	ENSP00000270301:E526K	E	+	1	0	WDR62	41267420	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	7.272000	0.78516	2.558000	0.86282	0.561000	0.74099	GAG		0.617	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		A	36575580	G	A	36575580	3	1	61	1	0	0	0	0	1	0	0	0	17353	1059	37	1	1622	1	WDR62	19	36575580	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176934	36575580	22553403	11070	19055										
ZNF565	147929	broad.mit.edu	37	chr19	36673447	36673447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacactctctacattcgtaaGgtttgataccaggatgaatt	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36673447G>A	ENST00000355114.5	-	5	2267	c.1541C>T	c.(1540-1542)cCt>cTt	p.P514L	ZNF565_ENST00000304116.5_Missense_Mutation_p.P474L|ZNF565_ENST00000392173.2_Missense_Mutation_p.P474L			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P474L(1)		large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			ACATTCGTAAGGTTTGATACC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	99	103					19																	36673447		2203	4300	6503	41365287	SO:0001583	missense	147929			AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.1541C>T	19.37:g.36673447G>A	ENSP00000347234:p.Pro514Leu		41365287	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	37		.	.	.	.	.	.	.	.	.	.	g	13.68	2.308797	0.40895	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.27557	1.66;1.66;1.66	4.81	4.81	0.61882	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34435	N	0.003961	T	0.37785	0.1016	L	0.42686	1.345	0.41034	D	0.985172	P	0.50528	0.936	P	0.50490	0.642	T	0.17961	-1.0352	10	0.62326	D	0.03	.	15.8101	0.78552	0.0:0.0:1.0:0.0	.	474	Q8N9K5	ZN565_HUMAN	L	474;474;514	ENSP00000376013:P474L;ENSP00000306869:P474L;ENSP00000347234:P514L	ENSP00000306869:P474L	P	-	2	0	ZNF565	41365287	1.000000	0.71417	0.947000	0.38551	0.098000	0.18820	5.181000	0.65054	2.673000	0.90976	0.650000	0.86243	CCT		0.423	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		A	36673447	G	A	36673447	3	1	61	1	0	0	0	0	1	0	0	0	18035	1000	35	3	82	3	ZNF565	19	36673447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	97867	36673447	22455536	11071	19056										
ZNF565	147929	broad.mit.edu	37	chr19	36685205	36685205	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttgctccaataaggagacGacatcaggcttagaaatgga	10	9	1	2	rs139103330	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36685205G>A	ENST00000355114.5	-	4	1008	c.282C>T	c.(280-282)gtC>gtT	p.V94V	ZNF565_ENST00000304116.5_Silent_p.V54V|ZNF565_ENST00000392173.2_Silent_p.V54V			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	94	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V54V(1)		large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			ATAAGGAGACGACATCAGGCT	0.507													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		18987	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G	,	1,4405	2.1+/-5.4	0,1,2202	74	60	65		162,162	1.6	1	19	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ZNF565	NM_001042474.1,NM_152477.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	54/500,54/500	36685205	1,13005	2203	4300	6503	41377045	SO:0001819	synonymous_variant	147929			AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.282C>T	19.37:g.36685205G>A			41377045	B3KQ35|Q6NUS2	Silent	SNP	ENST00000355114.5	37																																																																																					0.507	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		A	36685205	G	A	36685205	2	1	61	1	0	0	0	0	0	0	0	1	18035	1045	37	1		1	ZNF565	19	36685205	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11758	36685205	22443778	11072	19057										
ZFP14	57677	broad.mit.edu	37	chr19	36831229	36831229	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctcaccagtatgaattCtctggtgttgagtaagaaat	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36831229C>A	ENST00000270001.7	-	5	1614	c.1499G>T	c.(1498-1500)aGa>aTa	p.R500I		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	500					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R500I(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					AGTATGAATTCTCTGGTGTTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	69	70					19																	36831229		2203	4300	6503	41523069	SO:0001583	missense	57677			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.1499G>T	19.37:g.36831229C>A	ENSP00000270001:p.Arg500Ile		41523069	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	c	16.12	3.034027	0.54896	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.24908	1.83	3.93	3.93	0.45458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000243	T	0.48786	0.1519	M	0.76002	2.32	0.80722	D	1	D;D	0.62365	0.99;0.991	D;D	0.66497	0.94;0.944	T	0.52909	-0.8512	10	0.51188	T	0.08	.	15.22	0.73303	0.0:1.0:0.0:0.0	.	500;500	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	I	500	ENSP00000270001:R500I	ENSP00000270001:R500I	R	-	2	0	ZFP14	41523069	0.000000	0.05858	1.000000	0.80357	0.994000	0.84299	0.471000	0.22100	2.177000	0.69029	0.551000	0.68910	AGA		0.388	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		A	36831229	C	A	36831229	3	1	61	1	0	0	0	0	1	0	0	0	17678	913	32	2	106	2	ZFP14	19	36831229	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	146024	36831229	22297754	11073	19058										
ZFP14	57677	broad.mit.edu	37	chr19	36831575	36831575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtatgtattctctgatggcGaactagttgttgtcttaatc	9	6	2	1	rs571512137		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36831575G>A	ENST00000270001.7	-	5	1268	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R385C(2)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					CTCTGATGGCGAACTAGTTGT	0.388													G|||	1	0.000199681	0	0	5008	,	,		22777	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	19											109	101	104					19																	36831575		2203	4300	6503	41523415	SO:0001583	missense	57677			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.1153C>T	19.37:g.36831575G>A	ENSP00000270001:p.Arg385Cys		41523415	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	g	13.75	2.331050	0.41297	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.26660	1.72	4.1	4.1	0.47936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43919	D	0.000513	T	0.44138	0.1279	M	0.75884	2.315	0.21325	N	0.999727	D;D	0.76494	0.999;0.999	D;D	0.65987	0.94;0.94	T	0.27191	-1.0081	10	0.59425	D	0.04	.	7.4247	0.27092	0.0:0.1812:0.632:0.1868	.	385;385	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	C	385	ENSP00000270001:R385C	ENSP00000270001:R385C	R	-	1	0	ZFP14	41523415	0.000000	0.05858	1.000000	0.80357	0.989000	0.77384	-0.099000	0.11007	2.270000	0.75569	0.643000	0.83706	CGC		0.388	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		A	36831575	G	A	36831575	3	1	61	1	0	0	0	0	1	0	0	0	17678	1058	37	1	452	1	ZFP14	19	36831575	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	346	36831575	22297408	11074	19059										
ZFP14	57677	broad.mit.edu	37	chr19	36832181	36832181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgactaagtgttgagcgacGaataaaggtcttcctacact	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36832181G>A	ENST00000270001.7	-	5	662	c.547C>T	c.(547-549)Cgt>Tgt	p.R183C		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R183C(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					GTTGAGCGACGAATAAAGGTC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											158	151	153					19																	36832181		2203	4300	6503	41524021	SO:0001583	missense	57677			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.547C>T	19.37:g.36832181G>A	ENSP00000270001:p.Arg183Cys		41524021	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	g	9.322	1.058214	0.19987	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.36340	1.26	3.85	2.81	0.32909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46145	D	0.000302	T	0.28732	0.0712	L	0.28458	0.855	0.20403	N	0.999909	D;D	0.69078	0.997;0.993	P;P	0.49708	0.62;0.519	T	0.06570	-1.0819	10	0.37606	T	0.19	.	6.1661	0.20390	0.1056:0.0:0.7051:0.1893	.	183;183	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	C	183	ENSP00000270001:R183C	ENSP00000270001:R183C	R	-	1	0	ZFP14	41524021	0.001000	0.12720	1.000000	0.80357	0.983000	0.72400	0.866000	0.27954	2.139000	0.66308	0.549000	0.68633	CGT		0.403	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		A	36832181	G	A	36832181	3	1	61	1	0	0	0	0	1	0	0	0	17678	1058	37	1	1058	1	ZFP14	19	36832181	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	606	36832181	22296802	11075	19060										
ZFP82	284406	broad.mit.edu	37	chr19	36883819	36883819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacactcaaagggtttttCgccagtatgaatgctctgat	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36883819C>T	ENST00000392161.3	-	5	1665	c.1423G>A	c.(1423-1425)Gaa>Aaa	p.E475K	ZFP82_ENST00000392171.1_Missense_Mutation_p.E475K	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E475K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AAGGGTTTTTCGCCAGTATGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											92	90	90					19																	36883819		2203	4300	6503	41575659	SO:0001583	missense	284406			AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1423G>A	19.37:g.36883819C>T	ENSP00000431265:p.Glu475Lys		41575659	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	37	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.726789	0.69074	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.24350	1.86;1.86	4.2	4.2	0.49525	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42420	D	0.000718	T	0.43590	0.1254	L	0.48260	1.515	0.41362	D	0.987434	D	0.89917	1.0	D	0.91635	0.999	T	0.39542	-0.9609	10	0.66056	D	0.02	.	14.447	0.67359	0.0:1.0:0.0:0.0	.	475	Q8N141	ZFP82_HUMAN	K	475	ENSP00000431265:E475K;ENSP00000446080:E475K	ENSP00000431265:E475K	E	-	1	0	ZFP82	41575659	0.982000	0.34865	0.999000	0.59377	0.959000	0.62525	3.735000	0.55044	2.352000	0.79861	0.591000	0.81541	GAA		0.383	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		T	36883819	C	T	36883819	3	4	61	1	0	0	0	0	1	0	0	0	17692	893	31	1	179	1	ZFP82	19	36883819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51638	36883819	22245164	11076	19061										
ZFP82	284406	broad.mit.edu	37	chr19	36898878	36898878	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtattcccactcttctggaGagaagtctatggatacatca	9	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:36898878G>T	ENST00000392161.3	-	3	289	c.47C>A	c.(46-48)tCt>tAt	p.S16Y	ZFP82_ENST00000392171.1_Missense_Mutation_p.S16Y	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S16Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CTCTTCTGGAGAGAAGTCTAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											125	109	114					19																	36898878		2203	4300	6503	41590718	SO:0001583	missense	284406			AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.47C>A	19.37:g.36898878G>T	ENSP00000431265:p.Ser16Tyr		41590718	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	37	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352269	0.41700	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.02944	4.1;4.1	3.08	3.08	0.35506	Krueppel-associated box (4);	.	.	.	.	T	0.24928	0.0605	H	0.98866	4.355	0.33845	D	0.631987	D	0.71674	0.998	D	0.71414	0.973	T	0.54070	-0.8348	9	0.87932	D	0	.	9.8948	0.41311	0.0:0.0:1.0:0.0	.	16	Q8N141	ZFP82_HUMAN	Y	16	ENSP00000431265:S16Y;ENSP00000446080:S16Y	ENSP00000431265:S16Y	S	-	2	0	ZFP82	41590718	0.997000	0.39634	0.996000	0.52242	0.461000	0.32589	3.113000	0.50376	2.034000	0.60081	0.591000	0.81541	TCT		0.398	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		T	36898878	G	T	36898878	3	4	61	1	0	0	0	0	1	0	0	0	17692	942	33	2	1563	2	ZFP82	19	36898878	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15059	36898878	22230105	11077	19062										
ZNF260	339324	broad.mit.edu	37	chr19	37006040	37006040	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcttcaggctaaaagttTttctacattcattacattca	4	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37006040T>G	ENST00000523638.1	-	3	1222	c.101A>C	c.(100-102)aAa>aCa	p.K34T	ZNF260_ENST00000593142.1_Missense_Mutation_p.K34T|ZNF260_ENST00000592282.1_Missense_Mutation_p.K34T|ZNF260_ENST00000588993.1_Missense_Mutation_p.K34T	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	34					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K34T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					GCTAAAAGTTTTTCTACATTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											94	94	94					19																	37006040		2203	4300	6503	41697880	SO:0001583	missense	339324			AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"Zinc fingers, C2H2-type"	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.101A>C	19.37:g.37006040T>G	ENSP00000429803:p.Lys34Thr		41697880	Q0VF43	Missense_Mutation	SNP	ENST00000523638.1	37	CCDS33003.1	.	.	.	.	.	.	.	.	.	.	T	6.859	0.527758	0.13127	.	.	ENSG00000254004	ENST00000523638	T	0.27890	1.64	4.32	0.986	0.19784	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42314	0.1197	M	0.88105	2.93	0.24335	N	0.994988	B	0.26512	0.151	B	0.37888	0.26	T	0.51379	-0.8713	9	0.72032	D	0.01	.	4.268	0.10773	0.149:0.174:0.0:0.6771	.	34	Q3ZCT1	ZN260_HUMAN	T	34	ENSP00000429803:K34T	ENSP00000429803:K34T	K	-	2	0	ZNF260	41697880	0.944000	0.32072	0.000000	0.03702	0.007000	0.05969	3.200000	0.51051	0.003000	0.14656	-0.509000	0.04479	AAA		0.378	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756		G	37006040	T	G	37006040	3	3	61	1	0	0	0	0	1	0	0	0	17841	1841	64	4	1141	4	ZNF260	19	37006040	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	107162	37006040	22122943	11078	19063										
ZNF529	57711	broad.mit.edu	37	chr19	37038602	37038602	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctaaaggatttcccacaGaatgagcattcaaagtgttt	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37038602G>T	ENST00000591340.1	-	5	1016	c.858C>A	c.(856-858)ttC>ttA	p.F286L	ZNF529_ENST00000334116.7_Missense_Mutation_p.F181L	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F285L(1)|p.F286L(1)		breast(1)	1	Esophageal squamous(110;0.198)					ATTTCCCACAGAATGAGCATT	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	19											152	152	152					19																	37038602		1973	4201	6174	41730442	SO:0001583	missense	57711			AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"Zinc fingers, C2H2-type", "-"	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.858C>A	19.37:g.37038602G>T	ENSP00000465578:p.Phe286Leu		41730442	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	37	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381404	0.24944	.	.	ENSG00000186020	ENST00000334116	.	.	.	3.52	-0.555	0.11807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13200	0.0320	N	0.10733	0.035	0.09310	N	0.999995	P;P	0.36837	0.571;0.454	B;B	0.37780	0.168;0.258	T	0.17992	-1.0351	8	0.87932	D	0	.	0.813	0.01097	0.2326:0.3117:0.2756:0.18	.	181;253	Q6P280-2;Q6P280	.;ZN529_HUMAN	L	286	.	ENSP00000334695:F286L	F	-	3	2	ZNF529	41730442	.	.	0.635000	0.29338	0.669000	0.39330	.	.	0.157000	0.19338	0.591000	0.81541	TTC		0.373	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		T	37038602	G	T	37038602	3	4	61	1	0	0	0	0	1	0	0	0	18009	933	33	2	837	2	ZNF529	19	37038602	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	32562	37038602	22090381	11079	19064										
ZNF382	84911	broad.mit.edu	37	chr19	37117998	37117998	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctcattgatcaccagaGaactcacacaggagagaaac	7	11	3	3	rs4439880		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37117998G>A	ENST00000292928.2	+	5	1312	c.1199G>A	c.(1198-1200)aGa>aAa	p.R400K	ZNF382_ENST00000423582.1_Missense_Mutation_p.R351K|ZNF382_ENST00000439428.1_Missense_Mutation_p.R399K|ZNF382_ENST00000435416.1_Missense_Mutation_p.R399K|CTD-3234P18.2_ENST00000585467.1_lincRNA	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	400	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R400K(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GATCACCAGAGAACTCACACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	93	94					19																	37117998		2203	4300	6503	41809838	SO:0001583	missense	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1199G>A	19.37:g.37117998G>A	ENSP00000292928:p.Arg400Lys		41809838	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.516678	0.44763	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.02197	4.4;4.4;4.4;4.4	4.27	4.27	0.50696	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47455	D	0.000230	T	0.01940	0.0061	N	0.11892	0.195	0.30120	N	0.805805	B;B;B	0.29552	0.209;0.209;0.248	B;B;B	0.29862	0.066;0.066;0.108	T	0.37454	-0.9705	10	0.45353	T	0.12	.	14.5487	0.68050	0.0:0.0:1.0:0.0	rs4439880;rs4439880	399;399;400	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	K	351;400;399;399	ENSP00000389722:R351K;ENSP00000292928:R400K;ENSP00000407593:R399K;ENSP00000410113:R399K	ENSP00000292928:R400K	R	+	2	0	ZNF382	41809838	0.019000	0.18553	1.000000	0.80357	0.974000	0.67602	1.596000	0.36718	2.375000	0.81037	0.591000	0.81541	AGA		0.458	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		A	37117998	G	A	37117998	3	1	61	1	0	0	0	0	1	0	0	0	17912	942	33	3	1209	3	ZNF382	19	37117998	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79396	37117998	22010985	11080	19065										
ZNF382	84911	broad.mit.edu	37	chr19	37118166	37118166	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccctcactctccaccagaGaattcacacgggggaaaaac	7	14	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37118166G>T	ENST00000292928.2	+	5	1480	c.1367G>T	c.(1366-1368)aGa>aTa	p.R456I	ZNF382_ENST00000423582.1_Missense_Mutation_p.R407I|ZNF382_ENST00000439428.1_Missense_Mutation_p.R455I|ZNF382_ENST00000435416.1_Missense_Mutation_p.R455I|CTD-3234P18.2_ENST00000585467.1_lincRNA	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	456	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R456I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CTCCACCAGAGAATTCACACG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											50	54	53					19																	37118166		2203	4300	6503	41810006	SO:0001583	missense	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1367G>T	19.37:g.37118166G>T	ENSP00000292928:p.Arg456Ile		41810006	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.191384	0.58017	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.27	4.27	0.50696	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46145	D	0.000313	T	0.39436	0.1078	L	0.50333	1.59	0.46609	D	0.999129	D;D;D	0.67145	0.995;0.995;0.996	D;D;D	0.68943	0.934;0.934;0.961	T	0.15925	-1.0420	10	0.66056	D	0.02	.	8.2048	0.31446	0.1086:0.0:0.8914:0.0	.	455;455;456	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	I	407;456;455;455	ENSP00000389722:R407I;ENSP00000292928:R456I;ENSP00000407593:R455I;ENSP00000410113:R455I	ENSP00000292928:R456I	R	+	2	0	ZNF382	41810006	0.213000	0.23551	1.000000	0.80357	0.984000	0.73092	2.689000	0.46993	2.375000	0.81037	0.591000	0.81541	AGA		0.448	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		T	37118166	G	T	37118166	3	4	61	1	0	0	0	0	1	0	0	0	17912	942	33	2	1377	2	ZNF382	19	37118166	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	168	37118166	22010817	11081	19066										
ZNF790	388536	broad.mit.edu	37	chr19	37309700	37309700	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaagttgtgaaccccagaGaaaggcttttccacattctt	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37309700G>T	ENST00000356725.4	-	5	1666	c.1546C>A	c.(1546-1548)Ctc>Atc	p.L516I	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L516I(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GAACCCCAGAGAAAGGCTTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											118	111	114					19																	37309700		2203	4300	6503	42001540	SO:0001583	missense	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1546C>A	19.37:g.37309700G>T	ENSP00000349161:p.Leu516Ile		42001540		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	G	4.353	0.064993	0.08388	.	.	ENSG00000197863	ENST00000356725	T	0.06068	3.35	3.04	0.469	0.16741	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03520	0.0101	N	0.12920	0.275	0.09310	N	1	B	0.14012	0.009	B	0.19666	0.026	T	0.46679	-0.9174	9	0.23891	T	0.37	.	5.1103	0.14806	0.0:0.3169:0.3186:0.3645	.	516	Q6PG37	ZN790_HUMAN	I	516	ENSP00000349161:L516I	ENSP00000349161:L516I	L	-	1	0	ZNF790	42001540	0.000000	0.05858	0.833000	0.33012	0.982000	0.71751	-3.930000	0.00332	0.547000	0.28938	0.491000	0.48974	CTC		0.408	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		T	37309700	G	T	37309700	3	4	61	1	0	0	0	0	1	0	0	0	18201	942	33	2	368	2	ZNF790	19	37309700	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191534	37309700	21819283	11082	19067										
ZNF790	388536	broad.mit.edu	37	chr19	37309819	37309819	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attccttacattcatagtttCtctcaccagtatgaattttc	3	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37309819C>T	ENST00000356725.4	-	5	1547	c.1427G>A	c.(1426-1428)aGa>aAa	p.R476K	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R476K(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TTCATAGTTTCTCTCACCAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	70	70					19																	37309819		2203	4300	6503	42001659	SO:0001583	missense	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1427G>A	19.37:g.37309819C>T	ENSP00000349161:p.Arg476Lys		42001659		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	C	2.686	-0.274281	0.05679	.	.	ENSG00000197863	ENST00000356725	T	0.12361	2.69	3.14	-1.43	0.08884	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.01424	-0.875	0.09310	N	0.999999	B	0.13594	0.008	B	0.14023	0.01	T	0.43956	-0.9359	9	0.02654	T	1	.	7.9304	0.29899	0.0:0.3969:0.0:0.6031	.	476	Q6PG37	ZN790_HUMAN	K	476	ENSP00000349161:R476K	ENSP00000349161:R476K	R	-	2	0	ZNF790	42001659	0.000000	0.05858	0.079000	0.20413	0.588000	0.36517	-0.757000	0.04772	-0.072000	0.12864	0.491000	0.48974	AGA		0.368	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		T	37309819	C	T	37309819	3	4	61	1	0	0	0	0	1	0	0	0	18201	913	32	3	487	3	ZNF790	19	37309819	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	119	37309819	21819164	11083	19068										
ZNF790	388536	broad.mit.edu	37	chr19	37309942	37309942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcatgttgagcaagatacGaagcccaagtaaaagtcttc	8	9	2	2	rs551820063		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37309942G>A	ENST00000356725.4	-	5	1424	c.1304C>T	c.(1303-1305)tCg>tTg	p.S435L	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	435					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S435L(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGCAAGATACGAAGCCCAAGT	0.413													G|||	1	0.000199681	0	0	5008	,	,		20656	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19											92	93	92					19																	37309942		2203	4300	6503	42001782	SO:0001583	missense	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1304C>T	19.37:g.37309942G>A	ENSP00000349161:p.Ser435Leu		42001782		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094259	0.36952	.	.	ENSG00000197863	ENST00000356725	T	0.07444	3.19	3.14	3.14	0.36123	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18800	0.0451	L	0.61218	1.895	0.09310	N	1	D	0.65815	0.995	P	0.53809	0.735	T	0.04294	-1.0962	9	0.56958	D	0.05	.	13.5234	0.61580	0.0:0.0:1.0:0.0	.	435	Q6PG37	ZN790_HUMAN	L	435	ENSP00000349161:S435L	ENSP00000349161:S435L	S	-	2	0	ZNF790	42001782	0.000000	0.05858	0.002000	0.10522	0.491000	0.33493	-0.130000	0.10498	1.753000	0.51906	0.491000	0.48974	TCG		0.413	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		A	37309942	G	A	37309942	3	1	61	1	0	0	0	0	1	0	0	0	18201	1059	37	1	610	1	ZNF790	19	37309942	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123	37309942	21819041	11084	19069										
ZNF790	388536	broad.mit.edu	37	chr19	37310282	37310282	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtttaataagatgtgatcGctgactaaaggcctttctac	8	7	1	3	rs147290327	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37310282G>A	ENST00000356725.4	-	5	1084	c.964C>T	c.(964-966)Cga>Tga	p.R322*	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R322*(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGATGTGATCGCTGACTAAAG	0.393													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		20278	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	19						G	stop/ARG,stop/ARG,stop/ARG,stop/ARG	36,4370	40.8+/-73.8	1,34,2168	55	58	57		964,964,964,964	-2.2	0	19	dbSNP_134	57	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained,stop-gained	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	,,,	1,35,6467	AA,AG,GG		0.0116,0.8171,0.2845	,,,	322/637,322/637,322/637,322/637	37310282	37,12969	2203	4300	6503	42002122	SO:0001587	stop_gained	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.964C>T	19.37:g.37310282G>A	ENSP00000349161:p.Arg322*		42002122		Nonsense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	17.59	3.428399	0.62844	0.008171	1.16E-4	ENSG00000197863	ENST00000356725	.	.	.	2.97	-2.18	0.07037	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	7.024	0.24930	0.0:0.3657:0.3608:0.2735	.	.	.	.	X	322	.	ENSP00000349161:R322X	R	-	1	2	ZNF790	42002122	0.000000	0.05858	0.000000	0.03702	0.956000	0.61745	-0.761000	0.04751	-0.381000	0.07882	0.313000	0.20887	CGA		0.393	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		A	37310282	G	A	37310282	4	1	61	1	0	0	0	0	0	1	0	0	18201	1095	38	1	950	1	ZNF790	19	37310282	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	340	37310282	21818701	11085	19070										
ZNF790	388536	broad.mit.edu	37	chr19	37310403	37310403	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacattccttacattcataAgatttctcaccagtatgaat	3	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37310403A>C	ENST00000356725.4	-	5	963	c.843T>G	c.(841-843)tcT>tcG	p.S281S	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S281S(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TACATTCATAAGATTTCTCAC	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	19											54	56	55					19																	37310403		2203	4299	6502	42002243	SO:0001819	synonymous_variant	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.843T>G	19.37:g.37310403A>C			42002243		Silent	SNP	ENST00000356725.4	37	CCDS12496.1																																																																																				0.373	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		C	37310403	A	C	37310403	2	2	61	1	0	0	0	0	0	0	0	1	18201	59	3	4		4	ZNF790	19	37310403	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	121	37310403	21818580	11086	19071										
ZNF790	388536	broad.mit.edu	37	chr19	37314586	37314586	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacccagtgagaccatgttgCtgtagttctccaacatcaca	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37314586C>A	ENST00000356725.4	-	3	236	c.116G>T	c.(115-117)aGc>aTc	p.S39I	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S39I(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GACCATGTTGCTGTAGTTCTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											113	106	108					19																	37314586		2203	4300	6503	42006426	SO:0001583	missense	388536			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.116G>T	19.37:g.37314586C>A	ENSP00000349161:p.Ser39Ile		42006426		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849427	0.51270	.	.	ENSG00000197863	ENST00000356725;ENST00000528994;ENST00000525288;ENST00000527645	T;T;T;T	0.02140	4.43;4.43;4.43;4.43	3.57	1.4	0.22301	Krueppel-associated box (4);	.	.	.	.	T	0.10551	0.0258	M	0.85777	2.775	0.27712	N	0.945412	D	0.69078	0.997	D	0.65874	0.939	T	0.04976	-1.0914	9	0.62326	D	0.03	.	7.0269	0.24944	0.0:0.7654:0.0:0.2346	.	39	Q6PG37	ZN790_HUMAN	I	39	ENSP00000349161:S39I;ENSP00000435944:S39I;ENSP00000433389:S39I;ENSP00000434537:S39I	ENSP00000349161:S39I	S	-	2	0	ZNF790	42006426	0.000000	0.05858	0.984000	0.44739	0.990000	0.78478	0.252000	0.18278	0.300000	0.22699	0.585000	0.79938	AGC		0.408	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		A	37314586	C	A	37314586	3	1	61	1	0	0	0	0	1	0	0	0	18201	797	28	2	1806	2	ZNF790	19	37314586	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4183	37314586	21814397	11087	19072										
ZNF345	25850	broad.mit.edu	37	chr19	37368061	37368061	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaccttgcttaccatcaaaGaattcatactggtgagaagc	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37368061G>T	ENST00000529555.1	+	2	1117	c.329G>T	c.(328-330)aGa>aTa	p.R110I	ZNF345_ENST00000589046.1_Missense_Mutation_p.R110I|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.R110I			Q14585	ZN345_HUMAN	zinc finger protein 345	110					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R110I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TACCATCAAAGAATTCATACT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											65	67	66					19																	37368061		2203	4300	6503	42059901	SO:0001583	missense	25850			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.329G>T	19.37:g.37368061G>T	ENSP00000431202:p.Arg110Ile		42059901		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116117	0.56505	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000331800	T;T;T	0.24908	1.83;1.83;2.92	3.58	1.34	0.21922	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22975	0.0555	M	0.70595	2.14	0.40828	D	0.983562	B	0.23854	0.092	B	0.12156	0.007	T	0.04708	-1.0932	8	.	.	.	.	5.8434	0.18647	0.1098:0.0:0.6982:0.192	.	110	Q14585	ZN345_HUMAN	I	110	ENSP00000431216:R110I;ENSP00000431202:R110I;ENSP00000331120:R110I	.	R	+	2	0	ZNF345	42059901	0.000000	0.05858	0.999000	0.59377	0.973000	0.67179	0.220000	0.17660	0.451000	0.26802	0.561000	0.74099	AGA		0.428	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			T	37368061	G	T	37368061	3	4	61	1	0	0	0	0	1	0	0	0	17898	942	33	2	331	2	ZNF345	19	37368061	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53475	37368061	21760922	11088	19073										
ZNF345	25850	broad.mit.edu	37	chr19	37368733	37368733	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacttattcagcatcaaaGaatgcatactggagagaaac	7	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37368733G>T	ENST00000529555.1	+	2	1789	c.1001G>T	c.(1000-1002)aGa>aTa	p.R334I	ZNF345_ENST00000589046.1_Missense_Mutation_p.R334I|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.R334I			Q14585	ZN345_HUMAN	zinc finger protein 345	334					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R334I(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGCATCAAAGAATGCATACT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	19											71	77	75					19																	37368733		2203	4300	6503	42060573	SO:0001583	missense	25850			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1001G>T	19.37:g.37368733G>T	ENSP00000431202:p.Arg334Ile		42060573		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.199663	0.38905	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.02446	4.29;4.29	3.8	3.8	0.43715	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05090	0.0136	L	0.48877	1.53	0.38566	D	0.949823	D	0.56521	0.976	P	0.48677	0.586	T	0.33904	-0.9850	9	0.87932	D	0	.	8.8822	0.35380	0.0:0.0:0.7767:0.2233	.	334	Q14585	ZN345_HUMAN	I	334;334;98	ENSP00000431216:R334I;ENSP00000431202:R334I	ENSP00000442320:R98I	R	+	2	0	ZNF345	42060573	0.005000	0.15991	1.000000	0.80357	0.887000	0.51463	1.437000	0.34991	2.092000	0.63282	0.462000	0.41574	AGA		0.408	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			T	37368733	G	T	37368733	3	4	61	1	0	0	0	0	1	0	0	0	17898	942	33	2	1003	2	ZNF345	19	37368733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	672	37368733	21760250	11089	19074										
ZNF345	25850	broad.mit.edu	37	chr19	37368919	37368919	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaatccatactggtgaaaGaccctatgaatgtaaagaat	8	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37368919G>T	ENST00000529555.1	+	2	1975	c.1187G>T	c.(1186-1188)aGa>aTa	p.R396I	ZNF345_ENST00000589046.1_Missense_Mutation_p.R396I|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.R396I			Q14585	ZN345_HUMAN	zinc finger protein 345	396					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R396I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACTGGTGAAAGACCCTATGAA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	79	80					19																	37368919		2203	4300	6503	42060759	SO:0001583	missense	25850			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1187G>T	19.37:g.37368919G>T	ENSP00000431202:p.Arg396Ile		42060759		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.755416	0.31046	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.20332	2.08;2.08	3.93	2.91	0.33838	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32615	0.0835	M	0.90814	3.15	0.37278	D	0.907707	B	0.26041	0.14	B	0.32677	0.15	T	0.29488	-1.0010	9	0.87932	D	0	.	6.9575	0.24580	0.8815:0.0:0.1185:0.0	.	396	Q14585	ZN345_HUMAN	I	396;396;160	ENSP00000431216:R396I;ENSP00000431202:R396I	ENSP00000442320:R160I	R	+	2	0	ZNF345	42060759	0.141000	0.22595	0.981000	0.43875	0.733000	0.41908	0.545000	0.23268	0.669000	0.31146	-0.367000	0.07326	AGA		0.418	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			T	37368919	G	T	37368919	3	4	61	1	0	0	0	0	1	0	0	0	17898	942	33	2	1189	2	ZNF345	19	37368919	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	186	37368919	21760064	11090	19075										
ZNF829	374899	broad.mit.edu	37	chr19	37382597	37382597	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctgatgttgaataagttCtgagctctgaataaaggcct	9	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37382597C>T	ENST00000391711.3	-	6	1460	c.1096G>A	c.(1096-1098)Gaa>Aaa	p.E366K	ZNF829_ENST00000520965.1_Missense_Mutation_p.E447K|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E366K(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAATAAGTTCTGAGCTCTGA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	74	73					19																	37382597		2195	4293	6488	42074437	SO:0001583	missense	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.1096G>A	19.37:g.37382597C>T	ENSP00000429266:p.Glu366Lys		42074437	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	37	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	C	6.940	0.543156	0.13250	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.39229	1.09	3.05	1.6	0.23607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28200	0.0696	L	0.38838	1.175	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.25710	-1.0124	9	0.15952	T	0.53	.	6.7447	0.23454	0.1769:0.4903:0.3329:0.0	.	366	Q3KNS6	ZN829_HUMAN	K	366	ENSP00000429266:E366K	ENSP00000429266:E366K	E	-	1	0	ZNF829	42074437	0.000000	0.05858	0.988000	0.46212	0.958000	0.62258	-4.900000	0.00172	0.511000	0.28236	0.557000	0.71058	GAA		0.368	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		T	37382597	C	T	37382597	3	4	61	1	0	0	0	0	1	0	0	0	18221	922	32	3	206	3	ZNF829	19	37382597	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13678	37382597	21746386	11091	19076										
ZNF829	374899	broad.mit.edu	37	chr19	37383000	37383000	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcaccagtgtgaatcctCtgatgttgagaaaaatatga	8	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37383000C>T	ENST00000391711.3	-	6	1057	c.693G>A	c.(691-693)caG>caA	p.Q231Q	ZNF829_ENST00000520965.1_Silent_p.Q312Q|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	231					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q231Q(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTGAATCCTCTGATGTTGAG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	19											60	63	62					19																	37383000		2201	4297	6498	42074840	SO:0001819	synonymous_variant	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.693G>A	19.37:g.37383000C>T			42074840	Q3KNS7|Q6ZNN0|Q7Z657	Silent	SNP	ENST00000391711.3	37	CCDS42557.1																																																																																				0.383	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		T	37383000	C	T	37383000	2	4	61	1	0	0	0	0	0	0	0	1	18221	912	32	3		3	ZNF829	19	37383000	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	403	37383000	21745983	11092	19077										
ZNF829	374899	broad.mit.edu	37	chr19	37383266	37383266	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttttttgaggtggaataaGaaatgtgggctgaataaaag	13	1	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37383266G>T	ENST00000391711.3	-	6	791	c.427C>A	c.(427-429)Ctt>Att	p.L143I	ZNF829_ENST00000520965.1_Missense_Mutation_p.L224I|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	143					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L143I(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGTGGAATAAGAAATGTGGGC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	19											62	55	58					19																	37383266		1857	4097	5954	42075106	SO:0001583	missense	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.427C>A	19.37:g.37383266G>T	ENSP00000429266:p.Leu143Ile		42075106	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	37	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	G	7.228	0.598824	0.13939	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.40756	1.02	3.34	-1.8	0.07907	.	.	.	.	.	T	0.48714	0.1515	M	0.70108	2.13	0.09310	N	1	P	0.52692	0.955	P	0.54544	0.755	T	0.41680	-0.9495	9	0.56958	D	0.05	.	4.8759	0.13656	0.2798:0.0:0.5721:0.1481	.	143	Q3KNS6	ZN829_HUMAN	I	143	ENSP00000429266:L143I	ENSP00000429266:L143I	L	-	1	0	ZNF829	42075106	0.159000	0.22864	0.003000	0.11579	0.050000	0.14768	1.126000	0.31344	-0.207000	0.10187	0.650000	0.86243	CTT		0.338	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		T	37383266	G	T	37383266	3	4	61	1	0	0	0	0	1	0	0	0	18221	942	33	2	875	2	ZNF829	19	37383266	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	266	37383266	21745717	11093	19078										
ZNF829	374899	broad.mit.edu	37	chr19	37399238	37399238	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaatagttatccttacccaCtgaaaccaggttgctgaaat	8	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37399238C>A	ENST00000391711.3	-	4	584	c.220G>T	c.(220-222)Gtg>Ttg	p.V74L	ZNF829_ENST00000520965.1_Missense_Mutation_p.V155L|ZNF345_ENST00000432005.2_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V74L(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCCTTACCCACTGAAACCAGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											125	127	126					19																	37399238		2168	4280	6448	42091078	SO:0001583	missense	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.220G>T	19.37:g.37399238C>A	ENSP00000429266:p.Val74Leu		42091078	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	37	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	C	2.993	-0.207728	0.06180	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.01359	4.98	4.55	1.08	0.20341	Krueppel-associated box (4);	.	.	.	.	T	0.00440	0.0014	N	0.00595	-1.35	0.23043	N	0.99839	B	0.02656	0.0	B	0.06405	0.002	T	0.47235	-0.9133	9	0.02654	T	1	.	3.2799	0.06912	0.2077:0.5751:0.0:0.2172	.	74	Q3KNS6	ZN829_HUMAN	L	74	ENSP00000429266:V74L	ENSP00000429266:V74L	V	-	1	0	ZNF829	42091078	0.344000	0.24827	1.000000	0.80357	0.998000	0.95712	-0.150000	0.10189	0.657000	0.30906	0.591000	0.81541	GTG		0.408	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		A	37399238	C	A	37399238	3	1	61	1	0	0	0	0	1	0	0	0	18221	565	20	2	1090	2	ZNF829	19	37399238	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15972	37399238	21729745	11094	19079										
ZNF829	374899	broad.mit.edu	37	chr19	37399331	37399331	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattcctcttgagagaagtCtatggaaacatccctgaaca	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37399331C>A	ENST00000391711.3	-	4	491	c.127G>T	c.(127-129)Gac>Tac	p.D43Y	ZNF829_ENST00000520965.1_Missense_Mutation_p.D124Y|ZNF345_ENST00000432005.2_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D43Y(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAGAGAAGTCTATGGAAACA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	102	103					19																	37399331		2137	4267	6404	42091171	SO:0001583	missense	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.127G>T	19.37:g.37399331C>A	ENSP00000429266:p.Asp43Tyr		42091171	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	37	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.847084	0.51164	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.01887	4.58	4.47	3.41	0.39046	Krueppel-associated box (4);	.	.	.	.	T	0.04679	0.0127	L	0.57130	1.785	0.27620	N	0.948371	B	0.32893	0.389	B	0.43916	0.436	T	0.29150	-1.0021	9	0.45353	T	0.12	.	4.5143	0.11926	0.0:0.7717:0.0:0.2283	.	43	Q3KNS6	ZN829_HUMAN	Y	43	ENSP00000429266:D43Y	ENSP00000429266:D43Y	D	-	1	0	ZNF829	42091171	0.882000	0.30256	0.989000	0.46669	0.978000	0.69477	-0.074000	0.11450	1.067000	0.40740	0.591000	0.81541	GAC		0.433	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		A	37399331	C	A	37399331	3	1	61	1	0	0	0	0	1	0	0	0	18221	913	32	2	1183	2	ZNF829	19	37399331	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93	37399331	21729652	11095	19080										
ZNF568	374900	broad.mit.edu	37	chr19	37427721	37427721	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaatgaaacctgctcaaaGaaacttgtatcgagatgtga	9	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37427721G>T	ENST00000333987.7	+	5	715	c.209G>T	c.(208-210)aGa>aTa	p.R70I	ZNF568_ENST00000427117.1_Missense_Mutation_p.R70I|ZNF568_ENST00000415168.1_Missense_Mutation_p.R6I|ZNF568_ENST00000455427.2_Missense_Mutation_p.R6I	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	70	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R70I(1)|p.R6I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTGCTCAAAGAAACTTGTAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	19											108	108	108					19																	37427721		2203	4300	6503	42119561	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.209G>T	19.37:g.37427721G>T	ENSP00000334685:p.Arg70Ile		42119561	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748799	0.69533	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000415168;ENST00000444991;ENST00000455427	T;T;T;T;T	0.03035	4.07;4.07;4.07;4.07;4.07	4.69	2.52	0.30459	Krueppel-associated box (4);	0.000000	0.39274	N	0.001408	T	0.19886	0.0478	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.999;0.999	T	0.00724	-1.1593	10	0.87932	D	0	.	7.2825	0.26320	0.2058:0.0:0.7942:0.0	.	6;70;70	B4DS92;C9JZ58;Q3ZCX4	.;.;ZN568_HUMAN	I	70;70;6;70;6	ENSP00000407012:R70I;ENSP00000334685:R70I;ENSP00000394514:R6I;ENSP00000389794:R70I;ENSP00000413396:R6I	ENSP00000334685:R70I	R	+	2	0	ZNF568	42119561	0.961000	0.32948	1.000000	0.80357	0.937000	0.57800	1.416000	0.34759	1.191000	0.43056	0.655000	0.94253	AGA		0.413	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37427721	G	T	37427721	3	4	61	1	0	0	0	0	1	0	0	0	18038	942	33	2	219	2	ZNF568	19	37427721	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28390	37427721	21701262	11096	19081										
ZNF568	374900	broad.mit.edu	37	chr19	37440504	37440504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagaaaattctgataaaggAaaaagtcattgaatgtaaaa	7	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37440504A>G	ENST00000333987.7	+	7	955	c.449A>G	c.(448-450)gAa>gGa	p.E150G	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.E86G|ZNF568_ENST00000455427.2_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E150G(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGATAAAGGAAAAAGTCATT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	62	64					19																	37440504		1812	4081	5893	42132344	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.449A>G	19.37:g.37440504A>G	ENSP00000334685:p.Glu150Gly		42132344	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	A	11.28	1.592890	0.28357	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.07444	3.19;3.19	4.25	0.924	0.19418	.	0.199812	0.25025	N	0.033734	T	0.07279	0.0184	M	0.70275	2.135	0.09310	N	1	P	0.39782	0.688	B	0.24974	0.057	T	0.26815	-1.0092	10	0.48119	T	0.1	.	6.6131	0.22763	0.5864:0.0:0.4136:0.0	.	150	Q3ZCX4	ZN568_HUMAN	G	150;86	ENSP00000334685:E150G;ENSP00000394514:E86G	ENSP00000334685:E150G	E	+	2	0	ZNF568	42132344	0.000000	0.05858	0.288000	0.24862	0.973000	0.67179	0.094000	0.15107	0.230000	0.21059	0.533000	0.62120	GAA		0.353	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		G	37440504	A	G	37440504	3	3	61	1	0	0	0	0	1	0	0	0	18038	246	9	4	467	4	ZNF568	19	37440504	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	12783	37440504	21688479	11097	19082										
ZNF568	374900	broad.mit.edu	37	chr19	37441468	37441468	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaaaattcacactggagaGaaaccttatgaatgcagtga	9	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37441468G>T	ENST00000333987.7	+	7	1919	c.1413G>T	c.(1411-1413)gaG>gaT	p.E471D	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.E407D|ZNF568_ENST00000455427.2_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E471D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACACTGGAGAGAAACCTTATG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	59	57					19																	37441468		2202	4300	6502	42133308	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1413G>T	19.37:g.37441468G>T	ENSP00000334685:p.Glu471Asp		42133308	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867171	0.51588	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.26810	1.71;1.71	3.96	1.79	0.24919	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34178	N	0.004189	T	0.34308	0.0893	L	0.33485	1.01	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	T	0.05099	-1.0906	10	0.66056	D	0.02	.	8.2081	0.31467	0.2044:0.0:0.7956:0.0	.	471	Q3ZCX4	ZN568_HUMAN	D	471;407	ENSP00000334685:E471D;ENSP00000394514:E407D	ENSP00000334685:E471D	E	+	3	2	ZNF568	42133308	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	0.861000	0.27885	0.448000	0.26722	0.467000	0.42956	GAG		0.393	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37441468	G	T	37441468	3	4	61	1	0	0	0	0	1	0	0	0	18038	933	33	2	1431	2	ZNF568	19	37441468	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	964	37441468	21687515	11098	19083										
ZNF568	374900	broad.mit.edu	37	chr19	37441756	37441756	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaatgtggtaaagccttCtctcgaatctcatccctcac	6	12	3	1	rs367876051		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37441756C>A	ENST00000333987.7	+	7	2207	c.1701C>A	c.(1699-1701)ttC>ttA	p.F567L	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.F503L|ZNF568_ENST00000455427.2_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F567L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTAAAGCCTTCTCTCGAATCT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	81	78					19																	37441756		2181	4294	6475	42133596	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1701C>A	19.37:g.37441756C>A	ENSP00000334685:p.Phe567Leu		42133596	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.135581	0.56828	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.46063	0.88;0.88	4.13	-1.64	0.08318	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37483	N	0.002076	T	0.62514	0.2434	M	0.88450	2.955	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.63180	-0.6695	10	0.72032	D	0.01	.	8.3699	0.32408	0.0:0.3785:0.0:0.6215	.	567	Q3ZCX4	ZN568_HUMAN	L	567;503	ENSP00000334685:F567L;ENSP00000394514:F503L	ENSP00000334685:F567L	F	+	3	2	ZNF568	42133596	0.000000	0.05858	0.907000	0.35723	0.998000	0.95712	-1.860000	0.01656	-0.294000	0.08973	0.591000	0.81541	TTC		0.393	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		A	37441756	C	A	37441756	3	1	61	1	0	0	0	0	1	0	0	0	18038	912	32	2	1719	2	ZNF568	19	37441756	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	288	37441756	21687227	11099	19084										
ZNF420	147923	broad.mit.edu	37	chr19	37619445	37619445	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttactcagagttcacatCtttcccaacatcaaagactt	3	13	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37619445C>A	ENST00000337995.3	+	5	1767	c.1552C>A	c.(1552-1554)Ctt>Att	p.L518I	ZNF585A_ENST00000588723.1_Intron|CTC-454I21.4_ENST00000587645.1_RNA|ZNF420_ENST00000304239.7_Intron	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L518I(1)		breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAGTTCACATCTTTCCCAACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	85	86					19																	37619445		2203	4300	6503	42311285	SO:0001583	missense	147923			AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.1552C>A	19.37:g.37619445C>A	ENSP00000338770:p.Leu518Ile		42311285	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	37	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.447515	0.43429	.	.	ENSG00000197050	ENST00000337995	T	0.53857	0.6	4.32	3.28	0.37604	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71178	0.3309	M	0.90145	3.09	0.20196	N	0.999927	P	0.51653	0.947	P	0.58266	0.836	T	0.61879	-0.6972	8	.	.	.	.	8.3135	0.32086	0.0:0.8059:0.0:0.1941	.	518	Q8TAQ5	ZN420_HUMAN	I	518	ENSP00000338770:L518I	.	L	+	1	0	ZNF420	42311285	0.040000	0.19996	0.840000	0.33206	0.998000	0.95712	0.414000	0.21164	1.029000	0.39812	0.655000	0.94253	CTT		0.413	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		A	37619445	C	A	37619445	3	1	61	1	0	0	0	0	1	0	0	0	17936	913	32	2	1562	2	ZNF420	19	37619445	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177689	37619445	21509538	11100	19085										
ZNF420	147923	broad.mit.edu	37	chr19	37619881	37619881	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagctaactcaacatcagaGaattcatatcagtgagaaat	6	8	4	2	rs140027212		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37619881G>T	ENST00000337995.3	+	5	2203	c.1988G>T	c.(1987-1989)aGa>aTa	p.R663I	ZNF585A_ENST00000588723.1_Intron|ZNF420_ENST00000586540.1_Intron|CTC-454I21.4_ENST00000587645.1_RNA|ZNF420_ENST00000304239.7_Intron	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	663					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R663I(1)		breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAACATCAGAGAATTCATATC	0.378													G|||	1	0.000199681	0	0	5008	,	,		21752	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											86	87	86					19																	37619881		2203	4299	6502	42311721	SO:0001583	missense	147923			AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.1988G>T	19.37:g.37619881G>T	ENSP00000338770:p.Arg663Ile		42311721	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	37	CCDS12498.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.89	1.773212	0.31411	.	.	ENSG00000197050	ENST00000337995	T	0.10005	2.92	4.46	-0.533	0.11887	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10852	0.0265	M	0.78049	2.395	0.80722	D	1	B	0.24920	0.114	B	0.22880	0.042	T	0.11299	-1.0593	8	.	.	.	.	2.1726	0.03853	0.2501:0.13:0.4871:0.1327	.	663	Q8TAQ5	ZN420_HUMAN	I	663	ENSP00000338770:R663I	.	R	+	2	0	ZNF420	42311721	0.000000	0.05858	0.669000	0.29828	0.993000	0.82548	0.798000	0.27014	0.151000	0.19162	0.655000	0.94253	AGA		0.378	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		T	37619881	G	T	37619881	3	4	61	1	0	0	0	0	1	0	0	0	17936	942	33	2	1998	2	ZNF420	19	37619881	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	436	37619881	21509102	11101	19086										
ZNF585A	199704	broad.mit.edu	37	chr19	37642627	37642627	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggacctgtcagtaaaggccTtcccacactcagcacacacg	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37642627T>G	ENST00000356958.4	-	5	2432	c.2174A>C	c.(2173-2175)aAg>aCg	p.K725T	ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Missense_Mutation_p.K670T|ZNF585A_ENST00000392157.2_Missense_Mutation_p.K670T|ZNF585A_ENST00000355533.2_Missense_Mutation_p.K362T			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	725					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K670T(1)		breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTAAAGGCCTTCCCACACTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											188	151	164					19																	37642627		2203	4300	6503	42334467	SO:0001583	missense	199704			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.2174A>C	19.37:g.37642627T>G	ENSP00000349440:p.Lys725Thr		42334467	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	37		.	.	.	.	.	.	.	.	.	.	T	17.34	3.364209	0.61513	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	T;T;T;T	0.07908	3.15;3.15;3.15;3.15	3.05	3.05	0.35203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39083	N	0.001472	T	0.24699	0.0599	.	.	.	0.23271	N	0.998005	D	0.89917	1.0	D	0.97110	1.0	T	0.01208	-1.1418	9	0.72032	D	0.01	.	10.6216	0.45483	0.0:0.0:0.0:1.0	.	725	Q6P3V2	Z585A_HUMAN	T	725;670;670;362	ENSP00000349440:K725T;ENSP00000292841:K670T;ENSP00000375998:K670T;ENSP00000347724:K362T	ENSP00000292841:K670T	K	-	2	0	ZNF585A	42334467	1.000000	0.71417	0.997000	0.53966	0.876000	0.50452	3.443000	0.52907	1.387000	0.46486	0.533000	0.62120	AAG		0.463	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		G	37642627	T	G	37642627	3	3	61	1	0	0	0	0	1	0	0	0	18056	1609	56	4	139	4	ZNF585A	19	37642627	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	22746	37642627	21486356	11102	19087										
ZNF585B	92285	broad.mit.edu	37	chr19	37676583	37676583	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgatgcaccaggagctgaGacttggaggtaaaggacttc	14	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37676583G>T	ENST00000532828.2	-	5	2107	c.1856C>A	c.(1855-1857)tCt>tAt	p.S619Y	ZNF585B_ENST00000312908.5_Missense_Mutation_p.S207Y|ZNF585B_ENST00000531805.1_Missense_Mutation_p.S564Y|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	619					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S619Y(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGGAGCTGAGACTTGGAGGT	0.468																																					Melanoma(93;882 1454 18863 28917 48427)											1	Substitution - Missense(1)	large_intestine(1)	19											24	21	22					19																	37676583		2203	4297	6500	42368423	SO:0001583	missense	92285			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1856C>A	19.37:g.37676583G>T	ENSP00000433773:p.Ser619Tyr		42368423	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005571	0.35415	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000312908	T;T;T	0.37058	1.22;1.22;3.18	2.79	1.67	0.24075	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36519	N	0.002551	T	0.53270	0.1786	M	0.80508	2.5	0.09310	N	1	D;D	0.65815	0.995;0.995	P;P	0.60012	0.867;0.867	T	0.46707	-0.9172	10	0.72032	D	0.01	.	9.6677	0.39994	0.0:0.0:0.7893:0.2107	.	564;619	E9PQH3;Q52M93	.;Z585B_HUMAN	Y	564;619;207	ENSP00000436774:S564Y;ENSP00000433773:S619Y;ENSP00000442139:S207Y	ENSP00000442139:S207Y	S	-	2	0	ZNF585B	42368423	0.000000	0.05858	0.022000	0.16811	0.822000	0.46500	0.154000	0.16343	0.438000	0.26450	0.305000	0.20034	TCT		0.468	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		T	37676583	G	T	37676583	3	4	61	1	0	0	0	0	1	0	0	0	18057	942	33	2	457	2	ZNF585B	19	37676583	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33956	37676583	21452400	11103	19088										
ZNF585B	92285	broad.mit.edu	37	chr19	37677386	37677386	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtacatatggaagatttCtctctactttgaatcttctc	5	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37677386C>A	ENST00000532828.2	-	5	1304	c.1053G>T	c.(1051-1053)gaG>gaT	p.E351D	ZNF585B_ENST00000312908.5_5'UTR|ZNF585B_ENST00000531805.1_Missense_Mutation_p.E296D|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E351D(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGGAAGATTTCTCTCTACTTT	0.398																																					Melanoma(93;882 1454 18863 28917 48427)											1	Substitution - Missense(1)	large_intestine(1)	19											121	116	118					19																	37677386		2203	4300	6503	42369226	SO:0001583	missense	92285			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1053G>T	19.37:g.37677386C>A	ENSP00000433773:p.Glu351Asp		42369226	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964189	0.34659	.	.	ENSG00000245680	ENST00000531805;ENST00000532828	T;T	0.37058	1.22;1.22	2.93	0.652	0.17823	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38005	N	0.001847	T	0.45994	0.1370	L	0.54908	1.71	0.80722	D	1	D;P	0.56746	0.977;0.776	D;P	0.65140	0.932;0.734	T	0.35126	-0.9801	10	0.72032	D	0.01	.	6.7454	0.23458	0.0:0.7429:0.0:0.2571	.	296;351	E9PQH3;Q52M93	.;Z585B_HUMAN	D	296;351	ENSP00000436774:E296D;ENSP00000433773:E351D	ENSP00000436774:E296D	E	-	3	2	ZNF585B	42369226	0.954000	0.32549	0.958000	0.39756	0.518000	0.34316	0.689000	0.25437	0.099000	0.17552	-0.391000	0.06502	GAG		0.398	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37677386	C	A	37677386	3	1	61	1	0	0	0	0	1	0	0	0	18057	912	32	2	1260	2	ZNF585B	19	37677386	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	803	37677386	21451597	11104	19089										
ZNF585B	92285	broad.mit.edu	37	chr19	37677473	37677473	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtacatatatagggcttcacTcttgtgtgaacacgttgatg	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37677473T>G	ENST00000532828.2	-	5	1217	c.966A>C	c.(964-966)agA>agC	p.R322S	ZNF585B_ENST00000312908.5_5'UTR|ZNF585B_ENST00000531805.1_Missense_Mutation_p.R267S|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R322S(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGGGCTTCACTCTTGTGTGAA	0.373																																					Melanoma(93;882 1454 18863 28917 48427)											1	Substitution - Missense(1)	large_intestine(1)	19											207	190	196					19																	37677473		2203	4297	6500	42369313	SO:0001583	missense	92285			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.966A>C	19.37:g.37677473T>G	ENSP00000433773:p.Arg322Ser		42369313	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	3.861	-0.029952	0.07543	.	.	ENSG00000245680	ENST00000531805;ENST00000532828	T;T	0.52754	0.65;0.65	2.71	2.71	0.32032	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40908	D	0.000981	T	0.41166	0.1147	L	0.33245	0.995	0.80722	D	1	B;D	0.58970	0.269;0.984	B;P	0.51266	0.038;0.664	T	0.33599	-0.9862	10	0.72032	D	0.01	.	5.5829	0.17260	0.0:0.1405:0.0:0.8595	.	267;322	E9PQH3;Q52M93	.;Z585B_HUMAN	S	267;322	ENSP00000436774:R267S;ENSP00000433773:R322S	ENSP00000436774:R267S	R	-	3	2	ZNF585B	42369313	0.000000	0.05858	0.052000	0.19188	0.003000	0.03518	-0.114000	0.10757	1.228000	0.43614	0.374000	0.22700	AGA		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		G	37677473	T	G	37677473	3	3	61	1	0	0	0	0	1	0	0	0	18057	1548	54	4	1347	4	ZNF585B	19	37677473	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	87	37677473	21451510	11105	19090										
ZNF585B	92285	broad.mit.edu	37	chr19	37677556	37677556	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcattcatatggtttttCtccactatgaattcttcggt	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37677556C>A	ENST00000532828.2	-	5	1134	c.883G>T	c.(883-885)Gaa>Taa	p.E295*	ZNF585B_ENST00000312908.5_5'UTR|ZNF585B_ENST00000531805.1_Nonsense_Mutation_p.E240*|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E295*(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TATGGTTTTTCTCCACTATGA	0.413																																					Melanoma(93;882 1454 18863 28917 48427)											1	Substitution - Nonsense(1)	large_intestine(1)	19											244	233	237					19																	37677556		2203	4300	6503	42369396	SO:0001587	stop_gained	92285			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.883G>T	19.37:g.37677556C>A	ENSP00000433773:p.Glu295*		42369396	Q8IZD3|Q96JW6	Nonsense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	C	34	5.359907	0.95877	.	.	ENSG00000245680	ENST00000531805;ENST00000532828	.	.	.	2.71	2.71	0.32032	.	0.000000	0.38605	N	0.001629	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	12.5143	0.56024	0.0:1.0:0.0:0.0	.	.	.	.	X	240;295	.	ENSP00000436774:E240X	E	-	1	0	ZNF585B	42369396	1.000000	0.71417	0.936000	0.37596	0.021000	0.10359	4.096000	0.57734	1.501000	0.48654	0.455000	0.32223	GAA		0.413	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37677556	C	A	37677556	4	1	61	1	0	0	0	0	0	1	0	0	18057	922	32	2	1430	2	ZNF585B	19	37677556	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83	37677556	21451427	11106	19091										
HKR1	284459	broad.mit.edu	37	chr19	37853675	37853675	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaggacacactcaggggaGaaaccttatgtgtgcaagga	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37853675G>T	ENST00000324411.4	+	6	1247	c.978G>T	c.(976-978)gaG>gaT	p.E326D	HKR1_ENST00000392153.3_Missense_Mutation_p.E307D|HKR1_ENST00000591471.1_Missense_Mutation_p.E53D|HKR1_ENST00000541583.2_Missense_Mutation_p.E265D|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000589392.1_Missense_Mutation_p.E308D|HKR1_ENST00000544914.1_Missense_Mutation_p.E53D	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	326					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E326D(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACTCAGGGGAGAAACCTTATG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	99	100					19																	37853675		2203	4300	6503	42545515	SO:0001583	missense	284459			M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"Zinc fingers, C2H2-type", "-"	4928	protein-coding gene	gene with protein product	"oncogene HKR1"	165250	"GLI-Kruppel family member HKR1"			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.978G>T	19.37:g.37853675G>T	ENSP00000315505:p.Glu326Asp		42545515	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747310	0.49257	.	.	ENSG00000181666	ENST00000544914;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	3.05	2.0	0.26442	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38639	0.1048	L	0.45470	1.425	0.80722	D	1	B;D;B;D	0.71674	0.202;0.998;0.11;0.994	B;D;B;D	0.71184	0.376;0.972;0.244;0.949	T	0.14035	-1.0487	9	0.87932	D	0	-17.7737	9.0176	0.36179	0.1152:0.0:0.8848:0.0	.	265;307;326;308	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	D	53;307;362;326;265	ENSP00000437774:E53D;ENSP00000375994:E307D;ENSP00000315505:E326D;ENSP00000438261:E265D	ENSP00000315505:E326D	E	+	3	2	HKR1	42545515	1.000000	0.71417	0.992000	0.48379	0.952000	0.60782	2.242000	0.43106	0.611000	0.30052	0.650000	0.86243	GAG		0.512	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37853675	G	T	37853675	3	4	61	1	0	0	0	0	1	0	0	0	7215	933	33	2	992	2	HKR1	19	37853675	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	176119	37853675	21275308	11107	19092										
HKR1	284459	broad.mit.edu	37	chr19	37854384	37854384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagtgtggcagaaggtttCggcagaagcctaacctgttt	15	7	0	2	rs552933332		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37854384C>T	ENST00000324411.4	+	6	1956	c.1687C>T	c.(1687-1689)Cgg>Tgg	p.R563W	HKR1_ENST00000392153.3_Missense_Mutation_p.R544W|HKR1_ENST00000591471.1_Missense_Mutation_p.R290W|HKR1_ENST00000541583.2_Missense_Mutation_p.R502W|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000589392.1_Missense_Mutation_p.R545W|HKR1_ENST00000544914.1_Missense_Mutation_p.R290W	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	563					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R563W(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGAAGGTTTCGGCAGAAGCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	48	50					19																	37854384		2203	4300	6503	42546224	SO:0001583	missense	284459			M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"Zinc fingers, C2H2-type", "-"	4928	protein-coding gene	gene with protein product	"oncogene HKR1"	165250	"GLI-Kruppel family member HKR1"			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.1687C>T	19.37:g.37854384C>T	ENSP00000315505:p.Arg563Trp		42546224	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669051	0.29604	.	.	ENSG00000181666	ENST00000544914;ENST00000414402;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	2.77	-0.82	0.10826	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29321	0.0730	M	0.77616	2.38	0.09310	N	1	D;D;P;D	0.67145	0.996;0.995;0.741;0.983	P;P;B;P	0.58970	0.849;0.764;0.105;0.571	T	0.16424	-1.0403	9	0.72032	D	0.01	.	1.6277	0.02726	0.3892:0.3472:0.1077:0.156	.	502;544;563;545	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	W	290;342;544;599;563;502	ENSP00000437774:R290W;ENSP00000375994:R544W;ENSP00000315505:R563W;ENSP00000438261:R502W	ENSP00000315505:R563W	R	+	1	2	HKR1	42546224	0.000000	0.05858	0.289000	0.24876	0.899000	0.52679	-0.301000	0.08232	-0.247000	0.09597	-0.271000	0.10264	CGG		0.493	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37854384	C	T	37854384	3	4	61	1	0	0	0	0	1	0	0	0	7215	875	31	1	1701	1	HKR1	19	37854384	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	709	37854384	21274599	11108	19093										
ZNF569	148266	broad.mit.edu	37	chr19	37903515	37903515	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctaatgagtatgaattCtctggtgtctaacaaggtgc	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37903515C>A	ENST00000316950.6	-	6	2602	c.2045G>T	c.(2044-2046)aGa>aTa	p.R682I	ZNF569_ENST00000392149.2_Missense_Mutation_p.R682I|ZNF569_ENST00000392150.2_Missense_Mutation_p.R523I	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	682					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R682I(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTATGAATTCTCTGGTGTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											102	104	103					19																	37903515		2203	4300	6503	42595355	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.2045G>T	19.37:g.37903515C>A	ENSP00000325018:p.Arg682Ile		42595355	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996016	0.74703	.	.	ENSG00000196437	ENST00000316950;ENST00000392149;ENST00000392150	T;T	0.32753	1.44;2.21	4.16	4.16	0.48862	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36519	N	0.002551	T	0.48352	0.1495	M	0.70903	2.155	0.58432	D	0.999994	P;P	0.52842	0.658;0.956	B;P	0.59948	0.149;0.866	T	0.50440	-0.8828	10	0.66056	D	0.02	.	11.02	0.47711	0.1867:0.8133:0.0:0.0	.	523;682	Q17RR6;Q5MCW4	.;ZN569_HUMAN	I	682;338;523	ENSP00000325018:R682I;ENSP00000375993:R523I	ENSP00000325018:R682I	R	-	2	0	ZNF569	42595355	0.033000	0.19621	1.000000	0.80357	0.996000	0.88848	0.795000	0.26972	2.295000	0.77249	0.563000	0.77884	AGA		0.408	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		A	37903515	C	A	37903515	3	1	61	1	0	0	0	0	1	0	0	0	18039	913	32	2	19	2	ZNF569	19	37903515	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49131	37903515	21225468	11109	19094										
ZNF569	148266	broad.mit.edu	37	chr19	37904523	37904523	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttttctcctgtatgacttCtcatatgaagagcaagggat	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37904523C>A	ENST00000316950.6	-	6	1594	c.1037G>T	c.(1036-1038)aGa>aTa	p.R346I	ZNF569_ENST00000392149.2_Missense_Mutation_p.R346I|ZNF569_ENST00000392150.2_Missense_Mutation_p.R187I	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R346I(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTATGACTTCTCATATGAAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											105	102	103					19																	37904523		2203	4300	6503	42596363	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.1037G>T	19.37:g.37904523C>A	ENSP00000325018:p.Arg346Ile		42596363	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599629	0.46318	.	.	ENSG00000196437	ENST00000316950;ENST00000392149;ENST00000392150	T;T	0.24908	1.83;1.83	3.97	3.97	0.46021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36200	N	0.002721	T	0.46444	0.1393	M	0.75777	2.31	0.31897	N	0.616467	D;D	0.69078	0.997;0.997	D;D	0.64776	0.929;0.929	T	0.57021	-0.7882	10	0.54805	T	0.06	.	11.9001	0.52678	0.0:0.8219:0.1781:0.0	.	187;346	Q17RR6;Q5MCW4	.;ZN569_HUMAN	I	346;2;187	ENSP00000325018:R346I;ENSP00000375993:R187I	ENSP00000325018:R346I	R	-	2	0	ZNF569	42596363	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.754000	0.26390	2.204000	0.70986	0.655000	0.94253	AGA		0.373	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		A	37904523	C	A	37904523	3	1	61	1	0	0	0	0	1	0	0	0	18039	913	32	2	1027	2	ZNF569	19	37904523	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1008	37904523	21224460	11110	19095										
ZNF569	148266	broad.mit.edu	37	chr19	37904973	37904973	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatgaggtccaaagtctgaTtgaagccttttccacaatga	9	8	1	5	rs532445392		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37904973T>G	ENST00000316950.6	-	6	1144	c.587A>C	c.(586-588)aAt>aCt	p.N196T	ZNF569_ENST00000392149.2_Missense_Mutation_p.N196T|ZNF569_ENST00000392150.2_Missense_Mutation_p.N37T	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N196T(1)		breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAAAGTCTGATTGAAGCCTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	69	69					19																	37904973		2203	4300	6503	42596813	SO:0001583	missense	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.587A>C	19.37:g.37904973T>G	ENSP00000325018:p.Asn196Thr		42596813	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	3.773	-0.047323	0.07407	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	T;T	0.26810	1.71;3.19	3.73	-4.3	0.03710	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.218610	0.06049	N	0.656322	T	0.13543	0.0328	N	0.11106	0.095	0.09310	N	1	B;B	0.16603	0.018;0.0	B;B	0.14578	0.011;0.0	T	0.32981	-0.9886	10	0.23891	T	0.37	.	12.6716	0.56870	0.0:0.7009:0.0:0.2991	.	37;196	Q17RR6;Q5MCW4	.;ZN569_HUMAN	T	196;37	ENSP00000325018:N196T;ENSP00000375993:N37T	ENSP00000325018:N196T	N	-	2	0	ZNF569	42596813	0.000000	0.05858	0.016000	0.15963	0.975000	0.68041	-1.227000	0.02950	-0.898000	0.03906	0.482000	0.46254	AAT		0.378	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		G	37904973	T	G	37904973	3	3	61	1	0	0	0	0	1	0	0	0	18039	1493	52	4	1477	4	ZNF569	19	37904973	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	450	37904973	21224010	11111	19096										
ZNF570	148268	broad.mit.edu	37	chr19	37975237	37975237	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccttactcttcatcaaaGaattcatactggagagaaac	5	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37975237G>A	ENST00000330173.1	+	5	1242	c.713G>A	c.(712-714)aGa>aAa	p.R238K	ZNF570_ENST00000586475.1_Missense_Mutation_p.R294K|ZNF570_ENST00000388801.3_Missense_Mutation_p.R35K	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R238K(1)		endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTCATCAAAGAATTCATACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	99	95					19																	37975237		2203	4300	6503	42667077	SO:0001583	missense	148268			AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.713G>A	19.37:g.37975237G>A	ENSP00000331540:p.Arg238Lys		42667077	A1L472|B4DMP1	Missense_Mutation	SNP	ENST00000330173.1	37	CCDS12504.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.262798	0.59431	.	.	ENSG00000171827	ENST00000330173;ENST00000388801	T;T	0.18338	2.22;2.22	4.35	3.23	0.37069	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.359457	0.20424	N	0.092606	T	0.27454	0.0674	N	0.25485	0.75	0.30023	N	0.814201	D;D	0.63880	0.993;0.99	D;D	0.75484	0.986;0.975	T	0.02958	-1.1089	10	0.52906	T	0.07	.	13.8309	0.63380	0.0:0.1553:0.8447:0.0	.	35;238	B4DMP1;Q96NI8	.;ZN570_HUMAN	K	238;35	ENSP00000331540:R238K;ENSP00000373453:R35K	ENSP00000331540:R238K	R	+	2	0	ZNF570	42667077	0.001000	0.12720	1.000000	0.80357	0.997000	0.91878	1.096000	0.30976	2.410000	0.81850	0.563000	0.77884	AGA		0.388	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		A	37975237	G	A	37975237	3	1	61	1	0	0	0	0	1	0	0	0	18041	942	33	3	727	3	ZNF570	19	37975237	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	70264	37975237	21153746	11112	19097										
ZNF570	148268	broad.mit.edu	37	chr19	37975505	37975505	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagagttcacacgggagaGaaaccctatgaatgtatcga	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37975505G>T	ENST00000330173.1	+	5	1510	c.981G>T	c.(979-981)gaG>gaT	p.E327D	ZNF570_ENST00000586475.1_Missense_Mutation_p.E383D|ZNF570_ENST00000388801.3_Missense_Mutation_p.E124D	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E327D(1)		endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACACGGGAGAGAAACCCTATG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											93	88	90					19																	37975505		2203	4300	6503	42667345	SO:0001583	missense	148268			AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.981G>T	19.37:g.37975505G>T	ENSP00000331540:p.Glu327Asp		42667345	A1L472|B4DMP1	Missense_Mutation	SNP	ENST00000330173.1	37	CCDS12504.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805621	0.70682	.	.	ENSG00000171827	ENST00000330173;ENST00000388801	T;T	0.26810	1.71;1.71	4.18	3.14	0.36123	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43110	D	0.000608	T	0.35480	0.0933	L	0.43923	1.385	0.32676	N	0.516187	D;B	0.53312	0.959;0.235	P;B	0.59171	0.853;0.137	T	0.44143	-0.9347	10	0.59425	D	0.04	.	11.5514	0.50723	0.0961:0.0:0.9039:0.0	.	124;327	B4DMP1;Q96NI8	.;ZN570_HUMAN	D	327;124	ENSP00000331540:E327D;ENSP00000373453:E124D	ENSP00000331540:E327D	E	+	3	2	ZNF570	42667345	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.510000	0.45468	2.317000	0.78254	0.563000	0.77884	GAG		0.428	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		T	37975505	G	T	37975505	3	4	61	1	0	0	0	0	1	0	0	0	18041	933	33	2	995	2	ZNF570	19	37975505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	268	37975505	21153478	11113	19098										
ZNF570	148268	broad.mit.edu	37	chr19	37975755	37975755	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagagaattcatactggaGaaaaaccttataagtgtcag	8	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:37975755G>T	ENST00000330173.1	+	5	1760	c.1231G>T	c.(1231-1233)Gaa>Taa	p.E411*	ZNF570_ENST00000586475.1_Nonsense_Mutation_p.E467*|ZNF570_ENST00000388801.3_Nonsense_Mutation_p.E208*	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E411*(1)		endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCATACTGGAGAAAAACCTTA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											80	83	82					19																	37975755		2203	4300	6503	42667595	SO:0001587	stop_gained	148268			AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.1231G>T	19.37:g.37975755G>T	ENSP00000331540:p.Glu411*		42667595	A1L472|B4DMP1	Nonsense_Mutation	SNP	ENST00000330173.1	37	CCDS12504.1	.	.	.	.	.	.	.	.	.	.	G	42	9.621044	0.99221	.	.	ENSG00000171827	ENST00000330173;ENST00000388801	.	.	.	4.11	4.11	0.48088	.	0.164075	0.29028	N	0.013379	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	15.64	0.76989	0.0:0.0:1.0:0.0	.	.	.	.	X	411;208	.	ENSP00000331540:E411X	E	+	1	0	ZNF570	42667595	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.687000	0.91255	2.282000	0.76494	0.462000	0.41574	GAA		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		T	37975755	G	T	37975755	4	4	61	1	0	0	0	0	0	1	0	0	18041	943	33	2	1245	2	ZNF570	19	37975755	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	250	37975755	21153228	11114	19099										
ZNF793	390927	broad.mit.edu	37	chr19	38028458	38028458	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagaagtcacaccgcacaGaacatcagagaacacacaca	6	15	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38028458G>T	ENST00000587143.1	+	6	1133	c.898G>T	c.(898-900)Gaa>Taa	p.E300*	ZNF793_ENST00000542455.1_Nonsense_Mutation_p.E300*|ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000445217.1_Nonsense_Mutation_p.E300*|ZNF793_ENST00000588578.1_3'UTR			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	300					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E300*(1)		kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACACCGCACAGAACATCAGAG	0.443																																					Melanoma(44;400 1431 1499 19093)											1	Substitution - Nonsense(1)	large_intestine(1)	19											73	81	79					19																	38028458		2175	4286	6461	42720298	SO:0001587	stop_gained	390927			AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.898G>T	19.37:g.38028458G>T	ENSP00000468605:p.Glu300*		42720298	E9PGN4|Q7Z3Q9	Nonsense_Mutation	SNP	ENST00000587143.1	37	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	G	37	6.141587	0.97320	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	.	.	.	3.83	2.68	0.31781	.	0.000000	0.38436	N	0.001689	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	3.6281	0.08121	0.2133:0.2232:0.5634:0.0	.	.	.	.	X	300;300;300;299	.	ENSP00000318811:E299X	E	+	1	0	ZNF793	42720298	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	-1.167000	0.03126	2.117000	0.64856	0.637000	0.83480	GAA		0.443	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		T	38028458	G	T	38028458	4	4	61	1	0	0	0	0	0	1	0	0	18204	943	33	2	912	2	ZNF793	19	38028458	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52703	38028458	21100525	11115	19100										
ZNF571	51276	broad.mit.edu	37	chr19	38056602	38056602	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctcctgtatgaactCtctgatgttcagtgagctgt	9	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38056602C>A	ENST00000328550.2	-	4	827	c.728G>T	c.(727-729)aGa>aTa	p.R243I	ZNF571_ENST00000358744.3_Missense_Mutation_p.R243I|ZNF571_ENST00000593133.1_Missense_Mutation_p.R243I|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571-AS1_ENST00000589750.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.R243I|ZNF571-AS1_ENST00000591430.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	243					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R243I(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTATGAACTCTCTGATGTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	66	67					19																	38056602		2203	4299	6502	42748442	SO:0001583	missense	51276			AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"Zinc fingers, C2H2-type", "-"	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.728G>T	19.37:g.38056602C>A	ENSP00000333660:p.Arg243Ile		42748442	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.121817	0.56613	.	.	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.24908	1.83;1.83;1.83	3.75	1.53	0.23141	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24392	0.0591	M	0.66297	2.02	0.36747	D	0.882548	B	0.31599	0.33	B	0.29524	0.103	T	0.14839	-1.0458	9	0.87932	D	0	.	6.855	0.24036	0.1746:0.7266:0.0:0.0988	.	243	Q7Z3V5	ZN571_HUMAN	I	243	ENSP00000333660:R243I;ENSP00000392638:R243I;ENSP00000351594:R243I	ENSP00000333660:R243I	R	-	2	0	ZNF571	42748442	0.000000	0.05858	0.063000	0.19743	0.976000	0.68499	-0.716000	0.04991	0.239000	0.21243	0.313000	0.20887	AGA		0.353	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536		A	38056602	C	A	38056602	3	1	61	1	0	0	0	0	1	0	0	0	18042	913	32	2	1105	2	ZNF571	19	38056602	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28144	38056602	21072381	11116	19101										
ZNF540	163255	broad.mit.edu	37	chr19	38102729	38102729	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaacatgggaaaatagattCtgatgtgaaacatgattgta	9	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38102729C>A	ENST00000592533.1	+	5	880	c.548C>A	c.(547-549)tCt>tAt	p.S183Y	ZNF540_ENST00000316433.4_Missense_Mutation_p.S183Y|ZNF540_ENST00000589117.1_Missense_Mutation_p.S151Y|ZNF540_ENST00000343599.5_Missense_Mutation_p.S183Y|ZNF540_ENST00000586792.1_3'UTR	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	183					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.S183Y(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAATAGATTCTGATGTGAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19											58	58	58					19																	38102729		2203	4298	6501	42794569	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.548C>A	19.37:g.38102729C>A	ENSP00000466274:p.Ser183Tyr		42794569	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	C	8.905	0.957278	0.18507	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.09350	2.99	1.93	1.93	0.25924	.	.	.	.	.	T	0.12263	0.0298	L	0.57536	1.79	0.09310	N	1	P;P	0.40197	0.706;0.582	B;B	0.37888	0.26;0.133	T	0.14090	-1.0485	9	0.66056	D	0.02	.	9.4299	0.38604	0.0:1.0:0.0:0.0	.	151;183	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	Y	183;151	ENSP00000324598:S183Y	ENSP00000324598:S183Y	S	+	2	0	ZNF540	42794569	0.551000	0.26497	0.004000	0.12327	0.269000	0.26545	0.878000	0.28126	1.053000	0.40415	0.313000	0.20887	TCT		0.348	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		A	38102729	C	A	38102729	3	1	61	1	0	0	0	0	1	0	0	0	18014	913	32	2	562	2	ZNF540	19	38102729	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46127	38102729	21026254	11117	19102										
ZNF540	163255	broad.mit.edu	37	chr19	38103703	38103703	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagacctttagatttggtTtctaccttactgaacaccag	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38103703T>G	ENST00000592533.1	+	5	1854	c.1522T>G	c.(1522-1524)Ttc>Gtc	p.F508V	ZNF540_ENST00000316433.4_Missense_Mutation_p.F508V|ZNF540_ENST00000589117.1_Missense_Mutation_p.F476V|ZNF540_ENST00000343599.5_Missense_Mutation_p.F508V	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	508					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.F508V(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGATTTGGTTTCTACCTTAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											84	87	86					19																	38103703		2203	4300	6503	42795543	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.1522T>G	19.37:g.38103703T>G	ENSP00000466274:p.Phe508Val		42795543	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.119855	0.37436	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T;T	0.46063	3.19;0.88	2.39	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21509	0.0518	N	0.16478	0.41	0.09310	N	1	B;B	0.34147	0.438;0.311	B;B	0.29663	0.105;0.065	T	0.14755	-1.0461	9	0.54805	T	0.06	.	3.9402	0.09323	0.1975:0.0:0.2:0.6025	.	476;508	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	V	508;476	ENSP00000324598:F508V;ENSP00000343768:F476V	ENSP00000324598:F508V	F	+	1	0	ZNF540	42795543	0.000000	0.05858	0.002000	0.10522	0.981000	0.71138	0.216000	0.17585	1.081000	0.41110	0.254000	0.18369	TTC		0.378	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		G	38103703	T	G	38103703	3	3	61	1	0	0	0	0	1	0	0	0	18014	1841	64	4	1536	4	ZNF540	19	38103703	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	974	38103703	21025280	11118	19103										
ZNF540	163255	broad.mit.edu	37	chr19	38104066	38104066	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttactgaacatcagagaattCacactggtgagaaaccctat	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38104066C>A	ENST00000592533.1	+	5	2217	c.1885C>A	c.(1885-1887)Cac>Aac	p.H629N	ZNF540_ENST00000316433.4_Missense_Mutation_p.H629N|ZNF540_ENST00000589117.1_Missense_Mutation_p.H597N|ZNF540_ENST00000343599.5_Missense_Mutation_p.H629N	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	629					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.H629N(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCAGAGAATTCACACTGGTGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	42	42					19																	38104066		2203	4300	6503	42795906	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.1885C>A	19.37:g.38104066C>A	ENSP00000466274:p.His629Asn		42795906	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.915370	0.73098	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T;D	0.86865	-0.26;-2.18	2.8	0.395	0.16304	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93785	0.8013	H	0.95574	3.69	0.23616	N	0.997282	P;P	0.51449	0.933;0.945	P;P	0.61940	0.833;0.896	D	0.85611	0.1258	9	0.87932	D	0	.	7.674	0.28476	0.0:0.7648:0.0:0.2352	.	597;629	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	N	629;597	ENSP00000324598:H629N;ENSP00000343768:H597N	ENSP00000324598:H629N	H	+	1	0	ZNF540	42795906	0.011000	0.17503	0.001000	0.08648	0.871000	0.50021	0.546000	0.23284	-0.113000	0.11958	0.305000	0.20034	CAC		0.343	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		A	38104066	C	A	38104066	3	1	61	1	0	0	0	0	1	0	0	0	18014	826	29	2	1899	2	ZNF540	19	38104066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	363	38104066	21024917	11119	19104										
ZFP30	22835	broad.mit.edu	37	chr19	38125901	38125901	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaagttacattatgaattCgctgatggtaagtaagatgt	9	3	0	3	rs144294637	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38125901C>T	ENST00000351218.2	-	6	2098	c.1541G>A	c.(1540-1542)cGa>cAa	p.R514Q	ZFP30_ENST00000392144.1_Missense_Mutation_p.R514Q|ZFP30_ENST00000589018.1_Intron|ZFP30_ENST00000514101.2_Missense_Mutation_p.R514Q	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R514Q(1)		autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTATGAATTCGCTGATGGTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	58	56	57		1541	4.1	1	19	dbSNP_134	57	3,8595	3.0+/-9.4	0,3,4296	yes	missense	ZFP30	NM_014898.2	43	0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308	possibly-damaging	514/520	38125901	4,13000	2203	4299	6502	42817741	SO:0001583	missense	22835			AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.1541G>A	19.37:g.38125901C>T	ENSP00000343581:p.Arg514Gln		42817741	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	37	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.602021	0.46423	2.27E-4	3.49E-4	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144;ENST00000440715	T;T;T	0.35789	1.29;1.29;1.29	4.05	4.05	0.47172	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.414870	0.14693	N	0.304017	T	0.30230	0.0758	L	0.58101	1.795	0.31142	N	0.706531	P;P	0.48694	0.914;0.914	B;B	0.29716	0.106;0.106	T	0.50783	-0.8787	10	0.66056	D	0.02	.	14.0653	0.64824	0.0:1.0:0.0:0.0	.	514;514	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	Q	514;514;514;429	ENSP00000343581:R514Q;ENSP00000422930:R514Q;ENSP00000375988:R514Q	ENSP00000343581:R514Q	R	-	2	0	ZFP30	42817741	0.009000	0.17119	1.000000	0.80357	0.976000	0.68499	0.569000	0.23638	2.249000	0.74217	0.585000	0.79938	CGA		0.333	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		T	38125901	C	T	38125901	3	4	61	1	0	0	0	0	1	0	0	0	17683	884	31	1	22	1	ZFP30	19	38125901	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21835	38125901	21003082	11120	19105										
ZNF781	163115	broad.mit.edu	37	chr19	38160305	38160305	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttttcaccagtgtgaattCtctgatgtctattaaaatca	6	7	4	2	rs141004896		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38160305C>A	ENST00000590008.1	-	5	1597	c.745G>T	c.(745-747)Gaa>Taa	p.E249*	ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Nonsense_Mutation_p.E249*			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E249*(1)		NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						AGTGTGAATTCTCTGATGTCT	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	19						C	stop/GLU	0,4406		0,0,2203	61	65	64		745	-0.1	0	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	ZNF781	NM_152605.3		0,1,6502	AA,AC,CC		0.0116,0.0,0.0077		249/328	38160305	1,13005	2203	4300	6503	42852145	SO:0001587	stop_gained	163115			AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.745G>T	19.37:g.38160305C>A	ENSP00000466370:p.Glu249*		42852145	Q2VPJ8	Nonsense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	C	38	6.708432	0.97780	0.0	1.16E-4	ENSG00000196381	ENST00000358582;ENST00000545586	.	.	.	2.29	-0.0871	0.13678	.	.	.	.	.	.	.	.	.	.	.	0.49582	D	0.9998	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-3.211	2.7693	0.05329	0.2171:0.4889:0.0:0.294	.	.	.	.	X	249	.	ENSP00000351391:E249X	E	-	1	0	ZNF781	42852145	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.245000	0.18142	-0.107000	0.12088	-0.300000	0.09419	GAA		0.363	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		A	38160305	C	A	38160305	4	1	61	1	0	0	0	0	0	1	0	0	18193	922	32	2	242	2	ZNF781	19	38160305	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34404	38160305	20968678	11121	19106										
ZNF607	84775	broad.mit.edu	37	chr19	38188954	38188954	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctatcaaatatgaattCtctgatgtacttcaaggatg	6	7	4	2	rs368373326		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38188954C>A	ENST00000355202.4	-	5	2673	c.2078G>T	c.(2077-2079)aGa>aTa	p.R693I	ZNF607_ENST00000395835.3_Missense_Mutation_p.R692I|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	693					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R693I(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			AATATGAATTCTCTGATGTAC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	ILE/ARG,ILE/ARG	0,4406		0,0,2203	113	119	117		2075,2078	1.3	0.9	19		117	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	97,97	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	692/696,693/697	38188954	1,13005	2203	4300	6503	42880794	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.2078G>T	19.37:g.38188954C>A	ENSP00000347338:p.Arg693Ile		42880794	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.941964	0.53079	0.0	1.16E-4	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.32753	1.44;1.44	2.33	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37293	0.0998	M	0.77103	2.36	0.37746	D	0.925799	P;P	0.42757	0.789;0.746	B;P	0.47044	0.136;0.535	T	0.31166	-0.9953	9	0.51188	T	0.08	.	5.0145	0.14330	0.0:0.815:0.0:0.185	.	693;692	Q96SK3;F5H141	ZN607_HUMAN;.	I	693;692	ENSP00000347338:R693I;ENSP00000438015:R692I	ENSP00000347338:R693I	R	-	2	0	ZNF607	42880794	0.000000	0.05858	0.940000	0.37924	0.485000	0.33311	-0.048000	0.11944	0.302000	0.22762	-0.379000	0.06801	AGA		0.348	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38188954	C	A	38188954	3	1	61	1	0	0	0	0	1	0	0	0	18072	913	32	2	16	2	ZNF607	19	38188954	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28649	38188954	20940029	11122	19107										
ZNF607	84775	broad.mit.edu	37	chr19	38189206	38189206	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttatcactggtatgaattCtctcatgaataataagatgt	7	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38189206C>A	ENST00000355202.4	-	5	2421	c.1826G>T	c.(1825-1827)aGa>aTa	p.R609I	ZNF607_ENST00000395835.3_Missense_Mutation_p.R608I|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	609					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R609I(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			GGTATGAATTCTCTCATGAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	64	65					19																	38189206		2203	4300	6503	42881046	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1826G>T	19.37:g.38189206C>A	ENSP00000347338:p.Arg609Ile		42881046	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346199	0.61073	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.24908	1.83;1.83	1.96	0.862	0.19056	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37348	0.1000	L	0.50847	1.595	0.41997	D	0.990876	D;P	0.76494	0.999;0.883	D;P	0.68192	0.956;0.448	T	0.10567	-1.0624	9	0.56958	D	0.05	.	7.2809	0.26310	0.0:0.8485:0.0:0.1515	.	609;608	Q96SK3;F5H141	ZN607_HUMAN;.	I	609;608	ENSP00000347338:R609I;ENSP00000438015:R608I	ENSP00000347338:R609I	R	-	2	0	ZNF607	42881046	0.000000	0.05858	0.099000	0.21106	0.818000	0.46254	-0.341000	0.07811	0.154000	0.19237	0.462000	0.41574	AGA		0.378	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38189206	C	A	38189206	3	1	61	1	0	0	0	0	1	0	0	0	18072	913	32	2	268	2	ZNF607	19	38189206	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252	38189206	20939777	11123	19108										
ZNF607	84775	broad.mit.edu	37	chr19	38189709	38189709	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtttgtaaccagtatgaatTctgttatgatgggcaaggtg	13	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38189709T>G	ENST00000355202.4	-	5	1918	c.1323A>C	c.(1321-1323)agA>agC	p.R441S	ZNF607_ENST00000395835.3_Missense_Mutation_p.R440S|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R441S(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CAGTATGAATTCTGTTATGAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											100	102	101					19																	38189709		2203	4300	6503	42881549	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1323A>C	19.37:g.38189709T>G	ENSP00000347338:p.Arg441Ser		42881549	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.744674	0.49151	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.24151	1.87;1.87	2.38	1.19	0.21007	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35711	0.0941	L	0.49571	1.57	0.23879	N	0.996584	D;D	0.76494	0.999;0.998	P;P	0.61800	0.894;0.891	T	0.12400	-1.0549	9	0.59425	D	0.04	.	5.8678	0.18786	0.0:0.1675:0.0:0.8325	.	441;440	Q96SK3;F5H141	ZN607_HUMAN;.	S	441;440	ENSP00000347338:R441S;ENSP00000438015:R440S	ENSP00000347338:R441S	R	-	3	2	ZNF607	42881549	0.000000	0.05858	0.842000	0.33263	0.640000	0.38277	-1.067000	0.03451	0.114000	0.18032	0.459000	0.35465	AGA		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		G	38189709	T	G	38189709	3	3	61	1	0	0	0	0	1	0	0	0	18072	1780	62	4	771	4	ZNF607	19	38189709	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	503	38189709	20939274	11124	19109										
ZNF607	84775	broad.mit.edu	37	chr19	38190030	38190030	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttacattcatagtgtttCtcccctgaataaattctctg	4	10	4	1	rs369953157		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38190030C>A	ENST00000355202.4	-	5	1597	c.1002G>T	c.(1000-1002)gaG>gaT	p.E334D	ZNF607_ENST00000395835.3_Missense_Mutation_p.E333D|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	334					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E334D(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CATAGTGTTTCTCCCCTGAAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											110	110	110					19																	38190030		2203	4300	6503	42881870	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1002G>T	19.37:g.38190030C>A	ENSP00000347338:p.Glu334Asp		42881870	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.713848	0.30413	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.64085	-0.08;-0.08	1.63	0.507	0.16967	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69584	0.3127	M	0.62016	1.91	0.26517	N	0.974492	P;P	0.48294	0.89;0.908	P;P	0.60173	0.87;0.532	T	0.59495	-0.7444	9	0.72032	D	0.01	.	6.8178	0.23841	0.0:0.8357:0.0:0.1643	.	334;333	Q96SK3;F5H141	ZN607_HUMAN;.	D	334;333	ENSP00000347338:E334D;ENSP00000438015:E333D	ENSP00000347338:E334D	E	-	3	2	ZNF607	42881870	0.940000	0.31905	0.059000	0.19551	0.072000	0.16883	0.120000	0.15647	0.029000	0.15352	0.561000	0.74099	GAG		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38190030	C	A	38190030	3	1	61	1	0	0	0	0	1	0	0	0	18072	912	32	2	1092	2	ZNF607	19	38190030	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	321	38190030	20938953	11125	19110										
ZNF607	84775	broad.mit.edu	37	chr19	38190464	38190464	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtttctcaacatgaacttTcccatgttgagcaaggtttg	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38190464T>G	ENST00000355202.4	-	5	1163	c.568A>C	c.(568-570)Aaa>Caa	p.K190Q	ZNF607_ENST00000395835.3_Missense_Mutation_p.K189Q|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	190					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K190Q(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			ACATGAACTTTCCCATGTTGA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											117	109	112					19																	38190464		2203	4300	6503	42882304	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.568A>C	19.37:g.38190464T>G	ENSP00000347338:p.Lys190Gln		42882304	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.408706	0.42715	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.16196	2.36;2.36	1.91	1.91	0.25777	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19604	0.0471	L	0.55017	1.72	0.09310	N	1	P;P	0.41929	0.603;0.765	B;P	0.45406	0.097;0.479	T	0.13629	-1.0502	9	0.72032	D	0.01	.	5.0253	0.14381	0.0:0.1687:0.0:0.8313	.	190;189	Q96SK3;F5H141	ZN607_HUMAN;.	Q	190;189	ENSP00000347338:K190Q;ENSP00000438015:K189Q	ENSP00000347338:K190Q	K	-	1	0	ZNF607	42882304	0.000000	0.05858	0.004000	0.12327	0.100000	0.18952	0.525000	0.22956	0.869000	0.35703	0.459000	0.35465	AAA		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		G	38190464	T	G	38190464	3	3	61	1	0	0	0	0	1	0	0	0	18072	1792	62	4	1526	4	ZNF607	19	38190464	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	434	38190464	20938519	11126	19111										
ZNF607	84775	broad.mit.edu	37	chr19	38200709	38200709	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtctatggccacatccccGaatgttattgatccctgaaa	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38200709G>A	ENST00000355202.4	-	3	619	c.24C>T	c.(22-24)ttC>ttT	p.F8F	ZNF607_ENST00000395835.3_Silent_p.F8F|CTD-2528L19.4_ENST00000586606.2_Silent_p.F8F	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	8	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F8F(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CCACATCCCCGAATGTTATTG	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	19											102	90	94					19																	38200709		2203	4300	6503	42892549	SO:0001819	synonymous_variant	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.24C>T	19.37:g.38200709G>A			42892549	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Silent	SNP	ENST00000355202.4	37	CCDS33006.1																																																																																				0.498	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38200709	G	A	38200709	2	1	61	1	0	0	0	0	0	0	0	1	18072	1049	37	1		1	ZNF607	19	38200709	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10245	38200709	20928274	11127	19112										
ZNF573	126231	broad.mit.edu	37	chr19	38230298	38230298	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatacaaagtaaaggtttTcttacactccttacattcat	3	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38230298T>A	ENST00000590414.2	-	4	1114	c.1093A>T	c.(1093-1095)Aaa>Taa	p.K365*	ZNF573_ENST00000536220.1_Nonsense_Mutation_p.K277*|ZNF573_ENST00000357309.3_Nonsense_Mutation_p.K277*|ZNF573_ENST00000392138.1_Nonsense_Mutation_p.K278*|ZNF573_ENST00000339503.4_Nonsense_Mutation_p.K307*			Q86YE8	ZN573_HUMAN	zinc finger protein 573	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K307*(1)		NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			GTAAAGGTTTTCTTACACTCC	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											70	72	72					19																	38230298		2203	4300	6503	42922138	SO:0001587	stop_gained	126231			AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1093A>T	19.37:g.38230298T>A	ENSP00000465020:p.Lys365*		42922138	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Nonsense_Mutation	SNP	ENST00000590414.2	37	CCDS59381.1	.	.	.	.	.	.	.	.	.	.	T	35	5.560361	0.96527	.	.	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	.	.	.	2.02	2.02	0.26589	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4931	0.33112	0.0:0.0:0.0:1.0	.	.	.	.	X	278;277;277;307;277	.	ENSP00000340171:K307X	K	-	1	0	ZNF573	42922138	0.120000	0.22244	0.929000	0.37066	0.953000	0.61014	2.819000	0.48049	0.786000	0.33708	0.377000	0.23210	AAA		0.378	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		A	38230298	T	A	38230298	4	1	61	1	0	0	0	0	0	1	0	0	18044	1792	62	5	908	5	ZNF573	19	38230298	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	29589	38230298	20898685	11128	19113										
SPINT2	10653	broad.mit.edu	37	chr19	38780877	38780877	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaggctgccggggcaataaGaacagctaccgctctgagga	15	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38780877G>T	ENST00000301244.7	+	5	945	c.510G>T	c.(508-510)aaG>aaT	p.K170N	SPINT2_ENST00000454580.3_Missense_Mutation_p.K113N|SPINT2_ENST00000587090.1_Missense_Mutation_p.K120N|CTB-102L5.4_ENST00000591889.1_Missense_Mutation_p.R48I	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2	170	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.K170N(1)		large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GGGGCAATAAGAACAGCTACC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											52	52	52					19																	38780877		2203	4300	6503	43472717	SO:0001583	missense	10653			U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"placental bikunin"	605124	"serine protease inhibitor, Kunitz type, 2"			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.510G>T	19.37:g.38780877G>T	ENSP00000301244:p.Lys170Asn		43472717	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Missense_Mutation	SNP	ENST00000301244.7	37	CCDS12510.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.117213	0.37339	.	.	ENSG00000167642	ENST00000301244;ENST00000454580	T;T	0.57907	0.37;0.37	5.55	-3.44	0.04796	Proteinase inhibitor I2, Kunitz metazoa (5);Proteinase inhibitor I2, Kunitz, conserved site (1);	0.090718	0.48286	D	0.000199	T	0.49184	0.1542	L	0.41124	1.26	0.26891	N	0.967325	P;P	0.49862	0.899;0.929	B;P	0.54026	0.401;0.74	T	0.53251	-0.8465	10	0.39692	T	0.17	.	11.6325	0.51185	0.4575:0.0:0.5425:0.0	.	113;170	B4DLU1;O43291	.;SPIT2_HUMAN	N	170;113	ENSP00000301244:K170N;ENSP00000389788:K113N	ENSP00000301244:K170N	K	+	3	2	SPINT2	43472717	1.000000	0.71417	0.174000	0.22961	0.267000	0.26476	0.601000	0.24119	-0.517000	0.06461	-0.140000	0.14226	AAG		0.597	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2			T	38780877	G	T	38780877	3	4	61	1	0	0	0	0	1	0	0	0	15108	933	33	2	528	2	SPINT2	19	38780877	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	550579	38780877	20348106	11129	19114										
GGN	199720	broad.mit.edu	37	chr19	38877102	38877102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctccgccgccccccagcGaagctttggctgctaaggaa	11	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38877102G>A	ENST00000334928.6	-	3	932	c.800C>T	c.(799-801)tCg>tTg	p.S267L	AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank|GGN_ENST00000591809.1_Intron	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	267	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)		p.S267L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCCCCCCAGCGAAGCTTTGGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											20	24	23					19																	38877102		1955	3912	5867	43568942	SO:0001583	missense	199720			AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.800C>T	19.37:g.38877102G>A	ENSP00000334940:p.Ser267Leu		43568942	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	37	CCDS12516.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.200166	0.38905	.	.	ENSG00000179168	ENST00000334928	.	.	.	3.63	3.63	0.41609	.	0.424789	0.17486	N	0.172522	T	0.30230	0.0758	L	0.27053	0.805	0.27110	N	0.962403	D;P	0.57899	0.981;0.938	P;B	0.47206	0.541;0.363	T	0.08006	-1.0743	9	0.48119	T	0.1	-2.77	10.6653	0.45726	0.0:0.0:1.0:0.0	.	184;267	Q86UU5-2;Q86UU5	.;GGN_HUMAN	L	267	.	ENSP00000334940:S267L	S	-	2	0	GGN	43568942	0.846000	0.29590	0.427000	0.26684	0.784000	0.44337	2.006000	0.40874	1.848000	0.53677	0.462000	0.41574	TCG		0.647	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		A	38877102	G	A	38877102	3	1	61	1	0	0	0	0	1	0	0	0	6378	1059	37	1	1166	1	GGN	19	38877102	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	96225	38877102	20251881	11130	19115										
FAM98C	147965	broad.mit.edu	37	chr19	38897589	38897589	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcagtgctgatcccaattCgagaggttctgaccccagaa	12	11	1	4	rs180979305	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38897589C>T	ENST00000252530.5	+	7	809	c.790C>T	c.(790-792)Cga>Tga	p.R264*	FAM98C_ENST00000343358.7_Intron|FAM98C_ENST00000588262.1_Missense_Mutation_p.S130L	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	264								p.R264*(1)		endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GATCCCAATTCGAGAGGTTCT	0.617													C|||	2	0.000399361	0.0015	0	5008	,	,		19630	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	19						C	stop/ARG	9,4031		0,9,2011	99	102	101		790	4.9	1	19		101	0,8356		0,0,4178	yes	stop-gained	FAM98C	NM_174905.3		0,9,6189	TT,TC,CC		0.0,0.2228,0.0726		264/350	38897589	9,12387	2020	4178	6198	43589429	SO:0001587	stop_gained	147965				CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.790C>T	19.37:g.38897589C>T	ENSP00000252530:p.Arg264*		43589429	A6NMW3|Q66K45	Nonsense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	20.3	3.968479	0.74131	0.002228	0.0	ENSG00000130244	ENST00000252530	.	.	.	4.9	4.9	0.64082	.	0.229512	0.22316	N	0.061664	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.6392	15.6386	0.76977	0.0:1.0:0.0:0.0	.	.	.	.	X	264	.	ENSP00000252530:R264X	R	+	1	2	FAM98C	43589429	0.996000	0.38824	0.992000	0.48379	0.324000	0.28378	1.927000	0.40094	2.274000	0.75844	0.650000	0.86243	CGA		0.617	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		T	38897589	C	T	38897589	4	4	61	1	0	0	0	0	0	1	0	0	5677	876	31	1	816	1	FAM98C	19	38897589	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	20487	38897589	20231394	11131	19116										
RASGRP4	115727	broad.mit.edu	37	chr19	38901840	38901840	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccctggcctcttcttacaTtctaccttcacctggtctct	5	17	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38901840T>A	ENST00000587738.1	-	15	1837	c.1767A>T	c.(1765-1767)gaA>gaT	p.E589D	RASGRP4_ENST00000433821.2_Missense_Mutation_p.E497D|RASGRP4_ENST00000293062.9_Missense_Mutation_p.E492D|RASGRP4_ENST00000587753.1_Missense_Mutation_p.E520D|RASGRP4_ENST00000454404.2_Missense_Mutation_p.E555D|RASGRP4_ENST00000586305.1_Missense_Mutation_p.E575D|RASGRP4_ENST00000426920.2_Missense_Mutation_p.E400D			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	589					activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.E589D(1)		cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCTTCTTACATTCTACCTTCA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											78	84	82					19																	38901840		2023	4184	6207	43593680	SO:0001583	missense	115727			AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1767A>T	19.37:g.38901840T>A	ENSP00000465772:p.Glu589Asp		43593680	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	37	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967443	0.53507	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000454404	D;D;D	0.93763	-3.28;-3.28;-3.28	5.83	-1.39	0.08997	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.216830	0.47455	D	0.000232	D	0.92344	0.7571	L	0.33189	0.99	0.41286	D	0.986943	D;P;D;D;D;D;D	0.76494	0.998;0.597;0.998;0.998;0.998;0.997;0.999	D;P;D;D;D;D;D	0.80764	0.965;0.739;0.949;0.949;0.949;0.977;0.994	D	0.88520	0.3095	10	0.40728	T	0.16	-26.0779	9.2195	0.37368	0.0:0.4344:0.0:0.5656	.	400;492;497;555;520;575;589	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	D	497;492;400;589	ENSP00000411878:E497D;ENSP00000293062:E492D;ENSP00000445966:E400D	ENSP00000293062:E492D	E	-	3	2	RASGRP4	43593680	0.793000	0.28825	0.982000	0.44146	0.021000	0.10359	-0.100000	0.10990	-0.085000	0.12573	-0.285000	0.09966	GAA		0.607	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		A	38901840	T	A	38901840	3	1	61	1	0	0	0	0	1	0	0	0	13114	1490	52	5	266	5	RASGRP4	19	38901840	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4251	38901840	20227143	11132	19117										
RYR1	6261	broad.mit.edu	37	chr19	38943558	38943558	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagcctgcaggacctcatCatctacttcgagcctccctc	7	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38943558C>A	ENST00000359596.3	+	13	1344	c.1344C>A	c.(1342-1344)atC>atA	p.I448I	RYR1_ENST00000355481.4_Silent_p.I448I|RYR1_ENST00000360985.3_Silent_p.I448I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	448					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.I448I(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AGGACCTCATCATCTACTTCG	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	19											46	34	38					19																	38943558		2202	4300	6502	43635398	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1344C>A	19.37:g.38943558C>A			43635398	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.657	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38943558	C	A	38943558	2	1	61	1	0	0	0	0	0	0	0	1	13805	816	29	2		2	RYR1	19	38943558	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41718	38943558	20185425	11133	19118										
RYR1	6261	broad.mit.edu	37	chr19	38957016	38957016	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggctacggctacaacatCgagcctcctgaccaggagcc	11	15	0	1	rs368131832		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:38957016C>T	ENST00000359596.3	+	24	3156	c.3156C>T	c.(3154-3156)atC>atT	p.I1052I	RYR1_ENST00000355481.4_Silent_p.I1052I|RYR1_ENST00000360985.3_Silent_p.I1052I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1052	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.I1052I(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCTACAACATCGAGCCTCCTG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	19											20	20	20					19																	38957016		2175	4264	6439	43648856	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3156C>T	19.37:g.38957016C>T			43648856	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.667	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38957016	C	T	38957016	2	4	61	1	0	0	0	0	0	0	0	1	13805	874	31	1		1	RYR1	19	38957016	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13458	38957016	20171967	11134	19119										
RYR1	6261	broad.mit.edu	37	chr19	39063823	39063823	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcccactatccaggtgcccCtggtaatctttaagcgggag	10	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39063823C>A	ENST00000359596.3	+	96	14005	c.14005C>A	c.(14005-14007)Ctg>Atg	p.L4669M	RYR1_ENST00000355481.4_Missense_Mutation_p.L4664M|RYR1_ENST00000360985.3_Missense_Mutation_p.L4664M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4669					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.L4669M(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCAGGTGCCCCTGGTAATCTT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											79	76	77					19																	39063823		2203	4300	6503	43755663	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14005C>A	19.37:g.39063823C>A	ENSP00000352608:p.Leu4669Met		43755663	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.369012	0.24771	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97941	-4.62;-4.62;-4.62	4.39	3.36	0.38483	Ryanodine Receptor TM 4-6 (1);	0.000000	0.53938	U	0.000060	D	0.98523	0.9507	M	0.86651	2.83	0.42793	D	0.993905	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99019	1.0817	10	0.87932	D	0	.	9.8515	0.41059	0.0:0.8266:0.0:0.1734	.	4664;4669	P21817-2;P21817	.;RYR1_HUMAN	M	4669;4664;4664	ENSP00000352608:L4669M;ENSP00000347667:L4664M;ENSP00000354254:L4664M	ENSP00000347667:L4664M	L	+	1	2	RYR1	43755663	0.998000	0.40836	1.000000	0.80357	0.918000	0.54935	3.813000	0.55636	1.085000	0.41206	0.313000	0.20887	CTG		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39063823	C	A	39063823	3	1	61	1	0	0	0	0	1	0	0	0	13805	680	24	2	14387	2	RYR1	19	39063823	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	106807	39063823	20065160	11135	19120										
MAP4K1	11184	broad.mit.edu	37	chr19	39101941	39101941	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcttggtcatgaggaagaGaactctagaatagtagggaa	12	5	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39101941G>T	ENST00000591517.1	-	10	698	c.670C>A	c.(670-672)Ctc>Atc	p.L224I	MAP4K1_ENST00000589130.1_Missense_Mutation_p.L220I|MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000586296.1_Missense_Mutation_p.L224I|MAP4K1_ENST00000396857.2_Missense_Mutation_p.L224I	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.L224I(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ATGAGGAAGAGAACTCTAGAA	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	19											83	82	83					19																	39101941		1925	4131	6056	43793781	SO:0001583	missense	11184			U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.670C>A	19.37:g.39101941G>T	ENSP00000465039:p.Leu224Ile		43793781		Missense_Mutation	SNP	ENST00000591517.1	37	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076122	0.76415	.	.	ENSG00000104814	ENST00000396857;ENST00000221409	T	0.27256	1.68	4.13	4.13	0.48395	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.34542	0.0901	L	0.28054	0.825	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.87578	0.994;0.998	T	0.12243	-1.0555	10	0.87932	D	0	.	9.7435	0.40433	0.1017:0.0:0.8983:0.0	.	224;224	Q92918-2;Q92918	.;M4K1_HUMAN	I	224	ENSP00000380066:L224I	ENSP00000221409:L224I	L	-	1	0	MAP4K1	43793781	0.999000	0.42202	0.998000	0.56505	0.903000	0.53119	2.899000	0.48679	2.122000	0.65172	0.555000	0.69702	CTC		0.552	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		T	39101941	G	T	39101941	3	4	61	1	0	0	0	0	1	0	0	0	9289	942	33	2	1985	2	MAP4K1	19	39101941	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38118	39101941	20027042	11136	19121										
ACTN4	81	broad.mit.edu	37	chr19	39214690	39214690	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggacctccaggacatgttCatcgtccataccatcgagga	10	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39214690C>A	ENST00000252699.2	+	14	1741	c.1665C>A	c.(1663-1665)ttC>ttA	p.F555L	ACTN4_ENST00000390009.3_Missense_Mutation_p.F336L|ACTN4_ENST00000424234.2_Missense_Mutation_p.F165L	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	555					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.F555L(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGACATGTTCATCGTCCATA	0.642																																					Colon(168;199 1940 10254 46213 46384)											1	Substitution - Missense(1)	large_intestine(1)	19											63	64	64					19																	39214690		2203	4300	6503	43906530	SO:0001583	missense	81			D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1665C>A	19.37:g.39214690C>A	ENSP00000252699:p.Phe555Leu		43906530	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	37	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.101958	0.56183	.	.	ENSG00000130402	ENST00000252699;ENST00000424234;ENST00000390009	T;T;T	0.48836	0.8;0.8;0.8	3.75	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.61961	0.2389	M	0.86343	2.81	0.58432	D	0.999993	B	0.28783	0.222	B	0.42030	0.373	T	0.65463	-0.6162	10	0.35671	T	0.21	.	14.8549	0.70329	0.0:1.0:0.0:0.0	.	555	O43707	ACTN4_HUMAN	L	555;165;336	ENSP00000252699:F555L;ENSP00000411187:F165L;ENSP00000439497:F336L	ENSP00000252699:F555L	F	+	3	2	ACTN4	43906530	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.107000	0.50329	2.106000	0.64143	0.561000	0.74099	TTC		0.642	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			A	39214690	C	A	39214690	3	1	61	1	0	0	0	0	1	0	0	0	207	825	29	2	1719	2	ACTN4	19	39214690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	112749	39214690	19914293	11137	19122										
ZFP36	7538	broad.mit.edu	37	chr19	39899054	39899054	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccactgtcaccctctgccttCtctgctgcccctggcacccc	6	22	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39899054C>A	ENST00000248673.3	+	2	754	c.696C>A	c.(694-696)ttC>ttA	p.F232L	MIR4530_ENST00000581459.1_RNA|ZFP36_ENST00000597629.1_Missense_Mutation_p.F238L	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	232					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)	p.F232L(1)		large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCTCTGCCTTCTCTGCTGCCC	0.687																																					NSCLC(67;1164 1324 12056 21056 30097)											1	Substitution - Missense(1)	large_intestine(1)	19											41	48	45					19																	39899054		2203	4299	6502	44590894	SO:0001583	missense	7538			M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"RING-type (C3HC4) zinc fingers"	12862	protein-coding gene	gene with protein product		190700	"zinc finger protein 36, C3H type, homolog (mouse)"			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.696C>A	19.37:g.39899054C>A	ENSP00000248673:p.Phe232Leu		44590894	B2RA54	Missense_Mutation	SNP	ENST00000248673.3	37		.	.	.	.	.	.	.	.	.	.	C	14.09	2.433062	0.43224	.	.	ENSG00000128016	ENST00000248673	T	0.19669	2.13	4.35	3.31	0.37934	.	0.250559	0.33272	U	0.005084	T	0.27241	0.0668	L	0.44542	1.39	0.34663	D	0.722841	D	0.67145	0.996	P	0.58266	0.836	T	0.26360	-1.0105	10	0.14656	T	0.56	-15.9899	10.1418	0.42740	0.0:0.9:0.0:0.1	.	232	P26651	TTP_HUMAN	L	232	ENSP00000248673:F232L	ENSP00000248673:F232L	F	+	3	2	ZFP36	44590894	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.085000	0.41634	1.065000	0.40693	0.442000	0.29010	TTC		0.687	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	39899054	C	A	39899054	3	1	61	1	0	0	0	0	1	0	0	0	17684	912	32	2	702	2	ZFP36	19	39899054	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	684364	39899054	19229929	11138	19123										
PLEKHG2	64857	broad.mit.edu	37	chr19	39915227	39915227	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgcccctgccacaagtcCtcacagacatctgggtccaa	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39915227C>A	ENST00000409794.3	+	19	4304	c.3454C>A	c.(3454-3456)Ctc>Atc	p.L1152I	PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.L1093I|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.L1123I	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1152	Pro-rich.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1110I(1)|p.L1093I(1)|p.L1152I(1)		breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCCACAAGTCCTCACAGACAT	0.617																																																3	Substitution - Missense(3)	large_intestine(3)	19											94	89	90					19																	39915227		2203	4300	6503	44607067	SO:0001583	missense	64857			AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.3454C>A	19.37:g.39915227C>A	ENSP00000386733:p.Leu1152Ile		44607067	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273064	0.80580	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.75260	-0.77;-0.83;-0.92	4.11	3.06	0.35304	.	0.000000	0.35495	N	0.003161	T	0.79868	0.4520	L	0.52905	1.665	0.80722	D	1	D;D;D	0.67145	0.996;0.993;0.993	D;D;D	0.75484	0.986;0.967;0.967	T	0.77316	-0.2633	9	.	.	.	.	8.525	0.33300	0.0:0.8855:0.0:0.1145	.	1123;1152;1093	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	I	1152;1123;1093	ENSP00000386733:L1152I;ENSP00000392906:L1123I;ENSP00000408857:L1093I	.	L	+	1	0	PLEKHG2	44607067	0.116000	0.22171	0.661000	0.29709	0.612000	0.37316	1.443000	0.35057	1.044000	0.40200	0.205000	0.17691	CTC		0.617	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39915227	C	A	39915227	3	1	61	1	0	0	0	0	1	0	0	0	12100	681	24	2	3524	2	PLEKHG2	19	39915227	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16173	39915227	19213756	11139	19124										
SUPT5H	6829	broad.mit.edu	37	chr19	39960790	39960790	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcccagcccaggaacttaGaaaatacttcaagatggggg	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39960790G>T	ENST00000599117.1	+	18	1773	c.1406G>T	c.(1405-1407)aGa>aTa	p.R469I	SUPT5H_ENST00000432763.2_Missense_Mutation_p.R469I|SUPT5H_ENST00000598725.1_Missense_Mutation_p.R469I|SUPT5H_ENST00000402194.2_Missense_Mutation_p.R465I|SUPT5H_ENST00000359191.6_Missense_Mutation_p.R465I			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	469					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.R469I(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CAGGAACTTAGAAAATACTTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											119	113	115					19																	39960790		2203	4300	6503	44652630	SO:0001583	missense	6829			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.1406G>T	19.37:g.39960790G>T	ENSP00000470252:p.Arg469Ile		44652630	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892989	0.91889	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.63	5.63	0.86233	Translation protein SH3-like (1);	0.059925	0.64402	D	0.000004	D	0.83533	0.5275	M	0.85777	2.775	0.80722	D	1	D;P;P	0.89917	1.0;0.944;0.908	D;P;P	0.69654	0.965;0.729;0.692	D	0.84713	0.0735	8	.	.	.	-22.9872	18.4634	0.90747	0.0:0.0:1.0:0.0	.	261;465;469	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	I	469;465;447;469	.	.	R	+	2	0	SUPT5H	44652630	1.000000	0.71417	0.961000	0.40146	0.964000	0.63967	7.824000	0.86668	2.671000	0.90904	0.455000	0.32223	AGA		0.557	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		T	39960790	G	T	39960790	3	4	61	1	0	0	0	0	1	0	0	0	15438	942	33	2	1468	2	SUPT5H	19	39960790	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45563	39960790	19168193	11140	19125										
TIMM50	92609	broad.mit.edu	37	chr19	39976337	39976337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcccacagatgatcatcGagcccaccagcccttgcctt	6	18	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39976337G>A	ENST00000607714.1	+	6	404	c.382G>A	c.(382-384)Gag>Aag	p.E128K	TIMM50_ENST00000544017.1_Missense_Mutation_p.E15K|TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000314349.4_Missense_Mutation_p.E231K			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	128					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)	p.E231K(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GATGATCATCGAGCCCACCAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											94	78	83					19																	39976337		2203	4300	6503	44668177	SO:0001583	missense	92609			BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	23656	protein-coding gene	gene with protein product		607381	"translocase of inner mitochondrial membrane 50 homolog (yeast)"			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.382G>A	19.37:g.39976337G>A	ENSP00000475531:p.Glu128Lys		44668177	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Missense_Mutation	SNP	ENST00000607714.1	37		.	.	.	.	.	.	.	.	.	.	G	22.1	4.247382	0.80024	.	.	ENSG00000105197	ENST00000314349;ENST00000544017	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.57417	0.2052	L	0.59967	1.855	0.80722	D	1	P	0.50272	0.933	B	0.43155	0.41	T	0.60136	-0.7322	8	.	.	.	-20.7268	17.1668	0.86818	0.0:0.0:1.0:0.0	.	231	Q3ZCQ8-2	.	K	231;15	.	.	E	+	1	0	TIMM50	44668177	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.278000	0.78587	2.576000	0.86940	0.561000	0.74099	GAG		0.622	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		A	39976337	G	A	39976337	3	1	61	1	0	0	0	0	1	0	0	0	15952	1059	37	1	713	1	TIMM50	19	39976337	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15547	39976337	19152646	11141	19126										
TIMM50	92609	broad.mit.edu	37	chr19	39976926	39976926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatctttacgtcagagactGgcatggtgaggctctggggc	14	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:39976926G>A	ENST00000607714.1	+	7	614	c.592G>A	c.(592-594)Ggc>Agc	p.G198S	TIMM50_ENST00000544017.1_Missense_Mutation_p.G85S|TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000314349.4_Missense_Mutation_p.G301S			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	198	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)	p.G301S(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GTCAGAGACTGGCATGGTGAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											129	134	132					19																	39976926		2203	4300	6503	44668766	SO:0001583	missense	92609			BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	23656	protein-coding gene	gene with protein product		607381	"translocase of inner mitochondrial membrane 50 homolog (yeast)"			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.592G>A	19.37:g.39976926G>A	ENSP00000475531:p.Gly198Ser		44668766	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Missense_Mutation	SNP	ENST00000607714.1	37		.	.	.	.	.	.	.	.	.	.	G	21.1	4.093189	0.76756	.	.	ENSG00000105197	ENST00000314349;ENST00000544017	T;T	0.15834	2.39;2.39	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.22627	0.0546	N	0.16567	0.415	0.80722	D	1	P	0.49862	0.929	P	0.58172	0.834	T	0.03095	-1.1073	9	.	.	.	-23.5099	17.419	0.87510	0.0:0.0:1.0:0.0	.	301	Q3ZCQ8-2	.	S	301;85	ENSP00000318115:G301S;ENSP00000445806:G85S	.	G	+	1	0	TIMM50	44668766	1.000000	0.71417	0.989000	0.46669	0.554000	0.35429	9.117000	0.94347	2.649000	0.89929	0.462000	0.41574	GGC		0.562	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		A	39976926	G	A	39976926	3	1	61	1	0	0	0	0	1	0	0	0	15952	1348	47	3	927	3	TIMM50	19	39976926	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	589	39976926	19152057	11142	19127										
CLC	1178	broad.mit.edu	37	chr19	40222064	40222064	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatttggtcagggagatatCtctccacacttgcaccatct	7	11	3	1	rs368189111		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40222064C>A	ENST00000221804.4	-	4	460	c.385G>T	c.(385-387)Gat>Tat	p.D129Y		NM_001828.5	NP_001819.2	Q05315	LEG10_HUMAN	Charcot-Leyden crystal galectin	129	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				multicellular organismal development (GO:0007275)|regulation of activated T cell proliferation (GO:0046006)|regulation of T cell anergy (GO:0002667)|regulation of T cell cytokine production (GO:0002724)|T cell apoptotic process (GO:0070231)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)	p.D129Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)|stomach(1)	12	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)		AGGGAGATATCTCTCCACACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	TYR/ASP	1,4405		0,1,2202	196	191	193		385	0.7	0.8	19		193	0,8600		0,0,4300	no	missense	CLC	NM_001828.4	160	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging	129/143	40222064	1,13005	2203	4300	6503	44913904	SO:0001583	missense	1178			L01664	CCDS33025.1	19q13.1	2013-06-12	2013-06-12		ENSG00000105205	ENSG00000105205		"Lectins, galactoside-binding"	2014	protein-coding gene	gene with protein product	"eosinophil lysophospholipase", "lysolecithin acylhydrolase", "galectin 10", "lectin, galactoside-binding, soluble, 10"	153310	"Charcot-Leyden crystal protein"			1577491, 11834744	Standard	NM_001828		Approved	LGALS10, MGC149659, Gal-10	uc002omh.3	Q05315		ENST00000221804.4:c.385G>T	19.37:g.40222064C>A	ENSP00000221804:p.Asp129Tyr		44913904	C5HZ13|C5HZ14|Q0VDE3	Missense_Mutation	SNP	ENST00000221804.4	37	CCDS33025.1	.	.	.	.	.	.	.	.	.	.	.	12.17	1.857577	0.32791	2.27E-4	0.0	ENSG00000105205	ENST00000221804	T	0.25912	1.77	0.659	0.659	0.17861	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.55513	0.1925	M	0.92923	3.36	0.25594	N	0.986668	D	0.89917	1.0	D	0.91635	0.999	T	0.41197	-0.9522	8	0.87932	D	0	.	.	.	.	.	129	Q05315	LPPL_HUMAN	Y	129	ENSP00000221804:D129Y	ENSP00000221804:D129Y	D	-	1	0	CLC	44913904	0.519000	0.26242	0.836000	0.33094	0.176000	0.22953	1.079000	0.30766	0.608000	0.30000	0.187000	0.17357	GAT		0.418	CLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465225.1	NM_001828		A	40222064	C	A	40222064	3	1	61	1	0	0	0	0	1	0	0	0	3462	913	32	2	47	2	CLC	19	40222064	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	245138	40222064	18906919	11143	19128										
FCGBP	8857	broad.mit.edu	37	chr19	40366251	40366251	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcgtccgggccgccgaaGgactcctgctgctctggggt	16	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40366251G>T	ENST00000221347.6	-	30	13990	c.13983C>A	c.(13981-13983)tcC>tcA	p.S4661S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4661	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.S4661S(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			GGCCGCCGAAGGACTCCTGCT	0.736																																																1	Substitution - coding silent(1)	large_intestine(1)	19											28	39	35					19																	40366251		2202	4297	6499	45058091	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13983C>A	19.37:g.40366251G>T			45058091	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.736	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40366251	G	T	40366251	2	4	61	1	0	0	0	0	0	0	0	1	5797	987	35	2		2	FCGBP	19	40366251	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	144187	40366251	18762732	11144	19129										
FCGBP	8857	broad.mit.edu	37	chr19	40392191	40392191	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgactgttctgagggcatTccatggctgcaaggaggggg	17	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40392191T>G	ENST00000221347.6	-	17	8202	c.8195A>C	c.(8194-8196)gAa>gCa	p.E2732A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2732	Cys-rich.					extracellular vesicular exosome (GO:0070062)		p.E2732A(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			CTGAGGGCATTCCATGGCTGC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											10	11	11					19																	40392191		2131	4192	6323	45084031	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8195A>C	19.37:g.40392191T>G	ENSP00000221347:p.Glu2732Ala		45084031	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	T	4.342	0.062962	0.08388	.	.	ENSG00000090920	ENST00000221347	T	0.79247	-1.25	2.66	-1.58	0.08479	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (1);	0.975053	0.08364	U	0.957148	T	0.61451	0.2348	L	0.29908	0.895	0.09310	N	1	B	0.33120	0.398	B	0.39590	0.304	T	0.48937	-0.8990	10	0.10377	T	0.69	.	1.5738	0.02620	0.1613:0.1054:0.3306:0.4026	.	2732	Q9Y6R7	FCGBP_HUMAN	A	2732	ENSP00000221347:E2732A	ENSP00000221347:E2732A	E	-	2	0	FCGBP	45084031	0.000000	0.05858	0.024000	0.17045	0.013000	0.08279	-0.238000	0.08977	-0.635000	0.05531	0.248000	0.18094	GAA		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40392191	T	G	40392191	3	3	61	1	0	0	0	0	1	0	0	0	5797	1783	62	4	8102	4	FCGBP	19	40392191	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	25940	40392191	18736792	11145	19130										
FCGBP	8857	broad.mit.edu	37	chr19	40430320	40430320	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaacttcaccgcgggtcagCgacacagagtggctgtaggc	13	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40430320C>T	ENST00000221347.6	-	3	1630	c.1623G>A	c.(1621-1623)tcG>tcA	p.S541S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	541	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.S541S(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			CGCGGGTCAGCGACACAGAGT	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	19											49	41	44					19																	40430320		2203	4300	6503	45122160	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1623G>A	19.37:g.40430320C>T			45122160	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40430320	C	T	40430320	2	4	61	1	0	0	0	0	0	0	0	1	5797	755	27	1		1	FCGBP	19	40430320	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38129	40430320	18698663	11146	19131										
PSMC4	5704	broad.mit.edu	37	chr19	40486243	40486243	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggatccggccctgctacgGccaggacggctggaccgtaa	14	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40486243G>T	ENST00000157812.2	+	9	1167	c.969G>T	c.(967-969)cgG>cgT	p.R323R	PSMC4_ENST00000455878.2_Silent_p.R292R	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	323					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R323R(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CCCTGCTACGGCCAGGACGGC	0.542																																					Colon(105;1478 1543 4034 6132 38638)											1	Substitution - coding silent(1)	large_intestine(1)	19											122	126	124					19																	40486243		2203	4300	6503	45178083	SO:0001819	synonymous_variant	5704			U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.969G>T	19.37:g.40486243G>T			45178083	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																				0.542	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		T	40486243	G	T	40486243	2	4	61	1	0	0	0	0	0	0	0	1	12723	1190	42	2		2	PSMC4	19	40486243	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55923	40486243	18642740	11147	19132										
ZNF546	339327	broad.mit.edu	37	chr19	40512012	40512012	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccccccagccccggtttCtctggattctgtgcttctcc	7	18	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40512012C>A	ENST00000347077.4	+	4	310	c.94C>A	c.(94-96)Ctc>Atc	p.L32I	ZNF546_ENST00000600094.1_Missense_Mutation_p.L6I|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	32					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L32I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GCCCCGGTTTCTCTGGATTCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											130	122	124					19																	40512012		2203	4300	6503	45203852	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.94C>A	19.37:g.40512012C>A	ENSP00000339823:p.Leu32Ile		45203852	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	c	8.738	0.918269	0.17982	.	.	ENSG00000187187	ENST00000347077	T	0.06849	3.25	2.4	1.35	0.21983	.	.	.	.	.	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	B;B	0.30482	0.18;0.281	B;B	0.24974	0.057;0.057	T	0.45249	-0.9274	9	0.23891	T	0.37	.	5.2462	0.15498	0.0:0.8326:0.0:0.1674	.	6;32	B3KVL3;Q86UE3	.;ZN546_HUMAN	I	32	ENSP00000339823:L32I	ENSP00000339823:L32I	L	+	1	0	ZNF546	45203852	0.033000	0.19621	0.034000	0.17996	0.002000	0.02628	1.290000	0.33319	0.549000	0.28973	-0.150000	0.13652	CTC		0.418	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		A	40512012	C	A	40512012	3	1	61	1	0	0	0	0	1	0	0	0	18017	913	32	2	100	2	ZNF546	19	40512012	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25769	40512012	18616971	11148	19133										
ZNF546	339327	broad.mit.edu	37	chr19	40519887	40519887	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataccttattcaacatctgaGaattcacactggtgagagac	7	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40519887G>T	ENST00000347077.4	+	7	926	c.710G>T	c.(709-711)aGa>aTa	p.R237I	ZNF546_ENST00000600094.1_Missense_Mutation_p.R211I|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R237I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CAACATCTGAGAATTCACACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	86	85					19																	40519887		2203	4300	6503	45211727	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.710G>T	19.37:g.40519887G>T	ENSP00000339823:p.Arg237Ile		45211727	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	g	12.95	2.092822	0.36952	.	.	ENSG00000187187	ENST00000347077	T	0.24908	1.83	2.41	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23806	0.0576	M	0.81497	2.545	0.27381	N	0.955403	P;P	0.50710	0.938;0.626	B;B	0.38327	0.271;0.096	T	0.32455	-0.9906	9	0.56958	D	0.05	.	1.8957	0.03257	0.2732:0.0:0.4342:0.2926	.	211;237	B3KVL3;Q86UE3	.;ZN546_HUMAN	I	237	ENSP00000339823:R237I	ENSP00000339823:R237I	R	+	2	0	ZNF546	45211727	0.000000	0.05858	0.037000	0.18230	0.995000	0.86356	0.460000	0.21924	0.324000	0.23333	0.591000	0.81541	AGA		0.408	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		T	40519887	G	T	40519887	3	4	61	1	0	0	0	0	1	0	0	0	18017	942	33	2	728	2	ZNF546	19	40519887	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7875	40519887	18609096	11149	19134										
ZNF546	339327	broad.mit.edu	37	chr19	40520025	40520025	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatgtgggaaggcctttaGacttcattatcaccttactg	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40520025G>T	ENST00000347077.4	+	7	1064	c.848G>T	c.(847-849)aGa>aTa	p.R283I	ZNF546_ENST00000600094.1_Missense_Mutation_p.R257I|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	283					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R283I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AAGGCCTTTAGACTTCATTAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											104	104	104					19																	40520025		2203	4300	6503	45211865	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.848G>T	19.37:g.40520025G>T	ENSP00000339823:p.Arg283Ile		45211865	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	g	6.109	0.388276	0.11581	.	.	ENSG00000187187	ENST00000347077	T	0.08008	3.14	2.61	1.5	0.22942	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04861	0.0131	L	0.38531	1.155	0.20563	N	0.999883	P;B	0.39352	0.669;0.136	B;B	0.23716	0.028;0.048	T	0.39840	-0.9594	9	0.20046	T	0.44	.	8.066	0.30661	0.1347:0.0:0.8653:0.0	.	257;283	B3KVL3;Q86UE3	.;ZN546_HUMAN	I	283	ENSP00000339823:R283I	ENSP00000339823:R283I	R	+	2	0	ZNF546	45211865	0.000000	0.05858	0.759000	0.31340	0.994000	0.84299	-1.736000	0.01845	0.600000	0.29862	0.655000	0.94253	AGA		0.443	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		T	40520025	G	T	40520025	3	4	61	1	0	0	0	0	1	0	0	0	18017	942	33	2	866	2	ZNF546	19	40520025	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138	40520025	18608958	11150	19135										
ZNF546	339327	broad.mit.edu	37	chr19	40520541	40520541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcctttcgtcttcaaacggAacttactcggcatcatagaa	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40520541A>G	ENST00000347077.4	+	7	1580	c.1364A>G	c.(1363-1365)gAa>gGa	p.E455G	ZNF546_ENST00000600094.1_Missense_Mutation_p.E429G|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E455G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTTCAAACGGAACTTACTCGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	73	72					19																	40520541		2203	4300	6503	45212381	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.1364A>G	19.37:g.40520541A>G	ENSP00000339823:p.Glu455Gly		45212381	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	a	8.952	0.968454	0.18659	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.07800	3.16	2.67	1.59	0.23543	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04497	0.0123	N	0.10945	0.07	0.09310	N	1	P	0.38280	0.625	B	0.39738	0.308	T	0.43393	-0.9394	9	0.20046	T	0.44	.	6.1468	0.20291	0.7623:0.0:0.0:0.2377	.	455	Q86UE3	ZN546_HUMAN	G	455;92	ENSP00000339823:E455G	ENSP00000339823:E455G	E	+	2	0	ZNF546	45212381	0.000000	0.05858	0.042000	0.18584	0.932000	0.56968	0.073000	0.14640	0.397000	0.25310	0.533000	0.62120	GAA		0.393	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		G	40520541	A	G	40520541	3	3	61	1	0	0	0	0	1	0	0	0	18017	246	9	4	1382	4	ZNF546	19	40520541	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	516	40520541	18608442	11151	19136										
ZNF546	339327	broad.mit.edu	37	chr19	40520762	40520762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaccctacatatgtaacGaatgtggaaaagcctttcgt	8	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40520762G>A	ENST00000347077.4	+	7	1801	c.1585G>A	c.(1585-1587)Gaa>Aaa	p.E529K	ZNF546_ENST00000600094.1_Missense_Mutation_p.E503K|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	529					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E529K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CATATGTAACGAATGTGGAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	58	60					19																	40520762		2203	4300	6503	45212602	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.1585G>A	19.37:g.40520762G>A	ENSP00000339823:p.Glu529Lys		45212602	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	g	17.23	3.337392	0.60963	.	.	ENSG00000187187	ENST00000347077	T	0.07327	3.2	3.0	3.0	0.34707	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.20685	0.6	0.22710	N	0.99883	D	0.53745	0.962	P	0.45946	0.498	T	0.29912	-0.9996	9	0.48119	T	0.1	.	12.2301	0.54482	0.0:0.0:1.0:0.0	.	529	Q86UE3	ZN546_HUMAN	K	529	ENSP00000339823:E529K	ENSP00000339823:E529K	E	+	1	0	ZNF546	45212602	0.000000	0.05858	0.961000	0.40146	0.952000	0.60782	-0.204000	0.09425	1.969000	0.57287	0.655000	0.94253	GAA		0.403	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		A	40520762	G	A	40520762	3	1	61	1	0	0	0	0	1	0	0	0	18017	1059	37	1	1603	1	ZNF546	19	40520762	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	221	40520762	18608221	11152	19137										
ZNF780B	163131	broad.mit.edu	37	chr19	40541828	40541828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttggtaatgatatcgaaagGccatctcacattccctacat	7	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40541828G>A	ENST00000434248.1	-	5	1003	c.938C>T	c.(937-939)gCc>gTc	p.A313V	ZNF780B_ENST00000221355.6_Missense_Mutation_p.A165V	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A313V(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					ATATCGAAAGGCCATCTCACA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	19											120	120	120					19																	40541828		2203	4300	6503	45233668	SO:0001583	missense	163131			AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.938C>T	19.37:g.40541828G>A	ENSP00000391641:p.Ala313Val		45233668	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.419869	0.25552	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.08546	3.08;3.08	2.21	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05823	0.0152	L	0.41492	1.28	0.09310	N	1	P	0.47677	0.899	B	0.37601	0.254	T	0.34576	-0.9823	9	0.39692	T	0.17	.	4.2006	0.10464	0.0:0.2608:0.4743:0.2649	.	313	Q9Y6R6	Z780B_HUMAN	V	313;165	ENSP00000391641:A313V;ENSP00000221355:A165V	ENSP00000221355:A165V	A	-	2	0	ZNF780B	45233668	0.000000	0.05858	0.014000	0.15608	0.198000	0.23893	0.034000	0.13776	0.079000	0.16929	0.313000	0.20887	GCC		0.388	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		A	40541828	G	A	40541828	3	1	61	1	0	0	0	0	1	0	0	0	18192	1203	42	3	1567	3	ZNF780B	19	40541828	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21066	40541828	18587155	11153	19138										
ZNF780A	284323	broad.mit.edu	37	chr19	40580817	40580817	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaagttgtaggtaaagtCtaaaagccttcccacactcc	9	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40580817C>A	ENST00000595687.2	-	6	1741	c.1532G>T	c.(1531-1533)aGa>aTa	p.R511I	ZNF780A_ENST00000594395.1_Missense_Mutation_p.R512I|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Missense_Mutation_p.R511I|ZNF780A_ENST00000450241.2_Missense_Mutation_p.R477I|ZNF780A_ENST00000455521.1_Missense_Mutation_p.R512I|ZNF780A_ENST00000414720.2_Intron	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R477I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TAGGTAAAGTCTAAAAGCCTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19											80	82	82					19																	40580817		2203	4300	6503	45272657	SO:0001583	missense	284323			AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1532G>T	19.37:g.40580817C>A	ENSP00000472189:p.Arg511Ile		45272657	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	c	12.31	1.898464	0.33535	.	.	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	T;T	0.04917	3.53;3.53	1.93	-0.548	0.11833	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07773	0.0195	L	0.35487	1.065	0.19300	N	0.999971	B;D	0.67145	0.238;0.996	B;P	0.59115	0.082;0.852	T	0.30149	-0.9988	9	0.22109	T	0.4	.	0.5793	0.00709	0.249:0.3289:0.2453:0.1768	.	512;511	E9PB48;O75290	.;Z780A_HUMAN	I	511;512;511	ENSP00000400997:R512I;ENSP00000341507:R511I	ENSP00000341507:R511I	R	-	2	0	ZNF780A	45272657	0.000000	0.05858	0.186000	0.23195	0.740000	0.42216	-2.862000	0.00725	0.096000	0.17463	0.313000	0.20887	AGA		0.423	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40580817	C	A	40580817	3	1	61	1	0	0	0	0	1	0	0	0	18191	913	32	2	524	2	ZNF780A	19	40580817	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38989	40580817	18548166	11154	19139										
ZNF780A	284323	broad.mit.edu	37	chr19	40581460	40581460	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctcattggaatgaatttTctgatgctgaataaggtgtg	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40581460T>A	ENST00000595687.2	-	6	1098	c.889A>T	c.(889-891)Aaa>Taa	p.K297*	ZNF780A_ENST00000594395.1_Nonsense_Mutation_p.K298*|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Nonsense_Mutation_p.K297*|ZNF780A_ENST00000450241.2_Nonsense_Mutation_p.K263*|ZNF780A_ENST00000455521.1_Nonsense_Mutation_p.K298*|ZNF780A_ENST00000414720.2_Intron	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K263*(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GAATGAATTTTCTGATGCTGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											185	183	184					19																	40581460		2203	4300	6503	45273300	SO:0001587	stop_gained	284323			AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.889A>T	19.37:g.40581460T>A	ENSP00000472189:p.Lys297*		45273300	E9PB48|Q6ZN87	Nonsense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	T	38	6.943241	0.97952	.	.	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	.	.	.	1.92	1.92	0.25849	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	4.0966	0.09993	0.3139:0.0:0.0:0.6861	.	.	.	.	X	297;298;297	.	ENSP00000341507:K297X	K	-	1	0	ZNF780A	45273300	.	.	0.583000	0.28640	0.943000	0.58893	.	.	0.862000	0.35528	0.254000	0.18369	AAA		0.383	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40581460	T	A	40581460	4	1	61	1	0	0	0	0	0	1	0	0	18191	1792	62	5	1167	5	ZNF780A	19	40581460	Nonsense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	643	40581460	18547523	11155	19140										
AKT2	208	broad.mit.edu	37	chr19	40741000	40741000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggcggtaaattcatcatCgaagtaccttgtgtcgacct	10	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:40741000C>T	ENST00000392038.2	-	13	1616	c.1318G>A	c.(1318-1320)Gat>Aat	p.D440N	AKT2_ENST00000579047.1_Missense_Mutation_p.D378N|AKT2_ENST00000424901.1_Missense_Mutation_p.D440N|AKT2_ENST00000311278.6_Missense_Mutation_p.D397N	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	440	AGC-kinase C-terminal.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)	p.D440N(1)		breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			AATTCATCATCGAAGTACCTT	0.632			A		"ovarian, pancreatic "																																		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	1	Substitution - Missense(1)	large_intestine(1)	19											159	146	150					19																	40741000		2203	4300	6503	45432840	SO:0001583	missense	208			M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.1318G>A	19.37:g.40741000C>T	ENSP00000375892:p.Asp440Asn		45432840	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	37	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	C	36	5.963393	0.97151	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278	D;D;D	0.84800	-1.9;-1.9;-1.9	5.39	5.39	0.77823	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.044865	0.85682	D	0.000000	D	0.93485	0.7921	M	0.89968	3.075	0.80722	D	1	P;D;D	0.76494	0.909;0.999;0.992	B;D;P	0.66602	0.436;0.945;0.702	D	0.94334	0.7564	10	0.87932	D	0	.	18.0804	0.89440	0.0:1.0:0.0:0.0	.	378;397;440	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	N	440;341;440;397	ENSP00000375892:D440N;ENSP00000399532:D440N;ENSP00000309428:D397N	ENSP00000309428:D397N	D	-	1	0	AKT2	45432840	1.000000	0.71417	0.720000	0.30636	0.961000	0.63080	7.403000	0.79983	2.808000	0.96608	0.655000	0.94253	GAT		0.632	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		T	40741000	C	T	40741000	3	4	61	1	0	0	0	0	1	0	0	0	480	884	31	1	135	1	AKT2	19	40741000	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	159540	40741000	18387983	11156	19141										
RAB4B	53916	broad.mit.edu	37	chr19	41286341	41286341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagtttggatcccgggtggTcaacgtgggtgggaagactg	19	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41286341T>C	ENST00000594800.1	+	3	309	c.149T>C	c.(148-150)gTc>gCc	p.V50A	RAB4B_ENST00000602069.1_3'UTR|RAB4B-EGLN2_ENST00000601949.1_Intron|MIA-RAB4B_ENST00000600729.1_3'UTR|RAB4B_ENST00000357052.2_Missense_Mutation_p.V50A|RAB4B-EGLN2_ENST00000594136.1_Missense_Mutation_p.V50A			P61018	RAB4B_HUMAN	RAB4B, member RAS oncogene family	50					glucose import (GO:0046323)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	insulin-responsive compartment (GO:0032593)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	GTP binding (GO:0005525)	p.V85A(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	11			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TCCCGGGTGGTCAACGTGGGT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	73	79					19																	41286341		2203	4300	6503	45978181	SO:0001583	missense	53916			AF165522	CCDS33030.1	19q13.2	2012-10-15			ENSG00000167578	ENSG00000167578		"RAB, member RAS oncogene"	9782	protein-coding gene	gene with protein product	"ras-related GTP-binding protein 4b", "small GTP binding protein RAB4B"	612945					Standard	NM_016154		Approved	FLJ78649, MGC52123	uc002opd.2	P61018		ENST00000594800.1:c.149T>C	19.37:g.41286341T>C	ENSP00000470246:p.Val50Ala		45978181	P22750|Q7Z514|Q9HBR6	Missense_Mutation	SNP	ENST00000594800.1	37	CCDS33030.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.965876	0.74131	.	.	ENSG00000167578	ENST00000357052;ENST00000378307	D;D	0.81739	-1.53;-1.53	4.89	4.89	0.63831	Small GTP-binding protein domain (1);	0.069542	0.56097	D	0.000027	D	0.85031	0.5604	M	0.83384	2.64	0.80722	D	1	B;B	0.28820	0.224;0.094	B;B	0.39805	0.264;0.31	D	0.85962	0.1471	10	0.72032	D	0.01	.	13.6226	0.62146	0.0:0.0:0.0:1.0	.	85;50	P61018-2;P61018	.;RAB4B_HUMAN	A	50	ENSP00000349560:V50A;ENSP00000367557:V50A	ENSP00000349560:V50A	V	+	2	0	RAB4B	45978181	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.707000	0.84623	2.052000	0.61016	0.402000	0.26972	GTC		0.592	RAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463168.1	NM_016154		C	41286341	T	C	41286341	3	2	61	1	0	0	0	0	1	0	0	0	12984	1667	58	4	159	4	RAB4B	19	41286341	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	545341	41286341	17842642	11157	19142										
CYP2A6	1548	broad.mit.edu	37	chr19	41349804	41349804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgactgggaggacttgaggCggaagttctgcatgacggtg	18	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41349804C>T	ENST00000301141.5	-	9	1402	c.1382G>A	c.(1381-1383)cGc>cAc	p.R461H	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	461					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.R461H(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGACTTGAGGCGGAAGTTCTG	0.577																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	19											98	75	83					19																	41349804		2203	4297	6500	46041644	SO:0001583	missense	1548			AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1382G>A	19.37:g.41349804C>T	ENSP00000301141:p.Arg461His		46041644	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	3.742	-0.053278	0.07362	.	.	ENSG00000255974	ENST00000301141	T	0.01359	4.98	2.98	0.723	0.18231	.	0.904496	0.09385	N	0.809439	T	0.01320	0.0043	N	0.25789	0.76	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.47058	-0.9146	10	0.44086	T	0.13	.	6.1029	0.20057	0.0:0.5027:0.0:0.4973	.	461	P11509	CP2A6_HUMAN	H	461	ENSP00000301141:R461H	ENSP00000301141:R461H	R	-	2	0	CYP2A6	46041644	0.000000	0.05858	0.297000	0.24988	0.182000	0.23217	-1.176000	0.03099	-0.012000	0.14223	0.386000	0.25728	CGC		0.577	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41349804	C	T	41349804	3	4	61	1	0	0	0	0	1	0	0	0	4168	768	27	1	106	1	CYP2A6	19	41349804	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63463	41349804	17779179	11158	19143										
CYP2A6	1548	broad.mit.edu	37	chr19	41356251	41356251	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagcttccccttgctcttCctctgctgccaaacagacat	7	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41356251C>A	ENST00000301141.5	-	1	101	c.81G>T	c.(79-81)agG>agT	p.R27S	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	27					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.R27S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCTTGCTCTTCCTCTGCTGCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19											109	93	98					19																	41356251		2203	4299	6502	46048091	SO:0001583	missense	1548			AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.81G>T	19.37:g.41356251C>A	ENSP00000301141:p.Arg27Ser		46048091	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	0.153	-1.088942	0.01873	.	.	ENSG00000255974	ENST00000301141	T	0.70631	-0.5	2.86	-0.876	0.10624	.	0.712341	0.12950	U	0.425845	T	0.52948	0.1766	L	0.37630	1.12	0.09310	N	1	P	0.45283	0.855	B	0.43575	0.424	T	0.50329	-0.8841	10	0.06099	T	0.92	.	6.6343	0.22874	0.0:0.5929:0.0:0.4071	.	27	P11509	CP2A6_HUMAN	S	27	ENSP00000301141:R27S	ENSP00000301141:R27S	R	-	3	2	CYP2A6	46048091	0.000000	0.05858	0.069000	0.20011	0.024000	0.10985	-0.162000	0.10012	-0.003000	0.14444	0.173000	0.16961	AGG		0.547	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		A	41356251	C	A	41356251	3	1	61	1	0	0	0	0	1	0	0	0	4168	854	30	2	1439	2	CYP2A6	19	41356251	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6447	41356251	17772732	11159	19144										
CYP2A13	1553	broad.mit.edu	37	chr19	41594546	41594546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacagagcagatgtacaactCcctcatgaaggtgtcctaag	9	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41594546C>T	ENST00000330436.3	+	1	170	c.170C>T	c.(169-171)tCc>tTc	p.S57F		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	57					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.S57F(1)		breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	ATGTACAACTCCCTCATGAAG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	81	84					19																	41594546		2203	4300	6503	46286386	SO:0001583	missense	1553			U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.170C>T	19.37:g.41594546C>T	ENSP00000332679:p.Ser57Phe		46286386	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	14.55	2.567535	0.45694	.	.	ENSG00000197838	ENST00000330436	T	0.01203	5.18	3.43	3.43	0.39272	.	0.193852	0.43919	U	0.000502	T	0.04861	0.0131	L	0.58583	1.82	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.05989	-1.0852	10	0.72032	D	0.01	.	12.8036	0.57601	0.0:1.0:0.0:0.0	.	57	Q16696	CP2AD_HUMAN	F	57	ENSP00000332679:S57F	ENSP00000332679:S57F	S	+	2	0	CYP2A13	46286386	0.001000	0.12720	0.905000	0.35620	0.779000	0.44077	1.026000	0.30103	1.928000	0.55862	0.444000	0.29173	TCC		0.612	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		T	41594546	C	T	41594546	3	4	61	1	0	0	0	0	1	0	0	0	4167	855	30	3	172	3	CYP2A13	19	41594546	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	238295	41594546	17534437	11160	19145										
CYP2F1	1572	broad.mit.edu	37	chr19	41630644	41630644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgcgtgcaggaggagatcGacctcgtggtgggacgcgcg	18	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41630644G>A	ENST00000331105.2	+	8	1057	c.985G>A	c.(985-987)Gac>Aac	p.D329N		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	329					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.D329N(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						GGAGGAGATCGACCTCGTGGT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											15	16	16					19																	41630644		2197	4294	6491	46322484	SO:0001583	missense	1572			J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"Cytochrome P450s"	2632	protein-coding gene	gene with protein product		124070	"cytochrome P450, subfamily IIF, polypeptide 1"	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.985G>A	19.37:g.41630644G>A	ENSP00000333534:p.Asp329Asn		46322484	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	g	14.42	2.530500	0.45073	.	.	ENSG00000197446	ENST00000331105	T	0.71698	-0.59	3.13	3.13	0.36017	.	0.000000	0.85682	U	0.000000	T	0.79149	0.4397	M	0.84082	2.675	0.41508	D	0.98832	D	0.63880	0.993	P	0.54460	0.753	T	0.82406	-0.0473	10	0.54805	T	0.06	.	11.8716	0.52523	0.0:0.0:1.0:0.0	.	329	P24903	CP2F1_HUMAN	N	329	ENSP00000333534:D329N	ENSP00000333534:D329N	D	+	1	0	CYP2F1	46322484	0.855000	0.29742	0.994000	0.49952	0.179000	0.23085	2.238000	0.43070	1.618000	0.50286	0.089000	0.15464	GAC		0.672	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2			A	41630644	G	A	41630644	3	1	61	1	0	0	0	0	1	0	0	0	4177	1058	37	1	1011	1	CYP2F1	19	41630644	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36098	41630644	17498339	11161	19146										
AXL	558	broad.mit.edu	37	chr19	41726583	41726583	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgtgggcaacccagggaAtatcacaggtgcccggggac	14	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41726583A>C	ENST00000301178.4	+	2	318	c.128A>C	c.(127-129)aAt>aCt	p.N43T	CTD-2195B23.3_ENST00000598541.1_RNA|AXL_ENST00000594880.1_3'UTR|AXL_ENST00000359092.3_Missense_Mutation_p.N43T	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	43	Ig-like C2-type 1.|Interaction with GAS6.				apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N43T(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						AACCCAGGGAATATCACAGGT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											30	30	30					19																	41726583		2203	4298	6501	46418423	SO:0001583	missense	558			M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.128A>C	19.37:g.41726583A>C	ENSP00000301178:p.Asn43Thr		46418423	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.514875	0.27123	.	.	ENSG00000167601	ENST00000301178;ENST00000359092	T;T	0.64618	-0.11;-0.11	4.59	4.59	0.56863	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.228496	0.35040	N	0.003496	T	0.55625	0.1932	L	0.46947	1.48	0.33180	D	0.549424	B;B	0.30455	0.096;0.28	B;B	0.34873	0.12;0.191	T	0.66732	-0.5849	10	0.44086	T	0.13	-25.3566	10.3314	0.43825	1.0:0.0:0.0:0.0	.	43;43	P30530-2;P30530	.;UFO_HUMAN	T	43	ENSP00000301178:N43T;ENSP00000351995:N43T	ENSP00000301178:N43T	N	+	2	0	AXL	46418423	0.891000	0.30450	0.837000	0.33122	0.266000	0.26442	1.964000	0.40462	1.948000	0.56530	0.317000	0.21355	AAT		0.622	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			C	41726583	A	C	41726583	3	2	61	1	0	0	0	0	1	0	0	0	1239	101	4	4	134	4	AXL	19	41726583	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	95939	41726583	17402400	11162	19147										
AXL	558	broad.mit.edu	37	chr19	41765576	41765576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgcccaggagcctgacGaaatcctctatgtcaacatg	8	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41765576G>A	ENST00000301178.4	+	20	2642	c.2452G>A	c.(2452-2454)Gaa>Aaa	p.E818K	HNRNPUL1_ENST00000352456.3_5'Flank|AXL_ENST00000593513.1_Missense_Mutation_p.E550K|AXL_ENST00000359092.3_Missense_Mutation_p.E809K|HNRNPUL1_ENST00000595018.1_5'Flank	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	818					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E809K(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GGAGCCTGACGAAATCCTCTA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											80	78	79					19																	41765576		2203	4300	6503	46457416	SO:0001583	missense	558			M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.2452G>A	19.37:g.41765576G>A	ENSP00000301178:p.Glu818Lys		46457416	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889403	0.91889	.	.	ENSG00000167601	ENST00000301178;ENST00000359092	T;T	0.74737	-0.87;-0.83	4.85	3.78	0.43462	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.74015	0.3661	N	0.11845	0.185	0.47245	D	0.999366	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.78448	-0.2200	10	0.72032	D	0.01	-2.693	13.2094	0.59815	0.0:0.0:0.8391:0.1609	.	809;818	P30530-2;P30530	.;UFO_HUMAN	K	818;809	ENSP00000301178:E818K;ENSP00000351995:E809K	ENSP00000301178:E818K	E	+	1	0	AXL	46457416	1.000000	0.71417	0.828000	0.32881	0.986000	0.74619	9.030000	0.93725	1.204000	0.43247	0.591000	0.81541	GAA		0.572	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			A	41765576	G	A	41765576	3	1	61	1	0	0	0	0	1	0	0	0	1239	1059	37	1	2530	1	AXL	19	41765576	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38993	41765576	17363407	11163	19148										
CCDC97	90324	broad.mit.edu	37	chr19	41825733	41825733	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcttggaggaagaggaaGaggaggaggacagtgacgag	19	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:41825733G>A	ENST00000269967.3	+	3	879	c.757G>A	c.(757-759)Gag>Aag	p.E253K		NM_052848.1	NP_443080.1	Q96F63	CCD97_HUMAN	coiled-coil domain containing 97	253								p.E253K(1)		biliary_tract(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)	17						ggaagaggaagaggaggagga	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											22	21	21					19																	41825733		2203	4298	6501	46517573	SO:0001583	missense	90324			BC011577	CCDS12578.1	19q13.2	2008-02-05							28289	protein-coding gene	gene with protein product						12477932	Standard	NM_052848		Approved	FLJ40267, MGC20255	uc002oqg.3	Q96F63		ENST00000269967.3:c.757G>A	19.37:g.41825733G>A	ENSP00000269967:p.Glu253Lys		46517573	Q658N6|Q96IF3	Missense_Mutation	SNP	ENST00000269967.3	37	CCDS12578.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429604	0.83776	.	.	ENSG00000142039	ENST00000269967	.	.	.	4.85	4.85	0.62838	.	0.537521	0.17081	N	0.187772	T	0.72203	0.3431	L	0.50333	1.59	0.46499	D	0.999074	D	0.59767	0.986	P	0.61800	0.894	T	0.70364	-0.4892	9	0.37606	T	0.19	-28.06	16.7313	0.85435	0.0:0.0:1.0:0.0	.	253	Q96F63	CCD97_HUMAN	K	253	.	ENSP00000269967:E253K	E	+	1	0	CCDC97	46517573	1.000000	0.71417	0.965000	0.40720	0.462000	0.32619	7.609000	0.82925	2.250000	0.74265	0.462000	0.41574	GAG		0.607	CCDC97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463293.1	NM_052848		A	41825733	G	A	41825733	3	1	61	1	0	0	0	0	1	0	0	0	2881	943	33	3	767	3	CCDC97	19	41825733	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60157	41825733	17303250	11164	19149										
CEACAM21	90273	broad.mit.edu	37	chr19	42091817	42091817	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagcgatcagagtgacttCagggagcagcagcccccagc	13	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42091817C>A	ENST00000401445.2	+	5	845	c.819C>A	c.(817-819)ttC>ttA	p.F273L	CEACAM21_ENST00000187608.9_Missense_Mutation_p.F272L|CEACAM21_ENST00000407170.2_Missense_Mutation_p.F145L|CEACAM21_ENST00000482870.2_3'UTR			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21	273						integral component of membrane (GO:0016021)		p.F273L(2)		endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						AGAGTGACTTCAGGGAGCAGC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	19											61	71	67					19																	42091817		2184	4297	6481	46783657	SO:0001583	missense	90273			AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.819C>A	19.37:g.42091817C>A	ENSP00000385739:p.Phe273Leu		46783657	B7WNQ6|O75296|Q6UY47|Q96ER7	Missense_Mutation	SNP	ENST00000401445.2	37	CCDS46086.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.030555	0.00410	.	.	ENSG00000007129	ENST00000407170;ENST00000187608;ENST00000401445	T;T;T	0.29142	2.82;1.64;1.58	1.18	-0.211	0.13172	.	.	.	.	.	T	0.04952	0.0133	N	0.00151	-1.98	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38265	-0.9669	9	0.08179	T	0.78	.	3.2286	0.06740	0.0:0.5898:0.0:0.4102	.	272;273	Q3KPI0-2;Q3KPI0	.;CEA21_HUMAN	L	145;272;273	ENSP00000384380:F145L;ENSP00000187608:F272L;ENSP00000385739:F273L	ENSP00000187608:F272L	F	+	3	2	CEACAM21	46783657	0.001000	0.12720	0.001000	0.08648	0.138000	0.21146	-0.164000	0.09983	-0.016000	0.14127	0.123000	0.15791	TTC		0.547	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543		A	42091817	C	A	42091817	3	1	61	1	0	0	0	0	1	0	0	0	3198	825	29	2	837	2	CEACAM21	19	42091817	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	266084	42091817	17037166	11165	19150										
CEACAM4	1089	broad.mit.edu	37	chr19	42132031	42132031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtaactggcatttatggttCgtagggtgtaggatcctgcg	14	7	0	0	rs147125003	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42132031C>T	ENST00000221954.2	-	2	478	c.368G>A	c.(367-369)cGa>cAa	p.R123Q	CEACAM4_ENST00000600925.1_Missense_Mutation_p.R123Q	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	123	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.R123Q(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						ATTTATGGTTCGTAGGGTGTA	0.557													C|||	7	0.00139776	0	0.0101	5008	,	,		16994	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											194	164	174					19																	42132031		2203	4300	6503	46823871	SO:0001583	missense	1089			D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"Immunoglobulin superfamily / V-set domain containing"	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.368G>A	19.37:g.42132031C>T	ENSP00000221954:p.Arg123Gln		46823871	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.836839	0.00579	.	.	ENSG00000105352	ENST00000221954	T	0.64085	-0.08	1.82	-3.64	0.04515	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19565	0.0470	N	0.01686	-0.76	0.09310	N	1	B;B	0.30179	0.241;0.271	B;B	0.18871	0.021;0.023	T	0.17379	-1.0371	9	0.02654	T	1	.	0.3907	0.00410	0.2455:0.3191:0.1797:0.2558	.	123;123	E7EMX3;O75871	.;CEAM4_HUMAN	Q	123	ENSP00000221954:R123Q	ENSP00000221954:R123Q	R	-	2	0	CEACAM4	46823871	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.584000	0.05800	-2.152000	0.00794	-0.657000	0.03884	CGA		0.557	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		T	42132031	C	T	42132031	3	4	61	1	0	0	0	0	1	0	0	0	3200	884	31	1	390	1	CEACAM4	19	42132031	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40214	42132031	16996952	11166	19151										
CEACAM7	1087	broad.mit.edu	37	chr19	42190984	42190984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttacatatcctataattCgatagttggcatgcaccctt	5	9	0	0	rs201819691		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42190984C>T	ENST00000006724.3	-	2	434	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	CEACAM7_ENST00000401731.1_Missense_Mutation_p.R78Q|CEACAM7_ENST00000338196.4_Missense_Mutation_p.R78Q|CEACAM7_ENST00000599715.1_5'UTR|CEACAM7_ENST00000602225.1_Missense_Mutation_p.R78Q	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	78	Ig-like V-type.					anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R78Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		TCCTATAATTCGATAGTTGGC	0.463													C|||	1	0.000199681	0	0	5008	,	,		18263	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											132	141	138					19																	42190984		2203	4300	6503	46882824	SO:0001583	missense	1087			X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1819	protein-coding gene	gene with protein product	"carcinoembryonic antigen gene family member 2"			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.233G>A	19.37:g.42190984C>T	ENSP00000006724:p.Arg78Gln		46882824	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Missense_Mutation	SNP	ENST00000006724.3	37	CCDS12583.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	4.178	0.031543	0.08101	.	.	ENSG00000007306	ENST00000006724;ENST00000401731;ENST00000338196	T;T;T	0.65178	-0.14;-0.14;-0.14	1.68	-2.3	0.06785	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36908	0.0984	N	0.16708	0.43	0.09310	N	1	B;B	0.26876	0.162;0.02	B;B	0.22386	0.039;0.018	T	0.16541	-1.0399	9	0.20046	T	0.44	.	5.6702	0.17717	0.0:0.4738:0.0:0.5262	.	78;78	Q14002-2;Q14002	.;CEAM7_HUMAN	Q	78	ENSP00000006724:R78Q;ENSP00000385932:R78Q;ENSP00000343286:R78Q	ENSP00000006724:R78Q	R	-	2	0	CEACAM7	46882824	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-4.080000	0.00299	-0.761000	0.04670	0.313000	0.20887	CGA		0.463	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890		T	42190984	C	T	42190984	3	4	61	1	0	0	0	0	1	0	0	0	3203	884	31	1	576	1	CEACAM7	19	42190984	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58953	42190984	16937999	11167	19152										
CEACAM5	1048	broad.mit.edu	37	chr19	42224988	42224988	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcagcaacacacacaagttCtctttatcgccaaaatcacg	5	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42224988C>A	ENST00000221992.6	+	8	2032	c.1918C>A	c.(1918-1920)Ctc>Atc	p.L640I	CEACAM5_ENST00000405816.1_Missense_Mutation_p.L640I|CEACAM5_ENST00000398599.4_Missense_Mutation_p.L639I|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	640	Ig-like 7.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.L640I(2)		breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CACACAAGTTCTCTTTATCGC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	19											216	172	187					19																	42224988		2203	4300	6503	46916828	SO:0001583	missense	1048			M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1918C>A	19.37:g.42224988C>A	ENSP00000221992:p.Leu640Ile		46916828	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.06|15.06	2.722260|2.722260	0.48728|0.48728	.|.	.|.	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181|ENST00000398599	T;T|.	0.29917|.	1.55;1.55|.	2.44|2.44	2.44|2.44	0.29823|0.29823	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.65954|0.65954	0.2741|0.2741	M|M	0.91090|0.91090	3.175|3.175	0.09310|0.09310	N|N	0.999999|0.999999	P;D|.	0.71674|.	0.953;0.998|.	P;D|.	0.83275|.	0.649;0.996|.	T|T	0.57854|0.57854	-0.7739|-0.7739	9|5	0.87932|.	D|.	0|.	.|.	8.474|8.474	0.33001|0.33001	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	640;640|.	P06731;Q53G30|.	CEAM5_HUMAN;.|.	I|Y	640;640;358|635	ENSP00000221992:L640I;ENSP00000385072:L640I|.	ENSP00000221992:L640I|.	L|S	+|+	1|2	0|0	CEACAM5|CEACAM5	46916828|46916828	0.027000|0.027000	0.19231|0.19231	0.396000|0.396000	0.26296|0.26296	0.006000|0.006000	0.05464|0.05464	0.690000|0.690000	0.25451|0.25451	1.656000|1.656000	0.50722|0.50722	0.467000|0.467000	0.42956|0.42956	CTC|TCT		0.493	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42224988	C	A	42224988	3	1	61	1	0	0	0	0	1	0	0	0	3201	913	32	2	1948	2	CEACAM5	19	42224988	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34004	42224988	16903995	11168	19153										
ATP1A3	478	broad.mit.edu	37	chr19	42471437	42471437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggatgagtttgcggatttCgtcgtagacgaagatgagga	15	5	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42471437C>T	ENST00000302102.5	-	22	3127	c.2977G>A	c.(2977-2979)Gaa>Aaa	p.E993K	ATP1A3_ENST00000545399.1_Missense_Mutation_p.E1006K|ATP1A3_ENST00000602133.1_Missense_Mutation_p.E963K|ATP1A3_ENST00000543770.1_Missense_Mutation_p.E1004K	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	993					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.E993K(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						TTGCGGATTTCGTCGTAGACG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	41	41					19																	42471437		2203	4300	6503	47163277	SO:0001583	missense	478				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.2977G>A	19.37:g.42471437C>T	ENSP00000302397:p.Glu993Lys		47163277	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	37	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909094	0.92107	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	3.32	3.32	0.38043	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99074	0.9682	H	0.99261	4.49	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.988;0.999;1.0;0.999	D	0.98304	1.0520	10	0.87932	D	0	.	12.4936	0.55914	0.0:1.0:0.0:0.0	.	1006;1004;993;993	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	K	993;993;1006;963;1004	ENSP00000302397:E993K;ENSP00000411503:E993K;ENSP00000444688:E1006K;ENSP00000437577:E1004K	ENSP00000302397:E993K	E	-	1	0	ATP1A3	47163277	1.000000	0.71417	0.945000	0.38365	0.989000	0.77384	7.533000	0.81994	1.887000	0.54652	0.462000	0.41574	GAA		0.652	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		T	42471437	C	T	42471437	3	4	61	1	0	0	0	0	1	0	0	0	1131	893	31	1	72	1	ATP1A3	19	42471437	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	246449	42471437	16657546	11169	19154										
ATP1A3	478	broad.mit.edu	37	chr19	42489532	42489532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgagtgcagtcgggagagCgagtctggggctcggattcg	19	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42489532C>T	ENST00000302102.5	-	7	800	c.650G>A	c.(649-651)cGc>cAc	p.R217H	ATP1A3_ENST00000545399.1_Missense_Mutation_p.R230H|ATP1A3_ENST00000602133.1_Missense_Mutation_p.R187H|ATP1A3_ENST00000468774.2_5'Flank|ATP1A3_ENST00000543770.1_Missense_Mutation_p.R228H	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	217					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.R217H(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						GTCGGGAGAGCGAGTCTGGGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	79	82					19																	42489532		2203	4300	6503	47181372	SO:0001583	missense	478				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.650G>A	19.37:g.42489532C>T	ENSP00000302397:p.Arg217His		47181372	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	37	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733173	0.89482	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770	D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8	4.18	4.18	0.49190	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.96806	0.8957	H	0.96604	3.85	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.998;0.997	D	0.98016	1.0368	10	0.87932	D	0	.	14.3808	0.66908	0.0:1.0:0.0:0.0	.	230;228;217;217	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	H	217;217;230;187;228	ENSP00000302397:R217H;ENSP00000411503:R217H;ENSP00000444688:R230H;ENSP00000437577:R228H	ENSP00000302397:R217H	R	-	2	0	ATP1A3	47181372	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	5.972000	0.70448	2.072000	0.62099	0.478000	0.44815	CGC		0.597	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		T	42489532	C	T	42489532	3	4	61	1	0	0	0	0	1	0	0	0	1131	768	27	1	2459	1	ATP1A3	19	42489532	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18095	42489532	16639451	11170	19155										
GRIK5	2901	broad.mit.edu	37	chr19	42546895	42546895	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagttgggccggcgcatgaCgtatgggttctcctgggtgg	18	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42546895C>T	ENST00000262895.3	-	11	1281	c.1282G>A	c.(1282-1284)Gtc>Atc	p.V428I	GRIK5_ENST00000301218.4_Missense_Mutation_p.V428I|GRIK5_ENST00000593562.1_Missense_Mutation_p.V428I	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	428					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.V428I(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				CGGCGCATGACGTATGGGTTC	0.657																																																2	Substitution - Missense(2)	large_intestine(2)	19											29	25	26					19																	42546895		2203	4300	6503	47238735	SO:0001583	missense	2901				CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1282G>A	19.37:g.42546895C>T	ENSP00000262895:p.Val428Ile		47238735	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.794922	0.70452	.	.	ENSG00000105737	ENST00000262895;ENST00000301218	T;T	0.78595	-1.19;-1.19	6.17	6.17	0.99709	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.64402	D	0.000001	T	0.72938	0.3523	L	0.45581	1.43	0.37317	D	0.909407	P	0.38370	0.628	B	0.38264	0.269	T	0.78326	-0.2247	10	0.72032	D	0.01	.	12.9056	0.58149	0.0:0.9255:0.0:0.0745	.	428	Q16478	GRIK5_HUMAN	I	428	ENSP00000262895:V428I;ENSP00000301218:V428I	ENSP00000262895:V428I	V	-	1	0	GRIK5	47238735	0.887000	0.30362	0.979000	0.43373	0.931000	0.56810	1.602000	0.36783	2.941000	0.99782	0.655000	0.94253	GTC		0.657	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			T	42546895	C	T	42546895	3	4	61	1	0	0	0	0	1	0	0	0	6798	536	19	1	1696	1	GRIK5	19	42546895	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	57363	42546895	16582088	11171	19156										
POU2F2	5452	broad.mit.edu	37	chr19	42599739	42599739	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcgaagcggacgtttgtctcGatgctggtcctcttcttgcg	13	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42599739G>T	ENST00000526816.2	-	10	927	c.912C>A	c.(910-912)atC>atA	p.I304I	POU2F2_ENST00000529952.1_Silent_p.I304I|POU2F2_ENST00000560398.1_Silent_p.I310I|POU2F2_ENST00000560558.1_Silent_p.I249I|POU2F2_ENST00000529067.1_Silent_p.I288I|POU2F2_ENST00000389341.5_Silent_p.I288I|POU2F2_ENST00000342301.4_Silent_p.I304I|POU2F2_ENST00000533720.1_Silent_p.I288I			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	304					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I288I(1)		kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	CGTTTGTCTCGATGCTGGTCC	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	19											36	37	37					19																	42599739		2203	4300	6503	47291579	SO:0001819	synonymous_variant	5452				CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.912C>A	19.37:g.42599739G>T			47291579	Q16648|Q7M4M8|Q9BRS4	Silent	SNP	ENST00000526816.2	37	CCDS56095.1																																																																																				0.662	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			T	42599739	G	T	42599739	2	4	61	1	0	0	0	0	0	0	0	1	12303	1048	37	2		2	POU2F2	19	42599739	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52844	42599739	16529244	11172	19157										
POU2F2	5452	broad.mit.edu	37	chr19	42600042	42600042	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatggtcgtctggctgaagtCgttgccgtagagcttgccca	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42600042C>A	ENST00000526816.2	-	9	718	c.703G>T	c.(703-705)Gac>Tac	p.D235Y	POU2F2_ENST00000529952.1_Missense_Mutation_p.D235Y|POU2F2_ENST00000560398.1_Missense_Mutation_p.D241Y|POU2F2_ENST00000560558.1_Missense_Mutation_p.D180Y|POU2F2_ENST00000529067.1_Missense_Mutation_p.D219Y|POU2F2_ENST00000389341.5_Missense_Mutation_p.D219Y|POU2F2_ENST00000342301.4_Missense_Mutation_p.D235Y|POU2F2_ENST00000533720.1_Missense_Mutation_p.D219Y			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	235	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D219Y(1)		kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	TGGCTGAAGTCGTTGCCGTAG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											116	116	116					19																	42600042		2203	4300	6503	47291882	SO:0001583	missense	5452				CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.703G>T	19.37:g.42600042C>A	ENSP00000431603:p.Asp235Tyr		47291882	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225581	0.79576	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	4.38	3.29	0.37713	POU-specific (3);Lambda repressor-like, DNA-binding (2);	0.104975	0.64402	N	0.000007	D	0.88658	0.6496	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.89273	0.3606	10	0.87932	D	0	.	12.4954	0.55925	0.1689:0.8311:0.0:0.0	.	219;235;219	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	Y	219;235;235;219;234;219;235	ENSP00000373992:D219Y;ENSP00000339369:D235Y;ENSP00000437221:D219Y;ENSP00000437224:D219Y;ENSP00000436988:D235Y	ENSP00000292077:D235Y	D	-	1	0	POU2F2	47291882	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.604000	0.82830	1.132000	0.42129	0.555000	0.69702	GAC		0.637	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			A	42600042	C	A	42600042	3	1	61	1	0	0	0	0	1	0	0	0	12303	884	31	2	760	2	POU2F2	19	42600042	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	303	42600042	16528941	11173	19158										
POU2F2	5452	broad.mit.edu	37	chr19	42603753	42603753	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggtagctggaatagatTtggtgtcggtagcaggcctg	16	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42603753T>G	ENST00000526816.2	-	7	442	c.427A>C	c.(427-429)Aat>Cat	p.N143H	POU2F2_ENST00000529952.1_Missense_Mutation_p.N143H|POU2F2_ENST00000560398.1_Missense_Mutation_p.N165H|POU2F2_ENST00000560558.1_Missense_Mutation_p.N104H|POU2F2_ENST00000529067.1_Missense_Mutation_p.N143H|POU2F2_ENST00000389341.5_Missense_Mutation_p.N143H|POU2F2_ENST00000342301.4_Missense_Mutation_p.N143H|POU2F2_ENST00000533720.1_Missense_Mutation_p.N143H			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	143					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N143H(1)		kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	TGGAATAGATTTGGTGTCGGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	19											50	51	51					19																	42603753		2203	4300	6503	47295593	SO:0001583	missense	5452				CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.427A>C	19.37:g.42603753T>G	ENSP00000431603:p.Asn143His		47295593	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.302884	0.81136	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85258	-1.86;-1.95;-1.96;-1.65;-1.83	4.84	4.84	0.62591	.	0.749959	0.12478	N	0.465449	D	0.91085	0.7194	M	0.69523	2.12	0.54753	D	0.999981	D;D;D	0.65815	0.992;0.989;0.995	D;P;D	0.64776	0.922;0.726;0.929	D	0.90128	0.4204	10	0.62326	D	0.03	.	13.8397	0.63430	0.0:0.0:0.0:1.0	.	143;143;143	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	H	143;143;143;143;142;143;143	ENSP00000373992:N143H;ENSP00000339369:N143H;ENSP00000437221:N143H;ENSP00000437224:N143H;ENSP00000436988:N143H	ENSP00000292077:N143H	N	-	1	0	POU2F2	47295593	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.715000	0.68430	2.168000	0.68352	0.533000	0.62120	AAT		0.597	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			G	42603753	T	G	42603753	3	3	61	1	0	0	0	0	1	0	0	0	12303	1841	64	4	996	4	POU2F2	19	42603753	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3711	42603753	16525230	11174	19159										
DEDD2	162989	broad.mit.edu	37	chr19	42703605	42703605	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggatcaggaggcctctgtCgggcgccgccccccttcctc	12	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42703605C>T	ENST00000595337.1	-	5	1053	c.966G>A	c.(964-966)ccG>ccA	p.P322P	DEDD2_ENST00000593804.1_5'UTR|DEDD2_ENST00000336034.4_Silent_p.P317P|DEDD2_ENST00000596251.1_Silent_p.P322P	NM_001270614.1	NP_001257543.1	Q8WXF8	DEDD2_HUMAN	death effector domain containing 2	322					apoptotic nuclear changes (GO:0030262)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|RNA processing (GO:0006396)|rRNA catabolic process (GO:0016075)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|receptor signaling complex scaffold activity (GO:0030159)	p.P322P(1)		endometrium(1)|large_intestine(1)|ovary(1)|prostate(2)	5		Prostate(69;0.0704)				AGGCCTCTGTCGGGCGCCGCC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	19											12	13	12					19																	42703605		2194	4273	6467	47395445	SO:0001819	synonymous_variant	162989			AY125488	CCDS12597.1, CCDS59391.1	19q13.31	2008-02-05				ENSG00000160570			24450	protein-coding gene	gene with protein product						11965497, 12235123	Standard	NM_133328		Approved	FLAME-3	uc031rkv.1	Q8WXF8		ENST00000595337.1:c.966G>A	19.37:g.42703605C>T			47395445	Q8NBR2|Q8NES1|Q8TAA8|Q96D35	Silent	SNP	ENST00000595337.1	37	CCDS12597.1																																																																																				0.652	DEDD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463508.1	NM_133328		T	42703605	C	T	42703605	2	4	61	1	0	0	0	0	0	0	0	1	4391	871	31	1		1	DEDD2	19	42703605	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	99852	42703605	16425378	11175	19160										
ERF	2077	broad.mit.edu	37	chr19	42754575	42754575	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcagggtctttgatgacGaattccccgtagtccccctg	9	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42754575G>A	ENST00000222329.4	-	2	322	c.165C>T	c.(163-165)ttC>ttT	p.F55F	ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000440177.2_5'UTR	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	55					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)	p.F55F(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				CTTTGATGACGAATTCCCCGT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											59	55	57					19																	42754575		2203	4300	6503	47446415	SO:0001819	synonymous_variant	2077			U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.165C>T	19.37:g.42754575G>A			47446415	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Silent	SNP	ENST00000222329.4	37	CCDS12600.1																																																																																				0.612	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		A	42754575	G	A	42754575	2	1	61	1	0	0	0	0	0	0	0	1	5234	1049	37	1		1	ERF	19	42754575	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50970	42754575	16374408	11176	19161										
MEGF8	1954	broad.mit.edu	37	chr19	42854336	42854336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctggagccctaccgctcgTcgtcctgcacctcctattct	7	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42854336T>C	ENST00000251268.6	+	15	2536	c.2536T>C	c.(2536-2538)Tcg>Ccg	p.S846P	MEGF8_ENST00000334370.4_Missense_Mutation_p.S779P	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	846					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.S387P(1)|p.S846P(1)|p.S779P(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CTACCGCTCGTCGTCCTGCAC	0.647																																																3	Substitution - Missense(3)	large_intestine(3)	19											96	85	89					19																	42854336		2203	4300	6503	47546176	SO:0001583	missense	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2536T>C	19.37:g.42854336T>C	ENSP00000251268:p.Ser846Pro		47546176	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	T	8.045	0.764670	0.15914	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.21932	1.98;1.98	4.74	-1.87	0.07737	.	0.862860	0.10081	N	0.718438	T	0.11707	0.0285	N	0.08118	0	0.09310	N	1	B;B	0.27068	0.167;0.018	B;B	0.32465	0.046;0.146	T	0.38265	-0.9669	10	0.41790	T	0.15	0.0027	10.9015	0.47054	0.1158:0.0:0.6716:0.2125	.	846;779	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	P	779;846	ENSP00000334219:S779P;ENSP00000251268:S846P	ENSP00000251268:S846P	S	+	1	0	MEGF8	47546176	0.506000	0.26139	0.000000	0.03702	0.075000	0.17131	2.708000	0.47152	-0.360000	0.08138	-0.488000	0.04728	TCG		0.647	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		C	42854336	T	C	42854336	3	2	61	1	0	0	0	0	1	0	0	0	9493	1667	58	4	2389	4	MEGF8	19	42854336	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	99761	42854336	16274647	11177	19162										
MEGF8	1954	broad.mit.edu	37	chr19	42854509	42854509	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgcccactctgcgaggaGcatcgggactgccacgcctg	12	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42854509G>T	ENST00000251268.6	+	15	2709	c.2709G>T	c.(2707-2709)gaG>gaT	p.E903D	MEGF8_ENST00000334370.4_Missense_Mutation_p.E836D	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	903	PSI 3.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.E444D(1)|p.E836D(1)|p.E903D(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TCTGCGAGGAGCATCGGGACT	0.692																																																3	Substitution - Missense(3)	large_intestine(3)	19											14	15	15					19																	42854509		2200	4293	6493	47546349	SO:0001583	missense	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2709G>T	19.37:g.42854509G>T	ENSP00000251268:p.Glu903Asp		47546349	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	G	11.94	1.787320	0.31593	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20881	2.04;2.04	4.93	3.89	0.44902	.	0.000000	0.64402	D	0.000001	T	0.22859	0.0552	L	0.28274	0.84	0.80722	D	1	B;D	0.64830	0.236;0.994	B;P	0.60541	0.056;0.876	T	0.07121	-1.0789	10	0.13853	T	0.58	-23.7079	7.7426	0.28849	0.1908:0.0:0.8092:0.0	.	903;836	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	D	836;903	ENSP00000334219:E836D;ENSP00000251268:E903D	ENSP00000251268:E903D	E	+	3	2	MEGF8	47546349	0.997000	0.39634	1.000000	0.80357	0.871000	0.50021	0.290000	0.18975	1.076000	0.40961	0.561000	0.74099	GAG		0.692	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42854509	G	T	42854509	3	4	61	1	0	0	0	0	1	0	0	0	9493	962	34	2	2562	2	MEGF8	19	42854509	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	173	42854509	16274474	11178	19163										
MEGF8	1954	broad.mit.edu	37	chr19	42866667	42866667	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgggcagggaactgctcCgaggctgcgtgcggggctgc	18	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:42866667C>T	ENST00000251268.6	+	34	5976	c.5976C>T	c.(5974-5976)tcC>tcT	p.S1992S	MEGF8_ENST00000334370.4_Silent_p.S1925S	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1992					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.S1992S(1)|p.S1925S(1)|p.S1533S(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GGAACTGCTCCGAGGCTGCGT	0.622																																																3	Substitution - coding silent(3)	large_intestine(3)	19											99	89	92					19																	42866667		2203	4300	6503	47558507	SO:0001819	synonymous_variant	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.5976C>T	19.37:g.42866667C>T			47558507	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																					0.622	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42866667	C	T	42866667	2	4	61	1	0	0	0	0	0	0	0	1	9493	639	23	1		1	MEGF8	19	42866667	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12158	42866667	16262316	11179	19164										
PSG8	440533	broad.mit.edu	37	chr19	43259228	43259228	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcctgtttcatttctcgtGacactgggtagaatgaggat	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:43259228G>T	ENST00000306511.4	-	4	997	c.900C>A	c.(898-900)gtC>gtA	p.V300V	PSG8_ENST00000406636.3_Silent_p.V178V|PSG8_ENST00000401467.2_Silent_p.V207V|PSG8_ENST00000600709.1_Intron|PSG8_ENST00000404209.4_Silent_p.V300V	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	300	Ig-like C2-type 2.					extracellular region (GO:0005576)		p.V300V(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				CATTTCTCGTGACACTGGGTA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	19											124	126	126					19																	43259228		2203	4297	6500	47951068	SO:0001819	synonymous_variant	440533			M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.900C>A	19.37:g.43259228G>T			47951068	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																				0.478	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			T	43259228	G	T	43259228	2	4	61	1	0	0	0	0	0	0	0	1	12695	1277	45	2		2	PSG8	19	43259228	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	392561	43259228	15869755	11180	19165										
PSG1	5669	broad.mit.edu	37	chr19	43372314	43372314	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggctgagttacgaacagaGcaaacatagagcccgctatg	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:43372314G>A	ENST00000436291.2	-	5	1298	c.1182C>T	c.(1180-1182)tgC>tgT	p.C394C	PSG1_ENST00000244296.2_Silent_p.C394C|PSG1_ENST00000595356.1_Silent_p.C394C|PSG1_ENST00000312439.6_Silent_p.C394C|PSG1_ENST00000595124.1_Silent_p.C301C|PSG1_ENST00000403380.3_Silent_p.C301C	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	394	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.C394C(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TACGAACAGAGCAAACATAGA	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	19											200	203	202					19																	43372314		2202	4298	6500	48064154	SO:0001819	synonymous_variant	5669				CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.1182C>T	19.37:g.43372314G>A			48064154	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																				0.453	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			A	43372314	G	A	43372314	2	1	61	1	0	0	0	0	0	0	0	1	12687	963	34	3		3	PSG1	19	43372314	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113086	43372314	15756669	11181	19166										
PSG11	5680	broad.mit.edu	37	chr19	43519305	43519305	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggatgtggagctttcctcGccagtggctgagttacgagc	14	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:43519305G>A	ENST00000401740.1	-	4	1030	c.927C>T	c.(925-927)ggC>ggT	p.G309G	PSG11_ENST00000403486.1_Silent_p.G187G|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_Silent_p.G187G|PSG11_ENST00000320078.7_Silent_p.G309G			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	318	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G309G(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				AGCTTTCCTCGCCAGTGGCTG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	19											143	136	139					19																	43519305		2199	4296	6495	48211145	SO:0001819	synonymous_variant	5680			U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.927C>T	19.37:g.43519305G>A			48211145	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000401740.1	37	CCDS12614.2																																																																																				0.463	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		A	43519305	G	A	43519305	2	1	61	1	0	0	0	0	0	0	0	1	12688	1074	38	1		1	PSG11	19	43519305	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	146991	43519305	15609678	11182	19167										
PSG9	5678	broad.mit.edu	37	chr19	43772123	43772123	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttaccatcaactatataCgatataatgtaatggtagag	6	5	1	1	rs376642216		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:43772123C>T	ENST00000270077.3	-	2	339	c.243G>A	c.(241-243)tcG>tcA	p.S81S	PSG9_ENST00000291752.5_Silent_p.S81S|PSG9_ENST00000443718.3_Silent_p.S81S|PSG9_ENST00000593948.1_Silent_p.S81S|PSG9_ENST00000596730.1_Silent_p.S81S|PSG9_ENST00000418820.2_Silent_p.S81S|PSG9_ENST00000244293.7_Silent_p.S81S	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	81	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.S81S(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				CAACTATATACGATATAATGT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	19						T		0,4406		0,0,2203	176	178	178		243	-0.9	0	19		178	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	PSG9	NM_002784.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		81/427	43772123	4,13002	2203	4300	6503	48463963	SO:0001819	synonymous_variant	5678			M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.243G>A	19.37:g.43772123C>T			48463963	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000270077.3	37	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	t	0.903	-0.721690	0.03182	0.0	4.65E-4	ENSG00000183668	ENST00000418820	.	.	.	1.56	-0.884	0.10597	.	.	.	.	.	T	0.21468	0.0517	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19745	-1.0296	4	.	.	.	.	2.7007	0.05148	0.2008:0.2645:0.0:0.5347	.	.	.	.	H	68	.	.	R	-	2	0	PSG9	48463963	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.734000	0.04893	-2.083000	0.00867	-4.055000	0.00012	CGT		0.423	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		T	43772123	C	T	43772123	2	4	61	1	0	0	0	0	0	0	0	1	12696	523	19	1		1	PSG9	19	43772123	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252818	43772123	15356860	11183	19168										
PLAUR	5329	broad.mit.edu	37	chr19	44153066	44153066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccagaggagagtgcctccCcacagtctggcagtcattag	12	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44153066C>A	ENST00000340093.3	-	7	1213	c.984G>T	c.(982-984)tgG>tgT	p.W328C	PLAUR_ENST00000601723.1_Missense_Mutation_p.W279C|PLAUR_ENST00000221264.4_Missense_Mutation_p.W283C|PLAUR_ENST00000339082.3_Intron	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	328					attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)	p.W328C(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GAGTGCCTCCCCACAGTCTGG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											84	75	78					19																	44153066		2203	4300	6503	48844906	SO:0001583	missense	5329				CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"CD molecules"	9053	protein-coding gene	gene with protein product	"urokinase-type plasminogen activator (uPA) receptor", "urokinase plasminogen activator surface receptor"	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.984G>T	19.37:g.44153066C>A	ENSP00000339328:p.Trp328Cys		48844906	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357724	0.41801	.	.	ENSG00000011422	ENST00000340093;ENST00000221264	T;T	0.12039	2.73;2.72	3.84	2.8	0.32819	.	0.390578	0.19114	N	0.122347	T	0.27419	0.0673	M	0.62723	1.935	0.52501	D	0.999951	D;D	0.76494	0.999;0.998	D;P	0.64237	0.923;0.84	T	0.02009	-1.1230	10	0.87932	D	0	-14.1511	7.355	0.26714	0.0:0.88:0.0:0.12	.	283;328	Q03405-3;Q03405	.;UPAR_HUMAN	C	328;283	ENSP00000339328:W328C;ENSP00000221264:W283C	ENSP00000221264:W283C	W	-	3	0	PLAUR	48844906	1.000000	0.71417	0.953000	0.39169	0.744000	0.42396	2.913000	0.48790	1.199000	0.43173	0.313000	0.20887	TGG		0.632	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659		A	44153066	C	A	44153066	3	1	61	1	0	0	0	0	1	0	0	0	12054	624	22	2	123	2	PLAUR	19	44153066	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	380943	44153066	14975917	11184	19169										
ZNF283	284349	broad.mit.edu	37	chr19	44352357	44352357	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccttgttcaacatgaaaGaatccatacaggggagaaac	9	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44352357G>T	ENST00000324461.7	+	7	1901	c.1604G>T	c.(1603-1605)aGa>aTa	p.R535I	ZNF283_ENST00000588797.1_Missense_Mutation_p.R396I	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	535					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R535I(1)|p.R535K(1)		endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				CAACATGAAAGAATCCATACA	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	19											72	81	78					19																	44352357		2202	4296	6498	49044197	SO:0001583	missense	284349			AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"Zinc fingers, C2H2-type", "-"	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1604G>T	19.37:g.44352357G>T	ENSP00000327314:p.Arg535Ile		49044197	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.746595	0.49257	.	.	ENSG00000167637	ENST00000324461	T	0.24908	1.83	2.48	2.48	0.30137	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46288	0.1385	M	0.73430	2.235	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.46076	-0.9217	9	0.62326	D	0.03	.	9.1756	0.37109	0.0:0.226:0.774:0.0	.	535	Q8N7M2	ZN283_HUMAN	I	535	ENSP00000327314:R535I	ENSP00000327314:R535I	R	+	2	0	ZNF283	49044197	0.000000	0.05858	0.858000	0.33744	0.751000	0.42716	0.269000	0.18589	1.366000	0.46076	0.462000	0.41574	AGA		0.413	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845		T	44352357	G	T	44352357	3	4	61	1	0	0	0	0	1	0	0	0	17859	942	33	2	1618	2	ZNF283	19	44352357	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	199291	44352357	14776626	11185	19170										
ZNF283	284349	broad.mit.edu	37	chr19	44352544	44352544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagtccatactaatgagaaGtcttatgaatgtaaagactg	9	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44352544G>T	ENST00000324461.7	+	7	2088	c.1791G>T	c.(1789-1791)aaG>aaT	p.K597N	ZNF283_ENST00000588797.1_Missense_Mutation_p.K458N	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	597					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K597N(1)		endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				CTAATGAGAAGTCTTATGAAT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	100	97					19																	44352544		2164	4279	6443	49044384	SO:0001583	missense	284349			AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"Zinc fingers, C2H2-type", "-"	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1791G>T	19.37:g.44352544G>T	ENSP00000327314:p.Lys597Asn		49044384	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	.	.	.	.	.	.	.	.	.	.	G	4.372	0.068646	0.08436	.	.	ENSG00000167637	ENST00000324461	T	0.26067	1.76	2.2	-2.62	0.06152	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46014	0.1371	M	0.84585	2.705	0.58432	D	0.999992	P	0.46578	0.88	P	0.61477	0.889	T	0.48768	-0.9006	9	0.72032	D	0.01	.	8.4739	0.33001	0.5119:0.0:0.4881:0.0	.	597	Q8N7M2	ZN283_HUMAN	N	597	ENSP00000327314:K597N	ENSP00000327314:K597N	K	+	3	2	ZNF283	49044384	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-1.047000	0.03521	-0.858000	0.04110	-0.471000	0.05019	AAG		0.418	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845		T	44352544	G	T	44352544	3	4	61	1	0	0	0	0	1	0	0	0	17859	1020	36	2	1805	2	ZNF283	19	44352544	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187	44352544	14776439	11186	19171										
ZNF404	342908	broad.mit.edu	37	chr19	44377174	44377174	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattatctgatgttgaataaGatatgaatgaagcttaaaag	8	2	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44377174G>T	ENST00000587539.1	-	3	1191	c.1192C>A	c.(1192-1194)Ctt>Att	p.L398I	ZNF404_ENST00000324394.6_Missense_Mutation_p.L396I	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	398					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L396I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				TGTTGAATAAGATATGAATGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											33	35	35					19																	44377174		2189	4295	6484	49069014	SO:0001583	missense	342908			XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.1192C>A	19.37:g.44377174G>T	ENSP00000466051:p.Leu398Ile		49069014	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	.	.	.	.	.	.	.	.	.	.	G	9.790	1.177684	0.21787	.	.	ENSG00000176222	ENST00000324394	T	0.14640	2.49	2.17	2.17	0.27698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41396	0.1157	M	0.90198	3.095	0.09310	N	1	D	0.76494	0.999	D	0.85130	0.997	T	0.11203	-1.0597	9	0.72032	D	0.01	.	9.4773	0.38880	0.0:0.0:1.0:0.0	.	398	Q494X3	ZN404_HUMAN	I	396	ENSP00000319479:L396I	ENSP00000319479:L396I	L	-	1	0	ZNF404	49069014	0.995000	0.38212	0.877000	0.34402	0.344000	0.29017	2.823000	0.48081	1.193000	0.43086	0.404000	0.27445	CTT		0.378	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		T	44377174	G	T	44377174	3	4	61	1	0	0	0	0	1	0	0	0	17925	942	33	2	470	2	ZNF404	19	44377174	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24630	44377174	14751809	11187	19172										
ZNF404	342908	broad.mit.edu	37	chr19	44377349	44377349	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgtttaagaaggcttgaGcccttaccaaaagcctttcc	7	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44377349G>A	ENST00000587539.1	-	3	1016	c.1017C>T	c.(1015-1017)ggC>ggT	p.G339G	ZNF404_ENST00000324394.6_Silent_p.G337G	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G337G(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				GAAGGCTTGAGCCCTTACCAA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	19											63	69	67					19																	44377349		2095	4263	6358	49069189	SO:0001819	synonymous_variant	342908			XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.1017C>T	19.37:g.44377349G>A			49069189	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																				0.408	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		A	44377349	G	A	44377349	2	1	61	1	0	0	0	0	0	0	0	1	17925	958	34	3		3	ZNF404	19	44377349	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	175	44377349	14751634	11188	19173										
ZNF221	7638	broad.mit.edu	37	chr19	44469104	44469104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatgttggatattttaggaGgcagtgacattcaaggatgt	13	3	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44469104G>T	ENST00000251269.5	+	4	412	c.84G>T	c.(82-84)gaG>gaT	p.E28D	ZNF221_ENST00000587682.1_Missense_Mutation_p.E28D|ZNF221_ENST00000592350.1_Missense_Mutation_p.E28D	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E28D(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TATTTTAGGAGGCAGTGACAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											311	312	312					19																	44469104		2203	4300	6503	49160944	SO:0001583	missense	7638			AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.84G>T	19.37:g.44469104G>T	ENSP00000251269:p.Glu28Asp		49160944	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.422969	0.43020	.	.	ENSG00000159905	ENST00000539505;ENST00000251269	T	0.00824	5.65	2.64	-1.01	0.10169	Krueppel-associated box (1);	.	.	.	.	T	0.01765	0.0056	L	0.28740	0.885	0.09310	N	1	D	0.76494	0.999	D	0.66196	0.942	T	0.52109	-0.8619	9	0.33141	T	0.24	.	5.9363	0.19167	0.4019:0.0:0.5981:0.0	.	28	Q9UK13	ZN221_HUMAN	D	6;28	ENSP00000251269:E28D	ENSP00000251269:E28D	E	+	3	2	ZNF221	49160944	0.030000	0.19436	0.005000	0.12908	0.184000	0.23303	0.225000	0.17757	-0.267000	0.09325	0.462000	0.41574	GAG		0.478	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			T	44469104	G	T	44469104	3	4	61	1	0	0	0	0	1	0	0	0	17814	991	35	2	90	2	ZNF221	19	44469104	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91755	44469104	14659879	11189	19174										
ZNF221	7638	broad.mit.edu	37	chr19	44470048	44470048	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgggaacaaattgcaagtGacctaaccaggtctcaaaac	8	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44470048G>T	ENST00000251269.5	+	6	722	c.394G>T	c.(394-396)Gac>Tac	p.D132Y	ZNF221_ENST00000587682.1_Missense_Mutation_p.D132Y|ZNF221_ENST00000592350.1_Missense_Mutation_p.D132Y	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	132					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D132Y(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				AATTGCAAGTGACCTAACCAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											96	87	90					19																	44470048		2203	4300	6503	49161888	SO:0001583	missense	7638			AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.394G>T	19.37:g.44470048G>T	ENSP00000251269:p.Asp132Tyr		49161888	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	10.36	1.327705	0.24080	.	.	ENSG00000159905	ENST00000251269	T	0.06142	3.34	2.54	0.268	0.15626	.	.	.	.	.	T	0.09379	0.0231	L	0.38175	1.15	0.09310	N	1	D	0.76494	0.999	D	0.68353	0.957	T	0.09443	-1.0674	9	0.05436	T	0.98	.	5.6328	0.17520	0.2912:0.0:0.7088:0.0	.	132	Q9UK13	ZN221_HUMAN	Y	132	ENSP00000251269:D132Y	ENSP00000251269:D132Y	D	+	1	0	ZNF221	49161888	0.001000	0.12720	0.000000	0.03702	0.160000	0.22226	0.924000	0.28777	-0.001000	0.14495	-0.379000	0.06801	GAC		0.448	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			T	44470048	G	T	44470048	3	4	61	1	0	0	0	0	1	0	0	0	17814	1290	45	2	408	2	ZNF221	19	44470048	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	944	44470048	14658935	11190	19175										
ZNF221	7638	broad.mit.edu	37	chr19	44470321	44470321	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagagagtccatatgggaGaaaaatgctataagtgtgat	11	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44470321G>T	ENST00000251269.5	+	6	995	c.667G>T	c.(667-669)Gaa>Taa	p.E223*	ZNF221_ENST00000587682.1_Nonsense_Mutation_p.E223*|ZNF221_ENST00000592350.1_Nonsense_Mutation_p.E223*	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E223*(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				CCATATGGGAGAAAAATGCTA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											132	138	136					19																	44470321		2203	4300	6503	49162161	SO:0001587	stop_gained	7638			AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.667G>T	19.37:g.44470321G>T	ENSP00000251269:p.Glu223*		49162161	B2RAI6|Q2M2H2|Q9P1U8	Nonsense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	31	5.075493	0.94000	.	.	ENSG00000159905	ENST00000251269	.	.	.	2.65	-1.47	0.08772	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	7.7502	0.28892	0.3271:0.0:0.6729:0.0	.	.	.	.	X	223	.	ENSP00000251269:E223X	E	+	1	0	ZNF221	49162161	0.075000	0.21258	0.000000	0.03702	0.128000	0.20619	0.563000	0.23547	-0.327000	0.08551	0.462000	0.41574	GAA		0.413	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			T	44470321	G	T	44470321	4	4	61	1	0	0	0	0	0	1	0	0	17814	943	33	2	681	2	ZNF221	19	44470321	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273	44470321	14658662	11191	19176										
ZNF221	7638	broad.mit.edu	37	chr19	44470518	44470518	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tataattgtgaggaatgtggGaaagccttcattcatgattc	10	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44470518G>A	ENST00000251269.5	+	6	1192	c.864G>A	c.(862-864)ggG>ggA	p.G288G	ZNF221_ENST00000587682.1_Silent_p.G288G|ZNF221_ENST00000592350.1_Silent_p.G288G	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	288					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G288G(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				AGGAATGTGGGAAAGCCTTCA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	19											128	129	129					19																	44470518		2203	4300	6503	49162358	SO:0001819	synonymous_variant	7638			AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.864G>A	19.37:g.44470518G>A			49162358	B2RAI6|Q2M2H2|Q9P1U8	Silent	SNP	ENST00000251269.5	37	CCDS12633.1																																																																																				0.408	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			A	44470518	G	A	44470518	2	1	61	1	0	0	0	0	0	0	0	1	17814	1161	41	3		3	ZNF221	19	44470518	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	197	44470518	14658465	11192	19177										
ZNF222	7673	broad.mit.edu	37	chr19	44536220	44536220	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcagtgatgtttccttCtttgatcttcctcagcagtt	6	10	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44536220C>T	ENST00000187879.8	+	4	555	c.393C>T	c.(391-393)ttC>ttT	p.F131F	ZNF222_ENST00000391960.3_Silent_p.F171F|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F131F(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				ATGTTTCCTTCTTTGATCTTC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	19											132	134	133					19																	44536220		2203	4300	6503	49228060	SO:0001819	synonymous_variant	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.393C>T	19.37:g.44536220C>T			49228060	G5E9B9|Q8N6G7|Q9P1U5	Silent	SNP	ENST00000187879.8	37	CCDS33045.1																																																																																				0.398	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			T	44536220	C	T	44536220	2	4	61	1	0	0	0	0	0	0	0	1	17815	912	32	3		3	ZNF222	19	44536220	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65702	44536220	14592763	11193	19178										
ZNF222	7673	broad.mit.edu	37	chr19	44536702	44536702	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaatctgaaaagtatggaaGaggtttcattgataggctag	11	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44536702G>A	ENST00000187879.8	+	4	1037	c.875G>A	c.(874-876)aGa>aAa	p.R292K	ZNF222_ENST00000391960.3_Missense_Mutation_p.R332K|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R292K(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				AAGTATGGAAGAGGTTTCATT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											131	133	132					19																	44536702		2203	4300	6503	49228542	SO:0001583	missense	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.875G>A	19.37:g.44536702G>A	ENSP00000187879:p.Arg292Lys		49228542	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	37	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.513184	0.00975	.	.	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	T;T	0.34275	3.73;1.37	2.72	0.438	0.16560	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12347	0.0300	N	0.04994	-0.135	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.32025	-0.9922	9	0.02654	T	1	.	3.6429	0.08173	0.558:0.1965:0.2455:0.0	.	332;292	G5E9B9;Q9UK12	.;ZN222_HUMAN	K	332;292;238	ENSP00000375822:R332K;ENSP00000187879:R292K	ENSP00000187879:R292K	R	+	2	0	ZNF222	49228542	0.974000	0.33945	0.003000	0.11579	0.035000	0.12851	2.527000	0.45615	-0.106000	0.12110	0.205000	0.17691	AGA		0.383	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			A	44536702	G	A	44536702	3	1	61	1	0	0	0	0	1	0	0	0	17815	942	33	3	1028	3	ZNF222	19	44536702	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	482	44536702	14592281	11194	19179										
ZNF222	7673	broad.mit.edu	37	chr19	44536776	44536776	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaaccatataattgtaaaGaatgtgggaagagcttcaaa	9	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44536776G>T	ENST00000187879.8	+	4	1111	c.949G>T	c.(949-951)Gaa>Taa	p.E317*	ZNF222_ENST00000391960.3_Nonsense_Mutation_p.E357*|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E317*(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				TAATTGTAAAGAATGTGGGAA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											113	113	113					19																	44536776		2203	4300	6503	49228616	SO:0001587	stop_gained	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.949G>T	19.37:g.44536776G>T	ENSP00000187879:p.Glu317*		49228616	G5E9B9|Q8N6G7|Q9P1U5	Nonsense_Mutation	SNP	ENST00000187879.8	37	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	G	33	5.269292	0.95429	.	.	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	.	.	.	2.99	2.99	0.34606	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	13.1631	0.59554	0.0:0.0:1.0:0.0	.	.	.	.	X	357;317;263	.	ENSP00000187879:E317X	E	+	1	0	ZNF222	49228616	0.000000	0.05858	0.012000	0.15200	0.835000	0.47333	0.009000	0.13219	1.643000	0.50594	0.205000	0.17691	GAA		0.398	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			T	44536776	G	T	44536776	4	4	61	1	0	0	0	0	0	1	0	0	17815	943	33	2	1102	2	ZNF222	19	44536776	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74	44536776	14592207	11195	19180										
ZNF223	7766	broad.mit.edu	37	chr19	44570386	44570386	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgcccactcccaggttgaGgaaggactatctataatgca	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44570386G>A	ENST00000434772.3	+	5	660	c.405G>A	c.(403-405)gaG>gaA	p.E135E	ZNF223_ENST00000591793.1_Silent_p.E245E	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E135E(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				CCCAGGTTGAGGAAGGACTAT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	19											105	87	93					19																	44570386		2203	4300	6503	49262226	SO:0001819	synonymous_variant	7766			AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.405G>A	19.37:g.44570386G>A			49262226	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	37	CCDS12635.1																																																																																				0.433	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			A	44570386	G	A	44570386	2	1	61	1	0	0	0	0	0	0	0	1	17816	991	35	3		3	ZNF223	19	44570386	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33610	44570386	14558597	11196	19181										
ZNF284	342909	broad.mit.edu	37	chr19	44590315	44590315	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagaatccacactggagaGaaaccattcaaatgtgagca	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44590315G>T	ENST00000421176.3	+	5	900	c.684G>T	c.(682-684)gaG>gaT	p.E228D	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E228D(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				ACACTGGAGAGAAACCATTCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	77	74					19																	44590315		2199	4298	6497	49282155	SO:0001583	missense	342909			AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.684G>T	19.37:g.44590315G>T	ENSP00000411032:p.Glu228Asp		49282155	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	37	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559607	0.65538	.	.	ENSG00000186026	ENST00000421176	T	0.26810	1.71	2.59	1.52	0.23074	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39989	0.1099	L	0.54908	1.71	0.20638	N	0.999879	D	0.57257	0.979	D	0.63597	0.916	T	0.13872	-1.0493	9	0.72032	D	0.01	.	8.6192	0.33851	0.1258:0.0:0.8742:0.0	.	228	Q2VY69	ZN284_HUMAN	D	228	ENSP00000411032:E228D	ENSP00000411032:E228D	E	+	3	2	ZNF284	49282155	0.897000	0.30589	0.052000	0.19188	0.526000	0.34562	0.405000	0.21015	0.403000	0.25479	-0.448000	0.05591	GAG		0.403	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		T	44590315	G	T	44590315	3	4	61	1	0	0	0	0	1	0	0	0	17860	933	33	2	698	2	ZNF284	19	44590315	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19929	44590315	14538668	11197	19182										
ZNF284	342909	broad.mit.edu	37	chr19	44591113	44591113	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgggaagaggtttactgaGaattcaaaacttcgtttcca	10	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44591113G>T	ENST00000421176.3	+	5	1698	c.1482G>T	c.(1480-1482)gaG>gaT	p.E494D	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E494D(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GGTTTACTGAGAATTCAAAAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											49	52	51					19																	44591113		2143	4277	6420	49282953	SO:0001583	missense	342909			AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1482G>T	19.37:g.44591113G>T	ENSP00000411032:p.Glu494Asp		49282953	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	37	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	14.45	2.540453	0.45176	.	.	ENSG00000186026	ENST00000421176	T	0.14766	2.48	2.37	-0.272	0.12919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05318	0.0141	N	0.01493	-0.835	0.09310	N	1	B	0.33345	0.409	B	0.38755	0.281	T	0.40608	-0.9554	9	0.40728	T	0.16	.	6.3152	0.21186	0.0:0.3818:0.4237:0.1945	.	494	Q2VY69	ZN284_HUMAN	D	494	ENSP00000411032:E494D	ENSP00000411032:E494D	E	+	3	2	ZNF284	49282953	0.000000	0.05858	0.000000	0.03702	0.970000	0.65996	-1.789000	0.01761	-0.105000	0.12132	0.462000	0.41574	GAG		0.418	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		T	44591113	G	T	44591113	3	4	61	1	0	0	0	0	1	0	0	0	17860	933	33	2	1496	2	ZNF284	19	44591113	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	798	44591113	14537870	11198	19183										
ZNF224	7767	broad.mit.edu	37	chr19	44610659	44610659	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatttaaccaggtctcaaGacttgatgataaatagctct	8	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44610659G>T	ENST00000336976.6	+	6	600	c.346G>T	c.(346-348)Gac>Tac	p.D116Y	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	116					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D116Y(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				CAGGTCTCAAGACTTGATGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											80	79	79					19																	44610659		2203	4300	6503	49302499	SO:0001583	missense	7767			AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.346G>T	19.37:g.44610659G>T	ENSP00000337368:p.Asp116Tyr		49302499	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	.	.	.	.	.	.	.	.	.	.	g	13.54	2.269135	0.40095	.	.	ENSG00000186019	ENST00000336976	T	0.06528	3.29	2.88	0.603	0.17541	.	.	.	.	.	T	0.10121	0.0248	L	0.52905	1.665	0.09310	N	1	P	0.44659	0.84	P	0.47891	0.56	T	0.19063	-1.0317	9	0.72032	D	0.01	.	6.9297	0.24434	0.2455:0.0:0.7545:0.0	.	116	Q9NZL3	ZN224_HUMAN	Y	116	ENSP00000337368:D116Y	ENSP00000337368:D116Y	D	+	1	0	ZNF224	49302499	0.003000	0.15002	0.002000	0.10522	0.091000	0.18340	0.823000	0.27366	0.248000	0.21435	0.591000	0.81541	GAC		0.433	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		T	44610659	G	T	44610659	3	4	61	1	0	0	0	0	1	0	0	0	17817	942	33	2	360	2	ZNF224	19	44610659	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19546	44610659	14518324	11199	19184										
ZNF225	7768	broad.mit.edu	37	chr19	44635438	44635438	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatctgcaaattcatcagaGaatccacactggagagaaac	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44635438G>T	ENST00000262894.6	+	5	951	c.671G>T	c.(670-672)aGa>aTa	p.R224I	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Missense_Mutation_p.R224I	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R224I(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				ATTCATCAGAGAATCCACACT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											78	85	83					19																	44635438		2202	4300	6502	49327278	SO:0001583	missense	7768			AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.671G>T	19.37:g.44635438G>T	ENSP00000262894:p.Arg224Ile		49327278	A8K8S2|Q53F12|Q9NS46|Q9UID8	Missense_Mutation	SNP	ENST00000262894.6	37	CCDS46100.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800613	0.70567	.	.	ENSG00000256294	ENST00000262894;ENST00000544184	T	0.24908	1.83	2.97	-5.95	0.02241	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31482	0.0798	L	0.49350	1.555	0.09310	N	1	D	0.61080	0.989	D	0.66497	0.944	T	0.18116	-1.0347	9	0.52906	T	0.07	.	2.2958	0.04150	0.3514:0.1171:0.4138:0.1178	.	224	Q9UK10	ZN225_HUMAN	I	224;188	ENSP00000262894:R224I	ENSP00000262894:R224I	R	+	2	0	ZNF225	49327278	0.000000	0.05858	0.000000	0.03702	0.723000	0.41478	-2.856000	0.00729	-1.314000	0.02300	-0.258000	0.10820	AGA		0.413	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			T	44635438	G	T	44635438	3	4	61	1	0	0	0	0	1	0	0	0	17818	942	33	2	685	2	ZNF225	19	44635438	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24779	44635438	14493545	11200	19185										
ZNF225	7768	broad.mit.edu	37	chr19	44636464	44636464	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggtccacaccggagagaGaccttataattgtaaagaat	11	7	0	3	rs192190840	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44636464G>T	ENST00000262894.6	+	5	1977	c.1697G>T	c.(1696-1698)aGa>aTa	p.R566I	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Missense_Mutation_p.R566I	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	566					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R566I(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				ACCGGAGAGAGACCTTATAAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	79	77					19																	44636464		2200	4297	6497	49328304	SO:0001583	missense	7768			AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.1697G>T	19.37:g.44636464G>T	ENSP00000262894:p.Arg566Ile		49328304	A8K8S2|Q53F12|Q9NS46|Q9UID8	Missense_Mutation	SNP	ENST00000262894.6	37	CCDS46100.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.761129	0.49468	.	.	ENSG00000256294	ENST00000262894;ENST00000544184	T	0.20332	2.08	2.76	0.546	0.17196	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.44180	0.1281	M	0.86864	2.845	0.34810	D	0.737603	D	0.63046	0.992	D	0.69142	0.962	T	0.53725	-0.8398	9	0.87932	D	0	.	6.5561	0.22462	0.7952:0.0:0.2048:0.0	.	566	Q9UK10	ZN225_HUMAN	I	566;530	ENSP00000262894:R566I	ENSP00000262894:R566I	R	+	2	0	ZNF225	49328304	0.024000	0.19004	0.019000	0.16419	0.139000	0.21198	0.510000	0.22723	-0.061000	0.13110	-0.291000	0.09656	AGA		0.433	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			T	44636464	G	T	44636464	3	4	61	1	0	0	0	0	1	0	0	0	17818	942	33	2	1711	2	ZNF225	19	44636464	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1026	44636464	14492519	11201	19186										
ZNF227	7770	broad.mit.edu	37	chr19	44739551	44739551	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatcatacaggagagaagtCttatagatgcgacagttgcg	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44739551C>A	ENST00000313040.7	+	6	1173	c.968C>A	c.(967-969)tCt>tAt	p.S323Y	ZNF227_ENST00000391961.2_Missense_Mutation_p.S272Y|ZNF227_ENST00000589005.1_Missense_Mutation_p.S272Y	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S323Y(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GGAGAGAAGTCTTATAGATGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	66	65					19																	44739551		2203	4300	6503	49431391	SO:0001583	missense	7770			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.968C>A	19.37:g.44739551C>A	ENSP00000321049:p.Ser323Tyr		49431391	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.581879	0.28180	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.18338	2.22;2.22	4.79	3.73	0.42828	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31420	0.0796	L	0.60012	1.86	0.80722	D	1	P;P;P;P	0.49253	0.921;0.921;0.921;0.921	P;P;P;P	0.55222	0.771;0.771;0.771;0.771	T	0.07927	-1.0747	9	0.87932	D	0	.	14.0265	0.64588	0.0:0.847:0.153:0.0	.	244;302;275;323	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	Y	323;280;272;302;24	ENSP00000321049:S323Y;ENSP00000375823:S272Y	ENSP00000321049:S323Y	S	+	2	0	ZNF227	49431391	0.856000	0.29760	0.673000	0.29887	0.148000	0.21650	3.045000	0.49838	1.104000	0.41587	0.563000	0.77884	TCT		0.403	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		A	44739551	C	A	44739551	3	1	61	1	0	0	0	0	1	0	0	0	17820	913	32	2	982	2	ZNF227	19	44739551	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103087	44739551	14389432	11202	19187										
ZNF233	353355	broad.mit.edu	37	chr19	44778627	44778627	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaggcttcatctggaactCatatcttcatgttcatcaga	7	9	7	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44778627C>T	ENST00000391958.2	+	5	1941	c.1814C>T	c.(1813-1815)tCa>tTa	p.S605L	ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR|ZNF233_ENST00000334152.1_Missense_Mutation_p.S587L	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S605L(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				ATCTGGAACTCATATCTTCAT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											98	97	97					19																	44778627		2203	4300	6503	49470467	SO:0001583	missense	353355			AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"Zinc fingers, C2H2-type", "-"	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1814C>T	19.37:g.44778627C>T	ENSP00000375820:p.Ser605Leu		49470467	B2RN78|B2RN79|Q86WL8	Missense_Mutation	SNP	ENST00000391958.2	37	CCDS33047.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849577	0.51270	.	.	ENSG00000159915	ENST00000334152;ENST00000391958;ENST00000280305	T;T	0.07908	3.15;3.15	4.08	-0.951	0.10369	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08133	0.0203	M	0.63428	1.95	0.09310	N	1	B	0.25007	0.116	B	0.23852	0.049	T	0.37979	-0.9682	9	0.49607	T	0.09	-0.4458	2.081	0.03635	0.1414:0.3978:0.2775:0.1833	.	605	A6NK53	ZN233_HUMAN	L	587;605;500	ENSP00000334957:S587L;ENSP00000375820:S605L	ENSP00000280305:S500L	S	+	2	0	ZNF233	49470467	0.000000	0.05858	0.001000	0.08648	0.987000	0.75469	-0.120000	0.10660	0.306000	0.22856	-0.192000	0.12808	TCA		0.448	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756		T	44778627	C	T	44778627	3	4	61	1	0	0	0	0	1	0	0	0	17825	838	29	3	1828	3	ZNF233	19	44778627	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39076	44778627	14350356	11203	19188										
ZFP112	7771	broad.mit.edu	37	chr19	44831976	44831976	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgaactctcactgaaaccCtttgtacacacctcacattt	4	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44831976C>A	ENST00000337401.4	-	5	2440	c.2352G>T	c.(2350-2352)aaG>aaT	p.K784N	ZNF112_ENST00000354340.4_Missense_Mutation_p.K778N|ZNF112_ENST00000536500.1_Missense_Mutation_p.K801N	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	784					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K778N(1)									CACTGAAACCCTTTGTACACA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	19											218	207	211					19																	44831976		2203	4300	6503	49523816	SO:0001583	missense	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2352G>T	19.37:g.44831976C>A	ENSP00000337081:p.Lys784Asn		49523816	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.055721	0.55325	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.07908	3.15;3.15;3.15	5.18	2.7	0.31948	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35708	N	0.003029	T	0.29126	0.0724	M	0.89287	3.02	0.36406	D	0.863452	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.998	T	0.32402	-0.9908	10	0.87932	D	0	-24.3371	7.311	0.26475	0.0:0.6867:0.0:0.3133	.	783;801;784	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	N	784;784;778;801;783	ENSP00000337081:K784N;ENSP00000346305:K778N;ENSP00000441990:K801N	ENSP00000253426:K783N	K	-	3	2	ZNF285	49523816	0.005000	0.15991	1.000000	0.80357	0.960000	0.62799	0.060000	0.14342	1.328000	0.45358	-0.251000	0.11542	AAG		0.488	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		A	44831976	C	A	44831976	3	1	61	1	0	0	0	0	1	0	0	0	17677	680	24	2	393	2	ZFP112	19	44831976	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53349	44831976	14297007	11204	19189										
ZNF285	26974	broad.mit.edu	37	chr19	44892168	44892168	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacagttaaatcccggatcCtttgtttccaaatctgccag	6	12	2	0	rs73039940	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44892168C>A	ENST00000330997.4	-	4	303	c.239G>T	c.(238-240)aGg>aTg	p.R80M	ZNF285_ENST00000591679.1_Missense_Mutation_p.R87M|ZNF285_ENST00000544719.2_Missense_Mutation_p.R80M|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	80	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R80M(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						ATCCCGGATCCTTTGTTTCCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											89	91	90					19																	44892168		2203	4300	6503	49584008	SO:0001583	missense	26974			AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.239G>T	19.37:g.44892168C>A	ENSP00000333595:p.Arg80Met		49584008	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332817	0.24167	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.06933	3.24	3.14	-0.384	0.12474	Krueppel-associated box (1);	.	.	.	.	T	0.07007	0.0178	N	0.22421	0.69	0.09310	N	1	P;P	0.50943	0.94;0.94	P;P	0.47075	0.536;0.536	T	0.32719	-0.9896	9	0.46703	T	0.11	.	5.6402	0.17559	0.0:0.5993:0.0:0.4007	.	104;80	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	M	103;80	ENSP00000333595:R80M	ENSP00000333595:R80M	R	-	2	0	ZNF285	49584008	0.000000	0.05858	0.137000	0.22149	0.400000	0.30750	-3.112000	0.00599	-0.246000	0.09611	-0.396000	0.06452	AGG		0.433	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		A	44892168	C	A	44892168	3	1	61	1	0	0	0	0	1	0	0	0	17861	681	24	2	1537	2	ZNF285	19	44892168	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60192	44892168	14236815	11205	19190										
ZNF180	7733	broad.mit.edu	37	chr19	44981207	44981207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactaaaggatttcccacaCtgattgcattcatagggttt	8	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44981207C>T	ENST00000221327.4	-	5	1772	c.1491G>A	c.(1489-1491)caG>caA	p.Q497Q	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Silent_p.Q470Q|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Silent_p.Q472Q	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q497Q(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ATTTCCCACACTGATTGCATT	0.363																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - coding silent(1)	large_intestine(1)	19											70	69	69					19																	44981207		2203	4300	6503	49673047	SO:0001819	synonymous_variant	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1491G>A	19.37:g.44981207C>T			49673047	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																				0.363	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		T	44981207	C	T	44981207	2	4	61	1	0	0	0	0	0	0	0	1	17787	564	20	3		3	ZNF180	19	44981207	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89039	44981207	14147776	11206	19191										
ZNF180	7733	broad.mit.edu	37	chr19	44981328	44981328	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttctctccggtatgtgttCtttgatgtgcaataagttta	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44981328C>A	ENST00000221327.4	-	5	1651	c.1370G>T	c.(1369-1371)aGa>aTa	p.R457I	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Missense_Mutation_p.R430I|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.R432I	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R457I(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GGTATGTGTTCTTTGATGTGC	0.383																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - Missense(1)	large_intestine(1)	19											75	77	76					19																	44981328		2203	4299	6502	49673168	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1370G>T	19.37:g.44981328C>A	ENSP00000221327:p.Arg457Ile		49673168	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728086	0.69074	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.02446	4.29;4.29	5.2	5.2	0.72013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46145	D	0.000307	T	0.15262	0.0368	M	0.71296	2.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.998	T	0.00124	-1.2023	10	0.87932	D	0	-16.9226	17.5112	0.87760	0.0:1.0:0.0:0.0	.	432;456;457	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	I	457;432	ENSP00000221327:R457I;ENSP00000375818:R432I	ENSP00000221327:R457I	R	-	2	0	ZNF180	49673168	0.000000	0.05858	1.000000	0.80357	0.858000	0.48976	0.565000	0.23578	2.409000	0.81822	0.460000	0.39030	AGA		0.383	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44981328	C	A	44981328	3	1	61	1	0	0	0	0	1	0	0	0	17787	913	32	2	712	2	ZNF180	19	44981328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	121	44981328	14147655	11207	19192										
ZNF180	7733	broad.mit.edu	37	chr19	44981496	44981496	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgagttCtctgatgggaaacaaggtgc	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44981496C>A	ENST00000221327.4	-	5	1483	c.1202G>T	c.(1201-1203)aGa>aTa	p.R401I	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Missense_Mutation_p.R374I|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.R376I	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	401					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R401I(2)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AGTATGAGTTCTCTGATGGGA	0.448																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											2	Substitution - Missense(2)	large_intestine(2)	19											66	68	67					19																	44981496		2203	4300	6503	49673336	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1202G>T	19.37:g.44981496C>A	ENSP00000221327:p.Arg401Ile		49673336	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640143	0.67244	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.24908	1.83;1.83	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000344	T	0.56077	0.1961	M	0.84683	2.71	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	P;D;D	0.66979	0.877;0.948;0.948	T	0.63332	-0.6661	10	0.87932	D	0	-11.7145	17.8877	0.88862	0.0:1.0:0.0:0.0	.	376;400;401	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	I	401;376	ENSP00000221327:R401I;ENSP00000375818:R376I	ENSP00000221327:R401I	R	-	2	0	ZNF180	49673336	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.735000	0.26115	2.499000	0.84300	0.591000	0.81541	AGA		0.448	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44981496	C	A	44981496	3	1	61	1	0	0	0	0	1	0	0	0	17787	913	32	2	880	2	ZNF180	19	44981496	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168	44981496	14147487	11208	19193										
ZNF180	7733	broad.mit.edu	37	chr19	44981994	44981994	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcattaatcttctgatgaCtgtttacagcagcattaaga	6	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:44981994C>A	ENST00000221327.4	-	5	985	c.704G>T	c.(703-705)aGt>aTt	p.S235I	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Missense_Mutation_p.S208I|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.S210I	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S235I(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTTCTGATGACTGTTTACAGC	0.338																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - Missense(1)	large_intestine(1)	19											86	86	86					19																	44981994		2203	4300	6503	49673834	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.704G>T	19.37:g.44981994C>A	ENSP00000221327:p.Ser235Ile		49673834	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	C	4.018	0.000705	0.07819	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.08282	3.11;3.15	4.89	1.41	0.22369	.	0.430694	0.19962	N	0.102197	T	0.05731	0.0150	N	0.17278	0.47	0.09310	N	0.999999	P;P;P	0.42203	0.773;0.664;0.664	B;B;B	0.43701	0.428;0.246;0.246	T	0.32877	-0.9890	10	0.37606	T	0.19	-8.2258	6.3737	0.21495	0.0:0.6386:0.1876:0.1738	.	210;234;235	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	I	235;210	ENSP00000221327:S235I;ENSP00000375818:S210I	ENSP00000221327:S235I	S	-	2	0	ZNF180	49673834	0.000000	0.05858	0.239000	0.24122	0.579000	0.36224	-0.299000	0.08254	0.547000	0.28938	0.655000	0.94253	AGT		0.338	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44981994	C	A	44981994	3	1	61	1	0	0	0	0	1	0	0	0	17787	565	20	2	1378	2	ZNF180	19	44981994	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	498	44981994	14146989	11209	19194										
CEACAM20	125931	broad.mit.edu	37	chr19	45029247	45029247	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagggtgagctgggctgcaGctggaggactccatacggta	17	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:45029247G>T	ENST00000454753.1	-	0	361							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				CTGGGCTGCAGCTGGAGGACT	0.577																																																0			19											106	113	111					19																	45029247		2098	4216	6314	49721087			125931			AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Immunoglobulin superfamily / I-set domain containing"	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45029247G>T			49721087		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																					0.577	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		T	45029247	G	T	45029247	1	4	61	0	1	0	0	0	0	0	0	0	3197	971	34	2		2	CEACAM20	19	45029247	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	47253	45029247	14099736	11210	19195										
CKM	1158	broad.mit.edu	37	chr19	45810765	45810765	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggtgaggatctcctcgaaCttggggtgcttgctcaggtg	16	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:45810765C>A	ENST00000221476.3	-	7	1095	c.921G>T	c.(919-921)aaG>aaT	p.K307N		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	307	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.K307N(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	TCTCCTCGAACTTGGGGTGCT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	67	70					19																	45810765		2203	4300	6503	50502605	SO:0001583	missense	1158			M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.921G>T	19.37:g.45810765C>A	ENSP00000221476:p.Lys307Asn		50502605	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692932	0.68271	.	.	ENSG00000104879	ENST00000221476	T	0.11821	2.74	5.3	1.98	0.26296	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	M	0.73319	2.225	0.53688	D	0.999975	D	0.62365	0.991	D	0.66602	0.945	T	0.01460	-1.1349	10	0.59425	D	0.04	-34.2682	6.7082	0.23262	0.0:0.6375:0.0:0.3625	.	307	P06732	KCRM_HUMAN	N	307	ENSP00000221476:K307N	ENSP00000221476:K307N	K	-	3	2	CKM	50502605	0.535000	0.26370	1.000000	0.80357	0.998000	0.95712	-0.120000	0.10660	0.619000	0.30197	0.561000	0.74099	AAG		0.647	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			A	45810765	C	A	45810765	3	1	61	1	0	0	0	0	1	0	0	0	3454	564	20	2	232	2	CKM	19	45810765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	781518	45810765	13318218	11211	19196										
PPM1N	147699	broad.mit.edu	37	chr19	46002455	46002455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttacctacaaggaggctcCggggaggccccccgagctac	12	15	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46002455C>T	ENST00000451287.2	+	1	725	c.725C>T	c.(724-726)cCg>cTg	p.P242L	RTN2_ENST00000245923.4_5'Flank|PPM1N_ENST00000396735.2_5'Flank|PPM1N_ENST00000456399.2_Intron|PPM1N_ENST00000401593.1_5'Flank|RTN2_ENST00000590526.1_5'Flank|RTN2_ENST00000344680.4_5'Flank|PPM1N_ENST00000396737.2_Intron|PPM1N_ENST00000401705.1_Intron|PPM1N_ENST00000324688.4_Missense_Mutation_p.P164L|PPM1N_ENST00000396736.2_5'Flank|RTN2_ENST00000589384.1_5'Flank	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	242	PP2C-like.						magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)	p.P242L(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						AAGGAGGCTCCGGGGAGGCCC	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	19											18	21	20					19																	46002455		1898	4083	5981	50694295	SO:0001583	missense	147699			AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.725C>T	19.37:g.46002455C>T	ENSP00000397050:p.Pro242Leu		50694295	Q6P662	Missense_Mutation	SNP	ENST00000451287.2	37	CCDS46115.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.538576	0.27475	.	.	ENSG00000213889	ENST00000451287;ENST00000396734;ENST00000324688	T;T	0.17213	2.29;2.29	3.5	1.36	0.22044	Protein phosphatase 2C-like (5);	0.283230	0.28700	U	0.014423	T	0.09423	0.0232	L	0.39397	1.21	0.21950	N	0.999454	P	0.39520	0.676	B	0.30855	0.121	T	0.23547	-1.0185	10	0.29301	T	0.29	.	5.4895	0.16769	0.0:0.6385:0.0:0.3615	.	242	Q8N819	PPM1N_HUMAN	L	242;242;164	ENSP00000397050:P242L;ENSP00000321761:P164L	ENSP00000321761:P164L	P	+	2	0	PPM1N	50694295	0.000000	0.05858	0.450000	0.26969	0.912000	0.54170	1.223000	0.32527	0.487000	0.27698	0.313000	0.20887	CCG		0.697	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401		T	46002455	C	T	46002455	3	4	61	1	0	0	0	0	1	0	0	0	12380	652	23	1	727	1	PPM1N	19	46002455	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	191690	46002455	13126528	11212	19197										
DMWD	1762	broad.mit.edu	37	chr19	46289815	46289815	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacgcaggagcatggagtcGaagtggaagacgcgcaggca	16	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46289815G>A	ENST00000270223.6	-	3	984	c.939C>T	c.(937-939)ttC>ttT	p.F313F	DMWD_ENST00000377735.3_Silent_p.F313F|DMWD_ENST00000601370.1_5'Flank|AC011530.4_ENST00000593999.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	313								p.F313F(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GCATGGAGTCGAAGTGGAAGA	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	19											44	49	48					19																	46289815		2203	4300	6503	50981655	SO:0001819	synonymous_variant	1762			L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.939C>T	19.37:g.46289815G>A			50981655		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																				0.667	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		A	46289815	G	A	46289815	2	1	61	1	0	0	0	0	0	0	0	1	4604	1049	37	1		1	DMWD	19	46289815	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	287360	46289815	12839168	11213	19198										
NOVA2	4858	broad.mit.edu	37	chr19	46444012	46444012	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcttgtaccttctgcacGatggcgctcacggccttgtg	10	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46444012G>A	ENST00000263257.5	-	4	782	c.588C>T	c.(586-588)atC>atT	p.I196I		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	196	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.I196I(1)		endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		CCTTCTGCACGATGGCGCTCA	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	19											63	34	44					19																	46444012		2203	4300	6503	51135852	SO:0001819	synonymous_variant	4858			U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.588C>T	19.37:g.46444012G>A			51135852	O43267|Q9UEA1	Silent	SNP	ENST00000263257.5	37	CCDS12679.1																																																																																				0.662	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		A	46444012	G	A	46444012	2	1	61	1	0	0	0	0	0	0	0	1	10586	1048	37	1		1	NOVA2	19	46444012	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	154197	46444012	12684971	11214	19199										
HIF3A	64344	broad.mit.edu	37	chr19	46838171	46838171	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcccacagagtttccttCtgacaggaggaccagcccca	8	16	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46838171C>T	ENST00000377670.4	+	14	1871	c.1840C>T	c.(1840-1842)Ctg>Ttg	p.L614L	HIF3A_ENST00000600383.1_Silent_p.L545L|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000420102.2_Silent_p.L563L|HIF3A_ENST00000300862.3_Silent_p.L612L|HIF3A_ENST00000472815.1_Intron|HIF3A_ENST00000339613.2_Silent_p.L558L|HIF3A_ENST00000244303.6_Silent_p.L545L	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	614					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.L612L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		GAGTTTCCTTCTGACAGGAGG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	19											65	64	64					19																	46838171		2203	4300	6503	51530011	SO:0001819	synonymous_variant	64344			AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"Basic helix-loop-helix proteins"	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1840C>T	19.37:g.46838171C>T			51530011	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Silent	SNP	ENST00000377670.4	37	CCDS12681.2																																																																																				0.567	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			T	46838171	C	T	46838171	2	4	61	1	0	0	0	0	0	0	0	1	7126	912	32	3		3	HIF3A	19	46838171	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	394159	46838171	12290812	11215	19200										
PPP5C	5536	broad.mit.edu	37	chr19	46857194	46857194	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggttattaccgccgggctgCcagcaacatggcactgggca	14	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46857194C>A	ENST00000012443.4	+	2	414	c.311C>A	c.(310-312)gCc>gAc	p.A104D	PPP5C_ENST00000391919.1_5'UTR	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	104					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)	p.A104D(1)		endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		CGCCGGGCTGCCAGCAACATG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											31	24	27					19																	46857194		2202	4299	6501	51549034	SO:0001583	missense	5536				CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.311C>A	19.37:g.46857194C>A	ENSP00000012443:p.Ala104Asp		51549034	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	37	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737134	0.69304	.	.	ENSG00000011485	ENST00000012443;ENST00000451918	T	0.64618	-0.11	5.21	5.21	0.72293	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.061993	0.64402	D	0.000004	T	0.65873	0.2733	M	0.82056	2.57	0.80722	D	1	P;B	0.39535	0.677;0.003	B;B	0.38020	0.263;0.012	T	0.70128	-0.4957	10	0.44086	T	0.13	-18.3798	16.6324	0.85037	0.0:1.0:0.0:0.0	.	104;104	B2R6R6;P53041	.;PPP5_HUMAN	D	104;91	ENSP00000012443:A104D	ENSP00000012443:A104D	A	+	2	0	PPP5C	51549034	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.092000	0.76930	2.597000	0.87782	0.563000	0.77884	GCC		0.637	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		A	46857194	C	A	46857194	3	1	61	1	0	0	0	0	1	0	0	0	12440	739	26	2	317	2	PPP5C	19	46857194	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19023	46857194	12271789	11216	19201										
PNMAL2	57469	broad.mit.edu	37	chr19	46997934	46997934	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctctgcctcttctttcttCgatttgtcggtgacggtgac	9	11	4	2	rs35793066		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46997934C>T	ENST00000377655.2	-	1	734				PNMAL2_ENST00000594749.1_Intron|AC011484.1_ENST00000377652.3_Silent_p.F15F|PNMAL2_ENST00000599531.1_Silent_p.S263S			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2									p.F15F(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CTTCTTTCTTCGATTTGTCGG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	19											73	63	66					19																	46997934		2203	4300	6503	51689774	SO:0001627	intron_variant	57469			AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+54G>A	19.37:g.46997934C>T			51689774	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Silent	SNP	ENST00000377655.2	37																																																																																					0.592	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		T	46997934	C	T	46997934	1	4	61	0	1	0	0	0	0	0	0	0	12189	871	31	1		1	PNMAL2	19	46997934	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	140740	46997934	12131049	11217	19202										
PNMAL2	57469	broad.mit.edu	37	chr19	46998309	46998309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgttacctccccagaatcCtgggcctgcgtctccgaagc	9	17	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:46998309C>A	ENST00000377655.2	-	1	413	c.414G>T	c.(412-414)caG>caT	p.Q138H	PNMAL2_ENST00000594749.1_Intron|AC011484.1_ENST00000377652.3_Silent_p.S140S|PNMAL2_ENST00000599531.1_Missense_Mutation_p.Q138H			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2	138								p.Q138H(1)|p.S140S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CCCCAGAATCCTGGGCCTGCG	0.687																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	19											46	48	47					19																	46998309		2203	4300	6503	51690149	SO:0001583	missense	57469			AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.414G>T	19.37:g.46998309C>A	ENSP00000366883:p.Gln138His		51690149	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37		.	.	.	.	.	.	.	.	.	.	C	15.71	2.915225	0.52546	.	.	ENSG00000204851	ENST00000377655	T	0.10477	2.87	2.81	0.667	0.17907	.	.	.	.	.	T	0.10121	0.0248	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.59889	0.865	T	0.24297	-1.0164	9	0.59425	D	0.04	-8.1282	4.8671	0.13613	0.0:0.7018:0.0:0.2982	.	138	Q9ULN7	PNML2_HUMAN	H	138	ENSP00000366883:Q138H	ENSP00000366883:Q138H	Q	-	3	2	PNMAL2	51690149	0.486000	0.25980	0.008000	0.14137	0.662000	0.39071	1.054000	0.30455	0.241000	0.21283	0.561000	0.74099	CAG		0.687	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		A	46998309	C	A	46998309	3	1	61	1	0	0	0	0	1	0	0	0	12189	680	24	2	1497	2	PNMAL2	19	46998309	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	375	46998309	12130674	11218	19203										
STRN4	29888	broad.mit.edu	37	chr19	47241448	47241448	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacacatctgctttcttctCcccctggttcaggtctgtcc	7	15	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47241448C>A	ENST00000263280.6	-	3	482	c.433G>T	c.(433-435)Gag>Tag	p.E145*	STRN4_ENST00000539396.1_Nonsense_Mutation_p.E26*|Y_RNA_ENST00000410682.1_RNA|STRN4_ENST00000391910.3_Nonsense_Mutation_p.E145*	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	145						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.E145*(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		GCTTTCTTCTCCCCCTGGTTC	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											259	201	221					19																	47241448		2203	4300	6503	51933288	SO:0001587	stop_gained	29888			AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"WD repeat domain containing"	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.433G>T	19.37:g.47241448C>A	ENSP00000263280:p.Glu145*		51933288	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Nonsense_Mutation	SNP	ENST00000263280.6	37	CCDS12690.1	.	.	.	.	.	.	.	.	.	.	C	36	5.901109	0.97087	.	.	ENSG00000090372	ENST00000391910;ENST00000263280;ENST00000539396;ENST00000435164	.	.	.	5.05	4.02	0.46733	.	0.062935	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-32.6235	12.2573	0.54631	0.0:0.9161:0.0:0.0839	.	.	.	.	X	145;145;26;26	.	ENSP00000263280:E145X	E	-	1	0	STRN4	51933288	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.918000	0.75788	1.347000	0.45714	0.563000	0.77884	GAG		0.493	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2			A	47241448	C	A	47241448	4	1	61	1	0	0	0	0	0	1	0	0	15370	864	30	2	1909	2	STRN4	19	47241448	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	243139	47241448	11887535	11219	19204										
ARHGAP35	2909	broad.mit.edu	37	chr19	47422621	47422621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggttgtggagacctcagCgagatccaatgtaaacgtgg	13	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47422621C>T	ENST00000404338.3	+	1	689	c.689C>T	c.(688-690)gCg>gTg	p.A230V		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	230					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.A230V(1)									GAGACCTCAGCGAGATCCAAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											101	100	100					19																	47422621		1920	4134	6054	52114461	SO:0001583	missense	2909			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.689C>T	19.37:g.47422621C>T	ENSP00000385720:p.Ala230Val		52114461	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.126663	0.77549	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	D	0.90261	-2.64	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.96914	0.8992	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97473	1.0042	10	0.87932	D	0	-22.307	18.9906	0.92789	0.0:1.0:0.0:0.0	.	230	Q9NRY4-2	.	V	230	ENSP00000385720:A230V	ENSP00000324820:A230V	A	+	2	0	ARHGAP35	52114461	1.000000	0.71417	0.512000	0.27736	0.984000	0.73092	7.818000	0.86416	2.780000	0.95670	0.655000	0.94253	GCG		0.438	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47422621	C	T	47422621	3	4	61	1	0	0	0	0	1	0	0	0	6816	768	27	1	691	1	ARHGAP35	19	47422621	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	181173	47422621	11706362	11220	19205										
ARHGAP35	2909	broad.mit.edu	37	chr19	47423130	47423130	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acattgacaacatggaaaacGaacggattccctttgattta	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47423130G>A	ENST00000404338.3	+	1	1198	c.1198G>A	c.(1198-1200)Gaa>Aaa	p.E400K		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	400	FF 2.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.E400K(1)									CATGGAAAACGAACGGATTCC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											126	118	120					19																	47423130		1914	4138	6052	52114970	SO:0001583	missense	2909			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.1198G>A	19.37:g.47423130G>A	ENSP00000385720:p.Glu400Lys		52114970	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187731	0.38609	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.07216	3.21	6.03	6.03	0.97812	.	0.099760	0.64402	D	0.000002	T	0.09468	0.0233	L	0.38531	1.155	0.53688	D	0.999979	B	0.28900	0.227	B	0.22601	0.04	T	0.18398	-1.0338	10	0.33940	T	0.23	-35.5583	19.3283	0.94273	0.0:0.0:1.0:0.0	.	400	Q9NRY4-2	.	K	400	ENSP00000385720:E400K	ENSP00000324820:E400K	E	+	1	0	ARHGAP35	52114970	1.000000	0.71417	0.937000	0.37676	0.989000	0.77384	4.835000	0.62781	2.861000	0.98227	0.655000	0.94253	GAA		0.463	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		A	47423130	G	A	47423130	3	1	61	1	0	0	0	0	1	0	0	0	6816	1059	37	1	1200	1	ARHGAP35	19	47423130	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	509	47423130	11705853	11221	19206										
ARHGAP35	2909	broad.mit.edu	37	chr19	47424922	47424922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcttacagcctgtttcGagaagacacatcactgcctt	7	13	2	2	rs371941437		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47424922G>A	ENST00000404338.3	+	1	2990	c.2990G>A	c.(2989-2991)cGa>cAa	p.R997Q		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	997					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.R997Q(1)									AGCCTGTTTCGAGAAGACACA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	63	63					19																	47424922		1937	4149	6086	52116762	SO:0001583	missense	2909			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2990G>A	19.37:g.47424922G>A	ENSP00000385720:p.Arg997Gln		52116762	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.790576	0.31685	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.08102	3.13	5.76	5.76	0.90799	.	0.061993	0.64402	D	0.000005	T	0.08626	0.0214	L	0.43152	1.355	0.39874	D	0.973542	B	0.23442	0.085	B	0.19148	0.024	T	0.18903	-1.0322	10	0.29301	T	0.29	-7.3842	12.1257	0.53915	0.0796:0.0:0.9204:0.0	.	997	Q9NRY4-2	.	Q	997	ENSP00000385720:R997Q	ENSP00000324820:R997Q	R	+	2	0	ARHGAP35	52116762	0.993000	0.37304	0.999000	0.59377	0.995000	0.86356	7.298000	0.78815	2.726000	0.93360	0.655000	0.94253	CGA		0.478	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		A	47424922	G	A	47424922	3	1	61	1	0	0	0	0	1	0	0	0	6816	1058	37	1	2992	1	ARHGAP35	19	47424922	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1792	47424922	11704061	11222	19207										
ARHGAP35	2909	broad.mit.edu	37	chr19	47502610	47502610	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccttaaggaggtattaaaGaaatttccaaaggaaaacca	8	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47502610G>T	ENST00000404338.3	+	5	4086	c.4086G>T	c.(4084-4086)aaG>aaT	p.K1362N	ARHGAP35_ENST00000598548.1_3'UTR	NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	1362	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.K1362N(1)									AGGTATTAAAGAAATTTCCAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	54	54					19																	47502610		1872	4116	5988	52194450	SO:0001583	missense	2909			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.4086G>T	19.37:g.47502610G>T	ENSP00000385720:p.Lys1362Asn		52194450	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359245	0.61403	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.19669	2.13	5.09	5.09	0.68999	.	0.256729	0.34725	N	0.003737	T	0.13457	0.0326	N	0.25031	0.7	0.38613	D	0.950946	B	0.25809	0.135	B	0.24848	0.056	T	0.10019	-1.0648	10	0.40728	T	0.16	-23.2409	7.8985	0.29721	0.1771:0.0:0.8229:0.0	.	1362	Q9NRY4-2	.	N	1362	ENSP00000385720:K1362N	ENSP00000324820:K1362N	K	+	3	2	ARHGAP35	52194450	1.000000	0.71417	0.660000	0.29694	0.992000	0.81027	1.249000	0.32839	2.389000	0.81357	0.491000	0.48974	AAG		0.463	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47502610	G	T	47502610	3	4	61	1	0	0	0	0	1	0	0	0	6816	933	33	2	4104	2	ARHGAP35	19	47502610	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77688	47502610	11626373	11223	19208										
CCDC9	26093	broad.mit.edu	37	chr19	47774684	47774684	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaggaggaaccagcccaaGaccaccaagccccagaggct	11	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47774684G>T	ENST00000221922.6	+	12	1567	c.1345G>T	c.(1345-1347)Gac>Tac	p.D449Y		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	449							poly(A) RNA binding (GO:0044822)	p.D449Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		ACCAGCCCAAGACCACCAAGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											105	102	103					19																	47774684		2203	4300	6503	52466524	SO:0001583	missense	26093			AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1345G>T	19.37:g.47774684G>T	ENSP00000221922:p.Asp449Tyr		52466524		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	.	15.84	2.950784	0.53186	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.26223	1.75	4.31	4.31	0.51392	.	2.218800	0.02014	N	0.047234	T	0.40423	0.1116	L	0.54323	1.7	0.19775	N	0.999958	P	0.50528	0.936	P	0.48141	0.568	T	0.45920	-0.9228	10	0.66056	D	0.02	-13.8753	13.787	0.63117	0.0:0.0:1.0:0.0	.	449	Q9Y3X0	CCDC9_HUMAN	Y	449;431	ENSP00000221922:D449Y	ENSP00000221922:D449Y	D	+	1	0	CCDC9	52466524	0.233000	0.23772	0.032000	0.17829	0.151000	0.21798	1.987000	0.40687	2.213000	0.71641	0.305000	0.20034	GAC		0.622	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		T	47774684	G	T	47774684	3	4	61	1	0	0	0	0	1	0	0	0	2873	942	33	2	1387	2	CCDC9	19	47774684	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272074	47774684	11354299	11224	19209										
C5AR1	728	broad.mit.edu	37	chr19	47823317	47823317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctgcccatcttgttcacgTccattgtacagcatcaccac	6	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47823317T>C	ENST00000355085.3	+	2	305	c.283T>C	c.(283-285)Tcc>Ccc	p.S95P		NM_001736.3	NP_001727.1	P21730	C5AR1_HUMAN	complement component 5a receptor 1	95					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|cell proliferation in hindbrain (GO:0021534)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)|complement component C5a signaling pathway (GO:0038178)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ regeneration (GO:0031100)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)|complement component C5a receptor activity (GO:0004878)	p.S95P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)	20		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)		CTTGTTCACGTCCATTGTACA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											112	95	101					19																	47823317		2203	4300	6503	52515157	SO:0001583	missense	728				CCDS33063.1	19q13.3-q13.4	2012-08-10	2006-02-09	2006-02-09		ENSG00000197405		"CD molecules", "Complement system", "GPCR / Class A : Complement component receptors"	1338	protein-coding gene	gene with protein product		113995	"complement component 5 receptor 1 (C5a ligand)"	C5R1		1612600	Standard	NM_001736		Approved	C5A, C5AR, CD88	uc002pgj.1	P21730		ENST00000355085.3:c.283T>C	19.37:g.47823317T>C	ENSP00000347197:p.Ser95Pro		52515157		Missense_Mutation	SNP	ENST00000355085.3	37	CCDS33063.1	.	.	.	.	.	.	.	.	.	.	T	0.147	-1.095754	0.01858	.	.	ENSG00000197405	ENST00000355085	T	0.73047	-0.71	4.67	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.140754	0.48767	U	0.000179	T	0.58119	0.2100	M	0.62088	1.915	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.46176	-0.9210	10	0.31617	T	0.26	.	0.7132	0.00928	0.456:0.1283:0.1707:0.245	.	95	P21730	C5AR_HUMAN	P	95	ENSP00000347197:S95P	ENSP00000347197:S95P	S	+	1	0	C5AR1	52515157	0.000000	0.05858	0.005000	0.12908	0.057000	0.15508	-1.463000	0.02361	0.419000	0.25927	0.391000	0.25812	TCC		0.612	C5AR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466925.1	NM_001736		C	47823317	T	C	47823317	3	2	61	1	0	0	0	0	1	0	0	0	2287	1667	58	4	288	4	C5AR1	19	47823317	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	48633	47823317	11305666	11225	19210										
GPR77	27202	broad.mit.edu	37	chr19	47845011	47845011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggagtcccagggccaggacGaaagtgtggacagcaagaaa	16	8	0	1	rs529217199		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47845011G>A	ENST00000595464.1	+	2	1173	c.955G>A	c.(955-957)Gaa>Aaa	p.E319K	C5AR2_ENST00000600626.1_Missense_Mutation_p.E319K|C5AR2_ENST00000257267.2_Missense_Mutation_p.E319K	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	319					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of interleukin-8 secretion (GO:2000482)	apical part of cell (GO:0045177)|basal plasma membrane (GO:0009925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)	p.E319K(2)									GGGCCAGGACGAAAGTGTGGA	0.557													G|||	1	0.000199681	8e-04	0	5008	,	,		18010	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	19											54	43	46					19																	47845011		2203	4300	6503	52536851	SO:0001583	missense	27202			AB038237	CCDS12699.1	19q13.33	2013-01-28	2013-01-28	2013-01-28		ENSG00000134830		"GPCR / Class A : Complement component receptors"	4527	protein-coding gene	gene with protein product		609949	"G protein-coupled receptor 77"	GPR77		11165367	Standard	NM_018485		Approved	C5L2	uc010ela.1	Q9P296		ENST00000595464.1:c.955G>A	19.37:g.47845011G>A	ENSP00000472620:p.Glu319Lys		52536851	B2RA09	Missense_Mutation	SNP	ENST00000595464.1	37	CCDS12699.1	.	.	.	.	.	.	.	.	.	.	G	7.807	0.714959	0.15306	.	.	ENSG00000134830	ENST00000257267	T	0.49720	0.77	3.56	2.47	0.30058	.	0.768615	0.12267	U	0.484191	T	0.28797	0.0714	L	0.32530	0.975	0.09310	N	1	P	0.50066	0.931	B	0.34489	0.184	T	0.06127	-1.0844	10	0.24483	T	0.36	.	8.703	0.34338	0.0:0.2346:0.7654:0.0	.	319	Q9P296	C5ARL_HUMAN	K	319	ENSP00000257267:E319K	ENSP00000257267:E319K	E	+	1	0	GPR77	52536851	0.003000	0.15002	0.002000	0.10522	0.054000	0.15201	0.271000	0.18626	0.790000	0.33803	0.313000	0.20887	GAA		0.557	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485		A	47845011	G	A	47845011	3	1	61	1	0	0	0	0	1	0	0	0	6729	1059	37	1	957	1	GPR77	19	47845011	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21694	47845011	11283972	11226	19211										
NAPA	8775	broad.mit.edu	37	chr19	47996703	47996703	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccaactctgtctcataGatctcagcaatggagatgtg	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:47996703G>T	ENST00000263354.3	-	5	689	c.390C>A	c.(388-390)atC>atA	p.I130I	NAPA-AS1_ENST00000594367.1_RNA|NAPA-AS1_ENST00000593284.1_RNA|NAPA_ENST00000593785.1_5'Flank|NAPA_ENST00000595227.1_Silent_p.I91I	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	130					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)		p.I130I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		CTGTCTCATAGATCTCAGCAA	0.607																																					Ovarian(185;1135 2042 27703 31345 42493)											1	Substitution - coding silent(1)	large_intestine(1)	19											252	217	229					19																	47996703		2203	4300	6503	52688515	SO:0001819	synonymous_variant	8775			U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.390C>A	19.37:g.47996703G>T			52688515	A8K879|Q96IK3|Q9BVJ3	Silent	SNP	ENST00000263354.3	37	CCDS12702.1																																																																																				0.607	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		T	47996703	G	T	47996703	2	4	61	1	0	0	0	0	0	0	0	1	10191	932	33	2		2	NAPA	19	47996703	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151692	47996703	11132280	11227	19212										
EHD2	30846	broad.mit.edu	37	chr19	48220014	48220014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggggccttccactcgccgGccctggaggacgcagacttc	13	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48220014G>A	ENST00000263277.3	+	2	396	c.145G>A	c.(145-147)Gcc>Acc	p.A49T	EHD2_ENST00000538399.1_Intron|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	49					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.A49T(1)		endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		CCACTCGCCGGCCCTGGAGGA	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											37	30	32					19																	48220014		2203	4300	6503	52911826	SO:0001583	missense	30846			AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.145G>A	19.37:g.48220014G>A	ENSP00000263277:p.Ala49Thr		52911826	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	37	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	G	6.889	0.533563	0.13188	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364	T	0.17854	2.25	3.75	2.7	0.31948	.	0.123446	0.53938	D	0.000053	T	0.14227	0.0344	L	0.49640	1.575	0.80722	D	1	B	0.20780	0.048	B	0.14578	0.011	T	0.07065	-1.0792	10	0.21014	T	0.42	-36.9344	9.5824	0.39495	0.1082:0.0:0.8918:0.0	.	49	Q9NZN4	EHD2_HUMAN	T	49	ENSP00000263277:A49T	ENSP00000263277:A49T	A	+	1	0	EHD2	52911826	1.000000	0.71417	0.904000	0.35570	0.189000	0.23516	4.053000	0.57427	0.942000	0.37525	-0.567000	0.04161	GCC		0.662	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			A	48220014	G	A	48220014	3	1	61	1	0	0	0	0	1	0	0	0	4989	1203	42	3	147	3	EHD2	19	48220014	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	223311	48220014	10908969	11228	19213										
EHD2	30846	broad.mit.edu	37	chr19	48229161	48229161	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagctggagatctcggacGagttctcagaggccatcggc	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48229161G>A	ENST00000263277.3	+	4	846	c.595G>A	c.(595-597)Gag>Aag	p.E199K	EHD2_ENST00000538399.1_Missense_Mutation_p.E63K|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	199	Dynamin-type G.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.E199K(1)		endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GATCTCGGACGAGTTCTCAGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											49	40	43					19																	48229161		2203	4300	6503	52920973	SO:0001583	missense	30846			AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.595G>A	19.37:g.48229161G>A	ENSP00000263277:p.Glu199Lys		52920973	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	37	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522807	0.85600	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364;ENST00000538399	D;D	0.96041	-3.89;-3.89	3.66	3.66	0.41972	Dynamin, GTPase domain (1);	0.134193	0.48286	D	0.000187	D	0.97711	0.9249	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98400	1.0567	10	0.87932	D	0	-20.4498	13.284	0.60232	0.0:0.0:1.0:0.0	.	199	Q9NZN4	EHD2_HUMAN	K	199;199;189;63	ENSP00000263277:E199K;ENSP00000439036:E63K	ENSP00000263277:E199K	E	+	1	0	EHD2	52920973	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.668000	0.98619	1.793000	0.52555	0.456000	0.33151	GAG		0.632	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			A	48229161	G	A	48229161	3	1	61	1	0	0	0	0	1	0	0	0	4989	1059	37	1	605	1	EHD2	19	48229161	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9147	48229161	10899822	11229	19214										
GLTSCR2	29997	broad.mit.edu	37	chr19	48253450	48253450	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttagggctgacaaagaagaGaaccaaagtccagaagaagt	11	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48253450G>T	ENST00000246802.5	+	3	343	c.305G>T	c.(304-306)aGa>aTa	p.R102I	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	102						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.R102I(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		ACAAAGAAGAGAACCAAAGTC	0.522																																					Colon(58;613 1041 9473 10089 15241)											1	Substitution - Missense(1)	large_intestine(1)	19											72	64	67					19																	48253450		2203	4300	6503	52945262	SO:0001583	missense	29997			AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.305G>T	19.37:g.48253450G>T	ENSP00000246802:p.Arg102Ile		52945262	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	37	CCDS12705.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.290569	0.23564	.	.	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.35048	1.33	3.06	0.913	0.19354	.	0.544526	0.18342	N	0.144159	T	0.33440	0.0863	L	0.55743	1.74	0.28385	N	0.919368	P;P;P	0.46142	0.873;0.873;0.873	P;P;B	0.45998	0.5;0.5;0.377	T	0.22243	-1.0222	10	0.72032	D	0.01	-14.0242	4.9179	0.13854	0.2911:0.0:0.7089:0.0	.	102;102;100	Q53YP0;Q9NZM5;Q96CS0	.;GSCR2_HUMAN;.	I	102	ENSP00000246802:R102I	ENSP00000246802:R102I	R	+	2	0	GLTSCR2	52945262	0.067000	0.21026	0.011000	0.14972	0.446000	0.32137	0.025000	0.13577	0.323000	0.23307	0.462000	0.41574	AGA		0.522	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		T	48253450	G	T	48253450	3	4	61	1	0	0	0	0	1	0	0	0	6495	942	33	2	315	2	GLTSCR2	19	48253450	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24289	48253450	10875533	11230	19215										
CRX	1406	broad.mit.edu	37	chr19	48342775	48342775	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccctctgcccggcccctcaGgctccccaaccacggcagtg	9	22	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48342775G>T	ENST00000221996.7	+	4	657	c.451G>T	c.(451-453)Ggc>Tgc	p.G151C	CRX_ENST00000539067.1_Missense_Mutation_p.G151C|TPRX2P_ENST00000535362.1_Intron	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	151					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G151C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		CGGCCCCTCAGGCTCCCCAAC	0.667																																					Pancreas(57;461 1196 22201 40716 47188)											1	Substitution - Missense(1)	large_intestine(1)	19											39	43	41					19																	48342775		2203	4298	6501	53034587	SO:0001583	missense	1406			AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"Homeoboxes / PRD class"	2383	protein-coding gene	gene with protein product	"orthodenticle homeobox 3"	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.451G>T	19.37:g.48342775G>T	ENSP00000221996:p.Gly151Cys		53034587	Q0QD45	Missense_Mutation	SNP	ENST00000221996.7	37	CCDS12706.1	.	.	.	.	.	.	.	.	.	.	G	9.420	1.082887	0.20309	.	.	ENSG00000105392	ENST00000221996;ENST00000539067	D;D	0.91011	-2.77;-2.77	3.93	3.93	0.45458	.	0.566940	0.17433	N	0.174394	D	0.83533	0.5275	N	0.19112	0.55	0.09310	N	1	B	0.28512	0.214	B	0.27170	0.077	T	0.76753	-0.2843	10	0.51188	T	0.08	-2.7547	13.5154	0.61537	0.0:0.0:1.0:0.0	.	151	O43186	CRX_HUMAN	C	151	ENSP00000221996:G151C;ENSP00000445565:G151C	ENSP00000221996:G151C	G	+	1	0	CRX	53034587	0.653000	0.27358	0.525000	0.27900	0.876000	0.50452	3.992000	0.56980	2.024000	0.59613	0.467000	0.42956	GGC		0.667	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554		T	48342775	G	T	48342775	3	4	61	1	0	0	0	0	1	0	0	0	3908	1000	35	2	461	2	CRX	19	48342775	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89325	48342775	10786208	11231	19216										
CRX	1406	broad.mit.edu	37	chr19	48343094	48343094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctccctatcaggccagaGctatggcgcctacagccccg	9	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48343094G>T	ENST00000221996.7	+	4	976	c.770G>T	c.(769-771)aGc>aTc	p.S257I	CRX_ENST00000539067.1_Missense_Mutation_p.S257I|TPRX2P_ENST00000535362.1_Intron	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	257					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S257I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		TCAGGCCAGAGCTATGGCGCC	0.632																																					Pancreas(57;461 1196 22201 40716 47188)											1	Substitution - Missense(1)	large_intestine(1)	19											85	94	91					19																	48343094		2203	4299	6502	53034906	SO:0001583	missense	1406			AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"Homeoboxes / PRD class"	2383	protein-coding gene	gene with protein product	"orthodenticle homeobox 3"	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.770G>T	19.37:g.48343094G>T	ENSP00000221996:p.Ser257Ile		53034906	Q0QD45	Missense_Mutation	SNP	ENST00000221996.7	37	CCDS12706.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038901	0.55003	.	.	ENSG00000105392	ENST00000221996;ENST00000539067	D;D	0.90563	-2.69;-2.69	4.01	4.01	0.46588	.	0.057855	0.64402	D	0.000002	D	0.82545	0.5060	L	0.29908	0.895	0.33372	D	0.573741	P	0.50943	0.94	B	0.35413	0.202	D	0.88438	0.3040	10	0.59425	D	0.04	-10.6536	13.6636	0.62382	0.0:0.0:1.0:0.0	.	257	O43186	CRX_HUMAN	I	257	ENSP00000221996:S257I;ENSP00000445565:S257I	ENSP00000221996:S257I	S	+	2	0	CRX	53034906	1.000000	0.71417	0.956000	0.39512	0.945000	0.59286	8.852000	0.92215	2.059000	0.61396	0.467000	0.42956	AGC		0.632	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554		T	48343094	G	T	48343094	3	4	61	1	0	0	0	0	1	0	0	0	3908	971	34	2	780	2	CRX	19	48343094	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	319	48343094	10785889	11232	19217										
SULT2A1	6822	broad.mit.edu	37	chr19	48385390	48385390	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcccatgactttggtttCttaataaacttcatgttttt	4	8	3	1	rs371548779		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48385390C>A	ENST00000222002.3	-	3	562	c.423G>T	c.(421-423)aaG>aaT	p.K141N		NM_003167.3	NP_003158.2	Q06520	ST2A1_HUMAN	sulfotransferase family, cytosolic, 2A, dehydroepiandrosterone (DHEA)-preferring, member 1	141					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|bile acid catabolic process (GO:0030573)|cellular lipid metabolic process (GO:0044255)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	bile-salt sulfotransferase activity (GO:0047704)|sulfotransferase activity (GO:0008146)	p.K141N(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)	Abiraterone(DB05812)|Acetaminophen(DB00316)	ACTTTGGTTTCTTAATAAACT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	83	83					19																	48385390		2203	4300	6503	53077202	SO:0001583	missense	6822			X70222	CCDS12707.1	19q13.3	2014-05-21			ENSG00000105398	ENSG00000105398	2.8.2.2	"Sulfotransferases, cytosolic"	11458	protein-coding gene	gene with protein product		125263		STD		1588921, 7736787	Standard	NM_003167		Approved	DHEA-ST	uc002phr.2	Q06520	OTTHUMG00000162469	ENST00000222002.3:c.423G>T	19.37:g.48385390C>A	ENSP00000222002:p.Lys141Asn		53077202		Missense_Mutation	SNP	ENST00000222002.3	37	CCDS12707.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.173041	0.38413	.	.	ENSG00000105398	ENST00000222002	T	0.01613	4.73	4.15	0.739	0.18324	Sulfotransferase domain (1);	0.421521	0.21181	N	0.078813	T	0.05868	0.0153	M	0.78285	2.405	0.09310	N	1	D	0.60160	0.987	D	0.63283	0.913	T	0.22034	-1.0228	10	0.49607	T	0.09	.	3.3583	0.07177	0.204:0.5756:0.0:0.2204	.	141	Q06520	ST2A1_HUMAN	N	141	ENSP00000222002:K141N	ENSP00000222002:K141N	K	-	3	2	SULT2A1	53077202	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.167000	0.16602	0.144000	0.18951	0.655000	0.94253	AAG		0.373	SULT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369044.1	NM_003167		A	48385390	C	A	48385390	3	1	61	1	0	0	0	0	1	0	0	0	15420	912	32	2	450	2	SULT2A1	19	48385390	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	42296	48385390	10743593	11233	19218										
LIG1	3978	broad.mit.edu	37	chr19	48660284	48660284	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctcacctgtgcgacgcttCggaatccctgatggggaact	11	12	1	1	rs111516401	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48660284C>T	ENST00000263274.7	-	5	776	c.357G>A	c.(355-357)ccG>ccA	p.P119P	LIG1_ENST00000427526.2_Silent_p.P89P|LIG1_ENST00000599165.1_Intron|LIG1_ENST00000536218.1_Silent_p.P119P	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	119					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)	p.P119P(1)		breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	TGCGACGCTTCGGAATCCCTG	0.512								Nucleotide excision repair (NER)					C|||	3	0.000599042	0.0023	0	5008	,	,		13582	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		4,4402	6.2+/-15.9	0,4,2199	89	90	89		357	-3.6	1	19	dbSNP_132	89	0,8600		0,0,4300	no	coding-synonymous	LIG1	NM_000234.1		0,4,6499	TT,TC,CC		0.0,0.0908,0.0308		119/920	48660284	4,13002	2203	4300	6503	53352096	SO:0001819	synonymous_variant	3978				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.357G>A	19.37:g.48660284C>T			53352096	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																				0.512	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		T	48660284	C	T	48660284	2	4	61	1	0	0	0	0	0	0	0	1	8804	871	31	1		1	LIG1	19	48660284	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	274894	48660284	10468699	11234	19219										
CARD8	22900	broad.mit.edu	37	chr19	48734067	48734067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtgggggaggtggatttCggcgacagcctcctctggct	17	9	1	0	rs542641676	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48734067C>T	ENST00000359009.4	-	5	736	c.424G>A	c.(424-426)Gaa>Aaa	p.E142K	CARD8_ENST00000520015.1_Missense_Mutation_p.E247K|CARD8_ENST00000519940.1_Missense_Mutation_p.E247K|CARD8_ENST00000447740.2_Missense_Mutation_p.E197K|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000521613.1_Missense_Mutation_p.E197K|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000391898.3_Missense_Mutation_p.E247K|CARD8_ENST00000520753.1_Missense_Mutation_p.E247K|CARD8_ENST00000520153.1_Missense_Mutation_p.E197K			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	142					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)	p.E142K(1)		endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		AGGTGGATTTCGGCGACAGCC	0.632													C|||	2	0.000399361	0	0	5008	,	,		15438	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19											39	40	40					19																	48734067		2203	4300	6503	53425879	SO:0001583	missense	22900			AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.424G>A	19.37:g.48734067C>T	ENSP00000351901:p.Glu142Lys		53425879	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Missense_Mutation	SNP	ENST00000359009.4	37		.	.	.	.	.	.	.	.	.	.	C	5.118	0.207445	0.09704	.	.	ENSG00000105483	ENST00000447740;ENST00000391898;ENST00000359009;ENST00000520753;ENST00000520153;ENST00000520015;ENST00000521613;ENST00000519940	T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	1.89	0.741	0.18336	.	.	.	.	.	T	0.10551	0.0258	L	0.44542	1.39	0.09310	N	1	P;B;B;B;P;B;P;B	0.37233	0.563;0.38;0.38;0.38;0.588;0.195;0.507;0.095	B;B;B;B;B;B;B;B	0.28011	0.085;0.058;0.058;0.058;0.061;0.019;0.051;0.05	T	0.21895	-1.0232	9	0.39692	T	0.17	.	3.8717	0.09039	0.0:0.7388:0.0:0.2612	.	166;247;247;180;247;197;142;142	B5KVR7;E9PEM7;B5KVR6;Q6MZI8;Q9Y2G2-3;G3XAM9;Q9Y2G2-2;Q9Y2G2	.;.;.;.;.;.;.;CARD8_HUMAN	K	197;247;142;247;197;247;197;247	ENSP00000391248:E197K;ENSP00000375767:E247K;ENSP00000351901:E142K;ENSP00000429839:E247K;ENSP00000428736:E197K;ENSP00000430747:E247K;ENSP00000427858:E197K;ENSP00000428883:E247K	ENSP00000351901:E142K	E	-	1	0	CARD8	53425879	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	0.239000	0.18023	0.284000	0.22305	0.655000	0.94253	GAA		0.632	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959		T	48734067	C	T	48734067	3	4	61	1	0	0	0	0	1	0	0	0	2657	893	31	1	898	1	CARD8	19	48734067	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73783	48734067	10394916	11235	19220										
ZNF114	163071	broad.mit.edu	37	chr19	48785734	48785734	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacgtgatgctggaaaattCtaggaacttggcattcatag	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:48785734C>A	ENST00000595607.1	+	5	610	c.116C>A	c.(115-117)tCt>tAt	p.S39Y	ZNF114_ENST00000600687.1_Missense_Mutation_p.S39Y|ZNF114_ENST00000597695.1_Missense_Mutation_p.S5Y|ZNF114_ENST00000315849.1_Missense_Mutation_p.S39Y			Q8NC26	ZN114_HUMAN	zinc finger protein 114	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S39Y(1)		endometrium(1)|large_intestine(6)|lung(11)	18		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)		CTGGAAAATTCTAGGAACTTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	19											110	113	112					19																	48785734		2203	4300	6503	53477546	SO:0001583	missense	163071			BC014935	CCDS12713.1, CCDS74412.1	19q13.32	2013-01-08			ENSG00000178150	ENSG00000178150		"Zinc fingers, C2H2-type", "-"	12894	protein-coding gene	gene with protein product		603996					Standard	XM_005258580		Approved	MGC17986	uc002pim.1	Q8NC26		ENST00000595607.1:c.116C>A	19.37:g.48785734C>A	ENSP00000469998:p.Ser39Tyr		53477546	A8K6B0|Q08AQ6	Missense_Mutation	SNP	ENST00000595607.1	37	CCDS12713.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.346069	0.01266	.	.	ENSG00000178150	ENST00000315849	T	0.01234	5.13	2.07	-4.14	0.03892	Krueppel-associated box (4);	.	.	.	.	T	0.00271	0.0008	N	0.00034	-2.56	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44375	-0.9332	9	0.02654	T	1	.	0.0678	0.00019	0.2793:0.18:0.197:0.3436	.	39	Q8NC26	ZN114_HUMAN	Y	39	ENSP00000318898:S39Y	ENSP00000318898:S39Y	S	+	2	0	ZNF114	53477546	0.005000	0.15991	0.000000	0.03702	0.097000	0.18754	0.050000	0.14120	-1.141000	0.02873	0.205000	0.17691	TCT		0.532	ZNF114-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465601.1	NM_153608		A	48785734	C	A	48785734	3	1	61	1	0	0	0	0	1	0	0	0	17755	913	32	2	122	2	ZNF114	19	48785734	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51667	48785734	10343249	11236	19221										
IZUMO1	284359	broad.mit.edu	37	chr19	49247724	49247724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcaccctctttttggaatCgagcaacataggtggcaaag	9	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49247724C>T	ENST00000332955.2	-	4	930	c.383G>A	c.(382-384)cGa>cAa	p.R128Q		NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	128					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R128Q(1)		endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTTTTGGAATCGAGCAACATA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	19											121	113	116					19																	49247724		2203	4300	6503	53939536	SO:0001583	missense	284359			BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"-"	28539	protein-coding gene	gene with protein product	"oocyte binding/fusion factor"	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.383G>A	19.37:g.49247724C>T	ENSP00000327786:p.Arg128Gln		53939536	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	C	1.543	-0.541391	0.04053	.	.	ENSG00000182264	ENST00000332955	T	0.20332	2.08	5.21	-0.817	0.10836	.	1.186920	0.06191	N	0.681367	T	0.07324	0.0185	N	0.04355	-0.22	0.09310	N	1	B	0.18461	0.028	B	0.10450	0.005	T	0.30297	-0.9983	10	0.02654	T	1	-3.767	4.5294	0.11997	0.145:0.35:0.0:0.505	.	128	Q8IYV9	IZUM1_HUMAN	Q	128	ENSP00000327786:R128Q	ENSP00000327786:R128Q	R	-	2	0	IZUMO1	53939536	0.003000	0.15002	0.000000	0.03702	0.122000	0.20287	-0.201000	0.09464	-0.489000	0.06716	-0.367000	0.07326	CGA		0.517	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		T	49247724	C	T	49247724	3	4	61	1	0	0	0	0	1	0	0	0	7954	884	31	1	697	1	IZUMO1	19	49247724	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	461990	49247724	9881259	11237	19222										
FUT1	2523	broad.mit.edu	37	chr19	49253689	49253689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggtgtagcctcctgtccatCgccagcaaacgtcacatcgc	9	16	1	0	rs557041594		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49253689C>T	ENST00000310160.3	-	4	1824	c.850G>A	c.(850-852)Gat>Aat	p.D284N	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	284					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)	p.D284N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		TCCTGTCCATCGCCAGCAAAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											187	135	153					19																	49253689		2203	4300	6503	53945501	SO:0001583	missense	2523				CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.850G>A	19.37:g.49253689C>T	ENSP00000312021:p.Asp284Asn		53945501	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	37	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	0.389	-0.924284	0.02377	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.96587	-4.06	4.56	-3.63	0.04529	.	0.755603	0.11982	N	0.510713	D	0.88529	0.6461	N	0.11892	0.195	0.09310	N	1	B	0.23540	0.087	B	0.21360	0.034	T	0.76572	-0.2910	10	0.12103	T	0.63	-10.5985	12.4069	0.55445	0.0:0.7105:0.0:0.2895	.	284	P19526	FUT1_HUMAN	N	284;274	ENSP00000312021:D284N	ENSP00000312021:D284N	D	-	1	0	FUT1	53945501	0.001000	0.12720	0.001000	0.08648	0.024000	0.10985	-0.373000	0.07494	-0.612000	0.05701	-0.379000	0.06801	GAT		0.572	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		T	49253689	C	T	49253689	3	4	61	1	0	0	0	0	1	0	0	0	6120	884	31	1	251	1	FUT1	19	49253689	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5965	49253689	9875294	11238	19223										
FUT1	2523	broad.mit.edu	37	chr19	49254151	49254151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccacttctggggccagcaCgggcagggtgatgcggaata	16	10	1	1	rs368762099		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49254151C>T	ENST00000310160.3	-	4	1362	c.388G>A	c.(388-390)Gtg>Atg	p.V130M	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	130					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)	p.V130M(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		GGGGCCAGCACGGGCAGGGTG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	MET/VAL	0,4404		0,0,2202	54	63	60		388	2.2	1	19		60	1,8593	1.2+/-3.3	0,1,4296	no	missense	FUT1	NM_000148.3	21	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	130/366	49254151	1,12997	2202	4297	6499	53945963	SO:0001583	missense	2523				CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.388G>A	19.37:g.49254151C>T	ENSP00000312021:p.Val130Met		53945963	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	37	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436731	0.43224	0.0	1.16E-4	ENSG00000174951	ENST00000310160	D	0.97328	-4.34	4.37	2.17	0.27698	.	0.474683	0.17958	N	0.156295	D	0.98027	0.9350	M	0.86420	2.815	0.30071	N	0.810039	D	0.67145	0.996	D	0.65684	0.937	D	0.94939	0.8089	10	0.87932	D	0	-14.0076	9.1092	0.36716	0.0:0.8139:0.0:0.1861	.	130	P19526	FUT1_HUMAN	M	130	ENSP00000312021:V130M	ENSP00000312021:V130M	V	-	1	0	FUT1	53945963	0.874000	0.30092	0.967000	0.41034	0.163000	0.22366	1.541000	0.36126	0.584000	0.29591	0.563000	0.77884	GTG		0.662	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		T	49254151	C	T	49254151	3	4	61	1	0	0	0	0	1	0	0	0	6120	536	19	1	713	1	FUT1	19	49254151	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	462	49254151	9874832	11239	19224										
PLEKHA4	57664	broad.mit.edu	37	chr19	49364745	49364745	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacgctgcctaggacactCtcctcgcggctgtctgcaaa	11	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49364745C>A	ENST00000263265.6	-	5	834	c.279G>T	c.(277-279)gaG>gaT	p.E93D	PLEKHA4_ENST00000596713.1_5'Flank|PLEKHA4_ENST00000355496.5_Missense_Mutation_p.E93D	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	93	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)	p.E93D(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		CTAGGACACTCTCCTCGCGGC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											38	46	43					19																	49364745		2203	4300	6503	54056557	SO:0001583	missense	57664			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.279G>T	19.37:g.49364745C>A	ENSP00000263265:p.Glu93Asp		54056557	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	c	22.3	4.269148	0.80469	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.12774	2.65;2.65	4.56	2.43	0.29744	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000001	T	0.24890	0.0604	L	0.48877	1.53	0.41927	D	0.990542	P;P	0.44627	0.839;0.819	P;P	0.61477	0.873;0.889	T	0.01105	-1.1450	10	0.87932	D	0	.	8.7412	0.34558	0.0:0.8129:0.0:0.187	.	93;93	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	D	93	ENSP00000263265:E93D;ENSP00000347683:E93D	ENSP00000263265:E93D	E	-	3	2	PLEKHA4	54056557	0.988000	0.35896	1.000000	0.80357	0.967000	0.64934	0.647000	0.24812	0.669000	0.31146	0.457000	0.33378	GAG		0.632	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			A	49364745	C	A	49364745	3	1	61	1	0	0	0	0	1	0	0	0	12089	912	32	2	2124	2	PLEKHA4	19	49364745	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	110594	49364745	9764238	11240	19225										
PPP1R15A	23645	broad.mit.edu	37	chr19	49377853	49377853	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggatagtgaggataaggaaGatgattcagaagcagccttg	14	4	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49377853G>A	ENST00000200453.5	+	2	1632	c.1363G>A	c.(1363-1365)Gat>Aat	p.D455N		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	455	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)	p.D455N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GGATAAGGAAGATGATTCAGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											76	76	76					19																	49377853		2203	4300	6503	54069665	SO:0001583	missense	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1363G>A	19.37:g.49377853G>A	ENSP00000200453:p.Asp455Asn		54069665	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.397016	0.42512	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.07114	3.22	4.19	-0.967	0.10316	.	4.230020	0.01115	N	0.005679	T	0.07234	0.0183	L	0.40543	1.245	0.09310	N	1	B	0.18310	0.027	B	0.17722	0.019	T	0.31447	-0.9943	10	0.18710	T	0.47	6.3949	2.616	0.04903	0.0964:0.1594:0.417:0.3271	.	455	O75807	PR15A_HUMAN	N	455;295;413	ENSP00000200453:D455N	ENSP00000200453:D455N	D	+	1	0	PPP1R15A	54069665	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.225000	0.17757	-0.134000	0.11516	-0.302000	0.09304	GAT		0.572	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49377853	G	A	49377853	3	1	61	1	0	0	0	0	1	0	0	0	12397	942	33	3	1365	3	PPP1R15A	19	49377853	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13108	49377853	9751130	11241	19226										
TULP2	7288	broad.mit.edu	37	chr19	49391471	49391471	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtgtgctgctgaggagttCgtccctgtagactcagaggc	14	9	1	3	rs369432743		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49391471C>T	ENST00000221399.3	-	8	828	c.684G>A	c.(682-684)acG>acA	p.T228T		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	228					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.T228T(1)		NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CTGAGGAGTTCGTCCCTGTAG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	91	65	73		684	-4.8	0	19		73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TULP2	NM_003323.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		228/521	49391471	1,13005	2203	4300	6503	54083283	SO:0001819	synonymous_variant	7288			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.684G>A	19.37:g.49391471C>T			54083283	Q8TC50	Silent	SNP	ENST00000221399.3	37	CCDS12739.1																																																																																				0.562	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		T	49391471	C	T	49391471	2	4	61	1	0	0	0	0	0	0	0	1	16814	871	31	1		1	TULP2	19	49391471	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13618	49391471	9737512	11242	19227										
NUCB1	4924	broad.mit.edu	37	chr19	49404075	49404075	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctccctctgggccccgaGgaaccctccttctgttgccg	10	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49404075G>T	ENST00000405315.4	+	2	356	c.22G>T	c.(22-24)Gga>Tga	p.G8*	NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000407032.1_Nonsense_Mutation_p.G8*|NUCB1_ENST00000263273.5_Nonsense_Mutation_p.G8*|TULP2_ENST00000221399.3_5'Flank	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	8						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)	p.G8*(1)		cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		TGGGCCCCGAGGAACCCTCCT	0.652																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											66	51	56					19																	49404075		2203	4300	6503	54095887	SO:0001587	stop_gained	4924			BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.22G>T	19.37:g.49404075G>T	ENSP00000385923:p.Gly8*		54095887	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Nonsense_Mutation	SNP	ENST00000405315.4	37	CCDS12740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.73|15.73	2.919953|2.919953	0.52653|0.52653	.|.	.|.	ENSG00000104805|ENSG00000104805	ENST00000424608|ENST00000405315;ENST00000407032;ENST00000452087;ENST00000411700;ENST00000451312;ENST00000263273	.|.	.|.	.|.	4.08|4.08	-2.34|-2.34	0.06704|0.06704	.|.	.|2.229330	.|0.02019	.|N	.|0.047612	T|.	0.26159|.	0.0638|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.18147|.	-1.0346|.	3|.	.|0.41790	.|T	.|0.15	.|.	4.3321|4.3321	0.11069|0.11069	0.2916:0.3096:0.3988:0.0|0.2916:0.3096:0.3988:0.0	.|.	.|.	.|.	.|.	D|X	7|8	.|.	.|ENSP00000263273:G8X	E|G	+|+	3|1	2|0	NUCB1|NUCB1	54095887|54095887	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.131000|0.131000	0.20780|0.20780	0.270000|0.270000	0.18607|0.18607	-0.246000|-0.246000	0.09611|0.09611	0.549000|0.549000	0.68633|0.68633	GAG|GGA		0.652	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		T	49404075	G	T	49404075	4	4	61	1	0	0	0	0	0	1	0	0	10749	1001	35	2	24	2	NUCB1	19	49404075	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12604	49404075	9724908	11243	19228										
GYS1	2997	broad.mit.edu	37	chr19	49485577	49485577	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacccttgttggagaactCatagcggccggcgataaaga	12	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49485577C>A	ENST00000323798.3	-	7	1193	c.997G>T	c.(997-999)Gag>Tag	p.E333*	GYS1_ENST00000544287.1_5'UTR|GYS1_ENST00000540532.1_Missense_Mutation_p.M213I|GYS1_ENST00000541188.1_Nonsense_Mutation_p.E253*|GYS1_ENST00000263276.6_Nonsense_Mutation_p.E269*	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	333					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)	p.E333*(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		TTGGAGAACTCATAGCGGCCG	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											105	94	97					19																	49485577		2203	4300	6503	54177389	SO:0001587	stop_gained	2997				CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.997G>T	19.37:g.49485577C>A	ENSP00000317904:p.Glu333*		54177389	Q9BTT9	Nonsense_Mutation	SNP	ENST00000323798.3	37	CCDS12747.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	7.992054|7.992054	0.98599|0.98599	.|.	.|.	ENSG00000104812|ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188|ENST00000540532	.|T	.|0.21932	.|1.98	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.38214	.|0.1032	.|.	.|.	.|.	0.35151|0.35151	D|D	0.769791|0.769791	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.43814	.|-0.9368	.|6	0.87932|0.45353	D|T	0|0.12	-30.539|-30.539	16.6519|16.6519	0.85218|0.85218	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	333;269;253|213	.|ENSP00000445197:M213I	ENSP00000263276:E269X|ENSP00000445197:M213I	E|M	-|-	1|3	0|0	GYS1|GYS1	54177389|54177389	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.988000|0.988000	0.76386|0.76386	7.403000|7.403000	0.79983|0.79983	2.613000|2.613000	0.88420|0.88420	0.650000|0.650000	0.86243|0.86243	GAG|ATG		0.552	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		A	49485577	C	A	49485577	4	1	61	1	0	0	0	0	0	1	0	0	6933	835	29	2	1256	2	GYS1	19	49485577	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81502	49485577	9643406	11244	19229										
SNRNP70	6625	broad.mit.edu	37	chr19	49589812	49589812	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcgccgtacattcgagaGtttgaggtgagttcactgag	13	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49589812G>T	ENST00000598441.1	+	2	365	c.141G>T	c.(139-141)gaG>gaT	p.E47D	SNRNP70_ENST00000221448.5_Missense_Mutation_p.E47D			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	47					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E47D(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						ACATTCGAGAGTTTGAGGTGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19											182	178	179					19																	49589812		2203	4300	6503	54281624	SO:0001583	missense	6625				CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"RNA binding motif (RRM) containing"	11150	protein-coding gene	gene with protein product		180740	"small nuclear ribonucleoprotein 70kDa (RNP antigen)"	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.141G>T	19.37:g.49589812G>T	ENSP00000472998:p.Glu47Asp		54281624	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Missense_Mutation	SNP	ENST00000598441.1	37	CCDS12756.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.574984	0.45902	.	.	ENSG00000104852	ENST00000221448;ENST00000401730	T	0.16073	2.37	4.9	0.0252	0.14144	.	0.193064	0.43579	D	0.000548	T	0.11879	0.0289	L	0.33485	1.01	0.80722	D	1	B;B	0.23937	0.058;0.094	B;B	0.32342	0.144;0.032	T	0.18967	-1.0320	10	0.16420	T	0.52	-10.6801	8.8285	0.35069	0.517:0.0:0.483:0.0	.	47;47	P08621;P08621-2	RU17_HUMAN;.	D	47	ENSP00000221448:E47D	ENSP00000221448:E47D	E	+	3	2	SNRNP70	54281624	0.981000	0.34729	0.997000	0.53966	0.995000	0.86356	0.139000	0.16036	-0.075000	0.12798	0.561000	0.74099	GAG		0.537	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089		T	49589812	G	T	49589812	3	4	61	1	0	0	0	0	1	0	0	0	14895	1020	36	2	143	2	SNRNP70	19	49589812	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104235	49589812	9539171	11245	19230										
SNRNP70	6625	broad.mit.edu	37	chr19	49593555	49593555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttgttcccaggaccctcGagatgcccctcctccaactc	6	18	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49593555G>A	ENST00000598441.1	+	3	379	c.155G>A	c.(154-156)cGa>cAa	p.R52Q	SNRNP70_ENST00000221448.5_Missense_Mutation_p.R52Q			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	52					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R52Q(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						CAGGACCCTCGAGATGCCCCT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	71	75					19																	49593555		2203	4300	6503	54285367	SO:0001583	missense	6625				CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"RNA binding motif (RRM) containing"	11150	protein-coding gene	gene with protein product		180740	"small nuclear ribonucleoprotein 70kDa (RNP antigen)"	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.155G>A	19.37:g.49593555G>A	ENSP00000472998:p.Arg52Gln		54285367	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Missense_Mutation	SNP	ENST00000598441.1	37	CCDS12756.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.392554	0.62066	.	.	ENSG00000104852	ENST00000221448;ENST00000401730	T	0.14516	2.5	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	L	0.44542	1.39	0.80722	D	1	B;B	0.32365	0.258;0.367	B;B	0.25614	0.062;0.028	T	0.09037	-1.0693	10	0.20046	T	0.44	-3.8141	18.5311	0.90992	0.0:0.0:1.0:0.0	.	52;52	P08621;P08621-2	RU17_HUMAN;.	Q	52	ENSP00000221448:R52Q	ENSP00000221448:R52Q	R	+	2	0	SNRNP70	54285367	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.929000	0.75852	2.756000	0.94617	0.561000	0.74099	CGA		0.542	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089		A	49593555	G	A	49593555	3	1	61	1	0	0	0	0	1	0	0	0	14895	1058	37	1	161	1	SNRNP70	19	49593555	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3743	49593555	9535428	11246	19231										
SLC6A16	28968	broad.mit.edu	37	chr19	49796494	49796494	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcacctcctggccccataGgcccaggatacagccatggt	9	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49796494G>T	ENST00000335875.4	-	10	2005	c.1764C>A	c.(1762-1764)gcC>gcA	p.A588A	SLC6A16_ENST00000454748.3_Silent_p.A588A	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	588					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A588A(1)		NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		TGGCCCCATAGGCCCAGGATA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	19											65	66	65					19																	49796494		1934	4144	6078	54488306	SO:0001819	synonymous_variant	28968			AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.1764C>A	19.37:g.49796494G>T			54488306	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																				0.517	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		T	49796494	G	T	49796494	2	4	61	1	0	0	0	0	0	0	0	1	14716	987	35	2		2	SLC6A16	19	49796494	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202939	49796494	9332489	11247	19232										
SLC6A16	28968	broad.mit.edu	37	chr19	49812193	49812193	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggacacagaagttgaaaGatgtgaaaaccaacaaagtg	10	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49812193G>T	ENST00000335875.4	-	7	1410	c.1169C>A	c.(1168-1170)tCt>tAt	p.S390Y	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Missense_Mutation_p.S390Y	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	390					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)	p.S390Y(1)		NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		GAAGTTGAAAGATGTGAAAAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	19											105	101	103					19																	49812193		2025	4178	6203	54504005	SO:0001583	missense	28968			AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.1169C>A	19.37:g.49812193G>T	ENSP00000338627:p.Ser390Tyr		54504005	Q8IYV4|Q9Y5I9	Missense_Mutation	SNP	ENST00000335875.4	37	CCDS42590.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282602	0.40394	.	.	ENSG00000063127	ENST00000335875;ENST00000454748	T;T	0.73897	-0.79;-0.79	4.27	-1.53	0.08611	.	0.782162	0.11924	N	0.516412	T	0.75064	0.3799	L	0.39898	1.24	0.09310	N	1	D;D	0.63880	0.993;0.993	P;P	0.62089	0.898;0.854	T	0.65664	-0.6113	10	0.72032	D	0.01	.	8.3775	0.32451	0.5621:0.0:0.4379:0.0	.	390;390	Q8IYV4;Q9GZN6	.;S6A16_HUMAN	Y	390	ENSP00000338627:S390Y;ENSP00000404022:S390Y	ENSP00000338627:S390Y	S	-	2	0	SLC6A16	54504005	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.766000	0.26560	-0.130000	0.11599	-0.291000	0.09656	TCT		0.522	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		T	49812193	G	T	49812193	3	4	61	1	0	0	0	0	1	0	0	0	14716	942	33	2	1065	2	SLC6A16	19	49812193	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15699	49812193	9316790	11248	19233										
TEAD2	8463	broad.mit.edu	37	chr19	49858608	49858608	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtttggcctgcagagaaggCgcggagatgagctgggcaga	18	7	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49858608C>T	ENST00000311227.2	-	5	519	c.429G>A	c.(427-429)gcG>gcA	p.A143A	TEAD2_ENST00000539846.1_Silent_p.A12A|TEAD2_ENST00000601519.1_Silent_p.A143A|TEAD2_ENST00000598810.1_Silent_p.A147A|TEAD2_ENST00000598397.1_5'UTR|TEAD2_ENST00000377214.4_Silent_p.A143A|AC010524.4_ENST00000596488.1_RNA|TEAD2_ENST00000593945.1_Silent_p.A147A	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	143					gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P144fs*15(1)|p.A143A(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GCAGAGAAGGCGCGGAGATGA	0.607																																																2	Deletion - Frameshift(1)|Substitution - coding silent(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	19											116	97	103					19																	49858608		2203	4300	6503	54550420	SO:0001819	synonymous_variant	8463			X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.429G>A	19.37:g.49858608C>T			54550420	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Silent	SNP	ENST00000311227.2	37	CCDS12761.1																																																																																				0.607	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598		T	49858608	C	T	49858608	2	4	61	1	0	0	0	0	0	0	0	1	15778	755	27	1		1	TEAD2	19	49858608	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46415	49858608	9270375	11249	19234										
DKKL1	27120	broad.mit.edu	37	chr19	49868900	49868900	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctccagccacctccagatCgacaaggtgcctatgcaggg	10	15	1	1	rs34625472	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49868900C>T	ENST00000221498.2	+	3	723	c.318C>T	c.(316-318)atC>atT	p.I106I	DKKL1_ENST00000594268.1_Intron	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	106					anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)	p.I106I(1)		large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		ACCTCCAGATCGACAAGGTGC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19											87	78	81					19																	49868900		2203	4300	6503	54560712	SO:0001819	synonymous_variant	27120			AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"cancer/testis antigen 34", "soggy"	605418	"dickkopf-like 1 (soggy)"			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.318C>T	19.37:g.49868900C>T			54560712		Silent	SNP	ENST00000221498.2	37	CCDS12762.1																																																																																				0.617	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419		T	49868900	C	T	49868900	2	4	61	1	0	0	0	0	0	0	0	1	4559	874	31	1		1	DKKL1	19	49868900	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10292	49868900	9260083	11250	19235										
PIH1D1	55011	broad.mit.edu	37	chr19	49951296	49951296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcgctgttgacagctacgtCgtaggcggtacatccctggc	13	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:49951296C>T	ENST00000262265.5	-	4	596	c.361G>A	c.(361-363)Gac>Aac	p.D121N	PIH1D1_ENST00000596049.1_Missense_Mutation_p.D121N|PIH1D1_ENST00000602226.1_5'Flank	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	121					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)		p.D121N(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		ACAGCTACGTCGTAGGCGGTA	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	46	49					19																	49951296		2203	4300	6503	54643108	SO:0001583	missense	55011			AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.361G>A	19.37:g.49951296C>T	ENSP00000262265:p.Asp121Asn		54643108	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.452992	0.84209	.	.	ENSG00000104872	ENST00000262265	T	0.54479	0.57	4.68	4.68	0.58851	.	0.052908	0.64402	D	0.000001	T	0.73900	0.3646	M	0.87328	2.875	0.50813	D	0.999899	D	0.89917	1.0	D	0.70935	0.971	T	0.78745	-0.2084	10	0.72032	D	0.01	-32.0351	12.9694	0.58503	0.0:1.0:0.0:0.0	.	121	Q9NWS0	PIHD1_HUMAN	N	121	ENSP00000262265:D121N	ENSP00000262265:D121N	D	-	1	0	PIH1D1	54643108	1.000000	0.71417	0.991000	0.47740	0.837000	0.47467	4.411000	0.59781	2.423000	0.82170	0.655000	0.94253	GAC		0.657	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		T	49951296	C	T	49951296	3	4	61	1	0	0	0	0	1	0	0	0	11937	884	31	1	535	1	PIH1D1	19	49951296	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82396	49951296	9177687	11251	19236										
TSKS	60385	broad.mit.edu	37	chr19	50245144	50245144	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccatattccctggtaccaGaatcttcttgtgtagcctct	7	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50245144G>T	ENST00000246801.3	-	9	1577	c.1495C>A	c.(1495-1497)Ctg>Atg	p.L499M	TSKS_ENST00000358830.3_Missense_Mutation_p.L299M	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	499					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.L499M(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CCTGGTACCAGAATCTTCTTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											143	125	131					19																	50245144		2203	4300	6503	54936956	SO:0001583	missense	60385			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1495C>A	19.37:g.50245144G>T	ENSP00000246801:p.Leu499Met		54936956	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921961	0.52653	.	.	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.38077	1.16;1.16	4.43	4.43	0.53597	.	0.000000	0.41823	D	0.000810	T	0.45377	0.1339	L	0.29908	0.895	0.31664	N	0.645226	D	0.76494	0.999	D	0.85130	0.997	T	0.45527	-0.9255	10	0.35671	T	0.21	-17.2533	12.72	0.57137	0.0:0.0:1.0:0.0	.	499	Q9UJT2	TSKS_HUMAN	M	499;299	ENSP00000246801:L499M;ENSP00000351691:L299M	ENSP00000246801:L499M	L	-	1	2	TSKS	54936956	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	4.370000	0.59517	2.446000	0.82766	0.462000	0.41574	CTG		0.582	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50245144	G	T	50245144	3	4	61	1	0	0	0	0	1	0	0	0	16666	933	33	2	295	2	TSKS	19	50245144	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	293848	50245144	8883839	11252	19237										
TSKS	60385	broad.mit.edu	37	chr19	50247577	50247577	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagttctgaaattgccgcccGaactcctccagaatgggttt	10	11	1	2	rs149069102		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50247577G>A	ENST00000246801.3	-	8	1354	c.1272C>T	c.(1270-1272)ttC>ttT	p.F424F	TSKS_ENST00000358830.3_Silent_p.F224F	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	424					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.F424fs*11(2)|p.F424F(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ATTGCCGCCCGAACTCCTCCA	0.602																																																4	Deletion - Frameshift(2)|Substitution - coding silent(2)	large_intestine(2)|breast(2)	19						G		0,4406		0,0,2203	78	70	73		1272	-1.3	1	19	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TSKS	NM_021733.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		424/593	50247577	1,13005	2203	4300	6503	54939389	SO:0001819	synonymous_variant	60385			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1272C>T	19.37:g.50247577G>A			54939389	Q8WXJ0	Silent	SNP	ENST00000246801.3	37	CCDS12780.1																																																																																				0.602	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		A	50247577	G	A	50247577	2	1	61	1	0	0	0	0	0	0	0	1	16666	1049	37	1		1	TSKS	19	50247577	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2433	50247577	8881406	11253	19238										
IL4I1	259307	broad.mit.edu	37	chr19	50394668	50394668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatccccacttaccaagagCgtgtgcctttcaaacttctt	6	13	2	2	rs369542657		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50394668C>T	ENST00000391826.2	-	6	772	c.630G>A	c.(628-630)acG>acA	p.T210T	IL4I1_ENST00000595948.1_Silent_p.T232T|IL4I1_ENST00000341114.3_Silent_p.T232T	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	210						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)	p.T232T(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	TTACCAAGAGCGTGTGCCTTT	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19											234	180	198					19																	50394668		2203	4300	6503	55086480	SO:0001819	synonymous_variant	259307			AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.630G>A	19.37:g.50394668C>T			55086480	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																				0.562	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			T	50394668	C	T	50394668	2	4	61	1	0	0	0	0	0	0	0	1	7718	755	27	1		1	IL4I1	19	50394668	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147091	50394668	8734315	11254	19239										
IL4I1	259307	broad.mit.edu	37	chr19	50399151	50399151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacaatcaccctctggggcTtcagggtccgattgagcccc	10	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50399151T>C	ENST00000391826.2	-	3	315	c.173A>G	c.(172-174)aAg>aGg	p.K58R	IL4I1_ENST00000595948.1_Missense_Mutation_p.K80R|IL4I1_ENST00000341114.3_Missense_Mutation_p.K80R	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	58						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)	p.K80R(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	CCTCTGGGGCTTCAGGGTCCG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											108	113	111					19																	50399151		2203	4300	6503	55090963	SO:0001583	missense	259307			AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.173A>G	19.37:g.50399151T>C	ENSP00000375702:p.Lys58Arg		55090963	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	37	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	T	6.645	0.487441	0.12641	.	.	ENSG00000104951	ENST00000341114;ENST00000391826	T;T	0.34859	1.34;1.36	5.18	1.45	0.22620	.	0.941599	0.08972	N	0.867035	T	0.21103	0.0508	L	0.32530	0.975	0.09310	N	0.999998	B;B;B	0.16396	0.017;0.002;0.002	B;B;B	0.12156	0.007;0.003;0.003	T	0.30563	-0.9974	10	0.18276	T	0.48	-17.2856	0.457	0.00510	0.2173:0.1374:0.2247:0.4206	.	80;80;58	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	R	80;58	ENSP00000342557:K80R;ENSP00000375702:K58R	ENSP00000342557:K80R	K	-	2	0	IL4I1	55090963	0.001000	0.12720	0.334000	0.25495	0.291000	0.27294	-0.189000	0.09629	0.263000	0.21812	0.443000	0.29094	AAG		0.607	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			C	50399151	T	C	50399151	3	2	61	1	0	0	0	0	1	0	0	0	7718	1609	56	4	1554	4	IL4I1	19	50399151	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4483	50399151	8729832	11255	19240										
NUP62	23636	broad.mit.edu	37	chr19	50411700	50411700	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggacgtgttcaggtgctcGatgatgtccttgagatcctg	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50411700G>A	ENST00000596217.1	-	2	3252	c.1365C>T	c.(1363-1365)atC>atT	p.I455I	NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000597029.1_Silent_p.I455I|NUP62_ENST00000413454.1_Silent_p.I455I|NUP62_ENST00000422090.2_Silent_p.I455I|IL4I1_ENST00000595948.1_Intron|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.I455I|NUP62_ENST00000597723.1_Silent_p.I379I			P37198	NUP62_HUMAN	nucleoporin 62kDa	455					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)	p.I455I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TCAGGTGCTCGATGATGTCCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											181	164	170					19																	50411700		2203	4300	6503	55103512	SO:0001819	synonymous_variant	23636			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.1365C>T	19.37:g.50411700G>A			55103512	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																				0.587	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		A	50411700	G	A	50411700	2	1	61	1	0	0	0	0	0	0	0	1	10799	1048	37	1		1	NUP62	19	50411700	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12549	50411700	8717283	11256	19241										
SIGLEC11	114132	broad.mit.edu	37	chr19	50455574	50455574	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaagacgacaaggcaggAacagaaagcgagcagggcag	15	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50455574A>G	ENST00000447370.2	-	9	1819	c.1729T>C	c.(1729-1731)Tcc>Ccc	p.S577P	SIGLEC11_ENST00000426971.2_Missense_Mutation_p.S481P|U3_ENST00000408198.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	577					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.S565P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		ACAAGGCAGGAACAGAAAGCG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	81	81					19																	50455574		2203	4300	6503	55147386	SO:0001583	missense	114132			AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1729T>C	19.37:g.50455574A>G	ENSP00000412361:p.Ser577Pro		55147386		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	.	.	.	.	.	.	.	.	.	.	A	5.651	0.304747	0.10678	.	.	ENSG00000161640	ENST00000447370;ENST00000458019	T	0.53206	0.63	2.49	-4.97	0.03029	.	1.568680	0.03851	N	0.272311	T	0.26666	0.0652	L	0.34521	1.04	0.09310	N	1	B;P	0.38110	0.001;0.618	B;B	0.28553	0.001;0.091	T	0.09975	-1.0650	10	0.51188	T	0.08	.	0.2811	0.00245	0.2811:0.1567:0.3134:0.2488	.	481;577	Q96RL6-2;Q96RL6	.;SIG11_HUMAN	P	577;481	ENSP00000412361:S577P	ENSP00000412361:S577P	S	-	1	0	SIGLEC11	55147386	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.432000	0.06956	-2.843000	0.00334	0.379000	0.24179	TCC		0.627	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		G	50455574	A	G	50455574	3	3	61	1	0	0	0	0	1	0	0	0	14344	246	9	4	379	4	SIGLEC11	19	50455574	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	43874	50455574	8673409	11257	19242										
SIGLEC11	114132	broad.mit.edu	37	chr19	50462304	50462304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctgtcctgtttgcttggGaaaccatcactctcaggttc	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50462304G>A	ENST00000447370.2	-	6	1178	c.1088C>T	c.(1087-1089)tCc>tTc	p.S363F	SIGLEC11_ENST00000426971.2_Missense_Mutation_p.S363F|CTC-326K19.6_ENST00000451973.1_5'Flank	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	363	Ig-like C2-type 3.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.S351F(2)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		GTTTGCTTGGGAAACCATCAC	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	19											76	78	77					19																	50462304		2203	4297	6500	55154116	SO:0001583	missense	114132			AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1088C>T	19.37:g.50462304G>A	ENSP00000412361:p.Ser363Phe		55154116		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.87|14.87	2.664451|2.664451	0.47572|0.47572	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000426971|ENST00000447370;ENST00000458019	.|T	.|0.56941	.|0.43	2.33|2.33	-0.443|-0.443	0.12249|0.12249	.|Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.942626	.|0.08751	.|N	.|0.899091	T|T	0.45458|0.45458	0.1343|0.1343	N|N	0.17800|0.17800	0.525|0.525	0.09310|0.09310	N|N	1|1	.|D;D	.|0.67145	.|0.996;0.986	.|D;D	.|0.69654	.|0.965;0.923	T|T	0.42849|0.42849	-0.9427|-0.9427	5|10	.|0.09084	.|T	.|0.74	.|.	2.366|2.366	0.04319|0.04319	0.188:0.0:0.5184:0.2936|0.188:0.0:0.5184:0.2936	.|.	.|363;363	.|Q96RL6-2;Q96RL6	.|.;SIG11_HUMAN	S|F	353|363	.|ENSP00000412361:S363F	.|ENSP00000412361:S363F	P|S	-|-	1|2	0|0	SIGLEC11|SIGLEC11	55154116|55154116	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.863000|0.863000	0.49368|0.49368	-0.512000|-0.512000	0.06313|0.06313	0.268000|0.268000	0.21939|0.21939	-0.265000|-0.265000	0.10407|0.10407	CCC|TCC		0.582	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		A	50462304	G	A	50462304	3	1	61	1	0	0	0	0	1	0	0	0	14344	1174	41	3	1032	3	SIGLEC11	19	50462304	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6730	50462304	8666679	11258	19243										
ZNF473	25888	broad.mit.edu	37	chr19	50549648	50549648	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacccttttaaatgtaacGaatgcggaaagaccttcagc	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50549648G>A	ENST00000595661.1	+	6	2443	c.1948G>A	c.(1948-1950)Gaa>Aaa	p.E650K	ZNF473_ENST00000270617.3_Missense_Mutation_p.E650K|ZNF473_ENST00000601364.1_Intron|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000445728.3_Missense_Mutation_p.E638K|ZNF473_ENST00000391821.2_Missense_Mutation_p.E650K|CTD-2126E3.3_ENST00000599914.1_RNA			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	650					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E650K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		TAAATGTAACGAATGCGGAAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	19											75	70	71					19																	50549648		2203	4300	6503	55241460	SO:0001583	missense	25888			AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.1948G>A	19.37:g.50549648G>A	ENSP00000472808:p.Glu650Lys		55241460	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	37	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772596	0.31411	.	.	ENSG00000142528	ENST00000270617;ENST00000391821;ENST00000445728	T;T;T	0.61274	0.12;0.12;0.12	3.98	-3.78	0.04333	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.678532	0.12877	N	0.431794	T	0.44623	0.1302	L	0.53729	1.69	0.09310	N	1	B	0.17038	0.02	B	0.12837	0.008	T	0.38735	-0.9647	10	0.52906	T	0.07	-0.002	5.9296	0.19132	0.462:0.1332:0.4049:0.0	.	650	Q8WTR7	ZN473_HUMAN	K	650;650;638	ENSP00000270617:E650K;ENSP00000375697:E650K;ENSP00000388961:E638K	ENSP00000270617:E650K	E	+	1	0	ZNF473	55241460	0.000000	0.05858	0.000000	0.03702	0.883000	0.51084	-0.729000	0.04920	-0.595000	0.05828	-0.320000	0.08662	GAA		0.453	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		A	50549648	G	A	50549648	3	1	61	1	0	0	0	0	1	0	0	0	17970	1059	37	1	1962	1	ZNF473	19	50549648	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	87344	50549648	8579335	11259	19244										
MYH14	79784	broad.mit.edu	37	chr19	50784973	50784973	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctggcagaaaagacagaGaccgtggatcggctggagcg	16	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50784973G>T	ENST00000596571.1	+	30	4290	c.4290G>T	c.(4288-4290)gaG>gaT	p.E1430D	MYH14_ENST00000440075.2_Missense_Mutation_p.E1471D|MYH14_ENST00000262269.8_Missense_Mutation_p.E1471D|MYH14_ENST00000376970.2_Missense_Mutation_p.E1463D|MYH14_ENST00000601313.1_Missense_Mutation_p.E1471D|MYH14_ENST00000598205.1_Missense_Mutation_p.E1438D|MYH14_ENST00000425460.1_Missense_Mutation_p.E1438D			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1430					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.E1471D(1)|p.E1430D(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		AAAAGACAGAGACCGTGGATC	0.726																																																2	Substitution - Missense(2)	large_intestine(2)	19											11	16	15					19																	50784973		1952	4065	6017	55476785	SO:0001583	missense	79784			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4290G>T	19.37:g.50784973G>T	ENSP00000472819:p.Glu1430Asp		55476785	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.656842	0.29425	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000262269	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	3.75	1.58	0.23477	Myosin tail (1);	.	.	.	.	T	0.78496	0.4292	L	0.29908	0.895	0.09310	N	1	P;P;P	0.45474	0.859;0.542;0.486	P;B;B	0.48189	0.57;0.388;0.356	T	0.68780	-0.5318	9	0.87932	D	0	.	2.6745	0.05077	0.2578:0.0:0.515:0.2272	.	1471;1430;1438	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	D	1430;1471;1463;1438;1471	ENSP00000406273:E1471D;ENSP00000366169:E1463D;ENSP00000407879:E1438D;ENSP00000262269:E1471D	ENSP00000262269:E1471D	E	+	3	2	MYH14	55476785	0.000000	0.05858	0.192000	0.23308	0.951000	0.60555	-0.817000	0.04472	0.905000	0.36596	0.555000	0.69702	GAG		0.726	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50784973	G	T	50784973	3	4	61	1	0	0	0	0	1	0	0	0	10063	933	33	2	4539	2	MYH14	19	50784973	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	235325	50784973	8344010	11260	19245										
NAPSA	9476	broad.mit.edu	37	chr19	50865456	50865456	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttcgagagaggtacgaaGatgggcttgtccccagggga	16	7	0	2	rs199668068		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50865456G>T	ENST00000253719.2	-	2	406	c.198C>A	c.(196-198)atC>atA	p.I66I	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	66					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)	p.I66I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		GAGGTACGAAGATGGGCTTGT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											72	63	66					19																	50865456		2203	4300	6503	55557268	SO:0001819	synonymous_variant	9476			AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"kidney-derived aspartic protease-like protein"	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.198C>A	19.37:g.50865456G>T			55557268	Q8WWD9	Silent	SNP	ENST00000253719.2	37	CCDS12794.1																																																																																				0.587	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851		T	50865456	G	T	50865456	2	4	61	1	0	0	0	0	0	0	0	1	10196	932	33	2		2	NAPSA	19	50865456	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	80483	50865456	8263527	11261	19246										
MYBPC2	4606	broad.mit.edu	37	chr19	50964828	50964828	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtctatgaacgtaacagGcacactagctgtactgtgtc	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:50964828G>A	ENST00000357701.5	+	25	3012	c.2961G>A	c.(2959-2961)agG>agA	p.R987R		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	987	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R987R(1)		breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		AACGTAACAGGCACACTAGCT	0.527											OREG0025636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	19											109	105	106					19																	50964828		2063	4212	6275	55656640	SO:0001819	synonymous_variant	4606				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2961G>A	19.37:g.50964828G>A		973	55656640	A1L4G9	Silent	SNP	ENST00000357701.5	37	CCDS46152.1																																																																																				0.527	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		A	50964828	G	A	50964828	2	1	61	1	0	0	0	0	0	0	0	1	10042	1194	42	3		3	MYBPC2	19	50964828	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99372	50964828	8164155	11262	19247										
KLK2	3817	broad.mit.edu	37	chr19	51379920	51379920	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagagcctgccaagatcacAgatgttgtgaaggtcctggg	13	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51379920A>C	ENST00000325321.3	+	3	624	c.399A>C	c.(397-399)acA>acC	p.T133T	KLK2_ENST00000391810.2_Silent_p.T31T|AC037199.1_ENST00000594218.1_5'Flank|KLK2_ENST00000358049.4_Silent_p.T133T			P20151	KLK2_HUMAN	kallikrein-related peptidase 2	133	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)	p.T133T(1)	KLK2/ETV1(3)|KLK2/ETV4(2)	large_intestine(3)|lung(6)|ovary(1)|skin(1)	11		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)		CCAAGATCACAGATGTTGTGA	0.577			T	ETV4	prostate																																		Dom	yes		19	19q13.41	3817	kallikrein-related peptidase 2		E	1	Substitution - coding silent(1)	large_intestine(1)	19											59	55	57					19																	51379920		2203	4300	6503	56071732	SO:0001819	synonymous_variant	3817			M18157	CCDS12808.1, CCDS42597.1, CCDS58675.1	19q13.33	2008-02-05	2006-10-27				3.4.21.35	"Kallikreins"	6363	protein-coding gene	gene with protein product		147960	"kallikrein 2, prostatic"			2468530, 16800724, 16800723	Standard	NM_005551		Approved		uc002ptv.3	P20151		ENST00000325321.3:c.399A>C	19.37:g.51379920A>C			56071732	B4DU93|B4DUB0|F5H8L3|Q15946|Q9UJZ9	Silent	SNP	ENST00000325321.3	37	CCDS12808.1																																																																																				0.577	KLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464438.3	NM_005551.3		C	51379920	A	C	51379920	2	2	61	1	0	0	0	0	0	0	0	1	8425	175	7	4		4	KLK2	19	51379920	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	415092	51379920	7749063	11263	19248										
KLK4	9622	broad.mit.edu	37	chr19	51411894	51411894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccgcggtagggcactgcGaagcaatgctgatgctccgg	14	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51411894G>A	ENST00000324041.1	-	3	415	c.416C>T	c.(415-417)tCg>tTg	p.S139L	KLK4_ENST00000431178.2_Missense_Mutation_p.S90L|KLK4_ENST00000597441.1_5'Flank	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	139	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S139L(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		AGGGCACTGCGAAGCAATGCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											116	86	96					19																	51411894		2203	4300	6503	56103706	SO:0001583	missense	9622			AF113141	CCDS12809.1	19q13.41	2014-09-04	2006-10-27		ENSG00000167749	ENSG00000167749		"Kallikreins", "Serine peptidases / Serine peptidases"	6365	protein-coding gene	gene with protein product		603767	"kallikrein 4 (prostase, enamel matrix, prostate)"	PRSS17		10077646, 10438493, 16800724, 10863090, 9465170	Standard	XM_005259441		Approved	EMSP, EMSP1, PSTS, KLK-L1	uc002pua.1	Q9Y5K2	OTTHUMG00000182964	ENST00000324041.1:c.416C>T	19.37:g.51411894G>A	ENSP00000326159:p.Ser139Leu		56103706	Q4VB16|Q96RU5|Q9GZL6|Q9UBJ6	Missense_Mutation	SNP	ENST00000324041.1	37	CCDS12809.1	.	.	.	.	.	.	.	.	.	.	a	15.83	2.950468	0.53186	.	.	ENSG00000167749	ENST00000324041;ENST00000431178	D;D	0.89415	-2.51;-2.51	3.97	2.93	0.34026	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.480647	0.15950	N	0.236787	D	0.91710	0.7379	L	0.55103	1.725	0.09310	N	1	D;D	0.76494	0.999;0.998	D;D	0.65684	0.937;0.909	D	0.84162	0.0429	10	0.56958	D	0.05	.	12.2105	0.54377	0.0969:0.0:0.9031:0.0	.	90;139	Q96JD7;Q9Y5K2	.;KLK4_HUMAN	L	139;90	ENSP00000326159:S139L;ENSP00000399448:S90L	ENSP00000326159:S139L	S	-	2	0	KLK4	56103706	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	0.509000	0.22707	0.466000	0.27193	-0.945000	0.02674	TCG		0.587	KLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464449.1	NM_004917		A	51411894	G	A	51411894	3	1	61	1	0	0	0	0	1	0	0	0	8427	1059	37	1	360	1	KLK4	19	51411894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31974	51411894	7717089	11264	19249										
KLK6	5653	broad.mit.edu	37	chr19	51466793	51466793	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttatgcttccccaggaaGacctgaagattcctgggaag	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51466793G>T	ENST00000376851.3	-	4	649	c.210C>A	c.(208-210)gtC>gtA	p.V70V	CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000310157.2_Silent_p.V70V|KLK6_ENST00000391808.1_5'UTR|KLK6_ENST00000456750.2_5'Flank|KLK6_ENST00000424910.2_Missense_Mutation_p.S18Y|KLK6_ENST00000594641.1_Silent_p.V70V|KLK6_ENST00000376853.4_Intron	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	70	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)	p.V70V(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		TCCCCAGGAAGACCTGAAGAT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	19											45	46	46					19																	51466793		2203	4300	6503	56158605	SO:0001819	synonymous_variant	5653			U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.210C>A	19.37:g.51466793G>T			56158605	A6NJA1|A8MW09|Q6H301	Silent	SNP	ENST00000376851.3	37	CCDS12811.1	.	.	.	.	.	.	.	.	.	.	N	12.51	1.960554	0.34565	.	.	ENSG00000167755	ENST00000424910	.	.	.	4.54	-5.21	0.02815	.	.	.	.	.	T	0.35189	0.0923	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.50964	-0.8765	5	0.87932	D	0	.	6.2107	0.20628	0.3252:0.3553:0.3195:0.0	.	.	.	.	Y	18	.	ENSP00000396012:S18Y	S	-	2	0	KLK6	56158605	0.000000	0.05858	0.005000	0.12908	0.888000	0.51559	-0.695000	0.05109	-0.353000	0.08224	-0.336000	0.08194	TCT		0.582	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		T	51466793	G	T	51466793	2	4	61	1	0	0	0	0	0	0	0	1	8429	929	33	2		2	KLK6	19	51466793	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54899	51466793	7662190	11265	19250										
KLK12	43849	broad.mit.edu	37	chr19	51537862	51537862	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagaacacacaggagcaaaaAgatgctgagccccatggtgg	12	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51537862A>C	ENST00000525263.1	-	1	135	c.16T>G	c.(16-18)Ttt>Gtt	p.F6V	CTC-518B2.9_ENST00000594910.1_RNA|KLK12_ENST00000250352.11_5'UTR|KLK12_ENST00000250351.4_Missense_Mutation_p.F6V|KLK12_ENST00000529888.1_Missense_Mutation_p.F6V|KLK12_ENST00000319590.4_Missense_Mutation_p.F6V			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12	6					proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.F6V(1)		endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		AGGAGCAAAAAGATGCTGAGC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	65	67					19																	51537862		2203	4300	6503	56229674	SO:0001583	missense	43849				CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"Kallikreins"	6360	protein-coding gene	gene with protein product		605539	"kallikrein 12"			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.16T>G	19.37:g.51537862A>C	ENSP00000436458:p.Phe6Val		56229674	Q9UKR1|Q9UKR2	Missense_Mutation	SNP	ENST00000525263.1	37	CCDS12821.1	.	.	.	.	.	.	.	.	.	.	a	6.438	0.448991	0.12223	.	.	ENSG00000186474	ENST00000525263;ENST00000319590;ENST00000529888;ENST00000250351	D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02	4.11	-8.22	0.01037	.	1.521110	0.04667	N	0.410016	D	0.86251	0.5888	L	0.42245	1.32	0.09310	N	1	B;B;B	0.19935	0.04;0.01;0.007	B;B;B	0.19148	0.024;0.011;0.015	T	0.73742	-0.3887	10	0.49607	T	0.09	.	8.0123	0.30361	0.13:0.1109:0.6491:0.11	.	6;6;6	Q9UKR2;Q9UKR0-2;Q9UKR0	.;.;KLK12_HUMAN	V	6	ENSP00000436458:F6V;ENSP00000324181:F6V;ENSP00000434036:F6V;ENSP00000250351:F6V	ENSP00000250351:F6V	F	-	1	0	KLK12	56229674	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.923000	0.00692	-2.591000	0.00456	-1.007000	0.02485	TTT		0.607	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598		C	51537862	A	C	51537862	3	2	61	1	0	0	0	0	1	0	0	0	8421	72	3	4	812	4	KLK12	19	51537862	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	71069	51537862	7591121	11266	19251										
KLK13	26085	broad.mit.edu	37	chr19	51559891	51559891	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgggtttcatattttcGgattgtttcacggatccaca	9	9	2	0	rs536078012		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51559891G>A	ENST00000595793.1	-	5	829	c.787C>T	c.(787-789)Cga>Tga	p.R263*	KLK13_ENST00000595547.1_Nonsense_Mutation_p.R190*|KLK13_ENST00000335422.3_Nonsense_Mutation_p.R111*	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	263	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				protein processing (GO:0016485)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)	hydrolase activity (GO:0016787)|serine-type endopeptidase activity (GO:0004252)	p.R263*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		TCATATTTTCGGATTGTTTCA	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											250	235	240					19																	51559891		2203	4300	6503	56251703	SO:0001587	stop_gained	26085				CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759		"Kallikreins"	6361	protein-coding gene	gene with protein product		605505	"kallikrein 13"			16800724, 16800723	Standard	NM_015596		Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.787C>T	19.37:g.51559891G>A	ENSP00000470555:p.Arg263*		56251703	A7UNK6|Q86VI8|Q9Y433	Nonsense_Mutation	SNP	ENST00000595793.1	37	CCDS12822.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.133749	0.37630	.	.	ENSG00000167759	ENST00000156476;ENST00000335422	.	.	.	4.34	-0.69	0.11309	.	1.340470	0.05170	N	0.499377	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	1.0164	0.01508	0.2019:0.1496:0.4186:0.2298	.	.	.	.	X	263;111	.	ENSP00000156476:R263X	R	-	1	2	KLK13	56251703	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.475000	0.06599	-0.101000	0.12219	-0.143000	0.13931	CGA		0.507	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596		A	51559891	G	A	51559891	4	1	61	1	0	0	0	0	0	1	0	0	8422	1124	39	1	50	1	KLK13	19	51559891	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22029	51559891	7569092	11267	19252										
KLK13	26085	broad.mit.edu	37	chr19	51559985	51559985	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaagtctccccaggagacGatgccatacagtgttctgtt	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51559985G>A	ENST00000595793.1	-	5	735	c.693C>T	c.(691-693)atC>atT	p.I231I	KLK13_ENST00000595547.1_Silent_p.I158I|KLK13_ENST00000335422.3_Silent_p.I79I	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	231	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				protein processing (GO:0016485)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)	hydrolase activity (GO:0016787)|serine-type endopeptidase activity (GO:0004252)	p.I231I(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		CCCAGGAGACGATGCCATACA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	19											97	96	96					19																	51559985		2203	4300	6503	56251797	SO:0001819	synonymous_variant	26085				CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759		"Kallikreins"	6361	protein-coding gene	gene with protein product		605505	"kallikrein 13"			16800724, 16800723	Standard	NM_015596		Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.693C>T	19.37:g.51559985G>A			56251797	A7UNK6|Q86VI8|Q9Y433	Silent	SNP	ENST00000595793.1	37	CCDS12822.1																																																																																				0.552	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596		A	51559985	G	A	51559985	2	1	61	1	0	0	0	0	0	0	0	1	8422	1048	37	1		1	KLK13	19	51559985	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	94	51559985	7568998	11268	19253										
SIGLEC9	27180	broad.mit.edu	37	chr19	51629096	51629096	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaccttccctggggccagcGtgaccacgaacaagaccgtc	11	15	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51629096G>T	ENST00000250360.3	+	2	731	c.664G>T	c.(664-666)Gtg>Ttg	p.V222L	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.V222L	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	222	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.V222L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		TGGGGCCAGCGTGACCACGAA	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	82	83					19																	51629096		2203	4300	6503	56320908	SO:0001583	missense	27180			AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.664G>T	19.37:g.51629096G>T	ENSP00000250360:p.Val222Leu		56320908	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	5.711	0.315657	0.10789	.	.	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.03330	3.97;3.97	2.88	1.72	0.24424	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37261	N	0.002176	T	0.04998	0.0134	M	0.82923	2.615	0.09310	N	1	P	0.47484	0.896	B	0.34931	0.192	T	0.37888	-0.9686	10	0.87932	D	0	.	6.0163	0.19605	0.0:0.0:0.6616:0.3384	.	222	Q9Y336	SIGL9_HUMAN	L	222	ENSP00000413861:V222L;ENSP00000250360:V222L	ENSP00000250360:V222L	V	+	1	0	SIGLEC9	56320908	0.000000	0.05858	0.008000	0.14137	0.238000	0.25445	-0.116000	0.10724	1.425000	0.47237	0.514000	0.50259	GTG		0.662	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		T	51629096	G	T	51629096	3	4	61	1	0	0	0	0	1	0	0	0	14352	1145	40	2	670	2	SIGLEC9	19	51629096	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69111	51629096	7499887	11269	19254										
SIGLEC7	27036	broad.mit.edu	37	chr19	51645960	51645960	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgcaccctgagcatcagaGatgccagaatgagtgatgcg	12	9	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51645960G>A	ENST00000317643.6	+	1	403	c.334G>A	c.(334-336)Gat>Aat	p.D112N	SIGLEC7_ENST00000305628.7_Missense_Mutation_p.D112N|SIGLEC7_ENST00000600577.1_Missense_Mutation_p.D112N	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	112	Ig-like V-type.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.D112N(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		GAGCATCAGAGATGCCAGAAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	105	106					19																	51645960		2203	4300	6503	56337772	SO:0001583	missense	27036			AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.334G>A	19.37:g.51645960G>A	ENSP00000323328:p.Asp112Asn		56337772	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Missense_Mutation	SNP	ENST00000317643.6	37	CCDS12826.1	.	.	.	.	.	.	.	.	.	.	.	16.11	3.029445	0.54790	.	.	ENSG00000168995	ENST00000317643;ENST00000305628;ENST00000536156	T;T;T	0.43688	0.94;0.94;0.94	2.89	0.471	0.16752	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.377447	0.18948	N	0.126778	T	0.49133	0.1539	L	0.58510	1.815	0.09310	N	1	D;B;D	0.89917	0.996;0.116;1.0	P;B;D	0.87578	0.855;0.063;0.998	T	0.36016	-0.9765	10	0.22706	T	0.39	.	3.4048	0.07336	0.1478:0.0:0.6019:0.2503	.	112;112;112	Q9Y286-4;Q9Y286-2;Q9Y286	.;.;SIGL7_HUMAN	N	112	ENSP00000323328:D112N;ENSP00000306757:D112N;ENSP00000437609:D112N	ENSP00000306757:D112N	D	+	1	0	SIGLEC7	56337772	0.007000	0.16637	0.449000	0.26957	0.247000	0.25773	1.142000	0.31540	0.080000	0.16959	0.530000	0.56133	GAT		0.488	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		A	51645960	G	A	51645960	3	1	61	1	0	0	0	0	1	0	0	0	14350	942	33	3	336	3	SIGLEC7	19	51645960	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16864	51645960	7483023	11270	19255										
SIGLEC7	27036	broad.mit.edu	37	chr19	51650040	51650040	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctgtatcaggagtgttgCtgggggcggtcgggggagct	21	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51650040C>T	ENST00000317643.6	+	5	1126	c.1057C>T	c.(1057-1059)Ctg>Ttg	p.L353L	SIGLEC7_ENST00000305628.7_Silent_p.L260L|SIGLEC7_ENST00000600577.1_Intron	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	353					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.L353L(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		AGGAGTGTTGCTGGGGGCGGT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	19											86	85	86					19																	51650040		2203	4300	6503	56341852	SO:0001819	synonymous_variant	27036			AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1057C>T	19.37:g.51650040C>T			56341852	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																				0.547	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		T	51650040	C	T	51650040	2	4	61	1	0	0	0	0	0	0	0	1	14350	796	28	3		3	SIGLEC7	19	51650040	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4080	51650040	7478943	11271	19256										
SIGLEC7	27036	broad.mit.edu	37	chr19	51656391	51656391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcccactcctcaggggaGgaaagagagatccagtatgc	13	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51656391G>A	ENST00000317643.6	+	7	1362	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	CTD-3187F8.14_ENST00000600074.1_RNA|SIGLEC7_ENST00000305628.7_Silent_p.E338E|SIGLEC7_ENST00000600577.1_3'UTR	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	431					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.E431E(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		CCTCAGGGGAGGAAAGAGAGA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	19											121	118	119					19																	51656391		2203	4300	6503	56348203	SO:0001819	synonymous_variant	27036			AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1293G>A	19.37:g.51656391G>A			56348203	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																				0.537	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		A	51656391	G	A	51656391	2	1	61	1	0	0	0	0	0	0	0	1	14350	991	35	3		3	SIGLEC7	19	51656391	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6351	51656391	7472592	11272	19257										
LIM2	3982	broad.mit.edu	37	chr19	51883795	51883795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcactgccacccagcccaGgatgtaggaccaggaaaagc	12	13	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51883795G>A	ENST00000596399.1	-	4	471	c.424C>T	c.(424-426)Ctg>Ttg	p.L142L	LIM2_ENST00000221973.3_Silent_p.L184L	NM_001161748.1	NP_001155220.1	P55344	LMIP_HUMAN	lens intrinsic membrane protein 2, 19kDa	142					cell-cell junction assembly (GO:0007043)|lens development in camera-type eye (GO:0002088)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	structural constituent of eye lens (GO:0005212)	p.L184L(1)		endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000214)|OV - Ovarian serous cystadenocarcinoma(262;0.00985)		ACCCAGCCCAGGATGTAGGAC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											147	148	148					19																	51883795		2203	4300	6503	56575607	SO:0001819	synonymous_variant	3982				CCDS12831.1, CCDS59415.1	19q13.4	2008-07-17	2002-08-29			ENSG00000105370			6610	protein-coding gene	gene with protein product		154045	"lens intrinsic membrane protein 2 (19kD)"			1606837	Standard	NM_030657		Approved	MP19, MP17	uc002pwl.2	P55344		ENST00000596399.1:c.424C>T	19.37:g.51883795G>A			56575607	Q6B083|Q9BXD0|Q9HAR5	Silent	SNP	ENST00000596399.1	37	CCDS59415.1																																																																																				0.612	LIM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464247.1	NM_030657		A	51883795	G	A	51883795	2	1	61	1	0	0	0	0	0	0	0	1	8818	991	35	3		3	LIM2	19	51883795	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	227404	51883795	7245188	11273	19258										
SIGLEC10	89790	broad.mit.edu	37	chr19	51920402	51920402	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagcttcctctctccacccGaaagaagtactgtgactcat	6	13	2	2	rs374849658		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51920402G>A	ENST00000339313.5	-	2	471	c.355C>T	c.(355-357)Cgg>Tgg	p.R119W	SIGLEC10_ENST00000442846.3_Missense_Mutation_p.R119W|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.R119W|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.R119W|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.R119W|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.R119W|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.R119W|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.R119W|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.R119W			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	119	Ig-like V-type.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R119W(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CTCTCCACCCGAAAGAAGTAC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	19											64	65	65					19																	51920402		2203	4300	6503	56612214	SO:0001583	missense	89790			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.355C>T	19.37:g.51920402G>A	ENSP00000345243:p.Arg119Trp		56612214	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	14.28	2.488955	0.44249	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000530476	T;T;T;T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	4.85	2.53	0.30540	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000091	T	0.79100	0.4389	M	0.80183	2.485	0.39953	D	0.97456	P;P;D;P;D;D;D	0.89917	0.65;0.6;1.0;0.746;0.985;0.975;0.981	B;B;D;B;P;B;P	0.78314	0.359;0.32;0.991;0.262;0.772;0.446;0.907	T	0.80063	-0.1539	10	0.54805	T	0.06	.	9.3898	0.38365	0.0:0.0:0.6114:0.3886	.	119;119;119;119;119;119;119	C9JM10;E9PL79;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	W	119;119;119;119;119;119;119;119;119;86	ENSP00000342389:R119W;ENSP00000396742:R119W;ENSP00000395475:R119W;ENSP00000348646:R119W;ENSP00000408387:R119W;ENSP00000431444:R119W;ENSP00000389132:R119W;ENSP00000414324:R119W;ENSP00000345243:R119W;ENSP00000433838:R86W	ENSP00000345243:R119W	R	-	1	2	SIGLEC10	56612214	0.694000	0.27738	0.375000	0.26029	0.104000	0.19210	0.630000	0.24553	1.018000	0.39521	0.205000	0.17691	CGG		0.527	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		A	51920402	G	A	51920402	3	1	61	1	0	0	0	0	1	0	0	0	14343	1057	37	1	1778	1	SIGLEC10	19	51920402	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36607	51920402	7208581	11274	19259										
SIGLEC8	27181	broad.mit.edu	37	chr19	51961580	51961580	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaaccatccccatattgtCtgtctccctccatccccttt	3	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:51961580C>A	ENST00000321424.3	-	1	128	c.62G>T	c.(61-63)aGa>aTa	p.R21I	SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000430817.1_Missense_Mutation_p.R21I|SIGLEC8_ENST00000340550.5_Missense_Mutation_p.R21I	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	21					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R21I(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CCCATATTGTCTGTCTCCCTC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											93	89	90					19																	51961580		2203	4300	6503	56653392	SO:0001583	missense	27181			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.62G>T	19.37:g.51961580C>A	ENSP00000321077:p.Arg21Ile		56653392	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	.	.	.	.	.	.	.	.	.	.	.	7.298	0.612419	0.14066	.	.	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	T;T;T	0.62498	1.37;0.02;1.15	2.08	-4.15	0.03881	.	8.648920	0.00166	N	0.000000	T	0.41926	0.1180	L	0.38838	1.175	0.09310	N	1	B;P;B	0.35077	0.006;0.483;0.007	B;B;B	0.28232	0.001;0.087;0.006	T	0.15206	-1.0445	10	0.21014	T	0.42	.	0.9551	0.01384	0.4387:0.2486:0.1631:0.1496	.	21;21;21	C9JT30;Q9NYZ4-2;Q9NYZ4	.;.;SIGL8_HUMAN	I	21	ENSP00000389142:R21I;ENSP00000321077:R21I;ENSP00000339448:R21I	ENSP00000321077:R21I	R	-	2	0	SIGLEC8	56653392	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.286000	0.08399	-1.124000	0.02936	0.508000	0.49915	AGA		0.617	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		A	51961580	C	A	51961580	3	1	61	1	0	0	0	0	1	0	0	0	14351	913	32	2	1465	2	SIGLEC8	19	51961580	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41178	51961580	7167403	11275	19260										
SIGLEC6	946	broad.mit.edu	37	chr19	52033129	52033129	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcagggcggggaagccctgGaaccagctcaggtgtgcagg	17	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52033129G>A	ENST00000425629.3	-	5	1015	c.861C>T	c.(859-861)ttC>ttT	p.F287F	SIGLEC6_ENST00000391797.3_Silent_p.F276F|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000343300.4_Silent_p.F287F|SIGLEC6_ENST00000359982.4_Silent_p.F298F|SIGLEC6_ENST00000436458.1_Silent_p.F235F|SIGLEC6_ENST00000346477.3_Silent_p.F271F	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	287	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.F287F(1)|p.F260F(1)		endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GGAAGCCCTGGAACCAGCTCA	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	19											69	78	75					19																	52033129		2200	4298	6498	56724941	SO:0001819	synonymous_variant	946			D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.861C>T	19.37:g.52033129G>A			56724941	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	37	CCDS12834.3																																																																																				0.622	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		A	52033129	G	A	52033129	2	1	61	1	0	0	0	0	0	0	0	1	14349	1165	41	3		3	SIGLEC6	19	52033129	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71549	52033129	7095854	11276	19261										
ZNF175	7728	broad.mit.edu	37	chr19	52090274	52090274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgacgttgttgggtctggTcagctattcagccatagctc	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52090274T>C	ENST00000262259.2	+	5	1048	c.690T>C	c.(688-690)ggT>ggC	p.G230G	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	230					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G230G(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TTGGGTCTGGTCAGCTATTCA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	19											74	68	70					19																	52090274		2203	4299	6502	56782086	SO:0001819	synonymous_variant	7728			D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.690T>C	19.37:g.52090274T>C			56782086	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																				0.418	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		C	52090274	T	C	52090274	2	2	61	1	0	0	0	0	0	0	0	1	17784	1654	58	4		4	ZNF175	19	52090274	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	57145	52090274	7038709	11277	19262										
SIGLEC5	8778	broad.mit.edu	37	chr19	52115563	52115563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctccctcgacttcatctcaGaaaaactaagggaggcataa	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52115563G>T	ENST00000534261.2	-	10	1976	c.1577C>A	c.(1576-1578)tCt>tAt	p.S526Y	SIGLEC5_ENST00000429354.3_Missense_Mutation_p.S526Y|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.S526Y|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.S526Y|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.S526Y			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	526					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.S526Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		CTTCATCTCAGAAAAACTAAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	19											128	122	124					19																	52115563		2203	4300	6503	56807375	SO:0001583	missense	8778			U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1577C>A	19.37:g.52115563G>T	ENSP00000473238:p.Ser526Tyr		56807375		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	G	1.841	-0.467347	0.04476	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.04917	3.53;3.53	3.36	-3.4	0.04853	.	.	.	.	.	T	0.04048	0.0113	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41106	-0.9527	9	0.46703	T	0.11	.	2.8978	0.05696	0.1459:0.1027:0.4818:0.2695	.	526	O15389	SIGL5_HUMAN	Y	526	ENSP00000222107:S526Y;ENSP00000415200:S526Y	ENSP00000222107:S526Y	S	-	2	0	SIGLEC5	56807375	0.017000	0.18338	0.000000	0.03702	0.000000	0.00434	-0.155000	0.10115	-0.901000	0.03891	-1.036000	0.02392	TCT		0.552	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		T	52115563	G	T	52115563	3	4	61	1	0	0	0	0	1	0	0	0	14348	942	33	2	82	2	SIGLEC5	19	52115563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25289	52115563	7013420	11278	19263										
SIGLEC5	8778	broad.mit.edu	37	chr19	52131217	52131217	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtattggagatgggggtggcGttcagggcaggggagccctg	21	6	1	1	rs376870702	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52131217G>A	ENST00000534261.2	-	6	1266	c.867C>T	c.(865-867)aaC>aaT	p.N289N	SIGLEC5_ENST00000429354.3_Silent_p.N289N|SIGLEC5_ENST00000599649.1_Silent_p.N289N|SIGLEC5_ENST00000570106.2_Silent_p.N289N|SIGLEC5_ENST00000222107.4_Silent_p.N289N			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	289	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.N289N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGGGGTGGCGTTCAGGGCAG	0.647													G|||	5	0.000998403	0.003	0	5008	,	,		16602	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G		1,4405	2.1+/-5.4	0,1,2202	65	72	69		867	-5.3	0	19		69	0,8600		0,0,4300	no	coding-synonymous	SIGLEC5	NM_003830.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		289/552	52131217	1,13005	2203	4300	6503	56823029	SO:0001819	synonymous_variant	8778			U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.867C>T	19.37:g.52131217G>A			56823029		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																				0.647	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		A	52131217	G	A	52131217	2	1	61	1	0	0	0	0	0	0	0	1	14348	1136	40	1		1	SIGLEC5	19	52131217	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	15654	52131217	6997766	11279	19264										
HAS1	3036	broad.mit.edu	37	chr19	52222483	52222483	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtagtccaccgaatctccGagcgccttgaaggctgtgta	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52222483G>A	ENST00000222115.1	-	2	712	c.678C>T	c.(676-678)ctC>ctT	p.L226L	HAS1_ENST00000601714.1_Silent_p.L233L|HAS1_ENST00000594621.1_Silent_p.L80L|HAS1_ENST00000540069.2_Silent_p.L225L	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	226					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.L226L(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CCGAATCTCCGAGCGCCTTGA	0.627																																					NSCLC(132;636 2450 45807 47979)											1	Substitution - coding silent(1)	large_intestine(1)	19											45	39	41					19																	52222483		2200	4297	6497	56914295	SO:0001819	synonymous_variant	3036			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.678C>T	19.37:g.52222483G>A			56914295	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																				0.627	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52222483	G	A	52222483	2	1	61	1	0	0	0	0	0	0	0	1	6982	1045	37	1		1	HAS1	19	52222483	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91266	52222483	6906500	11280	19265										
FPR3	2359	broad.mit.edu	37	chr19	52327243	52327243	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgccatcctaccattccGaatggtctcagtcgccatga	8	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52327243G>A	ENST00000339223.4	+	2	421	c.242G>A	c.(241-243)cGa>cAa	p.R81Q	FPR3_ENST00000595991.1_Missense_Mutation_p.R81Q	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	81					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)	p.R81Q(1)		NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						CTACCATTCCGAATGGTCTCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	19											145	113	124					19																	52327243		2203	4300	6503	57019055	SO:0001583	missense	2359				CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"GPCR / Class A : Formyl peptide receptors"	3828	protein-coding gene	gene with protein product		136539	"formyl peptide receptor-like 2"	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.242G>A	19.37:g.52327243G>A	ENSP00000341821:p.Arg81Gln		57019055		Missense_Mutation	SNP	ENST00000339223.4	37	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	0.279	-0.987527	0.02180	.	.	ENSG00000187474	ENST00000339223	T	0.71934	-0.61	2.19	-2.25	0.06888	GPCR, rhodopsin-like superfamily (1);	0.937585	0.08941	N	0.871588	T	0.33990	0.0882	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13415	-1.0510	10	0.29301	T	0.29	.	3.7568	0.08588	0.3472:0.0:0.3885:0.2644	.	81	P25089	FPR3_HUMAN	Q	81	ENSP00000341821:R81Q	ENSP00000341821:R81Q	R	+	2	0	FPR3	57019055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.334000	0.07883	-0.879000	0.04002	-1.547000	0.00903	CGA		0.468	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		A	52327243	G	A	52327243	3	1	61	1	0	0	0	0	1	0	0	0	6059	1058	37	1	244	1	FPR3	19	52327243	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104760	52327243	6801740	11281	19266										
ZNF577	84765	broad.mit.edu	37	chr19	52375952	52375952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacatttctgcccactaggcGctcactcttgtttaacaatg	6	12	3	0	rs45526832		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52375952G>A	ENST00000301399.5	-	7	1656	c.1291C>T	c.(1291-1293)Cgc>Tgc	p.R431C	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.R372C|ZNF577_ENST00000451628.2_Missense_Mutation_p.R372C|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	431					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R424C(1)		breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CCCACTAGGCGCTCACTCTTG	0.413													G|||	1	0.000199681	0	0.0014	5008	,	,		19463	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											68	65	66					19																	52375952		2203	4300	6503	57067764	SO:0001583	missense	84765			AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1291C>T	19.37:g.52375952G>A	ENSP00000301399:p.Arg431Cys		57067764	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	6.487	0.458037	0.12342	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.06608	3.29;3.33;3.33;3.28	2.51	-4.19	0.03835	.	.	.	.	.	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	P;P	0.45044	0.765;0.849	B;B	0.34722	0.092;0.188	T	0.38564	-0.9655	9	0.66056	D	0.02	.	3.6054	0.08041	0.4995:0.0:0.3165:0.184	rs45526832	431;372	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	C	431;372;372;431	ENSP00000301399:R431C;ENSP00000413476:R372C;ENSP00000389652:R372C;ENSP00000404509:R431C	ENSP00000301399:R431C	R	-	1	0	ZNF577	57067764	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.632000	0.05489	-0.940000	0.03705	-0.150000	0.13652	CGC		0.413	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52375952	G	A	52375952	3	1	61	1	0	0	0	0	1	0	0	0	18048	1087	38	1	170	1	ZNF577	19	52375952	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	48709	52375952	6753031	11282	19267										
ZNF649	65251	broad.mit.edu	37	chr19	52395111	52395111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcagtattttttggtttTgcaagggctgctgcagatga	11	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52395111T>C	ENST00000354957.3	-	5	562	c.278A>G	c.(277-279)cAa>cGa	p.Q93R	CTC-429C10.2_ENST00000600329.1_RNA|ZNF649_ENST00000600738.1_Missense_Mutation_p.Q93R	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	93					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q93R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		TTTTTGGTTTTGCAAGGGCTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	100	101					19																	52395111		2203	4300	6503	57086923	SO:0001583	missense	65251			BC005368	CCDS12843.1	19q13.41	2013-01-08				ENSG00000198093		"Zinc fingers, C2H2-type", "-"	25741	protein-coding gene	gene with protein product		611903				15950191	Standard	NM_023074		Approved	FLJ12644	uc002pxy.3	Q9BS31		ENST00000354957.3:c.278A>G	19.37:g.52395111T>C	ENSP00000347043:p.Gln93Arg		57086923	A8MYJ5|B2RDC4|Q9H9N2	Missense_Mutation	SNP	ENST00000354957.3	37	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	T	9.389	1.074964	0.20227	.	.	ENSG00000198093	ENST00000354957	T	0.06142	3.34	2.49	2.49	0.30216	.	.	.	.	.	T	0.04092	0.0114	N	0.24115	0.695	0.09310	N	1	P	0.35575	0.51	B	0.29176	0.099	T	0.41980	-0.9478	9	0.30078	T	0.28	.	8.4888	0.33086	0.0:0.0:0.0:1.0	.	93	Q9BS31	ZN649_HUMAN	R	93	ENSP00000347043:Q93R	ENSP00000347043:Q93R	Q	-	2	0	ZNF649	57086923	0.000000	0.05858	0.015000	0.15790	0.051000	0.14879	0.649000	0.24843	1.150000	0.42419	0.332000	0.21555	CAA		0.388	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		C	52395111	T	C	52395111	3	2	61	1	0	0	0	0	1	0	0	0	18103	1812	63	4	1243	4	ZNF649	19	52395111	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	19159	52395111	6733872	11283	19268										
ZNF350	59348	broad.mit.edu	37	chr19	52469050	52469050	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggtgatcagttagccaaGacttcttgatgaaggctttc	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52469050G>T	ENST00000243644.4	-	5	883	c.656C>A	c.(655-657)tCt>tAt	p.S219Y	ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	219					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S219Y(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		AGTTAGCCAAGACTTCTTGAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											192	174	180					19																	52469050		2203	4300	6503	57160862	SO:0001583	missense	59348			AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.656C>A	19.37:g.52469050G>T	ENSP00000243644:p.Ser219Tyr		57160862	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	37	CCDS12845.1	.	.	.	.	.	.	.	.	.	.	G	9.729	1.161870	0.21538	.	.	ENSG00000256683	ENST00000243644	T	0.18502	2.21	3.09	2.02	0.26589	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36482	N	0.002573	T	0.34135	0.0887	M	0.88450	2.955	0.09310	N	1	D	0.61697	0.99	P	0.55615	0.78	T	0.15925	-1.0420	10	0.66056	D	0.02	.	5.4759	0.16695	0.117:0.4063:0.4767:0.0	.	219	Q9GZX5	ZN350_HUMAN	Y	219	ENSP00000243644:S219Y	ENSP00000243644:S219Y	S	-	2	0	ZNF350	57160862	0.000000	0.05858	0.245000	0.24217	0.254000	0.26022	0.022000	0.13511	0.634000	0.30469	0.591000	0.81541	TCT		0.428	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		T	52469050	G	T	52469050	3	4	61	1	0	0	0	0	1	0	0	0	17902	942	33	2	946	2	ZNF350	19	52469050	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73939	52469050	6659933	11284	19269										
ZNF615	284370	broad.mit.edu	37	chr19	52497070	52497070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctctccagtatgagttCgttgatgtaccatgagacag	10	8	1	3	rs142913953	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52497070C>T	ENST00000602063.1	-	6	1608	c.1259G>A	c.(1258-1260)cGa>cAa	p.R420Q	ZNF615_ENST00000594083.1_Missense_Mutation_p.R431Q|ZNF615_ENST00000376716.5_Missense_Mutation_p.R420Q|ZNF615_ENST00000391795.3_Missense_Mutation_p.R425Q|ZNF615_ENST00000598071.1_Missense_Mutation_p.R431Q			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	420					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R420Q(2)|p.R431Q(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		AGTATGAGTTCGTTGATGTAC	0.413													C|||	7	0.00139776	0	0	5008	,	,		22491	0.0069		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	19											86	77	80					19																	52497070		2203	4300	6503	57188882	SO:0001583	missense	284370			AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1259G>A	19.37:g.52497070C>T	ENSP00000473089:p.Arg420Gln		57188882	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	8	0.003663003663003663	0	0.0	0	0.0	8	0.013986013986013986	0	0.0	C	16.11	3.028894	0.54790	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.02369	4.32;4.32	2.99	1.93	0.25924	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01730	0.0055	L	0.49699	1.58	0.26239	N	0.978907	D;D;D;D	0.55800	0.973;0.966;0.966;0.973	B;B;B;B	0.31751	0.135;0.12;0.12;0.135	T	0.47861	-0.9084	9	0.87932	D	0	.	6.1114	0.20102	0.0:0.6902:0.1923:0.1175	.	425;427;431;420	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	Q	420;430;425;430	ENSP00000365906:R420Q;ENSP00000375672:R425Q	ENSP00000347019:R430Q	R	-	2	0	ZNF615	57188882	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.054000	0.14205	0.574000	0.29417	0.585000	0.79938	CGA		0.413	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		T	52497070	C	T	52497070	3	4	61	1	0	0	0	0	1	0	0	0	18079	884	31	1	940	1	ZNF615	19	52497070	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28020	52497070	6631913	11285	19270										
ZNF615	284370	broad.mit.edu	37	chr19	52497571	52497571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtttcagttctgtatgaGttctctgatggtccattagt	9	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52497571G>A	ENST00000602063.1	-	6	1107	c.758C>T	c.(757-759)aCt>aTt	p.T253I	ZNF615_ENST00000594083.1_Missense_Mutation_p.T264I|ZNF615_ENST00000376716.5_Missense_Mutation_p.T253I|ZNF615_ENST00000391795.3_Missense_Mutation_p.T258I|ZNF615_ENST00000598071.1_Missense_Mutation_p.T264I			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T253I(1)|p.T264I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TTCTGTATGAGTTCTCTGATG	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	19											157	147	150					19																	52497571		2203	4300	6503	57189383	SO:0001583	missense	284370			AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.758C>T	19.37:g.52497571G>A	ENSP00000473089:p.Thr253Ile		57189383	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.496506	0.00010	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.12672	2.66;2.66	3.42	-6.83	0.01693	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04363	0.0120	N	0.13299	0.325	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39800	-0.9596	9	0.02654	T	1	.	3.3289	0.07077	0.5067:0.1924:0.2041:0.0968	.	258;260;264;253	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	I	253;263;258;263	ENSP00000365906:T253I;ENSP00000375672:T258I	ENSP00000347019:T263I	T	-	2	0	ZNF615	57189383	0.000000	0.05858	0.002000	0.10522	0.313000	0.28021	-2.228000	0.01209	-2.298000	0.00660	-0.266000	0.10368	ACT		0.388	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52497571	G	A	52497571	3	1	61	1	0	0	0	0	1	0	0	0	18079	1029	36	3	1441	3	ZNF615	19	52497571	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	501	52497571	6631412	11286	19271										
ZNF614	80110	broad.mit.edu	37	chr19	52520188	52520188	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacaaatgttctcatggtaAatgagctgagacttcctaag	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52520188A>C	ENST00000270649.6	-	5	1207	c.663T>G	c.(661-663)atT>atG	p.I221M	ZNF614_ENST00000356322.6_Intron	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I221M(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TCTCATGGTAAATGAGCTGAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	87	90					19																	52520188		2203	4300	6503	57212000	SO:0001583	missense	80110			BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"Zinc fingers, C2H2-type", "-"	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.663T>G	19.37:g.52520188A>C	ENSP00000270649:p.Ile221Met		57212000	Q494T8|Q8TCF4|Q9BSN8	Missense_Mutation	SNP	ENST00000270649.6	37	CCDS12847.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.638722	0.47153	.	.	ENSG00000142556	ENST00000270649	T	0.15834	2.39	4.06	1.91	0.25777	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17023	0.0409	M	0.65975	2.015	0.09310	N	1	B	0.22480	0.07	B	0.18263	0.021	T	0.26985	-1.0087	9	0.51188	T	0.08	.	4.3182	0.11003	0.7235:0.0:0.1008:0.1756	.	221	Q8N883	ZN614_HUMAN	M	221	ENSP00000270649:I221M	ENSP00000270649:I221M	I	-	3	3	ZNF614	57212000	0.000000	0.05858	0.000000	0.03702	0.232000	0.25224	0.178000	0.16820	0.137000	0.18759	0.533000	0.62120	ATT		0.388	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040		C	52520188	A	C	52520188	3	2	61	1	0	0	0	0	1	0	0	0	18078	10	1	4	1098	4	ZNF614	19	52520188	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22617	52520188	6608795	11287	19272										
ZNF432	9668	broad.mit.edu	37	chr19	52537316	52537316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcactgcacataaagggtTtctctccagtatgagttcgc	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52537316T>C	ENST00000594154.1	-	5	1828	c.1616A>G	c.(1615-1617)aAa>aGa	p.K539R	ZNF432_ENST00000221315.5_Missense_Mutation_p.K539R			O94892	ZN432_HUMAN	zinc finger protein 432	539					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K539R(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		CATAAAGGGTTTCTCTCCAGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											106	98	100					19																	52537316		2203	4300	6503	57229128	SO:0001583	missense	9668			AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"Zinc fingers, C2H2-type", "-"	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.1616A>G	19.37:g.52537316T>C	ENSP00000470488:p.Lys539Arg		57229128		Missense_Mutation	SNP	ENST00000594154.1	37	CCDS12848.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.098387	0.37048	.	.	ENSG00000256087	ENST00000221315	T	0.24908	1.83	2.81	2.81	0.32909	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18882	0.0453	L	0.28458	0.855	0.20764	N	0.999855	B	0.18863	0.031	B	0.27262	0.078	T	0.19614	-1.0300	9	0.49607	T	0.09	.	6.1133	0.20112	0.0:0.1316:0.0:0.8684	.	539	O94892	ZN432_HUMAN	R	539	ENSP00000221315:K539R	ENSP00000221315:K539R	K	-	2	0	ZNF432	57229128	0.000000	0.05858	0.995000	0.50966	0.994000	0.84299	-0.226000	0.09139	1.292000	0.44672	0.533000	0.62120	AAA		0.388	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650		C	52537316	T	C	52537316	3	2	61	1	0	0	0	0	1	0	0	0	17945	1841	64	4	346	4	ZNF432	19	52537316	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	17128	52537316	6591667	11288	19273										
ZNF432	9668	broad.mit.edu	37	chr19	52538153	52538153	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacattcactgcatataaaaGatttctctcttttatgaatt	3	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52538153G>T	ENST00000594154.1	-	5	991	c.779C>A	c.(778-780)tCt>tAt	p.S260Y	ZNF432_ENST00000221315.5_Missense_Mutation_p.S260Y			O94892	ZN432_HUMAN	zinc finger protein 432	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S260Y(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		GCATATAAAAGATTTCTCTCT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											85	90	88					19																	52538153		2203	4300	6503	57229965	SO:0001583	missense	9668			AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"Zinc fingers, C2H2-type", "-"	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.779C>A	19.37:g.52538153G>T	ENSP00000470488:p.Ser260Tyr		57229965		Missense_Mutation	SNP	ENST00000594154.1	37	CCDS12848.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.248829	0.39797	.	.	ENSG00000256087	ENST00000221315	T	0.18338	2.22	2.9	2.9	0.33743	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30572	0.0769	L	0.45470	1.425	0.30676	N	0.752808	D	0.65815	0.995	P	0.60789	0.879	T	0.17410	-1.0370	9	0.72032	D	0.01	.	12.9715	0.58515	0.0:0.0:1.0:0.0	.	260	O94892	ZN432_HUMAN	Y	260	ENSP00000221315:S260Y	ENSP00000221315:S260Y	S	-	2	0	ZNF432	57229965	0.073000	0.21202	0.970000	0.41538	0.906000	0.53458	2.545000	0.45769	1.630000	0.50440	0.585000	0.79938	TCT		0.373	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650		T	52538153	G	T	52538153	3	4	61	1	0	0	0	0	1	0	0	0	17945	942	33	2	1183	2	ZNF432	19	52538153	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	837	52538153	6590830	11289	19274										
ZNF616	90317	broad.mit.edu	37	chr19	52618710	52618710	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtttctctccactatgaatTctccgatgcactgtaagacg	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52618710T>G	ENST00000600228.1	-	4	1968	c.1707A>C	c.(1705-1707)agA>agC	p.R569S	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	569					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R569S(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		CACTATGAATTCTCCGATGCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											114	100	105					19																	52618710		2203	4300	6503	57310522	SO:0001583	missense	90317			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.1707A>C	19.37:g.52618710T>G	ENSP00000471000:p.Arg569Ser		57310522	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.395576	0.25205	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.08	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49012	0.1532	L	0.52823	1.66	0.09310	N	1	D	0.53619	0.961	P	0.56648	0.803	T	0.32241	-0.9914	8	0.66056	D	0.02	.	7.6168	0.28163	0.0:0.0:0.0:1.0	.	569	Q08AN1	ZN616_HUMAN	S	569	.	ENSP00000328722:R569S	R	-	3	2	ZNF616	57310522	0.000000	0.05858	0.003000	0.11579	0.223000	0.24884	-0.967000	0.03821	0.736000	0.32559	0.254000	0.18369	AGA		0.433	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		G	52618710	T	G	52618710	3	3	61	1	0	0	0	0	1	0	0	0	18080	1780	62	4	642	4	ZNF616	19	52618710	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	80557	52618710	6510273	11290	19275										
ZNF616	90317	broad.mit.edu	37	chr19	52619479	52619479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaactgtctgatgaagtCtaagatggacacgctgacta	10	7	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52619479C>A	ENST00000600228.1	-	4	1199	c.938G>T	c.(937-939)aGa>aTa	p.R313I	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R313I(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		CTGATGAAGTCTAAGATGGAC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											109	105	106					19																	52619479		2203	4300	6503	57311291	SO:0001583	missense	90317			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.938G>T	19.37:g.52619479C>A	ENSP00000471000:p.Arg313Ile		57311291	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.722160	0.30503	.	.	ENSG00000204611	ENST00000330123	.	.	.	0.825	-1.65	0.08291	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13500	0.0327	N	0.11341	0.13	0.09310	N	1	B	0.17667	0.023	B	0.01281	0.0	T	0.29822	-0.9999	8	0.08179	T	0.78	.	3.7114	0.08421	0.2221:0.2714:0.5065:0.0	.	313	Q08AN1	ZN616_HUMAN	I	313	.	ENSP00000328722:R313I	R	-	2	0	ZNF616	57311291	0.000000	0.05858	0.001000	0.08648	0.936000	0.57629	-3.421000	0.00477	-0.763000	0.04658	0.305000	0.20034	AGA		0.413	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		A	52619479	C	A	52619479	3	1	61	1	0	0	0	0	1	0	0	0	18080	913	32	2	1411	2	ZNF616	19	52619479	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	769	52619479	6509504	11291	19276										
ZNF616	90317	broad.mit.edu	37	chr19	52619593	52619593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttttactaaaggacttgCcacattcattacatatgtag	5	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52619593C>T	ENST00000600228.1	-	4	1085	c.824G>A	c.(823-825)gGc>gAc	p.G275D	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	275					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G275D(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		AAAGGACTTGCCACATTCATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	72	72					19																	52619593		2203	4300	6503	57311405	SO:0001583	missense	90317			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.824G>A	19.37:g.52619593C>T	ENSP00000471000:p.Gly275Asp		57311405	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757233	0.49468	.	.	ENSG00000204611	ENST00000330123	.	.	.	0.954	0.954	0.19595	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50292	0.1607	L	0.49126	1.545	0.26583	N	0.973347	D	0.67145	0.996	P	0.59825	0.864	T	0.39396	-0.9616	8	0.66056	D	0.02	.	9.4055	0.38460	0.0:1.0:0.0:0.0	.	275	Q08AN1	ZN616_HUMAN	D	275	.	ENSP00000328722:G275D	G	-	2	0	ZNF616	57311405	0.000000	0.05858	0.008000	0.14137	0.241000	0.25554	0.005000	0.13129	0.809000	0.34255	0.305000	0.20034	GGC		0.378	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		T	52619593	C	T	52619593	3	4	61	1	0	0	0	0	1	0	0	0	18080	739	26	3	1525	3	ZNF616	19	52619593	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114	52619593	6509390	11292	19277										
ZNF616	90317	broad.mit.edu	37	chr19	52620049	52620049	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccttgactatgttgatctCttttaccagtaagattgttt	6	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52620049C>A	ENST00000600228.1	-	4	629	c.368G>T	c.(367-369)aGa>aTa	p.R123I	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R123I(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		ATGTTGATCTCTTTTACCAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											214	191	199					19																	52620049		2202	4300	6502	57311861	SO:0001583	missense	90317			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.368G>T	19.37:g.52620049C>A	ENSP00000471000:p.Arg123Ile		57311861	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	C	5.469	0.271644	0.10349	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.64	-3.27	0.05048	.	.	.	.	.	T	0.28400	0.0702	L	0.48642	1.525	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20505	-1.0273	8	0.38643	T	0.18	.	3.0698	0.06226	0.2042:0.5008:0.0:0.295	.	123	Q08AN1	ZN616_HUMAN	I	123	.	ENSP00000328722:R123I	R	-	2	0	ZNF616	57311861	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-4.362000	0.00246	-1.142000	0.02869	-0.680000	0.03767	AGA		0.368	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		A	52620049	C	A	52620049	3	1	61	1	0	0	0	0	1	0	0	0	18080	913	32	2	1981	2	ZNF616	19	52620049	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	456	52620049	6508934	11293	19278										
ZNF836	162962	broad.mit.edu	37	chr19	52659131	52659131	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctgcccagtatgaattCttagatgacgtgctaggcat	10	8	2	3	rs532993293	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52659131C>A	ENST00000322146.8	-	5	2326	c.1805G>T	c.(1804-1806)aGa>aTa	p.R602I	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.R602I	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	602					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R602I(1)		endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						AGTATGAATTCTTAGATGACG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											133	145	141					19																	52659131		2146	4275	6421	57350943	SO:0001583	missense	162962			BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.1805G>T	19.37:g.52659131C>A	ENSP00000325038:p.Arg602Ile		57350943		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.529915	0.27387	.	.	ENSG00000196267	ENST00000322146;ENST00000396443	T	0.24908	1.83	2.09	-4.17	0.03857	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20333	0.0489	L	0.52266	1.64	0.09310	N	1	P	0.38767	0.646	B	0.41946	0.371	T	0.12811	-1.0533	9	0.59425	D	0.04	.	1.8312	0.03130	0.1297:0.1595:0.3721:0.3386	.	602	Q6ZNA1	ZN836_HUMAN	I	602;176	ENSP00000325038:R602I	ENSP00000325038:R602I	R	-	2	0	ZNF836	57350943	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-3.849000	0.00351	-1.382000	0.02109	0.484000	0.47621	AGA		0.393	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52659131	C	A	52659131	3	1	61	1	0	0	0	0	1	0	0	0	18226	913	32	2	1007	2	ZNF836	19	52659131	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39082	52659131	6469852	11294	19279										
ZNF766	90321	broad.mit.edu	37	chr19	52794016	52794016	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggagaattcatacaggagaGaaactttacaaatgtaataa	8	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52794016G>T	ENST00000439461.1	+	4	1015	c.972G>T	c.(970-972)gaG>gaT	p.E324D	CTD-2525I3.5_ENST00000594865.1_RNA|ZNF766_ENST00000359102.4_Missense_Mutation_p.E339D|ZNF766_ENST00000599581.1_3'UTR|ZNF766_ENST00000593612.1_Missense_Mutation_p.E339D	NM_001010851.2	NP_001010851.1	Q5HY98	ZN766_HUMAN	zinc finger protein 766	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E324D(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	17				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		ATACAGGAGAGAAACTTTACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											29	32	31					19																	52794016		2122	4268	6390	57485828	SO:0001583	missense	90321			AK024074	CCDS46163.1	19q13.33	2013-01-08				ENSG00000196214		"Zinc fingers, C2H2-type", "-"	28063	protein-coding gene	gene with protein product							Standard	XM_006723458		Approved		uc002pyr.1	Q5HY98		ENST00000439461.1:c.972G>T	19.37:g.52794016G>T	ENSP00000409652:p.Glu324Asp		57485828	B2RNE0|Q7Z326	Missense_Mutation	SNP	ENST00000439461.1	37	CCDS46163.1	.	.	.	.	.	.	.	.	.	.	G	7.545	0.661443	0.14645	.	.	ENSG00000196214	ENST00000439461;ENST00000359102	T;T	0.26810	1.71;1.71	2.38	1.31	0.21738	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31358	0.0794	L	0.33485	1.01	0.23221	N	0.99809	P;D	0.58268	0.938;0.982	P;P	0.59012	0.616;0.85	T	0.12016	-1.0564	9	0.87932	D	0	.	7.8641	0.29526	0.137:0.0:0.863:0.0	.	339;324	G3XAE0;Q5HY98	.;ZN766_HUMAN	D	324;339	ENSP00000409652:E324D;ENSP00000352005:E339D	ENSP00000352005:E339D	E	+	3	2	ZNF766	57485828	1.000000	0.71417	0.033000	0.17914	0.046000	0.14306	1.277000	0.33167	0.318000	0.23185	0.650000	0.86243	GAG		0.363	ZNF766-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462764.1	NM_001010851		T	52794016	G	T	52794016	3	4	61	1	0	0	0	0	1	0	0	0	18179	933	33	2	986	2	ZNF766	19	52794016	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134885	52794016	6334967	11295	19280										
ZNF610	162963	broad.mit.edu	37	chr19	52869600	52869600	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtaatgagtgtggcaaGaacttcaggcacaaattttc	9	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52869600G>A	ENST00000403906.3	+	6	1425	c.969G>A	c.(967-969)aaG>aaA	p.K323K	ZNF610_ENST00000321287.8_Silent_p.K323K|ZNF610_ENST00000327920.8_Silent_p.K323K|ZNF610_ENST00000601151.1_Silent_p.K280K	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K323K(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		AGTGTGGCAAGAACTTCAGGC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	19											62	61	61					19																	52869600		2203	4300	6503	57561412	SO:0001819	synonymous_variant	162963			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"Zinc fingers, C2H2-type", "-"	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.969G>A	19.37:g.52869600G>A			57561412	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																				0.403	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		A	52869600	G	A	52869600	2	1	61	1	0	0	0	0	0	0	0	1	18075	933	33	3		3	ZNF610	19	52869600	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75584	52869600	6259383	11296	19281										
ZNF528	84436	broad.mit.edu	37	chr19	52918941	52918941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgtgacaaggtctttcGaagcagttcaaagcttgcac	10	8	2	2	rs202043315		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52918941G>A	ENST00000360465.3	+	7	1262	c.836G>A	c.(835-837)cGa>cAa	p.R279Q	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	279					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R279Q(2)		breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AAGGTCTTTCGAAGCAGTTCA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	19						G	GLN/ARG	0,4406		0,0,2203	95	99	98		836	-1.3	0	19		98	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF528	NM_032423.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	279/629	52918941	1,13005	2203	4300	6503	57610753	SO:0001583	missense	84436			AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.836G>A	19.37:g.52918941G>A	ENSP00000353652:p.Arg279Gln		57610753	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.454704	0.26161	0.0	1.16E-4	ENSG00000167555	ENST00000360465	T	0.18338	2.22	1.85	-1.26	0.09376	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10680	0.0261	L	0.39633	1.23	0.09310	N	1	P	0.49358	0.923	B	0.33620	0.167	T	0.25779	-1.0122	9	0.45353	T	0.12	.	9.7711	0.40589	0.0:0.7035:0.2965:0.0	.	279	Q3MIS6	ZN528_HUMAN	Q	279	ENSP00000353652:R279Q	ENSP00000353652:R279Q	R	+	2	0	ZNF528	57610753	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-5.127000	0.00148	0.086000	0.17137	0.491000	0.48974	CGA		0.388	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		A	52918941	G	A	52918941	3	1	61	1	0	0	0	0	1	0	0	0	18008	1058	37	1	850	1	ZNF528	19	52918941	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49341	52918941	6210042	11297	19282										
ZNF528	84436	broad.mit.edu	37	chr19	52919616	52919616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtggcaaggtcttcagtcGcagttcaaacctggtatgcc	11	10	3	0	rs372030934		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52919616G>A	ENST00000360465.3	+	7	1937	c.1511G>A	c.(1510-1512)cGc>cAc	p.R504H	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	504					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R504H(1)		breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		GTCTTCAGTCGCAGTTCAAAC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	HIS/ARG	0,4406		0,0,2203	50	50	50		1511	-3.7	0	19		50	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF528	NM_032423.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	504/629	52919616	1,13005	2203	4300	6503	57611428	SO:0001583	missense	84436			AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.1511G>A	19.37:g.52919616G>A	ENSP00000353652:p.Arg504His		57611428	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.364970	0.24684	0.0	1.16E-4	ENSG00000167555	ENST00000360465	T	0.05580	3.42	1.83	-3.66	0.04489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03564	0.0102	L	0.36672	1.1	0.09310	N	1	B	0.27229	0.172	B	0.22753	0.041	T	0.46541	-0.9184	9	0.13853	T	0.58	.	1.9599	0.03384	0.1367:0.1492:0.4568:0.2573	.	504	Q3MIS6	ZN528_HUMAN	H	504	ENSP00000353652:R504H	ENSP00000353652:R504H	R	+	2	0	ZNF528	57611428	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.827000	0.00096	-0.996000	0.03455	-0.312000	0.09012	CGC		0.398	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		A	52919616	G	A	52919616	3	1	61	1	0	0	0	0	1	0	0	0	18008	1087	38	1	1525	1	ZNF528	19	52919616	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	675	52919616	6209367	11298	19283										
ZNF534	147658	broad.mit.edu	37	chr19	52941430	52941430	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacgaatccatactggagaGaagccttacaaatataatga	7	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:52941430G>T	ENST00000332323.6	+	4	817	c.756G>T	c.(754-756)gaG>gaT	p.E252D	ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.E239D	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E252D(1)		central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						ATACTGGAGAGAAGCCTTACA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											55	50	52					19																	52941430		1568	3582	5150	57633242	SO:0001583	missense	147658			AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.756G>T	19.37:g.52941430G>T	ENSP00000327538:p.Glu252Asp		57633242	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	37	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	G	5.337	0.247580	0.10130	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.26810	1.71;1.71	1.81	0.705	0.18127	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41581	0.1165	M	0.69823	2.125	0.80722	D	1	D;P	0.63880	0.993;0.95	P;D	0.68765	0.878;0.96	T	0.22871	-1.0204	9	0.62326	D	0.03	.	5.4475	0.16544	0.3348:0.0:0.6652:0.0	.	239;252	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	D	252;239;251	ENSP00000327538:E252D;ENSP00000391358:E239D	ENSP00000327538:E252D	E	+	3	2	ZNF534	57633242	0.927000	0.31430	0.567000	0.28434	0.079000	0.17450	0.330000	0.19715	0.085000	0.17107	0.460000	0.39030	GAG		0.358	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		T	52941430	G	T	52941430	3	4	61	1	0	0	0	0	1	0	0	0	18012	933	33	2	770	2	ZNF534	19	52941430	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21814	52941430	6187553	11299	19284										
ZNF578	147660	broad.mit.edu	37	chr19	53014722	53014722	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccttagatgccatcgtaGacttcatactggaataaaac	6	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53014722G>T	ENST00000421239.2	+	6	1332	c.1088G>T	c.(1087-1089)aGa>aTa	p.R363I	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R363I(1)							GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TGCCATCGTAGACTTCATACT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	112	110					19																	53014722		2203	4299	6502	57706534	SO:0001583	missense	147660			AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1088G>T	19.37:g.53014722G>T	ENSP00000459216:p.Arg363Ile		57706534	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	7.227	0.598540	0.13939	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	0.322	0.15888	.	.	.	.	.	T	0.43010	0.1228	L	0.42632	1.34	0.09310	N	0.99999	D	0.76494	0.999	D	0.81914	0.995	T	0.21690	-1.0238	7	.	.	.	.	2.7717	0.05336	0.3481:0.2501:0.4018:0.0	.	363	G3V4F6	.	I	363	.	.	R	+	2	0	ZNF578	57706534	0.000000	0.05858	0.005000	0.12908	0.083000	0.17756	-0.725000	0.04942	-0.002000	0.14469	0.297000	0.19635	AGA		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014722	G	T	53014722	3	4	61	1	0	0	0	0	1	0	0	0	18049	942	33	2	1098	2	ZNF578	19	53014722	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73292	53014722	6114261	11300	19285										
ZNF701	55762	broad.mit.edu	37	chr19	53086657	53086657	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtggcaaggtttttaatCgaaaatcaaaccttgaacgt	8	6	1	1	rs370144367		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53086657C>T	ENST00000540331.1	+	5	1768	c.1543C>T	c.(1543-1545)Cga>Tga	p.R515*	ZNF701_ENST00000391785.3_Nonsense_Mutation_p.R449*|ZNF701_ENST00000301093.2_Nonsense_Mutation_p.R515*|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R449*(1)		endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GGTTTTTAATCGAAAATCAAA	0.358													C|||	1	0.000199681	0	0.0014	5008	,	,		22676	0		0	False		,,,				2504	0				NSCLC(89;451 1475 9611 20673 52284)											1	Substitution - Nonsense(1)	large_intestine(1)	19						C	stop/ARG,stop/ARG	0,4396		0,0,2198	41	41	41		1543,1345	0.6	0	19		41	1,8591	1.2+/-3.3	0,1,4295	no	stop-gained,stop-gained	ZNF701	NM_001172655.1,NM_018260.2	,	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	,	515/532,449/466	53086657	1,12987	2198	4296	6494	57778469	SO:0001587	stop_gained	55762			AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1543C>T	19.37:g.53086657C>T	ENSP00000444339:p.Arg515*		57778469	A2RRM8|B9EGF2|F5GZM6|Q66K42	Nonsense_Mutation	SNP	ENST00000540331.1	37	CCDS54311.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500805	0.85176	0.0	1.16E-4	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	.	.	.	1.81	0.618	0.17624	.	.	.	.	.	.	.	.	.	.	.	0.23834	N	0.996711	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	8.7109	0.34382	0.0:0.7615:0.2385:0.0	.	.	.	.	X	449;515;515	.	ENSP00000301093:R515X	R	+	1	2	ZNF701	57778469	.	.	0.000000	0.03702	0.027000	0.11550	.	.	0.072000	0.16694	0.306000	0.20318	CGA		0.358	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		T	53086657	C	T	53086657	4	4	61	1	0	0	0	0	0	1	0	0	18144	876	31	1	1557	1	ZNF701	19	53086657	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	71935	53086657	6042326	11301	19286										
ZNF83	55769	broad.mit.edu	37	chr19	53116556	53116556	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttctccagtatgaattCtccaatgatatgcaaggtat	6	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53116556C>A	ENST00000597597.1	-	2	3515	c.1262G>T	c.(1261-1263)aGa>aTa	p.R421I	ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.R421I|ZNF83_ENST00000301096.3_Missense_Mutation_p.R421I|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000545872.1_Missense_Mutation_p.R421I|ZNF83_ENST00000391789.4_Missense_Mutation_p.R393I|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Missense_Mutation_p.R421I|ZNF83_ENST00000544146.1_Missense_Mutation_p.R421I			P51522	ZNF83_HUMAN	zinc finger protein 83	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R421I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		AGTATGAATTCTCCAATGATA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	85	85					19																	53116556		2203	4300	6503	57808368	SO:0001583	missense	55769			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1262G>T	19.37:g.53116556C>A	ENSP00000472619:p.Arg421Ile		57808368	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	-	13.61	2.288823	0.40494	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83	2.2	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23492	0.0568	M	0.66506	2.035	0.09310	N	1	B;P	0.41643	0.24;0.758	B;B	0.39299	0.044;0.296	T	0.21759	-1.0236	9	0.59425	D	0.04	.	6.0377	0.19716	0.4773:0.3642:0.1584:0.0	.	393;421	P51522-2;P51522	.;ZNF83_HUMAN	I	421;421;421;393;421;421;393	ENSP00000445993:R421I;ENSP00000301096:R421I;ENSP00000445470:R421I;ENSP00000440713:R421I;ENSP00000439681:R421I;ENSP00000375666:R393I	ENSP00000301096:R421I	R	-	2	0	ZNF83	57808368	0.000000	0.05858	0.003000	0.11579	0.050000	0.14768	-1.811000	0.01728	-0.173000	0.10761	0.411000	0.27672	AGA		0.383	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		A	53116556	C	A	53116556	3	1	61	1	0	0	0	0	1	0	0	0	18222	913	32	2	292	2	ZNF83	19	53116556	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29899	53116556	6012427	11302	19287										
ZNF611	81856	broad.mit.edu	37	chr19	53208757	53208757	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgatttacgactgaaaacCttttcacattcatcacattt	3	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53208757C>A	ENST00000319783.1	-	7	1867	c.1551G>T	c.(1549-1551)aaG>aaT	p.K517N	ZNF611_ENST00000540744.1_Missense_Mutation_p.K517N|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000543227.1_Missense_Mutation_p.K517N|ZNF611_ENST00000602162.1_Missense_Mutation_p.K448N|ZNF611_ENST00000595798.1_Missense_Mutation_p.K448N|ZNF611_ENST00000453741.2_Missense_Mutation_p.K448N	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K517N(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		GACTGAAAACCTTTTCACATT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											119	118	119					19																	53208757		2203	4300	6503	57900569	SO:0001583	missense	81856			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1551G>T	19.37:g.53208757C>A	ENSP00000322427:p.Lys517Asn		57900569	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	10.83	1.459811	0.26248	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.27890	1.64;1.64;3.15;1.64	1.51	-3.03	0.05429	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41396	0.1157	M	0.91140	3.18	0.09310	N	1	B	0.29136	0.234	B	0.34931	0.192	T	0.50800	-0.8785	9	0.87932	D	0	.	7.7886	0.29106	0.0:0.5875:0.0:0.4125	.	517	Q8N823	ZN611_HUMAN	N	517;517;448;517	ENSP00000437616:K517N;ENSP00000439211:K517N;ENSP00000443505:K448N;ENSP00000322427:K517N	ENSP00000322427:K517N	K	-	3	2	ZNF611	57900569	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-2.242000	0.01195	-0.821000	0.04312	-1.021000	0.02439	AAG		0.368	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		A	53208757	C	A	53208757	3	1	61	1	0	0	0	0	1	0	0	0	18076	680	24	2	570	2	ZNF611	19	53208757	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	92201	53208757	5920226	11303	19288										
ZNF600	162966	broad.mit.edu	37	chr19	53270941	53270941	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgtgataactttgatatCtttgcaatgtccctgtgtgg	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53270941C>T	ENST00000338230.3	-	3	335	c.68G>A	c.(67-69)aGa>aAa	p.R23K		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	23					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R23K(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		ACTTTGATATCTTTGCAATGT	0.368																																					Esophageal Squamous(196;1235 2112 2375 33339 34207)											1	Substitution - Missense(1)	large_intestine(1)	19											159	165	163					19																	53270941		2203	4300	6503	57962753	SO:0001583	missense	162966			U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"Zinc fingers, C2H2-type"	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.68G>A	19.37:g.53270941C>T	ENSP00000344791:p.Arg23Lys		57962753	Q6MZR0	Missense_Mutation	SNP	ENST00000338230.3	37	CCDS12856.1	.	.	.	.	.	.	.	.	.	.	.	10.25	1.298515	0.23650	.	.	ENSG00000189190	ENST00000338230	T	0.09723	2.95	1.01	1.01	0.19927	.	.	.	.	.	T	0.16769	0.0403	M	0.64997	1.995	0.09310	N	1	P	0.44690	0.841	P	0.54210	0.745	T	0.18366	-1.0339	9	0.14656	T	0.56	.	5.0146	0.14330	0.0:0.6129:0.387:0.0	.	23	Q6ZNG1	ZN600_HUMAN	K	23	ENSP00000344791:R23K	ENSP00000344791:R23K	R	-	2	0	ZNF600	57962753	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	0.038000	0.13862	0.877000	0.35895	0.298000	0.19748	AGA		0.368	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457		T	53270941	C	T	53270941	3	4	61	1	0	0	0	0	1	0	0	0	18069	913	32	3	2104	3	ZNF600	19	53270941	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62184	53270941	5858042	11304	19289										
ZNF28	7576	broad.mit.edu	37	chr19	53303229	53303229	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatgaagcctacgatggatTataagcgatgatgtctgacg	12	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53303229T>G	ENST00000457749.2	-	4	1988	c.1869A>C	c.(1867-1869)atA>atC	p.I623I	ZNF28_ENST00000414252.2_Silent_p.I570I|ZNF28_ENST00000360272.4_Silent_p.I570I|ZNF28_ENST00000438150.2_Silent_p.I570I	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	623					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I570I(2)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TACGATGGATTATAAGCGATG	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	19											231	206	214					19																	53303229		2203	4300	6503	57995041	SO:0001819	synonymous_variant	7576			X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1869A>C	19.37:g.53303229T>G			57995041	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Silent	SNP	ENST00000457749.2	37	CCDS33093.2																																																																																				0.453	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		G	53303229	T	G	53303229	2	3	61	1	0	0	0	0	0	0	0	1	17852	1744	61	4		4	ZNF28	19	53303229	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	32288	53303229	5825754	11305	19290										
ZNF320	162967	broad.mit.edu	37	chr19	53384249	53384249	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtctctctccagtatgaactCtctgatgttctgcaagacgt	8	11	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53384249C>A	ENST00000595635.1	-	8	1631	c.1130G>T	c.(1129-1131)aGa>aTa	p.R377I	ZNF320_ENST00000391781.2_Missense_Mutation_p.R377I|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000597909.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R377I(1)		NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		AGTATGAACTCTCTGATGTTC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											120	114	116					19																	53384249		2203	4300	6503	58076061	SO:0001583	missense	162967			AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1130G>T	19.37:g.53384249C>A	ENSP00000473091:p.Arg377Ile		58076061	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	37	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	9.910	1.209322	0.22205	.	.	ENSG00000182986	ENST00000391781	T	0.24908	1.83	1.75	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47097	0.1427	M	0.80508	2.5	0.09310	N	0.999999	D	0.76494	0.999	D	0.69479	0.964	T	0.16748	-1.0392	9	0.51188	T	0.08	.	7.9287	0.29889	0.0:0.7417:0.2583:0.0	.	377	A2RRD8	ZN320_HUMAN	I	377	ENSP00000375660:R377I	ENSP00000375660:R377I	R	-	2	0	ZNF320	58076061	0.000000	0.05858	0.044000	0.18714	0.497000	0.33675	-0.662000	0.05305	0.960000	0.38005	0.194000	0.17425	AGA		0.413	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		A	53384249	C	A	53384249	3	1	61	1	0	0	0	0	1	0	0	0	17878	913	32	2	403	2	ZNF320	19	53384249	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81020	53384249	5744734	11306	19291										
ZNF816A	125893	broad.mit.edu	37	chr19	53453316	53453316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttgattaaaaaccttcGcacatttattacacttgtaa	3	8	0	1	rs376324036		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53453316G>A	ENST00000357666.4	-	5	2012	c.1712C>T	c.(1711-1713)gCg>gTg	p.A571V	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.A571V|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A571V(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AAAAACCTTCGCACATTTATT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	VAL/ALA,VAL/ALA,VAL/ALA,	1,4405		0,1,2202	69	70	70		1712,1712,1712,	1.8	0.2	19		70	0,8600		0,0,4300	no	missense,missense,missense,intron	ZNF816,ZNF816-ZNF321P	NM_001031665.2,NM_001202456.1,NM_001202457.1,NM_001202473.1	64,64,64,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,	571/652,571/652,571/652,	53453316	1,13005	2203	4300	6503	58145128	SO:0001583	missense	125893			BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.1712C>T	19.37:g.53453316G>A	ENSP00000350295:p.Ala571Val		58145128	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	37	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	14.25	2.479424	0.44044	2.27E-4	0.0	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.07908	3.15;3.15	1.79	1.79	0.24919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06554	0.0168	N	0.25992	0.78	0.80722	D	1	B	0.20887	0.049	B	0.25506	0.061	T	0.26643	-1.0097	9	0.87932	D	0	.	7.368	0.26785	0.0:0.7243:0.2757:0.0	.	571	Q0VGE8	ZN816_HUMAN	V	571	ENSP00000350295:A571V;ENSP00000403266:A571V	ENSP00000350295:A571V	A	-	2	0	ZNF816	58145128	0.000000	0.05858	0.164000	0.22755	0.285000	0.27093	-0.144000	0.10280	0.088000	0.17205	-0.980000	0.02579	GCG		0.378	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		A	53453316	G	A	53453316	3	1	61	1	0	0	0	0	1	0	0	0	18216	1087	38	1	247	1	ZNF816A	19	53453316	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	69067	53453316	5675667	11307	19292										
ZNF816A	125893	broad.mit.edu	37	chr19	53453856	53453856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtaaggtttctctccagtgTgaagtatatgatggcattga	11	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53453856T>C	ENST00000357666.4	-	5	1472	c.1172A>G	c.(1171-1173)cAc>cGc	p.H391R	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.H391R|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H391R(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						CTCTCCAGTGTGAAGTATATG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											140	140	140					19																	53453856		2203	4300	6503	58145668	SO:0001583	missense	125893			BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.1172A>G	19.37:g.53453856T>C	ENSP00000350295:p.His391Arg		58145668	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	37	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	15.04	2.714618	0.48622	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.67523	-0.27;-0.27	1.85	1.85	0.25348	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.82806	0.5117	M	0.92317	3.295	0.80722	D	1	D	0.71674	0.998	D	0.85130	0.997	T	0.83295	-0.0031	9	0.87932	D	0	.	8.4536	0.32886	0.0:0.0:0.0:1.0	.	391	Q0VGE8	ZN816_HUMAN	R	391	ENSP00000350295:H391R;ENSP00000403266:H391R	ENSP00000350295:H391R	H	-	2	0	ZNF816	58145668	1.000000	0.71417	0.122000	0.21767	0.021000	0.10359	4.274000	0.58921	0.833000	0.34828	0.260000	0.18958	CAC		0.393	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		C	53453856	T	C	53453856	3	2	61	1	0	0	0	0	1	0	0	0	18216	1696	59	4	787	4	ZNF816A	19	53453856	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	540	53453856	5675127	11308	19293										
ZNF160	90338	broad.mit.edu	37	chr19	53572255	53572255	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctttcccacactcattaCacttgtaaggtttctctcca	5	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53572255C>A	ENST00000429604.1	-	7	1947	c.1532G>T	c.(1531-1533)tGt>tTt	p.C511F	ZNF160_ENST00000599056.1_Missense_Mutation_p.C511F|ZNF160_ENST00000418871.1_Missense_Mutation_p.C511F|ZNF160_ENST00000601421.1_Missense_Mutation_p.C475F	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	511					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C511F(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		ACACTCATTACACTTGTAAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											102	103	102					19																	53572255		2203	4300	6503	58264067	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1532G>T	19.37:g.53572255C>A	ENSP00000406201:p.Cys511Phe		58264067	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.283981	0.40394	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	D;D	0.85088	-1.94;-1.94	2.47	2.47	0.30058	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93687	0.7983	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.94644	0.7833	9	0.87932	D	0	.	12.0276	0.53380	0.0:1.0:0.0:0.0	.	511	Q9HCG1	ZN160_HUMAN	F	511	ENSP00000406201:C511F;ENSP00000409597:C511F	ENSP00000409597:C511F	C	-	2	0	ZNF160	58264067	0.996000	0.38824	0.062000	0.19696	0.388000	0.30384	4.710000	0.61873	1.361000	0.45981	0.561000	0.74099	TGT		0.393	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		A	53572255	C	A	53572255	3	1	61	1	0	0	0	0	1	0	0	0	17778	478	17	2	928	2	ZNF160	19	53572255	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118399	53572255	5556728	11309	19294										
ZNF160	90338	broad.mit.edu	37	chr19	53572687	53572687	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcattacatttgaacggtTtttctccagtatgaattaac	5	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53572687T>C	ENST00000429604.1	-	7	1515	c.1100A>G	c.(1099-1101)aAa>aGa	p.K367R	ZNF160_ENST00000599056.1_Missense_Mutation_p.K367R|ZNF160_ENST00000418871.1_Missense_Mutation_p.K367R|ZNF160_ENST00000601421.1_Missense_Mutation_p.K331R	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	367					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K367R(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TTTGAACGGTTTTTCTCCAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	84	84					19																	53572687		2203	4300	6503	58264499	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1100A>G	19.37:g.53572687T>C	ENSP00000406201:p.Lys367Arg		58264499	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.852319	0.32699	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.24908	1.83;1.83	2.47	2.47	0.30058	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27063	0.0663	N	0.10685	0.025	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.11743	-1.0575	9	0.54805	T	0.06	.	9.5616	0.39373	0.0:0.0:0.0:1.0	.	367	Q9HCG1	ZN160_HUMAN	R	367	ENSP00000406201:K367R;ENSP00000409597:K367R	ENSP00000409597:K367R	K	-	2	0	ZNF160	58264499	0.002000	0.14202	0.094000	0.20943	0.083000	0.17756	0.178000	0.16820	1.118000	0.41863	0.459000	0.35465	AAA		0.373	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53572687	T	C	53572687	3	2	61	1	0	0	0	0	1	0	0	0	17778	1841	64	4	1360	4	ZNF160	19	53572687	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	432	53572687	5556296	11310	19295										
ZNF160	90338	broad.mit.edu	37	chr19	53572790	53572790	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctctccagtatgaattcGccgatgagttgcaaggtatg	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53572790G>A	ENST00000429604.1	-	7	1412	c.997C>T	c.(997-999)Cga>Tga	p.R333*	ZNF160_ENST00000599056.1_Nonsense_Mutation_p.R333*|ZNF160_ENST00000418871.1_Nonsense_Mutation_p.R333*|ZNF160_ENST00000601421.1_Nonsense_Mutation_p.R297*	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	333					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R333*(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		GTATGAATTCGCCGATGAGTT	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											95	93	93					19																	53572790		2203	4300	6503	58264602	SO:0001587	stop_gained	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.997C>T	19.37:g.53572790G>A	ENSP00000406201:p.Arg333*		58264602	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Nonsense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180302	0.78677	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	.	.	.	2.47	1.4	0.22301	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.2225	0.10565	0.0:0.139:0.4709:0.3901	.	.	.	.	X	333	.	ENSP00000409597:R333X	R	-	1	2	ZNF160	58264602	0.000000	0.05858	0.006000	0.13384	0.264000	0.26372	-0.192000	0.09587	0.193000	0.20303	-0.397000	0.06425	CGA		0.403	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		A	53572790	G	A	53572790	4	1	61	1	0	0	0	0	0	1	0	0	17778	1095	38	1	1463	1	ZNF160	19	53572790	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103	53572790	5556193	11311	19296										
ZNF415	55786	broad.mit.edu	37	chr19	53612174	53612174	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccccagtgtgaattctcTgatgagttgcaaggcttgaa	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53612174T>G	ENST00000500065.4	-	4	1457	c.1124A>C	c.(1123-1125)cAg>cCg	p.Q375P	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.Q387P|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000601493.1_Missense_Mutation_p.Q145P|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.Q423P|ZNF415_ENST00000440291.1_Missense_Mutation_p.Q362P|ZNF415_ENST00000243643.4_Missense_Mutation_p.Q375P|ZNF415_ENST00000455735.2_Missense_Mutation_p.Q423P	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q375P(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		GTGAATTCTCTGATGAGTTGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	59	61					19																	53612174		2203	4300	6503	58303986	SO:0001583	missense	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1124A>C	19.37:g.53612174T>G	ENSP00000439435:p.Gln375Pro		58303986	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.606858	0.28623	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18	2.67	-2.35	0.06684	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15089	0.0364	L	0.42581	1.335	0.09310	N	1	D;D;D;D;D;D	0.67145	0.99;0.996;0.991;0.995;0.99;0.984	P;D;P;D;P;P	0.68765	0.544;0.96;0.79;0.913;0.638;0.787	T	0.11891	-1.0569	9	0.72032	D	0.01	.	5.4893	0.16767	0.0:0.4494:0.1693:0.3813	.	375;423;423;375;362;387	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	P	375;375;423;387;423;362	ENSP00000243643:Q375P;ENSP00000439435:Q375P;ENSP00000396492:Q423P;ENSP00000395055:Q387P;ENSP00000388787:Q423P;ENSP00000414601:Q362P	ENSP00000243643:Q375P	Q	-	2	0	ZNF415	58303986	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-1.425000	0.02446	-0.871000	0.04042	0.397000	0.26171	CAG		0.418	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		G	53612174	T	G	53612174	3	3	61	1	0	0	0	0	1	0	0	0	17931	1580	55	4	547	4	ZNF415	19	53612174	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	39384	53612174	5516809	11312	19297										
ZNF415	55786	broad.mit.edu	37	chr19	53612426	53612426	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctccagtgtgaactctcCgatgtagtgcaaggcatgag	11	10	2	2	rs138480197	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53612426C>A	ENST00000500065.4	-	4	1205	c.872G>T	c.(871-873)cGg>cTg	p.R291L	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.R303L|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000601493.1_Missense_Mutation_p.R61L|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.R339L|ZNF415_ENST00000440291.1_Missense_Mutation_p.R278L|ZNF415_ENST00000243643.4_Missense_Mutation_p.R291L|ZNF415_ENST00000455735.2_Missense_Mutation_p.R339L	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R291L(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		GTGAACTCTCCGATGTAGTGC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											101	89	93					19																	53612426		2203	4300	6503	58304238	SO:0001583	missense	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.872G>T	19.37:g.53612426C>A	ENSP00000439435:p.Arg291Leu		58304238	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808715	0.31961	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51	2.78	-5.55	0.02536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11153	0.0272	N	0.13327	0.33	0.09310	N	1	B;P;B;P;B;B	0.43412	0.0;0.806;0.0;0.626;0.0;0.159	B;P;B;B;B;B	0.53649	0.001;0.731;0.001;0.28;0.001;0.076	T	0.20472	-1.0274	9	0.66056	D	0.02	.	4.0911	0.09970	0.2495:0.3289:0.0:0.4217	.	291;339;339;291;278;303	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	L	291;291;339;303;339;278	ENSP00000243643:R291L;ENSP00000439435:R291L;ENSP00000396492:R339L;ENSP00000395055:R303L;ENSP00000388787:R339L;ENSP00000414601:R278L	ENSP00000243643:R291L	R	-	2	0	ZNF415	58304238	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.175000	0.03102	-2.022000	0.00938	-0.332000	0.08345	CGG		0.418	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612426	C	A	53612426	3	1	61	1	0	0	0	0	1	0	0	0	17931	652	23	2	799	2	ZNF415	19	53612426	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	252	53612426	5516557	11313	19298										
ZNF415	55786	broad.mit.edu	37	chr19	53612635	53612635	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatgattcaaggctttgtcGcactcaatatatctgtaagg	8	9	3	1	rs375385270		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53612635G>A	ENST00000500065.4	-	4	996	c.663C>T	c.(661-663)tgC>tgT	p.C221C	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Silent_p.C233C|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000448501.1_Silent_p.C269C|ZNF415_ENST00000440291.1_Silent_p.C208C|ZNF415_ENST00000243643.4_Silent_p.C221C|ZNF415_ENST00000455735.2_Silent_p.C269C	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C221C(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		AGGCTTTGTCGCACTCAATAT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G	,,	1,4405	2.1+/-5.4	0,1,2202	154	123	134		663,663,663	-2.7	0	19		134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	221/556,221/556,221/556	53612635	1,13005	2203	4300	6503	58304447	SO:0001819	synonymous_variant	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.663C>T	19.37:g.53612635G>A			58304447	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																				0.378	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612635	G	A	53612635	2	1	61	1	0	0	0	0	0	0	0	1	17931	1079	38	1		1	ZNF415	19	53612635	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	209	53612635	5516348	11314	19299										
ZNF347	84671	broad.mit.edu	37	chr19	53643837	53643837	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcttgcaaggtgtgaattCtgagtgaagaccttcccaca	10	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53643837C>A	ENST00000334197.7	-	5	2312	c.2244G>T	c.(2242-2244)caG>caT	p.Q748H	ZNF347_ENST00000601469.2_Missense_Mutation_p.Q749H|ZNF347_ENST00000452676.2_Missense_Mutation_p.Q749H|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	748					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q748H(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		GGTGTGAATTCTGAGTGAAGA	0.423																																					Melanoma(64;205 1597 17324 45721)											1	Substitution - Missense(1)	large_intestine(1)	19											170	159	163					19																	53643837		2203	4300	6503	58335649	SO:0001583	missense	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2244G>T	19.37:g.53643837C>A	ENSP00000334146:p.Gln748His		58335649	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	3.266	-0.150157	0.06585	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07327	3.2;3.2	2.56	-3.11	0.05299	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02688	0.0081	N	0.04705	-0.18	0.09310	N	1	P;B	0.36753	0.568;0.001	B;B	0.34991	0.193;0.002	T	0.41142	-0.9525	9	0.13853	T	0.58	.	3.148	0.06478	0.1594:0.5095:0.1607:0.1703	.	749;748	G5E9N4;Q96SE7	.;ZN347_HUMAN	H	748;749	ENSP00000334146:Q748H;ENSP00000405218:Q749H	ENSP00000334146:Q748H	Q	-	3	2	ZNF347	58335649	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-7.779000	0.00030	-0.635000	0.05531	-0.302000	0.09304	CAG		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53643837	C	A	53643837	3	1	61	1	0	0	0	0	1	0	0	0	17900	912	32	2	279	2	ZNF347	19	53643837	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31202	53643837	5485146	11315	19300										
ZNF347	84671	broad.mit.edu	37	chr19	53644385	53644385	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attacatttgtaaggtttttCtccagtatggatgacctgat	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53644385C>A	ENST00000334197.7	-	5	1764	c.1696G>T	c.(1696-1698)Gaa>Taa	p.E566*	ZNF347_ENST00000601469.2_Nonsense_Mutation_p.E567*|ZNF347_ENST00000452676.2_Nonsense_Mutation_p.E567*|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	566					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E566*(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TAAGGTTTTTCTCCAGTATGG	0.413																																					Melanoma(64;205 1597 17324 45721)											1	Substitution - Nonsense(1)	large_intestine(1)	19											156	149	151					19																	53644385		2203	4300	6503	58336197	SO:0001587	stop_gained	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1696G>T	19.37:g.53644385C>A	ENSP00000334146:p.Glu566*		58336197	B3KU77|B9EG59|G5E9N4|Q8TCN1	Nonsense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	37	6.041210	0.97226	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	.	.	.	3.01	1.95	0.26073	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.4511	0.21903	0.0:0.7591:0.0:0.2409	.	.	.	.	X	566;567	.	ENSP00000334146:E566X	E	-	1	0	ZNF347	58336197	0.124000	0.22315	0.875000	0.34327	0.762000	0.43233	1.361000	0.34136	0.606000	0.29965	0.655000	0.94253	GAA		0.413	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53644385	C	A	53644385	4	1	61	1	0	0	0	0	0	1	0	0	17900	922	32	2	827	2	ZNF347	19	53644385	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	548	53644385	5484598	11316	19301										
ZNF665	79788	broad.mit.edu	37	chr19	53667893	53667893	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctccagtgtgaattcttCtatgatttgcaagatgtgaa	8	6	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53667893C>A	ENST00000600412.1	-	2	1770	c.1655G>T	c.(1654-1656)aGa>aTa	p.R552I	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.R617I			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R552I(1)|p.R617I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		GTGAATTCTTCTATGATTTGC	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	19											104	110	108					19																	53667893		2203	4300	6503	58359705	SO:0001583	missense	79788				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1655G>T	19.37:g.53667893C>A	ENSP00000469154:p.Arg552Ile		58359705	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	C	12.22	1.873693	0.33069	.	.	ENSG00000197497	ENST00000396424	T	0.15603	2.41	2.55	0.276	0.15663	.	.	.	.	.	T	0.12603	0.0306	N	0.16266	0.395	0.09310	N	1	P	0.47604	0.898	P	0.49799	0.622	T	0.14420	-1.0473	9	0.56958	D	0.05	.	2.6622	0.05030	0.1981:0.2562:0.0:0.5457	.	617	Q9H7R5-2	.	I	617	ENSP00000379702:R617I	ENSP00000379702:R617I	R	-	2	0	ZNF665	58359705	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.308000	0.01131	-0.124000	0.11724	-0.484000	0.04775	AGA		0.408	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53667893	C	A	53667893	3	1	61	1	0	0	0	0	1	0	0	0	18112	913	32	2	190	2	ZNF665	19	53667893	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23508	53667893	5461090	11317	19302										
ZNF665	79788	broad.mit.edu	37	chr19	53668389	53668389	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaggcttttctccagtatGaattgcctgatgggtagtta	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53668389G>A	ENST00000600412.1	-	2	1274	c.1159C>T	c.(1159-1161)Cat>Tat	p.H387Y	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.H452Y			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H387Y(1)|p.H452Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCTCCAGTATGAATTGCCTGA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	19											79	82	81					19																	53668389		2203	4300	6503	58360201	SO:0001583	missense	79788				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1159C>T	19.37:g.53668389G>A	ENSP00000469154:p.His387Tyr		58360201	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	G	14.44	2.535588	0.45176	.	.	ENSG00000197497	ENST00000396424	T	0.67523	-0.27	2.55	1.46	0.22682	.	.	.	.	.	D	0.85044	0.5607	H	0.95645	3.7	0.22996	N	0.998456	D	0.89917	1.0	D	0.91635	0.999	T	0.73579	-0.3938	9	0.87932	D	0	.	9.6412	0.39839	0.0:0.0:0.7901:0.2098	.	452	Q9H7R5-2	.	Y	452	ENSP00000379702:H452Y	ENSP00000379702:H452Y	H	-	1	0	ZNF665	58360201	1.000000	0.71417	0.001000	0.08648	0.002000	0.02628	4.319000	0.59197	0.382000	0.24878	0.543000	0.68304	CAT		0.428	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53668389	G	A	53668389	3	1	61	1	0	0	0	0	1	0	0	0	18112	1290	45	3	686	3	ZNF665	19	53668389	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	496	53668389	5460594	11318	19303										
ZNF665	79788	broad.mit.edu	37	chr19	53678753	53678753	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgtccctgtacaaagtcttCtgagcagggtccaggcatgt	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53678753C>A	ENST00000600412.1	-	2	63				ZNF665_ENST00000396424.3_Missense_Mutation_p.Q29H			Q9H7R5	ZN665_HUMAN	zinc finger protein 665						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q29H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		ACAAAGTCTTCTGAGCAGGGT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	19											133	137	136					19																	53678753		2203	4300	6503	58370565	SO:0001627	intron_variant	79788				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.53-9153G>T	19.37:g.53678753C>A			58370565	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	C	12.38	1.922002	0.33908	.	.	ENSG00000197497	ENST00000396424	T	0.09445	2.98	2.67	2.67	0.31697	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.24361	N	0.994877	D	0.76494	0.999	D	0.69479	0.964	T	0.02560	-1.1141	8	0.87932	D	0	.	11.0727	0.48012	0.0:1.0:0.0:0.0	.	29	Q9H7R5-2	.	H	29	ENSP00000379702:Q29H	ENSP00000379702:Q29H	Q	-	3	2	ZNF665	58370565	0.948000	0.32251	0.912000	0.35992	0.171000	0.22731	1.878000	0.39608	1.479000	0.48272	0.655000	0.94253	CAG		0.458	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53678753	C	A	53678753	1	1	61	0	1	0	0	0	0	0	0	0	18112	912	32	2		2	ZNF665	19	53678753	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10364	53678753	5450230	11319	19304										
ZNF677	342926	broad.mit.edu	37	chr19	53740628	53740628	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttttctccagtgtgaattCtctgatgttccacaagactt	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53740628C>A	ENST00000598513.1	-	5	1502	c.1352G>T	c.(1351-1353)aGa>aTa	p.R451I	ZNF677_ENST00000333952.4_Missense_Mutation_p.R451I	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R451I(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		AGTGTGAATTCTCTGATGTTC	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	19											51	49	50					19																	53740628		2203	4300	6503	58432440	SO:0001583	missense	342926			BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1352G>T	19.37:g.53740628C>A	ENSP00000469391:p.Arg451Ile		58432440		Missense_Mutation	SNP	ENST00000598513.1	37	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.640997	0.29157	.	.	ENSG00000197928	ENST00000333952	T	0.24908	1.83	2.21	2.21	0.28008	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38326	N	0.001728	T	0.39733	0.1089	M	0.67517	2.055	0.40570	D	0.981294	D	0.71674	0.998	D	0.64237	0.923	T	0.26467	-1.0102	10	0.49607	T	0.09	.	6.8865	0.24206	0.0:0.7088:0.2912:0.0	.	451	Q86XU0	ZN677_HUMAN	I	451	ENSP00000334394:R451I	ENSP00000334394:R451I	R	-	2	0	ZNF677	58432440	0.000000	0.05858	0.996000	0.52242	0.992000	0.81027	0.843000	0.27640	1.559000	0.49555	0.655000	0.94253	AGA		0.393	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		A	53740628	C	A	53740628	3	1	61	1	0	0	0	0	1	0	0	0	18123	913	32	2	406	2	ZNF677	19	53740628	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61875	53740628	5388355	11320	19305										
VN1R2	317701	broad.mit.edu	37	chr19	53762697	53762697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactgctgcactaatcattGcctgttttccaactattagc	5	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53762697G>A	ENST00000341702.3	+	1	1153	c.1069G>A	c.(1069-1071)Gcc>Acc	p.A357T	VN1R2_ENST00000598458.1_Intron	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	357					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.A357T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		ACTAATCATTGCCTGTTTTCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											232	211	218					19																	53762697		2203	4300	6503	58454509	SO:0001583	missense	317701			AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.1069G>A	19.37:g.53762697G>A	ENSP00000351244:p.Ala357Thr		58454509	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842979	0.32606	.	.	ENSG00000196131	ENST00000341702	T	0.09445	2.98	2.94	-2.78	0.05859	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.09423	0.0232	L	0.43757	1.38	0.09310	N	1	P	0.38250	0.624	B	0.39465	0.3	T	0.27739	-1.0065	9	0.45353	T	0.12	.	7.0517	0.25077	0.0:0.1546:0.3723:0.4731	.	357	Q8NFZ6	VN1R2_HUMAN	T	357	ENSP00000351244:A357T	ENSP00000351244:A357T	A	+	1	0	VN1R2	58454509	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.112000	0.15479	-0.371000	0.08004	0.596000	0.82720	GCC		0.443	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		A	53762697	G	A	53762697	3	1	61	1	0	0	0	0	1	0	0	0	17219	1319	46	3	1071	3	VN1R2	19	53762697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22069	53762697	5366286	11321	19306										
VN1R4	317703	broad.mit.edu	37	chr19	53770175	53770175	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacttggaaaaggcaggaGagagtgtaagaagacacaaa	12	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53770175G>T	ENST00000311170.4	-	1	797	c.744C>A	c.(742-744)ctC>ctA	p.L248L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	248					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.L248L(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		AAAGGCAGGAGAGAGTGTAAG	0.473										HNSCC(26;0.072)																																						1	Substitution - coding silent(1)	large_intestine(1)	19											51	45	47					19																	53770175		2203	4300	6503	58461987	SO:0001819	synonymous_variant	317703			AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.744C>A	19.37:g.53770175G>T			58461987	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Silent	SNP	ENST00000311170.4	37	CCDS33099.1																																																																																				0.473	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857		T	53770175	G	T	53770175	2	4	61	1	0	0	0	0	0	0	0	1	17220	929	33	2		2	VN1R4	19	53770175	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7478	53770175	5358808	11322	19307										
ZNF765	91661	broad.mit.edu	37	chr19	53911344	53911344	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggtttcaacagcccaaaGaatttcttgtaggcctgaaa	8	9	2	2	rs377536824		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53911344G>T	ENST00000396408.3	+	4	653	c.536G>T	c.(535-537)aGa>aTa	p.R179I	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R179I(1)		endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		ACAGCCCAAAGAATTTCTTGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	ILE/ARG	0,4390		0,0,2195	76	78	77		536	-1.2	0	19		77	1,8589	1.2+/-3.3	0,1,4294	no	missense	ZNF765	NM_001040185.1	97	0,1,6489	TT,TG,GG		0.0116,0.0,0.0077	benign	179/524	53911344	1,12979	2195	4295	6490	58603156	SO:0001583	missense	91661			BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"Zinc fingers, C2H2-type", "-"	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.536G>T	19.37:g.53911344G>T	ENSP00000379689:p.Arg179Ile		58603156	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	.	.	.	.	.	.	.	.	.	.	G	2.004	-0.428715	0.04701	0.0	1.16E-4	ENSG00000196417	ENST00000396408;ENST00000505866	T;T	0.08193	3.12;3.9	0.588	-1.18	0.09617	.	.	.	.	.	T	0.09423	0.0232	M	0.65677	2.01	0.09310	N	1	B	0.17852	0.024	B	0.26094	0.066	T	0.39272	-0.9622	7	.	.	.	.	.	.	.	.	179	Q7L2R6	ZN765_HUMAN	I	179;126	ENSP00000379689:R179I;ENSP00000421579:R126I	.	R	+	2	0	ZNF765	58603156	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	0.081000	0.14823	-0.427000	0.07350	0.174000	0.16983	AGA		0.373	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		T	53911344	G	T	53911344	3	4	61	1	0	0	0	0	1	0	0	0	18178	942	33	2	546	2	ZNF765	19	53911344	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	141169	53911344	5217639	11323	19308										
ZNF765	91661	broad.mit.edu	37	chr19	53911764	53911764	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcttcaaatacataggaGaattcatactggagagaaac	8	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53911764G>T	ENST00000396408.3	+	4	1073	c.956G>T	c.(955-957)aGa>aTa	p.R319I	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R319I(1)		endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		ATACATAGGAGAATTCATACT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	19											67	71	69					19																	53911764		2202	4298	6500	58603576	SO:0001583	missense	91661			BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"Zinc fingers, C2H2-type", "-"	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.956G>T	19.37:g.53911764G>T	ENSP00000379689:p.Arg319Ile		58603576	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	.	.	.	.	.	.	.	.	.	.	G	8.490	0.861704	0.17178	.	.	ENSG00000196417	ENST00000396408	T	0.02446	4.29	1.28	-0.0742	0.13731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04497	0.0123	M	0.70903	2.155	0.09310	N	0.999999	B	0.15141	0.012	B	0.24974	0.057	T	0.38757	-0.9646	8	.	.	.	.	6.5117	0.22226	0.1841:0.0:0.8159:0.0	.	319	Q7L2R6	ZN765_HUMAN	I	319	ENSP00000379689:R319I	.	R	+	2	0	ZNF765	58603576	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	-0.025000	0.12413	-0.193000	0.10415	0.289000	0.19496	AGA		0.403	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		T	53911764	G	T	53911764	3	4	61	1	0	0	0	0	1	0	0	0	18178	942	33	2	966	2	ZNF765	19	53911764	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	420	53911764	5217219	11324	19309										
ZNF761	388561	broad.mit.edu	37	chr19	53958429	53958429	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaatgagagtggcaaagCctttaattacagctcactct	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53958429C>T	ENST00000454407.1	+	0	1121							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A169V(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AGTGGCAAAGCCTTTAATTAC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19											105	107	106					19																	53958429		2203	4300	6503	58650241			388561			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958429C>T			58650241	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																					0.343	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		T	53958429	C	T	53958429	1	4	61	0	1	0	0	0	0	0	0	0	18175	739	26	3		3	ZNF761	19	53958429	RNA	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	46665	53958429	5170554	11325	19310										
ZNF813	126017	broad.mit.edu	37	chr19	53993651	53993651	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcttccaaatgcatgatGaaggagttctcatcaacagc	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53993651G>T	ENST00000396403.4	+	4	293	c.165G>T	c.(163-165)atG>atT	p.M55I	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M55I(1)		large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		AATGCATGATGAAGGAGTTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	85	84					19																	53993651		2181	4292	6473	58685463	SO:0001583	missense	126017			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.165G>T	19.37:g.53993651G>T	ENSP00000379684:p.Met55Ile		58685463		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.385891	0.01194	.	.	ENSG00000198346	ENST00000468450;ENST00000396403;ENST00000490956	T;T;T	0.13307	4.03;3.51;2.6	0.581	-1.16	0.09678	Krueppel-associated box (3);	.	.	.	.	T	0.03651	0.0104	N	0.00991	-1.07	0.09310	N	1	B	0.20671	0.047	B	0.23852	0.049	T	0.42344	-0.9457	8	0.27785	T	0.31	.	.	.	.	.	55	Q6ZN06	ZN813_HUMAN	I	2;55;86	ENSP00000419821:M2I;ENSP00000379684:M55I;ENSP00000418289:M86I	ENSP00000379684:M55I	M	+	3	0	ZNF813	58685463	0.006000	0.16342	0.003000	0.11579	0.297000	0.27493	-0.384000	0.07389	-0.422000	0.07405	0.134000	0.15878	ATG		0.383	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		T	53993651	G	T	53993651	3	4	61	1	0	0	0	0	1	0	0	0	18214	1290	45	2	175	2	ZNF813	19	53993651	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35222	53993651	5135332	11326	19311										
ZNF813	126017	broad.mit.edu	37	chr19	53994025	53994025	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcaacatcccaaagaaTttcttgtaggcccaaaaccc	4	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53994025T>G	ENST00000396403.4	+	4	667	c.539T>G	c.(538-540)aTt>aGt	p.I180S	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I180S(1)		large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TCCCAAAGAATTTCTTGTAGG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											96	107	103					19																	53994025		2180	4291	6471	58685837	SO:0001583	missense	126017			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.539T>G	19.37:g.53994025T>G	ENSP00000379684:p.Ile180Ser		58685837		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	T	6.680	0.493995	0.12702	.	.	ENSG00000198346	ENST00000396403	T	0.05649	3.41	0.75	-1.07	0.09968	.	.	.	.	.	T	0.11067	0.0270	M	0.83774	2.66	0.09310	N	1	B	0.34290	0.447	B	0.38921	0.285	T	0.19063	-1.0317	8	0.66056	D	0.02	.	.	.	.	.	180	Q6ZN06	ZN813_HUMAN	S	180	ENSP00000379684:I180S	ENSP00000379684:I180S	I	+	2	0	ZNF813	58685837	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.109000	0.10840	-0.317000	0.08677	0.172000	0.16884	ATT		0.393	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		G	53994025	T	G	53994025	3	3	61	1	0	0	0	0	1	0	0	0	18214	1493	52	4	549	4	ZNF813	19	53994025	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	374	53994025	5134958	11327	19312										
ZNF813	126017	broad.mit.edu	37	chr19	53994221	53994221	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagagaaacaatataaatgTgatgtatgtggcaaggtctt	12	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53994221T>G	ENST00000396403.4	+	4	863	c.735T>G	c.(733-735)tgT>tgG	p.C245W	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C245W(1)		large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		AATATAAATGTGATGTATGTG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	77	76					19																	53994221		2198	4299	6497	58686033	SO:0001583	missense	126017			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.735T>G	19.37:g.53994221T>G	ENSP00000379684:p.Cys245Trp		58686033		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.126479	0.37533	.	.	ENSG00000198346	ENST00000396403	D	0.85258	-1.96	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94748	0.8305	H	0.99130	4.44	0.23168	N	0.998186	D	0.89917	1.0	D	0.87578	0.998	D	0.85261	0.1050	9	0.87932	D	0	.	6.8716	0.24123	0.0:0.0:0.0:1.0	.	245	Q6ZN06	ZN813_HUMAN	W	245	ENSP00000379684:C245W	ENSP00000379684:C245W	C	+	3	2	ZNF813	58686033	0.010000	0.17322	0.300000	0.25030	0.310000	0.27922	-0.141000	0.10327	0.175000	0.19841	0.172000	0.16884	TGT		0.388	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		G	53994221	T	G	53994221	3	3	61	1	0	0	0	0	1	0	0	0	18214	1702	59	4	745	4	ZNF813	19	53994221	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	196	53994221	5134762	11328	19313										
ZNF813	126017	broad.mit.edu	37	chr19	53995298	53995298	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagacttcatactggagaGaaaccttacaagtttaatga	7	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:53995298G>T	ENST00000396403.4	+	4	1940	c.1812G>T	c.(1810-1812)gaG>gaT	p.E604D	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E604D(1)		large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATACTGGAGAGAAACCTTACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	19											34	36	35					19																	53995298		2188	4289	6477	58687110	SO:0001583	missense	126017			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.1812G>T	19.37:g.53995298G>T	ENSP00000379684:p.Glu604Asp		58687110		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	g	10.06	1.245986	0.22796	.	.	ENSG00000198346	ENST00000396403	T	0.26810	1.71	1.28	-0.0579	0.13799	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23846	0.0577	M	0.64630	1.985	0.80722	D	1	B	0.10296	0.003	B	0.19946	0.027	T	0.14504	-1.0470	9	0.72032	D	0.01	.	6.6473	0.22943	0.1887:0.0:0.8113:0.0	.	604	Q6ZN06	ZN813_HUMAN	D	604	ENSP00000379684:E604D	ENSP00000379684:E604D	E	+	3	2	ZNF813	58687110	0.015000	0.18098	0.018000	0.16275	0.186000	0.23388	0.093000	0.15086	0.455000	0.26910	0.187000	0.17357	GAG		0.363	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		T	53995298	G	T	53995298	3	4	61	1	0	0	0	0	1	0	0	0	18214	933	33	2	1822	2	ZNF813	19	53995298	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1077	53995298	5133685	11329	19314										
ZNF331	55422	broad.mit.edu	37	chr19	54079953	54079953	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgttcttttttcccagatTtggagtcagcatatgaaaat	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54079953T>C	ENST00000253144.9	+	7	1472	c.139T>C	c.(139-141)Ttg>Ctg	p.L47L	ZNF331_ENST00000513999.1_Silent_p.L47L|ZNF331_ENST00000512387.1_Silent_p.L47L|ZNF331_ENST00000511154.1_Silent_p.L47L|ZNF331_ENST00000511593.2_Silent_p.L47L|ZNF331_ENST00000411977.2_Silent_p.L47L|ZNF331_ENST00000449416.1_Silent_p.L47L|ZNF331_ENST00000513265.1_Silent_p.L47L	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L47L(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TTTCCCAGATTTGGAGTCAGC	0.323			T	?	follicular thyroid adenoma																																		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	1	Substitution - coding silent(1)	large_intestine(1)	19											37	41	40					19																	54079953		2202	4300	6502	58771765	SO:0001819	synonymous_variant	55422			AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.139T>C	19.37:g.54079953T>C			58771765	Q96GJ4	Silent	SNP	ENST00000253144.9	37	CCDS33102.1																																																																																				0.323	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		C	54079953	T	C	54079953	2	2	61	1	0	0	0	0	0	0	0	1	17888	1838	64	4		4	ZNF331	19	54079953	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	84655	54079953	5049030	11330	19315										
ZNF331	55422	broad.mit.edu	37	chr19	54081178	54081178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaccacctaaaccatctccGagaacatcagaggatccaca	5	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54081178G>A	ENST00000253144.9	+	7	2697	c.1364G>A	c.(1363-1365)cGa>cAa	p.R455Q	ZNF331_ENST00000513999.1_Missense_Mutation_p.R455Q|ZNF331_ENST00000512387.1_Missense_Mutation_p.R455Q|ZNF331_ENST00000511154.1_Missense_Mutation_p.R455Q|ZNF331_ENST00000511593.2_Missense_Mutation_p.R455Q|ZNF331_ENST00000411977.2_Missense_Mutation_p.R455Q|ZNF331_ENST00000449416.1_Missense_Mutation_p.R455Q	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R455Q(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		AACCATCTCCGAGAACATCAG	0.493			T	?	follicular thyroid adenoma																																		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	1	Substitution - Missense(1)	large_intestine(1)	19											56	50	52					19																	54081178		2203	4300	6503	58772990	SO:0001583	missense	55422			AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1364G>A	19.37:g.54081178G>A	ENSP00000253144:p.Arg455Gln		58772990	Q96GJ4	Missense_Mutation	SNP	ENST00000253144.9	37	CCDS33102.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194836	0.38806	.	.	ENSG00000130844	ENST00000253144;ENST00000511593;ENST00000449416;ENST00000411977;ENST00000511154;ENST00000513999;ENST00000512387	T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6	3.58	-5.19	0.02832	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.170740	0.06762	N	0.782032	T	0.19327	0.0464	L	0.35542	1.07	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.39542	-0.9609	10	0.66056	D	0.02	.	5.3595	0.16079	0.3089:0.449:0.2422:0.0	.	455	Q9NQX6	ZN331_HUMAN	Q	455	ENSP00000253144:R455Q;ENSP00000427439:R455Q;ENSP00000393817:R455Q;ENSP00000393336:R455Q;ENSP00000421014:R455Q;ENSP00000423156:R455Q;ENSP00000421728:R455Q	ENSP00000253144:R455Q	R	+	2	0	ZNF331	58772990	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.559000	0.02162	-0.596000	0.05821	0.655000	0.94253	CGA		0.493	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		A	54081178	G	A	54081178	3	1	61	1	0	0	0	0	1	0	0	0	17888	1058	37	1	1374	1	ZNF331	19	54081178	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1225	54081178	5047805	11331	19316										
NLRP12	91662	broad.mit.edu	37	chr19	54297342	54297342	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaggttttgttactcgaagCgctgccaacctactgtgggt	11	9	0	0	rs148506660		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54297342C>T	ENST00000324134.6	-	10	3315	c.3147G>A	c.(3145-3147)gcG>gcA	p.A1049A	NLRP12_ENST00000345770.5_Silent_p.A994A|NLRP12_ENST00000535162.1_Silent_p.A992A|NLRP12_ENST00000351894.4_Silent_p.A937A|NLRP12_ENST00000391775.3_Silent_p.A992A|NLRP12_ENST00000391772.1_Silent_p.A880A|NLRP12_ENST00000354278.3_Silent_p.A880A|NLRP12_ENST00000391773.1_Silent_p.A1050A	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	1049					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.A1049A(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TTACTCGAAGCGCTGCCAACC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C	,	0,4406		0,0,2203	176	140	152		825,3147	-8.9	0	19	dbSNP_134	152	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,coding-synonymous	NLRP12	NM_033297.2,NM_144687.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	275/288,1049/1062	54297342	1,13005	2203	4300	6503	58989154	SO:0001819	synonymous_variant	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.3147G>A	19.37:g.54297342C>T			58989154	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																				0.463	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54297342	C	T	54297342	2	4	61	1	0	0	0	0	0	0	0	1	10505	755	27	1		1	NLRP12	19	54297342	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	216164	54297342	4831641	11332	19317										
NLRP12	91662	broad.mit.edu	37	chr19	54310827	54310827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccggctgcccagggcatttCggtacagagacagctctatc	11	14	1	1	rs199475868	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54310827C>T	ENST00000324134.6	-	4	2333	c.2165G>A	c.(2164-2166)cGa>cAa	p.R722Q	NLRP12_ENST00000345770.5_Missense_Mutation_p.R723Q|NLRP12_ENST00000535162.1_Missense_Mutation_p.R722Q|NLRP12_ENST00000351894.4_Missense_Mutation_p.R722Q|NLRP12_ENST00000391775.3_Missense_Mutation_p.R722Q|NLRP12_ENST00000391772.1_Missense_Mutation_p.R723Q|NLRP12_ENST00000354278.3_Missense_Mutation_p.R722Q|NLRP12_ENST00000391773.1_Missense_Mutation_p.R723Q	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	722					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.R722Q(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CAGGGCATTTCGGTACAGAGA	0.582													C|||	4	0.000798722	0	0	5008	,	,		16994	0.002		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	19											81	72	75					19																	54310827		2203	4300	6503	59002639	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2165G>A	19.37:g.54310827C>T	ENSP00000319377:p.Arg722Gln		59002639	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.866	0.948186	0.18356	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	3.86	-2.13	0.07144	.	0.000000	0.35349	U	0.003273	T	0.81269	0.4787	N	0.25992	0.78	0.09310	N	0.999998	D;D;D;P	0.67145	0.996;0.973;0.996;0.913	P;P;P;P	0.58970	0.787;0.768;0.849;0.753	T	0.74850	-0.3524	10	0.11182	T	0.66	.	7.2272	0.26022	0.0:0.4228:0.0:0.5772	.	723;722;722;722	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	Q	722;722;722;722;722;723;723;723	ENSP00000319377:R722Q;ENSP00000438030:R722Q;ENSP00000340473:R722Q;ENSP00000346231:R722Q;ENSP00000375655:R722Q;ENSP00000375653:R723Q;ENSP00000375652:R723Q	ENSP00000319377:R722Q	R	-	2	0	NLRP12	59002639	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-1.645000	0.02000	-0.157000	0.11059	-0.300000	0.09419	CGA		0.582	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54310827	C	T	54310827	3	4	61	1	0	0	0	0	1	0	0	0	10505	884	31	1	1144	1	NLRP12	19	54310827	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13485	54310827	4818156	11333	19318										
NLRP12	91662	broad.mit.edu	37	chr19	54313811	54313811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtattccttcctttctgCctcagagaagcccaggatct	8	12	3	1	rs541068679		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54313811C>T	ENST00000324134.6	-	3	1270	c.1102G>A	c.(1102-1104)Gca>Aca	p.A368T	NLRP12_ENST00000345770.5_Missense_Mutation_p.A368T|NLRP12_ENST00000535162.1_Missense_Mutation_p.A368T|NLRP12_ENST00000351894.4_Missense_Mutation_p.A368T|NLRP12_ENST00000391775.3_Missense_Mutation_p.A368T|NLRP12_ENST00000391772.1_Missense_Mutation_p.A368T|NLRP12_ENST00000354278.3_Missense_Mutation_p.A368T|NLRP12_ENST00000391773.1_Missense_Mutation_p.A368T	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	368	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.A368T(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TTCCTTTCTGCCTCAGAGAAG	0.537													C|||	1	0.000199681	0	0	5008	,	,		19290	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19											160	166	164					19																	54313811		2203	4300	6503	59005623	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.1102G>A	19.37:g.54313811C>T	ENSP00000319377:p.Ala368Thr		59005623	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452618	0.26074	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.64	2.39	0.29439	NACHT nucleoside triphosphatase (1);	0.558998	0.14842	N	0.295206	T	0.81973	0.4936	L	0.49571	1.57	0.09310	N	1	D;D;D;D	0.76494	0.999;0.993;0.993;0.995	D;D;D;D	0.68039	0.947;0.934;0.934;0.955	T	0.67872	-0.5558	10	0.24483	T	0.36	.	4.8937	0.13740	0.0:0.6281:0.1777:0.1942	.	368;368;368;368	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	T	368	ENSP00000319377:A368T;ENSP00000438030:A368T;ENSP00000340473:A368T;ENSP00000346231:A368T;ENSP00000375655:A368T;ENSP00000375653:A368T;ENSP00000375652:A368T	ENSP00000319377:A368T	A	-	1	0	NLRP12	59005623	0.000000	0.05858	0.013000	0.15412	0.831000	0.47069	0.294000	0.19047	0.462000	0.27095	0.485000	0.47835	GCA		0.537	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54313811	C	T	54313811	3	4	61	1	0	0	0	0	1	0	0	0	10505	739	26	3	2211	3	NLRP12	19	54313811	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2984	54313811	4815172	11334	19319										
NLRP12	91662	broad.mit.edu	37	chr19	54314328	54314328	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcaaagagggtctctatCttgatggggctagcctggtg	15	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54314328C>A	ENST00000324134.6	-	3	753	c.585G>T	c.(583-585)aaG>aaT	p.K195N	NLRP12_ENST00000345770.5_Missense_Mutation_p.K195N|NLRP12_ENST00000535162.1_Missense_Mutation_p.K195N|NLRP12_ENST00000351894.4_Missense_Mutation_p.K195N|NLRP12_ENST00000391775.3_Missense_Mutation_p.K195N|NLRP12_ENST00000391772.1_Missense_Mutation_p.K195N|NLRP12_ENST00000354278.3_Missense_Mutation_p.K195N|NLRP12_ENST00000391773.1_Missense_Mutation_p.K195N	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	195					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.K195N(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GGGTCTCTATCTTGATGGGGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											104	83	90					19																	54314328		2203	4300	6503	59006140	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.585G>T	19.37:g.54314328C>A	ENSP00000319377:p.Lys195Asn		59006140	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	2.946	-0.217913	0.06101	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5	4.25	-0.955	0.10356	.	0.942177	0.08709	N	0.905185	T	0.72495	0.3467	N	0.05124	-0.11	0.09310	N	1	B;B;B;B	0.27068	0.167;0.097;0.167;0.121	B;B;B;B	0.21360	0.034;0.023;0.034;0.032	T	0.58482	-0.7629	10	0.25106	T	0.35	.	6.4605	0.21954	0.0:0.3343:0.4718:0.1939	.	195;195;195;195	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	N	195	ENSP00000319377:K195N;ENSP00000438030:K195N;ENSP00000340473:K195N;ENSP00000346231:K195N;ENSP00000375655:K195N;ENSP00000375653:K195N;ENSP00000375652:K195N	ENSP00000319377:K195N	K	-	3	2	NLRP12	59006140	0.000000	0.05858	0.575000	0.28536	0.199000	0.23934	-0.802000	0.04545	-0.293000	0.08986	-1.225000	0.01585	AAG		0.637	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54314328	C	A	54314328	3	1	61	1	0	0	0	0	1	0	0	0	10505	912	32	2	2728	2	NLRP12	19	54314328	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	517	54314328	4814655	11335	19320										
NLRP12	91662	broad.mit.edu	37	chr19	54327263	54327263	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgatgagcagctgggccaTttccaggggaccggccttct	15	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54327263T>G	ENST00000324134.6	-	1	334	c.166A>C	c.(166-168)Atg>Ctg	p.M56L	NLRP12_ENST00000345770.5_Missense_Mutation_p.M56L|NLRP12_ENST00000535162.1_Missense_Mutation_p.M56L|NLRP12_ENST00000351894.4_Missense_Mutation_p.M56L|NLRP12_ENST00000391775.3_Missense_Mutation_p.M56L|NLRP12_ENST00000391772.1_Missense_Mutation_p.M56L|NLRP12_ENST00000354278.3_Missense_Mutation_p.M56L|NLRP12_ENST00000391773.1_Missense_Mutation_p.M56L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	56	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.M56L(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGCTGGGCCATTTCCAGGGGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											77	74	75					19																	54327263		2203	4300	6503	59019075	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.166A>C	19.37:g.54327263T>G	ENSP00000319377:p.Met56Leu		59019075	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.354124	0.01256	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56	4.7	-0.261	0.12963	Pyrin (2);DEATH-like (2);	0.817960	0.10538	N	0.663031	T	0.08980	0.0222	N	0.03238	-0.38	0.29134	N	0.879425	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.08055	0.003;0.002;0.003;0.002	T	0.37502	-0.9703	10	0.02654	T	1	.	2.4669	0.04554	0.3528:0.205:0.0:0.4422	.	56;56;56;56	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	L	56	ENSP00000319377:M56L;ENSP00000438030:M56L;ENSP00000340473:M56L;ENSP00000346231:M56L;ENSP00000375655:M56L;ENSP00000375653:M56L;ENSP00000375652:M56L	ENSP00000319377:M56L	M	-	1	0	NLRP12	59019075	0.078000	0.21339	0.305000	0.25099	0.462000	0.32619	-0.068000	0.11561	-0.012000	0.14223	0.254000	0.18369	ATG		0.587	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		G	54327263	T	G	54327263	3	3	61	1	0	0	0	0	1	0	0	0	10505	1493	52	4	3155	4	NLRP12	19	54327263	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	12935	54327263	4801720	11336	19321										
PRKCG	5582	broad.mit.edu	37	chr19	54387447	54387447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggttcatcgacgatgccacGaatttgtgaccttcgagtgt	11	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54387447G>A	ENST00000263431.3	+	3	517	c.235G>A	c.(235-237)Gaa>Aaa	p.E79K	PRKCG_ENST00000540413.1_Missense_Mutation_p.E79K|PRKCG_ENST00000542049.1_Missense_Mutation_p.R3Q|PRKCG_ENST00000536044.1_Missense_Mutation_p.E79K	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	79					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.E79K(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	ACGATGCCACGAATTTGTGAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	81	84					19																	54387447		2203	4300	6503	59079259	SO:0001583	missense	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.235G>A	19.37:g.54387447G>A	ENSP00000263431:p.Glu79Lys		59079259	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.2|25.2	4.616599|4.616599	0.87359|0.87359	.|.	.|.	ENSG00000126583|ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000419486|ENST00000542049	D;D;D|T	0.92699|0.69561	-3.09;-3.09;-3.09|-0.41	4.68|4.68	4.68|4.68	0.58851|0.58851	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);|.	.|.	.|.	.|.	.|.	T|T	0.73361|0.73361	0.3577|0.3577	L|L	0.35593|0.35593	1.075|1.075	0.30700|0.30700	N|N	0.750409|0.750409	D;D;P;P|D	0.63046|0.69078	0.992;0.987;0.796;0.766|0.997	P;P;B;P|D	0.58820|0.67725	0.843;0.846;0.362;0.546|0.953	T|T	0.73742|0.73742	-0.3887|-0.3887	9|9	0.41790|0.87932	T|D	0.15|0	.|.	15.4645|15.4645	0.75387|0.75387	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	79;79;79;79|3	F5H5C4;B7Z870;B7Z3W6;P05129|B7Z8Q0	.;.;.;KPCG_HUMAN|.	K|Q	79;79;79;102|3	ENSP00000440541:E79K;ENSP00000443493:E79K;ENSP00000263431:E79K|ENSP00000438090:R3Q	ENSP00000263431:E79K|ENSP00000438090:R3Q	E|R	+|+	1|2	0|0	PRKCG|PRKCG	59079259|59079259	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.914000|0.914000	0.54420|0.54420	6.844000|6.844000	0.75390|0.75390	2.332000|2.332000	0.79248|0.79248	0.313000|0.313000	0.20887|0.20887	GAA|CGA		0.592	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54387447	G	A	54387447	3	1	61	1	0	0	0	0	1	0	0	0	12546	1059	37	1	245	1	PRKCG	19	54387447	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60184	54387447	4741536	11337	19322										
CACNG6	59285	broad.mit.edu	37	chr19	54501518	54501518	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactgcacctattttaaattCttcaccacgggggagaatgc	8	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54501518C>A	ENST00000252729.2	+	2	947	c.357C>A	c.(355-357)ttC>ttA	p.F119L	CACNG6_ENST00000346968.2_Missense_Mutation_p.F119L|CACNG6_ENST00000352529.1_Intron	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	119					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.F119L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	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;0.168)		ATTTTAAATTCTTCACCACGG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	95	100					19																	54501518		2203	4300	6503	59193330	SO:0001583	missense	59285			AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"Calcium channel subunits"	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.357C>A	19.37:g.54501518C>A	ENSP00000252729:p.Phe119Leu		59193330		Missense_Mutation	SNP	ENST00000252729.2	37	CCDS12870.1	.	.	.	.	.	.	.	.	.	.	.	20.7	4.041390	0.75732	.	.	ENSG00000130433	ENST00000252729;ENST00000346968	T;T	0.35789	1.31;1.29	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	L	0.57536	1.79	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.77004	0.98;0.989	T	0.40308	-0.9570	10	0.22706	T	0.39	-15.569	14.9705	0.71229	0.0:1.0:0.0:0.0	.	119;119	A6NFR2;Q9BXT2	.;CCG6_HUMAN	L	119	ENSP00000252729:F119L;ENSP00000319097:F119L	ENSP00000252729:F119L	F	+	3	2	CACNG6	59193330	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.127000	0.57944	2.685000	0.91497	0.655000	0.94253	TTC		0.507	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1			A	54501518	C	A	54501518	3	1	61	1	0	0	0	0	1	0	0	0	2567	912	32	2	363	2	CACNG6	19	54501518	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	114071	54501518	4627465	11338	19323										
TMC4	147798	broad.mit.edu	37	chr19	54667480	54667480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaggataaaaacgatctggCgactccgagtgtagccctcc	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54667480C>T	ENST00000376591.4	-	8	1402	c.1271G>A	c.(1270-1272)cGc>cAc	p.R424H	TMC4_ENST00000476013.2_5'Flank|TMC4_ENST00000416963.1_5'Flank|TMC4_ENST00000301187.4_Missense_Mutation_p.R418H	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	424					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R418H(1)		breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					AACGATCTGGCGACTCCGAGT	0.572											OREG0003641	type=REGULATORY REGION|Gene=AK124406|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Missense(1)	large_intestine(1)	19											104	96	98					19																	54667480		2203	4300	6503	59359292	SO:0001583	missense	147798			AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1271G>A	19.37:g.54667480C>T	ENSP00000365776:p.Arg424His	1002	59359292	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	.	.	.	.	.	.	.	.	.	.	C	4.375	0.069118	0.08436	.	.	ENSG00000167608	ENST00000301187;ENST00000376591	T;T	0.50001	0.76;0.76	5.21	-0.714	0.11219	.	1.813140	0.02102	N	0.054020	T	0.36771	0.0979	L	0.45228	1.405	0.49687	D	0.999819	B;B	0.12630	0.006;0.002	B;B	0.10450	0.001;0.005	T	0.23190	-1.0195	10	0.14656	T	0.56	-4.9514	4.3563	0.11179	0.2444:0.4698:0.0:0.2858	.	424;418	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	H	418;424	ENSP00000301187:R418H;ENSP00000365776:R424H	ENSP00000301187:R418H	R	-	2	0	TMC4	59359292	0.091000	0.21658	0.961000	0.40146	0.114000	0.19823	-0.459000	0.06728	-0.152000	0.11156	-0.219000	0.12488	CGC		0.572	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			T	54667480	C	T	54667480	3	4	61	1	0	0	0	0	1	0	0	0	16026	768	27	1	899	1	TMC4	19	54667480	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	165962	54667480	4461503	11339	19324										
RPS9	6203	broad.mit.edu	37	chr19	54705148	54705148	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccaagagctgaagctgatCggtgagtggccaaggcttcc	14	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54705148C>T	ENST00000302907.4	+	2	268	c.96C>T	c.(94-96)atC>atT	p.I32I	RPS9_ENST00000391753.2_Splice_Site_p.I32I|AC012314.20_ENST00000426213.1_RNA|RPS9_ENST00000391751.3_Splice_Site_p.I32I|RPS9_ENST00000391752.1_Splice_Site_p.I32I|RPS9_ENST00000441429.1_Splice_Site_p.I32I|RPS9_ENST00000402367.1_Splice_Site_p.I32I	NM_001013.3	NP_001004.2	P46781	RS9_HUMAN	ribosomal protein S9	32					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)	p.I32I(1)		NS(1)|breast(1)|kidney(11)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	20	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.18)		TGAAGCTGATCGGTGAGTGGC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	19											40	41	40					19																	54705148		2203	4300	6503	59396960	SO:0001630	splice_region_variant	6203			U14971	CCDS12884.1	19q13.4	2011-04-05			ENSG00000170889	ENSG00000170889		"S ribosomal proteins"	10442	protein-coding gene	gene with protein product	"40S ribosomal protein S9"	603631				7772601, 9582194	Standard	XM_005259135		Approved	S9	uc002qdx.3	P46781	OTTHUMG00000066618	ENST00000302907.4:c.97+1C>T	19.37:g.54705148C>T			59396960	A9C4C1|Q4QRK7|Q9BVZ0	Silent	SNP	ENST00000302907.4	37	CCDS12884.1																																																																																				0.572	RPS9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142834.3	NM_001013	Silent	T	54705148	C	T	54705148	5	4	61	1	0	0	0	0	0	0	1	0	13699	898	31	1	98	1	RPS9	19	54705148	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37668	54705148	4423835	11340	19325										
LILRA6	79168	broad.mit.edu	37	chr19	54746102	54746102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtactcctgggcctccaggCtcccctgacaccagatggtc	11	16	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54746102C>T	ENST00000396365.2	-	3	194	c.155G>A	c.(154-156)aGc>aAc	p.S52N	LILRA6_ENST00000391735.3_Missense_Mutation_p.S52N|LILRA6_ENST00000245621.5_Missense_Mutation_p.S52N|LILRA6_ENST00000440558.2_Missense_Mutation_p.S52N|LILRA6_ENST00000270464.5_Missense_Mutation_p.S52N|LILRA6_ENST00000419410.2_Missense_Mutation_p.S52N|LILRB3_ENST00000407860.2_Missense_Mutation_p.S52N	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	52					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.S52N(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGCCTCCAGGCTCCCCTGACA	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	19											210	211	211					19																	54746102		2203	4300	6503	59437914	SO:0001583	missense	11025			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15495	protein-coding gene	gene with protein product			"leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.155G>A	19.37:g.54746102C>T	ENSP00000379651:p.Ser52Asn		59437914		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	4.117	0.019982	0.08006	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62;2.62;2.62	3.19	0.725	0.18242	Immunoglobulin-like fold (1);	0.908784	0.09292	N	0.822121	T	0.09686	0.0238	L	0.31371	0.925	0.09310	N	1	B;B;B;B;B;B;B;B;B;B	0.24533	0.003;0.0;0.0;0.0;0.105;0.001;0.002;0.002;0.001;0.01	B;B;B;B;B;B;B;B;B;B	0.26517	0.01;0.003;0.003;0.003;0.07;0.006;0.012;0.004;0.016;0.015	T	0.40701	-0.9549	10	0.30854	T	0.27	.	5.5285	0.16970	0.0:0.2261:0.5469:0.227	.	52;52;52;52;52;52;52;52;52;52	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	N	52	ENSP00000384274:S52N;ENSP00000390120:S52N;ENSP00000270464:S52N;ENSP00000411227:S52N;ENSP00000375615:S52N;ENSP00000379651:S52N;ENSP00000245621:S52N	ENSP00000245621:S52N	S	-	2	0	LILRB3;LILRA6	59437914	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.668000	0.01959	0.162000	0.19483	-1.271000	0.01417	AGC		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		T	54746102	C	T	54746102	3	4	61	1	0	0	0	0	1	0	0	0	8812	797	28	3	1314	3	LILRA6	19	54746102	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40954	54746102	4382881	11341	19326										
LILRB5	10990	broad.mit.edu	37	chr19	54756374	54756374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcaggccctggtccttggGctctggccccgcagcccctg	13	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54756374G>A	ENST00000316219.5	-	10	1617	c.1510C>T	c.(1510-1512)Ccc>Tcc	p.P504S	LILRB5_ENST00000449561.2_Missense_Mutation_p.P505S|LILRB5_ENST00000345866.6_Missense_Mutation_p.P405S|LILRB5_ENST00000450632.1_Missense_Mutation_p.P496S|CTD-2337J16.1_ENST00000595133.1_lincRNA	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	504					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.P504S(1)|p.P496S(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTCCTTGGGCTCTGGCCCC	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	19											102	98	99					19																	54756374		2203	4300	6503	59448186	SO:0001583	missense	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1510C>T	19.37:g.54756374G>A	ENSP00000320390:p.Pro504Ser		59448186	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.578180	0.28180	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00475	7.22;7.17;7.21;7.24	2.08	-0.3	0.12804	.	.	.	.	.	T	0.00906	0.0030	M	0.70842	2.15	0.09310	N	1	D;P;B;P	0.89917	1.0;0.86;0.003;0.572	D;P;B;B	0.83275	0.996;0.661;0.007;0.052	T	0.51116	-0.8746	9	0.49607	T	0.09	.	3.2535	0.06823	0.1768:0.2791:0.5441:0.0	.	496;405;505;504	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	S	504;496;505;405	ENSP00000320390:P504S;ENSP00000414225:P496S;ENSP00000406478:P505S;ENSP00000263430:P405S	ENSP00000320390:P504S	P	-	1	0	LILRB5	59448186	0.006000	0.16342	0.001000	0.08648	0.001000	0.01503	0.707000	0.25704	-0.002000	0.14469	-0.291000	0.09656	CCC		0.617	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			A	54756374	G	A	54756374	3	1	61	1	0	0	0	0	1	0	0	0	8817	1203	42	3	278	3	LILRB5	19	54756374	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	10272	54756374	4372609	11342	19327										
LILRB5	10990	broad.mit.edu	37	chr19	54759181	54759181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtccagggggtcgctggggGccgaccacctaggggagagg	20	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54759181G>A	ENST00000316219.5	-	5	1027	c.920C>T	c.(919-921)gCc>gTc	p.A307V	LILRB5_ENST00000449561.2_Missense_Mutation_p.A307V|LILRB5_ENST00000345866.6_Missense_Mutation_p.A207V|LILRB5_ENST00000450632.1_Missense_Mutation_p.A298V	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	307	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.A298V(1)|p.A307V(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTCGCTGGGGGCCGACCACCT	0.672																																																2	Substitution - Missense(2)	large_intestine(2)	19											31	33	32					19																	54759181		2201	4298	6499	59450993	SO:0001583	missense	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.920C>T	19.37:g.54759181G>A	ENSP00000320390:p.Ala307Val		59450993	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621902	0.28889	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	2.62	0.228	0.15364	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.452860	0.05232	N	0.510635	T	0.39860	0.1094	M	0.89904	3.07	0.09310	N	1	D;P;D;D;D	0.76494	0.998;0.784;0.999;0.998;0.968	D;P;D;D;P	0.72625	0.978;0.465;0.919;0.952;0.831	T	0.09292	-1.0681	10	0.66056	D	0.02	.	3.0709	0.06230	0.1559:0.0:0.5821:0.2621	.	298;198;207;307;307	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	V	307;298;307;207	ENSP00000320390:A307V;ENSP00000414225:A298V;ENSP00000406478:A307V;ENSP00000263430:A207V	ENSP00000320390:A307V	A	-	2	0	LILRB5	59450993	0.075000	0.21258	0.067000	0.19924	0.009000	0.06853	0.266000	0.18534	0.137000	0.18759	0.446000	0.29264	GCC		0.672	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			A	54759181	G	A	54759181	3	1	61	1	0	0	0	0	1	0	0	0	8817	1203	42	3	891	3	LILRB5	19	54759181	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2807	54759181	4369802	11343	19328										
LILRA5	353514	broad.mit.edu	37	chr19	54822896	54822896	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagaatgaacctgtcgaatCtcagccgtgagccacactgg	10	12	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54822896C>A	ENST00000301219.3	-	5	619	c.500G>T	c.(499-501)aGa>aTa	p.R167I	LILRA5_ENST00000446712.3_Missense_Mutation_p.R155I|LILRA5_ENST00000346508.3_Missense_Mutation_p.R155I|LILRA5_ENST00000432233.3_Missense_Mutation_p.R167I|AC008984.2_ENST00000507363.1_RNA	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	167	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R167T(1)|p.R167I(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCTGTCGAATCTCAGCCGTGA	0.577																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	19											68	67	67					19																	54822896		2203	4300	6503	59514708	SO:0001583	missense	353514			AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.500G>T	19.37:g.54822896C>A	ENSP00000301219:p.Arg167Ile		59514708	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	37	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	C	9.706	1.155829	0.21454	.	.	ENSG00000187116	ENST00000301219;ENST00000346508;ENST00000446712;ENST00000432233	T;T;T;T	0.03004	4.08;4.08;4.08;4.08	3.14	-1.16	0.09678	Immunoglobulin-like fold (1);	2.567660	0.02050	U	0.049950	T	0.07503	0.0189	M	0.66939	2.045	0.09310	N	1	B;B;B;B	0.30542	0.156;0.073;0.284;0.048	B;B;B;B	0.29176	0.099;0.012;0.099;0.006	T	0.46331	-0.9199	10	0.87932	D	0	.	10.6179	0.45462	0.0:0.4078:0.5922:0.0	.	155;167;155;167	A6NI73-4;A6NI73-3;A6NI73-2;A6NI73	.;.;.;LIRA5_HUMAN	I	167;155;155;167	ENSP00000301219:R167I;ENSP00000302948:R155I;ENSP00000389499:R155I;ENSP00000404236:R167I	ENSP00000301219:R167I	R	-	2	0	LILRA5	59514708	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.008000	0.03663	-0.412000	0.07519	0.205000	0.17691	AGA		0.577	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		A	54822896	C	A	54822896	3	1	61	1	0	0	0	0	1	0	0	0	8811	913	32	2	497	2	LILRA5	19	54822896	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63715	54822896	4306087	11344	19329										
TTYH1	57348	broad.mit.edu	37	chr19	54942297	54942297	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcctctgctgtccttggaGgagactctgaatgtgacaga	12	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54942297G>T	ENST00000376530.3	+	10	1156	c.1053G>T	c.(1051-1053)gaG>gaT	p.E351D	TTYH1_ENST00000391739.3_Nonsense_Mutation_p.G382*|AC008746.3_ENST00000457113.1_RNA|TTYH1_ENST00000301194.4_Missense_Mutation_p.E351D|TTYH1_ENST00000376531.3_Missense_Mutation_p.E351D|TTYH1_ENST00000489425.1_3'UTR	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	351					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.E351D(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		TGTCCTTGGAGGAGACTCTGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	84	84					19																	54942297		2203	4300	6503	59634109	SO:0001583	missense	57348			AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.1053G>T	19.37:g.54942297G>T	ENSP00000365713:p.Glu351Asp		59634109	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	37	CCDS12893.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.232262|6.232262	0.97399|0.97399	.|.	.|.	ENSG00000167614|ENSG00000167614	ENST00000301194;ENST00000376530;ENST00000376531|ENST00000391739	T;T;T|.	0.11169|.	2.8;2.8;2.8|.	4.07|4.07	3.03|3.03	0.35002|0.35002	.|.	0.136231|.	0.48767|.	D|.	0.000172|.	T|.	0.35068|.	0.0919|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	A|A	1|1	P;D;P;P|.	0.53745|.	0.856;0.962;0.9;0.91|.	P;P;B;P|.	0.50082|.	0.605;0.605;0.39;0.63|.	T|.	0.33189|.	-0.9878|.	9|.	0.23302|0.16420	T|T	0.38|0.52	-11.679|-11.679	5.5772|5.5772	0.17231|0.17231	0.2192:0.0:0.7808:0.0|0.2192:0.0:0.7808:0.0	.|.	263;351;351;351|.	Q9H313-5;Q9H313-2;Q9H313-3;Q9H313|.	.;.;.;TTYH1_HUMAN|.	D|X	351|382	ENSP00000301194:E351D;ENSP00000365713:E351D;ENSP00000365714:E351D|.	ENSP00000301194:E351D|ENSP00000375619:G382X	E|G	+|+	3|1	2|0	TTYH1|TTYH1	59634109|59634109	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	1.358000|1.358000	0.34102|0.34102	2.254000|2.254000	0.74563|0.74563	0.561000|0.561000	0.74099|0.74099	GAG|GGA		0.627	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			T	54942297	G	T	54942297	3	4	61	1	0	0	0	0	1	0	0	0	16779	991	35	2	1091	2	TTYH1	19	54942297	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119401	54942297	4186686	11345	19330										
LENG9	94059	broad.mit.edu	37	chr19	54973714	54973714	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttctgagagggcactagGaagttggcgcagtgtggggc	19	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:54973714G>T	ENST00000333834.4	-	1	1180	c.1062C>A	c.(1060-1062)ttC>ttA	p.F354L		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	354							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)	p.F332L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		AGGGCACTAGGAAGTTGGCGC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	64	66					19																	54973714		2203	4299	6502	59665526	SO:0001583	missense	94059			AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.1062C>A	19.37:g.54973714G>T	ENSP00000331647:p.Phe354Leu		59665526	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	37	CCDS12895.2	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095661	0.36952	.	.	ENSG00000182909	ENST00000333834	T	0.60299	0.2	4.39	2.2	0.27929	RNA ligase/cyclic nucleotide phosphodiesterase (1);	0.816417	0.11187	U	0.590298	T	0.49081	0.1536	M	0.64997	1.995	0.22591	N	0.998956	P	0.35714	0.517	B	0.35931	0.214	T	0.31308	-0.9948	10	0.15499	T	0.54	-21.594	6.2872	0.21039	0.1044:0.1872:0.7084:0.0	.	354	Q96B70	LENG9_HUMAN	L	354	ENSP00000331647:F354L	ENSP00000331647:F354L	F	-	3	2	LENG9	59665526	0.753000	0.28349	0.275000	0.24674	0.017000	0.09413	4.069000	0.57541	0.405000	0.25532	-0.502000	0.04539	TTC		0.632	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988		T	54973714	G	T	54973714	3	4	61	1	0	0	0	0	1	0	0	0	8747	1165	41	2	447	2	LENG9	19	54973714	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31417	54973714	4155269	11346	19331										
LAIR2	3904	broad.mit.edu	37	chr19	55019239	55019239	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggaggatagagccaagtaCaaagatagttataatgtgtt	12	3	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55019239C>T	ENST00000301202.2	+	3	326	c.204C>T	c.(202-204)taC>taT	p.Y68Y	LAIR2_ENST00000351841.2_Silent_p.Y68Y	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	68	Ig-like C2-type.					extracellular region (GO:0005576)		p.Y68Y(1)		central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		GAGCCAAGTACAAAGATAGTT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	19											111	103	106					19																	55019239		2203	4300	6503	59711051	SO:0001819	synonymous_variant	3904			AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6478	protein-coding gene	gene with protein product		602993	"leukocyte-associated Ig-like receptor 2"			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.204C>T	19.37:g.55019239C>T			59711051	Q6PEZ4	Silent	SNP	ENST00000301202.2	37	CCDS12897.1																																																																																				0.527	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			T	55019239	C	T	55019239	2	4	61	1	0	0	0	0	0	0	0	1	8625	489	17	3		3	LAIR2	19	55019239	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	45525	55019239	4109744	11347	19332										
LILRA2	11027	broad.mit.edu	37	chr19	55086234	55086234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccctctcagctctgcccaGccctgtggtgaccttaggag	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55086234G>A	ENST00000251377.3	+	5	522	c.389G>A	c.(388-390)aGc>aAc	p.S130N	LILRA2_ENST00000391738.3_Missense_Mutation_p.S130N|LILRA2_ENST00000391737.1_Missense_Mutation_p.S118N|LILRA2_ENST00000495786.1_3'UTR|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.S130N|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	130	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.S130N(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GCTCTGCCCAGCCCTGTGGTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											134	127	129					19																	55086234		2203	4300	6503	59778046	SO:0001583	missense	11027			U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.389G>A	19.37:g.55086234G>A	ENSP00000251377:p.Ser130Asn		59778046	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.283268	0.23392	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.00848	5.62;5.62;5.62;5.62;5.62	2.93	0.528	0.17089	Immunoglobulin-like fold (1);	0.108353	0.41712	N	0.000836	T	0.03915	0.0110	M	0.91090	3.175	0.09310	N	1	B;B;P;B;B	0.40931	0.025;0.027;0.733;0.233;0.041	B;B;P;B;B	0.51866	0.022;0.039;0.682;0.16;0.065	T	0.05354	-1.0890	10	0.59425	D	0.04	.	7.5574	0.27833	0.0:0.0:0.5421:0.4579	.	130;130;118;130;130	Q99702;E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;.;LIRA2_HUMAN;.	N	130;130;130;130;118	ENSP00000388131:S130N;ENSP00000251377:S130N;ENSP00000375618:S130N;ENSP00000251376:S130N;ENSP00000375617:S118N	ENSP00000251376:S130N	S	+	2	0	LILRA2	59778046	0.013000	0.17824	0.015000	0.15790	0.003000	0.03518	1.491000	0.35583	0.078000	0.16900	-0.442000	0.05670	AGC		0.557	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			A	55086234	G	A	55086234	3	1	61	1	0	0	0	0	1	0	0	0	8808	971	34	3	403	3	LILRA2	19	55086234	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66995	55086234	4042749	11348	19333										
LILRB1	10859	broad.mit.edu	37	chr19	55145137	55145137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaggccccacctccacatCtggtgagtccctgaggcttc	9	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55145137C>A	ENST00000396331.1	+	9	1667	c.1310C>A	c.(1309-1311)tCt>tAt	p.S437Y	LILRB1_ENST00000434867.2_Missense_Mutation_p.S437Y|LILRB1_ENST00000396317.1_Intron|LILRB1_ENST00000427581.2_Missense_Mutation_p.S473Y|LILRB1_ENST00000324602.7_Missense_Mutation_p.S437Y|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Missense_Mutation_p.S437Y|LILRB1_ENST00000396327.3_Missense_Mutation_p.S437Y|LILRB1_ENST00000396332.4_Missense_Mutation_p.S437Y|LILRB1_ENST00000396315.1_Missense_Mutation_p.S437Y|LILRB1_ENST00000396321.2_Missense_Mutation_p.S437Y	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	437					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.S437Y(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		ACCTCCACATCTGGTGAGTCC	0.617										HNSCC(37;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	19											26	30	29					19																	55145137		1897	4121	6018	59836949	SO:0001583	missense	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1310C>A	19.37:g.55145137C>A	ENSP00000379622:p.Ser437Tyr		59836949	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	6.033	0.374394	0.11409	.	.	ENSG00000104972	ENST00000396321;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396315	T;T;T;T;T;T;T;T;T	0.00525	7.06;6.94;7.06;6.95;6.94;7.06;7.06;6.81;6.94	2.46	-1.69	0.08186	.	.	.	.	.	T	0.00552	0.0018	L	0.50333	1.59	0.09310	N	1	P;P;P;P;P	0.50819	0.595;0.939;0.829;0.939;0.938	B;P;B;P;B	0.46940	0.243;0.532;0.396;0.532;0.332	T	0.49428	-0.8941	9	0.66056	D	0.02	.	5.4755	0.16694	0.2115:0.3733:0.4152:0.0	.	437;437;437;437;437	D9IDM5;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	Y	437;437;437;437;437;437;437;473;437	ENSP00000379614:S437Y;ENSP00000409968:S437Y;ENSP00000379622:S437Y;ENSP00000379618:S437Y;ENSP00000315997:S437Y;ENSP00000405243:S437Y;ENSP00000379623:S437Y;ENSP00000395004:S473Y;ENSP00000379608:S437Y	ENSP00000315997:S437Y	S	+	2	0	LILRB1	59836949	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.545000	0.06069	-0.357000	0.08175	-1.098000	0.02139	TCT		0.617	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55145137	C	A	55145137	3	1	61	1	0	0	0	0	1	0	0	0	8813	913	32	2	1336	2	LILRB1	19	55145137	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	58903	55145137	3983846	11349	19334										
LILRB1	10859	broad.mit.edu	37	chr19	55146120	55146120	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcacctgggggttgtgatCggcatcttggtggccgtcat	16	9	2	1	rs200419876		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55146120C>T	ENST00000396331.1	+	11	1746	c.1389C>T	c.(1387-1389)atC>atT	p.I463I	LILRB1_ENST00000434867.2_Silent_p.I463I|LILRB1_ENST00000396317.1_Silent_p.I447I|LILRB1_ENST00000427581.2_Silent_p.I513I|LILRB1_ENST00000324602.7_Silent_p.I464I|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000418536.2_Silent_p.I447I|LILRB1_ENST00000448689.1_Silent_p.I463I|LILRB1_ENST00000396327.3_Silent_p.I464I|LILRB1_ENST00000396332.4_Silent_p.I463I|LILRB1_ENST00000396315.1_Silent_p.I464I|LILRB1_ENST00000396321.2_Silent_p.I463I	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	463					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.I463I(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGGTTGTGATCGGCATCTTGG	0.567										HNSCC(37;0.09)			c|||	1	0.000199681	0	0.0014	5008	,	,		17894	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											137	107	117					19																	55146120		2203	4300	6503	59837932	SO:0001819	synonymous_variant	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1389C>T	19.37:g.55146120C>T			59837932	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																				0.567	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55146120	C	T	55146120	2	4	61	1	0	0	0	0	0	0	0	1	8813	874	31	1		1	LILRB1	19	55146120	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	983	55146120	3982863	11350	19335										
LILRB1	10859	broad.mit.edu	37	chr19	55148247	55148247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacagcttgaccctcagacGggaggcaactgagcctcctc	11	15	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55148247G>A	ENST00000396331.1	+	16	2228	c.1871G>A	c.(1870-1872)cGg>cAg	p.R624Q	AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000434867.2_Missense_Mutation_p.R624Q|LILRB1_ENST00000396317.1_Missense_Mutation_p.R608Q|LILRB1_ENST00000427581.2_Missense_Mutation_p.R675Q|LILRB1_ENST00000324602.7_Missense_Mutation_p.R626Q|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000418536.2_Missense_Mutation_p.R608Q|LILRB1_ENST00000448689.1_3'UTR|LILRB1_ENST00000396327.3_Missense_Mutation_p.R625Q|LILRB1_ENST00000396332.4_Missense_Mutation_p.R625Q|LILRB1_ENST00000396315.1_Missense_Mutation_p.R626Q|LILRB1_ENST00000396321.2_Missense_Mutation_p.R624Q	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	624					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.R624Q(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		ACCCTCAGACGGGAGGCAACT	0.647										HNSCC(37;0.09)																																						1	Substitution - Missense(1)	large_intestine(1)	19											98	85	89					19																	55148247		2203	4300	6503	59840059	SO:0001583	missense	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1871G>A	19.37:g.55148247G>A	ENSP00000379622:p.Arg624Gln		59840059	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	G	5.915	0.352927	0.11182	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T	0.00481	7.18;7.11;7.18;7.17;7.16;7.18;7.17;7.15;7.11;7.16	2.1	-2.03	0.07365	.	.	.	.	.	T	0.00241	0.0007	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.30542	0.052;0.284;0.006;0.088;0.025	B;B;B;B;B	0.21546	0.023;0.035;0.009;0.021;0.004	T	0.28776	-1.0033	9	0.18710	T	0.47	.	2.1898	0.03896	0.3861:0.0:0.3599:0.2539	.	608;626;625;625;624	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	Q	624;608;624;625;626;624;625;675;608;626	ENSP00000379614:R624Q;ENSP00000391514:R608Q;ENSP00000379622:R624Q;ENSP00000379618:R625Q;ENSP00000315997:R626Q;ENSP00000405243:R624Q;ENSP00000379623:R625Q;ENSP00000395004:R675Q;ENSP00000379610:R608Q;ENSP00000379608:R626Q	ENSP00000315997:R626Q	R	+	2	0	LILRB1	59840059	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.020000	0.03618	-0.545000	0.06224	0.194000	0.17425	CGG		0.647	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55148247	G	A	55148247	3	1	61	1	0	0	0	0	1	0	0	0	8813	1116	39	1	1931	1	LILRB1	19	55148247	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2127	55148247	3980736	11351	19336										
KIR3DL1	3811	broad.mit.edu	37	chr19	55341721	55341721	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccagatccaaagttgtctcCtgcccatgagcaccacagtc	7	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55341721C>A	ENST00000391728.4	+	9	1359	c.1326C>A	c.(1324-1326)tcC>tcA	p.S442S	KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000541392.1_Silent_p.S425S|KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000326542.7_Silent_p.S425S|KIR3DL1_ENST00000538269.1_Silent_p.S442S|KIR3DL1_ENST00000358178.4_Silent_p.S347S	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	442					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.S442S(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		AAGTTGTCTCCTGCCCATGAG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	19											220	204	210					19																	55341721		2173	4170	6343	60033533	SO:0001819	synonymous_variant	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1326C>A	19.37:g.55341721C>A			60033533	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																				0.532	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		A	55341721	C	A	55341721	2	1	61	1	0	0	0	0	0	0	0	1	8341	668	24	2		2	KIR3DL1	19	55341721	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	193474	55341721	3787262	11352	19337										
NLRP7	199713	broad.mit.edu	37	chr19	55450611	55450611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggctctcttctcgttagCgaggccgaataagaagtgtc	11	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55450611C>T	ENST00000590030.1	-	3	1616	c.1576G>A	c.(1576-1578)Gct>Act	p.A526T	NLRP7_ENST00000340844.2_Missense_Mutation_p.A526T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A526T|NLRP7_ENST00000446217.1_Missense_Mutation_p.A554T|NLRP7_ENST00000448121.2_Missense_Mutation_p.A526T|NLRP7_ENST00000588756.1_Missense_Mutation_p.A526T|NLRP7_ENST00000592784.1_Missense_Mutation_p.A526T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	526							ATP binding (GO:0005524)	p.A526T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTCTCGTTAGCGAGGCCGAAT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	19											79	80	79					19																	55450611		2203	4300	6503	60142423	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1576G>A	19.37:g.55450611C>T	ENSP00000465520:p.Ala526Thr		60142423	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	5.333	0.246805	0.10130	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.73363	-0.68;-0.68;-0.74;-0.71	2.34	-4.67	0.03319	.	3.583670	0.01181	N	0.007097	T	0.53417	0.1795	N	0.19112	0.55	0.09310	N	1	P;P;P;P	0.48350	0.909;0.909;0.909;0.865	B;B;B;B	0.38500	0.255;0.255;0.255;0.275	T	0.55786	-0.8086	10	0.39692	T	0.17	.	2.61	0.04888	0.1697:0.4522:0.2391:0.139	.	554;526;526;526	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	T	526;526;526;554;293	ENSP00000329568:A526T;ENSP00000409137:A526T;ENSP00000339491:A526T;ENSP00000414273:A554T	ENSP00000329568:A526T	A	-	1	0	NLRP7	60142423	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.713000	0.00816	-1.982000	0.00988	-0.521000	0.04368	GCT		0.527	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55450611	C	T	55450611	3	4	61	1	0	0	0	0	1	0	0	0	10513	768	27	1	1569	1	NLRP7	19	55450611	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108890	55450611	3678372	11353	19338										
NLRP7	199713	broad.mit.edu	37	chr19	55451499	55451499	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctgcaattcaggccagtCtttggagatcagctctgcaa	9	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55451499C>A	ENST00000590030.1	-	3	728	c.688G>T	c.(688-690)Gac>Tac	p.D230Y	NLRP7_ENST00000340844.2_Missense_Mutation_p.D230Y|NLRP7_ENST00000328092.5_Missense_Mutation_p.D230Y|NLRP7_ENST00000446217.1_Missense_Mutation_p.D258Y|NLRP7_ENST00000448121.2_Missense_Mutation_p.D230Y|NLRP7_ENST00000588756.1_Missense_Mutation_p.D230Y|NLRP7_ENST00000592784.1_Missense_Mutation_p.D230Y			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	230	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)	p.D230Y(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TCAGGCCAGTCTTTGGAGATC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	19											115	114	114					19																	55451499		2203	4300	6503	60143311	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.688G>T	19.37:g.55451499C>A	ENSP00000465520:p.Asp230Tyr		60143311	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.706415	0.30232	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	1.88	-1.63	0.08345	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.86075	0.5846	L	0.59436	1.845	0.09310	N	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;D	0.77557	0.99;0.99;0.99;0.983	T	0.74968	-0.3483	9	0.66056	D	0.02	.	6.0467	0.19764	0.0:0.5882:0.0:0.4118	.	258;230;230;230	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	Y	230;230;230;258	ENSP00000329568:D230Y;ENSP00000409137:D230Y;ENSP00000339491:D230Y;ENSP00000414273:D258Y	ENSP00000329568:D230Y	D	-	1	0	NLRP7	60143311	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.066000	0.11598	-0.334000	0.08463	0.462000	0.41574	GAC		0.557	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55451499	C	A	55451499	3	1	61	1	0	0	0	0	1	0	0	0	10513	913	32	2	2457	2	NLRP7	19	55451499	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	888	55451499	3677484	11354	19339										
NLRP7	199713	broad.mit.edu	37	chr19	55451782	55451782	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctccttgccaaaaggtgttCttccagaccaaagactgttt	7	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55451782C>A	ENST00000590030.1	-	3	445	c.405G>T	c.(403-405)aaG>aaT	p.K135N	NLRP7_ENST00000340844.2_Missense_Mutation_p.K135N|NLRP7_ENST00000328092.5_Missense_Mutation_p.K135N|NLRP7_ENST00000446217.1_Missense_Mutation_p.K163N|NLRP7_ENST00000448121.2_Missense_Mutation_p.K135N|NLRP7_ENST00000588756.1_Missense_Mutation_p.K135N|NLRP7_ENST00000592784.1_Missense_Mutation_p.K135N			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	135							ATP binding (GO:0005524)	p.K135N(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		AAAAGGTGTTCTTCCAGACCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											295	323	313					19																	55451782		2203	4300	6503	60143594	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.405G>T	19.37:g.55451782C>A	ENSP00000465520:p.Lys135Asn		60143594	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	5.060	0.196795	0.09599	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.74106	-0.77;-0.77;-0.81;-0.78	1.87	-1.67	0.08238	.	.	.	.	.	T	0.59321	0.2185	N	0.08118	0	0.09310	N	1	D;P;P;D	0.59357	0.975;0.745;0.745;0.985	P;P;P;P	0.56916	0.556;0.448;0.448;0.809	T	0.52094	-0.8621	9	0.23891	T	0.37	.	3.2262	0.06732	0.0:0.3073:0.2271:0.4656	.	163;135;135;135	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	N	135;135;135;163	ENSP00000329568:K135N;ENSP00000409137:K135N;ENSP00000339491:K135N;ENSP00000414273:K163N	ENSP00000329568:K135N	K	-	3	2	NLRP7	60143594	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.089000	0.15002	-0.374000	0.07967	-0.300000	0.09419	AAG		0.448	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55451782	C	A	55451782	3	1	61	1	0	0	0	0	1	0	0	0	10513	912	32	2	2740	2	NLRP7	19	55451782	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	283	55451782	3677201	11355	19340										
NLRP2	55655	broad.mit.edu	37	chr19	55489157	55489157	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaccacctctagacgtggaCgaaatgctggagcgcttcaa	11	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55489157C>T	ENST00000543010.1	+	4	506	c.363C>T	c.(361-363)gaC>gaT	p.D121D	NLRP2_ENST00000448584.2_Silent_p.D121D|NLRP2_ENST00000427260.2_Silent_p.D98D|NLRP2_ENST00000339757.7_Silent_p.D121D|NLRP2_ENST00000263437.6_Silent_p.D121D|NLRP2_ENST00000538819.1_Intron|NLRP2_ENST00000391721.4_Intron|NLRP2_ENST00000537859.1_Silent_p.D121D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	121					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)	p.D121D(1)		large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TAGACGTGGACGAAATGCTGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	19											128	104	112					19																	55489157		2203	4300	6503	60180969	SO:0001819	synonymous_variant	55655			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.363C>T	19.37:g.55489157C>T			60180969	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																				0.547	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55489157	C	T	55489157	2	4	61	1	0	0	0	0	0	0	0	1	10508	535	19	1		1	NLRP2	19	55489157	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37375	55489157	3639826	11356	19341										
NLRP2	55655	broad.mit.edu	37	chr19	55508820	55508820	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaagatgctgtttgaaacCttgacatgttccagtggcac	11	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55508820C>A	ENST00000543010.1	+	12	3158	c.3015C>A	c.(3013-3015)acC>acA	p.T1005T	NLRP2_ENST00000448584.2_Silent_p.T1005T|NLRP2_ENST00000427260.2_Silent_p.T982T|NLRP2_ENST00000339757.7_Silent_p.T983T|NLRP2_ENST00000263437.6_Silent_p.T1002T|NLRP2_ENST00000538819.1_Silent_p.T981T|NLRP2_ENST00000391721.4_Silent_p.T981T|NLRP2_ENST00000537859.1_Silent_p.T983T	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	1005					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)	p.T1005T(2)		large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TGTTTGAAACCTTGACATGTT	0.522																																																2	Substitution - coding silent(2)	large_intestine(2)	19											213	192	199					19																	55508820		2203	4300	6503	60200632	SO:0001819	synonymous_variant	55655			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.3015C>A	19.37:g.55508820C>A			60200632	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																				0.522	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55508820	C	A	55508820	2	1	61	1	0	0	0	0	0	0	0	1	10508	668	24	2		2	NLRP2	19	55508820	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19663	55508820	3620163	11357	19342										
GP6	51206	broad.mit.edu	37	chr19	55527100	55527100	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcggtgatactcctagaagtCtctgggaaccaaacaaaggc	11	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55527100C>A	ENST00000417454.1	-	7	753	c.726G>T	c.(724-726)gaG>gaT	p.E242D	GP6_ENST00000333884.2_Splice_Site_p.E224D|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|GP6_ENST00000310373.3_Splice_Site_p.E242D	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	242					blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.E242D(1)		NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TCCTAGAAGTCTCTGGGAACC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	19											62	69	67					19																	55527100		1995	4165	6160	60218912	SO:0001630	splice_region_variant	51206			AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.725-1G>T	19.37:g.55527100C>A			60218912	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812812	0.32053	.	.	ENSG00000088053	ENST00000417454;ENST00000310373;ENST00000333884	T;T;T	0.00520	6.91;6.85;6.96	3.15	-0.412	0.12367	.	.	.	.	.	T	0.00356	0.0011	L	0.34521	1.04	0.09310	N	1	B;P;B	0.47253	0.418;0.892;0.244	B;B;B	0.41036	0.236;0.346;0.073	T	0.50268	-0.8848	9	0.62326	D	0.03	.	3.0873	0.06281	0.0:0.4768:0.2294:0.2938	.	224;242;242	Q9HCN6-2;Q9HCN6-3;Q9HCN6	.;.;GPVI_HUMAN	D	242;242;224	ENSP00000394922:E242D;ENSP00000308782:E242D;ENSP00000334552:E224D	ENSP00000308782:E242D	E	-	3	2	GP6	60218912	0.000000	0.05858	0.000000	0.03702	0.303000	0.27691	-0.134000	0.10436	-0.007000	0.14345	-0.175000	0.13238	GAG		0.522	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		Missense_Mutation	A	55527100	C	A	55527100	5	1	61	1	0	0	0	0	0	0	1	0	6604	927	32	2	1144	2	GP6	19	55527100	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18280	55527100	3601883	11358	19343										
PPP1R12C	54776	broad.mit.edu	37	chr19	55607513	55607513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaagtcctggagggaaatCttctcgcgactgctcagacg	12	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55607513C>A	ENST00000263433.3	-	8	1074	c.1059G>T	c.(1057-1059)aaG>aaT	p.K353N	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.K279N|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.K353N	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C									p.K353N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GGAGGGAAATCTTCTCGCGAC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	19											51	60	57					19																	55607513		2203	4300	6503	60299325	SO:0001583	missense	54776			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14947	protein-coding gene	gene with protein product	"myosin-binding subunit 85"	613245	"leukocyte receptor cluster (LRC) member 3", "protein phosphatase 1, regulatory (inhibitor) subunit 12C"	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1059G>T	19.37:g.55607513C>A	ENSP00000263433:p.Lys353Asn		60299325		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848950	0.71603	.	.	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.71222	-0.42;-0.5;-0.55	4.59	3.53	0.40419	.	0.128764	0.48767	D	0.000166	T	0.76169	0.3950	L	0.59436	1.845	0.46376	D	0.999019	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.991;0.999;0.997	T	0.71464	-0.4585	10	0.20046	T	0.44	.	7.6889	0.28557	0.0:0.8037:0.0:0.1963	.	279;353;353	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	N	353;353;279	ENSP00000263433:K353N;ENSP00000365573:K353N;ENSP00000387833:K279N	ENSP00000263433:K353N	K	-	3	2	PPP1R12C	60299325	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.366000	0.34193	2.261000	0.74972	0.655000	0.94253	AAG		0.677	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		A	55607513	C	A	55607513	3	1	61	1	0	0	0	0	1	0	0	0	12390	912	32	2	1349	2	PPP1R12C	19	55607513	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80413	55607513	3521470	11359	19344										
PTPRH	5794	broad.mit.edu	37	chr19	55713438	55713438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcacctgtggtggcatttCgagtctcccgggagctgttg	13	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55713438C>T	ENST00000376350.3	-	6	1161	c.1139G>A	c.(1138-1140)cGa>cAa	p.R380Q	PTPRH_ENST00000263434.5_Missense_Mutation_p.R202Q|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	380	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R380Q(1)		breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GGTGGCATTTCGAGTCTCCCG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	19											122	123	123					19																	55713438		2203	4300	6503	60405250	SO:0001583	missense	5794				CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1139G>A	19.37:g.55713438C>T	ENSP00000365528:p.Arg380Gln		60405250	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614971	0.28712	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.53423	0.62;0.62	4.79	-4.74	0.03249	Fibronectin, type III (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14830	0.0358	N	0.08118	0	0.09310	N	1	P;P;D	0.53619	0.884;0.929;0.961	B;B;B	0.36464	0.098;0.2;0.225	T	0.28332	-1.0047	9	0.12766	T	0.61	.	1.6028	0.02678	0.2485:0.2662:0.0812:0.4042	.	202;202;380	C9JCH2;Q9HD43-2;Q9HD43	.;.;PTPRH_HUMAN	Q	380;202	ENSP00000365528:R380Q;ENSP00000263434:R202Q	ENSP00000263434:R202Q	R	-	2	0	PTPRH	60405250	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.937000	0.03942	-1.466000	0.01897	-1.613000	0.00800	CGA		0.473	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			T	55713438	C	T	55713438	3	4	61	1	0	0	0	0	1	0	0	0	12840	884	31	1	2268	1	PTPRH	19	55713438	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	105925	55713438	3415545	11360	19345										
HSPBP1	23640	broad.mit.edu	37	chr19	55774019	55774019	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgggctggagaaacaggtcTgtagcagcttttcacagaac	12	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55774019T>C	ENST00000255631.5	-	9	1347	c.1037A>G	c.(1036-1038)cAg>cGg	p.Q346R	HSPBP1_ENST00000433386.2_Missense_Mutation_p.Q346R|HSPBP1_ENST00000587922.1_Missense_Mutation_p.Q346R|HSPBP1_ENST00000376343.3_Missense_Mutation_p.Q244R	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	349					negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)	p.Q346R(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		GAAACAGGTCTGTAGCAGCTT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	55	60					19																	55774019		2203	4300	6503	60465831	SO:0001583	missense	23640				CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"hsp70 interacting protein", "Hsp70 binding protein 1"	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.1037A>G	19.37:g.55774019T>C	ENSP00000255631:p.Gln346Arg		60465831	B3KQP0|B4DG11|O95351|Q6ZNU5	Missense_Mutation	SNP	ENST00000255631.5	37	CCDS33111.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.257489	0.22965	.	.	ENSG00000133265	ENST00000433386;ENST00000255631;ENST00000376343	T;T;T	0.51071	0.72;0.72;0.72	4.51	4.51	0.55191	Armadillo-type fold (1);	0.871117	0.10222	N	0.700778	T	0.34106	0.0886	L	0.29908	0.895	0.20638	N	0.99988	B;B	0.23891	0.049;0.093	B;B	0.23574	0.032;0.047	T	0.22103	-1.0226	10	0.15499	T	0.54	.	8.5332	0.33346	0.0:0.0:0.1957:0.8043	.	349;392	Q9NZL4;B4DG11	HPBP1_HUMAN;.	R	346;346;244	ENSP00000398244:Q346R;ENSP00000255631:Q346R;ENSP00000365521:Q244R	ENSP00000255631:Q346R	Q	-	2	0	HSPBP1	60465831	0.495000	0.26051	1.000000	0.80357	0.378000	0.30076	0.857000	0.27831	1.817000	0.53016	0.254000	0.18369	CAG		0.622	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267		C	55774019	T	C	55774019	3	2	61	1	0	0	0	0	1	0	0	0	7447	1580	55	4	46	4	HSPBP1	19	55774019	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	60581	55774019	3354964	11361	19346										
ZNF628	89887	broad.mit.edu	37	chr19	55992811	55992811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccctgctctaccaccagcGaggccacacgggcgagcggc	14	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:55992811G>A	ENST00000598519.1	+	3	804	c.251G>A	c.(250-252)cGa>cAa	p.R84Q	ZNF628_ENST00000391718.2_Missense_Mutation_p.R80Q			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	84					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R80Q(1)		endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TACCACCAGCGAGGCCACACG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	41	41					19																	55992811		2203	4298	6501	60684623	SO:0001583	missense	89887			AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.251G>A	19.37:g.55992811G>A	ENSP00000469591:p.Arg84Gln		60684623	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	37	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	15.14	2.744161	0.49151	.	.	ENSG00000197483	ENST00000391718	T	0.24723	1.84	3.56	3.56	0.40772	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42682	U	0.000666	T	0.44350	0.1289	L	0.56199	1.76	0.31650	N	0.646954	D	0.89917	1.0	D	0.85130	0.997	T	0.52533	-0.8563	10	0.72032	D	0.01	-15.9567	13.0316	0.58845	0.0:0.0:1.0:0.0	.	80	Q5EBL2	ZN628_HUMAN	Q	80	ENSP00000375598:R80Q	ENSP00000375598:R80Q	R	+	2	0	ZNF628	60684623	0.983000	0.35010	0.916000	0.36221	0.008000	0.06430	3.400000	0.52594	2.001000	0.58596	0.491000	0.48974	CGA		0.672	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		A	55992811	G	A	55992811	3	1	61	1	0	0	0	0	1	0	0	0	18091	1058	37	1	241	1	ZNF628	19	55992811	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	218792	55992811	3136172	11362	19347										
U2AF2	11338	broad.mit.edu	37	chr19	56180089	56180089	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggccttcaacctggtcaaGgacagtgccacggggctctc	12	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56180089G>T	ENST00000308924.4	+	9	916	c.876G>T	c.(874-876)aaG>aaT	p.K292N	CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000450554.2_Missense_Mutation_p.K292N|U2AF2_ENST00000590551.1_Missense_Mutation_p.K128N			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	292	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K292N(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		ACCTGGTCAAGGACAGTGCCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											63	61	62					19																	56180089		2203	4300	6503	60871901	SO:0001583	missense	11338			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.876G>T	19.37:g.56180089G>T	ENSP00000307863:p.Lys292Asn		60871901	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.740244	0.69304	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.75704	-0.96;1.15	4.4	3.33	0.38152	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.85957	0.5818	M	0.90019	3.08	0.53005	D	0.999964	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.98	D	0.86236	0.1640	10	0.49607	T	0.09	-31.7421	8.9744	0.35926	0.1838:0.0:0.8162:0.0	.	292;292	P26368;P26368-2	U2AF2_HUMAN;.	N	292	ENSP00000307863:K292N;ENSP00000388475:K292N	ENSP00000307863:K292N	K	+	3	2	U2AF2	60871901	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.778000	0.38614	2.184000	0.69523	0.655000	0.94253	AAG		0.632	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56180089	G	T	56180089	3	4	61	1	0	0	0	0	1	0	0	0	16863	991	35	2	910	2	U2AF2	19	56180089	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	187278	56180089	2948894	11363	19348										
NLRP9	338321	broad.mit.edu	37	chr19	56241247	56241247	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccagcgctttgcaaagaatCgccagggagggatcatcaag	13	10	2	1	rs201513039		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56241247C>T	ENST00000332836.2	-	3	1971	c.1944G>A	c.(1942-1944)gcG>gcA	p.A648A		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	648						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.A648A(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TGCAAAGAATCGCCAGGGAGG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	19											90	89	89					19																	56241247		2203	4300	6503	60933059	SO:0001819	synonymous_variant	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1944G>A	19.37:g.56241247C>T			60933059	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																				0.438	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56241247	C	T	56241247	2	4	61	1	0	0	0	0	0	0	0	1	10515	871	31	1		1	NLRP9	19	56241247	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61158	56241247	2887736	11364	19349										
NLRP9	338321	broad.mit.edu	37	chr19	56243394	56243394	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcctgagtcatctggaaaGatattctccacacacatgcg	7	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56243394G>T	ENST00000332836.2	-	2	1830	c.1803C>A	c.(1801-1803)atC>atA	p.I601I		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	601						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.I601I(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CATCTGGAAAGATATTCTCCA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	19											78	75	76					19																	56243394		2203	4300	6503	60935206	SO:0001819	synonymous_variant	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1803C>A	19.37:g.56243394G>T			60935206	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																				0.413	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56243394	G	T	56243394	2	4	61	1	0	0	0	0	0	0	0	1	10515	932	33	2		2	NLRP9	19	56243394	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2147	56243394	2885589	11365	19350										
NLRP9	338321	broad.mit.edu	37	chr19	56243505	56243505	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgaaaacttcttcaaaGaaattcatcactttggttac	4	7	4	2	rs145361464	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56243505G>T	ENST00000332836.2	-	2	1719	c.1692C>A	c.(1690-1692)ttC>ttA	p.F564L		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	564						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.F564L(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTTCTTCAAAGAAATTCATCA	0.353													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		21224	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						G	LEU/PHE	16,4390	22.3+/-47.3	0,16,2187	60	61	60		1692	2.2	0	19	dbSNP_134	60	0,8600		0,0,4300	yes	missense	NLRP9	NM_176820.2	22	0,16,6487	TT,TG,GG		0.0,0.3631,0.123	benign	564/992	56243505	16,12990	2203	4300	6503	60935317	SO:0001583	missense	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1692C>A	19.37:g.56243505G>T	ENSP00000331857:p.Phe564Leu		60935317	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	0.016	-1.515603	0.00975	0.003631	0.0	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.51817	0.69	2.23	2.23	0.28157	.	.	.	.	.	T	0.23766	0.0575	L	0.34521	1.04	0.09310	N	1	B	0.15719	0.014	B	0.15484	0.013	T	0.16689	-1.0394	9	0.10377	T	0.69	.	8.1026	0.30865	0.0:0.0:1.0:0.0	.	564	Q7RTR0	NALP9_HUMAN	L	564	ENSP00000331857:F564L	ENSP00000331857:F564L	F	-	3	2	NLRP9	60935317	0.069000	0.21087	0.047000	0.18901	0.008000	0.06430	0.436000	0.21526	1.588000	0.49971	0.644000	0.83932	TTC		0.353	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56243505	G	T	56243505	3	4	61	1	0	0	0	0	1	0	0	0	10515	933	33	2	1315	2	NLRP9	19	56243505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111	56243505	2885478	11366	19351										
NLRP9	338321	broad.mit.edu	37	chr19	56244544	56244544	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagaattctctctggctggGaaaaaatgtcttcgatcttc	8	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56244544G>A	ENST00000332836.2	-	2	680	c.653C>T	c.(652-654)tCc>tTc	p.S218F		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	218	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.S218F(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTCTGGCTGGGAAAAAATGTC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											31	32	32					19																	56244544		2203	4300	6503	60936356	SO:0001583	missense	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.653C>T	19.37:g.56244544G>A	ENSP00000331857:p.Ser218Phe		60936356	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795382	0.31777	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.64618	-0.11	2.46	2.46	0.29980	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.78259	0.4255	M	0.87682	2.9	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63699	-0.6578	9	0.87932	D	0	.	6.6558	0.22986	0.0:0.0:0.7174:0.2826	.	218	Q7RTR0	NALP9_HUMAN	F	218	ENSP00000331857:S218F	ENSP00000331857:S218F	S	-	2	0	NLRP9	60936356	0.000000	0.05858	0.048000	0.18961	0.008000	0.06430	-0.315000	0.08081	1.731000	0.51592	0.644000	0.83932	TCC		0.478	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56244544	G	A	56244544	3	1	61	1	0	0	0	0	1	0	0	0	10515	1174	41	3	2354	3	NLRP9	19	56244544	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1039	56244544	2884439	11367	19352										
NLRP11	204801	broad.mit.edu	37	chr19	56329310	56329310	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcctacaaagatcttccttAcgcatcattgaaaatatgct	4	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56329310A>C	ENST00000589093.1	-	2	324	c.231T>G	c.(229-231)cgT>cgG	p.R77R	NLRP11_ENST00000589824.2_Silent_p.R77R|NLRP11_ENST00000592953.1_Intron|NLRP11_ENST00000443188.1_Silent_p.R77R|NLRP11_ENST00000360133.3_Silent_p.R77R			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	77	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.R77R(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		GATCTTCCTTACGCATCATTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	19											126	114	118					19																	56329310		2203	4300	6503	61021122	SO:0001819	synonymous_variant	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.231T>G	19.37:g.56329310A>C			61021122	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																				0.448	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56329310	A	C	56329310	2	2	61	1	0	0	0	0	0	0	0	1	10504	378	14	4		4	NLRP11	19	56329310	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	84766	56329310	2799673	11368	19353										
NLRP4	147945	broad.mit.edu	37	chr19	56370017	56370017	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttttgtgaagacgacctcCggagaaatggggttgttgac	14	6	0	4	rs140509890	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56370017C>T	ENST00000301295.6	+	3	1680	c.1258C>T	c.(1258-1260)Cgg>Tgg	p.R420W	NLRP4_ENST00000587891.1_Missense_Mutation_p.R345W|NLRP4_ENST00000346986.5_Missense_Mutation_p.R420W	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	420	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.R420W(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		AGACGACCTCCGGAGAAATGG	0.582													C|||	2	0.000399361	0	0.0014	5008	,	,		18850	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19						C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	107	106	106		1258	-4.4	0	19	dbSNP_134	106	0,8600		0,0,4300	yes	missense	NLRP4	NM_134444.4	101	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	420/995	56370017	3,13003	2203	4300	6503	61061829	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1258C>T	19.37:g.56370017C>T	ENSP00000301295:p.Arg420Trp		61061829	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669306	0.47677	6.81E-4	0.0	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.84660	-1.88;-1.88	4.09	-4.44	0.03557	.	.	.	.	.	D	0.88976	0.6584	M	0.70108	2.13	0.09310	N	1	D;D;D	0.89917	0.991;1.0;1.0	P;D;D	0.87578	0.871;0.998;0.995	T	0.81978	-0.0685	9	0.87932	D	0	.	7.6799	0.28507	0.2079:0.5349:0.2572:0.0	.	420;345;420	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	W	420	ENSP00000301295:R420W;ENSP00000344787:R420W	ENSP00000301295:R420W	R	+	1	2	NLRP4	61061829	0.000000	0.05858	0.004000	0.12327	0.015000	0.08874	-0.323000	0.07997	-1.229000	0.02564	-0.275000	0.10095	CGG		0.582	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56370017	C	T	56370017	3	4	61	1	0	0	0	0	1	0	0	0	10510	643	23	1	1264	1	NLRP4	19	56370017	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	40707	56370017	2758966	11369	19354										
NLRP4	147945	broad.mit.edu	37	chr19	56370116	56370116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcctacgtgttcctccacGtgtgtatccaggagttctgt	10	12	1	0	rs140761924		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56370116G>A	ENST00000301295.6	+	3	1779	c.1357G>A	c.(1357-1359)Gtg>Atg	p.V453M	NLRP4_ENST00000587891.1_Missense_Mutation_p.V378M|NLRP4_ENST00000346986.5_Missense_Mutation_p.V453M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	453	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.V453M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GTTCCTCCACGTGTGTATCCA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	MET/VAL	0,4406		0,0,2203	146	139	141		1357	-8.2	0	19	dbSNP_134	141	2,8598	2.2+/-6.3	0,2,4298	yes	missense	NLRP4	NM_134444.4	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	453/995	56370116	2,13004	2203	4300	6503	61061928	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1357G>A	19.37:g.56370116G>A	ENSP00000301295:p.Val453Met		61061928	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	7.739	0.700821	0.15172	0.0	2.33E-4	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.84223	-1.82;-1.82	4.1	-8.19	0.01049	.	.	.	.	.	T	0.62950	0.2470	N	0.10972	0.075	0.09310	N	1	B;B;B	0.19200	0.034;0.027;0.012	B;B;B	0.15870	0.01;0.014;0.003	T	0.52200	-0.8607	9	0.49607	T	0.09	.	2.0714	0.03614	0.1069:0.2637:0.2298:0.3995	.	453;378;453	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	M	453	ENSP00000301295:V453M;ENSP00000344787:V453M	ENSP00000301295:V453M	V	+	1	0	NLRP4	61061928	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.589000	0.00900	-3.018000	0.00270	-0.302000	0.09304	GTG		0.537	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		A	56370116	G	A	56370116	3	1	61	1	0	0	0	0	1	0	0	0	10510	1145	40	1	1363	1	NLRP4	19	56370116	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	99	56370116	2758867	11370	19355										
NLRP13	126204	broad.mit.edu	37	chr19	56419202	56419202	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgtctcaaagctttaagAatcagggggacagtcattcc	11	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56419202A>C	ENST00000342929.3	-	7	2402	c.2403T>G	c.(2401-2403)atT>atG	p.I801M	NLRP13_ENST00000588751.1_Missense_Mutation_p.I801M	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	801							ATP binding (GO:0005524)	p.I801M(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AAGCTTTAAGAATCAGGGGGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											131	118	123					19																	56419202		2203	4300	6503	61111014	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2403T>G	19.37:g.56419202A>C	ENSP00000343891:p.Ile801Met		61111014	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	5.364	0.252449	0.10185	.	.	ENSG00000173572	ENST00000342929	T	0.56941	0.43	2.18	-4.35	0.03656	.	.	.	.	.	T	0.40670	0.1126	L	0.39898	1.24	0.09310	N	1	P	0.45348	0.856	B	0.43575	0.424	T	0.37798	-0.9690	9	0.66056	D	0.02	.	6.6016	0.22703	0.2256:0.1845:0.59:0.0	.	801	Q86W25	NAL13_HUMAN	M	801	ENSP00000343891:I801M	ENSP00000343891:I801M	I	-	3	3	NLRP13	61111014	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.173000	0.01265	-1.490000	0.01842	-0.334000	0.08254	ATT		0.493	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		C	56419202	A	C	56419202	3	2	61	1	0	0	0	0	1	0	0	0	10506	242	9	4	746	4	NLRP13	19	56419202	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	49086	56419202	2709781	11371	19356										
NLRP13	126204	broad.mit.edu	37	chr19	56423611	56423611	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacccccacagtcattgatCttttgaagaatattgaactc	5	11	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56423611C>A	ENST00000342929.3	-	5	1571	c.1572G>T	c.(1570-1572)aaG>aaT	p.K524N	NLRP13_ENST00000588751.1_Missense_Mutation_p.K524N	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	524	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)	p.K524N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGTCATTGATCTTTTGAAGAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	73	72					19																	56423611		2203	4300	6503	61115423	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1572G>T	19.37:g.56423611C>A	ENSP00000343891:p.Lys524Asn		61115423	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	C	11.21	1.570397	0.28003	.	.	ENSG00000173572	ENST00000342929	D	0.89270	-2.49	2.48	-4.6	0.03390	.	.	.	.	.	D	0.89996	0.6877	M	0.73598	2.24	0.09310	N	1	D	0.65815	0.995	P	0.59357	0.856	T	0.81640	-0.0841	9	0.54805	T	0.06	.	3.9552	0.09387	0.1797:0.4757:0.0:0.3447	.	524	Q86W25	NAL13_HUMAN	N	524	ENSP00000343891:K524N	ENSP00000343891:K524N	K	-	3	2	NLRP13	61115423	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.125000	0.15749	-1.050000	0.03230	-1.687000	0.00730	AAG		0.438	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		A	56423611	C	A	56423611	3	1	61	1	0	0	0	0	1	0	0	0	10506	912	32	2	1585	2	NLRP13	19	56423611	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4409	56423611	2705372	11372	19357										
NLRP13	126204	broad.mit.edu	37	chr19	56436023	56436023	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccctgggtctgcatattCcctgaaataaacattgacga	7	11	1	2	rs561628596		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56436023C>A	ENST00000342929.3	-	3	389	c.390G>T	c.(388-390)ggG>ggT	p.G130G	NLRP13_ENST00000588751.1_Splice_Site_p.G130G	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	130							ATP binding (GO:0005524)	p.G130G(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		TCTGCATATTCCCTGAAATAA	0.418													C|||	1	0.000199681	8e-04	0	5008	,	,		16333	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											208	163	179					19																	56436023		2203	4300	6503	61127835	SO:0001630	splice_region_variant	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.389-1G>T	19.37:g.56436023C>A			61127835	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																				0.418	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	Silent	A	56436023	C	A	56436023	5	1	61	1	0	0	0	0	0	0	1	0	10506	869	30	2	2775	2	NLRP13	19	56436023	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12412	56436023	2692960	11373	19358										
NLRP8	126205	broad.mit.edu	37	chr19	56467356	56467356	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacaaagaagttcaagtGtctgctttttgcctgaagcg	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56467356G>A	ENST00000291971.3	+	3	2003	c.1932G>A	c.(1930-1932)gtG>gtA	p.V644V	NLRP8_ENST00000590542.1_Silent_p.V644V	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	644					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.V644V(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AAGTTCAAGTGTCTGCTTTTT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	19											141	131	135					19																	56467356		2203	4300	6503	61159168	SO:0001819	synonymous_variant	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1932G>A	19.37:g.56467356G>A			61159168	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																				0.458	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56467356	G	A	56467356	2	1	61	1	0	0	0	0	0	0	0	1	10514	1364	48	3		3	NLRP8	19	56467356	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31333	56467356	2661627	11374	19359										
NLRP5	126206	broad.mit.edu	37	chr19	56515268	56515268	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcagacattcaaggaattActaaagaagaaatcttcaga	6	6	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56515268A>G	ENST00000390649.3	+	2	249	c.249A>G	c.(247-249)ttA>ttG	p.L83L		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	83	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.L83L(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TCAAGGAATTACTAAAGAAGA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	19											95	91	92					19																	56515268		1905	4128	6033	61207080	SO:0001819	synonymous_variant	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.249A>G	19.37:g.56515268A>G			61207080	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																				0.428	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		G	56515268	A	G	56515268	2	3	61	1	0	0	0	0	0	0	0	1	10511	388	14	4		4	NLRP5	19	56515268	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	47912	56515268	2613715	11375	19360										
NLRP5	126206	broad.mit.edu	37	chr19	56538691	56538691	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttcatcattgacggtttCgatgacctgggctctgtcct	10	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56538691C>T	ENST00000390649.3	+	7	1092	c.1092C>T	c.(1090-1092)ttC>ttT	p.F364F		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	364	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.F364F(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TTGACGGTTTCGATGACCTGG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	19											46	46	46					19																	56538691		2076	4215	6291	61230503	SO:0001819	synonymous_variant	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1092C>T	19.37:g.56538691C>T			61230503	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																				0.552	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56538691	C	T	56538691	2	4	61	1	0	0	0	0	0	0	0	1	10511	883	31	1		1	NLRP5	19	56538691	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23423	56538691	2590292	11376	19361										
NLRP5	126206	broad.mit.edu	37	chr19	56539418	56539418	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctggaaatcgagccagctCtctgccctctgtacgttgag	11	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56539418C>A	ENST00000390649.3	+	7	1819	c.1819C>A	c.(1819-1821)Ctc>Atc	p.L607I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	607					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.L607I(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CGAGCCAGCTCTCTGCCCTCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	66	66					19																	56539418		1971	4166	6137	61231230	SO:0001583	missense	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1819C>A	19.37:g.56539418C>A	ENSP00000375063:p.Leu607Ile		61231230	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	4.004	-0.001885	0.07819	.	.	ENSG00000171487	ENST00000390649	T	0.73047	-0.71	2.85	0.524	0.17066	.	3.228080	0.01119	N	0.005750	T	0.60143	0.2246	L	0.36672	1.1	0.09310	N	1	P	0.40211	0.707	B	0.40565	0.333	T	0.45527	-0.9255	10	0.22706	T	0.39	.	3.3341	0.07094	0.0:0.5515:0.2699:0.1786	.	607	P59047	NALP5_HUMAN	I	607	ENSP00000375063:L607I	ENSP00000375063:L607I	L	+	1	0	NLRP5	61231230	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.213000	0.02991	0.189000	0.20188	0.462000	0.41574	CTC		0.522	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56539418	C	A	56539418	3	1	61	1	0	0	0	0	1	0	0	0	10511	913	32	2	1845	2	NLRP5	19	56539418	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	727	56539418	2589565	11377	19362										
ZSCAN5B	342933	broad.mit.edu	37	chr19	56701593	56701593	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagctgggaaaaatacttaAatgatttattgcacacgtca	7	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56701593A>C	ENST00000586855.2	-	5	1404	c.1091T>G	c.(1090-1092)tTt>tGt	p.F364C	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.F364C			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	364					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.F364C(2)		breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AAAATACTTAAATGATTTATT	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	19											72	75	74					19																	56701593		2185	4283	6468	61393405	SO:0001583	missense	342933				CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"-", "Zinc fingers, C2H2-type"	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.1091T>G	19.37:g.56701593A>C	ENSP00000466072:p.Phe364Cys		61393405		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076799	0.36662	.	.	ENSG00000197213	ENST00000358992	T	0.14766	2.48	2.61	2.61	0.31194	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37265	0.0997	M	0.82517	2.595	0.09310	N	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.05037	-1.0910	9	0.87932	D	0	.	9.0502	0.36372	1.0:0.0:0.0:0.0	.	364	A6NJL1	ZSA5B_HUMAN	C	364	ENSP00000351883:F364C	ENSP00000351883:F364C	F	-	2	0	ZSCAN5B	61393405	0.962000	0.33011	0.006000	0.13384	0.011000	0.07611	3.124000	0.50461	1.448000	0.47680	0.254000	0.18369	TTT		0.547	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		C	56701593	A	C	56701593	3	2	61	1	0	0	0	0	1	0	0	0	18278	14	1	4	400	4	ZSCAN5B	19	56701593	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	162175	56701593	2427390	11378	19363										
ZSCAN5A	79149	broad.mit.edu	37	chr19	56733256	56733256	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaggctaataagctgcatGaagcgcttcccacagagatt	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56733256G>T	ENST00000587340.1	-	7	1874	c.1179C>A	c.(1177-1179)ttC>ttA	p.F393L	ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.F392L|ZSCAN5A_ENST00000254165.3_Missense_Mutation_p.F276L|ZSCAN5A_ENST00000587492.1_Missense_Mutation_p.F247L|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.F393L			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	393					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.F393L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TAAGCTGCATGAAGCGCTTCC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											66	64	65					19																	56733256		2203	4300	6503	61425068	SO:0001583	missense	79149			AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.1179C>A	19.37:g.56733256G>T	ENSP00000467631:p.Phe393Leu		61425068	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910190	0.52439	.	.	ENSG00000131848	ENST00000391713;ENST00000254165	T;T	0.41065	1.01;1.01	2.83	0.614	0.17603	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.59824	0.2222	M	0.82056	2.57	0.33325	D	0.567824	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.66093	-0.6009	9	0.87932	D	0	.	6.0718	0.19893	0.3096:0.0:0.6904:0.0	.	276;393	B4DX98;Q9BUG6	.;ZSA5A_HUMAN	L	393;276	ENSP00000375593:F393L;ENSP00000254165:F276L	ENSP00000254165:F276L	F	-	3	2	ZSCAN5A	61425068	0.964000	0.33143	0.013000	0.15412	0.019000	0.09904	1.998000	0.40796	0.495000	0.27882	0.561000	0.74099	TTC		0.502	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		T	56733256	G	T	56733256	3	4	61	1	0	0	0	0	1	0	0	0	18277	1281	45	2	315	2	ZSCAN5A	19	56733256	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31663	56733256	2395727	11379	19364										
ZSCAN5A	79149	broad.mit.edu	37	chr19	56734058	56734058	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtctgcttgggtctcagaGactttgggtcacctgttacg	13	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56734058G>T	ENST00000587340.1	-	6	1336	c.641C>A	c.(640-642)tCt>tAt	p.S214Y	ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.S214Y|ZSCAN5A_ENST00000254165.3_Missense_Mutation_p.S97Y|ZSCAN5A_ENST00000587492.1_Missense_Mutation_p.S68Y|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.S214Y			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	214					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S214Y(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGGTCTCAGAGACTTTGGGTC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	19											211	175	187					19																	56734058		2203	4300	6503	61425870	SO:0001583	missense	79149			AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.641C>A	19.37:g.56734058G>T	ENSP00000467631:p.Ser214Tyr		61425870	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	.	.	.	.	.	.	.	.	.	.	G	7.322	0.617077	0.14129	.	.	ENSG00000131848	ENST00000391713;ENST00000254165	T;T	0.06068	3.35;3.35	2.05	-3.32	0.04973	.	.	.	.	.	T	0.04227	0.0117	L	0.44542	1.39	0.09310	N	1	P;P	0.41748	0.761;0.641	B;B	0.35413	0.202;0.202	T	0.23583	-1.0184	9	0.72032	D	0.01	.	1.5805	0.02633	0.1932:0.2553:0.4021:0.1493	.	97;214	B4DX98;Q9BUG6	.;ZSA5A_HUMAN	Y	214;97	ENSP00000375593:S214Y;ENSP00000254165:S97Y	ENSP00000254165:S97Y	S	-	2	0	ZSCAN5A	61425870	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.394000	0.07296	-0.770000	0.04614	-1.157000	0.01802	TCT		0.498	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		T	56734058	G	T	56734058	3	4	61	1	0	0	0	0	1	0	0	0	18277	942	33	2	857	2	ZSCAN5A	19	56734058	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	802	56734058	2394925	11380	19365										
ZNF582	147948	broad.mit.edu	37	chr19	56895841	56895841	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgactaaaggttttcccacaTtccttgcatgcatagggttt	8	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56895841T>C	ENST00000301310.4	-	5	1103	c.945A>G	c.(943-945)gaA>gaG	p.E315E	ZNF582_ENST00000586929.1_Silent_p.E315E|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E315E(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		TTTTCCCACATTCCTTGCATG	0.398																																					Ovarian(183;1887 2032 4349 30507 51343)											1	Substitution - coding silent(1)	large_intestine(1)	19											88	86	87					19																	56895841		2203	4300	6503	61587653	SO:0001819	synonymous_variant	147948			AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.945A>G	19.37:g.56895841T>C			61587653	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	37	CCDS33121.1																																																																																				0.398	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		C	56895841	T	C	56895841	2	2	61	1	0	0	0	0	0	0	0	1	18053	1490	52	4		4	ZNF582	19	56895841	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	161783	56895841	2233142	11381	19366										
ZNF582	147948	broad.mit.edu	37	chr19	56901378	56901378	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctcactcacctggacacAggcctccagacaccactctc	5	19	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56901378A>T	ENST00000301310.4	-	4	382	c.224T>A	c.(223-225)cTg>cAg	p.L75Q	ZNF582_ENST00000586929.1_Missense_Mutation_p.L75Q|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	75	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L75Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		ACCTGGACACAGGCCTCCAGA	0.542																																					Ovarian(183;1887 2032 4349 30507 51343)											1	Substitution - Missense(1)	large_intestine(1)	19											105	90	95					19																	56901378		2203	4300	6503	61593190	SO:0001583	missense	147948			AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.224T>A	19.37:g.56901378A>T	ENSP00000301310:p.Leu75Gln		61593190	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.800016	0.31869	.	.	ENSG00000018869	ENST00000301310	T	0.06294	3.32	4.54	-9.09	0.00717	Krueppel-associated box (1);	.	.	.	.	T	0.02888	0.0086	N	0.20685	0.6	0.09310	N	1	B;B	0.15473	0.003;0.013	B;B	0.14578	0.011;0.011	T	0.42849	-0.9427	9	0.16420	T	0.52	.	5.9031	0.18978	0.3443:0.096:0.4652:0.0945	.	75;106	Q96NG8;B4DQZ9	ZN582_HUMAN;.	Q	75	ENSP00000301310:L75Q	ENSP00000301310:L75Q	L	-	2	0	ZNF582	61593190	0.000000	0.05858	0.000000	0.03702	0.667000	0.39255	-3.568000	0.00428	-2.017000	0.00944	0.533000	0.62120	CTG		0.542	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		T	56901378	A	T	56901378	3	4	61	1	0	0	0	0	1	0	0	0	18053	188	7	5	1337	5	ZNF582	19	56901378	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5537	56901378	2227605	11382	19367										
ZNF583	147949	broad.mit.edu	37	chr19	56934722	56934722	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcccttactcttcatcagaGaattcatactggagagaaac	6	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56934722G>T	ENST00000333201.9	+	5	905	c.695G>T	c.(694-696)aGa>aTa	p.R232I	ZNF583_ENST00000585612.1_3'UTR|ZNF583_ENST00000291598.7_Missense_Mutation_p.R232I	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R232I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		CTTCATCAGAGAATTCATACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											45	50	48					19																	56934722		2203	4297	6500	61626534	SO:0001583	missense	147949			AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.695G>T	19.37:g.56934722G>T	ENSP00000388502:p.Arg232Ile		61626534	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692434	0.68271	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.02446	4.29;4.29	4.43	-1.39	0.08997	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46758	D	0.000272	T	0.05914	0.0154	L	0.45422	1.42	0.45704	D	0.998612	D	0.76494	0.999	D	0.67548	0.952	T	0.42258	-0.9462	9	.	.	.	.	5.611	0.17406	0.3784:0.1299:0.4917:0.0	.	232	Q96ND8	ZN583_HUMAN	I	232	ENSP00000291598:R232I;ENSP00000388502:R232I	.	R	+	2	0	ZNF583	61626534	0.000000	0.05858	0.052000	0.19188	0.995000	0.86356	-2.160000	0.01279	-0.175000	0.10725	0.462000	0.41574	AGA		0.388	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		T	56934722	G	T	56934722	3	4	61	1	0	0	0	0	1	0	0	0	18054	942	33	2	709	2	ZNF583	19	56934722	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	33344	56934722	2194261	11383	19368										
ZNF583	147949	broad.mit.edu	37	chr19	56935000	56935000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactggagagagacctttcGaatgtattgaatgtggaaag	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56935000G>A	ENST00000333201.9	+	5	1183	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K	ZNF583_ENST00000585612.1_3'UTR|ZNF583_ENST00000291598.7_Missense_Mutation_p.E325K	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E325K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		GAGACCTTTCGAATGTATTGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											109	117	115					19																	56935000		2203	4299	6502	61626812	SO:0001583	missense	147949			AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.973G>A	19.37:g.56935000G>A	ENSP00000388502:p.Glu325Lys		61626812	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243854	0.22796	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.06608	3.28;3.28	4.33	2.01	0.26516	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46145	D	0.000317	T	0.04724	0.0128	N	0.01824	-0.7	0.09310	N	1	D	0.76494	0.999	D	0.70935	0.971	T	0.38887	-0.9640	9	.	.	.	.	3.0242	0.06085	0.1017:0.2385:0.5039:0.1559	.	325	Q96ND8	ZN583_HUMAN	K	325	ENSP00000291598:E325K;ENSP00000388502:E325K	.	E	+	1	0	ZNF583	61626812	0.000000	0.05858	0.037000	0.18230	0.989000	0.77384	-3.558000	0.00431	1.176000	0.42840	0.462000	0.41574	GAA		0.408	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		A	56935000	G	A	56935000	3	1	61	1	0	0	0	0	1	0	0	0	18054	1059	37	1	987	1	ZNF583	19	56935000	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	278	56935000	2193983	11384	19369										
ZNF667	63934	broad.mit.edu	37	chr19	56952547	56952547	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccttaggctttttcttcaGaatgtgtattctgatgtcga	8	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:56952547G>T	ENST00000504904.3	-	7	2536	c.1817C>A	c.(1816-1818)tCt>tAt	p.S606Y	ZNF667_ENST00000342634.3_Missense_Mutation_p.S734Y|ZNF667_ENST00000292069.6_Missense_Mutation_p.S606Y|ZNF667_ENST00000591790.1_3'UTR			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	606					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S606Y(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TTTTTCTTCAGAATGTGTATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	87	87					19																	56952547		2203	4300	6503	61644359	SO:0001583	missense	63934				CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1817C>A	19.37:g.56952547G>T	ENSP00000439402:p.Ser606Tyr		61644359	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.353251	0.41700	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518;ENST00000360227	T;T;T	0.05996	3.36;3.4;3.4	5.19	3.05	0.35203	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.791957	0.10736	N	0.640018	T	0.12603	0.0306	M	0.84433	2.695	0.09310	N	1	P;P	0.44578	0.838;0.736	B;B	0.41691	0.364;0.28	T	0.19712	-1.0297	10	0.87932	D	0	-0.0821	6.706	0.23250	0.0964:0.2005:0.7031:0.0	.	734;606	E7EPS0;Q5HYK9	.;ZN667_HUMAN	Y	734;606;606;388;321	ENSP00000344699:S734Y;ENSP00000439402:S606Y;ENSP00000292069:S606Y	ENSP00000292069:S606Y	S	-	2	0	ZNF667	61644359	.	.	0.007000	0.13788	0.969000	0.65631	.	.	0.753000	0.32945	0.563000	0.77884	TCT		0.338	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		T	56952547	G	T	56952547	3	4	61	1	0	0	0	0	1	0	0	0	18113	942	33	2	19	2	ZNF667	19	56952547	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17547	56952547	2176436	11385	19370										
ZNF471	57573	broad.mit.edu	37	chr19	57036281	57036281	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaccttattcagcatcaaaGaattcatactggagaaaaac	5	9	3	2	rs375659650		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57036281G>T	ENST00000308031.5	+	5	978	c.845G>T	c.(844-846)aGa>aTa	p.R282I	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Nonsense_Mutation_p.E142*	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R282I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CAGCATCAAAGAATTCATACT	0.393																																					Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)											1	Substitution - Missense(1)	large_intestine(1)	19						G	ILE/ARG	0,4406		0,0,2203	128	140	136		845	2.7	0.5	19		136	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF471	NM_020813.2	97	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	282/627	57036281	1,13005	2203	4300	6503	61728093	SO:0001583	missense	57573			AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.845G>T	19.37:g.57036281G>T	ENSP00000309161:p.Arg282Ile		61728093	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058668	0.55325	0.0	1.16E-4	ENSG00000196263	ENST00000308031	T	0.24908	1.83	3.71	2.68	0.31781	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41259	0.1151	M	0.66439	2.03	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	T	0.16719	-1.0393	9	0.49607	T	0.09	.	6.8525	0.24022	0.2199:0.0:0.7801:0.0	.	282	Q9BX82	ZN471_HUMAN	I	282	ENSP00000309161:R282I	ENSP00000309161:R282I	R	+	2	0	ZNF471	61728093	0.000000	0.05858	0.451000	0.26982	0.981000	0.71138	0.133000	0.15912	0.769000	0.33313	0.462000	0.41574	AGA		0.393	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		T	57036281	G	T	57036281	3	4	61	1	0	0	0	0	1	0	0	0	17969	942	33	2	859	2	ZNF471	19	57036281	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	83734	57036281	2092702	11386	19371										
ZFP28	140612	broad.mit.edu	37	chr19	57065487	57065487	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagagaattcacactggaGagaaaccttataaatgtaat	7	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57065487G>T	ENST00000301318.3	+	8	1404	c.1333G>T	c.(1333-1335)Gag>Tag	p.E445*	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E445*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		TCACACTGGAGAGAAACCTTA	0.423																																					Ovarian(124;554 1662 19430 21141 52494)											1	Substitution - Nonsense(1)	large_intestine(1)	19											55	58	57					19																	57065487		2203	4300	6503	61757299	SO:0001587	stop_gained	140612				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1333G>T	19.37:g.57065487G>T	ENSP00000301318:p.Glu445*		61757299	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Nonsense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	36	5.822301	0.96989	.	.	ENSG00000196867	ENST00000301318	.	.	.	4.47	4.47	0.54385	.	0.000000	0.46758	D	0.000274	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.9032	0.24295	0.19:0.0:0.81:0.0	.	.	.	.	X	445	.	ENSP00000301318:E445X	E	+	1	0	ZFP28	61757299	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.391000	0.97249	2.478000	0.83669	0.655000	0.94253	GAG		0.423	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		T	57065487	G	T	57065487	4	4	61	1	0	0	0	0	0	1	0	0	17681	943	33	2	1363	2	ZFP28	19	57065487	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29206	57065487	2063496	11387	19372										
ZFP28	140612	broad.mit.edu	37	chr19	57065728	57065728	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggcttaatcaacacaggaGaattcatactggagagaaac	10	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57065728G>T	ENST00000301318.3	+	8	1645	c.1574G>T	c.(1573-1575)aGa>aTa	p.R525I	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	525					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R525I(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		CAACACAGGAGAATTCATACT	0.428																																					Ovarian(124;554 1662 19430 21141 52494)											2	Substitution - Missense(2)	large_intestine(2)	19											64	57	60					19																	57065728		2203	4300	6503	61757540	SO:0001583	missense	140612				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1574G>T	19.37:g.57065728G>T	ENSP00000301318:p.Arg525Ile		61757540	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.307618	0.60305	.	.	ENSG00000196867	ENST00000301318	T	0.24908	1.83	4.3	3.27	0.37495	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000140	T	0.45796	0.1360	M	0.73430	2.235	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.43540	-0.9385	10	0.72032	D	0.01	.	8.3256	0.32156	0.1688:0.0:0.8312:0.0	.	525	Q8NHY6	ZFP28_HUMAN	I	525	ENSP00000301318:R525I	ENSP00000301318:R525I	R	+	2	0	ZFP28	61757540	0.001000	0.12720	0.999000	0.59377	0.995000	0.86356	1.073000	0.30691	2.390000	0.81377	0.650000	0.86243	AGA		0.428	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		T	57065728	G	T	57065728	3	4	61	1	0	0	0	0	1	0	0	0	17681	942	33	2	1604	2	ZFP28	19	57065728	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241	57065728	2063255	11388	19373										
ZNF470	388566	broad.mit.edu	37	chr19	57088467	57088467	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacaagcaagaccgtggaGaaaagaaacttttaaaatgt	8	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57088467G>T	ENST00000330619.8	+	6	1356	c.670G>T	c.(670-672)Gaa>Taa	p.E224*	ZNF470_ENST00000601902.1_Intron|ZNF470_ENST00000391709.3_Nonsense_Mutation_p.E224*	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E224*(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		AGACCGTGGAGAAAAGAAACT	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											39	41	40					19																	57088467		2203	4297	6500	61780279	SO:0001587	stop_gained	388566			AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.670G>T	19.37:g.57088467G>T	ENSP00000333223:p.Glu224*		61780279	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Nonsense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	G	38	6.851305	0.97885	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	.	.	.	3.76	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	10.6665	0.45734	0.0:0.1959:0.8041:0.0	.	.	.	.	X	224	.	ENSP00000333223:E224X	E	+	1	0	ZNF470	61780279	0.037000	0.19845	0.736000	0.30914	0.256000	0.26092	1.929000	0.40114	1.946000	0.56461	0.305000	0.20034	GAA		0.323	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		T	57088467	G	T	57088467	4	4	61	1	0	0	0	0	0	1	0	0	17968	943	33	2	684	2	ZNF470	19	57088467	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22739	57088467	2040516	11389	19374										
ZNF470	388566	broad.mit.edu	37	chr19	57088645	57088645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacacacaggagaaaaacCttttgaatgtactgaatgtg	8	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57088645C>A	ENST00000330619.8	+	6	1534	c.848C>A	c.(847-849)cCt>cAt	p.P283H	ZNF470_ENST00000601902.1_Intron|ZNF470_ENST00000391709.3_Missense_Mutation_p.P283H	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	283					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P283H(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		GGAGAAAAACCTTTTGAATGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											77	81	80					19																	57088645		2203	4300	6503	61780457	SO:0001583	missense	388566			AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.848C>A	19.37:g.57088645C>A	ENSP00000333223:p.Pro283His		61780457	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.817911	0.71028	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.17528	2.27;2.27	3.8	3.8	0.43715	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.52386	0.1731	M	0.93507	3.425	0.29428	N	0.8601	D	0.89917	1.0	D	0.97110	1.0	T	0.58869	-0.7560	9	0.72032	D	0.01	.	14.5658	0.68176	0.0:1.0:0.0:0.0	.	283	Q6ECI4	ZN470_HUMAN	H	283	ENSP00000375590:P283H;ENSP00000333223:P283H	ENSP00000333223:P283H	P	+	2	0	ZNF470	61780457	0.996000	0.38824	0.988000	0.46212	0.987000	0.75469	4.346000	0.59367	1.964000	0.57103	0.460000	0.39030	CCT		0.433	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		A	57088645	C	A	57088645	3	1	61	1	0	0	0	0	1	0	0	0	17968	681	24	2	862	2	ZNF470	19	57088645	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	178	57088645	2040338	11390	19375										
ZNF470	388566	broad.mit.edu	37	chr19	57088894	57088894	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggattcacactgggaaaaGaccttatgaatgtattgact	9	6	1	3	rs375575481		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57088894G>T	ENST00000330619.8	+	6	1783	c.1097G>T	c.(1096-1098)aGa>aTa	p.R366I	ZNF470_ENST00000601902.1_Intron|ZNF470_ENST00000391709.3_Missense_Mutation_p.R366I	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R366I(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		ACTGGGAAAAGACCTTATGAA	0.428													-|||	1	0.000199681	0	0.0014	5008	,	,		22453	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						A	ILE/ARG	1,4405		0,1,2202	89	84	86		1097	0.7	0	19		86	0,8600		0,0,4300	no	missense	ZNF470	NM_001001668.3	97	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging	366/718	57088894	1,13005	2203	4300	6503	61780706	SO:0001583	missense	388566			AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1097G>T	19.37:g.57088894G>T	ENSP00000333223:p.Arg366Ile		61780706	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	-	10.22	1.291107	0.23564	2.27E-4	0.0	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.20332	2.08;2.08	4.19	0.665	0.17896	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42832	0.1220	M	0.82823	2.61	0.26140	N	0.980295	D	0.76494	0.999	D	0.74348	0.983	T	0.15867	-1.0422	9	0.87932	D	0	.	5.6174	0.17438	0.5771:0.0:0.4229:0.0	.	366	Q6ECI4	ZN470_HUMAN	I	366	ENSP00000375590:R366I;ENSP00000333223:R366I	ENSP00000333223:R366I	R	+	2	0	ZNF470	61780706	0.001000	0.12720	0.014000	0.15608	0.007000	0.05969	0.046000	0.14035	0.412000	0.25729	-0.175000	0.13238	AGA		0.428	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		T	57088894	G	T	57088894	3	4	61	1	0	0	0	0	1	0	0	0	17968	942	33	2	1111	2	ZNF470	19	57088894	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	249	57088894	2040089	11391	19376										
ZNF835	90485	broad.mit.edu	37	chr19	57175816	57175816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggcgcacgcggagcactCgtagggcttctcaccggtgt	14	13	1	0	rs562824788		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57175816C>T	ENST00000537055.2	-	2	982	c.751G>A	c.(751-753)Gag>Aag	p.E251K		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E273K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						GCGGAGCACTCGTAGGGCTTC	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	40	41					19																	57175816		2203	4300	6503	61867628	SO:0001583	missense	90485			AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.751G>A	19.37:g.57175816C>T	ENSP00000444747:p.Glu251Lys		61867628	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	C	9.260	1.042895	0.19748	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06608	3.28	1.83	0.782	0.18567	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01523	0.0049	N	0.00869	-1.13	0.09310	N	1	P	0.37176	0.586	B	0.31812	0.136	T	0.39482	-0.9612	9	0.17832	T	0.49	.	3.9866	0.09519	0.0:0.6144:0.0:0.3856	.	273	Q9Y2P0	ZN835_HUMAN	K	273;251	ENSP00000444747:E251K	ENSP00000341756:E273K	E	-	1	0	ZNF835	61867628	0.000000	0.05858	0.001000	0.08648	0.647000	0.38526	-0.914000	0.04038	0.332000	0.23536	0.561000	0.74099	GAG		0.692	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175816	C	T	57175816	3	4	61	1	0	0	0	0	1	0	0	0	18225	893	31	1	864	1	ZNF835	19	57175816	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	86922	57175816	1953167	11392	19377										
ZIM2	23619	broad.mit.edu	37	chr19	57286090	57286090	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaacagttttctcttgaGaatggagttgataatgttga	9	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57286090G>A	ENST00000391708.3	-	12	2092	c.1550C>T	c.(1549-1551)tCt>tTt	p.S517F	AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.S517F|ZIM2_ENST00000601070.1_Missense_Mutation_p.S517F|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000599935.1_Missense_Mutation_p.S517F|ZIM2_ENST00000221722.5_Missense_Mutation_p.S517F	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S517F(1)|p.S517Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		TTTCTCTTGAGAATGGAGTTG	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	19											100	95	97					19																	57286090		2203	4300	6503	61977902	SO:0001583	missense	23619			AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1550C>T	19.37:g.57286090G>A	ENSP00000375589:p.Ser517Phe		61977902	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.346737	0.61073	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.16196	2.36;2.36	4.96	0.201	0.15186	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17662	0.0424	L	0.61036	1.89	.	.	.	B	0.09022	0.002	B	0.08055	0.003	T	0.11792	-1.0573	8	0.87932	D	0	.	8.3919	0.32533	0.3709:0.0:0.6291:0.0	.	517	Q9NZV7	ZIM2_HUMAN	F	517	ENSP00000375589:S517F;ENSP00000221722:S517F	ENSP00000221722:S517F	S	-	2	0	ZIM2	61977902	0.957000	0.32711	0.715000	0.30552	0.890000	0.51754	1.527000	0.35975	-0.103000	0.12175	-0.136000	0.14681	TCT		0.438	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			A	57286090	G	A	57286090	3	1	61	1	0	0	0	0	1	0	0	0	17723	942	33	3	37	3	ZIM2	19	57286090	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110274	57286090	1842893	11393	19378										
ZIM2	23619	broad.mit.edu	37	chr19	57286851	57286851	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttataggagtcaaaagtttCtcttggttgccctggtgtgg	13	6	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57286851C>A	ENST00000391708.3	-	12	1331	c.789G>T	c.(787-789)gaG>gaT	p.E263D	AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.E263D|ZIM2_ENST00000601070.1_Missense_Mutation_p.E263D|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000599935.1_Missense_Mutation_p.E263D|ZIM2_ENST00000221722.5_Missense_Mutation_p.E263D	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E263D(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		TCAAAAGTTTCTCTTGGTTGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											102	94	97					19																	57286851		2203	4300	6503	61978663	SO:0001583	missense	23619			AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.789G>T	19.37:g.57286851C>A	ENSP00000375589:p.Glu263Asp		61978663	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	C	9.211	1.030955	0.19590	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.04862	3.54;3.54	3.94	2.59	0.31030	.	.	.	.	.	T	0.03477	0.0100	N	0.14661	0.345	.	.	.	P	0.37781	0.608	B	0.35413	0.202	T	0.36016	-0.9765	8	0.18710	T	0.47	.	7.7356	0.28812	0.0:0.8273:0.0:0.1727	.	263	Q9NZV7	ZIM2_HUMAN	D	263	ENSP00000375589:E263D;ENSP00000221722:E263D	ENSP00000221722:E263D	E	-	3	2	ZIM2	61978663	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	0.140000	0.16056	0.914000	0.36822	0.655000	0.94253	GAG		0.463	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			A	57286851	C	A	57286851	3	1	61	1	0	0	0	0	1	0	0	0	17723	912	32	2	798	2	ZIM2	19	57286851	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	761	57286851	1842132	11394	19379										
PEG3	5178	broad.mit.edu	37	chr19	57325440	57325440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttctgggtcttcaataCctgcaccatctggctcatca	6	13	7	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57325440C>T	ENST00000326441.9	-	10	4733	c.4370G>A	c.(4369-4371)gGt>gAt	p.G1457D	PEG3_ENST00000423103.2_Missense_Mutation_p.G1457D|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.G1333D|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.G1331D	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1457	Glu-rich.				apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.G1457D(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GTCTTCAATACCTGCACCATC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	19											107	97	100					19																	57325440		2203	4300	6503	62017252	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4370G>A	19.37:g.57325440C>T	ENSP00000326581:p.Gly1457Asp		62017252	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576445	0.65878	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02345	4.33;4.33	4.25	4.25	0.50352	.	0.000000	0.46145	D	0.000317	T	0.06325	0.0163	L	0.27053	0.805	.	.	.	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.50693	-0.8798	9	0.12103	T	0.63	-39.6188	12.4664	0.55762	0.0:1.0:0.0:0.0	.	1333;1457;1392	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	D	1457	ENSP00000326581:G1457D;ENSP00000403051:G1457D	ENSP00000326581:G1457D	G	-	2	0	ZIM2	62017252	0.000000	0.05858	0.514000	0.27761	0.779000	0.44077	0.246000	0.18160	2.657000	0.90304	0.650000	0.86243	GGT		0.572	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57325440	C	T	57325440	3	4	61	1	0	0	0	0	1	0	0	0	11751	507	18	3	400	3	PEG3	19	57325440	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38589	57325440	1803543	11395	19380										
PEG3	5178	broad.mit.edu	37	chr19	57326133	57326134	+	Nonsense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtccacacaaaaggcatCgaatggccgacccagcaaga							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57326133_57326134CG>TA	ENST00000326441.9	-	10	4039_4040	c.3676_3677CG>TA	c.(3676-3678)CGa>TAa	p.R1226*	PEG3_ENST00000423103.2_Nonsense_Mutation_p.R1226*|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Nonsense_Mutation_p.R1102*|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Nonsense_Mutation_p.R1100*	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1226					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R1226>?(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CAAAAGGCATCGAATGGCCGAC	0.5																																																2	Complex(2)	large_intestine(2)	19																																								62017946	SO:0001587	stop_gained	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3676_3677delinsTA	19.37:g.57326133_57326134delinsTA	ENSP00000326581:p.Arg1226*		62017945	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Nonsense_Mutation	DNP	ENST00000326441.9	37	CCDS12948.1																																																																																				0.5	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			TA	57326134	CG	TA	57326133	4	4	61	1	0	0	0	0	0	1	0	0	11751	884	31	1	1093	1	PEG3	19	57326133	Nonsense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	693	57326133	1802850	11396	19381										
PEG3	5178	broad.mit.edu	37	chr19	57326492	57326492	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacagtcctcacattcataGattttgtcatcagggtcatc	6	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57326492G>T	ENST00000326441.9	-	10	3681	c.3318C>A	c.(3316-3318)atC>atA	p.I1106I	PEG3_ENST00000423103.2_Silent_p.I1106I|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Silent_p.I982I|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Silent_p.I980I	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1106					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.I1106I(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CACATTCATAGATTTTGTCAT	0.522																																																2	Substitution - coding silent(2)	large_intestine(2)	19											118	114	115					19																	57326492		2203	4300	6503	62018304	SO:0001819	synonymous_variant	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3318C>A	19.37:g.57326492G>T			62018304	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																				0.522	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57326492	G	T	57326492	2	4	61	1	0	0	0	0	0	0	0	1	11751	932	33	2		2	PEG3	19	57326492	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	359	57326492	1802491	11397	19382										
PEG3	5178	broad.mit.edu	37	chr19	57326642	57326642	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactcctcgccatgagacttCtcttggtcatagattttctg	8	11	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57326642C>A	ENST00000326441.9	-	10	3531	c.3168G>T	c.(3166-3168)gaG>gaT	p.E1056D	PEG3_ENST00000423103.2_Missense_Mutation_p.E1056D|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.E932D|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.E930D	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1056					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.E1056D(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CATGAGACTTCTCTTGGTCAT	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	19											142	128	133					19																	57326642		2203	4300	6503	62018454	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3168G>T	19.37:g.57326642C>A	ENSP00000326581:p.Glu1056Asp		62018454	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471293	0.43942	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02944	4.1;4.1	4.01	2.97	0.34412	.	0.000000	0.37348	N	0.002127	T	0.10809	0.0264	M	0.71581	2.175	.	.	.	D;D;D	0.76494	0.999;0.997;0.986	D;D;P	0.73380	0.98;0.978;0.643	T	0.05007	-1.0912	9	0.62326	D	0.03	.	7.9104	0.29787	0.0:0.8881:0.0:0.1119	.	932;1056;991	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	D	1056	ENSP00000326581:E1056D;ENSP00000403051:E1056D	ENSP00000326581:E1056D	E	-	3	2	ZIM2	62018454	0.001000	0.12720	0.907000	0.35723	0.139000	0.21198	-0.069000	0.11542	1.285000	0.44548	0.655000	0.94253	GAG		0.478	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57326642	C	A	57326642	3	1	61	1	0	0	0	0	1	0	0	0	11751	912	32	2	1602	2	PEG3	19	57326642	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	150	57326642	1802341	11398	19383										
PEG3	5178	broad.mit.edu	37	chr19	57327246	57327246	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggattctcccttctcattaGattccaccaattcatttcca	3	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57327246G>T	ENST00000326441.9	-	10	2927	c.2564C>A	c.(2563-2565)tCt>tAt	p.S855Y	PEG3_ENST00000423103.2_Missense_Mutation_p.S855Y|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.S731Y|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.S729Y	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	855					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S855Y(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CTTCTCATTAGATTCCACCAA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	19											108	102	104					19																	57327246		2203	4300	6503	62019058	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2564C>A	19.37:g.57327246G>T	ENSP00000326581:p.Ser855Tyr		62019058	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954012	0.53293	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02787	4.16;4.16	3.88	1.3	0.21679	.	0.532273	0.16207	N	0.224671	T	0.01870	0.0059	N	0.22421	0.69	.	.	.	B;P;B	0.38110	0.092;0.618;0.25	B;B;B	0.31016	0.024;0.123;0.07	T	0.39482	-0.9612	9	0.87932	D	0	-2.1892	5.6968	0.17861	0.0:0.6193:0.2256:0.155	.	731;855;790	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	Y	855	ENSP00000326581:S855Y;ENSP00000403051:S855Y	ENSP00000326581:S855Y	S	-	2	0	ZIM2	62019058	0.000000	0.05858	0.002000	0.10522	0.784000	0.44337	0.740000	0.26188	0.396000	0.25283	-0.282000	0.10007	TCT		0.438	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57327246	G	T	57327246	3	4	61	1	0	0	0	0	1	0	0	0	11751	942	33	2	2206	2	PEG3	19	57327246	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	604	57327246	1801737	11399	19384										
PEG3	5178	broad.mit.edu	37	chr19	57327485	57327485	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctatgaataacagacctCtcatatgattttgcctcata	5	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57327485C>A	ENST00000326441.9	-	10	2688	c.2325G>T	c.(2323-2325)gaG>gaT	p.E775D	PEG3_ENST00000423103.2_Missense_Mutation_p.E775D|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.E651D|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.E649D	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	775					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.E775D(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TAACAGACCTCTCATATGATT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	19											170	168	169					19																	57327485		2203	4300	6503	62019297	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2325G>T	19.37:g.57327485C>A	ENSP00000326581:p.Glu775Asp		62019297	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622003	0.28889	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02812	4.15;4.15	4.11	1.99	0.26369	.	0.134498	0.34314	N	0.004073	T	0.11793	0.0287	M	0.82323	2.585	.	.	.	P;D;D	0.71674	0.816;0.998;0.994	B;D;P	0.74674	0.307;0.984;0.736	T	0.14200	-1.0481	9	0.28530	T	0.3	-28.6504	8.2302	0.31593	0.0:0.7993:0.0:0.2007	.	651;775;710	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	D	775	ENSP00000326581:E775D;ENSP00000403051:E775D	ENSP00000326581:E775D	E	-	3	2	ZIM2	62019297	0.059000	0.20769	0.076000	0.20297	0.152000	0.21847	0.375000	0.20518	0.695000	0.31675	0.585000	0.79938	GAG		0.428	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57327485	C	A	57327485	3	1	61	1	0	0	0	0	1	0	0	0	11751	912	32	2	2445	2	PEG3	19	57327485	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	239	57327485	1801498	11400	19385										
USP29	57663	broad.mit.edu	37	chr19	57640286	57640286	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actttgaaaaacaacgtgttCttgtttattgacaaattatc	5	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57640286C>A	ENST00000254181.4	+	4	697	c.243C>A	c.(241-243)ttC>ttA	p.F81L	USP29_ENST00000598197.1_Missense_Mutation_p.F81L	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	81					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.F81L(2)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACAACGTGTTCTTGTTTATTG	0.348																																																2	Substitution - Missense(2)	large_intestine(2)	19											50	49	49					19																	57640286		2203	4300	6503	62332098	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.243C>A	19.37:g.57640286C>A	ENSP00000254181:p.Phe81Leu		62332098		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801786	0.31869	.	.	ENSG00000131864	ENST00000254181	T	0.51071	0.72	2.79	2.79	0.32731	.	1.327380	0.05735	U	0.600293	T	0.40839	0.1133	L	0.46157	1.445	0.09310	N	1	P	0.45126	0.851	B	0.37550	0.253	T	0.34601	-0.9822	10	0.41790	T	0.15	0.0857	9.2721	0.37677	0.0:1.0:0.0:0.0	.	81	Q9HBJ7	UBP29_HUMAN	L	81	ENSP00000254181:F81L	ENSP00000254181:F81L	F	+	3	2	USP29	62332098	0.004000	0.15560	0.007000	0.13788	0.007000	0.05969	0.303000	0.19210	1.828000	0.53243	0.591000	0.81541	TTC		0.348	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			A	57640286	C	A	57640286	3	1	61	1	0	0	0	0	1	0	0	0	17099	912	32	2	245	2	USP29	19	57640286	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	312801	57640286	1488697	11401	19386										
USP29	57663	broad.mit.edu	37	chr19	57641161	57641161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcaacatgcagaatgatgCtcatgagtttttaggtcagt	11	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57641161C>T	ENST00000254181.4	+	4	1572	c.1118C>T	c.(1117-1119)gCt>gTt	p.A373V	USP29_ENST00000598197.1_Missense_Mutation_p.A373V	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	373	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.A373V(1)|p.A373D(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CAGAATGATGCTCATGAGTTT	0.353																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											56	57	56					19																	57641161		2203	4299	6502	62332973	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1118C>T	19.37:g.57641161C>T	ENSP00000254181:p.Ala373Val		62332973		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.627122	0.46840	.	.	ENSG00000131864	ENST00000254181	D	0.81579	-1.51	2.69	2.69	0.31865	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.44902	U	0.000413	D	0.86372	0.5917	M	0.62266	1.93	0.31449	N	0.671013	D	0.89917	1.0	D	0.97110	1.0	D	0.85839	0.1396	10	0.87932	D	0	-13.9409	11.5376	0.50648	0.0:1.0:0.0:0.0	.	373	Q9HBJ7	UBP29_HUMAN	V	373	ENSP00000254181:A373V	ENSP00000254181:A373V	A	+	2	0	USP29	62332973	0.998000	0.40836	0.895000	0.35142	0.174000	0.22865	3.208000	0.51114	1.767000	0.52121	0.591000	0.81541	GCT		0.353	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			T	57641161	C	T	57641161	3	4	61	1	0	0	0	0	1	0	0	0	17099	797	28	3	1120	3	USP29	19	57641161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	875	57641161	1487822	11402	19387										
ZIM3	114026	broad.mit.edu	37	chr19	57646651	57646651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtgaattttctcatgatCgatgacattggatttctggg	11	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57646651C>T	ENST00000269834.1	-	5	1439	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	352					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D352N(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTCTCATGATCGATGACATTG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	19											166	163	164					19																	57646651		2203	4300	6503	62338463	SO:0001583	missense	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1054G>A	19.37:g.57646651C>T	ENSP00000269834:p.Asp352Asn		62338463	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	C	4.804	0.149574	0.09185	.	.	ENSG00000141946	ENST00000269834	T	0.35973	1.28	2.53	2.53	0.30540	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25269	0.0614	N	0.01576	-0.805	0.09310	N	1	D	0.67145	0.996	P	0.62560	0.904	T	0.20405	-1.0276	9	0.17369	T	0.5	.	10.7601	0.46259	0.0:1.0:0.0:0.0	.	352	Q96PE6	ZIM3_HUMAN	N	352	ENSP00000269834:D352N	ENSP00000269834:D352N	D	-	1	0	ZIM3	62338463	0.000000	0.05858	0.053000	0.19242	0.067000	0.16453	-1.106000	0.03319	1.400000	0.46741	0.313000	0.20887	GAT		0.383	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			T	57646651	C	T	57646651	3	4	61	1	0	0	0	0	1	0	0	0	17724	884	31	1	368	1	ZIM3	19	57646651	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5490	57646651	1482332	11403	19388										
ZIM3	114026	broad.mit.edu	37	chr19	57647330	57647330	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctatgcccagtggaagtatTttcttagatccgtcacattc	7	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57647330T>G	ENST00000269834.1	-	5	760	c.375A>C	c.(373-375)aaA>aaC	p.K125N	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K125N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGAAGTATTTTCTTAGATC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											227	219	221					19																	57647330		2203	4300	6503	62339142	SO:0001583	missense	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.375A>C	19.37:g.57647330T>G	ENSP00000269834:p.Lys125Asn		62339142	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	T	8.871	0.949333	0.18356	.	.	ENSG00000141946	ENST00000269834	T	0.04862	3.54	2.18	2.18	0.27775	.	.	.	.	.	T	0.04363	0.0120	N	0.20986	0.625	0.09310	N	1	B	0.29716	0.255	B	0.23275	0.045	T	0.36601	-0.9741	9	0.54805	T	0.06	.	6.7915	0.23701	0.0:0.0:0.2369:0.7631	.	125	Q96PE6	ZIM3_HUMAN	N	125	ENSP00000269834:K125N	ENSP00000269834:K125N	K	-	3	2	ZIM3	62339142	0.000000	0.05858	0.011000	0.14972	0.120000	0.20174	-0.011000	0.12721	1.248000	0.43934	0.260000	0.18958	AAA		0.388	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			G	57647330	T	G	57647330	3	3	61	1	0	0	0	0	1	0	0	0	17724	1838	64	4	1047	4	ZIM3	19	57647330	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	679	57647330	1481653	11404	19389										
DUXA	503835	broad.mit.edu	37	chr19	57666741	57666741	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcgattttggaaccaaatCtaagtggtaagacaaagaaa	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57666741C>A	ENST00000554048.2	-	5	438		c.e5-1			NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.?(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		GGAACCAAATCTAAGTGGTAA	0.378																																																1	Unknown(1)	large_intestine(1)	19											57	54	55					19																	57666741		2203	4300	6503	62358553	SO:0001630	splice_region_variant	503835				CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873		"Homeoboxes / PRD class"	32179	protein-coding gene	gene with protein product		611168					Standard	NM_001012729		Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.439-1G>T	19.37:g.57666741C>A			62358553		Splice_Site	SNP	ENST00000554048.2	37	CCDS33126.1	.	.	.	.	.	.	.	.	.	.	C	3.067	-0.191998	0.06299	.	.	ENSG00000258873	ENST00000554048	.	.	.	2.08	2.08	0.27032	.	.	.	.	.	.	.	.	.	.	.	0.44194	D	0.997014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7237	0.28746	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DUXA	62358553	0.604000	0.26932	0.240000	0.24138	0.207000	0.24258	1.488000	0.35551	1.455000	0.47813	0.514000	0.50259	.		0.378	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729	Intron	A	57666741	C	A	57666741	5	1	61	1	0	0	0	0	0	0	1	0	4845	927	32	2	184	2	DUXA	19	57666741	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19411	57666741	1462242	11405	19390										
ZNF264	9422	broad.mit.edu	37	chr19	57723831	57723831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactggagaaaagcctttcGagtgcaaagagtgtgggaaa	13	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57723831G>A	ENST00000263095.6	+	4	1780	c.1366G>A	c.(1366-1368)Gag>Aag	p.E456K	ZNF264_ENST00000536056.1_Missense_Mutation_p.E456K	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E456K(1)|p.E456*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		AAAGCCTTTCGAGTGCAAAGA	0.517																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	19											55	57	56					19																	57723831		2203	4300	6503	62415643	SO:0001583	missense	9422			AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"Zinc fingers, C2H2-type", "-"	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.1366G>A	19.37:g.57723831G>A	ENSP00000263095:p.Glu456Lys		62415643	A8K8Y9|Q9P1V0	Missense_Mutation	SNP	ENST00000263095.6	37	CCDS33127.1	.	.	.	.	.	.	.	.	.	.	G	8.397	0.841078	0.16891	.	.	ENSG00000083844	ENST00000263095;ENST00000536056	T;T	0.06608	3.28;3.28	2.35	1.3	0.21679	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01592	0.0051	N	0.00450	-1.49	0.09310	N	1	B	0.28850	0.225	B	0.31191	0.125	T	0.46020	-0.9221	9	0.18710	T	0.47	.	4.3259	0.11039	0.1349:0.0:0.6422:0.2228	.	456	O43296	ZN264_HUMAN	K	456	ENSP00000263095:E456K;ENSP00000440376:E456K	ENSP00000263095:E456K	E	+	1	0	ZNF264	62415643	0.000000	0.05858	0.807000	0.32361	0.772000	0.43724	-1.148000	0.03185	0.563000	0.29222	0.491000	0.48974	GAG		0.517	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			A	57723831	G	A	57723831	3	1	61	1	0	0	0	0	1	0	0	0	17843	1059	37	1	1380	1	ZNF264	19	57723831	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57090	57723831	1405152	11406	19391										
AURKC	6795	broad.mit.edu	37	chr19	57743431	57743431	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtcgatgactttgaaatCgggcgtcccctgggcaaggg	14	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57743431C>T	ENST00000302804.7	+	3	321	c.135C>T	c.(133-135)atC>atT	p.I45I	AURKC_ENST00000415300.2_Silent_p.I26I|AURKC_ENST00000448930.1_Silent_p.I11I|AURKC_ENST00000598785.1_Silent_p.I11I|AURKC_ENST00000599062.1_Silent_p.I42I	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	45	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.I45I(2)|p.I11I(2)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		ACTTTGAAATCGGGCGTCCCC	0.552																																																4	Substitution - coding silent(4)	large_intestine(4)	19											52	48	50					19																	57743431		2203	4300	6503	62435243	SO:0001819	synonymous_variant	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.135C>T	19.37:g.57743431C>T			62435243	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Silent	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																				0.552	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		T	57743431	C	T	57743431	2	4	61	1	0	0	0	0	0	0	0	1	1225	874	31	1		1	AURKC	19	57743431	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19600	57743431	1385552	11407	19392										
AURKC	6795	broad.mit.edu	37	chr19	57746297	57746297	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gactacttgccgccagaaatGattgaggggagaacatatga	12	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57746297G>T	ENST00000302804.7	+	6	816	c.630G>T	c.(628-630)atG>atT	p.M210I	AURKC_ENST00000415300.2_Missense_Mutation_p.M191I|AURKC_ENST00000448930.1_Missense_Mutation_p.M176I|AURKC_ENST00000598785.1_Missense_Mutation_p.M176I|AURKC_ENST00000599062.1_Missense_Mutation_p.M207I	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.M176I(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		CGCCAGAAATGATTGAGGGGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	19											143	117	126					19																	57746297		2203	4300	6503	62438109	SO:0001583	missense	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.630G>T	19.37:g.57746297G>T	ENSP00000302898:p.Met210Ile		62438109	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Missense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.896654	0.33535	.	.	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	T;T;T	0.62364	0.03;0.03;0.03	4.09	1.92	0.25849	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.076845	0.85682	N	0.000000	T	0.35189	0.0923	N	0.01631	-0.79	0.50813	D	0.999895	B;B;B	0.28378	0.072;0.157;0.209	B;B;B	0.37267	0.245;0.115;0.16	T	0.26916	-1.0089	10	0.66056	D	0.02	-33.7327	7.4897	0.27454	0.0959:0.1695:0.7346:0.0	.	207;210;191	Q5Y191;Q9UQB9;Q9UQB9-3	.;AURKC_HUMAN;.	I	191;176;210	ENSP00000407162:M191I;ENSP00000406798:M176I;ENSP00000302898:M210I	ENSP00000302898:M210I	M	+	3	0	AURKC	62438109	1.000000	0.71417	0.660000	0.29694	0.522000	0.34438	5.197000	0.65141	0.663000	0.31027	0.655000	0.94253	ATG		0.507	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		T	57746297	G	T	57746297	3	4	61	1	0	0	0	0	1	0	0	0	1225	1290	45	2	657	2	AURKC	19	57746297	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2866	57746297	1382686	11408	19393										
ZNF460	10794	broad.mit.edu	37	chr19	57802833	57802833	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaatgagaagaaacccttCgcatgcagcgaatgtggaaa	10	9	0	2	rs368085632		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57802833C>T	ENST00000360338.3	+	3	1246	c.924C>T	c.(922-924)ttC>ttT	p.F308F	ZNF460_ENST00000537645.1_Silent_p.F267F	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	308					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F308F(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAAACCCTTCGCATGCAGCG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4406		0,0,2203	102	90	94		924	-2.2	0	19		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		308/563	57802833	1,13005	2203	4300	6503	62494645	SO:0001819	synonymous_variant	10794			X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"Zinc fingers, C2H2-type", "-"	21628	protein-coding gene	gene with protein product		604755	"zinc finger protein 272"	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.924C>T	19.37:g.57802833C>T			62494645	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																				0.458	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635		T	57802833	C	T	57802833	2	4	61	1	0	0	0	0	0	0	0	1	17963	883	31	1		1	ZNF460	19	57802833	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56536	57802833	1326150	11409	19394										
ZNF547	284306	broad.mit.edu	37	chr19	57889375	57889375	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcctcattcaacaccaaaGagttcacactggagaacggc	8	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57889375G>T	ENST00000282282.3	+	4	1181	c.1031G>T	c.(1030-1032)aGa>aTa	p.R344I	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R344I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CAACACCAAAGAGTTCACACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											96	90	92					19																	57889375		2203	4300	6503	62581187	SO:0001583	missense	284306			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.1031G>T	19.37:g.57889375G>T	ENSP00000282282:p.Arg344Ile		62581187	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509180	0.64410	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.24908	1.83	1.87	-3.73	0.04398	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37865	0.1019	M	0.73430	2.235	0.19945	N	0.999946	D;P;P	0.62365	0.991;0.931;0.935	P;B;P	0.59643	0.861;0.378;0.508	T	0.24119	-1.0169	9	0.56958	D	0.05	.	4.9401	0.13961	0.512:0.1602:0.3278:0.0	.	344;344;344	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	I	344	ENSP00000282282:R344I	ENSP00000282282:R344I	R	+	2	0	ZNF547	62581187	0.000000	0.05858	0.000000	0.03702	0.961000	0.63080	-2.477000	0.00985	-0.977000	0.03537	0.491000	0.48974	AGA		0.463	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		T	57889375	G	T	57889375	3	4	61	1	0	0	0	0	1	0	0	0	18018	942	33	2	1041	2	ZNF547	19	57889375	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	86542	57889375	1239608	11410	19395										
ZNF548	147694	broad.mit.edu	37	chr19	57910407	57910407	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacagttcacactagtgaaaGgacttatgagtgcagagaat	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57910407G>T	ENST00000366197.5	+	3	1002	c.752G>T	c.(751-753)aGg>aTg	p.R251M	AC004076.7_ENST00000597410.1_Intron|ZNF548_ENST00000336128.7_Missense_Mutation_p.R263M|AC003002.6_ENST00000596400.1_Intron|AC003002.6_ENST00000600421.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R263M(1)		breast(1)	1		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)		ACTAGTGAAAGGACTTATGAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											45	46	45					19																	57910407		2195	4294	6489	62602219	SO:0001583	missense	147694			AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"Zinc fingers, C2H2-type", "-"	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.752G>T	19.37:g.57910407G>T	ENSP00000379482:p.Arg251Met		62602219	Q96M05	Missense_Mutation	SNP	ENST00000366197.5	37	CCDS46209.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957893	0.53400	.	.	ENSG00000188785	ENST00000336128;ENST00000366197	T;T	0.20332	2.08;2.08	2.28	2.28	0.28536	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40719	0.1128	M	0.87971	2.92	0.24484	N	0.994333	D;D	0.67145	0.995;0.996	P;P	0.59825	0.785;0.864	T	0.25047	-1.0143	9	0.62326	D	0.03	.	4.0389	0.09741	0.3053:0.0:0.6946:0.0	.	263;251	Q8NEK5-2;Q8NEK5	.;ZN548_HUMAN	M	263;251	ENSP00000337555:R263M;ENSP00000379482:R251M	ENSP00000337555:R263M	R	+	2	0	ZNF548	62602219	0.000000	0.05858	0.822000	0.32727	0.965000	0.64279	-0.586000	0.05787	1.628000	0.50416	0.655000	0.94253	AGG		0.398	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909		T	57910407	G	T	57910407	3	4	61	1	0	0	0	0	1	0	0	0	18019	1000	35	2	802	2	ZNF548	19	57910407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21032	57910407	1218576	11411	19396										
ZNF772	400720	broad.mit.edu	37	chr19	57984676	57984676	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtgtgaattttccagtggCggatgagggaagccctctgc	14	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:57984676C>T	ENST00000343280.4	-	5	1696	c.1436G>A	c.(1435-1437)cGc>cAc	p.R479H	ZNF772_ENST00000427512.2_Missense_Mutation_p.R367H|ZNF772_ENST00000356584.3_Missense_Mutation_p.R438H|ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000425074.3_3'UTR|AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000600175.1_Intron	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	479					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R479H(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		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)		TTTCCAGTGGCGGATGAGGGA	0.448																																					Melanoma(5;289 436 14293 15924 30817)											1	Substitution - Missense(1)	large_intestine(1)	19											67	59	62					19																	57984676		2203	4300	6503	62676488	SO:0001583	missense	400720			BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"Zinc fingers, C2H2-type", "-"	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.1436G>A	19.37:g.57984676C>T	ENSP00000341165:p.Arg479His		62676488	A6NJK9|B4DH56|B4DYS0	Missense_Mutation	SNP	ENST00000343280.4	37	CCDS33133.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.098874	0.37048	.	.	ENSG00000197128	ENST00000343280;ENST00000427512;ENST00000356584;ENST00000291809	T;T;T	0.07688	3.17;3.17;3.17	3.96	1.68	0.24146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19846	0.0477	M	0.66439	2.03	0.09310	N	1	D;D;D	0.76494	0.992;0.987;0.999	P;P;D	0.76071	0.821;0.666;0.987	T	0.10941	-1.0608	9	0.54805	T	0.06	.	2.6213	0.04917	0.2307:0.5083:0.0:0.2611	.	367;438;479	Q68DY9-2;A6NJK9;Q68DY9	.;.;ZN772_HUMAN	H	479;367;438;404	ENSP00000341165:R479H;ENSP00000395967:R367H;ENSP00000348992:R438H	ENSP00000291809:R404H	R	-	2	0	ZNF772	62676488	0.000000	0.05858	0.221000	0.23827	0.572000	0.35998	-2.261000	0.01176	0.892000	0.36259	0.289000	0.19496	CGC		0.448	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596		T	57984676	C	T	57984676	3	4	61	1	0	0	0	0	1	0	0	0	18184	768	27	1	37	1	ZNF772	19	57984676	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74269	57984676	1144307	11412	19397										
ZNF419	79744	broad.mit.edu	37	chr19	58004477	58004477	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggtgactcacacaggagaGaagtcacataggagctccaa	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58004477G>T	ENST00000221735.7	+	5	738	c.552G>T	c.(550-552)gaG>gaT	p.E184D	ZNF419_ENST00000426954.2_Missense_Mutation_p.E172D|ZNF419_ENST00000415379.2_Missense_Mutation_p.E138D|ZNF419_ENST00000424930.2_Missense_Mutation_p.E185D|ZNF419_ENST00000442920.2_Missense_Mutation_p.E171D|ZNF419_ENST00000354197.4_Missense_Mutation_p.E172D|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000347466.6_Missense_Mutation_p.E152D			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	184					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E152D(1)|p.E187D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		ACACAGGAGAGAAGTCACATA	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	19											42	44	43					19																	58004477		2203	4300	6503	62696289	SO:0001583	missense	79744			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.552G>T	19.37:g.58004477G>T	ENSP00000221735:p.Glu184Asp		62696289	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.355034	0.24512	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735;ENST00000521137	T;T;T;T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12;2.12;2.12;2.12	2.28	-3.46	0.04767	.	.	.	.	.	T	0.27967	0.0689	M	0.70275	2.135	0.09310	N	1	B;B;B;B;B;B;B	0.30889	0.012;0.012;0.03;0.012;0.0;0.023;0.299	B;B;B;B;B;B;P	0.44623	0.007;0.011;0.016;0.007;0.0;0.024;0.455	T	0.51865	-0.8651	9	0.62326	D	0.03	.	3.5302	0.07774	0.6229:0.0:0.2038:0.1734	.	138;138;171;172;185;152;184	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	D	187;185;172;172;171;185;152;138;184;151	ENSP00000388864:E185D;ENSP00000390916:E172D;ENSP00000346136:E172D;ENSP00000414709:E171D;ENSP00000299860:E152D;ENSP00000392129:E138D;ENSP00000221735:E184D;ENSP00000429628:E151D	ENSP00000221735:E184D	E	+	3	2	ZNF419	62696289	0.000000	0.05858	0.000000	0.03702	0.252000	0.25951	-0.294000	0.08309	-0.869000	0.04052	0.205000	0.17691	GAG		0.478	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		T	58004477	G	T	58004477	3	4	61	1	0	0	0	0	1	0	0	0	17935	933	33	2	573	2	ZNF419	19	58004477	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19801	58004477	1124506	11413	19398										
ZNF419	79744	broad.mit.edu	37	chr19	58004955	58004955	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactggagaaagaccttatAagtgcagtgaatgtggaaaa	11	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58004955A>C	ENST00000221735.7	+	5	1216	c.1030A>C	c.(1030-1032)Aag>Cag	p.K344Q	ZNF419_ENST00000426954.2_Missense_Mutation_p.K332Q|ZNF419_ENST00000415379.2_Missense_Mutation_p.K298Q|ZNF419_ENST00000424930.2_Missense_Mutation_p.K345Q|ZNF419_ENST00000442920.2_Missense_Mutation_p.K331Q|ZNF419_ENST00000354197.4_Missense_Mutation_p.K332Q|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000347466.6_Missense_Mutation_p.K312Q			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K319Q(1)|p.K312Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		AAGACCTTATAAGTGCAGTGA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	19											69	71	70					19																	58004955		2203	4300	6503	62696767	SO:0001583	missense	79744			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1030A>C	19.37:g.58004955A>C	ENSP00000221735:p.Lys344Gln		62696767	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	A	9.210	1.030793	0.19590	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.18810	3.1;3.1;3.1;3.1;3.1;2.19;3.1	2.36	-2.45	0.06481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11452	0.0279	L	0.28115	0.83	0.09310	N	1	B;B;B;B;B;B;B	0.22983	0.005;0.002;0.006;0.078;0.005;0.002;0.005	B;B;B;B;B;B;B	0.18561	0.001;0.001;0.003;0.022;0.002;0.001;0.002	T	0.27434	-1.0074	9	0.54805	T	0.06	.	3.0978	0.06315	0.1951:0.1578:0.4917:0.1555	.	298;298;331;332;345;312;344	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	Q	319;345;332;332;331;345;312;298;344	ENSP00000388864:K345Q;ENSP00000390916:K332Q;ENSP00000346136:K332Q;ENSP00000414709:K331Q;ENSP00000299860:K312Q;ENSP00000392129:K298Q;ENSP00000221735:K344Q	ENSP00000221735:K344Q	K	+	1	0	ZNF419	62696767	0.000000	0.05858	0.028000	0.17463	0.866000	0.49608	-4.228000	0.00270	-0.617000	0.05664	0.172000	0.16884	AAG		0.423	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		C	58004955	A	C	58004955	3	2	61	1	0	0	0	0	1	0	0	0	17935	363	13	4	1051	4	ZNF419	19	58004955	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	478	58004955	1124028	11414	19399										
ZNF419	79744	broad.mit.edu	37	chr19	58005122	58005122	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacactggagaaaagcctttTaagtgcaatgaatgtgggag	12	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58005122T>G	ENST00000221735.7	+	5	1383	c.1197T>G	c.(1195-1197)ttT>ttG	p.F399L	ZNF419_ENST00000426954.2_Missense_Mutation_p.F387L|ZNF419_ENST00000415379.2_Missense_Mutation_p.F353L|ZNF419_ENST00000424930.2_Missense_Mutation_p.F400L|ZNF419_ENST00000442920.2_Missense_Mutation_p.F386L|ZNF419_ENST00000354197.4_Missense_Mutation_p.F387L|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000347466.6_Missense_Mutation_p.F367L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F367L(1)|p.F374L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		AAAAGCCTTTTAAGTGCAATG	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	19											88	92	91					19																	58005122		2201	4300	6501	62696934	SO:0001583	missense	79744			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1197T>G	19.37:g.58005122T>G	ENSP00000221735:p.Phe399Leu		62696934	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.680762	0.47886	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98	2.19	2.19	0.27852	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20129	0.0484	L	0.49778	1.585	0.09310	N	1	B;B;P;B;P;B;P	0.38827	0.245;0.245;0.454;0.245;0.649;0.4;0.649	B;B;B;B;B;B;B	0.40602	0.184;0.184;0.334;0.253;0.157;0.173;0.157	T	0.17198	-1.0377	9	0.87932	D	0	.	5.346	0.16010	0.0:0.1564:0.0:0.8436	.	353;353;386;387;400;367;399	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	L	374;400;387;387;386;400;367;353;399	ENSP00000388864:F400L;ENSP00000390916:F387L;ENSP00000346136:F387L;ENSP00000414709:F386L;ENSP00000299860:F367L;ENSP00000392129:F353L;ENSP00000221735:F399L	ENSP00000221735:F399L	F	+	3	2	ZNF419	62696934	0.000000	0.05858	0.002000	0.10522	0.324000	0.28378	-0.874000	0.04210	0.988000	0.38734	0.172000	0.16884	TTT		0.443	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		G	58005122	T	G	58005122	3	3	61	1	0	0	0	0	1	0	0	0	17935	1751	61	4	1218	4	ZNF419	19	58005122	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	167	58005122	1123861	11415	19400										
ZNF773	374928	broad.mit.edu	37	chr19	58017811	58017811	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaacgttcagcaacaccaGaagcagcactgtggagagaa	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58017811G>T	ENST00000282292.4	+	4	488	c.348G>T	c.(346-348)caG>caT	p.Q116H	ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.Q115H	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q116H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		AGCAACACCAGAAGCAGCACT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	92	91					19																	58017811		2203	4300	6503	62709623	SO:0001583	missense	374928			BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.348G>T	19.37:g.58017811G>T	ENSP00000282292:p.Gln116His		62709623	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632434	0.46944	.	.	ENSG00000152439	ENST00000282292	T	0.06849	3.25	1.18	1.18	0.20946	.	.	.	.	.	T	0.16041	0.0386	L	0.45285	1.41	0.24162	N	0.99565	D;P	0.59357	0.985;0.93	P;P	0.61940	0.896;0.459	T	0.10222	-1.0639	9	0.56958	D	0.05	.	8.2465	0.31691	0.0:0.0:1.0:0.0	.	115;116	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	H	116	ENSP00000282292:Q116H	ENSP00000282292:Q116H	Q	+	3	2	ZNF773	62709623	0.001000	0.12720	0.007000	0.13788	0.536000	0.34869	0.401000	0.20948	0.950000	0.37743	0.313000	0.20887	CAG		0.502	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		T	58017811	G	T	58017811	3	4	61	1	0	0	0	0	1	0	0	0	18185	933	33	2	362	2	ZNF773	19	58017811	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	12689	58017811	1111172	11416	19401										
ZNF773	374928	broad.mit.edu	37	chr19	58018529	58018529	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attggcgtgttcacactggaGaaaggccttatgagtgcagt	13	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58018529G>T	ENST00000282292.4	+	4	1206	c.1066G>T	c.(1066-1068)Gaa>Taa	p.E356*	ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000598770.1_Nonsense_Mutation_p.E355*	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	356					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E356*(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		TCACACTGGAGAAAGGCCTTA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											107	110	109					19																	58018529		2203	4300	6503	62710341	SO:0001587	stop_gained	374928			BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.1066G>T	19.37:g.58018529G>T	ENSP00000282292:p.Glu356*		62710341	Q96DL8	Nonsense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862521	0.91511	.	.	ENSG00000152439	ENST00000282292	.	.	.	1.24	1.24	0.21308	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	10.0353	0.42125	0.0:0.0:1.0:0.0	.	.	.	.	X	356	.	ENSP00000282292:E356X	E	+	1	0	ZNF773	62710341	0.990000	0.36364	0.010000	0.14722	0.821000	0.46438	4.329000	0.59260	0.987000	0.38709	0.305000	0.20034	GAA		0.418	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		T	58018529	G	T	58018529	4	4	61	1	0	0	0	0	0	1	0	0	18185	943	33	2	1080	2	ZNF773	19	58018529	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	718	58018529	1110454	11417	19402										
ZNF773	374928	broad.mit.edu	37	chr19	58018596	58018596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaagcctcatgcaacatcGaaaagttcacactggagaaa	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58018596G>A	ENST00000282292.4	+	4	1273	c.1133G>A	c.(1132-1134)cGa>cAa	p.R378Q	ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.R377Q	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R378Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		ATGCAACATCGAAAAGTTCAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											111	114	113					19																	58018596		2203	4300	6503	62710408	SO:0001583	missense	374928			BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.1133G>A	19.37:g.58018596G>A	ENSP00000282292:p.Arg378Gln		62710408	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.789508	0.00623	.	.	ENSG00000152439	ENST00000282292	T	0.17691	2.26	1.03	-0.0823	0.13698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	N	0.04043	-0.29	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.06405	0.002;0.002	T	0.40136	-0.9579	9	0.02654	T	1	.	1.8888	0.03243	0.3967:0.0:0.3328:0.2705	.	377;378	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	Q	378	ENSP00000282292:R378Q	ENSP00000282292:R378Q	R	+	2	0	ZNF773	62710408	0.000000	0.05858	0.276000	0.24689	0.841000	0.47740	-1.620000	0.02046	-0.002000	0.14469	0.305000	0.20034	CGA		0.418	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		A	58018596	G	A	58018596	3	1	61	1	0	0	0	0	1	0	0	0	18185	1058	37	1	1147	1	ZNF773	19	58018596	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67	58018596	1110387	11418	19403										
ZNF549	256051	broad.mit.edu	37	chr19	58046547	58046547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggatattgctgtgtacttCtcccaggaggagtggggcct	15	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58046547C>A	ENST00000376233.3	+	3	289	c.108C>A	c.(106-108)ttC>ttA	p.F36L	ZNF549_ENST00000602149.1_Missense_Mutation_p.F36L|ZNF549_ENST00000240719.3_Missense_Mutation_p.F23L|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F23L(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		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)		CTGTGTACTTCTCCCAGGAGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											170	138	149					19																	58046547		2203	4300	6503	62738359	SO:0001583	missense	256051			AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.108C>A	19.37:g.58046547C>A	ENSP00000365407:p.Phe36Leu		62738359	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541807	0.65198	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.12879	2.64;2.64	2.58	1.5	0.22942	Krueppel-associated box (4);	.	.	.	.	T	0.37999	0.1024	M	0.89904	3.07	0.24096	N	0.995891	D;D	0.59357	0.985;0.981	P;D	0.65684	0.849;0.937	T	0.09662	-1.0664	9	0.62326	D	0.03	.	7.2421	0.26102	0.0:0.8545:0.0:0.1455	.	36;23	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	L	23;36	ENSP00000240719:F23L;ENSP00000365407:F36L	ENSP00000240719:F23L	F	+	3	2	ZNF549	62738359	0.665000	0.27466	0.908000	0.35775	0.998000	0.95712	0.887000	0.28254	0.420000	0.25954	0.655000	0.94253	TTC		0.502	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		A	58046547	C	A	58046547	3	1	61	1	0	0	0	0	1	0	0	0	18020	912	32	2	75	2	ZNF549	19	58046547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27951	58046547	1082436	11419	19404										
ZNF549	256051	broad.mit.edu	37	chr19	58048826	58048826	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaacctgcaacagcaccagAaccaggacagtggagagaaa	10	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58048826A>G	ENST00000376233.3	+	4	635	c.454A>G	c.(454-456)Aac>Gac	p.N152D	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.N139D|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	152					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N139D(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		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)		ACAGCACCAGAACCAGGACAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	77	80					19																	58048826		2203	4300	6503	62740638	SO:0001583	missense	256051			AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.454A>G	19.37:g.58048826A>G	ENSP00000365407:p.Asn152Asp		62740638	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	A	9.110	1.006367	0.19199	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.06142	3.36;3.34	2.03	-0.357	0.12579	.	.	.	.	.	T	0.04952	0.0133	L	0.27053	0.805	0.09310	N	1	B;P	0.37548	0.043;0.599	B;B	0.40901	0.033;0.343	T	0.36529	-0.9744	9	0.62326	D	0.03	.	2.2566	0.04057	0.3878:0.0:0.1548:0.4574	.	152;139	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	D	139;152	ENSP00000240719:N139D;ENSP00000365407:N152D	ENSP00000240719:N139D	N	+	1	0	ZNF549	62740638	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.338000	0.19858	-0.173000	0.10761	0.459000	0.35465	AAC		0.483	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		G	58048826	A	G	58048826	3	3	61	1	0	0	0	0	1	0	0	0	18020	246	9	4	425	4	ZNF549	19	58048826	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	2279	58048826	1080157	11420	19405										
ZNF549	256051	broad.mit.edu	37	chr19	58049294	58049294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggtcttatgtgtgcatcGaatgtgggaaatccttgagc	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58049294G>A	ENST00000376233.3	+	4	1103	c.922G>A	c.(922-924)Gaa>Aaa	p.E308K	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.E295K|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	308					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E295K(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		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)		TGTGTGCATCGAATGTGGGAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	101	102					19																	58049294		2203	4300	6503	62741106	SO:0001583	missense	256051			AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.922G>A	19.37:g.58049294G>A	ENSP00000365407:p.Glu308Lys		62741106	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	G	7.935	0.741549	0.15642	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.07327	3.2;3.2	2.6	0.707	0.18139	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09818	0.0241	L	0.39633	1.23	0.09310	N	1	P;D	0.53462	0.497;0.96	B;P	0.47915	0.023;0.561	T	0.25882	-1.0119	9	0.49607	T	0.09	.	7.9332	0.29914	0.1793:0.0:0.8207:0.0	.	308;295	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	K	295;308	ENSP00000240719:E295K;ENSP00000365407:E308K	ENSP00000240719:E295K	E	+	1	0	ZNF549	62741106	0.000000	0.05858	0.228000	0.23943	0.224000	0.24922	-1.725000	0.01863	0.254000	0.21573	0.585000	0.79938	GAA		0.413	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		A	58049294	G	A	58049294	3	1	61	1	0	0	0	0	1	0	0	0	18020	1059	37	1	893	1	ZNF549	19	58049294	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	468	58049294	1079689	11421	19406										
ZNF549	256051	broad.mit.edu	37	chr19	58049982	58049982	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcaatgaatgtggaaaagTcttcagccaccaaaaaagac	9	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58049982T>C	ENST00000376233.3	+	4	1791	c.1610T>C	c.(1609-1611)gTc>gCc	p.V537A	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.V524A|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V524A(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		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)		TGTGGAAAAGTCTTCAGCCAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	19											68	70	69					19																	58049982		2203	4300	6503	62741794	SO:0001583	missense	256051			AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.1610T>C	19.37:g.58049982T>C	ENSP00000365407:p.Val537Ala		62741794	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	T	2.495	-0.316613	0.05422	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.10005	2.92;2.92	2.6	-3.95	0.04118	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01940	0.0061	N	0.00656	-1.285	0.09310	N	1	B;B	0.15719	0.0;0.014	B;B	0.15484	0.0;0.013	T	0.38735	-0.9647	9	0.02654	T	1	.	4.1076	0.10043	0.0:0.4153:0.1745:0.4102	.	537;524	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	A	524;537	ENSP00000240719:V524A;ENSP00000365407:V537A	ENSP00000240719:V524A	V	+	2	0	ZNF549	62741794	0.000000	0.05858	0.001000	0.08648	0.851000	0.48451	-0.022000	0.12480	-0.947000	0.03673	-0.472000	0.04984	GTC		0.438	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		C	58049982	T	C	58049982	3	2	61	1	0	0	0	0	1	0	0	0	18020	1667	58	4	1581	4	ZNF549	19	58049982	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	688	58049982	1079001	11422	19407										
ZNF549	256051	broad.mit.edu	37	chr19	58050186	58050186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaacttgttgagcatcagcGaatccacaccggagaaaagc	9	11	1	2	rs534903585		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58050186G>A	ENST00000376233.3	+	4	1995	c.1814G>A	c.(1813-1815)cGa>cAa	p.R605Q	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.R592Q|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R592Q(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		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)		GAGCATCAGCGAATCCACACC	0.423													G|||	1	0.000199681	8e-04	0	5008	,	,		20218	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											79	69	72					19																	58050186		2203	4300	6503	62741998	SO:0001583	missense	256051			AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.1814G>A	19.37:g.58050186G>A	ENSP00000365407:p.Arg605Gln		62741998	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239612	0.79800	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.24723	1.84;1.84	2.35	1.25	0.21368	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32793	0.0841	L	0.33137	0.985	0.09310	N	1	D;D	0.89917	1.0;0.999	D;P	0.64877	0.93;0.888	T	0.11036	-1.0604	9	0.72032	D	0.01	.	6.8879	0.24212	0.1558:0.0:0.8442:0.0	.	605;592	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	Q	592;605	ENSP00000240719:R592Q;ENSP00000365407:R605Q	ENSP00000240719:R592Q	R	+	2	0	ZNF549	62741998	0.000000	0.05858	0.001000	0.08648	0.895000	0.52256	-0.794000	0.04584	0.326000	0.23384	0.585000	0.79938	CGA		0.423	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		A	58050186	G	A	58050186	3	1	61	1	0	0	0	0	1	0	0	0	18020	1058	37	1	1785	1	ZNF549	19	58050186	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	204	58050186	1078797	11423	19408										
ZNF416	55659	broad.mit.edu	37	chr19	58087211	58087211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagttctccagcatcacatCgcggtacaggagcctctgag	10	12	3	1	rs570790847		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58087211C>T	ENST00000196489.3	-	3	385	c.163G>A	c.(163-165)Gat>Aat	p.D55N		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D55N(1)|p.D55H(1)		breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		AGCATCACATCGCGGTACAGG	0.547													C|||	1	0.000199681	0	0	5008	,	,		20797	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19											195	172	180					19																	58087211		2203	4300	6503	62779023	SO:0001583	missense	55659			BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"Zinc fingers, C2H2-type", "-"	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.163G>A	19.37:g.58087211C>T	ENSP00000196489:p.Asp55Asn		62779023	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149275	0.57151	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.02498	4.27	3.66	-1.36	0.09085	Krueppel-associated box (4);	.	.	.	.	T	0.05640	0.0148	M	0.74467	2.265	0.09310	N	1	D	0.53745	0.962	P	0.47864	0.559	T	0.27468	-1.0073	9	0.37606	T	0.19	.	5.9177	0.19063	0.0:0.3351:0.4683:0.1966	.	55	Q9BWM5	ZN416_HUMAN	N	55;41;35	ENSP00000196489:D55N	ENSP00000196489:D55N	D	-	1	0	ZNF416	62779023	0.000000	0.05858	0.000000	0.03702	0.964000	0.63967	-0.773000	0.04689	-0.237000	0.09739	0.655000	0.94253	GAT		0.547	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		T	58087211	C	T	58087211	3	4	61	1	0	0	0	0	1	0	0	0	17932	884	31	1	1629	1	ZNF416	19	58087211	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37025	58087211	1041772	11424	19409										
ZIK1	284307	broad.mit.edu	37	chr19	58101755	58101755	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggtctttcctggaggcaaGaaacccggcacaattactga	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58101755G>T	ENST00000597850.1	+	4	791	c.576G>T	c.(574-576)aaG>aaT	p.K192N	ZIK1_ENST00000599456.1_Missense_Mutation_p.K137N|ZIK1_ENST00000536878.2_Missense_Mutation_p.K179N|ZIK1_ENST00000307468.4_3'UTR	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K192N(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CTGGAGGCAAGAAACCCGGCA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											69	70	70					19																	58101755		2203	4300	6503	62793567	SO:0001583	missense	284307			AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.576G>T	19.37:g.58101755G>T	ENSP00000472867:p.Lys192Asn		62793567	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	37	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.307656	0.23821	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.05447	3.44	2.88	2.88	0.33553	.	.	.	.	.	T	0.08088	0.0202	L	0.49126	1.545	0.09310	N	1	B;B	0.19817	0.039;0.011	B;B	0.23150	0.044;0.014	T	0.14727	-1.0462	9	0.72032	D	0.01	.	9.4658	0.38811	0.0:0.0:1.0:0.0	.	179;192	F5H435;Q3SY52	.;ZIK1_HUMAN	N	179;173;192	ENSP00000438487:K179N	ENSP00000303820:K192N	K	+	3	2	ZIK1	62793567	0.002000	0.14202	0.012000	0.15200	0.002000	0.02628	0.654000	0.24918	1.918000	0.55548	0.555000	0.69702	AAG		0.493	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		T	58101755	G	T	58101755	3	4	61	1	0	0	0	0	1	0	0	0	17722	933	33	2	590	2	ZIK1	19	58101755	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14544	58101755	1027228	11425	19410										
ZNF530	348327	broad.mit.edu	37	chr19	58117301	58117301	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcaaaccttcaccagctCcagaagcttgataatggaga	8	10	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58117301C>A	ENST00000332854.6	+	3	628	c.408C>A	c.(406-408)ctC>ctA	p.L136L	ZNF530_ENST00000597864.1_Intron	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L136L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTCACCAGCTCCAGAAGCTTG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	19											52	55	54					19																	58117301		2203	4300	6503	62809113	SO:0001819	synonymous_variant	348327			AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"Zinc fingers, C2H2-type", "-"	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.408C>A	19.37:g.58117301C>A			62809113	O43340|Q9P220	Silent	SNP	ENST00000332854.6	37	CCDS12955.1																																																																																				0.453	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880		A	58117301	C	A	58117301	2	1	61	1	0	0	0	0	0	0	0	1	18010	842	30	2		2	ZNF530	19	58117301	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15546	58117301	1011682	11426	19411										
ZNF530	348327	broad.mit.edu	37	chr19	58118544	58118544	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaggccttatgagtgcagaGaatgtgggaaatcttttacc	11	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58118544G>T	ENST00000332854.6	+	3	1871	c.1651G>T	c.(1651-1653)Gaa>Taa	p.E551*	ZNF530_ENST00000597864.1_Intron	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	551					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E551*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TGAGTGCAGAGAATGTGGGAA	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											73	73	73					19																	58118544		2203	4300	6503	62810356	SO:0001587	stop_gained	348327			AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"Zinc fingers, C2H2-type", "-"	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.1651G>T	19.37:g.58118544G>T	ENSP00000332861:p.Glu551*		62810356	O43340|Q9P220	Nonsense_Mutation	SNP	ENST00000332854.6	37	CCDS12955.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681331	0.88542	.	.	ENSG00000183647	ENST00000332854	.	.	.	2.48	-0.236	0.13067	.	.	.	.	.	.	.	.	.	.	.	0.51012	D	0.999903	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	9.4919	0.38965	0.0:0.0:0.6339:0.3661	.	.	.	.	X	551	.	ENSP00000332861:E551X	E	+	1	0	ZNF530	62810356	0.000000	0.05858	0.070000	0.20053	0.062000	0.15995	-1.735000	0.01847	0.342000	0.23796	0.543000	0.68304	GAA		0.448	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880		T	58118544	G	T	58118544	4	4	61	1	0	0	0	0	0	1	0	0	18010	943	33	2	1661	2	ZNF530	19	58118544	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1243	58118544	1010439	11427	19412										
ZSCAN4	201516	broad.mit.edu	37	chr19	58189969	58189969	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttattagctcaccagagaaGacacaggaatgagaggccat	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58189969G>T	ENST00000318203.5	+	5	1695	c.998G>T	c.(997-999)aGa>aTa	p.R333I		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	333					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R333I(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CACCAGAGAAGACACAGGAAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	80	80					19																	58189969		2203	4300	6503	62881781	SO:0001583	missense	201516			AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.998G>T	19.37:g.58189969G>T	ENSP00000321963:p.Arg333Ile		62881781	Q3MIQ2	Missense_Mutation	SNP	ENST00000318203.5	37	CCDS12958.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523938	0.44866	.	.	ENSG00000180532	ENST00000318203	T	0.17213	2.29	4.83	3.71	0.42584	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.126087	0.37623	N	0.002007	T	0.04770	0.0129	N	0.00677	-1.265	0.32425	N	0.548761	B	0.31931	0.347	B	0.35353	0.201	T	0.20472	-1.0274	10	0.06494	T	0.89	-4.7718	12.4389	0.55614	0.0:0.0:0.7815:0.2185	.	333	Q8NAM6	ZSCA4_HUMAN	I	333	ENSP00000321963:R333I	ENSP00000321963:R333I	R	+	2	0	ZSCAN4	62881781	0.004000	0.15560	1.000000	0.80357	0.883000	0.51084	0.074000	0.14662	2.669000	0.90835	0.655000	0.94253	AGA		0.428	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		T	58189969	G	T	58189969	3	4	61	1	0	0	0	0	1	0	0	0	18276	942	33	2	1008	2	ZSCAN4	19	58189969	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	71425	58189969	939014	11428	19413										
ZNF551	90233	broad.mit.edu	37	chr19	58198272	58198272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagccacacagtagcagcaGcaagcatatacaggcatttt	10	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58198272G>A	ENST00000282296.5	+	3	814	c.629G>A	c.(628-630)aGc>aAc	p.S210N	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron|ZNF551_ENST00000356715.4_Missense_Mutation_p.S194N			Q7Z340	ZN551_HUMAN	zinc finger protein 551	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S194N(1)		endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AGTAGCAGCAGCAAGCATATA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	66	65					19																	58198272		2202	4299	6501	62890084	SO:0001583	missense	90233			BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.629G>A	19.37:g.58198272G>A	ENSP00000282296:p.Ser210Asn		62890084	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	37	CCDS12959.2	.	.	.	.	.	.	.	.	.	.	G	1.257	-0.616895	0.03663	.	.	ENSG00000204519	ENST00000356715;ENST00000282296;ENST00000359821	.	.	.	1.63	-2.06	0.07298	.	.	.	.	.	T	0.14874	0.0359	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.18366	-1.0339	8	0.37606	T	0.19	.	2.6392	0.04966	0.3761:0.2628:0.3611:0.0	.	210	Q7Z340	ZN551_HUMAN	N	210;194;104	.	ENSP00000282296:S194N	S	+	2	0	ZNF551	62890084	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.135000	0.01306	-0.508000	0.06540	0.561000	0.74099	AGC		0.483	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		A	58198272	G	A	58198272	3	1	61	1	0	0	0	0	1	0	0	0	18022	971	34	3	591	3	ZNF551	19	58198272	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8303	58198272	930711	11429	19414										
ZNF154	7710	broad.mit.edu	37	chr19	58213222	58213222	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agactggagctgtagggaaaGaacttcccacattcactgca	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58213222G>T	ENST00000512439.2	-	3	1291	c.1095C>A	c.(1093-1095)ttC>ttA	p.F365L	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron|ZNF154_ENST00000426889.1_Missense_Mutation_p.F365L			Q13106	ZN154_HUMAN	zinc finger protein 154	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F365L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		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;0.0257)		TGTAGGGAAAGAACTTCCCAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	19											90	94	92					19																	58213222		2200	4300	6500	62905034	SO:0001583	missense	7710			U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"Zinc fingers, C2H2-type", "-"	12939	protein-coding gene	gene with protein product		604085	"zinc finger protein 154 (pHZ-92)"			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.1095C>A	19.37:g.58213222G>T	ENSP00000421258:p.Phe365Leu		62905034	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	G	0.600	-0.829455	0.02734	.	.	ENSG00000179909	ENST00000512439;ENST00000426889	T;T	0.06933	3.24;3.24	2.99	-3.67	0.04476	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02649	0.0080	N	0.03029	-0.43	0.09310	N	1	B	0.23990	0.095	B	0.22601	0.04	T	0.41034	-0.9531	9	0.72032	D	0.01	.	1.0212	0.01518	0.4268:0.1592:0.2522:0.1618	.	365	Q13106	ZN154_HUMAN	L	365	ENSP00000421258:F365L;ENSP00000442370:F365L	ENSP00000442370:F365L	F	-	3	2	ZNF154	62905034	0.000000	0.05858	0.013000	0.15412	0.066000	0.16364	-4.301000	0.00257	-0.632000	0.05553	-0.258000	0.10820	TTC		0.488	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			T	58213222	G	T	58213222	3	4	61	1	0	0	0	0	1	0	0	0	17774	933	33	2	222	2	ZNF154	19	58213222	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14950	58213222	915761	11430	19415										
ZNF671	79891	broad.mit.edu	37	chr19	58232190	58232190	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcactcataaggcctttCtccagtgtgagttcgttggt	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58232190C>A	ENST00000317398.6	-	4	1359	c.1264G>T	c.(1264-1266)Gaa>Taa	p.E422*	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF671_ENST00000335820.3_Nonsense_Mutation_p.E324*|ZNF671_ENST00000594803.1_5'Flank	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E422*(1)		kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TAAGGCCTTTCTCCAGTGTGA	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											122	99	107					19																	58232190		2203	4300	6503	62924002	SO:0001587	stop_gained	79891				CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"Zinc fingers, C2H2-type", "-"	26279	protein-coding gene	gene with protein product	"hypothetical protein FLJ23506"					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.1264G>T	19.37:g.58232190C>A	ENSP00000321848:p.Glu422*		62924002	A6NF07|Q9H5E9	Nonsense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	.	.	.	.	.	.	.	.	.	.	C	37	6.197636	0.97367	.	.	ENSG00000083814	ENST00000317398;ENST00000335820	.	.	.	1.88	0.819	0.18785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.3264	0.21246	0.0:0.8266:0.0:0.1734	.	.	.	.	X	422;324	.	ENSP00000321848:E422X	E	-	1	0	ZNF671	62924002	0.003000	0.15002	0.949000	0.38748	0.994000	0.84299	1.340000	0.33896	0.352000	0.24053	0.467000	0.42956	GAA		0.483	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833		A	58232190	C	A	58232190	4	1	61	1	0	0	0	0	0	1	0	0	18117	922	32	2	344	2	ZNF671	19	58232190	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18968	58232190	896793	11431	19416										
ZNF671	79891	broad.mit.edu	37	chr19	58232304	58232304	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttcctggtgtcgaatgaGattagacttactgctaaaaa	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58232304G>T	ENST00000317398.6	-	4	1245	c.1150C>A	c.(1150-1152)Ctc>Atc	p.L384I	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF671_ENST00000335820.3_Missense_Mutation_p.L286I|ZNF671_ENST00000594803.1_5'Flank	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	384					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L384I(1)		kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TGTCGAATGAGATTAGACTTA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	19											80	67	72					19																	58232304		2203	4300	6503	62924116	SO:0001583	missense	79891				CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"Zinc fingers, C2H2-type", "-"	26279	protein-coding gene	gene with protein product	"hypothetical protein FLJ23506"					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.1150C>A	19.37:g.58232304G>T	ENSP00000321848:p.Leu384Ile		62924116	A6NF07|Q9H5E9	Missense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555028	0.65425	.	.	ENSG00000083814	ENST00000317398;ENST00000335820	T;T	0.53857	0.6;0.6	1.88	0.79	0.18613	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69735	0.3144	M	0.92169	3.28	0.09310	N	1	P	0.42357	0.777	P	0.53722	0.733	T	0.60732	-0.7205	9	0.87932	D	0	.	6.346	0.21349	0.1748:0.0:0.8252:0.0	.	384	Q8TAW3	ZN671_HUMAN	I	384;286	ENSP00000321848:L384I;ENSP00000338670:L286I	ENSP00000321848:L384I	L	-	1	0	ZNF671	62924116	0.720000	0.27996	0.039000	0.18376	0.934000	0.57294	1.302000	0.33459	0.336000	0.23639	0.467000	0.42956	CTC		0.473	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833		T	58232304	G	T	58232304	3	4	61	1	0	0	0	0	1	0	0	0	18117	942	33	2	458	2	ZNF671	19	58232304	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114	58232304	896679	11432	19417										
ZNF671	79891	broad.mit.edu	37	chr19	58232505	58232505	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgaagaatttcccacattCgttacactcataaggccttt	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58232505C>A	ENST00000317398.6	-	4	1044	c.949G>T	c.(949-951)Gaa>Taa	p.E317*	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF671_ENST00000335820.3_Nonsense_Mutation_p.E219*|ZNF671_ENST00000594803.1_5'Flank	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E317*(1)		kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTCCCACATTCGTTACACTCA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											102	96	98					19																	58232505		2203	4300	6503	62924317	SO:0001587	stop_gained	79891				CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"Zinc fingers, C2H2-type", "-"	26279	protein-coding gene	gene with protein product	"hypothetical protein FLJ23506"					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.949G>T	19.37:g.58232505C>A	ENSP00000321848:p.Glu317*		62924317	A6NF07|Q9H5E9	Nonsense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750918	0.89753	.	.	ENSG00000083814	ENST00000317398;ENST00000335820	.	.	.	1.94	-0.399	0.12415	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	4.9122	0.13827	0.0:0.6351:0.2185:0.1464	.	.	.	.	X	317;219	.	ENSP00000321848:E317X	E	-	1	0	ZNF671	62924317	0.000000	0.05858	0.072000	0.20136	0.903000	0.53119	-3.549000	0.00434	-0.015000	0.14150	0.467000	0.42956	GAA		0.473	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833		A	58232505	C	A	58232505	4	1	61	1	0	0	0	0	0	1	0	0	18117	893	31	2	659	2	ZNF671	19	58232505	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	201	58232505	896478	11433	19418										
ZNF417	147687	broad.mit.edu	37	chr19	58420013	58420013	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtacattcataaggcctttCtccagtgtgaattctcctgt	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58420013C>A	ENST00000312026.5	-	3	1797	c.1633G>T	c.(1633-1635)Gaa>Taa	p.E545*	CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Nonsense_Mutation_p.E346*|ZNF417_ENST00000595559.1_Nonsense_Mutation_p.E544*	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	545					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E545*(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		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;0.0151)		TAAGGCCTTTCTCCAGTGTGA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											116	115	115					19																	58420013		2203	4300	6503	63111825	SO:0001587	stop_gained	147687			BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"Zinc fingers, C2H2-type", "-"	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1633G>T	19.37:g.58420013C>A	ENSP00000311319:p.Glu545*		63111825	B4DEU1	Nonsense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	42	9.742544	0.99252	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	.	.	.	2.52	0.231	0.15377	.	.	.	.	.	.	.	.	.	.	.	0.43536	D	0.995827	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	5.726	0.18013	0.0:0.5965:0.0:0.4035	.	.	.	.	X	545;346	.	ENSP00000311319:E545X	E	-	1	0	ZNF417	63111825	0.195000	0.23338	0.000000	0.03702	0.304000	0.27724	0.810000	0.27183	-0.003000	0.14444	0.306000	0.20318	GAA		0.413	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475		A	58420013	C	A	58420013	4	1	61	1	0	0	0	0	0	1	0	0	17933	922	32	2	98	2	ZNF417	19	58420013	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	187508	58420013	708970	11434	19419										
C19orf18	147685	broad.mit.edu	37	chr19	58477955	58477955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgctgaaggctacgctcGaaattaaaattactttaaca	6	8	0	1	rs200742590		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58477955G>A	ENST00000314391.3	-	4	415	c.314C>T	c.(313-315)tCg>tTg	p.S105L		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	105						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.S105L(1)		large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)		GGCTACGCTCGAAATTAAAAT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	LEU/SER	0,4406		0,0,2203	75	74	75		314	3	0	19		75	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C19orf18	NM_152474.4	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	105/216	58477955	1,13005	2203	4300	6503	63169767	SO:0001583	missense	147685			BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.314C>T	19.37:g.58477955G>A	ENSP00000321519:p.Ser105Leu		63169767		Missense_Mutation	SNP	ENST00000314391.3	37	CCDS12967.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.517451	0.27123	0.0	1.16E-4	ENSG00000177025	ENST00000314391	T	0.58797	0.31	4.1	3.05	0.35203	.	0.340109	0.21511	N	0.073370	T	0.37461	0.1004	L	0.27053	0.805	0.09310	N	1	P	0.42692	0.787	B	0.32090	0.14	T	0.33929	-0.9849	10	0.66056	D	0.02	-4.6675	9.9264	0.41494	0.0:0.2264:0.7736:0.0	.	105	Q8NEA5	CS018_HUMAN	L	105	ENSP00000321519:S105L	ENSP00000321519:S105L	S	-	2	0	C19orf18	63169767	0.003000	0.15002	0.004000	0.12327	0.063000	0.16089	1.345000	0.33953	1.296000	0.44742	0.644000	0.83932	TCG		0.348	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	NM_152474		A	58477955	G	A	58477955	3	1	61	1	0	0	0	0	1	0	0	0	1916	1059	37	1	345	1	C19orf18	19	58477955	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	57942	58477955	651028	11435	19420										
ZNF606	80095	broad.mit.edu	37	chr19	58489760	58489760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacattcactgcatataaagCgtttctctccactatgcatt	4	12	2	0	rs373070463		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58489760C>T	ENST00000341164.4	-	7	2908	c.2288G>A	c.(2287-2289)cGc>cAc	p.R763H	ZNF606_ENST00000536132.1_Missense_Mutation_p.R673H	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	763					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R763H(2)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		GCATATAAAGCGTTTCTCTCC	0.373																																																2	Substitution - Missense(2)	large_intestine(2)	19						C	HIS/ARG	0,4406		0,0,2203	115	114	114		2288	3.6	1	19		114	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF606	NM_025027.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	763/793	58489760	1,13005	2203	4300	6503	63181572	SO:0001583	missense	80095			AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2288G>A	19.37:g.58489760C>T	ENSP00000343617:p.Arg763His		63181572	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008480	0.35415	0.0	1.16E-4	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.10477	2.87;2.87	4.66	3.63	0.41609	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.679844	0.12984	N	0.422987	T	0.07098	0.0180	N	0.16602	0.42	0.32142	N	0.585392	B	0.15141	0.012	B	0.06405	0.002	T	0.05666	-1.0871	10	0.87932	D	0	.	7.001	0.24809	0.0:0.6169:0.2887:0.0944	.	763	Q8WXB4	ZN606_HUMAN	H	763;673	ENSP00000343617:R763H;ENSP00000445624:R673H	ENSP00000343617:R763H	R	-	2	0	ZNF606	63181572	0.322000	0.24634	1.000000	0.80357	0.992000	0.81027	0.396000	0.20867	1.296000	0.44742	0.650000	0.86243	CGC		0.373	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		T	58489760	C	T	58489760	3	4	61	1	0	0	0	0	1	0	0	0	18071	768	27	1	94	1	ZNF606	19	58489760	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11805	58489760	639223	11436	19421										
ZNF606	80095	broad.mit.edu	37	chr19	58490360	58490360	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttatatggttttgctccaGaatgagttctttcatgttta	7	5	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58490360G>T	ENST00000341164.4	-	7	2308	c.1688C>A	c.(1687-1689)tCt>tAt	p.S563Y	ZNF606_ENST00000536132.1_Missense_Mutation_p.S473Y	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S563Y(2)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		TTTTGCTCCAGAATGAGTTCT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	19											66	66	66					19																	58490360		2203	4300	6503	63182172	SO:0001583	missense	80095			AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.1688C>A	19.37:g.58490360G>T	ENSP00000343617:p.Ser563Tyr		63182172	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561739	0.45590	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.19938	2.11;2.11	4.71	4.71	0.59529	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.299887	0.24513	N	0.037875	T	0.35098	0.0920	L	0.43923	1.385	0.33955	D	0.64489	D	0.71674	0.998	D	0.66196	0.942	T	0.45469	-0.9259	10	0.87932	D	0	.	12.0649	0.53581	0.0:0.0:0.8273:0.1727	.	563	Q8WXB4	ZN606_HUMAN	Y	563;473	ENSP00000343617:S563Y;ENSP00000445624:S473Y	ENSP00000343617:S563Y	S	-	2	0	ZNF606	63182172	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.571000	0.53841	2.597000	0.87782	0.561000	0.74099	TCT		0.398	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		T	58490360	G	T	58490360	3	4	61	1	0	0	0	0	1	0	0	0	18071	942	33	2	694	2	ZNF606	19	58490360	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	600	58490360	638623	11437	19422										
ZSCAN1	284312	broad.mit.edu	37	chr19	58563961	58563961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagagtctgcacaccagggCggaggccgaagcgccccgcg	16	15	1	1	rs372048643		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58563961C>T	ENST00000282326.1	+	5	816	c.569C>T	c.(568-570)gCg>gTg	p.A190V		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	190					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)	p.A190V(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		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)		CACACCAGGGCGGAGGCCGAA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	VAL/ALA	0,4406		0,0,2203	31	35	34		569	-3.6	0	19		34	1,8597		0,1,4298	no	missense	ZSCAN1	NM_182572.3	64	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	190/409	58563961	1,13003	2203	4299	6502	63255773	SO:0001583	missense	284312			AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.569C>T	19.37:g.58563961C>T	ENSP00000282326:p.Ala190Val		63255773	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	C	0.525	-0.860550	0.02610	0.0	1.16E-4	ENSG00000152467	ENST00000282326	T	0.04083	3.71	1.9	-3.56	0.04626	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.09310	N	1	B	0.17038	0.02	B	0.11329	0.006	T	0.46289	-0.9202	9	0.29301	T	0.29	.	2.1121	0.03705	0.2479:0.332:0.0:0.4202	.	190	Q8NBB4	ZSCA1_HUMAN	V	190	ENSP00000282326:A190V	ENSP00000282326:A190V	A	+	2	0	ZSCAN1	63255773	0.002000	0.14202	0.001000	0.08648	0.009000	0.06853	-1.920000	0.01571	-0.414000	0.07495	0.305000	0.20034	GCG		0.612	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		T	58563961	C	T	58563961	3	4	61	1	0	0	0	0	1	0	0	0	18265	768	27	1	579	1	ZSCAN1	19	58563961	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73601	58563961	565022	11438	19423										
ZSCAN1	284312	broad.mit.edu	37	chr19	58564950	58564950	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtccccgaaggagaaacaGgaacactgaccagagcggcc	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58564950G>T	ENST00000282326.1	+	6	1005	c.758G>T	c.(757-759)aGg>aTg	p.R253M		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	253					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)	p.R253M(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		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)		AGGAGAAACAGGAACACTGAC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											64	66	65					19																	58564950		2203	4300	6503	63256762	SO:0001583	missense	284312			AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.758G>T	19.37:g.58564950G>T	ENSP00000282326:p.Arg253Met		63256762	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	4.840	0.156109	0.09236	.	.	ENSG00000152467	ENST00000282326	T	0.04758	3.56	1.14	0.0741	0.14393	.	.	.	.	.	T	0.02342	0.0072	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.45789	-0.9237	9	0.36615	T	0.2	.	3.609	0.08053	0.265:0.0:0.735:0.0	.	253	Q8NBB4	ZSCA1_HUMAN	M	253	ENSP00000282326:R253M	ENSP00000282326:R253M	R	+	2	0	ZSCAN1	63256762	0.004000	0.15560	0.001000	0.08648	0.002000	0.02628	0.535000	0.23114	0.067000	0.16545	-0.333000	0.08304	AGG		0.622	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		T	58564950	G	T	58564950	3	4	61	1	0	0	0	0	1	0	0	0	18265	1000	35	2	772	2	ZSCAN1	19	58564950	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	989	58564950	564033	11439	19424										
ZNF329	79673	broad.mit.edu	37	chr19	58640441	58640441	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggtatttgtagggcttctCtctcactggatttcttccat	9	9	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58640441C>A	ENST00000598312.1	-	4	663	c.430G>T	c.(430-432)Gag>Tag	p.E144*	ZNF329_ENST00000358067.4_Nonsense_Mutation_p.E144*	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E144*(1)		NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		TAGGGCTTCTCTCTCACTGGA	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											93	90	91					19																	58640441		2203	4300	6503	63332253	SO:0001587	stop_gained	79673			AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"Zinc fingers, C2H2-type"	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.430G>T	19.37:g.58640441C>A	ENSP00000470008:p.Glu144*		63332253	B3KR32|Q9H9R7	Nonsense_Mutation	SNP	ENST00000598312.1	37	CCDS12972.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.467738	0.63625	.	.	ENSG00000181894	ENST00000358067;ENST00000500161	.	.	.	4.39	4.39	0.52855	.	0.294536	0.24472	N	0.038227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-5.8394	16.9533	0.86251	0.0:1.0:0.0:0.0	.	.	.	.	X	144	.	ENSP00000350773:E144X	E	-	1	0	ZNF329	63332253	0.957000	0.32711	0.714000	0.30535	0.043000	0.13939	4.146000	0.58072	2.730000	0.93505	0.655000	0.94253	GAG		0.383	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620		A	58640441	C	A	58640441	4	1	61	1	0	0	0	0	0	1	0	0	17886	922	32	2	1199	2	ZNF329	19	58640441	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75491	58640441	488542	11440	19425										
ZNF544	27300	broad.mit.edu	37	chr19	58773400	58773400	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaagtccttcagccaaagCtatgagttagttacacataa	8	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58773400C>A	ENST00000596652.1	+	6	1662	c.1428C>A	c.(1426-1428)agC>agA	p.S476R	ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000415203.2_Missense_Mutation_p.S448R|ZNF544_ENST00000600044.1_Missense_Mutation_p.S448R|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000269829.4_Missense_Mutation_p.S476R|ZNF544_ENST00000599953.1_Missense_Mutation_p.S334R|ZNF544_ENST00000600220.1_Missense_Mutation_p.S448R|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596825.1_3'UTR			Q6NX49	ZN544_HUMAN	zinc finger protein 544	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S476R(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TCAGCCAAAGCTATGAGTTAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	19											86	88	88					19																	58773400		2203	4300	6503	63465212	SO:0001583	missense	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1428C>A	19.37:g.58773400C>A	ENSP00000469635:p.Ser476Arg		63465212	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	C	0.596	-0.830868	0.02713	.	.	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.42900	0.96;0.96	2.53	-0.0757	0.13725	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17323	0.0416	N	0.16478	0.41	0.09310	N	1	B;B;B	0.31485	0.325;0.008;0.022	B;B;B	0.22152	0.038;0.004;0.004	T	0.20306	-1.0279	9	0.06494	T	0.89	.	5.1939	0.15225	0.0:0.6412:0.2132:0.1456	.	448;448;476	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	R	476;448;140	ENSP00000269829:S476R;ENSP00000394341:S448R	ENSP00000269829:S476R	S	+	3	2	ZNF544	63465212	0.000000	0.05858	0.018000	0.16275	0.077000	0.17291	-0.210000	0.09345	0.386000	0.24997	0.462000	0.41574	AGC		0.418	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58773400	C	A	58773400	3	1	61	1	0	0	0	0	1	0	0	0	18016	796	28	2	1442	2	ZNF544	19	58773400	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132959	58773400	355583	11441	19426										
ZNF544	27300	broad.mit.edu	37	chr19	58773781	58773781	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcacactggagaaaagccCtatgaatgtaacgagtgtgg	11	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58773781C>A	ENST00000596652.1	+	6	2043	c.1809C>A	c.(1807-1809)ccC>ccA	p.P603P	ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000415203.2_Silent_p.P575P|ZNF544_ENST00000600044.1_Silent_p.P575P|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000269829.4_Silent_p.P603P|ZNF544_ENST00000599953.1_Silent_p.P461P|ZNF544_ENST00000600220.1_Silent_p.P575P|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596825.1_3'UTR			Q6NX49	ZN544_HUMAN	zinc finger protein 544	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P603P(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		GAGAAAAGCCCTATGAATGTA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	19											96	88	90					19																	58773781		2203	4300	6503	63465593	SO:0001819	synonymous_variant	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1809C>A	19.37:g.58773781C>A			63465593	A8K6J1|Q9UEX4	Silent	SNP	ENST00000596652.1	37	CCDS12973.1																																																																																				0.448	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58773781	C	A	58773781	2	1	61	1	0	0	0	0	0	0	0	1	18016	668	24	2		2	ZNF544	19	58773781	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	381	58773781	355202	11442	19427										
ZSCAN22	342945	broad.mit.edu	37	chr19	58849905	58849905	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgcctcgaggaacagttCtagtgcgtggccaaacctca	12	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58849905C>A	ENST00000329665.4	+	3	836	c.689C>A	c.(688-690)tCt>tAt	p.S230Y		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	230					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S230Y(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		AGGAACAGTTCTAGTGCGTGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	19											165	172	169					19																	58849905		2203	4300	6503	63541717	SO:0001583	missense	342945			M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.689C>A	19.37:g.58849905C>A	ENSP00000332433:p.Ser230Tyr		63541717	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	37	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.323862	0.01309	.	.	ENSG00000182318	ENST00000329665	T	0.08807	3.05	4.02	1.83	0.25207	.	.	.	.	.	T	0.03871	0.0109	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.46020	-0.9221	9	0.06099	T	0.92	.	2.773	0.05340	0.1862:0.5288:0.1811:0.1039	.	230	P10073	ZSC22_HUMAN	Y	230	ENSP00000332433:S230Y	ENSP00000332433:S230Y	S	+	2	0	ZSCAN22	63541717	0.000000	0.05858	0.001000	0.08648	0.176000	0.22953	-0.728000	0.04925	0.344000	0.23847	0.313000	0.20887	TCT		0.517	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58849905	C	A	58849905	3	1	61	1	0	0	0	0	1	0	0	0	18273	913	32	2	695	2	ZSCAN22	19	58849905	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	76124	58849905	279078	11443	19428										
ZSCAN22	342945	broad.mit.edu	37	chr19	58850605	58850605	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccacacgggagagaagccTtataagtgcagcgactgtgg	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58850605T>G	ENST00000329665.4	+	3	1536	c.1389T>G	c.(1387-1389)ccT>ccG	p.P463P		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	463					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P463P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		GAGAGAAGCCTTATAAGTGCA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	19											77	70	72					19																	58850605		2203	4300	6503	63542417	SO:0001819	synonymous_variant	342945			M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.1389T>G	19.37:g.58850605T>G			63542417	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	37	CCDS12975.1																																																																																				0.552	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		G	58850605	T	G	58850605	2	3	61	1	0	0	0	0	0	0	0	1	18273	1596	56	4		4	ZSCAN22	19	58850605	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	700	58850605	278378	11444	19429										
ZNF132	7691	broad.mit.edu	37	chr19	58945961	58945961	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtatttccccagtgtgaaActttttattaccaaggattg	9	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58945961A>T	ENST00000254166.3	-	3	1250	c.850T>A	c.(850-852)Ttt>Att	p.F284I		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F284I(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		CCAGTGTGAAACTTTTTATTA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19											57	64	61					19																	58945961		2203	4299	6502	63637773	SO:0001583	missense	7691			U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.850T>A	19.37:g.58945961A>T	ENSP00000254166:p.Phe284Ile		63637773	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	37	CCDS12980.1	.	.	.	.	.	.	.	.	.	.	A	0.035	-1.313246	0.01331	.	.	ENSG00000131849	ENST00000254166;ENST00000391695	T	0.12672	2.66	3.27	-1.98	0.07480	.	.	.	.	.	T	0.01730	0.0055	N	0.00205	-1.85	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.41787	-0.9489	9	0.02654	T	1	.	0.0799	0.00030	0.293:0.164:0.2216:0.3214	.	284	P52740	ZN132_HUMAN	I	284;195	ENSP00000254166:F284I	ENSP00000254166:F284I	F	-	1	0	ZNF132	63637773	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.211000	0.09332	-0.272000	0.09259	-0.274000	0.10170	TTT		0.423	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		T	58945961	A	T	58945961	3	4	61	1	0	0	0	0	1	0	0	0	17761	43	2	5	1274	5	ZNF132	19	58945961	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	95356	58945961	183022	11445	19430										
ZNF132	7691	broad.mit.edu	37	chr19	58946044	58946044	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatctcttcagagtgagttCtcagatggttggggagagtg	15	5	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:58946044C>A	ENST00000254166.3	-	3	1167	c.767G>T	c.(766-768)aGa>aTa	p.R256I		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R256I(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		AGAGTGAGTTCTCAGATGGTT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	98	97					19																	58946044		2203	4300	6503	63637856	SO:0001583	missense	7691			U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.767G>T	19.37:g.58946044C>A	ENSP00000254166:p.Arg256Ile		63637856	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	37	CCDS12980.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.239972	0.39598	.	.	ENSG00000131849	ENST00000254166;ENST00000391695	T	0.18502	2.21	3.41	-2.99	0.05497	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18841	0.0452	M	0.85462	2.755	0.36379	D	0.861789	B	0.20261	0.043	B	0.20767	0.031	T	0.07501	-1.0769	9	0.44086	T	0.13	.	3.8206	0.08833	0.4473:0.3435:0.0:0.2092	.	256	P52740	ZN132_HUMAN	I	256;167	ENSP00000254166:R256I	ENSP00000254166:R256I	R	-	2	0	ZNF132	63637856	0.000000	0.05858	0.207000	0.23584	0.385000	0.30292	-2.170000	0.01268	-0.667000	0.05303	0.655000	0.94253	AGA		0.448	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		A	58946044	C	A	58946044	3	1	61	1	0	0	0	0	1	0	0	0	17761	913	32	2	1357	2	ZNF132	19	58946044	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	83	58946044	182939	11446	19431										
SLC27A5	10998	broad.mit.edu	37	chr19	59022255	59022255	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagcagcggatgttctcaGcctgcagcttgggaaggatc	14	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:59022255G>T	ENST00000263093.2	-	2	840	c.731C>A	c.(730-732)gCt>gAt	p.A244D	SLC27A5_ENST00000601355.1_Missense_Mutation_p.A160D	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	244					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.A244D(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GATGTTCTCAGCCTGCAGCTT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	19											35	36	36					19																	59022255		2203	4300	6503	63714067	SO:0001583	missense	10998			AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.731C>A	19.37:g.59022255G>T	ENSP00000263093:p.Ala244Asp		63714067	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	g	10.71	1.428029	0.25726	.	.	ENSG00000083807	ENST00000263093	T	0.43688	0.94	4.59	2.2	0.27929	AMP-dependent synthetase/ligase (1);	0.128198	0.51477	D	0.000097	T	0.31263	0.0791	N	0.17082	0.46	0.33018	D	0.52842	P	0.37276	0.589	P	0.46208	0.507	T	0.39210	-0.9625	10	0.25106	T	0.35	-11.8543	9.1664	0.37054	0.0:0.0:0.6066:0.3934	.	244	Q9Y2P5	S27A5_HUMAN	D	244	ENSP00000263093:A244D	ENSP00000263093:A244D	A	-	2	0	SLC27A5	63714067	0.185000	0.23213	0.793000	0.32043	0.997000	0.91878	2.136000	0.42121	1.214000	0.43395	0.491000	0.48974	GCT		0.632	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		T	59022255	G	T	59022255	3	4	61	1	0	0	0	0	1	0	0	0	14566	971	34	2	1377	2	SLC27A5	19	59022255	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	76211	59022255	106728	11447	19432										
CHMP2A	27243	broad.mit.edu	37	chr19	59065428	59065428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccatctggccttgcttgGccatcttcttaatgtctgca	7	13	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr19:59065428G>A	ENST00000600118.1	-	1	577	c.152C>T	c.(151-153)gCc>gTc	p.A51V	CHMP2A_ENST00000601220.1_Missense_Mutation_p.A51V|CHMP2A_ENST00000312547.2_Missense_Mutation_p.A51V			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	51					endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)	p.A51V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GCCTTGCTTGGCCATCTTCTT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19											198	167	178					19																	59065428		2203	4300	6503	63757240	SO:0001583	missense	27243			AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"Charged multivesicular body proteins"	30216	protein-coding gene	gene with protein product	"putative breast adenocarcinoma marker (32kD)", "VPS2 homolog A (S. cerevisiae)"	610893	"chromatin modifying protein 2A"			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.152C>T	19.37:g.59065428G>A	ENSP00000469240:p.Ala51Val		63757240	B2R4W6|Q3ZTT0	Missense_Mutation	SNP	ENST00000600118.1	37	CCDS12986.1	.	.	.	.	.	.	.	.	.	.	G	36	5.748044	0.96882	.	.	ENSG00000130724	ENST00000312547	T	0.74002	-0.8	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.89030	0.6599	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91262	0.5037	10	0.87932	D	0	.	16.618	0.84922	0.0:0.0:1.0:0.0	.	51	O43633	CHM2A_HUMAN	V	51	ENSP00000310440:A51V	ENSP00000310440:A51V	A	-	2	0	CHMP2A	63757240	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.788000	0.91834	2.601000	0.87937	0.655000	0.94253	GCC		0.547	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453		A	59065428	G	A	59065428	3	1	61	1	0	0	0	0	1	0	0	0	3360	1203	42	3	536	3	CHMP2A	19	59065428	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43173	59065428	63555	11448	19433										
TRIB3	57761	broad.mit.edu	37	chr20	368760	368760	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcccgtccagaaacgagctCgaagtgggccccagcccaga	12	15	0	2	rs150841542	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:368760C>T	ENST00000217233.3	+	2	659	c.106C>T	c.(106-108)Cga>Tga	p.R36*	TRIB3_ENST00000422053.2_Nonsense_Mutation_p.R63*|TRIB3_ENST00000485293.1_3'UTR	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	36	Interaction with DDIT3/CHOP.				cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)	p.R36*(1)		breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		GAAACGAGCTCGAAGTGGGCC	0.632																																					Melanoma(101;421 2374 19538)											1	Substitution - Nonsense(1)	large_intestine(1)	20						C	stop/ARG	5,4401	9.9+/-24.2	0,5,2198	81	79	80		106	2.5	0.9	20	dbSNP_134	80	0,8600		0,0,4300	yes	stop-gained	TRIB3	NM_021158.3		0,5,6498	TT,TC,CC		0.0,0.1135,0.0384		36/359	368760	5,13001	2203	4300	6503	316760	SO:0001587	stop_gained	57761			AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"chromosome 20 open reading frame 97", "tribbles homolog 3 (Drosophila)"	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.106C>T	20.37:g.368760C>T	ENSP00000217233:p.Arg36*		316760	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Nonsense_Mutation	SNP	ENST00000217233.3	37	CCDS12997.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949461	0.92660	0.001135	0.0	ENSG00000101255	ENST00000217233;ENST00000449710;ENST00000422053	.	.	.	4.49	2.45	0.29901	.	0.276960	0.19290	N	0.117908	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.7288	7.4018	0.26969	0.1882:0.4736:0.3381:0.0	.	.	.	.	X	36;36;63	.	ENSP00000217233:R36X	R	+	1	2	TRIB3	316760	0.004000	0.15560	0.939000	0.37840	0.630000	0.37929	1.547000	0.36190	0.447000	0.26695	0.561000	0.74099	CGA		0.632	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158		T	368760	C	T	368760	4	4	61	1	0	0	0	0	0	1	0	0	16524	876	31	1	108	1	TRIB3	20	368760	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		368760	62656760	11449	19434										
ANGPT4	51378	broad.mit.edu	37	chr20	853726	853726	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagcgtggtagtagacgccGttgaggtttgacaggccaca	16	8	0	3	rs375636235		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:853726G>A	ENST00000381922.3	-	9	1491	c.1389C>T	c.(1387-1389)aaC>aaT	p.N463N	ANGPT4_ENST00000546022.1_3'UTR	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	463	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.N463N(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						AGTAGACGCCGTTGAGGTTTG	0.612																																					Pancreas(181;481 2077 3259 31286 49856)											1	Substitution - coding silent(1)	large_intestine(1)	20						G		1,4405	2.1+/-5.4	0,1,2202	84	76	79		1389	-8.8	0.3	20		79	0,8600		0,0,4300	no	coding-synonymous	ANGPT4	NM_015985.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		463/504	853726	1,13005	2203	4300	6503	801726	SO:0001819	synonymous_variant	51378			AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1389C>T	20.37:g.853726G>A			801726	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																				0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		A	853726	G	A	853726	2	1	61	1	0	0	0	0	0	0	0	1	612	1136	40	1		1	ANGPT4	20	853726	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	484966	853726	62171794	11450	19435										
ANGPT4	51378	broad.mit.edu	37	chr20	870988	870988	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgctccagcttcgacctcaaGatcgtcttgatggccctctc	8	15	3	2	rs370865591		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:870988G>T	ENST00000381922.3	-	2	435	c.333C>A	c.(331-333)atC>atA	p.I111I	ANGPT4_ENST00000546022.1_Silent_p.I111I	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	111					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.I111I(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						TCGACCTCAAGATCGTCTTGA	0.647																																					Pancreas(181;481 2077 3259 31286 49856)											1	Substitution - coding silent(1)	large_intestine(1)	20								0,4406		0,0,2203	74	65	68		333	3.5	0.3	20		68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ANGPT4	NM_015985.2		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		111/504	870988	1,13005	2203	4300	6503	818988	SO:0001819	synonymous_variant	51378			AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.333C>A	20.37:g.870988G>T			818988	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																				0.647	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		T	870988	G	T	870988	2	4	61	1	0	0	0	0	0	0	0	1	612	932	33	2		2	ANGPT4	20	870988	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17262	870988	62154532	11451	19436										
PSMF1	9491	broad.mit.edu	37	chr20	1106243	1106243	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataaggatgggtccagaaagCtccttgtgaaagccatcacc	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1106243C>T	ENST00000335877.6	+	2	408	c.232C>T	c.(232-234)Ctc>Ttc	p.L78F	PSMF1_ENST00000246015.4_Missense_Mutation_p.L78F|PSMF1_ENST00000333082.3_Missense_Mutation_p.L78F|PSMF1_ENST00000438768.2_Missense_Mutation_p.L78F|PSMF1_ENST00000381898.4_5'UTR	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	78	Important for homodimerization and interaction with FBXO7.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)	p.L78F(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						GTCCAGAAAGCTCCTTGTGAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											133	112	119					20																	1106243		2203	4300	6503	1054243	SO:0001583	missense	9491			D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"Proteasome (prosome, macropain) subunits"	9571	protein-coding gene	gene with protein product	"proteasome inhibitor hP131 subunit"					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.232C>T	20.37:g.1106243C>T	ENSP00000338039:p.Leu78Phe		1054243	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	37	CCDS13010.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801539	0.50315	.	.	ENSG00000125818	ENST00000333082;ENST00000381899;ENST00000246015;ENST00000335877;ENST00000438768	T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000002	T	0.36908	0.0984	L	0.39633	1.23	0.80722	D	1	P;B;B	0.50443	0.935;0.226;0.226	P;B;B	0.45712	0.491;0.109;0.109	T	0.07290	-1.0780	10	0.10377	T	0.69	-20.4883	15.1704	0.72869	0.0:1.0:0.0:0.0	.	78;78;78	E7ER20;Q5QPM7;Q92530	.;.;PSMF1_HUMAN	F	78	ENSP00000327704:L78F;ENSP00000371324:L78F;ENSP00000246015:L78F;ENSP00000338039:L78F;ENSP00000401404:L78F	ENSP00000246015:L78F	L	+	1	0	PSMF1	1054243	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.348000	0.52209	2.562000	0.86427	0.585000	0.79938	CTC		0.507	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578		T	1106243	C	T	1106243	3	4	61	1	0	0	0	0	1	0	0	0	12744	797	28	3	238	3	PSMF1	20	1106243	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235255	1106243	61919277	11452	19437										
SNPH	9751	broad.mit.edu	37	chr20	1285732	1285732	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgtggacatcaacatccaGaacaagaagctggagacgct	10	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1285732G>A	ENST00000381873.3	+	6	755	c.519G>A	c.(517-519)caG>caA	p.Q173Q	SNPH_ENST00000381867.1_Silent_p.Q217Q	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	173					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)	p.Q217Q(1)|p.Q173Q(1)		endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TCAACATCCAGAACAAGAAGC	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	20											118	94	102					20																	1285732		2203	4300	6503	1233732	SO:0001819	synonymous_variant	9751				CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.519G>A	20.37:g.1285732G>A			1233732	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																				0.567	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723		A	1285732	G	A	1285732	2	1	61	1	0	0	0	0	0	0	0	1	14887	933	33	3		3	SNPH	20	1285732	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	179489	1285732	61739788	11453	19438										
SIRPB2	284759	broad.mit.edu	37	chr20	1460486	1460486	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ataatcacaattcagtggttCtgatgtccgttggatcatgg	10	7	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1460486C>A	ENST00000359801.3	-	2	346	c.310G>T	c.(310-312)Gaa>Taa	p.E104*	SIRPB2_ENST00000444444.2_Intron|SIRPB2_ENST00000537284.1_Intron|SIRPB2_ENST00000608747.1_Intron	NM_001122962.1	NP_001116434.1	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein beta 2	97	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E203*(1)|p.E104*(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTCAGTGGTTCTGATGTCCGT	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	20											142	126	131					20																	1460486		1568	3582	5150	1408486	SO:0001587	stop_gained	284759			AL109658	CCDS42849.1, CCDS46570.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000196209	ENSG00000196209		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16247	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type 1-like", "protein tyrosine phosphatase, non-receptor type substrate 1-like 3"	PTPN1L, PTPNS1L3		16339511	Standard	NM_001122962		Approved	dJ776F14.2	uc002wfg.2	Q5JXA9	OTTHUMG00000031670	ENST00000359801.3:c.310G>T	20.37:g.1460486C>A	ENSP00000352849:p.Glu104*		1408486	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Nonsense_Mutation	SNP	ENST00000359801.3	37	CCDS42849.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980424	0.74474	.	.	ENSG00000196209	ENST00000359801	.	.	.	4.13	4.13	0.48395	.	0.952302	0.08635	N	0.916503	.	.	.	.	.	.	0.44214	D	0.997042	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-24.4079	12.0631	0.53574	0.0:1.0:0.0:0.0	.	.	.	.	X	104	.	ENSP00000352849:E104X	E	-	1	0	SIRPB2	1408486	0.001000	0.12720	0.020000	0.16555	0.853000	0.48598	0.747000	0.26290	2.312000	0.78011	0.655000	0.94253	GAA		0.453	SIRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077544.1	NM_178459		A	1460486	C	A	1460486	4	1	61	1	0	0	0	0	0	1	0	0	14371	922	32	2	734	2	SIRPB2	20	1460486	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	174754	1460486	61565034	11454	19439										
SIRPB2	284759	broad.mit.edu	37	chr20	1460689	1460689	+	De_novo_Start_OutOfFrame	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcacctgccagtcattcCtgctgctctgcccagaggca	10	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1460689C>A	ENST00000537284.1	-	0	160				SIRPB2_ENST00000444444.2_Missense_Mutation_p.R36M|SIRPB2_ENST00000608747.1_5'UTR|SIRPB2_ENST00000359801.3_Missense_Mutation_p.R36M			Q9P1W8	SIRPG_HUMAN	signal-regulatory protein beta 2						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R135M(1)|p.R36M(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CCAGTCATTCCTGCTGCTCTG	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	20											43	40	41					20																	1460689		1568	3581	5149	1408689			284759			AL109658	CCDS42849.1, CCDS46570.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000196209	ENSG00000196209		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16247	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type 1-like", "protein tyrosine phosphatase, non-receptor type substrate 1-like 3"	PTPN1L, PTPNS1L3		16339511	Standard	NM_001122962		Approved	dJ776F14.2	uc002wfg.2	Q5JXA9	OTTHUMG00000031670	ENST00000537284.1:c.-177G>T	20.37:g.1460689C>A			1408689	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000537284.1	37		.	.	.	.	.	.	.	.	.	.	C	10.73	1.432341	0.25813	.	.	ENSG00000196209	ENST00000359801;ENST00000444444;ENST00000381630;ENST00000381628	T;T;T	0.02682	4.66;4.2;4.29	4.44	-2.43	0.06522	Immunoglobulin-like (1);	1.935470	0.02296	N	0.070752	T	0.01976	0.0062	N	0.17474	0.49	0.18873	N	0.999988	B;P	0.39576	0.0;0.679	B;B	0.38500	0.001;0.275	T	0.30179	-0.9987	10	0.32370	T	0.25	-8.4472	0.2245	0.00172	0.3024:0.2764:0.148:0.2732	.	36;36	E9PCW6;Q5JXA9	.;SIRB2_HUMAN	M	36	ENSP00000352849:R36M;ENSP00000402438:R36M;ENSP00000371043:R36M	ENSP00000352849:R36M	R	-	2	0	SIRPB2	1408689	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.299000	0.08254	-0.266000	0.09339	0.655000	0.94253	AGG		0.537	SIRPB2-201	KNOWN	basic	protein_coding	protein_coding		NM_178459		A	1460689	C	A	1460689	1	1	61	1	0	1	0	0	0	0	0	0	14371	681	24	2		2	SIRPB2	20	1460689	De_novo_Start_OutOfFrame	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203	1460689	61564831	11455	19440										
SIRPB1	10326	broad.mit.edu	37	chr20	1552399	1552399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agacaagttggcagtcccacGaagagggtccccctgcaagg	13	12	0	2	rs142083473	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1552399G>A	ENST00000381605.4	-	3	782	c.718C>T	c.(718-720)Cgt>Tgt	p.R240C	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	240	Ig-like C1-type 1.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R240C(1)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GCAGTCCCACGAAGAGGGTCC	0.627													.|||	4	0.000798722	0.003	0	5008	,	,		19667	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20						G	,CYS/ARG	11,4395		0,11,2192	106	95	99		,718	1.5	0.9	20	dbSNP_134	99	0,8600		0,0,4300	no	intron,missense	SIRPB1	NM_001083910.2,NM_006065.3	,180	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	,probably-damaging	,240/399	1552399	11,12995	2203	4300	6503	1500399	SO:0001583	missense	10326			Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.718C>T	20.37:g.1552399G>A	ENSP00000371018:p.Arg240Cys		1500399	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	.	12.42	1.932274	0.34096	0.002497	0.0	ENSG00000101307	ENST00000381605	T	0.02812	4.15	2.47	1.5	0.22942	Immunoglobulin-like (1);	0.229512	0.29205	N	0.012832	T	0.11623	0.0283	M	0.85197	2.74	0.54753	D	0.999984	D	0.89917	1.0	D	0.66351	0.943	T	0.00726	-1.1592	10	0.72032	D	0.01	.	5.4858	0.16749	0.1673:0.0:0.8327:0.0	.	240	O00241	SIRB1_HUMAN	C	240	ENSP00000371018:R240C	ENSP00000371018:R240C	R	-	1	0	SIRPB1	1500399	0.005000	0.15991	0.932000	0.37286	0.452000	0.32318	0.255000	0.18333	0.387000	0.25024	-0.380000	0.06706	CGT		0.627	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		A	1552399	G	A	1552399	3	1	61	1	0	0	0	0	1	0	0	0	14370	1058	37	1	490	1	SIRPB1	20	1552399	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91710	1552399	61473121	11456	19441										
SIRPG	55423	broad.mit.edu	37	chr20	1629888	1629888	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggggaagtggccttctttTtgattgtagattaattcccg	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1629888T>G	ENST00000303415.3	-	2	304	c.240A>C	c.(238-240)caA>caC	p.Q80H	SIRPG_ENST00000216927.4_Missense_Mutation_p.Q80H|SIRPG_ENST00000344103.4_Missense_Mutation_p.Q80H|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381580.1_Missense_Mutation_p.Q47H|SIRPG_ENST00000381583.2_Missense_Mutation_p.Q80H	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	80	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.Q80H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GGCCTTCTTTTTGATTGTAGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20											215	191	199					20																	1629888		2203	4300	6503	1577888	SO:0001583	missense	55423			AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.240A>C	20.37:g.1629888T>G	ENSP00000305529:p.Gln80His		1577888	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	5.707	0.314961	0.10789	.	.	ENSG00000089012	ENST00000381580;ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	1.93	-0.372	0.12520	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.317880	0.04801	N	0.433402	T	0.57431	0.2053	L	0.50333	1.59	0.09310	N	1	B;B;B	0.16603	0.006;0.018;0.01	B;B;B	0.14023	0.003;0.006;0.01	T	0.29427	-1.0012	10	0.23891	T	0.37	.	6.0232	0.19640	0.0:0.0:0.437:0.563	.	80;80;80	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	H	47;80;80;80;80	ENSP00000370992:Q47H;ENSP00000342759:Q80H;ENSP00000305529:Q80H;ENSP00000370995:Q80H;ENSP00000216927:Q80H	ENSP00000216927:Q80H	Q	-	3	2	SIRPG	1577888	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	0.084000	0.14891	-0.059000	0.13154	0.164000	0.16699	CAA		0.522	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		G	1629888	T	G	1629888	3	3	61	1	0	0	0	0	1	0	0	0	14373	1838	64	4	939	4	SIRPG	20	1629888	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	77489	1629888	61395632	11457	19442										
SIRPG	55423	broad.mit.edu	37	chr20	1638306	1638306	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtaagtcccagcagtaGagtcagaagcaggaaaggac	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1638306G>T	ENST00000303415.3	-	1	119	c.55C>A	c.(55-57)Cta>Ata	p.L19I	SIRPG_ENST00000216927.4_Missense_Mutation_p.L19I|SIRPG_ENST00000344103.4_Missense_Mutation_p.L19I|SIRPG_ENST00000381583.2_Missense_Mutation_p.L19I	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	19					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L19I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						CCCAGCAGTAGAGTCAGAAGC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	20											127	113	118					20																	1638306		2203	4300	6503	1586306	SO:0001583	missense	55423			AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.55C>A	20.37:g.1638306G>T	ENSP00000305529:p.Leu19Ile		1586306	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	10.80	1.453520	0.26161	.	.	ENSG00000089012	ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T	0.16324	3.84;2.35;4.62;4.62	2.29	1.33	0.21861	Immunoglobulin-like (1);	2.788340	0.02080	N	0.052245	T	0.43612	0.1255	M	0.80847	2.515	0.09310	N	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.85130	0.996;0.932;0.997	T	0.02789	-1.1110	10	0.66056	D	0.02	.	4.8961	0.13751	0.1819:0.0:0.8181:0.0	.	19;19;19	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	I	19	ENSP00000342759:L19I;ENSP00000305529:L19I;ENSP00000370995:L19I;ENSP00000216927:L19I	ENSP00000216927:L19I	L	-	1	2	SIRPG	1586306	0.015000	0.18098	0.003000	0.11579	0.108000	0.19459	0.348000	0.20031	0.526000	0.28541	0.543000	0.68304	CTA		0.547	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		T	1638306	G	T	1638306	3	4	61	1	0	0	0	0	1	0	0	0	14373	933	33	2	1128	2	SIRPG	20	1638306	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8418	1638306	61387214	11458	19443										
SIRPA	140885	broad.mit.edu	37	chr20	1905475	1905475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgtgcaccttgctggtgGccctactgatggcggccctc	14	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:1905475G>A	ENST00000358771.4	+	5	1305	c.1153G>A	c.(1153-1155)Gcc>Acc	p.A385T	SIRPA_ENST00000356025.3_Missense_Mutation_p.A385T|SIRPA_ENST00000400068.3_Missense_Mutation_p.A385T	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	385					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.A385T(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CTTGCTGGTGGCCCTACTGAT	0.537																																					GBM(155;1668 1920 5945 42733 48121)											1	Substitution - Missense(1)	large_intestine(1)	20											236	179	198					20																	1905475		2203	4300	6503	1853475	SO:0001583	missense	140885			D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	9662	protein-coding gene	gene with protein product		602461	"protein tyrosine phosphatase, non-receptor type substrate 1"	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.1153G>A	20.37:g.1905475G>A	ENSP00000351621:p.Ala385Thr		1853475	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.367067	0.41902	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.19250	2.16;2.16;2.16	4.99	3.04	0.35103	.	0.610713	0.14551	N	0.312659	T	0.12475	0.0303	N	0.24115	0.695	0.23720	N	0.997027	P;B;P	0.43094	0.704;0.019;0.799	B;B;B	0.37650	0.215;0.031;0.255	T	0.11567	-1.0582	10	0.31617	T	0.26	.	8.0976	0.30837	0.1839:0.0:0.8161:0.0	.	365;385;385	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	T	385	ENSP00000382941:A385T;ENSP00000348307:A385T;ENSP00000351621:A385T	ENSP00000348307:A385T	A	+	1	0	SIRPA	1853475	0.992000	0.36948	1.000000	0.80357	0.473000	0.32948	1.613000	0.36900	0.807000	0.34208	0.591000	0.81541	GCC		0.537	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		A	1905475	G	A	1905475	3	1	61	1	0	0	0	0	1	0	0	0	14369	1203	42	3	1171	3	SIRPA	20	1905475	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	267169	1905475	61120045	11459	19444										
TGM3	7053	broad.mit.edu	37	chr20	2290453	2290453	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggccttggctctaacgaaaGactggagttcattgtctcca	10	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2290453G>T	ENST00000381458.5	+	2	221	c.158G>T	c.(157-159)aGa>aTa	p.R53I		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	53					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)	p.R53I(1)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	TCTAACGAAAGACTGGAGTTC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	20											133	116	122					20																	2290453		2203	4300	6503	2238453	SO:0001583	missense	7053			L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.158G>T	20.37:g.2290453G>T	ENSP00000370867:p.Arg53Ile		2238453	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.754490	0.31046	.	.	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.85088	-1.94	5.53	-7.14	0.01527	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.521290	0.03087	N	0.159309	T	0.75034	0.3795	L	0.40543	1.245	0.09310	N	1	B	0.30439	0.279	B	0.23574	0.047	T	0.62134	-0.6918	10	0.33940	T	0.23	-24.6445	8.3049	0.32036	0.5667:0.1991:0.2342:0.0	.	53	Q08188	TGM3_HUMAN	I	53	ENSP00000370867:R53I	ENSP00000370867:R53I	R	+	2	0	TGM3	2238453	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.191000	0.09601	-0.929000	0.03757	-0.305000	0.09177	AGA		0.498	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2290453	G	T	2290453	3	4	61	1	0	0	0	0	1	0	0	0	15870	942	33	2	164	2	TGM3	20	2290453	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	384978	2290453	60735067	11460	19445										
SNRPB	6628	broad.mit.edu	37	chr20	2448314	2448314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgtgcttgtcaaaagcctTgaaggtgccaatgaagatcc	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2448314T>C	ENST00000438552.2	-	2	256	c.94A>G	c.(94-96)Aag>Gag	p.K32E	SNRPB_ENST00000339610.6_5'UTR|RP4-734P14.4_ENST00000461548.1_3'UTR|SNRPB_ENST00000381342.2_Missense_Mutation_p.K32E	NM_198216.1	NP_937859.1	P14678	RSMB_HUMAN	small nuclear ribonucleoprotein polypeptides B and B1	32					gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	histone pre-mRNA DCP binding (GO:0071208)|poly(A) RNA binding (GO:0044822)	p.K32E(1)		kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	10						TCAAAAGCCTTGAAGGTGCCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20											131	104	113					20																	2448314		2203	4300	6503	2396314	SO:0001583	missense	6628				CCDS13026.1, CCDS13027.1	20p13	2011-10-11			ENSG00000125835	ENSG00000125835			11153	protein-coding gene	gene with protein product		182282		SNRPB1		1376292	Standard	NM_003091		Approved	COD, SmB/SmB', Sm-B/B', snRNP-B	uc002wfz.1	P14678	OTTHUMG00000031694	ENST00000438552.2:c.94A>G	20.37:g.2448314T>C	ENSP00000412566:p.Lys32Glu		2396314	Q15490|Q6IB35|Q9UIS5	Missense_Mutation	SNP	ENST00000438552.2	37	CCDS13026.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.975868	0.74360	.	.	ENSG00000125835	ENST00000381342;ENST00000438552;ENST00000303103	T;T	0.44881	0.91;0.91	5.81	4.71	0.59529	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.61837	0.2379	M	0.75884	2.315	0.80722	D	1	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	D;D;D;D	0.77557	0.966;0.99;0.99;0.99	T	0.64305	-0.6439	10	0.87932	D	0	.	10.1652	0.42875	0.0:0.079:0.0:0.921	.	32;32;32;32	E7ENP4;B4DVS0;Q66K91;P14678	.;.;.;RSMB_HUMAN	E	32	ENSP00000370746:K32E;ENSP00000412566:K32E	ENSP00000303591:K32E	K	-	1	0	SNRPB	2396314	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	7.994000	0.88315	1.014000	0.39417	0.528000	0.53228	AAG		0.522	SNRPB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077585.2			C	2448314	T	C	2448314	3	2	61	1	0	0	0	0	1	0	0	0	14898	1821	63	4	667	4	SNRPB	20	2448314	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	157861	2448314	60577206	11461	19446										
TMC2	117532	broad.mit.edu	37	chr20	2596830	2596830	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaatgtgctgggtttgatCttcaaccaaggaatgatctg	12	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2596830C>A	ENST00000358864.1	+	15	1935	c.1920C>A	c.(1918-1920)atC>atA	p.I640I	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	640					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)	p.I640I(1)		NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGGGTTTGATCTTCAACCAAG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	20											214	181	192					20																	2596830		2203	4300	6503	2544830	SO:0001819	synonymous_variant	117532			AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1920C>A	20.37:g.2596830C>A			2544830	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	37	CCDS13029.2																																																																																				0.433	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			A	2596830	C	A	2596830	2	1	61	1	0	0	0	0	0	0	0	1	16024	903	32	2		2	TMC2	20	2596830	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	148516	2596830	60428690	11462	19447										
NOP56	10528	broad.mit.edu	37	chr20	2637782	2637782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagaaacaggagaagaaacGcttaaagaaggaaaagaaac	12	4	0	5	rs143140440		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2637782G>A	ENST00000329276.5	+	11	1853	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	SNORD57_ENST00000448188.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORA51_ENST00000606420.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	446	Lys-rich.				cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)	p.R446H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GAGAAGAAACGCTTAAAGAAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	20						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	78	78	78		1337	4.8	1	20	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	missense	NOP56	NM_006392.3	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	446/595	2637782	2,13004	2203	4300	6503	2585782	SO:0001583	missense	10528			Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1337G>A	20.37:g.2637782G>A	ENSP00000370589:p.Arg446His		2585782	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.22|15.22	2.769168|2.769168	0.49680|0.49680	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000101361|ENSG00000101361	ENST00000415272|ENST00000329276;ENST00000381169	.|T	.|0.47177	.|0.85	5.71|5.71	4.75|4.75	0.60458|0.60458	.|.	.|0.052450	.|0.64402	.|D	.|0.000001	T|T	0.46229|0.46229	0.1382|0.1382	L|L	0.34521|0.34521	1.04|1.04	0.46356|0.46356	D|D	0.999001|0.999001	.|D;D	.|0.59767	.|0.964;0.986	.|B;P	.|0.50791	.|0.215;0.65	T|T	0.47086|0.47086	-0.9144|-0.9144	5|10	.|0.56958	.|D	.|0.05	-3.4286|-3.4286	12.4334|12.4334	0.55586|0.55586	0.0:0.0:0.8323:0.1677|0.0:0.0:0.8323:0.1677	.|.	.|193;446	.|E9PDI8;O00567	.|.;NOP56_HUMAN	T|H	187|446;193	.|ENSP00000370589:R446H	.|ENSP00000370589:R446H	A|R	+|+	1|2	0|0	NOP56|NOP56	2585782|2585782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.179000|2.179000	0.42528|0.42528	1.541000|1.541000	0.49316|0.49316	0.650000|0.650000	0.86243|0.86243	GCT|CGC		0.512	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		A	2637782	G	A	2637782	3	1	61	1	0	0	0	0	1	0	0	0	10570	1087	38	1	1379	1	NOP56	20	2637782	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	40952	2637782	60387738	11463	19448										
NOP56	10528	broad.mit.edu	37	chr20	2638841	2638841	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaagaaaaagaggaaattCtccaaagaggagccggtcag	11	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2638841C>A	ENST00000329276.5	+	12	2202	c.1686C>A	c.(1684-1686)ttC>ttA	p.F562L	SNORD57_ENST00000448188.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	562	Lys-rich.				cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)	p.F562L(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						AGAGGAAATTCTCCAAAGAGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	20											13	14	14					20																	2638841		2196	4299	6495	2586841	SO:0001583	missense	10528			Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1686C>A	20.37:g.2638841C>A	ENSP00000370589:p.Phe562Leu		2586841	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	7.770	0.707293	0.15239	.	.	ENSG00000101361	ENST00000329276	T	0.56444	0.46	5.07	-6.96	0.01622	.	1.505710	0.03166	N	0.170076	T	0.25975	0.0633	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17410	-1.0370	10	0.12430	T	0.62	0.2929	7.2685	0.26244	0.0:0.2517:0.3975:0.3508	.	562	O00567	NOP56_HUMAN	L	562	ENSP00000370589:F562L	ENSP00000370589:F562L	F	+	3	2	NOP56	2586841	0.000000	0.05858	0.022000	0.16811	0.443000	0.32047	-1.755000	0.01814	-1.329000	0.02258	-0.208000	0.12717	TTC		0.498	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		A	2638841	C	A	2638841	3	1	61	1	0	0	0	0	1	0	0	0	10570	912	32	2	1732	2	NOP56	20	2638841	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1059	2638841	60386679	11464	19449										
NOP56	10528	broad.mit.edu	37	chr20	2638897	2638897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcggttggcaagagcagctCcaagaagaagaaaaagttcc	13	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2638897C>T	ENST00000329276.5	+	12	2258	c.1742C>T	c.(1741-1743)tCc>tTc	p.S581F	SNORD57_ENST00000448188.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	581	Lys-rich.				cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)	p.S581F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						AAGAGCAGCTCCAAGAAGAAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											7	9	9					20																	2638897		2125	4241	6366	2586897	SO:0001583	missense	10528			Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1742C>T	20.37:g.2638897C>T	ENSP00000370589:p.Ser581Phe		2586897	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.637642	0.67130	.	.	ENSG00000101361	ENST00000329276	T	0.58940	0.3	5.27	5.27	0.74061	.	2.465540	0.01080	N	0.004972	T	0.51941	0.1704	N	0.14661	0.345	0.26380	N	0.976757	B	0.26258	0.145	B	0.31016	0.123	T	0.48917	-0.8992	10	0.87932	D	0	1.337	14.6769	0.68986	0.0:1.0:0.0:0.0	.	581	O00567	NOP56_HUMAN	F	581	ENSP00000370589:S581F	ENSP00000370589:S581F	S	+	2	0	NOP56	2586897	0.185000	0.23213	0.576000	0.28549	0.769000	0.43574	1.642000	0.37207	2.932000	0.99384	0.644000	0.83932	TCC		0.507	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		T	2638897	C	T	2638897	3	4	61	1	0	0	0	0	1	0	0	0	10570	855	30	3	1788	3	NOP56	20	2638897	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56	2638897	60386623	11465	19450										
CPXM1	56265	broad.mit.edu	37	chr20	2775011	2775011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccgtgtcactgaatggtagCcctcggcactggcagtcacc	11	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2775011C>T	ENST00000380605.2	-	14	2094	c.2030G>A	c.(2029-2031)gGc>gAc	p.G677D		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	677					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.G677D(1)		endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TGAATGGTAGCCCTCGGCACT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	20											60	58	58					20																	2775011		2203	4300	6503	2723011	SO:0001583	missense	56265			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.2030G>A	20.37:g.2775011C>T	ENSP00000369979:p.Gly677Asp		2723011	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973722	0.92919	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	T	0.61742	0.08	5.12	5.12	0.69794	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.000000	0.85682	D	0.000000	D	0.82531	0.5057	H	0.94734	3.575	0.53005	D	0.999967	D	0.89917	1.0	D	0.91635	0.999	D	0.86812	0.1999	10	0.72032	D	0.01	-26.6541	16.4323	0.83853	0.0:1.0:0.0:0.0	.	677	Q96SM3	CPXM1_HUMAN	D	677;373	ENSP00000369979:G677D	ENSP00000369979:G677D	G	-	2	0	CPXM1	2723011	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.536000	0.82023	2.821000	0.97095	0.651000	0.88453	GGC		0.597	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		T	2775011	C	T	2775011	3	4	61	1	0	0	0	0	1	0	0	0	3843	739	26	3	178	3	CPXM1	20	2775011	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	136114	2775011	60250509	11466	19451										
VPS16	64601	broad.mit.edu	37	chr20	2841680	2841680	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgtctccttcacctaccGacacctggcactcttcacag	7	17	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:2841680G>A	ENST00000380445.3	+	7	767	c.695G>A	c.(694-696)cGa>cAa	p.R232Q	VPS16_ENST00000380443.3_5'Flank|VPS16_ENST00000380469.3_Missense_Mutation_p.R232Q|VPS16_ENST00000481812.2_3'UTR	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	232					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)		p.R232Q(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						TTCACCTACCGACACCTGGCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											128	118	122					20																	2841680		2203	4300	6503	2789680	SO:0001583	missense	64601			AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.695G>A	20.37:g.2841680G>A	ENSP00000369810:p.Arg232Gln		2789680	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation	SNP	ENST00000380445.3	37	CCDS13036.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.061124	0.55432	.	.	ENSG00000215305	ENST00000380445;ENST00000380469;ENST00000453689;ENST00000417508	T;T	0.45668	0.89;0.89	5.82	4.87	0.63330	Vps16, N-terminal (1);	0.064498	0.64402	D	0.000004	T	0.39784	0.1091	L	0.35644	1.08	0.80722	D	1	P;D	0.64830	0.953;0.994	B;P	0.53450	0.199;0.726	T	0.17837	-1.0356	10	0.18276	T	0.48	-5.3516	7.7451	0.28864	0.081:0.0:0.7555:0.1634	.	232;232	Q9H269-2;Q9H269	.;VPS16_HUMAN	Q	232;232;114;114	ENSP00000369810:R232Q;ENSP00000369836:R232Q	ENSP00000369810:R232Q	R	+	2	0	VPS16	2789680	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.600000	0.67599	1.464000	0.47987	0.467000	0.42956	CGA		0.587	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575		A	2841680	G	A	2841680	3	1	61	1	0	0	0	0	1	0	0	0	17233	1058	37	1	721	1	VPS16	20	2841680	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	66669	2841680	60183840	11467	19452										
UBOX5	22888	broad.mit.edu	37	chr20	3102194	3102194	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttcagcctgctctatcttcCttttctgagagggcagaaca	9	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3102194C>A	ENST00000217173.2	-	3	1562	c.1091G>T	c.(1090-1092)aGg>aTg	p.R364M	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.R364M	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5									p.R364M(1)		endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						CTCTATCTTCCTTTTCTGAGA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	20											71	55	61					20																	3102194		2203	4300	6503	3050194	SO:0001583	missense	22888			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.1091G>T	20.37:g.3102194C>A	ENSP00000217173:p.Arg364Met		3050194		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.416316	0.62511	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.37058	1.38;1.22	5.43	5.43	0.79202	.	0.585491	0.17077	U	0.187959	T	0.53012	0.1770	L	0.34521	1.04	0.40614	D	0.9817	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.56257	-0.8009	10	0.87932	D	0	-12.258	19.2596	0.93962	0.0:1.0:0.0:0.0	.	364;364;364	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	M	364	ENSP00000217173:R364M;ENSP00000311726:R364M	ENSP00000217173:R364M	R	-	2	0	UBOX5	3050194	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.891000	0.56227	2.543000	0.85770	0.655000	0.94253	AGG		0.517	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102194	C	A	3102194	3	1	61	1	0	0	0	0	1	0	0	0	16934	681	24	2	546	2	UBOX5	20	3102194	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	260514	3102194	59923326	11468	19453										
UBOX5	22888	broad.mit.edu	37	chr20	3102535	3102535	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaatgatctcggccagcttCtgcaggctggagggagcctg	15	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3102535C>A	ENST00000217173.2	-	3	1221	c.750G>T	c.(748-750)caG>caT	p.Q250H	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.Q250H	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5									p.Q250H(1)		endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						CGGCCAGCTTCTGCAGGCTGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	20											42	41	41					20																	3102535		2203	4300	6503	3050535	SO:0001583	missense	22888			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.750G>T	20.37:g.3102535C>A	ENSP00000217173:p.Gln250His		3050535		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.619731	0.28801	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.32272	1.46;1.46	5.42	3.5	0.40072	.	0.438978	0.18757	U	0.132014	T	0.19525	0.0469	L	0.27053	0.805	0.23459	N	0.997631	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.08055	0.002;0.003;0.002	T	0.16188	-1.0411	10	0.44086	T	0.13	-2.5058	6.5425	0.22388	0.0:0.5885:0.2466:0.1648	.	250;250;250	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	H	250	ENSP00000217173:Q250H;ENSP00000311726:Q250H	ENSP00000217173:Q250H	Q	-	3	2	UBOX5	3050535	0.994000	0.37717	0.987000	0.45799	0.784000	0.44337	1.372000	0.34261	0.666000	0.31087	0.563000	0.77884	CAG		0.607	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102535	C	A	3102535	3	1	61	1	0	0	0	0	1	0	0	0	16934	912	32	2	887	2	UBOX5	20	3102535	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	341	3102535	59922985	11469	19454										
UBOX5	22888	broad.mit.edu	37	chr20	3102794	3102794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacgtggctaagggaaagaGcccctttattccagagctcc	10	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3102794G>T	ENST00000217173.2	-	3	962	c.491C>A	c.(490-492)gCt>gAt	p.A164D	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.A164D	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5									p.A164D(1)		endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						AAGGGAAAGAGCCCCTTTATT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	20											62	59	60					20																	3102794		2203	4300	6503	3050794	SO:0001583	missense	22888			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.491C>A	20.37:g.3102794G>T	ENSP00000217173:p.Ala164Asp		3050794		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267800	0.40095	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.34072	1.38;1.38	5.32	4.38	0.52667	.	0.215721	0.39544	U	0.001326	T	0.30198	0.0757	L	0.36672	1.1	0.23192	N	0.998143	B;B;B	0.29341	0.242;0.112;0.112	B;B;B	0.26416	0.034;0.069;0.034	T	0.27365	-1.0076	10	0.72032	D	0.01	-0.8402	13.9373	0.64032	0.0733:0.0:0.9267:0.0	.	164;164;164	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	D	164	ENSP00000217173:A164D;ENSP00000311726:A164D	ENSP00000217173:A164D	A	-	2	0	UBOX5	3050794	0.703000	0.27826	1.000000	0.80357	0.916000	0.54674	3.836000	0.55813	1.237000	0.43756	0.563000	0.77884	GCT		0.592	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		T	3102794	G	T	3102794	3	4	61	1	0	0	0	0	1	0	0	0	16934	971	34	2	1146	2	UBOX5	20	3102794	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259	3102794	59922726	11470	19455										
UBOX5	22888	broad.mit.edu	37	chr20	3103974	3103974	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaccttgttgcagtgaattCttggtctgaactgtgggagg	13	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3103974C>A	ENST00000217173.2	-	2	509	c.38G>T	c.(37-39)aGa>aTa	p.R13I	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.R13I	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5									p.R13I(1)		endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						GCAGTGAATTCTTGGTCTGAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	20											186	174	178					20																	3103974		2203	4300	6503	3051974	SO:0001583	missense	22888			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.38G>T	20.37:g.3103974C>A	ENSP00000217173:p.Arg13Ile		3051974		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467642	0.84533	.	.	ENSG00000185019	ENST00000217173;ENST00000348031;ENST00000449731	T;T;T	0.36878	1.23;1.23;1.23	5.69	5.69	0.88448	.	0.120519	0.56097	U	0.000037	T	0.63674	0.2531	M	0.73962	2.25	0.58432	D	0.99999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65742	-0.6094	10	0.87932	D	0	-6.931	19.8045	0.96525	0.0:1.0:0.0:0.0	.	13;13;13	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	I	13	ENSP00000217173:R13I;ENSP00000311726:R13I;ENSP00000404364:R13I	ENSP00000217173:R13I	R	-	2	0	UBOX5	3051974	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.204000	0.65180	2.676000	0.91093	0.655000	0.94253	AGA		0.353	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3103974	C	A	3103974	3	1	61	1	0	0	0	0	1	0	0	0	16934	913	32	2	1603	2	UBOX5	20	3103974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1180	3103974	59921546	11471	19456										
SLC4A11	83959	broad.mit.edu	37	chr20	3215517	3215517	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcgggcttcgaaggtgtCatctgtgtcacacttgtagt	11	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3215517C>A	ENST00000380056.3	-	2	207	c.160G>T	c.(160-162)Gac>Tac	p.D54Y	SLC4A11_ENST00000380059.3_Missense_Mutation_p.D81Y|SLC4A11_ENST00000539553.2_Missense_Mutation_p.D38Y	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	54					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.D54Y(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TCGAAGGTGTCATCTGTGTCA	0.557																																					NSCLC(190;922 2139 10266 10292 38692)											1	Substitution - Missense(1)	large_intestine(1)	20											102	94	97					20																	3215517		2203	4300	6503	3163517	SO:0001583	missense	83959			AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.160G>T	20.37:g.3215517C>A	ENSP00000369396:p.Asp54Tyr		3163517	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956424	0.34565	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553;ENST00000437836	D;D;D;D	0.85088	-1.86;-1.86;-1.8;-1.94	4.55	3.59	0.41128	.	0.323511	0.30949	N	0.008546	T	0.82240	0.4994	L	0.60455	1.87	0.45718	D	0.998622	B;B;B	0.12630	0.005;0.006;0.001	B;B;B	0.14023	0.01;0.003;0.002	T	0.79155	-0.1920	10	0.87932	D	0	.	12.6927	0.56985	0.1665:0.8335:0.0:0.0	.	38;81;54	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	Y	81;54;38;38	ENSP00000369399:D81Y;ENSP00000369396:D54Y;ENSP00000441370:D38Y;ENSP00000404271:D38Y	ENSP00000369396:D54Y	D	-	1	0	SLC4A11	3163517	0.223000	0.23663	0.262000	0.24481	0.893000	0.52053	1.672000	0.37523	0.883000	0.36040	0.655000	0.94253	GAC		0.557	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			A	3215517	C	A	3215517	3	1	61	1	0	0	0	0	1	0	0	0	14689	826	29	2	2587	2	SLC4A11	20	3215517	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111543	3215517	59810003	11472	19457										
SLC4A11	83959	broad.mit.edu	37	chr20	3218200	3218200	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtactcacttgaatcctcGaagtatccattctgcgacat	7	11	2	1	rs35732230	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3218200G>A	ENST00000380056.3	-	1	173	c.126C>T	c.(124-126)ttC>ttT	p.F42F	SLC4A11_ENST00000380059.3_Silent_p.F69F|SLC4A11_ENST00000539553.2_Silent_p.F26F	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	42					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.F42F(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TTGAATCCTCGAAGTATCCAT	0.562													A|||	4	0.000798722	0.003	0	5008	,	,		19005	0		0	False		,,,				2504	0				NSCLC(190;922 2139 10266 10292 38692)											1	Substitution - coding silent(1)	large_intestine(1)	20						A	,,	3,4403	825.9+/-416.6	0,3,2200	169	140	149		78,207,126	0.4	0.2	20	dbSNP_126	149	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	,,	26/876,69/919,42/892	3218200	4,13002	2203	4300	6503	3166200	SO:0001819	synonymous_variant	83959			AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.126C>T	20.37:g.3218200G>A			3166200	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																				0.562	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			A	3218200	G	A	3218200	2	1	61	1	0	0	0	0	0	0	0	1	14689	1049	37	1		1	SLC4A11	20	3218200	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2683	3218200	59807320	11473	19458										
C20orf194	25943	broad.mit.edu	37	chr20	3295716	3295716	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtagattgctggaataaaGatatgctccttctcctcctg	8	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3295716G>T	ENST00000252032.9	-	20	1709	c.1642C>A	c.(1642-1644)Ctt>Att	p.L548I	C20orf194_ENST00000453730.2_Missense_Mutation_p.L286I|C20orf194_ENST00000498079.1_5'UTR	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	548								p.L548I(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						CTGGAATAAAGATATGCTCCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	20											143	141	142					20																	3295716		1890	4107	5997	3243716	SO:0001583	missense	25943			AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1642C>A	20.37:g.3295716G>T	ENSP00000252032:p.Leu548Ile		3243716	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.816115	0.32145	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.34667	2.12;1.35	5.02	4.01	0.46588	.	0.273852	0.35615	N	0.003086	T	0.20659	0.0497	N	0.16656	0.425	0.38803	D	0.955249	B;B	0.14012	0.009;0.009	B;B	0.18561	0.022;0.013	T	0.08289	-1.0729	10	0.18276	T	0.48	.	10.3567	0.43969	0.0:0.0:0.6651:0.3349	.	287;548	Q0IIP3;Q5TEA3	.;CT194_HUMAN	I	548;286	ENSP00000252032:L548I;ENSP00000407229:L286I	ENSP00000252032:L548I	L	-	1	0	C20orf194	3243716	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	3.399000	0.52586	2.591000	0.87537	0.650000	0.86243	CTT		0.408	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		T	3295716	G	T	3295716	3	4	61	1	0	0	0	0	1	0	0	0	2105	942	33	2	1963	2	C20orf194	20	3295716	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77516	3295716	59729804	11474	19459										
C20orf194	25943	broad.mit.edu	37	chr20	3321279	3321279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagaacaaatggctgccGgttagggctagagagggaag	16	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3321279G>A	ENST00000252032.9	-	10	920	c.853C>T	c.(853-855)Cgg>Tgg	p.R285W	C20orf194_ENST00000453730.2_Missense_Mutation_p.R24W	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	285								p.R285W(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						AATGGCTGCCGGTTAGGGCTA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	20											80	78	78					20																	3321279		1886	4113	5999	3269279	SO:0001583	missense	25943			AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.853C>T	20.37:g.3321279G>A	ENSP00000252032:p.Arg285Trp		3269279	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571622	0.45798	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.38240	2.0;1.15	5.79	3.57	0.40892	.	0.117980	0.53938	D	0.000045	T	0.56156	0.1966	M	0.62723	1.935	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.95	T	0.57768	-0.7754	10	0.87932	D	0	.	13.4982	0.61438	0.0:0.0:0.4724:0.5276	.	24;285	Q0IIP3;Q5TEA3	.;CT194_HUMAN	W	285;24	ENSP00000252032:R285W;ENSP00000407229:R24W	ENSP00000252032:R285W	R	-	1	2	C20orf194	3269279	1.000000	0.71417	0.996000	0.52242	0.363000	0.29612	1.168000	0.31859	0.511000	0.28236	-0.457000	0.05445	CGG		0.463	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		A	3321279	G	A	3321279	3	1	61	1	0	0	0	0	1	0	0	0	2105	1115	39	1	2792	1	C20orf194	20	3321279	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	25563	3321279	59704241	11475	19460										
ATRN	8455	broad.mit.edu	37	chr20	3553521	3553521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtgtgtggaacacagggtCgtctcagtgtatctcgtggg	16	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3553521C>T	ENST00000262919.5	+	12	2083	c.2015C>T	c.(2014-2016)tCg>tTg	p.S672L	ATRN_ENST00000446916.2_Missense_Mutation_p.S672L	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	672					cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.S672L(1)		breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						AACACAGGGTCGTCTCAGTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	20											159	128	138					20																	3553521		2203	4300	6503	3501521	SO:0001583	missense	8455			AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2015C>T	20.37:g.3553521C>T	ENSP00000262919:p.Ser672Leu		3501521	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	C	3.800	-0.041791	0.07452	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.06218	3.33;3.41	5.65	-0.738	0.11125	.	1.110700	0.06576	N	0.749436	T	0.05044	0.0135	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45381	-0.9265	10	0.30078	T	0.28	2.3127	7.2151	0.25955	0.0:0.2946:0.1274:0.578	.	672;672	O75882;O75882-2	ATRN_HUMAN;.	L	672;672;598	ENSP00000262919:S672L;ENSP00000416587:S672L	ENSP00000262919:S672L	S	+	2	0	ATRN	3501521	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.060000	0.11712	-0.058000	0.13177	-0.302000	0.09304	TCG		0.448	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		T	3553521	C	T	3553521	3	4	61	1	0	0	0	0	1	0	0	0	1207	893	31	1	2061	1	ATRN	20	3553521	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	232242	3553521	59471999	11476	19461										
ATRN	8455	broad.mit.edu	37	chr20	3559320	3559320	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgacaatgctaaattgttCtgtaggaaccacaatgccct	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3559320C>A	ENST00000262919.5	+	15	2513	c.2445C>A	c.(2443-2445)ttC>ttA	p.F815L	ATRN_ENST00000446916.2_Missense_Mutation_p.F815L	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	815	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.F815L(1)		breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						CTAAATTGTTCTGTAGGAACC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	20											102	96	98					20																	3559320		2203	4300	6503	3507320	SO:0001583	missense	8455			AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2445C>A	20.37:g.3559320C>A	ENSP00000262919:p.Phe815Leu		3507320	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.414138	0.42817	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.55052	0.54;0.54	5.42	5.42	0.78866	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.255939	0.40818	N	0.001007	T	0.45357	0.1338	L	0.39245	1.2	0.32356	N	0.557756	B;B	0.09022	0.002;0.001	B;B	0.14578	0.011;0.003	T	0.46456	-0.9190	10	0.12430	T	0.62	-7.9714	18.8161	0.92077	0.0:1.0:0.0:0.0	.	815;815	O75882;O75882-2	ATRN_HUMAN;.	L	815;815;741	ENSP00000262919:F815L;ENSP00000416587:F815L	ENSP00000262919:F815L	F	+	3	2	ATRN	3507320	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.829000	0.39121	2.534000	0.85438	0.655000	0.94253	TTC		0.398	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		A	3559320	C	A	3559320	3	1	61	1	0	0	0	0	1	0	0	0	1207	912	32	2	2503	2	ATRN	20	3559320	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5799	3559320	59466200	11477	19462										
ATRN	8455	broad.mit.edu	37	chr20	3559394	3559394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttgtccttaagcagctgcGaataatgcagtcatctcaga	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3559394G>A	ENST00000262919.5	+	15	2587	c.2519G>A	c.(2518-2520)cGa>cAa	p.R840Q	ATRN_ENST00000446916.2_Missense_Mutation_p.R840Q	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	840	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R840Q(1)		breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						AAGCAGCTGCGAATAATGCAG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	20											76	72	73					20																	3559394		2203	4300	6503	3507394	SO:0001583	missense	8455			AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2519G>A	20.37:g.3559394G>A	ENSP00000262919:p.Arg840Gln		3507394	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082314	0.36758	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.18016	2.24;2.24	5.56	4.61	0.57282	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.199871	0.43416	D	0.000565	T	0.04318	0.0119	N	0.00605	-1.335	0.36903	D	0.890522	B;B	0.11235	0.004;0.001	B;B	0.06405	0.001;0.002	T	0.26916	-1.0089	10	0.15066	T	0.55	-5.0244	7.037	0.24998	0.289:0.0:0.711:0.0	.	840;840	O75882;O75882-2	ATRN_HUMAN;.	Q	840;840;766	ENSP00000262919:R840Q;ENSP00000416587:R840Q	ENSP00000262919:R840Q	R	+	2	0	ATRN	3507394	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	3.195000	0.51013	1.362000	0.46000	0.655000	0.94253	CGA		0.413	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		A	3559394	G	A	3559394	3	1	61	1	0	0	0	0	1	0	0	0	1207	1058	37	1	2577	1	ATRN	20	3559394	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74	3559394	59466126	11478	19463										
SIGLEC1	6614	broad.mit.edu	37	chr20	3682019	3682019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtccagggtggaggttgCatttccaagggagttggtgg	18	5	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3682019C>T	ENST00000344754.4	-	6	1497	c.1498G>A	c.(1498-1500)Gca>Aca	p.A500T	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.A500T	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	500	Ig-like C2-type 4.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.A500T(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						GTGGAGGTTGCATTTCCAAGG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											80	64	70					20																	3682019		2203	4300	6503	3630019	SO:0001583	missense	6614			AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1498G>A	20.37:g.3682019C>T	ENSP00000341141:p.Ala500Thr		3630019	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387390	0.61956	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.68903	-0.36;-0.36	5.69	-0.303	0.12792	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.976540	0.08323	N	0.963596	T	0.73606	0.3608	M	0.65975	2.015	0.09310	N	1	P;P	0.49559	0.925;0.846	P;P	0.53760	0.734;0.611	T	0.64791	-0.6324	10	0.17832	T	0.49	.	15.7684	0.78146	0.6833:0.3167:0.0:0.0	.	500;500	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	T	500	ENSP00000341141:A500T;ENSP00000202578:A500T	ENSP00000202578:A500T	A	-	1	0	SIGLEC1	3630019	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	-1.114000	0.03293	-0.342000	0.08363	0.655000	0.94253	GCA		0.587	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3682019	C	T	3682019	3	4	61	1	0	0	0	0	1	0	0	0	14342	710	25	3	3695	3	SIGLEC1	20	3682019	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	122625	3682019	59343501	11479	19464										
MAVS	57506	broad.mit.edu	37	chr20	3844907	3844907	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttttccaccggcaggtgcGacctccagcctcacaccatc	8	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3844907G>A	ENST00000428216.2	+	6	758	c.630G>A	c.(628-630)gcG>gcA	p.A210A	MAVS_ENST00000358134.6_3'UTR|MAVS_ENST00000416600.2_Silent_p.A69A	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	210					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.A210A(1)		autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CGGCAGGTGCGACCTCCAGCC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	20											87	89	89					20																	3844907		2203	4300	6503	3792907	SO:0001819	synonymous_variant	57506			DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"virus-induced signaling adaptor", "IFN-B promoter stimulator 1", "CARD adaptor inducing IFN-beta"	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.630G>A	20.37:g.3844907G>A			3792907	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Silent	SNP	ENST00000428216.2	37	CCDS33437.1																																																																																				0.612	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746		A	3844907	G	A	3844907	2	1	61	1	0	0	0	0	0	0	0	1	9368	1045	37	1		1	MAVS	20	3844907	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	162888	3844907	59180613	11480	19465										
PANK2	80025	broad.mit.edu	37	chr20	3888859	3888859	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagagataaaaacttctcGagtctccacactgtcttttg	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:3888859G>A	ENST00000316562.4	+	2	921	c.915G>A	c.(913-915)tcG>tcA	p.S305S	PANK2_ENST00000610179.1_Silent_p.S182S|PANK2_ENST00000497424.1_Silent_p.S14S	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	305					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.S305S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						AAAACTTCTCGAGTCTCCACA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	20											100	92	95					20																	3888859		2203	4300	6503	3836859	SO:0001819	synonymous_variant	80025			AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.915G>A	20.37:g.3888859G>A			3836859	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Silent	SNP	ENST00000316562.4	37	CCDS13071.2																																																																																				0.418	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		A	3888859	G	A	3888859	2	1	61	1	0	0	0	0	0	0	0	1	11448	1045	37	1		1	PANK2	20	3888859	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43952	3888859	59136661	11481	19466										
SMOX	54498	broad.mit.edu	37	chr20	4162483	4162483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaggagttcttccggcacGataaaccagtcaatgctgaa	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:4162483G>A	ENST00000305958.4	+	4	694	c.469G>A	c.(469-471)Gat>Aat	p.D157N	SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000278795.3_Missense_Mutation_p.D157N|SMOX_ENST00000339123.6_Missense_Mutation_p.D157N|SMOX_ENST00000346595.2_Intron|SMOX_ENST00000379460.2_Missense_Mutation_p.D157N	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	157					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)	p.D157N(2)		breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	CTTCCGGCACGATAAACCAGT	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	20											96	94	95					20																	4162483		2203	4300	6503	4110483	SO:0001583	missense	54498			AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.469G>A	20.37:g.4162483G>A	ENSP00000307252:p.Asp157Asn		4110483	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	37	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375210	0.42105	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	D;D;D;D;T	0.92595	-3.07;-3.07;-3.07;-3.07;1.56	5.44	5.44	0.79542	Amine oxidase (1);	0.049971	0.85682	D	0.000000	D	0.87605	0.6219	L	0.32530	0.975	0.30041	N	0.81258	B;B;B;B;B	0.30033	0.12;0.266;0.12;0.004;0.136	B;B;B;B;B	0.27608	0.043;0.043;0.081;0.0;0.027	T	0.83223	-0.0067	10	0.33940	T	0.23	-1.5446	16.8098	0.85716	0.0:0.0:1.0:0.0	.	134;157;157;157;157	B4DE63;Q9NWM0-6;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;SMOX_HUMAN;.;.	N	157;157;157;157;14	ENSP00000344595:D157N;ENSP00000307252:D157N;ENSP00000278795:D157N;ENSP00000368773:D157N;ENSP00000407269:D14N	ENSP00000278795:D157N	D	+	1	0	SMOX	4110483	1.000000	0.71417	0.998000	0.56505	0.791000	0.44710	6.834000	0.75339	2.576000	0.86940	0.558000	0.71614	GAT		0.532	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		A	4162483	G	A	4162483	3	1	61	1	0	0	0	0	1	0	0	0	14840	1058	37	1	479	1	SMOX	20	4162483	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273624	4162483	58863037	11482	19467										
PRNP	5621	broad.mit.edu	37	chr20	4679943	4679943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggcctctgcaagaagcgccCgaagcctggaggatggaaca	15	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:4679943C>T	ENST00000379440.4	+	2	364	c.77C>T	c.(76-78)cCg>cTg	p.P26L	PRNP_ENST00000430350.2_Missense_Mutation_p.P26L	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	0	Trp-rich.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)		p.P26L(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						AAGAAGCGCCCGAAGCCTGGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	20											39	49	45					20																	4679943		2200	4298	6498	4627943	SO:0001583	missense	5621			M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"CD molecules"	9449	protein-coding gene	gene with protein product	"Creutzfeldt-Jakob disease", "Gerstmann-Strausler-Scheinker syndrome", "fatal familial insomnia", "p27-30"	176640	"prion protein (p27-30)"	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.77C>T	20.37:g.4679943C>T	ENSP00000368752:p.Pro26Leu		4627943		Missense_Mutation	SNP	ENST00000379440.4	37	CCDS13080.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.664633	0.67700	.	.	ENSG00000171867	ENST00000379440;ENST00000430350;ENST00000424424;ENST00000457586	D;D;D;D	0.96334	-2.92;-2.92;-3.14;-3.98	5.02	5.02	0.67125	.	0.211349	0.32015	N	0.006706	D	0.97225	0.9093	L	0.54323	1.7	0.41406	D	0.987708	D;D;P	0.89917	1.0;0.998;0.875	D;D;B	0.91635	0.999;0.979;0.393	D	0.97781	1.0232	10	0.87932	D	0	-0.667	14.1892	0.65628	0.0:1.0:0.0:0.0	.	26;26;26	B2NI04;P04156;O75942	.;PRIO_HUMAN;.	L	26	ENSP00000368752:P26L;ENSP00000399376:P26L;ENSP00000411599:P26L;ENSP00000415284:P26L	ENSP00000368752:P26L	P	+	2	0	PRNP	4627943	0.798000	0.28890	0.316000	0.25252	0.870000	0.49936	2.149000	0.42244	2.496000	0.84212	0.655000	0.94253	CCG		0.627	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311		T	4679943	C	T	4679943	3	4	61	1	0	0	0	0	1	0	0	0	12578	652	23	1	79	1	PRNP	20	4679943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	517460	4679943	58345577	11483	19468										
RASSF2	9770	broad.mit.edu	37	chr20	4764984	4764984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcattagccggagcacggTgtacctggagacaagaaaca	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:4764984T>C	ENST00000379400.3	-	12	1111	c.916A>G	c.(916-918)Acc>Gcc	p.T306A	RASSF2_ENST00000379376.2_Missense_Mutation_p.T306A|RASSF2_ENST00000478553.1_5'UTR	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	306	SARAH. {ECO:0000255|PROSITE- ProRule:PRU00310}.				bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T306A(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						CGGAGCACGGTGTACCTGGAG	0.592																																					Melanoma(158;1891 3343 50738)											1	Substitution - Missense(1)	large_intestine(1)	20											99	89	92					20																	4764984		2203	4300	6503	4712984	SO:0001583	missense	9770			D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"centromere protein 34"	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.916A>G	20.37:g.4764984T>C	ENSP00000368710:p.Thr306Ala		4712984	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Missense_Mutation	SNP	ENST00000379400.3	37	CCDS13083.1	.	.	.	.	.	.	.	.	.	.	T	7.685	0.689863	0.15039	.	.	ENSG00000101265	ENST00000379400;ENST00000379376	T;T	0.09163	3.01;3.01	5.21	5.21	0.72293	SARAH (1);	0.334600	0.34067	N	0.004296	T	0.05090	0.0136	N	0.12182	0.205	0.43175	D	0.994981	B	0.10296	0.003	B	0.10450	0.005	T	0.24905	-1.0147	10	0.06365	T	0.9	.	8.4109	0.32642	0.1739:0.0:0.0:0.8261	.	306	P50749	RASF2_HUMAN	A	306	ENSP00000368710:T306A;ENSP00000368684:T306A	ENSP00000368684:T306A	T	-	1	0	RASSF2	4712984	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	2.719000	0.47244	2.186000	0.69663	0.533000	0.62120	ACC		0.592	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		C	4764984	T	C	4764984	3	2	61	1	0	0	0	0	1	0	0	0	13123	1696	59	4	68	4	RASSF2	20	4764984	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	85041	4764984	58260536	11484	19469										
RASSF2	9770	broad.mit.edu	37	chr20	4766954	4766954	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttttaagtaccggcatctcGaactttatatactgggccac	7	11	1	0	rs200418178	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:4766954G>A	ENST00000379400.3	-	11	1029	c.834C>T	c.(832-834)ttC>ttT	p.F278F	RASSF2_ENST00000379376.2_Silent_p.F278F|RASSF2_ENST00000478553.1_5'UTR	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	278	SARAH. {ECO:0000255|PROSITE- ProRule:PRU00310}.				bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F278F(2)		endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						CCGGCATCTCGAACTTTATAT	0.468													G|||	2	0.000399361	0.0015	0	5008	,	,		20066	0		0	False		,,,				2504	0				Melanoma(158;1891 3343 50738)											2	Substitution - coding silent(2)	large_intestine(2)	20											146	161	156					20																	4766954		2203	4300	6503	4714954	SO:0001819	synonymous_variant	9770			D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"centromere protein 34"	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.834C>T	20.37:g.4766954G>A			4714954	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	37	CCDS13083.1																																																																																				0.468	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		A	4766954	G	A	4766954	2	1	61	1	0	0	0	0	0	0	0	1	13123	1049	37	1		1	RASSF2	20	4766954	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1970	4766954	58258566	11485	19470										
SLC23A2	9962	broad.mit.edu	37	chr20	4880249	4880249	+	Frame_Shift_Del	DEL	A	A	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagtgattcccacacagaagAaaatggtcccaatgagctgg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:4880249delA	ENST00000379333.1	-	6	826	c.434delT	c.(433-435)ttcfs	p.F146fs	SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Frame_Shift_Del_p.F146fs|SLC23A2_ENST00000338244.1_Frame_Shift_Del_p.F146fs	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	146					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.F145fs*38(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CACACAGAAGAAAATGGTCCC	0.552																																																1	Deletion - Frameshift(1)	large_intestine(1)	20											196	181	186					20																	4880249		2203	4300	6503	4828249	SO:0001589	frameshift_variant	9962			AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"Solute carriers"	10973	protein-coding gene	gene with protein product		603791	"solute carrier family 23 (nucleobase transporters), member 1"	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.434delT	20.37:g.4880249delA	ENSP00000368637:p.Phe146fs		4828249	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Frame_Shift_Del	DEL	ENST00000379333.1	37	CCDS13085.1																																																																																				0.552	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			-	4880249	A	-	4880249	7	5	61	1	0	1	0	1	0	0	0	0	14500	246	9	0	1566	0	SLC23A2	20	4880249	Frame_Shift_Del	DEL	A	TCGA-AG-A002-01A-01W-A00K-09	113295	4880249	58145271	11486	19471										
PROKR2	128674	broad.mit.edu	37	chr20	5282738	5282738	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtgggcaccccgttggttCtgaggtcaaggtcagcactg	15	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:5282738C>A	ENST00000217270.3	-	2	1102	c.1103G>T	c.(1102-1104)aGa>aTa	p.R368I	PROKR2_ENST00000546004.1_Missense_Mutation_p.R368I	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	368					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.R368I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						CCCGTTGGTTCTGAGGTCAAG	0.542										HNSCC(71;0.22)																																						1	Substitution - Missense(1)	large_intestine(1)	20											151	126	135					20																	5282738		2203	4300	6503	5230738	SO:0001583	missense	128674			AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"GPCR / Class A : Prokineticin receptors"	15836	protein-coding gene	gene with protein product		607123	"G protein-coupled receptor 73-like 1", "Kallmann syndrome 3 (autosomal dominant)"	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.1103G>T	20.37:g.5282738C>A	ENSP00000217270:p.Arg368Ile		5230738	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	37	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	C	9.371	1.070465	0.20147	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.71698	-0.59;-0.59	5.2	-0.0662	0.13765	.	0.176394	0.51477	D	0.000093	T	0.56702	0.2003	L	0.40543	1.245	0.34295	D	0.683731	P	0.36330	0.548	B	0.35470	0.203	T	0.60296	-0.7291	10	0.72032	D	0.01	.	8.6631	0.34103	0.0:0.3282:0.0:0.6718	.	368	Q8NFJ6	PKR2_HUMAN	I	368	ENSP00000440790:R368I;ENSP00000217270:R368I	ENSP00000217270:R368I	R	-	2	0	PROKR2	5230738	0.968000	0.33430	0.560000	0.28344	0.017000	0.09413	0.675000	0.25232	-0.247000	0.09597	-0.290000	0.09829	AGA		0.542	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		A	5282738	C	A	5282738	3	1	61	1	0	0	0	0	1	0	0	0	12587	913	32	2	54	2	PROKR2	20	5282738	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	402489	5282738	57742782	11487	19472										
PROKR2	128674	broad.mit.edu	37	chr20	5283115	5283115	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccgggagatcctggcataGcacagggtcatggtgaccac	13	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:5283115G>T	ENST00000217270.3	-	2	725	c.726C>A	c.(724-726)tgC>tgA	p.C242*	PROKR2_ENST00000546004.1_Nonsense_Mutation_p.C242*	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	242					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.C242*(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						TCCTGGCATAGCACAGGGTCA	0.597										HNSCC(71;0.22)																																						1	Substitution - Nonsense(1)	large_intestine(1)	20											91	84	86					20																	5283115		2203	4300	6503	5231115	SO:0001587	stop_gained	128674			AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"GPCR / Class A : Prokineticin receptors"	15836	protein-coding gene	gene with protein product		607123	"G protein-coupled receptor 73-like 1", "Kallmann syndrome 3 (autosomal dominant)"	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.726C>A	20.37:g.5283115G>T	ENSP00000217270:p.Cys242*		5231115	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Nonsense_Mutation	SNP	ENST00000217270.3	37	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	G	37	6.073376	0.97256	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	.	.	.	5.16	2.91	0.33838	.	0.088999	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.123	0.20164	0.1332:0.1983:0.6685:0.0	.	.	.	.	X	242	.	ENSP00000217270:C242X	C	-	3	2	PROKR2	5231115	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	0.494000	0.22467	1.151000	0.42436	0.655000	0.94253	TGC		0.597	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		T	5283115	G	T	5283115	4	4	61	1	0	0	0	0	0	1	0	0	12587	963	34	2	431	2	PROKR2	20	5283115	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	377	5283115	57742405	11488	19473										
GPCPD1	56261	broad.mit.edu	37	chr20	5539375	5539375	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcattgcaatgggggttgtCcgagatctgaggtccatgag	14	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:5539375C>A	ENST00000379019.4	-	18	1835	c.1623G>T	c.(1621-1623)cgG>cgT	p.R541R	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	541	GP-PDE.				glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)	p.R541R(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TGGGGGTTGTCCGAGATCTGA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	20											69	72	71					20																	5539375		2203	4300	6503	5487375	SO:0001819	synonymous_variant	56261				CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.1623G>T	20.37:g.5539375C>A			5487375	D3DW06|Q9BQL8|Q9NUX0	Silent	SNP	ENST00000379019.4	37	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	C	9.604	1.129522	0.21041	.	.	ENSG00000125772	ENST00000418646	.	.	.	5.22	3.28	0.37604	.	.	.	.	.	T	0.45736	0.1357	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35699	-0.9778	4	.	.	.	-15.1843	2.239	0.04015	0.2751:0.4566:0.1145:0.1539	.	.	.	.	Y	133	.	.	D	-	1	0	GPCPD1	5487375	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.703000	0.25646	0.698000	0.31739	0.655000	0.94253	GAC		0.348	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		A	5539375	C	A	5539375	2	1	61	1	0	0	0	0	0	0	0	1	6623	842	30	2		2	GPCPD1	20	5539375	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	256260	5539375	57486145	11489	19474										
C20orf196	149840	broad.mit.edu	37	chr20	5844088	5844088	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcatttcctcttgcagcaGaatgtaatgaaagacctgta	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:5844088G>A	ENST00000303142.6	+	3	684	c.597G>A	c.(595-597)caG>caA	p.Q199Q		NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	199								p.Q199Q(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						TCTTGCAGCAGAATGTAATGA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	20											85	82	83					20																	5844088		2202	4299	6501	5792088	SO:0001819	synonymous_variant	149840			AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984			26318	protein-coding gene	gene with protein product						12477932	Standard	NM_152504		Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.597G>A	20.37:g.5844088G>A			5792088	A8K9J3|Q5TGA9|Q96LU1	Silent	SNP	ENST00000303142.6	37	CCDS13091.1																																																																																				0.502	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504		A	5844088	G	A	5844088	2	1	61	1	0	0	0	0	0	0	0	1	2107	933	33	3		3	C20orf196	20	5844088	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	304713	5844088	57181432	11490	19475										
MCM8	84515	broad.mit.edu	37	chr20	5966767	5966767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagctggaatctttgattcGtctgacagaggtttgtttct	11	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:5966767G>A	ENST00000378896.3	+	16	2530	c.2153G>A	c.(2152-2154)cGt>cAt	p.R718H	MCM8_ENST00000378886.2_Missense_Mutation_p.R758H|MCM8_ENST00000378883.1_Missense_Mutation_p.R671H|MCM8_ENST00000265187.4_Missense_Mutation_p.R702H	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	718					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R702H(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TCTTTGATTCGTCTGACAGAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	20											103	98	100					20																	5966767		2203	4300	6503	5914767	SO:0001583	missense	84515			AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2153G>A	20.37:g.5966767G>A	ENSP00000368174:p.Arg718His		5914767	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.696208	0.88830	.	.	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.15139	2.45;2.45;2.45;2.45	5.65	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.56688	0.2002	H	0.97186	3.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.996;1.0	T	0.73668	-0.3910	10	0.87932	D	0	-13.2564	14.947	0.71039	0.0687:0.0:0.9313:0.0	.	671;758;702;718	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	H	718;671;758;702	ENSP00000368174:R718H;ENSP00000368161:R671H;ENSP00000368164:R758H;ENSP00000265187:R702H	ENSP00000265187:R702H	R	+	2	0	MCM8	5914767	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.648000	0.98483	1.531000	0.49152	-0.140000	0.14226	CGT		0.418	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		A	5966767	G	A	5966767	3	1	61	1	0	0	0	0	1	0	0	0	9423	1145	40	1	2211	1	MCM8	20	5966767	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	122679	5966767	57058753	11491	19476										
BMP2	650	broad.mit.edu	37	chr20	6759694	6759694	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgaaaaggttgtattaaaGaactatcaggacatggttgt	10	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:6759694G>T	ENST00000378827.4	+	3	2368	c.1149G>T	c.(1147-1149)aaG>aaT	p.K383N		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	383					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)	p.K383N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						TTGTATTAAAGAACTATCAGG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	20											72	69	70					20																	6759694		2203	4300	6503	6707694	SO:0001583	missense	650				CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"Bone morphogenetic proteins", "Endogenous ligands"	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.1149G>T	20.37:g.6759694G>T	ENSP00000368104:p.Lys383Asn		6707694		Missense_Mutation	SNP	ENST00000378827.4	37	CCDS13099.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.929420	0.52759	.	.	ENSG00000125845	ENST00000378827	D	0.84730	-1.89	5.76	4.81	0.61882	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93953	0.8064	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94637	0.7827	10	0.87932	D	0	.	10.4547	0.44544	0.15:0.0:0.85:0.0	.	383	P12643	BMP2_HUMAN	N	383	ENSP00000368104:K383N	ENSP00000368104:K383N	K	+	3	2	BMP2	6707694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.578000	0.60929	1.546000	0.49388	0.650000	0.86243	AAG		0.353	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3			T	6759694	G	T	6759694	3	4	61	1	0	0	0	0	1	0	0	0	1460	933	33	2	1155	2	BMP2	20	6759694	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	792927	6759694	56265826	11492	19477										
HAO1	54363	broad.mit.edu	37	chr20	7866189	7866189	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcagagccatggccaaccGgaattcttcctttagtatct	7	12	3	1	rs573481520		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:7866189G>T	ENST00000378789.3	-	7	1072	c.1021C>A	c.(1021-1023)Cgg>Agg	p.R341R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	341	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)	p.R341R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ATGGCCAACCGGAATTCTTCC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	20											121	106	111					20																	7866189		2203	4300	6503	7814189	SO:0001819	synonymous_variant	54363			AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.1021C>A	20.37:g.7866189G>T			7814189	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																				0.398	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			T	7866189	G	T	7866189	2	4	61	1	0	0	0	0	0	0	0	1	6972	1115	39	2		2	HAO1	20	7866189	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1106495	7866189	55159331	11493	19478										
PLCB1	23236	broad.mit.edu	37	chr20	8719982	8719982	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcattggccaccgtatCttgccagtgcaagccattcg	8	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:8719982C>A	ENST00000338037.6	+	21	2310	c.2283C>A	c.(2281-2283)atC>atA	p.I761I	PLCB1_ENST00000378641.3_Silent_p.I761I|PLCB1_ENST00000378637.2_Silent_p.I761I|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	761	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.I761I(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						GCCACCGTATCTTGCCAGTGC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	20											93	89	90					20																	8719982		2203	4300	6503	8667982	SO:0001819	synonymous_variant	23236			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2283C>A	20.37:g.8719982C>A			8667982	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																				0.408	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			A	8719982	C	A	8719982	2	1	61	1	0	0	0	0	0	0	0	1	12058	903	32	2		2	PLCB1	20	8719982	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	853793	8719982	54305538	11494	19479										
PLCB1	23236	broad.mit.edu	37	chr20	8722118	8722118	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccctatttagatgtcatCgaagctttatcaaacccaat	4	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:8722118C>T	ENST00000338037.6	+	23	2448	c.2421C>T	c.(2419-2421)atC>atT	p.I807I	PLCB1_ENST00000378641.3_Silent_p.I807I|PLCB1_ENST00000378637.2_Silent_p.I807I|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	807					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.I807I(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TAGATGTCATCGAAGCTTTAT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	20											115	103	107					20																	8722118		2203	4300	6503	8670118	SO:0001819	synonymous_variant	23236			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2421C>T	20.37:g.8722118C>T			8670118	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																				0.383	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8722118	C	T	8722118	2	4	61	1	0	0	0	0	0	0	0	1	12058	874	31	1		1	PLCB1	20	8722118	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2136	8722118	54303402	11495	19480										
PLCB4	5332	broad.mit.edu	37	chr20	9401961	9401961	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggttatatcaggtcaattCttatcagataagaaaattgg	8	5	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:9401961C>A	ENST00000378493.1	+	23	2151	c.2136C>A	c.(2134-2136)ttC>ttA	p.F712L	PLCB4_ENST00000378473.3_Missense_Mutation_p.F724L|PLCB4_ENST00000278655.4_Missense_Mutation_p.F712L|PLCB4_ENST00000414679.2_Missense_Mutation_p.F724L|PLCB4_ENST00000334005.3_Missense_Mutation_p.F712L|PLCB4_ENST00000378501.2_Missense_Mutation_p.F712L|PLCB4_ENST00000492632.1_3'UTR			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	712	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.F712L(1)		NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CAGGTCAATTCTTATCAGATA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	20											88	85	86					20																	9401961		2203	4300	6503	9349961	SO:0001583	missense	5332				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.2136C>A	20.37:g.9401961C>A	ENSP00000367754:p.Phe712Leu		9349961	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398525	0.83120	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58	5.68	4.71	0.59529	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093709	0.85682	D	0.000000	T	0.30324	0.0761	L	0.49640	1.575	0.80722	D	1	D;P;D;D	0.89917	1.0;0.825;0.989;0.99	D;B;D;P	0.87578	0.998;0.278;0.983;0.857	T	0.01734	-1.1285	10	0.66056	D	0.02	.	11.9572	0.52988	0.0:0.8512:0.0:0.1488	.	724;559;712;712	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	L	712;724;712;712;712;560	ENSP00000334105:F712L;ENSP00000367734:F724L;ENSP00000278655:F712L;ENSP00000367754:F712L;ENSP00000367762:F712L;ENSP00000390616:F560L	ENSP00000278655:F712L	F	+	3	2	PLCB4	9349961	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.603000	0.36794	1.350000	0.45770	0.467000	0.42956	TTC		0.403	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9401961	C	A	9401961	3	1	61	1	0	0	0	0	1	0	0	0	12061	912	32	2	2266	2	PLCB4	20	9401961	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	679843	9401961	53623559	11496	19481										
C20orf103	24141	broad.mit.edu	37	chr20	9498747	9498747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtcacccccgctgggaagtCctatgagtgtcaagctcaac	11	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:9498747C>T	ENST00000246070.2	+	5	1028	c.536C>T	c.(535-537)tCc>tTc	p.S179F	LAMP5_ENST00000427562.2_Missense_Mutation_p.S135F	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	179						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)		p.S179F(1)									GCTGGGAAGTCCTATGAGTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	20											122	96	105					20																	9498747		2203	4300	6503	9446747	SO:0001583	missense	24141			AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.536C>T	20.37:g.9498747C>T	ENSP00000246070:p.Ser179Phe		9446747	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041945	0.93685	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.57436	0.4;0.4	5.93	5.93	0.95920	.	0.049906	0.85682	D	0.000000	T	0.63022	0.2476	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.961	T	0.57757	-0.7756	9	.	.	.	-13.5095	20.3539	0.98825	0.0:1.0:0.0:0.0	.	135;179	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	F	179;135	ENSP00000246070:S179F;ENSP00000406360:S135F	.	S	+	2	0	C20orf103	9446747	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.361000	0.79497	2.826000	0.97356	0.655000	0.94253	TCC		0.537	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		T	9498747	C	T	9498747	3	4	61	1	0	0	0	0	1	0	0	0	2081	855	30	3	554	3	C20orf103	20	9498747	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	96786	9498747	53526773	11497	19482										
PAK7	57144	broad.mit.edu	37	chr20	9561309	9561309	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtggctgcctctataatacGgatccagatcatctccatag	8	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:9561309G>A	ENST00000378429.3	-	5	1019	c.473C>T	c.(472-474)cCg>cTg	p.P158L	PAK7_ENST00000378423.1_Missense_Mutation_p.P158L|RP5-986I17.2_ENST00000428769.1_RNA|PAK7_ENST00000353224.5_Missense_Mutation_p.P158L	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	158	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P158L(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TCTATAATACGGATCCAGATC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	20											185	178	180					20																	9561309		2203	4300	6503	9509309	SO:0001583	missense	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.473C>T	20.37:g.9561309G>A	ENSP00000367686:p.Pro158Leu		9509309	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	G	0.771	-0.765859	0.02974	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.40225	1.04;1.04;1.04	5.31	0.942	0.19525	.	0.839167	0.10931	N	0.618373	T	0.18299	0.0439	N	0.04959	-0.14	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.26677	-1.0096	9	.	.	.	.	5.6268	0.17487	0.4021:0.2538:0.3441:0.0	.	158;158	B0AZM9;Q9P286	.;PAK7_HUMAN	L	158;158;158;106	ENSP00000367686:P158L;ENSP00000322957:P158L;ENSP00000367679:P158L	.	P	-	2	0	PAK7	9509309	0.002000	0.14202	0.005000	0.12908	0.073000	0.16967	1.427000	0.34881	0.241000	0.21283	-0.280000	0.10049	CCG		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9561309	G	A	9561309	3	1	61	1	0	0	0	0	1	0	0	0	11436	1116	39	1	1714	1	PAK7	20	9561309	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62562	9561309	53464211	11498	19483										
PAK7	57144	broad.mit.edu	37	chr20	9561418	9561418	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggtgatgaagccattttCttccgcgtggcctggaccgt	13	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:9561418C>A	ENST00000378429.3	-	5	910	c.364G>T	c.(364-366)Gaa>Taa	p.E122*	PAK7_ENST00000378423.1_Nonsense_Mutation_p.E122*|PAK7_ENST00000353224.5_Nonsense_Mutation_p.E122*	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	122	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E122*(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			AAGCCATTTTCTTCCGCGTGG	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											186	188	187					20																	9561418		2203	4300	6503	9509418	SO:0001587	stop_gained	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.364G>T	20.37:g.9561418C>A	ENSP00000367686:p.Glu122*		9509418	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Nonsense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.377642	0.97520	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	.	.	.	5.22	5.22	0.72569	.	0.046001	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7962	0.91995	0.0:1.0:0.0:0.0	.	.	.	.	X	122;122;122;70	.	.	E	-	1	0	PAK7	9509418	1.000000	0.71417	0.997000	0.53966	0.338000	0.28826	5.777000	0.68931	2.445000	0.82738	0.563000	0.77884	GAA		0.527	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9561418	C	A	9561418	4	1	61	1	0	0	0	0	0	1	0	0	11436	922	32	2	1823	2	PAK7	20	9561418	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	109	9561418	53464102	11499	19484										
ANKRD5	63926	broad.mit.edu	37	chr20	10019076	10019076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accctgaactaatcaattatAcagaacccattaatggactt	4	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10019076A>G	ENST00000378380.3	+	2	456	c.127A>G	c.(127-129)Aca>Gca	p.T43A	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Missense_Mutation_p.T43A	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	43							calcium ion binding (GO:0005509)	p.T43A(1)									AATCAATTATACAGAACCCAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	20											106	102	103					20																	10019076		2203	4300	6503	9967076	SO:0001583	missense	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.127A>G	20.37:g.10019076A>G	ENSP00000367631:p.Thr43Ala		9967076	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.627386	0.66901	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.70631	-0.5;-0.5	5.93	5.93	0.95920	Ankyrin repeat-containing domain (3);	0.091306	0.85682	D	0.000000	T	0.69672	0.3137	N	0.25144	0.715	0.58432	D	0.999994	D	0.56746	0.977	P	0.55011	0.766	T	0.68573	-0.5373	9	.	.	.	.	16.3709	0.83357	1.0:0.0:0.0:0.0	.	43	Q9NU02	ANKR5_HUMAN	A	43	ENSP00000367644:T43A;ENSP00000367631:T43A	.	T	+	1	0	ANKRD5	9967076	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.008000	0.70739	2.261000	0.74972	0.528000	0.53228	ACA		0.413	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		G	10019076	A	G	10019076	3	3	61	1	0	0	0	0	1	0	0	0	676	391	14	4	129	4	ANKRD5	20	10019076	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	457658	10019076	53006444	11500	19485										
ANKRD5	63926	broad.mit.edu	37	chr20	10025099	10025099	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggggtagtggaaatagttCgaggcatattggaaagagga	16	2	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10025099C>T	ENST00000378380.3	+	4	933	c.604C>T	c.(604-606)Cga>Tga	p.R202*	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Nonsense_Mutation_p.R202*	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	202							calcium ion binding (GO:0005509)	p.R202*(1)									GGAAATAGTTCGAGGCATATT	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											213	194	200					20																	10025099		2203	4300	6503	9973099	SO:0001587	stop_gained	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.604C>T	20.37:g.10025099C>T	ENSP00000367631:p.Arg202*		9973099	B3KUQ0|Q9H6Y9	Nonsense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	C	39	7.529295	0.98339	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	.	.	.	5.24	4.29	0.51040	.	0.171354	0.49916	D	0.000138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-2.1216	15.4315	0.75102	0.1403:0.8597:0.0:0.0	.	.	.	.	X	202	.	ENSP00000367631:R202X	R	+	1	2	ANKRD5	9973099	1.000000	0.71417	0.976000	0.42696	0.720000	0.41350	3.999000	0.57031	1.313000	0.45069	0.655000	0.94253	CGA		0.438	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		T	10025099	C	T	10025099	4	4	61	1	0	0	0	0	0	1	0	0	676	876	31	1	614	1	ANKRD5	20	10025099	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6023	10025099	53000421	11501	19486										
ANKRD5	63926	broad.mit.edu	37	chr20	10030099	10030099	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggctgtggctaaggaaggCggcttcaaagcagcaagcaa	15	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10030099C>T	ENST00000378380.3	+	6	1211	c.882C>T	c.(880-882)ggC>ggT	p.G294G	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Silent_p.G294G	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	294							calcium ion binding (GO:0005509)	p.G294G(1)									CTAAGGAAGGCGGCTTCAAAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	20											96	110	106					20																	10030099		2203	4300	6503	9978099	SO:0001819	synonymous_variant	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.882C>T	20.37:g.10030099C>T			9978099	B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	37	CCDS13108.1																																																																																				0.448	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		T	10030099	C	T	10030099	2	4	61	1	0	0	0	0	0	0	0	1	676	755	27	1		1	ANKRD5	20	10030099	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5000	10030099	52995421	11502	19487										
ANKRD5	63926	broad.mit.edu	37	chr20	10030617	10030617	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatgtcactgatagcagccGgtttaatagagatcatcccc	9	10	2	2	rs148551222		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10030617G>T	ENST00000378380.3	+	6	1729	c.1400G>T	c.(1399-1401)cGg>cTg	p.R467L	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Missense_Mutation_p.R467L	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	467							calcium ion binding (GO:0005509)	p.R467L(1)									GATAGCAGCCGGTTTAATAGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	20											141	126	131					20																	10030617		2203	4300	6503	9978617	SO:0001583	missense	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1400G>T	20.37:g.10030617G>T	ENSP00000367631:p.Arg467Leu		9978617	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586890	0.28268	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.69926	-0.44;-0.44	5.77	4.82	0.62117	Ankyrin repeat-containing domain (1);	0.162599	0.52532	D	0.000078	T	0.76140	0.3946	M	0.70275	2.135	0.22280	N	0.999234	D	0.64830	0.994	P	0.57911	0.829	T	0.69522	-0.5123	10	0.66056	D	0.02	-0.6943	12.9385	0.58329	0.1272:0.0:0.8727:0.0	.	467	Q9NU02	ANKR5_HUMAN	L	467	ENSP00000367644:R467L;ENSP00000367631:R467L	ENSP00000367631:R467L	R	+	2	0	ANKRD5	9978617	0.698000	0.27777	0.088000	0.20740	0.003000	0.03518	3.343000	0.52167	2.885000	0.99019	0.655000	0.94253	CGG		0.443	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		T	10030617	G	T	10030617	3	4	61	1	0	0	0	0	1	0	0	0	676	1116	39	2	1418	2	ANKRD5	20	10030617	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	518	10030617	52994903	11503	19488										
C20orf94	128710	broad.mit.edu	37	chr20	10603735	10603735	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaccaccacgggagagtttCtcttggaagtgatcgattag	12	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10603735C>A	ENST00000334534.5	+	8	1115	c.935C>A	c.(934-936)tCt>tAt	p.S312Y		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	312								p.S312Y(1)									GGGAGAGTTTCTCTTGGAAGT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	20											88	99	95					20																	10603735		2203	4300	6503	10551735	SO:0001583	missense	128710			AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346			16225	protein-coding gene	gene with protein product		615958	"chromosome 20 open reading frame 94"	C20orf94		19596235	Standard	XM_005260664		Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.935C>A	20.37:g.10603735C>A	ENSP00000335557:p.Ser312Tyr		10551735	Q05CG2|Q05CT9	Missense_Mutation	SNP	ENST00000334534.5	37	CCDS33439.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692476	0.68271	.	.	ENSG00000149346	ENST00000334534	T	0.56941	0.43	5.96	5.03	0.67393	.	0.241828	0.36555	N	0.002521	T	0.53433	0.1796	L	0.59436	1.845	0.33769	D	0.622828	P	0.45827	0.867	P	0.46253	0.509	T	0.69745	-0.5062	10	0.72032	D	0.01	-0.9988	9.7797	0.40640	0.0:0.7871:0.1399:0.0729	.	312	Q5VYV7	CT094_HUMAN	Y	312	ENSP00000335557:S312Y	ENSP00000335557:S312Y	S	+	2	0	C20orf94	10551735	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	1.603000	0.36794	1.533000	0.49186	0.650000	0.86243	TCT		0.483	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3	NM_001009608		A	10603735	C	A	10603735	3	1	61	1	0	0	0	0	1	0	0	0	2127	913	32	2	961	2	C20orf94	20	10603735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	573118	10603735	52421785	11504	19489										
JAG1	182	broad.mit.edu	37	chr20	10629720	10629720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttacatacccgacaggaggCgtcattctgacactggccaa	9	12	2	1	rs201667840		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:10629720C>T	ENST00000254958.5	-	11	1899	c.1384G>A	c.(1384-1386)Gcc>Acc	p.A462T	JAG1_ENST00000488480.1_RNA|JAG1_ENST00000423891.2_Missense_Mutation_p.A303T	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	462	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.A462T(4)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CGACAGGAGGCGTCATTCTGA	0.353									Alagille Syndrome				C|||	1	0.000199681	0	0	5008	,	,		18871	0		0.001	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	20											51	54	53					20																	10629720		2203	4300	6503	10577720	SO:0001583	missense	182	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.1384G>A	20.37:g.10629720C>T	ENSP00000254958:p.Ala462Thr		10577720	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	29.8	5.033955	0.93575	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.94232	-3.38;-3.38	6.07	6.07	0.98685	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.047852	0.85682	D	0.000000	D	0.97337	0.9129	M	0.93062	3.375	0.52099	D	0.999949	D	0.69078	0.997	P	0.59424	0.857	D	0.97462	1.0035	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	462	P78504	JAG1_HUMAN	T	462;303	ENSP00000254958:A462T;ENSP00000389519:A303T	ENSP00000254958:A462T	A	-	1	0	JAG1	10577720	1.000000	0.71417	0.949000	0.38748	0.981000	0.71138	7.786000	0.85741	2.884000	0.98904	0.655000	0.94253	GCC		0.353	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10629720	C	T	10629720	3	4	61	1	0	0	0	0	1	0	0	0	7955	768	27	1	2336	1	JAG1	20	10629720	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	25985	10629720	52395800	11505	19490										
SPTLC3	55304	broad.mit.edu	37	chr20	13140674	13140674	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcaaggcatatgctagaGaaaaaaattggagtggtggt	13	3	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:13140674G>T	ENST00000399002.2	+	11	1714	c.1440G>T	c.(1438-1440)gaG>gaT	p.E480D	SPTLC3_ENST00000378194.4_3'UTR	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	480					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)	p.E480D(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						ATATGCTAGAGAAAAAAATTG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	20											83	84	83					20																	13140674		1802	4078	5880	13088674	SO:0001583	missense	55304			AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"chromosome 20 open reading frame 38", "serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.1440G>T	20.37:g.13140674G>T	ENSP00000381968:p.Glu480Asp		13088674	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.68|14.68	2.608639|2.608639	0.46527|0.46527	.|.	.|.	ENSG00000172296|ENSG00000172296	ENST00000399002|ENST00000431275	D|.	0.91521|.	-2.86|.	5.84|5.84	-2.74|-2.74	0.05932|0.05932	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.600804|.	0.19225|.	N|.	0.119574|.	T|T	0.38772|0.38772	0.1053|0.1053	L|L	0.39633|0.39633	1.23|1.23	0.80722|0.80722	D|D	1|1	B|.	0.09022|.	0.002|.	B|.	0.17979|.	0.02|.	T|T	0.34279|0.34279	-0.9835|-0.9835	10|5	0.41790|.	T|.	0.15|.	-0.1086|-0.1086	1.3341|1.3341	0.02141|0.02141	0.1747:0.326:0.2396:0.2597|0.1747:0.326:0.2396:0.2597	.|.	480|.	Q9NUV7|.	SPTC3_HUMAN|.	D|I	480|78	ENSP00000381968:E480D|.	ENSP00000381968:E480D|.	E|R	+|+	3|2	2|0	SPTLC3|SPTLC3	13088674|13088674	0.464000|0.464000	0.25807|0.25807	0.074000|0.074000	0.20217|0.20217	0.785000|0.785000	0.44390|0.44390	-0.086000|-0.086000	0.11233|0.11233	-0.265000|-0.265000	0.09352|0.09352	0.655000|0.655000	0.94253|0.94253	GAG|AGA		0.433	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327		T	13140674	G	T	13140674	3	4	61	1	0	0	0	0	1	0	0	0	15164	933	33	2	1482	2	SPTLC3	20	13140674	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2510954	13140674	49884846	11506	19491										
ISM1	140862	broad.mit.edu	37	chr20	13279839	13279839	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctccatgctgtccctggaGagcaccacgctggcggcaca	12	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:13279839G>A	ENST00000262487.4	+	6	1134	c.1128G>A	c.(1126-1128)gaG>gaA	p.E376E	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	376	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)		p.E376E(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						TGTCCCTGGAGAGCACCACGC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	20											24	28	27					20																	13279839		2167	4273	6440	13227839	SO:0001819	synonymous_variant	140862			AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"chromosome 20 open reading frame 82", "isthmin 1 homolog (zebrafish)"	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.1128G>A	20.37:g.13279839G>A			13227839	Q8WVH9	Silent	SNP	ENST00000262487.4	37	CCDS46579.1																																																																																				0.647	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2			A	13279839	G	A	13279839	2	1	61	1	0	0	0	0	0	0	0	1	7881	933	33	3		3	ISM1	20	13279839	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	139165	13279839	49745681	11507	19492										
SEL1L2	80343	broad.mit.edu	37	chr20	13839926	13839926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctttgtgatgcctaagccGtgttcatacatataagccag	8	10	1	1	rs372265984		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:13839926G>A	ENST00000284951.5	-	18	1874	c.1800C>T	c.(1798-1800)caC>caT	p.H600H	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Intron			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	600						integral component of membrane (GO:0016021)		p.H600H(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TGCCTAAGCCGTGTTCATACA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G		1,4043		0,1,2021	181	164	169		1800	-11	0	20		169	0,8358		0,0,4179	no	coding-synonymous	SEL1L2	NM_025229.1		0,1,6200	AA,AG,GG		0.0,0.0247,0.0081		600/689	13839926	1,12401	2022	4179	6201	13787926	SO:0001819	synonymous_variant	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1800C>T	20.37:g.13839926G>A			13787926	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																					0.393	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13839926	G	A	13839926	2	1	61	1	0	0	0	0	0	0	0	1	14048	1136	40	1		1	SEL1L2	20	13839926	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	560087	13839926	49185594	11508	19493										
SEL1L2	80343	broad.mit.edu	37	chr20	13846146	13846146	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccagtggcctagttcacaGacacctttataaagctgtac	8	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:13846146G>T	ENST00000284951.5	-	16	1493	c.1419C>A	c.(1417-1419)gtC>gtA	p.V473V	SEL1L2_ENST00000486903.1_Intron|SEL1L2_ENST00000378072.5_Intron			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	473						integral component of membrane (GO:0016021)		p.V473V(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTAGTTCACAGACACCTTTAT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	20											69	65	66					20																	13846146		1880	4105	5985	13794146	SO:0001819	synonymous_variant	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1419C>A	20.37:g.13846146G>T			13794146	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																					0.438	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		T	13846146	G	T	13846146	2	4	61	1	0	0	0	0	0	0	0	1	14048	929	33	2		2	SEL1L2	20	13846146	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6220	13846146	49179374	11509	19494										
SEL1L2	80343	broad.mit.edu	37	chr20	13971174	13971174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctattaacagagacaaggGcttcatcttctcttaagcag	7	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:13971174G>A	ENST00000284951.5	-	1	81	c.7C>T	c.(7-9)Ccc>Tcc	p.P3S	SEL1L2_ENST00000486903.1_Intron|SEL1L2_ENST00000378072.5_Missense_Mutation_p.P3S			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	3						integral component of membrane (GO:0016021)		p.P3S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						AGAGACAAGGGCTTCATCTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	20											102	95	97					20																	13971174		1872	4111	5983	13919174	SO:0001583	missense	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.7C>T	20.37:g.13971174G>A	ENSP00000284951:p.Pro3Ser		13919174	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	G	18.95	3.731538	0.69189	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.26067	1.76;2.16	6.07	4.14	0.48551	.	0.599158	0.15906	N	0.238833	T	0.16685	0.0401	N	0.19112	0.55	0.23192	N	0.998144	B;B	0.13594	0.008;0.008	B;B	0.12156	0.007;0.007	T	0.17319	-1.0373	10	0.46703	T	0.11	2.5839	8.8731	0.35327	0.1685:0.0:0.8315:0.0	.	3;3	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	S	3	ENSP00000367312:P3S;ENSP00000284951:P3S	ENSP00000284951:P3S	P	-	1	0	SEL1L2	13919174	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.401000	0.34589	0.904000	0.36572	0.585000	0.79938	CCC		0.438	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13971174	G	A	13971174	3	1	61	1	0	0	0	0	1	0	0	0	14048	1203	42	3	2139	3	SEL1L2	20	13971174	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	125028	13971174	49054346	11510	19495										
KIF16B	55614	broad.mit.edu	37	chr20	16493483	16493483	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccctacctgacttcagttCgaaaagaagcttcatcccat	7	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:16493483C>T	ENST00000354981.2	-	5	591	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.R145Q|KIF16B_ENST00000408042.1_Missense_Mutation_p.R145Q	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	145	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.R145Q(3)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GACTTCAGTTCGAAAAGAAGC	0.483																																																3	Substitution - Missense(3)	large_intestine(3)	20											107	93	98					20																	16493483		2203	4300	6503	16441483	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.434G>A	20.37:g.16493483C>T	ENSP00000347076:p.Arg145Gln		16441483	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	C	35	5.593849	0.96602	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	T;T;T	0.74737	-0.87;-0.87;-0.87	5.79	5.79	0.91817	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.77505	0.4140	N	0.13327	0.33	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.978;0.978;0.983;0.99	T	0.81118	-0.1078	10	0.72032	D	0.01	.	18.2217	0.89904	0.0:1.0:0.0:0.0	.	145;145;145;145	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	Q	145	ENSP00000347076:R145Q;ENSP00000347995:R145Q;ENSP00000384164:R145Q	ENSP00000347076:R145Q	R	-	2	0	KIF16B	16441483	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	7.482000	0.81143	2.739000	0.93911	0.655000	0.94253	CGA		0.483	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		T	16493483	C	T	16493483	3	4	61	1	0	0	0	0	1	0	0	0	8299	884	31	1	3607	1	KIF16B	20	16493483	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2522309	16493483	46532037	11511	19496										
KIF16B	55614	broad.mit.edu	37	chr20	16506742	16506742	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaatatcatataccatttCttgtgaaacgtaatctgggc	7	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:16506742C>A	ENST00000354981.2	-	3	383	c.226G>T	c.(226-228)Gaa>Taa	p.E76*	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Nonsense_Mutation_p.E76*|KIF16B_ENST00000408042.1_Nonsense_Mutation_p.E76*	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	76	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.E76*(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TATACCATTTCTTGTGAAACG	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											112	115	114					20																	16506742		2203	4300	6503	16454742	SO:0001587	stop_gained	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.226G>T	20.37:g.16506742C>A	ENSP00000347076:p.Glu76*		16454742	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Nonsense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	C	32	5.193130	0.94960	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	16.3705	0.83355	0.0:1.0:0.0:0.0	.	.	.	.	X	76	.	ENSP00000347076:E76X	E	-	1	0	KIF16B	16454742	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	5.383000	0.66219	2.584000	0.87258	0.557000	0.71058	GAA		0.338	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16506742	C	A	16506742	4	1	61	1	0	0	0	0	0	1	0	0	8299	922	32	2	3823	2	KIF16B	20	16506742	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13259	16506742	46518778	11512	19497										
PCSK2	5126	broad.mit.edu	37	chr20	17445972	17445972	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgcttcctgtatccagcCtgggtctgacctggcgggac	12	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17445972C>A	ENST00000262545.2	+	11	1519	c.1204C>A	c.(1204-1206)Ctg>Atg	p.L402M	PCSK2_ENST00000377899.1_Splice_Site_p.L383M|PCSK2_ENST00000536609.1_Splice_Site_p.L367M|PCSK2_ENST00000459871.1_3'UTR	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	402	Peptidase S8.				cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.L402M(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	TGTATCCAGCCTGGGTCTGAC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	20											61	47	52					20																	17445972		2203	4300	6503	17393972	SO:0001630	splice_region_variant	5126			AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1203-1C>A	20.37:g.17445972C>A			17393972	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	37	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471733	0.43942	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.42131	0.98;0.98;0.98	5.61	1.13	0.20643	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.264406	0.37623	N	0.002016	T	0.21921	0.0528	N	0.16656	0.425	0.33324	D	0.567652	B;B;B	0.11235	0.002;0.004;0.0	B;B;B	0.16722	0.016;0.01;0.005	T	0.07966	-1.0745	10	0.62326	D	0.03	-6.6611	3.3222	0.07054	0.1294:0.4733:0.2516:0.1457	.	367;383;402	B4DFQ3;B1ANH9;P16519	.;.;NEC2_HUMAN	M	383;402;367	ENSP00000367131:L383M;ENSP00000262545:L402M;ENSP00000437458:L367M	ENSP00000262545:L402M	L	+	1	2	PCSK2	17393972	0.990000	0.36364	0.822000	0.32727	0.984000	0.73092	0.831000	0.27476	0.285000	0.22329	0.555000	0.69702	CTG		0.562	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	Missense_Mutation	A	17445972	C	A	17445972	5	1	61	1	0	0	0	0	0	0	1	0	11632	695	24	2	1246	2	PCSK2	20	17445972	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	939230	17445972	45579548	11513	19498										
BFSP1	631	broad.mit.edu	37	chr20	17474974	17474974	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcaggtatagatggttcCtctgcaccgggtgtgaccat	13	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17474974C>A	ENST00000377873.3	-	8	1782	c.1743G>T	c.(1741-1743)gaG>gaT	p.E581D	BFSP1_ENST00000377868.2_Missense_Mutation_p.E456D|BFSP1_ENST00000536626.1_Missense_Mutation_p.E442D|BFSP1_ENST00000544874.1_Missense_Mutation_p.E442D	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	581	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.E581D(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						TAGATGGTTCCTCTGCACCGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	20											122	121	122					20																	17474974		2203	4300	6503	17422974	SO:0001583	missense	631			Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"Intermediate filaments type VI, eye lens intermediate filaments"	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1743G>T	20.37:g.17474974C>A	ENSP00000367104:p.Glu581Asp		17422974	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Missense_Mutation	SNP	ENST00000377873.3	37	CCDS13126.1	.	.	.	.	.	.	.	.	.	.	C	8.864	0.947714	0.18356	.	.	ENSG00000125864	ENST00000377873;ENST00000377868;ENST00000536626;ENST00000544874	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	4.76	-0.239	0.13050	.	0.761961	0.12979	N	0.423466	T	0.30103	0.0754	L	0.41824	1.3	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.25257	-1.0137	10	0.11182	T	0.66	-9.9217	5.4762	0.16697	0.4522:0.3711:0.0:0.1767	.	456;581	Q12934-2;Q12934	.;BFSP1_HUMAN	D	581;456;442;442	ENSP00000367104:E581D;ENSP00000367099:E456D;ENSP00000442522:E442D;ENSP00000439870:E442D	ENSP00000367099:E456D	E	-	3	2	BFSP1	17422974	0.000000	0.05858	0.396000	0.26296	0.260000	0.26232	0.261000	0.18442	0.051000	0.15978	0.655000	0.94253	GAG		0.592	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195		A	17474974	C	A	17474974	3	1	61	1	0	0	0	0	1	0	0	0	1416	680	24	2	258	2	BFSP1	20	17474974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29002	17474974	45550546	11514	19499										
BFSP1	631	broad.mit.edu	37	chr20	17505516	17505516	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttaagccgttcaagcatttCttttagcaggagttgacatt	9	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17505516C>A	ENST00000377873.3	-	2	454	c.415G>T	c.(415-417)Gaa>Taa	p.E139*	BFSP1_ENST00000377868.2_Nonsense_Mutation_p.E14*|BFSP1_ENST00000473415.1_5'UTR|BFSP1_ENST00000536626.1_5'UTR|BFSP1_ENST00000544874.1_5'UTR	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	139	Coil 1B.|Rod.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.E139*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						TCAAGCATTTCTTTTAGCAGG	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											239	186	204					20																	17505516		2203	4300	6503	17453516	SO:0001587	stop_gained	631			Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"Intermediate filaments type VI, eye lens intermediate filaments"	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.415G>T	20.37:g.17505516C>A	ENSP00000367104:p.Glu139*		17453516	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Nonsense_Mutation	SNP	ENST00000377873.3	37	CCDS13126.1	.	.	.	.	.	.	.	.	.	.	C	37	6.065802	0.97251	.	.	ENSG00000125864	ENST00000377873;ENST00000377868	.	.	.	5.21	5.21	0.72293	.	0.394331	0.29868	N	0.010991	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-5.6219	15.8484	0.78907	0.0:1.0:0.0:0.0	.	.	.	.	X	139;14	.	ENSP00000367099:E14X	E	-	1	0	BFSP1	17453516	1.000000	0.71417	0.981000	0.43875	0.991000	0.79684	2.539000	0.45718	2.595000	0.87683	0.557000	0.71058	GAA		0.418	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195		A	17505516	C	A	17505516	4	1	61	1	0	0	0	0	0	1	0	0	1416	922	32	2	1610	2	BFSP1	20	17505516	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30542	17505516	45520004	11515	19500										
DSTN	11034	broad.mit.edu	37	chr20	17581440	17581440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttttatgacatgaaagttCgtaaatgctccacaccagaa	6	8	0	3	rs138670114		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17581440C>T	ENST00000246069.7	+	2	407	c.61C>T	c.(61-63)Cgt>Tgt	p.R21C	DSTN_ENST00000474024.1_Missense_Mutation_p.R4C	NM_006870.3	NP_006861.1	P60981	DEST_HUMAN	destrin (actin depolymerizing factor)	21	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|actin filament severing (GO:0051014)|actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|positive regulation of actin filament depolymerization (GO:0030836)	actin cytoskeleton (GO:0015629)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)		p.R21C(2)		endometrium(1)|large_intestine(5)|lung(8)|skin(1)	15						CATGAAAGTTCGTAAATGCTC	0.358																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	20											38	38	38					20																	17581440		2203	4296	6499	17529440	SO:0001583	missense	11034			S65738	CCDS13127.1, CCDS46580.1	20p12.1	2010-08-20			ENSG00000125868	ENSG00000125868			15750	protein-coding gene	gene with protein product		609114				8399167, 2156828	Standard	NM_006870		Approved	ADF, ACTDP	uc002wpr.3	P60981	OTTHUMG00000031947	ENST00000246069.7:c.61C>T	20.37:g.17581440C>T	ENSP00000246069:p.Arg21Cys		17529440	B2R6N2|B4DYA6|P18282|Q5W166|Q6IAW2	Missense_Mutation	SNP	ENST00000246069.7	37	CCDS13127.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747540	0.30955	.	.	ENSG00000125868	ENST00000246069;ENST00000543261	T;T	0.32753	1.44;1.44	5.65	0.0598	0.14334	Actin-binding, cofilin/tropomyosin type (2);	0.167420	0.50627	D	0.000107	T	0.24812	0.0602	L	0.46614	1.455	0.48341	D	0.999637	B	0.15141	0.012	B	0.19666	0.026	T	0.06356	-1.0831	10	0.54805	T	0.06	-0.2453	9.4785	0.38887	0.4798:0.4556:0.0:0.0646	.	21	P60981	DEST_HUMAN	C	21;4	ENSP00000246069:R21C;ENSP00000444808:R4C	ENSP00000246069:R21C	R	+	1	0	DSTN	17529440	1.000000	0.71417	0.993000	0.49108	0.783000	0.44284	1.890000	0.39728	-0.192000	0.10432	-0.309000	0.09137	CGT		0.358	DSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078131.6	NM_001011546		T	17581440	C	T	17581440	3	4	61	1	0	0	0	0	1	0	0	0	4795	884	31	1	67	1	DSTN	20	17581440	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75924	17581440	45444080	11516	19501										
C20orf72	27131	broad.mit.edu	37	chr20	17950834	17950834	+	5'Flank	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatccagagagaagtgataAaccaaatgcaagtgatcctt	8	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17950834A>C	ENST00000377768.3	-	0	0				SNX5_ENST00000486039.1_5'Flank|MGME1_ENST00000377710.5_Missense_Mutation_p.K111T|SNX5_ENST00000481323.1_5'Flank|MGME1_ENST00000377709.1_Intron|SNX5_ENST00000377759.4_5'Flank|MGME1_ENST00000377704.4_Missense_Mutation_p.K111T|MGME1_ENST00000467391.1_3'UTR|SNX5_ENST00000606602.1_5'Flank|SNX5_ENST00000606557.1_5'Flank	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)	p.K111T(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						AGAAGTGATAAACCAAATGCA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	20											76	80	79					20																	17950834		2203	4300	6503	17898834	SO:0001631	upstream_gene_variant	92667			AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953		20.37:g.17950834A>C	Exception_encountered		17898834	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	A	1.789	-0.480107	0.04383	.	.	ENSG00000125871	ENST00000377710;ENST00000377704	T;T	0.47528	0.9;0.84	5.6	-8.29	0.01009	.	2.378200	0.01173	N	0.006919	T	0.33760	0.0874	L	0.53249	1.67	0.09310	N	1	B	0.26318	0.146	B	0.19148	0.024	T	0.10177	-1.0641	10	0.23302	T	0.38	0.2299	3.7189	0.08449	0.1126:0.3661:0.3168:0.2044	.	111	Q9BQP7	CT072_HUMAN	T	111	ENSP00000366939:K111T;ENSP00000366933:K111T	ENSP00000366933:K111T	K	+	2	0	C20orf72	17898834	0.000000	0.05858	0.000000	0.03702	0.435000	0.31806	-0.416000	0.07097	-1.208000	0.02634	0.459000	0.35465	AAA		0.463	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			C	17950834	A	C	17950834	1	2	61	0	1	0	0	0	0	0	0	0	2124	14	1	4		4	C20orf72	20	17950834	5'Flank	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	369394	17950834	45074686	11517	19502										
C20orf72	92667	broad.mit.edu	37	chr20	17970589	17970589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttcttcctaggttcaatGtggcttaattgtggtggcct	11	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:17970589G>A	ENST00000377710.5	+	5	1160	c.872G>A	c.(871-873)tGt>tAt	p.C291Y	MGME1_ENST00000377709.1_Missense_Mutation_p.C211Y|MGME1_ENST00000377704.4_Missense_Mutation_p.M173I|MGME1_ENST00000467391.1_3'UTR	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1									p.C291Y(1)									TAGGTTCAATGTGGCTTAATT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	20											135	127	130					20																	17970589		2203	4300	6503	17918589	SO:0001583	missense	92667				CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"chromosome 20 open reading frame 72"	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.872G>A	20.37:g.17970589G>A	ENSP00000366939:p.Cys291Tyr		17918589		Missense_Mutation	SNP	ENST00000377710.5	37	CCDS13131.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.69|12.69	2.014806|2.014806	0.35511|0.35511	.|.	.|.	ENSG00000125871|ENSG00000125871	ENST00000377710;ENST00000377709|ENST00000377704	T;T|T	0.43688|0.45668	0.94;0.98|0.89	6.04|6.04	4.09|4.09	0.47781|0.47781	.|.	0.130549|.	0.64402|.	D|.	0.000001|.	T|T	0.45617|0.45617	0.1351|0.1351	L|L	0.59912|0.59912	1.85|1.85	0.25091|0.25091	N|N	0.990858|0.990858	D|.	0.71674|.	0.998|.	D|.	0.71184|.	0.972|.	T|T	0.28459|0.28459	-1.0043|-1.0043	10|7	0.36615|0.24483	T|T	0.2|0.36	-6.9004|-6.9004	11.3115|11.3115	0.49366|0.49366	0.0694:0.1275:0.8032:0.0|0.0694:0.1275:0.8032:0.0	.|.	291|.	Q9BQP7|.	CT072_HUMAN|.	Y|I	291;211|173	ENSP00000366939:C291Y;ENSP00000366938:C211Y|ENSP00000366933:M173I	ENSP00000366938:C211Y|ENSP00000366933:M173I	C|M	+|+	2|3	0|0	C20orf72|C20orf72	17918589|17918589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.903000|0.903000	0.53119|0.53119	3.787000|3.787000	0.55439|0.55439	0.880000|0.880000	0.35969|0.35969	0.563000|0.563000	0.77884|0.77884	TGT|ATG		0.468	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865		A	17970589	G	A	17970589	3	1	61	1	0	0	0	0	1	0	0	0	2124	1377	48	3	886	3	C20orf72	20	17970589	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	19755	17970589	45054931	11518	19503										
OVOL2	58495	broad.mit.edu	37	chr20	18005407	18005407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgcccggatgggcactgTtcacgtgcaggtacaggtcc	14	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:18005407T>C	ENST00000278780.6	-	4	943	c.701A>G	c.(700-702)aAc>aGc	p.N234S	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	234					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)	p.N234S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						ATGGGCACTGTTCACGTGCAG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20											87	79	82					20																	18005407		2203	4300	6503	17953407	SO:0001583	missense	58495			AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"Zinc fingers, C2H2-type"	15804	protein-coding gene	gene with protein product			"zinc finger protein 339", "ovo-like 2 (Drosophila)"	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.701A>G	20.37:g.18005407T>C	ENSP00000278780:p.Asn234Ser		17953407	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Missense_Mutation	SNP	ENST00000278780.6	37	CCDS13132.1	.	.	.	.	.	.	.	.	.	.	T	7.371	0.626824	0.14257	.	.	ENSG00000125850	ENST00000278780	T	0.50277	0.75	5.25	4.15	0.48705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.291252	0.38436	N	0.001694	T	0.21841	0.0526	N	0.03608	-0.345	0.09310	N	1	B	0.18461	0.028	B	0.21360	0.034	T	0.07712	-1.0758	10	0.35671	T	0.21	-41.6472	6.4377	0.21833	0.0:0.1864:0.0:0.8136	.	234	Q9BRP0	OVOL2_HUMAN	S	234	ENSP00000278780:N234S	ENSP00000278780:N234S	N	-	2	0	OVOL2	17953407	0.084000	0.21492	1.000000	0.80357	0.170000	0.22686	0.852000	0.27764	1.966000	0.57179	0.460000	0.39030	AAC		0.577	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220		C	18005407	T	C	18005407	3	2	61	1	0	0	0	0	1	0	0	0	11358	1725	60	4	130	4	OVOL2	20	18005407	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	34818	18005407	45020113	11519	19504										
CSRP2BP	57325	broad.mit.edu	37	chr20	18143396	18143396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagctcggagactgaaacGcaaactgattgtcagacaag	12	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:18143396G>A	ENST00000435364.3	+	6	1819	c.1478G>A	c.(1477-1479)cGc>cAc	p.R493H	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.R492H|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.R365H	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	493					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)	p.R493H(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGACTGAAACGCAAACTGATT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	20											121	97	105					20																	18143396		2203	4300	6503	18091396	SO:0001583	missense	57325			AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1478G>A	20.37:g.18143396G>A	ENSP00000392318:p.Arg493His		18091396	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	G	32	5.186845	0.94923	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.27402	1.67;1.67;1.67;1.68	6.03	6.03	0.97812	.	0.063402	0.64402	D	0.000003	T	0.58177	0.2104	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.71414	0.973;0.908	T	0.57382	-0.7821	10	0.87932	D	0	-26.6549	20.5568	0.99304	0.0:0.0:1.0:0.0	.	365;493	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	H	493;492;493;365	ENSP00000278816:R493H;ENSP00000366909:R492H;ENSP00000392318:R493H;ENSP00000425909:R365H	ENSP00000278816:R493H	R	+	2	0	CSRP2BP	18091396	1.000000	0.71417	0.972000	0.41901	0.992000	0.81027	9.060000	0.93907	2.861000	0.98227	0.655000	0.94253	CGC		0.473	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		A	18143396	G	A	18143396	3	1	61	1	0	0	0	0	1	0	0	0	3974	1087	38	1	1500	1	CSRP2BP	20	18143396	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	137989	18143396	44882124	11520	19505										
C20orf12	55184	broad.mit.edu	37	chr20	18396009	18396009	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagaaggacgcctcccagaGattccagcgaccacatctgt	10	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:18396009G>T	ENST00000358866.6	-	10	1061	c.1039C>A	c.(1039-1041)Ctc>Atc	p.L347I	DZANK1_ENST00000262547.5_Missense_Mutation_p.L347I|DZANK1_ENST00000329494.5_Missense_Mutation_p.L349I|DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000357236.4_Missense_Mutation_p.L233I			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	347							zinc ion binding (GO:0008270)	p.L347I(2)		NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GCCTCCCAGAGATTCCAGCGA	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	20											84	95	92					20																	18396009		1924	4122	6046	18344009	SO:0001583	missense	55184			AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1039C>A	20.37:g.18396009G>T	ENSP00000351734:p.Leu347Ile		18344009	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	G	6.040	0.375747	0.11409	.	.	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000357236	T;T;T;T	0.63417	0.13;-0.04;0.64;0.11	5.71	2.63	0.31362	.	0.881954	0.10286	N	0.692908	T	0.46521	0.1397	N	0.26042	0.785	0.09310	N	1	P;P;B	0.38767	0.551;0.646;0.421	B;B;B	0.37144	0.242;0.161;0.052	T	0.16719	-1.0393	10	0.20519	T	0.43	0.0499	9.8774	0.41211	0.0715:0.2657:0.6628:0.0	.	366;233;347	B7Z631;Q9NVP4-4;Q9NVP4	.;.;DZAN1_HUMAN	I	174;347;349;173;233	ENSP00000366857:L174I;ENSP00000262547:L347I;ENSP00000328866:L349I;ENSP00000349774:L233I	ENSP00000262547:L347I	L	-	1	0	C20orf12	18344009	0.944000	0.32072	0.001000	0.08648	0.182000	0.23217	1.568000	0.36418	0.726000	0.32339	0.467000	0.42956	CTC		0.552	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		T	18396009	G	T	18396009	3	4	61	1	0	0	0	0	1	0	0	0	2091	942	33	2	1263	2	C20orf12	20	18396009	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	252613	18396009	44629511	11521	19506										
DTD1	92675	broad.mit.edu	37	chr20	18608841	18608841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaccatagagctggaatcGccagctcccggcactgctac	11	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:18608841G>A	ENST00000377452.3	+	4	621	c.441G>A	c.(439-441)tcG>tcA	p.S147S	DTD1_ENST00000494921.1_3'UTR	NM_080820.4	NP_543010.3	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1	147					D-amino acid catabolic process (GO:0019478)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)	p.S147S(1)		large_intestine(4)|lung(1)|ovary(2)	7						AGCTGGAATCGCCAGCTCCCG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	20											99	88	91					20																	18608841		2203	4300	6503	18556841	SO:0001819	synonymous_variant	92675			AF332356	CCDS13138.1	20p11.23	2012-09-25	2012-09-25	2007-02-23	ENSG00000125821	ENSG00000125821			16219	protein-coding gene	gene with protein product		610996	"chromosome 20 open reading frame 88", "D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae)"	C20orf88, HARS2			Standard	NM_080820		Approved	DUEB, MGC119131, MGC41905, bA379J5.3, bA555E18.1, pqn-68	uc002wrf.4	Q8TEA8	OTTHUMG00000031980	ENST00000377452.3:c.441G>A	20.37:g.18608841G>A			18556841	A8K5X5|D3DW37|Q496D1|Q5W184|Q8WXU8|Q9BW67|Q9H464|Q9H474	Silent	SNP	ENST00000377452.3	37	CCDS13138.1																																																																																				0.542	DTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078189.3	NM_080820		A	18608841	G	A	18608841	2	1	61	1	0	0	0	0	0	0	0	1	4797	1074	38	1		1	DTD1	20	18608841	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	212832	18608841	44416679	11522	19507										
SLC24A3	57419	broad.mit.edu	37	chr20	19665962	19665962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaggaggaagaggaggaCgaggatgatgatgaaggacc	19	3	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:19665962C>T	ENST00000328041.6	+	12	1478	c.1281C>T	c.(1279-1281)gaC>gaT	p.D427D		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	427	Poly-Glu.				ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.D427D(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						aagaggaggacgaggatgatg	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	20											166	142	150					20																	19665962		2203	4300	6503	19613962	SO:0001819	synonymous_variant	57419			AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1281C>T	20.37:g.19665962C>T			19613962	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	37	CCDS13140.1																																																																																				0.512	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689		T	19665962	C	T	19665962	2	4	61	1	0	0	0	0	0	0	0	1	14504	535	19	1		1	SLC24A3	20	19665962	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1057121	19665962	43359558	11523	19508										
RIN2	54453	broad.mit.edu	37	chr20	19955749	19955749	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcccatccctccaccccgGctgaagaagcaggcttcttt	7	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:19955749G>A	ENST00000255006.6	+	8	1376	c.1227G>A	c.(1225-1227)cgG>cgA	p.R409R	RIN2_ENST00000440354.2_Intron|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	360					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)	p.R360R(1)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CTCCACCCCGGCTGAAGAAGC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	20											73	78	77					20																	19955749		1938	4131	6069	19903749	SO:0001819	synonymous_variant	54453			AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1227G>A	20.37:g.19955749G>A			19903749	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																				0.607	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			A	19955749	G	A	19955749	2	1	61	1	0	0	0	0	0	0	0	1	13409	1190	42	3		3	RIN2	20	19955749	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	289787	19955749	43069771	11524	19509										
CRNKL1	51340	broad.mit.edu	37	chr20	20018118	20018118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccttttcttcacagtttCgcatggttttgttagcttct	6	10	3	0	rs375673644		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:20018118C>T	ENST00000377340.2	-	14	2259	c.2228G>A	c.(2227-2229)cGa>cAa	p.R743Q	CRNKL1_ENST00000377327.4_Missense_Mutation_p.R731Q|CRNKL1_ENST00000521379.1_5'UTR|CRNKL1_ENST00000536226.1_Missense_Mutation_p.R582Q	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	743					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R743Q(1)		breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TTCACAGTTTCGCATGGTTTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	GLN/ARG	0,4406		0,0,2203	190	186	187		2228	5	1	20		187	1,8599	1.2+/-3.3	0,1,4299	no	missense	CRNKL1	NM_016652.4	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	743/849	20018118	1,13005	2203	4300	6503	19966118	SO:0001583	missense	51340			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.2228G>A	20.37:g.20018118C>T	ENSP00000366557:p.Arg743Gln		19966118	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.584891	0.65992	0.0	1.16E-4	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.57907	0.37;0.37;0.37	5.02	5.02	0.67125	.	0.051632	0.85682	D	0.000000	T	0.47673	0.1458	L	0.49778	1.585	0.50467	D	0.999876	B	0.33135	0.399	B	0.22880	0.042	T	0.53373	-0.8448	10	0.62326	D	0.03	-10.4844	18.5163	0.90936	0.0:1.0:0.0:0.0	.	743	Q9BZJ0	CRNL1_HUMAN	Q	731;743;582	ENSP00000366544:R731Q;ENSP00000366557:R743Q;ENSP00000440733:R582Q	ENSP00000366544:R731Q	R	-	2	0	CRNKL1	19966118	1.000000	0.71417	0.995000	0.50966	0.901000	0.52897	4.618000	0.61211	2.596000	0.87737	0.484000	0.47621	CGA		0.383	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			T	20018118	C	T	20018118	3	4	61	1	0	0	0	0	1	0	0	0	3897	884	31	1	326	1	CRNKL1	20	20018118	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62369	20018118	43007402	11525	19510										
C20orf26	26074	broad.mit.edu	37	chr20	20278871	20278871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaatgggacttacttccGaattcatattaacaagtata	6	6	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:20278871G>A	ENST00000245957.5	+	25	3339	c.3263G>A	c.(3262-3264)cGa>cAa	p.R1088Q	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1088								p.R1088Q(3)|p.R1088P(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		ACTTACTTCCGAATTCATATT	0.458																																																4	Substitution - Missense(4)	large_intestine(3)|lung(1)	20											78	75	76					20																	20278871		2203	4300	6503	20226871	SO:0001583	missense	26074																														ENST00000245957.5:c.3263G>A	20.37:g.20278871G>A	ENSP00000245957:p.Arg1088Gln		20226871	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678484	0.88542	.	.	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.47528	0.84	5.27	5.27	0.74061	.	0.300219	0.31922	N	0.006857	T	0.61211	0.2329	M	0.72894	2.215	0.80722	D	1	D	0.69078	0.997	P	0.51701	0.677	T	0.65784	-0.6084	10	0.62326	D	0.03	.	19.2438	0.93893	0.0:0.0:1.0:0.0	.	1088	Q8NHU2	CT026_HUMAN	Q	1028;1054;1088	ENSP00000245957:R1088Q	ENSP00000245957:R1088Q	R	+	2	0	C20orf26	20226871	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	6.069000	0.71209	2.628000	0.89032	0.655000	0.94253	CGA		0.458	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			A	20278871	G	A	20278871	3	1	61	1	0	0	0	0	1	0	0	0	2112	1058	37	1	3389	1	C20orf26	20	20278871	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	260753	20278871	42746649	11526	19511										
RALGAPA2	57186	broad.mit.edu	37	chr20	20475785	20475785	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtttcttcgttatcgcgatGaagaacatgtgattcttcat	9	7	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:20475785G>T	ENST00000202677.7	-	36	5350	c.5343C>A	c.(5341-5343)ttC>ttA	p.F1781L		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1781	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.F1781L(2)		endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						TTATCGCGATGAAGAACATGT	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	20											145	139	141					20																	20475785		1893	4122	6015	20423785	SO:0001583	missense	57186			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.5343C>A	20.37:g.20475785G>T	ENSP00000202677:p.Phe1781Leu		20423785	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.00|14.00	2.404398|2.404398	0.42613|0.42613	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000417022;ENST00000202677|ENST00000430436;ENST00000427175	D;D|.	0.94931|.	-3.56;-3.56|.	5.29|5.29	-2.15|-2.15	0.07102|0.07102	Rap/ran-GAP (2);|.	0.103686|.	0.64402|.	D|.	0.000002|.	T|.	0.44993|.	0.1320|.	N|N	0.21373|0.21373	0.66|0.66	0.38733|0.38733	D|D	0.953718|0.953718	B;D;P|.	0.76494|.	0.046;0.999;0.869|.	B;D;P|.	0.80764|.	0.208;0.994;0.707|.	T|.	0.33777|.	-0.9855|.	10|.	0.44086|.	T|.	0.13|.	.|.	12.1617|12.1617	0.54107|0.54107	0.4598:0.0:0.5401:0.0|0.4598:0.0:0.5401:0.0	.|.	1619;1781;1781|.	A8MSM5;Q2PPJ7-2;Q2PPJ7|.	.;.;RGPA2_HUMAN|.	L|X	211;1781|1598;192	ENSP00000408332:F211L;ENSP00000202677:F1781L|.	ENSP00000202677:F1781L|.	F|S	-|-	3|2	2|0	RALGAPA2|RALGAPA2	20423785|20423785	1.000000|1.000000	0.71417|0.71417	0.653000|0.653000	0.29593|0.29593	0.932000|0.932000	0.56968|0.56968	1.535000|1.535000	0.36061|0.36061	-0.317000|-0.317000	0.08677|0.08677	-0.471000|-0.471000	0.05019|0.05019	TTC|TCA		0.398	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20475785	G	T	20475785	3	4	61	1	0	0	0	0	1	0	0	0	13051	1281	45	2	294	2	RALGAPA2	20	20475785	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	196914	20475785	42549735	11527	19512										
RALGAPA2	57186	broad.mit.edu	37	chr20	20484032	20484032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catctgagtctgacggcattCgagtggaaacatggaaaatc	11	8	2	2	rs200369501		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:20484032C>T	ENST00000202677.7	-	35	5178	c.5171G>A	c.(5170-5172)cGa>cAa	p.R1724Q		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1724	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.R1724Q(2)		endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						TGACGGCATTCGAGTGGAAAC	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	20						C	GLN/ARG	0,3944		0,0,1972	91	91	91		5171	5.8	1	20		91	2,8300		0,2,4149	yes	missense	RALGAPA2	NM_020343.3	43	0,2,6121	TT,TC,CC		0.0241,0.0,0.0163	probably-damaging	1724/1874	20484032	2,12244	1972	4151	6123	20432032	SO:0001583	missense	57186			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.5171G>A	20.37:g.20484032C>T	ENSP00000202677:p.Arg1724Gln		20432032	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.872882|5.872882	0.97049|0.97049	0.0|0.0	2.41E-4|2.41E-4	ENSG00000188559|ENSG00000188559	ENST00000430436;ENST00000427175|ENST00000417022;ENST00000202677	.|D;D	.|0.95069	.|-3.6;-3.6	5.85|5.85	5.85|5.85	0.93711|0.93711	.|Rap/ran-GAP (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97021|0.97021	0.9027|0.9027	M|M	0.69358|0.69358	2.11|2.11	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.997;0.998;1.0	D|D	0.96843|0.96843	0.9619|0.9619	5|10	.|0.62326	.|D	.|0.03	.|.	20.1731|20.1731	0.98165|0.98165	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1562;1724;1724	.|A8MSM5;Q2PPJ7-2;Q2PPJ7	.|.;.;RGPA2_HUMAN	K|Q	1541;135|154;1724	.|ENSP00000408332:R154Q;ENSP00000202677:R1724Q	.|ENSP00000202677:R1724Q	E|R	-|-	1|2	0|0	RALGAPA2|RALGAPA2	20432032|20432032	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.764000|7.764000	0.85297|0.85297	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.542	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20484032	C	T	20484032	3	4	61	1	0	0	0	0	1	0	0	0	13051	884	31	1	470	1	RALGAPA2	20	20484032	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8247	20484032	42541488	11528	19513										
RALGAPA2	57186	broad.mit.edu	37	chr20	20585835	20585835	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atacctttgcctcgttgcttCttttccttttgttcacttaa	4	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:20585835C>A	ENST00000202677.7	-	15	2029	c.2022G>T	c.(2020-2022)aaG>aaT	p.K674N	RALGAPA2_ENST00000495793.1_5'UTR	NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	674					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.K674N(2)		endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						CTCGTTGCTTCTTTTCCTTTT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	20											85	80	81					20																	20585835		1892	4121	6013	20533835	SO:0001583	missense	57186			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.2022G>T	20.37:g.20585835C>A	ENSP00000202677:p.Lys674Asn		20533835	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.05|19.05	3.751092|3.751092	0.69533|0.69533	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	D|.	0.96856|.	-4.15|.	5.28|5.28	4.33|4.33	0.51752|0.51752	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74007|0.74007	0.3660|0.3660	M|M	0.85041|0.85041	2.73|2.73	0.45295|0.45295	D|D	0.998297|0.998297	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.81914|.	0.995;0.995|.	T|T	0.75932|0.75932	-0.3143|-0.3143	10|5	0.54805|.	T|.	0.06|.	.|.	8.1127|8.1127	0.30924|0.30924	0.0:0.8147:0.0:0.1853|0.0:0.8147:0.0:0.1853	.|.	512;674|.	A8MSM5;Q2PPJ7|.	.;RGPA2_HUMAN|.	N|I	674|491	ENSP00000202677:K674N|.	ENSP00000202677:K674N|.	K|R	-|-	3|2	2|0	RALGAPA2|RALGAPA2	20533835|20533835	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	1.951000|1.951000	0.40333|0.40333	2.474000|2.474000	0.83562|0.83562	0.460000|0.460000	0.39030|0.39030	AAG|AGA		0.428	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		A	20585835	C	A	20585835	3	1	61	1	0	0	0	0	1	0	0	0	13051	912	32	2	3699	2	RALGAPA2	20	20585835	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101803	20585835	42439685	11529	19514										
PLK1S1	101929591	broad.mit.edu	37	chr20	21142892	21142892	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtaacacacgtcatggcaaGagtaatttatctgaaggcaa	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:21142892G>T	ENST00000591761.1	-	0	5142				RP5-872K7.7_ENST00000425746.2_RNA|PLK1S1_ENST00000457464.1_RNA																							GTCATGGCAAGAGTAATTTAT	0.423																																																0			20											157	155	156					20																	21142892		1916	4124	6040	21090892			55857																															20.37:g.21142892G>T			21090892		Missense_Mutation	SNP	ENST00000591761.1	37																																																																																					0.423	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			T	21142892	G	T	21142892	1	4	61	0	1	0	0	0	0	0	0	0	12126	933	33	2		2	PLK1S1	20	21142892	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	557057	21142892	41882628	11530	19515										
PLK1S1	101929591	broad.mit.edu	37	chr20	21186155	21186155	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaacaccagactcagacGtaccgaggcacaggtgggtc	12	12	1	2	rs368781277		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:21186155G>A	ENST00000591761.1	-	0	231				PLK1S1_ENST00000457464.1_RNA|RP4-777D9.2_ENST00000443753.1_RNA|RP4-777D9.2_ENST00000433213.2_RNA																							AGACTCAGACGTACCGAGGCA	0.398																																																0			20						G	ILE/VAL,ILE/VAL,ILE/VAL	0,3760		0,0,1880	62	58	59		1069,979,1378	-1.1	0	20		59	1,8239		0,1,4119	no	missense,missense,missense	PLK1S1	NM_001163022.1,NM_001163023.1,NM_018474.4	29,29,29	0,1,5999	AA,AG,GG		0.0121,0.0,0.0083	benign,benign,benign	357/571,327/541,460/674	21186155	1,11999	1880	4120	6000	21134155			55857																															20.37:g.21186155G>A			21134155		Missense_Mutation	SNP	ENST00000591761.1	37																																																																																					0.398	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			A	21186155	G	A	21186155	1	1	61	0	1	0	0	0	0	0	0	0	12126	1145	40	1		1	PLK1S1	20	21186155	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43263	21186155	41839365	11531	19516										
XRN2	22803	broad.mit.edu	37	chr20	21314218	21314218	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtcttccttgtgcagaaGgagagtttatcttccttcgg	10	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:21314218G>T	ENST00000377191.3	+	10	990	c.895G>T	c.(895-897)Gga>Tga	p.G299*	XRN2_ENST00000430571.2_Nonsense_Mutation_p.G223*|XRN2_ENST00000539513.1_Nonsense_Mutation_p.G245*	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	299					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G299*(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						TTGTGCAGAAGGAGAGTTTAT	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											241	223	229					20																	21314218		2203	4300	6503	21262218	SO:0001587	stop_gained	22803			AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.895G>T	20.37:g.21314218G>T	ENSP00000366396:p.Gly299*		21262218	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Nonsense_Mutation	SNP	ENST00000377191.3	37	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	G	38	7.090699	0.98055	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	.	.	.	5.73	5.73	0.89815	.	0.099149	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-20.4747	14.3506	0.66699	0.0:0.2637:0.7363:0.0	.	.	.	.	X	299;223;245	.	ENSP00000366396:G299X	G	+	1	0	XRN2	21262218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.385000	0.66231	2.709000	0.92574	0.655000	0.94253	GGA		0.408	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		T	21314218	G	T	21314218	4	4	61	1	0	0	0	0	0	1	0	0	17500	1001	35	2	933	2	XRN2	20	21314218	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128063	21314218	41711302	11532	19517										
XRN2	22803	broad.mit.edu	37	chr20	21367627	21367627	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtatccacccagacgagatGatcgtggagggagacaggta	15	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:21367627G>T	ENST00000377191.3	+	29	2865	c.2770G>T	c.(2770-2772)Gat>Tat	p.D924Y	XRN2_ENST00000430571.2_Missense_Mutation_p.D848Y|XRN2_ENST00000539513.1_Missense_Mutation_p.D870Y	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	924					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D924Y(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						CAGACGAGATGATCGTGGAGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	20											94	87	89					20																	21367627		2203	4300	6503	21315627	SO:0001583	missense	22803			AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2770G>T	20.37:g.21367627G>T	ENSP00000366396:p.Asp924Tyr		21315627	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	37	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427261	0.62733	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.32023	1.47;1.47;1.47	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	N	0.19112	0.55	0.47949	D	0.999559	D	0.76494	0.999	D	0.77557	0.99	T	0.32719	-0.9896	10	0.52906	T	0.07	-25.8238	18.5737	0.91147	0.0:0.0:1.0:0.0	.	924	Q9H0D6	XRN2_HUMAN	Y	924;848;870	ENSP00000366396:D924Y;ENSP00000413548:D848Y;ENSP00000441113:D870Y	ENSP00000366396:D924Y	D	+	1	0	XRN2	21315627	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.899000	0.63245	2.824000	0.97209	0.655000	0.94253	GAT		0.498	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		T	21367627	G	T	21367627	3	4	61	1	0	0	0	0	1	0	0	0	17500	1290	45	2	2884	2	XRN2	20	21367627	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	53409	21367627	41657893	11533	19518										
CD93	22918	broad.mit.edu	37	chr20	23065795	23065795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtcctggcattcatccacGtccacacagtccagctgact	8	15	1	1	rs368417861		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:23065795G>A	ENST00000246006.4	-	1	1182	c.1035C>T	c.(1033-1035)gaC>gaT	p.D345D		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	345	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)	p.D345D(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					ATTCATCCACGTCCACACAGT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G		0,4406		0,0,2203	34	37	36		1035	-9.8	0	20		36	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CD93	NM_012072.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		345/653	23065795	1,13005	2203	4300	6503	23013795	SO:0001819	synonymous_variant	22918			U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.1035C>T	20.37:g.23065795G>A			23013795	O00274	Silent	SNP	ENST00000246006.4	37	CCDS13149.1																																																																																				0.652	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		A	23065795	G	A	23065795	2	1	61	1	0	0	0	0	0	0	0	1	3053	1136	40	1		1	CD93	20	23065795	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1698168	23065795	39959725	11534	19519										
CSTL1	128817	broad.mit.edu	37	chr20	23424576	23424576	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgattctcggcagctgacGacgggagtggagtatatagt	14	7	1	2	rs529625349		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:23424576G>A	ENST00000246020.2	+	2	245	c.225G>A	c.(223-225)acG>acA	p.T75T	CSTL1_ENST00000347397.1_Silent_p.T75T			Q9H114	CST1L_HUMAN	cystatin-like 1	75						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.T75T(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					GGCAGCTGACGACGGGAGTGG	0.522													G|||	1	0.000199681	0	0	5008	,	,		18945	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	20											100	85	90					20																	23424576		2203	4300	6503	23372576	SO:0001819	synonymous_variant	128817			AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.225G>A	20.37:g.23424576G>A			23372576	Q17RA8|Q64FF7	Silent	SNP	ENST00000246020.2	37	CCDS13153.1																																																																																				0.522	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1			A	23424576	G	A	23424576	2	1	61	1	0	0	0	0	0	0	0	1	3993	1045	37	1		1	CSTL1	20	23424576	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	358781	23424576	39600944	11535	19520										
CST9L	128821	broad.mit.edu	37	chr20	23548861	23548861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaacctgctccttccagGaattcaagatgtgccccagt	7	15	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:23548861G>T	ENST00000376979.3	-	1	525	c.227C>A	c.(226-228)tCc>tAc	p.S76Y		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	76						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.S76Y(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CTCCTTCCAGGAATTCAAGAT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	20											143	115	125					20																	23548861		2203	4300	6503	23496861	SO:0001583	missense	128821				CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.227C>A	20.37:g.23548861G>T	ENSP00000366178:p.Ser76Tyr		23496861	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	37	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	G	7.587	0.669942	0.14776	.	.	ENSG00000101435	ENST00000376979	T	0.12569	2.67	1.75	-0.401	0.12407	Proteinase inhibitor I25, cystatin (2);	0.284905	0.19012	N	0.125047	T	0.21590	0.0520	M	0.80982	2.52	0.09310	N	1	P	0.47762	0.9	P	0.50352	0.638	T	0.08554	-1.0716	10	0.72032	D	0.01	.	4.0703	0.09879	0.4548:0.0:0.5452:0.0	.	76	Q9H4G1	CST9L_HUMAN	Y	76	ENSP00000366178:S76Y	ENSP00000366178:S76Y	S	-	2	0	CST9L	23496861	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.798000	0.04565	-0.110000	0.12022	-0.657000	0.03884	TCC		0.547	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		T	23548861	G	T	23548861	3	4	61	1	0	0	0	0	1	0	0	0	3986	1174	41	2	228	2	CST9L	20	23548861	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	124285	23548861	39476659	11536	19521										
CST3	1471	broad.mit.edu	37	chr20	23616002	23616002	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtagttcaccccagctacGatctacacatgtgaaagagc	8	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:23616002G>A	ENST00000398411.1	-	2	328	c.246C>T	c.(244-246)atC>atT	p.I82I	CST3_ENST00000398409.1_Silent_p.I82I|CST3_ENST00000376925.3_Silent_p.I82I			P01034	CYTC_HUMAN	cystatin C	82					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell activation (GO:0001775)|cellular response to hydrogen peroxide (GO:0070301)|circadian sleep/wake cycle, REM sleep (GO:0042747)|defense response (GO:0006952)|embryo implantation (GO:0007566)|extracellular fibril organization (GO:0043206)|eye development (GO:0001654)|negative regulation of blood vessel remodeling (GO:0060313)|negative regulation of cell death (GO:0060548)|negative regulation of collagen catabolic process (GO:0010711)|negative regulation of elastin catabolic process (GO:0060311)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|regulation of programmed cell death (GO:0043067)|regulation of tissue remodeling (GO:0034103)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|salivary gland development (GO:0007431)|Sertoli cell development (GO:0060009)	basement membrane (GO:0005604)|cell projection (GO:0042995)|contractile fiber (GO:0043292)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)	p.I82I(1)		large_intestine(2)|lung(1)|ovary(1)	4	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CCCCAGCTACGATCTACACAT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	20											110	84	93					20																	23616002		2203	4300	6503	23564002	SO:0001819	synonymous_variant	1471				CCDS13158.1	20p11.2	2008-04-15	2008-04-15		ENSG00000101439	ENSG00000101439			2475	protein-coding gene	gene with protein product		604312	"cystatin C (amyloid angiopathy and cerebral hemorrhage)"			8486384	Standard	NM_000099		Approved		uc002wtn.1	P01034	OTTHUMG00000032080	ENST00000398411.1:c.246C>T	20.37:g.23616002G>A			23564002	B2R5J9|D3DW42|Q6FGW9	Silent	SNP	ENST00000398411.1	37	CCDS13158.1																																																																																				0.567	CST3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256831.1	NM_000099		A	23616002	G	A	23616002	2	1	61	1	0	0	0	0	0	0	0	1	3979	1048	37	1		1	CST3	20	23616002	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67141	23616002	39409518	11537	19522										
VSX1	30813	broad.mit.edu	37	chr20	25056898	25056898	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagtgggacctgtgggtctCatgtggctcccaccttccct	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25056898C>A	ENST00000376709.4	-	5	1360	c.1097G>T	c.(1096-1098)tGa>tTa	p.*366L	VSX1_ENST00000451258.1_Intron|VSX1_ENST00000424574.1_Intron|VSX1_ENST00000444511.2_Intron|VSX1_ENST00000429762.3_Intron	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	0					neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.*366L(1)		central_nervous_system(1)|large_intestine(3)|lung(2)	6						CTGTGGGTCTCATGTGGCTCC	0.537																																																1	Nonstop extension(1)	large_intestine(1)	20											44	49	47					20																	25056898		2203	4300	6503	25004898	SO:0001578	stop_lost	30813			AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"Homeoboxes / PRD class"	12723	protein-coding gene	gene with protein product		605020	"posterior polymorphous corneal dystrophy", "visual system homeobox 1 homolog, CHX10-like (zebrafish)"	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.1097G>T	20.37:g.25056898C>A			25004898	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Nonstop_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	.	.	.	.	.	.	.	.	.	.	C	9.296	1.051802	0.19827	.	.	ENSG00000100987	ENST00000376709	.	.	.	4.35	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.20403	N	0.99991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3872	0.32508	0.0:0.8882:0.0:0.1118	.	.	.	.	L	366	.	.	X	-	2	2	VSX1	25004898	0.022000	0.18835	0.109000	0.21407	0.020000	0.10135	0.184000	0.16939	2.254000	0.74563	0.655000	0.94253	TGA		0.537	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3			A	25056898	C	A	25056898	4	1	61	1	0	0	0	0	0	0	0	0	17271	837	29	2	4	2	VSX1	20	25056898	Nonstop_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1440896	25056898	37968622	11538	19523										
ENTPD6	955	broad.mit.edu	37	chr20	25201875	25201875	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctctgtttcagctaaggaTggaaaggagttggtcagccc	12	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25201875T>C	ENST00000376652.4	+	11	1114	c.951T>C	c.(949-951)gaT>gaC	p.D317D	ENTPD6_ENST00000360031.2_Silent_p.D316D|ENTPD6_ENST00000354989.5_Silent_p.D300D|ENTPD6_ENST00000433259.2_Intron			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	317					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)	p.D317D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						CAGCTAAGGATGGAAAGGAGT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	20											159	141	147					20																	25201875		2203	4300	6503	25149875	SO:0001819	synonymous_variant	955			AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.951T>C	20.37:g.25201875T>C			25149875	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Silent	SNP	ENST00000376652.4	37	CCDS13170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.004|8.004	0.756135|0.756135	0.15846|0.15846	.|.	.|.	ENSG00000197586|ENSG00000197586	ENST00000433417|ENST00000376666	.|.	.|.	.|.	5.6|5.6	-2.56|-2.56	0.06268|0.06268	.|.	.|.	.|.	.|.	.|.	T|T	0.17662|0.17662	0.0424|0.0424	.|.	.|.	.|.	0.19775|0.19775	N|N	0.99995|0.99995	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.26643|0.26643	-1.0097|-1.0097	4|4	.|.	.|.	.|.	-9.7144|-9.7144	0.2069|0.2069	0.00152|0.00152	0.2481:0.23:0.2559:0.266|0.2481:0.23:0.2559:0.266	.|.	.|.	.|.	.|.	T|R	238|141	.|.	.|.	M|W	+|+	2|1	0|0	ENTPD6|ENTPD6	25149875|25149875	0.999000|0.999000	0.42202|0.42202	0.088000|0.088000	0.20740|0.20740	0.935000|0.935000	0.57460|0.57460	0.429000|0.429000	0.21412|0.21412	-0.092000|-0.092000	0.12417|0.12417	0.454000|0.454000	0.30748|0.30748	ATG|TGG		0.517	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			C	25201875	T	C	25201875	2	2	61	1	0	0	0	0	0	0	0	1	5156	1461	51	4		4	ENTPD6	20	25201875	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	144977	25201875	37823645	11539	19524										
NINL	22981	broad.mit.edu	37	chr20	25443036	25443036	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctgctgctgcccactgcGaaccacctcctccaggctct	7	20	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25443036G>A	ENST00000278886.6	-	20	3638	c.3565C>T	c.(3565-3567)Cgc>Tgc	p.R1189C	NINL_ENST00000422516.1_Missense_Mutation_p.R840C	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1189					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.R1189C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TGCCCACTGCGAACCACCTCC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											97	74	82					20																	25443036		2203	4300	6503	25391036	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3565C>T	20.37:g.25443036G>A	ENSP00000278886:p.Arg1189Cys		25391036	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	9.646|9.646	1.140305|1.140305	0.21205|0.21205	.|.	.|.	ENSG00000101004|ENSG00000101004	ENST00000278886;ENST00000422516|ENST00000336104	T;T|.	0.34667|.	3.38;1.35|.	4.89|4.89	-7.0|-7.0	0.01599|0.01599	.|.	2.186810|.	0.01520|.	N|.	0.018313|.	T|T	0.10937|0.10937	0.0267|0.0267	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.23583|0.23583	-1.0184|-1.0184	10|5	0.41790|.	T|.	0.15|.	1.2992|1.2992	4.5416|4.5416	0.12059|0.12059	0.4528:0.0914:0.3631:0.0926|0.4528:0.0914:0.3631:0.0926	.|.	840;1189|.	Q9Y2I6-2;Q9Y2I6|.	.;NINL_HUMAN|.	C|L	1189;840|141	ENSP00000278886:R1189C;ENSP00000410431:R840C|.	ENSP00000278886:R1189C|.	R|S	-|-	1|2	0|0	NINL|NINL	25391036|25391036	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.398000|-1.398000	0.02509|0.02509	-1.805000|-1.805000	0.01239|0.01239	-2.347000|-2.347000	0.00243|0.00243	CGC|TCG		0.617	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		A	25443036	G	A	25443036	3	1	61	1	0	0	0	0	1	0	0	0	10451	1058	37	1	603	1	NINL	20	25443036	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	241161	25443036	37582484	11540	19525										
NINL	22981	broad.mit.edu	37	chr20	25457525	25457525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctcctcgagggccaacGatacgcacatctgggcgcgc	11	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25457525G>A	ENST00000278886.6	-	17	2475	c.2402C>T	c.(2401-2403)tCg>tTg	p.S801L	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	801					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.S801L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GAGGGCCAACGATACGCACAT	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	20											48	40	43					20																	25457525		2203	4300	6503	25405525	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2402C>T	20.37:g.25457525G>A	ENSP00000278886:p.Ser801Leu		25405525	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	g	9.510	1.105531	0.20632	.	.	ENSG00000101004	ENST00000278886	T	0.34667	1.35	3.48	-0.0352	0.13893	.	2.445680	0.01324	N	0.011021	T	0.18002	0.0432	L	0.27053	0.805	0.09310	N	1	P	0.44260	0.83	B	0.27262	0.078	T	0.19943	-1.0290	10	0.21540	T	0.41	0.6603	2.9605	0.05890	0.2965:0.2398:0.4637:0.0	.	801	Q9Y2I6	NINL_HUMAN	L	801	ENSP00000278886:S801L	ENSP00000278886:S801L	S	-	2	0	NINL	25405525	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.157000	0.10085	0.181000	0.19994	-0.355000	0.07637	TCG		0.677	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		A	25457525	G	A	25457525	3	1	61	1	0	0	0	0	1	0	0	0	10451	1059	37	1	1778	1	NINL	20	25457525	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14489	25457525	37567995	11541	19526										
NINL	22981	broad.mit.edu	37	chr20	25462682	25462682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccggttcttgggcagccGcgcccacaggccttccagct	13	16	1	0	rs142777399		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25462682G>A	ENST00000278886.6	-	14	1805	c.1732C>T	c.(1732-1734)Cgg>Tgg	p.R578W	NINL_ENST00000422516.1_Missense_Mutation_p.R578W	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	578					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.R578W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TTGGGCAGCCGCGCCCACAGG	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	20						G	TRP/ARG	0,4406		0,0,2203	42	46	44		1732	3.8	0	20	dbSNP_134	44	1,8593	1.2+/-3.3	0,1,4296	no	missense	NINL	NM_025176.4	101	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	578/1383	25462682	1,12999	2203	4297	6500	25410682	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.1732C>T	20.37:g.25462682G>A	ENSP00000278886:p.Arg578Trp		25410682	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382077	0.24944	0.0	1.16E-4	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.35048	1.61;1.33	4.73	3.77	0.43336	.	0.801057	0.11241	N	0.584667	T	0.33147	0.0853	L	0.44542	1.39	0.09310	N	1	B;B	0.21381	0.055;0.036	B;B	0.12156	0.007;0.003	T	0.28902	-1.0029	10	0.87932	D	0	-13.6426	12.3268	0.55015	0.0845:0.0:0.9155:0.0	.	578;578	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	W	578	ENSP00000278886:R578W;ENSP00000410431:R578W	ENSP00000278886:R578W	R	-	1	2	NINL	25410682	0.593000	0.26840	0.001000	0.08648	0.242000	0.25591	1.919000	0.40015	1.207000	0.43291	0.555000	0.69702	CGG		0.682	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		A	25462682	G	A	25462682	3	1	61	1	0	0	0	0	1	0	0	0	10451	1086	38	1	2460	1	NINL	20	25462682	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5157	25462682	37562838	11542	19527										
ZNF337	26152	broad.mit.edu	37	chr20	25655992	25655994	+	In_Frame_Del	DEL	GAG	GAG	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtgtgtcctctggtgtgtGaggagatttcccttccagtt							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	GAG	GAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:25655992_25655994delGAG	ENST00000376436.1	-	4	2469_2471	c.1930_1932delCTC	c.(1930-1932)ctcdel	p.L644del	RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA|ZNF337_ENST00000538750.1_In_Frame_Del_p.L612del|RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000252979.5_In_Frame_Del_p.L644del|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L644delL(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TCTGGTGTGTGAGGAGATTTCCC	0.527																																																1	Deletion - In frame(1)	large_intestine(1)	20								0,4264		0,0,2132						1.1	0			87	4,8250		0,4,4123	no	coding	ZNF337	NM_015655.2		0,4,6255	A1A1,A1R,RR		0.0485,0.0,0.032				4,12514				25603994	SO:0001651	inframe_deletion	26152				CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1930_1932delCTC	20.37:g.25655995_25655997delGAG	ENSP00000365619:p.Leu644del		25603992	B4DSM2|Q9Y3Y5	In_Frame_Del	DEL	ENST00000376436.1	37	CCDS13174.1																																																																																				0.527	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			-	25655994	GAG	-	25655992	7	5	61	1	0	1	0	1	0	0	0	0	17892	1277	45	0	327	0	ZNF337	20	25655992	In_Frame_Del	DEL	GAG	TCGA-AG-A002-01A-01W-A00K-09	193310	25655992	37369528	11543	19528										
DEFB116	245930	broad.mit.edu	37	chr20	29891068	29891068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacaagttggagttagagtCgtaatcctccttcacatttt	8	8	1	2	rs181424547		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:29891068C>T	ENST00000400549.1	-	2	255	c.256G>A	c.(256-258)Gac>Aac	p.D86N		NM_001037731.1	NP_001032820.1	Q30KQ4	DB116_HUMAN	defensin, beta 116	86					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.D86N(1)		kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GAGTTAGAGTCGTAATCCTCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	ASN/ASP	0,3716		0,0,1858	286	260	268		256	-2.2	0	20		268	2,8206		0,2,4102	no	missense	DEFB116	NM_001037731.1	23	0,2,5960	TT,TC,CC		0.0244,0.0,0.0168	benign	86/103	29891068	2,11922	1858	4104	5962	29354729	SO:0001583	missense	245930			DQ012020	CCDS42860.1	20q11.21	2008-07-17			ENSG00000215545	ENSG00000215545		"Defensins, beta"	18097	protein-coding gene	gene with protein product	"defensin, beta 16"					11854508, 16033865	Standard	NM_001037731		Approved	DEFB-16	uc010ztm.2	Q30KQ4	OTTHUMG00000159285	ENST00000400549.1:c.256G>A	20.37:g.29891068C>T	ENSP00000383396:p.Asp86Asn		29354729		Missense_Mutation	SNP	ENST00000400549.1	37	CCDS42860.1	.	.	.	.	.	.	.	.	.	.	C	6.071	0.381348	0.11466	0.0	2.44E-4	ENSG00000215545	ENST00000400549	T	0.20200	2.09	3.61	-2.19	0.07015	.	.	.	.	.	T	0.11623	0.0283	N	0.24115	0.695	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.34403	-0.9830	9	0.24483	T	0.36	.	7.9397	0.29950	0.0:0.3474:0.0:0.6526	.	86	Q30KQ4	DB116_HUMAN	N	86	ENSP00000383396:D86N	ENSP00000383396:D86N	D	-	1	0	DEFB116	29354729	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.427000	0.06999	-0.410000	0.07542	0.655000	0.94253	GAC		0.373	DEFB116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354403.1	NM_001037731		T	29891068	C	T	29891068	3	4	61	1	0	0	0	0	1	0	0	0	4415	884	31	1	55	1	DEFB116	20	29891068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4235076	29891068	33134452	11544	19529										
REM1	28954	broad.mit.edu	37	chr20	30070143	30070143	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggcagtgcctatgtcatCgtatactccatcgcagaccg	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30070143C>T	ENST00000201979.2	+	4	770	c.477C>T	c.(475-477)atC>atT	p.I159I		NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	159					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)	p.I159I(1)		kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CCTATGTCATCGTATACTCCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	20											90	82	85					20																	30070143		2203	4300	6503	29533804	SO:0001819	synonymous_variant	28954			AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.477C>T	20.37:g.30070143C>T			29533804	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	37	CCDS13181.1																																																																																				0.597	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		T	30070143	C	T	30070143	2	4	61	1	0	0	0	0	0	0	0	1	13259	874	31	1		1	REM1	20	30070143	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179075	30070143	32955377	11545	19530										
REM1	28954	broad.mit.edu	37	chr20	30070204	30070204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagctccgcatccagctgCggcgcacacatcaggcagac	11	16	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30070204C>T	ENST00000201979.2	+	4	831	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W		NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	180					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)	p.R180W(1)|p.R180R(1)		kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CATCCAGCTGCGGCGCACACA	0.607																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	20											92	81	85					20																	30070204		2203	4300	6503	29533865	SO:0001583	missense	28954			AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.538C>T	20.37:g.30070204C>T	ENSP00000201979:p.Arg180Trp		29533865	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Missense_Mutation	SNP	ENST00000201979.2	37	CCDS13181.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.995929	0.74703	.	.	ENSG00000088320	ENST00000201979	T	0.80566	-1.39	5.01	2.98	0.34508	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89392	0.6702	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89663	0.3878	10	0.87932	D	0	.	11.9775	0.53100	0.4709:0.5291:0.0:0.0	.	180	O75628	REM1_HUMAN	W	180	ENSP00000201979:R180W	ENSP00000201979:R180W	R	+	1	2	REM1	29533865	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.835000	0.39181	0.602000	0.29896	0.563000	0.77884	CGG		0.607	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		T	30070204	C	T	30070204	3	4	61	1	0	0	0	0	1	0	0	0	13259	759	27	1	548	1	REM1	20	30070204	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61	30070204	32955316	11546	19531										
COX4I2	84701	broad.mit.edu	37	chr20	30231305	30231305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcttcttcattggattcGcagctctggtgatttggtgg	11	8	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30231305G>A	ENST00000376075.3	+	4	421	c.346G>A	c.(346-348)Gca>Aca	p.A116T	COX4I2_ENST00000490030.1_Intron	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	116					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)	p.A116T(1)		breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CATTGGATTCGCAGCTCTGGT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	20											204	166	179					20																	30231305		2203	4300	6503	29694966	SO:0001583	missense	84701			AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"Mitochondrial respiratory chain complex / Complex IV"	16232	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit IV-like 2"	607976	"cytochrome c oxidase subunit IV isoform 2"	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.346G>A	20.37:g.30231305G>A	ENSP00000365243:p.Ala116Thr		29694966	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	37	CCDS13187.1	.	.	.	.	.	.	.	.	.	.	G	0.943	-0.708995	0.03230	.	.	ENSG00000131055	ENST00000376075	T	0.53423	0.62	4.97	2.65	0.31530	.	0.060906	0.64402	N	0.000005	T	0.12475	0.0303	N	0.00707	-1.245	0.30199	N	0.798826	B	0.06786	0.001	B	0.04013	0.001	T	0.33979	-0.9847	10	0.02654	T	1	-11.2899	6.7193	0.23321	0.8306:0.0:0.1694:0.0	.	116	Q96KJ9	COX42_HUMAN	T	116	ENSP00000365243:A116T	ENSP00000365243:A116T	A	+	1	0	COX4I2	29694966	0.996000	0.38824	0.985000	0.45067	0.407000	0.30961	3.004000	0.49513	0.385000	0.24970	-0.424000	0.05967	GCA		0.557	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609		A	30231305	G	A	30231305	3	1	61	1	0	0	0	0	1	0	0	0	3776	1087	38	1	356	1	COX4I2	20	30231305	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	161101	30231305	32794215	11547	19532										
TPX2	22974	broad.mit.edu	37	chr20	30347927	30347927	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagggctttttcagggcaaAactcctttgagaaaggctaa	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30347927A>T	ENST00000300403.6	+	4	702	c.174A>T	c.(172-174)aaA>aaT	p.K58N	TPX2_ENST00000340513.4_Missense_Mutation_p.K58N	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	58					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)	p.K58N(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TTCAGGGCAAAACTCCTTTGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	20											127	130	129					20																	30347927		2203	4300	6503	29811588	SO:0001583	missense	22974			AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.174A>T	20.37:g.30347927A>T	ENSP00000300403:p.Lys58Asn		29811588	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.839181	0.51057	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.32988	1.43	4.95	0.345	0.16011	Aurora-A binding (1);	0.362480	0.26875	N	0.022049	T	0.30166	0.0756	N	0.24115	0.695	0.09310	N	1	D;P	0.62365	0.991;0.684	P;B	0.62089	0.898;0.419	T	0.10894	-1.0610	10	0.36615	T	0.2	-8.2154	6.9812	0.24704	0.5708:0.0:0.4292:0.0	.	58;58	Q96RR5;Q9ULW0	.;TPX2_HUMAN	N	58	ENSP00000341145:K58N	ENSP00000300403:K58N	K	+	3	2	TPX2	29811588	0.993000	0.37304	0.019000	0.16419	0.948000	0.59901	0.674000	0.25218	0.143000	0.18926	0.482000	0.46254	AAA		0.413	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30347927	A	T	30347927	3	4	61	1	0	0	0	0	1	0	0	0	16472	11	1	5	180	5	TPX2	20	30347927	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116622	30347927	32677593	11548	19533										
TTLL9	164395	broad.mit.edu	37	chr20	30458989	30458989	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgccattaggtgccccaaGaaattacaggtgaatgttgg	11	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30458989G>T	ENST00000375938.4	+	2	313	c.60G>T	c.(58-60)aaG>aaT	p.K20N	DUSP15_ENST00000486996.1_5'Flank|TTLL9_ENST00000375921.2_5'UTR|DUSP15_ENST00000278979.3_5'Flank|TTLL9_ENST00000535842.1_Missense_Mutation_p.K20N|DUSP15_ENST00000398084.2_5'Flank|TTLL9_ENST00000310998.4_5'UTR|DUSP15_ENST00000493115.1_5'Flank|DUSP15_ENST00000375966.4_5'Flank|DUSP15_ENST00000398083.1_5'Flank|DUSP15_ENST00000339738.5_5'Flank			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	20					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.K20N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GGTGCCCCAAGAAATTACAGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	20											139	140	139					20																	30458989		1879	4118	5997	29922650	SO:0001583	missense	164395			AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.60G>T	20.37:g.30458989G>T	ENSP00000365105:p.Lys20Asn		29922650	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.233546	0.22626	.	.	ENSG00000131044	ENST00000375938;ENST00000535842	T;T	0.03745	3.82;3.82	3.68	1.69	0.24217	.	.	.	.	.	T	0.01835	0.0058	N	0.08118	0	0.09310	N	0.999997	B	0.06786	0.001	B	0.04013	0.001	T	0.49194	-0.8965	9	0.19147	T	0.46	.	4.1416	0.10196	0.124:0.0:0.6237:0.2523	.	20	Q3SXZ7	TTLL9_HUMAN	N	20	ENSP00000365105:K20N;ENSP00000442515:K20N	ENSP00000365105:K20N	K	+	3	2	TTLL9	29922650	0.003000	0.15002	0.001000	0.08648	0.016000	0.09150	0.556000	0.23438	0.512000	0.28257	0.491000	0.48974	AAG		0.532	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		T	30458989	G	T	30458989	3	4	61	1	0	0	0	0	1	0	0	0	16774	933	33	2	62	2	TTLL9	20	30458989	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111062	30458989	32566531	11549	19534										
TTLL9	164395	broad.mit.edu	37	chr20	30522647	30522647	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagtgacaagcactgcttCgagctgtacggctatgacat	10	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30522647C>T	ENST00000375938.4	+	12	1213	c.960C>T	c.(958-960)ttC>ttT	p.F320F	TTLL9_ENST00000375934.4_3'UTR|TTLL9_ENST00000375921.2_Intron|TTLL9_ENST00000375922.4_Silent_p.F262F|TTLL9_ENST00000535842.1_Silent_p.F320F|TTLL9_ENST00000310998.4_Silent_p.F285F			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	320	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.F309F(1)|p.F320F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			AGCACTGCTTCGAGCTGTACG	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	20											119	119	119					20																	30522647		2091	4218	6309	29986308	SO:0001819	synonymous_variant	164395			AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.960C>T	20.37:g.30522647C>T			29986308	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Silent	SNP	ENST00000375938.4	37	CCDS42863.1																																																																																				0.547	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		T	30522647	C	T	30522647	2	4	61	1	0	0	0	0	0	0	0	1	16774	883	31	1		1	TTLL9	20	30522647	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63658	30522647	32502873	11550	19535										
TTLL9	164395	broad.mit.edu	37	chr20	30527047	30527047	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacctgtcgggaatgggaaaCtttgtgaccaacacacatct	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30527047C>A	ENST00000375938.4	+	14	1474	c.1221C>A	c.(1219-1221)aaC>aaA	p.N407K	TTLL9_ENST00000375934.4_3'UTR|TTLL9_ENST00000375921.2_3'UTR|TTLL9_ENST00000375922.4_Intron|TTLL9_ENST00000535842.1_Missense_Mutation_p.N407K			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	407					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.N407K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GAATGGGAAACTTTGTGACCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											66	74	72					20																	30527047		2003	4176	6179	29990708	SO:0001583	missense	164395			AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.1221C>A	20.37:g.30527047C>A	ENSP00000365105:p.Asn407Lys		29990708	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185107	0.38609	.	.	ENSG00000131044	ENST00000375938;ENST00000535842	T;T	0.03580	3.88;3.88	5.88	4.94	0.65067	.	1.024030	0.07700	N	0.940258	T	0.02494	0.0076	N	0.17474	0.49	0.80722	D	1	B;P	0.40000	0.062;0.698	B;B	0.29862	0.021;0.108	T	0.50964	-0.8765	10	0.07482	T	0.82	.	12.2334	0.54500	0.0:0.9209:0.0:0.0791	.	407;309	Q3SXZ7;B1ANK8	TTLL9_HUMAN;.	K	407	ENSP00000365105:N407K;ENSP00000442515:N407K	ENSP00000365105:N407K	N	+	3	2	TTLL9	29990708	0.994000	0.37717	0.997000	0.53966	0.849000	0.48306	1.306000	0.33505	1.502000	0.48669	0.561000	0.74099	AAC		0.587	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		A	30527047	C	A	30527047	3	1	61	1	0	0	0	0	1	0	0	0	16774	564	20	2	1271	2	TTLL9	20	30527047	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4400	30527047	32498473	11551	19536										
TM9SF4	9777	broad.mit.edu	37	chr20	30745656	30745656	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgggatctccctgcccctCgtctacttgggctactactt	8	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:30745656C>T	ENST00000398022.2	+	14	1624	c.1389C>T	c.(1387-1389)ctC>ctT	p.L463L	TM9SF4_ENST00000217315.5_Silent_p.L446L	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	463						integral component of membrane (GO:0016021)		p.L446L(1)		central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CCCTGCCCCTCGTCTACTTGG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	20											177	164	168					20																	30745656		2203	4300	6503	30209317	SO:0001819	synonymous_variant	9777			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.1389C>T	20.37:g.30745656C>T			30209317	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	37	CCDS13196.2																																																																																				0.607	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30745656	C	T	30745656	2	4	61	1	0	0	0	0	0	0	0	1	16019	871	31	1		1	TM9SF4	20	30745656	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	218609	30745656	32279864	11552	19537										
ASXL1	171023	broad.mit.edu	37	chr20	31016150	31016150	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctcttgatgaaacatcttcGaacgcatcctgttctacaga	6	11	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31016150G>A	ENST00000375687.4	+	6	820	c.396G>A	c.(394-396)tcG>tcA	p.S132S	ASXL1_ENST00000306058.5_Silent_p.S127S|ASXL1_ENST00000470145.1_3'UTR|ASXL1_ENST00000542461.1_3'UTR	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	132					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.S132S(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						AAACATCTTCGAACGCATCCT	0.488			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	2	Substitution - coding silent(2)	large_intestine(2)	20											221	203	209					20																	31016150		2203	4300	6503	30479811	SO:0001819	synonymous_variant	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.396G>A	20.37:g.31016150G>A			30479811	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																				0.488	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31016150	G	A	31016150	2	1	61	1	0	0	0	0	0	0	0	1	1067	1045	37	1		1	ASXL1	20	31016150	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	270494	31016150	32009370	11553	19538										
DNMT3B	1789	broad.mit.edu	37	chr20	31368226	31368226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgcagcgaccagtcctccGactcgcccccaatcctggag	9	19	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31368226G>A	ENST00000328111.2	+	2	418	c.97G>A	c.(97-99)Gac>Aac	p.D33N	DNMT3B_ENST00000348286.2_Missense_Mutation_p.D33N|DNMT3B_ENST00000375623.4_Missense_Mutation_p.D33N|DNMT3B_ENST00000201963.3_Missense_Mutation_p.D45N|DNMT3B_ENST00000353855.2_Missense_Mutation_p.D33N|DNMT3B_ENST00000456297.2_Missense_Mutation_p.D33N|DNMT3B_ENST00000443239.3_Missense_Mutation_p.D33N|DNMT3B_ENST00000344505.4_Missense_Mutation_p.D33N	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	33	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.D33N(1)|p.D45N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCAGTCCTCCGACTCGCCCCC	0.642																																																2	Substitution - Missense(2)	large_intestine(2)	20											33	35	34					20																	31368226		2203	4300	6503	30831887	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.97G>A	20.37:g.31368226G>A	ENSP00000328547:p.Asp33Asn		30831887	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.139254	0.37728	.	.	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000375623;ENST00000201963	D;D;D;D;D;D;T;D	0.97976	-4.61;-4.61;-4.57;-4.64;-4.51;-4.46;-0.71;-4.62	4.39	2.21	0.28008	.	0.598323	0.16958	N	0.192607	D	0.93344	0.7878	N	0.24115	0.695	0.09310	N	0.999999	P;P;P;P;P;P	0.50710	0.509;0.776;0.733;0.848;0.683;0.938	B;B;B;B;B;B	0.43018	0.043;0.1;0.232;0.169;0.052;0.405	D	0.87804	0.2627	10	0.30078	T	0.28	-23.2374	8.3391	0.32232	0.0:0.1589:0.6577:0.1833	.	33;33;45;33;33;33	E9PBF2;E7EN63;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;DNM3B_HUMAN	N	33;119;33;33;33;33;33;33;45	ENSP00000328547:D33N;ENSP00000313397:D33N;ENSP00000337764:D33N;ENSP00000403169:D33N;ENSP00000412305:D33N;ENSP00000345105:D33N;ENSP00000364774:D33N;ENSP00000201963:D45N	ENSP00000201963:D45N	D	+	1	0	DNMT3B	30831887	0.979000	0.34478	0.160000	0.22671	0.524000	0.34500	2.227000	0.42972	1.159000	0.42565	0.462000	0.41574	GAC		0.642	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31368226	G	A	31368226	3	1	61	1	0	0	0	0	1	0	0	0	4688	1058	37	1	139	1	DNMT3B	20	31368226	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	352076	31368226	31657294	11554	19539										
DNMT3B	1789	broad.mit.edu	37	chr20	31379489	31379489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caataagctcgtctcctatcGaaaagccatgtaccatgctc	6	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31379489G>A	ENST00000328111.2	+	8	1217	c.896G>A	c.(895-897)cGa>cAa	p.R299Q	DNMT3B_ENST00000348286.2_Missense_Mutation_p.R299Q|DNMT3B_ENST00000375623.4_Missense_Mutation_p.R257Q|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R311Q|DNMT3B_ENST00000353855.2_Missense_Mutation_p.R299Q|DNMT3B_ENST00000456297.2_Missense_Mutation_p.R223Q|DNMT3B_ENST00000443239.3_Missense_Mutation_p.R257Q|DNMT3B_ENST00000344505.4_Missense_Mutation_p.R299Q	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	299					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.R299Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTCTCCTATCGAAAAGCCATG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	20											128	99	109					20																	31379489		2203	4300	6503	30843150	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.896G>A	20.37:g.31379489G>A	ENSP00000328547:p.Arg299Gln		30843150	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	35	5.528178	0.96446	.	.	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000375623;ENST00000201963	T;T;T;T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.82549	0.5061	M	0.70275	2.135	0.53688	D	0.999973	D;D;D;D;D;D	0.89917	0.997;0.994;0.994;0.999;0.994;1.0	P;P;B;P;B;P	0.61397	0.585;0.468;0.406;0.763;0.406;0.888	T	0.82579	-0.0387	10	0.54805	T	0.06	-35.0289	19.1516	0.93491	0.0:0.0:1.0:0.0	.	223;257;311;299;299;299	E9PBF2;E7EN63;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;DNM3B_HUMAN	Q	299;385;299;299;257;223;299;257;311	ENSP00000328547:R299Q;ENSP00000313397:R299Q;ENSP00000337764:R299Q;ENSP00000403169:R257Q;ENSP00000412305:R223Q;ENSP00000345105:R299Q;ENSP00000364774:R257Q;ENSP00000201963:R311Q	ENSP00000201963:R311Q	R	+	2	0	DNMT3B	30843150	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	5.228000	0.65310	2.773000	0.95371	0.655000	0.94253	CGA		0.502	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31379489	G	A	31379489	3	1	61	1	0	0	0	0	1	0	0	0	4688	1058	37	1	962	1	DNMT3B	20	31379489	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11263	31379489	31646031	11555	19540										
DNMT3B	1789	broad.mit.edu	37	chr20	31384645	31384645	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgtgtccttccaccctctCtttgagggggggctctgtca	11	15	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31384645C>A	ENST00000328111.2	+	13	1668	c.1347C>A	c.(1345-1347)ctC>ctA	p.L449L	DNMT3B_ENST00000348286.2_Silent_p.L429L|DNMT3B_ENST00000375623.4_Missense_Mutation_p.L332I|DNMT3B_ENST00000201963.3_Silent_p.L441L|DNMT3B_ENST00000353855.2_Silent_p.L429L|DNMT3B_ENST00000456297.2_Silent_p.L353L|DNMT3B_ENST00000443239.3_Silent_p.L387L|DNMT3B_ENST00000344505.4_Silent_p.L429L	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	449	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.L449L(1)|p.L441L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCACCCTCTCTTTGAGGGGG	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	20											87	89	89					20																	31384645		2203	4300	6503	30848306	SO:0001819	synonymous_variant	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1347C>A	20.37:g.31384645C>A			30848306	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465496	0.43839	.	.	ENSG00000088305	ENST00000375623	T	0.68181	-0.31	4.88	-0.787	0.10943	.	0.000000	0.64402	D	0.000001	T	0.67078	0.2855	.	.	.	0.23936	N	0.996414	.	.	.	.	.	.	T	0.64521	-0.6388	7	0.87932	D	0	-25.7854	11.4838	0.50342	0.0:0.3794:0.4849:0.1357	.	.	.	.	I	332	ENSP00000364774:L332I	ENSP00000364774:L332I	L	+	1	0	DNMT3B	30848306	0.416000	0.25424	0.968000	0.41197	0.921000	0.55340	-0.496000	0.06436	-0.450000	0.07107	-0.795000	0.03280	CTT		0.557	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31384645	C	A	31384645	2	1	61	1	0	0	0	0	0	0	0	1	4688	900	32	2		2	DNMT3B	20	31384645	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5156	31384645	31640875	11556	19541										
BPIL3	128859	broad.mit.edu	37	chr20	31619469	31619469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccatgctgcggatcctgTgcctggcactctgcagcctg	13	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31619469T>C	ENST00000349552.1	+	1	16	c.16T>C	c.(16-18)Tgc>Cgc	p.C6R		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	6						extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.C6R(1)									GCGGATCCTGTGCCTGGCACT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	20											36	28	31					20																	31619469		2203	4300	6503	31083130	SO:0001583	missense	128859			AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"BPI fold containing"	16504	protein-coding gene	gene with protein product		614110	"bactericidal/permeability-increasing protein-like 3"	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.16T>C	20.37:g.31619469T>C	ENSP00000344929:p.Cys6Arg		31083130		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	T	7.590	0.670595	0.14776	.	.	ENSG00000167104	ENST00000349552	T	0.01252	5.1	4.85	2.5	0.30297	.	0.703302	0.12534	N	0.460493	T	0.01661	0.0053	L	0.44542	1.39	0.30590	N	0.761597	P	0.37015	0.578	B	0.36186	0.219	T	0.39742	-0.9599	10	0.45353	T	0.12	.	5.6857	0.17801	0.1685:0.0:0.1759:0.6557	.	6	Q8NFQ5	BPIB6_HUMAN	R	6	ENSP00000344929:C6R	ENSP00000344929:C6R	C	+	1	0	BPIFB6	31083130	0.639000	0.27234	0.757000	0.31301	0.166000	0.22503	0.221000	0.17680	0.184000	0.20083	-0.429000	0.05907	TGC		0.642	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		C	31619469	T	C	31619469	3	2	61	1	0	0	0	0	1	0	0	0	1496	1696	59	4	18	4	BPIL3	20	31619469	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	234824	31619469	31406051	11557	19542										
C20orf185	359710	broad.mit.edu	37	chr20	31656648	31656648	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaccagcaactcctactgTtcctgcgggtgagggaagct	12	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31656648T>C	ENST00000375494.3	+	10	1018	c.1018T>C	c.(1018-1020)Ttc>Ctc	p.F340L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	340					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.F340L(1)									ACTCCTACTGTTCCTGCGGGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	20											102	74	84					20																	31656648		2203	4300	6503	31120309	SO:0001583	missense	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1018T>C	20.37:g.31656648T>C	ENSP00000364643:p.Phe340Leu		31120309	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	T	5.777	0.327706	0.10956	.	.	ENSG00000186190	ENST00000375494	T	0.08193	3.12	4.25	1.81	0.25067	.	1.057110	0.07501	N	0.907244	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46652	-0.9176	10	0.11794	T	0.64	-1.3124	3.1464	0.06473	0.2075:0.1134:0.0:0.6791	.	340	P59826	BPIB3_HUMAN	L	340	ENSP00000364643:F340L	ENSP00000364643:F340L	F	+	1	0	BPIFB3	31120309	0.001000	0.12720	0.010000	0.14722	0.011000	0.07611	0.694000	0.25512	0.793000	0.33875	-0.326000	0.08463	TTC		0.572	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		C	31656648	T	C	31656648	3	2	61	1	0	0	0	0	1	0	0	0	2103	1725	60	4	1056	4	C20orf185	20	31656648	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	37179	31656648	31368872	11558	19543										
C20orf71	128861	broad.mit.edu	37	chr20	31805421	31805421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccacacaagcagccttggCctggcctggcccaagcccac	9	19	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31805421C>T	ENST00000375454.3	+	1	289	c.79C>T	c.(79-81)Cct>Tct	p.P27S	BPIFA3_ENST00000375452.3_Missense_Mutation_p.P27S|BPIFA3_ENST00000490499.1_3'UTR|RP11-49G10.3_ENST00000419613.1_RNA	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	27						extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.P27S(1)									GCAGCCTTGGCCTGGCCTGGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											96	85	88					20																	31805421		2203	4300	6503	31269082	SO:0001583	missense	128861				CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"BPI fold containing"	16204	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 71"	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.79C>T	20.37:g.31805421C>T	ENSP00000364603:p.Pro27Ser		31269082	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	.	.	.	.	.	.	.	.	.	.	C	0.318	-0.963446	0.02249	.	.	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.32023	1.47;1.69	4.14	-2.22	0.06952	.	0.773311	0.11064	N	0.603622	T	0.14874	0.0359	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.001	T	0.20974	-1.0259	10	0.48119	T	0.1	-9.0E-4	5.2532	0.15532	0.0:0.5144:0.1513:0.3343	.	27;27	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	S	27	ENSP00000364603:P27S;ENSP00000364601:P27S	ENSP00000364601:P27S	P	+	1	0	BPIFA3	31269082	0.498000	0.26075	0.146000	0.22360	0.001000	0.01503	-0.483000	0.06536	-0.291000	0.09012	-1.170000	0.01741	CCT		0.617	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		T	31805421	C	T	31805421	3	4	61	1	0	0	0	0	1	0	0	0	2123	739	26	3	81	3	C20orf71	20	31805421	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	148773	31805421	31220099	11559	19544										
PLUNC	51297	broad.mit.edu	37	chr20	31829239	31829239	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggacagcctcacagggatCttgaataaagtcctgcctga	10	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:31829239C>A	ENST00000354297.4	+	6	701	c.630C>A	c.(628-630)atC>atA	p.I210I	BPIFA1_ENST00000375413.4_Silent_p.I210I|BPIFA1_ENST00000375422.2_Silent_p.I210I	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	210					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.I210I(1)									TCACAGGGATCTTGAATAAAG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	20											209	201	204					20																	31829239		2203	4300	6503	31292900	SO:0001819	synonymous_variant	51297			AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.630C>A	20.37:g.31829239C>A			31292900	A8K9R3|E1P5M9|Q9NZT0	Silent	SNP	ENST00000354297.4	37	CCDS13217.1																																																																																				0.507	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		A	31829239	C	A	31829239	2	1	61	1	0	0	0	0	0	0	0	1	12146	903	32	2		2	PLUNC	20	31829239	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23818	31829239	31196281	11560	19545										
SNTA1	6640	broad.mit.edu	37	chr20	32000579	32000579	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaccatctgccgagcagatCtccagatacctgcaggcaca	9	14	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:32000579C>A	ENST00000217381.2	-	4	982	c.711G>T	c.(709-711)gaG>gaT	p.E237D		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	237	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)	p.E237D(1)		breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						CCGAGCAGATCTCCAGATACC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											33	23	26					20																	32000579		2203	4300	6503	31464240	SO:0001583	missense	6640			U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"pro-TGF-alpha cytoplasmic domain-interacting protein 1", "dystrophin-associated protein A1, 59kDa, acidic component"	601017	"syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.711G>T	20.37:g.32000579C>A	ENSP00000217381:p.Glu237Asp		31464240	A8K7H9|B4DX40|E1P5N1|Q16438	Missense_Mutation	SNP	ENST00000217381.2	37	CCDS13220.1	.	.	.	.	.	.	.	.	.	.	c	24.1	4.493667	0.84962	.	.	ENSG00000101400	ENST00000217381	D	0.81659	-1.52	5.08	5.08	0.68730	Pleckstrin homology domain (2);	0.121922	0.53938	D	0.000044	D	0.88228	0.6380	M	0.74881	2.28	0.80722	D	1	P;B	0.46064	0.872;0.336	D;B	0.64506	0.926;0.135	D	0.89072	0.3470	10	0.72032	D	0.01	-1.3506	12.5685	0.56323	0.0:0.9185:0.0:0.0815	.	237;237	B4DX40;Q13424	.;SNTA1_HUMAN	D	237	ENSP00000217381:E237D	ENSP00000217381:E237D	E	-	3	2	SNTA1	31464240	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	2.053000	0.41326	2.356000	0.79943	0.556000	0.70494	GAG		0.587	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098		A	32000579	C	A	32000579	3	1	61	1	0	0	0	0	1	0	0	0	14908	912	32	2	826	2	SNTA1	20	32000579	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171340	32000579	31024941	11561	19546										
NECAB3	63941	broad.mit.edu	37	chr20	32258514	32258514	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagatgcccatcaatgccgCtgaacagttcctgcagctcc	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:32258514C>A	ENST00000246190.6	-	3	294	c.239G>T	c.(238-240)aGc>aTc	p.S80I	NECAB3_ENST00000375238.4_Missense_Mutation_p.S80I	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	80					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S80I(1)		large_intestine(3)|lung(5)|skin(2)	10						ATCAATGCCGCTGAACAGTTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20											65	68	67					20																	32258514		1967	4157	6124	31722175	SO:0001583	missense	63941			AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	15851	protein-coding gene	gene with protein product	"EF-hand calcium binding protein 3"	612478	"amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.239G>T	20.37:g.32258514C>A	ENSP00000246190:p.Ser80Ile		31722175	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Missense_Mutation	SNP	ENST00000246190.6	37	CCDS42866.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.268607	0.59540	.	.	ENSG00000125967	ENST00000375238;ENST00000246190;ENST00000439478	T;T;T	0.10382	2.88;2.88;2.88	4.81	3.86	0.44501	EF-hand-like domain (1);	0.326534	0.33959	N	0.004388	T	0.22704	0.0548	M	0.62723	1.935	0.38660	D	0.952055	D;P;P	0.58970	0.984;0.715;0.708	P;B;B	0.59056	0.851;0.342;0.419	T	0.02115	-1.1211	10	0.72032	D	0.01	-19.4326	8.6614	0.34095	0.0:0.8203:0.0:0.1797	.	80;80;80	Q96P71-3;Q96P71;Q96P71-2	.;NECA3_HUMAN;.	I	80	ENSP00000364386:S80I;ENSP00000246190:S80I;ENSP00000392064:S80I	ENSP00000246190:S80I	S	-	2	0	NECAB3	31722175	0.629000	0.27146	0.899000	0.35326	0.881000	0.50899	1.052000	0.30429	1.023000	0.39654	0.462000	0.41574	AGC		0.577	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2			A	32258514	C	A	32258514	3	1	61	1	0	0	0	0	1	0	0	0	10337	797	28	2	991	2	NECAB3	20	32258514	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	257935	32258514	30767006	11562	19547										
NCOA6	23054	broad.mit.edu	37	chr20	33328554	33328554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctttctcaagagagcctgTaactttcttacatgccttgg	7	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33328554T>C	ENST00000374796.2	-	12	8076	c.5506A>G	c.(5506-5508)Aca>Gca	p.T1836A	NCOA6_ENST00000359003.2_Missense_Mutation_p.T1836A			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1836	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.T1836A(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						AGAGAGCCTGTAACTTTCTTA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											130	132	131					20																	33328554		2203	4300	6503	32792215	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5506A>G	20.37:g.33328554T>C	ENSP00000363929:p.Thr1836Ala		32792215	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.046979	0.75846	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.27557	1.66;1.66	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.43255	0.1239	L	0.27053	0.805	0.49213	D	0.999761	D	0.69078	0.997	D	0.75020	0.985	T	0.34279	-0.9835	10	0.52906	T	0.07	-7.8358	16.0399	0.80667	0.0:0.0:0.0:1.0	.	1836	Q14686	NCOA6_HUMAN	A	1836	ENSP00000363929:T1836A;ENSP00000351894:T1836A	ENSP00000351894:T1836A	T	-	1	0	NCOA6	32792215	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.330000	0.65899	2.371000	0.80710	0.533000	0.62120	ACA		0.507	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33328554	T	C	33328554	3	2	61	1	0	0	0	0	1	0	0	0	10264	1638	57	4	705	4	NCOA6	20	33328554	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1070040	33328554	29696966	11563	19548										
NCOA6	23054	broad.mit.edu	37	chr20	33328934	33328934	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggcggtacaggagcagaaGaaaattttatgttctgaggt	13	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33328934G>T	ENST00000374796.2	-	12	7696	c.5126C>A	c.(5125-5127)tCt>tAt	p.S1709Y	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1709Y			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1709	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.S1709Y(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						AGGAGCAGAAGAAAATTTTAT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20											110	117	115					20																	33328934		2203	4300	6503	32792595	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5126C>A	20.37:g.33328934G>T	ENSP00000363929:p.Ser1709Tyr		32792595	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560720	0.65538	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.34859	1.34;1.34	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	T	0.40423	0.1116	L	0.27053	0.805	0.49213	D	0.999762	D	0.56521	0.976	P	0.51016	0.656	T	0.30387	-0.9980	10	0.87932	D	0	-10.4838	19.4628	0.94924	0.0:0.0:1.0:0.0	.	1709	Q14686	NCOA6_HUMAN	Y	1709	ENSP00000363929:S1709Y;ENSP00000351894:S1709Y	ENSP00000351894:S1709Y	S	-	2	0	NCOA6	32792595	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	8.415000	0.90241	2.837000	0.97791	0.655000	0.94253	TCT		0.522	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		T	33328934	G	T	33328934	3	4	61	1	0	0	0	0	1	0	0	0	10264	942	33	2	1085	2	NCOA6	20	33328934	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	380	33328934	29696586	11564	19549										
NCOA6	23054	broad.mit.edu	37	chr20	33329436	33329436	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttagggaattagaaggttCtttagaagaagacagatcct	11	4	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33329436C>A	ENST00000374796.2	-	12	7194	c.4624G>T	c.(4624-4626)Gaa>Taa	p.E1542*	NCOA6_ENST00000359003.2_Nonsense_Mutation_p.E1542*			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1542					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.E1542*(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TTAGAAGGTTCTTTAGAAGAA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											136	136	136					20																	33329436		2203	4300	6503	32793097	SO:0001587	stop_gained	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4624G>T	20.37:g.33329436C>A	ENSP00000363929:p.Glu1542*		32793097	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Nonsense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	C	57	27.387461	0.99971	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	.	.	.	5.55	5.55	0.83447	.	0.138727	0.49916	D	0.000135	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-5.578	19.7069	0.96076	0.0:1.0:0.0:0.0	.	.	.	.	X	1542	.	ENSP00000351894:E1542X	E	-	1	0	NCOA6	32793097	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.754000	0.55189	2.894000	0.99253	0.591000	0.81541	GAA		0.453	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33329436	C	A	33329436	4	1	61	1	0	0	0	0	0	1	0	0	10264	922	32	2	1587	2	NCOA6	20	33329436	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	502	33329436	29696084	11565	19550										
NCOA6	23054	broad.mit.edu	37	chr20	33330140	33330140	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccagaattcactaccacaGaatctaatttgtgagtttgt	6	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33330140G>T	ENST00000374796.2	-	12	6490	c.3920C>A	c.(3919-3921)tCt>tAt	p.S1307Y	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1307Y			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1307	NCOA1-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.S1307Y(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CACTACCACAGAATCTAATTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	20											121	125	124					20																	33330140		2203	4300	6503	32793801	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3920C>A	20.37:g.33330140G>T	ENSP00000363929:p.Ser1307Tyr		32793801	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.779968	0.49891	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.30182	1.54;1.54	5.98	5.98	0.97165	.	0.174016	0.40144	N	0.001163	T	0.31482	0.0798	N	0.19112	0.55	0.44736	D	0.997732	D	0.56521	0.976	P	0.51016	0.656	T	0.03651	-1.1016	10	0.66056	D	0.02	-11.4843	15.2611	0.73625	0.0:0.1495:0.8505:0.0	.	1307	Q14686	NCOA6_HUMAN	Y	1307	ENSP00000363929:S1307Y;ENSP00000351894:S1307Y	ENSP00000351894:S1307Y	S	-	2	0	NCOA6	32793801	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	2.653000	0.46691	2.847000	0.97988	0.591000	0.81541	TCT		0.458	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		T	33330140	G	T	33330140	3	4	61	1	0	0	0	0	1	0	0	0	10264	942	33	2	2291	2	NCOA6	20	33330140	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	704	33330140	29695380	11566	19551										
NCOA6	23054	broad.mit.edu	37	chr20	33330703	33330703	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtggcgagctggaaggattCtgcgggctctcctgatagac	15	9	2	2	rs75120685		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33330703C>A	ENST00000374796.2	-	12	5927	c.3357G>T	c.(3355-3357)caG>caT	p.Q1119H	NCOA6_ENST00000359003.2_Missense_Mutation_p.Q1119H			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1119	NCOA1-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1119H(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TGGAAGGATTCTGCGGGCTCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	20											97	96	96					20																	33330703		2203	4300	6503	32794364	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3357G>T	20.37:g.33330703C>A	ENSP00000363929:p.Gln1119His		32794364	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.224142	0.58668	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.26957	1.7;1.7	6.06	5.12	0.69794	.	0.173554	0.41294	D	0.000909	T	0.37404	0.1002	L	0.29908	0.895	0.80722	D	1	D	0.67145	0.996	D	0.64042	0.921	T	0.22103	-1.0226	10	0.66056	D	0.02	-3.5051	15.1122	0.72368	0.0:0.9328:0.0:0.0672	.	1119	Q14686	NCOA6_HUMAN	H	1119	ENSP00000363929:Q1119H;ENSP00000351894:Q1119H	ENSP00000351894:Q1119H	Q	-	3	2	NCOA6	32794364	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	2.346000	0.44027	1.579000	0.49836	0.655000	0.94253	CAG		0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33330703	C	A	33330703	3	1	61	1	0	0	0	0	1	0	0	0	10264	912	32	2	2854	2	NCOA6	20	33330703	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	563	33330703	29694817	11567	19552										
GGT7	2686	broad.mit.edu	37	chr20	33449333	33449333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caattaggtggctctcatttCgtcggatgtcatgtaccagc	10	10	2	0	rs199747158		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33449333C>T	ENST00000336431.5	-	4	634	c.590G>A	c.(589-591)cGa>cAa	p.R197Q		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	197					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.R197Q(1)		NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						GCTCTCATTTCGTCGGATGTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	20						C	GLN/ARG	0,4406		0,0,2203	74	70	71		590	4.8	0.3	20		71	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GGT7	NM_178026.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	197/663	33449333	1,13005	2203	4300	6503	32912994	SO:0001583	missense	2686			AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"Gamma-glutamyltransferases"	4259	protein-coding gene	gene with protein product		612342	"gamma-glutamyltransferase-like 3"	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.590G>A	20.37:g.33449333C>T	ENSP00000338964:p.Arg197Gln		32912994	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	37	CCDS13242.2	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013360	0.35511	0.0	1.16E-4	ENSG00000131067	ENST00000336431	T	0.21543	2.0	5.74	4.81	0.61882	.	0.239802	0.39274	N	0.001408	T	0.11153	0.0272	N	0.20807	0.61	0.21719	N	0.999578	B;B;B	0.19935	0.04;0.016;0.008	B;B;B	0.12837	0.005;0.008;0.005	T	0.30416	-0.9979	10	0.14252	T	0.57	-22.091	6.8106	0.23802	0.0:0.7062:0.0:0.2938	.	197;197;197	Q9UJ14-5;A4FU32;Q9UJ14	.;.;GGT7_HUMAN	Q	197	ENSP00000338964:R197Q	ENSP00000338964:R197Q	R	-	2	0	GGT7	32912994	0.885000	0.30320	0.322000	0.25334	0.987000	0.75469	2.920000	0.48844	1.430000	0.47334	0.655000	0.94253	CGA		0.562	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026		T	33449333	C	T	33449333	3	4	61	1	0	0	0	0	1	0	0	0	6384	884	31	1	1446	1	GGT7	20	33449333	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	118630	33449333	29576187	11568	19553										
ACSS2	55902	broad.mit.edu	37	chr20	33509399	33509399	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacacccatgaaacccggttCtgctgtgagtgatgcttccc	9	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33509399C>A	ENST00000360596.2	+	12	1674	c.1463C>A	c.(1462-1464)tCt>tAt	p.S488Y	ACSS2_ENST00000336325.4_Missense_Mutation_p.S438Y|ACSS2_ENST00000253382.5_Missense_Mutation_p.S501Y|ACSS2_ENST00000476922.1_Intron	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	488					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)	p.S488Y(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AAACCCGGTTCTGCTGTGAGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	20											156	145	149					20																	33509399		2203	4300	6503	32973060	SO:0001583	missense	55902			AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"Acyl-CoA synthetase family"	15814	protein-coding gene	gene with protein product		605832	"acetyl-Coenzyme A synthetase 2 (ADP forming)"	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.1463C>A	20.37:g.33509399C>A	ENSP00000353804:p.Ser488Tyr		32973060	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	37	CCDS13243.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506575	0.85282	.	.	ENSG00000131069	ENST00000336325;ENST00000360596;ENST00000374693;ENST00000542204;ENST00000253382	T;T;T	0.52057	0.68;0.68;0.68	5.42	5.42	0.78866	AMP-dependent synthetase/ligase (1);	0.109014	0.64402	D	0.000003	T	0.75049	0.3797	M	0.90425	3.115	0.80722	D	1	D;D	0.65815	0.995;0.987	D;D	0.67725	0.953;0.926	T	0.79923	-0.1598	10	0.87932	D	0	-17.1668	19.4079	0.94655	0.0:1.0:0.0:0.0	.	501;488	Q5QPH3;Q9NR19	.;ACSA_HUMAN	Y	438;488;486;196;501	ENSP00000337190:S438Y;ENSP00000353804:S488Y;ENSP00000253382:S501Y	ENSP00000253382:S501Y	S	+	2	0	ACSS2	32973060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.536000	0.82023	2.819000	0.97034	0.650000	0.86243	TCT		0.537	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677		A	33509399	C	A	33509399	3	1	61	1	0	0	0	0	1	0	0	0	189	913	32	2	1552	2	ACSS2	20	33509399	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	60066	33509399	29516121	11569	19554										
MYH7B	57644	broad.mit.edu	37	chr20	33577698	33577698	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcaagtaccaggcccacttCgaggtggtccactacgcagg	12	14	0	0	rs369651613		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33577698C>T	ENST00000262873.7	+	18	1961	c.1869C>T	c.(1867-1869)ttC>ttT	p.F623F	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	581	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.F623F(1)		NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			AGGCCCACTTCGAGGTGGTCC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	20						C		1,4295		0,1,2147	44	49	47		1869	-0.3	1	20		47	0,8540		0,0,4270	no	coding-synonymous	MYH7B	NM_020884.3		0,1,6417	TT,TC,CC		0.0,0.0233,0.0078		623/1984	33577698	1,12835	2148	4270	6418	33041359	SO:0001819	synonymous_variant	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1869C>T	20.37:g.33577698C>T			33041359	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																				0.657	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33577698	C	T	33577698	2	4	61	1	0	0	0	0	0	0	0	1	10070	883	31	1		1	MYH7B	20	33577698	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	68299	33577698	29447822	11570	19555										
MYH7B	57644	broad.mit.edu	37	chr20	33578085	33578085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagcgtaagaaggcagcatCgttccagacggtgtcccagc	13	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33578085C>T	ENST00000262873.7	+	20	2167	c.2075C>T	c.(2074-2076)tCg>tTg	p.S692L	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	650	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S692L(1)		NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			AAGGCAGCATCGTTCCAGACG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											93	98	96					20																	33578085		2203	4300	6503	33041746	SO:0001583	missense	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2075C>T	20.37:g.33578085C>T	ENSP00000262873:p.Ser692Leu		33041746	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692504	0.88735	.	.	ENSG00000078814	ENST00000262873	D	0.87650	-2.28	4.39	4.39	0.52855	Myosin head, motor domain (2);	0.000000	0.31922	N	0.006860	D	0.94814	0.8325	M	0.90922	3.16	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95975	0.8973	10	0.87932	D	0	.	17.5203	0.87784	0.0:1.0:0.0:0.0	.	650	A7E2Y1	MYH7B_HUMAN	L	692	ENSP00000262873:S692L	ENSP00000262873:S692L	S	+	2	0	MYH7B	33041746	1.000000	0.71417	0.231000	0.23993	0.882000	0.50991	5.923000	0.70045	2.445000	0.82738	0.511000	0.50034	TCG		0.617	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33578085	C	T	33578085	3	4	61	1	0	0	0	0	1	0	0	0	10070	893	31	1	2153	1	MYH7B	20	33578085	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	387	33578085	29447435	11571	19556										
TRPC4AP	26133	broad.mit.edu	37	chr20	33609059	33609059	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttccagtttgtacatgatCtcatgcataatcttcattga	5	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33609059C>T	ENST00000252015.2	-	9	1241	c.1152G>A	c.(1150-1152)gaG>gaA	p.E384E	TRPC4AP_ENST00000451813.2_Silent_p.E376E|TRPC4AP_ENST00000539834.1_Intron|TRPC4AP_ENST00000432634.2_Silent_p.E345E			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	384	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)	p.E384E(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TGTACATGATCTCATGCATAA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	20											126	101	109					20																	33609059		2203	4300	6503	33072720	SO:0001819	synonymous_variant	26133			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1152G>A	20.37:g.33609059C>T			33072720	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																				0.577	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33609059	C	T	33609059	2	4	61	1	0	0	0	0	0	0	0	1	16621	912	32	3		3	TRPC4AP	20	33609059	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	30974	33609059	29416461	11572	19557										
TRPC4AP	26133	broad.mit.edu	37	chr20	33657149	33657149	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtatttggataagtggtttCttgggtaagtttcctctctt	10	5	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:33657149C>A	ENST00000252015.2	-	3	453	c.364G>T	c.(364-366)Gaa>Taa	p.E122*	TRPC4AP_ENST00000451813.2_Nonsense_Mutation_p.E122*|TRPC4AP_ENST00000432634.2_Intron			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	122	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)	p.E122*(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TAAGTGGTTTCTTGGGTAAGT	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											129	132	131					20																	33657149		2203	4300	6503	33120810	SO:0001587	stop_gained	26133			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.364G>T	20.37:g.33657149C>A	ENSP00000252015:p.Glu122*		33120810	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Nonsense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	C	35	5.488151	0.96323	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000541994	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.3348	0.90283	0.0:1.0:0.0:0.0	.	.	.	.	X	122;122;107	.	ENSP00000252015:E122X	E	-	1	0	TRPC4AP	33120810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.854000	0.75440	2.868000	0.98415	0.555000	0.69702	GAA		0.328	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33657149	C	A	33657149	4	1	61	1	0	0	0	0	0	1	0	0	16621	922	32	2	2097	2	TRPC4AP	20	33657149	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48090	33657149	29368371	11573	19558										
GDF5	8200	broad.mit.edu	37	chr20	34022112	34022112	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaggtactcatacacggtCttatcgtcctggccagagcg	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34022112C>A	ENST00000374372.1	-	4	1604	c.1101G>T	c.(1099-1101)aaG>aaT	p.K367N	GDF5OS_ENST00000374375.1_Silent_p.V52V|GDF5_ENST00000374369.3_Missense_Mutation_p.K367N			P43026	GDF5_HUMAN	growth differentiation factor 5	367					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)	p.K367N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CATACACGGTCTTATCGTCCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	20											93	93	93					20																	34022112		2203	4300	6503	33485526	SO:0001583	missense	8200			X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.1101G>T	20.37:g.34022112C>A	ENSP00000363492:p.Lys367Asn		33485526	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043370	0.36085	.	.	ENSG00000125965	ENST00000374369;ENST00000374372	T;T	0.80909	-1.43;-1.43	4.44	4.44	0.53790	.	0.129237	0.49916	D	0.000128	T	0.65133	0.2662	N	0.19112	0.55	0.46823	D	0.999213	P;P	0.50710	0.83;0.938	B;B	0.42916	0.402;0.25	T	0.66019	-0.6027	10	0.46703	T	0.11	.	5.2624	0.15582	0.0:0.7455:0.0:0.2545	.	367;367	F1T0J1;P43026	.;GDF5_HUMAN	N	367	ENSP00000363489:K367N;ENSP00000363492:K367N	ENSP00000363489:K367N	K	-	3	2	GDF5	33485526	1.000000	0.71417	1.000000	0.80357	0.413000	0.31143	1.598000	0.36740	2.288000	0.76882	0.491000	0.48974	AAG		0.597	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			A	34022112	C	A	34022112	3	1	61	1	0	0	0	0	1	0	0	0	6336	912	32	2	408	2	GDF5	20	34022112	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	364963	34022112	29003408	11574	19559										
CEP250	11190	broad.mit.edu	37	chr20	34065891	34065891	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatctcagggacatccaaGaagagaaggaagaaattcaa	10	7	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34065891G>T	ENST00000397527.1	+	17	2779	c.2059G>T	c.(2059-2061)Gaa>Taa	p.E687*	RP3-477O4.14_ENST00000444933.1_RNA|CEP250_ENST00000342580.4_Nonsense_Mutation_p.E687*|RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	687	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.E687*(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GGACATCCAAGAAGAGAAGGA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											41	45	44					20																	34065891		2203	4300	6503	33529305	SO:0001587	stop_gained	11190			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.2059G>T	20.37:g.34065891G>T	ENSP00000380661:p.Glu687*		33529305	E1P5Q3|O14812|O60588|Q9H450	Nonsense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.58|12.58	1.979760|1.979760	0.34942|0.34942	.|.	.|.	ENSG00000126001|ENSG00000126001	ENST00000397527;ENST00000342580|ENST00000425096	.|.	.|.	.|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.106399|.	0.41194|.	D|.	0.000933|.	.|T	.|0.73497	.|0.3594	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73043	.|-0.4107	.|3	0.56958|.	D|.	0.05|.	.|.	17.1083|17.1083	0.86669|0.86669	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	687|200	.|.	ENSP00000341541:E687X|.	E|R	+|+	1|2	0|0	CEP250|CEP250	33529305|33529305	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.707000|0.707000	0.40811|0.40811	4.188000|4.188000	0.58351|0.58351	2.564000|2.564000	0.86499|0.86499	0.557000|0.557000	0.71058|0.71058	GAA|AGA		0.453	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34065891	G	T	34065891	4	4	61	1	0	0	0	0	0	1	0	0	3258	943	33	2	2113	2	CEP250	20	34065891	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43779	34065891	28959629	11575	19560										
ERGIC3	51614	broad.mit.edu	37	chr20	34130142	34130142	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtattacctcaccacggaGgtaaggggcggggcttagtg	15	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34130142G>T	ENST00000348547.2	+	2	236	c.159G>T	c.(157-159)gaG>gaT	p.E53D	ERGIC3_ENST00000357394.4_Splice_Site_p.E53D|ERGIC3_ENST00000279052.6_Splice_Site_p.E53D|ERGIC3_ENST00000447986.1_Splice_Site_p.E53D	NM_015966.2	NP_057050.1	Q9Y282	ERGI3_HUMAN	ERGIC and golgi 3	53					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.E53D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)	16	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			TCACCACGGAGGTAAGGGGCG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	20											88	85	86					20																	34130142		2203	4300	6503	33593556	SO:0001630	splice_region_variant	51614			AF077030	CCDS13257.1, CCDS13258.1	20q11.22	2013-09-19	2006-01-19	2006-01-19	ENSG00000125991	ENSG00000125991			15927	protein-coding gene	gene with protein product			"serologically defined breast cancer antigen 84", "chromosome 20 open reading frame 47"	SDBCAG84, C20orf47		10810093	Standard	NM_015966		Approved	CGI-54, PRO0989, NY-BR-84, Erv46	uc002xcs.3	Q9Y282	OTTHUMG00000032346	ENST00000348547.2:c.159+1G>T	20.37:g.34130142G>T			33593556	Q5JWS3|Q6ZWP7|Q9H276|Q9P1L3	Missense_Mutation	SNP	ENST00000348547.2	37	CCDS13257.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	14.97|14.97|14.97	2.693158|2.693158|2.693158	0.48202|0.48202|0.48202	.|.|.	.|.|.	ENSG00000125991|ENSG00000125991|ENSG00000125991	ENST00000348547;ENST00000357394;ENST00000447986;ENST00000279052;ENST00000411577|ENST00000413587|ENST00000416206	T;T;T;T;T|.|.	0.45276|.|.	0.91;0.9;0.91;0.9;0.91|.|.	4.75|4.75|4.75	4.75|4.75|4.75	0.60458|0.60458|0.60458	.|.|.	0.052711|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.50718|0.50718|0.50718	0.1632|0.1632|0.1632	N|N|N	0.26042|0.26042|0.26042	0.785|0.785|0.785	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B;B;B;P;B|.|.	0.34587|.|.	0.012;0.101;0.145;0.003;0.458;0.145|.|.	B;B;B;B;B;B|.|.	0.31390|.|.	0.02;0.09;0.066;0.011;0.129;0.066|.|.	T|T|T	0.41556|0.41556|0.41556	-0.9502|-0.9502|-0.9502	10|5|5	0.13470|.|.	T|.|.	0.59|.|.	-19.1073|-19.1073|-19.1073	11.7532|11.7532|11.7532	0.51859|0.51859|0.51859	0.0809:0.0:0.9191:0.0|0.0809:0.0:0.9191:0.0|0.0809:0.0:0.9191:0.0	.|.|.	53;53;53;53;53;53|.|.	B4DV36;E9PFA8;Q9Y282;Q9Y282-3;Q9Y282-2;A2TJK5|.|.	.;.;ERGI3_HUMAN;.;.;.|.|.	D|C|M	53;53;53;53;47|43|52	ENSP00000341358:E53D;ENSP00000349970:E53D;ENSP00000392341:E53D;ENSP00000279052:E53D;ENSP00000414490:E47D|.|.	ENSP00000279052:E53D|.|.	E|G|R	+|+|+	3|1|2	2|0|0	ERGIC3|ERGIC3|ERGIC3	33593556|33593556|33593556	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.981000|0.981000|0.981000	0.71138|0.71138|0.71138	5.280000|5.280000|5.280000	0.65603|0.65603|0.65603	2.623000|2.623000|2.623000	0.88846|0.88846|0.88846	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	GAG|GGT|AGG		0.582	ERGIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078880.2	NM_015966	Missense_Mutation	T	34130142	G	T	34130142	5	4	61	1	0	0	0	0	0	0	1	0	5238	1014	35	2	165	2	ERGIC3	20	34130142	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64251	34130142	28895378	11576	19561										
RBM12	10137	broad.mit.edu	37	chr20	34241693	34241693	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagttctgcagtctttttcGaatcatatctatcttttcta	5	8	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34241693G>A	ENST00000374114.3	-	3	1815	c.1552C>T	c.(1552-1554)Cga>Tga	p.R518*	RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000359646.1_Nonsense_Mutation_p.R518*|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397445.1_Intron|RBM12_ENST00000374104.3_Nonsense_Mutation_p.R518*|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397446.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	518						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R518*(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			AGTCTTTTTCGAATCATATCT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											179	174	175					20																	34241693		2203	4300	6503	33705107	SO:0001587	stop_gained	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1552C>T	20.37:g.34241693G>A	ENSP00000363228:p.Arg518*		33705107	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Nonsense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	36	5.676604	0.96764	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	.	.	.	4.64	2.59	0.31030	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5429	12.819	0.57681	0.0:0.0:0.6381:0.3619	.	.	.	.	X	518;518;518;317	.	ENSP00000339879:R317X	R	-	1	2	RBM12	33705107	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.077000	0.57598	0.459000	0.27016	0.561000	0.74099	CGA		0.398	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		A	34241693	G	A	34241693	4	1	61	1	0	0	0	0	0	1	0	0	13150	1066	37	1	1250	1	RBM12	20	34241693	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111551	34241693	28783827	11577	19562										
RBM39	9584	broad.mit.edu	37	chr20	34302298	34302298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagcctttttggcacatTctgagtcagaaaactacatg	7	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34302298T>C	ENST00000253363.6	-	11	928	c.905A>G	c.(904-906)gAa>gGa	p.E302G	RBM39_ENST00000407261.4_Missense_Mutation_p.E145G|RBM39_ENST00000361162.6_Missense_Mutation_p.E302G|snoU13_ENST00000459110.1_RNA|RBM39_ENST00000528062.3_Missense_Mutation_p.E280G			Q14498	RBM39_HUMAN	RNA binding motif protein 39	302	Activating domain. {ECO:0000250}.|Interaction with JUN. {ECO:0000250}.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E302G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TTTGGCACATTCTGAGTCAGA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	20											63	55	58					20																	34302298		2203	4300	6503	33765712	SO:0001583	missense	9584			L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.905A>G	20.37:g.34302298T>C	ENSP00000253363:p.Glu302Gly		33765712	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Missense_Mutation	SNP	ENST00000253363.6	37	CCDS13266.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686530	0.88639	.	.	ENSG00000131051	ENST00000253363;ENST00000361162;ENST00000528062;ENST00000407261	D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.092847	0.85682	D	0.000000	D	0.88288	0.6396	L	0.35723	1.085	0.80722	D	1	B;P;P;P;B	0.40282	0.43;0.617;0.475;0.711;0.071	P;P;B;P;B	0.48304	0.517;0.573;0.2;0.534;0.337	D	0.88336	0.2971	10	0.46703	T	0.11	.	15.3991	0.74823	0.0:0.0:0.0:1.0	.	280;280;302;302;278	B4DRA0;A2RRD3;Q14498-2;Q14498;B3KWX7	.;.;.;RBM39_HUMAN;.	G	302;302;280;145	ENSP00000253363:E302G;ENSP00000354437:E302G;ENSP00000436747:E280G;ENSP00000384541:E145G	ENSP00000253363:E302G	E	-	2	0	RBM39	33765712	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.778000	0.85637	2.234000	0.73211	0.533000	0.62120	GAA		0.353	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		C	34302298	T	C	34302298	3	2	61	1	0	0	0	0	1	0	0	0	13170	1783	62	4	715	4	RBM39	20	34302298	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	60605	34302298	28723222	11578	19563										
RBM39	9584	broad.mit.edu	37	chr20	34326903	34326903	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactcactttttgctacgttCttcatggccgttggcactgc	8	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34326903C>A	ENST00000253363.6	-	3	111	c.88G>T	c.(88-90)Gaa>Taa	p.E30*	RBM39_ENST00000407261.4_5'UTR|RBM39_ENST00000397370.3_Nonsense_Mutation_p.E30*|RBM39_ENST00000361162.6_Nonsense_Mutation_p.E30*|RBM39_ENST00000463098.1_5'Flank|RBM39_ENST00000528062.3_Nonsense_Mutation_p.E30*			Q14498	RBM39_HUMAN	RNA binding motif protein 39	30					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E30*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TTGCTACGTTCTTCATGGCCG	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											143	120	127					20																	34326903		2203	4300	6503	33790317	SO:0001587	stop_gained	9584			L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.88G>T	20.37:g.34326903C>A	ENSP00000253363:p.Glu30*		33790317	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Nonsense_Mutation	SNP	ENST00000253363.6	37	CCDS13266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.553835|5.553835	0.96501|0.96501	.|.	.|.	ENSG00000131051|ENSG00000131051	ENST00000253363;ENST00000361162;ENST00000528062;ENST00000374038;ENST00000427743;ENST00000434927;ENST00000397370|ENST00000426951	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.097095|.	0.64402|.	D|.	0.000002|.	.|T	.|0.75133	.|0.3808	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73649	.|-0.3916	.|4	0.27082|.	T|.	0.32|.	.|.	19.1783|19.1783	0.93612|0.93612	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	30|17	.|.	ENSP00000253363:E30X|.	E|K	-|-	1|3	0|2	RBM39|RBM39	33790317|33790317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.247000|7.247000	0.78257|0.78257	2.523000|2.523000	0.85059|0.85059	0.591000|0.591000	0.81541|0.81541	GAA|AAG		0.443	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		A	34326903	C	A	34326903	4	1	61	1	0	0	0	0	0	1	0	0	13170	922	32	2	1564	2	RBM39	20	34326903	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24605	34326903	28698617	11579	19564										
PHF20	51230	broad.mit.edu	37	chr20	34459740	34459740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggaattacaagagatttCgactgtggaaggttcatatt	11	4	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34459740C>T	ENST00000374012.3	+	9	1400	c.1271C>T	c.(1270-1272)tCg>tTg	p.S424L	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	424					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S424L(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CAAGAGATTTCGACTGTGGAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	20											82	85	84					20																	34459740		2203	4300	6503	33923154	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1271C>T	20.37:g.34459740C>T	ENSP00000363124:p.Ser424Leu		33923154	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.222971	0.39300	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.58060	1.12;0.36;0.36	5.56	5.56	0.83823	.	0.256554	0.33610	N	0.004735	T	0.48040	0.1478	L	0.46157	1.445	0.80722	D	1	P;D	0.59357	0.897;0.985	B;B	0.42386	0.122;0.386	T	0.48525	-0.9028	10	0.40728	T	0.16	.	15.0108	0.71547	0.0:1.0:0.0:0.0	.	424;424	Q9BVI0;Q66K49	PHF20_HUMAN;.	L	424	ENSP00000363124:S424L;ENSP00000341900:S424L;ENSP00000363112:S424L	ENSP00000341900:S424L	S	+	2	0	PHF20	33923154	0.991000	0.36638	0.924000	0.36721	0.107000	0.19398	3.776000	0.55356	2.617000	0.88574	0.591000	0.81541	TCG		0.378	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		T	34459740	C	T	34459740	3	4	61	1	0	0	0	0	1	0	0	0	11862	893	31	1	1301	1	PHF20	20	34459740	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	132837	34459740	28565780	11580	19565										
PHF20	51230	broad.mit.edu	37	chr20	34515779	34515779	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcccgagaaatacacctgTtatgtttgccaagaccctcc	8	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34515779T>G	ENST00000374012.3	+	14	2211	c.2082T>G	c.(2080-2082)tgT>tgG	p.C694W	RNU6-937P_ENST00000384325.1_RNA|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	694					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.C694W(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AATACACCTGTTATGTTTGCC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	20											135	132	133					20																	34515779		2203	4300	6503	33979193	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.2082T>G	20.37:g.34515779T>G	ENSP00000363124:p.Cys694Trp		33979193	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686670	0.68157	.	.	ENSG00000025293	ENST00000374012	D	0.99667	-6.34	5.91	2.37	0.29283	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99725	0.9893	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98258	1.0497	10	0.87932	D	0	.	6.6393	0.22901	0.0:0.4451:0.0:0.5549	.	694	Q9BVI0	PHF20_HUMAN	W	694	ENSP00000363124:C694W	ENSP00000363124:C694W	C	+	3	2	PHF20	33979193	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.881000	0.28173	0.517000	0.28361	0.533000	0.62120	TGT		0.458	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		G	34515779	T	G	34515779	3	3	61	1	0	0	0	0	1	0	0	0	11862	1731	60	4	2132	4	PHF20	20	34515779	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	56039	34515779	28509741	11581	19566										
EPB41L1	2036	broad.mit.edu	37	chr20	34765945	34765945	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctagagaaggactacttCggcctgaccttctgtgatgc	10	12	1	3	rs373620188		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:34765945C>T	ENST00000338074.2	+	4	575	c.414C>T	c.(412-414)ttC>ttT	p.F138F	EPB41L1_ENST00000202028.5_Silent_p.F76F|EPB41L1_ENST00000373946.3_Silent_p.F107F|EPB41L1_ENST00000373941.1_Silent_p.F138F|EPB41L1_ENST00000441639.1_Silent_p.F76F|EPB41L1_ENST00000373950.2_Intron	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	138	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.F138F(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					AGGACTACTTCGGCCTGACCT	0.582													C|||	1	0.000199681	0	0	5008	,	,		19685	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	20						C	,	0,4406		0,0,2203	117	93	101		414,228	0.4	1	20		101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	EPB41L1	NM_012156.2,NM_177996.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	138/882,76/780	34765945	1,13005	2203	4300	6503	34229359	SO:0001819	synonymous_variant	2036			AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.414C>T	20.37:g.34765945C>T			34229359	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1																																																																																				0.582	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		T	34765945	C	T	34765945	2	4	61	1	0	0	0	0	0	0	0	1	5165	883	31	1		1	EPB41L1	20	34765945	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	250166	34765945	28259575	11582	19567										
NDRG3	57446	broad.mit.edu	37	chr20	35288785	35288785	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggcgggaattgcattcGacctaaaatttaaaaaaaga	8	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35288785G>A	ENST00000349004.1	-	13	894	c.813C>T	c.(811-813)gtC>gtT	p.V271V	NDRG3_ENST00000359675.2_Silent_p.V259V|NDRG3_ENST00000373773.3_Silent_p.V176V|NDRG3_ENST00000373803.2_Silent_p.V271V|NDRG3_ENST00000540765.1_Silent_p.V167V	NM_032013.3	NP_114402.1	Q9UGV2	NDRG3_HUMAN	NDRG family member 3	271					cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.V271V(1)		endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Myeloproliferative disorder(115;0.00878)				AATTGCATTCGACCTAAAATT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	20											82	82	82					20																	35288785		2203	4300	6503	34722199	SO:0001819	synonymous_variant	57446			AL031662	CCDS13284.1, CCDS13285.1	20q11.21-q11.23	2008-07-28			ENSG00000101079	ENSG00000101079			14462	protein-coding gene	gene with protein product		605273				10831399, 17998568	Standard	NM_032013		Approved		uc002xfw.3	Q9UGV2	OTTHUMG00000032398	ENST00000349004.1:c.813C>T	20.37:g.35288785G>A			34722199	A2A2S8|E1P5U7|E1P5U8|Q5TH32|Q96PL8|Q96SM2|Q9BXY7|Q9H3N7|Q9H411|Q9H8J6	Silent	SNP	ENST00000349004.1	37	CCDS13285.1																																																																																				0.353	NDRG3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079053.2			A	35288785	G	A	35288785	2	1	61	1	0	0	0	0	0	0	0	1	10284	1045	37	1		1	NDRG3	20	35288785	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	522840	35288785	27736735	11583	19568										
SAMHD1	25939	broad.mit.edu	37	chr20	35545400	35545400	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caatgccatttcttttattaGatactatctcataaaggaag	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35545400G>T	ENST00000262878.4	-	8	1104	c.905C>A	c.(904-906)tCt>tAt	p.S302Y	SAMHD1_ENST00000373694.5_Missense_Mutation_p.S87Y	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	302	HD.				dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S302Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				TCTTTTATTAGATACTATCTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	20											59	55	57					20																	35545400		2203	4300	6503	34978814	SO:0001583	missense	25939			AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.905C>A	20.37:g.35545400G>T	ENSP00000262878:p.Ser302Tyr		34978814	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.955363	0.92726	.	.	ENSG00000101347	ENST00000262878;ENST00000373694	D;D	0.96459	-4.02;-4.02	5.67	5.67	0.87782	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.206543	0.49916	D	0.000130	D	0.97939	0.9322	M	0.83852	2.665	0.58432	D	0.999995	D	0.56746	0.977	P	0.59171	0.853	D	0.98350	1.0543	10	0.87932	D	0	-9.7048	19.7192	0.96135	0.0:0.0:1.0:0.0	.	302	Q9Y3Z3	SAMH1_HUMAN	Y	302;87	ENSP00000262878:S302Y;ENSP00000362798:S87Y	ENSP00000262878:S302Y	S	-	2	0	SAMHD1	34978814	1.000000	0.71417	0.990000	0.47175	0.834000	0.47266	9.671000	0.98627	2.823000	0.97156	0.591000	0.81541	TCT		0.363	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		T	35545400	G	T	35545400	3	4	61	1	0	0	0	0	1	0	0	0	13865	942	33	2	1011	2	SAMHD1	20	35545400	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	256615	35545400	27480120	11584	19569										
RBL1	5933	broad.mit.edu	37	chr20	35646765	35646765	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttttcagcagaacacttCtatatacctacatgccagag	5	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35646765C>A	ENST00000373664.3	-	19	2705	c.2639G>T	c.(2638-2640)aGa>aTa	p.R880I	RBL1_ENST00000344359.3_Missense_Mutation_p.R880I	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	880	Domain B.|Pocket; binds T and E1A.				chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)	p.R880I(1)		NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				CAGAACACTTCTATATACCTA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	20											67	67	67					20																	35646765		2201	4298	6499	35080179	SO:0001583	missense	5933			L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.2639G>T	20.37:g.35646765C>A	ENSP00000362768:p.Arg880Ile		35080179	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	37	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710185	0.68730	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	D;D	0.92595	-3.07;-3.07	4.85	4.85	0.62838	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.96522	0.8865	M	0.89353	3.025	0.80722	D	1	D;D	0.63046	0.971;0.992	P;D	0.70227	0.687;0.968	D	0.97228	0.9882	10	0.87932	D	0	-20.8994	17.199	0.86901	0.0:1.0:0.0:0.0	.	880;880	P28749-2;P28749	.;RBL1_HUMAN	I	880	ENSP00000362768:R880I;ENSP00000343646:R880I	ENSP00000343646:R880I	R	-	2	0	RBL1	35080179	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	4.578000	0.60929	2.529000	0.85273	0.460000	0.39030	AGA		0.333	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		A	35646765	C	A	35646765	3	1	61	1	0	0	0	0	1	0	0	0	13146	913	32	2	592	2	RBL1	20	35646765	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101365	35646765	27378755	11585	19570										
RBL1	5933	broad.mit.edu	37	chr20	35651162	35651162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacacgtccatatcttccttCgtaactcatttgaaacatcc	3	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35651162C>T	ENST00000373664.3	-	17	2516	c.2450G>A	c.(2449-2451)cGa>cAa	p.R817Q	RBL1_ENST00000344359.3_Missense_Mutation_p.R817Q	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	817	Domain B.|Pocket; binds T and E1A.				chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)	p.R817Q(1)		NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				TATCTTCCTTCGTAACTCATT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	20											120	107	111					20																	35651162		2203	4300	6503	35084576	SO:0001583	missense	5933			L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.2450G>A	20.37:g.35651162C>T	ENSP00000362768:p.Arg817Gln		35084576	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	37	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084246	0.94100	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	D;D	0.91631	-2.88;-2.88	5.39	4.45	0.53987	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.070349	0.56097	D	0.000022	D	0.94178	0.8132	M	0.63428	1.95	0.54753	D	0.999989	D;P	0.76494	0.999;0.819	D;P	0.63192	0.912;0.575	D	0.92626	0.6112	10	0.25751	T	0.34	-4.1047	15.4901	0.75600	0.1397:0.8603:0.0:0.0	.	817;817	P28749-2;P28749	.;RBL1_HUMAN	Q	817	ENSP00000362768:R817Q;ENSP00000343646:R817Q	ENSP00000343646:R817Q	R	-	2	0	RBL1	35084576	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.928000	0.70088	1.274000	0.44362	0.555000	0.69702	CGA		0.373	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		T	35651162	C	T	35651162	3	4	61	1	0	0	0	0	1	0	0	0	13146	884	31	1	789	1	RBL1	20	35651162	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4397	35651162	27374358	11586	19571										
C20orf132	140699	broad.mit.edu	37	chr20	35740792	35740792	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatctttggagtacacttCttggggcagcttccacttca	11	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35740792C>A	ENST00000400441.3	-	21	2748	c.2749G>T	c.(2749-2751)Gaa>Taa	p.E917*	MROH8_ENST00000217333.8_Nonsense_Mutation_p.E746*|MROH8_ENST00000441008.2_Nonsense_Mutation_p.E903*			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	0								p.E917*(1)									GAGTACACTTCTTGGGGCAGC	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											110	101	104					20																	35740792		1889	4117	6006	35174206	SO:0001587	stop_gained	140699			AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.2749G>T	20.37:g.35740792C>A	ENSP00000383291:p.Glu917*		35174206	Q5JYQ6	Nonsense_Mutation	SNP	ENST00000400441.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	38|38|38	6.666690|6.666690|6.666690	0.97747|0.97747|0.97747	.|.|.	.|.|.	ENSG00000101353|ENSG00000101353|ENSG00000101353	ENST00000441008;ENST00000400441;ENST00000217333|ENST00000343811|ENST00000417458	.|.|.	.|.|.	.|.|.	5.57|5.57|5.57	3.49|3.49|3.49	0.39957|0.39957|0.39957	.|.|.	0.618437|.|.	0.16759|.|.	N|.|.	0.200709|.|.	.|T|T	.|0.54695|0.54695	.|0.1874|0.1874	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.64445|0.64445	.|-0.6406|-0.6406	.|3|3	0.10377|.|.	T|.|.	0.69|.|.	0.0564|0.0564|0.0564	11.7616|11.7616|11.7616	0.51908|0.51908|0.51908	0.0:0.6566:0.3434:0.0|0.0:0.6566:0.3434:0.0|0.0:0.6566:0.3434:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	903;917;746|943|544	.|.|.	ENSP00000217333:E746X|.|.	E|K|R	-|-|-	1|3|2	0|2|0	C20orf132|C20orf132|C20orf132	35174206|35174206|35174206	0.907000|0.907000|0.907000	0.30839|0.30839|0.30839	0.904000|0.904000|0.904000	0.35570|0.35570|0.35570	0.786000|0.786000|0.786000	0.44442|0.44442|0.44442	0.782000|0.782000|0.782000	0.26788|0.26788|0.26788	1.311000|1.311000|1.311000	0.45024|0.45024|0.45024	0.511000|0.511000|0.511000	0.50034|0.50034|0.50034	GAA|AAG|AGA		0.418	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		A	35740792	C	A	35740792	4	1	61	1	0	0	0	0	0	1	0	0	2092	922	32	2	395	2	C20orf132	20	35740792	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	89630	35740792	27284728	11587	19572										
RPN2	6185	broad.mit.edu	37	chr20	35857024	35857024	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgagccagacaacaagaaCgtgtacaagtttgaactgga	11	9	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:35857024C>T	ENST00000237530.6	+	12	1682	c.1371C>T	c.(1369-1371)aaC>aaT	p.N457N	RPN2_ENST00000373622.5_Silent_p.N425N	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	457					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)	p.N457N(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				ACAACAAGAACGTGTACAAGT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	20											119	113	115					20																	35857024		2203	4300	6503	35290438	SO:0001819	synonymous_variant	6185			Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1371C>T	20.37:g.35857024C>T			35290438	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Silent	SNP	ENST00000237530.6	37	CCDS13291.1																																																																																				0.423	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		T	35857024	C	T	35857024	2	4	61	1	0	0	0	0	0	0	0	1	13645	535	19	1		1	RPN2	20	35857024	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116232	35857024	27168496	11588	19573										
TGM2	7052	broad.mit.edu	37	chr20	36760871	36760871	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaaggcagtcacggtatttCtcatagaggatgcaaagagg	13	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:36760871C>A	ENST00000361475.2	-	11	1820	c.1647G>T	c.(1645-1647)gaG>gaT	p.E549D	TGM2_ENST00000536701.1_Missense_Mutation_p.E468D|TGM2_ENST00000536724.1_Missense_Mutation_p.E489D	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	549					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.E549D(1)		endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	CACGGTATTTCTCATAGAGGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	20											178	178	178					20																	36760871		2203	4300	6503	36194285	SO:0001583	missense	7052			M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"Transglutaminases"	11778	protein-coding gene	gene with protein product	"C polypeptide, protein-glutamine-gamma-glutamyltransferase"	190196	"transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1647G>T	20.37:g.36760871C>A	ENSP00000355330:p.Glu549Asp		36194285	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Missense_Mutation	SNP	ENST00000361475.2	37	CCDS13302.1	.	.	.	.	.	.	.	.	.	.	C	3.021	-0.201695	0.06219	.	.	ENSG00000198959	ENST00000361475;ENST00000536701;ENST00000536724	T;T;T	0.29917	1.55;1.55;1.55	4.67	-1.27	0.09347	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.693293	0.14694	N	0.303994	T	0.23846	0.0577	M	0.64997	1.995	0.19300	N	0.99997	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.12156	0.003;0.007;0.005;0.004	T	0.27226	-1.0080	10	0.19590	T	0.45	-11.674	6.0283	0.19667	0.0:0.4563:0.2416:0.3021	.	489;468;489;549	F5H6P0;B4DIT7;B4DTN7;P21980	.;.;.;TGM2_HUMAN	D	549;468;489	ENSP00000355330:E549D;ENSP00000444701:E468D;ENSP00000437479:E489D	ENSP00000355330:E549D	E	-	3	2	TGM2	36194285	0.840000	0.29493	0.508000	0.27688	0.056000	0.15407	-0.119000	0.10676	0.121000	0.18284	0.561000	0.74099	GAG		0.542	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951		A	36760871	C	A	36760871	3	1	61	1	0	0	0	0	1	0	0	0	15869	912	32	2	428	2	TGM2	20	36760871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	903847	36760871	26264649	11589	19574										
KIAA1755	85449	broad.mit.edu	37	chr20	36869698	36869698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctctcttgggaaaagcctaGgagagccacatagtctccct	10	12	2	1	rs201894627		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:36869698G>T	ENST00000279024.4	-	3	1106	c.835C>A	c.(835-837)Cta>Ata	p.L279I		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	279								p.L279I(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GAAAAGCCTAGGAGAGCCACA	0.572													G|||	1	0.000199681	0	0	5008	,	,		18456	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											106	104	105					20																	36869698		2203	4300	6503	36303112	SO:0001583	missense	85449			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.835C>A	20.37:g.36869698G>T	ENSP00000279024:p.Leu279Ile		36303112	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.42	2.528603	0.44969	.	.	ENSG00000149633	ENST00000279024	T	0.14266	2.52	5.07	4.1	0.47936	.	0.000000	0.38605	N	0.001621	T	0.29126	0.0724	M	0.66939	2.045	0.34108	D	0.662606	D	0.67145	0.996	P	0.57283	0.817	T	0.49466	-0.8937	10	0.72032	D	0.01	.	12.9373	0.58322	0.0:0.1626:0.8374:0.0	.	279	Q5JYT7	K1755_HUMAN	I	279	ENSP00000279024:L279I	ENSP00000279024:L279I	L	-	1	2	KIAA1755	36303112	1.000000	0.71417	0.954000	0.39281	0.543000	0.35085	2.033000	0.41136	1.320000	0.45209	0.655000	0.94253	CTA		0.572	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36869698	G	T	36869698	3	4	61	1	0	0	0	0	1	0	0	0	8278	991	35	2	2815	2	KIAA1755	20	36869698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	108827	36869698	26155822	11590	19575										
BPI	671	broad.mit.edu	37	chr20	36932652	36932652	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggggcccttgcaacgcgccGagatgggcgtccctgatggt	16	12	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:36932652G>A	ENST00000262865.4	+	1	128	c.39G>A	c.(37-39)ccG>ccA	p.P13P	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	13					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.P13P(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				GCAACGCGCCGAGATGGGCGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	20											74	73	73					20																	36932652		2203	4300	6503	36366066	SO:0001819	synonymous_variant	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.39G>A	20.37:g.36932652G>A			36366066	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1																																																																																				0.617	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		A	36932652	G	A	36932652	2	1	61	1	0	0	0	0	0	0	0	1	1493	1045	37	1		1	BPI	20	36932652	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	62954	36932652	26092868	11591	19576										
BPI	671	broad.mit.edu	37	chr20	36954708	36954708	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgaagatacagatccatgtCtcagcctccaccccgccaca	6	16	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:36954708C>A	ENST00000262865.4	+	10	1136	c.1047C>A	c.(1045-1047)gtC>gtA	p.V349V	BPI_ENST00000489102.1_3'UTR|CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	349					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.V349V(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				AGATCCATGTCTCAGCCTCCA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	20											90	72	79					20																	36954708		2203	4300	6503	36388122	SO:0001819	synonymous_variant	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1047C>A	20.37:g.36954708C>A			36388122	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1	.	.	.	.	.	.	.	.	.	.	C	3.713	-0.059072	0.07317	.	.	ENSG00000101425	ENST00000417318	.	.	.	4.52	-4.11	0.03928	.	.	.	.	.	T	0.34424	0.0897	.	.	.	0.20703	N	0.999864	.	.	.	.	.	.	T	0.40534	-0.9558	4	.	.	.	-2.001	12.2187	0.54420	0.0:0.1784:0.6704:0.1511	.	.	.	.	Y	175	.	.	S	+	2	0	BPI	36388122	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.323000	0.01117	-0.575000	0.05982	-0.127000	0.14921	TCT		0.557	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		A	36954708	C	A	36954708	2	1	61	1	0	0	0	0	0	0	0	1	1493	900	32	2		2	BPI	20	36954708	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22056	36954708	26070812	11592	19577										
BPI	671	broad.mit.edu	37	chr20	36964001	36964001	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcggtctctgtcacagaGaaactacagaaaggcttccc	8	13	2	2	rs142119049		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:36964001G>T	ENST00000262865.4	+	14	1439	c.1350G>T	c.(1348-1350)gaG>gaT	p.E450D	BPI_ENST00000489102.1_3'UTR	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	450					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.E450D(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				CTGTCACAGAGAAACTACAGA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20						G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	93	91	92		1350	2.7	0.8	20	dbSNP_134	92	0,8600		0,0,4300	no	missense-near-splice	BPI	NM_001725.2	45	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging	450/488	36964001	1,13005	2203	4300	6503	36397415	SO:0001630	splice_region_variant	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1349-1G>T	20.37:g.36964001G>T			36397415	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.62|10.62	1.400504|1.400504	0.25291|0.25291	2.27E-4|2.27E-4	0.0|0.0	ENSG00000101425|ENSG00000101425	ENST00000262865|ENST00000417318	T|.	0.06849|.	3.25|.	3.65|3.65	2.65|2.65	0.31530|0.31530	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);|.	0.292311|.	0.27991|.	N|.	0.017036|.	T|T	0.45776|0.45776	0.1359|0.1359	L|L	0.41632|0.41632	1.29|1.29	0.37138|0.37138	D|D	0.901584|0.901584	P|.	0.46457|.	0.878|.	P|.	0.51657|.	0.676|.	T|T	0.45026|0.45026	-0.9289|-0.9289	10|5	0.22109|.	T|.	0.4|.	.|.	5.9472|5.9472	0.19225|0.19225	0.1559:0.0:0.8441:0.0|0.1559:0.0:0.8441:0.0	.|.	450|.	P17213|.	BPI_HUMAN|.	D|I	450|276	ENSP00000262865:E450D|.	ENSP00000262865:E450D|.	E|R	+|+	3|2	2|0	BPI|BPI	36397415|36397415	0.966000|0.966000	0.33281|0.33281	0.840000|0.840000	0.33206|0.33206	0.183000|0.183000	0.23260|0.23260	1.531000|1.531000	0.36018|0.36018	1.030000|1.030000	0.39839|0.39839	0.455000|0.455000	0.32223|0.32223	GAG|AGA		0.577	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	Missense_Mutation	T	36964001	G	T	36964001	5	4	61	1	0	0	0	0	0	0	1	0	1493	956	33	2	1404	2	BPI	20	36964001	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9293	36964001	26061519	11593	19578										
RALGAPB	57148	broad.mit.edu	37	chr20	37144971	37144971	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctgcctcaaatattttttCgtgccatgcgtggaatcagc	8	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37144971C>T	ENST00000262879.6	+	7	1293	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	RALGAPB_ENST00000537204.1_Missense_Mutation_p.R337C|RALGAPB_ENST00000397042.3_Missense_Mutation_p.R337C|MIR548O2_ENST00000583129.1_RNA|RALGAPB_ENST00000397040.1_Missense_Mutation_p.R337C|RALGAPB_ENST00000397038.1_Missense_Mutation_p.R115C			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	337					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.R337C(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						AATATTTTTTCGTGCCATGCG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	20											208	192	198					20																	37144971		2203	4300	6503	36578385	SO:0001583	missense	57148			AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1009C>T	20.37:g.37144971C>T	ENSP00000262879:p.Arg337Cys		36578385	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648404	0.87958	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000537204;ENST00000397040;ENST00000438490	.	.	.	5.48	5.48	0.80851	.	0.048056	0.85682	D	0.000000	T	0.64789	0.2630	L	0.47716	1.5	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.997;0.994;0.997;0.997	P;P;P;P;P	0.56474	0.799;0.799;0.742;0.799;0.799	T	0.66567	-0.5891	9	0.66056	D	0.02	.	14.5378	0.67973	0.1464:0.8535:0.0:0.0	.	337;165;337;337;337	B4E2E8;A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;.;RLGPB_HUMAN	C	337;337;337;115;337;337;165	.	ENSP00000262879:R337C	R	+	1	0	RALGAPB	36578385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.645000	0.61404	2.722000	0.93159	0.467000	0.42956	CGT		0.413	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		T	37144971	C	T	37144971	3	4	61	1	0	0	0	0	1	0	0	0	13052	884	31	1	1031	1	RALGAPB	20	37144971	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	180970	37144971	25880549	11594	19579										
SLC32A1	140679	broad.mit.edu	37	chr20	37356137	37356137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctacgccatcctgcacggcGgctacctggggttgtttctc	11	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37356137G>T	ENST00000217420.1	+	2	696	c.433G>T	c.(433-435)Ggc>Tgc	p.G145C		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	145					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)	p.G145C(1)		breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CCTGCACGGCGGCTACCTGGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											67	55	59					20																	37356137		2203	4299	6502	36789551	SO:0001583	missense	140679			AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.433G>T	20.37:g.37356137G>T	ENSP00000217420:p.Gly145Cys		36789551	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024038	0.75390	.	.	ENSG00000101438	ENST00000217420	T	0.64260	-0.09	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.80686	0.4670	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84237	0.0470	10	0.87932	D	0	-20.9238	14.9054	0.70715	0.0:0.0:1.0:0.0	.	145	Q9H598	VIAAT_HUMAN	C	145	ENSP00000217420:G145C	ENSP00000217420:G145C	G	+	1	0	SLC32A1	36789551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.631000	0.98424	2.387000	0.81309	0.563000	0.77884	GGC		0.617	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		T	37356137	G	T	37356137	3	4	61	1	0	0	0	0	1	0	0	0	14602	1116	39	2	439	2	SLC32A1	20	37356137	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	211166	37356137	25669383	11595	19580										
SLC32A1	140679	broad.mit.edu	37	chr20	37356420	37356420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcccggggctgcccgtgtCgcagaagtcctggtccatta	12	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37356420C>T	ENST00000217420.1	+	2	979	c.716C>T	c.(715-717)tCg>tTg	p.S239L		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	239					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)	p.S239L(1)		breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CTGCCCGTGTCGCAGAAGTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	20											107	76	87					20																	37356420		2203	4300	6503	36789834	SO:0001583	missense	140679			AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.716C>T	20.37:g.37356420C>T	ENSP00000217420:p.Ser239Leu		36789834	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.243760	0.79912	.	.	ENSG00000101438	ENST00000217420	T	0.02682	4.2	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.06872	0.0175	L	0.54323	1.7	0.80722	D	1	D	0.56746	0.977	P	0.48552	0.581	T	0.14727	-1.0462	10	0.56958	D	0.05	-10.3087	15.8477	0.78903	0.0:1.0:0.0:0.0	.	239	Q9H598	VIAAT_HUMAN	L	239	ENSP00000217420:S239L	ENSP00000217420:S239L	S	+	2	0	SLC32A1	36789834	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.756000	0.85195	2.428000	0.82296	0.563000	0.77884	TCG		0.582	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		T	37356420	C	T	37356420	3	4	61	1	0	0	0	0	1	0	0	0	14602	893	31	1	722	1	SLC32A1	20	37356420	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	283	37356420	25669100	11596	19581										
PPP1R16B	26051	broad.mit.edu	37	chr20	37546912	37546912	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctccggtcagtgcctaccAgtatgcgctggccaacgggg	15	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37546912A>G	ENST00000299824.1	+	11	1496	c.1307A>G	c.(1306-1308)cAg>cGg	p.Q436R	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.Q394R	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	436					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.Q436R(1)		biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				AGTGCCTACCAGTATGCGCTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											157	151	153					20																	37546912		2203	4300	6503	36980326	SO:0001583	missense	26051			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1307A>G	20.37:g.37546912A>G	ENSP00000299824:p.Gln436Arg		36980326	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.677|9.677	1.148191|1.148191	0.21288|0.21288	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	T;T|.	0.71341|.	-0.34;-0.56|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.073163|.	0.56097|.	D|.	0.000032|.	T|T	0.39572|0.39572	0.1083|0.1083	L|L	0.36672|0.36672	1.1|1.1	0.21841|0.21841	N|N	0.999515|0.999515	B;B|.	0.30281|.	0.0;0.275|.	B;B|.	0.21708|.	0.0;0.036|.	T|T	0.28681|0.28681	-1.0036|-1.0036	10|5	0.14656|.	T|.	0.56|.	.|.	11.1731|11.1731	0.48584|0.48584	0.847:0.153:0.0:0.0|0.847:0.153:0.0:0.0	.|.	394;436|.	E9PFS8;Q96T49|.	.;PP16B_HUMAN|.	R|G	436;394|337	ENSP00000299824:Q436R;ENSP00000362428:Q394R|.	ENSP00000299824:Q436R|.	Q|S	+|+	2|1	0|0	PPP1R16B|PPP1R16B	36980326|36980326	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	2.103000|2.103000	0.41806|0.41806	2.002000|2.002000	0.58637|0.58637	0.533000|0.533000	0.62120|0.62120	CAG|AGT		0.617	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		G	37546912	A	G	37546912	3	3	61	1	0	0	0	0	1	0	0	0	12400	188	7	4	1345	4	PPP1R16B	20	37546912	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	190492	37546912	25478608	11597	19582										
FAM83D	81610	broad.mit.edu	37	chr20	37576594	37576594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agattattgggaaggttcacGaaaagttcacgttgattgat	11	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37576594G>A	ENST00000217429.4	+	3	858	c.817G>A	c.(817-819)Gaa>Aaa	p.E273K		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	243					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E273K(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				GAAGGTTCACGAAAAGTTCAC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	20											116	111	113					20																	37576594		1967	4144	6111	37010008	SO:0001583	missense	81610			AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.817G>A	20.37:g.37576594G>A	ENSP00000217429:p.Glu273Lys		37010008	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	.	.	.	.	.	.	.	.	.	.	G	37	6.176831	0.97348	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.13089	2.62	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.40522	0.1120	M	0.86651	2.83	0.80722	D	1	D	0.58268	0.982	P	0.55222	0.771	T	0.31194	-0.9952	10	0.72032	D	0.01	-4.6384	20.4702	0.99162	0.0:0.0:1.0:0.0	.	243	Q9H4H8	FA83D_HUMAN	K	273;227	ENSP00000217429:E273K	ENSP00000217429:E273K	E	+	1	0	FAM83D	37010008	1.000000	0.71417	0.991000	0.47740	0.973000	0.67179	9.441000	0.97557	2.937000	0.99478	0.650000	0.86243	GAA		0.438	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			A	37576594	G	A	37576594	3	1	61	1	0	0	0	0	1	0	0	0	5655	1059	37	1	827	1	FAM83D	20	37576594	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29682	37576594	25448926	11598	19583										
DHX35	60625	broad.mit.edu	37	chr20	37632401	37632401	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacgtctttaggaagaggtaGaaactgttgtgtcgatgctc	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:37632401G>T	ENST00000252011.3	+	11	895	c.862G>T	c.(862-864)Gaa>Taa	p.E288*	DHX35_ENST00000373323.4_Nonsense_Mutation_p.E257*|DHX35_ENST00000373325.2_Nonsense_Mutation_p.E288*	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	288	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.E288*(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				GGAAGAGGTAGAAACTGTTGT	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											143	135	138					20																	37632401		2203	4300	6503	37065815	SO:0001587	stop_gained	60625			AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.862G>T	20.37:g.37632401G>T	ENSP00000252011:p.Glu288*		37065815	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Nonsense_Mutation	SNP	ENST00000252011.3	37	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	G	36	5.599435	0.96614	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000441485	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.3593	0.98849	0.0:0.0:1.0:0.0	.	.	.	.	X	288;288;257;253	.	ENSP00000252011:E288X	E	+	1	0	DHX35	37065815	1.000000	0.71417	0.735000	0.30896	0.948000	0.59901	9.869000	0.99810	2.807000	0.96579	0.591000	0.81541	GAA		0.453	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37632401	G	T	37632401	4	4	61	1	0	0	0	0	0	1	0	0	4519	943	33	2	904	2	DHX35	20	37632401	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	55807	37632401	25393119	11599	19584										
TOP1	7150	broad.mit.edu	37	chr20	39713125	39713125	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaaattgaaaaaacccaaGaataaagataaagataaaaa	6	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:39713125G>T	ENST00000361337.2	+	8	781	c.531G>T	c.(529-531)aaG>aaT	p.K177N		NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	177	Lys-rich.				chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)	p.K177N(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	AAAAACCCAAGAATAAAGATA	0.378			T	NUP98	AML*																																		Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	1	Substitution - Missense(1)	large_intestine(1)	20											44	43	43					20																	39713125		2200	4297	6497	39146539	SO:0001583	missense	7150				CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.531G>T	20.37:g.39713125G>T	ENSP00000354522:p.Lys177Asn		39146539	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Missense_Mutation	SNP	ENST00000361337.2	37	CCDS13312.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630911	0.46944	.	.	ENSG00000198900	ENST00000361337	T	0.25579	1.79	5.33	5.33	0.75918	.	0.103535	0.64402	D	0.000003	T	0.30696	0.0773	L	0.57536	1.79	0.54753	D	0.999984	P	0.51791	0.948	B	0.43783	0.431	T	0.04946	-1.0916	10	0.44086	T	0.13	-16.5097	15.7241	0.77740	0.0:0.0:1.0:0.0	.	177	P11387	TOP1_HUMAN	N	177	ENSP00000354522:K177N	ENSP00000354522:K177N	K	+	3	2	TOP1	39146539	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.775000	0.55349	2.493000	0.84123	0.591000	0.81541	AAG		0.378	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2			T	39713125	G	T	39713125	3	4	61	1	0	0	0	0	1	0	0	0	16403	933	33	2	561	2	TOP1	20	39713125	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2080724	39713125	23312395	11600	19585										
TOP1	7150	broad.mit.edu	37	chr20	39741565	39741565	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctgtacttcatcgacaaGgtgagagcatcttcccatcg	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:39741565G>T	ENST00000361337.2	+	14	1702	c.1452G>T	c.(1450-1452)aaG>aaT	p.K484N	RP1-1J6.2_ENST00000454626.1_RNA	NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	484					chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)	p.K484N(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	TCATCGACAAGGTGAGAGCAT	0.488			T	NUP98	AML*																																		Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	1	Substitution - Missense(1)	large_intestine(1)	20											84	74	77					20																	39741565		2203	4300	6503	39174979	SO:0001630	splice_region_variant	7150				CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.1452+1G>T	20.37:g.39741565G>T			39174979	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Missense_Mutation	SNP	ENST00000361337.2	37	CCDS13312.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301974	0.81136	.	.	ENSG00000198900	ENST00000361337	T	0.44083	0.93	5.3	5.3	0.74995	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, eukaryotic-type (1);DNA topoisomerase I, C-terminal (1);DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (1);	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78329	-0.2246	10	0.87932	D	0	-17.1921	13.6261	0.62165	0.0747:0.0:0.9252:0.0	.	484	P11387	TOP1_HUMAN	N	484	ENSP00000354522:K484N	ENSP00000354522:K484N	K	+	3	2	TOP1	39174979	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.651000	0.46674	2.633000	0.89246	0.650000	0.86243	AAG		0.488	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2		Missense_Mutation	T	39741565	G	T	39741565	5	4	61	1	0	0	0	0	0	0	1	0	16403	1014	35	2	1506	2	TOP1	20	39741565	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28440	39741565	23283955	11601	19586										
PLCG1	5335	broad.mit.edu	37	chr20	39795391	39795391	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgctagggaactcggagttCgacagccttgttgacctcat	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:39795391C>T	ENST00000373271.1	+	19	2598	c.2193C>T	c.(2191-2193)ttC>ttT	p.F731F	PLCG1_ENST00000244007.3_Silent_p.F731F|PLCG1_ENST00000373272.2_Silent_p.F731F	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	731	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)	p.F731F(1)		breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				ACTCGGAGTTCGACAGCCTTG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	20											142	128	133					20																	39795391		2203	4300	6503	39228805	SO:0001819	synonymous_variant	5335			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2193C>T	20.37:g.39795391C>T			39228805	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																				0.527	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39795391	C	T	39795391	2	4	61	1	0	0	0	0	0	0	0	1	12066	883	31	1		1	PLCG1	20	39795391	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53826	39795391	23230129	11602	19587										
ZHX3	23051	broad.mit.edu	37	chr20	39831594	39831594	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaaaccagctatcaatttCtcgtcgggtcattttggttt	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:39831594C>A	ENST00000309060.3	-	4	2378	c.1963G>T	c.(1963-1965)Gaa>Taa	p.E655*	ZHX3_ENST00000540170.1_Nonsense_Mutation_p.E655*|ZHX3_ENST00000559234.1_Nonsense_Mutation_p.E655*|ZHX3_ENST00000432768.2_Nonsense_Mutation_p.E655*|ZHX3_ENST00000544979.2_Nonsense_Mutation_p.E655*|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000560361.1_Nonsense_Mutation_p.E655*			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	655					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E655*(1)		endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CTATCAATTTCTCGTCGGGTC	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											151	163	159					20																	39831594		2203	4300	6503	39265008	SO:0001587	stop_gained	23051			AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.1963G>T	20.37:g.39831594C>A	ENSP00000312222:p.Glu655*		39265008	E1P5W5|F5H820|O43145|Q6NUJ7	Nonsense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.757538|9.757538	0.99256|0.99256	.|.	.|.	ENSG00000174306|ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262|ENST00000421422	.|D	.|0.96802	.|-4.13	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|D	.|0.98226	.|0.9413	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.98419	.|1.0576	.|5	0.51188|0.72032	T|D	0.08|0.01	-22.6534|-22.6534	20.2348|20.2348	0.98355|0.98355	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	655;655;655;655;433|363	.|ENSP00000405421:R363I	ENSP00000312222:E655X|ENSP00000405421:R363I	E|R	-|-	1|2	0|0	ZHX3|ZHX3	39265008|39265008	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.994000|0.994000	0.84299|0.84299	7.473000|7.473000	0.81007|0.81007	2.879000|2.879000	0.98667|0.98667	0.650000|0.650000	0.86243|0.86243	GAA|AGA		0.502	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		A	39831594	C	A	39831594	4	1	61	1	0	0	0	0	0	1	0	0	17716	922	32	2	915	2	ZHX3	20	39831594	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36203	39831594	23193926	11603	19588										
CHD6	84181	broad.mit.edu	37	chr20	40122242	40122242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taacttttgcaggatctacaTcttcctctagctcccacgtg	6	13	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:40122242T>C	ENST00000373233.3	-	10	1427	c.1250A>G	c.(1249-1251)gAt>gGt	p.D417G	CHD6_ENST00000309279.7_Missense_Mutation_p.D417G	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	417	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.D417G(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGGATCTACATCTTCCTCTAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	20											120	111	114					20																	40122242		2203	4300	6503	39555656	SO:0001583	missense	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.1250A>G	20.37:g.40122242T>C	ENSP00000362330:p.Asp417Gly		39555656	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.9|27.9	4.877030|4.877030	0.91664|0.91664	.|.	.|.	ENSG00000124177|ENSG00000124177	ENST00000373233;ENST00000309279|ENST00000440697	T;T|.	0.73897|.	-0.79;-0.79|.	5.68|5.68	5.68|5.68	0.88126|0.88126	Chromo domain (1);Chromo domain/shadow (2);|.	0.000000|.	0.56097|.	D|.	0.000027|.	D|D	0.85592|0.85592	0.5732|0.5732	M|M	0.92923|0.92923	3.36|3.36	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.89237|0.89237	0.3581|0.3581	10|5	0.87932|.	D|.	0|.	-17.6989|-17.6989	15.9211|15.9211	0.79575|0.79575	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	417|.	Q8TD26|.	CHD6_HUMAN|.	G|V	417|120	ENSP00000362330:D417G;ENSP00000308684:D417G|.	ENSP00000308684:D417G|.	D|M	-|-	2|1	0|0	CHD6|CHD6	39555656|39555656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	7.997000|7.997000	0.88414|0.88414	2.156000|2.156000	0.67533|0.67533	0.459000|0.459000	0.35465|0.35465	GAT|ATG		0.418	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40122242	T	C	40122242	3	2	61	1	0	0	0	0	1	0	0	0	3335	1435	50	4	7009	4	CHD6	20	40122242	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	290648	40122242	22903278	11604	19589										
PTPRT	11122	broad.mit.edu	37	chr20	40827909	40827909	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacgtcctgagaactagaaGagaagccttcatcattgcgg	11	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:40827909G>A	ENST00000373187.1	-	16	2461	c.2462C>T	c.(2461-2463)tCt>tTt	p.S821F	PTPRT_ENST00000373193.3_Missense_Mutation_p.S824F|PTPRT_ENST00000373201.1_Missense_Mutation_p.S811F|PTPRT_ENST00000373198.4_Missense_Mutation_p.S840F|PTPRT_ENST00000373190.1_Missense_Mutation_p.S821F|PTPRT_ENST00000356100.2_Missense_Mutation_p.S830F|PTPRT_ENST00000373184.1_Missense_Mutation_p.S811F			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	821					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.S843F(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGAACTAGAAGAGAAGCCTTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	20											319	324	322					20																	40827909		2054	4204	6258	40261323	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2462C>T	20.37:g.40827909G>A	ENSP00000362283:p.Ser821Phe		40261323	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896523	0.72639	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.38887	1.11;1.17;1.19;1.21;1.19;1.21;1.21	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	L	0.34521	1.04	0.80722	D	1	D;D	0.62365	0.991;0.985	P;P	0.61592	0.891;0.781	T	0.51702	-0.8672	10	0.56958	D	0.05	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	843;821	O14522-1;O14522	.;PTPRT_HUMAN	F	821;821;824;830;843;811;811	ENSP00000362286:S821F;ENSP00000362283:S821F;ENSP00000362289:S824F;ENSP00000348408:S830F;ENSP00000362294:S843F;ENSP00000362280:S811F;ENSP00000362297:S811F	ENSP00000348408:S830F	S	-	2	0	PTPRT	40261323	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.030000	0.93725	2.861000	0.98227	0.655000	0.94253	TCT		0.572	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40827909	G	A	40827909	3	1	61	1	0	0	0	0	1	0	0	0	12849	942	33	3	1927	3	PTPRT	20	40827909	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	705667	40827909	22197611	11605	19590										
SFRS6	6431	broad.mit.edu	37	chr20	42089365	42089365	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggtcgcggagcaaaggtCgatcacgttctcgatcaaaa	11	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42089365C>T	ENST00000244020.3	+	6	803	c.697C>T	c.(697-699)Cga>Tga	p.R233*		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	233	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.R233*(2)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						GAGCAAAGGTCGATCACGTTC	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	20											57	52	54					20																	42089365		2203	4300	6503	41522779	SO:0001587	stop_gained	6431			U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.697C>T	20.37:g.42089365C>T	ENSP00000244020:p.Arg233*		41522779	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Nonsense_Mutation	SNP	ENST00000244020.3	37	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	C	36	5.714380	0.96830	.	.	ENSG00000124193	ENST00000244020	.	.	.	5.97	5.97	0.96955	.	0.192641	0.41938	D	0.000782	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2039	0.93722	0.0:1.0:0.0:0.0	.	.	.	.	X	233	.	ENSP00000244020:R233X	R	+	1	2	SRSF6	41522779	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.672000	0.68102	2.833000	0.97629	0.585000	0.79938	CGA		0.433	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		T	42089365	C	T	42089365	4	4	61	1	0	0	0	0	0	1	0	0	14218	876	31	1	719	1	SFRS6	20	42089365	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1261456	42089365	20936155	11606	19591										
SGK2	10110	broad.mit.edu	37	chr20	42199679	42199679	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagggatctgaaaccagaGaacattctcttggactgcca	10	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42199679G>T	ENST00000341458.4	+	7	888	c.669G>T	c.(667-669)gaG>gaT	p.E223D	SGK2_ENST00000423407.3_Missense_Mutation_p.E163D|SGK2_ENST00000426287.1_Missense_Mutation_p.E189D|SGK2_ENST00000373077.1_Missense_Mutation_p.E162D|SGK2_ENST00000373100.1_Missense_Mutation_p.E163D|SGK2_ENST00000373092.3_Missense_Mutation_p.E163D	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	223	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.E223D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TGAAACCAGAGAACATTCTCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											123	115	118					20																	42199679		2203	4300	6503	41633093	SO:0001583	missense	10110			AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.669G>T	20.37:g.42199679G>T	ENSP00000340608:p.Glu223Asp		41633093	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.646433	0.67358	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69;1.69;1.69	4.22	1.22	0.21188	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.105668	0.64402	D	0.000002	T	0.28566	0.0707	L	0.38692	1.165	0.58432	D	0.999997	P;P;B	0.46142	0.814;0.873;0.382	P;P;B	0.55260	0.662;0.772;0.283	T	0.03463	-1.1034	10	0.87932	D	0	.	6.1795	0.20463	0.4318:0.0:0.5682:0.0	.	189;223;163	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	D	163;163;162;162;163;223;189	ENSP00000362192:E163D;ENSP00000362184:E163D;ENSP00000362168:E162D;ENSP00000396222:E162D;ENSP00000392795:E163D;ENSP00000340608:E223D;ENSP00000412214:E189D	ENSP00000340608:E223D	E	+	3	2	SGK2	41633093	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	0.815000	0.27253	0.320000	0.23234	-0.258000	0.10820	GAG		0.507	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			T	42199679	G	T	42199679	3	4	61	1	0	0	0	0	1	0	0	0	14246	933	33	2	695	2	SGK2	20	42199679	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	110314	42199679	20825841	11607	19592										
MYBL2	4605	broad.mit.edu	37	chr20	42328485	42328485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttgcagcagccaccacatCgaaggaacaggagcccatcg	10	14	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42328485C>T	ENST00000217026.4	+	7	879	c.752C>T	c.(751-753)tCg>tTg	p.S251L	MYBL2_ENST00000396863.4_Missense_Mutation_p.S227L	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	251					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S251L(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GCCACCACATCGAAGGAACAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											80	68	72					20																	42328485		2203	4300	6503	41761899	SO:0001583	missense	4605				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.752C>T	20.37:g.42328485C>T	ENSP00000217026:p.Ser251Leu		41761899	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	C	8.819	0.937043	0.18206	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.15017	2.46;2.46	4.77	1.74	0.24563	.	1.612220	0.03310	N	0.190431	T	0.14141	0.0342	L	0.43152	1.355	0.09310	N	1	B;B	0.32781	0.042;0.384	B;B	0.16289	0.009;0.015	T	0.24440	-1.0160	10	0.34782	T	0.22	-1.1699	6.5378	0.22363	0.0:0.6828:0.1483:0.1689	.	227;251	F8W6N6;P10244	.;MYBB_HUMAN	L	227;251	ENSP00000380072:S227L;ENSP00000217026:S251L	ENSP00000217026:S251L	S	+	2	0	MYBL2	41761899	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.073000	0.14640	0.289000	0.22422	-0.889000	0.02933	TCG		0.567	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42328485	C	T	42328485	3	4	61	1	0	0	0	0	1	0	0	0	10040	893	31	1	778	1	MYBL2	20	42328485	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128806	42328485	20697035	11608	19593										
GTSF1L	149699	broad.mit.edu	37	chr20	42355026	42355026	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagcgccatcgacattccaGatatcggggctgggaaggca	13	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42355026G>T	ENST00000373003.1	-	1	612	c.309C>A	c.(307-309)atC>atA	p.I103I	GTSF1L_ENST00000373005.2_Intron	NM_001008901.1|NM_176791.3	NP_001008901.1|NP_789761.1	Q9H1H1	GTSFL_HUMAN	gametocyte specific factor 1-like	103							metal ion binding (GO:0046872)	p.I103I(1)		endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CGACATTCCAGATATCGGGGC	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	20											117	100	106					20																	42355026		2203	4300	6503	41788440	SO:0001819	synonymous_variant	149699			AK058060	CCDS13323.1, CCDS33471.1	20q13.12	2007-11-27	2007-11-27	2007-11-27	ENSG00000124196	ENSG00000124196			16198	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 65", "family with sequence similarity 112, member A"	C20orf65, FAM112A			Standard	NM_176791		Approved	dJ1028D15.4	uc002xld.3	Q9H1H1	OTTHUMG00000032510	ENST00000373003.1:c.309C>A	20.37:g.42355026G>T			41788440	Q5JWH5	Silent	SNP	ENST00000373003.1	37	CCDS13323.1																																																																																				0.483	GTSF1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079313.1	NM_176791		T	42355026	G	T	42355026	2	4	61	1	0	0	0	0	0	0	0	1	6908	932	33	2		2	GTSF1L	20	42355026	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26541	42355026	20670494	11609	19594										
JPH2	57158	broad.mit.edu	37	chr20	42788637	42788637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcggcctctcccaggctggCggtggacgcggcgtcgctgg	19	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42788637C>T	ENST00000372980.3	-	2	1662	c.790G>A	c.(790-792)Gcc>Acc	p.A264T		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	264					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.A264T(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CCCAGGCTGGCGGTGGACGCG	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	20											14	16	15					20																	42788637		2193	4277	6470	42222051	SO:0001583	missense	57158			AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.790G>A	20.37:g.42788637C>T	ENSP00000362071:p.Ala264Thr		42222051	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	37	CCDS13325.1	.	.	.	.	.	.	.	.	.	.	c	2.776	-0.254671	0.05829	.	.	ENSG00000149596	ENST00000372980	T	0.60040	0.22	3.03	-0.447	0.12234	.	0.478986	0.22078	U	0.064929	T	0.27933	0.0688	N	0.04880	-0.145	0.58432	D	0.999998	B	0.21071	0.051	B	0.08055	0.003	T	0.06023	-1.0850	10	0.14252	T	0.57	.	9.102	0.36673	0.0:0.6896:0.0:0.3104	.	264	Q9BR39	JPH2_HUMAN	T	264	ENSP00000362071:A264T	ENSP00000362071:A264T	A	-	1	0	JPH2	42222051	0.977000	0.34250	0.208000	0.23602	0.088000	0.18126	0.905000	0.28504	0.066000	0.16515	-0.755000	0.03482	GCC		0.706	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			T	42788637	C	T	42788637	3	4	61	1	0	0	0	0	1	0	0	0	7982	768	27	1	1316	1	JPH2	20	42788637	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	433611	42788637	20236883	11610	19595										
GDAP1L1	78997	broad.mit.edu	37	chr20	42893093	42893093	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgcccccaggccaagatCttggagcatgatgatgtgag	12	11	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:42893093C>A	ENST00000342560.5	+	5	742	c.654C>A	c.(652-654)atC>atA	p.I218I	GDAP1L1_ENST00000537864.1_Silent_p.I26I	NM_001256737.1|NM_024034.4	NP_001243666.1|NP_076939.3	Q96MZ0	GD1L1_HUMAN	ganglioside induced differentiation associated protein 1-like 1	218	GST C-terminal.							p.I218I(1)		endometrium(1)|large_intestine(5)|lung(10)|pancreas(1)|prostate(1)	18		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			AGGCCAAGATCTTGGAGCATG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	20											62	56	58					20																	42893093		2203	4300	6503	42326507	SO:0001819	synonymous_variant	78997				CCDS13328.1, CCDS74725.1, CCDS74726.1, CCDS74727.1	20q12	2012-02-09	2012-02-09		ENSG00000124194	ENSG00000124194			4213	protein-coding gene	gene with protein product							Standard	NM_024034		Approved		uc010zwl.3	Q96MZ0	OTTHUMG00000032530	ENST00000342560.5:c.654C>A	20.37:g.42893093C>A			42326507	B7Z621|Q5TE60|Q68CW7|Q9BQJ7|Q9BQV4|Q9BWJ4|Q9H3Y2|Q9H4G5	Silent	SNP	ENST00000342560.5	37	CCDS13328.1	.	.	.	.	.	.	.	.	.	.	C	9.964	1.223532	0.22457	.	.	ENSG00000124194	ENST00000445952	.	.	.	5.31	2.28	0.28536	.	.	.	.	.	T	0.52468	0.1736	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42241	-0.9463	4	.	.	.	.	5.4234	0.16413	0.2844:0.567:0.0:0.1486	.	.	.	.	I	165	.	.	L	+	1	0	GDAP1L1	42326507	0.400000	0.25295	1.000000	0.80357	0.994000	0.84299	0.465000	0.22004	0.605000	0.29947	0.491000	0.48974	CTT		0.552	GDAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079356.1	NM_024034		A	42893093	C	A	42893093	2	1	61	1	0	0	0	0	0	0	0	1	6328	903	32	2		2	GDAP1L1	20	42893093	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	104456	42893093	20132427	11611	19596										
HNF4A	3172	broad.mit.edu	37	chr20	43036049	43036049	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagtgcgtggtggacaaaGacaagaggaaccagtgccgc	16	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43036049G>T	ENST00000316099.4	+	3	408	c.319G>T	c.(319-321)Gac>Tac	p.D107Y	MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000316673.4_Missense_Mutation_p.D85Y|HNF4A_ENST00000443598.2_Missense_Mutation_p.D107Y|HNF4A_ENST00000609795.1_Missense_Mutation_p.D85Y|HNF4A_ENST00000415691.2_Missense_Mutation_p.D107Y|HNF4A_ENST00000457232.1_Missense_Mutation_p.D85Y	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	107					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.D107Y(1)|p.D85Y(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GGTGGACAAAGACAAGAGGAA	0.587																																					Colon(79;2 1269 8820 14841 52347)											2	Substitution - Missense(2)	large_intestine(2)	20											79	64	69					20																	43036049		2203	4300	6503	42469463	SO:0001583	missense	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.319G>T	20.37:g.43036049G>T	ENSP00000312987:p.Asp107Tyr		42469463	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	37	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.969638	0.92855	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31	5.69	5.69	0.88448	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.97926	0.9318	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;0.997;0.997;0.998;1.0;0.998;0.995	D	0.98771	1.0728	10	0.72032	D	0.01	.	19.8064	0.96533	0.0:0.0:1.0:0.0	.	100;107;107;107;85;85;85	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	Y	85;85;107;107;137;107	ENSP00000315180:D85Y;ENSP00000396216:D85Y;ENSP00000312987:D107Y;ENSP00000410911:D107Y;ENSP00000412111:D107Y	ENSP00000312987:D107Y	D	+	1	0	HNF4A	42469463	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.859000	0.99545	2.679000	0.91253	0.643000	0.83706	GAC		0.587	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43036049	G	T	43036049	3	4	61	1	0	0	0	0	1	0	0	0	7274	942	33	2	382	2	HNF4A	20	43036049	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	142956	43036049	19989471	11612	19597										
SERINC3	10955	broad.mit.edu	37	chr20	43150569	43150569	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacccagctggcgagggaGaagacacccagcacagcccc	11	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43150569G>T	ENST00000342374.4	-	1	181	c.24C>A	c.(22-24)ttC>ttA	p.F8L	SERINC3_ENST00000468234.1_5'UTR|SERINC3_ENST00000541235.1_5'UTR|SERINC3_ENST00000255175.1_Missense_Mutation_p.F8L	NM_006811.2	NP_006802.1	Q13530	SERC3_HUMAN	serine incorporator 3	8					phosphatidylserine metabolic process (GO:0006658)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)	p.F8L(1)		endometrium(4)|large_intestine(2)|lung(8)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			TGGCGAGGGAGAAGACACCCA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	20											64	58	60					20																	43150569		2201	4299	6500	42583983	SO:0001583	missense	10955			U49188	CCDS13333.1	20q13.12	2008-05-14	2005-11-15	2005-11-15	ENSG00000132824	ENSG00000132824			11699	protein-coding gene	gene with protein product		607165	"tumor differentially expressed 1"	TDE1		10559794	Standard	NM_006811		Approved	DIFF33, TDE, SBBI99, TMS-1, AIGP1	uc002xme.3	Q13530	OTTHUMG00000033087	ENST00000342374.4:c.24C>A	20.37:g.43150569G>T	ENSP00000340243:p.Phe8Leu		42583983	B4DUE9|O43717|Q9BR33	Missense_Mutation	SNP	ENST00000342374.4	37	CCDS13333.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.081063	0.55753	.	.	ENSG00000132824	ENST00000255175;ENST00000342374	T;T	0.12672	2.66;2.66	4.7	4.7	0.59300	.	0.453474	0.26792	N	0.022462	T	0.06690	0.0171	N	0.05441	-0.05	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30880	-0.9963	10	0.10902	T	0.67	-13.4592	12.2851	0.54788	0.0832:0.0:0.9168:0.0	.	8	Q13530	SERC3_HUMAN	L	8	ENSP00000255175:F8L;ENSP00000340243:F8L	ENSP00000255175:F8L	F	-	3	2	SERINC3	42583983	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.878000	0.39608	2.586000	0.87340	0.591000	0.81541	TTC		0.652	SERINC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080544.3	NM_006811		T	43150569	G	T	43150569	3	4	61	1	0	0	0	0	1	0	0	0	14118	933	33	2	1437	2	SERINC3	20	43150569	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	114520	43150569	19874951	11613	19598										
ADA	100	broad.mit.edu	37	chr20	43251230	43251230	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggggaacagagctcaccGaatgactgcatgctccgtgt	12	12	1	2	rs559798694		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43251230G>A	ENST00000372874.4	-	9	978	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	PKIG_ENST00000372882.3_Intron|ADA_ENST00000464097.1_5'UTR|ADA_ENST00000537820.1_Splice_Site_p.R258W|PKIG_ENST00000372887.1_Intron	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	282					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)	p.R282W(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	AGAGCTCACCGAATGACTGCA	0.577									Adenosine Deaminase Deficiency				G|||	1	0.000199681	0	0	5008	,	,		18824	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	20											59	56	57					20																	43251230		2203	4300	6503	42684644	SO:0001630	splice_region_variant	100	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.845+1C>T	20.37:g.43251230G>A			42684644	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294207	0.60086	.	.	ENSG00000196839	ENST00000372874;ENST00000537820	D;D	0.95554	-3.74;-3.74	5.13	4.11	0.48088	Adenosine/AMP deaminase (1);	0.169822	0.52532	D	0.000080	D	0.97321	0.9124	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	D	0.97451	1.0028	10	0.66056	D	0.02	-16.3693	13.1529	0.59500	0.0:0.0:0.7278:0.2722	.	282	P00813	ADA_HUMAN	W	282;258	ENSP00000361965:R282W;ENSP00000441818:R258W	ENSP00000361965:R282W	R	-	1	2	ADA	42684644	1.000000	0.71417	0.987000	0.45799	0.519000	0.34347	3.291000	0.51764	2.388000	0.81334	0.561000	0.74099	CGG		0.577	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	Missense_Mutation	A	43251230	G	A	43251230	5	1	61	1	0	0	0	0	0	0	1	0	230	1072	37	1	263	1	ADA	20	43251230	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100661	43251230	19774290	11614	19599										
RIMS4	140730	broad.mit.edu	37	chr20	43385613	43385613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggtccagcgacttgcgagCgactttggtcttcttcttgg	13	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43385613C>T	ENST00000372851.3	-	5	583	c.517G>A	c.(517-519)Gct>Act	p.A173T	RIMS4_ENST00000541604.2_Missense_Mutation_p.A174T	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	173	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)		p.A173T(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				GACTTGCGAGCGACTTTGGTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											298	270	279					20																	43385613		2203	4300	6503	42819027	SO:0001583	missense	140730				CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546	ENST00000372851.3:c.517G>A	20.37:g.43385613C>T	ENSP00000361942:p.Ala173Thr		42819027	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	33	5.279098	0.95489	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	T;T	0.79141	-1.24;-1.24	5.38	5.38	0.77491	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.052363	0.85682	D	0.000000	T	0.76765	0.4033	L	0.60904	1.88	0.80722	D	1	P;P	0.48640	0.913;0.822	B;B	0.40901	0.343;0.242	T	0.80405	-0.1396	10	0.59425	D	0.04	.	19.1287	0.93396	0.0:1.0:0.0:0.0	.	174;173	E1P613;Q9H426	.;RIMS4_HUMAN	T	173;174	ENSP00000361942:A173T;ENSP00000439287:A174T	ENSP00000361942:A173T	A	-	1	0	RIMS4	42819027	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	7.792000	0.85828	2.510000	0.84645	0.462000	0.41574	GCT		0.567	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		T	43385613	C	T	43385613	3	4	61	1	0	0	0	0	1	0	0	0	13407	768	27	1	300	1	RIMS4	20	43385613	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	134383	43385613	19639907	11615	19600										
TOMM34	10953	broad.mit.edu	37	chr20	43580536	43580536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatctctttgtggttctccGaaggcaaggaattccacctc	8	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43580536G>A	ENST00000372813.3	-	4	640	c.488C>T	c.(487-489)tCg>tTg	p.S163L	PABPC1L_ENST00000372819.1_Intron|PABPC1L_ENST00000490798.1_Intron	NM_006809.4	NP_006800.2	Q15785	TOM34_HUMAN	translocase of outer mitochondrial membrane 34	163					protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)	p.S163L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	11		Myeloproliferative disorder(115;0.0122)				GTGGTTCTCCGAAGGCAAGGA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	20											173	134	147					20																	43580536		2203	4300	6503	43013950	SO:0001583	missense	10953			U58970	CCDS13340.1	20q12-q13.1	2013-01-10			ENSG00000025772	ENSG00000025772		"Tetratricopeptide (TTC) repeat domain containing"	15746	protein-coding gene	gene with protein product	"outer mitochondrial membrane translocase (34kD)"					9324309	Standard	NM_006809		Approved	TOM34, HTOM34P	uc002xmy.3	Q15785	OTTHUMG00000032552	ENST00000372813.3:c.488C>T	20.37:g.43580536G>A	ENSP00000361900:p.Ser163Leu		43013950	Q53GH9|Q6IBN7|Q9NTZ3	Missense_Mutation	SNP	ENST00000372813.3	37	CCDS13340.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.298010	0.23650	.	.	ENSG00000025772	ENST00000372813	T	0.78595	-1.19	5.14	0.816	0.18768	.	0.903830	0.09496	N	0.794277	T	0.54334	0.1852	N	0.04880	-0.145	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.39354	-0.9618	10	0.27082	T	0.32	-37.1747	6.8513	0.24016	0.1495:0.2681:0.5824:0.0	.	163	Q15785	TOM34_HUMAN	L	163	ENSP00000361900:S163L	ENSP00000361900:S163L	S	-	2	0	TOMM34	43013950	0.810000	0.29049	0.008000	0.14137	0.003000	0.03518	1.320000	0.33666	0.346000	0.23899	-0.172000	0.13284	TCG		0.527	TOMM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079390.3	NM_006809		A	43580536	G	A	43580536	3	1	61	1	0	0	0	0	1	0	0	0	16396	1059	37	1	457	1	TOMM34	20	43580536	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194923	43580536	19444984	11616	19601										
PI3	5266	broad.mit.edu	37	chr20	43804616	43804616	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcaaagcgcaagagccagTcaaaggtccagtctccacta	9	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:43804616T>C	ENST00000243924.3	+	2	241	c.194T>C	c.(193-195)gTc>gCc	p.V65A		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	65	2 X tandem repeats of SVP-1 like motif.				copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.V65A(1)		large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CAAGAGCCAGTCAAAGGTCCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	20											131	112	118					20																	43804616		2203	4300	6503	43238030	SO:0001583	missense	5266			D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"WAP four-disulfide core domain containing"	8947	protein-coding gene	gene with protein product	"skin-derived antileukoproteinase", "trappin-2"	182257	"protease inhibitor 3, skin-derived (SKALP)"			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.194T>C	20.37:g.43804616T>C	ENSP00000243924:p.Val65Ala		43238030	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	.	.	.	.	.	.	.	.	.	.	T	5.257	0.232805	0.09969	.	.	ENSG00000124102	ENST00000243924	T	0.59906	0.23	3.18	0.762	0.18454	Whey acidic protein, 4-disulphide core (1);	5.059960	0.00822	N	0.001580	T	0.55033	0.1895	M	0.70787	2.145	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.08126	-1.0737	10	0.25751	T	0.34	.	3.8429	0.08922	0.2168:0.0:0.2249:0.5583	.	65	P19957	ELAF_HUMAN	A	65	ENSP00000243924:V65A	ENSP00000243924:V65A	V	+	2	0	PI3	43238030	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.073000	0.11468	0.129000	0.18514	0.528000	0.53228	GTC		0.488	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638		C	43804616	T	C	43804616	3	2	61	1	0	0	0	0	1	0	0	0	11901	1667	58	4	200	4	PI3	20	43804616	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	224080	43804616	19220904	11617	19602										
PIGT	51604	broad.mit.edu	37	chr20	44049313	44049313	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaacatccagctcaagtGgaagagacccccagagaatg	9	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44049313G>T	ENST00000279036.6	+	8	1093	c.1013G>T	c.(1012-1014)tGg>tTg	p.W338L	PIGT_ENST00000543458.2_Missense_Mutation_p.W282L|PIGT_ENST00000545755.1_Missense_Mutation_p.W76L|PIGT_ENST00000341555.5_Missense_Mutation_p.W144L|PIGT_ENST00000372689.5_Missense_Mutation_p.W338L|PIGT_ENST00000535404.1_Missense_Mutation_p.W183L|PIGT_ENST00000279035.9_Missense_Mutation_p.W236L	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	338					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)	p.W338L(1)		breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				CAGCTCAAGTGGAAGAGACCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	20											98	81	87					20																	44049313		2203	4300	6503	43482727	SO:0001583	missense	51604				CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"Phosphatidylinositol glycan anchor biosynthesis"	14938	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610272	"phosphatidylinositol glycan, class T"			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.1013G>T	20.37:g.44049313G>T	ENSP00000279036:p.Trp338Leu		43482727	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Missense_Mutation	SNP	ENST00000279036.6	37	CCDS13353.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620846	0.87460	.	.	ENSG00000124155	ENST00000543458;ENST00000372689;ENST00000279035;ENST00000279036;ENST00000455050;ENST00000545755;ENST00000341555;ENST00000535404	T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.66713	0.2817	M	0.85462	2.755	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;0.971;1.0;1.0;0.996;1.0;1.0;0.992;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;0.923;0.999;0.999;0.958;0.999;0.997;0.956;0.999	T	0.63180	-0.6695	10	0.12103	T	0.63	-15.1324	18.3101	0.90195	0.0:0.0:1.0:0.0	.	176;236;183;282;76;144;194;76;338	B7Z3L1;Q969N2-4;F5GWY0;B7Z3N1;B7ZAP3;Q969N2-2;Q969N2-3;B7Z1N3;Q969N2	.;.;.;.;.;.;.;.;PIGT_HUMAN	L	282;338;236;338;236;76;144;183	ENSP00000441577:W282L;ENSP00000361774:W338L;ENSP00000279035:W236L;ENSP00000279036:W338L;ENSP00000443963:W76L;ENSP00000343783:W144L;ENSP00000440528:W183L	ENSP00000279035:W236L	W	+	2	0	PIGT	43482727	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.454000	0.80714	2.793000	0.96121	0.655000	0.94253	TGG		0.517	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937		T	44049313	G	T	44049313	3	4	61	1	0	0	0	0	1	0	0	0	11930	1357	47	2	1043	2	PIGT	20	44049313	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244697	44049313	18976207	11618	19603										
WFDC10A	140832	broad.mit.edu	37	chr20	44258515	44258515	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgctgcaggcccagggAggataccgtgacaagaagag	15	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44258515A>G	ENST00000372643.3	+	1	351	c.63A>G	c.(61-63)ggA>ggG	p.G21G	WFDC9_ENST00000326000.1_Intron	NM_080753.2	NP_542791.1	Q9H1F0	WF10A_HUMAN	WAP four-disulfide core domain 10A	21						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G21G(1)		large_intestine(2)	2		Myeloproliferative disorder(115;0.0122)				AGGCCCAGGGAGGATACCGTG	0.592											OREG0025983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	20											154	119	131					20																	44258515		2203	4300	6503	43691929	SO:0001819	synonymous_variant	140832			AL031671	CCDS13363.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000180305	ENSG00000180305		"WAP four-disulfide core domain containing"	16139	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 146"	C20orf146		12206714	Standard	NM_080753		Approved	dJ688G8.3, WAP10	uc002xoz.3	Q9H1F0	OTTHUMG00000046331	ENST00000372643.3:c.63A>G	20.37:g.44258515A>G		922	43691929	A2RRE9|Q5TGZ7	Silent	SNP	ENST00000372643.3	37	CCDS13363.1																																																																																				0.592	WFDC10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106944.2			G	44258515	A	G	44258515	2	3	61	1	0	0	0	0	0	0	0	1	17387	291	11	4		4	WFDC10A	20	44258515	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	209202	44258515	18767005	11619	19604										
WFDC3	140686	broad.mit.edu	37	chr20	44418549	44418549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaccatgttctcctgcagtTatccaggattccagagaccc	7	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44418549T>C	ENST00000243938.4	-	2	149	c.66A>G	c.(64-66)atA>atG	p.I22M	WFDC3_ENST00000372632.2_Missense_Mutation_p.I22M|WFDC3_ENST00000372630.2_Missense_Mutation_p.I22M|WFDC3_ENST00000481847.1_Intron|DNTTIP1_ENST00000372622.3_5'Flank	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	22						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.I22M(1)		endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				CTCCTGCAGTTATCCAGGATT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	20											118	99	105					20																	44418549		2203	4300	6503	43851956	SO:0001583	missense	140686			AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.66A>G	20.37:g.44418549T>C	ENSP00000243938:p.Ile22Met		43851956	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	37	CCDS33478.1	.	.	.	.	.	.	.	.	.	.	T	4.383	0.070753	0.08436	.	.	ENSG00000124116	ENST00000243938;ENST00000372630;ENST00000372632	T;T;T	0.22945	1.94;1.93;1.95	4.02	-0.712	0.11226	Whey acidic protein, 4-disulphide core (1);	1.041310	0.07697	N	0.939738	T	0.14399	0.0348	N	0.22421	0.69	0.09310	N	1	B	0.26400	0.148	B	0.18871	0.023	T	0.28332	-1.0047	10	0.51188	T	0.08	-2.0444	3.7759	0.08660	0.221:0.5013:0.0:0.2778	.	22	Q8IUB2	WFDC3_HUMAN	M	22	ENSP00000243938:I22M;ENSP00000361713:I22M;ENSP00000361715:I22M	ENSP00000243938:I22M	I	-	3	3	WFDC3	43851956	0.733000	0.28132	0.014000	0.15608	0.209000	0.24338	0.078000	0.14761	-0.114000	0.11936	0.533000	0.62120	ATA		0.488	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1			C	44418549	T	C	44418549	3	2	61	1	0	0	0	0	1	0	0	0	17393	1744	61	4	653	4	WFDC3	20	44418549	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	160034	44418549	18606971	11620	19605										
PLTP	5360	broad.mit.edu	37	chr20	44534981	44534981	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagtcaatgccaacaagctCgtccacagaactgcgcactg	8	13	1	1	rs370983158		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44534981C>T	ENST00000477313.1	-	7	1225	c.631G>A	c.(631-633)Gag>Aag	p.E211K	PLTP_ENST00000354050.4_Missense_Mutation_p.E159K|PLTP_ENST00000542937.1_Missense_Mutation_p.E231K|PLTP_ENST00000372431.3_Missense_Mutation_p.E211K|PLTP_ENST00000372420.1_Missense_Mutation_p.E123K|PLTP_ENST00000420868.2_Missense_Mutation_p.E116K			P55058	PLTP_HUMAN	phospholipid transfer protein	211					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.E211K(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				CCAACAAGCTCGTCCACAGAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	20											103	78	87					20																	44534981		2203	4300	6503	43968388	SO:0001583	missense	5360			L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.631G>A	20.37:g.44534981C>T	ENSP00000417138:p.Glu211Lys		43968388	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	C	7.706	0.694073	0.15039	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.04360	3.64;3.64;3.64;3.64;3.64;3.64	5.25	0.493	0.16878	Lipid-binding serum glycoprotein, N-terminal (1);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.090600	0.06695	N	0.770434	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B	0.19935	0.04;0.04;0.013;0.013;0.021;0.013;0.013	B;B;B;B;B;B;B	0.12156	0.003;0.003;0.005;0.003;0.007;0.003;0.003	T	0.46665	-0.9175	10	0.16420	T	0.52	-3.1236	7.9374	0.29937	0.0:0.5597:0.2841:0.1561	.	116;116;123;211;159;211;231	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	K	123;211;159;211;231;116	ENSP00000361497:E123K;ENSP00000361508:E211K;ENSP00000335290:E159K;ENSP00000417138:E211K;ENSP00000440296:E231K;ENSP00000411671:E116K	ENSP00000335290:E159K	E	-	1	0	PLTP	43968388	0.000000	0.05858	0.004000	0.12327	0.767000	0.43475	-0.371000	0.07513	0.596000	0.29794	0.555000	0.69702	GAG		0.562	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44534981	C	T	44534981	3	4	61	1	0	0	0	0	1	0	0	0	12145	893	31	1	886	1	PLTP	20	44534981	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	116432	44534981	18490539	11621	19606										
PLTP	5360	broad.mit.edu	37	chr20	44539867	44539867	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtctccagctcttgctccaGaaagcgcagcccctcctgct	8	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44539867G>T	ENST00000477313.1	-	2	718	c.124C>A	c.(124-126)Ctg>Atg	p.L42M	PLTP_ENST00000354050.4_Missense_Mutation_p.L42M|PLTP_ENST00000542937.1_Missense_Mutation_p.L62M|PLTP_ENST00000372431.3_Missense_Mutation_p.L42M|PLTP_ENST00000372420.1_5'Flank|PLTP_ENST00000420868.2_Missense_Mutation_p.L42M			P55058	PLTP_HUMAN	phospholipid transfer protein	42					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.L42M(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				TCTTGCTCCAGAAAGCGCAGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											78	80	79					20																	44539867		2203	4300	6503	43973274	SO:0001583	missense	5360			L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.124C>A	20.37:g.44539867G>T	ENSP00000417138:p.Leu42Met		43973274	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.662327	0.67700	.	.	ENSG00000100979	ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74	5.2	2.12	0.27331	Lipid-binding serum glycoprotein, conserved site (1);Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.065184	0.64402	D	0.000012	T	0.29491	0.0735	M	0.74881	2.28	0.34609	D	0.717416	D;D;D;D;D;D	0.71674	0.988;0.993;0.998;0.997;0.998;0.998	P;P;D;D;D;D	0.69479	0.691;0.855;0.964;0.939;0.964;0.964	T	0.35101	-0.9802	10	0.56958	D	0.05	-17.7892	6.0452	0.19755	0.2505:0.2354:0.5141:0.0	.	42;42;42;42;42;62	E7EV16;B4DRB4;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;PLTP_HUMAN;.	M	42;42;42;62;42	ENSP00000361508:L42M;ENSP00000335290:L42M;ENSP00000417138:L42M;ENSP00000440296:L62M;ENSP00000411671:L42M	ENSP00000335290:L42M	L	-	1	2	PLTP	43973274	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	1.119000	0.31258	0.755000	0.32990	0.563000	0.77884	CTG		0.617	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44539867	G	T	44539867	3	4	61	1	0	0	0	0	1	0	0	0	12145	933	33	2	1413	2	PLTP	20	44539867	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4886	44539867	18485653	11622	19607										
PLTP	5360	broad.mit.edu	37	chr20	44540080	44540080	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcgctaggaagagggccccGaagagggccatggcgagcgg	19	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44540080G>A	ENST00000477313.1	-	1	606	c.12C>T	c.(10-12)ttC>ttT	p.F4F	PLTP_ENST00000354050.4_Silent_p.F4F|PLTP_ENST00000542937.1_Silent_p.F24F|PLTP_ENST00000372431.3_Silent_p.F4F|PLTP_ENST00000372420.1_5'Flank|PLTP_ENST00000420868.2_Silent_p.F4F			P55058	PLTP_HUMAN	phospholipid transfer protein	4					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.F4F(2)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				AGAGGGCCCCGAAGAGGGCCA	0.642																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	20											28	34	32					20																	44540080		2175	4269	6444	43973487	SO:0001819	synonymous_variant	5360			L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.12C>T	20.37:g.44540080G>A			43973487	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	37	CCDS13386.1																																																																																				0.642	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		A	44540080	G	A	44540080	2	1	61	1	0	0	0	0	0	0	0	1	12145	1049	37	1		1	PLTP	20	44540080	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	213	44540080	18485440	11623	19608										
PCIF1	63935	broad.mit.edu	37	chr20	44569521	44569521	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaggaaccccaacgctgaAgatgtggggtacgtcccctg	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44569521A>C	ENST00000372409.3	+	6	825	c.461A>C	c.(460-462)aAg>aCg	p.K154T		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	154					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.K154T(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CCAACGCTGAAGATGTGGGGT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	20											103	93	97					20																	44569521		2203	4300	6503	44002928	SO:0001583	missense	63935			AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.461A>C	20.37:g.44569521A>C	ENSP00000361486:p.Lys154Thr		44002928	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.260294	0.80246	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	L	0.51422	1.61	0.49213	D	0.999761	P	0.37466	0.596	B	0.26864	0.074	T	0.54682	-0.8257	9	0.59425	D	0.04	-32.9898	12.7964	0.57562	1.0:0.0:0.0:0.0	.	154	Q9H4Z3	PCIF1_HUMAN	T	154	.	ENSP00000361486:K154T	K	+	2	0	PCIF1	44002928	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.173000	0.65010	2.152000	0.67230	0.533000	0.62120	AAG		0.552	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		C	44569521	A	C	44569521	3	2	61	1	0	0	0	0	1	0	0	0	11611	72	3	4	475	4	PCIF1	20	44569521	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	29441	44569521	18455999	11624	19609										
PCIF1	63935	broad.mit.edu	37	chr20	44571740	44571740	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcctgtcctgcaggcatTgagcctccacgggagtcttt	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44571740T>C	ENST00000372409.3	+	8	1042	c.678T>C	c.(676-678)atT>atC	p.I226I		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	226					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.I226I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CTGCAGGCATTGAGCCTCCAC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	20											44	38	40					20																	44571740		2203	4300	6503	44005147	SO:0001819	synonymous_variant	63935			AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.678T>C	20.37:g.44571740T>C			44005147	E1P5P1|Q54AB9|Q9NT85	Silent	SNP	ENST00000372409.3	37	CCDS13388.1																																																																																				0.547	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		C	44571740	T	C	44571740	2	2	61	1	0	0	0	0	0	0	0	1	11611	1800	63	4		4	PCIF1	20	44571740	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2219	44571740	18453780	11625	19610										
MMP9	4318	broad.mit.edu	37	chr20	44639180	44639180	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacgacgcctttgcccgcGccttcgcactgtggagcgcg	13	15	0	1	rs199948478		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44639180G>A	ENST00000372330.3	+	3	449	c.430G>A	c.(430-432)Gcc>Acc	p.A144T	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	144					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A144T(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CTTTGCCCGCGCCTTCGCACT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	20											46	46	46					20																	44639180		2203	4300	6503	44072587	SO:0001583	missense	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.430G>A	20.37:g.44639180G>A	ENSP00000361405:p.Ala144Thr		44072587	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	35	5.418671	0.96092	.	.	ENSG00000100985	ENST00000372330	T	0.41400	1.0	4.72	4.72	0.59763	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.100224	0.64402	D	0.000002	T	0.73598	0.3607	H	0.97516	4.02	0.80722	D	1	D	0.64830	0.994	P	0.58013	0.831	D	0.84516	0.0625	10	0.87932	D	0	.	17.198	0.86899	0.0:0.0:1.0:0.0	.	144	P14780	MMP9_HUMAN	T	144	ENSP00000361405:A144T	ENSP00000361405:A144T	A	+	1	0	MMP9	44072587	1.000000	0.71417	0.999000	0.59377	0.682000	0.39822	9.317000	0.96327	2.597000	0.87782	0.555000	0.69702	GCC		0.602	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			A	44639180	G	A	44639180	3	1	61	1	0	0	0	0	1	0	0	0	9699	1087	38	1	440	1	MMP9	20	44639180	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67440	44639180	18386340	11626	19611										
MMP9	4318	broad.mit.edu	37	chr20	44642416	44642416	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgaggagcggctctccaaGaagcttttcttcttctctgg	10	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44642416G>T	ENST00000372330.3	+	10	1750	c.1731G>T	c.(1729-1731)aaG>aaT	p.K577N	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	577					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K577N(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	GGCTCTCCAAGAAGCTTTTCT	0.607											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	20											50	50	50					20																	44642416		2203	4300	6503	44075823	SO:0001583	missense	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1731G>T	20.37:g.44642416G>T	ENSP00000361405:p.Lys577Asn	925	44075823	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.875782	0.72180	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.02103	4.45	4.85	4.85	0.62838	Hemopexin/matrixin (2);	0.048577	0.85682	D	0.000000	T	0.03220	0.0094	L	0.49699	1.58	0.58432	D	0.999999	P	0.39116	0.66	B	0.32465	0.146	T	0.56013	-0.8049	10	0.42905	T	0.14	.	16.7107	0.85384	0.0:0.0:1.0:0.0	.	577	P14780	MMP9_HUMAN	N	577;147	ENSP00000361405:K577N	ENSP00000361405:K577N	K	+	3	2	MMP9	44075823	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	3.347000	0.52200	2.497000	0.84241	0.655000	0.94253	AAG		0.607	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			T	44642416	G	T	44642416	3	4	61	1	0	0	0	0	1	0	0	0	9699	933	33	2	1769	2	MMP9	20	44642416	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3236	44642416	18383104	11627	19612										
SLC12A5	57468	broad.mit.edu	37	chr20	44671881	44671881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccgatggcactcctatcGacatggaccacccttatgtc	9	14	0	0	rs200798560		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44671881G>A	ENST00000454036.2	+	9	1274	c.1225G>A	c.(1225-1227)Gac>Aac	p.D409N	SLC12A5_ENST00000243964.3_Missense_Mutation_p.D386N	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	409					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.D386N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CACTCCTATCGACATGGACCA	0.567													G|||	1	0.000199681	0	0	5008	,	,		19769	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											298	252	267					20																	44671881		2203	4300	6503	44105288	SO:0001583	missense	57468			AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1225G>A	20.37:g.44671881G>A	ENSP00000387694:p.Asp409Asn		44105288	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	7.655	0.683796	0.14907	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	D;D	0.84070	-1.8;-1.8	4.47	2.51	0.30379	.	0.251988	0.40728	N	0.001040	T	0.67449	0.2894	N	0.22421	0.69	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.57900	-0.7731	10	0.20046	T	0.44	.	7.9208	0.29846	0.2631:0.0:0.7369:0.0	.	409;386	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	N	409;386	ENSP00000387694:D409N;ENSP00000243964:D386N	ENSP00000243964:D386N	D	+	1	0	SLC12A5	44105288	0.992000	0.36948	0.838000	0.33150	0.372000	0.29890	2.720000	0.47252	1.226000	0.43582	0.462000	0.41574	GAC		0.567	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			A	44671881	G	A	44671881	3	1	61	1	0	0	0	0	1	0	0	0	14423	1058	37	1	1315	1	SLC12A5	20	44671881	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29465	44671881	18353639	11628	19613										
CD40	958	broad.mit.edu	37	chr20	44751836	44751836	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaatgtgtcatctgctttcGaaaaatgtcacccttggaca	7	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:44751836G>A	ENST00000372285.3	+	5	547	c.475G>A	c.(475-477)Gaa>Aaa	p.E159K	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Missense_Mutation_p.E159K	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	159					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)	p.E159K(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				ATCTGCTTTCGAAAAATGTCA	0.532									Immune Deficiency with Hyper-IgM																																							1	Substitution - Missense(1)	large_intestine(1)	20											238	220	226					20																	44751836		2203	4300	6503	44185243	SO:0001583	missense	958	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.475G>A	20.37:g.44751836G>A	ENSP00000361359:p.Glu159Lys		44185243	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Missense_Mutation	SNP	ENST00000372285.3	37	CCDS13393.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176576	0.57692	.	.	ENSG00000101017	ENST00000372285;ENST00000372276	T;T	0.62788	-0.0;-0.0	4.76	4.76	0.60689	TNFR/CD27/30/40/95 cysteine-rich region (2);	0.440664	0.22780	N	0.055739	T	0.74854	0.3771	M	0.67517	2.055	0.47584	D	0.999469	D;D	0.89917	1.0;0.999	D;P	0.68039	0.955;0.866	T	0.75566	-0.3273	10	0.51188	T	0.08	-19.735	13.1257	0.59354	0.0:0.0:1.0:0.0	.	159;159	P25942-2;P25942	.;TNR5_HUMAN	K	159	ENSP00000361359:E159K;ENSP00000361350:E159K	ENSP00000361350:E159K	E	+	1	0	CD40	44185243	0.997000	0.39634	0.936000	0.37596	0.037000	0.13140	3.282000	0.51693	2.475000	0.83589	0.471000	0.43371	GAA		0.532	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		A	44751836	G	A	44751836	3	1	61	1	0	0	0	0	1	0	0	0	3021	1059	37	1	493	1	CD40	20	44751836	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79955	44751836	18273684	11629	19614										
SLC13A3	64849	broad.mit.edu	37	chr20	45216772	45216772	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaggatggcaaacatgcaGaaaaggatgaaaacagcctg	13	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45216772G>A	ENST00000279027.4	-	8	1065	c.1047C>T	c.(1045-1047)ttC>ttT	p.F349F	SLC13A3_ENST00000372121.1_Silent_p.F299F|SLC13A3_ENST00000495082.1_Silent_p.F302F|SLC13A3_ENST00000413164.2_Silent_p.F299F|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000290317.5_Silent_p.F302F|SLC13A3_ENST00000396360.1_Intron|SLC13A3_ENST00000472148.1_Intron|SLC13A3_ENST00000464518.1_5'Flank	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	349					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.F349F(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAAACATGCAGAAAAGGATGA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	20											91	82	85					20																	45216772		2203	4300	6503	44650179	SO:0001819	synonymous_variant	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1047C>T	20.37:g.45216772G>A			44650179	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																				0.592	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45216772	G	A	45216772	2	1	61	1	0	0	0	0	0	0	0	1	14430	933	33	3		3	SLC13A3	20	45216772	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	464936	45216772	17808748	11630	19615										
SLC13A3	64849	broad.mit.edu	37	chr20	45239190	45239190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcatcatggcagtggaggCggtgttgctcagccacatgg	15	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45239190C>T	ENST00000279027.4	-	3	454	c.436G>A	c.(436-438)Gcc>Acc	p.A146T	SLC13A3_ENST00000372121.1_Missense_Mutation_p.A146T|SLC13A3_ENST00000339636.3_Missense_Mutation_p.A146T|SLC13A3_ENST00000495082.1_Missense_Mutation_p.A99T|SLC13A3_ENST00000413164.2_Missense_Mutation_p.A146T|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000290317.5_Missense_Mutation_p.A99T|SLC13A3_ENST00000396360.1_Missense_Mutation_p.A99T|SLC13A3_ENST00000472148.1_Missense_Mutation_p.A99T|SLC13A3_ENST00000417157.2_Missense_Mutation_p.A99T	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	146					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.A146T(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	GCAGTGGAGGCGGTGTTGCTC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	20											183	164	170					20																	45239190		2203	4300	6503	44672597	SO:0001583	missense	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.436G>A	20.37:g.45239190C>T	ENSP00000279027:p.Ala146Thr		44672597	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749661	0.69533	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121;ENST00000417157;ENST00000339636	T;T;T;T;T;T;T;T;T;T;T	0.03496	3.91;3.91;3.91;3.91;3.91;3.91;3.91;3.91;3.91;3.91;3.91	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.23846	0.0577	M	0.84773	2.715	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.97;0.977;1.0;0.993	T	0.00402	-1.1762	10	0.87932	D	0	-29.4	20.0396	0.97574	0.0:1.0:0.0:0.0	.	146;99;99;99;146	B4DIR8;Q8WWT9-3;F6WI18;C9J4A3;Q8WWT9	.;.;.;.;S13A3_HUMAN	T	99;99;146;99;146;99;99;109;146;99;146	ENSP00000290317:A99T;ENSP00000379648:A99T;ENSP00000279027:A146T;ENSP00000420177:A99T;ENSP00000415852:A146T;ENSP00000419621:A99T;ENSP00000417784:A99T;ENSP00000395095:A109T;ENSP00000361193:A146T;ENSP00000397955:A99T;ENSP00000344912:A146T	ENSP00000279027:A146T	A	-	1	0	SLC13A3	44672597	1.000000	0.71417	0.967000	0.41034	0.076000	0.17211	5.880000	0.69698	2.814000	0.96858	0.563000	0.77884	GCC		0.547	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45239190	C	T	45239190	3	4	61	1	0	0	0	0	1	0	0	0	14430	768	27	1	1416	1	SLC13A3	20	45239190	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22418	45239190	17786330	11631	19616										
EYA2	2139	broad.mit.edu	37	chr20	45633581	45633581	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttccctctttccacacagAtcttgcccacgtgtcctccc	4	19	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45633581A>G	ENST00000327619.5	+	4	530	c.156A>G	c.(154-156)agA>agG	p.R52R	EYA2_ENST00000317304.6_Splice_Site_p.R52R|EYA2_ENST00000357410.3_Splice_Site_p.R52R	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	52					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)	p.R52R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				TTCCACACAGATCTTGCCCAC	0.557																																					Pancreas(120;56 1725 18501 25218 43520)											1	Substitution - coding silent(1)	large_intestine(1)	20											87	92	90					20																	45633581		2203	4300	6503	45066988	SO:0001630	splice_region_variant	2139				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.156-1A>G	20.37:g.45633581A>G			45066988	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																				0.557	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244	Silent	G	45633581	A	G	45633581	5	3	61	1	0	0	0	0	0	0	1	0	5342	347	12	4	166	4	EYA2	20	45633581	Splice_Site	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	394391	45633581	17391939	11632	19617										
EYA2	2139	broad.mit.edu	37	chr20	45717939	45717939	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagggagacacagacaggccGcaccgggcctccgacgggaa	16	13	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45717939G>A	ENST00000327619.5	+	8	1097	c.723G>A	c.(721-723)ccG>ccA	p.P241P	EYA2_ENST00000317304.6_Silent_p.P241P|EYA2_ENST00000357410.3_Silent_p.P241P	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	241					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)	p.P241P(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				CAGACAGGCCGCACCGGGCCT	0.572																																					Pancreas(120;56 1725 18501 25218 43520)											1	Substitution - coding silent(1)	large_intestine(1)	20											76	78	77					20																	45717939		2203	4300	6503	45151346	SO:0001819	synonymous_variant	2139				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.723G>A	20.37:g.45717939G>A			45151346	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																				0.572	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244		A	45717939	G	A	45717939	2	1	61	1	0	0	0	0	0	0	0	1	5342	1074	38	1		1	EYA2	20	45717939	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84358	45717939	17307581	11633	19618										
EYA2	2139	broad.mit.edu	37	chr20	45771716	45771716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacaccacgacgtccgtgCgcattggccttatgatggaa	12	11	0	1	rs368297287		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45771716C>T	ENST00000327619.5	+	10	1281	c.907C>T	c.(907-909)Cgc>Tgc	p.R303C	EYA2_ENST00000317304.6_Intron|EYA2_ENST00000357410.3_Missense_Mutation_p.R303C	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	303					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)	p.R303C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				GACGTCCGTGCGCATTGGCCT	0.488													C|||	1	0.000199681	8e-04	0	5008	,	,		19649	0		0	False		,,,				2504	0				Pancreas(120;56 1725 18501 25218 43520)											1	Substitution - Missense(1)	large_intestine(1)	20						C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	197	148	165		907,907	4	1	20		165	0,8600		0,0,4300	no	missense,missense	EYA2	NM_005244.4,NM_172110.3	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	303/539,303/460	45771716	1,13005	2203	4300	6503	45205123	SO:0001583	missense	2139				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.907C>T	20.37:g.45771716C>T	ENSP00000333640:p.Arg303Cys		45205123	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Missense_Mutation	SNP	ENST00000327619.5	37	CCDS13403.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.953744	0.53293	2.27E-4	0.0	ENSG00000064655	ENST00000327619;ENST00000357410;ENST00000458636	D;D;D	0.81821	-1.54;-1.54;-1.54	6.08	3.97	0.46021	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.105617	0.64402	D	0.000005	D	0.86155	0.5865	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.68765	0.96;0.928;0.928	D	0.87928	0.2708	10	0.72032	D	0.01	-22.8238	15.728	0.77777	0.3686:0.6314:0.0:0.0	.	303;303;303	O00167-3;A8KAG7;O00167	.;.;EYA2_HUMAN	C	303;303;174	ENSP00000333640:R303C;ENSP00000349986:R303C;ENSP00000395427:R174C	ENSP00000333640:R303C	R	+	1	0	EYA2	45205123	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	0.791000	0.26915	1.521000	0.48983	0.655000	0.94253	CGC		0.488	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244		T	45771716	C	T	45771716	3	4	61	1	0	0	0	0	1	0	0	0	5342	768	27	1	941	1	EYA2	20	45771716	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53777	45771716	17253804	11634	19619										
ZMYND8	23613	broad.mit.edu	37	chr20	45919007	45919007	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtgcagccatacattttCtttttcgcattctgggaaga	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:45919007C>A	ENST00000311275.7	-	7	865	c.612G>T	c.(610-612)aaG>aaT	p.K204N	ZMYND8_ENST00000458360.2_Missense_Mutation_p.K199N|ZMYND8_ENST00000372023.3_Missense_Mutation_p.K199N|ZMYND8_ENST00000355972.4_Missense_Mutation_p.K204N|ZMYND8_ENST00000352431.2_Missense_Mutation_p.K224N|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000262975.4_Missense_Mutation_p.K204N|ZMYND8_ENST00000536340.1_Missense_Mutation_p.K231N|ZMYND8_ENST00000396281.4_Missense_Mutation_p.K204N|ZMYND8_ENST00000540497.1_Missense_Mutation_p.K199N|ZMYND8_ENST00000471951.2_Missense_Mutation_p.K224N|ZMYND8_ENST00000461685.1_Missense_Mutation_p.K224N|ZMYND8_ENST00000446994.2_Missense_Mutation_p.K141N|ZMYND8_ENST00000360911.3_Missense_Mutation_p.K199N	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	204	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.K224N(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			CATACATTTTCTTTTTCGCAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	20											97	82	87					20																	45919007		2203	4300	6503	45352414	SO:0001583	missense	23613			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.612G>T	20.37:g.45919007C>A	ENSP00000312237:p.Lys204Asn		45352414	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.47|19.47	3.833868|3.833868	0.71258|0.71258	.|.	.|.	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.27256	.|1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68	6.16|6.16	5.22|5.22	0.72569|0.72569	.|Bromodomain (5);	.|0.047277	.|0.85682	.|D	.|0.000000	.|T	.|0.33059	.|0.0850	N|N	0.12502|0.12502	0.225|0.225	0.49213|0.49213	D|D	0.999769|0.999769	.|B;B;D;D;D;B;D;B;B;D;D;D;D;B;B;B;B	.|0.71674	.|0.389;0.151;0.994;0.994;0.998;0.014;0.996;0.151;0.021;0.996;0.997;0.994;0.994;0.424;0.028;0.182;0.182	.|B;B;D;D;D;B;P;B;B;D;D;D;D;P;B;B;B	.|0.71656	.|0.143;0.07;0.961;0.952;0.974;0.032;0.886;0.052;0.024;0.92;0.952;0.952;0.931;0.523;0.017;0.087;0.115	.|T	.|0.28332	.|-1.0047	.|10	.|0.36615	.|T	.|0.2	-24.9249|-24.9249	17.0691|17.0691	0.86568|0.86568	0.128:0.872:0.0:0.0|0.128:0.872:0.0:0.0	.|.	.|199;231;199;199;198;224;204;199;224;224;204;141;199;199;224;199;204	.|B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	X|N	131|199;204;199;204;224;224;204;231;204;141;224;199;199	.|ENSP00000354166:K199N;ENSP00000312237:K204N;ENSP00000392964:K199N;ENSP00000262975:K204N;ENSP00000420095:K224N;ENSP00000335537:K224N;ENSP00000379577:K204N;ENSP00000439800:K231N;ENSP00000348246:K204N;ENSP00000396725:K141N;ENSP00000418210:K224N;ENSP00000361093:K199N;ENSP00000443086:K199N	.|ENSP00000262975:K204N	E|K	-|-	1|3	0|2	ZMYND8|ZMYND8	45352414|45352414	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.886000|0.886000	0.51366|0.51366	3.183000|3.183000	0.50918|0.50918	1.606000|1.606000	0.50161|0.50161	0.650000|0.650000	0.86243|0.86243	GAA|AAG		0.438	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		A	45919007	C	A	45919007	3	1	61	1	0	0	0	0	1	0	0	0	17750	912	32	2	2962	2	ZMYND8	20	45919007	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147291	45919007	17106513	11635	19620										
NCOA3	8202	broad.mit.edu	37	chr20	46252792	46252792	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaatgtgcgattttaaaggAaacagtaagacagatacgtc	9	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:46252792A>C	ENST00000371998.3	+	4	412	c.221A>C	c.(220-222)gAa>gCa	p.E74A	NCOA3_ENST00000341724.6_Missense_Mutation_p.E74A|NCOA3_ENST00000371997.3_Missense_Mutation_p.E74A|NCOA3_ENST00000372004.3_Missense_Mutation_p.E74A			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	74	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.E74A(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ATTTTAAAGGAAACAGTAAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	20											75	72	73					20																	46252792		2203	4300	6503	45686199	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.221A>C	20.37:g.46252792A>C	ENSP00000361066:p.Glu74Ala		45686199	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	A	32	5.154802	0.94686	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02498	4.29;4.46;4.46;4.27	6.17	6.17	0.99709	Helix-loop-helix DNA-binding (4);	0.000000	0.85682	D	0.000000	T	0.11965	0.0291	L	0.48642	1.525	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.994;0.985;0.997;0.998	D;D;D;D;D	0.91635	0.999;0.968;0.949;0.986;0.968	T	0.00436	-1.1740	10	0.72032	D	0.01	-31.0307	16.8222	0.85835	1.0:0.0:0.0:0.0	.	74;78;74;74;74	Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;NCOA3_HUMAN	A	74	ENSP00000342123:E74A;ENSP00000361073:E74A;ENSP00000361066:E74A;ENSP00000361065:E74A	ENSP00000345671:E74A	E	+	2	0	NCOA3	45686199	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	GAA		0.358	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		C	46252792	A	C	46252792	3	2	61	1	0	0	0	0	1	0	0	0	10261	246	9	4	227	4	NCOA3	20	46252792	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	333785	46252792	16772728	11636	19621										
NCOA3	8202	broad.mit.edu	37	chr20	46255881	46255881	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaatatcttacatgaagaaGacagaaaggattttcttaag	7	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:46255881G>T	ENST00000371998.3	+	6	684	c.493G>T	c.(493-495)Gac>Tac	p.D165Y	NCOA3_ENST00000497292.1_3'UTR|NCOA3_ENST00000341724.6_Missense_Mutation_p.D165Y|NCOA3_ENST00000371997.3_Missense_Mutation_p.D165Y|NCOA3_ENST00000372004.3_Missense_Mutation_p.D165Y			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	165	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.D165Y(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ACATGAAGAAGACAGAAAGGA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	20											86	83	84					20																	46255881		2203	4300	6503	45689288	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.493G>T	20.37:g.46255881G>T	ENSP00000361066:p.Asp165Tyr		45689288	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.826880	0.90955	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	6.17	6.17	0.99709	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.70544	0.3236	H	0.95437	3.67	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.81914	0.98;0.995;0.995;0.991;0.995	T	0.77970	-0.2387	10	0.87932	D	0	-29.5936	20.8794	0.99867	0.0:0.0:1.0:0.0	.	165;169;165;165;165	Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;NCOA3_HUMAN	Y	165	ENSP00000342123:D165Y;ENSP00000361073:D165Y;ENSP00000361066:D165Y;ENSP00000361065:D165Y	ENSP00000345671:D165Y	D	+	1	0	NCOA3	45689288	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GAC		0.308	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46255881	G	T	46255881	3	4	61	1	0	0	0	0	1	0	0	0	10261	942	33	2	507	2	NCOA3	20	46255881	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3089	46255881	16769639	11637	19622										
NCOA3	8202	broad.mit.edu	37	chr20	46256397	46256397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacaccacatgatattctgGaagacataaacgccagtcct	6	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:46256397G>A	ENST00000371998.3	+	7	816	c.625G>A	c.(625-627)Gaa>Aaa	p.E209K	NCOA3_ENST00000497292.1_3'UTR|NCOA3_ENST00000341724.6_Missense_Mutation_p.E209K|NCOA3_ENST00000371997.3_Missense_Mutation_p.E209K|NCOA3_ENST00000372004.3_Missense_Mutation_p.E209K			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	209					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.E209K(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGATATTCTGGAAGACATAAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	20											101	98	99					20																	46256397		2203	4300	6503	45689804	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.625G>A	20.37:g.46256397G>A	ENSP00000361066:p.Glu209Lys		45689804	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	36	5.663136	0.96745	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02369	4.34;4.5;4.5;4.32	6.16	6.16	0.99307	.	0.220942	0.46758	D	0.000271	T	0.07458	0.0188	L	0.42245	1.32	0.80722	D	1	P;P;P;P;P;P	0.52061	0.578;0.95;0.578;0.578;0.523;0.578	P;P;P;P;P;P	0.48873	0.593;0.574;0.593;0.593;0.457;0.593	T	0.02190	-1.1198	10	0.72032	D	0.01	-22.2162	20.8598	0.99761	0.0:0.0:1.0:0.0	.	209;209;213;209;209;209	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	K	209	ENSP00000342123:E209K;ENSP00000361073:E209K;ENSP00000361066:E209K;ENSP00000361065:E209K	ENSP00000345671:E209K	E	+	1	0	NCOA3	45689804	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.727000	0.98787	2.937000	0.99478	0.650000	0.86243	GAA		0.428	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		A	46256397	G	A	46256397	3	1	61	1	0	0	0	0	1	0	0	0	10261	1175	41	3	643	3	NCOA3	20	46256397	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	516	46256397	16769123	11638	19623										
NCOA3	8202	broad.mit.edu	37	chr20	46262273	46262273	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatagatacaaattcactgaGatcctccatgaggcctggct	8	10	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:46262273G>A	ENST00000371998.3	+	9	1048	c.857G>A	c.(856-858)aGa>aAa	p.R286K	NCOA3_ENST00000341724.6_Missense_Mutation_p.R286K|NCOA3_ENST00000371997.3_Missense_Mutation_p.R286K|NCOA3_ENST00000372004.3_Missense_Mutation_p.R286K			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	286					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.R286K(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						AATTCACTGAGATCCTCCATG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	20											84	89	87					20																	46262273		2203	4300	6503	45695680	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.857G>A	20.37:g.46262273G>A	ENSP00000361066:p.Arg286Lys		45695680	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550909	0.86127	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997;ENST00000542882	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.4	5.4	0.78164	.	0.057212	0.64402	D	0.000002	T	0.37571	0.1008	M	0.76170	2.325	0.53005	D	0.999969	P;P;P;P;P;P	0.49862	0.929;0.923;0.761;0.761;0.846;0.761	P;B;B;B;P;B	0.48089	0.566;0.364;0.299;0.299;0.494;0.299	T	0.31833	-0.9929	10	0.72032	D	0.01	-25.5358	19.1741	0.93597	0.0:0.0:1.0:0.0	.	286;286;290;286;286;286	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	K	286;286;286;286;286;52	ENSP00000342123:R286K;ENSP00000361073:R286K;ENSP00000361066:R286K;ENSP00000361065:R286K	ENSP00000345671:R286K	R	+	2	0	NCOA3	45695680	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.509000	0.81698	2.530000	0.85305	0.655000	0.94253	AGA		0.378	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		A	46262273	G	A	46262273	3	1	61	1	0	0	0	0	1	0	0	0	10261	942	33	3	883	3	NCOA3	20	46262273	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5876	46262273	16763247	11639	19624										
NCOA3	8202	broad.mit.edu	37	chr20	46275934	46275934	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacaggggcctccaatgcaaGgaggctttcatcttcaggga	12	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:46275934G>T	ENST00000371998.3	+	18	3561	c.3370G>T	c.(3370-3372)Gga>Tga	p.G1124*	NCOA3_ENST00000341724.6_Nonsense_Mutation_p.G1054*|NCOA3_ENST00000371997.3_Nonsense_Mutation_p.G1119*|NCOA3_ENST00000372004.3_Nonsense_Mutation_p.G1124*			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1124	Acetyltransferase.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.G1124*(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TCCAATGCAAGGAGGCTTTCA	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											116	99	105					20																	46275934		2203	4300	6503	45709341	SO:0001587	stop_gained	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3370G>T	20.37:g.46275934G>T	ENSP00000361066:p.Gly1124*		45709341	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Nonsense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	43	10.034015	0.99321	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	.	.	.	5.57	5.57	0.84162	.	0.074687	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-18.1331	19.6117	0.95608	0.0:0.0:1.0:0.0	.	.	.	.	X	1124;1054;1124;1124;1119	.	ENSP00000345671:G1124X	G	+	1	0	NCOA3	45709341	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.561000	0.53770	2.650000	0.89964	0.586000	0.80456	GGA		0.473	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46275934	G	T	46275934	4	4	61	1	0	0	0	0	0	1	0	0	10261	1001	35	2	3462	2	NCOA3	20	46275934	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13661	46275934	16749586	11640	19625										
PREX1	57580	broad.mit.edu	37	chr20	47249038	47249038	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcctgaagctcacctttCgtgaacagcgctgtgtgcag	12	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47249038C>T	ENST00000371941.3	-	34	4429	c.4407G>A	c.(4405-4407)acG>acA	p.T1469T	PREX1_ENST00000396220.1_Silent_p.T1469T	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1469					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T1469T(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCTCACCTTTCGTGAACAGCG	0.677																																																2	Substitution - coding silent(2)	large_intestine(2)	20											44	43	43					20																	47249038		2203	4300	6503	46682445	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.4407G>A	20.37:g.47249038C>T			46682445	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																				0.677	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47249038	C	T	47249038	2	4	61	1	0	0	0	0	0	0	0	1	12510	871	31	1		1	PREX1	20	47249038	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	973104	47249038	15776482	11641	19626										
PREX1	57580	broad.mit.edu	37	chr20	47258745	47258745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggaaatgcttggtctcttCgaaagcccggctcatgactg	12	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47258745C>T	ENST00000371941.3	-	29	3758	c.3736G>A	c.(3736-3738)Gaa>Aaa	p.E1246K	PREX1_ENST00000396220.1_Missense_Mutation_p.E1246K|PREX1_ENST00000496915.1_5'UTR	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1246					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E1246K(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TTGGTCTCTTCGAAAGCCCGG	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	20											107	98	101					20																	47258745		2203	4300	6503	46692152	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3736G>A	20.37:g.47258745C>T	ENSP00000361009:p.Glu1246Lys		46692152	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	c	21.9	4.217559	0.79352	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.48522	0.81;0.81	5.4	5.4	0.78164	.	0.104988	0.39210	N	0.001440	T	0.47210	0.1433	L	0.60455	1.87	0.58432	D	0.999999	B;B	0.33044	0.279;0.395	B;B	0.27380	0.051;0.079	T	0.51220	-0.8733	10	0.62326	D	0.03	.	19.2615	0.93970	0.0:1.0:0.0:0.0	.	1246;543	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	K	1246	ENSP00000361009:E1246K;ENSP00000379522:E1246K	ENSP00000361009:E1246K	E	-	1	0	PREX1	46692152	1.000000	0.71417	0.954000	0.39281	0.618000	0.37518	7.379000	0.79691	2.538000	0.85594	0.639000	0.83563	GAA		0.587	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47258745	C	T	47258745	3	4	61	1	0	0	0	0	1	0	0	0	12510	893	31	1	1291	1	PREX1	20	47258745	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9707	47258745	15766775	11642	19627										
PREX1	57580	broad.mit.edu	37	chr20	47276508	47276508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttgaagtcgttgcgaagCtgtttgttcttgctgctggt	13	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47276508C>T	ENST00000371941.3	-	16	1852	c.1830G>A	c.(1828-1830)caG>caA	p.Q610Q	PREX1_ENST00000396220.1_Silent_p.Q610Q	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	610					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Q610Q(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGTTGCGAAGCTGTTTGTTCT	0.572																																																2	Substitution - coding silent(2)	large_intestine(2)	20											181	139	153					20																	47276508		2203	4300	6503	46709915	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1830G>A	20.37:g.47276508C>T			46709915	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																				0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47276508	C	T	47276508	2	4	61	1	0	0	0	0	0	0	0	1	12510	796	28	3		3	PREX1	20	47276508	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	17763	47276508	15749012	11643	19628										
ARFGEF2	10564	broad.mit.edu	37	chr20	47589745	47589745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttaaatgctgctaacatttTtgagcgccttgtaaatgatt	7	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47589745T>C	ENST00000371917.4	+	12	1589	c.1589T>C	c.(1588-1590)tTt>tCt	p.F530S		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	530					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.F530S(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GCTAACATTTTTGAGCGCCTT	0.388																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)											1	Substitution - Missense(1)	large_intestine(1)	20											99	95	96					20																	47589745		2203	4300	6503	47023152	SO:0001583	missense	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1589T>C	20.37:g.47589745T>C	ENSP00000360985:p.Phe530Ser		47023152	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.789584	0.90367	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.52057	0.68	5.5	5.5	0.81552	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77294	0.4109	H	0.95004	3.61	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.84430	0.0576	10	0.87932	D	0	.	15.6362	0.76953	0.0:0.0:0.0:1.0	.	530	Q9Y6D5	BIG2_HUMAN	S	530	ENSP00000360985:F530S	ENSP00000360985:F530S	F	+	2	0	ARFGEF2	47023152	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	8.040000	0.89188	2.090000	0.63153	0.460000	0.39030	TTT		0.388	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		C	47589745	T	C	47589745	3	2	61	1	0	0	0	0	1	0	0	0	853	1841	64	4	1635	4	ARFGEF2	20	47589745	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	313237	47589745	15435775	11644	19629										
ARFGEF2	10564	broad.mit.edu	37	chr20	47607666	47607667	+	Missense_Mutation	DNP	CG	CG	TA													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaatgaagcagaaaaacatCgacaccattaagacgcttat					rs138056947		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47607666_47607667CG>TA	ENST00000371917.4	+	21	2904_2905	c.2904_2905CG>TA	c.(2902-2907)atCGac>atTAac	p.D969N		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	969					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.I968>?(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGAAAAACATCGACACCATTAA	0.48																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)											1	Complex(1)	large_intestine(1)	20																																								47041074	SO:0001583	missense	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	Exception_encountered	20.37:g.47607666_47607667delinsTA	ENSP00000360985:p.Asp969Asn		47041073	Q5TFT9|Q9NTS1	Missense_Mutation	DNP	ENST00000371917.4	37	CCDS13411.1																																																																																				0.48	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		TA	47607667	CG	TA	47607666	3	4	61	1	0	0	0	0	1	0	0	0	853	874	31	1	2986	1	ARFGEF2	20	47607666	Missense_Mutation	DNP	CG	TCGA-AG-A002-01A-01W-A00K-09	17921	47607666	15417854	11645	19630										
ARFGEF2	10564	broad.mit.edu	37	chr20	47645144	47645144	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgtttgaggatcctgtttCgaatgtatgttgatgagaac	12	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47645144C>T	ENST00000371917.4	+	37	5002	c.5002C>T	c.(5002-5004)Cga>Tga	p.R1668*		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1668					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.R1668*(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GATCCTGTTTCGAATGTATGT	0.388																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)											1	Substitution - Nonsense(1)	large_intestine(1)	20											84	80	81					20																	47645144		2203	4300	6503	47078551	SO:0001587	stop_gained	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.5002C>T	20.37:g.47645144C>T	ENSP00000360985:p.Arg1668*		47078551	Q5TFT9|Q9NTS1	Nonsense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	C	44	10.958251	0.99494	.	.	ENSG00000124198	ENST00000371917	.	.	.	5.71	4.75	0.60458	.	0.060119	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6488	0.77076	0.1423:0.8577:0.0:0.0	.	.	.	.	X	1668	.	ENSP00000360985:R1668X	R	+	1	2	ARFGEF2	47078551	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.895000	0.56258	1.366000	0.46076	0.655000	0.94253	CGA		0.388	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		T	47645144	C	T	47645144	4	4	61	1	0	0	0	0	0	1	0	0	853	876	31	1	5148	1	ARFGEF2	20	47645144	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37478	47645144	15380376	11646	19631										
STAU1	6780	broad.mit.edu	37	chr20	47782583	47782583	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagagggtaaagcagagttTtgaatgggtctacctgcatt	13	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47782583T>G	ENST00000371856.2	-	3	566	c.156A>C	c.(154-156)caA>caC	p.Q52H	STAU1_ENST00000360426.4_Intron|STAU1_ENST00000371828.3_Intron|STAU1_ENST00000371802.1_Intron|STAU1_ENST00000347458.5_Intron|STAU1_ENST00000340954.7_Intron|STAU1_ENST00000371792.1_Intron	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	52					intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.Q52H(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			AAGCAGAGTTTTGAATGGGTC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	20											197	201	200					20																	47782583		2203	4300	6503	47215990	SO:0001583	missense	6780				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.156A>C	20.37:g.47782583T>G	ENSP00000360922:p.Gln52His		47215990	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	37	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451121	0.43531	.	.	ENSG00000124214	ENST00000371856	T	0.36340	1.26	5.96	2.38	0.29361	.	0.317648	0.32357	N	0.006217	T	0.21550	0.0519	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04579	-1.0941	10	0.41790	T	0.15	-8.3595	6.991	0.24755	0.0:0.1878:0.1144:0.6978	.	52	O95793	STAU1_HUMAN	H	52	ENSP00000360922:Q52H	ENSP00000360922:Q52H	Q	-	3	2	STAU1	47215990	0.998000	0.40836	0.999000	0.59377	0.961000	0.63080	0.410000	0.21098	0.127000	0.18452	0.533000	0.62120	CAA		0.418	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		G	47782583	T	G	47782583	3	3	61	1	0	0	0	0	1	0	0	0	15311	1838	64	4	1643	4	STAU1	20	47782583	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	137439	47782583	15242937	11647	19632										
ZNFX1	57169	broad.mit.edu	37	chr20	47864158	47864158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttgttcatcctcttgggtGaacttacatgttttctcaag	8	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47864158G>T	ENST00000396105.1	-	14	5649	c.5403C>A	c.(5401-5403)ttC>ttA	p.F1801L	ZNFX1_ENST00000469991.1_5'Flank|ZNFX1_ENST00000371752.1_Missense_Mutation_p.F1801L|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1801							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F1801L(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CCTCTTGGGTGAACTTACATG	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	20											143	144	143					20																	47864158		2203	4300	6503	47297565	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.5403C>A	20.37:g.47864158G>T	ENSP00000379412:p.Phe1801Leu		47297565	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893085	0.52121	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.85861	-2.04;-2.04	6.17	4.22	0.49857	.	0.053649	0.85682	D	0.000000	D	0.88183	0.6368	L	0.59436	1.845	0.42989	D	0.994481	D	0.63880	0.993	P	0.60682	0.878	D	0.85534	0.1211	10	0.26408	T	0.33	-24.6932	12.3692	0.55246	0.1382:0.0:0.8618:0.0	.	1801	Q9P2E3	ZNFX1_HUMAN	L	1801	ENSP00000360817:F1801L;ENSP00000379412:F1801L	ENSP00000360817:F1801L	F	-	3	2	ZNFX1	47297565	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.838000	0.55828	0.924000	0.37069	-0.140000	0.14226	TTC		0.478	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		T	47864158	G	T	47864158	3	4	61	1	0	0	0	0	1	0	0	0	18244	1281	45	2	357	2	ZNFX1	20	47864158	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	81575	47864158	15161362	11648	19633										
ZNFX1	57169	broad.mit.edu	37	chr20	47872433	47872433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcatggtgttcagtttgcGaagctcatccttcactcttt	8	10	5	0	rs553344985		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47872433G>A	ENST00000396105.1	-	9	2962	c.2716C>T	c.(2716-2718)Cgc>Tgc	p.R906C	ZNFX1_ENST00000371752.1_Missense_Mutation_p.R906C|ZNFX1_ENST00000371754.4_Missense_Mutation_p.R906C	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	906							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R906C(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTCAGTTTGCGAAGCTCATCC	0.507													G|||	1	0.000199681	0	0	5008	,	,		22358	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(2)	20											184	133	150					20																	47872433		2203	4300	6503	47305840	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.2716C>T	20.37:g.47872433G>A	ENSP00000379412:p.Arg906Cys		47305840	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822292	0.71028	.	.	ENSG00000124201	ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744	T;D;D;T	0.87103	1.76;-2.21;-2.21;-0.88	5.74	5.74	0.90152	.	0.390499	0.28119	N	0.016535	D	0.86401	0.5924	L	0.52126	1.63	0.40286	D	0.978456	D	0.61697	0.99	P	0.47376	0.545	D	0.87865	0.2667	10	0.66056	D	0.02	-11.7563	13.4489	0.61158	0.0:0.0:0.8432:0.1568	.	906	Q9P2E3	ZNFX1_HUMAN	C	906	ENSP00000360819:R906C;ENSP00000360817:R906C;ENSP00000379412:R906C;ENSP00000360809:R906C	ENSP00000360809:R906C	R	-	1	0	ZNFX1	47305840	0.942000	0.31987	1.000000	0.80357	0.484000	0.33280	1.874000	0.39568	2.709000	0.92574	0.655000	0.94253	CGC		0.507	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		A	47872433	G	A	47872433	3	1	61	1	0	0	0	0	1	0	0	0	18244	1058	37	1	3064	1	ZNFX1	20	47872433	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8275	47872433	15153087	11649	19634										
ZNFX1	57169	broad.mit.edu	37	chr20	47881340	47881340	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttagggtgaactgcttcagGatttcactgttgctccttcc	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47881340G>A	ENST00000396105.1	-	5	2310	c.2064C>T	c.(2062-2064)atC>atT	p.I688I	ZNFX1_ENST00000371752.1_Silent_p.I688I|ZNFX1_ENST00000371754.4_Silent_p.I688I	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	688							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.I688I(4)|p.I492I(1)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACTGCTTCAGGATTTCACTGT	0.552																																																5	Substitution - coding silent(5)	large_intestine(5)	20											173	141	151					20																	47881340		2203	4300	6503	47314747	SO:0001819	synonymous_variant	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.2064C>T	20.37:g.47881340G>A			47314747	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Silent	SNP	ENST00000396105.1	37	CCDS13417.1																																																																																				0.552	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		A	47881340	G	A	47881340	2	1	61	1	0	0	0	0	0	0	0	1	18244	1164	41	3		3	ZNFX1	20	47881340	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8907	47881340	15144180	11650	19635										
ZNFX1	57169	broad.mit.edu	37	chr20	47882686	47882686	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tattaccttccagaaactggTccaaagcatgattagtataa	6	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47882686T>C	ENST00000396105.1	-	4	2234	c.1988A>G	c.(1987-1989)gAc>gGc	p.D663G	ZNFX1_ENST00000371752.1_Missense_Mutation_p.D663G|ZNFX1_ENST00000371754.4_Missense_Mutation_p.D663G	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	663							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D663G(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CAGAAACTGGTCCAAAGCATG	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	20											98	95	96					20																	47882686		2203	4300	6503	47316093	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.1988A>G	20.37:g.47882686T>C	ENSP00000379412:p.Asp663Gly		47316093	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.879983	0.91740	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744;ENST00000455070	D;D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73;-2.73	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.96685	0.8918	M	0.94142	3.5	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97629	1.0141	10	0.87932	D	0	-32.7924	15.4485	0.75253	0.0:0.0:0.0:1.0	.	663	Q9P2E3	ZNFX1_HUMAN	G	663;663;663;663;663;467	ENSP00000360819:D663G;ENSP00000360817:D663G;ENSP00000379412:D663G;ENSP00000360809:D663G;ENSP00000413800:D467G	ENSP00000360809:D663G	D	-	2	0	ZNFX1	47316093	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.395000	0.79876	2.323000	0.78572	0.528000	0.53228	GAC		0.393	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		C	47882686	T	C	47882686	3	2	61	1	0	0	0	0	1	0	0	0	18244	1667	58	4	3812	4	ZNFX1	20	47882686	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1346	47882686	15142834	11651	19636										
ZNFX1	57169	broad.mit.edu	37	chr20	47887775	47887775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttggagctacaagccttccGaagaacctgacagatgagct	10	10	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47887775G>A	ENST00000396105.1	-	3	820	c.574C>T	c.(574-576)Cgg>Tgg	p.R192W	ZNFX1_ENST00000371752.1_Missense_Mutation_p.R192W|ZNFX1_ENST00000371754.4_Missense_Mutation_p.R192W	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	192							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R192W(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CAAGCCTTCCGAAGAACCTGA	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	20											110	113	112					20																	47887775		2203	4300	6503	47321182	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.574C>T	20.37:g.47887775G>A	ENSP00000379412:p.Arg192Trp		47321182	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814701	0.50527	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.86	3.72	0.42706	.	0.166435	0.53938	D	0.000058	T	0.69531	0.3121	L	0.56769	1.78	0.35896	D	0.830042	D	0.65815	0.995	P	0.53490	0.727	T	0.77493	-0.2567	10	0.66056	D	0.02	-23.9939	9.187	0.37176	0.0744:0.0:0.6497:0.2759	.	192	Q9P2E3	ZNFX1_HUMAN	W	192	ENSP00000360819:R192W;ENSP00000360817:R192W;ENSP00000379412:R192W;ENSP00000360809:R192W	ENSP00000360809:R192W	R	-	1	2	ZNFX1	47321182	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.955000	0.40372	1.468000	0.48064	0.655000	0.94253	CGG		0.448	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		A	47887775	G	A	47887775	3	1	61	1	0	0	0	0	1	0	0	0	18244	1057	37	1	5230	1	ZNFX1	20	47887775	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5089	47887775	15137745	11652	19637										
KCNB1	3745	broad.mit.edu	37	chr20	47990141	47990141	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttggggctctcgatgaaGaaactagagtgctggctggc	14	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:47990141G>T	ENST00000371741.4	-	2	2122	c.1956C>A	c.(1954-1956)ttC>ttA	p.F652L		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	652					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)	p.F652L(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	TCTCGATGAAGAAACTAGAGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	20											49	50	50					20																	47990141		2203	4300	6503	47423548	SO:0001583	missense	3745			AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1956C>A	20.37:g.47990141G>T	ENSP00000360806:p.Phe652Leu		47423548	Q14193	Missense_Mutation	SNP	ENST00000371741.4	37	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	G	1.185	-0.637085	0.03557	.	.	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.22134	1.97	5.7	5.7	0.88788	.	1.176120	0.05811	N	0.614031	T	0.21841	0.0526	L	0.51422	1.61	0.42521	D	0.993009	B	0.06786	0.001	B	0.09377	0.004	T	0.27938	-1.0059	10	0.11182	T	0.66	.	10.0263	0.42074	0.151:0.0:0.849:0.0	.	652	Q14721	KCNB1_HUMAN	L	652;607	ENSP00000360806:F652L	ENSP00000360806:F652L	F	-	3	2	KCNB1	47423548	1.000000	0.71417	1.000000	0.80357	0.493000	0.33554	2.774000	0.47694	2.692000	0.91855	0.655000	0.94253	TTC		0.572	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		T	47990141	G	T	47990141	3	4	61	1	0	0	0	0	1	0	0	0	8033	933	33	2	624	2	KCNB1	20	47990141	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	102366	47990141	15035379	11653	19638										
SLC9A8	23315	broad.mit.edu	37	chr20	48456127	48456127	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagagtttaaaaaactggcGaattggaaggtaggtttgcc	12	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:48456127G>A	ENST00000361573.2	+	4	381	c.339G>A	c.(337-339)gcG>gcA	p.A113A	SLC9A8_ENST00000539601.1_5'UTR|SLC9A8_ENST00000417961.1_Silent_p.A113A|SLC9A8_ENST00000541138.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	113					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)	p.A113A(2)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			AAAAACTGGCGAATTGGAAGG	0.299																																																2	Substitution - coding silent(2)	large_intestine(2)	20											76	83	80					20																	48456127		2203	4300	6503	47889534	SO:0001819	synonymous_variant	23315			AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.339G>A	20.37:g.48456127G>A			47889534	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																				0.299	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		A	48456127	G	A	48456127	2	1	61	1	0	0	0	0	0	0	0	1	14757	1045	37	1		1	SLC9A8	20	48456127	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	465986	48456127	14569393	11654	19639										
SPATA2	9825	broad.mit.edu	37	chr20	48523206	48523206	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctagcatctgctcacactcGactttggccagaaagagctc	8	13	3	2	rs143602566		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:48523206G>A	ENST00000422556.1	-	3	862	c.513C>T	c.(511-513)gtC>gtT	p.V171V	SPATA2_ENST00000289431.5_Silent_p.V171V|SPATA2_ENST00000543716.1_Silent_p.V34V	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	171					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.V171V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCTCACACTCGACTTTGGCCA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G	,	0,4406		0,0,2203	66	63	64		513,513	-8	0.7	20	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SPATA2	NM_001135773.1,NM_006038.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	171/521,171/521	48523206	1,13005	2203	4300	6503	47956613	SO:0001819	synonymous_variant	9825			AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 145"	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.513C>T	20.37:g.48523206G>A			47956613	E1P626|O94857	Silent	SNP	ENST00000422556.1	37	CCDS13422.1																																																																																				0.547	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038		A	48523206	G	A	48523206	2	1	61	1	0	0	0	0	0	0	0	1	15044	1045	37	1		1	SPATA2	20	48523206	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	67079	48523206	14502314	11655	19640										
TMEM189-UBE2V1	7335	broad.mit.edu	37	chr20	48700676	48700676	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaacttaccactccattaGaactatttactccattcata	1	12	1	1	rs544624018		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:48700676G>T	ENST00000371674.3	-	3	331	c.287C>A	c.(286-288)tCt>tAt	p.S96Y	TMEM189_ENST00000557021.1_Missense_Mutation_p.S319Y|UBE2V1_ENST00000340309.3_Missense_Mutation_p.S119Y|UBE2V1_ENST00000371677.3_Missense_Mutation_p.S119Y|TMEM189-UBE2V1_ENST00000341698.2_Missense_Mutation_p.S319Y|UBE2V1_ENST00000420027.2_Missense_Mutation_p.S52Y|UBE2V1_ENST00000371657.5_Intron|UBE2V1_ENST00000415862.2_Missense_Mutation_p.S52Y|UBE2V1_ENST00000396059.3_5'UTR	NM_001032288.2|NM_001257395.1	NP_001027459.1|NP_001244324.1	Q13404	UB2V1_HUMAN	ubiquitin-conjugating enzyme E2 variant 1	96					cell differentiation (GO:0030154)|error-free postreplication DNA repair (GO:0042275)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of DNA repair (GO:0006282)|regulation of transcription, DNA-templated (GO:0006355)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-UEV1A complex (GO:0035370)|ubiquitin conjugating enzyme complex (GO:0031371)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ubiquitin-protein transferase activity (GO:0004842)	p.S319Y(1)|p.S119Y(1)		endometrium(2)|large_intestine(3)|lung(4)	9			BRCA - Breast invasive adenocarcinoma(9;4.74e-06)			CACTCCATTAGAACTATTTAC	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	20											96	97	96					20																	48700676		2203	4300	6503	48134083	SO:0001583	missense	387522			U39360	CCDS13426.1, CCDS13427.1, CCDS33483.1, CCDS58775.1, CCDS74740.1	20q13.2	2007-07-18			ENSG00000244687	ENSG00000244687		"Ubiquitin-conjugating enzymes E2"	12494	protein-coding gene	gene with protein product		602995		UBE2V		9418904, 9305758	Standard	NM_001032288		Approved	UEV-1, CROC-1, UEV1A, CROC1		Q13404	OTTHUMG00000152626	ENST00000371674.3:c.287C>A	20.37:g.48700676G>T	ENSP00000360739:p.Ser96Tyr		48134083	E1P629|Q13403|Q13532|Q5TGE0|Q5TGE3|Q96H34|Q9GZT0|Q9GZW1|Q9H4J3|Q9H4J4|Q9UKL1|Q9UM48|Q9UM49|Q9UM50	Missense_Mutation	SNP	ENST00000371674.3	37	CCDS33483.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932337	0.92389	.	.	ENSG00000124208;ENSG00000244687;ENSG00000244687;ENSG00000244687;ENSG00000244687;ENSG00000244687;ENSG00000244687;ENSG00000240849	ENST00000341698;ENST00000371674;ENST00000340309;ENST00000415862;ENST00000371677;ENST00000420027;ENST00000354374;ENST00000557021	T;T;T;T;T;T;T	0.38887	2.76;2.76;2.76;1.11;2.76;1.11;2.76	5.49	5.49	0.81192	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.51477	U	0.000096	T	0.69522	0.3120	M	0.82323	2.585	0.80722	D	1	D;D;P;P	0.89917	1.0;0.984;0.929;0.75	D;D;D;P	0.85130	0.997;0.935;0.915;0.86	T	0.73094	-0.4091	10	0.62326	D	0.03	-9.4273	19.3809	0.94532	0.0:0.0:1.0:0.0	.	319;119;52;96	G3V2F7;Q13404-7;Q13404-6;Q13404	.;.;.;UB2V1_HUMAN	Y	319;96;119;52;119;52;52;319	ENSP00000344166:S319Y;ENSP00000360739:S96Y;ENSP00000340305:S119Y;ENSP00000407770:S52Y;ENSP00000360742:S119Y;ENSP00000395264:S52Y;ENSP00000450635:S319Y	ENSP00000344166:S319Y	S	-	2	0	TMEM189-UBE2V1;UBE2V1;TMEM189	48134083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.573000	0.86826	0.650000	0.86243	TCT		0.383	UBE2V1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080530.1	NM_021988		T	48700676	G	T	48700676	3	4	61	1	0	0	0	0	1	0	0	0	16151	942	33	2	164	2	TMEM189-UBE2V1	20	48700676	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	177470	48700676	14324844	11656	19641										
PTPN1	5770	broad.mit.edu	37	chr20	49191098	49191098	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaaagaagaaaaagagatGatctttgaagacacaaattt	7	4	1	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49191098G>T	ENST00000371621.3	+	5	573	c.399G>T	c.(397-399)atG>atT	p.M133I	PTPN1_ENST00000541713.1_Missense_Mutation_p.M60I|RP4-530I15.9_ENST00000431019.1_RNA	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	133	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)	p.M133I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	aaaaagagatgatctttgaag	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	20											82	82	82					20																	49191098		2203	4300	6503	48624505	SO:0001583	missense	5770				CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.399G>T	20.37:g.49191098G>T	ENSP00000360683:p.Met133Ile		48624505	Q5TGD8|Q9BQV9|Q9NQQ4	Missense_Mutation	SNP	ENST00000371621.3	37	CCDS13430.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228526	0.58777	.	.	ENSG00000196396	ENST00000371621;ENST00000541713	D;D	0.83419	-1.72;-1.72	5.37	5.37	0.77165	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.80581	0.4650	L	0.47078	1.49	0.53688	D	0.999977	B	0.12013	0.005	B	0.19666	0.026	T	0.76013	-0.3114	10	0.52906	T;T	0.07;0.07	.	18.0368	0.89307	0.0:0.0:1.0:0.0	.	133	P18031	PTN1_HUMAN	I	133;60	ENSP00000360683:M133I;ENSP00000437732:M60I	ENSP00000360683:M133I;ENSP00000360683:M133I	M	+	3	0	PTPN1	48624505	1.000000	0.71417	0.999000	0.59377	0.903000	0.53119	7.050000	0.76620	2.676000	0.91093	0.561000	0.74099	ATG		0.338	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			T	49191098	G	T	49191098	3	4	61	1	0	0	0	0	1	0	0	0	12814	1290	45	2	417	2	PTPN1	20	49191098	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	490422	49191098	13834422	11657	19642										
ADNP	23394	broad.mit.edu	37	chr20	49508261	49508261	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgctttgggaagactcgtcaGaccaggttcctggtttcatt	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49508261G>T	ENST00000396029.3	-	5	3557	c.2990C>A	c.(2989-2991)tCt>tAt	p.S997Y	ADNP_ENST00000371602.4_Missense_Mutation_p.S997Y|ADNP_ENST00000396032.3_Missense_Mutation_p.S997Y|ADNP_ENST00000349014.3_Missense_Mutation_p.S997Y	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	997					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S997Y(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						AGACTCGTCAGACCAGGTTCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	20											106	95	99					20																	49508261		2203	4300	6503	48941668	SO:0001583	missense	23394			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2990C>A	20.37:g.49508261G>T	ENSP00000379346:p.Ser997Tyr		48941668	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710512	0.30322	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	6.17	6.17	0.99709	.	0.095171	0.46145	D	0.000301	T	0.28034	0.0691	N	0.08118	0	0.35570	D	0.805367	B	0.32693	0.38	B	0.25140	0.058	T	0.40776	-0.9545	9	0.59425	D	0.04	0.3422	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	997	Q9H2P0	ADNP_HUMAN	Y	997	.	ENSP00000342905:S997Y	S	-	2	0	ADNP	48941668	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	5.119000	0.64679	2.941000	0.99782	0.655000	0.94253	TCT		0.493	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		T	49508261	G	T	49508261	3	4	61	1	0	0	0	0	1	0	0	0	323	942	33	2	322	2	ADNP	20	49508261	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	317163	49508261	13517259	11658	19643										
ADNP	23394	broad.mit.edu	37	chr20	49508542	49508542	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctctgggttatcgttagaGattttaggttcaacttcaaa	8	7	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49508542G>T	ENST00000396029.3	-	5	3276	c.2709C>A	c.(2707-2709)atC>atA	p.I903I	ADNP_ENST00000371602.4_Silent_p.I903I|ADNP_ENST00000396032.3_Silent_p.I903I|ADNP_ENST00000349014.3_Silent_p.I903I	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	903					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I903I(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						TATCGTTAGAGATTTTAGGTT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	20											148	148	148					20																	49508542		2203	4300	6503	48941949	SO:0001819	synonymous_variant	23394			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2709C>A	20.37:g.49508542G>T			48941949	E1P5Y2|O94881|Q5BKU2|Q9UG34	Silent	SNP	ENST00000396029.3	37	CCDS13433.1																																																																																				0.398	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		T	49508542	G	T	49508542	2	4	61	1	0	0	0	0	0	0	0	1	323	932	33	2		2	ADNP	20	49508542	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	281	49508542	13516978	11659	19644										
ADNP	23394	broad.mit.edu	37	chr20	49509723	49509723	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatggacaagacagaccatGaattaacatatggttgagca	9	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49509723G>T	ENST00000396029.3	-	5	2095	c.1528C>A	c.(1528-1530)Cat>Aat	p.H510N	ADNP_ENST00000371602.4_Missense_Mutation_p.H510N|ADNP_ENST00000396032.3_Missense_Mutation_p.H510N|ADNP_ENST00000349014.3_Missense_Mutation_p.H510N	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	510					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H510N(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GACAGACCATGAATTAACATA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	20											184	186	185					20																	49509723		2203	4300	6503	48943130	SO:0001583	missense	23394			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1528C>A	20.37:g.49509723G>T	ENSP00000379346:p.His510Asn		48943130	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486161	0.63962	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	6.01	6.01	0.97437	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.76919	0.4055	L	0.49126	1.545	0.58432	D	0.999999	D	0.69078	0.997	D	0.79784	0.993	T	0.76454	-0.2953	9	0.72032	D	0.01	-1.8897	20.5211	0.99222	0.0:0.0:1.0:0.0	.	510	Q9H2P0	ADNP_HUMAN	N	510	.	ENSP00000342905:H510N	H	-	1	0	ADNP	48943130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.630000	0.83225	2.861000	0.98227	0.650000	0.86243	CAT		0.398	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		T	49509723	G	T	49509723	3	4	61	1	0	0	0	0	1	0	0	0	323	1290	45	2	1784	2	ADNP	20	49509723	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1181	49509723	13515797	11660	19645										
ADNP	23394	broad.mit.edu	37	chr20	49509856	49509856	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagctttatgttctttttcGaagtgcacactatagacatt	6	8	2	1	rs375629425		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49509856G>A	ENST00000396029.3	-	5	1962	c.1395C>T	c.(1393-1395)ttC>ttT	p.F465F	ADNP_ENST00000371602.4_Silent_p.F465F|ADNP_ENST00000396032.3_Silent_p.F465F|ADNP_ENST00000349014.3_Silent_p.F465F	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	465					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.F465F(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GTTCTTTTTCGAAGTGCACAC	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G	,	1,4405	2.1+/-5.4	0,1,2202	156	164	161		1395,1395	3.6	1	20		161	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADNP	NM_015339.2,NM_181442.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	465/1103,465/1103	49509856	1,13005	2203	4300	6503	48943263	SO:0001819	synonymous_variant	23394			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1395C>T	20.37:g.49509856G>A			48943263	E1P5Y2|O94881|Q5BKU2|Q9UG34	Silent	SNP	ENST00000396029.3	37	CCDS13433.1																																																																																				0.388	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		A	49509856	G	A	49509856	2	1	61	1	0	0	0	0	0	0	0	1	323	1049	37	1		1	ADNP	20	49509856	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	133	49509856	13515664	11661	19646										
KCNG1	3755	broad.mit.edu	37	chr20	49626408	49626408	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgtccaggtggtcctccgcGatgccccagtacagcagctc	11	17	0	0	rs147442458		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:49626408G>A	ENST00000371571.4	-	2	753	c.468C>T	c.(466-468)atC>atT	p.I156I	KCNG1_ENST00000506387.1_5'Flank|RP5-955M13.4_ENST00000424566.1_RNA|KCNG1_ENST00000396017.3_Silent_p.I156I	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	156					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.I156I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GGTCCTCCGCGATGCCCCAGT	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G		0,4404		0,0,2202	39	40	40		468	3.6	1	20	dbSNP_134	40	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	KCNG1	NM_002237.3		0,1,6499	AA,AG,GG		0.0116,0.0,0.0077		156/514	49626408	1,12999	2202	4298	6500	49059815	SO:0001819	synonymous_variant	3755			AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.468C>T	20.37:g.49626408G>A			49059815	A8K3S4|O43528|Q5JXL5|Q9BRC1	Silent	SNP	ENST00000371571.4	37	CCDS13436.1																																																																																				0.662	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		A	49626408	G	A	49626408	2	1	61	1	0	0	0	0	0	0	0	1	8048	1048	37	1		1	KCNG1	20	49626408	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	116552	49626408	13399112	11662	19647										
NFATC2	4773	broad.mit.edu	37	chr20	50048815	50048815	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctggtggtgcctggtgcGaaattctcgcagtacatgat	14	8	2	1	rs199948885		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:50048815G>A	ENST00000396009.3	-	9	2730	c.2511C>T	c.(2509-2511)ttC>ttT	p.F837F	NFATC2_ENST00000414705.1_Silent_p.F817F|NFATC2_ENST00000609507.1_Silent_p.F618F|NFATC2_ENST00000610033.1_Silent_p.F618F|NFATC2_ENST00000609943.1_Silent_p.F817F|NFATC2_ENST00000371564.3_Silent_p.F837F	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	837					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F837F(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					TGCCTGGTGCGAAATTCTCGC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G	,,	0,4406		0,0,2203	66	65	65		2451,2511,2511	-3.1	0	20		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	817/902,837/922,837/926	50048815	1,13005	2203	4300	6503	49482222	SO:0001819	synonymous_variant	4773			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2511C>T	20.37:g.50048815G>A			49482222	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	37	CCDS13437.1																																																																																				0.617	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		A	50048815	G	A	50048815	2	1	61	1	0	0	0	0	0	0	0	1	10393	1049	37	1		1	NFATC2	20	50048815	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	422407	50048815	12976705	11663	19648										
ATP9A	10079	broad.mit.edu	37	chr20	50217793	50217793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggggagagaaccgtcttCgcaggtacttgaggacatag	16	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:50217793C>T	ENST00000338821.5	-	28	3365	c.3101G>A	c.(3100-3102)cGa>cAa	p.R1034Q	ATP9A_ENST00000402822.1_Missense_Mutation_p.R913Q|ATP9A_ENST00000311637.5_Missense_Mutation_p.R898Q	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	1034					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1034Q(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GAACCGTCTTCGCAGGTACTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											76	58	64					20																	50217793		2203	4300	6503	49651200	SO:0001583	missense	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.3101G>A	20.37:g.50217793C>T	ENSP00000342481:p.Arg1034Gln		49651200	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084718	0.76642	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.36520	1.25;1.25;1.25	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.27866	0.0686	L	0.31804	0.96	0.80722	D	1	P;P	0.46327	0.876;0.776	B;B	0.36092	0.132;0.217	T	0.11567	-1.0582	10	0.48119	T	0.1	-13.0378	18.4646	0.90750	0.0:1.0:0.0:0.0	.	913;1034	O75110-2;O75110	.;ATP9A_HUMAN	Q	898;1034;913	ENSP00000309086:R898Q;ENSP00000342481:R1034Q;ENSP00000385875:R913Q	ENSP00000309086:R898Q	R	-	2	0	ATP9A	49651200	1.000000	0.71417	0.958000	0.39756	0.965000	0.64279	7.760000	0.85248	2.434000	0.82447	0.655000	0.94253	CGA		0.567	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50217793	C	T	50217793	3	4	61	1	0	0	0	0	1	0	0	0	1199	884	31	1	46	1	ATP9A	20	50217793	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168978	50217793	12807727	11664	19649										
ATP9A	10079	broad.mit.edu	37	chr20	50292678	50292678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcgtacacaccttacttCggggatttgaggtattcatg	9	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:50292678C>T	ENST00000338821.5	-	10	1133	c.869G>A	c.(868-870)cGa>cAa	p.R290Q	ATP9A_ENST00000402822.1_Missense_Mutation_p.R169Q|ATP9A_ENST00000311637.5_Missense_Mutation_p.R154Q	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	290					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R290Q(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CACCTTACTTCGGGGATTTGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	20											92	84	87					20																	50292678		2203	4300	6503	49726085	SO:0001583	missense	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.869G>A	20.37:g.50292678C>T	ENSP00000342481:p.Arg290Gln		49726085	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999953	0.74818	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.89810	-2.38;-2.57;-2.38	5.61	5.61	0.85477	ATPase, P-type, ATPase-associated domain (1);	0.050166	0.85682	D	0.000000	D	0.88164	0.6363	L	0.50993	1.605	0.46203	D	0.998921	P;P	0.46512	0.879;0.489	B;B	0.42386	0.133;0.386	D	0.88899	0.3351	10	0.56958	D	0.05	-15.1243	19.6283	0.95689	0.0:1.0:0.0:0.0	.	169;290	O75110-2;O75110	.;ATP9A_HUMAN	Q	154;290;169	ENSP00000309086:R154Q;ENSP00000342481:R290Q;ENSP00000385875:R169Q	ENSP00000309086:R154Q	R	-	2	0	ATP9A	49726085	0.998000	0.40836	0.637000	0.29366	0.702000	0.40608	4.598000	0.61069	2.627000	0.88993	0.655000	0.94253	CGA		0.438	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50292678	C	T	50292678	3	4	61	1	0	0	0	0	1	0	0	0	1199	884	31	1	2350	1	ATP9A	20	50292678	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74885	50292678	12732842	11665	19650										
ZFP64	55734	broad.mit.edu	37	chr20	50769234	50769234	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcacctgatgcccaacgatGattttgactcttccctcgct	8	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:50769234G>T	ENST00000216923.4	-	6	1846	c.1497C>A	c.(1495-1497)atC>atA	p.I499I	ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000346617.4_Silent_p.I445I|ZFP64_ENST00000371515.4_Silent_p.I497I|ZFP64_ENST00000477786.1_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	499					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I499I(2)		breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GCCCAACGATGATTTTGACTC	0.657																																																2	Substitution - coding silent(2)	large_intestine(2)	20											29	31	30					20																	50769234		2203	4300	6503	50202641	SO:0001819	synonymous_variant	55734			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1497C>A	20.37:g.50769234G>T			50202641	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																				0.657	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		T	50769234	G	T	50769234	2	4	61	1	0	0	0	0	0	0	0	1	17691	1280	45	2		2	ZFP64	20	50769234	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	476556	50769234	12256286	11666	19651										
ZNF217	7764	broad.mit.edu	37	chr20	52193013	52193013	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actagagaggggaggcacatCttttcccagcaacgctggcg	13	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:52193013C>A	ENST00000371471.2	-	4	2715	c.2290G>T	c.(2290-2292)Gat>Tat	p.D764Y	ZNF217_ENST00000302342.3_Missense_Mutation_p.D764Y|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	764					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.D764Y(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GGAGGCACATCTTTTCCCAGC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	20											64	63	63					20																	52193013		2203	4300	6503	51626420	SO:0001583	missense	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2290G>T	20.37:g.52193013C>A	ENSP00000360526:p.Asp764Tyr		51626420	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.290765	0.80914	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.16324	2.35;2.35	5.45	5.45	0.79879	.	0.070853	0.56097	D	0.000022	T	0.44456	0.1294	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.37709	-0.9694	10	0.87932	D	0	-44.5444	18.8963	0.92424	0.0:1.0:0.0:0.0	.	764	O75362	ZN217_HUMAN	Y	764	ENSP00000360526:D764Y;ENSP00000304308:D764Y	ENSP00000304308:D764Y	D	-	1	0	ZNF217	51626420	1.000000	0.71417	0.024000	0.17045	0.017000	0.09413	7.092000	0.76930	2.553000	0.86117	0.555000	0.69702	GAT		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52193013	C	A	52193013	3	1	61	1	0	0	0	0	1	0	0	0	17811	913	32	2	864	2	ZNF217	20	52193013	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1423779	52193013	10832507	11667	19652										
ZNF217	7764	broad.mit.edu	37	chr20	52198015	52198015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttacccagatggattccttCgggaagcccatcctcagatc	8	14	1	2	rs200131894		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:52198015C>T	ENST00000371471.2	-	2	1776	c.1351G>A	c.(1351-1353)Gaa>Aaa	p.E451K	ZNF217_ENST00000302342.3_Missense_Mutation_p.E451K|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	451					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E451K(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TGGATTCCTTCGGGAAGCCCA	0.602													C|||	1	0.000199681	0	0	5008	,	,		15468	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											66	62	63					20																	52198015		2203	4300	6503	51631422	SO:0001583	missense	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1351G>A	20.37:g.52198015C>T	ENSP00000360526:p.Glu451Lys		51631422	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	14.46	2.541356	0.45280	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.10005	2.92;2.92	5.7	5.7	0.88788	.	0.494970	0.22437	N	0.060078	T	0.10723	0.0262	L	0.47716	1.5	0.39132	D	0.961874	P	0.48640	0.913	B	0.34038	0.174	T	0.13098	-1.0522	10	0.38643	T	0.18	-22.3892	17.6057	0.88036	0.0:1.0:0.0:0.0	.	451	O75362	ZN217_HUMAN	K	451	ENSP00000360526:E451K;ENSP00000304308:E451K	ENSP00000304308:E451K	E	-	1	0	ZNF217	51631422	0.988000	0.35896	0.199000	0.23439	0.303000	0.27691	6.374000	0.73132	2.686000	0.91538	0.591000	0.81541	GAA		0.602	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52198015	C	T	52198015	3	4	61	1	0	0	0	0	1	0	0	0	17811	893	31	1	1811	1	ZNF217	20	52198015	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5002	52198015	10827505	11668	19653										
CYP24A1	1591	broad.mit.edu	37	chr20	52775534	52775534	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggcttttaaatacggcatAttcctcaaatcttctgcccg	6	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:52775534A>C	ENST00000216862.3	-	8	1512	c.1119T>G	c.(1117-1119)aaT>aaG	p.N373K	CYP24A1_ENST00000460643.1_5'Flank|CYP24A1_ENST00000395954.3_Missense_Mutation_p.N231K|CYP24A1_ENST00000395955.3_Missense_Mutation_p.N373K	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	373					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)	p.N373K(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	AATACGGCATATTCCTCAAAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	20											129	135	133					20																	52775534		2203	4300	6503	52208941	SO:0001583	missense	1591			U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"Cytochrome P450s"	2602	protein-coding gene	gene with protein product		126065	"cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.1119T>G	20.37:g.52775534A>C	ENSP00000216862:p.Asn373Lys		52208941	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457285	0.26161	.	.	ENSG00000019186	ENST00000216862;ENST00000395955;ENST00000395954	T;T;T	0.77750	0.06;5.15;-1.12	5.43	-7.08	0.01558	.	0.044769	0.85682	D	0.000000	T	0.47967	0.1474	N	0.17082	0.46	0.40148	D	0.976913	B;B;B	0.13594	0.008;0.002;0.003	B;B;B	0.16289	0.015;0.01;0.01	T	0.51601	-0.8685	10	0.02654	T	1	-21.4374	7.8659	0.29537	0.4046:0.0:0.4318:0.1636	.	373;373;231	Q32ML3;Q07973;Q5I2W7	.;CP24A_HUMAN;.	K	373;373;231	ENSP00000216862:N373K;ENSP00000379285:N373K;ENSP00000379284:N231K	ENSP00000216862:N373K	N	-	3	2	CYP24A1	52208941	0.993000	0.37304	0.013000	0.15412	0.487000	0.33371	0.368000	0.20399	-1.972000	0.01001	-0.297000	0.09499	AAT		0.388	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			C	52775534	A	C	52775534	3	2	61	1	0	0	0	0	1	0	0	0	4160	446	16	4	441	4	CYP24A1	20	52775534	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	577519	52775534	10249986	11669	19654										
CASS4	57091	broad.mit.edu	37	chr20	55027937	55027937	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtcatggtggcacggatgCttccagaagacatcaagagg	13	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:55027937C>A	ENST00000360314.3	+	6	1930	c.1705C>A	c.(1705-1707)Ctt>Att	p.L569I	CASS4_ENST00000371336.3_Missense_Mutation_p.L569I|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	569					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)	p.L569I(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						GGCACGGATGCTTCCAGAAGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	20											88	81	83					20																	55027937		2203	4300	6503	54461344	SO:0001583	missense	57091			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1705C>A	20.37:g.55027937C>A	ENSP00000353462:p.Leu569Ile		54461344	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	C	5.333	0.246810	0.10130	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.22336	1.96;1.96	6.17	2.74	0.32292	Serine rich protein interaction (1);	0.235357	0.42420	N	0.000710	T	0.06872	0.0175	N	0.04297	-0.235	0.28438	N	0.916922	B;B;B	0.15473	0.013;0.001;0.0	B;B;B	0.17098	0.017;0.001;0.001	T	0.30563	-0.9974	10	0.10636	T	0.68	-11.7544	3.0569	0.06187	0.3977:0.2446:0.3577:0.0	.	515;569;569	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	I	569	ENSP00000353462:L569I;ENSP00000360387:L569I	ENSP00000353462:L569I	L	+	1	0	CASS4	54461344	0.997000	0.39634	0.986000	0.45419	0.829000	0.46940	2.641000	0.46587	0.858000	0.35431	-0.976000	0.02587	CTT		0.488	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		A	55027937	C	A	55027937	3	1	61	1	0	0	0	0	1	0	0	0	2689	797	28	2	1723	2	CASS4	20	55027937	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2252403	55027937	7997583	11670	19655										
SPO11	23626	broad.mit.edu	37	chr20	55910508	55910508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcgaatattcaaggaattCggagtatcctttaagtggga	10	6	1	0	rs28368082	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:55910508C>T	ENST00000371263.3	+	7	740	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	SPO11_ENST00000345868.4_Missense_Mutation_p.R173W|SPO11_ENST00000371260.4_Missense_Mutation_p.R173W	NM_012444.2	NP_036576.1	Q9Y5K1	SPO11_HUMAN	SPO11 meiotic protein covalently bound to DSB	211			R -> W (in dbSNP:rs28368082).		DNA catabolic process, endonucleolytic (GO:0000737)|female gamete generation (GO:0007292)|male meiosis I (GO:0007141)|ovarian follicle development (GO:0001541)|protein localization to chromosome (GO:0034502)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|hydrolase activity (GO:0016787)	p.R211W(1)		autonomic_ganglia(1)|breast(3)|large_intestine(4)|lung(8)|skin(2)	18	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)			TCAAGGAATTCGGAGTATCCT	0.303								Editing and processing nucleases					C|||	2	0.000399361	0	0	5008	,	,		19526	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	20											63	59	60					20																	55910508		2202	4300	6502	55343915	SO:0001583	missense	23626			AF169385	CCDS13456.1, CCDS13457.1	20q13.31	2013-06-05	2013-06-05		ENSG00000054796	ENSG00000054796			11250	protein-coding gene	gene with protein product	"cancer/testis antigen 35", "spermatogenesis associated 43"	605114	"SPO11, meiotic protein covalently bound to DSB (S. cerevisiae)-like", "SPO11 meiotic protein covalently bound to DSB-like (S. cerevisiae)", "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)"			10534401	Standard	NM_012444		Approved	CT35, SPATA43, TOPVIA	uc002xye.3	Q9Y5K1	OTTHUMG00000032817	ENST00000371263.3:c.631C>T	20.37:g.55910508C>T	ENSP00000360310:p.Arg211Trp		55343915	Q5TCI1|Q8N4V0|Q9NQM7|Q9NQM8	Missense_Mutation	SNP	ENST00000371263.3	37	CCDS13456.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.47	2.247781	0.39697	.	.	ENSG00000054796	ENST00000371263;ENST00000345868;ENST00000371260;ENST00000418127	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.5	-1.73	0.08081	.	0.904071	0.09523	N	0.790690	T	0.45558	0.1348	L	0.34521	1.04	0.39544	D	0.968868	B;B	0.20164	0.042;0.014	B;B	0.08055	0.003;0.001	T	0.34229	-0.9837	10	0.59425	D	0.04	2.9152	5.8689	0.18793	0.5109:0.2761:0.0:0.213	rs28368082;rs28368082	173;211	Q9Y5K1-2;Q9Y5K1	.;SPO11_HUMAN	W	211;173;173;189	ENSP00000360310:R211W;ENSP00000316034:R173W;ENSP00000360307:R173W;ENSP00000413185:R189W	ENSP00000316034:R173W	R	+	1	2	SPO11	55343915	0.996000	0.38824	0.193000	0.23327	0.978000	0.69477	1.447000	0.35101	-0.124000	0.11724	-0.463000	0.05309	CGG		0.303	SPO11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079836.2	NM_012444		T	55910508	C	T	55910508	3	4	61	1	0	0	0	0	1	0	0	0	15116	875	31	1	657	1	SPO11	20	55910508	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	882571	55910508	7115012	11671	19656										
RAE1	8480	broad.mit.edu	37	chr20	55948750	55948750	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttcacctttaaatgtcatCgatctaatggaaccaacact	4	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:55948750C>T	ENST00000395841.2	+	10	1201	c.781C>T	c.(781-783)Cga>Tga	p.R261*	RAE1_ENST00000371242.2_Nonsense_Mutation_p.R261*|RAE1_ENST00000395840.2_Nonsense_Mutation_p.R261*|RAE1_ENST00000527947.1_Nonsense_Mutation_p.R261*	NM_003610.3	NP_003601.1	P78406	RAE1L_HUMAN	ribonucleic acid export 1	261					carbohydrate metabolic process (GO:0005975)|cellular response to organic cyclic compound (GO:0071407)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|nuclear pore (GO:0005643)|nucleolus (GO:0005730)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|RNA binding (GO:0003723)	p.R261*(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(6)|prostate(3)|skin(2)	21	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			TAAATGTCATCGATCTAATGG	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											224	215	218					20																	55948750		2203	4300	6503	55382157	SO:0001587	stop_gained	8480			U84720	CCDS13458.1	20q13.31	2013-08-28	2013-08-28		ENSG00000101146	ENSG00000101146		"WD repeat domain containing"	9828	protein-coding gene	gene with protein product		603343	"RAE1 (RNA export 1, S.pombe) homolog", "RAE1 RNA export 1 homolog (S. pombe)"			9370289, 9256445	Standard	XM_005260582		Approved	Mnrp41	uc002xyi.3	P78406	OTTHUMG00000032819	ENST00000395841.2:c.781C>T	20.37:g.55948750C>T	ENSP00000379182:p.Arg261*		55382157	A8K882|O15306|Q3SYL7|Q5TCH8|Q6V708|Q9H100|Q9NQM6	Nonsense_Mutation	SNP	ENST00000395841.2	37	CCDS13458.1	.	.	.	.	.	.	.	.	.	.	C	38	7.231739	0.98150	.	.	ENSG00000101146	ENST00000395841;ENST00000371242;ENST00000527947;ENST00000395840	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.6719	19.9598	0.97242	0.0:1.0:0.0:0.0	.	.	.	.	X	261	.	ENSP00000360286:R261X	R	+	1	2	RAE1	55382157	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.794000	0.62482	2.716000	0.92895	0.655000	0.94253	CGA		0.403	RAE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079842.2			T	55948750	C	T	55948750	4	4	61	1	0	0	0	0	0	1	0	0	13035	876	31	1	815	1	RAE1	20	55948750	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38242	55948750	7076770	11672	19657										
RBM38	55544	broad.mit.edu	37	chr20	55982857	55982857	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcacccgcgggcaccactttCgtgcagtaccaggcgccgca	12	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:55982857C>T	ENST00000356208.5	+	4	850	c.675C>T	c.(673-675)ttC>ttT	p.F225F	RBM38_ENST00000371219.2_Silent_p.F144F	NM_017495.5	NP_059965.2	Q9H0Z9	RBM38_HUMAN	RNA binding motif protein 38	225					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell cycle (GO:0007049)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|regulation of myotube differentiation (GO:0010830)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.F225F(1)		large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			GCACCACTTTCGTGCAGTACC	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	20											8	11	10					20																	55982857		2013	4148	6161	55416263	SO:0001819	synonymous_variant	55544			X75314	CCDS46617.1, CCDS46618.1	20q13.31	2013-02-12	2006-07-11	2006-07-11	ENSG00000132819	ENSG00000132819		"RNA binding motif (RRM) containing"	15818	protein-coding gene	gene with protein product		612428	"RNA-binding region (RNP1, RRM) containing 1"	RNPC1			Standard	NM_017495		Approved	HSRNASEB, SEB4D, seb4B, dJ800J21.2	uc010zzj.2	Q9H0Z9	OTTHUMG00000032820	ENST00000356208.5:c.675C>T	20.37:g.55982857C>T			55416263	A6NDK1|A6NMU6|Q15350|Q15351|Q9BYK3|Q9BYK4	Silent	SNP	ENST00000356208.5	37	CCDS46617.1																																																																																				0.682	RBM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079843.4	NM_183425		T	55982857	C	T	55982857	2	4	61	1	0	0	0	0	0	0	0	1	13169	883	31	1		1	RBM38	20	55982857	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34107	55982857	7042663	11673	19658										
PCK1	5105	broad.mit.edu	37	chr20	56138152	56138152	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccacctgcctgaccgcagaGagatcatctcctttggcagt	9	15	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:56138152G>T	ENST00000319441.4	+	5	843	c.679G>T	c.(679-681)Gag>Tag	p.E227*	PCK1_ENST00000535860.1_Nonsense_Mutation_p.E95*|PCK1_ENST00000543666.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	227					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)	p.E227*(1)		endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TGACCGCAGAGAGATCATCTC	0.617																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											75	78	77					20																	56138152		2203	4300	6503	55571558	SO:0001587	stop_gained	5105				CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.679G>T	20.37:g.56138152G>T	ENSP00000319814:p.Glu227*		55571558	A8K437|B4DT64|Q8TCA3|Q9UJD2	Nonsense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	37	6.270652	0.97431	.	.	ENSG00000124253	ENST00000319441;ENST00000535860	.	.	.	5.06	5.06	0.68205	.	0.108146	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-36.278	18.8029	0.92025	0.0:0.0:1.0:0.0	.	.	.	.	X	227;95	.	ENSP00000319814:E227X	E	+	1	0	PCK1	55571558	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.693000	0.54735	2.520000	0.84964	0.655000	0.94253	GAG		0.617	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56138152	G	T	56138152	4	4	61	1	0	0	0	0	0	1	0	0	11612	943	33	2	693	2	PCK1	20	56138152	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	155295	56138152	6887368	11674	19659										
ZNF831	128611	broad.mit.edu	37	chr20	57766269	57766269	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccatcccactgtaccacacGgtgcctcccgggggcctcca	9	20	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:57766269G>A	ENST00000371030.2	+	1	195	c.195G>A	c.(193-195)acG>acA	p.T65T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	65	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.T65T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TGTACCACACGGTGCCTCCCG	0.692																																																1	Substitution - coding silent(1)	large_intestine(1)	20											11	13	12					20																	57766269		1871	4074	5945	57199664	SO:0001819	synonymous_variant	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.195G>A	20.37:g.57766269G>A			57199664	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																				0.692	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57766269	G	A	57766269	2	1	61	1	0	0	0	0	0	0	0	1	18224	1103	39	1		1	ZNF831	20	57766269	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1628117	57766269	5259251	11675	19660										
ZNF831	128611	broad.mit.edu	37	chr20	57767958	57767958	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtacggggatgagacgttCaaaaggatctaccagaaaat	12	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:57767958C>A	ENST00000371030.2	+	1	1884	c.1884C>A	c.(1882-1884)ttC>ttA	p.F628L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	628							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.F628L(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					ATGAGACGTTCAAAAGGATCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											60	69	66					20																	57767958		2048	4188	6236	57201353	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1884C>A	20.37:g.57767958C>A	ENSP00000360069:p.Phe628Leu		57201353	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.174363	0.57692	.	.	ENSG00000124203	ENST00000371030	T	0.09445	2.98	5.21	0.539	0.17156	.	0.000000	0.56097	D	0.000028	T	0.21347	0.0514	L	0.54323	1.7	0.35309	D	0.783748	D	0.89917	1.0	D	0.83275	0.996	T	0.10660	-1.0620	10	0.40728	T	0.16	-25.8782	7.4794	0.27395	0.0:0.4815:0.0:0.5185	.	628	Q5JPB2	ZN831_HUMAN	L	628	ENSP00000360069:F628L	ENSP00000360069:F628L	F	+	3	2	ZNF831	57201353	1.000000	0.71417	0.034000	0.17996	0.543000	0.35085	0.780000	0.26760	0.212000	0.20703	0.655000	0.94253	TTC		0.587	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767958	C	A	57767958	3	1	61	1	0	0	0	0	1	0	0	0	18224	825	29	2	1886	2	ZNF831	20	57767958	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1689	57767958	5257562	11676	19661										
ZNF831	128611	broad.mit.edu	37	chr20	57829673	57829673	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaagccagagcagcccataGaaattcctgaagccccttct	7	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:57829673G>T	ENST00000371030.2	+	5	4909	c.4909G>T	c.(4909-4911)Gaa>Taa	p.E1637*		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1637							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.E1637*(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCAGCCCATAGAAATTCCTGA	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											64	62	63					20																	57829673		1844	4103	5947	57263068	SO:0001587	stop_gained	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4909G>T	20.37:g.57829673G>T	ENSP00000360069:p.Glu1637*		57263068	Q5TDR4|Q8TCP0	Nonsense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	41	8.737360	0.98935	.	.	ENSG00000124203	ENST00000371030	.	.	.	5.66	3.67	0.42095	.	0.581837	0.15403	N	0.264198	.	.	.	.	.	.	0.51482	D	0.999925	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-5.5073	8.548	0.33433	0.0839:0.152:0.7641:0.0	.	.	.	.	X	1637	.	ENSP00000360069:E1637X	E	+	1	0	ZNF831	57263068	0.011000	0.17503	0.004000	0.12327	0.426000	0.31534	1.884000	0.39668	1.373000	0.46208	0.650000	0.86243	GAA		0.488	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57829673	G	T	57829673	4	4	61	1	0	0	0	0	0	1	0	0	18224	943	33	2	4927	2	ZNF831	20	57829673	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61715	57829673	5195847	11677	19662										
EDN3	1908	broad.mit.edu	37	chr20	57876616	57876616	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcgaggggactgtggccccGacagcactgcagggtccaag	17	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:57876616G>A	ENST00000337938.2	+	2	590	c.204G>A	c.(202-204)ccG>ccA	p.P68P	EDN3_ENST00000371028.2_Silent_p.P68P|EDN3_ENST00000395654.3_Silent_p.P68P|EDN3_ENST00000311585.7_Silent_p.P68P|EDN3_ENST00000371025.3_Silent_p.P68P	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	68					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.P68P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CTGTGGCCCCGACAGCACTGC	0.697																																																1	Substitution - coding silent(1)	large_intestine(1)	20											37	41	39					20																	57876616		2202	4299	6501	57310011	SO:0001819	synonymous_variant	1908			X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.204G>A	20.37:g.57876616G>A			57310011	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Silent	SNP	ENST00000337938.2	37	CCDS13477.1																																																																																				0.697	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		A	57876616	G	A	57876616	2	1	61	1	0	0	0	0	0	0	0	1	4929	1045	37	1		1	EDN3	20	57876616	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	46943	57876616	5148904	11678	19663										
PHACTR3	116154	broad.mit.edu	37	chr20	58381133	58381133	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcaagaaggagctcctggcCgtgaagctaaggaaccggcc	14	11	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58381133C>T	ENST00000371015.1	+	8	1679	c.1212C>T	c.(1210-1212)gcC>gcT	p.A404A	PHACTR3_ENST00000355648.4_Silent_p.A363A|PHACTR3_ENST00000361300.4_Silent_p.A293A|PHACTR3_ENST00000541461.1_Silent_p.A363A|PHACTR3_ENST00000395636.2_Silent_p.A363A|PHACTR3_ENST00000359926.3_Silent_p.A401A|PHACTR3_ENST00000395639.4_Silent_p.A293A	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	404						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.A404A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AGCTCCTGGCCGTGAAGCTAA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	20											167	179	175					20																	58381133		2203	4300	6503	57814528	SO:0001819	synonymous_variant	116154			AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1212C>T	20.37:g.58381133C>T			57814528	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Silent	SNP	ENST00000371015.1	37	CCDS13480.1																																																																																				0.537	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58381133	C	T	58381133	2	4	61	1	0	0	0	0	0	0	0	1	11842	639	23	1		1	PHACTR3	20	58381133	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	504517	58381133	4644387	11679	19664										
PHACTR3	116154	broad.mit.edu	37	chr20	58416501	58416501	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagacagaaaaattctgataCgattcagtgattacgtggaa	10	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58416501C>T	ENST00000371015.1	+	11	1965	c.1498C>T	c.(1498-1500)Cga>Tga	p.R500*	PHACTR3_ENST00000355648.4_Nonsense_Mutation_p.R459*|PHACTR3_ENST00000361300.4_Nonsense_Mutation_p.R389*|PHACTR3_ENST00000541461.1_Nonsense_Mutation_p.R459*|PHACTR3_ENST00000395636.2_Nonsense_Mutation_p.R459*|PHACTR3_ENST00000359926.3_Nonsense_Mutation_p.R497*|PHACTR3_ENST00000395639.4_Nonsense_Mutation_p.R389*	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	500	Required for PP1CA binding and inhibition of PP1 activity.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.R500*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AATTCTGATACGATTCAGTGA	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											92	86	88					20																	58416501		2203	4300	6503	57849896	SO:0001587	stop_gained	116154			AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1498C>T	20.37:g.58416501C>T	ENSP00000360054:p.Arg500*		57849896	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Nonsense_Mutation	SNP	ENST00000371015.1	37	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	C	40	8.353681	0.98774	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3716	18.0796	0.89438	0.0:1.0:0.0:0.0	.	.	.	.	X	497;500;389;459;459;459;389	.	ENSP00000347866:R459X	R	+	1	2	PHACTR3	57849896	1.000000	0.71417	0.987000	0.45799	0.999000	0.98932	7.713000	0.84693	2.584000	0.87258	0.655000	0.94253	CGA		0.408	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58416501	C	T	58416501	4	4	61	1	0	0	0	0	0	1	0	0	11842	528	19	1	1540	1	PHACTR3	20	58416501	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35368	58416501	4609019	11680	19665										
PHACTR3	116154	broad.mit.edu	37	chr20	58420259	58420259	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaggcagcaattcgtaaaGaattaaatgagtacaaaagt	8	5	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58420259G>T	ENST00000371015.1	+	12	2070	c.1603G>T	c.(1603-1605)Gaa>Taa	p.E535*	PHACTR3_ENST00000355648.4_Nonsense_Mutation_p.E494*|PHACTR3_ENST00000361300.4_Nonsense_Mutation_p.E424*|PHACTR3_ENST00000541461.1_Nonsense_Mutation_p.E494*|PHACTR3_ENST00000395636.2_Nonsense_Mutation_p.E494*|PHACTR3_ENST00000359926.3_Nonsense_Mutation_p.E532*|PHACTR3_ENST00000395639.4_Nonsense_Mutation_p.E424*	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	535						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.E535*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AATTCGTAAAGAATTAAATGA	0.299																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											66	69	68					20																	58420259		2203	4299	6502	57853654	SO:0001587	stop_gained	116154			AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1603G>T	20.37:g.58420259G>T	ENSP00000360054:p.Glu535*		57853654	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Nonsense_Mutation	SNP	ENST00000371015.1	37	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	G	39	7.693958	0.98438	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	.	.	.	5.07	4.12	0.48240	.	0.155907	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.0201	12.963	0.58468	0.0787:0.0:0.9213:0.0	.	.	.	.	X	532;535;424;494;494;494;424	.	ENSP00000347866:E494X	E	+	1	0	PHACTR3	57853654	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	9.727000	0.98787	1.276000	0.44395	0.306000	0.20318	GAA		0.299	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58420259	G	T	58420259	4	4	61	1	0	0	0	0	0	1	0	0	11842	943	33	2	1649	2	PHACTR3	20	58420259	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3758	58420259	4605261	11681	19666										
SYCP2	10388	broad.mit.edu	37	chr20	58442857	58442857	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttgccaggtctcccaaGgaatagaaaagtcatttgtt	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58442857G>T	ENST00000357552.3	-	39	4259	c.4034C>A	c.(4033-4035)cCt>cAt	p.P1345H	SYCP2_ENST00000371001.2_Missense_Mutation_p.P1345H			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1345					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.P1345H(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GGTCTCCCAAGGAATAGAAAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	20											55	57	56					20																	58442857		2202	4294	6496	57876252	SO:0001583	missense	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4034C>A	20.37:g.58442857G>T	ENSP00000350162:p.Pro1345His		57876252	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	5.233	0.228494	0.09916	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000412613	T;T	0.16743	2.32;2.32	5.25	3.07	0.35406	.	0.402704	0.21198	N	0.078501	T	0.11879	0.0289	L	0.38531	1.155	0.09310	N	1	B	0.16802	0.019	B	0.18561	0.022	T	0.30621	-0.9972	10	0.24483	T	0.36	-1.1574	6.4249	0.21764	0.0846:0.0:0.5101:0.4053	.	1345	Q9BX26	SYCP2_HUMAN	H	1345;1345;31	ENSP00000360040:P1345H;ENSP00000350162:P1345H	ENSP00000350162:P1345H	P	-	2	0	SYCP2	57876252	0.930000	0.31532	0.022000	0.16811	0.381000	0.30169	0.480000	0.22244	0.397000	0.25310	-0.293000	0.09583	CCT		0.328	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		T	58442857	G	T	58442857	3	4	61	1	0	0	0	0	1	0	0	0	15471	1000	35	2	586	2	SYCP2	20	58442857	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22598	58442857	4582663	11682	19667										
SYCP2	10388	broad.mit.edu	37	chr20	58476736	58476736	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctatgtttagttgcaccaAaaattttttgagttacatta	5	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58476736A>C	ENST00000357552.3	-	16	1388	c.1163T>G	c.(1162-1164)tTt>tGt	p.F388C	SYCP2_ENST00000371001.2_Missense_Mutation_p.F388C			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	388					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.F388C(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			AGTTGCACCAAAAATTTTTTG	0.269																																																1	Substitution - Missense(1)	large_intestine(1)	20											55	55	55					20																	58476736		2198	4286	6484	57910131	SO:0001583	missense	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1163T>G	20.37:g.58476736A>C	ENSP00000350162:p.Phe388Cys		57910131	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112856	0.56398	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.24151	2.12;2.12;1.87	5.59	4.46	0.54185	.	0.090637	0.48767	D	0.000166	T	0.41789	0.1174	L	0.59436	1.845	0.30890	N	0.730422	D;D	0.89917	1.0;1.0	D;D	0.70935	0.964;0.971	T	0.46830	-0.9163	10	0.87932	D	0	-8.5737	7.6619	0.28409	0.7181:0.0:0.0:0.2819	.	388;388	A2A341;Q9BX26	.;SYCP2_HUMAN	C	388	ENSP00000360040:F388C;ENSP00000350162:F388C;ENSP00000402456:F388C	ENSP00000350162:F388C	F	-	2	0	SYCP2	57910131	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	3.828000	0.55753	2.111000	0.64477	0.528000	0.53228	TTT		0.269	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		C	58476736	A	C	58476736	3	2	61	1	0	0	0	0	1	0	0	0	15471	14	1	4	3549	4	SYCP2	20	58476736	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	33879	58476736	4548784	11683	19668										
C20orf177	63939	broad.mit.edu	37	chr20	58519764	58519764	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagcttttcaccatgaaGaaatccacccatcacattat	4	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58519764G>T	ENST00000358293.3	+	5	1181	c.766G>T	c.(766-768)Gaa>Taa	p.E256*	FAM217B_ENST00000469084.1_3'UTR|FAM217B_ENST00000360816.3_Nonsense_Mutation_p.E256*	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	256								p.E256*(1)									TCACCATGAAGAAATCCACCC	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											92	96	95					20																	58519764		2203	4300	6503	57953159	SO:0001587	stop_gained	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.766G>T	20.37:g.58519764G>T	ENSP00000351040:p.Glu256*		57953159	B3KWH1|Q9NTA3	Nonsense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.484582	0.84854	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	.	.	.	5.8	3.83	0.44106	.	0.251761	0.27861	N	0.017560	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-16.477	11.5436	0.50679	0.0644:0.3514:0.5842:0.0	.	.	.	.	X	256	.	ENSP00000351040:E256X	E	+	1	0	C20orf177	57953159	0.944000	0.32072	0.015000	0.15790	0.011000	0.07611	2.490000	0.45294	0.765000	0.33221	-0.165000	0.13383	GAA		0.473	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		T	58519764	G	T	58519764	4	4	61	1	0	0	0	0	0	1	0	0	2102	943	33	2	768	2	C20orf177	20	58519764	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43028	58519764	4505756	11684	19669										
C20orf177	63939	broad.mit.edu	37	chr20	58519883	58519883	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggacagaagaaaagaaaaaGaaatcaagtaagagtacgaa	10	3	1	5	rs141403856	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58519883G>T	ENST00000358293.3	+	5	1300	c.885G>T	c.(883-885)aaG>aaT	p.K295N	FAM217B_ENST00000469084.1_3'UTR|FAM217B_ENST00000360816.3_Missense_Mutation_p.K295N	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	295	Poly-Lys.							p.K295N(1)									AAAAGAAAAAGAAATCAAGTA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	20											45	47	47					20																	58519883		2203	4300	6503	57953278	SO:0001583	missense	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.885G>T	20.37:g.58519883G>T	ENSP00000351040:p.Lys295Asn		57953278	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612923	0.46631	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.25749	1.78;1.78	5.3	3.27	0.37495	.	0.291697	0.28365	N	0.015607	T	0.33265	0.0857	L	0.36672	1.1	0.26017	N	0.981911	D	0.57257	0.979	P	0.59487	0.858	T	0.07558	-1.0766	10	0.48119	T	0.1	-11.9661	10.332	0.43829	0.2314:0.0:0.7686:0.0	.	295	Q9NTX9	CT177_HUMAN	N	295	ENSP00000351040:K295N;ENSP00000354056:K295N	ENSP00000351040:K295N	K	+	3	2	C20orf177	57953278	0.952000	0.32445	0.058000	0.19502	0.460000	0.32559	1.397000	0.34543	0.540000	0.28808	-0.345000	0.07892	AAG		0.483	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		T	58519883	G	T	58519883	3	4	61	1	0	0	0	0	1	0	0	0	2102	933	33	2	887	2	C20orf177	20	58519883	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119	58519883	4505637	11685	19670										
C20orf177	63939	broad.mit.edu	37	chr20	58520099	58520099	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgccactgtatcgagtgaGaaaaaactgaaaacaaacgg	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:58520099G>T	ENST00000358293.3	+	5	1516	c.1101G>T	c.(1099-1101)gaG>gaT	p.E367D	FAM217B_ENST00000360816.3_Missense_Mutation_p.E367D	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	367								p.E367D(1)									TATCGAGTGAGAAAAAACTGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	20											47	48	48					20																	58520099		2203	4300	6503	57953494	SO:0001583	missense	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.1101G>T	20.37:g.58520099G>T	ENSP00000351040:p.Glu367Asp		57953494	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973136	0.53614	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.33654	1.4;1.4	5.35	5.35	0.76521	.	0.130623	0.34580	N	0.003851	T	0.24928	0.0605	L	0.34521	1.04	0.28750	N	0.901508	P	0.35507	0.506	B	0.31812	0.136	T	0.16808	-1.0390	10	0.33940	T	0.23	-41.9123	9.6756	0.40039	0.0:0.1934:0.6735:0.1331	.	367	Q9NTX9	CT177_HUMAN	D	367	ENSP00000351040:E367D;ENSP00000354056:E367D	ENSP00000351040:E367D	E	+	3	2	C20orf177	57953494	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.517000	0.35867	2.497000	0.84241	0.591000	0.81541	GAG		0.403	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		T	58520099	G	T	58520099	3	4	61	1	0	0	0	0	1	0	0	0	2102	933	33	2	1103	2	C20orf177	20	58520099	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	216	58520099	4505421	11686	19671										
CDH4	1002	broad.mit.edu	37	chr20	60503345	60503345	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaaggaggcgcagatctgCgagaagcccaacctgaacgc	12	14	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:60503345C>T	ENST00000360469.5	+	12	1957	c.1869C>T	c.(1867-1869)tgC>tgT	p.C623C	CDH4_ENST00000543233.1_Silent_p.C549C	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	623	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C623C(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CGCAGATCTGCGAGAAGCCCA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	20											116	119	118					20																	60503345		2203	4300	6503	59936740	SO:0001819	synonymous_variant	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1869C>T	20.37:g.60503345C>T			59936740	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																				0.642	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60503345	C	T	60503345	2	4	61	1	0	0	0	0	0	0	0	1	3118	776	27	1		1	CDH4	20	60503345	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1983246	60503345	2522175	11687	19672										
CDH4	1002	broad.mit.edu	37	chr20	60504733	60504733	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgtatgacgtccccatcaTcgtcacagactctggaaacc	8	13	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:60504733T>G	ENST00000360469.5	+	13	2160	c.2072T>G	c.(2071-2073)aTc>aGc	p.I691S	CDH4_ENST00000543233.1_Missense_Mutation_p.I617S	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	691	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I691S(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GTCCCCATCATCGTCACAGAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	20											175	127	144					20																	60504733		2203	4300	6503	59938128	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2072T>G	20.37:g.60504733T>G	ENSP00000353656:p.Ile691Ser		59938128	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	T	4.737	0.137012	0.09032	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.60797	0.16;0.16	4.08	1.76	0.24704	Cadherin (3);Cadherin-like (1);	0.327701	0.30185	N	0.010217	T	0.41236	0.1150	L	0.52364	1.645	0.42982	D	0.994469	B	0.31318	0.319	B	0.24541	0.054	T	0.12192	-1.0557	9	.	.	.	.	3.8372	0.08899	0.1554:0.1748:0.0:0.6698	.	691	P55283	CADH4_HUMAN	S	691;599;617	ENSP00000353656:I691S;ENSP00000443301:I617S	.	I	+	2	0	CDH4	59938128	0.000000	0.05858	0.715000	0.30552	0.864000	0.49448	-0.019000	0.12546	0.044000	0.15775	0.459000	0.35465	ATC		0.542	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		G	60504733	T	G	60504733	3	3	61	1	0	0	0	0	1	0	0	0	3118	1435	50	4	2122	4	CDH4	20	60504733	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1388	60504733	2520787	11688	19673										
CDH4	1002	broad.mit.edu	37	chr20	60504841	60504841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccattggcgcagtggcagCggctggtctgggcaccggtg	17	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:60504841C>T	ENST00000360469.5	+	13	2268	c.2180C>T	c.(2179-2181)gCg>gTg	p.A727V	CDH4_ENST00000543233.1_Missense_Mutation_p.A653V	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	727					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A727V(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GCAGTGGCAGCGGCTGGTCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	20											122	93	103					20																	60504841		2203	4300	6503	59938236	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2180C>T	20.37:g.60504841C>T	ENSP00000353656:p.Ala727Val		59938236	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	8.403	0.842411	0.16963	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.57907	0.37;0.39	4.14	4.14	0.48551	.	0.184484	0.47093	D	0.000247	T	0.34454	0.0898	L	0.34521	1.04	0.50813	D	0.999899	P	0.39116	0.66	B	0.26202	0.067	T	0.20174	-1.0283	9	.	.	.	.	12.3418	0.55099	0.0:0.8295:0.1705:0.0	.	727	P55283	CADH4_HUMAN	V	727;635;653	ENSP00000353656:A727V;ENSP00000443301:A653V	.	A	+	2	0	CDH4	59938236	1.000000	0.71417	0.110000	0.21437	0.182000	0.23217	4.633000	0.61318	1.855000	0.53841	0.561000	0.74099	GCG		0.607	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60504841	C	T	60504841	3	4	61	1	0	0	0	0	1	0	0	0	3118	768	27	1	2230	1	CDH4	20	60504841	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	108	60504841	2520679	11689	19674										
PSMA7	5688	broad.mit.edu	37	chr20	60713265	60713265	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccagcttaatggtcagatCatctgtttcaatggcttcgt	8	10	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:60713265C>A	ENST00000370873.4	-	5	679	c.553G>T	c.(553-555)Gat>Tat	p.D185Y	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370861.1_Missense_Mutation_p.D115Y	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	185					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)	p.D185Y(2)		large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			ATGGTCAGATCATCTGTTTCA	0.483																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	20											214	138	164					20																	60713265		2203	4300	6503	60146660	SO:0001583	missense	5688			AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.553G>T	20.37:g.60713265C>A	ENSP00000359910:p.Asp185Tyr		60146660	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	37	CCDS13489.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.84|16.84	3.232981|3.232981	0.58777|0.58777	.|.	.|.	ENSG00000101182|ENSG00000101182	ENST00000370873;ENST00000370861|ENST00000442551	T;T|.	0.26067|.	1.76;1.76|.	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	0.088174|.	0.85682|.	D|.	0.000000|.	D|D	0.84942|0.84942	0.5584|0.5584	M|M	0.90019|0.90019	3.08|3.08	0.80722|0.80722	D|D	1|1	P|.	0.42248|.	0.774|.	P|.	0.48873|.	0.593|.	D|D	0.87826|0.87826	0.2641|0.2641	10|5	0.62326|.	D|.	0.03|.	.|.	18.563|18.563	0.91107|0.91107	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	185|.	O14818|.	PSA7_HUMAN|.	Y|I	185;115|110	ENSP00000359910:D185Y;ENSP00000359898:D115Y|.	ENSP00000359898:D115Y|.	D|M	-|-	1|3	0|0	PSMA7|PSMA7	60146660|60146660	1.000000|1.000000	0.71417|0.71417	0.053000|0.053000	0.19242|0.19242	0.693000|0.693000	0.40251|0.40251	4.646000|4.646000	0.61411|0.61411	2.401000|2.401000	0.81631|0.81631	0.563000|0.563000	0.77884|0.77884	GAT|ATG		0.483	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		A	60713265	C	A	60713265	3	1	61	1	0	0	0	0	1	0	0	0	12706	826	29	2	205	2	PSMA7	20	60713265	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	208424	60713265	2312255	11690	19675										
OSBPL2	9885	broad.mit.edu	37	chr20	60864312	60864312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcaacgagctggagacagGcatggagaagaccctgccac	12	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:60864312G>A	ENST00000313733.3	+	12	1377	c.1175G>A	c.(1174-1176)gGc>gAc	p.G392D	OSBPL2_ENST00000358053.2_Missense_Mutation_p.G380D|OSBPL2_ENST00000439951.2_Intron	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2	392					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.G392D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			CTGGAGACAGGCATGGAGAAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											84	64	71					20																	60864312		2203	4300	6503	60297707	SO:0001583	missense	9885			AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"Oxysterol binding proteins"	15761	protein-coding gene	gene with protein product		606731	"oxysterol-binding protein-like 2"			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.1175G>A	20.37:g.60864312G>A	ENSP00000316649:p.Gly392Asp		60297707	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Missense_Mutation	SNP	ENST00000313733.3	37	CCDS13495.1	.	.	.	.	.	.	.	.	.	.	G	7.512	0.654919	0.14580	.	.	ENSG00000130703	ENST00000358053;ENST00000313733	T;T	0.28454	1.61;1.61	4.22	3.27	0.37495	.	0.052181	0.85682	D	0.000000	T	0.17746	0.0426	N	0.21583	0.68	0.80722	D	1	B;B	0.13594	0.007;0.008	B;B	0.23150	0.036;0.044	T	0.05716	-1.0868	10	0.12103	T	0.63	-8.2166	8.5256	0.33302	0.1817:0.0:0.8183:0.0	.	380;392	Q9H1P3-2;Q9H1P3	.;OSBL2_HUMAN	D	380;392	ENSP00000350755:G380D;ENSP00000316649:G392D	ENSP00000316649:G392D	G	+	2	0	OSBPL2	60297707	1.000000	0.71417	0.874000	0.34290	0.987000	0.75469	3.435000	0.52849	0.900000	0.36469	0.561000	0.74099	GGC		0.587	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835		A	60864312	G	A	60864312	3	1	61	1	0	0	0	0	1	0	0	0	11309	1203	42	3	1217	3	OSBPL2	20	60864312	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151047	60864312	2161208	11691	19676										
TCFL5	10732	broad.mit.edu	37	chr20	61473391	61473391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggacaggtcaccaaggagTccggtctggtcagctttagc	13	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:61473391T>C	ENST00000335351.3	-	6	1531	c.1439A>G	c.(1438-1440)gAc>gGc	p.D480G		NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	480					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D480G(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					CACCAAGGAGTCCGGTCTGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	20											109	92	97					20																	61473391		2203	4300	6503	60943836	SO:0001583	missense	10732			AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"Basic helix-loop-helix proteins"	11646	protein-coding gene	gene with protein product	"HPV-16 E2 binding protein 1"	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.1439A>G	20.37:g.61473391T>C	ENSP00000334294:p.Asp480Gly		60943836	O94771|Q9BYW0	Missense_Mutation	SNP	ENST00000335351.3	37	CCDS13506.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311815	0.81358	.	.	ENSG00000101190	ENST00000335351	T	0.39406	1.08	5.93	5.93	0.95920	.	0.103063	0.42053	D	0.000774	T	0.33323	0.0859	N	0.24115	0.695	0.80722	D	1	P	0.45348	0.856	B	0.42625	0.393	T	0.07868	-1.0750	10	0.34782	T	0.22	-20.2662	14.9446	0.71020	0.0:0.0:0.0:1.0	.	480	Q9UL49	TCFL5_HUMAN	G	480	ENSP00000334294:D480G	ENSP00000334294:D480G	D	-	2	0	TCFL5	60943836	1.000000	0.71417	0.985000	0.45067	0.925000	0.55904	4.942000	0.63547	2.273000	0.75805	0.482000	0.46254	GAC		0.517	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602		C	61473391	T	C	61473391	3	2	61	1	0	0	0	0	1	0	0	0	15738	1667	58	4	67	4	TCFL5	20	61473391	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	609079	61473391	1552129	11692	19677										
DIDO1	11083	broad.mit.edu	37	chr20	61524262	61524262	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaaatggtgctgagtcGagacaaaaagagggtcgtgt	13	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:61524262G>A	ENST00000266070.4	-	13	3479	c.3154C>T	c.(3154-3156)Cga>Tga	p.R1052*	DIDO1_ENST00000395340.1_Nonsense_Mutation_p.R1052*|DIDO1_ENST00000395335.2_Nonsense_Mutation_p.R1052*|DIDO1_ENST00000395343.1_Nonsense_Mutation_p.R1052*	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1052					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R1052*(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GTGCTGAGTCGAGACAAAAAG	0.423																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											1	Substitution - Nonsense(1)	large_intestine(1)	20											117	105	109					20																	61524262		2203	4300	6503	60994707	SO:0001587	stop_gained	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3154C>T	20.37:g.61524262G>A	ENSP00000266070:p.Arg1052*		60994707	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Nonsense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	45	11.559260	0.99576	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	.	.	.	5.88	4.94	0.65067	.	0.000000	0.36519	U	0.002550	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.5963	15.002	0.71479	0.0681:0.0:0.9319:0.0	.	.	.	.	X	1052	.	ENSP00000266070:R1052X	R	-	1	2	DIDO1	60994707	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	3.587000	0.53957	1.504000	0.48704	-0.229000	0.12294	CGA		0.423	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61524262	G	A	61524262	4	1	61	1	0	0	0	0	0	1	0	0	4533	1066	37	1	3613	1	DIDO1	20	61524262	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	50871	61524262	1501258	11693	19678										
SLC17A9	63910	broad.mit.edu	37	chr20	61596508	61596508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagccatcacggtgcggaAgctcatgcaggtaggagaat	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:61596508A>C	ENST00000370351.4	+	9	1066	c.935A>C	c.(934-936)aAg>aCg	p.K312T	SLC17A9_ENST00000370349.3_Missense_Mutation_p.K306T|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	312					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.K312T(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						ACGGTGCGGAAGCTCATGCAG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	20											89	94	92					20																	61596508		1958	4143	6101	61066953	SO:0001583	missense	63910			AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.935A>C	20.37:g.61596508A>C	ENSP00000359376:p.Lys312Thr		61066953	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.317806	0.81469	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.57107	0.42;0.42	5.14	5.14	0.70334	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78188	0.4244	M	0.92459	3.31	0.80722	D	1	D;D;D	0.69078	0.997;0.99;0.987	D;D;D	0.77004	0.982;0.989;0.968	D	0.84062	0.0375	10	0.87932	D	0	.	14.1381	0.65300	1.0:0.0:0.0:0.0	.	332;312;306	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	T	312;306	ENSP00000359376:K312T;ENSP00000359374:K306T	ENSP00000359374:K306T	K	+	2	0	SLC17A9	61066953	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.666000	0.74446	1.927000	0.55829	0.459000	0.35465	AAG		0.582	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		C	61596508	A	C	61596508	3	2	61	1	0	0	0	0	1	0	0	0	14461	72	3	4	969	4	SLC17A9	20	61596508	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	72246	61596508	1429012	11694	19679										
YTHDF1	54915	broad.mit.edu	37	chr20	61834779	61834779	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggggccttgctgagggtgtcGctgtgaaagcctggctgccc	17	11	0	2	rs147844381	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:61834779G>A	ENST00000370339.3	-	4	854	c.513C>T	c.(511-513)agC>agT	p.S171S	YTHDF1_ENST00000370333.4_Silent_p.S121S|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	171							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)	p.S171S(1)|p.A70V(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						TGAGGGTGTCGCTGTGAAAGC	0.647													G|||	3	0.000599042	0	0.0029	5008	,	,		16897	0		0.001	False		,,,				2504	0															2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	20						G		3,4401		0,3,2199	40	37	38		513	-7.9	0.1	20	dbSNP_134	38	10,8590		0,10,4290	no	coding-synonymous	YTHDF1	NM_017798.3		0,13,6489	AA,AG,GG		0.1163,0.0681,0.1		171/560	61834779	13,12991	2202	4300	6502	61305224	SO:0001819	synonymous_variant	54915			AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.513C>T	20.37:g.61834779G>A			61305224	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1	4	0.0018315018315018315	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	G	7.724	0.697853	0.15106	6.81E-4	0.001163	ENSG00000149658	ENST00000342761	.	.	.	5.15	-7.94	0.01152	.	.	.	.	.	T	0.51244	0.1663	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63659	-0.6587	5	0.25106	T	0.35	-8.8652	15.2669	0.73669	0.4313:0.0:0.5687:0.0	.	.	.	.	V	70	.	ENSP00000339489:A70V	A	-	2	0	YTHDF1	61305224	0.974000	0.33945	0.125000	0.21846	0.919000	0.55068	0.341000	0.19909	-1.754000	0.01321	-0.658000	0.03865	GCG		0.647	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		A	61834779	G	A	61834779	2	1	61	1	0	0	0	0	0	0	0	1	17538	1078	38	1		1	YTHDF1	20	61834779	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	238271	61834779	1190741	11695	19680										
YTHDF1	54915	broad.mit.edu	37	chr20	61834908	61834908	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtcccccatgctgagaaCgcagggttttcagggaaaaa	11	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:61834908C>T	ENST00000370339.3	-	4	725	c.384G>A	c.(382-384)gcG>gcA	p.A128A	YTHDF1_ENST00000370333.4_Silent_p.A78A|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	128							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)	p.A128A(1)|p.R27H(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						ATGCTGAGAACGCAGGGTTTT	0.567																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	20											57	53	54					20																	61834908		2203	4300	6503	61305353	SO:0001819	synonymous_variant	54915			AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.384G>A	20.37:g.61834908C>T			61305353	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	C	8.104	0.777287	0.16120	.	.	ENSG00000149658	ENST00000342761	.	.	.	5.15	-7.07	0.01563	.	.	.	.	.	T	0.49677	0.1571	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60717	-0.7208	5	0.87932	D	0	-15.007	1.515	0.02504	0.1898:0.1569:0.3619:0.2914	.	.	.	.	H	27	.	ENSP00000339489:R27H	R	-	2	0	YTHDF1	61305353	0.416000	0.25424	0.943000	0.38184	0.912000	0.54170	-0.223000	0.09177	-0.789000	0.04498	-1.310000	0.01310	CGT		0.567	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		T	61834908	C	T	61834908	2	4	61	1	0	0	0	0	0	0	0	1	17538	523	19	1		1	YTHDF1	20	61834908	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	129	61834908	1190612	11696	19681										
ZGPAT	84619	broad.mit.edu	37	chr20	62340508	62340508	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaagtgccgctttaaggaGaactgcaggtaaagcccttt	12	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62340508G>A	ENST00000328969.5	+	2	703	c.576G>A	c.(574-576)gaG>gaA	p.E192E	RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.R98K|ARFRP1_ENST00000609142.1_5'Flank|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000357119.4_Silent_p.E192E|ZGPAT_ENST00000355969.6_Silent_p.E192E|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.E192E|ARFRP1_ENST00000607873.1_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.E192E|ZGPAT_ENST00000478385.1_3'UTR|ARFRP1_ENST00000324228.2_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	192					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E192E(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GCTTTAAGGAGAACTGCAGGT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	20											69	70	70					20																	62340508		2203	4300	6503	61810952	SO:0001819	synonymous_variant	84619			AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.576G>A	20.37:g.62340508G>A			61810952	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	37	CCDS13534.1																																																																																				0.582	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62340508	G	A	62340508	2	1	61	1	0	0	0	0	0	0	0	1	17713	933	33	3		3	ZGPAT	20	62340508	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	505600	62340508	685012	11697	19682										
ZBTB46	140685	broad.mit.edu	37	chr20	62422078	62422078	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaggtgccggtagtgggaCgtgatttccatatcttcctt	12	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62422078C>T	ENST00000245663.4	-	2	183	c.33G>A	c.(31-33)acG>acA	p.T11T	ZBTB46_ENST00000480766.1_5'Flank|ZBTB46_ENST00000302995.2_Silent_p.T11T|ZBTB46_ENST00000395104.1_Silent_p.T11T	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	11			T -> A (in dbSNP:rs2281929). {ECO:0000269|PubMed:15489334}.		negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.T11T(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GGTAGTGGGACGTGATTTCCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	20											44	31	35					20																	62422078		2203	4299	6502	61892522	SO:0001819	synonymous_variant	140685			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.33G>A	20.37:g.62422078C>T			61892522	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																				0.572	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62422078	C	T	62422078	2	4	61	1	0	0	0	0	0	0	0	1	17586	523	19	1		1	ZBTB46	20	62422078	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81570	62422078	603442	11698	19683										
ZBTB46	140685	broad.mit.edu	37	chr20	62422100	62422100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgatttccatatcttcctttCggttgttcatttggaagccc	7	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62422100C>T	ENST00000245663.4	-	2	161	c.11G>A	c.(10-12)cGa>cAa	p.R4Q	ZBTB46_ENST00000480766.1_5'Flank|ZBTB46_ENST00000302995.2_Missense_Mutation_p.R4Q|ZBTB46_ENST00000395104.1_Missense_Mutation_p.R4Q	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	4					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.R4Q(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					ATCTTCCTTTCGGTTGTTCAT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	20											33	22	25					20																	62422100		2202	4294	6496	61892544	SO:0001583	missense	140685			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.11G>A	20.37:g.62422100C>T	ENSP00000245663:p.Arg4Gln		61892544	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250940	0.59212	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.13901	2.55;2.55;2.55	5.16	4.19	0.49359	BTB/POZ fold (1);	0.075973	0.52532	D	0.000076	T	0.10337	0.0253	L	0.39898	1.24	0.46458	D	0.999053	B	0.30193	0.272	B	0.15484	0.013	T	0.14783	-1.0460	10	0.21540	T	0.41	.	11.8377	0.52336	0.0:0.9112:0.0:0.0888	.	4	Q86UZ6	ZBT46_HUMAN	Q	4	ENSP00000245663:R4Q;ENSP00000303102:R4Q;ENSP00000378536:R4Q	ENSP00000245663:R4Q	R	-	2	0	ZBTB46	61892544	1.000000	0.71417	0.903000	0.35520	0.774000	0.43823	4.888000	0.63164	1.121000	0.41925	0.491000	0.48974	CGA		0.572	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62422100	C	T	62422100	3	4	61	1	0	0	0	0	1	0	0	0	17586	884	31	1	1774	1	ZBTB46	20	62422100	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22	62422100	603420	11699	19684										
PRPF6	57473	broad.mit.edu	37	chr20	62631085	62631085	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caagtagctcggaaccttatCatgaaggggacggagatgtg	14	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62631085C>A	ENST00000450537.1	-	2	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.I332I			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I332I(1)		NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GGAACCTTATCATGAAGGGGA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	20											67	57	60					20																	62631085		2203	4300	6503	62101529	SO:0001627	intron_variant	24148			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-31777G>T	20.37:g.62631085C>A			62101529	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																				0.562	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		A	62631085	C	A	62631085	1	1	61	0	1	0	0	0	0	0	0	0	12608	816	29	2		2	PRPF6	20	62631085	Intron	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	208985	62631085	394435	11700	19685										
TCEA2	6919	broad.mit.edu	37	chr20	62703269	62703269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgaccacctttgttgtctGcaacgagtgtggaaaccgct	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62703269G>A	ENST00000343484.5	+	9	1035	c.866G>A	c.(865-867)tGc>tAc	p.C289Y	TCEA2_ENST00000361317.2_Missense_Mutation_p.C262Y|TCEA2_ENST00000465111.1_3'UTR|TCEA2_ENST00000395053.3_3'UTR|RGS19_ENST00000493165.1_5'Flank	NM_003195.4	NP_003186.1	Q15560	TCEA2_HUMAN	transcription elongation factor A (SII), 2	289					DNA-templated transcription, elongation (GO:0006354)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)	centrosome (GO:0005813)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.C289Y(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)	12	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					TTTGTTGTCTGCAACGAGTGT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	20											84	71	76					20																	62703269		2203	4300	6503	62173713	SO:0001583	missense	6919			U86749	CCDS13553.1, CCDS13554.1	20q13.33	2011-01-25			ENSG00000171703	ENSG00000171703			11614	protein-coding gene	gene with protein product		604784				9441762, 8566795	Standard	NM_003195		Approved	TFIIS	uc021wgq.1	Q15560	OTTHUMG00000033026	ENST00000343484.5:c.866G>A	20.37:g.62703269G>A	ENSP00000343515:p.Cys289Tyr		62173713	B3KNM1|Q8TD37|Q8TD38	Missense_Mutation	SNP	ENST00000343484.5	37	CCDS13553.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233006	0.79688	.	.	ENSG00000171703	ENST00000361317;ENST00000343484;ENST00000458442	.	.	.	3.99	3.99	0.46301	Zinc finger, TFIIS-type (4);	0.000000	0.85682	D	0.000000	D	0.90827	0.7119	H	0.99299	4.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95088	0.8219	9	0.87932	D	0	-0.1823	16.4271	0.83817	0.0:0.0:1.0:0.0	.	289;289;262	Q15560;Q6IB64;B3KNM1	TCEA2_HUMAN;.;.	Y	262;289;262	.	ENSP00000343515:C289Y	C	+	2	0	TCEA2	62173713	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.550000	0.98110	1.953000	0.56701	0.313000	0.20887	TGC		0.622	TCEA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080277.2	NM_198723		A	62703269	G	A	62703269	3	1	61	1	0	0	0	0	1	0	0	0	15707	1319	46	3	900	3	TCEA2	20	62703269	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	72184	62703269	322251	11701	19686										
MYT1	4661	broad.mit.edu	37	chr20	62839449	62839449	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggaggaggaagaggaagaGgaagaggaggaggaggaggc	24	1	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62839449G>T	ENST00000328439.1	+	7	1264	c.900G>T	c.(898-900)gaG>gaT	p.E300D	MYT1_ENST00000360149.4_Intron|MYT1_ENST00000536311.1_Missense_Mutation_p.E300D	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E300D(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					aagaggaagaggaagaggagg	0.572																																					GBM(59;481 1041 20555 21139 33705)											1	Substitution - Missense(1)	large_intestine(1)	20											57	57	57					20																	62839449		2203	4300	6503	62309893	SO:0001583	missense	4661			M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.900G>T	20.37:g.62839449G>T	ENSP00000327465:p.Glu300Asp		62309893	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	g	0.588	-0.834161	0.02713	.	.	ENSG00000196132	ENST00000328439;ENST00000536311	T;T	0.73047	-0.71;-0.71	3.61	-4.9	0.03094	.	2.701810	0.01172	N	0.006892	T	0.57140	0.2033	L	0.38531	1.155	0.80722	D	1	B	0.14012	0.009	B	0.10450	0.005	T	0.28776	-1.0033	10	0.17369	T	0.5	-1.6302	7.9983	0.30282	0.6473:0.0:0.2362:0.1165	.	300	Q01538	MYT1_HUMAN	D	300	ENSP00000327465:E300D;ENSP00000442412:E300D	ENSP00000327465:E300D	E	+	3	2	MYT1	62309893	0.001000	0.12720	0.007000	0.13788	0.057000	0.15508	-2.123000	0.01319	-1.069000	0.03153	0.282000	0.19409	GAG		0.572	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62839449	G	T	62839449	3	4	61	1	0	0	0	0	1	0	0	0	10136	991	35	2	918	2	MYT1	20	62839449	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136180	62839449	186071	11702	19687										
MYT1	4661	broad.mit.edu	37	chr20	62848610	62848610	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaaagattcagaccagcGaaacctcacctaaagccttt	5	15	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr20:62848610G>A	ENST00000328439.1	+	11	2186	c.1822G>A	c.(1822-1824)Gaa>Aaa	p.E608K	MYT1_ENST00000360149.4_Missense_Mutation_p.E310K|MYT1_ENST00000536311.1_Missense_Mutation_p.E608K	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E608K(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					TCAGACCAGCGAAACCTCACC	0.498																																					GBM(59;481 1041 20555 21139 33705)											1	Substitution - Missense(1)	large_intestine(1)	20											89	85	87					20																	62848610		2203	4300	6503	62319054	SO:0001583	missense	4661			M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1822G>A	20.37:g.62848610G>A	ENSP00000327465:p.Glu608Lys		62319054	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470894	0.84533	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.47869	0.83;0.83;0.83	5.55	5.55	0.83447	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	N	0.25890	0.77	0.80722	D	1	D;D;D	0.89917	1.0;0.995;1.0	D;P;D	0.83275	0.973;0.806;0.996	T	0.52682	-0.8543	10	0.28530	T	0.3	-19.0414	19.5144	0.95157	0.0:0.0:1.0:0.0	.	608;608;310	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	K	310;608;608	ENSP00000353269:E310K;ENSP00000327465:E608K;ENSP00000442412:E608K	ENSP00000327465:E608K	E	+	1	0	MYT1	62319054	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.725000	0.98778	2.618000	0.88619	0.655000	0.94253	GAA		0.498	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62848610	G	A	62848610	3	1	61	1	0	0	0	0	1	0	0	0	10136	1059	37	1	1856	1	MYT1	20	62848610	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9161	62848610	176910	11703	19688										
TPTE	7179	broad.mit.edu	37	chr21	10916378	10916378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaagcacttacgaggaatcGaataaataatgaagtgtttt	8	4	0	1	rs570468666		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:10916378G>A	ENST00000361285.4	-	20	1597	c.1268C>T	c.(1267-1269)tCg>tTg	p.S423L	TPTE_ENST00000298232.7_Missense_Mutation_p.S405L|TPTE_ENST00000415664.2_Intron|TPTE_ENST00000342420.5_Missense_Mutation_p.S385L	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	423	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S405L(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACGAGGAATCGAATAAATAAT	0.388													.|||	1	0.000199681	8e-04	0	5008	,	,		47548	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	21																																								9938249	SO:0001583	missense	7179			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1268C>T	21.37:g.10916378G>A	ENSP00000355208:p.Ser423Leu		9938249	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	13.90	2.374557	0.42105	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.86562	-2.14;-2.14;-2.14	1.79	1.79	0.24919	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.062472	0.64402	D	0.000003	D	0.90892	0.7138	M	0.81942	2.565	0.46028	D	0.998829	D;D;D	0.71674	0.998;0.998;0.978	D;D;P	0.65323	0.934;0.934;0.739	D	0.89728	0.3924	10	0.62326	D	0.03	-4.5869	7.1115	0.25392	0.0:0.0:1.0:0.0	.	385;405;423	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	L	405;423;385	ENSP00000298232:S405L;ENSP00000355208:S423L;ENSP00000344441:S385L	ENSP00000298232:S405L	S	-	2	0	TPTE	9938249	0.992000	0.36948	0.708000	0.30435	0.064000	0.16182	2.621000	0.46418	1.313000	0.45069	0.184000	0.17185	TCG		0.388	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			A	10916378	G	A	10916378	3	1	61	1	0	0	0	0	1	0	0	0	16470	1059	37	1	407	1	TPTE	21	10916378	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		10916378	37213517	11704	19689										
TPTE	7179	broad.mit.edu	37	chr21	10943004	10943004	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataataagtcgtagaagtcGaagtaaatgtgtccatctaa	8	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:10943004G>A	ENST00000361285.4	-	12	912	c.583C>T	c.(583-585)Cga>Tga	p.R195*	TPTE_ENST00000298232.7_Nonsense_Mutation_p.R177*|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Nonsense_Mutation_p.R157*	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	195			R -> Q (in dbSNP:rs1810856).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R177*(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CGTAGAAGTCGAAGTAAATGT	0.308																																																2	Substitution - Nonsense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	21											71	65	67					21																	10943004		2203	4299	6502	9964875	SO:0001587	stop_gained	7179			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.583C>T	21.37:g.10943004G>A	ENSP00000355208:p.Arg195*		9964875	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Nonsense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	22.4	4.278363	0.80692	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	.	.	.	2.07	2.07	0.26955	.	0.072998	0.56097	U	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7066	10.2257	0.43225	0.0:0.0:1.0:0.0	.	.	.	.	X	177;195;157	.	ENSP00000298232:R177X	R	-	1	2	TPTE	9964875	0.009000	0.17119	0.034000	0.17996	0.036000	0.12997	1.383000	0.34385	1.470000	0.48102	0.194000	0.17425	CGA		0.308	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			A	10943004	G	A	10943004	4	1	61	1	0	0	0	0	0	1	0	0	16470	1066	37	1	1124	1	TPTE	21	10943004	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	26626	10943004	37186891	11705	19690										
TPTE	7179	broad.mit.edu	37	chr21	10951393	10951393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taggtcggcaaggatgagagTgacatccagtaagaccagga	14	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:10951393T>C	ENST00000361285.4	-	10	648	c.319A>G	c.(319-321)Act>Gct	p.T107A	TPTE_ENST00000298232.7_Missense_Mutation_p.T89A|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.T69A	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	107					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.T89A(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGGATGAGAGTGACATCCAGT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	21											134	138	137					21																	10951393		2203	4300	6503	9973264	SO:0001583	missense	7179			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.319A>G	21.37:g.10951393T>C	ENSP00000355208:p.Thr107Ala		9973264	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	0.028	-1.351227	0.01256	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420;ENST00000328758	D;D;D	0.97279	-4.32;-4.32;-4.32	1.8	-1.16	0.09678	.	0.778417	0.11366	U	0.571402	D	0.87997	0.6319	N	0.08118	0	0.09310	N	1	B;B;B	0.11235	0.004;0.004;0.003	B;B;B	0.09377	0.004;0.004;0.004	T	0.79006	-0.1979	10	0.13108	T	0.6	-0.3163	2.39	0.04376	0.4411:0.2732:0.0:0.2857	.	69;89;107	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	A	89;107;69;89	ENSP00000298232:T89A;ENSP00000355208:T107A;ENSP00000344441:T69A	ENSP00000298232:T89A	T	-	1	0	TPTE	9973264	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.978000	0.03778	-0.262000	0.09392	0.163000	0.16589	ACT		0.338	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			C	10951393	T	C	10951393	3	2	61	1	0	0	0	0	1	0	0	0	16470	1696	59	4	1396	4	TPTE	21	10951393	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8389	10951393	37178502	11706	19691										
POTED	317754	broad.mit.edu	37	chr21	14982911	14982911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagcaacgtgggcgcttgggGagactacgaccacagcgcct	15	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:14982911G>A	ENST00000299443.5	+	1	414	c.362G>A	c.(361-363)gGa>gAa	p.G121E		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	121						plasma membrane (GO:0005886)		p.G121E(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						GGCGCTTGGGGAGACTACGAC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	21											30	47	43					21																	14982911		829	3142	3971	13904782	SO:0001583	missense	317754			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	23822	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 1"	607549	"ankyrin repeat domain 21", "ANKRD26-like family B, member 3"	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.362G>A	21.37:g.14982911G>A	ENSP00000299443:p.Gly121Glu		13904782	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	G	0.621	-0.821034	0.02755	.	.	ENSG00000166351	ENST00000299443	T	0.27890	1.64	0.637	-1.27	0.09347	.	.	.	.	.	T	0.25344	0.0616	N	0.11427	0.14	0.09310	N	1	D	0.64830	0.994	D	0.65010	0.931	T	0.12400	-1.0549	8	0.35671	T	0.21	.	.	.	.	.	121	Q86YR6	POTED_HUMAN	E	121	ENSP00000299443:G121E	ENSP00000299443:G121E	G	+	2	0	POTED	13904782	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.848000	0.01673	-1.131000	0.02910	-1.109000	0.02080	GGA		0.587	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981		A	14982911	G	A	14982911	3	1	61	1	0	0	0	0	1	0	0	0	12294	1174	41	3	364	3	POTED	21	14982911	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4031518	14982911	33146984	11707	19692										
POTED	317754	broad.mit.edu	37	chr21	14987509	14987509	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaactcctgctggacagacGatgtcaacttaatgtccttg	8	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:14987509G>A	ENST00000299443.5	+	2	639	c.587G>A	c.(586-588)cGa>cAa	p.R196Q		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	196						plasma membrane (GO:0005886)		p.R196Q(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						CTGGACAGACGATGTCAACTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	21											0	1	1					21																	14987509		0	1	1	13909380	SO:0001583	missense	317754			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	23822	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 1"	607549	"ankyrin repeat domain 21", "ANKRD26-like family B, member 3"	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.587G>A	21.37:g.14987509G>A	ENSP00000299443:p.Arg196Gln		13909380	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	G	5.966	0.362244	0.11296	.	.	ENSG00000166351	ENST00000299443	T	0.52057	0.68	1.4	0.186	0.15105	Ankyrin repeat-containing domain (4);	0.674489	0.12697	N	0.446625	T	0.30262	0.0759	N	0.17248	0.465	0.09310	N	1	P	0.48640	0.913	P	0.47645	0.553	T	0.11203	-1.0597	10	0.27082	T	0.32	.	3.1236	0.06400	0.7252:0.0:0.2748:0.0	.	196	Q86YR6	POTED_HUMAN	Q	196	ENSP00000299443:R196Q	ENSP00000299443:R196Q	R	+	2	0	POTED	13909380	0.950000	0.32346	0.001000	0.08648	0.016000	0.09150	1.452000	0.35156	0.046000	0.15833	0.184000	0.17185	CGA		0.403	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981		A	14987509	G	A	14987509	3	1	61	1	0	0	0	0	1	0	0	0	12294	1058	37	1	593	1	POTED	21	14987509	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4598	14987509	33142386	11708	19693										
POTED	317754	broad.mit.edu	37	chr21	14990767	14990767	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttaaatgtacttgataGatatggaaggtatggttatt	9	1	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:14990767G>T	ENST00000299443.5	+	4	960	c.908G>T	c.(907-909)aGa>aTa	p.R303I		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	303						plasma membrane (GO:0005886)		p.R303I(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						GTACTTGATAGATATGGAAGG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	21											1	1	1					21																	14990767		14	69	83	13912638	SO:0001583	missense	317754			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	23822	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 1"	607549	"ankyrin repeat domain 21", "ANKRD26-like family B, member 3"	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.908G>T	21.37:g.14990767G>T	ENSP00000299443:p.Arg303Ile		13912638	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	G	4.957	0.177696	0.09443	.	.	ENSG00000166351	ENST00000299443	T	0.52754	0.65	1.4	-1.87	0.07737	Ankyrin repeat-containing domain (4);	0.718507	0.10344	U	0.685945	T	0.20170	0.0485	N	0.17379	0.485	0.09310	N	1	P	0.41008	0.735	B	0.29440	0.102	T	0.11446	-1.0587	10	0.48119	T	0.1	.	2.2179	0.03965	0.4493:0.3188:0.2319:0.0	.	303	Q86YR6	POTED_HUMAN	I	303	ENSP00000299443:R303I	ENSP00000299443:R303I	R	+	2	0	POTED	13912638	0.006000	0.16342	0.001000	0.08648	0.114000	0.19823	0.391000	0.20784	-0.428000	0.07339	0.184000	0.17185	AGA		0.299	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981		T	14990767	G	T	14990767	3	4	61	1	0	0	0	0	1	0	0	0	12294	942	33	2	922	2	POTED	21	14990767	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3258	14990767	33139128	11709	19694										
POTED	317754	broad.mit.edu	37	chr21	15013696	15013696	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcataagaaagaagaagatCtcttgcgtgaaaacagcgtg	11	6	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:15013696C>T	ENST00000299443.5	+	11	1616	c.1564C>T	c.(1564-1566)Ctc>Ttc	p.L522F		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	522						plasma membrane (GO:0005886)		p.L522I(1)|p.L522F(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						AGAAGAAGATCTCTTGCGTGA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	21											18	24	23					21																	15013696		829	3062	3891	13935567	SO:0001583	missense	317754			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	23822	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 1"	607549	"ankyrin repeat domain 21", "ANKRD26-like family B, member 3"	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.1564C>T	21.37:g.15013696C>T	ENSP00000299443:p.Leu522Phe		13935567	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.355033	0.24512	.	.	ENSG00000166351	ENST00000299443	T	0.48201	0.82	2.1	1.19	0.21007	.	.	.	.	.	T	0.43255	0.1239	M	0.72118	2.19	0.09310	N	1	B	0.27286	0.174	B	0.22601	0.04	T	0.39502	-0.9611	9	0.56958	D	0.05	.	6.7502	0.23483	0.0:0.8402:0.0:0.1598	.	522	Q86YR6	POTED_HUMAN	F	522	ENSP00000299443:L522F	ENSP00000299443:L522F	L	+	1	0	POTED	13935567	0.955000	0.32602	0.002000	0.10522	0.000000	0.00434	0.801000	0.27055	0.235000	0.21160	-0.460000	0.05396	CTC		0.333	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981		T	15013696	C	T	15013696	3	4	61	1	0	0	0	0	1	0	0	0	12294	913	32	3	1606	3	POTED	21	15013696	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22929	15013696	33116199	11710	19695										
LIPI	149998	broad.mit.edu	37	chr21	15524982	15524982	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catagttttatctggaacaaTtatactgagaacaaaataat	5	5	1	1	rs202154453		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:15524982T>G	ENST00000536861.1	-	8	1029	c.1030A>C	c.(1030-1032)Att>Ctt	p.I344L	LIPI_ENST00000344577.2_Missense_Mutation_p.I365L			Q6XZB0	LIPI_HUMAN	lipase, member I	344					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.I365L(1)		endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TCTGGAACAATTATACTGAGA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	21											28	29	29					21																	15524982		2198	4260	6458	14446853	SO:0001583	missense	149998			BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1030A>C	21.37:g.15524982T>G	ENSP00000440381:p.Ile344Leu		14446853	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		.	.	.	.	.	.	.	.	.	.	T	4.002	-0.002315	0.07819	.	.	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.87571	-2.27;-2.26	5.34	0.358	0.16084	.	0.597916	0.18513	N	0.139017	T	0.75845	0.3905	L	0.42245	1.32	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.55354	-0.8154	10	0.09084	T	0.74	.	4.7831	0.13211	0.0:0.2703:0.1794:0.5502	.	365	Q6XZB0-2	.	L	365;344	ENSP00000343331:I365L;ENSP00000440381:I344L	ENSP00000343331:I365L	I	-	1	0	LIPI	14446853	0.004000	0.15560	0.003000	0.11579	0.039000	0.13416	0.168000	0.16622	-0.026000	0.13895	0.528000	0.53228	ATT		0.254	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		G	15524982	T	G	15524982	3	3	61	1	0	0	0	0	1	0	0	0	8849	1493	52	4	364	4	LIPI	21	15524982	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	511286	15524982	32604913	11711	19696										
LIPI	149998	broad.mit.edu	37	chr21	15561499	15561499	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcattcagcaaaatccttacGaagttctgaagccataatgg	7	9	3	1	rs548960957		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:15561499G>A	ENST00000536861.1	-	2	287	c.288C>T	c.(286-288)ttC>ttT	p.F96F	LIPI_ENST00000344577.2_Silent_p.F117F			Q6XZB0	LIPI_HUMAN	lipase, member I	96					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.F117F(1)		endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		AAATCCTTACGAAGTTCTGAA	0.368													G|||	1	0.000199681	0	0	5008	,	,		16208	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	21											98	92	94					21																	15561499		2203	4300	6503	14483370	SO:0001819	synonymous_variant	149998			BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.288C>T	21.37:g.15561499G>A			14483370	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	37																																																																																					0.368	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		A	15561499	G	A	15561499	2	1	61	1	0	0	0	0	0	0	0	1	8849	1049	37	1		1	LIPI	21	15561499	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36517	15561499	32568396	11712	19697										
SAMSN1	64092	broad.mit.edu	37	chr21	15872865	15872865	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacctgcagatgaatcctCtctaggaactcctgcagagt	8	13	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:15872865C>A	ENST00000400566.1	-	6	834	c.753G>T	c.(751-753)gaG>gaT	p.E251D	SAMSN1_ENST00000285670.2_Missense_Mutation_p.E319D|SAMSN1_ENST00000463807.1_5'UTR|SAMSN1_ENST00000400564.1_Missense_Mutation_p.E83D	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	251	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)	p.E251D(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GATGAATCCTCTCTAGGAACT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	21											94	88	90					21																	15872865		1845	4098	5943	14794736	SO:0001583	missense	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.753G>T	21.37:g.15872865C>A	ENSP00000383411:p.Glu251Asp		14794736	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085351	0.55861	.	.	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	D;D;D	0.85171	-1.95;-1.95;-1.95	5.63	4.71	0.59529	Src homology-3 domain (1);Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.094388	0.64402	D	0.000001	D	0.90542	0.7036	M	0.75884	2.315	0.40983	D	0.984798	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.982;0.996;0.996	D	0.89573	0.3815	10	0.36615	T	0.2	-23.7698	10.2128	0.43152	0.0:0.8193:0.0:0.1807	.	83;319;251	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	D	319;251;83	ENSP00000285670:E319D;ENSP00000383411:E251D;ENSP00000383409:E83D	ENSP00000285670:E319D	E	-	3	2	SAMSN1	14794736	0.497000	0.26067	0.999000	0.59377	0.905000	0.53344	0.333000	0.19768	1.302000	0.44855	0.650000	0.86243	GAG		0.443	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			A	15872865	C	A	15872865	3	1	61	1	0	0	0	0	1	0	0	0	13867	912	32	2	380	2	SAMSN1	21	15872865	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	311366	15872865	32257030	11713	19698										
NRIP1	8204	broad.mit.edu	37	chr21	16339697	16339697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactgctgcaaatgggcttCgcttgacagaagtaatgcta	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:16339697C>T	ENST00000400202.1	-	3	1529	c.817G>A	c.(817-819)Gaa>Aaa	p.E273K	NRIP1_ENST00000318948.4_Missense_Mutation_p.E273K|NRIP1_ENST00000400199.1_Missense_Mutation_p.E273K			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	273	Interaction with ZNF366.|Repression domain 1.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.E273K(1)		cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				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)		AAATGGGCTTCGCTTGACAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	21											152	139	143					21																	16339697		2203	4300	6503	15261568	SO:0001583	missense	8204			X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"receptor interacting protein 140", "nuclear factor RIP140"	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.817G>A	21.37:g.16339697C>T	ENSP00000383063:p.Glu273Lys		15261568	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848687	0.91277	.	.	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.23950	1.88;1.88;1.88	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.52484	0.1737	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48317	-0.9046	10	0.87932	D	0	-17.3029	20.4753	0.99175	0.0:1.0:0.0:0.0	.	273	P48552	NRIP1_HUMAN	K	273	ENSP00000383060:E273K;ENSP00000383063:E273K;ENSP00000327213:E273K	ENSP00000327213:E273K	E	-	1	0	NRIP1	15261568	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	7.487000	0.81328	2.844000	0.97970	0.650000	0.86243	GAA		0.453	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		T	16339697	C	T	16339697	3	4	61	1	0	0	0	0	1	0	0	0	10683	893	31	1	2663	1	NRIP1	21	16339697	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	466832	16339697	31790198	11714	19699										
USP25	29761	broad.mit.edu	37	chr21	17163895	17163895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagtttggagggattctcGaaacccttatgatagaaaaa	10	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:17163895G>A	ENST00000285679.6	+	5	836	c.467G>A	c.(466-468)cGa>cAa	p.R156Q	USP25_ENST00000400183.2_Missense_Mutation_p.R156Q|USP25_ENST00000285681.2_Missense_Mutation_p.R156Q|USP25_ENST00000547201.1_3'UTR|USP25_ENST00000351097.5_Missense_Mutation_p.R156Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	156					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.R156Q(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		AGGGATTCTCGAAACCCTTAT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	21											152	154	153					21																	17163895		2203	4300	6503	16085766	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.467G>A	21.37:g.17163895G>A	ENSP00000285679:p.Arg156Gln		16085766	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167131	0.57476	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.30448	1.97;1.97;1.53;1.97	5.25	4.35	0.52113	.	0.112431	0.64402	D	0.000009	T	0.17577	0.0422	N	0.12182	0.205	0.32263	N	0.569897	P;B;P;B	0.37997	0.614;0.395;0.471;0.004	B;B;B;B	0.36922	0.236;0.019;0.158;0.0	T	0.13098	-1.0522	10	0.29301	T	0.29	.	12.3586	0.55190	0.0:0.4309:0.5691:0.0	.	156;156;156;156	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	156	ENSP00000285681:R156Q;ENSP00000285679:R156Q;ENSP00000299574:R156Q;ENSP00000383044:R156Q	ENSP00000285679:R156Q	R	+	2	0	USP25	16085766	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.269000	0.65542	2.467000	0.83353	0.585000	0.79938	CGA		0.393	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			A	17163895	G	A	17163895	3	1	61	1	0	0	0	0	1	0	0	0	17096	1058	37	1	485	1	USP25	21	17163895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	824198	17163895	30966000	11715	19700										
USP25	29761	broad.mit.edu	37	chr21	17205776	17205776	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgatttgaaaaagaactagaAgaatgggatgcacaacttgc	10	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:17205776A>G	ENST00000285679.6	+	17	2472	c.2103A>G	c.(2101-2103)gaA>gaG	p.E701E	USP25_ENST00000400183.2_Silent_p.E701E|USP25_ENST00000285681.2_Silent_p.E701E|USP25_ENST00000351097.5_Intron	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	701					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.E701E(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		AAGAACTAGAAGAATGGGATG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	21											67	70	69					21																	17205776		2203	4300	6503	16127647	SO:0001819	synonymous_variant	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2103A>G	21.37:g.17205776A>G			16127647	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																				0.418	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17205776	A	G	17205776	2	3	61	1	0	0	0	0	0	0	0	1	17096	69	3	4		4	USP25	21	17205776	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	41881	17205776	30924119	11716	19701										
USP25	29761	broad.mit.edu	37	chr21	17214800	17214800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaagaagaaactattcaaAtaattaccaaggcatcacat	5	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:17214800A>G	ENST00000285679.6	+	18	2647	c.2278A>G	c.(2278-2280)Ata>Gta	p.I760V	USP25_ENST00000400183.2_Missense_Mutation_p.I760V|USP25_ENST00000285681.2_Missense_Mutation_p.I760V|USP25_ENST00000351097.5_Intron	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	760					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.I760V(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		AACTATTCAAATAATTACCAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	21											114	117	116					21																	17214800		2203	4300	6503	16136671	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2278A>G	21.37:g.17214800A>G	ENSP00000285679:p.Ile760Val		16136671	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	A	7.765	0.706272	0.15239	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	T;T;T	0.21543	2.0;2.02;2.0	5.32	-6.2	0.02072	.	0.557741	0.20055	N	0.100219	T	0.04634	0.0126	N	0.00926	-1.1	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.12156	0.007;0.0;0.0	T	0.36553	-0.9743	10	0.08179	T	0.78	.	12.1029	0.53794	0.1268:0.0:0.7656:0.1076	.	760;760;760	Q9UHP3-3;Q9UHP3-1;Q9UHP3	.;.;UBP25_HUMAN	V	760	ENSP00000285681:I760V;ENSP00000285679:I760V;ENSP00000383044:I760V	ENSP00000285679:I760V	I	+	1	0	USP25	16136671	1.000000	0.71417	0.901000	0.35422	0.987000	0.75469	1.035000	0.30216	-1.056000	0.03205	-0.177000	0.13119	ATA		0.393	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17214800	A	G	17214800	3	3	61	1	0	0	0	0	1	0	0	0	17096	101	4	4	2348	4	USP25	21	17214800	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	9024	17214800	30915095	11717	19702										
USP25	29761	broad.mit.edu	37	chr21	17250704	17250704	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagtttccatgagccaccGaagttaccttcatattccac	5	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:17250704G>A	ENST00000285679.6	+	24	3447	c.3078G>A	c.(3076-3078)ccG>ccA	p.P1026P	USP25_ENST00000400183.2_Silent_p.P1096P|USP25_ENST00000285681.2_Silent_p.P1058P|USP25_ENST00000351097.5_Silent_p.P421P	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	1026					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.P1026P(2)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		ATGAGCCACCGAAGTTACCTT	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	21											106	95	99					21																	17250704		2203	4300	6503	16172575	SO:0001819	synonymous_variant	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.3078G>A	21.37:g.17250704G>A			16172575	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																				0.423	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			A	17250704	G	A	17250704	2	1	61	1	0	0	0	0	0	0	0	1	17096	1045	37	1		1	USP25	21	17250704	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35904	17250704	30879191	11718	19703										
USP25	29761	broad.mit.edu	37	chr21	17250772	17250772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcatgttgtccctcagtcGaactcctgctgatggaagat	9	10	2	2	rs549945211	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:17250772G>A	ENST00000285679.6	+	24	3515	c.3146G>A	c.(3145-3147)cGa>cAa	p.R1049Q	USP25_ENST00000400183.2_Missense_Mutation_p.R1119Q|USP25_ENST00000285681.2_Missense_Mutation_p.R1081Q|USP25_ENST00000351097.5_Missense_Mutation_p.R444Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	1049					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.R1049Q(2)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		TCCCTCAGTCGAACTCCTGCT	0.438													G|||	2	0.000399361	0	0	5008	,	,		17817	0		0	False		,,,				2504	0.002															2	Substitution - Missense(2)	large_intestine(2)	21											110	100	103					21																	17250772		2203	4300	6503	16172643	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.3146G>A	21.37:g.17250772G>A	ENSP00000285679:p.Arg1049Gln		16172643	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560817	0.65538	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.33216	1.82;1.83;1.42;1.82	5.92	5.92	0.95590	.	0.233302	0.42821	D	0.000646	T	0.43722	0.1260	L	0.41236	1.265	0.38800	D	0.955174	D;D;D;P	0.71674	0.998;0.996;0.979;0.955	P;P;P;B	0.56563	0.759;0.801;0.638;0.357	T	0.10245	-1.0638	10	0.36615	T	0.2	-10.4026	20.3172	0.98658	0.0:0.0:1.0:0.0	.	1119;444;1081;1049	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	1081;1049;444;1119	ENSP00000285681:R1081Q;ENSP00000285679:R1049Q;ENSP00000299574:R444Q;ENSP00000383044:R1119Q	ENSP00000285679:R1049Q	R	+	2	0	USP25	16172643	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.325000	0.65869	2.801000	0.96364	0.650000	0.86243	CGA		0.438	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			A	17250772	G	A	17250772	3	1	61	1	0	0	0	0	1	0	0	0	17096	1058	37	1	3240	1	USP25	21	17250772	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68	17250772	30879123	11719	19704										
CXADR	1525	broad.mit.edu	37	chr21	18924145	18924145	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtacattttacgagtaatGatctcaaatctggtgatgca	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:18924145G>T	ENST00000284878.7	+	3	1037	c.289G>T	c.(289-291)Gat>Tat	p.D97Y	CXADR_ENST00000400169.1_Missense_Mutation_p.D97Y|CXADR_ENST00000356275.6_Intron|CXADR_ENST00000400166.1_Missense_Mutation_p.D97Y|CXADR_ENST00000306618.10_Missense_Mutation_p.D97Y|CXADR_ENST00000400165.1_Missense_Mutation_p.D97Y	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	97	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)	p.D97Y(1)		endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		TACGAGTAATGATCTCAAATC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	21											66	64	64					21																	18924145		2203	4300	6503	17846016	SO:0001583	missense	1525			Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.289G>T	21.37:g.18924145G>T	ENSP00000284878:p.Asp97Tyr		17846016	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	37	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.866099	0.71949	.	.	ENSG00000154639	ENST00000284878;ENST00000400166;ENST00000400169;ENST00000400165;ENST00000306618	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.04	4.15	0.48705	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.043023	0.85682	D	0.000000	T	0.73040	0.3536	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.991;0.997;0.996;0.996	T	0.73395	-0.3996	10	0.02654	T	1	.	12.9804	0.58559	0.0788:0.0:0.9212:0.0	.	97;97;97;97	P78310-4;B7WPI3;P78310;P78310-5	.;.;CXAR_HUMAN;.	Y	97	ENSP00000284878:D97Y;ENSP00000383030:D97Y;ENSP00000383033:D97Y;ENSP00000383029:D97Y;ENSP00000303395:D97Y	ENSP00000284878:D97Y	D	+	1	0	CXADR	17846016	1.000000	0.71417	0.716000	0.30569	0.984000	0.73092	6.152000	0.71812	1.428000	0.47296	0.655000	0.94253	GAT		0.333	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			T	18924145	G	T	18924145	3	4	61	1	0	0	0	0	1	0	0	0	4082	1290	45	2	299	2	CXADR	21	18924145	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1673373	18924145	29205750	11720	19705										
TMPRSS15	5651	broad.mit.edu	37	chr21	19698871	19698871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaacacatcctttactgggCcaggccctgtgtacacagct	9	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19698871C>A	ENST00000284885.3	-	16	1832	c.1799G>T	c.(1798-1800)gGc>gTc	p.G600V		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	600	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.G600V(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTTTACTGGGCCAGGCCCTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	21											162	135	144					21																	19698871		2203	4300	6503	18620742	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1799G>T	21.37:g.19698871C>A	ENSP00000284885:p.Gly600Val		18620742	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734889	0.48939	.	.	ENSG00000154646	ENST00000284885	T	0.18657	2.2	5.27	4.39	0.52855	CUB (5);	0.063724	0.64402	D	0.000011	T	0.32763	0.0840	L	0.42529	1.33	0.28940	N	0.891055	D	0.76494	0.999	D	0.75020	0.985	T	0.08452	-1.0721	9	.	.	.	.	7.7185	0.28719	0.0:0.7471:0.1646:0.0882	.	600	P98073	ENTK_HUMAN	V	600	ENSP00000284885:G600V	.	G	-	2	0	TMPRSS15	18620742	0.003000	0.15002	0.141000	0.22245	0.858000	0.48976	0.713000	0.25794	1.351000	0.45789	0.650000	0.86243	GGC		0.448	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19698871	C	A	19698871	3	1	61	1	0	0	0	0	1	0	0	0	16285	739	26	2	1300	2	TMPRSS15	21	19698871	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	774726	19698871	28431024	11721	19706										
TMPRSS15	5651	broad.mit.edu	37	chr21	19701534	19701534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcttatttcaactacatCgttaatattttctaagtcaa	2	8	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19701534C>T	ENST00000284885.3	-	15	1765	c.1732G>A	c.(1732-1734)Gat>Aat	p.D578N		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	578	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.D578N(2)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCAACTACATCGTTAATATTT	0.308																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	21											91	88	89					21																	19701534		2203	4298	6501	18623405	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1732G>A	21.37:g.19701534C>T	ENSP00000284885:p.Asp578Asn		18623405	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.758031	0.69648	.	.	ENSG00000154646	ENST00000284885	T	0.33865	1.39	5.53	5.53	0.82687	CUB (5);	0.000000	0.85682	D	0.000000	T	0.71443	0.3340	H	0.94345	3.525	0.53005	D	0.999961	D	0.89917	1.0	D	0.97110	1.0	T	0.79598	-0.1737	9	.	.	.	.	17.3132	0.87215	0.0:1.0:0.0:0.0	.	578	P98073	ENTK_HUMAN	N	578	ENSP00000284885:D578N	.	D	-	1	0	TMPRSS15	18623405	1.000000	0.71417	0.983000	0.44433	0.332000	0.28634	5.609000	0.67661	2.758000	0.94735	0.655000	0.94253	GAT		0.308	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19701534	C	T	19701534	3	4	61	1	0	0	0	0	1	0	0	0	16285	884	31	1	1371	1	TMPRSS15	21	19701534	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2663	19701534	28428361	11722	19707										
TMPRSS15	5651	broad.mit.edu	37	chr21	19713769	19713769	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttggcaccaaagttggttCtggataaagactcccattgc	10	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19713769C>A	ENST00000284885.3	-	13	1558	c.1525G>T	c.(1525-1527)Gaa>Taa	p.E509*		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	509						brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.E509*(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						AAAGTTGGTTCTGGATAAAGA	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											161	153	156					21																	19713769		2203	4300	6503	18635640	SO:0001587	stop_gained	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1525G>T	21.37:g.19713769C>A	ENSP00000284885:p.Glu509*		18635640	Q2NKL7	Nonsense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	39	7.647139	0.98409	.	.	ENSG00000154646	ENST00000284885	.	.	.	5.64	5.64	0.86602	.	0.185138	0.44902	D	0.000417	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6798	0.91543	0.0:1.0:0.0:0.0	.	.	.	.	X	509	.	.	E	-	1	0	TMPRSS15	18635640	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.974000	0.56852	2.659000	0.90383	0.484000	0.47621	GAA		0.398	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19713769	C	A	19713769	4	1	61	1	0	0	0	0	0	1	0	0	16285	922	32	2	1586	2	TMPRSS15	21	19713769	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12235	19713769	28416126	11723	19708										
TMPRSS15	5651	broad.mit.edu	37	chr21	19716325	19716325	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaaagggaggcttaaaagCcccactcgttcttgtctccc	8	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19716325C>T	ENST00000284885.3	-	11	1257	c.1224G>A	c.(1222-1224)ggG>ggA	p.G408G		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	408	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.G408G(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GGCTTAAAAGCCCCACTCGTT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	21											114	119	117					21																	19716325		2203	4300	6503	18638196	SO:0001819	synonymous_variant	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1224G>A	21.37:g.19716325C>T			18638196	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																				0.393	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19716325	C	T	19716325	2	4	61	1	0	0	0	0	0	0	0	1	16285	726	26	3		3	TMPRSS15	21	19716325	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2556	19716325	28413570	11724	19709										
TMPRSS15	5651	broad.mit.edu	37	chr21	19770231	19770231	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgagttcttatattcattCttcagattgcttgatagaaa	6	6	4	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19770231C>A	ENST00000284885.3	-	3	342	c.309G>T	c.(307-309)aaG>aaT	p.K103N		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	103	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.K103N(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TATATTCATTCTTCAGATTGC	0.234																																																1	Substitution - Missense(1)	large_intestine(1)	21											16	17	17					21																	19770231		2133	4216	6349	18692102	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.309G>T	21.37:g.19770231C>A	ENSP00000284885:p.Lys103Asn		18692102	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239047	0.58995	.	.	ENSG00000154646	ENST00000284885;ENST00000422787	T;T	0.33865	1.39;1.39	4.78	3.83	0.44106	SEA (3);	0.352689	0.29529	N	0.011900	T	0.45677	0.1354	M	0.62723	1.935	0.30545	N	0.76601	P	0.51653	0.947	P	0.58391	0.838	T	0.49513	-0.8932	9	.	.	.	.	4.4344	0.11544	0.0:0.7772:0.0:0.2228	.	103	P98073	ENTK_HUMAN	N	103;58	ENSP00000284885:K103N;ENSP00000398253:K58N	.	K	-	3	2	TMPRSS15	18692102	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.198000	0.17217	1.208000	0.43306	0.643000	0.83706	AAG		0.234	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19770231	C	A	19770231	3	1	61	1	0	0	0	0	1	0	0	0	16285	912	32	2	2842	2	TMPRSS15	21	19770231	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	53906	19770231	28359664	11725	19710										
TMPRSS15	5651	broad.mit.edu	37	chr21	19775917	19775917	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagagaatgatgcctagaaGatatgcctcttttcgacccc	9	10	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:19775917G>T	ENST00000284885.3	-	1	56	c.23C>A	c.(22-24)tCt>tAt	p.S8Y		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	8						brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.S8Y(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						ATGCCTAGAAGATATGCCTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	21											141	134	136					21																	19775917		2203	4300	6503	18697788	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.23C>A	21.37:g.19775917G>T	ENSP00000284885:p.Ser8Tyr		18697788	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.958005	0.34565	.	.	ENSG00000154646	ENST00000284885	D	0.86694	-2.16	5.16	4.28	0.50868	.	0.738938	0.12956	N	0.425456	T	0.80221	0.4583	L	0.29908	0.895	0.09310	N	1	P	0.44877	0.845	B	0.41571	0.36	T	0.68891	-0.5289	9	.	.	.	.	9.55	0.39304	0.0943:0.0:0.9057:0.0	.	8	P98073	ENTK_HUMAN	Y	8	ENSP00000284885:S8Y	.	S	-	2	0	TMPRSS15	18697788	0.001000	0.12720	0.008000	0.14137	0.063000	0.16089	0.552000	0.23376	1.428000	0.47296	0.563000	0.77884	TCT		0.383	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19775917	G	T	19775917	3	4	61	1	0	0	0	0	1	0	0	0	16285	942	33	2	3136	2	TMPRSS15	21	19775917	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5686	19775917	28353978	11726	19711										
NCAM2	4685	broad.mit.edu	37	chr21	22656657	22656657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagaagatgcagggatatatCgttgtcaagcaacagatgcc	11	7	1	3	rs566399279		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:22656657C>T	ENST00000400546.1	+	3	523	c.274C>T	c.(274-276)Cgt>Tgt	p.R92C	NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000535285.1_Missense_Mutation_p.R117C	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	92	Ig-like C2-type 1.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R92C(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGGGATATATCGTTGTCAAGC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	21											92	86	88					21																	22656657		1872	4105	5977	21578528	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.274C>T	21.37:g.22656657C>T	ENSP00000383392:p.Arg92Cys		21578528	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313730	0.81358	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	T;T	0.28454	1.61;1.61	5.58	5.58	0.84498	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.56307	0.1976	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.57785	-0.7751	10	0.87932	D	0	-12.539	18.134	0.89612	0.0:1.0:0.0:0.0	.	117;92	B7Z841;O15394	.;NCAM2_HUMAN	C	92;117	ENSP00000383392:R92C;ENSP00000441887:R117C	ENSP00000383392:R92C	R	+	1	0	NCAM2	21578528	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.204000	0.32296	2.632000	0.89209	0.591000	0.81541	CGT		0.348	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22656657	C	T	22656657	3	4	61	1	0	0	0	0	1	0	0	0	10234	884	31	1	284	1	NCAM2	21	22656657	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2880740	22656657	25473238	11727	19712										
NCAM2	4685	broad.mit.edu	37	chr21	22746300	22746300	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgcaagcagaattggaGggcatcaaaagagcatgtac	12	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:22746300G>T	ENST00000400546.1	+	9	1411	c.1162G>T	c.(1162-1164)Ggg>Tgg	p.G388W	NCAM2_ENST00000284894.7_Missense_Mutation_p.G246W|NCAM2_ENST00000535285.1_Missense_Mutation_p.G413W	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	388	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G388W(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		CAGAATTGGAGGGCATCAAAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	21											177	168	171					21																	22746300		1905	4136	6041	21668171	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1162G>T	21.37:g.22746300G>T	ENSP00000383392:p.Gly388Trp		21668171	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.656242	0.88056	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.67523	-0.27;-0.27;-0.27	5.54	5.54	0.83059	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79563	0.4467	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.80600	-0.1310	10	0.72032	D	0.01	-15.0922	18.1211	0.89572	0.0:0.0:1.0:0.0	.	413;246;388	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	W	388;246;413	ENSP00000383392:G388W;ENSP00000284894:G246W;ENSP00000441887:G413W	ENSP00000284894:G246W	G	+	1	0	NCAM2	21668171	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.226000	0.95229	2.618000	0.88619	0.644000	0.83932	GGG		0.363	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22746300	G	T	22746300	3	4	61	1	0	0	0	0	1	0	0	0	10234	1000	35	2	1196	2	NCAM2	21	22746300	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89643	22746300	25383595	11728	19713										
NCAM2	4685	broad.mit.edu	37	chr21	22906955	22906955	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtaaatgagccaaatgaaAccacaccactgacagaacct	6	12	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:22906955A>G	ENST00000400546.1	+	17	2629	c.2380A>G	c.(2380-2382)Acc>Gcc	p.T794A	NCAM2_ENST00000284894.7_Missense_Mutation_p.T652A	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	794					axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T794A(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GCCAAATGAAACCACACCACT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	21											111	106	108					21																	22906955		1926	4131	6057	21828826	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.2380A>G	21.37:g.22906955A>G	ENSP00000383392:p.Thr794Ala		21828826	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.616795	0.66672	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.54866	0.55;0.55	5.49	5.49	0.81192	.	0.241745	0.41605	D	0.000848	T	0.68742	0.3034	M	0.62723	1.935	0.80722	D	1	P;D	0.58970	0.765;0.984	B;D	0.68192	0.22;0.956	T	0.71354	-0.4618	10	0.62326	D	0.03	-17.4856	14.4086	0.67101	1.0:0.0:0.0:0.0	.	652;794	B7Z5K2;O15394	.;NCAM2_HUMAN	A	794;652	ENSP00000383392:T794A;ENSP00000284894:T652A	ENSP00000284894:T652A	T	+	1	0	NCAM2	21828826	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.605000	0.90883	2.088000	0.63022	0.377000	0.23210	ACC		0.388	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		G	22906955	A	G	22906955	3	3	61	1	0	0	0	0	1	0	0	0	10234	43	2	4	2446	4	NCAM2	21	22906955	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	160655	22906955	25222940	11729	19714										
MRPL39	54148	broad.mit.edu	37	chr21	26969724	26969724	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtgaaggaacgtaagttCtccttaaaaatgaaagtaat	8	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:26969724C>A	ENST00000352957.4	-	6	632	c.591G>T	c.(589-591)gaG>gaT	p.E197D	MRPL39_ENST00000307301.7_Missense_Mutation_p.E197D	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	197						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E197D(2)		endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						AACGTAAGTTCTCCTTAAAAA	0.328																																																2	Substitution - Missense(2)	large_intestine(2)	21											38	36	37					21																	26969724		2198	4293	6491	25891595	SO:0001583	missense	54148			AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"Mitochondrial ribosomal proteins / large subunits"	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.591G>T	21.37:g.26969724C>A	ENSP00000284967:p.Glu197Asp		25891595	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Missense_Mutation	SNP	ENST00000352957.4	37	CCDS13573.1	.	.	.	.	.	.	.	.	.	.	C	9.883	1.202022	0.22121	.	.	ENSG00000154719	ENST00000352957;ENST00000307301;ENST00000419219	T;T;T	0.51574	0.72;0.7;0.78	4.49	3.51	0.40186	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.053337	0.64402	D	0.000001	T	0.32793	0.0841	L	0.39397	1.21	0.51482	D	0.999929	B;B	0.20368	0.044;0.044	B;B	0.20577	0.03;0.03	T	0.12889	-1.0530	10	0.22706	T	0.39	-24.3188	5.8757	0.18828	0.0:0.6521:0.1917:0.1562	.	197;197	Q9NYK5;Q9NYK5-2	RM39_HUMAN;.	D	197;197;187	ENSP00000284967:E197D;ENSP00000305682:E197D;ENSP00000404426:E187D	ENSP00000305682:E197D	E	-	3	2	MRPL39	25891595	1.000000	0.71417	1.000000	0.80357	0.464000	0.32679	0.542000	0.23222	2.331000	0.79229	0.585000	0.79938	GAG		0.328	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446		A	26969724	C	A	26969724	3	1	61	1	0	0	0	0	1	0	0	0	9832	912	32	2	538	2	MRPL39	21	26969724	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4062769	26969724	21160171	11730	19715										
APP	351	broad.mit.edu	37	chr21	27327992	27327992	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaccatgcgcacatgctcGaaatgctttagggtgtgctg	11	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:27327992G>A	ENST00000346798.3	-	12	1569	c.1536C>T	c.(1534-1536)ttC>ttT	p.F512F	APP_ENST00000357903.3_Silent_p.F493F|APP_ENST00000354192.3_Silent_p.F381F|APP_ENST00000358918.3_Silent_p.F512F|APP_ENST00000448388.2_Silent_p.F402F|APP_ENST00000359726.3_Silent_p.F456F|APP_ENST00000440126.3_Silent_p.F488F|APP_ENST00000439274.2_Silent_p.F456F|APP_ENST00000348990.5_Silent_p.F437F	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	512	Heparin-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.F512F(2)		endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				GCACATGCTCGAAATGCTTTA	0.493																																																2	Substitution - coding silent(2)	large_intestine(2)	21											217	169	185					21																	27327992		2203	4300	6503	26249863	SO:0001819	synonymous_variant	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1536C>T	21.37:g.27327992G>A			26249863	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	G	5.958	0.360705	0.11296	.	.	ENSG00000142192	ENST00000448850	.	.	.	5.45	0.505	0.16953	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.1801	9.3162	0.37934	0.5085:0.0:0.4915:0.0	.	.	.	.	X	415	.	.	R	-	1	2	APP	26249863	0.984000	0.35163	1.000000	0.80357	0.467000	0.32768	0.330000	0.19715	0.182000	0.20032	-0.302000	0.09304	CGA		0.493	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		A	27327992	G	A	27327992	2	1	61	1	0	0	0	0	0	0	0	1	815	1049	37	1		1	APP	21	27327992	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	358268	27327992	20801903	11731	19716										
APP	351	broad.mit.edu	37	chr21	27425560	27425560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgggctggtacctctttggCgacggtgtgccagtgaagat	15	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:27425560C>T	ENST00000346798.3	-	4	493	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	APP_ENST00000357903.3_Missense_Mutation_p.A154T|APP_ENST00000474136.1_5'UTR|APP_ENST00000354192.3_Missense_Mutation_p.A98T|APP_ENST00000358918.3_Missense_Mutation_p.A154T|APP_ENST00000448388.2_Missense_Mutation_p.A119T|APP_ENST00000359726.3_Missense_Mutation_p.A154T|APP_ENST00000440126.3_Missense_Mutation_p.A149T|APP_ENST00000439274.2_Missense_Mutation_p.A98T|APP_ENST00000348990.5_Missense_Mutation_p.A154T	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	154					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.A154T(1)		endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				ACCTCTTTGGCGACGGTGTGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	21											162	157	159					21																	27425560		2203	4300	6503	26347431	SO:0001583	missense	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.460G>A	21.37:g.27425560C>T	ENSP00000284981:p.Ala154Thr		26347431	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.711729|5.711729	0.96830|0.96830	.|.	.|.	ENSG00000142192|ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274|ENST00000448850	D;D;D;D;D;D;D;D;D|.	0.97888|.	-2.57;-4.49;-4.55;-2.59;-2.37;-4.59;-4.47;-2.57;-2.52|.	5.78|5.78	5.78|5.78	0.91487|0.91487	Amyloidogenic glycoprotein, extracellular (1);Amyloidogenic glycoprotein, copper-binding (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77818|0.77818	0.4187|0.4187	M|M	0.74647|0.74647	2.275|2.275	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;0.999;0.984;1.0|.	D;D;D;D;D;D;P;D|.	0.85130|.	0.997;0.991;0.991;0.994;0.985;0.91;0.879;0.991|.	T|T	0.75614|0.75614	-0.3257|-0.3257	10|5	0.87932|.	D|.	0|.	-18.9998|-18.9998	19.9618|19.9618	0.97254|0.97254	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	154;119;98;149;98;154;154;154|.	P05067-2;E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067|.	.;.;.;.;.;.;.;A4_HUMAN|.	T|H	154;98;154;154;154;154;119;149;98|75	ENSP00000284981:A154T;ENSP00000346129:A98T;ENSP00000345463:A154T;ENSP00000350578:A154T;ENSP00000351796:A154T;ENSP00000352760:A154T;ENSP00000388538:A119T;ENSP00000387483:A149T;ENSP00000398879:A98T|.	ENSP00000284981:A154T|.	A|R	-|-	1|2	0|0	APP|APP	26347431|26347431	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	7.776000|7.776000	0.85560|0.85560	2.894000|2.894000	0.99253|0.99253	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.448	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		T	27425560	C	T	27425560	3	4	61	1	0	0	0	0	1	0	0	0	815	768	27	1	1912	1	APP	21	27425560	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	97568	27425560	20704335	11732	19717										
CYYR1	116159	broad.mit.edu	37	chr21	27840832	27840832	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatagattatttccttgcGtttccaggataaggaggggg	14	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:27840832G>A	ENST00000299340.4	-	4	796	c.453C>T	c.(451-453)aaC>aaT	p.N151N	AP001596.6_ENST00000421771.1_RNA|AP001597.1_ENST00000357401.3_RNA|AP001596.6_ENST00000429340.1_RNA|AP001597.1_ENST00000414486.1_RNA|CYYR1_ENST00000435845.2_3'UTR|AP001596.6_ENST00000444306.1_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	151						integral component of membrane (GO:0016021)		p.N151N(1)		large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						ATTTCCTTGCGTTTCCAGGAT	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	21											75	70	72					21																	27840832		2203	4300	6503	26762703	SO:0001819	synonymous_variant	116159			AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"cysteine and tyrosine-rich 1"	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.453C>T	21.37:g.27840832G>A			26762703	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Silent	SNP	ENST00000299340.4	37	CCDS13578.1																																																																																				0.512	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954		A	27840832	G	A	27840832	2	1	61	1	0	0	0	0	0	0	0	1	4217	1136	40	1		1	CYYR1	21	27840832	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	415272	27840832	20289063	11733	19718										
ADAMTS1	9510	broad.mit.edu	37	chr21	28214671	28214671	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcttacctgtctggtgaaaAgaattgctgtgtcatagtgc	10	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:28214671A>C	ENST00000284984.3	-	2	1518	c.1064T>G	c.(1063-1065)cTt>cGt	p.L355R		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	355	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.L355R(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TCTGGTGAAAAGAATTGCTGT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	21											80	56	64					21																	28214671		2203	4300	6503	27136542	SO:0001583	missense	9510			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1064T>G	21.37:g.28214671A>C	ENSP00000284984:p.Leu355Arg		27136542	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	37	CCDS33524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.85|18.85	3.711865|3.711865	0.68730|0.68730	.|.	.|.	ENSG00000154734|ENSG00000154734	ENST00000451462|ENST00000284984;ENST00000517777;ENST00000517452	.|T;T;T	.|0.79454	.|-1.27;-1.27;-1.27	5.27|5.27	5.27|5.27	0.74061|0.74061	.|Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.|.	.|.	.|.	.|.	D|D	0.90875|0.90875	0.7133|0.7133	M|M	0.94021|0.94021	3.485|3.485	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.93211|0.93211	0.6600|0.6600	5|9	.|0.87932	.|D	.|0	.|.	15.3726|15.3726	0.74577|0.74577	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|355	.|Q9UHI8	.|ATS1_HUMAN	V|R	137|355;93;117	.|ENSP00000284984:L355R;ENSP00000429557:L93R;ENSP00000431065:L117R	.|ENSP00000284984:L355R	F|L	-|-	1|2	0|0	ADAMTS1|ADAMTS1	27136542|27136542	1.000000|1.000000	0.71417|0.71417	0.907000|0.907000	0.35723|0.35723	0.589000|0.589000	0.36550|0.36550	9.139000|9.139000	0.94554|0.94554	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	TTT|CTT		0.488	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			C	28214671	A	C	28214671	3	2	61	1	0	0	0	0	1	0	0	0	255	72	3	4	1871	4	ADAMTS1	21	28214671	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	373839	28214671	19915224	11734	19719										
ADAMTS1	9510	broad.mit.edu	37	chr21	28214980	28214980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggtgactggacacaaatCgcttctttcttatgcttcca	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:28214980C>T	ENST00000284984.3	-	2	1209	c.755G>A	c.(754-756)cGa>cAa	p.R252Q		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	252					heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R252Q(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		GGACACAAATCGCTTCTTTCT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	21											55	54	55					21																	28214980		2203	4300	6503	27136851	SO:0001583	missense	9510			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.755G>A	21.37:g.28214980C>T	ENSP00000284984:p.Arg252Gln		27136851	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	37	CCDS33524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.733797|5.733797	0.96865|0.96865	.|.	.|.	ENSG00000154734|ENSG00000154734	ENST00000451462|ENST00000284984;ENST00000517452	.|T;D	.|0.85013	.|-0.25;-1.93	5.38|5.38	5.38|5.38	0.77491|0.77491	.|Metallopeptidase, catalytic domain (1);	.|.	.|.	.|.	.|.	D|D	0.85191|0.85191	0.5640|0.5640	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.69307	.|0.963	D|D	0.88628|0.88628	0.3167|0.3167	5|9	.|0.87932	.|D	.|0	.|.	19.3096|19.3096	0.94182|0.94182	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|252	.|Q9UHI8	.|ATS1_HUMAN	N|Q	34|252;14	.|ENSP00000284984:R252Q;ENSP00000431065:R14Q	.|ENSP00000284984:R252Q	D|R	-|-	1|2	0|0	ADAMTS1|ADAMTS1	27136851|27136851	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.320000|7.320000	0.79064|0.79064	2.792000|2.792000	0.96026|0.96026	0.655000|0.655000	0.94253|0.94253	GAT|CGA		0.433	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28214980	C	T	28214980	3	4	61	1	0	0	0	0	1	0	0	0	255	884	31	1	2180	1	ADAMTS1	21	28214980	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	309	28214980	19914915	11735	19720										
RNF160	26046	broad.mit.edu	37	chr21	30325676	30325676	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaattcttcacaccactgCagtgaataaagcagttctgc	6	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30325676C>T	ENST00000361371.5	-	17	3181	c.3102G>A	c.(3100-3102)ctG>ctA	p.L1034L	LTN1_ENST00000389194.2_Silent_p.L1080L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	1034					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.L1034L(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						CACACCACTGCAGTGAATAAA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	21											58	59	59					21																	30325676		2202	4300	6502	29247547	SO:0001819	synonymous_variant	26046			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.3102G>A	21.37:g.30325676C>T			29247547	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	37																																																																																					0.343	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		T	30325676	C	T	30325676	2	4	61	1	0	0	0	0	0	0	0	1	13492	697	25	3		3	RNF160	21	30325676	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2110696	30325676	17804219	11736	19721										
RNF160	26046	broad.mit.edu	37	chr21	30332891	30332891	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaagagtccatctttctgaGaagtgagattctgaagatac	10	6	3	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30332891G>T	ENST00000361371.5	-	12	2380	c.2301C>A	c.(2299-2301)ttC>ttA	p.F767L	LTN1_ENST00000389194.2_Missense_Mutation_p.F813L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	767					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.F767L(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						ATCTTTCTGAGAAGTGAGATT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	21											102	91	95					21																	30332891		2203	4300	6503	29254762	SO:0001583	missense	26046			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.2301C>A	21.37:g.30332891G>T	ENSP00000354977:p.Phe767Leu		29254762	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	G	6.729	0.503284	0.12822	.	.	ENSG00000198862	ENST00000389194;ENST00000361371	T;T	0.15718	2.4;2.41	5.25	1.41	0.22369	.	0.553031	0.21217	N	0.078213	T	0.06234	0.0161	N	0.08118	0	0.09310	N	0.999999	B	0.15473	0.013	B	0.11329	0.006	T	0.40421	-0.9564	10	0.11485	T	0.65	.	4.7757	0.13178	0.3561:0.0:0.5012:0.1427	.	767	O94822	LTN1_HUMAN	L	813;767	ENSP00000373846:F813L;ENSP00000354977:F767L	ENSP00000354977:F767L	F	-	3	2	LTN1	29254762	0.969000	0.33509	0.779000	0.31741	0.949000	0.60115	1.320000	0.33666	0.152000	0.19188	0.591000	0.81541	TTC		0.393	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		T	30332891	G	T	30332891	3	4	61	1	0	0	0	0	1	0	0	0	13492	933	33	2	3075	2	RNF160	21	30332891	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7215	30332891	17797004	11737	19722										
RNF160	26046	broad.mit.edu	37	chr21	30341850	30341850	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttgctgcattataaaacGtaagcattcaaaaaaagcag	7	6	1	0	rs369131368		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30341850G>A	ENST00000361371.5	-	9	1328	c.1249C>T	c.(1249-1251)Cgt>Tgt	p.R417C	LTN1_ENST00000389194.2_Missense_Mutation_p.R463C|LTN1_ENST00000389195.2_Missense_Mutation_p.R463C			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	417					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R417C(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						ATTATAAAACGTAAGCATTCA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	21						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	115	112	113		1387	4.9	1	21		113	0,8600		0,0,4300	no	missense	LTN1	NM_015565.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	463/1813	30341850	1,13005	2203	4300	6503	29263721	SO:0001583	missense	26046			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1249C>T	21.37:g.30341850G>A	ENSP00000354977:p.Arg417Cys		29263721	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	G	17.10	3.302471	0.60195	2.27E-4	0.0	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.66815	3.56;3.56;-0.23	4.91	4.91	0.64330	Armadillo-type fold (1);	0.117788	0.56097	D	0.000030	T	0.58133	0.2101	L	0.49126	1.545	0.80722	D	1	B	0.33135	0.399	B	0.23275	0.045	T	0.59674	-0.7410	10	0.39692	T	0.17	.	15.4727	0.75453	0.0:0.0:1.0:0.0	.	417	O94822	LTN1_HUMAN	C	463;417;419;463	ENSP00000373846:R463C;ENSP00000354977:R417C;ENSP00000373847:R463C	ENSP00000354977:R417C	R	-	1	0	LTN1	29263721	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	3.225000	0.51246	2.721000	0.93114	0.655000	0.94253	CGT		0.363	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		A	30341850	G	A	30341850	3	1	61	1	0	0	0	0	1	0	0	0	13492	1145	40	1	4139	1	RNF160	21	30341850	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8959	30341850	17788045	11738	19723										
USP16	10694	broad.mit.edu	37	chr21	30426503	30426503	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctattttatgagagaataCtgtaataatatcaaaagcac	5	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30426503C>A	ENST00000286788.4	-	0	2005				USP16_ENST00000399975.3_Missense_Mutation_p.L822M|USP16_ENST00000334352.4_Missense_Mutation_p.L823M|USP16_ENST00000535828.1_Missense_Mutation_p.L452M|CCT8_ENST00000470450.1_5'Flank|USP16_ENST00000399976.2_Missense_Mutation_p.L823M	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)						'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)	p.L823M(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						TGAGAGAATACTGTAATAATA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	21											47	47	47					21																	30426503		2203	4300	6503	29348374	SO:0001628	intergenic_variant	10600			Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"Heat Shock Proteins / Chaperonins"	1623	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 112"	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595		21.37:g.30426503C>A			29348374	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.011207	0.35511	.	.	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352;ENST00000535828	T;T;T;T	0.55413	2.57;2.56;2.56;0.52	5.05	0.0295	0.14163	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (1);	0.164922	0.41294	D	0.000920	T	0.65502	0.2697	M	0.75777	2.31	0.41614	D	0.988924	D;D;D;D	0.89917	0.995;1.0;1.0;1.0	D;D;D;D	0.91635	0.917;0.999;0.991;0.987	T	0.63310	-0.6666	10	0.72032	D	0.01	.	6.9802	0.24698	0.0:0.6226:0.1143:0.2631	.	452;808;822;823	B4DUS4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;.;UBP16_HUMAN	M	822;823;823;452	ENSP00000382857:L822M;ENSP00000382858:L823M;ENSP00000334808:L823M;ENSP00000442855:L452M	ENSP00000334808:L823M	L	+	1	2	USP16	29348374	0.996000	0.38824	0.442000	0.26870	0.420000	0.31355	1.222000	0.32515	-0.090000	0.12462	-0.263000	0.10527	CTG		0.338	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			A	30426503	C	A	30426503	1	1	61	0	1	0	0	0	0	0	0	0	17087	564	20	2		2	USP16	21	30426503	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	84653	30426503	17703392	11739	19724										
BACH1	571	broad.mit.edu	37	chr21	30698986	30698986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgatgttaaaatgtgacGaaagtaaattagcaatggaa	11	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30698986G>A	ENST00000399921.1	+	3	1084	c.841G>A	c.(841-843)Gaa>Aaa	p.E281K	BACH1_ENST00000286800.3_Missense_Mutation_p.E281K	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E281K(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						AAAATGTGACGAAAGTAAATT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	21											69	69	69					21																	30698986		2203	4300	6503	29620857	SO:0001583	missense	571			AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.841G>A	21.37:g.30698986G>A	ENSP00000382805:p.Glu281Lys		29620857	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	CCDS13585.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.291368	0.40494	.	.	ENSG00000156273	ENST00000286800;ENST00000399921	T;T	0.71698	-0.59;-0.59	5.65	5.65	0.86999	.	0.332804	0.33253	N	0.005109	T	0.48750	0.1517	L	0.27053	0.805	0.30854	N	0.734309	P	0.41710	0.76	B	0.22152	0.038	T	0.54925	-0.8220	10	0.15066	T	0.55	-10.8092	14.091	0.64990	0.071:0.0:0.929:0.0	.	281	O14867	BACH1_HUMAN	K	281	ENSP00000286800:E281K;ENSP00000382805:E281K	ENSP00000286800:E281K	E	+	1	0	BACH1	29620857	0.975000	0.34042	0.438000	0.26821	0.581000	0.36288	2.559000	0.45888	2.941000	0.99782	0.655000	0.94253	GAA		0.428	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		A	30698986	G	A	30698986	3	1	61	1	0	0	0	0	1	0	0	0	1284	1059	37	1	847	1	BACH1	21	30698986	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272483	30698986	17430909	11740	19725										
BACH1	571	broad.mit.edu	37	chr21	30701851	30701851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acggataatttcactgtctcGaaatgattttcagtccttgt	7	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:30701851G>A	ENST00000399921.1	+	4	1856	c.1613G>A	c.(1612-1614)cGa>cAa	p.R538Q	BACH1_ENST00000286800.3_Missense_Mutation_p.R538Q	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R538Q(2)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						TCACTGTCTCGAAATGATTTT	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	21											75	72	73					21																	30701851		2203	4299	6502	29623722	SO:0001583	missense	571			AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1613G>A	21.37:g.30701851G>A	ENSP00000382805:p.Arg538Gln		29623722	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	CCDS13585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.582710|5.582710	0.96578|0.96578	.|.	.|.	ENSG00000156273|ENSG00000156273	ENST00000551628|ENST00000286800;ENST00000399921	.|D;D	.|0.91945	.|-2.94;-2.94	5.43|5.43	5.43|5.43	0.79202|0.79202	.|Eukaryotic transcription factor, Skn-1-like, DNA-binding (2);	.|0.000000	.|0.64402	.|D	.|0.000008	D|D	0.95456|0.95456	0.8524|0.8524	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.74023	.|0.982	D|D	0.95612|0.95612	0.8673|0.8673	5|10	.|0.72032	.|D	.|0.01	-13.3532|-13.3532	19.2326|19.2326	0.93846|0.93846	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|538	.|O14867	.|BACH1_HUMAN	K|Q	32|538	.|ENSP00000286800:R538Q;ENSP00000382805:R538Q	.|ENSP00000286800:R538Q	E|R	+|+	1|2	0|0	BACH1|BACH1	29623722|29623722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.814000|9.814000	0.99346|0.99346	2.553000|2.553000	0.86117|0.86117	0.585000|0.585000	0.79938|0.79938	GAA|CGA		0.318	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		A	30701851	G	A	30701851	3	1	61	1	0	0	0	0	1	0	0	0	1284	1058	37	1	1623	1	BACH1	21	30701851	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2865	30701851	17428044	11741	19726										
KRTAP23-1	337963	broad.mit.edu	37	chr21	31720883	31720883	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcacaggtagccctcacaGgaatgggaggagaagtttcc	13	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:31720883G>T	ENST00000334160.4	-	1	41	c.42C>A	c.(40-42)tcC>tcA	p.S14S		NM_181624.1	NP_853655.1	A1A580	KR231_HUMAN	keratin associated protein 23-1	14						intermediate filament (GO:0005882)		p.S14S(1)		large_intestine(1)|lung(4)|prostate(1)	6						AGCCCTCACAGGAATGGGAGG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	21											169	129	143					21																	31720883		2203	4300	6503	30642754	SO:0001819	synonymous_variant	337963			AP001708	CCDS33533.1	21q22.1	2008-05-21			ENSG00000186980	ENSG00000186980		"Keratin associated proteins"	18928	protein-coding gene	gene with protein product						12359730	Standard	NM_181624		Approved	KAP23.1	uc002yny.1	A1A580	OTTHUMG00000057792	ENST00000334160.4:c.42C>A	21.37:g.31720883G>T			30642754		Silent	SNP	ENST00000334160.4	37	CCDS33533.1																																																																																				0.552	KRTAP23-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128244.4			T	31720883	G	T	31720883	2	4	61	1	0	0	0	0	0	0	0	1	8563	987	35	2		2	KRTAP23-1	21	31720883	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1019032	31720883	16409012	11742	19727										
KRTAP13-4	284827	broad.mit.edu	37	chr21	31802974	31802974	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttttccttccctgagttaCggatccagattctgctaccc	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:31802974C>T	ENST00000334068.2	+	1	403	c.381C>T	c.(379-381)taC>taT	p.Y127Y		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	127						intermediate filament (GO:0005882)		p.Y127Y(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CCCTGAGTTACGGATCCAGAT	0.498																																					NSCLC(196;2401 3038 18004 35753)											1	Substitution - coding silent(1)	large_intestine(1)	21											106	93	97					21																	31802974		2203	4300	6503	30724845	SO:0001819	synonymous_variant	284827			AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"Keratin associated proteins"	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.381C>T	21.37:g.31802974C>T			30724845	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																				0.498	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			T	31802974	C	T	31802974	2	4	61	1	0	0	0	0	0	0	0	1	8546	547	19	1		1	KRTAP13-4	21	31802974	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	82091	31802974	16326921	11743	19728										
KRTAP6-2	337967	broad.mit.edu	37	chr21	31971175	31971175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtcgccgtagtagtttcCgtagtagctgccgcacatcg	12	11	0	0	rs199532937		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:31971175C>T	ENST00000334897.3	-	1	44	c.19G>A	c.(19-21)Gga>Aga	p.G7R	KRTAP22-1_ENST00000334680.2_5'Flank	NM_181604.1	NP_853635.1	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	7						intermediate filament (GO:0005882)		p.G7R(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11						TAGTAGTTTCCGTAGTAGCTG	0.522													C|||	1	0.000199681	0	0	5008	,	,		18364	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21											202	167	179					21																	31971175		2203	4300	6503	30893046	SO:0001583	missense	337967			AP001708	CCDS13600.1	21q22.1	2011-02-10			ENSG00000186930	ENSG00000186930		"Keratin associated proteins"	18932	protein-coding gene	gene with protein product						12359730	Standard	NM_181604		Approved	KAP6.2	uc011adc.2	Q3LI66	OTTHUMG00000057794	ENST00000334897.3:c.19G>A	21.37:g.31971175C>T	ENSP00000334560:p.Gly7Arg		30893046		Missense_Mutation	SNP	ENST00000334897.3	37	CCDS13600.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	10.21	1.286253	0.23478	.	.	ENSG00000186930	ENST00000334897	T	0.09538	2.97	4.47	0.564	0.17302	.	0.000000	0.38164	U	0.001792	T	0.06188	0.0160	.	.	.	0.25362	N	0.988776	P	0.43352	0.804	B	0.37144	0.242	T	0.31280	-0.9949	9	0.87932	D	0	.	1.4449	0.02362	0.1748:0.4664:0.1694:0.1895	.	7	Q3LI66	KRA62_HUMAN	R	7	ENSP00000334560:G7R	ENSP00000334560:G7R	G	-	1	0	KRTAP6-2	30893046	0.851000	0.29673	0.929000	0.37066	0.734000	0.41952	0.238000	0.18004	0.100000	0.17581	0.650000	0.86243	GGA		0.522	KRTAP6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128246.3			T	31971175	C	T	31971175	3	4	61	1	0	0	0	0	1	0	0	0	8592	661	23	1	172	1	KRTAP6-2	21	31971175	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168201	31971175	16158720	11744	19729										
KRTAP8-1	337879	broad.mit.edu	37	chr21	32185526	32185526	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagacagccccggggaagtTgtcgcagagcatggtgtcgg	17	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:32185526T>A	ENST00000329621.4	-	1	44	c.13A>T	c.(13-15)Aac>Tac	p.N5Y		NM_175857.3	NP_787053.1	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1	5						intermediate filament (GO:0005882)		p.N5Y(1)		central_nervous_system(1)|large_intestine(1)|lung(4)	6						CCGGGGAAGTTGTCGCAGAGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	21											77	67	71					21																	32185526		2203	4300	6503	31107397	SO:0001583	missense	337879			AJ457064	CCDS13607.1	21q22.1	2006-03-13			ENSG00000183640	ENSG00000183640		"Keratin associated proteins"	18935	protein-coding gene	gene with protein product						12359730	Standard	NM_175857		Approved	KAP8.1	uc002you.3	Q8IUC2	OTTHUMG00000057771	ENST00000329621.4:c.13A>T	21.37:g.32185526T>A	ENSP00000332805:p.Asn5Tyr		31107397	Q3LI57	Missense_Mutation	SNP	ENST00000329621.4	37	CCDS13607.1	.	.	.	.	.	.	.	.	.	.	T	0.661	-0.805694	0.02819	.	.	ENSG00000183640	ENST00000329621	.	.	.	4.36	0.552	0.17230	.	1.358030	0.04605	N	0.399143	T	0.30978	0.0782	.	.	.	0.09310	N	1	B	0.27286	0.174	B	0.30646	0.118	T	0.30707	-0.9969	8	0.51188	T	0.08	-6.0673	2.3992	0.04397	0.4261:0.1438:0.0:0.4301	.	5	Q8IUC2	KRA81_HUMAN	Y	5	.	ENSP00000332805:N5Y	N	-	1	0	KRTAP8-1	31107397	0.022000	0.18835	0.003000	0.11579	0.008000	0.06430	-0.184000	0.09698	0.085000	0.17107	0.455000	0.32223	AAC		0.552	KRTAP8-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128223.1			A	32185526	T	A	32185526	3	1	61	1	0	0	0	0	1	0	0	0	8594	1812	63	5	182	5	KRTAP8-1	21	32185526	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	214351	32185526	15944369	11745	19730										
TIAM1	7074	broad.mit.edu	37	chr21	32508292	32508292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctttttccacttgcccagcGaggccggcgggttcagccag	12	15	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:32508292G>A	ENST00000286827.3	-	24	4313	c.3842C>T	c.(3841-3843)tCg>tTg	p.S1281L	TIAM1_ENST00000541036.1_Missense_Mutation_p.S1221L	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1281	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S1281L(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CTTGCCCAGCGAGGCCGGCGG	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	21											98	95	96					21																	32508292		2203	4300	6503	31430163	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3842C>T	21.37:g.32508292G>A	ENSP00000286827:p.Ser1281Leu		31430163	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372194	0.82573	.	.	ENSG00000156299	ENST00000286827;ENST00000541036	T;T	0.49432	0.78;0.81	5.49	5.49	0.81192	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.51736	0.1692	M	0.72894	2.215	0.80722	D	1	D;D;D	0.63046	0.992;0.987;0.987	B;B;B	0.41440	0.357;0.195;0.195	T	0.60475	-0.7256	10	0.54805	T	0.06	.	19.3968	0.94610	0.0:0.0:1.0:0.0	.	1221;1221;1281	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	L	1281;1221	ENSP00000286827:S1281L;ENSP00000441570:S1221L	ENSP00000286827:S1281L	S	-	2	0	TIAM1	31430163	1.000000	0.71417	0.934000	0.37439	0.759000	0.43091	9.810000	0.99221	2.565000	0.86533	0.655000	0.94253	TCG		0.502	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32508292	G	A	32508292	3	1	61	1	0	0	0	0	1	0	0	0	15929	1059	37	1	957	1	TIAM1	21	32508292	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	322766	32508292	15621603	11746	19731										
TIAM1	7074	broad.mit.edu	37	chr21	32582480	32582480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atactcgtggacccaaatgtCgcagtcagggttgtgctggt	13	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:32582480C>T	ENST00000286827.3	-	12	2740	c.2269G>A	c.(2269-2271)Gac>Aac	p.D757N	TIAM1_ENST00000469412.1_5'Flank|TIAM1_ENST00000541036.1_Missense_Mutation_p.D732N	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	757					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D757N(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						ACCCAAATGTCGCAGTCAGGG	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	21											139	120	126					21																	32582480		2203	4300	6503	31504351	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.2269G>A	21.37:g.32582480C>T	ENSP00000286827:p.Asp757Asn		31504351	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183263	0.94885	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.39997	1.31;1.05	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.55178	0.1904	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;P	0.63703	0.917;0.829;0.829	T	0.54050	-0.8351	10	0.62326	D	0.03	.	20.3324	0.98724	0.0:1.0:0.0:0.0	.	732;732;757	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	N	757;598;732	ENSP00000286827:D757N;ENSP00000441570:D732N	ENSP00000286827:D757N	D	-	1	0	TIAM1	31504351	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.465000	0.80898	2.799000	0.96334	0.650000	0.86243	GAC		0.532	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32582480	C	T	32582480	3	4	61	1	0	0	0	0	1	0	0	0	15929	884	31	1	2578	1	TIAM1	21	32582480	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	74188	32582480	15547415	11747	19732										
TIAM1	7074	broad.mit.edu	37	chr21	32617957	32617957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagacctgccgtcgctctcGtagaaaaatagcgtgcatcc	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:32617957G>A	ENST00000286827.3	-	7	1902	c.1431C>T	c.(1429-1431)taC>taT	p.Y477Y	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Silent_p.Y477Y	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	477	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Y477Y(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CGTCGCTCTCGTAGAAAAATA	0.527																																																2	Substitution - coding silent(2)	large_intestine(2)	21											63	55	58					21																	32617957		2203	4300	6503	31539828	SO:0001819	synonymous_variant	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1431C>T	21.37:g.32617957G>A			31539828	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.527	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32617957	G	A	32617957	2	1	61	1	0	0	0	0	0	0	0	1	15929	1140	40	1		1	TIAM1	21	32617957	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35477	32617957	15511938	11748	19733										
TIAM1	7074	broad.mit.edu	37	chr21	32638995	32638995	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtgtaagacacaggtctCaagcccatgtccactcggtc	9	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:32638995C>A	ENST00000286827.3	-	5	765	c.294G>T	c.(292-294)ttG>ttT	p.L98F	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.L98F	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	98					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L98F(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						ACACAGGTCTCAAGCCCATGT	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	21											81	75	77					21																	32638995		2203	4300	6503	31560866	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.294G>T	21.37:g.32638995C>A	ENSP00000286827:p.Leu98Phe		31560866	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443115	0.83993	.	.	ENSG00000156299	ENST00000286827;ENST00000541036;ENST00000455508	T;T	0.57273	0.46;0.41	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000002	T	0.68723	0.3032	L	0.53249	1.67	0.80722	D	1	D;D;D	0.69078	0.997;0.995;0.995	D;P;P	0.65987	0.94;0.873;0.873	T	0.71347	-0.4620	10	0.87932	D	0	.	19.0706	0.93134	0.0:1.0:0.0:0.0	.	98;98;98	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	F	98	ENSP00000286827:L98F;ENSP00000441570:L98F	ENSP00000286827:L98F	L	-	3	2	TIAM1	31560866	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.851000	0.48302	2.505000	0.84491	0.591000	0.81541	TTG		0.577	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32638995	C	A	32638995	3	1	61	1	0	0	0	0	1	0	0	0	15929	825	29	2	4581	2	TIAM1	21	32638995	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	21038	32638995	15490900	11749	19734										
HUNK	30811	broad.mit.edu	37	chr21	33346966	33346966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacactgtgctctccaaccgCgcctgccacatcctggccat	7	18	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:33346966C>T	ENST00000270112.2	+	7	1470	c.1110C>T	c.(1108-1110)cgC>cgT	p.R370R	HUNK_ENST00000465574.1_3'UTR	NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	370					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R370R(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						TCTCCAACCGCGCCTGCCACA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	21											95	85	88					21																	33346966		2203	4300	6503	32268837	SO:0001819	synonymous_variant	30811			AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1110C>T	21.37:g.33346966C>T			32268837		Silent	SNP	ENST00000270112.2	37	CCDS13610.1																																																																																				0.542	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33346966	C	T	33346966	2	4	61	1	0	0	0	0	0	0	0	1	7479	755	27	1		1	HUNK	21	33346966	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	707971	33346966	14782929	11750	19735										
C21orf63	59271	broad.mit.edu	37	chr21	33840103	33840103	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctgcgacctacggcaggaGgacccaggaaagggacatct	13	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:33840103G>T	ENST00000300255.2	+	4	1054	c.581G>T	c.(580-582)aGg>aTg	p.R194M	EVA1C_ENST00000401402.3_Missense_Mutation_p.R194M|EVA1C_ENST00000382699.3_Missense_Mutation_p.R194M	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	194	SUEL-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.R194M(1)									TACGGCAGGAGGACCCAGGAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	21											81	65	70					21																	33840103		2203	4300	6503	32761974	SO:0001583	missense	59271			AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.581G>T	21.37:g.33840103G>T	ENSP00000300255:p.Arg194Met		32761974	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479122	0.44044	.	.	ENSG00000166979	ENST00000300255;ENST00000401402;ENST00000382699;ENST00000412833	T;T;T;T	0.18174	2.23;3.08;2.23;2.23	5.61	-0.224	0.13115	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.571397	0.20776	N	0.085895	T	0.19765	0.0475	L	0.58583	1.82	0.27810	N	0.942185	P;P;P	0.45348	0.854;0.808;0.856	P;P;B	0.51550	0.673;0.663;0.423	T	0.06427	-1.0827	10	0.34782	T	0.22	-5.9658	3.0333	0.06113	0.2475:0.2286:0.4295:0.0944	.	194;194;194	A6ND58;P58658;B5MC74	.;CU063_HUMAN;.	M	194;194;194;99	ENSP00000300255:R194M;ENSP00000384594:R194M;ENSP00000372146:R194M;ENSP00000389269:R99M	ENSP00000300255:R194M	R	+	2	0	C21orf63	32761974	0.881000	0.30235	0.999000	0.59377	0.921000	0.55340	0.308000	0.19314	0.276000	0.22118	0.650000	0.86243	AGG		0.512	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		T	33840103	G	T	33840103	3	4	61	1	0	0	0	0	1	0	0	0	2137	1000	35	2	595	2	C21orf63	21	33840103	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	493137	33840103	14289792	11751	19736										
C21orf63	59271	broad.mit.edu	37	chr21	33876261	33876261	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttcgacccaagcggatcGaaggttctgaggaaagatgg	13	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:33876261G>A	ENST00000300255.2	+	7	1358	c.885G>A	c.(883-885)tcG>tcA	p.S295S	EVA1C_ENST00000401402.3_Silent_p.S247S|EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000382699.3_Silent_p.S292S	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	295						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.S295S(1)									CAAGCGGATCGAAGGTTCTGA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	21											140	133	136					21																	33876261		2203	4300	6503	32798132	SO:0001819	synonymous_variant	59271			AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.885G>A	21.37:g.33876261G>A			32798132	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																				0.423	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		A	33876261	G	A	33876261	2	1	61	1	0	0	0	0	0	0	0	1	2137	1045	37	1		1	C21orf63	21	33876261	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36158	33876261	14253634	11752	19737										
SYNJ1	8867	broad.mit.edu	37	chr21	34050985	34050985	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagtagttaaaagtgctcGagctttgtcagctaaatcac	8	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34050985G>A	ENST00000322229.7	-	11	1479	c.1480C>T	c.(1480-1482)Cga>Tga	p.R494*	SYNJ1_ENST00000357345.3_Nonsense_Mutation_p.R494*|SYNJ1_ENST00000433931.2_Nonsense_Mutation_p.R533*|SYNJ1_ENST00000382499.2_Nonsense_Mutation_p.R533*|SYNJ1_ENST00000382491.3_Nonsense_Mutation_p.R497*			O43426	SYNJ1_HUMAN	synaptojanin 1	494					cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.R494*(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						AAAAGTGCTCGAGCTTTGTCA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											89	84	86					21																	34050985		2203	4300	6503	32972856	SO:0001587	stop_gained	8867			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1480C>T	21.37:g.34050985G>A	ENSP00000322234:p.Arg494*		32972856	O43425|O94984|Q4KMR1	Nonsense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	G	37	6.327611	0.97476	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236	.	.	.	5.99	4.15	0.48705	.	0.058295	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2515	0.66023	0.0:0.0:0.6088:0.3912	.	.	.	.	X	497;494;533;533;494;497	.	ENSP00000322234:R494X	R	-	1	2	SYNJ1	32972856	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.570000	0.67398	0.828000	0.34709	-0.127000	0.14921	CGA		0.353	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34050985	G	A	34050985	4	1	61	1	0	0	0	0	0	1	0	0	15491	1066	37	1	3350	1	SYNJ1	21	34050985	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	174724	34050985	14078910	11753	19738										
SYNJ1	8867	broad.mit.edu	37	chr21	34072370	34072370	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcttgaatttttccaacaGacatacatccagtgactagg	6	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34072370G>T	ENST00000322229.7	-	3	256	c.257C>A	c.(256-258)tCt>tAt	p.S86Y	SYNJ1_ENST00000357345.3_Missense_Mutation_p.S86Y|SYNJ1_ENST00000433931.2_Missense_Mutation_p.S125Y|SYNJ1_ENST00000382499.2_Missense_Mutation_p.S125Y|SYNJ1_ENST00000382491.3_Missense_Mutation_p.S86Y			O43426	SYNJ1_HUMAN	synaptojanin 1	86					cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.S86Y(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TTTTCCAACAGACATACATCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	21											68	72	70					21																	34072370		2203	4300	6503	32994241	SO:0001583	missense	8867			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.257C>A	21.37:g.34072370G>T	ENSP00000322234:p.Ser86Tyr		32994241	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821844	0.90873	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236;ENST00000456084	T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.6	5.6	0.85130	Synaptojanin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79003	0.4373	M	0.79805	2.47	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.997;1.0;0.998;0.998	T	0.81120	-0.1077	10	0.87932	D	0	.	19.6209	0.95654	0.0:0.0:1.0:0.0	.	86;125;86;86;86	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	Y	86;86;125;125;86;86;86	ENSP00000371931:S86Y;ENSP00000349903:S86Y;ENSP00000371939:S125Y;ENSP00000409667:S125Y;ENSP00000322234:S86Y;ENSP00000413649:S86Y;ENSP00000412707:S86Y	ENSP00000322234:S86Y	S	-	2	0	SYNJ1	32994241	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.328000	0.96403	2.646000	0.89796	0.585000	0.79938	TCT		0.373	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34072370	G	T	34072370	3	4	61	1	0	0	0	0	1	0	0	0	15491	942	33	2	4614	2	SYNJ1	21	34072370	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21385	34072370	14057525	11754	19739										
GCFC1	94104	broad.mit.edu	37	chr21	34107272	34107272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcatagatctattttccttCgatcaaagacttaaattctt	3	9	4	2	rs143512881		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34107272C>T	ENST00000331923.4	-	18	2932	c.2743G>A	c.(2743-2745)Gaa>Aaa	p.E915K	PAXBP1-AS1_ENST00000440052.1_RNA|PAXBP1-AS1_ENST00000455170.1_RNA|PAXBP1-AS1_ENST00000458479.1_RNA	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	915					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E915K(1)									TATTTTCCTTCGATCAAAGAC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	21											88	81	84					21																	34107272		2202	4299	6501	33029143	SO:0001583	missense	94104			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.2743G>A	21.37:g.34107272C>T	ENSP00000328992:p.Glu915Lys		33029143	D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.652357	0.67472	.	.	ENSG00000159086	ENST00000331923	T	0.26223	1.75	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.37839	0.1018	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.71184	0.972;0.691	T	0.03453	-1.1035	10	0.14252	T	0.57	-28.1019	19.072	0.93143	0.0:1.0:0.0:0.0	.	915;424	Q9Y5B6;B3KSC0	GCFC1_HUMAN;.	K	915	ENSP00000328992:E915K	ENSP00000328992:E915K	E	-	1	0	GCFC1	33029143	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	6.059000	0.71133	2.688000	0.91661	0.551000	0.68910	GAA		0.318	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		T	34107272	C	T	34107272	3	4	61	1	0	0	0	0	1	0	0	0	6309	893	31	1	14	1	GCFC1	21	34107272	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34902	34107272	14022623	11755	19740										
GCFC1	94104	broad.mit.edu	37	chr21	34123228	34123228	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccaaataaatgtctaacCtttttccagattgaaattag	4	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34123228C>T	ENST00000331923.4	-	10	1912	c.1723G>A	c.(1723-1725)Gat>Aat	p.D575N	PAXBP1_ENST00000290178.4_Splice_Site_p.D575N	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	575					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D575N(1)									AATGTCTAACCTTTTTCCAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	21											86	87	87					21																	34123228		2203	4300	6503	33045099	SO:0001630	splice_region_variant	94104			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1723+1G>A	21.37:g.34123228C>T			33045099	D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	C	34	5.370176	0.95900	.	.	ENSG00000159086	ENST00000331923;ENST00000290178	T;T	0.36340	1.66;1.26	5.46	5.46	0.80206	.	0.094831	0.64402	D	0.000001	T	0.51024	0.1650	M	0.72118	2.19	0.80722	D	1	D;P;P	0.56035	0.974;0.956;0.915	P;P;B	0.50659	0.647;0.63;0.321	T	0.50734	-0.8793	9	.	.	.	-22.1055	18.9016	0.92444	0.0:1.0:0.0:0.0	.	575;575;84	Q9Y5B6-2;Q9Y5B6;B3KSC0	.;GCFC1_HUMAN;.	N	575	ENSP00000328992:D575N;ENSP00000290178:D575N	.	D	-	1	0	GCFC1	33045099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.336000	0.79245	2.574000	0.86865	0.557000	0.71058	GAT		0.358	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	Missense_Mutation	T	34123228	C	T	34123228	5	4	61	1	0	0	0	0	0	0	1	0	6309	695	24	3	1184	3	GCFC1	21	34123228	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15956	34123228	14006667	11756	19741										
GCFC1	94104	broad.mit.edu	37	chr21	34134471	34134471	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaaaactatccggcgtttCtcatcgtcatcttcatcatc	5	12	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34134471C>T	ENST00000331923.4	-	4	996	c.807G>A	c.(805-807)gaG>gaA	p.E269E	PAXBP1_ENST00000290178.4_Silent_p.E269E|PAXBP1_ENST00000472588.1_5'UTR	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	269					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E269E(1)									TCCGGCGTTTCTCATCGTCAT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	21											130	131	131					21																	34134471		2203	4300	6503	33056342	SO:0001819	synonymous_variant	94104			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.807G>A	21.37:g.34134471C>T			33056342	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																				0.383	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		T	34134471	C	T	34134471	2	4	61	1	0	0	0	0	0	0	0	1	6309	912	32	3		3	GCFC1	21	34134471	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11243	34134471	13995424	11757	19742										
IFNAR2	3455	broad.mit.edu	37	chr21	34617284	34617284	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgaatcttgcactttcaaGatatcattgcgaaatttccg	7	8	3	2	rs9754221		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34617284G>T	ENST00000342136.4	+	4	452	c.126G>T	c.(124-126)aaG>aaT	p.K42N	IFNAR2_ENST00000420068.1_Intron|IFNAR2_ENST00000382241.3_Missense_Mutation_p.K42N|AP000295.9_ENST00000433395.2_5'Flank|IFNAR2_ENST00000342101.3_Missense_Mutation_p.K42N|IFNAR2_ENST00000404220.3_Missense_Mutation_p.K42N|IFNAR2_ENST00000413881.1_5'UTR|IFNAR2_ENST00000382264.3_Missense_Mutation_p.K42N			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	42					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)	p.K42N(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	GCACTTTCAAGATATCATTGC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	21											160	154	156					21																	34617284		2202	4298	6500	33539154	SO:0001583	missense	3455				CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"Interferons"	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.126G>T	21.37:g.34617284G>T	ENSP00000343957:p.Lys42Asn		33539154	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Missense_Mutation	SNP	ENST00000342136.4	37	CCDS13621.1	.	.	.	.	.	.	.	.	.	.	G	7.187	0.590751	0.13812	.	.	ENSG00000159110	ENST00000382264;ENST00000404220;ENST00000382241;ENST00000342136;ENST00000342101;ENST00000447980	T;T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82;-0.82	4.81	-3.22	0.05125	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.035900	0.07553	N	0.915813	T	0.52885	0.1762	L	0.27053	0.805	0.09310	N	1	B;B;B	0.23854	0.092;0.049;0.04	B;B;B	0.27887	0.084;0.08;0.055	T	0.35798	-0.9774	10	0.12430	T	0.62	.	1.9816	0.03427	0.2467:0.3856:0.2364:0.1312	.	42;42;42	P48551-3;P48551;P48551-2	.;INAR2_HUMAN;.	N	42;42;42;42;42;66	ENSP00000371699:K42N;ENSP00000384309:K42N;ENSP00000371676:K42N;ENSP00000343957:K42N;ENSP00000343289:K42N;ENSP00000402311:K66N	ENSP00000343289:K42N	K	+	3	2	IFNAR2	33539154	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.698000	0.05092	-0.994000	0.03463	-0.291000	0.09656	AAG		0.373	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1			T	34617284	G	T	34617284	3	4	61	1	0	0	0	0	1	0	0	0	7566	933	33	2	136	2	IFNAR2	21	34617284	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	482813	34617284	13512611	11758	19743										
IFNAR2	3455	broad.mit.edu	37	chr21	34632960	34632960	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtttttgatagcattggtCttgacaagcaccatagtgac	10	7	1	3	rs567371989		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34632960C>A	ENST00000342136.4	+	8	1094	c.768C>A	c.(766-768)gtC>gtA	p.V256V	IFNAR2_ENST00000382241.3_Silent_p.V256V|AP000295.9_ENST00000433395.2_Intron|IFNAR2_ENST00000342101.3_Intron|IFNAR2_ENST00000404220.3_Silent_p.V256V|IFNAR2_ENST00000413881.1_Intron|IFNAR2_ENST00000382264.3_Silent_p.V256V			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	256					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)	p.V256V(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	TAGCATTGGTCTTGACAAGCA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	21											136	138	137					21																	34632960		2203	4299	6502	33554830	SO:0001819	synonymous_variant	3455				CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"Interferons"	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.768C>A	21.37:g.34632960C>A			33554830	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Silent	SNP	ENST00000342136.4	37	CCDS13621.1																																																																																				0.323	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1			A	34632960	C	A	34632960	2	1	61	1	0	0	0	0	0	0	0	1	7566	900	32	2		2	IFNAR2	21	34632960	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	15676	34632960	13496935	11759	19744										
IL10RB	3588	broad.mit.edu	37	chr21	34655474	34655474	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacttattgtgttcaagttCgagggtttcttcctgatcgg	10	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34655474C>T	ENST00000290200.2	+	5	682	c.574C>T	c.(574-576)Cga>Tga	p.R192*	AP000295.9_ENST00000433395.2_Silent_p.F319F	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	192	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R192*(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						TGTTCAAGTTCGAGGGTTTCT	0.463																																					Melanoma(67;315 1275 21667 21943 44564)											2	Substitution - Nonsense(2)	large_intestine(2)	21											150	131	137					21																	34655474		2203	4300	6503	33577344	SO:0001587	stop_gained	3588			U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"Interleukins and interleukin receptors", "CD molecules"	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.574C>T	21.37:g.34655474C>T	ENSP00000290200:p.Arg192*		33577344	Q9BUU4	Nonsense_Mutation	SNP	ENST00000290200.2	37	CCDS13623.1	.	.	.	.	.	.	.	.	.	.	C	35	5.585763	0.96578	.	.	ENSG00000243646	ENST00000290200;ENST00000539894	.	.	.	5.39	5.39	0.77823	.	0.644606	0.16041	N	0.232422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-0.3172	14.674	0.68964	0.0:1.0:0.0:0.0	.	.	.	.	X	192	.	ENSP00000290200:R192X	R	+	1	2	IL10RB	33577344	0.972000	0.33761	0.970000	0.41538	0.987000	0.75469	4.136000	0.58004	2.526000	0.85167	0.561000	0.74099	CGA		0.463	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3			T	34655474	C	T	34655474	4	4	61	1	0	0	0	0	0	1	0	0	7642	876	31	1	592	1	IL10RB	21	34655474	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22514	34655474	13474421	11760	19745										
IFNGR2	3460	broad.mit.edu	37	chr21	34805069	34805069	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctccgtgggaacattttCgttgctgtcggtgctggcag	14	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34805069C>A	ENST00000290219.6	+	6	1418	c.770C>A	c.(769-771)tCg>tAg	p.S257*	IFNGR2_ENST00000381995.1_Nonsense_Mutation_p.S276*|IFNGR2_ENST00000405436.1_Nonsense_Mutation_p.S178*	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	257					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)	p.S257*(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	GGAACATTTTCGTTGCTGTCG	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											146	137	140					21																	34805069		2203	4300	6503	33726939	SO:0001587	stop_gained	3460				CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"Interferons", "Fibronectin type III domain containing"	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.770C>A	21.37:g.34805069C>A	ENSP00000290219:p.Ser257*		33726939	Q9BTL5	Nonsense_Mutation	SNP	ENST00000290219.6	37	CCDS33544.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.7|26.7	4.765975|4.765975	0.90020|0.90020	.|.	.|.	ENSG00000159128|ENSG00000159128	ENST00000421802|ENST00000290219;ENST00000381995;ENST00000405436	.|.	.|.	.|.	5.53|5.53	-0.485|-0.485	0.12067|0.12067	.|.	.|2.142320	.|0.01825	.|N	.|0.034334	T|.	0.20700|.	0.0498|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.14868|.	-1.0457|.	4|.	.|0.12103	.|T	.|0.63	-22.2222|-22.2222	8.9566|8.9566	0.35820|0.35820	0.0:0.4158:0.0:0.5842|0.0:0.4158:0.0:0.5842	.|.	.|.	.|.	.|.	S|X	23|257;276;178	.|.	.|ENSP00000290219:S257X	R|S	+|+	1|2	0|0	IFNGR2|IFNGR2	33726939|33726939	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.160000|0.160000	0.22226|0.22226	-0.002000|-0.002000	0.12924|0.12924	-0.019000|-0.019000	0.14055|0.14055	0.563000|0.563000	0.77884|0.77884	CGT|TCG		0.473	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1			A	34805069	C	A	34805069	4	1	61	1	0	0	0	0	0	1	0	0	7571	893	31	2	792	2	IFNGR2	21	34805069	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	149595	34805069	13324826	11761	19746										
SON	6651	broad.mit.edu	37	chr21	34921915	34921915	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagaagaaagaaaaggaAaaaaaatataaaagacagcc	7	3	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34921915A>C	ENST00000356577.4	+	3	853	c.378A>C	c.(376-378)gaA>gaC	p.E126D	SON_ENST00000300278.4_Missense_Mutation_p.E126D|SON_ENST00000290239.6_Missense_Mutation_p.E126D|SON_ENST00000381679.4_Missense_Mutation_p.E126D|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	126				E -> K (in Ref. 7; BAB14985). {ECO:0000305}.	cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E126D(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						aagaaaaggaaaaaaaaTATA	0.299											OREG0003562	type=REGULATORY REGION|Gene=AK091233|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				2	Substitution - Missense(2)	large_intestine(2)	21											23	26	25					21																	34921915		2192	4296	6488	33843785	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.378A>C	21.37:g.34921915A>C	ENSP00000348984:p.Glu126Asp	851	33843785	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464359	0.63513	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.77	0.535	0.17133	.	0.106418	0.41938	D	0.000791	T	0.22166	0.0534	L	0.27053	0.805	0.22521	N	0.999026	D;D;D	0.69078	0.995;0.997;0.997	D;D;D	0.78314	0.98;0.991;0.991	T	0.05733	-1.0867	10	0.41790	T	0.15	.	7.9612	0.30072	0.4419:0.0:0.5581:0.0	.	126;126;126	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	D	126	ENSP00000348984:E126D;ENSP00000290239:E126D;ENSP00000300278:E126D;ENSP00000371095:E126D	ENSP00000290239:E126D	E	+	3	2	SON	33843785	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	1.196000	0.32198	0.192000	0.20272	0.533000	0.62120	GAA		0.299	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34921915	A	C	34921915	3	2	61	1	0	0	0	0	1	0	0	0	14963	11	1	4	388	4	SON	21	34921915	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116846	34921915	13207980	11762	19747										
SON	6651	broad.mit.edu	37	chr21	34925830	34925830	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagtccttcaaccttctatGattgtttcagaaccatctgt	5	11	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34925830G>T	ENST00000356577.4	+	3	4768	c.4293G>T	c.(4291-4293)atG>atT	p.M1431I	SON_ENST00000300278.4_Missense_Mutation_p.M1431I|SON_ENST00000290239.6_Missense_Mutation_p.M1431I|SON_ENST00000381679.4_Missense_Mutation_p.M1431I|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1431					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.M1431I(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						AACCTTCTATGATTGTTTCAG	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	21											109	96	100					21																	34925830		2203	4300	6503	33847700	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4293G>T	21.37:g.34925830G>T	ENSP00000348984:p.Met1431Ile		33847700	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.824|5.824	0.336281|0.336281	0.11013|0.11013	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679|ENST00000436227	T;T;T;T|.	0.11821|.	2.95;2.93;2.92;2.74|.	5.19|5.19	3.37|3.37	0.38596|0.38596	.|.	0.854617|.	0.10417|.	N|.	0.677185|.	T|.	0.38665|.	0.1049|.	L|L	0.44542|0.44542	1.39|1.39	0.25969|0.25969	N|N	0.982526|0.982526	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.04013|.	0.001;0.0;0.001;0.001;0.001|.	T|.	0.22487|.	-1.0215|.	10|.	0.19147|.	T|.	0.46|.	.|.	8.0736|8.0736	0.30704|0.30704	0.0835:0.0:0.758:0.1585|0.0835:0.0:0.758:0.1585	.|.	1431;1431;1112;1431;1431|.	P18583-10;P18583;P18583-2;P18583-3;P18583-6|.	.;SON_HUMAN;.;.;.|.	I|L	1431|426	ENSP00000348984:M1431I;ENSP00000290239:M1431I;ENSP00000300278:M1431I;ENSP00000371095:M1431I|.	ENSP00000290239:M1431I|.	M|X	+|+	3|2	0|2	SON|SON	33847700|33847700	0.978000|0.978000	0.34361|0.34361	0.599000|0.599000	0.28851|0.28851	0.622000|0.622000	0.37654|0.37654	1.612000|1.612000	0.36889|0.36889	0.748000|0.748000	0.32831|0.32831	-0.182000|-0.182000	0.12963|0.12963	ATG|TGA		0.493	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34925830	G	T	34925830	3	4	61	1	0	0	0	0	1	0	0	0	14963	1290	45	2	4303	2	SON	21	34925830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3915	34925830	13204065	11763	19748										
SON	6651	broad.mit.edu	37	chr21	34927647	34927647	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctcccatccgtcgtaaaaGatccaggtcttctgaacgag	8	12	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34927647G>T	ENST00000356577.4	+	3	6585	c.6110G>T	c.(6109-6111)aGa>aTa	p.R2037I	SON_ENST00000300278.4_Missense_Mutation_p.R2037I|SON_ENST00000290239.6_Missense_Mutation_p.R2037I|SON_ENST00000381679.4_Missense_Mutation_p.R2037I|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2037	3 X tandem repeats of [ST]-P-[VLI]-R- [RL]-[RK]-[RF]-S-R.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R2037I(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CGTCGTAAAAGATCCAGGTCT	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	21											78	75	76					21																	34927647		2203	4300	6503	33849517	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6110G>T	21.37:g.34927647G>T	ENSP00000348984:p.Arg2037Ile		33849517	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.15|16.15	3.040804|3.040804	0.55003|0.55003	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679;ENST00000421541	.|T;T;T;T	.|0.24908	.|2.33;2.33;2.32;1.83	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.000000	.|0.49305	.|D	.|0.000159	T|T	0.47655|0.47655	0.1457|0.1457	L|L	0.49778|0.49778	1.585|1.585	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|0.999;0.999;1.0;1.0;1.0	.|D;D;D;D;D	.|0.85130	.|0.996;0.994;0.997;0.997;0.997	T|T	0.38045|0.38045	-0.9679|-0.9679	5|10	.|0.62326	.|D	.|0.03	.|.	18.0847|18.0847	0.89454|0.89454	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2037;2037;1718;2037;2037	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	Y|I	1032|2037;2037;2037;2037;98	.|ENSP00000348984:R2037I;ENSP00000290239:R2037I;ENSP00000300278:R2037I;ENSP00000371095:R2037I	.|ENSP00000290239:R2037I	D|R	+|+	1|2	0|0	SON|SON	33849517|33849517	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.920000|6.920000	0.75799|0.75799	2.628000|2.628000	0.89032|0.89032	0.650000|0.650000	0.86243|0.86243	GAT|AGA		0.423	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34927647	G	T	34927647	3	4	61	1	0	0	0	0	1	0	0	0	14963	942	33	2	6120	2	SON	21	34927647	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1817	34927647	13202248	11764	19749										
SON	6651	broad.mit.edu	37	chr21	34929576	34929576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccacctactatagaagagaAagttgctaaaaagtcaggag	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34929576A>G	ENST00000356577.4	+	4	6750	c.6275A>G	c.(6274-6276)aAa>aGa	p.K2092R	SON_ENST00000300278.4_Missense_Mutation_p.K2092R|SON_ENST00000290239.6_Missense_Mutation_p.K2092R|SON_ENST00000381679.4_Missense_Mutation_p.K2092R|SON_ENST00000381692.2_Missense_Mutation_p.K120R	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2092					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K2092R(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						ATAGAAGAGAAAGTTGCTAAA	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	21											63	60	61					21																	34929576		2203	4300	6503	33851446	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6275A>G	21.37:g.34929576A>G	ENSP00000348984:p.Lys2092Arg		33851446	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.26|14.26	2.483827|2.483827	0.44147|0.44147	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000381692;ENST00000300278;ENST00000381679;ENST00000421541	T|T;T;T;T	0.26518|0.20738	1.73|2.72;2.69;2.66;2.05	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.000000|0.000000	0.56097|0.56097	D|D	0.000022|0.000022	T|T	0.41971|0.41971	0.1182|0.1182	L|L	0.50333|0.50333	1.59|1.59	0.40805|0.40805	D|D	0.983377|0.983377	.|D;P;D;D;D;D	.|0.89917	.|1.0;0.948;0.997;0.998;0.998;0.998	.|D;B;D;D;D;D	.|0.85130	.|0.997;0.431;0.985;0.994;0.994;0.994	T|T	0.33497|0.33497	-0.9866|-0.9866	8|10	0.72032|0.72032	D|D	0.01|0.01	.|.	15.7499|15.7499	0.77976|0.77976	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2092;120;2092;1773;2092;2092	.|P18583-10;Q6ZRV7;P18583;P18583-2;P18583-3;P18583-6	.|.;.;SON_HUMAN;.;.;.	E|R	1087|2092;2092;120;2092;2092;153	ENSP00000400985:K1087E|ENSP00000348984:K2092R;ENSP00000290239:K2092R;ENSP00000300278:K2092R;ENSP00000371095:K2092R	ENSP00000400985:K1087E|ENSP00000290239:K2092R	K|K	+|+	1|2	0|0	SON|SON	33851446|33851446	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.184000|7.184000	0.77705|0.77705	2.188000|2.188000	0.69820|0.69820	0.533000|0.533000	0.62120|0.62120	AAG|AAA		0.413	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34929576	A	G	34929576	3	3	61	1	0	0	0	0	1	0	0	0	14963	14	1	4	6289	4	SON	21	34929576	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1929	34929576	13200319	11765	19750										
DONSON	29980	broad.mit.edu	37	chr21	34951865	34951865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcttcacattcacactccGtgccttcatgaaaatgtaaa	5	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34951865G>A	ENST00000303071.5	-	9	1420	c.1354C>T	c.(1354-1356)Cgg>Tgg	p.R452W	DONSON_ENST00000453626.1_Intron|DONSON_ENST00000432378.1_Intron|DONSON_ENST00000303113.6_Missense_Mutation_p.R438W	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	452					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.R452W(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						TTCACACTCCGTGCCTTCATG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	21											104	97	99					21																	34951865		2203	4300	6503	33873735	SO:0001583	missense	29980			AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.1354C>T	21.37:g.34951865G>A	ENSP00000307143:p.Arg452Trp		33873735	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Missense_Mutation	SNP	ENST00000303071.5	37	CCDS13632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.22|16.22	3.061039|3.061039	0.55432|0.55432	.|.	.|.	ENSG00000159147|ENSG00000159147	ENST00000303113;ENST00000303071|ENST00000440810	.|.	.|.	.|.	5.8|5.8	3.95|3.95	0.45737|0.45737	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77831|0.77831	0.4189|0.4189	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.79752|0.79752	-0.1671|-0.1671	9|5	0.72032|.	D|.	0.01|.	-14.1603|-14.1603	13.628|13.628	0.62178|0.62178	0.0:0.0:0.5927:0.4073|0.0:0.0:0.5927:0.4073	.|.	438;452|.	F8W8A5;Q9NYP3|.	.;DONS_HUMAN|.	W|M	438;452|223	.|.	ENSP00000307143:R452W|.	R|T	-|-	1|2	2|0	DONSON|DONSON	33873735|33873735	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.393000|0.393000	0.30537|0.30537	3.631000|3.631000	0.54280|0.54280	0.760000|0.760000	0.33108|0.33108	0.453000|0.453000	0.30009|0.30009	CGG|ACG		0.383	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		A	34951865	G	A	34951865	3	1	61	1	0	0	0	0	1	0	0	0	4717	1144	40	1	354	1	DONSON	21	34951865	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	22289	34951865	13178030	11766	19751										
DONSON	29980	broad.mit.edu	37	chr21	34954270	34954270	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatacagcttgatagaaaGtatgtctggctttttaattt	9	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:34954270G>T	ENST00000303071.5	-	7	1204	c.1138C>A	c.(1138-1140)Ctt>Att	p.L380I	DONSON_ENST00000453626.1_Missense_Mutation_p.L380I|DONSON_ENST00000432378.1_Missense_Mutation_p.L380I|DONSON_ENST00000303113.6_Missense_Mutation_p.L366I	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	380					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)		p.L380I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						TTGATAGAAAGTATGTCTGGC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	21											90	90	90					21																	34954270		2203	4300	6503	33876140	SO:0001583	missense	29980			AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.1138C>A	21.37:g.34954270G>T	ENSP00000307143:p.Leu380Ile		33876140	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Missense_Mutation	SNP	ENST00000303071.5	37	CCDS13632.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	5.329|5.329|5.329	0.246081|0.246081|0.246081	0.10077|0.10077|0.10077	.|.|.	.|.|.	ENSG00000159147|ENSG00000159147|ENSG00000159147	ENST00000303113;ENST00000453626;ENST00000303071;ENST00000432378|ENST00000440810|ENST00000437395	.|.|.	.|.|.	.|.|.	5.09|5.09|5.09	3.06|3.06|3.06	0.35304|0.35304|0.35304	.|.|.	0.382752|.|.	0.27406|.|.	N|.|.	0.019516|.|.	T|T|.	0.31231|0.31231|.	0.0790|0.0790|.	N|N|N	0.26130|0.26130|0.26130	0.795|0.795|0.795	0.09310|0.09310|0.09310	N|N|N	1|1|1	B;B|.|.	0.06786|.|.	0.001;0.001|.|.	B;B|.|.	0.08055|.|.	0.003;0.003|.|.	T|T|.	0.17319|0.17319|.	-1.0373|-1.0373|.	9|5|.	0.22109|.|.	T|.|.	0.4|.|.	-48.8622|-48.8622|-48.8622	8.0614|8.0614|8.0614	0.30635|0.30635|0.30635	0.0:0.127:0.3905:0.4825|0.0:0.127:0.3905:0.4825|0.0:0.127:0.3905:0.4825	.|.|.	366;380|.|.	F8W8A5;Q9NYP3|.|.	.;DONS_HUMAN|.|.	I|N|X	366;380;380;380|151|350	.|.|.	ENSP00000307143:L380I|.|.	L|T|Y	-|-|-	1|2|3	0|0|2	DONSON|DONSON|DONSON	33876140|33876140|33876140	0.228000|0.228000|0.228000	0.23718|0.23718|0.23718	0.023000|0.023000|0.023000	0.16930|0.16930|0.16930	0.860000|0.860000|0.860000	0.49131|0.49131|0.49131	1.644000|1.644000|1.644000	0.37228|0.37228|0.37228	1.402000|1.402000|1.402000	0.46780|0.46780|0.46780	0.467000|0.467000|0.467000	0.42956|0.42956|0.42956	CTT|ACT|TAC		0.353	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		T	34954270	G	T	34954270	3	4	61	1	0	0	0	0	1	0	0	0	4717	1029	36	2	578	2	DONSON	21	34954270	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2405	34954270	13175625	11767	19752										
ITSN1	6453	broad.mit.edu	37	chr21	35140024	35140024	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccgcaattgcagaagagttCgatctggcagtggtatatct	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35140024C>T	ENST00000381318.3	+	11	1222	c.934C>T	c.(934-936)Cga>Tga	p.R312*	ITSN1_ENST00000379960.5_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399367.3_Nonsense_Mutation_p.R312*|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000488166.1_3'UTR|ITSN1_ENST00000381291.4_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399338.4_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399326.3_Nonsense_Mutation_p.R312*|ITSN1_ENST00000437442.2_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399355.2_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399352.1_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399353.1_Nonsense_Mutation_p.R275*|ITSN1_ENST00000381285.4_Nonsense_Mutation_p.R312*|ITSN1_ENST00000399349.1_Nonsense_Mutation_p.R312*	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	312					apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R312*(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CAGAAGAGTTCGATCTGGCAG	0.388																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											86	83	84					21																	35140024		2203	4300	6503	34061894	SO:0001587	stop_gained	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.934C>T	21.37:g.35140024C>T	ENSP00000370719:p.Arg312*		34061894	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Nonsense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	C	40	7.958791	0.98583	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000381283;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	.	.	.	5.71	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0996	0.81163	0.1351:0.8649:0.0:0.0	.	.	.	.	X	275;312;312;312;312;312;312;312;312;312;252;312;312;312;312	.	ENSP00000369294:R312X	R	+	1	2	ITSN1	34061894	0.981000	0.34729	0.943000	0.38184	0.994000	0.84299	1.919000	0.40015	1.407000	0.46875	0.462000	0.41574	CGA		0.388	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		T	35140024	C	T	35140024	4	4	61	1	0	0	0	0	0	1	0	0	7947	876	31	1	972	1	ITSN1	21	35140024	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	185754	35140024	12989871	11768	19753										
ITSN1	6453	broad.mit.edu	37	chr21	35144467	35144467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcgcaaggagcaggagcGcctggcccagctggagcggg	19	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35144467G>A	ENST00000381318.3	+	12	1433	c.1145G>A	c.(1144-1146)cGc>cAc	p.R382H	ITSN1_ENST00000379960.5_Missense_Mutation_p.R382H|ITSN1_ENST00000399367.3_Missense_Mutation_p.R382H|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000488166.1_3'UTR|ITSN1_ENST00000381291.4_Missense_Mutation_p.R382H|ITSN1_ENST00000399338.4_Missense_Mutation_p.R382H|ITSN1_ENST00000399326.3_Missense_Mutation_p.R382H|ITSN1_ENST00000437442.2_Missense_Mutation_p.R382H|ITSN1_ENST00000399355.2_Missense_Mutation_p.R382H|ITSN1_ENST00000399352.1_Missense_Mutation_p.R382H|ITSN1_ENST00000399353.1_Missense_Mutation_p.R345H|ITSN1_ENST00000381285.4_Missense_Mutation_p.R382H|ITSN1_ENST00000399349.1_Missense_Mutation_p.R382H	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	382	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R382H(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GAGCAGGAGCGCCTGGCCCAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	21											52	58	56					21																	35144467		2203	4300	6503	34066337	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1145G>A	21.37:g.35144467G>A	ENSP00000370719:p.Arg382His		34066337	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818434	0.90790	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000381283;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T;T	0.51325	1.52;0.71;0.77;0.71;1.52;1.52;0.75;1.52;1.39;1.52;1.52;1.52;1.52	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.69557	0.3124	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;0.999;1.0;0.999;0.999;0.999;0.999	D;D;D;D;D;D;D;D;D;D	0.80764	0.987;0.987;0.987;0.987;0.994;0.991;0.987;0.987;0.994;0.987	T	0.72523	-0.4267	10	0.87932	D	0	.	19.2198	0.93791	0.0:0.0:1.0:0.0	.	345;345;345;382;382;382;382;382;382;345	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	H	345;382;382;382;382;382;382;382;382;382;322;382;382;382;382	ENSP00000382290:R345H;ENSP00000370719:R382H;ENSP00000370691:R382H;ENSP00000370685:R382H;ENSP00000382301:R382H;ENSP00000382289:R382H;ENSP00000382292:R382H;ENSP00000382286:R382H;ENSP00000370683:R322H;ENSP00000382275:R382H;ENSP00000387377:R382H;ENSP00000382265:R382H;ENSP00000369294:R382H	ENSP00000369294:R382H	R	+	2	0	ITSN1	34066337	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.619000	0.98369	2.616000	0.88540	0.455000	0.32223	CGC		0.572	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35144467	G	A	35144467	3	1	61	1	0	0	0	0	1	0	0	0	7947	1087	38	1	1187	1	ITSN1	21	35144467	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4443	35144467	12985428	11769	19754										
ITSN1	6453	broad.mit.edu	37	chr21	35147383	35147383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagagagttgagaattgccGaaatcacccatctacagcaa	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35147383G>A	ENST00000381318.3	+	14	1855	c.1567G>A	c.(1567-1569)Gaa>Aaa	p.E523K	ITSN1_ENST00000379960.5_Missense_Mutation_p.E523K|ITSN1_ENST00000399367.3_Missense_Mutation_p.E523K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.E523K|ITSN1_ENST00000399338.4_Missense_Mutation_p.E523K|ITSN1_ENST00000399326.3_Missense_Mutation_p.E523K|ITSN1_ENST00000437442.2_Missense_Mutation_p.E523K|ITSN1_ENST00000399355.2_Missense_Mutation_p.E523K|ITSN1_ENST00000399352.1_Missense_Mutation_p.E523K|ITSN1_ENST00000399353.1_Missense_Mutation_p.E486K|ITSN1_ENST00000381285.4_Missense_Mutation_p.E523K|ITSN1_ENST00000399349.1_Missense_Mutation_p.E523K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	523	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E523K(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GAGAATTGCCGAAATCACCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	21											99	102	101					21																	35147383		2203	4300	6503	34069253	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1567G>A	21.37:g.35147383G>A	ENSP00000370719:p.Glu523Lys		34069253	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	36	5.698354	0.96802	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.52526	1.64;0.66;0.68;0.66;1.64;1.64;0.66;1.64;1.64;1.64;1.64;1.64	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.70185	0.3195	M	0.76002	2.32	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.99;0.998;1.0;0.999;0.999;0.999;1.0;1.0	D;P;P;P;D;P;P;P;D;P	0.83275	0.941;0.879;0.548;0.874;0.973;0.798;0.84;0.84;0.996;0.879	T	0.74556	-0.3626	10	0.87932	D	0	.	18.4476	0.90690	0.0:0.0:1.0:0.0	.	486;486;486;523;523;523;523;523;523;486	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	K	486;523;523;523;523;523;523;523;523;523;523;523;523;523	ENSP00000382290:E486K;ENSP00000370719:E523K;ENSP00000370691:E523K;ENSP00000370685:E523K;ENSP00000382301:E523K;ENSP00000382289:E523K;ENSP00000382292:E523K;ENSP00000382286:E523K;ENSP00000382275:E523K;ENSP00000387377:E523K;ENSP00000382265:E523K;ENSP00000369294:E523K	ENSP00000369294:E523K	E	+	1	0	ITSN1	34069253	1.000000	0.71417	0.939000	0.37840	0.934000	0.57294	9.694000	0.98686	2.356000	0.79943	0.591000	0.81541	GAA		0.368	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35147383	G	A	35147383	3	1	61	1	0	0	0	0	1	0	0	0	7947	1059	37	1	1617	1	ITSN1	21	35147383	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2916	35147383	12982512	11770	19755										
ITSN1	6453	broad.mit.edu	37	chr21	35153769	35153769	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccttccttcccaggaatCtcagcaaatgcttggaagac	7	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35153769C>A	ENST00000381318.3	+	15	1889	c.1601C>A	c.(1600-1602)tCt>tAt	p.S534Y	ITSN1_ENST00000379960.5_Missense_Mutation_p.S534Y|ITSN1_ENST00000399367.3_Missense_Mutation_p.S534Y|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.S534Y|ITSN1_ENST00000399338.4_Missense_Mutation_p.S534Y|ITSN1_ENST00000399326.3_Missense_Mutation_p.S534Y|ITSN1_ENST00000437442.2_Missense_Mutation_p.S534Y|ITSN1_ENST00000399355.2_Missense_Mutation_p.S534Y|ITSN1_ENST00000399352.1_Missense_Mutation_p.S534Y|ITSN1_ENST00000399353.1_Missense_Mutation_p.S497Y|ITSN1_ENST00000381285.4_Missense_Mutation_p.S534Y|ITSN1_ENST00000399349.1_Missense_Mutation_p.S534Y	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	534	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S534Y(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						TCCCAGGAATCTCAGCAAATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	21											113	111	112					21																	35153769		2203	4300	6503	34075639	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1601C>A	21.37:g.35153769C>A	ENSP00000370719:p.Ser534Tyr		34075639	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.383016	0.25031	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.44482	2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.02;2.48;2.48;0.92	5.33	5.33	0.75918	.	0.053438	0.85682	D	0.000000	T	0.28499	0.0705	N	0.00690	-1.25	0.53005	D	0.99996	D;D;P;P;D;P;D;D;D;D	0.71674	0.998;0.992;0.937;0.919;0.997;0.612;0.992;0.992;0.993;0.992	P;P;P;P;P;B;P;P;D;P	0.64042	0.901;0.901;0.585;0.709;0.868;0.226;0.858;0.858;0.921;0.901	T	0.40021	-0.9585	10	0.02654	T	1	.	19.3849	0.94553	0.0:1.0:0.0:0.0	.	497;497;497;534;534;534;534;534;534;497	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	Y	497;534;534;534;534;534;534;534;534;534;534;534;534;534	ENSP00000382290:S497Y;ENSP00000370719:S534Y;ENSP00000370691:S534Y;ENSP00000370685:S534Y;ENSP00000382301:S534Y;ENSP00000382289:S534Y;ENSP00000382292:S534Y;ENSP00000382286:S534Y;ENSP00000382275:S534Y;ENSP00000387377:S534Y;ENSP00000382265:S534Y;ENSP00000369294:S534Y	ENSP00000369294:S534Y	S	+	2	0	ITSN1	34075639	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.615000	0.61190	2.632000	0.89209	0.557000	0.71058	TCT		0.388	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35153769	C	A	35153769	3	1	61	1	0	0	0	0	1	0	0	0	7947	913	32	2	1655	2	ITSN1	21	35153769	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6386	35153769	12976126	11771	19756										
ITSN1	6453	broad.mit.edu	37	chr21	35154339	35154339	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagagccttagaagcaaaaGaactagctcggcagcaccta	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35154339G>T	ENST00000381318.3	+	16	2014	c.1726G>T	c.(1726-1728)Gaa>Taa	p.E576*	ITSN1_ENST00000379960.5_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399367.3_Nonsense_Mutation_p.E576*|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399338.4_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399326.3_Nonsense_Mutation_p.E576*|ITSN1_ENST00000437442.2_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399355.2_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399352.1_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399353.1_Nonsense_Mutation_p.E539*|ITSN1_ENST00000381285.4_Nonsense_Mutation_p.E576*|ITSN1_ENST00000399349.1_Nonsense_Mutation_p.E576*	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	576	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E576*(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AGAAGCAAAAGAACTAGCTCG	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											83	83	83					21																	35154339		2203	4300	6503	34076209	SO:0001587	stop_gained	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1726G>T	21.37:g.35154339G>T	ENSP00000370719:p.Glu576*		34076209	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Nonsense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	42	9.404861	0.99161	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	.	.	.	5.83	5.83	0.93111	.	0.101968	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	20.1195	0.97955	0.0:0.0:1.0:0.0	.	.	.	.	X	539;576;576;576;576;576;576;576;576;576;576;576;576;576	.	ENSP00000369294:E576X	E	+	1	0	ITSN1	34076209	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.639000	0.83342	2.759000	0.94783	0.650000	0.86243	GAA		0.363	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		T	35154339	G	T	35154339	4	4	61	1	0	0	0	0	0	1	0	0	7947	943	33	2	1784	2	ITSN1	21	35154339	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	570	35154339	12975556	11772	19757										
ITSN1	6453	broad.mit.edu	37	chr21	35208896	35208896	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggggctcttcccatccaaTtatgtgaagctgaccacaga	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35208896T>G	ENST00000381318.3	+	29	3909	c.3621T>G	c.(3619-3621)aaT>aaG	p.N1207K	ITSN1_ENST00000379960.5_3'UTR|ITSN1_ENST00000399367.3_Missense_Mutation_p.N1202K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.N1207K|ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000437442.2_Missense_Mutation_p.N1202K|ITSN1_ENST00000399355.2_Missense_Mutation_p.N1136K|ITSN1_ENST00000399352.1_Missense_Mutation_p.N1202K|ITSN1_ENST00000399353.1_Missense_Mutation_p.N1165K|ITSN1_ENST00000381285.4_Missense_Mutation_p.N1207K|ITSN1_ENST00000399349.1_Missense_Mutation_p.N1131K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1207	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N1207K(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						TCCCATCCAATTATGTGAAGC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	21											113	102	106					21																	35208896		2203	4300	6503	34130766	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.3621T>G	21.37:g.35208896T>G	ENSP00000370719:p.Asn1207Lys		34130766	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870329	0.51588	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000437442	T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	4.37	-2.25	0.06888	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.69269	0.3092	M	0.82923	2.615	0.80722	D	1	D;D;P;D;D;D;D;D;D	0.89917	0.992;0.999;0.865;0.999;0.999;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D;D;D	0.91635	0.952;0.998;0.877;0.996;0.992;0.998;0.998;0.999;0.999	T	0.71199	-0.4663	10	0.87932	D	0	.	11.9827	0.53129	0.0:0.71:0.0:0.29	.	1099;1170;1094;1202;1136;1202;1207;1131;1165	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;ITSN1_HUMAN;.;.	K	1165;1207;1207;1207;1136;1202;1202;1136;1131;1202	ENSP00000382290:N1165K;ENSP00000370719:N1207K;ENSP00000370691:N1207K;ENSP00000370685:N1207K;ENSP00000382301:N1202K;ENSP00000382289:N1202K;ENSP00000382292:N1136K;ENSP00000382286:N1131K;ENSP00000387377:N1202K	ENSP00000370685:N1207K	N	+	3	2	ITSN1	34130766	0.976000	0.34144	0.989000	0.46669	0.994000	0.84299	0.214000	0.17541	-0.483000	0.06772	-0.276000	0.10085	AAT		0.532	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		G	35208896	T	G	35208896	3	3	61	1	0	0	0	0	1	0	0	0	7947	1490	52	4	3731	4	ITSN1	21	35208896	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	54557	35208896	12920999	11773	19758										
ITSN1	6453	broad.mit.edu	37	chr21	35230996	35230996	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctgcatctgtagatttttCaaaaacccctgatggagtct	7	9	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35230996C>A	ENST00000381318.3	+	31	4078	c.3790C>A	c.(3790-3792)Caa>Aaa	p.Q1264K	ITSN1_ENST00000399367.3_Missense_Mutation_p.Q1259K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000437442.2_Missense_Mutation_p.Q1259K|ITSN1_ENST00000381285.4_Missense_Mutation_p.Q1264K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1264	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Q1264K(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GTAGATTTTTCAAAAACCCCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	21											86	92	90					21																	35230996		2203	4300	6503	34152866	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.3790C>A	21.37:g.35230996C>A	ENSP00000370719:p.Gln1264Lys		34152866	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.610578	0.66558	.	.	ENSG00000205726	ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.65	5.65	0.86999	Dbl homology (DH) domain (5);	0.064586	0.64402	D	0.000004	T	0.61776	0.2374	N	0.17674	0.51	0.80722	D	1	D;P;D	0.61697	0.99;0.932;0.969	P;B;P	0.53809	0.735;0.381;0.586	T	0.61128	-0.7125	10	0.36615	T	0.2	.	19.7274	0.96170	0.0:1.0:0.0:0.0	.	1259;1259;1264	A8CTY3;A8CTX8;Q15811	.;.;ITSN1_HUMAN	K	1264;1264;1193;1259;1259	ENSP00000370719:Q1264K;ENSP00000370685:Q1264K;ENSP00000382301:Q1259K;ENSP00000387377:Q1259K	ENSP00000370685:Q1264K	Q	+	1	0	ITSN1	34152866	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.455000	0.80726	2.663000	0.90544	0.563000	0.77884	CAA		0.428	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35230996	C	A	35230996	3	1	61	1	0	0	0	0	1	0	0	0	7947	827	29	2	3914	2	ITSN1	21	35230996	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22100	35230996	12898899	11774	19759										
ITSN1	6453	broad.mit.edu	37	chr21	35260545	35260545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaagtgtcttctgctgcacGaagtccccacgggagagatt	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:35260545G>A	ENST00000381318.3	+	40	5395	c.5107G>A	c.(5107-5109)Gaa>Aaa	p.E1703K	ITSN1_ENST00000399367.3_Missense_Mutation_p.E1698K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000437442.2_Missense_Mutation_p.E1642K|ITSN1_ENST00000381285.4_Missense_Mutation_p.E1703K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1703					apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E1703K(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						TCTGCTGCACGAAGTCCCCAC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	21											80	69	73					21																	35260545		2203	4300	6503	34182415	SO:0001583	missense	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.5107G>A	21.37:g.35260545G>A	ENSP00000370719:p.Glu1703Lys		34182415	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	36	5.858220	0.97036	.	.	ENSG00000205726	ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.65	5.65	0.86999	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.80460	0.4627	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.72625	0.978;0.954;0.954	T	0.81355	-0.0970	10	0.87932	D	0	.	19.7272	0.96168	0.0:0.0:1.0:0.0	.	1642;1698;1703	A8CTY3;A8CTX8;Q15811	.;.;ITSN1_HUMAN	K	1703;1703;1632;1698;1642	ENSP00000370719:E1703K;ENSP00000370685:E1703K;ENSP00000382301:E1698K;ENSP00000387377:E1642K	ENSP00000370685:E1703K	E	+	1	0	ITSN1	34182415	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	9.441000	0.97557	2.646000	0.89796	0.655000	0.94253	GAA		0.572	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35260545	G	A	35260545	3	1	61	1	0	0	0	0	1	0	0	0	7947	1059	37	1	5267	1	ITSN1	21	35260545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29549	35260545	12869350	11775	19760										
SETD4	54093	broad.mit.edu	37	chr21	37420633	37420633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtatgcccctaagtagcttCgaatcactgtgtccgtggtg	11	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:37420633C>T	ENST00000399215.1	-	4	1641	c.269G>A	c.(268-270)cGa>cAa	p.R90Q	SETD4_ENST00000399205.1_Missense_Mutation_p.R66Q|SETD4_ENST00000399208.2_Missense_Mutation_p.R90Q|SETD4_ENST00000399212.1_Missense_Mutation_p.R66Q|SETD4_ENST00000481477.1_Intron|SETD4_ENST00000332131.4_Missense_Mutation_p.R90Q|SETD4_ENST00000399207.1_Missense_Mutation_p.R90Q|SETD4_ENST00000399201.1_Missense_Mutation_p.R66Q			Q9NVD3	SETD4_HUMAN	SET domain containing 4	90	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)	p.R90Q(2)		autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						TAAGTAGCTTCGAATCACTGT	0.463																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	21											386	318	341					21																	37420633		2203	4300	6503	36342503	SO:0001583	missense	54093			AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.269G>A	21.37:g.37420633C>T	ENSP00000382163:p.Arg90Gln		36342503	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	C	5.507	0.278582	0.10403	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131;ENST00000399205;ENST00000399208;ENST00000399201;ENST00000399207;ENST00000424303;ENST00000429161;ENST00000446166;ENST00000442559	D;D;D;D;D;D;D;T;T;T;T	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;2.57;2.57;2.57;2.57	5.25	-0.836	0.10770	SET domain (1);	0.397866	0.27664	N	0.018362	T	0.59376	0.2189	N	0.12961	0.28	0.09310	N	1	B;B;B;B	0.21753	0.06;0.029;0.048;0.0	B;B;B;B	0.16289	0.015;0.004;0.009;0.002	T	0.43782	-0.9370	10	0.13108	T	0.6	8.0285	11.2508	0.49024	0.0:0.4034:0.0:0.5966	.	66;90;66;90	A8MTS1;C9JWV5;Q9NVD3-3;Q9NVD3	.;.;.;SETD4_HUMAN	Q	90;66;90;66;90;66;90;90;90;66;66	ENSP00000382163:R90Q;ENSP00000382161:R66Q;ENSP00000329189:R90Q;ENSP00000382156:R66Q;ENSP00000382159:R90Q;ENSP00000382152:R66Q;ENSP00000382158:R90Q;ENSP00000399998:R90Q;ENSP00000396837:R90Q;ENSP00000413318:R66Q;ENSP00000394822:R66Q	ENSP00000329189:R90Q	R	-	2	0	SETD4	36342503	0.000000	0.05858	0.057000	0.19452	0.487000	0.33371	-0.245000	0.08890	0.002000	0.14630	-1.012000	0.02466	CGA		0.463	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		T	37420633	C	T	37420633	3	4	61	1	0	0	0	0	1	0	0	0	14170	884	31	1	1104	1	SETD4	21	37420633	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2160088	37420633	10709262	11776	19761										
DOPEY2	9980	broad.mit.edu	37	chr21	37661103	37661103	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctaaaagatgaagatgagtCattgaggtaagcagtacaag	11	4	2	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:37661103C>A	ENST00000399151.3	+	34	6432	c.6347C>A	c.(6346-6348)tCa>tAa	p.S2116*		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	2116					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)		p.S2116*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GAAGATGAGTCATTGAGGTAA	0.343																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											84	78	80					21																	37661103		2203	4300	6503	36582973	SO:0001587	stop_gained	9980			AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.6347C>A	21.37:g.37661103C>A	ENSP00000382104:p.Ser2116*		36582973	D3DSG5|Q6PJQ7|Q9UEZ3	Nonsense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	C	47	13.736124	0.99760	.	.	ENSG00000142197	ENST00000399151	.	.	.	5.74	2.92	0.33932	.	0.698869	0.14367	N	0.324071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2736	9.7534	0.40490	0.0:0.6656:0.2635:0.071	.	.	.	.	X	2116	.	ENSP00000382104:S2116X	S	+	2	0	DOPEY2	36582973	0.003000	0.15002	0.001000	0.08648	0.909000	0.53808	1.644000	0.37228	0.342000	0.23796	0.655000	0.94253	TCA		0.343	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37661103	C	A	37661103	4	1	61	1	0	0	0	0	0	1	0	0	4719	838	29	2	6477	2	DOPEY2	21	37661103	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240470	37661103	10468792	11777	19762										
MORC3	23515	broad.mit.edu	37	chr21	37705952	37705952	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgtttcagctttgcccGaagtttttacatacaaattc	6	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:37705952G>A	ENST00000400485.1	+	2	124	c.48G>A	c.(46-48)ccG>ccA	p.P16P	MORC3_ENST00000487909.1_Intron	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	16					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)	p.P16P(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						AGCTTTGCCCGAAGTTTTTAC	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	21											142	131	134					21																	37705952		1822	4086	5908	36627822	SO:0001819	synonymous_variant	23515			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.48G>A	21.37:g.37705952G>A			36627822	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																				0.328	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37705952	G	A	37705952	2	1	61	1	0	0	0	0	0	0	0	1	9733	1045	37	1		1	MORC3	21	37705952	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	44849	37705952	10423943	11778	19763										
MORC3	23515	broad.mit.edu	37	chr21	37716992	37716992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catcgaacgtgatgtttatcGaccaaaatttttagtatcct	6	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:37716992G>A	ENST00000400485.1	+	7	948	c.872G>A	c.(871-873)cGa>cAa	p.R291Q	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	291					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)	p.R291Q(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						GATGTTTATCGACCAAAATTT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	21											106	97	100					21																	37716992		1871	4107	5978	36638862	SO:0001583	missense	23515			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.872G>A	21.37:g.37716992G>A	ENSP00000383333:p.Arg291Gln		36638862	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	32	5.182037	0.94885	.	.	ENSG00000159256	ENST00000400485	T	0.15718	2.4	5.49	5.49	0.81192	ATPase-like, ATP-binding domain (1);	0.052118	0.85682	D	0.000000	T	0.37544	0.1007	M	0.65677	2.01	0.46011	D	0.998812	D	0.89917	1.0	D	0.66351	0.943	T	0.08146	-1.0736	10	0.72032	D	0.01	-11.58	12.6853	0.56944	0.0753:0.0:0.9247:0.0	.	291	Q14149	MORC3_HUMAN	Q	291	ENSP00000383333:R291Q	ENSP00000383333:R291Q	R	+	2	0	MORC3	36638862	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	6.031000	0.70911	2.582000	0.87167	0.655000	0.94253	CGA		0.388	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37716992	G	A	37716992	3	1	61	1	0	0	0	0	1	0	0	0	9733	1058	37	1	898	1	MORC3	21	37716992	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11040	37716992	10412903	11779	19764										
MORC3	23515	broad.mit.edu	37	chr21	37728940	37728940	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacaataacagcactaggaGaaaagctgaatgattactgg	9	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:37728940G>A	ENST00000400485.1	+	10	1202	c.1126G>A	c.(1126-1128)Gaa>Aaa	p.E376K	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	376					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)	p.E376K(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						AGCACTAGGAGAAAAGCTGAA	0.254																																																1	Substitution - Missense(1)	large_intestine(1)	21											78	75	76					21																	37728940		1796	4050	5846	36650810	SO:0001583	missense	23515			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1126G>A	21.37:g.37728940G>A	ENSP00000383333:p.Glu376Lys		36650810	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012538	0.35511	.	.	ENSG00000159256	ENST00000400485	T	0.15718	2.4	5.92	5.92	0.95590	.	0.672641	0.16216	N	0.224279	T	0.17831	0.0428	L	0.36672	1.1	0.39286	D	0.964655	B	0.13145	0.007	B	0.10450	0.005	T	0.14392	-1.0474	10	0.18276	T	0.48	-5.9813	20.3151	0.98650	0.0:0.0:1.0:0.0	.	376	Q14149	MORC3_HUMAN	K	376	ENSP00000383333:E376K	ENSP00000383333:E376K	E	+	1	0	MORC3	36650810	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.175000	0.50855	2.809000	0.96659	0.467000	0.42956	GAA		0.254	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37728940	G	A	37728940	3	1	61	1	0	0	0	0	1	0	0	0	9733	943	33	3	1164	3	MORC3	21	37728940	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11948	37728940	10400955	11780	19765										
HLCS	3141	broad.mit.edu	37	chr21	38302646	38302646	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatctctctaaggacttCgtatcttctaaaattgcttg	6	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38302646C>T	ENST00000399120.1	-	6	2314	c.1084G>A	c.(1084-1086)Gaa>Aaa	p.E362K	HLCS_ENST00000482273.1_5'UTR|HLCS_ENST00000336648.4_Missense_Mutation_p.E362K	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	362					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)	p.E362K(3)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CTAAGGACTTCGTATCTTCTA	0.458																																																3	Substitution - Missense(3)	large_intestine(3)	21											95	91	93					21																	38302646		2203	4300	6503	37224516	SO:0001583	missense	3141				CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.1084G>A	21.37:g.38302646C>T	ENSP00000382071:p.Glu362Lys		37224516	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	37	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.211684	0.39102	.	.	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98362	-4.89;-4.89	5.22	4.34	0.51931	.	0.158532	0.56097	D	0.000030	D	0.95815	0.8638	M	0.76574	2.34	0.45272	D	0.99827	P;P	0.44986	0.847;0.717	B;B	0.28553	0.091;0.075	D	0.94019	0.7291	10	0.33940	T	0.23	.	11.0911	0.48117	0.0:0.8482:0.0:0.1518	.	362;362	B2RAH1;P50747	.;BPL1_HUMAN	K	362	ENSP00000382071:E362K;ENSP00000338387:E362K	ENSP00000338387:E362K	E	-	1	0	HLCS	37224516	0.998000	0.40836	0.793000	0.32043	0.399000	0.30720	4.020000	0.57189	1.332000	0.45431	0.650000	0.86243	GAA		0.458	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			T	38302646	C	T	38302646	3	4	61	1	0	0	0	0	1	0	0	0	7234	893	31	1	1124	1	HLCS	21	38302646	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	573706	38302646	9827249	11781	19766										
TTC3	7267	broad.mit.edu	37	chr21	38494279	38494279	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaaatagaagacctacaaGgtatttcacctaagattctt	5	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38494279G>T	ENST00000399017.2	+	12	3810	c.1063G>T	c.(1063-1065)Ggt>Tgt	p.G355C	TTC3_ENST00000355666.1_Splice_Site_p.G355C|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Splice_Site_p.G45C|TTC3_ENST00000354749.2_Splice_Site_p.G355C	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	355					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G355C(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AGACCTACAAGGTATTTCACC	0.363																																					Ovarian(38;194 1649 35661)											1	Substitution - Missense(1)	large_intestine(1)	21											58	59	59					21																	38494279		2203	4300	6503	37416149	SO:0001630	splice_region_variant	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1063+1G>T	21.37:g.38494279G>T			37416149	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183022	0.78677	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.57595	1.1;1.1;1.1;2.9;0.39;2.9;2.9	5.41	5.41	0.78517	.	0.119040	0.37178	N	0.002215	T	0.61664	0.2365	L	0.27053	0.805	0.47276	D	0.99937	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65240	-0.6216	10	0.72032	D	0.01	-16.0166	16.1082	0.81241	0.0:0.0:1.0:0.0	.	45;355	B4DSZ9;P53804	.;TTC3_HUMAN	C	355;355;337;355;45;355;355	ENSP00000403943:G355C;ENSP00000408456:G355C;ENSP00000391891:G337C;ENSP00000347889:G355C;ENSP00000442875:G45C;ENSP00000381981:G355C;ENSP00000346791:G355C	ENSP00000346791:G355C	G	+	1	0	TTC3	37416149	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.651000	0.74372	2.552000	0.86080	0.650000	0.86243	GGT		0.363	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Missense_Mutation	T	38494279	G	T	38494279	5	4	61	1	0	0	0	0	0	0	1	0	16737	1014	35	2	1105	2	TTC3	21	38494279	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191633	38494279	9635616	11782	19767										
TTC3	7267	broad.mit.edu	37	chr21	38507697	38507697	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggattttgctaatataatGaaaatgctgagaagcttaat	8	4	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38507697G>T	ENST00000399017.2	+	18	4208	c.1461G>T	c.(1459-1461)atG>atT	p.M487I	TTC3_ENST00000355666.1_Missense_Mutation_p.M487I|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Missense_Mutation_p.M177I|TTC3_ENST00000354749.2_Missense_Mutation_p.M487I	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	487					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M487I(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CTAATATAATGAAAATGCTGA	0.368																																					Ovarian(38;194 1649 35661)											1	Substitution - Missense(1)	large_intestine(1)	21											41	44	43					21																	38507697		2203	4300	6503	37429567	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1461G>T	21.37:g.38507697G>T	ENSP00000381981:p.Met487Ile		37429567	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340030	0.41398	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.41400	2.82;1.0;2.82;3.16;1.01;3.16;3.16	5.49	4.37	0.52481	.	0.297392	0.28766	N	0.014212	T	0.21801	0.0525	N	0.19112	0.55	0.27240	N	0.959177	B;P	0.35844	0.001;0.524	B;B	0.31946	0.001;0.138	T	0.06807	-1.0806	10	0.34782	T	0.22	-21.0079	4.5614	0.12161	0.1327:0.0:0.5919:0.2754	.	177;487	B4DSZ9;P53804	.;TTC3_HUMAN	I	487;487;469;487;177;487;487	ENSP00000403943:M487I;ENSP00000408456:M487I;ENSP00000391891:M469I;ENSP00000347889:M487I;ENSP00000442875:M177I;ENSP00000381981:M487I;ENSP00000346791:M487I	ENSP00000346791:M487I	M	+	3	0	TTC3	37429567	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.973000	0.40550	2.728000	0.93425	0.655000	0.94253	ATG		0.368	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38507697	G	T	38507697	3	4	61	1	0	0	0	0	1	0	0	0	16737	1290	45	2	1527	2	TTC3	21	38507697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13418	38507697	9622198	11783	19768										
TTC3	7267	broad.mit.edu	37	chr21	38537937	38537937	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatatgagtttttcccagaaGaaactcgacagatactagaa	7	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38537937G>T	ENST00000399017.2	+	33	6168	c.3421G>T	c.(3421-3423)Gaa>Taa	p.E1141*	TTC3_ENST00000355666.1_Nonsense_Mutation_p.E1141*|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Nonsense_Mutation_p.E1141*	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1141					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E1141*(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTTCCCAGAAGAAACTCGACA	0.388																																					Ovarian(38;194 1649 35661)											1	Substitution - Nonsense(1)	large_intestine(1)	21											136	150	145					21																	38537937		2203	4300	6503	37459807	SO:0001587	stop_gained	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3421G>T	21.37:g.38537937G>T	ENSP00000381981:p.Glu1141*		37459807	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Nonsense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.135671|8.135671	0.98670|0.98670	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749|ENST00000411496	.|.	.|.	.|.	4.75|4.75	4.75|4.75	0.60458|0.60458	.|.	0.195065|.	0.35903|.	N|.	0.002918|.	.|T	.|0.71609	.|0.3360	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71090	.|-0.4693	.|4	0.87932|.	D|.	0|.	-26.0179|-26.0179	16.2538|16.2538	0.82501|0.82501	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	1141;1123;1141;1141;1141|296	.|.	ENSP00000346791:E1141X|.	E|K	+|+	1|3	0|2	TTC3|TTC3	37459807|37459807	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	7.387000|7.387000	0.79785|0.79785	2.352000|2.352000	0.79861|0.79861	0.591000|0.591000	0.81541|0.81541	GAA|AAG		0.388	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38537937	G	T	38537937	4	4	61	1	0	0	0	0	0	1	0	0	16737	943	33	2	3547	2	TTC3	21	38537937	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30240	38537937	9591958	11784	19769										
DSCR3	10311	broad.mit.edu	37	chr21	38610883	38610883	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttccccggcttcaccatttCtatggtgctgttgataatct	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38610883C>A	ENST00000309117.6	-	3	466	c.229G>T	c.(229-231)Gaa>Taa	p.E77*	DSCR3_ENST00000288304.5_Nonsense_Mutation_p.E35*|DSCR3_ENST00000398998.1_Nonsense_Mutation_p.E29*|DSCR3_ENST00000539844.1_Intron|AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000399000.3_5'UTR|DSCR3_ENST00000399001.1_Intron|DSCR3_ENST00000476950.1_Nonsense_Mutation_p.E77*	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	77						nucleus (GO:0005634)		p.E77*(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						TTCACCATTTCTATGGTGCTG	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											104	108	106					21																	38610883		2203	4300	6503	37532753	SO:0001587	stop_gained	10311			D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538			3044	protein-coding gene	gene with protein product		605298				9399594	Standard	NM_006052		Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.229G>T	21.37:g.38610883C>A	ENSP00000311399:p.Glu77*		37532753	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Nonsense_Mutation	SNP	ENST00000309117.6	37	CCDS33553.1	.	.	.	.	.	.	.	.	.	.	C	44	10.696723	0.99452	.	.	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000476950;ENST00000398998	.	.	.	5.41	5.41	0.78517	.	0.049641	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-1.3018	19.5612	0.95373	0.0:1.0:0.0:0.0	.	.	.	.	X	77;35;77;29	.	ENSP00000288304:E35X	E	-	1	0	DSCR3	37532753	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.748000	0.68697	2.687000	0.91594	0.655000	0.94253	GAA		0.408	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1			A	38610883	C	A	38610883	4	1	61	1	0	0	0	0	0	1	0	0	4782	922	32	2	688	2	DSCR3	21	38610883	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72946	38610883	9519012	11785	19770										
DYRK1A	1859	broad.mit.edu	37	chr21	38884507	38884507	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccacagtcaccactccatGacatccctgtcttcctcaac	5	18	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:38884507G>T	ENST00000398960.2	+	11	2040	c.1965G>T	c.(1963-1965)atG>atT	p.M655I	DYRK1A_ENST00000455387.2_Missense_Mutation_p.M427I|DYRK1A_ENST00000338785.3_3'UTR|DYRK1A_ENST00000339659.4_Missense_Mutation_p.M646I	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	655					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)	p.M655I(1)		breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCACTCCATGACATCCCTGT	0.517																																					Melanoma(114;464 1602 31203 43785 45765)											1	Substitution - Missense(1)	large_intestine(1)	21											164	141	149					21																	38884507		2203	4300	6503	37806377	SO:0001583	missense	1859			U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1965G>T	21.37:g.38884507G>T	ENSP00000381932:p.Met655Ile		37806377	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.839719	0.51057	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.55760	0.5;0.53;1.05	5.73	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.38453	0.1041	N	0.24115	0.695	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14337	-1.0476	10	0.19147	T	0.46	.	14.9122	0.70767	0.0689:0.0:0.9311:0.0	.	655;646	Q13627;Q13627-2	DYR1A_HUMAN;.	I	646;655;427	ENSP00000340373:M646I;ENSP00000381932:M655I;ENSP00000407854:M427I	ENSP00000340373:M646I	M	+	3	0	DYRK1A	37806377	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.357000	0.97099	1.433000	0.47394	-0.150000	0.13652	ATG		0.517	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38884507	G	T	38884507	3	4	61	1	0	0	0	0	1	0	0	0	4865	1290	45	2	2091	2	DYRK1A	21	38884507	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	273624	38884507	9245388	11786	19771										
KCNJ6	3763	broad.mit.edu	37	chr21	39086848	39086848	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcactgcatgggtggaaaaGaccagggtctctgccctctt	11	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:39086848G>T	ENST00000609713.1	-	3	1201	c.612C>A	c.(610-612)gtC>gtA	p.V204V	KCNJ6-IT1_ENST00000435001.1_RNA|KCNJ6_ENST00000288309.6_Silent_p.V204V	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	204					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)	p.V204V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	GGGTGGAAAAGACCAGGGTCT	0.493																																					Pancreas(48;379 1118 2936 19024 28214)											1	Substitution - coding silent(1)	large_intestine(1)	21											57	56	56					21																	39086848		1937	4167	6104	38008718	SO:0001819	synonymous_variant	3763			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.612C>A	21.37:g.39086848G>T			38008718	Q3MJ74|Q53WW6	Silent	SNP	ENST00000609713.1	37	CCDS42927.1																																																																																				0.493	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		T	39086848	G	T	39086848	2	4	61	1	0	0	0	0	0	0	0	1	8076	929	33	2		2	KCNJ6	21	39086848	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	202341	39086848	9043047	11787	19772										
KCNJ6	3763	broad.mit.edu	37	chr21	39087225	39087225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cactaatgtggtgaagatatCggtcaggtagcgataggtct	13	6	2	2	rs143219969		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:39087225C>T	ENST00000609713.1	-	3	824	c.235G>A	c.(235-237)Gat>Aat	p.D79N	KCNJ6-IT1_ENST00000435001.1_RNA|KCNJ6_ENST00000288309.6_Missense_Mutation_p.D79N	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	79					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)	p.D79N(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	GTGAAGATATCGGTCAGGTAG	0.463																																					Pancreas(48;379 1118 2936 19024 28214)											2	Substitution - Missense(2)	large_intestine(1)|skin(1)	21											221	208	212					21																	39087225		2006	4153	6159	38009095	SO:0001583	missense	3763			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.235G>A	21.37:g.39087225C>T	ENSP00000477437:p.Asp79Asn		38009095	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	37	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.030635	0.93575	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.97066	-4.23;-4.23	5.95	5.95	0.96441	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.000000	0.85682	D	0.000000	D	0.98969	0.9649	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99218	1.0878	10	0.87932	D	0	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	79	P48051	IRK6_HUMAN	N	79	ENSP00000383330:D79N;ENSP00000288309:D79N	ENSP00000288309:D79N	D	-	1	0	KCNJ6	38009095	1.000000	0.71417	0.939000	0.37840	0.977000	0.68977	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	GAT		0.463	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		T	39087225	C	T	39087225	3	4	61	1	0	0	0	0	1	0	0	0	8076	884	31	1	1044	1	KCNJ6	21	39087225	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	377	39087225	9042670	11788	19773										
DSCR4	10281	broad.mit.edu	37	chr21	39427068	39427068	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccaaaattgctgcccctCtctggttctgagtggaaagg	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:39427068C>A	ENST00000328264.3	-	3	342	c.238G>T	c.(238-240)Gag>Tag	p.E80*	DSCR4_ENST00000398948.1_Intron	NM_005867.2	NP_005858.1	P56555	DSCR4_HUMAN	Down syndrome critical region gene 4	80								p.E80*(1)		large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	6						TGCTGCCCCTCTCTGGTTCTG	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											152	138	143					21																	39427068		2203	4300	6503	38348938	SO:0001587	stop_gained	10281			AB000099	CCDS33554.1	21q22.2	2012-04-19			ENSG00000184029	ENSG00000184029			3045	protein-coding gene	gene with protein product		604829				9455479	Standard	NM_005867		Approved	DCRB	uc002ywp.3	P56555	OTTHUMG00000086673	ENST00000328264.3:c.238G>T	21.37:g.39427068C>A	ENSP00000328676:p.Glu80*		38348938	Q4VB31	Nonsense_Mutation	SNP	ENST00000328264.3	37	CCDS33554.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.058594	0.36277	.	.	ENSG00000184029	ENST00000328264	.	.	.	3.89	1.99	0.26369	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.7018	0.17887	0.0:0.7393:0.0:0.2607	.	.	.	.	X	80	.	ENSP00000328676:E80X	E	-	1	0	DSCR4	38348938	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.383000	0.20651	0.540000	0.28808	0.563000	0.77884	GAG		0.428	DSCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000194834.1	NM_005867		A	39427068	C	A	39427068	4	1	61	1	0	0	0	0	0	1	0	0	4783	922	32	2	122	2	DSCR4	21	39427068	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	339843	39427068	8702827	11789	19774										
KCNJ15	3772	broad.mit.edu	37	chr21	39672277	39672277	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatcagagggaaagagaacTgaggacacttttattacaac	11	6	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:39672277T>G	ENST00000328656.4	+	4	1397	c.1094T>G	c.(1093-1095)cTg>cGg	p.L365R	KCNJ15_ENST00000398938.2_Missense_Mutation_p.L365R|KCNJ15_ENST00000398932.1_Missense_Mutation_p.L365R|KCNJ15_ENST00000398934.1_Missense_Mutation_p.L365R|KCNJ15_ENST00000398930.1_Missense_Mutation_p.L365R	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	365					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.L365R(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GAAAGAGAACTGAGGACACTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	21											47	50	49					21																	39672277		2203	4300	6503	38594147	SO:0001583	missense	3772			Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.1094T>G	21.37:g.39672277T>G	ENSP00000331698:p.Leu365Arg		38594147	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	T	3.749	-0.052068	0.07362	.	.	ENSG00000157551	ENST00000328656;ENST00000398938;ENST00000398932;ENST00000398930;ENST00000398934	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54	5.83	5.83	0.93111	.	0.396031	0.21811	N	0.068762	T	0.80808	0.4694	N	0.22421	0.69	0.33660	D	0.609612	B	0.06786	0.001	B	0.10450	0.005	T	0.79027	-0.1971	9	.	.	.	.	11.4501	0.50147	0.0:0.0:0.1501:0.8499	.	365	Q99712	IRK15_HUMAN	R	365	ENSP00000331698:L365R;ENSP00000381911:L365R;ENSP00000381905:L365R;ENSP00000381904:L365R;ENSP00000381907:L365R	.	L	+	2	0	KCNJ15	38594147	0.998000	0.40836	0.950000	0.38849	0.972000	0.66771	1.465000	0.35299	2.236000	0.73375	0.533000	0.62120	CTG		0.468	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		G	39672277	T	G	39672277	3	3	61	1	0	0	0	0	1	0	0	0	8070	1580	55	4	1096	4	KCNJ15	21	39672277	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	245209	39672277	8457618	11790	19775										
BRWD1	54014	broad.mit.edu	37	chr21	40559097	40559097	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttttcttagccgcagcaGaagcatttcgatggggcagt	11	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40559097G>T	ENST00000333229.2	-	42	7145	c.6818C>A	c.(6817-6819)tCt>tAt	p.S2273Y	AF129408.17_ENST00000608767.1_RNA	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2273					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S2273Y(1)|p.S2273C(1)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AGCCGCAGCAGAAGCATTTCG	0.323																																					Melanoma(170;988 1986 4794 16843 39731)											2	Substitution - Missense(2)	large_intestine(1)|lung(1)	21											74	77	76					21																	40559097		2201	4297	6498	39480967	SO:0001583	missense	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6818C>A	21.37:g.40559097G>T	ENSP00000330753:p.Ser2273Tyr		39480967	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.864773	0.71949	.	.	ENSG00000185658	ENST00000333229	T	0.60171	0.21	5.12	5.12	0.69794	.	0.121502	0.37348	N	0.002123	T	0.65270	0.2675	L	0.58101	1.795	0.80722	D	1	P	0.51791	0.948	P	0.50791	0.65	T	0.69899	-0.5020	10	0.87932	D	0	-8.6834	17.1329	0.86730	0.0:0.0:1.0:0.0	.	2273	Q9NSI6	BRWD1_HUMAN	Y	2273	ENSP00000330753:S2273Y	ENSP00000330753:S2273Y	S	-	2	0	BRWD1	39480967	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	3.336000	0.52113	2.542000	0.85734	0.650000	0.86243	TCT		0.323	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40559097	G	T	40559097	3	4	61	1	0	0	0	0	1	0	0	0	1528	942	33	2	148	2	BRWD1	21	40559097	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	886820	40559097	7570798	11791	19776										
BRWD1	54014	broad.mit.edu	37	chr21	40570895	40570895	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgagtcactcagaatcttgGtttttttaaagaaactcgca	7	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40570895G>T	ENST00000333229.2	-	40	5774	c.5447C>A	c.(5446-5448)aCc>aAc	p.T1816N	BRWD1_ENST00000342449.3_Missense_Mutation_p.T1816N|BRWD1_ENST00000380800.3_Missense_Mutation_p.T1816N	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1816					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T1816N(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CAGAATCTTGGTTTTTTTAAA	0.388																																					Melanoma(170;988 1986 4794 16843 39731)											2	Substitution - Missense(2)	large_intestine(2)	21											121	123	122					21																	40570895		2203	4300	6503	39492765	SO:0001583	missense	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.5447C>A	21.37:g.40570895G>T	ENSP00000330753:p.Thr1816Asn		39492765	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.966851	0.34659	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.54071	0.59;0.61;0.69	5.48	5.48	0.80851	.	0.374434	0.25820	N	0.028090	T	0.45357	0.1338	L	0.29908	0.895	0.80722	D	1	P;B	0.34757	0.467;0.072	B;B	0.34652	0.187;0.032	T	0.49254	-0.8959	10	0.66056	D	0.02	-3.482	17.5514	0.87876	0.0:0.0:1.0:0.0	.	1816;1816	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	N	1816	ENSP00000330753:T1816N;ENSP00000344333:T1816N;ENSP00000370178:T1816N	ENSP00000330753:T1816N	T	-	2	0	BRWD1	39492765	1.000000	0.71417	1.000000	0.80357	0.189000	0.23516	3.508000	0.53378	2.576000	0.86940	0.655000	0.94253	ACC		0.388	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40570895	G	T	40570895	3	4	61	1	0	0	0	0	1	0	0	0	1528	1261	44	2	1766	2	BRWD1	21	40570895	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11798	40570895	7559000	11792	19777										
BRWD1	54014	broad.mit.edu	37	chr21	40587276	40587276	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatctgacttcccaaactaaCgcagacagcctccttcaaaa	4	14	2	2	rs148823718		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40587276C>T	ENST00000333229.2	-	32	3999	c.3672G>A	c.(3670-3672)gcG>gcA	p.A1224A	BRWD1_ENST00000342449.3_Silent_p.A1224A|BRWD1_ENST00000380800.3_Silent_p.A1224A|BRWD1-IT1_ENST00000435608.1_RNA	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1224	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A1224A(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CCCAAACTAACGCAGACAGCC	0.348																																					Melanoma(170;988 1986 4794 16843 39731)											2	Substitution - coding silent(2)	large_intestine(2)	21						C	,	0,4406		0,0,2203	114	104	107		3672,3672	-6.4	1	21	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	1224/2321,1224/2270	40587276	1,13005	2203	4300	6503	39509146	SO:0001819	synonymous_variant	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3672G>A	21.37:g.40587276C>T			39509146	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169045	0.38315	0.0	1.16E-4	ENSG00000185658	ENST00000424441	.	.	.	5.55	-6.45	0.01914	.	.	.	.	.	T	0.38746	0.1052	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	.	3.838	0.08902	0.0825:0.1851:0.1614:0.5709	.	.	.	.	I	210	.	.	V	-	1	0	BRWD1	39509146	0.752000	0.28338	0.989000	0.46669	0.960000	0.62799	-0.193000	0.09573	-0.497000	0.06641	-1.417000	0.01113	GTT		0.348	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40587276	C	T	40587276	2	4	61	1	0	0	0	0	0	0	0	1	1528	523	19	1		1	BRWD1	21	40587276	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16381	40587276	7542619	11793	19778										
LCA5L	150082	broad.mit.edu	37	chr21	40778280	40778280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtctgagggggcctttcGtgtagggagcagtgcctttg	16	7	1	1	rs147712761	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40778280G>A	ENST00000358268.2	-	10	2069	c.1541C>T	c.(1540-1542)aCg>aTg	p.T514M	WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'UTR|LCA5L_ENST00000288350.3_Missense_Mutation_p.T514M|LCA5L_ENST00000380671.2_Missense_Mutation_p.T514M			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	514								p.T514M(2)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				GGGGCCTTTCGTGTAGGGAGC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	21						G	MET/THR	0,4406		0,0,2203	117	96	103		1541	-7.8	0	21	dbSNP_134	103	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LCA5L	NM_152505.3	81	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	possibly-damaging	514/671	40778280	4,13002	2203	4300	6503	39700150	SO:0001583	missense	150082			AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1541C>T	21.37:g.40778280G>A	ENSP00000351008:p.Thr514Met		39700150	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721846	0.30503	0.0	4.65E-4	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	T;T;T	0.55588	0.51;0.51;0.51	3.9	-7.8	0.01214	.	3.687670	0.00919	N	0.002568	T	0.33177	0.0854	L	0.29908	0.895	0.09310	N	1	P	0.45768	0.866	B	0.39185	0.293	T	0.48387	-0.9040	10	0.48119	T	0.1	9.9576	3.7432	0.08539	0.2114:0.2418:0.4499:0.0969	.	514	O95447	LCA5L_HUMAN	M	514	ENSP00000288350:T514M;ENSP00000370046:T514M;ENSP00000351008:T514M	ENSP00000288350:T514M	T	-	2	0	LCA5L	39700150	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.496000	0.06436	-1.076000	0.03125	-0.258000	0.10820	ACG		0.478	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		A	40778280	G	A	40778280	3	1	61	1	0	0	0	0	1	0	0	0	8679	1145	40	1	475	1	LCA5L	21	40778280	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	191004	40778280	7351615	11794	19779										
LCA5L	150082	broad.mit.edu	37	chr21	40783686	40783686	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtaaatttttaagtattcGatgactatagatgtttttaa	6	2	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40783686G>A	ENST00000358268.2	-	7	1546	c.1018C>T	c.(1018-1020)Cga>Tga	p.R340*	WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'Flank|LCA5L_ENST00000288350.3_Nonsense_Mutation_p.R340*|LCA5L_ENST00000380671.2_Nonsense_Mutation_p.R340*			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	340								p.R340*(2)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				TTAAGTATTCGATGACTATAG	0.294																																																2	Substitution - Nonsense(2)	large_intestine(2)	21											70	71	71					21																	40783686		2201	4291	6492	39705556	SO:0001587	stop_gained	150082			AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1018C>T	21.37:g.40783686G>A	ENSP00000351008:p.Arg340*		39705556	D3DSI0|Q3ZCT0	Nonsense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	G	39	7.895382	0.98548	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	.	.	.	5.52	3.66	0.41972	.	0.000000	0.51477	D	0.000083	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8473	12.1077	0.53821	0.0:0.0:0.688:0.312	.	.	.	.	X	340	.	ENSP00000288350:R340X	R	-	1	2	LCA5L	39705556	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	3.043000	0.49823	0.668000	0.31126	0.650000	0.86243	CGA		0.294	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		A	40783686	G	A	40783686	4	1	61	1	0	0	0	0	0	1	0	0	8679	1066	37	1	1010	1	LCA5L	21	40783686	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5406	40783686	7346209	11795	19780										
LCA5L	150082	broad.mit.edu	37	chr21	40795153	40795153	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagccataatttgaggtaGattattttgtgaattctcat	7	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40795153G>T	ENST00000358268.2	-	5	1114	c.586C>A	c.(586-588)Cta>Ata	p.L196I	LCA5L_ENST00000485895.2_Missense_Mutation_p.L196I|LCA5L_ENST00000288350.3_Missense_Mutation_p.L196I|LCA5L_ENST00000380671.2_Missense_Mutation_p.L196I			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	196								p.L196I(2)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				ATTTGAGGTAGATTATTTTGT	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	21											94	89	91					21																	40795153		2203	4299	6502	39717023	SO:0001583	missense	150082			AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.586C>A	21.37:g.40795153G>T	ENSP00000351008:p.Leu196Ile		39717023	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.057284	0.55325	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	D;D;D	0.83673	-1.75;-1.75;-1.75	4.95	1.54	0.23209	.	0.216608	0.32769	N	0.005673	T	0.76335	0.3973	L	0.38953	1.18	0.31051	N	0.715192	D	0.60575	0.988	P	0.53224	0.721	T	0.71262	-0.4645	10	0.28530	T	0.3	-6.9345	2.6427	0.04975	0.2392:0.1326:0.4931:0.135	.	196	O95447	LCA5L_HUMAN	I	196	ENSP00000288350:L196I;ENSP00000370046:L196I;ENSP00000351008:L196I	ENSP00000288350:L196I	L	-	1	2	LCA5L	39717023	0.161000	0.22892	0.991000	0.47740	0.972000	0.66771	0.462000	0.21956	0.576000	0.29452	0.655000	0.94253	CTA		0.318	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		T	40795153	G	T	40795153	3	4	61	1	0	0	0	0	1	0	0	0	8679	933	33	2	1450	2	LCA5L	21	40795153	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11467	40795153	7334742	11796	19781										
SH3BGR	6450	broad.mit.edu	37	chr21	40847088	40847088	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actctttcttctctgcaaaaGaagagaatattatttattcc	4	8	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:40847088G>T	ENST00000333634.4	+	3	526	c.448G>T	c.(448-450)Gaa>Taa	p.E150*	SH3BGR_ENST00000380637.3_Nonsense_Mutation_p.E39*|SH3BGR_ENST00000380631.1_Nonsense_Mutation_p.E39*|SH3BGR_ENST00000458295.1_Nonsense_Mutation_p.E39*|SH3BGR_ENST00000380634.1_Nonsense_Mutation_p.E39*	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	150					positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)	p.E150*(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		CTCTGCAAAAGAAGAGAATAT	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											108	103	104					21																	40847088		2203	4300	6503	39768958	SO:0001587	stop_gained	6450				CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"21-glutamic acid-rich protein"	602230	"SH3 domain binding glutamic acid-rich protein"			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.448G>T	21.37:g.40847088G>T	ENSP00000332513:p.Glu150*		39768958	A6ND59|D3DSI2|Q9BRB8	Nonsense_Mutation	SNP	ENST00000333634.4	37	CCDS13666.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.988325|6.988325	0.97983|0.97983	.|.	.|.	ENSG00000185437|ENSG00000185437	ENST00000380637;ENST00000380634;ENST00000458295;ENST00000440288;ENST00000380631;ENST00000333634|ENST00000452550	.|.	.|.	.|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	0.088452|.	0.85682|.	D|.	0.000000|.	.|T	.|0.72020	.|0.3409	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72779	.|-0.4190	.|3	0.87932|.	D|.	0|.	.|.	16.3563|16.3563	0.83236|0.83236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	39;39;39;39;39;150|78	.|.	ENSP00000332513:E150X|.	E|R	+|+	1|2	0|0	SH3BGR|SH3BGR	39768958|39768958	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.970000|4.970000	0.63742|0.63742	2.715000|2.715000	0.92844|0.92844	0.655000|0.655000	0.94253|0.94253	GAA|AGA		0.358	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341		T	40847088	G	T	40847088	4	4	61	1	0	0	0	0	0	1	0	0	14277	943	33	2	458	2	SH3BGR	21	40847088	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	51935	40847088	7282807	11797	19782										
B3GALT5	10317	broad.mit.edu	37	chr21	41032830	41032830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggaccaggagagccagcGacacggggacattatccaga	15	10	0	2	rs371497510		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41032830G>A	ENST00000380620.4	+	5	936	c.344G>A	c.(343-345)cGa>cAa	p.R115Q	AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000398714.2_Missense_Mutation_p.R115Q|B3GALT5_ENST00000343118.4_Missense_Mutation_p.R115Q|B3GALT5_ENST00000380618.1_Missense_Mutation_p.R115Q			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	115					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.R115Q(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				GAGAGCCAGCGACACGGGGAC	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	21											83	85	84					21																	41032830		2203	4300	6503	39954700	SO:0001583	missense	10317			AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"Beta 3-glycosyltransferases"	920	protein-coding gene	gene with protein product	"homolog of C. elegans Bt toxin resistance gene bre-5", "GlcNAc-beta-1,3-galactosyltransferase 5"	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.344G>A	21.37:g.41032830G>A	ENSP00000369994:p.Arg115Gln		39954700	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	37	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	G	7.774	0.708108	0.15239	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.72	-5.23	0.02798	.	1.444890	0.04540	N	0.388012	T	0.14743	0.0356	N	0.03084	-0.415	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.16630	-1.0396	10	0.08837	T	0.75	.	3.749	0.08559	0.2505:0.1045:0.4404:0.2046	.	115	Q9Y2C3	B3GT5_HUMAN	Q	115	ENSP00000369994:R115Q;ENSP00000369992:R115Q;ENSP00000343318:R115Q;ENSP00000381699:R115Q	ENSP00000343318:R115Q	R	+	2	0	B3GALT5	39954700	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.650000	0.05378	-0.767000	0.04633	-0.181000	0.13052	CGA		0.517	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170		A	41032830	G	A	41032830	3	1	61	1	0	0	0	0	1	0	0	0	1251	1058	37	1	346	1	B3GALT5	21	41032830	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	185742	41032830	7097065	11798	19783										
B3GALT5	10317	broad.mit.edu	37	chr21	41033164	41033164	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgttttctggcgacgtggcGagtcaggtgtacaatgtctc	14	8	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41033164G>A	ENST00000380620.4	+	5	1270	c.678G>A	c.(676-678)gcG>gcA	p.A226A	AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000398714.2_Silent_p.A226A|B3GALT5_ENST00000343118.4_Silent_p.A226A|B3GALT5_ENST00000380618.1_Silent_p.A226A			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	226					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.A226A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				GCGACGTGGCGAGTCAGGTGT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	21											86	86	86					21																	41033164		2203	4300	6503	39955034	SO:0001819	synonymous_variant	10317			AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"Beta 3-glycosyltransferases"	920	protein-coding gene	gene with protein product	"homolog of C. elegans Bt toxin resistance gene bre-5", "GlcNAc-beta-1,3-galactosyltransferase 5"	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.678G>A	21.37:g.41033164G>A			39955034	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Silent	SNP	ENST00000380620.4	37	CCDS13667.1																																																																																				0.522	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170		A	41033164	G	A	41033164	2	1	61	1	0	0	0	0	0	0	0	1	1251	1045	37	1		1	B3GALT5	21	41033164	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	334	41033164	7096731	11799	19784										
B3GALT5	10317	broad.mit.edu	37	chr21	41033348	41033348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgtggcctgccacttcatcAagcctcggactctcttggac	9	15	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41033348A>G	ENST00000380620.4	+	5	1454	c.862A>G	c.(862-864)Aag>Gag	p.K288E	AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000398714.2_Missense_Mutation_p.K288E|B3GALT5_ENST00000343118.4_Missense_Mutation_p.K288E|B3GALT5_ENST00000380618.1_Missense_Mutation_p.K288E			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	288					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.K288E(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				CCACTTCATCAAGCCTCGGAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	21											56	56	56					21																	41033348		2203	4299	6502	39955218	SO:0001583	missense	10317			AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"Beta 3-glycosyltransferases"	920	protein-coding gene	gene with protein product	"homolog of C. elegans Bt toxin resistance gene bre-5", "GlcNAc-beta-1,3-galactosyltransferase 5"	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.862A>G	21.37:g.41033348A>G	ENSP00000369994:p.Lys288Glu		39955218	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	37	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324352	0.41197	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.51	1.82	0.25136	.	0.191405	0.34628	N	0.003805	T	0.28797	0.0714	M	0.65320	2	0.32986	D	0.524349	B	0.27380	0.177	B	0.25405	0.06	T	0.29274	-1.0017	10	0.18710	T	0.47	.	6.4848	0.22083	0.7143:0.1445:0.1412:0.0	.	288	Q9Y2C3	B3GT5_HUMAN	E	288	ENSP00000369994:K288E;ENSP00000369992:K288E;ENSP00000343318:K288E;ENSP00000381699:K288E	ENSP00000343318:K288E	K	+	1	0	B3GALT5	39955218	0.002000	0.14202	0.002000	0.10522	0.010000	0.07245	1.363000	0.34159	0.062000	0.16340	0.459000	0.35465	AAG		0.582	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170		G	41033348	A	G	41033348	3	3	61	1	0	0	0	0	1	0	0	0	1251	131	5	4	864	4	B3GALT5	21	41033348	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	184	41033348	7096547	11800	19785										
IGSF5	150084	broad.mit.edu	37	chr21	41137531	41137531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctgaagggctcccaggctcGcttcaactgcaccgtctccc	9	18	2	1	rs372378189		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41137531G>A	ENST00000380588.4	+	3	273	c.170G>A	c.(169-171)cGc>cAc	p.R57H	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	57	Ig-like V-type 1.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R57H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				TCCCAGGCTCGCTTCAACTGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	21						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	71	63	66		170	2.2	1	21		66	0,8600		0,0,4300	no	missense	IGSF5	NM_001080444.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	57/408	41137531	1,13005	2203	4300	6503	40059401	SO:0001583	missense	150084				CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.170G>A	21.37:g.41137531G>A	ENSP00000369962:p.Arg57His		40059401		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693871	0.30052	2.27E-4	0.0	ENSG00000183067	ENST00000380588	T	0.28069	1.63	4.05	2.18	0.27775	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.290921	0.33631	N	0.004711	T	0.20210	0.0486	L	0.36672	1.1	0.32231	N	0.573921	P	0.39665	0.682	B	0.35312	0.2	T	0.19516	-1.0303	10	0.33940	T	0.23	-12.2058	9.2585	0.37597	0.1767:0.0:0.8233:0.0	.	57	Q9NSI5	IGSF5_HUMAN	H	57	ENSP00000369962:R57H	ENSP00000369962:R57H	R	+	2	0	IGSF5	40059401	0.998000	0.40836	0.999000	0.59377	0.533000	0.34776	1.174000	0.31932	0.430000	0.26230	-0.142000	0.14014	CGC		0.527	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			A	41137531	G	A	41137531	3	1	61	1	0	0	0	0	1	0	0	0	7623	1087	38	1	180	1	IGSF5	21	41137531	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	104183	41137531	6992364	11801	19786										
IGSF5	150084	broad.mit.edu	37	chr21	41151230	41151230	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgctgtagaagaaaaaGaggtaatttttttgttcatt	8	3	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41151230G>T	ENST00000380588.4	+	5	1035	c.932G>T	c.(931-933)aGa>aTa	p.R311I	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	311					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R311I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				AGAAGAAAAAGAGGTAATTTT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	21											59	53	55					21																	41151230		2203	4300	6503	40073100	SO:0001583	missense	150084				CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.932G>T	21.37:g.41151230G>T	ENSP00000369962:p.Arg311Ile		40073100		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	G	5.532	0.283067	0.10458	.	.	ENSG00000183067	ENST00000380588	T	0.06371	3.31	4.24	1.88	0.25563	.	0.552019	0.20487	N	0.091372	T	0.02688	0.0081	N	0.08118	0	0.38994	D	0.959216	B	0.30361	0.277	B	0.25405	0.06	T	0.52139	-0.8615	10	0.42905	T	0.14	-8.0378	3.9995	0.09574	0.6732:0.214:0.1128:0.0	.	311	Q9NSI5	IGSF5_HUMAN	I	311	ENSP00000369962:R311I	ENSP00000369962:R311I	R	+	2	0	IGSF5	40073100	0.998000	0.40836	0.598000	0.28837	0.014000	0.08584	1.160000	0.31761	0.408000	0.25621	-0.302000	0.09304	AGA		0.413	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			T	41151230	G	T	41151230	3	4	61	1	0	0	0	0	1	0	0	0	7623	942	33	2	950	2	IGSF5	21	41151230	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13699	41151230	6978665	11802	19787										
DSCAM	1826	broad.mit.edu	37	chr21	41385275	41385275	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accacctcggtttaacaaaaAgtccattctaaggtatggag	8	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41385275A>C	ENST00000400454.1	-	33	6202	c.5725T>G	c.(5725-5727)Ttt>Gtt	p.F1909V		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1909				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.F1909V(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTTAACAAAAAGTCCATTCTA	0.502																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - Missense(1)	large_intestine(1)	21											47	47	47					21																	41385275		1979	4144	6123	40307145	SO:0001583	missense	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5725T>G	21.37:g.41385275A>C	ENSP00000383303:p.Phe1909Val		40307145	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	.	15.28	2.787378	0.49997	.	.	ENSG00000171587	ENST00000400454	T	0.58210	0.35	5.39	5.39	0.77823	.	0.103096	0.64402	D	0.000002	T	0.59155	0.2173	L	0.27053	0.805	0.48511	D	0.999663	D	0.57899	0.981	D	0.67900	0.954	T	0.58880	-0.7558	10	0.37606	T	0.19	.	15.4428	0.75200	1.0:0.0:0.0:0.0	.	1909	O60469	DSCAM_HUMAN	V	1909	ENSP00000383303:F1909V	ENSP00000383303:F1909V	F	-	1	0	DSCAM	40307145	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.721000	0.91446	2.044000	0.60594	0.460000	0.39030	TTT		0.502	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41385275	A	C	41385275	3	2	61	1	0	0	0	0	1	0	0	0	4779	72	3	4	317	4	DSCAM	21	41385275	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	234045	41385275	6744620	11803	19788										
DSCAM	1826	broad.mit.edu	37	chr21	41447046	41447046	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagcaagacccccaccagGatacaggagatggtcaccag	11	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41447046G>A	ENST00000400454.1	-	27	5283	c.4806C>T	c.(4804-4806)atC>atT	p.I1602I		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1602					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.I1602I(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCCCCACCAGGATACAGGAGA	0.567																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - coding silent(1)	large_intestine(1)	21											109	123	118					21																	41447046		2100	4221	6321	40368916	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4806C>T	21.37:g.41447046G>A			40368916	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.567	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41447046	G	A	41447046	2	1	61	1	0	0	0	0	0	0	0	1	4779	1164	41	3		3	DSCAM	21	41447046	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61771	41447046	6682849	11804	19789										
DSCAM	1826	broad.mit.edu	37	chr21	41450636	41450636	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatcgtagttcagcgtagcGaagttggcctgcttctccgc	11	13	2	0	rs201376842		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41450636G>A	ENST00000400454.1	-	26	5166	c.4689C>T	c.(4687-4689)ttC>ttT	p.F1563F		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1563	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.F1563F(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TCAGCGTAGCGAAGTTGGCCT	0.592																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - coding silent(1)	large_intestine(1)	21											81	85	83					21																	41450636		2190	4288	6478	40372506	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4689C>T	21.37:g.41450636G>A			40372506	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.592	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41450636	G	A	41450636	2	1	61	1	0	0	0	0	0	0	0	1	4779	1049	37	1		1	DSCAM	21	41450636	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3590	41450636	6679259	11805	19790										
DSCAM	1826	broad.mit.edu	37	chr21	41457622	41457622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtcttctgctttcaccgtgcGaataatgaagcttccgttgc	9	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41457622G>A	ENST00000400454.1	-	23	4516	c.4039C>T	c.(4039-4041)Cgc>Tgc	p.R1347C		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1347	Ig-like C2-type 10.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R1347C(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTCACCGTGCGAATAATGAAG	0.438																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - Missense(1)	large_intestine(1)	21											103	99	101					21																	41457622		1904	4131	6035	40379492	SO:0001583	missense	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4039C>T	21.37:g.41457622G>A	ENSP00000383303:p.Arg1347Cys		40379492	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542721	0.85917	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.68479	-0.33;-0.33	5.41	5.41	0.78517	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.058746	0.64402	D	0.000003	T	0.78892	0.4355	M	0.69463	2.115	0.80722	D	1	D	0.89917	1.0	D	0.63793	0.918	T	0.80901	-0.1175	10	0.72032	D	0.01	.	15.573	0.76354	0.0:0.0:0.8618:0.1382	.	1347	O60469	DSCAM_HUMAN	C	1347;1099	ENSP00000383303:R1347C;ENSP00000385342:R1099C	ENSP00000383303:R1347C	R	-	1	0	DSCAM	40379492	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.730000	0.84881	2.523000	0.85059	0.655000	0.94253	CGC		0.438	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41457622	G	A	41457622	3	1	61	1	0	0	0	0	1	0	0	0	4779	1058	37	1	2043	1	DSCAM	21	41457622	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6986	41457622	6672273	11806	19791										
DSCAM	1826	broad.mit.edu	37	chr21	41561162	41561162	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataggatgttatcatcgcaGgaactgaaaaagcaaaaggg	12	5	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:41561162G>T	ENST00000400454.1	-	12	2837	c.2360C>A	c.(2359-2361)cCt>cAt	p.P787H		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	787	Ig-like C2-type 9.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.P787H(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TATCATCGCAGGAACTGAAAA	0.473																																					Melanoma(134;970 1778 1785 21664 32388)											1	Substitution - Missense(1)	large_intestine(1)	21											68	66	67					21																	41561162		1940	4135	6075	40483032	SO:0001583	missense	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.2360C>A	21.37:g.41561162G>T	ENSP00000383303:p.Pro787His		40483032	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.164677	0.57476	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.52295	0.67;0.67	5.28	5.28	0.74379	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059233	0.64402	D	0.000001	T	0.70081	0.3183	M	0.89163	3.01	0.58432	D	0.999999	D	0.65815	0.995	P	0.55667	0.781	T	0.77819	-0.2446	10	0.87932	D	0	.	18.9074	0.92467	0.0:0.0:1.0:0.0	.	787	O60469	DSCAM_HUMAN	H	787;539	ENSP00000383303:P787H;ENSP00000385342:P539H	ENSP00000383303:P787H	P	-	2	0	DSCAM	40483032	1.000000	0.71417	0.988000	0.46212	0.037000	0.13140	9.704000	0.98716	2.441000	0.82636	0.561000	0.74099	CCT		0.473	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41561162	G	T	41561162	3	4	61	1	0	0	0	0	1	0	0	0	4779	1000	35	2	3766	2	DSCAM	21	41561162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103540	41561162	6568733	11807	19792										
MX2	4600	broad.mit.edu	37	chr21	42778810	42778810	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaagtccgagaagagatttTtaaccctctggggacgcctt	11	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:42778810T>G	ENST00000330714.3	+	13	1974	c.1790T>G	c.(1789-1791)tTt>tGt	p.F597C		NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	597					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F597C(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GAAGAGATTTTTAACCCTCTG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	21											126	124	125					21																	42778810		2203	4300	6503	41700680	SO:0001583	missense	4600				CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"interferon-regulated resistance GTP-binding protein MXB", "second interferon-induced protein p78"	147890	"myxovirus (influenza) resistance 2, homolog of murine", "myxovirus (influenza virus) resistance 2 (mouse)"			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.1790T>G	21.37:g.42778810T>G	ENSP00000333657:p.Phe597Cys		41700680	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	37	CCDS13672.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746245	0.30955	.	.	ENSG00000183486	ENST00000330714;ENST00000398632	D	0.89810	-2.57	3.11	-3.14	0.05250	.	1.316200	0.06722	U	0.775121	D	0.83257	0.5215	N	0.14661	0.345	0.09310	N	1	P	0.52170	0.951	P	0.59115	0.852	T	0.71580	-0.4550	10	0.44086	T	0.13	.	0.3606	0.00363	0.1887:0.2525:0.1926:0.3662	.	597	P20592	MX2_HUMAN	C	597;71	ENSP00000333657:F597C	ENSP00000333657:F597C	F	+	2	0	MX2	41700680	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.068000	0.11561	-0.612000	0.05701	0.477000	0.44152	TTT		0.413	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463		G	42778810	T	G	42778810	3	3	61	1	0	0	0	0	1	0	0	0	10028	1841	64	4	1836	4	MX2	21	42778810	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1217648	42778810	5351085	11808	19793										
TMPRSS2	7113	broad.mit.edu	37	chr21	42852441	42852441	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggccgcccgcccgtagttCtcgttccagtcgtcttggca	11	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:42852441C>A	ENST00000332149.5	-	6	668	c.534G>T	c.(532-534)gaG>gaT	p.E178D	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.E215D|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.E178D	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	178	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.E178D(2)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GCCCGTAGTTCTCGTTCCAGT	0.572			T	"ERG, ETV1, ETV4, ETV5"	prostate																																		Dom	yes		21	21q22.3	7113	"transmembrane protease, serine 2"		E	2	Substitution - Missense(2)	large_intestine(2)	21											61	55	57					21																	42852441		2203	4300	6503	41774311	SO:0001583	missense	7113			U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"Serine peptidases / Transmembrane"	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.534G>T	21.37:g.42852441C>A	ENSP00000330330:p.Glu178Asp		41774311	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.637259	0.00799	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	5.12	-5.23	0.02798	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.259165	0.31542	N	0.007477	T	0.12178	0.0296	N	0.01771	-0.73	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.34551	-0.9824	10	0.02654	T	1	.	6.395	0.21607	0.1572:0.2134:0.5431:0.0862	.	215;178	F8WES1;O15393	.;TMPS2_HUMAN	D	178;215;178;178;138	ENSP00000330330:E178D;ENSP00000381588:E215D;ENSP00000391216:E178D;ENSP00000389006:E178D;ENSP00000397846:E138D	ENSP00000330330:E178D	E	-	3	2	TMPRSS2	41774311	0.000000	0.05858	0.002000	0.10522	0.058000	0.15608	-0.420000	0.07062	-0.746000	0.04766	0.561000	0.74099	GAG		0.572	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1			A	42852441	C	A	42852441	3	1	61	1	0	0	0	0	1	0	0	0	16286	912	32	2	980	2	TMPRSS2	21	42852441	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	73631	42852441	5277454	11809	19794										
UMODL1	89766	broad.mit.edu	37	chr21	43522304	43522304	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtatttgaagtcacaataaaGattgtaaaccacaacctgac	6	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43522304G>T	ENST00000408910.2	+	8	1215	c.1215G>T	c.(1213-1215)aaG>aaT	p.K405N	UMODL1_ENST00000408989.2_Missense_Mutation_p.K405N|UMODL1_ENST00000400424.2_Missense_Mutation_p.K333N|C21orf128_ENST00000329015.2_3'UTR|UMODL1_ENST00000400427.1_Missense_Mutation_p.K333N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	405	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)	p.K333N(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TCACAATAAAGATTGTAAACC	0.428																																					Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)											1	Substitution - Missense(1)	large_intestine(1)	21											94	93	94					21																	43522304		1902	4111	6013	42395373	SO:0001583	missense	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1215G>T	21.37:g.43522304G>T	ENSP00000386147:p.Lys405Asn		42395373	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.596153	0.28445	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	3.99	3.99	0.46301	SEA (1);	0.121858	0.35677	N	0.003044	T	0.42086	0.1187	L	0.40543	1.245	0.80722	D	1	B;B;B	0.26120	0.142;0.039;0.048	B;B;B	0.38020	0.135;0.12;0.263	T	0.49513	-0.8932	10	0.87932	D	0	-17.1138	13.8624	0.63569	0.0:0.0:1.0:0.0	.	333;405;405	Q5DID0-3;Q5DID0-2;Q5DID0	.;.;UROL1_HUMAN	N	333;333;405;405	ENSP00000383279:K333N;ENSP00000383276:K333N;ENSP00000386126:K405N;ENSP00000386147:K405N	ENSP00000383276:K333N	K	+	3	2	UMODL1	42395373	0.998000	0.40836	0.257000	0.24404	0.222000	0.24845	1.199000	0.32235	2.173000	0.68751	0.655000	0.94253	AAG		0.428	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43522304	G	T	43522304	3	4	61	1	0	0	0	0	1	0	0	0	17020	933	33	2	1245	2	UMODL1	21	43522304	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	669863	43522304	4607591	11810	19795										
ABCG1	9619	broad.mit.edu	37	chr21	43714699	43714699	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatcccggtgctcctgttCtcggggttcttcgtcagctt	11	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43714699C>A	ENST00000361802.2	+	14	1882	c.1737C>A	c.(1735-1737)ttC>ttA	p.F579L	ABCG1_ENST00000343687.3_Missense_Mutation_p.F578L|ABCG1_ENST00000347800.2_Missense_Mutation_p.F564L|ABCG1_ENST00000340588.4_Missense_Mutation_p.F687L|ABCG1_ENST00000398449.3_Missense_Mutation_p.F567L|ABCG1_ENST00000398457.2_Missense_Mutation_p.F569L|ABCG1_ENST00000398437.1_Missense_Mutation_p.F725L|ABCG1_ENST00000462050.1_3'UTR	NM_004915.3	NP_004906.3	P45844	ABCG1_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 1	579	ABC transmembrane type-2.				amyloid precursor protein catabolic process (GO:0042987)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|detection of hormone stimulus (GO:0009720)|glycoprotein transport (GO:0034436)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of cholesterol efflux (GO:0010875)|regulation of cholesterol esterification (GO:0010872)|regulation of transcription, DNA-templated (GO:0006355)|response to high density lipoprotein particle (GO:0055099)|response to lipid (GO:0033993)|response to organic substance (GO:0010033)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|glycoprotein transporter activity (GO:0034437)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sterol-transporting ATPase activity (GO:0034041)|toxin transporter activity (GO:0019534)	p.F569L(1)|p.F579L(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(3)|prostate(2)|stomach(1)	29					Adenosine triphosphate(DB00171)	TGCTCCTGTTCTCGGGGTTCT	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	21											140	110	120					21																	43714699		2203	4300	6503	42587768	SO:0001583	missense	9619			U34919	CCDS13681.1, CCDS13682.1, CCDS13683.1, CCDS42937.1, CCDS42938.1	21q22.3	2012-03-14			ENSG00000160179	ENSG00000160179		"ATP binding cassette transporters / subfamily G"	73	protein-coding gene	gene with protein product	"ATP-binding cassette transporter 8"	603076				8659545, 16870176	Standard	NM_016818		Approved	ABC8	uc002zaq.3	P45844	OTTHUMG00000086791	ENST00000361802.2:c.1737C>A	21.37:g.43714699C>A	ENSP00000354995:p.Phe579Leu		42587768	Q86SU8|Q96L76|Q9BXK6|Q9BXK7|Q9BXK8|Q9BXK9|Q9BXL0|Q9BXL1|Q9BXL2|Q9BXL3|Q9BXL4	Missense_Mutation	SNP	ENST00000361802.2	37	CCDS13682.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.77|15.77	2.932966|2.932966	0.52866|0.52866	.|.	.|.	ENSG00000160179|ENSG00000160179	ENST00000398457;ENST00000347800;ENST00000398449;ENST00000361802;ENST00000343687;ENST00000398437;ENST00000340588|ENST00000489035;ENST00000469119	T;T;T;T;T;T;T|.	0.69926|.	-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44|.	4.55|4.55	3.67|3.67	0.42095|0.42095	ABC-2 type transporter (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60011|0.60011	0.2236|0.2236	L|L	0.58428|0.58428	1.81|1.81	0.58432|0.58432	D|D	0.999994|0.999994	P;P;D;B;B;D|.	0.56035|.	0.546;0.713;0.97;0.163;0.349;0.974|.	P;P;P;B;B;D|.	0.70487|.	0.464;0.479;0.859;0.17;0.331;0.969|.	T|T	0.56619|0.56619	-0.7949|-0.7949	9|5	.|.	.|.	.|.	-38.7267|-38.7267	8.7425|8.7425	0.34567|0.34567	0.0:0.7581:0.0:0.2419|0.0:0.7581:0.0:0.2419	.|.	590;578;579;567;564;569|.	B4DPT7;P45844-2;P45844;P45844-4;P45844-5;P45844-3|.	.;.;ABCG1_HUMAN;.;.;.|.	L|I	569;564;567;579;578;725;687|315;303	ENSP00000381475:F569L;ENSP00000291524:F564L;ENSP00000381467:F567L;ENSP00000354995:F579L;ENSP00000339744:F578L;ENSP00000381464:F725L;ENSP00000343820:F687L|.	.|.	F|L	+|+	3|1	2|0	ABCG1|ABCG1	42587768|42587768	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.696000|0.696000	0.40369|0.40369	2.429000|2.429000	0.44758|0.44758	1.039000|1.039000	0.40074|0.40074	0.484000|0.484000	0.47621|0.47621	TTC|CTC		0.617	ABCG1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195318.2	NM_207174		A	43714699	C	A	43714699	3	1	61	1	0	0	0	0	1	0	0	0	68	912	32	2	1959	2	ABCG1	21	43714699	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192395	43714699	4415196	11811	19796										
ABCG1	9619	broad.mit.edu	37	chr21	43716283	43716283	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcctcctaggtatgggttCgaaggggtcatcctctccat	10	11	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43716283C>T	ENST00000361802.2	+	15	1963	c.1818C>T	c.(1816-1818)ttC>ttT	p.F606F	ABCG1_ENST00000343687.3_Silent_p.F605F|ABCG1_ENST00000347800.2_Silent_p.F591F|ABCG1_ENST00000340588.4_Silent_p.F714F|ABCG1_ENST00000398449.3_Silent_p.F594F|ABCG1_ENST00000398457.2_Silent_p.F596F|ABCG1_ENST00000398437.1_Silent_p.F752F|ABCG1_ENST00000462050.1_3'UTR	NM_004915.3	NP_004906.3	P45844	ABCG1_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 1	606	ABC transmembrane type-2.				amyloid precursor protein catabolic process (GO:0042987)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|detection of hormone stimulus (GO:0009720)|glycoprotein transport (GO:0034436)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of cholesterol efflux (GO:0010875)|regulation of cholesterol esterification (GO:0010872)|regulation of transcription, DNA-templated (GO:0006355)|response to high density lipoprotein particle (GO:0055099)|response to lipid (GO:0033993)|response to organic substance (GO:0010033)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|glycoprotein transporter activity (GO:0034437)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sterol-transporting ATPase activity (GO:0034041)|toxin transporter activity (GO:0019534)	p.F596F(2)|p.F606F(2)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(3)|prostate(2)|stomach(1)	29					Adenosine triphosphate(DB00171)	GGTATGGGTTCGAAGGGGTCA	0.587																																																4	Substitution - coding silent(4)	large_intestine(4)	21											110	90	97					21																	43716283		2203	4300	6503	42589352	SO:0001819	synonymous_variant	9619			U34919	CCDS13681.1, CCDS13682.1, CCDS13683.1, CCDS42937.1, CCDS42938.1	21q22.3	2012-03-14			ENSG00000160179	ENSG00000160179		"ATP binding cassette transporters / subfamily G"	73	protein-coding gene	gene with protein product	"ATP-binding cassette transporter 8"	603076				8659545, 16870176	Standard	NM_016818		Approved	ABC8	uc002zaq.3	P45844	OTTHUMG00000086791	ENST00000361802.2:c.1818C>T	21.37:g.43716283C>T			42589352	Q86SU8|Q96L76|Q9BXK6|Q9BXK7|Q9BXK8|Q9BXK9|Q9BXL0|Q9BXL1|Q9BXL2|Q9BXL3|Q9BXL4	Silent	SNP	ENST00000361802.2	37	CCDS13682.1																																																																																				0.587	ABCG1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195318.2	NM_207174		T	43716283	C	T	43716283	2	4	61	1	0	0	0	0	0	0	0	1	68	883	31	1		1	ABCG1	21	43716283	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1584	43716283	4413612	11812	19797										
UBASH3A	53347	broad.mit.edu	37	chr21	43836697	43836697	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgcagcactctactcccgaGacatgcgctttgtgcactac	8	16	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43836697G>T	ENST00000319294.6	+	6	845	c.814G>T	c.(814-816)Gac>Tac	p.D272Y	UBASH3A_ENST00000398367.1_Missense_Mutation_p.D234Y|UBASH3A_ENST00000291535.6_Missense_Mutation_p.D234Y|RNU6-1149P_ENST00000516810.1_RNA	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	272					negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.D272Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CTACTCCCGAGACATGCGCTT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	21											32	30	31					21																	43836697		2203	4300	6503	42709766	SO:0001583	missense	53347			AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.814G>T	21.37:g.43836697G>T	ENSP00000317327:p.Asp272Tyr		42709766	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Missense_Mutation	SNP	ENST00000319294.6	37	CCDS13687.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703397	0.88924	.	.	ENSG00000160185	ENST00000291535;ENST00000319294;ENST00000398367	T;T;T	0.17528	2.46;2.38;2.27	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000017	T	0.46870	0.1415	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.52895	-0.8514	10	0.87932	D	0	-50.2448	18.4014	0.90518	0.0:0.0:1.0:0.0	.	234;234;272	G5E9E4;P57075-2;P57075	.;.;UBS3A_HUMAN	Y	234;272;234	ENSP00000291535:D234Y;ENSP00000317327:D272Y;ENSP00000381408:D234Y	ENSP00000291535:D234Y	D	+	1	0	UBASH3A	42709766	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.201000	0.95017	2.336000	0.79503	0.591000	0.81541	GAC		0.617	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895		T	43836697	G	T	43836697	3	4	61	1	0	0	0	0	1	0	0	0	16879	942	33	2	836	2	UBASH3A	21	43836697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	120414	43836697	4293198	11813	19798										
UBASH3A	53347	broad.mit.edu	37	chr21	43864744	43864744	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggggattttgcccaactCgtgagaaaggtacgcgccca	13	10	0	1	rs61735848		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43864744C>T	ENST00000319294.6	+	14	1870	c.1839C>T	c.(1837-1839)ctC>ctT	p.L613L	UBASH3A_ENST00000398367.1_Intron|UBASH3A_ENST00000291535.6_Silent_p.L575L	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	613	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.L613L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						TTGCCCAACTCGTGAGAAAGG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	21											74	79	77					21																	43864744		2203	4300	6503	42737813	SO:0001819	synonymous_variant	53347			AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1839C>T	21.37:g.43864744C>T			42737813	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																				0.557	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895		T	43864744	C	T	43864744	2	4	61	1	0	0	0	0	0	0	0	1	16879	871	31	1		1	UBASH3A	21	43864744	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28047	43864744	4265151	11814	19799										
RSPH1	89765	broad.mit.edu	37	chr21	43913086	43913086	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cggttctgacctggccatgtCttttaccgaattcgtagctc	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:43913086C>A	ENST00000291536.3	-	2	325	c.158G>T	c.(157-159)aGa>aTa	p.R53I	RSPH1_ENST00000398352.3_Intron	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	53					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.R53I(1)		large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						CTGGCCATGTCTTTTACCGAA	0.488																																					Esophageal Squamous(23;63 706 6286 10288 12913)											1	Substitution - Missense(1)	large_intestine(1)	21											245	211	222					21																	43913086		2203	4300	6503	42786155	SO:0001583	missense	89765			AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"meichroacidin"	609314	"testis specific A2 homolog (mouse)"	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.158G>T	21.37:g.43913086C>A	ENSP00000291536:p.Arg53Ile		42786155	A8MWV0|B2RBN9|Q3MJA1	Missense_Mutation	SNP	ENST00000291536.3	37	CCDS13688.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.767810	0.90020	.	.	ENSG00000160188	ENST00000291536	T	0.59083	0.29	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	L	0.49455	1.56	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66122	-0.6002	10	0.23891	T	0.37	.	17.868	0.88801	0.0:1.0:0.0:0.0	.	53	Q8WYR4	RSPH1_HUMAN	I	53	ENSP00000291536:R53I	ENSP00000291536:R53I	R	-	2	0	RSPH1	42786155	0.999000	0.42202	0.953000	0.39169	0.912000	0.54170	6.691000	0.74573	2.284000	0.76573	0.462000	0.41574	AGA		0.488	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1			A	43913086	C	A	43913086	3	1	61	1	0	0	0	0	1	0	0	0	13739	913	32	2	803	2	RSPH1	21	43913086	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	48342	43913086	4216809	11815	19800										
PDE9A	5152	broad.mit.edu	37	chr21	44180989	44180989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgacagcggccatctgccacGatctggaccatcccggctac	10	16	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:44180989G>A	ENST00000291539.6	+	13	1117	c.1057G>A	c.(1057-1059)Gat>Aat	p.D353N	PDE9A_ENST00000335512.4_Missense_Mutation_p.D293N|PDE9A_ENST00000398227.3_Missense_Mutation_p.D193N|PDE9A_ENST00000349112.3_Missense_Mutation_p.D225N|PDE9A_ENST00000539837.1_Missense_Mutation_p.D225N|PDE9A_ENST00000398236.3_Missense_Mutation_p.D267N|PDE9A_ENST00000398232.3_Missense_Mutation_p.D286N|PDE9A_ENST00000335440.6_Missense_Mutation_p.D251N|PDE9A_ENST00000398229.3_Missense_Mutation_p.D219N|PDE9A_ENST00000328862.6_Missense_Mutation_p.D327N|PDE9A_ENST00000398224.3_Missense_Mutation_p.D226N|PDE9A_ENST00000398234.3_Missense_Mutation_p.D252N|PDE9A_ENST00000380328.2_Missense_Mutation_p.D300N|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398225.3_Missense_Mutation_p.D312N	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	353	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)	p.D353N(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CATCTGCCACGATCTGGACCA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	21											131	110	117					21																	44180989		2203	4300	6503	43054058	SO:0001583	missense	5152			AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1057G>A	21.37:g.44180989G>A	ENSP00000291539:p.Asp353Asn		43054058	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	G	32	5.166043	0.94768	.	.	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	5.15	5.15	0.70609	Metal-dependent phosphohydrolase, HD domain (1);-cyclic nucleotide phosphodiesterase, conserved site (1);5&apos (3);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (3);	0.000000	0.85682	D	0.000000	D	0.97448	0.9165	H	0.99609	4.655	0.58432	D	0.999993	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.998;0.998;0.999;0.998;0.997;0.997;0.998;0.953;0.998;0.998;0.998;0.996;0.998;0.998;0.99	D	0.99797	1.1034	10	0.87932	D	0	.	18.6364	0.91380	0.0:0.0:1.0:0.0	.	225;286;267;252;327;312;245;293;136;193;219;225;251;300;226;353	F5GWD0;O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	N	293;225;353;300;286;252;267;327;251;312;219;193;225;226	ENSP00000335242:D293N;ENSP00000441899:D225N;ENSP00000291539:D353N;ENSP00000369685:D300N;ENSP00000381287:D286N;ENSP00000381289:D252N;ENSP00000381291:D267N;ENSP00000328699:D327N;ENSP00000335365:D251N;ENSP00000381281:D312N;ENSP00000381285:D219N;ENSP00000381283:D193N;ENSP00000344730:D225N;ENSP00000381280:D226N	ENSP00000291539:D353N	D	+	1	0	PDE9A	43054058	1.000000	0.71417	0.621000	0.29145	0.894000	0.52154	8.887000	0.92456	2.382000	0.81193	0.655000	0.94253	GAT		0.493	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			A	44180989	G	A	44180989	3	1	61	1	0	0	0	0	1	0	0	0	11686	1058	37	1	1187	1	PDE9A	21	44180989	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	267903	44180989	3948906	11816	19801										
WDR4	10785	broad.mit.edu	37	chr21	44293684	44293684	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acactcagacattgccatggTtttgtacggaaaagaatcag	9	8	2	2	rs565775371		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:44293684T>C	ENST00000398208.2	-	3	332	c.273A>G	c.(271-273)aaA>aaG	p.K91K	WDR4_ENST00000492742.1_Intron|WDR4_ENST00000330317.2_Silent_p.K91K	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4									p.K91K(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		ATTGCCATGGTTTTGTACGGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	21											261	227	238					21																	44293684		2203	4300	6503	43166753	SO:0001819	synonymous_variant	10785			AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"WD repeat domain containing"	12756	protein-coding gene	gene with protein product	"TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.273A>G	21.37:g.44293684T>C			43166753		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																				0.478	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1			C	44293684	T	C	44293684	2	2	61	1	0	0	0	0	0	0	0	1	17333	1722	60	4		4	WDR4	21	44293684	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	112695	44293684	3836211	11817	19802										
NDUFV3	4731	broad.mit.edu	37	chr21	44317064	44317064	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccaggaagcccaggtgtttCgaggacttgcttctacggtt	12	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:44317064C>T	ENST00000340344.4	+	2	142	c.76C>T	c.(76-78)Cga>Tga	p.R26*	NDUFV3_ENST00000460259.1_3'UTR|NDUFV3_ENST00000354250.2_Nonsense_Mutation_p.R26*	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa	26					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)	p.R26*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		CCAGGTGTTTCGAGGACTTGC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											85	84	84					21																	44317064		2203	4300	6503	43190133	SO:0001587	stop_gained	4731				CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.76C>T	21.37:g.44317064C>T	ENSP00000342895:p.Arg26*		43190133	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Nonsense_Mutation	SNP	ENST00000340344.4	37	CCDS33573.1	.	.	.	.	.	.	.	.	.	.	C	35	5.564933	0.96527	.	.	ENSG00000160194	ENST00000354250;ENST00000340344;ENST00000398198	.	.	.	5.3	4.42	0.53409	.	0.616872	0.16245	N	0.222979	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-5.639	9.8864	0.41264	0.0:0.905:0.0:0.095	.	.	.	.	X	26;26;9	.	ENSP00000342895:R26X	R	+	1	2	NDUFV3	43190133	0.995000	0.38212	0.926000	0.36857	0.849000	0.48306	2.984000	0.49353	1.353000	0.45828	0.655000	0.94253	CGA		0.393	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			T	44317064	C	T	44317064	4	4	61	1	0	0	0	0	0	1	0	0	10332	876	31	1	82	1	NDUFV3	21	44317064	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23380	44317064	3812831	11818	19803										
U2AF1	7307	broad.mit.edu	37	chr21	44513342	44513342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaacgacgctcccgggatCgggatcttgatctatgcctg	13	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:44513342C>T	ENST00000291552.4	-	8	685	c.593G>A	c.(592-594)cGa>cAa	p.R198Q	U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.R198Q|U2AF1_ENST00000459639.1_Missense_Mutation_p.R125Q|U2AF1_ENST00000398137.1_Missense_Mutation_p.R125Q	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	198	Arg/Gly/Ser-rich (RS domain).				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R198Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						CTCCCGGGATCGGGATCTTGA	0.622			Mis		"CLL, MDS"																																		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	1	Substitution - Missense(1)	large_intestine(1)	21											49	55	53					21																	44513342		2203	4300	6503	43386411	SO:0001583	missense	7307			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"RNA binding motif (RRM) containing"	12453	protein-coding gene	gene with protein product		191317	"U2(RNU2) small nuclear RNA auxiliary factor binding protein", "U2(RNU2) small nuclear RNA auxiliary factor 1"	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.593G>A	21.37:g.44513342C>T	ENSP00000291552:p.Arg198Gln		43386411	Q701P4|Q71RF1	Missense_Mutation	SNP	ENST00000291552.4	37	CCDS13694.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.956055	0.73902	.	.	ENSG00000160201	ENST00000459639;ENST00000380276;ENST00000291552;ENST00000398137	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	4.81	4.81	0.61882	.	0.052628	0.64402	D	0.000002	T	0.20414	0.0491	L	0.54323	1.7	0.80722	D	1	P;P	0.50369	0.934;0.934	P;P	0.49528	0.614;0.614	T	0.00770	-1.1573	10	0.56958	D	0.05	-11.7919	18.2435	0.89977	0.0:1.0:0.0:0.0	.	198;198	Q01081;Q701P4	U2AF1_HUMAN;.	Q	125;198;198;125	ENSP00000418705:R125Q;ENSP00000369629:R198Q;ENSP00000291552:R198Q;ENSP00000381205:R125Q	ENSP00000291552:R198Q	R	-	2	0	U2AF1	43386411	1.000000	0.71417	0.994000	0.49952	0.850000	0.48378	6.219000	0.72231	2.371000	0.80710	0.563000	0.77884	CGA		0.622	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195541.1	NM_006758		T	44513342	C	T	44513342	3	4	61	1	0	0	0	0	1	0	0	0	16861	884	31	1	133	1	U2AF1	21	44513342	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	196278	44513342	3616553	11819	19804										
DNMT3L	29947	broad.mit.edu	37	chr21	45671557	45671557	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtgtggcgccgtacacaaGatcgaagggtccccactcct	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:45671557G>T	ENST00000418993.1	-	9	1201	c.718C>A	c.(718-720)Ctt>Att	p.L240I	AP001059.5_ENST00000442785.1_RNA|DNMT3L_ENST00000270172.3_Missense_Mutation_p.L240I	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	240					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)	p.L240I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		CCGTACACAAGATCGAAGGGT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	21											99	72	81					21																	45671557		2203	4300	6503	44495985	SO:0001583	missense	29947			AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"cytosine-5-methyltransferase 3-like protein", "human cytosine-5-methyltransferase 3-like protein"	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.718C>A	21.37:g.45671557G>T	ENSP00000412862:p.Leu240Ile		44495985	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666510	0.29604	.	.	ENSG00000142182	ENST00000270172;ENST00000418993;ENST00000431166	T;T;T	0.80393	-1.37;-1.37;-1.37	2.81	1.9	0.25705	.	0.000000	0.64402	D	0.000012	D	0.87196	0.6117	M	0.82716	2.605	0.39612	D	0.96989	D;D	0.61697	0.99;0.99	D;D	0.85130	0.997;0.997	D	0.85050	0.0928	10	0.48119	T	0.1	-29.334	6.0894	0.19985	0.1469:0.0:0.8531:0.0	.	240;240	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	I	240;240;225	ENSP00000270172:L240I;ENSP00000412862:L240I;ENSP00000400242:L225I	ENSP00000270172:L240I	L	-	1	0	DNMT3L	44495985	1.000000	0.71417	0.325000	0.25375	0.005000	0.04900	1.247000	0.32815	0.720000	0.32209	0.561000	0.74099	CTT		0.652	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369		T	45671557	G	T	45671557	3	4	61	1	0	0	0	0	1	0	0	0	4689	942	33	2	461	2	DNMT3L	21	45671557	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1158215	45671557	2458338	11820	19805										
TRPM2	7226	broad.mit.edu	37	chr21	45833864	45833864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgacgcgacgcagcagaggcCggccttccctgagtggctga	15	14	0	3	rs145947009	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:45833864C>T	ENST00000397928.1	+	20	3498	c.3053C>T	c.(3052-3054)cCg>cTg	p.P1018L	AP001065.2_ENST00000423310.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.P1018L|TRPM2_ENST00000397932.2_Missense_Mutation_p.P1018L|AP001065.2_ENST00000456880.1_RNA|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.P998L	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1018					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.P1018L(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CAGCAGAGGCCGGCCTTCCCT	0.617													C|||	35	0.00698882	0	0	5008	,	,		17763	0.0337		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	21	GRCh37	CM086006	TRPM2	M	rs145947009	C	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	227	229	229		3053	4.9	0.1	21	dbSNP_134	229	0,8600		0,0,4300	yes	missense	TRPM2	NM_003307.3	98	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	1018/1504	45833864	2,13004	2203	4300	6503	44658292	SO:0001583	missense	7226			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.3053C>T	21.37:g.45833864C>T	ENSP00000381023:p.Pro1018Leu		44658292	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	14	0.00641025641025641	2	0.0040650406504065045	0	0.0	11	0.019230769230769232	1	0.0013192612137203166	C	17.80	3.478135	0.63849	4.54E-4	0.0	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	4.93	4.93	0.64822	Ion transport (1);	0.333938	0.27782	N	0.017870	T	0.68430	0.3000	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.78244	-0.2279	10	0.59425	D	0.04	-22.3206	18.5231	0.90960	0.0:1.0:0.0:0.0	.	1018;804;1018	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	L	1018;1018;998;1018	ENSP00000300482:P1018L;ENSP00000381023:P1018L;ENSP00000300481:P998L;ENSP00000381026:P1018L	ENSP00000300481:P998L	P	+	2	0	TRPM2	44658292	1.000000	0.71417	0.092000	0.20876	0.141000	0.21300	7.109000	0.77062	2.455000	0.83008	0.591000	0.81541	CCG		0.617	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		T	45833864	C	T	45833864	3	4	61	1	0	0	0	0	1	0	0	0	16626	652	23	1	3131	1	TRPM2	21	45833864	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	162307	45833864	2296031	11821	19806										
C21orf29	54084	broad.mit.edu	37	chr21	45945672	45945672	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccatttgtaaatgacagaGaactcctgacccttctcatc	5	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:45945672G>T	ENST00000323084.4	-	8	1265	c.1200C>A	c.(1198-1200)ttC>ttA	p.F400L	TSPEAR_ENST00000397916.1_Missense_Mutation_p.F332L|C21orf90_ENST00000465978.1_Intron	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	400					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)		p.F400L(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						AAATGACAGAGAACTCCTGAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	21											173	174	174					21																	45945672		2203	4300	6503	44770100	SO:0001583	missense	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1200C>A	21.37:g.45945672G>T	ENSP00000321987:p.Phe400Leu		44770100		Missense_Mutation	SNP	ENST00000323084.4	37	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	G	9.144	1.014480	0.19277	.	.	ENSG00000175894	ENST00000323084;ENST00000397918;ENST00000397916;ENST00000341581	T;T	0.14266	2.53;2.52	4.34	4.34	0.51931	.	0.441828	0.25738	N	0.028638	T	0.11580	0.0282	L	0.43152	1.355	0.80722	D	1	B	0.09022	0.002	B	0.17979	0.02	T	0.07290	-1.0780	10	0.10636	T	0.68	-9.5219	11.8346	0.52316	0.0861:0.0:0.9139:0.0	.	400	Q8WU66	TSEAR_HUMAN	L	400;253;332;401	ENSP00000321987:F400L;ENSP00000381012:F332L	ENSP00000321987:F400L	F	-	3	2	TSPEAR	44770100	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.966000	0.29331	2.128000	0.65567	0.591000	0.81541	TTC		0.522	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		T	45945672	G	T	45945672	3	4	61	1	0	0	0	0	1	0	0	0	2130	933	33	2	829	2	C21orf29	21	45945672	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	111808	45945672	2184223	11822	19807										
C21orf29	54084	broad.mit.edu	37	chr21	45947241	45947241	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggatgttctgatatgagacGaacttctcttcggtccactt	10	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:45947241G>A	ENST00000323084.4	-	7	1148	c.1083C>T	c.(1081-1083)ttC>ttT	p.F361F	TSPEAR_ENST00000397916.1_Silent_p.F293F	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	361					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)		p.F361F(2)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GATATGAGACGAACTTCTCTT	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	21											275	254	261					21																	45947241		2203	4300	6503	44771669	SO:0001819	synonymous_variant	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1083C>T	21.37:g.45947241G>A			44771669		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																				0.552	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45947241	G	A	45947241	2	1	61	1	0	0	0	0	0	0	0	1	2130	1049	37	1		1	C21orf29	21	45947241	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1569	45947241	2182654	11823	19808										
KRTAP10-7	386675	broad.mit.edu	37	chr21	46021524	46021524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcccgtcccctcctgctgcGcccccacctcctcctgccag	7	24	0	0	rs369025844		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:46021524G>A	ENST00000380102.2	+	1	1028	c.1003G>A	c.(1003-1005)Gcc>Acc	p.A335T	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	335	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.A335T(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						CTCCTGCTGCGCCCCCACCTC	0.716													-|||	1	0.000199681	8e-04	0	5008	,	,		14870	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21						G	THR/ALA,	0,4398		0,0,2199	38	42	41		1003,	0.3	0.1	21		41	1,8575	1.2+/-3.3	0,1,4287	no	missense,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	58,	0,1,6486	AA,AG,GG		0.0117,0.0,0.0077	possibly-damaging,	335/376,	46021524	1,12973	2199	4288	6487	44845952	SO:0001583	missense	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.1003G>A	21.37:g.46021524G>A	ENSP00000369445:p.Ala335Thr		44845952	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		.	.	.	.	.	.	.	.	.	.	g	4.807	0.150053	0.09185	0.0	1.17E-4	ENSG00000205441	ENST00000380102	T	0.01359	4.98	2.36	0.298	0.15766	.	.	.	.	.	T	0.01222	0.0040	L	0.54323	1.7	0.09310	N	1	P	0.40681	0.727	B	0.29176	0.099	T	0.48186	-0.9057	9	0.25751	T	0.34	.	3.5945	0.08001	0.3042:0.2145:0.4813:0.0	.	330	P60409-2	.	T	335	ENSP00000369445:A335T	ENSP00000369445:A335T	A	+	1	0	KRTAP10-7	44845952	0.001000	0.12720	0.065000	0.19835	0.107000	0.19398	0.309000	0.19332	0.122000	0.18314	0.467000	0.42956	GCC		0.716	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		A	46021524	G	A	46021524	3	1	61	1	0	0	0	0	1	0	0	0	8535	1087	38	1	994	1	KRTAP10-7	21	46021524	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	74283	46021524	2108371	11824	19809										
MCM3AP	8888	broad.mit.edu	37	chr21	47655303	47655303	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctagacacgttcctgtcGcctctgacagctgcagttgc	10	15	1	2	rs17183403	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:47655303G>A	ENST00000397708.1	-	29	6076	c.5822C>T	c.(5821-5823)gCg>gTg	p.A1941V	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.A1941V|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1941			A -> V (in dbSNP:rs17183403). {ECO:0000269|Ref.2}.		DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.A1941V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CGTTCCTGTCGCCTCTGACAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	21											104	77	86					21																	47655303		2203	4300	6503	46479731	SO:0001583	missense	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.5822C>T	21.37:g.47655303G>A	ENSP00000380820:p.Ala1941Val		46479731	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657420	0.29425	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03580	3.88;3.88	4.94	-4.41	0.03590	.	1.268580	0.05297	N	0.522328	T	0.02494	0.0076	L	0.27053	0.805	0.09310	N	1	B;B	0.13145	0.0;0.007	B;B	0.06405	0.0;0.002	T	0.46498	-0.9187	10	0.39692	T	0.17	-0.342	1.1882	0.01859	0.4096:0.0987:0.1888:0.3029	rs17183403	1941;436	O60318;B3KT88	MCM3A_HUMAN;.	V	1941;1941;436	ENSP00000380820:A1941V;ENSP00000291688:A1941V	ENSP00000291688:A1941V	A	-	2	0	MCM3AP	46479731	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.693000	0.05121	-0.699000	0.05077	-0.137000	0.14449	GCG		0.488	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47655303	G	A	47655303	3	1	61	1	0	0	0	0	1	0	0	0	9418	1087	38	1	124	1	MCM3AP	21	47655303	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1633779	47655303	474592	11825	19810										
MCM3AP	8888	broad.mit.edu	37	chr21	47660879	47660879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagttacggtgcatgtgaaGcaatggtatgggaaaattgt	13	5	0	1	rs575883540		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:47660879G>A	ENST00000397708.1	-	27	5733	c.5479C>T	c.(5479-5481)Ctt>Ttt	p.L1827F	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.L1827F|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1827					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.L1827F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					TGCATGTGAAGCAATGGTATG	0.438													G|||	1	0.000199681	0	0	5008	,	,		23993	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21											187	167	174					21																	47660879		2203	4300	6503	46485307	SO:0001583	missense	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.5479C>T	21.37:g.47660879G>A	ENSP00000380820:p.Leu1827Phe		46485307	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243254	0.22796	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03772	3.81;3.81	5.5	3.67	0.42095	.	0.611144	0.17348	N	0.177520	T	0.04634	0.0126	L	0.32530	0.975	0.09310	N	1	B;B	0.24368	0.002;0.102	B;B	0.23018	0.005;0.043	T	0.31971	-0.9924	10	0.59425	D	0.04	-2.8571	8.2686	0.31831	0.2486:0.0:0.7514:0.0	.	1827;322	O60318;B3KT88	MCM3A_HUMAN;.	F	1827;1827;322	ENSP00000380820:L1827F;ENSP00000291688:L1827F	ENSP00000291688:L1827F	L	-	1	0	MCM3AP	46485307	0.276000	0.24211	0.006000	0.13384	0.024000	0.10985	1.482000	0.35486	1.307000	0.44944	0.650000	0.86243	CTT		0.438	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47660879	G	A	47660879	3	1	61	1	0	0	0	0	1	0	0	0	9418	971	34	3	475	3	MCM3AP	21	47660879	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5576	47660879	469016	11826	19811										
MCM3AP	8888	broad.mit.edu	37	chr21	47704009	47704009	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttctctctactttcagtttCttcctctttattcacacctg	2	14	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:47704009C>A	ENST00000397708.1	-	2	1446	c.1192G>T	c.(1192-1194)Gaa>Taa	p.E398*	MCM3AP_ENST00000291688.1_Nonsense_Mutation_p.E398*|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397692.1_5'Flank|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397701.4_5'Flank|YBEY_ENST00000397694.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	398					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.E398*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CTTTCAGTTTCTTCCTCTTTA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	21											84	88	86					21																	47704009		2203	4300	6503	46528437	SO:0001587	stop_gained	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.1192G>T	21.37:g.47704009C>A	ENSP00000380820:p.Glu398*		46528437	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Nonsense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	36	5.675724	0.96764	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	.	.	.	5.33	4.44	0.53790	.	0.630430	0.16885	N	0.195547	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-20.336	10.5565	0.45121	0.0:0.9095:0.0:0.0905	.	.	.	.	X	398	.	ENSP00000291688:E398X	E	-	1	0	MCM3AP	46528437	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.298000	0.51818	2.490000	0.84030	0.563000	0.77884	GAA		0.463	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47704009	C	A	47704009	4	1	61	1	0	0	0	0	0	1	0	0	9418	922	32	2	4862	2	MCM3AP	21	47704009	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43130	47704009	425886	11827	19812										
DIP2A	23181	broad.mit.edu	37	chr21	47904673	47904673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccattgttgttttaggtgAcatcactcaaaaaggatatg	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr21:47904673A>G	ENST00000417564.2	+	2	116	c.95A>G	c.(94-96)gAc>gGc	p.D32G	DIP2A_ENST00000435722.3_Missense_Mutation_p.D32G|DIP2A_ENST00000457905.3_Missense_Mutation_p.D32G|DIP2A_ENST00000427143.2_Intron|DIP2A_ENST00000466639.1_Missense_Mutation_p.D32G|DIP2A_ENST00000400274.1_Missense_Mutation_p.D32G|DIP2A_ENST00000318711.7_Missense_Mutation_p.D32G			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	32	DMAP-interaction.				multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.D32G(2)		cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GTTTTAGGTGACATCACTCAA	0.318																																																2	Substitution - Missense(2)	large_intestine(2)	21											63	57	59					21																	47904673		1902	4152	6054	46729101	SO:0001583	missense	23181			AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.95A>G	21.37:g.47904673A>G	ENSP00000392066:p.Asp32Gly		46729101	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202246	0.79127	.	.	ENSG00000160305	ENST00000400274;ENST00000318711;ENST00000358985;ENST00000457905;ENST00000466639;ENST00000435722;ENST00000417564	T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53	5.95	5.95	0.96441	DMAP1-binding (1);	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.78456	2.415	0.80722	D	1	P;B;P;D;P	0.61697	0.889;0.009;0.801;0.99;0.849	P;B;P;D;P	0.65233	0.842;0.016;0.79;0.933;0.615	T	0.73751	-0.3884	10	0.87932	D	0	-31.3793	10.3918	0.44175	0.9236:0.0:0.0764:0.0	.	32;32;32;32;32	E9PER1;Q14689-3;Q14689;Q14689-4;Q14689-2	.;.;DIP2A_HUMAN;.;.	G	32	ENSP00000383133:D32G;ENSP00000323633:D32G;ENSP00000393434:D32G;ENSP00000430249:D32G;ENSP00000415089:D32G;ENSP00000392066:D32G	ENSP00000323633:D32G	D	+	2	0	DIP2A	46729101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.056000	0.71111	2.277000	0.76020	0.533000	0.62120	GAC		0.318	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		G	47904673	A	G	47904673	3	3	61	1	0	0	0	0	1	0	0	0	4538	275	10	4	101	4	DIP2A	21	47904673	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	200664	47904673	225222	11828	19813										
XKR3	150165	broad.mit.edu	37	chr22	17264659	17264659	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctgattttcagtacgtccTggcaacactttgcctgactg	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:17264659T>G	ENST00000331428.5	-	4	1332	c.1230A>C	c.(1228-1230)ccA>ccC	p.P410P		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	410						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P410P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CAGTACGTCCTGGCAACACTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	22											5	5	5					22																	17264659		403	1263	1666	15644659	SO:0001819	synonymous_variant	150165			AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.1230A>C	22.37:g.17264659T>G			15644659	B2RPN1|Q52PG8|Q8N7E1	Silent	SNP	ENST00000331428.5	37	CCDS42975.1																																																																																				0.423	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		G	17264659	T	G	17264659	2	3	61	1	0	0	0	0	0	0	0	1	17472	1567	55	4		4	XKR3	22	17264659	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09		17264659	34039907	11829	19814										
XKR3	150165	broad.mit.edu	37	chr22	17288683	17288683	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagtaatgcagccttatttCtcctcaagtctttgttgaaa	6	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:17288683C>A	ENST00000331428.5	-	2	383	c.281G>T	c.(280-282)aGa>aTa	p.R94I		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R94I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				AGCCTTATTTCTCCTCAAGTC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	22											91	87	88					22																	17288683		1842	4087	5929	15668683	SO:0001583	missense	150165			AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.281G>T	22.37:g.17288683C>A	ENSP00000331704:p.Arg94Ile		15668683	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	.	.	.	.	.	.	.	.	.	.	.	12.16	1.855656	0.32791	.	.	ENSG00000172967	ENST00000331428	T	0.64438	-0.1	0.473	0.473	0.16763	.	0.153277	0.37809	U	0.001938	T	0.50360	0.1611	L	0.41492	1.28	0.19575	N	0.999966	D	0.59357	0.985	P	0.45577	0.486	T	0.47484	-0.9114	10	0.62326	D	0.03	.	6.8307	0.23909	0.0:0.9998:0.0:2.0E-4	.	94	Q5GH77	XKR3_HUMAN	I	94	ENSP00000331704:R94I	ENSP00000331704:R94I	R	-	2	0	XKR3	15668683	0.697000	0.27767	0.023000	0.16930	0.102000	0.19082	1.225000	0.32551	0.524000	0.28502	0.134000	0.15878	AGA		0.358	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		A	17288683	C	A	17288683	3	1	61	1	0	0	0	0	1	0	0	0	17472	913	32	2	1110	2	XKR3	22	17288683	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24024	17288683	34015883	11830	19815										
CECR1	51816	broad.mit.edu	37	chr22	17670853	17670853	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggtcaaaccctgccaccacCgtggggaacttgattcggag	12	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:17670853C>T	ENST00000399839.1	-	6	1221	c.951G>A	c.(949-951)acG>acA	p.T317T	CECR1_ENST00000480276.1_5'UTR|CECR1_ENST00000399837.2_Silent_p.T317T|CECR1_ENST00000449907.2_Silent_p.T275T|CECR1_ENST00000262607.3_Silent_p.T317T|CECR1_ENST00000330232.4_Silent_p.T76T	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	317					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.T317T(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CTGCCACCACCGTGGGGAACT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	22											145	113	124					22																	17670853		2203	4300	6503	16050853	SO:0001819	synonymous_variant	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.951G>A	22.37:g.17670853C>T			16050853	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																				0.577	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			T	17670853	C	T	17670853	2	4	61	1	0	0	0	0	0	0	0	1	3211	639	23	1		1	CECR1	22	17670853	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382170	17670853	33633713	11831	19816										
CECR2	27443	broad.mit.edu	37	chr22	17976597	17976597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattaccggctggatgcagaCgatgtcttcgatcttctaaa	10	9	3	1	rs546492180		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:17976597C>T	ENST00000400573.5	+	3	325	c.318C>T	c.(316-318)gaC>gaT	p.D106D	CECR2_ENST00000342247.5_Silent_p.D86D|CECR2_ENST00000262608.8_Silent_p.D87D|CECR2_ENST00000400585.2_5'UTR|CECR2_ENST00000497534.1_3'UTR			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	128					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.D106D(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		TGGATGCAGACGATGTCTTCG	0.512													C|||	1	0.000199681	0	0	5008	,	,		19219	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	22											100	102	102					22																	17976597		2024	4179	6203	16356597	SO:0001819	synonymous_variant	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400573.5:c.318C>T	22.37:g.17976597C>T			16356597	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Silent	SNP	ENST00000400573.5	37																																																																																					0.512	CECR2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316104.5	NM_031413		T	17976597	C	T	17976597	2	4	61	1	0	0	0	0	0	0	0	1	3212	535	19	1		1	CECR2	22	17976597	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	305744	17976597	33327969	11832	19817										
CECR2	27443	broad.mit.edu	37	chr22	18028174	18028174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagcatctccttgtggatCggaggggaagggccttggta	17	7	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:18028174C>T	ENST00000400585.2	+	17	3143	c.2705C>T	c.(2704-2706)tCg>tTg	p.S902L	CECR2_ENST00000262608.8_Missense_Mutation_p.S1045L|CECR2_ENST00000400573.5_Missense_Mutation_p.S1044L			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1086					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.S1044L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		CCTTGTGGATCGGAGGGGAAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	22											33	37	36					22																	18028174		2094	4224	6318	16408174	SO:0001583	missense	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.2705C>T	22.37:g.18028174C>T	ENSP00000383428:p.Ser902Leu		16408174	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	C	11.04	1.521077	0.27211	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.29917	1.67;1.67;1.55	4.26	4.26	0.50523	.	0.358748	0.20295	N	0.095145	T	0.27027	0.0662	L	0.60455	1.87	0.18873	N	0.999987	D;D;D	0.52996	0.957;0.957;0.957	B;B;B	0.33799	0.17;0.17;0.17	T	0.39522	-0.9610	10	0.59425	D	0.04	-12.4732	14.9759	0.71273	0.0:1.0:0.0:0.0	.	1086;902;1044	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	L	902;1044;1045	ENSP00000383428:S902L;ENSP00000383417:S1044L;ENSP00000262608:S1045L	ENSP00000262608:S1045L	S	+	2	0	CECR2	16408174	0.029000	0.19370	0.483000	0.27378	0.196000	0.23810	3.047000	0.49854	2.352000	0.79861	0.561000	0.74099	TCG		0.622	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		T	18028174	C	T	18028174	3	4	61	1	0	0	0	0	1	0	0	0	3212	893	31	1	3195	1	CECR2	22	18028174	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	51577	18028174	33276392	11833	19818										
BCL2L13	23786	broad.mit.edu	37	chr22	18185121	18185121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacatacctggaggactattCggcagagtacatcattcagc	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:18185121C>T	ENST00000317582.5	+	6	916	c.569C>T	c.(568-570)tCg>tTg	p.S190L	BCL2L13_ENST00000355028.3_Intron|BCL2L13_ENST00000418951.2_Intron|BCL2L13_ENST00000538149.1_Missense_Mutation_p.S66L|BCL2L13_ENST00000399782.1_Missense_Mutation_p.S190L|BCL2L13_ENST00000493680.1_Missense_Mutation_p.S190L|BCL2L13_ENST00000337612.5_Missense_Mutation_p.S28L|BCL2L13_ENST00000543133.1_Missense_Mutation_p.S28L	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	190					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.S190L(1)		breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		GAGGACTATTCGGCAGAGTAC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	22											105	97	100					22																	18185121		2203	4300	6503	16565121	SO:0001583	missense	23786			AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.569C>T	22.37:g.18185121C>T	ENSP00000318883:p.Ser190Leu		16565121	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Missense_Mutation	SNP	ENST00000317582.5	37	CCDS13746.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747535	0.49257	.	.	ENSG00000099968	ENST00000399782;ENST00000317582;ENST00000543133;ENST00000538149;ENST00000337612;ENST00000493680	T;T;T;T;T;T	0.03124	4.04;4.04;4.04;4.04;4.04;4.04	5.95	4.93	0.64822	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.528419	0.21221	N	0.078148	T	0.03220	0.0094	N	0.22421	0.69	0.09310	N	1	P;B;B	0.35944	0.529;0.386;0.052	B;B;B	0.29440	0.102;0.102;0.023	T	0.44528	-0.9322	10	0.31617	T	0.26	-3.0865	15.4096	0.74908	0.0:0.8618:0.1382:0.0	.	66;190;190	B7Z238;Q9BXK5;Q9BXK5-2	.;B2L13_HUMAN;.	L	190;190;28;66;28;190	ENSP00000382682:S190L;ENSP00000318883:S190L;ENSP00000437667:S28L;ENSP00000441344:S66L;ENSP00000338932:S28L;ENSP00000434764:S190L	ENSP00000318883:S190L	S	+	2	0	BCL2L13	16565121	0.980000	0.34600	0.025000	0.17156	0.756000	0.42949	2.844000	0.48246	1.501000	0.48654	0.655000	0.94253	TCG		0.393	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		T	18185121	C	T	18185121	3	4	61	1	0	0	0	0	1	0	0	0	1372	893	31	1	587	1	BCL2L13	22	18185121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	156947	18185121	33119445	11834	19819										
BID	637	broad.mit.edu	37	chr22	18220849	18220849	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaattcactgttgtgtgaaaGacatcacggagcaaggacgg	12	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:18220849G>T	ENST00000399774.3	-	5	679	c.510C>A	c.(508-510)gtC>gtA	p.V170V	BID_ENST00000551952.1_Silent_p.V170V|BID_ENST00000317361.7_Silent_p.V216V|BID_ENST00000399767.1_Silent_p.V74V|BID_ENST00000473439.1_5'UTR|BID_ENST00000399765.1_Silent_p.V74V|BID_ENST00000342111.5_3'UTR	NM_001196.3|NM_001244569.1	NP_001187.1|NP_001231498.1	P55957	BID_HUMAN	BH3 interacting domain death agonist	170					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|brain development (GO:0007420)|establishment of protein localization to membrane (GO:0090150)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|intrinsic apoptotic signaling pathway (GO:0097193)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of cell proliferation (GO:0042127)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|release of cytochrome c from mitochondria (GO:0001836)|response to estradiol (GO:0032355)|signal transduction in response to DNA damage (GO:0042770)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial membrane (GO:0032592)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	death receptor binding (GO:0005123)	p.V216V(1)		large_intestine(2)|ovary(1)	3		all_epithelial(15;0.198)		Lung(27;0.0419)		TTGTGTGAAAGACATCACGGA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	22											121	116	118					22																	18220849		2203	4300	6503	16600849	SO:0001819	synonymous_variant	637			AF042083	CCDS13747.1, CCDS13748.1, CCDS13749.1	22q11.2	2014-03-07			ENSG00000015475	ENSG00000015475		"Endogenous ligands"	1050	protein-coding gene	gene with protein product		601997				8918887, 9721221	Standard	NM_001244567		Approved		uc002znc.2	P55957	OTTHUMG00000150087	ENST00000399774.3:c.510C>A	22.37:g.18220849G>T			16600849	Q549M7|Q71T04|Q7Z4M9|Q8IY86	Silent	SNP	ENST00000399774.3	37	CCDS13748.1																																																																																				0.532	BID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316178.1	NM_197966		T	18220849	G	T	18220849	2	4	61	1	0	0	0	0	0	0	0	1	1431	929	33	2		2	BID	22	18220849	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35728	18220849	33083717	11835	19820										
PEX26	55670	broad.mit.edu	37	chr22	18562752	18562752	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtattaccaggtccctgaaAagctaccccccaaagtcctg	7	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:18562752A>C	ENST00000329627.7	+	3	549	c.343A>C	c.(343-345)Aag>Cag	p.K115Q	XXbac-B476C20.9_ENST00000426483.1_RNA|XXbac-B476C20.9_ENST00000607927.1_RNA|PEX26_ENST00000399744.3_Missense_Mutation_p.K115Q|PEX26_ENST00000428061.2_Missense_Mutation_p.K115Q	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	115					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.K115Q(1)		breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GGTCCCTGAAAAGCTACCCCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	22											103	84	90					22																	18562752		2203	4300	6503	16942752	SO:0001583	missense	55670			AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"peroxisome biogenesis factor 26"			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.343A>C	22.37:g.18562752A>C	ENSP00000331106:p.Lys115Gln		16942752	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	A	17.02	3.281588	0.59758	.	.	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.94457	-3.43;-3.43;-3.43	5.44	4.34	0.51931	.	0.565422	0.16515	U	0.211067	D	0.92453	0.7604	M	0.71581	2.175	0.25218	N	0.989921	P;P	0.39535	0.627;0.677	B;B	0.37091	0.155;0.241	D	0.86860	0.2029	10	0.36615	T	0.2	-18.4396	10.7287	0.46083	0.7781:0.2219:0.0:0.0	.	115;115	F6UBB5;Q7Z412	.;PEX26_HUMAN	Q	115	ENSP00000331106:K115Q;ENSP00000382648:K115Q;ENSP00000412441:K115Q	ENSP00000331106:K115Q	K	+	1	0	PEX26	16942752	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.437000	0.34991	2.193000	0.70182	0.402000	0.26972	AAG		0.512	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929		C	18562752	A	C	18562752	3	2	61	1	0	0	0	0	1	0	0	0	11777	15	1	4	349	4	PEX26	22	18562752	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	341903	18562752	32741814	11836	19821										
CLTCL1	8218	broad.mit.edu	37	chr22	19175076	19175076	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cccaggccaccaaccttgtaGagatgatccttcttgcagag	9	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19175076G>T	ENST00000263200.10	-	29	4671	c.4599C>A	c.(4597-4599)ctC>ctA	p.L1533L	CLTCL1_ENST00000427926.1_Silent_p.L1533L|CLTCL1_ENST00000353891.5_Intron|CLTCL1_ENST00000442042.2_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1533	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)	p.L1533L(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CAACCTTGTAGAGATGATCCT	0.552			T	?	ALCL																																		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	1	Substitution - coding silent(1)	large_intestine(1)	22											97	106	103					22																	19175076		2062	4193	6255	17555076	SO:0001819	synonymous_variant	8218				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4599C>A	22.37:g.19175076G>T			17555076	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																				0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		T	19175076	G	T	19175076	2	4	61	1	0	0	0	0	0	0	0	1	3573	929	33	2		2	CLTCL1	22	19175076	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	612324	19175076	32129490	11837	19822										
CLTCL1	8218	broad.mit.edu	37	chr22	19217448	19217448	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcttcaaggcatccaataaGaaggaagtacactgctgaat	8	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19217448G>A	ENST00000263200.10	-	11	1767	c.1695C>T	c.(1693-1695)ttC>ttT	p.F565F	CLTCL1_ENST00000427926.1_Silent_p.F565F|CLTCL1_ENST00000353891.5_Silent_p.F565F	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	565	Distal segment.|Heavy chain arm.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)	p.F565F(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CATCCAATAAGAAGGAAGTAC	0.428			T	?	ALCL																																		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	1	Substitution - coding silent(1)	large_intestine(1)	22											58	55	56					22																	19217448		1930	4150	6080	17597448	SO:0001819	synonymous_variant	8218				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1695C>T	22.37:g.19217448G>A			17597448	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																				0.428	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19217448	G	A	19217448	2	1	61	1	0	0	0	0	0	0	0	1	3573	933	33	3		3	CLTCL1	22	19217448	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42372	19217448	32087118	11838	19823										
CLTCL1	8218	broad.mit.edu	37	chr22	19220769	19220769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcttggcacatttgcccGaaggtacacactcagagcga	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19220769G>A	ENST00000263200.10	-	9	1513	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	CLTCL1_ENST00000427926.1_Missense_Mutation_p.R481W|CLTCL1_ENST00000353891.5_Missense_Mutation_p.R481W	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	481	Flexible linker.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)	p.R481W(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					ACATTTGCCCGAAGGTACACA	0.498			T	?	ALCL																																		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	1	Substitution - Missense(1)	large_intestine(1)	22											143	140	141					22																	19220769		1960	4163	6123	17600769	SO:0001583	missense	8218				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1441C>T	22.37:g.19220769G>A	ENSP00000445677:p.Arg481Trp		17600769	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276926	0.59758	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.52295	0.67;0.67;0.67	3.92	2.89	0.33648	Armadillo-type fold (2);	0.000000	0.64402	D	0.000002	T	0.72724	0.3496	M	0.93106	3.38	0.58432	D	0.999991	D;D	0.76494	0.997;0.999	D;D	0.74674	0.984;0.947	T	0.79072	-0.1953	10	0.87932	D	0	-21.811	11.9849	0.53142	0.0867:0.0:0.9133:0.0	.	481;481	P53675-2;P53675	.;CLH2_HUMAN	W	481	ENSP00000439662:R481W;ENSP00000445677:R481W;ENSP00000441158:R481W	ENSP00000445677:R481W	R	-	1	2	CLTCL1	17600769	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	2.512000	0.45485	0.982000	0.38575	0.591000	0.81541	CGG		0.498	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19220769	G	A	19220769	3	1	61	1	0	0	0	0	1	0	0	0	3573	1057	37	1	3577	1	CLTCL1	22	19220769	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3321	19220769	32083797	11839	19824										
HIRA	7290	broad.mit.edu	37	chr22	19340888	19340888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagcctcaccttcgtttaCgaggtaccgtgcgtagacga	12	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19340888C>T	ENST00000263208.5	-	23	3095	c.2839G>A	c.(2839-2841)Gta>Ata	p.V947I	HIRA_ENST00000541063.1_Missense_Mutation_p.V903I|HIRA_ENST00000546308.1_3'UTR|HIRA_ENST00000340170.4_Missense_Mutation_p.V740I	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	947	Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.V947I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CCTTCGTTTACGAGGTACCGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	22											75	51	59					22																	19340888		2203	4300	6503	17720888	SO:0001583	missense	7290			X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2839G>A	22.37:g.19340888C>T	ENSP00000263208:p.Val947Ile		17720888	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	37	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386606	0.82902	.	.	ENSG00000100084	ENST00000340170;ENST00000263208;ENST00000541063;ENST00000539600	T;T;T	0.71817	-0.32;-0.6;-0.45	4.94	4.94	0.65067	TUP1-like enhancer of split (1);	0.000000	0.85682	D	0.000000	T	0.81866	0.4913	M	0.70595	2.14	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.79784	0.991;0.981;0.993	T	0.76990	-0.2754	10	0.12766	T	0.61	-16.3814	18.3537	0.90348	0.0:1.0:0.0:0.0	.	903;740;947	F5H4M2;P54198-2;P54198	.;.;HIRA_HUMAN	I	740;947;903;456	ENSP00000345350:V740I;ENSP00000263208:V947I;ENSP00000446073:V903I	ENSP00000263208:V947I	V	-	1	0	HIRA	17720888	1.000000	0.71417	0.839000	0.33178	0.590000	0.36582	7.076000	0.76806	2.577000	0.86979	0.563000	0.77884	GTA		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		T	19340888	C	T	19340888	3	4	61	1	0	0	0	0	1	0	0	0	7141	536	19	1	226	1	HIRA	22	19340888	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	120119	19340888	31963678	11840	19825										
UFD1L	7353	broad.mit.edu	37	chr22	19444434	19444434	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtagcccaggggagcatcaAagtccacctgtgtttccagg	12	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19444434A>C	ENST00000263202.10	-	8	701	c.572T>G	c.(571-573)tTt>tGt	p.F191C	AC000068.10_ENST00000608816.1_RNA|UFD1L_ENST00000399523.1_Missense_Mutation_p.F191C|UFD1L_ENST00000360834.4_Missense_Mutation_p.F180C|AC000068.9_ENST00000607934.1_RNA	NM_001035247.2|NM_005659.6	NP_001030324.2|NP_005650.2	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1 like (yeast)	191					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.F191C(1)		large_intestine(3)|upper_aerodigestive_tract(1)	4	Colorectal(54;0.0993)					gggagcatcaaagtccacctg	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	22											84	58	67					22																	19444434		2198	4297	6495	17824434	SO:0001583	missense	7353			AJ239058	CCDS13761.1, CCDS33600.1, CCDS33600.2	22q11.2	2014-05-02	2005-10-10		ENSG00000070010	ENSG00000070010			12520	protein-coding gene	gene with protein product		601754	"ubiquitin fusion degradation 1-like"			9063746	Standard	NM_005659		Approved	UFD1	uc002zpm.2	Q92890	OTTHUMG00000150130	ENST00000263202.10:c.572T>G	22.37:g.19444434A>C	ENSP00000263202:p.Phe191Cys		17824434	A8MW31|Q9Y5N0	Missense_Mutation	SNP	ENST00000263202.10	37	CCDS13761.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983204	0.74474	.	.	ENSG00000070010	ENST00000263202;ENST00000360834;ENST00000399523;ENST00000399525;ENST00000447868;ENST00000421968	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.80232	0.4585	H	0.96208	3.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86181	0.1606	10	0.87932	D	0	.	13.0648	0.59028	1.0:0.0:0.0:0.0	.	191;191	B4E3I3;Q92890	.;UFD1_HUMAN	C	191;180;191;227;95;180	ENSP00000263202:F191C;ENSP00000354079:F180C;ENSP00000382439:F191C;ENSP00000402136:F95C;ENSP00000406680:F180C	ENSP00000263202:F191C	F	-	2	0	UFD1L	17824434	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.882000	0.63121	2.153000	0.67306	0.533000	0.62120	TTT		0.433	UFD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316460.6			C	19444434	A	C	19444434	3	2	61	1	0	0	0	0	1	0	0	0	16975	14	1	4	371	4	UFD1L	22	19444434	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	103546	19444434	31860132	11841	19826										
UFD1L	7353	broad.mit.edu	37	chr22	19445656	19445656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtctccatcacacgcagttCgtagatctgtggggcaaaca	11	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19445656C>T	ENST00000263202.10	-	7	631	c.502G>A	c.(502-504)Gaa>Aaa	p.E168K	AC000068.10_ENST00000608816.1_RNA|UFD1L_ENST00000399523.1_Missense_Mutation_p.E168K|UFD1L_ENST00000360834.4_Missense_Mutation_p.E157K	NM_001035247.2|NM_005659.6	NP_001030324.2|NP_005650.2	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1 like (yeast)	168					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.E168K(1)		large_intestine(3)|upper_aerodigestive_tract(1)	4	Colorectal(54;0.0993)					ACACGCAGTTCGTAGATCTGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											232	155	181					22																	19445656		2203	4300	6503	17825656	SO:0001583	missense	7353			AJ239058	CCDS13761.1, CCDS33600.1, CCDS33600.2	22q11.2	2014-05-02	2005-10-10		ENSG00000070010	ENSG00000070010			12520	protein-coding gene	gene with protein product		601754	"ubiquitin fusion degradation 1-like"			9063746	Standard	NM_005659		Approved	UFD1	uc002zpm.2	Q92890	OTTHUMG00000150130	ENST00000263202.10:c.502G>A	22.37:g.19445656C>T	ENSP00000263202:p.Glu168Lys		17825656	A8MW31|Q9Y5N0	Missense_Mutation	SNP	ENST00000263202.10	37	CCDS13761.1	.	.	.	.	.	.	.	.	.	.	C	33	5.242912	0.95272	.	.	ENSG00000070010	ENST00000263202;ENST00000360834;ENST00000399523;ENST00000399525;ENST00000447868;ENST00000421968	T;T;T;D;D	0.96522	0.97;0.97;0.97;-4.04;-4.04	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	D	0.97480	0.9175	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.976	D	0.96788	0.9580	10	0.33141	T	0.24	.	18.0026	0.89202	0.0:1.0:0.0:0.0	.	168;168	B4E3I3;Q92890	.;UFD1_HUMAN	K	168;157;168;204;72;157	ENSP00000263202:E168K;ENSP00000354079:E157K;ENSP00000382439:E168K;ENSP00000402136:E72K;ENSP00000406680:E157K	ENSP00000263202:E168K	E	-	1	0	UFD1L	17825656	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	7.163000	0.77524	2.487000	0.83934	0.655000	0.94253	GAA		0.537	UFD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316460.6			T	19445656	C	T	19445656	3	4	61	1	0	0	0	0	1	0	0	0	16975	893	31	1	445	1	UFD1L	22	19445656	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1222	19445656	31858910	11842	19827										
UFD1L	7353	broad.mit.edu	37	chr22	19463072	19463072	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcagcggtactgtgtggaGaagcggttttggaagaccct	15	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19463072G>T	ENST00000263202.10	-	2	186	c.57C>A	c.(55-57)ttC>ttA	p.F19L	UFD1L_ENST00000484101.1_5'UTR|UFD1L_ENST00000399523.1_Missense_Mutation_p.F19L|UFD1L_ENST00000360834.4_Missense_Mutation_p.F19L	NM_001035247.2|NM_005659.6	NP_001030324.2|NP_005650.2	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1 like (yeast)	19					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.F19L(1)		large_intestine(3)|upper_aerodigestive_tract(1)	4	Colorectal(54;0.0993)					ACTGTGTGGAGAAGCGGTTTT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	22											137	124	128					22																	19463072		2203	4300	6503	17843072	SO:0001583	missense	7353			AJ239058	CCDS13761.1, CCDS33600.1, CCDS33600.2	22q11.2	2014-05-02	2005-10-10		ENSG00000070010	ENSG00000070010			12520	protein-coding gene	gene with protein product		601754	"ubiquitin fusion degradation 1-like"			9063746	Standard	NM_005659		Approved	UFD1	uc002zpm.2	Q92890	OTTHUMG00000150130	ENST00000263202.10:c.57C>A	22.37:g.19463072G>T	ENSP00000263202:p.Phe19Leu		17843072	A8MW31|Q9Y5N0	Missense_Mutation	SNP	ENST00000263202.10	37	CCDS13761.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.877510	0.91664	.	.	ENSG00000070010	ENST00000263202;ENST00000360834;ENST00000399523;ENST00000399525;ENST00000421968;ENST00000494054	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.72	3.59	0.41128	.	0.000000	0.85682	D	0.000000	T	0.67618	0.2912	M	0.89658	3.05	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.71192	-0.4665	10	0.72032	D	0.01	.	10.1998	0.43075	0.2289:0.0:0.7711:0.0	.	19;19	B4E3I3;Q92890	.;UFD1_HUMAN	L	19;19;19;19;19;14	ENSP00000263202:F19L;ENSP00000354079:F19L;ENSP00000382439:F19L;ENSP00000406680:F19L;ENSP00000418390:F14L	ENSP00000263202:F19L	F	-	3	2	UFD1L	17843072	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.793000	0.55484	0.709000	0.31976	0.655000	0.94253	TTC		0.443	UFD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316460.6			T	19463072	G	T	19463072	3	4	61	1	0	0	0	0	1	0	0	0	16975	933	33	2	910	2	UFD1L	22	19463072	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	17416	19463072	31841494	11843	19828										
TXNRD2	10587	broad.mit.edu	37	chr22	19898902	19898902	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcacgcgcaggccttacgtTtttccaggggattccttcag	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:19898902T>G	ENST00000400521.1	-	8	666	c.660A>C	c.(658-660)aaA>aaC	p.K220N	TXNRD2_ENST00000400519.1_Missense_Mutation_p.K219N|TXNRD2_ENST00000542719.1_Missense_Mutation_p.K190N|TXNRD2_ENST00000535882.1_Missense_Mutation_p.K219N|TXNRD2_ENST00000491939.1_5'UTR|TXNRD2_ENST00000400518.1_Missense_Mutation_p.K190N|TXNRD2_ENST00000334363.9_Missense_Mutation_p.K220N	NM_006440.3	NP_006431.2	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2	220					cell redox homeostasis (GO:0045454)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|response to oxygen radical (GO:0000305)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|thioredoxin-disulfide reductase activity (GO:0004791)	p.K220N(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|urinary_tract(2)	30	Colorectal(54;0.0993)					GGCCTTACGTTTTTCCAGGGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	22											87	93	91					22																	19898902		1983	4156	6139	18278902	SO:0001583	missense	10587			AF106697	CCDS42981.1, CCDS63402.1	22q11.21	2014-09-17			ENSG00000184470	ENSG00000184470			18155	protein-coding gene	gene with protein product	"thioredoxin reductase beta", "selenoprotein Z"	606448				9923614, 10215850, 11012661	Standard	NM_006440		Approved	TR, TRXR2, TR3	uc021wlj.1	Q9NNW7	OTTHUMG00000149975	ENST00000400521.1:c.660A>C	22.37:g.19898902T>G	ENSP00000383365:p.Lys220Asn		18278902	O95840|Q96IJ2|Q9H2Z5|Q9NZV3|Q9NZV4|Q9P2Y0|Q9P2Y1|Q9UQU8	Missense_Mutation	SNP	ENST00000400521.1	37	CCDS42981.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391109	0.82902	.	.	ENSG00000184470	ENST00000400518;ENST00000538798;ENST00000400521;ENST00000400525;ENST00000540474;ENST00000400519;ENST00000535882;ENST00000542719;ENST00000334363	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.57	3.22	0.36961	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.118609	0.56097	D	0.000032	T	0.71467	0.3343	M	0.92738	3.34	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;0.991;0.991;1.0	D;P;P;D	0.79108	0.992;0.829;0.889;0.992	T	0.72187	-0.4366	10	0.66056	D	0.02	-25.0123	8.3183	0.32113	0.0:0.2599:0.0:0.7401	.	220;220;188;219	Q9NNW7;E7EWK1;Q6M1B7;D3YTF9	TRXR2_HUMAN;.;.;.	N	190;220;220;197;124;219;219;190;220	ENSP00000383362:K190N;ENSP00000383365:K220N;ENSP00000383369:K197N;ENSP00000383363:K219N;ENSP00000439314:K219N;ENSP00000439570:K190N;ENSP00000334451:K220N	ENSP00000334451:K220N	K	-	3	2	TXNRD2	18278902	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.356000	0.44116	0.402000	0.25451	0.533000	0.62120	AAA		0.527	TXNRD2-003	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000314903.3	NM_006440		G	19898902	T	G	19898902	3	3	61	1	0	0	0	0	1	0	0	0	16848	1838	64	4	954	4	TXNRD2	22	19898902	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	435830	19898902	31405664	11844	19829										
DGCR8	54487	broad.mit.edu	37	chr22	20077238	20077238	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgcccgacgggtggatcatGacattccataactctggagt	11	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:20077238G>T	ENST00000351989.3	+	4	1356	c.927G>T	c.(925-927)atG>atT	p.M309I	DGCR8_ENST00000383024.2_Missense_Mutation_p.M309I|DGCR8_ENST00000407755.1_Missense_Mutation_p.M309I	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	309	Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with NCL.|WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)	p.M309I(1)		NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GGTGGATCATGACATTCCATA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											114	105	108					22																	20077238		2203	4300	6503	18457238	SO:0001583	missense	54487			AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"chromosome 22 open reading frame 12", "DiGeorge syndrome critical region gene 8"	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.927G>T	22.37:g.20077238G>T	ENSP00000263209:p.Met309Ile		18457238	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Missense_Mutation	SNP	ENST00000351989.3	37	CCDS13773.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891026	0.91889	.	.	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	T;T;T	0.33438	1.44;1.41;1.41	5.68	5.68	0.88126	WW/Rsp5/WWP (3);	0.000000	0.85682	D	0.000000	T	0.40570	0.1122	N	0.14661	0.345	0.80722	D	1	P;P	0.52577	0.954;0.817	D;B	0.66351	0.943;0.36	T	0.38001	-0.9681	10	0.52906	T	0.07	-18.5149	19.3812	0.94536	0.0:0.0:1.0:0.0	.	309;309	Q8WYQ5-3;Q8WYQ5	.;DGCR8_HUMAN	I	309	ENSP00000263209:M309I;ENSP00000372488:M309I;ENSP00000384726:M309I	ENSP00000263209:M309I	M	+	3	0	DGCR8	18457238	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.354000	0.97083	2.677000	0.91161	0.650000	0.86243	ATG		0.537	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1			T	20077238	G	T	20077238	3	4	61	1	0	0	0	0	1	0	0	0	4475	1290	45	2	937	2	DGCR8	22	20077238	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	178336	20077238	31227328	11845	19830										
PI4KA	5297	broad.mit.edu	37	chr22	21104265	21104265	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcatcccacagcgtgcagcGaagtccttcacaatgctctg	8	14	3	0	rs146663036		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:21104265G>A	ENST00000572273.1	-	28	3227	c.2997C>T	c.(2995-2997)ttC>ttT	p.F999F	PI4KA_ENST00000255882.6_Silent_p.F1057F			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	999					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.F999F(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			AGCGTGCAGCGAAGTCCTTCA	0.537													G|||	1	0.000199681	0	0	5008	,	,		19869	0		0.001	False		,,,				2504	0				GBM(136;1332 1831 3115 23601 50806)											2	Substitution - coding silent(2)	large_intestine(2)	22						G		1,4405	2.1+/-5.4	0,1,2202	99	79	86		2997	-7.5	0.7	22	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PI4KA	NM_058004.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		999/2045	21104265	2,13004	2203	4300	6503	19434265	SO:0001819	synonymous_variant	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2997C>T	22.37:g.21104265G>A			19434265	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																					0.537	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21104265	G	A	21104265	2	1	61	1	0	0	0	0	0	0	0	1	11904	1049	37	1		1	PI4KA	22	21104265	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1027027	21104265	30200301	11846	19831										
PI4KA	5297	broad.mit.edu	37	chr22	21115658	21115658	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacctggaagcgatcaggatCtgttgaacgcagtaccctaa	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:21115658C>A	ENST00000572273.1	-	23	2781	c.2551G>T	c.(2551-2553)Gat>Tat	p.D851Y	PI4KA_ENST00000255882.6_Missense_Mutation_p.D909Y|PI4KA_ENST00000466162.1_5'UTR			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	851					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.D851Y(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CGATCAGGATCTGTTGAACGC	0.388																																					GBM(136;1332 1831 3115 23601 50806)											2	Substitution - Missense(2)	large_intestine(2)	22											94	85	88					22																	21115658		2203	4300	6503	19445658	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2551G>T	22.37:g.21115658C>A	ENSP00000458238:p.Asp851Tyr		19445658	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	C	25.7	4.664545	0.88251	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.29	5.29	0.74685	.	0.047754	0.85682	D	0.000000	T	0.66577	0.2803	L	0.43152	1.355	0.80722	D	1	B	0.32543	0.375	B	0.43728	0.429	T	0.67662	-0.5613	9	0.66056	D	0.02	-20.2127	19.1301	0.93402	0.0:1.0:0.0:0.0	.	851	P42356	PI4KA_HUMAN	Y	851	.	ENSP00000255882:D851Y	D	-	1	0	PI4KA	19445658	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.266000	0.78452	2.767000	0.95098	0.655000	0.94253	GAT		0.388	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21115658	C	A	21115658	3	1	61	1	0	0	0	0	1	0	0	0	11904	913	32	2	3715	2	PI4KA	22	21115658	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	11393	21115658	30188908	11847	19832										
CRKL	1399	broad.mit.edu	37	chr22	21288475	21288475	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagaatggacctgtctttgcGaaagcaatccagaaaagagt	10	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:21288475G>A	ENST00000354336.3	+	2	1229	c.720G>A	c.(718-720)gcG>gcA	p.A240A		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	240	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.A240A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			CTGTCTTTGCGAAAGCAATCC	0.478																																					Pancreas(85;3 1441 23889 42519 42763)											1	Substitution - coding silent(1)	large_intestine(1)	22											98	88	91					22																	21288475		2203	4300	6503	19618475	SO:0001819	synonymous_variant	1399				CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"SH2 domain containing"	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.720G>A	22.37:g.21288475G>A			19618475	A8KA44|D3DX35	Silent	SNP	ENST00000354336.3	37	CCDS13785.1																																																																																				0.478	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207		A	21288475	G	A	21288475	2	1	61	1	0	0	0	0	0	0	0	1	3891	1045	37	1		1	CRKL	22	21288475	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	172817	21288475	30016091	11848	19833										
CCDC116	164592	broad.mit.edu	37	chr22	21988735	21988735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgccatagcagcctcatggCcggctgtctgggctcccaca	11	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:21988735C>T	ENST00000292779.3	+	3	658	c.497C>T	c.(496-498)gCc>gTc	p.A166V	CCDC116_ENST00000607942.1_Missense_Mutation_p.A166V	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	166								p.A166V(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AGCCTCATGGCCGGCTGTCTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	22											56	63	61					22																	21988735		2202	4299	6501	20318735	SO:0001583	missense	164592			BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.497C>T	22.37:g.21988735C>T	ENSP00000292779:p.Ala166Val		20318735	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.728766	0.48833	.	.	ENSG00000161180	ENST00000292779	T	0.21031	2.03	4.42	-0.521	0.11931	.	0.393903	0.21692	N	0.070551	T	0.17066	0.0410	L	0.46157	1.445	0.09310	N	1	P;P	0.44816	0.703;0.844	B;P	0.47015	0.319;0.534	T	0.08207	-1.0733	9	.	.	.	-61.6135	1.0615	0.01601	0.1836:0.4296:0.1789:0.2079	.	166;166	B7Z7H5;Q8IYX3-2	.;.	V	166	ENSP00000292779:A166V	.	A	+	2	0	CCDC116	20318735	0.000000	0.05858	0.009000	0.14445	0.565000	0.35776	0.048000	0.14078	0.205000	0.20568	0.491000	0.48974	GCC		0.617	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		T	21988735	C	T	21988735	3	4	61	1	0	0	0	0	1	0	0	0	2759	739	26	3	503	3	CCDC116	22	21988735	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	700260	21988735	29315831	11849	19834										
YPEL1	29799	broad.mit.edu	37	chr22	22057727	22057727	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaccgcatgcagcccggtgaGaaggaccctctcctctgcag	11	15	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:22057727G>T	ENST00000339468.3	-	4	585	c.202C>A	c.(202-204)Ctc>Atc	p.L68I		NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)	68						nucleus (GO:0005634)		p.L68I(1)		breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					AGCCCGGTGAGAAGGACCCTC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	22											120	101	107					22																	22057727		2203	4300	6503	20387727	SO:0001583	missense	29799			AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"yippee (Drosophila) homolog-like 1"			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830	ENST00000339468.3:c.202C>A	22.37:g.22057727G>T	ENSP00000342832:p.Leu68Ile		20387727	Q65ZA1|Q6GLI6	Missense_Mutation	SNP	ENST00000339468.3	37	CCDS13794.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188326	0.57909	.	.	ENSG00000100027	ENST00000339468	.	.	.	4.07	4.07	0.47477	.	0.150778	0.44688	D	0.000436	T	0.57198	0.2037	L	0.49350	1.555	0.80722	D	1	B	0.23591	0.088	B	0.32677	0.15	T	0.53760	-0.8393	9	0.29301	T	0.29	.	12.1692	0.54148	0.0851:0.0:0.9149:0.0	.	68	O60688	YPEL1_HUMAN	I	68	.	ENSP00000342832:L68I	L	-	1	0	YPEL1	20387727	1.000000	0.71417	0.485000	0.27403	0.854000	0.48673	6.507000	0.73717	2.575000	0.86900	0.558000	0.71614	CTC		0.672	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313		T	22057727	G	T	22057727	3	4	61	1	0	0	0	0	1	0	0	0	17529	942	33	2	165	2	YPEL1	22	22057727	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68992	22057727	29246839	11850	19835										
ZNF280A	129025	broad.mit.edu	37	chr22	22868699	22868699	+	Frame_Shift_Del	DEL	T	T	-													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacaaagcaaattctttgtgTtttcatggcacgttctaaaa							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:22868699delT	ENST00000302097.3	-	2	1508	c.1256delA	c.(1255-1257)aacfs	p.N419fs		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	419					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N419fs*21(1)		endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	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)		ATTCTTTGTGTTTTCATGGCA	0.433																																																1	Deletion - Frameshift(1)	large_intestine(1)	22											121	109	113					22																	22868699		2203	4300	6503	21198699	SO:0001589	frameshift_variant	129025			D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"zinc finger protein 280", "suppressor of hairy wing homolog 1 (Drosophila)"	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1256delA	22.37:g.22868699delT	ENSP00000302855:p.Asn419fs		21198699		Frame_Shift_Del	DEL	ENST00000302097.3	37	CCDS13800.1																																																																																				0.433	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740		-	22868699	T	-	22868699	7	5	61	1	0	1	0	1	0	0	0	0	17853	1725	60	0	376	0	ZNF280A	22	22868699	Frame_Shift_Del	DEL	T	TCGA-AG-A002-01A-01W-A00K-09	810972	22868699	28435867	11851	19836										
PRAME	23532	broad.mit.edu	37	chr22	22892289	22892289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaatgtaggaagatgcaTggatgtgggagaggaggagt	20	1	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:22892289T>C	ENST00000398741.1	-	5	1118	c.812A>G	c.(811-813)cAt>cGt	p.H271R	PRAME_ENST00000539862.1_Missense_Mutation_p.H255R|PRAME_ENST00000543184.1_Missense_Mutation_p.H271R|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.H255R|PRAME_ENST00000398743.2_Missense_Mutation_p.H271R|PRAME_ENST00000402697.1_Missense_Mutation_p.H271R|PRAME_ENST00000405655.3_Missense_Mutation_p.H271R	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	271					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.H271R(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		GGAAGATGCATGGATGTGGGA	0.512																																					Melanoma(73;1707 1838 15168 27201)											1	Substitution - Missense(1)	large_intestine(1)	22											110	97	102					22																	22892289		2203	4300	6503	21222289	SO:0001583	missense	23532			U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.812A>G	22.37:g.22892289T>C	ENSP00000381726:p.His271Arg		21222289	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	T	7.817	0.716909	0.15306	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69;2.69;2.69	3.78	-4.04	0.04010	.	0.521356	0.19712	N	0.107788	T	0.07728	0.0194	L	0.38531	1.155	0.09310	N	1	B	0.16166	0.016	B	0.17722	0.019	T	0.17167	-1.0378	10	0.39692	T	0.17	.	4.0435	0.09761	0.3099:0.4011:0.0:0.289	.	271	P78395	PRAME_HUMAN	R	271;271;271;271;255;271;255	ENSP00000381728:H271R;ENSP00000445675:H271R;ENSP00000381726:H271R;ENSP00000384343:H271R;ENSP00000445097:H255R;ENSP00000385198:H271R;ENSP00000407342:H255R	ENSP00000381726:H271R	H	-	2	0	PRAME	21222289	0.008000	0.16893	0.001000	0.08648	0.004000	0.04260	-0.192000	0.09587	-1.061000	0.03185	0.533000	0.62120	CAT		0.512	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		C	22892289	T	C	22892289	3	2	61	1	0	0	0	0	1	0	0	0	12458	1464	51	4	725	4	PRAME	22	22892289	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	23590	22892289	28412277	11852	19837										
PRAME	23532	broad.mit.edu	37	chr22	22892481	22892481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcagcttcttacagcacaggCgtagtacatttttctttcgc	7	11	3	0	rs116965324	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:22892481C>T	ENST00000398741.1	-	5	926	c.620G>A	c.(619-621)cGc>cAc	p.R207H	PRAME_ENST00000539862.1_Missense_Mutation_p.R191H|PRAME_ENST00000543184.1_Missense_Mutation_p.R207H|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.R191H|PRAME_ENST00000398743.2_Missense_Mutation_p.R207H|PRAME_ENST00000402697.1_Missense_Mutation_p.R207H|PRAME_ENST00000405655.3_Missense_Mutation_p.R207H	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	207					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.R207H(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		ACAGCACAGGCGTAGTACATT	0.443													C|||	2	0.000399361	0	0	5008	,	,		20030	0		0.002	False		,,,				2504	0				Melanoma(73;1707 1838 15168 27201)											1	Substitution - Missense(1)	large_intestine(1)	22											143	140	141					22																	22892481		2203	4300	6503	21222481	SO:0001583	missense	23532			U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.620G>A	22.37:g.22892481C>T	ENSP00000381726:p.Arg207His		21222481	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	0.004	-2.275362	0.00257	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63;2.63	3.56	0.203	0.15195	.	0.828357	0.10766	N	0.636584	T	0.01835	0.0058	N	0.00059	-2.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43621	-0.9380	10	0.02654	T	1	.	6.1532	0.20322	0.0:0.3452:0.0:0.6548	.	207	P78395	PRAME_HUMAN	H	207;207;207;207;191;207;191	ENSP00000381728:R207H;ENSP00000445675:R207H;ENSP00000381726:R207H;ENSP00000384343:R207H;ENSP00000445097:R191H;ENSP00000385198:R207H;ENSP00000407342:R191H	ENSP00000381726:R207H	R	-	2	0	PRAME	21222481	0.000000	0.05858	0.016000	0.15963	0.034000	0.12701	-1.596000	0.02091	-0.045000	0.13468	-0.285000	0.09966	CGC		0.443	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		T	22892481	C	T	22892481	3	4	61	1	0	0	0	0	1	0	0	0	12458	768	27	1	917	1	PRAME	22	22892481	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192	22892481	28412085	11853	19838										
RTDR1	27156	broad.mit.edu	37	chr22	23401654	23401654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagggctcagggtttgaactCgatgacactgatggcgatcc	13	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:23401654C>T	ENST00000216036.4	-	7	1229	c.1033G>A	c.(1033-1035)Gag>Aag	p.E345K		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		345								p.E345K(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		GGTTTGAACTCGATGACACTG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											116	114	115					22																	23401654		2203	4300	6503	21731654	SO:0001583	missense	27156																														ENST00000216036.4:c.1033G>A	22.37:g.23401654C>T	ENSP00000216036:p.Glu345Lys		21731654		Missense_Mutation	SNP	ENST00000216036.4	37	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389726	0.25118	.	.	ENSG00000100218	ENST00000216036	T	0.30182	1.54	5.08	3.98	0.46160	.	0.696409	0.14346	N	0.325405	T	0.19805	0.0476	L	0.43923	1.385	0.80722	D	1	P	0.49635	0.926	B	0.33960	0.173	T	0.03922	-1.0992	10	0.16896	T	0.51	-38.5646	10.9851	0.47518	0.0:0.811:0.189:0.0	.	345	Q9UHP6	RTDR1_HUMAN	K	345	ENSP00000216036:E345K	ENSP00000216036:E345K	E	-	1	0	RTDR1	21731654	0.230000	0.23740	0.961000	0.40146	0.054000	0.15201	0.582000	0.23834	2.533000	0.85409	0.561000	0.74099	GAG		0.537	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			T	23401654	C	T	23401654	3	4	61	1	0	0	0	0	1	0	0	0	13756	893	31	1	17	1	RTDR1	22	23401654	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	509173	23401654	27902912	11854	19839										
RTDR1	27156	broad.mit.edu	37	chr22	23406139	23406139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttctggttggcgctgaggagCttctgcttcaggacaagcac	13	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:23406139C>A	ENST00000216036.4	-	5	790	c.594G>T	c.(592-594)aaG>aaT	p.K198N		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		198								p.K198N(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		CGCTGAGGAGCTTCTGCTTCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											113	96	102					22																	23406139		2203	4300	6503	21736139	SO:0001583	missense	27156																														ENST00000216036.4:c.594G>T	22.37:g.23406139C>A	ENSP00000216036:p.Lys198Asn		21736139		Missense_Mutation	SNP	ENST00000216036.4	37	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431441	0.25813	.	.	ENSG00000100218	ENST00000216036	T	0.48836	0.8	4.77	0.0395	0.14205	Armadillo-like helical (1);Armadillo-type fold (1);	0.781774	0.11720	N	0.536024	T	0.55737	0.1939	L	0.61036	1.89	0.51233	D	0.999917	D	0.71674	0.998	D	0.66351	0.943	T	0.53844	-0.8381	10	0.29301	T	0.29	-15.7646	4.9132	0.13833	0.0:0.5754:0.1532:0.2714	.	198	Q9UHP6	RTDR1_HUMAN	N	198	ENSP00000216036:K198N	ENSP00000216036:K198N	K	-	3	2	RTDR1	21736139	0.075000	0.21258	0.459000	0.27081	0.018000	0.09664	-0.089000	0.11180	-0.061000	0.13110	-0.266000	0.10368	AAG		0.612	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			A	23406139	C	A	23406139	3	1	61	1	0	0	0	0	1	0	0	0	13756	796	28	2	464	2	RTDR1	22	23406139	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4485	23406139	27898427	11855	19840										
RGL4	266747	broad.mit.edu	37	chr22	24034556	24034556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgttcaactggccccccGaaaacacttcagtttactat	5	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:24034556G>A	ENST00000290691.5	+	2	1384	c.214G>A	c.(214-216)Gaa>Aaa	p.E72K	AP000347.2_ENST00000417194.1_RNA|KB-1572G7.2_ENST00000421064.1_RNA|GUSBP11_ENST00000455485.1_RNA|RGL4_ENST00000401461.1_5'UTR	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	72					small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.E72K(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						CTGGCCCCCCGAAAACACTTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											217	210	212					22																	24034556		2203	4300	6503	22364556	SO:0001583	missense	266747				CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"RalGDS related oncogene"	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.214G>A	22.37:g.24034556G>A	ENSP00000290691:p.Glu72Lys		22364556	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	37	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	g	10.51	1.371445	0.24771	.	.	ENSG00000159496	ENST00000290691;ENST00000382833;ENST00000423392	T;T	0.34275	1.37;1.37	1.43	-2.87	0.05700	.	1.400230	0.05020	U	0.472576	T	0.39655	0.1086	L	0.29908	0.895	0.09310	N	1	D;D	0.76494	0.997;0.999	P;P	0.58077	0.721;0.832	T	0.50030	-0.8875	10	0.62326	D	0.03	.	6.4568	0.21934	0.2206:0.5314:0.2481:0.0	.	72;72	E9PH87;Q8IZJ4	.;RGDSR_HUMAN	K	72	ENSP00000290691:E72K;ENSP00000402142:E72K	ENSP00000290691:E72K	E	+	1	0	RGL4	22364556	0.773000	0.28580	0.000000	0.03702	0.000000	0.00434	0.522000	0.22909	-3.032000	0.00266	-1.255000	0.01485	GAA		0.572	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615		A	24034556	G	A	24034556	3	1	61	1	0	0	0	0	1	0	0	0	13316	1059	37	1	220	1	RGL4	22	24034556	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	628417	24034556	27270010	11856	19841										
MMP11	4320	broad.mit.edu	37	chr22	24122865	24122865	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgagaaggggatgtccacttCgactatgatgagacctggac	13	9	0	3	rs369986636		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:24122865C>T	ENST00000215743.3	+	4	631	c.579C>T	c.(577-579)ttC>ttT	p.F193F	MMP11_ENST00000477567.1_3'UTR	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	193					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.F193F(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	ATGTCCACTTCGACTATGATG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	22						C		0,4406		0,0,2203	71	70	70		579	-3	1	22		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MMP11	NM_005940.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		193/489	24122865	1,13005	2203	4300	6503	22452865	SO:0001819	synonymous_variant	4320				CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.579C>T	22.37:g.24122865C>T			22452865	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	37	CCDS13816.1																																																																																				0.577	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		T	24122865	C	T	24122865	2	4	61	1	0	0	0	0	0	0	0	1	9680	883	31	1		1	MMP11	22	24122865	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88309	24122865	27181701	11857	19842										
GGT5	2687	broad.mit.edu	37	chr22	24622608	24622608	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcaacctcacctggagcttCgggtggcttcgagggtcccc	13	14	1	0	rs58692741		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:24622608C>T	ENST00000327365.4	-	7	1445	c.1029G>A	c.(1027-1029)ccG>ccA	p.P343P	GGT5_ENST00000263112.7_Silent_p.P311P|GGT5_ENST00000398292.3_Silent_p.P343P|GGT5_ENST00000418439.2_Silent_p.P266P	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	343					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.P343P(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						CCTGGAGCTTCGGGTGGCTTC	0.627													C|||	1	0.000199681	0	0	5008	,	,		15626	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	22											74	70	71					22																	24622608		2203	4300	6503	22952608	SO:0001819	synonymous_variant	2687			M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.1029G>A	22.37:g.24622608C>T			22952608	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1																																																																																				0.627	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		T	24622608	C	T	24622608	2	4	61	1	0	0	0	0	0	0	0	1	6382	871	31	1		1	GGT5	22	24622608	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	499743	24622608	26681958	11858	19843										
ADORA2A	135	broad.mit.edu	37	chr22	24837060	24837060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtcctctcccacaccaattCggttgtgaatcccttcatct	5	16	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:24837060C>T	ENST00000337539.7	+	3	1301	c.842C>T	c.(841-843)tCg>tTg	p.S281L	ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	281					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)	p.S281L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CACACCAATTCGGTTGTGAAT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											94	87	90					22																	24837060		2203	4300	6503	23167060	SO:0001583	missense	135			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.842C>T	22.37:g.24837060C>T	ENSP00000336630:p.Ser281Leu		23167060	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175577	0.94807	.	.	ENSG00000128271	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596	T;T	0.79554	-1.28;-1.28	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.92912	0.7745	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94994	0.8137	10	0.87932	D	0	-28.2139	17.5681	0.87926	0.0:1.0:0.0:0.0	.	281	P29274	AA2AR_HUMAN	L	281	ENSP00000414802:S281L;ENSP00000336630:S281L	ENSP00000336630:S281L	S	+	2	0	ADORA2A	23167060	1.000000	0.71417	0.663000	0.29738	0.985000	0.73830	7.590000	0.82653	2.385000	0.81259	0.462000	0.41574	TCG		0.567	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24837060	C	T	24837060	3	4	61	1	0	0	0	0	1	0	0	0	327	893	31	1	848	1	ADORA2A	22	24837060	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	214452	24837060	26467506	11859	19844										
ADORA2A	135	broad.mit.edu	37	chr22	24837121	24837121	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttccgccagaccttccgcaaGatcattcgcagccacgtcct	7	17	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:24837121G>T	ENST00000337539.7	+	3	1362	c.903G>T	c.(901-903)aaG>aaT	p.K301N	ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	301					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)	p.K301N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CCTTCCGCAAGATCATTCGCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	22											75	64	68					22																	24837121		2203	4300	6503	23167121	SO:0001583	missense	135			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.903G>T	22.37:g.24837121G>T	ENSP00000336630:p.Lys301Asn		23167121	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805952	0.50421	.	.	ENSG00000128271	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596	T;T	0.41065	1.01;1.01	4.75	4.75	0.60458	.	0.101533	0.64402	D	0.000003	T	0.37919	0.1021	M	0.61703	1.905	0.58432	D	0.999993	B	0.32051	0.354	B	0.28638	0.092	T	0.31779	-0.9931	10	0.46703	T	0.11	-29.7135	10.2491	0.43358	0.1:0.0:0.9:0.0	.	301	P29274	AA2AR_HUMAN	N	301	ENSP00000414802:K301N;ENSP00000336630:K301N	ENSP00000336630:K301N	K	+	3	2	ADORA2A	23167121	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.503000	0.53340	2.473000	0.83533	0.462000	0.41574	AAG		0.587	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24837121	G	T	24837121	3	4	61	1	0	0	0	0	1	0	0	0	327	933	33	2	909	2	ADORA2A	22	24837121	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	61	24837121	26467445	11860	19845										
PIWIL3	440822	broad.mit.edu	37	chr22	25115745	25115745	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatacatgtggcatagacaAtatgttaaacgctgtactgt	8	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25115745A>G	ENST00000332271.5	-	20	2918	c.2502T>C	c.(2500-2502)taT>taC	p.Y834Y	PIWIL3_ENST00000533313.1_Silent_p.Y716Y|PIWIL3_ENST00000527701.1_Silent_p.Y716Y|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	834	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.Y834Y(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GGCATAGACAATATGTTAAAC	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	22											98	95	96					22																	25115745		2203	4300	6503	23445745	SO:0001819	synonymous_variant	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.2502T>C	22.37:g.25115745A>G			23445745		Silent	SNP	ENST00000332271.5	37	CCDS33623.1																																																																																				0.363	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		G	25115745	A	G	25115745	2	3	61	1	0	0	0	0	0	0	0	1	11990	108	4	4		4	PIWIL3	22	25115745	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	278624	25115745	26188821	11861	19846										
PIWIL3	440822	broad.mit.edu	37	chr22	25150797	25150797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttttggtataatagttgcGaccaacttgttcaaaatcca	6	8	1	0	rs142590557		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25150797G>A	ENST00000332271.5	-	7	1143	c.727C>T	c.(727-729)Cgc>Tgc	p.R243C	PIWIL3_ENST00000533313.1_Missense_Mutation_p.R134C|PIWIL3_ENST00000527701.1_Missense_Mutation_p.R134C|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	243					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.R243C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TAATAGTTGCGACCAACTTGT	0.348													G|||	1	0.000199681	8e-04	0	5008	,	,		18387	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	115	117	116		727	2.4	0.9	22	dbSNP_134	116	0,8600		0,0,4300	yes	missense	PIWIL3	NM_001008496.2	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	243/883	25150797	2,13004	2203	4300	6503	23480797	SO:0001583	missense	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.727C>T	22.37:g.25150797G>A	ENSP00000330031:p.Arg243Cys		23480797		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	14.97	2.694675	0.48202	4.54E-4	0.0	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.20069	2.1;2.1;2.1	2.41	2.41	0.29592	Argonaute/Dicer protein, PAZ (1);	0.000000	0.85682	U	0.000000	T	0.48295	0.1492	M	0.90369	3.11	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.55016	-0.8206	10	0.87932	D	0	-3.4366	8.428	0.32739	0.0:0.0:1.0:0.0	.	134;243;243	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	C	243;134;134	ENSP00000330031:R243C;ENSP00000431843:R134C;ENSP00000435718:R134C	ENSP00000330031:R243C	R	-	1	0	PIWIL3	23480797	1.000000	0.71417	0.878000	0.34440	0.032000	0.12392	2.018000	0.40991	1.673000	0.50895	0.455000	0.32223	CGC		0.348	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25150797	G	A	25150797	3	1	61	1	0	0	0	0	1	0	0	0	11990	1058	37	1	1981	1	PIWIL3	22	25150797	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	35052	25150797	26153769	11862	19847										
PIWIL3	440822	broad.mit.edu	37	chr22	25151834	25151834	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aactcaactgtaatcttcacGatgtttttgtctttggttgt	7	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25151834G>A	ENST00000332271.5	-	6	1025	c.609C>T	c.(607-609)atC>atT	p.I203I	PIWIL3_ENST00000533313.1_Silent_p.I94I|PIWIL3_ENST00000527701.1_Silent_p.I94I|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	203					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.I203I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TAATCTTCACGATGTTTTTGT	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	22											145	137	140					22																	25151834		2203	4300	6503	23481834	SO:0001819	synonymous_variant	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.609C>T	22.37:g.25151834G>A			23481834		Silent	SNP	ENST00000332271.5	37	CCDS33623.1																																																																																				0.373	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25151834	G	A	25151834	2	1	61	1	0	0	0	0	0	0	0	1	11990	1048	37	1		1	PIWIL3	22	25151834	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1037	25151834	26152732	11863	19848										
SGSM1	129049	broad.mit.edu	37	chr22	25264350	25264350	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggtggcggcagttgacagCggcgggacagtggtattggt	20	6	0	1	rs375206010		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25264350C>T	ENST00000400359.4	+	11	1009	c.1002C>T	c.(1000-1002)agC>agT	p.S334S	SGSM1_ENST00000400358.4_Silent_p.S334S	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	334	Required for interaction with RAP family members.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.S334S(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CAGTTGACAGCGGCGGGACAG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	22						C	,,,	0,4084		0,0,2042	31	35	34		1002,1002,1002,1002	2.8	1	22		34	1,8363		0,1,4181	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	0,1,6223	TT,TC,CC		0.012,0.0,0.0080	,,,	334/1149,334/1094,334/1033,334/1088	25264350	1,12447	2042	4182	6224	23594350	SO:0001819	synonymous_variant	129049			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1002C>T	22.37:g.25264350C>T			23594350	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																				0.647	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		T	25264350	C	T	25264350	2	4	61	1	0	0	0	0	0	0	0	1	14259	767	27	1		1	SGSM1	22	25264350	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	112516	25264350	26040216	11864	19849										
SGSM1	129049	broad.mit.edu	37	chr22	25301121	25301121	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtccagggcatgtgtgatCttctggctccactgctggtc	12	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25301121C>A	ENST00000400359.4	+	22	2957	c.2950C>A	c.(2950-2952)Ctt>Att	p.L984I	SGSM1_ENST00000400358.4_Missense_Mutation_p.L929I	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	984	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.L929I(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CATGTGTGATCTTCTGGCTCC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											283	275	278					22																	25301121		2143	4253	6396	23631121	SO:0001583	missense	129049			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.2950C>A	22.37:g.25301121C>A	ENSP00000383212:p.Leu984Ile		23631121	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676477	0.88445	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.05258	3.47;3.47	5.62	5.62	0.85841	Rab-GAP/TBC domain (4);	0.055931	0.64402	D	0.000001	T	0.25938	0.0632	M	0.66560	2.04	0.58432	D	0.999998	P;P;P;D	0.89917	0.933;0.714;0.928;1.0	P;P;P;D	0.91635	0.784;0.737;0.885;0.999	T	0.00059	-1.2166	10	0.87932	D	0	-28.6862	19.0368	0.92982	0.0:1.0:0.0:0.0	.	929;984;1001;984	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	I	984;929;984	ENSP00000383211:L929I;ENSP00000383212:L984I	ENSP00000383211:L929I	L	+	1	0	SGSM1	23631121	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.660000	0.61511	2.823000	0.97156	0.643000	0.83706	CTT		0.537	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		A	25301121	C	A	25301121	3	1	61	1	0	0	0	0	1	0	0	0	14259	913	32	2	3036	2	SGSM1	22	25301121	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	36771	25301121	26003445	11865	19850										
SGSM1	129049	broad.mit.edu	37	chr22	25315920	25315920	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taccgtgacatcattttggaGaacaacatggatttcacaga	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:25315920G>T	ENST00000400359.4	+	25	3325	c.3318G>T	c.(3316-3318)gaG>gaT	p.E1106D	SGSM1_ENST00000400358.4_Missense_Mutation_p.E1051D	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	1106						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.E1051D(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TCATTTTGGAGAACAACATGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	22											90	83	85					22																	25315920		2063	4209	6272	23645920	SO:0001583	missense	129049			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.3318G>T	22.37:g.25315920G>T	ENSP00000383212:p.Glu1106Asp		23645920	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	g	4.826	0.153656	0.09185	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.25250	1.81;1.81	5.53	1.88	0.25563	Rab-GAP/TBC domain (2);	0.000000	0.85682	D	0.000000	T	0.16041	0.0386	N	0.03224	-0.385	0.45791	D	0.99867	B;B;D;P	0.60575	0.02;0.024;0.988;0.462	B;B;P;B	0.59221	0.07;0.024;0.854;0.065	T	0.07558	-1.0766	10	0.02654	T	1	-32.9947	10.1692	0.42900	0.2704:0.0:0.7296:0.0	.	1051;1106;1123;1106	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	D	1106;1051;1106	ENSP00000383211:E1051D;ENSP00000383212:E1106D	ENSP00000383211:E1051D	E	+	3	2	SGSM1	23645920	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.422000	0.34826	0.832000	0.34804	-0.140000	0.14226	GAG		0.527	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		T	25315920	G	T	25315920	3	4	61	1	0	0	0	0	1	0	0	0	14259	933	33	2	3416	2	SGSM1	22	25315920	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14799	25315920	25988646	11866	19851										
MYO18B	84700	broad.mit.edu	37	chr22	26157081	26157081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggccatctcatcacgcctcGccctgtgggagcagaaggaa	12	13	2	1	rs139296373	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26157081G>A	ENST00000407587.2	+	2	191	c.22G>A	c.(22-24)Gcc>Acc	p.A8T	MYO18B_ENST00000335473.7_Missense_Mutation_p.A8T|MYO18B_ENST00000536101.1_Missense_Mutation_p.A8T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	8						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A8T(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ATCACGCCTCGCCCTGTGGGA	0.592													G|||	2	0.000399361	0	0.0014	5008	,	,		21771	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						G	THR/ALA	0,4378		0,0,2189	102	103	102		22	5.3	1	22	dbSNP_134	102	2,8558	2.2+/-6.3	0,2,4278	no	missense	MYO18B	NM_032608.5	58	0,2,6467	AA,AG,GG		0.0234,0.0,0.0155	benign	8/2568	26157081	2,12936	2189	4280	6469	24487081	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.22G>A	22.37:g.26157081G>A	ENSP00000386096:p.Ala8Thr		24487081	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	27.9	4.874543	0.91664	0.0	2.34E-4	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.88896	-2.42;-2.42;-2.44	5.3	5.3	0.74995	.	0.000000	0.36101	N	0.002800	D	0.92909	0.7744	L	0.56769	1.78	0.34314	D	0.685746	D	0.89917	1.0	D	0.87578	0.998	D	0.95653	0.8708	10	0.87932	D	0	.	14.4541	0.67404	0.0:0.0:1.0:0.0	.	8	F5GYU7	.	T	8	ENSP00000441229:A8T;ENSP00000334563:A8T;ENSP00000386096:A8T	ENSP00000334563:A8T	A	+	1	0	MYO18B	24487081	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.191000	0.65110	2.487000	0.83934	0.591000	0.81541	GCC		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26157081	G	A	26157081	3	1	61	1	0	0	0	0	1	0	0	0	10096	1087	38	1	24	1	MYO18B	22	26157081	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	841161	26157081	25147485	11867	19852										
MYO18B	84700	broad.mit.edu	37	chr22	26164630	26164630	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggggcttgggacccccaaGaccacagagctgaaagaggc	14	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26164630G>T	ENST00000407587.2	+	4	916	c.747G>T	c.(745-747)aaG>aaT	p.K249N	MYO18B_ENST00000335473.7_Missense_Mutation_p.K249N|MYO18B_ENST00000536101.1_Missense_Mutation_p.K249N			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	249						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K249N(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GGACCCCCAAGACCACAGAGC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	22											23	29	27					22																	26164630		1907	4109	6016	24494630	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.747G>T	22.37:g.26164630G>T	ENSP00000386096:p.Lys249Asn		24494630	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	g	4.652	0.121179	0.08881	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86956	-2.17;-2.17;-2.19	4.81	2.71	0.32032	.	0.904474	0.08975	N	0.866627	T	0.76026	0.3930	N	0.14661	0.345	0.09310	N	1	B;B;B	0.29037	0.148;0.231;0.231	B;B;B	0.21546	0.016;0.035;0.035	T	0.61173	-0.7116	10	0.42905	T	0.14	.	9.3296	0.38014	0.1459:0.1233:0.7308:0.0	.	249;249;249	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	N	249	ENSP00000441229:K249N;ENSP00000334563:K249N;ENSP00000386096:K249N	ENSP00000334563:K249N	K	+	3	2	MYO18B	24494630	0.986000	0.35501	0.823000	0.32752	0.016000	0.09150	2.040000	0.41203	0.125000	0.18397	-1.829000	0.00594	AAG		0.652	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26164630	G	T	26164630	3	4	61	1	0	0	0	0	1	0	0	0	10096	933	33	2	757	2	MYO18B	22	26164630	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7549	26164630	25139936	11868	19853										
MYO18B	84700	broad.mit.edu	37	chr22	26165302	26165302	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccagcctgctctggagaaGgatgcagaaaggcctcggat	14	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26165302G>T	ENST00000407587.2	+	4	1588	c.1419G>T	c.(1417-1419)aaG>aaT	p.K473N	MYO18B_ENST00000335473.7_Missense_Mutation_p.K473N|MYO18B_ENST00000536101.1_Missense_Mutation_p.K473N			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	473						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K473N(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCTGGAGAAGGATGCAGAAA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	22											12	15	14					22																	26165302		2013	4161	6174	24495302	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1419G>T	22.37:g.26165302G>T	ENSP00000386096:p.Lys473Asn		24495302	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	9.425	1.084084	0.20309	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87029	-2.18;-2.18;-2.2	4.53	1.04	0.20106	.	2.990260	0.00979	N	0.003342	T	0.77552	0.4147	N	0.22421	0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.59445	-0.7453	10	0.27082	T	0.32	.	2.3434	0.04265	0.131:0.3768:0.3187:0.1736	.	473;473;473	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	N	473	ENSP00000441229:K473N;ENSP00000334563:K473N;ENSP00000386096:K473N	ENSP00000334563:K473N	K	+	3	2	MYO18B	24495302	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.428000	0.06991	0.076000	0.16826	0.491000	0.48974	AAG		0.642	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26165302	G	T	26165302	3	4	61	1	0	0	0	0	1	0	0	0	10096	991	35	2	1429	2	MYO18B	22	26165302	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	672	26165302	25139264	11869	19854										
MYO18B	84700	broad.mit.edu	37	chr22	26294417	26294417	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgaaaccatgagctggagaaGaagcagaagaagtgagttgc	14	6	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26294417G>T	ENST00000407587.2	+	29	4984	c.4815G>T	c.(4813-4815)aaG>aaT	p.K1605N	CTA-125H2.2_ENST00000600211.1_RNA|CTA-125H2.2_ENST00000600903.1_RNA|CTA-125H2.2_ENST00000596813.1_RNA|CTA-125H2.2_ENST00000608921.1_RNA|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000595102.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000609809.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.K1604N|CTA-125H2.2_ENST00000595093.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.K1604N|CTA-125H2.2_ENST00000599792.1_RNA|CTA-125H2.2_ENST00000594856.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000608507.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|CTA-125H2.2_ENST00000593715.1_RNA|CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000594542.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000597614.2_RNA|CTA-125H2.2_ENST00000609820.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1604	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K1605N(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGCTGGAGAAGAAGCAGAAGA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	22											118	117	117					22																	26294417		2070	4204	6274	24624417	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4815G>T	22.37:g.26294417G>T	ENSP00000386096:p.Lys1605Asn		24624417	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	20.8	4.050103	0.75846	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;T	0.89617	-2.54;-2.54;-1.2	5.9	4.89	0.63831	.	0.322332	0.28198	N	0.016232	D	0.91590	0.7343	M	0.76574	2.34	0.41153	D	0.98604	P;P;D;D	0.54601	0.943;0.945;0.959;0.967	P;P;P;P	0.56127	0.736;0.625;0.714;0.792	D	0.91941	0.5563	10	0.87932	D	0	.	9.1682	0.37065	0.1634:0.0:0.8366:0.0	.	1117;1604;1605;1604	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	N	1604;1604;1605	ENSP00000441229:K1604N;ENSP00000334563:K1604N;ENSP00000386096:K1605N	ENSP00000334563:K1604N	K	+	3	2	MYO18B	24624417	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.713000	0.47194	1.501000	0.48654	0.655000	0.94253	AAG		0.522	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26294417	G	T	26294417	3	4	61	1	0	0	0	0	1	0	0	0	10096	933	33	2	4922	2	MYO18B	22	26294417	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	129115	26294417	25010149	11870	19855										
MYO18B	84700	broad.mit.edu	37	chr22	26423385	26423385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaaacggaagaggctaaccGttcctttctctcggggatca	11	10	2	2	rs577931213		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26423385G>A	ENST00000407587.2	+	43	7617	c.7448G>A	c.(7447-7449)cGt>cAt	p.R2483H	MYO18B_ENST00000335473.7_Missense_Mutation_p.R2482H|MYO18B_ENST00000536101.1_Missense_Mutation_p.R2482H			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2482						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R2483H(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GAGGCTAACCGTTCCTTTCTC	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		20053	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											80	82	81					22																	26423385		1999	4158	6157	24753385	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7448G>A	22.37:g.26423385G>A	ENSP00000386096:p.Arg2483His		24753385	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.424|3.424	-0.117597|-0.117597	0.06838|0.06838	.|.	.|.	ENSG00000133454|ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587|ENST00000543971	D;D;D|.	0.86865|.	-2.17;-2.17;-2.18|.	5.17|5.17	3.05|3.05	0.35203|0.35203	.|.	0.458028|.	0.16030|.	N|.	0.232938|.	T|T	0.41650|0.41650	0.1168|0.1168	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.32829|.	0.252;0.267;0.267;0.386;0.386|.	B;B;B;B;B|.	0.21917|.	0.026;0.016;0.016;0.037;0.037|.	T|T	0.31613|0.31613	-0.9937|-0.9937	10|5	0.72032|.	D|.	0.01|.	.|.	4.7489|4.7489	0.13050|0.13050	0.2408:0.0:0.605:0.1541|0.2408:0.0:0.605:0.1541	.|.	1995;2484;2482;2483;2482|.	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7|.	.;.;MY18B_HUMAN;.;.|.	H|I	2482;2482;2483|432	ENSP00000441229:R2482H;ENSP00000334563:R2482H;ENSP00000386096:R2483H|.	ENSP00000334563:R2482H|.	R|V	+|+	2|1	0|0	MYO18B|MYO18B	24753385|24753385	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.016000|0.016000	0.09150|0.09150	0.342000|0.342000	0.19926|0.19926	1.169000|1.169000	0.42739|0.42739	0.561000|0.561000	0.74099|0.74099	CGT|GTT		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26423385	G	A	26423385	3	1	61	1	0	0	0	0	1	0	0	0	10096	1145	40	1	7611	1	MYO18B	22	26423385	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	128968	26423385	24881181	11871	19856										
SEZ6L	23544	broad.mit.edu	37	chr22	26688897	26688897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaatctcccccttcacttCgcagccctatgtggcccaca	6	18	2	0	rs200293457		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26688897C>T	ENST00000248933.6	+	2	715	c.620C>T	c.(619-621)tCg>tTg	p.S207L	SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000404234.3_Missense_Mutation_p.S207L|SEZ6L_ENST00000360929.3_Missense_Mutation_p.S207L|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000529632.2_Missense_Mutation_p.S207L|SEZ6L_ENST00000343706.4_Missense_Mutation_p.S207L			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	207					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.S207L(2)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCCTTCACTTCGCAGCCCTAT	0.662																																																2	Substitution - Missense(2)	large_intestine(2)	22											53	57	56					22																	26688897		2201	4293	6494	25018897	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.620C>T	22.37:g.26688897C>T	ENSP00000248933:p.Ser207Leu		25018897	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.659530	0.29515	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.29655	1.82;1.93;2.0;1.82;1.56	4.49	4.49	0.54785	.	0.387872	0.18853	N	0.129344	T	0.14830	0.0358	N	0.08118	0	0.19945	N	0.999948	B;B;B;B;B;B	0.21309	0.004;0.01;0.054;0.025;0.01;0.01	B;B;B;B;B;B	0.12156	0.001;0.001;0.004;0.007;0.001;0.001	T	0.08006	-1.0743	10	0.42905	T	0.14	.	7.4189	0.27061	0.1661:0.7452:0.0:0.0887	.	207;207;207;207;207;207	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	L	207	ENSP00000384772:S207L;ENSP00000437037:S207L;ENSP00000354185:S207L;ENSP00000248933:S207L;ENSP00000342661:S207L	ENSP00000248933:S207L	S	+	2	0	SEZ6L	25018897	0.001000	0.12720	0.606000	0.28943	0.694000	0.40290	0.781000	0.26774	2.216000	0.71823	0.508000	0.49915	TCG		0.662	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			T	26688897	C	T	26688897	3	4	61	1	0	0	0	0	1	0	0	0	14180	893	31	1	626	1	SEZ6L	22	26688897	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	265512	26688897	24615669	11872	19857										
SEZ6L	23544	broad.mit.edu	37	chr22	26736453	26736453	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctacgatggcgacgaggtCatgccccacatcttggggca	12	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26736453C>A	ENST00000248933.6	+	10	2162	c.2067C>A	c.(2065-2067)gtC>gtA	p.V689V	SEZ6L_ENST00000402979.1_Silent_p.V462V|SEZ6L_ENST00000404234.3_Silent_p.V689V|SEZ6L_ENST00000360929.3_Silent_p.V689V|SEZ6L_ENST00000403121.1_Silent_p.V462V|SEZ6L_ENST00000529632.2_Silent_p.V689V|SEZ6L_ENST00000343706.4_Silent_p.V689V			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	689	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.V689V(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GCGACGAGGTCATGCCCCACA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	22											150	137	141					22																	26736453		2203	4300	6503	25066453	SO:0001819	synonymous_variant	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2067C>A	22.37:g.26736453C>A			25066453	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																				0.537	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26736453	C	A	26736453	2	1	61	1	0	0	0	0	0	0	0	1	14180	813	29	2		2	SEZ6L	22	26736453	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	47556	26736453	24568113	11873	19858										
SEZ6L	23544	broad.mit.edu	37	chr22	26771561	26771561	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagcagaagcggcagcagagAcgtcgctggaaggggggaac	18	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26771561A>G	ENST00000248933.6	+	15	2943	c.2848A>G	c.(2848-2850)Acg>Gcg	p.T950A	SEZ6L_ENST00000494013.1_3'UTR|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T722A|SEZ6L_ENST00000404234.3_Missense_Mutation_p.T949A|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T875A|SEZ6L_ENST00000411842.2_Intron|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T646A|SEZ6L_ENST00000529632.2_Missense_Mutation_p.T939A|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T874A			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	950					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.T950A(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGCAGCAGAGACGTCGCTGGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											99	81	87					22																	26771561		2203	4300	6503	25101561	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2848A>G	22.37:g.26771561A>G	ENSP00000248933:p.Thr950Ala		25101561	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908429	0.52333	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.28069	1.94;2.02;2.11;1.92;1.66;1.63;1.92	5.33	0.563	0.17296	.	0.221905	0.29775	N	0.011232	T	0.17619	0.0423	N	0.22421	0.69	0.80722	D	1	P;P;B;B;B;P;P	0.39940	0.512;0.696;0.023;0.3;0.3;0.563;0.563	B;B;B;B;B;B;B	0.34722	0.13;0.188;0.008;0.066;0.066;0.188;0.188	T	0.02654	-1.1128	10	0.52906	T	0.07	.	10.8069	0.46522	0.5403:0.0:0.0:0.4597	.	937;939;646;874;875;949;950	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	A	949;939;875;950;874;646;722	ENSP00000384772:T949A;ENSP00000437037:T939A;ENSP00000354185:T875A;ENSP00000248933:T950A;ENSP00000342661:T874A;ENSP00000384838:T646A;ENSP00000384733:T722A	ENSP00000248933:T950A	T	+	1	0	SEZ6L	25101561	1.000000	0.71417	0.912000	0.35992	0.992000	0.81027	3.702000	0.54800	-0.264000	0.09365	-0.531000	0.04308	ACG		0.572	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			G	26771561	A	G	26771561	3	3	61	1	0	0	0	0	1	0	0	0	14180	275	10	4	2906	4	SEZ6L	22	26771561	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	35108	26771561	24533005	11874	19859										
HPS4	89781	broad.mit.edu	37	chr22	26860708	26860708	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattccacatggccagtggcGttttctttcagggcagatgt	12	9	2	1	rs138343171	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:26860708G>A	ENST00000398145.2	-	11	1504	c.888C>T	c.(886-888)aaC>aaT	p.N296N	HPS4_ENST00000398141.1_Silent_p.N309N|HPS4_ENST00000336873.5_Silent_p.N296N|HPS4_ENST00000493455.2_5'Flank|HPS4_ENST00000402105.3_Silent_p.N291N	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	296					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)	p.N309N(1)|p.N296N(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GGCCAGTGGCGTTTTCTTTCA	0.567									Hermansky-Pudlak syndrome				G|||	5	0.000998403	0	0	5008	,	,		22214	0		0.005	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	22						G	,	1,4405	2.1+/-5.4	0,1,2202	109	90	96		888,873	-8.7	0	22	dbSNP_134	96	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	HPS4	NM_022081.4,NM_152841.1	,	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	,	296/709,291/704	26860708	15,12991	2203	4300	6503	25190708	SO:0001819	synonymous_variant	89781	Familial Cancer Database	HPS, HPS1-8		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.888C>T	22.37:g.26860708G>A			25190708	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	37	CCDS13835.1																																																																																				0.567	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		A	26860708	G	A	26860708	2	1	61	1	0	0	0	0	0	0	0	1	7362	1136	40	1		1	HPS4	22	26860708	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	89147	26860708	24443858	11875	19860										
CRYBB1	1414	broad.mit.edu	37	chr22	27003956	27003956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaggatgaacatctccccgCggaagttggactgctcaaag	11	12	2	1	rs533532537		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:27003956C>T	ENST00000215939.2	-	4	459	c.329G>A	c.(328-330)cGc>cAc	p.R110H		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	110	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.R110H(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						CATCTCCCCGCGGAAGTTGGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											89	72	78					22																	27003956		2203	4300	6503	25333956	SO:0001583	missense	1414				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.329G>A	22.37:g.27003956C>T	ENSP00000215939:p.Arg110His		25333956		Missense_Mutation	SNP	ENST00000215939.2	37	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.731951	0.48939	.	.	ENSG00000100122	ENST00000215939	T	0.78126	-1.15	4.64	2.55	0.30701	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.409242	0.27686	N	0.018280	T	0.78259	0.4255	M	0.88241	2.94	0.52501	D	0.999951	B	0.28552	0.215	B	0.26202	0.067	T	0.75019	-0.3465	10	0.46703	T	0.11	.	9.6196	0.39712	0.0:0.8304:0.0:0.1696	.	110	P53674	CRBB1_HUMAN	H	110	ENSP00000215939:R110H	ENSP00000215939:R110H	R	-	2	0	CRYBB1	25333956	0.869000	0.29996	0.714000	0.30535	0.955000	0.61496	2.265000	0.43311	0.571000	0.29365	0.585000	0.79938	CGC		0.567	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887		T	27003956	C	T	27003956	3	4	61	1	0	0	0	0	1	0	0	0	3916	768	27	1	441	1	CRYBB1	22	27003956	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	143248	27003956	24300610	11876	19861										
CRYBB1	1414	broad.mit.edu	37	chr22	27008142	27008142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccctggaagttttccagttCgaagaccaccagctgcagga	11	12	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:27008142C>T	ENST00000215939.2	-	3	323	c.193G>A	c.(193-195)Gaa>Aaa	p.E65K		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	65	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.E65K(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						TTTTCCAGTTCGAAGACCACC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	22											56	51	53					22																	27008142		2203	4300	6503	25338142	SO:0001583	missense	1414				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.193G>A	22.37:g.27008142C>T	ENSP00000215939:p.Glu65Lys		25338142		Missense_Mutation	SNP	ENST00000215939.2	37	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995809	0.93167	.	.	ENSG00000100122	ENST00000215939	T	0.80824	-1.42	4.02	4.02	0.46733	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.112768	0.64402	D	0.000015	D	0.91888	0.7432	H	0.94925	3.6	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	D	0.94318	0.7551	10	0.87932	D	0	.	15.3041	0.73979	0.0:1.0:0.0:0.0	.	65	P53674	CRBB1_HUMAN	K	65	ENSP00000215939:E65K	ENSP00000215939:E65K	E	-	1	0	CRYBB1	25338142	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	6.730000	0.74780	2.072000	0.62099	0.491000	0.48974	GAA		0.537	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887		T	27008142	C	T	27008142	3	4	61	1	0	0	0	0	1	0	0	0	3916	893	31	1	581	1	CRYBB1	22	27008142	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4186	27008142	24296424	11877	19862										
MN1	4330	broad.mit.edu	37	chr22	28196070	28196070	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccctggctctccgccatgtgCtcatagccctcggcgaaggg	12	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:28196070C>T	ENST00000302326.4	-	1	1416	c.462G>A	c.(460-462)gaG>gaA	p.E154E		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	154					intramembranous ossification (GO:0001957)			p.E154E(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						CCGCCATGTGCTCATAGCCCT	0.746			T	ETV6	"AML, meningioma"																																		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	1	Substitution - coding silent(1)	large_intestine(1)	22											7	9	8					22																	28196070		1858	4047	5905	26526070	SO:0001819	synonymous_variant	4330			X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"probable tumor suppressor protein MN1"	156100	"meningioma chromosome region"	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.462G>A	22.37:g.28196070C>T			26526070	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																				0.746	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		T	28196070	C	T	28196070	2	4	61	1	0	0	0	0	0	0	0	1	9703	796	28	3		3	MN1	22	28196070	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1187928	28196070	23108496	11878	19863										
PITPNB	23760	broad.mit.edu	37	chr22	28250906	28250906	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcagcagccgacgtgcctcGaacggaacccctcttacgca	9	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:28250906G>A	ENST00000335272.5	-	11	866	c.790C>T	c.(790-792)Cga>Tga	p.R264*	PITPNB_ENST00000455418.3_Nonsense_Mutation_p.R266*|PITPNB_ENST00000320996.10_Intron	NM_012399.3	NP_036531.1	P48739	PIPNB_HUMAN	phosphatidylinositol transfer protein, beta	264					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|lipid metabolic process (GO:0006629)|phospholipid metabolic process (GO:0006644)|phospholipid transport (GO:0015914)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	lipid binding (GO:0008289)	p.R264*(1)		large_intestine(4)|lung(3)|skin(1)	8						GACGTGCCTCGAACGGAACCC	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	22																																								26580906	SO:0001587	stop_gained	23760			D30037	CCDS13842.1, CCDS63433.1	22q12.1	2006-12-15			ENSG00000180957	ENSG00000180957			9002	protein-coding gene	gene with protein product		606876				10591208	Standard	NM_012399		Approved	VIB1B	uc003adk.3	P48739	OTTHUMG00000150976	ENST00000335272.5:c.790C>T	22.37:g.28250906G>A	ENSP00000334738:p.Arg264*		26580906	B3KYB8|B7Z7Q0|Q8N5W1	Nonsense_Mutation	SNP	ENST00000335272.5	37	CCDS13842.1	.	.	.	.	.	.	.	.	.	.	G	35	5.454711	0.96223	.	.	ENSG00000180957	ENST00000335272;ENST00000455418	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.0426	0.93006	0.0:0.0:1.0:0.0	.	.	.	.	X	264;266	.	ENSP00000334738:R264X	R	-	1	2	PITPNB	26580906	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.269000	0.78482	2.748000	0.94277	0.655000	0.94253	CGA		0.438	PITPNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320740.1			A	28250906	G	A	28250906	4	1	61	1	0	0	0	0	0	1	0	0	11979	1066	37	1	29	1	PITPNB	22	28250906	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	54836	28250906	23053660	11879	19864										
CCDC117	150275	broad.mit.edu	37	chr22	29182259	29182259	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcggccaacagggatgtCtctttataatagtttggaga	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:29182259C>A	ENST00000249064.4	+	5	961	c.785C>A	c.(784-786)tCt>tAt	p.S262Y	CCDC117_ENST00000421503.2_Missense_Mutation_p.S187Y|CCDC117_ENST00000443309.2_Missense_Mutation_p.S130Y|CCDC117_ENST00000448492.2_Missense_Mutation_p.S244Y	NM_001284263.1|NM_001284265.1|NM_173510.2	NP_001271192.1|NP_001271194.1|NP_775781.1	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	262								p.S262Y(1)		breast(1)|kidney(1)|large_intestine(4)|upper_aerodigestive_tract(1)	7						ACAGGGATGTCTCTTTATAAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	22											79	78	78					22																	29182259		2203	4300	6503	27512259	SO:0001583	missense	150275			AK091133	CCDS13846.1, CCDS63435.1, CCDS63436.1	22q12.1	2006-06-27			ENSG00000159873	ENSG00000159873			26599	protein-coding gene	gene with protein product						12477932	Standard	NM_001284263		Approved	FLJ33814	uc003aeb.3	Q8IWD4	OTTHUMG00000151091	ENST00000249064.4:c.785C>A	22.37:g.29182259C>A	ENSP00000249064:p.Ser262Tyr		27512259	A8K0F1|B7Z2V1|B7Z860|Q6ICA7|Q8N278	Missense_Mutation	SNP	ENST00000249064.4	37	CCDS13846.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.279259	0.40294	.	.	ENSG00000159873	ENST00000249064;ENST00000448492;ENST00000421503;ENST00000443309	T;T;T;T	0.36157	1.27;1.31;1.28;1.32	5.94	5.94	0.96194	.	0.258919	0.38778	N	0.001574	T	0.32194	0.0821	N	0.14661	0.345	0.25110	N	0.990721	P;P;P	0.42649	0.786;0.786;0.786	P;P;P	0.47251	0.542;0.542;0.542	T	0.29058	-1.0024	10	0.72032	D	0.01	.	14.8966	0.70649	0.0:0.8573:0.1427:0.0	.	187;244;262	B7Z2V1;B7Z860;Q8IWD4	.;.;CC117_HUMAN	Y	262;244;187;130	ENSP00000249064:S262Y;ENSP00000389478:S244Y;ENSP00000387827:S187Y;ENSP00000399363:S130Y	ENSP00000249064:S262Y	S	+	2	0	CCDC117	27512259	1.000000	0.71417	0.867000	0.34043	0.385000	0.30292	5.000000	0.63940	2.816000	0.96949	0.561000	0.74099	TCT		0.433	CCDC117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321258.1	NM_173510		A	29182259	C	A	29182259	3	1	61	1	0	0	0	0	1	0	0	0	2760	913	32	2	803	2	CCDC117	22	29182259	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	931353	29182259	22122307	11880	19865										
C22orf31	25770	broad.mit.edu	37	chr22	29454761	29454761	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctttaacttgggccatttcTtgagtacaggctcctcgtgg	10	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:29454761T>G	ENST00000216071.4	-	3	893	c.842A>C	c.(841-843)aAg>aCg	p.K281T		NM_015370.1	NP_056185.1	O95567	CV031_HUMAN	chromosome 22 open reading frame 31	281								p.K281T(1)		cervix(1)|endometrium(1)|kidney(17)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	27						GGGCCATTTCTTGAGTACAGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	22											121	105	110					22																	29454761		2203	4300	6503	27784761	SO:0001583	missense	25770			AL035364	CCDS13848.1	22q12.1	2006-07-05			ENSG00000100249	ENSG00000100249			26931	protein-coding gene	gene with protein product						15461802	Standard	XM_005261490		Approved	HS747E2A, bK747E2.1	uc003aej.1	O95567	OTTHUMG00000151011	ENST00000216071.4:c.842A>C	22.37:g.29454761T>G	ENSP00000216071:p.Lys281Thr		27784761	A0AV97	Missense_Mutation	SNP	ENST00000216071.4	37	CCDS13848.1	.	.	.	.	.	.	.	.	.	.	T	4.399	0.073720	0.08485	.	.	ENSG00000100249	ENST00000216071	T	0.35973	1.28	5.25	4.21	0.49690	.	0.924506	0.09158	N	0.840608	T	0.32823	0.0842	N	0.24115	0.695	0.09310	N	0.999999	P	0.46784	0.884	P	0.48677	0.586	T	0.11891	-1.0569	10	0.40728	T	0.16	-2.2026	7.6837	0.28528	0.0:0.0936:0.0:0.9064	.	281	O95567	CV031_HUMAN	T	281	ENSP00000216071:K281T	ENSP00000216071:K281T	K	-	2	0	C22orf31	27784761	0.749000	0.28305	0.706000	0.30403	0.027000	0.11550	1.069000	0.30641	1.123000	0.41961	0.533000	0.62120	AAG		0.483	C22orf31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320952.1	NM_015370		G	29454761	T	G	29454761	3	3	61	1	0	0	0	0	1	0	0	0	2149	1609	56	4	34	4	C22orf31	22	29454761	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	272502	29454761	21849805	11881	19866										
C22orf31	25770	broad.mit.edu	37	chr22	29455128	29455128	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatatctgtcctcaagatCttggcggactgttagttttt	9	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:29455128C>A	ENST00000216071.4	-	3	526	c.475G>T	c.(475-477)Gat>Tat	p.D159Y		NM_015370.1	NP_056185.1	O95567	CV031_HUMAN	chromosome 22 open reading frame 31	159								p.D159Y(1)		cervix(1)|endometrium(1)|kidney(17)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	27						TCCTCAAGATCTTGGCGGACT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	22											150	137	142					22																	29455128		2203	4300	6503	27785128	SO:0001583	missense	25770			AL035364	CCDS13848.1	22q12.1	2006-07-05			ENSG00000100249	ENSG00000100249			26931	protein-coding gene	gene with protein product						15461802	Standard	XM_005261490		Approved	HS747E2A, bK747E2.1	uc003aej.1	O95567	OTTHUMG00000151011	ENST00000216071.4:c.475G>T	22.37:g.29455128C>A	ENSP00000216071:p.Asp159Tyr		27785128	A0AV97	Missense_Mutation	SNP	ENST00000216071.4	37	CCDS13848.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.910473	0.72983	.	.	ENSG00000100249	ENST00000216071	T	0.40476	1.03	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000015	T	0.53174	0.1780	L	0.29908	0.895	0.37550	D	0.918645	D	0.89917	1.0	D	0.97110	1.0	T	0.58200	-0.7678	10	0.87932	D	0	-16.8634	15.0734	0.72056	0.0:1.0:0.0:0.0	.	159	O95567	CV031_HUMAN	Y	159	ENSP00000216071:D159Y	ENSP00000216071:D159Y	D	-	1	0	C22orf31	27785128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.347000	0.52200	2.937000	0.99478	0.650000	0.86243	GAT		0.493	C22orf31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320952.1	NM_015370		A	29455128	C	A	29455128	3	1	61	1	0	0	0	0	1	0	0	0	2149	913	32	2	401	2	C22orf31	22	29455128	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	367	29455128	21849438	11882	19867										
RFPL1	5988	broad.mit.edu	37	chr22	29837868	29837868	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgccgctgactttcctcttCgtagaccgcaagttacagcg	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:29837868C>T	ENST00000354373.2	+	2	920	c.711C>T	c.(709-711)ttC>ttT	p.F237F	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	237	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.F237F(1)		endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						CTTTCCTCTTCGTAGACCGCA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	22											127	108	114					22																	29837868		2203	4300	6503	28167868	SO:0001819	synonymous_variant	5988			AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"RING-type (C3HC4) zinc fingers"	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.711C>T	22.37:g.29837868C>T			28167868	Q6IC06|Q9UJ97	Silent	SNP	ENST00000354373.2	37	CCDS13857.2																																																																																				0.512	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026		T	29837868	C	T	29837868	2	4	61	1	0	0	0	0	0	0	0	1	13290	883	31	1		1	RFPL1	22	29837868	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	382740	29837868	21466698	11883	19868										
NEFH	4744	broad.mit.edu	37	chr22	29881820	29881820	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaagatggctctggatataGagatagccgcttacaggtga	12	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:29881820G>T	ENST00000310624.6	+	3	1225	c.1192G>T	c.(1192-1194)Gag>Tag	p.E398*		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	398	Coil 2B.|Rod.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E398*(1)		cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TCTGGATATAGAGATAGCCGC	0.547																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											83	73	77					22																	29881820		2203	4300	6503	28211820	SO:0001587	stop_gained	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1192G>T	22.37:g.29881820G>T	ENSP00000311997:p.Glu398*		28211820	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Nonsense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	38	6.802418	0.97849	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	.	.	.	5.67	4.66	0.58398	.	0.269718	0.26314	N	0.025100	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.5401	0.67987	0.07:0.0:0.93:0.0	.	.	.	.	X	398	.	ENSP00000311997:E398X	E	+	1	0	NEFH	28211820	1.000000	0.71417	0.971000	0.41717	0.911000	0.54048	9.863000	0.99569	1.419000	0.47118	0.650000	0.86243	GAG		0.547	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		T	29881820	G	T	29881820	4	4	61	1	0	0	0	0	0	1	0	0	10345	943	33	2	1202	2	NEFH	22	29881820	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	43952	29881820	21422746	11884	19869										
NF2	4771	broad.mit.edu	37	chr22	30035126	30035126	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccagtcacctttcacttCttggccaaattttatcctga	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30035126C>A	ENST00000338641.4	+	3	729	c.288C>A	c.(286-288)ttC>ttA	p.F96L	NF2_ENST00000403435.1_Missense_Mutation_p.F96L|NF2_ENST00000353887.4_Intron|NF2_ENST00000334961.7_Intron|NF2_ENST00000413209.2_Missense_Mutation_p.F96L|NF2_ENST00000361166.4_Missense_Mutation_p.F96L|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Intron|NF2_ENST00000397789.3_Missense_Mutation_p.F96L|NF2_ENST00000403999.3_Missense_Mutation_p.F96L|NF2_ENST00000361676.4_Missense_Mutation_p.F54L	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	96	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		Missing (in NF2 and in sporadic meningioma). {ECO:0000269|PubMed:7913580, ECO:0000269|PubMed:8655144}.		actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.F96del(2)|p.V86_Q111>E(1)|p.L97fs*22(1)|p.H84_F100del(1)|p.F96L(1)|p.H95fs*3(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						CCTTTCACTTCTTGGCCAAAT	0.433			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	10	Unknown(3)|Deletion - In frame(3)|Deletion - Frameshift(2)|Substitution - Missense(1)|Complex - deletion inframe(1)	meninges(3)|soft_tissue(3)|large_intestine(2)|stomach(1)|lung(1)	22	GRCh37	CD941738	NF2	D							137	119	125					22																	30035126		2203	4300	6503	28365126	SO:0001583	missense	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.288C>A	22.37:g.30035126C>A	ENSP00000344666:p.Phe96Leu		28365126	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.588532	0.66105	.	.	ENSG00000186575	ENST00000413209;ENST00000338641;ENST00000403435;ENST00000397822;ENST00000403999;ENST00000397789;ENST00000361676;ENST00000361166	T;T;T;T;T;D;T	0.89415	-0.74;-0.74;-0.74;-0.74;-0.74;-2.51;-0.74	6.17	-0.577	0.11727	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);FERM conserved site (1);	0.092891	0.85682	D	0.000000	D	0.87481	0.6188	M	0.64567	1.98	0.80722	D	1	P;P;P;P;P	0.44195	0.75;0.65;0.597;0.801;0.828	P;B;B;B;B	0.48030	0.564;0.408;0.285;0.244;0.232	T	0.83090	-0.0133	9	.	.	.	.	10.0552	0.42241	0.0:0.5588:0.0:0.4412	.	96;96;96;54;96	P35240-9;P35240;P35240-2;P35240-6;P35240-3	.;MERL_HUMAN;.;.;.	L	96;96;96;96;96;96;54;96	ENSP00000409921:F96L;ENSP00000344666:F96L;ENSP00000384029:F96L;ENSP00000384797:F96L;ENSP00000380891:F96L;ENSP00000355183:F54L;ENSP00000354529:F96L	.	F	+	3	2	NF2	28365126	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.985000	0.29578	-0.010000	0.14271	0.655000	0.94253	TTC		0.433	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		A	30035126	C	A	30035126	3	1	61	1	0	0	0	0	1	0	0	0	10388	912	32	2	298	2	NF2	22	30035126	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	153306	30035126	21269440	11885	19870										
NF2	4771	broad.mit.edu	37	chr22	30069405	30069405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcgcacggaggaggagaagCgcctgatggagcagaaggtg	18	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30069405C>T	ENST00000338641.4	+	12	1711	c.1270C>T	c.(1270-1272)Cgc>Tgc	p.R424C	NF2_ENST00000403435.1_Missense_Mutation_p.R395C|NF2_ENST00000353887.4_Missense_Mutation_p.R341C|NF2_ENST00000334961.7_Missense_Mutation_p.R341C|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_Missense_Mutation_p.R424C|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Missense_Mutation_p.R383C|NF2_ENST00000397789.3_Missense_Mutation_p.R424C|NF2_ENST00000403999.3_Missense_Mutation_p.R424C|NF2_ENST00000361676.4_Missense_Mutation_p.R382C	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	424	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.R424C(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GGAGGAGAAGCGCCTGATGGA	0.627			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	4	Unknown(3)|Substitution - Missense(1)	large_intestine(2)|stomach(1)|central_nervous_system(1)	22											56	48	51					22																	30069405		2203	4300	6503	28399405	SO:0001583	missense	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.1270C>T	22.37:g.30069405C>T	ENSP00000344666:p.Arg424Cys		28399405	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757698	0.89843	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	D;D;D;D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	6.06	6.06	0.98353	Ezrin/radixin/moesin, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89736	0.6801	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;0.994;0.994;0.995;0.997;0.998;1.0;0.997	P;P;P;P;P;P;D;P	0.65010	0.892;0.764;0.764;0.901;0.764;0.857;0.931;0.799	D	0.87720	0.2572	9	.	.	.	.	20.2159	0.98296	0.0:1.0:0.0:0.0	.	399;395;383;424;424;382;341;424	B7Z4B6;P35240-8;P35240-5;P35240;P35240-2;P35240-6;P35240-4;P35240-3	.;.;.;MERL_HUMAN;.;.;.;.	C	424;395;383;399;424;341;341;424;382;424	ENSP00000344666:R424C;ENSP00000384029:R395C;ENSP00000354897:R383C;ENSP00000384797:R424C;ENSP00000335652:R341C;ENSP00000340626:R341C;ENSP00000380891:R424C;ENSP00000355183:R382C;ENSP00000354529:R424C	.	R	+	1	0	NF2	28399405	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.294000	0.43567	2.882000	0.98803	0.655000	0.94253	CGC		0.627	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		T	30069405	C	T	30069405	3	4	61	1	0	0	0	0	1	0	0	0	10388	768	27	1	1316	1	NF2	22	30069405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	34279	30069405	21235161	11886	19871										
ASCC2	84164	broad.mit.edu	37	chr22	30186483	30186483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttggcgagaaaggccatgcGcctggcttctgccttctctc	11	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30186483G>A	ENST00000397771.2	-	20	2254	c.2077C>T	c.(2077-2079)Cgc>Tgc	p.R693C	ASCC2_ENST00000542393.1_Missense_Mutation_p.R617C|ASCC2_ENST00000307790.3_Missense_Mutation_p.R693C			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	693					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.R693C(1)		endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			AAGGCCATGCGCCTGGCTTCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	22											58	51	53					22																	30186483		2203	4300	6503	28516483	SO:0001583	missense	84164			AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"ASC 1 complex subunit P100"	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.2077C>T	22.37:g.30186483G>A	ENSP00000380877:p.Arg693Cys		28516483	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	37	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029259	0.75504	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393	T;T;T	0.11169	2.8;2.8;2.81	5.76	4.69	0.59074	.	0.048539	0.85682	D	0.000000	T	0.28234	0.0697	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.976;0.964	T	0.00192	-1.1935	10	0.39692	T	0.17	-20.8225	12.4244	0.55538	0.0:0.0:0.7164:0.2836	.	617;693	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	C	693;693;617	ENSP00000305502:R693C;ENSP00000380877:R693C;ENSP00000437570:R617C	ENSP00000305502:R693C	R	-	1	0	ASCC2	28516483	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	2.077000	0.41557	2.713000	0.92767	0.655000	0.94253	CGC		0.597	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204		A	30186483	G	A	30186483	3	1	61	1	0	0	0	0	1	0	0	0	1033	1087	38	1	204	1	ASCC2	22	30186483	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	117078	30186483	21118083	11887	19872										
HORMAD2	150280	broad.mit.edu	37	chr22	30517626	30517626	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttttctgtgtagtcataGcagcagtacaagctttgaaa	8	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30517626G>T	ENST00000336726.6	+	9	771	c.416G>T	c.(415-417)aGc>aTc	p.S139I	HORMAD2_ENST00000403975.1_Missense_Mutation_p.S139I	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	139	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)		p.S139I(1)		large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			TGTAGTCATAGCAGCAGTACA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	22											60	51	54					22																	30517626		1846	4096	5942	28847626	SO:0001583	missense	150280			AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.416G>T	22.37:g.30517626G>T	ENSP00000336984:p.Ser139Ile		28847626	B5MEB2|Q8NHR2	Missense_Mutation	SNP	ENST00000336726.6	37	CCDS46683.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.229216	0.39399	.	.	ENSG00000176635	ENST00000336726;ENST00000403975	T;T	0.33216	1.42;1.42	4.63	4.63	0.57726	DNA-binding HORMA (4);	0.075873	0.45361	D	0.000380	T	0.48169	0.1485	L	0.49126	1.545	0.46458	D	0.999059	D	0.89917	1.0	D	0.76071	0.987	T	0.33929	-0.9849	10	0.37606	T	0.19	-2.5911	14.7834	0.69784	0.0:0.0:1.0:0.0	.	139	Q8N7B1	HORM2_HUMAN	I	139	ENSP00000336984:S139I;ENSP00000385055:S139I	ENSP00000336984:S139I	S	+	2	0	HORMAD2	28847626	0.988000	0.35896	0.158000	0.22627	0.039000	0.13416	2.834000	0.48167	2.414000	0.81942	0.655000	0.94253	AGC		0.333	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510		T	30517626	G	T	30517626	3	4	61	1	0	0	0	0	1	0	0	0	7308	971	34	2	446	2	HORMAD2	22	30517626	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	331143	30517626	20786940	11888	19873										
OSM	5008	broad.mit.edu	37	chr22	30660019	30660019	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgctgaagacccgccccacTgagtgcatgaagcgatggta	12	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30660019T>C	ENST00000215781.2	-	3	652	c.612A>G	c.(610-612)tcA>tcG	p.S204S	OSM_ENST00000403389.1_Silent_p.S183S	NM_020530.4	NP_065391.1	P13725	ONCM_HUMAN	oncostatin M	204					behavioral response to pain (GO:0048266)|cell proliferation (GO:0008283)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|peripheral nervous system development (GO:0007422)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|response to heat (GO:0009408)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	extracellular space (GO:0005615)|oncostatin-M receptor complex (GO:0005900)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|oncostatin-M receptor binding (GO:0005147)	p.S204S(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(3)|skin(3)	11			Epithelial(10;0.206)			CCCGCCCCACTGAGTGCATGA	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	22											38	42	40					22																	30660019		2203	4300	6503	28990019	SO:0001819	synonymous_variant	5008			AF129855	CCDS13873.1	22q12.2	2011-07-21			ENSG00000099985	ENSG00000099985			8506	protein-coding gene	gene with protein product		165095				1717982	Standard	NM_020530		Approved	MGC20461	uc003ahb.3	P13725	OTTHUMG00000150913	ENST00000215781.2:c.612A>G	22.37:g.30660019T>C			28990019	Q6FHP8|Q9UCP6	Silent	SNP	ENST00000215781.2	37	CCDS13873.1																																																																																				0.677	OSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320512.1	NM_020530		C	30660019	T	C	30660019	2	2	61	1	0	0	0	0	0	0	0	1	11322	1567	55	4		4	OSM	22	30660019	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	142393	30660019	20644547	11889	19874										
SF3A1	10291	broad.mit.edu	37	chr22	30735169	30735169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accgatcttcttaccaatggCtgtttcctctacaccgaaga	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30735169C>T	ENST00000215793.8	-	10	1601	c.1447G>A	c.(1447-1449)Gcc>Acc	p.A483T	SF3A1_ENST00000439242.1_Missense_Mutation_p.A418T	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	483					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A483T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						TTACCAATGGCTGTTTCCTCT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	22											249	199	216					22																	30735169		2203	4300	6503	29065169	SO:0001583	missense	10291			X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.1447G>A	22.37:g.30735169C>T	ENSP00000215793:p.Ala483Thr		29065169	E9PAW1	Missense_Mutation	SNP	ENST00000215793.8	37	CCDS13875.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.293805	0.80914	.	.	ENSG00000099995	ENST00000439242;ENST00000215793;ENST00000536049	T;T	0.33216	1.42;1.43	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.52869	0.1761	M	0.64404	1.975	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.25950	-1.0117	10	0.18710	T	0.47	-23.8074	20.3248	0.98698	0.0:1.0:0.0:0.0	.	483	Q15459	SF3A1_HUMAN	T	418;483;380	ENSP00000390336:A418T;ENSP00000215793:A483T	ENSP00000215793:A483T	A	-	1	0	SF3A1	29065169	1.000000	0.71417	0.970000	0.41538	0.793000	0.44817	7.601000	0.82783	2.818000	0.97014	0.655000	0.94253	GCC		0.522	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		T	30735169	C	T	30735169	3	4	61	1	0	0	0	0	1	0	0	0	14183	797	28	3	962	3	SF3A1	22	30735169	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	75150	30735169	20569397	11890	19875										
CCDC157	550631	broad.mit.edu	37	chr22	30765460	30765460	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctgtatgagctacttggaGaaccttggctcagagcagat	12	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30765460G>T	ENST00000405659.1	+	4	997	c.288G>T	c.(286-288)gaG>gaT	p.E96D	CCDC157_ENST00000338306.3_Missense_Mutation_p.E96D			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	96								p.E45D(1)|p.E96D(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						GCTACTTGGAGAACCTTGGCT	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	22											65	62	63					22																	30765460		2203	4300	6503	29095460	SO:0001583	missense	550631			BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.288G>T	22.37:g.30765460G>T	ENSP00000385357:p.Glu96Asp		29095460	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440483	0.43326	.	.	ENSG00000187860	ENST00000405659;ENST00000338306;ENST00000445005;ENST00000430839	T;T;T;T	0.35421	1.64;1.64;1.32;1.31	5.52	-0.39	0.12450	.	0.057804	0.64402	D	0.000003	T	0.24431	0.0592	L	0.39397	1.21	0.80722	D	1	B	0.32693	0.38	B	0.34452	0.183	T	0.04140	-1.0974	10	0.22109	T	0.4	-32.4151	8.3686	0.32402	0.3311:0.1293:0.5396:0.0	.	96	Q569K6	CC157_HUMAN	D	96	ENSP00000385357:E96D;ENSP00000343087:E96D;ENSP00000387491:E96D;ENSP00000401837:E96D	ENSP00000343087:E96D	E	+	3	2	CCDC157	29095460	0.194000	0.23325	0.987000	0.45799	0.692000	0.40212	-0.015000	0.12634	0.063000	0.16370	0.462000	0.41574	GAG		0.627	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		T	30765460	G	T	30765460	3	4	61	1	0	0	0	0	1	0	0	0	2795	933	33	2	294	2	CCDC157	22	30765460	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	30291	30765460	20539106	11891	19876										
SEC14L4	284904	broad.mit.edu	37	chr22	30888505	30888505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgtctcctcactcatgaacGacttgaccaagttgaaggcc	9	12	3	3	rs145618105	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30888505G>A	ENST00000255858.7	-	8	703	c.620C>T	c.(619-621)tCg>tTg	p.S207L	RP4-539M6.14_ENST00000610156.1_RNA|SEC14L4_ENST00000540456.1_Missense_Mutation_p.S192L|SEC14L4_ENST00000392772.2_Missense_Mutation_p.S153L|SEC14L4_ENST00000381982.3_Missense_Mutation_p.S207L|RP4-539M6.14_ENST00000442126.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	207	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.S207L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	ACTCATGAACGACTTGACCAA	0.537													G|||	8	0.00159744	0.0061	0	5008	,	,		21357	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						G	LEU/SER,LEU/SER	29,4377	34.3+/-65.2	1,27,2175	131	92	106		620,620	3.8	0.5	22	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	SEC14L4	NM_001161368.1,NM_174977.3	145,145	1,28,6474	AA,AG,GG		0.0116,0.6582,0.2307	benign,benign	207/361,207/407	30888505	30,12976	2203	4300	6503	29218505	SO:0001583	missense	284904			AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.620C>T	22.37:g.30888505G>A	ENSP00000255858:p.Ser207Leu		29218505	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	14.89	2.671284	0.47781	0.006582	1.16E-4	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	4.93	3.78	0.43462	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.417696	0.25987	N	0.027037	T	0.15609	0.0376	L	0.60845	1.875	0.80722	D	1	B;B;B	0.16396	0.006;0.017;0.002	B;B;B	0.15484	0.013;0.008;0.009	T	0.13124	-1.0521	10	0.56958	D	0.05	6.3659	3.0631	0.06206	0.1131:0.1589:0.565:0.163	.	153;192;207	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	L	207;192;153;207	ENSP00000255858:S207L;ENSP00000440848:S192L;ENSP00000376525:S153L;ENSP00000371412:S207L	ENSP00000255858:S207L	S	-	2	0	SEC14L4	29218505	0.896000	0.30565	0.517000	0.27799	0.988000	0.76386	2.405000	0.44548	0.945000	0.37605	0.591000	0.81541	TCG		0.537	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		A	30888505	G	A	30888505	3	1	61	1	0	0	0	0	1	0	0	0	14021	1059	37	1	626	1	SEC14L4	22	30888505	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123045	30888505	20416061	11892	19877										
GAL3ST1	9514	broad.mit.edu	37	chr22	30951608	30951608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgttggggtcgtagtagcGatccgggtcttgcaggaact	16	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:30951608G>A	ENST00000402321.1	-	3	921	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	GAL3ST1_ENST00000406955.1_Missense_Mutation_p.R202C|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.R202C|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.R202C|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.R202C|GAL3ST1_ENST00000338911.5_Missense_Mutation_p.R202C|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.R202C			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	202					galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)	p.R202C(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						TCGTAGTAGCGATCCGGGTCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	22											76	67	70					22																	30951608		2202	4298	6500	29281608	SO:0001583	missense	9514			D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"Sulfotransferases, membrane-bound"	24240	protein-coding gene	gene with protein product	"cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.604C>T	22.37:g.30951608G>A	ENSP00000385735:p.Arg202Cys		29281608	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.209264	0.58343	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111;ENST00000441967;ENST00000431313;ENST00000452827	T;T;T;T;T;T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42	5.25	5.25	0.73442	.	0.502792	0.24083	N	0.041709	T	0.34978	0.0916	L	0.61218	1.895	0.58432	D	0.999997	D	0.76494	0.999	P	0.60682	0.878	T	0.03619	-1.1019	10	0.62326	D	0.03	-2.1162	13.3882	0.60807	0.0:0.0:0.8422:0.1578	.	202	Q99999	G3ST1_HUMAN	C	202;202;202;202;202;202;202;202;203;202	ENSP00000385825:R202C;ENSP00000385735:R202C;ENSP00000384122:R202C;ENSP00000384388:R202C;ENSP00000343234:R202C;ENSP00000385207:R202C;ENSP00000402587:R202C;ENSP00000390545:R202C;ENSP00000395080:R203C;ENSP00000405017:R202C	ENSP00000343234:R202C	R	-	1	0	GAL3ST1	29281608	0.999000	0.42202	0.959000	0.39883	0.880000	0.50808	3.176000	0.50863	2.457000	0.83068	0.484000	0.47621	CGC		0.617	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861		A	30951608	G	A	30951608	3	1	61	1	0	0	0	0	1	0	0	0	6217	1058	37	1	671	1	GAL3ST1	22	30951608	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	63103	30951608	20352958	11893	19878										
MORC2	22880	broad.mit.edu	37	chr22	31332542	31332542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctggcgaattttctctgTcagttgtttctgcttctctt	8	10	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:31332542T>C	ENST00000397641.3	-	17	2101	c.1693A>G	c.(1693-1695)Aca>Gca	p.T565A	MORC2_ENST00000469915.1_5'Flank|MORC2_ENST00000215862.4_Missense_Mutation_p.T503A			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	565						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.T503A(1)		breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						ATTTTCTCTGTCAGTTGTTTC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	22											195	167	176					22																	31332542		2203	4300	6503	29662542	SO:0001583	missense	22880			AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1693A>G	22.37:g.31332542T>C	ENSP00000380763:p.Thr565Ala		29662542	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	37		.	.	.	.	.	.	.	.	.	.	T	10.25	1.298235	0.23650	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.11385	2.78;2.78	6.06	5.01	0.66863	.	0.198918	0.52532	D	0.000062	T	0.10165	0.0249	L	0.49350	1.555	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.09292	-1.0681	10	0.09590	T	0.72	.	10.9399	0.47268	0.2493:0.0:0.0:0.7507	.	565	Q9Y6X9	MORC2_HUMAN	A	565;503	ENSP00000380763:T565A;ENSP00000215862:T503A	ENSP00000215862:T503A	T	-	1	0	MORC2	29662542	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.464000	0.35288	1.068000	0.40764	0.533000	0.62120	ACA		0.527	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		C	31332542	T	C	31332542	3	2	61	1	0	0	0	0	1	0	0	0	9732	1667	58	4	1445	4	MORC2	22	31332542	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	380934	31332542	19972024	11894	19879										
LIMK2	3985	broad.mit.edu	37	chr22	31663018	31663018	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtcatgaaagagttaattCgatgtgatgaggagacccag	13	5	1	5	rs114127458		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:31663018C>T	ENST00000331728.4	+	9	1204	c.1090C>T	c.(1090-1092)Cga>Tga	p.R364*	LIMK2_ENST00000406516.1_Nonsense_Mutation_p.R286*|LIMK2_ENST00000340552.4_Nonsense_Mutation_p.R343*|LIMK2_ENST00000444929.2_Nonsense_Mutation_p.R118*|LIMK2_ENST00000333611.4_Nonsense_Mutation_p.R343*	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	364	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.R364*(1)		endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						AGAGTTAATTCGATGTGATGA	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											77	63	68					22																	31663018		2203	4300	6503	29993018	SO:0001587	stop_gained	3985			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1090C>T	22.37:g.31663018C>T	ENSP00000332687:p.Arg364*		29993018	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Nonsense_Mutation	SNP	ENST00000331728.4	37	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	.	39	7.766604	0.98477	.	.	ENSG00000182541	ENST00000406516;ENST00000444929;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	.	.	.	5.76	4.75	0.60458	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.943	13.8451	0.63463	0.0:0.927:0.0:0.073	.	.	.	.	X	286;118;364;396;343;343	.	ENSP00000332687:R364X	R	+	1	2	LIMK2	29993018	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.487000	0.81328	1.444000	0.47605	0.650000	0.86243	CGA		0.493	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		T	31663018	C	T	31663018	4	4	61	1	0	0	0	0	0	1	0	0	8825	876	31	1	1181	1	LIMK2	22	31663018	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	330476	31663018	19641548	11895	19880										
PATZ1	23598	broad.mit.edu	37	chr22	31723166	31723166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actccattttgtttttggggActgccatgtcgcaggagaaa	11	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:31723166A>G	ENST00000266269.5	-	5	2404	c.1775T>C	c.(1774-1776)gTc>gCc	p.V592A	PATZ1_ENST00000351933.4_Missense_Mutation_p.V546A|PATZ1_ENST00000405309.3_3'UTR|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	592					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V592A(1)	EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GTTTTTGGGGACTGCCATGTC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	22											128	130	129					22																	31723166		2203	4300	6503	30053166	SO:0001583	missense	23598			AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13071	protein-coding gene	gene with protein product		605165	"zinc finger protein 278"	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1775T>C	22.37:g.31723166A>G	ENSP00000266269:p.Val592Ala		30053166	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Missense_Mutation	SNP	ENST00000266269.5	37	CCDS13894.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240329	0.58995	.	.	ENSG00000100105	ENST00000266269;ENST00000351933	T;T	0.10099	2.91;3.03	5.8	5.8	0.92144	.	0.234528	0.36268	N	0.002693	T	0.08492	0.0211	N	0.14661	0.345	0.80722	D	1	B;B	0.31817	0.341;0.177	B;B	0.30646	0.118;0.053	T	0.21759	-1.0236	10	0.87932	D	0	-19.3936	15.3242	0.74147	1.0:0.0:0.0:0.0	.	546;592	Q9HBE1-3;Q9HBE1	.;PATZ1_HUMAN	A	592;546	ENSP00000266269:V592A;ENSP00000337520:V546A	ENSP00000266269:V592A	V	-	2	0	PATZ1	30053166	1.000000	0.71417	0.985000	0.45067	0.947000	0.59692	3.374000	0.52402	2.206000	0.71126	0.528000	0.53228	GTC		0.512	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052		G	31723166	A	G	31723166	3	3	61	1	0	0	0	0	1	0	0	0	11507	275	10	4	292	4	PATZ1	22	31723166	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	60148	31723166	19581400	11896	19881										
SFI1	9814	broad.mit.edu	37	chr22	31927078	31927078	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agttcttatatttatggattCgaatgacttttggaagagta	9	3	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:31927078C>T	ENST00000400288.2	+	4	406	c.301C>T	c.(301-303)Cga>Tga	p.R101*	SFI1_ENST00000443326.1_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000432498.1_Nonsense_Mutation_p.R101*|SFI1_ENST00000540643.1_Intron	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	101					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.R101*(2)		NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						TTTATGGATTCGAATGACTTT	0.323																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											120	112	115					22																	31927078		1830	4079	5909	30257078	SO:0001587	stop_gained	9814			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.301C>T	22.37:g.31927078C>T	ENSP00000383145:p.Arg101*		30257078	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Nonsense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.976926	0.53720	.	.	ENSG00000198089	ENST00000432498;ENST00000400288;ENST00000450787	.	.	.	4.26	3.15	0.36227	.	0.274240	0.27151	N	0.020686	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.831	0.35085	0.2239:0.7761:0.0:0.0	.	.	.	.	X	101;101;52	.	ENSP00000383145:R101X	R	+	1	2	SFI1	30257078	0.920000	0.31207	1.000000	0.80357	0.976000	0.68499	1.841000	0.39240	2.377000	0.81083	0.442000	0.29010	CGA		0.323	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		T	31927078	C	T	31927078	4	4	61	1	0	0	0	0	0	1	0	0	14193	876	31	1	311	1	SFI1	22	31927078	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203912	31927078	19377488	11897	19882										
PISD	23761	broad.mit.edu	37	chr22	32015711	32015711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtggagcccaggttgaactCgcccaggtgctcgcccttac	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32015711C>T	ENST00000439502.2	-	8	1340	c.1117G>A	c.(1117-1119)Gag>Aag	p.E373K	PISD_ENST00000397500.1_3'UTR|PISD_ENST00000382151.2_Missense_Mutation_p.E339K|PISD_ENST00000478893.1_5'Flank|PISD_ENST00000336566.4_Missense_Mutation_p.E372K|PISD_ENST00000266095.5_Missense_Mutation_p.E339K			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	373					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)	p.E339K(1)		central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	AGGTTGAACTCGCCCAGGTGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	22											129	109	116					22																	32015711		2203	4300	6503	30345711	SO:0001583	missense	23761				CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.1117G>A	22.37:g.32015711C>T	ENSP00000391739:p.Glu373Lys		30345711	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Missense_Mutation	SNP	ENST00000439502.2	37		.	.	.	.	.	.	.	.	.	.	C	26.3	4.722565	0.89298	.	.	ENSG00000241878	ENST00000382151;ENST00000266095;ENST00000439502;ENST00000336566	.	.	.	5.29	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.76681	0.4021	M	0.79011	2.435	0.80722	D	1	D;D;P	0.71674	0.998;0.978;0.56	D;P;P	0.69824	0.966;0.833;0.474	T	0.76266	-0.3022	9	0.34782	T	0.22	-26.6751	12.903	0.58135	0.0:0.9214:0.0:0.0786	.	325;373;339	B1AJZ0;Q9UG56;Q9UG56-2	.;PISD_HUMAN;.	K	339;339;373;372	.	ENSP00000266095:E339K	E	-	1	0	PISD	30345711	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.480000	0.81109	1.227000	0.43598	0.591000	0.81541	GAG		0.562	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4			T	32015711	C	T	32015711	3	4	61	1	0	0	0	0	1	0	0	0	11977	893	31	1	116	1	PISD	22	32015711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	88633	32015711	19288855	11898	19883										
DEPDC5	9681	broad.mit.edu	37	chr22	32188763	32188763	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataaaccgagcctcaattCgacaggatcacaaggggaga	10	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32188763C>T	ENST00000382112.3	+	11	797	c.727C>T	c.(727-729)Cga>Tga	p.R243*	DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000400242.3_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000536766.1_Nonsense_Mutation_p.R215*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.R243*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	243					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.R243*(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGCCTCAATTCGACAGGATCA	0.353																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											130	122	124					22																	32188763		1804	4082	5886	30518763	SO:0001587	stop_gained	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.727C>T	22.37:g.32188763C>T	ENSP00000371546:p.Arg243*		30518763	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	-	38	6.701398	0.97772	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000400242;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.	.	.	5.29	1.87	0.25490	.	0.117813	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	13.4713	0.61283	0.6194:0.3806:0.0:0.0	.	.	.	.	X	243;215;243;243;243;243;243;243;243;243;243	.	ENSP00000266091:R243X	R	+	1	2	DEPDC5	30518763	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	1.746000	0.38288	0.154000	0.19237	0.567000	0.79289	CGA		0.353	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32188763	C	T	32188763	4	4	61	1	0	0	0	0	0	1	0	0	4453	876	31	1	769	1	DEPDC5	22	32188763	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173052	32188763	19115803	11899	19884										
DEPDC5	9681	broad.mit.edu	37	chr22	32215144	32215144	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagcactgattaaccccttCgctccctctcggatgcccat	7	16	1	2	rs368563183		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32215144C>T	ENST00000382112.3	+	21	1873	c.1803C>T	c.(1801-1803)ttC>ttT	p.F601F	DEPDC5_ENST00000400249.2_Silent_p.F601F|DEPDC5_ENST00000536766.1_Silent_p.F573F|DEPDC5_ENST00000400248.2_Silent_p.F601F|DEPDC5_ENST00000382105.2_Silent_p.F601F|DEPDC5_ENST00000266091.3_Silent_p.F601F|DEPDC5_ENST00000400246.1_Silent_p.F601F|DEPDC5_ENST00000382111.2_Silent_p.F601F|DEPDC5_ENST00000535622.1_Silent_p.F601F	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	601					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.F601F(3)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TTAACCCCTTCGCTCCCTCTC	0.542																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	22						C	,,,	0,4122		0,0,2061	141	141	141		1803,1803,1803,1803	-5.4	0.8	22		141	1,8419		0,1,4209	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEPDC5	NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,	0,1,6270	TT,TC,CC		0.0119,0.0,0.0080	,,,	601/1595,601/1604,601/1504,601/1573	32215144	1,12541	2061	4210	6271	30545144	SO:0001819	synonymous_variant	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1803C>T	22.37:g.32215144C>T			30545144	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1																																																																																				0.542	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32215144	C	T	32215144	2	4	61	1	0	0	0	0	0	0	0	1	4453	883	31	1		1	DEPDC5	22	32215144	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26381	32215144	19089422	11900	19885										
DEPDC5	9681	broad.mit.edu	37	chr22	32218747	32218747	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggaacagaggagctttCtgtcggcctgcttagcaaca	12	10	1	1	rs199783404	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32218747C>A	ENST00000382112.3	+	23	2145	c.2075C>A	c.(2074-2076)tCt>tAt	p.S692Y	DEPDC5_ENST00000400249.2_Missense_Mutation_p.S692Y|DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000400248.2_Missense_Mutation_p.S692Y|DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000266091.3_Missense_Mutation_p.S692Y|DEPDC5_ENST00000400246.1_Missense_Mutation_p.S692Y|DEPDC5_ENST00000382111.2_Missense_Mutation_p.S692Y|DEPDC5_ENST00000535622.1_Intron	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	692					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.S692F(1)|p.S692Y(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GAGGAGCTTTCTGTCGGCCTG	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	22											79	77	77					22																	32218747		1972	4162	6134	30548747	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2075C>A	22.37:g.32218747C>A	ENSP00000371546:p.Ser692Tyr		30548747	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.1|21.1	4.096108|4.096108	0.76870|0.76870	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000266091;ENST00000400249;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248	.|T;T;T;T;T;T	.|0.26957	.|1.85;1.7;1.84;1.71;1.84;1.7	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.416827	.|0.29119	.|N	.|0.013100	T|T	0.37433|0.37433	0.1003|0.1003	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P	.|0.52692	.|0.936;0.874;0.955;0.681;0.681	.|P;B;P;B;B	.|0.53102	.|0.718;0.322;0.542;0.254;0.34	T|T	0.06679|0.06679	-1.0813|-1.0813	5|10	.|0.66056	.|D	.|0.02	.|.	16.1893|16.1893	0.81975|0.81975	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|13;692;692;692;692	.|B4DSS1;B9EGN9;O75140-4;A8MPX9;O75140	.|.;.;.;.;DEPD5_HUMAN	L|Y	89|692	.|ENSP00000266091:S692Y;ENSP00000383108:S692Y;ENSP00000383105:S692Y;ENSP00000371546:S692Y;ENSP00000371545:S692Y;ENSP00000383107:S692Y	.|ENSP00000266091:S692Y	F|S	+|+	3|2	2|0	DEPDC5|DEPDC5	30548747|30548747	0.840000|0.840000	0.29493|0.29493	0.975000|0.975000	0.42487|0.42487	0.937000|0.937000	0.57800|0.57800	2.772000|2.772000	0.47678|0.47678	2.665000|2.665000	0.90641|0.90641	0.591000|0.591000	0.81541|0.81541	TTC|TCT		0.527	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		A	32218747	C	A	32218747	3	1	61	1	0	0	0	0	1	0	0	0	4453	913	32	2	2183	2	DEPDC5	22	32218747	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3603	32218747	19085819	11901	19886										
RFPL2	10739	broad.mit.edu	37	chr22	32586963	32586963	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaacgttctgcatgcccatAtccagaaaaatccccactcg	6	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32586963A>C	ENST00000400237.1	-	5	1868	c.933T>G	c.(931-933)gaT>gaG	p.D311E	RFPL2_ENST00000248980.4_Missense_Mutation_p.D250E|RFPL2_ENST00000248983.4_Missense_Mutation_p.D221E|RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000400236.3_Missense_Mutation_p.D221E			O75678	RFPL2_HUMAN	ret finger protein-like 2	311	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.D221E(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						GCATGCCCATATCCAGAAAAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	22											40	57	52					22																	32586963		2203	4297	6500	30916963	SO:0001583	missense	10739			AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.933T>G	22.37:g.32586963A>C	ENSP00000383096:p.Asp311Glu		30916963		Missense_Mutation	SNP	ENST00000400237.1	37	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	A	14.94	2.685909	0.47991	.	.	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	0.351	0.351	0.16042	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	D	0.89870	0.6840	M	0.93550	3.43	0.21064	N	0.999791	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.77587	-0.2532	9	0.87932	D	0	.	5.016	0.14337	0.9998:0.0:2.0E-4:0.0	.	311;250	O75678;O75678-3	RFPL2_HUMAN;.	E	250;221;221;311	ENSP00000248980:D250E;ENSP00000248983:D221E;ENSP00000383095:D221E;ENSP00000383096:D311E	ENSP00000248980:D250E	D	-	3	2	RFPL2	30916963	0.176000	0.23096	0.287000	0.24848	0.283000	0.27025	1.609000	0.36858	0.338000	0.23692	0.332000	0.21555	GAT		0.517	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		C	32586963	A	C	32586963	3	2	61	1	0	0	0	0	1	0	0	0	13291	446	16	4	207	4	RFPL2	22	32586963	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	368216	32586963	18717603	11902	19887										
BPIL2	254240	broad.mit.edu	37	chr22	32831742	32831742	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagctgtgaaatgagcaaaGgacgcagatttaaagaaata	10	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32831742G>T	ENST00000397452.1	-	9	983	c.873C>A	c.(871-873)tcC>tcA	p.S291S	BPIFC_ENST00000534972.1_Silent_p.S15S|BPIFC_ENST00000432451.2_Silent_p.S105S|BPIFC_ENST00000300399.3_Silent_p.S291S			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	291						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)	p.S291S(1)									AATGAGCAAAGGACGCAGATT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	22											79	80	80					22																	32831742		2203	4300	6503	31161742	SO:0001819	synonymous_variant	254240			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.873C>A	22.37:g.32831742G>T			31161742	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																				0.488	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		T	32831742	G	T	32831742	2	4	61	1	0	0	0	0	0	0	0	1	1495	987	35	2		2	BPIL2	22	32831742	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	244779	32831742	18472824	11903	19888										
BPIL2	254240	broad.mit.edu	37	chr22	32841835	32841835	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctctcattcacctgagttCtccggaaaatgagacgtggg	12	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32841835C>A	ENST00000397452.1	-	5	633	c.523G>T	c.(523-525)Gaa>Taa	p.E175*	BPIFC_ENST00000534972.1_Intron|BPIFC_ENST00000432451.2_5'UTR|BPIFC_ENST00000300399.3_Nonsense_Mutation_p.E175*			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	175						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)	p.E175*(1)									CACCTGAGTTCTCCGGAAAAT	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											59	56	57					22																	32841835		2203	4300	6503	31171835	SO:0001587	stop_gained	254240			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.523G>T	22.37:g.32841835C>A	ENSP00000380594:p.Glu175*		31171835	A2RRF1	Nonsense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	C	37	6.092962	0.97276	.	.	ENSG00000184459	ENST00000397452;ENST00000300399	.	.	.	5.6	2.19	0.27852	.	0.333371	0.33127	N	0.005260	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-2.187	6.4602	0.21952	0.0:0.6664:0.1619:0.1717	.	.	.	.	X	175	.	ENSP00000300399:E175X	E	-	1	0	BPIFC	31171835	0.976000	0.34144	0.527000	0.27925	0.881000	0.50899	0.870000	0.28010	0.676000	0.31285	0.650000	0.86243	GAA		0.512	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32841835	C	A	32841835	4	1	61	1	0	0	0	0	0	1	0	0	1495	922	32	2	1048	2	BPIL2	22	32841835	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10093	32841835	18462731	11904	19889										
FBXO7	25793	broad.mit.edu	37	chr22	32894280	32894280	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgccttcctccaggaattatCgggggtgaatatgaccaaag	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:32894280C>T	ENST00000266087.7	+	9	1659	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	FBXO7_ENST00000382058.3_Silent_p.I365I|FBXO7_ENST00000397426.1_Silent_p.I330I	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	444	Important for interaction with CDK6.|Pro-rich.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.I444I(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGGAATTATCGGGGGTGAAT	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	22											137	133	134					22																	32894280		2203	4300	6503	31224280	SO:0001819	synonymous_variant	25793			AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.1332C>T	22.37:g.32894280C>T			31224280	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	37	CCDS13907.1																																																																																				0.532	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			T	32894280	C	T	32894280	2	4	61	1	0	0	0	0	0	0	0	1	5779	874	31	1		1	FBXO7	22	32894280	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	52445	32894280	18410286	11905	19890										
TIMP3	7078	broad.mit.edu	37	chr22	33255356	33255356	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcatcatcaatgccacaGacccctgagcgccagaccct	7	16	2	3	rs1804709		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:33255356G>T	ENST00000266085.6	+	5	929	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	SYN3_ENST00000332840.5_Intron|SYN3_ENST00000358763.2_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	210					cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.D210Y(1)		endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						CAATGCCACAGACCCCTGAGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	22											46	37	40					22																	33255356		2203	4300	6503	31585356	SO:0001583	missense	7078				CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.628G>T	22.37:g.33255356G>T	ENSP00000266085:p.Asp210Tyr		31585356	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Missense_Mutation	SNP	ENST00000266085.6	37	CCDS13911.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192152	0.58017	.	.	ENSG00000100234	ENST00000266085;ENST00000538671	D	0.95980	-3.87	3.91	3.91	0.45181	.	0.194271	0.46442	D	0.000300	D	0.97448	0.9165	M	0.80183	2.485	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.98366	1.0551	10	0.87932	D	0	-15.5028	16.1096	0.81250	0.0:0.0:1.0:0.0	rs1804709	210	P35625	TIMP3_HUMAN	Y	210;144	ENSP00000266085:D210Y	ENSP00000266085:D210Y	D	+	1	0	TIMP3	31585356	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.648000	0.98483	2.019000	0.59389	0.561000	0.74099	GAC		0.577	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362		T	33255356	G	T	33255356	3	4	61	1	0	0	0	0	1	0	0	0	15958	942	33	2	646	2	TIMP3	22	33255356	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	361076	33255356	18049210	11906	19891										
LARGE	9215	broad.mit.edu	37	chr22	33733727	33733727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggtcaggtagaggttgcGaaaaaactccacatgcttgt	12	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:33733727G>A	ENST00000354992.2	-	11	1763	c.1192C>T	c.(1192-1194)Cgc>Tgc	p.R398C	LARGE_ENST00000397394.2_Missense_Mutation_p.R398C|LARGE_ENST00000402320.1_Intron|LARGE_ENST00000452586.2_Missense_Mutation_p.R197C|LARGE_ENST00000337431.2_Intron|LARGE_ENST00000437602.2_Missense_Mutation_p.R398C	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	398					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.R398C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TAGAGGTTGCGAAAAAACTCC	0.527																																					Colon(70;397 1175 4573 19089 45288)											1	Substitution - Missense(1)	large_intestine(1)	22											97	85	89					22																	33733727		2203	4300	6503	32063727	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1192C>T	22.37:g.33733727G>A	ENSP00000347088:p.Arg398Cys		32063727	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	37	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084878	0.55861	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000445431;ENST00000354992;ENST00000397394;ENST00000452586;ENST00000437602	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.22	4.21	0.49690	.	0.052159	0.85682	D	0.000000	T	0.52240	0.1722	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.98;0.988	T	0.59284	-0.7483	10	0.87932	D	0	-1.2839	13.7369	0.62824	0.074:0.0:0.926:0.0	.	398;197;398	B7Z2I9;E9PH73;O95461	.;.;LARGE_HUMAN	C	75;75;75;398;398;197;398	ENSP00000347088:R398C;ENSP00000380549:R398C;ENSP00000407917:R197C;ENSP00000388544:R398C	ENSP00000347088:R398C	R	-	1	0	LARGE	32063727	1.000000	0.71417	1.000000	0.80357	0.473000	0.32948	3.889000	0.56212	1.209000	0.43321	-0.136000	0.14681	CGC		0.527	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	33733727	G	A	33733727	3	1	61	1	0	0	0	0	1	0	0	0	8649	1058	37	1	1102	1	LARGE	22	33733727	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	478371	33733727	17570839	11907	19892										
HMGXB4	10042	broad.mit.edu	37	chr22	35661203	35661203	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtctgacgcctcccagttCgcagagtcccacagtgctaa	11	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:35661203C>T	ENST00000216106.5	+	5	950	c.822C>T	c.(820-822)ttC>ttT	p.F274F	HMGXB4_ENST00000444518.2_Silent_p.F165F	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	274					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)	p.F274F(1)		breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCTCCCAGTTCGCAGAGTCCC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	22											75	73	73					22																	35661203		2203	4300	6503	33991203	SO:0001819	synonymous_variant	10042			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.822C>T	22.37:g.35661203C>T			33991203	O75672|O75673|Q9UMT5	Silent	SNP	ENST00000216106.5	37	CCDS33641.1																																																																																				0.522	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		T	35661203	C	T	35661203	2	4	61	1	0	0	0	0	0	0	0	1	7260	883	31	1		1	HMGXB4	22	35661203	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1927476	35661203	15643363	11908	19893										
MCM5	4174	broad.mit.edu	37	chr22	35812760	35812760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccatcttgtcgcgcttcGacatgatcttcatcgtcaag	7	14	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:35812760G>A	ENST00000216122.4	+	12	1697	c.1543G>A	c.(1543-1545)Gac>Aac	p.D515N	MCM5_ENST00000382011.5_Missense_Mutation_p.D472N	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	515	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.D515N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						GTCGCGCTTCGACATGATCTT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	22											138	108	118					22																	35812760		2203	4300	6503	34142760	SO:0001583	missense	4174				CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.1543G>A	22.37:g.35812760G>A	ENSP00000216122:p.Asp515Asn		34142760	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	G	31	5.069615	0.93950	.	.	ENSG00000100297	ENST00000216122;ENST00000382011	T;T	0.18174	2.23;2.23	5.77	5.77	0.91146	.	0.043472	0.85682	D	0.000000	T	0.66177	0.2763	H	0.99874	4.875	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;D	0.67548	0.952;0.952;0.952;0.952	T	0.83247	-0.0055	10	0.87932	D	0	-29.443	20.0628	0.97684	0.0:0.0:1.0:0.0	.	515;515;472;515	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	N	515;472	ENSP00000216122:D515N;ENSP00000371441:D472N	ENSP00000216122:D515N	D	+	1	0	MCM5	34142760	1.000000	0.71417	0.990000	0.47175	0.475000	0.33008	9.691000	0.98679	2.741000	0.93983	0.650000	0.86243	GAC		0.597	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			A	35812760	G	A	35812760	3	1	61	1	0	0	0	0	1	0	0	0	9420	1058	37	1	1585	1	MCM5	22	35812760	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151557	35812760	15491806	11909	19894										
MCM5	4174	broad.mit.edu	37	chr22	35819257	35819257	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggagatgctgagccgcatcGagaagcagctcaagcgccgc	14	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:35819257G>A	ENST00000216122.4	+	16	2180	c.2026G>A	c.(2026-2028)Gag>Aag	p.E676K	MCM5_ENST00000382011.5_Missense_Mutation_p.E633K	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	676					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.E676K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						GAGCCGCATCGAGAAGCAGCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	22											84	68	74					22																	35819257		2203	4300	6503	34149257	SO:0001583	missense	4174				CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.2026G>A	22.37:g.35819257G>A	ENSP00000216122:p.Glu676Lys		34149257	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.843003|4.843003	0.91197|0.91197	.|.	.|.	ENSG00000100297|ENSG00000100297	ENST00000216122;ENST00000382011|ENST00000444582	T;T|.	0.03860|.	4.1;3.78|.	4.55|4.55	3.51|3.51	0.40186|0.40186	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85944|0.85944	0.5815|0.5815	H|H	0.95712|0.95712	3.71|3.71	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	D|D	0.90131|0.90131	0.4206|0.4206	10|6	0.87932|0.72032	D|D	0|0.01	-37.4913|-37.4913	14.5473|14.5473	0.68041|0.68041	0.0:0.1472:0.8528:0.0|0.0:0.1472:0.8528:0.0	.|.	676;633;676|.	B1AHB0;B1AHB1;P33992|.	.;.;MCM5_HUMAN|.	K|Q	676;633|360	ENSP00000216122:E676K;ENSP00000371441:E633K|.	ENSP00000216122:E676K|ENSP00000397217:R360Q	E|R	+|+	1|2	0|0	MCM5|MCM5	34149257|34149257	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.983000|0.983000	0.72400|0.72400	8.528000|8.528000	0.90598|0.90598	1.109000|1.109000	0.41680|0.41680	0.561000|0.561000	0.74099|0.74099	GAG|CGA		0.617	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			A	35819257	G	A	35819257	3	1	61	1	0	0	0	0	1	0	0	0	9420	1059	37	1	2084	1	MCM5	22	35819257	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6497	35819257	15485309	11910	19895										
APOL5	80831	broad.mit.edu	37	chr22	36122298	36122298	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagttggaaaattaacaaTttgatgtcaactgtccacag	8	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:36122298T>C	ENST00000249044.2	+	3	183	c.183T>C	c.(181-183)aaT>aaC	p.N61N		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	61					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)	p.N61N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						AAATTAACAATTTGATGTCAA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	22											122	110	114					22																	36122298		2203	4300	6503	34452244	SO:0001819	synonymous_variant	80831			AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"Apolipoproteins"	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.183T>C	22.37:g.36122298T>C			34452244	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																				0.453	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642		C	36122298	T	C	36122298	2	2	61	1	0	0	0	0	0	0	0	1	809	1490	52	4		4	APOL5	22	36122298	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	303041	36122298	15182268	11911	19896										
APOL2	23780	broad.mit.edu	37	chr22	36627418	36627418	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagcagccacgaatccattCcaggcttcatcatcagtcag	8	14	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:36627418C>T	ENST00000249066.6	-	5	581	c.105G>A	c.(103-105)tgG>tgA	p.W35*	APOL2_ENST00000451256.2_Nonsense_Mutation_p.W147*|APOL2_ENST00000358502.5_Nonsense_Mutation_p.W35*	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	35					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)	p.W35*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						CGAATCCATTCCAGGCTTCAT	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											75	77	77					22																	36627418		2203	4300	6503	34957364	SO:0001587	stop_gained	23780			AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"Apolipoproteins"	619	protein-coding gene	gene with protein product	"apolipoprotein L-II"	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.105G>A	22.37:g.36627418C>T	ENSP00000249066:p.Trp35*		34957364	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Nonsense_Mutation	SNP	ENST00000249066.6	37	CCDS43014.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991418	0.54041	.	.	ENSG00000128335	ENST00000358502;ENST00000249066;ENST00000451256;ENST00000529194;ENST00000454728	.	.	.	3.8	3.8	0.43715	.	0.489529	0.19362	N	0.116120	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4907	0.50379	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;147;35;35	.	ENSP00000249066:W35X	W	-	3	0	APOL2	34957364	0.004000	0.15560	0.183000	0.23137	0.006000	0.05464	1.045000	0.30341	1.817000	0.53016	0.411000	0.27672	TGG		0.512	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637		T	36627418	C	T	36627418	4	4	61	1	0	0	0	0	0	1	0	0	806	856	30	3	916	3	APOL2	22	36627418	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	505120	36627418	14677148	11912	19897										
MYH9	4627	broad.mit.edu	37	chr22	36684378	36684378	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctccaggtccttcaggtCcatctccagcttcttccggg	9	17	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:36684378C>A	ENST00000216181.5	-	34	5082	c.4852G>T	c.(4852-4854)Gac>Tac	p.D1618Y	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1618					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.D1618Y(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TCCTTCAGGTCCATCTCCAGC	0.632			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																														Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	22											114	92	99					22																	36684378		2203	4300	6503	35014324	SO:0001583	missense	4627	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4852G>T	22.37:g.36684378C>A	ENSP00000216181:p.Asp1618Tyr		35014324	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.722745	0.89298	.	.	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	D	0.85629	-2.01	5.5	4.47	0.54385	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.94085	0.8104	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95523	0.8596	10	0.87932	D	0	.	15.0008	0.71469	0.0:0.9309:0.0:0.0691	.	1618	P35579	MYH9_HUMAN	Y	1040;220;1618	ENSP00000216181:D1618Y	ENSP00000216181:D1618Y	D	-	1	0	MYH9	35014324	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	1.442000	0.47568	0.655000	0.94253	GAC		0.632	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		A	36684378	C	A	36684378	3	1	61	1	0	0	0	0	1	0	0	0	10072	855	30	2	1062	2	MYH9	22	36684378	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	56960	36684378	14620188	11913	19898										
MYH9	4627	broad.mit.edu	37	chr22	36689510	36689510	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggctcagcttctgccggttCtcctcctgcagcagctccta	9	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:36689510C>A	ENST00000216181.5	-	30	4190	c.3960G>T	c.(3958-3960)gaG>gaT	p.E1320D		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1320					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.E1320D(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TCTGCCGGTTCTCCTCCTGCA	0.617			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																														Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	22											90	84	86					22																	36689510		2203	4300	6503	35019456	SO:0001583	missense	4627	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.3960G>T	22.37:g.36689510C>A	ENSP00000216181:p.Glu1320Asp		35019456	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168118	0.78339	.	.	ENSG00000100345	ENST00000216181	D	0.89485	-2.52	4.98	4.98	0.66077	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	M	0.89353	3.025	0.80722	D	1	D	0.59357	0.985	D	0.63381	0.914	D	0.94196	0.7445	10	0.87932	D	0	.	9.4288	0.38597	0.0:0.8415:0.0:0.1585	.	1320	P35579	MYH9_HUMAN	D	1320	ENSP00000216181:E1320D	ENSP00000216181:E1320D	E	-	3	2	MYH9	35019456	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.771000	0.55318	2.454000	0.82982	0.561000	0.74099	GAG		0.617	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		A	36689510	C	A	36689510	3	1	61	1	0	0	0	0	1	0	0	0	10072	912	32	2	1970	2	MYH9	22	36689510	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5132	36689510	14615056	11914	19899										
CACNG2	10369	broad.mit.edu	37	chr22	36962445	36962445	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actcaggatgatgttgtgtcGagttttgtagaactcgctgg	13	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:36962445G>A	ENST00000300105.6	-	3	1372	c.391C>T	c.(391-393)Cga>Tga	p.R131*		NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	131					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R131*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						ATGTTGTGTCGAGTTTTGTAG	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											109	102	104					22																	36962445		2203	4300	6503	35292391	SO:0001587	stop_gained	10369			AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.391C>T	22.37:g.36962445G>A	ENSP00000300105:p.Arg131*		35292391	Q2M1M1|Q5TGT3|Q9UGZ7	Nonsense_Mutation	SNP	ENST00000300105.6	37	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	G	45	11.914536	0.99617	.	.	ENSG00000166862	ENST00000300105	.	.	.	4.79	4.79	0.61399	.	0.140129	0.49305	D	0.000143	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.1808	18.2288	0.89927	0.0:0.0:1.0:0.0	.	.	.	.	X	131	.	ENSP00000300105:R131X	R	-	1	2	CACNG2	35292391	1.000000	0.71417	0.988000	0.46212	0.968000	0.65278	9.476000	0.97823	2.377000	0.81083	0.557000	0.71058	CGA		0.562	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			A	36962445	G	A	36962445	4	1	61	1	0	0	0	0	0	1	0	0	2563	1066	37	1	588	1	CACNG2	22	36962445	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	272935	36962445	14342121	11915	19900										
CACNG2	10369	broad.mit.edu	37	chr22	37098606	37098606	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taaaagcatttgaacacctcGatcaaacagccccataattc	4	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:37098606G>A	ENST00000300105.6	-	1	997	c.16C>T	c.(16-18)Cga>Tga	p.R6*	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	6					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R6*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TGAACACCTCGATCAAACAGC	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											104	98	100					22																	37098606		2203	4300	6503	35428552	SO:0001587	stop_gained	10369			AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.16C>T	22.37:g.37098606G>A	ENSP00000300105:p.Arg6*		35428552	Q2M1M1|Q5TGT3|Q9UGZ7	Nonsense_Mutation	SNP	ENST00000300105.6	37	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	g	46	12.212487	0.99647	.	.	ENSG00000166862	ENST00000300105	.	.	.	4.77	3.71	0.42584	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.8246	11.8841	0.52592	0.0:0.0:0.689:0.311	.	.	.	.	X	6	.	ENSP00000300105:R6X	R	-	1	2	CACNG2	35428552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.780000	0.55386	2.180000	0.69256	0.546000	0.68486	CGA		0.468	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			A	37098606	G	A	37098606	4	1	61	1	0	0	0	0	0	1	0	0	2563	1066	37	1	971	1	CACNG2	22	37098606	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	136161	37098606	14205960	11916	19901										
TMPRSS6	164656	broad.mit.edu	37	chr22	37499285	37499285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagagtagcacccccgccGaagccagcacgagcagggcc	12	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:37499285G>A	ENST00000346753.3	-	2	316	c.200C>T	c.(199-201)tCg>tTg	p.S67L	TMPRSS6_ENST00000381792.2_Missense_Mutation_p.S58L|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.S67L|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.S58L|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.S58L	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	67					angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.S67L(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CACCCCCGCCGAAGCCAGCAC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	22											51	53	52					22																	37499285		2203	4300	6503	35829231	SO:0001583	missense	164656			AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.200C>T	22.37:g.37499285G>A	ENSP00000334962:p.Ser67Leu		35829231	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.344171	0.01277	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782;ENST00000423761	D;D;D;D;T;D	0.91351	-2.83;-2.82;-2.83;-2.83;-0.79;-2.4	4.39	1.05	0.20165	.	0.286415	0.28927	N	0.013696	D	0.84388	0.5461	L	0.51422	1.61	0.09310	N	1	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.71454	-0.4588	10	0.33940	T	0.23	.	7.0854	0.25254	0.3083:0.0:0.6917:0.0	.	67;58;67	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	L	58;67;58;58;67;58	ENSP00000371211:S58L;ENSP00000334962:S67L;ENSP00000385453:S58L;ENSP00000384964:S58L;ENSP00000397691:S67L;ENSP00000400317:S58L	ENSP00000334962:S67L	S	-	2	0	TMPRSS6	35829231	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.794000	0.26958	0.327000	0.23409	-0.272000	0.10252	TCG		0.627	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		A	37499285	G	A	37499285	3	1	61	1	0	0	0	0	1	0	0	0	16290	1059	37	1	2303	1	TMPRSS6	22	37499285	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	400679	37499285	13805281	11917	19902										
C1QTNF6	114904	broad.mit.edu	37	chr22	37578569	37578569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggttcacaaagaccctttCgaagagcagcgtctggaagt	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:37578569C>T	ENST00000337843.2	-	3	571	c.496G>A	c.(496-498)Gaa>Aaa	p.E166K	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.E166K|C1QTNF6_ENST00000255836.6_Missense_Mutation_p.E42K|C1QTNF6_ENST00000470655.1_5'UTR|RP1-151B14.6_ENST00000419128.1_RNA	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	147	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)		p.E166K(1)		breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						AAGACCCTTTCGAAGAGCAGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	22											60	62	61					22																	37578569		2203	4300	6503	35908515	SO:0001583	missense	114904			AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.496G>A	22.37:g.37578569C>T	ENSP00000338812:p.Glu166Lys		35908515	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380130	0.61845	.	.	ENSG00000133466	ENST00000397110;ENST00000337843;ENST00000255836	T;T;T	0.21191	2.02;2.02;2.02	5.14	5.14	0.70334	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.052099	0.85682	D	0.000000	T	0.16557	0.0398	N	0.11927	0.2	0.47547	D	0.999458	P;P	0.42973	0.74;0.796	B;B	0.41135	0.348;0.294	T	0.07539	-1.0767	10	0.87932	D	0	.	18.6158	0.91302	0.0:1.0:0.0:0.0	.	166;147	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	K	166;166;42	ENSP00000380299:E166K;ENSP00000338812:E166K;ENSP00000255836:E42K	ENSP00000255836:E42K	E	-	1	0	C1QTNF6	35908515	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	7.818000	0.86416	2.393000	0.81446	0.555000	0.69702	GAA		0.622	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486		T	37578569	C	T	37578569	3	4	61	1	0	0	0	0	1	0	0	0	1973	893	31	1	344	1	C1QTNF6	22	37578569	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	79284	37578569	13725997	11918	19903										
PDXP	57026	broad.mit.edu	37	chr22	38061644	38061644	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcccagcccctacatgttCgagtgcatcacggagaactt	9	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38061644C>T	ENST00000215904.6	+	2	713	c.657C>T	c.(655-657)ttC>ttT	p.F219F	PDXP_ENST00000403251.1_Silent_p.F2F|SH3BP1_ENST00000599616.1_Silent_p.F528F	NM_020315.4	NP_064711.1	Q96GD0	PLPP_HUMAN	pyridoxal (pyridoxine, vitamin B6) phosphatase	219					actin rod assembly (GO:0031247)|cellular response to ATP (GO:0071318)|positive regulation of actin filament depolymerization (GO:0030836)|protein dephosphorylation (GO:0006470)|pyridoxal phosphate catabolic process (GO:0032361)|regulation of cytokinesis (GO:0032465)|regulation of mitosis (GO:0007088)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heat shock protein binding (GO:0031072)|magnesium ion binding (GO:0000287)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|pyridoxal phosphatase activity (GO:0033883)	p.F219F(1)		kidney(1)|large_intestine(1)|lung(5)|ovary(2)	9	Melanoma(58;0.0574)					CCTACATGTTCGAGTGCATCA	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	22											94	81	85					22																	38061644		2203	4300	6503	36391590	SO:0001819	synonymous_variant	23616			BC064922	CCDS13953.1	22q12.3	2005-08-16			ENSG00000241360	ENSG00000241360			30259	protein-coding gene	gene with protein product		609246				14522954	Standard	NM_020315		Approved	dJ37E16.5, FLJ32703		Q96GD0	OTTHUMG00000044618	ENST00000215904.6:c.657C>T	22.37:g.38061644C>T			36391590	Q9UGY2	Silent	SNP	ENST00000215904.6	37	CCDS13953.1																																																																																				0.652	PDXP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104105.2	NM_020315		T	38061644	C	T	38061644	2	4	61	1	0	0	0	0	0	0	0	1	11729	883	31	1		1	PDXP	22	38061644	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	483075	38061644	13242922	11919	19904										
TRIOBP	11078	broad.mit.edu	37	chr22	38121768	38121768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgtgcattggacaccgaGatgccccccgggcgtcctcg	13	15	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38121768G>T	ENST00000406386.3	+	7	3460	c.3205G>T	c.(3205-3207)Gat>Tat	p.D1069Y		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1069					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.D1069Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TGGACACCGAGATGCCCCCCG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	22											51	57	55					22																	38121768		1871	4078	5949	36451714	SO:0001583	missense	11078			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3205G>T	22.37:g.38121768G>T	ENSP00000384312:p.Asp1069Tyr		36451714	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603883	0.46423	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.39592	1.07	4.67	4.67	0.58626	.	.	.	.	.	T	0.52933	0.1765	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.51911	-0.8645	9	0.51188	T	0.08	.	12.9924	0.58627	0.0:0.0:1.0:0.0	.	1069	Q9H2D6	TARA_HUMAN	Y	1069	ENSP00000384312:D1069Y	ENSP00000384312:D1069Y	D	+	1	0	TRIOBP	36451714	0.996000	0.38824	0.979000	0.43373	0.362000	0.29581	3.084000	0.50143	2.426000	0.82243	0.449000	0.29647	GAT		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38121768	G	T	38121768	3	4	61	1	0	0	0	0	1	0	0	0	16593	942	33	2	3223	2	TRIOBP	22	38121768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	60124	38121768	13182798	11920	19905										
TRIOBP	11078	broad.mit.edu	37	chr22	38150918	38150918	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcaccaccacctctacttCgcagtggaagaaacattggt	8	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38150918C>T	ENST00000406386.3	+	13	5669	c.5414C>T	c.(5413-5415)tCg>tTg	p.S1805L	TRIOBP_ENST00000403663.2_Missense_Mutation_p.S92L|TRIOBP_ENST00000407319.2_Missense_Mutation_p.S92L	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1805	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.S1805L(1)|p.S92L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					ACCTCTACTTCGCAGTGGAAG	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	22											173	131	145					22																	38150918		2203	4300	6503	36480864	SO:0001583	missense	11078			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.5414C>T	22.37:g.38150918C>T	ENSP00000384312:p.Ser1805Leu		36480864	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.633413	0.29068	.	.	ENSG00000100106	ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000452519;ENST00000417857	T;T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96;-0.96	4.98	2.86	0.33363	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	T	0.49184	0.1542	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.15473	0.001;0.002;0.013	B;B;B	0.14578	0.001;0.002;0.011	T	0.39502	-0.9611	9	0.45353	T	0.12	.	6.3865	0.21563	0.0:0.6061:0.134:0.2598	.	92;92;1805	F8W6V6;F2Z2W0;Q9H2D6	.;.;TARA_HUMAN	L	1805;92;92;51;21;21	ENSP00000384312:S1805L;ENSP00000383913:S92L;ENSP00000386026:S92L;ENSP00000396946:S51L;ENSP00000407542:S21L;ENSP00000387881:S21L	ENSP00000386026:S92L	S	+	2	0	TRIOBP	36480864	0.000000	0.05858	0.011000	0.14972	0.179000	0.23085	0.075000	0.14686	1.090000	0.41315	0.655000	0.94253	TCG		0.517	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38150918	C	T	38150918	3	4	61	1	0	0	0	0	1	0	0	0	16593	893	31	1	5643	1	TRIOBP	22	38150918	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	29150	38150918	13153648	11921	19906										
C22orf23	84645	broad.mit.edu	37	chr22	38343425	38343425	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgcttggaaggtaagactCtctggctggatgttgggctg	15	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38343425C>A	ENST00000249079.2	-	4	468	c.212G>T	c.(211-213)aGa>aTa	p.R71I	C22orf23_ENST00000403026.1_Missense_Mutation_p.R71I|C22orf23_ENST00000403305.1_Missense_Mutation_p.R71I			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	71								p.R71I(1)		endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					AGGTAAGACTCTCTGGCTGGA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	22											117	102	107					22																	38343425		2203	4300	6503	36673371	SO:0001583	missense	84645			AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.212G>T	22.37:g.38343425C>A	ENSP00000249079:p.Arg71Ile		36673371	Q5JYU9|Q96M68	Missense_Mutation	SNP	ENST00000249079.2	37	CCDS13962.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.775117	0.49786	.	.	ENSG00000128346	ENST00000403305;ENST00000249079;ENST00000403026;ENST00000418863;ENST00000422191	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	5.38	3.07	0.35406	.	0.630831	0.15901	N	0.239100	T	0.31575	0.0801	L	0.55103	1.725	0.39278	D	0.964511	P	0.45634	0.863	B	0.38378	0.272	T	0.33007	-0.9885	10	0.62326	D	0.03	-6.0969	3.0052	0.06026	0.0:0.4969:0.3013:0.2018	.	71	Q9BZE7	EVG1_HUMAN	I	71	ENSP00000384667:R71I;ENSP00000249079:R71I;ENSP00000384618:R71I;ENSP00000395077:R71I;ENSP00000407707:R71I	ENSP00000249079:R71I	R	-	2	0	C22orf23	36673371	0.091000	0.21658	0.735000	0.30896	0.691000	0.40173	0.554000	0.23407	1.215000	0.43411	0.555000	0.69702	AGA		0.557	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561		A	38343425	C	A	38343425	3	1	61	1	0	0	0	0	1	0	0	0	2143	913	32	2	457	2	C22orf23	22	38343425	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	192507	38343425	12961141	11922	19907										
PLA2G6	8398	broad.mit.edu	37	chr22	38516880	38516880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaacacctcatccttcatgCgaaagtacatgccgcgcatg	9	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38516880C>T	ENST00000332509.3	-	12	1811	c.1628G>A	c.(1627-1629)cGc>cAc	p.R543H	PLA2G6_ENST00000490473.1_5'Flank|PLA2G6_ENST00000335539.3_Missense_Mutation_p.R489H|PLA2G6_ENST00000402064.1_Missense_Mutation_p.R489H	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	543	Patatin.				cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)	p.R543H(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	ATCCTTCATGCGAAAGTACAT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	22											86	88	87					22																	38516880		2203	4300	6503	36846826	SO:0001583	missense	8398			AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.1628G>A	22.37:g.38516880C>T	ENSP00000333142:p.Arg543His		36846826	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	37	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378566	0.82682	.	.	ENSG00000184381	ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064	T;T;T	0.78003	-1.14;-1.14;-1.14	5.45	5.45	0.79879	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.207337	0.49305	D	0.000145	D	0.88771	0.6527	M	0.77406	2.37	0.80722	D	1	D;B	0.89917	1.0;0.335	D;B	0.87578	0.998;0.24	D	0.89463	0.3738	10	0.66056	D	0.02	-33.0529	19.3415	0.94344	0.0:1.0:0.0:0.0	.	489;543	O60733-2;O60733	.;PA2G6_HUMAN	H	543;404;489;489	ENSP00000333142:R543H;ENSP00000335149:R489H;ENSP00000386100:R489H	ENSP00000333142:R543H	R	-	2	0	PLA2G6	36846826	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.073000	0.76784	2.560000	0.86352	0.555000	0.69702	CGC		0.617	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		T	38516880	C	T	38516880	3	4	61	1	0	0	0	0	1	0	0	0	12039	768	27	1	816	1	PLA2G6	22	38516880	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	173455	38516880	12787686	11923	19908										
CSNK1E	1454	broad.mit.edu	37	chr22	38694791	38694791	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcctccaggtgactcacGaatttcagcatgttccagtc	9	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:38694791G>A	ENST00000396832.1	-	7	1145	c.885C>T	c.(883-885)ttC>ttT	p.F295F	CSNK1E_ENST00000359867.3_Splice_Site_p.F295F|CSNK1E_ENST00000403904.1_Splice_Site_p.F295F|CSNK1E_ENST00000498529.1_5'UTR|CSNK1E_ENST00000400206.2_Splice_Site_p.F295F|CSNK1E_ENST00000413574.2_Splice_Site_p.F295F|CSNK1E_ENST00000405675.3_Splice_Site_p.F295F	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	295					cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F295F(3)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GGTGACTCACGAATTTCAGCA	0.602											OREG0026559	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)											3	Substitution - coding silent(3)	large_intestine(3)	22											106	105	105					22																	38694791		2203	4300	6503	37024737	SO:0001630	splice_region_variant	1454				CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.885+1C>T	22.37:g.38694791G>A		880	37024737		Silent	SNP	ENST00000396832.1	37	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.56|15.56	2.868564|2.868564	0.51588|0.51588	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000431632|ENST00000451964	.|.	.|.	.|.	5.14|5.14	4.12|4.12	0.48240|0.48240	.|.	.|.	.|.	.|.	.|.	T|T	0.55369|0.55369	0.1916|0.1916	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52079|0.52079	-0.8623|-0.8623	4|4	.|.	.|.	.|.	.|.	6.2469|6.2469	0.20823|0.20823	0.3229:0.0:0.6771:0.0|0.3229:0.0:0.6771:0.0	.|.	.|.	.|.	.|.	W|L	23|233	.|.	.|.	R|S	-|-	1|2	2|0	CSNK1E|CSNK1E	37024737|37024737	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	3.806000|3.806000	0.55583|0.55583	1.167000|1.167000	0.42706|0.42706	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.602	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894	Silent	A	38694791	G	A	38694791	5	1	61	1	0	0	0	0	0	0	1	0	3959	1072	37	1	381	1	CSNK1E	22	38694791	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	177911	38694791	12609775	11924	19909										
TOMM22	56993	broad.mit.edu	37	chr22	39078348	39078348	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctagatgagaccctgtcggaGagactatggggcctgacgga	15	9	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39078348G>T	ENST00000216034.4	+	2	169	c.138G>T	c.(136-138)gaG>gaT	p.E46D	RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000412067.1_RNA	NM_020243.4	NP_064628.1	Q9NS69	TOM22_HUMAN	translocase of outer mitochondrial membrane 22 homolog (yeast)	46	Import sequence; necessary for mitochondrion outer membrane localization and integration in the TOM complex. {ECO:0000250}.				cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)	p.E46D(1)		large_intestine(1)|lung(2)	3	Melanoma(58;0.04)					CCCTGTCGGAGAGACTATGGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	22											42	45	44					22																	39078348		2203	4300	6503	37408294	SO:0001583	missense	56993			AB040119	CCDS13975.1	22q12-q13	2010-07-29			ENSG00000100216	ENSG00000100216			18002	protein-coding gene	gene with protein product		607046				10982837, 10900208	Standard	NM_020243		Approved	TOM22	uc003awe.3	Q9NS69	OTTHUMG00000150991	ENST00000216034.4:c.138G>T	22.37:g.39078348G>T	ENSP00000216034:p.Glu46Asp		37408294		Missense_Mutation	SNP	ENST00000216034.4	37	CCDS13975.1	.	.	.	.	.	.	.	.	.	.	G	31	5.093600	0.94149	.	.	ENSG00000100216	ENST00000216034	.	.	.	5.4	3.29	0.37713	.	0.000000	0.85682	D	0.000000	T	0.78792	0.4339	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80108	-0.1520	9	0.45353	T	0.12	-20.9465	11.8792	0.52564	0.144:0.0:0.856:0.0	.	46	Q9NS69	TOM22_HUMAN	D	46	.	ENSP00000216034:E46D	E	+	3	2	TOMM22	37408294	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.074000	0.57577	1.269000	0.44280	0.563000	0.77884	GAG		0.597	TOMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320842.1			T	39078348	G	T	39078348	3	4	61	1	0	0	0	0	1	0	0	0	16395	933	33	2	144	2	TOMM22	22	39078348	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	383557	39078348	12226218	11925	19910										
APOBEC3D	140564	broad.mit.edu	37	chr22	39421629	39421629	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcatgccttggtacaaattCgatgacaattatgcatccct	6	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39421629C>T	ENST00000216099.8	+	4	965	c.558C>T	c.(556-558)ttC>ttT	p.F186F	APOBEC3D_ENST00000381568.4_Silent_p.F186F|APOBEC3D_ENST00000427494.2_Intron	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	186					defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.F186F(1)|p.F255F(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					GGTACAAATTCGATGACAATT	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	22											333	289	304					22																	39421629		2203	4300	6503	37751575	SO:0001819	synonymous_variant	140564			BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"Apolipoprotein B mRNA editing enzymes"	17354	protein-coding gene	gene with protein product		609900	"apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)", "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.558C>T	22.37:g.39421629C>T			37751575	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Silent	SNP	ENST00000216099.8	37	CCDS46709.1																																																																																				0.512	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426		T	39421629	C	T	39421629	2	4	61	1	0	0	0	0	0	0	0	1	792	883	31	1		1	APOBEC3D	22	39421629	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	343281	39421629	11882937	11926	19911										
APOBEC3F	200316	broad.mit.edu	37	chr22	39445500	39445500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctacgcaaagcctatggtCggaacgaaagctggctgtgc	12	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39445500C>T	ENST00000308521.5	+	5	994	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	213					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R213W(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					AGCCTATGGTCGGAACGAAAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	22											151	137	142					22																	39445500		2203	4300	6503	37775446	SO:0001583	missense	200316			BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"Apolipoprotein B mRNA editing enzymes"	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.637C>T	22.37:g.39445500C>T	ENSP00000309749:p.Arg213Trp		37775446	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	.	.	.	.	.	.	.	.	.	.	.	11.62	1.692785	0.30052	.	.	ENSG00000128394	ENST00000308521	T	0.74421	-0.84	1.75	-0.824	0.10812	APOBEC-like, N-terminal (1);	.	.	.	.	T	0.81936	0.4928	M	0.81497	2.545	0.09310	N	1	D	0.89917	1.0	D	0.65323	0.934	T	0.69745	-0.5062	9	0.87932	D	0	.	5.9096	0.19020	0.5538:0.4462:0.0:0.0	.	213	Q8IUX4	ABC3F_HUMAN	W	213	ENSP00000309749:R213W	ENSP00000309749:R213W	R	+	1	2	APOBEC3F	37775446	0.013000	0.17824	0.000000	0.03702	0.001000	0.01503	0.367000	0.20382	-0.109000	0.12044	-0.470000	0.05040	CGG		0.488	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298		T	39445500	C	T	39445500	3	4	61	1	0	0	0	0	1	0	0	0	793	875	31	1	794	1	APOBEC3F	22	39445500	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	23871	39445500	11859066	11927	19912										
APOBEC3G	60489	broad.mit.edu	37	chr22	39477045	39477045	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggtcacctggtacatatcCtggagcccctgcacaaagtg	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39477045C>A	ENST00000407997.3	+	3	636	c.279C>A	c.(277-279)tcC>tcA	p.S93S	APOBEC3G_ENST00000461827.1_3'UTR|APOBEC3G_ENST00000452957.2_Silent_p.S93S	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	93	CMP/dCMP deaminase zinc-binding 1.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S93S(2)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					GGTACATATCCTGGAGCCCCT	0.532																																																2	Substitution - coding silent(2)	large_intestine(2)	22											98	84	89					22																	39477045		2203	4300	6503	37806991	SO:0001819	synonymous_variant	60489			AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.279C>A	22.37:g.39477045C>A			37806991	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	37	CCDS13984.1																																																																																				0.532	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		A	39477045	C	A	39477045	2	1	61	1	0	0	0	0	0	0	0	1	794	668	24	2		2	APOBEC3G	22	39477045	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31545	39477045	11827521	11928	19913										
APOBEC3G	60489	broad.mit.edu	37	chr22	39482506	39482506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatctatgatgatcaaggaAgatgtcaggaggggctgcgc	15	7	3	3	rs371126678		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39482506A>G	ENST00000407997.3	+	6	1315	c.958A>G	c.(958-960)Aga>Gga	p.R320G	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.R320G	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	320	Interaction with DNA. {ECO:0000305}.|Necessary for homooligomerization.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R320G(2)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TGATCAAGGAAGATGTCAGGA	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	22						A	GLY/ARG	0,4406		0,0,2203	114	123	120		958	-2.4	0	22		120	1,8599		0,1,4299	no	missense	APOBEC3G	NM_021822.3	125	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	320/385	39482506	1,13005	2203	4300	6503	37812452	SO:0001583	missense	60489			AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.958A>G	22.37:g.39482506A>G	ENSP00000385057:p.Arg320Gly		37812452	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	0.168	-1.073953	0.01918	0.0	1.16E-4	ENSG00000239713	ENST00000452957;ENST00000407997	T;T	0.66995	-0.24;-0.24	1.39	-2.44	0.06502	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.44008	0.1273	N	0.25332	0.735	0.09310	N	1	B	0.06786	0.001	B	0.17433	0.018	T	0.22871	-1.0204	9	0.17832	T	0.49	.	3.3744	0.07232	0.3387:0.2194:0.4419:0.0	.	320	Q9HC16	ABC3G_HUMAN	G	320	ENSP00000413376:R320G;ENSP00000385057:R320G	ENSP00000385057:R320G	R	+	1	2	APOBEC3G	37812452	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.561000	0.02158	-0.604000	0.05760	-0.756000	0.03474	AGA		0.512	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		G	39482506	A	G	39482506	3	3	61	1	0	0	0	0	1	0	0	0	794	64	3	4	980	4	APOBEC3G	22	39482506	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	5461	39482506	11822060	11929	19914										
MGAT3	4248	broad.mit.edu	37	chr22	39884258	39884258	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcacccaggacggcgtctcGcggctgcgcaacctgcggcc	13	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:39884258G>A	ENST00000341184.6	+	2	1121	c.906G>A	c.(904-906)tcG>tcA	p.S302S		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	302					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)	p.S302S(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					ACGGCGTCTCGCGGCTGCGCA	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	22											58	61	60					22																	39884258		2202	4294	6496	38214204	SO:0001819	synonymous_variant	4248			D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.906G>A	22.37:g.39884258G>A			38214204	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Silent	SNP	ENST00000341184.6	37	CCDS13994.2																																																																																				0.657	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		A	39884258	G	A	39884258	2	1	61	1	0	0	0	0	0	0	0	1	9574	1074	38	1		1	MGAT3	22	39884258	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	401752	39884258	11420308	11930	19915										
CACNA1I	8911	broad.mit.edu	37	chr22	40078593	40078593	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgtctcgccggatccagaGaacttcctgtgtgagatgga	13	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40078593G>T	ENST00000402142.3	+	35	5757	c.5757G>T	c.(5755-5757)gaG>gaT	p.E1919D	CACNA1I_ENST00000407673.1_Missense_Mutation_p.E1884D|CACNA1I_ENST00000400164.3_Missense_Mutation_p.E1884D|CACNA1I_ENST00000401624.1_Missense_Mutation_p.E1919D|CACNA1I_ENST00000336649.4_Missense_Mutation_p.E1925D|CACNA1I_ENST00000404898.1_Missense_Mutation_p.E1884D	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1919					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.E1884D(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CGGATCCAGAGAACTTCCTGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											68	72	70					22																	40078593		2016	4164	6180	38408539	SO:0001583	missense	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.5757G>T	22.37:g.40078593G>T	ENSP00000385019:p.Glu1919Asp		38408539	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	G	9.827	1.187380	0.21870	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97114	-4.22;-4.19;-4.21;-4.17;-4.25;-4.15	4.94	4.94	0.65067	.	7739.210000	0.00166	N	0.000000	D	0.93618	0.7962	L	0.31294	0.92	0.30133	N	0.804617	B;B;B;B	0.15930	0.002;0.015;0.015;0.009	B;B;B;B	0.16722	0.006;0.011;0.016;0.007	T	0.81780	-0.0776	10	0.02654	T	1	.	9.0757	0.36519	0.0838:0.1619:0.7543:0.0	.	1884;1919;1884;1919	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	D	1919;1884;1919;1884;1925;1884	ENSP00000385019:E1919D;ENSP00000384093:E1884D;ENSP00000383887:E1919D;ENSP00000385680:E1884D;ENSP00000337829:E1925D;ENSP00000383028:E1884D	ENSP00000337829:E1925D	E	+	3	2	CACNA1I	38408539	1.000000	0.71417	0.997000	0.53966	0.711000	0.40976	1.366000	0.34193	2.286000	0.76751	0.655000	0.94253	GAG		0.612	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		T	40078593	G	T	40078593	3	4	61	1	0	0	0	0	1	0	0	0	2552	933	33	2	5895	2	CACNA1I	22	40078593	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	194335	40078593	11225973	11931	19916										
ENTHD1	150350	broad.mit.edu	37	chr22	40139830	40139830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagatcttcatgtaatctagCgatcgcacgttttacctccc	6	13	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40139830C>T	ENST00000325157.6	-	7	1928	c.1678G>A	c.(1678-1680)Gct>Act	p.A560T		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	560								p.A560T(1)		breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					TGTAATCTAGCGATCGCACGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	22											140	119	126					22																	40139830		2203	4300	6503	38469776	SO:0001583	missense	150350			AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.1678G>A	22.37:g.40139830C>T	ENSP00000317431:p.Ala560Thr		38469776	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	37	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	C	7.826	0.718899	0.15372	.	.	ENSG00000176177	ENST00000325157	T	0.30981	1.51	5.76	2.53	0.30540	.	0.831724	0.10467	N	0.671219	T	0.12646	0.0307	N	0.08118	0	0.09310	N	1	P	0.39094	0.659	B	0.24848	0.056	T	0.08764	-1.0706	10	0.40728	T	0.16	-0.2732	8.4405	0.32812	0.0:0.7508:0.0:0.2492	.	560	Q8IYW4	ENTD1_HUMAN	T	560	ENSP00000317431:A560T	ENSP00000317431:A560T	A	-	1	0	ENTHD1	38469776	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.679000	0.05203	0.786000	0.33708	0.655000	0.94253	GCT		0.408	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		T	40139830	C	T	40139830	3	4	61	1	0	0	0	0	1	0	0	0	5150	768	27	1	149	1	ENTHD1	22	40139830	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61237	40139830	11164736	11932	19917										
ENTHD1	150350	broad.mit.edu	37	chr22	40140215	40140215	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gataagagatgagctgacttCtctggagaggctaaatcagg	13	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40140215C>A	ENST00000325157.6	-	7	1543	c.1293G>T	c.(1291-1293)gaG>gaT	p.E431D		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	431								p.E431D(1)		breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					GAGCTGACTTCTCTGGAGAGG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	22											66	63	64					22																	40140215		2203	4300	6503	38470161	SO:0001583	missense	150350			AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.1293G>T	22.37:g.40140215C>A	ENSP00000317431:p.Glu431Asp		38470161	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	37	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.499851	0.26861	.	.	ENSG00000176177	ENST00000325157	T	0.66280	-0.2	5.64	3.16	0.36331	.	0.354113	0.23797	N	0.044479	T	0.45054	0.1323	L	0.29908	0.895	0.22933	N	0.998541	B	0.18461	0.028	B	0.17433	0.018	T	0.22977	-1.0201	10	0.26408	T	0.33	-2.9461	7.9788	0.30170	0.0:0.7365:0.1662:0.0973	.	431	Q8IYW4	ENTD1_HUMAN	D	431	ENSP00000317431:E431D	ENSP00000317431:E431D	E	-	3	2	ENTHD1	38470161	0.982000	0.34865	0.653000	0.29593	0.703000	0.40648	0.235000	0.17948	1.341000	0.45600	0.650000	0.86243	GAG		0.418	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		A	40140215	C	A	40140215	3	1	61	1	0	0	0	0	1	0	0	0	5150	912	32	2	534	2	ENTHD1	22	40140215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	385	40140215	11164351	11933	19918										
ENTHD1	150350	broad.mit.edu	37	chr22	40231926	40231926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtaggcaaatgaacatcttgGcaatgctcttgtttcaatcc	8	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40231926G>A	ENST00000325157.6	-	4	880	c.630C>T	c.(628-630)tgC>tgT	p.C210C		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	210								p.C210C(2)		breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					GAACATCTTGGCAATGCTCTT	0.358																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	22											284	260	268					22																	40231926		2203	4300	6503	38561872	SO:0001819	synonymous_variant	150350			AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.630C>T	22.37:g.40231926G>A			38561872	B0QYD5|Q5H9F7|Q96LK3	Silent	SNP	ENST00000325157.6	37	CCDS13998.1																																																																																				0.358	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		A	40231926	G	A	40231926	2	1	61	1	0	0	0	0	0	0	0	1	5150	1195	42	3		3	ENTHD1	22	40231926	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	91711	40231926	11072640	11934	19919										
GRAP2	9402	broad.mit.edu	37	chr22	40351888	40351888	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggaaggatatgtgcccaaGaatttcatagacatccagtt	9	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40351888G>T	ENST00000344138.4	+	3	407	c.144G>T	c.(142-144)aaG>aaT	p.K48N	GRAP2_ENST00000407075.3_Missense_Mutation_p.K48N|GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000544756.1_Intron|GRAP2_ENST00000543252.1_Missense_Mutation_p.K48N|GRAP2_ENST00000540310.1_Intron|GRAP2_ENST00000478445.1_3'UTR	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	48	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)	p.K48N(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						ATGTGCCCAAGAATTTCATAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	22											107	94	98					22																	40351888		2203	4300	6503	38681834	SO:0001583	missense	9402			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.144G>T	22.37:g.40351888G>T	ENSP00000339186:p.Lys48Asn		38681834	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702122	0.68501	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000420971;ENST00000407075	T;T;T;T	0.30182	1.54;1.94;1.94;1.54	5.46	4.45	0.53987	Src homology-3 domain (2);	0.093973	0.64402	D	0.000001	T	0.41971	0.1182	L	0.37750	1.13	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.64410	0.925;0.925	T	0.32295	-0.9912	10	0.66056	D	0.02	-31.1498	11.9833	0.53131	0.0808:0.0:0.9192:0.0	.	48;48	Q6FI14;O75791	.;GRAP2_HUMAN	N	48	ENSP00000339186:K48N;ENSP00000446350:K48N;ENSP00000396355:K48N;ENSP00000385607:K48N	ENSP00000339186:K48N	K	+	3	2	GRAP2	38681834	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.846000	0.39289	1.311000	0.45024	0.655000	0.94253	AAG		0.453	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40351888	G	T	40351888	3	4	61	1	0	0	0	0	1	0	0	0	6775	933	33	2	150	2	GRAP2	22	40351888	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119962	40351888	10952678	11935	19920										
GRAP2	9402	broad.mit.edu	37	chr22	40356095	40356095	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctcgacaccaggcagaGaacttactcatgggcaagga	10	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40356095G>T	ENST00000344138.4	+	4	470	c.207G>T	c.(205-207)gaG>gaT	p.E69D	GRAP2_ENST00000407075.3_Missense_Mutation_p.E69D|GRAP2_ENST00000399090.2_Nonsense_Mutation_p.E13*|GRAP2_ENST00000544756.1_5'UTR|GRAP2_ENST00000543252.1_Intron|GRAP2_ENST00000540310.1_Intron|GRAP2_ENST00000478445.1_3'UTR|RP3-370M22.8_ENST00000424496.1_RNA	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	69	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)	p.E69D(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						ACCAGGCAGAGAACTTACTCA	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	22											255	263	260					22																	40356095		2203	4300	6503	38686041	SO:0001583	missense	9402			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.207G>T	22.37:g.40356095G>T	ENSP00000339186:p.Glu69Asp		38686041	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.187696|6.187696	0.97357|0.97357	.|.	.|.	ENSG00000100351|ENSG00000100351	ENST00000344138;ENST00000544006;ENST00000420971;ENST00000407075|ENST00000399090	D;D;D|.	0.91894|.	-2.93;-2.93;-2.93|.	5.31|5.31	3.22|3.22	0.36961|0.36961	SH2 motif (5);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.73458|.	0.3589|.	M|M	0.83483|0.83483	2.645|2.645	0.80722|0.80722	D|D	1|1	D;P|.	0.89917|.	1.0;0.845|.	D;B|.	0.87578|.	0.998;0.346|.	T|.	0.76152|.	-0.3064|.	10|.	0.87932|0.87932	D|D	0|0	-27.6342|-27.6342	9.0202|9.0202	0.36195|0.36195	0.2372:0.0:0.7628:0.0|0.2372:0.0:0.7628:0.0	.|.	43;69|.	B7Z8F8;O75791|.	.;GRAP2_HUMAN|.	D|X	69;43;69;69|13	ENSP00000339186:E69D;ENSP00000396355:E69D;ENSP00000385607:E69D|.	ENSP00000339186:E69D|ENSP00000382040:E13X	E|E	+|+	3|1	2|0	GRAP2|GRAP2	38686041|38686041	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.375000|2.375000	0.44283|0.44283	1.208000|1.208000	0.43306|0.43306	0.655000|0.655000	0.94253|0.94253	GAG|GAA		0.547	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40356095	G	T	40356095	3	4	61	1	0	0	0	0	1	0	0	0	6775	933	33	2	217	2	GRAP2	22	40356095	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4207	40356095	10948471	11936	19921										
GRAP2	9402	broad.mit.edu	37	chr22	40362101	40362101	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagctggtagactactacaGgacaaattccatctccagac	7	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40362101G>T	ENST00000344138.4	+	5	661	c.398G>T	c.(397-399)aGg>aTg	p.R133M	GRAP2_ENST00000407075.3_Missense_Mutation_p.R133M|GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000544756.1_Missense_Mutation_p.R61M|GRAP2_ENST00000543252.1_Missense_Mutation_p.R93M|GRAP2_ENST00000540310.1_Missense_Mutation_p.R67M|GRAP2_ENST00000478445.1_3'UTR|RP3-370M22.8_ENST00000424496.1_RNA	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	133	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)	p.R133M(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GACTACTACAGGACAAATTCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	22											115	99	104					22																	40362101		2203	4300	6503	38692047	SO:0001583	missense	9402			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.398G>T	22.37:g.40362101G>T	ENSP00000339186:p.Arg133Met		38692047	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114780	0.77210	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000407075	T;D;D;D;T	0.82619	-0.04;-1.63;-1.63;-1.63;-0.04	6.03	2.85	0.33270	SH2 motif (4);	0.311047	0.40469	N	0.001096	D	0.85652	0.5746	L	0.52126	1.63	0.45899	D	0.998745	D;D;D;D	0.76494	0.983;0.999;0.998;0.983	P;D;P;P	0.65874	0.569;0.939;0.87;0.569	D	0.85007	0.0903	10	0.87932	D	0	-26.0301	8.5737	0.33585	0.3879:0.0:0.6121:0.0	.	133;67;107;133	Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;GRAP2_HUMAN	M	133;93;107;67;61;133	ENSP00000339186:R133M;ENSP00000446350:R93M;ENSP00000444734:R67M;ENSP00000442195:R61M;ENSP00000385607:R133M	ENSP00000339186:R133M	R	+	2	0	GRAP2	38692047	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.635000	0.37134	0.887000	0.36136	0.655000	0.94253	AGG		0.448	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40362101	G	T	40362101	3	4	61	1	0	0	0	0	1	0	0	0	6775	1000	35	2	412	2	GRAP2	22	40362101	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6006	40362101	10942465	11937	19922										
TNRC6B	23112	broad.mit.edu	37	chr22	40662788	40662788	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccacctccaggcaacgttCgaccttccaattccagctgg	7	17	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40662788C>T	ENST00000454349.2	+	5	2765	c.2554C>T	c.(2554-2556)Cga>Tga	p.R852*	TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Nonsense_Mutation_p.R852*|TNRC6B_ENST00000301923.9_Intron	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	852	Interaction with argonaute proteins.|Pro-rich.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R866*(2)		breast(1)	1						AGGCAACGTTCGACCTTCCAA	0.617																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											31	37	35					22																	40662788		2107	4216	6323	38992734	SO:0001587	stop_gained	23112			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.2554C>T	22.37:g.40662788C>T	ENSP00000401946:p.Arg852*		38992734	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Nonsense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	43	10.036531	0.99323	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	.	.	.	5.46	4.4	0.53042	.	0.062472	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-4.4001	12.7472	0.57287	0.4244:0.5756:0.0:0.0	.	.	.	.	X	852	.	ENSP00000338371:R852X	R	+	1	2	TNRC6B	38992734	1.000000	0.71417	0.936000	0.37596	0.986000	0.74619	2.771000	0.47670	1.230000	0.43646	0.561000	0.74099	CGA		0.617	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40662788	C	T	40662788	4	4	61	1	0	0	0	0	0	1	0	0	16380	876	31	1	2693	1	TNRC6B	22	40662788	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	300687	40662788	10641778	11938	19923										
SGSM3	27352	broad.mit.edu	37	chr22	40801147	40801147	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccgatggctgcctgacagatCgagaaggacctgctccgcac	12	14	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:40801147C>T	ENST00000248929.9	+	7	666	c.477C>T	c.(475-477)atC>atT	p.I159I	SGSM3_ENST00000454798.2_Silent_p.I92I	NM_015705.4	NP_056520.2			small G protein signaling modulator 3									p.I159I(1)		cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						CCTGACAGATCGAGAAGGACC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	22											52	56	54					22																	40801147		2203	4300	6503	39131093	SO:0001819	synonymous_variant	27352			AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.477C>T	22.37:g.40801147C>T			39131093		Silent	SNP	ENST00000248929.9	37	CCDS14002.1																																																																																				0.657	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		T	40801147	C	T	40801147	2	4	61	1	0	0	0	0	0	0	0	1	14261	874	31	1		1	SGSM3	22	40801147	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	138359	40801147	10503419	11939	19924										
MCHR1	2847	broad.mit.edu	37	chr22	41077326	41077326	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtccaccccatctcttccacGaagttccggaagccctctgt	7	17	2	0	rs200370529		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41077326G>A	ENST00000249016.4	+	2	1359	c.663G>A	c.(661-663)acG>acA	p.T221T	MCHR1_ENST00000381433.2_Intron|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	221					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.T221T(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						TCTCTTCCACGAAGTTCCGGA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	22											153	129	137					22																	41077326		2203	4300	6503	39407272	SO:0001819	synonymous_variant	2847				CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"GPCR / Class A : MCH receptors"	4479	protein-coding gene	gene with protein product		601751	"G protein-coupled receptor 24"	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.663G>A	22.37:g.41077326G>A			39407272	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Silent	SNP	ENST00000249016.4	37	CCDS14004.1																																																																																				0.592	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		A	41077326	G	A	41077326	2	1	61	1	0	0	0	0	0	0	0	1	9412	1045	37	1		1	MCHR1	22	41077326	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	276179	41077326	10227240	11940	19925										
SLC25A17	10478	broad.mit.edu	37	chr22	41188666	41188666	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatcactggaaaccaccctCgatatggtgccaggctaggg	11	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41188666C>T	ENST00000435456.2	-	4	330	c.197G>A	c.(196-198)cGa>cAa	p.R66Q	SLC25A17_ENST00000544408.1_Missense_Mutation_p.R29Q|SLC25A17_ENST00000542412.1_Intron|SLC25A17_ENST00000491545.1_5'UTR	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	66	Necessary for targeting to peroxisomes and interaction with PEX19.				ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|cellular lipid metabolic process (GO:0044255)|coenzyme A transmembrane transport (GO:0035349)|FAD transmembrane transport (GO:0035350)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|fatty acid transport (GO:0015908)|NAD transport (GO:0043132)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|chaperone binding (GO:0051087)|coenzyme A transmembrane transporter activity (GO:0015228)|FAD transmembrane transporter activity (GO:0015230)|FMN transmembrane transporter activity (GO:0044610)|NAD transporter activity (GO:0051724)	p.R66Q(1)		central_nervous_system(1)|large_intestine(4)|lung(2)|skin(1)	8						aaaccaccctcgatatggtgc	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	22											71	69	70					22																	41188666		2203	4300	6503	39518612	SO:0001583	missense	10478			Y12860	CCDS14005.1, CCDS74868.1	22q13.2	2013-05-22	2002-08-29		ENSG00000100372	ENSG00000100372		"Solute carriers"	10987	protein-coding gene	gene with protein product	"peroxisomal membrane protein (34kD)"	606795	"solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kD), member 17"			9874197	Standard	NM_006358		Approved	PMP34	uc003azc.3	O43808	OTTHUMG00000151139	ENST00000435456.2:c.197G>A	22.37:g.41188666C>T	ENSP00000390722:p.Arg66Gln		39518612	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Missense_Mutation	SNP	ENST00000435456.2	37	CCDS14005.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.400618	0.25291	.	.	ENSG00000100372	ENST00000435456;ENST00000544408;ENST00000434185	D;D;D	0.81659	-1.52;-1.52;-1.52	1.83	1.83	0.25207	Mitochondrial carrier domain (2);	0.063358	0.64402	D	0.000006	T	0.78672	0.4320	M	0.69358	2.11	0.52099	D	0.999947	D;P	0.56035	0.974;0.895	P;P	0.49226	0.593;0.603	T	0.75485	-0.3301	10	0.33940	T	0.23	-26.2165	7.2262	0.26016	0.0:1.0:0.0:0.0	.	29;66	B4DU97;O43808	.;PM34_HUMAN	Q	66;29;49	ENSP00000390722:R66Q;ENSP00000438355:R29Q;ENSP00000404200:R49Q	ENSP00000394539:R66Q	R	-	2	0	SLC25A17	39518612	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.930000	0.40124	1.347000	0.45714	0.398000	0.26397	CGA		0.418	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358		T	41188666	C	T	41188666	3	4	61	1	0	0	0	0	1	0	0	0	14516	884	31	1	750	1	SLC25A17	22	41188666	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	111340	41188666	10115900	11941	19926										
XPNPEP3	63929	broad.mit.edu	37	chr22	41305159	41305159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccgggctcgtggcgcagacAttttagcctatccacctgtg	12	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41305159A>G	ENST00000357137.4	+	6	973	c.889A>G	c.(889-891)Att>Gtt	p.I297V	XPNPEP3_ENST00000544094.1_Missense_Mutation_p.I274V	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	297					glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)	p.I297V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						TGGCGCAGACATTTTAGCCTA	0.478																																					Ovarian(145;306 1841 7037 21878 30110)											1	Substitution - Missense(1)	large_intestine(1)	22											190	168	175					22																	41305159		2203	4300	6503	39635105	SO:0001583	missense	63929				CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236			28052	protein-coding gene	gene with protein product		613553				15708373, 20179356	Standard	NM_022098		Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.889A>G	22.37:g.41305159A>G	ENSP00000349658:p.Ile297Val		39635105	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	Missense_Mutation	SNP	ENST00000357137.4	37	CCDS14007.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.208039	0.39003	.	.	ENSG00000196236	ENST00000357137;ENST00000544094	T;T	0.76448	-1.02;-1.02	5.58	5.58	0.84498	Peptidase M24, structural domain (3);	0.046354	0.85682	D	0.000000	T	0.72684	0.3491	L	0.28556	0.865	0.47547	D	0.999458	P	0.49961	0.93	P	0.48425	0.577	T	0.69602	-0.5101	10	0.19147	T	0.46	.	15.4153	0.74962	1.0:0.0:0.0:0.0	.	297	Q9NQH7	XPP3_HUMAN	V	297;274	ENSP00000349658:I297V;ENSP00000441942:I274V	ENSP00000349658:I297V	I	+	1	0	XPNPEP3	39635105	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.980000	0.70516	2.134000	0.65973	0.459000	0.35465	ATT		0.478	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322201.2	NM_022098		G	41305159	A	G	41305159	3	3	61	1	0	0	0	0	1	0	0	0	17484	217	8	4	911	4	XPNPEP3	22	41305159	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	116493	41305159	9999407	11942	19927										
EP300	2033	broad.mit.edu	37	chr22	41545903	41545903	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcctgtacctagtcgtaccCccacccctcaccatactccc	4	22	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41545903C>A	ENST00000263253.7	+	14	3737	c.2518C>A	c.(2518-2520)Ccc>Acc	p.P840T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	840					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.P840T(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TAGTCGTACCCCCACCCCTCA	0.582			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	22											113	70	85					22																	41545903		2203	4300	6503	39875849	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2518C>A	22.37:g.41545903C>A	ENSP00000263253:p.Pro840Thr		39875849	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236326	0.58886	.	.	ENSG00000100393	ENST00000263253	D	0.84516	-1.86	6.08	6.08	0.98989	.	0.000000	0.48286	D	0.000186	D	0.85695	0.5756	N	0.08118	0	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	D	0.85655	0.1285	10	0.33141	T	0.24	-8.1572	20.6721	0.99693	0.0:1.0:0.0:0.0	.	840	Q09472	EP300_HUMAN	T	840	ENSP00000263253:P840T	ENSP00000263253:P840T	P	+	1	0	EP300	39875849	1.000000	0.71417	0.995000	0.50966	0.829000	0.46940	6.899000	0.75682	2.894000	0.99253	0.591000	0.81541	CCC		0.582	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41545903	C	A	41545903	3	1	61	1	0	0	0	0	1	0	0	0	5161	623	22	2	2572	2	EP300	22	41545903	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240744	41545903	9758663	11943	19928										
EP300	2033	broad.mit.edu	37	chr22	41574836	41574836	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccagaattcaatgctttCtcagcttgctagcaatccag	8	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41574836C>A	ENST00000263253.7	+	31	8340	c.7121C>A	c.(7120-7122)tCt>tAt	p.S2374Y	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2374					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.S2374Y(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TCAATGCTTTCTCAGCTTGCT	0.547			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	22											50	52	51					22																	41574836		2203	4300	6503	39904782	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.7121C>A	22.37:g.41574836C>A	ENSP00000263253:p.Ser2374Tyr		39904782	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900466	0.52227	.	.	ENSG00000100393	ENST00000263253	D	0.86366	-2.11	5.65	5.65	0.86999	.	0.000000	0.45867	D	0.000322	D	0.89815	0.6824	L	0.46157	1.445	0.52099	D	0.999947	D	0.61697	0.99	P	0.54664	0.758	D	0.90516	0.4485	10	0.87932	D	0	-10.4503	19.717	0.96124	0.0:1.0:0.0:0.0	.	2374	Q09472	EP300_HUMAN	Y	2374	ENSP00000263253:S2374Y	ENSP00000263253:S2374Y	S	+	2	0	EP300	39904782	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.944000	0.70219	2.661000	0.90470	0.655000	0.94253	TCT		0.547	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41574836	C	A	41574836	3	1	61	1	0	0	0	0	1	0	0	0	5161	913	32	2	7243	2	EP300	22	41574836	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	28933	41574836	9729730	11944	19929										
ZC3H7B	23264	broad.mit.edu	37	chr22	41742114	41742114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaagggcaccctcaaccgcGacctgctcttcgacccgctg	11	17	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41742114G>A	ENST00000352645.4	+	14	1824	c.1567G>A	c.(1567-1569)Gac>Aac	p.D523N	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.D523N	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	539					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D523N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						CCTCAACCGCGACCTGCTCTT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	22											157	125	136					22																	41742114		2203	4300	6503	40072060	SO:0001583	missense	23264				CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.1567G>A	22.37:g.41742114G>A	ENSP00000345793:p.Asp523Asn		40072060	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	37	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123437	0.94429	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.19105	2.17;2.17	5.36	5.36	0.76844	.	0.044939	0.85682	D	0.000000	T	0.25975	0.0633	L	0.46157	1.445	0.58432	D	0.999995	P	0.50272	0.933	B	0.43155	0.41	T	0.02539	-1.1144	10	0.66056	D	0.02	-34.013	19.0939	0.93242	0.0:0.0:1.0:0.0	.	523	Q9UGR2-2	.	N	523	ENSP00000345793:D523N;ENSP00000263243:D523N	ENSP00000263243:D523N	D	+	1	0	ZC3H7B	40072060	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.987000	0.88182	2.523000	0.85059	0.555000	0.69702	GAC		0.607	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		A	41742114	G	A	41742114	3	1	61	1	0	0	0	0	1	0	0	0	17612	1058	37	1	1617	1	ZC3H7B	22	41742114	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	167278	41742114	9562452	11945	19930										
PMM1	5372	broad.mit.edu	37	chr22	41979978	41979978	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtaccttgtccagttcggaGaactcgatcctctcctccag	9	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:41979978G>T	ENST00000216259.7	-	5	543	c.459C>A	c.(457-459)ttC>ttA	p.F153L	PMM1_ENST00000466645.1_5'Flank	NM_002676.2	NP_002667.2	Q92871	PMM1_HUMAN	phosphomannomutase 1	153					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	metal ion binding (GO:0046872)|phosphomannomutase activity (GO:0004615)	p.F153L(1)		NS(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(2)	11						CCAGTTCGGAGAACTCGATCC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	22											111	97	102					22																	41979978		2203	4300	6503	40309924	SO:0001583	missense	5372				CCDS14020.1	22q13	2008-12-01			ENSG00000100417	ENSG00000100417	5.4.2.8		9114	protein-coding gene	gene with protein product	"brain glucose-1,6-bisphosphatase"	601786				9070917, 9271215	Standard	NM_002676		Approved	Sec53	uc003bal.2	Q92871	OTTHUMG00000150972	ENST00000216259.7:c.459C>A	22.37:g.41979978G>T	ENSP00000216259:p.Phe153Leu		40309924	A8K003|Q92586	Missense_Mutation	SNP	ENST00000216259.7	37	CCDS14020.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.836597	0.71373	.	.	ENSG00000100417	ENST00000216259	D	0.98987	-5.3	5.41	3.27	0.37495	HAD-like domain (1);	0.094859	0.85682	N	0.000000	D	0.98197	0.9404	M	0.91459	3.21	0.80722	D	1	B	0.15473	0.013	B	0.18263	0.021	D	0.96304	0.9223	10	0.87932	D	0	-22.2686	5.1571	0.15040	0.2207:0.0:0.6325:0.1468	.	153	Q92871	PMM1_HUMAN	L	153	ENSP00000216259:F153L	ENSP00000216259:F153L	F	-	3	2	PMM1	40309924	1.000000	0.71417	0.998000	0.56505	0.584000	0.36387	2.238000	0.43070	0.624000	0.30286	0.563000	0.77884	TTC		0.512	PMM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320711.3	NM_002676		T	41979978	G	T	41979978	3	4	61	1	0	0	0	0	1	0	0	0	12167	933	33	2	345	2	PMM1	22	41979978	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	237864	41979978	9324588	11946	19931										
XRCC6	2547	broad.mit.edu	37	chr22	42032768	42032768	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaaagccggtgatctccgaGatacaggtgggcatatttcc	11	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42032768G>T	ENST00000359308.4	+	4	1238	c.583G>T	c.(583-585)Gat>Tat	p.D195Y	XRCC6_ENST00000402580.3_Missense_Mutation_p.D154Y|XRCC6_ENST00000405506.1_Missense_Mutation_p.D145Y|XRCC6_ENST00000360079.3_Missense_Mutation_p.D195Y|XRCC6_ENST00000405878.1_Missense_Mutation_p.D195Y|XRCC6_ENST00000428575.2_Missense_Mutation_p.D62Y			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	195					brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)	p.D195H(1)|p.D195Y(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TGATCTCCGAGATACAGGTGG	0.453								Non-homologous end-joining																																								2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	22											55	57	57					22																	42032768		2203	4300	6503	40362714	SO:0001583	missense	2547			J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"Ku autoantigen, 70kDa"	152690	"thyroid autoantigen 70kD (Ku antigen)", "thyroid autoantigen 70kDa (Ku antigen)"	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.583G>T	22.37:g.42032768G>T	ENSP00000352257:p.Asp195Tyr		40362714	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Missense_Mutation	SNP	ENST00000359308.4	37	CCDS14021.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625223	0.66901	.	.	ENSG00000196419	ENST00000360079;ENST00000402580;ENST00000428575;ENST00000359308;ENST00000405878;ENST00000402409;ENST00000405506	.	.	.	5.39	5.39	0.77823	Ku70/Ku80, N-terminal alpha/beta (1);	0.101533	0.64402	D	0.000002	D	0.83613	0.5292	M	0.82716	2.605	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.78314	0.99;0.988;0.99;0.991	D	0.84618	0.0682	9	0.51188	T	0.08	-23.5411	19.1841	0.93635	0.0:0.0:1.0:0.0	.	145;195;154;195	B1AHC9;B1AHC7;B1AHC8;P12956	.;.;.;XRCC6_HUMAN	Y	195;154;62;195;195;195;145	.	ENSP00000352257:D195Y	D	+	1	0	XRCC6	40362714	1.000000	0.71417	0.999000	0.59377	0.312000	0.27988	9.476000	0.97823	2.537000	0.85549	0.655000	0.94253	GAT		0.453	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469		T	42032768	G	T	42032768	3	4	61	1	0	0	0	0	1	0	0	0	17497	942	33	2	597	2	XRCC6	22	42032768	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	52790	42032768	9271798	11947	19932										
MEI1	150365	broad.mit.edu	37	chr22	42141907	42141907	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggttggctatagaattccaGagtgagccttcagcccagga	12	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42141907G>T	ENST00000401548.3	+	14	1597	c.1557G>T	c.(1555-1557)caG>caT	p.Q519H	MEI1_ENST00000400107.1_5'UTR|MEI1_ENST00000540833.1_Missense_Mutation_p.Q259H|MEI1_ENST00000300398.4_5'UTR|Y_RNA_ENST00000384086.1_RNA	NM_152513.3	NP_689726.3			meiosis inhibitor 1									p.Q519H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TAGAATTCCAGAGTGAGCCTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	22											66	67	67					22																	42141907		1912	4139	6051	40471853	SO:0001583	missense	150365			AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.1557G>T	22.37:g.42141907G>T	ENSP00000384115:p.Gln519His		40471853		Missense_Mutation	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.322496	0.60634	.	.	ENSG00000167077	ENST00000401548;ENST00000540833	T;T	0.48836	1.79;0.8	5.43	4.41	0.53225	Armadillo-type fold (1);	0.152448	0.44902	D	0.000405	T	0.62344	0.2420	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.85130	0.976;0.997	T	0.64045	-0.6499	10	0.72032	D	0.01	-6.6768	8.7957	0.34878	0.1773:0.0:0.8227:0.0	.	519;519	Q5TIA1;Q5TIA1-4	MEI1_HUMAN;.	H	519;259	ENSP00000384115:Q519H;ENSP00000444225:Q259H	ENSP00000384115:Q519H	Q	+	3	2	MEI1	40471853	1.000000	0.71417	0.920000	0.36463	0.998000	0.95712	1.948000	0.40303	1.249000	0.43950	0.655000	0.94253	CAG		0.498	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		T	42141907	G	T	42141907	3	4	61	1	0	0	0	0	1	0	0	0	9495	933	33	2	1611	2	MEI1	22	42141907	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	109139	42141907	9162659	11948	19933										
CCDC134	79879	broad.mit.edu	37	chr22	42205912	42205912	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttgaggtgaagcggcggGagcagctgttggcactgaag	18	6	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42205912G>T	ENST00000255784.5	+	3	237	c.133G>T	c.(133-135)Gag>Tag	p.E45*	CCDC134_ENST00000402061.3_Nonsense_Mutation_p.E45*	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	45						extracellular region (GO:0005576)|membrane (GO:0016020)		p.E45*(1)		large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GAAGCGGCGGGAGCAGCTGTT	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											68	61	63					22																	42205912		2203	4300	6503	40535858	SO:0001587	stop_gained	79879			AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.133G>T	22.37:g.42205912G>T	ENSP00000255784:p.Glu45*		40535858		Nonsense_Mutation	SNP	ENST00000255784.5	37	CCDS33654.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532339	0.45073	.	.	ENSG00000100147	ENST00000402061;ENST00000255784;ENST00000429249	.	.	.	4.84	4.84	0.62591	.	0.103349	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-32.6239	18.495	0.90861	0.0:0.0:1.0:0.0	.	.	.	.	X	45	.	ENSP00000255784:E45X	E	+	1	0	CCDC134	40535858	1.000000	0.71417	0.983000	0.44433	0.320000	0.28249	8.823000	0.92018	2.683000	0.91414	0.655000	0.94253	GAG		0.522	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821		T	42205912	G	T	42205912	4	4	61	1	0	0	0	0	0	1	0	0	2774	1175	41	2	139	2	CCDC134	22	42205912	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64005	42205912	9098654	11949	19934										
TCF20	6942	broad.mit.edu	37	chr22	42606743	42606743	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggagggaaaccctcttgcttCggtgaaatcgtcactgtatc	11	10	2	1	rs142330661	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42606743C>T	ENST00000359486.3	-	1	4705	c.4569G>A	c.(4567-4569)ccG>ccA	p.P1523P	TCF20_ENST00000335626.4_Silent_p.P1523P|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.P1523P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CCTCTTGCTTCGGTGAAATCG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	22						C	,	1,4405	2.1+/-5.4	0,1,2202	108	92	97		4569,4569	-0.4	1	22	dbSNP_134	97	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TCF20	NM_005650.1,NM_181492.1	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	1523/1961,1523/1939	42606743	3,13003	2203	4300	6503	40936687	SO:0001819	synonymous_variant	6942			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4569G>A	22.37:g.42606743C>T			40936687	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																				0.488	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		T	42606743	C	T	42606743	2	4	61	1	0	0	0	0	0	0	0	1	15729	871	31	1		1	TCF20	22	42606743	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	400831	42606743	8697823	11950	19935										
TCF20	6942	broad.mit.edu	37	chr22	42609650	42609650	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccggtgaggagccagctttCtcagaggctccacccttgta	12	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42609650C>A	ENST00000359486.3	-	1	1798	c.1662G>T	c.(1660-1662)gaG>gaT	p.E554D	TCF20_ENST00000335626.4_Missense_Mutation_p.E554D	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	554					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E554D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						AGCCAGCTTTCTCAGAGGCTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	22											85	84	84					22																	42609650		2203	4300	6503	40939594	SO:0001583	missense	6942			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.1662G>T	22.37:g.42609650C>A	ENSP00000352463:p.Glu554Asp		40939594	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	37	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786009	0.31593	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.32515	1.45;1.45	6.17	2.96	0.34315	.	0.071629	0.56097	D	0.000023	T	0.36110	0.0955	N	0.24115	0.695	0.80722	D	1	D;D	0.67145	0.996;0.994	D;D	0.76071	0.987;0.97	T	0.04467	-1.0949	10	0.30078	T	0.28	-25.5522	10.55	0.45083	0.0:0.7413:0.0:0.2587	.	554;554	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	D	554	ENSP00000352463:E554D;ENSP00000335561:E554D	ENSP00000335561:E554D	E	-	3	2	TCF20	40939594	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	0.820000	0.27323	0.952000	0.37798	0.655000	0.94253	GAG		0.592	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		A	42609650	C	A	42609650	3	1	61	1	0	0	0	0	1	0	0	0	15729	912	32	2	4258	2	TCF20	22	42609650	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2907	42609650	8694916	11951	19936										
POLDIP3	84271	broad.mit.edu	37	chr22	42998975	42998975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttccctttgattcgaaatCgggcatctttctgcaaaagc	7	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:42998975C>T	ENST00000252115.5	-	2	355	c.251G>A	c.(250-252)cGa>cAa	p.R84Q	POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000451060.2_5'Flank|POLDIP3_ENST00000348657.2_Missense_Mutation_p.R84Q|POLDIP3_ENST00000339677.6_Missense_Mutation_p.R84Q	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	84					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R84Q(2)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						GATTCGAAATCGGGCATCTTT	0.562																																					Ovarian(52;967 1128 5875 19997 42537)											2	Substitution - Missense(2)	large_intestine(2)	22											100	98	99					22																	42998975		2203	4300	6503	41328919	SO:0001583	missense	84271				CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.251G>A	22.37:g.42998975C>T	ENSP00000252115:p.Arg84Gln		41328919	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148352	0.94603	.	.	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	6.08	6.08	0.98989	.	0.055197	0.85682	D	0.000000	T	0.80407	0.4617	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.999;0.996	T	0.80004	-0.1564	9	0.72032	D	0.01	-15.0671	20.6721	0.99693	0.0:1.0:0.0:0.0	.	84;84;84;84	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	Q	84	.	ENSP00000252115:R84Q	R	-	2	0	POLDIP3	41328919	0.999000	0.42202	0.946000	0.38457	0.669000	0.39330	4.939000	0.63526	2.894000	0.99253	0.591000	0.81541	CGA		0.562	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		T	42998975	C	T	42998975	3	4	61	1	0	0	0	0	1	0	0	0	12226	884	31	1	1046	1	POLDIP3	22	42998975	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	389325	42998975	8305591	11952	19937										
PACSIN2	11252	broad.mit.edu	37	chr22	43287079	43287079	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccagttcttgatcttctcGaagtcatcgttcatcagtga	8	10	6	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43287079G>A	ENST00000263246.3	-	4	528	c.327C>T	c.(325-327)ttC>ttT	p.F109F	PACSIN2_ENST00000407585.1_Silent_p.F109F|PACSIN2_ENST00000403744.3_Silent_p.F109F|PACSIN2_ENST00000402229.1_Silent_p.F109F|PACSIN2_ENST00000337959.4_Silent_p.F109F	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	109	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)	p.F109F(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				TGATCTTCTCGAAGTCATCGT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	22											86	85	86					22																	43287079		2174	4293	6467	41617023	SO:0001819	synonymous_variant	11252			AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"syndapin II"	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.327C>T	22.37:g.43287079G>A			41617023	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	37	CCDS43023.1																																																																																				0.567	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229		A	43287079	G	A	43287079	2	1	61	1	0	0	0	0	0	0	0	1	11406	1049	37	1		1	PACSIN2	22	43287079	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	288104	43287079	8017487	11953	19938										
SCUBE1	80274	broad.mit.edu	37	chr22	43735138	43735138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcttgccttcccccttgtaGcctggcttgcagaggcattt	10	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43735138G>A	ENST00000360835.4	-	2	318	c.192C>T	c.(190-192)ggC>ggT	p.G64G	SCUBE1_ENST00000290460.7_Silent_p.G64G	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	64	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.G64G(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CCCCCTTGTAGCCTGGCTTGC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	22											183	131	149					22																	43735138		2203	4300	6503	42065082	SO:0001819	synonymous_variant	80274				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.192C>T	22.37:g.43735138G>A			42065082	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																				0.622	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		A	43735138	G	A	43735138	2	1	61	1	0	0	0	0	0	0	0	1	13981	958	34	3		3	SCUBE1	22	43735138	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	448059	43735138	7569428	11954	19939										
MPPED1	758	broad.mit.edu	37	chr22	43831029	43831029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgtctctgatacccactcGaggacggaccccatccagat	9	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43831029G>A	ENST00000417669.2	+	3	744	c.300G>A	c.(298-300)tcG>tcA	p.S100S	MPPED1_ENST00000538182.1_Silent_p.S133S|MPPED1_ENST00000443721.1_Silent_p.S100S|MPPED1_ENST00000439548.1_Intron|MPPED1_ENST00000542779.1_Silent_p.S100S|MPPED1_ENST00000414469.2_5'UTR			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	100							hydrolase activity (GO:0016787)	p.S100S(1)		endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				ATACCCACTCGAGGACGGACC	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	22											108	124	118					22																	43831029		2133	4224	6357	42160973	SO:0001819	synonymous_variant	758			U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"chromosome 22 open reading frame 1"	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.300G>A	22.37:g.43831029G>A			42160973	A8K159|B7Z2S9|Q8N361	Silent	SNP	ENST00000417669.2	37	CCDS46723.1																																																																																				0.627	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370		A	43831029	G	A	43831029	2	1	61	1	0	0	0	0	0	0	0	1	9771	1045	37	1		1	MPPED1	22	43831029	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95891	43831029	7473537	11955	19940										
EFCAB6	64800	broad.mit.edu	37	chr22	43950925	43950925	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgtcggctgtggccttggGagaggtaggcggcgggcctt	19	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43950925G>T	ENST00000262726.7	-	27	3725	c.3472C>A	c.(3472-3474)Ccc>Acc	p.P1158T	EFCAB6_ENST00000461800.1_5'UTR|EFCAB6_ENST00000396231.2_Missense_Mutation_p.P1006T	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.P1158T(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				GTGGCCTTGGGAGAGGTAGGC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	22											87	80	82					22																	43950925		2203	4300	6503	42282258	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3472C>A	22.37:g.43950925G>T	ENSP00000262726:p.Pro1158Thr		42282258	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323238	0.24080	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.17213	2.32;2.29	4.88	0.277	0.15668	.	0.583885	0.16357	N	0.217950	T	0.14614	0.0353	L	0.45581	1.43	0.28123	N	0.930522	P;B	0.45531	0.86;0.319	P;B	0.47075	0.536;0.075	T	0.14254	-1.0479	10	0.14252	T	0.57	-13.1876	4.2727	0.10794	0.3639:0.1634:0.4727:0.0	.	1006;1158	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	T	1006;1158	ENSP00000379533:P1006T;ENSP00000262726:P1158T	ENSP00000262726:P1158T	P	-	1	0	EFCAB6	42282258	0.037000	0.19845	0.019000	0.16419	0.057000	0.15508	0.084000	0.14891	0.281000	0.22233	0.655000	0.94253	CCC		0.507	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43950925	G	T	43950925	3	4	61	1	0	0	0	0	1	0	0	0	4950	1174	41	2	1057	2	EFCAB6	22	43950925	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	119896	43950925	7353641	11956	19941										
EFCAB6	64800	broad.mit.edu	37	chr22	43972305	43972305	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgtaacagaaatccttaaGaacttgtccgaattctgtag	7	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43972305G>T	ENST00000262726.7	-	26	3545	c.3292C>A	c.(3292-3294)Ctt>Att	p.L1098I	EFCAB6_ENST00000396231.2_Missense_Mutation_p.L946I	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1098	EF-hand 12. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L1098I(1)|p.L1098V(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AAATCCTTAAGAACTTGTCCG	0.313																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	22											66	70	69					22																	43972305		2203	4299	6502	42303638	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3292C>A	22.37:g.43972305G>T	ENSP00000262726:p.Leu1098Ile		42303638	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.800011	0.31869	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.12774	2.65;2.65	5.4	3.19	0.36642	EF-hand-like domain (1);	0.153404	0.43110	N	0.000616	T	0.24699	0.0599	L	0.56769	1.78	0.26817	N	0.968879	P;P	0.44946	0.724;0.846	B;P	0.52309	0.292;0.695	T	0.03249	-1.1056	10	0.51188	T	0.08	-19.2094	14.0077	0.64475	0.0:0.0:0.6951:0.3049	.	946;1098	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	I	946;1098	ENSP00000379533:L946I;ENSP00000262726:L1098I	ENSP00000262726:L1098I	L	-	1	0	EFCAB6	42303638	0.986000	0.35501	0.490000	0.27465	0.939000	0.58152	2.915000	0.48805	1.468000	0.48064	-0.274000	0.10170	CTT		0.313	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43972305	G	T	43972305	3	4	61	1	0	0	0	0	1	0	0	0	4950	942	33	2	1241	2	EFCAB6	22	43972305	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21380	43972305	7332261	11957	19942										
EFCAB6	64800	broad.mit.edu	37	chr22	43996032	43996032	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctttgtaaaatgacccatGaagttgaaataatcctctgc	8	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:43996032G>T	ENST00000262726.7	-	23	3046	c.2793C>A	c.(2791-2793)ttC>ttA	p.F931L	EFCAB6_ENST00000396231.2_Missense_Mutation_p.F779L	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	931					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.F931L(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AATGACCCATGAAGTTGAAAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	22											197	196	197					22																	43996032		2203	4300	6503	42327365	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.2793C>A	22.37:g.43996032G>T	ENSP00000262726:p.Phe931Leu		42327365	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.567993	0.65651	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.38722	1.12;1.12	5.26	5.26	0.73747	.	0.177155	0.39544	N	0.001335	T	0.49898	0.1584	L	0.46157	1.445	0.80722	D	1	D;P	0.71674	0.998;0.584	D;B	0.80764	0.994;0.16	T	0.38887	-0.9640	10	0.08837	T	0.75	-25.6401	9.7616	0.40534	0.0908:0.0:0.9092:0.0	.	779;931	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	L	779;931	ENSP00000379533:F779L;ENSP00000262726:F931L	ENSP00000262726:F931L	F	-	3	2	EFCAB6	42327365	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.407000	0.44565	2.731000	0.93534	0.650000	0.86243	TTC		0.478	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43996032	G	T	43996032	3	4	61	1	0	0	0	0	1	0	0	0	4950	1281	45	2	1752	2	EFCAB6	22	43996032	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23727	43996032	7308534	11958	19943										
EFCAB6	64800	broad.mit.edu	37	chr22	44031028	44031028	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagctcatcccttccttctcGaagcctattttagtggtcag	7	12	3	0	rs201541665		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44031028G>A	ENST00000262726.7	-	18	2305	c.2052C>T	c.(2050-2052)ttC>ttT	p.F684F	EFCAB6_ENST00000396231.2_Silent_p.F532F	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	684					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.F684F(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				CTTCCTTCTCGAAGCCTATTT	0.537													G|||	1	0.000199681	0	0	5008	,	,		22706	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	22											248	182	204					22																	44031028		2203	4300	6503	42362361	SO:0001819	synonymous_variant	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.2052C>T	22.37:g.44031028G>A			42362361	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	37	CCDS14049.1																																																																																				0.537	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44031028	G	A	44031028	2	1	61	1	0	0	0	0	0	0	0	1	4950	1049	37	1		1	EFCAB6	22	44031028	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34996	44031028	7273538	11959	19944										
EFCAB6	64800	broad.mit.edu	37	chr22	44074010	44074010	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcaatttagaatatatcGaaattcttctcttgttatcg	5	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44074010G>A	ENST00000262726.7	-	13	1538	c.1285C>T	c.(1285-1287)Cga>Tga	p.R429*	EFCAB6_ENST00000358439.4_3'UTR|EFCAB6_ENST00000396231.2_Nonsense_Mutation_p.R277*	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	429	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R429*(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AGAATATATCGAAATTCTTCT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											90	90	90					22																	44074010		2203	4300	6503	42405343	SO:0001587	stop_gained	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1285C>T	22.37:g.44074010G>A	ENSP00000262726:p.Arg429*		42405343	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Nonsense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873062	0.91664	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	.	.	.	4.96	2.83	0.33086	.	0.632034	0.14820	N	0.296533	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-2.8467	6.0296	0.19673	0.0952:0.0:0.7174:0.1874	.	.	.	.	X	277;429	.	ENSP00000262726:R429X	R	-	1	2	EFCAB6	42405343	0.069000	0.21087	0.025000	0.17156	0.044000	0.14063	1.192000	0.32150	0.766000	0.33244	0.650000	0.86243	CGA		0.363	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44074010	G	A	44074010	4	1	61	1	0	0	0	0	0	1	0	0	4950	1066	37	1	3300	1	EFCAB6	22	44074010	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42982	44074010	7230556	11960	19945										
EFCAB6	64800	broad.mit.edu	37	chr22	44083429	44083429	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgttagaaattgcttcCaattgattttagtggtggct	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44083429C>T	ENST00000262726.7	-	11	1317	c.1064G>A	c.(1063-1065)tGg>tAg	p.W355*	EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000396231.2_Nonsense_Mutation_p.W203*	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	355					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.W355*(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AAATTGCTTCCAATTGATTTT	0.313																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											61	61	61					22																	44083429		2203	4300	6503	42414762	SO:0001587	stop_gained	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1064G>A	22.37:g.44083429C>T	ENSP00000262726:p.Trp355*		42414762	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Nonsense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	38	6.649931	0.97734	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	.	.	.	4.68	4.68	0.58851	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-16.5501	13.2831	0.60226	0.0:1.0:0.0:0.0	.	.	.	.	X	203;355	.	ENSP00000262726:W355X	W	-	2	0	EFCAB6	42414762	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	2.942000	0.49018	2.595000	0.87683	0.655000	0.94253	TGG		0.313	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	44083429	C	T	44083429	4	4	61	1	0	0	0	0	0	1	0	0	4950	595	21	3	3529	3	EFCAB6	22	44083429	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	9419	44083429	7221137	11961	19946										
EFCAB6	64800	broad.mit.edu	37	chr22	44107477	44107477	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccctgcactgagggccttTtcaaccttttcataagactt	6	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44107477T>C	ENST00000262726.7	-	10	1162	c.909A>G	c.(907-909)gaA>gaG	p.E303E	EFCAB6_ENST00000358439.4_Silent_p.E197E|EFCAB6_ENST00000396231.2_Silent_p.E151E	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	303	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.E303E(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TGAGGGCCTTTTCAACCTTTT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	22											59	61	61					22																	44107477		2203	4300	6503	42438810	SO:0001819	synonymous_variant	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.909A>G	22.37:g.44107477T>C			42438810	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	37	CCDS14049.1																																																																																				0.368	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		C	44107477	T	C	44107477	2	2	61	1	0	0	0	0	0	0	0	1	4950	1838	64	4		4	EFCAB6	22	44107477	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	24048	44107477	7197089	11962	19947										
EFCAB6	64800	broad.mit.edu	37	chr22	44131804	44131804	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccttcttagctcctgcggtcGaaccagtccagtcttgttaa	8	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44131804G>A	ENST00000262726.7	-	7	830	c.577C>T	c.(577-579)Cga>Tga	p.R193*	EFCAB6_ENST00000358439.4_Nonsense_Mutation_p.R87*|EFCAB6_ENST00000356087.4_Nonsense_Mutation_p.R87*|EFCAB6_ENST00000396231.2_Nonsense_Mutation_p.R41*	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	193	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R193*(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TCCTGCGGTCGAACCAGTCCA	0.403																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											133	128	130					22																	44131804		2203	4300	6503	42463137	SO:0001587	stop_gained	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.577C>T	22.37:g.44131804G>A	ENSP00000262726:p.Arg193*		42463137	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Nonsense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	37	5.994794	0.97184	.	.	ENSG00000186976	ENST00000396231;ENST00000262726;ENST00000358439;ENST00000356087	.	.	.	5.0	3.99	0.46301	.	0.184905	0.34088	N	0.004278	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-6.2807	13.4571	0.61206	0.0766:0.0:0.9234:0.0	.	.	.	.	X	41;193;87;87	.	ENSP00000262726:R193X	R	-	1	2	EFCAB6	42463137	0.060000	0.20803	0.002000	0.10522	0.666000	0.39218	1.203000	0.32284	1.482000	0.48325	0.491000	0.48974	CGA		0.403	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44131804	G	A	44131804	4	1	61	1	0	0	0	0	0	1	0	0	4950	1066	37	1	4032	1	EFCAB6	22	44131804	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	24327	44131804	7172762	11963	19948										
PNPLA3	80339	broad.mit.edu	37	chr22	44342082	44342082	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctccccatgcacacctgaGcaggactggccctgctggac	11	17	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44342082G>A	ENST00000216180.3	+	9	1439	c.1266G>A	c.(1264-1266)gaG>gaA	p.E422E	PNPLA3_ENST00000423180.2_Silent_p.E418E	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	422					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.E422E(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				GCACACCTGAGCAGGACTGGC	0.622											OREG0026623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	22											135	136	135					22																	44342082		2203	4300	6503	42673415	SO:0001819	synonymous_variant	80339				CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"Patatin-like phospholipase domain containing"	18590	protein-coding gene	gene with protein product		609567	"chromosome 22 open reading frame 20", "adiponutrin"	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.1266G>A	22.37:g.44342082G>A		923	42673415	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Silent	SNP	ENST00000216180.3	37	CCDS14054.1																																																																																				0.622	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225		A	44342082	G	A	44342082	2	1	61	1	0	0	0	0	0	0	0	1	12197	962	34	3		3	PNPLA3	22	44342082	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210278	44342082	6962484	11964	19949										
LDOC1L	84247	broad.mit.edu	37	chr22	44892990	44892990	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgtgggggatagcccacttCtccgcctccccagtcagtcg	11	15	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:44892990C>A	ENST00000341255.3	-	2	956	c.447G>T	c.(445-447)gaG>gaT	p.E149D		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	149								p.E149D(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		TAGCCCACTTCTCCGCCTCCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	22											43	44	44					22																	44892990		2203	4300	6503	43271654	SO:0001583	missense	84247			CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.447G>T	22.37:g.44892990C>A	ENSP00000340434:p.Glu149Asp		43271654	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	37	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.474917	0.63737	.	.	ENSG00000188636	ENST00000341255	T	0.18960	2.18	3.27	3.27	0.37495	.	0.293400	0.22855	N	0.054820	T	0.13756	0.0333	N	0.24115	0.695	0.29683	N	0.841518	P	0.47253	0.892	B	0.44085	0.44	T	0.03344	-1.1046	10	0.12766	T	0.61	-16.6304	10.3019	0.43656	0.0:1.0:0.0:0.0	.	149	Q6ICC9	LDOCL_HUMAN	D	149	ENSP00000340434:E149D	ENSP00000340434:E149D	E	-	3	2	LDOC1L	43271654	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	2.775000	0.47702	2.139000	0.66308	0.591000	0.81541	GAG		0.602	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		A	44892990	C	A	44892990	3	1	61	1	0	0	0	0	1	0	0	0	8732	912	32	2	276	2	LDOC1L	22	44892990	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	550908	44892990	6411576	11965	19950										
SMC1B	27127	broad.mit.edu	37	chr22	45795097	45795097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccagggcttttatatcatCttcctgtttagaacattgtt	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:45795097C>A	ENST00000357450.4	-	6	990	c.991G>T	c.(991-993)Gat>Tat	p.D331Y	SMC1B_ENST00000404354.3_Missense_Mutation_p.D331Y	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	331					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.D331Y(2)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTTATATCATCTTCCTGTTTA	0.363																																																2	Substitution - Missense(2)	large_intestine(2)	22											205	182	189					22																	45795097		1840	4092	5932	44173761	SO:0001583	missense	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.991G>T	22.37:g.45795097C>A	ENSP00000350036:p.Asp331Tyr		44173761	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.813978	0.50527	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.79845	-1.31;-1.16	5.7	5.7	0.88788	RecF/RecN/SMC (1);	0.443883	0.21317	N	0.076536	T	0.76069	0.3936	L	0.36672	1.1	0.34187	D	0.671587	B;P;P	0.48089	0.093;0.905;0.587	B;B;B	0.43575	0.158;0.424;0.424	D	0.84186	0.0442	10	0.66056	D	0.02	.	15.2296	0.73378	0.0:0.7528:0.2472:0.0	.	331;331;331	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	Y	331	ENSP00000350036:D331Y;ENSP00000385902:D331Y	ENSP00000350036:D331Y	D	-	1	0	SMC1B	44173761	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.577000	0.36515	2.692000	0.91855	0.655000	0.94253	GAT		0.363	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		A	45795097	C	A	45795097	3	1	61	1	0	0	0	0	1	0	0	0	14819	913	32	2	2796	2	SMC1B	22	45795097	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	902107	45795097	5509469	11966	19951										
FBLN1	2192	broad.mit.edu	37	chr22	45931216	45931216	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctctaggcaactgtatTggtaagaggtgtgccgccag	14	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:45931216T>C	ENST00000327858.6	+	8	1016	c.921T>C	c.(919-921)atT>atC	p.I307I	FBLN1_ENST00000348697.2_Splice_Site_p.I307I|FBLN1_ENST00000340923.5_Splice_Site_p.I307I|FBLN1_ENST00000442170.2_Splice_Site_p.I307I|FBLN1_ENST00000262722.7_Splice_Site_p.I307I|FBLN1_ENST00000402984.3_Splice_Site_p.I345I	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	307	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.I307I(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GCAACTGTATTGGTAAGAGGT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	22											64	59	60					22																	45931216		2203	4300	6503	44309880	SO:0001630	splice_region_variant	2192				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.922+1T>C	22.37:g.45931216T>C			44309880	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	37	CCDS14067.1																																																																																				0.547	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	Silent	C	45931216	T	C	45931216	5	2	61	1	0	0	0	0	0	0	1	0	5717	1826	63	4	951	4	FBLN1	22	45931216	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	136119	45931216	5373350	11967	19952										
FBLN1	2192	broad.mit.edu	37	chr22	45937194	45937194	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggctcctacacgtgccagaaGaacgtgcccaactgtggccg	12	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:45937194G>T	ENST00000327858.6	+	9	1103	c.1008G>T	c.(1006-1008)aaG>aaT	p.K336N	FBLN1_ENST00000348697.2_Missense_Mutation_p.K336N|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000340923.5_Missense_Mutation_p.K336N|FBLN1_ENST00000442170.2_Missense_Mutation_p.K336N|FBLN1_ENST00000262722.7_Missense_Mutation_p.K336N|FBLN1_ENST00000402984.3_Missense_Mutation_p.K374N	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	336	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.K336N(2)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CGTGCCAGAAGAACGTGCCCA	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	22											139	113	121					22																	45937194		2203	4300	6503	44315858	SO:0001583	missense	2192				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1008G>T	22.37:g.45937194G>T	ENSP00000331544:p.Lys336Asn		44315858	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.657843	0.67586	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.87491	-1.65;-2.08;-1.96;-2.26;-1.71;-1.62	5.41	3.18	0.36537	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.145467	0.64402	D	0.000013	T	0.80454	0.4626	N	0.03608	-0.345	0.34514	D	0.70746	D;D;D;D	0.69078	0.993;0.993;0.987;0.997	P;P;P;P	0.62184	0.886;0.899;0.886;0.888	D	0.83463	0.0055	10	0.59425	D	0.04	.	6.5854	0.22618	0.3606:0.0:0.6394:0.0	.	374;336;336;336	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	N	336;374;336;336;336;336	ENSP00000262723:K336N;ENSP00000385521:K374N;ENSP00000262722:K336N;ENSP00000331544:K336N;ENSP00000393812:K336N;ENSP00000342212:K336N	ENSP00000262722:K336N	K	+	3	2	FBLN1	44315858	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.482000	0.45224	1.290000	0.44636	0.655000	0.94253	AAG		0.502	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45937194	G	T	45937194	3	4	61	1	0	0	0	0	1	0	0	0	5717	933	33	2	1042	2	FBLN1	22	45937194	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5978	45937194	5367372	11968	19953										
FBLN1	2192	broad.mit.edu	37	chr22	45960776	45960776	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttccaggcagaaatccaaGaagggaaggcagaacacccc	11	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:45960776G>T	ENST00000327858.6	+	15	1792				FBLN1_ENST00000348697.2_Missense_Mutation_p.K570N|FBLN1_ENST00000442170.2_Missense_Mutation_p.K570N	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1						embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.K570N(2)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		AGAAATCCAAGAAGGGAAGGC	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	22											90	81	84					22																	45960776		2203	4300	6503	44339440	SO:0001627	intron_variant	2192				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1698-9615G>T	22.37:g.45960776G>T			44339440	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	2.602	-0.292663	0.05568	.	.	ENSG00000077942	ENST00000348697;ENST00000442170	D;D	0.83250	-1.63;-1.7	0.889	-0.249	0.13011	.	.	.	.	.	T	0.69205	0.3085	L	0.39397	1.21	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.49606	-0.8922	9	0.16896	T	0.51	.	3.2644	0.06860	0.3207:0.0:0.6793:0.0	.	570	B1AHL4	.	N	570	ENSP00000262723:K570N;ENSP00000393812:K570N	ENSP00000262723:K570N	K	+	3	2	FBLN1	44339440	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	1.214000	0.32419	-0.061000	0.13110	-0.373000	0.07131	AAG		0.527	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45960776	G	T	45960776	1	4	61	0	1	0	0	0	0	0	0	0	5717	933	33	2		2	FBLN1	22	45960776	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	23582	45960776	5343790	11969	19954										
PPARA	5465	broad.mit.edu	37	chr22	46628102	46628102	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaactggatgacagtgatatCtccctttttgtggctgctat	10	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46628102C>A	ENST00000396000.2	+	7	1390	c.1125C>A	c.(1123-1125)atC>atA	p.I375I	PPARA_ENST00000402126.1_Silent_p.I375I|PPARA_ENST00000262735.5_Silent_p.I375I|PPARA_ENST00000434345.2_3'UTR|PPARA_ENST00000407236.1_Silent_p.I375I			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	375	Ligand-binding.|Required for heterodimerization with RXRA.				behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.I375I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	ACAGTGATATCTCCCTTTTTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	22											226	204	212					22																	46628102		2203	4300	6503	45006766	SO:0001819	synonymous_variant	5465			L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"Nuclear hormone receptors"	9232	protein-coding gene	gene with protein product		170998	"peroxisome proliferative activated receptor, alpha"	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.1125C>A	22.37:g.46628102C>A			45006766	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Silent	SNP	ENST00000396000.2	37	CCDS33669.1																																																																																				0.413	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928		A	46628102	C	A	46628102	2	1	61	1	0	0	0	0	0	0	0	1	12328	903	32	2		2	PPARA	22	46628102	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	667326	46628102	4676464	11970	19955										
PKDREJ	10343	broad.mit.edu	37	chr22	46653093	46653093	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatgtgatctacctgagaaaCtgcatgaaagggaatgaagt	11	5	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46653093C>A	ENST00000253255.5	-	1	6126	c.6127G>T	c.(6127-6129)Gtt>Ttt	p.V2043F		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2043					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.V2043F(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACCTGAGAAACTGCATGAAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	22											85	87	86					22																	46653093		2203	4300	6503	45031757	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6127G>T	22.37:g.46653093C>A	ENSP00000253255:p.Val2043Phe		45031757	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.473460	0.43942	.	.	ENSG00000130943	ENST00000253255	T	0.73575	-0.76	5.81	2.19	0.27852	Polycystin cation channel, PKD1/PKD2 (1);	0.218239	0.31507	N	0.007533	T	0.81730	0.4884	M	0.67953	2.075	0.09310	N	1	D	0.64830	0.994	D	0.70935	0.971	T	0.71520	-0.4568	10	0.72032	D	0.01	-20.5036	9.8069	0.40799	0.0:0.7412:0.0:0.2588	.	2043	Q9NTG1	PKDRE_HUMAN	F	2043	ENSP00000253255:V2043F	ENSP00000253255:V2043F	V	-	1	0	PKDREJ	45031757	0.178000	0.23122	0.019000	0.16419	0.608000	0.37181	0.409000	0.21082	0.822000	0.34565	0.508000	0.49915	GTT		0.408	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46653093	C	A	46653093	3	1	61	1	0	0	0	0	1	0	0	0	12001	565	20	2	638	2	PKDREJ	22	46653093	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	24991	46653093	4651473	11971	19956										
PKDREJ	10343	broad.mit.edu	37	chr22	46653325	46653325	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatggccacatacaagtaGatttctgctgaagcttttct	8	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46653325G>T	ENST00000253255.5	-	1	5894	c.5895C>A	c.(5893-5895)atC>atA	p.I1965I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1965					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.I1965I(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CATACAAGTAGATTTCTGCTG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	22											54	57	56					22																	46653325		2200	4300	6500	45031989	SO:0001819	synonymous_variant	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5895C>A	22.37:g.46653325G>T			45031989	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																				0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46653325	G	T	46653325	2	4	61	1	0	0	0	0	0	0	0	1	12001	932	33	2		2	PKDREJ	22	46653325	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	232	46653325	4651241	11972	19957										
PKDREJ	10343	broad.mit.edu	37	chr22	46653409	46653409	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgacaactcctaactgagaGacttcaaatatgaccgaaat	6	9	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46653409G>T	ENST00000253255.5	-	1	5810	c.5811C>A	c.(5809-5811)gtC>gtA	p.V1937V		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1937					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.V1937V(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CTAACTGAGAGACTTCAAATA	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	22											79	83	82					22																	46653409		2203	4300	6503	45032073	SO:0001819	synonymous_variant	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5811C>A	22.37:g.46653409G>T			45032073	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																				0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46653409	G	T	46653409	2	4	61	1	0	0	0	0	0	0	0	1	12001	929	33	2		2	PKDREJ	22	46653409	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	84	46653409	4651157	11973	19958										
PKDREJ	10343	broad.mit.edu	37	chr22	46654832	46654832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagaggatgcttttgaggaGatacctcctttagatccgct	10	8	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46654832G>T	ENST00000253255.5	-	1	4387	c.4388C>A	c.(4387-4389)tCt>tAt	p.S1463Y		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1463					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.S1463Y(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CTTTTGAGGAGATACCTCCTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	22											107	100	103					22																	46654832		2203	4300	6503	45033496	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4388C>A	22.37:g.46654832G>T	ENSP00000253255:p.Ser1463Tyr		45033496	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751894	0.49362	.	.	ENSG00000130943	ENST00000253255	T	0.37411	1.2	4.84	3.82	0.43975	.	0.993298	0.08162	N	0.988314	T	0.35970	0.0950	L	0.50333	1.59	0.09310	N	1	P	0.46277	0.875	B	0.41510	0.359	T	0.15037	-1.0451	10	0.36615	T	0.2	-2.61	11.0976	0.48155	0.0867:0.0:0.9133:0.0	.	1463	Q9NTG1	PKDRE_HUMAN	Y	1463	ENSP00000253255:S1463Y	ENSP00000253255:S1463Y	S	-	2	0	PKDREJ	45033496	0.000000	0.05858	0.005000	0.12908	0.180000	0.23129	0.332000	0.19751	1.170000	0.42753	0.561000	0.74099	TCT		0.428	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46654832	G	T	46654832	3	4	61	1	0	0	0	0	1	0	0	0	12001	942	33	2	2377	2	PKDREJ	22	46654832	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1423	46654832	4649734	11974	19959										
PKDREJ	10343	broad.mit.edu	37	chr22	46655124	46655124	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccacatgtggtttttccggaGattactactcacatctataa	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46655124G>T	ENST00000253255.5	-	1	4095	c.4096C>A	c.(4096-4098)Ctc>Atc	p.L1366I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1366					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.L1366I(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TTTTTCCGGAGATTACTACTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	22											65	68	67					22																	46655124		2203	4300	6503	45033788	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4096C>A	22.37:g.46655124G>T	ENSP00000253255:p.Leu1366Ile		45033788	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774187	0.49786	.	.	ENSG00000130943	ENST00000253255	T	0.48522	0.81	5.09	0.385	0.16249	.	0.147317	0.31450	N	0.007639	T	0.55194	0.1905	M	0.62209	1.925	0.09310	N	1	D	0.76494	0.999	D	0.63113	0.911	T	0.45991	-0.9223	10	0.62326	D	0.03	-12.0809	6.131	0.20204	0.2176:0.0:0.6515:0.1309	.	1366	Q9NTG1	PKDRE_HUMAN	I	1366	ENSP00000253255:L1366I	ENSP00000253255:L1366I	L	-	1	0	PKDREJ	45033788	0.645000	0.27286	0.000000	0.03702	0.007000	0.05969	0.966000	0.29331	-0.012000	0.14223	0.511000	0.50034	CTC		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46655124	G	T	46655124	3	4	61	1	0	0	0	0	1	0	0	0	12001	942	33	2	2669	2	PKDREJ	22	46655124	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	292	46655124	4649442	11975	19960										
PKDREJ	10343	broad.mit.edu	37	chr22	46655967	46655967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attgagcttcatgacaaaacGaggtgcctgcagaactatgg	11	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46655967G>A	ENST00000253255.5	-	1	3252	c.3253C>T	c.(3253-3255)Cgt>Tgt	p.R1085C		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1085					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.R1085C(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ATGACAAAACGAGGTGCCTGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	22											62	56	58					22																	46655967		2203	4300	6503	45034631	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.3253C>T	22.37:g.46655967G>A	ENSP00000253255:p.Arg1085Cys		45034631	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.138986	0.21123	.	.	ENSG00000130943	ENST00000253255	T	0.37411	1.2	5.2	1.79	0.24919	.	0.740118	0.12898	N	0.430054	T	0.33673	0.0871	M	0.61703	1.905	0.09310	N	1	D	0.61697	0.99	B	0.43809	0.432	T	0.15838	-1.0423	10	0.38643	T	0.18	-2.0166	6.6372	0.22889	0.1176:0.0:0.5874:0.295	.	1085	Q9NTG1	PKDRE_HUMAN	C	1085	ENSP00000253255:R1085C	ENSP00000253255:R1085C	R	-	1	0	PKDREJ	45034631	0.003000	0.15002	0.001000	0.08648	0.023000	0.10783	1.249000	0.32839	0.660000	0.30964	-0.538000	0.04264	CGT		0.502	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46655967	G	A	46655967	3	1	61	1	0	0	0	0	1	0	0	0	12001	1058	37	1	3512	1	PKDREJ	22	46655967	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	843	46655967	4648599	11976	19961										
PKDREJ	10343	broad.mit.edu	37	chr22	46656825	46656825	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatttctatttgttcagatcGaaagcgtttatctttttgct	7	6	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46656825G>A	ENST00000253255.5	-	1	2394	c.2395C>T	c.(2395-2397)Cga>Tga	p.R799*		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	799	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.R799*(2)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TGTTCAGATCGAAAGCGTTTA	0.388																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											71	75	74					22																	46656825		2203	4300	6503	45035489	SO:0001587	stop_gained	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2395C>T	22.37:g.46656825G>A	ENSP00000253255:p.Arg799*		45035489	B1AJY3|O95850	Nonsense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	36	5.763605	0.96906	.	.	ENSG00000130943	ENST00000253255	.	.	.	5.31	-0.988	0.10245	.	1.194380	0.05773	N	0.607068	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-1.171	1.5651	0.02602	0.1676:0.1274:0.2767:0.4283	.	.	.	.	X	799	.	ENSP00000253255:R799X	R	-	1	2	PKDREJ	45035489	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.072000	0.11486	-0.246000	0.09611	-0.274000	0.10170	CGA		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46656825	G	A	46656825	4	1	61	1	0	0	0	0	0	1	0	0	12001	1066	37	1	4370	1	PKDREJ	22	46656825	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	858	46656825	4647741	11977	19962										
TTC38	55020	broad.mit.edu	37	chr22	46671279	46671279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgagagattctgttgctcGaatttaccccttctggacac	9	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46671279G>A	ENST00000381031.3	+	5	576	c.500G>A	c.(499-501)cGa>cAa	p.R167Q	TTC38_ENST00000445282.2_Intron	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	167						extracellular vesicular exosome (GO:0070062)		p.R167Q(1)		endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						TCTGTTGCTCGAATTTACCCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	22											114	112	113					22																	46671279		1882	4102	5984	45049943	SO:0001583	missense	55020				CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.500G>A	22.37:g.46671279G>A	ENSP00000370419:p.Arg167Gln		45049943	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	34	5.311838	0.95655	.	.	ENSG00000075234	ENST00000381031;ENST00000421359	T	0.44083	0.93	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.83953	2.67	0.80722	D	1	D	0.56035	0.974	P	0.49683	0.619	T	0.63576	-0.6606	9	.	.	.	-10.2422	18.8363	0.92164	0.0:0.0:1.0:0.0	.	167	Q5R3I4	TTC38_HUMAN	Q	167	ENSP00000370419:R167Q	.	R	+	2	0	TTC38	45049943	1.000000	0.71417	0.962000	0.40283	0.978000	0.69477	9.189000	0.94928	2.705000	0.92388	0.650000	0.86243	CGA		0.443	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		A	46671279	G	A	46671279	3	1	61	1	0	0	0	0	1	0	0	0	16746	1058	37	1	518	1	TTC38	22	46671279	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	14454	46671279	4633287	11978	19963										
GTSE1	51512	broad.mit.edu	37	chr22	46712304	46712304	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttaaaattcctaagttttCtattggtgagtaatagatac	6	4	1	2	rs563396011		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46712304C>A	ENST00000454366.1	+	7	1639	c.1427C>A	c.(1426-1428)tCt>tAt	p.S476Y		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	457					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)		p.S457Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CCTAAGTTTTCTATTGGTGAG	0.294																																					GBM(153;542 1915 12487 29016 50495)											1	Substitution - Missense(1)	large_intestine(1)	22											76	83	81					22																	46712304		1955	4186	6141	45090968	SO:0001583	missense	51512			AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1427C>A	22.37:g.46712304C>A	ENSP00000415430:p.Ser476Tyr		45090968	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	C	11.92	1.783530	0.31593	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.08634	3.07	4.96	2.71	0.32032	.	0.497643	0.21782	N	0.069193	T	0.21468	0.0517	M	0.64997	1.995	0.09310	N	1	D;P	0.57257	0.979;0.946	P;P	0.56960	0.81;0.74	T	0.06770	-1.0808	10	0.72032	D	0.01	-10.2378	16.3893	0.83528	0.0:0.7501:0.2499:0.0	.	457;436	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	Y	476;436	ENSP00000415430:S476Y	ENSP00000354634:S436Y	S	+	2	0	GTSE1	45090968	0.013000	0.17824	0.068000	0.19968	0.445000	0.32107	1.043000	0.30316	0.608000	0.30000	-0.810000	0.03169	TCT		0.294	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		A	46712304	C	A	46712304	3	1	61	1	0	0	0	0	1	0	0	0	6906	913	32	2	1449	2	GTSE1	22	46712304	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	41025	46712304	4592262	11979	19964										
GTSE1	51512	broad.mit.edu	37	chr22	46722482	46722482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccccaaaacgatgcccagggCcgtgggctctcccctgtgtg	12	16	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:46722482C>T	ENST00000454366.1	+	9	1867	c.1655C>T	c.(1654-1656)gCc>gTc	p.A552V		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	533					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)		p.A533V(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		ATGCCCAGGGCCGTGGGCTCT	0.612																																					GBM(153;542 1915 12487 29016 50495)											1	Substitution - Missense(1)	large_intestine(1)	22											55	51	52					22																	46722482		2203	4300	6503	45101146	SO:0001583	missense	51512			AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1655C>T	22.37:g.46722482C>T	ENSP00000415430:p.Ala552Val		45101146	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987528	0.35036	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07688	3.17	3.84	2.83	0.33086	.	1.239290	0.05284	N	0.519847	T	0.19485	0.0468	M	0.62723	1.935	0.09310	N	1	P;P	0.52061	0.793;0.95	B;P	0.52066	0.272;0.689	T	0.18209	-1.0344	10	0.59425	D	0.04	-3.7404	9.4031	0.38444	0.0:0.8955:0.0:0.1045	.	533;512	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	V	552;512	ENSP00000415430:A552V	ENSP00000354634:A512V	A	+	2	0	GTSE1	45101146	0.003000	0.15002	0.016000	0.15963	0.029000	0.11900	1.352000	0.34033	1.211000	0.43351	0.491000	0.48974	GCC		0.612	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		T	46722482	C	T	46722482	3	4	61	1	0	0	0	0	1	0	0	0	6906	739	26	3	1685	3	GTSE1	22	46722482	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10178	46722482	4582084	11980	19965										
GRAMD4	23151	broad.mit.edu	37	chr22	47022795	47022795	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctcggacaccgaatgcagCgacgaaatccccctgaaggt	11	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:47022795C>T	ENST00000406902.1	+	2	312	c.99C>T	c.(97-99)agC>agT	p.S33S	GRAMD4_ENST00000490378.1_3'UTR|GRAMD4_ENST00000361034.3_Silent_p.S33S			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4	33					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.S33S(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		CCGAATGCAGCGACGAAATCC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	22											141	114	123					22																	47022795		2203	4300	6503	45401459	SO:0001819	synonymous_variant	23151				CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240			29113	protein-coding gene	gene with protein product	"death-inducing-protein"	613691				15565177	Standard	NM_015124		Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.99C>T	22.37:g.47022795C>T			45401459	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	Silent	SNP	ENST00000406902.1	37	CCDS33672.1																																																																																				0.597	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317969.1	NM_015124		T	47022795	C	T	47022795	2	4	61	1	0	0	0	0	0	0	0	1	6773	767	27	1		1	GRAMD4	22	47022795	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	300313	47022795	4281771	11981	19966										
ZBED4	9889	broad.mit.edu	37	chr22	50277400	50277400	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagaagaggaagatgatgaTggaattcctcctgatagttt	11	4	0	6			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50277400T>C	ENST00000216268.5	+	2	567	c.90T>C	c.(88-90)gaT>gaC	p.D30D		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	30	Asp/Glu-rich (acidic).					cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D30D(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		AAGATGATGATGGAATTCCTC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	22											62	73	70					22																	50277400		2203	4300	6503	48663404	SO:0001819	synonymous_variant	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.90T>C	22.37:g.50277400T>C			48663404	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																				0.443	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		C	50277400	T	C	50277400	2	2	61	1	0	0	0	0	0	0	0	1	17559	1461	51	4		4	ZBED4	22	50277400	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3254605	50277400	1027166	11982	19967										
MOV10L1	54456	broad.mit.edu	37	chr22	50547128	50547128	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaggaacggggtgttagagGaaagcatcttctttaccttg	13	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50547128G>T	ENST00000262794.5	+	5	681	c.598G>T	c.(598-600)Gaa>Taa	p.E200*	MOV10L1_ENST00000545383.1_Nonsense_Mutation_p.E200*|MOV10L1_ENST00000540615.1_Nonsense_Mutation_p.E180*|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Nonsense_Mutation_p.E200*	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	200					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E200*(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GGTGTTAGAGGAAAGCATCTT	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											139	121	127					22																	50547128		2203	4300	6503	48889255	SO:0001587	stop_gained	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.598G>T	22.37:g.50547128G>T	ENSP00000262794:p.Glu200*		48889255	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Nonsense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	g	23.6	4.438069	0.83885	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	.	.	.	5.28	3.2	0.36748	.	0.096709	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-31.6342	10.6893	0.45862	0.1572:0.0:0.8428:0.0	.	.	.	.	X	200;200;200;180	.	ENSP00000262794:E200X	E	+	1	0	MOV10L1	48889255	1.000000	0.71417	0.006000	0.13384	0.343000	0.28985	8.799000	0.91895	0.637000	0.30526	0.627000	0.83407	GAA		0.567	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50547128	G	T	50547128	4	4	61	1	0	0	0	0	0	1	0	0	9749	1175	41	2	657	2	MOV10L1	22	50547128	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	269728	50547128	757438	11983	19968										
MOV10L1	54456	broad.mit.edu	37	chr22	50555698	50555698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtcactaattgctgcgcgcGaaccattttcttggaaaaag	9	9	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50555698G>A	ENST00000262794.5	+	9	1455	c.1372G>A	c.(1372-1374)Gaa>Aaa	p.E458K	MOV10L1_ENST00000545383.1_Missense_Mutation_p.E458K|MOV10L1_ENST00000540615.1_Missense_Mutation_p.E438K|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.E458K	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	458					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E458K(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGCTGCGCGCGAACCATTTTC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	22											80	76	77					22																	50555698		2203	4300	6503	48897825	SO:0001583	missense	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1372G>A	22.37:g.50555698G>A	ENSP00000262794:p.Glu458Lys		48897825	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.637019	0.47049	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.85773	-1.84;-1.84;-1.43;-2.03	5.76	5.76	0.90799	.	0.237801	0.43260	D	0.000585	D	0.82861	0.5129	L	0.41961	1.31	0.80722	D	1	D;P;P;P	0.58268	0.982;0.951;0.918;0.918	P;B;B;B	0.45881	0.496;0.348;0.189;0.3	T	0.79495	-0.1780	10	0.16420	T	0.52	-29.9369	18.7444	0.91787	0.0:0.0:1.0:0.0	.	219;438;458;458	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	K	458;458;458;438	ENSP00000438978:E458K;ENSP00000262794:E458K;ENSP00000379199:E458K;ENSP00000438542:E438K	ENSP00000262794:E458K	E	+	1	0	MOV10L1	48897825	0.426000	0.25506	0.468000	0.27192	0.010000	0.07245	2.329000	0.43876	2.716000	0.92895	0.650000	0.86243	GAA		0.423	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		A	50555698	G	A	50555698	3	1	61	1	0	0	0	0	1	0	0	0	9749	1059	37	1	1447	1	MOV10L1	22	50555698	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8570	50555698	748868	11984	19969										
MOV10L1	54456	broad.mit.edu	37	chr22	50563956	50563956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggggatctgctggttctgGaggtcccagggttggccgaa	17	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50563956G>A	ENST00000262794.5	+	11	1788	c.1705G>A	c.(1705-1707)Gag>Aag	p.E569K	MOV10L1_ENST00000545383.1_Missense_Mutation_p.E569K|MOV10L1_ENST00000540615.1_Missense_Mutation_p.E549K|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.E569K	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	569					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E569K(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GCTGGTTCTGGAGGTCCCAGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	22											135	135	135					22																	50563956		2203	4300	6503	48906083	SO:0001583	missense	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1705G>A	22.37:g.50563956G>A	ENSP00000262794:p.Glu569Lys		48906083	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185144	0.78677	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.86432	-1.93;-1.93;-1.52;-2.12	5.41	5.41	0.78517	.	0.045500	0.85682	D	0.000000	D	0.92254	0.7543	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.982;0.993	D;D;P;P	0.79108	0.992;0.988;0.817;0.878	D	0.90661	0.4590	10	0.34782	T	0.22	-43.2942	18.3108	0.90199	0.0:0.0:1.0:0.0	.	330;549;569;569	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	K	569;569;569;549	ENSP00000438978:E569K;ENSP00000262794:E569K;ENSP00000379199:E569K;ENSP00000438542:E549K	ENSP00000262794:E569K	E	+	1	0	MOV10L1	48906083	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	7.303000	0.78871	2.679000	0.91253	0.544000	0.68410	GAG		0.488	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		A	50563956	G	A	50563956	3	1	61	1	0	0	0	0	1	0	0	0	9749	1175	41	3	1788	3	MOV10L1	22	50563956	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8258	50563956	740610	11985	19970										
MOV10L1	54456	broad.mit.edu	37	chr22	50564678	50564678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtacaatggacatgccatcGaatacatcagctacgtgact	8	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50564678G>A	ENST00000262794.5	+	12	1878	c.1795G>A	c.(1795-1797)Gaa>Aaa	p.E599K	MOV10L1_ENST00000545383.1_Missense_Mutation_p.E599K|MOV10L1_ENST00000540615.1_Missense_Mutation_p.E579K|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.E599K	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	599					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E599K(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		ACATGCCATCGAATACATCAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	22											123	102	109					22																	50564678		2203	4300	6503	48906805	SO:0001583	missense	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1795G>A	22.37:g.50564678G>A	ENSP00000262794:p.Glu599Lys		48906805	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690276	0.68271	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.85629	-1.82;-1.82;-1.41;-2.01	5.46	5.46	0.80206	.	0.098399	0.64402	D	0.000002	D	0.87083	0.6089	L	0.58669	1.825	0.80722	D	1	D;D;D;D	0.71674	0.998;0.994;0.98;0.98	P;P;B;B	0.56788	0.806;0.64;0.436;0.436	D	0.83584	0.0119	10	0.17369	T	0.5	-39.1041	12.5473	0.56208	0.0:0.1675:0.8325:0.0	.	360;579;599;599	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	K	599;599;599;579	ENSP00000438978:E599K;ENSP00000262794:E599K;ENSP00000379199:E599K;ENSP00000438542:E579K	ENSP00000262794:E599K	E	+	1	0	MOV10L1	48906805	1.000000	0.71417	0.890000	0.34922	0.929000	0.56500	4.187000	0.58344	2.542000	0.85734	0.655000	0.94253	GAA		0.383	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		A	50564678	G	A	50564678	3	1	61	1	0	0	0	0	1	0	0	0	9749	1059	37	1	1882	1	MOV10L1	22	50564678	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	722	50564678	739888	11986	19971										
MOV10L1	54456	broad.mit.edu	37	chr22	50572485	50572485	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgaacacgtcatccacttaGgtgtaaaaggtattactttt	7	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50572485G>T	ENST00000262794.5	+	14	2043	c.1960G>T	c.(1960-1962)Ggt>Tgt	p.G654C	MOV10L1_ENST00000545383.1_Missense_Mutation_p.G654C|MOV10L1_ENST00000540615.1_Missense_Mutation_p.G634C|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.G654C	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	654					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.G654C(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CATCCACTTAGGTGTAAAAGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	22											105	94	98					22																	50572485		2203	4300	6503	48914612	SO:0001583	missense	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1960G>T	22.37:g.50572485G>T	ENSP00000262794:p.Gly654Cys		48914612	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.883209	0.72410	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.87809	-2.12;-2.12;-1.71;-2.3	5.78	5.78	0.91487	.	0.276964	0.42821	D	0.000642	D	0.94255	0.8155	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;0.998	D	0.94319	0.7552	10	0.72032	D	0.01	-31.6025	19.6307	0.95700	0.0:0.0:1.0:0.0	.	415;634;654;654	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	C	654;654;654;634	ENSP00000438978:G654C;ENSP00000262794:G654C;ENSP00000379199:G654C;ENSP00000438542:G634C	ENSP00000262794:G654C	G	+	1	0	MOV10L1	48914612	1.000000	0.71417	0.328000	0.25416	0.955000	0.61496	5.084000	0.64462	2.730000	0.93505	0.655000	0.94253	GGT		0.338	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50572485	G	T	50572485	3	4	61	1	0	0	0	0	1	0	0	0	9749	1000	35	2	2055	2	MOV10L1	22	50572485	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7807	50572485	732081	11987	19972										
MOV10L1	54456	broad.mit.edu	37	chr22	50589166	50589166	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgggccctctgtgtgcagatCgtgctggcaggagaccccat	14	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50589166C>T	ENST00000262794.5	+	21	2813	c.2730C>T	c.(2728-2730)atC>atT	p.I910I	MOV10L1_ENST00000354853.2_Intron|MOV10L1_ENST00000545383.1_Silent_p.I910I|MOV10L1_ENST00000540615.1_Silent_p.I890I|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000395852.1_Silent_p.I37I|MOV10L1_ENST00000395858.3_Silent_p.I910I	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	910					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.I910I(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GTGTGCAGATCGTGCTGGCAG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	22											103	74	84					22																	50589166		2202	4300	6502	48931293	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2730C>T	22.37:g.50589166C>T			48931293	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.622	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50589166	C	T	50589166	2	4	61	1	0	0	0	0	0	0	0	1	9749	874	31	1		1	MOV10L1	22	50589166	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16681	50589166	715400	11988	19973										
TUBGCP6	85378	broad.mit.edu	37	chr22	50682563	50682563	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaccaggaggtccaaaacaGaccccacctccaaaagcgga	9	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50682563G>T	ENST00000248846.5	-	1	430	c.326C>A	c.(325-327)tCt>tAt	p.S109Y	HDAC10_ENST00000498366.1_5'Flank|TUBGCP6_ENST00000439308.2_Missense_Mutation_p.S109Y|MAPK12_ENST00000497036.1_5'Flank			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	109					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.S109Y(1)		breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		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)		GTCCAAAACAGACCCCACCTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	22											71	70	71					22																	50682563		2202	4300	6502	49024690	SO:0001583	missense	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.326C>A	22.37:g.50682563G>T	ENSP00000248846:p.Ser109Tyr		49024690	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874884	0.72180	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.16073	2.78;2.37	3.97	3.97	0.46021	.	0.542047	0.18440	N	0.141178	T	0.22859	0.0552	N	0.24115	0.695	0.09310	N	1	D;D;D	0.63880	0.993;0.981;0.981	P;P;P	0.55161	0.77;0.656;0.744	T	0.07654	-1.0761	10	0.72032	D	0.01	.	16.1987	0.82053	0.0:0.0:1.0:0.0	.	109;109;109	A7E2V7;B2RWN4;Q96RT7	.;.;GCP6_HUMAN	Y	109	ENSP00000248846:S109Y;ENSP00000397387:S109Y	ENSP00000248846:S109Y	S	-	2	0	TUBGCP6	49024690	0.957000	0.32711	0.004000	0.12327	0.995000	0.86356	5.772000	0.68889	2.212000	0.71576	0.561000	0.74099	TCT		0.582	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		T	50682563	G	T	50682563	3	4	61	1	0	0	0	0	1	0	0	0	16810	942	33	2	5233	2	TUBGCP6	22	50682563	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	93397	50682563	622003	11989	19974										
SBF1	6305	broad.mit.edu	37	chr22	50900671	50900671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttgctggcgctctccaggtCgcccagcccggcacgctccc	12	19	1	0	rs371155431		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chr22:50900671C>T	ENST00000390679.3	-	19	2543	c.2359G>A	c.(2359-2361)Gac>Aac	p.D787N	SBF1_ENST00000348911.6_Missense_Mutation_p.D788N|SBF1_ENST00000380817.3_Missense_Mutation_p.D787N			O95248	MTMR5_HUMAN	SET binding factor 1	787					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.D787N(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-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)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		CTCTCCAGGTCGCCCAGCCCG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	22						C	ASN/ASP	1,4179		0,1,2089	42	46	45		2359	4.5	1	22		45	0,8408		0,0,4204	no	missense	SBF1	NM_002972.2	23	0,1,6293	TT,TC,CC		0.0,0.0239,0.0079	probably-damaging	787/1894	50900671	1,12587	2090	4204	6294	49247537	SO:0001583	missense	6305			U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.2359G>A	22.37:g.50900671C>T	ENSP00000375097:p.Asp787Asn		49247537	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	20.8	4.056987	0.76074	2.39E-4	0.0	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	D;D;D	0.90444	-2.67;-2.65;-2.66	4.52	4.52	0.55395	.	0.192361	0.42964	D	0.000624	D	0.91590	0.7343	M	0.68952	2.095	0.80722	D	1	D;D;D	0.56287	0.975;0.969;0.958	P;B;B	0.48677	0.586;0.435;0.408	D	0.92023	0.5627	10	0.48119	T	0.1	.	17.0388	0.86483	0.0:1.0:0.0:0.0	.	787;788;787	O95248;G5E933;O95248-4	MTMR5_HUMAN;.;.	N	787;788;798;797;787	ENSP00000370196:D787N;ENSP00000252027:D788N;ENSP00000375097:D787N	ENSP00000336522:D797N	D	-	1	0	SBF1	49247537	1.000000	0.71417	0.978000	0.43139	0.832000	0.47134	7.403000	0.79983	2.366000	0.80165	0.655000	0.94253	GAC		0.687	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50900671	C	T	50900671	3	4	61	1	0	0	0	0	1	0	0	0	13895	884	31	1	3414	1	SBF1	22	50900671	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	218108	50900671	403895	11990	19975										
CSF2RA	1438	broad.mit.edu	37	chrX	1401670	1401670	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcctgatcccagagaaatCgggtaagtatggaaacctgg	11	10	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1401670C>T	ENST00000381524.3	+	3	260	c.74C>T	c.(73-75)tCg>tTg	p.S25L	CSF2RA_ENST00000381509.3_Missense_Mutation_p.S25L|CSF2RA_ENST00000417535.2_Missense_Mutation_p.S25L|CSF2RA_ENST00000494969.2_Missense_Mutation_p.S25L|CSF2RA_ENST00000355432.3_Missense_Mutation_p.S25L|CSF2RA_ENST00000432318.2_Missense_Mutation_p.S25L|CSF2RA_ENST00000361536.3_Missense_Mutation_p.S25L|CSF2RA_ENST00000355805.2_Missense_Mutation_p.S25L|CSF2RA_ENST00000381500.1_Missense_Mutation_p.S25L|CSF2RA_ENST00000501036.2_5'UTR|CSF2RA_ENST00000381529.3_Missense_Mutation_p.S25L			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	25					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.S25L(2)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	CCAGAGAAATCGGGTAAGTAT	0.532																																					Esophageal Squamous(131;723 1707 25334 40494 41806)											2	Substitution - Missense(2)	large_intestine(2)	X											238	239	239					X																	1401670		2203	4296	6499	1361670	SO:0001583	missense	1438			M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.74C>T	X.37:g.1401670C>T	ENSP00000370935:p.Ser25Leu		1361670	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	0.150	-1.092816	0.01858	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;D;D;T;T;D;T;T;D;D	0.94184	-3.08;-3.08;-3.37;-3.08;0.87;1.86;-3.14;0.85;1.11;-2.93;-3.37	1.21	-2.42	0.06542	.	.	.	.	.	D	0.84853	0.5564	.	.	.	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.65841	-0.6070	8	0.42905	T	0.14	.	0.1616	0.00104	0.3587:0.2211:0.2031:0.2171	.	25;25;25;25;25;25	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	L	25	ENSP00000370940:S25L;ENSP00000416437:S25L;ENSP00000354836:S25L;ENSP00000370935:S25L;ENSP00000410667:S25L;ENSP00000397452:S25L;ENSP00000370920:S25L;ENSP00000348058:S25L;ENSP00000347606:S25L;ENSP00000394227:S25L;ENSP00000370911:S25L	ENSP00000347606:S25L	S	+	2	0	CSF2RA	1361670	0.035000	0.19736	0.000000	0.03702	0.002000	0.02628	-0.475000	0.06599	-2.065000	0.00887	-0.630000	0.03990	TCG		0.532	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			T	1401670	C	T	1401670	3	4	61	1	0	0	0	0	1	0	0	0	3940	893	31	1	76	1	CSF2RA	23	1401670	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09		1401670	153868890	11991	19976										
CSF2RA	1438	broad.mit.edu	37	chrX	1407442	1407442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acgaatgttcgtgcacatttCgtgaaatttgtctgcatgaa	9	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1407442C>T	ENST00000381524.3	+	5	436	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	CSF2RA_ENST00000381509.3_Missense_Mutation_p.R84C|CSF2RA_ENST00000417535.2_Missense_Mutation_p.R84C|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355432.3_Missense_Mutation_p.R84C|CSF2RA_ENST00000432318.2_Missense_Mutation_p.R84C|CSF2RA_ENST00000361536.3_Missense_Mutation_p.R84C|CSF2RA_ENST00000355805.2_Missense_Mutation_p.R84C|CSF2RA_ENST00000381500.1_Missense_Mutation_p.R84C|CSF2RA_ENST00000501036.2_5'UTR|CSF2RA_ENST00000381529.3_Missense_Mutation_p.R84C			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	84					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.R84C(3)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	GTGCACATTTCGTGAAATTTG	0.428																																					Esophageal Squamous(131;723 1707 25334 40494 41806)											3	Substitution - Missense(3)	large_intestine(2)|skin(1)	X											365	335	345					X																	1407442		2203	4296	6499	1367442	SO:0001583	missense	1438			M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.250C>T	X.37:g.1407442C>T	ENSP00000370935:p.Arg84Cys		1367442	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	3.337	-0.135522	0.06711	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;D;D;T;T;D;T;T;D;D	0.94092	-3.11;-3.11;-3.35;-3.11;0.88;1.87;-3.13;0.86;1.17;-2.92;-3.35	0.912	-0.229	0.13094	.	14.760800	0.01967	U	0.043797	D	0.88633	0.6489	.	.	.	0.09310	N	0.999995	B;B;B;B;B;B	0.14438	0.01;0.005;0.002;0.002;0.002;0.0	B;B;B;B;B;B	0.08055	0.003;0.001;0.001;0.001;0.001;0.0	T	0.75213	-0.3397	9	0.66056	D	0.02	.	4.3815	0.11297	0.0:0.5726:0.4274:0.0	.	84;84;84;84;84;84	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	C	84	ENSP00000370940:R84C;ENSP00000416437:R84C;ENSP00000354836:R84C;ENSP00000370935:R84C;ENSP00000410667:R84C;ENSP00000397452:R84C;ENSP00000370920:R84C;ENSP00000348058:R84C;ENSP00000347606:R84C;ENSP00000394227:R84C;ENSP00000370911:R84C	ENSP00000347606:R84C	R	+	1	0	CSF2RA	1367442	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-2.265000	0.01172	-0.099000	0.12263	0.358000	0.22013	CGT		0.428	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			T	1407442	C	T	1407442	3	4	61	1	0	0	0	0	1	0	0	0	3940	884	31	1	260	1	CSF2RA	23	1407442	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5772	1407442	153863118	11992	19977										
CSF2RA	1438	broad.mit.edu	37	chrX	1428338	1428338	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggaagggaaaggctaccGcgaagaggtcttgaccgtga	16	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1428338G>A	ENST00000381524.3	+	13	1355	c.1169G>A	c.(1168-1170)cGc>cAc	p.R390H	CSF2RA_ENST00000417535.2_Missense_Mutation_p.R424H|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355432.3_Silent_p.P330P|CSF2RA_ENST00000432318.2_Missense_Mutation_p.R390H|CSF2RA_ENST00000498153.1_3'UTR|CSF2RA_ENST00000361536.3_3'UTR|CSF2RA_ENST00000355805.2_3'UTR|CSF2RA_ENST00000381500.1_3'UTR|CSF2RA_ENST00000501036.2_Missense_Mutation_p.R257H|CSF2RA_ENST00000381529.3_Missense_Mutation_p.R390H			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	390					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.P330P(1)|p.R390H(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	AAAGGCTACCGCGAAGAGGTC	0.547																																					Esophageal Squamous(131;723 1707 25334 40494 41806)											2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	X											198	186	190					X																	1428338		2203	4296	6499	1388338	SO:0001583	missense	1438			M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.1169G>A	X.37:g.1428338G>A	ENSP00000370935:p.Arg390His		1388338	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	4.342	0.062993	0.08388	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000501036;ENST00000381524;ENST00000417535	D;D;D;D;D	0.93859	-3.03;-3.03;-3.3;-3.03;-2.89	0.69	-0.885	0.10593	.	.	.	.	.	T	0.81259	0.4785	.	.	.	0.09310	N	1	B;B	0.31459	0.324;0.14	B;B	0.15484	0.013;0.009	T	0.68930	-0.5279	7	0.15066	T	0.55	.	.	.	.	.	424;390	A7J003;P15509	.;CSF2R_HUMAN	H	390;390;257;390;424	ENSP00000370940:R390H;ENSP00000416437:R390H;ENSP00000440491:R257H;ENSP00000370935:R390H;ENSP00000394227:R424H	ENSP00000370935:R390H	R	+	2	0	CSF2RA	1388338	0.001000	0.12720	0.000000	0.03702	0.068000	0.16541	0.125000	0.15749	-0.255000	0.09486	0.110000	0.15639	CGC		0.547	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			A	1428338	G	A	1428338	3	1	61	1	0	0	0	0	1	0	0	0	3940	1087	38	1	1429	1	CSF2RA	23	1428338	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20896	1428338	153842222	11993	19978										
IL3RA	3563	broad.mit.edu	37	chrX	1471018	1471018	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccttgggcaggtgcggaGaatctgacctgctggattca	14	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1471018G>T	ENST00000331035.4	+	5	673	c.324G>T	c.(322-324)gaG>gaT	p.E108D	IL3RA_ENST00000381469.2_Missense_Mutation_p.E30D	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	108					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)	p.E108D(1)		lung(1)|skin(2)	3		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)			Sargramostim(DB00020)	CAGGTGCGGAGAATCTGACCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	X											121	139	133					X																	1471018		2201	4294	6495	1431018	SO:0001583	missense	3563			M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"Pseudoautosomal regions / PAR1", "Interleukins and interleukin receptors", "CD molecules"	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.324G>T	X.37:g.1471018G>T	ENSP00000327890:p.Glu108Asp		1431018	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	.	.	.	.	.	.	.	.	.	.	.	9.616	1.132680	0.21041	.	.	ENSG00000185291	ENST00000331035;ENST00000432757;ENST00000381469	T;T;T	0.58060	0.36;0.36;0.36	1.88	-0.283	0.12874	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.604415	0.11433	U	0.564570	T	0.31918	0.0812	L	0.29908	0.895	0.09310	N	1	B;B	0.26445	0.072;0.149	B;B	0.25884	0.055;0.064	T	0.17410	-1.0370	10	0.23302	T	0.38	-12.4586	2.5259	0.04691	0.2301:0.3219:0.448:0.0	.	29;108	P26951-2;P26951	.;IL3RA_HUMAN	D	108;30;30	ENSP00000327890:E108D;ENSP00000414867:E30D;ENSP00000370878:E30D	ENSP00000327890:E108D	E	+	3	2	IL3RA	1431018	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.288000	0.01150	0.044000	0.15775	0.365000	0.22127	GAG		0.607	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3			T	1471018	G	T	1471018	3	4	61	1	0	0	0	0	1	0	0	0	7716	933	33	2	338	2	IL3RA	23	1471018	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42680	1471018	153799542	11994	19979										
P2RY8	286530	broad.mit.edu	37	chrX	1584787	1584787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccgtgcgcctcctccgtgCgcaacagcttgaggatggtg	15	13	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1584787C>T	ENST00000381297.4	-	2	875	c.665G>A	c.(664-666)cGc>cAc	p.R222H	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.R222H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		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)				CTCCTCCGTGCGCAACAGCTT	0.637			T	CRLF2	"B-ALL, Downs associated ALL"																																		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	1	Substitution - Missense(1)	large_intestine(1)	X											67	41	50					X																	1584787		2203	4293	6496	1544787	SO:0001583	missense	286530			AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.665G>A	X.37:g.1584787C>T	ENSP00000370697:p.Arg222His		1544787		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	5.192	0.220911	0.09863	.	.	ENSG00000182162	ENST00000381297	T	0.43688	0.94	2.41	0.46	0.16684	GPCR, rhodopsin-like superfamily (1);	0.805999	0.10272	U	0.694670	T	0.27866	0.0686	L	0.48642	1.525	0.09310	N	1	P	0.48350	0.909	B	0.34138	0.176	T	0.14615	-1.0466	10	0.48119	T	0.1	.	5.6054	0.17377	0.0:0.2906:0.0:0.7094	.	222	Q86VZ1	P2RY8_HUMAN	H	222	ENSP00000370697:R222H	ENSP00000370697:R222H	R	-	2	0	P2RY8	1544787	0.993000	0.37304	0.001000	0.08648	0.063000	0.16089	1.026000	0.30103	-0.003000	0.14444	0.279000	0.19357	CGC		0.637	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		T	1584787	C	T	1584787	3	4	61	1	0	0	0	0	1	0	0	0	11386	768	27	1	418	1	P2RY8	23	1584787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	113769	1584787	153685773	11995	19980										
SFRS17A	8227	broad.mit.edu	37	chrX	1712547	1712547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggtgcagaaccaccagttCtccacgctgcgtatttccaa	8	13	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:1712547C>A	ENST00000313871.3	+	2	388	c.192C>A	c.(190-192)ttC>ttA	p.F64L	AKAP17A_ENST00000381261.3_Missense_Mutation_p.F64L	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	64					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)	p.F64L(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						ACCACCAGTTCTCCACGCTGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	X											189	168	175					X																	1712547		2203	4296	6499	1672547	SO:0001583	missense	8227			L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.192C>A	X.37:g.1712547C>A	ENSP00000324827:p.Phe64Leu		1672547	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	37	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	c	10.01	1.234090	0.22626	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.34072	1.38;1.38	2.02	-0.481	0.12082	.	0.000000	0.64402	U	0.000002	T	0.49423	0.1556	.	.	.	0.09310	N	1	D;B	0.76494	0.999;0.267	D;B	0.83275	0.996;0.327	T	0.35201	-0.9798	9	0.87932	D	0	-16.8625	4.2662	0.10764	0.0:0.4496:0.1883:0.3621	.	64;64	Q02040-3;Q02040	.;AK17A_HUMAN	L	64	ENSP00000324827:F64L;ENSP00000370660:F64L	ENSP00000324827:F64L	F	+	3	2	AKAP17A	1672547	0.995000	0.38212	0.001000	0.08648	0.573000	0.36030	0.114000	0.15520	-0.095000	0.12351	0.100000	0.15512	TTC		0.592	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		A	1712547	C	A	1712547	3	1	61	1	0	0	0	0	1	0	0	0	14210	912	32	2	194	2	SFRS17A	23	1712547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	127760	1712547	153558013	11996	19981										
DHRSX	207063	broad.mit.edu	37	chrX	2139178	2139178	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgacgtggagggacttggtCtctttctcgttgtataggta	14	6	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:2139178C>A	ENST00000334651.5	-	7	949	c.897G>T	c.(895-897)gaG>gaT	p.E299D		NM_145177.2	NP_660160.2	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked	299							oxidoreductase activity (GO:0016491)	p.E299D(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)	16		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GGGACTTGGTCTCTTTCTCGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	X											305	263	277					X																	2139178		2203	4296	6499	2149178	SO:0001583	missense	207063			AJ293620	CCDS35195.1	Xp22.33 and Yp11.2	2014-05-07	2003-09-12		ENSG00000169084	ENSG00000169084		"Pseudoautosomal regions / PAR1"	18399	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 6", "short chain dehydrogenase/reductase family 46C, member 1", "dehydrogenase/reductase (SDR family) Y-linked"		"dehydrogenase/reductase (SDR family) X chromosome"			11731500, 19027726	Standard	NM_145177		Approved	DHRS5X, DHRSXY, DHRSY, DHRS5Y, SDR46C1, SDR7C6	uc004cqf.4	Q8N5I4	OTTHUMG00000021068	ENST00000334651.5:c.897G>T	X.37:g.2139178C>A	ENSP00000334113:p.Glu299Asp		2149178	Q6UWC7|Q8WUS4|Q96GR8|Q9NTF6	Missense_Mutation	SNP	ENST00000334651.5	37	CCDS35195.1	.	.	.	.	.	.	.	.	.	.	c	0.089	-1.169929	0.01660	.	.	ENSG00000169084	ENST00000334651	T	0.66995	-0.24	2.32	-2.95	0.05564	NAD(P)-binding domain (1);	0.350692	0.25250	U	0.032023	T	0.61236	0.2331	M	0.91818	3.245	0.09310	N	1	B	0.31026	0.304	B	0.25614	0.062	T	0.54490	-0.8286	10	0.13853	T	0.58	.	6.9197	0.24380	0.0:0.3985:0.4787:0.1229	.	299	Q8N5I4	DHRSX_HUMAN	D	299	ENSP00000334113:E299D	ENSP00000334113:E299D	E	-	3	2	DHRSX	2149178	0.996000	0.38824	0.222000	0.23844	0.407000	0.30961	0.560000	0.23500	-0.436000	0.07254	0.124000	0.15798	GAG		0.537	DHRSX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055617.3	NM_145177		A	2139178	C	A	2139178	3	1	61	1	0	0	0	0	1	0	0	0	4510	912	32	2	99	2	DHRSX	23	2139178	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	426631	2139178	153131382	11997	19982										
ZBED1	9189	broad.mit.edu	37	chrX	2407653	2407653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caccaagaccccggcgatgaCgaactgctgctccttgaggc	11	15	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:2407653C>T	ENST00000381223.4	-	2	1311	c.1108G>A	c.(1108-1110)Gtc>Atc	p.V370I	ZBED1_ENST00000381218.3_Missense_Mutation_p.V370I|ZBED1_ENST00000515319.1_5'Flank|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Missense_Mutation_p.V370I	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	370					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)	p.V370I(1)		endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		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)				CCGGCGATGACGAACTGCTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	X											58	46	50					X																	2407653		2203	4296	6499	2417653	SO:0001583	missense	9189			AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.1108G>A	X.37:g.2407653C>T	ENSP00000370621:p.Val370Ile		2417653	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	37	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	C	1.947	-0.442059	0.04604	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218	T;T;T	0.22336	1.96;1.96;1.96	3.06	1.82	0.25136	Ribonuclease H-like (1);	0.936228	0.08714	N	0.904469	T	0.13841	0.0335	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.24190	-1.0167	9	0.32370	T	0.25	-26.5599	7.9711	0.30127	0.0:0.736:0.0:0.264	.	370	O96006	ZBED1_HUMAN	I	370	ENSP00000370621:V370I;ENSP00000370620:V370I;ENSP00000370616:V370I	ENSP00000370616:V370I	V	-	1	0	ZBED1	2417653	0.155000	0.22806	0.053000	0.19242	0.016000	0.09150	1.924000	0.40065	1.155000	0.42497	0.519000	0.50382	GTC		0.657	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		T	2407653	C	T	2407653	3	4	61	1	0	0	0	0	1	0	0	0	17557	536	19	1	980	1	ZBED1	23	2407653	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	268475	2407653	152862907	11998	19983										
CD99	4267	broad.mit.edu	37	chrX	2644308	2644308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttcctcctgcagccgacgcCccaggcgtgatccccgggat	11	18	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:2644308C>T	ENST00000381192.3	+	8	551	c.369C>T	c.(367-369)gcC>gcT	p.A123A	CD99_ENST00000482405.2_3'UTR|CD99_ENST00000381187.3_Silent_p.A107A|CD99_ENST00000381184.1_Silent_p.A123A	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule	123					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.A123A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11						CAGCCGACGCCCCAGGCGTGA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	X											75	76	76					X																	2644308		2203	4296	6499	2654308	SO:0001819	synonymous_variant	4267			M16279	CCDS14119.1, CCDS48071.1, CCDS75947.1	Xp22.32 and Yp11.3	2012-10-02	2006-03-28	2003-02-14	ENSG00000002586	ENSG00000002586		"Pseudoautosomal regions / PAR1", "CD molecules"	7082	protein-coding gene	gene with protein product		313470, 450000	"antigen identified by monoclonal antibodies 12E7, F21 and O13", "CD99 antigen"	MIC2			Standard	NM_001122898		Approved		uc004cqm.3	P14209	OTTHUMG00000021073	ENST00000381192.3:c.369C>T	X.37:g.2644308C>T			2654308	A6NIW1|O00518|Q6ICV7	Silent	SNP	ENST00000381192.3	37	CCDS14119.1																																																																																				0.587	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	NM_001122898		T	2644308	C	T	2644308	2	4	61	1	0	0	0	0	0	0	0	1	3056	610	22	3		3	CD99	23	2644308	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	236655	2644308	152626252	11999	19984										
ARSF	416	broad.mit.edu	37	chrX	3019148	3019148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaagattcttgatgctatcGatgattttggcctaaggaac	10	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:3019148G>A	ENST00000381127.1	+	8	1209	c.988G>A	c.(988-990)Gat>Aat	p.D330N	ARSF_ENST00000359361.2_Missense_Mutation_p.D330N|ARSF_ENST00000537104.1_Missense_Mutation_p.D330N	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	330					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.D330N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		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)				TGATGCTATCGATGATTTTGG	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	X											134	110	118					X																	3019148		2203	4299	6502	3029148	SO:0001583	missense	416			X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"Arylsulfatase family"	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.988G>A	X.37:g.3019148G>A	ENSP00000370519:p.Asp330Asn		3029148	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263090	0.59431	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.94537	-3.45;-3.45;-3.45	2.81	2.81	0.32909	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.121890	0.52532	U	0.000068	D	0.93284	0.7860	M	0.77820	2.39	0.46874	D	0.999238	P	0.34724	0.465	B	0.34301	0.179	D	0.93227	0.6614	10	0.59425	D	0.04	.	13.1568	0.59522	0.0:0.0:1.0:0.0	.	330	P54793	ARSF_HUMAN	N	330	ENSP00000370519:D330N;ENSP00000445594:D330N;ENSP00000352319:D330N	ENSP00000352319:D330N	D	+	1	0	ARSF	3029148	1.000000	0.71417	0.003000	0.11579	0.001000	0.01503	6.964000	0.76061	1.300000	0.44818	0.534000	0.68092	GAT		0.413	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			A	3019148	G	A	3019148	3	1	61	1	0	0	0	0	1	0	0	0	992	1058	37	1	1014	1	ARSF	23	3019148	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	374840	3019148	152251412	12000	19985										
MXRA5	25878	broad.mit.edu	37	chrX	3229372	3229372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcgtccaccgctgtcatccGactgcatgaaggagttcacc	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:3229372G>A	ENST00000217939.6	-	7	7026	c.6872C>T	c.(6871-6873)tCg>tTg	p.S2291L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2291	Ig-like C2-type 7.					extracellular vesicular exosome (GO:0070062)		p.S2291L(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GCTGTCATCCGACTGCATGAA	0.577																																																2	Substitution - Missense(2)	large_intestine(2)	X											109	86	94					X																	3229372		2203	4300	6503	3239372	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6872C>T	X.37:g.3229372G>A	ENSP00000217939:p.Ser2291Leu		3239372	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.589036	0.28357	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.27557	1.66	4.28	3.37	0.38596	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.511109	0.14573	U	0.311316	T	0.37265	0.0997	L	0.39147	1.195	0.09310	N	0.999999	D	0.60160	0.987	P	0.52823	0.71	T	0.16424	-1.0403	10	0.51188	T	0.08	.	13.2913	0.60272	0.0:0.1564:0.8436:0.0	.	2291	Q9NR99	MXRA5_HUMAN	L	2291	ENSP00000217939:S2291L	ENSP00000217939:S2291L	S	-	2	0	MXRA5	3239372	1.000000	0.71417	0.004000	0.12327	0.022000	0.10575	4.728000	0.62000	0.605000	0.29947	0.509000	0.49947	TCG		0.577	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3229372	G	A	3229372	3	1	61	1	0	0	0	0	1	0	0	0	10033	1059	37	1	1618	1	MXRA5	23	3229372	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	210224	3229372	152041188	12001	19986										
MXRA5	25878	broad.mit.edu	37	chrX	3238514	3238514	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccaactgtggaaaagaaaGagtcttgttggtaaagaaag	11	5	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:3238514G>T	ENST00000217939.6	-	5	5366	c.5212C>A	c.(5212-5214)Ctt>Att	p.L1738I		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1738						extracellular vesicular exosome (GO:0070062)		p.L1738I(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGAAAAGAAAGAGTCTTGTTG	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	X											61	57	59					X																	3238514		2203	4300	6503	3248514	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5212C>A	X.37:g.3238514G>T	ENSP00000217939:p.Leu1738Ile		3248514	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	G	4.060	0.008964	0.07912	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62364	0.03	3.18	-0.779	0.10973	.	1.197160	0.06569	U	0.748265	T	0.34716	0.0907	N	0.08118	0	0.09310	N	1	B	0.26002	0.139	B	0.22386	0.039	T	0.16719	-1.0393	10	0.41790	T	0.15	.	0.2971	0.00267	0.2976:0.1299:0.2404:0.332	.	1738	Q9NR99	MXRA5_HUMAN	I	1738	ENSP00000217939:L1738I	ENSP00000217939:L1738I	L	-	1	0	MXRA5	3248514	0.000000	0.05858	0.005000	0.12908	0.538000	0.34931	-0.505000	0.06367	-0.248000	0.09583	0.287000	0.19450	CTT		0.468	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3238514	G	T	3238514	3	4	61	1	0	0	0	0	1	0	0	0	10033	942	33	2	3286	2	MXRA5	23	3238514	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9142	3238514	152032046	12002	19987										
MXRA5	25878	broad.mit.edu	37	chrX	3239636	3239636	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaggattcttccttaaattCtcccatagtggagaccaagg	9	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:3239636C>A	ENST00000217939.6	-	5	4244	c.4090G>T	c.(4090-4092)Gaa>Taa	p.E1364*		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1364						extracellular vesicular exosome (GO:0070062)		p.E1364*(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCCTTAAATTCTCCCATAGTG	0.468																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											54	51	52					X																	3239636		2203	4300	6503	3249636	SO:0001587	stop_gained	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4090G>T	X.37:g.3239636C>A	ENSP00000217939:p.Glu1364*		3249636	Q6P1M7|Q9Y3Y8	Nonsense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	40	8.377664	0.98784	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	.	.	.	2.92	2.92	0.33932	.	0.179456	0.26311	U	0.025113	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	7.5267	0.27660	0.0:0.8608:0.0:0.1392	.	.	.	.	X	1364	.	ENSP00000217939:E1364X	E	-	1	0	MXRA5	3249636	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.183000	0.16919	1.227000	0.43598	0.436000	0.28706	GAA		0.468	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3239636	C	A	3239636	4	1	61	1	0	0	0	0	0	1	0	0	10033	922	32	2	4408	2	MXRA5	23	3239636	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1122	3239636	152030924	12003	19988										
MXRA5	25878	broad.mit.edu	37	chrX	3248147	3248147	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagtaaagattctccagaagCggcatgttccgaagcatgct	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:3248147C>T	ENST00000217939.6	-	4	775	c.621G>A	c.(619-621)ccG>ccA	p.P207P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	207						extracellular vesicular exosome (GO:0070062)		p.P207P(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCTCCAGAAGCGGCATGTTCC	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	X											68	59	62					X																	3248147		2202	4300	6502	3258147	SO:0001819	synonymous_variant	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.621G>A	X.37:g.3248147C>T			3258147	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.453	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3248147	C	T	3248147	2	4	61	1	0	0	0	0	0	0	0	1	10033	755	27	1		1	MXRA5	23	3248147	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8511	3248147	152022413	12004	19989										
NLGN4X	57502	broad.mit.edu	37	chrX	5821228	5821228	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaccgatcatggggatgccGaagacataggggacctcatc	14	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:5821228G>A	ENST00000381095.3	-	5	2118	c.1491C>T	c.(1489-1491)ttC>ttT	p.F497F	NLGN4X_ENST00000381092.1_Silent_p.F497F|NLGN4X_ENST00000275857.6_Silent_p.F497F|NLGN4X_ENST00000381093.2_Silent_p.F517F|NLGN4X_ENST00000538097.1_Silent_p.F497F	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	497					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.F497F(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TGGGGATGCCGAAGACATAGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	X											96	80	85					X																	5821228		2203	4300	6503	5831228	SO:0001819	synonymous_variant	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1491C>T	X.37:g.5821228G>A			5831228	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.547	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5821228	G	A	5821228	2	1	61	1	0	0	0	0	0	0	0	1	10495	1049	37	1		1	NLGN4X	23	5821228	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2573081	5821228	149449332	12005	19990										
HDHD1A	8226	broad.mit.edu	37	chrX	7023671	7023671	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaccgcacctggcatgagCgcagccgtggggaacacttc	13	14	0	1	rs200144671		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:7023671C>T	ENST00000381077.5	-	2	346	c.270G>A	c.(268-270)gcG>gcA	p.A90A	HDHD1_ENST00000424830.2_Silent_p.A113A|HDHD1_ENST00000498474.2_5'UTR|HDHD1_ENST00000412827.2_Intron|HDHD1_ENST00000540122.1_Silent_p.A90A	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	90					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)	p.A76A(1)		breast(2)|large_intestine(1)|lung(3)	6						CTGGCATGAGCGCAGCCGTGG	0.483													c|||	1	0.000264901	0	0	3775	,	,		12654	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											52	55	54					X																	7023671		2003	4165	6168	7033671	SO:0001819	synonymous_variant	8226			M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"family with sequence similarity 16, member A, X-linked", "haloacid dehalogenase-like hydrolase domain containing 1A"	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.270G>A	X.37:g.7023671C>T			7033671	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																				0.483	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080		T	7023671	C	T	7023671	2	4	61	1	0	0	0	0	0	0	0	1	7043	755	27	1		1	HDHD1A	23	7023671	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1202443	7023671	148246889	12006	19991										
VCX	26609	broad.mit.edu	37	chrX	7811750	7811750	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gacccagcacgaccccctgaGtcaggaggccgagctggagg	15	14	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:7811750G>T	ENST00000381059.3	+	3	533	c.314G>T	c.(313-315)aGt>aTt	p.S105I	VCX_ENST00000341408.4_Missense_Mutation_p.S105I	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	105	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S105I(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GACCCCCTGAGTCAGGAGGCC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	X											72	91	84					X																	7811750		2128	4069	6197	7771750	SO:0001583	missense	26609			AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"variable charge, X chromosome"			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.314G>T	X.37:g.7811750G>T	ENSP00000370447:p.Ser105Ile		7771750	A0JNS5|Q4V774|Q9P0H3	Missense_Mutation	SNP	ENST00000381059.3	37	CCDS14128.1	.	.	.	.	.	.	.	.	.	.	-	5.630	0.300866	0.10678	.	.	ENSG00000182583	ENST00000381059;ENST00000341408	T;T	0.29397	1.57;1.57	.	.	.	.	.	.	.	.	T	0.23054	0.0557	L	0.52573	1.65	0.09310	N	1	B	0.31174	0.311	B	0.23150	0.044	T	0.17837	-1.0356	8	0.66056	D	0.02	.	5.9618	0.19303	6.0E-4:0.0:0.9994:0.0	.	105	Q9H320	VCX1_HUMAN	I	105	ENSP00000370447:S105I;ENSP00000344144:S105I	ENSP00000344144:S105I	S	+	2	0	VCX	7771750	0.008000	0.16893	0.024000	0.17045	0.024000	0.10985	-0.099000	0.11007	0.161000	0.19458	0.164000	0.16699	AGT		0.677	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452		T	7811750	G	T	7811750	3	4	61	1	0	0	0	0	1	0	0	0	17182	1029	36	2	320	2	VCX	23	7811750	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	788079	7811750	147458810	12007	19992										
FAM9B	171483	broad.mit.edu	37	chrX	8997356	8997356	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgataccaacaattagttCttcctcttctccctcttctt	2	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:8997356C>A	ENST00000327220.5	-	6	749	c.385G>T	c.(385-387)Gaa>Taa	p.E129*	FAM9B_ENST00000362066.3_Nonsense_Mutation_p.E169*|FAM9B_ENST00000428477.1_Nonsense_Mutation_p.E129*			Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B	129						nucleus (GO:0005634)		p.E129*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11		Hepatocellular(5;0.219)				ACAATTAGttcttcctcttct	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											279	199	226					X																	8997356		2201	4300	6501	8957356	SO:0001587	stop_gained	171483				CCDS14132.1	Xp22.31	2014-02-17			ENSG00000177138	ENSG00000177138			18404	protein-coding gene	gene with protein product	"testis expressed 39B"	300478				12213195, 21085121, 21998597, 22936694	Standard	XM_005274456		Approved	TEX39B	uc011mhu.2	Q8IZU0	OTTHUMG00000021114	ENST00000327220.5:c.385G>T	X.37:g.8997356C>A	ENSP00000318716:p.Glu129*		8957356	Q0IJ68|Q8N7Z8	Nonsense_Mutation	SNP	ENST00000327220.5	37	CCDS14132.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.208151	0.39003	.	.	ENSG00000177138	ENST00000362066;ENST00000327220;ENST00000428477	.	.	.	0.43	-0.548	0.11833	.	.	.	.	.	.	.	.	.	.	.	0.52501	A	0.999951	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	169;129;129	.	ENSP00000318716:E129X	E	-	1	0	FAM9B	8957356	0.126000	0.22350	0.049000	0.19019	0.046000	0.14306	-0.336000	0.07863	-0.426000	0.07360	-0.422000	0.05995	GAA		0.383	FAM9B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055702.2	NM_205849		A	8997356	C	A	8997356	4	1	61	1	0	0	0	0	0	1	0	0	5679	922	32	2	187	2	FAM9B	23	8997356	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1185606	8997356	146273204	12008	19993										
WWC3	55841	broad.mit.edu	37	chrX	10047833	10047833	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacaaagaaaagggggtggaGaccctgcaagagtgagttgc	15	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10047833G>T	ENST00000380861.4	+	5	757	c.366G>T	c.(364-366)gaG>gaT	p.E122D	WWC3_ENST00000454666.1_Missense_Mutation_p.E122D	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	122					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.E122D(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						AGGGGGTGGAGACCCTGCAAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											75	64	67					X																	10047833		2203	4300	6503	10007833	SO:0001583	missense	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.366G>T	X.37:g.10047833G>T	ENSP00000370242:p.Glu122Asp		10007833	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092159	0.76756	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000398613	T;T	0.05786	3.39;3.39	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.10680	0.0261	L	0.42245	1.32	0.48395	D	0.99964	P	0.51147	0.942	P	0.54815	0.761	T	0.18335	-1.0340	10	0.23891	T	0.37	-33.0699	7.7635	0.28965	0.1844:0.0:0.8156:0.0	.	122	Q9ULE0	WWC3_HUMAN	D	122	ENSP00000370242:E122D;ENSP00000399584:E122D	ENSP00000370242:E122D	E	+	3	2	WWC3	10007833	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.283000	0.65621	2.366000	0.80165	0.544000	0.68410	GAG		0.423	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		T	10047833	G	T	10047833	3	4	61	1	0	0	0	0	1	0	0	0	17453	933	33	2	380	2	WWC3	23	10047833	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1050477	10047833	145222727	12009	19994										
CLCN4	1183	broad.mit.edu	37	chrX	10176600	10176600	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggcactgatcttcaaaatCgtcgttaccatatttacctt	5	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10176600C>T	ENST00000380833.4	+	9	1750	c.1359C>T	c.(1357-1359)atC>atT	p.I453I	CLCN4_ENST00000380829.1_Silent_p.I422I|CLCN4_ENST00000421085.2_Silent_p.I359I	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	453					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.I453I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TCTTCAAAATCGTCGTTACCA	0.537																																					Melanoma(74;1050 1296 1576 30544 38374)											1	Substitution - coding silent(1)	large_intestine(1)	X											66	65	65					X																	10176600		2203	4295	6498	10136600	SO:0001819	synonymous_variant	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1359C>T	X.37:g.10176600C>T			10136600	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																				0.537	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			T	10176600	C	T	10176600	2	4	61	1	0	0	0	0	0	0	0	1	3471	874	31	1		1	CLCN4	23	10176600	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	128767	10176600	145093960	12010	19995										
CLCN4	1183	broad.mit.edu	37	chrX	10188805	10188805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcccacatcccctgaagctgCggcgcatcctgaacctcagc	9	18	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10188805C>T	ENST00000380833.4	+	12	2471	c.2080C>T	c.(2080-2082)Cgg>Tgg	p.R694W	CLCN4_ENST00000380829.1_Missense_Mutation_p.R663W|CLCN4_ENST00000421085.2_Missense_Mutation_p.R600W	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	694					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R694W(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCTGAAGCTGCGGCGCATCCT	0.597																																					Melanoma(74;1050 1296 1576 30544 38374)											1	Substitution - Missense(1)	large_intestine(1)	X											140	113	122					X																	10188805		2203	4300	6503	10148805	SO:0001583	missense	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.2080C>T	X.37:g.10188805C>T	ENSP00000370213:p.Arg694Trp		10148805	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	c	18.79	3.699492	0.68501	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.94232	-3.38;-3.38;-3.38	5.36	-0.865	0.10662	Cystathionine beta-synthase, core (1);	0.000000	0.85682	D	0.000000	D	0.96682	0.8917	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95974	0.8972	10	0.87932	D	0	-36.9511	18.091	0.89475	0.4915:0.5085:0.0:0.0	.	694	P51793	CLCN4_HUMAN	W	694;663;600	ENSP00000370213:R694W;ENSP00000370209:R663W;ENSP00000405754:R600W	ENSP00000370209:R663W	R	+	1	2	CLCN4	10148805	1.000000	0.71417	0.972000	0.41901	0.912000	0.54170	1.473000	0.35387	-0.451000	0.07097	-0.950000	0.02660	CGG		0.597	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			T	10188805	C	T	10188805	3	4	61	1	0	0	0	0	1	0	0	0	3471	759	27	1	2118	1	CLCN4	23	10188805	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12205	10188805	145081755	12011	19996										
MID1	4281	broad.mit.edu	37	chrX	10417522	10417522	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggctgcgcaaatgcgacGtcgaaggtgtagaggtggat	16	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10417522G>A	ENST00000317552.4	-	10	2290	c.1890C>T	c.(1888-1890)gaC>gaT	p.D630D	MID1_ENST00000380785.1_Silent_p.D630D|MID1_ENST00000479925.1_5'UTR|MID1_ENST00000380779.1_Silent_p.D630D|MID1_ENST00000453318.2_Silent_p.D630D|MID1_ENST00000380780.1_Silent_p.D630D|MID1_ENST00000380782.2_3'UTR|MID1_ENST00000380787.1_Silent_p.D630D	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	630	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.D630D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						CAAATGCGACGTCGAAGGTGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	X											131	100	110					X																	10417522		2203	4300	6503	10377522	SO:0001819	synonymous_variant	4281			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1890C>T	X.37:g.10417522G>A			10377522	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	37	CCDS14138.1																																																																																				0.557	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10417522	G	A	10417522	2	1	61	1	0	0	0	0	0	0	0	1	9606	1136	40	1		1	MID1	23	10417522	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	228717	10417522	144853038	12012	19997										
MID1	4281	broad.mit.edu	37	chrX	10534931	10534931	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcggatcggactaaccttCaatttgtcatagcgctcact	9	11	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10534931C>A	ENST00000317552.4	-	2	1057	c.657G>T	c.(655-657)ttG>ttT	p.L219F	MID1_ENST00000380785.1_Missense_Mutation_p.L219F|MID1_ENST00000380779.1_Missense_Mutation_p.L219F|MID1_ENST00000453318.2_Missense_Mutation_p.L219F|MID1_ENST00000380780.1_Missense_Mutation_p.L219F|MID1_ENST00000380782.2_Missense_Mutation_p.L219F|MID1_ENST00000380787.1_Missense_Mutation_p.L219F	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	219					microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.L219F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						GACTAACCTTCAATTTGTCAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	78	85					X																	10534931		2203	4300	6503	10494931	SO:0001583	missense	4281			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.657G>T	X.37:g.10534931C>A	ENSP00000312678:p.Leu219Phe		10494931	B2RCG2|O75361|Q9BZX5	Missense_Mutation	SNP	ENST00000317552.4	37	CCDS14138.1	.	.	.	.	.	.	.	.	.	.	c	14.77	2.635484	0.47049	.	.	ENSG00000101871	ENST00000453318;ENST00000317552;ENST00000380785;ENST00000380779;ENST00000380787;ENST00000380780;ENST00000380782;ENST00000413894	T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.63	5.63	0.86233	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64821	0.2633	L	0.59436	1.845	0.53005	D	0.999962	D;D;D	0.71674	0.998;0.994;0.989	D;D;P	0.68621	0.959;0.921;0.837	T	0.67130	-0.5748	10	0.62326	D	0.03	.	8.861	0.35258	0.0:0.7812:0.0:0.2188	.	219;219;219	C9J453;O15344-2;O15344	.;.;TRI18_HUMAN	F	219	ENSP00000414521:L219F;ENSP00000312678:L219F;ENSP00000370162:L219F;ENSP00000370156:L219F;ENSP00000370164:L219F;ENSP00000370157:L219F;ENSP00000370159:L219F;ENSP00000391154:L219F	ENSP00000312678:L219F	L	-	3	2	MID1	10494931	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.213000	0.32407	2.383000	0.81215	0.597000	0.82753	TTG		0.478	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10534931	C	A	10534931	3	1	61	1	0	0	0	0	1	0	0	0	9606	825	29	2	1382	2	MID1	23	10534931	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117409	10534931	144735629	12013	19998										
MID1	4281	broad.mit.edu	37	chrX	10535339	10535339	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatgctttctggaacctgtcGatgatgttctgtagggtgac	13	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:10535339G>A	ENST00000317552.4	-	2	649	c.249C>T	c.(247-249)atC>atT	p.I83I	MID1_ENST00000380785.1_Silent_p.I83I|MID1_ENST00000380779.1_Silent_p.I83I|MID1_ENST00000453318.2_Silent_p.I83I|MID1_ENST00000380780.1_Silent_p.I83I|MID1_ENST00000380782.2_Silent_p.I83I|MID1_ENST00000380787.1_Silent_p.I83I	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	83					microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I83I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						GGAACCTGTCGATGATGTTCT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	X											133	105	115					X																	10535339		2203	4300	6503	10495339	SO:0001819	synonymous_variant	4281			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.249C>T	X.37:g.10535339G>A			10495339	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	37	CCDS14138.1																																																																																				0.627	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10535339	G	A	10535339	2	1	61	1	0	0	0	0	0	0	0	1	9606	1048	37	1		1	MID1	23	10535339	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	408	10535339	144735221	12014	19999										
ARHGAP6	395	broad.mit.edu	37	chrX	11206944	11206944	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagatgagttactgcttgaGagttctttgttttgtctttt	10	4	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:11206944G>T	ENST00000337414.4	-	4	1853	c.981C>A	c.(979-981)ctC>ctA	p.L327L	ARHGAP6_ENST00000380736.1_Silent_p.L124L|ARHGAP6_ENST00000380718.1_Silent_p.L327L|ARHGAP6_ENST00000534860.1_Silent_p.L152L|ARHGAP6_ENST00000303025.6_Silent_p.L124L|ARHGAP6_ENST00000413512.3_Silent_p.L136L|ARHGAP6_ENST00000380732.3_Silent_p.L359L	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	327					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)	p.L327L(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TACTGCTTGAGAGTTCTTTGT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	X											150	114	126					X																	11206944		2203	4300	6503	11116865	SO:0001819	synonymous_variant	395			AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"Rho GTPase activating proteins"	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.981C>A	X.37:g.11206944G>T			11116865	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Silent	SNP	ENST00000337414.4	37	CCDS14140.1																																																																																				0.498	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		T	11206944	G	T	11206944	2	4	61	1	0	0	0	0	0	0	0	1	887	929	33	2		2	ARHGAP6	23	11206944	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	671605	11206944	144063616	12015	20000										
FRMPD4	9758	broad.mit.edu	37	chrX	12725710	12725710	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttagccacgtcaacaggatCgaaatgttttccgaggagga	11	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12725710C>T	ENST00000380682.1	+	13	1916	c.1410C>T	c.(1408-1410)atC>atT	p.I470I		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	470	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I470I(1)|p.I460I(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TCAACAGGATCGAAATGTTTT	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	X											143	118	127					X																	12725710		2203	4300	6503	12635631	SO:0001819	synonymous_variant	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1410C>T	X.37:g.12725710C>T			12635631	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																				0.512	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12725710	C	T	12725710	2	4	61	1	0	0	0	0	0	0	0	1	6078	874	31	1		1	FRMPD4	23	12725710	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1518766	12725710	142544850	12016	20001										
FRMPD4	9758	broad.mit.edu	37	chrX	12736204	12736204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctggagagaactgcctttCgcaaggacagtcaaagatgg	12	8	2	2	rs141229690		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12736204C>T	ENST00000380682.1	+	16	3765	c.3259C>T	c.(3259-3261)Cgc>Tgc	p.R1087C		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1087					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R1077C(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						AACTGCCTTTCGCAAGGACAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X						C	CYS/ARG	1,3834		0,1,1631,571	126	122	123		3259	5.5	1	X	dbSNP_134	123	1,6727		0,1,2427,1872	no	missense	FRMPD4	NM_014728.3	180	0,2,4058,2443	TT,TC,CC,C		0.0149,0.0261,0.0189	probably-damaging	1087/1323	12736204	2,10561	2203	4300	6503	12646125	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3259C>T	X.37:g.12736204C>T	ENSP00000370057:p.Arg1087Cys		12646125	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756579	0.69648	2.61E-4	1.49E-4	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.08634	3.07	5.49	5.49	0.81192	.	0.060592	0.64402	D	0.000005	T	0.27205	0.0667	M	0.63428	1.95	0.52501	D	0.99995	D;D	0.89917	1.0;1.0	D;D	0.65443	0.935;0.935	T	0.00668	-1.1618	10	0.87932	D	0	-14.0944	18.464	0.90749	0.0:1.0:0.0:0.0	.	1079;1087	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	C	1087;1078;1076	ENSP00000370057:R1087C	ENSP00000304583:R1076C	R	+	1	0	FRMPD4	12646125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.631000	0.54280	2.301000	0.77427	0.600000	0.82982	CGC		0.483	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12736204	C	T	12736204	3	4	61	1	0	0	0	0	1	0	0	0	6078	884	31	1	3321	1	FRMPD4	23	12736204	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10494	12736204	142534356	12017	20002										
TLR7	51284	broad.mit.edu	37	chrX	12904027	12904027	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttatttaaaatccctttacCtggatggaaaccagctacta	5	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12904027C>A	ENST00000380659.3	+	3	539	c.400C>A	c.(400-402)Ctg>Atg	p.L134M		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	134					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.L134M(1)		NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	ATCCCTTTACCTGGATGGAAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	70	69					X																	12904027		2203	4300	6503	12813948	SO:0001583	missense	51284			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.400C>A	X.37:g.12904027C>A	ENSP00000370034:p.Leu134Met		12813948	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795161	0.50208	.	.	ENSG00000196664	ENST00000380659	T	0.09817	2.94	5.62	2.88	0.33553	.	0.000000	0.64402	D	0.000008	T	0.31263	0.0791	M	0.82923	2.615	0.46241	D	0.998948	D	0.89917	1.0	D	0.87578	0.998	T	0.02109	-1.1212	10	0.87932	D	0	.	7.8943	0.29697	0.0:0.5183:0.0:0.4817	.	134	Q9NYK1	TLR7_HUMAN	M	134	ENSP00000370034:L134M	ENSP00000370034:L134M	L	+	1	2	TLR7	12813948	0.238000	0.23825	1.000000	0.80357	0.986000	0.74619	0.509000	0.22707	0.555000	0.29079	-0.205000	0.12727	CTG		0.453	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12904027	C	A	12904027	3	1	61	1	0	0	0	0	1	0	0	0	15995	680	24	2	406	2	TLR7	23	12904027	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	167823	12904027	142366533	12018	20003										
TLR7	51284	broad.mit.edu	37	chrX	12904837	12904837	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaatcttgaagttcttgatCttggcactaactttataaaa	5	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12904837C>A	ENST00000380659.3	+	3	1349	c.1210C>A	c.(1210-1212)Ctt>Att	p.L404I		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	404					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.L404I(1)		NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	AGTTCTTGATCTTGGCACTAA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	X											66	73	71					X																	12904837		2201	4299	6500	12814758	SO:0001583	missense	51284			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.1210C>A	X.37:g.12904837C>A	ENSP00000370034:p.Leu404Ile		12814758	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008488	0.35415	.	.	ENSG00000196664	ENST00000380659	T	0.60424	0.19	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000001	T	0.64034	0.2562	M	0.80616	2.505	0.50313	D	0.999867	P	0.35107	0.484	B	0.42030	0.373	T	0.68202	-0.5471	10	0.62326	D	0.03	.	9.5943	0.39565	0.0:0.8416:0.0:0.1584	.	404	Q9NYK1	TLR7_HUMAN	I	404	ENSP00000370034:L404I	ENSP00000370034:L404I	L	+	1	0	TLR7	12814758	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.242000	0.43106	2.434000	0.82447	0.600000	0.82982	CTT		0.328	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12904837	C	A	12904837	3	1	61	1	0	0	0	0	1	0	0	0	15995	913	32	2	1216	2	TLR7	23	12904837	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	810	12904837	142365723	12019	20004										
TLR8	51311	broad.mit.edu	37	chrX	12939078	12939078	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattttcaaaggtctcaagaAtctgacacgtctggatttat	7	8	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12939078A>C	ENST00000218032.6	+	2	2006	c.1919A>C	c.(1918-1920)aAt>aCt	p.N640T	TLR8_ENST00000311912.5_Missense_Mutation_p.N658T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	640					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.N658T(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	GGTCTCAAGAATCTGACACGT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											60	60	60					X																	12939078		2203	4297	6500	12848999	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1919A>C	X.37:g.12939078A>C	ENSP00000218032:p.Asn640Thr		12848999	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	A	3.630	-0.075673	0.07184	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.60171	0.21;0.21	5.82	4.67	0.58626	.	0.000000	0.43416	D	0.000575	T	0.52964	0.1767	L	0.59912	1.85	0.34464	D	0.702109	B;B	0.22080	0.064;0.064	B;B	0.24848	0.056;0.056	T	0.59526	-0.7438	10	0.46703	T	0.11	.	9.7431	0.40431	0.8538:0.0:0.1462:0.0	.	640;658	Q9NR97;D1CS70	TLR8_HUMAN;.	T	640;658	ENSP00000218032:N640T;ENSP00000312082:N658T	ENSP00000218032:N640T	N	+	2	0	TLR8	12848999	0.867000	0.29959	0.004000	0.12327	0.011000	0.07611	2.562000	0.45914	0.836000	0.34901	0.486000	0.48141	AAT		0.398	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12939078	A	C	12939078	3	2	61	1	0	0	0	0	1	0	0	0	15996	101	4	4	1925	4	TLR8	23	12939078	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	34241	12939078	142331482	12020	20005										
TLR8	51311	broad.mit.edu	37	chrX	12939262	12939262	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttacgtggaaacaaactactCtttttaactgatagcctatc	5	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:12939262C>A	ENST00000218032.6	+	2	2190	c.2103C>A	c.(2101-2103)ctC>ctA	p.L701L	TLR8_ENST00000311912.5_Silent_p.L719L	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	701					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.L719L(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	ACAAACTACTCTTTTTAACTG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	X											100	97	98					X																	12939262		2203	4300	6503	12849183	SO:0001819	synonymous_variant	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2103C>A	X.37:g.12939262C>A			12849183	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																				0.393	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12939262	C	A	12939262	2	1	61	1	0	0	0	0	0	0	0	1	15996	900	32	2		2	TLR8	23	12939262	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	184	12939262	142331298	12021	20006										
ATXN3L	92552	broad.mit.edu	37	chrX	13337601	13337601	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgttgttgtaatcgagccaaGaaatttgcaaggcatgtatc	10	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13337601G>T	ENST00000380622.2	-	1	917	c.453C>A	c.(451-453)ttC>ttA	p.F151L	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	151	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.				protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)	p.F151L(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						ATCGAGCCAAGAAATTTGCAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											67	62	64					X																	13337601		1568	3582	5150	13247522	SO:0001583	missense	92552				CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.453C>A	X.37:g.13337601G>T	ENSP00000369996:p.Phe151Leu		13247522	B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.478045	0.26511	.	.	ENSG00000123594	ENST00000380622	T	0.50813	0.73	0.661	0.661	0.17874	.	0.090728	0.85682	D	0.000000	T	0.48660	0.1512	M	0.78916	2.43	0.51767	D	0.999934	B	0.29716	0.255	B	0.37780	0.258	T	0.50783	-0.8787	10	0.62326	D	0.03	.	6.936	0.24466	1.0E-4:0.0:0.9999:0.0	.	151	Q9H3M9	ATX3L_HUMAN	L	151	ENSP00000369996:F151L	ENSP00000369996:F151L	F	-	3	2	ATXN3L	13247522	1.000000	0.71417	0.002000	0.10522	0.001000	0.01503	1.154000	0.31688	0.579000	0.29504	0.422000	0.28245	TTC		0.398	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		T	13337601	G	T	13337601	3	4	61	1	0	0	0	0	1	0	0	0	1215	933	33	2	618	2	ATXN3L	23	13337601	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	398339	13337601	141932959	12022	20007										
EGFL6	25975	broad.mit.edu	37	chrX	13636108	13636108	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagaggggcttgaggatgaGaaaagagaagagaaagccct	15	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13636108G>T	ENST00000361306.1	+	8	1295	c.1038G>T	c.(1036-1038)gaG>gaT	p.E346D	EGFL6_ENST00000380602.3_Missense_Mutation_p.E346D	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	346					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.E346D(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						TTGAGGATGAGAAAAGAGAAG	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											53	56	55					X																	13636108		2203	4300	6503	13546029	SO:0001583	missense	25975			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"MAM and EGF domain containing"	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1038G>T	X.37:g.13636108G>T	ENSP00000355126:p.Glu346Asp		13546029	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Missense_Mutation	SNP	ENST00000361306.1	37	CCDS14155.1	.	.	.	.	.	.	.	.	.	.	G	3.174	-0.169386	0.06461	.	.	ENSG00000198759	ENST00000361306;ENST00000380602	T;T	0.70869	-0.52;-0.4	5.49	1.6	0.23607	.	0.686478	0.15092	N	0.281019	T	0.49779	0.1577	L	0.32530	0.975	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.12156	0.007;0.002	T	0.19943	-1.0290	10	0.14252	T	0.57	.	2.0237	0.03514	0.164:0.1223:0.4321:0.2816	.	346;346	Q8IUX8-2;Q8IUX8	.;EGFL6_HUMAN	D	346	ENSP00000355126:E346D;ENSP00000369976:E346D	ENSP00000355126:E346D	E	+	3	2	EGFL6	13546029	0.991000	0.36638	0.009000	0.14445	0.021000	0.10359	0.698000	0.25571	0.481000	0.27557	0.589000	0.80489	GAG		0.403	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		T	13636108	G	T	13636108	3	4	61	1	0	0	0	0	1	0	0	0	4974	933	33	2	1068	2	EGFL6	23	13636108	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	298507	13636108	141634452	12023	20008										
EGFL6	25975	broad.mit.edu	37	chrX	13645187	13645187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcacaagaaagacattggccGattgaaacttctcctacctg	7	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13645187G>A	ENST00000361306.1	+	11	1600	c.1343G>A	c.(1342-1344)cGa>cAa	p.R448Q	EGFL6_ENST00000380602.3_Missense_Mutation_p.R449Q	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	448	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.R448Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GACATTGGCCGATTGAAACTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	100	102					X																	13645187		2203	4300	6503	13555108	SO:0001583	missense	25975			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"MAM and EGF domain containing"	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1343G>A	X.37:g.13645187G>A	ENSP00000355126:p.Arg448Gln		13555108	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Missense_Mutation	SNP	ENST00000361306.1	37	CCDS14155.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829076	0.71258	.	.	ENSG00000198759	ENST00000361306;ENST00000380602	T;T	0.02158	4.42;4.42	4.85	3.98	0.46160	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.128919	0.51477	D	0.000093	T	0.12092	0.0294	M	0.79693	2.465	0.36203	D	0.850888	D;D	0.89917	0.996;1.0	P;D	0.81914	0.811;0.995	T	0.03503	-1.1030	10	0.59425	D	0.04	.	12.4872	0.55879	0.0838:0.0:0.9162:0.0	.	449;448	Q8IUX8-2;Q8IUX8	.;EGFL6_HUMAN	Q	448;449	ENSP00000355126:R448Q;ENSP00000369976:R449Q	ENSP00000355126:R448Q	R	+	2	0	EGFL6	13555108	0.999000	0.42202	0.022000	0.16811	0.747000	0.42532	4.015000	0.57152	0.839000	0.34971	0.600000	0.82982	CGA		0.458	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		A	13645187	G	A	13645187	3	1	61	1	0	0	0	0	1	0	0	0	4974	1058	37	1	1388	1	EGFL6	23	13645187	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	9079	13645187	141625373	12024	20009										
TCEANC	170082	broad.mit.edu	37	chrX	13681237	13681237	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggcaaaactttgcaagaGaaattgaagagcatgttttt	10	4	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13681237G>T	ENST00000380600.1	+	2	697	c.610G>T	c.(610-612)Gaa>Taa	p.E204*	TCEANC_ENST00000314720.4_Nonsense_Mutation_p.E234*|TCEANC_ENST00000545566.1_Nonsense_Mutation_p.E204*|TCEANC_ENST00000544987.1_Nonsense_Mutation_p.E204*|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	204	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E204*(2)		central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						CTTTGCAAGAGAAATTGAAGA	0.358																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											61	57	58					X																	13681237		1835	4083	5918	13591158	SO:0001587	stop_gained	170082				CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.610G>T	X.37:g.13681237G>T	ENSP00000369974:p.Glu204*		13591158	A6NI06|B2RDM3	Nonsense_Mutation	SNP	ENST00000380600.1	37		.	.	.	.	.	.	.	.	.	.	G	39	7.545359	0.98348	.	.	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	.	.	.	5.26	3.42	0.39159	.	0.394051	0.25135	N	0.032873	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	15.0911	0.72195	0.0:0.2603:0.7397:0.0	.	.	.	.	X	204;204;234;204	.	ENSP00000313886:E234X	E	+	1	0	TCEANC	13591158	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	2.678000	0.46900	0.489000	0.27749	0.600000	0.82982	GAA		0.358	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		T	13681237	G	T	13681237	4	4	61	1	0	0	0	0	0	1	0	0	15717	943	33	2	706	2	TCEANC	23	13681237	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36050	13681237	141589323	12025	20010										
RAB9A	9367	broad.mit.edu	37	chrX	13727175	13727175	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttaagtaactggaagaaaGaattcatatattatgcagat	7	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13727175G>T	ENST00000464506.1	+	3	589	c.310G>T	c.(310-312)Gaa>Taa	p.E104*	RAB9A_ENST00000243325.5_3'UTR	NM_001195328.1|NM_004251.4	NP_001182257.1|NP_004242.1	P51151	RAB9A_HUMAN	RAB9A, member RAS oncogene family	104					GTP catabolic process (GO:0006184)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E104*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						CTGGAAGAAAGAATTCATATA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											98	96	97					X																	13727175		2203	4300	6503	13637096	SO:0001587	stop_gained	9367			U44103	CCDS14156.1	Xp22.2	2010-04-19	2007-01-15	2007-01-15	ENSG00000123595	ENSG00000123595		"RAB, member RAS oncogene"	9792	protein-coding gene	gene with protein product		300284	"RAB9, member RAS oncogene family"	RAB9		9126495	Standard	NM_004251		Approved		uc010neh.3	P51151	OTTHUMG00000021156	ENST00000464506.1:c.310G>T	X.37:g.13727175G>T	ENSP00000420127:p.Glu104*		13637096	A8K390|Q6ICN1	Nonsense_Mutation	SNP	ENST00000464506.1	37	CCDS14156.1	.	.	.	.	.	.	.	.	.	.	G	37	5.996250	0.97184	.	.	ENSG00000123595	ENST00000464506	.	.	.	5.42	4.55	0.56014	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.6318	13.7172	0.62705	0.0772:0.0:0.9228:0.0	.	.	.	.	X	104	.	.	E	+	1	0	RAB9A	13637096	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.606000	0.98325	1.044000	0.40200	0.594000	0.82650	GAA		0.413	RAB9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055802.1	NM_004251		T	13727175	G	T	13727175	4	4	61	1	0	0	0	0	0	1	0	0	12995	943	33	2	312	2	RAB9A	23	13727175	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	45938	13727175	141543385	12026	20011										
OFD1	8481	broad.mit.edu	37	chrX	13762615	13762615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatggaaactcagacaagttCgacatttaacagagattctc	7	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13762615C>T	ENST00000340096.6	+	6	821	c.494C>T	c.(493-495)tCg>tTg	p.S165L	OFD1_ENST00000398395.3_Missense_Mutation_p.S165L|OFD1_ENST00000380567.1_Missense_Mutation_p.S25L|OFD1_ENST00000380550.3_Missense_Mutation_p.S165L|OFD1_ENST00000490265.1_3'UTR	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	165					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)	p.S165L(2)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CAGACAAGTTCGACATTTAAC	0.299																																																2	Substitution - Missense(2)	large_intestine(2)	X											70	60	63					X																	13762615		2203	4299	6502	13672536	SO:0001583	missense	8481			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.494C>T	X.37:g.13762615C>T	ENSP00000344314:p.Ser165Leu		13672536	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.197480	0.38806	.	.	ENSG00000046651	ENST00000380550;ENST00000398395;ENST00000340096;ENST00000380567;ENST00000543598	D;D;D;D	0.96168	-3.91;-3.68;-3.93;-1.75	5.34	3.58	0.41010	.	1.230950	0.05298	N	0.522451	D	0.91106	0.7200	L	0.38531	1.155	0.09310	N	1	P;B;B;B	0.35600	0.511;0.143;0.219;0.268	B;B;B;B	0.22601	0.04;0.017;0.034;0.023	T	0.79438	-0.1803	10	0.20519	T	0.43	1.239	10.9727	0.47448	0.0:0.8457:0.0:0.1543	.	165;165;25;165	A8K2T9;O75665-3;A6NF31;O75665	.;.;.;OFD1_HUMAN	L	165;165;165;25;28	ENSP00000369923:S165L;ENSP00000381432:S165L;ENSP00000344314:S165L;ENSP00000369941:S25L	ENSP00000344314:S165L	S	+	2	0	OFD1	13672536	0.010000	0.17322	0.005000	0.12908	0.316000	0.28119	0.936000	0.28938	0.623000	0.30267	0.544000	0.68410	TCG		0.299	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		T	13762615	C	T	13762615	3	4	61	1	0	0	0	0	1	0	0	0	10869	893	31	1	516	1	OFD1	23	13762615	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	35440	13762615	141507945	12027	20012										
OFD1	8481	broad.mit.edu	37	chrX	13769387	13769387	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggaaccagaagctccaggaaGaaaaacataaaagcataact	8	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:13769387G>T	ENST00000340096.6	+	10	1282	c.955G>T	c.(955-957)Gaa>Taa	p.E319*	OFD1_ENST00000398395.3_Nonsense_Mutation_p.E319*|OFD1_ENST00000380567.1_Nonsense_Mutation_p.E179*|OFD1_ENST00000380550.3_Intron|OFD1_ENST00000490265.1_3'UTR	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	319					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)	p.E319*(2)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						GCTCCAGGAAGAAAAACATAA	0.343																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											52	49	50					X																	13769387		2203	4299	6502	13679308	SO:0001587	stop_gained	8481			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.955G>T	X.37:g.13769387G>T	ENSP00000344314:p.Glu319*		13679308	B9ZVU5|O75666|Q4VAK4	Nonsense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	.	36	5.893911	0.97074	.	.	ENSG00000046651	ENST00000398395;ENST00000340096;ENST00000380567	.	.	.	5.76	3.96	0.45880	.	0.183254	0.56097	D	0.000022	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-10.8547	6.5561	0.22462	0.0722:0.1267:0.6671:0.134	.	.	.	.	X	319;319;179	.	ENSP00000344314:E319X	E	+	1	0	OFD1	13679308	1.000000	0.71417	0.153000	0.22517	0.380000	0.30137	4.925000	0.63425	0.574000	0.29417	0.600000	0.82982	GAA		0.343	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		T	13769387	G	T	13769387	4	4	61	1	0	0	0	0	0	1	0	0	10869	943	33	2	993	2	OFD1	23	13769387	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6772	13769387	141501173	12028	20013										
ASB11	140456	broad.mit.edu	37	chrX	15333668	15333668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaagcttaaagaaaaaaaaCgtagcaaacattgtaataaa	5	4	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:15333668C>T	ENST00000480796.1	-	1	110	c.60G>A	c.(58-60)acG>acA	p.T20T	ASB11_ENST00000537676.1_5'Flank|ASB11_ENST00000380470.3_Silent_p.T20T|ASB11_ENST00000344384.4_5'Flank			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase	20					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.T20T(1)		breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					AGAAAAAAAACGTAGCAAACA	0.333													G|||	2	0.000529801	8e-04	0	3775	,	,		13491	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X											77	77	77					X																	15333668		2202	4297	6499	15243589	SO:0001819	synonymous_variant	140456			AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"Ankyrin repeat domain containing"	17186	protein-coding gene	gene with protein product		300626	"ankyrin repeat and SOCS box-containing 11", "ankyrin repeat and SOCS box containing 11"			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.60G>A	X.37:g.15333668C>T			15243589	E9PEN1|Q3SYC4|Q7Z667	Silent	SNP	ENST00000480796.1	37	CCDS14164.1																																																																																				0.333	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2			T	15333668	C	T	15333668	2	4	61	1	0	0	0	0	0	0	0	1	1016	523	19	1		1	ASB11	23	15333668	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1564281	15333668	139936892	12029	20014										
FIGF	2277	broad.mit.edu	37	chrX	15376224	15376224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcacacaagggggcttgaaGaatgtgttggtactcttccc	11	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:15376224G>T	ENST00000297904.3	-	3	822	c.393C>A	c.(391-393)ttC>ttA	p.F131L		NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	131					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)	p.F131L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					GGGGCTTGAAGAATGTGTTGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											274	219	238					X																	15376224		2203	4300	6503	15286145	SO:0001583	missense	2277			AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.393C>A	X.37:g.15376224G>T	ENSP00000297904:p.Phe131Leu		15286145	B2R7Z3	Missense_Mutation	SNP	ENST00000297904.3	37	CCDS14166.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909213	0.72868	.	.	ENSG00000165197	ENST00000297904	.	.	.	5.11	4.24	0.50183	Platelet-derived growth factor (PDGF) (3);	0.000000	0.85682	D	0.000000	T	0.65112	0.2660	L	0.43646	1.37	0.46437	D	0.999044	D	0.76494	0.999	D	0.83275	0.996	T	0.63825	-0.6549	9	0.48119	T	0.1	-37.2445	8.2732	0.31857	0.261:0.0:0.739:0.0	.	131	O43915	VEGFD_HUMAN	L	131	.	ENSP00000297904:F131L	F	-	3	2	FIGF	15286145	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.090000	0.50191	1.057000	0.40506	0.529000	0.55759	TTC		0.498	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469		T	15376224	G	T	15376224	3	4	61	1	0	0	0	0	1	0	0	0	5908	933	33	2	691	2	FIGF	23	15376224	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	42556	15376224	139894336	12030	20015										
ACE2	59272	broad.mit.edu	37	chrX	15596329	15596329	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatccttcattagctccatTtcttagcagaaaaggttgtg	8	8	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:15596329T>G	ENST00000252519.3	-	9	1282	c.1180A>C	c.(1180-1182)Aat>Cat	p.N394H	ACE2_ENST00000427411.1_Missense_Mutation_p.N394H			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	394					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.N394H(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	TTAGCTCCATTTCTTAGCAGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											118	98	105					X																	15596329		2203	4300	6503	15506250	SO:0001583	missense	59272			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.1180A>C	X.37:g.15596329T>G	ENSP00000252519:p.Asn394His		15506250	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.532809	0.45073	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	T;T	0.35605	1.3;1.3	5.55	4.39	0.52855	.	0.258412	0.44483	D	0.000442	T	0.60958	0.2309	M	0.92923	3.36	0.27720	N	0.94517	D	0.63880	0.993	P	0.61070	0.883	T	0.61252	-0.7100	10	0.62326	D	0.03	-15.6043	7.2343	0.26062	0.0:0.2443:0.0:0.7557	.	394	Q9BYF1	ACE2_HUMAN	H	394	ENSP00000252519:N394H;ENSP00000389326:N394H	ENSP00000252519:N394H	N	-	1	0	ACE2	15506250	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.392000	0.34486	0.746000	0.32786	0.441000	0.28932	AAT		0.448	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1			G	15596329	T	G	15596329	3	3	61	1	0	0	0	0	1	0	0	0	137	1841	64	4	1277	4	ACE2	23	15596329	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	220105	15596329	139674231	12031	20016										
ACE2	59272	broad.mit.edu	37	chrX	15609836	15609836	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctacagatcagcaaacttacGatttgctcttgccatctcat	5	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:15609836G>A	ENST00000252519.3	-	4	685	c.583C>T	c.(583-585)Cat>Tat	p.H195Y	ACE2_ENST00000427411.1_Splice_Site_p.H195Y			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	195					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.H195Y(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	GCAAACTTACGATTTGCTCTT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											236	221	226					X																	15609836		2203	4300	6503	15519757	SO:0001630	splice_region_variant	59272			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.583+1C>T	X.37:g.15609836G>A			15519757	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	G	9.375	1.071565	0.20147	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	T;T	0.32988	1.43;1.43	5.84	0.868	0.19090	.	0.563891	0.20129	N	0.098638	T	0.18841	0.0452	L	0.36672	1.1	0.21527	N	0.999653	P	0.36465	0.554	B	0.32624	0.149	T	0.11941	-1.0567	9	.	.	.	-1.3945	7.5979	0.28058	0.0:0.4556:0.1322:0.4123	.	195	Q9BYF1	ACE2_HUMAN	Y	195	ENSP00000252519:H195Y;ENSP00000389326:H195Y	.	H	-	1	0	ACE2	15519757	0.885000	0.30320	0.012000	0.15200	0.393000	0.30537	0.246000	0.18160	-0.124000	0.11724	-1.105000	0.02106	CAT		0.498	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1		Missense_Mutation	A	15609836	G	A	15609836	5	1	61	1	0	0	0	0	0	0	1	0	137	1072	37	1	1894	1	ACE2	23	15609836	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	13507	15609836	139660724	12032	20017										
ACE2	59272	broad.mit.edu	37	chrX	15609913	15609913	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgcttgccgacctcagatCtccagctttcccaagcccag	8	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:15609913C>A	ENST00000252519.3	-	4	608	c.506G>T	c.(505-507)aGa>aTa	p.R169I	ACE2_ENST00000427411.1_Missense_Mutation_p.R169I			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	169					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.R169I(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	GACCTCAGATCTCCAGCTTTC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											217	208	211					X																	15609913		2203	4300	6503	15519834	SO:0001583	missense	59272			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.506G>T	X.37:g.15609913C>A	ENSP00000252519:p.Arg169Ile		15519834	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.039273	0.75617	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	T;T	0.38077	1.16;1.16	6.14	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.72653	0.3487	H	0.97051	3.93	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.82534	-0.0409	10	0.87932	D	0	-23.0782	14.4186	0.67168	0.0:0.9283:0.0:0.0717	.	169	Q9BYF1	ACE2_HUMAN	I	169	ENSP00000252519:R169I;ENSP00000389326:R169I	ENSP00000252519:R169I	R	-	2	0	ACE2	15519834	1.000000	0.71417	0.841000	0.33234	0.590000	0.36582	6.918000	0.75788	1.345000	0.45676	0.596000	0.82720	AGA		0.428	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1			A	15609913	C	A	15609913	3	1	61	1	0	0	0	0	1	0	0	0	137	913	32	2	1971	2	ACE2	23	15609913	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	77	15609913	139660647	12033	20018										
TXLNG	55787	broad.mit.edu	37	chrX	16857989	16857989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaaagaaacaataatttggCgtaccaaatgggaaaacaat	7	5	0	1	rs200810818		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:16857989C>T	ENST00000380122.5	+	9	1259	c.1198C>T	c.(1198-1200)Cgt>Tgt	p.R400C	TXLNG_ENST00000398155.4_Missense_Mutation_p.R268C|TXLNG_ENST00000485153.1_3'UTR	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	400					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)	p.R400C(1)		breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						AATAATTTGGCGTACCAAATG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	101	103					X																	16857989		2203	4300	6503	16767910	SO:0001583	missense	55787			AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"lipopolysaccharide specific response-5 protein", "factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"	300677	"chromosome X open reading frame 15"	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.1198C>T	X.37:g.16857989C>T	ENSP00000369465:p.Arg400Cys		16767910	Q2KQ75|Q5JNZ7|Q9P0X1	Missense_Mutation	SNP	ENST00000380122.5	37	CCDS14178.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740245	0.69304	.	.	ENSG00000086712	ENST00000380122;ENST00000398155	T;T	0.34072	1.38;1.38	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.54743	0.1877	M	0.78637	2.42	0.80722	D	1	D;D	0.62365	0.988;0.991	P;P	0.51777	0.55;0.679	T	0.61676	-0.7014	10	0.87932	D	0	-0.1479	18.8131	0.92065	0.0:1.0:0.0:0.0	.	268;400	Q9NUQ3-2;Q9NUQ3	.;TXLNG_HUMAN	C	400;268	ENSP00000369465:R400C;ENSP00000381222:R268C	ENSP00000369465:R400C	R	+	1	0	TXLNG	16767910	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.955000	0.63638	2.390000	0.81377	0.538000	0.68166	CGT		0.373	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360		T	16857989	C	T	16857989	3	4	61	1	0	0	0	0	1	0	0	0	16829	768	27	1	1232	1	TXLNG	23	16857989	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1248076	16857989	138412571	12034	20019										
RBBP7	5931	broad.mit.edu	37	chrX	16870700	16870700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcatctttatgagattCgaaggtatggagttttaatt	8	3	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:16870700C>T	ENST00000380087.2	-	8	1297	c.937G>A	c.(937-939)Gaa>Aaa	p.E313K	RBBP7_ENST00000380084.4_Missense_Mutation_p.E357K|RBBP7_ENST00000404022.1_Missense_Mutation_p.E304K			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	313					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)	p.E313K(2)		biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					TTATGAGATTCGAAGGTATGG	0.343																																																2	Substitution - Missense(2)	large_intestine(2)	X											63	59	60					X																	16870700		2203	4300	6503	16780621	SO:0001583	missense	5931			U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"WD repeat domain containing"	9890	protein-coding gene	gene with protein product	"G1/S transition control protein-binding protein RbAp46", "retinoblastoma-binding protein 7", "retinoblastoma-binding protein RbAp46", "histone acetyltransferase type B subunit 2", "retinoblastoma-binding protein p46"	300825	"retinoblastoma-binding protein 7"			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.937G>A	X.37:g.16870700C>T	ENSP00000369427:p.Glu313Lys		16780621	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354446	0.82243	.	.	ENSG00000102054	ENST00000380087;ENST00000380084;ENST00000404022;ENST00000444437	T;T;T;T	0.64438	-0.1;-0.1;-0.1;0.24	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.55481	0.1923	L	0.31845	0.965	0.80722	D	1	B;B;B	0.21452	0.056;0.035;0.028	B;B;B	0.21708	0.014;0.036;0.014	T	0.54437	-0.8294	10	0.72032	D	0.01	1.2052	17.6398	0.88132	0.0:1.0:0.0:0.0	.	304;313;357	E9PC52;Q16576;Q5JP00	.;RBBP7_HUMAN;.	K	313;357;304;117	ENSP00000369427:E313K;ENSP00000369424:E357K;ENSP00000386068:E304K;ENSP00000402796:E117K	ENSP00000369424:E357K	E	-	1	0	RBBP7	16780621	1.000000	0.71417	0.655000	0.29622	0.980000	0.70556	7.772000	0.85439	2.469000	0.83416	0.594000	0.82650	GAA		0.343	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		T	16870700	C	T	16870700	3	4	61	1	0	0	0	0	1	0	0	0	13141	893	31	1	360	1	RBBP7	23	16870700	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	12711	16870700	138399860	12035	20020										
SCML2	10389	broad.mit.edu	37	chrX	18264796	18264796	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtggtgcctggcacacttcGagaaaaatcctgggagactg	13	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:18264796G>A	ENST00000251900.4	-	13	1882	c.1723C>T	c.(1723-1725)Cga>Tga	p.R575*	SCML2_ENST00000398048.3_Nonsense_Mutation_p.R311*	NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	575					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R575*(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					GGCACACTTCGAGAAAAATCC	0.418																																					Esophageal Squamous(100;1252 1965 19021 35517)											1	Substitution - Nonsense(1)	large_intestine(1)	X											101	95	97					X																	18264796		2203	4300	6503	18174717	SO:0001587	stop_gained	10389			Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"Sterile alpha motif (SAM) domain containing"	10581	protein-coding gene	gene with protein product		300208	"sex comb on midleg (Drosophila)-like 2"			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.1723C>T	X.37:g.18264796G>A	ENSP00000251900:p.Arg575*		18174717	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Nonsense_Mutation	SNP	ENST00000251900.4	37	CCDS14185.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894599	0.52121	.	.	ENSG00000102098	ENST00000251900;ENST00000398048;ENST00000442000	.	.	.	5.72	-1.01	0.10169	.	4.120150	0.00166	N	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	9.5626	0.39378	0.1423:0.5378:0.3198:0.0	.	.	.	.	X	575;311;543	.	ENSP00000251900:R575X	R	-	1	2	SCML2	18174717	0.915000	0.31059	0.000000	0.03702	0.004000	0.04260	1.904000	0.39868	-0.764000	0.04651	-0.229000	0.12294	CGA		0.418	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055941.1	NM_006089		A	18264796	G	A	18264796	4	1	61	1	0	0	0	0	0	1	0	0	13947	1066	37	1	391	1	SCML2	23	18264796	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1394096	18264796	137005764	12036	20021										
CDKL5	6792	broad.mit.edu	37	chrX	18622822	18622822	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcacctcacgaatctttttCttatggactgggctacacca	7	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:18622822C>A	ENST00000379989.3	+	13	2063	c.1778C>A	c.(1777-1779)tCt>tAt	p.S593Y	CDKL5_ENST00000463994.1_3'UTR|CDKL5_ENST00000379996.3_Missense_Mutation_p.S593Y	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	593					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.S593Y(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					GAATCTTTTTCTTATGGACTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											166	162	163					X																	18622822		2203	4300	6503	18532743	SO:0001583	missense	6792			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.1778C>A	X.37:g.18622822C>A	ENSP00000369325:p.Ser593Tyr		18532743	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.423428	0.43020	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.71461	-0.57;-0.57	6.03	5.17	0.71159	.	0.353179	0.37437	N	0.002086	T	0.58764	0.2145	L	0.27053	0.805	0.26348	N	0.977256	P	0.45902	0.868	B	0.39068	0.289	T	0.57900	-0.7731	10	0.87932	D	0	-3.9713	14.3609	0.66771	0.0:0.9277:0.0:0.0723	.	593	O76039	CDKL5_HUMAN	Y	593	ENSP00000369332:S593Y;ENSP00000369325:S593Y	ENSP00000369325:S593Y	S	+	2	0	CDKL5	18532743	1.000000	0.71417	0.369000	0.25952	0.678000	0.39670	4.537000	0.60643	1.298000	0.44778	0.600000	0.82982	TCT		0.498	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		A	18622822	C	A	18622822	3	1	61	1	0	0	0	0	1	0	0	0	3163	913	32	2	1820	2	CDKL5	23	18622822	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	358026	18622822	136647738	12037	20022										
RS1	6247	broad.mit.edu	37	chrX	18660161	18660161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgcactccagcagctccatcCggatggcaatgcggacgtgc	12	15	0	0	rs281865364		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:18660161C>T	ENST00000379984.3	-	6	678	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	CDKL5_ENST00000379989.3_Intron|RS1_ENST00000476595.1_5'UTR|CDKL5_ENST00000379996.3_Intron	NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	213	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.		R -> Q (in XLRS1). {ECO:0000269|PubMed:17615541}.|R -> W (in XLRS1).		adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.R213Q(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					CAGCTCCATCCGGATGGCAAT	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CM981773	RS1	M							54	50	51					X																	18660161		2203	4300	6503	18570082	SO:0001583	missense	6247			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"retinoschisis (X-linked, juvenile) 1"	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.638G>A	X.37:g.18660161C>T	ENSP00000369320:p.Arg213Gln		18570082	Q0QD39	Missense_Mutation	SNP	ENST00000379984.3	37	CCDS14187.1	.	.	.	.	.	.	.	.	.	.	C	36	5.907797	0.97093	.	.	ENSG00000102104	ENST00000379984	D	0.98666	-5.06	5.63	5.63	0.86233	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.99495	0.9820	H	0.97131	3.945	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.98137	1.0434	10	0.87932	D	0	.	18.6736	0.91521	0.0:1.0:0.0:0.0	.	213	O15537	XLRS1_HUMAN	Q	213	ENSP00000369320:R213Q	ENSP00000369320:R213Q	R	-	2	0	RS1	18570082	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.353000	0.79882	0.594000	0.82650	CGG		0.682	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1			T	18660161	C	T	18660161	3	4	61	1	0	0	0	0	1	0	0	0	13730	652	23	1	40	1	RS1	23	18660161	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	37339	18660161	136610399	12038	20023										
PPEF1	5475	broad.mit.edu	37	chrX	18779678	18779678	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaaactggatgatctttTtttgatcttctacaaggtaa	9	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:18779678T>A	ENST00000361511.4	+	9	1036	c.542T>A	c.(541-543)tTt>tAt	p.F181Y	PPEF1_ENST00000359763.6_Missense_Mutation_p.F128Y|PPEF1_ENST00000349874.5_Missense_Mutation_p.F181Y|PPEF1_ENST00000544635.1_Missense_Mutation_p.F116Y|PPEF1_ENST00000543630.1_Missense_Mutation_p.F181Y	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	181	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.F181Y(1)		breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					GATGATCTTTTTTTGATCTTC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											148	133	138					X																	18779678		2203	4300	6503	18689599	SO:0001583	missense	5475			BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9243	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, alpha isozyme"	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.542T>A	X.37:g.18779678T>A	ENSP00000354871:p.Phe181Tyr		18689599	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	37	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.810642	0.50421	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000543630;ENST00000472826;ENST00000544635	T;T;T;T;T;T	0.05382	3.45;3.45;3.45;3.45;3.45;3.45	5.47	4.29	0.51040	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.626077	0.15941	N	0.237186	T	0.14614	0.0353	M	0.63843	1.955	0.09310	N	1	D;P;P	0.56746	0.977;0.927;0.933	P;P;P	0.54174	0.709;0.744;0.623	T	0.08432	-1.0722	10	0.87932	D	0	-3.0753	8.5938	0.33703	0.0:0.0:0.192:0.808	.	181;181;181	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	Y	181;128;181;181;91;116	ENSP00000354871:F181Y;ENSP00000352806:F128Y;ENSP00000341892:F181Y;ENSP00000437785:F181Y;ENSP00000419948:F91Y;ENSP00000441289:F116Y	ENSP00000341892:F181Y	F	+	2	0	PPEF1	18689599	1.000000	0.71417	0.015000	0.15790	0.555000	0.35460	5.958000	0.70330	0.698000	0.31739	-0.369000	0.07265	TTT		0.338	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240		A	18779678	T	A	18779678	3	1	61	1	0	0	0	0	1	0	0	0	12338	1841	64	5	564	5	PPEF1	23	18779678	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	119517	18779678	136490882	12039	20024										
PHKA2	5256	broad.mit.edu	37	chrX	18911622	18911622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctattgcatctggcagcccGaattgggcaacaattcctgc	9	13	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:18911622G>A	ENST00000379942.4	-	33	4354	c.3689C>T	c.(3688-3690)tCg>tTg	p.S1230L	PHKA2-AS1_ENST00000452900.1_RNA|PHKA2-AS1_ENST00000439295.1_RNA|PHKA2_ENST00000481718.1_5'UTR	NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1230					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.S1230L(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CTGGCAGCCCGAATTGGGCAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	X											157	142	147					X																	18911622		2203	4300	6503	18821543	SO:0001583	missense	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.3689C>T	X.37:g.18911622G>A	ENSP00000369274:p.Ser1230Leu		18821543	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189101	0.78789	.	.	ENSG00000044446	ENST00000379942	D	0.95853	-3.83	5.91	5.91	0.95273	.	0.249082	0.39274	N	0.001413	D	0.93746	0.8001	L	0.46741	1.465	0.49213	D	0.999769	B	0.27316	0.175	B	0.26416	0.069	D	0.91110	0.4921	10	0.49607	T	0.09	-8.7187	19.2757	0.94030	0.0:0.0:1.0:0.0	.	1230	P46019	KPB2_HUMAN	L	1230	ENSP00000369274:S1230L	ENSP00000369274:S1230L	S	-	2	0	PHKA2	18821543	0.998000	0.40836	0.951000	0.38953	0.936000	0.57629	4.971000	0.63749	2.504000	0.84457	0.600000	0.82982	TCG		0.512	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		A	18911622	G	A	18911622	3	1	61	1	0	0	0	0	1	0	0	0	11875	1059	37	1	22	1	PHKA2	23	18911622	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	131944	18911622	136358938	12040	20025										
GPR64	10149	broad.mit.edu	37	chrX	19028798	19028798	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgacttggttgatcatttCtcctgcgaggttaggctcca	11	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:19028798C>A	ENST00000379869.3	-	17	1361	c.1198G>T	c.(1198-1200)Gaa>Taa	p.E400*	GPR64_ENST00000379878.3_Nonsense_Mutation_p.E384*|GPR64_ENST00000357991.3_Nonsense_Mutation_p.E397*|GPR64_ENST00000379873.2_Nonsense_Mutation_p.E400*|GPR64_ENST00000379876.1_Nonsense_Mutation_p.E376*|GPR64_ENST00000357544.3_Nonsense_Mutation_p.E370*|GPR64_ENST00000354791.3_Nonsense_Mutation_p.E384*|GPR64_ENST00000360279.4_Nonsense_Mutation_p.E378*|GPR64_ENST00000340581.3_Nonsense_Mutation_p.E370*|GPR64_ENST00000356606.4_Nonsense_Mutation_p.E386*	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	400					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.E397*(1)		breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					TTGATCATTTCTCCTGCGAGG	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											208	156	174					X																	19028798		2203	4300	6503	18938719	SO:0001587	stop_gained	10149			X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.1198G>T	X.37:g.19028798C>A	ENSP00000369198:p.Glu400*		18938719	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Nonsense_Mutation	SNP	ENST00000379869.3	37	CCDS43923.1	.	.	.	.	.	.	.	.	.	.	C	36	5.632985	0.96682	.	.	ENSG00000173698	ENST00000379873;ENST00000379878;ENST00000354791;ENST00000379876;ENST00000357544;ENST00000379869;ENST00000360279;ENST00000357991;ENST00000356606;ENST00000340581	.	.	.	6.08	2.3	0.28687	.	0.691331	0.13712	N	0.368028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	1.1643	0.01812	0.2667:0.289:0.2796:0.1647	.	.	.	.	X	400;384;384;376;370;400;378;397;386;370	.	ENSP00000344972:E370X	E	-	1	0	GPR64	18938719	0.011000	0.17503	0.274000	0.24659	0.980000	0.70556	-0.133000	0.10451	0.260000	0.21731	0.600000	0.82982	GAA		0.522	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2			A	19028798	C	A	19028798	4	1	61	1	0	0	0	0	0	1	0	0	6725	922	32	2	1907	2	GPR64	23	19028798	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	117176	19028798	136241762	12041	20026										
PDHA1	5160	broad.mit.edu	37	chrX	19368189	19368189	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagatcagctgtataaacaGaaaattattcgtggtttctg	9	6	2	2	rs144828838	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:19368189G>T	ENST00000422285.2	+	3	357	c.252G>T	c.(250-252)caG>caT	p.Q84H	PDHA1_ENST00000540249.1_Missense_Mutation_p.Q84H|PDHA1_ENST00000545074.1_Missense_Mutation_p.Q84H|PDHA1_ENST00000379806.5_Missense_Mutation_p.Q122H|PDHA1_ENST00000379805.3_Missense_Mutation_p.Q84H			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	84					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)	p.Q84H(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)	18	Hepatocellular(33;0.183)					TGTATAAACAGAAAATTATTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											274	223	240					X																	19368189		2203	4300	6503	19278110	SO:0001583	missense	5160				CCDS14192.1, CCDS55380.1, CCDS55381.1, CCDS55382.1	Xp22.1	2008-02-05			ENSG00000131828	ENSG00000131828	1.2.4.1		8806	protein-coding gene	gene with protein product		300502		PDHA			Standard	NM_001173454		Approved		uc004czh.4	P08559	OTTHUMG00000021224	ENST00000422285.2:c.252G>T	X.37:g.19368189G>T	ENSP00000394382:p.Gln84His		19278110	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Missense_Mutation	SNP	ENST00000422285.2	37	CCDS14192.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003776	0.74932	.	.	ENSG00000131828	ENST00000379806;ENST00000545074;ENST00000540249;ENST00000423505;ENST00000417819;ENST00000422285;ENST00000355808;ENST00000379815;ENST00000379805	D;D;D;D;D;D;D;D	0.99277	-4.41;-4.41;-4.41;-4.41;-5.67;-4.41;-4.41;-4.41	5.17	4.29	0.51040	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99269	0.9745	M	0.87547	2.89	0.58432	D	0.999998	P;D;D;D;D	0.64830	0.804;0.994;0.977;0.983;0.977	B;D;D;P;D	0.65140	0.413;0.932;0.929;0.887;0.929	D	0.98802	1.0740	10	0.62326	D	0.03	-20.6353	10.3178	0.43747	0.1616:0.0:0.8384:0.0	.	84;84;84;122;84	B7Z3X5;B7Z3T7;B2R5P7;A5YVE9;P08559	.;.;.;.;ODPA_HUMAN	H	122;84;84;122;112;84;84;112;84	ENSP00000369134:Q122H;ENSP00000438550:Q84H;ENSP00000440761:Q84H;ENSP00000406473:Q122H;ENSP00000404616:Q112H;ENSP00000394382:Q84H;ENSP00000348062:Q84H;ENSP00000369133:Q84H	ENSP00000348062:Q84H	Q	+	3	2	PDHA1	19278110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.291000	0.65667	2.283000	0.76528	0.600000	0.82982	CAG		0.443	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			T	19368189	G	T	19368189	3	4	61	1	0	0	0	0	1	0	0	0	11695	933	33	2	380	2	PDHA1	23	19368189	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	339391	19368189	135902371	12042	20027										
SH3KBP1	30011	broad.mit.edu	37	chrX	19725017	19725017	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctctcctaccacctctatGatgtcgccaactttcagctc	4	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:19725017G>T	ENST00000397821.3	-	4	662	c.372C>A	c.(370-372)atC>atA	p.I124I	SH3KBP1_ENST00000379697.3_Silent_p.I124I|SH3KBP1_ENST00000379698.4_Silent_p.I87I	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	124	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.I124I(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CCACCTCTATGATGTCGCCAA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	X											88	72	77					X																	19725017		2203	4300	6503	19634938	SO:0001819	synonymous_variant	30011			AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.372C>A	X.37:g.19725017G>T			19634938	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Silent	SNP	ENST00000397821.3	37	CCDS14193.1																																																																																				0.582	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		T	19725017	G	T	19725017	2	4	61	1	0	0	0	0	0	0	0	1	14292	1280	45	2		2	SH3KBP1	23	19725017	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	356828	19725017	135545543	12043	20028										
MAP7D2	256714	broad.mit.edu	37	chrX	20031204	20031204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacaaccagttttgtcttcTtttccacacacacagcaggc	7	13	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:20031204T>C	ENST00000379651.3	-	13	1748	c.1730A>G	c.(1729-1731)aAg>aGg	p.K577R	MAP7D2_ENST00000452324.3_Missense_Mutation_p.K525R|MAP7D2_ENST00000543767.1_Missense_Mutation_p.K462R|MAP7D2_ENST00000379643.5_Missense_Mutation_p.K618R|MAP7D2_ENST00000443379.3_Missense_Mutation_p.K532R	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	577					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)		p.K577R(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						TTTTGTCTTCTTTTCCACACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X											261	237	245					X																	20031204		2203	4300	6503	19941125	SO:0001583	missense	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1730A>G	X.37:g.20031204T>C	ENSP00000368972:p.Lys577Arg		19941125	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	T	11.13	1.549023	0.27652	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.23754	2.21;3.54;3.54;1.89;2.21	4.67	3.47	0.39725	.	0.212145	0.40908	D	0.000995	T	0.12518	0.0304	N	0.14661	0.345	0.22728	N	0.998804	B;B;B;B;B	0.31879	0.233;0.344;0.344;0.233;0.228	B;B;B;B;B	0.31191	0.059;0.125;0.125;0.059;0.125	T	0.25328	-1.0135	10	0.17832	T	0.49	-12.0492	7.7637	0.28968	0.0:0.0981:0.0:0.9019	.	532;525;618;577;462	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	R	577;618;462;532;260;525	ENSP00000368972:K577R;ENSP00000368964:K618R;ENSP00000440691:K462R;ENSP00000388239:K532R;ENSP00000413301:K525R	ENSP00000368964:K618R	K	-	2	0	MAP7D2	19941125	0.989000	0.36119	0.966000	0.40874	0.434000	0.31775	1.104000	0.31074	0.707000	0.31934	0.427000	0.28365	AAG		0.458	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		C	20031204	T	C	20031204	3	2	61	1	0	0	0	0	1	0	0	0	9298	1609	56	4	480	4	MAP7D2	23	20031204	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	306187	20031204	135239356	12044	20029										
MAP7D2	256714	broad.mit.edu	37	chrX	20034397	20034397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcgggcttcctcttctaggcGaagcctttcctcctctgcct	8	16	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:20034397G>A	ENST00000379651.3	-	10	1354	c.1336C>T	c.(1336-1338)Cgc>Tgc	p.R446C	MIR23C_ENST00000579846.1_RNA|MAP7D2_ENST00000452324.3_Missense_Mutation_p.R394C|MAP7D2_ENST00000543767.1_Missense_Mutation_p.R331C|MAP7D2_ENST00000379643.5_Missense_Mutation_p.R487C|MAP7D2_ENST00000443379.3_Missense_Mutation_p.R401C	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	446					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)		p.R446C(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						tcttctaggcgaagcctttcc	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	X											68	63	65					X																	20034397		2203	4300	6503	19944318	SO:0001583	missense	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1336C>T	X.37:g.20034397G>A	ENSP00000368972:p.Arg446Cys		19944318	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.716266	0.30413	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.19	3.37	0.38596	.	0.685242	0.14464	N	0.318001	T	0.35799	0.0944	M	0.86502	2.82	0.21652	N	0.99961	B;B;B;B;B	0.24675	0.109;0.012;0.089;0.109;0.022	B;B;B;B;B	0.16289	0.015;0.006;0.009;0.015;0.005	T	0.42632	-0.9440	10	0.87932	D	0	1.1329	5.5388	0.17026	0.1026:0.0:0.7017:0.1957	.	401;394;487;446;331	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	C	446;487;331;401;129;394	ENSP00000368972:R446C;ENSP00000368964:R487C;ENSP00000440691:R331C;ENSP00000388239:R401C;ENSP00000413301:R394C	ENSP00000368964:R487C	R	-	1	0	MAP7D2	19944318	0.977000	0.34250	0.027000	0.17364	0.733000	0.41908	2.150000	0.42254	0.646000	0.30693	0.540000	0.68198	CGC		0.468	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		A	20034397	G	A	20034397	3	1	61	1	0	0	0	0	1	0	0	0	9298	1058	37	1	886	1	MAP7D2	23	20034397	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3193	20034397	135236163	12045	20030										
MAP7D2	256714	broad.mit.edu	37	chrX	20062574	20062574	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttcttcttctcaatgtttcGagtgggtgaagacttgtaag	10	6	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:20062574G>A	ENST00000379651.3	-	6	682	c.664C>T	c.(664-666)Cga>Tga	p.R222*	MAP7D2_ENST00000452324.3_Nonsense_Mutation_p.R170*|MAP7D2_ENST00000543767.1_Nonsense_Mutation_p.R107*|MAP7D2_ENST00000379643.5_Nonsense_Mutation_p.R263*|MAP7D2_ENST00000443379.3_Nonsense_Mutation_p.R177*	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	222					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)		p.R222*(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						TCAATGTTTCGAGTGGGTGAA	0.463																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											208	185	193					X																	20062574		2203	4300	6503	19972495	SO:0001587	stop_gained	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.664C>T	X.37:g.20062574G>A	ENSP00000368972:p.Arg222*		19972495	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Nonsense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408777	0.62399	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000452324	.	.	.	5.1	2.18	0.27775	.	0.097082	0.44902	D	0.000407	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3162	8.4092	0.32634	0.0749:0.0:0.6521:0.273	.	.	.	.	X	222;263;107;177;170	.	ENSP00000368964:R263X	R	-	1	2	MAP7D2	19972495	1.000000	0.71417	0.136000	0.22124	0.051000	0.14879	1.764000	0.38471	0.368000	0.24481	-0.191000	0.12829	CGA		0.463	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		A	20062574	G	A	20062574	4	1	61	1	0	0	0	0	0	1	0	0	9298	1066	37	1	1574	1	MAP7D2	23	20062574	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	28177	20062574	135207986	12046	20031										
RPS6KA3	6197	broad.mit.edu	37	chrX	20185793	20185793	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagaaaaatttttgtctaaGaattttatccagcaattcac	5	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:20185793G>T	ENST00000379565.3	-	17	1723	c.1516C>A	c.(1516-1518)Ctt>Att	p.L506I	RPS6KA3_ENST00000379548.4_Missense_Mutation_p.L476I|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.L478I|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.L477I|RPS6KA3_ENST00000479809.1_5'UTR	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	506	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L506I(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTTTGTCTAAGAATTTTATCC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											164	172	169					X																	20185793		2203	4300	6503	20095714	SO:0001583	missense	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1516C>A	X.37:g.20185793G>T	ENSP00000368884:p.Leu506Ile		20095714	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408583	0.83340	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	5.8	5.8	0.92144	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	N	0.05467	-0.045	0.80722	D	1	B;B;D;P	0.67145	0.28;0.237;0.996;0.664	P;B;D;P	0.97110	0.538;0.35;1.0;0.635	T	0.66590	-0.5885	10	0.28530	T	0.3	.	18.9908	0.92791	0.0:0.0:1.0:0.0	.	477;476;478;506	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	I	506;478;476;477	ENSP00000368884:L506I;ENSP00000440220:L478I;ENSP00000368865:L476I;ENSP00000444837:L477I	ENSP00000368865:L476I	L	-	1	0	RPS6KA3	20095714	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.028000	0.88798	2.434000	0.82447	0.513000	0.50165	CTT		0.338	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		T	20185793	G	T	20185793	3	4	61	1	0	0	0	0	1	0	0	0	13689	942	33	2	730	2	RPS6KA3	23	20185793	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	123219	20185793	135084767	12047	20032										
ZNF645	158506	broad.mit.edu	37	chrX	22291957	22291957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctcagaaacagcattatgcGccacctccatctccatcatc	4	17	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:22291957G>A	ENST00000323684.1	+	1	893	c.849G>A	c.(847-849)gcG>gcA	p.A283A		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	283	Pro-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A283A(3)		cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						AGCATTATGCGCCACCTCCAT	0.473																																																3	Substitution - coding silent(3)	large_intestine(2)|urinary_tract(1)	X											150	116	127					X																	22291957		2203	4300	6503	22201878	SO:0001819	synonymous_variant	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.849G>A	X.37:g.22291957G>A			22201878	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																				0.473	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		A	22291957	G	A	22291957	2	1	61	1	0	0	0	0	0	0	0	1	18100	1074	38	1		1	ZNF645	23	22291957	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2106164	22291957	132978603	12048	20033										
CXorf58	254158	broad.mit.edu	37	chrX	23953382	23953382	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagctggcgcaaattaaatCttgaaaatattcccaggaca	7	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:23953382C>T	ENST00000379211.3	+	7	1174	c.625C>T	c.(625-627)Ctt>Ttt	p.L209F		NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	209								p.L209F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						CAAATTAAATCTTGAAAATAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											96	97	97					X																	23953382		2203	4300	6503	23863303	SO:0001583	missense	254158			AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.625C>T	X.37:g.23953382C>T	ENSP00000368511:p.Leu209Phe		23863303		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	c	13.02	2.112707	0.37242	.	.	ENSG00000165182	ENST00000379211	T	0.47528	0.84	5.91	5.91	0.95273	.	0.000000	0.56097	D	0.000022	T	0.66479	0.2793	M	0.71581	2.175	0.24646	N	0.993546	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63143	-0.6703	10	0.87932	D	0	-10.0909	11.9281	0.52831	0.0:0.9154:0.0:0.0846	.	209;209	B7ZLS7;Q96LI9	.;CX058_HUMAN	F	209	ENSP00000368511:L209F	ENSP00000368511:L209F	L	+	1	0	CXorf58	23863303	0.968000	0.33430	0.097000	0.21041	0.031000	0.12232	3.097000	0.50251	2.496000	0.84212	0.417000	0.27973	CTT		0.388	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761		T	23953382	C	T	23953382	3	4	61	1	0	0	0	0	1	0	0	0	4120	913	32	3	647	3	CXorf58	23	23953382	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1661425	23953382	131317178	12049	20034										
PDK3	5165	broad.mit.edu	37	chrX	24546235	24546235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccacttcgaaaaatagatCgtctttttaactacatgtat	4	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:24546235C>T	ENST00000379162.4	+	9	1130	c.895C>T	c.(895-897)Cgt>Tgt	p.R299C	PDK3_ENST00000441463.2_Missense_Mutation_p.R299C	NM_005391.4	NP_005382.1	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase, isozyme 3	299	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cell death (GO:0008219)|cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|peptidyl-serine phosphorylation (GO:0018105)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|regulation of reactive oxygen species metabolic process (GO:2000377)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.R299C(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AAAAATAGATCGTCTTTTTAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											147	121	130					X																	24546235		2203	4300	6503	24456156	SO:0001583	missense	5165			L42452	CCDS14212.1, CCDS48088.1	Xp22.12	2008-02-05	2005-11-16		ENSG00000067992	ENSG00000067992			8811	protein-coding gene	gene with protein product		300906	"pyruvate dehydrogenase kinase, isoenzyme 3"			7499431	Standard	NM_001142386		Approved		uc004dbh.3	Q15120	OTTHUMG00000021269	ENST00000379162.4:c.895C>T	X.37:g.24546235C>T	ENSP00000368460:p.Arg299Cys		24456156	B4DXG6	Missense_Mutation	SNP	ENST00000379162.4	37	CCDS14212.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.133463	0.56828	.	.	ENSG00000067992	ENST00000379162;ENST00000441463	T;T	0.79653	-1.29;-1.29	4.97	4.97	0.65823	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.86289	0.5897	H	0.96489	3.83	0.80722	D	1	P;P	0.43826	0.818;0.553	B;B	0.39660	0.306;0.206	D	0.90126	0.4203	10	0.72032	D	0.01	.	13.2895	0.60262	0.1686:0.8314:0.0:0.0	.	299;299	B4DXG6;Q15120	.;PDK3_HUMAN	C	299	ENSP00000368460:R299C;ENSP00000387536:R299C	ENSP00000368460:R299C	R	+	1	0	PDK3	24456156	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.247000	0.58750	2.305000	0.77605	0.513000	0.50165	CGT		0.423	PDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056097.1	NM_005391		T	24546235	C	T	24546235	3	4	61	1	0	0	0	0	1	0	0	0	11708	884	31	1	929	1	PDK3	23	24546235	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	592853	24546235	130724325	12050	20035										
DCAF8L1	139425	broad.mit.edu	37	chrX	27999204	27999204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaataaaccttcacccatgCtttcaagttcgacgtcttca	4	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:27999204C>T	ENST00000441525.1	-	1	362	c.248G>A	c.(247-249)aGc>aAc	p.S83N		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	83	Glu-rich.							p.S83N(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						TTCACCCATGCTTTCAAGTTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											183	137	152					X																	27999204		2202	4300	6502	27909125	SO:0001583	missense	139425				CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"WD repeat domain containing"	31810	protein-coding gene	gene with protein product			"WD repeat domain 42B"	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.248G>A	X.37:g.27999204C>T	ENSP00000405222:p.Ser83Asn		27909125	B3KXX1	Missense_Mutation	SNP	ENST00000441525.1	37	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	C	7.268	0.606493	0.14002	.	.	ENSG00000226372	ENST00000441525	T	0.67523	-0.27	0.842	-0.498	0.12019	.	0.352689	0.30118	N	0.010366	T	0.53417	0.1795	L	0.49350	1.555	0.21950	N	0.999452	B	0.19200	0.034	B	0.19391	0.025	T	0.43669	-0.9377	10	0.44086	T	0.13	-1.565	6.2033	0.20587	0.0:0.6862:0.3138:0.0	.	83	A6NGE4	DC8L1_HUMAN	N	83	ENSP00000405222:S83N	ENSP00000405222:S83N	S	-	2	0	DCAF8L1	27909125	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	2.664000	0.46783	-0.208000	0.10171	0.284000	0.19432	AGC		0.483	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		T	27999204	C	T	27999204	3	4	61	1	0	0	0	0	1	0	0	0	4283	797	28	3	1558	3	DCAF8L1	23	27999204	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3452969	27999204	127271356	12051	20036										
IL1RAPL1	11141	broad.mit.edu	37	chrX	29935661	29935661	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatttactggatgaaaggaGaaaaatttattgaagatctg	9	2	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:29935661G>A	ENST00000378993.1	+	7	1532	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.E287K	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	287	Ig-like C2-type 3.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.E287K(2)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						GATGAAAGGAGAAAAATTTAT	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	X											61	59	60					X																	29935661		2202	4300	6502	29845582	SO:0001583	missense	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.859G>A	X.37:g.29935661G>A	ENSP00000368278:p.Glu287Lys		29845582	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743894	0.89663	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.13901	2.55;2.55	5.78	5.78	0.91487	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051429	0.85682	D	0.000000	T	0.33527	0.0866	L	0.57536	1.79	0.58432	D	0.999996	D	0.59357	0.985	P	0.62885	0.908	T	0.00638	-1.1632	9	.	.	.	.	18.9267	0.92548	0.0:0.0:1.0:0.0	.	287	Q9NZN1	IRPL1_HUMAN	K	287	ENSP00000368278:E287K;ENSP00000305200:E287K	.	E	+	1	0	IL1RAPL1	29845582	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.476000	0.97823	2.417000	0.82017	0.600000	0.82982	GAA		0.368	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		A	29935661	G	A	29935661	3	1	61	1	0	0	0	0	1	0	0	0	7682	943	33	3	881	3	IL1RAPL1	23	29935661	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1936457	29935661	125334899	12052	20037										
IL1RAPL1	11141	broad.mit.edu	37	chrX	29973736	29973736	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tactaccgaagctatgagtaCgacgtacctcctaccggcac	8	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:29973736C>T	ENST00000378993.1	+	11	2563	c.1890C>T	c.(1888-1890)taC>taT	p.Y630Y	IL1RAPL1_ENST00000302196.4_Silent_p.Y630Y	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	630	Interaction with NCS1.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.Y630Y(1)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						GCTATGAGTACGACGTACCTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	X											91	44	60					X																	29973736		2202	4300	6502	29883657	SO:0001819	synonymous_variant	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1890C>T	X.37:g.29973736C>T			29883657	A0AVG4|Q9UJ53	Silent	SNP	ENST00000378993.1	37	CCDS14218.1																																																																																				0.517	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29973736	C	T	29973736	2	4	61	1	0	0	0	0	0	0	0	1	7682	547	19	1		1	IL1RAPL1	23	29973736	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	38075	29973736	125296824	12053	20038										
MAGEB2	4113	broad.mit.edu	37	chrX	30237186	30237186	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgagggcctcagtgttgtCtttggccttgagctgaataa	12	8	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:30237186C>A	ENST00000378988.4	+	2	590	c.489C>A	c.(487-489)gtC>gtA	p.V163V		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	163	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.V163V(2)		breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						TCAGTGTTGTCTTTGGCCTTG	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	X											51	46	48					X																	30237186		2202	4300	6502	30147107	SO:0001819	synonymous_variant	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.489C>A	X.37:g.30237186C>A			30147107	O75860	Silent	SNP	ENST00000378988.4	37	CCDS14219.1																																																																																				0.498	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		A	30237186	C	A	30237186	2	1	61	1	0	0	0	0	0	0	0	1	9206	900	32	2		2	MAGEB2	23	30237186	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	263450	30237186	125033374	12054	20039										
MAGEB1	4112	broad.mit.edu	37	chrX	30269013	30269013	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattatgaaggcagatatgCtgaaggttgttgatgaaaag	12	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:30269013C>T	ENST00000378981.3	+	4	724	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L	MAGEB1_ENST00000397548.2_Silent_p.L135L|MAGEB1_ENST00000397550.1_Silent_p.L135L	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	135	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.L135L(1)		NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						GGCAGATATGCTGAAGGTTGT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	X											63	49	54					X																	30269013		2202	4300	6502	30178934	SO:0001819	synonymous_variant	4112				CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 10", "cancer/testis antigen family 3, member 1"	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.403C>T	X.37:g.30269013C>T			30178934	B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Silent	SNP	ENST00000378981.3	37	CCDS14222.1																																																																																				0.463	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363		T	30269013	C	T	30269013	2	4	61	1	0	0	0	0	0	0	0	1	9202	796	28	3		3	MAGEB1	23	30269013	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	31827	30269013	125001547	12055	20040										
CXorf21	80231	broad.mit.edu	37	chrX	30577583	30577583	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctctatggatttacattgCtatactgagaaatatggaga	8	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:30577583C>A	ENST00000378962.3	-	3	1212	c.890G>T	c.(889-891)aGc>aTc	p.S297I		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	297								p.S297I(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						ATTTACATTGCTATACTGAGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	60	63					X																	30577583		2202	4300	6502	30487504	SO:0001583	missense	80231			BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.890G>T	X.37:g.30577583C>A	ENSP00000368245:p.Ser297Ile		30487504		Missense_Mutation	SNP	ENST00000378962.3	37	CCDS14224.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.714213	0.68730	.	.	ENSG00000120280	ENST00000378962	.	.	.	5.11	5.11	0.69529	.	0.297876	0.35525	N	0.003145	T	0.76926	0.4056	L	0.60455	1.87	0.46631	D	0.999138	D	0.76494	0.999	D	0.85130	0.997	T	0.79245	-0.1883	9	0.72032	D	0.01	-3.3288	17.6373	0.88125	0.0:1.0:0.0:0.0	.	297	Q9HAI6	CX021_HUMAN	I	297	.	ENSP00000368245:S297I	S	-	2	0	CXorf21	30487504	1.000000	0.71417	0.994000	0.49952	0.909000	0.53808	3.998000	0.57024	2.351000	0.79841	0.513000	0.50165	AGC		0.383	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159		A	30577583	C	A	30577583	3	1	61	1	0	0	0	0	1	0	0	0	4107	797	28	2	19	2	CXorf21	23	30577583	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	308570	30577583	124692977	12056	20041										
DMD	1756	broad.mit.edu	37	chrX	31947777	31947777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatcttgctcttctgggcttAtgggagcacttacaagcacg	10	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:31947777A>G	ENST00000357033.4	-	47	7054	c.6848T>C	c.(6847-6849)aTa>aCa	p.I2283T	DMD_ENST00000541735.1_5'UTR|DMD_ENST00000378677.2_Missense_Mutation_p.I2279T|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000474231.1_5'UTR|DMD_ENST00000359836.1_5'UTR|DMD_ENST00000343523.2_5'UTR	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2283					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.I2278T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				TTCTGGGCTTATGGGAGCACT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											211	166	181					X																	31947777		2202	4300	6502	31857698	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6848T>C	X.37:g.31947777A>G	ENSP00000354923:p.Ile2283Thr		31857698	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028615	0.35797	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.34472	1.36;1.36	5.02	3.85	0.44370	.	0.443560	0.15066	U	0.282484	T	0.22003	0.0530	N	0.21448	0.665	0.80722	D	1	B;B;B;B;B	0.10296	0.0;0.002;0.0;0.003;0.003	B;B;B;B;B	0.11329	0.002;0.004;0.004;0.006;0.006	T	0.04360	-1.0957	10	0.11794	T	0.64	.	9.5333	0.39207	0.915:0.0:0.085:0.0	.	2275;2283;2279;942;939	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	T	2275;942;939;2279;2283;2283;2160	ENSP00000367948:I2279T;ENSP00000354923:I2283T	ENSP00000354923:I2283T	I	-	2	0	DMD	31857698	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	5.061000	0.64319	1.763000	0.52060	0.486000	0.48141	ATA		0.428	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31947777	A	G	31947777	3	3	61	1	0	0	0	0	1	0	0	0	4591	449	16	4	4489	4	DMD	23	31947777	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1370194	31947777	123322783	12057	20042										
DMD	1756	broad.mit.edu	37	chrX	32361387	32361387	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctagagccttttttcttCtttgagacctcaaatcctgt	5	10	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:32361387C>T	ENST00000357033.4	-	40	5809	c.5603G>A	c.(5602-5604)aGa>aAa	p.R1868K	DMD_ENST00000378677.2_Missense_Mutation_p.R1864K	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1868	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R1863K(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CTTTTTTCTTCTTTGAGACCT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											98	88	91					X																	32361387		2202	4299	6501	32271308	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5603G>A	X.37:g.32361387C>T	ENSP00000354923:p.Arg1868Lys		32271308	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848459	0.71603	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000493412	T;T;T	0.58940	0.3;0.3;0.3	5.62	5.62	0.85841	.	0.000000	0.40554	U	0.001063	T	0.66790	0.2825	L	0.39898	1.24	0.80722	D	1	D;D;D;P;P	0.67145	0.996;0.996;0.994;0.956;0.956	D;P;D;D;D	0.76071	0.987;0.824;0.97;0.931;0.931	T	0.58685	-0.7593	10	0.09084	T	0.74	.	18.8812	0.92356	0.0:1.0:0.0:0.0	.	1860;1868;1864;527;524	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	K	1860;527;524;1864;1868;1868;1745;87	ENSP00000367948:R1864K;ENSP00000354923:R1868K;ENSP00000417725:R87K	ENSP00000354923:R1868K	R	-	2	0	DMD	32271308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.709000	0.74665	2.493000	0.84123	0.594000	0.82650	AGA		0.348	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32361387	C	T	32361387	3	4	61	1	0	0	0	0	1	0	0	0	4591	913	32	3	5762	3	DMD	23	32361387	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	413610	32361387	122909173	12058	20043										
DMD	1756	broad.mit.edu	37	chrX	32430296	32430296	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacattaaggaaataggctgGaaaaaaaattagcaaaatca	7	4	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:32430296G>T	ENST00000357033.4	-	30	4278				DMD_ENST00000378677.2_Intron	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin						cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.P11T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				AAATAGGCTGGAAAAAAAATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											66	56	59					X																	32430296		1863	4093	5956	32340217	SO:0001627	intron_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.4072-266C>A	X.37:g.32430296G>T			32340217	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.479609	0.01035	.	.	ENSG00000198947	ENST00000378682	.	.	.	5.3	-1.0	0.10196	.	.	.	.	.	T	0.15219	0.0367	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20706	-1.0267	8	0.62326	D	0.03	.	1.505	0.02484	0.2809:0.2296:0.3698:0.1197	.	11	E7EQS7	.	T	11	.	ENSP00000367953:P11T	P	-	1	0	DMD	32340217	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.651000	0.24873	-0.103000	0.12175	-1.236000	0.01555	CCA		0.338	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32430296	G	T	32430296	1	4	61	0	1	0	0	0	0	0	0	0	4591	1174	41	2		2	DMD	23	32430296	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68909	32430296	122840264	12059	20044										
DMD	1756	broad.mit.edu	37	chrX	32613885	32613885	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatctgaccttaagttgttCttccaaagcagcagttgcgt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:32613885C>A	ENST00000357033.4	-	13	1797	c.1591G>T	c.(1591-1593)Gaa>Taa	p.E531*	DMD_ENST00000378677.2_Nonsense_Mutation_p.E527*|DMD_ENST00000288447.4_Nonsense_Mutation_p.E523*	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	531			Missing (in BMD).		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E526*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				TTAAGTTGTTCTTCCAAAGCA	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											140	113	122					X																	32613885		2202	4300	6502	32523806	SO:0001587	stop_gained	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.1591G>T	X.37:g.32613885C>A	ENSP00000354923:p.Glu531*		32523806	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Nonsense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	39	7.338143	0.98221	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	.	.	.	5.74	3.65	0.41850	.	0.000000	0.37530	U	0.002044	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	7.632	0.28245	0.0:0.6781:0.14:0.1819	.	.	.	.	X	523;527;531;531;408;523	.	ENSP00000288447:E523X	E	-	1	0	DMD	32523806	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	1.731000	0.38135	1.178000	0.42870	0.538000	0.68166	GAA		0.328	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32613885	C	A	32613885	4	1	61	1	0	0	0	0	0	1	0	0	4591	922	32	2	9977	2	DMD	23	32613885	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	183589	32613885	122656675	12060	20045										
DMD	1756	broad.mit.edu	37	chrX	32834697	32834697	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgtcggacccagctcaggaGaatcttttcactgttggttt	10	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:32834697G>T	ENST00000357033.4	-	6	624	c.418C>A	c.(418-420)Ctc>Atc	p.L140I	DMD_ENST00000288447.4_Missense_Mutation_p.L132I|DMD_ENST00000378677.2_Missense_Mutation_p.L136I	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	140	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L135I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CAGCTCAGGAGAATCTTTTCA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											170	148	155					X																	32834697		2202	4300	6502	32744618	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.418C>A	X.37:g.32834697G>T	ENSP00000354923:p.Leu140Ile		32744618	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843419	0.71488	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	D;D;D	0.98028	-4.67;-4.67;-4.67	5.51	4.53	0.55603	Calponin homology domain (5);	0.000000	0.32935	U	0.005469	D	0.98538	0.9512	M	0.89785	3.06	0.80722	D	1	D;D;D;D;D	0.76494	0.996;0.997;0.996;0.999;0.997	D;D;D;D;D	0.91635	0.998;0.999;0.998;0.996;0.999	D	0.98888	1.0772	10	0.72032	D	0.01	.	6.5008	0.22168	0.3027:0.0:0.6973:0.0	.	140;132;132;140;136	F5H6K1;Q4G0X0;P11532-4;P11532;E9PDN5	.;.;.;DMD_HUMAN;.	I	132;136;140;140;17;132	ENSP00000367948:L136I;ENSP00000354923:L140I;ENSP00000288447:L132I	ENSP00000288447:L132I	L	-	1	0	DMD	32744618	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.647000	0.46639	2.300000	0.77407	0.600000	0.82982	CTC		0.388	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32834697	G	T	32834697	3	4	61	1	0	0	0	0	1	0	0	0	4591	942	33	2	11178	2	DMD	23	32834697	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	220812	32834697	122435863	12061	20046										
FAM47A	158724	broad.mit.edu	37	chrX	34148398	34148398	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttcctgtgagaagaatttGtcctcatccttttcatctag	6	9	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:34148398G>A	ENST00000346193.3	-	1	2049	c.1998C>T	c.(1996-1998)gaC>gaT	p.D666D		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	666								p.D666D(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						AGAAGAATTTGTCCTCATCCT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	X											90	90	90					X																	34148398		2196	4294	6490	34058319	SO:0001819	synonymous_variant	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1998C>T	X.37:g.34148398G>A			34058319	A8K8I9|Q8TAA0	Silent	SNP	ENST00000346193.3	37	CCDS43926.1																																																																																				0.448	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34148398	G	A	34148398	2	1	61	1	0	0	0	0	0	0	0	1	5588	1368	48	3		3	FAM47A	23	34148398	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1313701	34148398	121122162	12062	20047										
MAGEB16	139604	broad.mit.edu	37	chrX	35821084	35821084	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accaaagattttgtgaaggaGaagtacctggagtaccagca	11	7	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:35821084G>T	ENST00000399989.1	+	2	1050	c.771G>T	c.(769-771)gaG>gaT	p.E257D	MAGEB16_ENST00000399988.1_Missense_Mutation_p.E257D|MAGEB16_ENST00000399985.1_Missense_Mutation_p.E257D|MAGEB16_ENST00000399987.1_Missense_Mutation_p.E257D|MAGEB16_ENST00000399992.1_Missense_Mutation_p.E289D	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	257	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.E424D(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						TTGTGAAGGAGAAGTACCTGG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											39	39	39					X																	35821084		2190	4293	6483	35731005	SO:0001583	missense	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.771G>T	X.37:g.35821084G>T	ENSP00000382871:p.Glu257Asp		35731005	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288065	0.40494	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.05580	3.42;3.42;3.42;3.42;3.42	3.06	-2.37	0.06643	.	0.112463	0.64402	D	0.000010	T	0.11580	0.0282	M	0.86028	2.79	0.09310	N	1	P	0.52577	0.954	P	0.47251	0.542	T	0.06607	-1.0817	10	0.46703	T	0.11	.	7.8104	0.29228	0.4088:0.0:0.5912:0.0	.	257	A2A368	MAGBG_HUMAN	D	257;289;257;257;257	ENSP00000382870:E257D;ENSP00000382874:E289D;ENSP00000382869:E257D;ENSP00000382871:E257D;ENSP00000382867:E257D	ENSP00000382867:E257D	E	+	3	2	MAGEB16	35731005	0.001000	0.12720	0.000000	0.03702	0.297000	0.27493	0.019000	0.13444	-0.634000	0.05538	-0.482000	0.04802	GAG		0.483	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			T	35821084	G	T	35821084	3	4	61	1	0	0	0	0	1	0	0	0	9204	933	33	2	773	2	MAGEB16	23	35821084	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1672686	35821084	119449476	12063	20048										
CXorf22	170063	broad.mit.edu	37	chrX	35993925	35993925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttcatgaaaacatgttttCgggggacagttagattgtat	10	5	2	2	rs141343030	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:35993925C>T	ENST00000297866.5	+	15	2674	c.2608C>T	c.(2608-2610)Cgg>Tgg	p.R870W		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	870								p.R870W(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AACATGTTTTCGGGGGACAGT	0.433													C|||	5	0.0013245	0.0038	0	3775	,	,		12571	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X						C	TRP/ARG	9,3824		0,9,0,1622,571	179	158	165		2608	0.5	0	X	dbSNP_134	165	1,6727		0,0,1,2428,1871	yes	missense	CXorf22	NM_152632.3	101	0,9,1,4050,2442	TT,TC,T,CC,C		0.0149,0.2348,0.0947	probably-damaging	870/977	35993925	10,10551	2202	4300	6502	35903846	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2608C>T	X.37:g.35993925C>T	ENSP00000297866:p.Arg870Trp		35903846	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	C	7.029	0.560314	0.13498	0.002348	1.49E-4	ENSG00000165164	ENST00000297866	T	0.18502	2.21	5.14	0.539	0.17156	.	0.152729	0.56097	N	0.000023	T	0.14830	0.0358	M	0.71581	2.175	0.09310	N	1	P	0.42409	0.779	B	0.34489	0.184	T	0.14392	-1.0474	10	0.87932	D	0	-0.4751	6.3717	0.21485	0.2469:0.5224:0.0:0.2307	.	870	Q6ZTR5	CX022_HUMAN	W	870	ENSP00000297866:R870W	ENSP00000297866:R870W	R	+	1	2	CXorf22	35903846	0.969000	0.33509	0.005000	0.12908	0.058000	0.15608	0.674000	0.25218	-0.279000	0.09167	-0.191000	0.12829	CGG		0.433	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		T	35993925	C	T	35993925	3	4	61	1	0	0	0	0	1	0	0	0	4108	875	31	1	2666	1	CXorf22	23	35993925	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	172841	35993925	119276635	12064	20049										
FAM47C	442444	broad.mit.edu	37	chrX	37027491	37027491	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctccacccagagcctcccaaGactctggtgtccagtctcca	7	18	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:37027491G>T	ENST00000358047.3	+	1	1060	c.1008G>T	c.(1006-1008)aaG>aaT	p.K336N		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	336								p.K336N(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						AGCCTCCCAAGACTCTGGTGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	X											77	73	75					X																	37027491		2202	4299	6501	36937412	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1008G>T	X.37:g.37027491G>T	ENSP00000367913:p.Lys336Asn		36937412	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	g	7.970	0.748842	0.15710	.	.	ENSG00000198173	ENST00000358047	T	0.20200	2.09	0.95	0.95	0.19572	.	.	.	.	.	T	0.32346	0.0826	M	0.63843	1.955	0.09310	N	1	D	0.63046	0.992	D	0.65874	0.939	T	0.21895	-1.0232	9	0.16420	T	0.52	.	5.1634	0.15073	0.0:0.3706:0.6294:0.0	.	336	Q5HY64	FA47C_HUMAN	N	336	ENSP00000367913:K336N	ENSP00000367913:K336N	K	+	3	2	FAM47C	36937412	0.004000	0.15560	0.012000	0.15200	0.012000	0.07955	0.850000	0.27737	0.177000	0.19895	0.179000	0.17066	AAG		0.617	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37027491	G	T	37027491	3	4	61	1	0	0	0	0	1	0	0	0	5590	933	33	2	1010	2	FAM47C	23	37027491	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1033566	37027491	118243069	12065	20050										
PRRG1	5638	broad.mit.edu	37	chrX	37285205	37285205	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtgagtgcaaagaagaattCtgtacatttgaagaagcaag	11	5	1	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:37285205C>A	ENST00000542554.1	+	4	395	c.123C>A	c.(121-123)ttC>ttA	p.F41L	PRRG1_ENST00000463135.1_Missense_Mutation_p.F41L|PRRG1_ENST00000543642.1_Missense_Mutation_p.F41L|PRRG1_ENST00000449135.2_Missense_Mutation_p.F41L|PRRG1_ENST00000491253.1_Intron|TM4SF2_ENST00000465127.1_Missense_Mutation_p.F41L|PRRG1_ENST00000378628.4_Missense_Mutation_p.F41L	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	41	Gla. {ECO:0000255|PROSITE- ProRule:PRU00463}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.F41L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						AAGAAGAATTCTGTACATTTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	X											56	54	54					X																	37285205		2202	4300	6502	37170126	SO:0001583	missense	5638			AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.123C>A	X.37:g.37285205C>A	ENSP00000444278:p.Phe41Leu		37170126	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	37	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568986	0.28003	.	.	ENSG00000130962;ENSG00000130962;ENSG00000130962;ENSG00000130962;ENSG00000130962;ENSG00000130962;ENSG00000130962;ENSG00000250349	ENST00000378628;ENST00000466533;ENST00000542554;ENST00000543642;ENST00000484460;ENST00000449135;ENST00000463135;ENST00000465127	D;D;D;D;D;D;D;D	0.99005	-5.32;-5.32;-5.32;-5.32;-5.32;-5.32;-5.32;-5.32	4.94	1.54	0.23209	Gamma-carboxyglutamic acid-rich (GLA) domain (6);Coagulation factor, subgroup, Gla domain (1);	0.798476	0.11739	N	0.534198	D	0.91116	0.7203	N	0.00399	-1.545	0.23249	N	0.998042	B	0.02656	0.0	B	0.01281	0.0	D	0.87953	0.2725	10	0.20519	T	0.43	-2.4198	5.5445	0.17055	0.0:0.5975:0.152:0.2505	.	41	O14668	TMG1_HUMAN	L	41	ENSP00000367894:F41L;ENSP00000418384:F41L;ENSP00000444278:F41L;ENSP00000443271:F41L;ENSP00000420353:F41L;ENSP00000390332:F41L;ENSP00000419999:F41L;ENSP00000417050:F41L	ENSP00000367894:F41L	F	+	3	2	RP5-972B16.2;PRRG1	37170126	0.001000	0.12720	0.927000	0.36925	0.968000	0.65278	-0.157000	0.10085	0.170000	0.19704	0.544000	0.68410	TTC		0.348	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		A	37285205	C	A	37285205	3	1	61	1	0	0	0	0	1	0	0	0	12639	912	32	2	129	2	PRRG1	23	37285205	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	257714	37285205	117985355	12066	20051										
SYTL5	94122	broad.mit.edu	37	chrX	37913673	37913673	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcactgtctgtgacaaaatCgcgtgagtttcttgattttt	9	7	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:37913673C>T	ENST00000357972.5	+	3	873	c.327C>T	c.(325-327)atC>atT	p.I109I	SYTL5_ENST00000297875.2_Silent_p.I109I|SYTL5_ENST00000456733.2_Silent_p.I109I|TM4SF2_ENST00000465127.1_Intron			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	109	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.I109I(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						GTGACAAAATCGCGTGAGTTT	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	X											56	51	52					X																	37913673		2202	4300	6502	37798617	SO:0001819	synonymous_variant	94122				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"exophilin 9"						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.327C>T	X.37:g.37913673C>T			37798617	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																				0.478	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		T	37913673	C	T	37913673	2	4	61	1	0	0	0	0	0	0	0	1	15525	874	31	1		1	SYTL5	23	37913673	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	628468	37913673	117356887	12067	20052										
ATP6AP2	10159	broad.mit.edu	37	chrX	40464996	40464996	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgacaaaccagaagattCgaatggattgaatgttacct	10	6	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:40464996C>T	ENST00000378438.4	+	9	1200	c.1042C>T	c.(1042-1044)Cga>Tga	p.R348*	ATP6AP2_ENST00000544975.1_Nonsense_Mutation_p.R272*|ATP6AP2_ENST00000535539.1_Nonsense_Mutation_p.R316*|ATP6AP2_ENST00000535777.1_Nonsense_Mutation_p.R270*	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	348					angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)	p.R348*(2)		endometrium(1)|large_intestine(1)|lung(2)	4						CCAGAAGATTCGAATGGATTG	0.368																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											80	69	73					X																	40464996		2203	4300	6503	40349940	SO:0001587	stop_gained	10159			AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"prorenin receptor", "renin receptor"	300556	"ATPase, H+ transporting, lysosomal interacting protein 2"	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.1042C>T	X.37:g.40464996C>T	ENSP00000367697:p.Arg348*		40349940	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Nonsense_Mutation	SNP	ENST00000378438.4	37	CCDS14252.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508107	0.85282	.	.	ENSG00000182220	ENST00000535539;ENST00000378438;ENST00000544975;ENST00000535777	.	.	.	5.65	5.65	0.86999	.	0.103987	0.64402	D	0.000005	.	.	.	.	.	.	0.49389	D	0.999786	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-29.7493	11.8032	0.52139	0.3156:0.6844:0.0:0.0	.	.	.	.	X	316;348;272;270	.	ENSP00000367697:R348X	R	+	1	2	ATP6AP2	40349940	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.111000	0.50360	2.377000	0.81083	0.600000	0.82982	CGA		0.368	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060679.1	NM_005765		T	40464996	C	T	40464996	4	4	61	1	0	0	0	0	0	1	0	0	1168	876	31	1	1076	1	ATP6AP2	23	40464996	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2551323	40464996	114805564	12068	20053										
USP9X	8239	broad.mit.edu	37	chrX	41084340	41084340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tatgaactgcggccctatttGgatctgcttttgcaaatctt	8	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:41084340G>T	ENST00000324545.8	+	41	7644	c.7011G>T	c.(7009-7011)ttG>ttT	p.L2337F	USP9X_ENST00000378308.2_Missense_Mutation_p.L2337F	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	2337					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.L2330F(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						GGCCCTATTTGGATCTGCTTT	0.383																																					Ovarian(172;1807 2695 35459 49286)											1	Substitution - Missense(1)	large_intestine(1)	X											168	149	155					X																	41084340		2066	4202	6268	40969284	SO:0001583	missense	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.7011G>T	X.37:g.41084340G>T	ENSP00000316357:p.Leu2337Phe		40969284	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	G	9.487	1.099588	0.20552	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.03553	3.89;3.9	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.04092	0.0114	N	0.21097	0.63	0.80722	D	1	B;B	0.19445	0.029;0.036	B;B	0.19148	0.024;0.014	T	0.53648	-0.8409	10	0.23302	T	0.38	.	18.6323	0.91364	0.0:0.0:1.0:0.0	.	2337;2337	Q93008-1;Q93008	.;USP9X_HUMAN	F	2337	ENSP00000367558:L2337F;ENSP00000316357:L2337F	ENSP00000316357:L2337F	L	+	3	2	USP9X	40969284	1.000000	0.71417	0.998000	0.56505	0.002000	0.02628	6.234000	0.72326	2.344000	0.79699	0.544000	0.68410	TTG		0.383	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		T	41084340	G	T	41084340	3	4	61	1	0	0	0	0	1	0	0	0	17130	1339	47	2	7169	2	USP9X	23	41084340	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	619344	41084340	114186220	12069	20054										
GPR34	2857	broad.mit.edu	37	chrX	41555214	41555214	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcttctgcctccctttcCgaataatgtatcatattaac	3	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:41555214C>T	ENST00000378142.4	+	3	612	c.328C>T	c.(328-330)Cga>Tga	p.R110*	CASK_ENST00000361962.4_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000378166.4_Intron|GPR34_ENST00000378138.5_Nonsense_Mutation_p.R110*|CASK_ENST00000378163.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000318588.9_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	110					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.R110*(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						CCTCCCTTTCCGAATAATGTA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											152	141	145					X																	41555214		2203	4300	6503	41440158	SO:0001587	stop_gained	2857			AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"GPCR / Class A : Orphans"	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.328C>T	X.37:g.41555214C>T	ENSP00000367384:p.Arg110*		41440158	O95853	Nonsense_Mutation	SNP	ENST00000378142.4	37	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728854	0.96856	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7556	19.3529	0.94398	0.0:1.0:0.0:0.0	.	.	.	.	X	110;110;63	.	ENSP00000367378:R110X	R	+	1	2	GPR34	41440158	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.189000	0.50965	2.523000	0.85059	0.594000	0.82650	CGA		0.368	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		T	41555214	C	T	41555214	4	4	61	1	0	0	0	0	0	1	0	0	6709	644	23	1	330	1	GPR34	23	41555214	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	470874	41555214	113715346	12070	20055										
EFHC2	80258	broad.mit.edu	37	chrX	44037698	44037698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaacttttcgtgggccagtgCgattaagaaatccatatctg	10	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:44037698C>T	ENST00000420999.1	-	12	1947	c.1864G>A	c.(1864-1866)Gca>Aca	p.A622T	EFHC2_ENST00000343571.3_5'UTR	NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	622							calcium ion binding (GO:0005509)	p.A622T(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						TGGGCCAGTGCGATTAAGAAA	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											67	57	60					X																	44037698		1853	4087	5940	43922642	SO:0001583	missense	80258			AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1864G>A	X.37:g.44037698C>T	ENSP00000404232:p.Ala622Thr		43922642	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.55|13.55	2.269417|2.269417	0.40095|0.40095	.|.	.|.	ENSG00000183690|ENSG00000183690	ENST00000343571;ENST00000333807;ENST00000420999|ENST00000441230	T;T;T|.	0.80033|.	0.89;-1.33;-1.33|.	5.53|5.53	1.28|1.28	0.21552|0.21552	EF-hand-like domain (1);|.	0.244018|.	0.40385|.	N|.	0.001108|.	T|T	0.44265|0.44265	0.1285|0.1285	M|M	0.65498|0.65498	2.005|2.005	0.18873|0.18873	N|N	0.999983|0.999983	P|.	0.42296|.	0.775|.	B|.	0.28916|.	0.096|.	T|T	0.34825|0.34825	-0.9813|-0.9813	10|5	0.52906|.	T|.	0.07|.	-9.3455|-9.3455	6.0251|6.0251	0.19650|0.19650	0.4592:0.4437:0.0:0.0971|0.4592:0.4437:0.0:0.0971	.|.	622|.	Q5JST6|.	EFHC2_HUMAN|.	T|H	35;622;650|602	ENSP00000340643:A35T;ENSP00000333823:A622T;ENSP00000404232:A650T|.	ENSP00000333823:A622T|.	A|R	-|-	1|2	0|0	EFHC2|EFHC2	43922642|43922642	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.032000|0.032000	0.12392|0.12392	-0.256000|-0.256000	0.08757|0.08757	0.171000|0.171000	0.19730|0.19730	0.594000|0.594000	0.82650|0.82650	GCA|CGC		0.393	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		T	44037698	C	T	44037698	3	4	61	1	0	0	0	0	1	0	0	0	4958	768	27	1	401	1	EFHC2	23	44037698	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2482484	44037698	111232862	12071	20056										
ZNF674	641339	broad.mit.edu	37	chrX	46360481	46360481	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgaagattataatggagGcatactttccaatatgcctt	7	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:46360481G>A	ENST00000523374.1	-	6	753	c.543C>T	c.(541-543)tgC>tgT	p.C181C	ZNF674_ENST00000414387.2_Silent_p.C175C|ZNF674_ENST00000518795.1_5'Flank	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	181					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						TATAATGGAGGCATACTTTCC	0.378																																																0			X											64	53	57					X																	46360481		1965	4146	6111	46245425	SO:0001819	synonymous_variant	641339			AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"Zinc fingers, C2H2-type", "-"	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.543C>T	X.37:g.46360481G>A			46245425	B4DHE2|E9PHQ4	Silent	SNP	ENST00000523374.1	37	CCDS48099.1																																																																																				0.378	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056357.2	NM_001039891		A	46360481	G	A	46360481	2	1	61	1	0	0	0	0	0	0	0	1	18120	1195	42	3		3	ZNF674	23	46360481	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2322783	46360481	108910079	12072	20057										
RP2	6102	broad.mit.edu	37	chrX	46713160	46713160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattagcctgccaacaatttCgtgtgcgagattgtagaaag	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:46713160C>T	ENST00000218340.3	+	2	513	c.352C>T	c.(352-354)Cgt>Tgt	p.R118C		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	118	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.		R -> C (in RP2). {ECO:0000269|PubMed:12657579}.|R -> H (in RP2; reduces affinity for ARL3 800-fold; loss of stimulation of tubulin GTPase activity; no effect on subcellular location). {ECO:0000269|PubMed:10090907, ECO:0000269|PubMed:10520237, ECO:0000269|PubMed:10937588, ECO:0000269|PubMed:11992260, ECO:0000269|PubMed:12657579, ECO:0000269|PubMed:14564670, ECO:0000269|PubMed:9697692}.|R -> L (in RP2; dbSNP:rs28933687). {ECO:0000269|PubMed:11462235}.		cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)	p.R118C(1)		NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						CCAACAATTTCGTGTGCGAGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CM033008|CM077334	RP2	M							130	118	122					X																	46713160		2203	4300	6503	46598104	SO:0001583	missense	6102			AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.352C>T	X.37:g.46713160C>T	ENSP00000218340:p.Arg118Cys		46598104	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	37	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.594517	0.86953	.	.	ENSG00000102218	ENST00000218340	D	0.90844	-2.74	5.62	5.62	0.85841	CARP motif (1);Tubulin binding cofactor C (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	D	0.96938	0.9000	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97354	0.9965	10	0.49607	T	0.09	-6.3424	18.6553	0.91450	0.0:1.0:0.0:0.0	.	118	O75695	XRP2_HUMAN	C	118	ENSP00000218340:R118C	ENSP00000218340:R118C	R	+	1	0	RP2	46598104	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.371000	0.79600	2.349000	0.79799	0.513000	0.50165	CGT		0.418	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		T	46713160	C	T	46713160	3	4	61	1	0	0	0	0	1	0	0	0	13571	884	31	1	358	1	RP2	23	46713160	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	352679	46713160	108557400	12073	20058										
PHF16	9767	broad.mit.edu	37	chrX	46913788	46913788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcctgcgggcacagaagcttCgggagctggaggaggagttc	18	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:46913788C>T	ENST00000218343.4	+	9	1499	c.1201C>T	c.(1201-1203)Cgg>Tgg	p.R401W	PHF16_ENST00000397189.1_Missense_Mutation_p.R401W	NM_014735.3	NP_055550.1												p.R401W(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						ACAGAAGCTTCGGGAGCTGGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	X											62	59	60					X																	46913788		2203	4300	6503	46798732	SO:0001583	missense	9767																														ENST00000218343.4:c.1201C>T	X.37:g.46913788C>T	ENSP00000218343:p.Arg401Trp		46798732		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.167592	0.57476	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.52983	0.64;0.64	4.99	0.203	0.15195	.	0.448812	0.25068	N	0.033393	T	0.49541	0.1563	L	0.59436	1.845	0.09310	N	0.99999	D	0.64830	0.994	P	0.51657	0.676	T	0.46610	-0.9179	10	0.59425	D	0.04	.	9.7666	0.40565	0.4846:0.4391:0.0:0.0763	.	401	Q92613	JADE3_HUMAN	W	401	ENSP00000380373:R401W;ENSP00000218343:R401W	ENSP00000218343:R401W	R	+	1	2	PHF16	46798732	0.935000	0.31712	0.183000	0.23137	0.969000	0.65631	0.596000	0.24044	0.086000	0.17137	-0.174000	0.13273	CGG		0.537	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			T	46913788	C	T	46913788	3	4	61	1	0	0	0	0	1	0	0	0	11858	875	31	1	1231	1	PHF16	23	46913788	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	200628	46913788	108356772	12074	20059										
PHF16	9767	broad.mit.edu	37	chrX	46918268	46918268	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtagacaggttctcaggcGgtctgcagggagagctccat	16	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:46918268G>A	ENST00000218343.4	+	11	2559	c.2261G>A	c.(2260-2262)cGg>cAg	p.R754Q	PHF16_ENST00000397189.1_Missense_Mutation_p.R754Q	NM_014735.3	NP_055550.1												p.R754Q(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						GTTCTCAGGCGGTCTGCAGGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											49	43	45					X																	46918268		2203	4300	6503	46803212	SO:0001583	missense	9767																														ENST00000218343.4:c.2261G>A	X.37:g.46918268G>A	ENSP00000218343:p.Arg754Gln		46803212		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	G	9.061	0.994469	0.19043	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.51817	0.69;0.69	5.72	3.58	0.41010	.	1.354970	0.04425	N	0.368291	T	0.27697	0.0681	N	0.19112	0.55	0.09310	N	1	P	0.37158	0.585	B	0.23852	0.049	T	0.18147	-1.0346	10	0.16896	T	0.51	.	6.1687	0.20404	0.1109:0.0:0.6992:0.1899	.	754	Q92613	JADE3_HUMAN	Q	754	ENSP00000380373:R754Q;ENSP00000218343:R754Q	ENSP00000218343:R754Q	R	+	2	0	PHF16	46803212	0.235000	0.23794	0.964000	0.40570	0.966000	0.64601	0.857000	0.27831	1.140000	0.42260	0.594000	0.82650	CGG		0.488	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			A	46918268	G	A	46918268	3	1	61	1	0	0	0	0	1	0	0	0	11858	1116	39	1	2299	1	PHF16	23	46918268	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4480	46918268	108352292	12075	20060										
RBM10	8241	broad.mit.edu	37	chrX	47045658	47045658	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtgcaccgcccctgcagaGacttcgagcagcctactcgg	11	16	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47045658G>T	ENST00000377604.3	+	23	3281	c.2539G>T	c.(2539-2541)Gac>Tac	p.D847Y	RBM10_ENST00000345781.6_Splice_Site_p.D770Y|RBM10_ENST00000329236.7_Splice_Site_p.D769Y	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	847					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.D847Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CCCCTGCAGAGACTTCGAGCA	0.692																																					Melanoma(171;120 2705 19495 39241)											1	Substitution - Missense(1)	large_intestine(1)	X											36	38	37					X																	47045658		2198	4299	6497	46930602	SO:0001630	splice_region_variant	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.2538-1G>T	X.37:g.47045658G>T			46930602	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.636567	0.67130	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.20332	2.75;2.08;2.35	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000011	T	0.32823	0.0842	L	0.29908	0.895	0.43693	D	0.996149	D;D;D;D;P	0.69078	0.997;0.972;0.964;0.997;0.939	D;P;P;D;P	0.65010	0.931;0.781;0.601;0.931;0.781	T	0.03103	-1.1072	10	0.66056	D	0.02	-37.8434	14.385	0.66938	0.0:0.0:1.0:0.0	.	770;912;846;769;847	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	Y	847;769;770	ENSP00000366829:D847Y;ENSP00000328848:D769Y;ENSP00000329659:D770Y	ENSP00000328848:D769Y	D	+	1	0	RBM10	46930602	0.998000	0.40836	1.000000	0.80357	0.965000	0.64279	2.830000	0.48136	2.562000	0.86427	0.600000	0.82982	GAC		0.692	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	Missense_Mutation	T	47045658	G	T	47045658	5	4	61	1	0	0	0	0	0	0	1	0	13148	956	33	2	2625	2	RBM10	23	47045658	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	127390	47045658	108224902	12076	20061										
UBA1	7317	broad.mit.edu	37	chrX	47062533	47062533	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctccctttgcattccttagCgccagaaccgttatgacggg	9	14	0	2	rs570568650		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47062533C>T	ENST00000335972.6	+	13	1522	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	INE1_ENST00000456273.1_RNA|UBA1_ENST00000490869.1_3'UTR|UBA1_ENST00000377351.4_Splice_Site_p.R447C	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	447	2 approximate repeats.		R -> H (in dbSNP:rs2070169).		cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)	p.R447C(1)		breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CATTCCTTAGCGCCAGAACCG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	X											125	100	109					X																	47062533		2203	4300	6503	46947477	SO:0001630	splice_region_variant	7317			AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1339-1C>T	X.37:g.47062533C>T			46947477	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	C	6.164	0.398495	0.11696	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.20738	2.05;2.05	5.42	3.61	0.41365	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.098654	0.64402	N	0.000005	T	0.19765	0.0475	M	0.64170	1.965	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04767	-1.0928	9	.	.	.	-3.192	7.6391	0.28284	0.1634:0.7473:0.0:0.0894	.	447	P22314	UBA1_HUMAN	C	447	ENSP00000366568:R447C;ENSP00000338413:R447C	.	R	+	1	0	UBA1	46947477	0.997000	0.39634	0.764000	0.31436	0.032000	0.12392	1.004000	0.29822	0.543000	0.28864	0.597000	0.82753	CGC		0.557	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	Missense_Mutation	T	47062533	C	T	47062533	5	4	61	1	0	0	0	0	0	0	1	0	16867	782	27	1	1385	1	UBA1	23	47062533	Splice_Site	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	16875	47062533	108208027	12077	20062										
USP11	8237	broad.mit.edu	37	chrX	47107215	47107215	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcagcctatgtcctcttCtaccaacgccaggacgtggc	10	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47107215C>A	ENST00000218348.3	+	21	2778	c.2778C>A	c.(2776-2778)ttC>ttA	p.F926L	USP11_ENST00000377107.2_Missense_Mutation_p.F883L	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	926	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.F926L(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						ATGTCCTCTTCTACCAACGCC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	X											75	59	64					X																	47107215		2203	4300	6503	46992159	SO:0001583	missense	8237			U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.2778C>A	X.37:g.47107215C>A	ENSP00000218348:p.Phe926Leu		46992159	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.977146	0.74360	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.39056	1.1;1.1	4.89	4.03	0.46877	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.218384	0.37178	N	0.002207	T	0.57917	0.2086	M	0.69185	2.1	0.39671	D	0.97075	D;D	0.89917	1.0;1.0	D;D	0.79784	0.991;0.993	T	0.61267	-0.7097	10	0.87932	D	0	-21.7709	7.7986	0.29162	0.0:0.8029:0.0:0.1971	.	652;926	B3KP28;P51784	.;UBP11_HUMAN	L	883;926	ENSP00000366311:F883L;ENSP00000218348:F926L	ENSP00000218348:F926L	F	+	3	2	USP11	46992159	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	4.317000	0.59184	1.046000	0.40249	0.431000	0.28591	TTC		0.642	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		A	47107215	C	A	47107215	3	1	61	1	0	0	0	0	1	0	0	0	17082	912	32	2	2860	2	USP11	23	47107215	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	44682	47107215	108163345	12078	20063										
ZNF157	7712	broad.mit.edu	37	chrX	47272616	47272616	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccatcagagaattcacacaGgagagaaaccttacgaatgt	8	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47272616G>T	ENST00000377073.3	+	4	1230	c.1144G>T	c.(1144-1146)Gga>Tga	p.G382*		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	382					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G382*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						AATTCACACAGGAGAGAAACC	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											51	47	49					X																	47272616		2203	4300	6503	47157560	SO:0001587	stop_gained	7712			U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"Zinc fingers, C2H2-type", "-"	12942	protein-coding gene	gene with protein product		300024	"zinc finger protein 157 (HZF22)"			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1144G>T	X.37:g.47272616G>T	ENSP00000366273:p.Gly382*		47157560	Q96LE9	Nonsense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.940319	0.92526	.	.	ENSG00000147117	ENST00000377073	.	.	.	3.18	2.3	0.28687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	7.681	0.28513	0.1367:0.0:0.8633:0.0	.	.	.	.	X	382	.	ENSP00000366273:G382X	G	+	1	0	ZNF157	47157560	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.595000	0.67563	0.718000	0.32166	0.600000	0.82982	GGA		0.428	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		T	47272616	G	T	47272616	4	4	61	1	0	0	0	0	0	1	0	0	17776	1001	35	2	1158	2	ZNF157	23	47272616	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165401	47272616	107997944	12079	20064										
ZNF41	7592	broad.mit.edu	37	chrX	47307476	47307476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttctgatgtattttgaggcGcgacttccatatgaaggctt	10	7	1	3	rs376568507		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47307476G>A	ENST00000377065.4	-	5	2332	c.1693C>T	c.(1693-1695)Cgc>Tgc	p.R565C	ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000397050.2_Missense_Mutation_p.R575C|ZNF41_ENST00000313116.7_Missense_Mutation_p.R565C	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	607					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R565C(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				ATTTTGAGGCGCGACTTCCAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	CYS/ARG,CYS/ARG	0,3835		0,0,0,1632,571	83	71	75		1693,1693	2.1	0.5	X		75	1,6727		0,0,1,2428,1871	no	missense,missense	ZNF41	NM_007130.2,NM_153380.2	180,180	0,0,1,4060,2442	AA,AG,A,GG,G		0.0149,0.0,0.0095	probably-damaging,probably-damaging	565/780,565/780	47307476	1,10562	2203	4300	6503	47192420	SO:0001583	missense	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1693C>T	X.37:g.47307476G>A	ENSP00000366265:p.Arg565Cys		47192420	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.906458	0.33628	0.0	1.49E-4	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.08102	3.13;3.13;3.13	3.98	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35838	N	0.002955	T	0.10337	0.0253	N	0.10664	0.02	0.09310	N	1	D;D;D;D;D	0.89917	0.991;0.991;1.0;0.997;0.994	P;P;D;P;P	0.66196	0.666;0.666;0.942;0.747;0.563	T	0.16988	-1.0384	10	0.51188	T	0.08	.	11.1003	0.48170	0.0:0.3475:0.6525:0.0	.	565;567;575;599;607	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	C	565;565;575	ENSP00000315173:R565C;ENSP00000366265:R565C;ENSP00000380243:R575C	ENSP00000315173:R565C	R	-	1	0	ZNF41	47192420	0.000000	0.05858	0.533000	0.28001	0.990000	0.78478	-3.144000	0.00585	0.430000	0.26230	0.600000	0.82982	CGC		0.423	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		A	47307476	G	A	47307476	3	1	61	1	0	0	0	0	1	0	0	0	17928	1087	38	1	650	1	ZNF41	23	47307476	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	34860	47307476	107963084	12080	20065										
SYN1	6853	broad.mit.edu	37	chrX	47464411	47464411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggggtagaaggtctgatcaAttagagggaattcttctgtc	13	5	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47464411A>G	ENST00000295987.7	-	5	864	c.740T>C	c.(739-741)aTt>aCt	p.I247T	SYN1_ENST00000340666.4_Missense_Mutation_p.I247T	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	247	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)	p.I247T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						GGTCTGATCAATTAGAGGGAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											129	105	113					X																	47464411		2203	4300	6503	47349355	SO:0001583	missense	6853				CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.740T>C	X.37:g.47464411A>G	ENSP00000295987:p.Ile247Thr		47349355	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	37	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043739	0.75732	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.38401	1.6;1.14	4.88	4.88	0.63580	ATP-grasp fold, subdomain 2 (1);Synapsin, ATP-binding domain (1);	0.000000	0.64402	D	0.000002	T	0.62429	0.2427	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	0.965;1.0	D;D	0.97110	0.971;1.0	T	0.68591	-0.5368	10	0.87932	D	0	-1.8326	11.6533	0.51301	1.0:0.0:0.0:0.0	.	247;247	P17600;P17600-2	SYN1_HUMAN;.	T	247	ENSP00000295987:I247T;ENSP00000343206:I247T	ENSP00000295987:I247T	I	-	2	0	SYN1	47349355	1.000000	0.71417	0.978000	0.43139	0.982000	0.71751	8.816000	0.91979	1.723000	0.51488	0.441000	0.28932	ATT		0.438	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		G	47464411	A	G	47464411	3	3	61	1	0	0	0	0	1	0	0	0	15479	101	4	4	1413	4	SYN1	23	47464411	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	156935	47464411	107806149	12081	20066										
CFP	5199	broad.mit.edu	37	chrX	47485784	47485784	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgttgcccggcacatcGatgtccgtcaaacttgcggc	11	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47485784G>A	ENST00000396992.3	-	7	1195	c.1075C>T	c.(1075-1077)Cga>Tga	p.R359*	CFP_ENST00000377005.2_Nonsense_Mutation_p.R359*|CFP_ENST00000247153.3_Nonsense_Mutation_p.R359*|CFP_ENST00000480317.1_5'Flank	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	359	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R359*(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						CCGGCACATCGATGTCCGTCA	0.612																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											63	54	57					X																	47485784		2203	4300	6503	47370728	SO:0001587	stop_gained	5199			M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"Complement system"	8864	protein-coding gene	gene with protein product		300383	"properdin P factor, complement"	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.1075C>T	X.37:g.47485784G>A	ENSP00000380189:p.Arg359*		47370728	O15134|O15135|O15136|O75826	Nonsense_Mutation	SNP	ENST00000396992.3	37	CCDS14282.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181472	0.78677	.	.	ENSG00000126759	ENST00000396992;ENST00000247153;ENST00000377005	.	.	.	5.28	5.28	0.74379	.	0.504643	0.20634	N	0.088532	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	13.5045	0.61477	0.0:0.0:1.0:0.0	.	.	.	.	X	359	.	ENSP00000247153:R359X	R	-	1	2	CFP	47370728	0.066000	0.20996	0.008000	0.14137	0.066000	0.16364	2.434000	0.44802	2.344000	0.79699	0.468000	0.43344	CGA		0.612	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621		A	47485784	G	A	47485784	4	1	61	1	0	0	0	0	0	1	0	0	3299	1066	37	1	346	1	CFP	23	47485784	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	21373	47485784	107784776	12082	20067										
ZNF81	347344	broad.mit.edu	37	chrX	47775202	47775202	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatactggagaaaaactctTtgaatgcagtgaatgtggta	10	5	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47775202T>G	ENST00000376954.1	+	6	1525	c.1157T>G	c.(1156-1158)tTt>tGt	p.F386C	ZNF81_ENST00000338637.7_Missense_Mutation_p.F386C			P51508	ZNF81_HUMAN	zinc finger protein 81	386					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F386C(1)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				GAAAAACTCTTTGAATGCAGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											59	58	58					X																	47775202		2190	4295	6485	47660146	SO:0001583	missense	347344			AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"Zinc fingers, C2H2-type", "-"	13156	protein-coding gene	gene with protein product		314998	"zinc finger protein 81 (HFZ20)", "mental retardation, X-linked 45"	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.1157T>G	X.37:g.47775202T>G	ENSP00000366153:p.Phe386Cys		47660146	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	.	.	.	.	.	.	.	.	.	.	T	8.224	0.803049	0.16397	.	.	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.24908	1.83;1.83	4.16	1.77	0.24775	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.191498	0.26038	N	0.026715	T	0.28928	0.0718	M	0.86573	2.825	0.22911	N	0.998571	B	0.06786	0.001	B	0.12156	0.007	T	0.40496	-0.9560	10	0.87932	D	0	.	2.9291	0.05794	0.463:0.0:0.1157:0.4213	.	386	P51508	ZNF81_HUMAN	C	386	ENSP00000366153:F386C;ENSP00000341151:F386C	ENSP00000341151:F386C	F	+	2	0	ZNF81	47660146	0.000000	0.05858	0.999000	0.59377	0.947000	0.59692	-0.912000	0.04046	0.248000	0.21435	-0.400000	0.06385	TTT		0.408	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137		G	47775202	T	G	47775202	3	3	61	1	0	0	0	0	1	0	0	0	18213	1841	64	4	1171	4	ZNF81	23	47775202	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	289418	47775202	107495358	12083	20068										
ZNF182	7569	broad.mit.edu	37	chrX	47836690	47836690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctaaaagcttttccacattCggtacatccaaaaggtttct	6	10	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47836690C>T	ENST00000396965.1	-	7	1146	c.796G>A	c.(796-798)Gaa>Aaa	p.E266K	ZNF182_ENST00000376943.3_Missense_Mutation_p.E247K|ZNF182_ENST00000305127.6_Missense_Mutation_p.E266K	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E266K(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						TTTCCACATTCGGTACATCCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											74	71	72					X																	47836690		2203	4300	6503	47721634	SO:0001583	missense	7569			AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"Zinc fingers, C2H2-type", "-"	13001	protein-coding gene	gene with protein product		314993	"zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)"	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.796G>A	X.37:g.47836690C>T	ENSP00000380165:p.Glu266Lys		47721634	A2IDD7|Q3KP67|Q96QH7	Missense_Mutation	SNP	ENST00000396965.1	37	CCDS35236.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.074066	0.55646	.	.	ENSG00000147118	ENST00000376943;ENST00000396965;ENST00000305127	T;T;T	0.23552	1.9;1.9;1.9	4.36	4.36	0.52297	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24160	0.0585	N	0.25201	0.72	0.27650	N	0.947434	D;P;P	0.54397	0.966;0.926;0.935	P;P;B	0.47102	0.482;0.537;0.323	T	0.06734	-1.0810	9	0.59425	D	0.04	.	13.5566	0.61763	0.0:1.0:0.0:0.0	.	246;247;266	B4DRM0;Q96QH7;P17025	.;.;ZN182_HUMAN	K	247;266;266	ENSP00000366142:E247K;ENSP00000380165:E266K;ENSP00000306351:E266K	ENSP00000306351:E266K	E	-	1	0	ZNF182	47721634	0.000000	0.05858	0.940000	0.37924	0.993000	0.82548	0.117000	0.15583	2.156000	0.67533	0.594000	0.82650	GAA		0.423	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962		T	47836690	C	T	47836690	3	4	61	1	0	0	0	0	1	0	0	0	17789	893	31	1	1127	1	ZNF182	23	47836690	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	61488	47836690	107433870	12084	20069										
ZNF630	57232	broad.mit.edu	37	chrX	47918227	47918227	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtttctcccctgtgtgaactCtcagatgaataatgaggagt	10	8	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:47918227C>A	ENST00000409324.3	-	5	1830	c.1604G>T	c.(1603-1605)aGa>aTa	p.R535I	ZNF630_ENST00000276054.4_Missense_Mutation_p.R411I|ZNF630_ENST00000442455.3_Missense_Mutation_p.R521I|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	535					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R535I(1)		endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TGTGTGAACTCTCAGATGAAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											52	49	50					X																	47918227		2193	4286	6479	47803171	SO:0001583	missense	57232			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1604G>T	X.37:g.47918227C>A	ENSP00000386393:p.Arg535Ile		47803171	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	12.21	1.869689	0.33069	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324	T;T;T	0.24908	1.83;1.83;1.83	2.31	1.4	0.22301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38825	0.1055	L	0.58969	1.84	0.34491	D	0.70495	D	0.71674	0.998	D	0.66084	0.941	T	0.52503	-0.8567	9	0.72032	D	0.01	.	6.2102	0.20626	0.0:0.8168:0.0:0.1832	.	535	Q2M218	ZN630_HUMAN	I	521;411;535	ENSP00000393163:R521I;ENSP00000354683:R411I;ENSP00000386393:R535I	ENSP00000354683:R411I	R	-	2	0	ZNF630	47803171	0.000000	0.05858	0.968000	0.41197	0.102000	0.19082	0.718000	0.25866	1.179000	0.42884	0.544000	0.68410	AGA		0.453	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		A	47918227	C	A	47918227	3	1	61	1	0	0	0	0	1	0	0	0	18093	913	32	2	373	2	ZNF630	23	47918227	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	81537	47918227	107352333	12085	20070										
GATA1	2623	broad.mit.edu	37	chrX	48652425	48652425	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtactgcccatctctaccaaGgcctgggccctgtggtgctg	12	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:48652425G>T	ENST00000376670.3	+	6	1207	c.1096G>T	c.(1096-1098)Ggc>Tgc	p.G366C	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	366					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.G366C(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						TCTCTACCAAGGCCTGGGCCC	0.652			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																Pancreas(9;429 505 11287 29617)		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	1	Substitution - Missense(1)	large_intestine(1)	X											34	31	32					X																	48652425		2203	4300	6503	48537369	SO:0001583	missense	2623			X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.1096G>T	X.37:g.48652425G>T	ENSP00000365858:p.Gly366Cys		48537369	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	37	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	g	15.11	2.735357	0.48939	.	.	ENSG00000102145	ENST00000376670	D	0.97575	-4.44	4.73	3.64	0.41730	.	0.789532	0.11313	U	0.576937	D	0.94525	0.8237	N	0.14661	0.345	0.44042	D	0.996778	D	0.69078	0.997	P	0.53912	0.737	D	0.92229	0.5791	10	0.66056	D	0.02	-12.1236	7.8196	0.29280	0.1437:0.0:0.8563:0.0	.	366	P15976	GATA1_HUMAN	C	366	ENSP00000365858:G366C	ENSP00000365858:G366C	G	+	1	0	GATA1	48537369	1.000000	0.71417	0.989000	0.46669	0.773000	0.43773	1.654000	0.37334	1.941000	0.56285	0.365000	0.22127	GGC		0.652	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		T	48652425	G	T	48652425	3	4	61	1	0	0	0	0	1	0	0	0	6273	1000	35	2	1114	2	GATA1	23	48652425	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	734198	48652425	106618135	12086	20071										
HDAC6	10013	broad.mit.edu	37	chrX	48661318	48661318	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agccgttccccgctctatccCcaatctagcggaggtaaaga	9	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:48661318C>A	ENST00000334136.5	+	3	312	c.134C>A	c.(133-135)cCc>cAc	p.P45H	HDAC6_ENST00000413163.2_5'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.P45H|HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000444343.2_Missense_Mutation_p.P59H			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	45					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)	p.P45H(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CGCTCTATCCCCAATCTAGCG	0.522																																					Pancreas(112;205 1675 2305 8976 15959)											1	Substitution - Missense(1)	large_intestine(1)	X											55	46	49					X																	48661318		2202	4300	6502	48546262	SO:0001583	missense	10013			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.134C>A	X.37:g.48661318C>A	ENSP00000334061:p.Pro45His		48546262	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217150	0.58560	.	.	ENSG00000094631	ENST00000423941;ENST00000438518;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T	0.60672	0.17;0.18;0.18	4.42	4.42	0.53409	.	0.547076	0.17305	N	0.179118	T	0.65954	0.2741	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.921;0.921;0.999	T	0.66799	-0.5832	10	0.54805	T	0.06	-21.0505	13.6369	0.62227	0.0:1.0:0.0:0.0	.	35;45;45	B4DZN1;Q9UBN7;Q9BRX7	.;HDAC6_HUMAN;.	H	45;45;45;59;45;45;45;45;45;45;45;45	ENSP00000398566:P59H;ENSP00000334061:P45H;ENSP00000365804:P45H	ENSP00000334061:P45H	P	+	2	0	HDAC6	48546262	0.340000	0.24792	0.721000	0.30653	0.718000	0.41266	0.495000	0.22483	2.176000	0.68965	0.600000	0.82982	CCC		0.522	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		A	48661318	C	A	48661318	3	1	61	1	0	0	0	0	1	0	0	0	7032	623	22	2	140	2	HDAC6	23	48661318	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	8893	48661318	106609242	12087	20072										
HDAC6	10013	broad.mit.edu	37	chrX	48681938	48681938	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgcagggaactacaccccaGatatctcccagtacactgat	8	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:48681938G>T	ENST00000334136.5	+	25	3307	c.3129G>T	c.(3127-3129)caG>caT	p.Q1043H	HDAC6_ENST00000376619.2_Missense_Mutation_p.Q1043H|HDAC6_ENST00000444343.2_Missense_Mutation_p.Q1057H			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	1043					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)	p.Q1043H(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CTACACCCCAGATATCTCCCA	0.592																																					Pancreas(112;205 1675 2305 8976 15959)											1	Substitution - Missense(1)	large_intestine(1)	X											24	20	21					X																	48681938		2203	4292	6495	48566882	SO:0001583	missense	10013			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.3129G>T	X.37:g.48681938G>T	ENSP00000334061:p.Gln1043His		48566882	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.76|12.76	2.035652|2.035652	0.35893|0.35893	.|.	.|.	ENSG00000094631|ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619|ENST00000430858	T;T;T|.	0.60920|.	0.15;0.16;0.16|.	4.06|4.06	0.166|0.166	0.14999|0.14999	.|.	1.121610|.	0.06706|.	N|.	0.772318|.	T|T	0.19046|0.19046	0.0457|0.0457	N|N	0.17082|0.17082	0.46|0.46	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.10296|.	0.001;0.003;0.001;0.001|.	B;B;B;B|.	0.09377|.	0.001;0.004;0.002;0.001|.	T|T	0.25641|0.25641	-1.0126|-1.0126	10|5	0.13853|.	T|.	0.58|.	-0.8251|-0.8251	4.3404|4.3404	0.11106|0.11106	0.3167:0.371:0.3123:0.0|0.3167:0.371:0.3123:0.0	.|.	1033;406;691;1043|.	B4DZN1;B3KY98;B3KVK5;Q9UBN7|.	.;.;.;HDAC6_HUMAN|.	H|I	1057;1043;1043|4	ENSP00000398566:Q1057H;ENSP00000334061:Q1043H;ENSP00000365804:Q1043H|.	ENSP00000334061:Q1043H|.	Q|R	+|+	3|2	2|0	HDAC6|HDAC6	48566882|48566882	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.744000|0.744000	0.42396|0.42396	-0.032000|-0.032000	0.12266|0.12266	-0.106000|-0.106000	0.12110|0.12110	0.600000|0.600000	0.82982|0.82982	CAG|AGA		0.592	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		T	48681938	G	T	48681938	3	4	61	1	0	0	0	0	1	0	0	0	7032	933	33	2	3223	2	HDAC6	23	48681938	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20620	48681938	106588622	12088	20073										
GRIPAP1	56850	broad.mit.edu	37	chrX	48847364	48847364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccttgcagctgttcccagaGcaatctcttctcctctttct	6	15	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:48847364G>T	ENST00000376441.1	-	7	650	c.616C>A	c.(616-618)Ctc>Atc	p.L206I	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.L206I|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.L161I|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.L153I|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	206						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.L153I(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TGTTCCCAGAGCAATCTCTTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	X											127	109	115					X																	48847364		2203	4300	6503	48732308	SO:0001583	missense	56850			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.616C>A	X.37:g.48847364G>T	ENSP00000365624:p.Leu206Ile		48732308	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907000	0.72868	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	T	0.41650	0.1168	L	0.35723	1.085	0.34219	D	0.675192	D;D;P	0.71674	0.998;0.996;0.946	D;D;B	0.83275	0.996;0.994;0.41	T	0.54043	-0.8352	10	0.46703	T	0.11	-4.4649	8.7286	0.34485	0.1066:0.0:0.8934:0.0	.	153;96;206	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	I	206;161;206;206;153	ENSP00000365608:L206I;ENSP00000365627:L161I;ENSP00000365624:L206I;ENSP00000365606:L153I	ENSP00000365606:L153I	L	-	1	0	GRIPAP1	48732308	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.919000	0.70005	2.089000	0.63090	0.556000	0.70494	CTC		0.592	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		T	48847364	G	T	48847364	3	4	61	1	0	0	0	0	1	0	0	0	6810	971	34	2	2043	2	GRIPAP1	23	48847364	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	165426	48847364	106423196	12089	20074										
CACNA1F	778	broad.mit.edu	37	chrX	49083497	49083497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgagtgatccagtccaggTagccccgcaggtcttcctcc	10	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:49083497T>C	ENST00000376265.2	-	9	1272	c.1211A>G	c.(1210-1212)tAc>tGc	p.Y404C	CACNA1F_ENST00000323022.5_Missense_Mutation_p.Y404C|CACNA1F_ENST00000376251.1_Missense_Mutation_p.Y339C	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	404	Binding to the beta subunit. {ECO:0000250}.				axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.Y404C(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CCAGTCCAGGTAGCCCCGCAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	X											66	45	52					X																	49083497		2203	4300	6503	48970441	SO:0001583	missense	778			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.1211A>G	X.37:g.49083497T>C	ENSP00000365441:p.Tyr404Cys		48970441	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029618	0.54790	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.94537	-3.45;-3.45;-3.45	5.03	5.03	0.67393	.	0.188616	0.47852	D	0.000217	D	0.97489	0.9178	M	0.89715	3.055	0.51482	D	0.999924	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.98166	1.0449	10	0.87932	D	0	.	12.8428	0.57813	0.0:0.0:0.0:1.0	.	404;404	F5CIQ9;O60840	.;CAC1F_HUMAN	C	339;404;404	ENSP00000365427:Y339C;ENSP00000321618:Y404C;ENSP00000365441:Y404C	ENSP00000321618:Y404C	Y	-	2	0	CACNA1F	48970441	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	7.943000	0.87716	1.671000	0.50874	0.347000	0.21830	TAC		0.607	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		C	49083497	T	C	49083497	3	2	61	1	0	0	0	0	1	0	0	0	2549	1638	57	4	4882	4	CACNA1F	23	49083497	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	236133	49083497	106187063	12090	20075										
CLCN5	1184	broad.mit.edu	37	chrX	49854843	49854843	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggtggcttagaatacatCgtgcctctgatggctgcagc	12	10	1	2	rs150674219		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:49854843C>T	ENST00000307367.2	+	10	1896	c.1605C>T	c.(1603-1605)atC>atT	p.I535I	CLCN5_ENST00000376091.3_Silent_p.I605I|CLCN5_ENST00000376088.3_Silent_p.I605I|CLCN5_ENST00000376108.3_Silent_p.I535I			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	535					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.I535I(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TAGAATACATCGTGCCTCTGA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	X						C	,,	1,3834		0,1,1631,571	153	140	145		1605,1815,1815	-0.3	1	X	dbSNP_134	145	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	CLCN5	NM_000084.2,NM_001127898.1,NM_001127899.1	,,	0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095	,,	535/747,605/817,605/817	49854843	1,10562	2203	4300	6503	49741583	SO:0001819	synonymous_variant	1184			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1605C>T	X.37:g.49854843C>T			49741583	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	37	CCDS14328.1																																																																																				0.507	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			T	49854843	C	T	49854843	2	4	61	1	0	0	0	0	0	0	0	1	3472	874	31	1		1	CLCN5	23	49854843	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	771346	49854843	105415717	12091	20076										
AKAP4	8852	broad.mit.edu	37	chrX	49957288	49957288	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatctataaattgcccgttCgcttgcttcatcccactggt	6	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:49957288C>T	ENST00000376056.2	-	5	2199	c.2049G>A	c.(2047-2049)gcG>gcA	p.A683A	AKAP4_ENST00000376064.3_Silent_p.A683A|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Silent_p.A309A|AKAP4_ENST00000358526.2_Silent_p.A692A					A kinase (PRKA) anchor protein 4									p.A692A(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					ATTGCCCGTTCGCTTGCTTCA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											114	88	97					X																	49957288		2203	4300	6503	49844028	SO:0001819	synonymous_variant	8852			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.2049G>A	X.37:g.49957288C>T			49844028		Silent	SNP	ENST00000376056.2	37	CCDS14330.1																																																																																				0.473	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		T	49957288	C	T	49957288	2	4	61	1	0	0	0	0	0	0	0	1	453	871	31	1		1	AKAP4	23	49957288	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	102445	49957288	105313272	12092	20077										
CCNB3	85417	broad.mit.edu	37	chrX	50052384	50052384	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagccattagtattgcaggaGatcacctctggagagaagtc	11	8	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:50052384G>T	ENST00000376042.1	+	6	1513	c.1215G>T	c.(1213-1215)gaG>gaT	p.E405D	CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.E405D			Q8WWL7	CCNB3_HUMAN	cyclin B3	405					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)		p.E405D(2)		breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TATTGCAGGAGATCACCTCTG	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	X											79	71	74					X																	50052384		2203	4300	6503	50069124	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.1215G>T	X.37:g.50052384G>T	ENSP00000365210:p.Glu405Asp		50069124	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	G	9.018	0.984093	0.18889	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.36520	1.25;1.25	3.63	-4.18	0.03846	.	5.142410	0.00664	N	0.000610	T	0.11793	0.0287	N	0.01874	-0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07986	-1.0744	9	.	.	.	.	1.145	0.01773	0.3848:0.2693:0.2082:0.1377	.	405	Q8WWL7	CCNB3_HUMAN	D	405	ENSP00000365210:E405D;ENSP00000276014:E405D	.	E	+	3	2	CCNB3	50069124	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.095000	0.15127	-1.356000	0.02183	-1.037000	0.02385	GAG		0.478	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			T	50052384	G	T	50052384	3	4	61	1	0	0	0	0	1	0	0	0	2920	933	33	2	1229	2	CCNB3	23	50052384	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95096	50052384	105218176	12093	20078										
CCNB3	85417	broad.mit.edu	37	chrX	50052743	50052743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acttattaaggagccactgcCctttaaagaagaaaaagtgt	8	7	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:50052743C>T	ENST00000376042.1	+	6	1872	c.1574C>T	c.(1573-1575)cCc>cTc	p.P525L	CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.P525L			Q8WWL7	CCNB3_HUMAN	cyclin B3	525					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)		p.P525L(4)		breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					GAGCCACTGCCCTTTAAAGAA	0.413																																																4	Substitution - Missense(4)	large_intestine(2)|skin(2)	X											36	34	35					X																	50052743		2203	4300	6503	50069483	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.1574C>T	X.37:g.50052743C>T	ENSP00000365210:p.Pro525Leu		50069483	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	8.573	0.880561	0.17467	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.22945	1.93;1.93	3.19	1.35	0.21983	.	433.910000	0.00166	N	0.000000	T	0.13243	0.0321	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.17018	-1.0383	9	.	.	.	.	3.3851	0.07269	0.2514:0.6055:0.0:0.1431	.	525	Q8WWL7	CCNB3_HUMAN	L	525	ENSP00000365210:P525L;ENSP00000276014:P525L	.	P	+	2	0	CCNB3	50069483	0.000000	0.05858	0.009000	0.14445	0.061000	0.15899	-0.214000	0.09292	0.237000	0.21200	-0.213000	0.12676	CCC		0.413	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			T	50052743	C	T	50052743	3	4	61	1	0	0	0	0	1	0	0	0	2920	623	22	3	1588	3	CCNB3	23	50052743	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	359	50052743	105217817	12094	20079										
DGKK	139189	broad.mit.edu	37	chrX	50121639	50121639	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gccatctgcacagaaccaaaGattgccaccacctccagttt	6	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:50121639G>T	ENST00000376025.2	-	0	2972							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.I767I(1)		central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					CAGAACCAAAGATTGCCACCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	X											105	96	99					X																	50121639		2075	4181	6256	50138379			139189			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50121639G>T			50138379	B2RP91	Silent	SNP	ENST00000376025.2	37																																																																																					0.542	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742		T	50121639	G	T	50121639	1	4	61	0	1	0	0	0	0	0	0	0	4483	932	33	2		2	DGKK	23	50121639	RNA	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68896	50121639	105148921	12095	20080										
TSPYL2	64061	broad.mit.edu	37	chrX	53114424	53114424	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagattatcaagaatgatCtgtgggttaaccctctacgc	8	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:53114424C>A	ENST00000375442.4	+	5	1291	c.1159C>A	c.(1159-1161)Ctg>Atg	p.L387M		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	387					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)	p.L387M(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						CAAGAATGATCTGTGGGTTAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	93	97					X																	53114424		2203	4300	6503	53131149	SO:0001583	missense	64061			AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.1159C>A	X.37:g.53114424C>A	ENSP00000364591:p.Leu387Met		53131149	O94799|Q96DG7|Q9BZW6	Missense_Mutation	SNP	ENST00000375442.4	37	CCDS14350.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.035313	0.35893	.	.	ENSG00000184205	ENST00000375442	T	0.41065	1.01	3.33	1.54	0.23209	.	0.000000	0.31976	N	0.006778	T	0.56543	0.1992	M	0.74467	2.265	0.47153	D	0.999338	D	0.89917	1.0	D	0.91635	0.999	T	0.53308	-0.8457	10	0.59425	D	0.04	-10.9848	4.8909	0.13726	0.0:0.7012:0.0:0.2988	.	387	Q9H2G4	TSYL2_HUMAN	M	387	ENSP00000364591:L387M	ENSP00000364591:L387M	L	+	1	2	TSPYL2	53131149	0.999000	0.42202	1.000000	0.80357	0.919000	0.55068	0.841000	0.27613	0.284000	0.22305	0.513000	0.50165	CTG		0.453	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		A	53114424	C	A	53114424	3	1	61	1	0	0	0	0	1	0	0	0	16700	912	32	2	1177	2	TSPYL2	23	53114424	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2992785	53114424	102156136	12096	20081										
RIBC1	158787	broad.mit.edu	37	chrX	53457715	53457715	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaggatccttcaaccagcaGctggctaatgagcaaaaagc	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:53457715G>A	ENST00000375327.3	+	7	1188	c.1035G>A	c.(1033-1035)caG>caA	p.Q345Q	HSD17B10_ENST00000495986.1_5'Flank|RP3-339A18.6_ENST00000418049.1_RNA|RIBC1_ENST00000414955.2_Silent_p.Q230Q	NM_001031745.2	NP_001026915.1	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1	345								p.Q345Q(1)		lung(2)	2						TCAACCAGCAGCTGGCTAATG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	X											66	51	56					X																	53457715		2203	4300	6503	53474440	SO:0001819	synonymous_variant	158787			AK057345	CCDS14353.1, CCDS35299.1, CCDS59168.1	Xp11.23	2006-04-12			ENSG00000158423	ENSG00000158423			26537	protein-coding gene	gene with protein product							Standard	NM_144968		Approved	FLJ32783	uc004dsk.4	Q8N443	OTTHUMG00000021615	ENST00000375327.3:c.1035G>A	X.37:g.53457715G>A			53474440	B4E297|E9PDU2|Q5H931|Q96A80	Silent	SNP	ENST00000375327.3	37	CCDS35299.1																																																																																				0.532	RIBC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056762.1	NM_144968		A	53457715	G	A	53457715	2	1	61	1	0	0	0	0	0	0	0	1	13389	962	34	3		3	RIBC1	23	53457715	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	343291	53457715	101812845	12097	20082										
HUWE1	10075	broad.mit.edu	37	chrX	53561010	53561010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctgtggacctgtcatctCgatggatctgaaacttctga	10	9	5	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:53561010C>T	ENST00000342160.3	-	82	13437	c.12980G>A	c.(12979-12981)cGa>cAa	p.R4327Q	HUWE1_ENST00000262854.6_Missense_Mutation_p.R4327Q			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4327	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.R4217Q(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CCTGTCATCTCGATGGATCTG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X											157	119	132					X																	53561010		2203	4300	6503	53577735	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12980G>A	X.37:g.53561010C>T	ENSP00000340648:p.Arg4327Gln		53577735	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837361	0.50951	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.60548	0.18;0.18	5.42	5.42	0.78866	HECT (4);	0.000000	0.64402	D	0.000001	T	0.77253	0.4103	M	0.82323	2.585	0.80722	D	1	D;D	0.69078	0.997;0.997	D;P	0.64506	0.926;0.879	T	0.81143	-0.1067	10	0.87932	D	0	.	17.2866	0.87143	0.0:1.0:0.0:0.0	.	4327;4311	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	Q	4327	ENSP00000340648:R4327Q;ENSP00000262854:R4327Q	ENSP00000262854:R4327Q	R	-	2	0	HUWE1	53577735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.959000	0.76031	2.436000	0.82500	0.529000	0.55759	CGA		0.493	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53561010	C	T	53561010	3	4	61	1	0	0	0	0	1	0	0	0	7482	884	31	1	152	1	HUWE1	23	53561010	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	103295	53561010	101709550	12098	20083										
HUWE1	10075	broad.mit.edu	37	chrX	53574917	53574917	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaaggagtctgaggagtttCtcagttaagagagagctccg	14	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:53574917C>A	ENST00000342160.3	-	67	10810	c.10353G>T	c.(10351-10353)gaG>gaT	p.E3451D	HUWE1_ENST00000262854.6_Missense_Mutation_p.E3451D|HUWE1_ENST00000474288.1_5'UTR			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3451					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.E3341D(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGAGGAGTTTCTCAGTTAAGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	X											61	51	54					X																	53574917		2203	4300	6503	53591642	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.10353G>T	X.37:g.53574917C>A	ENSP00000340648:p.Glu3451Asp		53591642	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.00|13.00	2.105161|2.105161	0.37145|0.37145	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052;ENST00000426907	T;T|.	0.20881|.	2.04;2.04|.	5.18|5.18	4.31|4.31	0.51392|0.51392	.|.	0.440632|0.440632	0.23046|0.23046	N|N	0.052546|0.052546	T|.	0.37320|.	0.0999|.	N|N	0.08118|0.08118	0|0	0.47862|0.47862	D|D	0.999538|0.999538	P;D|.	0.56035|.	0.956;0.974|.	P;D|.	0.67725|.	0.899;0.953|.	T|.	0.36212|.	-0.9757|.	10|.	0.07644|0.72032	T|D	0.81|0.01	.|.	8.4734|8.4734	0.32999|0.32999	0.0:0.8127:0.0:0.1873|0.0:0.8127:0.0:0.1873	.|.	3451;3435|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	D|X	3451|2485;289	ENSP00000340648:E3451D;ENSP00000262854:E3451D|.	ENSP00000262854:E3451D|ENSP00000403236:E289X	E|E	-|-	3|1	2|0	HUWE1|HUWE1	53591642|53591642	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	0.745000|0.745000	0.26259|0.26259	0.974000|0.974000	0.38366|0.38366	0.429000|0.429000	0.28392|0.28392	GAG|GAA		0.537	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53574917	C	A	53574917	3	1	61	1	0	0	0	0	1	0	0	0	7482	912	32	2	2839	2	HUWE1	23	53574917	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	13907	53574917	101695643	12099	20084										
WNK3	65267	broad.mit.edu	37	chrX	54263616	54263616	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtttcccagcagtcaatatCtctctctctttaagcaacag	5	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:54263616C>T	ENST00000375159.2	-	19	4382	c.4383G>A	c.(4381-4383)gaG>gaA	p.E1461E	WNK3_ENST00000354646.2_Silent_p.E1461E|WNK3_ENST00000375169.3_Silent_p.E1414E			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1461					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1461E(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						CAGTCAATATCTCTCTCTCTT	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	X											98	85	89					X																	54263616		2203	4300	6503	54280341	SO:0001819	synonymous_variant	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4383G>A	X.37:g.54263616C>T			54280341	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	37	CCDS14357.1																																																																																				0.453	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54263616	C	T	54263616	2	4	61	1	0	0	0	0	0	0	0	1	17419	912	32	3		3	WNK3	23	54263616	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	688699	54263616	101006944	12100	20085										
WNK3	65267	broad.mit.edu	37	chrX	54278091	54278091	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttctacaaatttttctttCtcactttccagcacaaagtt	2	11	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:54278091C>A	ENST00000375159.2	-	13	2396	c.2397G>T	c.(2395-2397)gaG>gaT	p.E799D	WNK3_ENST00000375169.3_Missense_Mutation_p.E799D|WNK3_ENST00000354646.2_Missense_Mutation_p.E799D			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	799					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E799D(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						ATTTTTCTTTCTCACTTTCCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	X											71	68	69					X																	54278091		2203	4300	6503	54294816	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.2397G>T	X.37:g.54278091C>A	ENSP00000364301:p.Glu799Asp		54294816	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461462	0.63513	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.35605	1.3;1.3;1.3	5.31	2.46	0.29980	.	0.000000	0.56097	D	0.000021	T	0.42832	0.1220	L	0.32530	0.975	0.27988	N	0.935772	D;D	0.76494	0.999;0.999	D;D	0.73380	0.98;0.939	T	0.20371	-1.0277	10	0.56958	D	0.05	-12.5176	7.6797	0.28507	0.0:0.6229:0.0:0.3771	.	799;799	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	D	799	ENSP00000364312:E799D;ENSP00000346667:E799D;ENSP00000364301:E799D	ENSP00000346667:E799D	E	-	3	2	WNK3	54294816	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	0.924000	0.28777	0.405000	0.25532	0.422000	0.28245	GAG		0.358	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		A	54278091	C	A	54278091	3	1	61	1	0	0	0	0	1	0	0	0	17419	912	32	2	3049	2	WNK3	23	54278091	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	14475	54278091	100992469	12101	20086										
FGD1	2245	broad.mit.edu	37	chrX	54481894	54481894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taagtacctggcctggagctCgagggagcgctgctttcctg	14	11	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:54481894C>T	ENST00000375135.3	-	12	2735	c.2002G>A	c.(2002-2004)Gag>Aag	p.E668K		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	668	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.E668K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GCCTGGAGCTCGAGGGAGCGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	X											110	80	91					X																	54481894		2203	4300	6503	54498619	SO:0001583	missense	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.2002G>A	X.37:g.54481894C>T	ENSP00000364277:p.Glu668Lys		54498619	Q5H999|Q8N4D9	Missense_Mutation	SNP	ENST00000375135.3	37	CCDS14359.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756829	0.89843	.	.	ENSG00000102302	ENST00000375135	D	0.88431	-2.38	5.01	5.01	0.66863	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.51477	D	0.000081	D	0.94905	0.8353	M	0.86740	2.835	0.58432	D	0.99999	D;D	0.89917	1.0;0.999	D;D	0.74674	0.981;0.984	D	0.95643	0.8700	10	0.72032	D	0.01	-7.8323	16.1456	0.81563	0.0:1.0:0.0:0.0	.	426;668	B4DS99;P98174	.;FGD1_HUMAN	K	668	ENSP00000364277:E668K	ENSP00000364277:E668K	E	-	1	0	FGD1	54498619	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.172000	0.77604	2.328000	0.79073	0.600000	0.82982	GAG		0.552	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		T	54481894	C	T	54481894	3	4	61	1	0	0	0	0	1	0	0	0	5851	893	31	1	911	1	FGD1	23	54481894	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	203803	54481894	100788666	12102	20087										
GNL3L	54552	broad.mit.edu	37	chrX	54559005	54559005	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcaagctggtcatcatgatGaaacttagacacagtgagtt	9	7	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:54559005G>T	ENST00000336470.4	+	2	145	c.6G>T	c.(4-6)atG>atT	p.M2I	GNL3L_ENST00000360845.2_Missense_Mutation_p.M2I|GNL3L_ENST00000489691.1_3'UTR	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	2					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.M2I(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						TCATCATGATGAAACTTAGAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											160	137	145					X																	54559005		2203	4300	6503	54575730	SO:0001583	missense	54552			AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.6G>T	X.37:g.54559005G>T	ENSP00000338573:p.Met2Ile		54575730		Missense_Mutation	SNP	ENST00000336470.4	37	CCDS14360.1	.	.	.	.	.	.	.	.	.	.	G	8.330	0.826334	0.16749	.	.	ENSG00000130119	ENST00000336470;ENST00000360845	T;T	0.16743	2.32;2.32	3.39	3.39	0.38822	.	0.607526	0.14835	N	0.295615	T	0.11067	0.0270	N	0.19112	0.55	0.27457	N	0.953263	B	0.10296	0.003	B	0.08055	0.003	T	0.10154	-1.0642	10	0.44086	T	0.13	-1.5884	9.3943	0.38392	0.0:0.0:1.0:0.0	.	2	Q9NVN8	GNL3L_HUMAN	I	2	ENSP00000338573:M2I;ENSP00000354091:M2I	ENSP00000338573:M2I	M	+	3	0	GNL3L	54575730	1.000000	0.71417	0.986000	0.45419	0.640000	0.38277	3.817000	0.55668	1.957000	0.56846	0.600000	0.82982	ATG		0.388	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067		T	54559005	G	T	54559005	3	4	61	1	0	0	0	0	1	0	0	0	6558	1290	45	2	8	2	GNL3L	23	54559005	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	77111	54559005	100711555	12103	20088										
ALAS2	212	broad.mit.edu	37	chrX	55043972	55043972	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttgggtatcttagggttaGacttctctagaagtttcttt	9	5	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:55043972G>T	ENST00000330807.5	-	7	1087	c.950C>A	c.(949-951)tCt>tAt	p.S317Y	ALAS2_ENST00000498636.1_5'UTR|ALAS2_ENST00000396198.3_Missense_Mutation_p.S304Y|ALAS2_ENST00000335854.4_Missense_Mutation_p.S280Y	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	317					cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)	p.S317Y(1)		central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	CTTAGGGTTAGACTTCTCTAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	X											248	201	217					X																	55043972		2203	4300	6503	55060697	SO:0001583	missense	212				CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"sideroblastic/hypochromic anemia"	301300	"aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.950C>A	X.37:g.55043972G>T	ENSP00000332369:p.Ser317Tyr		55060697	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Missense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	.	.	.	.	.	.	.	.	.	.	G	7.276	0.608157	0.14002	.	.	ENSG00000158578	ENST00000330807;ENST00000396198;ENST00000335854	D;D;D	0.95342	-3.68;-3.68;-3.68	5.24	5.24	0.73138	Aminotransferase, class I/classII (1);Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.164661	0.56097	D	0.000035	D	0.92166	0.7516	L	0.45352	1.415	0.47341	D	0.999397	B;B;B	0.27498	0.169;0.169;0.18	B;B;B	0.38921	0.285;0.285;0.285	D	0.87353	0.2339	10	0.02654	T	1	-24.0967	16.8746	0.86048	0.0:0.0:1.0:0.0	.	280;304;317	A8K6C4;Q5JZF5;P22557	.;.;HEM0_HUMAN	Y	317;304;280	ENSP00000332369:S317Y;ENSP00000379501:S304Y;ENSP00000337131:S280Y	ENSP00000332369:S317Y	S	-	2	0	ALAS2	55060697	1.000000	0.71417	0.052000	0.19188	0.823000	0.46562	7.912000	0.87465	2.333000	0.79357	0.513000	0.50165	TCT		0.433	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		T	55043972	G	T	55043972	3	4	61	1	0	0	0	0	1	0	0	0	485	942	33	2	833	2	ALAS2	23	55043972	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	484967	55043972	100226588	12104	20089										
USP51	158880	broad.mit.edu	37	chrX	55513912	55513912	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gattgcaggccacctgtaaaGatttggtctatgatgcagtt	11	7	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:55513912G>T	ENST00000500968.3	-	2	1543	c.1461C>A	c.(1459-1461)atC>atA	p.I487I	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	487	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.I487I(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CACCTGTAAAGATTTGGTCTA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	X											141	100	114					X																	55513912		2203	4300	6503	55530637	SO:0001819	synonymous_variant	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1461C>A	X.37:g.55513912G>T			55530637	Q8IWJ8	Silent	SNP	ENST00000500968.3	37	CCDS14370.1																																																																																				0.468	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		T	55513912	G	T	55513912	2	4	61	1	0	0	0	0	0	0	0	1	17123	932	33	2		2	USP51	23	55513912	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	469940	55513912	99756648	12105	20090										
USP51	158880	broad.mit.edu	37	chrX	55513974	55513974	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgcccaccactatcatCtttgctgtgtctatgtagca	6	14	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:55513974C>A	ENST00000500968.3	-	2	1481	c.1399G>T	c.(1399-1401)Gat>Tat	p.D467Y	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	467	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.D467Y(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CCACTATCATCTTTGCTGTGT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	X											139	109	119					X																	55513974		2203	4300	6503	55530699	SO:0001583	missense	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1399G>T	X.37:g.55513974C>A	ENSP00000423333:p.Asp467Tyr		55530699	Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	16.36	3.101680	0.56183	.	.	ENSG00000247746	ENST00000500968	T	0.31769	1.48	3.04	3.04	0.35103	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.344332	0.29293	U	0.012573	T	0.44414	0.1292	M	0.68952	2.095	0.43936	D	0.996597	D	0.58970	0.984	P	0.56163	0.793	T	0.49194	-0.8965	10	0.72032	D	0.01	.	11.3014	0.49309	0.0:1.0:0.0:0.0	.	467	Q70EK9	UBP51_HUMAN	Y	467	ENSP00000423333:D467Y	ENSP00000423333:D467Y	D	-	1	0	USP51	55530699	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.668000	0.74457	1.796000	0.52611	0.508000	0.49915	GAT		0.463	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		A	55513974	C	A	55513974	3	1	61	1	0	0	0	0	1	0	0	0	17123	913	32	2	740	2	USP51	23	55513974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	62	55513974	99756586	12106	20091										
ZXDA	7789	broad.mit.edu	37	chrX	57935660	57935660	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcactcactgtgataaatgTcttcttgcagccagaaaacg	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:57935660T>G	ENST00000358697.4	-	1	1407	c.1195A>C	c.(1195-1197)Aca>Cca	p.T399P		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	399	Required for interaction with ZXDC.				positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T399P(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						GTGATAAATGTCTTCTTGCAG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	X											125	113	117					X																	57935660		2203	4300	6503	57952385	SO:0001583	missense	7789			L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"Zinc fingers, C2H2-type"	13198	protein-coding gene	gene with protein product	"zinc finger protein 896"	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.1195A>C	X.37:g.57935660T>G	ENSP00000351530:p.Thr399Pro		57952385	Q9UJP7	Missense_Mutation	SNP	ENST00000358697.4	37	CCDS14376.1	.	.	.	.	.	.	.	.	.	.	.	15.07	2.723543	0.48728	.	.	ENSG00000198205	ENST00000358697	T	0.36340	1.26	3.45	3.45	0.39498	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.110563	0.64402	D	0.000010	T	0.45637	0.1352	L	0.44542	1.39	0.53688	D	0.999971	D	0.71674	0.998	D	0.67725	0.953	T	0.29941	-0.9995	9	.	.	.	.	9.4267	0.38583	0.0:0.0:0.0:1.0	.	399	P98168	ZXDA_HUMAN	P	399	ENSP00000351530:T399P	.	T	-	1	0	ZXDA	57952385	1.000000	0.71417	0.983000	0.44433	0.956000	0.61745	2.665000	0.46791	1.580000	0.49851	0.339000	0.21740	ACA		0.557	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156		G	57935660	T	G	57935660	3	3	61	1	0	0	0	0	1	0	0	0	18289	1667	58	4	1208	4	ZXDA	23	57935660	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	2421686	57935660	97334900	12107	20092										
ARHGEF9	23229	broad.mit.edu	37	chrX	62885871	62885871	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccccagtgtagatcagctcCgagctcctgtctaggatgtc	10	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:62885871C>T	ENST00000253401.6	-	7	1751	c.951G>A	c.(949-951)tcG>tcA	p.S317S	ARHGEF9_ENST00000437457.2_Silent_p.S264S|ARHGEF9_ENST00000433323.2_Intron|ARHGEF9_ENST00000374878.1_Silent_p.S315S|ARHGEF9_ENST00000495564.1_Intron|ARHGEF9_ENST00000374870.4_Silent_p.S215S|ARHGEF9_ENST00000374872.1_Silent_p.S296S	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	317					apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S315S(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						AGATCAGCTCCGAGCTCCTGT	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	X											134	104	114					X																	62885871		2203	4300	6503	62802596	SO:0001819	synonymous_variant	23229			AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.951G>A	X.37:g.62885871C>T			62802596	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Silent	SNP	ENST00000253401.6	37	CCDS35315.1																																																																																				0.597	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			T	62885871	C	T	62885871	2	4	61	1	0	0	0	0	0	0	0	1	912	639	23	1		1	ARHGEF9	23	62885871	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	4950211	62885871	92384689	12108	20093										
FAM123B	139285	broad.mit.edu	37	chrX	63411708	63411708	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccctgcggacaagccccaGggcctcacctgaatcatcct	8	17	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63411708G>A	ENST00000330258.3	-	2	1731	c.1459C>T	c.(1459-1461)Ctg>Ttg	p.L487L	AMER1_ENST00000374869.3_Silent_p.L487L|AMER1_ENST00000403336.1_Silent_p.L487L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	487					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.L487L(2)									ACAAGCCCCAGGGCCTCACCT	0.517																																																69	Whole gene deletion(67)|Substitution - coding silent(2)	kidney(65)|large_intestine(3)|ovary(1)	X											63	51	55					X																	63411708		2203	4300	6503	63328433	SO:0001819	synonymous_variant	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1459C>T	X.37:g.63411708G>A			63328433	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																				0.517	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411708	G	A	63411708	2	1	61	1	0	0	0	0	0	0	0	1	5439	991	35	3		3	FAM123B	23	63411708	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	525837	63411708	91858852	12109	20094										
FAM123B	139285	broad.mit.edu	37	chrX	63411948	63411948	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcagtttcccacagatattCtaagtcatcatcttcttcct	5	12	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63411948C>A	ENST00000330258.3	-	2	1491	c.1219G>T	c.(1219-1221)Gaa>Taa	p.E407*	AMER1_ENST00000374869.3_Nonsense_Mutation_p.E407*|AMER1_ENST00000403336.1_Nonsense_Mutation_p.E407*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	407	Glu-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.E407*(2)									CACAGATATTCTAAGTCATCA	0.502																																																69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											239	225	230					X																	63411948		2203	4300	6503	63328673	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1219G>T	X.37:g.63411948C>A	ENSP00000329117:p.Glu407*		63328673	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	39	7.298972	0.98196	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.17	5.17	0.71159	.	0.213952	0.33110	N	0.005263	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-8.7807	8.6586	0.34079	0.0:0.8975:0.0:0.1025	.	.	.	.	X	407	.	ENSP00000329117:E407X	E	-	1	0	FAM123B	63328673	0.210000	0.23517	1.000000	0.80357	0.913000	0.54294	1.491000	0.35583	2.551000	0.86045	0.600000	0.82982	GAA		0.502	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411948	C	A	63411948	4	1	61	1	0	0	0	0	0	1	0	0	5439	922	32	2	2192	2	FAM123B	23	63411948	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	240	63411948	91858612	12110	20095										
FAM123B	139285	broad.mit.edu	37	chrX	63412493	63412493	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggggttagcattttcctttCtaggggcttggaaggtctcc	14	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63412493C>A	ENST00000330258.3	-	2	946	c.674G>T	c.(673-675)aGa>aTa	p.R225I	AMER1_ENST00000374869.3_Missense_Mutation_p.R225I|AMER1_ENST00000403336.1_Missense_Mutation_p.R225I	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	225					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R225I(2)									ATTTTCCTTTCTAGGGGCTTG	0.567																																																69	Whole gene deletion(67)|Substitution - Missense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											64	63	63					X																	63412493		2196	4290	6486	63329218	SO:0001583	missense	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.674G>T	X.37:g.63412493C>A	ENSP00000329117:p.Arg225Ile		63329218	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	2.976	-0.211449	0.06140	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.19938	2.11;2.11;2.11	5.13	-5.29	0.02747	.	1.668050	0.02405	N	0.081017	T	0.17831	0.0428	M	0.63428	1.95	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.17289	-1.0374	10	0.32370	T	0.25	0.7982	1.0744	0.01629	0.3802:0.2181:0.0932:0.3085	.	225	Q5JTC6	F123B_HUMAN	I	225	ENSP00000364003:R225I;ENSP00000329117:R225I;ENSP00000384722:R225I	ENSP00000329117:R225I	R	-	2	0	FAM123B	63329218	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	0.279000	0.18771	-1.140000	0.02877	-0.956000	0.02647	AGA		0.567	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63412493	C	A	63412493	3	1	61	1	0	0	0	0	1	0	0	0	5439	913	32	2	2737	2	FAM123B	23	63412493	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	545	63412493	91858067	12111	20096										
ASB12	142689	broad.mit.edu	37	chrX	63445504	63445504	+	5'Flank	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgatgtccatgaggttcatCttggctaattggagaactat	11	6	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63445504C>A	ENST00000396130.2	-	0	0				MTMR8_ENST00000453546.1_Missense_Mutation_p.K384N|ASB12_ENST00000362002.2_Missense_Mutation_p.K9N			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12						intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)|p.K384N(2)|p.K9N(2)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						TGAGGTTCATCTTGGCTAATT	0.493																																																6	Substitution - Missense(4)|Whole gene deletion(2)	large_intestine(3)|lung(2)|ovary(1)	X											41	32	35					X																	63445504		2203	4298	6501	63362229	SO:0001631	upstream_gene_variant	142689			AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705		X.37:g.63445504C>A	Exception_encountered		63362229	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	37		.	.	.	.	.	.	.	.	.	.	C	9.710	1.156862	0.21454	.	.	ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000361287;ENST00000453546	T;T	0.76839	-0.0;-1.05	4.36	0.196	0.15159	.	0.221056	0.45606	N	0.000351	T	0.57621	0.2066	N	0.22421	0.69	0.26697	N	0.971249	B	0.10296	0.003	B	0.10450	0.005	T	0.39683	-0.9602	10	0.32370	T	0.25	.	5.0044	0.14280	0.0:0.2973:0.1789:0.5237	.	384	B4DQL0	.	N	9;9;384	ENSP00000355195:K9N;ENSP00000394003:K384N	ENSP00000354626:K9N	K	-	3	2	ASB12;MTMR8	63362229	0.996000	0.38824	0.962000	0.40283	0.870000	0.49936	0.222000	0.17699	-0.214000	0.10078	0.529000	0.55759	AAG		0.493	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	63445504	C	A	63445504	1	1	61	0	1	0	0	0	0	0	0	0	1017	928	32	2		2	ASB12	23	63445504	5'Flank	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	33011	63445504	91825056	12112	20097										
MTMR8	55613	broad.mit.edu	37	chrX	63488679	63488679	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatatttatggccctaaggCtgcccacaatctcacaacag	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63488679C>T	ENST00000374852.3	-	14	1920	c.1853G>A	c.(1852-1854)aGc>aAc	p.S618N	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	618						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)|p.S618N(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						GGCCCTAAGGCTGCCCACAAT	0.537																																																3	Whole gene deletion(2)|Substitution - Missense(1)	large_intestine(2)|ovary(1)	X											82	63	70					X																	63488679		2203	4300	6503	63405404	SO:0001583	missense	55613			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1853G>A	X.37:g.63488679C>T	ENSP00000363985:p.Ser618Asn		63405404	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	8.122	0.781089	0.16120	.	.	ENSG00000102043	ENST00000374852;ENST00000247400	D	0.94687	-3.49	2.5	-0.491	0.12045	.	0.439792	0.17497	U	0.172153	D	0.82481	0.5046	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.70321	-0.4904	10	0.30078	T	0.28	.	2.5766	0.04807	0.2278:0.309:0.0:0.4632	.	618	Q96EF0	MTMR8_HUMAN	N	618;504	ENSP00000363985:S618N	ENSP00000247400:S504N	S	-	2	0	MTMR8	63405404	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.688000	0.05150	-0.251000	0.09542	0.436000	0.28706	AGC		0.537	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63488679	C	T	63488679	3	4	61	1	0	0	0	0	1	0	0	0	9979	797	28	3	265	3	MTMR8	23	63488679	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43175	63488679	91781881	12113	20098										
MTMR8	55613	broad.mit.edu	37	chrX	63563587	63563587	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aattcactcattgttggagtTttcaattcacaaactaaggt	6	7	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63563587T>G	ENST00000374852.3	-	8	946	c.879A>C	c.(877-879)aaA>aaC	p.K293N	MTMR8_ENST00000453546.1_Missense_Mutation_p.K293N|MTMR8_ENST00000478487.1_5'UTR	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	293	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)|p.K293N(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TTGTTGGAGTTTTCAATTCAC	0.373																																																2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	X											52	43	46					X																	63563587		2203	4299	6502	63480312	SO:0001583	missense	55613			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.879A>C	X.37:g.63563587T>G	ENSP00000363985:p.Lys293Asn		63480312	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.87|15.87	2.960446|2.960446	0.53400|0.53400	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400|ENST00000442913	D;D|.	0.92545|.	-3.06;-3.06|.	3.34|3.34	3.34|3.34	0.38264|0.38264	Myotubularin phosphatase domain (1);|.	0.000000|.	0.53938|.	U|.	0.000050|.	T|T	0.53916|0.53916	0.1826|0.1826	L|L	0.48642|0.48642	1.525|1.525	0.46874|0.46874	D|D	0.999236|0.999236	D;D|.	0.54772|.	0.966;0.968|.	P;P|.	0.55087|.	0.501;0.768|.	T|T	0.49826|0.49826	-0.8898|-0.8898	10|5	0.87932|.	D|.	0|.	.|.	6.2344|6.2344	0.20754|0.20754	0.0:0.127:0.0:0.873|0.0:0.127:0.0:0.873	.|.	293;293|.	B4DQL0;Q96EF0|.	.;MTMR8_HUMAN|.	N|H	293;293;179|97	ENSP00000394003:K293N;ENSP00000363985:K293N|.	ENSP00000247400:K179N|.	K|N	-|-	3|1	2|0	MTMR8|MTMR8	63480312|63480312	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.566000|0.566000	0.23593|0.23593	1.360000|1.360000	0.45960|0.45960	0.417000|0.417000	0.27973|0.27973	AAA|AAC		0.373	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		G	63563587	T	G	63563587	3	3	61	1	0	0	0	0	1	0	0	0	9979	1838	64	4	1263	4	MTMR8	23	63563587	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	74908	63563587	91706973	12114	20099										
MTMR8	55613	broad.mit.edu	37	chrX	63568625	63568625	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagagctcatcatctacaCagcgagtgtaaaatccagag	8	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63568625C>G	ENST00000374852.3	-	6	714	c.647G>C	c.(646-648)tGt>tCt	p.C216S	MTMR8_ENST00000453546.1_Missense_Mutation_p.C216S	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	216	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.C216S(1)|p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						ATCATCTACACAGCGAGTGTA	0.443																																																2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	X											118	94	102					X																	63568625		2203	4300	6503	63485350	SO:0001583	missense	55613			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.647G>C	X.37:g.63568625C>G	ENSP00000363985:p.Cys216Ser		63485350	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	6.128	0.391905	0.11581	.	.	ENSG00000102043	ENST00000453546;ENST00000374852	D;D	0.89485	-2.52;-2.52	2.68	0.707	0.18139	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.107747	0.37261	N	0.002168	T	0.76572	0.4006	N	0.20445	0.575	0.51767	D	0.999938	B;P	0.36909	0.0;0.573	B;B	0.38106	0.002;0.265	T	0.63541	-0.6614	10	0.20519	T	0.43	.	5.6116	0.17408	0.0:0.6504:0.2177:0.1318	.	216;216	B4DQL0;Q96EF0	.;MTMR8_HUMAN	S	216	ENSP00000394003:C216S;ENSP00000363985:C216S	ENSP00000363985:C216S	C	-	2	0	MTMR8	63485350	0.971000	0.33674	0.006000	0.13384	0.975000	0.68041	2.326000	0.43849	-0.065000	0.13021	0.506000	0.49869	TGT		0.443	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		G	63568625	C	G	63568625	3	3	61	1	0	0	0	0	1	0	0	0	9979	478	17	5	1503	5	MTMR8	23	63568625	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5038	63568625	91701935	12115	20100										
MTMR8	55613	broad.mit.edu	37	chrX	63574764	63574764	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatccactttccctcatctCttttgaggatttgggattat	6	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:63574764C>A	ENST00000374852.3	-	4	428	c.361G>T	c.(361-363)Gag>Tag	p.E121*	MTMR8_ENST00000453546.1_Nonsense_Mutation_p.E121*	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	121						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.E121*(1)|p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TCCCTCATCTCTTTTGAGGAT	0.388																																																2	Substitution - Nonsense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	X											93	74	80					X																	63574764		2203	4300	6503	63491489	SO:0001587	stop_gained	55613			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.361G>T	X.37:g.63574764C>A	ENSP00000363985:p.Glu121*		63491489	Q5JT99|Q9NXP6	Nonsense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.0|22.0	4.226560|4.226560	0.79576|0.79576	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400|ENST00000442913	.|.	.|.	.|.	2.96|2.96	1.16|1.16	0.20824|0.20824	.|.	0.380677|.	0.19703|.	U|.	0.107989|.	.|T	.|0.39118	.|0.1066	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.44682	.|-0.9312	.|3	0.23302|.	T|.	0.38|.	.|.	6.0279|6.0279	0.19665|0.19665	0.0:0.6126:0.0:0.3874|0.0:0.6126:0.0:0.3874	.|.	.|.	.|.	.|.	X|I	121;121;120|37	.|.	ENSP00000247400:E120X|.	E|R	-|-	1|2	0|0	MTMR8|MTMR8	63491489|63491489	0.996000|0.996000	0.38824|0.38824	0.703000|0.703000	0.30354|0.30354	0.919000|0.919000	0.55068|0.55068	1.445000|1.445000	0.35079|0.35079	0.178000|0.178000	0.19917|0.19917	0.506000|0.506000	0.49869|0.49869	GAG|AGA		0.388	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		A	63574764	C	A	63574764	4	1	61	1	0	0	0	0	0	1	0	0	9979	922	32	2	1797	2	MTMR8	23	63574764	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	6139	63574764	91695796	12116	20101										
HEPH	9843	broad.mit.edu	37	chrX	65483520	65483520	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaccgtcatcaccaaagaGactgaaaaaggtacgtaaaa	7	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:65483520G>T	ENST00000343002.2	+	19	3898	c.3234G>T	c.(3232-3234)gaG>gaT	p.E1078D	HEPH_ENST00000419594.1_Missense_Mutation_p.E889D|HEPH_ENST00000519389.1_Missense_Mutation_p.E1132D|HEPH_ENST00000374727.3_Missense_Mutation_p.E1081D|HEPH_ENST00000336279.5_Missense_Mutation_p.E811D|HEPH_ENST00000441993.2_Missense_Mutation_p.E1081D			Q9BQS7	HEPH_HUMAN	hephaestin	1078	Plastocyanin-like 6.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)	p.E1078D(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						TCACCAAAGAGACTGAAAAAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											214	149	171					X																	65483520		2203	4300	6503	65400245	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.3234G>T	X.37:g.65483520G>T	ENSP00000343939:p.Glu1078Asp		65400245	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	G	2.027	-0.423305	0.04734	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002	D;D;D;D;D;D	0.99264	-5.65;-5.63;-5.63;-5.63;-5.64;-5.63	3.95	3.09	0.35607	.	0.381500	0.24983	N	0.034057	D	0.95865	0.8654	N	0.22421	0.69	0.09310	N	0.999998	B;B;B	0.21452	0.0;0.056;0.0	B;B;B	0.15484	0.001;0.013;0.0	D	0.89927	0.4063	10	0.13108	T	0.6	.	6.7121	0.23282	0.1299:0.0:0.8701:0.0	.	1132;889;1078	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	D	1132;1081;811;1081;889;1078	ENSP00000430620:E1132D;ENSP00000363859:E1081D;ENSP00000337418:E811D;ENSP00000411687:E1081D;ENSP00000413211:E889D;ENSP00000343939:E1078D	ENSP00000337418:E811D	E	+	3	2	HEPH	65400245	0.940000	0.31905	0.320000	0.25306	0.169000	0.22640	0.383000	0.20651	1.028000	0.39785	0.600000	0.82982	GAG		0.448	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65483520	G	T	65483520	3	4	61	1	0	0	0	0	1	0	0	0	7075	933	33	2	3474	2	HEPH	23	65483520	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1908756	65483520	89787040	12117	20102										
HEPH	9843	broad.mit.edu	37	chrX	65486346	65486346	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatgcagatccccataaaGaatgttgagatgctggcctc	11	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:65486346G>T	ENST00000343002.2	+	20	3973	c.3309G>T	c.(3307-3309)aaG>aaT	p.K1103N	HEPH_ENST00000419594.1_Missense_Mutation_p.K914N|HEPH_ENST00000519389.1_Missense_Mutation_p.K1157N|HEPH_ENST00000374727.3_Missense_Mutation_p.K1106N|HEPH_ENST00000336279.5_Missense_Mutation_p.K836N|HEPH_ENST00000441993.2_Missense_Mutation_p.K1105N			Q9BQS7	HEPH_HUMAN	hephaestin	1103					cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)	p.K1103N(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						TCCCCATAAAGAATGTTGAGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											307	207	241					X																	65486346		2203	4300	6503	65403071	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.3309G>T	X.37:g.65486346G>T	ENSP00000343939:p.Lys1103Asn		65403071	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	.	16.77	3.213853	0.58452	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002	D;D;D;D;D;D	0.99298	-5.71;-5.7;-5.7;-5.66;-5.71;-5.7	5.11	2.34	0.29019	.	0.364044	0.23474	N	0.047797	D	0.97210	0.9088	L	0.29908	0.895	0.09310	N	1	B;D;B	0.56035	0.201;0.974;0.18	B;P;B	0.49752	0.055;0.621;0.056	D	0.93950	0.7231	10	0.13470	T	0.59	.	7.8552	0.29478	0.2813:0.0:0.7187:0.0	.	1157;914;1103	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	N	1157;1106;836;1105;914;1103	ENSP00000430620:K1157N;ENSP00000363859:K1106N;ENSP00000337418:K836N;ENSP00000411687:K1105N;ENSP00000413211:K914N;ENSP00000343939:K1103N	ENSP00000337418:K836N	K	+	3	2	HEPH	65403071	0.033000	0.19621	0.051000	0.19133	0.982000	0.71751	1.140000	0.31516	0.557000	0.29117	0.600000	0.82982	AAG		0.483	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65486346	G	T	65486346	3	4	61	1	0	0	0	0	1	0	0	0	7075	933	33	2	3553	2	HEPH	23	65486346	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2826	65486346	89784214	12118	20103										
PJA1	64219	broad.mit.edu	37	chrX	68381193	68381193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcggcacacggggcaggtgCctgacttctgaagccagatg	15	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:68381193C>T	ENST00000361478.1	-	2	2266	c.1889G>A	c.(1888-1890)gGc>gAc	p.G630D	PJA1_ENST00000374571.4_Missense_Mutation_p.G575D|PJA1_ENST00000374583.1_Missense_Mutation_p.G630D|PJA1_ENST00000374584.3_Missense_Mutation_p.G442D|PJA1_ENST00000477231.1_5'Flank	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	630					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G630D(1)|p.G442D(1)|p.G442V(1)		endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						GGGGCAGGTGCCTGACTTCTG	0.537																																																3	Substitution - Missense(3)	large_intestine(2)|ovary(1)	X											51	41	44					X																	68381193		2203	4300	6503	68297918	SO:0001583	missense	64219			AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1889G>A	X.37:g.68381193C>T	ENSP00000355014:p.Gly630Asp		68297918	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	37	CCDS14393.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.950458	0.34377	.	.	ENSG00000181191	ENST00000396010;ENST00000374584;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	3.68	3.68	0.42216	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.132235	0.33127	U	0.005257	T	0.66117	0.2757	N	0.12637	0.245	0.46678	D	0.999158	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.71407	-0.4602	10	0.62326	D	0.03	-12.9359	12.5562	0.56254	0.0:1.0:0.0:0.0	.	630;442	Q8NG27;Q8NG27-2	PJA1_HUMAN;.	D	545;442;630;630;575	ENSP00000363712:G442D;ENSP00000363711:G630D;ENSP00000355014:G630D;ENSP00000363699:G575D	ENSP00000355014:G630D	G	-	2	0	PJA1	68297918	1.000000	0.71417	0.995000	0.50966	0.011000	0.07611	4.683000	0.61679	2.115000	0.64714	0.544000	0.68410	GGC		0.537	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		T	68381193	C	T	68381193	3	4	61	1	0	0	0	0	1	0	0	0	11992	739	26	3	46	3	PJA1	23	68381193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2894847	68381193	86889367	12119	20104										
PJA1	64219	broad.mit.edu	37	chrX	68382762	68382762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattcctcttctgctacccGaagctctgtactctcttggc	6	16	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:68382762G>A	ENST00000361478.1	-	2	697	c.320C>T	c.(319-321)tCg>tTg	p.S107L	PJA1_ENST00000374571.4_Missense_Mutation_p.S52L|PJA1_ENST00000374583.1_Missense_Mutation_p.S107L|PJA1_ENST00000374584.3_Intron|PJA1_ENST00000477231.1_5'UTR	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	107					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S107L(1)		endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TCTGCTACCCGAAGCTCTGTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	X											85	77	80					X																	68382762		2203	4300	6503	68299487	SO:0001583	missense	64219			AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.320C>T	X.37:g.68382762G>A	ENSP00000355014:p.Ser107Leu		68299487	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	37	CCDS14393.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308994	0.23821	.	.	ENSG00000181191	ENST00000396010;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T	0.14766	2.48;2.48;2.48	3.25	2.38	0.29361	.	0.761458	0.10268	N	0.695152	T	0.11153	0.0272	L	0.46157	1.445	0.18873	N	0.999983	B	0.12013	0.005	B	0.04013	0.001	T	0.38779	-0.9645	10	0.17832	T	0.49	-3.6457	5.658	0.17652	0.1538:0.0:0.8462:0.0	.	107	Q8NG27	PJA1_HUMAN	L	52;107;107;52	ENSP00000363711:S107L;ENSP00000355014:S107L;ENSP00000363699:S52L	ENSP00000355014:S107L	S	-	2	0	PJA1	68299487	0.501000	0.26099	0.555000	0.28281	0.928000	0.56348	0.976000	0.29462	0.789000	0.33779	0.534000	0.68092	TCG		0.522	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		A	68382762	G	A	68382762	3	1	61	1	0	0	0	0	1	0	0	0	11992	1059	37	1	1615	1	PJA1	23	68382762	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1569	68382762	86887798	12120	20105										
EDA	1896	broad.mit.edu	37	chrX	68836510	68836510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcagccattggaaccgggaGaagccgcactccactctgac	11	14	1	2	rs369801319		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:68836510G>T	ENST00000374552.4	+	1	600	c.358G>T	c.(358-360)Gaa>Taa	p.E120*	EDA_ENST00000527388.1_Nonsense_Mutation_p.E120*|EDA_ENST00000374553.2_Nonsense_Mutation_p.E120*|EDA_ENST00000525810.1_Nonsense_Mutation_p.E120*|EDA_ENST00000502251.1_3'UTR|EDA_ENST00000524573.1_Nonsense_Mutation_p.E120*|EDA_ENST00000338901.3_Nonsense_Mutation_p.E120*	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	120					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.E120*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						GGAACCGGGAGAAGCCGCACT	0.687																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											32	36	34					X																	68836510		2203	4298	6501	68753235	SO:0001587	stop_gained	1896			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.358G>T	X.37:g.68836510G>T	ENSP00000363680:p.Glu120*		68753235	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Nonsense_Mutation	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	G	38	6.930571	0.97944	.	.	ENSG00000158813	ENST00000513754;ENST00000338901;ENST00000374552;ENST00000374553;ENST00000525810;ENST00000527388;ENST00000524573	.	.	.	4.97	4.97	0.65823	.	0.271711	0.30949	N	0.008543	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.5556	12.243	0.54553	0.0:0.0:1.0:0.0	.	.	.	.	X	120	.	ENSP00000340611:E120X	E	+	1	0	EDA	68753235	0.996000	0.38824	0.365000	0.25901	0.895000	0.52256	4.615000	0.61190	2.279000	0.76181	0.600000	0.82982	GAA		0.687	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		T	68836510	G	T	68836510	4	4	61	1	0	0	0	0	0	1	0	0	4914	943	33	2	360	2	EDA	23	68836510	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	453748	68836510	86434050	12121	20106										
AWAT2	158835	broad.mit.edu	37	chrX	69261787	69261787	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctggcttggattctcaatCttgggcattggtagaggctc	12	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69261787C>A	ENST00000276101.3	-	7	878	c.873G>T	c.(871-873)aaG>aaT	p.K291N		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	291					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)	p.K291N(1)		endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						GATTCTCAATCTTGGGCATTG	0.478																																					NSCLC(80;1334 1436 9350 24214 26427)											1	Substitution - Missense(1)	large_intestine(1)	X											128	98	108					X																	69261787		2203	4300	6503	69178512	SO:0001583	missense	158835			BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"multifunctional O-acyltransferase"	300925	"diacylglycerol O-acyltransferase 2-like 4"	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.873G>T	X.37:g.69261787C>A	ENSP00000421172:p.Lys291Asn		69178512	Q6IEE3|Q6P437	Missense_Mutation	SNP	ENST00000276101.3	37	CCDS35320.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744846	0.49151	.	.	ENSG00000147160	ENST00000276101	T	0.20069	2.1	4.83	3.97	0.46021	.	0.071454	0.56097	D	0.000022	T	0.33702	0.0872	M	0.89030	3	0.51012	D	0.999909	P	0.41498	0.752	B	0.42625	0.393	T	0.30765	-0.9967	10	0.66056	D	0.02	.	9.9007	0.41346	0.0:0.8984:0.0:0.1016	.	291	Q6E213	AWAT2_HUMAN	N	291	ENSP00000421172:K291N	ENSP00000421172:K291N	K	-	3	2	AWAT2	69178512	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.862000	0.39448	1.163000	0.42636	0.600000	0.82982	AAG		0.478	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		A	69261787	C	A	69261787	3	1	61	1	0	0	0	0	1	0	0	0	1236	912	32	2	132	2	AWAT2	23	69261787	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	425277	69261787	86008773	12122	20107										
AWAT2	158835	broad.mit.edu	37	chrX	69263346	69263346	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgtagacattacatattCtctgaggaaaggcatccaga	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69263346C>A	ENST00000276101.3	-	4	459	c.454G>T	c.(454-456)Gaa>Taa	p.E152*		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	152					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)	p.E152*(1)		endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						ATTACATATTCTCTGAGGAAA	0.493																																					NSCLC(80;1334 1436 9350 24214 26427)											1	Substitution - Nonsense(1)	large_intestine(1)	X											36	32	33					X																	69263346		2203	4299	6502	69180071	SO:0001587	stop_gained	158835			BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"multifunctional O-acyltransferase"	300925	"diacylglycerol O-acyltransferase 2-like 4"	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.454G>T	X.37:g.69263346C>A	ENSP00000421172:p.Glu152*		69180071	Q6IEE3|Q6P437	Nonsense_Mutation	SNP	ENST00000276101.3	37	CCDS35320.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908906	0.52439	.	.	ENSG00000147160	ENST00000276101	.	.	.	5.02	5.02	0.67125	.	0.593663	0.16144	N	0.227580	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.5334	0.67942	0.0:1.0:0.0:0.0	.	.	.	.	X	152	.	ENSP00000421172:E152X	E	-	1	0	AWAT2	69180071	1.000000	0.71417	0.408000	0.26446	0.031000	0.12232	5.401000	0.66326	2.307000	0.77673	0.513000	0.50165	GAA		0.493	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		A	69263346	C	A	69263346	4	1	61	1	0	0	0	0	0	1	0	0	1236	922	32	2	563	2	AWAT2	23	69263346	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1559	69263346	86007214	12123	20108										
OTUD6A	139562	broad.mit.edu	37	chrX	69282896	69282896	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagatgctgcgctgccgcacCgccagctacatgaagaagca	12	13	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69282896C>T	ENST00000338352.2	+	1	556	c.522C>T	c.(520-522)acC>acT	p.T174T		NM_207320.1	NP_997203.1	Q7L8S5	OTU6A_HUMAN	OTU deubiquitinase 6A	174	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)		ubiquitin-specific protease activity (GO:0004843)	p.T174T(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(3)|urinary_tract(1)	23						GCTGCCGCACCGCCAGCTACA	0.602													C|||	1	0.000264901	8e-04	0	3775	,	,		14125	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											54	40	45					X																	69282896		2203	4300	6503	69199621	SO:0001819	synonymous_variant	139562			AK098697	CCDS14395.1	Xq13.1	2014-02-24	2014-02-24			ENSG00000189401		"OTU domain containing"	32312	protein-coding gene	gene with protein product		300714	"OTU domain containing 6A"			23827681	Standard	NM_207320		Approved	FLJ25831, HSHIN6, DUBA2	uc004dxu.1	Q7L8S5		ENST00000338352.2:c.522C>T	X.37:g.69282896C>T			69199621	B2RPB7	Silent	SNP	ENST00000338352.2	37	CCDS14395.1																																																																																				0.602	OTUD6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358763.1	NM_207320		T	69282896	C	T	69282896	2	4	61	1	0	0	0	0	0	0	0	1	11347	639	23	1		1	OTUD6A	23	69282896	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	19550	69282896	85987664	12124	20109										
IGBP1	3476	broad.mit.edu	37	chrX	69353825	69353825	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggacgagttacagctgCcgcggctccccgagctgttc	13	14	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69353825C>T	ENST00000342206.6	+	1	527	c.28C>T	c.(28-30)Ccg>Tcg	p.P10S	IGBP1_ENST00000356413.4_Missense_Mutation_p.P10S			P78318	IGBP1_HUMAN	immunoglobulin (CD79A) binding protein 1	10					B cell activation (GO:0042113)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dephosphorylation (GO:0035306)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microtubule-based movement (GO:0060632)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	protein phosphatase type 2A regulator activity (GO:0008601)	p.P10S(1)		kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(2)	11						GTTACAGCTGCCGCGGCTCCC	0.547											OREG0019849	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									NSCLC(167;1189 1558 6576 8216 30387 37980 41450)											1	Substitution - Missense(1)	large_intestine(1)	X											25	23	24					X																	69353825		2203	4300	6503	69270550	SO:0001583	missense	3476			Y08915	CCDS14396.1	Xq13.1-q13.3	2008-02-05			ENSG00000089289	ENSG00000089289			5461	protein-coding gene	gene with protein product	"alpha 4"	300139		IBP1		9441740	Standard	NM_001551		Approved		uc004dxw.3	P78318	OTTHUMG00000021767	ENST00000342206.6:c.28C>T	X.37:g.69353825C>T	ENSP00000363661:p.Pro10Ser	1114	69270550	Q8TAB2	Missense_Mutation	SNP	ENST00000342206.6	37	CCDS14396.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376810	0.24857	.	.	ENSG00000089289	ENST00000342206;ENST00000356413	T;T	0.41065	1.01;1.01	4.75	3.87	0.44632	.	0.164239	0.53938	D	0.000041	T	0.41119	0.1145	M	0.76574	2.34	0.39266	D	0.964293	B	0.33345	0.409	B	0.33799	0.17	T	0.44636	-0.9315	10	0.56958	D	0.05	.	7.1915	0.25828	0.1945:0.6206:0.1848:0.0	.	10	P78318	IGBP1_HUMAN	S	10	ENSP00000363661:P10S;ENSP00000348784:P10S	ENSP00000363661:P10S	P	+	1	0	IGBP1	69270550	0.880000	0.30214	0.616000	0.29078	0.238000	0.25445	1.907000	0.39897	1.098000	0.41479	0.600000	0.82982	CCG		0.547	IGBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057052.1			T	69353825	C	T	69353825	3	4	61	1	0	0	0	0	1	0	0	0	7588	739	26	3	30	3	IGBP1	23	69353825	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	70929	69353825	85916735	12125	20110										
AWAT1	158833	broad.mit.edu	37	chrX	69455608	69455608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cgtctacctgctgtttacatCcttgtggccgctaccagtgc	9	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69455608C>A	ENST00000374521.3	+	2	160	c.119C>A	c.(118-120)tCc>tAc	p.S40Y	AWAT1_ENST00000480702.1_3'UTR	NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	40					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)	p.S120Y(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						CTGTTTACATCCTTGTGGCCG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											311	231	258					X																	69455608		2203	4300	6503	69372333	SO:0001583	missense	158833			BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"diacylglycerol O-acyltransferase 2-like 3"	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.119C>A	X.37:g.69455608C>A	ENSP00000363645:p.Ser40Tyr		69372333	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	.	.	.	.	.	.	.	.	.	.	c	9.817	1.184780	0.21870	.	.	ENSG00000204195	ENST00000374521	T	0.14391	2.51	5.03	2.1	0.27182	.	0.923652	0.09145	N	0.842354	T	0.14356	0.0347	L	0.54323	1.7	0.09310	N	1	P	0.35155	0.487	B	0.34536	0.185	T	0.22487	-1.0215	10	0.06625	T	0.88	-1.181	14.9996	0.71462	0.0:0.4495:0.5505:0.0	.	40	Q58HT5	AWAT1_HUMAN	Y	40	ENSP00000363645:S40Y	ENSP00000363645:S40Y	S	+	2	0	AWAT1	69372333	0.000000	0.05858	0.037000	0.18230	0.068000	0.16541	-0.155000	0.10115	0.115000	0.18071	-0.231000	0.12243	TCC		0.498	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579		A	69455608	C	A	69455608	3	1	61	1	0	0	0	0	1	0	0	0	1235	855	30	2	125	2	AWAT1	23	69455608	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	101783	69455608	85814952	12126	20111										
DLG3	1741	broad.mit.edu	37	chrX	69669296	69669296	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatctttattaccaagattAtccctggtggagcagctgcc	9	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69669296A>T	ENST00000374360.3	+	3	729	c.496A>T	c.(496-498)Atc>Ttc	p.I166F	DLG3_ENST00000374355.3_5'Flank|RNU4-81P_ENST00000363561.1_RNA|DLG3_ENST00000194900.4_Missense_Mutation_p.I184F	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	166	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)	p.I166F(1)		endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					TACCAAGATTATCCCTGGTGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	X											81	65	71					X																	69669296		2203	4300	6503	69586021	SO:0001583	missense	1741			U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"neuroendocrine-dlg", "protein phosphatase 1, regulatory subunit 82"	300189	"discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.496A>T	X.37:g.69669296A>T	ENSP00000363480:p.Ile166Phe		69586021	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Missense_Mutation	SNP	ENST00000374360.3	37	CCDS14403.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.895938	0.72639	.	.	ENSG00000082458	ENST00000194900;ENST00000374360	T;T	0.27720	1.65;1.65	4.2	4.2	0.49525	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.45696	0.1355	L	0.46885	1.475	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.30208	-0.9986	9	.	.	.	.	11.738	0.51775	1.0:0.0:0.0:0.0	.	166	Q92796	DLG3_HUMAN	F	184;166	ENSP00000194900:I184F;ENSP00000363480:I166F	.	I	+	1	0	DLG3	69586021	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.661000	0.91125	1.555000	0.49500	0.356000	0.21956	ATC		0.582	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		T	69669296	A	T	69669296	3	4	61	1	0	0	0	0	1	0	0	0	4567	449	16	5	506	5	DLG3	23	69669296	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	213688	69669296	85601264	12127	20112										
DLG3	1741	broad.mit.edu	37	chrX	69712393	69712393	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaaaagaaagaaagagctCgattgaaaactgtgaagttc	11	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69712393C>T	ENST00000374360.3	+	12	1953	c.1720C>T	c.(1720-1722)Cga>Tga	p.R574*	DLG3_ENST00000374355.3_Nonsense_Mutation_p.R237*|DLG3_ENST00000542398.1_Nonsense_Mutation_p.R91*|DLG3_ENST00000194900.4_Nonsense_Mutation_p.R592*	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	574					axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)	p.R574*(2)		endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					AGAAAGAGCTCGATTGAAAAC	0.488																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											68	61	63					X																	69712393		2203	4300	6503	69629118	SO:0001587	stop_gained	1741			U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"neuroendocrine-dlg", "protein phosphatase 1, regulatory subunit 82"	300189	"discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.1720C>T	X.37:g.69712393C>T	ENSP00000363480:p.Arg574*		69629118	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Nonsense_Mutation	SNP	ENST00000374360.3	37	CCDS14403.1	.	.	.	.	.	.	.	.	.	.	C	34	5.403825	0.96051	.	.	ENSG00000082458	ENST00000194900;ENST00000374360;ENST00000374355;ENST00000542398	.	.	.	5.09	4.23	0.50019	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8911	0.52630	0.0:0.9147:0.0:0.0853	.	.	.	.	X	592;574;237;91	.	.	R	+	1	2	DLG3	69629118	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.456000	0.44997	1.146000	0.42352	0.600000	0.82982	CGA		0.488	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		T	69712393	C	T	69712393	4	4	61	1	0	0	0	0	0	1	0	0	4567	876	31	1	1904	1	DLG3	23	69712393	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43097	69712393	85558167	12128	20113										
TEX11	56159	broad.mit.edu	37	chrX	69749825	69749825	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggacttgaccatcagccagaGaatctccatttctgggtagt	10	10	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69749825G>T	ENST00000395889.2	-	30	2745	c.2590C>A	c.(2590-2592)Ctc>Atc	p.L864I	TEX11_ENST00000374320.2_Missense_Mutation_p.L539I|TEX11_ENST00000344304.3_Missense_Mutation_p.L864I|TEX11_ENST00000374333.2_Missense_Mutation_p.L849I	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	864					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.L849I(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					ATCAGCCAGAGAATCTCCATT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	86	93					X																	69749825		2203	4300	6503	69666550	SO:0001583	missense	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2590C>A	X.37:g.69749825G>T	ENSP00000379226:p.Leu864Ile		69666550	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521667	0.44866	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.47869	1.43;1.43;0.83;1.43	4.33	1.37	0.22104	.	0.337752	0.23791	U	0.044525	T	0.38639	0.1048	L	0.43152	1.355	0.23784	N	0.996854	P;P	0.50156	0.932;0.889	P;B	0.46543	0.52;0.444	T	0.21143	-1.0254	9	.	.	.	-0.1706	5.0998	0.14753	0.2134:0.2166:0.5699:0.0	.	849;864	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	I	849;864;539;864	ENSP00000363453:L849I;ENSP00000379226:L864I;ENSP00000363440:L539I;ENSP00000340995:L864I	.	L	-	1	0	TEX11	69666550	1.000000	0.71417	0.636000	0.29352	0.882000	0.50991	2.082000	0.41605	-0.046000	0.13446	0.500000	0.49745	CTC		0.438	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	69749825	G	T	69749825	3	4	61	1	0	0	0	0	1	0	0	0	15813	942	33	2	240	2	TEX11	23	69749825	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	37432	69749825	85520735	12129	20114										
TEX11	56159	broad.mit.edu	37	chrX	69960608	69960608	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	taatatttggtgtcatcccaAtccaaataattcgtggctaa	6	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:69960608A>G	ENST00000395889.2	-	12	986	c.831T>C	c.(829-831)gaT>gaC	p.D277D	TEX11_ENST00000344304.3_Silent_p.D277D|TEX11_ENST00000374333.2_Silent_p.D262D	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	277					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.D262D(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TGTCATCCCAATCCAAATAAT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	X											96	80	86					X																	69960608		2203	4300	6503	69877333	SO:0001819	synonymous_variant	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.831T>C	X.37:g.69960608A>G			69877333	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	37	CCDS35323.1																																																																																				0.323	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			G	69960608	A	G	69960608	2	3	61	1	0	0	0	0	0	0	0	1	15813	98	4	4		4	TEX11	23	69960608	Silent	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	210783	69960608	85309952	12130	20115										
TEX11	56159	broad.mit.edu	37	chrX	70026590	70026590	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttcttcatatttattattCttctgggtttctactccaaa	3	9	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70026590C>A	ENST00000395889.2	-	10	857	c.702G>T	c.(700-702)aaG>aaT	p.K234N	TEX11_ENST00000344304.3_Missense_Mutation_p.K234N|TEX11_ENST00000374333.2_Missense_Mutation_p.K219N	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	234					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.K219N(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					ATTTATTATTCTTCTGGGTTT	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	X											34	29	31					X																	70026590		2187	4270	6457	69943315	SO:0001583	missense	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.702G>T	X.37:g.70026590C>A	ENSP00000379226:p.Lys234Asn		69943315	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.559756	0.00910	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.63580	-0.05;-0.05;-0.05	4.07	-2.94	0.05581	Tetratricopeptide-like helical (1);	0.479220	0.21291	N	0.076965	T	0.36880	0.0983	L	0.35414	1.06	0.09310	N	1	B;P	0.43826	0.037;0.818	B;B	0.38985	0.018;0.287	T	0.33854	-0.9852	9	.	.	.	-0.037	0.1433	0.00085	0.3046:0.2314:0.1488:0.3152	.	219;234	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	N	219;234;234	ENSP00000363453:K219N;ENSP00000379226:K234N;ENSP00000340995:K234N	.	K	-	3	2	TEX11	69943315	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.891000	0.04135	-0.597000	0.05813	-0.434000	0.05882	AAG		0.299	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			A	70026590	C	A	70026590	3	1	61	1	0	0	0	0	1	0	0	0	15813	912	32	2	2208	2	TEX11	23	70026590	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	65982	70026590	85243970	12131	20116										
FOXO4	4303	broad.mit.edu	37	chrX	70316638	70316638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccagcccggaatcctgggggCtgtaacaggtcctcggaagg	15	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70316638C>T	ENST00000374259.3	+	1	592	c.260C>T	c.(259-261)gCt>gTt	p.A87V	FOXO4_ENST00000466874.1_Intron|FOXO4_ENST00000341558.3_Intron	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	87					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.A87V(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					ATCCTGGGGGCTGTAACAGGT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	X											14	14	14					X																	70316638		1828	4059	5887	70233363	SO:0001583	missense	4303				CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.260C>T	X.37:g.70316638C>T	ENSP00000363377:p.Ala87Val		70233363	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	37	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332242	0.41297	.	.	ENSG00000184481	ENST00000374259	D	0.95518	-3.73	4.83	4.83	0.62350	.	0.439725	0.19255	N	0.118838	D	0.89431	0.6713	N	0.22421	0.69	0.80722	D	1	B;B	0.26445	0.121;0.149	B;B	0.24394	0.024;0.053	D	0.85144	0.0982	10	0.16420	T	0.52	-13.6019	10.0088	0.41972	0.2015:0.7985:0.0:0.0	.	87;87	B4DTB6;P98177	.;FOXO4_HUMAN	V	87	ENSP00000363377:A87V	ENSP00000363377:A87V	A	+	2	0	FOXO4	70233363	0.647000	0.27304	0.997000	0.53966	0.577000	0.36160	0.010000	0.13242	2.130000	0.65690	0.594000	0.82650	GCT		0.652	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		T	70316638	C	T	70316638	3	4	61	1	0	0	0	0	1	0	0	0	6044	797	28	3	262	3	FOXO4	23	70316638	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	290048	70316638	84953922	12132	20117										
NLGN3	54413	broad.mit.edu	37	chrX	70389218	70389218	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaccagctctaccttcacatCgggctgaaaccaagggtccg	10	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70389218C>T	ENST00000358741.3	+	8	2121	c.1818C>T	c.(1816-1818)atC>atT	p.I606I	NLGN3_ENST00000374051.3_Silent_p.I586I|NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000536169.1_Silent_p.I566I	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	606					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.I586I(1)		biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					ACCTTCACATCGGGCTGAAAC	0.542																																					Esophageal Squamous(103;760 1488 16849 22250 40351)											1	Substitution - coding silent(1)	large_intestine(1)	X											56	44	48					X																	70389218		2203	4300	6503	70305943	SO:0001819	synonymous_variant	54413			AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.1818C>T	X.37:g.70389218C>T			70305943	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Silent	SNP	ENST00000358741.3	37	CCDS55441.1																																																																																				0.542	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		T	70389218	C	T	70389218	2	4	61	1	0	0	0	0	0	0	0	1	10494	874	31	1		1	NLGN3	23	70389218	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	72580	70389218	84881342	12133	20118										
ZMYM3	9203	broad.mit.edu	37	chrX	70464709	70464709	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctaccaggccacaatcaaaGaggaagtctacactgggatt	9	11	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70464709G>T	ENST00000353904.2	-	19	3229	c.3042C>A	c.(3040-3042)ctC>ctA	p.L1014L	ZMYM3_ENST00000373988.1_Silent_p.L1016L|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373998.1_Silent_p.L1002L|ZMYM3_ENST00000314425.5_Silent_p.L1014L|ZMYM3_ENST00000373984.3_Silent_p.L1016L	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	1014					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1014L(1)		breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					CACAATCAAAGAGGAAGTCTA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											62	48	53					X																	70464709		2203	4300	6503	70381434	SO:0001819	synonymous_variant	9203			AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"Zinc fingers, MYM type"	13054	protein-coding gene	gene with protein product		300061	"zinc finger protein 261"	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.3042C>A	X.37:g.70464709G>T			70381434	D3DVV3|O15089|Q96E26	Silent	SNP	ENST00000353904.2	37	CCDS14409.1																																																																																				0.473	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		T	70464709	G	T	70464709	2	4	61	1	0	0	0	0	0	0	0	1	17740	929	33	2		2	ZMYM3	23	70464709	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75491	70464709	84805851	12134	20119										
TAF1	6872	broad.mit.edu	37	chrX	70603905	70603905	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaaagatggtgatcttattCttgcagaatatagtgaggaa	11	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70603905C>A	ENST00000373790.4	+	13	2089	c.2038C>A	c.(2038-2040)Ctt>Att	p.L680I	TAF1_ENST00000276072.3_Missense_Mutation_p.L701I|TAF1_ENST00000423759.1_Missense_Mutation_p.L701I|TAF1_ENST00000449580.1_Missense_Mutation_p.L680I	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	680	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.L680I(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TGATCTTATTCTTGCAGAATA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											171	140	150					X																	70603905		2203	4300	6503	70520630	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2038C>A	X.37:g.70603905C>A	ENSP00000362895:p.Leu680Ile		70520630	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	24.4	4.525781	0.85600	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.88	5.88	0.94601	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.60907	0.2305	H	0.94423	3.535	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.968	T	0.72459	-0.4287	10	0.72032	D	0.01	.	19.1532	0.93499	0.0:1.0:0.0:0.0	.	680;701	P21675;P21675-2	TAF1_HUMAN;.	I	680;680;701;701	ENSP00000362895:L680I;ENSP00000389000:L680I;ENSP00000406549:L701I;ENSP00000276072:L701I	ENSP00000276072:L701I	L	+	1	0	TAF1	70520630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.632000	0.67819	2.474000	0.83562	0.600000	0.82982	CTT		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70603905	C	A	70603905	3	1	61	1	0	0	0	0	1	0	0	0	15552	913	32	2	2151	2	TAF1	23	70603905	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	139196	70603905	84666655	12135	20120										
TAF1	6872	broad.mit.edu	37	chrX	70608139	70608139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agatcggccacggaggatacGaatggaagatataaaaaaag	12	5	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70608139G>A	ENST00000373790.4	+	16	2528	c.2477G>A	c.(2476-2478)cGa>cAa	p.R826Q	TAF1_ENST00000276072.3_Missense_Mutation_p.R847Q|TAF1_ENST00000423759.1_Missense_Mutation_p.R847Q|TAF1_ENST00000449580.1_Missense_Mutation_p.R826Q	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	826	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R826Q(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CGGAGGATACGAATGGAAGAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											63	62	62					X																	70608139		2203	4300	6503	70524864	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2477G>A	X.37:g.70608139G>A	ENSP00000362895:p.Arg826Gln		70524864	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	21.3	4.132914	0.77662	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	4.52	4.52	0.55395	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.35856	0.0946	M	0.79475	2.455	0.80722	D	1	D;P	0.57571	0.98;0.89	P;P	0.59643	0.861;0.559	T	0.34204	-0.9838	10	0.72032	D	0.01	.	16.7873	0.85577	0.0:0.0:1.0:0.0	.	826;847	P21675;P21675-2	TAF1_HUMAN;.	Q	826;826;847;847	ENSP00000362895:R826Q;ENSP00000389000:R826Q;ENSP00000406549:R847Q;ENSP00000276072:R847Q	ENSP00000276072:R847Q	R	+	2	0	TAF1	70524864	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	9.476000	0.97823	1.966000	0.57179	0.284000	0.19432	CGA		0.423	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70608139	G	A	70608139	3	1	61	1	0	0	0	0	1	0	0	0	15552	1058	37	1	2602	1	TAF1	23	70608139	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4234	70608139	84662421	12136	20121										
TAF1	6872	broad.mit.edu	37	chrX	70614068	70614068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtgaacgggaggaacaggagCggaaggaactacagcgaatg	17	6	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:70614068C>T	ENST00000373790.4	+	22	3427	c.3376C>T	c.(3376-3378)Cgg>Tgg	p.R1126W	TAF1_ENST00000276072.3_Missense_Mutation_p.R1147W|TAF1_ENST00000423759.1_Missense_Mutation_p.R1147W|TAF1_ENST00000449580.1_Missense_Mutation_p.R1126W	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1126					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R1126W(2)|p.R1147W(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GGAACAGGAGCGGAAGGAACT	0.443																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	X											114	93	100					X																	70614068		2203	4300	6503	70530793	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3376C>T	X.37:g.70614068C>T	ENSP00000362895:p.Arg1126Trp		70530793	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	18.31	3.595568	0.66219	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.24	2.34	0.29019	.	0.000000	0.85682	D	0.000000	T	0.42314	0.1197	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.994;0.996	T	0.30909	-0.9962	10	0.62326	D	0.03	.	13.2791	0.60205	0.5508:0.4492:0.0:0.0	.	1126;1126;1147	P21675-4;P21675;P21675-2	.;TAF1_HUMAN;.	W	1126;1126;1147;1147	ENSP00000362895:R1126W;ENSP00000389000:R1126W;ENSP00000406549:R1147W;ENSP00000276072:R1147W	ENSP00000276072:R1147W	R	+	1	2	TAF1	70530793	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.851000	0.39338	0.045000	0.15804	-0.353000	0.07706	CGG		0.443	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		T	70614068	C	T	70614068	3	4	61	1	0	0	0	0	1	0	0	0	15552	759	27	1	3525	1	TAF1	23	70614068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5929	70614068	84656492	12137	20122										
NHSL2	340527	broad.mit.edu	37	chrX	71360158	71360158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaccactccctcaagacagCtacacggtagtgcggaaacc	9	14	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:71360158C>A	ENST00000373677.1	+	2	2924	c.1662C>A	c.(1660-1662)agC>agA	p.S554R	NHSL2_ENST00000535692.1_Missense_Mutation_p.S554R|NHSL2_ENST00000510661.1_Missense_Mutation_p.S689R|NHSL2_ENST00000540800.1_Missense_Mutation_p.S920R			Q5HYW2	NHSL2_HUMAN	NHS-like 2	554								p.S551R(1)|p.S920R(1)		NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CTCAAGACAGCTACACGGTAG	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	X											90	69	76					X																	71360158		2203	4300	6503	71276883	SO:0001583	missense	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1662C>A	X.37:g.71360158C>A	ENSP00000362781:p.Ser554Arg		71276883	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	37		.	.	.	.	.	.	.	.	.	.	C	4.698	0.129698	0.08981	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.46063	1.48;0.9;0.88;0.9	6.17	2.44	0.29823	.	0.528168	0.20071	N	0.099878	T	0.24122	0.0584	N	0.22421	0.69	0.27144	N	0.961589	B;B;B	0.32526	0.091;0.145;0.374	B;B;B	0.31614	0.064;0.133;0.133	T	0.13388	-1.0511	10	0.51188	T	0.08	1.9062	3.9834	0.09504	0.1315:0.5947:0.1248:0.149	.	920;689;554	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	R	920;554;689;554	ENSP00000444617:S920R;ENSP00000362781:S554R;ENSP00000424079:S689R;ENSP00000444914:S554R	ENSP00000362781:S554R	S	+	3	2	NHSL2	71276883	0.909000	0.30893	0.059000	0.19551	0.470000	0.32858	0.166000	0.16583	0.313000	0.23062	0.600000	0.82982	AGC		0.542	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71360158	C	A	71360158	3	1	61	1	0	0	0	0	1	0	0	0	10443	796	28	2	2782	2	NHSL2	23	71360158	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	746090	71360158	83910402	12138	20123										
ERCC6L	54821	broad.mit.edu	37	chrX	71427573	71427573	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggcatcaacatctggattCttttcattaagtctggcctc	7	10	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:71427573C>A	ENST00000334463.3	-	2	1179	c.1044G>T	c.(1042-1044)aaG>aaT	p.K348N	ERCC6L_ENST00000373657.1_Missense_Mutation_p.K225N|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	348					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.K348N(1)		breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					CATCTGGATTCTTTTCATTAA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	X											160	158	159					X																	71427573		2199	4294	6493	71344298	SO:0001583	missense	54821			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.1044G>T	X.37:g.71427573C>A	ENSP00000334675:p.Lys348Asn		71344298	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	C	8.257	0.810252	0.16537	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	D;D	0.91740	-2.86;-2.9	5.97	2.03	0.26663	.	.	.	.	.	D	0.89822	0.6826	M	0.72118	2.19	0.09310	N	1	P	0.35226	0.491	B	0.34652	0.187	T	0.78375	-0.2228	9	0.37606	T	0.19	0.0317	9.4516	0.38729	0.5388:0.3319:0.1293:0.0	.	348	Q2NKX8	ERC6L_HUMAN	N	225;348	ENSP00000362761:K225N;ENSP00000334675:K348N	ENSP00000334675:K348N	K	-	3	2	ERCC6L	71344298	0.000000	0.05858	0.009000	0.14445	0.504000	0.33889	-0.836000	0.04382	-0.029000	0.13827	0.600000	0.82982	AAG		0.358	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		A	71427573	C	A	71427573	3	1	61	1	0	0	0	0	1	0	0	0	5231	912	32	2	2712	2	ERCC6L	23	71427573	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	67415	71427573	83842987	12139	20124										
PHKA1	5255	broad.mit.edu	37	chrX	71802290	71802290	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggcaatatgcactattttTtccacagcaatgatgcttcc	6	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:71802290T>G	ENST00000373542.4	-	31	3615	c.3456A>C	c.(3454-3456)gaA>gaC	p.E1152D	PHKA1_ENST00000373539.3_Missense_Mutation_p.E1169D|PHKA1_ENST00000541944.1_Missense_Mutation_p.E1080D|PHKA1_ENST00000373545.3_Missense_Mutation_p.E1110D|PHKA1_ENST00000339490.3_Missense_Mutation_p.E1139D	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1152					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.E1152D(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GCACTATTTTTTCCACAGCAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											116	86	96					X																	71802290		2203	4300	6503	71719015	SO:0001583	missense	5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3456A>C	X.37:g.71802290T>G	ENSP00000362643:p.Glu1152Asp		71719015	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	6.436	0.448631	0.12223	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.89552	-2.42;-2.53;-2.47;-2.45;-2.45	5.17	-0.704	0.11256	.	0.000000	0.85682	D	0.000000	T	0.63896	0.2550	N	0.03209	-0.39	0.29032	N	0.885623	P;B;B;B	0.39116	0.66;0.001;0.001;0.005	B;B;B;B	0.30716	0.119;0.005;0.003;0.013	T	0.70081	-0.4970	10	0.02654	T	1	-14.5656	9.3011	0.37847	0.0:0.3869:0.0:0.6131	.	1080;1110;1139;1152	B7ZL07;A6NIT2;P46020-2;P46020	.;.;.;KPB1_HUMAN	D	1110;1152;1080;1139;1169	ENSP00000362646:E1110D;ENSP00000362643:E1152D;ENSP00000441251:E1080D;ENSP00000342469:E1139D;ENSP00000362640:E1169D	ENSP00000342469:E1139D	E	-	3	2	PHKA1	71719015	0.045000	0.20229	0.995000	0.50966	0.982000	0.71751	-0.670000	0.05256	-0.107000	0.12088	0.437000	0.28790	GAA		0.428	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			G	71802290	T	G	71802290	3	3	61	1	0	0	0	0	1	0	0	0	11874	1838	64	4	223	4	PHKA1	23	71802290	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	374717	71802290	83468270	12140	20125										
PHKA1	5255	broad.mit.edu	37	chrX	71822975	71822975	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttattcaatctcaccgcttcGttccactccaaactccttgc	3	16	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:71822975G>A	ENST00000373542.4	-	26	3070	c.2911C>T	c.(2911-2913)Cga>Tga	p.R971*	PHKA1_ENST00000373539.3_Nonsense_Mutation_p.R971*|PHKA1_ENST00000541944.1_Nonsense_Mutation_p.R912*|PHKA1_ENST00000373545.3_Nonsense_Mutation_p.R912*|PHKA1_ENST00000339490.3_Nonsense_Mutation_p.R971*	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	971					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R971*(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TCACCGCTTCGTTCCACTCCA	0.423																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											127	98	107					X																	71822975		2203	4300	6503	71739700	SO:0001587	stop_gained	5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2911C>T	X.37:g.71822975G>A	ENSP00000362643:p.Arg971*		71739700	B7ZL05|B7ZL07|Q2M3D7	Nonsense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	43	10.468460	0.99411	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	.	.	.	5.64	2.62	0.31277	.	0.053778	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0938	11.4523	0.50160	0.0:0.0:0.4858:0.5142	.	.	.	.	X	912;971;912;971;971	.	ENSP00000342469:R971X	R	-	1	2	PHKA1	71739700	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.545000	0.36169	1.138000	0.42230	-0.222000	0.12452	CGA		0.423	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71822975	G	A	71822975	4	1	61	1	0	0	0	0	0	1	0	0	11874	1153	40	1	788	1	PHKA1	23	71822975	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20685	71822975	83447585	12141	20126										
PHKA1	5255	broad.mit.edu	37	chrX	71825180	71825180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttgtatgatcagaccaattCgaagtcgaaacatttcagca	7	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:71825180C>T	ENST00000373542.4	-	25	2915	c.2756G>A	c.(2755-2757)cGa>cAa	p.R919Q	PHKA1_ENST00000373539.3_Missense_Mutation_p.R919Q|PHKA1_ENST00000541944.1_Missense_Mutation_p.R860Q|PHKA1_ENST00000373545.3_Missense_Mutation_p.R860Q|PHKA1_ENST00000339490.3_Missense_Mutation_p.R919Q	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	919					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R919Q(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					CAGACCAATTCGAAGTCGAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	87	93					X																	71825180		2203	4300	6503	71741905	SO:0001583	missense	5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2756G>A	X.37:g.71825180C>T	ENSP00000362643:p.Arg919Gln		71741905	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	36	5.619200	0.96649	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62	5.8	5.8	0.92144	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.75884	2.315	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94612	0.7805	10	0.48119	T	0.1	-3.7822	16.2856	0.82720	0.0:1.0:0.0:0.0	.	860;919;919	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	Q	860;919;860;919;919	ENSP00000362646:R860Q;ENSP00000362643:R919Q;ENSP00000441251:R860Q;ENSP00000342469:R919Q;ENSP00000362640:R919Q	ENSP00000342469:R919Q	R	-	2	0	PHKA1	71741905	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.691000	0.84191	2.450000	0.82876	0.594000	0.82650	CGA		0.403	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71825180	C	T	71825180	3	4	61	1	0	0	0	0	1	0	0	0	11874	884	31	1	947	1	PHKA1	23	71825180	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2205	71825180	83445380	12142	20127										
NAP1L2	4674	broad.mit.edu	37	chrX	72433068	72433068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcatcattaacttctctaaCtaccccctcctgctgagatt	4	14	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:72433068C>T	ENST00000373517.3	-	1	1616	c.1261G>A	c.(1261-1263)Gtt>Att	p.V421I	NAP1L2_ENST00000536638.1_Missense_Mutation_p.V279I	NM_021963.3	NP_068798.1	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	421					nucleosome assembly (GO:0006334)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of neuron differentiation (GO:0045666)|regulation of stem cell division (GO:2000035)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.V421I(1)		NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3)	29	Renal(35;0.156)					ACTTCTCTAACTACCCCCTCC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	X											72	65	67					X																	72433068		2203	4300	6503	72349793	SO:0001583	missense	4674			AF136178	CCDS14423.1	Xq13	2008-02-05			ENSG00000186462	ENSG00000186462			7638	protein-coding gene	gene with protein product		300026				8789438	Standard	NM_021963		Approved	BPX, MGC26243	uc004ebi.3	Q9ULW6	OTTHUMG00000021827	ENST00000373517.3:c.1261G>A	X.37:g.72433068C>T	ENSP00000362616:p.Val421Ile		72349793	B2RE61|B4E161|Q8TAN6	Missense_Mutation	SNP	ENST00000373517.3	37	CCDS14423.1	.	.	.	.	.	.	.	.	.	.	c	6.901	0.535840	0.13188	.	.	ENSG00000186462	ENST00000373517;ENST00000536638	T;T	0.36340	1.5;1.26	3.03	1.23	0.21249	.	0.262478	0.35291	N	0.003313	T	0.14917	0.0360	N	0.08118	0	0.23966	N	0.996321	B	0.09022	0.002	B	0.06405	0.002	T	0.14337	-1.0476	10	0.30854	T	0.27	-6.4708	4.8582	0.13570	0.0:0.5344:0.0:0.4655	.	421	Q9ULW6	NP1L2_HUMAN	I	421;279	ENSP00000362616:V421I;ENSP00000441555:V279I	ENSP00000362616:V421I	V	-	1	0	NAP1L2	72349793	0.925000	0.31364	0.997000	0.53966	0.996000	0.88848	0.585000	0.23879	0.185000	0.20105	0.513000	0.50165	GTT		0.343	NAP1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057225.1	NM_021963		T	72433068	C	T	72433068	3	4	61	1	0	0	0	0	1	0	0	0	10187	565	20	3	125	3	NAP1L2	23	72433068	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	607888	72433068	82837492	12143	20128										
RLIM	51132	broad.mit.edu	37	chrX	73811991	73811991	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accagtatttaagattctacGaatgggaattctgatggtac	9	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:73811991G>A	ENST00000332687.6	-	4	1377	c.1159C>T	c.(1159-1161)Cgt>Tgt	p.R387C	RLIM_ENST00000349225.2_Missense_Mutation_p.R387C	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	387					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R387C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AAGATTCTACGAATGGGAATT	0.403																																					Esophageal Squamous(169;1899 1923 14997 18818 32118)											1	Substitution - Missense(1)	large_intestine(1)	X											105	95	98					X																	73811991		2203	4300	6503	73728716	SO:0001583	missense	51132			AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1159C>T	X.37:g.73811991G>A	ENSP00000328059:p.Arg387Cys		73728716	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085876	0.36758	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.11930	2.73;2.73	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13926	-1.0491	10	0.87932	D	0	-2.7021	13.8021	0.63206	0.0:0.0:0.8471:0.1529	.	387	Q9NVW2	RNF12_HUMAN	C	387	ENSP00000328059:R387C;ENSP00000253571:R387C	ENSP00000328059:R387C	R	-	1	0	RLIM	73728716	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.155000	0.71833	2.406000	0.81754	0.600000	0.82982	CGT		0.403	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811991	G	A	73811991	3	1	61	1	0	0	0	0	1	0	0	0	13427	1058	37	1	719	1	RLIM	23	73811991	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1378923	73811991	81458569	12144	20129										
KIAA2022	340533	broad.mit.edu	37	chrX	73963428	73963428	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caaaagagtagtcttgtctcGaacattgtcctgaaaggatt	9	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:73963428G>A	ENST00000055682.6	-	3	1575	c.964C>T	c.(964-966)Cga>Tga	p.R322*		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	322					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.R322*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GTCTTGTCTCGAACATTGTCC	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											91	78	83					X																	73963428		2203	4300	6503	73880153	SO:0001587	stop_gained	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.964C>T	X.37:g.73963428G>A	ENSP00000055682:p.Arg322*		73880153	A7YY87|Q5JUX9|Q8IVE9	Nonsense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	G	41	8.972748	0.99021	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	.	.	.	5.83	5.83	0.93111	.	0.085176	0.44902	D	0.000414	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4723	13.402	0.60889	0.0:0.0:0.6959:0.3041	.	.	.	.	X	322	.	ENSP00000055682:R322X	R	-	1	2	KIAA2022	73880153	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.941000	0.56607	2.453000	0.82957	0.600000	0.82982	CGA		0.438	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73963428	G	A	73963428	4	1	61	1	0	0	0	0	0	1	0	0	8290	1066	37	1	3594	1	KIAA2022	23	73963428	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	151437	73963428	81307132	12145	20130										
KIAA2022	340533	broad.mit.edu	37	chrX	73963725	73963725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcctccaagtcaatgtcagGtttctcagtttctcgtctgt	7	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:73963725G>A	ENST00000055682.6	-	3	1278	c.667C>T	c.(667-669)Cct>Tct	p.P223S		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	223					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.P223S(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TCAATGTCAGGTTTCTCAGTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											144	130	135					X																	73963725		2203	4300	6503	73880450	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.667C>T	X.37:g.73963725G>A	ENSP00000055682:p.Pro223Ser		73880450	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	G	0.034	-1.318453	0.01320	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.25250	1.81;1.81	5.97	-0.989	0.10242	.	0.568971	0.20308	N	0.094889	T	0.07007	0.0178	N	0.02539	-0.55	0.23023	N	0.998417	B	0.02656	0.0	B	0.04013	0.001	T	0.38650	-0.9651	10	0.06757	T	0.87	0.0363	7.2518	0.26154	0.6861:0.1456:0.1683:0.0	.	223	Q5QGS0	K2022_HUMAN	S	223	ENSP00000362567:P223S;ENSP00000055682:P223S	ENSP00000055682:P223S	P	-	1	0	KIAA2022	73880450	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	0.984000	0.29565	-0.237000	0.09739	0.600000	0.82982	CCT		0.453	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73963725	G	A	73963725	3	1	61	1	0	0	0	0	1	0	0	0	8290	1261	44	3	3891	3	KIAA2022	23	73963725	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297	73963725	81306835	12146	20131										
ABCB7	22	broad.mit.edu	37	chrX	74282176	74282176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacttacctcttcagtaatcGaatctaacgatgaagtagct	6	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:74282176G>A	ENST00000373394.3	-	14	1929	c.1922C>T	c.(1921-1923)tCg>tTg	p.S641L	ABCB7_ENST00000534570.1_5'Flank|ABCB7_ENST00000339447.4_Missense_Mutation_p.S601L|ABCB7_ENST00000253577.3_Missense_Mutation_p.S642L			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	641	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)	p.S642L(1)		breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						TTCAGTAATCGAATCTAACGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	X											77	69	72					X																	74282176		2203	4300	6503	74198901	SO:0001583	missense	22			AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1922C>T	X.37:g.74282176G>A	ENSP00000362492:p.Ser641Leu		74198901	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Missense_Mutation	SNP	ENST00000373394.3	37		.	.	.	.	.	.	.	.	.	.	G	27.4	4.828296	0.90955	.	.	ENSG00000131269	ENST00000535115;ENST00000253577;ENST00000339447;ENST00000373394;ENST00000529949	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.32	5.32	0.75619	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.85745	0.5768	N	0.25957	0.775	0.80722	D	1	D;D;D;P;D	0.76494	0.972;0.999;0.999;0.953;0.995	P;D;D;B;P	0.69479	0.629;0.964;0.921;0.425;0.896	D	0.88001	0.2756	10	0.87932	D	0	-21.4512	16.9284	0.86183	0.0:0.0:1.0:0.0	.	615;601;642;641;642	G3V1J3;G3XAC4;B3KM98;O75027;O75027-2	.;.;.;ABCB7_HUMAN;.	L	615;642;601;641;615	ENSP00000253577:S642L;ENSP00000343849:S601L;ENSP00000362492:S641L;ENSP00000436586:S615L	ENSP00000253577:S642L	S	-	2	0	ABCB7	74198901	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.320000	0.96346	2.204000	0.70986	0.594000	0.82650	TCG		0.358	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		A	74282176	G	A	74282176	3	1	61	1	0	0	0	0	1	0	0	0	46	1059	37	1	348	1	ABCB7	23	74282176	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	318451	74282176	80988384	12147	20132										
ZDHHC15	158866	broad.mit.edu	37	chrX	74644554	74644554	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaatcacaaggctgacaaaAaacatgcaggccacaaagag	9	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:74644554A>C	ENST00000373367.3	-	8	899	c.669T>G	c.(667-669)ttT>ttG	p.F223L	ZDHHC15_ENST00000373361.3_Missense_Mutation_p.F183C|ZDHHC15_ENST00000541184.1_Missense_Mutation_p.F214L	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	223					establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.F223L(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						GGCTGACAAAAAACATGCAGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	X											84	65	72					X																	74644554		2203	4300	6503	74561279	SO:0001583	missense	158866			AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383		"Zinc fingers, DHHC-type"	20342	protein-coding gene	gene with protein product		300576					Standard	NM_144969		Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.669T>G	X.37:g.74644554A>C	ENSP00000362465:p.Phe223Leu		74561279	B3KVG7|Q3SY30|Q6UWH3	Missense_Mutation	SNP	ENST00000373367.3	37	CCDS14430.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.21|14.21	2.467744|2.467744	0.43839|0.43839	.|.	.|.	ENSG00000102383|ENSG00000102383	ENST00000373361|ENST00000373367;ENST00000541184	T|T;T	0.59906|0.24723	0.23|1.84;1.84	5.88|5.88	3.54|3.54	0.40534|0.40534	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	M|M	0.65498|0.65498	2.005|2.005	0.24410|0.24410	N|N	0.994666|0.994666	.|D;D	.|0.89917	.|0.975;1.0	.|D;D	.|0.81914	.|0.925;0.995	T|T	0.18935|0.18935	-1.0321|-1.0321	8|10	0.87932|0.24483	D|T	0|0.36	-9.7298|-9.7298	5.4781|5.4781	0.16708|0.16708	0.6283:0.0:0.3717:0.0|0.6283:0.0:0.3717:0.0	.|.	.|214;223	.|B3KVG7;Q96MV8	.|.;ZDH15_HUMAN	C|L	183|223;214	ENSP00000362459:F183C|ENSP00000362465:F223L;ENSP00000445420:F214L	ENSP00000362459:F183C|ENSP00000362465:F223L	F|F	-|-	2|3	0|2	ZDHHC15|ZDHHC15	74561279|74561279	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.079000|2.079000	0.41577|0.41577	0.843000|0.843000	0.35070|0.35070	0.486000|0.486000	0.48141|0.48141	TTT|TTT		0.363	ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057283.1	NM_144969		C	74644554	A	C	74644554	3	2	61	1	0	0	0	0	1	0	0	0	17644	11	1	4	360	4	ZDHHC15	23	74644554	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	362378	74644554	80626006	12148	20133										
MAGEE2	139599	broad.mit.edu	37	chrX	75004692	75004692	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcaggacctccaggtcattCgggtcctgaacggcctggga	13	12	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:75004692C>T	ENST00000373359.2	-	1	387	c.195G>A	c.(193-195)ccG>ccA	p.P65P		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	65								p.P65P(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCAGGTCATTCGGGTCCTGAA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	X											39	36	37					X																	75004692		2203	4300	6503	74921417	SO:0001819	synonymous_variant	139599			AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.195G>A	X.37:g.75004692C>T			74921417	Q5JSI5	Silent	SNP	ENST00000373359.2	37	CCDS14431.1																																																																																				0.587	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703		T	75004692	C	T	75004692	2	4	61	1	0	0	0	0	0	0	0	1	9216	871	31	1		1	MAGEE2	23	75004692	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	360138	75004692	80265868	12149	20134										
MAGEE1	57692	broad.mit.edu	37	chrX	75649460	75649460	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctgatggatcggacacctcCgtgccgcccactcctggtga	11	15	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:75649460C>T	ENST00000361470.2	+	1	1415	c.1137C>T	c.(1135-1137)tcC>tcT	p.S379S		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	379	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.S379S(2)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CGGACACCTCCGTGCCGCCCA	0.677																																																2	Substitution - coding silent(2)	large_intestine(2)	X											39	28	32					X																	75649460		2203	4299	6502	75565864	SO:0001819	synonymous_variant	57692			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1137C>T	X.37:g.75649460C>T			75565864	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																				0.677	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		T	75649460	C	T	75649460	2	4	61	1	0	0	0	0	0	0	0	1	9215	639	23	1		1	MAGEE1	23	75649460	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	644768	75649460	79621100	12150	20135										
MAGEE1	57692	broad.mit.edu	37	chrX	75650296	75650296	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgagtttttctggggcccaaGatcccacctagaaaccacca	8	13	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:75650296G>T	ENST00000361470.2	+	1	2251	c.1973G>T	c.(1972-1974)aGa>aTa	p.R658I		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	658	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.R658I(2)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						TGGGGCCCAAGATCCCACCTA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	X											42	39	40					X																	75650296		2203	4300	6503	75566700	SO:0001583	missense	57692			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1973G>T	X.37:g.75650296G>T	ENSP00000354912:p.Arg658Ile		75566700	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Missense_Mutation	SNP	ENST00000361470.2	37	CCDS14433.1	.	.	.	.	.	.	.	.	.	.	G	8.972	0.973191	0.18736	.	.	ENSG00000198934	ENST00000361470	T	0.22743	1.94	2.34	1.46	0.22682	.	.	.	.	.	T	0.47525	0.1450	M	0.92026	3.265	0.21579	N	0.999631	D	0.65815	0.995	D	0.72075	0.976	T	0.27905	-1.0060	9	0.87932	D	0	.	4.2562	0.10719	0.2085:0.0:0.7915:0.0	.	658	Q9HCI5	MAGE1_HUMAN	I	658	ENSP00000354912:R658I	ENSP00000354912:R658I	R	+	2	0	MAGEE1	75566700	0.936000	0.31750	0.048000	0.18961	0.310000	0.27922	2.592000	0.46171	0.407000	0.25591	0.594000	0.82650	AGA		0.428	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		T	75650296	G	T	75650296	3	4	61	1	0	0	0	0	1	0	0	0	9215	942	33	2	1975	2	MAGEE1	23	75650296	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	836	75650296	79620264	12151	20136										
MAGEE1	57692	broad.mit.edu	37	chrX	75651050	75651050	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctagagcccgtttggaaacCtctaagatgaaagccttgcg	10	11	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:75651050C>A	ENST00000361470.2	+	1	3005	c.2727C>A	c.(2725-2727)acC>acA	p.T909T		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	909	Interaction with DTNA. {ECO:0000250}.|MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.T909T(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						GTTTGGAAACCTCTAAGATGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	X											77	73	75					X																	75651050		2203	4300	6503	75567454	SO:0001819	synonymous_variant	57692			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.2727C>A	X.37:g.75651050C>A			75567454	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																				0.488	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75651050	C	A	75651050	2	1	61	1	0	0	0	0	0	0	0	1	9215	668	24	2		2	MAGEE1	23	75651050	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	754	75651050	79619510	12152	20137										
LPAR4	2846	broad.mit.edu	37	chrX	78010800	78010800	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggccattgtctatccttttcGatctcgtactattaggacta	7	10	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:78010800G>A	ENST00000435339.3	+	2	820	c.434G>A	c.(433-435)cGa>cAa	p.R145Q		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	145					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R145Q(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						TATCCTTTTCGATCTCGTACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	X											216	147	170					X																	78010800		2203	4300	6503	77897456	SO:0001583	missense	2846			U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.434G>A	X.37:g.78010800G>A	ENSP00000408205:p.Arg145Gln		77897456	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	37	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725257	0.68959	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.40756	1.02;1.02	4.21	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.074980	0.56097	N	0.000035	T	0.42630	0.1211	L	0.41906	1.305	0.45354	D	0.998343	D	0.56746	0.977	P	0.52066	0.689	T	0.27157	-1.0082	10	0.52906	T	0.07	.	9.927	0.41498	0.1045:0.0:0.8955:0.0	.	145	Q99677	LPAR4_HUMAN	Q	145	ENSP00000408205:R145Q;ENSP00000362398:R145Q	ENSP00000362398:R145Q	R	+	2	0	LPAR4	77897456	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	5.028000	0.64115	0.790000	0.33803	0.422000	0.28245	CGA		0.463	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		A	78010800	G	A	78010800	3	1	61	1	0	0	0	0	1	0	0	0	8936	1058	37	1	436	1	LPAR4	23	78010800	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2359750	78010800	77259760	12153	20138										
FAM46D	169966	broad.mit.edu	37	chrX	79698517	79698517	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggaagaatttagaactaaAatttgtgagttcactcagac	9	5	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:79698517A>C	ENST00000308293.5	+	3	718	c.479A>C	c.(478-480)aAa>aCa	p.K160T	FAM46D_ENST00000538312.1_Missense_Mutation_p.K160T	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	160								p.K160T(1)		kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						TTAGAACTAAAATTTGTGAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											83	81	82					X																	79698517		2202	4299	6501	79585173	SO:0001583	missense	169966			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.479A>C	X.37:g.79698517A>C	ENSP00000308575:p.Lys160Thr		79585173	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.701333	0.48307	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.35605	1.3;1.3	4.8	4.8	0.61643	Domain of unknown function DUF1693 (1);	0.056200	0.64402	D	0.000001	T	0.63450	0.2512	M	0.88704	2.975	0.58432	D	0.999994	D	0.76494	0.999	D	0.68943	0.961	T	0.71220	-0.4657	10	0.87932	D	0	-17.8212	12.2722	0.54712	1.0:0.0:0.0:0.0	.	160	Q8NEK8	FA46D_HUMAN	T	160	ENSP00000443410:K160T;ENSP00000308575:K160T	ENSP00000308575:K160T	K	+	2	0	FAM46D	79585173	1.000000	0.71417	0.997000	0.53966	0.650000	0.38633	6.640000	0.74319	1.774000	0.52232	0.481000	0.45027	AAA		0.373	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		C	79698517	A	C	79698517	3	2	61	1	0	0	0	0	1	0	0	0	5587	14	1	4	481	4	FAM46D	23	79698517	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1687717	79698517	75572043	12154	20139										
FAM46D	169966	broad.mit.edu	37	chrX	79699082	79699082	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acacaaaaggtaacttgcttTtatcagcctgctccgtactt	6	11	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:79699082T>G	ENST00000308293.5	+	3	1283	c.1044T>G	c.(1042-1044)ttT>ttG	p.F348L	FAM46D_ENST00000538312.1_Missense_Mutation_p.F348L	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	348								p.F348L(1)		kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						TAACTTGCTTTTATCAGCCTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											80	71	74					X																	79699082		2203	4298	6501	79585738	SO:0001583	missense	169966			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.1044T>G	X.37:g.79699082T>G	ENSP00000308575:p.Phe348Leu		79585738	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.729168	0.48833	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.24151	1.87;1.87	4.25	4.25	0.50352	.	0.383824	0.26979	N	0.021532	T	0.23727	0.0574	M	0.63843	1.955	0.45528	D	0.998486	P	0.42456	0.78	B	0.34931	0.192	T	0.05370	-1.0889	10	0.40728	T	0.16	-5.6845	11.4362	0.50070	0.0:0.0:0.0:1.0	.	348	Q8NEK8	FA46D_HUMAN	L	348	ENSP00000443410:F348L;ENSP00000308575:F348L	ENSP00000308575:F348L	F	+	3	2	FAM46D	79585738	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	1.324000	0.33712	1.569000	0.49696	0.481000	0.45027	TTT		0.448	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		G	79699082	T	G	79699082	3	3	61	1	0	0	0	0	1	0	0	0	5587	1838	64	4	1046	4	FAM46D	23	79699082	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	565	79699082	75571478	12155	20140										
BRWD3	254065	broad.mit.edu	37	chrX	79999689	79999689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatttcagcagagtgtccacGaagtgtagcaagaaggcgtc	12	8	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:79999689G>A	ENST00000373275.4	-	8	871	c.655C>T	c.(655-657)Cgt>Tgt	p.R219C		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	219					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.R219C(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						GAGTGTCCACGAAGTGTAGCA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											121	108	113					X																	79999689		2203	4300	6503	79886345	SO:0001583	missense	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.655C>T	X.37:g.79999689G>A	ENSP00000362372:p.Arg219Cys		79886345	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962280	0.74016	.	.	ENSG00000165288	ENST00000373275	T	0.20738	2.05	4.42	2.53	0.30540	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);WD40-repeat-containing domain (1);	0.077607	0.52532	D	0.000070	T	0.48021	0.1477	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.50415	-0.8831	9	.	.	.	-8.4293	12.4102	0.55464	0.0:0.0:0.6667:0.3333	.	219	Q6RI45	BRWD3_HUMAN	C	219	ENSP00000362372:R219C	.	R	-	1	0	BRWD3	79886345	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.812000	0.55628	0.369000	0.24510	0.415000	0.27848	CGT		0.403	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		A	79999689	G	A	79999689	3	1	61	1	0	0	0	0	1	0	0	0	1529	1058	37	1	4889	1	BRWD3	23	79999689	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	300607	79999689	75270871	12156	20141										
HMGN5	79366	broad.mit.edu	37	chrX	80370582	80370582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccagcttcccctttctcttCgttttgatcttcttcatctt	3	14	5	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:80370582C>T	ENST00000358130.2	-	7	743	c.415G>A	c.(415-417)Gaa>Aaa	p.E139K	HMGN5_ENST00000491275.1_5'Flank	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	139					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.E139K(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						cctttctcttcgttttgatct	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											132	98	109					X																	80370582		2046	3960	6006	80257238	SO:0001583	missense	79366			AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"High-mobility group / Canonical"	8013	protein-coding gene	gene with protein product		300385	"nucleosomal binding protein 1", "high-mobility group nucleosome binding domain 5"	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.415G>A	X.37:g.80370582C>T	ENSP00000350848:p.Glu139Lys		80257238	Q5JSL1	Missense_Mutation	SNP	ENST00000358130.2	37	CCDS14448.1	.	.	.	.	.	.	.	.	.	.	C	2.902	-0.227180	0.06022	.	.	ENSG00000198157	ENST00000358130;ENST00000447319;ENST00000373250;ENST00000430960	.	.	.	3.62	-2.54	0.06307	.	1.437710	0.05237	N	0.511522	T	0.13329	0.0323	N	0.02539	-0.55	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.15521	-1.0434	9	0.22706	T	0.39	.	4.54	0.12052	0.1653:0.2948:0.0:0.5399	.	139	P82970	HMGN5_HUMAN	K	139;119;129;139	.	ENSP00000350848:E139K	E	-	1	0	HMGN5	80257238	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-0.825000	0.04433	-0.891000	0.03940	-0.735000	0.03563	GAA		0.378	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763		T	80370582	C	T	80370582	3	4	61	1	0	0	0	0	1	0	0	0	7259	893	31	1	437	1	HMGN5	23	80370582	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	370893	80370582	74899978	12157	20142										
CYLC1	1538	broad.mit.edu	37	chrX	83126529	83126529	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttcccaaaccactccagaGaggtacaaatgataaatcaa	5	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:83126529G>T	ENST00000329312.4	+	3	165	c.128G>T	c.(127-129)aGa>aTa	p.R43I		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	43					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R42I(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CCACTCCAGAGAGGTACAAAT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	X											64	59	61					X																	83126529		2202	4295	6497	83013185	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.128G>T	X.37:g.83126529G>T	ENSP00000331556:p.Arg43Ile		83013185	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	7.940	0.742521	0.15642	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.47177	0.85	4.59	3.72	0.42706	.	.	.	.	.	T	0.32645	0.0836	N	0.22421	0.69	0.34165	D	0.669172	P;P	0.35982	0.531;0.531	B;B	0.34242	0.178;0.178	T	0.49283	-0.8956	9	0.72032	D	0.01	-6.3975	9.5381	0.39235	0.0:0.7787:0.2213:0.0	.	43;43	P35663;F5H4V5	CYLC1_HUMAN;.	I	43	ENSP00000331556:R43I	ENSP00000331556:R43I	R	+	2	0	CYLC1	83013185	1.000000	0.71417	0.975000	0.42487	0.022000	0.10575	0.884000	0.28214	1.048000	0.40298	-0.216000	0.12614	AGA		0.308	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83126529	G	T	83126529	3	4	61	1	0	0	0	0	1	0	0	0	4147	942	33	2	138	2	CYLC1	23	83126529	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2755947	83126529	72144031	12158	20143										
HDX	139324	broad.mit.edu	37	chrX	83576992	83576992	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgattgaaatccatttcctCtaattcaggaggtaaatctg	7	7	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:83576992C>A	ENST00000297977.5	-	10	2089	c.1978G>T	c.(1978-1980)Gag>Tag	p.E660*	HDX_ENST00000373177.2_Nonsense_Mutation_p.E660*|HDX_ENST00000506585.2_Nonsense_Mutation_p.E602*	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	660						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E660*(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TCCATTTCCTCTAATTCAGGA	0.328																																					Pancreas(53;231 1169 36156 43751 51139)											1	Substitution - Nonsense(1)	large_intestine(1)	X											65	54	58					X																	83576992		2203	4299	6502	83463648	SO:0001587	stop_gained	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1978G>T	X.37:g.83576992C>A	ENSP00000297977:p.Glu660*		83463648	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Nonsense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	37	6.360262	0.97502	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	.	.	.	5.52	5.52	0.82312	.	0.265952	0.38111	N	0.001818	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-19.2186	18.5022	0.90886	0.0:1.0:0.0:0.0	.	.	.	.	X	660;602;660	.	ENSP00000297977:E660X	E	-	1	0	HDX	83463648	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.181000	0.65054	2.311000	0.77944	0.600000	0.82982	GAG		0.328	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83576992	C	A	83576992	4	1	61	1	0	0	0	0	0	1	0	0	7047	922	32	2	98	2	HDX	23	83576992	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	450463	83576992	71693568	12159	20144										
HDX	139324	broad.mit.edu	37	chrX	83599313	83599313	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcatcatttctgtcattatcCtctcctacttcaggcccagc	4	15	6	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:83599313C>A	ENST00000297977.5	-	6	1716	c.1605G>T	c.(1603-1605)gaG>gaT	p.E535D	HDX_ENST00000373177.2_Missense_Mutation_p.E535D|HDX_ENST00000506585.2_Missense_Mutation_p.E477D	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	535						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E535D(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TGTCATTATCCTCTCCTACTT	0.443																																					Pancreas(53;231 1169 36156 43751 51139)											1	Substitution - Missense(1)	large_intestine(1)	X											113	101	105					X																	83599313		2203	4300	6503	83485969	SO:0001583	missense	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1605G>T	X.37:g.83599313C>A	ENSP00000297977:p.Glu535Asp		83485969	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.529834	0.27387	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.32515	1.47;1.45;1.47	5.46	-3.32	0.04973	.	0.345509	0.31566	N	0.007423	T	0.13114	0.0318	N	0.20986	0.625	0.31715	N	0.639039	B	0.14012	0.009	B	0.10450	0.005	T	0.07868	-1.0750	10	0.27082	T	0.32	-12.3221	2.4393	0.04490	0.2566:0.1615:0.0924:0.4895	.	535	Q7Z353	HDX_HUMAN	D	535;477;535	ENSP00000297977:E535D;ENSP00000362272:E477D;ENSP00000423670:E535D	ENSP00000297977:E535D	E	-	3	2	HDX	83485969	0.839000	0.29477	0.895000	0.35142	0.968000	0.65278	-0.209000	0.09358	-1.130000	0.02914	0.597000	0.82753	GAG		0.443	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83599313	C	A	83599313	3	1	61	1	0	0	0	0	1	0	0	0	7047	680	24	2	487	2	HDX	23	83599313	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	22321	83599313	71671247	12160	20145										
HDX	139324	broad.mit.edu	37	chrX	83723656	83723656	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtacattgtctgacatatCtctaatattcaccatttgtg	5	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:83723656C>A	ENST00000297977.5	-	3	1186	c.1075G>T	c.(1075-1077)Gat>Tat	p.D359Y	HDX_ENST00000373177.2_Missense_Mutation_p.D359Y|HDX_ENST00000506585.2_Missense_Mutation_p.D301Y	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	359						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D359Y(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TCTGACATATCTCTAATATTC	0.393																																					Pancreas(53;231 1169 36156 43751 51139)											1	Substitution - Missense(1)	large_intestine(1)	X											152	127	136					X																	83723656		2203	4300	6503	83610312	SO:0001583	missense	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1075G>T	X.37:g.83723656C>A	ENSP00000297977:p.Asp359Tyr		83610312	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.093372	0.36952	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.39592	1.13;1.07;1.13	5.43	5.43	0.79202	.	0.295020	0.33327	N	0.005036	T	0.53286	0.1787	L	0.54323	1.7	0.44531	D	0.997487	D	0.71674	0.998	P	0.57371	0.819	T	0.56811	-0.7917	10	0.87932	D	0	-1.9988	12.5908	0.56441	0.0:0.9187:0.0:0.0813	.	359	Q7Z353	HDX_HUMAN	Y	359;301;359	ENSP00000297977:D359Y;ENSP00000362272:D301Y;ENSP00000423670:D359Y	ENSP00000297977:D359Y	D	-	1	0	HDX	83610312	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	3.584000	0.53936	2.258000	0.74832	0.415000	0.27848	GAT		0.393	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83723656	C	A	83723656	3	1	61	1	0	0	0	0	1	0	0	0	7047	913	32	2	1029	2	HDX	23	83723656	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	124343	83723656	71546904	12161	20146										
HDX	139324	broad.mit.edu	37	chrX	83723827	83723827	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcatattcatcctcagcatCtccagtctccattgcaatgg	7	13	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:83723827C>A	ENST00000297977.5	-	3	1015	c.904G>T	c.(904-906)Gat>Tat	p.D302Y	HDX_ENST00000373177.2_Missense_Mutation_p.D302Y|HDX_ENST00000506585.2_Missense_Mutation_p.D244Y	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	302						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D302Y(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TCCTCAGCATCTCCAGTCTCC	0.488																																					Pancreas(53;231 1169 36156 43751 51139)											1	Substitution - Missense(1)	large_intestine(1)	X											112	96	101					X																	83723827		2203	4300	6503	83610483	SO:0001583	missense	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.904G>T	X.37:g.83723827C>A	ENSP00000297977:p.Asp302Tyr		83610483	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545679	0.45280	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.51817	0.79;0.69;0.79	4.94	4.04	0.47022	.	0.169084	0.51477	D	0.000083	T	0.54481	0.1861	L	0.59436	1.845	0.49915	D	0.999836	D	0.65815	0.995	P	0.53401	0.725	T	0.57682	-0.7769	10	0.87932	D	0	-8.6306	11.2817	0.49199	0.0:0.9029:0.0:0.0971	.	302	Q7Z353	HDX_HUMAN	Y	302;244;302	ENSP00000297977:D302Y;ENSP00000362272:D244Y;ENSP00000423670:D302Y	ENSP00000297977:D302Y	D	-	1	0	HDX	83610483	0.983000	0.35010	1.000000	0.80357	0.959000	0.62525	2.488000	0.45276	0.897000	0.36392	0.422000	0.28245	GAT		0.488	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83723827	C	A	83723827	3	1	61	1	0	0	0	0	1	0	0	0	7047	913	32	2	1200	2	HDX	23	83723827	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	171	83723827	71546733	12162	20147										
CHM	1121	broad.mit.edu	37	chrX	85149241	85149241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaacataactcaatgacccGaacagcaaaagttcctggtt	7	10	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:85149241G>A	ENST00000357749.2	-	12	1491	c.1462C>T	c.(1462-1464)Cgg>Tgg	p.R488W	CHM_ENST00000537751.1_Missense_Mutation_p.R340W|CHM_ENST00000467744.2_Intron	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	488					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.R488W(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				TCAATGACCCGAACAGCAAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											148	122	131					X																	85149241		2203	4300	6503	85035897	SO:0001583	missense	1121			X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.1462C>T	X.37:g.85149241G>A	ENSP00000350386:p.Arg488Trp		85035897	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	37	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.249888	0.22880	.	.	ENSG00000188419	ENST00000357749;ENST00000537751	D;D	0.85411	-1.98;-1.98	5.11	4.25	0.50352	.	0.422409	0.26808	N	0.022393	D	0.91243	0.7240	M	0.87180	2.865	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.83027	-0.0164	10	0.46703	T	0.11	-0.5221	5.9672	0.19332	0.3663:0.0:0.6337:0.0	.	488	P24386	RAE1_HUMAN	W	488;340	ENSP00000350386:R488W;ENSP00000441728:R340W	ENSP00000350386:R488W	R	-	1	2	CHM	85035897	0.999000	0.42202	0.014000	0.15608	0.005000	0.04900	1.846000	0.39289	0.942000	0.37525	0.600000	0.82982	CGG		0.378	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		A	85149241	G	A	85149241	3	1	61	1	0	0	0	0	1	0	0	0	3356	1057	37	1	515	1	CHM	23	85149241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1425414	85149241	70121319	12163	20148										
CHM	1121	broad.mit.edu	37	chrX	85156154	85156154	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tccacgaggaaatgctcagaGattattctctgaccaaactg	8	10	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:85156154G>T	ENST00000357749.2	-	10	1313	c.1284C>A	c.(1282-1284)atC>atA	p.I428I	CHM_ENST00000537751.1_Silent_p.I280I|MIR361_ENST00000362181.1_RNA|CHM_ENST00000467744.2_Intron	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	428					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.I428I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AATGCTCAGAGATTATTCTCT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	X											69	56	60					X																	85156154		2203	4300	6503	85042810	SO:0001819	synonymous_variant	1121			X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.1284C>A	X.37:g.85156154G>T			85042810	A1L4D2|O43732	Silent	SNP	ENST00000357749.2	37	CCDS14454.1																																																																																				0.378	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		T	85156154	G	T	85156154	2	4	61	1	0	0	0	0	0	0	0	1	3356	932	33	2		2	CHM	23	85156154	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6913	85156154	70114406	12164	20149										
DACH2	117154	broad.mit.edu	37	chrX	85403761	85403761	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctaatatgatcaatagttTcgtggttaataaccacagca	6	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:85403761T>G	ENST00000373125.4	+	1	137	c.137T>G	c.(136-138)tTc>tGc	p.F46C	DACH2_ENST00000373131.1_Missense_Mutation_p.F46C	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	46					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F46C(2)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						ATCAATAGTTTCGTGGTTAAT	0.607																																																2	Substitution - Missense(2)	large_intestine(2)	X											45	38	41					X																	85403761		2203	4300	6503	85290417	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.137T>G	X.37:g.85403761T>G	ENSP00000362217:p.Phe46Cys		85290417	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.801253	0.31869	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	D;D	0.83992	-1.79;-1.79	4.49	4.49	0.54785	Transforming protein Ski (1);	0.000000	0.51477	D	0.000088	D	0.88811	0.6538	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.993;0.996	D	0.87896	0.2687	10	0.38643	T	0.18	.	12.1654	0.54127	0.0:0.0:0.0:1.0	.	46;46	Q96NX9-2;Q96NX9	.;DACH2_HUMAN	C	46	ENSP00000362223:F46C;ENSP00000362217:F46C	ENSP00000345134:F46C	F	+	2	0	DACH2	85290417	1.000000	0.71417	0.987000	0.45799	0.030000	0.12068	6.238000	0.72350	1.659000	0.50751	0.437000	0.28790	TTC		0.607	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		G	85403761	T	G	85403761	3	3	61	1	0	0	0	0	1	0	0	0	4227	1783	62	4	139	4	DACH2	23	85403761	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	247607	85403761	69866799	12165	20150										
DACH2	117154	broad.mit.edu	37	chrX	85969625	85969625	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctgcatcagttgccatgGcaatgaatcagatgaaccat	8	11	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:85969625G>T	ENST00000373125.4	+	6	1006	c.1006G>T	c.(1006-1008)Gca>Tca	p.A336S	DACH2_ENST00000510272.1_Missense_Mutation_p.A117S|DACH2_ENST00000373131.1_Missense_Mutation_p.A323S|DACH2_ENST00000508860.1_Missense_Mutation_p.A169S	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	336					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A323S(1)|p.A336S(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AGTTGCCATGGCAATGAATCA	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	X											181	145	157					X																	85969625		2203	4300	6503	85856281	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1006G>T	X.37:g.85969625G>T	ENSP00000362217:p.Ala336Ser		85856281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.048143	0.75846	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297	D;D	0.87179	-2.22;-2.2	5.02	5.02	0.67125	.	0.180392	0.37348	N	0.002126	D	0.92149	0.7511	M	0.64404	1.975	0.58432	D	0.999999	D;D;D;D	0.89917	0.994;0.997;1.0;0.99	P;P;D;P	0.91635	0.887;0.804;0.999;0.844	D	0.91035	0.4867	10	0.32370	T	0.25	.	17.5775	0.87955	0.0:0.0:1.0:0.0	.	202;336;323;336	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	S	336;323;336;169;117;169	ENSP00000362223:A323S;ENSP00000362217:A336S	ENSP00000345134:A336S	A	+	1	0	DACH2	85856281	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	8.894000	0.92506	2.079000	0.62486	0.513000	0.50165	GCA		0.453	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	85969625	G	T	85969625	3	4	61	1	0	0	0	0	1	0	0	0	4227	1203	42	2	1028	2	DACH2	23	85969625	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	565864	85969625	69300935	12166	20151										
PABPC5	140886	broad.mit.edu	37	chrX	90690928	90690928	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaaacctggacaaatccataGacaatagggccctgttttac	7	10	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:90690928G>T	ENST00000312600.3	+	2	566	c.352G>T	c.(352-354)Gac>Tac	p.D118Y	PABPC5-AS1_ENST00000456187.1_RNA|PABPC5_ENST00000373105.1_Intron	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	118	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.D118Y(1)		central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						CAAATCCATAGACAATAGGGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											82	76	78					X																	90690928		2203	4300	6503	90577584	SO:0001583	missense	140886			AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.352G>T	X.37:g.90690928G>T	ENSP00000308012:p.Asp118Tyr		90577584	A8K240|Q5JQF4|Q6P529|Q9UFE5	Missense_Mutation	SNP	ENST00000312600.3	37	CCDS14460.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374140	0.61735	.	.	ENSG00000174740	ENST00000312600;ENST00000402906	T	0.17528	2.27	4.43	4.43	0.53597	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.044885	0.85682	D	0.000000	T	0.49457	0.1558	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60662	-0.7219	10	0.87932	D	0	.	13.8905	0.63736	0.0:0.0:1.0:0.0	.	118	Q96DU9	PABP5_HUMAN	Y	118;86	ENSP00000308012:D118Y	ENSP00000308012:D118Y	D	+	1	0	PABPC5	90577584	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.240000	0.95396	2.450000	0.82876	0.600000	0.82982	GAC		0.423	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		T	90690928	G	T	90690928	3	4	61	1	0	0	0	0	1	0	0	0	11398	942	33	2	354	2	PABPC5	23	90690928	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4721303	90690928	64579632	12167	20152										
RPA4	29935	broad.mit.edu	37	chrX	96139422	96139422	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcctgctattaagacccaaaGacctaaggtccgaattcagg	8	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:96139422G>T	ENST00000373040.3	+	1	516	c.113G>T	c.(112-114)aGa>aTa	p.R38I	DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000324765.8_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373054.4_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	38					DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)	p.R38I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						AAGACCCAAAGACCTAAGGTC	0.488								Other identified genes with known or suspected DNA repair function																																								1	Substitution - Missense(1)	large_intestine(1)	X											141	114	123					X																	96139422		2203	4300	6503	96026078	SO:0001583	missense	29935			U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"replication protein A4, 34kDa"			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.113G>T	X.37:g.96139422G>T	ENSP00000362131:p.Arg38Ile		96026078	Q3SY03	Missense_Mutation	SNP	ENST00000373040.3	37	CCDS35345.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362941	0.41902	.	.	ENSG00000204086	ENST00000373040	T	0.19250	2.16	3.48	2.48	0.30137	.	.	.	.	.	T	0.12433	0.0302	N	0.22421	0.69	0.09310	N	1	B	0.30584	0.286	B	0.20384	0.029	T	0.19745	-1.0296	9	0.87932	D	0	-34.8002	6.8459	0.23988	0.0:0.0:0.6219:0.3781	.	38	Q13156	RFA4_HUMAN	I	38	ENSP00000362131:R38I	ENSP00000362131:R38I	R	+	2	0	RPA4	96026078	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.401000	0.20948	0.673000	0.31224	0.600000	0.82982	AGA		0.488	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347		T	96139422	G	T	96139422	3	4	61	1	0	0	0	0	1	0	0	0	13576	942	33	2	115	2	RPA4	23	96139422	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	5448494	96139422	59131138	12168	20153										
DIAPH2	1730	broad.mit.edu	37	chrX	96684688	96684688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatggataatcttctagaagCcctacaatcaggtgcagcat	9	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:96684688C>T	ENST00000324765.8	+	26	3532	c.3185C>T	c.(3184-3186)gCc>gTc	p.A1062V	DIAPH2_ENST00000373061.3_Missense_Mutation_p.A1062V|DIAPH2_ENST00000373049.4_Missense_Mutation_p.A1062V|DIAPH2-AS1_ENST00000439759.2_RNA|DIAPH2_ENST00000355827.4_Missense_Mutation_p.A1062V|DIAPH2_ENST00000373054.4_Missense_Mutation_p.A1058V			O60879	DIAP2_HUMAN	diaphanous-related formin 2	1062	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)	p.A1062V(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						CTTCTAGAAGCCCTACAATCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											84	75	78					X																	96684688		2203	4300	6503	96571344	SO:0001583	missense	1730			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.3185C>T	X.37:g.96684688C>T	ENSP00000321348:p.Ala1062Val		96571344	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	37	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411070	0.83340	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	D;D;D;D;D	0.83250	-1.7;-1.69;-1.65;-1.65;-1.7	5.31	5.31	0.75309	DRF autoregulatory (1);Actin-binding FH2/DRF autoregulatory (1);Diaphanous autoregulatory (1);	0.000000	0.85682	D	0.000000	D	0.92364	0.7577	M	0.87180	2.865	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.986	D	0.93623	0.6949	10	0.87932	D	0	.	18.3124	0.90204	0.0:1.0:0.0:0.0	.	1062;1062	O60879;O60879-2	DIAP2_HUMAN;.	V	1062;1058;1062;1062;1062;1069	ENSP00000362152:A1062V;ENSP00000362145:A1058V;ENSP00000348082:A1062V;ENSP00000362140:A1062V;ENSP00000321348:A1062V	ENSP00000321348:A1062V	A	+	2	0	DIAPH2	96571344	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.639000	0.74314	2.351000	0.79841	0.600000	0.82982	GCC		0.398	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		T	96684688	C	T	96684688	3	4	61	1	0	0	0	0	1	0	0	0	4530	739	26	3	3287	3	DIAPH2	23	96684688	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	545266	96684688	58585872	12169	20154										
PCDH19	57526	broad.mit.edu	37	chrX	99551365	99551365	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgacctcatgcatgactttCtcgctatcagctccacgggg	9	14	3	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:99551365C>A	ENST00000373034.4	-	6	5032	c.3357G>T	c.(3355-3357)gaG>gaT	p.E1119D	PCDH19_ENST00000464981.1_5'Flank|PCDH19_ENST00000255531.7_Missense_Mutation_p.E1072D|PCDH19_ENST00000420881.2_Missense_Mutation_p.E1071D	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1119					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1119D(1)|p.E572D(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GCATGACTTTCTCGCTATCAG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	X											126	118	121					X																	99551365		2034	4183	6217	99438021	SO:0001583	missense	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3357G>T	X.37:g.99551365C>A	ENSP00000362125:p.Glu1119Asp		99438021	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526229	0.44969	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.59502	0.26;0.36;0.26	5.52	1.58	0.23477	.	0.000000	0.85682	D	0.000000	T	0.59595	0.2205	L	0.29908	0.895	0.54753	D	0.999983	D;D;D	0.61697	0.984;0.99;0.984	D;D;D	0.70935	0.956;0.971;0.935	T	0.57177	-0.7856	10	0.62326	D	0.03	.	8.578	0.33609	0.0:0.4656:0.0:0.5344	.	1119;1072;1071	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	D	1071;1119;1072	ENSP00000400327:E1071D;ENSP00000362125:E1119D;ENSP00000255531:E1072D	ENSP00000255531:E1072D	E	-	3	2	PCDH19	99438021	0.998000	0.40836	0.984000	0.44739	0.970000	0.65996	0.456000	0.21859	0.108000	0.17862	0.600000	0.82982	GAG		0.547	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99551365	C	A	99551365	3	1	61	1	0	0	0	0	1	0	0	0	11545	912	32	2	93	2	PCDH19	23	99551365	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2866677	99551365	55719195	12170	20155										
TSPAN6	7105	broad.mit.edu	37	chrX	99887533	99887533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcaacgactcccatttctgaCtctataatggtcatcacctt	5	13	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:99887533C>A	ENST00000373020.4	-	6	729	c.618G>T	c.(616-618)gaG>gaT	p.E206D	TSPAN6_ENST00000496771.1_5'Flank	NM_001278740.1|NM_001278741.1|NM_003270.2	NP_001265669.1|NP_001265670.1|NP_003261.1	O43657	TSN6_HUMAN	tetraspanin 6	206					negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway (GO:0039532)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)	p.E206D(1)		endometrium(2)|kidney(3)|large_intestine(6)|ovary(1)	12						CCATTTCTGACTCTATAATGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	X											64	59	61					X																	99887533		2203	4300	6503	99774189	SO:0001583	missense	7105			AF043906	CCDS14470.1, CCDS76001.1	Xq22	2013-02-14	2005-03-21	2005-03-21	ENSG00000000003	ENSG00000000003		"Tetraspanins"	11858	protein-coding gene	gene with protein product		300191	"transmembrane 4 superfamily member 6"	TM4SF6		9782095	Standard	NM_003270		Approved	T245, TSPAN-6	uc004ega.1	O43657	OTTHUMG00000022002	ENST00000373020.4:c.618G>T	X.37:g.99887533C>A	ENSP00000362111:p.Glu206Asp		99774189	Q54A42|Q6IAN9	Missense_Mutation	SNP	ENST00000373020.4	37	CCDS14470.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.045718	0.55110	.	.	ENSG00000000003	ENST00000373020;ENST00000431386	T	0.79749	-1.3	5.5	1.47	0.22746	Tetraspanin, EC2 domain (1);	0.344862	0.36200	N	0.002726	T	0.81950	0.4931	M	0.78344	2.41	0.54753	D	0.999981	B	0.31227	0.314	B	0.42163	0.378	T	0.75611	-0.3258	9	.	.	.	.	9.8988	0.41335	0.0:0.6577:0.0:0.3423	.	206	O43657	TSN6_HUMAN	D	206;188	ENSP00000362111:E206D	.	E	-	3	2	TSPAN6	99774189	0.705000	0.27846	1.000000	0.80357	0.549000	0.35272	-0.159000	0.10056	0.165000	0.19558	0.513000	0.50165	GAG		0.363	TSPAN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057483.1			A	99887533	C	A	99887533	3	1	61	1	0	0	0	0	1	0	0	0	16691	564	20	2	127	2	TSPAN6	23	99887533	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336168	99887533	55383027	12171	20156										
DRP2	1821	broad.mit.edu	37	chrX	100503513	100503513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttaaacctagtggtcgcagcGgaaagatgcgggcattgtct	13	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100503513G>A	ENST00000395209.3	+	14	1992	c.1465G>A	c.(1465-1467)Gga>Aga	p.G489R	DRP2_ENST00000538510.1_Missense_Mutation_p.G489R|DRP2_ENST00000541709.1_Missense_Mutation_p.G411R|DRP2_ENST00000402866.1_Missense_Mutation_p.G489R	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	489					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.G486R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						TGGTCGCAGCGGAAAGATGCG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	X											247	232	237					X																	100503513		2203	4300	6503	100390169	SO:0001583	missense	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.1465G>A	X.37:g.100503513G>A	ENSP00000378635:p.Gly489Arg		100390169	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564325	0.86335	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.07	5.07	0.68467	EF-hand domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93621	0.7963	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94917	0.8070	10	0.87932	D	0	-10.0215	17.6826	0.88248	0.0:0.0:1.0:0.0	.	489	Q13474	DRP2_HUMAN	R	489;489;411;489	ENSP00000385038:G489R;ENSP00000378635:G489R;ENSP00000444752:G411R;ENSP00000441051:G489R	ENSP00000378635:G489R	G	+	1	0	DRP2	100390169	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.624000	0.98398	2.104000	0.64026	0.513000	0.50165	GGA		0.433	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		A	100503513	G	A	100503513	3	1	61	1	0	0	0	0	1	0	0	0	4775	1117	39	1	1511	1	DRP2	23	100503513	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	615980	100503513	54767047	12172	20157										
BTK	695	broad.mit.edu	37	chrX	100608290	100608290	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcagtctcactgttagtaaaTctctcatatggcatcttccc	6	12	4	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100608290T>C	ENST00000308731.7	-	18	1963	c.1800A>G	c.(1798-1800)agA>agG	p.R600R	BTK_ENST00000372880.1_Silent_p.R424R	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)	p.R600R(1)		breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TGTTAGTAAATCTCTCATATG	0.418									Agammaglobulinemia, X-linked																																							1	Substitution - coding silent(1)	large_intestine(1)	X											236	212	220					X																	100608290		2203	4300	6503	100494946	SO:0001819	synonymous_variant	695	Familial Cancer Database	Bruton Type Agammaglobulinemia	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1800A>G	X.37:g.100608290T>C			100494946	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																				0.418	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		C	100608290	T	C	100608290	2	2	61	1	0	0	0	0	0	0	0	1	1560	1432	50	4		4	BTK	23	100608290	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	104777	100608290	54662270	12173	20158										
BTK	695	broad.mit.edu	37	chrX	100612498	100612498	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagagaaataaggagttaccGtatcccaggcctgcagtgga	12	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100612498G>A	ENST00000308731.7	-	13	1339	c.1176C>T	c.(1174-1176)taC>taT	p.Y392Y	BTK_ENST00000372880.1_Intron	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	392					adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)	p.Y392Y(1)		breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						AGGAGTTACCGTATCCCAGGC	0.493									Agammaglobulinemia, X-linked																																							1	Substitution - coding silent(1)	large_intestine(1)	X	GRCh37	CM015165	BTK	M							265	195	219					X																	100612498		2203	4300	6503	100499154	SO:0001630	splice_region_variant	695	Familial Cancer Database	Bruton Type Agammaglobulinemia	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1177+1C>T	X.37:g.100612498G>A			100499154	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																				0.493	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	Silent	A	100612498	G	A	100612498	5	1	61	1	0	0	0	0	0	0	1	0	1560	1159	40	1	831	1	BTK	23	100612498	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	4208	100612498	54658062	12174	20159										
BTK	695	broad.mit.edu	37	chrX	100613405	100613405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggaacacacaacataatgaCgtatcaccccttgagggtcc	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100613405C>T	ENST00000308731.7	-	12	1158	c.995G>A	c.(994-996)cGt>cAt	p.R332H	BTK_ENST00000372880.1_Missense_Mutation_p.R332H	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	332	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)	p.R332H(2)		breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						AACATAATGACGTATCACCCC	0.478									Agammaglobulinemia, X-linked																																							2	Substitution - Missense(2)	large_intestine(1)|breast(1)	X											164	137	147					X																	100613405		2203	4300	6503	100500061	SO:0001583	missense	695	Familial Cancer Database	Bruton Type Agammaglobulinemia	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.995G>A	X.37:g.100613405C>T	ENSP00000308176:p.Arg332His		100500061	B2RAW1|Q32ML5	Missense_Mutation	SNP	ENST00000308731.7	37	CCDS14482.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357494	0.82243	.	.	ENSG00000010671	ENST00000372880;ENST00000372855;ENST00000372859;ENST00000372860;ENST00000395179;ENST00000372869;ENST00000443591;ENST00000308731;ENST00000540426	D;D	0.88818	-2.43;-2.43	6.06	6.06	0.98353	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.93864	0.8037	M	0.64676	1.99	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	P;D;D;D	0.77557	0.814;0.99;0.982;0.98	D	0.94009	0.7282	10	0.87932	D	0	.	19.1109	0.93315	0.0:1.0:0.0:0.0	.	3;332;332;332	Q3MS94;Q5JY90;B2RAW1;Q06187	.;.;.;BTK_HUMAN	H	332;3;3;1;3;3;3;332;2	ENSP00000361971:R332H;ENSP00000308176:R332H	ENSP00000308176:R332H	R	-	2	0	BTK	100500061	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.571000	0.60879	2.562000	0.86427	0.600000	0.82982	CGT		0.478	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		T	100613405	C	T	100613405	3	4	61	1	0	0	0	0	1	0	0	0	1560	536	19	1	1016	1	BTK	23	100613405	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	907	100613405	54657155	12175	20160										
BTK	695	broad.mit.edu	37	chrX	100629581	100629581	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accactgtttcaacacaagtGatcttctcaacatctattga	4	11	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100629581G>T	ENST00000308731.7	-	3	346	c.183C>A	c.(181-183)atC>atA	p.I61I	BTK_ENST00000464567.1_5'UTR|BTK_ENST00000372880.1_Silent_p.I61I	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	61	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		I -> N (in XLA). {ECO:0000269|PubMed:9445504}.		adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)	p.I61I(1)		breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CAACACAAGTGATCTTCTCAA	0.408									Agammaglobulinemia, X-linked																																							1	Substitution - coding silent(1)	large_intestine(1)	X											245	231	236					X																	100629581		2203	4300	6503	100516237	SO:0001819	synonymous_variant	695	Familial Cancer Database	Bruton Type Agammaglobulinemia	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.183C>A	X.37:g.100629581G>T			100516237	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																				0.408	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		T	100629581	G	T	100629581	2	4	61	1	0	0	0	0	0	0	0	1	1560	1280	45	2		2	BTK	23	100629581	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	16176	100629581	54640979	12176	20161										
HNRNPH2	3188	broad.mit.edu	37	chrX	100668018	100668018	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgtggcagctatggcaaaaGacaaagctaatatgcaacac	9	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100668018G>T	ENST00000316594.5	+	2	1120	c.1042G>T	c.(1042-1044)Gac>Tac	p.D348Y		NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	348	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D348Y(1)		breast(3)|large_intestine(2)|lung(6)|skin(1)	12						TATGGCAAAAGACAAAGCTAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											108	96	100					X																	100668018		2203	4300	6503	100554674	SO:0001583	missense	3188			U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"RNA binding motif (RRM) containing"	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.1042G>T	X.37:g.100668018G>T	ENSP00000361927:p.Asp348Tyr		100554674	A1L400|Q9HHA7	Missense_Mutation	SNP	ENST00000316594.5	37	CCDS14485.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.551521	0.45487	.	.	ENSG00000126945	ENST00000457902;ENST00000316594	T	0.34472	1.36	4.62	3.74	0.42951	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.58293	0.2112	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.62765	-0.6785	10	0.87932	D	0	-19.9042	11.5945	0.50964	0.0:0.1771:0.8229:0.0	.	348	P55795	HNRH2_HUMAN	Y	303;348	ENSP00000361927:D348Y	ENSP00000361927:D348Y	D	+	1	0	HNRNPH2	100554674	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.562000	0.98145	1.055000	0.40461	0.513000	0.50165	GAC		0.423	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597		T	100668018	G	T	100668018	3	4	61	1	0	0	0	0	1	0	0	0	7288	942	33	2	1044	2	HNRNPH2	23	100668018	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38437	100668018	54602542	12177	20162										
ARMCX3	51566	broad.mit.edu	37	chrX	100880063	100880063	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atagactgactaggggaagaAaacagaacaaggaaaaaatg	11	4	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:100880063A>T	ENST00000341189.4	+	5	960	c.94A>T	c.(94-96)Aaa>Taa	p.K32*	ARMCX3_ENST00000471229.2_Nonsense_Mutation_p.K32*|ARMCX3-AS1_ENST00000454228.1_RNA|ARMCX3_ENST00000537169.1_Nonsense_Mutation_p.K32*|RP4-545K15.5_ENST00000564612.1_RNA	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	32					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)		p.K32*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						TAGGGGAAGAAAACAGAACAA	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											88	86	86					X																	100880063		2203	4300	6503	100766719	SO:0001587	stop_gained	51566			AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.94A>T	X.37:g.100880063A>T	ENSP00000340672:p.Lys32*		100766719	Q53HC6|Q7LCF5|Q9NPE4	Nonsense_Mutation	SNP	ENST00000341189.4	37	CCDS14489.1	.	.	.	.	.	.	.	.	.	.	A	36	5.802021	0.96960	.	.	ENSG00000102401	ENST00000341189;ENST00000537169	.	.	.	4.36	3.16	0.36331	.	0.408970	0.28225	N	0.016125	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-17.6618	6.9349	0.24461	0.7675:0.2325:0.0:0.0	.	.	.	.	X	32	.	ENSP00000340672:K32X	K	+	1	0	ARMCX3	100766719	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.950000	0.56676	0.767000	0.33267	0.481000	0.45027	AAA		0.527	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		T	100880063	A	T	100880063	4	4	61	1	0	0	0	0	0	1	0	0	962	15	1	5	96	5	ARMCX3	23	100880063	Nonsense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	212045	100880063	54390497	12178	20163										
GPRASP2	114928	broad.mit.edu	37	chrX	101969951	101969951	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctactggggcaaggcccaaaActgagaccaagtctgtgcct	11	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:101969951A>C	ENST00000535209.1	+	4	985	c.154A>C	c.(154-156)Act>Cct	p.T52P	GPRASP2_ENST00000332262.5_Missense_Mutation_p.T52P|GPRASP2_ENST00000543253.1_Missense_Mutation_p.T52P			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	52						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)	p.T52P(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						AAGGCCCAAAACTGAGACCAA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	99	102					X																	101969951		2203	4300	6503	101856607	SO:0001583	missense	114928			AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.154A>C	X.37:g.101969951A>C	ENSP00000437394:p.Thr52Pro		101856607	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042371	0.55003	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.08282	3.11;3.11;3.11	4.82	2.15	0.27550	.	0.000000	0.45361	D	0.000378	T	0.07188	0.0182	L	0.27053	0.805	0.32598	N	0.526247	P	0.52316	0.952	P	0.49140	0.601	T	0.27905	-1.0060	10	0.24483	T	0.36	.	5.5028	0.16838	0.6542:0.1742:0.0:0.1716	.	52	Q96D09	GASP2_HUMAN	P	52	ENSP00000437872:T52P;ENSP00000437394:T52P;ENSP00000339057:T52P	ENSP00000339057:T52P	T	+	1	0	GPRASP2	101856607	0.026000	0.19158	0.998000	0.56505	0.833000	0.47200	0.126000	0.15769	0.714000	0.32081	0.430000	0.28490	ACT		0.567	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		C	101969951	A	C	101969951	3	2	61	1	0	0	0	0	1	0	0	0	6744	43	2	4	156	4	GPRASP2	23	101969951	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	1089888	101969951	53300609	12179	20164										
GPRASP2	114928	broad.mit.edu	37	chrX	101970983	101970983	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cctggttctgggcagaaaaaGaggccagtttggagggtgga	17	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:101970983G>T	ENST00000535209.1	+	4	2017	c.1186G>T	c.(1186-1188)Gag>Tag	p.E396*	GPRASP2_ENST00000332262.5_Nonsense_Mutation_p.E396*|GPRASP2_ENST00000543253.1_Nonsense_Mutation_p.E396*			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	396						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)	p.E396*(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGCAGAAAAAGAGGCCAGTTT	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											60	62	61					X																	101970983		2203	4300	6503	101857639	SO:0001587	stop_gained	114928			AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1186G>T	X.37:g.101970983G>T	ENSP00000437394:p.Glu396*		101857639	D3DXA0|Q8NAB4	Nonsense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	G	42	9.206793	0.99099	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	.	.	.	4.44	4.44	0.53790	.	0.000000	0.48767	D	0.000164	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	7.365	0.26768	0.1155:0.0:0.8845:0.0	.	.	.	.	X	396	.	ENSP00000339057:E396X	E	+	1	0	GPRASP2	101857639	1.000000	0.71417	0.986000	0.45419	0.883000	0.51084	5.441000	0.66569	2.458000	0.83093	0.600000	0.82982	GAG		0.527	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		T	101970983	G	T	101970983	4	4	61	1	0	0	0	0	0	1	0	0	6744	943	33	2	1188	2	GPRASP2	23	101970983	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1032	101970983	53299577	12180	20165										
GPRASP2	114928	broad.mit.edu	37	chrX	101971499	101971499	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	accggtcagtccgggaaattCgagagcatcttagggccagg	14	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:101971499C>T	ENST00000535209.1	+	4	2533	c.1702C>T	c.(1702-1704)Cga>Tga	p.R568*	GPRASP2_ENST00000332262.5_Nonsense_Mutation_p.R568*|GPRASP2_ENST00000543253.1_Nonsense_Mutation_p.R568*			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	568						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)	p.R568*(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CCGGGAAATTCGAGAGCATCT	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											99	94	96					X																	101971499		2203	4300	6503	101858155	SO:0001587	stop_gained	114928			AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1702C>T	X.37:g.101971499C>T	ENSP00000437394:p.Arg568*		101858155	D3DXA0|Q8NAB4	Nonsense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	C	42	9.193336	0.99096	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	.	.	.	4.33	3.46	0.39613	.	0.000000	0.39615	N	0.001319	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5543	0.33471	0.229:0.771:0.0:0.0	.	.	.	.	X	568	.	ENSP00000339057:R568X	R	+	1	2	GPRASP2	101858155	1.000000	0.71417	0.989000	0.46669	0.815000	0.46073	0.913000	0.28611	1.162000	0.42619	0.600000	0.82982	CGA		0.483	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		T	101971499	C	T	101971499	4	4	61	1	0	0	0	0	0	1	0	0	6744	876	31	1	1704	1	GPRASP2	23	101971499	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	516	101971499	53299061	12181	20166										
NXF3	56000	broad.mit.edu	37	chrX	102334943	102334943	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attcccagggatacttactgCtgcaggaattgcaggaccag	11	10	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:102334943C>A	ENST00000395065.3	-	12	1151	c.1050G>T	c.(1048-1050)caG>caT	p.Q350H	NXF3_ENST00000425644.1_Intron	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	350	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)	p.Q350H(1)		NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						ATACTTACTGCTGCAGGAATT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											170	168	169					X																	102334943		2203	4300	6503	102221599	SO:0001583	missense	56000			AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1050G>T	X.37:g.102334943C>A	ENSP00000378504:p.Gln350His		102221599	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	37	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.577|8.577	0.881365|0.881365	0.17467|0.17467	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000427570|ENST00000395065	.|T	.|0.63096	.|-0.02	4.44|4.44	-0.61|-0.61	0.11604|0.11604	.|Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);	.|0.701713	.|0.14481	.|N	.|0.316928	T|T	0.62048|0.62048	0.2396|0.2396	M|M	0.90145|0.90145	3.09|3.09	0.80722|0.80722	D|D	1|1	.|B;B	.|0.23128	.|0.027;0.08	.|B;B	.|0.24394	.|0.012;0.053	T|T	0.56312|0.56312	-0.8000|-0.8000	5|10	.|0.51188	.|T	.|0.08	-3.3183|-3.3183	4.0231|4.0231	0.09675|0.09675	0.0:0.3753:0.1795:0.4451|0.0:0.3753:0.1795:0.4451	.|.	.|246;350	.|E9PEY7;Q9H4D5	.|.;NXF3_HUMAN	S|H	227|350	.|ENSP00000378504:Q350H	.|ENSP00000378504:Q350H	A|Q	-|-	1|3	0|2	NXF3|NXF3	102221599|102221599	1.000000|1.000000	0.71417|0.71417	0.447000|0.447000	0.26932|0.26932	0.587000|0.587000	0.36485|0.36485	0.940000|0.940000	0.28992|0.28992	-0.157000|-0.157000	0.11059|0.11059	-0.912000|-0.912000	0.02778|0.02778	GCA|CAG		0.483	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		A	102334943	C	A	102334943	3	1	61	1	0	0	0	0	1	0	0	0	10816	796	28	2	577	2	NXF3	23	102334943	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	363444	102334943	52935617	12182	20167										
TMEM31	203562	broad.mit.edu	37	chrX	102968621	102968621	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacatccagcgacagaacgAtcaaccttcttgaagtcctt	6	13	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:102968621A>C	ENST00000319560.6	+	3	393	c.202A>C	c.(202-204)Atc>Ctc	p.I68L	GLRA4_ENST00000372617.4_Intron	NM_182541.2	NP_872347.2	Q5JXX7	TMM31_HUMAN	transmembrane protein 31	68						integral component of membrane (GO:0016021)		p.I68L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						CGACAGAACGATCAACCTTCT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											285	200	229					X																	102968621		2203	4300	6503	102855277	SO:0001583	missense	203562			BC029575	CCDS35359.1	Xq22.2	2008-02-05			ENSG00000179363	ENSG00000179363			28601	protein-coding gene	gene with protein product						12477932	Standard	NM_182541		Approved	MGC39655	uc004elh.3	Q5JXX7	OTTHUMG00000022109	ENST00000319560.6:c.202A>C	X.37:g.102968621A>C	ENSP00000316940:p.Ile68Leu		102855277	Q8NHR4	Missense_Mutation	SNP	ENST00000319560.6	37	CCDS35359.1	.	.	.	.	.	.	.	.	.	.	A	7.596	0.671691	0.14776	.	.	ENSG00000179363	ENST00000319560	.	.	.	4.81	-0.623	0.11556	.	0.774336	0.10566	N	0.659696	T	0.18087	0.0434	N	0.08118	0	0.09310	N	1	B	0.24368	0.102	B	0.21151	0.033	T	0.20806	-1.0264	9	0.87932	D	0	-0.3048	7.9194	0.29837	0.5532:0.0:0.4468:0.0	.	68	Q5JXX7	TMM31_HUMAN	L	68	.	ENSP00000316940:I68L	I	+	1	0	TMEM31	102855277	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.091000	0.15046	-0.335000	0.08451	-1.043000	0.02367	ATC		0.483	TMEM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057741.1	NM_182541		C	102968621	A	C	102968621	3	2	61	1	0	0	0	0	1	0	0	0	16194	333	12	4	208	4	TMEM31	23	102968621	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	633678	102968621	52301939	12183	20168										
H2BFWT	158983	broad.mit.edu	37	chrX	103267811	103267811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccggcagcagcaggcgcacaGccatccgggtctcccaggca	13	17	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:103267811G>A	ENST00000217926.5	-	1	448	c.422C>T	c.(421-423)gCt>gTt	p.A141V	H2BFM_ENST00000243297.5_5'Flank	NM_001002916.3	NP_001002916.3	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	141						membrane (GO:0016020)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A141V(1)		breast(2)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	16						CAGGCGCACAGCCATCCGGGT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	X											28	28	28					X																	103267811		2203	4299	6502	103154467	SO:0001583	missense	158983			BC038109	CCDS35362.1	Xq22.2	2011-01-27			ENSG00000123569	ENSG00000123569		"Histones / Replication-independent"	27252	protein-coding gene	gene with protein product		300507				12477932	Standard	NM_001002916		Approved		uc004elr.3	Q7Z2G1	OTTHUMG00000022120	ENST00000217926.5:c.422C>T	X.37:g.103267811G>A	ENSP00000354723:p.Ala141Val		103154467	B1AK72|Q147W3	Missense_Mutation	SNP	ENST00000217926.5	37	CCDS35362.1	.	.	.	.	.	.	.	.	.	.	.	21.0	4.083089	0.76642	.	.	ENSG00000123569	ENST00000217926	T	0.55413	0.52	2.84	2.84	0.33178	Histone-fold (2);Histone core (1);	0.151282	0.21747	N	0.069729	T	0.71500	0.3347	M	0.85299	2.745	0.45150	D	0.998166	D	0.69078	0.997	D	0.70487	0.969	T	0.76372	-0.2983	10	0.87932	D	0	.	10.9533	0.47343	0.0:0.0:1.0:0.0	.	141	Q7Z2G1	H2BWT_HUMAN	V	141	ENSP00000354723:A141V	ENSP00000354723:A141V	A	-	2	0	H2BFWT	103154467	1.000000	0.71417	0.002000	0.10522	0.001000	0.01503	7.628000	0.83189	1.705000	0.51264	0.600000	0.82982	GCT		0.647	H2BFWT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057756.2	NM_001002916		A	103267811	G	A	103267811	3	1	61	1	0	0	0	0	1	0	0	0	6953	971	34	3	113	3	H2BFWT	23	103267811	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	299190	103267811	52002749	12184	20169										
IL1RAPL2	26280	broad.mit.edu	37	chrX	104999214	104999214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctcttacacaaaagtggaCcaagatactttagactgtga	7	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:104999214C>A	ENST00000372582.1	+	10	1992	c.1236C>A	c.(1234-1236)gaC>gaA	p.D412E	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.D412E|IL1RAPL2_ENST00000485671.1_3'UTR	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	412	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.D412E(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAAAAGTGGACCAAGATACTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											126	115	119					X																	104999214		2203	4300	6503	104885870	SO:0001583	missense	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1236C>A	X.37:g.104999214C>A	ENSP00000361663:p.Asp412Glu		104885870	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841352	0.32513	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.04654	3.68;3.68;3.58	5.62	-8.98	0.00754	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.087212	0.49305	N	0.000152	T	0.03739	0.0106	M	0.67517	2.055	0.49798	D	0.99982	B	0.02656	0.0	B	0.06405	0.002	T	0.31861	-0.9928	10	0.39692	T	0.17	.	3.2374	0.06770	0.2583:0.0911:0.0906:0.56	.	412	Q9NP60	IRPL2_HUMAN	E	412;412;17	ENSP00000361663:D412E;ENSP00000344976:D412E;ENSP00000445576:D17E	ENSP00000344976:D412E	D	+	3	2	IL1RAPL2	104885870	0.996000	0.38824	0.648000	0.29521	0.982000	0.71751	0.396000	0.20867	-2.081000	0.00869	-1.067000	0.02272	GAC		0.373	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		A	104999214	C	A	104999214	3	1	61	1	0	0	0	0	1	0	0	0	7683	506	18	2	1270	2	IL1RAPL2	23	104999214	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1731403	104999214	50271346	12185	20170										
NRK	203447	broad.mit.edu	37	chrX	105137871	105137871	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttcggtcactgatgtagtgaGaatgaccagtaatcagagtt	11	6	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105137871G>T	ENST00000243300.9	+	6	728	c.425G>T	c.(424-426)aGa>aTa	p.R142I	NRK_ENST00000536164.1_Missense_Mutation_p.R142I|NRK_ENST00000428173.2_Missense_Mutation_p.R142I	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	142	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R142I(3)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						GATGTAGTGAGAATGACCAGT	0.378										HNSCC(51;0.14)																																						3	Substitution - Missense(3)	large_intestine(2)|upper_aerodigestive_tract(1)	X											135	122	126					X																	105137871		1898	4099	5997	105024527	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.425G>T	X.37:g.105137871G>T	ENSP00000434830:p.Arg142Ile		105024527	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	G	16.40	3.113018	0.56398	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000536164	T;T;T	0.66099	-0.19;-0.19;-0.19	5.65	2.53	0.30540	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000094	T	0.63105	0.2483	L	0.41356	1.27	0.80722	D	1	D	0.58970	0.984	P	0.60541	0.876	T	0.62172	-0.6910	10	0.87932	D	0	.	5.4999	0.16823	0.5144:0.0:0.4856:0.0	.	142	Q7Z2Y5	NRK_HUMAN	I	142	ENSP00000434830:R142I;ENSP00000438378:R142I;ENSP00000438785:R142I	ENSP00000434830:R142I	R	+	2	0	NRK	105024527	1.000000	0.71417	0.978000	0.43139	0.980000	0.70556	6.193000	0.72075	0.553000	0.29044	0.594000	0.82650	AGA		0.378	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105137871	G	T	105137871	3	4	61	1	0	0	0	0	1	0	0	0	10686	942	33	2	447	2	NRK	23	105137871	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	138657	105137871	50132689	12186	20171										
NRK	203447	broad.mit.edu	37	chrX	105167407	105167407	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgtttgtaaagaccatGatgatgacaacaataagttt	8	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105167407G>T	ENST00000243300.9	+	18	3211	c.2908G>T	c.(2908-2910)Gat>Tat	p.D970Y	NRK_ENST00000428173.2_Missense_Mutation_p.D971Y	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	970	Asp-rich.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.D971Y(1)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						taaagaccatgatgatgacaa	0.343										HNSCC(51;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	X											87	76	79					X																	105167407		1747	3700	5447	105054063	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2908G>T	X.37:g.105167407G>T	ENSP00000434830:p.Asp970Tyr		105054063	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	G	5.102	0.204526	0.09704	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.78003	-1.13;-1.14	3.06	1.23	0.21249	.	1.133850	0.06755	N	0.780718	T	0.59676	0.2211	N	0.14661	0.345	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.10450	0.005;0.001	T	0.48186	-0.9057	10	0.48119	T	0.1	.	3.0693	0.06225	0.1519:0.0:0.583:0.2652	.	638;970	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	Y	970;971	ENSP00000434830:D970Y;ENSP00000438378:D971Y	ENSP00000434830:D970Y	D	+	1	0	NRK	105054063	0.003000	0.15002	0.001000	0.08648	0.036000	0.12997	0.921000	0.28718	0.190000	0.20209	0.597000	0.82753	GAT		0.343	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105167407	G	T	105167407	3	4	61	1	0	0	0	0	1	0	0	0	10686	1290	45	2	2978	2	NRK	23	105167407	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	29536	105167407	50103153	12187	20172										
NRK	203447	broad.mit.edu	37	chrX	105189939	105189939	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatacgaatactggcaaaaAtacaggcagctgatccagtg	9	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105189939A>C	ENST00000243300.9	+	25	4438	c.4135A>C	c.(4135-4137)Ata>Cta	p.I1379L	NRK_ENST00000540278.1_5'Flank|NRK_ENST00000428173.2_Missense_Mutation_p.I1380L	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1379	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.I1379L(1)|p.I1380L(1)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ACTGGCAAAAATACAGGCAGC	0.443										HNSCC(51;0.14)																																						2	Substitution - Missense(2)	large_intestine(2)	X											103	89	93					X																	105189939		1885	4111	5996	105076595	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.4135A>C	X.37:g.105189939A>C	ENSP00000434830:p.Ile1379Leu		105076595	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	A	15.85	2.953558	0.53293	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.79845	-1.3;-1.31	4.33	4.33	0.51752	Citron-like (2);	0.000000	0.56097	D	0.000032	T	0.76814	0.4040	N	0.08118	0	0.80722	D	1	D	0.58620	0.983	D	0.73708	0.981	T	0.79029	-0.1970	10	0.59425	D	0.04	.	8.821	0.35025	1.0:0.0:0.0:0.0	.	1379	Q7Z2Y5	NRK_HUMAN	L	1379;1380	ENSP00000434830:I1379L;ENSP00000438378:I1380L	ENSP00000434830:I1379L	I	+	1	0	NRK	105076595	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.608000	0.54109	1.904000	0.55121	0.486000	0.48141	ATA		0.443	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		C	105189939	A	C	105189939	3	2	61	1	0	0	0	0	1	0	0	0	10686	101	4	4	4233	4	NRK	23	105189939	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	22532	105189939	50080621	12188	20173										
SERPINA7	6906	broad.mit.edu	37	chrX	105281011	105281011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagtggattgtagcatgaagCccaagtaccaagagaaccag	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105281011C>T	ENST00000327674.4	-	1	374	c.39G>A	c.(37-39)ggG>ggA	p.G13G	SERPINA7_ENST00000372563.1_Silent_p.G13G|SERPINA7_ENST00000487487.1_5'Flank			P05543	THBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	13					aging (GO:0007568)|negative regulation of endopeptidase activity (GO:0010951)|post-embryonic development (GO:0009791)|regulation of proteolysis (GO:0030162)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to peptide hormone (GO:0043434)|response to prostaglandin E (GO:0034695)|response to vitamin A (GO:0033189)|thyroid hormone transport (GO:0070327)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone binding (GO:0042562)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G13G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|skin(3)	24					Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TAGCATGAAGCCCAAGTACCA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	X											105	92	97					X																	105281011		2203	4300	6503	105167667	SO:0001819	synonymous_variant	6906			M14091	CCDS14518.1	Xq21-q22	2014-02-18	2005-08-18		ENSG00000123561	ENSG00000123561		"Serine (or cysteine) peptidase inhibitors"	11583	protein-coding gene	gene with protein product	"thyroxin-binding globulin", "thyroxine-binding globulin", "alpha-1 antiproteinase, antitrypsin"	314200	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	TBG		24172014	Standard	NM_000354		Approved		uc004eme.2	P05543	OTTHUMG00000022144	ENST00000327674.4:c.39G>A	X.37:g.105281011C>T			105167667	D3DUX1	Silent	SNP	ENST00000327674.4	37	CCDS14518.1																																																																																				0.438	SERPINA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057790.1	NM_000354		T	105281011	C	T	105281011	2	4	61	1	0	0	0	0	0	0	0	1	14131	726	26	3		3	SERPINA7	23	105281011	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	91072	105281011	49989549	12189	20174										
MUM1L1	139221	broad.mit.edu	37	chrX	105449658	105449658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actacagtcagaggacagtgCtccacctacagaggaaactg	10	11	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105449658C>T	ENST00000357175.2	+	4	882	c.233C>T	c.(232-234)gCt>gTt	p.A78V	MUM1L1_ENST00000337685.2_Missense_Mutation_p.A78V|MUM1L1_ENST00000372552.1_Missense_Mutation_p.A78V	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	78						extracellular vesicular exosome (GO:0070062)		p.A78V(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						GAGGACAGTGCTCCACCTACA	0.398																																																2	Substitution - Missense(2)	large_intestine(2)	X											47	40	42					X																	105449658		1920	4117	6037	105336314	SO:0001583	missense	139221			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.233C>T	X.37:g.105449658C>T	ENSP00000349699:p.Ala78Val		105336314	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	C	3.423	-0.117751	0.06838	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.52983	0.64;0.64;0.64	4.71	-9.43	0.00607	.	1.228550	0.05914	N	0.632267	T	0.25644	0.0624	L	0.43923	1.385	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.34079	-0.9843	10	0.02654	T	1	-28.9621	3.7572	0.08589	0.4986:0.1263:0.2835:0.0916	.	78	Q5H9M0	MUML1_HUMAN	V	78	ENSP00000349699:A78V;ENSP00000338641:A78V;ENSP00000361632:A78V	ENSP00000338641:A78V	A	+	2	0	MUM1L1	105336314	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.601000	0.00418	-2.295000	0.00662	0.600000	0.82982	GCT		0.398	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		T	105449658	C	T	105449658	3	4	61	1	0	0	0	0	1	0	0	0	10016	797	28	3	235	3	MUM1L1	23	105449658	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	168647	105449658	49820902	12190	20175										
MUM1L1	139221	broad.mit.edu	37	chrX	105450221	105450221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggatacctgcctagagaccCtggctgttccctctgaatgc	10	13	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105450221C>A	ENST00000357175.2	+	4	1445	c.796C>A	c.(796-798)Ctg>Atg	p.L266M	MUM1L1_ENST00000337685.2_Missense_Mutation_p.L266M|MUM1L1_ENST00000372552.1_Missense_Mutation_p.L266M	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	266						extracellular vesicular exosome (GO:0070062)		p.L266M(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCTAGAGACCCTGGCTGTTCC	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	X											49	43	45					X																	105450221		1882	4102	5984	105336877	SO:0001583	missense	139221			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.796C>A	X.37:g.105450221C>A	ENSP00000349699:p.Leu266Met		105336877	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	C	8.269	0.812940	0.16537	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.24908	1.83;1.83;1.83	4.95	0.734	0.18294	.	1.314640	0.05538	N	0.565225	T	0.21718	0.0523	L	0.53249	1.67	0.09310	N	1	B	0.32101	0.356	B	0.26770	0.073	T	0.24977	-1.0145	10	0.45353	T	0.12	-34.6797	3.3821	0.07259	0.4391:0.3566:0.0:0.2043	.	266	Q5H9M0	MUML1_HUMAN	M	266	ENSP00000349699:L266M;ENSP00000338641:L266M;ENSP00000361632:L266M	ENSP00000338641:L266M	L	+	1	2	MUM1L1	105336877	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.293000	0.08320	0.094000	0.17404	-0.222000	0.12452	CTG		0.463	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		A	105450221	C	A	105450221	3	1	61	1	0	0	0	0	1	0	0	0	10016	680	24	2	798	2	MUM1L1	23	105450221	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	563	105450221	49820339	12191	20176										
CXorf57	55086	broad.mit.edu	37	chrX	105875933	105875933	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtgaaaccagaatggagacTgccaaagctaaatcaccgat	10	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:105875933T>G	ENST00000372548.4	+	4	1167	c.1058T>G	c.(1057-1059)cTg>cGg	p.L353R	CXorf57_ENST00000372544.2_Missense_Mutation_p.L353R	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	353							poly(A) RNA binding (GO:0044822)	p.L353R(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						GAATGGAGACTGCCAAAGCTA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	X											41	41	41					X																	105875933		2201	4297	6498	105762589	SO:0001583	missense	55086			AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1058T>G	X.37:g.105875933T>G	ENSP00000361628:p.Leu353Arg		105762589	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118297	0.56505	.	.	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.61859	0.07;0.07;0.25	4.08	4.08	0.47627	.	0.075648	0.53938	D	0.000044	T	0.71962	0.3402	M	0.66939	2.045	0.36710	D	0.880602	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.79162	-0.1917	10	0.87932	D	0	-7.7931	11.6472	0.51267	0.0:0.0:0.0:1.0	.	353;353;353	A8K6R5;Q6NSI4;Q6NSI4-2	.;CX057_HUMAN;.	R	353;353;161	ENSP00000361623:L353R;ENSP00000361628:L353R;ENSP00000405866:L161R	ENSP00000361623:L353R	L	+	2	0	CXorf57	105762589	1.000000	0.71417	0.992000	0.48379	0.908000	0.53690	4.853000	0.62911	1.579000	0.49836	0.412000	0.27726	CTG		0.318	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015		G	105875933	T	G	105875933	3	3	61	1	0	0	0	0	1	0	0	0	4119	1580	55	4	1072	4	CXorf57	23	105875933	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	425712	105875933	49394627	12192	20177										
TEX13B	56156	broad.mit.edu	37	chrX	107224541	107224541	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatctttctccctctgccccGcaaaggtgtaatttgcctgc	8	14	3	0	rs41300888		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107224541G>A	ENST00000302917.1	-	3	800	c.708C>T	c.(706-708)tgC>tgT	p.C236C		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	236								p.C236C(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						CCTCTGCCCCGCAAAGGTGTA	0.592													G|||	1	0.000264901	0	0	3775	,	,		13852	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											140	128	132					X																	107224541		2198	4300	6498	107111197	SO:0001819	synonymous_variant	56156			AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"testis expressed sequence 13B"			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.708C>T	X.37:g.107224541G>A			107111197	Q5JYF6	Silent	SNP	ENST00000302917.1	37	CCDS14534.1																																																																																				0.592	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057857.1			A	107224541	G	A	107224541	2	1	61	1	0	0	0	0	0	0	0	1	15816	1079	38	1		1	TEX13B	23	107224541	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1348608	107224541	48046019	12193	20178										
VSIG1	340547	broad.mit.edu	37	chrX	107320327	107320327	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaagcgaagcaatgccaagaGaagacgctacccaactagaa	9	10	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107320327G>T	ENST00000217957.5	+	7	997	c.880G>T	c.(880-882)Gaa>Taa	p.E294*	VSIG1_ENST00000415430.3_Nonsense_Mutation_p.E330*	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	294						integral component of membrane (GO:0016021)		p.E330*(1)|p.E294*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						AATGCCAAGAGAAGACGCTAC	0.463																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											106	98	101					X																	107320327		2203	4300	6503	107206983	SO:0001587	stop_gained	340547			BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.880G>T	X.37:g.107320327G>T	ENSP00000217957:p.Glu294*		107206983	C9J4P2|Q6MZS4	Nonsense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.747673	0.69533	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	.	.	.	4.12	3.16	0.36331	.	11.257100	0.00166	N	0.000001	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	8.0985	0.30844	0.0:0.2438:0.7562:0.0	.	.	.	.	X	330;294	.	ENSP00000217957:E294X	E	+	1	0	VSIG1	107206983	0.376000	0.25098	0.003000	0.11579	0.015000	0.08874	2.531000	0.45650	2.016000	0.59253	0.466000	0.42574	GAA		0.463	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607		T	107320327	G	T	107320327	4	4	61	1	0	0	0	0	0	1	0	0	17262	943	33	2	1018	2	VSIG1	23	107320327	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	95786	107320327	47950233	12194	20179										
ATG4A	115201	broad.mit.edu	37	chrX	107369366	107369366	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actacctagaagaatatccaGatacagatgagctggtatgg	10	7	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107369366G>T	ENST00000372232.3	+	2	229	c.70G>T	c.(70-72)Gat>Tat	p.D24Y	ATG4A_ENST00000345734.3_Missense_Mutation_p.D24Y|ATG4A_ENST00000372254.3_Missense_Mutation_p.D24Y|ATG4A_ENST00000545696.1_5'UTR	NM_052936.3	NP_443168.2	Q8WYN0	ATG4A_HUMAN	autophagy related 4A, cysteine peptidase	24					autophagy (GO:0006914)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)	p.D24Y(2)		endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)	11						AGAATATCCAGATACAGATGA	0.368																																																2	Substitution - Missense(2)	large_intestine(2)	X											87	75	79					X																	107369366		2203	4300	6503	107256022	SO:0001583	missense	115201			AJ320508	CCDS14538.1, CCDS14539.1	Xq22.1-q22.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000101844	ENSG00000101844			16489	protein-coding gene	gene with protein product		300663	"AUT-like 2, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog A (S. cerevisiae)", "ATG4 autophagy related 4 homolog A (S. cerevisiae)"	AUTL2, APG4A		12446702, 12473658	Standard	NM_052936		Approved		uc004enr.3	Q8WYN0	OTTHUMG00000022176	ENST00000372232.3:c.70G>T	X.37:g.107369366G>T	ENSP00000361306:p.Asp24Tyr		107256022	A6NCH2|B2RAZ7|D3DUY0|O95534|Q5JYY9|Q5JYZ0|Q86VE5|Q96KQ0|Q96KQ1	Missense_Mutation	SNP	ENST00000372232.3	37	CCDS14538.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.86|19.86	3.905232|3.905232	0.72868|0.72868	.|.	.|.	ENSG00000101844|ENSG00000101844	ENST00000372232;ENST00000345734;ENST00000372254|ENST00000394892	T;T;T|.	0.56103|.	0.89;0.88;0.48|.	5.7|5.7	4.84|4.84	0.62591|0.62591	.|.	0.109676|.	0.64402|.	D|.	0.000017|.	T|T	0.62708|0.62708	0.2450|0.2450	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	B;B|.	0.31949|.	0.348;0.019|.	B;B|.	0.40038|.	0.317;0.017|.	T|T	0.59904|0.59904	-0.7366|-0.7366	10|5	0.52906|.	T|.	0.07|.	-13.1196|-13.1196	12.8694|12.8694	0.57957|0.57957	0.082:0.0:0.918:0.0|0.082:0.0:0.918:0.0	.|.	24;24|.	Q8WYN0-2;Q8WYN0|.	.;ATG4A_HUMAN|.	Y|H	24|20	ENSP00000361306:D24Y;ENSP00000298131:D24Y;ENSP00000361328:D24Y|.	ENSP00000341833:D24Y|.	D|Q	+|+	1|3	0|2	ATG4A|ATG4A	107256022|107256022	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	6.498000|6.498000	0.73679|0.73679	1.165000|1.165000	0.42670|0.42670	-0.190000|-0.190000	0.12839|0.12839	GAT|CAG		0.368	ATG4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057860.1	NM_052936		T	107369366	G	T	107369366	3	4	61	1	0	0	0	0	1	0	0	0	1097	942	33	2	76	2	ATG4A	23	107369366	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	49039	107369366	47901194	12195	20180										
COL4A5	1287	broad.mit.edu	37	chrX	107824241	107824241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggcaaagatggagaaaatgGccaaccaggaattcctgtaa	11	7	0	2	rs104886082		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107824241G>A	ENST00000361603.2	+	16	1164	c.920G>A	c.(919-921)gGc>gAc	p.G307D	COL4A5_ENST00000328300.6_Missense_Mutation_p.G307D	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	307	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.G307D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGAGAAAATGGCCAACCAGGA	0.383									Alport syndrome with Diffuse Leiomyomatosis																																							1	Substitution - Missense(1)	large_intestine(1)	X											119	104	109					X																	107824241		2203	4300	6503	107710897	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.920G>A	X.37:g.107824241G>A	ENSP00000354505:p.Gly307Asp		107710897	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.383177	0.61845	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99532	-6.1;-6.1	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.99819	0.9920	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96661	0.9489	10	0.87932	D	0	.	18.4042	0.90528	0.0:0.0:1.0:0.0	.	307;307	E7EVY4;P29400	.;CO4A5_HUMAN	D	307	ENSP00000331902:G307D;ENSP00000354505:G307D	ENSP00000331902:G307D	G	+	2	0	COL4A5	107710897	1.000000	0.71417	0.999000	0.59377	0.688000	0.40055	6.474000	0.73578	2.286000	0.76751	0.600000	0.82982	GGC		0.383	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107824241	G	A	107824241	3	1	61	1	0	0	0	0	1	0	0	0	3700	1203	42	3	982	3	COL4A5	23	107824241	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	454875	107824241	47446319	12196	20181										
COL4A5	1287	broad.mit.edu	37	chrX	107910364	107910364	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttgttttgtactctgacaggTcaaccaggctttggaaaccc	9	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107910364T>C	ENST00000361603.2	+	40	3799	c.3555T>C	c.(3553-3555)ggT>ggC	p.G1185G	COL4A5_ENST00000328300.6_Splice_Site_p.G1185G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1185	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.G1185G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CTCTGACAGGTCAACCAGGCT	0.343									Alport syndrome with Diffuse Leiomyomatosis																																							1	Substitution - coding silent(1)	large_intestine(1)	X											66	69	68					X																	107910364		2203	4300	6503	107797020	SO:0001630	splice_region_variant	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.3554-1T>C	X.37:g.107910364T>C			107797020	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1																																																																																				0.343	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		Silent	C	107910364	T	C	107910364	5	2	61	1	0	0	0	0	0	0	1	0	3700	1681	58	4	3713	4	COL4A5	23	107910364	Splice_Site	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	86123	107910364	47360196	12197	20182										
COL4A5	1287	broad.mit.edu	37	chrX	107938088	107938088	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atcgcagttcacagtcagacGatccagattccccattgtcc	7	14	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107938088G>A	ENST00000361603.2	+	49	4984	c.4740G>A	c.(4738-4740)acG>acA	p.T1580T	COL4A5_ENST00000328300.6_Silent_p.T1586T	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1580	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.T1580T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						ACAGTCAGACGATCCAGATTC	0.443									Alport syndrome with Diffuse Leiomyomatosis																																							1	Substitution - coding silent(1)	large_intestine(1)	X											342	228	267					X																	107938088		2203	4300	6503	107824744	SO:0001819	synonymous_variant	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4740G>A	X.37:g.107938088G>A			107824744	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1																																																																																				0.443	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107938088	G	A	107938088	2	1	61	1	0	0	0	0	0	0	0	1	3700	1045	37	1		1	COL4A5	23	107938088	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	27724	107938088	47332472	12198	20183										
IRS4	8471	broad.mit.edu	37	chrX	107977570	107977570	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atctttcacttctttggcttCtttgcattctttcgtggctc	6	11	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107977570C>A	ENST00000372129.2	-	1	2081	c.2005G>T	c.(2005-2007)Gaa>Taa	p.E669*	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	669					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.E669*(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TCTTTGGCTTCTTTGCATTCT	0.507																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											276	277	277					X																	107977570		2203	4300	6503	107864226	SO:0001587	stop_gained	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2005G>T	X.37:g.107977570C>A	ENSP00000361202:p.Glu669*		107864226		Nonsense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470291	0.84533	.	.	ENSG00000133124	ENST00000372129	.	.	.	4.9	4.9	0.64082	.	0.486350	0.19522	N	0.112247	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-7.1869	11.6749	0.51424	0.0:0.9137:0.0:0.0863	.	.	.	.	X	669	.	ENSP00000361202:E669X	E	-	1	0	IRS4	107864226	1.000000	0.71417	0.998000	0.56505	0.129000	0.20672	4.078000	0.57606	2.257000	0.74773	0.600000	0.82982	GAA		0.507	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107977570	C	A	107977570	4	1	61	1	0	0	0	0	0	1	0	0	7863	922	32	2	1772	2	IRS4	23	107977570	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	39482	107977570	47292990	12199	20184										
IRS4	8471	broad.mit.edu	37	chrX	107977986	107977986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catttgagccctgaccacctCgggatccctgtccctcgcct	8	18	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107977986C>T	ENST00000372129.2	-	1	1665	c.1589G>A	c.(1588-1590)cGa>cAa	p.R530Q	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	530					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.R530Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTGACCACCTCGGGATCCCTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	X											139	139	139					X																	107977986		2203	4300	6503	107864642	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1589G>A	X.37:g.107977986C>T	ENSP00000361202:p.Arg530Gln		107864642		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	8.479	0.859443	0.17178	.	.	ENSG00000133124	ENST00000372129	T	0.34859	1.34	4.01	3.13	0.36017	.	0.811623	0.10552	N	0.661316	T	0.17280	0.0415	N	0.08118	0	0.18873	N	0.999982	B	0.33044	0.395	B	0.21360	0.034	T	0.09975	-1.0650	10	0.52906	T	0.07	-0.3908	8.5711	0.33569	0.0:0.7698:0.2302:0.0	.	530	O14654	IRS4_HUMAN	Q	530	ENSP00000361202:R530Q	ENSP00000361202:R530Q	R	-	2	0	IRS4	107864642	0.001000	0.12720	0.216000	0.23742	0.122000	0.20287	0.194000	0.17135	1.022000	0.39626	0.600000	0.82982	CGA		0.632	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107977986	C	T	107977986	3	4	61	1	0	0	0	0	1	0	0	0	7863	884	31	1	2188	1	IRS4	23	107977986	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	416	107977986	47292574	12200	20185										
IRS4	8471	broad.mit.edu	37	chrX	107978275	107978275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgggctgggtgctaagcggcGaaaaaagctggccggcactg	17	9	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107978275G>A	ENST00000372129.2	-	1	1376	c.1300C>T	c.(1300-1302)Cgc>Tgc	p.R434C	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	434					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.R434C(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GCTAAGCGGCGAAAAAAGCTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	X											62	54	57					X																	107978275		2203	4300	6503	107864931	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1300C>T	X.37:g.107978275G>A	ENSP00000361202:p.Arg434Cys		107864931		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	G	9.918	1.211337	0.22289	.	.	ENSG00000133124	ENST00000372129	T	0.40476	1.03	4.59	4.59	0.56863	.	0.662691	0.13958	N	0.351073	T	0.42494	0.1205	L	0.32530	0.975	0.19300	N	0.999979	D	0.67145	0.996	P	0.47528	0.549	T	0.38950	-0.9637	10	0.62326	D	0.03	-8.6902	17.0086	0.86400	0.0:0.0:1.0:0.0	.	434	O14654	IRS4_HUMAN	C	434	ENSP00000361202:R434C	ENSP00000361202:R434C	R	-	1	0	IRS4	107864931	0.439000	0.25610	0.006000	0.13384	0.003000	0.03518	3.824000	0.55723	2.281000	0.76405	0.596000	0.82720	CGC		0.632	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107978275	G	A	107978275	3	1	61	1	0	0	0	0	1	0	0	0	7863	1058	37	1	2477	1	IRS4	23	107978275	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	289	107978275	47292285	12201	20186										
IRS4	8471	broad.mit.edu	37	chrX	107978378	107978378	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaggctcgctgggtgttacGaagcgcctggtgaaaagcat	14	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:107978378G>A	ENST00000372129.2	-	1	1273	c.1197C>T	c.(1195-1197)ttC>ttT	p.F399F	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	399					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.F399F(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TGGGTGTTACGAAGCGCCTGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	X											54	47	50					X																	107978378		2203	4300	6503	107865034	SO:0001819	synonymous_variant	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1197C>T	X.37:g.107978378G>A			107865034		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																				0.632	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107978378	G	A	107978378	2	1	61	1	0	0	0	0	0	0	0	1	7863	1049	37	1		1	IRS4	23	107978378	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	103	107978378	47292182	12202	20187										
GUCY2F	2986	broad.mit.edu	37	chrX	108638580	108638580	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagtccttacctggttaaatAtttcatcaaaagttggtcgt	8	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:108638580A>T	ENST00000218006.2	-	12	2705	c.2414T>A	c.(2413-2415)aTa>aAa	p.I805K		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	805	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.I805K(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						CTGGTTAAATATTTCATCAAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											152	123	133					X																	108638580		2203	4300	6503	108525236	SO:0001583	missense	2986			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.2414T>A	X.37:g.108638580A>T	ENSP00000218006:p.Ile805Lys		108525236	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592516	0.66219	.	.	ENSG00000101890	ENST00000218006	D	0.85339	-1.97	4.14	2.97	0.34412	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.147943	0.56097	D	0.000024	D	0.93628	0.7965	H	0.96861	3.895	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	D	0.92253	0.5810	10	0.87932	D	0	.	7.1365	0.25531	0.8884:0.0:0.1116:0.0	.	805	P51841	GUC2F_HUMAN	K	805	ENSP00000218006:I805K	ENSP00000218006:I805K	I	-	2	0	GUCY2F	108525236	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.666000	0.74446	0.727000	0.32360	0.412000	0.27726	ATA		0.488	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108638580	A	T	108638580	3	4	61	1	0	0	0	0	1	0	0	0	6919	449	16	5	944	5	GUCY2F	23	108638580	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	660202	108638580	46631980	12203	20188										
RGAG1	57529	broad.mit.edu	37	chrX	109693871	109693871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatacccttacattcactgcGattcaacaatacaatgaggg	6	10	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109693871G>A	ENST00000465301.2	+	3	272	c.26G>A	c.(25-27)cGa>cAa	p.R9Q	RGAG1_ENST00000540313.1_Missense_Mutation_p.R9Q	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	9								p.R9Q(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CATTCACTGCGATTCAACAAT	0.453											OREG0019909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	X											166	153	158					X																	109693871		2203	4300	6503	109580527	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.26G>A	X.37:g.109693871G>A	ENSP00000419786:p.Arg9Gln	1421	109580527	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.707007	0.00719	.	.	ENSG00000243978	ENST00000520821;ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.48836	0.8;0.8	4.16	-5.69	0.02428	.	1.785780	0.03625	N	0.236953	T	0.25044	0.0608	N	0.08118	0	0.09310	N	1	B	0.17268	0.021	B	0.10450	0.005	T	0.21552	-1.0242	9	.	.	.	0.4227	9.6297	0.39772	0.696:0.1203:0.1837:0.0	.	9	Q8NET4	RGAG1_HUMAN	Q	9	ENSP00000419786:R9Q;ENSP00000441452:R9Q	.	R	+	2	0	RGAG1	109580527	0.366000	0.25014	0.000000	0.03702	0.000000	0.00434	-0.478000	0.06575	-1.989000	0.00979	-0.909000	0.02823	CGA		0.453	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109693871	G	A	109693871	3	1	61	1	0	0	0	0	1	0	0	0	13311	1058	37	1	28	1	RGAG1	23	109693871	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1055291	109693871	45576689	12204	20189										
RGAG1	57529	broad.mit.edu	37	chrX	109693932	109693932	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacaagcagatggccttctgTagaccaatgacagagaccag	10	10	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109693932T>C	ENST00000465301.2	+	3	333	c.87T>C	c.(85-87)tgT>tgC	p.C29C	RGAG1_ENST00000540313.1_Silent_p.C29C	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	29								p.C29C(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						TGGCCTTCTGTAGACCAATGA	0.468											OREG0019909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	X											208	180	190					X																	109693932		2203	4300	6503	109580588	SO:0001819	synonymous_variant	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.87T>C	X.37:g.109693932T>C		1421	109580588	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																				0.468	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		C	109693932	T	C	109693932	2	2	61	1	0	0	0	0	0	0	0	1	13311	1644	57	4		4	RGAG1	23	109693932	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	61	109693932	45576628	12205	20190										
RGAG1	57529	broad.mit.edu	37	chrX	109694869	109694869	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattaccaaagccagctccaGatgctgaagcaatgtcccca	7	14	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109694869G>T	ENST00000465301.2	+	3	1270	c.1024G>T	c.(1024-1026)Gat>Tat	p.D342Y	RGAG1_ENST00000540313.1_Missense_Mutation_p.D342Y	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	342								p.D342Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						GCCAGCTCCAGATGCTGAAGC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	X											240	224	229					X																	109694869		2203	4300	6503	109581525	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1024G>T	X.37:g.109694869G>T	ENSP00000419786:p.Asp342Tyr		109581525	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894427	0.52121	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.55413	0.52;0.52	4.42	1.74	0.24563	.	0.387744	0.18799	N	0.130840	T	0.51261	0.1664	L	0.29908	0.895	0.09310	N	1	D	0.71674	0.998	D	0.63192	0.912	T	0.34900	-0.9810	9	.	.	.	-2.1781	6.274	0.20971	0.4329:0.0:0.5671:0.0	.	342	Q8NET4	RGAG1_HUMAN	Y	342	ENSP00000419786:D342Y;ENSP00000441452:D342Y	.	D	+	1	0	RGAG1	109581525	0.001000	0.12720	0.001000	0.08648	0.527000	0.34593	0.879000	0.28146	0.234000	0.21139	-0.190000	0.12839	GAT		0.547	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109694869	G	T	109694869	3	4	61	1	0	0	0	0	1	0	0	0	13311	942	33	2	1026	2	RGAG1	23	109694869	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	937	109694869	45575691	12206	20191										
RGAG1	57529	broad.mit.edu	37	chrX	109696765	109696765	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtcagccatggcttctggaGagatgtctatgccgctaatg	12	9	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109696765G>T	ENST00000465301.2	+	3	3166	c.2920G>T	c.(2920-2922)Gag>Tag	p.E974*	RGAG1_ENST00000540313.1_Nonsense_Mutation_p.E974*	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	974								p.E974*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						GGCTTCTGGAGAGATGTCTAT	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											145	136	139					X																	109696765		2203	4300	6503	109583421	SO:0001587	stop_gained	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2920G>T	X.37:g.109696765G>T	ENSP00000419786:p.Glu974*		109583421	Q9P2M8	Nonsense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	36	5.626739	0.96671	.	.	ENSG00000243978	ENST00000465301;ENST00000540313	.	.	.	3.89	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3015	8.6038	0.33760	0.0:0.2303:0.7697:0.0	.	.	.	.	X	974	.	.	E	+	1	0	RGAG1	109583421	1.000000	0.71417	0.978000	0.43139	0.022000	0.10575	4.681000	0.61663	2.174000	0.68829	0.600000	0.82982	GAG		0.502	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109696765	G	T	109696765	4	4	61	1	0	0	0	0	0	1	0	0	13311	943	33	2	2922	2	RGAG1	23	109696765	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1896	109696765	45573795	12207	20192										
RGAG1	57529	broad.mit.edu	37	chrX	109697344	109697344	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctcatgctctgtggaggaaGagatggagattgatgaggag	17	4	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109697344G>T	ENST00000465301.2	+	3	3745	c.3499G>T	c.(3499-3501)Gag>Tag	p.E1167*	RGAG1_ENST00000540313.1_Nonsense_Mutation_p.E1167*	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1167								p.E1167*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						TGTGGAGGAAGAGATGGAGAT	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											100	93	96					X																	109697344		2203	4300	6503	109584000	SO:0001587	stop_gained	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3499G>T	X.37:g.109697344G>T	ENSP00000419786:p.Glu1167*		109584000	Q9P2M8	Nonsense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	40	8.343758	0.98769	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	.	.	.	4.02	4.02	0.46733	.	0.000000	0.37483	N	0.002070	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.8423	10.5265	0.44952	0.0:0.0:1.0:0.0	.	.	.	.	X	1167;1167;728	.	.	E	+	1	0	RGAG1	109584000	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	1.606000	0.36826	2.243000	0.73865	0.600000	0.82982	GAG		0.512	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109697344	G	T	109697344	4	4	61	1	0	0	0	0	0	1	0	0	13311	943	33	2	3501	2	RGAG1	23	109697344	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	579	109697344	45573216	12208	20193										
RGAG1	57529	broad.mit.edu	37	chrX	109697507	109697507	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaataaatctttcctgagaaGatcccagggcatatatgact	7	8	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109697507G>A	ENST00000465301.2	+	3	3908	c.3662G>A	c.(3661-3663)aGa>aAa	p.R1221K	RGAG1_ENST00000540313.1_Missense_Mutation_p.R1221K	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1221								p.R1221K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						TTCCTGAGAAGATCCCAGGGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	103	105					X																	109697507		2203	4300	6503	109584163	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3662G>A	X.37:g.109697507G>A	ENSP00000419786:p.Arg1221Lys		109584163	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427677	0.25726	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.42131	0.98;0.98	4.26	4.26	0.50523	.	0.000000	0.45361	D	0.000379	T	0.45276	0.1334	N	0.19112	0.55	0.20873	N	0.999835	D	0.76494	0.999	D	0.80764	0.994	T	0.23619	-1.0183	9	.	.	.	-20.326	10.9798	0.47488	0.0:0.0:1.0:0.0	.	1221	Q8NET4	RGAG1_HUMAN	K	1221;1221;782	ENSP00000419786:R1221K;ENSP00000441452:R1221K	.	R	+	2	0	RGAG1	109584163	0.998000	0.40836	0.484000	0.27391	0.911000	0.54048	2.399000	0.44495	2.356000	0.79943	0.600000	0.82982	AGA		0.463	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109697507	G	A	109697507	3	1	61	1	0	0	0	0	1	0	0	0	13311	942	33	3	3664	3	RGAG1	23	109697507	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	163	109697507	45573053	12209	20194										
CHRDL1	91851	broad.mit.edu	37	chrX	109931907	109931907	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggtatcgattggggcagtgGattttcttacactcttgctt	12	7	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:109931907G>A	ENST00000372045.1	-	9	1013	c.882C>T	c.(880-882)atC>atT	p.I294I	CHRDL1_ENST00000444321.2_Silent_p.I300I|CHRDL1_ENST00000218054.4_Silent_p.I300I|CHRDL1_ENST00000372042.1_Silent_p.I301I|CHRDL1_ENST00000434224.1_Silent_p.I221I|CHRDL1_ENST00000394797.4_Silent_p.I300I|CHRDL1_ENST00000482160.1_Silent_p.I221I			Q9BU40	CRDL1_HUMAN	chordin-like 1	294	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.I300I(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						TGGGGCAGTGGATTTTCTTAC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											193	176	182					X																	109931907		2203	4300	6503	109818563	SO:0001819	synonymous_variant	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.882C>T	X.37:g.109931907G>A			109818563	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Silent	SNP	ENST00000372045.1	37																																																																																					0.473	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		A	109931907	G	A	109931907	2	1	61	1	0	0	0	0	0	0	0	1	3379	1164	41	3		3	CHRDL1	23	109931907	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	234400	109931907	45338653	12210	20195										
CHRDL1	91851	broad.mit.edu	37	chrX	110035400	110035400	+	5'UTR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catgcctcccattttccactTttttctcatttggaccactg	4	14	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:110035400T>G	ENST00000372045.1	-	0	123				CHRDL1_ENST00000444321.2_Missense_Mutation_p.K4Q|CHRDL1_ENST00000218054.4_Missense_Mutation_p.K4Q|CHRDL1_ENST00000372042.1_Missense_Mutation_p.K4Q|CHRDL1_ENST00000434224.1_Missense_Mutation_p.K4Q|CHRDL1_ENST00000394797.4_Missense_Mutation_p.K4Q|CHRDL1_ENST00000482160.1_Missense_Mutation_p.K4Q			Q9BU40	CRDL1_HUMAN	chordin-like 1						BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.K4Q(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						ATTTTCCACTTTTTTCTCATT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	X											88	73	78					X																	110035400		2203	4300	6503	109922056	SO:0001623	5_prime_UTR_variant	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.-9A>C	X.37:g.110035400T>G			109922056	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Missense_Mutation	SNP	ENST00000372045.1	37		.	.	.	.	.	.	.	.	.	.	T	10.92	1.486897	0.26686	.	.	ENSG00000101938	ENST00000434224;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000482160;ENST00000444321	T;T;T;T;T;T	0.32988	1.43;2.18;2.18;2.45;1.43;2.18	5.19	2.53	0.30540	.	0.740498	0.13784	N	0.363030	T	0.16896	0.0406	N	0.19112	0.55	0.29198	N	0.875426	B;B;P	0.49185	0.019;0.019;0.92	B;B;B	0.40901	0.011;0.011;0.343	T	0.06092	-1.0846	9	.	.	.	-3.0497	5.4898	0.16769	0.0:0.0962:0.171:0.7328	.	4;4;4	E9PGS5;D3DUY6;D3YTA8	.;.;.	Q	4	ENSP00000389627:K4Q;ENSP00000218054:K4Q;ENSP00000378276:K4Q;ENSP00000361112:K4Q;ENSP00000418443:K4Q;ENSP00000399739:K4Q	.	K	-	1	0	CHRDL1	109922056	1.000000	0.71417	0.992000	0.48379	0.818000	0.46254	1.806000	0.38892	0.806000	0.34183	0.481000	0.45027	AAG		0.388	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		G	110035400	T	G	110035400	1	3	61	0	1	0	0	0	0	0	0	0	3379	1850	64	4		4	CHRDL1	23	110035400	5'UTR	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	103493	110035400	45235160	12211	20196										
PAK3	5063	broad.mit.edu	37	chrX	110439116	110439116	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcaaaccaggtgatccataGagatataaagagtgacaata	8	7	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:110439116G>A	ENST00000372010.1	+	16	1644	c.1202G>A	c.(1201-1203)aGa>aAa	p.R401K	PAK3_ENST00000360648.4_Missense_Mutation_p.R422K|PAK3_ENST00000519681.1_Missense_Mutation_p.R407K|PAK3_ENST00000372007.5_Missense_Mutation_p.R386K|PAK3_ENST00000262836.4_Missense_Mutation_p.R401K|PAK3_ENST00000417227.1_Missense_Mutation_p.R407K|PAK3_ENST00000425146.1_Missense_Mutation_p.R386K|PAK3_ENST00000446737.1_Missense_Mutation_p.R386K|PAK3_ENST00000518291.1_Missense_Mutation_p.R422K			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	401	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R386K(1)		breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						GTGATCCATAGAGATATAAAG	0.338										TSP Lung(19;0.15)																																						1	Substitution - Missense(1)	large_intestine(1)	X											127	125	126					X																	110439116		2203	4300	6503	110325772	SO:0001583	missense	5063			AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1202G>A	X.37:g.110439116G>A	ENSP00000361080:p.Arg401Lys		110325772	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	37	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	34	5.292768	0.95546	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	H	0.94925	3.6	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;0.999;1.0;0.999	T	0.78768	-0.2075	10	0.87932	D	0	.	18.5792	0.91165	0.0:0.0:1.0:0.0	.	407;422;401;386;401	O75914-4;O75914-3;O75914;O75914-2;B1GX77	.;.;PAK3_HUMAN;.;.	K	386;386;401;407;386;422;422;407;401	ENSP00000410853:R386K;ENSP00000401982:R386K;ENSP00000361080:R401K;ENSP00000429113:R407K;ENSP00000361077:R386K;ENSP00000428921:R422K;ENSP00000353864:R422K;ENSP00000389172:R407K;ENSP00000262836:R401K	ENSP00000262836:R401K	R	+	2	0	PAK3	110325772	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.281000	0.95811	2.417000	0.82017	0.594000	0.82650	AGA		0.338	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110439116	G	A	110439116	3	1	61	1	0	0	0	0	1	0	0	0	11433	942	33	3	1315	3	PAK3	23	110439116	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	403716	110439116	44831444	12212	20197										
DCX	1641	broad.mit.edu	37	chrX	110653358	110653358	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggttgatgttgtcagacagaGatcgcgtcaggtcagccagc	14	9	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:110653358G>T	ENST00000338081.3	-	2	683	c.512C>A	c.(511-513)tCt>tAt	p.S171Y	DCX_ENST00000356915.2_Missense_Mutation_p.S90Y|DCX_ENST00000488120.1_Missense_Mutation_p.S90Y|DCX_ENST00000371993.2_Missense_Mutation_p.S90Y|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000356220.3_Missense_Mutation_p.S90Y	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	171	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)	p.S171Y(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						GTCAGACAGAGATCGCGTCAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											227	169	189					X																	110653358		2203	4300	6503	110540014	SO:0001583	missense	1641			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.512C>A	X.37:g.110653358G>T	ENSP00000337697:p.Ser171Tyr		110540014	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	37	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.2|25.2	4.612915|4.612915	0.87258|0.87258	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000358070|ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120;ENST00000468911	.|D;D;D;D;D;D	.|0.93426	.|-2.15;-2.15;-2.15;-2.15;-2.15;-3.22	5.5|5.5	5.5|5.5	0.81552|0.81552	.|Doublecortin domain (5);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96442|0.96442	0.8839|0.8839	M|M	0.76002|0.76002	2.32|2.32	0.80722|0.80722	D|D	1|1	.|P;D	.|0.69078	.|0.593;0.997	.|P;D	.|0.78314	.|0.694;0.991	D|D	0.95807|0.95807	0.8838|0.8838	5|10	.|0.42905	.|T	.|0.14	.|.	18.4403|18.4403	0.90664|0.90664	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|159;171	.|B4DM53;O43602	.|.;DCX_HUMAN	I|Y	163|90;90;171;90;90;90	.|ENSP00000349385:S90Y;ENSP00000361061:S90Y;ENSP00000337697:S171Y;ENSP00000348553:S90Y;ENSP00000419861:S90Y;ENSP00000418811:S90Y	.|ENSP00000337697:S171Y	L|S	-|-	1|2	0|0	DCX|DCX	110540014|110540014	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.657000|9.657000	0.98554|0.98554	2.551000|2.551000	0.86045|0.86045	0.600000|0.600000	0.82982|0.82982	CTC|TCT		0.517	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		T	110653358	G	T	110653358	3	4	61	1	0	0	0	0	1	0	0	0	4324	942	33	2	852	2	DCX	23	110653358	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	214242	110653358	44617202	12213	20198										
DCX	1641	broad.mit.edu	37	chrX	110653451	110653451	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgaagtagcggtccccattgCggtagaaacgtaccttcttg	11	10	1	2	rs122457137		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:110653451C>T	ENST00000338081.3	-	2	590	c.419G>A	c.(418-420)cGc>cAc	p.R140H	DCX_ENST00000356915.2_Missense_Mutation_p.R59H|DCX_ENST00000488120.1_Missense_Mutation_p.R59H|DCX_ENST00000371993.2_Missense_Mutation_p.R59H|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000356220.3_Missense_Mutation_p.R59H	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	140	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.		R -> H (in SBHX). {ECO:0000269|PubMed:11175293}.|R -> L (in LISX1 and SBHX). {ECO:0000269|PubMed:9489700}.		axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)	p.R140H(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						GTCCCCATTGCGGTAGAAACG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CM010014	DCX	M	rs122457137						310	225	254					X																	110653451		2203	4300	6503	110540107	SO:0001583	missense	1641			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.419G>A	X.37:g.110653451C>T	ENSP00000337697:p.Arg140His		110540107	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	37	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.1|29.1	4.979578|4.979578	0.92982|0.92982	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000358070|ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120;ENST00000468911	.|D;D;D;D;D;D	.|0.94793	.|-2.46;-2.46;-2.46;-2.46;-2.46;-3.52	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Doublecortin domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.98021|0.98021	0.9348|0.9348	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.81914	.|0.974;0.995	D|D	0.98991|0.98991	1.0808|1.0808	5|10	.|0.72032	.|D	.|0.01	.|.	18.1845|18.1845	0.89789|0.89789	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|128;140	.|B4DM53;O43602	.|.;DCX_HUMAN	T|H	132|59;59;140;59;59;59	.|ENSP00000349385:R59H;ENSP00000361061:R59H;ENSP00000337697:R140H;ENSP00000348553:R59H;ENSP00000419861:R59H;ENSP00000418811:R59H	.|ENSP00000337697:R140H	A|R	-|-	1|2	0|0	DCX|DCX	110540107|110540107	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.651000|7.651000	0.83577|0.83577	2.487000|2.487000	0.83934|0.83934	0.513000|0.513000	0.50165|0.50165	GCA|CGC		0.542	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		T	110653451	C	T	110653451	3	4	61	1	0	0	0	0	1	0	0	0	4324	768	27	1	945	1	DCX	23	110653451	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	93	110653451	44617109	12214	20199										
ZCCHC16	340595	broad.mit.edu	37	chrX	111698217	111698217	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttgacagctctccaaatCtctaatcctgcaaatgatgc	5	12	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:111698217C>A	ENST00000340433.2	+	1	491	c.261C>A	c.(259-261)atC>atA	p.I87I		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	87							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.I87I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						CTCTCCAAATCTCTAATCCTG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	X											121	98	106					X																	111698217		2203	4300	6503	111584873	SO:0001819	synonymous_variant	340595			AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"Zinc fingers, CCHC domain containing"	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.261C>A	X.37:g.111698217C>A			111584873	B2RPG1	Silent	SNP	ENST00000340433.2	37	CCDS35369.1																																																																																				0.448	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308		A	111698217	C	A	111698217	2	1	61	1	0	0	0	0	0	0	0	1	17623	903	32	2		2	ZCCHC16	23	111698217	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1044766	111698217	43572343	12215	20200										
HTR2C	3358	broad.mit.edu	37	chrX	113965950	113965950	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaattacttcttaatgtccCtagccattgctgatatgcta	5	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:113965950C>A	ENST00000276198.1	+	4	1011	c.283C>A	c.(283-285)Cta>Ata	p.L95I	HTR2C_ENST00000371950.3_Missense_Mutation_p.L95I|HTR2C_ENST00000371951.1_Missense_Mutation_p.L95I	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	95					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.L95I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CTTAATGTCCCTAGCCATTGC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											209	163	179					X																	113965950		2203	4300	6503	113872206	SO:0001583	missense	3358				CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5295	protein-coding gene	gene with protein product		312861	"5-hydroxytryptamine (serotonin) receptor 2C"	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.283C>A	X.37:g.113965950C>A	ENSP00000276198:p.Leu95Ile		113872206	B1AMW4|Q5VUF8|Q9NP28	Missense_Mutation	SNP	ENST00000276198.1	37	CCDS14564.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.186543	0.78789	.	.	ENSG00000147246	ENST00000276198;ENST00000371951;ENST00000371950	D;D;D	0.91124	-2.79;-2.79;-2.79	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	D	0.97508	0.9184	H	0.99182	4.46	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.98908	1.0779	10	0.87932	D	0	.	15.3884	0.74723	0.0:1.0:0.0:0.0	.	95;95	B1AMW4;P28335	.;5HT2C_HUMAN	I	95	ENSP00000276198:L95I;ENSP00000361019:L95I;ENSP00000361018:L95I	ENSP00000276198:L95I	L	+	1	2	HTR2C	113872206	0.992000	0.36948	1.000000	0.80357	0.929000	0.56500	2.987000	0.49378	2.520000	0.84964	0.594000	0.82650	CTA		0.403	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868		A	113965950	C	A	113965950	3	1	61	1	0	0	0	0	1	0	0	0	7464	680	24	2	289	2	HTR2C	23	113965950	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2267733	113965950	41304610	12216	20201										
HTR2C	3358	broad.mit.edu	37	chrX	114141428	114141428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaatacggccgaggaagagaActctgcaaaccctaaccaag	10	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:114141428A>G	ENST00000276198.1	+	6	1555	c.827A>G	c.(826-828)aAc>aGc	p.N276S	HTR2C_ENST00000371950.3_Silent_p.E244E|HTR2C_ENST00000371951.1_Missense_Mutation_p.N276S	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	276					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.N276S(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GAGGAAGAGAACTCTGCAAAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											137	130	132					X																	114141428		2203	4300	6503	114047684	SO:0001583	missense	3358				CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5295	protein-coding gene	gene with protein product		312861	"5-hydroxytryptamine (serotonin) receptor 2C"	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.827A>G	X.37:g.114141428A>G	ENSP00000276198:p.Asn276Ser		114047684	B1AMW4|Q5VUF8|Q9NP28	Missense_Mutation	SNP	ENST00000276198.1	37	CCDS14564.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.263726	0.00262	.	.	ENSG00000147246	ENST00000276198;ENST00000371951	T;T	0.57436	0.4;0.4	4.51	0.419	0.16438	GPCR, rhodopsin-like superfamily (1);	1.061680	0.07225	N	0.861537	T	0.21962	0.0529	N	0.04820	-0.15	0.21105	N	0.999788	B	0.14012	0.009	B	0.14023	0.01	T	0.24404	-1.0161	10	0.05620	T	0.96	.	0.611	0.00761	0.4087:0.1731:0.1114:0.3068	.	276	P28335	5HT2C_HUMAN	S	276	ENSP00000276198:N276S;ENSP00000361019:N276S	ENSP00000276198:N276S	N	+	2	0	HTR2C	114047684	0.102000	0.21896	0.055000	0.19348	0.212000	0.24457	0.911000	0.28584	0.205000	0.20568	0.381000	0.24937	AAC		0.517	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868		G	114141428	A	G	114141428	3	3	61	1	0	0	0	0	1	0	0	0	7464	43	2	4	841	4	HTR2C	23	114141428	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	175478	114141428	41129132	12217	20202										
IL13RA2	3598	broad.mit.edu	37	chrX	114239865	114239865	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaacgtagcaaagttttcttCgataggtcttcacctaggat	8	8	3	0	rs368591186		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:114239865C>T	ENST00000371936.1	-	10	1260	c.1011G>A	c.(1009-1011)tcG>tcA	p.S337S	IL13RA2_ENST00000243213.1_Silent_p.S337S			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	337					cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)	p.S337S(2)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						AAGTTTTCTTCGATAGGTCTT	0.353																																																2	Substitution - coding silent(2)	large_intestine(2)	X						C		0,3835		0,0,1632,571	68	65	66		1011	3.8	0	X		66	1,6727		0,1,2427,1872	no	coding-synonymous	IL13RA2	NM_000640.2		0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095		337/381	114239865	1,10562	2203	4300	6503	114146121	SO:0001819	synonymous_variant	3598			X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.1011G>A	X.37:g.114239865C>T			114146121	A8K7E2|O00667	Silent	SNP	ENST00000371936.1	37	CCDS14565.1																																																																																				0.353	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		T	114239865	C	T	114239865	2	4	61	1	0	0	0	0	0	0	0	1	7651	871	31	1		1	IL13RA2	23	114239865	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	98437	114239865	41030695	12218	20203										
IL13RA2	3598	broad.mit.edu	37	chrX	114251824	114251824	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catccgatagccaagcaaacGaaagccatttctccgagatt	7	12	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:114251824G>A	ENST00000371936.1	-	3	258	c.9C>T	c.(7-9)ttC>ttT	p.F3F	IL13RA2_ENST00000468224.1_5'UTR|IL13RA2_ENST00000243213.1_Silent_p.F3F			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	3					cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)	p.F3F(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						CCAAGCAAACGAAAGCCATTT	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	X											88	76	80					X																	114251824		2203	4300	6503	114158080	SO:0001819	synonymous_variant	3598			X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.9C>T	X.37:g.114251824G>A			114158080	A8K7E2|O00667	Silent	SNP	ENST00000371936.1	37	CCDS14565.1																																																																																				0.328	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		A	114251824	G	A	114251824	2	1	61	1	0	0	0	0	0	0	0	1	7651	1049	37	1		1	IL13RA2	23	114251824	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	11959	114251824	41018736	12219	20204										
PLS3	5358	broad.mit.edu	37	chrX	114864191	114864191	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actggataaacaaagctttgGaaaatgatcctgattgtaga	9	5	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:114864191G>T	ENST00000420625.2	+	5	546	c.412G>T	c.(412-414)Gaa>Taa	p.E138*	PLS3_ENST00000539310.1_Nonsense_Mutation_p.E93*|PLS3_ENST00000355899.3_Nonsense_Mutation_p.E138*|PLS3_ENST00000289290.3_Nonsense_Mutation_p.E93*|PLS3_ENST00000537301.1_Nonsense_Mutation_p.E116*	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	138	Actin-binding 1.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.E138*(1)		NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						CAAAGCTTTGGAAAATGATCC	0.313																																					Colon(160;1047 1864 8490 12969 29601)											1	Substitution - Nonsense(1)	large_intestine(1)	X											195	181	186					X																	114864191		2203	4300	6503	114770447	SO:0001587	stop_gained	5358			L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.412G>T	X.37:g.114864191G>T	ENSP00000398945:p.Glu138*		114770447	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Nonsense_Mutation	SNP	ENST00000420625.2	37	CCDS14568.1	.	.	.	.	.	.	.	.	.	.	G	37	6.381021	0.97520	.	.	ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-4.8889	16.8052	0.85625	0.0:0.0:1.0:0.0	.	.	.	.	X	138;116;93;138;93	.	ENSP00000289290:E93X	E	+	1	0	PLS3	114770447	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.279000	0.76181	0.600000	0.82982	GAA		0.313	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			T	114864191	G	T	114864191	4	4	61	1	0	0	0	0	0	1	0	0	12139	1175	41	2	426	2	PLS3	23	114864191	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	612367	114864191	40406369	12220	20205										
AGTR2	186	broad.mit.edu	37	chrX	115303593	115303593	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attaccagcggtcttcacttCgggcttgtgaacatctctgg	10	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:115303593C>T	ENST00000371906.4	+	3	250	c.60C>T	c.(58-60)ttC>ttT	p.F20F		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	20					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)	p.F20F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	GTCTTCACTTCGGGCTTGTGA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	X											93	81	85					X																	115303593		2203	4300	6503	115217621	SO:0001819	synonymous_variant	186			AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.60C>T	X.37:g.115303593C>T			115217621	B2R9V1|Q13016|Q6FGY7	Silent	SNP	ENST00000371906.4	37	CCDS14569.1																																																																																				0.423	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		T	115303593	C	T	115303593	2	4	61	1	0	0	0	0	0	0	0	1	402	883	31	1		1	AGTR2	23	115303593	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	439402	115303593	39966967	12221	20206										
WDR44	54521	broad.mit.edu	37	chrX	117527157	117527157	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctcctagacccccacctcCttctcgacctgctccaccac	3	23	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:117527157C>A	ENST00000254029.3	+	4	1144	c.749C>A	c.(748-750)cCt>cAt	p.P250H	WDR44_ENST00000493448.1_3'UTR|WDR44_ENST00000371825.3_Missense_Mutation_p.P250H|WDR44_ENST00000371822.5_Missense_Mutation_p.P225H	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	250	Pro-rich.			P -> L (in Ref. 2; CAL38662). {ECO:0000305}.		endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.P250H(2)		breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						CCCCCACCTCCTTCTCGACCT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	X											125	129	128					X																	117527157		2203	4300	6503	117411185	SO:0001583	missense	54521			AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.749C>A	X.37:g.117527157C>A	ENSP00000254029:p.Pro250His		117411185	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	CCDS14572.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798801	0.90538	.	.	ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825	D;D;D	0.89746	-2.56;-1.94;-1.78	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.92044	0.7479	L	0.36672	1.1	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.987	D	0.92252	0.5809	10	0.51188	T	0.08	-14.3141	18.783	0.91942	0.0:1.0:0.0:0.0	.	225;250;250	F8W913;Q5JSH3-2;Q5JSH3	.;.;WDR44_HUMAN	H	225;250;250	ENSP00000360887:P225H;ENSP00000254029:P250H;ENSP00000360890:P250H	ENSP00000254029:P250H	P	+	2	0	WDR44	117411185	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.415000	0.80131	2.383000	0.81215	0.541000	0.68203	CCT		0.468	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		A	117527157	C	A	117527157	3	1	61	1	0	0	0	0	1	0	0	0	17336	681	24	2	763	2	WDR44	23	117527157	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2223564	117527157	37743403	12222	20207										
DOCK11	139818	broad.mit.edu	37	chrX	117733155	117733155	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagctgattcagtcaggctcGaaagaagttccaggggagct	13	9	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:117733155G>A	ENST00000276202.7	+	23	2589	c.2526G>A	c.(2524-2526)tcG>tcA	p.S842S	DOCK11_ENST00000276204.6_Silent_p.S842S	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	842					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S842S(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AGTCAGGCTCGAAAGAAGTTC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	X											65	57	60					X																	117733155		2203	4300	6503	117617183	SO:0001819	synonymous_variant	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.2526G>A	X.37:g.117733155G>A			117617183	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																				0.393	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117733155	G	A	117733155	2	1	61	1	0	0	0	0	0	0	0	1	4697	1045	37	1		1	DOCK11	23	117733155	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	205998	117733155	37537405	12223	20208										
DOCK11	139818	broad.mit.edu	37	chrX	117783028	117783028	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagcatctgcacttttgtatCttttgatgagaaacaacttt	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:117783028C>A	ENST00000276202.7	+	41	4582	c.4519C>A	c.(4519-4521)Ctt>Att	p.L1507I	DOCK11_ENST00000276204.6_Missense_Mutation_p.L1507I	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1507					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1507I(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						ACTTTTGTATCTTTTGATGAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											146	143	144					X																	117783028		2203	4300	6503	117667056	SO:0001583	missense	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.4519C>A	X.37:g.117783028C>A	ENSP00000276202:p.Leu1507Ile		117667056	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831100	0.71258	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.01933	4.55;4.55	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.09291	0.0229	M	0.80028	2.48	0.52099	D	0.999942	P;P	0.50819	0.897;0.939	B;P	0.50537	0.441;0.643	T	0.05115	-1.0905	10	0.39692	T	0.17	-6.5469	18.7528	0.91821	0.0:1.0:0.0:0.0	.	1507;1507	A6NIW2;Q5JSL3	.;DOC11_HUMAN	I	1507	ENSP00000276204:L1507I;ENSP00000276202:L1507I	ENSP00000276202:L1507I	L	+	1	0	DOCK11	117667056	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.821000	0.39041	2.374000	0.81015	0.429000	0.28392	CTT		0.383	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117783028	C	A	117783028	3	1	61	1	0	0	0	0	1	0	0	0	4697	913	32	2	4681	2	DOCK11	23	117783028	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	49873	117783028	37487532	12224	20209										
DOCK11	139818	broad.mit.edu	37	chrX	117809974	117809974	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttatgcatacaaaaaagagaCttttaggcactttcttcaga	6	7	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:117809974C>A	ENST00000276202.7	+	47	5338	c.5275C>A	c.(5275-5277)Ctt>Att	p.L1759I	DOCK11_ENST00000276204.6_Missense_Mutation_p.L1759I	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1759	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1759I(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AAAAAAGAGACTTTTAGGCAC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	X											41	40	40					X																	117809974		2202	4295	6497	117694002	SO:0001583	missense	139818			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.5275C>A	X.37:g.117809974C>A	ENSP00000276202:p.Leu1759Ile		117694002	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.121481	0.77436	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.19669	2.13;2.13	5.57	5.57	0.84162	.	0.065871	0.64402	D	0.000010	T	0.39200	0.1069	M	0.62154	1.92	0.49299	D	0.999778	P;P	0.47545	0.897;0.897	P;P	0.55161	0.77;0.77	T	0.04621	-1.0938	10	0.39692	T	0.17	-9.555	17.4003	0.87458	0.0:1.0:0.0:0.0	.	1759;1759	A6NIW2;Q5JSL3	.;DOC11_HUMAN	I	1759	ENSP00000276204:L1759I;ENSP00000276202:L1759I	ENSP00000276202:L1759I	L	+	1	0	DOCK11	117694002	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.724000	0.54962	2.322000	0.78497	0.600000	0.82982	CTT		0.299	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		A	117809974	C	A	117809974	3	1	61	1	0	0	0	0	1	0	0	0	4697	565	20	2	5461	2	DOCK11	23	117809974	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	26946	117809974	37460586	12225	20210										
IL13RA1	3597	broad.mit.edu	37	chrX	117910396	117910396	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgttttcttaaaggctcaaGattattatattccctccaat	4	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:117910396G>T	ENST00000371666.3	+	10	1180	c.1113G>T	c.(1111-1113)aaG>aaT	p.K371N	IL13RA1_ENST00000371637.3_Missense_Mutation_p.K170N	NM_001560.2	NP_001551.1	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1	371					cell surface receptor signaling pathway (GO:0007166)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin production (GO:0002639)	interleukin-13 receptor complex (GO:0005898)|plasma membrane (GO:0005886)	interleukin-13 receptor activity (GO:0016515)	p.K371N(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(7)	12						AAAGGCTCAAGATTATTATAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											70	62	65					X																	117910396		2203	4300	6503	117794424	SO:0001583	missense	3597			U62858	CCDS14573.1	Xq24	2008-02-05			ENSG00000131724	ENSG00000131724		"Interleukins and interleukin receptors", "CD molecules"	5974	protein-coding gene	gene with protein product	"IL13 receptor alpha-1 chain", "CD213a1 antigen"	300119				8910586, 9013879	Standard	NM_001560		Approved	IL-13Ra, NR4, CD213a1	uc004eqs.3	P78552	OTTHUMG00000022258	ENST00000371666.3:c.1113G>T	X.37:g.117910396G>T	ENSP00000360730:p.Lys371Asn		117794424	O95646|Q5JSL4|Q99656|Q9UDY5	Missense_Mutation	SNP	ENST00000371666.3	37	CCDS14573.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.273340	0.59649	.	.	ENSG00000131724	ENST00000371666;ENST00000371637	D	0.91686	-2.89	5.37	3.58	0.41010	.	0.078682	0.52532	D	0.000061	D	0.94225	0.8146	M	0.69823	2.125	0.34591	D	0.715487	D;D	0.89917	1.0;1.0	D;D	0.69307	0.963;0.963	D	0.95422	0.8508	10	0.87932	D	0	-21.3326	7.9716	0.30130	0.2055:0.0:0.7945:0.0	.	371;371	Q5JSL4;P78552	.;I13R1_HUMAN	N	371;170	ENSP00000360730:K371N	ENSP00000360700:K170N	K	+	3	2	IL13RA1	117794424	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.649000	0.46656	1.168000	0.42723	0.500000	0.49745	AAG		0.378	IL13RA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058009.1	NM_001560		T	117910396	G	T	117910396	3	4	61	1	0	0	0	0	1	0	0	0	7650	933	33	2	1151	2	IL13RA1	23	117910396	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	100422	117910396	37360164	12226	20211										
LONRF3	79836	broad.mit.edu	37	chrX	118145802	118145802	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataagaatgtgcctattttCgtgtgtactatggcctatcc	8	8	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:118145802C>T	ENST00000371628.3	+	8	1708	c.1677C>T	c.(1675-1677)ttC>ttT	p.F559F	LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000304778.7_Silent_p.F518F|LONRF3_ENST00000422289.2_Silent_p.F303F	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	559	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.F518F(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						TGCCTATTTTCGTGTGTACTA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	X											339	255	283					X																	118145802		2203	4300	6503	118029830	SO:0001819	synonymous_variant	79836			AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.1677C>T	X.37:g.118145802C>T			118029830	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.365347	0.24684	.	.	ENSG00000175556	ENST00000439603	.	.	.	6.07	-1.72	0.08107	.	.	.	.	.	T	0.58595	0.2133	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55685	-0.8102	4	.	.	.	-36.6924	12.4269	0.55553	0.0:0.1977:0.0:0.8023	.	.	.	.	C	325	.	.	R	+	1	0	LONRF3	118029830	0.870000	0.30015	0.982000	0.44146	0.983000	0.72400	-0.007000	0.12810	-0.416000	0.07473	-0.199000	0.12753	CGT		0.443	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		T	118145802	C	T	118145802	2	4	61	1	0	0	0	0	0	0	0	1	8925	883	31	1		1	LONRF3	23	118145802	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	235406	118145802	37124758	12227	20212										
KIAA1210	57481	broad.mit.edu	37	chrX	118220598	118220598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caacgtaagatattttggtgAggttccctgcagcatccagg	11	9	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:118220598A>G	ENST00000402510.2	-	11	4594	c.4595T>C	c.(4594-4596)cTc>cCc	p.L1532P		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1532								p.L1532P(1)|p.L1356P(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TATTTTGGTGAGGTTCCCTGC	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	X											85	77	79					X																	118220598		1912	4118	6030	118104626	SO:0001583	missense	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4595T>C	X.37:g.118220598A>G	ENSP00000384670:p.Leu1532Pro		118104626	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.721024	0.30503	.	.	ENSG00000250423	ENST00000402510	T	0.13420	2.59	5.07	1.2	0.21068	.	.	.	.	.	T	0.18841	0.0452	L	0.36672	1.1	0.18873	N	0.999988	D	0.69078	0.997	D	0.65010	0.931	T	0.13282	-1.0515	8	.	.	.	.	2.8126	0.05446	0.5659:0.0:0.2418:0.1923	.	1532	Q9ULL0	K1210_HUMAN	P	1532	ENSP00000384670:L1532P	.	L	-	2	0	RP13-347D8.6	118104626	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.351000	0.20096	-0.004000	0.14419	0.417000	0.27973	CTC		0.517	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118220598	A	G	118220598	3	3	61	1	0	0	0	0	1	0	0	0	8235	304	11	4	550	4	KIAA1210	23	118220598	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	74796	118220598	37049962	12228	20213										
KIAA1210	57481	broad.mit.edu	37	chrX	118239094	118239094	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgatgctgagtcggcgtCggcgcgatggtgggttctgt	19	7	1	2	rs376855405		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:118239094C>A	ENST00000402510.2	-	7	928	c.929G>T	c.(928-930)cGa>cTa	p.R310L		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	310								p.R310L(1)|p.R170L(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						GAGTCGGCGTCGGCGCGATGG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	X											117	119	118					X																	118239094		2009	4158	6167	118123122	SO:0001583	missense	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.929G>T	X.37:g.118239094C>A	ENSP00000384670:p.Arg310Leu		118123122	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	C	7.024	0.559290	0.13436	.	.	ENSG00000250423;ENSG00000241087	ENST00000402510;ENST00000420240	T	0.10288	2.89	4.55	0.185	0.15096	.	.	.	.	.	T	0.05044	0.0135	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.42582	-0.9443	9	0.31617	T	0.26	.	6.7523	0.23493	0.0:0.2938:0.2522:0.454	.	310	Q9ULL0	K1210_HUMAN	L	310;146	ENSP00000384670:R310L	ENSP00000396164:R146L	R	-	2	0	RP13-347D8.5;RP13-347D8.6	118123122	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.143000	0.10296	-0.136000	0.11475	-2.708000	0.00134	CGA		0.413	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		A	118239094	C	A	118239094	3	1	61	1	0	0	0	0	1	0	0	0	8235	884	31	2	4232	2	KIAA1210	23	118239094	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	18496	118239094	37031466	12229	20214										
FAM70A	55026	broad.mit.edu	37	chrX	119410866	119410866	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttggcaactgctgacatcGatgtattcgtagtacccacc	8	12	1	1	rs201573550		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:119410866G>A	ENST00000309720.5	-	8	744	c.621C>T	c.(619-621)atC>atT	p.I207I	TMEM255A_ENST00000440464.1_Intron|TMEM255A_ENST00000371369.4_Silent_p.I183I|TMEM255A_ENST00000371352.1_Silent_p.I43I	NM_017938.3	NP_060408.3	Q5JRV8	T255A_HUMAN	transmembrane protein 255A	207						integral component of membrane (GO:0016021)		p.I207I(1)									TGCTGACATCGATGTATTCGT	0.587													G|||	3	0.000794702	0	0.0029	3775	,	,		14117	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	X											258	187	211					X																	119410866		2203	4300	6503	119294894	SO:0001819	synonymous_variant	55026			BC047054	CCDS14597.1, CCDS43986.1, CCDS48157.1	Xq24	2012-11-30	2012-11-30	2012-11-30	ENSG00000125355	ENSG00000125355			26086	protein-coding gene	gene with protein product			"family with sequence similarity 70, member A"	FAM70A		12477932	Standard	NM_017938		Approved	FLJ20716	uc004eso.4	Q5JRV8	OTTHUMG00000022298	ENST00000309720.5:c.621C>T	X.37:g.119410866G>A			119294894	A8K0W9|B1APR4|B3KPI6|E9PAR3|Q86Y72|Q9NWN8	Silent	SNP	ENST00000309720.5	37	CCDS14597.1																																																																																				0.587	TMEM255A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058091.1	NM_017938		A	119410866	G	A	119410866	2	1	61	1	0	0	0	0	0	0	0	1	5624	1048	37	1		1	FAM70A	23	119410866	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1171772	119410866	35859694	12230	20215										
CUL4B	8450	broad.mit.edu	37	chrX	119708410	119708410	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tagttcatttactcaccaccGtctttagaggtagtagcctc	7	11	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:119708410G>A	ENST00000404115.3	-	2	464	c.63C>T	c.(61-63)gaC>gaT	p.D21D	CUL4B_ENST00000486604.1_5'UTR	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	21	Ser-rich.				cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.D21D(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ACTCACCACCGTCTTTAGAGG	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	X											181	146	158					X																	119708410		2203	4300	6503	119592438	SO:0001819	synonymous_variant	8450			U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.63C>T	X.37:g.119708410G>A			119592438	B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	Silent	SNP	ENST00000404115.3	37	CCDS35379.1																																																																																				0.458	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588		A	119708410	G	A	119708410	2	1	61	1	0	0	0	0	0	0	0	1	4064	1136	40	1		1	CUL4B	23	119708410	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	297544	119708410	35562150	12231	20216										
THOC2	57187	broad.mit.edu	37	chrX	122757090	122757090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctttgtgatgaaactcatttTcaggtatcatgtatgacttt	7	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:122757090T>C	ENST00000245838.8	-	29	3579	c.3548A>G	c.(3547-3549)gAa>gGa	p.E1183G	THOC2_ENST00000355725.4_Missense_Mutation_p.E1183G|THOC2_ENST00000491737.1_Missense_Mutation_p.E1068G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1183					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)	p.E1104G(1)|p.E1183G(1)		breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AAACTCATTTTCAGGTATCAT	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	X											154	139	144					X																	122757090		1866	4085	5951	122584771	SO:0001583	missense	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3548A>G	X.37:g.122757090T>C	ENSP00000245838:p.Glu1183Gly		122584771	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.6|20.6	4.025263|4.025263	0.75390|0.75390	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000438358	.|.	.|.	.|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|.	0.57636|.	0.2067|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D|.	0.60575|.	0.988|.	P|.	0.60345|.	0.873|.	T|.	0.54410|.	-0.8298|.	9|.	0.30078|.	T|.	0.28|.	-19.9423|-19.9423	15.5329|15.5329	0.75977|0.75977	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1183|.	Q8NI27|.	THOC2_HUMAN|.	G|W	1183;1183;1068|277	.|.	ENSP00000245838:E1183G|.	E|X	-|-	2|3	0|0	THOC2|THOC2	122584771|122584771	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.816000|7.816000	0.86201|0.86201	2.053000|2.053000	0.61076|0.61076	0.437000|0.437000	0.28790|0.28790	GAA|TGA		0.413	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122757090	T	C	122757090	3	2	61	1	0	0	0	0	1	0	0	0	15904	1783	62	4	1273	4	THOC2	23	122757090	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	3048680	122757090	32513470	12232	20217										
ODZ1	10178	broad.mit.edu	37	chrX	123515051	123515051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cttccctccttcaaggcaccGtccatcattgtatcggggag	9	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:123515051G>A	ENST00000371130.3	-	31	7576	c.7513C>T	c.(7513-7515)Cgg>Tgg	p.R2505W	TENM1_ENST00000422452.2_Missense_Mutation_p.R2512W|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2505					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R2507W(1)									TCAAGGCACCGTCCATCATTG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X											135	129	131					X																	123515051		2201	4299	6500	123342732	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7513C>T	X.37:g.123515051G>A	ENSP00000360171:p.Arg2505Trp		123342732	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.449402	0.43531	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86030	-2.06;-2.03	5.83	2.78	0.32641	.	0.317683	0.35151	N	0.003413	T	0.81631	0.4863	N	0.24115	0.695	0.31384	N	0.678691	D;D;D	0.63046	0.978;0.978;0.992	B;B;P	0.51657	0.39;0.39;0.676	T	0.82926	-0.0215	10	0.72032	D	0.01	.	13.2906	0.60269	0.0:0.0:0.2875:0.7125	.	2511;2512;2505	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	W	2505;2512	ENSP00000360171:R2505W;ENSP00000403954:R2512W	ENSP00000360171:R2505W	R	-	1	2	ODZ1	123342732	0.994000	0.37717	0.999000	0.59377	0.999000	0.98932	2.565000	0.45939	0.585000	0.29608	0.600000	0.82982	CGG		0.458	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123515051	G	A	123515051	3	1	61	1	0	0	0	0	1	0	0	0	10865	1144	40	1	668	1	ODZ1	23	123515051	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	757961	123515051	31755509	12233	20218										
ODZ1	10178	broad.mit.edu	37	chrX	123519908	123519908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctggctgtgtaggagaagcaTcacagactgaaacgagacaa	12	8	1	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:123519908T>C	ENST00000371130.3	-	28	5737	c.5674A>G	c.(5674-5676)Atg>Gtg	p.M1892V	TENM1_ENST00000422452.2_Missense_Mutation_p.M1899V|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1892					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.M1894V(1)									AGGAGAAGCATCACAGACTGA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	X											81	68	73					X																	123519908		2203	4300	6503	123347589	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5674A>G	X.37:g.123519908T>C	ENSP00000360171:p.Met1892Val		123347589	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	0.716	-0.785193	0.02907	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.84442	-1.85;-1.81	5.42	5.42	0.78866	.	0.079368	0.85682	D	0.000000	T	0.70919	0.3279	N	0.16066	0.365	0.40539	D	0.981004	B;B;B	0.29716	0.255;0.255;0.013	B;B;B	0.29598	0.104;0.104;0.008	T	0.68957	-0.5272	10	0.02654	T	1	.	14.533	0.67939	0.0:0.0:0.0:1.0	.	1898;1899;1892	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	1892;1899	ENSP00000360171:M1892V;ENSP00000403954:M1899V	ENSP00000360171:M1892V	M	-	1	0	ODZ1	123347589	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.153000	0.50685	1.812000	0.52913	0.486000	0.48141	ATG		0.433	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123519908	T	C	123519908	3	2	61	1	0	0	0	0	1	0	0	0	10865	1435	50	4	2519	4	ODZ1	23	123519908	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	4857	123519908	31750652	12234	20219										
ODZ1	10178	broad.mit.edu	37	chrX	123779183	123779183	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaccacacagcacagggcaGgaatctgaaggttggcaaat	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:123779183G>T	ENST00000371130.3	-	10	1749	c.1686C>A	c.(1684-1686)tcC>tcA	p.S562S	TENM1_ENST00000422452.2_Silent_p.S562S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	562	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S564S(1)									GCACAGGGCAGGAATCTGAAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	X											161	144	150					X																	123779183		2203	4300	6503	123606864	SO:0001819	synonymous_variant	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.1686C>A	X.37:g.123779183G>T			123606864	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.448	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123779183	G	T	123779183	2	4	61	1	0	0	0	0	0	0	0	1	10865	987	35	2		2	ODZ1	23	123779183	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	259275	123779183	31491377	12235	20220										
DCAF12L2	340578	broad.mit.edu	37	chrX	125299656	125299656	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggcgctccgtcagcagctcGggcagcctctggacggcgta	15	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:125299656G>A	ENST00000360028.2	-	1	278	c.252C>T	c.(250-252)ccC>ccT	p.P84P	DCAF12L2_ENST00000538699.1_Silent_p.P84P			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	84								p.P84P(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						TCAGCAGCTCGGGCAGCCTCT	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	X											29	30	29					X																	125299656		2194	4281	6475	125127337	SO:0001819	synonymous_variant	340578			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.252C>T	X.37:g.125299656G>A			125127337	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																				0.687	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		A	125299656	G	A	125299656	2	1	61	1	0	0	0	0	0	0	0	1	4271	1103	39	1		1	DCAF12L2	23	125299656	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1520473	125299656	29970904	12236	20221										
SMARCA1	6594	broad.mit.edu	37	chrX	128645905	128645905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgtgaggtccaggaatatttCggtagtgtttcaggtaacca	12	6	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:128645905C>T	ENST00000371122.4	-	6	815	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371123.1_Missense_Mutation_p.R229Q|SMARCA1_ENST00000371121.3_Missense_Mutation_p.R229Q	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	229	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R229Q(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						AGGAATATTTCGGTAGTGTTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											216	218	217					X																	128645905		2203	4300	6503	128473586	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.686G>A	X.37:g.128645905C>T	ENSP00000360163:p.Arg229Gln		128473586	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520992	0.85495	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	5.5	5.5	0.81552	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.53938	D	0.000047	D	0.89329	0.6684	N	0.25380	0.74	0.58432	D	0.999997	P;P;P;P	0.41947	0.766;0.766;0.723;0.766	B;B;B;B	0.38880	0.284;0.284;0.187;0.284	D	0.89990	0.4107	10	0.49607	T	0.09	-7.189	18.3709	0.90406	0.0:1.0:0.0:0.0	.	208;229;229;229	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	Q	229;229;229;208	ENSP00000360162:R229Q;ENSP00000360164:R229Q;ENSP00000360163:R229Q;ENSP00000404275:R208Q	ENSP00000360162:R229Q	R	-	2	0	SMARCA1	128473586	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.807000	0.86032	2.279000	0.76181	0.600000	0.82982	CGA		0.383	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		T	128645905	C	T	128645905	3	4	61	1	0	0	0	0	1	0	0	0	14805	884	31	1	2554	1	SMARCA1	23	128645905	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3346249	128645905	26624655	12237	20222										
OCRL	4952	broad.mit.edu	37	chrX	128720981	128720981	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tacttttccatctattaggaGaaatcccttctgcaaatggt	6	9	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:128720981G>T	ENST00000371113.4	+	20	2307	c.2142G>T	c.(2140-2142)gaG>gaT	p.E714D	OCRL_ENST00000357121.5_Missense_Mutation_p.E706D	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	714					cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.E714D(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						TCTATTAGGAGAAATCCCTTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											187	197	193					X																	128720981		2203	4300	6503	128548662	SO:0001583	missense	4952			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.2142G>T	X.37:g.128720981G>T	ENSP00000360154:p.Glu714Asp		128548662	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.106953	0.37145	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94793	-3.47;-3.52	4.93	3.17	0.36434	Rho GTPase activation protein (1);	1.285610	0.05366	N	0.534558	D	0.94719	0.8296	L	0.54323	1.7	0.48762	D	0.999703	D;B	0.56521	0.976;0.016	P;B	0.52066	0.689;0.005	D	0.86025	0.1509	10	0.40728	T	0.16	.	9.2686	0.37657	0.1806:0.0:0.8194:0.0	.	706;714	Q01968-2;Q01968	.;OCRL_HUMAN	D	714;706	ENSP00000360154:E714D;ENSP00000349635:E706D	ENSP00000349635:E706D	E	+	3	2	OCRL	128548662	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	2.622000	0.46427	0.506000	0.28125	0.594000	0.82650	GAG		0.408	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		T	128720981	G	T	128720981	3	4	61	1	0	0	0	0	1	0	0	0	10854	933	33	2	2220	2	OCRL	23	128720981	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	75076	128720981	26549579	12238	20223										
ZDHHC9	51114	broad.mit.edu	37	chrX	128957704	128957704	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaggcccggggaggccggaaGatcttgcatgtgtaacagta	16	8	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:128957704G>T	ENST00000357166.6	-	5	829	c.438C>A	c.(436-438)atC>atA	p.I146I	ZDHHC9_ENST00000491039.1_5'UTR|AL359542.1_ENST00000582964.1_RNA|ZDHHC9_ENST00000371064.3_Silent_p.I146I	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	146					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)	p.I146I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						GAGGCCGGAAGATCTTGCATG	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	X											140	130	134					X																	128957704		2203	4300	6503	128785385	SO:0001819	synonymous_variant	51114			AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.438C>A	X.37:g.128957704G>T			128785385	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Silent	SNP	ENST00000357166.6	37	CCDS35395.1	.	.	.	.	.	.	.	.	.	.	g	9.364	1.068720	0.20147	.	.	ENSG00000188706	ENST00000433917	.	.	.	5.66	4.79	0.61399	.	.	.	.	.	T	0.70527	0.3234	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69228	-0.5200	4	.	.	.	-17.4512	14.7758	0.69732	0.0:0.0:0.8543:0.1457	.	.	.	.	Y	106	.	.	S	-	2	0	ZDHHC9	128785385	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.614000	0.54160	1.133000	0.42147	-0.229000	0.12294	TCT		0.512	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		T	128957704	G	T	128957704	2	4	61	1	0	0	0	0	0	0	0	1	17661	932	33	2		2	ZDHHC9	23	128957704	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	236723	128957704	26312856	12239	20224										
ELF4	2000	broad.mit.edu	37	chrX	129205132	129205132	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcctttctctcgctgggtcCacttgatgtacttgggacag	11	11	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:129205132C>A	ENST00000308167.5	-	7	1071	c.692G>T	c.(691-693)tGg>tTg	p.W231L	ELF4_ENST00000335997.7_Missense_Mutation_p.W231L	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)									p.W231L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TCGCTGGGTCCACTTGATGTA	0.537			T	ERG	AML																																		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	1	Substitution - Missense(1)	large_intestine(1)	X											149	123	132					X																	129205132		2203	4300	6503	129032813	SO:0001583	missense	2000			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.692G>T	X.37:g.129205132C>A	ENSP00000311280:p.Trp231Leu		129032813		Missense_Mutation	SNP	ENST00000308167.5	37	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935349	0.92458	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	D;D	0.88509	-2.39;-2.39	5.45	5.45	0.79879	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (3);	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.93462	3.42	0.80722	D	1	D	0.60160	0.987	D	0.76575	0.988	D	0.96875	0.9642	10	0.87932	D	0	.	15.6014	0.76628	0.0:1.0:0.0:0.0	.	231	Q99607	ELF4_HUMAN	L	231	ENSP00000338608:W231L;ENSP00000311280:W231L	ENSP00000311280:W231L	W	-	2	0	ELF4	129032813	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.792000	0.85828	2.278000	0.76064	0.513000	0.50165	TGG		0.537	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		A	129205132	C	A	129205132	3	1	61	1	0	0	0	0	1	0	0	0	5069	595	21	2	1311	2	ELF4	23	129205132	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	247428	129205132	26065428	12240	20225										
RAB33A	9363	broad.mit.edu	37	chrX	129318615	129318615	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcttgccgattgaaggcccaGaaatccctgctgtatcgtga	11	11	0	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:129318615G>T	ENST00000257017.4	+	2	1029	c.615G>T	c.(613-615)caG>caT	p.Q205H		NM_004794.2	NP_004785.1	Q14088	RB33A_HUMAN	RAB33A, member RAS oncogene family	205					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.Q205H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						TGAAGGCCCAGAAATCCCTGC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	X											83	73	76					X																	129318615		2203	4300	6503	129146296	SO:0001583	missense	9363			D14889	CCDS14621.1	Xq26	2008-02-05			ENSG00000134594	ENSG00000134594		"RAB, member RAS oncogene"	9773	protein-coding gene	gene with protein product		300333				7688322, 9512502	Standard	NM_004794		Approved	RabS10	uc004evl.3	Q14088	OTTHUMG00000022391	ENST00000257017.4:c.615G>T	X.37:g.129318615G>T	ENSP00000257017:p.Gln205His		129146296	Q5JUZ6|Q92465	Missense_Mutation	SNP	ENST00000257017.4	37	CCDS14621.1	.	.	.	.	.	.	.	.	.	.	G	7.795	0.712391	0.15306	.	.	ENSG00000134594	ENST00000257017	T	0.79845	-1.31	5.26	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	N	0.08118	0	0.58432	D	0.999999	B	0.15719	0.014	B	0.15484	0.013	T	0.52917	-0.8511	10	0.26408	T	0.33	-11.242	9.4102	0.38487	0.1666:0.0:0.8334:0.0	.	205	Q14088	RB33A_HUMAN	H	205	ENSP00000257017:Q205H	ENSP00000257017:Q205H	Q	+	3	2	RAB33A	129146296	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.573000	0.53856	1.000000	0.39049	0.436000	0.28706	CAG		0.512	RAB33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058246.1	NM_004794		T	129318615	G	T	129318615	3	4	61	1	0	0	0	0	1	0	0	0	12959	933	33	2	621	2	RAB33A	23	129318615	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	113483	129318615	25951945	12241	20226										
ZNF280C	55609	broad.mit.edu	37	chrX	129339345	129339345	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccatacgatctaagccggaaGaatcagctaggaaatcacat	8	10	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:129339345G>T	ENST00000370978.4	-	17	2240	c.2087C>A	c.(2086-2088)tCt>tAt	p.S696Y		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	696					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S696Y(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TAAGCCGGAAGAATCAGCTAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	86	91					X																	129339345		2203	4299	6502	129167026	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.2087C>A	X.37:g.129339345G>T	ENSP00000360017:p.Ser696Tyr		129167026	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.513755	0.27123	.	.	ENSG00000056277	ENST00000370978	T	0.02709	4.19	3.66	1.79	0.24919	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.05044	0.0135	L	0.36672	1.1	0.22531	N	0.999016	P	0.50819	0.939	P	0.55667	0.781	T	0.40021	-0.9585	9	0.72032	D	0.01	.	2.8874	0.05665	0.2514:0.2566:0.492:0.0	.	696	Q8ND82	Z280C_HUMAN	Y	696	ENSP00000360017:S696Y	ENSP00000360017:S696Y	S	-	2	0	ZNF280C	129167026	1.000000	0.71417	0.903000	0.35520	0.577000	0.36160	1.430000	0.34914	0.665000	0.31066	0.292000	0.19580	TCT		0.318	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129339345	G	T	129339345	3	4	61	1	0	0	0	0	1	0	0	0	17855	942	33	2	138	2	ZNF280C	23	129339345	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	20730	129339345	25931215	12242	20227										
SLC25A14	9016	broad.mit.edu	37	chrX	129483269	129483269	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcatcatatggcaccattaAaattgggatttaccaaagct	7	8	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:129483269A>C	ENST00000218197.5	+	4	589	c.362A>C	c.(361-363)aAa>aCa	p.K121T	SLC25A14_ENST00000543953.1_Missense_Mutation_p.K86T|SLC25A14_ENST00000361980.5_Missense_Mutation_p.K118T|SLC25A14_ENST00000545805.1_Missense_Mutation_p.K121T|SLC25A14_ENST00000467496.1_3'UTR|SLC25A14_ENST00000339231.3_Missense_Mutation_p.K118T	NM_001282195.1|NM_001282196.1|NM_001282198.1	NP_001269124.1|NP_001269125.1|NP_001269127.1	O95258	UCP5_HUMAN	solute carrier family 25 (mitochondrial carrier, brain), member 14	121					aerobic respiration (GO:0009060)|mitochondrial transport (GO:0006839)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.K121T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)	22						GGCACCATTAAAATTGGGATT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	X											125	99	108					X																	129483269		2203	4300	6503	129310950	SO:0001583	missense	9016			AF078544	CCDS14623.1, CCDS14624.1, CCDS76020.1, CCDS76021.1	Xq24	2013-05-22			ENSG00000102078	ENSG00000102078		"Solute carriers"	10984	protein-coding gene	gene with protein product		300242				9852133	Standard	XM_005262485		Approved	BMCP1, UCP5	uc004evp.1	O95258	OTTHUMG00000022394	ENST00000218197.5:c.362A>C	X.37:g.129483269A>C	ENSP00000218197:p.Lys121Thr		129310950	D3DTG2|Q0VDH7|Q9HC60|Q9HC61	Missense_Mutation	SNP	ENST00000218197.5	37	CCDS14623.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306097	0.81247	.	.	ENSG00000102078	ENST00000424447;ENST00000545805;ENST00000543953;ENST00000218197;ENST00000361980;ENST00000339231	T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22	4.96	4.96	0.65561	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.81697	0.4877	L	0.35341	1.055	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.83722	0.0193	10	0.87932	D	0	-11.3458	12.6529	0.56772	1.0:0.0:0.0:0.0	.	86;118;118;121	B7Z996;O95258-3;O95258-2;O95258	.;.;.;UCP5_HUMAN	T	121;121;86;121;118;118	ENSP00000402578:K121T;ENSP00000444642:K121T;ENSP00000445225:K86T;ENSP00000218197:K121T;ENSP00000354455:K118T;ENSP00000342797:K118T	ENSP00000218197:K121T	K	+	2	0	SLC25A14	129310950	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.325000	0.90007	1.831000	0.53308	0.486000	0.48141	AAA		0.338	SLC25A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058253.1	NM_022810, NM_003951		C	129483269	A	C	129483269	3	2	61	1	0	0	0	0	1	0	0	0	14513	14	1	4	376	4	SLC25A14	23	129483269	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	143924	129483269	25787291	12243	20228										
GPR119	139760	broad.mit.edu	37	chrX	129519301	129519301	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cagattcaaggtgaagcagaGactgacaccatcattcttgt	9	9	3	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:129519301G>T	ENST00000276218.2	-	1	210	c.121C>A	c.(121-123)Ctc>Atc	p.L41I		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	41					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)	p.L41I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						GTGAAGCAGAGACTGACACCA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											227	194	205					X																	129519301		2203	4300	6503	129346982	SO:0001583	missense	139760			AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"GPCR / Class A : Orphans"	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.121C>A	X.37:g.129519301G>T	ENSP00000276218:p.Leu41Ile		129346982	Q495H7|Q4VBN3	Missense_Mutation	SNP	ENST00000276218.2	37	CCDS14625.1	.	.	.	.	.	.	.	.	.	.	G	11.22	1.575760	0.28092	.	.	ENSG00000147262	ENST00000276218	T	0.37411	1.2	5.06	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.332151	0.30320	N	0.009892	T	0.44561	0.1299	L	0.44542	1.39	0.27040	N	0.964029	D	0.63880	0.993	P	0.60609	0.877	T	0.31280	-0.9949	10	0.87932	D	0	-14.9141	8.1218	0.30976	0.1899:0.0:0.8101:0.0	.	41	Q8TDV5	GP119_HUMAN	I	41	ENSP00000276218:L41I	ENSP00000276218:L41I	L	-	1	0	GPR119	129346982	1.000000	0.71417	0.395000	0.26283	0.838000	0.47535	5.246000	0.65411	1.122000	0.41944	0.513000	0.50165	CTC		0.542	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471		T	129519301	G	T	129519301	3	4	61	1	0	0	0	0	1	0	0	0	6654	942	33	2	890	2	GPR119	23	129519301	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	36032	129519301	25751259	12244	20229										
IGSF1	3547	broad.mit.edu	37	chrX	130413158	130413158	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cattgcacagtcctgcaaaaGaaattgctgccaggactcgg	10	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:130413158G>T	ENST00000361420.3	-	11	1797				IGSF1_ENST00000370903.3_Missense_Mutation_p.S575Y|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370904.1_Intron|IGSF1_ENST00000370910.1_Intron			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1						regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)	p.?(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						TCCTGCAAAAGAAATTGCTGC	0.572																																																1	Unknown(1)	large_intestine(1)	X											110	111	111					X																	130413158		2203	4300	6503	130240839	SO:0001627	intron_variant	3547			AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.1718-9C>A	X.37:g.130413158G>T			130240839	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	37	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.558878	0.45590	.	.	ENSG00000147255	ENST00000370903	T	0.00682	5.86	4.38	4.38	0.52667	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.20196	N	0.99992	D	0.65815	0.995	D	0.72982	0.979	T	0.66830	-0.5824	8	.	.	.	.	11.2268	0.48888	0.0:0.0:1.0:0.0	.	14	C9JP68	.	Y	575	ENSP00000359940:S575Y	.	S	-	2	0	IGSF1	130240839	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.528000	0.45624	2.419000	0.82065	0.594000	0.82650	TCT		0.572	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			T	130413158	G	T	130413158	1	4	61	0	1	0	0	0	0	0	0	0	7617	942	33	2		2	IGSF1	23	130413158	Intron	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	893857	130413158	24857402	12245	20230										
IGSF1	3547	broad.mit.edu	37	chrX	130415813	130415813	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctctttcttcccattccagaGaaaattccagtactggatga	6	11	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:130415813G>T	ENST00000361420.3	-	8	1431	c.1352C>A	c.(1351-1353)tCt>tAt	p.S451Y	IGSF1_ENST00000370903.3_Missense_Mutation_p.S451Y|IGSF1_ENST00000370904.1_Missense_Mutation_p.S442Y|IGSF1_ENST00000370910.1_Missense_Mutation_p.S442Y			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	451	Ig-like C2-type 5.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)	p.S451Y(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						CCATTCCAGAGAAAATTCCAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											99	80	87					X																	130415813		2203	4300	6503	130243494	SO:0001583	missense	3547			AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.1352C>A	X.37:g.130415813G>T	ENSP00000355010:p.Ser451Tyr		130243494	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	37	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933955	0.34096	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.03496	3.91;3.91;3.91;3.91	4.35	1.5	0.22942	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.697090	0.13215	N	0.404834	T	0.04048	0.0113	L	0.45352	1.415	0.31592	N	0.653768	B;B	0.27910	0.003;0.193	B;B	0.33890	0.005;0.172	T	0.31888	-0.9927	10	0.23891	T	0.37	.	5.5701	0.17192	0.113:0.3879:0.4991:0.0	.	442;451	Q8N6C5-2;Q8N6C5	.;IGSF1_HUMAN	Y	442;451;442;451	ENSP00000359947:S442Y;ENSP00000355010:S451Y;ENSP00000359941:S442Y;ENSP00000359940:S451Y	ENSP00000355010:S451Y	S	-	2	0	IGSF1	130243494	0.927000	0.31430	0.923000	0.36655	0.992000	0.81027	0.045000	0.14013	0.187000	0.20147	0.594000	0.82650	TCT		0.483	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			T	130415813	G	T	130415813	3	4	61	1	0	0	0	0	1	0	0	0	7617	942	33	2	2725	2	IGSF1	23	130415813	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2655	130415813	24854747	12246	20231										
IGSF1	3547	broad.mit.edu	37	chrX	130419171	130419171	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acctgctacaaccagcttcaGggggttgctgggctctgacc	12	13	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:130419171G>A	ENST00000361420.3	-	5	728	c.649C>T	c.(649-651)Ctg>Ttg	p.L217L	IGSF1_ENST00000370903.3_Silent_p.L217L|IGSF1_ENST00000370904.1_Silent_p.L208L|IGSF1_ENST00000370900.1_Silent_p.L217L|IGSF1_ENST00000370910.1_Silent_p.L208L|IGSF1_ENST00000370901.4_Silent_p.L217L			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	217	Ig-like C2-type 2.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)	p.L217L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ACCAGCTTCAGGGGGTTGCTG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	X											96	74	81					X																	130419171		2203	4300	6503	130246852	SO:0001819	synonymous_variant	3547			AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.649C>T	X.37:g.130419171G>A			130246852	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	37	CCDS14629.1																																																																																				0.537	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			A	130419171	G	A	130419171	2	1	61	1	0	0	0	0	0	0	0	1	7617	991	35	3		3	IGSF1	23	130419171	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3358	130419171	24851389	12247	20232										
OR13H1	347468	broad.mit.edu	37	chrX	130678061	130678061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gggaaagatggccatggacaAtgtcacagcagtgtttcagt	13	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:130678061A>G	ENST00000338616.3	+	1	112	c.14A>G	c.(13-15)aAt>aGt	p.N5S		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N5S(1)		endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					GCCATGGACAATGTCACAGCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											203	158	174					X																	130678061		2203	4300	6503	130505742	SO:0001583	missense	347468				CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"GPCR / Class A : Olfactory receptors"	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.14A>G	X.37:g.130678061A>G	ENSP00000340748:p.Asn5Ser		130505742	B2RNQ3|Q6IET8|Q96R12	Missense_Mutation	SNP	ENST00000338616.3	37	CCDS35396.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.280621	0.23392	.	.	ENSG00000171054	ENST00000338616	T	0.02158	4.42	4.63	3.42	0.39159	.	0.356725	0.20241	U	0.096292	T	0.06735	0.0172	M	0.81614	2.55	0.09310	N	1	D	0.54207	0.965	P	0.50314	0.637	T	0.15093	-1.0449	10	0.66056	D	0.02	.	7.7699	0.29001	0.8967:0.0:0.1033:0.0	.	5	Q8NG92	O13H1_HUMAN	S	5	ENSP00000340748:N5S	ENSP00000340748:N5S	N	+	2	0	OR13H1	130505742	0.345000	0.24835	0.002000	0.10522	0.143000	0.21401	2.211000	0.42825	0.580000	0.29522	0.417000	0.27973	AAT		0.408	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1			G	130678061	A	G	130678061	3	3	61	1	0	0	0	0	1	0	0	0	10974	101	4	4	16	4	OR13H1	23	130678061	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	258890	130678061	24592499	12248	20233										
OR13H1	347468	broad.mit.edu	37	chrX	130678729	130678729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctatggctatcataaggattCgctcactccagggcaggctc	10	12	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:130678729C>T	ENST00000338616.3	+	1	780	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R228C(1)		endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					CATAAGGATTCGCTCACTCCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	X											214	187	196					X																	130678729		2203	4300	6503	130506410	SO:0001583	missense	347468				CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"GPCR / Class A : Olfactory receptors"	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.682C>T	X.37:g.130678729C>T	ENSP00000340748:p.Arg228Cys		130506410	B2RNQ3|Q6IET8|Q96R12	Missense_Mutation	SNP	ENST00000338616.3	37	CCDS35396.1	.	.	.	.	.	.	.	.	.	.	C	8.365	0.833907	0.16820	.	.	ENSG00000171054	ENST00000338616	T	0.40225	1.04	4.87	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.181151	0.26812	U	0.022362	T	0.55832	0.1945	M	0.70275	2.135	0.09310	N	1	D	0.71674	0.998	P	0.62740	0.906	T	0.48352	-0.9043	10	0.87932	D	0	.	7.5844	0.27985	0.0:0.7427:0.1626:0.0947	.	228	Q8NG92	O13H1_HUMAN	C	228	ENSP00000340748:R228C	ENSP00000340748:R228C	R	+	1	0	OR13H1	130506410	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	0.324000	0.19610	0.471000	0.27319	-0.185000	0.12909	CGC		0.468	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1			T	130678729	C	T	130678729	3	4	61	1	0	0	0	0	1	0	0	0	10974	884	31	1	684	1	OR13H1	23	130678729	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	668	130678729	24591831	12249	20234										
MST4	90167	broad.mit.edu	37	chrX	131208175	131208175	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttataggtgttcagcagaCgaatccccctaagaaactta	7	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:131208175C>T	ENST00000298542.4	-	0	3198				MST4_ENST00000481105.1_Silent_p.D435D|MST4_ENST00000394335.2_Silent_p.D336D|MST4_ENST00000496850.1_Silent_p.D351D|MST4_ENST00000354719.6_Silent_p.D389D|MST4_ENST00000394334.2_Silent_p.D413D	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7						regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.D413D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GTTCAGCAGACGAATCCCCCT	0.363													C|||	1	0.000264901	0	0.0014	3775	,	,		11124	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											99	97	98					X																	131208175		2203	4298	6501	131035856	SO:0001628	intergenic_variant	51765			AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421		X.37:g.131208175C>T			131035856	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																				0.363	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		T	131208175	C	T	131208175	1	4	61	0	1	0	0	0	0	0	0	0	9922	535	19	1		1	MST4	23	131208175	IGR	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	529446	131208175	24062385	12250	20235										
CCDC160	347475	broad.mit.edu	37	chrX	133379235	133379235	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctaagacaagacataagaaaGaaatttatggaaagaatgtc	8	4	0	5			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:133379235G>T	ENST00000517294.1	+	3	788	c.405G>T	c.(403-405)aaG>aaT	p.K135N	CCDC160_ENST00000370809.4_Missense_Mutation_p.K135N			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	135								p.K135N(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						ACATAAGAAAGAAATTTATGG	0.333													G|||	1	0.000264901	0	0	3775	,	,		12742	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	X											21	19	20					X																	133379235		1819	4055	5874	133206901	SO:0001583	missense	347475			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.405G>T	X.37:g.133379235G>T	ENSP00000427951:p.Lys135Asn		133206901		Missense_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710382	0.48517	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	.	.	.	5.12	2.93	0.34026	.	0.000000	0.53938	D	0.000042	T	0.17023	0.0409	L	0.34521	1.04	0.20638	N	0.99987	P	0.40731	0.728	B	0.33254	0.16	T	0.13361	-1.0512	9	0.46703	T	0.11	-17.5512	5.212	0.15322	0.1472:0.0:0.6533:0.1994	.	135	A6NGH7	CC160_HUMAN	N	135	.	ENSP00000359845:K135N	K	+	3	2	CCDC160	133206901	1.000000	0.71417	0.206000	0.23566	0.004000	0.04260	1.257000	0.32932	1.045000	0.40225	-0.205000	0.12727	AAG		0.333	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		T	133379235	G	T	133379235	3	4	61	1	0	0	0	0	1	0	0	0	2798	933	33	2	407	2	CCDC160	23	133379235	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2171060	133379235	21891325	12251	20236										
CCDC160	347475	broad.mit.edu	37	chrX	133379515	133379515	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aacagctccagcaagccaaaGaagtcatccacaaattgaac	6	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:133379515G>T	ENST00000517294.1	+	3	1068	c.685G>T	c.(685-687)Gaa>Taa	p.E229*	CCDC160_ENST00000370809.4_Nonsense_Mutation_p.E229*			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	229								p.E229*(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GCAAGCCAAAGAAGTCATCCA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											29	24	25					X																	133379515		1823	4062	5885	133207181	SO:0001587	stop_gained	347475			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.685G>T	X.37:g.133379515G>T	ENSP00000427951:p.Glu229*		133207181		Nonsense_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441466	0.83993	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	.	.	.	5.23	5.23	0.72850	.	0.119612	0.37136	N	0.002228	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-19.8773	16.5553	0.84483	0.0:0.0:1.0:0.0	.	.	.	.	X	229	.	ENSP00000359845:E229X	E	+	1	0	CCDC160	133207181	0.998000	0.40836	0.993000	0.49108	0.060000	0.15804	1.397000	0.34543	2.303000	0.77524	0.513000	0.50165	GAA		0.363	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		T	133379515	G	T	133379515	4	4	61	1	0	0	0	0	0	1	0	0	2798	943	33	2	687	2	CCDC160	23	133379515	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	280	133379515	21891045	12252	20237										
HPRT1	3251	broad.mit.edu	37	chrX	133627615	133627615	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatccaaagatggtcaaggtCgcaaggtatgtatgacattt	10	6	1	2	rs148780933	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:133627615C>T	ENST00000298556.7	+	6	639	c.480C>T	c.(478-480)gtC>gtT	p.V160V	HPRT1_ENST00000462974.1_3'UTR	NM_000194.2	NP_000185.1	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1	160					adenine salvage (GO:0006168)|central nervous system neuron development (GO:0021954)|cerebral cortex neuron differentiation (GO:0021895)|cytolysis (GO:0019835)|dendrite morphogenesis (GO:0048813)|dopamine metabolic process (GO:0042417)|GMP catabolic process (GO:0046038)|GMP salvage (GO:0032263)|grooming behavior (GO:0007625)|guanine salvage (GO:0006178)|hypoxanthine metabolic process (GO:0046100)|hypoxanthine salvage (GO:0043103)|IMP metabolic process (GO:0046040)|IMP salvage (GO:0032264)|locomotory behavior (GO:0007626)|lymphocyte proliferation (GO:0046651)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of dopamine metabolic process (GO:0045964)|protein homotetramerization (GO:0051289)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside salvage (GO:0006166)|purine-containing compound salvage (GO:0043101)|response to amphetamine (GO:0001975)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanine phosphoribosyltransferase activity (GO:0052657)|hypoxanthine phosphoribosyltransferase activity (GO:0004422)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)	p.V160V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(192;0.000127)				Azathioprine(DB00993)|Mercaptopurine(DB01033)|Tioguanine(DB00352)	TGGTCAAGGTCGCAAGGTATG	0.353													C|||	6	0.0015894	0.0045	0	3775	,	,		13264	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X	GRCh37	CI070553	HPRT1	I	rs148780933	C		33,3802		0,30,3,1602,568	166	148	154		480	-10.8	0.5	X	dbSNP_134	154	0,6728		0,0,0,2428,1872	no	coding-synonymous	HPRT1	NM_000194.2		0,30,3,4030,2440	TT,TC,T,CC,C		0.0,0.8605,0.3124		160/219	133627615	33,10530	2203	4300	6503	133455281	SO:0001819	synonymous_variant	3251			M26434	CCDS14641.1	Xq26.2	2012-10-02	2008-08-01		ENSG00000165704	ENSG00000165704	2.4.2.8		5157	protein-coding gene	gene with protein product	"Lesch-Nyhan syndrome"	308000		HPRT		12175903	Standard	NM_000194		Approved	HGPRT	uc004exl.4	P00492	OTTHUMG00000022452	ENST00000298556.7:c.480C>T	X.37:g.133627615C>T			133455281	A6NHF0|B2R8M9	Silent	SNP	ENST00000298556.7	37	CCDS14641.1																																																																																				0.353	HPRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058361.1	NM_000194		T	133627615	C	T	133627615	2	4	61	1	0	0	0	0	0	0	0	1	7359	871	31	1		1	HPRT1	23	133627615	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	248100	133627615	21642945	12253	20238										
ZNF75D	7626	broad.mit.edu	37	chrX	134421114	134421114	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccttcttctgtggagtttCtggtgtctaagaaggctcga	11	9	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:134421114C>A	ENST00000370766.3	-	7	4197	c.1488G>T	c.(1486-1488)caG>caT	p.Q496H	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Missense_Mutation_p.Q401H	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	496					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q496H(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TGTGGAGTTTCTGGTGTCTAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	X											132	120	124					X																	134421114		2203	4300	6503	134248780	SO:0001583	missense	7626			S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"Zinc fingers, C2H2-type", "-", "-", "-"	13145	protein-coding gene	gene with protein product		314997	"zinc finger protein 75 (D8C6)"	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.1488G>T	X.37:g.134421114C>A	ENSP00000359802:p.Gln496His		134248780	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Missense_Mutation	SNP	ENST00000370766.3	37	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331310	0.41297	.	.	ENSG00000186376	ENST00000370766;ENST00000370764	T;T	0.36520	3.17;1.25	3.14	-0.838	0.10762	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.271300	0.19696	N	0.108149	T	0.31734	0.0806	M	0.79123	2.44	0.25444	N	0.988061	B;B	0.24043	0.096;0.096	B;B	0.16722	0.016;0.016	T	0.24190	-1.0167	10	0.49607	T	0.09	.	4.3891	0.11332	0.0:0.4888:0.1693:0.3419	.	496;401	P51815;A6NK62	ZN75D_HUMAN;.	H	496;401	ENSP00000359802:Q496H;ENSP00000359800:Q401H	ENSP00000359800:Q401H	Q	-	3	2	ZNF75D	134248780	0.466000	0.25823	0.560000	0.28344	0.644000	0.38419	1.551000	0.36233	-0.340000	0.08388	0.422000	0.28245	CAG		0.413	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131		A	134421114	C	A	134421114	3	1	61	1	0	0	0	0	1	0	0	0	18173	912	32	2	48	2	ZNF75D	23	134421114	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	793499	134421114	20849446	12254	20239										
ZNF449	203523	broad.mit.edu	37	chrX	134494640	134494640	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatcttatagggcaccagaGaacccattctgaagaagaaa	8	9	2	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:134494640G>T	ENST00000339249.4	+	5	1336	c.1196G>T	c.(1195-1197)aGa>aTa	p.R399I		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	399					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R399I(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GGGCACCAGAGAACCCATTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											89	91	90					X																	134494640		2203	4299	6502	134322306	SO:0001583	missense	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.1196G>T	X.37:g.134494640G>T	ENSP00000339585:p.Arg399Ile		134322306	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	37	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.272403	0.59649	.	.	ENSG00000173275	ENST00000339249	T	0.07688	3.17	4.39	4.39	0.52855	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000160	T	0.27866	0.0686	M	0.87328	2.875	0.80722	D	1	D	0.65815	0.995	P	0.57371	0.819	T	0.13124	-1.0521	10	0.87932	D	0	.	13.6946	0.62569	0.0:0.0:1.0:0.0	.	399	Q6P9G9	ZN449_HUMAN	I	399	ENSP00000339585:R399I	ENSP00000339585:R399I	R	+	2	0	ZNF449	134322306	0.956000	0.32656	1.000000	0.80357	0.827000	0.46813	2.340000	0.43974	2.190000	0.69967	0.529000	0.55759	AGA		0.403	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		T	134494640	G	T	134494640	3	4	61	1	0	0	0	0	1	0	0	0	17959	942	33	2	1210	2	ZNF449	23	134494640	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	73526	134494640	20775920	12255	20240										
ZNF449	203523	broad.mit.edu	37	chrX	134494720	134494720	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gatcaagtcttaaaagacatCtgaaaactcatacaggtgaa	7	7	4	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:134494720C>T	ENST00000339249.4	+	5	1416	c.1276C>T	c.(1276-1278)Ctg>Ttg	p.L426L		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	426					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L426L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					TAAAAGACATCTGAAAACTCA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	X											75	79	77					X																	134494720		2203	4297	6500	134322386	SO:0001819	synonymous_variant	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.1276C>T	X.37:g.134494720C>T			134322386	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																				0.378	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		T	134494720	C	T	134494720	2	4	61	1	0	0	0	0	0	0	0	1	17959	912	32	3		3	ZNF449	23	134494720	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	80	134494720	20775840	12256	20241										
SAGE1	55511	broad.mit.edu	37	chrX	134992598	134992598	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgcagtcactcacaacatccGtgaagagaagataaataaca	7	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:134992598G>A	ENST00000370709.3	+	15	1889	c.1889G>A	c.(1888-1890)cGt>cAt	p.R630H	SAGE1_ENST00000537770.1_Missense_Mutation_p.R254H|SAGE1_ENST00000324447.3_Missense_Mutation_p.R630H|SAGE1_ENST00000535938.1_Missense_Mutation_p.R630H			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	630						nucleus (GO:0005634)		p.R630H(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CACAACATCCGTGAAGAGAAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											137	110	119					X																	134992598		2203	4300	6503	134820264	SO:0001583	missense	55511			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1889G>A	X.37:g.134992598G>A	ENSP00000359743:p.Arg630His		134820264	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	G	4.723	0.134429	0.09032	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.35605	1.3;1.3;1.43;1.3	1.22	-0.186	0.13272	.	0.000000	0.64402	U	0.000002	T	0.12050	0.0293	N	0.04880	-0.145	0.09310	N	1	B;B	0.16396	0.017;0.005	B;B	0.15052	0.012;0.005	T	0.18903	-1.0322	10	0.13108	T	0.6	.	2.966	0.05908	0.6768:0.0:0.3232:0.0	.	254;630	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	H	630;630;254;630	ENSP00000323191:R630H;ENSP00000445959:R630H;ENSP00000438276:R254H;ENSP00000359743:R630H	ENSP00000323191:R630H	R	+	2	0	SAGE1	134820264	0.006000	0.16342	0.005000	0.12908	0.009000	0.06853	-0.158000	0.10070	-0.068000	0.12953	0.181000	0.17075	CGT		0.488	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		A	134992598	G	A	134992598	3	1	61	1	0	0	0	0	1	0	0	0	13846	1145	40	1	1947	1	SAGE1	23	134992598	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	497878	134992598	20277962	12257	20242										
FHL1	2273	broad.mit.edu	37	chrX	135288732	135288732	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtggaatgccgcaagcccatCggtgcggactccaaggtaac	13	12	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135288732C>T	ENST00000345434.3	+	2	222	c.141C>T	c.(139-141)atC>atT	p.I47I	FHL1_ENST00000543669.1_Silent_p.I47I|FHL1_ENST00000370676.3_Silent_p.I63I|FHL1_ENST00000535737.1_Silent_p.I47I|FHL1_ENST00000370690.3_Silent_p.I47I|FHL1_ENST00000370683.1_Silent_p.I63I|FHL1_ENST00000394153.2_Silent_p.I47I|FHL1_ENST00000394155.2_Silent_p.I47I|FHL1_ENST00000539015.1_Silent_p.I76I|FHL1_ENST00000477080.1_3'UTR			Q13642	FHL1_HUMAN	four and a half LIM domains 1	47	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)	p.I47I(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					GCAAGCCCATCGGTGCGGACT	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	X											165	147	153					X																	135288732		2203	4300	6503	135116398	SO:0001819	synonymous_variant	2273			U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"Four-and-a-half LIM domains 1", "LIM protein SLIMMER"	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.141C>T	X.37:g.135288732C>T			135116398	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Silent	SNP	ENST00000345434.3	37	CCDS55507.1																																																																																				0.562	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449		T	135288732	C	T	135288732	2	4	61	1	0	0	0	0	0	0	0	1	5897	874	31	1		1	FHL1	23	135288732	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	296134	135288732	19981828	12258	20243										
MAP7D3	79649	broad.mit.edu	37	chrX	135326916	135326916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttttcatattggagcttggTctttctttctttttcaagta	6	6	5	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135326916T>C	ENST00000316077.9	-	4	512	c.292A>G	c.(292-294)Acc>Gcc	p.T98A	MAP7D3_ENST00000370661.1_Missense_Mutation_p.T98A|MAP7D3_ENST00000370663.5_Missense_Mutation_p.T80A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	98					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.T395A(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TGGAGCTTGGTCTTTCTTTCT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	X											148	126	133					X																	135326916		1827	4076	5903	135154582	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.292A>G	X.37:g.135326916T>C	ENSP00000318086:p.Thr98Ala		135154582	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	0.423	-0.907137	0.02434	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.23	-0.559	0.11792	.	.	.	.	.	T	0.01976	0.0062	N	0.01576	-0.805	0.22787	N	0.998737	B;B;B;B	0.23591	0.053;0.088;0.053;0.088	B;B;B;B	0.25140	0.026;0.058;0.026;0.058	T	0.45614	-0.9249	9	0.02654	T	1	-7.285	9.144	0.36921	0.1457:0.6832:0.0:0.1712	.	80;98;98;98	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	A	98;98;80;98	ENSP00000359695:T98A;ENSP00000318086:T98A;ENSP00000359697:T80A;ENSP00000359694:T98A	ENSP00000318086:T98A	T	-	1	0	MAP7D3	135154582	0.842000	0.29525	0.003000	0.11579	0.408000	0.30992	0.783000	0.26802	-0.206000	0.10203	-0.513000	0.04457	ACC		0.353	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135326916	T	C	135326916	3	2	61	1	0	0	0	0	1	0	0	0	9299	1667	58	4	2398	4	MAP7D3	23	135326916	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	38184	135326916	19943644	12259	20244										
GPR112	139378	broad.mit.edu	37	chrX	135405088	135405088	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcaaggtattggatggccttCtcttatattactaataacgc	7	8	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135405088C>A	ENST00000394143.1	+	5	513	c.222C>A	c.(220-222)ttC>ttA	p.F74L	GPR112_ENST00000370652.1_Missense_Mutation_p.F74L|GPR112_ENST00000287534.4_Missense_Mutation_p.F11L|GPR112_ENST00000394141.1_Intron|GPR112_ENST00000412101.1_Intron	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	74					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F74L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GGATGGCCTTCTCTTATATTA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											116	110	112					X																	135405088		2203	4300	6503	135232754	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.222C>A	X.37:g.135405088C>A	ENSP00000377699:p.Phe74Leu		135232754	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604457	0.46423	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000287534	T;T;T	0.63744	3.08;3.08;-0.06	5.62	1.37	0.22104	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.69405	0.3107	M	0.62723	1.935	0.19300	N	0.999976	D	0.57257	0.979	P	0.60473	0.875	T	0.57341	-0.7828	9	0.87932	D	0	.	6.3431	0.21335	0.0:0.3904:0.0:0.6096	.	74	Q8IZF6	GP112_HUMAN	L	74;74;11	ENSP00000377699:F74L;ENSP00000359686:F74L;ENSP00000287534:F11L	ENSP00000287534:F11L	F	+	3	2	GPR112	135232754	0.997000	0.39634	0.902000	0.35471	0.319000	0.28217	0.399000	0.20916	0.192000	0.20272	0.513000	0.50165	TTC		0.438	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			A	135405088	C	A	135405088	3	1	61	1	0	0	0	0	1	0	0	0	6649	912	32	2	228	2	GPR112	23	135405088	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	78172	135405088	19865472	12260	20245										
GPR112	139378	broad.mit.edu	37	chrX	135432547	135432547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggactccacaccttcctttCtatctacggaagcatcgact	6	14	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135432547C>A	ENST00000394143.1	+	6	6973	c.6682C>A	c.(6682-6684)Cta>Ata	p.L2228I	GPR112_ENST00000370652.1_Missense_Mutation_p.L2228I|GPR112_ENST00000287534.4_Missense_Mutation_p.L2165I|GPR112_ENST00000394141.1_Missense_Mutation_p.L2023I|GPR112_ENST00000412101.1_Missense_Mutation_p.L2023I	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2228					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L2228I(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ACCTTCCTTTCTATCTACGGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	X											143	118	127					X																	135432547		2203	4300	6503	135260213	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.6682C>A	X.37:g.135432547C>A	ENSP00000377699:p.Leu2228Ile		135260213	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	4.870	0.161794	0.09287	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.34859	1.39;1.39;1.34;1.53;1.34	3.77	-7.55	0.01327	.	.	.	.	.	T	0.16642	0.0400	L	0.29908	0.895	0.09310	N	1	B;B;P	0.34977	0.23;0.123;0.478	B;B;B	0.28139	0.086;0.023;0.056	T	0.11690	-1.0577	9	0.48119	T	0.1	.	2.8105	0.05440	0.372:0.161:0.3676:0.0994	.	2165;2023;2228	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	I	2228;2228;2023;2165;2023	ENSP00000377699:L2228I;ENSP00000359686:L2228I;ENSP00000416526:L2023I;ENSP00000287534:L2165I;ENSP00000377697:L2023I	ENSP00000287534:L2165I	L	+	1	2	GPR112	135260213	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.488000	0.02308	-1.456000	0.01921	-0.557000	0.04193	CTA		0.468	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			A	135432547	C	A	135432547	3	1	61	1	0	0	0	0	1	0	0	0	6649	912	32	2	6692	2	GPR112	23	135432547	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	27459	135432547	19838013	12261	20246										
GPR112	139378	broad.mit.edu	37	chrX	135487987	135487987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aatcccaaatccagaagactCggcggaagatgatcctgcat	9	11	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135487987C>T	ENST00000394143.1	+	23	9082	c.8791C>T	c.(8791-8793)Cgg>Tgg	p.R2931W	GPR112_ENST00000370652.1_Missense_Mutation_p.R2931W|GPR112_ENST00000287534.4_Missense_Mutation_p.R2684W|GPR112_ENST00000394141.1_Missense_Mutation_p.R2726W|GPR112_ENST00000412101.1_Missense_Mutation_p.R2726W	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2931					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R2931W(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CCAGAAGACTCGGCGGAAGAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	X											151	132	138					X																	135487987		2203	4300	6503	135315653	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.8791C>T	X.37:g.135487987C>T	ENSP00000377699:p.Arg2931Trp		135315653	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896092	0.33442	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	4.71	1.75	0.24633	GPCR, family 2-like (1);	.	.	.	.	T	0.35624	0.0938	N	0.17723	0.515	0.09310	N	1	P;B	0.44776	0.843;0.289	P;P	0.50231	0.466;0.635	T	0.15867	-1.0422	9	0.54805	T	0.06	.	7.4137	0.27032	0.0:0.4385:0.0:0.5615	.	2726;2931	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	W	2931;2931;2726;2684;2726	ENSP00000377699:R2931W;ENSP00000359686:R2931W;ENSP00000416526:R2726W;ENSP00000287534:R2684W;ENSP00000377697:R2726W	ENSP00000287534:R2684W	R	+	1	2	GPR112	135315653	0.000000	0.05858	0.315000	0.25238	0.332000	0.28634	-0.774000	0.04684	0.306000	0.22856	-0.380000	0.06706	CGG		0.458	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135487987	C	T	135487987	3	4	61	1	0	0	0	0	1	0	0	0	6649	875	31	1	8869	1	GPR112	23	135487987	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	55440	135487987	19782573	12262	20247										
BRS3	680	broad.mit.edu	37	chrX	135570623	135570623	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaggatggctgttcggaaGaattggttgtaaggtgctct	15	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135570623G>A	ENST00000370648.3	+	1	578	c.350G>A	c.(349-351)aGa>aAa	p.R117K	Z97632.1_ENST00000580943.1_RNA	NM_001727.1	NP_001718.1	P32247	BRS3_HUMAN	bombesin-like receptor 3	117					adult feeding behavior (GO:0008343)|glucose metabolic process (GO:0006006)|regulation of blood pressure (GO:0008217)	integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)	p.R117K(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(1)	23	Acute lymphoblastic leukemia(192;0.000127)					CTGTTCGGAAGAATTGGTTGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											152	140	144					X																	135570623		2203	4300	6503	135398289	SO:0001583	missense	680				CCDS14656.1	Xq26.3	2014-02-21			ENSG00000102239	ENSG00000102239		"GPCR / Class A : Bombesin receptors"	1113	protein-coding gene	gene with protein product		300107				8383682	Standard	NM_001727		Approved	BB3	uc004ezv.1	P32247	OTTHUMG00000022726	ENST00000370648.3:c.350G>A	X.37:g.135570623G>A	ENSP00000359682:p.Arg117Lys		135398289		Missense_Mutation	SNP	ENST00000370648.3	37	CCDS14656.1	.	.	.	.	.	.	.	.	.	.	G	10.90	1.482485	0.26598	.	.	ENSG00000102239	ENST00000370648	T	0.71934	-0.61	5.92	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.131409	0.52532	N	0.000065	T	0.53481	0.1799	L	0.31926	0.97	0.33043	D	0.531687	B	0.10296	0.003	B	0.15052	0.012	T	0.50676	-0.8800	10	0.08381	T	0.77	-3.5829	9.1616	0.37025	0.2384:0.0:0.7616:0.0	.	117	P32247	BRS3_HUMAN	K	117	ENSP00000359682:R117K	ENSP00000359682:R117K	R	+	2	0	BRS3	135398289	1.000000	0.71417	0.960000	0.40013	0.992000	0.81027	3.585000	0.53943	0.274000	0.22072	0.594000	0.82650	AGA		0.453	BRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059005.1	NM_001727		A	135570623	G	A	135570623	3	1	61	1	0	0	0	0	1	0	0	0	1525	942	33	3	352	3	BRS3	23	135570623	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	82636	135570623	19699937	12263	20248										
BRS3	680	broad.mit.edu	37	chrX	135574341	135574341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tctctactggctgagcaaaaGcttccagaagcattttaaag	8	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135574341G>T	ENST00000370648.3	+	3	1235	c.1007G>T	c.(1006-1008)aGc>aTc	p.S336I		NM_001727.1	NP_001718.1	P32247	BRS3_HUMAN	bombesin-like receptor 3	336					adult feeding behavior (GO:0008343)|glucose metabolic process (GO:0006006)|regulation of blood pressure (GO:0008217)	integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)	p.S336I(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(1)	23	Acute lymphoblastic leukemia(192;0.000127)					CTGAGCAAAAGCTTCCAGAAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	X											145	133	137					X																	135574341		2203	4300	6503	135402007	SO:0001583	missense	680				CCDS14656.1	Xq26.3	2014-02-21			ENSG00000102239	ENSG00000102239		"GPCR / Class A : Bombesin receptors"	1113	protein-coding gene	gene with protein product		300107				8383682	Standard	NM_001727		Approved	BB3	uc004ezv.1	P32247	OTTHUMG00000022726	ENST00000370648.3:c.1007G>T	X.37:g.135574341G>T	ENSP00000359682:p.Ser336Ile		135402007		Missense_Mutation	SNP	ENST00000370648.3	37	CCDS14656.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.776479	0.31411	.	.	ENSG00000102239	ENST00000370648	T	0.38401	1.14	5.81	4.01	0.46588	.	0.213183	0.39210	N	0.001422	T	0.35828	0.0945	L	0.38175	1.15	0.23361	N	0.997838	P	0.36789	0.57	B	0.40066	0.318	T	0.18178	-1.0345	10	0.54805	T	0.06	-8.034	17.6475	0.88152	0.0:0.4432:0.5568:0.0	.	336	P32247	BRS3_HUMAN	I	336	ENSP00000359682:S336I	ENSP00000359682:S336I	S	+	2	0	BRS3	135402007	0.988000	0.35896	1.000000	0.80357	0.627000	0.37826	0.575000	0.23729	0.571000	0.29365	-0.185000	0.12909	AGC		0.502	BRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059005.1	NM_001727		T	135574341	G	T	135574341	3	4	61	1	0	0	0	0	1	0	0	0	1525	971	34	2	1017	2	BRS3	23	135574341	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	3718	135574341	19696219	12264	20249										
ARHGEF6	9459	broad.mit.edu	37	chrX	135751652	135751652	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttttattacctgcttcagttCtctgacctcgtccttcaagg	6	12	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135751652C>A	ENST00000250617.6	-	21	3384	c.2179G>T	c.(2179-2181)Gaa>Taa	p.E727*	ARHGEF6_ENST00000535227.1_Nonsense_Mutation_p.E600*|ARHGEF6_ENST00000370622.1_Nonsense_Mutation_p.E573*|ARHGEF6_ENST00000370620.1_Nonsense_Mutation_p.E573*	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	727					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E727*(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TGCTTCAGTTCTCTGACCTCG	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											100	92	94					X																	135751652		2203	4300	6503	135579318	SO:0001587	stop_gained	9459			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.2179G>T	X.37:g.135751652C>A	ENSP00000250617:p.Glu727*		135579318	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Nonsense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	42	9.244519	0.99111	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	18.8569	0.92255	0.0:1.0:0.0:0.0	.	.	.	.	X	727;573;573;573;600	.	ENSP00000250617:E727X	E	-	1	0	ARHGEF6	135579318	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	6.947000	0.75959	2.399000	0.81585	0.506000	0.49869	GAA		0.398	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		A	135751652	C	A	135751652	4	1	61	1	0	0	0	0	0	1	0	0	910	922	32	2	159	2	ARHGEF6	23	135751652	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	177311	135751652	19518908	12265	20250										
ARHGEF6	9459	broad.mit.edu	37	chrX	135757193	135757193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atggccttgttgaaaatttgCgctggtgcagtaggcttcga	13	7	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:135757193C>T	ENST00000250617.6	-	19	3213	c.2008G>A	c.(2008-2010)Gca>Aca	p.A670T	ARHGEF6_ENST00000535227.1_Missense_Mutation_p.A543T|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.A516T|ARHGEF6_ENST00000370620.1_Missense_Mutation_p.A516T	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	670					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A670T(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TGAAAATTTGCGCTGGTGCAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											156	136	142					X																	135757193		2203	4300	6503	135584859	SO:0001583	missense	9459			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.2008G>A	X.37:g.135757193C>T	ENSP00000250617:p.Ala670Thr		135584859	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.897056	0.52121	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.55413	0.53;0.62;0.62;0.52	5.52	4.66	0.58398	.	0.096519	0.64402	N	0.000001	T	0.64170	0.2574	L	0.45698	1.435	0.58432	D	0.999997	D;D	0.89917	1.0;0.998	D;P	0.91635	0.999;0.844	T	0.60347	-0.7281	10	0.30078	T	0.28	.	13.3755	0.60736	0.0:0.9224:0.0:0.0776	.	543;670	B7Z3C7;Q15052	.;ARHG6_HUMAN	T	670;516;516;516;543	ENSP00000250617:A670T;ENSP00000359654:A516T;ENSP00000359656:A516T;ENSP00000439483:A543T	ENSP00000250617:A670T	A	-	1	0	ARHGEF6	135584859	1.000000	0.71417	0.076000	0.20297	0.069000	0.16628	4.389000	0.59639	1.095000	0.41419	0.600000	0.82982	GCA		0.398	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		T	135757193	C	T	135757193	3	4	61	1	0	0	0	0	1	0	0	0	910	768	27	1	338	1	ARHGEF6	23	135757193	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	5541	135757193	19513367	12266	20251										
GPR101	83550	broad.mit.edu	37	chrX	136113163	136113163	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcttgacattgtacagcagaGcatgctgcctccgggctgca	11	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:136113163G>A	ENST00000298110.1	-	1	670	c.671C>T	c.(670-672)gCt>gTt	p.A224V		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.A224V(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GTACAGCAGAGCATGCTGCCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	88	92					X																	136113163		2203	4300	6503	135940829	SO:0001583	missense	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.671C>T	X.37:g.136113163G>A	ENSP00000298110:p.Ala224Val		135940829	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.303045	0.81136	.	.	ENSG00000165370	ENST00000298110	T	0.37235	1.21	5.39	5.39	0.77823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33610	N	0.004736	T	0.56001	0.1956	L	0.52905	1.665	0.53005	D	0.999961	D	0.89917	1.0	D	0.91635	0.999	T	0.57923	-0.7727	10	0.66056	D	0.02	-11.9732	15.4692	0.75429	0.0:0.0:1.0:0.0	.	224	Q96P66	GP101_HUMAN	V	224	ENSP00000298110:A224V	ENSP00000298110:A224V	A	-	2	0	GPR101	135940829	1.000000	0.71417	0.987000	0.45799	0.938000	0.57974	5.711000	0.68400	2.245000	0.73994	0.600000	0.82982	GCT		0.517	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			A	136113163	G	A	136113163	3	1	61	1	0	0	0	0	1	0	0	0	6642	971	34	3	858	3	GPR101	23	136113163	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	355970	136113163	19157397	12267	20252										
GPR101	83550	broad.mit.edu	37	chrX	136113507	136113507	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaggcgaacaggtgggtgagGctaaccagggccgtgcagaa	17	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:136113507G>A	ENST00000298110.1	-	1	326	c.327C>T	c.(325-327)agC>agT	p.S109S		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.S109S(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GGTGGGTGAGGCTAACCAGGG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	X											72	54	60					X																	136113507		2203	4300	6503	135941173	SO:0001819	synonymous_variant	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.327C>T	X.37:g.136113507G>A			135941173	Q5JSM8|Q8NG93	Silent	SNP	ENST00000298110.1	37	CCDS14662.1																																																																																				0.612	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			A	136113507	G	A	136113507	2	1	61	1	0	0	0	0	0	0	0	1	6642	1194	42	3		3	GPR101	23	136113507	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	344	136113507	19157053	12268	20253										
FGF13	2258	broad.mit.edu	37	chrX	137717685	137717685	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acatggttgcctttcatgatCtctccttctttgttcagacc	6	12	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:137717685C>A	ENST00000315930.6	-	4	1195	c.534G>T	c.(532-534)gaG>gaT	p.E178D	FGF13_ENST00000541469.1_Missense_Mutation_p.E132D|FGF13_ENST00000370603.3_Missense_Mutation_p.E188D|FGF13_ENST00000441825.2_Missense_Mutation_p.E159D|FGF13_ENST00000305414.4_Missense_Mutation_p.E125D	NM_004114.3	NP_004105.1	Q92913	FGF13_HUMAN	fibroblast growth factor 13	178	Mediates interaction with sodium channels.				cell-cell signaling (GO:0007267)|cerebral cortex cell migration (GO:0021795)|establishment of neuroblast polarity (GO:0045200)|hippocampus development (GO:0021766)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|microtubule polymerization (GO:0046785)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of microtubule depolymerization (GO:0007026)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|positive regulation of protein kinase activity (GO:0045860)|protein localization to plasma membrane (GO:0072659)|signal transduction (GO:0007165)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|filopodium (GO:0030175)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|microtubule (GO:0005874)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-tubulin binding (GO:0048487)|growth factor activity (GO:0008083)|ion channel binding (GO:0044325)|microtubule binding (GO:0008017)|protein kinase activator activity (GO:0030295)|sodium channel regulator activity (GO:0017080)	p.E178D(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	24	Acute lymphoblastic leukemia(192;0.000127)					CTTTCATGATCTCTCCTTCTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	X											213	178	190					X																	137717685		2203	4300	6503	137545351	SO:0001583	missense	2258			BC034340	CCDS14664.1, CCDS14665.1, CCDS55511.1	Xq26.3	2008-02-05			ENSG00000129682	ENSG00000129682			3670	protein-coding gene	gene with protein product	"fibroblast growth factor homologous factor 2"	300070				8790420	Standard	NM_033642		Approved	FHF2, FGF2	uc011mwj.2	Q92913	OTTHUMG00000022532	ENST00000315930.6:c.534G>T	X.37:g.137717685C>A	ENSP00000322390:p.Glu178Asp		137545351	B1AK18|B7Z4M7|B7Z8N0|D3DWH4|O95830|Q9NZH9|Q9NZI0	Missense_Mutation	SNP	ENST00000315930.6	37	CCDS14665.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910084	0.52439	.	.	ENSG00000129682	ENST00000315930;ENST00000305414;ENST00000441825;ENST00000370603;ENST00000541469;ENST00000436198;ENST00000455663	D;D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	6.17	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.67979	0.2951	L	0.32530	0.975	0.52099	D	0.999944	B;B;B;B	0.19583	0.007;0.037;0.003;0.003	B;B;B;B	0.27500	0.017;0.08;0.006;0.024	T	0.61232	-0.7104	10	0.32370	T	0.25	.	4.3126	0.10977	0.0:0.5501:0.0:0.4499	.	132;188;125;178	B7Z8N0;B7Z4M7;Q92913-2;Q92913	.;.;.;FGF13_HUMAN	D	178;125;159;188;132;188;194	ENSP00000322390:E178D;ENSP00000303391:E125D;ENSP00000409276:E159D;ENSP00000359635:E188D;ENSP00000437903:E132D;ENSP00000396198:E188D;ENSP00000406916:E194D	ENSP00000303391:E125D	E	-	3	2	FGF13	137545351	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.534000	0.45676	1.352000	0.45808	0.600000	0.82982	GAG		0.408	FGF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058534.2	NM_004114		A	137717685	C	A	137717685	3	1	61	1	0	0	0	0	1	0	0	0	5861	912	32	2	211	2	FGF13	23	137717685	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1604178	137717685	17552875	12269	20254										
ATP11C	286410	broad.mit.edu	37	chrX	138825742	138825742	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agggttacagtgaatactaaGactgtaaaaacaatggttcc	9	6	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:138825742G>T	ENST00000327569.3	-	26	3113	c.3015C>A	c.(3013-3015)gtC>gtA	p.V1005V	ATP11C_ENST00000370543.1_Silent_p.V1005V|ATP11C_ENST00000359686.2_Silent_p.V1005V|ATP11C_ENST00000370557.1_Silent_p.V999V|ATP11C_ENST00000361648.2_Silent_p.V1005V|ATP11C_ENST00000460773.1_5'UTR	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	1005					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V1005V(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TGAATACTAAGACTGTAAAAA	0.259																																																1	Substitution - coding silent(1)	large_intestine(1)	X											42	34	37					X																	138825742		2195	4272	6467	138653408	SO:0001819	synonymous_variant	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.3015C>A	X.37:g.138825742G>T			138653408	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Silent	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	G	8.536	0.872127	0.17322	.	.	ENSG00000101974	ENST00000433868	.	.	.	5.57	4.7	0.59300	.	.	.	.	.	T	0.47967	0.1474	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48937	-0.8990	4	.	.	.	.	3.46	0.07529	0.0935:0.1788:0.5637:0.1641	.	.	.	.	I	38	.	.	L	-	1	0	ATP11C	138653408	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.451000	0.21779	2.349000	0.79799	0.529000	0.55759	CTT		0.259	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		T	138825742	G	T	138825742	2	4	61	1	0	0	0	0	0	0	0	1	1122	929	33	2		2	ATP11C	23	138825742	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1108057	138825742	16444818	12270	20255										
CXorf66	347487	broad.mit.edu	37	chrX	139038777	139038777	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tgccctttctggactcgatgAatcagatgacttgtctgcag	10	10	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:139038777A>C	ENST00000370540.1	-	3	387	c.364T>G	c.(364-366)Tca>Gca	p.S122A		NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN	chromosome X open reading frame 66	122	Ser-rich.					integral component of membrane (GO:0016021)		p.S122A(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						GGACTCGATGAATCAGATGAC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											242	199	214					X																	139038777		2203	4300	6503	138866443	SO:0001583	missense	347487				CCDS35411.1	Xq27.1	2014-05-30			ENSG00000203933	ENSG00000203933			33743	protein-coding gene	gene with protein product	"secreted glycoprotein, X-linked"					24709545	Standard	NM_001013403		Approved	RP11-35F15.2, SGPX	uc004fbb.3	Q5JRM2	OTTHUMG00000022539	ENST00000370540.1:c.364T>G	X.37:g.139038777A>C	ENSP00000359571:p.Ser122Ala		138866443		Missense_Mutation	SNP	ENST00000370540.1	37	CCDS35411.1	.	.	.	.	.	.	.	.	.	.	A	3.431	-0.116101	0.06881	.	.	ENSG00000203933	ENST00000370540	T	0.43688	0.94	4.21	1.27	0.21489	.	1.837470	0.03168	N	0.170302	T	0.26376	0.0644	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.14309	-1.0477	9	.	.	.	0.2858	5.9878	0.19444	0.1175:0.4652:0.4173:0.0	.	122	Q5JRM2	CX066_HUMAN	A	122	ENSP00000359571:S122A	.	S	-	1	0	CXorf66	138866443	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	0.304000	0.19228	0.106000	0.17784	-0.290000	0.09829	TCA		0.443	CXorf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058572.1	NM_001013403		C	139038777	A	C	139038777	3	2	61	1	0	0	0	0	1	0	0	0	4124	246	9	4	725	4	CXorf66	23	139038777	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	213035	139038777	16231783	12271	20256										
MAGEC3	139081	broad.mit.edu	37	chrX	140985436	140985436	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccattcagaggccagcaagaGaagtcttagagtttttatcc	9	9	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:140985436G>T	ENST00000298296.1	+	8	1750	c.1750G>T	c.(1750-1752)Gaa>Taa	p.E584*	MAGEC3_ENST00000536088.1_Missense_Mutation_p.R333I|MAGEC3_ENST00000409007.1_Missense_Mutation_p.R333I|MAGEC3_ENST00000443323.2_Missense_Mutation_p.R253I|MAGEC3_ENST00000544766.1_Missense_Mutation_p.R333I	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	584	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.E584*(1)|p.R333I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GCCAGCAAGAGAAGTCTTAGA	0.493																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(2)	X											71	72	71					X																	140985436		2203	4300	6503	140813102	SO:0001587	stop_gained	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1750G>T	X.37:g.140985436G>T	ENSP00000298296:p.Glu584*		140813102	Q3SYA7|Q5JZ43|Q9BZ80	Nonsense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	13.00|13.00	2.106433|2.106433	0.37145|0.37145	.|.	.|.	ENSG00000165509|ENSG00000165509	ENST00000298296|ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	.|T;T;T;T	.|0.04970	.|3.52;3.52;3.52;3.52	1.25|1.25	-2.5|-2.5	0.06384|0.06384	.|.	.|.	.|.	.|.	.|.	.|T	.|0.06416	.|0.0165	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B	.|0.22346	.|0.068	.|B	.|0.34346	.|0.18	.|T	.|0.45352	.|-0.9267	.|8	0.02654|0.87932	T|D	1|0	.|.	5.2174|5.2174	0.15350|0.15350	0.0:0.0:0.4599:0.5401|0.0:0.0:0.4599:0.5401	.|.	.|333	.|Q3SYA7	.|.	X|I	584|333;253;333;333	.|ENSP00000441107:R333I;ENSP00000438254:R253I;ENSP00000440444:R333I;ENSP00000386566:R333I	ENSP00000298296:E584X|ENSP00000386566:R333I	E|R	+|+	1|2	0|0	MAGEC3|MAGEC3	140813102|140813102	0.000000|0.000000	0.05858|0.05858	0.125000|0.125000	0.21846|0.21846	0.052000|0.052000	0.14988|0.14988	-1.250000|-1.250000	0.02885|0.02885	-0.878000|-0.878000	0.04007|0.04007	0.284000|0.284000	0.19432|0.19432	GAA|AGA		0.493	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140985436	G	T	140985436	4	4	61	1	0	0	0	0	0	1	0	0	9212	943	33	2	2147	2	MAGEC3	23	140985436	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	1946659	140985436	14285124	12272	20257										
MAGEC1	9947	broad.mit.edu	37	chrX	140994174	140994174	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tcccctgagagaactcacagTacttttgagggttttcccca	8	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:140994174T>C	ENST00000285879.4	+	4	1270	c.984T>C	c.(982-984)agT>agC	p.S328S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	328								p.S328S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GAACTCACAGTACTTTTGAGG	0.478										HNSCC(15;0.026)																																						1	Substitution - coding silent(1)	large_intestine(1)	X											114	115	114					X																	140994174		2201	4293	6494	140821840	SO:0001819	synonymous_variant	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.984T>C	X.37:g.140994174T>C			140821840	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	37	CCDS35417.1																																																																																				0.478	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		C	140994174	T	C	140994174	2	2	61	1	0	0	0	0	0	0	0	1	9210	1635	57	4		4	MAGEC1	23	140994174	Silent	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	8738	140994174	14276386	12273	20258										
MAGEC2	51438	broad.mit.edu	37	chrX	141291179	141291179	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaagtggtcagggcccacttCtatcagggcaaggccaaaaa	12	10	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:141291179C>A	ENST00000247452.3	-	3	942	c.595G>T	c.(595-597)Gaa>Taa	p.E199*		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	199	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.E199*(1)		NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					GGGCCCACTTCTATCAGGGCA	0.483										HNSCC(46;0.14)																																						1	Substitution - Nonsense(1)	large_intestine(1)	X											116	111	113					X																	141291179		2203	4300	6503	141118845	SO:0001587	stop_gained	51438			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.595G>T	X.37:g.141291179C>A	ENSP00000354660:p.Glu199*		141118845	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Nonsense_Mutation	SNP	ENST00000247452.3	37	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	22.6	4.313698	0.81358	.	.	ENSG00000046774	ENST00000247452	.	.	.	0.988	0.988	0.19796	.	0.064372	0.64402	U	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	4.9988	0.14253	0.0:1.0:0.0:0.0	.	.	.	.	X	199	.	ENSP00000354660:E199X	E	-	1	0	MAGEC2	141118845	0.000000	0.05858	0.005000	0.12908	0.184000	0.23303	-0.045000	0.12003	0.770000	0.33336	0.284000	0.19432	GAA		0.483	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		A	141291179	C	A	141291179	4	1	61	1	0	0	0	0	0	1	0	0	9211	922	32	2	530	2	MAGEC2	23	141291179	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	297005	141291179	13979381	12274	20259										
SPANXN4	441525	broad.mit.edu	37	chrX	142121906	142121906	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttagtgttttactgcaggaaGaataagaaaagaaattcaaa	8	3	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:142121906G>T	ENST00000446864.1	+	2	271	c.174G>T	c.(172-174)aaG>aaT	p.K58N	SPANXN4_ENST00000370504.3_Missense_Mutation_p.K57N	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	58								p.K58N(1)		endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					ACTGCAGGAAGAATAAGAAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											48	43	44					X																	142121906		1878	4087	5965	141949572	SO:0001583	missense	441525			DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 9"	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.174G>T	X.37:g.142121906G>T	ENSP00000405210:p.Lys58Asn		141949572	Q0ZNK6|Q5W0S6	Missense_Mutation	SNP	ENST00000446864.1	37	CCDS48178.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.937097	0.34189	.	.	ENSG00000189326	ENST00000446864;ENST00000370504	T;T	0.09350	2.99;2.99	0.766	0.766	0.18476	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.09310	N	1	P	0.47350	0.894	B	0.39027	0.288	T	0.34179	-0.9839	7	0.34782	T	0.22	.	.	.	.	.	58	Q5MJ08	SPXN4_HUMAN	N	58;57	ENSP00000405210:K58N;ENSP00000359535:K57N	ENSP00000359535:K57N	K	+	3	2	SPANXN4	141949572	0.015000	0.18098	0.017000	0.16124	0.450000	0.32258	0.007000	0.13174	0.640000	0.30582	0.179000	0.17066	AAG		0.403	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613		T	142121906	G	T	142121906	3	4	61	1	0	0	0	0	1	0	0	0	15032	933	33	2	180	2	SPANXN4	23	142121906	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	830727	142121906	13148654	12275	20260										
SPANXN4	441525	broad.mit.edu	37	chrX	142121985	142121985	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atccaatcaaagagaaaggaGacctagacatatctgcagga	9	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:142121985G>T	ENST00000446864.1	+	2	350	c.253G>T	c.(253-255)Gac>Tac	p.D85Y	SPANXN4_ENST00000370504.3_Missense_Mutation_p.D84Y	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	85								p.D85Y(1)		endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGAAAGGAGACCTAGACAT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											45	44	45					X																	142121985		2029	4140	6169	141949651	SO:0001583	missense	441525			DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 9"	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.253G>T	X.37:g.142121985G>T	ENSP00000405210:p.Asp85Tyr		141949651	Q0ZNK6|Q5W0S6	Missense_Mutation	SNP	ENST00000446864.1	37	CCDS48178.1	.	.	.	.	.	.	.	.	.	.	G	9.359	1.067591	0.20067	.	.	ENSG00000189326	ENST00000446864;ENST00000370504	T;T	0.09073	3.02;3.02	1.35	0.429	0.16506	.	.	.	.	.	T	0.17577	0.0422	.	.	.	0.09310	N	1	D	0.63880	0.993	P	0.62885	0.908	T	0.12528	-1.0544	8	0.87932	D	0	.	3.2352	0.06762	0.31:0.0:0.69:0.0	.	85	Q5MJ08	SPXN4_HUMAN	Y	85;84	ENSP00000405210:D85Y;ENSP00000359535:D84Y	ENSP00000359535:D84Y	D	+	1	0	SPANXN4	141949651	0.214000	0.23563	0.001000	0.08648	0.003000	0.03518	0.226000	0.17776	0.063000	0.16370	0.418000	0.28097	GAC		0.398	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613		T	142121985	G	T	142121985	3	4	61	1	0	0	0	0	1	0	0	0	15032	942	33	2	259	2	SPANXN4	23	142121985	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	79	142121985	13148575	12276	20261										
SPANXN3	139067	broad.mit.edu	37	chrX	142596917	142596917	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgaggtaatacacaaatatTattggatattctgatgtttt	7	4	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:142596917T>C	ENST00000370503.2	-	2	236	c.153A>G	c.(151-153)atA>atG	p.I51M	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	51								p.I51M(1)		endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					ACACAAATATTATTGGATATT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											122	109	113					X																	142596917		2203	4300	6503	142424583	SO:0001583	missense	139067				CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 8"	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.153A>G	X.37:g.142596917T>C	ENSP00000359534:p.Ile51Met		142424583	Q0ZNK4	Missense_Mutation	SNP	ENST00000370503.2	37	CCDS35418.1	.	.	.	.	.	.	.	.	.	.	t	12.56	1.974292	0.34848	.	.	ENSG00000189252	ENST00000370503	T	0.07327	3.2	3.04	-2.5	0.06384	.	.	.	.	.	T	0.06826	0.0174	L	0.29908	0.895	0.09310	N	1	D	0.53151	0.958	P	0.48334	0.574	T	0.17837	-1.0356	9	0.87932	D	0	.	1.1165	0.01715	0.1908:0.1298:0.3852:0.2942	.	51	Q5MJ09	SPXN3_HUMAN	M	51	ENSP00000359534:I51M	ENSP00000359534:I51M	I	-	3	3	SPANXN3	142424583	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.637000	0.05459	-0.661000	0.05345	0.475000	0.43553	ATA		0.398	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609		C	142596917	T	C	142596917	3	2	61	1	0	0	0	0	1	0	0	0	15031	1744	61	4	276	4	SPANXN3	23	142596917	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	474932	142596917	12673643	12277	20262										
SLITRK4	139065	broad.mit.edu	37	chrX	142718688	142718688	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	actgcatgtgaaaaattcaaGaatgtatttggatacagaat	8	4	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:142718688G>T	ENST00000381779.4	-	2	462	c.237C>A	c.(235-237)ttC>ttA	p.F79L	SLITRK4_ENST00000338017.4_Missense_Mutation_p.F79L|SLITRK4_ENST00000356928.1_Missense_Mutation_p.F79L	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	79						integral component of membrane (GO:0016021)		p.F79L(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					AAAAATTCAAGAATGTATTTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											45	47	46					X																	142718688		2201	4298	6499	142546354	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.237C>A	X.37:g.142718688G>T	ENSP00000371198:p.Phe79Leu		142546354	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654079	0.47362	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.67698	-0.28;-0.28;-0.28	5.61	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.79094	0.4388	M	0.81239	2.535	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.80271	-0.1452	10	0.62326	D	0.03	-12.3426	6.8091	0.23794	0.2074:0.0:0.7926:0.0	.	79	Q8IW52	SLIK4_HUMAN	L	79	ENSP00000371198:F79L;ENSP00000349400:F79L;ENSP00000336627:F79L	ENSP00000336627:F79L	F	-	3	2	SLITRK4	142546354	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.471000	0.45127	2.345000	0.79718	0.600000	0.82982	TTC		0.373	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		T	142718688	G	T	142718688	3	4	61	1	0	0	0	0	1	0	0	0	14782	933	33	2	2280	2	SLITRK4	23	142718688	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	121771	142718688	12551872	12278	20263										
UBE2NL	389898	broad.mit.edu	37	chrX	142967459	142967459	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aaatgtagacaagttggaaaGaataagtttagatattttga	9	1	0	4			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:142967459G>T	ENST00000370494.1	+	1	287	c.257G>T	c.(256-258)aGa>aTa	p.R86I		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	86						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)	p.R86I(2)		breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					AAGTTGGAAAGAATAAGTTTA	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	X											83	77	79					X																	142967459		2203	4300	6503	142795125	SO:0001583	missense	389898					Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"Ubiquitin-conjugating enzymes E2"	31710	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2N-like"			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.257G>T	X.37:g.142967459G>T	ENSP00000359525:p.Arg86Ile		142795125	E9KL27	Missense_Mutation	SNP	ENST00000370494.1	37	CCDS35420.1	.	.	.	.	.	.	.	.	.	.	g	6.782	0.513231	0.12944	.	.	ENSG00000102069	ENST00000370494	T	0.39592	1.07	1.06	-1.02	0.10135	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.113720	0.31685	N	0.007227	T	0.69504	0.3118	H	0.98487	4.245	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.63659	-0.6587	10	0.87932	D	0	-0.0347	3.2831	0.06922	0.1844:0.0:0.5664:0.2492	.	86	Q5JXB2	UE2NL_HUMAN	I	86	ENSP00000359525:R86I	ENSP00000359525:R86I	R	+	2	0	UBE2NL	142795125	1.000000	0.71417	0.907000	0.35723	0.000000	0.00434	4.953000	0.63624	-0.433000	0.07286	-3.074000	0.00066	AGA		0.403	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989		T	142967459	G	T	142967459	3	4	61	1	0	0	0	0	1	0	0	0	16907	942	33	2	259	2	UBE2NL	23	142967459	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	248771	142967459	12303101	12279	20264										
SLITRK2	84631	broad.mit.edu	37	chrX	144904653	144904653	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctagacaccataactgtttTtgtgggagagattgtctgtg	12	6	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:144904653T>G	ENST00000370490.1	+	1	4965	c.710T>G	c.(709-711)tTt>tGt	p.F237C	SLITRK2_ENST00000434188.2_Missense_Mutation_p.F237C|SLITRK2_ENST00000428560.2_Missense_Mutation_p.F237C|SLITRK2_ENST00000447897.2_Missense_Mutation_p.F237C|SLITRK2_ENST00000413937.2_Missense_Mutation_p.F237C			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	237	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.F237C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					ATAACTGTTTTTGTGGGAGAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											109	102	105					X																	144904653		2203	4300	6503	144712345	SO:0001583	missense	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.710T>G	X.37:g.144904653T>G	ENSP00000359521:p.Phe237Cys		144712345	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.924540	0.52653	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65	5.0	5.0	0.66597	Cysteine-rich flanking region, C-terminal (1);	0.057956	0.64402	D	0.000001	T	0.50154	0.1599	L	0.45352	1.415	0.48632	D	0.999687	D	0.54397	0.966	P	0.52672	0.706	T	0.47736	-0.9094	10	0.40728	T	0.16	-8.7477	11.659	0.51334	0.0:0.0:0.0:1.0	.	237	Q9H156	SLIK2_HUMAN	C	237	ENSP00000334374:F237C;ENSP00000411681:F237C;ENSP00000359521:F237C;ENSP00000397015:F237C;ENSP00000407347:F237C;ENSP00000412010:F237C	ENSP00000334374:F237C	F	+	2	0	SLITRK2	144712345	1.000000	0.71417	0.982000	0.44146	0.993000	0.82548	6.170000	0.71920	1.653000	0.50694	0.486000	0.48141	TTT		0.483	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		G	144904653	T	G	144904653	3	3	61	1	0	0	0	0	1	0	0	0	14780	1841	64	4	712	4	SLITRK2	23	144904653	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1937194	144904653	10365907	12280	20265										
FMR1	2332	broad.mit.edu	37	chrX	147010319	147010319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggatgtgccagaagacttacGgcaaatgtaagttgatacac	11	7	0	3	rs200163413		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147010319G>A	ENST00000370475.4	+	5	541	c.413G>A	c.(412-414)cGg>cAg	p.R138Q	FMR1_ENST00000439526.2_Missense_Mutation_p.R138Q|FMR1_ENST00000218200.8_Missense_Mutation_p.R138Q|FMR1_ENST00000370477.1_Missense_Mutation_p.R138Q|FMR1_ENST00000370470.1_Missense_Mutation_p.R138Q|FMR1_ENST00000334557.6_Missense_Mutation_p.R138Q|FMR1_ENST00000440235.2_5'Flank|FMR1_ENST00000370471.3_Missense_Mutation_p.R138Q	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	138			R -> Q (rare variant found in a developmentally delayed male; unknown pathological significance). {ECO:0000269|PubMed:20799337}.		central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R138Q(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GAAGACTTACGGCAAATGTAA	0.338									Fragile X syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	X						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,3834		0,0,1632,570	86	78	81		413,413,413,413,413	5.2	1	X		81	1,6727		0,1,2427,1872	yes	missense,missense,missense,missense,missense	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	43,43,43,43,43	0,1,4059,2442	AA,AG,GG,G		0.0149,0.0,0.0095	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	138/538,138/612,138/517,138/587,138/633	147010319	1,10561	2202	4300	6502	146818011	SO:0001583	missense	2332	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.413G>A	X.37:g.147010319G>A	ENSP00000359506:p.Arg138Gln		146818011	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219402	0.58560	0.0	1.49E-4	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.58210	1.09;0.35;1.13;1.1;1.41;1.12;1.13	5.25	5.25	0.73442	.	0.051505	0.64402	D	0.000001	T	0.43322	0.1242	L	0.40543	1.245	0.80722	D	1	B;P;P;P	0.48911	0.187;0.669;0.911;0.917	B;B;B;B	0.36989	0.029;0.153;0.238;0.168	T	0.45145	-0.9281	10	0.40728	T	0.16	-23.9308	16.9579	0.86264	0.0:0.0:1.0:0.0	.	138;138;138;138	Q8IXW7;Q06787;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.	Q	138	ENSP00000218200:R138Q;ENSP00000359502:R138Q;ENSP00000359508:R138Q;ENSP00000359506:R138Q;ENSP00000355115:R138Q;ENSP00000395923:R138Q;ENSP00000359501:R138Q	ENSP00000218200:R138Q	R	+	2	0	FMR1	146818011	1.000000	0.71417	0.951000	0.38953	0.834000	0.47266	7.790000	0.85794	2.299000	0.77371	0.538000	0.68166	CGG		0.338	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		A	147010319	G	A	147010319	3	1	61	1	0	0	0	0	1	0	0	0	5979	1116	39	1	431	1	FMR1	23	147010319	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	2105666	147010319	8260241	12281	20266										
FMR1	2332	broad.mit.edu	37	chrX	147018985	147018985	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gttttctgttttttaccaagGaaattatgccaccaaattcc	5	9	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147018985G>A	ENST00000370475.4	+	11	1119	c.991G>A	c.(991-993)Gaa>Aaa	p.E331K	FMR1_ENST00000439526.2_Splice_Site_p.E329K|FMR1_ENST00000218200.8_Splice_Site_p.E331K|FMR1_ENST00000370477.1_Splice_Site_p.E331K|FMR1_ENST00000370470.1_Splice_Site_p.E331K|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000370471.3_Splice_Site_p.E331K	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	331					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E331K(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTACCAAGGAAATTATGCC	0.308									Fragile X syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	X											63	64	64					X																	147018985		2199	4294	6493	146826677	SO:0001630	splice_region_variant	2332	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.991-1G>A	X.37:g.147018985G>A			146826677	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800500	0.50315	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000439526;ENST00000370470	T;T;T;T;T;T	0.56941	1.25;0.43;1.25;1.22;1.26;1.25	5.26	5.26	0.73747	K Homology (1);K Homology, type 1 (1);	0.247227	0.34603	N	0.003837	T	0.60637	0.2284	L	0.38175	1.15	0.80722	D	1	B;B;P;D	0.56035	0.008;0.02;0.578;0.974	B;B;B;D	0.67725	0.047;0.035;0.146;0.953	T	0.57843	-0.7741	9	.	.	.	-35.8459	13.4146	0.60961	0.0:0.0:1.0:0.0	.	331;247;331;329	Q06787;Q59GC1;Q06787-8;G3V0J0	FMR1_HUMAN;.;.;.	K	331;331;331;331;329;331	ENSP00000218200:E331K;ENSP00000359502:E331K;ENSP00000359508:E331K;ENSP00000359506:E331K;ENSP00000395923:E329K;ENSP00000359501:E331K	.	E	+	1	0	FMR1	146826677	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.046000	0.64226	2.320000	0.78422	0.506000	0.49869	GAA		0.308	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	Missense_Mutation	A	147018985	G	A	147018985	5	1	61	1	0	0	0	0	0	0	1	0	5979	1188	41	3	1033	3	FMR1	23	147018985	Splice_Site	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	8666	147018985	8251575	12282	20267										
FMR1	2332	broad.mit.edu	37	chrX	147026497	147026497	+	Missense_Mutation	SNP	G	G	A													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agagagggagagcttcctgcGcagaggagacggacggcggc							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147026497G>A	ENST00000370475.4	+	15	1708	c.1580G>A	c.(1579-1581)cGc>cAc	p.R527H	FMR1-IT1_ENST00000441414.1_RNA|FMR1_ENST00000439526.2_Missense_Mutation_p.R504H|FMR1_ENST00000218200.8_Missense_Mutation_p.R506H|FMR1_ENST00000370477.1_Missense_Mutation_p.R494H|FMR1_ENST00000370470.1_Missense_Mutation_p.R502H|FMR1_ENST00000440235.2_Missense_Mutation_p.R174H|FMR1_ENST00000370471.3_Missense_Mutation_p.A437T	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	527	Interaction with RANBP9.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R527H(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTTCCTGCGCAGAGGAGAC	0.512									Fragile X syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	X											63	62	62					X																	147026497		2203	4300	6503	146834189	SO:0001583	missense	2332	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.1580G>A	X.37:g.147026497G>A	ENSP00000359506:p.Arg527His		146834189	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.69|11.69	1.713899|1.713899	0.30413|0.30413	.|.	.|.	ENSG00000102081|ENSG00000102081	ENST00000370471|ENST00000218200;ENST00000370477;ENST00000370475;ENST00000439526;ENST00000370470;ENST00000440235	T|T;T;T;T;T;T	0.57436|0.35789	0.4|1.29;1.29;1.29;1.29;1.29;1.29	5.96|5.96	4.2|4.2	0.49525|0.49525	.|.	.|0.050584	.|0.85682	.|D	.|0.000000	T|T	0.46386|0.46386	0.1390|0.1390	L|L	0.34521|0.34521	1.04|1.04	0.43902|0.43902	D|D	0.996531|0.996531	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;0.997	.|D;D;D;D;P	.|0.91635	.|0.996;0.999;0.983;0.997;0.823	T|T	0.29058|0.29058	-1.0024|-1.0024	7|10	0.38643|0.44086	T|T	0.18|0.13	-36.4109|-36.4109	11.074|11.074	0.48021|0.48021	0.1521:0.0:0.8479:0.0|0.1521:0.0:0.8479:0.0	.|.	.|174;527;422;481;504	.|F8W871;Q06787;Q59GC1;Q06787-8;G3V0J0	.|.;FMR1_HUMAN;.;.;.	T|H	437|506;494;527;504;502;174	ENSP00000359502:A437T|ENSP00000218200:R506H;ENSP00000359508:R494H;ENSP00000359506:R527H;ENSP00000395923:R504H;ENSP00000359501:R502H;ENSP00000413764:R174H	ENSP00000359502:A437T|ENSP00000218200:R506H	A|R	+|+	1|2	0|0	FMR1|FMR1	146834189|146834189	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.082000|0.082000	0.17680|0.17680	5.543000|5.543000	0.67225|0.67225	0.651000|0.651000	0.30788|0.30788	-0.199000|-0.199000	0.12753|0.12753	GCA|CGC		0.512	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		A	147026497	G	A	147026497	3	1	61	1	0	0	0	0	1	0	0	0	5979	1087	38	1	1638	1	FMR1	23	147026497	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	7512	147026497	8244063	12283	20268	20	2								
FMR1	2332	broad.mit.edu	37	chrX	147026507	147026507	+	Silent	SNP	C	C	T													0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agcttcctgcgcagaggagaCggacggcggcgtggaggggg							TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147026507C>T	ENST00000370475.4	+	15	1718	c.1590C>T	c.(1588-1590)gaC>gaT	p.D530D	FMR1-IT1_ENST00000441414.1_RNA|FMR1_ENST00000439526.2_Silent_p.D507D|FMR1_ENST00000218200.8_Silent_p.D509D|FMR1_ENST00000370477.1_Silent_p.D497D|FMR1_ENST00000370470.1_Silent_p.D505D|FMR1_ENST00000440235.2_Silent_p.D177D|FMR1_ENST00000370471.3_Missense_Mutation_p.T440M	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	530	Interaction with RANBP9.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D530D(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GCAGAGGAGACGGACGGCGGC	0.507									Fragile X syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	X											64	64	64					X																	147026507		2203	4300	6503	146834199	SO:0001819	synonymous_variant	2332	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.1590C>T	X.37:g.147026507C>T			146834199	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.346921	0.24426	.	.	ENSG00000102081	ENST00000370471	T	0.56444	0.46	5.7	-0.359	0.12571	.	.	.	.	.	T	0.55705	0.1937	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56232	-0.8013	6	0.87932	D	0	-34.8962	6.987	0.24733	0.0:0.4031:0.1171:0.4798	.	.	.	.	M	440	ENSP00000359502:T440M	ENSP00000359502:T440M	T	+	2	0	FMR1	146834199	0.995000	0.38212	0.724000	0.30704	0.193000	0.23685	0.313000	0.19415	-0.042000	0.13535	0.415000	0.27848	ACG		0.507	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		T	147026507	C	T	147026507	2	4	61	1	0	0	0	0	0	0	0	1	5979	536	19	1		1	FMR1	23	147026507	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	10	147026507	8244053	12284	20269	20	2								
FMR1NB	158521	broad.mit.edu	37	chrX	147090223	147090223	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atttattgccgctctcttttCtggaggaggtaggtgaacat	11	7	2	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147090223C>A	ENST00000370467.3	+	4	698	c.624C>A	c.(622-624)ttC>ttA	p.F208L	5S_rRNA_ENST00000364415.1_RNA	NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	208						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)		p.F208L(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTCTTTTCTGGAGGAGGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											218	159	179					X																	147090223		2203	4300	6503	146897915	SO:0001583	missense	158521				CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"cancer/testis antigen 37"					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.624C>A	X.37:g.147090223C>A	ENSP00000359498:p.Phe208Leu		146897915	D3DWT3	Missense_Mutation	SNP	ENST00000370467.3	37	CCDS14683.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450792	0.26074	.	.	ENSG00000176988	ENST00000370467	T	0.28895	1.59	5.52	0.147	0.14838	.	0.782604	0.10897	N	0.622019	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.15484	0.013	T	0.27872	-1.0061	10	0.31617	T	0.26	-2.3661	9.4007	0.38431	0.0:0.3144:0.5938:0.0918	.	208	Q8N0W7	FMR1N_HUMAN	L	208	ENSP00000359498:F208L	ENSP00000359498:F208L	F	+	3	2	FMR1NB	146897915	0.033000	0.19621	0.000000	0.03702	0.579000	0.36224	-0.100000	0.10990	-0.103000	0.12175	0.544000	0.68410	TTC		0.378	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578		A	147090223	C	A	147090223	3	1	61	1	0	0	0	0	1	0	0	0	5980	912	32	2	638	2	FMR1NB	23	147090223	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	63716	147090223	8180337	12285	20270										
AFF2	2334	broad.mit.edu	37	chrX	147743545	147743545	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	cacctagtgggaattccaaaGaattctgtgccccagaatcc	8	12	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147743545G>T	ENST00000370460.2	+	3	776	c.297G>T	c.(295-297)aaG>aaT	p.K99N	AFF2_ENST00000342251.3_Missense_Mutation_p.K95N|AFF2_ENST00000370458.1_Missense_Mutation_p.K95N|AFF2_ENST00000370457.5_Missense_Mutation_p.K95N	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	99					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.K99N(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GAATTCCAAAGAATTCTGTGC	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											139	142	141					X																	147743545		2203	4300	6503	147551237	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.297G>T	X.37:g.147743545G>T	ENSP00000359489:p.Lys99Asn		147551237	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.275785	0.59649	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.63	5.63	0.86233	.	0.050951	0.85682	D	0.000000	T	0.78685	0.4322	L	0.46157	1.445	0.80722	D	1	D;D;D;D;D;D	0.89917	0.96;0.96;0.96;0.96;0.968;1.0	P;P;P;P;P;D	0.91635	0.643;0.643;0.643;0.643;0.757;0.999	T	0.80374	-0.1409	10	0.87932	D	0	.	18.7175	0.91680	0.0:0.0:1.0:0.0	.	99;95;95;95;99;95	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	N	99;95;95;95	ENSP00000359489:K99N;ENSP00000359486:K95N;ENSP00000345459:K95N;ENSP00000359487:K95N	ENSP00000345459:K95N	K	+	3	2	AFF2	147551237	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.393000	0.59665	2.365000	0.80145	0.600000	0.82982	AAG		0.398	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	147743545	G	T	147743545	3	4	61	1	0	0	0	0	1	0	0	0	357	933	33	2	307	2	AFF2	23	147743545	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	653322	147743545	7527015	12286	20271										
AFF2	2334	broad.mit.edu	37	chrX	147891438	147891438	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ccaagctgtgttgaagaaatCttgcgggtgagtttaaacct	11	7	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:147891438C>A	ENST00000370460.2	+	4	1559	c.1080C>A	c.(1078-1080)atC>atA	p.I360I	AFF2_ENST00000342251.3_Silent_p.I356I|AFF2_ENST00000286437.5_Silent_p.I30I|AFF2_ENST00000370458.1_Silent_p.I356I|AFF2_ENST00000370457.5_Silent_p.I356I	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	360					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.I360I(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					TTGAAGAAATCTTGCGGGTGA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	X											211	181	191					X																	147891438		2203	4300	6503	147699130	SO:0001819	synonymous_variant	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1080C>A	X.37:g.147891438C>A			147699130	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																				0.333	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	147891438	C	A	147891438	2	1	61	1	0	0	0	0	0	0	0	1	357	903	32	2		2	AFF2	23	147891438	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	147893	147891438	7379122	12287	20272										
MAGEA8	4107	broad.mit.edu	37	chrX	149013407	149013407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agaaagtggctgagttagttCgtttcctgctccgcaaatat	10	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:149013407C>T	ENST00000542674.1	+	3	882	c.361C>T	c.(361-363)Cgt>Tgt	p.R121C	MAGEA8_ENST00000535454.1_Missense_Mutation_p.R121C|MAGEA8_ENST00000286482.1_Missense_Mutation_p.R121C	NM_001166401.1	NP_001159873.1	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	121	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		R -> H (in dbSNP:rs35744768).					p.R121C(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)					TGAGTTAGTTCGTTTCCTGCT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X											92	91	91					X																	149013407		2203	4298	6501	148774065	SO:0001583	missense	4107				CCDS14692.1	Xq28	2009-03-13			ENSG00000156009	ENSG00000156009			6806	protein-coding gene	gene with protein product	"MAGE-8 antigen", "cancer/testis antigen family 1, member 8"	300341		MAGE8		8575766	Standard	NM_005364		Approved	MGC2182, CT1.8	uc004fdw.2	P43361	OTTHUMG00000022635	ENST00000542674.1:c.361C>T	X.37:g.149013407C>T	ENSP00000443776:p.Arg121Cys		148774065	Q9BUN9	Missense_Mutation	SNP	ENST00000542674.1	37	CCDS14692.1	.	.	.	.	.	.	.	.	.	.	.	14.49	2.552118	0.45487	.	.	ENSG00000156009	ENST00000535454;ENST00000542674;ENST00000286482	T;T;T	0.07800	3.16;3.16;3.16	0.436	0.436	0.16549	.	1.662530	0.03524	N	0.221529	T	0.18215	0.0437	L	0.55990	1.75	0.09310	N	1	D	0.60575	0.988	P	0.55011	0.766	T	0.20538	-1.0272	9	0.87932	D	0	.	.	.	.	.	121	P43361	MAGA8_HUMAN	C	121	ENSP00000438293:R121C;ENSP00000443776:R121C;ENSP00000286482:R121C	ENSP00000286482:R121C	R	+	1	0	MAGEA8	148774065	0.000000	0.05858	0.011000	0.14972	0.510000	0.34073	-1.649000	0.01993	0.431000	0.26258	0.190000	0.17370	CGT		0.493	MAGEA8-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058728.1	NM_005364		T	149013407	C	T	149013407	3	4	61	1	0	0	0	0	1	0	0	0	9201	884	31	1	363	1	MAGEA8	23	149013407	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	1121969	149013407	6257153	12288	20273										
MAMLD1	10046	broad.mit.edu	37	chrX	149638106	149638106	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aataaaattaagaggccttgCcttgaagatgtcacccttgc	8	9	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:149638106C>A	ENST00000370401.2	+	4	571	c.261C>A	c.(259-261)tgC>tgA	p.C87*	MAMLD1_ENST00000262858.5_Nonsense_Mutation_p.C87*|MAMLD1_ENST00000432680.2_Nonsense_Mutation_p.C62*|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000468306.1_3'UTR|MAMLD1_ENST00000426613.2_Nonsense_Mutation_p.C62*			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	87					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.C14*(1)|p.C87*(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGCCTTGCCTTGAAGATG	0.498																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											104	103	103					X																	149638106		2203	4300	6503	149388764	SO:0001587	stop_gained	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.261C>A	X.37:g.149638106C>A	ENSP00000359428:p.Cys87*		149388764	B2RCQ4|B4DG93|B9EGA5	Nonsense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824442	0.71143	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000358892;ENST00000262858;ENST00000426613	.	.	.	5.36	4.49	0.54785	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-22.7405	9.849	0.41046	0.0:0.8347:0.0:0.1653	.	.	.	.	X	49;87;62;87;87;62	.	ENSP00000262858:C87X	C	+	3	2	MAMLD1	149388764	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.944000	0.29043	2.237000	0.73441	0.600000	0.82982	TGC		0.498	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		A	149638106	C	A	149638106	4	1	61	1	0	0	0	0	0	1	0	0	9238	747	26	2	271	2	MAMLD1	23	149638106	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	624699	149638106	5632454	12289	20274										
MTMR1	8776	broad.mit.edu	37	chrX	149895775	149895775	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aagctgtacttcaaaaatgtCgagagggtgagttttttaaa	10	4	1	2	rs372879184		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:149895775C>T	ENST00000370390.3	+	4	574	c.417C>T	c.(415-417)gtC>gtT	p.V139V	MTMR1_ENST00000542156.1_Silent_p.V139V|MTMR1_ENST00000544228.1_Silent_p.V139V|MTMR1_ENST00000451863.2_Silent_p.V139V|MTMR1_ENST00000541925.1_Silent_p.V45V|MTMR1_ENST00000445323.2_Silent_p.V147V|MTMR1_ENST00000538506.1_Silent_p.V26V	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	139	GRAM.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)	p.V139V(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					TCAAAAATGTCGAGAGGGTGA	0.358													c|||	2	0.000529801	0.0015	0	3775	,	,		12266	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X						C		1,3834		0,1,1631,571	120	99	106		417	-8.8	0	X		106	0,6728		0,0,2428,1872	no	coding-synonymous	MTMR1	NM_003828.2		0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095		139/666	149895775	1,10562	2203	4300	6503	149646433	SO:0001819	synonymous_variant	8776			U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.417C>T	X.37:g.149895775C>T			149646433	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Silent	SNP	ENST00000370390.3	37	CCDS14695.1																																																																																				0.358	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		T	149895775	C	T	149895775	2	4	61	1	0	0	0	0	0	0	0	1	9968	871	31	1		1	MTMR1	23	149895775	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	257669	149895775	5374785	12290	20275										
MAGEA4	4103	broad.mit.edu	37	chrX	151092276	151092276	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctcctcctcctctcctctggTccctggcaccctggaggaag	9	18	2	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:151092276T>C	ENST00000360243.2	+	3	407	c.140T>C	c.(139-141)gTc>gCc	p.V47A	MAGEA4_ENST00000276344.2_Missense_Mutation_p.V47A|MAGEA4_ENST00000370337.4_Missense_Mutation_p.V47A|MAGEA4_ENST00000370340.3_Missense_Mutation_p.V47A|MAGEA4_ENST00000393920.1_Missense_Mutation_p.V47A|MAGEA4_ENST00000370335.1_Missense_Mutation_p.V47A|MAGEA4_ENST00000393921.1_Missense_Mutation_p.V47A	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	47								p.V47A(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TCTCCTCTGGTCCCTGGCACC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	X											61	57	59					X																	151092276		2203	4300	6503	150842932	SO:0001583	missense	4103				CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"melanoma-associated antigen 4", "cancer/testis antigen family 1, member 4"	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.140T>C	X.37:g.151092276T>C	ENSP00000353379:p.Val47Ala		150842932	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.992716	0.35131	.	.	ENSG00000147381	ENST00000431963;ENST00000276344;ENST00000448295;ENST00000393921;ENST00000430273;ENST00000370337;ENST00000441865;ENST00000393920;ENST00000370340;ENST00000416020;ENST00000425182;ENST00000457310;ENST00000370335;ENST00000360243;ENST00000431971	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.04917	3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53	2.4	-0.994	0.10225	Melanoma associated antigen, MAGE, N-terminal (1);	3.846200	0.00848	N	0.001812	T	0.12347	0.0300	M	0.80982	2.52	0.09310	N	1	P	0.46512	0.879	B	0.43508	0.422	T	0.35895	-0.9770	10	0.30078	T	0.28	.	5.5502	0.17086	0.0:0.5516:0.0:0.4484	.	47	P43358	MAGA4_HUMAN	A	47	ENSP00000387777:V47A;ENSP00000276344:V47A;ENSP00000391904:V47A;ENSP00000377498:V47A;ENSP00000394149:V47A;ENSP00000359362:V47A;ENSP00000402624:V47A;ENSP00000377497:V47A;ENSP00000359365:V47A;ENSP00000394073:V47A;ENSP00000400900:V47A;ENSP00000402186:V47A;ENSP00000359360:V47A;ENSP00000353379:V47A;ENSP00000390096:V47A	ENSP00000276344:V47A	V	+	2	0	MAGEA4	150842932	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.556000	0.05992	-0.365000	0.08076	0.356000	0.21956	GTC		0.627	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		C	151092276	T	C	151092276	3	2	61	1	0	0	0	0	1	0	0	0	9198	1667	58	4	142	4	MAGEA4	23	151092276	Missense_Mutation	SNP	T	TCGA-AG-A002-01A-01W-A00K-09	1196501	151092276	4178284	12291	20276										
GABRE	2564	broad.mit.edu	37	chrX	151131056	151131056	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acaagagactcaaaggtgtcGttgtaacagaggcgttcgtc	12	8	1	2	rs200914254		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:151131056G>A	ENST00000370328.3	-	4	455	c.402C>T	c.(400-402)aaC>aaT	p.N134N	GABRE_ENST00000393914.3_De_novo_Start_InFrame|GABRE_ENST00000370325.1_Silent_p.N134N|MIR452_ENST00000385020.1_RNA	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	134					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.N21N(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAAAGGTGTCGTTGTAACAGA	0.483													G|||	2	0.000529801	0	0	3775	,	,		16784	0.001		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											191	152	165					X																	151131056		2203	4300	6503	150881712	SO:0001819	synonymous_variant	2564			Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4085	protein-coding gene	gene with protein product	"GABA(A) receptor, epsilon"	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.402C>T	X.37:g.151131056G>A			150881712	E7ET93|O15345|O15346|Q6PCD2|Q99520	Silent	SNP	ENST00000370328.3	37	CCDS14703.1																																																																																				0.483	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984		A	151131056	G	A	151131056	2	1	61	1	0	0	0	0	0	0	0	1	6189	1136	40	1		1	GABRE	23	151131056	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	38780	151131056	4139504	12292	20277										
GABRA3	2556	broad.mit.edu	37	chrX	151532994	151532994	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gagaatattaatcaggaaaaGaatcccaaggctggtcatgt	10	6	2	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:151532994G>T	ENST00000370314.4	-	2	287	c.49C>A	c.(49-51)Ctt>Att	p.L17I	GABRA3_ENST00000535043.1_Missense_Mutation_p.L17I	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	17					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L17I(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	ATCAGGAAAAGAATCCCAAGG	0.453																																					NSCLC(142;2578 2613 10251 16743)											1	Substitution - Missense(1)	large_intestine(1)	X											160	139	146					X																	151532994		2203	4300	6503	151283650	SO:0001583	missense	2556				CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4077	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 3"	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.49C>A	X.37:g.151532994G>T	ENSP00000359337:p.Leu17Ile		151283650	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	37	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657851	0.29425	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	T;T;T	0.72615	-0.67;-0.67;-0.67	5.29	5.29	0.74685	.	1.807920	0.02759	N	0.118416	T	0.77558	0.4148	N	0.19112	0.55	0.24883	N	0.992215	P	0.46578	0.88	P	0.62184	0.899	T	0.67845	-0.5565	10	0.72032	D	0.01	.	13.1956	0.59736	0.0:0.0:1.0:0.0	.	17	P34903	GBRA3_HUMAN	I	17	ENSP00000359337:L17I;ENSP00000359334:L17I;ENSP00000443527:L17I	ENSP00000359334:L17I	L	-	1	0	GABRA3	151283650	1.000000	0.71417	1.000000	0.80357	0.467000	0.32768	2.982000	0.49337	2.175000	0.68902	0.600000	0.82982	CTT		0.453	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		T	151532994	G	T	151532994	3	4	61	1	0	0	0	0	1	0	0	0	6181	942	33	2	1465	2	GABRA3	23	151532994	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	401938	151532994	3737566	12293	20278										
MAGEA6	4105	broad.mit.edu	37	chrX	151869683	151869683	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	attttctgctcctcaagtatCgagccagggagccggtcaca	10	12	3	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:151869683C>T	ENST00000329342.5	+	3	598	c.373C>T	c.(373-375)Cga>Tga	p.R125*		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	125	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.R125*(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCAAGTATCGAGCCAGGGA	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	X											130	121	124					X																	151869683		2202	4300	6502	151620339	SO:0001587	stop_gained	4105				CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"MAGE-6 antigen", "melanoma-associated antigen 6", "melanoma antigen family A 6", "cancer/testis antigen family 1, member 6"	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.373C>T	X.37:g.151869683C>T	ENSP00000329199:p.Arg125*		151620339	A8IF93|Q6NW44	Nonsense_Mutation	SNP	ENST00000329342.5	37	CCDS14708.1	.	.	.	.	.	.	.	.	.	.	c	15.38	2.817397	0.50633	.	.	ENSG00000197172	ENST00000329342;ENST00000412733;ENST00000457643	.	.	.	0.605	-0.583	0.11706	.	0.363429	0.27294	N	0.020029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	125	.	ENSP00000329199:R125X	R	+	1	2	MAGEA6	151620339	0.017000	0.18338	0.026000	0.17262	0.207000	0.24258	-0.551000	0.06027	-0.314000	0.08716	0.181000	0.17075	CGA		0.527	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363		T	151869683	C	T	151869683	4	4	61	1	0	0	0	0	0	1	0	0	9200	876	31	1	375	1	MAGEA6	23	151869683	Nonsense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	336689	151869683	3400877	12294	20279										
NSDHL	50814	broad.mit.edu	37	chrX	152031184	152031184	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgtcatctttgagggcgtCgatatcaagaatggaactga	12	6	3	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:152031184C>T	ENST00000370274.3	+	5	653	c.459C>T	c.(457-459)gtC>gtT	p.V153V	NSDHL_ENST00000440023.1_Silent_p.V153V	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	153					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)	p.V153V(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TTGAGGGCGTCGATATCAAGA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	X											164	142	149					X																	152031184		2203	4300	6503	151781840	SO:0001819	synonymous_variant	50814			X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	13398	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 31E, member 1"	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.459C>T	X.37:g.152031184C>T			151781840	D3DWT6|O00344	Silent	SNP	ENST00000370274.3	37	CCDS14717.1																																																																																				0.408	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922		T	152031184	C	T	152031184	2	4	61	1	0	0	0	0	0	0	0	1	10701	871	31	1		1	NSDHL	23	152031184	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	161501	152031184	3239376	12295	20280										
NSDHL	50814	broad.mit.edu	37	chrX	152034497	152034497	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	aggaacggcaagatgaagttCgtgattgggtgagtcagccc	15	7	1	4	rs147293409	byFrequency	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:152034497C>T	ENST00000370274.3	+	6	872	c.678C>T	c.(676-678)ttC>ttT	p.F226F	NSDHL_ENST00000440023.1_Silent_p.F226F	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	226					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)	p.F226F(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					AGATGAAGTTCGTGATTGGGT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	X							,	6,3829		0,6,1626,571	97	86	90		678,678	-5.9	0	X	dbSNP_134	90	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous	NSDHL	NM_001129765.1,NM_015922.2	,	0,6,4054,2443	TT,TC,CC,C		0.0,0.1565,0.0568	,	226/374,226/374	152034497	6,10557	2203	4300	6503	151785153	SO:0001819	synonymous_variant	50814			X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	13398	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 31E, member 1"	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.678C>T	X.37:g.152034497C>T			151785153	D3DWT6|O00344	Silent	SNP	ENST00000370274.3	37	CCDS14717.1																																																																																				0.572	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922		T	152034497	C	T	152034497	2	4	61	1	0	0	0	0	0	0	0	1	10701	883	31	1		1	NSDHL	23	152034497	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	3313	152034497	3236063	12296	20281										
ATP2B3	492	broad.mit.edu	37	chrX	152825354	152825354	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atgatgaagaacattctgggCcacgccgtgtaccagctcgc	11	12	1	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:152825354C>T	ENST00000349466.2	+	17	3119	c.2793C>T	c.(2791-2793)ggC>ggT	p.G931G	ATP2B3_ENST00000393842.1_Silent_p.G917G|ATP2B3_ENST00000370181.2_Silent_p.G917G|ATP2B3_ENST00000370186.1_Silent_p.G917G|ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000359149.3_Silent_p.G931G|ATP2B3_ENST00000263519.4_Silent_p.G931G			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	931					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.G931G(2)|p.G917G(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACATTCTGGGCCACGCCGTGT	0.642																																																3	Substitution - coding silent(3)	large_intestine(3)	X											105	77	86					X																	152825354		2203	4300	6503	152478548	SO:0001819	synonymous_variant	492			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2793C>T	X.37:g.152825354C>T			152478548	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																				0.642	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152825354	C	T	152825354	2	4	61	1	0	0	0	0	0	0	0	1	1142	726	26	3		3	ATP2B3	23	152825354	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	790857	152825354	2445206	12297	20282										
SLC6A8	6535	broad.mit.edu	37	chrX	152959632	152959632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggcctcctcgacctcctcccGgcctcctactacttccgttt	6	20	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:152959632G>A	ENST00000253122.5	+	9	1778	c.1302G>A	c.(1300-1302)ccG>ccA	p.P434P	SLC6A8_ENST00000485324.1_3'UTR|SLC6A8_ENST00000430077.2_Silent_p.P319P	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	434				P -> R (in Ref. 9; AAH81558). {ECO:0000305}.	cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)	p.P434P(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	ACCTCCTCCCGGCCTCCTACT	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	X											66	64	65					X																	152959632		2203	4300	6503	152612826	SO:0001819	synonymous_variant	6535				CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.1302G>A	X.37:g.152959632G>A			152612826	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Silent	SNP	ENST00000253122.5	37	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	g	8.837	0.941415	0.18281	.	.	ENSG00000130821	ENST00000442457	.	.	.	5.25	3.37	0.38596	.	.	.	.	.	T	0.46600	0.1401	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38265	-0.9669	4	.	.	.	.	3.1875	0.06606	0.2851:0.0:0.5236:0.1913	.	.	.	.	Q	119	.	.	R	+	2	0	SLC6A8	152612826	0.119000	0.22226	1.000000	0.80357	0.997000	0.91878	-0.000000	0.12993	1.003000	0.39130	0.529000	0.55759	CGG		0.612	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			A	152959632	G	A	152959632	2	1	61	1	0	0	0	0	0	0	0	1	14727	1103	39	1		1	SLC6A8	23	152959632	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	134278	152959632	2310928	12298	20283										
OPN1LW	5956	broad.mit.edu	37	chrX	153421916	153421916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ctgctgccaaccctggttacGccttccaccctttgatggct	8	16	0	1	rs1065440		TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:153421916G>A	ENST00000369951.4	+	5	952	c.892G>A	c.(892-894)Gcc>Acc	p.A298T		NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	298			A -> P (in dbSNP:rs1065440).		phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.A298T(1)		endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CCCTGGTTACGCCTTCCACCC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											378	335	350					X																	153421916		2196	4272	6468	153075110	SO:0001583	missense	5956			Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"GPCR / Class A : Opsin receptors"	9936	protein-coding gene	gene with protein product	"cone dystrophy 5 (X-linked)"	300822	"color blindness, protan", "red cone photoreceptor pigment"	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.892G>A	X.37:g.153421916G>A	ENSP00000358967:p.Ala298Thr		153075110		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132483	0.77662	.	.	ENSG00000102076	ENST00000369951	T	0.72167	-0.63	4.57	0.2	0.15181	GPCR, rhodopsin-like superfamily (1);	0.295627	0.36778	N	0.002418	T	0.57770	0.2076	L	0.46614	1.455	0.35163	D	0.770884	P	0.36587	0.559	B	0.33690	0.168	T	0.60890	-0.7173	10	0.52906	T	0.07	.	9.1823	0.37149	0.0:0.122:0.3792:0.4988	.	298	P04000	OPSR_HUMAN	T	298	ENSP00000358967:A298T	ENSP00000358967:A298T	A	+	1	0	OPN1LW	153075110	0.000000	0.05858	0.954000	0.39281	0.661000	0.39034	-0.274000	0.08537	-0.006000	0.14370	-0.401000	0.06369	GCC		0.542	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061		A	153421916	G	A	153421916	3	1	61	1	0	0	0	0	1	0	0	0	10908	1087	38	1	910	1	OPN1LW	23	153421916	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	462284	153421916	1848644	12299	20284										
TKTL1	8277	broad.mit.edu	37	chrX	153537783	153537783	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gcatatactggcaagtacttCgacagggccaggtgaggttc	13	9	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:153537783C>T	ENST00000369915.3	+	3	528	c.339C>T	c.(337-339)ttC>ttT	p.F113F	TKTL1_ENST00000217905.7_Intron|TKTL1_ENST00000369912.2_Silent_p.F57F	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	113					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.F113F(1)		NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCAAGTACTTCGACAGGGCCA	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	X											252	213	226					X																	153537783		2203	4300	6503	153190977	SO:0001819	synonymous_variant	8277			X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.339C>T	X.37:g.153537783C>T			153190977	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	C	4.122	0.020848	0.08006	.	.	ENSG00000007350	ENST00000426203	.	.	.	4.64	-1.03	0.10102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.2143	4.8078	0.13328	0.0:0.2949:0.1505:0.5547	.	.	.	.	X	96	.	.	R	+	1	2	TKTL1	153190977	0.998000	0.40836	0.927000	0.36925	0.416000	0.31233	0.367000	0.20382	-0.364000	0.08088	-0.380000	0.06706	CGA		0.537	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		T	153537783	C	T	153537783	2	4	61	1	0	0	0	0	0	0	0	1	15974	883	31	1		1	TKTL1	23	153537783	Silent	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	115867	153537783	1732777	12300	20285										
SLC10A3	8273	broad.mit.edu	37	chrX	153716926	153716926	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	caggttatagcactcacgttCttgatggtcagcacctctgt	9	11	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:153716926C>A	ENST00000393587.4	-	3	617	c.354G>T	c.(352-354)aaG>aaT	p.K118N	SLC10A3_ENST00000393586.1_Missense_Mutation_p.K173N|UBL4A_ENST00000369653.4_5'Flank|SLC10A3_ENST00000263512.4_Missense_Mutation_p.K118N|UBL4A_ENST00000369660.4_5'Flank|UBL4A_ENST00000477777.1_5'Flank|SLC10A3_ENST00000369649.4_Missense_Mutation_p.K118N	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	118					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)	p.K118N(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CACTCACGTTCTTGATGGTCA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	X											88	75	80					X																	153716926		2203	4300	6503	153370120	SO:0001583	missense	8273			X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"Solute carriers"	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.354G>T	X.37:g.153716926C>A	ENSP00000377212:p.Lys118Asn		153370120	Q5HY79|Q9BSL2	Missense_Mutation	SNP	ENST00000393587.4	37	CCDS14755.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.798944	0.31777	.	.	ENSG00000126903	ENST00000369649;ENST00000393586;ENST00000263512;ENST00000393587;ENST00000453912	T;T;T;T	0.09817	2.94;2.99;3.04;3.04	5.23	4.35	0.52113	.	0.403926	0.24217	U	0.040478	T	0.14830	0.0358	M	0.70595	2.14	0.30685	N	0.751915	P;P	0.35656	0.454;0.514	B;B	0.37650	0.198;0.255	T	0.05099	-1.0906	10	0.17832	T	0.49	-16.5243	12.3521	0.55155	0.0:0.9132:0.0:0.0868	.	118;118	Q9BSL2;P09131	.;P3_HUMAN	N	118;173;118;118;118	ENSP00000358663:K118N;ENSP00000377211:K173N;ENSP00000263512:K118N;ENSP00000377212:K118N	ENSP00000263512:K118N	K	-	3	2	SLC10A3	153370120	0.786000	0.28738	0.992000	0.48379	0.968000	0.65278	0.478000	0.22212	0.963000	0.38082	0.529000	0.55759	AAG		0.637	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3	NM_019848		A	153716926	C	A	153716926	3	1	61	1	0	0	0	0	1	0	0	0	14412	912	32	2	1083	2	SLC10A3	23	153716926	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	179143	153716926	1553634	12301	20286										
G6PD	2539	broad.mit.edu	37	chrX	153760920	153760920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agctcgttgcgcttgcactgCtggtggaagatgtcgccggc	15	11	0	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:153760920C>A	ENST00000393564.2	-	10	1261	c.1149G>T	c.(1147-1149)caG>caT	p.Q383H	G6PD_ENST00000369620.2_Missense_Mutation_p.Q429H|G6PD_ENST00000497281.1_5'Flank|G6PD_ENST00000393562.2_Missense_Mutation_p.Q413H	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	383					carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.Q383H(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTTGCACTGCTGGTGGAAGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	X											59	49	52					X																	153760920		2203	4300	6503	153414114	SO:0001583	missense	2539			X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.1149G>T	X.37:g.153760920C>A	ENSP00000377194:p.Gln383His		153414114	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	37	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780985	0.31502	.	.	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620	D;D;D	0.99820	-6.93;-6.93;-6.93	5.82	2.97	0.34412	Glucose-6-phosphate dehydrogenase, C-terminal (1);	0.552015	0.20125	N	0.098718	D	0.98664	0.9552	L	0.37630	1.12	0.22771	N	0.99876	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	D	0.99958	1.1662	10	0.54805	T	0.06	.	3.7683	0.08632	0.1382:0.3994:0.367:0.0954	.	383;413	P11413;P11413-3	G6PD_HUMAN;.	H	413;383;383;429	ENSP00000377192:Q413H;ENSP00000377194:Q383H;ENSP00000358633:Q429H	ENSP00000291567:Q383H	Q	-	3	2	G6PD	153414114	0.000000	0.05858	1.000000	0.80357	0.927000	0.56198	-0.707000	0.05041	0.582000	0.29556	0.597000	0.82753	CAG		0.622	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402		A	153760920	C	A	153760920	3	1	61	1	0	0	0	0	1	0	0	0	6165	796	28	2	414	2	G6PD	23	153760920	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	43994	153760920	1509640	12302	20287										
MPP1	4354	broad.mit.edu	37	chrX	154009980	154009980	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tggtagctgccaaactccaaGaactcattggcagagatgtt	10	9	1	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154009980G>A	ENST00000369534.3	-	10	1191	c.1044C>T	c.(1042-1044)ttC>ttT	p.F348F	MPP1_ENST00000462825.1_5'Flank|MPP1_ENST00000413259.3_Silent_p.F318F|MPP1_ENST00000393531.1_Silent_p.F328F	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	348	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|Interaction with MPP5.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.F348F(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CAAACTCCAAGAACTCATTGG	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	X											339	245	277					X																	154009980		2203	4300	6503	153663174	SO:0001819	synonymous_variant	4354				CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.1044C>T	X.37:g.154009980G>A			153663174	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Silent	SNP	ENST00000369534.3	37	CCDS14762.1																																																																																				0.478	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		A	154009980	G	A	154009980	2	1	61	1	0	0	0	0	0	0	0	1	9763	933	33	3		3	MPP1	23	154009980	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	249060	154009980	1260580	12303	20288										
F8	2157	broad.mit.edu	37	chrX	154088801	154088801	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	catacatgctggtaagcagaGattttactccctgagtagtt	9	8	0	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154088801G>T	ENST00000360256.4	-	25	7006	c.6806C>A	c.(6805-6807)tCt>tAt	p.S2269Y	F8_ENST00000330287.6_Missense_Mutation_p.S134Y	NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	2269	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.S2269Y(4)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GGTAAGCAGAGATTTTACTCC	0.443																																																4	Substitution - Missense(4)	large_intestine(4)	X											162	140	147					X																	154088801		2203	4300	6503	153741995	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.6806C>A	X.37:g.154088801G>T	ENSP00000353393:p.Ser2269Tyr		153741995	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	g	17.30	3.354918	0.61293	.	.	ENSG00000185010	ENST00000330287;ENST00000360256	D;D	0.98419	-4.92;-4.92	5.33	3.55	0.40652	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.242538	0.43110	D	0.000607	D	0.98343	0.9450	M	0.70275	2.135	0.47153	D	0.999332	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.994	D	0.98214	1.0474	10	0.66056	D	0.02	-13.5887	8.3699	0.32408	0.1958:0.0:0.8042:0.0	.	2269;134	P00451;Q14286	FA8_HUMAN;.	Y	134;2269	ENSP00000327895:S134Y;ENSP00000353393:S2269Y	ENSP00000327895:S134Y	S	-	2	0	F8	153741995	0.269000	0.24143	1.000000	0.80357	0.977000	0.68977	2.762000	0.47597	1.032000	0.39892	0.544000	0.68410	TCT		0.443	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154088801	G	T	154088801	3	4	61	1	0	0	0	0	1	0	0	0	5363	942	33	2	257	2	F8	23	154088801	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	78821	154088801	1181759	12304	20289										
F8	2157	broad.mit.edu	37	chrX	154157349	154157349	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ttggagggagtctttgcagaGctttctgttgctactctcag	12	8	3	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154157349G>A	ENST00000360256.4	-	14	4916	c.4716C>T	c.(4714-4716)agC>agT	p.S1572S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1572	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.S1572S(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCTTTGCAGAGCTTTCTGTTG	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	X											153	151	152					X																	154157349		2203	4300	6503	153810543	SO:0001819	synonymous_variant	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4716C>T	X.37:g.154157349G>A			153810543	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																				0.468	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			A	154157349	G	A	154157349	2	1	61	1	0	0	0	0	0	0	0	1	5363	962	34	3		3	F8	23	154157349	Silent	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	68548	154157349	1113211	12305	20290										
F8	2157	broad.mit.edu	37	chrX	154159392	154159392	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gaaactttgaaatcaagtttCttcaactctgttgctgcagt	7	8	4	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154159392C>A	ENST00000360256.4	-	14	2873	c.2673G>T	c.(2671-2673)aaG>aaT	p.K891N		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	891	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.K891N(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	AATCAAGTTTCTTCAACTCTG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	X											54	49	50					X																	154159392		2203	4300	6503	153812586	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.2673G>T	X.37:g.154159392C>A	ENSP00000353393:p.Lys891Asn		153812586	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.469939	0.01044	.	.	ENSG00000185010	ENST00000360256	D	0.99382	-5.8	4.81	-4.37	0.03633	.	0.544852	0.17943	N	0.156777	D	0.95497	0.8537	L	0.29908	0.895	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	D	0.90008	0.4119	10	0.36615	T	0.2	-0.1397	2.5007	0.04632	0.4229:0.3195:0.1037:0.1539	.	891	P00451	FA8_HUMAN	N	891	ENSP00000353393:K891N	ENSP00000353393:K891N	K	-	3	2	F8	153812586	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.997000	0.03705	-1.410000	0.02035	-1.195000	0.01675	AAG		0.403	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			A	154159392	C	A	154159392	3	1	61	1	0	0	0	0	1	0	0	0	5363	912	32	2	4462	2	F8	23	154159392	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	2043	154159392	1111168	12306	20291										
TMLHE	55217	broad.mit.edu	37	chrX	154743711	154743711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	agtgggagggacattttctaCgaatgcaattccatagagca	11	7	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154743711C>T	ENST00000334398.3	-	4	719	c.574G>A	c.(574-576)Gta>Ata	p.V192I	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.V192I	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	192					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)	p.V192I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	ACATTTTCTACGAATGCAATT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											129	116	121					X																	154743711		2203	4300	6503	154396905	SO:0001583	missense	55217			AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.574G>A	X.37:g.154743711C>T	ENSP00000335261:p.Val192Ile		154396905	A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Missense_Mutation	SNP	ENST00000334398.3	37	CCDS14768.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088053	0.76642	.	.	ENSG00000185973	ENST00000334398;ENST00000369439	D;D	0.81821	-1.54;-1.54	3.92	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.80939	0.4720	L	0.37561	1.115	0.80722	D	1	D;D;D	0.64830	0.992;0.994;0.992	P;P;P	0.59643	0.779;0.861;0.636	T	0.77544	-0.2548	10	0.23302	T	0.38	-9.7994	13.0094	0.58724	0.0:1.0:0.0:0.0	.	192;192;192	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	I	192	ENSP00000335261:V192I;ENSP00000358447:V192I	ENSP00000335261:V192I	V	-	1	0	TMLHE	154396905	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.130000	0.64745	1.709000	0.51313	0.513000	0.50165	GTA		0.418	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196		T	154743711	C	T	154743711	3	4	61	1	0	0	0	0	1	0	0	0	16271	536	19	1	851	1	TMLHE	23	154743711	Missense_Mutation	SNP	C	TCGA-AG-A002-01A-01W-A00K-09	584319	154743711	526849	12307	20292										
TMLHE	55217	broad.mit.edu	37	chrX	154774795	154774795	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gctgccaagcacaagtcagaGacttggaggctgtatggtgc	14	9	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:154774795G>T	ENST00000334398.3	-	2	288	c.143C>A	c.(142-144)tCt>tAt	p.S48Y	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.S48Y	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	48					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)	p.S48Y(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	ACAAGTCAGAGACTTGGAGGC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	91	96					X																	154774795		2202	4292	6494	154427989	SO:0001583	missense	55217			AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.143C>A	X.37:g.154774795G>T	ENSP00000335261:p.Ser48Tyr		154427989	A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Missense_Mutation	SNP	ENST00000334398.3	37	CCDS14768.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.036878	0.00040	.	.	ENSG00000185973	ENST00000334398;ENST00000369439	D;T	0.83837	-1.77;-1.24	3.92	2.12	0.27331	Domain of unknown function, DUF971 (1);	0.555420	0.18767	N	0.131709	T	0.75606	0.3872	L	0.60455	1.87	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.64774	-0.6328	10	0.49607	T	0.09	-0.94	4.3818	0.11297	0.1226:0.0:0.6566:0.2208	.	48;48;48	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	Y	48	ENSP00000335261:S48Y;ENSP00000358447:S48Y	ENSP00000335261:S48Y	S	-	2	0	TMLHE	154427989	0.935000	0.31712	0.059000	0.19551	0.004000	0.04260	0.816000	0.27267	0.299000	0.22661	-0.315000	0.08773	TCT		0.438	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196		T	154774795	G	T	154774795	3	4	61	1	0	0	0	0	1	0	0	0	16271	942	33	2	1290	2	TMLHE	23	154774795	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	31084	154774795	495765	12308	20293										
SPRY3	10251	broad.mit.edu	37	chrX	155004379	155004379	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	ggtagtgcacccttccccaaGgcccaggaaaagtctgtatg	11	12	1	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrX:155004379G>T	ENST00000302805.2	+	2	1277	c.846G>T	c.(844-846)aaG>aaT	p.K282N		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	282					multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.K282N(1)				all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCTTCCCCAAGGCCCAGGAAA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	X											105	106	105					X																	155004379		2203	4296	6499	154657573	SO:0001583	missense	10251			AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.846G>T	X.37:g.155004379G>T	ENSP00000302978:p.Lys282Asn		154657573	A8K0H8	Missense_Mutation	SNP	ENST00000302805.2	37	CCDS14769.4	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553855	0.27739	.	.	ENSG00000168939	ENST00000302805	T	0.57752	0.38	3.12	3.12	0.35913	.	0.221748	0.36444	N	0.002583	T	0.42720	0.1215	.	.	.	0.09310	N	1	B	0.31893	0.345	B	0.32289	0.143	T	0.45571	-0.9252	9	0.59425	D	0.04	-21.4755	11.3145	0.49383	0.0:0.0:1.0:0.0	.	282	O43610	SPY3_HUMAN	N	282	ENSP00000302978:K282N	ENSP00000302978:K282N	K	+	3	2	SPRY3	154657573	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.511000	0.45476	1.581000	0.49865	0.279000	0.19357	AAG		0.547	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		T	155004379	G	T	155004379	3	4	61	1	0	0	0	0	1	0	0	0	15146	991	35	2	848	2	SPRY3	23	155004379	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	229584	155004379	266181	12309	20294										
TBL1Y	90665	broad.mit.edu	37	chrY	6942631	6942631	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	tttgggatgctcacacaggaGaagccaaacagcagtttcct	10	10	1	1			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrY:6942631G>T	ENST00000383032.1	+	13	1572	c.925G>T	c.(925-927)Gaa>Taa	p.E309*	TBL1Y_ENST00000355162.2_Nonsense_Mutation_p.E309*|TBL1Y_ENST00000346432.3_Nonsense_Mutation_p.E309*	NM_033284.1	NP_150600.1	Q9BQ87	TBL1Y_HUMAN	transducin (beta)-like 1, Y-linked	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.E309*(1)		kidney(1)|large_intestine(4)|lung(2)|skin(1)	8						TCACACAGGAGAAGCCAAACA	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	Y											122	133	130					Y																	6942631		639	1996	2635	7002631	SO:0001587	stop_gained	90665			AF332220	CCDS14779.1	Yp11.2	2013-01-10	2009-12-17		ENSG00000092377	ENSG00000092377		"WD repeat domain containing"	18502	protein-coding gene	gene with protein product		400033					Standard	NM_033284		Approved	TBL1	uc004frd.3	Q9BQ87	OTTHUMG00000035299	ENST00000383032.1:c.925G>T	Y.37:g.6942631G>T	ENSP00000372499:p.Glu309*		7002631	A1L4B3	Nonsense_Mutation	SNP	ENST00000383032.1	37	CCDS14779.1																																																																																				0.368	TBL1Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085360.1	NM_033284		T	6942631	G	T	6942631	4	4	61	1	0	0	0	0	0	1	0	0	15680	943	33	2	955	2	TBL1Y	24	6942631	Nonsense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09		6942631	52430935	12310	20295										
USP9Y	8287	broad.mit.edu	37	chrY	14887456	14887456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	acagagctatagatcttcttAaagagatatacacaaacctt	5	8	2	3			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrY:14887456A>G	ENST00000338981.3	+	18	3328	c.2383A>G	c.(2383-2385)Aaa>Gaa	p.K795E	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	795					BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)	p.K795E(2)		kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AGATCTTCTTAAAGAGATATA	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	Y																																								13396850	SO:0001583	missense	8287			Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.2383A>G	Y.37:g.14887456A>G	ENSP00000342812:p.Lys795Glu		13396850	O14601	Missense_Mutation	SNP	ENST00000338981.3	37	CCDS14781.1																																																																																				0.353	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		G	14887456	A	G	14887456	3	3	61	1	0	0	0	0	1	0	0	0	17131	363	13	4	2445	4	USP9Y	24	14887456	Missense_Mutation	SNP	A	TCGA-AG-A002-01A-01W-A00K-09	7944825	14887456	44486110	12311	20296										
USP9Y	8287	broad.mit.edu	37	chrY	14951946	14951946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	atatgggaccttacacagtaGcaggtgttgcaaacctggaa	11	8	0	0			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrY:14951946G>T	ENST00000338981.3	+	36	6439	c.5494G>T	c.(5494-5496)Gca>Tca	p.A1832S	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	1832	USP.				BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)	p.A1832S(1)		kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TTACACAGTAGCAGGTGTTGC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	Y											72	64	66					Y																	14951946		597	1947	2544	13461340	SO:0001583	missense	8287			Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.5494G>T	Y.37:g.14951946G>T	ENSP00000342812:p.Ala1832Ser		13461340	O14601	Missense_Mutation	SNP	ENST00000338981.3	37	CCDS14781.1																																																																																				0.388	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		T	14951946	G	T	14951946	3	4	61	1	0	0	0	0	1	0	0	0	17131	971	34	2	5628	2	USP9Y	24	14951946	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	64490	14951946	44421620	12312	20297										
KDM5D	8284	broad.mit.edu	37	chrY	21870162	21870162	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0329759584145549	406	1	0.415048904303878	0	0.41693720687123	7.67023552891641e-127	9.35768734527802e-125	0	gtagcaagaattcttcttgaGaaaggtcttggaggccttct	11	7	4	2			TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A002-01A-01W-A00K-09	TCGA-AG-A002-10A-01W-A00K-09	g.chrY:21870162G>T	ENST00000317961.4	-	22	3500	c.3229C>A	c.(3229-3231)Ctc>Atc	p.L1077I	KDM5D_ENST00000382806.2_Missense_Mutation_p.L1020I|KDM5D_ENST00000541639.1_Missense_Mutation_p.L1108I	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	1077					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.L1077I(2)		kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	TTCTTCTTGAGAAAGGTCTTG	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	Y											39	42	41					Y																	21870162		573	1913	2486	20329550	SO:0001583	missense	8284			U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.3229C>A	Y.37:g.21870162G>T	ENSP00000322408:p.Leu1077Ile		20329550	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Missense_Mutation	SNP	ENST00000317961.4	37	CCDS14794.1																																																																																				0.552	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		T	21870162	G	T	21870162	3	4	61	1	0	0	0	0	1	0	0	0	8157	942	33	2	1414	2	KDM5D	24	21870162	Missense_Mutation	SNP	G	TCGA-AG-A002-01A-01W-A00K-09	6918216	21870162	37503404	12313	20298										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24981534	24981534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tcctgcaactccaccacccaAaactcggcattcccctacac	3	20	0	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:24981534A>G	ENST00000323848.9	+	9	1544	c.1229A>G	c.(1228-1230)aAa>aGa	p.K410R	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.K405R|SRRM1_ENST00000537199.1_Missense_Mutation_p.K292E|SRRM1_ENST00000447431.2_Missense_Mutation_p.K410R	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	410	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.K410R(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CCACCACCCAAAACTCGGCAT	0.512																																					Ovarian(68;897 1494 3282 17478)											1	Substitution - Missense(1)	large_intestine(1)	1											108	102	104					1																	24981534		2203	4300	6503	24854121	SO:0001583	missense	10250			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1229A>G	1.37:g.24981534A>G	ENSP00000326261:p.Lys410Arg		24854121	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.92|18.92	3.726304|3.726304	0.69074|0.69074	.|.	.|.	ENSG00000133226|ENSG00000133226	ENST00000537199|ENST00000323848;ENST00000447431;ENST00000374389	T|T;T;T	0.54071|0.50277	0.59|0.83;0.79;0.75	5.84|5.84	4.7|4.7	0.59300|0.59300	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.40886|0.40886	0.1135|0.1135	L|L	0.38175|0.38175	1.15|1.15	0.22571|0.22571	N|N	0.998972|0.998972	.|D;P	.|0.52996	.|0.957;0.928	.|P;B	.|0.45946	.|0.498;0.302	T|T	0.20273|0.20273	-1.0280|-1.0280	8|10	0.87932|0.23302	D|T	0|0.38	-4.0339|-4.0339	12.056|12.056	0.53536|0.53536	0.8706:0.0:0.0:0.1294|0.8706:0.0:0.0:0.1294	.|.	.|410;410	.|E9PCT1;Q8IYB3	.|.;SRRM1_HUMAN	E|R	292|410;410;405	ENSP00000441776:K292E|ENSP00000326261:K410R;ENSP00000391430:K410R;ENSP00000363510:K405R	ENSP00000441776:K292E|ENSP00000326261:K410R	K|K	+|+	1|2	0|0	SRRM1|SRRM1	24854121|24854121	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.213000|7.213000	0.77950|0.77950	1.008000|1.008000	0.39264|0.39264	0.528000|0.528000	0.53228|0.53228	AAA|AAA		0.512	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		G	24981534	A	G	24981534	3	3	62	1	0	0	0	0	1	0	0	0	15207	14	1	4	1263	4	SRRM1	1	24981534	Missense_Mutation	SNP	A	TCGA-AG-A008-01A-01W-A005-10		24981534	224269087	1	20299										
SNX27	81609	hgsc.bcm.edu	37	chr1	151630869	151630869	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tcagaacaacaattagatgcCcgacgtcggggattggaaga	12	8	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:151630869C>T	ENST00000458013.2	+	3	822	c.702C>T	c.(700-702)gcC>gcT	p.A234A	SNX27_ENST00000368843.3_Silent_p.A234A|SNX27_ENST00000368838.1_Silent_p.A141A			Q96L92	SNX27_HUMAN	sorting nexin family member 27	234	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)	p.A234A(1)		central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AATTAGATGCCCGACGTCGGG	0.408																																					Colon(46;291 966 40145 41237 41888)											1	Substitution - coding silent(1)	large_intestine(1)	1											103	101	102					1																	151630869		2203	4300	6503	149897493	SO:0001819	synonymous_variant	81609			AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376		"Sorting nexins"	20073	protein-coding gene	gene with protein product		611541				12461558	Standard	XM_005245509		Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000458013.2:c.702C>T	1.37:g.151630869C>T			149897493	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Silent	SNP	ENST00000458013.2	37																																																																																					0.408	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		T	151630869	C	T	151630869	2	4	62	1	0	0	0	0	0	0	0	1	14934	610	22	3		3	SNX27	1	151630869	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10	126649335	151630869	97619752	2	20300										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669588	158669588	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctatagataatggggttgaaGaagggagacaaaactgcaaa	12	4	0	4			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:158669588G>C	ENST00000359610.2	-	1	898	c.855C>G	c.(853-855)ttC>ttG	p.F285L		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F285L(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TGGGGTTGAAGAAGGGAGACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	87	88					1																	158669588		2203	4300	6503	156936212	SO:0001583	missense	81448			BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.855C>G	1.37:g.158669588G>C	ENSP00000352626:p.Phe285Leu		156936212	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	G	2.299	-0.360602	0.05103	.	.	ENSG00000196171	ENST00000359610	T	0.35789	1.29	4.94	0.457	0.16661	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43110	D	0.000613	T	0.03695	0.0105	N	0.04705	-0.18	0.20563	N	0.999883	B	0.20052	0.041	B	0.24006	0.05	T	0.41980	-0.9478	10	0.07990	T	0.79	-13.8805	4.6112	0.12404	0.4096:0.2585:0.332:0.0	.	285	Q8NGY2	OR6K2_HUMAN	L	285	ENSP00000352626:F285L	ENSP00000352626:F285L	F	-	3	2	OR6K2	156936212	0.000000	0.05858	0.999000	0.59377	0.978000	0.69477	-1.619000	0.02048	0.208000	0.20626	0.655000	0.94253	TTC		0.413	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		C	158669588	G	C	158669588	3	2	62	1	0	0	0	0	1	0	0	0	11233	933	33	5	123	5	OR6K2	1	158669588	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	7038719	158669588	90581033	3	20301										
ABL2	27	hgsc.bcm.edu	37	chr1	179077641	179077641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gtgagtggttgggaggacggGggcagccttggctggagaag	22	5	0	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:179077641G>A	ENST00000502732.1	-	12	2964	c.2761C>T	c.(2761-2763)Ccc>Tcc	p.P921S	ABL2_ENST00000367623.4_Missense_Mutation_p.P900S|ABL2_ENST00000511413.1_Missense_Mutation_p.P818S|ABL2_ENST00000507173.1_Missense_Mutation_p.P797S|ABL2_ENST00000504405.1_Missense_Mutation_p.P782S|ABL2_ENST00000512653.1_Missense_Mutation_p.P906S|ABL2_ENST00000344730.3_Missense_Mutation_p.P803S|ABL2_ENST00000408940.3_Missense_Mutation_p.P885S	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	921	F-actin-binding. {ECO:0000250}.|Pro-rich.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)	p.P885S(1)		breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GGGAGGACGGGGGCAGCCTTG	0.582			T	ETV6	AML																																		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	1	Substitution - Missense(1)	large_intestine(1)	1											78	74	76					1																	179077641		2203	4300	6503	177344264	SO:0001583	missense	27			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.2761C>T	1.37:g.179077641G>A	ENSP00000427562:p.Pro921Ser		177344264	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	37	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.368995	0.01225	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.72942	-0.69;-0.7;-0.67;-0.7;-0.67;-0.69;-0.66;-0.67	5.1	-1.88	0.07713	.	0.283763	0.24245	U	0.040240	T	0.36358	0.0964	N	0.04508	-0.205	0.09310	N	1	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.11108	-1.0601	10	0.25751	T	0.34	.	1.865	0.03196	0.1276:0.4096:0.2369:0.2258	.	900;797;818;782;921;906;885;803	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	S	921;885;803;906;782;900;797;818	ENSP00000427562:P921S;ENSP00000386152:P885S;ENSP00000339209:P803S;ENSP00000423578:P906S;ENSP00000426831:P782S;ENSP00000356595:P900S;ENSP00000423413:P797S;ENSP00000424697:P818S	ENSP00000339209:P803S	P	-	1	0	ABL2	177344264	0.004000	0.15560	0.000000	0.03702	0.122000	0.20287	0.163000	0.16520	-0.278000	0.09180	-0.165000	0.13383	CCC		0.582	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		A	179077641	G	A	179077641	3	1	62	1	0	0	0	0	1	0	0	0	93	1232	43	3	791	3	ABL2	1	179077641	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	20408053	179077641	70172980	4	20302										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233497916	233497916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gcgagatcgacgtgctggagCgggaacttaacattctgata	13	8	1	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:233497916C>T	ENST00000366624.3	+	5	1690	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	MLK4_ENST00000366623.3_Missense_Mutation_p.R477W	NM_032435.2	NP_115811.2												p.R477W(2)									CGTGCTGGAGCGGGAACTTAA	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	1											64	62	62					1																	233497916		2203	4300	6503	231564539	SO:0001583	missense	84451																														ENST00000366624.3:c.1429C>T	1.37:g.233497916C>T	ENSP00000355583:p.Arg477Trp		231564539		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.455729	0.84209	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.12774	2.65;2.65	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.40145	0.1105	M	0.80183	2.485	0.80722	D	1	D;D	0.71674	0.998;0.971	D;P	0.66351	0.943;0.823	T	0.37502	-0.9703	10	0.66056	D	0.02	.	18.2298	0.89931	0.0:1.0:0.0:0.0	.	477;477	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	W	477	ENSP00000355582:R477W;ENSP00000355583:R477W	ENSP00000355582:R477W	R	+	1	2	RP5-862P8.2	231564539	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.760000	0.55235	2.525000	0.85131	0.655000	0.94253	CGG		0.532	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233497916	C	T	233497916	3	4	62	1	0	0	0	0	1	0	0	0	8280	759	27	1	1447	1	KIAA1804	1	233497916	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	54420275	233497916	15752705	5	20303										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234582611	234582611	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gcttcaacagcagctggaggCatctgtcagtcttcagcaag	11	11	5	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr1:234582611C>A	ENST00000040877.1	-	12	2071	c.2072G>T	c.(2071-2073)tGc>tTc	p.C691F		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	691					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)	p.C691F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			CAGCTGGAGGCATCTGTCAGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											169	146	153					1																	234582611		2203	4300	6503	232649234	SO:0001583	missense	6894				CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2072G>T	1.37:g.234582611C>A	ENSP00000040877:p.Cys691Phe		232649234	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500301	0.64298	.	.	ENSG00000059588	ENST00000040877	T	0.07567	3.18	5.2	5.2	0.72013	.	0.136561	0.64402	D	0.000006	T	0.11707	0.0285	L	0.60455	1.87	0.39453	D	0.967432	P	0.49961	0.93	B	0.41571	0.36	T	0.05852	-1.0860	10	0.35671	T	0.21	-21.7959	15.7522	0.77994	0.0:1.0:0.0:0.0	.	691	Q13395	TARB1_HUMAN	F	691	ENSP00000040877:C691F	ENSP00000040877:C691F	C	-	2	0	TARBP1	232649234	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.834000	0.62774	2.716000	0.92895	0.655000	0.94253	TGC		0.443	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234582611	C	A	234582611	3	1	62	1	0	0	0	0	1	0	0	0	15594	710	25	2	2869	2	TARBP1	1	234582611	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	1084695	234582611	14668010	6	20304										
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9098695	9098695	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	catgtcttataaaagagctaGttttgcttgaatgtagataa	8	4	1	3	rs142344615		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr2:9098695G>A	ENST00000305997.3	-	2	350	c.152C>T	c.(151-153)aCt>aTt	p.T51I	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	51					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.T51I(1)	MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AAAAGAGCTAGTTTTGCTTGA	0.338																																					Ovarian(194;1699 3813 22401)											1	Substitution - Missense(1)	large_intestine(1)	2											77	78	78					2																	9098695		2203	4300	6503	9016146	SO:0001583	missense	129642			BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.152C>T	2.37:g.9098695G>A	ENSP00000302177:p.Thr51Ile		9016146	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074770	0.76415	.	.	ENSG00000143797	ENST00000305997	T	0.10668	2.85	6.03	6.03	0.97812	.	0.048017	0.85682	D	0.000000	T	0.23330	0.0564	L	0.55103	1.725	0.80722	D	1	P;P	0.51933	0.901;0.949	P;P	0.52957	0.573;0.714	T	0.00075	-1.2121	10	0.28530	T	0.3	-18.9371	20.5568	0.99304	0.0:0.0:1.0:0.0	.	51;51	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	I	51	ENSP00000302177:T51I	ENSP00000302177:T51I	T	-	2	0	MBOAT2	9016146	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.861000	0.98227	0.655000	0.94253	ACT		0.338	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		A	9098695	G	A	9098695	3	1	62	1	0	0	0	0	1	0	0	0	9387	1029	36	3	1458	3	MBOAT2	2	9098695	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		9098695	234100678	7	20305										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163292022	163292022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gcattagaacagcagcgccaTattctgaatatcgatccagt	8	10	1	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr2:163292022T>C	ENST00000332142.5	-	8	1739	c.1640A>G	c.(1639-1641)tAt>tGt	p.Y547C	KCNH7_ENST00000328032.4_Missense_Mutation_p.Y540C	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	547					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.Y547C(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AGCAGCGCCATATTCTGAATA	0.458																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	large_intestine(1)	2											80	77	78					2																	163292022		2203	4300	6503	163000268	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1640A>G	2.37:g.163292022T>C	ENSP00000331727:p.Tyr547Cys		163000268	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.343841	0.82022	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.98493	-4.96;-4.96	5.9	5.9	0.94986	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99257	0.9741	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.99056	1.0829	10	0.62326	D	0.03	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	540;547	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	C	547;540	ENSP00000331727:Y547C;ENSP00000333781:Y540C	ENSP00000333781:Y540C	Y	-	2	0	KCNH7	163000268	1.000000	0.71417	0.999000	0.59377	0.924000	0.55760	8.040000	0.89188	2.251000	0.74343	0.528000	0.53228	TAT		0.458	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		C	163292022	T	C	163292022	3	2	62	1	0	0	0	0	1	0	0	0	8058	1406	49	4	2052	4	KCNH7	2	163292022	Missense_Mutation	SNP	T	TCGA-AG-A008-01A-01W-A005-10	154193327	163292022	79907351	8	20306										
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234198609	234198609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tctcaaactctgggatctacGcagcaaagtctgtgaggaaa	10	9	4	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr2:234198609G>A	ENST00000392017.4	+	13	1570	c.1313G>A	c.(1312-1314)cGc>cAc	p.R438H	ATG16L1_ENST00000392018.1_Missense_Mutation_p.R455H|ATG16L1_ENST00000347464.5_Missense_Mutation_p.R275H|SCARNA6_ENST00000515982.1_RNA|ATG16L1_ENST00000392020.4_Missense_Mutation_p.R419H|ATG16L1_ENST00000373525.5_Missense_Mutation_p.R259H	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	438					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)	p.R438H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		TGGGATCTACGCAGCAAAGTC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	2											103	93	96					2																	234198609		2203	4300	6503	233863348	SO:0001583	missense	55054			AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.1313G>A	2.37:g.234198609G>A	ENSP00000375872:p.Arg438His		233863348	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	37	CCDS2503.2	.	.	.	.	.	.	.	.	.	.	G	29.7	5.027325	0.93518	.	.	ENSG00000085978	ENST00000392017;ENST00000347464;ENST00000373525;ENST00000392020;ENST00000392018;ENST00000334050	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.9	5.01	0.66863	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051121	0.85682	D	0.000000	T	0.45074	0.1324	M	0.78637	2.42	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.996;0.996;0.993;0.985	D;D;D;P;P	0.66497	0.915;0.921;0.944;0.835;0.844	T	0.27157	-1.0082	10	0.42905	T	0.14	.	14.4791	0.67567	0.0697:0.0:0.9303:0.0	.	392;419;259;438;275	B7ZLM5;Q676U5-2;Q676U5-4;Q676U5;A3EXL0	.;.;.;A16L1_HUMAN;.	H	438;275;259;419;455;97	ENSP00000375872:R438H;ENSP00000318259:R275H;ENSP00000362625:R259H;ENSP00000375875:R419H;ENSP00000375873:R455H	ENSP00000334016:R97H	R	+	2	0	ATG16L1	233863348	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.889000	0.87307	2.788000	0.95919	0.650000	0.86243	CGC		0.493	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		A	234198609	G	A	234198609	3	1	62	1	0	0	0	0	1	0	0	0	1092	1087	38	1	1363	1	ATG16L1	2	234198609	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	70906587	234198609	9000764	9	20307										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242283192	242283192	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	catcccattctctgtggttgGatccaatcagttgattgaag	9	9	2	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr2:242283192G>C	ENST00000391973.2	+	9	1250	c.722G>C	c.(721-723)gGa>gCa	p.G241A	SEPT2_ENST00000407971.1_Missense_Mutation_p.G201A|SEPT2_ENST00000360051.3_Missense_Mutation_p.G241A|SEPT2_ENST00000401990.1_Missense_Mutation_p.G251A|SEPT2_ENST00000402092.2_Missense_Mutation_p.G241A|SEPT2_ENST00000391971.2_Missense_Mutation_p.G241A	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	241	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)	p.G241A(1)		central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TCTGTGGTTGGATCCAATCAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	2											340	347	344					2																	242283192		2203	4300	6503	241931865	SO:0001583	missense	4735			D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.722G>C	2.37:g.242283192G>C	ENSP00000375834:p.Gly241Ala		241931865	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Missense_Mutation	SNP	ENST00000391973.2	37	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	G	34	5.332952	0.95758	.	.	ENSG00000168385	ENST00000391973;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717	T;T;T;T;T;T;T	0.58210	1.34;1.34;1.34;1.34;0.35;1.34;0.35	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.74642	0.3743	M	0.81112	2.525	0.80722	D	1	D;D;P	0.67145	0.996;0.969;0.828	D;P;P	0.64042	0.921;0.564;0.631	T	0.76531	-0.2925	10	0.87932	D	0	.	20.3789	0.98926	0.0:0.0:1.0:0.0	.	276;201;241	Q15019-2;B5MCX3;Q15019	.;.;SEPT2_HUMAN	A	241;241;241;251;201;241;276;96	ENSP00000375834:G241A;ENSP00000353157:G241A;ENSP00000375832:G241A;ENSP00000385109:G251A;ENSP00000384525:G201A;ENSP00000385172:G241A;ENSP00000408296:G96A	ENSP00000353157:G241A	G	+	2	0	SEPT2	241931865	1.000000	0.71417	0.557000	0.28306	0.944000	0.59088	9.553000	0.98118	2.826000	0.97356	0.563000	0.77884	GGA		0.512	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		C	242283192	G	C	242283192	3	2	62	1	0	0	0	0	1	0	0	0	14101	1174	41	5	752	5	SEPT2	2	242283192	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	8084583	242283192	916181	10	20308										
CCBP2	1238	hgsc.bcm.edu	37	chr3	42906467	42906467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctaccacaggctgaggacccGggccaagagcctgctccttg	12	15	0	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr3:42906467G>A	ENST00000422265.1	+	3	648	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	RP11-141M3.5_ENST00000471537.1_RNA|KRBOX1_ENST00000426937.1_Intron|ACKR2_ENST00000442925.1_Missense_Mutation_p.R158Q|ACKR2_ENST00000273145.2_Missense_Mutation_p.R158Q|CYP8B1_ENST00000437102.1_Intron	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	158					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.R158Q(1)									CTGAGGACCCGGGCCAAGAGC	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	3											77	80	79					3																	42906467		2203	4300	6503	42881471	SO:0001583	missense	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.473G>A	3.37:g.42906467G>A	ENSP00000416996:p.Arg158Gln		42881471	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331196	0.24167	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.72282	-0.64;-0.64;-0.64	5.02	0.735	0.18300	GPCR, rhodopsin-like superfamily (1);	0.327353	0.21462	N	0.074150	T	0.54334	0.1852	L	0.49699	1.58	0.09310	N	0.999996	P	0.38078	0.617	B	0.30029	0.11	T	0.42258	-0.9462	9	.	.	.	.	6.6831	0.23131	0.0754:0.4651:0.3401:0.1194	.	158	O00590	CCBP2_HUMAN	Q	158	ENSP00000396150:R158Q;ENSP00000416996:R158Q;ENSP00000273145:R158Q	.	R	+	2	0	CCBP2	42881471	0.000000	0.05858	0.513000	0.27749	0.323000	0.28346	-0.484000	0.06528	0.109000	0.17891	0.563000	0.77884	CGG		0.507	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		A	42906467	G	A	42906467	3	1	62	1	0	0	0	0	1	0	0	0	2740	1116	39	1	475	1	CCBP2	3	42906467	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		42906467	155115963	11	20309										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467878	66467878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gcagtcccgcagggtaaattTgagttctatgaagattctgg	12	7	2	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr4:66467878T>C	ENST00000273854.3	-	3	991	c.391A>G	c.(391-393)Aaa>Gaa	p.K131E	EPHA5_ENST00000354839.4_Missense_Mutation_p.K131E|EPHA5_ENST00000432638.2_Missense_Mutation_p.K131E|EPHA5_ENST00000511294.1_Missense_Mutation_p.K131E	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	131	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.K131E(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						AGGGTAAATTTGAGTTCTATG	0.433										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4											85	89	88					4																	66467878		2203	4300	6503	66150473	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.391A>G	4.37:g.66467878T>C	ENSP00000273854:p.Lys131Glu		66150473	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248964	0.80024	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.03745	3.82;3.82;3.82;3.82	5.67	5.67	0.87782	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000004	T	0.17238	0.0414	M	0.66378	2.025	0.58432	D	0.999998	D;D;D;D	0.76494	0.999;0.985;0.998;0.996	D;D;D;D	0.91635	0.999;0.963;0.998;0.964	T	0.00089	-1.2089	10	0.87932	D	0	.	15.9044	0.79412	0.0:0.0:0.0:1.0	.	131;131;131;131	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	E	131	ENSP00000273854:K131E;ENSP00000389208:K131E;ENSP00000346899:K131E;ENSP00000427638:K131E	ENSP00000273854:K131E	K	-	1	0	EPHA5	66150473	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	8.040000	0.89188	2.162000	0.67917	0.528000	0.53228	AAA		0.433	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		C	66467878	T	C	66467878	3	2	62	1	0	0	0	0	1	0	0	0	5183	1821	63	4	2786	4	EPHA5	4	66467878	Missense_Mutation	SNP	T	TCGA-AG-A008-01A-01W-A005-10		66467878	124686398	12	20310										
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68810250	68810250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gactcaccaaattttcggtcGtctctcgtaagtccttaagt	7	11	2	0	rs187902089	byFrequency	TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr4:68810250G>A	ENST00000334830.7	-	3	985	c.239C>T	c.(238-240)aCg>aTg	p.T80M	TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.T79M|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.T80M|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	80	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.T80M(1)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						ATTTTCGGTCGTCTCTCGTAA	0.333													G|||	3	0.000599042	0.0023	0	5008	,	,		18220	0		0	False		,,,				2504	0				NSCLC(26;2 894 10941 14480 22546)											1	Substitution - Missense(1)	large_intestine(1)	4						G	MET/THR,MET/THR	0,4406		0,0,2203	172	174	174		239,239	-0.5	0.1	4		174	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	TMPRSS11A	NM_001114387.1,NM_182606.3	81,81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	80/419,80/422	68810250	2,13004	2203	4300	6503	68492845	SO:0001583	missense	339967			AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.239C>T	4.37:g.68810250G>A	ENSP00000334611:p.Thr80Met		68492845	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	4.509	0.094364	0.08632	0.0	2.33E-4	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.28	-0.487	0.12060	SEA (1);	0.704877	0.13093	N	0.414366	T	0.13713	0.0332	N	0.02736	-0.51	0.22240	N	0.999269	B;B	0.18610	0.029;0.029	B;B	0.12156	0.007;0.007	T	0.16305	-1.0407	10	0.27082	T	0.32	.	0.9486	0.01371	0.5034:0.1596:0.1827:0.1543	.	80;80	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	M	79;80;80;60	ENSP00000426911:T79M;ENSP00000334611:T80M;ENSP00000379491:T80M;ENSP00000427621:T60M	ENSP00000334611:T80M	T	-	2	0	TMPRSS11A	68492845	0.184000	0.23200	0.098000	0.21074	0.312000	0.27988	0.074000	0.14662	0.085000	0.17107	-0.302000	0.09304	ACG		0.333	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		A	68810250	G	A	68810250	3	1	62	1	0	0	0	0	1	0	0	0	16278	1145	40	1	1058	1	TMPRSS11A	4	68810250	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	2342372	68810250	122344026	13	20311										
FBXO8	26269	hgsc.bcm.edu	37	chr4	175183938	175183938	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tgccagagaagttcatcattCgcaaggtcctgccaaacaca	8	12	2	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr4:175183938C>T	ENST00000393674.2	-	2	1168	c.306G>A	c.(304-306)gcG>gcA	p.A102A	FBXO8_ENST00000503293.1_Silent_p.A61A	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	102	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.A102A(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		GTTCATCATTCGCAAGGTCCT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	4											86	76	79					4																	175183938		2203	4300	6503	175420513	SO:0001819	synonymous_variant	26269			AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"F-boxes /  "other""	13587	protein-coding gene	gene with protein product		605649	"F-box only protein 8"			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.306G>A	4.37:g.175183938C>T			175420513	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Silent	SNP	ENST00000393674.2	37	CCDS3820.1	.	.	.	.	.	.	.	.	.	.	C	3.728	-0.056095	0.07362	.	.	ENSG00000164117	ENST00000296517	.	.	.	5.63	-11.3	0.00108	.	.	.	.	.	T	0.26846	0.0657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41466	-0.9507	5	0.13470	T	0.59	.	3.0214	0.06077	0.1881:0.2461:0.3821:0.1836	.	.	.	.	Q	16	.	ENSP00000296517:R16Q	R	-	2	0	FBXO8	175420513	0.000000	0.05858	0.004000	0.12327	0.778000	0.44026	-1.846000	0.01676	-4.071000	0.00076	-2.689000	0.00140	CGA		0.388	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180		T	175183938	C	T	175183938	2	4	62	1	0	0	0	0	0	0	0	1	5780	871	31	1		1	FBXO8	4	175183938	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10	106373688	175183938	15970338	14	20312										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71757093	71757093	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gtgggcatgctcttccgtttCctagaccctgctccttcgaa	9	14	1	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr5:71757093C>T	ENST00000318442.5	-	2	721	c.231G>A	c.(229-231)agG>agA	p.R77R		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	77					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.R77R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCTTCCGTTTCCTAGACCCTG	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	5											168	176	173					5																	71757093		2203	4300	6503	71792849	SO:0001819	synonymous_variant	167465			AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.231G>A	5.37:g.71757093C>T			71792849	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																				0.572	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71757093	C	T	71757093	2	4	62	1	0	0	0	0	0	0	0	1	17909	854	30	3		3	ZNF366	5	71757093	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10		71757093	109158167	15	20313										
APC	324	hgsc.bcm.edu	37	chr5	112174544	112174544	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	atactgagagcactgatgatAaacacctcaagttccaacca	6	11	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr5:112174544A>T	ENST00000457016.1	+	16	3633	c.3253A>T	c.(3253-3255)Aaa>Taa	p.K1085*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.K1085*|APC_ENST00000257430.4_Nonsense_Mutation_p.K1085*			P25054	APC_HUMAN	adenomatous polyposis coli	1085	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1085fs*34(1)|p.K1085*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CACTGATGATAAACACCTCAA	0.393		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(1)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(2)|skin(1)	5	GRCh37	CI012706|CI972533	APC	I							83	79	80					5																	112174544		2202	4300	6502	112202443	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3253A>T	5.37:g.112174544A>T	ENSP00000413133:p.Lys1085*		112202443	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	38	7.244952	0.98161	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.8674	15.4753	0.75474	1.0:0.0:0.0:0.0	.	.	.	.	X	1085;1067;1085;1085;1085	.	ENSP00000257430:K1085X	K	+	1	0	APC	112202443	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	5.708000	0.68377	2.146000	0.66826	0.533000	0.62120	AAA		0.393	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174544	A	T	112174544	4	4	62	1	0	0	0	0	0	1	0	0	763	363	13	5	3311	5	APC	5	112174544	Nonsense_Mutation	SNP	A	TCGA-AG-A008-01A-01W-A005-10	40417451	112174544	68740716	16	20314										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140869933	140869933	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tggggttgtttaatgtgcgaGaccgggactcaggtagaaat	15	5	1	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr5:140869933G>C	ENST00000252087.1	+	1	1126	c.1126G>C	c.(1126-1128)Gac>Cac	p.D376H	PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	376	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D376H(2)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATGTGCGAGACCGGGACTC	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	5											135	137	136					5																	140869933		2203	4300	6503	140850117	SO:0001583	missense	56097			AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1126G>C	5.37:g.140869933G>C	ENSP00000252087:p.Asp376His		140850117	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711854	0.68730	.	.	ENSG00000240764	ENST00000252087	D	0.83163	-1.69	5.56	5.56	0.83823	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000011	D	0.95680	0.8595	H	0.99487	4.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97253	0.9899	10	0.87932	D	0	.	19.3074	0.94169	0.0:0.0:1.0:0.0	.	376;376	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	H	376	ENSP00000252087:D376H	ENSP00000252087:D376H	D	+	1	0	PCDHGC5	140850117	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.610000	0.98337	2.890000	0.99128	0.655000	0.94253	GAC		0.517	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		C	140869933	G	C	140869933	3	2	62	1	0	0	0	0	1	0	0	0	11602	942	33	5	1128	5	PCDHGC5	5	140869933	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	28695389	140869933	40045327	17	20315										
FAT2	2196	hgsc.bcm.edu	37	chr5	150925224	150925224	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	catctctgatacaatggttaGggttcccatgctgggatcaa	10	9	2	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr5:150925224G>A	ENST00000261800.5	-	9	5476	c.5464C>T	c.(5464-5466)Cta>Tta	p.L1822L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1822	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1822L(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACAATGGTTAGGGTTCCCATG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	5											55	57	56					5																	150925224		2203	4300	6503	150905417	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5464C>T	5.37:g.150925224G>A			150905417	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.438	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150925224	G	A	150925224	2	1	62	1	0	0	0	0	0	0	0	1	5709	991	35	3		3	FAT2	5	150925224	Silent	SNP	G	TCGA-AG-A008-01A-01W-A005-10	10055291	150925224	29990036	18	20316										
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179302062	179302062	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctcgaagggcatgacgctgaGgaagagggtcaggaaccagg	17	8	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr5:179302062G>A	ENST00000356834.3	-	12	2063	c.2026C>T	c.(2026-2028)Ctc>Ttc	p.L676F	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.L676F	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	676	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.L676F(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATGACGCTGAGGAAGAGGGTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	5											103	94	97					5																	179302062		2203	4300	6503	179234668	SO:0001583	missense	23061			AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2026C>T	5.37:g.179302062G>A	ENSP00000349291:p.Leu676Phe		179234668	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	37	CCDS43408.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.364011	0.82353	.	.	ENSG00000197226	ENST00000356834;ENST00000355235	T;T	0.12672	2.66;2.66	5.29	5.29	0.74685	Rab-GAP/TBC domain (4);	0.079970	0.51477	D	0.000083	T	0.35248	0.0925	M	0.70787	2.145	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.03555	-1.1025	10	0.56958	D	0.05	-31.8058	12.31	0.54924	0.0776:0.0:0.9224:0.0	.	676;676;676	A1L3A9;Q66K14-2;Q66K14	.;.;TBC9B_HUMAN	F	676	ENSP00000349291:L676F;ENSP00000347375:L676F	ENSP00000347375:L676F	L	-	1	0	TBC1D9B	179234668	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.690000	0.74567	2.469000	0.83416	0.491000	0.48974	CTC		0.607	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179302062	G	A	179302062	3	1	62	1	0	0	0	0	1	0	0	0	15667	1000	35	3	1770	3	TBC1D9B	5	179302062	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	28376838	179302062	1613198	19	20317										
UTRN	7402	hgsc.bcm.edu	37	chr6	145073029	145073029	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tgtctccacttgacctgcatCcctctctaaagatgtctcgc	6	15	3	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr6:145073029C>A	ENST00000367545.3	+	55	8296	c.8296C>A	c.(8296-8298)Ccc>Acc	p.P2766T	UTRN_ENST00000367526.4_Missense_Mutation_p.P321T	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2766					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.P2766T(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TGACCTGCATCCCTCTCTAAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	6											104	94	98					6																	145073029		2203	4300	6503	145114722	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.8296C>A	6.37:g.145073029C>A	ENSP00000356515:p.Pro2766Thr		145114722	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.288912	0.40494	.	.	ENSG00000152818	ENST00000367545;ENST00000367526	T;T	0.46451	0.87;0.87	5.99	4.23	0.50019	.	0.000000	0.49916	D	0.000140	T	0.34803	0.0910	L	0.36672	1.1	0.35536	D	0.802649	D	0.55385	0.971	P	0.56343	0.796	T	0.34750	-0.9816	10	0.66056	D	0.02	.	12.7663	0.57393	0.0:0.8683:0.0:0.1317	.	2766	P46939	UTRO_HUMAN	T	2766;321	ENSP00000356515:P2766T;ENSP00000356496:P321T	ENSP00000356496:P321T	P	+	1	0	UTRN	145114722	1.000000	0.71417	0.764000	0.31436	0.003000	0.03518	7.142000	0.77339	0.882000	0.36016	-0.140000	0.14226	CCC		0.403	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	145073029	C	A	145073029	3	1	62	1	0	0	0	0	1	0	0	0	17143	855	30	2	8514	2	UTRN	6	145073029	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10		145073029	26042038	20	20318										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91631629	91631629	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tacatactcctgttagccaaGaagaaagattgattttctta	6	7	1	4			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr7:91631629G>A	ENST00000359028.2	+	9	2659	c.2434G>A	c.(2434-2436)Gaa>Aaa	p.E812K	AKAP9_ENST00000356239.3_Missense_Mutation_p.E800K|AKAP9_ENST00000358100.2_Missense_Mutation_p.E812K			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	812	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.E800K(1)|p.E812K(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGTTAGCCAAGAAGAAAGATT	0.333			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - Missense(2)	large_intestine(2)	7											69	77	74					7																	91631629		2203	4296	6499	91469565	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.2434G>A	7.37:g.91631629G>A	ENSP00000351922:p.Glu812Lys		91469565	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	G	15.13	2.741964	0.49151	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.04706	3.59;3.59;3.57	5.55	5.55	0.83447	.	0.165679	0.28778	N	0.014176	T	0.18718	0.0449	M	0.65975	2.015	0.42420	D	0.992637	D;D;D;P	0.63880	0.988;0.993;0.993;0.909	P;P;P;P	0.60541	0.755;0.876;0.876;0.61	T	0.00020	-1.2354	10	0.87932	D	0	.	18.0566	0.89365	0.0:0.0:1.0:0.0	.	812;800;800;812	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	K	800;812;812;812;812	ENSP00000348573:E800K;ENSP00000351922:E812K;ENSP00000350813:E812K	ENSP00000348573:E800K	E	+	1	0	AKAP9	91469565	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.835000	0.55805	2.768000	0.95171	0.655000	0.94253	GAA		0.333	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91631629	G	A	91631629	3	1	62	1	0	0	0	0	1	0	0	0	459	943	33	3	2428	3	AKAP9	7	91631629	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		91631629	67507034	21	20319										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147926773	147926773	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gatacaacctgggtggcaccCgagagccatacaatattgac	10	11	0	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr7:147926773C>T	ENST00000361727.3	+	20	3799	c.3283C>T	c.(3283-3285)Cga>Tga	p.R1095*	CNTNAP2_ENST00000538075.1_Nonsense_Mutation_p.R154*	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1095	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.R1095*(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GGGTGGCACCCGAGAGCCATA	0.448										HNSCC(39;0.1)																																						1	Substitution - Nonsense(1)	large_intestine(1)	7											108	101	104					7																	147926773		2203	4300	6503	147557706	SO:0001587	stop_gained	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3283C>T	7.37:g.147926773C>T	ENSP00000354778:p.Arg1095*		147557706	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Nonsense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	C	39	7.690872	0.98434	.	.	ENSG00000174469	ENST00000361727;ENST00000538075	.	.	.	5.66	-1.49	0.08718	.	0.271225	0.34133	N	0.004228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	16.5713	0.84613	0.3188:0.6811:0.0:0.0	.	.	.	.	X	1095;154	.	ENSP00000354778:R1095X	R	+	1	2	CNTNAP2	147557706	0.034000	0.19679	0.539000	0.28077	0.610000	0.37248	1.513000	0.35823	-0.503000	0.06586	0.455000	0.32223	CGA		0.448	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	147926773	C	T	147926773	4	4	62	1	0	0	0	0	0	1	0	0	3653	644	23	1	3361	1	CNTNAP2	7	147926773	Nonsense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	56295144	147926773	11211890	22	20320										
XKR6	286046	hgsc.bcm.edu	37	chr8	10782302	10782302	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gtcgctggtgttccttccgcCgctggctctgaatccccagg	12	15	1	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr8:10782302C>T	ENST00000416569.2	-	2	829	c.803G>A	c.(802-804)cGg>cAg	p.R268Q	XKR6_ENST00000304437.2_5'UTR	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	268						integral component of membrane (GO:0016021)		p.R268Q(2)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		TTCCTTCCGCCGCTGGCTCTG	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	8											103	90	94					8																	10782302		2203	4300	6503	10819712	SO:0001583	missense	286046			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.803G>A	8.37:g.10782302C>T	ENSP00000416707:p.Arg268Gln		10819712	Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	37	CCDS5978.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	21.1|21.1	4.098619|4.098619	0.76870|0.76870	.|.	.|.	ENSG00000171044|ENSG00000171044	ENST00000382461|ENST00000416569	.|T	.|0.63913	.|-0.07	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.000000	.|0.64402	.|U	.|0.000003	T|T	0.61652|0.61652	0.2364|0.2364	N|N	0.20445|0.20445	0.575|0.575	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.63381	.|0.914	T|T	0.55964|0.55964	-0.8057|-0.8057	5|10	.|0.10111	.|T	.|0.7	1.7456|1.7456	16.6436|16.6436	0.85155|0.85155	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|268	.|Q5GH73	.|XKR6_HUMAN	S|Q	45|268	.|ENSP00000416707:R268Q	.|ENSP00000416707:R268Q	G|R	-|-	1|2	0|0	XKR6|XKR6	10819712|10819712	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.639000|7.639000	0.83342|0.83342	2.156000|2.156000	0.67533|0.67533	0.457000|0.457000	0.33378|0.33378	GGC|CGG		0.597	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		T	10782302	C	T	10782302	3	4	62	1	0	0	0	0	1	0	0	0	17475	652	23	1	1130	1	XKR6	8	10782302	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10		10782302	135581720	23	20321										
BAG1	573	hgsc.bcm.edu	37	chr9	33255912	33255912	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tcaatctactgtctttgaaaTtttctggcaggatctatgga	8	7	5	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr9:33255912T>A	ENST00000379704.2	-	6	987	c.554A>T	c.(553-555)aAt>aTt	p.N185I	BAG1_ENST00000467389.2_5'UTR|BAG1_ENST00000472232.3_Missense_Mutation_p.N300I			Q99933	BAG1_HUMAN	BCL2-associated athanogene	300	Interaction with HSPA8.|Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|chaperone cofactor-dependent protein refolding (GO:0070389)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor signaling protein activity (GO:0005057)	p.N300I(1)		endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00506)			GTCTTTGAAATTTTCTGGCAG	0.338																																					GBM(77;1066 1502 5858 12192)											1	Substitution - Missense(1)	large_intestine(1)	9											146	133	137					9																	33255912		2202	4298	6500	33245912	SO:0001583	missense	573			AF022224	CCDS35004.1, CCDS55301.1	9p12	2010-12-09			ENSG00000107262	ENSG00000107262			937	protein-coding gene	gene with protein product		601497				7834747	Standard	NM_004323		Approved		uc003zsj.3	Q99933	OTTHUMG00000019766	ENST00000379704.2:c.554A>T	9.37:g.33255912T>A	ENSP00000369026:p.Asn185Ile		33245912	O75315|Q14414|Q53H32|Q5VZE8|Q5VZE9|Q5VZF0|Q96TG2|Q9Y2V4	Missense_Mutation	SNP	ENST00000379704.2	37	CCDS55301.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.734935	0.69189	.	.	ENSG00000107262	ENST00000472232;ENST00000379700;ENST00000379704	D;D	0.88354	-2.37;-2.37	4.78	3.58	0.41010	BAG domain (3);	0.143965	0.64402	D	0.000007	D	0.90386	0.6991	L	0.56769	1.78	0.44395	D	0.997303	D;D	0.60160	0.969;0.987	P;P	0.57620	0.513;0.824	D	0.90691	0.4613	10	0.87932	D	0	-2.8431	9.971	0.41754	0.0:0.0:0.1691:0.8309	.	229;300	Q99933-3;Q99933	.;BAG1_HUMAN	I	300;185;185	ENSP00000420514:N300I;ENSP00000369026:N185I	ENSP00000369022:N185I	N	-	2	0	BAG1	33245912	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.388000	0.52509	2.022000	0.59522	0.533000	0.62120	AAT		0.338	BAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052042.3	NM_004323		A	33255912	T	A	33255912	3	1	62	1	0	0	0	0	1	0	0	0	1287	1493	52	5	146	5	BAG1	9	33255912	Missense_Mutation	SNP	T	TCGA-AG-A008-01A-01W-A005-10		33255912	107957519	24	20322										
TNC	3371	hgsc.bcm.edu	37	chr9	117798501	117798501	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tccactgtgttcccggacacCgtgcgtgtaatttctggcac	10	13	1	0	rs200409463		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr9:117798501C>T	ENST00000350763.4	-	21	5943	c.5532G>A	c.(5530-5532)acG>acA	p.T1844T	TNC_ENST00000537320.1_Silent_p.T1207T|TNC_ENST00000423613.2_Silent_p.T1571T|TNC_ENST00000340094.3_Silent_p.T1480T|TNC_ENST00000535648.1_Silent_p.T1389T|TNC_ENST00000341037.4_Silent_p.T1662T|TNC_ENST00000346706.3_Silent_p.T1298T|TNC_ENST00000345230.3_Silent_p.T1207T|TNC_ENST00000542877.1_Silent_p.T1481T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1844	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.T1844T(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCCCGGACACCGTGCGTGTAA	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	9											157	130	139					9																	117798501		2203	4300	6503	116838322	SO:0001819	synonymous_variant	3371				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5532G>A	9.37:g.117798501C>T			116838322	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	6.488	0.458154	0.12342	.	.	ENSG00000041982	ENST00000544972	.	.	.	5.38	-8.71	0.00848	.	.	.	.	.	T	0.49626	0.1568	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58115	-0.7693	4	.	.	.	.	10.219	0.43186	0.0:0.1848:0.3055:0.5097	.	.	.	.	S	407	.	.	G	-	1	0	TNC	116838322	0.000000	0.05858	0.152000	0.22495	0.877000	0.50540	-2.828000	0.00745	-1.821000	0.01213	-0.878000	0.02970	GGT		0.517	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117798501	C	T	117798501	2	4	62	1	0	0	0	0	0	0	0	1	16309	639	23	1		1	TNC	9	117798501	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10	84542589	117798501	23414930	25	20323										
MYPN	84665	hgsc.bcm.edu	37	chr10	69926073	69926073	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	aatgaggacctcagcaacaaCgggtctcttcactcagccaa	8	13	4	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr10:69926073C>T	ENST00000358913.5	+	10	2111	c.1623C>T	c.(1621-1623)aaC>aaT	p.N541N	MYPN_ENST00000354393.2_Silent_p.N266N|MYPN_ENST00000540630.1_Silent_p.N541N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	541					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.N541N(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TCAGCAACAACGGGTCTCTTC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	10											84	69	74					10																	69926073		2203	4300	6503	69596079	SO:0001819	synonymous_variant	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1623C>T	10.37:g.69926073C>T			69596079	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																				0.547	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69926073	C	T	69926073	2	4	62	1	0	0	0	0	0	0	0	1	10128	535	19	1		1	MYPN	10	69926073	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10		69926073	65608674	26	20324										
MYST4	23522	hgsc.bcm.edu	37	chr10	76789361	76789361	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	acgctcgacgattgccaacaGtcggaccacagtagcccagt	10	14	0	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr10:76789361G>A	ENST00000287239.4	+	18	5268	c.4779G>A	c.(4777-4779)caG>caA	p.Q1593Q	KAT6B_ENST00000372714.1_Silent_p.Q1301Q|KAT6B_ENST00000372711.1_Silent_p.Q1410Q|KAT6B_ENST00000372724.1_Silent_p.Q1301Q|KAT6B_ENST00000372725.1_Silent_p.Q1301Q	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1593	Interaction with RUNX1 and RUNX2.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.Q1593Q(1)									ATTGCCAACAGTCGGACCACA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	10											140	126	131					10																	76789361		2203	4300	6503	76459367	SO:0001819	synonymous_variant	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4779G>A	10.37:g.76789361G>A			76459367	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	37	CCDS7345.1																																																																																				0.557	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76789361	G	A	76789361	2	1	62	1	0	0	0	0	0	0	0	1	10135	1020	36	3		3	MYST4	10	76789361	Silent	SNP	G	TCGA-AG-A008-01A-01W-A005-10	6863288	76789361	58745386	27	20325										
GFRA1	2674	hgsc.bcm.edu	37	chr10	117849328	117849328	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctggccccaggggcttgttcTtaacccggagggcagtggtg	16	11	1	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr10:117849328T>G	ENST00000355422.6	-	9	1671	c.1121A>C	c.(1120-1122)aAg>aCg	p.K374T	GFRA1_ENST00000544592.1_Missense_Mutation_p.K253T|GFRA1_ENST00000369236.1_Missense_Mutation_p.K369T|GFRA1_ENST00000439649.3_Missense_Mutation_p.K369T	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	374					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.K369T(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		GGGCTTGTTCTTAACCCGGAG	0.547																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - Missense(1)	large_intestine(1)	10											69	69	69					10																	117849328		2203	4300	6503	117839318	SO:0001583	missense	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.1121A>C	10.37:g.117849328T>G	ENSP00000347591:p.Lys374Thr		117839318	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.128847	0.37533	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.47528	1.45;0.84	6.17	3.87	0.44632	.	0.342580	0.35870	N	0.002935	T	0.36853	0.0982	L	0.43152	1.355	0.38955	D	0.958426	P;B	0.43094	0.799;0.131	B;B	0.40901	0.343;0.062	T	0.17137	-1.0379	10	0.23891	T	0.37	-17.0835	8.4142	0.32662	0.0:0.1944:0.0:0.8056	.	374;369	P56159;P56159-2	GFRA1_HUMAN;.	T	374;369;369;253;369	ENSP00000358239:K369T;ENSP00000442179:K253T	ENSP00000347591:K369T	K	-	2	0	GFRA1	117839318	1.000000	0.71417	0.997000	0.53966	0.722000	0.41435	1.490000	0.35573	1.166000	0.42689	0.533000	0.62120	AAG		0.547	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		G	117849328	T	G	117849328	3	3	62	1	0	0	0	0	1	0	0	0	6367	1609	56	4	288	4	GFRA1	10	117849328	Missense_Mutation	SNP	T	TCGA-AG-A008-01A-01W-A005-10	41059967	117849328	17685419	28	20326										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121663616	121663616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ttcagccagatccggagagcGtggttcttggcacggatgga	15	9	2	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr10:121663616G>A	ENST00000369075.3	+	4	1000	c.928G>A	c.(928-930)Gtg>Atg	p.V310M	SEC23IP_ENST00000543134.1_Missense_Mutation_p.V99M	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	310	Interaction with SEC23A.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.V310M(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TCCGGAGAGCGTGGTTCTTGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	10											108	99	102					10																	121663616		2203	4300	6503	121653606	SO:0001583	missense	11196			AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.928G>A	10.37:g.121663616G>A	ENSP00000358071:p.Val310Met		121653606	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	37	CCDS7618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.518354|4.518354	0.85495|0.85495	.|.	.|.	ENSG00000107651|ENSG00000107651	ENST00000442952|ENST00000369075;ENST00000543134;ENST00000446561	.|T;T;T	.|0.48201	.|1.31;1.37;0.82	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72463|0.72463	0.3463|0.3463	M|M	0.86178|0.86178	2.8|2.8	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.68192	.|0.956;0.945	T|T	0.74688|0.74688	-0.3581|-0.3581	5|10	.|0.48119	.|T	.|0.1	-16.5517|-16.5517	19.3947|19.3947	0.94603|0.94603	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|99;310	.|F5H0L8;Q9Y6Y8	.|.;S23IP_HUMAN	H|M	75|310;99;44	.|ENSP00000358071:V310M;ENSP00000438773:V99M;ENSP00000396906:V44M	.|ENSP00000358071:V310M	R|V	+|+	2|1	0|0	SEC23IP|SEC23IP	121653606|121653606	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.885000|0.885000	0.51271|0.51271	9.254000|9.254000	0.95512|0.95512	2.644000|2.644000	0.89710|0.89710	0.563000|0.563000	0.77884|0.77884	CGT|GTG		0.493	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			A	121663616	G	A	121663616	3	1	62	1	0	0	0	0	1	0	0	0	14030	1145	40	1	942	1	SEC23IP	10	121663616	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	3814288	121663616	13871131	29	20327										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46782198	46782198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tgtcctcagctggtcccttgCgtaacatgttggcattggag	12	10	1	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr11:46782198C>T	ENST00000529230.1	-	33	4404	c.4358G>A	c.(4357-4359)cGc>cAc	p.R1453H	CKAP5_ENST00000415402.1_Missense_Mutation_p.R1453H|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1453H|SNORD67_ENST00000516618.1_RNA|SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1453H			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1453					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)		p.R1453H(1)		breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TGGTCCCTTGCGTAACATGTT	0.483																																					Ovarian(4;85 273 2202 4844 13323)											1	Substitution - Missense(1)	large_intestine(1)	11											233	192	206					11																	46782198		2201	4299	6500	46738774	SO:0001583	missense	9793				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.4358G>A	11.37:g.46782198C>T	ENSP00000432768:p.Arg1453His		46738774	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.807005	0.90623	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876	T;T;T;T	0.50277	0.75;0.77;0.77;0.77	6.03	6.03	0.97812	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60051	0.2239	L	0.32530	0.975	0.80722	D	1	D;D;P	0.89917	1.0;0.965;0.941	D;P;P	0.65684	0.937;0.681;0.482	T	0.56595	-0.7953	10	0.48119	T	0.1	-10.0088	20.5666	0.99351	0.0:1.0:0.0:0.0	.	1453;1453;1453	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	H	1453;1453;1453;1453;176	ENSP00000432768:R1453H;ENSP00000395302:R1453H;ENSP00000310227:R1453H;ENSP00000346566:R1453H	ENSP00000310227:R1453H	R	-	2	0	CKAP5	46738774	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.835000	0.69368	2.854000	0.98071	0.655000	0.94253	CGC		0.483	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		T	46782198	C	T	46782198	3	4	62	1	0	0	0	0	1	0	0	0	3451	768	27	1	1788	1	CKAP5	11	46782198	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10		46782198	88224318	30	20328										
LRMP	4033	hgsc.bcm.edu	37	chr12	25254244	25254244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	agaatgaaaggtctttcaatCctcttgaagatgatggtaat	9	5	3	5			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr12:25254244C>T	ENST00000354454.3	+	15	1703	c.874C>T	c.(874-876)Cct>Tct	p.P292S	LRMP_ENST00000548766.1_Missense_Mutation_p.P292S|LRMP_ENST00000547044.1_Missense_Mutation_p.P292S|RP11-713N11.4_ENST00000555862.1_RNA	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	348					immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P292S(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					GTCTTTCAATCCTCTTGAAGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											71	71	71					12																	25254244		2203	4300	6503	25145511	SO:0001583	missense	4033				CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.874C>T	12.37:g.25254244C>T	ENSP00000346442:p.Pro292Ser		25145511	A0AVM2|B4E077|Q8N301	Missense_Mutation	SNP	ENST00000354454.3	37	CCDS8701.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.852430	0.00563	.	.	ENSG00000118308	ENST00000354454;ENST00000536173;ENST00000548766;ENST00000547044	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	5.51	0.213	0.15244	.	0.399073	0.28847	N	0.013944	T	0.11452	0.0279	N	0.11201	0.11	0.09310	N	0.999998	B	0.10296	0.003	B	0.11329	0.006	T	0.21655	-1.0239	10	0.02654	T	1	-4.6117	1.0607	0.01600	0.15:0.3481:0.1459:0.356	.	348	Q12912	LRMP_HUMAN	S	292;239;292;292	ENSP00000346442:P292S;ENSP00000444056:P239S;ENSP00000446496:P292S;ENSP00000450246:P292S	ENSP00000346442:P292S	P	+	1	0	LRMP	25145511	0.018000	0.18449	0.956000	0.39512	0.180000	0.23129	0.745000	0.26259	0.367000	0.24454	0.462000	0.41574	CCT		0.333	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152		T	25254244	C	T	25254244	3	4	62	1	0	0	0	0	1	0	0	0	8979	855	30	3	916	3	LRMP	12	25254244	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10		25254244	108597651	31	20329										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	62	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	144040	25398284	108453611	32	20330										
TUBA1C	84790	hgsc.bcm.edu	37	chr12	49663626	49663626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tccagatgaagttcgcactgGcacttaccgccagctcttcc	8	15	1	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr12:49663626G>A	ENST00000301072.6	+	3	517	c.242G>A	c.(241-243)gGc>gAc	p.G81D	TUBA1C_ENST00000549183.1_Missense_Mutation_p.G81D|TUBA1C_ENST00000541364.1_Missense_Mutation_p.G151D|RP11-161H23.5_ENST00000550468.2_RNA	NM_032704.3	NP_116093.1	Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	81					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G81D(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						GTTCGCACTGGCACTTACCGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	12											106	101	103					12																	49663626		2203	4300	6503	47949893	SO:0001583	missense	84790			BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553		"Tubulins"	20768	protein-coding gene	gene with protein product			"tubulin, alpha 6"	TUBA6		7821789	Standard	NM_032704		Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000301072.6:c.242G>A	12.37:g.49663626G>A	ENSP00000301072:p.Gly81Asp		47949893		Missense_Mutation	SNP	ENST00000301072.6	37	CCDS8782.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841545	0.71488	.	.	ENSG00000167553	ENST00000541364;ENST00000301072;ENST00000549183;ENST00000321665	T;T;T	0.67345	-0.26;-0.26;-0.26	4.32	4.32	0.51571	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.86506	0.5949	H	0.96748	3.875	0.80722	D	1	P;P	0.52463	0.953;0.812	P;P	0.60682	0.878;0.564	D	0.91037	0.4868	10	0.87932	D	0	.	16.7781	0.85557	0.0:0.0:1.0:0.0	.	151;81	F5H5D3;Q9BQE3	.;TBA1C_HUMAN	D	151;81;81;81	ENSP00000443475:G151D;ENSP00000301072:G81D;ENSP00000448211:G81D	ENSP00000301072:G81D	G	+	2	0	TUBA1C	47949893	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.391000	0.97249	2.679000	0.91253	0.555000	0.69702	GGC		0.592	TUBA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404424.1	NM_032704		A	49663626	G	A	49663626	3	1	62	1	0	0	0	0	1	0	0	0	16785	1203	42	3	252	3	TUBA1C	12	49663626	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	24265342	49663626	84188269	33	20331										
KRT81	3887	hgsc.bcm.edu	37	chr12	52681407	52681407	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ttggcattctccacctcggcCgtcagcctttggatcatgcg	10	14	3	0	rs557990688		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr12:52681407C>T	ENST00000327741.5	-	6	1067	c.999G>A	c.(997-999)acG>acA	p.T333T	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	333	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.T333T(1)		breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCACCTCGGCCGTCAGCCTTT	0.587													.|||	1	0.000199681	0	0.0014	5008	,	,		19855	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12											95	82	87					12																	52681407		2203	4300	6503	50967674	SO:0001819	synonymous_variant	3887			X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.999G>A	12.37:g.52681407C>T			50967674	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																				0.587	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		T	52681407	C	T	52681407	2	4	62	1	0	0	0	0	0	0	0	1	8516	639	23	1		1	KRT81	12	52681407	Silent	SNP	C	TCGA-AG-A008-01A-01W-A005-10	3017781	52681407	81170488	34	20332										
MYF5	4617	hgsc.bcm.edu	37	chr12	81112717	81112717	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	accggatcacctcctcagagCaacctgggttgcctctccag	9	16	3	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr12:81112717C>T	ENST00000228644.3	+	3	807	c.655C>T	c.(655-657)Caa>Taa	p.Q219*		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	219					camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.Q219*(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						CTCCTCAGAGCAACCTGGGTT	0.493																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											106	102	103					12																	81112717		2203	4300	6503	79636848	SO:0001587	stop_gained	4617				CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.655C>T	12.37:g.81112717C>T	ENSP00000228644:p.Gln219*		79636848	Q6ISR9	Nonsense_Mutation	SNP	ENST00000228644.3	37	CCDS9020.1	.	.	.	.	.	.	.	.	.	.	C	36	5.847927	0.97023	.	.	ENSG00000111049	ENST00000228644	.	.	.	6.06	6.06	0.98353	.	0.240656	0.42548	D	0.000684	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-0.035	19.3923	0.94587	0.0:1.0:0.0:0.0	.	.	.	.	X	219	.	ENSP00000228644:Q219X	Q	+	1	0	MYF5	79636848	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.154000	0.50693	2.882000	0.98803	0.655000	0.94253	CAA		0.493	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		T	81112717	C	T	81112717	4	4	62	1	0	0	0	0	0	1	0	0	10057	711	25	3	665	3	MYF5	12	81112717	Nonsense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	28431310	81112717	52739178	35	20333										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70990285	70990285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	tattccctggatatggaggcGgttgaatacataatccacta	9	8	0	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr14:70990285G>A	ENST00000256389.3	-	2	1584	c.1340C>T	c.(1339-1341)cCg>cTg	p.P447L	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	397	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P447L(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ATATGGAGGCGGTTGAATACA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											178	118	138					14																	70990285		2203	4300	6503	70060038	SO:0001583	missense	8748			AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1340C>T	14.37:g.70990285G>A	ENSP00000256389:p.Pro447Leu		70060038	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	G	5.612	0.297729	0.10622	.	.	ENSG00000134007	ENST00000256389	T	0.00882	5.58	4.54	-1.19	0.09585	.	2.601280	0.02003	N	0.046465	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.47275	-0.9130	10	0.33940	T	0.23	.	5.7307	0.18038	0.2159:0.0:0.2594:0.5247	.	397	O43506	ADA20_HUMAN	L	447	ENSP00000256389:P447L	ENSP00000256389:P447L	P	-	2	0	ADAM20	70060038	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.364000	0.07583	-0.184000	0.10567	-1.185000	0.01705	CCG		0.423	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			A	70990285	G	A	70990285	3	1	62	1	0	0	0	0	1	0	0	0	242	1116	39	1	994	1	ADAM20	14	70990285	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		70990285	36359255	36	20334										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25926044	25926044	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ccccaggtaaacaggtccacGttcgagtcatagtaggcctg	11	12	1	0			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr15:25926044G>A	ENST00000356865.6	-	19	3702	c.3591C>T	c.(3589-3591)aaC>aaT	p.N1197N		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1197					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.N1197N(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ACAGGTCCACGTTCGAGTCAT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	15											114	109	111					15																	25926044		2203	4300	6503	23477137	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3591C>T	15.37:g.25926044G>A			23477137	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.557	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25926044	G	A	25926044	2	1	62	1	0	0	0	0	0	0	0	1	1117	1136	40	1		1	ATP10A	15	25926044	Silent	SNP	G	TCGA-AG-A008-01A-01W-A005-10		25926044	76605348	37	20335										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68156207	68156207	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	atgacccagaacgggaatttTtggaaaggccttctagagat	11	7	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr16:68156207T>C	ENST00000346183.3	+	2	445	c.421T>C	c.(421-423)Ttg>Ctg	p.L141L	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000349223.5_Silent_p.L141L|NFATC3_ENST00000575270.1_Silent_p.L141L|RP11-67A1.2_ENST00000548144.1_RNA|NFATC3_ENST00000329524.4_Silent_p.L141L	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	141					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L141L(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		ACGGGAATTTTTGGAAAGGCC	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	16											83	84	84					16																	68156207		2198	4300	6498	66713708	SO:0001819	synonymous_variant	4775			L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.421T>C	16.37:g.68156207T>C			66713708	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																				0.438	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		C	68156207	T	C	68156207	2	2	62	1	0	0	0	0	0	0	0	1	10395	1838	64	4		4	NFATC3	16	68156207	Silent	SNP	T	TCGA-AG-A008-01A-01W-A005-10		68156207	22198546	38	20336										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32959756	32959756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	gtgactacgtgtttgtgagtGgaaaagagtctcgagggtcc	15	6	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr17:32959756G>A	ENST00000321639.5	+	7	1574	c.1246G>A	c.(1246-1248)Gga>Aga	p.G416R		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	416						integral component of membrane (GO:0016021)		p.G416R(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		GTTTGTGAGTGGAAAAGAGTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	17											178	140	153					17																	32959756		2203	4300	6503	29983869	SO:0001583	missense	124842			BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1246G>A	17.37:g.32959756G>A	ENSP00000316532:p.Gly416Arg		29983869	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970319	0.92919	.	.	ENSG00000181291	ENST00000321639	T	0.35048	1.33	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.65729	0.2719	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73509	-0.3960	10	0.87932	D	0	-12.9424	16.6219	0.84932	0.0:0.0:1.0:0.0	.	416	Q6IEE7	T132E_HUMAN	R	416	ENSP00000316532:G416R	ENSP00000316532:G416R	G	+	1	0	TMEM132E	29983869	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	9.657000	0.98554	2.388000	0.81334	0.551000	0.68910	GGA		0.572	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32959756	G	A	32959756	3	1	62	1	0	0	0	0	1	0	0	0	16087	1349	47	3	1272	3	TMEM132E	17	32959756	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		32959756	48235454	39	20337										
CCDC103	388389	hgsc.bcm.edu	37	chr17	42980015	42980015	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	taagcctgctgagccgggcaGagagagagagctgcaagggc	17	9	0	4			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr17:42980015G>A	ENST00000417826.2	+	4	654	c.559G>A	c.(559-561)Gag>Aag	p.E187K	EFTUD2_ENST00000426333.2_5'Flank|AC015936.3_ENST00000441312.1_RNA|CCDC103_ENST00000410006.2_Missense_Mutation_p.E187K|FAM187A_ENST00000412523.2_Intron|FAM187A_ENST00000331733.4_5'UTR	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	Q8IW40	CC103_HUMAN	coiled-coil domain containing 103	187					axonemal dynein complex assembly (GO:0070286)|cell projection organization (GO:0030030)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|outer dynein arm assembly (GO:0036158)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein homodimerization activity (GO:0042803)	p.E187K(1)		endometrium(1)|kidney(1)|large_intestine(3)|prostate(1)|skin(1)	7		Prostate(33;0.109)				GAGCCGGGCAGAGAGAGAGAG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											37	39	38					17																	42980015		2203	4300	6503	40335541	SO:0001583	missense	388389			AK023156	CCDS11490.1, CCDS58554.1	17q21.31	2013-02-22			ENSG00000167131	ENSG00000167131			32700	protein-coding gene	gene with protein product		614677				22581229	Standard	NM_213607		Approved	FLJ13094, FLJ34211, PR46b, CILD17	uc031ray.1	Q8IW40	OTTHUMG00000154264	ENST00000417826.2:c.559G>A	17.37:g.42980015G>A	ENSP00000391692:p.Glu187Lys		40335541	A8K145|B8ZZU0	Missense_Mutation	SNP	ENST00000417826.2	37	CCDS11490.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.147083	0.77888	.	.	ENSG00000167131	ENST00000357776;ENST00000417826;ENST00000410006	T;T;T	0.60797	0.16;0.16;0.16	5.64	5.64	0.86602	.	0.000000	0.53938	U	0.000058	T	0.76183	0.3952	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.76884	-0.2794	10	0.72032	D	0.01	3.1677	18.0636	0.89384	0.0:0.0:1.0:0.0	.	187	Q8IW40	CC103_HUMAN	K	187	ENSP00000350420:E187K;ENSP00000391692:E187K;ENSP00000387252:E187K	ENSP00000350420:E187K	E	+	1	0	CCDC103	40335541	1.000000	0.71417	0.953000	0.39169	0.078000	0.17371	6.205000	0.72148	2.937000	0.99478	0.650000	0.86243	GAG		0.647	CCDC103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334578.1	NM_213607		A	42980015	G	A	42980015	3	1	62	1	0	0	0	0	1	0	0	0	2744	943	33	3	569	3	CCDC103	17	42980015	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	10020259	42980015	38215195	40	20338										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48604787	48604787	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	accgggccctccagctcctaGacgaagtacttcataccatg	8	15	1	1	rs377767385		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr18:48604787G>T	ENST00000342988.3	+	12	2147	c.1609G>T	c.(1609-1611)Gac>Tac	p.D537Y	SMAD4_ENST00000588745.1_Missense_Mutation_p.D441Y|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.D537Y	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	537	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.D537Y(3)|p.?(2)|p.L536fs*11(1)|p.L536fs*14(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CCAGCTCCTAGACGAAGTACT	0.488																																																43	Whole gene deletion(36)|Substitution - Missense(3)|Deletion - Frameshift(2)|Unknown(2)	pancreas(26)|large_intestine(7)|lung(3)|breast(3)|stomach(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											79	82	81					18																	48604787		2203	4300	6503	46858785	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1609G>T	18.37:g.48604787G>T	ENSP00000341551:p.Asp537Tyr		46858785	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.860918	0.71834	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98090	-4.71;-4.71	6.07	6.07	0.98685	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (1);	0.000000	0.85682	D	0.000000	D	0.99133	0.9701	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99323	1.0907	10	0.87932	D	0	.	19.4308	0.94765	0.0:0.0:1.0:0.0	.	537	Q13485	SMAD4_HUMAN	Y	537	ENSP00000341551:D537Y;ENSP00000381452:D537Y	ENSP00000341551:D537Y	D	+	1	0	SMAD4	46858785	1.000000	0.71417	0.972000	0.41901	0.957000	0.61999	9.633000	0.98432	2.885000	0.99019	0.655000	0.94253	GAC		0.488	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48604787	G	T	48604787	3	4	62	1	0	0	0	0	1	0	0	0	14797	942	33	2	1651	2	SMAD4	18	48604787	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		48604787	29472461	41	20339										
B3GNT3	10331	hgsc.bcm.edu	37	chr19	17922476	17922476	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	cacacacagacaacatggtcTtctacctgcaggaccatgac	7	14	2	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr19:17922476T>G	ENST00000318683.6	+	3	811	c.664T>G	c.(664-666)Ttc>Gtc	p.F222V	B3GNT3_ENST00000595387.1_Missense_Mutation_p.F222V	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	222					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)	p.F222V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						CAACATGGTCTTCTACCTGCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											103	80	88					19																	17922476		2203	4300	6503	17783476	SO:0001583	missense	10331			AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"Beta 3-glycosyltransferases"	13528	protein-coding gene	gene with protein product	"putative type II membrane protein", "beta-1,3-N-acetylglucosaminyltransferase bGnT-3", "transmembrane protein 3"	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.664T>G	19.37:g.17922476T>G	ENSP00000321874:p.Phe222Val		17783476	B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Missense_Mutation	SNP	ENST00000318683.6	37	CCDS12364.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.569251	0.28003	.	.	ENSG00000179913	ENST00000318683	T	0.41400	1.0	5.31	-5.34	0.02705	.	0.795762	0.10951	N	0.616056	T	0.12603	0.0306	N	0.01109	-1.01	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28332	-1.0047	10	0.32370	T	0.25	.	8.7885	0.34837	0.2946:0.0:0.5751:0.1303	.	222	Q9Y2A9	B3GN3_HUMAN	V	222	ENSP00000321874:F222V	ENSP00000321874:F222V	F	+	1	0	B3GNT3	17783476	0.000000	0.05858	0.159000	0.22649	0.788000	0.44548	-0.099000	0.11007	-1.554000	0.01700	0.454000	0.30748	TTC		0.572	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256		G	17922476	T	G	17922476	3	3	62	1	0	0	0	0	1	0	0	0	1259	1609	56	4	670	4	B3GNT3	19	17922476	Missense_Mutation	SNP	T	TCGA-AG-A008-01A-01W-A005-10		17922476	41206507	42	20340										
KIR3DL2	3812	hgsc.bcm.edu	37	chr19	55365348	55365348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctgaggacccctcacgcctcGttggacagatccatgatggg	12	13	1	3			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr19:55365348G>A	ENST00000326321.3	+	4	535	c.502G>A	c.(502-504)Gtt>Att	p.V168I	KIR3DL2_ENST00000270442.5_Missense_Mutation_p.V168I|KIR3DL1_ENST00000402254.2_Intron	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	168	Ig-like C2-type 2.				cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V168I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		CTCACGCCTCGTTGGACAGAT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19																																								60057160	SO:0001583	missense	3812			L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.502G>A	19.37:g.55365348G>A	ENSP00000325525:p.Val168Ile		60057160	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	g	1.603	-0.525953	0.04141	.	.	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.03004	4.08;4.08	2.06	-4.0	0.04057	Immunoglobulin-like fold (1);	.	.	.	.	T	0.01353	0.0044	N	0.02275	-0.615	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.45381	-0.9265	9	0.41790	T	0.15	.	2.7398	0.05250	0.5071:0.0:0.27:0.2229	.	168;168	Q95366;P43630	.;KI3L2_HUMAN	I	168	ENSP00000325525:V168I;ENSP00000270442:V168I	ENSP00000270442:V168I	V	+	1	0	KIR3DL2	60057160	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.408000	0.01042	-0.716000	0.04962	-1.051000	0.02340	GTT		0.512	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1			A	55365348	G	A	55365348	3	1	62	1	0	0	0	0	1	0	0	0	8342	1145	40	1	516	1	KIR3DL2	19	55365348	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10	37442872	55365348	3763635	43	20341										
SYN3	8224	hgsc.bcm.edu	37	chr22	32909719	32909719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	caaaagacttcctcaggttgCggatggtttcagccttggcc	11	11	2	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr22:32909719C>T	ENST00000358763.2	-	14	1945	c.1703G>A	c.(1702-1704)cGc>cAc	p.R568H	SYN3_ENST00000332840.5_Missense_Mutation_p.R568H|SYN3_ENST00000467095.1_5'UTR	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	568	E.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)	p.R568H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CCTCAGGTTGCGGATGGTTTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											160	115	130					22																	32909719		2203	4300	6503	31239719	SO:0001583	missense	8224			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.1703G>A	22.37:g.32909719C>T	ENSP00000351614:p.Arg568His		31239719	B1B1F9	Missense_Mutation	SNP	ENST00000358763.2	37	CCDS13908.1	.	.	.	.	.	.	.	.	.	.	C	35	5.518069	0.96416	.	.	ENSG00000185666	ENST00000358763;ENST00000332840;ENST00000445154	T;T	0.53640	0.61;0.61	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.69797	0.3151	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.72141	-0.4380	10	0.87932	D	0	-4.6075	19.5608	0.95371	0.0:1.0:0.0:0.0	.	567;568	Q17R54;O14994	.;SYN3_HUMAN	H	568;568;174	ENSP00000351614:R568H;ENSP00000330219:R568H	ENSP00000330219:R568H	R	-	2	0	SYN3	31239719	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.469000	0.80959	2.698000	0.92095	0.561000	0.74099	CGC		0.572	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4			T	32909719	C	T	32909719	3	4	62	1	0	0	0	0	1	0	0	0	15481	768	27	1	43	1	SYN3	22	32909719	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10		32909719	18394847	44	20342										
NFAM1	150372	hgsc.bcm.edu	37	chr22	42828276	42828276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ggtcccgggcagcagcagcaCgccaaggaggagccaggggg	19	12	0	0	rs138744630	byFrequency	TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chr22:42828276C>T	ENST00000329021.5	-	1	125	c.88G>A	c.(88-90)Gtg>Atg	p.V30M		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	30					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.V30M(1)		large_intestine(1)|lung(3)	4						AGCAGCAGCACGCCAAGGAGG	0.672													G|||	2	0.000399361	0.0015	0	5008	,	,		13444	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						G	MET/VAL	3,4375		0,3,2186	16	19	18		88	-3.1	0	22	dbSNP_134	18	0,8562		0,0,4281	yes	missense	NFAM1	NM_145912.5	21	0,3,6467	TT,TC,CC		0.0,0.0685,0.0232	benign	30/271	42828276	3,12937	2189	4281	6470	41158220	SO:0001583	missense	150372			BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.88G>A	22.37:g.42828276C>T	ENSP00000333680:p.Val30Met		41158220	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Missense_Mutation	SNP	ENST00000329021.5	37	CCDS14034.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720128	0.48728	6.85E-4	0.0	ENSG00000235568	ENST00000329021	T	0.33438	1.41	3.18	-3.09	0.05331	.	0.000000	0.30437	U	0.009627	T	0.10165	0.0249	N	0.08118	0	0.09310	N	1	B	0.32128	0.357	B	0.18871	0.023	T	0.09271	-1.0682	10	0.48119	T	0.1	-0.1179	6.0185	0.19616	0.242:0.3179:0.4401:0.0	.	30	Q8NET5	NFAM1_HUMAN	M	30	ENSP00000333680:V30M	ENSP00000333680:V30M	V	-	1	0	NFAM1	41158220	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.906000	0.04071	-1.310000	0.02312	-1.168000	0.01747	GTG		0.672	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912		T	42828276	C	T	42828276	3	4	62	1	0	0	0	0	1	0	0	0	10389	536	19	1	748	1	NFAM1	22	42828276	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	9918557	42828276	8476290	45	20343										
TIMP1	7076	hgsc.bcm.edu	37	chrX	47444707	47444707	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	cttccacaggtcccacaaccGcagcgaggagtttctcattg	9	14	1	0	rs140600134		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chrX:47444707G>A	ENST00000218388.4	+	4	475	c.305G>A	c.(304-306)cGc>cAc	p.R102H	TIMP1_ENST00000377017.1_Missense_Mutation_p.R38H|MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000340666.4_Intron|TIMP1_ENST00000377018.2_Missense_Mutation_p.A26T|TIMP1_ENST00000456754.2_Missense_Mutation_p.R102H|SYN1_ENST00000295987.7_Intron	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	102	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.R102H(1)		endometrium(1)|large_intestine(2)	3						TCCCACAACCGCAGCGAGGAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	X							HIS/ARG,,	0,3835		0,0,1632,571	55	48	51		305,,	1.8	1	X	dbSNP_134	51	1,6727		0,1,2427,1872	no	missense,intron,intron	SYN1,TIMP1	NM_003254.2,NM_006950.3,NM_133499.2	29,,	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	probably-damaging,,	102/208,,	47444707	1,10562	2203	4300	6503	47329651	SO:0001583	missense	7076				CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.305G>A	X.37:g.47444707G>A	ENSP00000218388:p.Arg102His		47329651	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	37	CCDS14281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	23.1|23.1	4.379827|4.379827	0.82682|0.82682	0.0|0.0	1.49E-4|1.49E-4	ENSG00000102265|ENSG00000102265	ENST00000377018|ENST00000218388;ENST00000456754;ENST00000377017	.|D;D;D	.|0.94376	.|-3.41;-3.41;-3.41	5.01|5.01	1.76|1.76	0.24704|0.24704	.|Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	.|0.147317	.|0.31909	.|N	.|0.006865	D|D	0.93374|0.93374	0.7887|0.7887	L|L	0.57536|0.57536	1.79|1.79	0.24761|0.24761	N|N	0.992929|0.992929	P|D	0.51537|0.71674	0.946|0.998	B|P	0.37387|0.62382	0.248|0.901	D|D	0.85652|0.85652	0.1283|0.1283	8|10	0.87932|0.45353	D|T	0|0.12	.|.	5.4077|5.4077	0.16330|0.16330	0.4296:0.0:0.5704:0.0|0.4296:0.0:0.5704:0.0	.|.	26|102	B4DJK3|P01033	.|TIMP1_HUMAN	T|H	26|102;102;38	.|ENSP00000218388:R102H;ENSP00000406671:R102H;ENSP00000366216:R38H	ENSP00000366217:A26T|ENSP00000218388:R102H	A|R	+|+	1|2	0|0	TIMP1|TIMP1	47329651|47329651	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	1.187000|1.187000	0.32090|0.32090	0.461000|0.461000	0.27071|0.27071	0.591000|0.591000	0.81541|0.81541	GCA|CGC		0.632	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254		A	47444707	G	A	47444707	3	1	62	1	0	0	0	0	1	0	0	0	15956	1087	38	1	315	1	TIMP1	23	47444707	Missense_Mutation	SNP	G	TCGA-AG-A008-01A-01W-A005-10		47444707	107825853	46	20344										
VSIG4	11326	hgsc.bcm.edu	37	chrX	65242693	65242693	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	actttcttacctggctgcttCgtagacatgctctagaaaaa	7	10	2	2			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chrX:65242693C>T	ENST00000374737.4	-	7	1060	c.952G>A	c.(952-954)Gaa>Aaa	p.E318K	VSIG4_ENST00000412866.2_Missense_Mutation_p.E224K|VSIG4_ENST00000455586.2_Missense_Mutation_p.E318K	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	318					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.E318K(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTGGCTGCTTCGTAGACATGC	0.473													C|||	2	0.000529801	0.0015	0	3775	,	,		14284	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											93	86	88					X																	65242693		2203	4300	6503	65159418	SO:0001583	missense	11326			AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.952G>A	X.37:g.65242693C>T	ENSP00000363869:p.Glu318Lys		65159418	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.82|13.82	2.351334|2.351334	0.41700|0.41700	.|.	.|.	ENSG00000155659|ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866|ENST00000427538	T;T;T|.	0.41065|.	1.56;1.01;1.63|.	4.71|4.71	3.84|3.84	0.44239|0.44239	.|.	0.340529|.	0.21244|.	N|.	0.077776|.	T|T	0.53334|0.53334	0.1790|0.1790	M|M	0.69823|0.69823	2.125|2.125	0.26363|0.26363	N|N	0.97701|0.97701	D;D;D;D|.	0.89917|.	0.996;0.998;0.997;1.0|.	P;P;P;D|.	0.66351|.	0.611;0.833;0.839;0.943|.	T|T	0.46638|0.46638	-0.9177|-0.9177	10|5	0.48119|.	T|.	0.1|.	-6.4465|-6.4465	8.154|8.154	0.31158|0.31158	0.0:0.883:0.0:0.117|0.0:0.883:0.0:0.117	.|.	224;308;224;318|.	C9J1L3;C9JH67;Q9Y279-3;Q9Y279|.	.;.;.;VSIG4_HUMAN|.	K|Q	318;318;224|244	ENSP00000363869:E318K;ENSP00000411581:E318K;ENSP00000394143:E224K|.	ENSP00000363869:E318K|.	E|R	-|-	1|2	0|0	VSIG4|VSIG4	65159418|65159418	0.995000|0.995000	0.38212|0.38212	0.944000|0.944000	0.38274|0.38274	0.077000|0.077000	0.17291|0.17291	0.628000|0.628000	0.24522|0.24522	1.068000|1.068000	0.40764|0.40764	0.509000|0.509000	0.49947|0.49947	GAA|CGA		0.473	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		T	65242693	C	T	65242693	3	4	62	1	0	0	0	0	1	0	0	0	17265	893	31	1	259	1	VSIG4	23	65242693	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	17797986	65242693	90027867	47	20345										
CPXCR1	53336	hgsc.bcm.edu	37	chrX	88009103	88009103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	ctaaagggaaatgtagattcCgtgctattgtgaggtctgtg	13	5	1	2	rs191294021		TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chrX:88009103C>T	ENST00000276127.4	+	3	947	c.688C>T	c.(688-690)Cgt>Tgt	p.R230C	CPXCR1_ENST00000373111.1_Missense_Mutation_p.R230C	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	230							metal ion binding (GO:0046872)	p.R230C(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						ATGTAGATTCCGTGCTATTGT	0.378													C|||	1	0.000264901	8e-04	0	3775	,	,		13600	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											66	53	58					X																	88009103		2203	4300	6503	87895759	SO:0001583	missense	53336			AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.688C>T	X.37:g.88009103C>T	ENSP00000276127:p.Arg230Cys		87895759	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.956	1.221395	0.22457	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.26223	1.75;1.75	3.57	2.71	0.32032	.	0.914662	0.09093	N	0.849544	T	0.15478	0.0373	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	B	0.43783	0.431	T	0.09250	-1.0683	9	.	.	.	-0.6198	6.2592	0.20891	0.0:0.8593:0.0:0.1407	.	230	Q8N123	CPXCR_HUMAN	C	230	ENSP00000276127:R230C;ENSP00000362203:R230C	.	R	+	1	0	CPXCR1	87895759	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.134000	0.15932	0.885000	0.36088	-0.215000	0.12644	CGT		0.378	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		T	88009103	C	T	88009103	3	4	62	1	0	0	0	0	1	0	0	0	3842	652	23	1	690	1	CPXCR1	23	88009103	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	22766410	88009103	67261457	48	20346										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120182923	120182923	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.102040816326531	5	1	0.923572579201718	4.55629139072848	0.603038566419945	1	1	0	cttcaaatatgaaagggattCtaactaccacttgctcctgt	6	10	2	1			TCGA-AG-A008-01A-01W-A005-10	TCGA-AG-A008-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	2221cfc4-b324-4329-ad37-3dd9a5adf36e	0f0138d4-f6d2-43c6-aee3-42a62686c23a	g.chrX:120182923C>T	ENST00000328078.1	+	1	1462	c.1385C>T	c.(1384-1386)tCt>tTt	p.S462F		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	462					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)	p.S462F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						GAAAGGGATTCTAACTACCAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											164	145	151					X																	120182923		2203	4300	6503	120010604	SO:0001583	missense	2747			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1385C>T	X.37:g.120182923C>T	ENSP00000327589:p.Ser462Phe		120010604	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.984794	0.53934	.	.	ENSG00000182890	ENST00000328078	D	0.96041	-3.89	2.14	2.14	0.27477	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.052175	0.85682	N	0.000000	D	0.97692	0.9243	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.97373	0.9977	10	0.87932	D	0	-7.638	9.6173	0.39698	0.0:1.0:0.0:0.0	.	462	P49448	DHE4_HUMAN	F	462	ENSP00000327589:S462F	ENSP00000327589:S462F	S	+	2	0	GLUD2	120010604	0.999000	0.42202	0.990000	0.47175	0.964000	0.63967	4.990000	0.63876	1.126000	0.42016	0.472000	0.43445	TCT		0.418	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		T	120182923	C	T	120182923	3	4	62	1	0	0	0	0	1	0	0	0	6497	913	32	3	1387	3	GLUD2	23	120182923	Missense_Mutation	SNP	C	TCGA-AG-A008-01A-01W-A005-10	32173820	120182923	35087637	49	20347										
C1orf63	57035	hgsc.bcm.edu	37	chr1	25571716	25571716	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gaaggaacagttctgagactAgctggcaagtcaatgttggt	13	6	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:25571716A>C	ENST00000243189.7	-	3	873	c.597T>G	c.(595-597)gcT>gcG	p.A199A	C1orf63_ENST00000431849.2_Silent_p.A199A|C1orf63_ENST00000417642.2_Silent_p.A192A|RP3-465N24.6_ENST00000607698.1_lincRNA	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		199								p.A199A(1)		breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTCTGAGACTAGCTGGCAAGT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	1											162	146	152					1																	25571716		2203	4300	6503	25444303	SO:0001819	synonymous_variant	57035																														ENST00000243189.7:c.597T>G	1.37:g.25571716A>C			25444303	A8K917|Q49AA4|Q5TH71|Q9GZP6	Silent	SNP	ENST00000243189.7	37	CCDS260.1																																																																																				0.403	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2			C	25571716	A	C	25571716	2	2	63	1	0	0	0	0	0	0	0	1	2059	407	15	4		4	C1orf63	1	25571716	Silent	SNP	A	TCGA-AG-A00C-01A-01W-A005-10		25571716	223678905	1	20348										
CATSPER4	378807	hgsc.bcm.edu	37	chr1	26527378	26527378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	cactggtgcattgtgtggtcGcccgctcggagaaatctggt	14	10	1	1	rs551550512		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:26527378G>A	ENST00000456354.2	+	8	1112	c.1045G>A	c.(1045-1047)Gcc>Acc	p.A349T		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	349					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.A349T(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TTGTGTGGTCGCCCGCTCGGA	0.597													G|||	1	0.000199681	0	0	5008	,	,		16263	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											56	58	57					1																	26527378		2203	4300	6503	26399965	SO:0001583	missense	378807			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1045G>A	1.37:g.26527378G>A	ENSP00000390423:p.Ala349Thr		26399965	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.006003	0.35415	.	.	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97598	-4.44;-4.45	3.83	1.76	0.24704	.	0.720448	0.11874	N	0.521186	D	0.91898	0.7435	L	0.31926	0.97	0.09310	N	1	B;B	0.22983	0.047;0.078	B;B	0.14023	0.007;0.01	T	0.82973	-0.0191	10	0.23302	T	0.38	-12.5042	4.2592	0.10733	0.1211:0.0:0.6553:0.2235	.	349;333	Q7RTX7;Q7RTX7-2	CTSR4_HUMAN;.	T	349	ENSP00000341006:A349T;ENSP00000390423:A349T	ENSP00000341006:A349T	A	+	1	0	CATSPER4	26399965	0.763000	0.28462	0.120000	0.21714	0.112000	0.19704	1.696000	0.37773	0.962000	0.38057	-0.657000	0.03884	GCC		0.597	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		A	26527378	G	A	26527378	3	1	63	1	0	0	0	0	1	0	0	0	2696	1087	38	1	1075	1	CATSPER4	1	26527378	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	955662	26527378	222723243	2	20349										
CYP2J2	1573	hgsc.bcm.edu	37	chr1	60377922	60377922	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tttcctaaaccaaagttcctTagtgctgtcagagtgaacct	7	10	1	2	rs111798172		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:60377922T>C	ENST00000371204.3	-	3	478	c.435A>G	c.(433-435)ctA>ctG	p.L145L	CYP2J2_ENST00000492633.1_5'UTR	NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	145					arachidonic acid metabolic process (GO:0019369)|epoxygenase P450 pathway (GO:0019373)|icosanoid metabolic process (GO:0006690)|linoleic acid metabolic process (GO:0043651)|regulation of heart contraction (GO:0008016)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	arachidonic acid 11,12-epoxygenase activity (GO:0008405)|arachidonic acid 14,15-epoxygenase activity (GO:0008404)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|linoleic acid epoxygenase activity (GO:0071614)	p.L145L(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|skin(1)	26	all_cancers(7;0.000396)				Apixaban(DB06605)|Astemizole(DB00637)|Cholecalciferol(DB00169)|Levomilnacipran(DB08918)|Masoprocol(DB00179)|Rivaroxaban(DB06228)	CAAAGTTCCTTAGTGCTGTCA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	1											203	168	180					1																	60377922		2203	4300	6503	60150510	SO:0001819	synonymous_variant	1573			BC032594	CCDS613.1	1p31.3-p31.2	2008-02-05	2003-01-14		ENSG00000134716	ENSG00000134716		"Cytochrome P450s"	2634	protein-coding gene	gene with protein product		601258	"cytochrome P450, subfamily IIJ (arachidonic acid epoxygenase) polypeptide 2"			9570962	Standard	NM_000775		Approved		uc001czq.3	P51589	OTTHUMG00000008991	ENST00000371204.3:c.435A>G	1.37:g.60377922T>C			60150510	B2RD33|Q8TF13	Silent	SNP	ENST00000371204.3	37	CCDS613.1																																																																																				0.448	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775		C	60377922	T	C	60377922	2	2	63	1	0	0	0	0	0	0	0	1	4178	1741	61	4		4	CYP2J2	1	60377922	Silent	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	33850544	60377922	188872699	3	20350										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82408914	82408914	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ggtgtatgatggtgctgtctTctttaacaaagaaagaacga	11	5	2	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:82408914T>C	ENST00000370728.1	+	8	1304	c.659T>C	c.(658-660)tTc>tCc	p.F220S	LPHN2_ENST00000335786.5_Missense_Mutation_p.F220S|LPHN2_ENST00000370725.1_Missense_Mutation_p.F220S|LPHN2_ENST00000370717.2_Missense_Mutation_p.F220S|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370727.1_Missense_Mutation_p.F220S|LPHN2_ENST00000370730.1_Missense_Mutation_p.F220S|LPHN2_ENST00000370721.1_Missense_Mutation_p.F224S|LPHN2_ENST00000370715.1_Missense_Mutation_p.F220S|LPHN2_ENST00000271029.4_Missense_Mutation_p.F220S|LPHN2_ENST00000370723.1_Missense_Mutation_p.F220S|LPHN2_ENST00000359929.3_Missense_Mutation_p.F220S|LPHN2_ENST00000370713.1_Missense_Mutation_p.F220S|LPHN2_ENST00000394879.1_Missense_Mutation_p.F220S|LPHN2_ENST00000319517.6_Missense_Mutation_p.F220S			O95490	LPHN2_HUMAN	latrophilin 2	220	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.F220S(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GGTGCTGTCTTCTTTAACAAA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	125	126					1																	82408914		2203	4300	6503	82181502	SO:0001583	missense	23266			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.659T>C	1.37:g.82408914T>C	ENSP00000359763:p.Phe220Ser		82181502	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.66|18.66	3.672066|3.672066	0.67928|0.67928	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000449420	D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.90133|.	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62|.	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	0.053768|.	0.85682|.	D|.	0.000000|.	T|T	0.66548|0.66548	0.2800|0.2800	M|M	0.68593|0.68593	2.085|2.085	0.80722|0.80722	D|D	1|1	B;B;B|.	0.32620|.	0.378;0.204;0.378|.	B;B;B|.	0.36808|.	0.233;0.076;0.233|.	T|T	0.66677|0.66677	-0.5863|-0.5863	10|5	0.59425|.	D|.	0.04|.	.|.	16.3322|16.3322	0.83039|0.83039	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	220;220;220|.	O95490-3;O95490-4;O95490-2|.	.;.;.|.	S|P	224;220;220;220;220;220;220;220;220;220;220;220;220;220|88	ENSP00000359756:F224S;ENSP00000359763:F220S;ENSP00000359765:F220S;ENSP00000359762:F220S;ENSP00000359760:F220S;ENSP00000359758:F220S;ENSP00000353006:F220S;ENSP00000359750:F220S;ENSP00000359748:F220S;ENSP00000322270:F220S;ENSP00000359752:F220S;ENSP00000378344:F220S;ENSP00000271029:F220S;ENSP00000337306:F220S|.	ENSP00000271029:F220S|.	F|S	+|+	2|1	0|0	LPHN2|LPHN2	82181502|82181502	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.040000|8.040000	0.89188|0.89188	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	TTC|TCT		0.373	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		C	82408914	T	C	82408914	3	2	63	1	0	0	0	0	1	0	0	0	8945	1783	62	4	673	4	LPHN2	1	82408914	Missense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	22030992	82408914	166841707	4	20351										
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110740094	110740094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gacggagatgctgggcttccGcccctaccgcttctatttct	10	14	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:110740094G>A	ENST00000331565.4	+	11	2173	c.1688G>A	c.(1687-1689)cGc>cAc	p.R563H		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	563					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)	p.R563H(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTGGGCTTCCGCCCCTACCGC	0.597											OREG0013652	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											92	78	83					1																	110740094		2203	4299	6502	110541617	SO:0001583	missense	388662				CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1688G>A	1.37:g.110740094G>A	ENSP00000330199:p.Arg563His	1429	110541617	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.506460	0.85282	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.76709	-1.04	5.03	0.392	0.16288	.	0.674841	0.14226	N	0.333085	T	0.81950	0.4931	M	0.90483	3.12	0.37863	D	0.929781	D	0.67145	0.996	P	0.60173	0.87	T	0.80919	-0.1167	10	0.72032	D	0.01	.	8.079	0.30733	0.4243:0.0:0.5757:0.0	.	563	Q9H1V8	S6A17_HUMAN	H	563	ENSP00000330199:R563H	ENSP00000330199:R563H	R	+	2	0	SLC6A17	110541617	0.706000	0.27856	0.987000	0.45799	0.994000	0.84299	1.050000	0.30404	0.020000	0.15106	0.557000	0.71058	CGC		0.597	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110740094	G	A	110740094	3	1	63	1	0	0	0	0	1	0	0	0	14717	1087	38	1	1726	1	SLC6A17	1	110740094	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	28331180	110740094	138510527	5	20352										
VTCN1	79679	hgsc.bcm.edu	37	chr1	117695864	117695864	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ctggtattggagacttccgaGaagttggctccctggtcaac	12	10	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr1:117695864G>T	ENST00000369458.3	-	4	651	c.573C>A	c.(571-573)ttC>ttA	p.F191L	VTCN1_ENST00000359008.4_Missense_Mutation_p.F194L|VTCN1_ENST00000463461.1_5'UTR|VTCN1_ENST00000539893.1_Missense_Mutation_p.F96L|VTCN1_ENST00000328189.3_Missense_Mutation_p.F75L	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1									p.F191L(1)		large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	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)		AGACTTCCGAGAAGTTGGCTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	102	104					1																	117695864		2203	4300	6503	117497387	SO:0001583	missense	79679			BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28873	protein-coding gene	gene with protein product	"B7 family member, H4", "B7 superfamily member 1"	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.573C>A	1.37:g.117695864G>T	ENSP00000358470:p.Phe191Leu		117497387		Missense_Mutation	SNP	ENST00000369458.3	37	CCDS894.1	.	.	.	.	.	.	.	.	.	.	G	4.078	0.012318	0.07912	.	.	ENSG00000134258	ENST00000369458;ENST00000359008;ENST00000328189;ENST00000539893	T;T;T;T	0.18174	3.74;3.73;2.23;4.12	5.34	2.48	0.30137	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.090168	0.49305	D	0.000159	T	0.01254	0.0041	N	0.01874	-0.695	0.30785	N	0.741619	B;B	0.23128	0.08;0.055	B;B	0.22386	0.039;0.018	T	0.45600	-0.9250	10	0.08837	T	0.75	-18.4057	4.6641	0.12657	0.2591:0.1737:0.5672:0.0	.	75;191	Q7Z7D3-2;Q7Z7D3	.;VTCN1_HUMAN	L	191;194;75;96	ENSP00000358470:F191L;ENSP00000351899:F194L;ENSP00000328168:F75L;ENSP00000444724:F96L	ENSP00000328168:F75L	F	-	3	2	VTCN1	117497387	0.991000	0.36638	1.000000	0.80357	0.859000	0.49053	0.072000	0.14617	0.948000	0.37687	-0.128000	0.14901	TTC		0.517	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626		T	117695864	G	T	117695864	3	4	63	1	0	0	0	0	1	0	0	0	17274	933	33	2	283	2	VTCN1	1	117695864	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	6955770	117695864	131554757	6	20353										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69053220	69053220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agccctagagatcagcctccGcaacatggagcgctcccggg	12	15	1	1	rs374053151		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr2:69053220G>A	ENST00000295381.3	+	11	2251	c.1832G>A	c.(1831-1833)cGc>cAc	p.R611H	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.R612H|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.R604H|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.R605H|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.R305H|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.R572H	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	611					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R605H(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						ATCAGCCTCCGCAACATGGAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	110	115	114		1835,1814,1715,1811	3.9	1	2		114	0,8600		0,0,4300	no	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	612/647,605/640,572/607,604/639	69053220	1,13005	2203	4300	6503	68906724	SO:0001583	missense	9938			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1832G>A	2.37:g.69053220G>A	ENSP00000295381:p.Arg611His		68906724	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.76|15.76	2.927955|2.927955	0.52759|0.52759	2.27E-4|2.27E-4	0.0|0.0	ENSG00000163219|ENSG00000163219	ENST00000497259|ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000543533;ENST00000479844	.|T;T;T;T;T;T	.|0.53640	.|0.61;0.61;0.61;0.61;0.61;0.61	5.95|5.95	3.94|3.94	0.45596|0.45596	.|.	.|0.420768	.|0.26224	.|N	.|0.025620	T|T	0.43787|0.43787	0.1263|0.1263	L|L	0.46819|0.46819	1.47|1.47	0.80722|0.80722	D|D	1|1	.|D;B;B;B;B	.|0.60160	.|0.987;0.015;0.004;0.004;0.146	.|P;B;B;B;B	.|0.50754	.|0.649;0.007;0.004;0.004;0.053	T|T	0.48479|0.48479	-0.9032|-0.9032	5|10	.|0.72032	.|D	.|0.01	.|.	2.5196|2.5196	0.04676|0.04676	0.3246:0.0:0.4597:0.2157|0.3246:0.0:0.4597:0.2157	.|.	.|572;612;605;604;611	.|E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.|.;.;.;.;RHG25_HUMAN	T|H	471|611;612;572;604;605;596;305	.|ENSP00000295381:R611H;ENSP00000386911:R612H;ENSP00000420583:R572H;ENSP00000386863:R604H;ENSP00000386241:R605H;ENSP00000417467:R305H	.|ENSP00000295381:R611H	A|R	+|+	1|2	0|0	ARHGAP25|ARHGAP25	68906724|68906724	0.024000|0.024000	0.19004|0.19004	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.051000|1.051000	0.30417|0.30417	1.533000|1.533000	0.49186|0.49186	-0.137000|-0.137000	0.14449|0.14449	GCA|CGC		0.483	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		A	69053220	G	A	69053220	3	1	63	1	0	0	0	0	1	0	0	0	874	1087	38	1	1917	1	ARHGAP25	2	69053220	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		69053220	174146153	7	20354										
STAT4	6775	hgsc.bcm.edu	37	chr2	191929644	191929644	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gcatggtgttcattaacaggTctgtctcatggatgatttgg	12	6	3	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr2:191929644T>G	ENST00000392320.2	-	8	985	c.671A>C	c.(670-672)gAc>gCc	p.D224A	STAT4_ENST00000358470.4_Missense_Mutation_p.D224A	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	224					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.D224A(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CATTAACAGGTCTGTCTCATG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											150	159	156					2																	191929644		2203	4300	6503	191637889	SO:0001583	missense	6775				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.671A>C	2.37:g.191929644T>G	ENSP00000376134:p.Asp224Ala		191637889	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	37	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248461	0.39797	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	T;T	0.60171	0.21;0.21	5.2	5.2	0.72013	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.154695	0.56097	D	0.000035	T	0.57784	0.2077	M	0.68952	2.095	0.80722	D	1	P;P;P	0.47484	0.896;0.822;0.822	B;B;B	0.40825	0.341;0.341;0.341	T	0.66276	-0.5964	10	0.72032	D	0.01	-14.9661	15.2326	0.73404	0.0:0.0:0.0:1.0	.	133;224;224	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	A	224	ENSP00000351255:D224A;ENSP00000376134:D224A	ENSP00000351255:D224A	D	-	2	0	STAT4	191637889	1.000000	0.71417	0.655000	0.29622	0.111000	0.19643	7.518000	0.81795	2.176000	0.68965	0.523000	0.50628	GAC		0.468	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		G	191929644	T	G	191929644	3	3	63	1	0	0	0	0	1	0	0	0	15306	1667	58	4	1643	4	STAT4	2	191929644	Missense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	122876424	191929644	51269729	8	20355										
PGAP1	80055	hgsc.bcm.edu	37	chr2	197735683	197735683	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	acctgtccaagtatttgtgaAaaggaagtcttaactgtcac	8	8	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr2:197735683A>G	ENST00000354764.4	-	19	1863	c.1749T>C	c.(1747-1749)ttT>ttC	p.F583F	PGAP1_ENST00000409475.1_Silent_p.F583F	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	583					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.F583F(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						GTATTTGTGAAAAGGAAGTCT	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	2											76	81	80					2																	197735683		2203	4300	6503	197443928	SO:0001819	synonymous_variant	80055				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1749T>C	2.37:g.197735683A>G			197443928	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Silent	SNP	ENST00000354764.4	37	CCDS2318.1																																																																																				0.313	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		G	197735683	A	G	197735683	2	3	63	1	0	0	0	0	0	0	0	1	11808	11	1	4		4	PGAP1	2	197735683	Silent	SNP	A	TCGA-AG-A00C-01A-01W-A005-10	5806039	197735683	45463690	9	20356										
RNF123	63891	hgsc.bcm.edu	37	chr3	49742129	49742129	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtgatcgacccactggagctCcagtcaaccgccatggatga	11	13	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr3:49742129C>A	ENST00000327697.6	+	22	2043	c.1899C>A	c.(1897-1899)ctC>ctA	p.L633L	RNF123_ENST00000432042.1_Silent_p.L487L	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	633					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.L633L(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CACTGGAGCTCCAGTCAACCG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	3											52	43	46					3																	49742129		2201	4300	6501	49717133	SO:0001819	synonymous_variant	63891			AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1899C>A	3.37:g.49742129C>A			49717133	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																				0.612	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49742129	C	A	49742129	2	1	63	1	0	0	0	0	0	0	0	1	13470	842	30	2		2	RNF123	3	49742129	Silent	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		49742129	148280301	10	20357										
IFT122	55764	hgsc.bcm.edu	37	chr3	129221592	129221592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	caaactggacaaggctgagcGcgagcccctgctgctgtgcg	14	13	0	1	rs372519478		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr3:129221592G>A	ENST00000348417.2	+	20	2491	c.2414G>A	c.(2413-2415)cGc>cAc	p.R805H	IFT122_ENST00000347300.2_Missense_Mutation_p.R746H|IFT122_ENST00000431818.2_Missense_Mutation_p.R655H|IFT122_ENST00000296266.3_Missense_Mutation_p.R856H|IFT122_ENST00000349441.2_Missense_Mutation_p.R694H|IFT122_ENST00000507564.1_Missense_Mutation_p.R797H|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000440957.2_Missense_Mutation_p.R596H|IFT122_ENST00000504021.1_Missense_Mutation_p.R681H	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	805					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.R856H(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						AAGGCTGAGCGCGAGCCCCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	111	103	106		2237,2567,2414,2081	6.2	1	3		106	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	IFT122	NM_018262.2,NM_052985.2,NM_052989.1,NM_052990.1	29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	746/1183,856/1293,805/1242,694/1132	129221592	1,13005	2203	4300	6503	130704282	SO:0001583	missense	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2414G>A	3.37:g.129221592G>A	ENSP00000324005:p.Arg805His		130704282	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516768	0.85495	0.0	1.16E-4	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522;ENST00000507221	T;T;T;T;T;T;T;T;T	0.62364	0.69;0.03;0.17;0.21;0.83;0.81;0.68;0.23;0.85	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	L	0.60845	1.875	0.80722	D	1	D;P;D;P;B;P;P;P;D;D	0.89917	1.0;0.579;0.999;0.724;0.347;0.563;0.563;0.478;1.0;1.0	D;B;D;B;B;B;B;B;D;D	0.83275	0.996;0.166;0.988;0.15;0.037;0.066;0.055;0.052;0.991;0.996	T	0.69150	-0.5221	10	0.24483	T	0.36	-25.3104	20.8794	0.99867	0.0:0.0:1.0:0.0	.	596;131;797;192;681;645;694;746;805;856	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	H	746;856;797;746;655;681;694;805;645;596;302;167	ENSP00000323973:R746H;ENSP00000296266:R856H;ENSP00000425536:R797H;ENSP00000410946:R655H;ENSP00000422179:R681H;ENSP00000324165:R694H;ENSP00000324005:R805H;ENSP00000401569:R596H;ENSP00000424727:R302H	ENSP00000296266:R856H	R	+	2	0	IFT122	130704282	1.000000	0.71417	0.999000	0.59377	0.792000	0.44763	9.587000	0.98229	2.941000	0.99782	0.655000	0.94253	CGC		0.607	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		A	129221592	G	A	129221592	3	1	63	1	0	0	0	0	1	0	0	0	7576	1087	38	1	2649	1	IFT122	3	129221592	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	79479463	129221592	68800838	11	20358										
MSL2	55167	hgsc.bcm.edu	37	chr3	135913926	135913926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	actaggcggctcgcggaaatGtagagagcagtagcattcac	13	9	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr3:135913926G>A	ENST00000309993.2	-	1	762	c.30C>T	c.(28-30)taC>taT	p.Y10Y	MSL2_ENST00000434835.2_5'Flank	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	10	Sufficient for interaction with MSL1.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.Y10Y(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						TCGCGGAAATGTAGAGAGCAG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											176	188	184					3																	135913926		2203	4300	6503	137396616	SO:0001819	synonymous_variant	55167			AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"RING-type (C3HC4) zinc fingers"	25544	protein-coding gene	gene with protein product	"male-specific lethal-2 homolog (Drosophila)"	614802	"ring finger protein 184", "male-specific lethal 2-like 1 (Drosophila)"	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.30C>T	3.37:g.135913926G>A			137396616	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Silent	SNP	ENST00000309993.2	37	CCDS33861.1																																																																																				0.527	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		A	135913926	G	A	135913926	2	1	63	1	0	0	0	0	0	0	0	1	9908	1372	48	3		3	MSL2	3	135913926	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	6692334	135913926	62108504	12	20359										
MFN1	55669	hgsc.bcm.edu	37	chr3	179096132	179096132	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tttaccattgttaacaggaaTtaaataagcacatagaggat	7	5	0	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr3:179096132T>C	ENST00000471841.1	+	13	1459	c.1333T>C	c.(1333-1335)Tta>Cta	p.L445L	MFN1_ENST00000280653.7_Intron|MFN1_ENST00000263969.5_Silent_p.L445L	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	445					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L445L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TTAACAGGAATTAAATAAGCA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	3											88	91	90					3																	179096132		2203	4300	6503	180578826	SO:0001819	synonymous_variant	55669			AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1333T>C	3.37:g.179096132T>C			180578826	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Silent	SNP	ENST00000471841.1	37	CCDS3228.1																																																																																				0.333	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		C	179096132	T	C	179096132	2	2	63	1	0	0	0	0	0	0	0	1	9553	1490	52	4		4	MFN1	3	179096132	Silent	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	43182206	179096132	18926298	13	20360										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46053442	46053442	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	atttttctttttaacataccGaggctttattttttagcttt	4	6	1	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr4:46053442G>T	ENST00000295452.4	-	8	1297	c.1130C>A	c.(1129-1131)tCg>tAg	p.S377*		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	377					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S377*(2)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTAACATACCGAGGCTTTATT	0.318																																																2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	4											43	41	41					4																	46053442		2201	4297	6498	45748199	SO:0001630	splice_region_variant	2565			BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1131+1C>A	4.37:g.46053442G>T			45748199	Q5H9T8	Nonsense_Mutation	SNP	ENST00000295452.4	37	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552629	0.86127	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	.	.	.	5.63	3.83	0.44106	.	0.782790	0.11568	N	0.551119	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	12.6897	0.56968	0.0:0.1312:0.7472:0.1217	.	.	.	.	X	377	.	ENSP00000295452:S377X	S	-	2	0	GABRG1	45748199	0.997000	0.39634	0.999000	0.59377	0.389000	0.30415	2.376000	0.44292	2.659000	0.90383	0.650000	0.86243	TCG		0.318	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	Nonsense_Mutation	T	46053442	G	T	46053442	5	4	63	1	0	0	0	0	0	0	1	0	6190	1072	37	2	275	2	GABRG1	4	46053442	Splice_Site	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		46053442	145100834	14	20361										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113539677	113539677	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ttaagactttcattatccatTttactttcagaaatcatgtc	3	8	3	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr4:113539677T>G	ENST00000505019.1	-	6	1646	c.1521A>C	c.(1519-1521)aaA>aaC	p.K507N	C4orf21_ENST00000445203.2_Missense_Mutation_p.K476N|C4orf21_ENST00000309071.5_Missense_Mutation_p.K507N	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		507						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.K507N(2)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CATTATCCATTTTACTTTCAG	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	4											81	83	82					4																	113539677		2202	4300	6502	113759126	SO:0001583	missense	55345																														ENST00000505019.1:c.1521A>C	4.37:g.113539677T>G	ENSP00000424737:p.Lys507Asn		113759126	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		.	.	.	.	.	.	.	.	.	.	T	8.686	0.906209	0.17760	.	.	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	D;T;T	0.81821	-1.54;1.95;1.54	5.42	-10.6	0.00265	.	1.668670	0.02986	N	0.146337	T	0.46718	0.1407	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47045	-0.9147	10	0.08179	T	0.78	0.9682	7.7091	0.28667	0.2782:0.0:0.3705:0.3513	.	507;507	Q86YA3;G5EA02	CD021_HUMAN;.	N	507;507;476	ENSP00000424737:K507N;ENSP00000309095:K507N;ENSP00000390505:K476N	ENSP00000309095:K507N	K	-	3	2	C4orf21	113759126	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-1.568000	0.02144	-1.527000	0.01758	-0.646000	0.03943	AAA		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			G	113539677	T	G	113539677	3	3	63	1	0	0	0	0	1	0	0	0	2260	1838	64	4	4885	4	C4orf21	4	113539677	Missense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	67486235	113539677	77614599	15	20362										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155180709	155180709	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tctgttacctgtatgacatgAgcattgtagagttggctttc	10	7	1	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr4:155180709A>T	ENST00000357232.4	-	20	5411	c.5412T>A	c.(5410-5412)gcT>gcA	p.A1804A		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1804	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A1804A(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTATGACATGAGCATTGTAGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	4											178	163	168					4																	155180709		2203	4300	6503	155400159	SO:0001819	synonymous_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5412T>A	4.37:g.155180709A>T			155400159	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.403	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155180709	A	T	155180709	2	4	63	1	0	0	0	0	0	0	0	1	4294	291	11	5		5	DCHS2	4	155180709	Silent	SNP	A	TCGA-AG-A00C-01A-01W-A005-10	41641032	155180709	35973567	16	20363										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170628172	170628172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	catttatgaagcacacatccGattaaatggataccctttct	5	10	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr4:170628172G>A	ENST00000513761.1	+	11	2463	c.1904G>A	c.(1903-1905)cGa>cAa	p.R635Q	CLCN3_ENST00000347613.4_Missense_Mutation_p.R635Q|CLCN3_ENST00000504131.2_Missense_Mutation_p.R618Q|CLCN3_ENST00000360642.3_Missense_Mutation_p.R608Q	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	635					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.R635Q(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GCACACATCCGATTAAATGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											176	156	163					4																	170628172		2203	4300	6503	170864747	SO:0001583	missense	1182			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1904G>A	4.37:g.170628172G>A	ENSP00000424603:p.Arg635Gln		170864747	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129739	0.77549	.	.	ENSG00000109572	ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131;ENST00000507875	D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12	5.48	5.48	0.80851	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.89829	0.6828	L	0.47716	1.5	0.80722	D	1	B;B;B;B;B	0.24258	0.027;0.027;0.1;0.027;0.046	B;B;B;B;B	0.19148	0.006;0.006;0.016;0.006;0.024	D	0.86065	0.1534	10	0.42905	T	0.14	-4.2017	19.3596	0.94431	0.0:0.0:1.0:0.0	.	608;618;608;635;635	B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.;.;.;CLCN3_HUMAN;.	Q	635;635;608;618;608	ENSP00000424603:R635Q;ENSP00000261514:R635Q;ENSP00000353857:R608Q;ENSP00000424540:R618Q;ENSP00000425323:R608Q	ENSP00000261514:R635Q	R	+	2	0	CLCN3	170864747	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.877000	0.87225	2.568000	0.86640	0.655000	0.94253	CGA		0.463	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			A	170628172	G	A	170628172	3	1	63	1	0	0	0	0	1	0	0	0	3470	1058	37	1	1942	1	CLCN3	4	170628172	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	15447463	170628172	20526104	17	20364										
TMEM167A	153339	hgsc.bcm.edu	37	chr5	82357695	82357695	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agggagattatagacacttaCcaattctggcacacttccaa	7	10	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr5:82357695C>A	ENST00000502346.1	-	3	321		c.e3+1		SCARNA18_ENST00000459004.1_RNA|TMEM167A_ENST00000511450.1_Splice_Site	NM_174909.4	NP_777569.1	Q8TBQ9	KISHA_HUMAN	transmembrane protein 167A							Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.?(1)		large_intestine(1)|lung(1)	2						TAGACACTTACCAATTCTGGC	0.318																																																1	Unknown(1)	large_intestine(1)	5											63	61	62					5																	82357695		2203	4300	6503	82393451	SO:0001630	splice_region_variant	153339			BC107575, AK055070	CCDS34198.1	5q14.2	2008-06-06	2008-06-06	2008-06-06	ENSG00000174695	ENSG00000174695			28330	protein-coding gene	gene with protein product			"transmembrane protein 167"	TMEM167		1316117	Standard	NM_174909		Approved	FLJ30508, MGC23909	uc003khx.4	Q8TBQ9	OTTHUMG00000162570	ENST00000502346.1:c.148+1G>T	5.37:g.82357695C>A			82393451	Q0P692	Splice_Site	SNP	ENST00000502346.1	37	CCDS34198.1	.	.	.	.	.	.	.	.	.	.	c	22.9	4.345899	0.82022	.	.	ENSG00000174695	ENST00000502346	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2045	0.98273	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM167A	82393451	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.473000	0.73572	2.876000	0.98609	0.645000	0.84053	.		0.318	TMEM167A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369631.2	NM_174909	Intron	A	82357695	C	A	82357695	5	1	63	1	0	0	0	0	0	0	1	0	16120	521	18	2	77	2	TMEM167A	5	82357695	Splice_Site	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		82357695	98557565	18	20365										
APC	324	hgsc.bcm.edu	37	chr5	112174916	112174916	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ctggacaaagcagtaaaaccGaacatatgtcttcaagcagt	8	9	2	0	rs201185479		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr5:112174916G>T	ENST00000457016.1	+	16	4005	c.3625G>T	c.(3625-3627)Gaa>Taa	p.E1209*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1209*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1209*			P25054	APC_HUMAN	adenomatous polyposis coli	1209	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1209*(3)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGTAAAACCGAACATATGTC	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Substitution - Nonsense(3)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD011096	APC	D							83	83	83					5																	112174916		2202	4300	6502	112202815	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3625G>T	5.37:g.112174916G>T	ENSP00000413133:p.Glu1209*		112202815	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782541	0.90282	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.91	5.91	0.95273	.	0.056678	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.108	15.437	0.75155	0.0681:0.0:0.9319:0.0	.	.	.	.	X	1209	.	.	E	+	1	0	APC	112202815	1.000000	0.71417	0.997000	0.53966	0.068000	0.16541	6.778000	0.75043	2.802000	0.96397	0.655000	0.94253	GAA		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174916	G	T	112174916	4	4	63	1	0	0	0	0	0	1	0	0	763	1059	37	2	3683	2	APC	5	112174916	Nonsense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	29817221	112174916	68740344	19	20366										
APC	324	hgsc.bcm.edu	37	chr5	112175480	112175480	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tcagttcacttgatagttttGagagtcgttcgattgccagc	10	8	2	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr5:112175480G>T	ENST00000457016.1	+	16	4569	c.4189G>T	c.(4189-4191)Gag>Tag	p.E1397*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1397*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1397*			P25054	APC_HUMAN	adenomatous polyposis coli	1397	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1399fs*9(18)|p.E1397*(8)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.E1397fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATAGTTTTGAGAGTCGTTC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Deletion - Frameshift(20)|Substitution - Nonsense(8)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(28)|soft_tissue(1)|skin(1)	5	GRCh37	CM992136	APC	M							104	98	100					5																	112175480		2202	4300	6502	112203379	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4189G>T	5.37:g.112175480G>T	ENSP00000413133:p.Glu1397*		112203379	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	41	8.742411	0.98937	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.111909	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.9405	20.4898	0.99202	0.0:0.0:1.0:0.0	.	.	.	.	X	1397	.	.	E	+	1	0	APC	112203379	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.281000	0.78621	2.941000	0.99782	0.655000	0.94253	GAG		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175480	G	T	112175480	4	4	63	1	0	0	0	0	0	1	0	0	763	1291	45	2	4247	2	APC	5	112175480	Nonsense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	564	112175480	68739780	20	20367										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140261917	140261917	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tgctctggcttctgatcctcGcagcctgggagacgggtagt	14	11	2	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr5:140261917G>T	ENST00000289272.2	+	1	64	c.64G>T	c.(64-66)Gca>Tca	p.A22S	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.A22S|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	22					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A22S(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGATCCTCGCAGCCTGGGA	0.592																																					Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - Missense(1)	large_intestine(1)	5											119	124	122					5																	140261917		2203	4300	6503	140242101	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.64G>T	5.37:g.140261917G>T	ENSP00000289272:p.Ala22Ser		140242101	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	1.697	-0.502443	0.04261	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.50277	0.75;0.81	5.4	-1.6	0.08426	.	.	.	.	.	T	0.33206	0.0855	L	0.43923	1.385	0.09310	N	1	B;B;B	0.20988	0.003;0.012;0.05	B;B;B	0.18871	0.005;0.01;0.023	T	0.23583	-1.0184	9	0.34782	T	0.22	.	4.8164	0.13369	0.5479:0.0:0.1816:0.2704	.	22;22;22	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	S	22	ENSP00000386821:A22S;ENSP00000289272:A22S	ENSP00000289272:A22S	A	+	1	0	PCDHA13	140242101	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-1.906000	0.01590	-0.202000	0.10268	-0.219000	0.12488	GCA		0.592	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140261917	G	T	140261917	3	4	63	1	0	0	0	0	1	0	0	0	11554	1087	38	2	66	2	PCDHA13	5	140261917	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	28086437	140261917	40653343	21	20368										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176016083	176016083	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tcatcctgttctccatcctcCgagtagacttcatctctaag	5	14	4	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr5:176016083C>T	ENST00000510636.1	+	22	3182	c.2908C>T	c.(2908-2910)Cga>Tga	p.R970*	CDHR2_ENST00000261944.5_Nonsense_Mutation_p.R970*|CDHR2_ENST00000506348.1_Nonsense_Mutation_p.R970*	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	970	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R970*(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTCCATCCTCCGAGTAGACTT	0.577																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											240	228	233					5																	176016083		2203	4300	6503	175948689	SO:0001587	stop_gained	54825			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2908C>T	5.37:g.176016083C>T	ENSP00000424565:p.Arg970*		175948689	A1L3U4|A6NC80|Q9NXP8	Nonsense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	c	37	6.625925	0.97714	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	.	.	.	4.76	1.49	0.22878	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	0.4428	7.4755	0.27374	0.6197:0.2918:0.0:0.0885	.	.	.	.	X	970	.	ENSP00000261944:R970X	R	+	1	2	CDHR2	175948689	0.000000	0.05858	0.033000	0.17914	0.661000	0.39034	0.160000	0.16462	0.442000	0.26555	0.543000	0.68304	CGA		0.577	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	176016083	C	T	176016083	4	4	63	1	0	0	0	0	0	1	0	0	3125	644	23	1	2990	1	CDHR2	5	176016083	Nonsense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	35754166	176016083	4899177	22	20369										
LHFPL5	222662	hgsc.bcm.edu	37	chr6	35773558	35773558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	accctcaccatctgcttctcCgtactggtcatggccctctt	6	17	5	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr6:35773558C>T	ENST00000373853.1	+	1	489	c.111C>T	c.(109-111)tcC>tcT	p.S37S	LHFPL5_ENST00000360215.1_Silent_p.S37S			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	37					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)		p.S37S(1)		endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						TCTGCTTCTCCGTACTGGTCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	6											232	200	211					6																	35773558		2203	4300	6503	35881536	SO:0001819	synonymous_variant	222662			BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"deafness, autosomal recessive 67"	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.111C>T	6.37:g.35773558C>T			35881536	B3KX66	Silent	SNP	ENST00000373853.1	37	CCDS4812.1																																																																																				0.602	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548		T	35773558	C	T	35773558	2	4	63	1	0	0	0	0	0	0	0	1	8791	639	23	1		1	LHFPL5	6	35773558	Silent	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		35773558	135341509	23	20370										
TREML1	340205	hgsc.bcm.edu	37	chr6	41118572	41118572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	cctaccttgtttcctcttggCcatcacagcaaacagcacca	5	16	2	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr6:41118572C>A	ENST00000426005.2	-	4	596	c.553G>T	c.(553-555)Gcc>Tcc	p.A185S	TREML1_ENST00000373127.4_Missense_Mutation_p.A185S|TREML1_ENST00000437044.2_Missense_Mutation_p.A74S	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	185					calcium-mediated signaling (GO:0019722)|innate immune response (GO:0045087)|platelet activation (GO:0030168)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)		p.A185S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TTCCTCTTGGCCATCACAGCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											130	109	116					6																	41118572		2203	4300	6503	41226550	SO:0001583	missense	340205			AF534822	CCDS4851.1, CCDS64420.1, CCDS64421.1	6p21.1	2013-01-11			ENSG00000161911	ENSG00000161911		"Immunoglobulin superfamily / V-set domain containing"	20434	protein-coding gene	gene with protein product	"TREM-like transcript 1"	609714				12393607, 12645956	Standard	NM_178174		Approved	TLT1, dJ238O23.3	uc011duc.3	Q86YW5	OTTHUMG00000016231	ENST00000426005.2:c.553G>T	6.37:g.41118572C>A	ENSP00000402855:p.Ala185Ser		41226550	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	37	CCDS4851.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.157949	0.57368	.	.	ENSG00000161911	ENST00000373127;ENST00000437044;ENST00000426005	T;T;T	0.56776	1.43;0.44;1.43	5.38	2.39	0.29439	.	0.233852	0.30410	N	0.009697	T	0.34308	0.0893	L	0.49350	1.555	0.32039	N	0.598471	P;D;P	0.62365	0.738;0.991;0.496	B;P;B	0.53689	0.283;0.732;0.184	T	0.12293	-1.0553	10	0.23891	T	0.37	.	4.6754	0.12710	0.1731:0.6404:0.0:0.1865	.	74;185;185	Q86YW5-3;Q86YW5;Q86YW5-2	.;TRML1_HUMAN;.	S	185;74;185	ENSP00000362219:A185S;ENSP00000400405:A74S;ENSP00000402855:A185S	ENSP00000362219:A185S	A	-	1	0	TREML1	41226550	0.654000	0.27367	1.000000	0.80357	0.822000	0.46500	0.184000	0.16939	1.270000	0.44297	0.655000	0.94253	GCC		0.557	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174		A	41118572	C	A	41118572	3	1	63	1	0	0	0	0	1	0	0	0	16512	739	26	2	392	2	TREML1	6	41118572	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	5345014	41118572	129996495	24	20371										
ICK	22858	hgsc.bcm.edu	37	chr6	52905984	52905984	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	atgcttcttcccagcaggacGgaaccgtaggttccatcccc	9	15	1	0	rs373305658		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr6:52905984G>A	ENST00000350082.5	-	2	397	c.51C>T	c.(49-51)tcC>tcT	p.S17S	ICK_ENST00000356971.3_Silent_p.S17S	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	17	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S17S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					CCAGCAGGACGGAACCGTAGG	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	0,4406		0,0,2203	157	147	150		51,51	1	1	6		150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ICK	NM_014920.3,NM_016513.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	17/633,17/633	52905984	1,13005	2203	4300	6503	53013943	SO:0001819	synonymous_variant	22858			AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.51C>T	6.37:g.52905984G>A			53013943	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Silent	SNP	ENST00000350082.5	37	CCDS4949.1																																																																																				0.493	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513		A	52905984	G	A	52905984	2	1	63	1	0	0	0	0	0	0	0	1	7505	1103	39	1		1	ICK	6	52905984	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	11787412	52905984	118209083	25	20372										
CBX3	11335	hgsc.bcm.edu	37	chr7	26246116	26246116	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtggaatatttcctgaagtgGaagggatttacagagtaaga	13	3	0	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr7:26246116G>C	ENST00000337620.4	+	3	581	c.153G>C	c.(151-153)tgG>tgC	p.W51C	CBX3_ENST00000497498.1_3'UTR|CBX3_ENST00000409747.1_Missense_Mutation_p.W51C|CBX3_ENST00000396386.2_Missense_Mutation_p.W51C	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	51	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)	p.W51C(1)		endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						TCCTGAAGTGGAAGGGATTTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											138	143	141					7																	26246116		2203	4300	6503	26212641	SO:0001583	missense	11335			U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.153G>C	7.37:g.26246116G>C	ENSP00000336687:p.Trp51Cys		26212641	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Missense_Mutation	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.432242	0.83776	.	.	ENSG00000122565	ENST00000337620;ENST00000396386;ENST00000456948;ENST00000409747	D;D;D;D	0.94232	-3.38;-3.38;-2.23;-2.23	5.75	5.75	0.90469	Chromo domain (1);Chromo domain subgroup (1);Chromo domain-like (1);Chromo domain/shadow (2);Chromo domain, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98871	0.9618	H	0.99987	5.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98621	1.0667	10	0.87932	D	0	.	20.312	0.98644	0.0:0.0:1.0:0.0	.	51;51	B8ZZ43;Q13185	.;CBX3_HUMAN	C	51	ENSP00000336687:W51C;ENSP00000379670:W51C;ENSP00000408672:W51C;ENSP00000387348:W51C	ENSP00000336687:W51C	W	+	3	0	CBX3	26212641	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.843000	0.99491	2.880000	0.98712	0.655000	0.94253	TGG		0.368	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276		C	26246116	G	C	26246116	3	2	63	1	0	0	0	0	1	0	0	0	2725	1183	41	5	159	5	CBX3	7	26246116	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		26246116	132892547	26	20373										
SPDYE1	285955	hgsc.bcm.edu	37	chr7	44042292	44042292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gaggaggagccacggaaggtGctcgcccctgagcctgagga	17	11	0	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr7:44042292G>A	ENST00000258704.3	+	2	500	c.363G>A	c.(361-363)gtG>gtA	p.V121V	POLR2J4_ENST00000427076.1_RNA|RP5-1165K10.2_ENST00000454572.1_RNA|AC004951.6_ENST00000447643.1_lincRNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	121								p.V121V(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						CACGGAAGGTGCTCGCCCCTG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	7											47	39	42					7																	44042292		1380	2329	3709	44008817	SO:0001819	synonymous_variant	285955			AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"Speedy homologs"	16408	protein-coding gene	gene with protein product	"Speedy E"		"Williams Beuren syndrome chromosome region 19", "speedy homolog E1 (Xenopus laevis)"	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.363G>A	7.37:g.44042292G>A			44008817	Q9NTH5	Silent	SNP	ENST00000258704.3	37	CCDS5475.1																																																																																				0.612	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064		A	44042292	G	A	44042292	2	1	63	1	0	0	0	0	0	0	0	1	15068	1306	46	3		3	SPDYE1	7	44042292	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	17796176	44042292	115096371	27	20374										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98445721	98445721	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gacttatagaggggcgggagCagcccgtggttctcacgaac	15	10	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr7:98445721C>A	ENST00000416379.2	-	8	1270	c.1266G>T	c.(1264-1266)ctG>ctT	p.L422L	TMEM130_ENST00000546258.1_Silent_p.L391L|TMEM130_ENST00000450876.1_Silent_p.L326L|TMEM130_ENST00000339375.4_Silent_p.L410L|TMEM130_ENST00000345589.4_Silent_p.L308L|TMEM130_ENST00000474857.1_5'Flank			Q8N3G9	TM130_HUMAN	transmembrane protein 130	422						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.L410L(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGGGCGGGAGCAGCCCGTGGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	7											56	55	55					7																	98445721		2203	4300	6503	98283657	SO:0001819	synonymous_variant	222865				CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.1266G>T	7.37:g.98445721C>A			98283657	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Silent	SNP	ENST00000416379.2	37	CCDS47650.1																																																																																				0.557	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		A	98445721	C	A	98445721	2	1	63	1	0	0	0	0	0	0	0	1	16082	697	25	2		2	TMEM130	7	98445721	Silent	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	54403429	98445721	60692942	28	20375										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763829	110763829	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	caatgcatttttcagactccCcaagctggaatcactcatgc	6	13	3	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr7:110763829C>G	ENST00000422987.3	+	2	1832	c.1001C>G	c.(1000-1002)cCc>cGc	p.P334R	IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.P334R|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.P334R|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	334					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P334R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TTCAGACTCCCCAAGCTGGAA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											102	100	101					7																	110763829		2203	4300	6503	110551065	SO:0001583	missense	54674			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1001C>G	7.37:g.110763829C>G	ENSP00000412417:p.Pro334Arg		110551065	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.320246	0.60634	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.58940	0.3;0.3;0.3	5.81	5.81	0.92471	.	0.000000	0.64402	D	0.000010	T	0.69459	0.3113	L	0.39085	1.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65183	-0.6230	10	0.35671	T	0.21	.	20.0656	0.97703	0.0:1.0:0.0:0.0	.	334	Q9H3W5	LRRN3_HUMAN	R	334	ENSP00000312001:P334R;ENSP00000397312:P334R;ENSP00000412417:P334R	ENSP00000312001:P334R	P	+	2	0	LRRN3	110551065	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.747000	0.94245	0.650000	0.86243	CCC		0.438	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110763829	C	G	110763829	3	3	63	1	0	0	0	0	1	0	0	0	9065	623	22	5	1003	5	LRRN3	7	110763829	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	12318108	110763829	48374834	29	20376										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136699684	136699684	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tataagacatttgaagtggtGtttattgtcctggtggctgg	13	4	0	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr7:136699684G>T	ENST00000445907.2	+	3	600	c.72G>T	c.(70-72)gtG>gtT	p.V24V	hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000397608.3_Silent_p.V24V|CHRM2_ENST00000320658.5_Silent_p.V24V|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000402486.3_Silent_p.V24V|CHRM2_ENST00000401861.1_Silent_p.V24V|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000453373.1_Silent_p.V24V	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	24					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.V24V(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TTGAAGTGGTGTTTATTGTCC	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	7											121	115	117					7																	136699684		2203	4300	6503	136350224	SO:0001819	synonymous_variant	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.72G>T	7.37:g.136699684G>T			136350224	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	37	CCDS5843.1																																																																																				0.438	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136699684	G	T	136699684	2	4	63	1	0	0	0	0	0	0	0	1	3383	1364	48	2		2	CHRM2	7	136699684	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	25935855	136699684	22438979	30	20377										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35400422	35400422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ctctcatcaagacctttgtgCgctcgcagaccacccaaggt	8	15	2	2	rs150259776		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr9:35400422C>T	ENST00000378495.3	+	36	4441	c.4219C>T	c.(4219-4221)Cgc>Tgc	p.R1407C	UNC13B_ENST00000396787.1_Missense_Mutation_p.R1419C|UNC13B_ENST00000378496.4_Missense_Mutation_p.R1407C	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1407					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.R1407C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GACCTTTGTGCGCTCGCAGAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	CYS/ARG	0,4406		0,0,2203	233	207	216		4219	5.1	1	9	dbSNP_134	216	1,8599	1.2+/-3.3	0,1,4299	no	missense	UNC13B	NM_006377.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1407/1592	35400422	1,13005	2203	4300	6503	35390422	SO:0001583	missense	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4219C>T	9.37:g.35400422C>T	ENSP00000367756:p.Arg1407Cys		35390422	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064873	0.55432	0.0	1.16E-4	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	D;D;D	0.83992	-1.67;-1.58;-1.79	5.08	5.08	0.68730	.	0.348813	0.34088	N	0.004269	T	0.69468	0.3114	N	0.11427	0.14	0.47065	D	0.999304	D;B	0.54964	0.969;0.001	B;B	0.37780	0.258;0.001	T	0.77264	-0.2652	10	0.62326	D	0.03	-9.0844	19.0356	0.92976	0.0:1.0:0.0:0.0	.	1407;1407	F8W8M9;O14795	.;UN13B_HUMAN	C	1419;1407;1407;994	ENSP00000380006:R1419C;ENSP00000367756:R1407C;ENSP00000367757:R1407C	ENSP00000367756:R1407C	R	+	1	0	UNC13B	35390422	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.739000	0.55075	2.814000	0.96858	0.563000	0.77884	CGC		0.522	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35400422	C	T	35400422	3	4	63	1	0	0	0	0	1	0	0	0	17025	768	27	1	4361	1	UNC13B	9	35400422	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		35400422	105813009	31	20378										
RALGPS1	9649	hgsc.bcm.edu	37	chr9	129796780	129796780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	taacgttgtggcctttacccGgaggtttaaccaggtaagca	11	9	0	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr9:129796780G>A	ENST00000259351.5	+	5	554	c.287G>A	c.(286-288)cGg>cAg	p.R96Q	RALGPS1_ENST00000394022.3_Missense_Mutation_p.R96Q|RALGPS1_ENST00000373434.1_Missense_Mutation_p.R96Q|RALGPS1_ENST00000373436.1_Missense_Mutation_p.R96Q|RALGPS1_ENST00000424082.2_Missense_Mutation_p.R96Q	NM_014636.2	NP_055451.1	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	96	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ral GTPase activity (GO:0032852)|regulation of Ral protein signal transduction (GO:0032485)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.R96Q(2)		kidney(2)|large_intestine(6)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						GCCTTTACCCGGAGGTTTAAC	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	9											183	128	147					9																	129796780		2203	4300	6503	128836601	SO:0001583	missense	9649			AB002349	CCDS35143.1, CCDS55344.1, CCDS55345.1, CCDS55346.1	9q33.3	2013-01-10			ENSG00000136828	ENSG00000136828		"Pleckstrin homology (PH) domain containing"	16851	protein-coding gene	gene with protein product		614444				9205841, 10747847	Standard	NM_001190728		Approved	RALGPS1A, RALGEF2, KIAA0351	uc004bqo.2	Q5JS13	OTTHUMG00000020696	ENST00000259351.5:c.287G>A	9.37:g.129796780G>A	ENSP00000259351:p.Arg96Gln		128836601	B4DR86|E9PBQ5|O15059|Q5JT60|Q5JT65|Q5JUG5|Q8N4S6|Q8N5H4|Q8WUV7|Q9NZ16	Missense_Mutation	SNP	ENST00000259351.5	37	CCDS35143.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.681043	0.68042	.	.	ENSG00000136828	ENST00000259351;ENST00000424082;ENST00000394022;ENST00000373439;ENST00000319107;ENST00000373436;ENST00000373434	T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57	4.98	4.98	0.66077	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.066674	0.56097	D	0.000033	T	0.19886	0.0478	L	0.27975	0.815	0.58432	D	0.999999	P;P;P;P	0.43909	0.541;0.679;0.679;0.821	B;B;B;B	0.31442	0.077;0.046;0.046;0.13	T	0.04333	-1.0959	10	0.31617	T	0.26	.	17.4041	0.87468	0.0:0.0:1.0:0.0	.	96;96;96;96	E9PBQ5;Q5JS13-3;Q5JS13-2;Q5JS13	.;.;.;RGPS1_HUMAN	Q	96	ENSP00000259351:R96Q;ENSP00000415630:R96Q;ENSP00000377590:R96Q;ENSP00000317149:R96Q;ENSP00000362535:R96Q;ENSP00000362533:R96Q	ENSP00000259351:R96Q	R	+	2	0	RALGPS1	128836601	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.955000	0.93058	2.470000	0.83445	0.563000	0.77884	CGG		0.527	RALGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054133.1	NM_014636		A	129796780	G	A	129796780	3	1	63	1	0	0	0	0	1	0	0	0	13054	1116	39	1	301	1	RALGPS1	9	129796780	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	94396358	129796780	11416651	32	20379										
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6557001	6557001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tgattcgacatactctttgaCgagcacagcacagtaagggt	10	9	1	2	rs372791078		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr10:6557001C>T	ENST00000263125.5	-	2	196	c.97G>A	c.(97-99)Gtc>Atc	p.V33I	PRKCQ_ENST00000397176.2_Missense_Mutation_p.V33I|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	33	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.V33I(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TACTCTTTGACGAGCACAGCA	0.507																																					Ovarian(50;572 1126 10530 25349 30594)											1	Substitution - Missense(1)	large_intestine(1)	10						C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	96	94	95		97,97	5.2	1	10		95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PRKCQ	NM_001242413.1,NM_006257.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	33/644,33/707	6557001	1,13005	2203	4300	6503	6597007	SO:0001583	missense	5588			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.97G>A	10.37:g.6557001C>T	ENSP00000263125:p.Val33Ile		6597007	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	37	CCDS7079.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273281	0.40194	0.0	1.16E-4	ENSG00000065675	ENST00000263125;ENST00000397176	T;T	0.70164	-0.46;-0.41	5.2	5.2	0.72013	C2 calcium/lipid-binding domain, CaLB (1);	0.054615	0.64402	D	0.000001	T	0.50684	0.1630	L	0.38175	1.15	0.80722	D	1	B;P	0.43938	0.006;0.822	B;B	0.32342	0.033;0.144	T	0.55244	-0.8171	10	0.39692	T	0.17	.	12.4743	0.55803	0.0:0.9234:0.0:0.0765	.	33;33	Q04759-2;Q04759	.;KPCT_HUMAN	I	33	ENSP00000263125:V33I;ENSP00000380361:V33I	ENSP00000263125:V33I	V	-	1	0	PRKCQ	6597007	1.000000	0.71417	0.960000	0.40013	0.768000	0.43524	4.158000	0.58150	2.584000	0.87258	0.563000	0.77884	GTC		0.507	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		T	6557001	C	T	6557001	3	4	63	1	0	0	0	0	1	0	0	0	12549	536	19	1	2091	1	PRKCQ	10	6557001	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		6557001	128977746	33	20380										
GPR158	57512	hgsc.bcm.edu	37	chr10	25861747	25861747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agatttcacttattggccagGggaaaacatccgatcacctc	8	11	2	1	rs371219715		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr10:25861747G>A	ENST00000376351.3	+	7	2043	c.1684G>A	c.(1684-1686)Ggg>Agg	p.G562R		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	562					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G562R(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						TATTGGCCAGGGGAAAACATC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	10						G	ARG/GLY	0,4406		0,0,2203	193	143	160		1684	5.7	1	10		160	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR158	NM_020752.2	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	562/1216	25861747	1,13005	2203	4300	6503	25901753	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1684G>A	10.37:g.25861747G>A	ENSP00000365529:p.Gly562Arg		25901753	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772800	0.90108	0.0	1.16E-4	ENSG00000151025	ENST00000376351	D	0.87571	-2.27	5.67	5.67	0.87782	GPCR, family 3, C-terminal (2);	0.137662	0.48767	D	0.000173	D	0.93061	0.7791	M	0.81239	2.535	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.93144	0.6544	10	0.59425	D	0.04	.	13.0255	0.58812	0.0737:0.0:0.9262:0.0	.	562	Q5T848	GP158_HUMAN	R	562	ENSP00000365529:G562R	ENSP00000365529:G562R	G	+	1	0	GPR158	25901753	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.677000	0.91161	0.557000	0.71058	GGG		0.448	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25861747	G	A	25861747	3	1	63	1	0	0	0	0	1	0	0	0	6683	1232	43	3	1710	3	GPR158	10	25861747	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	19304746	25861747	109673000	34	20381										
PPYR1	5540	hgsc.bcm.edu	37	chr10	47087186	47087186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ccatcctctcgctcgtcctcGtggccctggagaggcatcag	11	16	2	1	rs144429123		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr10:47087186G>A	ENST00000395716.1	+	2	488	c.403G>A	c.(403-405)Gtg>Atg	p.V135M	NPY4R_ENST00000374312.1_Missense_Mutation_p.V135M			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	135					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)	p.V135M(1)									GCTCGTCCTCGTGGCCCTGGA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	10											288	256	267					10																	47087186		2203	4300	6503	46507192	SO:0001583	missense	5540				CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.403G>A	10.37:g.47087186G>A	ENSP00000379066:p.Val135Met		46507192	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978308	0.53720	.	.	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.70986	-0.53;-0.53	4.93	4.01	0.46588	GPCR, rhodopsin-like superfamily (1);	0.136285	0.49916	D	0.000137	T	0.70141	0.3190	N	0.26042	0.785	0.40798	D	0.983314	D	0.76494	0.999	D	0.64687	0.928	T	0.72734	-0.4204	10	0.87932	D	0	.	8.1752	0.31278	0.1832:0.0:0.8168:0.0	.	135	P50391	NPY4R_HUMAN	M	135	ENSP00000363431:V135M;ENSP00000379066:V135M	ENSP00000363431:V135M	V	+	1	0	PPYR1	46507192	1.000000	0.71417	0.981000	0.43875	0.539000	0.34962	6.054000	0.71096	2.464000	0.83262	0.609000	0.83330	GTG		0.572	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			A	47087186	G	A	47087186	3	1	63	1	0	0	0	0	1	0	0	0	12450	1145	40	1	405	1	PPYR1	10	47087186	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	21225439	47087186	88447561	35	20382										
TET1	80312	hgsc.bcm.edu	37	chr10	70432671	70432671	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtcgtacctgtacatgtcaaGgaattgatccagagacttgt	10	8	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr10:70432671G>T	ENST00000373644.4	+	8	4902	c.4693G>T	c.(4693-4695)Gga>Tga	p.G1565*		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1565					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.G1565*(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TACATGTCAAGGAATTGATCC	0.398																																																2	Substitution - Nonsense(2)	large_intestine(2)	10											220	205	210					10																	70432671		2203	4300	6503	70102677	SO:0001587	stop_gained	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4693G>T	10.37:g.70432671G>T	ENSP00000362748:p.Gly1565*		70102677	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Nonsense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	46	12.865106	0.99702	.	.	ENSG00000138336	ENST00000373644;ENST00000545846	.	.	.	5.35	5.35	0.76521	.	0.122186	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.4244	0.94735	0.0:0.0:1.0:0.0	.	.	.	.	X	1565;37	.	ENSP00000362748:G1565X	G	+	1	0	TET1	70102677	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	9.741000	0.98843	2.667000	0.90743	0.585000	0.79938	GGA		0.398	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70432671	G	T	70432671	4	4	63	1	0	0	0	0	0	1	0	0	15808	1001	35	2	4719	2	TET1	10	70432671	Nonsense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	23345485	70432671	65102076	36	20383										
CLPB	81570	hgsc.bcm.edu	37	chr11	72004494	72004494	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gctgtccttgtcgatgatctCcagacgcagcttggggaggc	14	11	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr11:72004494C>G	ENST00000294053.3	-	17	2214	c.2041G>C	c.(2041-2043)Gag>Cag	p.E681Q	CLPB_ENST00000340729.5_Missense_Mutation_p.E622Q|CLPB_ENST00000437826.2_Missense_Mutation_p.E636Q|CLPB_ENST00000538021.1_Missense_Mutation_p.E289Q|CLPB_ENST00000538039.1_Missense_Mutation_p.E651Q|CLPB_ENST00000543042.1_Missense_Mutation_p.E480Q	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	681					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.E681Q(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						TCGATGATCTCCAGACGCAGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											126	99	108					11																	72004494		2200	4293	6493	71682142	SO:0001583	missense	81570			BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"Ankyrin repeat domain containing"	30664	protein-coding gene	gene with protein product	"suppressor of potassium transport defect 3"					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.2041G>C	11.37:g.72004494C>G	ENSP00000294053:p.Glu681Gln		71682142	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	37	CCDS8215.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.498817	0.44455	.	.	ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000535990;ENST00000340729;ENST00000437826;ENST00000543042;ENST00000538021	T;T;T;T;T;T	0.65364	1.92;1.13;2.1;-0.15;2.38;0.44	5.86	5.86	0.93980	.	0.053279	0.64402	D	0.000001	T	0.56321	0.1977	L	0.27053	0.805	0.50171	D	0.999859	P;P;P;P;P;B	0.39352	0.669;0.48;0.533;0.669;0.539;0.075	B;B;B;B;B;B	0.41440	0.357;0.12;0.083;0.122;0.085;0.01	T	0.56661	-0.7942	10	0.45353	T	0.12	-29.1719	18.7645	0.91866	0.0:1.0:0.0:0.0	.	480;622;636;651;681;289	B4DXW4;F8W7P6;E7EWN6;Q9H078-2;Q9H078;Q7Z777	.;.;.;.;CLPB_HUMAN;.	Q	681;651;686;622;636;480;289	ENSP00000294053:E681Q;ENSP00000441518:E651Q;ENSP00000443822:E686Q;ENSP00000340385:E622Q;ENSP00000407296:E636Q;ENSP00000439746:E480Q	ENSP00000294053:E681Q	E	-	1	0	CLPB	71682142	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	5.891000	0.69782	2.781000	0.95711	0.650000	0.86243	GAG		0.587	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813		G	72004494	C	G	72004494	3	3	63	1	0	0	0	0	1	0	0	0	3557	864	30	5	86	5	CLPB	11	72004494	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		72004494	63002022	37	20384										
DPAGT1	1798	hgsc.bcm.edu	37	chr11	118971067	118971067	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ttcctgctaggatattgatgGcattggtacagaacactgcc	10	9	0	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr11:118971067G>C	ENST00000409993.2	-	6	2099	c.548C>G	c.(547-549)gCc>gGc	p.A183G	DPAGT1_ENST00000432443.2_Missense_Mutation_p.A76G|DPAGT1_ENST00000445653.1_5'Flank|DPAGT1_ENST00000354202.4_Missense_Mutation_p.A183G			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	183					cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)	p.A183G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GATATTGATGGCATTGGTACA	0.502											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	11											98	95	96					11																	118971067		2200	4295	6495	118476277	SO:0001583	missense	1798			Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.548C>G	11.37:g.118971067G>C	ENSP00000386597:p.Ala183Gly	1492	118476277	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097188	0.94197	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.94966	-3.57;-3.57;-3.57	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.97607	0.9216	M	0.90145	3.09	0.80722	D	1	P;P	0.50272	0.933;0.529	P;P	0.62014	0.897;0.617	D	0.97789	1.0237	10	0.56958	D	0.05	-15.8663	18.6977	0.91607	0.0:0.0:1.0:0.0	.	76;183	E7EW40;Q9H3H5	.;GPT_HUMAN	G	183;183;76	ENSP00000386597:A183G;ENSP00000346142:A183G;ENSP00000404036:A76G	ENSP00000346142:A183G	A	-	2	0	DPAGT1	118476277	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.652000	0.90054	0.655000	0.94253	GCC		0.502	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		C	118971067	G	C	118971067	3	2	63	1	0	0	0	0	1	0	0	0	4721	1203	42	5	702	5	DPAGT1	11	118971067	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	46966573	118971067	16035449	38	20385										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	63	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		25398284	108453611	39	20386										
DBX2	440097	hgsc.bcm.edu	37	chr12	45410113	45410113	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	cttgcttccagcttcttcttCagaacataaatataaggcac	5	11	3	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr12:45410113C>A	ENST00000332700.6	-	4	1147	c.976G>T	c.(976-978)Gaa>Taa	p.E326*		NM_001004329.2	NP_001004329.2	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	326					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.E326*(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	22	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)		GCTTCTTCTTCAGAACATAAA	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											85	84	85					12																	45410113		2203	4300	6503	43696380	SO:0001587	stop_gained	440097				CCDS31781.1	12q12	2011-06-20				ENSG00000185610		"Homeoboxes / ANTP class : NKL subclass"	33186	protein-coding gene	gene with protein product						11239429	Standard	NM_001004329		Approved	FLJ16139	uc001rok.1	Q6ZNG2	OTTHUMG00000169559	ENST00000332700.6:c.976G>T	12.37:g.45410113C>A	ENSP00000331470:p.Glu326*		43696380		Nonsense_Mutation	SNP	ENST00000332700.6	37	CCDS31781.1	.	.	.	.	.	.	.	.	.	.	C	35	5.475224	0.96291	.	.	ENSG00000185610	ENST00000332700	.	.	.	5.95	4.11	0.48088	.	0.563382	0.18208	N	0.148297	.	.	.	.	.	.	0.42614	D	0.993328	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-3.0825	9.4015	0.38435	0.0:0.63:0.2965:0.0735	.	.	.	.	X	326	.	ENSP00000331470:E326X	E	-	1	0	DBX2	43696380	1.000000	0.71417	0.016000	0.15963	0.979000	0.70002	2.504000	0.45416	0.822000	0.34565	0.650000	0.86243	GAA		0.448	DBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404810.1	NM_001004329		A	45410113	C	A	45410113	4	1	63	1	0	0	0	0	0	1	0	0	4266	835	29	2	47	2	DBX2	12	45410113	Nonsense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	20011829	45410113	88441782	40	20387										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56577682	56577682	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ccagtgcagaagaacctgctTatccctcttcatgactggtc	8	13	2	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr12:56577682T>A	ENST00000267064.4	-	7	681	c.595A>T	c.(595-597)Aag>Tag	p.K199*	SMARCC2_ENST00000394023.3_Nonsense_Mutation_p.K199*|SMARCC2_ENST00000550859.1_Intron|SMARCC2_ENST00000347471.4_Nonsense_Mutation_p.K199*|SMARCC2_ENST00000550164.1_Nonsense_Mutation_p.K199*|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	199					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.K199*(2)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			AGAACCTGCTTATCCCTCTTC	0.483																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											84	78	80					12																	56577682		2203	4300	6503	54863949	SO:0001587	stop_gained	6601			U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.595A>T	12.37:g.56577682T>A	ENSP00000267064:p.Lys199*		54863949	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Nonsense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.015128	0.93404	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.4528	13.8694	0.63610	0.0:0.0:0.0:1.0	.	.	.	.	X	199	.	ENSP00000267064:K199X	K	-	1	0	SMARCC2	54863949	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.710000	0.68392	2.172000	0.68678	0.459000	0.35465	AAG		0.483	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			A	56577682	T	A	56577682	4	1	63	1	0	0	0	0	0	1	0	0	14813	1763	61	5	3234	5	SMARCC2	12	56577682	Nonsense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	11167569	56577682	77274213	41	20388										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671151	25671151	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agctcagaaaaaagtggaacGgcagacggaacttaagcgca	12	8	1	2	rs368285293		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr13:25671151G>A	ENST00000281589.3	+	1	852	c.815G>A	c.(814-816)cGg>cAg	p.R272Q		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	272					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)	p.R272Q(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAAGTGGAACGGCAGACGGAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											157	147	150					13																	25671151		2203	4300	6503	24569151	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.815G>A	13.37:g.25671151G>A	ENSP00000281589:p.Arg272Gln		24569151	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676067	0.67928	.	.	ENSG00000151846	ENST00000281589	T	0.06371	3.31	0.875	0.875	0.19130	.	0.000000	0.43416	U	0.000579	T	0.32912	0.0845	H	0.98295	4.195	0.46416	D	0.999035	D	0.89917	1.0	D	0.67548	0.952	T	0.38329	-0.9666	10	0.87932	D	0	.	7.5489	0.27783	0.0:0.0:1.0:0.0	.	272	Q9H361	PABP3_HUMAN	Q	272	ENSP00000281589:R272Q	ENSP00000281589:R272Q	R	+	2	0	PABPC3	24569151	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	6.590000	0.74085	0.759000	0.33084	0.313000	0.20887	CGG		0.398	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25671151	G	A	25671151	3	1	63	1	0	0	0	0	1	0	0	0	11396	1116	39	1	817	1	PABPC3	13	25671151	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		25671151	89498727	42	20389										
POMP	51371	hgsc.bcm.edu	37	chr13	29238656	29238656	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtcctttcagtttttcttgtGtgaaaaatgaacttttgcct	7	7	2	2	rs148838797		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr13:29238656G>C	ENST00000380842.4	+	3	193	c.112G>C	c.(112-114)Gtg>Ctg	p.V38L	POMP_ENST00000460403.1_3'UTR	NM_015932.5	NP_057016.1	Q9Y244	POMP_HUMAN	proteasome maturation protein	38					proteasome assembly (GO:0043248)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.V38L(1)		endometrium(2)|kidney(1)|large_intestine(1)	4		Lung SC(185;0.0367)		all cancers(112;0.141)|OV - Ovarian serous cystadenocarcinoma(117;0.216)		TTTTTCTTGTGTGAAAAATGA	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	LEU/VAL	0,4390		0,0,2195	29	33	32		112	6	1	13	dbSNP_134	32	1,8581	1.2+/-3.3	0,1,4290	no	missense	POMP	NM_015932.5	32	0,1,6485	CC,CG,GG		0.0117,0.0,0.0077	possibly-damaging	38/142	29238656	1,12971	2195	4291	6486	28136656	SO:0001583	missense	51371			AF077200	CCDS9331.1	13q12.13	2013-11-11	2006-07-04	2006-07-04	ENSG00000132963	ENSG00000132963			20330	protein-coding gene	gene with protein product	"proteassemblin"	613386	"chromosome 13 open reading frame 12"	C13orf12		11042152	Standard	NM_015932		Approved	HSPC014, UMP1	uc001usf.3	Q9Y244	OTTHUMG00000016652	ENST00000380842.4:c.112G>C	13.37:g.29238656G>C	ENSP00000370222:p.Val38Leu		28136656	A5HKJ2|D6MXU3|Q9HB69	Missense_Mutation	SNP	ENST00000380842.4	37	CCDS9331.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934937	0.73442	0.0	1.17E-4	ENSG00000132963	ENST00000380842	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.63965	0.2556	M	0.65975	2.015	0.80722	D	1	B	0.30563	0.285	B	0.33196	0.159	T	0.59989	-0.7350	9	0.33141	T	0.24	-10.9309	17.3175	0.87228	0.0:0.0:1.0:0.0	.	38	Q9Y244	POMP_HUMAN	L	38	.	ENSP00000370222:V38L	V	+	1	0	POMP	28136656	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.052000	0.89448	2.826000	0.97356	0.655000	0.94253	GTG		0.274	POMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044327.1	NM_015932		C	29238656	G	C	29238656	3	2	63	1	0	0	0	0	1	0	0	0	12275	1377	48	5	122	5	POMP	13	29238656	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	3567505	29238656	85931222	43	20390										
BRCA2	675	hgsc.bcm.edu	37	chr13	32929036	32929036	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agagatacagaatccaaattTtaccgcacctggtcaagaat	7	9	1	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr13:32929036T>G	ENST00000380152.3	+	14	7279	c.7046T>G	c.(7045-7047)tTt>tGt	p.F2349C	BRCA2_ENST00000544455.1_Missense_Mutation_p.F2349C			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2349					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.F2349C(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AATCCAAATTTTACCGCACCT	0.328			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - Missense(2)	large_intestine(2)	13											86	91	89					13																	32929036		2203	4300	6503	31827036	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.7046T>G	13.37:g.32929036T>G	ENSP00000369497:p.Phe2349Cys		31827036	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.209106	0.39003	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.80123	-1.34;-1.34	5.66	4.46	0.54185	.	0.699272	0.14460	N	0.318254	T	0.79730	0.4496	M	0.72118	2.19	0.20975	N	0.999813	B	0.18741	0.03	B	0.17098	0.017	T	0.71613	-0.4540	10	0.72032	D	0.01	.	11.7578	0.51886	0.0:0.0:0.1472:0.8528	.	2349	P51587	BRCA2_HUMAN	C	2349	ENSP00000369497:F2349C;ENSP00000439902:F2349C	ENSP00000369497:F2349C	F	+	2	0	BRCA2	31827036	0.577000	0.26708	0.055000	0.19348	0.963000	0.63663	3.557000	0.53741	1.048000	0.40298	0.528000	0.53228	TTT		0.328	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32929036	T	G	32929036	3	3	63	1	0	0	0	0	1	0	0	0	1502	1841	64	4	7096	4	BRCA2	13	32929036	Missense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10	3690380	32929036	82240842	44	20391										
MESDC2	23184	hgsc.bcm.edu	37	chr15	81271755	81271755	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tgaccgaccaaaaagtccttGatctcccaggcgtagctccc	8	15	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr15:81271755G>C	ENST00000261758.4	-	3	596	c.510C>G	c.(508-510)atC>atG	p.I170M	MESDC2_ENST00000560244.1_5'Flank	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	170	Escort domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)		p.I170M(1)		cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						AAAAGTCCTTGATCTCCCAGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	15											77	72	74					15																	81271755		2203	4300	6503	79058810	SO:0001583	missense	23184			D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.510C>G	15.37:g.81271755G>C	ENSP00000261758:p.Ile170Met		79058810	B4DW84|D3DW96|Q969U1	Missense_Mutation	SNP	ENST00000261758.4	37	CCDS32308.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.656572	0.47467	.	.	ENSG00000117899	ENST00000261758	.	.	.	5.9	3.02	0.34903	.	0.165679	0.53938	D	0.000056	T	0.53997	0.1831	L	0.55481	1.735	0.44079	D	0.99683	P	0.35307	0.494	B	0.40009	0.316	T	0.51568	-0.8689	9	0.52906	T	0.07	-8.843	9.6714	0.40015	0.2652:0.0:0.7348:0.0	.	170	Q14696	MESD_HUMAN	M	170	.	ENSP00000261758:I170M	I	-	3	3	MESDC2	79058810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.885000	0.28227	0.418000	0.25898	-0.145000	0.13849	ATC		0.512	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		C	81271755	G	C	81271755	3	2	63	1	0	0	0	0	1	0	0	0	9511	1280	45	5	198	5	MESDC2	15	81271755	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		81271755	21259637	45	20392										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	63	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		7578406	73616804	46	20393										
MPP2	4355	hgsc.bcm.edu	37	chr17	41981824	41981824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	cagagttggtggcggcaaccGgcatggtgaaggaggcaagg	19	7	0	2	rs146765164	byFrequency	TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr17:41981824G>A	ENST00000461854.1	-	2	90	c.5C>T	c.(4-6)cCg>cTg	p.P2L	MPP2_ENST00000523501.1_Intron|MPP2_ENST00000536246.1_5'Flank|MPP2_ENST00000473246.1_5'Flank|MPP2_ENST00000520305.1_5'UTR|MPP2_ENST00000518766.1_Missense_Mutation_p.P47L|MPP2_ENST00000269095.4_Missense_Mutation_p.P2L			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	2					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.P2L(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GGCGGCAACCGGCATGGTGAA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	17											114	97	102					17																	41981824		2203	4300	6503	39337350	SO:0001583	missense	4355				CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 2", "discs large, homolog 2"	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.5C>T	17.37:g.41981824G>A	ENSP00000428286:p.Pro2Leu		39337350	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	37		.	.	.	.	.	.	.	.	.	.	G	16.22	3.062694	0.55432	.	.	ENSG00000108852	ENST00000269095;ENST00000461854;ENST00000518766;ENST00000520406;ENST00000523934;ENST00000520241;ENST00000521178;ENST00000522172;ENST00000518478	T;T;T;T;T;T;T	0.52057	3.09;2.67;3.05;0.72;0.72;0.68;0.71	4.9	4.9	0.64082	.	.	.	.	.	T	0.31979	0.0814	N	0.19112	0.55	0.80722	D	1	B	0.30211	0.273	B	0.14578	0.011	T	0.25082	-1.0142	9	0.87932	D	0	.	13.438	0.61094	0.0:0.0:1.0:0.0	.	47	E7EV80	.	L	2;2;47;2;2;2;2;2;2	ENSP00000269095:P2L;ENSP00000428286:P2L;ENSP00000428182:P47L;ENSP00000428354:P2L;ENSP00000430797:P2L;ENSP00000428938:P2L;ENSP00000430443:P2L	ENSP00000269095:P2L	P	-	2	0	MPP2	39337350	0.999000	0.42202	0.987000	0.45799	0.901000	0.52897	4.597000	0.61062	2.539000	0.85634	0.561000	0.74099	CCG		0.557	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374		A	41981824	G	A	41981824	3	1	63	1	0	0	0	0	1	0	0	0	9764	1116	39	1	1701	1	MPP2	17	41981824	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	34403418	41981824	39213386	47	20394										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51900564	51900564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	cagagaaaactattgggtcaCggtagagtgggtggagaaag	16	4	1	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr17:51900564C>T	ENST00000268919.4	+	1	326	c.170C>T	c.(169-171)aCg>aTg	p.T57M		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	57					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T57M(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TATTGGGTCACGGTAGAGTGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											159	135	143					17																	51900564		2203	4300	6503	49255563	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.170C>T	17.37:g.51900564C>T	ENSP00000268919:p.Thr57Met		49255563	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.092687	0.36952	.	.	ENSG00000141200	ENST00000268919	T	0.77489	-1.1	4.96	2.97	0.34412	.	0.134922	0.33161	N	0.005204	D	0.83147	0.5191	L	0.59436	1.845	0.29612	N	0.846835	D	0.89917	1.0	D	0.76071	0.987	T	0.77640	-0.2512	10	0.66056	D	0.02	.	8.8332	0.35096	0.0:0.8242:0.0:0.1758	.	57	Q8N4N8	KIF2B_HUMAN	M	57	ENSP00000268919:T57M	ENSP00000268919:T57M	T	+	2	0	KIF2B	49255563	0.993000	0.37304	0.906000	0.35671	0.964000	0.63967	2.880000	0.48530	0.781000	0.33589	-0.137000	0.14449	ACG		0.532	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51900564	C	T	51900564	3	4	63	1	0	0	0	0	1	0	0	0	8319	536	19	1	172	1	KIF2B	17	51900564	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	9918740	51900564	29294646	48	20395										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67215769	67215769	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gcaacatttaatgatgcaaaGtatataaaagaagagaaaga	8	3	0	4			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr17:67215769G>T	ENST00000269081.4	-	7	1356	c.447C>A	c.(445-447)taC>taA	p.Y149*	ABCA10_ENST00000416101.2_Nonsense_Mutation_p.Y149*|ABCA10_ENST00000432313.2_Nonsense_Mutation_p.Y149*	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	149					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.Y149*(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					ATGATGCAAAGTATATAAAAG	0.333																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											57	62	61					17																	67215769		2203	4294	6497	64727364	SO:0001587	stop_gained	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.447C>A	17.37:g.67215769G>T	ENSP00000269081:p.Tyr149*		64727364	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Nonsense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	35	5.480397	0.96307	.	.	ENSG00000154263	ENST00000269081;ENST00000416101;ENST00000432313	.	.	.	3.66	-7.33	0.01431	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.6486	0.56748	0.2104:0.0:0.6802:0.1094	.	.	.	.	X	149	.	ENSP00000269081:Y149X	Y	-	3	2	ABCA10	64727364	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-2.285000	0.01153	-2.742000	0.00379	-0.942000	0.02676	TAC		0.333	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67215769	G	T	67215769	4	4	63	1	0	0	0	0	0	1	0	0	29	1024	36	2	4320	2	ABCA10	17	67215769	Nonsense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	15315205	67215769	13979441	49	20396										
TGIF1	7050	hgsc.bcm.edu	37	chr18	3457387	3457387	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtaactggttcatcaacgccCgccgcaggctcctccctgac	9	17	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr18:3457387C>G	ENST00000330513.5	+	3	958	c.655C>G	c.(655-657)Cgc>Ggc	p.R219G	TGIF1_ENST00000343820.5_Missense_Mutation_p.R90G|TGIF1_ENST00000345133.5_Missense_Mutation_p.R70G|TGIF1_ENST00000551541.1_Missense_Mutation_p.R70G|TGIF1_ENST00000400167.2_Missense_Mutation_p.R70G|TGIF1_ENST00000401449.1_Missense_Mutation_p.R70G|TGIF1_ENST00000405385.3_Missense_Mutation_p.R70G|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000407501.2_Missense_Mutation_p.R90G|TGIF1_ENST00000472042.1_Missense_Mutation_p.R70G|TGIF1_ENST00000548489.2_Missense_Mutation_p.R104G	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	219					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R219G(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				CATCAACGCCCGCCGCAGGCT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	18	GRCh37	CM020381	TGIF1	M							46	49	48					18																	3457387		2203	4300	6503	3447387	SO:0001583	missense	7050			X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"Homeoboxes / TALE class"	11776	protein-coding gene	gene with protein product		602630	"TGFB-induced factor (TALE family homeobox)"	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.655C>G	18.37:g.3457387C>G	ENSP00000327959:p.Arg219Gly		3447387	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.488574	0.64074	.	.	ENSG00000177426	ENST00000552383;ENST00000401449;ENST00000550958;ENST00000548489;ENST00000549780;ENST00000549253;ENST00000405385;ENST00000343820;ENST00000407501;ENST00000546979;ENST00000551541;ENST00000345133;ENST00000330513;ENST00000549546;ENST00000549468;ENST00000400167;ENST00000551333;ENST00000472042	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99841	-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09;-7.09	5.77	4.89	0.63831	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.102168	0.64402	D	0.000002	D	0.99917	0.9961	H	0.99609	4.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95724	0.8769	10	0.87932	D	0	-26.357	16.5235	0.84322	0.1319:0.8681:0.0:0.0	.	219;90;104	Q15583;Q15583-2;F8VZB6	TGIF1_HUMAN;.;.	G	70;70;70;104;70;93;70;90;90;90;70;70;219;70;70;70;70;70	ENSP00000449287:R70G;ENSP00000385206:R70G;ENSP00000449531:R70G;ENSP00000447747:R104G;ENSP00000448121:R70G;ENSP00000384970:R70G;ENSP00000339631:R90G;ENSP00000384133:R90G;ENSP00000448934:R90G;ENSP00000450025:R70G;ENSP00000343969:R70G;ENSP00000327959:R219G;ENSP00000449580:R70G;ENSP00000449722:R70G;ENSP00000383031:R70G;ENSP00000446838:R70G;ENSP00000449501:R70G	ENSP00000327959:R219G	R	+	1	0	TGIF1	3447387	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.445000	0.80570	1.557000	0.49525	-0.182000	0.12963	CGC		0.488	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		G	3457387	C	G	3457387	3	3	63	1	0	0	0	0	1	0	0	0	15864	652	23	5	747	5	TGIF1	18	3457387	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		3457387	74619861	50	20397										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34298151	34298151	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	atgctgagcccaatgacaagGtcccagaaacagcgccggtg	12	12	0	3			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr18:34298151G>A	ENST00000359247.4	+	15	2314	c.2314G>A	c.(2314-2316)Gtc>Atc	p.V772I	FHOD3_ENST00000257209.4_Missense_Mutation_p.V789I|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000590592.1_Missense_Mutation_p.V964I|FHOD3_ENST00000592128.1_5'Flank|FHOD3_ENST00000445677.1_Missense_Mutation_p.V751I	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	772					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.V789I(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CAATGACAAGGTCCCAGAAAC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	18											85	89	88					18																	34298151		2203	4300	6503	32552149	SO:0001583	missense	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.2314G>A	18.37:g.34298151G>A	ENSP00000352186:p.Val772Ile		32552149	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	6.538	0.467587	0.12402	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.30714	1.52;1.52;1.53	4.63	4.63	0.57726	.	0.566002	0.17821	N	0.160845	T	0.25494	0.0620	L	0.44542	1.39	0.09310	N	1	B;B;B	0.22211	0.066;0.039;0.003	B;B;B	0.21360	0.031;0.034;0.003	T	0.09952	-1.0651	10	0.34782	T	0.22	.	9.8497	0.41048	0.0965:0.0:0.9034:0.0	.	751;772;789	Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;FHOD3_HUMAN;.	I	789;772;751	ENSP00000257209:V789I;ENSP00000352186:V772I;ENSP00000411430:V751I	ENSP00000257209:V789I	V	+	1	0	FHOD3	32552149	0.519000	0.26242	0.352000	0.25734	0.548000	0.35241	1.666000	0.37460	2.116000	0.64780	0.455000	0.32223	GTC		0.522	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34298151	G	A	34298151	3	1	63	1	0	0	0	0	1	0	0	0	5902	1261	44	3	2427	3	FHOD3	18	34298151	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	30840764	34298151	43779097	51	20398										
ZNF540	163255	hgsc.bcm.edu	37	chr19	38103365	38103365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tgggaaatcatttaatgtgcGtggacagcttaatcggcata	11	6	1	0	rs200091894		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr19:38103365G>A	ENST00000592533.1	+	5	1516	c.1184G>A	c.(1183-1185)cGt>cAt	p.R395H	ZNF540_ENST00000316433.4_Missense_Mutation_p.R395H|ZNF540_ENST00000343599.5_Missense_Mutation_p.R395H|ZNF540_ENST00000589117.1_Missense_Mutation_p.R363H	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	395					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.R395H(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTAATGTGCGTGGACAGCTT	0.378													G|||	1	0.000199681	0	0	5008	,	,		21533	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											116	111	113					19																	38103365		2203	4300	6503	42795205	SO:0001583	missense	163255			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.1184G>A	19.37:g.38103365G>A	ENSP00000466274:p.Arg395His		42795205	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.32	1.604075	0.28534	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.08370	3.1	2.26	-0.13	0.13498	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05181	0.0138	L	0.35593	1.075	0.09310	N	1	B;B	0.22983	0.078;0.047	B;B	0.13407	0.009;0.004	T	0.46456	-0.9190	9	0.13853	T	0.58	.	5.0857	0.14680	0.4857:0.0:0.5143:0.0	.	363;395	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	H	395;363	ENSP00000324598:R395H	ENSP00000324598:R395H	R	+	2	0	ZNF540	42795205	0.000000	0.05858	0.000000	0.03702	0.683000	0.39861	0.068000	0.14531	-0.098000	0.12285	0.305000	0.20034	CGT		0.378	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		A	38103365	G	A	38103365	3	1	63	1	0	0	0	0	1	0	0	0	18014	1145	40	1	1198	1	ZNF540	19	38103365	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		38103365	21025618	52	20399										
TTYH1	57348	hgsc.bcm.edu	37	chr19	54941756	54941756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agctattatctcctctgcaaCcgggccgtctccaacccctt	6	17	3	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr19:54941756C>A	ENST00000376530.3	+	8	1015	c.912C>A	c.(910-912)aaC>aaA	p.N304K	TTYH1_ENST00000376531.3_Missense_Mutation_p.N304K|TTYH1_ENST00000301194.4_Missense_Mutation_p.N304K|TTYH1_ENST00000489425.1_3'UTR|TTYH1_ENST00000391739.3_Intron|AC008746.3_ENST00000457113.1_RNA	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	304					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.N304K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		TCCTCTGCAACCGGGCCGTCT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											143	153	150					19																	54941756		2203	4300	6503	59633568	SO:0001583	missense	57348			AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.912C>A	19.37:g.54941756C>A	ENSP00000365713:p.Asn304Lys		59633568	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	37	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.280704	0.59758	.	.	ENSG00000167614	ENST00000301194;ENST00000376530;ENST00000376531	T;T;T	0.11604	2.76;2.76;2.76	4.43	3.39	0.38822	.	0.192344	0.45867	D	0.000340	T	0.18882	0.0453	M	0.68952	2.095	0.80722	D	1	P;D;D;P	0.61697	0.95;0.99;0.99;0.896	P;P;P;B	0.52909	0.713;0.713;0.628;0.334	T	0.01146	-1.1437	10	0.40728	T	0.16	-9.9911	8.4332	0.32771	0.0:0.8893:0.0:0.1107	.	216;304;304;304	Q9H313-5;Q9H313-2;Q9H313-3;Q9H313	.;.;.;TTYH1_HUMAN	K	304	ENSP00000301194:N304K;ENSP00000365713:N304K;ENSP00000365714:N304K	ENSP00000301194:N304K	N	+	3	2	TTYH1	59633568	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.756000	0.38390	0.981000	0.38548	0.561000	0.74099	AAC		0.652	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			A	54941756	C	A	54941756	3	1	63	1	0	0	0	0	1	0	0	0	16779	506	18	2	942	2	TTYH1	19	54941756	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	16838391	54941756	4187227	53	20400										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56473561	56473561	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tccttttttgaaggctctcgCggccgcactgaggcaccctc	10	15	1	2	rs147934431	byFrequency	TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr19:56473561C>T	ENST00000291971.3	+	4	2242	c.2171C>T	c.(2170-2172)gCg>gTg	p.A724V	NLRP8_ENST00000590542.1_Missense_Mutation_p.A724V	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	724					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.A724V(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AAGGCTCTCGCGGCCGCACTG	0.483													C|||	2	0.000399361	8e-04	0	5008	,	,		20031	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	19											123	105	111					19																	56473561		2203	4300	6503	61165373	SO:0001583	missense	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2171C>T	19.37:g.56473561C>T	ENSP00000291971:p.Ala724Val		61165373	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	2.342	-0.350932	0.05173	.	.	ENSG00000179709	ENST00000291971	D	0.87650	-2.28	1.93	-0.552	0.11818	.	.	.	.	.	T	0.78591	0.4307	L	0.36672	1.1	0.09310	N	1	P;B	0.47106	0.89;0.049	B;B	0.43274	0.414;0.03	T	0.67593	-0.5631	9	0.39692	T	0.17	.	4.0585	0.09827	0.2704:0.4646:0.2651:0.0	.	724;724	Q86W28-2;Q86W28	.;NALP8_HUMAN	V	724	ENSP00000291971:A724V	ENSP00000291971:A724V	A	+	2	0	NLRP8	61165373	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.206000	0.17375	-0.051000	0.13334	0.508000	0.49915	GCG		0.483	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		T	56473561	C	T	56473561	3	4	63	1	0	0	0	0	1	0	0	0	10514	768	27	1	2185	1	NLRP8	19	56473561	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	1531805	56473561	2655422	54	20401										
TMC2	117532	hgsc.bcm.edu	37	chr20	2582875	2582875	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ttgtgtggaagtgggtacctCatttactttgtggttaagcg	13	5	1	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr20:2582875C>A	ENST00000358864.1	+	11	1356	c.1341C>A	c.(1339-1341)ctC>ctA	p.L447L	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	447					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)	p.L447L(1)		NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GTGGGTACCTCATTTACTTTG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	20											183	158	166					20																	2582875		2203	4300	6503	2530875	SO:0001819	synonymous_variant	117532			AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1341C>A	20.37:g.2582875C>A			2530875	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	37	CCDS13029.2																																																																																				0.398	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			A	2582875	C	A	2582875	2	1	63	1	0	0	0	0	0	0	0	1	16024	813	29	2		2	TMC2	20	2582875	Silent	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		2582875	60442645	55	20402										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62298882	62298882	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gccgacatcatattcatgccGtacaattacttgttggatgc	8	10	2	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr20:62298882G>A	ENST00000360203.5	+	8	1000	c.675G>A	c.(673-675)ccG>ccA	p.P225P	RTEL1_ENST00000370018.3_Silent_p.P225P|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.P225P|RTEL1_ENST00000508582.2_Silent_p.P249P|RTEL1_ENST00000318100.4_Silent_p.P225P					regulator of telomere elongation helicase 1									p.P225P(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			TATTCATGCCGTACAATTACT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	20											246	210	222					20																	62298882		2203	4300	6503	61769326	SO:0001819	synonymous_variant	51750			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.675G>A	20.37:g.62298882G>A			61769326		Silent	SNP	ENST00000360203.5	37																																																																																					0.572	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62298882	G	A	62298882	2	1	63	1	0	0	0	0	0	0	0	1	13757	1132	40	1		1	RTEL1	20	62298882	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	59716007	62298882	726638	56	20403										
USP25	29761	hgsc.bcm.edu	37	chr21	17198645	17198645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tgacgatattgacgctagttCcccacctagtggttccatac	8	12	0	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr21:17198645C>T	ENST00000285679.6	+	13	1796	c.1427C>T	c.(1426-1428)tCc>tTc	p.S476F	USP25_ENST00000285681.2_Missense_Mutation_p.S476F|USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Missense_Mutation_p.S476F	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	476	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.S476F(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		GACGCTAGTTCCCCACCTAGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	21											209	172	185					21																	17198645		2203	4300	6503	16120516	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.1427C>T	21.37:g.17198645C>T	ENSP00000285679:p.Ser476Phe		16120516	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146650	0.57151	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	T;T;T	0.24723	1.84;1.85;1.86	5.71	5.71	0.89125	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.095808	0.64402	D	0.000001	T	0.31606	0.0802	N	0.22421	0.69	0.53688	D	0.999977	P;P;P	0.50819	0.899;0.828;0.939	B;P;P	0.52267	0.435;0.652;0.694	T	0.01252	-1.1405	10	0.44086	T	0.13	.	20.2344	0.98354	0.0:1.0:0.0:0.0	.	476;476;476	Q9UHP3-3;Q9UHP3-1;Q9UHP3	.;.;UBP25_HUMAN	F	476	ENSP00000285681:S476F;ENSP00000285679:S476F;ENSP00000383044:S476F	ENSP00000285679:S476F	S	+	2	0	USP25	16120516	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	7.245000	0.78237	2.854000	0.98071	0.655000	0.94253	TCC		0.413	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17198645	C	T	17198645	3	4	63	1	0	0	0	0	1	0	0	0	17096	855	30	3	1477	3	USP25	21	17198645	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10		17198645	30931250	57	20404										
CHODL	140578	hgsc.bcm.edu	37	chr21	19629035	19629035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ccgggacagggatttctgatGgtgatttctggatagggctt	15	6	2	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr21:19629035G>T	ENST00000299295.2	+	2	680	c.289G>T	c.(289-291)Ggt>Tgt	p.G97C	CHODL_ENST00000400127.1_Missense_Mutation_p.G56C|CHODL_ENST00000338326.3_Missense_Mutation_p.G56C|CHODL_ENST00000400131.1_Missense_Mutation_p.G56C|CHODL_ENST00000543733.1_Missense_Mutation_p.G78C|CHODL_ENST00000400135.1_Missense_Mutation_p.G56C|CHODL_ENST00000400128.1_Missense_Mutation_p.G56C	NM_001204175.1|NM_024944.2	NP_001191104.1|NP_079220.2	Q9H9P2	CHODL_HUMAN	chondrolectin	97	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)	p.G97C(1)		kidney(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		GATTTCTGATGGTGATTTCTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	21											109	118	115					21																	19629035		2203	4300	6503	18550906	SO:0001583	missense	140578			AF257472	CCDS13570.1, CCDS56208.1, CCDS56209.1, CCDS56210.1	21q11.2	2006-04-03	2002-07-04		ENSG00000154645	ENSG00000154645			17807	protein-coding gene	gene with protein product		607247	"chromosome 21 open reading frame 68"	C21orf68		12079284	Standard	NM_024944		Approved	FLJ12627, PRED12, MT75	uc021whs.1	Q9H9P2	OTTHUMG00000074519	ENST00000299295.2:c.289G>T	21.37:g.19629035G>T	ENSP00000299295:p.Gly97Cys		18550906	B2R9C0|B4DJB8|Q7Z798|Q7Z799|Q7Z7A0|Q9HCY3	Missense_Mutation	SNP	ENST00000299295.2	37	CCDS13570.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286821	0.80803	.	.	ENSG00000154645	ENST00000400128;ENST00000400131;ENST00000400135;ENST00000400127;ENST00000299295;ENST00000338326;ENST00000543733	T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.82	4.95	0.65309	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.044128	0.85682	D	0.000000	T	0.53594	0.1806	M	0.90814	3.15	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.977;1.0	T	0.63928	-0.6526	9	.	.	.	-15.5347	14.05	0.64730	0.072:0.0:0.928:0.0	.	97;78;56	Q9H9P2;B4DJB8;Q9H9P2-3	CHODL_HUMAN;.;.	C	56;56;56;56;97;56;78	ENSP00000382993:G56C;ENSP00000382996:G56C;ENSP00000383001:G56C;ENSP00000382992:G56C;ENSP00000299295:G97C;ENSP00000339975:G56C;ENSP00000443566:G78C	.	G	+	1	0	CHODL	18550906	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.654000	0.83653	1.478000	0.48253	0.557000	0.71058	GGT		0.498	CHODL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158232.1	NM_024944		T	19629035	G	T	19629035	3	4	63	1	0	0	0	0	1	0	0	0	3370	1348	47	2	295	2	CHODL	21	19629035	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	2430390	19629035	28500860	58	20405										
WBP2NL	164684	hgsc.bcm.edu	37	chr22	42422878	42422878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	aggaaatgaaggcccgcctgTgggatacagagcctcacctg	13	11	1	2			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chr22:42422878T>C	ENST00000328823.9	+	6	654	c.623T>C	c.(622-624)gTg>gCg	p.V208A	WBP2NL_ENST00000543212.1_Missense_Mutation_p.V134A	NM_152613.2	NP_689826.2	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	208	10 X 7 AA tandem repeat of Y-G-X-P-P-X-G.|Gly-rich.				egg activation (GO:0007343)|male pronucleus assembly (GO:0035039)|meiotic nuclear division (GO:0007126)	perinuclear theca (GO:0033011)	WW domain binding (GO:0050699)	p.V208A(1)		breast(2)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)	14						GGCCCGCCTGTGGGATACAGA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											115	131	126					22																	42422878		2203	4300	6503	40752824	SO:0001583	missense	164684			BC022546	CCDS14029.1	22q13.2	2007-07-18			ENSG00000183066	ENSG00000183066			28389	protein-coding gene	gene with protein product	"postacrosomal sheath WW domain-binding protein"	610981				17289678	Standard	NM_152613		Approved	FLJ26145, MGC26816, PAWP	uc003bbt.3	Q6ICG8	OTTHUMG00000151270	ENST00000328823.9:c.623T>C	22.37:g.42422878T>C	ENSP00000332983:p.Val208Ala		40752824	A3KFF7|A8MSG5|B3KXX4|Q8TBF0|Q8TBF3	Missense_Mutation	SNP	ENST00000328823.9	37	CCDS14029.1	.	.	.	.	.	.	.	.	.	.	T	3.746	-0.052576	0.07362	.	.	ENSG00000183066	ENST00000328823;ENST00000543212	T;T	0.27402	1.67;1.67	3.38	-6.75	0.01738	WW-domain-binding protein (1);	.	.	.	.	T	0.09468	0.0233	N	0.04090	-0.28	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.19877	-1.0292	9	0.11182	T	0.66	.	4.6842	0.12750	0.1837:0.5948:0.0923:0.1292	.	208	Q6ICG8	WBP2L_HUMAN	A	208;134	ENSP00000332983:V208A;ENSP00000442447:V134A	ENSP00000332983:V208A	V	+	2	0	WBP2NL	40752824	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.941000	0.00683	-3.007000	0.00274	-0.701000	0.03672	GTG		0.612	WBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322037.1	NM_152613		C	42422878	T	C	42422878	3	2	63	1	0	0	0	0	1	0	0	0	17300	1696	59	4	645	4	WBP2NL	22	42422878	Missense_Mutation	SNP	T	TCGA-AG-A00C-01A-01W-A005-10		42422878	8881688	59	20406										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5947388	5947388	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	tagcttgccaaaatgctgccGtcaatcatgttgccggtgcc	10	12	2	0	rs145911431	byFrequency	TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:5947388G>A	ENST00000381095.3	-	3	1185	c.558C>T	c.(556-558)gaC>gaT	p.D186D	NLGN4X_ENST00000381092.1_Silent_p.D186D|NLGN4X_ENST00000275857.6_Silent_p.D186D|NLGN4X_ENST00000381093.2_Silent_p.D206D|NLGN4X_ENST00000538097.1_Silent_p.D186D	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	186					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.D186D(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						AAATGCTGCCGTCAATCATGT	0.448													G|||	22	0.00582781	0.0159	0.0014	3775	,	,		13665	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X						G	,	42,3793		0,37,5,1595,566	155	116	129		558,558	-1.1	0	X	dbSNP_134	129	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	NLGN4X	NM_020742.2,NM_181332.1	,	0,37,6,4023,2437	AA,AG,A,GG,G		0.0149,1.0952,0.4071	,	186/817,186/817	5947388	43,10520	2203	4300	6503	5957388	SO:0001819	synonymous_variant	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.558C>T	X.37:g.5947388G>A			5957388	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.448	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5947388	G	A	5947388	2	1	63	1	0	0	0	0	0	0	0	1	10495	1136	40	1		1	NLGN4X	23	5947388	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10		5947388	149323172	60	20407										
CLCN4	1183	hgsc.bcm.edu	37	chrX	10176319	10176319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	acatcgcctggtgcaggaggCgcaagaccaccaggctgggg	16	12	0	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:10176319C>T	ENST00000380833.4	+	9	1469	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	CLCN4_ENST00000380829.1_Missense_Mutation_p.R329C|CLCN4_ENST00000421085.2_Missense_Mutation_p.R266C	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	360					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R360C(2)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GTGCAGGAGGCGCAAGACCAC	0.597																																					Melanoma(74;1050 1296 1576 30544 38374)											2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	X											107	102	104					X																	10176319		2203	4300	6503	10136319	SO:0001583	missense	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1078C>T	X.37:g.10176319C>T	ENSP00000370213:p.Arg360Cys		10136319	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	c	21.6	4.168308	0.78339	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.94828	-3.48;-3.53;-3.48	5.71	5.71	0.89125	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.98704	0.9565	H	0.99238	4.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99628	1.0985	10	0.87932	D	0	-28.1314	18.999	0.92826	0.0:1.0:0.0:0.0	.	360	P51793	CLCN4_HUMAN	C	360;329;266	ENSP00000370213:R360C;ENSP00000370209:R329C;ENSP00000405754:R266C	ENSP00000370209:R329C	R	+	1	0	CLCN4	10136319	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.188000	0.50958	2.436000	0.82500	0.592000	0.82586	CGC		0.597	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			T	10176319	C	T	10176319	3	4	63	1	0	0	0	0	1	0	0	0	3471	768	27	1	1104	1	CLCN4	23	10176319	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	4228931	10176319	145094241	61	20408										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937238	12937238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gttcctgtgagttatgcgccGaagaaaatttttctagaagc	10	7	1	3	rs144647258		TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:12937238G>A	ENST00000218032.6	+	2	166	c.79G>A	c.(79-81)Gaa>Aaa	p.E27K	TLR8_ENST00000311912.5_Missense_Mutation_p.E45K	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	27					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.E45K(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	GTTATGCGCCGAAGAAAATTT	0.413													G|||	1	0.000264901	8e-04	0	3775	,	,		14651	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X						G	LYS/GLU	2,3833		0,2,1630,571	78	77	77		79	2	0	X	dbSNP_134	77	0,6728		0,0,2428,1872	no	missense	TLR8	NM_138636.4	56	0,2,4058,2443	AA,AG,GG,G		0.0,0.0522,0.0189	benign	27/1042	12937238	2,10561	2203	4300	6503	12847159	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.79G>A	X.37:g.12937238G>A	ENSP00000218032:p.Glu27Lys		12847159	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	0.042	-1.280276	0.01398	5.22E-4	0.0	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.41400	1.0;1.0	5.22	2.03	0.26663	.	0.756830	0.11275	N	0.580985	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.017	B;B	0.06405	0.002;0.002	T	0.28038	-1.0056	10	0.13108	T	0.6	.	5.4335	0.16466	0.5625:0.0:0.4375:0.0	.	27;45	Q9NR97;D1CS70	TLR8_HUMAN;.	K	27;45	ENSP00000218032:E27K;ENSP00000312082:E45K	ENSP00000218032:E27K	E	+	1	0	TLR8	12847159	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.460000	0.21924	0.436000	0.26393	0.523000	0.50628	GAA		0.413	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12937238	G	A	12937238	3	1	63	1	0	0	0	0	1	0	0	0	15996	1059	37	1	85	1	TLR8	23	12937238	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	2760919	12937238	142333322	62	20409										
NR0B1	190	hgsc.bcm.edu	37	chrX	30322817	30322817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	atctcagcaggaaaagggtaCtattaagttcgatgaatctg	10	6	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:30322817C>T	ENST00000378970.4	-	2	1526	c.1292G>A	c.(1291-1293)aGt>aAt	p.S431N		NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	431	Ligand-binding. {ECO:0000250}.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.S431N(1)		central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	GAAAAGGGTACTATTAAGTTC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CD951561	NR0B1	D							192	156	168					X																	30322817		2202	4300	6502	30232738	SO:0001583	missense	190			S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"Nuclear hormone receptors"	7960	protein-coding gene	gene with protein product		300473	"dosage-sensitive sex reversal"	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.1292G>A	X.37:g.30322817C>T	ENSP00000368253:p.Ser431Asn		30232738	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	37	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.973958	0.53720	.	.	ENSG00000169297	ENST00000378970	D	0.96856	-4.15	5.39	3.47	0.39725	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.354113	0.34088	N	0.004268	D	0.95567	0.8559	L	0.54323	1.7	0.80722	D	1	D	0.56287	0.975	P	0.55055	0.767	D	0.94497	0.7706	10	0.72032	D	0.01	-23.4654	6.7752	0.23617	0.4283:0.4489:0.1228:0.0	.	431	P51843	NR0B1_HUMAN	N	431	ENSP00000368253:S431N	ENSP00000368253:S431N	S	-	2	0	NR0B1	30232738	0.679000	0.27596	0.207000	0.23584	0.353000	0.29299	3.671000	0.54576	2.276000	0.75962	0.523000	0.50628	AGT		0.473	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		T	30322817	C	T	30322817	3	4	63	1	0	0	0	0	1	0	0	0	10644	565	20	3	124	3	NR0B1	23	30322817	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	17385579	30322817	124947743	63	20410										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028881	37028881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ctcgtcgagtgtccagtctcCgcctggagcctcccaagact	10	16	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:37028881C>T	ENST00000358047.3	+	1	2450	c.2398C>T	c.(2398-2400)Cgc>Tgc	p.R800C		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	800								p.R800C(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTCCAGTCTCCGCCTGGAGCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	X											42	42	42					X																	37028881		2202	4300	6502	36938802	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2398C>T	X.37:g.37028881C>T	ENSP00000367913:p.Arg800Cys		36938802	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	C	4.680	0.126435	0.08931	.	.	ENSG00000198173	ENST00000358047	T	0.21543	2.0	0.217	0.217	0.15264	.	.	.	.	.	T	0.09291	0.0229	N	0.08118	0	0.09310	N	1	B	0.23650	0.089	B	0.19148	0.024	T	0.31613	-0.9937	9	0.36615	T	0.2	.	6.1626	0.20372	0.0:0.9996:0.0:4.0E-4	.	800	Q5HY64	FA47C_HUMAN	C	800	ENSP00000367913:R800C	ENSP00000367913:R800C	R	+	1	0	FAM47C	36938802	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	-0.306000	0.08178	0.273000	0.22049	0.277000	0.19347	CGC		0.592	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37028881	C	T	37028881	3	4	63	1	0	0	0	0	1	0	0	0	5590	652	23	1	2400	1	FAM47C	23	37028881	Missense_Mutation	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	6706064	37028881	118241679	64	20411										
WNK3	65267	hgsc.bcm.edu	37	chrX	54275519	54275519	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ttccaggacagtagtgggttGaagggtagttggttcaaggc	16	5	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:54275519G>T	ENST00000375159.2	-	16	3261	c.3262C>A	c.(3262-3264)Caa>Aaa	p.Q1088K	WNK3_ENST00000375169.3_Missense_Mutation_p.Q1088K|WNK3_ENST00000354646.2_Missense_Mutation_p.Q1088K			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1088					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q1088K(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GTAGTGGGTTGAAGGGTAGTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	X											97	85	89					X																	54275519		2203	4300	6503	54292244	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3262C>A	X.37:g.54275519G>T	ENSP00000364301:p.Gln1088Lys		54292244	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	0.169	-1.073147	0.01918	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.47528	0.84;0.84;0.84	5.02	1.03	0.20045	.	1.000500	0.08068	N	0.999430	T	0.28400	0.0702	N	0.14661	0.345	0.21553	N	0.999641	B;B	0.21520	0.039;0.057	B;B	0.20955	0.032;0.014	T	0.24621	-1.0155	10	0.24483	T	0.36	-0.4997	6.7939	0.23715	0.1625:0.2621:0.5754:0.0	.	1088;1088	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	K	1088	ENSP00000364312:Q1088K;ENSP00000346667:Q1088K;ENSP00000364301:Q1088K	ENSP00000346667:Q1088K	Q	-	1	0	WNK3	54292244	1.000000	0.71417	0.000000	0.03702	0.259000	0.26198	3.566000	0.53805	-0.242000	0.09667	0.422000	0.28245	CAA		0.428	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54275519	G	T	54275519	3	4	63	1	0	0	0	0	1	0	0	0	17419	1299	45	2	2172	2	WNK3	23	54275519	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	17246638	54275519	100995041	65	20412										
RAB40A	142684	hgsc.bcm.edu	37	chrX	102755559	102755559	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	atccccccgagatggctgtaCggggactcagctgcaccatc	11	15	1	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:102755559C>T	ENST00000372633.1	-	1	2244	c.126G>A	c.(124-126)ccG>ccA	p.P42P	RAB40A_ENST00000304236.1_Silent_p.P42P|LL0XNC01-250H12.3_ENST00000445990.1_RNA			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	42					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.P42P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						GATGGCTGTACGGGGACTCAG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	X											125	110	115					X																	102755559		2203	4300	6503	102642215	SO:0001819	synonymous_variant	142684			AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"RAB, member RAS oncogene"	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.126G>A	X.37:g.102755559C>T			102642215	O00407|Q17RQ5|Q6DK06|Q8TF06	Silent	SNP	ENST00000372633.1	37	CCDS35357.1																																																																																				0.607	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1			T	102755559	C	T	102755559	2	4	63	1	0	0	0	0	0	0	0	1	12976	523	19	1		1	RAB40A	23	102755559	Silent	SNP	C	TCGA-AG-A00C-01A-01W-A005-10	48480040	102755559	52515001	66	20413										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114249076	114249076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	gtaaaagcgtgtgtatcttcGcttcaatgcccttgttaaga	9	8	2	1			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:114249076G>A	ENST00000371936.1	-	5	557	c.308C>T	c.(307-309)gCg>gTg	p.A103V	IL13RA2_ENST00000243213.1_Missense_Mutation_p.A103V|IL13RA2_ENST00000468224.1_5'Flank			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	103	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)	p.A103V(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						GTGTATCTTCGCTTCAATGCC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	X											143	117	126					X																	114249076		2203	4300	6503	114155332	SO:0001583	missense	3598			X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.308C>T	X.37:g.114249076G>A	ENSP00000361004:p.Ala103Val		114155332	A8K7E2|O00667	Missense_Mutation	SNP	ENST00000371936.1	37	CCDS14565.1	.	.	.	.	.	.	.	.	.	.	G	0.738	-0.777342	0.02929	.	.	ENSG00000123496	ENST00000371936;ENST00000243213	D;D	0.90955	-2.76;-2.76	5.18	4.3	0.51218	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.257726	0.40554	N	0.001070	T	0.74794	0.3763	N	0.25286	0.73	0.29795	N	0.832866	P;P	0.52577	0.954;0.893	B;B	0.22601	0.04;0.022	T	0.71961	-0.4434	10	0.10111	T	0.7	-12.3356	10.1799	0.42961	0.0:0.2036:0.7964:0.0	.	103;103	D0EFR8;Q14627	.;I13R2_HUMAN	V	103	ENSP00000361004:A103V;ENSP00000243213:A103V	ENSP00000243213:A103V	A	-	2	0	IL13RA2	114155332	1.000000	0.71417	0.992000	0.48379	0.260000	0.26232	1.890000	0.39728	1.134000	0.42165	0.538000	0.68166	GCG		0.373	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		A	114249076	G	A	114249076	3	1	63	1	0	0	0	0	1	0	0	0	7651	1087	38	1	862	1	IL13RA2	23	114249076	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	11493517	114249076	41021484	67	20414										
MBNL3	55796	hgsc.bcm.edu	37	chrX	131520695	131520695	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	agctgtgttctcacctgcagGgataaatgccggctgtggga	14	9	1	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:131520695G>A	ENST00000370853.3	-	5	994	c.916C>T	c.(916-918)Cct>Tct	p.P306S	RAP2C-AS1_ENST00000441399.2_RNA|MBNL3_ENST00000370849.3_Missense_Mutation_p.P256S|MBNL3_ENST00000370844.1_Missense_Mutation_p.P210S|MBNL3_ENST00000394311.2_Missense_Mutation_p.P210S|MBNL3_ENST00000370839.3_Missense_Mutation_p.P271S|MBNL3_ENST00000370857.3_Missense_Mutation_p.P306S|RAP2C-AS1_ENST00000421483.2_RNA|MBNL3_ENST00000538204.1_Missense_Mutation_p.P256S	NM_018388.3	NP_060858.2	Q9NUK0	MBNL3_HUMAN	muscleblind-like splicing regulator 3	306					mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|negative regulation of myoblast differentiation (GO:0045662)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P306S(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)	16	Acute lymphoblastic leukemia(192;0.000127)					TCACCTGCAGGGATAAATGCC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											90	79	83					X																	131520695		2203	4300	6503	131348376	SO:0001583	missense	55796			AF491305	CCDS14633.1, CCDS14634.1, CCDS55492.1, CCDS55493.1, CCDS55494.1	Xq26.2	2013-01-18	2012-02-23		ENSG00000076770	ENSG00000076770		"Zinc fingers, CCCH-type domain containing"	20564	protein-coding gene	gene with protein product		300413	"muscleblind-like 3 (Drosophila)"			12297108, 10970838	Standard	NM_018388		Approved	CHCR, FLJ11316, MBLX39, MBXL	uc004ewv.4	Q9NUK0	OTTHUMG00000022426	ENST00000370853.3:c.916C>T	X.37:g.131520695G>A	ENSP00000359890:p.Pro306Ser		131348376	Q5JXN8|Q5JXN9|Q5JXP4|Q6UDQ1|Q8IUR4|Q8TAD9|Q8TAF4|Q9H0Z7|Q9UF37	Missense_Mutation	SNP	ENST00000370853.3	37	CCDS14633.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.471855	0.84533	.	.	ENSG00000076770	ENST00000394311;ENST00000538204;ENST00000370857;ENST00000370853;ENST00000370849;ENST00000370839;ENST00000370844;ENST00000442191;ENST00000436215;ENST00000421707	T;T;T	0.57107	0.42;0.6;0.84	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.73118	0.3546	M	0.72894	2.215	0.58432	D	0.999995	D;B;D;P;D	0.89917	0.994;0.286;1.0;0.538;0.997	P;B;D;B;D	0.91635	0.858;0.396;0.999;0.396;0.919	T	0.73382	-0.4000	10	0.49607	T	0.09	-13.0011	18.9172	0.92510	0.0:0.0:1.0:0.0	.	256;306;271;256;210	Q9NUK0-4;Q9NUK0;Q9NUK0-2;Q9NUK0-3;Q8IUR4	.;MBNL3_HUMAN;.;.;.	S	210;256;306;306;256;271;210;87;210;210	ENSP00000359894:P306S;ENSP00000359890:P306S;ENSP00000359876:P271S	ENSP00000359876:P271S	P	-	1	0	MBNL3	131348376	1.000000	0.71417	0.774000	0.31636	0.954000	0.61252	8.009000	0.88606	2.415000	0.81967	0.600000	0.82982	CCT		0.498	MBNL3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058319.1	NM_018388		A	131520695	G	A	131520695	3	1	63	1	0	0	0	0	1	0	0	0	9385	1232	43	3	225	3	MBNL3	23	131520695	Missense_Mutation	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	17271619	131520695	23749865	68	20415										
MAMLD1	10046	hgsc.bcm.edu	37	chrX	149639582	149639582	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.186447368421053	1.06541353383459	0	1	1	0	ctgcagcagccgacaccaacGcaggcctcctcagccactgc	9	19	1	0			TCGA-AG-A00C-01A-01W-A005-10	TCGA-AG-A00C-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	1a4f95be-32d3-4202-a0e7-507181b3fb86	231b9dfb-c5a5-4c82-8271-b693b8d907a0	g.chrX:149639582G>A	ENST00000370401.2	+	4	2047	c.1737G>A	c.(1735-1737)acG>acA	p.T579T	MAMLD1_ENST00000455522.2_Silent_p.T60T|MAMLD1_ENST00000432680.2_Silent_p.T554T|MAMLD1_ENST00000426613.2_Silent_p.T554T|MAMLD1_ENST00000262858.5_Silent_p.T579T			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	579					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.T506T(1)|p.T579T(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					CGACACCAACGCAGGCCTCCT	0.617																																																2	Substitution - coding silent(2)	large_intestine(2)	X											72	66	68					X																	149639582		2203	4300	6503	149390240	SO:0001819	synonymous_variant	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1737G>A	X.37:g.149639582G>A			149390240	B2RCQ4|B4DG93|B9EGA5	Silent	SNP	ENST00000370401.2	37	CCDS14693.2																																																																																				0.617	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		A	149639582	G	A	149639582	2	1	63	1	0	0	0	0	0	0	0	1	9238	1074	38	1		1	MAMLD1	23	149639582	Silent	SNP	G	TCGA-AG-A00C-01A-01W-A005-10	18118887	149639582	5630978	69	20416										
ARID1A	8289	broad.mit.edu	37	chr1	27088759	27088759	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	caggcatgggctcctaccagCagaactccatggggagctat	12	12	0	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:27088759C>T	ENST00000324856.7	+	7	2739	c.2368C>T	c.(2368-2370)Cag>Tag	p.Q790*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q407*|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q790*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	790					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q790*(2)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		CTCCTACCAGCAGAACTCCAT	0.587			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	1											63	65	64					1																	27088759		2203	4300	6503	26961346	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2368C>T	1.37:g.27088759C>T	ENSP00000320485:p.Gln790*		26961346	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	39	7.350800	0.98228	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	.	.	.	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-6.9554	18.667	0.91493	0.0:1.0:0.0:0.0	.	.	.	.	X	790;790;407	.	ENSP00000320485:Q790X	Q	+	1	0	ARID1A	26961346	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.498000	0.66931	2.824000	0.97209	0.655000	0.94253	CAG		0.587	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27088759	C	T	27088759	4	4	64	1	0	0	0	0	0	1	0	0	913	711	25	3	2394	3	ARID1A	1	27088759	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		27088759	222161862	1	20417										
OLFM3	118427	broad.mit.edu	37	chr1	102296359	102296359	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agttctcaagtttaagacttCaatagactgggacatgttct	8	7	3	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:102296359C>A	ENST00000338858.5	-	3	300	c.301G>T	c.(301-303)Gaa>Taa	p.E101*	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Nonsense_Mutation_p.E81*|OLFM3_ENST00000359814.3_Nonsense_Mutation_p.E101*|OLFM3_ENST00000536598.1_Nonsense_Mutation_p.E6*			Q96PB7	NOE3_HUMAN	olfactomedin 3	101					eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)		p.E101*(1)|p.E81*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		TTTAAGACTTCAATAGACTGG	0.348																																																2	Substitution - Nonsense(2)	large_intestine(2)	1											106	107	107					1																	102296359		2203	4300	6503	102068947	SO:0001587	stop_gained	118427			AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.301G>T	1.37:g.102296359C>A	ENSP00000345192:p.Glu101*		102068947	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Nonsense_Mutation	SNP	ENST00000338858.5	37		.	.	.	.	.	.	.	.	.	.	C	37	6.082726	0.97267	.	.	ENSG00000118733	ENST00000370103;ENST00000338858;ENST00000536598;ENST00000359814	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0172	0.97481	0.0:1.0:0.0:0.0	.	.	.	.	X	81;101;6;101	.	ENSP00000345192:E101X	E	-	1	0	OLFM3	102068947	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.962000	0.70364	2.814000	0.96858	0.585000	0.79938	GAA		0.348	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			A	102296359	C	A	102296359	4	1	64	1	0	0	0	0	0	1	0	0	10885	835	29	2	1151	2	OLFM3	1	102296359	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	75207600	102296359	146954262	2	20418										
TRIM33	51592	broad.mit.edu	37	chr1	115005840	115005840	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ggcagaaaacagggcgttgaCcagatgctccaacagactct	11	11	1	4			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:115005840C>G	ENST00000358465.2	-	4	892	c.809G>C	c.(808-810)gGt>gCt	p.G270A	TRIM33_ENST00000450349.2_5'UTR|TRIM33_ENST00000369543.2_Missense_Mutation_p.G270A	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	270					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G270A(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		AGGGCGTTGACCAGATGCTCC	0.343			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	1	Substitution - Missense(1)	large_intestine(1)	1											62	58	59					1																	115005840		2203	4300	6503	114807363	SO:0001583	missense	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.809G>C	1.37:g.115005840C>G	ENSP00000351250:p.Gly270Ala		114807363	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.1|26.1	4.702771|4.702771	0.88924|0.88924	.|.	.|.	ENSG00000197323|ENSG00000197323	ENST00000358465;ENST00000369543|ENST00000448034	T;T|.	0.56611|.	0.45;0.45|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Zinc finger, RING-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.47135|0.47135	0.1429|0.1429	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	D|D	1|1	D;B|.	0.89917|.	1.0;0.066|.	D;B|.	0.87578|.	0.998;0.105|.	T|T	0.38134|0.38134	-0.9675|-0.9675	10|5	0.16896|.	T|.	0.51|.	-14.4216|-14.4216	19.7863|19.7863	0.96440|0.96440	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	270;270|.	Q9UPN9-2;Q9UPN9|.	.;TRI33_HUMAN|.	A|L	270|7	ENSP00000351250:G270A;ENSP00000358556:G270A|.	ENSP00000351250:G270A|.	G|V	-|-	2|1	0|0	TRIM33|TRIM33	114807363|114807363	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.871000|4.871000	0.63042|0.63042	2.665000|2.665000	0.90641|0.90641	0.655000|0.655000	0.94253|0.94253	GGT|GTC		0.343	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		G	115005840	C	G	115005840	3	3	64	1	0	0	0	0	1	0	0	0	16547	507	18	5	2642	5	TRIM33	1	115005840	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	12709481	115005840	134244781	3	20419										
ITGA10	8515	broad.mit.edu	37	chr1	145533128	145533128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	atggcttgaaggaggccaccGccttttccccccacgaatgg	11	14	0	1	rs587701227		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:145533128G>A	ENST00000369304.3	+	11	1398	c.1223G>A	c.(1222-1224)cGc>cAc	p.R408H	ITGA10_ENST00000538811.1_Missense_Mutation_p.R277H|ITGA10_ENST00000539363.1_Missense_Mutation_p.R265H	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	408					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.R408H(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGAGGCCACCGCCTTTTCCCC	0.577													G|||	1	0.000199681	0	0.0014	5008	,	,		14990	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											62	58	59					1																	145533128		2203	4300	6503	144244485	SO:0001583	missense	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.1223G>A	1.37:g.145533128G>A	ENSP00000358310:p.Arg408His		144244485	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	8.976	0.974056	0.18736	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.25085	1.82;1.82;1.82	4.71	-2.28	0.06826	.	0.719495	0.13270	N	0.400596	T	0.05318	0.0141	L	0.46741	1.465	0.29451	N	0.858498	B;B;B;B	0.21753	0.06;0.016;0.059;0.006	B;B;B;B	0.20767	0.031;0.013;0.009;0.008	T	0.44862	-0.9300	10	0.08837	T	0.75	.	7.5075	0.27553	0.3853:0.11:0.5047:0.0	.	374;277;265;408	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	H	408;374;265;277	ENSP00000358310:R408H;ENSP00000439894:R265H;ENSP00000440011:R277H	ENSP00000358310:R408H	R	+	2	0	ITGA10	144244485	0.001000	0.12720	0.557000	0.28306	0.563000	0.35712	0.248000	0.18198	-0.810000	0.04375	-0.797000	0.03246	CGC		0.577	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145533128	G	A	145533128	3	1	64	1	0	0	0	0	1	0	0	0	7894	1087	38	1	1265	1	ITGA10	1	145533128	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	30527288	145533128	103717493	4	20420										
ASTN1	460	broad.mit.edu	37	chr1	176838004	176838004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gacctaactcatcctcacatCgccaggtgaattccccaaaa	5	15	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:176838004C>T	ENST00000367654.3	-	22	3858	c.3647G>A	c.(3646-3648)cGa>cAa	p.R1216Q	ASTN1_ENST00000424564.2_Missense_Mutation_p.R1208Q|ASTN1_ENST00000367657.3_Missense_Mutation_p.R1208Q|ASTN1_ENST00000361833.2_Missense_Mutation_p.R1208Q	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1216					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.R1208Q(3)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						ATCCTCACATCGCCAGGTGAA	0.468																																																3	Substitution - Missense(3)	ovary(1)|large_intestine(1)|endometrium(1)	1											119	117	117					1																	176838004		2203	4300	6503	175104627	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3647G>A	1.37:g.176838004C>T	ENSP00000356626:p.Arg1216Gln		175104627	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	C	36	5.937872	0.97122	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.27557	1.66;2.07;2.07;1.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.48333	0.1494	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.99	T	0.43343	-0.9397	10	0.87932	D	0	-29.5501	19.9003	0.96983	0.0:1.0:0.0:0.0	.	1208;1208	O14525-2;B1AJS1	.;.	Q	1208;1208;1216;1208;1208	ENSP00000356629:R1208Q;ENSP00000354536:R1208Q;ENSP00000356626:R1216Q;ENSP00000395041:R1208Q	ENSP00000354536:R1208Q	R	-	2	0	ASTN1	175104627	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.679000	0.84048	2.808000	0.96608	0.655000	0.94253	CGA		0.468	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176838004	C	T	176838004	3	4	64	1	0	0	0	0	1	0	0	0	1065	884	31	1	273	1	ASTN1	1	176838004	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	31304876	176838004	72412617	5	20421										
RASSF5	83593	broad.mit.edu	37	chr1	206757739	206757739	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agtgaagacggcacctacacGggtttcatcaaagtgcatct	10	10	3	2	rs372473374		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr1:206757739G>A	ENST00000355294.4	+	4	768	c.711G>A	c.(709-711)acG>acA	p.T237T	RASSF5_ENST00000367117.3_Silent_p.T237T|RASSF5_ENST00000304534.8_Silent_p.T84T|RASSF5_ENST00000491368.1_3'UTR|EIF2D_ENST00000472709.2_Intron	NM_182663.2	NP_872604.1	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family member 5	237					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein localization to nucleus (GO:1900180)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.T237T(1)|p.T84T(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	8	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			GCACCTACACGGGTTTCATCA	0.612											OREG0014174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(162;656 1984 11916 22872 31529)											2	Substitution - coding silent(2)	large_intestine(2)	1						G	,,	1,4405	2.1+/-5.4	0,1,2202	45	48	47		711,711,252	-9.4	0.8	1		47	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	RASSF5	NM_182663.2,NM_182664.2,NM_182665.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	237/419,237/337,84/266	206757739	1,13005	2203	4300	6503	204824362	SO:0001819	synonymous_variant	83593			BC004270	CCDS1463.1, CCDS1464.1, CCDS30998.1	1q31	2014-04-10	2008-02-22		ENSG00000136653	ENSG00000266094			17609	protein-coding gene	gene with protein product		607020				11978988, 11965544	Standard	NM_182663		Approved	Maxp1, NORE1, RAPL	uc001hed.3	Q8WWW0	OTTHUMG00000184616	ENST00000355294.4:c.711G>A	1.37:g.206757739G>A		2162	204824362	A8K1E6|Q5SY32|Q8WWV9|Q8WXF4|Q9BT99	Silent	SNP	ENST00000355294.4	37	CCDS30998.1																																																																																				0.612	RASSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088469.1	NM_031437		A	206757739	G	A	206757739	2	1	64	1	0	0	0	0	0	0	0	1	13126	1103	39	1		1	RASSF5	1	206757739	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	29919735	206757739	42492882	6	20422										
PXDN	7837	broad.mit.edu	37	chr2	1667405	1667405	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tgcacagtcaggtgggccacGaccttctgggagccgatgat	14	11	2	1	rs202202761		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr2:1667405G>A	ENST00000252804.4	-	12	1589	c.1539C>T	c.(1537-1539)gtC>gtT	p.V513V	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	513	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.V513V(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGTGGGCCACGACCTTCTGGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		0,4064		0,0,2032	84	92	89		1539	-11.6	0	2		89	1,8323		0,1,4161	no	coding-synonymous	PXDN	NM_012293.1		0,1,6193	AA,AG,GG		0.012,0.0,0.0081		513/1480	1667405	1,12387	2032	4162	6194	1646412	SO:0001819	synonymous_variant	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1539C>T	2.37:g.1667405G>A			1646412	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	8.726	0.915479	0.17907	0.0	1.2E-4	ENSG00000130508	ENST00000433670	.	.	.	5.79	-11.6	0.00059	.	.	.	.	.	T	0.50854	0.1640	.	.	.	0.35671	D	0.813346	.	.	.	.	.	.	T	0.69924	-0.5013	4	.	.	.	-32.7278	14.2933	0.66295	0.3444:0.4676:0.188:0.0	.	.	.	.	L	509	.	.	S	-	2	0	PXDN	1646412	0.000000	0.05858	0.015000	0.15790	0.901000	0.52897	-1.548000	0.02184	-3.704000	0.00118	-0.136000	0.14681	TCG		0.547	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1667405	G	A	1667405	2	1	64	1	0	0	0	0	0	0	0	1	12884	1045	37	1		1	PXDN	2	1667405	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		1667405	241531968	7	20423										
TTC27	55622	broad.mit.edu	37	chr2	32958948	32958948	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tctgtattggaacgcctgaaGattttctattgctgtcaagt	9	7	3	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr2:32958948G>T	ENST00000317907.4	+	11	1518	c.1287G>T	c.(1285-1287)aaG>aaT	p.K429N		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	429								p.K429N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AACGCCTGAAGATTTTCTATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	2											152	140	144					2																	32958948		2203	4300	6503	32812452	SO:0001583	missense	55622			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1287G>T	2.37:g.32958948G>T	ENSP00000313953:p.Lys429Asn		32812452	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.985332	0.53934	.	.	ENSG00000018699	ENST00000317907	T	0.31510	1.49	5.42	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.49389	0.1554	M	0.69823	2.125	0.48395	D	0.999642	D	0.76494	0.999	D	0.68943	0.961	T	0.48151	-0.9060	10	0.49607	T	0.09	-17.7025	8.6741	0.34167	0.1752:0.0:0.8248:0.0	.	429	Q6P3X3	TTC27_HUMAN	N	429	ENSP00000313953:K429N	ENSP00000313953:K429N	K	+	3	2	TTC27	32812452	1.000000	0.71417	0.947000	0.38551	0.385000	0.30292	2.039000	0.41193	1.260000	0.44134	0.650000	0.86243	AAG		0.358	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	32958948	G	T	32958948	3	4	64	1	0	0	0	0	1	0	0	0	16735	933	33	2	1329	2	TTC27	2	32958948	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	31291543	32958948	210240425	8	20424										
SP140L	93349	broad.mit.edu	37	chr2	231254710	231254710	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	acctgtggtggggtgaagggAattttacataaggagaaatt	14	3	0	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr2:231254710A>T	ENST00000415673.2	+	11	1022	c.936A>T	c.(934-936)ggA>ggT	p.G312G	SP140L_ENST00000396563.4_Intron|SP140L_ENST00000243810.6_Silent_p.G312G|SP140L_ENST00000444636.1_Silent_p.G312G	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	312	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G312G(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GGGTGAAGGGAATTTTACATA	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	2											111	102	105					2																	231254710		1831	4096	5927	230962954	SO:0001819	synonymous_variant	93349			BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.936A>T	2.37:g.231254710A>T			230962954	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																				0.398	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		T	231254710	A	T	231254710	2	4	64	1	0	0	0	0	0	0	0	1	15000	233	9	5		5	SP140L	2	231254710	Silent	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	198295762	231254710	11944663	9	20425										
SLC6A1	6529	broad.mit.edu	37	chr3	11070971	11070971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccccaggctcctccgcaaccGcagagagctcttcattgctg	9	17	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:11070971G>A	ENST00000287766.4	+	12	1677	c.1256G>A	c.(1255-1257)cGc>cAc	p.R419H	SLC6A1_ENST00000536032.1_Missense_Mutation_p.R241H	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	419					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R419H(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	CTCCGCAACCGCAGAGAGCTC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3											89	77	81					3																	11070971		2203	4300	6503	11045971	SO:0001583	missense	6529				CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"Solute carriers"	11042	protein-coding gene	gene with protein product	"GABA transporter 1"	137165	"solute carrier family 6 (neurotransmitter transporter, GABA), member 1"			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.1256G>A	3.37:g.11070971G>A	ENSP00000287766:p.Arg419His		11045971	Q8N4K8	Missense_Mutation	SNP	ENST00000287766.4	37	CCDS2603.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.534134	0.85812	.	.	ENSG00000157103	ENST00000287766;ENST00000536032	T;T	0.75589	-0.95;-0.95	5.69	5.69	0.88448	.	0.089576	0.48286	D	0.000186	D	0.84129	0.5404	L	0.55017	1.72	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.83182	-0.0088	10	0.48119	T	0.1	.	19.8099	0.96542	0.0:0.0:1.0:0.0	.	419	P30531	SC6A1_HUMAN	H	419;241	ENSP00000287766:R419H;ENSP00000445171:R241H	ENSP00000287766:R419H	R	+	2	0	SLC6A1	11045971	0.998000	0.40836	0.999000	0.59377	0.997000	0.91878	7.837000	0.86796	2.691000	0.91804	0.655000	0.94253	CGC		0.572	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		A	11070971	G	A	11070971	3	1	64	1	0	0	0	0	1	0	0	0	14710	1087	38	1	1294	1	SLC6A1	3	11070971	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		11070971	186951459	10	20426										
ARPP21	10777	broad.mit.edu	37	chr3	35833951	35833951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agccacctcagagtcagaacGtgataaataaccaacaagga	8	10	2	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:35833951G>A	ENST00000187397.4	+	19	2566	c.2110G>A	c.(2110-2112)Gtg>Atg	p.V704M	ARPP21_ENST00000444190.1_Missense_Mutation_p.V685M|ARPP21_ENST00000337271.5_Missense_Mutation_p.V685M|ARPP21_ENST00000458225.1_Missense_Mutation_p.V705M|ARPP21_ENST00000476052.1_3'UTR|ARPP21_ENST00000417925.1_Missense_Mutation_p.V705M	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	704	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.V704M(2)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						GAGTCAGAACGTGATAAATAA	0.468																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	3											158	145	149					3																	35833951		2203	4300	6503	35808955	SO:0001583	missense	10777			AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.2110G>A	3.37:g.35833951G>A	ENSP00000187397:p.Val704Met		35808955	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.949519	0.34377	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.71	0.437	0.16555	.	0.331639	0.25964	N	0.027168	T	0.37732	0.1014	L	0.36672	1.1	0.09310	N	0.999992	P;D;P;P	0.53619	0.906;0.961;0.848;0.906	B;P;B;B	0.44359	0.329;0.447;0.163;0.329	T	0.26677	-1.0096	10	0.45353	T	0.12	-2.568	4.5612	0.12161	0.1534:0.3192:0.4348:0.0926	.	705;227;704;685	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	M	705;685;685;704;705	ENSP00000414351:V705M;ENSP00000337792:V685M;ENSP00000405276:V685M;ENSP00000187397:V704M;ENSP00000412326:V705M	ENSP00000187397:V704M	V	+	1	0	ARPP21	35808955	0.141000	0.22595	0.043000	0.18650	0.772000	0.43724	0.441000	0.21611	0.048000	0.15891	0.655000	0.94253	GTG		0.468	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		A	35833951	G	A	35833951	3	1	64	1	0	0	0	0	1	0	0	0	979	1145	40	1	2189	1	ARPP21	3	35833951	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	24762980	35833951	162188479	11	20427										
CCBP2	1238	broad.mit.edu	37	chr3	42906323	42906323	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	catctccgtggcctggcattGggtcttcgggagtttcttgt	13	10	3	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:42906323G>T	ENST00000422265.1	+	3	504	c.329G>T	c.(328-330)tGg>tTg	p.W110L	ACKR2_ENST00000273145.2_Missense_Mutation_p.W110L|CYP8B1_ENST00000437102.1_Intron|ACKR2_ENST00000442925.1_Missense_Mutation_p.W110L|KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	110					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.W110L(1)									GCCTGGCATTGGGTCTTCGGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											155	155	155					3																	42906323		2203	4300	6503	42881327	SO:0001583	missense	1238			U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.329G>T	3.37:g.42906323G>T	ENSP00000416996:p.Trp110Leu		42881327	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691509	0.88735	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.77358	-1.09;-1.09;-1.09	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000279	D	0.92054	0.7482	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94434	0.7652	9	.	.	.	.	17.485	0.87684	0.0:0.0:1.0:0.0	.	110;110	O00590;Q7Z7I1	CCBP2_HUMAN;.	L	110	ENSP00000396150:W110L;ENSP00000416996:W110L;ENSP00000273145:W110L	.	W	+	2	0	CCBP2	42881327	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.596000	0.67570	2.477000	0.83638	0.563000	0.77884	TGG		0.493	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		T	42906323	G	T	42906323	3	4	64	1	0	0	0	0	1	0	0	0	2740	1357	47	2	331	2	CCBP2	3	42906323	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	7072372	42906323	155116107	12	20428										
ALAS1	211	broad.mit.edu	37	chr3	52236599	52236599	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccagatggcacacagcttccGtctggacaccccttgcctgc	9	17	1	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:52236599G>A	ENST00000394965.2	+	4	636	c.276G>A	c.(274-276)ccG>ccA	p.P92P	ALAS1_ENST00000484952.1_Silent_p.P92P|ALAS1_ENST00000469224.1_Silent_p.P92P|ALAS1_ENST00000310271.2_Silent_p.P92P	NM_000688.5	NP_000679.1	P13196	HEM1_HUMAN	aminolevulinate, delta-, synthase 1	92					cellular lipid metabolic process (GO:0044255)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5-aminolevulinate synthase activity (GO:0003870)|pyridoxal phosphate binding (GO:0030170)	p.P92P(1)		endometrium(3)|kidney(3)|large_intestine(7)|liver(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)	CACAGCTTCCGTCTGGACACC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	3											69	62	65					3																	52236599		2203	4300	6503	52211639	SO:0001819	synonymous_variant	211			X56351	CCDS2847.1	3p21	2004-11-18			ENSG00000023330	ENSG00000023330	2.3.1.37		396	protein-coding gene	gene with protein product		125290		ALAS3, ALAS			Standard	NM_000688		Approved		uc003dcz.2	P13196	OTTHUMG00000158108	ENST00000394965.2:c.276G>A	3.37:g.52236599G>A			52211639		Silent	SNP	ENST00000394965.2	37	CCDS2847.1	.	.	.	.	.	.	.	.	.	.	G	9.103	1.004600	0.19199	.	.	ENSG00000023330	ENST00000441729	.	.	.	5.23	-7.82	0.01205	.	.	.	.	.	T	0.49253	0.1546	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60073	-0.7334	5	0.72032	D	0.01	-12.7331	1.7733	0.03016	0.4731:0.1778:0.1121:0.237	.	.	.	.	H	92	.	ENSP00000392725:R92H	R	+	2	0	ALAS1	52211639	0.000000	0.05858	0.402000	0.26371	0.984000	0.73092	-3.366000	0.00496	-1.170000	0.02769	-0.123000	0.14984	CGT		0.537	ALAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350207.1			A	52236599	G	A	52236599	2	1	64	1	0	0	0	0	0	0	0	1	484	1132	40	1		1	ALAS1	3	52236599	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	9330276	52236599	145785831	13	20429										
PIK3CA	5290	broad.mit.edu	37	chr3	178921553	178921553	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ctttgtgcaacctacgtgaaTgtaaatattcgagacattga	8	7	0	3	rs121913284		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:178921553T>A	ENST00000263967.3	+	5	1192	c.1035T>A	c.(1033-1035)aaT>aaA	p.N345K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	345	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N345K(44)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CCTACGTGAATGTAAATATTC	0.308		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	44	Substitution - Missense(44)	breast(27)|endometrium(6)|large_intestine(6)|central_nervous_system(5)	3											67	66	66					3																	178921553		1807	4074	5881	180404247	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1035T>A	3.37:g.178921553T>A	ENSP00000263967:p.Asn345Lys		180404247	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.002090	0.54254	.	.	ENSG00000121879	ENST00000263967	T	0.70164	-0.46	5.41	3.03	0.35002	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75465	-0.3308	10	0.49607	T	0.09	-21.0442	9.7159	0.40274	0.0:0.1415:0.0:0.8585	.	345	P42336	PK3CA_HUMAN	K	345	ENSP00000263967:N345K	ENSP00000263967:N345K	N	+	3	2	PIK3CA	180404247	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.030000	0.41108	0.441000	0.26529	0.402000	0.26972	AAT		0.308	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178921553	T	A	178921553	3	1	64	1	0	0	0	0	1	0	0	0	11944	1461	51	5	1049	5	PIK3CA	3	178921553	Missense_Mutation	SNP	T	TCGA-AG-A00H-01A-01W-A00E-09	126684954	178921553	19100877	14	20430										
RNF168	165918	broad.mit.edu	37	chr3	196214300	196214300	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	cttagctttcttgccagttcCtcatcacttttcagttgttc	5	12	4	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr3:196214300C>A	ENST00000318037.3	-	3	1122	c.528G>T	c.(526-528)gaG>gaT	p.E176D		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	176	Glu-rich.				cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E176D(1)		NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		TTGCCAGTTCCTCATCACTTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3											551	510	524					3																	196214300		2203	4300	6503	197698697	SO:0001583	missense	165918			AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.528G>T	3.37:g.196214300C>A	ENSP00000320898:p.Glu176Asp		197698697	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	37	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.784725	0.70222	.	.	ENSG00000163961	ENST00000318037	T	0.10860	2.83	5.41	-1.32	0.09201	.	0.000000	0.56097	D	0.000022	T	0.27629	0.0679	M	0.80183	2.485	0.43782	D	0.996314	D	0.76494	0.999	P	0.62885	0.908	T	0.05194	-1.0900	10	0.66056	D	0.02	-12.0857	12.4329	0.55583	0.0:0.5338:0.0:0.4662	.	176	Q8IYW5	RN168_HUMAN	D	176	ENSP00000320898:E176D	ENSP00000320898:E176D	E	-	3	2	RNF168	197698697	0.986000	0.35501	0.846000	0.33378	0.956000	0.61745	0.474000	0.22148	-0.340000	0.08388	-0.238000	0.12139	GAG		0.453	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		A	196214300	C	A	196214300	3	1	64	1	0	0	0	0	1	0	0	0	13496	680	24	2	1203	2	RNF168	3	196214300	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	17292747	196214300	1808130	15	20431										
CRMP1	1400	broad.mit.edu	37	chr4	5862769	5862769	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tcactgatcatcgtggtcccGcccaccagtgccgccctggt	10	17	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr4:5862769G>A	ENST00000397890.2	-	3	511	c.297C>T	c.(295-297)ggC>ggT	p.G99G	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.G213G|CRMP1_ENST00000512574.1_Silent_p.G97G	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	99					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.G213G(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TCGTGGTCCCGCCCACCAGTG	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	4											91	83	86					4																	5862769		2203	4300	6503	5913670	SO:0001819	synonymous_variant	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.297C>T	4.37:g.5862769G>A			5913670	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																				0.577	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5862769	G	A	5862769	2	1	64	1	0	0	0	0	0	0	0	1	3896	1074	38	1		1	CRMP1	4	5862769	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		5862769	185291507	16	20432										
LRRTM2	26045	broad.mit.edu	37	chr5	138208732	138208732	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tctttgtatggcagctgctgAcacttgcactgtccataacc	8	12	1	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr5:138208732A>C	ENST00000274711.6	-	2	1896	c.1518T>G	c.(1516-1518)tgT>tgG	p.C506W	CTNNA1_ENST00000540387.1_5'Flank|LRRTM2_ENST00000521094.2_Missense_Mutation_p.C67W|LRRTM2_ENST00000523537.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000520400.1_Intron|LRRTM2_ENST00000518785.1_3'UTR|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000518825.1_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	506					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.C506W(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GCAGCTGCTGACACTTGCACT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											167	161	163					5																	138208732		1905	4129	6034	138236631	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.1518T>G	5.37:g.138208732A>C	ENSP00000274711:p.Cys506Trp		138236631	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611738	0.28712	.	.	ENSG00000146006	ENST00000521094;ENST00000274711	T	0.51325	0.71	5.79	2.19	0.27852	.	0.000000	0.85682	D	0.000000	T	0.48804	0.1520	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.83275	0.984;0.996	T	0.33317	-0.9873	10	0.33141	T	0.24	.	8.9717	0.35910	0.7878:0.0:0.2122:0.0	.	372;506	B7Z4G4;O43300	.;LRRT2_HUMAN	W	67;506	ENSP00000274711:C506W	ENSP00000274711:C506W	C	-	3	2	LRRTM2	138236631	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.039000	0.41193	0.469000	0.27268	0.533000	0.62120	TGT		0.373	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			C	138208732	A	C	138208732	3	2	64	1	0	0	0	0	1	0	0	0	9069	273	10	4	36	4	LRRTM2	5	138208732	Missense_Mutation	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09		138208732	42706528	17	20433										
CYFIP2	26999	broad.mit.edu	37	chr5	156751064	156751064	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aacagtccttcttcttcacaCatctgctcaacatcagtggt	5	13	6	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr5:156751064C>T	ENST00000521420.1	+	15	1820	c.1729C>T	c.(1729-1731)Cat>Tat	p.H577Y	CYFIP2_ENST00000318218.6_Missense_Mutation_p.H628Y|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000522463.1_Missense_Mutation_p.H407Y|CYFIP2_ENST00000541131.1_Missense_Mutation_p.H528Y|CYFIP2_ENST00000435847.2_Missense_Mutation_p.H302Y|CYFIP2_ENST00000520960.1_3'UTR|CYFIP2_ENST00000377576.3_Missense_Mutation_p.H603Y|CYFIP2_ENST00000347377.6_Missense_Mutation_p.H603Y					cytoplasmic FMR1 interacting protein 2									p.H628Y(2)		breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTCTTCACACATCTGCTCAA	0.552																																																2	Substitution - Missense(2)	large_intestine(2)	5											85	82	83					5																	156751064		2016	4178	6194	156683642	SO:0001583	missense	26999			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1729C>T	5.37:g.156751064C>T	ENSP00000430904:p.His577Tyr		156683642		Missense_Mutation	SNP	ENST00000521420.1	37		.	.	.	.	.	.	.	.	.	.	C	9.790	1.177791	0.21787	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03;2.03;2.03	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.21062	0.0507	N	0.04355	-0.22	0.80722	D	1	B;B;B;B;B;P	0.40180	0.027;0.009;0.014;0.007;0.0;0.705	B;B;B;B;B;P	0.55785	0.016;0.042;0.02;0.014;0.001;0.784	T	0.03221	-1.1059	10	0.05833	T	0.94	-34.3135	20.2963	0.98556	0.0:1.0:0.0:0.0	.	467;407;577;603;603;628	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	Y	628;407;577;603;603;528;302	ENSP00000325817:H628Y;ENSP00000428009:H407Y;ENSP00000430904:H577Y;ENSP00000313567:H603Y;ENSP00000366799:H603Y;ENSP00000444645:H528Y;ENSP00000403793:H302Y	ENSP00000325817:H628Y	H	+	1	0	CYFIP2	156683642	1.000000	0.71417	0.830000	0.32933	0.935000	0.57460	7.776000	0.85560	2.813000	0.96785	0.655000	0.94253	CAT		0.552	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156751064	C	T	156751064	3	4	64	1	0	0	0	0	1	0	0	0	4144	478	17	3	1865	3	CYFIP2	5	156751064	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	18542332	156751064	24164196	18	20434										
ODZ2	57451	broad.mit.edu	37	chr5	167617454	167617454	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	atcattcagcagggccagacGgattggcccgcagtgaagtc	13	11	2	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr5:167617454G>A	ENST00000518659.1	+	14	2721	c.2682G>A	c.(2680-2682)acG>acA	p.T894T	TENM2_ENST00000403607.2_Silent_p.T718T|CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000520394.1_Silent_p.T662T|TENM2_ENST00000519204.1_Silent_p.T773T|TENM2_ENST00000545108.1_Silent_p.T894T	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	894					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.T894T(1)|p.T727T(1)									AGGGCCAGACGGATTGGCCCG	0.572																																																2	Substitution - coding silent(2)	large_intestine(2)	5											51	51	51					5																	167617454		1958	4144	6102	167550032	SO:0001819	synonymous_variant	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.2682G>A	5.37:g.167617454G>A			167550032	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																					0.572	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167617454	G	A	167617454	2	1	64	1	0	0	0	0	0	0	0	1	10866	1103	39	1		1	ODZ2	5	167617454	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	10866390	167617454	13297806	19	20435										
GABBR1	2550	broad.mit.edu	37	chr6	29576462	29576462	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gcagctaaagccagtgagcaGcccacagcagtcaggttgtt	12	11	1	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:29576462G>A	ENST00000377034.4	-	16	2243	c.1908C>T	c.(1906-1908)ggC>ggT	p.G636G	GABBR1_ENST00000377012.4_Silent_p.G519G|GABBR1_ENST00000377016.4_Silent_p.G574G|GABBR1_ENST00000355973.3_Silent_p.G519G|GABBR1_ENST00000376977.3_3'UTR	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	636					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.G636G(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CCAGTGAGCAGCCCACAGCAG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	6											141	112	122					6																	29576462		1511	2709	4220	29684441	SO:0001819	synonymous_variant	2550			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1908C>T	6.37:g.29576462G>A			29684441	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																				0.562	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			A	29576462	G	A	29576462	2	1	64	1	0	0	0	0	0	0	0	1	6174	958	34	3		3	GABBR1	6	29576462	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		29576462	141538605	20	20436										
SKIV2L	6499	broad.mit.edu	37	chr6	31930842	31930842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ctgagtgccaccgtccccaaCgcccttgagtttgctgactg	10	15	0	3	rs377050125		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:31930842C>T	ENST00000375394.2	+	13	1490	c.1377C>T	c.(1375-1377)aaC>aaT	p.N459N	SKIV2L_ENST00000544581.1_Silent_p.N266N	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	459	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.N459N(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						CCGTCCCCAACGCCCTTGAGT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		0,3022		0,0,1511	124	94	105		1377	-9.7	0.1	6		105	1,5417		0,1,2708	no	coding-synonymous	SKIV2L	NM_006929.4		0,1,4219	TT,TC,CC		0.0185,0.0,0.0118		459/1247	31930842	1,8439	1511	2709	4220	32038821	SO:0001819	synonymous_variant	6499				CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1377C>T	6.37:g.31930842C>T			32038821	O15005|Q12902|Q15476|Q5ST66	Silent	SNP	ENST00000375394.2	37	CCDS4731.1																																																																																				0.582	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			T	31930842	C	T	31930842	2	4	64	1	0	0	0	0	0	0	0	1	14396	535	19	1		1	SKIV2L	6	31930842	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	2354380	31930842	139184225	21	20437										
PTK7	5754	broad.mit.edu	37	chr6	43111350	43111351	+	Missense_Mutation	DNP	GC	GC	CT													0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	cgaggagccagagatggaatGcctcaacggtgaggggccct					rs139041676		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:43111350_43111351GC>CT	ENST00000230419.4	+	14	2464_2465	c.2243_2244GC>CT	c.(2242-2244)tGC>tCT	p.C748S	PTK7_ENST00000349241.2_Missense_Mutation_p.C618S|PTK7_ENST00000352931.2_Missense_Mutation_p.C692S|PTK7_ENST00000481273.1_Missense_Mutation_p.C756S|PTK7_ENST00000345201.2_Missense_Mutation_p.C708S	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	748					actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.C748>?(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			GAGATGGAATGCCTCAACGGTG	0.658											OREG0017450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Complex(1)	large_intestine(1)	6																																								43219329	SO:0001583	missense	5754			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	Exception_encountered	6.37:g.43111350_43111351delinsCT	ENSP00000230419:p.Cys748Ser	913	43219328	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	DNP	ENST00000230419.4	37	CCDS4884.1																																																																																				0.658	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			CT	43111351	GC	CT	43111350	3	2	64	1	0	0	0	0	1	0	0	0	12800	1319	46	5	2297	5	PTK7	6	43111350	Missense_Mutation	DNP	GC	TCGA-AG-A00H-01A-01W-A00E-09	11180508	43111350	128003717	22	20438										
COL12A1	1303	broad.mit.edu	37	chr6	75851849	75851849	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agaagaggtctttgagggaaGtgctggtctctgatctgtcc	14	7	3	4			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:75851849G>C	ENST00000322507.8	-	27	5165	c.4856C>G	c.(4855-4857)aCt>aGt	p.T1619S	COL12A1_ENST00000345356.6_Missense_Mutation_p.T455S|COL12A1_ENST00000416123.2_Missense_Mutation_p.T1619S|COL12A1_ENST00000483888.2_Missense_Mutation_p.T1619S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1619	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.T1619S(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTTGAGGGAAGTGCTGGTCTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											206	202	203					6																	75851849		2131	4252	6383	75908569	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4856C>G	6.37:g.75851849G>C	ENSP00000325146:p.Thr1619Ser		75908569	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.633|6.633	0.485183|0.485183	0.12641|0.12641	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|T;T;T;T	.|0.57436	.|0.4;0.4;0.4;0.4	6.16|6.16	0.422|0.422	0.16457|0.16457	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.167788	.|0.49916	.|D	.|0.000131	T|T	0.33323|0.33323	0.0859|0.0859	M|M	0.82823|0.82823	2.61|2.61	0.09310|0.09310	N|N	0.999994|0.999994	.|B;B	.|0.25235	.|0.099;0.121	.|B;B	.|0.29663	.|0.102;0.105	T|T	0.44236|0.44236	-0.9341|-0.9341	5|10	.|0.22706	.|T	.|0.39	.|.	11.7829|11.7829	0.52026|0.52026	0.3836:0.0:0.6164:0.0|0.3836:0.0:0.6164:0.0	.|.	.|455;1619	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	Q|S	360|1619;1619;455;1619;1619	.|ENSP00000325146:T1619S;ENSP00000305147:T455S;ENSP00000412864:T1619S;ENSP00000421216:T1619S	.|ENSP00000325146:T1619S	H|T	-|-	3|2	2|0	COL12A1|COL12A1	75908569|75908569	0.070000|0.070000	0.21116|0.21116	0.039000|0.039000	0.18376|0.18376	0.442000|0.442000	0.32017|0.32017	0.419000|0.419000	0.21247|0.21247	-0.136000|-0.136000	0.11475|0.11475	-0.142000|-0.142000	0.14014|0.14014	CAC|ACT		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75851849	G	C	75851849	3	2	64	1	0	0	0	0	1	0	0	0	3675	1029	36	5	4495	5	COL12A1	6	75851849	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	32740499	75851849	95263218	23	20439										
GJA10	84694	broad.mit.edu	37	chr6	90605410	90605410	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tcttcatagtcactgcagagAcagtgaaggcagcatgagag	12	8	3	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:90605410A>T	ENST00000369352.1	+	1	1223	c.1223A>T	c.(1222-1224)gAc>gTc	p.D408V	Y_RNA_ENST00000517082.1_RNA	NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	396					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.D408V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		CACTGCAGAGACAGTGAAGGC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											79	77	77					6																	90605410		2203	4300	6503	90662131	SO:0001583	missense	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.1223A>T	6.37:g.90605410A>T	ENSP00000358358:p.Asp408Val		90662131	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.884251	0.33255	.	.	ENSG00000135355	ENST00000369352	D	0.97752	-4.52	5.39	-4.11	0.03928	.	1.727610	0.03040	N	0.153244	D	0.89283	0.6671	L	0.44542	1.39	0.09310	N	0.999998	B	0.12013	0.005	B	0.10450	0.005	D	0.84350	0.0532	10	0.30078	T	0.28	.	3.7367	0.08514	0.4261:0.1121:0.362:0.0999	.	408	Q969M2	CXA10_HUMAN	V	408	ENSP00000358358:D408V	ENSP00000358358:D408V	D	+	2	0	GJA10	90662131	0.001000	0.12720	0.173000	0.22940	0.845000	0.48019	0.069000	0.14552	-0.460000	0.07003	0.460000	0.39030	GAC		0.537	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90605410	A	T	90605410	3	4	64	1	0	0	0	0	1	0	0	0	6421	275	10	5	1225	5	GJA10	6	90605410	Missense_Mutation	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	14753561	90605410	80509657	24	20440										
C6orf204	387119	broad.mit.edu	37	chr6	118786676	118786676	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	cacacatctgacagctttttAgtgagtgtttctgtgctgtg	10	8	2	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:118786676A>G	ENST00000368491.3	-	13	2931	c.2310T>C	c.(2308-2310)acT>acC	p.T770T	CEP85L_ENST00000368488.5_Silent_p.T773T	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	770						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.T770T(1)									ACAGCTTTTTAGTGAGTGTTT	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	6											233	221	225					6																	118786676		1970	4166	6136	118893369	SO:0001819	synonymous_variant	387119			AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.2310T>C	6.37:g.118786676A>G			118893369	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Silent	SNP	ENST00000368491.3	37	CCDS43498.1																																																																																				0.393	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		G	118786676	A	G	118786676	2	3	64	1	0	0	0	0	0	0	0	1	2359	407	15	4		4	C6orf204	6	118786676	Silent	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	28181266	118786676	52328391	25	20441										
EYA4	2070	broad.mit.edu	37	chr6	133789714	133789714	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	attgtttcaggattatccatCctatacagcctttggccaaa	6	10	1	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr6:133789714C>A	ENST00000367895.5	+	11	1279	c.815C>A	c.(814-816)tCc>tAc	p.S272Y	EYA4_ENST00000355167.3_Missense_Mutation_p.S272Y|EYA4_ENST00000355286.6_Missense_Mutation_p.S249Y|EYA4_ENST00000452339.2_Missense_Mutation_p.S218Y|EYA4_ENST00000531901.1_Missense_Mutation_p.S272Y|EYA4_ENST00000431403.2_Missense_Mutation_p.S272Y|EYA4_ENST00000430974.2_Missense_Mutation_p.S218Y|EYA4_ENST00000525849.1_Missense_Mutation_p.S249Y	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	272					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)	p.S272Y(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GATTATCCATCCTATACAGCC	0.388																																					Melanoma(57;398 1237 3528 4702 7415)											1	Substitution - Missense(1)	large_intestine(1)	6											107	98	101					6																	133789714		2203	4299	6502	133831407	SO:0001583	missense	2070			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.815C>A	6.37:g.133789714C>A	ENSP00000356870:p.Ser272Tyr		133831407	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950617	0.73787	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.87406	0.6169	L	0.46741	1.465	0.80722	D	1	D;D;D;D;D;D	0.76494	0.997;0.999;0.998;0.998;0.998;0.997	D;D;D;D;D;D	0.74348	0.976;0.983;0.952;0.952;0.976;0.964	D	0.87935	0.2713	10	0.87932	D	0	-12.1799	19.7445	0.96247	0.0:1.0:0.0:0.0	.	272;218;218;249;272;272	F2Z2Y1;E7ESD5;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;.;EYA4_HUMAN	Y	218;218;272;272;249;272;249;272	ENSP00000395916:S218Y;ENSP00000388670:S218Y;ENSP00000356870:S272Y;ENSP00000347294:S272Y;ENSP00000347434:S249Y;ENSP00000432770:S272Y;ENSP00000433219:S249Y;ENSP00000404558:S272Y	ENSP00000347294:S272Y	S	+	2	0	EYA4	133831407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.739000	0.93911	0.655000	0.94253	TCC		0.388	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		A	133789714	C	A	133789714	3	1	64	1	0	0	0	0	1	0	0	0	5344	855	30	2	853	2	EYA4	6	133789714	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	15003038	133789714	37325353	26	20442										
MACC1	346389	broad.mit.edu	37	chr7	20199081	20199081	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	atttctgtcatgacttggctGaaaggatcctttcttacttc	7	9	3	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr7:20199081G>C	ENST00000400331.5	-	5	1211	c.903C>G	c.(901-903)ttC>ttG	p.F301L	MACC1_ENST00000589011.1_Missense_Mutation_p.F301L|MACC1_ENST00000332878.4_Missense_Mutation_p.F301L	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	301					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F301L(1)		endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						TGACTTGGCTGAAAGGATCCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	7											60	58	58					7																	20199081		2203	4300	6503	20165606	SO:0001583	missense	346389				CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.903C>G	7.37:g.20199081G>C	ENSP00000383185:p.Phe301Leu		20165606	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	G	8.423	0.846822	0.17034	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.08634	3.07;3.07	5.47	2.15	0.27550	.	0.638880	0.17736	N	0.163738	T	0.05273	0.0140	N	0.21583	0.68	0.26618	N	0.972717	B	0.02656	0.0	B	0.04013	0.001	T	0.40794	-0.9544	10	0.18710	T	0.47	-4.8921	8.5006	0.33156	0.2081:0.1268:0.6651:0.0	.	301	Q6ZN28	MACC1_HUMAN	L	301	ENSP00000383185:F301L;ENSP00000328410:F301L	ENSP00000328410:F301L	F	-	3	2	MACC1	20165606	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.931000	0.28871	0.652000	0.30806	0.585000	0.79938	TTC		0.418	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		C	20199081	G	C	20199081	3	2	64	1	0	0	0	0	1	0	0	0	9173	1281	45	5	1667	5	MACC1	7	20199081	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		20199081	138939582	27	20443										
CYP3A7	1551	broad.mit.edu	37	chr7	99315163	99315163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tcatacctccttgagttttcCgctggtgaatgttggagaca	10	9	1	3	rs139250712	byFrequency	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr7:99315163C>T	ENST00000336374.2	-	5	420	c.418G>A	c.(418-420)Gga>Aga	p.G140R		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	140					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.G140R(1)		autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TTGAGTTTTCCGCTGGTGAAT	0.408													C|||	3	0.000599042	0	0	5008	,	,		20102	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	7						C	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	93	83	87		418	4	1	7	dbSNP_134	87	0,8600		0,0,4300	no	missense	CYP3A7	NM_000765.3	125	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	140/504	99315163	2,13004	2203	4300	6503	99153099	SO:0001583	missense	1551			AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"Cytochrome P450s"	2640	protein-coding gene	gene with protein product		605340	"cytochrome P450, subfamily IIIA, polypeptide 7"			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.418G>A	7.37:g.99315163C>T	ENSP00000337450:p.Gly140Arg		99153099	A4D288|Q9H241	Missense_Mutation	SNP	ENST00000336374.2	37	CCDS5673.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929871	0.52759	4.54E-4	0.0	ENSG00000160870	ENST00000292414;ENST00000336374	T	0.68765	-0.35	3.98	3.98	0.46160	.	0.000000	0.85682	D	0.000000	D	0.84488	0.5483	M	0.93898	3.47	0.58432	D	0.999998	D	0.71674	0.998	D	0.65773	0.938	D	0.88940	0.3379	10	0.87932	D	0	.	13.8757	0.63651	0.0:1.0:0.0:0.0	.	140	P24462	CP3A7_HUMAN	R	140	ENSP00000337450:G140R	ENSP00000292414:G140R	G	-	1	0	CYP3A7	99153099	1.000000	0.71417	0.996000	0.52242	0.072000	0.16883	7.369000	0.79578	1.901000	0.55032	0.462000	0.41574	GGA		0.408	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			T	99315163	C	T	99315163	3	4	64	1	0	0	0	0	1	0	0	0	4187	661	23	1	1129	1	CYP3A7	7	99315163	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	79116082	99315163	59823500	28	20444										
ADAM2	2515	broad.mit.edu	37	chr8	39645654	39645654	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aaaacaagataagatgttttCcatcttaaaaatgtgtgtaa	6	4	1	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr8:39645654C>T	ENST00000265708.4	-	9	862	c.759G>A	c.(757-759)tgG>tgA	p.W253*	ADAM2_ENST00000521880.1_Nonsense_Mutation_p.W253*|ADAM2_ENST00000379853.2_Intron|ADAM2_ENST00000347580.4_Nonsense_Mutation_p.W234*	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	253	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.W253*(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		AAGATGTTTTCCATCTTAAAA	0.294																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											92	92	92					8																	39645654		2202	4286	6488	39764811	SO:0001587	stop_gained	2515			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.759G>A	8.37:g.39645654C>T	ENSP00000265708:p.Trp253*		39764811	P78326|Q9UQQ8	Nonsense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.194304	0.78902	.	.	ENSG00000104755	ENST00000347580;ENST00000265708;ENST00000521880	.	.	.	4.57	3.69	0.42338	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9245	0.47184	0.0:0.8092:0.1908:0.0	.	.	.	.	X	234;253;253	.	.	W	-	3	0	ADAM2	39764811	1.000000	0.71417	0.944000	0.38274	0.501000	0.33797	1.379000	0.34340	1.027000	0.39758	0.460000	0.39030	TGG		0.294	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		T	39645654	C	T	39645654	4	4	64	1	0	0	0	0	0	1	0	0	241	856	30	3	1496	3	ADAM2	8	39645654	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		39645654	106718368	29	20445										
KCNB2	9312	broad.mit.edu	37	chr8	73480241	73480241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gaacgagtatttctttgatcGgcatccaggagccttcactt	9	10	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr8:73480241G>A	ENST00000523207.1	+	2	860	c.272G>A	c.(271-273)cGg>cAg	p.R91Q		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	91					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R91Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TTCTTTGATCGGCATCCAGGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	8											82	81	81					8																	73480241		2203	4300	6503	73642795	SO:0001583	missense	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.272G>A	8.37:g.73480241G>A	ENSP00000430846:p.Arg91Gln		73642795	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122195	0.94429	.	.	ENSG00000182674	ENST00000523207	D	0.90069	-2.61	5.93	5.05	0.67936	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.497156	0.14582	U	0.310783	D	0.96367	0.8815	H	0.95260	3.645	0.48288	D	0.999627	D	0.76494	0.999	D	0.73708	0.981	D	0.96805	0.9592	10	0.87932	D	0	.	16.8752	0.86050	0.0:0.1284:0.8716:0.0	.	91	Q92953	KCNB2_HUMAN	Q	91	ENSP00000430846:R91Q	ENSP00000430846:R91Q	R	+	2	0	KCNB2	73642795	1.000000	0.71417	0.964000	0.40570	0.989000	0.77384	9.869000	0.99810	1.513000	0.48852	0.655000	0.94253	CGG		0.483	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73480241	G	A	73480241	3	1	64	1	0	0	0	0	1	0	0	0	8034	1116	39	1	274	1	KCNB2	8	73480241	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	33834587	73480241	72883781	30	20446										
ZFHX4	79776	broad.mit.edu	37	chr8	77766101	77766101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	caacatgcagtaccagtgtaAaaagtgcaatgtggttttcc	9	8	0	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr8:77766101A>G	ENST00000521891.2	+	10	7392	c.6944A>G	c.(6943-6945)aAa>aGa	p.K2315R	ZFHX4_ENST00000050961.6_Missense_Mutation_p.K2270R|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K2270R|ZFHX4_ENST00000518282.1_Missense_Mutation_p.K2289R	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.K2299R(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TACCAGTGTAAAAAGTGCAAT	0.383										HNSCC(33;0.089)																																						1	Substitution - Missense(1)	large_intestine(1)	8											104	101	102					8																	77766101		1956	4148	6104	77928656	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6944A>G	8.37:g.77766101A>G	ENSP00000430497:p.Lys2315Arg		77928656	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659011	0.67586	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.34	4.34	0.51931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.47455	U	0.000237	T	0.56659	0.2000	M	0.81497	2.545	0.58432	D	0.99999	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.80764	0.994;0.99;0.99	T	0.63708	-0.6576	10	0.72032	D	0.01	.	13.9681	0.64221	1.0:0.0:0.0:0.0	.	2270;2270;2315	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	R	2315;2299;2270;2270;2289	ENSP00000430497:K2315R;ENSP00000399605:K2270R;ENSP00000050961:K2270R;ENSP00000430848:K2289R	ENSP00000050961:K2270R	K	+	2	0	ZFHX4	77928656	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.087000	0.94110	1.956000	0.56807	0.528000	0.53228	AAA		0.383	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77766101	A	G	77766101	3	3	64	1	0	0	0	0	1	0	0	0	17674	14	1	4	6978	4	ZFHX4	8	77766101	Missense_Mutation	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	4285860	77766101	68597921	31	20447										
COL22A1	169044	broad.mit.edu	37	chr8	139626111	139626111	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gtcgcaaagcaaaactcaccGgtgggccccttggtccttgg	12	13	1	0	rs202129460		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr8:139626111G>A	ENST00000303045.6	-	56	4423	c.3977C>T	c.(3976-3978)cCg>cTg	p.P1326L	COL22A1_ENST00000435777.1_Splice_Site_p.P1306L|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1326	Collagen-like 13.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.P1326L(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			AAAACTCACCGGTGGGCCCCT	0.478										HNSCC(7;0.00092)																																						1	Substitution - Missense(1)	large_intestine(1)	8						G	LEU/PRO	0,4406		0,0,2203	132	139	137		3977	4.8	1	8		137	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	COL22A1	NM_152888.1	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	1326/1627	139626111	1,13005	2203	4300	6503	139695293	SO:0001630	splice_region_variant	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3978+1C>T	8.37:g.139626111G>A			139695293	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318246	0.40996	0.0	1.16E-4	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.96685	-4.09;-4.09	4.75	4.75	0.60458	.	0.283649	0.24999	N	0.033932	D	0.95274	0.8467	M	0.83852	2.665	0.53688	D	0.999976	P;P	0.45126	0.82;0.851	B;B	0.37047	0.155;0.24	D	0.95619	0.8679	10	0.66056	D	0.02	.	13.1056	0.59246	0.0:0.0:1.0:0.0	.	1306;1326	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	L	1326;1306;1019	ENSP00000303153:P1326L;ENSP00000387655:P1306L	ENSP00000303153:P1326L	P	-	2	0	COL22A1	139695293	1.000000	0.71417	0.978000	0.43139	0.989000	0.77384	3.017000	0.49615	2.446000	0.82766	0.555000	0.69702	CCG		0.478	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Missense_Mutation	A	139626111	G	A	139626111	5	1	64	1	0	0	0	0	0	0	1	0	3687	1130	39	1	943	1	COL22A1	8	139626111	Splice_Site	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	61860010	139626111	6737911	32	20448										
CNTLN	54875	broad.mit.edu	37	chr9	17457636	17457636	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aaaattcccaggtaacatttCcacggatacaagttacatca	5	10	1	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr9:17457636C>A	ENST00000380647.3	+	19	3313	c.3229C>A	c.(3229-3231)Cca>Aca	p.P1077T	CNTLN_ENST00000262360.5_Missense_Mutation_p.P1077T|CNTLN_ENST00000425824.1_Missense_Mutation_p.P1077T			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1077					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.P1077T(1)		breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GGTAACATTTCCACGGATACA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	9											76	75	76					9																	17457636		1816	4081	5897	17447636	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.3229C>A	9.37:g.17457636C>A	ENSP00000370021:p.Pro1077Thr		17447636	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348547	0.41599	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.18657	2.2;2.2;2.47	5.37	4.46	0.54185	.	.	.	.	.	T	0.32194	0.0821	M	0.67953	2.075	0.22933	N	0.998547	D;B;B	0.60575	0.988;0.004;0.004	P;B;B	0.58721	0.844;0.018;0.012	T	0.17410	-1.0370	9	0.18710	T	0.47	.	4.9122	0.13827	0.133:0.5886:0.1974:0.081	.	1077;1077;1077	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	T	1077	ENSP00000370021:P1077T;ENSP00000392798:P1077T;ENSP00000262360:P1077T	ENSP00000262360:P1077T	P	+	1	0	CNTLN	17447636	0.345000	0.24835	0.899000	0.35326	0.794000	0.44872	0.741000	0.26202	1.373000	0.46208	0.591000	0.81541	CCA		0.353	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17457636	C	A	17457636	3	1	64	1	0	0	0	0	1	0	0	0	3645	855	30	2	3333	2	CNTLN	9	17457636	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		17457636	123755795	33	20449										
NPR2	4882	broad.mit.edu	37	chr9	35792684	35792684	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ctcaagctgtaccatgacccCgacctgctgttaggtcccgg	10	15	1	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr9:35792684C>T	ENST00000342694.2	+	1	534	c.279C>T	c.(277-279)ccC>ccT	p.P93P		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	93					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.P93P(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ACCATGACCCCGACCTGCTGT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	9											118	107	110					9																	35792684		2203	4300	6503	35782684	SO:0001819	synonymous_variant	4882			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.279C>T	9.37:g.35792684C>T			35782684	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																				0.652	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35792684	C	T	35792684	2	4	64	1	0	0	0	0	0	0	0	1	10626	639	23	1		1	NPR2	9	35792684	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	18335048	35792684	105420747	34	20450										
APBA1	320	broad.mit.edu	37	chr9	72131035	72131035	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ggggtgtaaggcgaacggatGgtcctggttttcacctcctc	14	10	1	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr9:72131035G>A	ENST00000265381.4	-	2	1314	c.1092C>T	c.(1090-1092)acC>acT	p.T364T		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	364					axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.T364T(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						GCGAACGGATGGTCCTGGTTT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	9											139	106	117					9																	72131035		2203	4300	6503	71320855	SO:0001819	synonymous_variant	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1092C>T	9.37:g.72131035G>A			71320855	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	37	CCDS6630.1																																																																																				0.632	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72131035	G	A	72131035	2	1	64	1	0	0	0	0	0	0	0	1	756	1335	47	3		3	APBA1	9	72131035	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	36338351	72131035	69082396	35	20451										
C9orf171	389799	broad.mit.edu	37	chr9	135413023	135413023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ctttgatctgctgcagcaccGgtacctgcagctgtgggtac	12	12	1	1	rs375659445		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr9:135413023G>A	ENST00000343036.2	+	5	716	c.668G>A	c.(667-669)cGg>cAg	p.R223Q	C9orf171_ENST00000393216.2_Missense_Mutation_p.R187Q	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	223								p.R223Q(1)		large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						CTGCAGCACCGGTACCTGCAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	9						G	GLN/ARG	0,4406		0,0,2203	103	104	104		668	2.1	1	9		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	C9orf171	NM_207417.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	223/321	135413023	1,13005	2203	4300	6503	134402844	SO:0001583	missense	389799			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.668G>A	9.37:g.135413023G>A	ENSP00000343290:p.Arg223Gln		134402844	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257966	0.80246	0.0	1.16E-4	ENSG00000188523	ENST00000343036;ENST00000393216	T;T	0.22539	1.95;1.95	5.36	2.13	0.27403	.	0.236354	0.30920	N	0.008601	T	0.27524	0.0676	L	0.54323	1.7	0.27912	N	0.938567	P;D	0.69078	0.948;0.997	B;P	0.53549	0.322;0.729	T	0.06516	-1.0822	10	0.66056	D	0.02	.	7.2066	0.25911	0.4083:0.0:0.5917:0.0	.	187;223	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	Q	223;187	ENSP00000343290:R223Q;ENSP00000376909:R187Q	ENSP00000343290:R223Q	R	+	2	0	C9orf171	134402844	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.008000	0.29872	0.640000	0.30582	0.591000	0.81541	CGG		0.572	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		A	135413023	G	A	135413023	3	1	64	1	0	0	0	0	1	0	0	0	2476	1116	39	1	686	1	C9orf171	9	135413023	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	63281988	135413023	5800408	36	20452										
P4HA1	5033	broad.mit.edu	37	chr10	74810943	74810943	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gaagcagacttattgacatcTttttctttagccattatata	5	7	2	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr10:74810943T>C	ENST00000307116.2	-	7	884	c.768A>G	c.(766-768)aaA>aaG	p.K256K	P4HA1_ENST00000440381.1_Silent_p.K256K|P4HA1_ENST00000412021.2_Silent_p.K256K|P4HA1_ENST00000394890.2_Silent_p.K256K|P4HA1_ENST00000263556.3_Silent_p.K256K|P4HA1_ENST00000373008.2_Silent_p.K256K			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	256					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.K256K(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TATTGACATCTTTTTCTTTAG	0.373																																					Colon(147;367 2405 2662 52127)											2	Substitution - coding silent(2)	large_intestine(2)	10											139	139	139					10																	74810943		2203	4300	6503	74480949	SO:0001819	synonymous_variant	5033				CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.768A>G	10.37:g.74810943T>C			74480949	C9JL12|Q15082|Q15083|Q5VSQ5	Silent	SNP	ENST00000307116.2	37																																																																																					0.373	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		C	74810943	T	C	74810943	2	2	64	1	0	0	0	0	0	0	0	1	11387	1606	56	4		4	P4HA1	10	74810943	Silent	SNP	T	TCGA-AG-A00H-01A-01W-A00E-09		74810943	60723804	37	20453										
CNNM2	54805	broad.mit.edu	37	chr10	104679743	104679743	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tttgtcaaagacttggccttCgtggatcccgatgactgtac	10	10	1	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr10:104679743C>T	ENST00000369878.4	+	1	1694	c.1506C>T	c.(1504-1506)ttC>ttT	p.F502F	CNNM2_ENST00000369875.3_Silent_p.F502F|CNNM2_ENST00000433628.2_Silent_p.F502F	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	502	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)	p.F502F(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		ACTTGGCCTTCGTGGATCCCG	0.502																																																2	Substitution - coding silent(2)	large_intestine(2)	10											124	126	125					10																	104679743		2203	4300	6503	104669733	SO:0001819	synonymous_variant	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1506C>T	10.37:g.104679743C>T			104669733	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																				0.502	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104679743	C	T	104679743	2	4	64	1	0	0	0	0	0	0	0	1	3619	883	31	1		1	CNNM2	10	104679743	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	29868800	104679743	30855004	38	20454										
ADD3	120	broad.mit.edu	37	chr10	111883966	111883966	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tggctgaactcaccaaatacTtacatgaaagtgaatgtgcc	8	9	1	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr10:111883966T>C	ENST00000356080.4	+	10	1702	c.1335T>C	c.(1333-1335)acT>acC	p.T445T	ADD3_ENST00000277900.8_Silent_p.T445T|ADD3_ENST00000360162.3_Silent_p.T445T	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	445						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.T445T(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		CACCAAATACTTACATGAAAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	10											116	105	109					10																	111883966		2203	4300	6503	111873956	SO:0001819	synonymous_variant	120			U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1335T>C	10.37:g.111883966T>C			111873956	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Silent	SNP	ENST00000356080.4	37	CCDS7561.1																																																																																				0.438	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		C	111883966	T	C	111883966	2	2	64	1	0	0	0	0	0	0	0	1	306	1596	56	4		4	ADD3	10	111883966	Silent	SNP	T	TCGA-AG-A00H-01A-01W-A00E-09	7204223	111883966	23650781	39	20455										
ZRANB1	54764	broad.mit.edu	37	chr10	126655346	126655346	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tatgctagcaatattgcttaCagaggtaagtttggcgtttt	10	5	0	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr10:126655346C>G	ENST00000359653.4	+	2	1369	c.998C>G	c.(997-999)aCa>aGa	p.T333R		NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	333					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.T333R(1)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		ATATTGCTTACAGAGGTAAGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	10											179	151	160					10																	126655346		2203	4300	6503	126645336	SO:0001583	missense	54764			AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"Zinc fingers, RAN-binding domain containing", "OTU domain containing"	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.998C>G	10.37:g.126655346C>G	ENSP00000352676:p.Thr333Arg		126645336	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Missense_Mutation	SNP	ENST00000359653.4	37	CCDS7642.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380898	0.82792	.	.	ENSG00000019995	ENST00000359653	T	0.18016	2.24	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.65987	0.94	T	0.05162	-1.0902	10	0.72032	D	0.01	-2.6552	20.2789	0.98501	0.0:1.0:0.0:0.0	.	333	Q9UGI0	ZRAN1_HUMAN	R	333	ENSP00000352676:T333R	ENSP00000352676:T333R	T	+	2	0	ZRANB1	126645336	1.000000	0.71417	0.982000	0.44146	0.638000	0.38207	7.461000	0.80834	2.788000	0.95919	0.650000	0.86243	ACA		0.353	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		G	126655346	C	G	126655346	3	3	64	1	0	0	0	0	1	0	0	0	18261	478	17	5	1004	5	ZRANB1	10	126655346	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	14771380	126655346	8879401	40	20456										
OR52L1	338751	broad.mit.edu	37	chr11	6007249	6007249	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccatagacaagaggattgagCgcaggtggcatgaggagata	15	6	0	5			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr11:6007249C>T	ENST00000332249.4	-	1	966	c.912G>A	c.(910-912)gcG>gcA	p.A304A		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A289A(2)|p.A304A(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGGATTGAGCGCAGGTGGCA	0.473																																					Melanoma(121;653 1666 10547 22796 51255)											3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	11											66	67	67					11																	6007249		2073	4230	6303	5963825	SO:0001819	synonymous_variant	338751			AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.912G>A	11.37:g.6007249C>T			5963825	B2RPA6|Q6IFK9	Silent	SNP	ENST00000332249.4	37	CCDS44529.1																																																																																				0.473	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		T	6007249	C	T	6007249	2	4	64	1	0	0	0	0	0	0	0	1	11156	755	27	1		1	OR52L1	11	6007249	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		6007249	128999267	41	20457										
C11orf49	79096	broad.mit.edu	37	chr11	47176746	47176746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ggattgtgctcatggacgatGccatggactgcttgatgtct	13	8	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr11:47176746G>A	ENST00000278460.7	+	5	444	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	C11orf49_ENST00000536126.1_Missense_Mutation_p.A32T|C11orf49_ENST00000378618.2_Missense_Mutation_p.A129T|C11orf49_ENST00000543718.1_Missense_Mutation_p.A45T|C11orf49_ENST00000378615.3_Missense_Mutation_p.A129T|C11orf49_ENST00000395460.2_Missense_Mutation_p.A129T|C11orf49_ENST00000527268.1_3'UTR	NM_001003677.1|NM_024113.3	NP_001003677.1|NP_077018.1	Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49	129						nucleus (GO:0005634)		p.A129T(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						CATGGACGATGCCATGGACTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	11											341	284	304					11																	47176746		2201	4299	6500	47133322	SO:0001583	missense	79096			AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179			28720	protein-coding gene	gene with protein product							Standard	NM_001003677		Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000278460.7:c.385G>A	11.37:g.47176746G>A	ENSP00000278460:p.Ala129Thr		47133322	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	Missense_Mutation	SNP	ENST00000278460.7	37	CCDS7925.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678672	0.88542	.	.	ENSG00000149179	ENST00000536126;ENST00000278460;ENST00000378618;ENST00000395460;ENST00000378615;ENST00000543718;ENST00000526827	T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81	5.66	5.66	0.87406	.	0.050511	0.85682	D	0.000000	T	0.54791	0.1880	M	0.74881	2.28	0.80722	D	1	D;D;P;D;D	0.89917	1.0;1.0;0.865;0.998;0.999	D;D;B;D;D	0.87578	0.998;0.998;0.391;0.972;0.981	T	0.56105	-0.8034	10	0.72032	D	0.01	-17.9197	19.756	0.96291	0.0:0.0:1.0:0.0	.	45;45;129;129;129	F5H6E0;B4DEG1;E9PAX7;Q9H6J7-2;Q9H6J7	.;.;.;.;CK049_HUMAN	T	32;129;129;129;129;45;55	ENSP00000438207:A32T;ENSP00000278460:A129T;ENSP00000367881:A129T;ENSP00000378844:A129T;ENSP00000367878:A129T;ENSP00000437689:A45T;ENSP00000433707:A55T	ENSP00000278460:A129T	A	+	1	0	C11orf49	47133322	1.000000	0.71417	0.938000	0.37757	0.620000	0.37586	6.982000	0.76173	2.665000	0.90641	0.655000	0.94253	GCC		0.522	C11orf49-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391218.1	NM_024113		A	47176746	G	A	47176746	3	1	64	1	0	0	0	0	1	0	0	0	1649	1319	46	3	403	3	C11orf49	11	47176746	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	41169497	47176746	87829770	42	20458										
MS4A13	503497	broad.mit.edu	37	chr11	60285636	60285636	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aattaaaggagcctttggaaCgtatgaacctgtaacttaca	8	7	0	1	rs184120879	byFrequency	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr11:60285636C>T	ENST00000527948.1	+	2	638	c.80C>T	c.(79-81)aCg>aTg	p.T27M	MS4A13_ENST00000378186.2_Missense_Mutation_p.T27M|MS4A13_ENST00000437058.2_Missense_Mutation_p.T27M|MS4A13_ENST00000378185.2_Missense_Mutation_p.T27M			Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	72						integral component of membrane (GO:0016021)		p.T27M(1)		endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						GCCTTTGGAACGTATGAACCT	0.308													C|||	2	0.000399361	0	0	5008	,	,		18587	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											117	119	119					11																	60285636		2203	4300	6503	60042212	SO:0001583	missense	503497			AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000527948.1:c.80C>T	11.37:g.60285636C>T	ENSP00000432713:p.Thr27Met		60042212	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000527948.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	0.426	-0.905724	0.02453	.	.	ENSG00000204979	ENST00000378186;ENST00000378185;ENST00000437058;ENST00000527948	T;T;T;T	0.35789	2.17;1.84;1.41;1.29	5.65	-5.08	0.02929	.	0.752361	0.12237	N	0.486851	T	0.26231	0.0640	L	0.60455	1.87	0.09310	N	1	B;B;B	0.31548	0.28;0.28;0.328	B;B;B	0.28139	0.051;0.082;0.086	T	0.14008	-1.0488	10	0.87932	D	0	-4.4699	5.2451	0.15493	0.2808:0.3386:0.0:0.3805	.	27;27;27	Q5J8X5-3;Q5J8X5-2;Q5J8X5	.;.;M4A13_HUMAN	M	27	ENSP00000367428:T27M;ENSP00000367427:T27M;ENSP00000415535:T27M;ENSP00000432713:T27M	ENSP00000367427:T27M	T	+	2	0	MS4A13	60042212	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.604000	0.02076	-1.268000	0.02439	-2.086000	0.00376	ACG		0.308	MS4A13-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000395411.1	NM_001012417		T	60285636	C	T	60285636	3	4	64	1	0	0	0	0	1	0	0	0	9887	536	19	1	82	1	MS4A13	11	60285636	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	13108890	60285636	74720880	43	20459										
ALDH3B1	221	broad.mit.edu	37	chr11	67789269	67789269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	caaccagaaacagttccagcGgctgcgggcattgctgggct	13	12	0	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr11:67789269G>A	ENST00000539229.1	+	8	991	c.875G>A	c.(874-876)cGg>cAg	p.R292Q	ALDH3B1_ENST00000342456.6_Missense_Mutation_p.R256Q|ALDH3B1_ENST00000316367.6_Intron|ALDH3B1_ENST00000434449.1_3'UTR|ALDH3B1_ENST00000007633.8_Missense_Mutation_p.R292Q	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	293					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										CAGTTCCAGCGGCTGCGGGCA	0.642																																																0			11											52	62	59					11																	67789269		2200	4294	6494	67545845	SO:0001583	missense	221			U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.875G>A	11.37:g.67789269G>A	ENSP00000474034:p.Arg292Gln		67545845	A3FMP9|Q53XL5|Q8N515|Q96CK8	Missense_Mutation	SNP	ENST00000539229.1	37																																																																																					0.642	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694		A	67789269	G	A	67789269	3	1	64	1	0	0	0	0	1	0	0	0	499	1116	39	1	899	1	ALDH3B1	11	67789269	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	7503633	67789269	67217247	44	20460										
MMP7	4316	broad.mit.edu	37	chr11	102401356	102401356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccactgtagctcactcatgcCtcccgcctcctgaggcagcg	9	18	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr11:102401356C>T	ENST00000260227.4	-	1	128	c.76G>A	c.(76-78)Ggc>Agc	p.G26S		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	26					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G26S(1)		large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	TCACTCATGCCTCCCGCCTCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	61	65					11																	102401356		2203	4299	6502	101906566	SO:0001583	missense	4316			Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"matrix metalloproteinase 7 (matrilysin, uterine)"	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.76G>A	11.37:g.102401356C>T	ENSP00000260227:p.Gly26Ser		101906566	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	37	CCDS8317.1	.	.	.	.	.	.	.	.	.	.	C	9.762	1.170479	0.21621	.	.	ENSG00000137673	ENST00000260227	T	0.38240	1.15	4.98	4.05	0.47172	Peptidoglycan binding-like (1);	1.077680	0.07196	N	0.856659	T	0.31071	0.0785	L	0.57536	1.79	0.09310	N	1	B;P;B	0.37781	0.172;0.608;0.144	B;B;B	0.32980	0.041;0.156;0.024	T	0.17776	-1.0358	10	0.08179	T	0.78	1.0644	9.827	0.40919	0.0:0.8992:0.0:0.1008	.	26;26;26	B4DDW4;Q53GF1;P09237	.;.;MMP7_HUMAN	S	26	ENSP00000260227:G26S	ENSP00000260227:G26S	G	-	1	0	MMP7	101906566	0.005000	0.15991	0.027000	0.17364	0.405000	0.30901	0.740000	0.26188	2.482000	0.83794	0.655000	0.94253	GGC		0.547	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2			T	102401356	C	T	102401356	3	4	64	1	0	0	0	0	1	0	0	0	9697	681	24	3	751	3	MMP7	11	102401356	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	34612087	102401356	32605160	45	20461										
KRAS	3845	broad.mit.edu	37	chr12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	acttacctgtcttgtctttgCtgatgtttcaataaaaggaa	7	7	3	1	rs121913527		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	12											207	188	195					12																	25378562		2203	4300	6503	25269829	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr		25269829	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA		0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25378562	C	T	25378562	3	4	64	1	0	0	0	0	1	0	0	0	8459	797	28	3	262	3	KRAS	12	25378562	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		25378562	108473333	46	20462										
TMBIM4	51643	broad.mit.edu	37	chr12	66541706	66541706	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	accaacaactgccacagtcaGagcttccaacagcgtctaat	6	14	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr12:66541706G>C	ENST00000358230.3	-	4	448	c.328C>G	c.(328-330)Ctg>Gtg	p.L110V	TMBIM4_ENST00000556010.1_Missense_Mutation_p.L110V|TMBIM4_ENST00000286424.7_Missense_Mutation_p.L157V|TMBIM4_ENST00000542724.1_Missense_Mutation_p.L79V|TMBIM4_ENST00000398033.4_Missense_Mutation_p.L110V|TMBIM4_ENST00000539652.1_Missense_Mutation_p.L110V|TMBIM4_ENST00000544599.1_5'UTR	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	110					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)		p.L110V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		GCCACAGTCAGAGCTTCCAAC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	12											44	43	43					12																	66541706		1817	4081	5898	64827973	SO:0001583	missense	51643			AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.328C>G	12.37:g.66541706G>C	ENSP00000350965:p.Leu110Val		64827973	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	37	CCDS41805.1	.	.	.	.	.	.	.	.	.	.	G	9.667	1.145724	0.21288	.	.	ENSG00000155957	ENST00000556010;ENST00000358230;ENST00000426857;ENST00000286424;ENST00000398033;ENST00000539043;ENST00000539427;ENST00000542724	T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86	5.19	3.31	0.37934	.	0.457457	0.21973	N	0.066433	T	0.34861	0.0912	L	0.39326	1.205	0.36374	D	0.861509	B;B;B;B;B	0.16166	0.003;0.003;0.001;0.016;0.0	B;B;B;B;B	0.17979	0.02;0.011;0.02;0.009;0.012	T	0.24476	-1.0159	9	.	.	.	1.7822	8.175	0.31276	0.082:0.3025:0.6155:0.0	.	110;157;110;79;110	E7EWY5;G3XAA5;E7EQ00;G3V1M2;Q9HC24	.;.;.;.;TMBI4_HUMAN	V	110;110;110;157;110;110;156;79	ENSP00000451688:L110V;ENSP00000350965:L110V;ENSP00000286424:L157V;ENSP00000381114:L110V;ENSP00000441291:L79V	.	L	-	1	2	TMBIM4	64827973	0.998000	0.40836	0.995000	0.50966	0.815000	0.46073	0.646000	0.24797	0.663000	0.31027	0.585000	0.79938	CTG		0.323	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		C	66541706	G	C	66541706	3	2	64	1	0	0	0	0	1	0	0	0	16021	933	33	5	404	5	TMBIM4	12	66541706	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	41163144	66541706	67310189	47	20463										
SACS	26278	broad.mit.edu	37	chr13	23914840	23914840	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aaagagatcctttagtacttCtatatcagggtcaaagagtt	8	6	3	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr13:23914840C>G	ENST00000382292.3	-	9	3448	c.3175G>C	c.(3175-3177)Gaa>Caa	p.E1059Q	SACS_ENST00000382298.3_Missense_Mutation_p.E1059Q|SACS_ENST00000402364.1_Missense_Mutation_p.E309Q			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1059					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.E912Q(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTAGTACTTCTATATCAGGG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											111	114	113					13																	23914840		2203	4300	6503	22812840	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.3175G>C	13.37:g.23914840C>G	ENSP00000371729:p.Glu1059Gln		22812840	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399570	0.42512	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.89552	-2.37;-2.53;-2.37	5.96	4.21	0.49690	.	0.107333	0.64402	D	0.000006	D	0.82765	0.5108	L	0.34521	1.04	0.38552	D	0.949482	B	0.23735	0.09	B	0.20384	0.029	T	0.81300	-0.0995	10	0.49607	T	0.09	.	12.338	0.55079	0.0:0.8167:0.1185:0.0648	.	1059	Q9NZJ4	SACS_HUMAN	Q	1059;309;1059	ENSP00000371729:E1059Q;ENSP00000385844:E309Q;ENSP00000371735:E1059Q	ENSP00000371729:E1059Q	E	-	1	0	SACS	22812840	1.000000	0.71417	0.580000	0.28601	0.923000	0.55619	4.489000	0.60309	1.519000	0.48950	0.585000	0.79938	GAA		0.383	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23914840	C	G	23914840	3	3	64	1	0	0	0	0	1	0	0	0	13841	922	32	5	10568	5	SACS	13	23914840	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		23914840	91255038	48	20464										
NBEA	26960	broad.mit.edu	37	chr13	35770298	35770298	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tagtcaaaccaaaggcatcaAtgtgaaggaaatactgaaaa	8	6	2	2	rs368594146		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr13:35770298A>T	ENST00000400445.3	+	31	5759	c.5225A>T	c.(5224-5226)aAt>aTt	p.N1742I	NBEA_ENST00000379939.2_Missense_Mutation_p.N1739I|NBEA_ENST00000310336.4_Missense_Mutation_p.N1742I|NBEA_ENST00000540320.1_Missense_Mutation_p.N1742I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1742					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.N1742I(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AAAGGCATCAATGTGAAGGAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	13											85	83	83					13																	35770298		1889	4135	6024	34668298	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5225A>T	13.37:g.35770298A>T	ENSP00000383295:p.Asn1742Ile		34668298	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.341628	0.81911	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.63417	-0.04;-0.04;-0.03;-0.04	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.77260	0.4104	M	0.67397	2.05	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68765	0.96;0.959	T	0.79524	-0.1768	10	0.72032	D	0.01	.	16.179	0.81887	1.0:0.0:0.0:0.0	.	1742;1739	Q8NFP9;Q5T321	NBEA_HUMAN;.	I	1742;1742;1739;1742;369	ENSP00000440951:N1742I;ENSP00000383295:N1742I;ENSP00000369271:N1739I;ENSP00000308534:N1742I	ENSP00000308534:N1742I	N	+	2	0	NBEA	34668298	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	8.730000	0.91510	2.232000	0.73038	0.477000	0.44152	AAT		0.423	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35770298	A	T	35770298	3	4	64	1	0	0	0	0	1	0	0	0	10217	101	4	5	5347	5	NBEA	13	35770298	Missense_Mutation	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	11855458	35770298	79399580	49	20465										
EDNRB	1910	broad.mit.edu	37	chr13	78477673	78477673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	actcagcacagtgattcccaCagaggctttctgtatgaaag	9	10	2	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr13:78477673C>T	ENST00000334286.5	-	2	789	c.553G>A	c.(553-555)Gtg>Atg	p.V185M	EDNRB_ENST00000446573.1_Missense_Mutation_p.V185M|EDNRB_ENST00000377211.4_Missense_Mutation_p.V275M	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	185					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.V185M(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	GTGATTCCCACAGAGGCTTTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13	GRCh37	CM081580	EDNRB	M							75	72	73					13																	78477673		2203	4300	6503	77375674	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.553G>A	13.37:g.78477673C>T	ENSP00000335311:p.Val185Met		77375674	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.884180	0.91814	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.72167	-0.63;-0.63;-0.63	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82848	0.5126	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;0.991;1.0	D;D;D	0.81914	0.991;0.937;0.995	D	0.83797	0.0234	10	0.87932	D	0	-18.3762	19.6906	0.95999	0.0:1.0:0.0:0.0	.	185;275;185	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	M	275;185;185	ENSP00000366416:V275M;ENSP00000403401:V185M;ENSP00000335311:V185M	ENSP00000335311:V185M	V	-	1	0	EDNRB	77375674	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	7.484000	0.81180	2.627000	0.88993	0.650000	0.86243	GTG		0.433	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			T	78477673	C	T	78477673	3	4	64	1	0	0	0	0	1	0	0	0	4931	478	17	3	920	3	EDNRB	13	78477673	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	42707375	78477673	36692205	50	20466										
NAA30	122830	broad.mit.edu	37	chr14	57876139	57876139	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	caaataagtccgctttgaaaCtttatgaaaatcttggtttt	6	6	1	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr14:57876139C>G	ENST00000556492.1	+	5	1148	c.994C>G	c.(994-996)Ctt>Gtt	p.L332V	NAA30_ENST00000555166.1_Missense_Mutation_p.L74V|NAA30_ENST00000554703.1_3'UTR	NM_001011713.2	NP_001011713.2	Q147X3	NAA30_HUMAN	N(alpha)-acetyltransferase 30, NatC catalytic subunit	332	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				metabolic process (GO:0008152)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)	peptide alpha-N-acetyltransferase activity (GO:0004596)	p.L332V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	13						CGCTTTGAAACTTTATGAAAA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	14											78	75	76					14																	57876139		2203	4300	6503	56945892	SO:0001583	missense	122830			AK092674	CCDS32088.1	14q22.2	2010-05-07	2010-01-14	2010-01-14		ENSG00000139977	2.3.1.88	"N(alpha)-acetyltransferase subunits"	19844	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 35", "N-acetyltransferase 12", "N-acetyltransferase 12 (GCN5-related, putative)"	C14orf35, NAT12		19660095	Standard	NM_001011713		Approved	FLJ35355, MAK3, Mak3p	uc001xcx.4	Q147X3		ENST00000556492.1:c.994C>G	14.37:g.57876139C>G	ENSP00000452521:p.Leu332Val		56945892	Q0IIN2	Missense_Mutation	SNP	ENST00000556492.1	37	CCDS32088.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.10|17.10	3.303408|3.303408	0.60195|0.60195	.|.	.|.	ENSG00000139977|ENSG00000139977	ENST00000555166;ENST00000556492;ENST00000395257|ENST00000298406	T;T|.	0.28454|.	1.61;1.61|.	5.04|5.04	5.04|5.04	0.67666|0.67666	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83353|0.83353	0.5236|0.5236	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	D|.	0.60160|.	0.987|.	D|.	0.67900|.	0.954|.	D|D	0.85792|0.85792	0.1368|0.1368	10|5	0.87932|.	D|.	0|.	-3.9384|-3.9384	18.7312|18.7312	0.91735|0.91735	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	332|.	Q147X3|.	NAA30_HUMAN|.	V|K	74;332;295|143	ENSP00000450939:L74V;ENSP00000452521:L332V|.	ENSP00000298406:L332V|.	L|N	+|+	1|3	0|2	NAA30|NAA30	56945892|56945892	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.591000|5.591000	0.67536|0.67536	2.486000|2.486000	0.83907|0.83907	0.555000|0.555000	0.69702|0.69702	CTT|AAC		0.313	NAA30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412925.1	NM_001011713		G	57876139	C	G	57876139	3	3	64	1	0	0	0	0	1	0	0	0	10152	565	20	5	1008	5	NAA30	14	57876139	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		57876139	49473401	51	20467										
TGM5	9333	broad.mit.edu	37	chr15	43531101	43531101	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	taaaattgccaacagaactcGtgtcctggtgaagcttctgc	9	10	1	2	rs140691294		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr15:43531101G>T	ENST00000220420.5	-	9	1266	c.1259C>A	c.(1258-1260)aCg>aAg	p.T420K	TGM5_ENST00000349114.4_Missense_Mutation_p.T338K	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	420					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T420K(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	AACAGAACTCGTGTCCTGGTG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	15											188	149	163					15																	43531101		2202	4299	6501	41318393	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1259C>A	15.37:g.43531101G>T	ENSP00000220420:p.Thr420Lys		41318393	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176291	0.57692	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.66099	-0.19;-0.19	5.55	5.55	0.83447	.	0.504943	0.19830	N	0.105102	T	0.71576	0.3356	L	0.39514	1.22	0.41761	D	0.989711	D;D	0.71674	0.969;0.998	P;D	0.63793	0.904;0.918	T	0.73917	-0.3831	10	0.87932	D	0	-16.5279	17.0051	0.86391	0.0:0.0:1.0:0.0	.	338;420	O43548-2;O43548	.;TGM5_HUMAN	K	420;338;419	ENSP00000220420:T420K;ENSP00000220419:T338K	ENSP00000220420:T420K	T	-	2	0	TGM5	41318393	1.000000	0.71417	0.923000	0.36655	0.113000	0.19764	5.198000	0.65147	2.620000	0.88729	0.563000	0.77884	ACG		0.493	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43531101	G	T	43531101	3	4	64	1	0	0	0	0	1	0	0	0	15872	1145	40	2	923	2	TGM5	15	43531101	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		43531101	59000291	52	20468										
LONP2	83752	broad.mit.edu	37	chr16	48295390	48295390	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tatctcaggtactttagaagAtgaagatgaagatgaagata	10	3	1	8			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr16:48295390A>G	ENST00000285737.4	+	5	872	c.779A>G	c.(778-780)gAt>gGt	p.D260G	LONP2_ENST00000535754.1_Missense_Mutation_p.D216G	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal									p.D260G(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ACTTTAGAAGATGAAGATGAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	16											153	152	152					16																	48295390		2200	4300	6500	46852891	SO:0001583	missense	83752			AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.779A>G	16.37:g.48295390A>G	ENSP00000285737:p.Asp260Gly		46852891		Missense_Mutation	SNP	ENST00000285737.4	37	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.513586	0.44763	.	.	ENSG00000102910	ENST00000285737;ENST00000535754;ENST00000416006	T;T	0.33438	1.41;1.43	5.88	5.88	0.94601	.	0.377476	0.32624	N	0.005843	T	0.30696	0.0773	L	0.43152	1.355	0.44006	D	0.996711	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04373	-1.0956	10	0.87932	D	0	-18.7683	16.2898	0.82742	1.0:0.0:0.0:0.0	.	216;260	B7ZKL7;Q86WA8	.;LONP2_HUMAN	G	260;216;216	ENSP00000285737:D260G;ENSP00000445426:D216G	ENSP00000285737:D260G	D	+	2	0	LONP2	46852891	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.630000	0.61297	2.250000	0.74265	0.482000	0.46254	GAT		0.348	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		G	48295390	A	G	48295390	3	3	64	1	0	0	0	0	1	0	0	0	8922	333	12	4	797	4	LONP2	16	48295390	Missense_Mutation	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09		48295390	42059363	53	20469										
CES1	1066	broad.mit.edu	37	chr16	55844459	55844459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccgggccacaatcacagatgGgacaccaaacatcacatctg	8	14	3	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr16:55844459G>A	ENST00000361503.4	-	11	1415	c.1285C>T	c.(1285-1287)Cca>Tca	p.P429S	CES1_ENST00000422046.2_Missense_Mutation_p.P428S|CES1_ENST00000360526.3_Missense_Mutation_p.P430S			P23141	EST1_HUMAN	carboxylesterase 1	429					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.P430S(1)							all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	ATCACAGATGGGACACCAAAC	0.517																																					NSCLC(162;1801 2756 42904 52896)											1	Substitution - Missense(1)	large_intestine(1)	16											176	181	180					16																	55844459		2198	4300	6498	54401960	SO:0001583	missense	1066			BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.1285C>T	16.37:g.55844459G>A	ENSP00000355193:p.Pro429Ser		54401960	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	18.50	3.637158	0.67130	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.71461	-0.57;-0.57;-0.57	4.69	4.69	0.59074	Carboxylesterase, type B (1);	0.000000	0.64402	D	0.000008	T	0.80979	0.4728	M	0.75447	2.3	0.47862	D	0.999538	D;D;P	0.63046	0.96;0.992;0.951	P;P;P	0.61592	0.827;0.891;0.735	T	0.83003	-0.0176	10	0.59425	D	0.04	.	13.1724	0.59606	0.0:0.0:1.0:0.0	.	428;429;430	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	S	430;429;428;294	ENSP00000353720:P430S;ENSP00000355193:P429S;ENSP00000390492:P428S	ENSP00000353720:P430S	P	-	1	0	CES1	54401960	1.000000	0.71417	0.426000	0.26672	0.020000	0.10135	3.285000	0.51716	2.182000	0.69389	0.456000	0.33151	CCA		0.517	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		A	55844459	G	A	55844459	3	1	64	1	0	0	0	0	1	0	0	0	3275	1232	43	3	434	3	CES1	16	55844459	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	7549069	55844459	34510294	54	20470										
TERF2IP	54386	broad.mit.edu	37	chr16	75690361	75690361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ggctacttccgccttcttagCgtctggtcagagagctgatg	12	11	3	2	rs367821647		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr16:75690361C>T	ENST00000300086.4	+	3	1149	c.1052C>T	c.(1051-1053)gCg>gTg	p.A351V		NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	351					negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A351V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						GCCTTCTTAGCGTCTGGTCAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	VAL/ALA	0,4396		0,0,2198	171	177	175		1052	2.3	1	16		175	1,8599	1.2+/-3.3	0,1,4299	no	missense	TERF2IP	NM_018975.3	64	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	benign	351/400	75690361	1,12995	2198	4300	6498	74247862	SO:0001583	missense	54386			AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.1052C>T	16.37:g.75690361C>T	ENSP00000300086:p.Ala351Val		74247862	B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	Missense_Mutation	SNP	ENST00000300086.4	37	CCDS32491.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714504	0.48622	0.0	1.16E-4	ENSG00000166848	ENST00000300086	T	0.41400	1.0	5.75	2.31	0.28768	.	0.377447	0.30528	N	0.009429	T	0.20251	0.0487	N	0.08118	0	0.26290	N	0.978138	B	0.23249	0.082	B	0.12837	0.008	T	0.14559	-1.0468	10	0.56958	D	0.05	-16.531	7.3858	0.26882	0.6076:0.3156:0.0767:0.0	.	351	Q9NYB0	TE2IP_HUMAN	V	351	ENSP00000300086:A351V	ENSP00000300086:A351V	A	+	2	0	TERF2IP	74247862	1.000000	0.71417	0.977000	0.42913	0.930000	0.56654	2.109000	0.41863	0.454000	0.26884	0.591000	0.81541	GCG		0.433	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975		T	75690361	C	T	75690361	3	4	64	1	0	0	0	0	1	0	0	0	15802	768	27	1	1062	1	TERF2IP	16	75690361	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	19845902	75690361	14664392	55	20471										
ALKBH5	54890	broad.mit.edu	37	chr17	18110226	18110226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gcctgtcaggaaacaacaggGaccctgctctgaaacccaag	10	13	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:18110226G>A	ENST00000399138.4	+	3	954	c.949G>A	c.(949-951)Gac>Aac	p.D317N	ALKBH5_ENST00000541285.1_5'UTR	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	317					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)	p.D317N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AAACAACAGGGACCCTGCTCT	0.567																																					Ovarian(166;154 1953 40235 46283 46309)											1	Substitution - Missense(1)	large_intestine(1)	17											176	182	180					17																	18110226		1935	4121	6056	18050951	SO:0001583	missense	54890			AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.949G>A	17.37:g.18110226G>A	ENSP00000382091:p.Asp317Asn		18050951	B4DVJ4|D3DXC6|Q9NXD6	Missense_Mutation	SNP	ENST00000399138.4	37	CCDS42272.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745487	0.49151	.	.	ENSG00000091542	ENST00000261650;ENST00000500385;ENST00000399138	.	.	.	5.56	5.56	0.83823	.	0.296096	0.37857	N	0.001902	T	0.36744	0.0978	N	0.19112	0.55	0.38740	D	0.953873	B	0.32160	0.358	B	0.26770	0.073	T	0.31998	-0.9923	9	0.31617	T	0.26	-14.2187	15.0521	0.71881	0.0:0.1416:0.8584:0.0	.	317	Q6P6C2-2	.	N	317;306;317	.	ENSP00000261650:D317N	D	+	1	0	ALKBH5	18050951	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.309000	0.51903	2.618000	0.88619	0.655000	0.94253	GAC		0.567	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		A	18110226	G	A	18110226	3	1	64	1	0	0	0	0	1	0	0	0	530	1174	41	3	959	3	ALKBH5	17	18110226	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		18110226	63084984	56	20472										
CCDC144NL	339184	broad.mit.edu	37	chr17	20799111	20799111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aagatcttccaggcggacatCgtgctggagctggtctaagg	14	9	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:20799111C>A	ENST00000327925.5	-	1	342	c.223G>T	c.(223-225)Gat>Tat	p.D75Y	RP11-344E13.3_ENST00000417232.2_RNA|RP11-344E13.3_ENST00000582324.1_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	75								p.D75Y(1)		large_intestine(3)|lung(3)|skin(1)	7						AGGCGGACATCGTGCTGGAGC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											70	84	79					17																	20799111		2203	4292	6495	20739703	SO:0001583	missense	339184				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.223G>T	17.37:g.20799111C>A	ENSP00000328054:p.Asp75Tyr		20739703		Missense_Mutation	SNP	ENST00000327925.5	37	CCDS32591.1	.	.	.	.	.	.	.	.	.	.	c	8.955	0.969182	0.18659	.	.	ENSG00000205212	ENST00000327925	T	0.24151	1.87	.	.	.	.	.	.	.	.	T	0.28764	0.0713	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.18304	-1.0341	7	0.66056	D	0.02	.	.	.	.	.	75	Q6NUI1	C144L_HUMAN	Y	75	ENSP00000328054:D75Y	ENSP00000328054:D75Y	D	-	1	0	CCDC144NL	20739703	0.065000	0.20965	0.002000	0.10522	0.047000	0.14425	0.160000	0.16462	-0.401000	0.07644	0.154000	0.16183	GAT		0.652	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306		A	20799111	C	A	20799111	3	1	64	1	0	0	0	0	1	0	0	0	2785	884	31	2	458	2	CCDC144NL	17	20799111	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	2688885	20799111	60396099	57	20473										
ACCN1	40	broad.mit.edu	37	chr17	32483463	32483463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gcccatacacgaagatgtggCggatgccatggagggtggag	17	8	0	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:32483463C>T	ENST00000359872.6	-	1	850	c.89G>A	c.(88-90)cGc>cAc	p.R30H		NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	30					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)	p.R30H(1)								Amiloride(DB00594)	GAAGATGTGGCGGATGCCATG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											45	52	50					17																	32483463		2200	4296	6496	29507576	SO:0001583	missense	40			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.89G>A	17.37:g.32483463C>T	ENSP00000352934:p.Arg30His		29507576	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537527	0.45176	.	.	ENSG00000108684	ENST00000359872	T	0.64991	-0.13	4.96	4.96	0.65561	.	.	.	.	.	T	0.69851	0.3157	L	0.45470	1.425	0.53005	D	0.999962	D	0.62365	0.991	P	0.60236	0.871	T	0.67968	-0.5533	9	0.37606	T	0.19	.	15.7471	0.77955	0.0:1.0:0.0:0.0	.	30	Q16515	ACCN1_HUMAN	H	30	ENSP00000352934:R30H	ENSP00000352934:R30H	R	-	2	0	ACCN1	29507576	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.647000	0.83462	2.559000	0.86315	0.655000	0.94253	CGC		0.627	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		T	32483463	C	T	32483463	3	4	64	1	0	0	0	0	1	0	0	0	128	768	27	1	2201	1	ACCN1	17	32483463	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	11684352	32483463	48711747	58	20474										
CSH1	1442	broad.mit.edu	37	chr17	61972821	61972821	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ccaggattggtgacccctggCgccaccctcacccccatcag	9	19	2	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:61972821C>T	ENST00000316193.8	-	4	598				CSH1_ENST00000453363.3_Intron|CSH1_ENST00000329882.8_Silent_p.A156A	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						TGACCCCTGGCGCCACCCTCA	0.567									Russell-Silver syndrome																																							0			17											73	75	74					17																	61972821		2194	4300	6494	59326553	SO:0001627	intron_variant	1442	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.456+11G>A	17.37:g.61972821C>T			59326553	P01243|Q0VDB1|Q14407	Silent	SNP	ENST00000316193.8	37	CCDS11649.1																																																																																				0.567	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		T	61972821	C	T	61972821	1	4	64	0	1	0	0	0	0	0	0	0	3946	755	27	1		1	CSH1	17	61972821	Intron	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	29489358	61972821	19222389	59	20475										
PRKAR1A	5573	broad.mit.edu	37	chr17	66518949	66518949	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agcaggcactcgtacagactCaagggaggatgagatttctc	12	9	2	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:66518949C>G	ENST00000589228.1	+	3	358	c.230C>G	c.(229-231)tCa>tGa	p.S77*	PRKAR1A_ENST00000536854.2_Nonsense_Mutation_p.S77*|PRKAR1A_ENST00000588188.2_Nonsense_Mutation_p.S77*|PRKAR1A_ENST00000358598.2_Nonsense_Mutation_p.S77*|PRKAR1A_ENST00000586397.1_Nonsense_Mutation_p.S77*|PRKAR1A_ENST00000392711.1_Nonsense_Mutation_p.S77*	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	77	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.S77*(2)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					CGTACAGACTCAAGGGAGGAT	0.498			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	17											84	81	82					17																	66518949		2203	4300	6503	64030544	SO:0001587	stop_gained	5573	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.230C>G	17.37:g.66518949C>G	ENSP00000464977:p.Ser77*		64030544	K7ER48|Q567S7	Nonsense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	C	38	7.031972	0.98013	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	.	.	.	5.96	5.96	0.96718	.	0.055972	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-23.3383	20.3866	0.98944	0.0:1.0:0.0:0.0	.	.	.	.	X	77	.	ENSP00000351410:S77X	S	+	2	0	PRKAR1A	64030544	1.000000	0.71417	0.961000	0.40146	0.861000	0.49209	7.818000	0.86416	2.826000	0.97356	0.650000	0.86243	TCA		0.498	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			G	66518949	C	G	66518949	4	3	64	1	0	0	0	0	0	1	0	0	12537	838	29	5	236	5	PRKAR1A	17	66518949	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	4546128	66518949	14676261	60	20476										
RAB37	326624	broad.mit.edu	37	chr17	72736994	72736994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tcctgtccggaaccttcataGccaccgtcggcatagacttc	8	15	1	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr17:72736994G>T	ENST00000392613.5	+	2	237	c.181G>T	c.(181-183)Gcc>Tcc	p.A61S	RAB37_ENST00000392614.4_Missense_Mutation_p.A66S|RAB37_ENST00000392612.3_Intron|RAB37_ENST00000392610.1_Missense_Mutation_p.A61S|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000340415.3_Intron|RAB37_ENST00000392615.5_Intron|RAB37_ENST00000528438.1_Missense_Mutation_p.A34S	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	61					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)	p.A61S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						AACCTTCATAGCCACCGTCGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	17											106	104	104					17																	72736994		2203	4300	6503	70248589	SO:0001583	missense	326624			BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"RAB, member RAS oncogene"	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.181G>T	17.37:g.72736994G>T	ENSP00000376389:p.Ala61Ser		70248589	A8MXF5|A8MYT0|Q8IWA7	Missense_Mutation	SNP	ENST00000392613.5	37	CCDS32722.1	.	.	.	.	.	.	.	.	.	.	G	9.308	1.054918	0.19907	.	.	ENSG00000172794	ENST00000528438;ENST00000392614;ENST00000392613;ENST00000533530;ENST00000392610	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.1	5.1	0.69264	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	N	0.05012	-0.13	0.80722	D	1	B;B	0.22604	0.072;0.033	B;B	0.27887	0.084;0.062	T	0.60954	-0.7160	10	0.02654	T	1	.	17.2957	0.87170	0.0:0.0:1.0:0.0	.	66;61	A8MYT0;Q96AX2	.;RAB37_HUMAN	S	34;66;61;61;61	ENSP00000432086:A34S;ENSP00000376390:A66S;ENSP00000376389:A61S;ENSP00000376387:A61S	ENSP00000376387:A61S	A	+	1	0	RAB37	70248589	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	7.309000	0.78937	2.386000	0.81285	0.561000	0.74099	GCC		0.597	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		T	72736994	G	T	72736994	3	4	64	1	0	0	0	0	1	0	0	0	12964	971	34	2	490	2	RAB37	17	72736994	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	6218045	72736994	8458216	61	20477										
MUC16	94025	broad.mit.edu	37	chr19	9067143	9067143	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agtgtggaaattcctgagtcGccatcgagtgtgttcctgcc	12	10	0	1	rs369202278		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr19:9067143G>A	ENST00000397910.4	-	3	20506	c.20303C>T	c.(20302-20304)gCg>gTg	p.A6768V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6770	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A6768V(2)|p.A2401V(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCCTGAGTCGCCATCGAGTG	0.483													g|||	1	0.000199681	8e-04	0	5008	,	,		22952	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	large_intestine(3)	19						G	VAL/ALA	2,4400	4.2+/-10.8	0,2,2199	242	239	240		20303	-4.1	0	19		240	1,8591	1.2+/-3.3	0,1,4295	no	missense	MUC16	NM_024690.2	64	0,3,6494	AA,AG,GG		0.0116,0.0454,0.0231	possibly-damaging	6768/14508	9067143	3,12991	2201	4296	6497	8928143	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20303C>T	19.37:g.9067143G>A	ENSP00000381008:p.Ala6768Val		8928143	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.799	-0.756034	0.03019	4.54E-4	1.16E-4	ENSG00000181143	ENST00000397910	T	0.20881	2.04	2.06	-4.13	0.03904	.	.	.	.	.	T	0.07638	0.0192	N	0.04508	-0.205	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.25082	-1.0142	8	0.87932	D	0	.	2.4153	0.04435	0.1704:0.4376:0.2467:0.1454	.	6768	B5ME49	.	V	6768	ENSP00000381008:A6768V	ENSP00000381008:A6768V	A	-	2	0	MUC16	8928143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.664000	0.00848	-3.322000	0.00187	-2.165000	0.00325	GCG		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9067143	G	A	9067143	3	1	64	1	0	0	0	0	1	0	0	0	10003	1087	38	1	23548	1	MUC16	19	9067143	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		9067143	50061840	62	20478										
FCGBP	8857	broad.mit.edu	37	chr19	40433293	40433293	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gtaggggtcataagtcacttCattccttatggcacctgtgc	10	10	3	0			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr19:40433293C>A	ENST00000221347.6	-	2	983	c.976G>T	c.(976-978)Gaa>Taa	p.E326*		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	326	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)		p.E326*(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			TAAGTCACTTCATTCCTTATG	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											59	57	58					19																	40433293		2203	4300	6503	45125133	SO:0001587	stop_gained	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.976G>T	19.37:g.40433293C>A	ENSP00000221347:p.Glu326*		45125133	O95784	Nonsense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.107475	0.37145	.	.	ENSG00000090920	ENST00000221347	.	.	.	4.36	-6.28	0.02020	.	1.918070	0.02669	N	0.108397	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	3.0838	0.06271	0.0995:0.1575:0.3074:0.4355	.	.	.	.	X	326	.	ENSP00000221347:E326X	E	-	1	0	FCGBP	45125133	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-2.828000	0.00745	-1.081000	0.03105	-0.727000	0.03589	GAA		0.562	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40433293	C	A	40433293	4	1	64	1	0	0	0	0	0	1	0	0	5797	835	29	2	15381	2	FCGBP	19	40433293	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	31366150	40433293	18695690	63	20479										
XRCC1	7515	broad.mit.edu	37	chr19	44051065	44051065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aagcttgggggcttcatctcCgctgccaccgctgtgagagg	14	12	2	1	rs371113463		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr19:44051065C>T	ENST00000262887.5	-	11	1811	c.1264G>A	c.(1264-1266)Gga>Aga	p.G422R	XRCC1_ENST00000543982.1_Missense_Mutation_p.G391R			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	422					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)	p.G422R(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				GCTTCATCTCCGCTGCCACCG	0.612								Other BER factors																																								1	Substitution - Missense(1)	large_intestine(1)	19						C	ARG/GLY	0,4406		0,0,2203	63	61	62		1264	5.2	0.1	19		62	1,8599	1.2+/-3.3	0,1,4299	no	missense	XRCC1	NM_006297.2	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	422/634	44051065	1,13005	2203	4300	6503	48742905	SO:0001583	missense	7515			M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.1264G>A	19.37:g.44051065C>T	ENSP00000262887:p.Gly422Arg		48742905	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	37	CCDS12624.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.246610	0.22796	0.0	1.16E-4	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982	T;T	0.02606	4.24;4.23	5.19	5.19	0.71726	.	0.679576	0.15363	N	0.266295	T	0.03739	0.0106	L	0.57536	1.79	0.18873	N	0.999982	P;B	0.46656	0.882;0.065	B;B	0.34824	0.19;0.01	T	0.50030	-0.8875	10	0.17369	T	0.5	-13.0362	14.9526	0.71086	0.0:1.0:0.0:0.0	.	391;422	F5H8D7;P18887	.;XRCC1_HUMAN	R	436;422;391	ENSP00000262887:G422R;ENSP00000443671:G391R	ENSP00000262887:G422R	G	-	1	0	XRCC1	48742905	0.777000	0.28628	0.112000	0.21494	0.089000	0.18198	3.384000	0.52478	2.804000	0.96469	0.655000	0.94253	GGA		0.612	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297		T	44051065	C	T	44051065	3	4	64	1	0	0	0	0	1	0	0	0	17492	661	23	1	665	1	XRCC1	19	44051065	Missense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	3617772	44051065	15077918	64	20480										
NLRP7	199713	broad.mit.edu	37	chr19	55450436	55450436	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	acggggccaccaccaccttcGccagctcctcctcctgagac	8	20	0	1			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr19:55450436G>A	ENST00000590030.1	-	3	1791	c.1751C>T	c.(1750-1752)gCg>gTg	p.A584V	NLRP7_ENST00000448121.2_Missense_Mutation_p.A584V|NLRP7_ENST00000588756.1_Missense_Mutation_p.A584V|NLRP7_ENST00000328092.5_Missense_Mutation_p.A584V|NLRP7_ENST00000340844.2_Missense_Mutation_p.A584V|NLRP7_ENST00000592784.1_Missense_Mutation_p.A584V|NLRP7_ENST00000446217.1_Missense_Mutation_p.A612V			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	584							ATP binding (GO:0005524)	p.A584V(3)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CACCACCTTCGCCAGCTCCTC	0.493																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	19											77	73	75					19																	55450436		2203	4300	6503	60142248	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1751C>T	19.37:g.55450436G>A	ENSP00000465520:p.Ala584Val		60142248	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.134757	0.00338	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	1.92	-0.316	0.12743	.	0.288824	0.18777	N	0.131456	T	0.16896	0.0406	N	0.05306	-0.075	0.09310	N	1	B;B;B;B	0.17667	0.007;0.007;0.007;0.023	B;B;B;B	0.09377	0.001;0.002;0.002;0.004	T	0.28004	-1.0057	10	0.02654	T	1	.	5.1222	0.14865	0.794:0.0:0.206:0.0	.	612;584;584;584	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	V	584;584;584;612;351	ENSP00000329568:A584V;ENSP00000409137:A584V;ENSP00000339491:A584V;ENSP00000414273:A612V	ENSP00000329568:A584V	A	-	2	0	NLRP7	60142248	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.136000	0.15974	-0.148000	0.11234	-1.263000	0.01449	GCG		0.493	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55450436	G	A	55450436	3	1	64	1	0	0	0	0	1	0	0	0	10513	1087	38	1	1394	1	NLRP7	19	55450436	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	11399371	55450436	3678547	65	20481										
C20orf186	149954	broad.mit.edu	37	chr20	31670792	31670792	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tgctctccactcggccctgaGagaggtgcccttgggtaaag	13	12	1	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr20:31670792G>A	ENST00000375483.3	+	2	155	c.155G>A	c.(154-156)aGa>aAa	p.R52K		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	52						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.R13K(1)									TCGGCCCTGAGAGAGGTGCCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	20											109	95	99					20																	31670792		2203	4300	6503	31134453	SO:0001583	missense	149954			AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.155G>A	20.37:g.31670792G>A	ENSP00000364632:p.Arg52Lys		31134453	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	g	11.33	1.607313	0.28623	.	.	ENSG00000186191	ENST00000375483	T	0.01015	5.44	3.41	3.41	0.39046	.	0.000000	0.33732	U	0.004601	T	0.01800	0.0057	L	0.29908	0.895	0.22435	N	0.999102	P	0.44690	0.841	P	0.54210	0.745	T	0.46219	-0.9207	10	0.87932	D	0	-8.2401	10.1934	0.43041	0.0:0.0:1.0:0.0	.	52	P59827	BPIB4_HUMAN	K	52	ENSP00000364632:R52K	ENSP00000364632:R52K	R	+	2	0	BPIFB4	31134453	1.000000	0.71417	0.999000	0.59377	0.425000	0.31504	2.477000	0.45180	1.729000	0.51567	0.306000	0.20318	AGA		0.607	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		A	31670792	G	A	31670792	3	1	64	1	0	0	0	0	1	0	0	0	2104	942	33	3	161	3	C20orf186	20	31670792	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09		31670792	31354728	66	20482										
CSE1L	1434	broad.mit.edu	37	chr20	47682749	47682749	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gttgaagatgaaccaaacaaAatttgtgaagccgatcgagt	10	6	0	4			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr20:47682749A>G	ENST00000262982.2	+	4	372	c.249A>G	c.(247-249)aaA>aaG	p.K83K	CSE1L_ENST00000396192.3_Silent_p.K83K|CSE1L_ENST00000542325.1_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	83	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)	p.K83K(1)		breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AACCAAACAAAATTTGTGAAG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	20											81	76	78					20																	47682749		2203	4300	6503	47116156	SO:0001819	synonymous_variant	1434			U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.249A>G	20.37:g.47682749A>G			47116156	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	37	CCDS13412.1																																																																																				0.398	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47682749	A	G	47682749	2	3	64	1	0	0	0	0	0	0	0	1	3936	11	1	4		4	CSE1L	20	47682749	Silent	SNP	A	TCGA-AG-A00H-01A-01W-A00E-09	16011957	47682749	15342771	67	20483										
KCNB1	3745	broad.mit.edu	37	chr20	47990218	47990218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	actggcacccagagctccccGccagcccacttctggggctg	11	18	1	1	rs554351105		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr20:47990218G>A	ENST00000371741.4	-	2	2045	c.1879C>T	c.(1879-1881)Cgg>Tgg	p.R627W		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	627					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)	p.R627W(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	AGAGCTCCCCGCCAGCCCACT	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		15901	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											30	32	31					20																	47990218		2203	4300	6503	47423625	SO:0001583	missense	3745			AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1879C>T	20.37:g.47990218G>A	ENSP00000360806:p.Arg627Trp		47423625	Q14193	Missense_Mutation	SNP	ENST00000371741.4	37	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	G	14.86	2.660566	0.47572	.	.	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.23950	1.88	5.7	3.68	0.42216	.	1.383220	0.04370	N	0.358880	T	0.37156	0.0993	L	0.43152	1.355	0.34369	D	0.691791	D	0.56968	0.978	P	0.49301	0.606	T	0.37709	-0.9694	10	0.72032	D	0.01	.	14.4842	0.67606	0.0:0.0:0.591:0.409	.	627	Q14721	KCNB1_HUMAN	W	627;582	ENSP00000360806:R627W	ENSP00000360806:R627W	R	-	1	2	KCNB1	47423625	0.329000	0.24696	1.000000	0.80357	0.915000	0.54546	0.798000	0.27014	1.410000	0.46936	-0.152000	0.13540	CGG		0.612	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		A	47990218	G	A	47990218	3	1	64	1	0	0	0	0	1	0	0	0	8033	1086	38	1	701	1	KCNB1	20	47990218	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	307469	47990218	15035302	68	20484										
PHACTR3	116154	broad.mit.edu	37	chr20	58416497	58416497	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ttaagagacagaaaaattctGatacgattcagtgattacgt	8	5	2	4			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr20:58416497G>A	ENST00000371015.1	+	11	1961	c.1494G>A	c.(1492-1494)ctG>ctA	p.L498L	PHACTR3_ENST00000361300.4_Silent_p.L387L|PHACTR3_ENST00000359926.3_Silent_p.L495L|PHACTR3_ENST00000395636.2_Silent_p.L457L|PHACTR3_ENST00000541461.1_Silent_p.L457L|PHACTR3_ENST00000355648.4_Silent_p.L457L|PHACTR3_ENST00000395639.4_Silent_p.L387L	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	498	Required for PP1CA binding and inhibition of PP1 activity.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.L498L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			GAAAAATTCTGATACGATTCA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	20											90	85	87					20																	58416497		2203	4300	6503	57849892	SO:0001819	synonymous_variant	116154			AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1494G>A	20.37:g.58416497G>A			57849892	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Silent	SNP	ENST00000371015.1	37	CCDS13480.1																																																																																				0.403	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		A	58416497	G	A	58416497	2	1	64	1	0	0	0	0	0	0	0	1	11842	1277	45	3		3	PHACTR3	20	58416497	Silent	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	10426279	58416497	4609023	69	20485										
CRYBB2	1415	broad.mit.edu	37	chr22	25625450	25625450	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	tatgaaaaccccaacttcacCgggaagaagatggaaatcat	8	9	2	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr22:25625450C>T	ENST00000398215.2	+	5	525	c.354C>T	c.(352-354)acC>acT	p.T118T		NM_000496.2	NP_000487.1	P43320	CRBB2_HUMAN	crystallin, beta B2	118	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		identical protein binding (GO:0042802)|structural constituent of eye lens (GO:0005212)|structural molecule activity (GO:0005198)	p.T118T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	10						CCAACTTCACCGGGAAGAAGA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	22											43	33	37					22																	25625450		2201	4279	6480	23955450	SO:0001819	synonymous_variant	1415				CCDS13831.1	22q11.23	2008-06-10			ENSG00000244752	ENSG00000244752			2398	protein-coding gene	gene with protein product		123620		CCA2, CRYB2A, CRYB2		9158139, 8224918	Standard	XM_006724141		Approved		uc003abp.1	P43320	OTTHUMG00000150905	ENST00000398215.2:c.354C>T	22.37:g.25625450C>T			23955450	Q9UCM8	Silent	SNP	ENST00000398215.2	37	CCDS13831.1																																																																																				0.547	CRYBB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320350.1	NM_000496		T	25625450	C	T	25625450	2	4	64	1	0	0	0	0	0	0	0	1	3917	639	23	1		1	CRYBB2	22	25625450	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		25625450	25679116	70	20486										
EFCAB6	64800	broad.mit.edu	37	chr22	43950938	43950938	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	gccttgggagaggtaggcggCgggcctttgggcattttctc	17	9	1	1	rs142712637		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chr22:43950938C>T	ENST00000262726.7	-	27	3712	c.3459G>A	c.(3457-3459)ccG>ccA	p.P1153P	EFCAB6_ENST00000461800.1_5'UTR|EFCAB6_ENST00000396231.2_Silent_p.P1001P	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1153					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.P1153P(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AGGTAGGCGGCGGGCCTTTGG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	22						C	,	1,4405	2.1+/-5.4	0,1,2202	74	69	71		3459,3003	-9.8	0	22	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EFCAB6	NM_022785.3,NM_198856.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	1153/1502,1001/1350	43950938	1,13005	2203	4300	6503	42282271	SO:0001819	synonymous_variant	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3459G>A	22.37:g.43950938C>T			42282271	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	37	CCDS14049.1																																																																																				0.527	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43950938	C	T	43950938	2	4	64	1	0	0	0	0	0	0	0	1	4950	755	27	1		1	EFCAB6	22	43950938	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	18325488	43950938	7353628	71	20487										
NLGN4X	57502	broad.mit.edu	37	chrX	5811130	5811130	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	ctgcagagacatgatctcttCgttctggatgtgagcgatat	11	8	2	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chrX:5811130C>A	ENST00000381095.3	-	6	2806	c.2179G>T	c.(2179-2181)Gaa>Taa	p.E727*	NLGN4X_ENST00000381092.1_Nonsense_Mutation_p.E727*|NLGN4X_ENST00000538097.1_Nonsense_Mutation_p.E727*|NLGN4X_ENST00000275857.6_Nonsense_Mutation_p.E727*|NLGN4X_ENST00000381093.2_Nonsense_Mutation_p.E747*	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	727					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.E727*(1)|p.E727K(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						ATGATCTCTTCGTTCTGGATG	0.552																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(2)	X											156	116	130					X																	5811130		2203	4300	6503	5821130	SO:0001587	stop_gained	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.2179G>T	X.37:g.5811130C>A	ENSP00000370485:p.Glu727*		5821130	Q6UX10|Q9ULG0	Nonsense_Mutation	SNP	ENST00000381095.3	37	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	C	41	8.696672	0.98918	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	.	.	.	3.82	3.82	0.43975	.	0.489617	0.15194	N	0.275364	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.222	0.65833	0.0:1.0:0.0:0.0	.	.	.	.	X	727;747;727;727;727	.	ENSP00000275857:E727X	E	-	1	0	NLGN4X	5821130	1.000000	0.71417	0.906000	0.35671	0.071000	0.16799	6.528000	0.73807	1.508000	0.48769	0.513000	0.50165	GAA		0.552	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5811130	C	A	5811130	4	1	64	1	0	0	0	0	0	1	0	0	10495	893	31	2	275	2	NLGN4X	23	5811130	Nonsense_Mutation	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09		5811130	149459430	72	20488										
PHKA2	5256	broad.mit.edu	37	chrX	18923928	18923928	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	agaatatggtgcaggagattTttcatatcgaaagggctgag	13	4	1	3			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chrX:18923928T>C	ENST00000379942.4	-	26	3521	c.2856A>G	c.(2854-2856)aaA>aaG	p.K952K		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	952					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.K952K(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					GCAGGAGATTTTTCATATCGA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	X											164	148	153					X																	18923928		2203	4300	6503	18833849	SO:0001819	synonymous_variant	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.2856A>G	X.37:g.18923928T>C			18833849	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Silent	SNP	ENST00000379942.4	37	CCDS14190.1																																																																																				0.448	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		C	18923928	T	C	18923928	2	2	64	1	0	0	0	0	0	0	0	1	11875	1838	64	4		4	PHKA2	23	18923928	Silent	SNP	T	TCGA-AG-A00H-01A-01W-A00E-09	13112798	18923928	136346632	73	20489										
FAM47B	170062	broad.mit.edu	37	chrX	34962201	34962201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	cctgaagcctcccaagactcGtcgggtgtccagtctctgcc	10	16	1	2			TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chrX:34962201G>A	ENST00000329357.5	+	1	1289	c.1253G>A	c.(1252-1254)cGt>cAt	p.R418H		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	418								p.R418H(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						CCCAAGACTCGTCGGGTGTCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	61	63					X																	34962201		2202	4300	6502	34872122	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1253G>A	X.37:g.34962201G>A	ENSP00000328307:p.Arg418His		34872122	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	G	2.596	-0.294170	0.05568	.	.	ENSG00000189132	ENST00000329357	T	0.16457	2.34	0.158	-0.317	0.12736	.	.	.	.	.	T	0.16257	0.0391	M	0.78049	2.395	0.09310	N	1	B	0.31174	0.311	B	0.24974	0.057	T	0.22034	-1.0228	8	0.46703	T	0.11	.	.	.	.	.	418	Q8NA70	FA47B_HUMAN	H	418	ENSP00000328307:R418H	ENSP00000328307:R418H	R	+	2	0	FAM47B	34872122	0.039000	0.19947	0.002000	0.10522	0.003000	0.03518	-0.809000	0.04510	-1.095000	0.03050	-1.093000	0.02169	CGT		0.562	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34962201	G	A	34962201	3	1	64	1	0	0	0	0	1	0	0	0	5589	1145	40	1	1255	1	FAM47B	23	34962201	Missense_Mutation	SNP	G	TCGA-AG-A00H-01A-01W-A00E-09	16038273	34962201	120308359	74	20490										
F8	2157	broad.mit.edu	37	chrX	154158723	154158723	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.08	6	1	0.728731161886242	3.09710743801653	0.28810301748991	0.619909502262444	1	0	aagaatagcatcttaaagaaCgacatatctggattttgtgc	8	6	2	2	rs200593763		TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A00H-01A-01W-A00E-09	TCGA-AG-A00H-10A-01W-A00E-09	g.chrX:154158723C>T	ENST00000360256.4	-	14	3542	c.3342G>A	c.(3340-3342)tcG>tcA	p.S1114S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1114	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.S1114S(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCTTAAAGAACGACATATCTG	0.413																																																2	Substitution - coding silent(2)	large_intestine(2)	X						T		0,3835		0,0,1632,571	72	67	69		3342	-3	0	X		69	1,6724		0,1,2426,1871	no	coding-synonymous	F8	NM_000132.3		0,1,4058,2442	TT,TC,CC,C		0.0149,0.0,0.0095		1114/2352	154158723	1,10559	2203	4298	6501	153811917	SO:0001819	synonymous_variant	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3342G>A	X.37:g.154158723C>T			153811917	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																				0.413	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154158723	C	T	154158723	2	4	64	1	0	0	0	0	0	0	0	1	5363	523	19	1		1	F8	23	154158723	Silent	SNP	C	TCGA-AG-A00H-01A-01W-A00E-09	119196522	154158723	1111837	75	20491										
CCNL2	81669	hgsc.bcm.edu	37	chr1	1322887	1322892	+	In_Frame_Del	DEL	CGGTGG	CGGTGG	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcgctgcggggggcctgtctCggtggggagtcactcctgct					rs368716428|rs577659961		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CGGTGG	CGGTGG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:1322887_1322892delCGGTGG	ENST00000400809.3	-	11	1287_1292	c.1282_1287delCCACCG	c.(1282-1287)ccaccgdel	p.PP428del	CCNL2_ENST00000505849.1_5'UTR|CCNL2_ENST00000408952.5_In_Frame_Del_p.PP206del	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	428					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P428_P429delPP(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		GGGCCTGTCTCGGTGGGGAGTCACTC	0.626																																																1	Deletion - In frame(1)	large_intestine(1)	1																																								1312755	SO:0001651	inframe_deletion	81669			AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.1282_1287delCCACCG	1.37:g.1322887_1322892delCGGTGG	ENSP00000383611:p.Pro428_Pro429del		1312750	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	In_Frame_Del	DEL	ENST00000400809.3	37	CCDS30557.1																																																																																				0.626	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		-	1322892	CGGTGG	-	1322887	7	5	65	1	0	1	0	1	0	0	0	0	2938	871	31	0	279	0	CCNL2	1	1322887	In_Frame_Del	DEL	CGGTGG	TCGA-AG-A00Y-01A-02W-A005-10		1322887	247927734	1	20492										
ECE1	1889	hgsc.bcm.edu	37	chr1	21599259	21599259	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aaggtcccccagcgtgagtgGccatcagggactgggttggc	16	11	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:21599259G>A	ENST00000374893.6	-	4	500	c.426C>T	c.(424-426)ggC>ggT	p.G142G	ECE1_ENST00000357071.4_Silent_p.G130G|ECE1_ENST00000436918.2_Silent_p.G142G|ECE1_ENST00000415912.2_Silent_p.G126G|ECE1_ENST00000264205.6_Silent_p.G139G	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	142					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)	p.G142G(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGCGTGAGTGGCCATCAGGGA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											153	136	142					1																	21599259		2203	4300	6503	21471846	SO:0001819	synonymous_variant	1889			D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.426C>T	1.37:g.21599259G>A			21471846	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	37	CCDS215.1																																																																																				0.577	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		A	21599259	G	A	21599259	2	1	65	1	0	0	0	0	0	0	0	1	4900	1190	42	3		3	ECE1	1	21599259	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	20276372	21599259	227651362	2	20493										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27440563	27440563	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cccaccacggcaaagatcagGatggtgcccaggttttctgt	11	12	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:27440563G>C	ENST00000263980.3	-	2	1142	c.567C>G	c.(565-567)atC>atG	p.I189M	SLC9A1_ENST00000545949.1_Intron|SLC9A1_ENST00000374086.3_Missense_Mutation_p.I189M	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	189					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)	p.I189M(1)		central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				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)	CAAAGATCAGGATGGTGCCCA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	70	75					1																	27440563		2203	4300	6503	27313150	SO:0001583	missense	6548			M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.567C>G	1.37:g.27440563G>C	ENSP00000263980:p.Ile189Met		27313150	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	37	CCDS295.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123183	0.94429	.	.	ENSG00000090020	ENST00000263980;ENST00000374086	T;T	0.20200	2.09;2.09	5.8	5.8	0.92144	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.59770	0.2218	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	0.985;1.0	P;D	0.77557	0.897;0.99	T	0.69811	-0.5044	10	0.87932	D	0	.	19.0453	0.93018	0.0:0.0:1.0:0.0	.	189;189	P19634-2;P19634	.;SL9A1_HUMAN	M	189	ENSP00000263980:I189M;ENSP00000363199:I189M	ENSP00000263980:I189M	I	-	3	3	SLC9A1	27313150	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.700000	0.74619	2.751000	0.94390	0.655000	0.94253	ATC		0.607	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		C	27440563	G	C	27440563	3	2	65	1	0	0	0	0	1	0	0	0	14746	1164	41	5	1924	5	SLC9A1	1	27440563	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	5841304	27440563	221810058	3	20494										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66838194	66838195	+	Frame_Shift_Ins	INS	-	-	T													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggagaagtttcagtttgaacINStgactctcgatgaggaagat					rs34469235	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:66838194_66838195insT	ENST00000329654.4	+	17	2231_2232	c.2044_2045insT	c.(2044-2046)ctgfs	p.L682fs	PDE4B_ENST00000371045.5_Frame_Shift_Ins_p.L510fs|PDE4B_ENST00000423207.2_Frame_Shift_Ins_p.L667fs|PDE4B_ENST00000371049.3_Frame_Shift_Ins_p.L682fs|PDE4B_ENST00000480109.2_Frame_Shift_Ins_p.L449fs	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	682					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.T511fs*4(1)|p.T683fs*4(1)|p.T668fs*4(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	TCAGTTTGAACTGACTCTCGAT	0.495																																																3	Insertion - Frameshift(3)	large_intestine(3)	1																																								66610783	SO:0001589	frameshift_variant	5142			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.2045dupT	1.37:g.66838195_66838195dupT	ENSP00000332116:p.Leu682fs		66610782	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Frame_Shift_Ins	INS	ENST00000329654.4	37	CCDS632.1																																																																																				0.495	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		T	66838195	-	T	66838194	7	5	65	1	0	1	1	0	0	0	0	0	11671	564	20	0	2464	0	PDE4B	1	66838194	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	39397631	66838194	182412427	4	20495										
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90179160	90179160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cttatactggctgttctaccGttctctacgggaatattcct	7	11	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:90179160G>A	ENST00000370454.4	+	3	1286	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	344					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R344H(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CTGTTCTACCGTTCTCTACGG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											69	59	63					1																	90179160		2203	4300	6503	89951748	SO:0001583	missense	84230				CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1031G>A	1.37:g.90179160G>A	ENSP00000359483:p.Arg344His		89951748	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425343	0.62733	.	.	ENSG00000171488	ENST00000370454	T	0.52295	0.67	5.77	5.77	0.91146	.	0.146393	0.64402	D	0.000007	T	0.60945	0.2308	M	0.64404	1.975	0.53005	D	0.999963	D	0.89917	1.0	D	0.67725	0.953	T	0.58216	-0.7675	10	0.48119	T	0.1	.	19.9923	0.97371	0.0:0.0:1.0:0.0	.	344	Q8TDW0	LRC8C_HUMAN	H	344	ENSP00000359483:R344H	ENSP00000359483:R344H	R	+	2	0	LRRC8C	89951748	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.874000	0.87199	2.729000	0.93468	0.585000	0.79938	CGT		0.388	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		A	90179160	G	A	90179160	3	1	65	1	0	0	0	0	1	0	0	0	9052	1145	40	1	1037	1	LRRC8C	1	90179160	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	23340966	90179160	159071461	5	20496										
PALMD	54873	hgsc.bcm.edu	37	chr1	100152323	100152323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agaaactaaagtcaattgagCggacaacagaagacattata	8	6	1	4			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:100152323C>T	ENST00000263174.4	+	4	718	c.343C>T	c.(343-345)Cgg>Tgg	p.R115W	PALMD_ENST00000605497.1_Missense_Mutation_p.R115W	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	115					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)		p.R115W(2)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		GTCAATTGAGCGGACAACAGA	0.333																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	1											83	91	88					1																	100152323		2203	4300	6503	99924911	SO:0001583	missense	54873			AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.343C>T	1.37:g.100152323C>T	ENSP00000263174:p.Arg115Trp		99924911	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	37	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772301	0.69992	.	.	ENSG00000099260	ENST00000263174	T	0.17370	2.28	5.87	3.52	0.40303	.	0.191850	0.56097	D	0.000039	T	0.24547	0.0595	L	0.56769	1.78	0.34706	D	0.727288	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.984	T	0.08743	-1.0707	10	0.87932	D	0	-9.4698	13.0487	0.58942	0.735:0.2649:0.0:0.0	.	115;35	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	W	115	ENSP00000263174:R115W	ENSP00000263174:R115W	R	+	1	2	PALMD	99924911	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.301000	0.51842	0.545000	0.28902	-0.262000	0.10625	CGG		0.333	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		T	100152323	C	T	100152323	3	4	65	1	0	0	0	0	1	0	0	0	11442	759	27	1	357	1	PALMD	1	100152323	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	9973163	100152323	149098298	6	20497										
S1PR1	1901	hgsc.bcm.edu	37	chr1	101705672	101705672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccattatgtcttctggaaacGtcaactcttcttcctagaac	5	12	5	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:101705672G>A	ENST00000305352.6	+	2	1507	c.1132G>A	c.(1132-1134)Gtc>Atc	p.V378I		NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	378					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.V378I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						TTCTGGAAACGTCAACTCTTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											38	36	37					1																	101705672		2093	4143	6236	101478260	SO:0001583	missense	1901			M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate", "CD molecules"	3165	protein-coding gene	gene with protein product		601974	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.1132G>A	1.37:g.101705672G>A	ENSP00000305416:p.Val378Ile		101478260	D3DT66|Q9BYY4|Q9NYN8	Missense_Mutation	SNP	ENST00000305352.6	37	CCDS777.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830396	0.32329	.	.	ENSG00000170989	ENST00000305352	T	0.72051	-0.62	5.38	5.38	0.77491	.	0.207523	0.40640	N	0.001056	T	0.40398	0.1115	N	0.16478	0.41	0.36239	D	0.853157	B	0.06786	0.001	B	0.04013	0.001	T	0.34153	-0.9840	10	0.13470	T	0.59	.	19.1353	0.93426	0.0:0.0:1.0:0.0	.	378	P21453	S1PR1_HUMAN	I	378	ENSP00000305416:V378I	ENSP00000305416:V378I	V	+	1	0	S1PR1	101478260	0.994000	0.37717	1.000000	0.80357	0.973000	0.67179	2.153000	0.42282	2.524000	0.85096	0.305000	0.20034	GTC		0.532	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400		A	101705672	G	A	101705672	3	1	65	1	0	0	0	0	1	0	0	0	13830	1145	40	1	1134	1	S1PR1	1	101705672	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	1553349	101705672	147544949	7	20498										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380601	147380601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtgggccactacttcctgtaCgggttccggatcctgcctct	11	14	1	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:147380601C>T	ENST00000369235.1	+	1	519	c.519C>T	c.(517-519)taC>taT	p.Y173Y	GJA8_ENST00000240986.4_Silent_p.Y173Y			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	173					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)	p.Y173Y(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					ACTTCCTGTACGGGTTCCGGA	0.597																																					Melanoma(76;1255 1795 8195 52096)											2	Substitution - coding silent(2)	large_intestine(2)	1											107	101	103					1																	147380601		2203	4300	6503	145847225	SO:0001819	synonymous_variant	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.519C>T	1.37:g.147380601C>T			145847225	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																				0.597	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380601	C	T	147380601	2	4	65	1	0	0	0	0	0	0	0	1	6425	547	19	1		1	GJA8	1	147380601	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	45674929	147380601	101870020	8	20499										
KPRP	448834	hgsc.bcm.edu	37	chr1	152733396	152733396	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccagcactacgtccaacaccGcggccagttccccttcctcg	7	20	0	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:152733396G>T	ENST00000606109.1	+	1	1360	c.1332G>T	c.(1330-1332)ccG>ccT	p.P444P	KPRP_ENST00000368773.1_Silent_p.P444P			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	444	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.P444P(1)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCAACACCGCGGCCAGTTC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											173	173	173					1																	152733396		2203	4300	6503	151000020	SO:0001819	synonymous_variant	448834			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1332G>T	1.37:g.152733396G>T			151000020		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																				0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152733396	G	T	152733396	2	4	65	1	0	0	0	0	0	0	0	1	8457	1074	38	2		2	KPRP	1	152733396	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	5352795	152733396	96517225	9	20500										
APOA1BP	128240	hgsc.bcm.edu	37	chr1	156562358	156562358	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttcttcctagggctacgagCcaaccatctattaccccaaa	5	14	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:156562358C>G	ENST00000368235.3	+	4	455	c.412C>G	c.(412-414)Cca>Gca	p.P138A	APOA1BP_ENST00000368234.3_Missense_Mutation_p.P138A|APOA1BP_ENST00000368233.3_Missense_Mutation_p.P138A|APOA1BP_ENST00000467374.1_3'UTR	NM_144772.2	NP_658985.2			apolipoprotein A-I binding protein									p.P138A(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCTACGAGCCAACCATCTA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											173	173	173					1																	156562358		2203	4300	6503	154828982	SO:0001583	missense	128240			AJ315849	CCDS1145.1	1q21	2008-08-14			ENSG00000163382	ENSG00000163382			18453	protein-coding gene	gene with protein product	"apoA-I binding protein"	608862				11991719, 17533573	Standard	NM_144772		Approved	AIBP, MGC119143, MGC119144, MGC119145, YJEFN1	uc001fph.3	Q8NCW5	OTTHUMG00000033206	ENST00000368235.3:c.412C>G	1.37:g.156562358C>G	ENSP00000357218:p.Pro138Ala		154828982		Missense_Mutation	SNP	ENST00000368235.3	37	CCDS1145.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337500	0.60963	.	.	ENSG00000163382	ENST00000446584;ENST00000368234;ENST00000368235;ENST00000368233	T;T;T	0.39056	1.1;1.1;1.1	4.08	4.08	0.47627	YjeF-related protein, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	M	0.89030	3	0.80722	D	1	P;P;D	0.89917	0.738;0.927;1.0	P;P;D	0.97110	0.672;0.762;1.0	T	0.64262	-0.6449	10	0.30854	T	0.27	.	15.0102	0.71545	0.0:1.0:0.0:0.0	.	138;138;138	Q5T3I3;Q8NCW5;Q5T3I4	.;AIBP_HUMAN;.	A	156;138;138;138	ENSP00000357217:P138A;ENSP00000357218:P138A;ENSP00000357216:P138A	ENSP00000357216:P138A	P	+	1	0	APOA1BP	154828982	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	7.582000	0.82546	2.104000	0.64026	0.655000	0.94253	CCA		0.542	APOA1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081044.1	NM_144772		G	156562358	C	G	156562358	3	3	65	1	0	0	0	0	1	0	0	0	781	739	26	5	426	5	APOA1BP	1	156562358	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	3828962	156562358	92688263	10	20501										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157497673	157497673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccctgagggtgaggatggggCgagacactggaactgagaga	18	7	0	5	rs376321602		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:157497673C>T	ENST00000361835.3	-	9	1851	c.1694G>A	c.(1693-1695)cGc>cAc	p.R565H	FCRL5_ENST00000368190.3_Missense_Mutation_p.R565H|FCRL5_ENST00000356953.4_Missense_Mutation_p.R565H|FCRL5_ENST00000368191.3_Missense_Mutation_p.R480H	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	565					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.R565H(2)|p.R565P(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GAGGATGGGGCGAGACACTGG	0.527																																																3	Substitution - Missense(3)	ovary(1)|large_intestine(1)|kidney(1)	1						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	44	49	47		1694,1694	1.6	0.9	1		47	2,8598		0,2,4298	no	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	565/999,565/978	157497673	2,13004	2203	4300	6503	155764297	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1694G>A	1.37:g.157497673C>T	ENSP00000354691:p.Arg565His		155764297	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	7.816	0.716824	0.15306	0.0	2.33E-4	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191	T;T;T;T	0.03496	3.91;3.91;3.91;3.91	3.53	1.59	0.23543	.	0.445392	0.16880	N	0.195724	T	0.01523	0.0049	L	0.45352	1.415	0.80722	D	1	P;P;P;P	0.51057	0.514;0.941;0.783;0.783	B;B;B;B	0.43809	0.167;0.432;0.38;0.38	T	0.63152	-0.6701	10	0.30854	T	0.27	.	6.3384	0.21309	0.0:0.7603:0.0:0.2397	.	480;565;565;565	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9	.;.;.;FCRL5_HUMAN	H	565;565;565;480	ENSP00000354691:R565H;ENSP00000349434:R565H;ENSP00000357173:R565H;ENSP00000357174:R480H	ENSP00000349434:R565H	R	-	2	0	FCRL5	155764297	0.001000	0.12720	0.922000	0.36590	0.821000	0.46438	-2.375000	0.01071	0.293000	0.22520	0.650000	0.86243	CGC		0.527	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157497673	C	T	157497673	3	4	65	1	0	0	0	0	1	0	0	0	5817	768	27	1	1275	1	FCRL5	1	157497673	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	935315	157497673	91752948	11	20502										
CD5L	922	hgsc.bcm.edu	37	chr1	157804357	157804357	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttgttgcagcgtttttgagtCagtacagccctcccacatcc	8	13	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:157804357C>A	ENST00000368174.4	-	4	654	c.558G>T	c.(556-558)ctG>ctT	p.L186L	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	186	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.L186L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GTTTTTGAGTCAGTACAGCCC	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											97	87	91					1																	157804357		2203	4300	6503	156070981	SO:0001819	synonymous_variant	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.558G>T	1.37:g.157804357C>A			156070981	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	37	CCDS1171.1																																																																																				0.577	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157804357	C	A	157804357	2	1	65	1	0	0	0	0	0	0	0	1	3033	813	29	2		2	CD5L	1	157804357	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	306684	157804357	91446264	12	20503										
ASTN1	460	hgsc.bcm.edu	37	chr1	176833480	176833480	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctcagggtctgctcctcacaCgtcttcctgaggtcccggct	10	16	4	1	rs144824957	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:176833480C>T	ENST00000367654.3	-	23	4060	c.3849G>A	c.(3847-3849)acG>acA	p.T1283T	ASTN1_ENST00000367657.3_Intron|ASTN1_ENST00000361833.2_Silent_p.T1275T	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1283					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.T1275T(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GCTCCTCACACGTCTTCCTGA	0.582													C|||	9	0.00179712	0	0	5008	,	,		17840	0		0.001	False		,,,				2504	0.0082															1	Substitution - coding silent(1)	large_intestine(1)	1						C		2,4404	4.2+/-10.8	0,2,2201	126	121	123		3825	-9.2	0.6	1	dbSNP_134	123	34,8566	24.0+/-70.4	0,34,4266	no	coding-synonymous	ASTN1	NM_004319.1		0,36,6467	TT,TC,CC		0.3953,0.0454,0.2768		1275/1295	176833480	36,12970	2203	4300	6503	175100103	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3849G>A	1.37:g.176833480C>T			175100103	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.582	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176833480	C	T	176833480	2	4	65	1	0	0	0	0	0	0	0	1	1065	523	19	1		1	ASTN1	1	176833480	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	19029123	176833480	72417141	13	20504										
C4BPA	722	hgsc.bcm.edu	37	chr1	207318002	207318002	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tataagctgtctctggaaatTgaacaactggaactacagag	9	7	1	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:207318002T>A	ENST00000367070.3	+	12	1928	c.1734T>A	c.(1732-1734)atT>atA	p.I578I		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	578					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.I578I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						CTCTGGAAATTGAACAACTGG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	1											55	53	54					1																	207318002		2203	4300	6503	205384625	SO:0001819	synonymous_variant	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1734T>A	1.37:g.207318002T>A			205384625	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																				0.438	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			A	207318002	T	A	207318002	2	1	65	1	0	0	0	0	0	0	0	1	2255	1800	63	5		5	C4BPA	1	207318002	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	30484522	207318002	41932619	14	20505										
PLD5	200150	hgsc.bcm.edu	37	chr1	242277226	242277226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gctggagataggcaggtagtCcatgacagcgatgtacacat	13	8	0	2	rs201629512		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:242277226C>T	ENST00000536534.2	-	7	1277	c.1036G>A	c.(1036-1038)Gac>Aac	p.D346N	PLD5_ENST00000427495.1_Missense_Mutation_p.D284N|PLD5_ENST00000442594.2_Missense_Mutation_p.D254N			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	346						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.D254N(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GGCAGGTAGTCCATGACAGCG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											190	142	158					1																	242277226		2203	4300	6503	240343849	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1036G>A	1.37:g.242277226C>T	ENSP00000440896:p.Asp346Asn		240343849	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568102	0.86439	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.22945	1.93;1.93;1.93	5.48	5.48	0.80851	Phospholipase D/viral envelope (1);	0.000000	0.85682	D	0.000000	T	0.47322	0.1439	L	0.60455	1.87	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.984;0.989;0.984	T	0.17930	-1.0353	10	0.30854	T	0.27	-15.3805	17.1341	0.86734	0.0:1.0:0.0:0.0	.	254;346;284	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	N	284;254;346	ENSP00000401285:D284N;ENSP00000414188:D254N;ENSP00000440896:D346N	ENSP00000401285:D284N	D	-	1	0	PLD5	240343849	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	6.251000	0.72441	2.569000	0.86673	0.643000	0.83706	GAC		0.473	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		T	242277226	C	T	242277226	3	4	65	1	0	0	0	0	1	0	0	0	12080	855	30	3	590	3	PLD5	1	242277226	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	34959224	242277226	6973395	15	20506										
CNST	163882	hgsc.bcm.edu	37	chr1	246810608	246810608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agctgctctgcagcgctgaaGccacgttagcgctccacacc	10	16	1	1	rs369168079		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr1:246810608G>T	ENST00000366513.4	+	9	1374	c.1105G>T	c.(1105-1107)Gcc>Tcc	p.A369S	CNST_ENST00000366512.3_Missense_Mutation_p.A369S|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	369					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)	p.A369S(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						CAGCGCTGAAGCCACGTTAGC	0.582											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											83	85	84					1																	246810608		2203	4300	6503	244877231	SO:0001583	missense	163882			AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1105G>T	1.37:g.246810608G>T	ENSP00000355470:p.Ala369Ser	2468	244877231	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	G	4.396	0.073089	0.08485	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.16073	2.37;2.42	5.39	1.95	0.26073	.	0.735360	0.13405	N	0.390356	T	0.10508	0.0257	L	0.41356	1.27	0.09310	N	0.999997	B;B	0.23377	0.084;0.084	B;B	0.18561	0.022;0.022	T	0.38607	-0.9653	10	0.05721	T	0.95	5.7986	6.7202	0.23327	0.1696:0.0:0.6407:0.1896	.	369;369	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	S	369	ENSP00000355470:A369S;ENSP00000355469:A369S	ENSP00000355469:A369S	A	+	1	0	CNST	244877231	0.337000	0.24766	0.004000	0.12327	0.012000	0.07955	1.258000	0.32944	0.739000	0.32628	0.467000	0.42956	GCC		0.582	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		T	246810608	G	T	246810608	3	4	65	1	0	0	0	0	1	0	0	0	3640	971	34	2	1135	2	CNST	1	246810608	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	4533382	246810608	2440013	16	20507										
KLF11	8462	hgsc.bcm.edu	37	chr2	10186545	10186545	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cttccattctttatcgactcTggtaagaggaggtgggaggg	14	7	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:10186545T>A	ENST00000305883.1	+	2	473	c.311T>A	c.(310-312)cTg>cAg	p.L104Q	KLF11_ENST00000540845.1_Splice_Site_p.L87Q|KLF11_ENST00000535335.1_Splice_Site_p.L87Q	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	104					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.L104Q(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		TTATCGACTCTGGTAAGAGGA	0.502																																					Melanoma(56;431 1507 23687 50789)											1	Substitution - Missense(1)	large_intestine(1)	2											82	76	78					2																	10186545		2203	4300	6503	10103996	SO:0001630	splice_region_variant	8462			AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.312+1T>A	2.37:g.10186545T>A			10103996	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	37	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.579376	0.86645	.	.	ENSG00000172059	ENST00000401510;ENST00000305883;ENST00000448523;ENST00000540845;ENST00000440320;ENST00000535335	T;T;T;T;T;T	0.75154	-0.86;1.77;-0.91;1.78;-0.84;1.78	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.86180	0.5871	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88115	0.2828	10	0.87932	D	0	.	15.4155	0.74962	0.0:0.0:0.0:1.0	.	104	O14901	KLF11_HUMAN	Q	87;104;87;87;87;87	ENSP00000386058:L87Q;ENSP00000307023:L104Q;ENSP00000387866:L87Q;ENSP00000444690:L87Q;ENSP00000388263:L87Q;ENSP00000442722:L87Q	ENSP00000307023:L104Q	L	+	2	0	KLF11	10103996	1.000000	0.71417	0.994000	0.49952	0.901000	0.52897	7.593000	0.82686	2.038000	0.60285	0.379000	0.24179	CTG		0.502	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597	Missense_Mutation	A	10186545	T	A	10186545	5	1	65	1	0	0	0	0	0	0	1	0	8360	1594	55	5	317	5	KLF11	2	10186545	Splice_Site	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10		10186545	233012828	17	20508										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44051053	44051053	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccagcacgtgggcacttacaCagattcacagcgttcagcat	9	13	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:44051053C>A	ENST00000260645.1	-	9	1462	c.1323G>T	c.(1321-1323)ctG>ctT	p.L441L	ABCG5_ENST00000543989.1_Splice_Site_p.L46L|ABCG5_ENST00000405322.1_Splice_Site_p.L270L	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	441	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)	p.L441L(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	GGCACTTACACAGATTCACAG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	2											74	59	64					2																	44051053		2203	4300	6503	43904557	SO:0001630	splice_region_variant	64240			T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1324+1G>T	2.37:g.44051053C>A			43904557	Q2T9G2|Q96QZ2|Q96QZ3	Silent	SNP	ENST00000260645.1	37	CCDS1814.1																																																																																				0.507	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436	Silent	A	44051053	C	A	44051053	5	1	65	1	0	0	0	0	0	0	1	0	71	492	17	2	652	2	ABCG5	2	44051053	Splice_Site	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	33864508	44051053	199148320	18	20509										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012713	99012713	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tacagtctctactggtccacCttgacccttaccaccattgg	6	15	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:99012713C>A	ENST00000272602.2	+	7	1119	c.1080C>A	c.(1078-1080)acC>acA	p.T360T	CNGA3_ENST00000409937.1_Silent_p.T364T|CNGA3_ENST00000393504.1_Silent_p.T360T|CNGA3_ENST00000436404.2_Silent_p.T342T			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	360					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.T360T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						ACTGGTCCACCTTGACCCTTA	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	2											82	82	82					2																	99012713		2203	4300	6503	98379145	SO:0001819	synonymous_variant	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1080C>A	2.37:g.99012713C>A			98379145	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																				0.507	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	99012713	C	A	99012713	2	1	65	1	0	0	0	0	0	0	0	1	3604	668	24	2		2	CNGA3	2	99012713	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	54961660	99012713	144186660	19	20510										
IL1R2	7850	hgsc.bcm.edu	37	chr2	102642616	102642616	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	actacattgaagtgccattgAtttttgatcctgtcacaaga	7	8	1	4			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:102642616A>T	ENST00000332549.3	+	8	1160	c.931A>T	c.(931-933)Att>Ttt	p.I311F	IL1R2_ENST00000393414.2_Missense_Mutation_p.I311F|IL1R2_ENST00000485335.1_3'UTR	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	311	Ig-like C2-type 3.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.I311F(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						AGTGCCATTGATTTTTGATCC	0.358																																					Pancreas(106;189 1628 2302 5133 12295)											1	Substitution - Missense(1)	large_intestine(1)	2											129	125	126					2																	102642616		2203	4300	6503	102009048	SO:0001583	missense	7850			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.931A>T	2.37:g.102642616A>T	ENSP00000330959:p.Ile311Phe		102009048	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	A	18.96	3.733531	0.69189	.	.	ENSG00000115590	ENST00000332549;ENST00000393414	T;T	0.20738	2.05;2.05	5.95	0.486	0.16836	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.282439	0.34460	N	0.003957	T	0.30916	0.0780	M	0.63843	1.955	0.80722	D	1	D	0.69078	0.997	P	0.62649	0.905	T	0.06427	-1.0827	10	0.30854	T	0.27	.	5.0998	0.14753	0.6045:0.1447:0.2508:0.0	.	311	P27930	IL1R2_HUMAN	F	311	ENSP00000330959:I311F;ENSP00000377066:I311F	ENSP00000330959:I311F	I	+	1	0	IL1R2	102009048	1.000000	0.71417	0.926000	0.36857	0.958000	0.62258	0.623000	0.24447	0.076000	0.16826	0.533000	0.62120	ATT		0.358	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		T	102642616	A	T	102642616	3	4	65	1	0	0	0	0	1	0	0	0	7680	333	12	5	957	5	IL1R2	2	102642616	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	3629903	102642616	140556757	20	20511										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157184440	157184441	+	Frame_Shift_Ins	INS	-	-	TA													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcactgatcagactcaccggINSgggcgaagggggagagggct							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:157184440_157184441insTA	ENST00000339562.4	-	5	1442_1443	c.1080_1081insTA	c.(1078-1083)cccccgfs	p.P361fs	NR4A2_ENST00000426264.1_Frame_Shift_Ins_p.P298fs|NR4A2_ENST00000539077.1_Frame_Shift_Ins_p.P372fs|NR4A2_ENST00000429376.1_Frame_Shift_Ins_p.P298fs|NR4A2_ENST00000409108.2_Frame_Shift_Ins_p.P361fs|NR4A2_ENST00000409572.1_Frame_Shift_Ins_p.P361fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	361	Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.P361fs*3(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						AGACTCACCGGGGGCGAAGGGG	0.604																																																1	Insertion - Frameshift(1)	large_intestine(1)	2																																								156892687	SO:0001589	frameshift_variant	4929			X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.1080_1081insTA	2.37:g.157184440_157184441insTA	ENSP00000344479:p.Pro361fs		156892686	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Ins	INS	ENST00000339562.4	37	CCDS2201.1																																																																																				0.604	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			TA	157184441	-	TA	157184440	7	5	65	1	0	1	1	0	0	0	0	0	10664	1232	43	0	731	0	NR4A2	2	157184440	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	54541824	157184440	86014933	21	20512										
TTN	7273	hgsc.bcm.edu	37	chr2	179666973	179666973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggcggggatcgtcagtttagCgcggccatcgctaaaggaga	16	9	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:179666973C>T	ENST00000591111.1	-	3	411	c.187G>A	c.(187-189)Gct>Act	p.A63T	TTN_ENST00000589042.1_Missense_Mutation_p.A63T|TTN_ENST00000360870.5_Missense_Mutation_p.A63T|TTN_ENST00000342175.6_Missense_Mutation_p.A63T|TTN_ENST00000342992.6_Missense_Mutation_p.A63T|TTN_ENST00000359218.5_Missense_Mutation_p.A63T|TTN_ENST00000460472.2_Missense_Mutation_p.A63T			Q8WZ42	TITIN_HUMAN	titin	32675	Ig-like 1.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A63T(8)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCAGTTTAGCGCGGCCATCG	0.537																																																8	Substitution - Missense(8)	large_intestine(4)|NS(4)	2											121	107	112					2																	179666973		2203	4300	6503	179375218	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.187G>A	2.37:g.179666973C>T	ENSP00000465570:p.Ala63Thr		179375218	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.076214	0.76415	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50394	0.1613	N	0.12746	0.255	0.48762	D	0.999704	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.998	T	0.59204	-0.7498	9	0.87932	D	0	.	19.919	0.97077	0.0:1.0:0.0:0.0	.	63;63;63;63;63	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	63	ENSP00000343764:A63T;ENSP00000434586:A63T;ENSP00000340554:A63T;ENSP00000352154:A63T;ENSP00000354117:A63T	ENSP00000340554:A63T	A	-	1	0	TTN	179375218	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.818000	0.86416	2.707000	0.92482	0.655000	0.94253	GCT		0.537	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179666973	C	T	179666973	3	4	65	1	0	0	0	0	1	0	0	0	16775	768	27	1	111241	1	TTN	2	179666973	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	22482533	179666973	63532400	22	20513										
TNS1	7145	hgsc.bcm.edu	37	chr2	218679672	218679674	+	In_Frame_Del	DEL	AGA	AGA	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tcaggcttgtaccaatacttAgaagtgtcctggacaaactt					rs201496749		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	AGA	AGA	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr2:218679672_218679674delAGA	ENST00000171887.4	-	25	4830_4832	c.4378_4380delTCT	c.(4378-4380)tctdel	p.S1460del	TNS1_ENST00000430930.1_In_Frame_Del_p.S1439del|TNS1_ENST00000419504.1_In_Frame_Del_p.S1447del	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1460					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.S1460delS(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		ACCAATACTTAGAAGTGTCCTGG	0.522																																																1	Deletion - In frame(1)	large_intestine(1)	2																																								218387919	SO:0001651	inframe_deletion	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4378_4380delTCT	2.37:g.218679672_218679674delAGA	ENSP00000171887:p.Ser1460del		218387917	Q4ZG71|Q6IPI5	In_Frame_Del	DEL	ENST00000171887.4	37	CCDS2407.1																																																																																				0.522	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		-	218679674	AGA	-	218679672	7	5	65	1	0	1	0	1	0	0	0	0	16382	407	15	0	863	0	TNS1	2	218679672	In_Frame_Del	DEL	AGA	TCGA-AG-A00Y-01A-02W-A005-10	39012699	218679672	24519701	23	20514										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38518793	38518794	+	Frame_Shift_Ins	INS	-	-	C													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acaggctctgggcgtggggaINSggctgagacacgggagtgca							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:38518793_38518794insC	ENST00000352511.4	+	2	540_541	c.68_69insC	c.(67-72)gaggctfs	p.EA23fs		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	23					activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.E23fs*3(1)		lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		GGGCGTGGGGAGGCTGAGACAC	0.649																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								38493798	SO:0001589	frameshift_variant	93			X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	Exception_encountered	3.37:g.38518793_38518794insC	ENSP00000340361:p.Glu23fs		38493797	Q4VAV0	Frame_Shift_Ins	INS	ENST00000352511.4	37	CCDS2679.1																																																																																				0.649	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		C	38518794	-	C	38518793	7	5	65	1	0	1	1	0	0	0	0	0	224	304	11	0	74	0	ACVR2B	3	38518793	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10		38518793	159503637	24	20515										
MAP4	4134	hgsc.bcm.edu	37	chr3	47957778	47957778	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acatccttgcccagagccatTtctgtttctgatagtggaga	9	10	2	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:47957778T>C	ENST00000360240.6	-	7	2057	c.1539A>G	c.(1537-1539)gaA>gaG	p.E513E	MAP4_ENST00000395734.3_Silent_p.E513E|MAP4_ENST00000426837.2_Silent_p.E530E|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	513	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.E513E(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	CCAGAGCCATTTCTGTTTCTG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	3											172	162	165					3																	47957778		2203	4300	6503	47932782	SO:0001819	synonymous_variant	4134				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1539A>G	3.37:g.47957778T>C			47932782	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Silent	SNP	ENST00000360240.6	37	CCDS33750.1																																																																																				0.502	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		C	47957778	T	C	47957778	2	2	65	1	0	0	0	0	0	0	0	1	9288	1838	64	4		4	MAP4	3	47957778	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	9438985	47957778	150064652	25	20516										
PTPRG	5793	hgsc.bcm.edu	37	chr3	62189363	62189364	+	Frame_Shift_Ins	INS	-	-	G													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cacaccctcgtctcctaacaINSggactgccgagggagggcat							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:62189363_62189364insG	ENST00000474889.1	+	12	2271_2272	c.1894_1895insG	c.(1894-1896)aggfs	p.R632fs	PTPRG_ENST00000295874.10_Frame_Shift_Ins_p.R632fs	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	632					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T633fs*13(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		GTCTCCTAACAGGACTGCCGAG	0.634																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								62164404	SO:0001589	frameshift_variant	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.1896dupG	3.37:g.62189365_62189365dupG	ENSP00000418112:p.Arg632fs		62164403	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Frame_Shift_Ins	INS	ENST00000474889.1	37	CCDS2895.1																																																																																				0.634	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		G	62189364	-	G	62189363	7	5	65	1	0	1	1	0	0	0	0	0	12839	179	7	0	1940	0	PTPRG	3	62189363	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	14231585	62189363	135833067	26	20517										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89391122	89391122	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	accaacaccacggtgacagtGacagaccttctggcacatac	8	14	1	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:89391122G>T	ENST00000336596.2	+	5	1413	c.1188G>T	c.(1186-1188)gtG>gtT	p.V396V	EPHA3_ENST00000494014.1_Silent_p.V396V|EPHA3_ENST00000452448.2_Silent_p.V396V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	396	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.V396V(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CGGTGACAGTGACAGACCTTC	0.502										TSP Lung(6;0.00050)																																						1	Substitution - coding silent(1)	large_intestine(1)	3											103	86	92					3																	89391122		2203	4300	6503	89473812	SO:0001819	synonymous_variant	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1188G>T	3.37:g.89391122G>T			89473812	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																				0.502	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89391122	G	T	89391122	2	4	65	1	0	0	0	0	0	0	0	1	5181	1277	45	2		2	EPHA3	3	89391122	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	27201759	89391122	108631308	27	20518										
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955262	113955262	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	taaaaacctttcccacattcTttgcactcgtagggctttcc	5	13	1	0	rs568691849		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:113955262T>C	ENST00000482457.2	-	1	1163	c.660A>G	c.(658-660)aaA>aaG	p.K220K	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	220					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K220K(1)		NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TCCCACATTCTTTGCACTCGT	0.483																																					GBM(23;986 1114 21716)											1	Substitution - coding silent(1)	large_intestine(1)	3											109	111	110					3																	113955262		2203	4300	6503	115437952	SO:0001819	synonymous_variant	7634			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.660A>G	3.37:g.113955262T>C			115437952	Q6NSW4|Q6NT14	Silent	SNP	ENST00000482457.2	37	CCDS2979.1																																																																																				0.483	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		C	113955262	T	C	113955262	2	2	65	1	0	0	0	0	0	0	0	1	18207	1606	56	4		4	ZNF80	3	113955262	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	24564140	113955262	84067168	28	20519										
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955774	113955774	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gctcccacattccttgcattTgtaggtcttcccctcacgaa	6	15	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:113955774T>C	ENST00000482457.2	-	1	651	c.148A>G	c.(148-150)Aaa>Gaa	p.K50E	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K50E(1)		NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TCCTTGCATTTGTAGGTCTTC	0.488																																					GBM(23;986 1114 21716)											1	Substitution - Missense(1)	large_intestine(1)	3											126	112	117					3																	113955774		2203	4300	6503	115438464	SO:0001583	missense	7634			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.148A>G	3.37:g.113955774T>C	ENSP00000417192:p.Lys50Glu		115438464	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	.	.	.	.	.	.	.	.	.	.	T	4.955	0.177330	0.09443	.	.	ENSG00000174255	ENST00000482457	T	0.28895	1.59	2.77	0.389	0.16269	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10852	0.0265	N	0.05124	-0.11	0.09310	N	1	B	0.13594	0.008	B	0.16289	0.015	T	0.35549	-0.9784	9	0.02654	T	1	.	5.8301	0.18577	0.0:0.2574:0.0:0.7426	.	50	P51504	ZNF80_HUMAN	E	50	ENSP00000417192:K50E	ENSP00000309812:K50E	K	-	1	0	ZNF80	115438464	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-1.113000	0.03296	0.075000	0.16796	0.533000	0.62120	AAA		0.488	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		C	113955774	T	C	113955774	3	2	65	1	0	0	0	0	1	0	0	0	18207	1821	63	4	677	4	ZNF80	3	113955774	Missense_Mutation	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	512	113955774	84066656	29	20520										
PCCB	5096	hgsc.bcm.edu	37	chr3	136046079	136046080	+	Frame_Shift_Ins	INS	-	-	T													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aggcaactgtacccaaagtcINSacagtcatcaccaggaaggt							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:136046079_136046080insT	ENST00000251654.4	+	12	1351_1352	c.1281_1282insT	c.(1282-1284)acafs	p.T428fs	PCCB_ENST00000474833.1_Intron|PCCB_ENST00000490504.1_Frame_Shift_Ins_p.T371fs|PCCB_ENST00000469217.1_Frame_Shift_Ins_p.T448fs|PCCB_ENST00000462637.1_Frame_Shift_Ins_p.T405fs|PCCB_ENST00000466072.1_Frame_Shift_Ins_p.T448fs|PCCB_ENST00000468777.1_Frame_Shift_Ins_p.T459fs|PCCB_ENST00000478469.1_Intron|PCCB_ENST00000483687.1_Frame_Shift_Ins_p.T409fs|PCCB_ENST00000482086.1_Frame_Shift_Ins_p.T312fs|PCCB_ENST00000471595.1_Frame_Shift_Ins_p.T428fs	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	428	Carboxyltransferase.		T -> I (in PA-2; dbSNP:rs28934887). {ECO:0000269|PubMed:12189489, ECO:0000269|PubMed:15059621}.		biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)	p.T428fs*13(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	TACCCAAAGTCACAGTCATCAC	0.54																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								137528770	SO:0001589	frameshift_variant	5096				CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"propionyl Coenzyme A carboxylase, beta polypeptide"			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	Exception_encountered	3.37:g.136046079_136046080insT	ENSP00000251654:p.Thr428fs		137528769	B7Z2Z4|Q16813|Q96CX0	Frame_Shift_Ins	INS	ENST00000251654.4	37	CCDS3089.1																																																																																				0.54	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1			T	136046080	-	T	136046079	7	5	65	1	0	1	1	0	0	0	0	0	11536	813	29	0	1391	0	PCCB	3	136046079	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	22090305	136046079	61976351	30	20521										
ATR	545	hgsc.bcm.edu	37	chr3	142211989	142211989	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cttgccttatattttttcatAattgcattgctttcaaagtt	4	7	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr3:142211989A>G	ENST00000350721.4	-	35	6184	c.6063T>C	c.(6061-6063)atT>atC	p.I2021I	ATR_ENST00000383101.3_Silent_p.I1957I	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2021	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I2021I(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATTTTTTCATAATTGCATTGC	0.358								Other conserved DNA damage response genes																																								1	Substitution - coding silent(1)	large_intestine(1)	3											80	83	82					3																	142211989		2203	4300	6503	143694679	SO:0001819	synonymous_variant	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6063T>C	3.37:g.142211989A>G			143694679	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																				0.358	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		G	142211989	A	G	142211989	2	3	65	1	0	0	0	0	0	0	0	1	1205	358	13	4		4	ATR	3	142211989	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	6165910	142211989	55810441	31	20522										
KIT	3815	hgsc.bcm.edu	37	chr4	55599316	55599316	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atttgtgattttggtctagcCagagacatcaagaatgattc	9	6	2	4			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:55599316C>T	ENST00000288135.5	+	17	2539	c.2442C>T	c.(2440-2442)gcC>gcT	p.A814A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	814	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A814A(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTGGTCTAGCCAGAGACATCA	0.398		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - coding silent(1)	large_intestine(1)	4											139	141	140					4																	55599316		2203	4300	6503	55294073	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2442C>T	4.37:g.55599316C>T			55294073	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.398	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55599316	C	T	55599316	2	4	65	1	0	0	0	0	0	0	0	1	8350	581	21	3		3	KIT	4	55599316	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		55599316	135554960	32	20523										
ANK2	287	hgsc.bcm.edu	37	chr4	114278110	114278111	+	Frame_Shift_Del	DEL	CC	CC	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgatggccatggatgtgaggCcatgagtcctagcagctcag							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CC	CC	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:114278110_114278111delCC	ENST00000357077.4	+	38	8389_8390	c.8336_8337delCC	c.(8335-8337)gccfs	p.A2779fs	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Frame_Shift_Del_p.A2746fs	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2779					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A2779fs*4(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GGATGTGAGGCCATGAGTCCTA	0.47																																																1	Deletion - Frameshift(1)	large_intestine(1)	4																																								114497560	SO:0001589	frameshift_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8336_8337delCC	4.37:g.114278110_114278111delCC	ENSP00000349588:p.Ala2779fs		114497559	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	37	CCDS3702.1																																																																																				0.47	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114278111	CC	-	114278110	7	5	65	1	0	1	0	1	0	0	0	0	621	739	26	0	8551	0	ANK2	4	114278110	Frame_Shift_Del	DEL	CC	TCGA-AG-A00Y-01A-02W-A005-10	58678794	114278110	76876166	33	20524										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155253904	155253905	+	Frame_Shift_Del	DEL	GG	GG	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctaaaattatatgtttgggtGgattcatagtcaaactgtcg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	GG	GG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:155253904_155253905delGG	ENST00000357232.4	-	9	1957_1958	c.1958_1959delCC	c.(1957-1959)tccfs	p.S653fs	DCHS2_ENST00000507542.1_5'Flank|DCHS2_ENST00000339452.1_Frame_Shift_Del_p.S1152fs	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	653	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S653fs*5(1)|p.S1152fs*5(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATGTTTGGGTGGATTCATAGTC	0.47																																																2	Deletion - Frameshift(2)	large_intestine(2)	4																																								155473355	SO:0001589	frameshift_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.1958_1959delCC	4.37:g.155253904_155253905delGG	ENSP00000349768:p.Ser653fs		155473354	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	37	CCDS3785.1																																																																																				0.47	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		-	155253905	GG	-	155253904	7	5	65	1	0	1	0	1	0	0	0	0	4294	1335	47	0	6955	0	DCHS2	4	155253904	Frame_Shift_Del	DEL	GG	TCGA-AG-A00Y-01A-02W-A005-10	40975794	155253904	35900372	34	20525										
HAND2	9464	hgsc.bcm.edu	37	chr4	174450034	174450034	+	Missense_Mutation	SNP	G	G	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggcgcagggtcttgattttgGagagtttggtgtcggcgggt							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:174450034G>A	ENST00000359562.4	-	1	1346	c.407C>T	c.(406-408)tCc>tTc	p.S136F	HAND2-AS1_ENST00000503474.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502896.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	136	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.S136F(1)		endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		CTTGATTTTGGAGAGTTTGGT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	4											171	161	164					4																	174450034		2203	4300	6503	174686609	SO:0001583	missense	9464			AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.407C>T	4.37:g.174450034G>A	ENSP00000352565:p.Ser136Phe		174686609	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	37	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665065	0.67700	.	.	ENSG00000164107	ENST00000359562;ENST00000393686;ENST00000535864	D	0.98937	-5.25	4.63	4.63	0.57726	Helix-loop-helix DNA-binding (5);	0.057435	0.64402	D	0.000001	D	0.99462	0.9809	H	0.97103	3.94	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98145	1.0438	10	0.87932	D	0	-24.7867	17.6856	0.88255	0.0:0.0:1.0:0.0	.	136;136	B6ECG9;P61296	.;HAND2_HUMAN	F	136;105;84	ENSP00000352565:S136F	ENSP00000352565:S136F	S	-	2	0	HAND2	174686609	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.666000	0.83877	2.398000	0.81561	0.561000	0.74099	TCC		0.627	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			A	174450034	G	A	174450034	3	1	65	1	0	0	0	0	1	0	0	0	6971	1174	41	3	254	3	HAND2	4	174450034	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	19196130	174450034	16704242	35	20526	21	2								
HAND2	9464	hgsc.bcm.edu	37	chr4	174450036	174450036	+	Silent	SNP	G	G	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cgcagggtcttgattttggaGagtttggtgtcggcgggtac							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:174450036G>A	ENST00000359562.4	-	1	1344	c.405C>T	c.(403-405)ctC>ctT	p.L135L	HAND2-AS1_ENST00000503474.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502896.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	135	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.L135L(1)		endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		TGATTTTGGAGAGTTTGGTGT	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	4											170	160	164					4																	174450036		2203	4300	6503	174686611	SO:0001819	synonymous_variant	9464			AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.405C>T	4.37:g.174450036G>A			174686611	B6ECG9|O95300|O95301|P97833|Q494T1	Silent	SNP	ENST00000359562.4	37	CCDS3819.1																																																																																				0.632	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			A	174450036	G	A	174450036	2	1	65	1	0	0	0	0	0	0	0	1	6971	929	33	3		3	HAND2	4	174450036	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	2	174450036	16704240	36	20527	21	2								
HAND2	9464	hgsc.bcm.edu	37	chr4	174450096	174450096	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agttcggcgaaggcgctgttGatgctctgagtcctgcgccg	15	11	1	2	rs144784937		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr4:174450096G>A	ENST00000359562.4	-	1	1284	c.345C>T	c.(343-345)atC>atT	p.I115I	HAND2-AS1_ENST00000503474.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502896.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	115	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.I115I(1)		endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		AGGCGCTGTTGATGCTCTGAG	0.711																																																1	Substitution - coding silent(1)	large_intestine(1)	4											127	121	123					4																	174450096		2203	4300	6503	174686671	SO:0001819	synonymous_variant	9464			AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.345C>T	4.37:g.174450096G>A			174686671	B6ECG9|O95300|O95301|P97833|Q494T1	Silent	SNP	ENST00000359562.4	37	CCDS3819.1																																																																																				0.711	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			A	174450096	G	A	174450096	2	1	65	1	0	0	0	0	0	0	0	1	6971	1280	45	3		3	HAND2	4	174450096	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	60	174450096	16704180	37	20528										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32098677	32098678	+	Frame_Shift_Ins	INS	-	-	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gccctctgcccggcaggagcINSctcccacagccaatgggaag							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:32098677_32098678insA	ENST00000438447.1	+	23	8543_8544	c.8155_8156insA	c.(8155-8157)cctfs	p.P2719fs	PDZD2_ENST00000282493.3_Frame_Shift_Ins_p.P2719fs			O15018	PDZD2_HUMAN	PDZ domain containing 2	2719					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.P2719fs*34(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CCGGCAGGAGCCTCCCACAGCC	0.564																																																1	Insertion - Frameshift(1)	large_intestine(1)	5																																								32134435	SO:0001589	frameshift_variant	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		Exception_encountered	5.37:g.32098677_32098678insA	ENSP00000402033:p.Pro2719fs		32134434	Q9BXD4	Frame_Shift_Ins	INS	ENST00000438447.1	37	CCDS34137.1																																																																																				0.564	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32098678	-	A	32098677	7	5	65	1	0	1	1	0	0	0	0	0	11732	739	26	0	8241	0	PDZD2	5	32098677	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10		32098677	148816583	38	20529										
BHMT2	23743	hgsc.bcm.edu	37	chr5	78365614	78365614	+	Silent	SNP	T	T	C													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agccgcggcaccatggcaccTgctggacgcccgggggccaa							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:78365614T>C	ENST00000255192.3	+	1	75	c.9T>C	c.(7-9)ccT>ccC	p.P3P	BHMT2_ENST00000521567.1_Silent_p.P3P|DMGDH_ENST00000380311.4_5'Flank|DMGDH_ENST00000520388.1_Intron|DMGDH_ENST00000540686.1_5'Flank|DMGDH_ENST00000255189.3_5'Flank	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	3					L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.P3P(1)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		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)	CCATGGCACCTGCTGGACGCC	0.761																																																1	Substitution - coding silent(1)	large_intestine(1)	5											16	16	16					5																	78365614		2084	4083	6167	78401370	SO:0001819	synonymous_variant	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.9T>C	5.37:g.78365614T>C			78401370	B7Z516|Q9NXX7	Silent	SNP	ENST00000255192.3	37	CCDS4045.1																																																																																				0.761	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		C	78365614	T	C	78365614	2	2	65	1	0	0	0	0	0	0	0	1	1427	1567	55	4		4	BHMT2	5	78365614	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	46266937	78365614	102549646	39	20530	22	2								
BHMT2	23743	hgsc.bcm.edu	37	chr5	78365621	78365621	+	Missense_Mutation	SNP	C	C	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcaccatggcacctgctggaCgcccgggggccaagaaggtg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:78365621C>A	ENST00000255192.3	+	1	82	c.16C>A	c.(16-18)Cgc>Agc	p.R6S	BHMT2_ENST00000521567.1_Missense_Mutation_p.R6S|DMGDH_ENST00000380311.4_5'Flank|DMGDH_ENST00000520388.1_Intron|DMGDH_ENST00000540686.1_5'Flank|DMGDH_ENST00000255189.3_5'Flank	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	6					L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.R6S(1)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		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)	ACCTGCTGGACGCCCGGGGGC	0.741																																																1	Substitution - Missense(1)	large_intestine(1)	5											17	17	17					5																	78365621		2096	4105	6201	78401377	SO:0001583	missense	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.16C>A	5.37:g.78365621C>A	ENSP00000255192:p.Arg6Ser		78401377	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	37	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	C	9.297	1.052226	0.19827	.	.	ENSG00000132840	ENST00000255192;ENST00000521567	T;T	0.29142	1.58;1.6	3.59	-0.524	0.11920	.	1.838300	0.03176	N	0.171417	T	0.13286	0.0322	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.15263	-1.0443	10	0.14656	T	0.56	0.3423	4.1752	0.10348	0.3248:0.1849:0.4903:0.0	.	6;6	B7Z516;Q9H2M3	.;BHMT2_HUMAN	S	6	ENSP00000255192:R6S;ENSP00000430278:R6S	ENSP00000255192:R6S	R	+	1	0	BHMT2	78401377	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.070000	0.11523	-0.251000	0.09542	-0.502000	0.04539	CGC		0.741	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		A	78365621	C	A	78365621	3	1	65	1	0	0	0	0	1	0	0	0	1427	536	19	2	18	2	BHMT2	5	78365621	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	7	78365621	102549639	40	20531	22	2								
TCERG1	10915	hgsc.bcm.edu	37	chr5	145838521	145838521	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gttaaggttattcagcaatcAgaactgacacctatgcttgc	8	9	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:145838521A>T	ENST00000296702.5	+	4	551	c.513A>T	c.(511-513)tcA>tcT	p.S171S	TCERG1_ENST00000394421.2_Silent_p.S171S	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	171	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.S171S(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCAGCAATCAGAACTGACAC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	5											106	99	101					5																	145838521		2203	4300	6503	145818714	SO:0001819	synonymous_variant	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.513A>T	5.37:g.145838521A>T			145818714	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																				0.542	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145838521	A	T	145838521	2	4	65	1	0	0	0	0	0	0	0	1	15724	175	7	5		5	TCERG1	5	145838521	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	67472900	145838521	35076739	41	20532										
FAT2	2196	hgsc.bcm.edu	37	chr5	150948423	150948424	+	Frame_Shift_Ins	INS	-	-	T													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcagaggaggagagaatcccINSttctagaggcttctcacagg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:150948423_150948424insT	ENST00000261800.5	-	1	81_82	c.69_70insA	c.(67-72)gaagggfs	p.G24fs		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	24					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G24fs*21(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGAGAATCCCTTCTAGAGGCT	0.485																																																1	Insertion - Frameshift(1)	large_intestine(1)	5																																								150928617	SO:0001589	frameshift_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.70dupA	5.37:g.150948425_150948425dupT	ENSP00000261800:p.Gly24fs		150928616	O75091|Q9NSR7	Frame_Shift_Ins	INS	ENST00000261800.5	37	CCDS4317.1																																																																																				0.485	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150948424	-	T	150948423	7	5	65	1	0	1	1	0	0	0	0	0	5709	681	24	0	13071	0	FAT2	5	150948423	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	5109902	150948423	29966837	42	20533										
C5orf54	63920	hgsc.bcm.edu	37	chr5	159822060	159822060	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atttcatcaattctagaatgGatcacatcatctgataaggg	7	7	6	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:159822060G>A	ENST00000408953.3	-	2	945	c.438C>T	c.(436-438)atC>atT	p.I146I	C5orf54_ENST00000523213.1_Silent_p.I146I	NM_022090.3	NP_071373.2												p.I146I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						ttctagaatggatcacatcat	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	5											91	92	92					5																	159822060		2203	4300	6503	159754638	SO:0001819	synonymous_variant	63920																														ENST00000408953.3:c.438C>T	5.37:g.159822060G>A			159754638		Silent	SNP	ENST00000408953.3	37	CCDS34283.1																																																																																				0.393	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1			A	159822060	G	A	159822060	2	1	65	1	0	0	0	0	0	0	0	1	2316	1164	41	3		3	C5orf54	5	159822060	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	8873637	159822060	21093200	43	20534										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161580174	161580174	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cacaccttcaagagagagatGaagagtacggctatgagtgt	12	7	1	5			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr5:161580174G>A	ENST00000361925.4	+	9	1424	c.1204G>A	c.(1204-1206)Gaa>Aaa	p.E402K	GABRG2_ENST00000414552.2_Missense_Mutation_p.E450K|GABRG2_ENST00000356592.3_Missense_Mutation_p.E410K|GABRG2_ENST00000393933.4_Missense_Mutation_p.E307K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	402					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.E410K(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	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)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGAGAGAGATGAAGAGTACGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	5											182	166	171					5																	161580174		2203	4300	6503	161512752	SO:0001583	missense	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1204G>A	5.37:g.161580174G>A	ENSP00000354651:p.Glu402Lys		161512752	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.997428	0.35226	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88	5.95	5.08	0.68730	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.047726	0.85682	D	0.000000	D	0.82375	0.5023	L	0.50333	1.59	0.80722	D	1	B;B;B	0.27679	0.185;0.048;0.039	B;B;B	0.35550	0.205;0.158;0.098	T	0.76702	-0.2862	10	0.10636	T	0.68	.	15.3601	0.74464	0.0668:0.0:0.9332:0.0	.	450;402;410	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	K	410;450;402;307	ENSP00000349000:E410K;ENSP00000410732:E450K;ENSP00000354651:E402K;ENSP00000377510:E307K	ENSP00000349000:E410K	E	+	1	0	GABRG2	161512752	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.751000	0.98889	1.526000	0.49068	0.655000	0.94253	GAA		0.488	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161580174	G	A	161580174	3	1	65	1	0	0	0	0	1	0	0	0	6191	1291	45	3	1390	3	GABRG2	5	161580174	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	1758114	161580174	19335086	44	20535										
JARID2	3720	hgsc.bcm.edu	37	chr6	15501452	15501452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agttccaccctctgccccgcTtcgagcccaagaatgggctc	9	17	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:15501452T>C	ENST00000341776.2	+	8	2504	c.2260T>C	c.(2260-2262)Ttc>Ctc	p.F754L	JARID2_ENST00000397311.3_Missense_Mutation_p.F582L|JARID2_ENST00000541660.1_Missense_Mutation_p.F716L	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	754				F -> L (in Ref. 1; AAC50822). {ECO:0000305}.	central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.F754L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TCTGCCCCGCTTCGAGCCCAA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6											88	95	93					6																	15501452		2203	4300	6503	15609431	SO:0001583	missense	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2260T>C	6.37:g.15501452T>C	ENSP00000341280:p.Phe754Leu		15609431	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470174	0.63625	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	D;D;D	0.88277	-1.71;-1.71;-2.36	5.05	5.05	0.67936	.	0.056142	0.64402	D	0.000001	T	0.73202	0.3557	L	0.36672	1.1	0.49213	D	0.999768	B;B	0.33171	0.4;0.085	B;B	0.30855	0.121;0.039	T	0.74153	-0.3757	10	0.11794	T	0.64	-11.9726	14.7923	0.69851	0.0:0.0:0.0:1.0	.	716;754	F5H590;Q92833	.;JARD2_HUMAN	L	754;582;716	ENSP00000341280:F754L;ENSP00000380478:F582L;ENSP00000444623:F716L	ENSP00000341280:F754L	F	+	1	0	JARID2	15609431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.809000	0.86057	1.895000	0.54865	0.459000	0.35465	TTC		0.642	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		C	15501452	T	C	15501452	3	2	65	1	0	0	0	0	1	0	0	0	7966	1609	56	4	2290	4	JARID2	6	15501452	Missense_Mutation	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10		15501452	155613615	45	20536										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33052768	33052768	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccccctccaagaaggggcccTtgcagcaccacaacctgctt	8	18	0	1	rs1042187	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:33052768T>C	ENST00000418931.2	+	3	522	c.406T>C	c.(406-408)Ttg>Ctg	p.L136L		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	136	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.L136L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GAAGGGGCCCTTGCAGCACCA	0.502													.|||	2322	0.463658	0.5976	0.3314	5008	,	,		18424	0.621		0.3151	False		,,,				2504	0.3671															1	Substitution - coding silent(1)	large_intestine(1)	6											74	95	87					6																	33052768		1510	2709	4219	33160746	SO:0001819	synonymous_variant	3115				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.406T>C	6.37:g.33052768T>C			33160746	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1																																																																																				0.502	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		C	33052768	T	C	33052768	2	2	65	1	0	0	0	0	0	0	0	1	7224	1606	56	4		4	HLA-DPB1	6	33052768	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	17551316	33052768	138062299	46	20537										
PTK7	5754	hgsc.bcm.edu	37	chr6	43126674	43126674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cagagacaagtgaaggtgtcTgccctgggcctcagcaagga	14	10	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:43126674T>C	ENST00000230419.4	+	18	3062	c.2841T>C	c.(2839-2841)tcT>tcC	p.S947S	PTK7_ENST00000481273.1_Silent_p.S955S|PTK7_ENST00000345201.2_Silent_p.S907S|PTK7_ENST00000349241.2_Silent_p.S817S|PTK7_ENST00000352931.2_Silent_p.S891S	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	947	Interaction with CTNNB1.|Protein kinase; inactive. {ECO:0000255|PROSITE-ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S947S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			TGAAGGTGTCTGCCCTGGGCC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	6											84	75	78					6																	43126674		2203	4300	6503	43234652	SO:0001819	synonymous_variant	5754			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2841T>C	6.37:g.43126674T>C			43234652	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1	.	.	.	.	.	.	.	.	.	.	T	7.746	0.702334	0.15172	.	.	ENSG00000112655	ENST00000489707	.	.	.	5.93	-10.3	0.00346	.	.	.	.	.	T	0.17450	0.0419	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41070	-0.9529	4	.	.	.	.	2.975	0.05935	0.4391:0.2027:0.2293:0.1289	.	.	.	.	P	242	.	.	L	+	2	0	PTK7	43234652	0.000000	0.05858	0.234000	0.24042	0.890000	0.51754	-2.129000	0.01313	-1.942000	0.01040	-1.392000	0.01152	CTG		0.582	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			C	43126674	T	C	43126674	2	2	65	1	0	0	0	0	0	0	0	1	12800	1567	55	4		4	PTK7	6	43126674	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	10073906	43126674	127988393	47	20538										
BAI3	577	hgsc.bcm.edu	37	chr6	70071193	70071193	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcatgaaaggctattgcactAcaaagtaaaccctgaattca	7	9	1	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:70071193A>G	ENST00000370598.1	+	29	4849	c.4028A>G	c.(4027-4029)tAc>tGc	p.Y1343C	BAI3_ENST00000546190.1_Missense_Mutation_p.Y307C|BAI3_ENST00000238918.8_Missense_Mutation_p.Y549C	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1343					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Y1343C(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CTATTGCACTACAAAGTAAAC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	81	82					6																	70071193		2203	4299	6502	70127914	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4028A>G	6.37:g.70071193A>G	ENSP00000359630:p.Tyr1343Cys		70127914	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.947328	0.34377	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.05786	3.39;3.39;3.39	5.8	5.8	0.92144	.	0.057754	0.64402	D	0.000001	T	0.02267	0.0070	N	0.16478	0.41	0.53688	D	0.999979	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.0	T	0.48725	-0.9010	10	0.38643	T	0.18	.	16.1965	0.82029	1.0:0.0:0.0:0.0	.	549;1343	B7Z356;O60242	.;BAI3_HUMAN	C	1343;549;307	ENSP00000359630:Y1343C;ENSP00000238918:Y549C;ENSP00000441821:Y307C	ENSP00000238918:Y549C	Y	+	2	0	BAI3	70127914	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.146000	0.77373	2.232000	0.73038	0.529000	0.55759	TAC		0.408	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	70071193	A	G	70071193	3	3	65	1	0	0	0	0	1	0	0	0	1301	391	14	4	4134	4	BAI3	6	70071193	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	26944519	70071193	101043874	48	20539										
CD109	135228	hgsc.bcm.edu	37	chr6	74497111	74497111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aacacatctgggagaaattcCtatcacagtcacagctcttt	6	11	4	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:74497111C>A	ENST00000287097.5	+	21	2604	c.2492C>A	c.(2491-2493)cCt>cAt	p.P831H	CD109_ENST00000437994.2_Missense_Mutation_p.P831H|CD109_ENST00000422508.2_Missense_Mutation_p.P754H			Q6YHK3	CD109_HUMAN	CD109 molecule	831					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)	p.P831H(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGAGAAATTCCTATCACAGTC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	6											115	111	112					6																	74497111		2203	4300	6503	74553832	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2492C>A	6.37:g.74497111C>A	ENSP00000287097:p.Pro831His		74553832	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.770118	0.49680	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.25579	1.8;2.01;1.79	5.45	4.58	0.56647	.	0.228496	0.46758	D	0.000267	T	0.38665	0.1049	M	0.77313	2.365	0.50467	D	0.999876	D;P;P	0.56746	0.977;0.869;0.841	P;P;P	0.59171	0.842;0.853;0.538	T	0.45205	-0.9277	10	0.66056	D	0.02	.	15.7273	0.77770	0.1376:0.8624:0.0:0.0	.	754;831;831	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	H	831;754;831	ENSP00000388062:P831H;ENSP00000404475:P754H;ENSP00000287097:P831H	ENSP00000287097:P831H	P	+	2	0	CD109	74553832	0.996000	0.38824	0.782000	0.31804	0.064000	0.16182	3.419000	0.52728	1.504000	0.48704	0.650000	0.86243	CCT		0.448	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		A	74497111	C	A	74497111	3	1	65	1	0	0	0	0	1	0	0	0	2969	681	24	2	2574	2	CD109	6	74497111	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	4425918	74497111	96617956	49	20540										
BEND3	57673	hgsc.bcm.edu	37	chr6	107391651	107391651	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgcttgagctctgcggctgtGagctggtactcagggggcgg	18	9	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:107391651G>A	ENST00000369042.1	-	4	934	c.744C>T	c.(742-744)ctC>ctT	p.L248L	BEND3_ENST00000429433.2_Silent_p.L248L			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	248	BEN 1. {ECO:0000255|PROSITE- ProRule:PRU00784}.							p.L248L(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						CTGCGGCTGTGAGCTGGTACT	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	6											39	35	36					6																	107391651		2203	4300	6503	107498344	SO:0001819	synonymous_variant	57673			AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.744C>T	6.37:g.107391651G>A			107498344	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																				0.637	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		A	107391651	G	A	107391651	2	1	65	1	0	0	0	0	0	0	0	1	1400	1277	45	3		3	BEND3	6	107391651	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	32894540	107391651	63723416	50	20541										
GPR6	2830	hgsc.bcm.edu	37	chr6	110301320	110301320	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tatgccttccgcaaccaggaGatccagcgcgccctgtggct	11	15	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:110301320G>A	ENST00000275169.3	+	1	1023	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	GPR6_ENST00000414000.2_Silent_p.E350E	NM_005284.3	NP_005275.1	P46095	GPR6_HUMAN	G protein-coupled receptor 6	335					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.E335E(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;1.64e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;2.83e-05)|all_lung(197;0.00016)|Lung NSC(302;0.000318)|Colorectal(196;0.0488)		BRCA - Breast invasive adenocarcinoma(108;8.01e-05)|Epithelial(106;8.76e-05)|all cancers(137;0.000197)|OV - Ovarian serous cystadenocarcinoma(136;0.0307)		GCAACCAGGAGATCCAGCGCG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	6											107	110	109					6																	110301320		2203	4300	6503	110408013	SO:0001819	synonymous_variant	2830				CCDS5079.1, CCDS69172.1	6q21	2012-08-21				ENSG00000146360		"GPCR / Class A : Orphans"	4515	protein-coding gene	gene with protein product		600553				8530049	Standard	NM_001286099		Approved		uc003ptu.3	P46095	OTTHUMG00000015354	ENST00000275169.3:c.1005G>A	6.37:g.110301320G>A			110408013	B4DHS9|J3KQR3|Q17RJ7|Q5SYL0	Silent	SNP	ENST00000275169.3	37	CCDS5079.1																																																																																				0.612	GPR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041774.1			A	110301320	G	A	110301320	2	1	65	1	0	0	0	0	0	0	0	1	6721	933	33	3		3	GPR6	6	110301320	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	2909669	110301320	60813747	51	20542										
REV3L	5980	hgsc.bcm.edu	37	chr6	111632322	111632322	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cctggtttataagaaaaactTcctctgtattccttggcaaa	6	9	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:111632322T>A	ENST00000358835.3	-	30	9199	c.8745A>T	c.(8743-8745)ggA>ggT	p.G2915G	RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000435970.1_Silent_p.G2837G|REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000368805.1_Silent_p.G2915G|REV3L_ENST00000368802.3_Silent_p.G2915G			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2915					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.G2837G(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AAGAAAAACTTCCTCTGTATT	0.413								DNA polymerases (catalytic subunits)																																								1	Substitution - coding silent(1)	large_intestine(1)	6											161	162	162					6																	111632322		2203	4300	6503	111739015	SO:0001819	synonymous_variant	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8745A>T	6.37:g.111632322T>A			111739015	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																				0.413	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111632322	T	A	111632322	2	1	65	1	0	0	0	0	0	0	0	1	13277	1770	62	5		5	REV3L	6	111632322	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	1331002	111632322	59482745	52	20543										
ZDHHC14	79683	hgsc.bcm.edu	37	chr6	158066850	158066850	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cacacctacttgatcagctcCaaccagacaacaaatgagga	6	13	1	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:158066850C>G	ENST00000359775.5	+	6	1723	c.834C>G	c.(832-834)tcC>tcG	p.S278S	ZDHHC14_ENST00000414563.2_Silent_p.S278S|ZDHHC14_ENST00000341375.8_3'UTR			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	278					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.S278S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		TGATCAGCTCCAACCAGACAA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	6											161	121	135					6																	158066850		2203	4296	6499	157986838	SO:0001819	synonymous_variant	79683			AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"Zinc fingers, DHHC-type"	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.834C>G	6.37:g.158066850C>G			157986838	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Silent	SNP	ENST00000359775.5	37	CCDS5252.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.519183	0.27211	.	.	ENSG00000175048	ENST00000340347	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56208	-0.8017	4	.	.	.	-34.8274	12.9264	0.58262	0.1625:0.8375:0.0:0.0	.	.	.	.	R	103	.	.	P	+	2	0	ZDHHC14	157986838	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.361000	0.52306	2.043000	0.60533	0.459000	0.35465	CCA		0.522	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		G	158066850	C	G	158066850	2	3	65	1	0	0	0	0	0	0	0	1	17643	581	21	5		5	ZDHHC14	6	158066850	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	46434528	158066850	13048217	53	20544										
SYTL3	94120	hgsc.bcm.edu	37	chr6	159084381	159084382	+	Frame_Shift_Del	DEL	GG	GG	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtcctgtaccgagaccaggcGgttcaaaacacagaggagga					rs560281807	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	GG	GG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:159084381_159084382delGG	ENST00000297239.9	+	3	275_276	c.81_82delGG	c.(79-84)gcggttfs	p.V28fs	SYTL3_ENST00000360448.3_Frame_Shift_Del_p.V28fs|SYTL3_ENST00000367081.3_5'UTR			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	28	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)	p.V28fs*94(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		GAGACCAGGCGGTTCAAAACAC	0.559																																																1	Deletion - Frameshift(1)	large_intestine(1)	6																																								159004370	SO:0001589	frameshift_variant	94120			AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.81_82delGG	6.37:g.159084381_159084382delGG	ENSP00000297239:p.Val28fs		159004369	Q496J4|Q496J6|Q5U3B9	Frame_Shift_Del	DEL	ENST00000297239.9	37	CCDS56458.1																																																																																				0.559	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1			-	159084382	GG	-	159084381	7	5	65	1	0	1	0	1	0	0	0	0	15523	1103	39	0	83	0	SYTL3	6	159084381	Frame_Shift_Del	DEL	GG	TCGA-AG-A00Y-01A-02W-A005-10	1017531	159084381	12030686	54	20545										
PARK2	5071	hgsc.bcm.edu	37	chr6	162864376	162864376	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cattcctcagctccttccctGcgaaaatcacacgcaactgg	6	16	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr6:162864376G>T	ENST00000366898.1	-	2	239	c.137C>A	c.(136-138)gCa>gAa	p.A46E	PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366896.1_Missense_Mutation_p.A46E|PARK2_ENST00000366897.1_Missense_Mutation_p.A46E|PARK2_ENST00000366892.1_Missense_Mutation_p.A46E|PARK2_ENST00000366894.1_5'UTR	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	46	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.		A -> P (in PARK2). {ECO:0000269|PubMed:12362318}.		adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)	p.A46E(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CTCCTTCCCTGCGAAAATCAC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	6											142	121	128					6																	162864376		2203	4300	6503	162784366	SO:0001583	missense	5071				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.137C>A	6.37:g.162864376G>T	ENSP00000355865:p.Ala46Glu		162784366	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769564	0.90020	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366892;ENST00000542682	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.63	5.63	0.86233	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.85682	D	0.000000	D	0.89227	0.6655	M	0.92122	3.275	0.49213	D	0.999766	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.999;0.993;0.997;0.998	D	0.90699	0.4619	10	0.87932	D	0	.	20.0401	0.97581	0.0:0.0:1.0:0.0	.	46;46;46;46	O60260-5;Q5VVX3;Q5VVX4;O60260	.;.;.;PRKN2_HUMAN	E	46;46;46;46;45	ENSP00000355865:A46E;ENSP00000355863:A46E;ENSP00000355862:A46E;ENSP00000355858:A46E	ENSP00000355858:A46E	A	-	2	0	PARK2	162784366	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.633000	0.83260	2.805000	0.96524	0.655000	0.94253	GCA		0.597	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			T	162864376	G	T	162864376	3	4	65	1	0	0	0	0	1	0	0	0	11480	1319	46	2	1304	2	PARK2	6	162864376	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	3779995	162864376	8250691	55	20546										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86542401	86542401	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cctggagggcaggggacacaCgatgaacccgactgttcaga	14	11	1	2	rs369087183		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:86542401C>T	ENST00000450689.2	-	14	2036	c.1851G>A	c.(1849-1851)tcG>tcA	p.S617S	KIAA1324L_ENST00000416314.1_Silent_p.S450S|KIAA1324L_ENST00000297222.6_Silent_p.S377S|KIAA1324L_ENST00000444627.1_Intron|KIAA1324L_ENST00000490995.1_5'UTR	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	617						integral component of membrane (GO:0016021)		p.S377S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					AGGGGACACACGATGAACCCG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	7						C	,	1,4405	2.1+/-5.4	0,1,2202	157	130	139		1851,1350	0.5	1	7		139	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KIAA1324L	NM_001142749.2,NM_152748.3	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	617/1030,450/863	86542401	2,13004	2203	4300	6503	86380337	SO:0001819	synonymous_variant	222223			AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1851G>A	7.37:g.86542401C>T			86380337	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Silent	SNP	ENST00000450689.2	37	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	C	9.993	1.231426	0.22626	2.27E-4	1.16E-4	ENSG00000164659	ENST00000423294	.	.	.	5.82	0.506	0.16961	.	.	.	.	.	T	0.43144	0.1234	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25676	-1.0125	4	.	.	.	.	2.5706	0.04794	0.1114:0.4305:0.2392:0.2188	.	.	.	.	M	578	.	.	V	-	1	0	KIAA1324L	86380337	0.902000	0.30710	1.000000	0.80357	0.972000	0.66771	-0.060000	0.11712	0.360000	0.24265	-0.878000	0.02970	GTG		0.522	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		T	86542401	C	T	86542401	2	4	65	1	0	0	0	0	0	0	0	1	8245	523	19	1		1	KIAA1324L	7	86542401	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		86542401	72596262	56	20547										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726506	91726506	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atgcatgagctccagtccaaAgtggaagatcttcagcgcca	10	11	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:91726506A>G	ENST00000359028.2	+	41	10470	c.10245A>G	c.(10243-10245)aaA>aaG	p.K3415K	AKAP9_ENST00000358100.2_Silent_p.K3361K|AKAP9_ENST00000356239.3_Silent_p.K3411K			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3415					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K3411K(1)|p.K3415K(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCCAGTCCAAAGTGGAAGATC	0.448			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - coding silent(2)	large_intestine(2)	7											42	44	44					7																	91726506		2203	4299	6502	91564442	SO:0001819	synonymous_variant	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10245A>G	7.37:g.91726506A>G			91564442	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																					0.448	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91726506	A	G	91726506	2	3	65	1	0	0	0	0	0	0	0	1	459	69	3	4		4	AKAP9	7	91726506	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	5184105	91726506	67412157	57	20548										
TAF6	6878	hgsc.bcm.edu	37	chr7	99710479	99710479	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttcaggggtccgtcttcctcCtggcctggcttggctgactt	12	13	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:99710479C>T	ENST00000344095.4	-	6	1041	c.516G>A	c.(514-516)caG>caA	p.Q172Q	TAF6_ENST00000418432.2_Silent_p.Q96Q|TAF6_ENST00000472509.1_Silent_p.Q229Q|TAF6_ENST00000452041.1_Silent_p.Q172Q|TAF6_ENST00000497233.1_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000453269.2_Silent_p.Q172Q|TAF6_ENST00000437822.2_Silent_p.Q209Q	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	172					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q172Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGTCTTCCTCCTGGCCTGGCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	7											186	182	183					7																	99710479		2203	4300	6503	99548415	SO:0001819	synonymous_variant	6878				CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.516G>A	7.37:g.99710479C>T			99548415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Silent	SNP	ENST00000344095.4	37	CCDS5686.1																																																																																				0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		T	99710479	C	T	99710479	2	4	65	1	0	0	0	0	0	0	0	1	15569	680	24	3		3	TAF6	7	99710479	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	7983973	99710479	59428184	58	20549										
MEPCE	56257	hgsc.bcm.edu	37	chr7	100030612	100030613	+	Frame_Shift_Ins	INS	-	-	G													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tatgatgtggtgctctgcctINScagcctcaccaagtgggtgc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:100030612_100030613insG	ENST00000310512.2	+	2	2130_2131	c.1742_1743insG	c.(1741-1746)ctcagcfs	p.S582fs	RP11-758P17.2_ENST00000492523.1_RNA|MEPCE_ENST00000414441.1_Frame_Shift_Ins_p.S113fs|PPP1R35_ENST00000476185.1_5'Flank	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	582	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.S582fs*81(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTGCTCTGCCTCAGCCTCACCA	0.589																																																1	Insertion - Frameshift(1)	large_intestine(1)	7																																								99868549	SO:0001589	frameshift_variant	56257			AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"bin3, bicoid-interacting 3, homolog (Drosophila)"	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	Exception_encountered	7.37:g.100030612_100030613insG	ENSP00000308546:p.Ser582fs		99868548	B3KP86|D6W5V7|Q9NPD4	Frame_Shift_Ins	INS	ENST00000310512.2	37	CCDS5693.1																																																																																				0.589	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			G	100030613	-	G	100030612	7	5	65	1	0	1	1	0	0	0	0	0	9507	1551	54	0	1748	0	MEPCE	7	100030612	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	320133	100030612	59108051	59	20550										
SRRT	51593	hgsc.bcm.edu	37	chr7	100482167	100482167	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gatgagaagaaggaagacggCaagcaggtccgagccctggg	17	8	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:100482167C>A	ENST00000347433.4	+	7	1094	c.936C>A	c.(934-936)ggC>ggA	p.G312G	SRRT_ENST00000457580.2_Silent_p.G312G|SRRT_ENST00000432932.1_Silent_p.G312G|SRRT_ENST00000388793.4_Silent_p.G312G			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	312	Glu-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.G312G(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AGGAAGACGGCAAGCAGGTCC	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	7											44	46	45					7																	100482167		2199	4300	6499	100320103	SO:0001819	synonymous_variant	51593				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.936C>A	7.37:g.100482167C>A			100320103	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Silent	SNP	ENST00000347433.4	37	CCDS34709.1																																																																																				0.632	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100482167	C	A	100482167	2	1	65	1	0	0	0	0	0	0	0	1	15211	697	25	2		2	SRRT	7	100482167	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	451555	100482167	58656496	60	20551										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107717485	107717485	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgtacatctggttctaaacaGatgggtgtgggaagcagcat	13	6	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:107717485G>A	ENST00000388781.3	-	17	2111	c.2028C>T	c.(2026-2028)atC>atT	p.I676I	LAMB4_ENST00000388780.3_Silent_p.I676I|LAMB4_ENST00000418464.1_Silent_p.I676I|LAMB4_ENST00000205386.4_Silent_p.I676I|LAMB4_ENST00000414450.2_Silent_p.I676I	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	676	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.I676I(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GTTCTAAACAGATGGGTGTGG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	7											97	102	101					7																	107717485		2203	4300	6503	107504721	SO:0001819	synonymous_variant	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2028C>T	7.37:g.107717485G>A			107504721	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																				0.383	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107717485	G	A	107717485	2	1	65	1	0	0	0	0	0	0	0	1	8635	932	33	3		3	LAMB4	7	107717485	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	7235318	107717485	51421178	61	20552										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107880469	107880469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aatcaggggcactctgcccgCagataagcgcttctttttcg	10	12	3	1	rs535571962		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:107880469C>T	ENST00000425651.2	-	1	39	c.40G>A	c.(40-42)Gcg>Acg	p.A14T	NRCAM_ENST00000379024.4_Missense_Mutation_p.A14T|NRCAM_ENST00000351718.4_Missense_Mutation_p.A14T|NRCAM_ENST00000379022.4_Missense_Mutation_p.A14T|NRCAM_ENST00000379028.3_Missense_Mutation_p.A14T|NRCAM_ENST00000413765.2_Missense_Mutation_p.A14T	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	14					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)	p.A14T(1)		breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ACTCTGCCCGCAGATAAGCGC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	7											125	125	125					7																	107880469		2203	4300	6503	107667705	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.40G>A	7.37:g.107880469C>T	ENSP00000401244:p.Ala14Thr		107667705	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365137	0.41902	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979;ENST00000417701;ENST00000442580;ENST00000419936;ENST00000456431;ENST00000418239	T;T;T;T;T;T;T;T;T;T	0.74737	0.33;0.6;0.32;0.42;0.33;0.36;-0.28;-0.85;-0.87;-0.87	5.87	4.06	0.47325	.	0.644642	0.16184	N	0.225690	T	0.50633	0.1627	N	0.04959	-0.14	0.26752	N	0.970184	B;B;B;B;B	0.09022	0.002;0.001;0.001;0.002;0.002	B;B;B;B;B	0.17979	0.013;0.02;0.006;0.02;0.01	T	0.36601	-0.9741	10	0.29301	T	0.29	.	7.1413	0.25558	0.0:0.6736:0.1278:0.1986	.	14;14;14;14;14	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	T	14	ENSP00000368314:A14T;ENSP00000407858:A14T;ENSP00000325269:A14T;ENSP00000368310:A14T;ENSP00000401244:A14T;ENSP00000368308:A14T;ENSP00000390421:A14T;ENSP00000390868:A14T;ENSP00000397544:A14T;ENSP00000408203:A14T	ENSP00000325269:A14T	A	-	1	0	NRCAM	107667705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.654000	0.37334	1.633000	0.50488	0.655000	0.94253	GCG		0.423	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107880469	C	T	107880469	3	4	65	1	0	0	0	0	1	0	0	0	10675	710	25	3	4024	3	NRCAM	7	107880469	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	162984	107880469	51258194	62	20553										
FOXP2	93986	hgsc.bcm.edu	37	chr7	114268633	114268633	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atgatgactccccaggtgatCacccctcagcaaatgcagca	8	14	2	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr7:114268633C>T	ENST00000393494.2	+	4	576	c.297C>T	c.(295-297)atC>atT	p.I99I	FOXP2_ENST00000393489.3_Silent_p.I7I|FOXP2_ENST00000393500.3_Silent_p.I7I|FOXP2_ENST00000403559.4_Silent_p.I99I|FOXP2_ENST00000350908.4_Silent_p.I99I|FOXP2_ENST00000378237.3_Silent_p.I99I|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000390668.3_Silent_p.I123I|FOXP2_ENST00000360232.4_Silent_p.I99I|FOXP2_ENST00000459666.1_3'UTR|FOXP2_ENST00000408937.3_Silent_p.I124I|FOXP2_ENST00000393491.3_Silent_p.I7I|FOXP2_ENST00000393498.2_Silent_p.I99I			O15409	FOXP2_HUMAN	forkhead box P2	99	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I124I(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						CCCAGGTGATCACCCCTCAGC	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	7											206	176	186					7																	114268633		2203	4300	6503	114055869	SO:0001819	synonymous_variant	93986			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.297C>T	7.37:g.114268633C>T			114055869	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	CCDS5760.1																																																																																				0.493	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		T	114268633	C	T	114268633	2	4	65	1	0	0	0	0	0	0	0	1	6046	816	29	3		3	FOXP2	7	114268633	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	6388164	114268633	44870030	63	20554										
PRSS55	203074	hgsc.bcm.edu	37	chr8	10387198	10387198	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gcggctcactgcttatattcCgaggagctgttgtaagtacc	11	10	1	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:10387198C>T	ENST00000328655.3	+	2	376	c.336C>T	c.(334-336)tcC>tcT	p.S112S	PRSS55_ENST00000522210.1_Silent_p.S112S|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	112	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.S112S(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GCTTATATTCCGAGGAGCTGT	0.592																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	8											156	160	159					8																	10387198		2203	4300	6503	10424608	SO:0001819	synonymous_variant	203074			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.336C>T	8.37:g.10387198C>T			10424608	E5RJX5	Silent	SNP	ENST00000328655.3	37	CCDS5976.1																																																																																				0.592	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		T	10387198	C	T	10387198	2	4	65	1	0	0	0	0	0	0	0	1	12668	639	23	1		1	PRSS55	8	10387198	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		10387198	135976824	64	20555										
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19250959	19250959	+	Silent	SNP	T	T	C													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tcggaggacggctgtaaacaTttcctcatcgatgcctctgc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:19250959T>C	ENST00000265807.3	+	9	1590	c.1179T>C	c.(1177-1179)caT>caC	p.H393H	SH2D4A_ENST00000519207.1_Silent_p.H393H|SH2D4A_ENST00000518040.1_Silent_p.H348H	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	393	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)	p.H393H(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		GCTGTAAACATTTCCTCATCG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	8											105	95	99					8																	19250959		2203	4300	6503	19295239	SO:0001819	synonymous_variant	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.1179T>C	8.37:g.19250959T>C			19295239	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	37	CCDS6009.1																																																																																				0.537	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		C	19250959	T	C	19250959	2	2	65	1	0	0	0	0	0	0	0	1	14272	1490	52	4		4	SH2D4A	8	19250959	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	8863761	19250959	127113063	65	20556	23	2								
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19250967	19250967	+	Missense_Mutation	SNP	T	T	G													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cggctgtaaacatttcctcaTcgatgcctctgcagacgcct					rs147445565	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:19250967T>G	ENST00000265807.3	+	9	1598	c.1187T>G	c.(1186-1188)aTc>aGc	p.I396S	SH2D4A_ENST00000519207.1_Missense_Mutation_p.I396S|SH2D4A_ENST00000518040.1_Missense_Mutation_p.I351S	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	396	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)	p.I396S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		CATTTCCTCATCGATGCCTCT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	8											100	90	93					8																	19250967		2203	4300	6503	19295247	SO:0001583	missense	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.1187T>G	8.37:g.19250967T>G	ENSP00000265807:p.Ile396Ser		19295247	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.585145	0.46110	.	.	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;T;T	0.75938	-0.98;-0.98;-0.98	5.89	4.73	0.59995	SH2 motif (4);	0.124363	0.52532	N	0.000067	D	0.90625	0.7060	H	0.98238	4.18	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92289	0.5840	10	0.87932	D	0	.	11.503	0.50448	0.1345:0.0:0.0:0.8655	.	351;396	B4DDR1;Q9H788	.;SH24A_HUMAN	S	396;351;396	ENSP00000265807:I396S;ENSP00000429482:I351S;ENSP00000428684:I396S	ENSP00000265807:I396S	I	+	2	0	SH2D4A	19295247	1.000000	0.71417	0.782000	0.31804	0.011000	0.07611	6.742000	0.74843	1.035000	0.39972	-0.354000	0.07668	ATC		0.532	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		G	19250967	T	G	19250967	3	3	65	1	0	0	0	0	1	0	0	0	14272	1435	50	4	1267	4	SH2D4A	8	19250967	Missense_Mutation	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	8	19250967	127113055	66	20557	23	2								
NRG1	3084	hgsc.bcm.edu	37	chr8	32621746	32621747	+	Frame_Shift_Ins	INS	-	-	G													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cagaagatgaaagagtaggtINSgaagatacgcctttcctggg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:32621746_32621747insG	ENST00000405005.3	+	12	1749_1750	c.1749_1750insG	c.(1750-1752)gaafs	p.E584fs	NRG1_ENST00000356819.4_Frame_Shift_Ins_p.E589fs|NRG1_ENST00000287842.3_Frame_Shift_Ins_p.E581fs|NRG1_ENST00000338921.4_Frame_Shift_Ins_p.E592fs|NRG1_ENST00000519301.1_Frame_Shift_Ins_p.E534fs|NRG1_ENST00000539990.1_Frame_Shift_Ins_p.E427fs|NRG1_ENST00000341377.5_3'UTR|RP11-1002K11.1_ENST00000607314.1_lincRNA|NRG1_ENST00000287845.5_Frame_Shift_Ins_p.E555fs			Q02297	NRG1_HUMAN	neuregulin 1	584					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.E589fs*17(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		AAAGAGTAGGTGAAGATACGCC	0.545																																																1	Insertion - Frameshift(1)	large_intestine(1)	8																																								32741289	SO:0001589	frameshift_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.1750dupG	8.37:g.32621747_32621747dupG	ENSP00000384620:p.Glu584fs		32741288	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Frame_Shift_Ins	INS	ENST00000405005.3	37	CCDS6085.1																																																																																				0.545	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			G	32621747	-	G	32621746	7	5	65	1	0	1	1	0	0	0	0	0	10678	1683	59	0	3520	0	NRG1	8	32621746	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	13370779	32621746	113742276	67	20558										
ST18	9705	hgsc.bcm.edu	37	chr8	53084623	53084623	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggctgggcattgccatccagGggttctgcgagagcattctg	15	10	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:53084623G>A	ENST00000276480.7	-	10	1481	c.798C>T	c.(796-798)ccC>ccT	p.P266P		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	266					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P266P(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGCCATCCAGGGGTTCTGCGA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	8											97	100	99					8																	53084623		2203	4300	6503	53247176	SO:0001819	synonymous_variant	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.798C>T	8.37:g.53084623G>A			53247176	Q17RY1	Silent	SNP	ENST00000276480.7	37	CCDS6149.1																																																																																				0.493	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			A	53084623	G	A	53084623	2	1	65	1	0	0	0	0	0	0	0	1	15251	1219	43	3		3	ST18	8	53084623	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	20462877	53084623	93279399	68	20559										
PLAG1	5324	hgsc.bcm.edu	37	chr8	57080762	57080762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttggtttcaccacgcttacGtttccctgaagggactttct	8	11	2	1	rs144724863		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:57080762G>A	ENST00000316981.3	-	4	546	c.67C>T	c.(67-69)Cgt>Tgt	p.R23C	PLAG1_ENST00000423799.2_Intron|PLAG1_ENST00000429357.2_Missense_Mutation_p.R23C	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	23	Interacts with KPNA2.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R23C(1)	CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CCACGCTTACGTTTCCCTGAA	0.448			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	1	Substitution - Missense(1)	large_intestine(1)	8						G	CYS/ARG,,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	115	104	108		67,,67	5.5	1	8	dbSNP_134	108	0,8600		0,0,4300	no	missense,intron,missense	PLAG1	NM_001114634.1,NM_001114635.1,NM_002655.2	180,,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,,probably-damaging	23/501,,23/501	57080762	1,13005	2203	4300	6503	57243316	SO:0001583	missense	5324			U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.67C>T	8.37:g.57080762G>A	ENSP00000325546:p.Arg23Cys		57243316	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	37	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509050	0.64410	2.27E-4	0.0	ENSG00000181690	ENST00000316981;ENST00000429357	T;T	0.13901	2.55;2.55	5.46	5.46	0.80206	.	0.052285	0.85682	D	0.000000	T	0.20820	0.0501	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	P	0.58928	0.848	T	0.05852	-1.0860	10	0.87932	D	0	-17.9986	19.6662	0.95894	0.0:0.0:1.0:0.0	.	23	Q6DJT9	PLAG1_HUMAN	C	23	ENSP00000325546:R23C;ENSP00000416537:R23C	ENSP00000325546:R23C	R	-	1	0	PLAG1	57243316	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.650000	0.83521	2.695000	0.91970	0.563000	0.77884	CGT		0.448	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		A	57080762	G	A	57080762	3	1	65	1	0	0	0	0	1	0	0	0	12049	1145	40	1	1443	1	PLAG1	8	57080762	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	3996139	57080762	89283260	69	20560										
CA8	767	hgsc.bcm.edu	37	chr8	61178527	61178527	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	taaccgtgtgctcagaaccaCgctggttttctcttccccag	8	14	2	1	rs200882621		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:61178527C>T	ENST00000317995.4	-	3	638	c.374G>A	c.(373-375)cGt>cAt	p.R125H		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	125					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.R125H(1)		endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	CTCAGAACCACGCTGGTTTTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											79	76	77					8																	61178527		2203	4300	6503	61341081	SO:0001583	missense	767			L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"Carbonic anhydrases"	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.374G>A	8.37:g.61178527C>T	ENSP00000314407:p.Arg125His		61341081	A8K0A5|B3KQZ7|Q32MY2	Missense_Mutation	SNP	ENST00000317995.4	37	CCDS6174.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870337	0.51588	.	.	ENSG00000178538	ENST00000317995	T	0.66995	-0.24	5.58	5.58	0.84498	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	T	0.73737	0.3625	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.65541	-0.6143	10	0.02654	T	1	.	19.5923	0.95520	0.0:1.0:0.0:0.0	.	125	P35219	CAH8_HUMAN	H	125	ENSP00000314407:R125H	ENSP00000314407:R125H	R	-	2	0	CA8	61341081	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.644000	0.89710	0.557000	0.71058	CGT		0.383	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1			T	61178527	C	T	61178527	3	4	65	1	0	0	0	0	1	0	0	0	2529	536	19	1	522	1	CA8	8	61178527	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	4097765	61178527	85185495	70	20561										
TTPA	7274	hgsc.bcm.edu	37	chr8	63998434	63998434	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aggaaccgcagcaggaaggaGtcggtgagcggcagcggcgc	19	10	0	1	rs199805621	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr8:63998434G>C	ENST00000260116.4	-	1	178	c.147C>G	c.(145-147)gaC>gaG	p.D49E	TTPA_ENST00000521138.1_5'UTR	NM_000370.3	NP_000361.1	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	49					embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)	p.D49E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	GCAGGAAGGAGTCGGTGAGCG	0.746																																																1	Substitution - Missense(1)	large_intestine(1)	8											3	3	3					8																	63998434		1417	2680	4097	64160988	SO:0001583	missense	7274			BC058000	CCDS6178.1	8q12.3	2007-07-18	2007-07-16			ENSG00000137561			12404	protein-coding gene	gene with protein product		600415	"ataxia (Friedreich-like) with vitamin E deficiency"	AVED		7719340, 7887897	Standard	NM_000370		Approved		uc003xux.2	P49638		ENST00000260116.4:c.147C>G	8.37:g.63998434G>C	ENSP00000260116:p.Asp49Glu		64160988	Q71V64	Missense_Mutation	SNP	ENST00000260116.4	37	CCDS6178.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.839185	0.51057	.	.	ENSG00000137561	ENST00000260116	D	0.92446	-3.04	4.29	3.39	0.38822	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.562105	0.19880	N	0.103997	D	0.92107	0.7498	M	0.80746	2.51	0.35346	D	0.786964	P	0.35612	0.512	B	0.43360	0.417	D	0.93262	0.6644	10	0.48119	T	0.1	.	7.0014	0.24811	0.195:0.0:0.805:0.0	.	49	P49638	TTPA_HUMAN	E	49	ENSP00000260116:D49E	ENSP00000260116:D49E	D	-	3	2	TTPA	64160988	0.995000	0.38212	0.986000	0.45419	0.146000	0.21551	1.075000	0.30716	2.190000	0.69967	0.460000	0.39030	GAC		0.746	TTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378460.1	NM_000370		C	63998434	G	C	63998434	3	2	65	1	0	0	0	0	1	0	0	0	16776	1020	36	5	709	5	TTPA	8	63998434	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	2819907	63998434	82365588	71	20562										
RRAGA	54801	hgsc.bcm.edu	37	chr9	19050161	19050161	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acgtccatctgggatgagacGctctacaaagcctggtccag	11	12	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr9:19050161G>A	ENST00000380502.3	-	0	6536				RRAGA_ENST00000380527.1_Silent_p.T168T	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.T168T(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGGATGAGACGCTCTACAAAG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	9											66	64	65					9																	19050161		2203	4300	6503	19040161	SO:0001628	intergenic_variant	10670			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622		9.37:g.19050161G>A			19040161	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																				0.522	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		A	19050161	G	A	19050161	1	1	65	0	1	0	0	0	0	0	0	0	13709	1074	38	1		1	RRAGA	9	19050161	IGR	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10		19050161	122163270	72	20563										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74324230	74324230	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acttagacacatttacacagCttggatggcggatcaggtag	11	8	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr9:74324230C>G	ENST00000377044.4	-	17	3469	c.2930G>C	c.(2929-2931)aGc>aCc	p.S977T	TMEM2_ENST00000377066.5_Missense_Mutation_p.S914T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	977					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.S977T(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		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)		ATTTACACAGCTTGGATGGCG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	9											251	211	225					9																	74324230		2203	4300	6503	73514050	SO:0001583	missense	23670				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2930G>C	9.37:g.74324230C>G	ENSP00000366243:p.Ser977Thr		73514050	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.635235	0.29068	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000377055;ENST00000377043	T;T;T;T	0.72615	-0.67;-0.6;1.5;0.92	5.67	1.01	0.19927	.	0.642633	0.18162	N	0.149726	T	0.52403	0.1732	N	0.22421	0.69	0.32739	N	0.507953	B;B	0.12630	0.001;0.006	B;B	0.13407	0.002;0.009	T	0.53788	-0.8389	10	0.59425	D	0.04	.	7.5777	0.27946	0.0:0.2757:0.0:0.7243	.	977;914	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	T	977;914;6;78	ENSP00000366243:S977T;ENSP00000366266:S914T;ENSP00000366254:S6T;ENSP00000366242:S78T	ENSP00000366242:S78T	S	-	2	0	TMEM2	73514050	0.014000	0.17966	0.983000	0.44433	0.942000	0.58702	0.195000	0.17155	0.283000	0.22279	-0.259000	0.10710	AGC		0.458	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		G	74324230	C	G	74324230	3	3	65	1	0	0	0	0	1	0	0	0	16160	797	28	5	1253	5	TMEM2	9	74324230	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	55274069	74324230	66889201	73	20564										
ZBTB26	57684	hgsc.bcm.edu	37	chr9	125681862	125681862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccacagggcctgtgtgcaccGttctacaatgtggctcatct	10	13	3	0	rs559840108		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr9:125681862G>A	ENST00000373656.3	-	2	425	c.352C>T	c.(352-354)Cgg>Tgg	p.R118W	ZBTB26_ENST00000373654.1_Missense_Mutation_p.R118W	NM_020924.2	NP_065975.1	Q9HCK0	ZBT26_HUMAN	zinc finger and BTB domain containing 26	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R118W(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)	11						TGTGTGCACCGTTCTACAATG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											132	116	121					9																	125681862		2203	4300	6503	124721683	SO:0001583	missense	57684			AB046792	CCDS6847.1	9q34.11	2013-01-08	2004-04-15	2004-04-16	ENSG00000171448	ENSG00000171448		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	23383	protein-coding gene	gene with protein product			"zinc finger protein 481"	ZNF481			Standard	NM_020924		Approved		uc004bnk.3	Q9HCK0	OTTHUMG00000020627	ENST00000373656.3:c.352C>T	9.37:g.125681862G>A	ENSP00000362760:p.Arg118Trp		124721683	B3KQ53|Q8WTR1	Missense_Mutation	SNP	ENST00000373656.3	37	CCDS6847.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738653	0.49045	.	.	ENSG00000171448	ENST00000373656;ENST00000373654	T;T	0.68181	-0.31;-0.31	5.54	4.59	0.56863	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.068526	0.64402	D	0.000015	T	0.76076	0.3937	L	0.52573	1.65	0.48762	D	0.999706	D	0.89917	1.0	D	0.76071	0.987	T	0.77645	-0.2510	10	0.72032	D	0.01	.	13.0917	0.59169	0.0:0.0:0.719:0.281	.	118	Q9HCK0	ZBT26_HUMAN	W	118	ENSP00000362760:R118W;ENSP00000362758:R118W	ENSP00000362758:R118W	R	-	1	2	ZBTB26	124721683	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.606000	0.54095	2.605000	0.88082	0.591000	0.81541	CGG		0.443	ZBTB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053960.1	NM_020924		A	125681862	G	A	125681862	3	1	65	1	0	0	0	0	1	0	0	0	17572	1144	40	1	977	1	ZBTB26	9	125681862	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	51357632	125681862	15531569	74	20565										
C9orf114	51490	hgsc.bcm.edu	37	chr9	131589352	131589352	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tcaaacaccacgatctcatcCacacagaagatggcacaggc	7	14	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr9:131589352C>A	ENST00000361256.5	-	4	367	c.327G>T	c.(325-327)gtG>gtT	p.V109V		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	109							poly(A) RNA binding (GO:0044822)	p.V109V(1)		kidney(2)|large_intestine(4)|ovary(1)	7						CGATCTCATCCACACAGAAGA	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	9											144	124	131					9																	131589352		2203	4300	6503	130629173	SO:0001819	synonymous_variant	51490				CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"centromere protein 32"					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.327G>T	9.37:g.131589352C>A			130629173	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	ENST00000361256.5	37	CCDS6913.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359525	0.24598	.	.	ENSG00000198917	ENST00000372618	.	.	.	5.5	5.5	0.81552	.	0.340815	0.39274	N	0.001401	T	0.56292	0.1975	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49390	-0.8945	6	0.20519	T	0.43	-8.6629	11.8536	0.52425	0.0:0.9206:0.0:0.0794	.	.	.	.	L	109	.	ENSP00000361701:W109L	W	-	2	0	C9orf114	130629173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.182000	0.32029	2.602000	0.87976	0.650000	0.86243	TGG		0.627	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390		A	131589352	C	A	131589352	2	1	65	1	0	0	0	0	0	0	0	1	2455	581	21	2		2	C9orf114	9	131589352	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	5907490	131589352	9624079	75	20566										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7618864	7618864	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttccccgcaatgatgatctcCgagccgttgaagtagttggg	12	10	1	3	rs578011384		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr10:7618864C>T	ENST00000256861.6	-	10	1608	c.1530G>A	c.(1528-1530)tcG>tcA	p.S510S	ITIH5_ENST00000298441.6_Silent_p.S296S|ITIH5_ENST00000397145.2_Silent_p.S510S|ITIH5_ENST00000446830.2_Silent_p.S292S|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.S510S	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	510					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S510S(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TGATGATCTCCGAGCCGTTGA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	10											77	73	74					10																	7618864		2203	4300	6503	7658870	SO:0001819	synonymous_variant	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1530G>A	10.37:g.7618864C>T			7658870	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																					0.557	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7618864	C	T	7618864	2	4	65	1	0	0	0	0	0	0	0	1	7928	639	23	1		1	ITIH5	10	7618864	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		7618864	127915883	76	20567										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88213443	88213449	+	Frame_Shift_Del	DEL	CGATGAT	CGATGAT	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agttaaattaagcaacacccCgatgatggccctcatgcagt					rs367828346|rs371694095		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CGATGAT	CGATGAT	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr10:88213443_88213449delCGATGAT	ENST00000298767.5	-	13	3269_3275	c.2797_2803delATCATCG	c.(2797-2805)atcatcgggfs	p.IIG933fs	WAPAL_ENST00000372075.1_Frame_Shift_Del_p.IIG200fs|WAPAL_ENST00000263070.7_Frame_Shift_Del_p.IIG200fs	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	933	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)		p.I933fs*6(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AGCAACACCCCGATGATGGCCCTCATG	0.391																																																1	Deletion - Frameshift(1)	large_intestine(1)	10																																								88203429	SO:0001589	frameshift_variant	23063			AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2797_2803delATCATCG	10.37:g.88213443_88213449delCGATGAT	ENSP00000298767:p.Ile933fs		88203423	A7E2B5|Q5VSK5|Q8IX10|Q92549	Frame_Shift_Del	DEL	ENST00000298767.5	37	CCDS7375.1																																																																																				0.391	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		-	88213449	CGATGAT	-	88213443	7	5	65	1	0	1	0	1	0	0	0	0	17288	652	23	0	797	0	WAPAL	10	88213443	Frame_Shift_Del	DEL	CGATGAT	TCGA-AG-A00Y-01A-02W-A005-10	80594579	88213443	47321304	77	20568										
CARS	833	hgsc.bcm.edu	37	chr11	3041471	3041471	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttccccaagggcacggccaGgacggttctccgggcttaga	13	13	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:3041471G>A	ENST00000397111.5	-	10	1241	c.996C>T	c.(994-996)tcC>tcT	p.S332S	CARS_ENST00000397114.3_Silent_p.S322S|CARS_ENST00000401769.3_Silent_p.S345S|CARS_ENST00000380525.4_Silent_p.S415S|CARS_ENST00000278224.9_Silent_p.S332S			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	332					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.S332S(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	GGCACGGCCAGGACGGTTCTC	0.627			T	ALK	ALCL																																Ovarian(61;932 1157 5961 20446 52152)		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	1	Substitution - coding silent(1)	large_intestine(1)	11											115	92	100					11																	3041471		2202	4298	6500	2998047	SO:0001819	synonymous_variant	833			AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	1493	protein-coding gene	gene with protein product	"cysteine tRNA ligase 1, cytoplasmic"	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.996C>T	11.37:g.3041471G>A			2998047	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Silent	SNP	ENST00000397111.5	37	CCDS7742.1																																																																																				0.627	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751		A	3041471	G	A	3041471	2	1	65	1	0	0	0	0	0	0	0	1	2663	987	35	3		3	CARS	11	3041471	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10		3041471	131965045	78	20569										
ILK	3611	hgsc.bcm.edu	37	chr11	6629429	6629429	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gccagtcatggacaccgtgaTattgtacagaaggtacgtac	11	9	1	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:6629429T>C	ENST00000396751.2	+	2	699	c.243T>C	c.(241-243)gaT>gaC	p.D81D	ILK_ENST00000299421.4_Silent_p.D81D|ILK_ENST00000528995.1_Silent_p.D81D|ILK_ENST00000537806.1_Intron|TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000420936.2_Silent_p.D81D|RP11-732A19.2_ENST00000527398.1_RNA	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	81	Interaction with LIMS1.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.D81D(1)		central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		GACACCGTGATATTGTACAGA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	11											95	84	88					11																	6629429		2201	4296	6497	6586005	SO:0001819	synonymous_variant	3611			U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"Ankyrin repeat domain containing"	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.243T>C	11.37:g.6629429T>C			6586005	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																				0.502	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517		C	6629429	T	C	6629429	2	2	65	1	0	0	0	0	0	0	0	1	7734	1403	49	4		4	ILK	11	6629429	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	3587958	6629429	128377087	79	20570										
MRGPRX4	117196	hgsc.bcm.edu	37	chr11	18195753	18195754	+	In_Frame_Ins	INS	-	-	TAC													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gaaagcctggagctgtcgggINSaagcagattggggccatgag							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:18195753_18195754insTAC	ENST00000314254.3	+	1	1370_1371	c.950_951insTAC	c.(949-954)ggaagc>ggTACaagc	p.317_318GS>GTS	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	317				S -> R (in Ref. 2; AAL86882). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G317_S318insT(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GAGCTGTCGGGAAGCAGATTGG	0.559																																																1	Insertion - In frame(1)	large_intestine(1)	11																																								18152330	SO:0001652	inframe_insertion	117196			AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	Exception_encountered	11.37:g.18195753_18195754insTAC	ENSP00000314042:p.Gly317_Ser318insThr		18152329	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	In_Frame_Ins	INS	ENST00000314254.3	37	CCDS7831.1																																																																																				0.559	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		TAC	18195754	-	TAC	18195753	7	5	65	1	0	1	1	0	0	0	0	0	9799	1174	41	0	952	0	MRGPRX4	11	18195753	In_Frame_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	11566324	18195753	116810763	80	20571										
MAPK8IP1	9479	hgsc.bcm.edu	37	chr11	45927227	45927227	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttccagcagttctacaagcaGtttgtggagtacacctgccc	9	12	1	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:45927227G>A	ENST00000241014.2	+	12	2261	c.2091G>A	c.(2089-2091)caG>caA	p.Q697Q	MAPK8IP1_ENST00000395629.2_Silent_p.Q687Q|RP11-618K13.2_ENST00000533218.1_RNA	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	697	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)	p.Q697Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		TCTACAAGCAGTTTGTGGAGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	11											215	197	203					11																	45927227		2203	4299	6502	45883803	SO:0001819	synonymous_variant	9479				CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.2091G>A	11.37:g.45927227G>A			45883803	D3DQP4|O43407	Silent	SNP	ENST00000241014.2	37	CCDS7916.1																																																																																				0.597	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		A	45927227	G	A	45927227	2	1	65	1	0	0	0	0	0	0	0	1	9314	1020	36	3		3	MAPK8IP1	11	45927227	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	27731474	45927227	89079289	81	20572										
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45946111	45946112	+	Frame_Shift_Ins	INS	-	-	GG													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cggcctctatgggctaatgaINSagctggtgctgcccagtgcc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:45946111_45946112insGG	ENST00000531526.1	+	5	658_659	c.547_548insGG	c.(547-549)aagfs	p.K183fs	GYLTL1B_ENST00000401752.1_Frame_Shift_Ins_p.K183fs|GYLTL1B_ENST00000529052.1_Frame_Shift_Ins_p.K152fs|GYLTL1B_ENST00000389968.3_5'UTR|GYLTL1B_ENST00000325468.5_Frame_Shift_Ins_p.K183fs|GYLTL1B_ENST00000536139.1_Frame_Shift_Ins_p.K152fs	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	183					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.K183fs*77(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		TGGGCTAATGAAGCTGGTGCTG	0.614																																																1	Insertion - Frameshift(1)	large_intestine(1)	11																																								45902688	SO:0001589	frameshift_variant	120071				CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	Exception_encountered	11.37:g.45946111_45946112insGG	ENSP00000432869:p.Lys183fs		45902687	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Frame_Shift_Ins	INS	ENST00000531526.1	37	CCDS31473.1																																																																																				0.614	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		GG	45946112	-	GG	45946111	7	5	65	1	0	1	1	0	0	0	0	0	6928	247	9	0	561	0	GYLTL1B	11	45946111	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	18884	45946111	89060405	82	20573	24	2								
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45946116	45946116	+	Silent	SNP	G	G	C													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctctatgggctaatgaagctGgtgctgcccagtgccttgcc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:45946116G>C	ENST00000531526.1	+	5	663	c.552G>C	c.(550-552)ctG>ctC	p.L184L	GYLTL1B_ENST00000401752.1_Silent_p.L184L|GYLTL1B_ENST00000529052.1_Silent_p.L153L|GYLTL1B_ENST00000389968.3_5'UTR|GYLTL1B_ENST00000325468.5_Silent_p.L184L|GYLTL1B_ENST00000536139.1_Silent_p.L153L	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	184					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.L184L(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		TAATGAAGCTGGTGCTGCCCA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	11											88	85	86					11																	45946116		2203	4299	6502	45902692	SO:0001819	synonymous_variant	120071				CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.552G>C	11.37:g.45946116G>C			45902692	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	ENST00000531526.1	37	CCDS31473.1																																																																																				0.612	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		C	45946116	G	C	45946116	2	2	65	1	0	0	0	0	0	0	0	1	6928	1335	47	5		5	GYLTL1B	11	45946116	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	5	45946116	89060400	83	20574	24	2								
MS4A10	341116	hgsc.bcm.edu	37	chr11	60559758	60559758	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttctcatttcagggatcttGgcgataacaatgaagacctt	8	8	3	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:60559758G>A	ENST00000308287.1	+	4	420	c.324G>A	c.(322-324)ttG>ttA	p.L108L		NM_206893.3	NP_996776.2	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member 10	108						integral component of membrane (GO:0016021)		p.L108L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|skin(2)	21						CAGGGATCTTGGCGATAACAA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	11											190	174	179					11																	60559758		2203	4300	6503	60316334	SO:0001819	synonymous_variant	341116			AK122633	CCDS7992.1	11q12.2	2008-02-05				ENSG00000172689			13368	protein-coding gene	gene with protein product		608403				11486273, 11401424	Standard	NM_206893		Approved	CD20L7, MS4A9	uc001npz.1	Q96PG2		ENST00000308287.1:c.324G>A	11.37:g.60559758G>A			60316334	B2RP45|Q96PG3	Silent	SNP	ENST00000308287.1	37	CCDS7992.1																																																																																				0.453	MS4A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395619.1	NM_206893		A	60559758	G	A	60559758	2	1	65	1	0	0	0	0	0	0	0	1	9885	1339	47	3		3	MS4A10	11	60559758	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	14613642	60559758	74446758	84	20575										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288674	62288674	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccttccactttgggcagagaGacatccacatcacctttcac	6	15	2	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:62288674G>A	ENST00000378024.4	-	5	13489	c.13215C>T	c.(13213-13215)gtC>gtT	p.V4405V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4405					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V4405V(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGGGCAGAGAGACATCCACAT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	11											145	152	150					11																	62288674		2202	4299	6501	62045250	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13215C>T	11.37:g.62288674G>A			62045250	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.468	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62288674	G	A	62288674	2	1	65	1	0	0	0	0	0	0	0	1	414	929	33	3		3	AHNAK	11	62288674	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	1728916	62288674	72717842	85	20576										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62298736	62298736	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggcatcttaaacttcgggccTttcaacttcccttcaggtcc	7	14	3	0	rs116435570		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:62298736T>C	ENST00000378024.4	-	5	3427	c.3153A>G	c.(3151-3153)aaA>aaG	p.K1051K	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1051					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.K1051K(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ACTTCGGGCCTTTCAACTTCC	0.443													T|||	1	0.000199681	8e-04	0	5008	,	,		21229	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11											92	91	91					11																	62298736		2202	4299	6501	62055312	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3153A>G	11.37:g.62298736T>C			62055312	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.443	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62298736	T	C	62298736	2	2	65	1	0	0	0	0	0	0	0	1	414	1606	56	4		4	AHNAK	11	62298736	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	10062	62298736	72707780	86	20577										
RBM4B	83759	hgsc.bcm.edu	37	chr11	66436369	66436370	+	Frame_Shift_Ins	INS	-	-	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	taggtgtctgtcatagggatINScaacagaagtagagttgagg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:66436369_66436370insA	ENST00000525754.1	-	2	1473_1474	c.805_806insT	c.(805-807)gatfs	p.D269fs	RP11-658F2.8_ENST00000548810.1_RNA|RP11-658F2.8_ENST00000550837.1_RNA|RBM4B_ENST00000529195.2_5'Flank|RBM4B_ENST00000310046.4_Frame_Shift_Ins_p.D269fs|RBM4B_ENST00000531969.1_Intron			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	269	Interaction with TNPO3. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D269fs*4(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						GTCATAGGGATCAACAGAAGTA	0.545																																																1	Insertion - Frameshift(1)	large_intestine(1)	11																																								66192946	SO:0001589	frameshift_variant	83759			AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	28842	protein-coding gene	gene with protein product			"RNA binding motif protein 30"	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.805_806insT	11.37:g.66436369_66436370insA	ENSP00000433071:p.Asp269fs		66192945	B3KT83	Frame_Shift_Ins	INS	ENST00000525754.1	37	CCDS8149.1																																																																																				0.545	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492		A	66436370	-	A	66436369	7	5	65	1	0	1	1	0	0	0	0	0	13179	1435	50	0	277	0	RBM4B	11	66436369	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	4137633	66436369	68570147	87	20578										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110451496	110451497	+	Frame_Shift_Ins	INS	-	-	CA													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acagctggacttgcgtagctINSttttctgataaaactccctg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:110451496_110451497insCA	ENST00000260283.4	-	16	2457_2458	c.2173_2174insTG	c.(2173-2175)aagfs	p.K725fs	ARHGAP20_ENST00000533353.1_Frame_Shift_Ins_p.K699fs|ARHGAP20_ENST00000527598.1_Frame_Shift_Ins_p.K689fs|ARHGAP20_ENST00000528829.1_Frame_Shift_Ins_p.K689fs|ARHGAP20_ENST00000529591.1_Frame_Shift_Ins_p.K268fs|ARHGAP20_ENST00000524756.1_Frame_Shift_Ins_p.K702fs|ARHGAP20_ENST00000357139.3_Frame_Shift_Ins_p.K699fs	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	725					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.K725fs*20(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CTTGCGTAGCTTTTTCTGATAA	0.45																																																1	Insertion - Frameshift(1)	large_intestine(1)	11																																								109956707	SO:0001589	frameshift_variant	57569			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2173_2174insTG	11.37:g.110451496_110451497insCA	ENSP00000260283:p.Lys725fs		109956706	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Frame_Shift_Ins	INS	ENST00000260283.4	37	CCDS31673.1																																																																																				0.45	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		CA	110451497	-	CA	110451496	7	5	65	1	0	1	1	0	0	0	0	0	870	1609	56	0	1405	0	ARHGAP20	11	110451496	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	44015127	110451496	24555020	88	20579										
PANX3	116337	hgsc.bcm.edu	37	chr11	124481615	124481615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgctgatgtccctggcattcGcccaggagttctcctctggt	11	13	2	1	rs142639637	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr11:124481615G>A	ENST00000284288.2	+	1	230	c.163G>A	c.(163-165)Gcc>Acc	p.A55T		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	55					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)	p.A55T(2)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		CCTGGCATTCGCCCAGGAGTT	0.587													G|||	10	0.00199681	0.0076	0	5008	,	,		15784	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	11						G	THR/ALA	37,4365	42.3+/-75.8	1,35,2165	84	87	86		163	4.8	1	11	dbSNP_134	86	0,8598		0,0,4299	yes	missense	PANX3	NM_052959.2	58	1,35,6464	AA,AG,GG		0.0,0.8405,0.2846	probably-damaging	55/393	124481615	37,12963	2201	4299	6500	123986825	SO:0001583	missense	116337			AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"Ion channels / Pannexins"	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.163G>A	11.37:g.124481615G>A	ENSP00000284288:p.Ala55Thr		123986825		Missense_Mutation	SNP	ENST00000284288.2	37	CCDS8447.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	25.4	4.635799	0.87760	0.008405	0.0	ENSG00000154143	ENST00000284288	T	0.38887	1.11	4.78	4.78	0.61160	.	0.051343	0.85682	D	0.000000	T	0.51312	0.1667	L	0.50333	1.59	0.58432	D	0.999995	D	0.89917	1.0	D	0.75020	0.985	T	0.57300	-0.7835	10	0.51188	T	0.08	-16.2529	18.0228	0.89260	0.0:0.0:1.0:0.0	.	55	Q96QZ0	PANX3_HUMAN	T	55	ENSP00000284288:A55T	ENSP00000284288:A55T	A	+	1	0	PANX3	123986825	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.461000	0.97646	2.476000	0.83614	0.655000	0.94253	GCC		0.587	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			A	124481615	G	A	124481615	3	1	65	1	0	0	0	0	1	0	0	0	11453	1087	38	1	165	1	PANX3	11	124481615	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	14030119	124481615	10524901	89	20580										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	65	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		25398284	108453611	90	20581										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40713873	40713873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtggaaaaatttctttcaaaAaaaaggaaatttccaaagaa	6	4	2	1	rs11176013	byFrequency	TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:40713873A>G	ENST00000298910.7	+	34	4969	c.4911A>G	c.(4909-4911)aaA>aaG	p.K1637K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1637					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.K1637K(1)|p.K1649K(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTCTTTCAAAAAAAAGGAAAT	0.358											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2933	0.585663	0.587	0.6052	5008	,	,		14667	0.501		0.5427	False		,,,				2504	0.7014															2	Substitution - coding silent(2)	large_intestine(2)	12						G		2529,1869	498.4+/-364.1	744,1041,414	54	64	60		4911	5.5	1	12	dbSNP_120	60	4638,3954	529.1+/-381.5	1240,2158,898	no	coding-synonymous	LRRK2	NM_198578.3		1984,3199,1312	GG,GA,AA		46.0196,42.4966,44.8268		1637/2528	40713873	7167,5823	2199	4296	6495	39000140	SO:0001819	synonymous_variant	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4911A>G	12.37:g.40713873A>G		895	39000140	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																				0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		G	40713873	A	G	40713873	2	3	65	1	0	0	0	0	0	0	0	1	9062	11	1	4		4	LRRK2	12	40713873	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	15315589	40713873	93138022	91	20582										
TROAP	10024	hgsc.bcm.edu	37	chr12	49724135	49724136	+	Frame_Shift_Ins	INS	-	-	CA													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acactcagggctgccaaagcINScctgtcttccagaggagtgc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:49724135_49724136insCA	ENST00000257909.3	+	13	1583_1584	c.1507_1508insCA	c.(1507-1509)cccfs	p.P503fs	TROAP_ENST00000547923.1_Frame_Shift_Ins_p.P211fs|TROAP_ENST00000551245.1_Frame_Shift_Ins_p.P503fs	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	503					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)		p.C504fs*54(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						GCTGCCAAAGCCCTGTCTTCCA	0.589																																																1	Insertion - Frameshift(1)	large_intestine(1)	12																																								48010403	SO:0001589	frameshift_variant	10024			U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	Exception_encountered	12.37:g.49724135_49724136insCA	ENSP00000257909:p.Pro503fs		48010402	F8VSF9|Q6PJU7|Q8N5B2	Frame_Shift_Ins	INS	ENST00000257909.3	37	CCDS8784.1																																																																																				0.589	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		CA	49724136	-	CA	49724135	7	5	65	1	0	1	1	0	0	0	0	0	16615	739	26	0	1655	0	TROAP	12	49724135	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	9010262	49724135	84127760	92	20583										
DEPDC4	120863	hgsc.bcm.edu	37	chr12	100649877	100649877	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctgtctaggcaagtgttagtGataacaagatcttcctcttt	8	8	3	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:100649877G>A	ENST00000416321.1	-	4	830	c.828C>T	c.(826-828)atC>atT	p.I276I	Y_RNA_ENST00000384063.1_RNA	NM_152317.2	NP_689530.1	Q8N2C3	DEPD4_HUMAN	DEP domain containing 4	276					intracellular signal transduction (GO:0035556)			p.I276I(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)|urinary_tract(1)	15						AAGTGTTAGTGATAACAAGAT	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	12											173	153	160					12																	100649877		2203	4298	6501	99174008	SO:0001819	synonymous_variant	120863			AK090824	CCDS9075.1	12q23	2006-03-30				ENSG00000166153			22952	protein-coding gene	gene with protein product						12477932	Standard	XM_005268628		Approved	DEP.4, FLJ33505	uc001thi.3	Q8N2C3		ENST00000416321.1:c.828C>T	12.37:g.100649877G>A			99174008	Q496C8|Q96BW0	Silent	SNP	ENST00000416321.1	37	CCDS9075.1	.	.	.	.	.	.	.	.	.	.	g	0.016	-1.525995	0.00959	.	.	ENSG00000166153	ENST00000548313	.	.	.	4.96	-2.66	0.06077	.	.	.	.	.	T	0.29355	0.0731	.	.	.	0.24357	N	0.994892	.	.	.	.	.	.	T	0.26292	-1.0107	4	.	.	.	.	7.1104	0.25386	0.5139:0.0:0.374:0.1121	.	.	.	.	L	87	.	.	S	-	2	0	DEPDC4	99174008	0.947000	0.32204	0.002000	0.10522	0.001000	0.01503	0.034000	0.13776	-1.493000	0.01835	-1.203000	0.01651	TCA		0.333	DEPDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408482.1	NM_152317		A	100649877	G	A	100649877	2	1	65	1	0	0	0	0	0	0	0	1	4452	1280	45	3		3	DEPDC4	12	100649877	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	50925742	100649877	33202018	93	20584										
STAB2	55576	hgsc.bcm.edu	37	chr12	104089565	104089565	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gccgatgcctacacagtgttTgctccaaacaacaatgccat	7	13	0	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:104089565T>C	ENST00000388887.2	+	33	3729	c.3525T>C	c.(3523-3525)ttT>ttC	p.F1175F		NM_017564.9	NP_060034.9			stabilin 2									p.F1175F(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ACACAGTGTTTGCTCCAAACA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	12											113	108	110					12																	104089565		2203	4300	6503	102613695	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3525T>C	12.37:g.104089565T>C			102613695		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.423	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104089565	T	C	104089565	2	2	65	1	0	0	0	0	0	0	0	1	15277	1809	63	4		4	STAB2	12	104089565	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	3439688	104089565	29762330	94	20585										
FICD	11153	hgsc.bcm.edu	37	chr12	108913103	108913103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tggaagctgccaacgagggcGacgtgaggcctttcattcgc	14	11	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:108913103G>A	ENST00000552695.1	+	3	1463	c.1228G>A	c.(1228-1230)Gac>Aac	p.D410N	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	410	Fido. {ECO:0000255|PROSITE- ProRule:PRU00791}.				negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)	p.D410N(1)		NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						CAACGAGGGCGACGTGAGGCC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	12											100	93	95					12																	108913103		2203	4300	6503	107437233	SO:0001583	missense	11153			AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"huntingtin interacting protein 13", "fic S-phase protein cell division homolog (E. coli)"					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.1228G>A	12.37:g.108913103G>A	ENSP00000446479:p.Asp410Asn		107437233	O75406	Missense_Mutation	SNP	ENST00000552695.1	37	CCDS9116.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271747	0.80469	.	.	ENSG00000198855	ENST00000552695	.	.	.	6.02	6.02	0.97574	Filamentation induced by cAMP/death on curing-related (2);	0.000000	0.85682	D	0.000000	T	0.72890	0.3517	L	0.42487	1.325	0.80722	D	1	D	0.76494	0.999	P	0.62649	0.905	T	0.68401	-0.5418	9	0.38643	T	0.18	-50.3835	20.5407	0.99260	0.0:0.0:1.0:0.0	.	410	Q9BVA6	FICD_HUMAN	N	410	.	ENSP00000446479:D410N	D	+	1	0	FICD	107437233	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	9.869000	0.99810	2.865000	0.98341	0.655000	0.94253	GAC		0.587	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076		A	108913103	G	A	108913103	3	1	65	1	0	0	0	0	1	0	0	0	5906	1058	37	1	1234	1	FICD	12	108913103	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	4823538	108913103	24938792	95	20586										
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110811952	110811952	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atggagctgccgccccctcaCtgcatgccgaaccactgctc	9	18	1	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:110811952C>T	ENST00000455511.3	-	11	1797	c.1797G>A	c.(1795-1797)caG>caA	p.Q599Q	ANAPC7_ENST00000481473.1_5'UTR	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	599					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.Q565Q(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						CGCCCCCTCACTGCATGCCGA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	12											97	80	85					12																	110811952		2203	4300	6503	109296335	SO:0001819	synonymous_variant	51434			AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1797G>A	12.37:g.110811952C>T			109296335	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Silent	SNP	ENST00000455511.3	37	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	C	2.940	-0.219100	0.06101	.	.	ENSG00000196510	ENST00000552087	.	.	.	5.88	4.07	0.47477	.	.	.	.	.	T	0.71745	0.3376	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68907	-0.5285	4	.	.	.	-24.4285	15.8897	0.79286	0.0:0.8836:0.0:0.1164	.	.	.	.	M	149	.	.	V	-	1	0	ANAPC7	109296335	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	3.520000	0.53465	0.418000	0.25898	-2.069000	0.00389	GTG		0.632	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		T	110811952	C	T	110811952	2	4	65	1	0	0	0	0	0	0	0	1	606	564	20	3		3	ANAPC7	12	110811952	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	1898849	110811952	23039943	96	20587										
DHX37	57647	hgsc.bcm.edu	37	chr12	125441655	125441655	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agaagggcttccacggagggGggcgtcgggaaggggaagtt	21	6	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:125441655G>A	ENST00000308736.2	-	17	2282	c.2184C>T	c.(2182-2184)ccC>ccT	p.P728P	DHX37_ENST00000544745.1_Silent_p.P515P	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	728							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.P728P(2)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCACGGAGGGGGGCGTCGGGA	0.612																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	12											68	69	69					12																	125441655		2203	4300	6503	124007608	SO:0001819	synonymous_variant	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2184C>T	12.37:g.125441655G>A			124007608	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																				0.612	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125441655	G	A	125441655	2	1	65	1	0	0	0	0	0	0	0	1	4521	1219	43	3		3	DHX37	12	125441655	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	14629703	125441655	8410240	97	20588										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129563262	129563262	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aggatggtgtctgacagaggAgacaggatctggagggcaga	18	5	2	4			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr12:129563262A>G	ENST00000422113.2	-	8	2258	c.1932T>C	c.(1930-1932)tcT>tcC	p.S644S	TMEM132D_ENST00000389441.4_Silent_p.S182S	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	644					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.S644S(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		CTGACAGAGGAGACAGGATCT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	12											131	111	118					12																	129563262		2203	4300	6503	128129215	SO:0001819	synonymous_variant	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1932T>C	12.37:g.129563262A>G			128129215	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.577	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	129563262	A	G	129563262	2	3	65	1	0	0	0	0	0	0	0	1	16086	291	11	4		4	TMEM132D	12	129563262	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	4121607	129563262	4288633	98	20589										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25480370	25480370	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttgcagatctgttgatccctTtctaagattttcagtacaaa	6	8	3	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr13:25480370T>C	ENST00000381884.4	-	7	1991	c.1806A>G	c.(1804-1806)gaA>gaG	p.E602E	CENPJ_ENST00000545981.1_Silent_p.E602E	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	602					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)	p.E602E(1)		endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GTTGATCCCTTTCTAAGATTT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	13											67	69	68					13																	25480370		2203	4300	6503	24378370	SO:0001819	synonymous_variant	55835			AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1806A>G	13.37:g.25480370T>C			24378370	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1																																																																																				0.378	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		C	25480370	T	C	25480370	2	2	65	1	0	0	0	0	0	0	0	1	3240	1838	64	4		4	CENPJ	13	25480370	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10		25480370	89689508	99	20590										
DGKH	160851	hgsc.bcm.edu	37	chr13	42795469	42795469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttgggagagtacaaagataTcttcatccgtcatgacatca	8	8	4	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr13:42795469T>C	ENST00000337343.4	+	29	3533	c.3512T>C	c.(3511-3513)aTc>aCc	p.I1171T	DGKH_ENST00000538674.1_Intron|DGKH_ENST00000498255.2_Intron|DGKH_ENST00000536612.1_Missense_Mutation_p.I1035T|DGKH_ENST00000540693.1_Intron|DGKH_ENST00000261491.5_Intron|DGKH_ENST00000379274.2_Missense_Mutation_p.I1035T	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1171	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.I1171T(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TACAAAGATATCTTCATCCGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	13											205	186	193					13																	42795469		2203	4300	6503	41693469	SO:0001583	missense	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3512T>C	13.37:g.42795469T>C	ENSP00000337572:p.Ile1171Thr		41693469	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643348	0.29246	.	.	ENSG00000102780	ENST00000337343;ENST00000379274;ENST00000536612	D;D;D	0.85088	-1.94;-1.94;-1.94	5.58	-0.00731	0.14009	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.746103	0.13084	N	0.415114	T	0.67078	0.2855	N	0.11892	0.195	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.15484	0.005;0.013	T	0.52601	-0.8554	10	0.07175	T	0.84	.	9.5856	0.39514	0.0:0.2906:0.0:0.7094	.	1035;1171	Q86XP1-3;Q86XP1	.;DGKH_HUMAN	T	1171;1035;1035	ENSP00000337572:I1171T;ENSP00000368576:I1035T;ENSP00000445114:I1035T	ENSP00000337572:I1171T	I	+	2	0	DGKH	41693469	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	0.706000	0.25690	0.022000	0.15160	-0.441000	0.05720	ATC		0.418	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		C	42795469	T	C	42795469	3	2	65	1	0	0	0	0	1	0	0	0	4481	1435	50	4	3626	4	DGKH	13	42795469	Missense_Mutation	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	17315099	42795469	72374409	100	20591										
RB1	5925	hgsc.bcm.edu	37	chr13	48953741	48953741	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgtttgtagcgatacaaactTggagttcgcttgtattaccg	10	7	0	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr13:48953741T>G	ENST00000267163.4	+	14	1482	c.1344T>G	c.(1342-1344)ctT>ctG	p.L448L		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	448	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.L448L(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GATACAAACTTGGAGTTCGCT	0.348		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	24	Whole gene deletion(15)|Unknown(8)|Substitution - coding silent(1)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											21	21	21					13																	48953741		2201	4300	6501	47851742	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1344T>G	13.37:g.48953741T>G			47851742	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.348	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48953741	T	G	48953741	2	3	65	1	0	0	0	0	0	0	0	1	13135	1799	63	4		4	RB1	13	48953741	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	6158272	48953741	66216137	101	20592										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61985847	61985847	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccagttttagggtcaatcctGaaggactcaggcctaggacc	11	11	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr13:61985847G>A	ENST00000409186.1	-	5	4490	c.2385C>T	c.(2383-2385)ttC>ttT	p.F795F	PCDH20_ENST00000409204.4_Silent_p.F795F			Q8N6Y1	PCD20_HUMAN	protocadherin 20	795	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.F795F(1)|p.F768F(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GGTCAATCCTGAAGGACTCAG	0.478																																																2	Substitution - coding silent(2)	large_intestine(2)	13											84	82	82					13																	61985847		2203	4300	6503	60883848	SO:0001819	synonymous_variant	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.2385C>T	13.37:g.61985847G>A			60883848	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	37	CCDS9442.2																																																																																				0.478	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		A	61985847	G	A	61985847	2	1	65	1	0	0	0	0	0	0	0	1	11546	1281	45	3		3	PCDH20	13	61985847	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	13032106	61985847	53184031	102	20593										
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454911	84454912	+	Frame_Shift_Del	DEL	GG	GG	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tctttaccctgcagtctggtGggggcttcgcagaccactcg							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	GG	GG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr13:84454911_84454912delGG	ENST00000377084.2	-	1	1616_1617	c.731_732delCC	c.(730-732)cccfs	p.P244fs		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	244	LRRCT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.P244fs*6(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GCAGTCTGGTGGGGGCTTCGCA	0.55																																																1	Deletion - Frameshift(1)	large_intestine(1)	13																																								83352913	SO:0001589	frameshift_variant	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.731_732delCC	13.37:g.84454913_84454914delGG	ENSP00000366288:p.Pro244fs		83352912	Q5U5I6|Q96SF9	Frame_Shift_Del	DEL	ENST00000377084.2	37	CCDS9464.1																																																																																				0.55	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		-	84454912	GG	-	84454911	7	5	65	1	0	1	0	1	0	0	0	0	14779	1335	47	0	1362	0	SLITRK1	13	84454911	Frame_Shift_Del	DEL	GG	TCGA-AG-A00Y-01A-02W-A005-10	22469064	84454911	30714967	103	20594										
MMP14	4323	hgsc.bcm.edu	37	chr14	23311706	23311706	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtgtgggagagtgccacaccActgcgcttccgcgaggtgcc	15	13	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr14:23311706A>T	ENST00000311852.6	+	4	729	c.468A>T	c.(466-468)ccA>ccT	p.P156P	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	156					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P156P(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	GTGCCACACCACTGCGCTTCC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	14											82	57	65					14																	23311706		2203	4300	6503	22381546	SO:0001819	synonymous_variant	4323				CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.468A>T	14.37:g.23311706A>T			22381546	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	37	CCDS9577.1																																																																																				0.602	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		T	23311706	A	T	23311706	2	4	65	1	0	0	0	0	0	0	0	1	9683	146	6	5		5	MMP14	14	23311706	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10		23311706	84037834	104	20595										
ZFYVE1	53349	hgsc.bcm.edu	37	chr14	73441537	73441537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgtcacagacccgcactggcGcagggccccagccccgctca	11	19	2	1	rs142709121		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr14:73441537G>A	ENST00000556143.1	-	10	2657	c.1937C>T	c.(1936-1938)gCg>gTg	p.A646V	ZFYVE1_ENST00000554145.1_5'UTR|ZFYVE1_ENST00000555072.1_Missense_Mutation_p.A231V|ZFYVE1_ENST00000553891.1_Missense_Mutation_p.A646V|ZFYVE1_ENST00000318876.5_Missense_Mutation_p.A632V|ZFYVE1_ENST00000394207.2_Missense_Mutation_p.A231V	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	646					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)	p.A646V(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		CCGCACTGGCGCAGGGCCCCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14						G	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	85	82	83		1937,692	5.2	1	14	dbSNP_134	83	0,8600		0,0,4300	no	missense,missense	ZFYVE1	NM_021260.2,NM_178441.1	64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	646/778,231/363	73441537	1,13005	2203	4300	6503	72511290	SO:0001583	missense	53349			AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"Zinc fingers, FYVE domain containing"	13180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 172"	605471	"zinc finger protein, subfamily 2A (FYVE domain containing), 1"	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1937C>T	14.37:g.73441537G>A	ENSP00000450742:p.Ala646Val		72511290	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Missense_Mutation	SNP	ENST00000556143.1	37	CCDS9811.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.929917	0.73327	2.27E-4	0.0	ENSG00000165861	ENST00000553891;ENST00000318876;ENST00000556143;ENST00000394207;ENST00000555072	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66	6.07	5.18	0.71444	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.222755	0.46145	N	0.000306	T	0.54208	0.1844	N	0.20483	0.58	0.45139	D	0.998151	B;B	0.34200	0.441;0.386	B;B	0.25884	0.05;0.064	T	0.55256	-0.8169	10	0.38643	T	0.18	-24.1912	15.3906	0.74741	0.0664:0.0:0.9336:0.0	.	646;646	G3V5N8;Q9HBF4	.;ZFYV1_HUMAN	V	646;632;646;231;231	ENSP00000452442:A646V;ENSP00000326921:A632V;ENSP00000450742:A646V;ENSP00000377757:A231V;ENSP00000452232:A231V	ENSP00000326921:A646V	A	-	2	0	ZFYVE1	72511290	1.000000	0.71417	0.994000	0.49952	0.962000	0.63368	5.635000	0.67841	1.578000	0.49821	0.655000	0.94253	GCG		0.612	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260		A	73441537	G	A	73441537	3	1	65	1	0	0	0	0	1	0	0	0	17702	1087	38	1	408	1	ZFYVE1	14	73441537	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	50129831	73441537	33908003	105	20596										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92139281	92139281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atgttagcacagttggaaaaAtttttattcctttaaaaatg	6	4	0	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr14:92139281A>G	ENST00000256343.3	-	13	1214	c.1058T>C	c.(1057-1059)aTt>aCt	p.I353T		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	353					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.I353T(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				AGTTGGAAAAATTTTTATTCC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	14											76	83	80					14																	92139281		2203	4298	6501	91209034	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1058T>C	14.37:g.92139281A>G	ENSP00000256343:p.Ile353Thr		91209034	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.330614	0.00227	.	.	ENSG00000133962	ENST00000256343	T	0.43294	0.95	5.43	-10.9	0.00192	.	15.000100	0.00166	N	0.000000	T	0.11410	0.0278	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37502	-0.9703	10	0.33141	T	0.24	2.2839	1.8133	0.03095	0.3809:0.0856:0.2912:0.2423	.	353	Q9H7T0	CTSRB_HUMAN	T	353	ENSP00000256343:I353T	ENSP00000256343:I353T	I	-	2	0	CATSPERB	91209034	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.220000	0.00271	-3.843000	0.00100	-3.094000	0.00064	ATT		0.363	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		G	92139281	A	G	92139281	3	3	65	1	0	0	0	0	1	0	0	0	2697	101	4	4	2352	4	CATSPERB	14	92139281	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	18697744	92139281	15210259	106	20597										
OCA2	4948	hgsc.bcm.edu	37	chr15	28196949	28196949	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccaagatcaagatgaatgccAgggacaaacgaattgaggaa	11	7	1	4			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:28196949A>C	ENST00000354638.3	-	18	2087	c.1932T>G	c.(1930-1932)ccT>ccG	p.P644P	OCA2_ENST00000382996.2_Silent_p.P644P|OCA2_ENST00000353809.5_Silent_p.P620P	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	644					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.P644P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GATGAATGCCAGGGACAAACG	0.443									Oculocutaneous Albinism																																							1	Substitution - coding silent(1)	large_intestine(1)	15											166	128	141					15																	28196949		2203	4300	6503	25870544	SO:0001819	synonymous_variant	4948	Familial Cancer Database			CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1932T>G	15.37:g.28196949A>C			25870544	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																				0.443	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		C	28196949	A	C	28196949	2	2	65	1	0	0	0	0	0	0	0	1	10846	175	7	4		4	OCA2	15	28196949	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10		28196949	74334443	107	20598										
CYP19A1	1588	hgsc.bcm.edu	37	chr15	51510831	51510831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	atgcatcaaaataaccttggAttttaaccacgatagcactt	5	9	1	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:51510831A>G	ENST00000396402.1	-	6	803	c.650T>C	c.(649-651)aTc>aCc	p.I217T	RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000396404.4_Missense_Mutation_p.I217T|CYP19A1_ENST00000260433.2_Missense_Mutation_p.I217T|CYP19A1_ENST00000559878.1_Missense_Mutation_p.I217T	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	217					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.I217T(1)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	ATAACCTTGGATTTTAACCAC	0.378																																					Melanoma(142;1016 1807 39614 48966 51721)											1	Substitution - Missense(1)	large_intestine(1)	15											67	65	65					15																	51510831		2196	4293	6489	49298123	SO:0001583	missense	1588			D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"Cytochrome P450s"	2594	protein-coding gene	gene with protein product		107910	"cytochrome P450, subfamily XIX (aromatization of androgens)"	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.650T>C	15.37:g.51510831A>G	ENSP00000379683:p.Ile217Thr		49298123	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	37	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214745	0.79352	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000396404;ENST00000420301;ENST00000439712	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.85864	0.5796	M	0.91090	3.175	0.80722	D	1	P	0.50617	0.937	D	0.78314	0.991	D	0.88774	0.3266	10	0.87932	D	0	-30.3607	16.2631	0.82557	1.0:0.0:0.0:0.0	.	217	P11511	CP19A_HUMAN	T	217	ENSP00000379683:I217T;ENSP00000260433:I217T;ENSP00000379685:I217T;ENSP00000390614:I217T	ENSP00000260433:I217T	I	-	2	0	CYP19A1	49298123	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.960000	0.76036	2.239000	0.73571	0.528000	0.53228	ATC		0.378	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1			G	51510831	A	G	51510831	3	3	65	1	0	0	0	0	1	0	0	0	4154	333	12	4	881	4	CYP19A1	15	51510831	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	23313882	51510831	51020561	108	20599										
AQP9	366	hgsc.bcm.edu	37	chr15	58467169	58467169	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctgatcgtgggagaaaatgcAacagcacacatttttgcaac	9	9	0	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:58467169A>G	ENST00000219919.4	+	4	799	c.429A>G	c.(427-429)gcA>gcG	p.A143A	ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000536493.1_Silent_p.A143A|AQP9_ENST00000558772.1_Silent_p.A78A	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	143					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)	p.A143A(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		GAGAAAATGCAACAGCACACA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	15											162	144	150					15																	58467169		2192	4292	6484	56254461	SO:0001819	synonymous_variant	366			AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"Ion channels / Aquaporins"	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.429A>G	15.37:g.58467169A>G			56254461	Q9NP32	Silent	SNP	ENST00000219919.4	37	CCDS10165.1																																																																																				0.433	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980		G	58467169	A	G	58467169	2	3	65	1	0	0	0	0	0	0	0	1	833	117	5	4		4	AQP9	15	58467169	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	6956338	58467169	44064223	109	20600										
CILP	8483	hgsc.bcm.edu	37	chr15	65496628	65496628	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gccctcacaaactctgccttGatggtggctgccttcaggct	10	14	3	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65496628G>A	ENST00000261883.4	-	6	1063	c.897C>T	c.(895-897)atC>atT	p.I299I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	299					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.I299I(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						ACTCTGCCTTGATGGTGGCTG	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	15											86	84	85					15																	65496628		2201	4299	6500	63283681	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.897C>T	15.37:g.65496628G>A			63283681	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.473	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65496628	G	A	65496628	2	1	65	1	0	0	0	0	0	0	0	1	3435	1280	45	3		3	CILP	15	65496628	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	7029459	65496628	37034764	110	20601			1	9		5	4	226	N	G	2.087026e-10
CILP	8483	hgsc.bcm.edu	37	chr15	65496664	65496664	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aggctagtcttgggcattgtGagtacaatgggggcaaactt	14	6	1	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65496664G>A	ENST00000261883.4	-	6	1027	c.861C>T	c.(859-861)ctC>ctT	p.L287L		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	287					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.L287L(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						TGGGCATTGTGAGTACAATGG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	15											108	98	101					15																	65496664		2201	4299	6500	63283717	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.861C>T	15.37:g.65496664G>A			63283717	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.517	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65496664	G	A	65496664	2	1	65	1	0	0	0	0	0	0	0	1	3435	1277	45	3		3	CILP	15	65496664	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	36	65496664	37034728	111	20602			1	9		5	4	226	N	G	2.087026e-10
CILP	8483	hgsc.bcm.edu	37	chr15	65496694	65496694	+	Silent	SNP	G	G	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggggcaaacttgacctttgtGatcttcaggatgcttttgcc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65496694G>A	ENST00000261883.4	-	6	997	c.831C>T	c.(829-831)atC>atT	p.I277I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	277					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.I277I(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						TGACCTTTGTGATCTTCAGGA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	15											126	110	115					15																	65496694		2201	4299	6500	63283747	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.831C>T	15.37:g.65496694G>A			63283747	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.522	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65496694	G	A	65496694	2	1	65	1	0	0	0	0	0	0	0	1	3435	1280	45	3		3	CILP	15	65496694	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	30	65496694	37034698	112	20603	25	2	1	9		5	4	226	N	G	2.087026e-10
CILP	8483	hgsc.bcm.edu	37	chr15	65496703	65496703	+	Silent	SNP	G	G	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttgacctttgtgatcttcagGatgcttttgccatcagggca					rs377719940		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65496703G>A	ENST00000261883.4	-	6	988	c.822C>T	c.(820-822)atC>atT	p.I274I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	274					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.I274I(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						TGATCTTCAGGATGCTTTTGC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	15											132	115	121					15																	65496703		2201	4299	6500	63283756	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.822C>T	15.37:g.65496703G>A			63283756	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.532	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65496703	G	A	65496703	2	1	65	1	0	0	0	0	0	0	0	1	3435	1164	41	3		3	CILP	15	65496703	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	9	65496703	37034689	113	20604	25	2	1	9		5	4	226	N	G	2.087026e-10
CILP	8483	hgsc.bcm.edu	37	chr15	65496853	65496853	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gagacagccccatgaagcatGaagtcctggcacatgcaggc	12	12	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65496853G>A	ENST00000261883.4	-	6	838	c.672C>T	c.(670-672)ttC>ttT	p.F224F		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	224					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.F224F(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						CATGAAGCATGAAGTCCTGGC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	15											71	68	69					15																	65496853		2201	4299	6500	63283906	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.672C>T	15.37:g.65496853G>A			63283906	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.597	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65496853	G	A	65496853	2	1	65	1	0	0	0	0	0	0	0	1	3435	1281	45	3		3	CILP	15	65496853	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	150	65496853	37034539	114	20605			1	9		5	4	226	N	G	2.087026e-10
DPP8	54878	hgsc.bcm.edu	37	chr15	65773927	65773927	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	agaatctcaaaaggttgaatTagttccttatctatgacatc	6	7	2	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:65773927T>G	ENST00000341861.5	-	9	2672	c.1092A>C	c.(1090-1092)ctA>ctC	p.L364L	DPP8_ENST00000321147.6_Silent_p.L364L|DPP8_ENST00000321118.7_Silent_p.L364L|DPP8_ENST00000559233.1_Silent_p.L364L|DPP8_ENST00000358939.4_Silent_p.L348L|DPP8_ENST00000300141.6_Silent_p.L348L|DPP8_ENST00000339244.5_Intron	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	364					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)	p.L348L(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AAGGTTGAATTAGTTCCTTAT	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	15											81	85	84					15																	65773927		2201	4298	6499	63560980	SO:0001819	synonymous_variant	54878			AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.1092A>C	15.37:g.65773927T>G			63560980	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Silent	SNP	ENST00000341861.5	37	CCDS10207.1																																																																																				0.294	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		G	65773927	T	G	65773927	2	3	65	1	0	0	0	0	0	0	0	1	4743	1741	61	4		4	DPP8	15	65773927	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	277074	65773927	36757465	115	20606										
POLG	5428	hgsc.bcm.edu	37	chr15	89866641	89866641	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gacccaggacacaccttgtgAggcagcttgaaaaaccagca	10	12	0	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr15:89866641A>T	ENST00000268124.5	-	13	2592	c.2259T>A	c.(2257-2259)ccT>ccA	p.P753P	POLG_ENST00000442287.2_Silent_p.P753P	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	753					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)	p.P753P(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			ACACCTTGTGAGGCAGCTTGA	0.572								DNA polymerases (catalytic subunits)																													Colon(73;648 1203 11348 18386 27782)											1	Substitution - coding silent(1)	large_intestine(1)	15											156	109	125					15																	89866641		2200	4299	6499	87667645	SO:0001819	synonymous_variant	5428			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2259T>A	15.37:g.89866641A>T			87667645	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																				0.572	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		T	89866641	A	T	89866641	2	4	65	1	0	0	0	0	0	0	0	1	12231	291	11	5		5	POLG	15	89866641	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	24092714	89866641	12664751	116	20607										
C16orf93	90835	hgsc.bcm.edu	37	chr16	30770990	30770990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctgaccctgactccatggcaAaaaaggacactggtgaagta	10	10	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:30770990A>G	ENST00000543610.1	-	5	1486	c.525T>C	c.(523-525)ttT>ttC	p.F175F	RNF40_ENST00000563683.1_5'Flank|PHKG2_ENST00000563588.1_3'UTR|PHKG2_ENST00000424889.3_Intron|RNF40_ENST00000324685.6_5'Flank|C16orf93_ENST00000541260.1_Silent_p.F175F|RNF40_ENST00000357890.5_5'Flank|RNF40_ENST00000402121.3_5'Flank	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	175								p.F138F(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						CTCCATGGCAAAAAAGGACAC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	16											101	85	91					16																	30770990		2197	4300	6497	30678491	SO:0001819	synonymous_variant	90835			BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.525T>C	16.37:g.30770990A>G			30678491	A1A4V8|F5GX13|Q569G2	Silent	SNP	ENST00000543610.1	37	CCDS32434.2	.	.	.	.	.	.	.	.	.	.	A	10.37	1.330450	0.24167	.	.	ENSG00000196118	ENST00000535476	.	.	.	5.34	-2.87	0.05700	.	0.165039	0.43260	D	0.000598	T	0.59459	0.2195	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59322	-0.7476	6	0.52906	T	0.07	-14.619	9.8784	0.41218	0.2248:0.1464:0.6288:0.0	.	.	.	.	S	72	.	ENSP00000442644:F72S	F	-	2	0	C16orf93	30678491	0.959000	0.32827	0.985000	0.45067	0.972000	0.66771	0.019000	0.13444	-0.484000	0.06763	0.459000	0.35465	TTT		0.532	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979		G	30770990	A	G	30770990	2	3	65	1	0	0	0	0	0	0	0	1	1850	11	1	4		4	C16orf93	16	30770990	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10		30770990	59583763	117	20608										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56906570	56906571	+	Frame_Shift_Del	DEL	GA	GA	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	caggccttgcttttccagcgGacatttttgtccagaacttg					rs534168507		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	GA	GA	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:56906570_56906571delGA	ENST00000563236.1	+	8	992_993	c.967_968delGA	c.(967-969)gacfs	p.D323fs	SLC12A3_ENST00000438926.2_Frame_Shift_Del_p.D323fs|SLC12A3_ENST00000566786.1_Frame_Shift_Del_p.D322fs|SLC12A3_ENST00000262502.5_Frame_Shift_Del_p.D322fs			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	323					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)	p.D323fs*9(1)		breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	TTTTCCAGCGGACATTTTTGTC	0.594																																																1	Deletion - Frameshift(1)	large_intestine(1)	16																																								55464072	SO:0001589	frameshift_variant	6559				CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.967_968delGA	16.37:g.56906570_56906571delGA	ENSP00000456149:p.Asp323fs		55464071	A8MSJ2|C9JNN9	Frame_Shift_Del	DEL	ENST00000563236.1	37	CCDS58464.1																																																																																				0.594	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			-	56906571	GA	-	56906570	7	5	65	1	0	1	0	1	0	0	0	0	14421	1174	41	0	997	0	SLC12A3	16	56906570	Frame_Shift_Del	DEL	GA	TCGA-AG-A00Y-01A-02W-A005-10	26135580	56906570	33448183	118	20609										
NAE1	8883	hgsc.bcm.edu	37	chr16	66855428	66855428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gatcaaaagaggaatctgggAattccagaggacatctgcta	11	7	3	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:66855428A>G	ENST00000290810.3	-	7	533	c.436T>C	c.(436-438)Tcc>Ccc	p.S146P	NAE1_ENST00000394074.2_Missense_Mutation_p.S57P|NAE1_ENST00000379463.2_Missense_Mutation_p.S140P|NAE1_ENST00000564040.2_5'UTR|NAE1_ENST00000359087.4_Missense_Mutation_p.S149P			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	146					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)	p.S146P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	GGAATCTGGGAATTCCAGAGG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	16											93	87	89					16																	66855428		2200	4300	6500	65412929	SO:0001583	missense	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.436T>C	16.37:g.66855428A>G	ENSP00000290810:p.Ser146Pro		65412929	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Missense_Mutation	SNP	ENST00000290810.3	37	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.026195	0.35701	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463;ENST00000394074	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.63	3.45	0.39498	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.124475	0.56097	D	0.000040	T	0.35098	0.0920	L	0.47716	1.5	0.44595	D	0.997568	B;B;B;B	0.26602	0.154;0.001;0.086;0.059	B;B;B;B	0.27380	0.021;0.007;0.049;0.079	T	0.18116	-1.0347	10	0.30854	T	0.27	.	11.8359	0.52323	0.802:0.198:0.0:0.0	.	57;149;146;140	A8MU28;A6NCK0;Q13564;A6NFN4	.;.;ULA1_HUMAN;.	P	149;146;140;57	ENSP00000351990:S149P;ENSP00000290810:S146P;ENSP00000368776:S140P;ENSP00000377637:S57P	ENSP00000290810:S146P	S	-	1	0	NAE1	65412929	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	1.930000	0.40124	1.836000	0.53414	0.455000	0.32223	TCC		0.348	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905		G	66855428	A	G	66855428	3	3	65	1	0	0	0	0	1	0	0	0	10169	246	9	4	1224	4	NAE1	16	66855428	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	9948858	66855428	23499325	119	20610										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67578878	67578878	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtggtgcagttctcggcctcTcggcctggcttcctgacctt	12	14	2	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:67578878T>G	ENST00000379312.3	+	17	3022	c.2901T>G	c.(2899-2901)tcT>tcG	p.S967S	FAM65A_ENST00000540839.3_Silent_p.S982S|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000428437.2_Silent_p.S977S|FAM65A_ENST00000422602.2_Silent_p.S983S|FAM65A_ENST00000042381.4_Silent_p.S963S|CTD-2012K14.4_ENST00000564717.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	967						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.S963S(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		TCTCGGCCTCTCGGCCTGGCT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	16											149	150	150					16																	67578878		2198	4300	6498	66136379	SO:0001819	synonymous_variant	79567			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2901T>G	16.37:g.67578878T>G			66136379	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Silent	SNP	ENST00000379312.3	37	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	T	3.843	-0.033350	0.07543	.	.	ENSG00000039523	ENST00000428437	.	.	.	5.44	1.67	0.24075	.	0.324995	0.33327	N	0.005040	T	0.35770	0.0943	.	.	.	0.52099	D	0.999942	.	.	.	.	.	.	T	0.04440	-1.0951	6	0.13108	T	0.6	-13.3653	4.7889	0.13239	0.0:0.1999:0.2996:0.5005	.	.	.	.	A	957	.	ENSP00000389456:S957A	S	+	1	0	FAM65A	66136379	0.063000	0.20901	1.000000	0.80357	0.681000	0.39784	0.053000	0.14184	0.905000	0.36596	0.533000	0.62120	TCG		0.602	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		G	67578878	T	G	67578878	2	3	65	1	0	0	0	0	0	0	0	1	5618	1538	54	4		4	FAM65A	16	67578878	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	723450	67578878	22775875	120	20611										
GFOD2	81577	hgsc.bcm.edu	37	chr16	67709586	67709586	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acgtgccggatgccacggatGgcagcgttctgcctcacgaa	13	13	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:67709586G>C	ENST00000268797.7	-	3	975	c.630C>G	c.(628-630)gcC>gcG	p.A210A	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	210					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)	p.A210A(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		TGCCACGGATGGCAGCGTTCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	16											77	68	71					16																	67709586		2198	4300	6498	66267087	SO:0001819	synonymous_variant	81577			AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.630C>G	16.37:g.67709586G>C			66267087	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Silent	SNP	ENST00000268797.7	37	CCDS10845.1																																																																																				0.582	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819		C	67709586	G	C	67709586	2	2	65	1	0	0	0	0	0	0	0	1	6364	1335	47	5		5	GFOD2	16	67709586	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	130708	67709586	22645167	121	20612										
FANCA	2175	hgsc.bcm.edu	37	chr16	89851304	89851304	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aaaggcacgagttctgacaaGaacgtaaacaggaagaccag	11	8	1	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr16:89851304G>C	ENST00000389301.3	-	15	1458	c.1428C>G	c.(1426-1428)ttC>ttG	p.F476L	FANCA_ENST00000568369.1_Missense_Mutation_p.F476L	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	476					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.F476L(1)		breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GTTCTGACAAGAACGTAAACA	0.567			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	1	Substitution - Missense(1)	large_intestine(1)	16											170	152	158					16																	89851304		2198	4300	6498	88378805	SO:0001583	missense	2175	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1428C>G	16.37:g.89851304G>C	ENSP00000373952:p.Phe476Leu		88378805	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106773	0.56291	.	.	ENSG00000187741	ENST00000389301	D	0.98717	-5.09	5.58	4.43	0.53597	.	0.000000	0.64402	D	0.000008	D	0.98438	0.9480	M	0.80847	2.515	0.80722	D	1	D;D	0.62365	0.991;0.991	P;P	0.53593	0.73;0.73	D	0.98052	1.0388	10	0.72032	D	0.01	-36.8373	10.9233	0.47178	0.1594:0.0:0.8406:0.0	.	476;476	B4DRI7;O15360	.;FANCA_HUMAN	L	476	ENSP00000373952:F476L	ENSP00000373952:F476L	F	-	3	2	FANCA	88378805	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	4.071000	0.57556	2.643000	0.89663	0.549000	0.68633	TTC		0.567	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			C	89851304	G	C	89851304	3	2	65	1	0	0	0	0	1	0	0	0	5681	933	33	5	3055	5	FANCA	16	89851304	Missense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	22141718	89851304	503449	122	20613										
SLC43A2	124935	hgsc.bcm.edu	37	chr17	1519953	1519954	+	Frame_Shift_Ins	INS	-	-	AG													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	aaggagcccacagtgaaggcINScaaatttagcatctcgtcct					rs376006102		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:1519953_1519954insAG	ENST00000301335.5	-	3	358_359	c.270_271insCT	c.(268-273)ttggccfs	p.A91fs	SLC43A2_ENST00000382147.4_Frame_Shift_Ins_p.A91fs|snoU13_ENST00000459614.1_RNA|SLC43A2_ENST00000571650.1_Frame_Shift_Ins_p.A91fs	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	91					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)	p.A91fs*43(1)		endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		ACAGTGAAGGCCAAATTTAGCA	0.624																																																1	Insertion - Frameshift(1)	large_intestine(1)	17																																								1466704	SO:0001589	frameshift_variant	124935			BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"Solute carriers"	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.270_271insCT	17.37:g.1519953_1519954insAG	ENSP00000301335:p.Ala91fs		1466703	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Frame_Shift_Ins	INS	ENST00000301335.5	37	CCDS11006.1																																																																																				0.624	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		AG	1519954	-	AG	1519953	7	5	65	1	0	1	1	0	0	0	0	0	14670	739	26	0	1486	0	SLC43A2	17	1519953	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10		1519953	79675257	123	20614										
TP53	7157	hgsc.bcm.edu	37	chr17	7577082	7577082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tttcttgcggagattctcttCctctgtgcgccggtctctcc	9	14	4	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:7577082C>T	ENST00000269305.4	-	8	1045	c.856G>A	c.(856-858)Gaa>Aaa	p.E286K	TP53_ENST00000359597.4_Missense_Mutation_p.E286K|TP53_ENST00000445888.2_Missense_Mutation_p.E286K|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.E286K|TP53_ENST00000455263.2_Missense_Mutation_p.E286K	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E286K(58)|p.E286*(22)|p.0?(8)|p.E286Q(5)|p.?(2)|p.E286fs*59(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.G279fs*59(1)|p.R283fs*59(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGATTCTCTTCCTCTGTGCGC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	112	Substitution - Missense(63)|Substitution - Nonsense(22)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(2)	lung(18)|upper_aerodigestive_tract(13)|breast(10)|large_intestine(9)|urinary_tract(9)|skin(9)|oesophagus(9)|haematopoietic_and_lymphoid_tissue(8)|liver(7)|central_nervous_system(6)|bone(4)|ovary(3)|stomach(2)|vulva(1)|soft_tissue(1)|eye(1)|biliary_tract(1)|endometrium(1)	17	GRCh37	CM076567	TP53	M							95	81	86					17																	7577082		2203	4300	6503	7517807	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.856G>A	17.37:g.7577082C>T	ENSP00000269305:p.Glu286Lys		7517807	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.310731	0.81358	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	4.99	4.99	0.66335	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92077	3.27	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.77557	0.983;0.985;0.982;0.99	D	0.96355	0.9261	10	0.87932	D	0	-23.2961	15.807	0.78520	0.0:1.0:0.0:0.0	.	286;286;286;286	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	K	286;286;286;286;286;275;154	ENSP00000352610:E286K;ENSP00000269305:E286K;ENSP00000398846:E286K;ENSP00000391127:E286K;ENSP00000391478:E286K;ENSP00000425104:E154K	ENSP00000269305:E286K	E	-	1	0	TP53	7517807	1.000000	0.71417	0.972000	0.41901	0.455000	0.32408	7.587000	0.82613	2.579000	0.87056	0.462000	0.41574	GAA		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577082	C	T	7577082	3	4	65	1	0	0	0	0	1	0	0	0	16421	864	30	3	430	3	TP53	17	7577082	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	6057129	7577082	73618128	124	20615										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12028610	12028610	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acacttgtctttatgttccaGcctgaaagaatagacccaag	7	10	1	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:12028610G>T	ENST00000353533.5	+	8	876		c.e8-1		MAP2K4_ENST00000581941.1_Splice_Site|MAP2K4_ENST00000415385.3_Splice_Site	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4						apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(2)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTATGTTCCAGCCTGAAAGAA	0.428			"D, Mis, N"		"pancreatic, breast, colorectal"																																		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	12	Whole gene deletion(10)|Unknown(2)	ovary(4)|breast(4)|large_intestine(2)|biliary_tract(1)|pancreas(1)	17											188	152	164					17																	12028610		2203	4300	6503	11969335	SO:0001630	splice_region_variant	6416			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.814-1G>T	17.37:g.12028610G>T			11969335	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Splice_Site	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263678	0.59431	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8064	0.88602	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP2K4	11969335	1.000000	0.71417	0.998000	0.56505	0.604000	0.37047	9.561000	0.98142	2.814000	0.96858	0.563000	0.77884	.		0.428	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1		Intron	T	12028610	G	T	12028610	5	4	65	1	0	0	0	0	0	0	1	0	9269	985	34	2	843	2	MAP2K4	17	12028610	Splice_Site	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	4451528	12028610	69166600	125	20616										
PHF12	57649	hgsc.bcm.edu	37	chr17	27241005	27241005	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccgtcccgaatggccgcgggTgcaatgagagggggtggaaa	18	9	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:27241005T>C	ENST00000332830.4	-	8	1995	c.1185A>G	c.(1183-1185)gcA>gcG	p.A395A	PHF12_ENST00000577226.1_Silent_p.A395A|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000268756.3_Silent_p.A395A	NM_001033561.1	NP_001028733.1			PHD finger protein 12									p.A395A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	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)			TGGCCGCGGGTGCAATGAGAG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	17											95	93	93					17																	27241005		2203	4300	6503	24265131	SO:0001819	synonymous_variant	57649			AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"Zinc fingers, PHD-type"	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.1185A>G	17.37:g.27241005T>C			24265131		Silent	SNP	ENST00000332830.4	37	CCDS32598.1																																																																																				0.517	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		C	27241005	T	C	27241005	2	2	65	1	0	0	0	0	0	0	0	1	11854	1683	59	4		4	PHF12	17	27241005	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	15212395	27241005	53954205	126	20617										
ACACA	31	hgsc.bcm.edu	37	chr17	35454825	35454825	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgcaagtcagcaaactgcacGgctacctgatggtaaatggg	12	9	1	1	rs548821816		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:35454825G>A	ENST00000394406.2	-	53	6739	c.6549C>T	c.(6547-6549)gcC>gcT	p.A2183A	ACACA_ENST00000335166.5_Silent_p.A2105A|ACACA_ENST00000360679.3_Silent_p.A2125A|ACACA_ENST00000353139.5_Silent_p.A2220A|ACACA_ENST00000361253.5_Silent_p.A309A	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2183	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.A2125A(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CAAACTGCACGGCTACCTGAT	0.522																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											1	Substitution - coding silent(1)	large_intestine(1)	17											170	143	152					17																	35454825		2203	4300	6503	32528938	SO:0001819	synonymous_variant	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6549C>T	17.37:g.35454825G>A			32528938	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.522	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35454825	G	A	35454825	2	1	65	1	0	0	0	0	0	0	0	1	106	1103	39	1		1	ACACA	17	35454825	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	8213820	35454825	45740385	127	20618										
MED24	9862	hgsc.bcm.edu	37	chr17	38189334	38189335	+	Frame_Shift_Del	DEL	TG	TG	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgcgcttcaccatcgtcagcTgctccaccagggactgcgtc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	TG	TG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:38189334_38189335delTG	ENST00000394128.2	-	8	877_878	c.796_797delCA	c.(796-798)cagfs	p.Q266fs	MED24_ENST00000501516.3_Frame_Shift_Del_p.Q285fs|MED24_ENST00000479829.1_5'Flank|MED24_ENST00000356271.3_Frame_Shift_Del_p.Q253fs|MED24_ENST00000394127.2_Frame_Shift_Del_p.Q253fs|MED24_ENST00000394126.1_Frame_Shift_Del_p.Q291fs	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	266					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.Q266fs*29(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CATCGTCAGCTGCTCCACCAGG	0.644																																																1	Deletion - Frameshift(1)	large_intestine(1)	17																																								35442861	SO:0001589	frameshift_variant	9862			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.796_797delCA	17.37:g.38189334_38189335delTG	ENSP00000377686:p.Gln266fs		35442860	A8K4S5|B3KMR9|Q14143|Q9NNY5	Frame_Shift_Del	DEL	ENST00000394128.2	37	CCDS11359.1																																																																																				0.644	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		-	38189335	TG	-	38189334	7	5	65	1	0	1	0	1	0	0	0	0	9472	1580	55	0	2248	0	MED24	17	38189334	Frame_Shift_Del	DEL	TG	TCGA-AG-A00Y-01A-02W-A005-10	2734509	38189334	43005876	128	20619										
GAST	2520	hgsc.bcm.edu	37	chr17	39872082	39872082	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gaagaagaagaagcctatggAtggatggacttcggccgccg	15	8	0	3	rs535385347		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:39872082A>G	ENST00000329402.3	+	3	331	c.264A>G	c.(262-264)ggA>ggG	p.G88G	JUP_ENST00000540235.1_Intron|RNA5SP442_ENST00000365050.1_RNA	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	88					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.G88G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			AAGCCTATGGATGGATGGACT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	17											80	81	80					17																	39872082		2203	4300	6503	37125608	SO:0001819	synonymous_variant	2520				CCDS11404.1	17q21.2	2013-02-26	2005-06-14	2005-06-14	ENSG00000184502	ENSG00000184502		"Endogenous ligands"	4164	protein-coding gene	gene with protein product	"preprogastrin"	137250		GAS			Standard	NM_000805		Approved		uc002hxl.3	P01350	OTTHUMG00000133496	ENST00000329402.3:c.264A>G	17.37:g.39872082A>G			37125608	P78463|P78464	Silent	SNP	ENST00000329402.3	37	CCDS11404.1																																																																																				0.577	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1			G	39872082	A	G	39872082	2	3	65	1	0	0	0	0	0	0	0	1	6272	320	12	4		4	GAST	17	39872082	Silent	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	1682748	39872082	41323128	129	20620										
PPY	5539	hgsc.bcm.edu	37	chr17	42018858	42018858	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctggtcagcatgttgatgtaTctacggagatcagctgcata	11	8	3	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:42018858T>C	ENST00000591228.1	-	2	252	c.165A>G	c.(163-165)agA>agG	p.R55R	PPY_ENST00000225992.3_Silent_p.R55R|PPY_ENST00000587006.1_Silent_p.R55R			P01298	PAHO_HUMAN	pancreatic polypeptide	55					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.R55R(1)		large_intestine(2)|lung(1)|skin(1)	4		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TGTTGATGTATCTACGGAGAT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	17											152	141	145					17																	42018858		2203	4300	6503	39374384	SO:0001819	synonymous_variant	5539				CCDS11472.1	17q21.31	2013-02-28			ENSG00000108849	ENSG00000108849		"Endogenous ligands"	9327	protein-coding gene	gene with protein product	"pancreatic polypeptide Y", "prepro-PP (prepropancreatic polypeptide)"	167780				3753985	Standard	NM_002722		Approved	PNP	uc002iep.3	P01298		ENST00000591228.1:c.165A>G	17.37:g.42018858T>C			39374384		Silent	SNP	ENST00000591228.1	37	CCDS11472.1																																																																																				0.622	PPY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457656.1	NM_002722		C	42018858	T	C	42018858	2	2	65	1	0	0	0	0	0	0	0	1	12449	1432	50	4		4	PPY	17	42018858	Silent	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	2146776	42018858	39176352	130	20621										
MRC2	9902	hgsc.bcm.edu	37	chr17	60743538	60743539	+	In_Frame_Ins	INS	-	-	TCT													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccagtggttccacggctgcaINSccagcacgggccgcgaggat							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:60743538_60743539insTCT	ENST00000303375.5	+	3	1006_1007	c.604_605insTCT	c.(604-606)acc>aTCTcc	p.202_202T>IS		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	202	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)	p.T202>IS(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCACGGCTGCACCAGCACGGGC	0.609																																																1	Complex - insertion inframe(1)	large_intestine(1)	17																																								58097271	SO:0001652	inframe_insertion	9902			AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		Exception_encountered	17.37:g.60743538_60743539insTCT	ENSP00000307513:p.Thr202delinsIleSer		58097270	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	In_Frame_Ins	INS	ENST00000303375.5	37	CCDS11634.1																																																																																				0.609	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			TCT	60743539	-	TCT	60743538	7	5	65	1	0	1	1	0	0	0	0	0	9788	159	6	0	614	0	MRC2	17	60743538	In_Frame_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	18724680	60743538	20451672	131	20622										
NAT9	26151	hgsc.bcm.edu	37	chr17	72768361	72768362	+	Frame_Shift_Ins	INS	-	-	T													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctcacactttcttaccgtaaINSgacagcatcgcgagaacggc					rs566744182		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:72768361_72768362insT	ENST00000357814.3	-	5	462_463	c.389_390insA	c.(388-390)tctfs	p.S130fs	NAT9_ENST00000578822.1_Frame_Shift_Ins_p.S135fs|NAT9_ENST00000582524.1_Frame_Shift_Ins_p.S130fs|NAT9_ENST00000582870.1_Frame_Shift_Ins_p.S134fs|NAT9_ENST00000583476.1_Frame_Shift_Ins_p.S130fs|NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000580632.1_Intron|NAT9_ENST00000580301.1_Frame_Shift_Ins_p.S129fs|NAT9_ENST00000581136.1_Frame_Shift_Ins_p.S130fs|NAT9_ENST00000583757.1_Frame_Shift_Ins_p.S129fs	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	130	N-acetyltransferase.					protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)	p.Y131fs*12(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						TCTTACCGTAAGACAGCATCGC	0.609																																																1	Insertion - Frameshift(1)	large_intestine(1)	17																																								70279957	SO:0001589	frameshift_variant	26151			AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.389_390insA	17.37:g.72768361_72768362insT	ENSP00000350467:p.Ser130fs		70279956	B2R7F0|Q9BTD0|Q9Y3T3	Frame_Shift_Ins	INS	ENST00000357814.3	37	CCDS11706.1																																																																																				0.609	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		T	72768362	-	T	72768361	7	5	65	1	0	1	1	0	0	0	0	0	10212	59	3	0	245	0	NAT9	17	72768361	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	12024823	72768361	8426849	132	20623										
TMEM104	54868	hgsc.bcm.edu	37	chr17	72832329	72832330	+	In_Frame_Ins	INS	-	-	ACTGCA													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	catcttctgcttccgcggcgINSacagcctcatggacatgtac					rs574674425		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:72832329_72832330insACTGCA	ENST00000335464.5	+	10	1156_1157	c.994_995insACTGCA	c.(994-996)gac>gACTGCAac	p.332_333insCN	TMEM104_ENST00000582330.1_In_Frame_Ins_p.332_333insCN|TMEM104_ENST00000582773.1_Intron|TMEM104_ENST00000417024.2_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	332						integral component of membrane (GO:0016021)		p.D332_S333insCN(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CTTCCGCGGCGACAGCCTCATG	0.619																																																1	Insertion - In frame(1)	large_intestine(1)	17																																								70343925	SO:0001652	inframe_insertion	54868			AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		Exception_encountered	17.37:g.72832329_72832330insACTGCA	ENSP00000334849:p.Asp332_Ser333insCysAsn		70343924	Q8TEU1|Q9NT56|Q9NXH1	In_Frame_Ins	INS	ENST00000335464.5	37	CCDS32723.1																																																																																				0.619	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		ACTGCA	72832330	-	ACTGCA	72832329	7	5	65	1	0	1	1	0	0	0	0	0	16057	1058	37	0	1028	0	TMEM104	17	72832329	In_Frame_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	63968	72832329	8362881	133	20624										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73826131	73826132	+	Frame_Shift_Ins	INS	-	-	C													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tcaaaggtctcatcaaacaaINStgggtgaaggtccttcttgt							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr17:73826131_73826132insC	ENST00000207549.4	-	30	3310_3311	c.2931_2932insG	c.(2929-2934)ccattgfs	p.L978fs	UNC13D_ENST00000412096.2_Frame_Shift_Ins_p.L978fs	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	978	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)		p.L978fs*3(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCATCAAACAATGGGTGAAGGT	0.609									Familial Hemophagocytic Lymphohistiocytosis																																							1	Insertion - Frameshift(1)	large_intestine(1)	17																																								71337727	SO:0001589	frameshift_variant	201294	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2931_2932insG	17.37:g.73826131_73826132insC	ENSP00000207549:p.Leu978fs		71337726	B4DWG9|Q9H7K5	Frame_Shift_Ins	INS	ENST00000207549.4	37	CCDS11730.1																																																																																				0.609	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		C	73826132	-	C	73826131	7	5	65	1	0	1	1	0	0	0	0	0	17027	98	4	0	352	0	UNC13D	17	73826131	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	993802	73826131	7369079	134	20625										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5410583	5410583	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acctcagtggcagtggtctcCccgtcggctgcggtgtccgt	14	14	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr18:5410583C>T	ENST00000341928.2	-	14	2443	c.2103G>A	c.(2101-2103)ggG>ggA	p.G701G	EPB41L3_ENST00000342933.3_Silent_p.G701G|EPB41L3_ENST00000540638.2_Silent_p.G532G|EPB41L3_ENST00000544123.1_Silent_p.G532G|EPB41L3_ENST00000427684.2_5'UTR|EPB41L3_ENST00000400111.3_Silent_p.G532G|EPB41L3_ENST00000542146.1_5'UTR|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	701	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.G701G(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CAGTGGTCTCCCCGTCGGCTG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	18											101	66	78					18																	5410583		2203	4300	6503	5400583	SO:0001819	synonymous_variant	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2103G>A	18.37:g.5410583C>T			5400583	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	CCDS11838.1																																																																																				0.537	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5410583	C	T	5410583	2	4	65	1	0	0	0	0	0	0	0	1	5167	610	22	3		3	EPB41L3	18	5410583	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		5410583	72666665	135	20626										
MUM1	84939	hgsc.bcm.edu	37	chr19	1366323	1366327	+	Frame_Shift_Del	DEL	GAGAT	GAGAT	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggtcaaaagcgtcaggcagaGagataagaaagcaagtgtgc					rs373401790|rs376603583		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	GAGAT	GAGAT	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:1366323_1366327delGAGAT	ENST00000415183.3	+	7	1333_1337	c.1307_1311delGAGAT	c.(1306-1311)agagatfs	p.RD436fs	MUM1_ENST00000591806.1_Frame_Shift_Del_p.RD436fs|MUM1_ENST00000311401.5_Frame_Shift_Del_p.RD367fs|MUM1_ENST00000344663.3_Frame_Shift_Del_p.RD436fs			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	435	PWWP.				chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)	p.R436fs*24(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)		GTCAGGCAGAGAGATAAGAAAGCAA	0.415																																																1	Deletion - Frameshift(1)	large_intestine(1)	19																																								1317327	SO:0001589	frameshift_variant	84939			AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1307_1311delGAGAT	19.37:g.1366323_1366327delGAGAT	ENSP00000394925:p.Arg436fs		1317323	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Frame_Shift_Del	DEL	ENST00000415183.3	37																																																																																					0.415	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		-	1366327	GAGAT	-	1366323	7	5	65	1	0	1	0	1	0	0	0	0	10015	942	33	0	1333	0	MUM1	19	1366323	Frame_Shift_Del	DEL	GAGAT	TCGA-AG-A00Y-01A-02W-A005-10		1366323	57762660	136	20627										
APC2	10297	hgsc.bcm.edu	37	chr19	1462030	1462030	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cacagcacagagaacaaggcGgccatctgccaggtggatgg	14	11	1	1	rs376388515		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:1462030G>A	ENST00000535453.1	+	13	3420	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A	C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Silent_p.A569A|APC2_ENST00000238483.4_Silent_p.A295A|CTB-25B13.12_ENST00000588225.1_RNA			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)	p.A569A(1)		breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAACAAGGCGGCCATCTGCC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	62	52	56		1707	-3.3	1	19		56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	APC2	NM_005883.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		569/2304	1462030	1,13005	2203	4300	6503	1413030	SO:0001819	synonymous_variant	10297				CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.1707G>A	19.37:g.1462030G>A			1413030	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																				0.652	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		A	1462030	G	A	1462030	2	1	65	1	0	0	0	0	0	0	0	1	764	1103	39	1		1	APC2	19	1462030	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	95707	1462030	57666953	137	20628										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2876218	2876218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tgggcctcccttttaggaaaAaattgggaagaacatagcgt	11	7	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:2876218A>C	ENST00000307635.2	+	3	345	c.258A>C	c.(256-258)aaA>aaC	p.K86N	ZNF556_ENST00000586426.1_Missense_Mutation_p.K86N	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K86N(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		TTTTAGGAAAAAATTGGGAAG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											131	144	139					19																	2876218		2203	4300	6503	2827218	SO:0001583	missense	80032			BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.258A>C	19.37:g.2876218A>C	ENSP00000302603:p.Lys86Asn		2827218	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.091731	0.36952	.	.	ENSG00000172000	ENST00000307635	T	0.06218	3.33	2.39	1.34	0.21922	.	.	.	.	.	T	0.08582	0.0213	M	0.77313	2.365	0.09310	N	1	B	0.28026	0.198	B	0.18263	0.021	T	0.22452	-1.0216	9	0.52906	T	0.07	.	5.4887	0.16763	0.8452:0.0:0.1548:0.0	.	86	Q9HAH1	ZN556_HUMAN	N	86	ENSP00000302603:K86N	ENSP00000302603:K86N	K	+	3	2	ZNF556	2827218	0.126000	0.22350	0.018000	0.16275	0.515000	0.34225	0.255000	0.18333	0.199000	0.20427	0.323000	0.21402	AAA		0.398	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		C	2876218	A	C	2876218	3	2	65	1	0	0	0	0	1	0	0	0	18026	11	1	4	268	4	ZNF556	19	2876218	Missense_Mutation	SNP	A	TCGA-AG-A00Y-01A-02W-A005-10	1414188	2876218	56252765	138	20629										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2878138	2878138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	catgagagaaagcacactggGgagaaacctgtaaatgcagc	12	8	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:2878138G>A	ENST00000307635.2	+	4	1269	c.1182G>A	c.(1180-1182)ggG>ggA	p.G394G	ZNF556_ENST00000586426.1_Silent_p.G393G	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G394G(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		AGCACACTGGGGAGAAACCTG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	19											83	86	85					19																	2878138		2203	4300	6503	2829138	SO:0001819	synonymous_variant	80032			BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.1182G>A	19.37:g.2878138G>A			2829138	Q96GM3	Silent	SNP	ENST00000307635.2	37	CCDS12097.1																																																																																				0.438	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		A	2878138	G	A	2878138	2	1	65	1	0	0	0	0	0	0	0	1	18026	1219	43	3		3	ZNF556	19	2878138	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	1920	2878138	56250845	139	20630										
C19orf10	56005	hgsc.bcm.edu	37	chr19	4660748	4660749	+	Frame_Shift_Ins	INS	-	-	CATC													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctgtgtgaagtacagataggINSacttcccctggggcctgcag							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:4660748_4660749insCATC	ENST00000262947.3	-	4	336_337	c.301_302insGATG	c.(301-303)tccfs	p.S101fs	C19orf10_ENST00000599630.1_Frame_Shift_Ins_p.S101fs	NM_019107.3	NP_061980.1	Q969H8	CS010_HUMAN	chromosome 19 open reading frame 10	101					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)		p.S101fs*1(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		GTACAGATAGGACTTCCCCTGG	0.644																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								4611749	SO:0001589	frameshift_variant	56005			AF282264	CCDS12133.1	19p13.3	2013-11-27	2003-06-25	2003-06-27	ENSG00000074842	ENSG00000074842			16948	protein-coding gene	gene with protein product		606746	"interleukin 27 working designation"	IL27, IL27w		17362502, 21128247	Standard	NM_019107		Approved	R33729_1, IL25, SF20, IL-25, IL-27	uc002may.3	Q969H8		ENST00000262947.3:c.301_302insGATG	19.37:g.4660748_4660749insCATC	ENSP00000262947:p.Ser101fs		4611748	D6W628|O75256|O75272|Q9BTK7|Q9NP69	Frame_Shift_Ins	INS	ENST00000262947.3	37	CCDS12133.1																																																																																				0.644	C19orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458937.1	NM_019107		CATC	4660749	-	CATC	4660748	7	5	65	1	0	1	1	0	0	0	0	0	1914	1174	41	0	231	0	C19orf10	19	4660748	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	1782610	4660748	54468235	140	20631										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768281	31768281	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	gtggacgtgggtgacagaagCactgaacccaaggagcagcc	15	10	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:31768281C>G	ENST00000240587.4	-	2	2745	c.2418G>C	c.(2416-2418)gtG>gtC	p.V806V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	806					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V623V(1)|p.V806V(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GTGACAGAAGCACTGAACCCA	0.547																																																2	Substitution - coding silent(2)	large_intestine(2)	19											109	91	97					19																	31768281		2203	4300	6503	36460121	SO:0001819	synonymous_variant	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2418G>C	19.37:g.31768281C>G			36460121	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																				0.547	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31768281	C	G	31768281	2	3	65	1	0	0	0	0	0	0	0	1	16665	697	25	5		5	TSHZ3	19	31768281	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	27107533	31768281	27360702	141	20632										
U2AF1L4	199746	hgsc.bcm.edu	37	chr19	36235245	36235245	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttgacatagacgttgcccacGaggtggtccccaaggttgtc	12	11	0	2			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:36235245G>A	ENST00000412391.2	-	5	340	c.327C>T	c.(325-327)ctC>ctT	p.L109L	IGFLR1_ENST00000588992.1_5'Flank|IGFLR1_ENST00000246532.1_5'Flank|U2AF1L4_ENST00000378975.3_Silent_p.L70L|PSENEN_ENST00000222266.2_5'Flank|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000592537.1_5'Flank|IGFLR1_ENST00000344990.3_5'Flank|PSENEN_ENST00000587708.2_5'Flank|AC002398.9_ENST00000591613.2_5'Flank|AC002398.11_ENST00000591091.1_RNA|U2AF1L4_ENST00000292879.5_Silent_p.L70L|U2AF1L4_ENST00000588100.1_5'Flank|AC002398.11_ENST00000585365.1_RNA|PSENEN_ENST00000591949.1_5'Flank			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4	109	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.			L -> V (in Ref. 3; AAH21186). {ECO:0000305}.	mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.L70L(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CGTTGCCCACGAGGTGGTCCC	0.557																																																2	Substitution - coding silent(2)	large_intestine(2)	19											128	122	124					19																	36235245		2203	4300	6503	40927085	SO:0001819	synonymous_variant	199746			BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"RNA binding motif (RRM) containing"	23020	protein-coding gene	gene with protein product		601080	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 3", "U2 small nuclear RNA auxiliary factor 1-like 3"	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68		ENST00000412391.2:c.327C>T	19.37:g.36235245G>A			40927085	A6NKI8|Q56UU3	Silent	SNP	ENST00000412391.2	37		.	.	.	.	.	.	.	.	.	.	G	1.823	-0.471745	0.04445	.	.	ENSG00000161265	ENST00000392196	.	.	.	5.41	-3.63	0.04529	.	.	.	.	.	T	0.36635	0.0974	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40327	-0.9569	4	.	.	.	-12.6686	0.8603	0.01191	0.1964:0.2557:0.3229:0.225	.	.	.	.	L	10	.	.	S	-	2	0	U2AF1L4	40927085	0.146000	0.22672	0.987000	0.45799	0.240000	0.25518	-0.723000	0.04952	-0.076000	0.12775	0.561000	0.74099	TCG		0.557	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144987		A	36235245	G	A	36235245	2	1	65	1	0	0	0	0	0	0	0	1	16862	1045	37	1		1	U2AF1L4	19	36235245	Silent	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10	4466964	36235245	22893738	142	20633										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44536830	44536831	+	Frame_Shift_Del	DEL	CA	CA	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ttttggtccatcaacgagtcCacactggagaaaagccatac							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CA	CA	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:44536830_44536831delCA	ENST00000187879.8	+	4	1165_1166	c.1003_1004delCA	c.(1003-1005)cacfs	p.H335fs	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Frame_Shift_Del_p.H375fs	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	335					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T336fs*8(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				TCAACGAGTCCACACTGGAGAA	0.431																																																1	Deletion - Frameshift(1)	large_intestine(1)	19																																								49228671	SO:0001589	frameshift_variant	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.1003_1004delCA	19.37:g.44536832_44536833delCA	ENSP00000187879:p.His335fs		49228670	G5E9B9|Q8N6G7|Q9P1U5	Frame_Shift_Del	DEL	ENST00000187879.8	37	CCDS33045.1																																																																																				0.431	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			-	44536831	CA	-	44536830	7	5	65	1	0	1	0	1	0	0	0	0	17815	594	21	0	1156	0	ZNF222	19	44536830	Frame_Shift_Del	DEL	CA	TCGA-AG-A00Y-01A-02W-A005-10	8301585	44536830	14592153	143	20634										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47214231	47214231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cagtgatcacagaaggcaggCgcccgataggagtgcaccgt	14	11	1	2	rs371861713		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:47214231C>T	ENST00000291281.4	-	3	669	c.444G>A	c.(442-444)gcG>gcA	p.A148A	PRKD2_ENST00000600194.1_5'UTR|PRKD2_ENST00000433867.1_Silent_p.A148A|PRKD2_ENST00000601806.1_5'UTR|PRKD2_ENST00000595515.1_Silent_p.A148A|MIR320E_ENST00000390179.3_RNA			Q9BZL6	KPCD2_HUMAN	protein kinase D2	148					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.A148A(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		AGAAGGCAGGCGCCCGATAGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C	,,,	1,4381		0,1,2190	31	25	27		444,444,,444	-11.2	0	19		27	0,8576		0,0,4288	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	PRKD2	NM_001079880.1,NM_001079881.1,NM_001079882.1,NM_016457.4	,,,	0,1,6478	TT,TC,CC		0.0,0.0228,0.0077	,,,	148/879,148/879,,148/879	47214231	1,12957	2191	4288	6479	51906071	SO:0001819	synonymous_variant	25865			AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.444G>A	19.37:g.47214231C>T			51906071	Q8TB08|Q9P0T6|Q9Y3X8	Silent	SNP	ENST00000291281.4	37	CCDS12689.1																																																																																				0.652	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		T	47214231	C	T	47214231	2	4	65	1	0	0	0	0	0	0	0	1	12553	755	27	1		1	PRKD2	19	47214231	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	2677401	47214231	11914752	144	20635										
NUP62	23636	hgsc.bcm.edu	37	chr19	50412684	50412685	+	Frame_Shift_Ins	INS	-	-	A													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cctggctggaggtgacggtgINSctcgatatggcattagtgag							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:50412684_50412685insA	ENST00000596217.1	-	2	2267_2268	c.380_381insT	c.(379-381)agcfs	p.S127fs	NUP62_ENST00000597029.1_Frame_Shift_Ins_p.S127fs|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Frame_Shift_Ins_p.S127fs|NUP62_ENST00000352066.3_Frame_Shift_Ins_p.S127fs|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000422090.2_Frame_Shift_Ins_p.S127fs|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000413454.1_Frame_Shift_Ins_p.S127fs			P37198	NUP62_HUMAN	nucleoporin 62kDa	127	15 X 9 AA approximate repeats.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)	p.T128fs*301(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		AGGTGACGGTGCTCGATATGGC	0.594																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								55104497	SO:0001589	frameshift_variant	23636			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.380_381insT	19.37:g.50412684_50412685insA	ENSP00000471191:p.Ser127fs		55104496	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Frame_Shift_Ins	INS	ENST00000596217.1	37	CCDS12788.1																																																																																				0.594	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		A	50412685	-	A	50412684	7	5	65	1	0	1	1	0	0	0	0	0	10799	1310	46	0	1191	0	NUP62	19	50412684	Frame_Shift_Ins	INS	-	TCGA-AG-A00Y-01A-02W-A005-10	3198453	50412684	8716299	145	20636										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56321102	56321105	+	Frame_Shift_Del	DEL	CCTC	CCTC	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	caaggtcgtgcagcaatctaCctctttcaagaacgttttta							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CCTC	CCTC	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr19:56321102_56321105delCCTC	ENST00000589093.1	-	3	964_967	c.871_874delGAGG	c.(871-876)gaggtafs	p.EV291fs	NLRP11_ENST00000589824.2_Frame_Shift_Del_p.EV291fs|NLRP11_ENST00000360133.3_Frame_Shift_Del_p.EV291fs|NLRP11_ENST00000443188.1_Frame_Shift_Del_p.EV291fs|NLRP11_ENST00000592953.1_Frame_Shift_Del_p.EV192fs			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	291	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.E291fs*1(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		CAGCAATCTACCTCTTTCAAGAAC	0.495																																																1	Deletion - Frameshift(1)	large_intestine(1)	19																																								61012917	SO:0001589	frameshift_variant	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.871_874delGAGG	19.37:g.56321102_56321105delCCTC	ENSP00000466285:p.Glu291fs		61012914	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Frame_Shift_Del	DEL	ENST00000589093.1	37	CCDS12935.1																																																																																				0.495	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		-	56321105	CCTC	-	56321102	7	5	65	1	0	1	0	1	0	0	0	0	10504	507	18	0	2259	0	NLRP11	19	56321102	Frame_Shift_Del	DEL	CCTC	TCGA-AG-A00Y-01A-02W-A005-10	5908418	56321102	2807881	146	20637										
KRTAP19-2	337969	hgsc.bcm.edu	37	chr21	31859611	31859611	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	tatctgcatccttcatagccGcagccatagcccagtctgca	7	15	3	0	rs144891171		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chr21:31859611G>T	ENST00000334055.3	-	1	144	c.57C>A	c.(55-57)tgC>tgA	p.C19*		NM_181608.1	NP_853639.1	Q3LHN2	KR192_HUMAN	keratin associated protein 19-2	19						intermediate filament (GO:0005882)		p.C19C(1)|p.C19*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CTTCATAGCCGCAGCCATAGC	0.547																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(2)	21											157	154	155					21																	31859611		2203	4300	6503	30781482	SO:0001587	stop_gained	337969			AP001708	CCDS13595.1	21q22.1	2006-03-13			ENSG00000186965	ENSG00000186965		"Keratin associated proteins"	18937	protein-coding gene	gene with protein product						12359730	Standard	NM_181608		Approved	KAP19.2	uc011acy.2	Q3LHN2	OTTHUMG00000057772	ENST00000334055.3:c.57C>A	21.37:g.31859611G>T	ENSP00000335660:p.Cys19*		30781482		Nonsense_Mutation	SNP	ENST00000334055.3	37	CCDS13595.1	.	.	.	.	.	.	.	.	.	.	-	14.98	2.698191	0.48307	.	.	ENSG00000186965	ENST00000334055	.	.	.	4.41	4.41	0.53225	.	0.123452	0.36665	N	0.002468	.	.	.	.	.	.	0.29722	N	0.838535	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.9152	0.24355	0.8948:0.0:0.1052:0.0	.	.	.	.	X	19	.	ENSP00000335660:C19X	C	-	3	2	KRTAP19-2	30781482	0.000000	0.05858	0.025000	0.17156	0.280000	0.26924	0.181000	0.16880	0.846000	0.35142	-0.308000	0.09152	TGC		0.547	KRTAP19-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128224.3			T	31859611	G	T	31859611	4	4	65	1	0	0	0	0	0	1	0	0	8550	1079	38	2	103	2	KRTAP19-2	21	31859611	Nonsense_Mutation	SNP	G	TCGA-AG-A00Y-01A-02W-A005-10		31859611	16270284	147	20638										
KAL1	3730	hgsc.bcm.edu	37	chrX	8553403	8553403	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	actggtaccatcggctgggtCttatgtcagtcagttgaact	11	9	3	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:8553403C>T	ENST00000262648.3	-	6	910	c.761G>A	c.(760-762)aGa>aAa	p.R254K		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	254	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R254K(1)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						TCGGCTGGGTCTTATGTCAGT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	X											182	127	146					X																	8553403		2203	4300	6503	8513403	SO:0001583	missense	3730				CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.761G>A	X.37:g.8553403C>T	ENSP00000262648:p.Arg254Lys		8513403	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712423	0.68730	.	.	ENSG00000011201	ENST00000262648	T	0.56611	0.45	3.74	3.74	0.42951	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.057290	0.64402	D	0.000003	T	0.62344	0.2420	L	0.43152	1.355	0.53688	D	0.999978	D	0.67145	0.996	D	0.66602	0.945	T	0.64846	-0.6311	10	0.52906	T	0.07	.	14.1448	0.65344	0.0:1.0:0.0:0.0	.	254	P23352	KALM_HUMAN	K	254	ENSP00000262648:R254K	ENSP00000262648:R254K	R	-	2	0	KAL1	8513403	1.000000	0.71417	0.780000	0.31762	0.345000	0.29048	6.411000	0.73298	1.488000	0.48433	0.594000	0.82650	AGA		0.507	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		T	8553403	C	T	8553403	3	4	65	1	0	0	0	0	1	0	0	0	7995	913	32	3	1317	3	KAL1	23	8553403	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		8553403	146717157	148	20639										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64754516	64754517	+	Frame_Shift_Del	DEL	CA	CA	-													0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acgaccctttccctttaacgCactttccgtaccacgcactc							TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	CA	CA	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:64754516_64754517delCA	ENST00000374811.3	-	1	119_120	c.79_80delTG	c.(79-81)tgcfs	p.C27fs	LAS1L_ENST00000374804.5_Frame_Shift_Del_p.C27fs|LAS1L_ENST00000312391.8_Frame_Shift_Del_p.C27fs|LAS1L_ENST00000374807.5_Frame_Shift_Del_p.C27fs	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	27					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.C27fs*2(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CCCTTTAACGCACTTTCCGTAC	0.604																																																1	Deletion - Frameshift(1)	large_intestine(1)	X																																								64671242	SO:0001589	frameshift_variant	81887			BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.79_80delTG	X.37:g.64754516_64754517delCA	ENSP00000363944:p.Cys27fs		64671241	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Frame_Shift_Del	DEL	ENST00000374811.3	37	CCDS14381.1																																																																																				0.604	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		-	64754517	CA	-	64754516	7	5	65	1	0	1	0	1	0	0	0	0	8658	710	25	0	2180	0	LAS1L	23	64754516	Frame_Shift_Del	DEL	CA	TCGA-AG-A00Y-01A-02W-A005-10	56201113	64754516	90516044	149	20640										
ZCCHC5	203430	hgsc.bcm.edu	37	chrX	77912908	77912908	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ggaagtgggttgctacatgaCcctccccttggcagagttga	13	10	0	3			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:77912908C>A	ENST00000321110.1	-	2	1305	c.1010G>T	c.(1009-1011)gGt>gTt	p.G337V		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	337							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.G337V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						TGCTACATGACCCTCCCCTTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											85	70	75					X																	77912908		2203	4300	6503	77799564	SO:0001583	missense	203430			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"Zinc fingers, CCHC domain containing"	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.1010G>T	X.37:g.77912908C>A	ENSP00000316794:p.Gly337Val		77799564	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	C	2.062	-0.415224	0.04766	.	.	ENSG00000179300	ENST00000321110	T	0.19532	2.14	3.2	1.13	0.20643	.	0.507301	0.13804	U	0.361606	T	0.19565	0.0470	L	0.50333	1.59	0.09310	N	1	P	0.48911	0.917	P	0.46049	0.502	T	0.10520	-1.0626	10	0.40728	T	0.16	.	3.9579	0.09398	0.0:0.4061:0.0:0.5939	.	337	Q8N8U3	ZCHC5_HUMAN	V	337	ENSP00000316794:G337V	ENSP00000316794:G337V	G	-	2	0	ZCCHC5	77799564	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.167000	0.16602	0.133000	0.18654	0.506000	0.49869	GGT		0.448	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		A	77912908	C	A	77912908	3	1	65	1	0	0	0	0	1	0	0	0	17630	507	18	2	421	2	ZCCHC5	23	77912908	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	13158392	77912908	77357652	150	20641										
SATL1	340562	hgsc.bcm.edu	37	chrX	84362526	84362526	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	cctggctgactcggccccggTtcccatatgcctggttggcc	12	16	0	1			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:84362526T>G	ENST00000395409.3	-	1	1448	c.888A>C	c.(886-888)gaA>gaC	p.E296D	SATL1_ENST00000332921.5_Missense_Mutation_p.E296D|SATL1_ENST00000509231.1_Missense_Mutation_p.E483D			Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	296	Gln-rich.						N-acetyltransferase activity (GO:0008080)	p.E483D(1)		NS(1)|breast(5)|endometrium(2)|large_intestine(3)|lung(13)|skin(3)|stomach(1)|urinary_tract(1)	29						TCGGCCCCGGTTCCCATATGC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	X											116	94	101					X																	84362526		2203	4300	6503	84249182	SO:0001583	missense	340562			BC043215	CCDS35343.1, CCDS35343.2	Xq21	2008-02-05			ENSG00000184788	ENSG00000184788			27992	protein-coding gene	gene with protein product						12477932	Standard	NM_001012980		Approved		uc004een.3	Q86VE3	OTTHUMG00000021931	ENST00000395409.3:c.888A>C	X.37:g.84362526T>G	ENSP00000378804:p.Glu296Asp		84249182	A0AVK7|E9PB72|Q5H8V9	Missense_Mutation	SNP	ENST00000395409.3	37		.	.	.	.	.	.	.	.	.	.	T	14.59	2.579830	0.46006	.	.	ENSG00000184788	ENST00000395409;ENST00000332921;ENST00000509231	T;T;T	0.46451	0.87;0.87;0.87	3.48	0.972	0.19704	.	0.845116	0.09648	N	0.773992	T	0.37489	0.1005	L	0.46157	1.445	0.09310	N	1	P;P	0.47302	0.893;0.73	B;B	0.44315	0.446;0.263	T	0.21930	-1.0231	10	0.59425	D	0.04	-6.2099	6.2233	0.20693	0.0:0.2486:0.0:0.7514	.	296;483	Q86VE3;E9PB72	SATL1_HUMAN;.	D	296;296;483	ENSP00000378804:E296D;ENSP00000329115:E296D;ENSP00000425421:E483D	ENSP00000329115:E296D	E	-	3	2	SATL1	84249182	0.020000	0.18652	0.000000	0.03702	0.002000	0.02628	-0.022000	0.12480	-0.008000	0.14320	0.486000	0.48141	GAA		0.572	SATL1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_291339		G	84362526	T	G	84362526	3	3	65	1	0	0	0	0	1	0	0	0	13892	1722	60	4	469	4	SATL1	23	84362526	Missense_Mutation	SNP	T	TCGA-AG-A00Y-01A-02W-A005-10	6449618	84362526	70908034	151	20642										
DRP2	1821	hgsc.bcm.edu	37	chrX	100509467	100509467	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	acaaccttaaagaacaaattCcgctccaagcattatttcag	4	11	1	1	rs190486006		TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:100509467C>T	ENST00000395209.3	+	18	2558	c.2031C>T	c.(2029-2031)ttC>ttT	p.F677F	DRP2_ENST00000402866.1_Silent_p.F677F|DRP2_ENST00000538510.1_Silent_p.F677F|DRP2_ENST00000541709.1_Silent_p.F599F	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	677					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.F674F(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						AGAACAAATTCCGCTCCAAGC	0.502													C|||	1	0.000264901	0	0.0014	3775	,	,		13282	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	X											118	84	96					X																	100509467		2203	4300	6503	100396123	SO:0001819	synonymous_variant	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2031C>T	X.37:g.100509467C>T			100396123	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																				0.502	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100509467	C	T	100509467	2	4	65	1	0	0	0	0	0	0	0	1	4775	854	30	3		3	DRP2	23	100509467	Silent	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	16146941	100509467	54761093	152	20643										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118972444	118972444	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ccaatttcttggctttttctCttttgtccaattctttttca	3	10	4	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrX:118972444C>T	ENST00000276201.2	-	9	962	c.893G>A	c.(892-894)aGa>aAa	p.R298K	UPF3B_ENST00000345865.2_Missense_Mutation_p.R285K|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	298	Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R298K(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						GGCTTTTTCTCTTTTGTCCAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	X											199	174	182					X																	118972444		2203	4300	6503	118856472	SO:0001583	missense	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.893G>A	X.37:g.118972444C>T	ENSP00000276201:p.Arg298Lys		118856472	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	5.293	0.239389	0.10023	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	T;T	0.75477	-0.94;-0.88	5.43	5.43	0.79202	.	0.042876	0.85682	D	0.000000	T	0.48892	0.1525	N	0.11756	0.17	0.36267	D	0.854915	B;B	0.23128	0.08;0.029	B;B	0.18561	0.022;0.006	T	0.51865	-0.8651	10	0.02654	T	1	.	7.6803	0.28509	0.0:0.817:0.0:0.183	.	285;298	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	K	298;285	ENSP00000276201:R298K;ENSP00000245418:R285K	ENSP00000276201:R298K	R	-	2	0	UPF3B	118856472	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.325000	0.43840	2.275000	0.75901	0.526000	0.51066	AGA		0.363	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			T	118972444	C	T	118972444	3	4	65	1	0	0	0	0	1	0	0	0	17046	913	32	3	570	3	UPF3B	23	118972444	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10	18462977	118972444	36298116	153	20644										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16734312	16734312	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.100671140939597	15	1	1.76807228915663	0.884036144578313	1.90407784986098	2.0077937570804e-05	0.000816502794546029	0	ctggcatccgaaatgctactCagttttctgctgtgtgcccc	9	13	2	0			TCGA-AG-A00Y-01A-02W-A005-10	TCGA-AG-A00Y-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	b50ae1df-ee6f-4a5e-ba4b-c962d740ab22	a5a6325b-e91e-41d7-86c7-5933c8c59c35	g.chrY:16734312C>A	ENST00000297967.5	+	1	412	c.313C>A	c.(313-315)Cag>Aag	p.Q105K	NLGN4Y_ENST00000476359.1_3'UTR	NM_001164238.1	NP_001157710.1	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked	105					learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.Q105K(2)		large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						AAATGCTACTCAGTTTTCTGC	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	Y											65	59	60					Y																	16734312		612	1959	2571	15243706	SO:0001583	missense	22829				CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000297967.5:c.313C>A	Y.37:g.16734312C>A	ENSP00000297967:p.Gln105Lys		15243706	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Missense_Mutation	SNP	ENST00000297967.5	37	CCDS55553.1																																																																																				0.522	NLGN4Y-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014893		A	16734312	C	A	16734312	3	1	65	1	0	0	0	0	1	0	0	0	10496	827	29	2	315	2	NLGN4Y	24	16734312	Missense_Mutation	SNP	C	TCGA-AG-A00Y-01A-02W-A005-10		16734312	42639254	154	20645										
USP48	84196	broad.mit.edu	37	chr1	22033300	22033300	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gcctttggaaagtactgctgCagtttgctccaagcctcttt	9	11	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:22033300C>A	ENST00000308271.9	-	16	2673	c.2025G>T	c.(2023-2025)ctG>ctT	p.L675L	USP48_ENST00000400301.1_Silent_p.L675L|USP48_ENST00000529637.1_Silent_p.L687L|USP48_ENST00000374732.3_Silent_p.L213L	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	675	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.L675L(1)		NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		AGTACTGCTGCAGTTTGCTCC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	1											122	115	118					1																	22033300		2203	4300	6503	21905887	SO:0001819	synonymous_variant	84196			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2025G>T	1.37:g.22033300C>A			21905887	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																				0.393	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		A	22033300	C	A	22033300	2	1	66	1	0	0	0	0	0	0	0	1	17119	697	25	2		2	USP48	1	22033300	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		22033300	227217321	1	20646										
WDTC1	23038	broad.mit.edu	37	chr1	27609910	27609910	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aagctgctctccatgcacacGggacacaccgcaaatatctt	7	14	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:27609910G>A	ENST00000319394.3	+	5	796	c.261G>A	c.(259-261)acG>acA	p.T87T	WDTC1_ENST00000361771.3_Silent_p.T87T	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	87					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.T87T(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CCATGCACACGGGACACACCG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	1											103	86	92					1																	27609910		2203	4300	6503	27482497	SO:0001819	synonymous_variant	23038			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.261G>A	1.37:g.27609910G>A			27482497	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Silent	SNP	ENST00000319394.3	37																																																																																					0.562	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27609910	G	A	27609910	2	1	66	1	0	0	0	0	0	0	0	1	17382	1103	39	1		1	WDTC1	1	27609910	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	5576610	27609910	221640711	2	20647										
ZSCAN20	7579	broad.mit.edu	37	chr1	33957183	33957183	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	agagatggatgagcaggaggAagggggctgggatcctgaag	20	4	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:33957183A>T	ENST00000361328.3	+	6	1478	c.1325A>T	c.(1324-1326)gAa>gTa	p.E442V	ZSCAN20_ENST00000373413.2_Missense_Mutation_p.E388V	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	442					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E442V(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GAGCAGGAGGAAGGGGGCTGG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	106	102					1																	33957183		1966	4155	6121	33729770	SO:0001583	missense	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.1325A>T	1.37:g.33957183A>T	ENSP00000355053:p.Glu442Val		33729770	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.278288	0.80692	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.02140	4.43	5.61	4.48	0.54585	.	0.187792	0.37906	N	0.001891	T	0.09555	0.0235	M	0.76838	2.35	0.39944	D	0.974457	D;D;D	0.69078	0.989;0.989;0.997	P;P;P	0.60789	0.836;0.776;0.879	T	0.01059	-1.1465	10	0.72032	D	0.01	-6.576	9.951	0.41638	0.9194:0.0:0.0805:0.0	.	442;388;442	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	V	388;442;388;376;376	ENSP00000362512:E388V	ENSP00000324450:E442V	E	+	2	0	ZSCAN20	33729770	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	1.904000	0.39868	1.076000	0.40961	0.459000	0.35465	GAA		0.612	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33957183	A	T	33957183	3	4	66	1	0	0	0	0	1	0	0	0	18271	246	9	5	1343	5	ZSCAN20	1	33957183	Missense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	6347273	33957183	215293438	3	20648										
GRIK3	2899	broad.mit.edu	37	chr1	37346292	37346292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cttgaggtactggaccaggtCgaggatggcatggctgagcg	17	8	0	2	rs148168675		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:37346292C>T	ENST00000373091.3	-	3	509	c.493G>A	c.(493-495)Gac>Aac	p.D165N	GRIK3_ENST00000373093.4_Missense_Mutation_p.D165N	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	165					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.D165N(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				TGGACCAGGTCGAGGATGGCA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	ASN/ASP	0,4406		0,0,2203	322	290	301		493	4.9	1	1	dbSNP_134	301	1,8599	1.2+/-3.3	0,1,4299	no	missense	GRIK3	NM_000831.3	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	165/920	37346292	1,13005	2203	4300	6503	37118879	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.493G>A	1.37:g.37346292C>T	ENSP00000362183:p.Asp165Asn		37118879	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	34	5.335527	0.95758	0.0	1.16E-4	ENSG00000163873	ENST00000373091;ENST00000373093	D;D	0.85013	-1.93;-1.93	4.88	4.88	0.63580	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93719	0.7993	M	0.90198	3.095	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.74348	0.975;0.983	D	0.94798	0.7968	10	0.66056	D	0.02	.	18.3912	0.90484	0.0:1.0:0.0:0.0	.	165;165	A9Z1Z8;Q13003	.;GRIK3_HUMAN	N	165	ENSP00000362183:D165N;ENSP00000362185:D165N	ENSP00000362183:D165N	D	-	1	0	GRIK3	37118879	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.410000	0.80065	2.426000	0.82243	0.561000	0.74099	GAC		0.622	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37346292	C	T	37346292	3	4	66	1	0	0	0	0	1	0	0	0	6796	884	31	1	2322	1	GRIK3	1	37346292	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	3389109	37346292	211904329	4	20649										
MACF1	23499	broad.mit.edu	37	chr1	39747978	39747978	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	acagctggttacacaggaatCaaatgcaccaacttttcctc	6	12	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:39747978C>G	ENST00000372915.3	+	6	729	c.642C>G	c.(640-642)atC>atG	p.I214M	MACF1_ENST00000536367.1_Missense_Mutation_p.I177M|MACF1_ENST00000545844.1_Missense_Mutation_p.I214M|MACF1_ENST00000539005.1_Missense_Mutation_p.I214M|MACF1_ENST00000361689.2_Missense_Mutation_p.I214M|MACF1_ENST00000317713.7_Missense_Mutation_p.I214M|MACF1_ENST00000564288.1_Missense_Mutation_p.I209M|MACF1_ENST00000567887.1_Missense_Mutation_p.I246M			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	214	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.I214M(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACACAGGAATCAAATGCACCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											130	116	121					1																	39747978		2203	4300	6503	39520565	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.642C>G	1.37:g.39747978C>G	ENSP00000362006:p.Ile214Met		39520565	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	21.5	4.163449	0.78226	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000536367;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D;D	0.95554	-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74	5.78	5.78	0.91487	.	.	.	.	.	D	0.96629	0.8900	M	0.66506	2.035	0.32588	N	0.527591	D;B;P	0.53151	0.958;0.012;0.905	P;B;P	0.61201	0.885;0.05;0.672	D	0.97496	1.0057	9	0.87932	D	0	.	11.5156	0.50520	0.1303:0.7278:0.1419:0.0	.	177;214;179	B4E2T3;F8W8Q1;Q9UPN3-3	.;.;.	M	214;214;214;230;214;214;172;177;363;374	ENSP00000439537:I214M;ENSP00000362006:I214M;ENSP00000354573:I214M;ENSP00000313438:I214M;ENSP00000444364:I214M;ENSP00000435070:I172M;ENSP00000440369:I177M;ENSP00000437059:I363M	ENSP00000313438:I214M	I	+	3	3	MACF1	39520565	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.688000	0.25422	2.729000	0.93468	0.650000	0.86243	ATC		0.473	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39747978	C	G	39747978	3	3	66	1	0	0	0	0	1	0	0	0	9174	816	29	5	664	5	MACF1	1	39747978	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	2401686	39747978	209502643	5	20650										
KCND3	3752	broad.mit.edu	37	chr1	112524802	112524802	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	agtcacgtagtagaagaccaGggccagcgtgctggtgtggg	17	8	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:112524802G>A	ENST00000315987.2	-	2	1026	c.547C>T	c.(547-549)Ctg>Ttg	p.L183L	KCND3_ENST00000369697.1_Silent_p.L183L|KCND3_ENST00000302127.4_Silent_p.L183L	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	183					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.L183L(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TAGAAGACCAGGGCCAGCGTG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	1											46	44	45					1																	112524802		2203	4300	6503	112326325	SO:0001819	synonymous_variant	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.547C>T	1.37:g.112524802G>A			112326325	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Silent	SNP	ENST00000315987.2	37	CCDS843.1																																																																																				0.632	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		A	112524802	G	A	112524802	2	1	66	1	0	0	0	0	0	0	0	1	8041	991	35	3		3	KCND3	1	112524802	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	72776824	112524802	136725819	6	20651										
SV2A	9900	broad.mit.edu	37	chr1	149884869	149884869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccacaccgtcagccatcagcGccagaccaagcacaaaatac	6	17	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:149884869G>T	ENST00000369146.3	-	2	1014	c.524C>A	c.(523-525)gCg>gAg	p.A175E	SV2A_ENST00000369145.1_Missense_Mutation_p.A175E	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	175					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)	p.A175E(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	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)	AGCCATCAGCGCCAGACCAAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	109	111					1																	149884869		2203	4300	6503	148151493	SO:0001583	missense	9900			AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.524C>A	1.37:g.149884869G>T	ENSP00000358142:p.Ala175Glu		148151493	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	37	CCDS940.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999399	0.93227	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.61392	0.11;0.11	5.02	5.02	0.67125	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.76176	0.3951	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.80317	-0.1433	10	0.72032	D	0.01	-21.4838	17.5091	0.87755	0.0:0.0:1.0:0.0	.	175	Q7L0J3	SV2A_HUMAN	E	175	ENSP00000358142:A175E;ENSP00000358141:A175E	ENSP00000358141:A175E	A	-	2	0	SV2A	148151493	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.657000	0.98554	2.606000	0.88127	0.655000	0.94253	GCG		0.567	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			T	149884869	G	T	149884869	3	4	66	1	0	0	0	0	1	0	0	0	15456	1087	38	2	1752	2	SV2A	1	149884869	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	37360067	149884869	99365752	7	20652										
FLG	2312	broad.mit.edu	37	chr1	152283611	152283611	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgattgttcctgtcccacctGtgagtgtctagagctgtcag	11	10	2	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:152283611G>T	ENST00000368799.1	-	3	3786	c.3751C>A	c.(3751-3753)Cag>Aag	p.Q1251K	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1251	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.Q1251K(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCCACCTGTGAGTGTCTA	0.557									Ichthyosis																																							1	Substitution - Missense(1)	large_intestine(1)	1											279	266	270					1																	152283611		2203	4300	6503	150550235	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3751C>A	1.37:g.152283611G>T	ENSP00000357789:p.Gln1251Lys		150550235	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	5.472	0.272146	0.10349	.	.	ENSG00000143631	ENST00000368799	T	0.01629	4.72	2.62	-2.28	0.06826	.	.	.	.	.	T	0.00580	0.0019	M	0.76002	2.32	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.50136	-0.8863	9	0.07482	T	0.82	.	3.5341	0.07788	0.0:0.292:0.4459:0.262	.	1251	P20930	FILA_HUMAN	K	1251	ENSP00000357789:Q1251K	ENSP00000357789:Q1251K	Q	-	1	0	FLG	150550235	0.003000	0.15002	0.000000	0.03702	0.005000	0.04900	0.726000	0.25984	-0.713000	0.04981	0.186000	0.17326	CAG		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152283611	G	T	152283611	3	4	66	1	0	0	0	0	1	0	0	0	5941	1386	48	2	8438	2	FLG	1	152283611	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	2398742	152283611	96967010	8	20653										
THBS3	7059	broad.mit.edu	37	chr1	155166871	155166871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gccggtgcagaagctgccagCgataggaggtcttgtcccgc	15	12	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:155166871C>T	ENST00000368378.3	-	21	2653	c.2633G>A	c.(2632-2634)cGc>cAc	p.R878H	THBS3_ENST00000541576.1_Missense_Mutation_p.R275H|THBS3_ENST00000457183.2_Missense_Mutation_p.R758H|MIR92B_ENST00000607575.1_RNA|THBS3_ENST00000541990.1_Missense_Mutation_p.R407H|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	878	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R878H(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)			AAGCTGCCAGCGATAGGAGGT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											82	73	76					1																	155166871		2203	4300	6503	153433495	SO:0001583	missense	7059			L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2633G>A	1.37:g.155166871C>T	ENSP00000357362:p.Arg878His		153433495	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	37	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860896	0.91433	.	.	ENSG00000169231	ENST00000368378;ENST00000541576;ENST00000457183;ENST00000541990	D;D;D;D	0.97328	-4.34;-4.34;-4.34;-4.34	4.54	4.54	0.55810	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98557	0.9518	M	0.90425	3.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.99346	1.0913	10	0.87932	D	0	-18.5283	15.1718	0.72878	0.0:1.0:0.0:0.0	.	758;878;878;878	B4DQ20;Q53FK6;Q2HIZ0;P49746	.;.;.;TSP3_HUMAN	H	878;275;758;407	ENSP00000357362:R878H;ENSP00000444792:R275H;ENSP00000392207:R758H;ENSP00000437353:R407H	ENSP00000357362:R878H	R	-	2	0	THBS3	153433495	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.647000	0.83462	2.527000	0.85204	0.591000	0.81541	CGC		0.607	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		T	155166871	C	T	155166871	3	4	66	1	0	0	0	0	1	0	0	0	15894	768	27	1	249	1	THBS3	1	155166871	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	2883260	155166871	94083750	9	20654										
C1orf129	80133	broad.mit.edu	37	chr1	170940994	170940994	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aagcatcattgggaatgtgtCacctcctctacattgcacgg	9	11	3	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:170940994C>T	ENST00000367758.3	+	8	685	c.586C>T	c.(586-588)Cac>Tac	p.H196Y	MROH9_ENST00000367759.4_Missense_Mutation_p.H196Y	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	196								p.H196Y(1)									GGGAATGTGTCACCTCCTCTA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											301	269	280					1																	170940994		1971	4150	6121	169207618	SO:0001583	missense	80133			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.586C>T	1.37:g.170940994C>T	ENSP00000356732:p.His196Tyr		169207618	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.895972	0.00522	.	.	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.66815	-0.23;1.46	5.25	0.805	0.18703	.	0.470904	0.19916	N	0.103192	T	0.20210	0.0486	N	0.12182	0.205	0.22796	N	0.998729	B;B	0.06786	0.001;0.001	B;B	0.09377	0.003;0.004	T	0.28427	-1.0044	10	0.22706	T	0.39	-4.2422	7.3735	0.26815	0.0:0.532:0.0:0.468	.	196;196	F5GWX6;Q5TGP6	.;CA129_HUMAN	Y	196	ENSP00000356733:H196Y;ENSP00000356732:H196Y	ENSP00000356732:H196Y	H	+	1	0	C1orf129	169207618	0.030000	0.19436	0.171000	0.22900	0.001000	0.01503	0.102000	0.15272	0.115000	0.18071	-0.126000	0.14955	CAC		0.443	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		T	170940994	C	T	170940994	3	4	66	1	0	0	0	0	1	0	0	0	2002	826	29	3	612	3	C1orf129	1	170940994	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	15774123	170940994	78309627	10	20655										
IPO9	55705	broad.mit.edu	37	chr1	201837787	201837787	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccacttcagatcccgtcgtcGcctcactggctcaggacatc	8	17	3	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:201837787G>T	ENST00000361565.4	+	16	1936	c.1867G>T	c.(1867-1869)Gcc>Tcc	p.A623S		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	623					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)	p.A623S(1)		cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						TCCCGTCGTCGCCTCACTGGC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											90	75	80					1																	201837787		2203	4300	6503	200104410	SO:0001583	missense	55705			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.1867G>T	1.37:g.201837787G>T	ENSP00000354742:p.Ala623Ser		200104410	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627121	0.66901	.	.	ENSG00000198700	ENST00000361565	T	0.65916	-0.18	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.47507	0.1449	N	0.24115	0.695	0.80722	D	1	B	0.28998	0.23	B	0.16722	0.016	T	0.40021	-0.9585	10	0.15066	T	0.55	-18.211	18.3732	0.90420	0.0:0.0:1.0:0.0	.	623	Q96P70	IPO9_HUMAN	S	623	ENSP00000354742:A623S	ENSP00000354742:A623S	A	+	1	0	IPO9	200104410	1.000000	0.71417	0.993000	0.49108	0.988000	0.76386	9.339000	0.96797	2.941000	0.99782	0.655000	0.94253	GCC		0.532	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		T	201837787	G	T	201837787	3	4	66	1	0	0	0	0	1	0	0	0	7820	1087	38	2	1929	2	IPO9	1	201837787	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	30896793	201837787	47412834	11	20656										
OR2M5	127059	broad.mit.edu	37	chr1	248309327	248309327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tcccctcatctacagcctccGcaacaaggaggtgaccagag	9	15	2	2	rs138811069	byFrequency	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr1:248309327G>A	ENST00000366476.1	+	1	878	c.878G>A	c.(877-879)cGc>cAc	p.R293H		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R293H(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			TACAGCCTCCGCAACAAGGAG	0.493													g|||	4	0.000798722	0	0	5008	,	,		17073	0.002		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	79	73	75		878	3	0.2	1	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR2M5	NM_001004690.1	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	293/313	248309327	2,13004	2203	4300	6503	246375950	SO:0001583	missense	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.878G>A	1.37:g.248309327G>A	ENSP00000355432:p.Arg293His		246375950		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	11.40	1.627916	0.28978	2.27E-4	1.16E-4	ENSG00000162727	ENST00000366476	T	0.41065	1.01	3.01	3.01	0.34805	.	.	.	.	.	T	0.58509	0.2127	H	0.96333	3.805	0.09310	N	1	B	0.21905	0.062	B	0.18263	0.021	T	0.60172	-0.7315	9	0.72032	D	0.01	.	13.8517	0.63501	0.0:0.0:1.0:0.0	.	293	A3KFT3	OR2M5_HUMAN	H	293	ENSP00000355432:R293H	ENSP00000355432:R293H	R	+	2	0	OR2M5	246375950	0.911000	0.30947	0.216000	0.23742	0.780000	0.44128	1.852000	0.39348	1.356000	0.45884	0.385000	0.25706	CGC		0.493	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		A	248309327	G	A	248309327	3	1	66	1	0	0	0	0	1	0	0	0	11044	1087	38	1	880	1	OR2M5	1	248309327	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	46471540	248309327	941294	12	20657										
SNTG2	54221	broad.mit.edu	37	chr2	1168837	1168837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cctctcccctctttgacagcGgtttgcatctgaacggaaac	8	14	3	2	rs567910526		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr2:1168837G>A	ENST00000308624.5	+	8	688	c.559G>A	c.(559-561)Ggt>Agt	p.G187S	SNTG2_ENST00000407292.1_Intron|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	187					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.G187S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CTTTGACAGCGGTTTGCATCT	0.468													G|||	1	0.000199681	8e-04	0	5008	,	,		18832	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											160	162	161					2																	1168837		1929	4127	6056	1158837	SO:0001583	missense	54221			AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.559G>A	2.37:g.1168837G>A	ENSP00000311837:p.Gly187Ser		1158837	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673037	0.47781	.	.	ENSG00000172554	ENST00000308624	T	0.38077	1.16	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.42426	0.1202	M	0.62723	1.935	0.80722	D	1	D	0.62365	0.991	P	0.48488	0.579	T	0.29488	-1.0010	10	0.19590	T	0.45	.	15.4969	0.75662	0.0:0.0:1.0:0.0	.	187	Q9NY99	SNTG2_HUMAN	S	187	ENSP00000311837:G187S	ENSP00000311837:G187S	G	+	1	0	SNTG2	1158837	1.000000	0.71417	0.650000	0.29550	0.185000	0.23345	6.238000	0.72350	2.151000	0.67156	0.643000	0.83706	GGT		0.468	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		A	1168837	G	A	1168837	3	1	66	1	0	0	0	0	1	0	0	0	14912	1116	39	1	589	1	SNTG2	2	1168837	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		1168837	242030536	13	20658										
TRIM43	129868	broad.mit.edu	37	chr2	96259783	96259783	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cttaggaaaatggactcagaCttctcacatgccttccagaa	7	11	2	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr2:96259783C>A	ENST00000272395.2	+	2	148	c.12C>A	c.(10-12)gaC>gaA	p.D4E		NM_001164464.1|NM_138800.1	NP_001157936.1|NP_620155.1	Q96BQ3	TRI43_HUMAN	tripartite motif containing 43	4						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.D4E(2)		breast(1)|large_intestine(3)|lung(7)|ovary(1)	12						TGGACTCAGACTTCTCACATG	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	2											85	88	87					2																	96259783		2201	4299	6500	95623510	SO:0001583	missense	129868			BK000505	CCDS2015.1	2q11	2014-02-17	2011-01-25		ENSG00000144015	ENSG00000144015		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19015	protein-coding gene	gene with protein product			"tripartite motif-containing 43"				Standard	NM_138800		Approved	TRIM43A	uc002suv.3	Q96BQ3	OTTHUMG00000130401	ENST00000272395.2:c.12C>A	2.37:g.96259783C>A	ENSP00000272395:p.Asp4Glu		95623510	Q53TJ7	Missense_Mutation	SNP	ENST00000272395.2	37	CCDS2015.1	.	.	.	.	.	.	.	.	.	.	.	0.377	-0.930930	0.02359	.	.	ENSG00000144015	ENST00000272395	T	0.66815	-0.23	1.18	1.18	0.20946	.	.	.	.	.	T	0.41213	0.1149	N	0.13003	0.285	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.22487	-1.0215	9	0.12103	T	0.63	-0.1596	4.5442	0.12073	0.3774:0.6226:0.0:0.0	.	4	Q96BQ3	TRI43_HUMAN	E	4	ENSP00000272395:D4E	ENSP00000272395:D4E	D	+	3	2	TRIM43	95623510	0.001000	0.12720	0.004000	0.12327	0.301000	0.27625	0.014000	0.13333	0.959000	0.37980	0.386000	0.25728	GAC		0.463	TRIM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252784.1	NM_138800		A	96259783	C	A	96259783	3	1	66	1	0	0	0	0	1	0	0	0	16558	564	20	2	14	2	TRIM43	2	96259783	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	95090946	96259783	146939590	14	20659										
ST6GAL2	84620	broad.mit.edu	37	chr2	107450536	107450536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgatgcgtatggtggttttaTtcccaacatctttctcataa	7	8	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr2:107450536T>C	ENST00000409382.3	-	3	1620	c.1010A>G	c.(1009-1011)aAt>aGt	p.N337S	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.N337S|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.N337S	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	337					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)	p.N337S(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						GGTGGTTTTATTCCCAACATC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	2											217	207	211					2																	107450536		2203	4300	6503	106816968	SO:0001583	missense	84620			AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1010A>G	2.37:g.107450536T>C	ENSP00000386942:p.Asn337Ser		106816968	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652538	0.29336	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.78364	-1.17;-1.17;-1.17	6.03	4.87	0.63330	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);	0.174254	0.64402	N	0.000011	T	0.56262	0.1973	N	0.11427	0.14	0.58432	D	0.999996	B;B	0.22003	0.063;0.002	B;B	0.18871	0.023;0.01	T	0.49753	-0.8906	10	0.08599	T	0.76	-28.4653	11.2601	0.49078	0.0:0.0709:0.0:0.9291	.	337;337	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	S	337	ENSP00000355273:N337S;ENSP00000386942:N337S;ENSP00000387332:N337S	ENSP00000355273:N337S	N	-	2	0	ST6GAL2	106816968	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	1.790000	0.38734	1.097000	0.41459	0.533000	0.62120	AAT		0.383	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		C	107450536	T	C	107450536	3	2	66	1	0	0	0	0	1	0	0	0	15261	1493	52	4	682	4	ST6GAL2	2	107450536	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	11190753	107450536	135748837	15	20660										
CAV3	859	broad.mit.edu	37	chr3	8787320	8787320	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccaagtactggtgctaccgtCtgttgtccacgctgctgggc	12	13	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:8787320C>A	ENST00000343849.2	+	2	300	c.223C>A	c.(223-225)Ctg>Atg	p.L75M	CAV3_ENST00000472766.1_Intron|SSUH2_ENST00000478513.1_5'Flank|CAV3_ENST00000397368.2_Missense_Mutation_p.L75M	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	75	Required for interaction with DAG1.				actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)	p.L75M(1)		breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						GTGCTACCGTCTGTTGTCCAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	81	90					3																	8787320		2203	4300	6503	8762320	SO:0001583	missense	859			AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"M-caveolin"	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.223C>A	3.37:g.8787320C>A	ENSP00000341940:p.Leu75Met		8762320	A8K777|Q3T1A4	Missense_Mutation	SNP	ENST00000343849.2	37	CCDS2569.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923787	0.34002	.	.	ENSG00000182533	ENST00000343849;ENST00000397368	D;D	0.94650	-3.48;-3.48	4.63	3.73	0.42828	.	0.190535	0.36338	N	0.002651	D	0.95978	0.8690	M	0.82630	2.6	0.44295	D	0.997164	D	0.53151	0.958	P	0.60345	0.873	D	0.95341	0.8438	10	0.72032	D	0.01	-3.4283	7.1701	0.25715	0.1679:0.7416:0.0:0.0905	.	75	P56539	CAV3_HUMAN	M	75	ENSP00000341940:L75M;ENSP00000380525:L75M	ENSP00000341940:L75M	L	+	1	2	CAV3	8762320	0.330000	0.24705	1.000000	0.80357	0.237000	0.25408	0.748000	0.26305	2.386000	0.81285	0.313000	0.20887	CTG		0.592	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337		A	8787320	C	A	8787320	3	1	66	1	0	0	0	0	1	0	0	0	2701	912	32	2	229	2	CAV3	3	8787320	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		8787320	189235110	16	20661										
NBEAL2	23218	broad.mit.edu	37	chr3	47030195	47030195	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgcagcagtggctgaaggccTttgtaggtgccttcaagaag	14	8	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:47030195T>G	ENST00000450053.3	+	2	267	c.88T>G	c.(88-90)Ttt>Gtt	p.F30V	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.F30V	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	30					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.F30V(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GCTGAAGGCCTTTGTAGGTGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											118	119	119					3																	47030195		2067	4189	6256	47005199	SO:0001583	missense	23218			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.88T>G	3.37:g.47030195T>G	ENSP00000415034:p.Phe30Val		47005199	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.049169	0.55110	.	.	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.75260	-0.92;-0.84	4.17	4.17	0.49024	.	.	.	.	.	T	0.80644	0.4662	M	0.73962	2.25	0.80722	D	1	D;B	0.63046	0.992;0.376	P;B	0.57101	0.813;0.115	T	0.80158	-0.1499	9	0.37606	T	0.19	.	10.7348	0.46117	0.0:0.0:0.0:1.0	.	23;30	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	V	30;30;23	ENSP00000292309:F30V;ENSP00000415034:F30V	ENSP00000292309:F30V	F	+	1	0	NBEAL2	47005199	1.000000	0.71417	0.895000	0.35142	0.435000	0.31806	3.930000	0.56522	1.767000	0.52121	0.459000	0.35465	TTT		0.582	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		G	47030195	T	G	47030195	3	3	66	1	0	0	0	0	1	0	0	0	10219	1609	56	4	94	4	NBEAL2	3	47030195	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	38242875	47030195	150992235	17	20662										
CSPG5	10675	broad.mit.edu	37	chr3	47614185	47614185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cacagactcacttggtcctaCgcagcttggtattctccgtc	8	14	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:47614185C>T	ENST00000383738.2	-	3	3471	c.1373G>A	c.(1372-1374)cGt>cAt	p.R458H	CSPG5_ENST00000456150.1_Missense_Mutation_p.R320H|CSPG5_ENST00000264723.4_Missense_Mutation_p.R458H	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	458	Interaction with GOPC.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)	p.R458H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CTTGGTCCTACGCAGCTTGGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	3											130	90	103					3																	47614185		2203	4300	6503	47589189	SO:0001583	missense	10675			AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.1373G>A	3.37:g.47614185C>T	ENSP00000373244:p.Arg458His		47589189	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.958418	0.92726	.	.	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.32023	1.49;1.57;1.47	5.25	5.25	0.73442	Neural chondroitin sulphate proteoglycan cytoplasmic (1);	0.133288	0.50627	D	0.000103	T	0.44808	0.1311	L	0.27053	0.805	0.46849	D	0.999225	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	T	0.46386	-0.9195	10	0.87932	D	0	-11.1723	17.4347	0.87548	0.0:1.0:0.0:0.0	.	458;458	O95196;O95196-2	CSPG5_HUMAN;.	H	320;458;458	ENSP00000392096:R320H;ENSP00000373244:R458H;ENSP00000264723:R458H	ENSP00000264723:R458H	R	-	2	0	CSPG5	47589189	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	5.439000	0.66556	2.455000	0.83008	0.561000	0.74099	CGT		0.602	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		T	47614185	C	T	47614185	3	4	66	1	0	0	0	0	1	0	0	0	3967	536	19	1	258	1	CSPG5	3	47614185	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	583990	47614185	150408245	18	20663										
MORC1	27136	broad.mit.edu	37	chr3	108813824	108813824	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ttttaaatggggagtatttaTaaattatagataattccatt	6	2	0	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:108813824T>A	ENST00000483760.1	-	7	558	c.515A>T	c.(514-516)tAt>tTt	p.Y172F	MORC1_ENST00000232603.5_Missense_Mutation_p.Y172F					MORC family CW-type zinc finger 1									p.Y172F(1)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GGAGTATTTATAAATTATAGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3											37	41	40					3																	108813824		2202	4296	6498	110296514	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.515A>T	3.37:g.108813824T>A	ENSP00000417282:p.Tyr172Phe		110296514		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	T	10.52	1.373837	0.24857	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05649	3.42;3.41	5.52	0.226	0.15353	ATPase-like, ATP-binding domain (1);	0.304109	0.24109	N	0.041477	T	0.04272	0.0118	L	0.33485	1.01	0.18873	N	0.999986	B;B	0.15141	0.012;0.001	B;B	0.11329	0.006;0.003	T	0.40979	-0.9534	10	0.25751	T	0.34	-4.4238	5.5909	0.17301	0.3985:0.0728:0.0:0.5287	.	172;172	E7ERX1;Q86VD1	.;MORC1_HUMAN	F	172	ENSP00000232603:Y172F;ENSP00000417282:Y172F	ENSP00000232603:Y172F	Y	-	2	0	MORC1	110296514	1.000000	0.71417	0.950000	0.38849	0.609000	0.37215	0.783000	0.26802	-0.096000	0.12329	0.528000	0.53228	TAT		0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108813824	T	A	108813824	3	1	66	1	0	0	0	0	1	0	0	0	9731	1406	49	5	2527	5	MORC1	3	108813824	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	61199639	108813824	89208606	19	20664										
NAALADL2	254827	broad.mit.edu	37	chr3	175455143	175455143	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	caacgaacctgttctgccctTtaatgcacttgatatagctt	6	11	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:175455143T>A	ENST00000454872.1	+	12	2074	c.1946T>A	c.(1945-1947)tTt>tAt	p.F649Y	snoU13_ENST00000606657.1_RNA	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	649						integral component of membrane (GO:0016021)		p.F649Y(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		GTTCTGCCCTTTAATGCACTT	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	3											114	108	110					3																	175455143		1822	4077	5899	176937837	SO:0001583	missense	254827				CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"glutamate carboxypeptidase II-type non-peptidase homologue"	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1946T>A	3.37:g.175455143T>A	ENSP00000404705:p.Phe649Tyr		176937837	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.271650	0.80469	.	.	ENSG00000177694	ENST00000454872	T	0.40225	1.04	5.38	5.38	0.77491	Transferrin receptor-like, dimerisation domain (1);	0.134368	0.48767	D	0.000168	T	0.37758	0.1015	L	0.32530	0.975	0.32674	N	0.516408	P	0.41475	0.751	B	0.42282	0.382	T	0.54529	-0.8280	10	0.56958	D	0.05	-9.7209	14.6487	0.68780	0.0:0.0:0.0:1.0	.	649	Q58DX5	NADL2_HUMAN	Y	649	ENSP00000404705:F649Y	ENSP00000404705:F649Y	F	+	2	0	NAALADL2	176937837	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.924000	0.63418	2.164000	0.68074	0.477000	0.44152	TTT		0.303	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		A	175455143	T	A	175455143	3	1	66	1	0	0	0	0	1	0	0	0	10160	1841	64	5	1992	5	NAALADL2	3	175455143	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	66641319	175455143	22567287	20	20665										
PYDC2	152138	broad.mit.edu	37	chr3	191179197	191179197	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tttgaaaagatgaatcaaacGcatctgtctgggagagctga	11	6	3	5			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr3:191179197G>A	ENST00000518817.1	+	1	246	c.246G>A	c.(244-246)acG>acA	p.T82T		NM_001083308.1	NP_001076777.1	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	82	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T82T(2)		breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10						TGAATCAAACGCATCTGTCTG	0.512																																																2	Substitution - coding silent(2)	large_intestine(1)|breast(1)	3											94	99	97					3																	191179197		2141	4280	6421	192661891	SO:0001819	synonymous_variant	152138					3q28	2008-07-29				ENSG00000253548			33512	protein-coding gene	gene with protein product		615701				17178784	Standard	NM_001083308		Approved	POP2	uc011bso.2	Q56P42		ENST00000518817.1:c.246G>A	3.37:g.191179197G>A			192661891		Silent	SNP	ENST00000518817.1	37																																																																																					0.512	PYDC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343231.2	NM_001083308		A	191179197	G	A	191179197	2	1	66	1	0	0	0	0	0	0	0	1	12896	1074	38	1		1	PYDC2	3	191179197	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	15724054	191179197	6843233	21	20666										
RNF212	285498	broad.mit.edu	37	chr4	1075217	1075217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	acccacacacctgtcgggggCtgatgagtgaggtggcagca	15	11	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:1075217C>A	ENST00000433731.2	-	7	515	c.454G>T	c.(454-456)Gcc>Tcc	p.A152S	RNF212_ENST00000382968.5_Missense_Mutation_p.A152S			Q495C1	RN212_HUMAN	ring finger protein 212	152					chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A152S(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		CTGTCGGGGGCTGATGAGTGA	0.562																																																2	Substitution - Missense(2)	large_intestine(2)	4											163	159	160					4																	1075217		2203	4300	6503	1065217	SO:0001583	missense	285498			AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"RING-type (C3HC4) zinc fingers"	27729	protein-coding gene	gene with protein product		612041	"hypothetical protein LOC285498"	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.454G>T	4.37:g.1075217C>A	ENSP00000389709:p.Ala152Ser		1065217	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Missense_Mutation	SNP	ENST00000433731.2	37	CCDS46996.1	.	.	.	.	.	.	.	.	.	.	c	0.703	-0.789979	0.02884	.	.	ENSG00000178222	ENST00000382968;ENST00000433731	T	0.47528	0.84	4.07	-0.156	0.13391	.	.	.	.	.	T	0.30230	0.0758	L	0.36672	1.1	0.09310	N	1	B;B	0.22414	0.02;0.069	B;B	0.24006	0.05;0.034	T	0.30966	-0.9960	9	0.07482	T	0.82	-0.5296	6.6308	0.22855	0.0:0.6467:0.1545:0.1988	.	152;152	Q495C1;Q495C1-5	RN212_HUMAN;.	S	152	ENSP00000389709:A152S	ENSP00000372428:A152S	A	-	1	0	RNF212	1065217	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.069000	0.01381	-0.141000	0.11374	-0.898000	0.02899	GCC		0.562	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439		A	1075217	C	A	1075217	3	1	66	1	0	0	0	0	1	0	0	0	13513	797	28	2	455	2	RNF212	4	1075217	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		1075217	190079059	22	20667										
PRDM5	11107	broad.mit.edu	37	chr4	121719559	121719559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gaaagacttattacaaatctCgcaattatagggtcgttttt	7	6	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:121719559C>T	ENST00000264808.3	-	10	1291	c.1051G>A	c.(1051-1053)Gag>Aag	p.E351K	PRDM5_ENST00000515109.1_Missense_Mutation_p.E320K|PRDM5_ENST00000428209.2_Missense_Mutation_p.E320K	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	351					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E351K(1)|p.E351*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTACAAATCTCGCAATTATAG	0.343																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	4											61	62	62					4																	121719559		2202	4300	6502	121939009	SO:0001583	missense	11107			AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"Zinc fingers, C2H2-type"	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1051G>A	4.37:g.121719559C>T	ENSP00000264808:p.Glu351Lys		121939009	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917941	0.73098	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.16597	2.33;3.28;3.28	5.63	5.63	0.86233	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.141585	0.64402	D	0.000007	T	0.22666	0.0547	L	0.28274	0.84	0.80722	D	1	D;D;D	0.64830	0.989;0.994;0.979	P;P;P	0.55749	0.683;0.783;0.594	T	0.01643	-1.1305	10	0.08599	T	0.76	-26.9094	20.0499	0.97621	0.0:1.0:0.0:0.0	.	320;320;351	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	K	351;320;320	ENSP00000264808:E351K;ENSP00000422309:E320K;ENSP00000404832:E320K	ENSP00000264808:E351K	E	-	1	0	PRDM5	121939009	1.000000	0.71417	0.996000	0.52242	0.780000	0.44128	7.578000	0.82498	2.798000	0.96311	0.655000	0.94253	GAG		0.343	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			T	121719559	C	T	121719559	3	4	66	1	0	0	0	0	1	0	0	0	12494	893	31	1	869	1	PRDM5	4	121719559	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	120644342	121719559	69434717	23	20668										
EXOSC9	5393	broad.mit.edu	37	chr4	122737580	122737580	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaatgatcattttggaaccaGacaagaatccaaagaaaata	6	6	1	4			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:122737580G>C	ENST00000243498.5	+	11	1321	c.1213G>C	c.(1213-1215)Gac>Cac	p.D405H	EXOSC9_ENST00000379663.3_Missense_Mutation_p.D422H|EXOSC9_ENST00000512454.1_Missense_Mutation_p.D389H	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	405					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D422H(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						TTTGGAACCAGACAAGAATCC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											66	77	73					4																	122737580		2197	4292	6489	122957030	SO:0001583	missense	5393			M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1213G>C	4.37:g.122737580G>C	ENSP00000243498:p.Asp405His		122957030	Q12883|Q4W5P5|Q86Y41|Q86Y48	Missense_Mutation	SNP	ENST00000243498.5	37	CCDS3722.2	.	.	.	.	.	.	.	.	.	.	G	19.77	3.888976	0.72524	.	.	ENSG00000123737	ENST00000243498;ENST00000379663;ENST00000512454	T;T;T	0.26223	1.76;1.77;1.75	6.08	6.08	0.98989	.	0.316334	0.36932	N	0.002321	T	0.21022	0.0506	N	0.14661	0.345	0.26612	N	0.972816	B;B;P	0.41569	0.412;0.214;0.755	B;B;B	0.44224	0.172;0.092;0.444	T	0.14227	-1.0480	10	0.59425	D	0.04	0.1626	13.9726	0.64250	0.0:0.1623:0.8377:0.0	.	389;405;422	D6RIY6;Q06265;Q06265-2	.;EXOS9_HUMAN;.	H	405;422;389	ENSP00000243498:D405H;ENSP00000368984:D422H;ENSP00000425782:D389H	ENSP00000243498:D405H	D	+	1	0	EXOSC9	122957030	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.410000	0.66381	2.894000	0.99253	0.655000	0.94253	GAC		0.279	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		C	122737580	G	C	122737580	3	2	66	1	0	0	0	0	1	0	0	0	5334	942	33	5	1310	5	EXOSC9	4	122737580	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	1018021	122737580	68416696	24	20669										
FBXW7	55294	broad.mit.edu	37	chr4	153245393	153245393	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccagattttaactgtagaatCtgcattcccagagacaagaa	7	9	1	4			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:153245393C>A	ENST00000281708.4	-	11	3027	c.1798G>T	c.(1798-1800)Gat>Tat	p.D600Y	FBXW7_ENST00000263981.5_Missense_Mutation_p.D520Y|FBXW7_ENST00000393956.3_Missense_Mutation_p.D424Y|FBXW7_ENST00000603841.1_Missense_Mutation_p.D600Y|FBXW7_ENST00000296555.5_Missense_Mutation_p.D482Y|FBXW7_ENST00000603548.1_Missense_Mutation_p.D600Y	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	600					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.D600Y(2)|p.D520Y(1)|p.D361Y(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTGTAGAATCTGCATTCCCA	0.388			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	5	Substitution - Missense(4)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)	4											125	116	119					4																	153245393		2203	4300	6503	153464843	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1798G>T	4.37:g.153245393C>A	ENSP00000281708:p.Asp600Tyr		153464843	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689117	0.88735	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.96969	0.9010	H	0.98133	4.155	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98335	1.0535	10	0.87932	D	0	-19.794	19.2767	0.94034	0.0:1.0:0.0:0.0	.	424;600;482;520	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	Y	600;482;520;424	ENSP00000281708:D600Y;ENSP00000296555:D482Y;ENSP00000263981:D520Y;ENSP00000377528:D424Y	ENSP00000263981:D520Y	D	-	1	0	FBXW7	153464843	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.547000	0.85894	0.655000	0.94253	GAT		0.388	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153245393	C	A	153245393	3	1	66	1	0	0	0	0	1	0	0	0	5788	913	32	2	333	2	FBXW7	4	153245393	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	30507813	153245393	37908883	25	20670										
FBXW7	55294	broad.mit.edu	37	chr4	153249469	153249469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gagtgtccgatctgtagatcCactaatgatgatgttgtctc	10	8	2	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:153249469C>T	ENST00000281708.4	-	9	2538	c.1309G>A	c.(1309-1311)Gga>Aga	p.G437R	FBXW7_ENST00000263981.5_Missense_Mutation_p.G357R|FBXW7_ENST00000393956.3_Missense_Mutation_p.G261R|FBXW7_ENST00000603841.1_Missense_Mutation_p.G437R|FBXW7_ENST00000296555.5_Missense_Mutation_p.G319R|FBXW7_ENST00000603548.1_Missense_Mutation_p.G437R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	437					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.G437R(2)|p.G357R(1)|p.?(1)|p.G198R(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TCTGTAGATCCACTAATGATG	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	5	Substitution - Missense(4)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)	4											313	265	281					4																	153249469		2203	4300	6503	153468919	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1309G>A	4.37:g.153249469C>T	ENSP00000281708:p.Gly437Arg		153468919	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977609	0.92982	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.91560	0.7334	H	0.98901	4.365	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.94264	0.7505	10	0.87932	D	0	-19.4993	20.2787	0.98501	0.0:1.0:0.0:0.0	.	261;437;319;357	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	R	437;319;357;261	ENSP00000281708:G437R;ENSP00000296555:G319R;ENSP00000263981:G357R;ENSP00000377528:G261R	ENSP00000263981:G357R	G	-	1	0	FBXW7	153468919	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	GGA		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153249469	C	T	153249469	3	4	66	1	0	0	0	0	1	0	0	0	5788	603	21	3	830	3	FBXW7	4	153249469	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	4076	153249469	37904807	26	20671										
GLRB	2743	broad.mit.edu	37	chr4	158073917	158073917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ctgagtgcacaacccttgccGctgagcttcccaaagtttcc	8	15	0	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:158073917G>A	ENST00000264428.4	+	9	1222	c.952G>A	c.(952-954)Gct>Act	p.A318T	GLRB_ENST00000512619.1_Intron|GLRB_ENST00000509282.1_Missense_Mutation_p.A318T|GLRB_ENST00000541722.1_Intron	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	318					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)	p.A318T(1)		central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	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)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	AACCCTTGCCGCTGAGCTTCC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	4											190	181	184					4																	158073917		2203	4300	6503	158293367	SO:0001583	missense	2743			U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.952G>A	4.37:g.158073917G>A	ENSP00000264428:p.Ala318Thr		158293367	A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	37	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073419	0.36566	.	.	ENSG00000109738	ENST00000264428;ENST00000509282	D;D	0.84223	-1.82;-1.82	5.61	5.61	0.85477	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.245990	0.42548	D	0.000681	T	0.77572	0.4150	N	0.21617	0.685	0.80722	D	1	B	0.23591	0.088	B	0.19946	0.027	T	0.74788	-0.3546	10	0.62326	D	0.03	.	15.1522	0.72709	0.0:0.1407:0.8593:0.0	.	318	P48167	GLRB_HUMAN	T	318	ENSP00000264428:A318T;ENSP00000427186:A318T	ENSP00000264428:A318T	A	+	1	0	GLRB	158293367	1.000000	0.71417	0.577000	0.28562	0.420000	0.31355	5.062000	0.64326	2.642000	0.89623	0.650000	0.86243	GCT		0.463	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		A	158073917	G	A	158073917	3	1	66	1	0	0	0	0	1	0	0	0	6478	1087	38	1	982	1	GLRB	4	158073917	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	4824448	158073917	33080359	27	20672										
ADAM29	11086	broad.mit.edu	37	chr4	175898763	175898763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tttattatgttgtctttatcGactttgtaaaaaaagtaaac	5	4	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr4:175898763G>A	ENST00000359240.3	+	5	2757	c.2087G>A	c.(2086-2088)cGa>cAa	p.R696Q	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Missense_Mutation_p.R696Q|ADAM29_ENST00000404450.4_Missense_Mutation_p.R696Q|ADAM29_ENST00000514159.1_Missense_Mutation_p.R696Q	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	696					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R696Q(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGTCTTTATCGACTTTGTAAA	0.343																																					Ovarian(140;1727 1835 21805 25838 41440)											1	Substitution - Missense(1)	large_intestine(1)	4											36	39	38					4																	175898763		2203	4300	6503	176135338	SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2087G>A	4.37:g.175898763G>A	ENSP00000352177:p.Arg696Gln		176135338	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	G	4.343	0.063028	0.08388	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01981	4.52;4.52;4.52;4.52	3.08	-6.16	0.02098	.	2.137520	0.03034	U	0.152525	T	0.01092	0.0036	N	0.14661	0.345	0.09310	N	1	P	0.42456	0.78	B	0.23419	0.046	T	0.44436	-0.9328	9	.	.	.	.	5.6034	0.17367	0.2097:0.0:0.1896:0.6008	.	696	Q9UKF5	ADA29_HUMAN	Q	696	ENSP00000352177:R696Q;ENSP00000414544:R696Q;ENSP00000384229:R696Q;ENSP00000423517:R696Q	.	R	+	2	0	ADAM29	176135338	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.938000	0.00684	-2.371000	0.00602	-0.196000	0.12772	CGA		0.343	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898763	G	A	175898763	3	1	66	1	0	0	0	0	1	0	0	0	247	1058	37	1	2089	1	ADAM29	4	175898763	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	17824846	175898763	15255513	28	20673										
LIFR	3977	broad.mit.edu	37	chr5	38490321	38490321	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ctatatatccaatcatggagCgtaataattgatatccttga	6	7	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr5:38490321C>A	ENST00000263409.4	-	15	2300	c.2138G>T	c.(2137-2139)cGc>cTc	p.R713L	LIFR_ENST00000503088.1_5'Flank|LIFR_ENST00000453190.2_Missense_Mutation_p.R713L	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	713	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.R713L(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					AATCATGGAGCGTAATAATTG	0.318			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	1	Substitution - Missense(1)	large_intestine(1)	5											97	106	103					5																	38490321		2202	4290	6492	38526078	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2138G>T	5.37:g.38490321C>A	ENSP00000263409:p.Arg713Leu		38526078	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.920870	0.73213	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.52754	0.65;0.65	6.05	6.05	0.98169	Fibronectin, type III (1);	0.390921	0.30285	N	0.009971	T	0.44746	0.1308	L	0.56769	1.78	0.28933	N	0.891453	D	0.54207	0.965	P	0.45071	0.468	T	0.52902	-0.8513	10	0.34782	T	0.22	-20.2531	7.9601	0.30066	0.0:0.8154:0.0:0.1846	.	713	P42702	LIFR_HUMAN	L	713	ENSP00000263409:R713L;ENSP00000398368:R713L	ENSP00000263409:R713L	R	-	2	0	LIFR	38526078	0.111000	0.22076	0.632000	0.29296	0.935000	0.57460	1.910000	0.39927	2.878000	0.98634	0.650000	0.86243	CGC		0.318	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38490321	C	A	38490321	3	1	66	1	0	0	0	0	1	0	0	0	8803	768	27	2	1179	2	LIFR	5	38490321	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		38490321	142424939	29	20674										
APC	324	broad.mit.edu	37	chr5	112173299	112173299	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaactttattacaacacttaAaatctcatagtttgacaata	2	7	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr5:112173299A>T	ENST00000457016.1	+	16	2388	c.2008A>T	c.(2008-2010)Aaa>Taa	p.K670*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.K670*|APC_ENST00000257430.4_Nonsense_Mutation_p.K670*			P25054	APC_HUMAN	adenomatous polyposis coli	670	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K670*(2)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACAACACTTAAAATCTCATAG	0.368		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(2)|Unknown(1)	large_intestine(2)|skin(1)	5											71	73	72					5																	112173299		2202	4300	6502	112201198	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2008A>T	5.37:g.112173299A>T	ENSP00000413133:p.Lys670*		112201198	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	37	6.015398	0.97205	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.4247	16.4943	0.84223	1.0:0.0:0.0:0.0	.	.	.	.	X	670;652;670;670;670	.	ENSP00000257430:K670X	K	+	1	0	APC	112201198	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.013000	0.76373	2.291000	0.77112	0.533000	0.62120	AAA		0.368	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173299	A	T	112173299	4	4	66	1	0	0	0	0	0	1	0	0	763	15	1	5	2066	5	APC	5	112173299	Nonsense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	73682978	112173299	68741961	30	20675										
APC	324	broad.mit.edu	37	chr5	112175507	112175507	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gttcgattgccagctccgttCagagtgaaccatgcagtgga	12	10	1	2	rs587782518		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr5:112175507C>T	ENST00000457016.1	+	16	4596	c.4216C>T	c.(4216-4218)Cag>Tag	p.Q1406*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1406*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1406*			P25054	APC_HUMAN	adenomatous polyposis coli	1406	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1406*(15)|p.Q1406fs*11(1)|p.?(1)|p.K1192fs*3(1)|p.I1401fs*2(1)|p.Y1376fs*41(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCTCCGTTCAGAGTGAACC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(15)|Deletion - Frameshift(3)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(18)|soft_tissue(1)|skin(1)	5	GRCh37	CI084250|CM023011	APC	I|M							113	105	108					5																	112175507		2202	4300	6502	112203406	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4216C>T	5.37:g.112175507C>T	ENSP00000413133:p.Gln1406*		112203406	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.658788	0.98903	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.187376	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.0613	15.6825	0.77381	0.0:0.8637:0.1363:0.0	.	.	.	.	X	1406	.	.	Q	+	1	0	APC	112203406	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.175000	0.77632	1.615000	0.50252	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175507	C	T	112175507	4	4	66	1	0	0	0	0	0	1	0	0	763	827	29	3	4274	3	APC	5	112175507	Nonsense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	2208	112175507	68739753	31	20676										
PCDHB4	56131	broad.mit.edu	37	chr5	140502512	140502512	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaaattggatttcgaaaaaaTtaaatcttaccatgtagaaa	5	4	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr5:140502512T>A	ENST00000194152.1	+	1	932	c.932T>A	c.(931-933)aTt>aAt	p.I311N	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	311	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I311N(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCGAAAAAATTAAATCTTAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											111	129	123					5																	140502512		2203	4300	6503	140482696	SO:0001583	missense	56131			AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.932T>A	5.37:g.140502512T>A	ENSP00000194152:p.Ile311Asn		140482696	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	T	7.613	0.675177	0.14841	.	.	ENSG00000081818	ENST00000194152	T	0.51817	0.69	4.41	1.89	0.25635	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.46927	0.1418	L	0.42529	1.33	0.09310	N	1	P	0.44195	0.828	P	0.52267	0.694	T	0.32402	-0.9908	9	0.54805	T	0.06	.	4.1179	0.10090	0.1906:0.239:0.0:0.5704	.	311	Q9Y5E5	PCDB4_HUMAN	N	311	ENSP00000194152:I311N	ENSP00000194152:I311N	I	+	2	0	PCDHB4	140482696	0.000000	0.05858	0.173000	0.22940	0.965000	0.64279	-1.008000	0.03663	0.293000	0.22520	0.528000	0.53228	ATT		0.373	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		A	140502512	T	A	140502512	3	1	66	1	0	0	0	0	1	0	0	0	11575	1493	52	5	934	5	PCDHB4	5	140502512	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	28327005	140502512	40412748	32	20677										
PCDHB8	56128	broad.mit.edu	37	chr5	140559748	140559748	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tcggtgctcctgttcgtggcGgtgctgctgtgtaggaggag	18	8	0	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr5:140559748G>A	ENST00000239444.2	+	1	2378	c.2133G>A	c.(2131-2133)gcG>gcA	p.A711A	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	711					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A711A(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTGGCGGTGCTGCTGT	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	5											93	95	95					5																	140559748		2202	4299	6501	140539932	SO:0001819	synonymous_variant	56128			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.2133G>A	5.37:g.140559748G>A			140539932	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																				0.677	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		A	140559748	G	A	140559748	2	1	66	1	0	0	0	0	0	0	0	1	11579	1103	39	1		1	PCDHB8	5	140559748	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	57236	140559748	40355512	33	20678										
HIST1H3D	8351	broad.mit.edu	37	chr6	26197369	26197369	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gccggtaacggtggggcttcTtcacgccgccggtggctgga	17	12	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr6:26197369T>A	ENST00000356476.2	-	1	109	c.110A>T	c.(109-111)aAg>aTg	p.K37M	HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000377831.5_Missense_Mutation_p.K37M			P68431	H31_HUMAN	histone cluster 1, H3d	37					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)	p.K37M(1)		NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)	14		all_hematologic(11;0.196)				GTGGGGCTTCTTCACGCCGCC	0.652																																					GBM(108;3816 4467)											1	Substitution - Missense(1)	large_intestine(1)	6											44	49	48					6																	26197369		2203	4298	6501	26305348	SO:0001583	missense	8351			Z80784	CCDS4590.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197409	ENSG00000197409		"Histones / Replication-dependent"	4767	protein-coding gene	gene with protein product		602811	"H3 histone family, member B", "histone 1, H3d"	H3FB		9119399, 12408966	Standard	NM_003530		Approved	H3/b	uc003ngv.4	P68431	OTTHUMG00000014433	ENST00000356476.2:c.110A>T	6.37:g.26197369T>A	ENSP00000366999:p.Lys37Met		26305348	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000356476.2	37	CCDS4590.1	.	.	.	.	.	.	.	.	.	.	.	15.18	2.755542	0.49362	.	.	ENSG00000197409	ENST00000356476;ENST00000377831	T;T	0.56776	0.44;0.44	4.14	2.96	0.34315	.	.	.	.	.	T	0.45657	0.1353	.	.	.	0.35625	D	0.809751	.	.	.	.	.	.	T	0.50346	-0.8839	6	0.87932	D	0	.	8.6974	0.34305	0.0:0.0929:0.0:0.9071	.	.	.	.	M	37	ENSP00000366999:K37M;ENSP00000367062:K37M	ENSP00000366999:K37M	K	-	2	0	HIST1H3D	26305348	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	5.801000	0.69115	0.565000	0.29255	0.533000	0.62120	AAG		0.652	HIST1H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040096.1	NM_003530		A	26197369	T	A	26197369	3	1	66	1	0	0	0	0	1	0	0	0	7179	1609	56	5	304	5	HIST1H3D	6	26197369	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09		26197369	144917698	34	20679										
MOG	4340	broad.mit.edu	37	chr6	29633972	29633972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggagtgctggttctcctcgcGgtgctgcctgtgctcctcct	13	14	1	0	rs148630553	byFrequency	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr6:29633972G>A	ENST00000376917.3	+	3	709	c.480G>A	c.(478-480)gcG>gcA	p.A160A	MOG_ENST00000396701.2_Silent_p.A160A|MOG_ENST00000376902.3_3'UTR|MOG_ENST00000431798.2_Silent_p.A160A|MOG_ENST00000494692.1_Silent_p.A160A|MOG_ENST00000376894.4_Silent_p.A160A|MOG_ENST00000490427.1_Silent_p.A44A|MOG_ENST00000416766.2_Intron|MOG_ENST00000396704.3_Silent_p.A160A|MOG_ENST00000376888.2_Silent_p.A44A|MOG_ENST00000376898.3_Silent_p.A160A|MOG_ENST00000376891.4_Silent_p.A160A|MOG_ENST00000483013.1_Silent_p.A44A|MOG_ENST00000533330.2_3'UTR	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	160					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A160A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						TTCTCCTCGCGGTGCTGCCTG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	6											297	250	267					6																	29633972		1511	2709	4220	29741951	SO:0001819	synonymous_variant	4340				CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099	ENST00000376917.3:c.480G>A	6.37:g.29633972G>A			29741951	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Silent	SNP	ENST00000376917.3	37	CCDS34370.1																																																																																				0.557	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		A	29633972	G	A	29633972	2	1	66	1	0	0	0	0	0	0	0	1	9723	1103	39	1		1	MOG	6	29633972	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	3436603	29633972	141481095	35	20680										
RBM16	22828	broad.mit.edu	37	chr6	155154100	155154100	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tttcggtctggaaactatcgAtttgatcctagaagtggtcc	10	8	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr6:155154100A>G	ENST00000367178.3	+	20	3963	c.3387A>G	c.(3385-3387)cgA>cgG	p.R1129R	SCAF8_ENST00000417268.1_Silent_p.R1129R|SCAF8_ENST00000367186.4_Silent_p.R1195R|TIAM2_ENST00000461783.3_5'UTR	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	1129	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)	p.R1129R(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						GAAACTATCGATTTGATCCTA	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	6											82	90	88					6																	155154100		2203	4300	6503	155195792	SO:0001819	synonymous_variant	22828			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.3387A>G	6.37:g.155154100A>G			155195792	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Silent	SNP	ENST00000367178.3	37	CCDS5247.1																																																																																				0.473	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		G	155154100	A	G	155154100	2	3	66	1	0	0	0	0	0	0	0	1	13155	320	12	4		4	RBM16	6	155154100	Silent	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	125520128	155154100	15960967	36	20681										
HERPUD2	64224	broad.mit.edu	37	chr7	35674865	35674865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	acatccagtctagccagtctCgattgaagtcttcttcattt	6	11	5	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:35674865C>T	ENST00000396081.1	-	6	1625	c.821G>A	c.(820-822)cGa>cAa	p.R274Q	HERPUD2_ENST00000311350.3_Missense_Mutation_p.R274Q|HERPUD2_ENST00000426180.1_5'UTR	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	274					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.R274Q(1)		kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						TAGCCAGTCTCGATTGAAGTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											205	194	198					7																	35674865		2203	4300	6503	35641390	SO:0001583	missense	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.821G>A	7.37:g.35674865C>T	ENSP00000379390:p.Arg274Gln		35641390	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	C	37	6.065724	0.97251	.	.	ENSG00000122557	ENST00000396081;ENST00000311350	T;T	0.20069	2.1;2.1	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.47728	0.1461	L	0.61036	1.89	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.22730	-1.0208	10	0.54805	T	0.06	-19.5002	20.422	0.99049	0.0:1.0:0.0:0.0	.	274	Q9BSE4	HERP2_HUMAN	Q	274	ENSP00000379390:R274Q;ENSP00000310729:R274Q	ENSP00000310729:R274Q	R	-	2	0	HERPUD2	35641390	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.072000	0.71238	2.832000	0.97577	0.655000	0.94253	CGA		0.433	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35674865	C	T	35674865	3	4	66	1	0	0	0	0	1	0	0	0	7085	884	31	1	411	1	HERPUD2	7	35674865	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		35674865	123463798	37	20682										
ABCA13	154664	broad.mit.edu	37	chr7	48427433	48427433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ttttaggaacatttggtttaCggaaaccatggtatttcccc	8	8	0	0	rs373647440		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:48427433C>T	ENST00000435803.1	+	36	11374	c.11350C>T	c.(11350-11352)Cgg>Tgg	p.R3784W		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3784					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R3784W(1)|p.R3729W(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTTGGTTTACGGAAACCATG	0.294																																																2	Substitution - Missense(2)	large_intestine(2)	7						C	TRP/ARG	0,3586		0,0,1793	97	86	89		11350	-3.4	0	7		89	1,8125		0,1,4062	no	missense	ABCA13	NM_152701.3	101	0,1,5855	TT,TC,CC		0.0123,0.0,0.0085	probably-damaging	3784/5059	48427433	1,11711	1793	4063	5856	48397979	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11350C>T	7.37:g.48427433C>T	ENSP00000411096:p.Arg3784Trp		48397979	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392525	0.42410	0.0	1.23E-4	ENSG00000179869	ENST00000435803	D	0.86297	-2.1	5.36	-3.39	0.04868	.	0.601905	0.15681	N	0.249939	D	0.87787	0.6265	M	0.69523	2.12	0.09310	N	1	D;D	0.76494	0.998;0.999	P;P	0.62298	0.9;0.849	T	0.78081	-0.2343	10	0.52906	T	0.07	.	2.4468	0.04508	0.3302:0.4:0.1493:0.1204	.	1486;3784	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	W	3784	ENSP00000411096:R3784W	ENSP00000411096:R3784W	R	+	1	2	ABCA13	48397979	0.127000	0.22367	0.003000	0.11579	0.008000	0.06430	0.419000	0.21247	-0.786000	0.04516	-2.245000	0.00285	CGG		0.294	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48427433	C	T	48427433	3	4	66	1	0	0	0	0	1	0	0	0	31	527	19	1	11321	1	ABCA13	7	48427433	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	12752568	48427433	110711230	38	20683										
SLC25A13	10165	broad.mit.edu	37	chr7	95820475	95820475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cagagtgctatagatctttcTaatgagttccatgttgttaa	8	6	2	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:95820475T>C	ENST00000265631.5	-	7	836	c.700A>G	c.(700-702)Aga>Gga	p.R234G	SLC25A13_ENST00000416240.2_Missense_Mutation_p.R234G|SLC25A13_ENST00000542654.1_Missense_Mutation_p.R126G			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	234					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)	p.R234G(1)		breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	TAGATCTTTCTAATGAGTTCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	7											178	177	177					7																	95820475		2203	4300	6503	95658411	SO:0001583	missense	10165			AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.700A>G	7.37:g.95820475T>C	ENSP00000265631:p.Arg234Gly		95658411	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.345787	0.41599	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.81247	-1.47;-1.47;-1.47	5.18	5.18	0.71444	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79493	0.4455	M	0.63428	1.95	0.52501	D	0.999959	P;P;P	0.39940	0.696;0.57;0.57	B;B;B	0.40602	0.333;0.334;0.334	T	0.78991	-0.1985	10	0.33940	T	0.23	-22.589	15.5118	0.75789	0.0:0.0:0.0:1.0	.	126;234;234	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	G	234;234;126	ENSP00000265631:R234G;ENSP00000400101:R234G;ENSP00000440484:R126G	ENSP00000265631:R234G	R	-	1	2	SLC25A13	95658411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.677000	0.46892	2.313000	0.78055	0.455000	0.32223	AGA		0.393	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		C	95820475	T	C	95820475	3	2	66	1	0	0	0	0	1	0	0	0	14512	1530	53	4	1378	4	SLC25A13	7	95820475	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	47393042	95820475	63318188	39	20684										
LMTK2	22853	broad.mit.edu	37	chr7	97823749	97823749	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gtgcccatcatcctcagcaaCgaggacggaaggcacctgcg	12	14	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:97823749C>T	ENST00000297293.5	+	11	4265	c.3972C>T	c.(3970-3972)aaC>aaT	p.N1324N		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1324					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)	p.N1324N(2)		NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	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)					TCCTCAGCAACGAGGACGGAA	0.637																																																2	Substitution - coding silent(2)	large_intestine(2)	7											105	101	102					7																	97823749		2203	4300	6503	97661685	SO:0001819	synonymous_variant	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3972C>T	7.37:g.97823749C>T			97661685	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																				0.637	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		T	97823749	C	T	97823749	2	4	66	1	0	0	0	0	0	0	0	1	8883	535	19	1		1	LMTK2	7	97823749	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	2003274	97823749	61314914	40	20685										
ARPC1B	10095	broad.mit.edu	37	chr7	98985759	98985759	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggccgcacatggaagcccacGctggtcatcctgcggatcaa	12	14	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:98985759G>A	ENST00000451682.1	+	6	576	c.267G>A	c.(265-267)acG>acA	p.T89T	ARPC1B_ENST00000252725.5_Silent_p.T89T|ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000474880.1_3'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	89					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)	p.T89T(2)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GGAAGCCCACGCTGGTCATCC	0.642																																																2	Substitution - coding silent(2)	large_intestine(2)	7											63	60	61					7																	98985759		2203	4300	6503	98823695	SO:0001819	synonymous_variant	10095			AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.267G>A	7.37:g.98985759G>A			98823695	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																				0.642	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		A	98985759	G	A	98985759	2	1	66	1	0	0	0	0	0	0	0	1	971	1074	38	1		1	ARPC1B	7	98985759	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	1162010	98985759	60152904	41	20686										
KCND2	3751	broad.mit.edu	37	chr7	120385934	120385934	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tccttcactgtcttcacaacAaggagtcaccagcacctgct	6	15	4	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:120385934A>T	ENST00000331113.4	+	5	2533	c.1568A>T	c.(1567-1569)cAa>cTa	p.Q523L	RP4-797C5.2_ENST00000450480.1_RNA	NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	523					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.Q523L(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TCTTCACAACAAGGAGTCACC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	7											146	122	130					7																	120385934		2203	4300	6503	120173170	SO:0001583	missense	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1568A>T	7.37:g.120385934A>T	ENSP00000333496:p.Gln523Leu		120173170	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.83|14.83	2.652305|2.652305	0.47362|0.47362	.|.	.|.	ENSG00000184408|ENSG00000184408	ENST00000425288|ENST00000331113	.|D	.|0.82803	.|-1.65	5.63|5.63	4.45|4.45	0.53987|0.53987	.|Potassium channel, voltage dependent, Kv4, C-terminal (1);	.|0.137306	.|0.51477	.|D	.|0.000098	.|T	.|0.76513	.|0.3998	L|L	0.38175|0.38175	1.15|1.15	0.41315|0.41315	D|D	0.987132|0.987132	.|B	.|0.17268	.|0.021	.|B	.|0.29524	.|0.103	.|T	.|0.68228	.|-0.5464	.|9	.|.	.|.	.|.	.|.	12.7549|12.7549	0.57328|0.57328	0.8628:0.1371:0.0:0.0|0.8628:0.1371:0.0:0.0	.|.	.|523	.|Q9NZV8	.|KCND2_HUMAN	X|L	109|523	.|ENSP00000333496:Q523L	.|.	K|Q	+|+	1|2	0|0	KCND2|KCND2	120173170|120173170	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.736000|3.736000	0.55052|0.55052	0.934000|0.934000	0.37316|0.37316	0.533000|0.533000	0.62120|0.62120	AAG|CAA		0.438	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	120385934	A	T	120385934	3	4	66	1	0	0	0	0	1	0	0	0	8040	130	5	5	1586	5	KCND2	7	120385934	Missense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	21400175	120385934	38752729	42	20687										
RBM33	155435	broad.mit.edu	37	chr7	155503909	155503909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ctccacagccccaggctcccCctccaccgccaccgccgcct	6	26	0	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr7:155503909C>T	ENST00000401878.3	+	8	1159	c.961C>T	c.(961-963)Cct>Tct	p.P321S	RBM33_ENST00000486747.1_3'UTR	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	321	Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P321S(2)		breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CCAGGCTCCCCCTCCACCGCC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	7											12	15	14					7																	155503909		1913	4118	6031	155196670	SO:0001583	missense	155435			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.961C>T	7.37:g.155503909C>T	ENSP00000384160:p.Pro321Ser		155196670	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	ENST00000401878.3	37	CCDS5941.2	.	.	.	.	.	.	.	.	.	.	C	6.800	0.516673	0.12944	.	.	ENSG00000184863	ENST00000401878;ENST00000440108	T	0.44482	0.92	4.64	4.64	0.57946	.	.	.	.	.	T	0.42245	0.1194	L	0.51422	1.61	0.80722	D	1	B;B	0.31174	0.311;0.311	B;B	0.39562	0.303;0.303	T	0.24548	-1.0157	9	0.23891	T	0.37	.	12.9926	0.58627	0.0:1.0:0.0:0.0	.	38;321	B4DVQ2;Q96EV2	.;RBM33_HUMAN	S	321;222	ENSP00000384160:P321S	ENSP00000384160:P321S	P	+	1	0	RBM33	155196670	0.177000	0.23109	0.045000	0.18777	0.190000	0.23558	2.825000	0.48096	2.144000	0.66660	0.557000	0.71058	CCT		0.547	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		T	155503909	C	T	155503909	3	4	66	1	0	0	0	0	1	0	0	0	13167	623	22	3	991	3	RBM33	7	155503909	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	35117975	155503909	3634754	43	20688										
PRKDC	5591	broad.mit.edu	37	chr8	48840396	48840396	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gtgtggcaaggacagaagaaAggtcaaacaagaggccaaaa	13	6	1	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:48840396A>C	ENST00000314191.2	-	20	2250	c.2194T>G	c.(2194-2196)Ttt>Gtt	p.F732V	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Missense_Mutation_p.F732V	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	732					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.F732V(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GACAGAAGAAAGGTCAAACAA	0.423								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											2	Substitution - Missense(2)	large_intestine(2)	8											141	148	146					8																	48840396		1989	4159	6148	49002949	SO:0001583	missense	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.2194T>G	8.37:g.48840396A>C	ENSP00000313420:p.Phe732Val		49002949	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	A	27.6	4.843556	0.91197	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.68331	4.16;-0.32	5.35	5.35	0.76521	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81254	0.4784	.	.	.	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.985	D;D;P	0.67103	0.949;0.948;0.783	D	0.84113	0.0402	9	0.87932	D	0	.	15.6202	0.76799	1.0:0.0:0.0:0.0	.	732;732;732	P78527-2;E7EUY0;P78527	.;.;PRKDC_HUMAN	V	732	ENSP00000313420:F732V;ENSP00000345182:F732V	ENSP00000313420:F732V	F	-	1	0	PRKDC	49002949	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.655000	0.91098	2.145000	0.66743	0.460000	0.39030	TTT		0.423	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		C	48840396	A	C	48840396	3	2	66	1	0	0	0	0	1	0	0	0	12555	72	3	4	10459	4	PRKDC	8	48840396	Missense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09		48840396	97523626	44	20689										
MATN2	4147	broad.mit.edu	37	chr8	99028888	99028888	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgaagatggaaaaacctgcaGaagtaagtttgtactggagc	12	5	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:99028888G>A	ENST00000520016.1	+	10	1818	c.1694G>A	c.(1693-1695)aGa>aAa	p.R565K	MATN2_ENST00000254898.5_Missense_Mutation_p.R565K|MATN2_ENST00000522025.2_Missense_Mutation_p.R281K|MATN2_ENST00000524308.1_Missense_Mutation_p.R524K|MATN2_ENST00000521689.1_Missense_Mutation_p.R565K			O00339	MATN2_HUMAN	matrilin 2	565	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.R565K(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AAAACCTGCAGAAGTAAGTTT	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	8											73	71	71					8																	99028888		1901	4117	6018	99098064	SO:0001583	missense	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1694G>A	8.37:g.99028888G>A	ENSP00000430487:p.Arg565Lys		99098064	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.401497	0.42613	.	.	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	D;D;D;D;D	0.97279	-2.2;-2.2;-4.32;-4.32;-2.2	5.68	1.9	0.25705	Epidermal growth factor-like (1);	0.357941	0.27388	N	0.019586	D	0.91533	0.7326	N	0.20685	0.6	0.35795	D	0.822685	B;B;B;B	0.11235	0.001;0.001;0.004;0.001	B;B;B;B	0.12837	0.002;0.002;0.007;0.008	D	0.86073	0.1539	10	0.32370	T	0.25	-11.6303	8.2239	0.31558	0.3965:0.0:0.6035:0.0	.	524;565;565;565	C9JH87;E9PF03;O00339-2;O00339	.;.;.;MATN2_HUMAN	K	565;565;524;524;281;565	ENSP00000429977:R565K;ENSP00000254898:R565K;ENSP00000430221:R524K;ENSP00000429010:R281K;ENSP00000430487:R565K	ENSP00000254898:R565K	R	+	2	0	MATN2	99098064	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	0.772000	0.26647	0.347000	0.23924	0.563000	0.77884	AGA		0.443	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			A	99028888	G	A	99028888	3	1	66	1	0	0	0	0	1	0	0	0	9364	942	33	3	1732	3	MATN2	8	99028888	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	50188492	99028888	47335134	45	20690										
CSMD3	114788	broad.mit.edu	37	chr8	113308235	113308235	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ctggaattccacaatgacccGctgaaatacgttataaagta	7	9	0	2	rs369949755		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:113308235G>T	ENST00000297405.5	-	54	8685	c.8441C>A	c.(8440-8442)gCg>gAg	p.A2814E	CSMD3_ENST00000352409.3_Splice_Site_p.A2744E|CSMD3_ENST00000343508.3_Splice_Site_p.A2774E|CSMD3_ENST00000455883.2_Splice_Site_p.A2645E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2814	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A2814V(1)|p.A2814E(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACAATGACCCGCTGAAATACG	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	8											57	56	56					8																	113308235		2203	4300	6503	113377411	SO:0001630	splice_region_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8441-1C>A	8.37:g.113308235G>T			113377411	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820679	0.71028	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	5.31	5.31	0.75309	Complement control module (2);Sushi/SCR/CCP (1);	0.000000	0.64402	D	0.000001	T	0.50480	0.1618	M	0.84156	2.68	0.80722	D	1	P;P;D	0.65815	0.937;0.896;0.995	P;P;D	0.65443	0.712;0.669;0.935	T	0.52419	-0.8578	10	0.07325	T	0.83	.	18.9718	0.92718	0.0:0.0:1.0:0.0	.	2645;2814;2774	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	2774;2814;2084;2645;2744	ENSP00000345799:A2774E;ENSP00000297405:A2814E;ENSP00000341558:A2084E;ENSP00000412263:A2645E;ENSP00000343124:A2744E	ENSP00000297405:A2814E	A	-	2	0	CSMD3	113377411	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	6.622000	0.74233	2.480000	0.83734	0.655000	0.94253	GCG		0.299	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Missense_Mutation	T	113308235	G	T	113308235	5	4	66	1	0	0	0	0	0	0	1	0	3952	1101	38	2	2754	2	CSMD3	8	113308235	Splice_Site	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	14279347	113308235	33055787	46	20691										
RAD21	5885	broad.mit.edu	37	chr8	117866561	117866561	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tcctcctgtctctttccacaTcatcaatttcttggtgggcg	7	13	4	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:117866561T>A	ENST00000297338.2	-	9	1371	c.1084A>T	c.(1084-1086)Atg>Ttg	p.M362L	RAD21_ENST00000523547.1_5'Flank|RAD21_ENST00000523986.1_5'Flank|RAD21_ENST00000518055.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	362	Interaction with STAG1.|Interaction with WAPAL and PDS5B.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.M362L(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TCTTTCCACATCATCAATTTC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8											113	113	113					8																	117866561		2203	4300	6503	117935742	SO:0001583	missense	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1084A>T	8.37:g.117866561T>A	ENSP00000297338:p.Met362Leu		117935742	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	T	9.386	1.074311	0.20227	.	.	ENSG00000164754	ENST00000297338	T	0.74209	-0.82	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.78972	0.4368	M	0.66939	2.045	0.80722	D	1	P	0.35745	0.518	P	0.47827	0.558	T	0.74038	-0.3793	10	0.11182	T	0.66	-1.4875	15.8526	0.78943	0.0:0.0:0.0:1.0	.	362	O60216	RAD21_HUMAN	L	362	ENSP00000297338:M362L	ENSP00000297338:M362L	M	-	1	0	RAD21	117935742	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.040000	0.89188	2.156000	0.67533	0.377000	0.23210	ATG		0.383	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117866561	T	A	117866561	3	1	66	1	0	0	0	0	1	0	0	0	13018	1435	50	5	835	5	RAD21	8	117866561	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	4558326	117866561	28497461	47	20692										
EXT1	2131	broad.mit.edu	37	chr8	118842542	118842542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	agaattgtgtctgctgtctaAgtgctaggattttatcctga	10	6	2	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:118842542A>G	ENST00000378204.2	-	4	2017	c.1211T>C	c.(1210-1212)cTt>cCt	p.L404P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	404					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)	p.L404P(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			CTGCTGTCTAAGTGCTAGGAT	0.388			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																													yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	1	Substitution - Missense(1)	large_intestine(1)	8											93	92	92					8																	118842542		2203	4300	6503	118911723	SO:0001583	missense	2131	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1211T>C	8.37:g.118842542A>G	ENSP00000367446:p.Leu404Pro		118911723	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	37	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	a	28.8	4.953446	0.92660	.	.	ENSG00000182197	ENST00000378204	D	0.96992	-4.2	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.97977	0.9334	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.98737	1.0715	10	0.87932	D	0	-12.9545	16.8061	0.85666	1.0:0.0:0.0:0.0	.	404	Q16394	EXT1_HUMAN	P	404	ENSP00000367446:L404P	ENSP00000367446:L404P	L	-	2	0	EXT1	118911723	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.335000	0.96500	2.367000	0.80283	0.528000	0.53228	CTT		0.388	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		G	118842542	A	G	118842542	3	3	66	1	0	0	0	0	1	0	0	0	5336	72	3	4	1061	4	EXT1	8	118842542	Missense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	975981	118842542	27521480	48	20693										
CYP11B1	1584	broad.mit.edu	37	chr8	143957761	143957761	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cacgatgctggtgtactgttGagggcggctgaaggccagtt	16	8	0	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr8:143957761G>A	ENST00000292427.4	-	5	882	c.850C>T	c.(850-852)Caa>Taa	p.Q284*	CYP11B1_ENST00000517471.1_Nonsense_Mutation_p.Q284*|CYP11B1_ENST00000377675.3_Nonsense_Mutation_p.Q355*	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	284					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.Q284*(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	GTGTACTGTTGAGGGCGGCTG	0.572									Familial Hyperaldosteronism type I																																							1	Substitution - Nonsense(1)	large_intestine(1)	8											116	97	103					8																	143957761		2203	4300	6503	143954763	SO:0001587	stop_gained	1584	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.850C>T	8.37:g.143957761G>A	ENSP00000292427:p.Gln284*		143954763	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Nonsense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	16.64	3.178836	0.57692	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	.	.	.	4.1	-1.72	0.08107	.	2.112300	0.02205	N	0.062592	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	0.8811	0.01234	0.1777:0.2647:0.2825:0.2751	.	.	.	.	X	284;284;355	.	ENSP00000292427:Q284X	Q	-	1	0	CYP11B1	143954763	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.016000	0.13377	-0.715000	0.04968	-0.913000	0.02753	CAA		0.572	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			A	143957761	G	A	143957761	4	1	66	1	0	0	0	0	0	1	0	0	4151	1299	45	3	681	3	CYP11B1	8	143957761	Nonsense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	25115219	143957761	2406261	49	20694										
FREM1	158326	broad.mit.edu	37	chr9	14868886	14868886	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cccttcatcaccctcaccccGcggttgatgctgatgaaggt	9	15	3	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr9:14868886G>A	ENST00000380880.3	-	2	873	c.90C>T	c.(88-90)cgC>cgT	p.R30R	FREM1_ENST00000380881.4_Silent_p.R30R|FREM1_ENST00000422223.2_Silent_p.R30R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	30					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.R30R(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		CCCTCACCCCGCGGTTGATGC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9											29	32	31					9																	14868886		1998	4172	6170	14858886	SO:0001819	synonymous_variant	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.90C>T	9.37:g.14868886G>A			14858886	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																				0.582	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		A	14868886	G	A	14868886	2	1	66	1	0	0	0	0	0	0	0	1	6063	1074	38	1		1	FREM1	9	14868886	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		14868886	126344545	50	20695										
ZNF483	158399	broad.mit.edu	37	chr9	114304173	114304173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaacttcagacttaattaaaCatctgagagtctacttgagg	7	7	3	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr9:114304173C>T	ENST00000309235.5	+	6	1116	c.958C>T	c.(958-960)Cat>Tat	p.H320Y	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	320					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H320Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						CTTAATTAAACATCTGAGAGT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	115	111					9																	114304173		2203	4300	6503	113343994	SO:0001583	missense	158399			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.958C>T	9.37:g.114304173C>T	ENSP00000311679:p.His320Tyr		113343994	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.265743	0.40095	.	.	ENSG00000173258	ENST00000309235	T	0.04758	3.56	4.33	1.51	0.23008	.	0.133398	0.34628	N	0.003803	T	0.08758	0.0217	M	0.86028	2.79	0.80722	D	1	B	0.15930	0.015	B	0.15052	0.012	T	0.04065	-1.0980	10	0.59425	D	0.04	-9.1043	7.999	0.30286	0.0:0.7218:0.0:0.2782	.	320	Q8TF39	ZN483_HUMAN	Y	320	ENSP00000311679:H320Y	ENSP00000311679:H320Y	H	+	1	0	ZNF483	113343994	0.808000	0.29022	0.867000	0.34043	0.387000	0.30353	2.434000	0.44802	0.365000	0.24400	-0.136000	0.14681	CAT		0.388	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		T	114304173	C	T	114304173	3	4	66	1	0	0	0	0	1	0	0	0	17975	478	17	3	976	3	ZNF483	9	114304173	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	99435287	114304173	26909258	51	20696										
ZNF483	158399	broad.mit.edu	37	chr9	114304373	114304373	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cgtcagaagattcatttgggGgataggtcccaaaaatgcag	12	7	2	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr9:114304373G>A	ENST00000309235.5	+	6	1316	c.1158G>A	c.(1156-1158)ggG>ggA	p.G386G	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	386					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G386G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						TTCATTTGGGGGATAGGTCCC	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	9											83	92	89					9																	114304373		2203	4300	6503	113344194	SO:0001819	synonymous_variant	158399			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1158G>A	9.37:g.114304373G>A			113344194	Q5VZN2|Q8NAE1	Silent	SNP	ENST00000309235.5	37	CCDS35106.1																																																																																				0.418	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		A	114304373	G	A	114304373	2	1	66	1	0	0	0	0	0	0	0	1	17975	1219	43	3		3	ZNF483	9	114304373	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	200	114304373	26909058	52	20697										
OR1K1	392392	broad.mit.edu	37	chr9	125562783	125562783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	atgactgctacgtggccatcCggcaccccctcccctatgcc	8	19	0	1	rs143894111		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr9:125562783C>T	ENST00000277309.2	+	1	414	c.382C>T	c.(382-384)Cgg>Tgg	p.R128W		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R128W(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						CGTGGCCATCCGGCACCCCCT	0.612													C|||	1	0.000199681	0	0.0014	5008	,	,		20798	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9						C	TRP/ARG	0,4406		0,0,2203	94	67	76		382	1.6	0.1	9	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	missense	OR1K1	NM_080859.1	101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	128/317	125562783	3,13003	2203	4300	6503	124602604	SO:0001583	missense	392392			AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.382C>T	9.37:g.125562783C>T	ENSP00000277309:p.Arg128Trp		124602604	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	37	CCDS35132.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	11.49	1.654119	0.29425	0.0	3.49E-4	ENSG00000165204	ENST00000277309	T	0.01455	4.87	4.49	1.64	0.23874	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35585	U	0.003114	T	0.02455	0.0075	N	0.12746	0.255	0.24930	N	0.991924	D	0.76494	0.999	P	0.60286	0.872	T	0.46076	-0.9217	10	0.87932	D	0	.	6.8581	0.24052	0.0:0.5241:0.0:0.4759	.	128	Q8NGR3	OR1K1_HUMAN	W	128	ENSP00000277309:R128W	ENSP00000277309:R128W	R	+	1	2	OR1K1	124602604	0.642000	0.27260	0.080000	0.20451	0.025000	0.11179	0.405000	0.21015	0.162000	0.19483	-0.251000	0.11542	CGG		0.612	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			T	125562783	C	T	125562783	3	4	66	1	0	0	0	0	1	0	0	0	10993	643	23	1	384	1	OR1K1	9	125562783	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	11258410	125562783	15650648	53	20698										
LARP4B	23185	broad.mit.edu	37	chr10	890957	890957	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgtttttttaagtacttctcGggggtcttcctggctgtctg	11	8	3	0	rs538826325		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr10:890957G>A	ENST00000316157.3	-	5	509	c.469C>T	c.(469-471)Cga>Tga	p.R157*		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	157	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.R157*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						AGTACTTCTCGGGGGTCTTCC	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											131	123	126					10																	890957		2203	4300	6503	880957	SO:0001587	stop_gained	23185			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.469C>T	10.37:g.890957G>A	ENSP00000326128:p.Arg157*		880957	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Nonsense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	G	36	5.822112	0.96989	.	.	ENSG00000107929	ENST00000316157	.	.	.	5.65	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-10.4542	16.1496	0.81605	0.0:0.0:0.8653:0.1347	.	.	.	.	X	157	.	ENSP00000326128:R157X	R	-	1	2	LARP4B	880957	1.000000	0.71417	0.989000	0.46669	0.937000	0.57800	3.884000	0.56175	1.483000	0.48342	0.563000	0.77884	CGA		0.363	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		A	890957	G	A	890957	4	1	66	1	0	0	0	0	0	1	0	0	8653	1124	39	1	1799	1	LARP4B	10	890957	Nonsense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		890957	134643790	54	20699										
AKR1C3	8644	broad.mit.edu	37	chr10	5138762	5138762	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gagagaagacatattctacaCttcaaaggtactgtgtctat	8	7	3	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr10:5138762C>A	ENST00000380554.3	+	2	897	c.245C>A	c.(244-246)aCt>aAt	p.T82N	AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.T59N	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	82					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.T82N(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	ATATTCTACACTTCAAAGGTA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											177	137	151					10																	5138762		2203	4300	6503	5128762	SO:0001583	missense	8644			L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.245C>A	10.37:g.5138762C>A	ENSP00000369927:p.Thr82Asn		5128762	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.341647	0.61073	.	.	ENSG00000196139	ENST00000380554	T	0.55413	0.52	2.0	2.0	0.26442	NADP-dependent oxidoreductase domain (3);	0.000000	0.56097	D	0.000030	T	0.72252	0.3437	M	0.90922	3.16	0.27770	N	0.943527	P;P	0.51537	0.946;0.859	P;P	0.62382	0.901;0.75	T	0.65932	-0.6048	10	0.72032	D	0.01	.	10.0149	0.42008	0.0:1.0:0.0:0.0	.	82;82	B4DKT3;P42330	.;AK1C3_HUMAN	N	82	ENSP00000369927:T82N	ENSP00000369927:T82N	T	+	2	0	AKR1C3	5128762	0.581000	0.26741	0.136000	0.22124	0.769000	0.43574	1.607000	0.36836	1.424000	0.47217	0.313000	0.20887	ACT		0.408	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		A	5138762	C	A	5138762	3	1	66	1	0	0	0	0	1	0	0	0	471	565	20	2	251	2	AKR1C3	10	5138762	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	4247805	5138762	130395985	55	20700										
OGDHL	55753	broad.mit.edu	37	chr10	50945842	50945842	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aggcacgtaccggataccatTtggtcaaagctggacttggc	12	10	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr10:50945842T>A	ENST00000374103.4	-	20	2665	c.2580A>T	c.(2578-2580)caA>caT	p.Q860H	OGDHL_ENST00000432695.1_Missense_Mutation_p.Q651H|OGDHL_ENST00000419399.1_Missense_Mutation_p.Q803H|OGDHL_ENST00000490844.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	860					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.Q860H(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CGGATACCATTTGGTCAAAGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	10											61	70	67					10																	50945842		2203	4300	6503	50615848	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2580A>T	10.37:g.50945842T>A	ENSP00000363216:p.Gln860His		50615848	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.902311	0.52227	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;T	0.11385	2.78;2.78;2.78	5.19	-10.0	0.00425	.	0.323215	0.31859	N	0.006948	T	0.08846	0.0219	L	0.47016	1.485	0.23221	N	0.998092	B;B;B	0.32031	0.352;0.067;0.128	B;B;B	0.42282	0.382;0.273;0.212	T	0.14839	-1.0458	10	0.87932	D	0	.	5.8303	0.18577	0.0846:0.4806:0.2543:0.1805	.	803;651;860	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	H	860;803;651	ENSP00000363216:Q860H;ENSP00000401356:Q803H;ENSP00000390240:Q651H	ENSP00000363216:Q860H	Q	-	3	2	OGDHL	50615848	0.297000	0.24408	0.845000	0.33349	0.976000	0.68499	-0.820000	0.04457	-1.467000	0.01895	-0.297000	0.09499	CAA		0.587	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50945842	T	A	50945842	3	1	66	1	0	0	0	0	1	0	0	0	10871	1838	64	5	468	5	OGDHL	10	50945842	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	45807080	50945842	84588905	56	20701										
CCKBR	887	broad.mit.edu	37	chr11	6292523	6292523	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgatggcccgggtgcacaccGagcactctcgggtgctccta	13	14	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:6292523G>A	ENST00000334619.2	+	5	1287	c.1094G>A	c.(1093-1095)cGa>cAa	p.R365Q	CCKBR_ENST00000525462.1_Missense_Mutation_p.R434Q|CCKBR_ENST00000532715.1_Missense_Mutation_p.R281Q	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	365					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)	p.R365Q(1)		NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		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)	GGTGCACACCGAGCACTCTCG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	11											156	125	135					11																	6292523		2201	4296	6497	6249099	SO:0001583	missense	887			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.1094G>A	11.37:g.6292523G>A	ENSP00000335544:p.Arg365Gln		6249099	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.780790	0.31502	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.37235	1.21;1.21;1.21	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.367899	0.29159	N	0.012964	T	0.24699	0.0599	N	0.26042	0.785	0.09310	N	1	P;P;P	0.42584	0.588;0.63;0.784	B;B;B	0.36335	0.222;0.119;0.189	T	0.20405	-1.0276	10	0.45353	T	0.12	.	12.4971	0.55933	0.0:0.0:0.8329:0.1671	.	434;299;365	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	Q	365;281;434	ENSP00000335544:R365Q;ENSP00000432079:R281Q;ENSP00000435534:R434Q	ENSP00000335544:R365Q	R	+	2	0	CCKBR	6249099	0.000000	0.05858	0.320000	0.25306	0.062000	0.15995	0.578000	0.23773	2.425000	0.82216	0.557000	0.71058	CGA		0.557	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		A	6292523	G	A	6292523	3	1	66	1	0	0	0	0	1	0	0	0	2887	1058	37	1	1112	1	CCKBR	11	6292523	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		6292523	128713993	57	20702										
NLRP10	338322	broad.mit.edu	37	chr11	7981697	7981697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ttctctgcgggactccttccCcagccggctttggtcctctt	9	16	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:7981697C>T	ENST00000328600.2	-	2	1623	c.1462G>A	c.(1462-1464)Ggg>Agg	p.G488R		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	488					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)	p.G488R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GACTCCTTCCCCAGCCGGCTT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	93	92					11																	7981697		2201	4296	6497	7938273	SO:0001583	missense	338322			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1462G>A	11.37:g.7981697C>T	ENSP00000327763:p.Gly488Arg		7938273	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	C	5.876	0.345695	0.11126	.	.	ENSG00000182261	ENST00000328600	D	0.87729	-2.29	3.57	2.65	0.31530	.	0.000000	0.37761	N	0.001946	D	0.84079	0.5393	L	0.48362	1.52	0.09310	N	1	P	0.46395	0.877	P	0.51453	0.67	T	0.72211	-0.4359	10	0.15952	T	0.53	.	6.9612	0.24597	0.0:0.8748:0.0:0.1252	.	488	Q86W26	NAL10_HUMAN	R	488	ENSP00000327763:G488R	ENSP00000327763:G488R	G	-	1	0	NLRP10	7938273	0.000000	0.05858	0.083000	0.20561	0.098000	0.18820	-0.213000	0.09305	1.091000	0.41335	-0.251000	0.11542	GGG		0.512	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		T	7981697	C	T	7981697	3	4	66	1	0	0	0	0	1	0	0	0	10503	623	22	3	509	3	NLRP10	11	7981697	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	1689174	7981697	127024819	58	20703										
CSTF3	1479	broad.mit.edu	37	chr11	33127570	33127570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggacataatttccattccaaTtttatccagtgcaaagtcat	5	9	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:33127570T>A	ENST00000323959.4	-	6	536	c.397A>T	c.(397-399)Att>Ttt	p.I133F	CSTF3_ENST00000524827.1_Missense_Mutation_p.I165F	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	133					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.I133F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						TCCATTCCAATTTTATCCAGT	0.259																																																1	Substitution - Missense(1)	large_intestine(1)	11											77	83	81					11																	33127570		2202	4297	6499	33084146	SO:0001583	missense	1479			U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.397A>T	11.37:g.33127570T>A	ENSP00000315791:p.Ile133Phe		33084146	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Missense_Mutation	SNP	ENST00000323959.4	37	CCDS7883.1	.	.	.	.	.	.	.	.	.	.	T	31	5.083805	0.94050	.	.	ENSG00000176102	ENST00000323959;ENST00000537832;ENST00000524827	T;T	0.35605	1.3;1.3	5.57	5.57	0.84162	.	0.049210	0.85682	D	0.000000	T	0.54806	0.1881	M	0.75150	2.29	0.80722	D	1	D	0.63880	0.993	P	0.55615	0.78	T	0.60677	-0.7216	10	0.72032	D	0.01	.	15.732	0.77814	0.0:0.0:0.0:1.0	.	133	Q12996	CSTF3_HUMAN	F	133;66;165	ENSP00000315791:I133F;ENSP00000431355:I165F	ENSP00000315791:I133F	I	-	1	0	CSTF3	33084146	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.035000	0.88872	2.123000	0.65237	0.477000	0.44152	ATT		0.259	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326		A	33127570	T	A	33127570	3	1	66	1	0	0	0	0	1	0	0	0	3992	1493	52	5	1820	5	CSTF3	11	33127570	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	25145873	33127570	101878946	59	20704										
OR8I2	120586	broad.mit.edu	37	chr11	55861213	55861213	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cccaaaaagtgtccaactggCtgggagtaatgccatatgtg	11	9	0	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:55861213C>T	ENST00000302124.2	+	1	461	c.430C>T	c.(430-432)Ctg>Ttg	p.L144L		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L144L(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GTCCAACTGGCTGGGAGTAAT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	11											147	135	139					11																	55861213		2201	4296	6497	55617789	SO:0001819	synonymous_variant	120586			AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.430C>T	11.37:g.55861213C>T			55617789	B2RNN4|Q6IFC0|Q96RC5	Silent	SNP	ENST00000302124.2	37	CCDS31517.1																																																																																				0.438	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		T	55861213	C	T	55861213	2	4	66	1	0	0	0	0	0	0	0	1	11271	796	28	3		3	OR8I2	11	55861213	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	22733643	55861213	79145303	60	20705										
OR4D11	219986	broad.mit.edu	37	chr11	59271156	59271156	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tttttatgtcttgtgtacatGacgactctgctgggaaacct	9	8	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:59271156G>C	ENST00000313253.1	+	1	108	c.108G>C	c.(106-108)atG>atC	p.M36I		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M36I(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						TTGTGTACATGACGACTCTGC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	11											147	138	141					11																	59271156		2201	4295	6496	59027732	SO:0001583	missense	219986			AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"GPCR / Class A : Olfactory receptors"	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.108G>C	11.37:g.59271156G>C	ENSP00000320077:p.Met36Ile		59027732		Missense_Mutation	SNP	ENST00000313253.1	37	CCDS31563.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.505978	0.00992	.	.	ENSG00000176200	ENST00000313253	T	0.02863	4.13	5.45	-2.59	0.06209	.	1.094760	0.06977	N	0.819116	T	0.01124	0.0037	N	0.05259	-0.085	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.46665	-0.9175	10	0.02654	T	1	0.5716	2.1716	0.03851	0.3459:0.1881:0.3615:0.1044	.	36	Q8NGI4	OR4DB_HUMAN	I	36	ENSP00000320077:M36I	ENSP00000320077:M36I	M	+	3	0	OR4D11	59027732	0.000000	0.05858	0.104000	0.21259	0.191000	0.23601	-3.239000	0.00544	0.031000	0.15407	0.563000	0.77884	ATG		0.458	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706		C	59271156	G	C	59271156	3	2	66	1	0	0	0	0	1	0	0	0	11086	1290	45	5	110	5	OR4D11	11	59271156	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	3409943	59271156	75735360	61	20706										
PKNOX2	63876	broad.mit.edu	37	chr11	125267931	125267931	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggggggccctactcccccaaCcagccctccatcaaccttca	7	20	2	0	rs377342245		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:125267931C>A	ENST00000298282.9	+	7	832	c.561C>A	c.(559-561)aaC>aaA	p.N187K	PKNOX2_ENST00000542175.1_Missense_Mutation_p.N123K|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	187					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.N187K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		ACTCCCCCAACCAGCCCTCCA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	80	78					11																	125267931		1939	4130	6069	124773141	SO:0001583	missense	63876			AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.561C>A	11.37:g.125267931C>A	ENSP00000298282:p.Asn187Lys		124773141	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	37	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	9.314	1.056244	0.19907	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.8	5.24	5.24	0.73138	.	0.217375	0.47852	D	0.000215	T	0.73590	0.3606	N	0.14661	0.345	0.58432	D	0.999999	B;B	0.28933	0.228;0.118	B;B	0.29862	0.108;0.039	T	0.70510	-0.4852	10	0.05721	T	0.95	-19.7188	19.2389	0.93873	0.0:1.0:0.0:0.0	.	123;187	F5GZ15;Q96KN3	.;PKNX2_HUMAN	K	158;158;187;123;175	ENSP00000434732:N158K;ENSP00000433971:N158K;ENSP00000298282:N187K;ENSP00000441470:N123K	ENSP00000298282:N187K	N	+	3	2	PKNOX2	124773141	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.067000	0.41461	2.604000	0.88044	0.650000	0.86243	AAC		0.557	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			A	125267931	C	A	125267931	3	1	66	1	0	0	0	0	1	0	0	0	12014	506	18	2	575	2	PKNOX2	11	125267931	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	65996775	125267931	9738585	62	20707										
ADAMTS15	170689	broad.mit.edu	37	chr11	130332087	130332087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gaccctcatccagatcgaccGtgccaacccctggtcagcct	8	18	2	1	rs200077954		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr11:130332087G>A	ENST00000299164.2	+	3	1196	c.1196G>A	c.(1195-1197)cGt>cAt	p.R399H		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	399	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R399H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		CAGATCGACCGTGCCAACCCC	0.607													G|||	1	0.000199681	0	0	5008	,	,		18020	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											119	97	105					11																	130332087		2201	4297	6498	129837297	SO:0001583	missense	170689			AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"ADAM metallopeptidases with thrombospondin type 1 motif"	16305	protein-coding gene	gene with protein product		607509	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.1196G>A	11.37:g.130332087G>A	ENSP00000299164:p.Arg399His		129837297	Q32MI6	Missense_Mutation	SNP	ENST00000299164.2	37	CCDS8488.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	15.85	2.954456	0.53293	.	.	ENSG00000166106	ENST00000299164	D	0.86164	-2.08	5.58	5.58	0.84498	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.77928	0.4204	N	0.13140	0.3	0.58432	D	0.999999	P	0.44627	0.839	B	0.40477	0.33	T	0.77707	-0.2487	9	0.25751	T	0.34	.	15.9302	0.79654	0.0:0.0:0.8646:0.1354	.	399	Q8TE58	ATS15_HUMAN	H	399	ENSP00000299164:R399H	ENSP00000299164:R399H	R	+	2	0	ADAMTS15	129837297	1.000000	0.71417	0.963000	0.40424	0.876000	0.50452	6.585000	0.74062	2.621000	0.88768	0.650000	0.86243	CGT		0.607	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		A	130332087	G	A	130332087	3	1	66	1	0	0	0	0	1	0	0	0	260	1145	40	1	1206	1	ADAMTS15	11	130332087	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	5064156	130332087	4674429	63	20708										
A2M	2	broad.mit.edu	37	chr12	9265980	9265980	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaggcgacacagtggagtacGtcattctccgcctccaggtc	11	13	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:9265980G>A	ENST00000318602.7	-	2	553	c.246C>T	c.(244-246)gaC>gaT	p.D82D		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	82				D -> V (in Ref. 3; AAT02228). {ECO:0000305}.	blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.D82D(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	AGTGGAGTACGTCATTCTCCG	0.483													G|||	2	0.000399361	0	0	5008	,	,		-128	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	12											121	121	121					12																	9265980		2203	4300	6503	9157247	SO:0001819	synonymous_variant	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.246C>T	12.37:g.9265980G>A			9157247	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	De_novo_Start_OutOfFrame	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																				0.483	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9265980	G	A	9265980	2	1	66	1	0	0	0	0	0	0	0	1	4	1136	40	1		1	A2M	12	9265980	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		9265980	124585915	64	20709										
TMTC1	83857	broad.mit.edu	37	chr12	29709923	29709923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gttgagcgcacttgcatggcGtggatacaacctgaaaagtt	12	8	0	2	rs141215209		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:29709923G>A	ENST00000539277.1	-	10	1601	c.1543C>T	c.(1543-1545)Cgc>Tgc	p.R515C	TMTC1_ENST00000381224.2_Missense_Mutation_p.R469C|TMTC1_ENST00000256062.5_Missense_Mutation_p.R407C|TMTC1_ENST00000551659.1_Missense_Mutation_p.R577C|TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000552618.1_Missense_Mutation_p.R539C	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	515						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.R407C(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					CTTGCATGGCGTGGATACAAC	0.448													G|||	1	0.000199681	0	0	5008	,	,		18748	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	146	130	135		1543,1219	5.5	1	12	dbSNP_134	135	0,8600		0,0,4300	yes	missense,missense	TMTC1	NM_001193451.1,NM_175861.3	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	515/883,407/775	29709923	1,13005	2203	4300	6503	29601190	SO:0001583	missense	83857				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1543C>T	12.37:g.29709923G>A	ENSP00000442046:p.Arg515Cys		29601190	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	20.9	4.071779	0.76301	2.27E-4	0.0	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.59772	0.24;0.24;0.6;0.24;0.24	5.48	5.48	0.80851	Tetratricopeptide-like helical (1);PIK-related kinase, FAT (1);Tetratricopeptide repeat-containing (1);	0.120205	0.64402	D	0.000018	T	0.70185	0.3195	M	0.66439	2.03	0.58432	D	0.999991	D;D;D	0.89917	0.999;1.0;0.999	P;P;P	0.62184	0.854;0.873;0.899	T	0.70310	-0.4907	9	.	.	.	-16.3665	12.9681	0.58497	0.0:0.0:0.8384:0.1616	.	469;515;577	Q8IUR5-3;Q8IUR5;F8VTQ9	.;TMTC1_HUMAN;.	C	278;407;577;539;515;469	ENSP00000256062:R407C;ENSP00000448112:R577C;ENSP00000449043:R539C;ENSP00000442046:R515C;ENSP00000370622:R469C	.	R	-	1	0	TMTC1	29601190	1.000000	0.71417	0.959000	0.39883	0.959000	0.62525	6.994000	0.76251	2.576000	0.86940	0.655000	0.94253	CGC		0.448	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		A	29709923	G	A	29709923	3	1	66	1	0	0	0	0	1	0	0	0	16299	1145	40	1	1141	1	TMTC1	12	29709923	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	20443943	29709923	104141972	65	20710										
ARID2	196528	broad.mit.edu	37	chr12	46230605	46230605	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	taacgatattgaaggacagcGggtacttcagattgcagtga	12	6	1	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:46230605G>A	ENST00000334344.6	+	8	1026	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	ARID2_ENST00000422737.1_Missense_Mutation_p.R136Q|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	285					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R285Q(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GAAGGACAGCGGGTACTTCAG	0.403			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)	12											157	153	155					12																	46230605		2203	4300	6503	44516872	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.854G>A	12.37:g.46230605G>A	ENSP00000335044:p.Arg285Gln		44516872	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	35	5.482817	0.96307	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	T;T	0.48522	0.81;0.81	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.71195	0.3311	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.72616	-0.4239	10	0.87932	D	0	-12.5418	20.2009	0.98259	0.0:0.0:1.0:0.0	.	285	Q68CP9	ARID2_HUMAN	Q	285;136	ENSP00000335044:R285Q;ENSP00000415650:R136Q	ENSP00000335044:R285Q	R	+	2	0	ARID2	44516872	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.822000	0.99363	2.767000	0.95098	0.591000	0.81541	CGG		0.403	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46230605	G	A	46230605	3	1	66	1	0	0	0	0	1	0	0	0	915	1116	39	1	884	1	ARID2	12	46230605	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	16520682	46230605	87621290	66	20711										
GLI1	2735	broad.mit.edu	37	chr12	57865076	57865076	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cagcctctcttttcccattaCccccagccctctcctcccca	2	23	2	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:57865076C>A	ENST00000228682.2	+	12	2644	c.2553C>A	c.(2551-2553)taC>taA	p.Y851*	GLI1_ENST00000546141.1_Nonsense_Mutation_p.Y810*|GLI1_ENST00000543426.1_Nonsense_Mutation_p.Y723*	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	851					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)	p.Y851*(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TTTCCCATTACCCCCAGCCCT	0.602																																					Pancreas(157;841 1936 10503 41495 50368)											1	Substitution - Nonsense(1)	large_intestine(1)	12											75	85	82					12																	57865076		2203	4300	6503	56151343	SO:0001587	stop_gained	2735				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.2553C>A	12.37:g.57865076C>A	ENSP00000228682:p.Tyr851*		56151343	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Nonsense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.745964	0.69418	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	.	.	.	4.44	-2.92	0.05615	.	0.196194	0.25456	N	0.030541	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.2153	0.25957	0.1296:0.2434:0.0:0.627	.	.	.	.	X	723;851;810;810;319	.	ENSP00000228682:Y851X	Y	+	3	2	GLI1	56151343	0.000000	0.05858	0.759000	0.31340	0.515000	0.34225	-1.397000	0.02511	-0.495000	0.06659	-0.439000	0.05793	TAC		0.602	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57865076	C	A	57865076	4	1	66	1	0	0	0	0	0	1	0	0	6457	518	18	2	2595	2	GLI1	12	57865076	Nonsense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	11634471	57865076	75986819	67	20712										
MON2	23041	broad.mit.edu	37	chr12	62938714	62938714	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	actctcgaatgagagaatggGgagcagaagctttaacttct	11	7	2	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:62938714G>T	ENST00000393632.2	+	21	2894	c.2503G>T	c.(2503-2505)Gga>Tga	p.G835*	MON2_ENST00000546600.1_Nonsense_Mutation_p.G835*|MON2_ENST00000393629.2_Nonsense_Mutation_p.G835*|RNU6-399P_ENST00000365164.1_RNA|MON2_ENST00000552738.1_Nonsense_Mutation_p.G812*|MON2_ENST00000552115.1_Nonsense_Mutation_p.G835*|MON2_ENST00000280379.6_Nonsense_Mutation_p.G836*|MON2_ENST00000393630.3_Nonsense_Mutation_p.G836*	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	835					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.G835*(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAGAGAATGGGGAGCAGAAGC	0.328																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											65	65	65					12																	62938714		2203	4300	6503	61224981	SO:0001587	stop_gained	23041				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.2503G>T	12.37:g.62938714G>T	ENSP00000377252:p.Gly835*		61224981	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Nonsense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	44	11.251642	0.99537	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.4591	19.9855	0.97347	0.0:0.0:1.0:0.0	.	.	.	.	X	835;836;836;835;812;835;835	.	.	G	+	1	0	MON2	61224981	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.715000	0.92844	0.655000	0.94253	GGA		0.328	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62938714	G	T	62938714	4	4	66	1	0	0	0	0	0	1	0	0	9730	1233	43	2	2585	2	MON2	12	62938714	Nonsense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	5073638	62938714	70913181	68	20713										
KRR1	11103	broad.mit.edu	37	chr12	75900604	75900604	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gctaacagttttatcagatcTctggccctaatgatgatata	7	8	2	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:75900604T>C	ENST00000229214.4	-	3	374	c.351A>G	c.(349-351)agA>agG	p.R117R	KRR1_ENST00000438169.2_Silent_p.R117R	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	117					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.R117R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						TTATCAGATCTCTGGCCCTAA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	12											130	122	125					12																	75900604		2203	4300	6503	74186871	SO:0001819	synonymous_variant	11103			U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.351A>G	12.37:g.75900604T>C			74186871	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																				0.378	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043		C	75900604	T	C	75900604	2	2	66	1	0	0	0	0	0	0	0	1	8467	1548	54	4		4	KRR1	12	75900604	Silent	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	12961890	75900604	57951291	69	20714										
C12orf12	196477	broad.mit.edu	37	chr12	91348043	91348043	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	acatccgctggcgggctccgCgggtaggagtggcgagggtg	20	10	0	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:91348043C>T	ENST00000358859.2	-	1	910	c.477G>A	c.(475-477)ccG>ccA	p.P159P	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	159								p.P159P(3)									GCGGGCTCCGCGGGTAGGAGT	0.706																																																3	Substitution - coding silent(3)	large_intestine(3)	12											21	24	23					12																	91348043		2198	4295	6493	89872174	SO:0001819	synonymous_variant	196477			BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.477G>A	12.37:g.91348043C>T			89872174	Q8TC47	Silent	SNP	ENST00000358859.2	37	CCDS9036.1																																																																																				0.706	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		T	91348043	C	T	91348043	2	4	66	1	0	0	0	0	0	0	0	1	1680	755	27	1		1	C12orf12	12	91348043	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	15447439	91348043	42503852	70	20715										
MPHOSPH9	10198	broad.mit.edu	37	chr12	123649915	123649915	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tatttttccctcatcaagttCttttaaagctctcatgatcg	4	10	4	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr12:123649915C>A	ENST00000606320.1	-	18	2907	c.2701G>T	c.(2701-2703)Gaa>Taa	p.E901*	MPHOSPH9_ENST00000302349.5_Nonsense_Mutation_p.E749*|MPHOSPH9_ENST00000541076.2_Nonsense_Mutation_p.E871*|MPHOSPH9_ENST00000392425.3_Nonsense_Mutation_p.E749*			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	901						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E749*(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		TCATCAAGTTCTTTTAAAGCT	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											116	116	116					12																	123649915		2203	4300	6503	122215868	SO:0001587	stop_gained	10198			X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2701G>T	12.37:g.123649915C>A	ENSP00000475489:p.Glu901*		122215868	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Nonsense_Mutation	SNP	ENST00000606320.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.725359	0.96847	.	.	ENSG00000051825	ENST00000302349;ENST00000541076	.	.	.	5.95	3.74	0.42951	.	0.283922	0.33290	N	0.005078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-20.0928	10.934	0.47235	0.0:0.7885:0.1334:0.0781	.	.	.	.	X	749	.	ENSP00000303597:E749X	E	-	1	0	MPHOSPH9	122215868	1.000000	0.71417	0.940000	0.37924	0.095000	0.18619	2.550000	0.45811	1.458000	0.47871	0.655000	0.94253	GAA		0.378	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2			A	123649915	C	A	123649915	4	1	66	1	0	0	0	0	0	1	0	0	9758	922	32	2	878	2	MPHOSPH9	12	123649915	Nonsense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	32301872	123649915	10201980	71	20716										
TBC1D4	9882	broad.mit.edu	37	chr13	75900518	75900518	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	caagctgaggacggtggggaCgctggcggtgtccctggtgg	20	9	0	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr13:75900518C>T	ENST00000377636.3	-	10	2194	c.1848G>A	c.(1846-1848)gcG>gcA	p.A616A	TBC1D4_ENST00000377625.2_Silent_p.A616A|TBC1D4_ENST00000431480.2_Silent_p.A616A|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	616					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.A616A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		ACGGTGGGGACGCTGGCGGTG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	13											77	81	80					13																	75900518		2024	4182	6206	74798519	SO:0001819	synonymous_variant	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.1848G>A	13.37:g.75900518C>T			74798519	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																				0.592	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	75900518	C	T	75900518	2	4	66	1	0	0	0	0	0	0	0	1	15661	523	19	1		1	TBC1D4	13	75900518	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		75900518	39269360	72	20717										
SLITRK1	114798	broad.mit.edu	37	chr13	84454333	84454333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cgaatttctcccgggacagcGtgtccaggtaattgctatcc	10	12	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr13:84454333G>A	ENST00000377084.2	-	1	2195	c.1310C>T	c.(1309-1311)aCg>aTg	p.T437M		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	437					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.T437M(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		CCGGGACAGCGTGTCCAGGTA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	13											138	131	133					13																	84454333		2203	4300	6503	83352334	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1310C>T	13.37:g.84454333G>A	ENSP00000366288:p.Thr437Met		83352334	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486035	0.44147	.	.	ENSG00000178235	ENST00000377084	T	0.58210	0.35	5.07	5.07	0.68467	.	0.051580	0.85682	D	0.000000	T	0.55940	0.1952	M	0.66939	2.045	0.80722	D	1	P	0.35551	0.509	B	0.37650	0.255	T	0.59606	-0.7423	10	0.48119	T	0.1	-7.3503	17.3701	0.87374	0.0:0.0:1.0:0.0	.	437	Q96PX8	SLIK1_HUMAN	M	437	ENSP00000366288:T437M	ENSP00000366288:T437M	T	-	2	0	SLITRK1	83352334	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.643000	0.74334	2.522000	0.85027	0.655000	0.94253	ACG		0.498	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454333	G	A	84454333	3	1	66	1	0	0	0	0	1	0	0	0	14779	1145	40	1	784	1	SLITRK1	13	84454333	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	8553815	84454333	30715545	73	20718										
PCCA	5095	broad.mit.edu	37	chr13	101020796	101020796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgcatgataaagttcataccGtagtagcatcaaacaatggg	9	7	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr13:101020796G>A	ENST00000376285.1	+	19	1752	c.1714G>A	c.(1714-1716)Gta>Ata	p.V572I	PCCA_ENST00000376286.4_Missense_Mutation_p.V546I|PCCA_ENST00000376279.3_Missense_Mutation_p.V572I	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	572					biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.V572I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	AGTTCATACCGTAGTAGCATC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	13											161	148	153					13																	101020796		2203	4300	6503	99818797	SO:0001583	missense	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1714G>A	13.37:g.101020796G>A	ENSP00000365462:p.Val572Ile		99818797	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.92|11.92	1.782310|1.782310	0.31502|0.31502	.|.	.|.	ENSG00000175198|ENSG00000175198	ENST00000458283;ENST00000413170|ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000536640	.|T;T;T;T	.|0.78595	.|-1.19;-1.19;-1.19;-1.19	4.77|4.77	3.9|3.9	0.45041|0.45041	.|.	.|0.063949	.|0.64402	.|D	.|0.000008	T|T	0.62466|0.62466	0.2430|0.2430	L|L	0.31664|0.31664	0.95|0.95	0.09310|0.09310	N|N	0.999997|0.999997	.|B;B;B	.|0.30870	.|0.204;0.298;0.107	.|B;B;B	.|0.27500	.|0.025;0.08;0.014	T|T	0.51204|0.51204	-0.8735|-0.8735	5|10	.|0.25106	.|T	.|0.35	.|.	9.8813|9.8813	0.41236|0.41236	0.0975:0.0:0.9025:0.0|0.0975:0.0:0.9025:0.0	.|.	.|572;546;572	.|C9JPQ8;P05165-2;P05165	.|.;.;PCCA_HUMAN	H|I	24;15|546;572;572;106;68	.|ENSP00000365463:V546I;ENSP00000365456:V572I;ENSP00000365462:V572I;ENSP00000396050:V106I	.|ENSP00000365456:V572I	R|V	+|+	2|1	0|0	PCCA|PCCA	99818797|99818797	0.639000|0.639000	0.27234|0.27234	0.038000|0.038000	0.18304|0.18304	0.057000|0.057000	0.15508|0.15508	1.976000|1.976000	0.40579|0.40579	2.356000|2.356000	0.79943|0.79943	0.563000|0.563000	0.77884|0.77884	CGT|GTA		0.328	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			A	101020796	G	A	101020796	3	1	66	1	0	0	0	0	1	0	0	0	11535	1145	40	1	1788	1	PCCA	13	101020796	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	16566463	101020796	14149082	74	20719										
C14orf93	60686	broad.mit.edu	37	chr14	23465438	23465438	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ataagcagggaccagaactcGctgtactgcaccctcagagg	11	12	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr14:23465438G>A	ENST00000299088.6	-	3	1066	c.637C>T	c.(637-639)Cga>Tga	p.R213*	RP11-298I3.4_ENST00000557615.1_RNA|C14orf93_ENST00000397379.3_Nonsense_Mutation_p.R213*|C14orf93_ENST00000406429.2_Nonsense_Mutation_p.R213*|C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000397377.1_Nonsense_Mutation_p.R33*|C14orf93_ENST00000397382.4_Nonsense_Mutation_p.R213*|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000341470.4_Nonsense_Mutation_p.R213*|RP11-298I3.4_ENST00000555294.1_RNA	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	213						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)	p.R213*(1)		kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		ACCAGAACTCGCTGTACTGCA	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	14											111	97	102					14																	23465438		2203	4300	6503	22535278	SO:0001587	stop_gained	60686			AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.637C>T	14.37:g.23465438G>A	ENSP00000299088:p.Arg213*		22535278	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Nonsense_Mutation	SNP	ENST00000299088.6	37	CCDS9583.1	.	.	.	.	.	.	.	.	.	.	G	39	7.302150	0.98196	.	.	ENSG00000100802	ENST00000299088;ENST00000341470;ENST00000397379;ENST00000397382;ENST00000397377;ENST00000406429;ENST00000397376	.	.	.	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.71	12.5442	0.56190	0.0:0.0:0.8338:0.1662	.	.	.	.	X	213;213;213;213;33;213;33	.	ENSP00000299088:R213X	R	-	1	2	C14orf93	22535278	1.000000	0.71417	0.997000	0.53966	0.778000	0.44026	3.353000	0.52247	2.769000	0.95229	0.655000	0.94253	CGA		0.512	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		A	23465438	G	A	23465438	4	1	66	1	0	0	0	0	0	1	0	0	1786	1095	38	1	999	1	C14orf93	14	23465438	Nonsense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		23465438	83884102	75	20720										
FAM179B	23116	broad.mit.edu	37	chr14	45535820	45535820	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gaagtcaccagaaaatcagtCcctcgtaattccttagaaag	7	10	2	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr14:45535820C>T	ENST00000361577.3	+	16	4654	c.4440C>T	c.(4438-4440)gtC>gtT	p.V1480V	FAM179B_ENST00000361462.2_Silent_p.V1533V|FAM179B_ENST00000382233.2_3'UTR	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1480								p.V1480V(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GAAAATCAGTCCCTCGTAATT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	14											121	121	121					14																	45535820		2203	4300	6503	44605570	SO:0001819	synonymous_variant	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4440C>T	14.37:g.45535820C>T			44605570	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																				0.343	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45535820	C	T	45535820	2	4	66	1	0	0	0	0	0	0	0	1	5522	842	30	3		3	FAM179B	14	45535820	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	22070382	45535820	61813720	76	20721										
AHNAK2	113146	broad.mit.edu	37	chr14	105411676	105411676	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccgggagcttcacgtccaccTggccagcctggacctccagg	12	17	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr14:105411676T>A	ENST00000333244.5	-	7	10231	c.10112A>T	c.(10111-10113)cAg>cTg	p.Q3371L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3371						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.Q3371L(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CACGTCCACCTGGCCAGCCTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	14											119	130	126					14																	105411676		1961	4135	6096	104482721	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10112A>T	14.37:g.105411676T>A	ENSP00000353114:p.Gln3371Leu		104482721	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	12.46	1.944814	0.34283	.	.	ENSG00000185567	ENST00000333244	T	0.00737	5.76	4.12	-1.37	0.09056	.	.	.	.	.	T	0.01765	0.0056	M	0.82923	2.615	0.09310	N	1	D	0.57899	0.981	P	0.53401	0.725	T	0.40664	-0.9551	9	0.27785	T	0.31	.	0.4756	0.00539	0.2506:0.2259:0.1284:0.3952	.	3371	Q8IVF2	AHNK2_HUMAN	L	3371	ENSP00000353114:Q3371L	ENSP00000353114:Q3371L	Q	-	2	0	AHNAK2	104482721	0.474000	0.25886	0.000000	0.03702	0.020000	0.10135	1.976000	0.40579	-0.118000	0.11851	0.402000	0.26972	CAG		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105411676	T	A	105411676	3	1	66	1	0	0	0	0	1	0	0	0	415	1580	55	5	7279	5	AHNAK2	14	105411676	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	59875856	105411676	1937864	77	20722										
RASGRP1	10125	broad.mit.edu	37	chr15	38793405	38793405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tggtctcttggaagttgtgaGgaaagcccaggcccagcttg	14	9	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr15:38793405G>A	ENST00000310803.5	-	13	1799	c.1622C>T	c.(1621-1623)cCt>cTt	p.P541L	RASGRP1_ENST00000450598.2_Missense_Mutation_p.P506L|RASGRP1_ENST00000539159.1_Missense_Mutation_p.P493L|RASGRP1_ENST00000558164.1_Missense_Mutation_p.P506L|RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000561180.1_Missense_Mutation_p.P592L|RASGRP1_ENST00000559830.1_Missense_Mutation_p.P506L	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	541					activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.P541L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		GAAGTTGTGAGGAAAGCCCAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	15											88	88	88					15																	38793405		1934	4148	6082	36580697	SO:0001583	missense	10125			AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1622C>T	15.37:g.38793405G>A	ENSP00000310244:p.Pro541Leu		36580697	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	37	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	G	7.285	0.609833	0.14066	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159	D;D;D	0.85171	-1.95;-1.95;-1.95	5.29	5.29	0.74685	Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Diacylglycerol/phorbol-ester binding (1);	0.218383	0.43416	D	0.000568	T	0.62109	0.2401	N	0.00926	-1.1	0.49051	D	0.999748	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.61461	-0.7058	10	0.21014	T	0.42	-8.0559	12.4472	0.55657	0.0759:0.0:0.9241:0.0	.	506;506;541;506	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	L	541;506;506;506;493	ENSP00000310244:P541L;ENSP00000388540:P506L;ENSP00000444762:P493L	ENSP00000310244:P541L	P	-	2	0	RASGRP1	36580697	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.280000	0.58959	2.752000	0.94435	0.655000	0.94253	CCT		0.522	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		A	38793405	G	A	38793405	3	1	66	1	0	0	0	0	1	0	0	0	13111	1000	35	3	791	3	RASGRP1	15	38793405	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		38793405	63737987	78	20723										
FAHD1	81889	broad.mit.edu	37	chr16	1877620	1877620	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	agcttcacggcgtcctgcccGgtcagcgcgttcgtgcccaa	12	16	2	0	rs144517611	byFrequency	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:1877620G>T	ENST00000427358.2	+	1	396	c.390G>T	c.(388-390)ccG>ccT	p.P130P	HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382668.4_Silent_p.P130P|HAGH_ENST00000397356.3_5'Flank|FAHD1_ENST00000382666.4_Silent_p.P130P|HAGH_ENST00000566709.1_5'Flank	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	130						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)	p.P130P(1)		NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						CGTCCTGCCCGGTCAGCGCGT	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	16											46	39	42					16																	1877620		2199	4300	6499	1817621	SO:0001819	synonymous_variant	81889			BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 36"	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.390G>T	16.37:g.1877620G>T			1817621	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																				0.617	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104		T	1877620	G	T	1877620	2	4	66	1	0	0	0	0	0	0	0	1	5388	1103	39	2		2	FAHD1	16	1877620	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		1877620	88477133	79	20724										
UBN1	29855	broad.mit.edu	37	chr16	4920956	4920956	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggacctcggaagaagttccaAtggaatgatgagatcaggtg	14	6	1	3	rs148310869		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:4920956A>G	ENST00000396658.4	+	10	2245	c.1542A>G	c.(1540-1542)caA>caG	p.Q514Q	UBN1_ENST00000590769.1_Silent_p.Q514Q|UBN1_ENST00000545171.1_Silent_p.Q514Q|UBN1_ENST00000262376.6_Silent_p.Q514Q	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	514					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q514Q(1)		NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						AGAAGTTCCAATGGAATGATG	0.522													A|||	1	0.000199681	8e-04	0	5008	,	,		19599	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16						A	,	1,4393	2.1+/-5.4	0,1,2196	73	72	72		1542,1542	2.9	1	16	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	UBN1	NM_001079514.1,NM_016936.3	,	0,2,6495	GG,GA,AA		0.0116,0.0228,0.0154	,	514/1135,514/1135	4920956	2,12992	2197	4300	6497	4860957	SO:0001819	synonymous_variant	29855			AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.1542A>G	16.37:g.4920956A>G			4860957	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																				0.522	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		G	4920956	A	G	4920956	2	3	66	1	0	0	0	0	0	0	0	1	16932	98	4	4		4	UBN1	16	4920956	Silent	SNP	A	TCGA-AG-A011-01A-01W-A00K-09	3043336	4920956	85433797	80	20725										
ABCC1	4363	broad.mit.edu	37	chr16	16142096	16142096	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gaggttcatggacttggccaCgtacattaacatgatctggt	11	8	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:16142096C>G	ENST00000399410.3	+	10	1491	c.1316C>G	c.(1315-1317)aCg>aGg	p.T439R	ABCC1_ENST00000346370.5_Missense_Mutation_p.T439R|ABCC1_ENST00000349029.5_Missense_Mutation_p.T439R|ABCC1_ENST00000399408.2_Missense_Mutation_p.T439R|ABCC1_ENST00000345148.5_Missense_Mutation_p.T439R|ABCC1_ENST00000351154.5_Missense_Mutation_p.T439R	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	439	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.T439R(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GACTTGGCCACGTACATTAAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											153	158	156					16																	16142096		2090	4226	6316	16049597	SO:0001583	missense	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1316C>G	16.37:g.16142096C>G	ENSP00000382342:p.Thr439Arg		16049597	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400815	0.62177	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	5.43	5.43	0.79202	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.095200	0.64402	D	0.000001	D	0.95771	0.8624	M	0.73319	2.225	0.53005	D	0.999961	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.991;0.991;0.971;1.0;0.991;1.0;1.0	D	0.95886	0.8903	10	0.66056	D	0.02	-18.473	18.245	0.89982	0.0:1.0:0.0:0.0	.	439;439;439;439;439;439;439	P33527-6;P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;.;MRP1_HUMAN;.	R	439;439;439;439;439;439;113	ENSP00000382342:T439R;ENSP00000382340:T439R;ENSP00000263019:T439R;ENSP00000263017:T439R;ENSP00000263014:T439R;ENSP00000263016:T439R	ENSP00000263014:T439R	T	+	2	0	ABCC1	16049597	1.000000	0.71417	0.980000	0.43619	0.400000	0.30750	4.884000	0.63135	2.561000	0.86390	0.561000	0.74099	ACG		0.542	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		G	16142096	C	G	16142096	3	3	66	1	0	0	0	0	1	0	0	0	49	536	19	5	1354	5	ABCC1	16	16142096	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	11221140	16142096	74212657	81	20726										
DNAH3	55567	broad.mit.edu	37	chr16	21078692	21078692	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gttggcttcttgaagcttctCtgccatccgtggctggtcgg	13	11	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:21078692C>T	ENST00000261383.3	-	24	3429	c.3430G>A	c.(3430-3432)Gag>Aag	p.E1144K	DNAH3_ENST00000415178.1_Missense_Mutation_p.E1144K	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1144	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.E1144K(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGAAGCTTCTCTGCCATCCGT	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	16											85	86	86					16																	21078692		2201	4300	6501	20986193	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3430G>A	16.37:g.21078692C>T	ENSP00000261383:p.Glu1144Lys		20986193	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.734719	0.69189	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61627	0.09;0.09	5.64	5.64	0.86602	Dynein heavy chain, domain-2 (1);	0.134633	0.49916	D	0.000138	T	0.54464	0.1860	L	0.43152	1.355	0.58432	D	0.999995	B	0.22003	0.063	B	0.20955	0.032	T	0.49744	-0.8907	10	0.49607	T	0.09	.	19.7101	0.96094	0.0:1.0:0.0:0.0	.	1144	Q8TD57	DYH3_HUMAN	K	1144	ENSP00000261383:E1144K;ENSP00000394245:E1144K	ENSP00000261383:E1144K	E	-	1	0	DNAH3	20986193	1.000000	0.71417	0.998000	0.56505	0.875000	0.50365	5.803000	0.69129	2.655000	0.90218	0.637000	0.83480	GAG		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21078692	C	T	21078692	3	4	66	1	0	0	0	0	1	0	0	0	4614	922	32	3	9075	3	DNAH3	16	21078692	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	4936596	21078692	69276061	82	20727										
MMP2	4313	broad.mit.edu	37	chr16	55527187	55527187	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cgctcagatccgtggtgagaTcttcttcttcaaggaccggt	11	11	5	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:55527187T>A	ENST00000219070.4	+	9	1963	c.1454T>A	c.(1453-1455)aTc>aAc	p.I485N	MMP2_ENST00000437642.2_Missense_Mutation_p.I435N|MMP2_ENST00000543485.1_Missense_Mutation_p.I409N|MMP2_ENST00000570308.1_Missense_Mutation_p.I409N	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	485	Required for inhibitor TIMP2 binding.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.I485N(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		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)	Captopril(DB01197)|Marimastat(DB00786)	CGTGGTGAGATCTTCTTCTTC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	16											219	201	207					16																	55527187		2198	4300	6498	54084688	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.1454T>A	16.37:g.55527187T>A	ENSP00000219070:p.Ile485Asn		54084688	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.323065	0.60634	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.02944	4.1;4.1;4.1	5.33	3.11	0.35812	Hemopexin/matrixin (2);	0.145432	0.64402	D	0.000008	T	0.13756	0.0333	M	0.86805	2.84	0.50467	D	0.999877	P;D	0.53885	0.956;0.963	D;P	0.65443	0.935;0.652	T	0.00112	-1.2043	10	0.87932	D	0	.	8.5836	0.33644	0.0:0.2507:0.0:0.7493	.	435;485	E9PE45;P08253	.;MMP2_HUMAN	N	485;409;435	ENSP00000219070:I485N;ENSP00000444143:I409N;ENSP00000394237:I435N	ENSP00000219070:I485N	I	+	2	0	MMP2	54084688	0.653000	0.27358	1.000000	0.80357	0.998000	0.95712	1.104000	0.31074	2.028000	0.59812	0.460000	0.39030	ATC		0.537	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			A	55527187	T	A	55527187	3	1	66	1	0	0	0	0	1	0	0	0	9688	1435	50	5	1495	5	MMP2	16	55527187	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	34448495	55527187	34827566	83	20728										
CDH8	1006	broad.mit.edu	37	chr16	61689492	61689492	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ccgtcattgctgcagccacaGaccctgattgtcaaggtgct	10	13	2	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:61689492G>C	ENST00000577390.1	-	11	2742	c.1788C>G	c.(1786-1788)gtC>gtG	p.V596V	CDH8_ENST00000577730.1_Silent_p.V596V|CDH8_ENST00000299345.6_Silent_p.V596V	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	596	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.V596V(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TGCAGCCACAGACCCTGATTG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	16											158	134	142					16																	61689492		2203	4300	6503	60246993	SO:0001819	synonymous_variant	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1788C>G	16.37:g.61689492G>C			60246993	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																				0.463	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61689492	G	C	61689492	2	2	66	1	0	0	0	0	0	0	0	1	3122	929	33	5		5	CDH8	16	61689492	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	6162305	61689492	28665261	84	20729										
NFATC3	4775	broad.mit.edu	37	chr16	68217251	68217251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggaaaaaaagccagtctcaaCgttttacttatacaccaggt	7	9	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr16:68217251C>T	ENST00000346183.3	+	8	2104	c.2080C>T	c.(2080-2082)Cgt>Tgt	p.R694C	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.R694C|NFATC3_ENST00000329524.4_Missense_Mutation_p.R694C|NFATC3_ENST00000349223.5_Missense_Mutation_p.R694C	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	694					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R694C(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CCAGTCTCAACGTTTTACTTA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	16											139	130	133					16																	68217251		2198	4300	6498	66774752	SO:0001583	missense	4775			L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2080C>T	16.37:g.68217251C>T	ENSP00000300659:p.Arg694Cys		66774752	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799395	0.50208	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.09445	2.98;2.98;2.98	5.05	4.09	0.47781	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.050045	0.85682	N	0.000000	T	0.10380	0.0254	L	0.54908	1.71	0.80722	D	1	P;P;P;P	0.46578	0.598;0.88;0.598;0.598	B;B;B;B	0.37550	0.065;0.253;0.065;0.065	T	0.04481	-1.0948	10	0.66056	D	0.02	-5.7809	8.6786	0.34194	0.1504:0.7727:0.0:0.077	.	694;694;694;694	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	C	694;694;694;215	ENSP00000264008:R694C;ENSP00000300659:R694C;ENSP00000331324:R694C	ENSP00000331324:R694C	R	+	1	0	NFATC3	66774752	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.375000	0.66173	1.245000	0.43885	0.563000	0.77884	CGT		0.383	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		T	68217251	C	T	68217251	3	4	66	1	0	0	0	0	1	0	0	0	10395	536	19	1	2110	1	NFATC3	16	68217251	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	6527759	68217251	22137502	85	20730										
NLRP1	22861	broad.mit.edu	37	chr17	5418225	5418225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tgaacagcttccgcatctggCtgggcctcgtgttctcagcc	11	14	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr17:5418225C>A	ENST00000572272.1	-	17	4270	c.4271G>T	c.(4270-4272)aGc>aTc	p.S1424I	NLRP1_ENST00000354411.3_Missense_Mutation_p.S1394I|RNU7-31P_ENST00000517262.1_RNA|NLRP1_ENST00000577119.1_Missense_Mutation_p.S1350I|NLRP1_ENST00000269280.4_Missense_Mutation_p.S1380I|NLRP1_ENST00000345221.3_Missense_Mutation_p.S1380I|NLRP1_ENST00000262467.5_Intron			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1424	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.S1424I(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CCGCATCTGGCTGGGCCTCGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	17											72	76	75					17																	5418225		2104	4230	6334	5358949	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.4271G>T	17.37:g.5418225C>A	ENSP00000460475:p.Ser1424Ile		5358949	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029510	0.54790	.	.	ENSG00000091592	ENST00000269280;ENST00000354411;ENST00000345221	T;T	0.25085	1.82;1.82	5.07	-10.1	0.00402	DEATH-like (2);Caspase Recruitment (2);	2.717470	0.01198	N	0.007507	T	0.41073	0.1143	L	0.55481	1.735	0.09310	N	1	D;D;D;D	0.69078	0.996;0.996;0.997;0.996	P;P;D;P	0.64506	0.878;0.878;0.926;0.878	T	0.65331	-0.6194	10	0.87932	D	0	.	12.8987	0.58113	0.0:0.1136:0.1792:0.7072	.	1350;1394;1424;1380	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2	.;.;NALP1_HUMAN;.	I	1424;1394;1380	ENSP00000346390:S1394I;ENSP00000324366:S1380I	ENSP00000269280:S1424I	S	-	2	0	NLRP1	5358949	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-1.974000	0.01499	-2.581000	0.00462	-0.145000	0.13849	AGC		0.577	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		A	5418225	C	A	5418225	3	1	66	1	0	0	0	0	1	0	0	0	10502	797	28	2	217	2	NLRP1	17	5418225	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		5418225	75776985	86	20731										
TP53	7157	broad.mit.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	66	1	0	0	0	0	1	0	0	0	16421	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	2159314	7577539	73617671	87	20732										
ALDOC	230	broad.mit.edu	37	chr17	26901111	26901111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cagctgggggcacagtgcgaCgcagggcagtgacagttgcc	17	11	0	1	rs145665688	byFrequency	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr17:26901111C>T	ENST00000226253.4	-	7	1248	c.773G>A	c.(772-774)cGt>cAt	p.R258H	PIGS_ENST00000543734.1_5'Flank|PIGS_ENST00000395346.2_5'Flank|ALDOC_ENST00000395321.2_Missense_Mutation_p.R258H|PIGS_ENST00000308360.7_5'Flank|RP11-192H23.5_ENST00000585189.1_RNA|ALDOC_ENST00000395319.3_Missense_Mutation_p.R230H	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	258					aging (GO:0007568)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|organ regeneration (GO:0031100)|protein heterotetramerization (GO:0051290)|protein homotetramerization (GO:0051289)|response to hypoxia (GO:0001666)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	cytoskeletal protein binding (GO:0008092)|fructose-bisphosphate aldolase activity (GO:0004332)	p.R258H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Lung NSC(42;0.00431)					CACAGTGCGACGCAGGGCAGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	130	131	131		773	5.3	1	17	dbSNP_134	131	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALDOC	NM_005165.2	29	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	possibly-damaging	258/365	26901111	3,13003	2203	4300	6503	23925238	SO:0001583	missense	230			AF054987	CCDS11236.1	17q11.2	2013-09-20			ENSG00000109107	ENSG00000109107	4.1.2.13		418	protein-coding gene	gene with protein product		103870					Standard	XM_005257947		Approved		uc002hbp.3	P09972	OTTHUMG00000132605	ENST00000226253.4:c.773G>A	17.37:g.26901111C>T	ENSP00000226253:p.Arg258His		23925238	B2R5R3|Q3SYL3|Q6FH94|Q6P0L5	Missense_Mutation	SNP	ENST00000226253.4	37	CCDS11236.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168568	0.78339	4.54E-4	1.16E-4	ENSG00000109107	ENST00000395319;ENST00000226253;ENST00000395321	D;D;D	0.86769	-2.17;-2.17;-2.17	5.28	5.28	0.74379	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.85915	0.5808	L	0.58428	1.81	0.80722	D	1	P;P	0.39131	0.616;0.661	B;B	0.37780	0.146;0.258	D	0.86179	0.1605	10	0.45353	T	0.12	-21.493	18.0486	0.89341	0.0:1.0:0.0:0.0	.	230;258	A8MVZ9;P09972	.;ALDOC_HUMAN	H	230;258;258	ENSP00000378729:R230H;ENSP00000226253:R258H;ENSP00000378731:R258H	ENSP00000226253:R258H	R	-	2	0	ALDOC	23925238	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.955000	0.63638	2.637000	0.89404	0.555000	0.69702	CGT		0.602	ALDOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255839.4			T	26901111	C	T	26901111	3	4	66	1	0	0	0	0	1	0	0	0	509	536	19	1	333	1	ALDOC	17	26901111	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	19323572	26901111	54294099	88	20733										
KIAA1267	284058	broad.mit.edu	37	chr17	44248500	44248500	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	actggctccgtggtctcaagGattccaagtttggcagtttg	12	9	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr17:44248500G>T	ENST00000262419.6	-	2	1480	c.1010C>A	c.(1009-1011)tCc>tAc	p.S337Y	KANSL1_ENST00000575318.1_Missense_Mutation_p.S337Y|KANSL1_ENST00000432791.1_Missense_Mutation_p.S337Y|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Missense_Mutation_p.S337Y|KANSL1_ENST00000572904.1_Missense_Mutation_p.S337Y|KANSL1_ENST00000576248.1_5'Flank	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	337					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S337Y(1)|p.S337C(1)									TGGTCTCAAGGATTCCAAGTT	0.493																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	17											78	95	90					17																	44248500		2203	4300	6503	41604277	SO:0001583	missense	284058			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1010C>A	17.37:g.44248500G>T	ENSP00000262419:p.Ser337Tyr		41604277	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374824	0.61735	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12569	2.67;2.67	5.94	5.94	0.96194	.	0.090582	0.49305	D	0.000143	T	0.17066	0.0410	N	0.19112	0.55	0.80722	D	1	D;B	0.54207	0.965;0.184	P;B	0.51135	0.66;0.082	T	0.00628	-1.1637	10	0.52906	T	0.07	-9.8513	17.0961	0.86635	0.0:0.0:1.0:0.0	.	337;337	C9JHY2;Q7Z3B3	.;K1267_HUMAN	Y	337	ENSP00000262419:S337Y;ENSP00000387393:S337Y	ENSP00000262419:S337Y	S	-	2	0	KIAA1267	41604277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.394000	0.73223	2.826000	0.97356	0.561000	0.74099	TCC		0.493	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		T	44248500	G	T	44248500	3	4	66	1	0	0	0	0	1	0	0	0	8240	1174	41	2	2363	2	KIAA1267	17	44248500	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	17347389	44248500	36946710	89	20734										
ANKFN1	162282	broad.mit.edu	37	chr17	54452001	54452001	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	caatgtctgtctcatggtaaCcagcagcacatcactcactg	7	13	4	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr17:54452001C>G	ENST00000318698.2	+	7	880	c.845C>G	c.(844-846)aCc>aGc	p.T282S	ANKFN1_ENST00000566473.2_Missense_Mutation_p.T282S	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	282	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.							p.T282S(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CTCATGGTAACCAGCAGCACA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	17											220	199	206					17																	54452001		2203	4300	6503	51807000	SO:0001583	missense	162282			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.845C>G	17.37:g.54452001C>G	ENSP00000321627:p.Thr282Ser		51807000		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.221629	0.39300	.	.	ENSG00000153930	ENST00000318698	T	0.57273	0.41	5.53	4.55	0.56014	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.188195	0.56097	N	0.000036	T	0.42765	0.1217	N	0.26092	0.79	0.39838	D	0.973077	B	0.26775	0.159	B	0.27887	0.084	T	0.34354	-0.9832	10	0.36615	T	0.2	-10.5003	16.9468	0.86232	0.0:0.8725:0.1275:0.0	.	282	Q8N957	ANKF1_HUMAN	S	282	ENSP00000321627:T282S	ENSP00000321627:T282S	T	+	2	0	ANKFN1	51807000	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.515000	0.60489	1.454000	0.47793	0.655000	0.94253	ACC		0.458	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		G	54452001	C	G	54452001	3	3	66	1	0	0	0	0	1	0	0	0	625	507	18	5	871	5	ANKFN1	17	54452001	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	10203501	54452001	26743209	90	20735										
SMAD4	4089	broad.mit.edu	37	chr18	48591919	48591919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggacccttctggaggagatcGcttttgtttgggtcaactct	12	9	3	1	rs377767347		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr18:48591919G>A	ENST00000342988.3	+	9	1620	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	SMAD4_ENST00000588745.1_Missense_Mutation_p.R265H|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361H	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	361	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		R -> C (in JPS; dbSNP:rs80338963). {ECO:0000269|PubMed:9811934}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R361H(12)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGAGATCGCTTTTGTTTG	0.413																																																50	Whole gene deletion(36)|Substitution - Missense(12)|Unknown(2)	pancreas(26)|large_intestine(13)|lung(3)|breast(3)|upper_aerodigestive_tract(2)|stomach(2)|oesophagus(1)	18	GRCh37	CM004254	SMAD4	M							167	138	148					18																	48591919		2203	4300	6503	46845917	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1082G>A	18.37:g.48591919G>A	ENSP00000341551:p.Arg361His		46845917	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477304	0.96291	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98120	-4.73;-4.73	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99741	1.1015	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	361	Q13485	SMAD4_HUMAN	H	361	ENSP00000341551:R361H;ENSP00000381452:R361H	ENSP00000341551:R361H	R	+	2	0	SMAD4	46845917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.828000	0.86729	2.771000	0.95319	0.563000	0.77884	CGC		0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48591919	G	A	48591919	3	1	66	1	0	0	0	0	1	0	0	0	14797	1087	38	1	1112	1	SMAD4	18	48591919	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09		48591919	29485329	91	20736										
THEG	51298	broad.mit.edu	37	chr19	374392	374392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ttgctttggtcatggtggtgCtggggagcttctggctgatg	17	6	2	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:374392C>T	ENST00000342640.4	-	2	380	c.338G>A	c.(337-339)aGc>aAc	p.S113N	THEG_ENST00000346878.2_Missense_Mutation_p.S113N	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	113					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)		p.S113N(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|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)		CATGGTGGTGCTGGGGAGCTT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											124	116	119					19																	374392		2203	4300	6503	325392	SO:0001583	missense	51298			AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"cancer/testis antigen 56"	609503	"Theg homolog (mouse)"			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.338G>A	19.37:g.374392C>T	ENSP00000340088:p.Ser113Asn		325392	A6NMJ8	Missense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	.	.	.	.	.	.	.	.	.	.	C	7.341	0.620813	0.14193	.	.	ENSG00000105549	ENST00000342640;ENST00000346878	T;T	0.21734	1.99;2.01	2.35	-1.73	0.08081	.	3.154090	0.00802	N	0.001427	T	0.15046	0.0363	L	0.36672	1.1	0.09310	N	1	P;B	0.36535	0.557;0.13	B;B	0.30572	0.117;0.034	T	0.18650	-1.0330	10	0.48119	T	0.1	-23.3107	4.4843	0.11781	0.0:0.3943:0.4525:0.1532	.	113;113	Q9P2T0-2;Q9P2T0	.;THEG_HUMAN	N	113	ENSP00000340088:S113N;ENSP00000264820:S113N	ENSP00000340088:S113N	S	-	2	0	THEG	325392	0.012000	0.17670	0.000000	0.03702	0.003000	0.03518	0.290000	0.18975	-0.255000	0.09486	0.511000	0.50034	AGC		0.582	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2			T	374392	C	T	374392	3	4	66	1	0	0	0	0	1	0	0	0	15896	797	28	3	829	3	THEG	19	374392	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		374392	58754591	92	20737										
PTPRS	5802	broad.mit.edu	37	chr19	5220326	5220326	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gggtcaggaattggcctccaCgagacttgcgcagtggcacc	14	12	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:5220326C>T	ENST00000587303.1	-	20	3593	c.3494G>A	c.(3493-3495)cGt>cAt	p.R1165H	PTPRS_ENST00000262963.6_Missense_Mutation_p.R1161H|PTPRS_ENST00000372412.4_Missense_Mutation_p.R1166H|PTPRS_ENST00000588012.1_Missense_Mutation_p.R1143H|PTPRS_ENST00000592099.1_Missense_Mutation_p.R734H|PTPRS_ENST00000348075.2_Missense_Mutation_p.R1143H|PTPRS_ENST00000353284.2_Missense_Mutation_p.R734H|PTPRS_ENST00000357368.4_Missense_Mutation_p.R1165H|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1165					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R1165H(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TTGGCCTCCACGAGACTTGCG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											52	50	50					19																	5220326		2203	4299	6502	5171326	SO:0001583	missense	5802			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.3494G>A	19.37:g.5220326C>T	ENSP00000467537:p.Arg1165His		5171326	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284294	0.40394	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.56776	0.61;0.6;0.56;0.44;0.54	3.92	3.92	0.45320	.	0.000000	0.64402	U	0.000003	T	0.67154	0.2863	L	0.59436	1.845	0.45914	D	0.998753	D;D;D;B;D;D	0.89917	0.997;0.996;0.997;0.26;0.995;1.0	D;P;P;B;P;P	0.66847	0.947;0.852;0.897;0.052;0.886;0.904	T	0.70324	-0.4903	10	0.51188	T	0.08	.	16.1393	0.81512	0.0:1.0:0.0:0.0	.	747;734;738;1143;1165;760	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	H	760;1166;1165;1165;1156;1161;1143;747;738;734	ENSP00000361489:R1166H;ENSP00000349932:R1165H;ENSP00000262963:R1161H;ENSP00000269907:R1143H;ENSP00000327313:R734H	ENSP00000262963:R1161H	R	-	2	0	PTPRS	5171326	0.882000	0.30256	0.806000	0.32338	0.031000	0.12232	2.134000	0.42102	2.027000	0.59764	0.655000	0.94253	CGT		0.582	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			T	5220326	C	T	5220326	3	4	66	1	0	0	0	0	1	0	0	0	12848	536	19	1	2424	1	PTPRS	19	5220326	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	4845934	5220326	53908657	93	20738										
PRAM1	84106	broad.mit.edu	37	chr19	8564402	8564402	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggaggtcagtgacctcaggcGgcgggggcttcttggggagg	21	8	3	1	rs200547271		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:8564402G>A	ENST00000423345.4	-	2	810	c.290C>T	c.(289-291)cCg>cTg	p.P97L	PRAM1_ENST00000255612.3_Missense_Mutation_p.P97L			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	145	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)	p.P97L(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GACCTCAGGCGGCGGGGGCTT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											14	15	14					19																	8564402		1118	2662	3780	8470402	SO:0001583	missense	84106			BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.290C>T	19.37:g.8564402G>A	ENSP00000408342:p.Pro97Leu		8470402	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	g	5.272	0.235589	0.10023	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.14022	2.54;2.54	3.16	-0.344	0.12628	.	0.453195	0.16503	N	0.211572	T	0.04907	0.0132	N	0.22421	0.69	0.09310	N	1	B;B	0.30482	0.281;0.221	B;B	0.19946	0.027;0.026	T	0.31971	-0.9924	10	0.09843	T	0.71	.	0.3139	0.00292	0.1928:0.253:0.2071:0.3471	.	97;145	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	L	97	ENSP00000255612:P97L;ENSP00000408342:P97L	ENSP00000255612:P97L	P	-	2	0	PRAM1	8470402	0.001000	0.12720	0.043000	0.18650	0.009000	0.06853	0.346000	0.19997	0.027000	0.15297	-0.781000	0.03364	CCG		0.642	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		A	8564402	G	A	8564402	3	1	66	1	0	0	0	0	1	0	0	0	12457	1116	39	1	1755	1	PRAM1	19	8564402	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	3344076	8564402	50564581	94	20739										
MUC16	94025	broad.mit.edu	37	chr19	9068541	9068541	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tggtccccacattggccactGctgtgtttatagaaggatgc	11	10	0	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:9068541G>T	ENST00000397910.4	-	3	19108	c.18905C>A	c.(18904-18906)gCa>gAa	p.A6302E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6304	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A6302E(2)|p.A1935E(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTGGCCACTGCTGTGTTTAT	0.443																																																3	Substitution - Missense(3)	large_intestine(3)	19											208	196	200					19																	9068541		2012	4181	6193	8929541	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18905C>A	19.37:g.9068541G>T	ENSP00000381008:p.Ala6302Glu		8929541	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.810	0.150613	0.09185	.	.	ENSG00000181143	ENST00000397910	T	0.30182	1.54	2.41	-0.0291	0.13919	.	.	.	.	.	T	0.33904	0.0879	L	0.43152	1.355	.	.	.	D	0.55172	0.97	P	0.57324	0.818	T	0.39663	-0.9603	8	0.87932	D	0	.	2.8625	0.05591	0.1643:0.0:0.566:0.2697	.	6302	B5ME49	.	E	6302	ENSP00000381008:A6302E	ENSP00000381008:A6302E	A	-	2	0	MUC16	8929541	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.430000	0.06973	0.073000	0.16731	0.195000	0.17529	GCA		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9068541	G	T	9068541	3	4	66	1	0	0	0	0	1	0	0	0	10003	1319	46	2	24946	2	MUC16	19	9068541	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	504139	9068541	50060442	95	20740										
RYR1	6261	broad.mit.edu	37	chr19	38956902	38956902	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gcagtgcaggacatcccagcGcgccgaaaccctcggctggt	13	15	0	0	rs2228074	byFrequency	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:38956902G>A	ENST00000359596.3	+	24	3042	c.3042G>A	c.(3040-3042)gcG>gcA	p.A1014A	RYR1_ENST00000355481.4_Silent_p.A1014A|RYR1_ENST00000360985.3_Silent_p.A1014A			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1014	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.A1014A(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACATCCCAGCGCGCCGAAACC	0.682													G|||	23	0.00459265	0.0174	0	5008	,	,		14338	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G	,	45,4353	46.7+/-81.2	0,45,2154	43	42	42		3042,3042	-7.6	0.4	19	dbSNP_98	42	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	0,45,6453	AA,AG,GG		0.0,1.0232,0.3463	,	1014/5039,1014/5034	38956902	45,12951	2199	4299	6498	43648742	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3042G>A	19.37:g.38956902G>A			43648742	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38956902	G	A	38956902	2	1	66	1	0	0	0	0	0	0	0	1	13805	1074	38	1		1	RYR1	19	38956902	Silent	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	29888361	38956902	20172081	96	20741										
RYR1	6261	broad.mit.edu	37	chr19	38976776	38976776	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gacggtgggcagcacgctcgCgaccccgtcgggggctccgt	17	15	0	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:38976776C>T	ENST00000359596.3	+	34	5481	c.5481C>T	c.(5479-5481)cgC>cgT	p.R1827R	RYR1_ENST00000355481.4_Silent_p.R1827R|RYR1_ENST00000360985.3_Silent_p.R1827R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1827	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R1827R(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AGCACGCTCGCGACCCCGTCG	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	19											84	83	83					19																	38976776		2191	4287	6478	43668616	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5481C>T	19.37:g.38976776C>T			43668616	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976776	C	T	38976776	2	4	66	1	0	0	0	0	0	0	0	1	13805	755	27	1		1	RYR1	19	38976776	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	19874	38976776	20152207	97	20742										
ZNF665	79788	broad.mit.edu	37	chr19	53668666	53668666	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cgccgatgctttgcaaggtaTgaattgtgcctgaagacctt	11	9	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:53668666T>C	ENST00000600412.1	-	2	997	c.882A>G	c.(880-882)tcA>tcG	p.S294S	ZNF665_ENST00000396424.3_Silent_p.S359S|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	294					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S294S(1)|p.S359S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TTGCAAGGTATGAATTGTGCC	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	19											106	106	106					19																	53668666		2203	4300	6503	58360478	SO:0001819	synonymous_variant	79788				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.882A>G	19.37:g.53668666T>C			58360478	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																					0.423	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		C	53668666	T	C	53668666	2	2	66	1	0	0	0	0	0	0	0	1	18112	1451	51	4		4	ZNF665	19	53668666	Silent	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	14691890	53668666	5460317	98	20743										
AURKC	6795	broad.mit.edu	37	chr19	57743436	57743436	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cgatgactttgaaatcgggcGtcccctgggcaaggggaaat	14	9	0	2	rs137858773		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr19:57743436G>A	ENST00000302804.7	+	3	326	c.140G>A	c.(139-141)cGt>cAt	p.R47H	AURKC_ENST00000448930.1_Missense_Mutation_p.R13H|AURKC_ENST00000599062.1_Missense_Mutation_p.R44H|AURKC_ENST00000415300.2_Missense_Mutation_p.R28H|AURKC_ENST00000598785.1_Missense_Mutation_p.R13H	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	47	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R13H(1)|p.R47H(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		GAAATCGGGCGTCCCCTGGGC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	19						G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	56	51	53		140,83,38	2.8	1	19	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	AURKC	NM_001015878.1,NM_001015879.1,NM_003160.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	47/310,28/291,13/276	57743436	1,13005	2203	4300	6503	62435248	SO:0001583	missense	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.140G>A	19.37:g.57743436G>A	ENSP00000302898:p.Arg47His		62435248	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Missense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617574	0.46736	0.0	1.16E-4	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	T;T;T	0.09073	3.02;3.02;3.02	3.79	2.76	0.32466	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117432	0.64402	N	0.000015	T	0.08268	0.0206	M	0.67517	2.055	0.54753	D	0.999981	P;P;P	0.48294	0.908;0.868;0.603	B;B;B	0.32583	0.148;0.118;0.092	T	0.16660	-1.0395	10	0.87932	D	0	-2.2481	9.6918	0.40134	0.1043:0.0:0.8957:0.0	.	44;47;28	Q5Y191;Q9UQB9;Q9UQB9-3	.;AURKC_HUMAN;.	H	28;13;47	ENSP00000407162:R28H;ENSP00000406798:R13H;ENSP00000302898:R47H	ENSP00000302898:R47H	R	+	2	0	AURKC	62435248	1.000000	0.71417	0.952000	0.39060	0.730000	0.41778	8.093000	0.89531	1.191000	0.43056	-0.266000	0.10368	CGT		0.547	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		A	57743436	G	A	57743436	3	1	66	1	0	0	0	0	1	0	0	0	1225	1145	40	1	155	1	AURKC	19	57743436	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	4074770	57743436	1385547	99	20744										
FERMT1	55612	broad.mit.edu	37	chr20	6065798	6065798	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tttcgagactggaagccaccTgagatgcagagttcctgttt	11	9	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr20:6065798T>G	ENST00000217289.4	-	12	2296	c.1508A>C	c.(1507-1509)cAg>cCg	p.Q503P	FERMT1_ENST00000536936.1_Missense_Mutation_p.Q246P|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	503	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)		p.Q503P(2)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GGAAGCCACCTGAGATGCAGA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	20											140	123	129					20																	6065798		2203	4300	6503	6013798	SO:0001583	missense	55612			AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"Fermitins", "Pleckstrin homology (PH) domain containing"	15889	protein-coding gene	gene with protein product	"kindlin-1", "kinderlin"	607900	"chromosome 20 open reading frame 42", "fermitin family homolog 1 (Drosophila)"	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1508A>C	20.37:g.6065798T>G	ENSP00000217289:p.Gln503Pro		6013798	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	.	.	.	.	.	.	.	.	.	.	t	5.221	0.226196	0.09916	.	.	ENSG00000101311	ENST00000217289;ENST00000536936;ENST00000339538	T;T	0.45668	0.89;1.5	5.17	-4.13	0.03904	Band 4.1 domain (1);FERM central domain (2);	0.316966	0.34828	N	0.003653	T	0.19765	0.0475	N	0.12637	0.245	0.39701	D	0.971189	B	0.02656	0.0	B	0.04013	0.001	T	0.05599	-1.0875	10	0.25106	T	0.35	-2.6837	12.0306	0.53396	0.1052:0.0:0.5846:0.3103	.	503	Q9BQL6	FERM1_HUMAN	P	503;246;503	ENSP00000217289:Q503P;ENSP00000441063:Q246P	ENSP00000217289:Q503P	Q	-	2	0	FERMT1	6013798	0.935000	0.31712	0.001000	0.08648	0.290000	0.27261	1.499000	0.35671	-1.022000	0.03346	0.454000	0.30748	CAG		0.458	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671		G	6065798	T	G	6065798	3	3	66	1	0	0	0	0	1	0	0	0	5836	1580	55	4	541	4	FERMT1	20	6065798	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09		6065798	56959722	100	20745										
PCSK2	5126	broad.mit.edu	37	chr20	17434431	17434431	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tacgtgtgggcctccggggaCggcggcagctatgacgactg	17	11	0	1	rs372965651		TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr20:17434431C>T	ENST00000262545.2	+	9	1245	c.930C>T	c.(928-930)gaC>gaT	p.D310D	PCSK2_ENST00000377899.1_Silent_p.D291D|PCSK2_ENST00000536609.1_Silent_p.D275D	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	310	Peptidase S8.				cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.D310D(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	CCTCCGGGGACGGCGGCAGCT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	20						C	,,	0,4406		0,0,2203	86	68	74		873,825,930	-4.1	0.6	20		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PCSK2	NM_001201528.1,NM_001201529.1,NM_002594.3	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	291/620,275/604,310/639	17434431	1,13005	2203	4300	6503	17382431	SO:0001819	synonymous_variant	5126			AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.930C>T	20.37:g.17434431C>T			17382431	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Silent	SNP	ENST00000262545.2	37	CCDS13125.1																																																																																				0.672	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17434431	C	T	17434431	2	4	66	1	0	0	0	0	0	0	0	1	11632	535	19	1		1	PCSK2	20	17434431	Silent	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	11368633	17434431	45591089	101	20746										
CTNNBL1	56259	broad.mit.edu	37	chr20	36361299	36361299	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	agcccaataggggcacaaaaCgtccccgggatgatgaagag	13	10	0	3			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr20:36361299C>T	ENST00000361383.6	+	2	166	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C	CTNNBL1_ENST00000405275.2_5'UTR	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	17					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)	p.R17C(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GGGCACAAAACGTCCCCGGGA	0.502																																					Ovarian(184;582 2038 3273 4106 42608)											1	Substitution - Missense(1)	large_intestine(1)	20											65	63	64					20																	36361299		2203	4300	6503	35794713	SO:0001583	missense	56259			AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"nuclear associated protein"	611537	"chromosome 20 open reading frame 33"	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.49C>T	20.37:g.36361299C>T	ENSP00000355050:p.Arg17Cys		35794713	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Missense_Mutation	SNP	ENST00000361383.6	37	CCDS13298.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150455	0.78001	.	.	ENSG00000132792	ENST00000361383	T	0.54866	0.55	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.73154	-0.4072	10	0.87932	D	0	-8.8664	14.1301	0.65247	0.1503:0.8497:0.0:0.0	.	17	Q8WYA6	CTBL1_HUMAN	C	17	ENSP00000355050:R17C	ENSP00000355050:R17C	R	+	1	0	CTNNBL1	35794713	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.821000	0.48065	2.606000	0.88127	0.561000	0.74099	CGT		0.502	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877		T	36361299	C	T	36361299	3	4	66	1	0	0	0	0	1	0	0	0	4024	536	19	1	55	1	CTNNBL1	20	36361299	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	18926868	36361299	26664221	102	20747										
SYS1	90196	broad.mit.edu	37	chr20	43995561	43995561	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	ggcgaggaaagcagtgtctgGatttcactgtcactgtccat	12	9	3	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr20:43995561G>T	ENST00000243918.5	+	4	568	c.277G>T	c.(277-279)Gat>Tat	p.D93Y	SYS1_ENST00000414310.1_Missense_Mutation_p.D72Y|SYS1_ENST00000372727.1_Missense_Mutation_p.D93Y|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1_ENST00000426004.1_Intron|SYS1_ENST00000479779.1_3'UTR|SYS1-DBNDD2_ENST00000475242.1_Intron	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	93					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)		p.D93Y(1)		cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GCAGTGTCTGGATTTCACTGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20											159	138	145					20																	43995561		2203	4300	6503	43428975	SO:0001583	missense	90196			AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"chromosome 20 open reading frame 169", "SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.277G>T	20.37:g.43995561G>T	ENSP00000243918:p.Asp93Tyr		43428975	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Missense_Mutation	SNP	ENST00000243918.5	37	CCDS13351.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.020245	0.93462	.	.	ENSG00000204070	ENST00000372727;ENST00000414310;ENST00000243918;ENST00000453003	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.86644	0.5982	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88101	0.2819	9	0.87932	D	0	-23.0603	19.8676	0.96824	0.0:0.0:1.0:0.0	.	93	Q8N2H4	SYS1_HUMAN	Y	93;72;93;93	.	ENSP00000243918:D93Y	D	+	1	0	SYS1	43428975	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.185000	0.94900	2.941000	0.99782	0.655000	0.94253	GAT		0.577	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542		T	43995561	G	T	43995561	3	4	66	1	0	0	0	0	1	0	0	0	15503	1174	41	2	287	2	SYS1	20	43995561	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	7634262	43995561	19029959	103	20748										
SON	6651	broad.mit.edu	37	chr21	34927006	34927006	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaaagagactcttcattaagAtctcgaagtaagcgttccaa	7	8	3	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr21:34927006A>T	ENST00000356577.4	+	3	5944	c.5469A>T	c.(5467-5469)agA>agT	p.R1823S	SON_ENST00000381679.4_Missense_Mutation_p.R1823S|SON_ENST00000300278.4_Missense_Mutation_p.R1823S|SON_ENST00000290239.6_Missense_Mutation_p.R1823S|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1823					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R1823S(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CTTCATTAAGATCTCGAAGTA	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	21											81	83	82					21																	34927006		2203	4300	6503	33848876	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.5469A>T	21.37:g.34927006A>T	ENSP00000348984:p.Arg1823Ser		33848876	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.79|13.79	2.341052|2.341052	0.41498|0.41498	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.17528	.|2.27;2.27;2.27;2.27	5.65|5.65	-0.63|-0.63	0.11530|0.11530	.|.	.|0.000000	.|0.56097	.|D	.|0.000035	T|T	0.30885|0.30885	0.0779|0.0779	L|L	0.56769|0.56769	1.78|1.78	0.32338|0.32338	N|N	0.560143|0.560143	.|D;D;D;D;D	.|0.76494	.|0.996;0.998;0.989;0.999;0.999	.|P;P;P;D;P	.|0.65684	.|0.9;0.778;0.756;0.937;0.889	T|T	0.34428|0.34428	-0.9829|-0.9829	5|10	.|0.49607	.|T	.|0.09	.|.	11.9736|11.9736	0.53078|0.53078	0.5087:0.0:0.4913:0.0|0.5087:0.0:0.4913:0.0	.|.	.|1823;1823;1504;1823;1823	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	V|S	818|1823	.|ENSP00000348984:R1823S;ENSP00000290239:R1823S;ENSP00000300278:R1823S;ENSP00000371095:R1823S	.|ENSP00000290239:R1823S	D|R	+|+	2|3	0|2	SON|SON	33848876|33848876	0.998000|0.998000	0.40836|0.40836	0.995000|0.995000	0.50966|0.50966	0.998000|0.998000	0.95712|0.95712	0.273000|0.273000	0.18662|0.18662	-0.107000|-0.107000	0.12088|0.12088	0.533000|0.533000	0.62120|0.62120	GAT|AGA		0.383	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34927006	A	T	34927006	3	4	66	1	0	0	0	0	1	0	0	0	14963	330	12	5	5479	5	SON	21	34927006	Missense_Mutation	SNP	A	TCGA-AG-A011-01A-01W-A00K-09		34927006	13202889	104	20749										
C2CD2	25966	broad.mit.edu	37	chr21	43342136	43342136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gccggcatccagcacccaagGcaggcgtctcgctgaccaag	12	16	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr21:43342136G>A	ENST00000380486.3	-	3	678	c.437C>T	c.(436-438)gCc>gTc	p.A146V	C2CD2_ENST00000329623.7_5'UTR	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	146						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.A146V(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						AGCACCCAAGGCAGGCGTCTC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	21											57	55	56					21																	43342136		2203	4300	6503	42215205	SO:0001583	missense	25966			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.437C>T	21.37:g.43342136G>A	ENSP00000369853:p.Ala146Val		42215205	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.900879	0.52227	.	.	ENSG00000157617	ENST00000380486	T	0.24723	1.84	4.73	4.73	0.59995	.	0.498237	0.20830	N	0.084908	T	0.25457	0.0619	L	0.54323	1.7	0.09310	N	1	P	0.43094	0.799	B	0.38562	0.276	T	0.17561	-1.0365	10	0.38643	T	0.18	-14.2407	13.567	0.61824	0.0:0.0:1.0:0.0	.	146	Q9Y426	CU025_HUMAN	V	146	ENSP00000369853:A146V	ENSP00000369853:A146V	A	-	2	0	C2CD2	42215205	0.032000	0.19561	0.005000	0.12908	0.007000	0.05969	2.150000	0.42254	2.325000	0.78763	0.655000	0.94253	GCC		0.532	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		A	43342136	G	A	43342136	3	1	66	1	0	0	0	0	1	0	0	0	2158	1203	42	3	1701	3	C2CD2	21	43342136	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	8415130	43342136	4787759	105	20750										
CCT8L2	150160	broad.mit.edu	37	chr22	17073278	17073278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	caccaggaacttctgccggcCgtgggggccatagcaaggcc	14	14	1	0			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr22:17073278C>T	ENST00000359963.3	-	1	422	c.163G>A	c.(163-165)Ggc>Agc	p.G55S		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	55					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)	p.G55S(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TTCTGCCGGCCGTGGGGGCCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	22											64	66	65					22																	17073278		2203	4300	6503	15453278	SO:0001583	missense	150160			AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.163G>A	22.37:g.17073278C>T	ENSP00000353048:p.Gly55Ser		15453278	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	15.91	2.972960	0.53614	.	.	ENSG00000198445	ENST00000359963	D	0.89681	-2.55	2.0	2.0	0.26442	.	0.000000	0.35466	U	0.003192	D	0.93012	0.7776	M	0.84433	2.695	0.37124	D	0.900969	D	0.69078	0.997	D	0.69307	0.963	D	0.93154	0.6552	10	0.87932	D	0	-11.292	7.4831	0.27417	0.0:1.0:0.0:0.0	.	55	Q96SF2	TCPQM_HUMAN	S	55	ENSP00000353048:G55S	ENSP00000353048:G55S	G	-	1	0	CCT8L2	15453278	0.121000	0.22262	0.958000	0.39756	0.698000	0.40448	2.840000	0.48215	1.126000	0.42016	0.393000	0.25936	GGC		0.642	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17073278	C	T	17073278	3	4	66	1	0	0	0	0	1	0	0	0	2967	652	23	1	1514	1	CCT8L2	22	17073278	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09		17073278	34231288	106	20751										
TNRC6B	23112	broad.mit.edu	37	chr22	40676034	40676034	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	aaaaatttgatgtggacaagCgagcgatgaatctcggggat	13	5	1	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chr22:40676034C>T	ENST00000454349.2	+	10	3509	c.3298C>T	c.(3298-3300)Cga>Tga	p.R1100*	TNRC6B_ENST00000335727.9_Nonsense_Mutation_p.R1047*|TNRC6B_ENST00000497559.1_3'UTR|TNRC6B_ENST00000402203.1_Nonsense_Mutation_p.R353*|TNRC6B_ENST00000301923.9_Nonsense_Mutation_p.R353*	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1100					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R1114*(1)		breast(1)	1						TGTGGACAAGCGAGCGATGAA	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											205	204	204					22																	40676034		1844	4092	5936	39005980	SO:0001587	stop_gained	23112			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3298C>T	22.37:g.40676034C>T	ENSP00000401946:p.Arg1100*		39005980	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Nonsense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	43	10.111934	0.99339	.	.	ENSG00000100354	ENST00000301923;ENST00000402203;ENST00000454349;ENST00000400140;ENST00000335727	.	.	.	5.93	3.79	0.43588	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.666	15.1162	0.72404	0.2658:0.7342:0.0:0.0	.	.	.	.	X	353;353;1100;1047;1047	.	ENSP00000306759:R353X	R	+	1	2	TNRC6B	39005980	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.562000	0.45914	0.775000	0.33450	0.655000	0.94253	CGA		0.433	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40676034	C	T	40676034	4	4	66	1	0	0	0	0	0	1	0	0	16380	760	27	1	3457	1	TNRC6B	22	40676034	Nonsense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	23602756	40676034	10628532	107	20752										
ZC3H12B	340554	broad.mit.edu	37	chrX	64709236	64709236	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	tctcttgaagatgaaatagaTaacagtgacaatttgaggcc	9	6	1	6			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chrX:64709236T>G	ENST00000338957.4	+	1	622	c.555T>G	c.(553-555)gaT>gaG	p.D185E	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.D174E	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	185							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.D35E(1)|p.D121E(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATGAAATAGATAACAGTGACA	0.438																																																2	Substitution - Missense(2)	large_intestine(2)	X											67	65	66					X																	64709236		1909	4101	6010	64625961	SO:0001583	missense	340554			BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.555T>G	X.37:g.64709236T>G	ENSP00000340839:p.Asp185Glu		64625961	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	37	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	T	15.23	2.772088	0.49680	.	.	ENSG00000102053	ENST00000338957;ENST00000423889;ENST00000218172	T;T	0.23552	1.9;1.9	5.05	2.36	0.29203	.	0.092939	0.64402	D	0.000001	T	0.38268	0.1034	L	0.49350	1.555	0.43857	D	0.996453	D	0.76494	0.999	D	0.78314	0.991	T	0.03453	-1.1035	10	0.33940	T	0.23	0.4858	7.9917	0.30244	0.0:0.6437:0.0:0.3563	.	174	Q5HYM0	ZC12B_HUMAN	E	185;174;121	ENSP00000340839:D185E;ENSP00000408077:D174E	ENSP00000218172:D121E	D	+	3	2	ZC3H12B	64625961	0.996000	0.38824	0.997000	0.53966	0.973000	0.67179	0.459000	0.21908	0.183000	0.20059	-0.298000	0.09462	GAT		0.438	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		G	64709236	T	G	64709236	3	3	66	1	0	0	0	0	1	0	0	0	17601	1403	49	4	557	4	ZC3H12B	23	64709236	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09		64709236	90561324	108	20753										
KIAA2022	340533	broad.mit.edu	37	chrX	73963619	73963619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	taaaagtctcgaagtaacccCaatcctgattggaatttgca	7	9	1	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chrX:73963619C>A	ENST00000055682.6	-	3	1384	c.773G>T	c.(772-774)tGg>tTg	p.W258L		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	258					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.W258L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GAAGTAACCCCAATCCTGATT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	X											128	118	121					X																	73963619		2203	4300	6503	73880344	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.773G>T	X.37:g.73963619C>A	ENSP00000055682:p.Trp258Leu		73880344	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671415	0.67814	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.60424	0.19;0.19	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.73410	0.3583	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74680	-0.3584	10	0.87932	D	0	-3.7722	19.3296	0.94280	0.0:1.0:0.0:0.0	.	258	Q5QGS0	K2022_HUMAN	L	258	ENSP00000362567:W258L;ENSP00000055682:W258L	ENSP00000055682:W258L	W	-	2	0	KIAA2022	73880344	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.517000	0.84864	0.600000	0.82982	TGG		0.398	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73963619	C	A	73963619	3	1	66	1	0	0	0	0	1	0	0	0	8290	595	21	2	3785	2	KIAA2022	23	73963619	Missense_Mutation	SNP	C	TCGA-AG-A011-01A-01W-A00K-09	9254383	73963619	81306941	109	20754										
POU3F4	5456	broad.mit.edu	37	chrX	82764140	82764140	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	cagggagcccgaccagcattGacaagatcgctgcacagggc	13	13	0	2			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chrX:82764140G>T	ENST00000373200.2	+	1	872	c.808G>T	c.(808-810)Gac>Tac	p.D270Y	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	270					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D270Y(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						GACCAGCATTGACAAGATCGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	X											47	41	43					X																	82764140		2203	4300	6503	82650796	SO:0001583	missense	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.808G>T	X.37:g.82764140G>T	ENSP00000362296:p.Asp270Tyr		82650796	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	37	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960594	0.74016	.	.	ENSG00000196767	ENST00000373200	D	0.95656	-3.77	5.07	5.07	0.68467	Homeodomain-related (1);	0.000000	0.85682	D	0.000000	D	0.97704	0.9247	M	0.83012	2.62	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	D	0.98645	1.0677	10	0.87932	D	0	.	17.4614	0.87620	0.0:0.0:1.0:0.0	.	270	P49335	PO3F4_HUMAN	Y	270	ENSP00000362296:D270Y	ENSP00000362296:D270Y	D	+	1	0	POU3F4	82650796	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.764000	0.85297	2.244000	0.73946	0.525000	0.51046	GAC		0.577	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82764140	G	T	82764140	3	4	66	1	0	0	0	0	1	0	0	0	12308	1290	45	2	810	2	POU3F4	23	82764140	Missense_Mutation	SNP	G	TCGA-AG-A011-01A-01W-A00K-09	8800521	82764140	72506420	110	20755										
MPP1	4354	broad.mit.edu	37	chrX	154019307	154019307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0810810810810811	9	1	1.06583737864078	5.05285868392664	0.653386898783618	1	1	0	gatttgtcacatttgtgccaTtgatttctaggatctcatcc	7	9	3	1			TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A011-01A-01W-A00K-09	TCGA-AG-A011-10A-01W-A00K-09	g.chrX:154019307T>C	ENST00000369534.3	-	4	509	c.362A>G	c.(361-363)aAt>aGt	p.N121S	MPP1_ENST00000413259.3_Missense_Mutation_p.N91S|MPP1_ENST00000462825.1_Intron|MPP1_ENST00000393531.1_Missense_Mutation_p.N121S	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	121	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.N121S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATTTGTGCCATTGATTTCTAG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X											299	241	261					X																	154019307		2203	4300	6503	153672501	SO:0001583	missense	4354				CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.362A>G	X.37:g.154019307T>C	ENSP00000358547:p.Asn121Ser		153672501	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Missense_Mutation	SNP	ENST00000369534.3	37	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200247	0.79015	.	.	ENSG00000130830	ENST00000369534;ENST00000413259;ENST00000393531;ENST00000393529;ENST00000369531	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	5.61	4.44	0.53790	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.80529	0.4640	H	0.94183	3.505	0.54753	D	0.999986	B;P;D;P	0.89917	0.41;0.902;1.0;0.902	B;P;D;P	0.97110	0.26;0.897;1.0;0.897	T	0.82436	-0.0458	10	0.87932	D	0	.	9.5197	0.39126	0.0:0.0848:0.0:0.9152	.	104;91;121;121	B4E325;B4DZV5;G3XAI1;Q00013	.;.;.;EM55_HUMAN	S	121;91;121;75;104	ENSP00000358547:N121S;ENSP00000400155:N91S;ENSP00000377165:N121S;ENSP00000377163:N75S;ENSP00000358544:N104S	ENSP00000358544:N104S	N	-	2	0	MPP1	153672501	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.558000	0.82253	0.751000	0.32900	0.481000	0.45027	AAT		0.418	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		C	154019307	T	C	154019307	3	2	66	1	0	0	0	0	1	0	0	0	9763	1493	52	4	1074	4	MPP1	23	154019307	Missense_Mutation	SNP	T	TCGA-AG-A011-01A-01W-A00K-09	71255167	154019307	1251253	111	20756										
ZBTB8A	653121	broad.mit.edu	37	chr1	33065909	33065909	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tggcacttgagtgaagatgaGaatagatcctatgtggagat	13	4	0	6			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:33065909G>A	ENST00000373510.4	+	5	1444	c.1215G>A	c.(1213-1215)gaG>gaA	p.E405E	ZBTB8OS_ENST00000341885.5_Missense_Mutation_p.S59F|ZBTB8A_ENST00000316459.4_3'UTR|RP1-27O5.3_ENST00000480336.1_3'UTR	NM_001040441.1	NP_001035531.1	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	405					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E405E(1)		cervix(2)|large_intestine(2)|lung(2)|prostate(1)	7						GTGAAGATGAGAATAGATCCT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	1											147	132	137					1																	33065909		2203	4300	6503	32838496	SO:0001819	synonymous_variant	653121			AF548353	CCDS30664.1	1p34.3	2013-01-08	2009-03-25	2009-03-25	ENSG00000160062	ENSG00000160062		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24172	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 8"	ZBTB8		12477932	Standard	NM_001040441		Approved	BOZF1, FLJ90065, ZNF916A	uc001bvn.3	Q96BR9	OTTHUMG00000007855	ENST00000373510.4:c.1215G>A	1.37:g.33065909G>A			32838496	Q8IUL5|Q8IWR9|Q8N2Y5|Q96BX0	Silent	SNP	ENST00000373510.4	37	CCDS30664.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476558	0.44044	.	.	ENSG00000176261	ENST00000341885	.	.	.	5.59	4.67	0.58626	.	.	.	.	.	T	0.63283	0.2498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65676	-0.6110	5	0.87932	D	0	-18.2496	7.0097	0.24855	0.1517:0.1662:0.682:0.0	.	.	.	.	F	59	.	ENSP00000343760:S59F	S	-	2	0	ZBTB8OS	32838496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.703000	0.37846	2.804000	0.96469	0.655000	0.94253	TCT		0.428	ZBTB8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021665.2	NM_144621		A	33065909	G	A	33065909	2	1	67	1	0	0	0	0	0	0	0	1	17595	933	33	3		3	ZBTB8A	1	33065909	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		33065909	216184712	1	20757										
COL9A2	1298	broad.mit.edu	37	chr1	40766888	40766888	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tggatccaggctctgtaaggCgggcagaggcataggccgaa	16	9	1	1	rs199897562		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:40766888C>G	ENST00000372748.3	-	32	2132	c.2036G>C	c.(2035-2037)cGc>cCc	p.R679P	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	679	Nonhelical region 1 (NC1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.R679P(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-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;2.08e-17)			CTCTGTAAGGCGGGCAGAGGC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	1											33	38	36					1																	40766888		2203	4300	6503	40539475	SO:0001583	missense	1298			M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.2036G>C	1.37:g.40766888C>G	ENSP00000361834:p.Arg679Pro		40539475	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	37	CCDS450.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025807	0.75390	.	.	ENSG00000049089	ENST00000372748	D	0.90324	-2.65	5.38	5.38	0.77491	.	0.107792	0.64402	D	0.000010	D	0.92433	0.7598	L	0.47716	1.5	0.48975	D	0.999735	D	0.76494	0.999	D	0.66084	0.941	D	0.92240	0.5800	10	0.54805	T	0.06	.	12.374	0.55269	0.0:0.8301:0.1699:0.0	.	679	Q14055	CO9A2_HUMAN	P	679	ENSP00000361834:R679P	ENSP00000361834:R679P	R	-	2	0	COL9A2	40539475	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.063000	0.57499	2.534000	0.85438	0.561000	0.74099	CGC		0.677	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		G	40766888	C	G	40766888	3	3	67	1	0	0	0	0	1	0	0	0	3714	768	27	5	37	5	COL9A2	1	40766888	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	7700979	40766888	208483733	2	20758										
CYP4B1	1580	broad.mit.edu	37	chr1	47280904	47280904	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cgttgtagagaggaggtccgCgagatcctaggggaccagga	17	8	0	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:47280904C>T	ENST00000271153.4	+	8	1074	c.1038C>T	c.(1036-1038)cgC>cgT	p.R346R	CYP4B1_ENST00000371919.4_Silent_p.R332R|CYP4B1_ENST00000452782.2_Silent_p.R184R|CYP4B1_ENST00000371923.4_Silent_p.R347R			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	346					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.R346R(2)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	AGGAGGTCCGCGAGATCCTAG	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	1											96	82	87					1																	47280904		2203	4300	6503	47053491	SO:0001819	synonymous_variant	1580			BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1038C>T	1.37:g.47280904C>T			47053491	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	37	CCDS542.1																																																																																				0.582	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		T	47280904	C	T	47280904	2	4	67	1	0	0	0	0	0	0	0	1	4191	755	27	1		1	CYP4B1	1	47280904	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	6514016	47280904	201969717	3	20759										
CD53	963	broad.mit.edu	37	chr1	111437611	111437611	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tatgtggctaagggtctgacCgacagcatccaccgttacca	10	12	1	1	rs201211085		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:111437611C>T	ENST00000271324.5	+	5	469	c.357C>T	c.(355-357)acC>acT	p.T119T	CD53_ENST00000429072.2_Intron|CD53_ENST00000497404.1_3'UTR	NM_000560.3|NM_001040033.1	NP_000551.1|NP_001035122.1	P19397	CD53_HUMAN	CD53 molecule	119					positive regulation of myoblast fusion (GO:1901741)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T119T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	17		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)		AGGGTCTGACCGACAGCATCC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	1											196	160	172					1																	111437611		2203	4300	6503	111239134	SO:0001819	synonymous_variant	963			BC040693	CCDS829.1	1p13	2013-02-14	2006-03-28		ENSG00000143119	ENSG00000143119		"CD molecules", "Tetraspanins"	1686	protein-coding gene	gene with protein product		151525	"CD53 antigen"	MOX44		8319976	Standard	XM_006711053		Approved	TSPAN25	uc001dzw.3	P19397	OTTHUMG00000048020	ENST00000271324.5:c.357C>T	1.37:g.111437611C>T			111239134	B2R905|Q5U0D6	Silent	SNP	ENST00000271324.5	37	CCDS829.1																																																																																				0.507	CD53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032931.1	NM_000560		T	111437611	C	T	111437611	2	4	67	1	0	0	0	0	0	0	0	1	3029	639	23	1		1	CD53	1	111437611	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	64156707	111437611	137813010	4	20760										
GBA	2629	broad.mit.edu	37	chr1	155209750	155209750	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccactgcgtgtactctcataGcggctgaaggtaccaagggc	12	12	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:155209750G>A	ENST00000327247.5	-	4	466	c.234C>T	c.(232-234)cgC>cgT	p.R78R	GBA_ENST00000493842.1_5'UTR|GBA_ENST00000427500.3_Silent_p.R78R|GBA_ENST00000428024.3_5'UTR|GBA_ENST00000536770.1_Intron|GBA_ENST00000368373.3_Silent_p.R78R	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	78					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)	p.R78R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	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)		Velaglucerase alfa(DB06720)	TACTCTCATAGCGGCTGAAGG	0.577									Gaucher disease type I																																							1	Substitution - coding silent(1)	large_intestine(1)	1											52	43	46					1																	155209750		2203	4300	6503	153476374	SO:0001819	synonymous_variant	2629	Familial Cancer Database	glucocerebrosidase insufficiency	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"glucosylceramidase", "glucosidase, beta; acid (includes glucosylceramidase)"	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.234C>T	1.37:g.155209750G>A			153476374	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Silent	SNP	ENST00000327247.5	37	CCDS1102.1																																																																																				0.577	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157		A	155209750	G	A	155209750	2	1	67	1	0	0	0	0	0	0	0	1	6286	958	34	3		3	GBA	1	155209750	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	43772139	155209750	94040871	5	20761										
NDUFS2	4720	broad.mit.edu	37	chr1	161179294	161179294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gctgtttggagaaatcacacGtttgttgaaccacatcatgg	10	8	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:161179294G>A	ENST00000367993.3	+	6	984	c.536G>A	c.(535-537)cGt>cAt	p.R179H	NDUFS2_ENST00000476409.2_Missense_Mutation_p.R81H|NDUFS2_ENST00000392179.4_Missense_Mutation_p.R179H	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	179					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)	p.R179H(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	GAAATCACACGTTTGTTGAAC	0.527											OREG0013941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											92	80	84					1																	161179294		2203	4300	6503	159445918	SO:0001583	missense	4720			BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.536G>A	1.37:g.161179294G>A	ENSP00000356972:p.Arg179His	1814	159445918	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982064	0.93044	.	.	ENSG00000158864	ENST00000367993;ENST00000392179;ENST00000476409	D;D;D	0.91180	-2.8;-2.8;-2.8	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	M	0.94063	3.49	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	D	0.97118	0.9809	9	0.87932	D	0	.	17.5462	0.87863	0.0:0.0:1.0:0.0	.	128;81;179;179	B7Z792;B7Z9L2;Q53HG2;O75306	.;.;.;NDUS2_HUMAN	H	179;179;81	ENSP00000356972:R179H;ENSP00000376018:R179H;ENSP00000446447:R81H	ENSP00000356972:R179H	R	+	2	0	NDUFS2	159445918	1.000000	0.71417	0.960000	0.40013	0.736000	0.42039	6.917000	0.75782	2.654000	0.90174	0.655000	0.94253	CGT		0.527	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		A	161179294	G	A	161179294	3	1	67	1	0	0	0	0	1	0	0	0	10323	1145	40	1	554	1	NDUFS2	1	161179294	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	5969544	161179294	88071327	6	20762										
C1orf129	80133	broad.mit.edu	37	chr1	170961432	170961432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acaccgtaacggaagggaaaCgtttctctcttgatattacc	8	10	2	1	rs553009271	byFrequency	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:170961432C>T	ENST00000367758.3	+	12	1255	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C	MROH9_ENST00000367759.4_Missense_Mutation_p.R386C	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	386								p.R386C(2)									GGAAGGGAAACGTTTCTCTCT	0.448													C|||	6	0.00119808	0	0	5008	,	,		20236	0		0	False		,,,				2504	0.0061															2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	1											168	170	169					1																	170961432		1969	4143	6112	169228056	SO:0001583	missense	80133			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1156C>T	1.37:g.170961432C>T	ENSP00000356732:p.Arg386Cys		169228056	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.385863	0.25031	.	.	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.16743	3.91;2.32	5.61	1.73	0.24493	.	0.405814	0.24014	N	0.042342	T	0.06962	0.0177	M	0.69823	2.125	0.09310	N	1	B;B	0.22541	0.071;0.032	B;B	0.18871	0.023;0.018	T	0.28490	-1.0042	10	0.46703	T	0.11	0.0523	7.4505	0.27235	0.0:0.655:0.0:0.345	.	386;386	F5GWX6;Q5TGP6	.;CA129_HUMAN	C	386	ENSP00000356733:R386C;ENSP00000356732:R386C	ENSP00000356732:R386C	R	+	1	0	C1orf129	169228056	0.134000	0.22483	0.000000	0.03702	0.001000	0.01503	0.897000	0.28390	0.073000	0.16731	-0.229000	0.12294	CGT		0.448	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		T	170961432	C	T	170961432	3	4	67	1	0	0	0	0	1	0	0	0	2002	536	19	1	1198	1	C1orf129	1	170961432	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	9782138	170961432	78289189	7	20763										
CACNA1E	777	broad.mit.edu	37	chr1	181741329	181741329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcggcaccgatctggcctacGtgtactttgtctccttcatc	9	14	3	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:181741329G>A	ENST00000367573.2	+	37	5101	c.5101G>A	c.(5101-5103)Gtg>Atg	p.V1701M	CACNA1E_ENST00000357570.5_Missense_Mutation_p.V1652M|CACNA1E_ENST00000526775.1_Missense_Mutation_p.V1682M|CACNA1E_ENST00000358338.5_Missense_Mutation_p.V1633M|CACNA1E_ENST00000360108.3_Missense_Mutation_p.V1682M|CACNA1E_ENST00000367567.4_Missense_Mutation_p.V1308M|RNA5SP70_ENST00000517168.1_RNA|CACNA1E_ENST00000367570.1_Missense_Mutation_p.V1701M	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1701					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.V1701M(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TCTGGCCTACGTGTACTTTGT	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											218	216	217					1																	181741329		2185	4277	6462	180007952	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5101G>A	1.37:g.181741329G>A	ENSP00000356545:p.Val1701Met		180007952	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921974	0.73213	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98684	-5.07;-5.07;-5.07;-5.07;-5.07;-5.07;-5.07	5.77	3.65	0.41850	Ion transport (1);	0.232379	0.42821	D	0.000642	D	0.97489	0.9178	L	0.32530	0.975	0.45415	D	0.998393	P;P;D	0.56287	0.839;0.907;0.975	P;P;P	0.51833	0.542;0.652;0.681	D	0.97562	1.0099	10	0.54805	T	0.06	.	15.8891	0.79279	0.0:0.0:0.7427:0.2573	.	1682;1701;1701	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	M	1701;1682;1652;1633;1308;1682;1701	ENSP00000356542:V1701M;ENSP00000434814:V1682M;ENSP00000350183:V1652M;ENSP00000351101:V1633M;ENSP00000356539:V1308M;ENSP00000353222:V1682M;ENSP00000356545:V1701M	ENSP00000350183:V1652M	V	+	1	0	CACNA1E	180007952	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.645000	0.67909	1.387000	0.46486	0.643000	0.83706	GTG		0.547	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181741329	G	A	181741329	3	1	67	1	0	0	0	0	1	0	0	0	2548	1145	40	1	5247	1	CACNA1E	1	181741329	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	10779897	181741329	67509292	8	20764										
KCNT2	343450	broad.mit.edu	37	chr1	196398809	196398809	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccgaagcccacagtagaaaaCgtcacaatgcagaaataaag	8	10	1	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:196398809C>A	ENST00000294725.9	-	9	1632	c.717G>T	c.(715-717)acG>acT	p.T239T	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000609185.1_Silent_p.T239T|KCNT2_ENST00000367433.5_Silent_p.T239T|KCNT2_ENST00000367431.4_Silent_p.T239T			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	239					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.T239T(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						CAGTAGAAAACGTCACAATGC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	1											109	95	99					1																	196398809		2203	4300	6503	194665432	SO:0001819	synonymous_variant	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.717G>T	1.37:g.196398809C>A			194665432	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																				0.413	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		A	196398809	C	A	196398809	2	1	67	1	0	0	0	0	0	0	0	1	8113	523	19	2		2	KCNT2	1	196398809	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	14657480	196398809	52851812	9	20765										
DISP1	84976	broad.mit.edu	37	chr1	223176891	223176891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	catgcattgtcattaagtttCgctacctttggctgttttgg	9	8	1	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:223176891C>T	ENST00000284476.6	+	8	2316	c.2152C>T	c.(2152-2154)Cgc>Tgc	p.R718C		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	718					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.R718C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		CATTAAGTTTCGCTACCTTTG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	1											163	160	161					1																	223176891		2203	4300	6503	221243514	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2152C>T	1.37:g.223176891C>T	ENSP00000284476:p.Arg718Cys		221243514	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065781	0.76187	.	.	ENSG00000154309	ENST00000284476	D	0.87334	-2.24	5.73	5.73	0.89815	.	0.046696	0.85682	D	0.000000	D	0.93409	0.7898	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93407	0.6765	10	0.72032	D	0.01	-35.9979	19.8966	0.96963	0.0:1.0:0.0:0.0	.	718	Q96F81	DISP1_HUMAN	C	718	ENSP00000284476:R718C	ENSP00000284476:R718C	R	+	1	0	DISP1	221243514	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.818000	0.86416	2.700000	0.92200	0.655000	0.94253	CGC		0.423	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		T	223176891	C	T	223176891	3	4	67	1	0	0	0	0	1	0	0	0	4550	884	31	1	2178	1	DISP1	1	223176891	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	26778082	223176891	26073730	10	20766										
HEATR1	55127	broad.mit.edu	37	chr1	236734962	236734962	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtgtattccatatttccctgCtcttgtggcaagggttctaa	9	9	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr1:236734962C>A	ENST00000366582.3	-	27	3846	c.3732G>T	c.(3730-3732)gaG>gaT	p.E1244D	HEATR1_ENST00000366581.2_Missense_Mutation_p.E1163D	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1244					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.E1244D(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TATTTCCCTGCTCTTGTGGCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											129	127	128					1																	236734962		2203	4300	6503	234801585	SO:0001583	missense	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.3732G>T	1.37:g.236734962C>A	ENSP00000355541:p.Glu1244Asp		234801585	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.120476	0.56613	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.66099	-0.19;3.4	5.58	2.64	0.31445	Armadillo-like helical (1);Armadillo-type fold (1);	0.214383	0.47093	N	0.000251	T	0.45538	0.1347	L	0.45470	1.425	0.80722	D	1	B;B	0.27765	0.188;0.075	B;B	0.22880	0.042;0.016	T	0.16364	-1.0405	10	0.17369	T	0.5	.	4.4388	0.11564	0.0:0.4851:0.1577:0.3572	.	1163;1244	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	D	1244;1163	ENSP00000355541:E1244D;ENSP00000355540:E1163D	ENSP00000355540:E1163D	E	-	3	2	HEATR1	234801585	0.931000	0.31567	0.993000	0.49108	0.893000	0.52053	0.026000	0.13599	0.291000	0.22468	0.585000	0.79938	GAG		0.383	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		A	236734962	C	A	236734962	3	1	67	1	0	0	0	0	1	0	0	0	7048	796	28	2	2778	2	HEATR1	1	236734962	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	13558071	236734962	12515659	11	20767										
CIB4	130106	broad.mit.edu	37	chr2	26818086	26818086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aatcttcaggcttgggcaggCctgctcgctgaacacagatg	12	11	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:26818086C>T	ENST00000288861.4	-	4	339	c.286G>A	c.(286-288)Gcc>Acc	p.A96T	CIB4_ENST00000405346.3_5'UTR	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	96							calcium ion binding (GO:0005509)	p.A96T(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGGGCAGGCCTGCTCGCTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	2											133	115	121					2																	26818086		2203	4300	6503	26671590	SO:0001583	missense	130106				CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"EF-hand domain containing"	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.286G>A	2.37:g.26818086C>T	ENSP00000288861:p.Ala96Thr		26671590	B2RU18	Missense_Mutation	SNP	ENST00000288861.4	37	CCDS33160.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929509	0.92389	.	.	ENSG00000157884	ENST00000288861;ENST00000403670;ENST00000405346	T	0.67865	-0.29	6.08	6.08	0.98989	EF-hand-like domain (1);	0.000000	0.64402	D	0.000009	D	0.82986	0.5156	M	0.83483	2.645	0.49299	D	0.999777	D	0.76494	0.999	D	0.72982	0.979	D	0.84553	0.0645	10	0.87932	D	0	.	16.1722	0.81825	0.0:1.0:0.0:0.0	.	96	A0PJX0	CIB4_HUMAN	T	96;51;98	ENSP00000288861:A96T	ENSP00000288861:A96T	A	-	1	0	CIB4	26671590	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.949000	0.56668	2.894000	0.99253	0.591000	0.81541	GCC		0.542	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1			T	26818086	C	T	26818086	3	4	67	1	0	0	0	0	1	0	0	0	3429	739	26	3	287	3	CIB4	2	26818086	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09		26818086	216381287	12	20768										
RETSAT	54884	broad.mit.edu	37	chr2	85578926	85578926	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgcagctgcagccaggccccCaaagccactgccaattacca	8	17	0	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:85578926C>G	ENST00000295802.4	-	2	344	c.232G>C	c.(232-234)Ggg>Cgg	p.G78R	ELMOD3_ENST00000409890.2_5'Flank|ELMOD3_ENST00000393852.4_5'Flank|ELMOD3_ENST00000428955.2_5'Flank|RETSAT_ENST00000263854.6_Missense_Mutation_p.G78R|ELMOD3_ENST00000315658.7_5'Flank|ELMOD3_ENST00000409344.3_5'Flank|RETSAT_ENST00000457495.2_Intron|ELMOD3_ENST00000409013.3_5'Flank	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	78					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)	p.G78R(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	GCCAGGCCCCCAAAGCCACTG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	2											84	80	81					2																	85578926		2203	4300	6503	85432437	SO:0001583	missense	54884			AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.232G>C	2.37:g.85578926C>G	ENSP00000295802:p.Gly78Arg		85432437	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	37	CCDS1972.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092561	0.94149	.	.	ENSG00000042445	ENST00000295802;ENST00000263854	D;D	0.81739	-1.53;-1.53	5.62	5.62	0.85841	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.054659	0.64402	D	0.000001	D	0.92172	0.7518	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93629	0.6954	10	0.87932	D	0	-20.9854	17.1641	0.86810	0.0:1.0:0.0:0.0	.	78	Q6NUM9	RETST_HUMAN	R	78	ENSP00000295802:G78R;ENSP00000263854:G78R	ENSP00000263854:G78R	G	-	1	0	RETSAT	85432437	1.000000	0.71417	0.995000	0.50966	0.942000	0.58702	7.655000	0.83696	2.665000	0.90641	0.650000	0.86243	GGG		0.557	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750		G	85578926	C	G	85578926	3	3	67	1	0	0	0	0	1	0	0	0	13275	594	21	5	1640	5	RETSAT	2	85578926	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	58760840	85578926	157620447	13	20769										
ZEB2	9839	broad.mit.edu	37	chr2	145155885	145155885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tacctgaaatccttgtttccGctggtactttctcctttgct	6	12	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:145155885G>A	ENST00000558170.2	-	8	4053	c.2869C>T	c.(2869-2871)Cgg>Tgg	p.R957W	ZEB2_ENST00000409487.3_Missense_Mutation_p.R957W|ZEB2_ENST00000539609.3_Missense_Mutation_p.R933W|ZEB2_ENST00000303660.4_Missense_Mutation_p.R957W	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	957					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.R957W(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CCTTGTTTCCGCTGGTACTTT	0.408																																					Melanoma(33;1235 1264 5755 16332)											1	Substitution - Missense(1)	large_intestine(1)	2											90	87	88					2																	145155885		2203	4300	6503	144872355	SO:0001583	missense	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.2869C>T	2.37:g.145155885G>A	ENSP00000454157:p.Arg957Trp		144872355	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.679129	0.47886	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487	T;T;T	0.14766	2.48;2.48;2.48	5.83	3.98	0.46160	.	0.000000	0.85682	D	0.000000	T	0.33702	0.0872	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.978;0.99;0.99;0.99	T	0.06092	-1.0846	10	0.87932	D	0	-6.4187	15.2553	0.73579	0.0:0.0:0.7445:0.2555	.	933;822;956;957	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	W	933;957;957	ENSP00000443792:R933W;ENSP00000302501:R957W;ENSP00000386854:R957W	ENSP00000302501:R957W	R	-	1	2	ZEB2	144872355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.825000	0.62708	0.756000	0.33013	0.563000	0.77884	CGG		0.408	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145155885	G	A	145155885	3	1	67	1	0	0	0	0	1	0	0	0	17663	1086	38	1	787	1	ZEB2	2	145155885	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	59576959	145155885	98043488	14	20770										
LRP2	4036	broad.mit.edu	37	chr2	170063145	170063145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cacattttggggtgtgcaatCcaggcagagcaaagcagaga	13	8	0	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:170063145C>T	ENST00000263816.3	-	39	7370	c.7085G>A	c.(7084-7086)gGa>gAa	p.G2362E		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2362	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.G2362E(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGTGTGCAATCCAGGCAGAGC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											72	66	68					2																	170063145		2203	4300	6503	169771391	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.7085G>A	2.37:g.170063145C>T	ENSP00000263816:p.Gly2362Glu		169771391	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	8.408	0.843470	0.16963	.	.	ENSG00000081479	ENST00000263816	D	0.95482	-3.72	6.07	0.456	0.16655	Epidermal growth factor-like (1);	0.506284	0.23551	N	0.046971	D	0.89210	0.6650	L	0.47078	1.49	0.58432	D	0.999997	B	0.10296	0.003	B	0.08055	0.003	T	0.76310	-0.3006	10	0.02654	T	1	.	6.4822	0.22069	0.0:0.3959:0.123:0.481	.	2362	P98164	LRP2_HUMAN	E	2362	ENSP00000263816:G2362E	ENSP00000263816:G2362E	G	-	2	0	LRP2	169771391	0.672000	0.27530	0.294000	0.24946	0.584000	0.36387	1.302000	0.33459	-0.198000	0.10333	0.655000	0.94253	GGA		0.488	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170063145	C	T	170063145	3	4	67	1	0	0	0	0	1	0	0	0	8985	855	30	3	7046	3	LRP2	2	170063145	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	24907260	170063145	73136228	15	20771										
PLCL1	5334	broad.mit.edu	37	chr2	198949476	198949476	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tcactactatatcaatgcctCtcataacacctatctaatag	2	12	4	0	rs374856574		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:198949476C>T	ENST00000428675.1	+	2	1633	c.1235C>T	c.(1234-1236)tCt>tTt	p.S412F	PLCL1_ENST00000437704.2_Missense_Mutation_p.S314F	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	412	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S314F(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	ATCAATGCCTCTCATAACACC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	PHE/SER	0,4406		0,0,2203	87	87	87		1235	5.9	1	2		87	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLCL1	NM_006226.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	412/1096	198949476	1,13005	2203	4300	6503	198657721	SO:0001583	missense	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1235C>T	2.37:g.198949476C>T	ENSP00000402861:p.Ser412Phe		198657721	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	C	18.71	3.682740	0.68157	0.0	1.16E-4	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.64618	-0.11;-0.11	5.94	5.94	0.96194	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.64402	D	0.000004	D	0.88119	0.6351	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91620	0.5310	9	.	.	.	.	20.3633	0.98874	0.0:1.0:0.0:0.0	.	412;338	Q15111;B4DYZ4	PLCL1_HUMAN;.	F	412;314	ENSP00000402861:S412F;ENSP00000414138:S314F	.	S	+	2	0	PLCL1	198657721	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.808000	0.86044	2.826000	0.97356	0.561000	0.74099	TCT		0.418	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		T	198949476	C	T	198949476	3	4	67	1	0	0	0	0	1	0	0	0	12070	913	32	3	1241	3	PLCL1	2	198949476	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	28886331	198949476	44249897	16	20772										
ACADL	33	broad.mit.edu	37	chr2	211069375	211069375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtagggcactagctggcaacCgtatatcttcaaagaatagt	10	8	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr2:211069375C>T	ENST00000233710.3	-	7	1027	c.800G>A	c.(799-801)cGg>cAg	p.R267Q	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	267					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)	p.R267Q(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AGCTGGCAACCGTATATCTTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	125	125					2																	211069375		2203	4300	6503	210777620	SO:0001583	missense	33			M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.800G>A	2.37:g.211069375C>T	ENSP00000233710:p.Arg267Gln		210777620	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737705	0.69304	.	.	ENSG00000115361	ENST00000233710	D	0.99259	-5.64	5.22	4.35	0.52113	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.056311	0.64402	D	0.000001	D	0.99202	0.9723	M	0.83953	2.67	0.48632	D	0.999688	D	0.63880	0.993	P	0.58454	0.839	D	0.98869	1.0765	10	0.72032	D	0.01	.	13.8394	0.63430	0.0:0.9258:0.0:0.0742	.	267	P28330	ACADL_HUMAN	Q	267	ENSP00000233710:R267Q	ENSP00000233710:R267Q	R	-	2	0	ACADL	210777620	1.000000	0.71417	0.968000	0.41197	0.938000	0.57974	5.735000	0.68587	1.215000	0.43411	0.579000	0.79373	CGG		0.373	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		T	211069375	C	T	211069375	3	4	67	1	0	0	0	0	1	0	0	0	112	652	23	1	512	1	ACADL	2	211069375	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	12119899	211069375	32129998	17	20773										
CAMKV	79012	broad.mit.edu	37	chr3	49898884	49898885	+	Frame_Shift_Ins	INS	-	-	A													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccctcaccttgagattcctgINStgcacgatcttgagtgagtg							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:49898884_49898885insA	ENST00000477224.1	-	5	906_907	c.428_429insT	c.(427-429)cacfs	p.H143fs	CAMKV_ENST00000463537.1_Frame_Shift_Ins_p.H143fs|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000498324.1_5'Flank|CAMKV_ENST00000488336.1_Frame_Shift_Ins_p.H143fs|CAMKV_ENST00000296471.7_Frame_Shift_Ins_p.H143fs|CAMKV_ENST00000466940.1_Intron|CAMKV_ENST00000467248.1_Frame_Shift_Ins_p.H68fs			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.R144fs*23(1)		central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TGAGATTCCTGTGCACGATCTT	0.604																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								49873889	SO:0001589	frameshift_variant	79012			BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.428_429insT	3.37:g.49898884_49898885insA	ENSP00000419195:p.His143fs		49873888	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Frame_Shift_Ins	INS	ENST00000477224.1	37	CCDS33762.1																																																																																				0.604	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046		A	49898885	-	A	49898884	7	5	67	1	0	1	1	0	0	0	0	0	2614	1368	48	0	1104	0	CAMKV	3	49898884	Frame_Shift_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09		49898884	148123546	18	20774	26	2								
CAMKV	79012	broad.mit.edu	37	chr3	49898887	49898887	+	Frame_Shift_Del	DEL	C	C	-													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctcaccttgagattcctgtgCacgatcttgagtgagtgcaa							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:49898887delC	ENST00000477224.1	-	5	904	c.426delG	c.(424-426)gtgfs	p.V142fs	CAMKV_ENST00000463537.1_Frame_Shift_Del_p.V142fs|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000498324.1_5'Flank|CAMKV_ENST00000488336.1_Frame_Shift_Del_p.V142fs|CAMKV_ENST00000296471.7_Frame_Shift_Del_p.V142fs|CAMKV_ENST00000466940.1_Intron|CAMKV_ENST00000467248.1_Frame_Shift_Del_p.V67fs			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	142	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.H143fs*15(1)		central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GATTCCTGTGCACGATCTTGA	0.602																																																1	Deletion - Frameshift(1)	large_intestine(1)	3											76	69	71					3																	49898887		2203	4300	6503	49873891	SO:0001589	frameshift_variant	79012			BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.426delG	3.37:g.49898887delC	ENSP00000419195:p.Val142fs		49873891	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Frame_Shift_Del	DEL	ENST00000477224.1	37	CCDS33762.1																																																																																				0.602	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046		-	49898887	C	-	49898887	7	5	67	1	0	1	0	1	0	0	0	0	2614	697	25	0	1107	0	CAMKV	3	49898887	Frame_Shift_Del	DEL	C	TCGA-AG-A014-01A-02W-A00K-09	3	49898887	148123543	19	20775	26	2								
ITIH3	3699	broad.mit.edu	37	chr3	52840399	52840399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agccccaggcacagtgctgcGccttattcaggatgcagtca	11	13	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:52840399G>A	ENST00000449956.2	+	18	2039	c.2033G>A	c.(2032-2034)cGc>cAc	p.R678H	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	678					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R678H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		ACAGTGCTGCGCCTTATTCAG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	3											44	44	44					3																	52840399		1954	4137	6091	52815439	SO:0001583	missense	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.2033G>A	3.37:g.52840399G>A	ENSP00000415769:p.Arg678His		52815439	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.679546	0.47886	.	.	ENSG00000162267	ENST00000273291;ENST00000449956	T	0.01705	4.68	5.38	4.27	0.50696	.	0.337826	0.33496	N	0.004854	T	0.03011	0.0089	M	0.74881	2.28	0.29739	N	0.837221	P	0.48016	0.904	B	0.37650	0.255	T	0.16988	-1.0384	10	0.52906	T	0.07	-10.1344	11.5428	0.50675	0.1232:0.0:0.8768:0.0	.	678	Q06033	ITIH3_HUMAN	H	673;678	ENSP00000415769:R678H	ENSP00000273291:R673H	R	+	2	0	ITIH3	52815439	0.786000	0.28738	1.000000	0.80357	0.106000	0.19336	1.342000	0.33919	2.692000	0.91855	0.561000	0.74099	CGC		0.612	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		A	52840399	G	A	52840399	3	1	67	1	0	0	0	0	1	0	0	0	7926	1087	38	1	2103	1	ITIH3	3	52840399	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	2941512	52840399	145182031	20	20776										
CPOX	1371	broad.mit.edu	37	chr3	98304422	98304422	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cgaaacacctcctccttggaCggagagtcaagatcatcaaa	8	12	3	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:98304422C>T	ENST00000264193.2	-	5	1253	c.1035G>A	c.(1033-1035)ccG>ccA	p.P345P		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	345					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)	p.P345P(1)		endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CCTCCTTGGACGGAGAGTCAA	0.493																																					Esophageal Squamous(75;7 1223 22300 43648 48951)											1	Substitution - coding silent(1)	large_intestine(1)	3											130	137	134					3																	98304422		2203	4300	6503	99787112	SO:0001819	synonymous_variant	1371			BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"coproporphyria"	612732	"coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.1035G>A	3.37:g.98304422C>T			99787112	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Silent	SNP	ENST00000264193.2	37	CCDS2932.1																																																																																				0.493	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097		T	98304422	C	T	98304422	2	4	67	1	0	0	0	0	0	0	0	1	3827	523	19	1		1	CPOX	3	98304422	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	45464023	98304422	99718008	21	20777										
PPP2R3A	5523	broad.mit.edu	37	chr3	135720430	135720431	+	Frame_Shift_Ins	INS	-	-	TG													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ttgaacaagctatacattatINStgcactggaacctgccacac							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-	-	TG	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:135720430_135720431insTG	ENST00000264977.3	+	2	707_708	c.90_91insTG	c.(91-93)tgcfs	p.C31fs	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	31					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)	p.T32fs*38(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CTATACATTATTGCACTGGAAC	0.45																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								137203121	SO:0001589	frameshift_variant	5523			L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.91_92dupTG	3.37:g.135720431_135720432dupTG	ENSP00000264977:p.Cys31fs		137203120	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Frame_Shift_Ins	INS	ENST00000264977.3	37	CCDS3087.1																																																																																				0.45	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		TG	135720431	-	TG	135720430	7	5	67	1	0	1	1	0	0	0	0	0	12422	1500	52	0	92	0	PPP2R3A	3	135720430	Frame_Shift_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09	37416008	135720430	62302000	22	20778										
DVL3	1857	broad.mit.edu	37	chr3	183884308	183884308	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cgggagattgtgcacaaaccGgggtatggatggaatggggc	18	6	0	1	rs186597752		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr3:183884308G>A	ENST00000313143.3	+	9	1226	c.978G>A	c.(976-978)ccG>ccA	p.P326P	EIF2B5_ENST00000444495.1_Intron|DVL3_ENST00000431765.1_Silent_p.P326P	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	326					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)	p.P326P(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			TGCACAAACCGGGGTATGGAT	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	3											145	145	145					3																	183884308		2203	4300	6503	185367002	SO:0001819	synonymous_variant	1857			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.978G>A	3.37:g.183884308G>A			185367002	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Silent	SNP	ENST00000313143.3	37	CCDS3253.1																																																																																				0.537	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		A	183884308	G	A	183884308	2	1	67	1	0	0	0	0	0	0	0	1	4848	1103	39	1		1	DVL3	3	183884308	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	48163878	183884308	14138122	23	20779										
NFXL1	152518	broad.mit.edu	37	chr4	47892713	47892713	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cacaaggtggacagtttccaGggcaacactgaagagaaagc	12	9	0	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr4:47892713G>T	ENST00000507489.1	-	12	1636	c.1460C>A	c.(1459-1461)cCt>cAt	p.P487H	NFXL1_ENST00000381538.3_Missense_Mutation_p.P487H|NFXL1_ENST00000329043.3_Missense_Mutation_p.P487H	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	487						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P487H(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						ACAGTTTCCAGGGCAACACTG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											85	79	81					4																	47892713		2203	4300	6503	47587470	SO:0001583	missense	152518			AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.1460C>A	4.37:g.47892713G>T	ENSP00000422037:p.Pro487His		47587470	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	37	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286782	0.80803	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.53423	0.62;0.62;0.62	5.26	5.26	0.73747	Zinc finger, NF-X1-type (1);	0.000000	0.85682	D	0.000000	T	0.69886	0.3161	M	0.88241	2.94	0.80722	D	1	D	0.63046	0.992	P	0.55785	0.784	T	0.76900	-0.2788	10	0.62326	D	0.03	-12.6511	18.8593	0.92266	0.0:0.0:1.0:0.0	.	487	Q6ZNB6	NFXL1_HUMAN	H	487	ENSP00000370949:P487H;ENSP00000422037:P487H;ENSP00000333113:P487H	ENSP00000333113:P487H	P	-	2	0	NFXL1	47587470	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.390000	0.97246	2.471000	0.83476	0.650000	0.86243	CCT		0.368	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		T	47892713	G	T	47892713	3	4	67	1	0	0	0	0	1	0	0	0	10419	1000	35	2	1323	2	NFXL1	4	47892713	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		47892713	143261563	24	20780										
SGCB	6443	broad.mit.edu	37	chr4	52899701	52899701	+	Frame_Shift_Del	DEL	T	T	-													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtggagacgatcttcatcaaTcggaatgtatccagctttaa							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr4:52899701delT	ENST00000381431.5	-	2	361	c.139delA	c.(139-141)attfs	p.I47fs	SGCB_ENST00000535450.1_Intron	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	47					cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.I47fs*11(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TCTTCATCAATCGGAATGTAT	0.418																																																1	Deletion - Frameshift(1)	large_intestine(1)	4											207	183	191					4																	52899701		2203	4300	6503	52594458	SO:0001589	frameshift_variant	6443			U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.139delA	4.37:g.52899701delT	ENSP00000370839:p.Ile47fs		52594458	B7Z635|O00661	Frame_Shift_Del	DEL	ENST00000381431.5	37	CCDS3488.1																																																																																				0.418	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			-	52899701	T	-	52899701	7	5	67	1	0	1	0	1	0	0	0	0	14237	1435	50	0	837	0	SGCB	4	52899701	Frame_Shift_Del	DEL	T	TCGA-AG-A014-01A-02W-A00K-09	5006988	52899701	138254575	25	20781			1	10		2	2	19	N	TAAA_T	7.093525e-05
SGCB	6443	broad.mit.edu	37	chr4	52899719	52899722	+	Frame_Shift_Del	DEL	TAAA	TAAA	-													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aatcggaatgtatccagcttTaaagttactgttgtgctctt							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	TAAA	TAAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr4:52899719_52899722delTAAA	ENST00000381431.5	-	2	340_343	c.118_121delTTTA	c.(118-123)tttaaafs	p.FK40fs	SGCB_ENST00000535450.1_Intron	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	40					cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.F40fs*17(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TATCCAGCTTTAAAGTTACTGTTG	0.397																																																1	Deletion - Frameshift(1)	large_intestine(1)	4																																								52594479	SO:0001589	frameshift_variant	6443			U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.118_121delTTTA	4.37:g.52899719_52899722delTAAA	ENSP00000370839:p.Phe40fs		52594476	B7Z635|O00661	Frame_Shift_Del	DEL	ENST00000381431.5	37	CCDS3488.1																																																																																				0.397	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			-	52899722	TAAA	-	52899719	7	5	67	1	0	1	0	1	0	0	0	0	14237	1763	61	0	855	0	SGCB	4	52899719	Frame_Shift_Del	DEL	TAAA	TCGA-AG-A014-01A-02W-A00K-09	18	52899719	138254557	26	20782			1	10		2	2	19	N	TAAA_T	7.093525e-05
GRIA2	2891	broad.mit.edu	37	chr4	158281128	158281128	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtgtttgtgaggactacggcCgaaggggtggctagagtgcg	19	6	0	2	rs143272523		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr4:158281128C>T	ENST00000264426.9	+	13	2403	c.2124C>T	c.(2122-2124)gcC>gcT	p.A708A	GRIA2_ENST00000393815.2_Silent_p.A661A|GRIA2_ENST00000449365.1_Silent_p.A661A|GRIA2_ENST00000507898.1_Silent_p.A661A|GRIA2_ENST00000296526.7_Silent_p.A708A|AC079233.1_ENST00000578227.1_RNA	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	708					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.A708A(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGACTACGGCCGAAGGGGTGG	0.502													C|||	1	0.000199681	0	0	5008	,	,		17949	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4						C	,,	0,4406		0,0,2203	108	106	107		2124,2124,1983	-10.2	0.3	4	dbSNP_134	107	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIA2	NM_000826.3,NM_001083619.1,NM_001083620.1	,,	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	,,	708/884,708/884,661/837	158281128	4,13002	2203	4300	6503	158500578	SO:0001819	synonymous_variant	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2124C>T	4.37:g.158281128C>T			158500578	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	37	CCDS43274.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	2.571	-0.299619	0.05532	0.0	4.65E-4	ENSG00000120251	ENST00000510854	.	.	.	5.69	-10.2	0.00374	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.7617	0.13111	0.3113:0.0969:0.0672:0.5246	.	.	.	.	X	39	.	.	R	+	1	2	GRIA2	158500578	0.000000	0.05858	0.316000	0.25252	0.978000	0.69477	-4.652000	0.00203	-1.729000	0.01364	-0.345000	0.07892	CGA		0.502	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			T	158281128	C	T	158281128	2	4	67	1	0	0	0	0	0	0	0	1	6789	639	23	1		1	GRIA2	4	158281128	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	105381409	158281128	32873148	27	20783										
C4orf41	60684	broad.mit.edu	37	chr4	184615782	184615782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aaaaatgttgtatgttcgctGtggaacagtgggttccagaa	12	5	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr4:184615782G>A	ENST00000334690.6	+	23	2736	c.2534G>A	c.(2533-2535)tGt>tAt	p.C845Y	TRAPPC11_ENST00000512476.1_Missense_Mutation_p.C451Y|TRAPPC11_ENST00000357207.4_Missense_Mutation_p.C845Y	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	845					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.C845Y(1)									TATGTTCGCTGTGGAACAGTG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	62	62					4																	184615782		2203	4294	6497	184852776	SO:0001583	missense	60684				CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"Trafficking protein particle complex"	25751	protein-coding gene	gene with protein product	"gryzun homolog (Drosophila)", "foie gras homolog (zebrafish)"	614138	"chromosome 4 open reading frame 41"	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.2534G>A	4.37:g.184615782G>A	ENSP00000335371:p.Cys845Tyr		184852776	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.319429	0.81469	.	.	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109;ENST00000512476	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.73946	0.3652	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.997	D;D;D;D	0.91635	0.989;0.999;0.983;0.994	T	0.67094	-0.5757	9	0.02654	T	1	.	19.1299	0.93400	0.0:0.0:1.0:0.0	.	576;451;845;845	B3KR79;D6RHE5;Q7Z392;Q7Z392-3	.;.;TPC11_HUMAN;.	Y	845;845;845;451	.	ENSP00000335371:C845Y	C	+	2	0	C4orf41	184852776	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.263000	0.95617	2.753000	0.94483	0.467000	0.42956	TGT		0.299	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942		A	184615782	G	A	184615782	3	1	67	1	0	0	0	0	1	0	0	0	2276	1377	48	3	2620	3	C4orf41	4	184615782	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	26334654	184615782	6538494	28	20784										
ADCY2	108	broad.mit.edu	37	chr5	7709437	7709438	+	Missense_Mutation	DNP	GC	GC	AA													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gagtcctggggggcagccaaGccctttgcacacctacatca							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:7709437_7709438GC>AA	ENST00000338316.4	+	10	1604_1605	c.1515_1516GC>AA	c.(1513-1518)aaGCcc>aaAAcc	p.P506T	ADCY2_ENST00000537121.1_Missense_Mutation_p.P326T|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	506					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.K505>?(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GGGCAGCCAAGCCCTTTGCACA	0.614																																																1	Complex(1)	large_intestine(1)	5																																								7762438	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	Exception_encountered	5.37:g.7709437_7709438delinsAA	ENSP00000342952:p.Pro506Thr		7762437	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	DNP	ENST00000338316.4	37	CCDS3872.2																																																																																				0.614	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		AA	7709438	GC	AA	7709437	3	1	67	1	0	0	0	0	1	0	0	0	294	962	34	3	1553	3	ADCY2	5	7709437	Missense_Mutation	DNP	GC	TCGA-AG-A014-01A-02W-A00K-09		7709437	173205823	29	20785										
DNAH5	1767	broad.mit.edu	37	chr5	13885213	13885213	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ttgaaatgagagagtaactcGcgggcttcttcccctaacat	9	10	1	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:13885213G>A	ENST00000265104.4	-	19	2972	c.2868C>T	c.(2866-2868)cgC>cgT	p.R956R	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	956	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R956R(2)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAGTAACTCGCGGGCTTCTT	0.443									Kartagener syndrome																																							2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	5											126	120	122					5																	13885213		2203	4300	6503	13938213	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2868C>T	5.37:g.13885213G>A			13938213	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13885213	G	A	13885213	2	1	67	1	0	0	0	0	0	0	0	1	4615	1074	38	1		1	DNAH5	5	13885213	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	6175776	13885213	167030047	30	20786										
ADAMTS12	81792	broad.mit.edu	37	chr5	33648973	33648973	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgggtccatattgtagctggCactggtggtgaacatcatag	13	7	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:33648973C>A	ENST00000504830.1	-	9	1768	c.1433G>T	c.(1432-1434)tGc>tTc	p.C478F	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.C478F	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	478	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.C478F(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TTGTAGCTGGCACTGGTGGTG	0.498										HNSCC(64;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	5											152	145	147					5																	33648973		2203	4300	6503	33684730	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1433G>T	5.37:g.33648973C>A	ENSP00000422554:p.Cys478Phe		33684730	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.679955	0.88542	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.09817	2.94;2.94	5.6	5.6	0.85130	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48943	0.1528	H	0.95294	3.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.64394	-0.6418	10	0.87932	D	0	.	19.6116	0.95608	0.0:1.0:0.0:0.0	.	478;478	P58397-3;P58397	.;ATS12_HUMAN	F	478	ENSP00000422554:C478F;ENSP00000344847:C478F	ENSP00000344847:C478F	C	-	2	0	ADAMTS12	33684730	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.629000	0.83207	2.641000	0.89580	0.549000	0.68633	TGC		0.498	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33648973	C	A	33648973	3	1	67	1	0	0	0	0	1	0	0	0	257	710	25	2	3415	2	ADAMTS12	5	33648973	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	19763760	33648973	147266287	31	20787										
RGMB	285704	broad.mit.edu	37	chr5	98129379	98129380	+	Frame_Shift_Ins	INS	-	-	A													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acattttccccagcagtggcINSaatgggactccccgtggagg							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:98129379_98129380insA	ENST00000513185.1	+	3	1672_1673	c.1236_1237insA	c.(1237-1239)aatfs	p.N413fs	RGMB_ENST00000308234.7_Frame_Shift_Ins_p.N454fs			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	413					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)	p.N454fs*9(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		CCAGCAGTGGCAATGGGACTCC	0.53																																																1	Insertion - Frameshift(1)	large_intestine(1)	5																																								98157280	SO:0001589	frameshift_variant	285704			AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.1238dupA	5.37:g.98129381_98129381dupA	ENSP00000423256:p.Asn413fs		98157279	D6R9A0|Q8NC92	Frame_Shift_Ins	INS	ENST00000513185.1	37																																																																																					0.53	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		A	98129380	-	A	98129379	7	5	67	1	0	1	1	0	0	0	0	0	13318	697	25	0	1373	0	RGMB	5	98129379	Frame_Shift_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09	64480406	98129379	82785881	32	20788										
SLCO6A1	133482	broad.mit.edu	37	chr5	101709056	101709057	+	Stop_Codon_Ins	INS	-	-	C													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ttacacaatgatgatccagtINStacaagtcagtttcttcttt					rs113965602		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:101709056_101709057insC	ENST00000506729.1	-	0	2330_2331				SLCO6A1_ENST00000379807.3_Stop_Codon_Ins|SLCO6A1_ENST00000379810.1_Stop_Codon_Ins|SLCO6A1_ENST00000389019.3_Stop_Codon_Ins|SLCO6A1_ENST00000513675.1_Stop_Codon_Ins			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.?(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GATGATCCAGTTACAAGTCAGT	0.267																																																1	Unknown(1)	large_intestine(1)	5																																								101736956	SO:0001567	stop_retained_variant	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.2158_2158insG	5.37:g.101709056_101709057insC			101736955	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Ins	INS	ENST00000506729.1	37	CCDS34206.1																																																																																				0.267	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		C	101709057	-	C	101709056	7	5	67	1	0	1	1	0	0	0	0	0	14769	1732	60	0	3	0	SLCO6A1	5	101709056	Stop_Codon_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09	3579677	101709056	79206204	33	20789										
APC	324	broad.mit.edu	37	chr5	112174916	112174916	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctggacaaagcagtaaaaccGaacatatgtcttcaagcagt	8	9	2	0	rs201185479		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:112174916G>T	ENST00000457016.1	+	16	4005	c.3625G>T	c.(3625-3627)Gaa>Taa	p.E1209*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1209*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1209*			P25054	APC_HUMAN	adenomatous polyposis coli	1209	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1209*(3)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGTAAAACCGAACATATGTC	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Substitution - Nonsense(3)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD011096	APC	D							83	83	83					5																	112174916		2202	4300	6502	112202815	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3625G>T	5.37:g.112174916G>T	ENSP00000413133:p.Glu1209*		112202815	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782541	0.90282	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.91	5.91	0.95273	.	0.056678	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.108	15.437	0.75155	0.0681:0.0:0.9319:0.0	.	.	.	.	X	1209	.	.	E	+	1	0	APC	112202815	1.000000	0.71417	0.997000	0.53966	0.068000	0.16541	6.778000	0.75043	2.802000	0.96397	0.655000	0.94253	GAA		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174916	G	T	112174916	4	4	67	1	0	0	0	0	0	1	0	0	763	1059	37	2	3683	2	APC	5	112174916	Nonsense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	10465860	112174916	68740344	34	20790										
CHSY3	337876	broad.mit.edu	37	chr5	129520136	129520136	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aagtgccctgatgagcaagcTcagtaacacagaagtgagca	11	9	1	4			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:129520136T>A	ENST00000305031.4	+	3	1659	c.1301T>A	c.(1300-1302)cTc>cAc	p.L434H	CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	434					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.L434H(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		ATGAGCAAGCTCAGTAACACA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	5											72	66	68					5																	129520136		2203	4300	6503	129548035	SO:0001583	missense	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1301T>A	5.37:g.129520136T>A	ENSP00000302629:p.Leu434His		129548035	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.825669	0.71143	.	.	ENSG00000198108	ENST00000305031	T	0.16897	2.31	4.5	4.5	0.54988	.	0.000000	0.51477	D	0.000084	T	0.30448	0.0765	M	0.69823	2.125	0.53005	D	0.999968	P	0.46784	0.884	P	0.49922	0.626	T	0.03795	-1.1003	9	.	.	.	-2.5329	14.8652	0.70409	0.0:0.0:0.0:1.0	.	434	Q70JA7	CHSS3_HUMAN	H	434	ENSP00000302629:L434H	.	L	+	2	0	CHSY3	129548035	0.997000	0.39634	1.000000	0.80357	0.912000	0.54170	2.400000	0.44504	2.243000	0.73865	0.528000	0.53228	CTC		0.493	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		A	129520136	T	A	129520136	3	1	67	1	0	0	0	0	1	0	0	0	3419	1551	54	5	1311	5	CHSY3	5	129520136	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	17345220	129520136	51395124	35	20791										
PSD2	84249	broad.mit.edu	37	chr5	139197135	139197135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ttctcgggcttgactctggaCggagcactcaggtcagtggg	15	10	4	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:139197135C>T	ENST00000274710.3	+	5	1291	c.1086C>T	c.(1084-1086)gaC>gaT	p.D362D		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	362	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.D362D(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTCTGGACGGAGCACTCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	5											84	79	81					5																	139197135		2203	4300	6503	139177319	SO:0001819	synonymous_variant	84249			AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1086C>T	5.37:g.139197135C>T			139177319	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	37	CCDS4216.1																																																																																				0.542	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139197135	C	T	139197135	2	4	67	1	0	0	0	0	0	0	0	1	12681	535	19	1		1	PSD2	5	139197135	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	9676999	139197135	41718125	36	20792										
JAKMIP2	9832	broad.mit.edu	37	chr5	147023718	147023718	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cttggtcgaggtcattcagaGattttaatttcttcaggggt	11	6	4	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:147023718G>T	ENST00000265272.5	-	7	1594	c.1127C>A	c.(1126-1128)tCt>tAt	p.S376Y	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.S334Y|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.S376Y	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	376						Golgi apparatus (GO:0005794)		p.S376Y(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCATTCAGAGATTTTAATTT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	5											121	117	119					5																	147023718		2203	4300	6503	147003911	SO:0001583	missense	9832			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1127C>A	5.37:g.147023718G>T	ENSP00000265272:p.Ser376Tyr		147003911	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764313	0.89932	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.35973	1.28;1.28;1.29	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.63954	0.2555	M	0.76838	2.35	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;D;D	0.74348	0.983;0.983;0.983;0.983	T	0.66685	-0.5861	10	0.87932	D	0	.	19.7462	0.96252	0.0:0.0:1.0:0.0	.	334;376;376;376	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	Y	376;376;334;376	ENSP00000421398:S376Y;ENSP00000265272:S376Y;ENSP00000328989:S334Y	ENSP00000265272:S376Y	S	-	2	0	JAKMIP2	147003911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.736000	0.93811	0.655000	0.94253	TCT		0.373	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		T	147023718	G	T	147023718	3	4	67	1	0	0	0	0	1	0	0	0	7962	942	33	2	1365	2	JAKMIP2	5	147023718	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	7826583	147023718	33891542	37	20793										
FOXI1	2299	broad.mit.edu	37	chr5	169533176	169533176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	caacgggcccaccatgacccCgccaccctacctgcccggcc	8	23	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:169533176C>T	ENST00000306268.6	+	1	276	c.215C>T	c.(214-216)cCg>cTg	p.P72L	FOXI1_ENST00000449804.2_Missense_Mutation_p.P72L			Q12951	FOXI1_HUMAN	forkhead box I1	72	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.P72L(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCATGACCCCGCCACCCTAC	0.731									Pendred syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											8	8	8					5																	169533176		2169	4252	6421	169465754	SO:0001583	missense	2299	Familial Cancer Database	Goiter-Deafness syndrome	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.215C>T	5.37:g.169533176C>T	ENSP00000304286:p.Pro72Leu		169465754	Q14518|Q66SR7|Q8N6L8	Missense_Mutation	SNP	ENST00000306268.6	37	CCDS4372.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141701	0.57044	.	.	ENSG00000168269	ENST00000306268;ENST00000449804	D;D	0.94931	-3.43;-3.56	5.06	5.06	0.68205	.	0.060050	0.64402	D	0.000002	D	0.93582	0.7951	M	0.72894	2.215	0.80722	D	1	D;D	0.56287	0.975;0.957	B;B	0.40134	0.32;0.17	D	0.94621	0.7813	10	0.72032	D	0.01	.	18.448	0.90693	0.0:1.0:0.0:0.0	.	72;72	Q12951-2;Q12951	.;FOXI1_HUMAN	L	72	ENSP00000304286:P72L;ENSP00000415483:P72L	ENSP00000304286:P72L	P	+	2	0	FOXI1	169465754	0.995000	0.38212	0.898000	0.35279	0.386000	0.30323	5.764000	0.68826	2.353000	0.79882	0.591000	0.81541	CCG		0.731	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		T	169533176	C	T	169533176	3	4	67	1	0	0	0	0	1	0	0	0	6028	652	23	1	217	1	FOXI1	5	169533176	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	22509458	169533176	11382084	38	20794										
KCNIP1	30820	broad.mit.edu	37	chr5	170160888	170160888	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	taactttagatgaatttcttGaatcatgtcaggaggtaagg	10	4	3	3	rs34559363		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:170160888G>T	ENST00000411494.1	+	8	622	c.622G>T	c.(622-624)Gaa>Taa	p.E208*	KCNIP1_ENST00000328939.4_Nonsense_Mutation_p.E197*|KCNIP1_ENST00000377360.4_Nonsense_Mutation_p.E206*|KCNIP1_ENST00000390656.4_Nonsense_Mutation_p.E197*|KCNIP1_ENST00000434108.1_Nonsense_Mutation_p.E222*|KCNIP1_ENST00000520740.1_Nonsense_Mutation_p.E169*			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	208	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)	p.E208*(1)		autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAATTTCTTGAATCATGTCA	0.423																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											111	105	107					5																	170160888		2203	4300	6503	170093466	SO:0001587	stop_gained	30820			AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.622G>T	5.37:g.170160888G>T	ENSP00000395323:p.Glu208*		170093466	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Nonsense_Mutation	SNP	ENST00000411494.1	37	CCDS34286.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.384700	0.82792	.	.	ENSG00000182132	ENST00000377360;ENST00000328939;ENST00000390656;ENST00000520740;ENST00000434108;ENST00000411494	.	.	.	5.66	5.66	0.87406	.	0.180712	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2591	0.87064	0.0:0.0:1.0:0.0	.	.	.	.	X	206;197;197;169;222;208	.	.	E	+	1	0	KCNIP1	170093466	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.209000	0.42806	2.668000	0.90789	0.650000	0.86243	GAA		0.423	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			T	170160888	G	T	170160888	4	4	67	1	0	0	0	0	0	1	0	0	8060	1291	45	2	744	2	KCNIP1	5	170160888	Nonsense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	627712	170160888	10754372	39	20795										
NSD1	64324	broad.mit.edu	37	chr5	176721701	176721701	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcactgaggcctgtggaccaGaatactcagtcaaaaaatag	10	9	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr5:176721701G>A	ENST00000439151.2	+	23	7377	c.7332G>A	c.(7330-7332)caG>caA	p.Q2444Q	NSD1_ENST00000361032.4_Silent_p.Q2341Q|NSD1_ENST00000354179.4_Silent_p.Q2175Q|NSD1_ENST00000347982.4_Silent_p.Q2175Q	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2444					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.Q2444Q(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	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)		CTGTGGACCAGAATACTCAGT	0.502			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Substitution - coding silent(2)	large_intestine(2)	5											51	55	54					5																	176721701		2203	4300	6503	176654307	SO:0001819	synonymous_variant	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7332G>A	5.37:g.176721701G>A			176654307	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																				0.502	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176721701	G	A	176721701	2	1	67	1	0	0	0	0	0	0	0	1	10700	933	33	3		3	NSD1	5	176721701	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	6560813	176721701	4193559	40	20796										
JARID2	3720	broad.mit.edu	37	chr6	15504789	15504789	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gaggaatatcatgagcatgtGtttcagcaaggagcctgccc	12	9	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:15504789G>C	ENST00000341776.2	+	9	2751	c.2507G>C	c.(2506-2508)tGt>tCt	p.C836S	JARID2_ENST00000474854.1_3'UTR|JARID2_ENST00000397311.3_Missense_Mutation_p.C664S|JARID2_ENST00000541660.1_Missense_Mutation_p.C798S	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	836					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.C836S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ATGAGCATGTGTTTCAGCAAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	6											72	76	75					6																	15504789		2203	4300	6503	15612768	SO:0001583	missense	3720			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2507G>C	6.37:g.15504789G>C	ENSP00000341280:p.Cys836Ser		15612768	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787195	0.70337	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	D;D;D	0.89270	-1.84;-1.84;-2.49	5.24	5.24	0.73138	.	0.043082	0.85682	D	0.000000	D	0.90542	0.7036	L	0.44542	1.39	0.53005	D	0.999969	D;D	0.67145	0.996;0.993	D;P	0.62955	0.909;0.813	D	0.91561	0.5264	10	0.72032	D	0.01	-9.9036	18.8078	0.92045	0.0:0.0:1.0:0.0	.	798;836	F5H590;Q92833	.;JARD2_HUMAN	S	836;664;798	ENSP00000341280:C836S;ENSP00000380478:C664S;ENSP00000444623:C798S	ENSP00000341280:C836S	C	+	2	0	JARID2	15612768	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.605000	0.74155	2.435000	0.82474	0.561000	0.74099	TGT		0.502	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		C	15504789	G	C	15504789	3	2	67	1	0	0	0	0	1	0	0	0	7966	1377	48	5	2541	5	JARID2	6	15504789	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		15504789	155610278	41	20797										
PHF1	5252	broad.mit.edu	37	chr6	33383799	33383799	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtcccgaggggaccctgtccGggtccttgctcggagagtac	15	13	0	1	rs147032936		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:33383799G>A	ENST00000374516.3	+	15	1899	c.1628G>A	c.(1627-1629)cGg>cAg	p.R543Q	PHF1_ENST00000374512.3_3'UTR|CUTA_ENST00000492510.1_5'Flank	NM_024165.2	NP_077084.1	O43189	PHF1_HUMAN	PHD finger protein 1	543					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of histone H3-K27 methylation (GO:0061087)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R543Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19		Ovarian(999;0.0443)				GACCCTGTCCGGGTCCTTGCT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	,GLN/ARG	0,4406		0,0,2203	86	86	86		,1628	4.5	1	6	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	utr-3,missense	PHF1	NM_002636.4,NM_024165.2	,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,possibly-damaging	,543/568	33383799	1,13005	2203	4300	6503	33491777	SO:0001583	missense	5252			AF029678	CCDS4777.1, CCDS4778.1	6p21.3	2013-01-28			ENSG00000112511	ENSG00000112511		"Tudor domain containing", "Zinc fingers, PHD-type"	8919	protein-coding gene	gene with protein product	"tudor domain containing 19C"	602881				9545646, 18385154	Standard	NM_024165		Approved	MTF2L2, TDRD19C	uc003oeh.3	O43189	OTTHUMG00000031105	ENST00000374516.3:c.1628G>A	6.37:g.33383799G>A	ENSP00000363640:p.Arg543Gln		33491777	B1AZX2|B1AZX3|O60929|Q5SU07|Q5SU08|Q96KM7	Missense_Mutation	SNP	ENST00000374516.3	37	CCDS4777.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191936	0.78902	0.0	1.16E-4	ENSG00000112511	ENST00000374516;ENST00000427826	T	0.24538	1.85	4.54	4.54	0.55810	.	0.000000	0.56097	D	0.000034	T	0.26666	0.0652	L	0.34521	1.04	0.46749	D	0.999181	D	0.71674	0.998	D	0.76575	0.988	T	0.01460	-1.1349	9	.	.	.	-13.2601	12.6788	0.56910	0.0:0.0:1.0:0.0	.	543	O43189	PHF1_HUMAN	Q	543;157	ENSP00000363640:R543Q	.	R	+	2	0	PHF1	33491777	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	2.973000	0.49264	2.365000	0.80145	0.655000	0.94253	CGG		0.647	PHF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076175.3			A	33383799	G	A	33383799	3	1	67	1	0	0	0	0	1	0	0	0	11851	1116	39	1	1682	1	PHF1	6	33383799	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	17879010	33383799	137731268	42	20798										
GPR111	222611	broad.mit.edu	37	chr6	47649059	47649059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aagcatctccaactggacttTcattcctgacagaaacagca	6	12	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:47649059T>C	ENST00000296862.1	+	6	764	c.764T>C	c.(763-765)tTc>tCc	p.F255S	GPR111_ENST00000507065.1_Missense_Mutation_p.F187S|GPR111_ENST00000398742.2_Missense_Mutation_p.F187S			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	255					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F187S(1)|p.F255S(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						AACTGGACTTTCATTCCTGAC	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	6											93	88	89					6																	47649059		1979	4171	6150	47757018	SO:0001583	missense	222611			AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"-", "GPCR / Class B : Orphans"	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.764T>C	6.37:g.47649059T>C	ENSP00000296862:p.Phe255Ser		47757018	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		.	.	.	.	.	.	.	.	.	.	T	18.40	3.615588	0.66672	.	.	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.23147	1.92;1.92;1.92	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000006	T	0.32763	0.0840	M	0.78637	2.42	0.31863	N	0.620724	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.991	T	0.33599	-0.9862	10	0.07644	T	0.81	.	14.2669	0.66123	0.0:0.0:0.0:1.0	.	187;255	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	S	187;255;187	ENSP00000422934:F187S;ENSP00000296862:F255S;ENSP00000381727:F187S	ENSP00000296862:F255S	F	+	2	0	GPR111	47757018	0.361000	0.24972	1.000000	0.80357	0.956000	0.61745	1.429000	0.34903	1.981000	0.57761	0.524000	0.50904	TTC		0.423	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839		C	47649059	T	C	47649059	3	2	67	1	0	0	0	0	1	0	0	0	6648	1783	62	4	578	4	GPR111	6	47649059	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	14265260	47649059	123466008	43	20799										
DST	667	broad.mit.edu	37	chr6	56327936	56327936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccatggtttaccataattgcGtgttaaaggatggagaatct	10	6	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:56327936G>A	ENST00000244364.6	-	82	15244	c.15037C>T	c.(15037-15039)Cgc>Tgc	p.R5013C	DST_ENST00000421834.2_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000312431.6_3'UTR	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	7442					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R5013C(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CCATAATTGCGTGTTAAAGGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	6											163	149	153					6																	56327936		1898	4124	6022	56435895	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000244364.6:c.15037C>T	6.37:g.56327936G>A	ENSP00000244364:p.Arg5013Cys		56435895	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000244364.6	37	CCDS47443.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236336	0.58886	.	.	ENSG00000151914	ENST00000244364	T	0.52983	0.64	5.79	5.79	0.91817	.	.	.	.	.	T	0.59074	0.2167	L	0.48642	1.525	0.19300	N	0.99998	D;D	0.89917	0.963;1.0	B;D	0.78314	0.36;0.991	T	0.60439	-0.7263	8	0.87932	D	0	.	20.0417	0.97594	0.0:0.0:1.0:0.0	.	5013;100	Q03001-8;Q86T18	.;.	C	5013	ENSP00000244364:R5013C	ENSP00000244364:R5013C	R	-	1	0	DST	56435895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.736000	0.93811	0.655000	0.94253	CGC		0.388	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723		A	56327936	G	A	56327936	3	1	67	1	0	0	0	0	1	0	0	0	4794	1145	40	1	490	1	DST	6	56327936	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	8678877	56327936	114787131	44	20800										
PGM3	23033	broad.mit.edu	37	chr6	83878990	83878990	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcctttctccaattcctccaGccagctgaaatactgccaag	6	15	1	1	rs541410808		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:83878990G>T	ENST00000349129.2	+	0	8210				PGM3_ENST00000513973.1_Missense_Mutation_p.A531D|PGM3_ENST00000506587.1_Missense_Mutation_p.A559D|DOPEY1_ENST00000484282.1_Intron|PGM3_ENST00000512866.1_Missense_Mutation_p.A531D|PGM3_ENST00000283977.4_Missense_Mutation_p.A450D	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1						protein transport (GO:0015031)			p.A531D(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AATTCCTCCAGCCAGCTGAAA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	6											65	62	63					6																	83878990		2203	4300	6503	83935709	SO:0001628	intergenic_variant	5238			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365		6.37:g.83878990G>T			83935709	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915627	0.92178	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.71151	0.3306	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77795	-0.2454	10	0.62326	D	0.03	-49.9041	19.2576	0.93952	0.0:0.0:1.0:0.0	.	559;531	E9PF86;O95394	.;AGM1_HUMAN	D	531;531;450;559	ENSP00000424874:A531D;ENSP00000421565:A531D;ENSP00000283977:A450D;ENSP00000425809:A559D	ENSP00000283977:A450D	A	-	2	0	PGM3	83935709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.273000	0.89887	2.789000	0.95967	0.655000	0.94253	GCT		0.383	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83878990	G	T	83878990	1	4	67	0	1	0	0	0	0	0	0	0	11831	971	34	2		2	PGM3	6	83878990	IGR	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	27551054	83878990	87236077	45	20801										
HTR1E	3354	broad.mit.edu	37	chr6	87725488	87725488	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccgcgctgatgatccttaccGtctggaccatctccattttc	7	15	2	2	rs200719637		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:87725488G>A	ENST00000305344.5	+	2	1139	c.436G>A	c.(436-438)Gtc>Atc	p.V146I		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	146					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.V146I(2)		breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	GATCCTTACCGTCTGGACCAT	0.582																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6											108	94	99					6																	87725488		2203	4300	6503	87782207	SO:0001583	missense	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.436G>A	6.37:g.87725488G>A	ENSP00000307766:p.Val146Ile		87782207	E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	37	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.640966	0.67244	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.73152	-0.72;-0.72	4.26	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	U	0.000069	T	0.78477	0.4289	M	0.69358	2.11	0.44834	D	0.997845	D	0.76494	0.999	D	0.68483	0.958	T	0.82133	-0.0608	10	0.72032	D	0.01	.	16.6564	0.85229	0.0:0.0:1.0:0.0	.	146	P28566	5HT1E_HUMAN	I	146	ENSP00000307766:V146I;ENSP00000358597:V146I	ENSP00000307766:V146I	V	+	1	0	HTR1E	87782207	1.000000	0.71417	0.986000	0.45419	0.941000	0.58515	7.241000	0.78201	1.929000	0.55896	0.404000	0.27445	GTC		0.582	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		A	87725488	G	A	87725488	3	1	67	1	0	0	0	0	1	0	0	0	7460	1145	40	1	438	1	HTR1E	6	87725488	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	3846498	87725488	83389579	46	20802										
ZNF292	23036	broad.mit.edu	37	chr6	87970724	87970724	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acgtgtgtatcagagagcaaTgataattcaagaacaacagc	9	7	2	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr6:87970724T>G	ENST00000369577.3	+	8	7420	c.7377T>G	c.(7375-7377)aaT>aaG	p.N2459K	ZNF292_ENST00000339907.4_Missense_Mutation_p.N2454K	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2459						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.N2314K(1)|p.N2459K(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CAGAGAGCAATGATAATTCAA	0.333																																																2	Substitution - Missense(2)	large_intestine(2)	6											33	30	31					6																	87970724		1886	4109	5995	88027443	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.7377T>G	6.37:g.87970724T>G	ENSP00000358590:p.Asn2459Lys		88027443	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	0.944	-0.708694	0.03230	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.06687	3.27;3.29	5.52	0.256	0.15567	.	1.028850	0.07618	N	0.926528	T	0.03434	0.0099	L	0.60455	1.87	0.09310	N	1	B	0.24258	0.1	B	0.19148	0.024	T	0.42699	-0.9436	10	0.45353	T	0.12	.	9.8865	0.41264	0.0:0.2594:0.0:0.7406	.	2459	O60281	ZN292_HUMAN	K	2459;2454	ENSP00000358590:N2459K;ENSP00000342847:N2454K	ENSP00000342847:N2454K	N	+	3	2	ZNF292	88027443	0.923000	0.31300	0.009000	0.14445	0.305000	0.27757	1.002000	0.29796	0.062000	0.16340	0.482000	0.46254	AAT		0.333	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87970724	T	G	87970724	3	3	67	1	0	0	0	0	1	0	0	0	17865	1461	51	4	7407	4	ZNF292	6	87970724	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	245236	87970724	83144343	47	20803										
CCM2	83605	broad.mit.edu	37	chr7	45109449	45109449	+	Frame_Shift_Del	DEL	C	C	-													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctgcggaggagctttgctgtCtgctaggccaggtcttccag							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:45109449delC	ENST00000258781.6	+	6	783	c.634delC	c.(634-636)ctgfs	p.L213fs	CCM2_ENST00000541586.1_Frame_Shift_Del_p.L155fs|CCM2_ENST00000381112.3_Frame_Shift_Del_p.L234fs|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Intron|CCM2_ENST00000475551.1_Frame_Shift_Del_p.L207fs|CCM2_ENST00000544363.1_Intron	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	213	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)		p.L233fs*2(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GCTTTGCTGTCTGCTAGGCCA	0.607																																																1	Deletion - Frameshift(1)	large_intestine(1)	7											129	120	123					7																	45109449		2203	4300	6503	45075974	SO:0001589	frameshift_variant	83605			BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.634delC	7.37:g.45109449delC	ENSP00000258781:p.Leu213fs		45075974	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Frame_Shift_Del	DEL	ENST00000258781.6	37	CCDS5500.1																																																																																				0.607	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443		-	45109449	C	-	45109449	7	5	67	1	0	1	0	1	0	0	0	0	2914	912	32	0	753	0	CCM2	7	45109449	Frame_Shift_Del	DEL	C	TCGA-AG-A014-01A-02W-A00K-09		45109449	114029214	48	20804										
PON2	5445	broad.mit.edu	37	chr7	95041017	95041017	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	atgcaacagagaattttctgCttcttcaaatttaaaaattt	4	6	3	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:95041017C>T	ENST00000222572.3	-	5	688	c.442G>A	c.(442-444)Gca>Aca	p.A148T	PON2_ENST00000483292.1_5'Flank|PON2_ENST00000433091.2_Missense_Mutation_p.A136T|PON2_ENST00000536183.1_Missense_Mutation_p.A169T			Q15165	PON2_HUMAN	paraoxonase 2	148			A -> G (associated with elevated mean fasting plasma glucose level; dbSNP:rs12026). {ECO:0000269|PubMed:9329371, ECO:0000269|PubMed:9714608, ECO:0000269|Ref.5}.		aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.A148T(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			GAATTTTCTGCTTCTTCAAAT	0.338																																					GBM(42;803 823 13649 23368 31463)											1	Substitution - Missense(1)	large_intestine(1)	7											70	72	72					7																	95041017		2203	4300	6503	94878953	SO:0001583	missense	5445			M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"Paraoxonases"	9205	protein-coding gene	gene with protein product	"paraoxonase nirs", "arylesterase 2"	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.442G>A	7.37:g.95041017C>T	ENSP00000222572:p.Ala148Thr		94878953	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.394005	0.25205	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.42513	2.28;0.97;2.28	4.94	4.06	0.47325	Six-bladed beta-propeller, TolB-like (1);	0.296339	0.41500	D	0.000871	T	0.25457	0.0619	N	0.12182	0.205	0.26467	N	0.975341	B;B	0.23591	0.043;0.088	B;B	0.22386	0.039;0.039	T	0.12192	-1.0557	10	0.25106	T	0.35	-16.649	13.8893	0.63729	0.0:0.9263:0.0:0.0737	.	148;148	A4D1H7;Q15165	.;PON2_HUMAN	T	169;146;136;148	ENSP00000440282:A169T;ENSP00000404622:A136T;ENSP00000222572:A148T	ENSP00000222572:A148T	A	-	1	0	PON2	94878953	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	5.401000	0.66326	1.456000	0.47831	-0.157000	0.13467	GCA		0.338	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		T	95041017	C	T	95041017	3	4	67	1	0	0	0	0	1	0	0	0	12280	797	28	3	642	3	PON2	7	95041017	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	49931568	95041017	64097646	49	20805										
CNPY4	245812	broad.mit.edu	37	chr7	99719968	99719968	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tggagctggggcaggtgctgGatacaggcaagaggaagaga	19	5	0	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:99719968G>T	ENST00000262932.3	+	2	337	c.205G>T	c.(205-207)Gat>Tat	p.D69Y	CNPY4_ENST00000480692.1_3'UTR|TAF6_ENST00000344095.4_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_5'Flank|TAF6_ENST00000418432.2_5'Flank|TAF6_ENST00000437822.2_5'Flank|TAF6_ENST00000453269.2_5'Flank	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	69						extracellular region (GO:0005576)		p.D69Y(1)		breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCAGGTGCTGGATACAGGCAA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	7											127	118	121					7																	99719968		2203	4300	6503	99557904	SO:0001583	missense	245812			AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"protein associated with TLR4"	610047	"canopy 4 homolog (zebrafish)"			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.205G>T	7.37:g.99719968G>T	ENSP00000262932:p.Asp69Tyr		99557904	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	37	CCDS34701.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.652763	0.88056	.	.	ENSG00000166997	ENST00000262932	T	0.42513	0.97	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.66137	0.2759	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70557	-0.4839	10	0.72032	D	0.01	-21.9607	14.3585	0.66754	0.0:0.0:1.0:0.0	.	69	Q8N129	CNPY4_HUMAN	Y	69	ENSP00000262932:D69Y	ENSP00000262932:D69Y	D	+	1	0	CNPY4	99557904	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.096000	0.76960	2.439000	0.82584	0.462000	0.41574	GAT		0.602	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		T	99719968	G	T	99719968	3	4	67	1	0	0	0	0	1	0	0	0	3636	1174	41	2	211	2	CNPY4	7	99719968	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	4678951	99719968	59418695	50	20806										
ZCWPW1	55063	broad.mit.edu	37	chr7	100013971	100013971	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aaggtgagtctattggatttCttcttagagggtgcaggatc	13	5	3	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:100013971C>T	ENST00000398027.2	-	7	835	c.588G>A	c.(586-588)aaG>aaA	p.K196K	ZCWPW1_ENST00000490721.1_Silent_p.K75K|ZCWPW1_ENST00000360951.4_Silent_p.K196K|ZCWPW1_ENST00000324725.6_Silent_p.K75K	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	196							zinc ion binding (GO:0008270)	p.K196K(1)		breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TATTGGATTTCTTCTTAGAGG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	7											153	142	145					7																	100013971		1868	4111	5979	99851907	SO:0001819	synonymous_variant	55063			AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.588G>A	7.37:g.100013971C>T			99851907	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Silent	SNP	ENST00000398027.2	37	CCDS43623.1																																																																																				0.438	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		T	100013971	C	T	100013971	2	4	67	1	0	0	0	0	0	0	0	1	17636	912	32	3		3	ZCWPW1	7	100013971	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	294003	100013971	59124692	51	20807										
C7orf66	154907	broad.mit.edu	37	chr7	108524118	108524118	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	taactgattggtttcttgtgGacaatccgtagatatgcacc	9	8	1	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:108524118G>C	ENST00000379007.2	-	2	348	c.294C>G	c.(292-294)gtC>gtG	p.V98V		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	98						integral component of membrane (GO:0016021)		p.V98V(1)		breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						GTTTCTTGTGGACAATCCGTA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	7											160	142	148					7																	108524118		2203	4300	6503	108311354	SO:0001819	synonymous_variant	154907			AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.294C>G	7.37:g.108524118G>C			108311354		Silent	SNP	ENST00000379007.2	37	CCDS34735.1																																																																																				0.348	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607		C	108524118	G	C	108524118	2	2	67	1	0	0	0	0	0	0	0	1	2418	1161	41	5		5	C7orf66	7	108524118	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	8510147	108524118	50614545	52	20808										
SLC13A1	6561	broad.mit.edu	37	chr7	122811857	122811857	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccaaccatcatcaccattttCagagcaattctcttgtgcaa	4	13	4	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:122811857C>T	ENST00000194130.2	-	3	369	c.330G>A	c.(328-330)ctG>ctA	p.L110L	SLC13A1_ENST00000539873.1_Silent_p.L46L	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	110					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.L110L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	TCACCATTTTCAGAGCAATTC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	7											238	212	221					7																	122811857		2203	4300	6503	122599093	SO:0001819	synonymous_variant	6561				CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.330G>A	7.37:g.122811857C>T			122599093	Q9H5Z0	Silent	SNP	ENST00000194130.2	37	CCDS5786.1																																																																																				0.378	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		T	122811857	C	T	122811857	2	4	67	1	0	0	0	0	0	0	0	1	14428	813	29	3		3	SLC13A1	7	122811857	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	14287739	122811857	36326806	53	20809										
AHCYL2	23382	broad.mit.edu	37	chr7	129066319	129066319	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcctacacctgcctacctttGatgcccacttgacagagctg	8	15	0	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr7:129066319G>A	ENST00000325006.3	+	16	1798	c.1744G>A	c.(1744-1746)Gat>Aat	p.D582N	AHCYL2_ENST00000490911.1_Missense_Mutation_p.D479N|AHCYL2_ENST00000474594.1_Missense_Mutation_p.D479N|AHCYL2_ENST00000446544.2_Missense_Mutation_p.D581N|AHCYL2_ENST00000446212.1_Missense_Mutation_p.D480N|AHCYL2_ENST00000531335.2_Missense_Mutation_p.D501N	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	582					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)	p.D582N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						GCCTACCTTTGATGCCCACTT	0.507																																					Pancreas(160;1736 1964 29875 40941 45605)											1	Substitution - Missense(1)	large_intestine(1)	7											149	129	136					7																	129066319		2203	4300	6503	128853555	SO:0001583	missense	23382			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"S-adenosylhomocysteine hydrolase-like 2"				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1744G>A	7.37:g.129066319G>A	ENSP00000315931:p.Asp582Asn		128853555	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872170	0.51695	.	.	ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911	T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.59878	0.2226	N	0.12853	0.265	0.80722	D	1	B;B;B;B;B	0.32693	0.017;0.004;0.38;0.004;0.328	B;B;B;B;B	0.32928	0.042;0.023;0.155;0.023;0.096	T	0.58375	-0.7647	10	0.25106	T	0.35	-19.105	18.2799	0.90096	0.0:0.0:1.0:0.0	.	479;480;582;479;581	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2	.;.;SAHH3_HUMAN;.;.	N	582;581;501;479;480;479	ENSP00000315931:D582N;ENSP00000413639:D581N;ENSP00000431787:D501N;ENSP00000420459:D479N;ENSP00000405267:D480N;ENSP00000420801:D479N	ENSP00000315931:D582N	D	+	1	0	AHCYL2	128853555	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.841000	0.99482	2.657000	0.90304	0.557000	0.71058	GAT		0.507	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1			A	129066319	G	A	129066319	3	1	67	1	0	0	0	0	1	0	0	0	411	1290	45	3	1928	3	AHCYL2	7	129066319	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	6254462	129066319	30072344	54	20810										
USP17L2	377630	broad.mit.edu	37	chr8	11995190	11995190	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcctgttgactcaggacagaAgtgatgctacaggcagtgac	13	9	1	4			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:11995190A>G	ENST00000333796.3	-	1	1396	c.1080T>C	c.(1078-1080)acT>acC	p.T360T	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	360	USP.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.T360T(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TCAGGACAGAAGTGATGCTAC	0.483																																																1	Substitution - coding silent(1)	large_intestine(1)	8											58	61	60					8																	11995190		1816	3997	5813	12032599	SO:0001819	synonymous_variant	377630			BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1080T>C	8.37:g.11995190A>G			12032599		Silent	SNP	ENST00000333796.3	37	CCDS43713.1																																																																																				0.483	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		G	11995190	A	G	11995190	2	3	67	1	0	0	0	0	0	0	0	1	17088	59	3	4		4	USP17L2	8	11995190	Silent	SNP	A	TCGA-AG-A014-01A-02W-A00K-09		11995190	134368832	55	20811										
EBF2	64641	broad.mit.edu	37	chr8	25718591	25718591	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tatttccttgtgttgactctGagatgctgaccccaagctgg	10	10	1	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:25718591G>C	ENST00000520164.1	-	13	1853	c.1316C>G	c.(1315-1317)tCa>tGa	p.S439*	EBF2_ENST00000535548.1_Nonsense_Mutation_p.S170*|EBF2_ENST00000408929.3_Nonsense_Mutation_p.S291*	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	439					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S439*(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TGTTGACTCTGAGATGCTGAC	0.488																																					Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)											2	Substitution - Nonsense(2)	large_intestine(2)	8											132	131	132					8																	25718591		1980	4171	6151	25774508	SO:0001587	stop_gained	64641			AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1316C>G	8.37:g.25718591G>C	ENSP00000430241:p.Ser439*		25774508	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Nonsense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	G	36	5.946411	0.97134	.	.	ENSG00000221818	ENST00000520164;ENST00000408929;ENST00000535548	.	.	.	5.29	5.29	0.74685	.	0.122041	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-23.7317	18.9368	0.92589	0.0:0.0:1.0:0.0	.	.	.	.	X	439;291;170	.	ENSP00000386178:S291X	S	-	2	0	EBF2	25774508	1.000000	0.71417	1.000000	0.80357	0.262000	0.26303	5.762000	0.68809	2.476000	0.83614	0.655000	0.94253	TCA		0.488	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		C	25718591	G	C	25718591	4	2	67	1	0	0	0	0	0	1	0	0	4892	1294	45	5	427	5	EBF2	8	25718591	Nonsense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	13723401	25718591	120645431	56	20812										
PRKDC	5591	broad.mit.edu	37	chr8	48866458	48866459	+	Missense_Mutation	DNP	AG	AG	CA													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cttcacccaataatcctaggAgctcatatactttttctaaa							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:48866458_48866459AG>CA	ENST00000314191.2	-	6	585_586	c.529_530CT>TG	c.(529-531)CTc>TGc	p.L177C	PRKDC_ENST00000338368.3_Missense_Mutation_p.L177C|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	177					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.L177>?(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TAATCCTAGGAGCTCATATACT	0.337								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											2	Complex(2)	large_intestine(2)	8																																								49029012	SO:0001583	missense	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.529_530delinsCA	8.37:g.48866458_48866459delinsCA	ENSP00000313420:p.Leu177Cys		49029011	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	DNP	ENST00000314191.2	37																																																																																					0.337	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		CA	48866459	AG	CA	48866458	3	2	67	1	0	0	0	0	1	0	0	0	12555	304	11	4	12179	4	PRKDC	8	48866458	Missense_Mutation	DNP	AG	TCGA-AG-A014-01A-02W-A00K-09	23147867	48866458	97497564	57	20813										
NSMAF	8439	broad.mit.edu	37	chr8	59535796	59535796	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tacctgtttttgtcaaatgaTgttctagctaaacgagactg	8	7	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:59535796T>C	ENST00000038176.3	-	9	752	c.540A>G	c.(538-540)acA>acG	p.T180T	NSMAF_ENST00000519858.1_5'UTR|NSMAF_ENST00000427130.2_Silent_p.T211T	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	180	GRAM.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.T180T(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGTCAAATGATGTTCTAGCTA	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	8											54	51	52					8																	59535796		2203	4300	6503	59698350	SO:0001819	synonymous_variant	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.540A>G	8.37:g.59535796T>C			59698350	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																				0.303	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		C	59535796	T	C	59535796	2	2	67	1	0	0	0	0	0	0	0	1	10705	1451	51	4		4	NSMAF	8	59535796	Silent	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	10669338	59535796	86828226	58	20814										
HEY1	23462	broad.mit.edu	37	chr8	80678909	80678909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tccctcctgccgtatgcagcAttttcaggtgatccacggtc	9	14	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:80678909A>G	ENST00000354724.3	-	4	507	c.308T>C	c.(307-309)aTg>aCg	p.M103T	RP11-26J3.1_ENST00000502766.2_lincRNA|HEY1_ENST00000337919.5_Missense_Mutation_p.M107T|RP11-27N21.3_ENST00000607172.1_lincRNA|HEY1_ENST00000435063.2_5'Flank|HEY1_ENST00000523976.1_5'Flank	NM_012258.3	NP_036390.3	Q9Y5J3	HEY1_HUMAN	hes-related family bHLH transcription factor with YRPW motif 1	103	Transcriptional repression and interaction with NCOR1 and SIN3A. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.M103T(1)	HEY1/NCOA2(10)	cervix(1)|kidney(2)|large_intestine(5)|lung(14)	22	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			CGTATGCAGCATTTTCAGGTG	0.502			T	NCOA2	mesenchymal chondrosarcoma																																		Dom	yes		8	8q21	23462	hairy/enhancer-of-split related with YRPW motif 1		M	1	Substitution - Missense(1)	large_intestine(1)	8											234	223	227					8																	80678909		2203	4300	6503	80841464	SO:0001583	missense	23462			AF151522	CCDS6225.1, CCDS43749.1, CCDS64915.1	8q21	2013-10-17	2013-10-17					"Basic helix-loop-helix proteins"	4880	protein-coding gene	gene with protein product		602953	"hairy/enhancer-of-split related with YRPW motif 1"			10415358, 10403790	Standard	NM_001040708		Approved	HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31	uc003ybl.3	Q9Y5J3		ENST00000354724.3:c.308T>C	8.37:g.80678909A>G	ENSP00000346761:p.Met103Thr		80841464	B2R883|Q5TZS3|Q8NAM2|Q9NYP4	Missense_Mutation	SNP	ENST00000354724.3	37	CCDS6225.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.515848	0.64634	.	.	ENSG00000164683	ENST00000354724;ENST00000542205;ENST00000337919;ENST00000518733	D;D;D	0.97811	-4.55;-4.55;-4.55	4.9	4.9	0.64082	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.95557	0.8556	N	0.02960	-0.455	0.80722	D	1	D;B	0.56521	0.976;0.228	D;B	0.65140	0.932;0.125	D	0.96333	0.9245	10	0.41790	T	0.15	-15.2159	14.5443	0.68017	1.0:0.0:0.0:0.0	.	103;107	Q9Y5J3;Q9Y5J3-2	HEY1_HUMAN;.	T	103;107;107;65	ENSP00000346761:M103T;ENSP00000338272:M107T;ENSP00000429705:M65T	ENSP00000338272:M107T	M	-	2	0	HEY1	80841464	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.927000	0.92846	1.825000	0.53177	0.459000	0.35465	ATG		0.502	HEY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379516.1	NM_012258		G	80678909	A	G	80678909	3	3	67	1	0	0	0	0	1	0	0	0	7099	217	8	4	614	4	HEY1	8	80678909	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	21143113	80678909	65685113	59	20815										
LY6D	8581	broad.mit.edu	37	chr8	143867013	143867013	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gatgctacccacctgtgttcGtggtcttgcagaagcgagag	13	10	1	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr8:143867013G>A	ENST00000301263.4	-	2	218	c.143C>T	c.(142-144)aCg>aTg	p.T48M	LY6D_ENST00000518434.1_5'UTR|RP11-706C16.8_ENST00000510610.2_RNA	NM_003695.2	NP_003686.1	Q14210	LY6D_HUMAN	lymphocyte antigen 6 complex, locus D	48	UPAR/Ly6.				cell adhesion (GO:0007155)|lymphocyte differentiation (GO:0030098)|response to stilbenoid (GO:0035634)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.T48M(1)		large_intestine(1)|lung(3)|prostate(1)	5	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACCTGTGTTCGTGGTCTTGCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	8											76	74	75					8																	143867013		2203	4300	6503	143864015	SO:0001583	missense	8581			U66837	CCDS6390.1	8q24	2004-07-06			ENSG00000167656	ENSG00000167656			13348	protein-coding gene	gene with protein product		606204				7790363, 9551972	Standard	NM_003695		Approved	E48	uc003yxf.1	Q14210	OTTHUMG00000164693	ENST00000301263.4:c.143C>T	8.37:g.143867013G>A	ENSP00000301263:p.Thr48Met		143864015	B2R5F1|D3DWJ0|O43783|Q6GTV9|Q8TBD4|Q92933	Missense_Mutation	SNP	ENST00000301263.4	37	CCDS6390.1	.	.	.	.	.	.	.	.	.	.	a	7.273	0.607634	0.14002	.	.	ENSG00000167656	ENST00000301263	T	0.70749	-0.51	3.15	0.199	0.15175	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);CD59 antigen (1);	1.524060	0.04307	N	0.348249	T	0.49167	0.1541	N	0.10972	0.075	0.09310	N	1	B	0.17038	0.02	B	0.06405	0.002	T	0.29640	-1.0005	10	0.41790	T	0.15	-3.9964	3.3197	0.07045	0.4462:0.222:0.3319:0.0	.	48	Q14210	LY6D_HUMAN	M	48	ENSP00000301263:T48M	ENSP00000301263:T48M	T	-	2	0	LY6D	143864015	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.090000	0.15025	-0.252000	0.09528	-0.379000	0.06801	ACG		0.642	LY6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379774.1	NM_003695		A	143867013	G	A	143867013	3	1	67	1	0	0	0	0	1	0	0	0	9120	1145	40	1	251	1	LY6D	8	143867013	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	63188104	143867013	2497009	60	20816										
DMRT2	10655	broad.mit.edu	37	chr9	1053815	1053815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccagtttgctggccaaaagcAttttagaaggtaaagcaaca	9	8	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr9:1053815A>G	ENST00000358146.2	+	2	619	c.619A>G	c.(619-621)Att>Gtt	p.I207V	DMRT2_ENST00000302441.6_Missense_Mutation_p.I207V|DMRT2_ENST00000412350.2_Missense_Mutation_p.I207V|DMRT2_ENST00000382251.3_Missense_Mutation_p.I207V|DMRT2_ENST00000382255.3_Missense_Mutation_p.I207V|DMRT2_ENST00000259622.6_Missense_Mutation_p.I207V			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	207					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I207V(2)		large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		GGCCAAAAGCATTTTAGAAGG	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	9											65	69	67					9																	1053815		2203	4300	6503	1043815	SO:0001583	missense	10655			AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"terra-like protein"	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.619A>G	9.37:g.1053815A>G	ENSP00000350865:p.Ile207Val		1043815	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.351262	0.61183	.	.	ENSG00000173253	ENST00000382255;ENST00000382251;ENST00000412350;ENST00000302441;ENST00000358146;ENST00000259622	T;T;T;T;T;T	0.54279	0.58;1.54;0.58;1.54;1.54;0.58	5.72	5.72	0.89469	.	0.246042	0.31673	N	0.007247	T	0.67692	0.2920	L	0.54323	1.7	0.58432	D	0.999996	B;D;D	0.67145	0.324;0.994;0.996	B;D;D	0.77557	0.133;0.978;0.99	T	0.66168	-0.5991	10	0.38643	T	0.18	-15.654	15.6654	0.77225	1.0:0.0:0.0:0.0	.	207;207;51	Q05C20;Q9Y5R5;Q5HYK2	.;DMRT2_HUMAN;.	V	207	ENSP00000371690:I207V;ENSP00000371686:I207V;ENSP00000397494:I207V;ENSP00000305785:I207V;ENSP00000350865:I207V;ENSP00000259622:I207V	ENSP00000259622:I207V	I	+	1	0	DMRT2	1043815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.018000	0.93657	2.174000	0.68829	0.454000	0.30748	ATT		0.413	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		G	1053815	A	G	1053815	3	3	67	1	0	0	0	0	1	0	0	0	4597	217	8	4	625	4	DMRT2	9	1053815	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09		1053815	140159616	61	20817										
KIAA1797	54914	broad.mit.edu	37	chr9	20929413	20929413	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcccgttctgctgccgccacGgctttgtctctccttgtgcc	10	17	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr9:20929413G>A	ENST00000380249.1	+	29	3499	c.3135G>A	c.(3133-3135)acG>acA	p.T1045T	FOCAD_ENST00000605086.1_Silent_p.T481T|FOCAD_ENST00000338382.6_Silent_p.T1045T	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1045						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.T1045T(1)									CTGCCGCCACGGCTTTGTCTC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	9											82	74	77					9																	20929413		2203	4300	6503	20919413	SO:0001819	synonymous_variant	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.3135G>A	9.37:g.20929413G>A			20919413	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																				0.473	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20929413	G	A	20929413	2	1	67	1	0	0	0	0	0	0	0	1	8279	1103	39	1		1	KIAA1797	9	20929413	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	19875598	20929413	120284018	62	20818										
TOPORS	10210	broad.mit.edu	37	chr9	32543404	32543404	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gaaggagcagggcaatcataAttggcatgctggtcaaaggc	14	7	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr9:32543404A>C	ENST00000360538.2	-	3	1235	c.1119T>G	c.(1117-1119)aaT>aaG	p.N373K	TOPORS_ENST00000379858.1_Missense_Mutation_p.N308K	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	373	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N373K(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		GGCAATCATAATTGGCATGCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											65	68	67					9																	32543404		2203	4300	6503	32533404	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1119T>G	9.37:g.32543404A>C	ENSP00000353735:p.Asn373Lys		32533404	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	A	0.023	-1.402193	0.01165	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.14022	2.54;2.54	5.93	5.93	0.95920	.	0.000000	0.53938	D	0.000047	T	0.11836	0.0288	L	0.27053	0.805	0.36995	D	0.894977	D	0.54397	0.966	P	0.46479	0.518	T	0.26360	-1.0105	10	0.22109	T	0.4	-29.3046	9.8027	0.40775	0.9226:0.0:0.0774:0.0	.	373	Q9NS56	TOPRS_HUMAN	K	373;308	ENSP00000353735:N373K;ENSP00000369187:N308K	ENSP00000353735:N373K	N	-	3	2	TOPORS	32533404	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	2.477000	0.45180	2.263000	0.75096	0.533000	0.62120	AAT		0.403	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543404	A	C	32543404	3	2	67	1	0	0	0	0	1	0	0	0	16410	98	4	4	2022	4	TOPORS	9	32543404	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	11613991	32543404	108670027	63	20819										
AKNA	80709	broad.mit.edu	37	chr9	117108256	117108257	+	Missense_Mutation	DNP	AA	AA	GT													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tggtcttgctcttctcagagAacagtggtagggagggcagc							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr9:117108256_117108257AA>GT	ENST00000307564.4	-	18	3708_3709	c.3547_3548TT>AC	c.(3547-3549)TTc>ACc	p.F1183T	AKNA_ENST00000223791.3_Missense_Mutation_p.F643T|AKNA_ENST00000374079.4_Missense_Mutation_p.F128T|AKNA_ENST00000374088.3_Missense_Mutation_p.F1183T|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374075.5_Missense_Mutation_p.F1102T	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1183					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.F1183>?(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTTCTCAGAGAACAGTGGTAGG	0.584																																																1	Complex(1)	large_intestine(1)	9																																								116148078	SO:0001583	missense	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3547_3548delinsGT	9.37:g.117108256_117108257delinsGT	ENSP00000303769:p.Phe1183Thr		116148077	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	DNP	ENST00000307564.4	37	CCDS6805.1																																																																																				0.584	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		GT	117108257	AA	GT	117108256	3	3	67	1	0	0	0	0	1	0	0	0	463	246	9	4	791	4	AKNA	9	117108256	Missense_Mutation	DNP	AA	TCGA-AG-A014-01A-02W-A00K-09	84564852	117108256	24105175	64	20820										
DAB2IP	153090	broad.mit.edu	37	chr9	124532879	124532880	+	Missense_Mutation	DNP	GC	GC	CG													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tcctgagggacgtccacacaGcactgagcaccccaggtagc							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr9:124532879_124532880GC>CG	ENST00000408936.3	+	11	2136_2137	c.1954_1955GC>CG	c.(1954-1956)GCa>CGa	p.A652R	DAB2IP_ENST00000259371.2_Missense_Mutation_p.A624R|DAB2IP_ENST00000309989.1_Missense_Mutation_p.A528R			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	652	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.A528>?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CGTCCACACAGCACTGAGCACC	0.614																																																1	Complex(1)	large_intestine(1)	9																																								123572701	SO:0001583	missense	153090			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	Exception_encountered	9.37:g.124532879_124532880delinsCG	ENSP00000386183:p.Ala652Arg		123572700	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	DNP	ENST00000408936.3	37																																																																																					0.614	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		CG	124532880	GC	CG	124532879	3	2	67	1	0	0	0	0	1	0	0	0	4225	971	34	5	1912	5	DAB2IP	9	124532879	Missense_Mutation	DNP	GC	TCGA-AG-A014-01A-02W-A00K-09	7424623	124532879	16680552	65	20821										
DIP2C	22982	broad.mit.edu	37	chr10	391004	391004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccgcctccctggaccgcagcAacttacagatcagctgtgtc	9	16	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr10:391004A>G	ENST00000280886.6	-	27	3365	c.3278T>C	c.(3277-3279)tTg>tCg	p.L1093S		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1093						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.L1093S(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GGACCGCAGCAACTTACAGAT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											58	49	52					10																	391004		2203	4300	6503	381004	SO:0001583	missense	22982			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3278T>C	10.37:g.391004A>G	ENSP00000280886:p.Leu1093Ser		381004	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.672554	0.88348	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.46063	0.88	5.59	5.59	0.84812	AMP-dependent synthetase/ligase (1);	0.000000	0.64402	D	0.000001	T	0.59473	0.2196	M	0.75615	2.305	0.80722	D	1	P	0.36974	0.576	P	0.50440	0.641	T	0.61113	-0.7128	10	0.52906	T	0.07	-23.6172	15.7635	0.78106	1.0:0.0:0.0:0.0	.	1093	Q9Y2E4	DIP2C_HUMAN	S	1093;18	ENSP00000280886:L1093S	ENSP00000280886:L1093S	L	-	2	0	DIP2C	381004	1.000000	0.71417	0.889000	0.34880	0.889000	0.51656	9.287000	0.95975	2.132000	0.65825	0.533000	0.62120	TTG		0.592	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		G	391004	A	G	391004	3	3	67	1	0	0	0	0	1	0	0	0	4540	131	5	4	1436	4	DIP2C	10	391004	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09		391004	135143743	66	20822										
POLL	27343	broad.mit.edu	37	chr10	103340040	103340041	+	Missense_Mutation	DNP	AT	AT	GG													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgtcaaggaggcggctgaagAtaccccggtgggaccggcca							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr10:103340040_103340041AT>GG	ENST00000370162.3	-	8	1821_1822	c.1327_1328AT>CC	c.(1327-1329)ATc>CCc	p.I443P	POLL_ENST00000463515.1_5'UTR|POLL_ENST00000370158.3_Missense_Mutation_p.I168P|DPCD_ENST00000416979.2_5'UTR|DPCD_ENST00000470165.1_3'UTR|POLL_ENST00000370169.1_Missense_Mutation_p.I443P|POLL_ENST00000456836.2_Missense_Mutation_p.I180P|POLL_ENST00000339310.3_Missense_Mutation_p.I166P|POLL_ENST00000370168.3_Missense_Mutation_p.I116P|POLL_ENST00000370172.1_Missense_Mutation_p.I355P|POLL_ENST00000299206.4_Missense_Mutation_p.I443P	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	443					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)	p.I443>?(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		GCGGCTGAAGATACCCCGGTGG	0.609								DNA polymerases (catalytic subunits)																																								1	Complex(1)	large_intestine(1)	10																																								103330031	SO:0001583	missense	27343			AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"DNA polymerases"	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.1327_1328delinsGG	10.37:g.103340040_103340041delinsGG	ENSP00000359181:p.Ile443Pro		103330030	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Missense_Mutation	DNP	ENST00000370162.3	37	CCDS7513.1																																																																																				0.609	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274		GG	103340041	AT	GG	103340040	3	3	67	1	0	0	0	0	1	0	0	0	12236	333	12	4	407	4	POLL	10	103340040	Missense_Mutation	DNP	AT	TCGA-AG-A014-01A-02W-A00K-09	102949036	103340040	32194707	67	20823										
GFRA1	2674	broad.mit.edu	37	chr10	117884988	117884988	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gcacggggtgatgtacgccgAcctgtacttcttgcaaatgt	12	10	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr10:117884988A>T	ENST00000355422.6	-	6	1064	c.514T>A	c.(514-516)Tcg>Acg	p.S172T	GFRA1_ENST00000369236.1_Missense_Mutation_p.S167T|GFRA1_ENST00000439649.3_Missense_Mutation_p.S167T|GFRA1_ENST00000544592.1_Missense_Mutation_p.S51T	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	172					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.S167T(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		ATGTACGCCGACCTGTACTTC	0.577																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - Missense(1)	large_intestine(1)	10											79	67	71					10																	117884988		2203	4300	6503	117874978	SO:0001583	missense	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.514T>A	10.37:g.117884988A>T	ENSP00000347591:p.Ser172Thr		117874978	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.539424	0.65085	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.64085	-0.08;-0.08	5.74	4.59	0.56863	GDNF/GAS1 (2);	0.120781	0.64402	D	0.000018	T	0.67524	0.2902	L	0.34521	1.04	0.58432	D	0.999992	D;D	0.69078	0.991;0.997	D;D	0.83275	0.996;0.996	T	0.63225	-0.6685	10	0.27082	T	0.32	-10.1407	12.1618	0.54107	0.8717:0.0:0.0:0.1283	.	172;167	P56159;P56159-2	GFRA1_HUMAN;.	T	172;167;167;51;167	ENSP00000358239:S167T;ENSP00000442179:S51T	ENSP00000347591:S167T	S	-	1	0	GFRA1	117874978	1.000000	0.71417	0.886000	0.34754	0.800000	0.45204	4.104000	0.57790	0.977000	0.38444	0.459000	0.35465	TCG		0.577	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		T	117884988	A	T	117884988	3	4	67	1	0	0	0	0	1	0	0	0	6367	275	10	5	907	5	GFRA1	10	117884988	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	14544948	117884988	17649759	68	20824										
OR51I2	390064	broad.mit.edu	37	chr11	5475386	5475386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctcctatgtgctcattctgcGttctgtcatggccactgctt	8	13	4	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:5475386G>A	ENST00000341449.2	+	1	749	c.668G>A	c.(667-669)cGt>cAt	p.R223H	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	223					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R223H(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCATTCTGCGTTCTGTCATG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											334	284	301					11																	5475386		2201	4297	6498	5431962	SO:0001583	missense	390064			BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.668G>A	11.37:g.5475386G>A	ENSP00000341987:p.Arg223His		5431962	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182284	0.01633	.	.	ENSG00000187918	ENST00000341449	T	0.39592	1.07	5.58	-8.98	0.00754	GPCR, rhodopsin-like superfamily (1);	0.640335	0.15500	N	0.259069	T	0.25680	0.0625	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.02132	-1.1208	10	0.33940	T	0.23	.	17.9915	0.89170	0.6218:0.0:0.3782:0.0	.	223	Q9H344	O51I2_HUMAN	H	223	ENSP00000341987:R223H	ENSP00000341987:R223H	R	+	2	0	OR51I2	5431962	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.817000	0.01719	-1.833000	0.01195	-1.021000	0.02439	CGT		0.448	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		A	5475386	G	A	5475386	3	1	67	1	0	0	0	0	1	0	0	0	11132	1145	40	1	670	1	OR51I2	11	5475386	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		5475386	129531130	69	20825										
NDUFS3	4722	broad.mit.edu	37	chr11	47603714	47603714	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tacacagatgagctgacgccCattgagtctgctgtctctgt	10	11	2	4			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:47603714C>G	ENST00000263774.4	+	5	538	c.456C>G	c.(454-456)ccC>ccG	p.P152P	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	152					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.P152P(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	AGCTGACGCCCATTGAGTCTG	0.527																																					Pancreas(15;551 601 22438 23457 52512)											1	Substitution - coding silent(1)	large_intestine(1)	11											162	148	153					11																	47603714		2201	4298	6499	47560290	SO:0001819	synonymous_variant	4722			AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.456C>G	11.37:g.47603714C>G			47560290	B2R9J1|B4DFM8|Q9UNQ8	Silent	SNP	ENST00000263774.4	37	CCDS7941.1																																																																																				0.527	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		G	47603714	C	G	47603714	2	3	67	1	0	0	0	0	0	0	0	1	10324	581	21	5		5	NDUFS3	11	47603714	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	42128328	47603714	87402802	70	20826										
FERMT3	83706	broad.mit.edu	37	chr11	63979205	63979205	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tcaagtactacagcttcttcGatttggatcccaaggtgggt	10	9	2	0	rs139416960		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:63979205G>T	ENST00000279227.5	+	6	867	c.772G>T	c.(772-774)Gat>Tat	p.D258Y	FERMT3_ENST00000345728.5_Missense_Mutation_p.D258Y	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	258	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)	p.D258Y(2)		breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CAGCTTCTTCGATTTGGATCC	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	11											100	91	94					11																	63979205		2201	4297	6498	63735781	SO:0001583	missense	83706			L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"Fermitins", "Pleckstrin homology (PH) domain containing"	23151	protein-coding gene	gene with protein product	"kindlin-3"	607901	"fermitin family homolog 3 (Drosophila)"				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.772G>T	11.37:g.63979205G>T	ENSP00000279227:p.Asp258Tyr		63735781	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.242660	0.79912	.	.	ENSG00000149781	ENST00000544997;ENST00000345728;ENST00000279227;ENST00000541252	D;D;D;T	0.83419	-1.72;-1.72;-1.72;0.14	3.6	3.6	0.41247	Band 4.1 domain (1);FERM central domain (2);	0.060767	0.64402	D	0.000009	D	0.90539	0.7035	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.973;0.993	D	0.92142	0.5721	10	0.87932	D	0	-30.8291	14.5431	0.68011	0.0:0.0:1.0:0.0	.	258;258	Q86UX7-2;Q86UX7	.;URP2_HUMAN	Y	258;258;258;78	ENSP00000445778:D258Y;ENSP00000339950:D258Y;ENSP00000279227:D258Y;ENSP00000438885:D78Y	ENSP00000279227:D258Y	D	+	1	0	FERMT3	63735781	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.336000	0.96533	2.032000	0.59987	0.462000	0.41574	GAT		0.627	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		T	63979205	G	T	63979205	3	4	67	1	0	0	0	0	1	0	0	0	5838	1058	37	2	790	2	FERMT3	11	63979205	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	16375491	63979205	71027311	71	20827										
ADRBK1	156	broad.mit.edu	37	chr11	67051781	67051781	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctgtcttcgacaccatcaacGctgagacagaccggctggag	11	13	2	2	rs139609139	byFrequency	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:67051781G>C	ENST00000308595.5	+	18	1881	c.1591G>C	c.(1591-1593)Gct>Cct	p.A531P	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	531					activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)	p.A531P(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CACCATCAACGCTGAGACAGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	70	73					11																	67051781		2200	4295	6495	66808357	SO:0001583	missense	156			X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1591G>C	11.37:g.67051781G>C	ENSP00000312262:p.Ala531Pro		66808357	B0ZBE1|Q13837|Q6GTT3	Missense_Mutation	SNP	ENST00000308595.5	37	CCDS8156.1	.	.	.	.	.	.	.	.	.	.	G	7.636	0.679876	0.14907	.	.	ENSG00000173020	ENST00000308595	T	0.24538	1.85	4.64	2.63	0.31362	AGC-kinase, C-terminal (1);Protein kinase-like domain (1);	0.141721	0.32918	N	0.005481	T	0.13970	0.0338	N	0.22421	0.69	0.19775	N	0.999955	P	0.36282	0.546	B	0.31245	0.126	T	0.15009	-1.0452	10	0.34782	T	0.22	-11.05	9.3996	0.38424	0.0806:0.0:0.7759:0.1435	.	531	P25098	ARBK1_HUMAN	P	531	ENSP00000312262:A531P	ENSP00000312262:A531P	A	+	1	0	ADRBK1	66808357	0.007000	0.16637	0.047000	0.18901	0.003000	0.03518	1.493000	0.35605	1.317000	0.45149	0.591000	0.81541	GCT		0.622	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		C	67051781	G	C	67051781	3	2	67	1	0	0	0	0	1	0	0	0	343	1087	38	5	1661	5	ADRBK1	11	67051781	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	3072576	67051781	67954735	72	20828										
SCN2B	6327	broad.mit.edu	37	chr11	118037796	118037796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	caccgtggagtcccgctcagGgggctctggaaaggaagcag	16	11	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:118037796G>A	ENST00000278947.5	-	4	695	c.454C>T	c.(454-456)Cct>Tct	p.P152S		NM_004588.4	NP_004579.1	O60939	SCN2B_HUMAN	sodium channel, voltage-gated, type II, beta subunit	152	Ig-like C2-type.				cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|nervous system development (GO:0007399)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	voltage-gated sodium channel complex (GO:0001518)	sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.P152S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	7	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;3.19e-05)|Epithelial(105;0.00117)	Valproic Acid(DB00313)|Zonisamide(DB00909)	TCCCGCTCAGGGGGCTCTGGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	11											49	52	51					11																	118037796		2200	4296	6496	117543006	SO:0001583	missense	6327			AY358945	CCDS8390.1	11q23.3	2013-09-19	2012-02-28		ENSG00000149575	ENSG00000149575		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	10589	protein-coding gene	gene with protein product		601327	"sodium channel, voltage-gated, type II, beta polypeptide", "sodium channel, voltage-gated, type II, beta"			10198179	Standard	NM_004588		Approved		uc001psf.2	O60939	OTTHUMG00000048248	ENST00000278947.5:c.454C>T	11.37:g.118037796G>A	ENSP00000278947:p.Pro152Ser		117543006	O75302|Q9UNN3	Missense_Mutation	SNP	ENST00000278947.5	37	CCDS8390.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681465	0.88542	.	.	ENSG00000149575	ENST00000278947	D	0.97455	-4.39	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.97464	0.9170	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.66716	0.946	D	0.95885	0.8902	10	0.10636	T	0.68	-18.7896	18.1626	0.89714	0.0:0.0:1.0:0.0	.	152	O60939	SCN2B_HUMAN	S	152	ENSP00000278947:P152S	ENSP00000278947:P152S	P	-	1	0	SCN2B	117543006	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.206000	0.89745	2.640000	0.89533	0.655000	0.94253	CCT		0.632	SCN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109748.2	NM_004588		A	118037796	G	A	118037796	3	1	67	1	0	0	0	0	1	0	0	0	13954	1232	43	3	197	3	SCN2B	11	118037796	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	50986015	118037796	16968720	73	20829										
HEPACAM	220296	broad.mit.edu	37	chr11	124794954	124794954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ggggctggtgatgttcacccCctccagggggtctgtgaaca	15	11	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:124794954C>T	ENST00000298251.4	-	2	502	c.97G>A	c.(97-99)Ggg>Agg	p.G33R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule									p.G33R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		ATGTTCACCCCCTCCAGGGGG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											31	30	30					11																	124794954		2201	4299	6500	124300164	SO:0001583	missense	220296			AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26361	protein-coding gene	gene with protein product	"glial cell adhesion molecule"	611642	"hepatocyte cell adhesion molecule"			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.97G>A	11.37:g.124794954C>T	ENSP00000298251:p.Gly33Arg		124300164		Missense_Mutation	SNP	ENST00000298251.4	37	CCDS8456.1	.	.	.	.	.	.	.	.	.	.	C	32	5.188787	0.94923	.	.	ENSG00000165478	ENST00000298251;ENST00000374961	T	0.50813	0.73	5.84	5.84	0.93424	.	0.148535	0.64402	D	0.000011	T	0.68888	0.3050	M	0.65498	2.005	0.52099	D	0.999948	D;D	0.69078	0.992;0.997	D;D	0.69824	0.962;0.966	T	0.68784	-0.5317	10	0.62326	D	0.03	-26.1067	20.1434	0.98067	0.0:1.0:0.0:0.0	.	33;33	Q14CZ8-2;Q14CZ8	.;HECAM_HUMAN	R	33	ENSP00000298251:G33R	ENSP00000298251:G33R	G	-	1	0	HEPACAM	124300164	0.946000	0.32159	1.000000	0.80357	0.872000	0.50106	6.049000	0.71053	2.769000	0.95229	0.563000	0.77884	GGG		0.602	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722		T	124794954	C	T	124794954	3	4	67	1	0	0	0	0	1	0	0	0	7073	623	22	3	1177	3	HEPACAM	11	124794954	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	6757158	124794954	10211562	74	20830										
FEZ1	9638	broad.mit.edu	37	chr11	125351506	125351506	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctgagagtgaagggatgtaaTtgtctgtcagagcatcccaa	12	7	2	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr11:125351506T>C	ENST00000278919.3	-	3	569	c.335A>G	c.(334-336)aAt>aGt	p.N112S	FEZ1_ENST00000527350.1_5'Flank	NM_005103.4	NP_005094.1	Q99689	FEZ1_HUMAN	fasciculation and elongation protein zeta 1 (zygin I)	112					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|establishment of mitochondrion localization (GO:0051654)|nervous system development (GO:0007399)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|transport (GO:0006810)	axon (GO:0030424)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)		p.N112S(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	24	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0934)		AGGGATGTAATTGTCTGTCAG	0.547																																					Melanoma(180;509 2033 10762 15939 24711)											1	Substitution - Missense(1)	large_intestine(1)	11											148	146	146					11																	125351506		2201	4299	6500	124856716	SO:0001583	missense	9638			U60060	CCDS31716.1, CCDS44758.1	11q24.2	2005-09-29			ENSG00000149557	ENSG00000149557			3659	protein-coding gene	gene with protein product		604825				9096408, 15843383	Standard	NM_005103		Approved		uc001qbx.3	Q99689	OTTHUMG00000165886	ENST00000278919.3:c.335A>G	11.37:g.125351506T>C	ENSP00000278919:p.Asn112Ser		124856716	O00679|O00728|Q6IBI7	Missense_Mutation	SNP	ENST00000278919.3	37	CCDS31716.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528157	0.64860	.	.	ENSG00000149557	ENST00000278919	T	0.52754	0.65	5.89	4.77	0.60923	.	0.121727	0.85682	N	0.000000	T	0.47040	0.1424	M	0.69248	2.105	0.80722	D	1	P;B	0.39094	0.659;0.43	B;B	0.40565	0.333;0.137	T	0.40739	-0.9547	9	.	.	.	-24.6226	9.7858	0.40675	0.0:0.1417:0.0:0.8583	.	112;112	B4DKG5;Q99689	.;FEZ1_HUMAN	S	112	ENSP00000278919:N112S	.	N	-	2	0	FEZ1	124856716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.352000	0.66028	1.060000	0.40578	0.533000	0.62120	AAT		0.547	FEZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386875.1	NM_005103		C	125351506	T	C	125351506	3	2	67	1	0	0	0	0	1	0	0	0	5842	1493	52	4	875	4	FEZ1	11	125351506	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	556552	125351506	9655010	75	20831										
SLC6A13	6540	broad.mit.edu	37	chr12	335654	335654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccacaaagctggtgccgctgTtgaggaagcagagggcgatg	16	9	0	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr12:335654T>C	ENST00000343164.4	-	9	1014	c.962A>G	c.(961-963)aAc>aGc	p.N321S	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Missense_Mutation_p.N229S	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	321				Missing (in Ref. 1; AAF64247). {ECO:0000305}.	neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.N321S(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GGTGCCGCTGTTGAGGAAGCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	12											61	53	56					12																	335654		2203	4300	6503	205915	SO:0001583	missense	6540			U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.962A>G	12.37:g.335654T>C	ENSP00000339260:p.Asn321Ser		205915	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.784247	0.90282	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	D;D	0.82433	-1.61;-1.61	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.94538	0.8241	H	0.98218	4.175	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.83275	0.973;0.996	D	0.96534	0.9395	10	0.87932	D	0	.	15.3028	0.73966	0.0:0.0:0.0:1.0	.	229;321	B4DJL1;Q9NSD5	.;S6A13_HUMAN	S	229;300;321	ENSP00000407104:N229S;ENSP00000339260:N321S	ENSP00000318097:N300S	N	-	2	0	SLC6A13	205915	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.974000	0.88039	2.010000	0.58986	0.402000	0.26972	AAC		0.617	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		C	335654	T	C	335654	3	2	67	1	0	0	0	0	1	0	0	0	14713	1725	60	4	874	4	SLC6A13	12	335654	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09		335654	133516241	76	20832										
KRAS	3845	broad.mit.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr12:25398285C>T	ENST00000256078.4	-	2	97	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	KRAS_ENST00000311936.3_Missense_Mutation_p.G12S|KRAS_ENST00000556131.1_Missense_Mutation_p.G12S|KRAS_ENST00000557334.1_Missense_Mutation_p.G12S	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>A	12.37:g.25398285C>T	ENSP00000256078:p.Gly12Ser		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441396	0.96187	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	L	0.28344	0.845	0.80722	D	1	P;P	0.39665	0.557;0.682	P;P	0.50570	0.525;0.644	T	0.80254	-0.1459	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	S	12	ENSP00000308495:G12S;ENSP00000452512:G12S;ENSP00000256078:G12S;ENSP00000451856:G12S	ENSP00000256078:G12S	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398285	C	T	25398285	3	4	67	1	0	0	0	0	1	0	0	0	8459	594	21	3	672	3	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	25062631	25398285	108453610	77	20833										
ACVRL1	94	broad.mit.edu	37	chr12	52309909	52309910	+	Missense_Mutation	DNP	GT	GT	TG													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agcggtacatggcacccgagGtgctggacgagcagatccgc							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr12:52309909_52309910GT>TG	ENST00000388922.4	+	8	1421_1422	c.1138_1139GT>TG	c.(1138-1140)GTg>TGg	p.V380W	ACVRL1_ENST00000550683.1_Missense_Mutation_p.V394W|ACVRL1_ENST00000419526.2_Missense_Mutation_p.V206W	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	380	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.V380>?(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	GGCACCCGAGGTGCTGGACGAG	0.619																																																1	Complex(1)	large_intestine(1)	12	GRCh37	CM050026	ACVRL1	M																																				50596177	SO:0001583	missense	94			L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	Exception_encountered	12.37:g.52309909_52309910delinsTG	ENSP00000373574:p.Val380Trp		50596176	A6NGA8	Missense_Mutation	DNP	ENST00000388922.4	37	CCDS31804.1																																																																																				0.619	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			TG	52309910	GT	TG	52309909	3	4	67	1	0	0	0	0	1	0	0	0	225	1261	44	2	1164	2	ACVRL1	12	52309909	Missense_Mutation	DNP	GT	TCGA-AG-A014-01A-02W-A00K-09	26911624	52309909	81541986	78	20834										
MYF5	4617	broad.mit.edu	37	chr12	81111304	81111304	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctgccgggacagagctgctcGgagcccaccagccccacctc	11	19	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr12:81111304G>A	ENST00000228644.3	+	1	614	c.462G>A	c.(460-462)tcG>tcA	p.S154S		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	154					camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.S154S(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						AGAGCTGCTCGGAGCCCACCA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	12											120	130	127					12																	81111304		2203	4300	6503	79635435	SO:0001819	synonymous_variant	4617				CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.462G>A	12.37:g.81111304G>A			79635435	Q6ISR9	Silent	SNP	ENST00000228644.3	37	CCDS9020.1																																																																																				0.542	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		A	81111304	G	A	81111304	2	1	67	1	0	0	0	0	0	0	0	1	10057	1103	39	1		1	MYF5	12	81111304	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	28801395	81111304	52740591	79	20835										
GLT8D2	83468	broad.mit.edu	37	chr12	104413414	104413414	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agttgaaatcttactttttcGtaacagagccatgtgtattc	7	7	1	2	rs527597208		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr12:104413414G>A	ENST00000360814.4	-	3	418	c.13C>T	c.(13-15)Cga>Tga	p.R5*	GLT8D2_ENST00000548660.1_Nonsense_Mutation_p.R5*|GLT8D2_ENST00000546436.1_Nonsense_Mutation_p.R5*|GLT8D2_ENST00000547583.1_Nonsense_Mutation_p.R5*	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	5						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.R5*(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						TTACTTTTTCGTAACAGAGCC	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											69	67	68					12																	104413414		2203	4300	6503	102937544	SO:0001587	stop_gained	83468			BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"Glycosyltransferase family 8 domain containing"	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.13C>T	12.37:g.104413414G>A	ENSP00000354053:p.Arg5*		102937544	Q96KA2	Nonsense_Mutation	SNP	ENST00000360814.4	37	CCDS9096.1	.	.	.	.	.	.	.	.	.	.	G	39	7.553357	0.98355	.	.	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660;ENST00000547583	.	.	.	4.29	4.29	0.51040	.	0.188567	0.41294	D	0.000902	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.489	0.67637	0.0:0.0:1.0:0.0	.	.	.	.	X	5	.	ENSP00000354053:R5X	R	-	1	2	GLT8D2	102937544	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.584000	0.36589	2.325000	0.78763	0.655000	0.94253	CGA		0.338	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302		A	104413414	G	A	104413414	4	1	67	1	0	0	0	0	0	1	0	0	6490	1153	40	1	1072	1	GLT8D2	12	104413414	Nonsense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	23302110	104413414	29438481	80	20836										
RXFP2	122042	broad.mit.edu	37	chr13	32351551	32351551	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aataaccagaatttcacagcGcttgtttacgggattaaatt	7	7	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr13:32351551G>A	ENST00000298386.2	+	8	751	c.680G>A	c.(679-681)cGc>cAc	p.R227H	RXFP2_ENST00000380314.1_Missense_Mutation_p.R227H	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	227					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)	p.R227H(1)		cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		ATTTCACAGCGCTTGTTTACG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	13											130	123	125					13																	32351551		2202	4298	6500	31249551	SO:0001583	missense	122042			AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.680G>A	13.37:g.32351551G>A	ENSP00000298386:p.Arg227His		31249551	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994465	0.35226	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.57752	0.38;3.6	4.96	-4.54	0.03452	.	0.839567	0.10978	N	0.612999	T	0.29423	0.0733	N	0.11756	0.17	0.09310	N	1	B;B	0.31879	0.344;0.195	B;B	0.26864	0.074;0.02	T	0.07809	-1.0753	10	0.45353	T	0.12	.	12.7777	0.57457	0.7608:0.0:0.2392:0.0	.	227;227	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	H	227	ENSP00000369670:R227H;ENSP00000298386:R227H	ENSP00000298386:R227H	R	+	2	0	RXFP2	31249551	0.206000	0.23470	0.029000	0.17559	0.995000	0.86356	-0.273000	0.08548	-0.901000	0.03891	0.655000	0.94253	CGC		0.333	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		A	32351551	G	A	32351551	3	1	67	1	0	0	0	0	1	0	0	0	13797	1087	38	1	710	1	RXFP2	13	32351551	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		32351551	82818327	81	20837										
ESD	2098	broad.mit.edu	37	chr13	47345618	47345618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aggttgcaatgaagtagtagCtatgatcataaccctagaag	10	6	1	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr13:47345618C>T	ENST00000378720.3	-	10	964	c.782G>A	c.(781-783)aGc>aAc	p.S261N	ESD_ENST00000378697.1_Missense_Mutation_p.S232N	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	261					formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)	p.S261N(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	GAAGTAGTAGCTATGATCATA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	13											152	154	153					13																	47345618		2203	4296	6499	46243619	SO:0001583	missense	2098			M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"S-formylglutathione hydrolase"	133280	"esterase D/formylglutathione hydrolase"				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.782G>A	13.37:g.47345618C>T	ENSP00000367992:p.Ser261Asn		46243619	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Missense_Mutation	SNP	ENST00000378720.3	37	CCDS9404.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344405	0.61073	.	.	ENSG00000139684	ENST00000378720;ENST00000378697	T;T	0.33216	1.42;1.42	6.17	5.17	0.71159	.	0.121779	0.85682	D	0.000000	T	0.45816	0.1361	M	0.91300	3.195	0.58432	D	0.999999	B	0.11235	0.004	B	0.15484	0.013	T	0.52003	-0.8633	10	0.72032	D	0.01	-2.4481	15.5559	0.76192	0.0:0.9239:0.0:0.0761	.	261	P10768	ESTD_HUMAN	N	261;232	ENSP00000367992:S261N;ENSP00000367969:S232N	ENSP00000367969:S232N	S	-	2	0	ESD	46243619	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.854000	0.69503	2.941000	0.99782	0.655000	0.94253	AGC		0.328	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1			T	47345618	C	T	47345618	3	4	67	1	0	0	0	0	1	0	0	0	5263	797	28	3	70	3	ESD	13	47345618	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	14994067	47345618	67824260	82	20838										
SLITRK1	114798	broad.mit.edu	37	chr13	84454465	84454465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tcttgtaatccacaaagtgcGattttcggatgctgtggatc	10	8	1	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr13:84454465G>A	ENST00000377084.2	-	1	2063	c.1178C>T	c.(1177-1179)tCg>tTg	p.S393L		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	393					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.S393L(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		CACAAAGTGCGATTTTCGGAT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	13											180	175	177					13																	84454465		2203	4300	6503	83352466	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1178C>T	13.37:g.84454465G>A	ENSP00000366288:p.Ser393Leu		83352466	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893641	0.33442	.	.	ENSG00000178235	ENST00000377084	T	0.60171	0.21	5.22	5.22	0.72569	.	0.214383	0.40728	N	0.001036	T	0.57784	0.2077	M	0.62266	1.93	0.40711	D	0.982577	B	0.25048	0.117	B	0.25884	0.064	T	0.58137	-0.7689	10	0.44086	T	0.13	-6.2556	17.3478	0.87314	0.0:0.0:1.0:0.0	.	393	Q96PX8	SLIK1_HUMAN	L	393	ENSP00000366288:S393L	ENSP00000366288:S393L	S	-	2	0	SLITRK1	83352466	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.049000	0.64244	2.448000	0.82819	0.555000	0.69702	TCG		0.453	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454465	G	A	84454465	3	1	67	1	0	0	0	0	1	0	0	0	14779	1059	37	1	916	1	SLITRK1	13	84454465	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	37108847	84454465	30715413	83	20839										
SLITRK5	26050	broad.mit.edu	37	chr13	88327927	88327927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtccggaaaccttttgaaccGtctctatcccaatgagtttg	8	11	1	2	rs370073384		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr13:88327927G>A	ENST00000325089.6	+	2	503	c.284G>A	c.(283-285)cGt>cAt	p.R95H	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	95					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)		p.R95H(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CTTTTGAACCGTCTCTATCCC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	HIS/ARG	1,4405		0,1,2202	155	162	159		284	5.9	1	13		159	0,8600		0,0,4300	no	missense	SLITRK5	NM_015567.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	95/959	88327927	1,13005	2203	4300	6503	87125928	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.284G>A	13.37:g.88327927G>A	ENSP00000366283:p.Arg95His		87125928	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688547	0.48097	2.27E-4	0.0	ENSG00000165300	ENST00000325089	T	0.52754	0.65	5.94	5.94	0.96194	.	0.056937	0.64402	D	0.000004	T	0.59959	0.2232	L	0.41356	1.27	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.52990	-0.8501	9	.	.	.	-6.5501	17.8571	0.88767	0.0:0.0:1.0:0.0	.	95	O94991	SLIK5_HUMAN	H	95	ENSP00000366283:R95H	.	R	+	2	0	SLITRK5	87125928	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.441000	0.59981	2.826000	0.97356	0.561000	0.74099	CGT		0.478	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88327927	G	A	88327927	3	1	67	1	0	0	0	0	1	0	0	0	14783	1145	40	1	286	1	SLITRK5	13	88327927	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	3873462	88327927	26841951	84	20840										
ACIN1	22985	broad.mit.edu	37	chr14	23564317	23564317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gagtcacctcctccagctccGccatcttgcgtgaggtactc	9	16	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr14:23564317G>A	ENST00000262710.1	-	1	506	c.179C>T	c.(178-180)gCg>gTg	p.A60V	C14orf119_ENST00000319074.4_5'UTR|ACIN1_ENST00000605057.1_Missense_Mutation_p.A2V|ACIN1_ENST00000457657.1_Missense_Mutation_p.A60V|ACIN1_ENST00000555053.1_Missense_Mutation_p.A60V|C14orf119_ENST00000554203.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	60					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A60V(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CTCCAGCTCCGCCATCTTGCG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	14											47	46	46					14																	23564317		2203	4300	6503	22634157	SO:0001583	missense	22985			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.179C>T	14.37:g.23564317G>A	ENSP00000262710:p.Ala60Val		22634157	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	G	35	5.535441	0.96460	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.24538	1.86;1.89;1.85	5.45	5.45	0.79879	.	0.000000	0.35870	N	0.002936	T	0.33585	0.0868	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.43718	-0.9374	10	0.87932	D	0	-11.0251	18.2118	0.89872	0.0:0.0:1.0:0.0	.	60;60	G3V3M7;Q9UKV3	.;ACINU_HUMAN	V	60	ENSP00000262710:A60V;ENSP00000405677:A60V;ENSP00000451328:A60V	ENSP00000262710:A60V	A	-	2	0	ACIN1	22634157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.140000	0.89616	2.837000	0.97791	0.591000	0.81541	GCG		0.652	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23564317	G	A	23564317	3	1	67	1	0	0	0	0	1	0	0	0	142	1087	38	1	4069	1	ACIN1	14	23564317	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		23564317	83785223	85	20841										
TRIP11	9321	broad.mit.edu	37	chr14	92471877	92471877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tttaagcttttcaataaaaaTttctttcttgtttataagtt	3	4	3	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr14:92471877T>C	ENST00000267622.4	-	11	2816	c.2443A>G	c.(2443-2445)Att>Gtt	p.I815V		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	815					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.I815V(1)		breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TCAATAAAAATTTCTTTCTTG	0.313			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	1	Substitution - Missense(1)	large_intestine(1)	14											67	73	71					14																	92471877		2203	4297	6500	91541630	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.2443A>G	14.37:g.92471877T>C	ENSP00000267622:p.Ile815Val		91541630	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.005|0.005	-2.135516|-2.135516	0.00335|0.00335	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.03772|.	3.81|.	5.77|5.77	-1.14|-1.14	0.09741|0.09741	.|.	0.714554|.	0.14207|.	N|.	0.334345|.	T|T	0.22282|0.22282	0.0537|0.0537	L|L	0.31926|0.31926	0.97|0.97	0.09310|0.09310	N|N	1|1	B;B|.	0.09022|.	0.001;0.002|.	B;B|.	0.06405|.	0.001;0.002|.	T|T	0.25222|0.25222	-1.0138|-1.0138	10|5	0.27082|.	T|.	0.32|.	.|.	1.3989|1.3989	0.02267|0.02267	0.1186:0.2406:0.2441:0.3968|0.1186:0.2406:0.2441:0.3968	.|.	551;815|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	V|S	815;551|530	ENSP00000267622:I815V|.	ENSP00000267622:I815V|.	I|N	-|-	1|2	0|0	TRIP11|TRIP11	91541630|91541630	0.000000|0.000000	0.05858|0.05858	0.031000|0.031000	0.17742|0.17742	0.601000|0.601000	0.36947|0.36947	-0.080000|-0.080000	0.11339|0.11339	-0.422000|-0.422000	0.07405|0.07405	0.254000|0.254000	0.18369|0.18369	ATT|AAT		0.313	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92471877	T	C	92471877	3	2	67	1	0	0	0	0	1	0	0	0	16595	1493	52	4	3540	4	TRIP11	14	92471877	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	68907560	92471877	14877663	86	20842										
SERPINA1	5265	broad.mit.edu	37	chr14	94848949	94848949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctttaaagaagatgtaattcAccagagcaaaaactgtgtct	7	7	2	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr14:94848949A>G	ENST00000448921.1	-	4	1198	c.626T>C	c.(625-627)gTg>gCg	p.V209A	SERPINA1_ENST00000404814.4_Missense_Mutation_p.V209A|SERPINA1_ENST00000393087.4_Missense_Mutation_p.V209A|SERPINA1_ENST00000393088.4_Missense_Mutation_p.V209A|SERPINA1_ENST00000437397.1_Missense_Mutation_p.V209A|SERPINA1_ENST00000449399.3_Missense_Mutation_p.V209A|SERPINA1_ENST00000402629.1_Missense_Mutation_p.V209A|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000355814.4_Missense_Mutation_p.V209A|SERPINA1_ENST00000440909.1_Missense_Mutation_p.V209A	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	209					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.V209A(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GATGTAATTCACCAGAGCAAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	14											106	109	108					14																	94848949		2203	4300	6503	93918702	SO:0001583	missense	5265			X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.626T>C	14.37:g.94848949A>G	ENSP00000416066:p.Val209Ala		93918702	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.929126	0.73327	.	.	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629	D;D;D;D;D;D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25	5.79	4.61	0.57282	Serpin domain (3);	0.473727	0.19413	N	0.114896	D	0.91536	0.7327	M	0.82433	2.59	0.32386	N	0.553927	P;P	0.49635	0.926;0.812	P;P	0.56823	0.768;0.807	D	0.91650	0.5334	10	0.38643	T	0.18	.	10.7189	0.46030	0.8656:0.0:0.1344:0.0	.	209;209	P01009-2;P01009	.;A1AT_HUMAN	A	209	ENSP00000390299:V209A;ENSP00000416066:V209A;ENSP00000408474:V209A;ENSP00000348068:V209A;ENSP00000376802:V209A;ENSP00000376803:V209A;ENSP00000385960:V209A;ENSP00000416354:V209A;ENSP00000386094:V209A	ENSP00000348068:V209A	V	-	2	0	SERPINA1	93918702	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	6.976000	0.76135	0.981000	0.38548	0.459000	0.35465	GTG		0.423	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		G	94848949	A	G	94848949	3	3	67	1	0	0	0	0	1	0	0	0	14123	159	6	4	646	4	SERPINA1	14	94848949	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	2377072	94848949	12500591	87	20843										
MAGEL2	54551	broad.mit.edu	37	chr15	23889919	23889919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgcgacctcagacacaactaCgggcagagagctccctgggc	12	14	1	2	rs372805925	byFrequency	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:23889919C>T	ENST00000532292.1	-	1	1256	c.1162G>A	c.(1162-1164)Gta>Ata	p.V388I		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	271	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		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)		GACACAACTACGGGCAGAGAG	0.642													C|||	2	0.000399361	0	0	5008	,	,		17883	0		0	False		,,,				2504	0.002															0			15						C	ILE/VAL	0,3856		0,0,1928	36	37	37		2971	-6.3	0	15		37	1,8269		0,1,4134	no	missense	MAGEL2	NM_019066.4	29	0,1,6062	TT,TC,CC		0.0121,0.0,0.0082	benign	991/1250	23889919	1,12125	1928	4135	6063	21441012	SO:0001583	missense	54551			AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1162G>A	15.37:g.23889919C>T	ENSP00000433433:p.Val388Ile		21441012		Missense_Mutation	SNP	ENST00000532292.1	37																																																																																					0.642	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		T	23889919	C	T	23889919	3	4	67	1	0	0	0	0	1	0	0	0	9219	536	19	1	782	1	MAGEL2	15	23889919	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09		23889919	78641473	88	20844										
C15orf2	23742	broad.mit.edu	37	chr15	24921147	24921147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ctcactctgtacccaccccgCgccctttccgcggcctgttc	7	21	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:24921147C>T	ENST00000329468.2	+	1	607	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	45					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R45C(1)									ACCCACCCCGCGCCCTTTCCG	0.761																																																1	Substitution - Missense(1)	large_intestine(1)	15											11	14	13					15																	24921147		2139	4164	6303	22472240	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.133C>T	15.37:g.24921147C>T	ENSP00000333735:p.Arg45Cys		22472240		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	13.85	2.361417	0.41801	.	.	ENSG00000185823	ENST00000329468	T	0.07327	3.2	2.14	-4.28	0.03732	.	2.777100	0.01720	N	0.028204	T	0.05914	0.0154	N	0.22421	0.69	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.35025	-0.9805	10	0.54805	T	0.06	.	3.9791	0.09487	0.0:0.2566:0.3614:0.382	.	45	Q9NZP6	CO002_HUMAN	C	45	ENSP00000333735:R45C	ENSP00000333735:R45C	R	+	1	0	C15orf2	22472240	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.364000	0.07583	-1.295000	0.02357	0.305000	0.20034	CGC		0.761	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921147	C	T	24921147	3	4	67	1	0	0	0	0	1	0	0	0	1788	768	27	1	135	1	C15orf2	15	24921147	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	1031228	24921147	77610245	89	20845										
C15orf41	84529	broad.mit.edu	37	chr15	36950064	36950064	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cgccctcattaatggctcggCttatactggagaggtttcta	10	10	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:36950064C>G	ENST00000566621.1	+	5	554	c.304C>G	c.(304-306)Ctt>Gtt	p.L102V	C15orf41_ENST00000569302.1_Missense_Mutation_p.L102V|C15orf41_ENST00000567389.1_Missense_Mutation_p.L4V|C15orf41_ENST00000562877.1_Missense_Mutation_p.L4V|C15orf41_ENST00000338183.4_Missense_Mutation_p.L4V|C15orf41_ENST00000437989.2_Missense_Mutation_p.L102V|RP11-16L14.2_ENST00000565366.1_RNA	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	102								p.L102V(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		AATGGCTCGGCTTATACTGGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											66	62	63					15																	36950064		1828	4076	5904	34737356	SO:0001583	missense	84529			BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.304C>G	15.37:g.36950064C>G	ENSP00000455397:p.Leu102Val		34737356	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	37	CCDS45215.1	.	.	.	.	.	.	.	.	.	.	C	3.072	-0.190834	0.06299	.	.	ENSG00000186073	ENST00000437989;ENST00000338183	T	0.47869	0.83	5.32	4.23	0.50019	.	.	.	.	.	T	0.38241	0.1033	L	0.35644	1.08	0.23969	N	0.996313	B	0.06786	0.001	B	0.06405	0.002	T	0.20174	-1.0283	9	0.28530	T	0.3	-0.4456	12.3195	0.54977	0.8391:0.1609:0.0:0.0	.	102	Q9Y2V0	CO041_HUMAN	V	102;4	ENSP00000401362:L102V	ENSP00000342433:L4V	L	+	1	0	C15orf41	34737356	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	1.512000	0.35812	1.040000	0.40099	0.650000	0.86243	CTT		0.398	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		G	36950064	C	G	36950064	3	3	67	1	0	0	0	0	1	0	0	0	1799	797	28	5	322	5	C15orf41	15	36950064	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	12028917	36950064	65581328	90	20846										
PLA2G4D	283748	broad.mit.edu	37	chr15	42379579	42379579	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtgagcgtcttggtcttaaaCttcattccaggtgcggtcga	12	9	3	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:42379579C>G	ENST00000290472.3	-	3	268	c.174G>C	c.(172-174)aaG>aaC	p.K58N		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	58	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.K58N(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		TGGTCTTAAACTTCATTCCAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	15											235	206	216					15																	42379579		2203	4299	6502	40166871	SO:0001583	missense	283748			AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.174G>C	15.37:g.42379579C>G	ENSP00000290472:p.Lys58Asn		40166871	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.860578	0.32884	.	.	ENSG00000159337	ENST00000290472	T	0.72051	-0.62	5.15	2.17	0.27698	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.231810	0.35585	N	0.003102	T	0.79364	0.4433	M	0.91818	3.245	0.09310	N	0.999996	P	0.47191	0.891	P	0.51324	0.666	T	0.70666	-0.4809	10	0.52906	T	0.07	-35.4794	7.2849	0.26333	0.0:0.6328:0.0:0.3672	.	58	Q86XP0	PA24D_HUMAN	N	58	ENSP00000290472:K58N	ENSP00000290472:K58N	K	-	3	2	PLA2G4D	40166871	0.007000	0.16637	0.590000	0.28732	0.274000	0.26718	0.053000	0.14184	0.667000	0.31107	-0.140000	0.14226	AAG		0.547	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		G	42379579	C	G	42379579	3	3	67	1	0	0	0	0	1	0	0	0	12035	564	20	5	2354	5	PLA2G4D	15	42379579	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	5429515	42379579	60151813	91	20847										
PRTG	283659	broad.mit.edu	37	chr15	55974598	55974598	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cgaggcctccatacttttacGtcggtgggctacagtggcag	13	11	0	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:55974598G>A	ENST00000389286.4	-	4	687	c.640C>T	c.(640-642)Cgt>Tgt	p.R214C	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin									p.R214C(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ATACTTTTACGTCGGTGGGCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	15											104	103	103					15																	55974598		1919	4126	6045	53761890	SO:0001583	missense	283659			AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.640C>T	15.37:g.55974598G>A	ENSP00000373937:p.Arg214Cys		53761890		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.714689	0.48622	.	.	ENSG00000166450	ENST00000389286	T	0.68025	-0.3	5.41	4.49	0.54785	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83547	0.5278	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	P	0.60173	0.87	D	0.87865	0.2667	10	0.72032	D	0.01	-14.6203	14.8166	0.70039	0.0:0.0:0.8555:0.1445	.	214	Q2VWP7	PRTG_HUMAN	C	214	ENSP00000373937:R214C	ENSP00000373937:R214C	R	-	1	0	PRTG	53761890	1.000000	0.71417	0.030000	0.17652	0.179000	0.23085	4.335000	0.59298	1.256000	0.44068	0.491000	0.48974	CGT		0.453	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		A	55974598	G	A	55974598	3	1	67	1	0	0	0	0	1	0	0	0	12672	1145	40	1	2880	1	PRTG	15	55974598	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	13595019	55974598	46556794	92	20848										
GCOM1	100820829	broad.mit.edu	37	chr15	57896494	57896494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tttgcagactacggctgaccGtacctcctgagagtccagtt	10	12	0	3			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:57896494G>A	ENST00000267853.5	+	2	197	c.103G>A	c.(103-105)Gta>Ata	p.V35I	MYZAP_ENST00000380565.4_Missense_Mutation_p.V35I|GCOM1_ENST00000396180.1_Missense_Mutation_p.V35I|GCOM1_ENST00000380569.2_Missense_Mutation_p.V35I|GCOM1_ENST00000574161.1_Missense_Mutation_p.V35I|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380560.2_Missense_Mutation_p.V35I|GCOM1_ENST00000380561.2_Missense_Mutation_p.V35I|GCOM1_ENST00000380568.3_Missense_Mutation_p.V35I|GCOM1_ENST00000587652.1_Missense_Mutation_p.V35I|GCOM1_ENST00000572390.1_Missense_Mutation_p.V35I			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	35					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)		p.V35I(1)									ACGGCTGACCGTACCTCCTGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	15											167	167	167					15																	57896494		2192	4292	6484	55683786	SO:0001583	missense	145781			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.103G>A	15.37:g.57896494G>A	ENSP00000267853:p.Val35Ile		55683786	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.914249	0.33815	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.32988	1.67;1.43;1.48;1.53;1.66;1.66;1.65	5.24	4.32	0.51571	.	0.244676	0.35040	N	0.003492	T	0.27629	0.0679	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.23854	0.092;0.038;0.038;0.018	B;B;B;B	0.15052	0.012;0.012;0.012;0.012	T	0.08186	-1.0734	10	0.48119	T	0.1	-18.6802	9.7885	0.40690	0.0931:0.0:0.9069:0.0	.	35;35;35;35	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	I	35	ENSP00000369943:V35I;ENSP00000369935:V35I;ENSP00000379483:V35I;ENSP00000369933:V35I;ENSP00000267853:V35I;ENSP00000369939:V35I;ENSP00000369942:V35I	ENSP00000267853:V35I	V	+	1	0	GCOM1	55683786	0.151000	0.22747	0.503000	0.27626	0.548000	0.35241	1.088000	0.30877	1.567000	0.49668	0.655000	0.94253	GTA		0.507	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		A	57896494	G	A	57896494	3	1	67	1	0	0	0	0	1	0	0	0	6324	1145	40	1	109	1	GCOM1	15	57896494	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	1921896	57896494	44634898	93	20849										
CYP1A2	1544	broad.mit.edu	37	chr15	75042288	75042289	+	Missense_Mutation	DNP	AG	AG	CC													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ggcactgtcaaggatgagccAgcgctacggggacgtcctgc					rs207475597		TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr15:75042288_75042289AG>CC	ENST00000343932.4	+	2	272_273	c.209_210AG>CC	c.(208-210)cAG>cCC	p.Q70P		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	70					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.Q70>?(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"	AGGATGAGCCAGCGCTACGGGG	0.668																																																1	Complex(1)	large_intestine(1)	15																																								72829342	SO:0001583	missense	1544			AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"Cytochrome P450s"	2596	protein-coding gene	gene with protein product		124060	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	Exception_encountered	15.37:g.75042288_75042289delinsCC	ENSP00000342007:p.Gln70Pro		72829341	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	DNP	ENST00000343932.4	37	CCDS32293.1																																																																																				0.668	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		CC	75042289	AG	CC	75042288	3	2	67	1	0	0	0	0	1	0	0	0	4156	188	7	4	211	4	CYP1A2	15	75042288	Missense_Mutation	DNP	AG	TCGA-AG-A014-01A-02W-A00K-09	17145794	75042288	27489104	94	20850										
AXIN1	8312	broad.mit.edu	37	chr16	396705	396706	+	Missense_Mutation	DNP	CT	CT	TA													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aagtcggcacagccctcctgCttcaggaaagtcctgaacag							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:396705_396706CT>TA	ENST00000262320.3	-	2	691_692	c.320_321AG>TA	c.(319-321)aAG>aTA	p.K107I	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.K107I	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	107	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.K107>?(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				AGCCCTCCTGCTTCAGGAAAGT	0.579											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Complex(1)	large_intestine(1)	16																																								336707	SO:0001583	missense	8312			AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.320_321delinsTA	16.37:g.396705_396706delinsTA	ENSP00000262320:p.Lys107Ile	588	336706	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	DNP	ENST00000262320.3	37	CCDS10405.1																																																																																				0.579	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			TA	396706	CT	TA	396705	3	4	67	1	0	0	0	0	1	0	0	0	1237	796	28	3	2307	3	AXIN1	16	396705	Missense_Mutation	DNP	CT	TCGA-AG-A014-01A-02W-A00K-09		396705	89958048	95	20851										
RPS2	6187	broad.mit.edu	37	chr16	2012734	2012735	+	Intron	INS	-	-	A													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccatcacctgccaccagcctINSaccttgcaagggacagtgtg							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:2012734_2012735insA	ENST00000343262.4	-	5	606				RPS2_ENST00000530225.1_Intron|SNHG9_ENST00000459373.1_lincRNA|RPS2_ENST00000529806.1_Intron|RPS2_ENST00000526522.1_Intron|SNORA64_ENST00000384674.1_RNA|SNORA10_ENST00000384084.1_RNA	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.?(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						GCCACCAGCCTACCTTGCAAGG	0.668																																																1	Unknown(1)	large_intestine(1)	16																																								1952736	SO:0001627	intron_variant	6187			AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"S ribosomal proteins"	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.549+1->T	16.37:g.2012735_2012735dupA			1952735	B2R5G0|D3DU82|Q3MIB1	Splice_Site	INS	ENST00000343262.4	37	CCDS10452.1																																																																																				0.668	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		A	2012735	-	A	2012734	6	5	67	0	1	1	1	0	0	0	0	0	13668	1537	53	0		0	RPS2	16	2012734	Intron	INS	-	TCGA-AG-A014-01A-02W-A00K-09	1616029	2012734	88342019	96	20852										
A2BP1	54715	broad.mit.edu	37	chr16	7760731	7760731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ataccgagggggatacaaccGttttgctccatactaaatga	9	9	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:7760731G>A	ENST00000550418.1	+	16	2166	c.1178G>A	c.(1177-1179)cGt>cAt	p.R393H	RBFOX1_ENST00000552089.1_3'UTR|RBFOX1_ENST00000547372.1_3'UTR|RBFOX1_ENST00000340209.4_Missense_Mutation_p.R398H|RBFOX1_ENST00000355637.4_3'UTR|RBFOX1_ENST00000553186.1_Missense_Mutation_p.R366H|RBFOX1_ENST00000311745.5_Missense_Mutation_p.R414H|RBFOX1_ENST00000547338.1_Missense_Mutation_p.R393H|RBFOX1_ENST00000436368.2_Missense_Mutation_p.R388H	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	393					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.R414H(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						GGATACAACCGTTTTGCTCCA	0.443																																					Ovarian(157;934 2567 15163 39509)											1	Substitution - Missense(1)	large_intestine(1)	16											149	134	139					16																	7760731		2197	4300	6497	7700732	SO:0001583	missense	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.1178G>A	16.37:g.7760731G>A	ENSP00000450031:p.Arg393His		7700732	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.219661	0.79464	.	.	ENSG00000078328	ENST00000550418;ENST00000553186;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000352951;ENST00000340209	T;T;T;T;T;T	0.50813	0.77;0.73;0.77;1.15;1.03;0.8	5.95	5.95	0.96441	.	0.104988	0.64402	D	0.000003	T	0.64091	0.2567	L	0.39245	1.2	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.939;0.996;0.996;0.988;0.983	T	0.63985	-0.6513	10	0.87932	D	0	-6.5935	20.3923	0.98948	0.0:0.0:1.0:0.0	.	387;414;388;366;393	F8WAC5;Q9NWB1-2;Q9NWB1-4;Q9NWB1-3;Q9NWB1	.;.;.;.;RFOX1_HUMAN	H	393;366;393;388;414;387;398	ENSP00000450031:R393H;ENSP00000447753:R366H;ENSP00000447717:R393H;ENSP00000402745:R388H;ENSP00000309117:R414H;ENSP00000344196:R398H	ENSP00000309117:R414H	R	+	2	0	RBFOX1	7700732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.014000	0.93635	2.831000	0.97527	0.609000	0.83330	CGT		0.443	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		A	7760731	G	A	7760731	3	1	67	1	0	0	0	0	1	0	0	0	3	1145	40	1	1423	1	A2BP1	16	7760731	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	5747997	7760731	82594022	97	20853										
RUNDC2A	92017	broad.mit.edu	37	chr16	12136895	12136895	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	caacgaacactccctggagcGctacctgcacatgctcctgg	9	16	0	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:12136895G>T	ENST00000566228.1	+	5	458	c.389G>T	c.(388-390)cGc>cTc	p.R130L	SNX29_ENST00000568359.1_3'UTR	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	130	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.R130L(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						TCCCTGGAGCGCTACCTGCAC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	16											35	29	31					16																	12136895		2197	4300	6497	12044396	SO:0001583	missense	84127			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.389G>T	16.37:g.12136895G>T	ENSP00000456480:p.Arg130Leu		12044396	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	34	5.319651	0.95682	.	.	ENSG00000140660	ENST00000268271	.	.	.	4.91	4.91	0.64330	.	0.071529	0.53938	D	0.000046	T	0.75079	0.3801	M	0.69823	2.125	0.80722	D	1	.	.	.	.	.	.	T	0.77378	-0.2610	7	0.59425	D	0.04	-0.7179	16.8321	0.85947	0.0:0.0:1.0:0.0	.	.	.	.	L	130	.	ENSP00000268271:R130L	R	+	2	0	RUNDC2A	12044396	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.354000	0.97083	2.555000	0.86185	0.462000	0.41574	CGC		0.652	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12136895	G	T	12136895	3	4	67	1	0	0	0	0	1	0	0	0	13780	1087	38	2	407	2	RUNDC2A	16	12136895	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	4376164	12136895	78217858	98	20854										
CMTM4	146223	broad.mit.edu	37	chr16	66656124	66656125	+	Splice_Site	DNP	AT	AT	CA													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cagtcgccaagaagccaaatAtctaaaaacacaccagcaca							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:66656124_66656125AT>CA	ENST00000330687.4	-	4	644_645	c.463_464AT>TG	c.(463-465)ATa>TGa	p.I155*	CMTM4_ENST00000563952.1_Splice_Site_p.I126*|CMTM4_ENST00000394106.2_Splice_Site_p.I155*	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	155	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.I155>?(1)		cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		GAAGCCAAATATCTAAAAACAC	0.559																																																1	Complex(1)	large_intestine(1)	16																																								65213626	SO:0001630	splice_region_variant	146223			AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.463_464delinsCA	16.37:g.66656124_66656125delinsCA			65213625	Q52M40|Q8IZR4|Q8IZV1	Nonsense_Mutation	DNP	ENST00000330687.4	37	CCDS10817.1																																																																																				0.559	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1		Nonsense_Mutation	CA	66656125	AT	CA	66656124	5	2	67	1	0	0	0	0	0	0	1	0	3591	463	16	4	252	4	CMTM4	16	66656124	Splice_Site	DNP	AT	TCGA-AG-A014-01A-02W-A00K-09	54519229	66656124	23698629	99	20855										
ZC3H18	124245	broad.mit.edu	37	chr16	88694438	88694439	+	Missense_Mutation	DNP	CC	CC	TT													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gggggaagtcctcccagcagCcctcgacaccccagcaggca							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr16:88694438_88694439CC>TT	ENST00000301011.5	+	15	2580_2581	c.2380_2381CC>TT	c.(2380-2382)CCc>TTc	p.P794F	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P818F	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	794						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P794>?(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CTCCCAGCAGCCCTCGACACCC	0.569																																					Ovarian(121;375 2276 20373 38669)											1	Complex(1)	large_intestine(1)	16																																								87221940	SO:0001583	missense	124245			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	Exception_encountered	16.37:g.88694438_88694439delinsTT	ENSP00000301011:p.Pro794Phe		87221939	Q96DG4|Q96MP7	Missense_Mutation	DNP	ENST00000301011.5	37	CCDS10967.1																																																																																				0.569	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		TT	88694439	CC	TT	88694438	3	4	67	1	0	0	0	0	1	0	0	0	17607	739	26	3	2434	3	ZC3H18	16	88694438	Missense_Mutation	DNP	CC	TCGA-AG-A014-01A-02W-A00K-09	22038314	88694438	1660315	100	20856										
TP53	7157	broad.mit.edu	37	chr17	7577118	7577118	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tctcccaggacaggcacaaaCacgcacctcaaagctgttcc	7	16	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:7577118C>G	ENST00000269305.4	-	8	1009	c.820G>C	c.(820-822)Gtt>Ctt	p.V274L	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.V274L|TP53_ENST00000455263.2_Missense_Mutation_p.V274L|TP53_ENST00000445888.2_Missense_Mutation_p.V274L|TP53_ENST00000359597.4_Missense_Mutation_p.V274L|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	274	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V274F(21)|p.V274L(11)|p.0?(8)|p.V274I(4)|p.?(2)|p.R273_C275delRVC(1)|p.V274fs*71(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.V274_P278del(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGCACAAACACGCACCTCA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	54	Substitution - Missense(36)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Unknown(2)	large_intestine(9)|breast(7)|upper_aerodigestive_tract(6)|ovary(4)|prostate(4)|bone(4)|central_nervous_system(3)|urinary_tract(3)|lung(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|skin(2)|adrenal_gland(1)|stomach(1)|soft_tissue(1)|liver(1)	17											69	60	63					17																	7577118		2203	4300	6503	7517843	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.820G>C	17.37:g.7577118C>G	ENSP00000269305:p.Val274Leu		7517843	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397576	0.42512	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99812	-6.88;-6.88;-6.88;-6.88;-6.88;-6.88	4.92	-0.763	0.11030	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.312804	0.33382	N	0.004980	D	0.99411	0.9792	M	0.87456	2.885	0.34283	D	0.682342	B;B;B;B	0.28584	0.216;0.067;0.087;0.049	B;B;B;B	0.40375	0.185;0.096;0.327;0.195	D	0.99980	1.2436	10	0.87932	D	0	-10.2267	9.2232	0.37390	0.0:0.5803:0.0:0.4197	.	274;274;274;274	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	L	274;274;274;274;274;263;142	ENSP00000352610:V274L;ENSP00000269305:V274L;ENSP00000398846:V274L;ENSP00000391127:V274L;ENSP00000391478:V274L;ENSP00000425104:V142L	ENSP00000269305:V274L	V	-	1	0	TP53	7517843	0.002000	0.14202	0.148000	0.22405	0.724000	0.41520	-0.002000	0.12924	-0.004000	0.14419	0.462000	0.41574	GTT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577118	C	G	7577118	3	3	67	1	0	0	0	0	1	0	0	0	16421	478	17	5	466	5	TP53	17	7577118	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09		7577118	73618092	101	20857										
KCNAB3	9196	broad.mit.edu	37	chr17	7829030	7829030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgtgctttcggcttaaacctCgctcggtttctgccctgtag	10	12	1	0	rs535006786	byFrequency	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:7829030C>T	ENST00000303790.2	-	7	508	c.509G>A	c.(508-510)cGa>cAa	p.R170Q		NM_004732.3	NP_004723.2	O43448	KCAB3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 3	170					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)	p.R170Q(1)		breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	8		Prostate(122;0.157)				GCTTAAACCTCGCTCGGTTTC	0.502													C|||	2	0.000399361	0	0	5008	,	,		16872	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17											210	210	210					17																	7829030		2203	4300	6503	7769755	SO:0001583	missense	9196			AF016411	CCDS11124.1	17p13.1	2006-11-29			ENSG00000170049	ENSG00000170049		"Potassium channels", "Aldo-keto reductases"	6230	protein-coding gene	gene with protein product		604111				9857044	Standard	NM_004732		Approved	AKR6A9, KCNA3B	uc002gjm.2	O43448	OTTHUMG00000108170	ENST00000303790.2:c.509G>A	17.37:g.7829030C>T	ENSP00000302719:p.Arg170Gln		7769755	Q4VAW0	Missense_Mutation	SNP	ENST00000303790.2	37	CCDS11124.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.353453	0.82243	.	.	ENSG00000170049	ENST00000303790	T	0.23754	1.89	5.83	4.86	0.63082	NADP-dependent oxidoreductase domain (3);	0.056844	0.64402	D	0.000003	T	0.20210	0.0486	L	0.35414	1.06	0.58432	D	0.999999	P	0.38300	0.626	B	0.32805	0.153	T	0.03008	-1.1083	10	0.62326	D	0.03	.	14.8413	0.70226	0.0:0.9297:0.0:0.0703	.	170	O43448	KCAB3_HUMAN	Q	170	ENSP00000302719:R170Q	ENSP00000302719:R170Q	R	-	2	0	KCNAB3	7769755	0.999000	0.42202	1.000000	0.80357	0.979000	0.70002	4.255000	0.58804	1.471000	0.48121	0.591000	0.81541	CGA		0.502	KCNAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226974.1	NM_004732		T	7829030	C	T	7829030	3	4	67	1	0	0	0	0	1	0	0	0	8032	884	31	1	737	1	KCNAB3	17	7829030	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	251912	7829030	73366180	102	20858										
GUCY2D	3000	broad.mit.edu	37	chr17	7907365	7907366	+	Missense_Mutation	DNP	AT	AT	CC													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ccagcttcgcagggcccacgAtgccgtgctcaccctcacgc							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:7907365_7907366AT>CC	ENST00000254854.4	+	3	1067_1068	c.917_918AT>CC	c.(916-918)gAT>gCC	p.D306A		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	306					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.D306>?(1)		skin(1)	1		Prostate(122;0.157)				AGGGCCCACGATGCCGTGCTCA	0.673																																																1	Complex(1)	large_intestine(1)	17																																								7848091	SO:0001583	missense	3000			L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	Exception_encountered	17.37:g.7907365_7907366delinsCC	ENSP00000254854:p.Asp306Ala		7848090	Q6LEA7	Missense_Mutation	DNP	ENST00000254854.4	37	CCDS11127.1																																																																																				0.673	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			CC	7907366	AT	CC	7907365	3	2	67	1	0	0	0	0	1	0	0	0	6918	333	12	4	923	4	GUCY2D	17	7907365	Missense_Mutation	DNP	AT	TCGA-AG-A014-01A-02W-A00K-09	78335	7907365	73287845	103	20859										
DHRS13	147015	broad.mit.edu	37	chr17	27225675	27225675	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agccctgccagcctcttgctGgcctcccatagccgatgggc	11	17	1	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:27225675G>A	ENST00000378895.4	-	5	1044	c.918C>T	c.(916-918)gcC>gcT	p.A306A	FLOT2_ENST00000577789.1_5'Flank|FLOT2_ENST00000394908.4_5'Flank|FLOT2_ENST00000585169.1_5'Flank|FLOT2_ENST00000394906.2_5'Flank|RP11-20B24.4_ENST00000579187.1_RNA|DHRS13_ENST00000426464.2_Silent_p.A225A|RP11-20B24.4_ENST00000580603.1_RNA|DHRS13_ENST00000581974.1_5'Flank|DHRS13_ENST00000394901.3_Silent_p.A256A	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	306						extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)	p.A306A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	9	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			GCCTCTTGCTGGCCTCCCATA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	17											14	16	16					17																	27225675		2199	4297	6496	24249801	SO:0001819	synonymous_variant	147015			BC015582	CCDS11246.2	17q11.2	2011-09-14			ENSG00000167536	ENSG00000167536	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	28326	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 5"					12975309, 19027726	Standard	NM_144683		Approved	MGC23280, SDR7C5	uc002hde.4	Q6UX07	OTTHUMG00000132678	ENST00000378895.4:c.918C>T	17.37:g.27225675G>A			24249801	Q96BH7	Silent	SNP	ENST00000378895.4	37	CCDS11246.2																																																																																				0.632	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1	NM_144683		A	27225675	G	A	27225675	2	1	67	1	0	0	0	0	0	0	0	1	4500	1335	47	3		3	DHRS13	17	27225675	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	19318310	27225675	53969535	104	20860										
C17orf102	400591	broad.mit.edu	37	chr17	32905944	32905944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cttccttccccagcaacagaAtaaataggtttcccacagct	5	14	0	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:32905944A>G	ENST00000357754.1	-	1	444	c.356T>C	c.(355-357)aTt>aCt	p.I119T	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	119								p.I119T(1)		central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						CAGCAACAGAATAAATAGGTT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											134	144	141					17																	32905944		1913	4117	6030	29930057	SO:0001583	missense	400591				CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.356T>C	17.37:g.32905944A>G	ENSP00000350392:p.Ile119Thr		29930057	A5PKX0|Q6ZTB3	Missense_Mutation	SNP	ENST00000357754.1	37	CCDS42297.1	.	.	.	.	.	.	.	.	.	.	A	8.115	0.779724	0.16120	.	.	ENSG00000197322	ENST00000357754	T	0.38722	1.12	3.4	-6.8	0.01709	.	5.024240	0.00897	U	0.002317	T	0.24084	0.0583	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13415	-1.0510	10	0.87932	D	0	.	2.1016	0.03681	0.2062:0.1226:0.4133:0.2579	.	119	A2RUQ5	CQ102_HUMAN	T	119	ENSP00000350392:I119T	ENSP00000350392:I119T	I	-	2	0	C17orf102	29930057	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.573000	0.05874	-2.676000	0.00411	-1.100000	0.02121	ATT		0.612	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454		G	32905944	A	G	32905944	3	3	67	1	0	0	0	0	1	0	0	0	1853	101	4	4	155	4	C17orf102	17	32905944	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	5680269	32905944	48289266	105	20861										
SLFN5	162394	broad.mit.edu	37	chr17	33585725	33585725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agaagatgagtcttaggattGatgtggatacaaactttcct	10	5	1	4			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:33585725G>T	ENST00000299977.4	+	2	164	c.16G>T	c.(16-18)Gat>Tat	p.D6Y	SLFN5_ENST00000592325.1_Missense_Mutation_p.D6Y|SLFN5_ENST00000542451.1_Missense_Mutation_p.D6Y	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	6					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.D6Y(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		TCTTAGGATTGATGTGGATAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	17											74	71	72					17																	33585725		2203	4300	6503	30609838	SO:0001583	missense	162394			BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.16G>T	17.37:g.33585725G>T	ENSP00000299977:p.Asp6Tyr		30609838	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314896	0.23908	.	.	ENSG00000166750	ENST00000299977;ENST00000542451	T;T	0.10860	4.09;2.83	3.76	0.44	0.16572	.	0.748090	0.10989	N	0.611857	T	0.21307	0.0513	M	0.75615	2.305	0.09310	N	1	P;P;D	0.56035	0.906;0.845;0.974	B;B;P	0.57244	0.431;0.273;0.816	T	0.12426	-1.0548	10	0.35671	T	0.21	.	4.2989	0.10915	0.2216:0.1881:0.5903:0.0	.	6;6;6	B4E128;Q08AF3;Q08AF3-2	.;SLFN5_HUMAN;.	Y	6	ENSP00000299977:D6Y;ENSP00000440537:D6Y	ENSP00000299977:D6Y	D	+	1	0	SLFN5	30609838	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	0.212000	0.17497	0.035000	0.15519	-0.140000	0.14226	GAT		0.458	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		T	33585725	G	T	33585725	3	4	67	1	0	0	0	0	1	0	0	0	14774	1290	45	2	18	2	SLFN5	17	33585725	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	679781	33585725	47609485	106	20862										
KRT37	8688	broad.mit.edu	37	chr17	39580043	39580043	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	aagtcatcagcagccagcttCgcgttgtcaatttgtacaat	8	10	3	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:39580043C>T	ENST00000225550.3	-	2	545	c.546G>A	c.(544-546)gcG>gcA	p.A182A	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	182	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.A182A(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				CAGCCAGCTTCGCGTTGTCAA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	17											125	104	111					17																	39580043		2203	4300	6503	36833569	SO:0001819	synonymous_variant	8688			Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.546G>A	17.37:g.39580043C>T			36833569		Silent	SNP	ENST00000225550.3	37	CCDS32653.1																																																																																				0.493	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39580043	C	T	39580043	2	4	67	1	0	0	0	0	0	0	0	1	8495	871	31	1		1	KRT37	17	39580043	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	5994318	39580043	41615167	107	20863										
STAT5B	6777	broad.mit.edu	37	chr17	40369193	40369193	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tttaccttgacttgaaaaacCagctcatttccaccaacact	3	13	1	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:40369193C>G	ENST00000293328.3	-	11	1533	c.1365G>C	c.(1363-1365)ctG>ctC	p.L455L		NM_012448.3	NP_036580.2	P51692	STA5B_HUMAN	signal transducer and activator of transcription 5B	455					2-oxoglutarate metabolic process (GO:0006103)|acute-phase response (GO:0006953)|allantoin metabolic process (GO:0000255)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|liver development (GO:0001889)|luteinization (GO:0001553)|natural killer cell differentiation (GO:0001779)|negative regulation of apoptotic process (GO:0043066)|negative regulation of erythrocyte differentiation (GO:0045647)|oxaloacetate metabolic process (GO:0006107)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cellular component movement (GO:0051272)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone metabolic process (GO:0042448)|prolactin signaling pathway (GO:0038161)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription from RNA polymerase II promoter (GO:0006366)|valine metabolic process (GO:0006573)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|glucocorticoid receptor binding (GO:0035259)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.L455L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	CTTGAAAAACCAGCTCATTTC	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	17											69	60	63					17																	40369193		2203	4300	6503	37622719	SO:0001819	synonymous_variant	6777			BC065227	CCDS11423.1	17q11.2	2014-09-17			ENSG00000173757	ENSG00000173757		"SH2 domain containing"	11367	protein-coding gene	gene with protein product		604260				8631883	Standard	NM_012448		Approved		uc002hzh.3	P51692	OTTHUMG00000150724	ENST00000293328.3:c.1365G>C	17.37:g.40369193C>G			37622719	Q8WWS8	Silent	SNP	ENST00000293328.3	37	CCDS11423.1																																																																																				0.428	STAT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319797.1	NM_012448		G	40369193	C	G	40369193	2	3	67	1	0	0	0	0	0	0	0	1	15308	581	21	5		5	STAT5B	17	40369193	Silent	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	789150	40369193	40826017	108	20864										
PSMC5	5705	broad.mit.edu	37	chr17	61908218	61908218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tgggaagacactgttggcccGggctgtggctcatcatacgg	15	10	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr17:61908218G>A	ENST00000310144.6	+	7	910	c.602G>A	c.(601-603)cGg>cAg	p.R201Q	FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000581882.1_Missense_Mutation_p.R193Q|PSMC5_ENST00000375812.4_Missense_Mutation_p.R193Q|PSMC5_ENST00000580864.1_Missense_Mutation_p.R193Q	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	201	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.R201Q(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						CTGTTGGCCCGGGCTGTGGCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	17											107	96	99					17																	61908218		2203	4300	6503	59261950	SO:0001583	missense	5705			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.602G>A	17.37:g.61908218G>A	ENSP00000310572:p.Arg201Gln		59261950	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	G	35	5.486317	0.96323	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.93712	-3.27;-3.27	6.17	5.2	0.72013	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.95385	0.8502	L	0.55213	1.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.95690	0.8739	10	0.87932	D	0	.	13.2422	0.60004	0.0761:0.0:0.9239:0.0	.	193;201	A8K3Z3;P62195	.;PRS8_HUMAN	Q	201;193	ENSP00000310572:R201Q;ENSP00000364970:R193Q	ENSP00000310572:R201Q	R	+	2	0	PSMC5	59261950	0.995000	0.38212	0.994000	0.49952	0.926000	0.56050	6.716000	0.74702	1.616000	0.50265	0.655000	0.94253	CGG		0.527	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		A	61908218	G	A	61908218	3	1	67	1	0	0	0	0	1	0	0	0	12724	1116	39	1	628	1	PSMC5	17	61908218	Missense_Mutation	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	21539025	61908218	19286992	109	20865										
SLC14A2	8170	broad.mit.edu	37	chr18	43247924	43247924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	catccagaacccctggtgggCgatctcaggctgcctgggta	13	13	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr18:43247924C>T	ENST00000255226.6	+	14	2660	c.1844C>T	c.(1843-1845)gCg>gTg	p.A615V	SLC14A2_ENST00000589658.1_Missense_Mutation_p.A92V|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000586448.1_Missense_Mutation_p.A615V	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	615					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.A615V(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCCTGGTGGGCGATCTCAGGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	18											137	131	133					18																	43247924		2203	4300	6503	41501922	SO:0001583	missense	8170			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1844C>T	18.37:g.43247924C>T	ENSP00000255226:p.Ala615Val		41501922	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	c	33	5.240137	0.95240	.	.	ENSG00000132874	ENST00000255226	T	0.57595	0.39	4.52	4.52	0.55395	.	0.129380	0.34906	N	0.003596	T	0.75860	0.3907	M	0.90369	3.11	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	T	0.81357	-0.0969	10	0.52906	T	0.07	-24.7051	17.468	0.87639	0.0:1.0:0.0:0.0	.	615	Q15849	UT2_HUMAN	V	615	ENSP00000255226:A615V	ENSP00000255226:A615V	A	+	2	0	SLC14A2	41501922	0.999000	0.42202	1.000000	0.80357	0.906000	0.53458	4.230000	0.58632	2.358000	0.79984	0.558000	0.71614	GCG		0.567	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43247924	C	T	43247924	3	4	67	1	0	0	0	0	1	0	0	0	14434	768	27	1	1894	1	SLC14A2	18	43247924	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09		43247924	34829324	110	20866										
ATP5A1	498	broad.mit.edu	37	chr18	43671703	43671703	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cttgaacattcctcagcccaTgtacgcgggcaataccatca	7	14	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr18:43671703T>C	ENST00000398752.6	-	3	375	c.254A>G	c.(253-255)cAt>cGt	p.H85R	ATP5A1_ENST00000593152.2_Missense_Mutation_p.H35R|ATP5A1_ENST00000282050.2_Missense_Mutation_p.H85R|ATP5A1_ENST00000591267.1_5'Flank|ATP5A1_ENST00000590665.1_Missense_Mutation_p.H85R	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	85					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.H85R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CCTCAGCCCATGTACGCGGGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	18											104	102	103					18																	43671703		2203	4300	6503	41925701	SO:0001583	missense	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.254A>G	18.37:g.43671703T>C	ENSP00000381736:p.His85Arg		41925701	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.851174	0.71719	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.85629	-2.01;-2.01	5.24	5.24	0.73138	ATPase, F1/A1 complex, alpha subunit, N-terminal (1);ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal (1);ATPase, F1/A1 complex, alpha/beta subunit, N-terminal (1);	0.189396	0.49305	D	0.000141	D	0.86686	0.5992	L	0.49699	1.58	0.43857	D	0.996455	B	0.27951	0.195	B	0.42593	0.392	D	0.86298	0.1678	10	0.66056	D	0.02	-18.3519	15.1468	0.72662	0.0:0.0:0.0:1.0	.	85	P25705	ATPA_HUMAN	R	85;85;35	ENSP00000282050:H85R;ENSP00000381736:H85R	ENSP00000282050:H85R	H	-	2	0	ATP5A1	41925701	1.000000	0.71417	0.964000	0.40570	0.969000	0.65631	7.992000	0.88273	1.975000	0.57531	0.533000	0.62120	CAT		0.393	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		C	43671703	T	C	43671703	3	2	67	1	0	0	0	0	1	0	0	0	1148	1464	51	4	1447	4	ATP5A1	18	43671703	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09	423779	43671703	34405545	111	20867										
ZFR2	23217	broad.mit.edu	37	chr19	3823262	3823262	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acctcctccacatattccggGcccaccggctgcgcatcaga	8	18	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr19:3823262G>T	ENST00000262961.4	-	8	1363	c.1353C>A	c.(1351-1353)ggC>ggA	p.G451G		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	451							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.G451G(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		CATATTCCGGGCCCACCGGCT	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	19											91	97	95					19																	3823262		1917	4120	6037	3774262	SO:0001819	synonymous_variant	23217			AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.1353C>A	19.37:g.3823262G>T			3774262		Silent	SNP	ENST00000262961.4	37	CCDS45921.1																																																																																				0.622	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		T	3823262	G	T	3823262	2	4	67	1	0	0	0	0	0	0	0	1	17699	1190	42	2		2	ZFR2	19	3823262	Silent	SNP	G	TCGA-AG-A014-01A-02W-A00K-09		3823262	55305721	112	20868										
HAUS8	93323	broad.mit.edu	37	chr19	17170455	17170455	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gtggcgtctttttgacgatgCttttgtctaagataaagcac	10	7	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr19:17170455C>A	ENST00000253669.5	-	6	522	c.332G>T	c.(331-333)aGc>aTc	p.S111I	HAUS8_ENST00000593360.1_Missense_Mutation_p.S50I|HAUS8_ENST00000448593.2_Missense_Mutation_p.S110I			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	111					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.S111I(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						TTTGACGATGCTTTTGTCTAA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	19											129	125	127					19																	17170455		2203	4300	6503	17031455	SO:0001583	missense	93323			BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"HAUS augmin-like complex subunits"	30532	protein-coding gene	gene with protein product		613434	"HEC1/NDC80 interacting, centrosome associated 1"	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.332G>T	19.37:g.17170455C>A	ENSP00000253669:p.Ser111Ile		17031455	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Missense_Mutation	SNP	ENST00000253669.5	37	CCDS32948.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235588	0.39498	.	.	ENSG00000131351	ENST00000253669;ENST00000448593	T;T	0.42900	0.96;0.96	2.84	2.84	0.33178	.	0.426114	0.22098	N	0.064654	T	0.51941	0.1704	L	0.49350	1.555	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.994;0.994	T	0.42982	-0.9419	10	0.27785	T	0.31	-8.1076	9.3687	0.38241	0.0:1.0:0.0:0.0	.	50;110;111	Q9BT25-2;C9JBZ4;Q9BT25	.;.;HAUS8_HUMAN	I	111;110	ENSP00000253669:S111I;ENSP00000395298:S110I	ENSP00000253669:S111I	S	-	2	0	HAUS8	17031455	0.053000	0.20554	0.250000	0.24296	0.106000	0.19336	1.265000	0.33027	1.910000	0.55303	0.561000	0.74099	AGC		0.398	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699		A	17170455	C	A	17170455	3	1	67	1	0	0	0	0	1	0	0	0	6993	797	28	2	924	2	HAUS8	19	17170455	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	13347193	17170455	41958528	113	20869										
ARRDC2	27106	broad.mit.edu	37	chr19	18120673	18120674	+	Missense_Mutation	DNP	AG	AG	GC													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	ggcagccgtggtgcagacacAgacgttcatggcccgaggcg							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr19:18120673_18120674AG>GC	ENST00000222250.4	+	5	817_818	c.674_675AG>GC	c.(673-675)cAG>cGC	p.Q225R	ARRDC2_ENST00000379656.3_Missense_Mutation_p.Q220R	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	225					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)		p.Q220>?(1)		endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						GTGCAGACACAGACGTTCATGG	0.693																																																1	Complex(1)	large_intestine(1)	19																																								17981674	SO:0001583	missense	27106				CCDS12370.1, CCDS32956.1	19p13.12	2008-02-05				ENSG00000105643			25225	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015683		Approved	CLONE24945, PP2703	uc002nhv.3	Q8TBH0		Exception_encountered	19.37:g.18120673_18120674delinsGC	ENSP00000222250:p.Gln225Arg		17981673	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Missense_Mutation	DNP	ENST00000222250.4	37	CCDS12370.1																																																																																				0.693	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683		GC	18120674	AG	GC	18120673	3	3	67	1	0	0	0	0	1	0	0	0	984	188	7	4	955	4	ARRDC2	19	18120673	Missense_Mutation	DNP	AG	TCGA-AG-A014-01A-02W-A00K-09	950218	18120673	41008310	114	20870										
TSHZ3	57616	broad.mit.edu	37	chr19	31769600	31769600	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gctggccccattctggtggcCgtaccgattatttggcgtga	13	11	1	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr19:31769600C>T	ENST00000240587.4	-	2	1426	c.1099G>A	c.(1099-1101)Ggc>Agc	p.G367S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	367					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G184S(2)|p.G367S(2)|p.Y366_G367>*(1)|p.Y183_G184>*(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TTCTGGTGGCCGTACCGATTA	0.557																																																6	Substitution - Missense(4)|Complex - deletion inframe(2)	large_intestine(2)|lung(2)|endometrium(2)	19											246	236	240					19																	31769600		2203	4300	6503	36461440	SO:0001583	missense	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1099G>A	19.37:g.31769600C>T	ENSP00000240587:p.Gly367Ser		36461440	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340420	0.41498	.	.	ENSG00000121297	ENST00000240587	T	0.15952	2.38	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.40619	0.1124	M	0.66297	2.02	0.80722	D	1	D	0.76494	0.999	D	0.63957	0.92	T	0.16129	-1.0413	10	0.54805	T	0.06	-41.6635	18.9894	0.92784	0.0:1.0:0.0:0.0	.	367	Q63HK5	TSH3_HUMAN	S	367	ENSP00000240587:G367S	ENSP00000240587:G367S	G	-	1	0	TSHZ3	36461440	1.000000	0.71417	0.999000	0.59377	0.033000	0.12548	7.461000	0.80834	2.468000	0.83385	0.655000	0.94253	GGC		0.557	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31769600	C	T	31769600	3	4	67	1	0	0	0	0	1	0	0	0	16665	652	23	1	2150	1	TSHZ3	19	31769600	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	13648927	31769600	27359383	115	20871										
PNMAL1	55228	broad.mit.edu	37	chr19	46973959	46973959	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	cccctcggcatccaggaattCattcagattttttaaaaact	5	11	2	1			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr19:46973959C>A	ENST00000313683.10	-	2	639	c.334G>T	c.(334-336)Gaa>Taa	p.E112*	PNMAL1_ENST00000438932.2_Nonsense_Mutation_p.E112*|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	112								p.E112*(2)		cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		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)		tccaggaattcattcagattt	0.577																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											42	44	43					19																	46973959		2203	4300	6503	51665799	SO:0001587	stop_gained	55228			BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"Paraneoplastic Ma antigens"	25578	protein-coding gene	gene with protein product			"PNMA-like 1"			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.334G>T	19.37:g.46973959C>A	ENSP00000318131:p.Glu112*		51665799	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Nonsense_Mutation	SNP	ENST00000313683.10	37	CCDS33059.1	.	.	.	.	.	.	.	.	.	.	C	38	6.932287	0.97944	.	.	ENSG00000182013	ENST00000438932;ENST00000313683;ENST00000417103	.	.	.	3.36	3.36	0.38483	.	0.206543	0.24298	N	0.039753	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-22.4724	10.5182	0.44903	0.0:1.0:0.0:0.0	.	.	.	.	X	112	.	ENSP00000318131:E112X	E	-	1	0	PNMAL1	51665799	0.463000	0.25799	0.517000	0.27799	0.898000	0.52572	1.152000	0.31663	2.185000	0.69588	0.655000	0.94253	GAA		0.577	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		A	46973959	C	A	46973959	4	1	67	1	0	0	0	0	0	1	0	0	12188	835	29	2	1015	2	PNMAL1	19	46973959	Nonsense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09	15204359	46973959	12155024	116	20872										
ZNF335	63925	broad.mit.edu	37	chr20	44588925	44588927	+	In_Frame_Del	DEL	GCT	GCT	-													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acaaaagctgcatttgaaggGcttgtcactgacgtgggaca							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	GCT	GCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr20:44588925_44588927delGCT	ENST00000322927.2	-	14	2040_2042	c.1940_1942delAGC	c.(1939-1944)aagccc>acc	p.647_648KP>T	ZNF335_ENST00000426788.1_In_Frame_Del_p.492_493KP>T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	647					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.K647_P648>T(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CATTTGAAGGGCTTGTCACTGAC	0.542																																																1	Complex - deletion inframe(1)	large_intestine(1)	20																																								44022334	SO:0001651	inframe_deletion	63925			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1940_1942delAGC	20.37:g.44588925_44588927delGCT	ENSP00000325326:p.Lys647_Pro648delinsThr		44022332	B4DLG7|Q548D0|Q9H684	In_Frame_Del	DEL	ENST00000322927.2	37	CCDS13389.1																																																																																				0.542	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		-	44588927	GCT	-	44588925	7	5	67	1	0	1	0	1	0	0	0	0	17891	1203	42	0	2146	0	ZNF335	20	44588925	In_Frame_Del	DEL	GCT	TCGA-AG-A014-01A-02W-A00K-09		44588925	18436595	117	20873	27	2								
ZNF335	63925	broad.mit.edu	37	chr20	44588930	44588931	+	Frame_Shift_Ins	INS	-	-	AGCG													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gctgcatttgaagggcttgtINScactgacgtgggacaactgg							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr20:44588930_44588931insAGCG	ENST00000322927.2	-	14	2036_2037	c.1936_1937insCGCT	c.(1936-1938)gacfs	p.D646fs	ZNF335_ENST00000426788.1_Frame_Shift_Ins_p.D491fs	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	646					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.D646fs*37(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GAAGGGCTTGTCACTGACGTGG	0.535																																																1	Insertion - Frameshift(1)	large_intestine(1)	20																																								44022338	SO:0001589	frameshift_variant	63925			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1936_1937insCGCT	20.37:g.44588930_44588931insAGCG	ENSP00000325326:p.Asp646fs		44022337	B4DLG7|Q548D0|Q9H684	Frame_Shift_Ins	INS	ENST00000322927.2	37	CCDS13389.1																																																																																				0.535	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		AGCG	44588931	-	AGCG	44588930	7	5	67	1	0	1	1	0	0	0	0	0	17891	1667	58	0	2151	0	ZNF335	20	44588930	Frame_Shift_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09	5	44588930	18436590	118	20874	27	2								
SLC2A10	81031	broad.mit.edu	37	chr20	45358112	45358112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gttggcagagatagaccagcAgttccagaagagacggtagg	15	7	0	4			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr20:45358112A>G	ENST00000359271.2	+	4	1782	c.1532A>G	c.(1531-1533)cAg>cGg	p.Q511R		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	511					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)	p.Q511R(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				ATAGACCAGCAGTTCCAGAAG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	20											56	55	55					20																	45358112		2203	4300	6503	44791519	SO:0001583	missense	81031			AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.1532A>G	20.37:g.45358112A>G	ENSP00000352216:p.Gln511Arg		44791519	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	37	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.419695	0.83559	.	.	ENSG00000197496	ENST00000359271	T	0.74002	-0.8	6.03	4.92	0.64577	Major facilitator superfamily domain, general substrate transporter (1);	0.264493	0.38778	N	0.001577	T	0.71600	0.3359	N	0.12920	0.275	0.38424	D	0.946263	D	0.64830	0.994	D	0.64595	0.927	T	0.69491	-0.5131	10	0.18710	T	0.47	-0.9788	12.7331	0.57208	0.8768:0.0:0.0:0.1232	.	511	O95528	GTR10_HUMAN	R	511	ENSP00000352216:Q511R	ENSP00000352216:Q511R	Q	+	2	0	SLC2A10	44791519	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.491000	0.73649	1.078000	0.41014	0.533000	0.62120	CAG		0.522	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			G	45358112	A	G	45358112	3	3	67	1	0	0	0	0	1	0	0	0	14576	188	7	4	1546	4	SLC2A10	20	45358112	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09	769182	45358112	17667408	119	20875										
ZNF295	49854	broad.mit.edu	37	chr21	43411789	43411789	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	gggcaaagaaaagttttcggTgggtgccatgttgttctgat	14	5	1	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr21:43411789T>G	ENST00000310826.5	-	3	2599	c.2416A>C	c.(2416-2418)Acc>Ccc	p.T806P	ZBTB21_ENST00000465968.1_5'UTR|ZBTB21_ENST00000398499.1_Missense_Mutation_p.T806P|ZBTB21_ENST00000398511.3_Missense_Mutation_p.T806P|ZBTB21_ENST00000398505.3_Missense_Mutation_p.T605P	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	806					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)	p.T806P(1)									AAGTTTTCGGTGGGTGCCATG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	21											125	121	123					21																	43411789		2203	4300	6503	42284858	SO:0001583	missense	49854			AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13083	protein-coding gene	gene with protein product			"zinc finger protein 295"	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.2416A>C	21.37:g.43411789T>G	ENSP00000308759:p.Thr806Pro		42284858	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	T	3.861	-0.029899	0.07543	.	.	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.07567	3.46;3.18;3.18;3.18	5.2	-4.28	0.03732	.	0.427176	0.22699	N	0.056702	T	0.03608	0.0103	N	0.22421	0.69	0.09310	N	1	B;B	0.28258	0.205;0.112	B;B	0.25759	0.059;0.063	T	0.26883	-1.0090	10	0.44086	T	0.13	-3.0782	2.0493	0.03567	0.1918:0.2213:0.1089:0.4779	.	605;806	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	P	605;806;806;806	ENSP00000381517:T605P;ENSP00000308759:T806P;ENSP00000381512:T806P;ENSP00000381523:T806P	ENSP00000308759:T806P	T	-	1	0	ZNF295	42284858	0.010000	0.17322	0.000000	0.03702	0.145000	0.21501	0.177000	0.16801	-0.783000	0.04534	-0.376000	0.06991	ACC		0.507	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		G	43411789	T	G	43411789	3	3	67	1	0	0	0	0	1	0	0	0	17866	1696	59	4	788	4	ZNF295	21	43411789	Missense_Mutation	SNP	T	TCGA-AG-A014-01A-02W-A00K-09		43411789	4718106	120	20876										
C22orf25	128989	broad.mit.edu	37	chr22	20030945	20030945	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	agttagctgacttctgggggAacaacaacgagatcctcagt	11	9	2	2			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr22:20030945A>G	ENST00000327374.4	+	3	302	c.124A>G	c.(124-126)Aac>Gac	p.N42D	TANGO2_ENST00000401833.1_Missense_Mutation_p.N83D|TANGO2_ENST00000434570.2_Missense_Mutation_p.N83D|TANGO2_ENST00000447208.2_Missense_Mutation_p.N42D|TANGO2_ENST00000420290.2_5'UTR|TANGO2_ENST00000456048.1_Missense_Mutation_p.N47D|TANGO2_ENST00000398042.2_Missense_Mutation_p.N42D|TANGO2_ENST00000432883.1_Missense_Mutation_p.N42D|TANGO2_ENST00000401886.1_Missense_Mutation_p.N42D|TANGO2_ENST00000479679.1_3'UTR	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	42								p.N42D(1)									CTTCTGGGGGAACAACAACGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	22											137	140	139					22																	20030945		2203	4300	6503	18410945	SO:0001583	missense	128989				CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 25"	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.124A>G	22.37:g.20030945A>G	ENSP00000332721:p.Asn42Asp		18410945	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	37	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	A	0.201	-1.045089	0.01997	.	.	ENSG00000183597	ENST00000401886;ENST00000432198;ENST00000447208;ENST00000398042;ENST00000450664;ENST00000327374;ENST00000432883;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000456048	T;T;T;T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	4.89	2.71	0.32032	.	0.683909	0.15490	N	0.259634	T	0.09379	0.0231	N	0.04335	-0.225	0.80722	D	1	B;B;B;B;B;B;B	0.11235	0.001;0.002;0.004;0.001;0.004;0.0;0.0	B;B;B;B;B;B;B	0.12156	0.004;0.007;0.003;0.004;0.007;0.002;0.001	T	0.24870	-1.0148	10	0.02654	T	1	-6.4641	7.9459	0.29987	0.8224:0.0:0.1776:0.0	.	42;83;42;83;42;42;42	B7Z9Q5;B7Z730;B7Z4A5;B7WNV6;Q6AHY1;Q6ICL3;Q6ICL3-2	.;.;.;.;.;CV025_HUMAN;.	D	42;42;42;42;42;42;42;83;42;83;47	ENSP00000385662:N42D;ENSP00000413850:N42D;ENSP00000389797:N42D;ENSP00000381122:N42D;ENSP00000415450:N42D;ENSP00000332721:N42D;ENSP00000402926:N42D;ENSP00000384827:N83D;ENSP00000411602:N42D;ENSP00000391262:N83D;ENSP00000403645:N47D	ENSP00000332721:N42D	N	+	1	0	C22orf25	18410945	0.587000	0.26791	0.164000	0.22755	0.043000	0.13939	1.382000	0.34374	0.292000	0.22492	0.459000	0.35465	AAC		0.567	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906		G	20030945	A	G	20030945	3	3	67	1	0	0	0	0	1	0	0	0	2145	246	9	4	130	4	C22orf25	22	20030945	Missense_Mutation	SNP	A	TCGA-AG-A014-01A-02W-A00K-09		20030945	31273621	121	20877										
ZMAT5	55954	broad.mit.edu	37	chr22	30127246	30127247	+	Frame_Shift_Ins	INS	-	-	C													0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	actctgggctgcagaggccaINSccccccaggtgggggtgccc							TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr22:30127246_30127247insC	ENST00000344318.3	-	6	596_597	c.480_481insG	c.(478-483)gggtggfs	p.W161fs	ZMAT5_ENST00000397781.3_Frame_Shift_Ins_p.W161fs|CABP7_ENST00000216144.3_3'UTR	NM_001003692.1	NP_001003692.1	Q9UDW3	ZMAT5_HUMAN	zinc finger, matrin-type 5	161					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	zinc ion binding (GO:0008270)	p.W161fs*>11(2)		large_intestine(1)|lung(1)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(5;0.000597)|all cancers(5;0.0534)|Epithelial(10;0.0574)			TGCAGAGGCCACCCCCCAGGTG	0.644																																																2	Insertion - Frameshift(2)	large_intestine(2)	22							,,	25,4229		1,23,2103					,,	5.1	1			37	23,8207		1,21,4093	no	utr-3,frameshift,frameshift	ZMAT5,CABP7	NM_182527.2,NM_019103.2,NM_001003692.1	,,	2,44,6196	A1A1,A1R,RR		0.2795,0.5877,0.3845	,,	,,		48,12436				28457247	SO:0001589	frameshift_variant	55954				CCDS13868.1	22q12.2	2013-09-20	2010-09-15		ENSG00000100319	ENSG00000100319		"Zinc fingers, matrin-type"	28046	protein-coding gene	gene with protein product	"U11/U12 snRNP 20K"					9847074	Standard	NM_019103		Approved	SNRNP20	uc003agn.3	Q9UDW3	OTTHUMG00000151292	ENST00000344318.3:c.481dupG	22.37:g.30127252_30127252dupC	ENSP00000344241:p.Trp161fs		28457246	A8K9F6	Frame_Shift_Ins	INS	ENST00000344318.3	37	CCDS13868.1																																																																																				0.644	ZMAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322114.1	NM_019103		C	30127247	-	C	30127246	7	5	67	1	0	1	1	0	0	0	0	0	17734	159	6	0	35	0	ZMAT5	22	30127246	Frame_Shift_Ins	INS	-	TCGA-AG-A014-01A-02W-A00K-09	10096301	30127246	21177320	122	20878										
CSF2RB	1439	broad.mit.edu	37	chr22	37331394	37331394	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	tctccccggctgctggaagtGctgcctatgtgggtgctggc	15	12	1	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chr22:37331394G>C	ENST00000403662.3	+	11	1539	c.1317G>C	c.(1315-1317)gtG>gtC	p.V439V	CSF2RB_ENST00000406230.1_Splice_Site_p.V445V|CSF2RB_ENST00000536485.1_Splice_Site_p.V386V|CSF2RB_ENST00000262825.5_Splice_Site_p.V445V			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	439					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.V439V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	TGCTGGAAGTGCTGCCTATGT	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	22											134	101	112					22																	37331394		2203	4300	6503	35661340	SO:0001630	splice_region_variant	1439			M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1316-1G>C	22.37:g.37331394G>C			35661340	Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	37	CCDS13936.1																																																																																				0.602	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	Silent	C	37331394	G	C	37331394	5	2	67	1	0	0	0	0	0	0	1	0	3941	1333	46	5	1355	5	CSF2RB	22	37331394	Splice_Site	SNP	G	TCGA-AG-A014-01A-02W-A00K-09	7204148	37331394	13973172	123	20879										
XKRX	402415	broad.mit.edu	37	chrX	100169628	100169628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	0.780410487857296	0.613179669030733	0.817572892040977	0.0634674922600621	0.351956093442163	0	acctcacactatagtgcaggCccatatgtccccagttctgc	7	15	2	0			TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A014-01A-02W-A00K-09	TCGA-AG-A014-10A-01W-A00K-09	g.chrX:100169628C>T	ENST00000372956.2	-	3	1653	c.1049G>A	c.(1048-1050)gGc>gAc	p.G350D	XKRX_ENST00000328526.5_Missense_Mutation_p.G363D|XKRX_ENST00000468904.1_3'UTR			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	350						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G363D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						ATAGTGCAGGCCCATATGTCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											182	163	169					X																	100169628		2203	4300	6503	100056284	SO:0001583	missense	402415			AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"X Kell blood group precursor-related, X-linked"				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.1049G>A	X.37:g.100169628C>T	ENSP00000362047:p.Gly350Asp		100056284	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	37	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192153	0.38707	.	.	ENSG00000182489	ENST00000328526;ENST00000372956	T;T	0.63255	-0.03;-0.03	5.74	2.86	0.33363	.	0.330090	0.35903	N	0.002909	T	0.43634	0.1256	N	0.08118	0	0.33382	D	0.574968	P	0.42584	0.784	P	0.45829	0.494	T	0.55049	-0.8201	10	0.35671	T	0.21	-4.1639	8.7787	0.34778	0.2078:0.4625:0.3297:0.0	.	350	Q6PP77	XKR2_HUMAN	D	363;350	ENSP00000327570:G363D;ENSP00000362047:G350D	ENSP00000327570:G363D	G	-	2	0	XKRX	100056284	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	3.193000	0.50997	1.148000	0.42385	0.544000	0.68410	GGC		0.448	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559		T	100169628	C	T	100169628	3	4	67	1	0	0	0	0	1	0	0	0	17479	739	26	3	304	3	XKRX	23	100169628	Missense_Mutation	SNP	C	TCGA-AG-A014-01A-02W-A00K-09		100169628	55100932	124	20880										
PADI3	51702	hgsc.bcm.edu	37	chr1	17603341	17603341	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aaaagcagaagtgtggccacGggagggccctcctgttccag	14	11	0	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr1:17603341G>C	ENST00000375460.3	+	13	1565	c.1525G>C	c.(1525-1527)Ggg>Cgg	p.G509R	MIR3972_ENST00000582732.1_RNA	NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	509			G -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.G509R(2)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GTGTGGCCACGGGAGGGCCCT	0.597																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	1											35	37	36					1																	17603341		2203	4300	6503	17475928	SO:0001583	missense	51702			AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1525G>C	1.37:g.17603341G>C	ENSP00000364609:p.Gly509Arg		17475928	Q58EY7|Q70SX5	Missense_Mutation	SNP	ENST00000375460.3	37	CCDS179.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822064	0.90873	.	.	ENSG00000142619	ENST00000375460	T	0.61859	0.07	4.79	4.79	0.61399	Protein-arginine deiminase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.90019	3.08	0.58432	D	0.999995	D	0.56968	0.978	D	0.68192	0.956	D	0.84506	0.0619	10	0.66056	D	0.02	-35.0556	16.7573	0.85503	0.0:0.0:1.0:0.0	.	509	Q9ULW8	PADI3_HUMAN	R	509	ENSP00000364609:G509R	ENSP00000364609:G509R	G	+	1	0	PADI3	17475928	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.916000	0.87491	2.377000	0.81083	0.555000	0.69702	GGG		0.597	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			C	17603341	G	C	17603341	3	2	68	1	0	0	0	0	1	0	0	0	11410	1116	39	5	1575	5	PADI3	1	17603341	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		17603341	231647280	1	20881										
BTBD8	284697	hgsc.bcm.edu	37	chr1	92612764	92612764	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ccagaacattgacgtctataCtagaatgcctgattattgct	7	9	1	4			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr1:92612764C>A	ENST00000342818.3	+	8	1194	c.958C>A	c.(958-960)Cta>Ata	p.L320I	BTBD8_ENST00000540648.1_3'UTR	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	320						nucleus (GO:0005634)		p.L320I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		GACGTCTATACTAGAATGCCT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	1											168	164	166					1																	92612764		2203	4300	6503	92385352	SO:0001583	missense	284697			AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"BTB/POZ domain containing"	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.958C>A	1.37:g.92612764C>A	ENSP00000343686:p.Leu320Ile		92385352	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	37	CCDS737.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926442	0.34002	.	.	ENSG00000189195	ENST00000342818	T	0.67171	-0.25	5.49	2.39	0.29439	.	0.000000	0.45867	D	0.000326	T	0.44222	0.1283	M	0.65498	2.005	0.80722	D	1	B	0.29766	0.256	B	0.24701	0.055	T	0.44907	-0.9297	10	0.59425	D	0.04	-0.9748	7.9997	0.30288	0.0:0.7161:0.1291:0.1548	.	320	Q5XKL5	BTBD8_HUMAN	I	320	ENSP00000343686:L320I	ENSP00000343686:L320I	L	+	1	2	BTBD8	92385352	0.634000	0.27190	0.242000	0.24170	0.583000	0.36354	1.031000	0.30165	0.295000	0.22570	0.557000	0.71058	CTA		0.328	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242		A	92612764	C	A	92612764	3	1	68	1	0	0	0	0	1	0	0	0	1550	564	20	2	988	2	BTBD8	1	92612764	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	75009423	92612764	156637857	2	20882										
UCHL5	51377	hgsc.bcm.edu	37	chr1	192985507	192985507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ggtttcctgagctttctttgCgttctgtttttcttttgcct	8	9	3	1	rs146351256	byFrequency	TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr1:192985507C>T	ENST00000367455.4	-	11	1199	c.964G>A	c.(964-966)Gca>Aca	p.A322T	UCHL5_ENST00000367451.4_Missense_Mutation_p.A348T|UCHL5_ENST00000367454.1_Missense_Mutation_p.A321T	NM_001199261.1|NM_015984.3	NP_001186190.1|NP_057068.1	Q9Y5K5	UCHL5_HUMAN	ubiquitin carboxyl-terminal hydrolase L5	322	Interaction with ADRM1.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|forebrain morphogenesis (GO:0048853)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein deubiquitination (GO:0016579)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	endopeptidase inhibitor activity (GO:0004866)|omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|proteasome binding (GO:0070628)|ubiquitin-specific protease activity (GO:0004843)	p.A322T(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(1)|lung(9)|ovary(1)	19						GCTTTCTTTGCGTTCTGTTTT	0.284													C|||	2	0.000399361	0.0015	0	5008	,	,		18037	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	225	219	221		964,961	5.5	1	1	dbSNP_134	221	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	UCHL5	NM_015984.3,NM_001199261.1	58,58	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign,benign	322/330,321/329	192985507	3,13003	2203	4300	6503	191252130	SO:0001583	missense	51377				CCDS1378.1, CCDS55668.1, CCDS55669.1, CCDS55670.1	1q32	2011-07-06			ENSG00000116750	ENSG00000116750		"INO80 complex subunits"	19678	protein-coding gene	gene with protein product	"INO80 complex subunit R"	610667				10810093, 16027725	Standard	NM_015984		Approved	UCH37, CGI-70, INO80R	uc001gsm.3	Q9Y5K5	OTTHUMG00000035561	ENST00000367455.4:c.964G>A	1.37:g.192985507C>T	ENSP00000356425:p.Ala322Thr		191252130	Q5LJA6|Q5LJA7|Q8TBS4|Q96BJ9|Q9H1W5|Q9P0I3|Q9UQN2	Missense_Mutation	SNP	ENST00000367455.4	37	CCDS1378.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	17.27	3.347450	0.61183	2.27E-4	2.33E-4	ENSG00000116750	ENST00000367455;ENST00000367454;ENST00000367450;ENST00000367451	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.5	5.5	0.81552	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.157689	0.56097	D	0.000028	T	0.34250	0.0891	L	0.40543	1.245	0.80722	D	1	B;B	0.15719	0.014;0.008	B;B	0.10450	0.005;0.002	T	0.08166	-1.0735	10	0.28530	T	0.3	-14.2017	12.7241	0.57159	0.0:0.9253:0.0:0.0747	.	321;322	Q9Y5K5-3;Q9Y5K5	.;UCHL5_HUMAN	T	322;321;361;348	ENSP00000356425:A322T;ENSP00000356424:A321T;ENSP00000356420:A361T;ENSP00000356421:A348T	ENSP00000356420:A361T	A	-	1	0	UCHL5	191252130	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.642000	0.61383	2.588000	0.87417	0.650000	0.86243	GCA		0.284	UCHL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086318.3	NM_015984		T	192985507	C	T	192985507	3	4	68	1	0	0	0	0	1	0	0	0	16962	768	27	1	29	1	UCHL5	1	192985507	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	100372743	192985507	56265114	3	20883										
APLF	200558	hgsc.bcm.edu	37	chr2	68740774	68740774	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ttggatgttagcagaacattTaagtgatcaaaacctttcag	8	6	2	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr2:68740774T>G	ENST00000303795.4	+	5	755	c.584T>G	c.(583-585)tTa>tGa	p.L195*		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	195					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.L195*(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GCAGAACATTTAAGTGATCAA	0.373																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											96	97	97					2																	68740774		2203	4299	6502	68594278	SO:0001587	stop_gained	200558			BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.584T>G	2.37:g.68740774T>G	ENSP00000307004:p.Leu195*		68594278	A8K476|Q53P47|Q53PB9|Q53QU0	Nonsense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	.	.	.	.	.	.	.	.	.	.	t	34	5.402069	0.96030	.	.	ENSG00000169621	ENST00000303795	.	.	.	6.17	-1.85	0.07784	.	0.712055	0.13786	N	0.362847	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4747	0.16690	0.1313:0.371:0.0:0.4978	.	.	.	.	X	195	.	ENSP00000307004:L195X	L	+	2	0	APLF	68594278	0.004000	0.15560	0.000000	0.03702	0.996000	0.88848	0.120000	0.15647	-0.539000	0.06273	0.533000	0.62120	TTA		0.373	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		G	68740774	T	G	68740774	4	3	68	1	0	0	0	0	0	1	0	0	776	1764	61	4	602	4	APLF	2	68740774	Nonsense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10		68740774	174458599	4	20884										
ANTXR1	84168	hgsc.bcm.edu	37	chr2	69409753	69409753	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aatctcaacaacaatatgcgTcggccttcttccccccggaa	6	15	2	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr2:69409753T>G	ENST00000303714.4	+	16	1636	c.1314T>G	c.(1312-1314)cgT>cgG	p.R438R	RNA5SP96_ENST00000516041.1_RNA|RNU6-1216P_ENST00000362590.2_RNA	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	438					actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)	p.R438R(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						ACAATATGCGTCGGCCTTCTT	0.438									Familial Infantile Hemangioma																																							1	Substitution - coding silent(1)	large_intestine(1)	2											124	120	122					2																	69409753		2203	4300	6503	69263257	SO:0001819	synonymous_variant	84168	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.1314T>G	2.37:g.69409753T>G			69263257	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Silent	SNP	ENST00000303714.4	37	CCDS1892.1																																																																																				0.438	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		G	69409753	T	G	69409753	2	3	68	1	0	0	0	0	0	0	0	1	711	1654	58	4		4	ANTXR1	2	69409753	Silent	SNP	T	TCGA-AG-A015-01A-01W-A005-10	668979	69409753	173789620	5	20885										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627527	187627527	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tctggaagaagcgagaggaaCgcccactgattcccataaat	10	10	1	3	rs148878744		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr2:187627527C>T	ENST00000304698.5	+	8	2661	c.2458C>T	c.(2458-2460)Cgc>Tgc	p.R820C		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	820						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.R820C(1)		NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCGAGAGGAACGCCCACTGAT	0.428													C|||	1	0.000199681	0	0	5008	,	,		19768	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	CYS/ARG	0,4406		0,0,2203	81	81	81		2458	5.1	1	2	dbSNP_134	81	1,8595	1.2+/-3.3	0,1,4297	no	missense	FAM171B	NM_177454.3	180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	820/827	187627527	1,13001	2203	4298	6501	187335772	SO:0001583	missense	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.2458C>T	2.37:g.187627527C>T	ENSP00000304108:p.Arg820Cys		187335772	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	16.14	3.038953	0.55003	0.0	1.16E-4	ENSG00000144369	ENST00000304698	T	0.58210	0.35	6.02	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.66406	0.2786	L	0.60455	1.87	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.64506	0.926;0.926	T	0.68070	-0.5506	10	0.87932	D	0	-12.2673	13.976	0.64273	0.2559:0.7441:0.0:0.0	.	820;821	Q6P995;A8K122	F171B_HUMAN;.	C	820	ENSP00000304108:R820C	ENSP00000304108:R820C	R	+	1	0	FAM171B	187335772	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.975000	0.40569	2.850000	0.98022	0.650000	0.86243	CGC		0.428	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		T	187627527	C	T	187627527	3	4	68	1	0	0	0	0	1	0	0	0	5507	536	19	1	2488	1	FAM171B	2	187627527	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	118217774	187627527	55571846	6	20886										
IGSF11	152404	hgsc.bcm.edu	37	chr3	118621493	118621493	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cgaggcttcctactgactgaGccattgctcctggacatcac	9	14	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr3:118621493G>T	ENST00000393775.2	-	7	1475	c.1170C>A	c.(1168-1170)ggC>ggA	p.G390G	IGSF11_ENST00000491903.1_Silent_p.G362G|IGSF11_ENST00000425327.2_Silent_p.G389G|IGSF11_ENST00000354673.2_Silent_p.G389G|IGSF11_ENST00000441144.2_Silent_p.G365G|IGSF11_ENST00000489689.1_Silent_p.G366G	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	390					cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G389G(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TACTGACTGAGCCATTGCTCC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	3											133	101	112					3																	118621493		2203	4300	6503	120104183	SO:0001819	synonymous_variant	152404			AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"Immunoglobulin superfamily / I-set domain containing"	16669	protein-coding gene	gene with protein product	"cancer/testis antigen 119"	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.1170C>A	3.37:g.118621493G>T			120104183	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Silent	SNP	ENST00000393775.2	37	CCDS46891.1																																																																																				0.537	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2			T	118621493	G	T	118621493	2	4	68	1	0	0	0	0	0	0	0	1	7619	958	34	2		2	IGSF11	3	118621493	Silent	SNP	G	TCGA-AG-A015-01A-01W-A005-10		118621493	79400937	7	20887										
SRPRB	58477	hgsc.bcm.edu	37	chr3	133534487	133534487	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ccagcgagaggtgaaagatgTggctgagtttctgtatcaag	14	6	2	4			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr3:133534487T>G	ENST00000466490.2	+	6	749	c.464T>G	c.(463-465)gTg>gGg	p.V155G		NM_021203.3	NP_067026.3	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, B subunit	155					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|small GTPase mediated signal transduction (GO:0007264)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)	p.V155G(1)		breast(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(2)	12						GTGAAAGATGTGGCTGAGTTT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											239	235	236					3																	133534487		2203	4300	6503	135017177	SO:0001583	missense	58477			AK075531	CCDS3081.1	3q22.1	2004-01-29			ENSG00000144867	ENSG00000144867			24085	protein-coding gene	gene with protein product						7844142, 10859309	Standard	NM_021203		Approved	APMCF1	uc003epx.2	Q9Y5M8	OTTHUMG00000159753	ENST00000466490.2:c.464T>G	3.37:g.133534487T>G	ENSP00000418401:p.Val155Gly		135017177	Q6P595|Q8N2D8	Missense_Mutation	SNP	ENST00000466490.2	37	CCDS3081.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.734273	0.89482	.	.	ENSG00000144867	ENST00000466490	T	0.17213	2.29	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.47135	0.1429	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51896	-0.8647	10	0.87932	D	0	-18.3908	16.3473	0.83146	0.0:0.0:0.0:1.0	.	155	Q9Y5M8	SRPRB_HUMAN	G	155	ENSP00000418401:V155G	ENSP00000418401:V155G	V	+	2	0	SRPRB	135017177	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.408000	0.80041	2.320000	0.78422	0.528000	0.53228	GTG		0.433	SRPRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357170.2			G	133534487	T	G	133534487	3	3	68	1	0	0	0	0	1	0	0	0	15202	1696	59	4	482	4	SRPRB	3	133534487	Missense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10	14912994	133534487	64487943	8	20888										
EVC2	132884	hgsc.bcm.edu	37	chr4	5667311	5667311	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aggaagagggcagcccaggtCagcacaagggagaggaggaa	18	7	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr4:5667311C>A	ENST00000344408.5	-	8	989	c.936G>T	c.(934-936)ctG>ctT	p.L312L	EVC2_ENST00000310917.2_Silent_p.L232L|EVC2_ENST00000344938.1_Silent_p.L312L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	312					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L312L(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CAGCCCAGGTCAGCACAAGGG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	4											160	103	122					4																	5667311		2203	4300	6503	5718212	SO:0001819	synonymous_variant	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.936G>T	4.37:g.5667311C>A			5718212	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																				0.567	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5667311	C	A	5667311	2	1	68	1	0	0	0	0	0	0	0	1	5299	813	29	2		2	EVC2	4	5667311	Silent	SNP	C	TCGA-AG-A015-01A-01W-A005-10		5667311	185486965	9	20889										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74008069	74008069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aacaacacttgtatggccacCttttgctgcttctatcaaca	5	12	2	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr4:74008069C>T	ENST00000358602.4	-	13	2235	c.2119G>A	c.(2119-2121)Ggt>Agt	p.G707S	ANKRD17_ENST00000330838.6_Missense_Mutation_p.G707S|ANKRD17_ENST00000514252.1_5'UTR|ANKRD17_ENST00000509867.2_Missense_Mutation_p.G594S	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	707					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.G707S(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTATGGCCACCTTTTGCTGCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	4											104	108	107					4																	74008069		2203	4300	6503	74226933	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2119G>A	4.37:g.74008069C>T	ENSP00000351416:p.Gly707Ser		74226933	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	33	5.229797	0.95173	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.62941	-0.01;-0.01;-0.01	5.53	5.53	0.82687	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000005	T	0.66858	0.2832	N	0.20881	0.62	0.52099	D	0.999945	D;P;D;D;D	0.89917	1.0;0.914;0.982;0.981;0.986	D;P;D;D;D	0.91635	0.999;0.863;0.972;0.968;0.968	T	0.57837	-0.7742	10	0.08599	T	0.76	.	19.8832	0.96905	0.0:1.0:0.0:0.0	.	228;707;707;707;594	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	S	707;707;707;594;707	ENSP00000351416:G707S;ENSP00000332265:G707S;ENSP00000427151:G594S	ENSP00000332265:G707S	G	-	1	0	ANKRD17	74226933	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.764000	0.85297	2.772000	0.95346	0.644000	0.83932	GGT		0.403	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		T	74008069	C	T	74008069	3	4	68	1	0	0	0	0	1	0	0	0	646	681	24	3	5780	3	ANKRD17	4	74008069	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	68340758	74008069	117146207	10	20890										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85661380	85661380	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	caagcagtgggccagacagcTaatgaattcttggtcatggt	12	8	2	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr4:85661380T>A	ENST00000295888.4	-	39	6831	c.6424A>T	c.(6424-6426)Agc>Tgc	p.S2142C	WDFY3_ENST00000322366.6_Missense_Mutation_p.S2142C	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2142					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.S2142C(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCCAGACAGCTAATGAATTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	4											134	134	134					4																	85661380		2203	4300	6503	85880404	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6424A>T	4.37:g.85661380T>A	ENSP00000295888:p.Ser2142Cys		85880404	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.621376	0.66787	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.64438	-0.1;-0.1	5.16	5.16	0.70880	.	0.095546	0.64402	D	0.000001	T	0.41213	0.1149	N	0.03608	-0.345	0.49213	D	0.99976	P	0.39903	0.694	B	0.40165	0.321	T	0.44697	-0.9311	10	0.25751	T	0.34	.	15.2795	0.73770	0.0:0.0:0.0:1.0	.	2142	Q8IZQ1	WDFY3_HUMAN	C	2142	ENSP00000318466:S2142C;ENSP00000295888:S2142C	ENSP00000295888:S2142C	S	-	1	0	WDFY3	85880404	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	4.672000	0.61597	2.067000	0.61834	0.383000	0.25322	AGC		0.423	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85661380	T	A	85661380	3	1	68	1	0	0	0	0	1	0	0	0	17310	1522	53	5	4276	5	WDFY3	4	85661380	Missense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10	11653311	85661380	105492896	11	20891										
BMPR1B	658	hgsc.bcm.edu	37	chr4	96035970	96035970	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gaaggctcagattttcagtgTcgggtaaggtagataacttg	13	5	2	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr4:96035970T>C	ENST00000515059.1	+	5	526	c.243T>C	c.(241-243)tgT>tgC	p.C81C	BMPR1B_ENST00000502683.1_Silent_p.C81C|BMPR1B_ENST00000440890.2_Silent_p.C111C|BMPR1B_ENST00000264568.4_Silent_p.C81C|BMPR1B_ENST00000394931.1_Silent_p.C81C	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	81					BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.C81C(1)		breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		ATTTTCAGTGTCGGGTAAGGT	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	4											227	223	224					4																	96035970		2203	4299	6502	96254993	SO:0001819	synonymous_variant	658			D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.243T>C	4.37:g.96035970T>C			96254993	B2R953|B4DSV1|P78366	Silent	SNP	ENST00000515059.1	37	CCDS3642.1																																																																																				0.428	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		C	96035970	T	C	96035970	2	2	68	1	0	0	0	0	0	0	0	1	1471	1673	58	4		4	BMPR1B	4	96035970	Silent	SNP	T	TCGA-AG-A015-01A-01W-A005-10	10374590	96035970	95118306	12	20892										
F2RL1	2150	hgsc.bcm.edu	37	chr5	76129107	76129107	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cctgccctgaacatcacgacCtgtcatgatgttttgcctga	8	13	2	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr5:76129107C>A	ENST00000296677.4	+	2	881	c.675C>A	c.(673-675)acC>acA	p.T225T		NM_005242.4	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	225					blood coagulation (GO:0007596)|chemokine (C-C motif) ligand 2 secretion (GO:0035926)|chemokine secretion (GO:0090195)|defense response to virus (GO:0051607)|establishment of endothelial barrier (GO:0061028)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|interleukin-1 beta secretion (GO:0050702)|interleukin-10 secretion (GO:0072608)|leukocyte migration (GO:0050900)|leukocyte proliferation (GO:0070661)|mature dendritic cell differentiation (GO:0097029)|negative regulation of chemokine secretion (GO:0090198)|negative regulation of JNK cascade (GO:0046329)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neutrophil activation (GO:0042119)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of cell migration (GO:0030335)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of eosinophil degranulation (GO:0043311)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of neutrophil mediated killing of gram-negative bacterium (GO:0070963)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of blood coagulation (GO:0030193)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of JNK cascade (GO:0046328)|T cell activation involved in immune response (GO:0002286)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)	p.T225T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	13		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)		ACATCACGACCTGTCATGATG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	5											111	97	102					5																	76129107		2203	4300	6503	76164863	SO:0001819	synonymous_variant	2150			BC018130	CCDS4033.1	5q13	2012-08-08			ENSG00000164251	ENSG00000164251		"GPCR / Class A : Protease activated receptors"	3538	protein-coding gene	gene with protein product	"proteinase-activated receptor-2"	600933		GPR11		7937743, 7556175	Standard	NM_005242		Approved	PAR2	uc003keo.3	P55085	OTTHUMG00000102118	ENST00000296677.4:c.675C>A	5.37:g.76129107C>A			76164863	Q13317|Q13346|Q53XJ8	Silent	SNP	ENST00000296677.4	37	CCDS4033.1																																																																																				0.502	F2RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219957.2			A	76129107	C	A	76129107	2	1	68	1	0	0	0	0	0	0	0	1	5357	668	24	2		2	F2RL1	5	76129107	Silent	SNP	C	TCGA-AG-A015-01A-01W-A005-10		76129107	104786153	13	20893										
APC	324	hgsc.bcm.edu	37	chr5	112175147	112175147	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ctttgtcatcagctgaagatGaaataggatgtaatcagacg	10	6	3	4			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr5:112175147G>T	ENST00000457016.1	+	16	4236	c.3856G>T	c.(3856-3858)Gaa>Taa	p.E1286*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1286*|APC_ENST00000257430.4_Nonsense_Mutation_p.E1286*			P25054	APC_HUMAN	adenomatous polyposis coli	1286	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1286*(7)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGCTGAAGATGAAATAGGATG	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	9	Substitution - Nonsense(7)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(7)|soft_tissue(1)|skin(1)	5	GRCh37	CM940071	APC	M							55	57	56					5																	112175147		2202	4300	6502	112203046	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3856G>T	5.37:g.112175147G>T	ENSP00000413133:p.Glu1286*		112203046	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	7.991415	0.98599	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.179817	0.47455	D	0.000223	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.935	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1286	.	.	E	+	1	0	APC	112203046	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.137000	0.71710	2.861000	0.98227	0.655000	0.94253	GAA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175147	G	T	112175147	4	4	68	1	0	0	0	0	0	1	0	0	763	1291	45	2	3914	2	APC	5	112175147	Nonsense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	36046040	112175147	68740113	14	20894										
GM2A	2760	hgsc.bcm.edu	37	chr5	150646436	150646436	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	agccctgcccagagcccctgCgtacctatgggcttccttgc	10	17	0	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr5:150646436C>T	ENST00000357164.3	+	3	713	c.388C>T	c.(388-390)Cgt>Tgt	p.R130C		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	130					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)	p.R130C(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGCCCCTGCGTACCTATGG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	5											100	98	99					5																	150646436		2203	4300	6503	150626629	SO:0001583	missense	2760				CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"cerebroside sulfate activator protein", "sphingolipid activator protein 3"	613109	"GM2 ganglioside activator protein"			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.388C>T	5.37:g.150646436C>T	ENSP00000349687:p.Arg130Cys		150626629	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.976121|3.976121	0.74360|0.74360	.|.	.|.	ENSG00000196743|ENSG00000196743	ENST00000523004|ENST00000523466;ENST00000357164	.|T;T	.|0.70399	.|-0.48;-0.48	5.7|5.7	4.83|4.83	0.62350|0.62350	.|MD-2-related lipid-recognition (1);	.|0.180058	.|0.64402	.|D	.|0.000012	T|T	0.67439|0.67439	0.2893|0.2893	L|L	0.27053|0.27053	0.805|0.805	0.41166|0.41166	D|D	0.986136|0.986136	.|D;D;D	.|0.89917	.|1.0;0.998;0.997	.|P;P;P	.|0.55455	.|0.776;0.448;0.491	T|T	0.70579|0.70579	-0.4833|-0.4833	5|10	.|0.72032	.|D	.|0.01	-9.6758|-9.6758	8.55|8.55	0.33447|0.33447	0.1519:0.77:0.0:0.0781|0.1519:0.77:0.0:0.0781	.|.	.|130;88;130	.|B4DQM5;Q14427;P17900	.|.;.;SAP3_HUMAN	V|C	88|145;130	.|ENSP00000429100:R145C;ENSP00000349687:R130C	.|ENSP00000349687:R130C	A|R	+|+	2|1	0|0	GM2A|GM2A	150626629|150626629	0.999000|0.999000	0.42202|0.42202	0.978000|0.978000	0.43139|0.43139	0.886000|0.886000	0.51366|0.51366	2.797000|2.797000	0.47877|0.47877	1.409000|1.409000	0.46915|0.46915	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.512	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405		T	150646436	C	T	150646436	3	4	68	1	0	0	0	0	1	0	0	0	6504	768	27	1	398	1	GM2A	5	150646436	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	38471289	150646436	30268824	15	20895										
RNF130	55819	hgsc.bcm.edu	37	chr5	179382668	179382668	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tcttcttcaaaaccattctaCcctatggaataaaaggaaaa	4	9	4	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr5:179382668C>A	ENST00000261947.4	-	8	1550	c.1152G>T	c.(1150-1152)agG>agT	p.R384S	RNF130_ENST00000520564.1_5'UTR|RNF130_ENST00000522208.2_Intron|RNF130_ENST00000521389.1_Splice_Site_p.V416L	NM_001280801.1	NP_001267730.1			ring finger protein 130									p.V416L(1)		breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AACCATTCTACCCTATGGAAT	0.368																																					GBM(24;432 554 38471 39699 51728)											1	Substitution - Missense(1)	large_intestine(1)	5											62	65	64					5																	179382668		2202	4300	6502	179315274	SO:0001630	splice_region_variant	55819			AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"RING-type (C3HC4) zinc fingers"	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.1151-1G>T	5.37:g.179382668C>A			179315274		Missense_Mutation	SNP	ENST00000261947.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.60|13.60	2.286063|2.286063	0.40394|0.40394	.|.	.|.	ENSG00000113269|ENSG00000113269	ENST00000261947|ENST00000521389	T|T	0.04454|0.04275	3.62|3.66	5.18|5.18	4.31|4.31	0.51392|0.51392	.|.	.|0.381207	.|0.25166	.|N	.|0.032632	T|T	0.03220|0.03220	0.0094|0.0094	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B|B	0.13594|0.02656	0.008|0.0	B|B	0.14578|0.04013	0.011|0.001	T|T	0.47156|0.47156	-0.9139|-0.9139	9|10	0.72032|0.59425	D|D	0.01|0.04	.|.	11.5252|11.5252	0.50576|0.50576	0.0:0.916:0.0:0.084|0.0:0.916:0.0:0.084	.|.	401|416	Q59EL1|Q86XS8	.|GOLI_HUMAN	S|L	384|416	ENSP00000261947:R384S|ENSP00000430237:V416L	ENSP00000261947:R384S|ENSP00000430237:V416L	R|V	-|-	3|1	2|0	RNF130|RNF130	179315274|179315274	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.807000|0.807000	0.45602|0.45602	2.045000|2.045000	0.41250|0.41250	1.297000|1.297000	0.44761|0.44761	0.591000|0.591000	0.81541|0.81541	AGG|GTA		0.368	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	Missense_Mutation	A	179382668	C	A	179382668	5	1	68	1	0	0	0	0	0	0	1	0	13475	521	18	2	17	2	RNF130	5	179382668	Splice_Site	SNP	C	TCGA-AG-A015-01A-01W-A005-10	28736232	179382668	1532592	16	20896										
PSMB8	5696	hgsc.bcm.edu	37	chr6	32810842	32810842	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gttcctttctccgtccccacCcagggactggaagaattctg	9	14	2	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:32810842C>A	ENST00000374882.3	-	2	222	c.172G>T	c.(172-174)Ggt>Tgt	p.G58C	TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_5'Flank|PSMB8_ENST00000395339.3_Missense_Mutation_p.G58C|PSMB8_ENST00000374881.2_Missense_Mutation_p.G54C	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	58					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.G54C(1)|p.G58C(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	CCGTCCCCACCCAGGGACTGG	0.498																																					NSCLC(48;53 1172 10859 13624 22883)											2	Substitution - Missense(2)	large_intestine(2)	6											76	73	74					6																	32810842		1511	2709	4220	32918820	SO:0001583	missense	5696				CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"Proteasome (prosome, macropain) subunits"	9545	protein-coding gene	gene with protein product		177046	"proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)", "large multifunctional peptidase 7"	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.172G>T	6.37:g.32810842C>A	ENSP00000364016:p.Gly58Cys		32918820	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Missense_Mutation	SNP	ENST00000374882.3	37	CCDS4757.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418005	0.25552	.	.	ENSG00000204264	ENST00000395339;ENST00000374882;ENST00000374881	T;T;T	0.38560	1.13;1.77;1.75	5.91	-1.26	0.09376	.	0.797554	0.11795	N	0.528734	T	0.09862	0.0242	L	0.33485	1.01	0.09310	N	1	B;B;B	0.19706	0.038;0.004;0.0	B;B;B	0.17433	0.013;0.018;0.002	T	0.29058	-1.0024	10	0.45353	T	0.12	-2.3013	2.4636	0.04547	0.1135:0.4458:0.1104:0.3303	.	58;54;58	B7Z6U7;P28062-2;P28062	.;.;PSB8_HUMAN	C	58;58;54	ENSP00000378748:G58C;ENSP00000364016:G58C;ENSP00000364015:G54C	ENSP00000364015:G54C	G	-	1	0	PSMB8	32918820	0.001000	0.12720	0.000000	0.03702	0.113000	0.19764	0.156000	0.16382	-0.624000	0.05611	-0.917000	0.02746	GGT		0.498	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919		A	32810842	C	A	32810842	3	1	68	1	0	0	0	0	1	0	0	0	12717	623	22	2	678	2	PSMB8	6	32810842	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10		32810842	138304225	17	20897										
VPS52	6293	hgsc.bcm.edu	37	chr6	33235080	33235080	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tggtgttcctgctgcggagcGatggctttgagaagaatcgt	15	7	0	2	rs377130721		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:33235080G>A	ENST00000445902.2	-	11	1228	c.1010C>T	c.(1009-1011)tCg>tTg	p.S337L	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000436044.2_Missense_Mutation_p.S212L|VPS52_ENST00000478934.1_Intron	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	337					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.S337L(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GCTGCGGAGCGATGGCTTTGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	83	77	79		1010	5.3	1	6		79	0,8600		0,0,4300	no	missense	VPS52	NM_022553.4	145	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	337/724	33235080	1,13005	2203	4300	6503	33343058	SO:0001583	missense	6293			AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"SAC2 suppressor of actin mutations 2-like (yeast)", "vacuolar protein sorting 52 (yeast)"	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.1010C>T	6.37:g.33235080G>A	ENSP00000409952:p.Ser337Leu		33343058	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Missense_Mutation	SNP	ENST00000445902.2	37	CCDS4770.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.193365	0.78902	2.27E-4	0.0	ENSG00000223501	ENST00000445902;ENST00000418054;ENST00000436044	.	.	.	5.3	5.3	0.74995	.	0.053410	0.85682	D	0.000000	T	0.44244	0.1284	M	0.75777	2.31	0.58432	D	0.999999	P	0.41929	0.765	B	0.34093	0.175	T	0.49123	-0.8972	9	0.30854	T	0.27	-18.6301	16.8656	0.86028	0.0:0.0:1.0:0.0	.	337	Q8N1B4	VPS52_HUMAN	L	337;315;212	.	ENSP00000414785:S315L	S	-	2	0	VPS52	33343058	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	7.437000	0.80417	2.932000	0.99384	0.643000	0.83706	TCG		0.562	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		A	33235080	G	A	33235080	3	1	68	1	0	0	0	0	1	0	0	0	17254	1059	37	1	1201	1	VPS52	6	33235080	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	424238	33235080	137879987	18	20898										
DAXX	1616	hgsc.bcm.edu	37	chr6	33288608	33288608	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tgcccacatctcggaaggcaTcctgagccatgagctggagc	12	13	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:33288608T>A	ENST00000374542.5	-	3	1148	c.944A>T	c.(943-945)gAt>gTt	p.D315V	DAXX_ENST00000266000.6_Missense_Mutation_p.D315V|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_Intron|DAXX_ENST00000414083.2_Missense_Mutation_p.D240V	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	315	Interaction with histone H3.3.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.D315V(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						TCGGAAGGCATCCTGAGCCAT	0.582			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	1	Substitution - Missense(1)	large_intestine(1)	6											103	95	98					6																	33288608		2203	4300	6503	33396586	SO:0001583	missense	1616			AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.944A>T	6.37:g.33288608T>A	ENSP00000363668:p.Asp315Val		33396586	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	37	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.855224	0.71719	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083	.	.	.	4.67	4.67	0.58626	.	0.051728	0.85682	D	0.000000	T	0.72550	0.3474	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	0.994;1.0;1.0	D;D;D	0.79784	0.937;0.993;0.993	T	0.77515	-0.2559	9	0.87932	D	0	-19.0275	12.1315	0.53946	0.0:0.0:0.0:1.0	.	327;315;315	B4E1C1;B2R7M0;Q9UER7	.;.;DAXX_HUMAN	V	315;315;240	.	ENSP00000266000:D315V	D	-	2	0	DAXX	33396586	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.613000	0.74192	1.974000	0.57490	0.523000	0.50628	GAT		0.582	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			A	33288608	T	A	33288608	3	1	68	1	0	0	0	0	1	0	0	0	4249	1435	50	5	1302	5	DAXX	6	33288608	Missense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10	53528	33288608	137826459	19	20899										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56918018	56918018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tagtgcataaacaaaataatAaaaatattgatgctactgta	5	4	0	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:56918018A>G	ENST00000370733.4	+	4	928	c.721A>G	c.(721-723)Aaa>Gaa	p.K241E	KIAA1586_ENST00000545356.1_Missense_Mutation_p.K214E	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	241							nucleic acid binding (GO:0003676)	p.K241E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ACAAAATAATAAAAATATTGA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	6											23	26	25					6																	56918018		2147	4254	6401	57025977	SO:0001583	missense	57691			AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.721A>G	6.37:g.56918018A>G	ENSP00000359768:p.Lys241Glu		57025977	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	2.456	-0.325239	0.05350	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.31247	1.51;1.5	4.07	1.58	0.23477	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	0.999991	B;B	0.23891	0.093;0.093	B;B	0.25987	0.065;0.065	T	0.45071	-0.9286	9	0.05721	T	0.95	-8.5602	3.0775	0.06251	0.673:0.0:0.1163:0.2108	.	214;241	F5H2N6;Q9HCI6	.;K1586_HUMAN	E	241;214	ENSP00000359768:K241E;ENSP00000445507:K214E	ENSP00000359768:K241E	K	+	1	0	KIAA1586	57025977	1.000000	0.71417	0.367000	0.25926	0.511000	0.34104	1.759000	0.38420	0.214000	0.20742	0.383000	0.25322	AAA		0.294	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		G	56918018	A	G	56918018	3	3	68	1	0	0	0	0	1	0	0	0	8266	363	13	4	735	4	KIAA1586	6	56918018	Missense_Mutation	SNP	A	TCGA-AG-A015-01A-01W-A005-10	23629410	56918018	114197049	20	20900										
SEC63	11231	hgsc.bcm.edu	37	chr6	108250659	108250659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tggctggggttttaataaccGtaaacgataccacatacacc	8	10	0	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:108250659G>A	ENST00000369002.4	-	2	363	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	RNU6-437P_ENST00000459408.1_RNA	NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	62					liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.R62W(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		TTTAATAACCGTAAACGATAC	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	6											157	158	158					6																	108250659		2202	4297	6499	108357352	SO:0001583	missense	11231			BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"Heat shock proteins / DNAJ (HSP40)"	21082	protein-coding gene	gene with protein product		608648	"SEC63-like (S. cerevisiae)"			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.184C>T	6.37:g.108250659G>A	ENSP00000357998:p.Arg62Trp		108357352	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Missense_Mutation	SNP	ENST00000369002.4	37	CCDS5061.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.394138	0.62066	.	.	ENSG00000025796	ENST00000369002;ENST00000429168	T;T	0.76448	-1.02;-0.17	5.48	3.64	0.41730	.	0.000000	0.85682	D	0.000000	T	0.67439	0.2893	L	0.34521	1.04	0.53688	D	0.99997	D	0.69078	0.997	P	0.52554	0.702	T	0.71810	-0.4480	10	0.72032	D	0.01	-14.1314	13.3702	0.60709	0.0:0.0:0.5862:0.4138	.	62	Q9UGP8	SEC63_HUMAN	W	62;6	ENSP00000357998:R62W;ENSP00000403144:R6W	ENSP00000357998:R62W	R	-	1	2	SEC63	108357352	1.000000	0.71417	0.999000	0.59377	0.744000	0.42396	2.026000	0.41069	0.631000	0.30412	0.557000	0.71058	CGG		0.299	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		A	108250659	G	A	108250659	3	1	68	1	0	0	0	0	1	0	0	0	14042	1144	40	1	2178	1	SEC63	6	108250659	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	51332641	108250659	62864408	21	20901										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151161631	151161631	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	agaaagttgtggtggtcaatAgaaatttacccttaaatgcc	9	6	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:151161631A>T	ENST00000358517.2	+	16	3968	c.3757A>T	c.(3757-3759)Aga>Tga	p.R1253*	PLEKHG1_ENST00000367328.1_Nonsense_Mutation_p.R1253*			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1253							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1253*(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GGTGGTCAATAGAAATTTACC	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											73	72	73					6																	151161631		2203	4300	6503	151203324	SO:0001587	stop_gained	57480			AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3757A>T	6.37:g.151161631A>T	ENSP00000351318:p.Arg1253*		151203324	Q5T1F2	Nonsense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	A	44	11.183252	0.99528	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	.	.	.	5.61	5.61	0.85477	.	0.133460	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0994	0.81158	1.0:0.0:0.0:0.0	.	.	.	.	X	1253	.	ENSP00000351318:R1253X	R	+	1	2	PLEKHG1	151203324	1.000000	0.71417	0.999000	0.59377	0.900000	0.52787	3.700000	0.54786	2.261000	0.74972	0.533000	0.62120	AGA		0.408	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			T	151161631	A	T	151161631	4	4	68	1	0	0	0	0	0	1	0	0	12099	412	15	5	3815	5	PLEKHG1	6	151161631	Nonsense_Mutation	SNP	A	TCGA-AG-A015-01A-01W-A005-10	42910972	151161631	19953436	22	20902										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152652170	152652170	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	agttcttgtaaccggtgactGcacttttgtaaaacactgtc	8	9	1	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr6:152652170G>T	ENST00000367255.5	-	78	14251	c.13650C>A	c.(13648-13650)tgC>tgA	p.C4550*	SYNE1_ENST00000448038.1_Nonsense_Mutation_p.C4479*|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.C4550*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.C4479*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4550					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.C4550*(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACCGGTGACTGCACTTTTGTA	0.413										HNSCC(10;0.0054)																																						2	Substitution - Nonsense(2)	large_intestine(2)	6											152	157	155					6																	152652170		2203	4300	6503	152693863	SO:0001587	stop_gained	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.13650C>A	6.37:g.152652170G>T	ENSP00000356224:p.Cys4550*		152693863	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	56	25.329121	0.99964	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038	.	.	.	6.03	-6.06	0.02165	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	19.4531	0.94876	0.2542:0.0:0.7458:0.0	.	.	.	.	X	4550;4479;4550;4479	.	ENSP00000265368:C4550X	C	-	3	2	SYNE1	152693863	0.784000	0.28713	0.225000	0.23894	0.578000	0.36192	0.116000	0.15561	-1.108000	0.03000	-0.302000	0.09304	TGC		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152652170	G	T	152652170	4	4	68	1	0	0	0	0	0	1	0	0	15484	1311	46	2	13092	2	SYNE1	6	152652170	Nonsense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	1490539	152652170	18462897	23	20903										
CARD11	84433	hgsc.bcm.edu	37	chr7	2977620	2977620	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tgtacatttcacagtcctttCccagggtcgagcacttgagc	9	12	1	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr7:2977620C>A	ENST00000396946.4	-	8	1467	c.1064G>T	c.(1063-1065)gGa>gTa	p.G355V		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	355					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.G348V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		ACAGTCCTTTCCCAGGGTCGA	0.562			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	1	Substitution - Missense(1)	large_intestine(1)	7											156	129	138					7																	2977620		2203	4300	6503	2944146	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1064G>T	7.37:g.2977620C>A	ENSP00000380150:p.Gly355Val		2944146	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	12.56	1.974817	0.34848	.	.	ENSG00000198286	ENST00000396946	T	0.33654	1.4	5.0	5.0	0.66597	.	0.464777	0.22197	N	0.063286	T	0.19327	0.0464	N	0.08118	0	0.50632	D	0.999888	B	0.18610	0.029	B	0.13407	0.009	T	0.06679	-1.0813	10	0.33141	T	0.24	-47.6073	10.8578	0.46808	0.0:0.9135:0.0:0.0865	.	355	Q9BXL7	CAR11_HUMAN	V	355	ENSP00000380150:G355V	ENSP00000380150:G355V	G	-	2	0	CARD11	2944146	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.636000	0.54317	2.318000	0.78349	0.591000	0.81541	GGA		0.562	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2977620	C	A	2977620	3	1	68	1	0	0	0	0	1	0	0	0	2651	855	30	2	2472	2	CARD11	7	2977620	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10		2977620	156161043	24	20904										
SP8	221833	hgsc.bcm.edu	37	chr7	20825258	20825258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	acccactacgttgcagctggCggaagaagaggacgaggagc	15	10	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr7:20825258C>A	ENST00000361443.4	-	3	361	c.124G>T	c.(124-126)Gcc>Tcc	p.A42S	SP8_ENST00000418710.2_Missense_Mutation_p.A60S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	42	Ser-rich.				dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A42S(1)|p.A60S(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						TTGCAGCTGGCGGAAGAAGAG	0.672																																																2	Substitution - Missense(2)	large_intestine(2)	7											43	43	43					7																	20825258		2203	4300	6503	20791783	SO:0001583	missense	221833				CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.124G>T	7.37:g.20825258C>A	ENSP00000354482:p.Ala42Ser		20791783	Q7Z615|Q7Z616|Q96MJ1	Missense_Mutation	SNP	ENST00000361443.4	37	CCDS5372.1	.	.	.	.	.	.	.	.	.	.	C	1.053	-0.675191	0.03378	.	.	ENSG00000164651	ENST00000297210;ENST00000418710;ENST00000361443	T;T	0.11385	2.84;2.78	3.35	2.45	0.29901	.	0.317189	0.33895	N	0.004442	T	0.04227	0.0117	N	0.08118	0	0.20873	N	0.999838	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.45760	-0.9239	10	0.09084	T	0.74	.	7.2589	0.26191	0.2981:0.6113:0.0:0.0906	.	42;42	Q7Z615;Q8IXZ3	.;SP8_HUMAN	S	60;60;42	ENSP00000408792:A60S;ENSP00000354482:A42S	ENSP00000297210:A60S	A	-	1	0	SP8	20791783	0.362000	0.24980	0.917000	0.36280	0.645000	0.38454	0.190000	0.17057	0.233000	0.21120	-2.157000	0.00329	GCC		0.672	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			A	20825258	C	A	20825258	3	1	68	1	0	0	0	0	1	0	0	0	15007	768	27	2	1352	2	SP8	7	20825258	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	17847638	20825258	138313405	25	20905										
ADCY1	107	hgsc.bcm.edu	37	chr7	45662340	45662340	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gcaagttcgatgaattagccAcggtaagtgcagcgtttttc	11	8	0	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr7:45662340A>C	ENST00000297323.7	+	4	1040	c.1018A>C	c.(1018-1020)Acg>Ccg	p.T340P	ADCY1_ENST00000432715.1_Missense_Mutation_p.T115P	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	340					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.T340P(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGAATTAGCCACGGTAAGTGC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											82	72	75					7																	45662340		2203	4300	6503	45628865	SO:0001583	missense	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1018A>C	7.37:g.45662340A>C	ENSP00000297323:p.Thr340Pro		45628865	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	37	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.494678	0.85069	.	.	ENSG00000164742	ENST00000432715;ENST00000297323;ENST00000545300	T;T	0.81247	-1.47;-1.47	5.03	5.03	0.67393	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.84037	0.5384	L	0.42245	1.32	0.80722	D	1	D;D	0.69078	0.997;0.962	D;P	0.67725	0.953;0.828	T	0.83129	-0.0114	10	0.37606	T	0.19	.	12.7639	0.57380	1.0:0.0:0.0:0.0	.	340;115	Q08828;C9J1J0	ADCY1_HUMAN;.	P	115;340;340	ENSP00000392721:T115P;ENSP00000297323:T340P	ENSP00000297323:T340P	T	+	1	0	ADCY1	45628865	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.299000	0.65716	2.093000	0.63338	0.533000	0.62120	ACG		0.483	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		C	45662340	A	C	45662340	3	2	68	1	0	0	0	0	1	0	0	0	292	159	6	4	1032	4	ADCY1	7	45662340	Missense_Mutation	SNP	A	TCGA-AG-A015-01A-01W-A005-10	24837082	45662340	113476323	26	20906										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70591848	70591848	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	acaggtgcattctgtataatTccgtatctaagtgagcaaaa	8	7	2	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr8:70591848T>G	ENST00000260126.4	-	8	2495	c.1789A>C	c.(1789-1791)Aat>Cat	p.N597H	SLCO5A1_ENST00000530307.1_Missense_Mutation_p.N542H|SLCO5A1_ENST00000524945.1_Missense_Mutation_p.N597H	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	597	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.N597H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TCTGTATAATTCCGTATCTAA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	8											115	111	112					8																	70591848		2203	4300	6503	70754402	SO:0001583	missense	81796			AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.1789A>C	8.37:g.70591848T>G	ENSP00000260126:p.Asn597His		70754402	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	37	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437223	0.83885	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.04317	3.65;3.65;3.65	5.8	5.8	0.92144	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.211465	0.46758	D	0.000279	T	0.19846	0.0477	M	0.79123	2.44	0.58432	D	0.999998	D;D;D	0.76494	0.998;0.999;0.993	D;D;D	0.70487	0.969;0.949;0.937	T	0.11372	-1.0590	10	0.15499	T	0.54	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	542;597;597	E9PKK5;Q9H2Y9;G3V1C0	.;SO5A1_HUMAN;.	H	597;597;542	ENSP00000260126:N597H;ENSP00000434422:N597H;ENSP00000431611:N542H	ENSP00000260126:N597H	N	-	1	0	SLCO5A1	70754402	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.985000	0.88162	2.209000	0.71365	0.533000	0.62120	AAT		0.413	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		G	70591848	T	G	70591848	3	3	68	1	0	0	0	0	1	0	0	0	14768	1783	62	4	769	4	SLCO5A1	8	70591848	Missense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10		70591848	75772174	27	20907										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92983013	92983013	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tgtcgtgggctttccgctccGcctcagacacggccttctgc	11	16	2	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr8:92983013G>A	ENST00000523629.1	-	11	1866	c.1412C>T	c.(1411-1413)gCg>gTg	p.A471V	RUNX1T1_ENST00000265814.3_Missense_Mutation_p.A471V|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.A434V|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.A434V|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.A482V|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.A444V|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.A444V|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.A434V	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	471			A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A434V(2)|p.A471V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TTTCCGCTCCGCCTCAGACAC	0.622																																																3	Substitution - Missense(3)	large_intestine(3)	8											81	65	70					8																	92983013		2203	4300	6503	93052189	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1412C>T	8.37:g.92983013G>A	ENSP00000428543:p.Ala471Val		93052189	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	37	5.997494	0.97184	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.74450	0.3718	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.988;0.994	T	0.76926	-0.2778	10	0.72032	D	0.01	-13.1985	20.2181	0.98305	0.0:0.0:1.0:0.0	.	482;434;471;444	E7EPN4;Q7Z4J5;Q06455;Q06455-2	.;.;MTG8_HUMAN;.	V	471;444;471;434;434;434;482;444	ENSP00000428543:A471V;ENSP00000379520:A444V;ENSP00000265814:A471V;ENSP00000353504:A434V;ENSP00000390137:A434V;ENSP00000428742:A434V;ENSP00000402257:A482V;ENSP00000430728:A444V	ENSP00000265814:A471V	A	-	2	0	RUNX1T1	93052189	1.000000	0.71417	0.974000	0.42286	0.987000	0.75469	9.869000	0.99810	2.785000	0.95823	0.655000	0.94253	GCG		0.622	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	92983013	G	A	92983013	3	1	68	1	0	0	0	0	1	0	0	0	13784	1087	38	1	410	1	RUNX1T1	8	92983013	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	22391165	92983013	53381009	28	20908										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133141602	133141602	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ccgctgggcgtgaaggggtcCgtgtctgtgtccgtctcacc	15	13	2	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr8:133141602C>T	ENST00000388996.4	-	15	2946	c.2526G>A	c.(2524-2526)acG>acA	p.T842T	KCNQ3_ENST00000521134.1_Silent_p.T722T|KCNQ3_ENST00000519445.1_Silent_p.T830T	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	842					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.T842T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGAAGGGGTCCGTGTCTGTGT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	8											83	70	75					8																	133141602		2203	4300	6503	133210784	SO:0001819	synonymous_variant	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2526G>A	8.37:g.133141602C>T			133210784	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																				0.572	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133141602	C	T	133141602	2	4	68	1	0	0	0	0	0	0	0	1	8105	639	23	1		1	KCNQ3	8	133141602	Silent	SNP	C	TCGA-AG-A015-01A-01W-A005-10	40158589	133141602	13222420	29	20909										
ECM2	1842	hgsc.bcm.edu	37	chr9	95277476	95277476	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	atgctataccactgagtagaGaataggagactaatgaccac	9	8	0	4			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr9:95277476G>T	ENST00000344604.5	-	4	640	c.491C>A	c.(490-492)tCt>tAt	p.S164Y	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	164					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.S164Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ACTGAGTAGAGAATAGGAGAC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	9											31	30	30					9																	95277476		2203	4300	6503	94317297	SO:0001583	missense	1842			AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"matrix glycoprotein SC1/ECM2"	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.491C>A	9.37:g.95277476G>T	ENSP00000344758:p.Ser164Tyr		94317297	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	G	10.91	1.485172	0.26598	.	.	ENSG00000106823	ENST00000344604	T	0.51325	0.71	5.32	0.134	0.14771	.	1.799990	0.02395	N	0.080075	T	0.31295	0.0792	N	0.14661	0.345	0.09310	N	1	P	0.44578	0.838	B	0.41988	0.372	T	0.11665	-1.0578	10	0.33141	T	0.24	.	3.9167	0.09227	0.3631:0.0:0.4798:0.157	.	164	O94769	ECM2_HUMAN	Y	164	ENSP00000344758:S164Y	ENSP00000344758:S164Y	S	-	2	0	ECM2	94317297	0.000000	0.05858	0.000000	0.03702	0.979000	0.70002	-0.341000	0.07811	-0.161000	0.10983	0.650000	0.86243	TCT		0.328	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		T	95277476	G	T	95277476	3	4	68	1	0	0	0	0	1	0	0	0	4909	942	33	2	1636	2	ECM2	9	95277476	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		95277476	45935955	30	20910										
SETX	23064	hgsc.bcm.edu	37	chr9	135172276	135172276	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gccctcacccatacctacctCtgtcagtagacgatagagga	8	14	3	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr9:135172276C>G	ENST00000224140.5	-	14	6129	c.5947G>C	c.(5947-5949)Gag>Cag	p.E1983Q	SETX_ENST00000372169.2_Missense_Mutation_p.E1983Q|SETX_ENST00000393220.1_Missense_Mutation_p.E1983Q	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1983					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.E1983Q(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATACCTACCTCTGTCAGTAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	9											139	113	122					9																	135172276		2203	4300	6503	134162097	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5947G>C	9.37:g.135172276C>G	ENSP00000224140:p.Glu1983Gln		134162097	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.134792	0.56828	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.53	5.53	0.82687	.	0.168428	0.40144	N	0.001164	D	0.86306	0.5901	N	0.25647	0.755	0.41871	D	0.990279	D;D;D	0.89917	0.98;1.0;1.0	D;D;D	0.91635	0.966;0.999;0.998	D	0.86889	0.2047	10	0.48119	T	0.1	.	18.0171	0.89245	0.0:1.0:0.0:0.0	.	1983;1983;1983	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	Q	1983;225;1983;1983	ENSP00000224140:E1983Q;ENSP00000409143:E225Q;ENSP00000361242:E1983Q;ENSP00000376913:E1983Q	ENSP00000224140:E1983Q	E	-	1	0	SETX	134162097	0.998000	0.40836	1.000000	0.80357	0.202000	0.24057	4.027000	0.57239	2.601000	0.87937	0.563000	0.77884	GAG		0.403	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135172276	C	G	135172276	3	3	68	1	0	0	0	0	1	0	0	0	14178	922	32	5	2138	5	SETX	9	135172276	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	39894800	135172276	6041155	31	20911										
MYPN	84665	hgsc.bcm.edu	37	chr10	69959139	69959139	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tattaggtgagtggtttaccGcccccggagctgacatggct	13	10	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr10:69959139G>A	ENST00000358913.5	+	17	3788	c.3300G>A	c.(3298-3300)ccG>ccA	p.P1100P	MYPN_ENST00000540630.1_Silent_p.P1100P|MYPN_ENST00000354393.2_Silent_p.P825P	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1100	Ig-like 4.|Interaction with ACTN.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.P1100P(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						GTGGTTTACCGCCCCCGGAGC	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	10											58	50	52					10																	69959139		2203	4300	6503	69629145	SO:0001819	synonymous_variant	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.3300G>A	10.37:g.69959139G>A			69629145	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																				0.512	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		A	69959139	G	A	69959139	2	1	68	1	0	0	0	0	0	0	0	1	10128	1074	38	1		1	MYPN	10	69959139	Silent	SNP	G	TCGA-AG-A015-01A-01W-A005-10		69959139	65575608	32	20912										
C10orf35	219738	hgsc.bcm.edu	37	chr10	71391546	71391546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aatcgtgcaggatgacgaccCccgagtgaggaccactaccc	11	14	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr10:71391546C>T	ENST00000373279.4	+	3	206	c.47C>T	c.(46-48)cCc>cTc	p.P16L	C10orf35_ENST00000491890.1_3'UTR	NM_145306.2	NP_660349.1	Q96D05	CJ035_HUMAN	chromosome 10 open reading frame 35	16						integral component of membrane (GO:0016021)		p.P16L(1)		breast(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						GATGACGACCCCCGAGTGAGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	10											160	118	132					10																	71391546		2203	4300	6503	71061552	SO:0001583	missense	219738			BC013587	CCDS7295.1	10q22.2	2003-11-21			ENSG00000171224	ENSG00000171224			23519	protein-coding gene	gene with protein product						12477932	Standard	NM_145306		Approved		uc001jpq.4	Q96D05	OTTHUMG00000018383	ENST00000373279.4:c.47C>T	10.37:g.71391546C>T	ENSP00000362376:p.Pro16Leu		71061552		Missense_Mutation	SNP	ENST00000373279.4	37	CCDS7295.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507392	0.85282	.	.	ENSG00000171224	ENST00000373279;ENST00000421716	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000008	T	0.77336	0.4115	M	0.63843	1.955	0.54753	D	0.999989	D	0.89917	1.0	D	0.87578	0.998	T	0.79050	-0.1962	9	0.72032	D	0.01	-7.6925	16.703	0.85364	0.0:1.0:0.0:0.0	.	16	Q96D05	CJ035_HUMAN	L	16;58	.	ENSP00000362376:P16L	P	+	2	0	C10orf35	71061552	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	4.829000	0.62737	2.551000	0.86045	0.491000	0.48974	CCC		0.597	C10orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048454.1	NM_145306		T	71391546	C	T	71391546	3	4	68	1	0	0	0	0	1	0	0	0	1607	623	22	3	49	3	C10orf35	10	71391546	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	1432407	71391546	64143201	33	20913										
CDCA5	113130	hgsc.bcm.edu	37	chr11	64846661	64846661	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	actcatccagctccgttttcTgagggaagagaaatgaggag	12	8	2	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr11:64846661T>C	ENST00000275517.3	-	6	851		c.e6-2		CDCA5_ENST00000404147.3_Missense_Mutation_p.Q281R	NM_080668.3	NP_542399.1	Q96FF9	CDCA5_HUMAN	cell division cycle associated 5						double-strand break repair (GO:0006302)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|regulation of cohesin localization to chromatin (GO:0071922)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.?(1)		large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						CTCCGTTTTCTGAGGGAAGAG	0.557																																																1	Unknown(1)	large_intestine(1)	11											50	44	46					11																	64846661		2201	4297	6498	64603237	SO:0001630	splice_region_variant	113130			BG354578	CCDS8091.1	11q13.1	2011-01-31			ENSG00000146670	ENSG00000146670			14626	protein-coding gene	gene with protein product	"sororin"	609374				12188893, 15837422	Standard	NM_080668		Approved		uc001ocp.2	Q96FF9	OTTHUMG00000150420	ENST00000275517.3:c.679-2A>G	11.37:g.64846661T>C			64603237	A8K625	Splice_Site	SNP	ENST00000275517.3	37	CCDS8091.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.73|14.73	2.623113|2.623113	0.46840|0.46840	.|.	.|.	ENSG00000146670|ENSG00000146670	ENST00000275517|ENST00000404147	.|T	.|0.47869	.|0.83	3.19|3.19	3.19|3.19	0.36642|0.36642	.|.	.|.	.|.	.|.	.|.	.|T	.|0.48447	.|0.1500	.|.	.|.	.|.	0.22171|0.22171	N|N	0.999311|0.999311	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.43718	.|-0.9374	.|6	.|0.87932	.|D	.|0	.|.	8.1541|8.1541	0.31158|0.31158	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|R	-1|281	.|ENSP00000385711:Q281R	.|ENSP00000385711:Q281R	.|Q	-|-	.|2	.|0	CDCA5|CDCA5	64603237|64603237	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	4.588000|4.588000	0.60999|0.60999	1.724000|1.724000	0.51502|0.51502	0.528000|0.528000	0.53228|0.53228	.|CAG		0.557	CDCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385186.1	NM_080668	Intron	C	64846661	T	C	64846661	5	2	68	1	0	0	0	0	0	0	1	0	3095	1594	55	4	85	4	CDCA5	11	64846661	Splice_Site	SNP	T	TCGA-AG-A015-01A-01W-A005-10		64846661	70159855	34	20914										
ME3	10873	hgsc.bcm.edu	37	chr11	86158123	86158123	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tgacctcggtgacccggtagCacttctcagccgtgcactcg	11	15	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr11:86158123C>A	ENST00000393324.3	-	11	1617	c.1364G>T	c.(1363-1365)tGc>tTc	p.C455F	ME3_ENST00000359636.2_Missense_Mutation_p.C455F|ME3_ENST00000543262.1_Missense_Mutation_p.C455F|RP11-317J19.1_ENST00000524610.1_RNA	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	455					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.C455F(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				GACCCGGTAGCACTTCTCAGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											66	58	60					11																	86158123		2202	4299	6501	85835771	SO:0001583	missense	10873			X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1364G>T	11.37:g.86158123C>A	ENSP00000376998:p.Cys455Phe		85835771	B7Z6V0|Q8TBJ0	Missense_Mutation	SNP	ENST00000393324.3	37	CCDS8277.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.958769	0.92726	.	.	ENSG00000151376	ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.23	5.23	0.72850	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.040960	0.85682	D	0.000000	T	0.66107	0.2756	M	0.83953	2.67	0.80722	D	1	D	0.53885	0.963	P	0.60068	0.868	T	0.68834	-0.5304	9	.	.	.	-5.7787	19.1755	0.93601	0.0:1.0:0.0:0.0	.	455	Q16798	MAON_HUMAN	F	455	ENSP00000352657:C455F;ENSP00000440246:C455F;ENSP00000376998:C455F;ENSP00000431182:C455F	.	C	-	2	0	ME3	85835771	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.619000	0.83057	2.584000	0.87258	0.650000	0.86243	TGC		0.562	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2			A	86158123	C	A	86158123	3	1	68	1	0	0	0	0	1	0	0	0	9449	710	25	2	466	2	ME3	11	86158123	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	21311462	86158123	48848393	35	20915										
TMEM225	338661	hgsc.bcm.edu	37	chr11	123753985	123753985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	attctcagattccttacattCgttgtcagatttatggatgt	7	7	2	2	rs77654932		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr11:123753985C>T	ENST00000375026.2	-	4	754	c.538G>A	c.(538-540)Gaa>Aaa	p.E180K		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	180					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.E180K(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						TCCTTACATTCGTTGTCAGAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	11											110	102	105					11																	123753985		2202	4299	6501	123259195	SO:0001583	missense	338661			AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"PMP22 claudin domain containing", "protein phosphatase 1, regulatory subunit 154"						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.538G>A	11.37:g.123753985C>T	ENSP00000364166:p.Glu180Lys		123259195		Missense_Mutation	SNP	ENST00000375026.2	37	CCDS31697.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.546781	0.27652	.	.	ENSG00000204300	ENST00000375026;ENST00000528595	T;T	0.34472	1.39;1.36	3.31	-2.27	0.06846	.	1.519590	0.03921	N	0.283618	T	0.23649	0.0572	N	0.20986	0.625	0.09310	N	1	B	0.25105	0.118	B	0.14578	0.011	T	0.20107	-1.0285	10	0.38643	T	0.18	2.5938	7.8188	0.29276	0.0:0.3397:0.0:0.6603	.	180	Q6GV28	TM225_HUMAN	K	180;130	ENSP00000364166:E180K;ENSP00000431282:E130K	ENSP00000364166:E180K	E	-	1	0	TMEM225	123259195	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.601000	0.05687	-0.512000	0.06505	-0.345000	0.07892	GAA		0.443	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743		T	123753985	C	T	123753985	3	4	68	1	0	0	0	0	1	0	0	0	16186	893	31	1	143	1	TMEM225	11	123753985	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	37595862	123753985	11252531	36	20916										
TAS2R10	50839	hgsc.bcm.edu	37	chr12	10978664	10978664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	atatatatttggagagaataTctgtataaatccatctgtaa	6	4	2	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:10978664T>C	ENST00000240619.2	-	1	293	c.205A>G	c.(205-207)Ata>Gta	p.I69V		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	69					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.I69V(1)		breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GGAGAGAATATCTGTATAAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											43	47	46					12																	10978664		2203	4299	6502	10869931	SO:0001583	missense	50839			AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.205A>G	12.37:g.10978664T>C	ENSP00000240619:p.Ile69Val		10869931	Q3MIM9|Q6NTD9	Missense_Mutation	SNP	ENST00000240619.2	37	CCDS8634.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.729998	0.00687	.	.	ENSG00000121318	ENST00000240619	T	0.37584	1.19	4.15	-1.3	0.09259	.	1.455470	0.04292	N	0.345755	T	0.12774	0.0310	N	0.03948	-0.315	0.09310	N	1	B	0.10296	0.003	B	0.16289	0.015	T	0.22626	-1.0211	10	0.02654	T	1	.	3.088	0.06284	0.1868:0.3221:0.0:0.4911	.	69	Q9NYW0	T2R10_HUMAN	V	69	ENSP00000240619:I69V	ENSP00000240619:I69V	I	-	1	0	TAS2R10	10869931	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.992000	0.01476	-0.012000	0.14223	-0.462000	0.05337	ATA		0.333	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			C	10978664	T	C	10978664	3	2	68	1	0	0	0	0	1	0	0	0	15605	1435	50	4	722	4	TAS2R10	12	10978664	Missense_Mutation	SNP	T	TCGA-AG-A015-01A-01W-A005-10		10978664	122873231	37	20917										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	68	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	14419620	25398284	108453611	38	20918										
TMEM117	84216	hgsc.bcm.edu	37	chr12	44770472	44770472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	caagattcctttcttccagaAaatcttcaaggaggaatatc	6	9	3	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:44770472A>G	ENST00000266534.3	+	7	990	c.863A>G	c.(862-864)aAa>aGa	p.K288R	TMEM117_ENST00000536799.1_Missense_Mutation_p.K184R|TMEM117_ENST00000551577.1_Intron|TMEM117_ENST00000546978.1_3'UTR	NM_032256.1	NP_115632.1	Q9H0C3	TM117_HUMAN	transmembrane protein 117	288						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.K288R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|urinary_tract(1)	23	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		TTCTTCCAGAAAATCTTCAAG	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	12											114	106	109					12																	44770472		2203	4300	6503	43056739	SO:0001583	missense	84216			BC060798	CCDS8745.1, CCDS73462.1	12q12	2006-02-03				ENSG00000139173			25308	protein-coding gene	gene with protein product						11230166	Standard	NM_001286211		Approved	DKFZp434K2435	uc001rod.3	Q9H0C3	OTTHUMG00000169427	ENST00000266534.3:c.863A>G	12.37:g.44770472A>G	ENSP00000266534:p.Lys288Arg		43056739		Missense_Mutation	SNP	ENST00000266534.3	37	CCDS8745.1	.	.	.	.	.	.	.	.	.	.	A	8.249	0.808581	0.16467	.	.	ENSG00000139173	ENST00000266534;ENST00000536799;ENST00000417623	T;T	0.42900	0.96;0.96	5.39	4.17	0.49024	.	0.254513	0.47093	D	0.000258	T	0.15998	0.0385	N	0.04880	-0.145	0.30660	N	0.754504	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.22243	-1.0222	10	0.07175	T	0.84	-13.0998	4.9853	0.14187	0.7158:0.0:0.1441:0.1401	.	184;288	F5H3Q2;Q9H0C3	.;TM117_HUMAN	R	288;184;36	ENSP00000266534:K288R;ENSP00000445243:K184R	ENSP00000266534:K288R	K	+	2	0	TMEM117	43056739	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.107000	0.50329	2.165000	0.68154	0.528000	0.53228	AAA		0.393	TMEM117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403969.1	NM_032256		G	44770472	A	G	44770472	3	3	68	1	0	0	0	0	1	0	0	0	16070	14	1	4	885	4	TMEM117	12	44770472	Missense_Mutation	SNP	A	TCGA-AG-A015-01A-01W-A005-10	19372188	44770472	89081423	39	20919										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63541337	63541337	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	acacagtcttgaaggagatgGccactaaaaaacatgtatat	8	7	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:63541337G>T	ENST00000299178.2	-	2	1164	c.1059C>A	c.(1057-1059)ggC>ggA	p.G353G		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	353					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)	p.G353G(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GAAGGAGATGGCCACTAAAAA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	12											161	153	156					12																	63541337		2203	4300	6503	61827604	SO:0001819	synonymous_variant	552			L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.1059C>A	12.37:g.63541337G>T			61827604		Silent	SNP	ENST00000299178.2	37	CCDS8965.1																																																																																				0.408	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			T	63541337	G	T	63541337	2	4	68	1	0	0	0	0	0	0	0	1	1232	1190	42	2		2	AVPR1A	12	63541337	Silent	SNP	G	TCGA-AG-A015-01A-01W-A005-10	18770865	63541337	70310558	40	20920										
C12orf26	84190	hgsc.bcm.edu	37	chr12	82796889	82796889	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ctaccacctcttatctgaagAatttgaaaaccagcataaag	5	10	2	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:82796889A>C	ENST00000248306.3	+	5	1328	c.1259A>C	c.(1258-1260)gAa>gCa	p.E420A	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	420							methyltransferase activity (GO:0008168)	p.E420A(1)									TTATCTGAAGAATTTGAAAAC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											86	81	83					12																	82796889		2203	4300	6503	81321020	SO:0001583	missense	84190			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1259A>C	12.37:g.82796889A>C	ENSP00000248306:p.Glu420Ala		81321020	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.818497	0.71028	.	.	ENSG00000127720	ENST00000248306;ENST00000550298	T;T	0.44881	1.36;0.91	5.49	5.49	0.81192	.	0.154834	0.53938	D	0.000042	T	0.47655	0.1457	M	0.64567	1.98	0.48395	D	0.99964	P	0.46621	0.881	P	0.47864	0.559	T	0.39231	-0.9624	10	0.15499	T	0.54	-15.5835	15.5739	0.76359	1.0:0.0:0.0:0.0	.	420	Q8N6Q8	CL026_HUMAN	A	420;55	ENSP00000248306:E420A;ENSP00000449730:E55A	ENSP00000248306:E420A	E	+	2	0	C12orf26	81321020	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.539000	0.90637	2.076000	0.62316	0.482000	0.46254	GAA		0.373	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		C	82796889	A	C	82796889	3	2	68	1	0	0	0	0	1	0	0	0	1683	246	9	4	1277	4	C12orf26	12	82796889	Missense_Mutation	SNP	A	TCGA-AG-A015-01A-01W-A005-10	19255552	82796889	51055006	41	20921										
GPR133	283383	hgsc.bcm.edu	37	chr12	131616324	131616324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tcatctcacagatcagcgccGacaactacaagatccatgga	7	13	3	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:131616324G>A	ENST00000261654.5	+	21	2789	c.2230G>A	c.(2230-2232)Gac>Aac	p.D744N	GPR133_ENST00000376682.4_Missense_Mutation_p.D430N|GPR133_ENST00000543617.1_Missense_Mutation_p.D263N|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000535015.1_Missense_Mutation_p.D776N	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	744					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D744N(1)		NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GATCAGCGCCGACAACTACAA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											204	149	167					12																	131616324		2203	4300	6503	130182277	SO:0001583	missense	283383			AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2230G>A	12.37:g.131616324G>A	ENSP00000261654:p.Asp744Asn		130182277	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593587	0.46214	.	.	ENSG00000111452	ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	T;T;T;T	0.41758	1.24;1.25;0.99;1.01	4.48	3.58	0.41010	GPCR, family 2-like (1);	0.115379	0.56097	U	0.000027	T	0.25005	0.0607	L	0.33293	1	0.48901	D	0.99972	P;B;B	0.37688	0.605;0.191;0.072	B;B;B	0.28011	0.085;0.031;0.021	T	0.03829	-1.1000	10	0.17832	T	0.49	.	10.3185	0.43751	0.0999:0.0:0.9001:0.0	.	776;97;744	B7ZLF7;Q9NSM3;Q6QNK2	.;.;GP133_HUMAN	N	744;776;430;263	ENSP00000261654:D744N;ENSP00000444425:D776N;ENSP00000365872:D430N;ENSP00000438021:D263N	ENSP00000261654:D744N	D	+	1	0	GPR133	130182277	1.000000	0.71417	0.233000	0.24025	0.985000	0.73830	8.150000	0.89634	0.845000	0.35118	0.491000	0.48974	GAC		0.577	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		A	131616324	G	A	131616324	3	1	68	1	0	0	0	0	1	0	0	0	6663	1058	37	1	2312	1	GPR133	12	131616324	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	48819435	131616324	2235571	42	20922										
EP400	57634	hgsc.bcm.edu	37	chr12	132490750	132490750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tcagttcaaagctgccgagaGgatgaatatcgggaagccaa	12	8	2	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr12:132490750G>A	ENST00000333577.4	+	15	3246	c.3137G>A	c.(3136-3138)aGg>aAg	p.R1046K	EP400_ENST00000389561.2_Missense_Mutation_p.R1010K|EP400_ENST00000330386.6_Missense_Mutation_p.R1010K|EP400_ENST00000389562.2_Missense_Mutation_p.R1009K|EP400_ENST00000332482.4_Missense_Mutation_p.R973K			Q96L91	EP400_HUMAN	E1A binding protein p400	1046	Interactions with RUVBL1 and RUVBL2.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R1009K(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		GCTGCCGAGAGGATGAATATC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											99	92	94					12																	132490750		2203	4300	6503	131056703	SO:0001583	missense	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.3137G>A	12.37:g.132490750G>A	ENSP00000333602:p.Arg1046Lys		131056703	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	14.65	2.599929	0.46318	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296;ENST00000542457	D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51	5.53	5.53	0.82687	.	0.142484	0.64402	D	0.000004	D	0.88897	0.6562	L	0.55103	1.725	0.34108	D	0.662706	P;P;P	0.46859	0.885;0.792;0.885	P;B;P	0.48189	0.57;0.415;0.57	D	0.87900	0.2690	10	0.10377	T	0.69	.	19.0592	0.93080	0.0:0.0:1.0:0.0	.	1010;1010;1009	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	K	1046;1010;1009;973;1010;1010;1010	ENSP00000333602:R1046K;ENSP00000374212:R1010K;ENSP00000374213:R1009K;ENSP00000331737:R973K;ENSP00000330620:R1010K	ENSP00000330620:R1010K	R	+	2	0	EP400	131056703	1.000000	0.71417	0.954000	0.39281	0.811000	0.45836	4.442000	0.59988	2.605000	0.88082	0.655000	0.94253	AGG		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132490750	G	A	132490750	3	1	68	1	0	0	0	0	1	0	0	0	5162	1000	35	3	3076	3	EP400	12	132490750	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	874426	132490750	1361145	43	20923										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63453899	63453899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gtgtcaatcgggcaaatttcGtccaaccttaaaaataagga	8	8	1	0	rs180894715		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr14:63453899G>A	ENST00000322893.7	-	5	708	c.440C>T	c.(439-441)aCg>aTg	p.T147M	KCNH5_ENST00000394968.1_Missense_Mutation_p.T89M|KCNH5_ENST00000420622.2_Missense_Mutation_p.T147M|KCNH5_ENST00000394964.2_Missense_Mutation_p.T89M	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	147					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.T147M(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGCAAATTTCGTCCAACCTTA	0.383													G|||	1	0.000199681	0	0.0014	5008	,	,		19251	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14						G	MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	82	78	80		440,440,266	5.7	1	14		80	2,8596	2.2+/-6.3	0,2,4297	no	missense,missense,missense	KCNH5	NM_139318.3,NM_172375.1,NM_172376.1	81,81,81	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	147/989,147/612,89/625	63453899	2,13002	2203	4299	6502	62523652	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.440C>T	14.37:g.63453899G>A	ENSP00000321427:p.Thr147Met		62523652	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.50	3.405912	0.62288	0.0	2.33E-4	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.98937	-5.25;-5.08;-5.08;-5.07	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.97380	0.9143	L	0.44542	1.39	0.80722	D	1	P;P;P;D	0.53885	0.892;0.889;0.759;0.963	B;B;B;B	0.43809	0.21;0.27;0.27;0.432	D	0.97467	1.0038	10	0.49607	T	0.09	.	19.85	0.96736	0.0:0.0:1.0:0.0	.	89;89;147;147	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	M	147;147;89;89	ENSP00000321427:T147M;ENSP00000395439:T147M;ENSP00000378419:T89M;ENSP00000378415:T89M	ENSP00000321427:T147M	T	-	2	0	KCNH5	62523652	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.559000	0.67326	2.697000	0.92050	0.563000	0.77884	ACG		0.383	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63453899	G	A	63453899	3	1	68	1	0	0	0	0	1	0	0	0	8056	1145	40	1	2588	1	KCNH5	14	63453899	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		63453899	43895641	44	20924										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24922476	24922476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gaggctcttataattcagtcGtaggagcagcgcctctcact	10	11	3	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr15:24922476G>A	ENST00000329468.2	+	1	1936	c.1462G>A	c.(1462-1464)Gta>Ata	p.V488I		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	488	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.V488I(2)									TAATTCAGTCGTAGGAGCAGC	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	15											188	198	195					15																	24922476		2203	4300	6503	22473569	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1462G>A	15.37:g.24922476G>A	ENSP00000333735:p.Val488Ile		22473569		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	8.200	0.798045	0.16327	.	.	ENSG00000185823	ENST00000329468	T	0.04917	3.53	2.07	-4.13	0.03904	.	6.428760	0.00447	N	0.000086	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	B	0.23854	0.092	B	0.13407	0.009	T	0.34875	-0.9811	10	0.15952	T	0.53	.	4.5352	0.12024	0.2848:0.2157:0.4995:0.0	.	488	Q9NZP6	CO002_HUMAN	I	488	ENSP00000333735:V488I	ENSP00000333735:V488I	V	+	1	0	C15orf2	22473569	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-2.612000	0.00884	-1.139000	0.02881	0.313000	0.20887	GTA		0.512	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24922476	G	A	24922476	3	1	68	1	0	0	0	0	1	0	0	0	1788	1145	40	1	1464	1	C15orf2	15	24922476	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		24922476	77608916	45	20925										
FBN1	2200	hgsc.bcm.edu	37	chr15	48760704	48760704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cacagttcccactgatgcacGtggttggatccaggcattca	10	12	1	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr15:48760704G>A	ENST00000316623.5	-	37	4942	c.4487C>T	c.(4486-4488)aCg>aTg	p.T1496M		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1496	EGF-like 26; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.T1496M(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ACTGATGCACGTGGTTGGATC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	15											118	95	103					15																	48760704		2198	4296	6494	46547996	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4487C>T	15.37:g.48760704G>A	ENSP00000325527:p.Thr1496Met		46547996	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145520	0.37825	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92965	-3.14	5.64	4.72	0.59763	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.297658	0.42053	N	0.000777	D	0.85860	0.5795	L	0.33710	1.025	0.80722	D	1	B	0.24675	0.109	B	0.17979	0.02	T	0.81752	-0.0789	10	0.33141	T	0.24	.	10.2982	0.43637	0.1495:0.0:0.8505:0.0	.	1496	P35555	FBN1_HUMAN	M	1496;64;386	ENSP00000325527:T1496M	ENSP00000325527:T1496M	T	-	2	0	FBN1	46547996	0.980000	0.34600	0.980000	0.43619	0.816000	0.46133	1.904000	0.39868	1.616000	0.50265	0.650000	0.86243	ACG		0.483	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48760704	G	A	48760704	3	1	68	1	0	0	0	0	1	0	0	0	5721	1145	40	1	4248	1	FBN1	15	48760704	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	23838228	48760704	53770688	46	20926										
HMG20A	10363	hgsc.bcm.edu	37	chr15	77770689	77770689	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	tccaacatggagtttgaggaGaggaatgcagccctgcaaaa	12	8	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr15:77770689G>C	ENST00000381714.3	+	9	1172	c.744G>C	c.(742-744)gaG>gaC	p.E248D	HMG20A_ENST00000336216.4_Missense_Mutation_p.E248D	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	248					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E248D(2)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						AGTTTGAGGAGAGGAATGCAG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	15											77	69	72					15																	77770689		2196	4294	6490	75557744	SO:0001583	missense	10363			AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.744G>C	15.37:g.77770689G>C	ENSP00000371133:p.Glu248Asp		75557744	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.368232	0.82463	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.70749	-0.51;-0.51	5.86	1.78	0.24846	.	0.000000	0.85682	D	0.000000	T	0.78470	0.4288	M	0.78456	2.415	0.52099	D	0.999947	D	0.60160	0.987	P	0.59424	0.857	T	0.75442	-0.3316	10	0.46703	T	0.11	-17.7482	9.244	0.37513	0.3499:0.0:0.6501:0.0	.	248	Q9NP66	HM20A_HUMAN	D	248	ENSP00000336856:E248D;ENSP00000371133:E248D	ENSP00000336856:E248D	E	+	3	2	HMG20A	75557744	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.837000	0.39201	0.073000	0.16731	0.563000	0.77884	GAG		0.557	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		C	77770689	G	C	77770689	3	2	68	1	0	0	0	0	1	0	0	0	7242	933	33	5	770	5	HMG20A	15	77770689	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	29009985	77770689	24760703	47	20927										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79749445	79749445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cctgaatccagtgtattcccCggttcctgacaaaaggcgag	10	12	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr15:79749445C>T	ENST00000305428.3	+	2	1031	c.956C>T	c.(955-957)cCg>cTg	p.P319L		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	319						integral component of membrane (GO:0016021)		p.P319L(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						GTGTATTCCCCGGTTCCTGAC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	136	134					15																	79749445		2196	4293	6489	77536500	SO:0001583	missense	23251			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.956C>T	15.37:g.79749445C>T	ENSP00000307461:p.Pro319Leu		77536500	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.866838	0.72065	.	.	ENSG00000169330	ENST00000305428	T	0.32272	1.46	5.01	5.01	0.66863	.	0.182021	0.48767	D	0.000164	T	0.54127	0.1839	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.53429	-0.8440	9	.	.	.	.	16.5141	0.84294	0.0:1.0:0.0:0.0	.	319	Q9UPX6	K1024_HUMAN	L	319	ENSP00000307461:P319L	.	P	+	2	0	KIAA1024	77536500	1.000000	0.71417	0.495000	0.27527	0.921000	0.55340	5.290000	0.65661	2.312000	0.78011	0.591000	0.81541	CCG		0.517	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		T	79749445	C	T	79749445	3	4	68	1	0	0	0	0	1	0	0	0	8226	652	23	1	958	1	KIAA1024	15	79749445	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	1978756	79749445	22781947	48	20928										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48175165	48175165	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aggatgttggccacgatgtcCatcaacacgcgtgtcctctg	11	12	2	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr16:48175165C>T	ENST00000311303.3	-	3	720	c.375G>A	c.(373-375)atG>atA	p.M125I	ABCC12_ENST00000448542.1_Missense_Mutation_p.M125I|ABCC12_ENST00000416054.1_Missense_Mutation_p.M125I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	125	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.M125I(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CCACGATGTCCATCAACACGC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											127	95	106					16																	48175165		2201	4300	6501	46732666	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.375G>A	16.37:g.48175165C>T	ENSP00000311030:p.Met125Ile		46732666	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	C	8.448	0.852361	0.17106	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054	D;D;D	0.89270	-2.49;-2.26;-2.26	5.75	4.8	0.61643	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, transmembrane domain (1);	0.153864	0.64402	D	0.000016	D	0.82370	0.5022	N	0.25890	0.77	0.45261	D	0.998266	B;B	0.18968	0.032;0.006	B;B	0.20577	0.018;0.03	T	0.77169	-0.2686	10	0.33940	T	0.23	.	13.7028	0.62620	0.0:0.9248:0.0:0.0752	.	125;125	Q96J65-2;Q96J65	.;MRP9_HUMAN	I	125	ENSP00000311030:M125I;ENSP00000401855:M125I;ENSP00000413046:M125I	ENSP00000311030:M125I	M	-	3	0	ABCC12	46732666	1.000000	0.71417	0.998000	0.56505	0.002000	0.02628	1.291000	0.33330	1.438000	0.47492	-0.253000	0.11424	ATG		0.572	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48175165	C	T	48175165	3	4	68	1	0	0	0	0	1	0	0	0	52	594	21	3	3812	3	ABCC12	16	48175165	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10		48175165	42179588	49	20929										
SALL1	6299	hgsc.bcm.edu	37	chr16	51174641	51174641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	agggtatttctctttgtggcGctgaaagtggactttcagat	12	6	2	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr16:51174641G>A	ENST00000251020.4	-	2	1525	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.R401C|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	498					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R498C(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TCTTTGTGGCGCTGAAAGTGG	0.512																																					GBM(103;1352 1446 1855 4775 8890)											1	Substitution - Missense(1)	large_intestine(1)	16											107	105	106					16																	51174641		2198	4300	6498	49732142	SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1492C>T	16.37:g.51174641G>A	ENSP00000251020:p.Arg498Cys		49732142	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.879139	0.72294	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07444	3.19;3.19	5.29	5.29	0.74685	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.34571	0.0902	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.09662	-1.0664	10	0.37606	T	0.19	.	18.9361	0.92586	0.0:0.0:1.0:0.0	.	498	Q9NSC2	SALL1_HUMAN	C	498;401;462	ENSP00000251020:R498C;ENSP00000407914:R401C	ENSP00000251020:R498C	R	-	1	0	SALL1	49732142	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.788000	0.75105	2.458000	0.83093	0.563000	0.77884	CGC		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51174641	G	A	51174641	3	1	68	1	0	0	0	0	1	0	0	0	13847	1087	38	1	2490	1	SALL1	16	51174641	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	2999476	51174641	39180112	50	20930										
BBS2	583	hgsc.bcm.edu	37	chr16	56545127	56545127	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ttgcagagcacaattgccacCaataatcgcaagaggggaag	11	9	0	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr16:56545127C>T	ENST00000245157.5	-	3	835	c.415G>A	c.(415-417)Ggt>Agt	p.G139S	BBS2_ENST00000561951.1_5'UTR|BBS2_ENST00000568104.1_Missense_Mutation_p.G139S	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	139					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.G139S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CAATTGCCACCAATAATCGCA	0.403									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	16											126	108	114					16																	56545127		2198	4300	6498	55102628	SO:0001583	missense	583	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.415G>A	16.37:g.56545127C>T	ENSP00000245157:p.Gly139Ser		55102628	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	C	36	5.838097	0.97009	.	.	ENSG00000125124	ENST00000245157	D	0.96041	-3.89	5.9	5.9	0.94986	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.98277	0.9429	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.98539	1.0631	10	0.72032	D	0.01	-21.0868	20.2799	0.98512	0.0:1.0:0.0:0.0	.	139;139	A8K0N9;Q9BXC9	.;BBS2_HUMAN	S	139	ENSP00000245157:G139S	ENSP00000245157:G139S	G	-	1	0	BBS2	55102628	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.695000	0.84257	2.800000	0.96347	0.643000	0.83706	GGT		0.403	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		T	56545127	C	T	56545127	3	4	68	1	0	0	0	0	1	0	0	0	1339	594	21	3	1810	3	BBS2	16	56545127	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	5370486	56545127	33809626	51	20931										
GLG1	2734	hgsc.bcm.edu	37	chr16	74499592	74499592	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	acctttatcatctgcttgcaGaccctcatgagggtgtagtc	9	11	3	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr16:74499592G>A	ENST00000422840.2	-	19	2648	c.2649C>T	c.(2647-2649)gtC>gtT	p.V883V	GLG1_ENST00000205061.5_Silent_p.V883V|Y_RNA_ENST00000384794.1_RNA|GLG1_ENST00000447066.2_Silent_p.V872V	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	883					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.V883V(1)		breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TCTGCTTGCAGACCCTCATGA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	16											210	203	205					16																	74499592		2198	4300	6498	73057093	SO:0001819	synonymous_variant	2734				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2649C>T	16.37:g.74499592G>A			73057093	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	37	CCDS45527.1																																																																																				0.488	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		A	74499592	G	A	74499592	2	1	68	1	0	0	0	0	0	0	0	1	6456	929	33	3		3	GLG1	16	74499592	Silent	SNP	G	TCGA-AG-A015-01A-01W-A005-10	17954465	74499592	15855161	52	20932										
NF1	4763	hgsc.bcm.edu	37	chr17	29654605	29654605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aaatgacatttattatgcttCggaaattgaagaaatctgcc	7	6	1	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr17:29654605C>T	ENST00000358273.4	+	38	5740	c.5357C>T	c.(5356-5358)tCg>tTg	p.S1786L	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Missense_Mutation_p.S1765L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1786	Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.S1786L(2)|p.S1786*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TATTATGCTTCGGAAATTGAA	0.458			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	14	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(2)|Substitution - Nonsense(1)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|ovary(1)	17	GRCh37	CS001442	NF1	S							88	86	86					17																	29654605		2203	4300	6503	26678731	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5357C>T	17.37:g.29654605C>T	ENSP00000351015:p.Ser1786Leu		26678731	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174632	0.94807	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.85629	-2.01;-2.01;-2.01	5.99	5.99	0.97316	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.93067	0.7793	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	P;D;D	0.71184	0.581;0.972;0.966	D	0.93103	0.6510	10	0.72032	D	0.01	.	19.5155	0.95162	0.0:1.0:0.0:0.0	.	815;1765;1786	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	L	1786;1765;1431	ENSP00000351015:S1786L;ENSP00000348498:S1765L;ENSP00000389907:S1431L	ENSP00000348498:S1765L	S	+	2	0	NF1	26678731	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.456000	0.80751	2.846000	0.97976	0.644000	0.83932	TCG		0.458	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29654605	C	T	29654605	3	4	68	1	0	0	0	0	1	0	0	0	10387	893	31	1	5568	1	NF1	17	29654605	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10		29654605	51540605	53	20933										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18547733	18547733	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cgcttgcatgtcattcagttCcttctgatgtttcactacca	6	12	4	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr18:18547733C>A	ENST00000399799.2	-	26	4112	c.3172G>T	c.(3172-3174)Gaa>Taa	p.E1058*		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1058					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1058*(2)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCATTCAGTTCCTTCTGATGT	0.343																																																2	Substitution - Nonsense(2)	large_intestine(2)	18											246	241	243					18																	18547733		2203	4300	6503	16801731	SO:0001587	stop_gained	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3172G>T	18.37:g.18547733C>A	ENSP00000382697:p.Glu1058*		16801731	B0YJ91|Q2KHM4|Q59GZ4	Nonsense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	49	15.574565	0.99838	.	.	ENSG00000067900	ENST00000399799	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.954	0.92650	0.0:1.0:0.0:0.0	.	.	.	.	X	1058	.	ENSP00000382697:E1058X	E	-	1	0	ROCK1	16801731	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.818000	0.86416	2.466000	0.83321	0.585000	0.79938	GAA		0.343	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		A	18547733	C	A	18547733	4	1	68	1	0	0	0	0	0	1	0	0	13554	864	30	2	924	2	ROCK1	18	18547733	Nonsense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10		18547733	59529515	54	20934										
CNDP2	55748	hgsc.bcm.edu	37	chr18	72178242	72178242	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aggggcatttgctactttttCatcgaggtacagtgccaagc	11	9	1	0			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr18:72178242C>A	ENST00000324262.4	+	6	967	c.651C>A	c.(649-651)ttC>ttA	p.F217L	CNDP2_ENST00000324301.8_Missense_Mutation_p.F133L|CNDP2_ENST00000579847.1_Missense_Mutation_p.F217L	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	217					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.F217L(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GCTACTTTTTCATCGAGGTAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	18											95	80	85					18																	72178242		2203	4300	6503	70329222	SO:0001583	missense	55748			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.651C>A	18.37:g.72178242C>A	ENSP00000325548:p.Phe217Leu		70329222	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.218595	0.39201	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.56776	0.44;0.44	6.08	5.04	0.67666	Peptidase M20, dimerisation (1);	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	M	0.79475	2.455	0.80722	D	1	B;B;B	0.29671	0.254;0.062;0.029	B;B;B	0.25884	0.064;0.046;0.025	T	0.48927	-0.8991	10	0.30078	T	0.28	1.1409	12.6212	0.56603	0.0:0.8609:0.0:0.1391	.	122;133;217	B4DPF1;Q96KP4-2;Q96KP4	.;.;CNDP2_HUMAN	L	217;133	ENSP00000325548:F217L;ENSP00000325756:F133L	ENSP00000325548:F217L	F	+	3	2	CNDP2	70329222	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.503000	0.35715	2.894000	0.99253	0.591000	0.81541	TTC		0.493	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		A	72178242	C	A	72178242	3	1	68	1	0	0	0	0	1	0	0	0	3600	825	29	2	669	2	CNDP2	18	72178242	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	53630509	72178242	5899006	55	20935										
ZNF345	25850	hgsc.bcm.edu	37	chr19	37367977	37367977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	agtccttgttcgacatcagcGaattcatactggtgagaaac	9	9	2	1	rs143253432		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr19:37367977G>A	ENST00000529555.1	+	2	1033	c.245G>A	c.(244-246)cGa>cAa	p.R82Q	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.R82Q|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.R82Q			Q14585	ZN345_HUMAN	zinc finger protein 345	82					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R82Q(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CGACATCAGCGAATTCATACT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	19						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	100	106	104		245,245,245,245,245	2.2	1	19	dbSNP_134	104	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	ZNF345	NM_001242472.1,NM_001242474.1,NM_001242475.1,NM_001242476.1,NM_003419.4	43,43,43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	82/489,82/489,82/489,82/489,82/489	37367977	1,13005	2203	4300	6503	42059817	SO:0001583	missense	25850			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.245G>A	19.37:g.37367977G>A	ENSP00000431202:p.Arg82Gln		42059817		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.438007	0.43326	2.27E-4	0.0	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000331800	T;T;T	0.24723	1.84;1.84;1.84	4.28	2.15	0.27550	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20170	0.0485	L	0.54908	1.71	0.24477	N	0.994366	B	0.31383	0.321	B	0.18561	0.022	T	0.10823	-1.0613	8	.	.	.	.	8.1552	0.31165	0.2079:0.0:0.7921:0.0	.	82	Q14585	ZN345_HUMAN	Q	82	ENSP00000431216:R82Q;ENSP00000431202:R82Q;ENSP00000331120:R82Q	.	R	+	2	0	ZNF345	42059817	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.278000	0.08490	1.128000	0.42052	0.655000	0.94253	CGA		0.403	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			A	37367977	G	A	37367977	3	1	68	1	0	0	0	0	1	0	0	0	17898	1058	37	1	247	1	ZNF345	19	37367977	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		37367977	21761006	56	20936										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10032527	10032527	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	ggtgctaaattccagctggaAaatagaaaaggtatgcgttc	11	6	0	1			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr20:10032527A>G	ENST00000378380.3	+	7	2189	c.1860A>G	c.(1858-1860)gaA>gaG	p.E620E	ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Silent_p.E620E|SNAP25-AS1_ENST00000603542.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	620							calcium ion binding (GO:0005509)	p.E620E(1)									TCCAGCTGGAAAATAGAAAAG	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	20											36	34	35					20																	10032527		2203	4299	6502	9980527	SO:0001819	synonymous_variant	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1860A>G	20.37:g.10032527A>G			9980527	B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	37	CCDS13108.1																																																																																				0.363	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		G	10032527	A	G	10032527	2	3	68	1	0	0	0	0	0	0	0	1	676	11	1	4		4	ANKRD5	20	10032527	Silent	SNP	A	TCGA-AG-A015-01A-01W-A005-10		10032527	52992993	57	20937										
CST2	1470	hgsc.bcm.edu	37	chr20	23805934	23805934	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gttcggcccacctctatgtcGaagaagtaattcaccccgcc	8	15	2	1	rs201981599		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr20:23805934G>A	ENST00000304725.2	-	2	325	c.255C>T	c.(253-255)ttC>ttT	p.F85F		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	85					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.F85F(1)		breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						CCTCTATGTCGAAGAAGTAAT	0.532																																					Pancreas(193;496 3017 22514 29918)											1	Substitution - coding silent(1)	large_intestine(1)	20											284	219	241					20																	23805934		2203	4300	6503	23753934	SO:0001819	synonymous_variant	1470			M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"cystatin 2"	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.255C>T	20.37:g.23805934G>A			23753934	Q9UCQ7	Silent	SNP	ENST00000304725.2	37	CCDS13161.1																																																																																				0.532	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2			A	23805934	G	A	23805934	2	1	68	1	0	0	0	0	0	0	0	1	3978	1049	37	1		1	CST2	20	23805934	Silent	SNP	G	TCGA-AG-A015-01A-01W-A005-10	13773407	23805934	39219586	58	20938										
CHD6	84181	hgsc.bcm.edu	37	chr20	40053862	40053862	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aggtccatttctgaggttctCctgaacatctcttcctgaac	7	12	3	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr20:40053862C>G	ENST00000373233.3	-	29	4479	c.4302G>C	c.(4300-4302)agG>agC	p.R1434S		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1434					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.R1434S(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CTGAGGTTCTCCTGAACATCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											131	110	117					20																	40053862		2203	4300	6503	39487276	SO:0001583	missense	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4302G>C	20.37:g.40053862C>G	ENSP00000362330:p.Arg1434Ser		39487276	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.963859	0.53507	.	.	ENSG00000124177	ENST00000373233	D	0.86562	-2.14	5.96	4.97	0.65823	.	0.000000	0.64402	D	0.000006	D	0.85885	0.5801	M	0.78801	2.425	0.80722	D	1	B	0.22909	0.077	B	0.24394	0.053	T	0.82252	-0.0549	10	0.42905	T	0.14	-19.0928	10.0896	0.42439	0.0:0.6818:0.2488:0.0694	.	1434	Q8TD26	CHD6_HUMAN	S	1434	ENSP00000362330:R1434S	ENSP00000362330:R1434S	R	-	3	2	CHD6	39487276	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.514000	0.22786	2.827000	0.97445	0.655000	0.94253	AGG		0.507	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			G	40053862	C	G	40053862	3	3	68	1	0	0	0	0	1	0	0	0	3335	854	30	5	3881	5	CHD6	20	40053862	Missense_Mutation	SNP	C	TCGA-AG-A015-01A-01W-A005-10	16247928	40053862	22971658	59	20939										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851148	43851148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aatatcatacccgtcttcacGtacagaagaaagacaacttc	5	11	3	3	rs145586123	byFrequency	TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chr20:43851148G>A	ENST00000372769.3	+	2	965	c.875G>A	c.(874-876)cGt>cAt	p.R292H		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	292	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.R292H(1)|p.R292L(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				CCGTCTTCACGTACAGAAGAA	0.398																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	20						G	HIS/ARG	0,4406	2.1+/-5.4	0,0,2203	94	88	90		875	-0.9	0	20	dbSNP_134	90	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SEMG2	NM_003008.2	29	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	292/583	43851148	4,13002	2203	4300	6503	43284562	SO:0001583	missense	6407				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.875G>A	20.37:g.43851148G>A	ENSP00000361855:p.Arg292His		43284562	Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	G	5.553	0.286965	0.10513	0.0	4.65E-4	ENSG00000124157	ENST00000372769	T	0.06449	3.3	1.28	-0.886	0.10590	.	.	.	.	.	T	0.03477	0.0100	N	0.14661	0.345	0.09310	N	1	B;B;B	0.14438	0.005;0.01;0.01	B;B;B	0.12156	0.007;0.007;0.007	T	0.42224	-0.9464	9	0.48119	T	0.1	.	4.015	0.09639	0.4624:0.0:0.5376:0.0	.	292;292;292	A8K6Z6;Q6IRW3;Q02383	.;.;SEMG2_HUMAN	H	292	ENSP00000361855:R292H	ENSP00000361855:R292H	R	+	2	0	SEMG2	43284562	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.964000	0.03833	-0.275000	0.09219	-0.194000	0.12790	CGT		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		A	43851148	G	A	43851148	3	1	68	1	0	0	0	0	1	0	0	0	14082	1145	40	1	881	1	SEMG2	20	43851148	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	3797286	43851148	19174372	60	20940										
CXorf58	254158	hgsc.bcm.edu	37	chrX	23945402	23945402	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	gggggaaaggaaatttcaccGtataattatggaagatgaac	12	4	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chrX:23945402G>A	ENST00000379211.3	+	6	1019	c.470G>A	c.(469-471)cGt>cAt	p.R157H		NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	157								p.R157H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						AAATTTCACCGTATAATTATG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	X											112	109	110					X																	23945402		2203	4299	6502	23855323	SO:0001583	missense	254158			AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.470G>A	X.37:g.23945402G>A	ENSP00000368511:p.Arg157His		23855323		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	G	2.468	-0.322641	0.05350	.	.	ENSG00000165182	ENST00000379211	T	0.29917	1.55	5.59	-2.49	0.06403	.	2.609730	0.01114	N	0.005649	T	0.09335	0.0230	N	0.00500	-1.43	0.09310	N	1	B;B	0.16396	0.017;0.017	B;B	0.10450	0.005;0.005	T	0.15780	-1.0425	10	0.30854	T	0.27	1.0927	5.1851	0.15180	0.4735:0.2577:0.2688:0.0	.	157;157	B7ZLS7;Q96LI9	.;CX058_HUMAN	H	157	ENSP00000368511:R157H	ENSP00000368511:R157H	R	+	2	0	CXorf58	23855323	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.253000	0.18296	-0.692000	0.05128	-0.512000	0.04463	CGT		0.328	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761		A	23945402	G	A	23945402	3	1	68	1	0	0	0	0	1	0	0	0	4120	1145	40	1	488	1	CXorf58	23	23945402	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10		23945402	131325158	61	20941										
PHF16	9767	hgsc.bcm.edu	37	chrX	46918065	46918065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	aaagacagctcgagtgagatGttctgtgaccaggagcctgt	13	8	1	3			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chrX:46918065G>A	ENST00000218343.4	+	11	2356	c.2058G>A	c.(2056-2058)atG>atA	p.M686I	PHF16_ENST00000397189.1_Missense_Mutation_p.M686I	NM_014735.3	NP_055550.1												p.M686I(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CGAGTGAGATGTTCTGTGACC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	X											52	45	48					X																	46918065		2203	4300	6503	46803009	SO:0001583	missense	9767																														ENST00000218343.4:c.2058G>A	X.37:g.46918065G>A	ENSP00000218343:p.Met686Ile		46803009		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	G	8.215	0.801249	0.16397	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.48522	0.81;0.81	5.73	3.77	0.43336	.	1.465190	0.03466	N	0.212969	T	0.32466	0.0830	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.17899	-1.0354	10	0.30854	T	0.27	.	5.8232	0.18538	0.2884:0.0:0.5625:0.149	.	686	Q92613	JADE3_HUMAN	I	686	ENSP00000380373:M686I;ENSP00000218343:M686I	ENSP00000218343:M686I	M	+	3	0	PHF16	46803009	0.002000	0.14202	0.120000	0.21714	0.945000	0.59286	-0.075000	0.11431	1.167000	0.42706	0.600000	0.82982	ATG		0.498	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			A	46918065	G	A	46918065	3	1	68	1	0	0	0	0	1	0	0	0	11858	1377	48	3	2096	3	PHF16	23	46918065	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	22972663	46918065	108352495	62	20942										
DRP2	1821	hgsc.bcm.edu	37	chrX	100492613	100492613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	actcattgtgtgcagcgctcGcctagaggccttctcagacc	10	14	2	2	rs144183424		TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chrX:100492613G>A	ENST00000395209.3	+	5	814	c.287G>A	c.(286-288)cGc>cAc	p.R96H	DRP2_ENST00000538510.1_Missense_Mutation_p.R96H|DRP2_ENST00000541709.1_Missense_Mutation_p.R18H|DRP2_ENST00000402866.1_Missense_Mutation_p.R96H	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	96					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R93H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						TGCAGCGCTCGCCTAGAGGCC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	X						G	HIS/ARG,HIS/ARG	1,3834		0,1,1631,571	95	89	91		53,287	5.9	1	X	dbSNP_134	91	0,6728		0,0,2428,1872	no	missense,missense	DRP2	NM_001171184.1,NM_001939.2	29,29	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	probably-damaging,probably-damaging	18/880,96/958	100492613	1,10562	2203	4300	6503	100379269	SO:0001583	missense	1821			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.287G>A	X.37:g.100492613G>A	ENSP00000378635:p.Arg96His		100379269	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	g	16.50	3.141959	0.57044	2.61E-4	0.0	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	L	0.42581	1.335	0.58432	D	0.999998	D	0.69078	0.997	P	0.56865	0.808	T	0.16482	-1.0401	10	0.13108	T	0.6	-13.8798	19.1513	0.93491	0.0:0.0:1.0:0.0	.	96	Q13474	DRP2_HUMAN	H	96;96;18;96	ENSP00000385038:R96H;ENSP00000378635:R96H;ENSP00000444752:R18H;ENSP00000441051:R96H	ENSP00000362007:R96H	R	+	2	0	DRP2	100379269	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.611000	0.82962	2.473000	0.83533	0.540000	0.68198	CGC		0.418	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		A	100492613	G	A	100492613	3	1	68	1	0	0	0	0	1	0	0	0	4775	1087	38	1	297	1	DRP2	23	100492613	Missense_Mutation	SNP	G	TCGA-AG-A015-01A-01W-A005-10	53574548	100492613	54777947	63	20943										
ZNF449	203523	hgsc.bcm.edu	37	chrX	134481166	134481166	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	0.557040998217469	3.06372549019608	0.211291413116971	1	1	0	cagttccagtacagagaagcAgctgggcctcatgaagcatt	11	10	1	2			TCGA-AG-A015-01A-01W-A005-10	TCGA-AG-A015-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	abb751f0-c4df-4556-ac9b-ad1e1971cccf	52e17ea0-09f5-49a3-838d-ecc142675bae	g.chrX:134481166A>T	ENST00000339249.4	+	2	263	c.123A>T	c.(121-123)gcA>gcT	p.A41A	ZNF449_ENST00000370760.3_Silent_p.A41A|ZNF449_ENST00000370761.3_Silent_p.A41A	NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	41	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A41A(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					ACAGAGAAGCAGCTGGGCCTC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											95	89	91					X																	134481166		2203	4300	6503	134308832	SO:0001819	synonymous_variant	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.123A>T	X.37:g.134481166A>T			134308832	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																				0.473	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		T	134481166	A	T	134481166	2	4	68	1	0	0	0	0	0	0	0	1	17959	175	7	5		5	ZNF449	23	134481166	Silent	SNP	A	TCGA-AG-A015-01A-01W-A005-10	33988553	134481166	20789394	64	20944										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41984117	41984117	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gcacccctgtctcttggcacTttttgctgtgggccttcgac	10	14	1	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:41984117T>A	ENST00000372583.1	-	7	6311	c.5426A>T	c.(5425-5427)aAg>aTg	p.K1809M	HIVEP3_ENST00000372584.1_Missense_Mutation_p.K1809M|HIVEP3_ENST00000247584.5_Missense_Mutation_p.K1809M|HIVEP3_ENST00000429157.2_Missense_Mutation_p.K1809M|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1809					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K1809M(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CTCTTGGCACTTTTTGCTGTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											163	139	147					1																	41984117		2203	4300	6503	41756704	SO:0001583	missense	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5426A>T	1.37:g.41984117T>A	ENSP00000361664:p.Lys1809Met		41756704	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.704336	0.88924	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	3.81	3.81	0.43845	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000347	T	0.25975	0.0633	M	0.69358	2.11	0.80722	D	1	D;D	0.64830	0.994;0.99	P;P	0.60415	0.874;0.751	T	0.02214	-1.1194	10	0.87932	D	0	-6.1405	12.4024	0.55420	0.0:0.0:0.0:1.0	.	1809;1809	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	M	1809	ENSP00000361665:K1809M;ENSP00000361664:K1809M;ENSP00000247584:K1809M;ENSP00000410828:K1809M	ENSP00000247584:K1809M	K	-	2	0	HIVEP3	41756704	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.577000	0.82486	1.593000	0.50029	0.533000	0.62120	AAG		0.547	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	41984117	T	A	41984117	3	1	69	1	0	0	0	0	1	0	0	0	7209	1609	56	5	1806	5	HIVEP3	1	41984117	Missense_Mutation	SNP	T	TCGA-AG-A016-01A-01W-A005-10		41984117	207266504	1	20945										
LRP8	7804	hgsc.bcm.edu	37	chr1	53729868	53729868	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gggggtcaacagcgatggccCggggttcactgaggttacgg	18	9	2	1	rs202186923		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:53729868C>G	ENST00000306052.6	-	10	1729	c.1628G>C	c.(1627-1629)cGg>cCg	p.R543P	LRP8_ENST00000347547.2_Missense_Mutation_p.R373P|LRP8_ENST00000354412.3_Missense_Mutation_p.R414P|LRP8_ENST00000371454.2_Missense_Mutation_p.R543P|LRP8_ENST00000465675.1_Missense_Mutation_p.R96P|LRP8_ENST00000460214.1_5'Flank	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	543					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.R543Q(1)|p.R543P(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						AGCGATGGCCCGGGGTTCACT	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	1											65	64	64					1																	53729868		2203	4300	6503	53502456	SO:0001583	missense	7804			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.1628G>C	1.37:g.53729868C>G	ENSP00000303634:p.Arg543Pro		53502456	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.275732|5.275732	0.95459|0.95459	.|.	.|.	ENSG00000157193|ENSG00000157193	ENST00000475501|ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	.|D;D;D;D;D	.|0.96745	.|-4.11;-4.11;-4.11;-4.11;-4.11	5.02|5.02	5.02|5.02	0.67125|0.67125	.|Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	.|.	.|.	.|.	.|.	D|D	0.98807|0.98807	0.9598|0.9598	H|H	0.96175|0.96175	3.78|3.78	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.97110	.|1.0;0.999;1.0;0.99;0.997;1.0	D|D	0.99505|0.99505	1.0954|1.0954	5|9	.|0.72032	.|D	.|0.01	.|.	18.5321|18.5321	0.90996|0.90996	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|96;414;373;543;543;96	.|B3KU40;Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.|.;.;.;.;LRP8_HUMAN;.	R|P	232|543;543;96;414;373	.|ENSP00000303634:R543P;ENSP00000360509:R543P;ENSP00000437009:R96P;ENSP00000346391:R414P;ENSP00000334522:R373P	.|ENSP00000303634:R543P	G|R	-|-	1|2	0|0	LRP8|LRP8	53502456|53502456	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	5.925000|5.925000	0.70062|0.70062	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	GGG|CGG		0.572	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		G	53729868	C	G	53729868	3	3	69	1	0	0	0	0	1	0	0	0	8992	652	23	5	1303	5	LRP8	1	53729868	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	11745751	53729868	195520753	2	20946										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86919148	86919148	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cagctcaggaggctccttttCagtgctgggagttccagctg	13	11	2	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:86919148C>T	ENST00000370565.4	+	13	2414	c.2252C>T	c.(2251-2253)tCa>tTa	p.S751L	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	751					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.S751L(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GGCTCCTTTTCAGTGCTGGGA	0.483																																					Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)											1	Substitution - Missense(1)	large_intestine(1)	1											85	87	86					1																	86919148		2203	4300	6503	86691736	SO:0001583	missense	9635				CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2252C>T	1.37:g.86919148C>T	ENSP00000359596:p.Ser751Leu		86691736	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276622	0.40294	.	.	ENSG00000137975	ENST00000370565	T	0.03035	4.07	5.72	2.68	0.31781	.	0.471865	0.21120	N	0.079833	T	0.01558	0.0050	M	0.73962	2.25	0.21652	N	0.999605	B	0.09022	0.002	B	0.08055	0.003	T	0.44390	-0.9331	10	0.25106	T	0.35	-7.1265	4.9091	0.13812	0.1399:0.5731:0.0:0.2871	.	751	Q9UQC9	CLCA2_HUMAN	L	751	ENSP00000359596:S751L	ENSP00000359596:S751L	S	+	2	0	CLCA2	86691736	0.044000	0.20184	0.933000	0.37362	0.966000	0.64601	0.396000	0.20867	0.898000	0.36418	0.650000	0.86243	TCA		0.483	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86919148	C	T	86919148	3	4	69	1	0	0	0	0	1	0	0	0	3464	838	29	3	2302	3	CLCA2	1	86919148	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	33189280	86919148	162331473	3	20947										
NTNG1	22854	hgsc.bcm.edu	37	chr1	107867346	107867346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	tgaaatcaaagacaggttcgCgttttttgctggacctcgcc	10	10	1	2	rs386352339		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:107867346C>T	ENST00000370068.1	+	3	1535	c.689C>T	c.(688-690)gCg>gTg	p.A230V	NTNG1_ENST00000370070.2_Missense_Mutation_p.A230V|NTNG1_ENST00000542803.1_Missense_Mutation_p.A230V|NTNG1_ENST00000370066.1_Missense_Mutation_p.A230V|NTNG1_ENST00000370071.2_Missense_Mutation_p.A230V|NTNG1_ENST00000370072.3_Missense_Mutation_p.A230V|NTNG1_ENST00000370065.1_Missense_Mutation_p.A230V|NTNG1_ENST00000477948.1_3'UTR|NTNG1_ENST00000370074.4_Missense_Mutation_p.A230V|NTNG1_ENST00000370067.1_Missense_Mutation_p.A230V|NTNG1_ENST00000370061.3_Missense_Mutation_p.A230V|NTNG1_ENST00000370073.2_Missense_Mutation_p.A230V			Q9Y2I2	NTNG1_HUMAN	netrin G1	230	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)		p.A230V(4)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GACAGGTTCGCGTTTTTTGCT	0.428																																																4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	1											97	93	95					1																	107867346		2203	4300	6503	107668869	SO:0001583	missense	22854			AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.689C>T	1.37:g.107867346C>T	ENSP00000359085:p.Ala230Val		107668869	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	37	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857515	0.91433	.	.	ENSG00000162631	ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065	T;T;T;T;T;T;T;T;T;T;T	0.75050	0.68;-0.48;0.63;0.02;-0.03;-0.66;-0.9;0.68;-0.66;-0.48;0.05	6.05	6.05	0.98169	Laminin, N-terminal (3);	0.000000	0.64402	D	0.000011	D	0.85801	0.5781	M	0.77616	2.38	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;P;D;P	0.91635	0.998;0.999;0.72;0.981;0.896	D	0.84823	0.0797	10	0.56958	D	0.05	.	20.6086	0.99469	0.0:1.0:0.0:0.0	.	230;230;230;230;230	B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1	.;NTNG1_HUMAN;.;.;.	V	230	ENSP00000359090:A230V;ENSP00000359088:A230V;ENSP00000440561:A230V;ENSP00000359078:A230V;ENSP00000359089:A230V;ENSP00000359087:A230V;ENSP00000359091:A230V;ENSP00000359085:A230V;ENSP00000359084:A230V;ENSP00000359083:A230V;ENSP00000359082:A230V	ENSP00000294649:A230V	A	+	2	0	NTNG1	107668869	1.000000	0.71417	0.096000	0.21009	0.994000	0.84299	7.818000	0.86416	2.880000	0.98712	0.655000	0.94253	GCG		0.428	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		T	107867346	C	T	107867346	3	4	69	1	0	0	0	0	1	0	0	0	10735	768	27	1	695	1	NTNG1	1	107867346	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	20948198	107867346	141383275	4	20948										
IL6R	3570	hgsc.bcm.edu	37	chr1	154401730	154401730	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agcgtgactctgacctgcccGggggtagagccggaagacaa	15	11	1	4			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:154401730G>A	ENST00000368485.3	+	2	581	c.144G>A	c.(142-144)ccG>ccA	p.P48P	IL6R_ENST00000344086.4_Silent_p.P48P	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	48	Ig-like C2-type.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)	p.P48P(1)	IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	TGACCTGCCCGGGGGTAGAGC	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	1											70	69	69					1																	154401730		2203	4300	6503	152668354	SO:0001819	synonymous_variant	3570			X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.144G>A	1.37:g.154401730G>A			152668354	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Silent	SNP	ENST00000368485.3	37	CCDS1067.1																																																																																				0.642	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		A	154401730	G	A	154401730	2	1	69	1	0	0	0	0	0	0	0	1	7723	1103	39	1		1	IL6R	1	154401730	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10	46534384	154401730	94848891	5	20949										
CD1A	909	hgsc.bcm.edu	37	chr1	158227281	158227281	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cttcttctgataggtcttgcGctttggttcaggaaacgctg	11	9	4	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:158227281G>A	ENST00000289429.5	+	5	1487	c.954G>A	c.(952-954)gcG>gcA	p.A318A		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	318					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.A318A(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TAGGTCTTGCGCTTTGGTTCA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											392	362	372					1																	158227281		2203	4300	6503	156493905	SO:0001819	synonymous_variant	909			M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.954G>A	1.37:g.158227281G>A			156493905	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Silent	SNP	ENST00000289429.5	37	CCDS1174.1																																																																																				0.458	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		A	158227281	G	A	158227281	2	1	69	1	0	0	0	0	0	0	0	1	2980	1074	38	1		1	CD1A	1	158227281	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10	3825551	158227281	91023340	6	20950										
OR6N2	81442	hgsc.bcm.edu	37	chr1	158746687	158746687	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cccaaagaagatgaggaccaCagcaagatgtgaggcacagg	13	9	0	5			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:158746687C>A	ENST00000339258.1	-	1	738	c.739G>T	c.(739-741)Gtg>Ttg	p.V247L		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V247L(1)		endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					ATGAGGACCACAGCAAGATGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	84	84					1																	158746687		2203	4300	6503	157013311	SO:0001583	missense	81442			BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"GPCR / Class A : Olfactory receptors"	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.739G>T	1.37:g.158746687C>A	ENSP00000344101:p.Val247Leu		157013311	Q6IFR2	Missense_Mutation	SNP	ENST00000339258.1	37	CCDS30906.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604909	0.46423	.	.	ENSG00000188340	ENST00000339258	T	0.00216	8.53	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34828	N	0.003651	T	0.00384	0.0012	M	0.91090	3.175	0.30609	N	0.759716	D	0.89917	1.0	D	0.87578	0.998	T	0.06320	-1.0833	10	0.87932	D	0	-14.1841	12.024	0.53360	0.173:0.827:0.0:0.0	.	247	Q8NGY6	OR6N2_HUMAN	L	247	ENSP00000344101:V247L	ENSP00000344101:V247L	V	-	1	0	OR6N2	157013311	0.243000	0.23878	1.000000	0.80357	0.333000	0.28666	1.997000	0.40786	2.500000	0.84329	0.650000	0.86243	GTG		0.443	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1			A	158746687	C	A	158746687	3	1	69	1	0	0	0	0	1	0	0	0	11238	478	17	2	217	2	OR6N2	1	158746687	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	519406	158746687	90503934	7	20951										
HIST3H2BB	128312	hgsc.bcm.edu	37	chr1	228645870	228645870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cggctcctgcgcccaagaagGgttctaaaaaggctgtcacc	11	13	2	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr1:228645870G>A	ENST00000369160.2	+	1	63	c.40G>A	c.(40-42)Ggt>Agt	p.G14S	HIST3H2A_ENST00000366695.2_5'Flank	NM_175055.2	NP_778225.1	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	14					chromatin organization (GO:0006325)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G14S(1)		skin(1)	1		Prostate(94;0.183)				GCCCAAGAAGGGTTCTAAAAA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											71	74	73					1																	228645870		2203	4300	6503	226712493	SO:0001583	missense	128312			AY131981	CCDS1574.1	1q42.13	2011-01-27	2006-10-11		ENSG00000196890	ENSG00000196890		"Histones / Replication-dependent"	20514	protein-coding gene	gene with protein product		615046	"histone 3, H2bb"			12408966	Standard	NM_175055		Approved		uc001hsz.3	Q8N257	OTTHUMG00000040045	ENST00000369160.2:c.40G>A	1.37:g.228645870G>A	ENSP00000375736:p.Gly14Ser		226712493	A4FU05|Q3ZCP6|Q5TA30	Missense_Mutation	SNP	ENST00000369160.2	37	CCDS1574.1	.	.	.	.	.	.	.	.	.	.	.	17.27	3.347492	0.61183	.	.	ENSG00000196890	ENST00000369160	T	0.22336	1.96	3.98	3.07	0.35406	Histone-fold (2);	0.000000	0.48286	D	0.000199	T	0.40956	0.1138	M	0.66378	2.025	0.43907	D	0.99654	D	0.76494	0.999	D	0.87578	0.998	T	0.30909	-0.9962	10	0.87932	D	0	.	9.9417	0.41585	0.1017:0.0:0.8983:0.0	.	14	Q8N257	H2B3B_HUMAN	S	14	ENSP00000375736:G14S	ENSP00000375736:G14S	G	+	1	0	HIST3H2BB	226712493	1.000000	0.71417	0.702000	0.30337	0.097000	0.18754	9.011000	0.93618	1.256000	0.44068	0.591000	0.81541	GGT		0.537	HIST3H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096597.1	NM_175055		A	228645870	G	A	228645870	3	1	69	1	0	0	0	0	1	0	0	0	7204	1232	43	3	42	3	HIST3H2BB	1	228645870	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	69899183	228645870	20604751	8	20952										
CHAC2	494143	hgsc.bcm.edu	37	chr2	54001633	54001633	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aattagtaaaggaacgtttaGaagggaaacagaacctcaat	9	5	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr2:54001633G>C	ENST00000295304.4	+	3	621	c.526G>C	c.(526-528)Gaa>Caa	p.E176Q	GPR75-ASB3_ENST00000406687.1_Intron|ASB3_ENST00000498475.2_Intron|GPR75-ASB3_ENST00000394717.2_Intron|GPR75-ASB3_ENST00000263634.3_Intron|ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron	NM_001008708.2	NP_001008708.1	Q8WUX2	CHAC2_HUMAN	ChaC, cation transport regulator homolog 2 (E. coli)	176								p.E176Q(1)		endometrium(1)|large_intestine(2)|lung(4)|prostate(1)	8			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GGAACGTTTAGAAGGGAAACA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											47	48	48					2																	54001633		2203	4300	6503	53855137	SO:0001583	missense	494143			BC025376	CCDS33196.1	2p16	2013-09-12	2006-09-12		ENSG00000143942	ENSG00000143942			32363	protein-coding gene	gene with protein product	"gamma-GCT acting on glutathione homolog 2"		"ChaC, cation transport regulator-like 2 (E. coli)"			23070364	Standard	NM_001008708		Approved		uc002rxk.1	Q8WUX2	OTTHUMG00000151824	ENST00000295304.4:c.526G>C	2.37:g.54001633G>C	ENSP00000295304:p.Glu176Gln		53855137	Q8WVI8	Missense_Mutation	SNP	ENST00000295304.4	37	CCDS33196.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.513728	0.44763	.	.	ENSG00000143942	ENST00000295304	T	0.44881	0.91	6.03	6.03	0.97812	.	0.304537	0.39834	N	0.001258	T	0.41419	0.1158	L	0.49350	1.555	0.41743	D	0.989624	B	0.11235	0.004	B	0.15052	0.012	T	0.27226	-1.0080	10	0.15952	T	0.53	-20.3398	20.5666	0.99351	0.0:0.0:1.0:0.0	.	176	Q8WUX2	CHAC2_HUMAN	Q	176	ENSP00000295304:E176Q	ENSP00000295304:E176Q	E	+	1	0	CHAC2	53855137	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.152000	0.31663	2.854000	0.98071	0.655000	0.94253	GAA		0.328	CHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324072.1	NM_001008708		C	54001633	G	C	54001633	3	2	69	1	0	0	0	0	1	0	0	0	3315	943	33	5	536	5	CHAC2	2	54001633	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10		54001633	189197740	9	20953										
DTYMK	1841	hgsc.bcm.edu	37	chr2	242619715	242619715	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gagggtcacgccctggctcaActtttccttaattaacggcc	9	13	2	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr2:242619715A>T	ENST00000305784.2	-	3	466	c.259T>A	c.(259-261)Ttg>Atg	p.L87M	DTYMK_ENST00000493095.1_5'Flank	NM_001165031.1|NM_012145.3	NP_001158503.1|NP_036277.2	P23919	KTHY_HUMAN	deoxythymidylate kinase (thymidylate kinase)	87					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|cellular response to growth factor stimulus (GO:0071363)|dTDP biosynthetic process (GO:0006233)|dTTP biosynthetic process (GO:0006235)|myoblast differentiation (GO:0045445)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside monophosphate phosphorylation (GO:0046940)|nucleotide phosphorylation (GO:0046939)|response to cadmium ion (GO:0046686)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|nucleoside phosphate kinase activity (GO:0050145)|thymidylate kinase activity (GO:0004798)	p.L87M(1)		NS(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.6e-33)|all cancers(36;3.57e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.23e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCCTGGCTCAACTTTTCCTTA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	2											117	98	105					2																	242619715		2203	4300	6503	242268388	SO:0001583	missense	1841			X54729	CCDS2552.1	2q37	2008-02-05			ENSG00000168393	ENSG00000168393	2.7.4.9		3061	protein-coding gene	gene with protein product	"dTMP kinase", "thymidylate (dTMP) kinase"	188345				2017365, 8024690	Standard	NM_001165031		Approved	CDC8, TYMK, TMPK	uc002wbz.2	P23919	OTTHUMG00000133409	ENST00000305784.2:c.259T>A	2.37:g.242619715A>T	ENSP00000304802:p.Leu87Met		242268388	B7ZW70|Q6FGX1|Q9BUX4	Missense_Mutation	SNP	ENST00000305784.2	37	CCDS2552.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.51|18.51	3.639326|3.639326	0.67244|0.67244	.|.	.|.	ENSG00000168393|ENSG00000168393	ENST00000305784|ENST00000420144	T|.	0.59083|.	0.29|.	5.48|5.48	-0.0802|-0.0802	0.13708|0.13708	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.77685|0.77685	0.4167|0.4167	M|M	0.91038|0.91038	3.17|3.17	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.79784|.	0.993;0.978|.	T|T	0.78814|0.78814	-0.2056|-0.2056	10|5	0.66056|.	D|.	0.02|.	-20.4296|-20.4296	10.862|10.862	0.46831|0.46831	0.5449:0.0:0.4551:0.0|0.5449:0.0:0.4551:0.0	.|.	87;87|.	B7ZW70;P23919|.	.;KTHY_HUMAN|.	M|R	87|82	ENSP00000304802:L87M|.	ENSP00000304802:L87M|.	L|S	-|-	1|3	2|2	DTYMK|DTYMK	242268388|242268388	0.974000|0.974000	0.33945|0.33945	0.997000|0.997000	0.53966|0.53966	0.940000|0.940000	0.58332|0.58332	0.165000|0.165000	0.16564|0.16564	0.000000|0.000000	0.14550|0.14550	0.533000|0.533000	0.62120|0.62120	TTG|AGT		0.532	DTYMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257266.2	NM_012145		T	242619715	A	T	242619715	3	4	69	1	0	0	0	0	1	0	0	0	4809	40	2	5	391	5	DTYMK	2	242619715	Missense_Mutation	SNP	A	TCGA-AG-A016-01A-01W-A005-10	188618082	242619715	579658	10	20954										
HRH1	3269	hgsc.bcm.edu	37	chr3	11301062	11301062	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gactatgtggccagcacagcGtccattttcagtgtcttcat	9	11	3	0	rs201790628	byFrequency	TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr3:11301062G>A	ENST00000397056.1	+	3	530	c.339G>A	c.(337-339)gcG>gcA	p.A113A	HRH1_ENST00000438284.2_Silent_p.A113A|HRH1_ENST00000431010.2_Silent_p.A113A	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	113					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)	p.A113A(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	CCAGCACAGCGTCCATTTTCA	0.542													G|||	6	0.00119808	0	0	5008	,	,		18426	0		0	False		,,,				2504	0.0061															1	Substitution - coding silent(1)	large_intestine(1)	3											215	208	210					3																	11301062		2203	4300	6503	11276062	SO:0001819	synonymous_variant	3269				CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"GPCR / Class A : Histamine receptors"	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.339G>A	3.37:g.11301062G>A			11276062	A8K047|Q6P9E5	Silent	SNP	ENST00000397056.1	37	CCDS2604.1																																																																																				0.542	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2			A	11301062	G	A	11301062	2	1	69	1	0	0	0	0	0	0	0	1	7376	1132	40	1		1	HRH1	3	11301062	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10		11301062	186721368	11	20955										
CPB1	1360	hgsc.bcm.edu	37	chr3	148562486	148562486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	ccgattttggagaaagactcGctccacccatactggatcta	8	12	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr3:148562486G>A	ENST00000491148.1	+	9	1044	c.710G>A	c.(709-711)cGc>cAc	p.R237H	CPB1_ENST00000282957.4_Missense_Mutation_p.R237H			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	237						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R237H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGAAAGACTCGCTCCACCCAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											115	114	114					3																	148562486		2203	4300	6503	150045176	SO:0001583	missense	1360			AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.710G>A	3.37:g.148562486G>A	ENSP00000417222:p.Arg237His		150045176	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	37	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	G	33	5.218427	0.95104	.	.	ENSG00000153002	ENST00000491148;ENST00000282957;ENST00000468341	T;T;T	0.24908	1.83;1.83;1.83	5.78	5.78	0.91487	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83501	0.0075	10	0.87932	D	0	.	20.0124	0.97464	0.0:0.0:1.0:0.0	.	237	P15086	CBPB1_HUMAN	H	237;237;203	ENSP00000417222:R237H;ENSP00000282957:R237H;ENSP00000419427:R203H	ENSP00000282957:R237H	R	+	2	0	CPB1	150045176	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	9.476000	0.97823	2.749000	0.94314	0.655000	0.94253	CGC		0.433	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		A	148562486	G	A	148562486	3	1	69	1	0	0	0	0	1	0	0	0	3802	1087	38	1	740	1	CPB1	3	148562486	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	137261424	148562486	49459944	12	20956										
RAB28	9364	hgsc.bcm.edu	37	chr4	13371557	13371557	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gtatgttgattttcttcttcCgggtacttcactatttctgc	7	9	4	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr4:13371557C>A	ENST00000330852.5	-	7	788				RAB28_ENST00000338176.4_Intron|RAB28_ENST00000288723.4_Silent_p.P202P	NM_001017979.2	NP_001017979.1	P51157	RAB28_HUMAN	RAB28, member RAS oncogene family						GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.P202P(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	8						TTTCTTCTTCCGGGTACTTCA	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	4											187	168	175					4																	13371557		2203	4300	6503	12980655	SO:0001627	intron_variant	9364			X94703	CCDS3409.1, CCDS33961.1, CCDS54741.1	4p16.1	2014-04-24			ENSG00000157869	ENSG00000157869		"RAB, member RAS oncogene"	9768	protein-coding gene	gene with protein product		612994				8647132	Standard	NM_004249		Approved		uc003gmu.2	P51157	OTTHUMG00000090543	ENST00000330852.5:c.574-1283G>T	4.37:g.13371557C>A			12980655	G8JLC5|Q8IYR8|Q8NI05	Silent	SNP	ENST00000330852.5	37	CCDS33961.1	.	.	.	.	.	.	.	.	.	.	C	8.717	0.913354	0.17907	.	.	ENSG00000157869	ENST00000511649	.	.	.	5.82	4.97	0.65823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1118	0.10062	0.3077:0.491:0.124:0.0774	.	.	.	.	X	125	.	.	G	-	1	0	RAB28	12980655	0.972000	0.33761	1.000000	0.80357	0.975000	0.68041	-0.002000	0.12924	2.754000	0.94517	0.591000	0.81541	GGA		0.353	RAB28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207068.2	NM_001017979		A	13371557	C	A	13371557	1	1	69	0	1	0	0	0	0	0	0	0	12953	639	23	2		2	RAB28	4	13371557	Intron	SNP	C	TCGA-AG-A016-01A-01W-A005-10		13371557	177782719	13	20957										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73205406	73205406	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	tcatcaaggccttccaggtcCgactctaataagagacaaaa	7	11	3	1	rs375370429		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr4:73205406C>T	ENST00000286657.4	-	5	702	c.666G>A	c.(664-666)tcG>tcA	p.S222S		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	222					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S222S(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTTCCAGGTCCGACTCTAATA	0.453																																					NSCLC(168;1941 2048 2918 13048 43078)											1	Substitution - coding silent(1)	large_intestine(1)	4						C		1,4405	2.1+/-5.4	0,1,2202	128	129	128		666	-7.2	0	4		128	0,8600		0,0,4300	no	coding-synonymous	ADAMTS3	NM_014243.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		222/1206	73205406	1,13005	2203	4300	6503	73424270	SO:0001819	synonymous_variant	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.666G>A	4.37:g.73205406C>T			73424270	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	37	CCDS3553.1																																																																																				0.453	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73205406	C	T	73205406	2	4	69	1	0	0	0	0	0	0	0	1	267	639	23	1		1	ADAMTS3	4	73205406	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10	59833849	73205406	117948870	14	20958										
SPARCL1	8404	hgsc.bcm.edu	37	chr4	88411522	88411522	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agatgacaggaactagcataGgtctgattgtcagtgccaca	11	8	2	3			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr4:88411522G>A	ENST00000282470.6	-	7	1904	c.1434C>T	c.(1432-1434)acC>acT	p.T478T	SPARCL1_ENST00000503414.1_Silent_p.T353T|SPARCL1_ENST00000418378.1_Silent_p.T478T	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	478	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.T478T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		AACTAGCATAGGTCTGATTGT	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	4											245	257	253					4																	88411522		2203	4300	6503	88630546	SO:0001819	synonymous_variant	8404			X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"EF-hand domain containing"	11220	protein-coding gene	gene with protein product		606041	"SPARC-like 1 (mast9, hevin)"			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1434C>T	4.37:g.88411522G>A			88630546	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	37	CCDS3622.1																																																																																				0.438	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2			A	88411522	G	A	88411522	2	1	69	1	0	0	0	0	0	0	0	1	15035	987	35	3		3	SPARCL1	4	88411522	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10	15206116	88411522	102742754	15	20959										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149357961	149357961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	ctgagaaacttgaccccaccGtctttccatatctagacctt	5	14	2	3			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr4:149357961G>A	ENST00000358102.3	-	2	414	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	NR3C2_ENST00000511528.1_Missense_Mutation_p.R18W|NR3C2_ENST00000344721.4_Missense_Mutation_p.R18W|NR3C2_ENST00000512865.1_Missense_Mutation_p.R18W|NR3C2_ENST00000355292.3_Missense_Mutation_p.R18W	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	18	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R18W(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	TGACCCCACCGTCTTTCCATA	0.433																																					Melanoma(27;428 957 40335 51025 51111)											1	Substitution - Missense(1)	large_intestine(1)	4											73	66	68					4																	149357961		2203	4300	6503	149577411	SO:0001583	missense	4306			M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.52C>T	4.37:g.149357961G>A	ENSP00000350815:p.Arg18Trp		149577411	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228252	0.39399	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.91996	-2.94;-2.95;-2.94;-2.56;-2.54;-2.95	6.02	4.3	0.51218	.	0.304661	0.35378	N	0.003252	D	0.88676	0.6501	L	0.50333	1.59	0.42714	D	0.993654	B;D	0.63046	0.004;0.992	B;B	0.42386	0.001;0.386	D	0.86266	0.1658	9	.	.	.	.	11.3953	0.49838	0.0648:0.0:0.8082:0.127	.	18;18	B0ZBF5;B0ZBF6	.;.	W	18	ENSP00000341390:R18W;ENSP00000347441:R18W;ENSP00000350815:R18W;ENSP00000423510:R18W;ENSP00000343907:R18W;ENSP00000421481:R18W	.	R	-	1	2	NR3C2	149577411	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.489000	0.66875	0.881000	0.35993	0.655000	0.94253	CGG		0.433	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149357961	G	A	149357961	3	1	69	1	0	0	0	0	1	0	0	0	10662	1144	40	1	2934	1	NR3C2	4	149357961	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	60946439	149357961	41796315	16	20960										
HMGB2	3148	hgsc.bcm.edu	37	chr4	174254768	174254768	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aaggcgtacgaggacattttGccccgcggcttgttggggtc	15	10	0	0	rs200580073		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr4:174254768G>T	ENST00000296503.5	-	2	906	c.33C>A	c.(31-33)ggC>ggA	p.G11G	HMGB2_ENST00000446922.2_Silent_p.G11G|HMGB2_ENST00000438704.2_Silent_p.G11G			P26583	HMGB2_HUMAN	high mobility group box 2	11					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)	p.G11G(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		AGGACATTTTGCCCCGCGGCT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	4											73	75	74					4																	174254768		2203	4300	6503	174491343	SO:0001819	synonymous_variant	3148				CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"High-mobility group / Canonical"	5000	protein-coding gene	gene with protein product		163906	"high-mobility group (nonhistone chromosomal) protein 2", "high-mobility group box 2"	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.33C>A	4.37:g.174254768G>T			174491343	B2R4K8|D3DP37|Q5U072	Silent	SNP	ENST00000296503.5	37	CCDS3816.1																																																																																				0.607	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		T	174254768	G	T	174254768	2	4	69	1	0	0	0	0	0	0	0	1	7247	1306	46	2		2	HMGB2	4	174254768	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10	24896807	174254768	16899508	17	20961										
HEXB	3074	hgsc.bcm.edu	37	chr5	74014148	74014148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	tattgcaaccataaacaaggGatccattgtctggcaggagg	11	8	1	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr5:74014148G>A	ENST00000261416.7	+	10	1319	c.1202G>A	c.(1201-1203)gGa>gAa	p.G401E	HEXB_ENST00000513539.1_3'UTR|HEXB_ENST00000511181.1_Missense_Mutation_p.G176E|GFM2_ENST00000515125.1_5'Flank|HEXB_ENST00000509579.1_5'Flank	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	401					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G401E(1)		endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		ATAAACAAGGGATCCATTGTC	0.308																																					Melanoma(66;841 1270 13391 18706 27225)											1	Substitution - Missense(1)	large_intestine(1)	5											105	112	110					5																	74014148		2203	4300	6503	74049904	SO:0001583	missense	3074			M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.1202G>A	5.37:g.74014148G>A	ENSP00000261416:p.Gly401Glu		74049904		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.322392	0.41096	.	.	ENSG00000049860	ENST00000511181;ENST00000261416	D;D	0.95035	-3.59;-3.59	5.95	1.02	0.19986	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.641465	0.17890	N	0.158557	D	0.92844	0.7724	L	0.45137	1.4	0.80722	D	1	P	0.47253	0.892	P	0.54346	0.749	D	0.87783	0.2613	10	0.37606	T	0.19	0.5847	6.4167	0.21719	0.3102:0.0:0.5785:0.1112	.	401	P07686	HEXB_HUMAN	E	176;401	ENSP00000426285:G176E;ENSP00000261416:G401E	ENSP00000261416:G401E	G	+	2	0	HEXB	74049904	0.959000	0.32827	0.032000	0.17829	0.985000	0.73830	1.763000	0.38461	-0.096000	0.12329	0.563000	0.77884	GGA		0.308	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521		A	74014148	G	A	74014148	3	1	69	1	0	0	0	0	1	0	0	0	7095	1174	41	3	1240	3	HEXB	5	74014148	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10		74014148	106901112	18	20962										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51923378	51923378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aaaccagtcagcagtgccgaCgctgatggaggccactttca	11	12	2	1	rs138672830	byFrequency	TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr6:51923378C>T	ENST00000371117.3	-	16	1530	c.1255G>A	c.(1255-1257)Gtc>Atc	p.V419I	PKHD1_ENST00000340994.4_Missense_Mutation_p.V419I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	419					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.V419I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCAGTGCCGACGCTGATGGAG	0.498													C|||	2	0.000399361	0.0015	0	5008	,	,		22269	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6						C	ILE/VAL,ILE/VAL	6,4400	11.4+/-27.6	0,6,2197	110	104	106		1255,1255	1.1	0	6	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	29,29	0,7,6496	TT,TC,CC		0.0116,0.1362,0.0538	benign,benign	419/4075,419/3397	51923378	7,12999	2203	4300	6503	52031337	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1255G>A	6.37:g.51923378C>T	ENSP00000360158:p.Val419Ile		52031337	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.637	-0.814936	0.02776	0.001362	1.16E-4	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88124	-2.34;-2.34	5.94	1.11	0.20524	.	0.796525	0.11432	N	0.564727	T	0.68751	0.3035	M	0.63428	1.95	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.06405	0.002;0.001	T	0.55636	-0.8110	10	0.22706	T	0.39	.	6.606	0.22726	0.114:0.6317:0.0:0.2544	.	419;419	P08F94-2;P08F94	.;PKHD1_HUMAN	I	419	ENSP00000360158:V419I;ENSP00000341097:V419I	ENSP00000341097:V419I	V	-	1	0	PKHD1	52031337	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.022000	0.13511	0.126000	0.18424	-0.897000	0.02905	GTC		0.498	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51923378	C	T	51923378	3	4	69	1	0	0	0	0	1	0	0	0	12002	536	19	1	11216	1	PKHD1	6	51923378	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10		51923378	119191689	19	20963										
NPY	4852	hgsc.bcm.edu	37	chr7	24331300	24331300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aggcttgaagaccctgcaatGtggtgatgggaaatgagact	14	6	0	4			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr7:24331300G>A	ENST00000407573.1	+	5	578	c.288G>A	c.(286-288)atG>atA	p.M96I	NPY_ENST00000242152.2_Missense_Mutation_p.M96I|NPY_ENST00000405982.1_Missense_Mutation_p.M96I			P01303	NPY_HUMAN	neuropeptide Y	96					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)	p.M96I(1)		breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						ACCCTGCAATGTGGTGATGGG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	7											233	195	208					7																	24331300		2203	4300	6503	24297825	SO:0001583	missense	4852			K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"Endogenous ligands"	7955	protein-coding gene	gene with protein product	"prepro-neuropeptide Y"	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.288G>A	7.37:g.24331300G>A	ENSP00000384364:p.Met96Ile		24297825		Missense_Mutation	SNP	ENST00000407573.1	37	CCDS5387.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.955481	0.53293	.	.	ENSG00000122585	ENST00000242152;ENST00000407573;ENST00000405982	T;T;T	0.11169	2.8;2.8;2.8	4.99	4.99	0.66335	.	0.348087	0.33854	N	0.004481	T	0.12774	0.0310	.	.	.	0.50632	D	0.999881	B	0.19445	0.036	B	0.15052	0.012	T	0.05419	-1.0886	9	0.56958	D	0.05	-7.0757	19.1499	0.93483	0.0:0.0:1.0:0.0	.	96	P01303	NPY_HUMAN	I	96	ENSP00000242152:M96I;ENSP00000384364:M96I;ENSP00000385282:M96I	ENSP00000242152:M96I	M	+	3	0	NPY	24297825	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.165000	0.77544	2.702000	0.92279	0.591000	0.81541	ATG		0.448	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905		A	24331300	G	A	24331300	3	1	69	1	0	0	0	0	1	0	0	0	10638	1377	48	3	298	3	NPY	7	24331300	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10		24331300	134807363	20	20964										
C7orf42	55069	hgsc.bcm.edu	37	chr7	66406936	66406936	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gtcttcatgatcagcgtaagCgccatggccatagctttcct	9	12	3	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr7:66406936C>T	ENST00000341567.4	+	2	339	c.84C>T	c.(82-84)agC>agT	p.S28S		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	28						integral component of membrane (GO:0016021)		p.S28S(1)									TCAGCGTAAGCGCCATGGCCA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	7											132	114	120					7																	66406936		2203	4300	6503	66044371	SO:0001819	synonymous_variant	55069				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.84C>T	7.37:g.66406936C>T			66044371	Q53H07|Q96FR2	Silent	SNP	ENST00000341567.4	37	CCDS5536.1																																																																																				0.502	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		T	66406936	C	T	66406936	2	4	69	1	0	0	0	0	0	0	0	1	2398	767	27	1		1	C7orf42	7	66406936	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10	42075636	66406936	92731727	21	20965										
CALN1	83698	hgsc.bcm.edu	37	chr7	71743767	71743767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	ccccttgtacaacaagccggCggtcacatggtggaacggca	12	13	1	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr7:71743767C>T	ENST00000329008.5	-	2	320	c.22G>A	c.(22-24)Gcc>Acc	p.A8T	CALN1_ENST00000405452.2_Missense_Mutation_p.A8T|CALN1_ENST00000412588.1_Missense_Mutation_p.A50T|CALN1_ENST00000395276.2_Missense_Mutation_p.A8T|CALN1_ENST00000395275.2_Missense_Mutation_p.A50T|CALN1_ENST00000431984.1_Missense_Mutation_p.A8T	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)	p.A8T(1)		biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				AACAAGCCGGCGGTCACATGG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	7											82	61	68					7																	71743767		2203	4300	6503	71381703	SO:0001583	missense	83698			AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166		"EF-hand domain containing"	13248	protein-coding gene	gene with protein product	"calcium-binding protein CABP8"	607176				11286509	Standard	NM_031468		Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.22G>A	7.37:g.71743767C>T	ENSP00000332498:p.Ala8Thr		71381703	J3KQA7	Missense_Mutation	SNP	ENST00000329008.5	37	CCDS5541.1	.	.	.	.	.	.	.	.	.	.	C	33	5.204046	0.95033	.	.	ENSG00000183166	ENST00000329008;ENST00000395275;ENST00000395276;ENST00000431984;ENST00000412588;ENST00000405452;ENST00000446128	T;T;T;T;T;T;T	0.74106	-0.4;-0.54;-0.4;-0.4;-0.54;-0.4;-0.81	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.60907	0.2305	N	0.24115	0.695	0.50313	D	0.999863	P;P	0.37688	0.605;0.605	B;B	0.22753	0.041;0.041	T	0.66740	-0.5847	10	0.87932	D	0	-4.0026	19.3475	0.94370	0.0:1.0:0.0:0.0	.	8;8	A4D1Z1;Q9BXU9	.;CABP8_HUMAN	T	8;50;8;8;50;8;8	ENSP00000332498:A8T;ENSP00000378690:A50T;ENSP00000378691:A8T;ENSP00000410704:A8T;ENSP00000391882:A50T;ENSP00000384354:A8T;ENSP00000411806:A8T	ENSP00000332498:A8T	A	-	1	0	CALN1	71381703	1.000000	0.71417	0.759000	0.31340	0.984000	0.73092	7.413000	0.80104	2.816000	0.96949	0.563000	0.77884	GCC		0.502	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320044.2	NM_031468		T	71743767	C	T	71743767	3	4	69	1	0	0	0	0	1	0	0	0	2597	768	27	1	657	1	CALN1	7	71743767	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	5336831	71743767	87394896	22	20966										
TRIM24	8805	hgsc.bcm.edu	37	chr7	138200067	138200067	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cagagggtaaagttcacaaaAgaccacactgtcagacagaa	9	9	2	4			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr7:138200067A>G	ENST00000343526.4	+	3	809	c.594A>G	c.(592-594)aaA>aaG	p.K198K	TRIM24_ENST00000497516.1_3'UTR|TRIM24_ENST00000415680.2_Silent_p.K198K			O15164	TIF1A_HUMAN	tripartite motif containing 24	198					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K198K(2)		breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						AGTTCACAAAAGACCACACTG	0.433																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)											2	Substitution - coding silent(2)	large_intestine(2)	7											136	125	129					7																	138200067		2203	4300	6503	137850607	SO:0001819	synonymous_variant	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.594A>G	7.37:g.138200067A>G			137850607	A4D1R7|A4D1R8|O95854	Silent	SNP	ENST00000343526.4	37	CCDS5847.1																																																																																				0.433	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		G	138200067	A	G	138200067	2	3	69	1	0	0	0	0	0	0	0	1	16538	69	3	4		4	TRIM24	7	138200067	Silent	SNP	A	TCGA-AG-A016-01A-01W-A005-10	66456300	138200067	20938596	23	20967										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21970974	21970974	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cccgcagccgcgcgcaggtaCcgtgcgacatcgcgatggcc	14	17	0	0	rs199901898		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr9:21970974C>T	ENST00000304494.5	-	2	654	c.384G>A	c.(382-384)cgG>cgA	p.R128R	CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000578845.2_Silent_p.R77R|CDKN2A_ENST00000530628.2_Splice_Site|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498124.1_Silent_p.R128R|CDKN2A_ENST00000579122.1_Splice_Site|CDKN2A_ENST00000479692.2_Silent_p.R77R|CDKN2A_ENST00000498628.2_Silent_p.R77R|CDKN2A_ENST00000494262.1_Silent_p.R77R|CDKN2A_ENST00000497750.1_Silent_p.R77R|CDKN2A_ENST00000446177.1_Silent_p.R128R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	128					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(13)|p.R128fs*12(3)|p.R128R(3)|p.R128fs*9(2)|p.0(1)|p.A118fs*10(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CGCGCAGGTACCGTGCGACAT	0.682		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1338	Whole gene deletion(1316)|Unknown(13)|Deletion - Frameshift(6)|Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(278)|skin(168)|central_nervous_system(164)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|upper_aerodigestive_tract(51)|oesophagus(48)|ovary(35)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|large_intestine(8)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9						C	,,,	0,4406		0,0,2203	29	31	31		384,384,,	-0.2	0.4	9		31	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,utr-3,utr-3	CDKN2A	NM_000077.4,NM_001195132.1,NM_058195.3,NM_058197.4	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	128/157,128/168,,	21970974	1,13005	2203	4300	6503	21960974	SO:0001819	synonymous_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.384G>A	9.37:g.21970974C>T			21960974	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Silent	SNP	ENST00000304494.5	37	CCDS6510.1																																																																																				0.682	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		T	21970974	C	T	21970974	2	4	69	1	0	0	0	0	0	0	0	1	3167	494	18	3		3	CDKN2A	9	21970974	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10		21970974	119242457	24	20968										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34512387	34512387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gaaggtggaaggcagcaccaCggaagttcctgaggggttgc	17	8	0	1	rs137935543		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr9:34512387C>T	ENST00000242317.4	+	15	1625	c.1454C>T	c.(1453-1455)aCg>aTg	p.T485M		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	485					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)	p.T485M(1)		autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GGCAGCACCACGGAAGTTCCT	0.612									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	9						C	MET/THR	3,4403	4.2+/-10.8	0,3,2200	76	59	65		1454	2.8	0	9	dbSNP_134	65	0,8600		0,0,4300	no	missense	DNAI1	NM_012144.2	81	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	485/700	34512387	3,13003	2203	4300	6503	34502387	SO:0001583	missense	27019	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1454C>T	9.37:g.34512387C>T	ENSP00000242317:p.Thr485Met		34502387	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.664465	0.47572	6.81E-4	0.0	ENSG00000122735	ENST00000379040;ENST00000242317	T	0.75938	-0.98	5.56	2.76	0.32466	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.540590	0.03463	N	0.212508	T	0.68824	0.3043	L	0.41236	1.265	0.09310	N	0.999999	B	0.20887	0.049	B	0.17433	0.018	T	0.52480	-0.8570	10	0.44086	T	0.13	.	9.2729	0.37681	0.0:0.7626:0.0:0.2374	.	485	Q9UI46	DNAI1_HUMAN	M	41;485	ENSP00000242317:T485M	ENSP00000242317:T485M	T	+	2	0	DNAI1	34502387	0.000000	0.05858	0.006000	0.13384	0.958000	0.62258	0.003000	0.13083	0.314000	0.23086	-0.150000	0.13652	ACG		0.612	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			T	34512387	C	T	34512387	3	4	69	1	0	0	0	0	1	0	0	0	4620	536	19	1	1512	1	DNAI1	9	34512387	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	12541413	34512387	106701044	25	20969										
IDI2	91734	hgsc.bcm.edu	37	chr10	1065499	1065499	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agctccacaaacggggtcacGtcatccaggtgaggccacca	11	14	2	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr10:1065499G>A	ENST00000277517.1	-	5	706	c.642C>T	c.(640-642)gaC>gaT	p.D214D	GTPBP4_ENST00000360803.4_3'UTR	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	214					cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)	p.D214D(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		ACGGGGTCACGTCATCCAGGT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	10											50	49	49					10																	1065499		2203	4300	6503	1055499	SO:0001819	synonymous_variant	91734			AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.642C>T	10.37:g.1065499G>A			1055499		Silent	SNP	ENST00000277517.1	37	CCDS7055.1																																																																																				0.572	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261		A	1065499	G	A	1065499	2	1	69	1	0	0	0	0	0	0	0	1	7521	1136	40	1		1	IDI2	10	1065499	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10		1065499	134469248	26	20970										
SORCS3	22986	hgsc.bcm.edu	37	chr10	107022163	107022163	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gatgattgggtcagtgagccAaagtgaaaacgcccccaaaa	11	9	1	3			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr10:107022163A>C	ENST00000369701.3	+	26	3745	c.3518A>C	c.(3517-3519)cAa>cCa	p.Q1173P		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1173					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.Q1173P(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TCAGTGAGCCAAAGTGAAAAC	0.507																																					NSCLC(116;1497 1690 7108 13108 14106)											1	Substitution - Missense(1)	large_intestine(1)	10											96	77	84					10																	107022163		2203	4300	6503	107012153	SO:0001583	missense	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3518A>C	10.37:g.107022163A>C	ENSP00000358715:p.Gln1173Pro		107012153	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.700712	0.48307	.	.	ENSG00000156395	ENST00000369701	T	0.15372	2.43	5.84	5.84	0.93424	.	0.061453	0.64402	D	0.000003	T	0.11623	0.0283	N	0.15975	0.35	0.47308	D	0.999381	B	0.06786	0.001	B	0.11329	0.006	T	0.18681	-1.0329	9	.	.	.	.	16.2322	0.82352	1.0:0.0:0.0:0.0	.	1173	Q9UPU3	SORC3_HUMAN	P	1173	ENSP00000358715:Q1173P	.	Q	+	2	0	SORCS3	107012153	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.716000	0.68437	2.233000	0.73108	0.454000	0.30748	CAA		0.507	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	107022163	A	C	107022163	3	2	69	1	0	0	0	0	1	0	0	0	14969	130	5	4	3620	4	SORCS3	10	107022163	Missense_Mutation	SNP	A	TCGA-AG-A016-01A-01W-A005-10	105956664	107022163	28512584	27	20971										
OR56A1	120796	hgsc.bcm.edu	37	chr11	6048641	6048641	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aagcaggcagggaagctgatCgacctaagatcataccagaa	11	9	1	3	rs368602860		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr11:6048641C>T	ENST00000316650.5	-	1	330	c.294G>A	c.(292-294)tcG>tcA	p.S98S		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S98S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGAAGCTGATCGACCTAAGAT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C		0,4402		0,0,2201	111	98	102		294	-2	0	11		102	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	OR56A1	NM_001001917.2		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		98/319	6048641	1,12993	2201	4296	6497	6005217	SO:0001819	synonymous_variant	120796			AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"GPCR / Class A : Olfactory receptors"	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.294G>A	11.37:g.6048641C>T			6005217	B2RNI2|Q6IFL0	Silent	SNP	ENST00000316650.5	37	CCDS31405.1																																																																																				0.547	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		T	6048641	C	T	6048641	2	4	69	1	0	0	0	0	0	0	0	1	11164	871	31	1		1	OR56A1	11	6048641	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10		6048641	128957875	28	20972										
SLC22A6	9356	hgsc.bcm.edu	37	chr11	62749369	62749369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gaccagtagctgcaggtggcGccagtggggcacagcgtagg	18	10	0	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr11:62749369G>A	ENST00000377871.3	-	4	1008	c.742C>T	c.(742-744)Cgc>Tgc	p.R248C	SLC22A6_ENST00000360421.4_Missense_Mutation_p.R248C|SLC22A6_ENST00000421062.2_Missense_Mutation_p.R248C|SLC22A6_ENST00000458333.2_Missense_Mutation_p.R248C|SLC22A6_ENST00000537349.1_5'UTR	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	248					alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R248C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	TGCAGGTGGCGCCAGTGGGGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											62	54	56					11																	62749369		2201	4298	6499	62505945	SO:0001583	missense	9356			AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901		"Solute carriers"	10970	protein-coding gene	gene with protein product		607582				9762842, 9950961	Standard	NM_004790		Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000377871.3:c.742C>T	11.37:g.62749369G>A	ENSP00000367102:p.Arg248Cys		62505945	A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	Missense_Mutation	SNP	ENST00000377871.3	37	CCDS31591.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.924218	0.73213	.	.	ENSG00000197901	ENST00000360421;ENST00000394651;ENST00000377871;ENST00000458333;ENST00000421062	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.21	4.3	0.51218	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.052199	0.64402	D	0.000001	D	0.84857	0.5565	H	0.95187	3.635	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.72338	0.961;0.977;0.969;0.947	D	0.87073	0.2161	10	0.66056	D	0.02	.	9.4909	0.38960	0.0951:0.0:0.9049:0.0	.	248;248;248;248	Q4U2R8-4;Q4U2R8-3;Q4U2R8;Q4U2R8-2	.;.;S22A6_HUMAN;.	C	248;227;248;248;248	ENSP00000353597:R248C;ENSP00000367102:R248C;ENSP00000396401:R248C;ENSP00000404441:R248C	ENSP00000353597:R248C	R	-	1	0	SLC22A6	62505945	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.902000	0.63266	1.433000	0.47394	0.491000	0.48974	CGC		0.617	SLC22A6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396186.1	NM_004790		A	62749369	G	A	62749369	3	1	69	1	0	0	0	0	1	0	0	0	14495	1087	38	1	977	1	SLC22A6	11	62749369	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	56700728	62749369	72257147	29	20973										
CBL	867	hgsc.bcm.edu	37	chr11	119148968	119148968	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gatgtaaagattgagccctgTggacacctcatgtgcacatc	10	10	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr11:119148968T>C	ENST00000264033.4	+	8	1564	c.1188T>C	c.(1186-1188)tgT>tgC	p.C396C		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	396	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E366_Q409del(13)|p.E369_Q409del(1)|p.C396C(1)|p.E366_K477del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TTGAGCCCTGTGGACACCTCA	0.383			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	16	Deletion - In frame(15)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(15)|large_intestine(1)	11											128	119	122					11																	119148968		2199	4295	6494	118654178	SO:0001819	synonymous_variant	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1188T>C	11.37:g.119148968T>C			118654178	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																				0.383	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119148968	T	C	119148968	2	2	69	1	0	0	0	0	0	0	0	1	2706	1702	59	4		4	CBL	11	119148968	Silent	SNP	T	TCGA-AG-A016-01A-01W-A005-10	56399599	119148968	15857548	30	20974										
PRMT8	56341	hgsc.bcm.edu	37	chr12	3702265	3702265	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gctctctctctgccttgcagCgagacctcgatttcacagta	8	14	3	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr12:3702265C>T	ENST00000382622.3	+	10	1492	c.1102C>T	c.(1102-1104)Cga>Tga	p.R368*	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Splice_Site_p.R359*	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	368	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.R368*(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			TGCCTTGCAGCGAGACCTCGA	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											85	69	75					12																	3702265		2203	4300	6503	3572526	SO:0001630	splice_region_variant	56341			AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1102-1C>T	12.37:g.3702265C>T			3572526	B2RDP0|Q8TBJ8	Nonsense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804512	0.90623	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	.	.	.	5.22	4.31	0.51392	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7323	0.57204	0.1657:0.8342:0.0:0.0	.	.	.	.	X	359;368	.	.	R	+	1	2	PRMT8	3572526	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.856000	0.62932	1.158000	0.42547	0.313000	0.20887	CGA		0.542	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	Nonsense_Mutation	T	3702265	C	T	3702265	5	4	69	1	0	0	0	0	0	0	1	0	12576	782	27	1	1140	1	PRMT8	12	3702265	Splice_Site	SNP	C	TCGA-AG-A016-01A-01W-A005-10		3702265	130149630	31	20975										
GPC5	2262	hgsc.bcm.edu	37	chr13	92380834	92380834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gaacacccacacaaagccccCgttgttcttttgatcagagc	7	14	2	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr13:92380834C>T	ENST00000377067.3	+	4	1441	c.1069C>T	c.(1069-1071)Cgt>Tgt	p.R357C	GPC5_ENST00000483422.1_3'UTR	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	357					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.R357C(1)		NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ACAAAGCCCCCGTTGTTCTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	13											125	129	128					13																	92380834		2203	4300	6503	91178835	SO:0001583	missense	2262			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1069C>T	13.37:g.92380834C>T	ENSP00000366267:p.Arg357Cys		91178835	B2R726|O60436|Q9BX27	Missense_Mutation	SNP	ENST00000377067.3	37	CCDS9468.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.803202	0.31869	.	.	ENSG00000179399	ENST00000377067	T	0.55588	0.51	5.88	5.02	0.67125	.	1.139230	0.06161	N	0.675933	T	0.52141	0.1716	L	0.58101	1.795	0.09310	N	0.999996	B	0.27351	0.176	B	0.26202	0.067	T	0.37842	-0.9688	10	0.38643	T	0.18	-2.7689	10.6536	0.45663	0.1259:0.7003:0.1738:0.0	.	357	P78333	GPC5_HUMAN	C	357	ENSP00000366267:R357C	ENSP00000366267:R357C	R	+	1	0	GPC5	91178835	0.001000	0.12720	0.824000	0.32777	0.986000	0.74619	0.310000	0.19356	2.792000	0.96026	0.557000	0.71058	CGT		0.408	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		T	92380834	C	T	92380834	3	4	69	1	0	0	0	0	1	0	0	0	6621	652	23	1	1083	1	GPC5	13	92380834	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10		92380834	22789044	32	20976										
LIG4	3981	hgsc.bcm.edu	37	chr13	108863418	108863418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aggaagaattagtctcattgCtggataaaaagagtctgtga	11	4	2	3			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr13:108863418C>T	ENST00000356922.4	-	2	471	c.199G>A	c.(199-201)Gca>Aca	p.A67T	LIG4_ENST00000405925.1_Missense_Mutation_p.A67T|LIG4_ENST00000442234.1_Missense_Mutation_p.A67T	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	67					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.A67T(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					AGTCTCATTGCTGGATAAAAA	0.343								Non-homologous end-joining																																								1	Substitution - Missense(1)	large_intestine(1)	13											95	98	97					13																	108863418		2203	4299	6502	107661419	SO:0001583	missense	3981			X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.199G>A	13.37:g.108863418C>T	ENSP00000349393:p.Ala67Thr		107661419	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036708	0.75617	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.18174	2.23;2.23;2.23	6.05	6.05	0.98169	DNA ligase, ATP-dependent, N-terminal (3);	0.050361	0.85682	D	0.000000	T	0.34483	0.0899	M	0.81341	2.54	0.80722	D	1	P	0.42871	0.792	P	0.47251	0.542	T	0.01889	-1.1253	10	0.27082	T	0.32	.	19.5914	0.95514	0.0:1.0:0.0:0.0	.	67	P49917	DNLI4_HUMAN	T	67	ENSP00000385955:A67T;ENSP00000402030:A67T;ENSP00000349393:A67T	ENSP00000349393:A67T	A	-	1	0	LIG4	107661419	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.424000	0.80242	2.875000	0.98604	0.643000	0.83706	GCA		0.343	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		T	108863418	C	T	108863418	3	4	69	1	0	0	0	0	1	0	0	0	8806	797	28	3	2540	3	LIG4	13	108863418	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	16482584	108863418	6306460	33	20977										
SLC39A2	29986	hgsc.bcm.edu	37	chr14	21469106	21469106	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gcccttctttttgtttctagAtggagtatccctatggagag	10	8	2	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr14:21469106A>G	ENST00000298681.4	+	4	455	c.298A>G	c.(298-300)Atg>Gtg	p.M100V	RP11-84C10.4_ENST00000557335.1_RNA|SLC39A2_ENST00000554422.1_3'UTR	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	100					transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)	p.M100V(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		TTGTTTCTAGATGGAGTATCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											356	370	365					14																	21469106		2203	4300	6503	20538946	SO:0001630	splice_region_variant	29986			AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"Solute carriers"	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.298-1A>G	14.37:g.21469106A>G			20538946	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	.	.	.	.	.	.	.	.	.	.	A	4.426	0.078770	0.08533	.	.	ENSG00000165794	ENST00000298681	T	0.07216	3.21	5.7	-3.79	0.04320	.	0.801903	0.12421	N	0.470412	T	0.02156	0.0067	N	0.00483	-1.445	0.22858	N	0.998646	B	0.02656	0.0	B	0.04013	0.001	T	0.46205	-0.9208	9	.	.	.	0.3638	15.4086	0.74900	0.2893:0.0:0.7107:0.0	.	100	Q9NP94	S39A2_HUMAN	V	100	ENSP00000298681:M100V	.	M	+	1	0	SLC39A2	20538946	0.002000	0.14202	0.185000	0.23176	0.733000	0.41908	-0.515000	0.06290	-0.669000	0.05289	-0.250000	0.11733	ATG		0.468	SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579	Missense_Mutation	G	21469106	A	G	21469106	5	3	69	1	0	0	0	0	0	0	1	0	14655	347	12	4	312	4	SLC39A2	14	21469106	Splice_Site	SNP	A	TCGA-AG-A016-01A-01W-A005-10		21469106	85880434	34	20978										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49325216	49325216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	ttttgatcgactatcaggacCtgctgcatttgtttctttct	7	9	3	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr15:49325216C>T	ENST00000559471.1	-	4	873	c.610G>A	c.(610-612)Ggt>Agt	p.G204S	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.G204S	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	204							poly(A) RNA binding (GO:0044822)	p.G204S(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						CTATCAGGACCTGCTGCATTT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											257	226	237					15																	49325216		2197	4295	6492	47112508	SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.610G>A	15.37:g.49325216C>T	ENSP00000453854:p.Gly204Ser		47112508	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.073811	0.55646	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.89485	-2.52	5.37	5.37	0.77165	.	0.101544	0.64402	D	0.000002	T	0.80859	0.4704	N	0.20986	0.625	0.44227	D	0.997068	B;B	0.31193	0.208;0.312	B;B	0.31812	0.112;0.136	T	0.76884	-0.2794	10	0.19147	T	0.46	.	12.4617	0.55734	0.0:0.9234:0.0:0.0766	.	204;204	Q93073;Q93073-2	SBP2L_HUMAN;.	S	204	ENSP00000261847:G204S	ENSP00000261847:G204S	G	-	1	0	SECISBP2L	47112508	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.085000	0.50151	2.513000	0.84729	0.491000	0.48974	GGT		0.383	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		T	49325216	C	T	49325216	3	4	69	1	0	0	0	0	1	0	0	0	14044	681	24	3	2616	3	SECISBP2L	15	49325216	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10		49325216	53206176	35	20979										
USP7	7874	hgsc.bcm.edu	37	chr16	8992421	8992421	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agtttcttaggttgtctaggCttgaagaactgtagaagatc	11	5	2	4			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr16:8992421C>T	ENST00000344836.4	-	24	2805	c.2607G>A	c.(2605-2607)aaG>aaA	p.K869K	USP7_ENST00000381886.4_Silent_p.K853K|USP7_ENST00000535863.1_Silent_p.K770K	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	869					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.K869K(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						GTTGTCTAGGCTTGAAGAACT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	16											72	76	75					16																	8992421		2197	4300	6497	8899922	SO:0001819	synonymous_variant	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.2607G>A	16.37:g.8992421C>T			8899922	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																				0.378	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			T	8992421	C	T	8992421	2	4	69	1	0	0	0	0	0	0	0	1	17128	796	28	3		3	USP7	16	8992421	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10		8992421	81362332	36	20980										
PHKB	5257	hgsc.bcm.edu	37	chr16	47727375	47727375	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agtgtggcagattctggagcGcacgcccaatgggatcattg	14	9	2	1	rs144689991		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr16:47727375G>A	ENST00000323584.5	+	28	2876	c.2852G>A	c.(2851-2853)cGc>cAc	p.R951H	PHKB_ENST00000455779.1_Missense_Mutation_p.R944H|PHKB_ENST00000299167.8_Missense_Mutation_p.R951H|PHKB_ENST00000566044.1_Missense_Mutation_p.R944H	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	951	Calmodulin-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R951H(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ATTCTGGAGCGCACGCCCAAT	0.502																																																2	Substitution - Missense(2)	large_intestine(2)	16											68	63	64					16																	47727375		2201	4300	6501	46284876	SO:0001583	missense	5257				CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2852G>A	16.37:g.47727375G>A	ENSP00000313504:p.Arg951His		46284876	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	35	5.516512	0.96402	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;T;T	0.91237	-2.81;-0.54;-0.54	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.93504	0.7927	L	0.43923	1.385	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.996;0.999	D	0.91066	0.4889	10	0.27082	T	0.32	-15.543	20.2985	0.98592	0.0:0.0:1.0:0.0	.	192;951;944	B3KVX5;Q93100;Q93100-4	.;KPBB_HUMAN;.	H	944;944;951	ENSP00000299167:R944H;ENSP00000414345:R944H;ENSP00000313504:R951H	ENSP00000299167:R944H	R	+	2	0	PHKB	46284876	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.370000	0.97159	2.793000	0.96121	0.655000	0.94253	CGC		0.502	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47727375	G	A	47727375	3	1	69	1	0	0	0	0	1	0	0	0	11876	1087	38	1	3116	1	PHKB	16	47727375	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	38734954	47727375	42627378	37	20981										
CDH8	1006	hgsc.bcm.edu	37	chr16	61935314	61935314	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	atttatttgaaatatggtccCagctccatcacctgatagga	7	9	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr16:61935314C>A	ENST00000577390.1	-	3	1270	c.316G>T	c.(316-318)Ggg>Tgg	p.G106W	CDH8_ENST00000577730.1_Missense_Mutation_p.G106W|CDH8_ENST00000299345.6_Missense_Mutation_p.G106W|CDH8_ENST00000584337.1_Missense_Mutation_p.G106W	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	106	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.G106W(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		AATATGGTCCCAGCTCCATCA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	16											107	102	104					16																	61935314		2203	4300	6503	60492815	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.316G>T	16.37:g.61935314C>A	ENSP00000462701:p.Gly106Trp		60492815	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215973	0.79352	.	.	ENSG00000150394	ENST00000299345	T	0.55234	0.53	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.044703	0.85682	D	0.000000	D	0.84047	0.5386	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88284	0.2938	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	106	P55286	CADH8_HUMAN	W	106	ENSP00000299345:G106W	ENSP00000299345:G106W	G	-	1	0	CDH8	60492815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.743000	0.68655	2.941000	0.99782	0.655000	0.94253	GGG		0.408	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		A	61935314	C	A	61935314	3	1	69	1	0	0	0	0	1	0	0	0	3122	594	21	2	2123	2	CDH8	16	61935314	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	14207939	61935314	28419439	38	20982										
LRRC36	55282	hgsc.bcm.edu	37	chr16	67375878	67375878	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agaactggtggagtctctttCattgcagggatcttatgctg	12	7	3	1			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr16:67375878C>T	ENST00000329956.6	+	2	108	c.89C>T	c.(88-90)tCa>tTa	p.S30L	LRRC36_ENST00000563303.1_Intron	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	30								p.S30L(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		GAGTCTCTTTCATTGCAGGGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	16											128	122	124					16																	67375878		2198	4300	6498	65933379	SO:0001583	missense	55282			BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.89C>T	16.37:g.67375878C>T	ENSP00000329943:p.Ser30Leu		65933379	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	37	CCDS32467.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.547022	0.45383	.	.	ENSG00000159708	ENST00000329956	T	0.24538	1.85	5.55	5.55	0.83447	.	0.160401	0.40818	N	0.001018	T	0.42017	0.1184	L	0.39397	1.21	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.09862	-1.0655	10	0.46703	T	0.11	-7.5457	15.0199	0.71621	0.0:1.0:0.0:0.0	.	30	Q1X8D7	LRC36_HUMAN	L	30	ENSP00000329943:S30L	ENSP00000329943:S30L	S	+	2	0	LRRC36	65933379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.761000	0.55242	2.614000	0.88457	0.563000	0.77884	TCA		0.398	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		T	67375878	C	T	67375878	3	4	69	1	0	0	0	0	1	0	0	0	9019	838	29	3	95	3	LRRC36	16	67375878	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	5440564	67375878	22978875	39	20983										
CHST4	10164	hgsc.bcm.edu	37	chr16	71571445	71571445	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cccctgtggcccagacttccCgaatgtatgaattcgtggga	11	12	0	2	rs144191969		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr16:71571445C>T	ENST00000338482.5	+	3	1208	c.865C>T	c.(865-867)Cga>Tga	p.R289*	RP11-510M2.5_ENST00000568523.1_RNA|CHST4_ENST00000572450.1_Nonsense_Mutation_p.R289*|ZNF19_ENST00000568446.1_Intron|CHST4_ENST00000539698.3_Nonsense_Mutation_p.R289*			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	289					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.R289*(1)		cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CCAGACTTCCCGAATGTATGA	0.567											OREG0023923	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	16						C	stop/ARG,stop/ARG	1,4395	2.1+/-5.4	0,1,2197	89	79	83		865,865	3.8	0.1	16	dbSNP_134	83	0,8600		0,0,4300	no	stop-gained,stop-gained	CHST4	NM_001166395.1,NM_005769.2	,	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	,	289/387,289/387	71571445	1,12995	2198	4300	6498	70128946	SO:0001587	stop_gained	10164			AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"Sulfotransferases, membrane-bound"	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.865C>T	16.37:g.71571445C>T	ENSP00000341206:p.Arg289*	1131	70128946	Q8IV46|Q9Y5R3	Nonsense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414643	0.62511	2.27E-4	0.0	ENSG00000140835	ENST00000338482;ENST00000539698	.	.	.	6.02	3.85	0.44370	.	0.648698	0.15268	N	0.271430	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-6.7456	14.3748	0.66867	0.286:0.714:0.0:0.0	.	.	.	.	X	289	.	ENSP00000341206:R289X	R	+	1	2	CHST4	70128946	0.000000	0.05858	0.064000	0.19789	0.047000	0.14425	0.380000	0.20602	1.498000	0.48600	0.655000	0.94253	CGA		0.567	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769		T	71571445	C	T	71571445	4	4	69	1	0	0	0	0	0	1	0	0	3412	644	23	1	867	1	CHST4	16	71571445	Nonsense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	4195567	71571445	18783308	40	20984										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000574684.1_5'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	69	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10		7578406	73616804	41	20985										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7701621	7701621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	tcgaggtcaccaaacattatCggaagcaggagttccgagat	11	9	1	1	rs138592684	byFrequency	TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr17:7701621C>T	ENST00000572933.1	+	54	9837	c.8377C>T	c.(8377-8379)Cgg>Tgg	p.R2793W	DNAH2_ENST00000389173.2_Missense_Mutation_p.R2793W			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2793	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2793W(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CAAACATTATCGGAAGCAGGA	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	TRP/ARG	3,4403		0,3,2200	42	41	41		8377	5.3	1	17	dbSNP_134	41	0,8598		0,0,4299	yes	missense	DNAH2	NM_020877.2	101	0,3,6499	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	2793/4428	7701621	3,13001	2203	4299	6502	7642346	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.8377C>T	17.37:g.7701621C>T	ENSP00000458355:p.Arg2793Trp		7642346	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069714	0.93950	6.81E-4	0.0	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.40476	1.03	5.3	5.3	0.74995	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.71854	0.3389	M	0.90595	3.13	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.78226	-0.2286	10	0.87932	D	0	.	18.0885	0.89466	0.0:1.0:0.0:0.0	.	2793	Q9P225	DYH2_HUMAN	W	2793	ENSP00000373825:R2793W	ENSP00000353818:R2793W	R	+	1	2	DNAH2	7642346	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	4.453000	0.60061	2.639000	0.89480	0.455000	0.32223	CGG		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7701621	C	T	7701621	3	4	69	1	0	0	0	0	1	0	0	0	4613	875	31	1	8587	1	DNAH2	17	7701621	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	123215	7701621	73493589	42	20986										
TTLL6	284076	hgsc.bcm.edu	37	chr17	46847280	46847280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gtgggcagaaaagattttaaCattttcttctgggttaagtg	11	4	2	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr17:46847280C>T	ENST00000393382.3	-	14	2361	c.2220G>A	c.(2218-2220)atG>atA	p.M740I	TTLL6_ENST00000433608.2_Missense_Mutation_p.M433I	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6									p.M692I(1)|p.M418I(1)		endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						AAGATTTTAACATTTTCTTCT	0.463																																																2	Substitution - Missense(2)	large_intestine(2)	17											84	85	85					17																	46847280		2203	4300	6503	44202279	SO:0001583	missense	284076			AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.2220G>A	17.37:g.46847280C>T	ENSP00000377043:p.Met740Ile		44202279		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	C	0.154	-1.088467	0.01873	.	.	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	.	.	.	4.48	-1.78	0.07957	.	96.862600	0.00166	U	0.000001	T	0.15305	0.0369	N	0.04880	-0.145	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.07404	-1.0774	9	0.16896	T	0.51	.	0.8629	0.01197	0.159:0.1958:0.3275:0.3177	.	692;433	Q8N841;G5E937	TTLL6_HUMAN;.	I	740;433;418;692	.	ENSP00000302547:M433I	M	-	3	0	TTLL6	44202279	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.112000	0.15479	-0.230000	0.09840	-1.224000	0.01588	ATG		0.463	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		T	46847280	C	T	46847280	3	4	69	1	0	0	0	0	1	0	0	0	16771	478	17	3	463	3	TTLL6	17	46847280	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	39145659	46847280	34347930	43	20987										
UBE2O	63893	hgsc.bcm.edu	37	chr17	74397133	74397133	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	cttgctcttggtgctgagcaCgggcttgacacctgacagcc	12	13	1	3			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr17:74397133C>T	ENST00000319380.7	-	6	917	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	285					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.V285M(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						GTGCTGAGCACGGGCTTGACA	0.587																																																2	Substitution - Missense(2)	large_intestine(2)	17											74	55	61					17																	74397133		2203	4300	6503	71908728	SO:0001583	missense	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.853G>A	17.37:g.74397133C>T	ENSP00000323687:p.Val285Met		71908728	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	37	CCDS32742.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.057956	0.76074	.	.	ENSG00000175931	ENST00000319380	T	0.72942	-0.7	5.07	5.07	0.68467	.	0.328060	0.27773	N	0.017914	T	0.73729	0.3624	N	0.17474	0.49	0.49389	D	0.999787	D	0.89917	1.0	D	0.83275	0.996	T	0.72883	-0.4157	10	0.27785	T	0.31	-10.4884	18.4527	0.90710	0.0:1.0:0.0:0.0	.	285	Q9C0C9	UBE2O_HUMAN	M	285	ENSP00000323687:V285M	ENSP00000323687:V285M	V	-	1	0	UBE2O	71908728	1.000000	0.71417	0.928000	0.36995	0.848000	0.48234	7.787000	0.85759	2.365000	0.80145	0.655000	0.94253	GTG		0.587	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		T	74397133	C	T	74397133	3	4	69	1	0	0	0	0	1	0	0	0	16908	536	19	1	3077	1	UBE2O	17	74397133	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	27549853	74397133	6798077	44	20988										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7033010	7033010	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gaggtccctgtgtagccttgCggacattcacagtgctccac	11	13	1	0	rs139988519		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr18:7033010C>T	ENST00000389658.3	-	15	2229	c.2136G>A	c.(2134-2136)ccG>ccA	p.P712P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	712	Laminin EGF-like 5; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.P712P(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGTAGCCTTGCGGACATTCAC	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	18											109	82	91					18																	7033010		2203	4300	6503	7023010	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2136G>A	18.37:g.7033010C>T			7023010		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.522	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7033010	C	T	7033010	2	4	69	1	0	0	0	0	0	0	0	1	8627	755	27	1		1	LAMA1	18	7033010	Silent	SNP	C	TCGA-AG-A016-01A-01W-A005-10		7033010	71044238	45	20989										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8819107	8819107	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gcagatgctgactccatcccGtttgaagaccggccgctgtc	11	14	0	4			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr18:8819107G>A	ENST00000306329.11	+	11	3963	c.3963G>A	c.(3961-3963)ccG>ccA	p.P1321P	SOGA2_ENST00000517570.1_Silent_p.P961P|SOGA2_ENST00000306285.7_Silent_p.P327P|SOGA2_ENST00000400050.3_Silent_p.P961P|SOGA2_ENST00000518815.1_Silent_p.P327P|SOGA2_ENST00000359865.3_Silent_p.P1002P														p.P1002P(1)									ACTCCATCCCGTTTGAAGACC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	18											50	46	47					18																	8819107		2203	4300	6503	8809107	SO:0001819	synonymous_variant	23255																														ENST00000306329.11:c.3963G>A	18.37:g.8819107G>A			8809107		Silent	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	G	8.967	0.971957	0.18736	.	.	ENSG00000168502	ENST00000519823	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.55465	0.1922	.	.	.	0.41738	D	0.989598	.	.	.	.	.	.	T	0.73742	-0.3887	4	.	.	.	-6.743	13.065	0.59028	0.0776:0.0797:0.6304:0.2123	.	.	.	.	I	108	.	.	V	+	1	0	CCDC165	8809107	0.003000	0.15002	0.000000	0.03702	0.180000	0.23129	-1.213000	0.02991	-3.970000	0.00086	-1.021000	0.02439	GTT		0.597	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			A	8819107	G	A	8819107	2	1	69	1	0	0	0	0	0	0	0	1	8215	1132	40	1		1	KIAA0802	18	8819107	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10	1786097	8819107	69258141	46	20990										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18550412	18550412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	actgttcttccagaaggcctCgcgccaactgctcagactca	8	15	3	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr18:18550412C>T	ENST00000399799.2	-	23	3657	c.2717G>A	c.(2716-2718)cGa>cAa	p.R906Q		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	906	Glu-rich.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R906Q(2)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					CAGAAGGCCTCGCGCCAACTG	0.383																																																2	Substitution - Missense(2)	large_intestine(2)	18											148	136	140					18																	18550412		2203	4300	6503	16804410	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.2717G>A	18.37:g.18550412C>T	ENSP00000382697:p.Arg906Gln		16804410	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	36	5.754285	0.96890	.	.	ENSG00000067900	ENST00000399799	T	0.13901	2.55	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.39963	0.1098	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.28202	-1.0051	10	0.87932	D	0	.	18.4587	0.90731	0.0:1.0:0.0:0.0	.	906	Q13464	ROCK1_HUMAN	Q	906	ENSP00000382697:R906Q	ENSP00000382697:R906Q	R	-	2	0	ROCK1	16804410	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.345000	0.79337	2.586000	0.87340	0.563000	0.77884	CGA		0.383	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		T	18550412	C	T	18550412	3	4	69	1	0	0	0	0	1	0	0	0	13554	884	31	1	1391	1	ROCK1	18	18550412	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	9731305	18550412	59526836	47	20991										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48573585	48573585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aaaaagatgaattggattctTtaataacagctataactaca	5	5	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr18:48573585T>G	ENST00000342988.3	+	2	707	c.169T>G	c.(169-171)Tta>Gta	p.L57V	SMAD4_ENST00000588745.1_Missense_Mutation_p.L57V|SMAD4_ENST00000398417.2_Missense_Mutation_p.L57V|SMAD4_ENST00000452201.2_Missense_Mutation_p.L57V|RP11-729L2.2_ENST00000590722.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	57	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(5)|p.L57V(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ATTGGATTCTTTAATAACAGC	0.363																																																42	Whole gene deletion(36)|Unknown(5)|Substitution - Missense(1)	pancreas(26)|large_intestine(4)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|oesophagus(1)|NS(1)	18											120	128	125					18																	48573585		2203	4300	6503	46827583	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.169T>G	18.37:g.48573585T>G	ENSP00000341551:p.Leu57Val		46827583	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.479970	0.63849	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	D;D;D	0.81659	-1.52;-1.52;-1.52	5.86	4.7	0.59300	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.64402	D	0.000001	D	0.90293	0.6964	M	0.91459	3.21	0.48975	D	0.999735	D	0.71674	0.998	D	0.87578	0.998	D	0.90288	0.4320	10	0.87932	D	0	.	8.3079	0.32053	0.0:0.1542:0.0:0.8458	.	57	Q13485	SMAD4_HUMAN	V	57	ENSP00000409551:L57V;ENSP00000341551:L57V;ENSP00000381452:L57V	ENSP00000341551:L57V	L	+	1	2	SMAD4	46827583	0.997000	0.39634	1.000000	0.80357	0.964000	0.63967	2.084000	0.41625	1.051000	0.40369	-0.250000	0.11733	TTA		0.363	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48573585	T	G	48573585	3	3	69	1	0	0	0	0	1	0	0	0	14797	1838	64	4	171	4	SMAD4	18	48573585	Missense_Mutation	SNP	T	TCGA-AG-A016-01A-01W-A005-10	30023173	48573585	29503663	48	20992										
TBCB	1155	hgsc.bcm.edu	37	chr19	36616654	36616654	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gtgacggtgggggacttcccGgaggaggactacgggttgga	20	7	0	1	rs141544940	byFrequency	TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr19:36616654G>A	ENST00000221855.3	+	6	1280	c.705G>A	c.(703-705)ccG>ccA	p.P235P	TBCB_ENST00000589996.1_3'UTR|TBCB_ENST00000585746.1_Silent_p.P184P|TBCB_ENST00000586868.1_3'UTR	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	235					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.P235P(1)		large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GGGACTTCCCGGAGGAGGACT	0.572													G|||	2	0.000399361	0.0015	0	5008	,	,		17610	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G		1,4405	2.1+/-5.4	0,1,2202	181	174	177		705	-9.6	0.5	19	dbSNP_134	177	0,8600		0,0,4300	no	coding-synonymous	TBCB	NM_001281.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		235/245	36616654	1,13005	2203	4300	6503	41308494	SO:0001819	synonymous_variant	1155			AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"cytoskeleton-associated protein 1", "cytoskeleton associated protein 1"	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.705G>A	19.37:g.36616654G>A			41308494	O00111|O00674|O14728|Q6FGY5	Silent	SNP	ENST00000221855.3	37	CCDS12488.1																																																																																				0.572	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281		A	36616654	G	A	36616654	2	1	69	1	0	0	0	0	0	0	0	1	15669	1103	39	1		1	TBCB	19	36616654	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10		36616654	22512329	49	20993										
ZNF420	147923	hgsc.bcm.edu	37	chr19	37619341	37619341	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	atgtaaggaatgtgggaaatCttttattcgtggttcccagc	11	6	1	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr19:37619341C>A	ENST00000337995.3	+	5	1663	c.1448C>A	c.(1447-1449)tCt>tAt	p.S483Y	ZNF585A_ENST00000588723.1_Intron|ZNF420_ENST00000304239.7_Intron|CTC-454I21.4_ENST00000587645.1_RNA	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	483					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S483Y(1)		breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTGGGAAATCTTTTATTCGT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19											72	65	67					19																	37619341		2203	4300	6503	42311181	SO:0001583	missense	147923			AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.1448C>A	19.37:g.37619341C>A	ENSP00000338770:p.Ser483Tyr		42311181	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	37	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.522812	0.27211	.	.	ENSG00000197050	ENST00000337995	T	0.08370	3.1	3.51	2.41	0.29592	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23492	0.0568	M	0.76838	2.35	0.09310	N	0.999999	D	0.89917	1.0	D	0.69307	0.963	T	0.03608	-1.1020	8	.	.	.	.	5.8512	0.18694	0.0:0.5542:0.3297:0.1161	.	483	Q8TAQ5	ZN420_HUMAN	Y	483	ENSP00000338770:S483Y	.	S	+	2	0	ZNF420	42311181	0.000000	0.05858	0.961000	0.40146	0.791000	0.44710	0.060000	0.14342	1.813000	0.52934	0.591000	0.81541	TCT		0.393	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		A	37619341	C	A	37619341	3	1	69	1	0	0	0	0	1	0	0	0	17936	913	32	2	1458	2	ZNF420	19	37619341	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	1002687	37619341	21509642	50	20994										
IRF3	3661	hgsc.bcm.edu	37	chr19	50166666	50166666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gctccggtcctctgctaaacGcaacccttctttgcggttga	9	14	2	1	rs377410193		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr19:50166666G>A	ENST00000597198.1	-	3	652	c.271C>T	c.(271-273)Cgt>Tgt	p.R91C	IRF3_ENST00000599680.1_5'Flank|IRF3_ENST00000599223.1_Missense_Mutation_p.R91C|BCL2L12_ENST00000441864.2_5'Flank|IRF3_ENST00000377135.4_Missense_Mutation_p.R91C|IRF3_ENST00000600911.1_Missense_Mutation_p.R91C|IRF3_ENST00000377139.3_Missense_Mutation_p.R91C|IRF3_ENST00000599144.1_Intron|IRF3_ENST00000593922.1_5'UTR|IRF3_ENST00000309877.7_Missense_Mutation_p.R91C|BCL2L12_ENST00000246785.3_5'Flank|IRF3_ENST00000598808.1_5'UTR|IRF3_ENST00000442265.2_Intron|IRF3_ENST00000601291.1_Missense_Mutation_p.R91C|IRF3_ENST00000600022.1_5'UTR|IRF3_ENST00000596822.1_5'UTR|IRF3_ENST00000596765.1_Intron|BCL2L12_ENST00000246784.3_5'Flank			Q14653	IRF3_HUMAN	interferon regulatory factor 3	91					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dsRNA (GO:0071359)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage apoptotic process (GO:0071888)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of interferon-beta biosynthetic process (GO:0045358)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|programmed necrotic cell death (GO:0097300)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.R91C(1)		breast(1)|large_intestine(2)|lung(4)|ovary(2)|stomach(1)	10		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)		TCTGCTAAACGCAACCCTTCT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19											73	66	68					19																	50166666		2203	4300	6503	54858478	SO:0001583	missense	3661				CCDS12775.1, CCDS56099.1, CCDS59407.1, CCDS59408.1, CCDS59409.1	19q13.3-q13.4	2008-07-16				ENSG00000126456			6118	protein-coding gene	gene with protein product		603734				8524823	Standard	NM_001571		Approved		uc002pow.3	Q14653		ENST00000597198.1:c.271C>T	19.37:g.50166666G>A	ENSP00000469113:p.Arg91Cys		54858478	A8K7L2|B2RAZ3|Q5FBY1|Q5FBY2|Q5FBY4|Q7Z5G6	Missense_Mutation	SNP	ENST00000597198.1	37	CCDS12775.1	.	.	.	.	.	.	.	.	.	.	G	2.853	-0.237954	0.05944	.	.	ENSG00000126456	ENST00000377139;ENST00000309877;ENST00000377135	D;D;D	0.98060	-4.69;-4.69;-4.69	4.92	2.76	0.32466	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	1.091900	0.06928	N	0.810588	D	0.95868	0.8655	L	0.60455	1.87	0.09310	N	0.999999	B;B;B;B;B	0.27791	0.189;0.019;0.019;0.128;0.002	B;B;B;B;B	0.24541	0.054;0.011;0.011;0.016;0.0	D	0.88983	0.3409	10	0.56958	D	0.05	-1.8841	7.3101	0.26469	0.1639:0.0:0.6989:0.1372	.	91;91;91;91;91	B2RAZ3;Q96GL3;Q7Z5G6;Q14653;Q5FBY1	.;.;.;IRF3_HUMAN;.	C	91	ENSP00000366344:R91C;ENSP00000310127:R91C;ENSP00000366339:R91C	ENSP00000310127:R91C	R	-	1	0	IRF3	54858478	0.045000	0.20229	0.008000	0.14137	0.001000	0.01503	1.801000	0.38843	0.232000	0.21100	-0.797000	0.03246	CGT		0.577	IRF3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465962.1	NM_001571		A	50166666	G	A	50166666	3	1	69	1	0	0	0	0	1	0	0	0	7852	1087	38	1	1036	1	IRF3	19	50166666	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	12547325	50166666	8962317	51	20995										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58153449	58153449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	tcaacaccgcagagttcacaCgggaaaaaggccttatcagt	9	11	3	1	rs149154202		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr19:58153449C>T	ENST00000347302.3	+	3	1774	c.1595C>T	c.(1594-1596)aCg>aTg	p.T532M	ZNF211_ENST00000420680.1_Missense_Mutation_p.T536M|ZNF211_ENST00000544273.1_Missense_Mutation_p.T544M|ZNF211_ENST00000391703.3_Missense_Mutation_p.T471M|ZNF211_ENST00000299871.5_Missense_Mutation_p.T597M|ZNF211_ENST00000240731.4_Missense_Mutation_p.T545M|ZNF211_ENST00000254182.7_Missense_Mutation_p.T523M|ZNF211_ENST00000541801.1_Missense_Mutation_p.T523M	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T545M(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		AGAGTTCACACGGGAAAAAGG	0.463													C|||	1	0.000199681	0	0	5008	,	,		21278	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						C	MET/THR,MET/THR	0,4406		0,0,2203	104	101	102		1634,1595	-0.3	0.1	19	dbSNP_134	102	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	81,81	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	probably-damaging,probably-damaging	545/578,532/565	58153449	6,13000	2203	4300	6503	62845261	SO:0001583	missense	10520			U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1595C>T	19.37:g.58153449C>T	ENSP00000339562:p.Thr532Met		62845261	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	24.5	4.533225	0.85812	0.0	6.98E-4	ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	3.23	-0.353	0.12594	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39733	0.1089	M	0.64404	1.975	0.27417	N	0.954402	D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0	D;D;P;D;D;D	0.72982	0.919;0.919;0.847;0.979;0.952;0.952	T	0.23619	-1.0183	9	0.87932	D	0	.	3.7567	0.08588	0.1672:0.5713:0.1623:0.0993	.	536;544;597;523;532;545	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1	.;.;.;.;ZN211_HUMAN;.	M	536;532;523;471;523;597;544;545	ENSP00000399193:T536M;ENSP00000339562:T532M;ENSP00000254182:T523M;ENSP00000375584:T471M;ENSP00000442601:T523M;ENSP00000299871:T597M;ENSP00000441386:T544M;ENSP00000240731:T545M	ENSP00000240731:T545M	T	+	2	0	ZNF211	62845261	0.001000	0.12720	0.087000	0.20705	0.961000	0.63080	-0.016000	0.12613	-0.078000	0.12730	0.585000	0.79938	ACG		0.463	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			T	58153449	C	T	58153449	3	4	69	1	0	0	0	0	1	0	0	0	17806	536	19	1	1648	1	ZNF211	19	58153449	Missense_Mutation	SNP	C	TCGA-AG-A016-01A-01W-A005-10	7986783	58153449	975534	52	20996										
C20orf151	140893	hgsc.bcm.edu	37	chr20	60992296	60992296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	ccacctgttctccagcacccGcaggttctccttcagtgtct	7	17	4	0			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr20:60992296G>A	ENST00000252998.1	-	4	340	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	62						extracellular space (GO:0005615)		p.R62W(1)									TCCAGCACCCGCAGGTTCTCC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	20											98	69	79					20																	60992296		2202	4296	6498	60425691	SO:0001583	missense	140893			AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"hypothetical protein LOC140893"		"chromosome 20 open reading frame 151"	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.184C>T	20.37:g.60992296G>A	ENSP00000252998:p.Arg62Trp		60425691	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775867	0.70107	.	.	ENSG00000130701	ENST00000252998	T	0.20881	2.04	4.54	2.14	0.27477	Tumour-suppressor protein CtIP N-terminal (1);	0.193749	0.41938	D	0.000798	T	0.37705	0.1013	L	0.54323	1.7	0.37382	D	0.912065	D	0.89917	1.0	D	0.85130	0.997	T	0.42447	-0.9451	10	0.87932	D	0	-27.0298	10.7743	0.46340	0.0:0.0:0.3752:0.6248	.	62	Q8NC74	CT151_HUMAN	W	62	ENSP00000252998:R62W	ENSP00000252998:R62W	R	-	1	2	C20orf151	60425691	0.230000	0.23740	0.998000	0.56505	0.805000	0.45488	1.552000	0.36244	0.998000	0.38996	0.561000	0.74099	CGG		0.612	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		A	60992296	G	A	60992296	3	1	69	1	0	0	0	0	1	0	0	0	2097	1086	38	1	1854	1	C20orf151	20	60992296	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10		60992296	2033224	53	20997										
AGPAT3	56894	hgsc.bcm.edu	37	chr21	45391327	45391327	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	aacaagaacccgtccctgctGgggatcctctacgggaagaa	11	12	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr21:45391327G>A	ENST00000398063.2	+	6	1215	c.723G>A	c.(721-723)ctG>ctA	p.L241L	AGPAT3_ENST00000291572.8_Silent_p.L241L|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000327505.2_Silent_p.L241L|AGPAT3_ENST00000398061.1_Silent_p.L241L|AGPAT3_ENST00000546158.1_Silent_p.L241L|AGPAT3_ENST00000398058.1_Silent_p.L241L	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	241					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.L241L(1)		large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		CGTCCCTGCTGGGGATCCTCT	0.612																																					Pancreas(60;623 1650 5574 52796)											1	Substitution - coding silent(1)	large_intestine(1)	21											139	137	137					21																	45391327		2203	4300	6503	44215755	SO:0001819	synonymous_variant	56894			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.723G>A	21.37:g.45391327G>A			44215755	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Silent	SNP	ENST00000398063.2	37	CCDS13703.1																																																																																				0.612	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132		A	45391327	G	A	45391327	2	1	69	1	0	0	0	0	0	0	0	1	388	1335	47	3		3	AGPAT3	21	45391327	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10		45391327	2738568	54	20998										
CECR1	51816	hgsc.bcm.edu	37	chr22	17663506	17663506	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	acacatacctggttagagatGggacagacttctatggggat	12	7	1	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr22:17663506G>A	ENST00000399839.1	-	8	1497	c.1227C>T	c.(1225-1227)ccC>ccT	p.P409P	CECR1_ENST00000399837.2_Silent_p.P409P|CECR1_ENST00000330232.4_Silent_p.P168P|CECR1_ENST00000449907.2_Silent_p.P367P|CECR1_ENST00000262607.3_Silent_p.P409P	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	409					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.P409P(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GGTTAGAGATGGGACAGACTT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	22											191	183	186					22																	17663506		2203	4300	6503	16043506	SO:0001819	synonymous_variant	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1227C>T	22.37:g.17663506G>A			16043506	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																				0.463	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			A	17663506	G	A	17663506	2	1	69	1	0	0	0	0	0	0	0	1	3211	1335	47	3		3	CECR1	22	17663506	Silent	SNP	G	TCGA-AG-A016-01A-01W-A005-10		17663506	33641060	55	20999										
PISD	23761	hgsc.bcm.edu	37	chr22	32016634	32016634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	gtcccccgtcaggaccacccGctcgttatggcagaagagct	11	15	1	2	rs370672474		TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chr22:32016634G>A	ENST00000439502.2	-	7	1133	c.910C>T	c.(910-912)Cgg>Tgg	p.R304W	PISD_ENST00000478893.1_5'UTR|PISD_ENST00000397500.1_Intron|PISD_ENST00000336566.4_Missense_Mutation_p.R303W|PISD_ENST00000266095.5_Missense_Mutation_p.R270W|PISD_ENST00000382151.2_Missense_Mutation_p.R270W			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	304					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)	p.R270W(1)		central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	AGGACCACCCGCTCGTTATGG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	22						G	TRP/ARG	0,4406		0,0,2203	125	106	112		808	4.6	1	22		112	1,8599	1.2+/-3.3	0,1,4299	no	missense	PISD	NM_014338.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	270/376	32016634	1,13005	2203	4300	6503	30346634	SO:0001583	missense	23761				CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.910C>T	22.37:g.32016634G>A	ENSP00000391739:p.Arg304Trp		30346634	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Missense_Mutation	SNP	ENST00000439502.2	37		.	.	.	.	.	.	.	.	.	.	G	27.0	4.790115	0.90367	0.0	1.16E-4	ENSG00000241878	ENST00000382151;ENST00000266095;ENST00000439502;ENST00000336566;ENST00000451635	.	.	.	5.6	4.55	0.56014	.	0.000000	0.85682	D	0.000000	D	0.90307	0.6968	H	0.98866	4.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93664	0.6984	9	0.87932	D	0	-24.5755	15.0179	0.71600	0.0:0.0:0.8575:0.1425	.	304;270	Q9UG56;Q9UG56-2	PISD_HUMAN;.	W	270;270;304;303;270	.	ENSP00000266095:R270W	R	-	1	2	PISD	30346634	1.000000	0.71417	0.982000	0.44146	0.800000	0.45204	7.532000	0.81985	2.645000	0.89757	0.467000	0.42956	CGG		0.592	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4			A	32016634	G	A	32016634	3	1	69	1	0	0	0	0	1	0	0	0	11977	1086	38	1	327	1	PISD	22	32016634	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10	14353128	32016634	19287932	56	21000										
PLS3	5358	hgsc.bcm.edu	37	chrX	114874777	114874777	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	3	1	0.447777777777778	3.35833333333333	0.312403100775194	1	1	0	caccaaaaggacaaaaggaaGgtgaaccacggatagatatt	10	7	0	2			TCGA-AG-A016-01A-01W-A005-10	TCGA-AG-A016-10A-01W-A005-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			SOLID	f20ae301-b10b-4dfa-9169-04bc6c3d103a	0635d391-58c8-4450-9be5-54e6620bb0a3	g.chrX:114874777G>A	ENST00000420625.2	+	9	1083	c.949G>A	c.(949-951)Ggt>Agt	p.G317S	PLS3_ENST00000289290.3_Missense_Mutation_p.G281S|PLS3_ENST00000537301.1_Missense_Mutation_p.G304S|PLS3_ENST00000543070.1_De_novo_Start_OutOfFrame|PLS3_ENST00000355899.3_Missense_Mutation_p.G317S|PLS3_ENST00000539310.1_Missense_Mutation_p.G272S	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	317	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.G317S(1)		NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						ACAAAAGGAAGGTGAACCACG	0.338																																					Colon(160;1047 1864 8490 12969 29601)											1	Substitution - Missense(1)	large_intestine(1)	X											172	147	156					X																	114874777		2203	4300	6503	114781033	SO:0001583	missense	5358			L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.949G>A	X.37:g.114874777G>A	ENSP00000398945:p.Gly317Ser		114781033	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Missense_Mutation	SNP	ENST00000420625.2	37	CCDS14568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.94|18.94	3.729294|3.729294	0.69074|0.69074	.|.	.|.	ENSG00000102024|ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310|ENST00000497870	T;D;D;T;D|.	0.85258|.	-0.47;-1.72;-1.94;-0.47;-1.96|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Calponin homology domain (5);|.	0.089981|.	0.85682|.	D|.	0.000000|.	T|T	0.71476|0.71476	0.3344|0.3344	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.31893|.	0.169;0.001;0.345;0.0|.	B;B;B;B|.	0.31614|.	0.133;0.01;0.119;0.006|.	T|T	0.69146|0.69146	-0.5222|-0.5222	10|5	0.59425|.	D|.	0.04|.	-16.7243|-16.7243	17.269|17.269	0.87096|0.87096	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	290;304;281;317|.	B4DPW9;B4DGB4;F8W8D8;P13797|.	.;.;.;PLST_HUMAN|.	S|K	317;304;281;317;272|37	ENSP00000348163:G317S;ENSP00000445105:G304S;ENSP00000289290:G281S;ENSP00000398945:G317S;ENSP00000445339:G272S|.	ENSP00000289290:G281S|.	G|R	+|+	1|2	0|0	PLS3|PLS3	114781033|114781033	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.711000|6.711000	0.74675|0.74675	2.394000|2.394000	0.81467|0.81467	0.600000|0.600000	0.82982|0.82982	GGT|AGG		0.338	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			A	114874777	G	A	114874777	3	1	69	1	0	0	0	0	1	0	0	0	12139	1000	35	3	979	3	PLS3	23	114874777	Missense_Mutation	SNP	G	TCGA-AG-A016-01A-01W-A005-10		114874777	40395783	57	21001										
EPHA10	284656	broad.mit.edu	37	chr1	38227114	38227114	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cgctcctggaatcccgcgctGcagctgcagcggcccacagg	13	17	0	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:38227114G>A	ENST00000373048.4	-	3	812	c.813C>T	c.(811-813)tgC>tgT	p.C271C	EPHA10_ENST00000427468.2_Silent_p.C271C|EPHA10_ENST00000319637.6_Silent_p.C271C	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	271					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)	p.C271C(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATCCCGCGCTGCAGCTGCAGC	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	1											31	34	33					1																	38227114		2164	4194	6358	37999701	SO:0001819	synonymous_variant	284656			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.813C>T	1.37:g.38227114G>A			37999701	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																				0.677	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		A	38227114	G	A	38227114	2	1	70	1	0	0	0	0	0	0	0	1	5179	1311	46	3		3	EPHA10	1	38227114	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		38227114	211023507	1	21002										
RIMKLA	284716	broad.mit.edu	37	chr1	42880166	42880166	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tccccacaggtggcgtgggcGtcaagtgtccgctgacagaa	14	12	1	2	rs536295712	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:42880166G>A	ENST00000431473.3	+	5	826	c.697G>A	c.(697-699)Gtc>Atc	p.V233I		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	233	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.V192I(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TGGCGTGGGCGTCAAGTGTCC	0.517													G|||	2	0.000399361	0	0	5008	,	,		20395	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	1											177	155	162					1																	42880166		2203	4300	6503	42652753	SO:0001583	missense	284716			BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"N-acetylaspartylglutamate synthetase II"		"family with sequence similarity 80, member A"	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.697G>A	1.37:g.42880166G>A	ENSP00000414330:p.Val233Ile		42652753	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	37	CCDS466.2	.	.	.	.	.	.	.	.	.	.	G	14.61	2.586955	0.46110	.	.	ENSG00000177181	ENST00000431473	.	.	.	5.22	5.22	0.72569	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 2 (1);	0.054243	0.64402	D	0.000001	T	0.40619	0.1124	N	0.21142	0.635	0.39778	D	0.972259	P	0.38617	0.64	B	0.36534	0.227	T	0.40683	-0.9550	9	0.38643	T	0.18	-4.5018	16.2864	0.82724	0.0:0.0:1.0:0.0	.	233	Q8IXN7	RIMKA_HUMAN	I	233	.	ENSP00000414330:V233I	V	+	1	0	RIMKLA	42652753	1.000000	0.71417	0.951000	0.38953	0.768000	0.43524	5.605000	0.67634	2.442000	0.82660	0.555000	0.69702	GTC		0.517	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642		A	42880166	G	A	42880166	3	1	70	1	0	0	0	0	1	0	0	0	13402	1145	40	1	715	1	RIMKLA	1	42880166	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	4653052	42880166	206370455	2	21003										
GBP1	2633	broad.mit.edu	37	chr1	89522749	89522749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctgggccaaggccaggactgCgttctccatgcacggcagat	13	13	1	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:89522749C>T	ENST00000370473.4	-	7	1162	c.943G>A	c.(943-945)Gca>Aca	p.A315T	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	315					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.A315T(1)		endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		GCCAGGACTGCGTTCTCCATG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	99	105					1																	89522749		2203	4300	6503	89295337	SO:0001583	missense	2633			BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"guanylate binding protein 1, interferon-inducible, 67kDa"			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.943G>A	1.37:g.89522749C>T	ENSP00000359504:p.Ala315Thr		89295337	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694842	0.48202	.	.	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.02944	4.1	4.8	4.8	0.61643	Guanylate-binding protein, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.05960	0.0155	M	0.90309	3.105	0.34370	D	0.691986	D	0.58268	0.982	P	0.47102	0.537	T	0.11084	-1.0602	10	0.52906	T	0.07	.	15.3412	0.74300	0.0:1.0:0.0:0.0	.	315	P32455	GBP1_HUMAN	T	315;278	ENSP00000359504:A315T	ENSP00000359504:A315T	A	-	1	0	GBP1	89295337	0.245000	0.23899	0.962000	0.40283	0.212000	0.24457	0.662000	0.25038	2.210000	0.71456	0.491000	0.48974	GCA		0.527	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		T	89522749	C	T	89522749	3	4	70	1	0	0	0	0	1	0	0	0	6293	768	27	1	855	1	GBP1	1	89522749	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	46642583	89522749	159727872	3	21004										
NRAS	4893	broad.mit.edu	37	chr1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	catggcactgtactcttcttGtccagctgtatccagtatgt	8	11	2	0	rs121913254		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:115256530G>T	ENST00000369535.4	-	3	434	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61K(595)|p.Q61E(9)|p.Q61L(3)|p.Q61R(2)|p.G60>?(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		TACTCTTCTTGTCCAGCTGTA	0.458	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	610	Substitution - Missense(609)|Complex(1)	skin(372)|haematopoietic_and_lymphoid_tissue(73)|thyroid(55)|NS(29)|large_intestine(28)|soft_tissue(16)|lung(12)|autonomic_ganglia(6)|liver(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|cervix(2)|endometrium(2)|pancreas(2)|meninges(1)|kidney(1)|biliary_tract(1)|stomach(1)|ovary(1)|bone(1)	1											180	156	164					1																	115256530		2203	4300	6503	115058053	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.181C>A	1.37:g.115256530G>T	ENSP00000358548:p.Gln61Lys		115058053	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	33	5.255564	0.95336	.	.	ENSG00000213281	ENST00000369535	D	0.83506	-1.73	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.91845	0.7419	H	0.95850	3.73	0.80722	D	1	P	0.51791	0.948	P	0.54759	0.76	D	0.93711	0.7024	10	0.62326	D	0.03	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	61	P01111	RASN_HUMAN	K	61	ENSP00000358548:Q61K	ENSP00000358548:Q61K	Q	-	1	0	NRAS	115058053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.520000	0.98027	2.624000	0.88883	0.655000	0.94253	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115256530	G	T	115256530	3	4	70	1	0	0	0	0	1	0	0	0	10671	1386	48	2	400	2	NRAS	1	115256530	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	25733781	115256530	133994091	4	21005										
FLG	2312	broad.mit.edu	37	chr1	152280074	152280074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tccagtgctggtcccggtccGtccatgggcggactcagact	13	14	1	1	rs140376327		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:152280074G>A	ENST00000368799.1	-	3	7323	c.7288C>T	c.(7288-7290)Cgg>Tgg	p.R2430W	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2430	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R2430W(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCCGGTCCGTCCATGGGCG	0.592									Ichthyosis				G|||	1	0.000199681	0	0	5008	,	,		20890	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	255	238	244		7288	1.6	0	1	dbSNP_134	244	4,8596	4.3+/-15.6	0,4,4296	no	missense	FLG	NM_002016.1	101	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	benign	2430/4062	152280074	5,13001	2203	4300	6503	150546698	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7288C>T	1.37:g.152280074G>A	ENSP00000357789:p.Arg2430Trp		150546698	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	7.286	0.610080	0.14066	2.27E-4	4.65E-4	ENSG00000143631	ENST00000368799	T	0.01745	4.66	4.55	1.57	0.23409	.	.	.	.	.	T	0.00666	0.0022	L	0.41027	1.25	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.45234	-0.9275	9	0.51188	T	0.08	.	7.4395	0.27174	0.0906:0.3128:0.5966:0.0	.	2430	P20930	FILA_HUMAN	W	2430	ENSP00000357789:R2430W	ENSP00000357789:R2430W	R	-	1	2	FLG	150546698	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.114000	0.10757	0.105000	0.17753	-0.347000	0.07816	CGG		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280074	G	A	152280074	3	1	70	1	0	0	0	0	1	0	0	0	5941	1144	40	1	4901	1	FLG	1	152280074	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	37023544	152280074	96970547	5	21006										
SPRR2E	6704	broad.mit.edu	37	chr1	153066193	153066193	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ggcacacaggaggtggctggCagggctgcttgcactgctgc	17	11	0	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:153066193C>A	ENST00000368751.1	-	2	109	c.35G>T	c.(34-36)tGc>tTc	p.C12F	SPRR2B_ENST00000368752.4_Intron|SPRR2E_ENST00000368750.3_Missense_Mutation_p.C12F			P22531	SPR2E_HUMAN	small proline-rich protein 2E	12					epidermis development (GO:0008544)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	structural molecule activity (GO:0005198)	p.C12S(1)|p.C12F(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTGGCTGGCAGGGCTGCTT	0.572																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											55	58	57					1																	153066193		2202	4292	6494	151332817	SO:0001583	missense	6704			AF333955	CCDS30866.1	1q21-q22	2008-02-05			ENSG00000203785	ENSG00000203785			11265	protein-coding gene	gene with protein product						8325635	Standard	NM_001024209		Approved		uc001fbh.3	P22531	OTTHUMG00000014397	ENST00000368751.1:c.35G>T	1.37:g.153066193C>A	ENSP00000357740:p.Cys12Phe		151332817	Q5T9T4|Q96RM2	Missense_Mutation	SNP	ENST00000368751.1	37	CCDS30866.1	.	.	.	.	.	.	.	.	.	.	C	8.180	0.793582	0.16327	.	.	ENSG00000203785	ENST00000368751;ENST00000368750	T;T	0.50548	0.74;0.74	4.17	4.17	0.49024	.	0.000000	0.38272	N	0.001742	T	0.57154	0.2034	.	.	.	0.31058	N	0.714417	D	0.76494	0.999	D	0.85130	0.997	T	0.59386	-0.7464	9	0.87932	D	0	.	11.9734	0.53075	0.0:1.0:0.0:0.0	.	12	P22531	SPR2E_HUMAN	F	12	ENSP00000357740:C12F;ENSP00000357739:C12F	ENSP00000357739:C12F	C	-	2	0	SPRR2E	151332817	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	1.222000	0.32515	1.865000	0.54081	0.411000	0.27672	TGC		0.572	SPRR2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040054.1			A	153066193	C	A	153066193	3	1	70	1	0	0	0	0	1	0	0	0	15139	710	25	2	187	2	SPRR2E	1	153066193	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	786119	153066193	96184428	6	21007										
C1orf65	164127	broad.mit.edu	37	chr1	223567884	223567884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	accagaggaccaggagagccCgcgccaggagaagctggaga	16	11	0	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:223567884C>T	ENST00000366875.3	+	1	1170	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		356								p.P356L(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CAGGAGAGCCCGCGCCAGGAG	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	1											12	16	15					1																	223567884		2191	4288	6479	221634507	SO:0001583	missense	164127																														ENST00000366875.3:c.1067C>T	1.37:g.223567884C>T	ENSP00000355840:p.Pro356Leu		221634507	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	C	1.799	-0.477609	0.04414	.	.	ENSG00000178395	ENST00000366875	T	0.19532	2.14	4.27	-4.2	0.03823	.	.	.	.	.	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33214	-0.9877	9	0.25106	T	0.35	.	0.6551	0.00833	0.3787:0.2702:0.1723:0.1789	.	356	Q8N715	CA065_HUMAN	L	356	ENSP00000355840:P356L	ENSP00000355840:P356L	P	+	2	0	C1orf65	221634507	0.000000	0.05858	0.001000	0.08648	0.214000	0.24535	-0.961000	0.03845	-0.862000	0.04089	-1.636000	0.00776	CCG		0.687	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223567884	C	T	223567884	3	4	70	1	0	0	0	0	1	0	0	0	2061	652	23	1	1069	1	C1orf65	1	223567884	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	70501691	223567884	25682737	7	21008										
MTR	4548	broad.mit.edu	37	chr1	236998969	236998969	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ttttgcaacttaattgcttcCgagccagacatcgcaaaggt	8	10	0	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr1:236998969C>T	ENST00000366577.5	+	14	1705	c.1311C>T	c.(1309-1311)tcC>tcT	p.S437S	MTR_ENST00000535889.1_Silent_p.S437S	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	437	Pterin-binding. {ECO:0000255|PROSITE- ProRule:PRU00334}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.S437S(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TAATTGCTTCCGAGCCAGACA	0.438																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	1											237	200	213					1																	236998969		2203	4300	6503	235065592	SO:0001819	synonymous_variant	4548			U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.1311C>T	1.37:g.236998969C>T			235065592	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	37	CCDS1614.1																																																																																				0.438	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		T	236998969	C	T	236998969	2	4	70	1	0	0	0	0	0	0	0	1	9988	639	23	1		1	MTR	1	236998969	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	13431085	236998969	12251652	8	21009										
INHBB	3625	broad.mit.edu	37	chr2	121106898	121106898	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	agggtggacctcaagcgcagCggctggcataccttcccact	12	14	1	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr2:121106898C>T	ENST00000295228.3	+	2	718	c.672C>T	c.(670-672)agC>agT	p.S224S		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	224					activin receptor signaling pathway (GO:0032924)|cell differentiation (GO:0030154)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|cellular response to starvation (GO:0009267)|defense response (GO:0006952)|fat cell differentiation (GO:0045444)|growth (GO:0040007)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of hepatocyte growth factor biosynthetic process (GO:0048178)|negative regulation of insulin secretion (GO:0046676)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|response to mechanical stimulus (GO:0009612)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|host cell surface receptor binding (GO:0046789)|protein homodimerization activity (GO:0042803)	p.S224S(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				TCAAGCGCAGCGGCTGGCATA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	2											106	106	106					2																	121106898		2203	4300	6503	120823368	SO:0001819	synonymous_variant	3625				CCDS2132.1	2q14.2	2014-01-30	2007-07-30		ENSG00000163083	ENSG00000163083		"Endogenous ligands"	6067	protein-coding gene	gene with protein product		147390	"inhibin, beta B (activin AB beta polypeptide)"			3345731	Standard	NM_002193		Approved		uc002tmn.2	P09529	OTTHUMG00000131437	ENST00000295228.3:c.672C>T	2.37:g.121106898C>T			120823368	Q53T31|Q8N1D3	Silent	SNP	ENST00000295228.3	37	CCDS2132.1																																																																																				0.637	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1			T	121106898	C	T	121106898	2	4	70	1	0	0	0	0	0	0	0	1	7763	767	27	1		1	INHBB	2	121106898	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		121106898	122092475	9	21010										
WIPF1	7456	broad.mit.edu	37	chr2	175431807	175431807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gaaatactcactccggctttCgtttcttgccagtttgctgg	9	11	2	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr2:175431807C>T	ENST00000392547.2	-	7	1546	c.1447G>A	c.(1447-1449)Gaa>Aaa	p.E483K	AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000467149.1_5'UTR|WIPF1_ENST00000359761.3_Missense_Mutation_p.E483K|WIPF1_ENST00000272746.5_Missense_Mutation_p.E483K|WIPF1_ENST00000392546.2_Missense_Mutation_p.E483K|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409891.1_Missense_Mutation_p.E483K	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	483					actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.E483K(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						CTCCGGCTTTCGTTTCTTGCC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											112	111	111					2																	175431807		2203	4300	6503	175140053	SO:0001583	missense	7456			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1447G>A	2.37:g.175431807C>T	ENSP00000376330:p.Glu483Lys		175140053	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	C	36	5.792639	0.96945	.	.	ENSG00000115935	ENST00000392547;ENST00000392548;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891	T;T;T;T;T	0.44083	1.51;1.51;1.51;1.51;0.93	5.78	5.78	0.91487	.	0.061993	0.64402	D	0.000004	T	0.58047	0.2095	M	0.65975	2.015	0.80722	D	1	D;D;D	0.65815	0.995;0.995;0.991	P;P;P	0.53760	0.734;0.668;0.546	T	0.57946	-0.7723	10	0.52906	T	0.07	.	20.0216	0.97506	0.0:1.0:0.0:0.0	.	483;483;483	O43516-3;O43516-2;O43516	.;.;WIPF1_HUMAN	K	483;339;483;483;483;483	ENSP00000376330:E483K;ENSP00000272746:E483K;ENSP00000352802:E483K;ENSP00000376329:E483K;ENSP00000386431:E483K	ENSP00000272746:E483K	E	-	1	0	WIPF1	175140053	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	6.262000	0.72514	2.735000	0.93741	0.650000	0.86243	GAA		0.473	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		T	175431807	C	T	175431807	3	4	70	1	0	0	0	0	1	0	0	0	17407	893	31	1	72	1	WIPF1	2	175431807	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	54324909	175431807	67767566	10	21011										
CCDC141	285025	broad.mit.edu	37	chr2	179730505	179730505	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cacacccacctcatttatctCgtctctcatggcgcagtact	5	16	4	0	rs150991367	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr2:179730505C>T	ENST00000420890.2	-	17	2830	c.2713G>A	c.(2713-2715)Gag>Aag	p.E905K	CCDC141_ENST00000295723.5_Missense_Mutation_p.E330K	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	905								p.E330K(1)|p.E905K(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCATTTATCTCGTCTCTCATG	0.522													C|||	3	0.000599042	8e-04	0.0014	5008	,	,		19796	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	2											357	321	333					2																	179730505		2203	4300	6503	179438750	SO:0001583	missense	285025			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2713G>A	2.37:g.179730505C>T	ENSP00000395995:p.Glu905Lys		179438750	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	25.6	4.653187	0.88056	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	T;T;T;T	0.57907	0.37;1.3;1.3;1.01	6.07	5.17	0.71159	.	0.264939	0.28921	N	0.013709	T	0.53738	0.1815	L	0.29908	0.895	0.30866	N	0.732976	D	0.65815	0.995	P	0.54499	0.754	T	0.59123	-0.7513	10	0.44086	T	0.13	-7.6071	14.5535	0.68084	0.0:0.9277:0.0:0.0723	.	330	Q6ZP82	CC141_HUMAN	K	905;349;330;905	ENSP00000395995:E905K;ENSP00000344627:E349K;ENSP00000295723:E330K;ENSP00000390190:E905K	ENSP00000295723:E330K	E	-	1	0	CCDC141	179438750	0.996000	0.38824	0.792000	0.32020	0.076000	0.17211	3.760000	0.55235	1.516000	0.48900	0.650000	0.86243	GAG		0.522	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179730505	C	T	179730505	3	4	70	1	0	0	0	0	1	0	0	0	2781	893	31	1	1667	1	CCDC141	2	179730505	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	4298698	179730505	63468868	11	21012										
B3GNT7	93010	broad.mit.edu	37	chr2	232262679	232262679	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	caggggccccaggcctgggaCgtgaccaccactaactgctc	12	16	0	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr2:232262679C>T	ENST00000287590.5	+	2	510	c.249C>T	c.(247-249)gaC>gaT	p.D83D	AC017104.6_ENST00000415129.1_RNA|B3GNT7_ENST00000479618.1_3'UTR	NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	83					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.D83D(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		AGGCCTGGGACGTGACCACCA	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	2											44	50	48					2																	232262679		1952	4133	6085	231970923	SO:0001819	synonymous_variant	93010			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"Beta 3-glycosyltransferases"	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.249C>T	2.37:g.232262679C>T			231970923	B3KWY4|B7WNP0	Silent	SNP	ENST00000287590.5	37	CCDS46540.1																																																																																				0.597	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236		T	232262679	C	T	232262679	2	4	70	1	0	0	0	0	0	0	0	1	1263	535	19	1		1	B3GNT7	2	232262679	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	52532174	232262679	10936694	12	21013										
PDZRN3	23024	broad.mit.edu	37	chr3	73432830	73432830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	catcttcatctcgctcaccgCgtcgtcgtcggtggtcatgc	10	15	5	0	rs150622040		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr3:73432830C>T	ENST00000263666.4	-	10	3001	c.2887G>A	c.(2887-2889)Gcg>Acg	p.A963T	PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Missense_Mutation_p.A685T|PDZRN3_ENST00000462146.2_Missense_Mutation_p.A620T|PDZRN3_ENST00000479530.1_Missense_Mutation_p.A680T|PDZRN3_ENST00000466780.1_Missense_Mutation_p.A620T	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	963					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A963T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCGCTCACCGCGTCGTCGTCG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	THR/ALA	0,4406		0,0,2203	72	70	71		2887	4.3	0.9	3	dbSNP_134	71	1,8599		0,1,4299	no	missense	PDZRN3	NM_015009.1	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	963/1067	73432830	1,13005	2203	4300	6503	73515520	SO:0001583	missense	23024			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2887G>A	3.37:g.73432830C>T	ENSP00000263666:p.Ala963Thr		73515520	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.32|14.32	2.498915|2.498915	0.44455|0.44455	0.0|0.0	1.16E-4|1.16E-4	ENSG00000121440|ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530|ENST00000416926	T;T;T;T;T|.	0.40476|.	1.03;1.03;1.03;1.03;1.03|.	5.21|5.21	4.34|4.34	0.51931|0.51931	.|.	0.105141|.	0.64402|.	D|.	0.000004|.	T|T	0.55862|0.55862	0.1947|0.1947	L|L	0.31371|0.31371	0.925|0.925	0.80722|0.80722	D|D	1|1	D;D;P;D|.	0.89917|.	0.985;1.0;0.871;1.0|.	P;D;B;D|.	0.87578|.	0.798;0.998;0.137;0.995|.	T|T	0.59123|0.59123	-0.7513|-0.7513	10|6	0.14656|0.59425	T|D	0.56|0.04	.|.	13.3663|13.3663	0.60687|0.60687	0.0:0.9231:0.0:0.0769|0.0:0.9231:0.0:0.0769	.|.	685;680;680;963|.	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7|.	.;.;.;PZRN3_HUMAN|.	T|H	963;685;620;620;680|682	ENSP00000263666:A963T;ENSP00000442026:A685T;ENSP00000418168:A620T;ENSP00000418484:A620T;ENSP00000418624:A680T|.	ENSP00000263666:A963T|ENSP00000392657:R682H	A|R	-|-	1|2	0|0	PDZRN3|PDZRN3	73515520|73515520	1.000000|1.000000	0.71417|0.71417	0.949000|0.949000	0.38748|0.38748	0.788000|0.788000	0.44548|0.44548	3.884000|3.884000	0.56175|0.56175	1.190000|1.190000	0.43042|0.43042	0.563000|0.563000	0.77884|0.77884	GCG|CGC		0.667	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73432830	C	T	73432830	3	4	70	1	0	0	0	0	1	0	0	0	11740	768	27	1	317	1	PDZRN3	3	73432830	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		73432830	124589600	13	21014										
SEMA5B	54437	broad.mit.edu	37	chr3	122634670	122634670	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gctcatgttggagctgtcctCgagtgtgctgcaacgttgct	13	10	1	0	rs557492984		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr3:122634670C>T	ENST00000357599.3	-	13	2142	c.1756G>A	c.(1756-1758)Gag>Aag	p.E586K	SEMA5B_ENST00000451055.2_Missense_Mutation_p.E640K|SEMA5B_ENST00000195173.4_Missense_Mutation_p.E586K	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	586					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.E640K(1)|p.E586K(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GAGCTGTCCTCGAGTGTGCTG	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		18020	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	3											138	130	133					3																	122634670		2203	4300	6503	124117360	SO:0001583	missense	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1756G>A	3.37:g.122634670C>T	ENSP00000350215:p.Glu586Lys		124117360	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277445	0.80580	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	4.64	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.37758	0.1015	L	0.55990	1.75	0.48395	D	0.999643	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.75020	0.962;0.978;0.985	T	0.05582	-1.0876	10	0.36615	T	0.2	.	11.8535	0.52425	0.0:0.8233:0.1767:0.0	.	528;586;586	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	K	586;586;528;640;586	ENSP00000350215:E586K;ENSP00000195173:E586K;ENSP00000389588:E640K;ENSP00000377208:E586K	ENSP00000195173:E586K	E	-	1	0	SEMA5B	124117360	1.000000	0.71417	0.805000	0.32314	0.992000	0.81027	5.197000	0.65141	1.147000	0.42369	0.561000	0.74099	GAG		0.607	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		T	122634670	C	T	122634670	3	4	70	1	0	0	0	0	1	0	0	0	14075	893	31	1	1743	1	SEMA5B	3	122634670	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	49201840	122634670	75387760	14	21015										
EPHB1	2047	broad.mit.edu	37	chr3	134884859	134884859	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctgcccctgattgctggctcGgcagcggccggggtcgtgtt	16	13	0	1	rs375267802	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr3:134884859G>A	ENST00000398015.3	+	8	2005	c.1635G>A	c.(1633-1635)tcG>tcA	p.S545S	EPHB1_ENST00000493838.1_Silent_p.S106S	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	545					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.S545S(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						TTGCTGGCTCGGCAGCGGCCG	0.552													G|||	2	0.000399361	0.0015	0	5008	,	,		16972	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	3						G		4,4234		0,4,2115	120	140	133		1635	-11.2	0.8	3		133	0,8478		0,0,4239	no	coding-synonymous	EPHB1	NM_004441.4		0,4,6354	AA,AG,GG		0.0,0.0944,0.0315		545/985	134884859	4,12712	2119	4239	6358	136367549	SO:0001819	synonymous_variant	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1635G>A	3.37:g.134884859G>A			136367549	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																				0.552	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134884859	G	A	134884859	2	1	70	1	0	0	0	0	0	0	0	1	5187	1103	39	1		1	EPHB1	3	134884859	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	12250189	134884859	63137571	15	21016										
PYDC2	152138	broad.mit.edu	37	chr3	191179140	191179140	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gaaatcttcaccagccactcCtgcagctactgggcagggat	10	13	2	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr3:191179140C>T	ENST00000518817.1	+	1	189	c.189C>T	c.(187-189)tcC>tcT	p.S63S		NM_001083308.1	NP_001076777.1	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	63	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S63S(1)		breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10						CCAGCCACTCCTGCAGCTACT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											74	82	79					3																	191179140		2175	4292	6467	192661834	SO:0001819	synonymous_variant	152138					3q28	2008-07-29				ENSG00000253548			33512	protein-coding gene	gene with protein product		615701				17178784	Standard	NM_001083308		Approved	POP2	uc011bso.2	Q56P42		ENST00000518817.1:c.189C>T	3.37:g.191179140C>T			192661834		Silent	SNP	ENST00000518817.1	37																																																																																					0.527	PYDC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343231.2	NM_001083308		T	191179140	C	T	191179140	2	4	70	1	0	0	0	0	0	0	0	1	12896	668	24	3		3	PYDC2	3	191179140	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	56294281	191179140	6843290	16	21017										
ATP13A5	344905	broad.mit.edu	37	chr3	193080216	193080216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	acccaatccaaatgtctgatGgatgtcagagcaggaattgc	10	9	2	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr3:193080216G>A	ENST00000342358.4	-	5	607	c.490C>T	c.(490-492)Cat>Tat	p.H164Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	164						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.H164Y(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		AATGTCTGATGGATGTCAGAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	3											149	139	143					3																	193080216		2203	4300	6503	194562910	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.490C>T	3.37:g.193080216G>A	ENSP00000341942:p.His164Tyr		194562910	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.661983	0.29515	.	.	ENSG00000187527	ENST00000342358	T	0.79033	-1.23	5.42	4.55	0.56014	ATPase, P-type cation-transporter, N-terminal (2);	0.163240	0.43416	N	0.000573	T	0.73799	0.3633	L	0.53249	1.67	0.40721	D	0.982664	B	0.21071	0.051	B	0.33799	0.17	T	0.66740	-0.5847	10	0.13108	T	0.6	-8.4755	12.4327	0.55583	0.0822:0.0:0.9178:0.0	.	164	Q4VNC0	AT135_HUMAN	Y	164	ENSP00000341942:H164Y	ENSP00000341942:H164Y	H	-	1	0	ATP13A5	194562910	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	4.415000	0.59809	1.431000	0.47355	0.655000	0.94253	CAT		0.423	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193080216	G	A	193080216	3	1	70	1	0	0	0	0	1	0	0	0	1128	1348	47	3	3268	3	ATP13A5	3	193080216	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	1901076	193080216	4942214	17	21018										
PTPN13	5783	broad.mit.edu	37	chr4	87726444	87726444	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gcttacagaatcttcaagaaTtaaaacctttggatcagtgt	7	7	3	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr4:87726444T>C	ENST00000411767.2	+	44	6730	c.6667T>C	c.(6667-6669)Tta>Cta	p.L2223L	PTPN13_ENST00000511467.1_Silent_p.L2228L|PTPN13_ENST00000316707.6_Silent_p.L2032L|PTPN13_ENST00000427191.2_Silent_p.L2204L|PTPN13_ENST00000436978.1_Silent_p.L2228L			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2223	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.L2228L(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TCTTCAAGAATTAAAACCTTT	0.318																																																1	Substitution - coding silent(1)	large_intestine(1)	4											66	65	65					4																	87726444		1800	4060	5860	87945468	SO:0001819	synonymous_variant	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6667T>C	4.37:g.87726444T>C			87945468	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																				0.318	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87726444	T	C	87726444	2	2	70	1	0	0	0	0	0	0	0	1	12817	1490	52	4		4	PTPN13	4	87726444	Silent	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09		87726444	103427832	18	21019										
PCDH10	57575	broad.mit.edu	37	chr4	134072724	134072724	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgtatgtgactgaaaacaacGtgcctggcgcctacatctac	9	11	1	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr4:134072724G>A	ENST00000264360.5	+	1	2255	c.1429G>A	c.(1429-1431)Gtg>Atg	p.V477M	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	477	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V477M(2)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		TGAAAACAACGTGCCTGGCGC	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	4											81	78	79					4																	134072724		2203	4300	6503	134292174	SO:0001583	missense	57575			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1429G>A	4.37:g.134072724G>A	ENSP00000264360:p.Val477Met		134292174	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.338613	0.60963	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.52983	0.64	4.71	4.71	0.59529	Cadherin (3);Cadherin-like (1);	0.000000	0.40818	N	0.001004	T	0.65396	0.2687	L	0.59436	1.845	0.54753	D	0.999987	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.931	T	0.67019	-0.5776	10	0.54805	T	0.06	.	16.6083	0.84837	0.0:0.0:1.0:0.0	.	477;477	Q9P2E7;Q96SF0	PCD10_HUMAN;.	M	477	ENSP00000264360:V477M	ENSP00000264360:V477M	V	+	1	0	PCDH10	134292174	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.821000	0.86641	2.436000	0.82500	0.655000	0.94253	GTG		0.597	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		A	134072724	G	A	134072724	3	1	70	1	0	0	0	0	1	0	0	0	11538	1145	40	1	1431	1	PCDH10	4	134072724	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	46346280	134072724	57081552	19	21020										
VEGFC	7424	broad.mit.edu	37	chr4	177649044	177649044	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gtttaaagaaggtgtttgtcGcgactccaaactccttcccc	8	12	0	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr4:177649044G>A	ENST00000280193.2	-	3	855	c.440C>T	c.(439-441)gCg>gTg	p.A147V	VEGFC_ENST00000507638.1_5'UTR	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	147					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.A147V(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		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)		GGTGTTTGTCGCGACTCCAAA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	4											116	118	118					4																	177649044		2005	4176	6181	177886038	SO:0001583	missense	7424			BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.440C>T	4.37:g.177649044G>A	ENSP00000280193:p.Ala147Val		177886038	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211846	0.58452	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.72	5.72	0.89469	Platelet-derived growth factor (PDGF) (3);	0.116055	0.64402	D	0.000015	T	0.40347	0.1113	L	0.33485	1.01	0.51482	D	0.999926	P	0.45044	0.849	B	0.30179	0.112	T	0.39375	-0.9617	9	0.40728	T	0.16	-16.2654	20.2406	0.98372	0.0:0.0:1.0:0.0	.	147	P49767	VEGFC_HUMAN	V	147	.	ENSP00000280193:A147V	A	-	2	0	VEGFC	177886038	1.000000	0.71417	0.982000	0.44146	0.361000	0.29550	7.273000	0.78527	2.857000	0.98124	0.650000	0.86243	GCG		0.493	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		A	177649044	G	A	177649044	3	1	70	1	0	0	0	0	1	0	0	0	17192	1087	38	1	842	1	VEGFC	4	177649044	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	43576320	177649044	13505232	20	21021										
TUBB4Q	56604	broad.mit.edu	37	chr4	190904398	190904398	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	atgcagaaggtctcatctgcGttttctatgagctggtggac	12	8	3	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr4:190904398G>A								FRG1 (20039 upstream) : RNA5SP174 (31894 downstream)																							TCTCATCTGCGTTTTCTATGA	0.512																																																0			4											20	32	29					4																	190904398		1806	3882	5688	191141392	SO:0001628	intergenic_variant	56604																															4.37:g.190904398G>A			191141392		Silent	SNP		37																																																																																				0	0.512									A	190904398	G	A	190904398	1	1	70	0	1	0	0	0	0	0	0	0	16799	1136	40	1		1	TUBB4Q	4	190904398	IGR	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	13255354	190904398	249878	21	21022										
C5orf49	134121	broad.mit.edu	37	chr5	7832094	7832094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctcaatgggctgattgatgcGcttcccatagacagaagacg	11	10	1	5	rs187132919	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:7832094G>A	ENST00000399810.2	-	3	781	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	C5orf49_ENST00000509627.1_Missense_Mutation_p.R103C	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	105								p.R105C(1)		large_intestine(3)|lung(5)|skin(1)	9						TGATTGATGCGCTTCCCATAG	0.542													G|||	2	0.000399361	0	0	5008	,	,		19571	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											156	162	160					5																	7832094		2036	4183	6219	7885094	SO:0001583	missense	134121				CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.313C>T	5.37:g.7832094G>A	ENSP00000382708:p.Arg105Cys		7885094		Missense_Mutation	SNP	ENST00000399810.2	37	CCDS43300.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	15.82	2.945505	0.53079	.	.	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.32753	1.44;1.44	4.72	3.85	0.44370	.	.	.	.	.	T	0.30293	0.0760	M	0.61703	1.905	0.50039	D	0.999847	B	0.25521	0.128	B	0.17722	0.019	T	0.13710	-1.0499	9	0.72032	D	0.01	-32.1385	10.3946	0.44192	0.0945:0.0:0.9055:0.0	.	105	A4QMS7	CE049_HUMAN	C	105;103	ENSP00000382708:R105C;ENSP00000426019:R103C	ENSP00000382708:R105C	R	-	1	0	C5orf49	7885094	0.998000	0.40836	0.994000	0.49952	0.457000	0.32468	3.291000	0.51764	1.117000	0.41842	0.555000	0.69702	CGC		0.542	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584		A	7832094	G	A	7832094	3	1	70	1	0	0	0	0	1	0	0	0	2313	1087	38	1	134	1	C5orf49	5	7832094	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		7832094	173083166	22	21023										
PRDM9	56979	broad.mit.edu	37	chr5	23527040	23527040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	atgtctgcagggagtgtgggCggggctttagccggcagtca	18	8	2	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:23527040C>T	ENST00000296682.3	+	11	2025	c.1843C>T	c.(1843-1845)Cgg>Tgg	p.R615W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	615					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R615W(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGAGTGTGGGCGGGGCTTTAG	0.627										HNSCC(3;0.000094)																																						1	Substitution - Missense(1)	large_intestine(1)	5											26	28	28					5																	23527040		1782	3781	5563	23562797	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1843C>T	5.37:g.23527040C>T	ENSP00000296682:p.Arg615Trp		23562797	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	9.892	1.204407	0.22205	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.36157	1.27	1.89	0.993	0.19825	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.440100	0.05127	N	0.491844	T	0.60314	0.2259	M	0.79926	2.475	0.35884	D	0.829131	D	0.89917	1.0	D	0.87578	0.998	T	0.53858	-0.8379	10	0.59425	D	0.04	-6.2673	6.3724	0.21489	0.5272:0.4728:0.0:0.0	.	615	Q9NQV7	PRDM9_HUMAN	W	615;381	ENSP00000296682:R615W	ENSP00000253473:R381W	R	+	1	2	PRDM9	23562797	0.624000	0.27102	0.974000	0.42286	0.229000	0.25112	1.799000	0.38824	0.343000	0.23821	-0.373000	0.07131	CGG		0.627	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23527040	C	T	23527040	3	4	70	1	0	0	0	0	1	0	0	0	12497	759	27	1	1881	1	PRDM9	5	23527040	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	15694946	23527040	157388220	23	21024										
OSMR	9180	broad.mit.edu	37	chr5	38924610	38924610	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	aagattactctactgaatctCaacctggttttatacaaggg	7	8	2	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:38924610C>T	ENST00000274276.3	+	14	2359	c.1957C>T	c.(1957-1959)Caa>Taa	p.Q653*		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	653	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)	p.Q653*(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TACTGAATCTCAACCTGGTTT	0.448																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											133	120	124					5																	38924610		2203	4300	6503	38960367	SO:0001587	stop_gained	9180			U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1957C>T	5.37:g.38924610C>T	ENSP00000274276:p.Gln653*		38960367	Q6P4E8|Q96QJ6	Nonsense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	.	.	.	.	.	.	.	.	.	.	C	41	8.875500	0.98986	.	.	ENSG00000145623	ENST00000274276	.	.	.	5.97	5.97	0.96955	.	0.057992	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.1328	0.86730	0.0:1.0:0.0:0.0	.	.	.	.	X	653	.	ENSP00000274276:Q653X	Q	+	1	0	OSMR	38960367	0.916000	0.31088	0.414000	0.26521	0.575000	0.36095	3.790000	0.55461	2.835000	0.97688	0.591000	0.81541	CAA		0.448	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		T	38924610	C	T	38924610	4	4	70	1	0	0	0	0	0	1	0	0	11323	827	29	3	2045	3	OSMR	5	38924610	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	15397570	38924610	141990650	24	21025										
CKMT2	1160	broad.mit.edu	37	chr5	80559399	80559399	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gccgcggtcgcagatgtgtaCgacatttccaacatagatag	11	10	0	2	rs150638385		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:80559399C>T	ENST00000424301.2	+	10	1342	c.1104C>T	c.(1102-1104)taC>taT	p.Y368Y	CKMT2-AS1_ENST00000505295.1_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Silent_p.Y368Y|CKMT2_ENST00000254035.4_Silent_p.Y368Y|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000511495.1_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	368	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.Y368Y(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	CAGATGTGTACGACATTTCCA	0.458													C|||	1	0.000199681	0	0	5008	,	,		12934	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C	,,	3,4403	6.2+/-15.9	0,3,2200	127	117	120		1104,1104,1104	-10.8	0.3	5	dbSNP_134	120	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CKMT2	NM_001099735.1,NM_001099736.1,NM_001825.2	,,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,,	368/420,368/420,368/420	80559399	3,13003	2203	4300	6503	80595155	SO:0001819	synonymous_variant	1160				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.1104C>T	5.37:g.80559399C>T			80595155	Q6ICS8|Q8N1E1	Silent	SNP	ENST00000424301.2	37	CCDS4053.1																																																																																				0.458	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		T	80559399	C	T	80559399	2	4	70	1	0	0	0	0	0	0	0	1	3457	547	19	1		1	CKMT2	5	80559399	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	41634789	80559399	100355861	25	21026										
APC	324	broad.mit.edu	37	chr5	112173797	112173798	+	Frame_Shift_Ins	INS	-	-	C													0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	agtgttacccagctcctcttINScatcaagaggaagcttagat							TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:112173797_112173798insC	ENST00000457016.1	+	16	2886_2887	c.2506_2507insC	c.(2506-2508)tcafs	p.S836fs	APC_ENST00000257430.4_Frame_Shift_Ins_p.S836fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Ins_p.S836fs			P25054	APC_HUMAN	adenomatous polyposis coli	836	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.S837fs*7(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCTCCTCTTCATCAAGAGGA	0.401		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Insertion - Frameshift(1)	large_intestine(1)|skin(1)	5	GRCh37	CM064976	APC	M																																				112201697	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2507dupC	5.37:g.112173798_112173798dupC	ENSP00000413133:p.Ser836fs		112201696	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.401	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112173798	-	C	112173797	7	5	70	1	0	1	1	0	0	0	0	0	763	1783	62	0	2564	0	APC	5	112173797	Frame_Shift_Ins	INS	-	TCGA-AG-A01L-01A-01W-A00K-09	31614398	112173797	68741463	26	21027										
HARS2	23438	broad.mit.edu	37	chr5	140075196	140075196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cccaaccatagtccaaggccGttatagggagttctgccagt	10	12	1	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:140075196G>A	ENST00000230771.3	+	5	726	c.503G>A	c.(502-504)cGt>cAt	p.R168H	HARS2_ENST00000435019.2_Missense_Mutation_p.R128H|HARS2_ENST00000508522.1_Missense_Mutation_p.R143H|HARS2_ENST00000437649.2_Intron|HARS2_ENST00000448069.2_Intron|HARS2_ENST00000432671.2_Intron	NM_012208.2	NP_036340.1	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2, mitochondrial	168					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)|poly(A) RNA binding (GO:0044822)	p.R168H(2)		NS(1)|endometrium(3)|large_intestine(5)|lung(10)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCAAGGCCGTTATAGGGAG	0.488																																																2	Substitution - Missense(2)	large_intestine(2)	5											141	136	138					5																	140075196		2203	4300	6503	140055380	SO:0001583	missense	23438			U18937	CCDS4238.1, CCDS64267.1	5q31.3	2012-07-20	2012-07-20	2007-02-23	ENSG00000112855	ENSG00000112855	6.1.1.21	"Aminoacyl tRNA synthetases / Class II"	4817	protein-coding gene	gene with protein product	"histidine tRNA ligase 2, mitochondrial (putative)"	600783	"histidyl-tRNA synthetase-like"	HARSL		7755634, 21464306	Standard	NM_012208		Approved	HO3, HARSR	uc003lgx.3	P49590	OTTHUMG00000129500	ENST00000230771.3:c.503G>A	5.37:g.140075196G>A	ENSP00000230771:p.Arg168His		140055380	B4DDY8	Missense_Mutation	SNP	ENST00000230771.3	37	CCDS4238.1	.	.	.	.	.	.	.	.	.	.	g	28.7	4.946222	0.92593	.	.	ENSG00000112855	ENST00000230771;ENST00000509299;ENST00000435019;ENST00000508522;ENST00000427675	T;D;T;T	0.96830	-0.48;-4.14;-0.48;-0.48	6.17	6.17	0.99709	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	H	0.98996	4.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.995;0.995;0.995	D	0.98667	1.0686	10	0.87932	D	0	-9.1108	20.8794	0.99867	0.0:0.0:1.0:0.0	.	54;143;168;168	E9PD60;B4DDY8;B2R7G6;P49590	.;.;.;SYHM_HUMAN	H	168;174;128;143;40	ENSP00000230771:R168H;ENSP00000425695:R174H;ENSP00000412887:R128H;ENSP00000423616:R143H	ENSP00000230771:R168H	R	+	2	0	HARS2	140055380	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	CGT		0.488	HARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251670.2	NM_012208		A	140075196	G	A	140075196	3	1	70	1	0	0	0	0	1	0	0	0	6981	1145	40	1	521	1	HARS2	5	140075196	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	27901399	140075196	40840064	27	21028										
PCDHA11	56138	broad.mit.edu	37	chr5	140250915	140250915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ccacgctggtgtgctcccgcGcggtggggagctggtcatac	16	13	1	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:140250915G>A	ENST00000398640.2	+	1	2227	c.2227G>A	c.(2227-2229)Gcg>Acg	p.A743T	PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	743	6 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A743T(2)		breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCTCCCGCGCGGTGGGGAG	0.682																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	5											29	31	31					5																	140250915		2203	4300	6503	140231099	SO:0001583	missense	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2227G>A	5.37:g.140250915G>A	ENSP00000381636:p.Ala743Thr		140231099	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627210	0.28978	.	.	ENSG00000249158	ENST00000398640	T	0.15139	2.45	4.6	4.6	0.57074	.	.	.	.	.	T	0.24851	0.0603	M	0.87971	2.92	0.23906	N	0.9965	B;B	0.31413	0.322;0.035	B;B	0.24394	0.053;0.033	T	0.15665	-1.0429	9	0.46703	T	0.11	.	10.6973	0.45907	0.0888:0.0:0.9112:0.0	.	743;743	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	T	743	ENSP00000381636:A743T	ENSP00000381636:A743T	A	+	1	0	PCDHA11	140231099	1.000000	0.71417	0.988000	0.46212	0.148000	0.21650	2.756000	0.47549	2.093000	0.63338	0.655000	0.94253	GCG		0.682	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140250915	G	A	140250915	3	1	70	1	0	0	0	0	1	0	0	0	11552	1087	38	1	2229	1	PCDHA11	5	140250915	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	175719	140250915	40664345	28	21029										
PCDHGB2	56103	broad.mit.edu	37	chr5	140740387	140740387	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	aaagtggcacgacccaaatcCgaatcaaagtcacggatgcc	9	12	2	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr5:140740387C>T	ENST00000522605.1	+	1	685	c.685C>T	c.(685-687)Cga>Tga	p.R229*	PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	229	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R229*(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACCCAAATCCGAATCAAAGT	0.542																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											84	85	84					5																	140740387		2037	4192	6229	140720571	SO:0001587	stop_gained	56103			AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.685C>T	5.37:g.140740387C>T	ENSP00000429018:p.Arg229*		140720571	Q3MIJ3|Q9UN65	Nonsense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740719	0.30865	.	.	ENSG00000253910	ENST00000522605	.	.	.	5.54	1.47	0.22746	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.2725	0.15632	0.4354:0.3857:0.1084:0.0705	.	.	.	.	X	229	.	ENSP00000429018:R229X	R	+	1	2	PCDHGB2	140720571	0.000000	0.05858	0.863000	0.33907	0.001000	0.01503	-2.801000	0.00761	0.776000	0.33473	-1.014000	0.02459	CGA		0.542	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		T	140740387	C	T	140740387	4	4	70	1	0	0	0	0	0	1	0	0	11594	644	23	1	687	1	PCDHGB2	5	140740387	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	489472	140740387	40174873	29	21030										
HIST1H4D	8360	broad.mit.edu	37	chr6	26189065	26189065	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	acgtccatggctgtgactgtCttgcgtttggcgtgttccgt	13	10	1	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr6:26189065C>T	ENST00000340756.2	-	1	239	c.240G>A	c.(238-240)aaG>aaA	p.K80K		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	80					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)	p.K80K(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)	8		all_hematologic(11;0.196)				CTGTGACTGTCTTGCGTTTGG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	6											140	120	127					6																	26189065		2203	4300	6503	26297044	SO:0001819	synonymous_variant	8360			X60482	CCDS4589.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000188987	ENSG00000277157		"Histones / Replication-dependent"	4782	protein-coding gene	gene with protein product		602823	"H4 histone family, member B", "histone 1, H4d"	H4FB		9119399, 12408966	Standard	NM_003539		Approved	H4/b	uc003ngu.3	P62805	OTTHUMG00000014423	ENST00000340756.2:c.240G>A	6.37:g.26189065C>T			26297044	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000340756.2	37	CCDS4589.1																																																																																				0.527	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539		T	26189065	C	T	26189065	2	4	70	1	0	0	0	0	0	0	0	1	7189	912	32	3		3	HIST1H4D	6	26189065	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		26189065	144926002	30	21031										
C6orf27	80737	broad.mit.edu	37	chr6	31735458	31735458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ggatccggactgtgatcttcTggagcagcccatccacgctg	12	13	2	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr6:31735458T>C	ENST00000375688.4	-	11	1777	c.1577A>G	c.(1576-1578)cAg>cGg	p.Q526R	VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000447450.1_Missense_Mutation_p.Q526R|SAPCD1-AS1_ENST00000419679.1_RNA|VWA7_ENST00000375686.3_Missense_Mutation_p.Q526R			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	526						extracellular region (GO:0005576)		p.Q526R(1)									TGTGATCTTCTGGAGCAGCCC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											118	118	118					6																	31735458		2203	4300	6503	31843437	SO:0001583	missense	80737				CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1577A>G	6.37:g.31735458T>C	ENSP00000364840:p.Gln526Arg		31843437	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	0.136	-1.107666	0.01813	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.29142	2.81;2.59;1.58	4.95	-2.9	0.05648	.	1.091170	0.06950	N	0.814491	T	0.07234	0.0183	L	0.39898	1.24	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37596	-0.9699	10	0.16896	T	0.51	-0.7677	7.725	0.28755	0.0:0.5182:0.1542:0.3276	.	526	Q9Y334	G7C_HUMAN	R	526	ENSP00000364840:Q526R;ENSP00000364838:Q526R;ENSP00000390554:Q526R	ENSP00000364838:Q526R	Q	-	2	0	C6orf27	31843437	0.007000	0.16637	0.033000	0.17914	0.349000	0.29174	-0.450000	0.06803	-0.714000	0.04975	-0.379000	0.06801	CAG		0.567	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31735458	T	C	31735458	3	2	70	1	0	0	0	0	1	0	0	0	2368	1580	55	4	1125	4	C6orf27	6	31735458	Missense_Mutation	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09	5546393	31735458	139379609	31	21032										
PRPH2	5961	broad.mit.edu	37	chr6	42689824	42689824	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ttggctgggtccagggcgtcGtagcagatcttcccagccag	14	12	1	1	rs61755775		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr6:42689824G>A	ENST00000230381.5	-	1	488	c.249C>T	c.(247-249)taC>taT	p.Y83Y		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	83					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.Y83Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			CCAGGGCGTCGTAGCAGATCT	0.517													G|||	1	0.000199681	0	0	5008	,	,		18497	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						G		0,4406		0,0,2203	89	72	78	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	249	-9	0	6	dbSNP_129	78	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	PRPH2	NM_000322.4		0,7,6496	AA,AG,GG		0.0814,0.0,0.0538		83/347	42689824	7,12999	2203	4300	6503	42797802	SO:0001819	synonymous_variant	5961				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.249C>T	6.37:g.42689824G>A			42797802	Q5TFH5|Q6DK65	Silent	SNP	ENST00000230381.5	37	CCDS4871.1																																																																																				0.517	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		A	42689824	G	A	42689824	2	1	70	1	0	0	0	0	0	0	0	1	12611	1140	40	1		1	PRPH2	6	42689824	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	10954366	42689824	128425243	32	21033										
GABRR1	2569	broad.mit.edu	37	chr6	89910948	89910948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgttctgactttgtcagaggCgatttggtgatgtcaggact	13	6	3	3	rs371490411		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr6:89910948C>T	ENST00000454853.2	-	3	320	c.210G>A	c.(208-210)tcG>tcA	p.S70S	GABRR1_ENST00000369451.3_5'UTR|GABRR1_ENST00000435811.1_Silent_p.S53S	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	70					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S64S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TTGTCAGAGGCGATTTGGTGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		1,4405	2.1+/-5.4	0,1,2202	240	204	216		210	-11.5	0.4	6		216	0,8600		0,0,4300	no	coding-synonymous	GABRR1	NM_002042.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		70/480	89910948	1,13005	2203	4300	6503	89967667	SO:0001819	synonymous_variant	2569				CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.210G>A	6.37:g.89910948C>T			89967667	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Silent	SNP	ENST00000454853.2	37	CCDS5019.2																																																																																				0.478	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			T	89910948	C	T	89910948	2	4	70	1	0	0	0	0	0	0	0	1	6195	755	27	1		1	GABRR1	6	89910948	Silent	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	47221124	89910948	81204119	33	21034										
SCML4	256380	broad.mit.edu	37	chr6	108042008	108042008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cagaagacatggggctagtgCggggaccaccagcggtggca	17	10	0	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr6:108042008C>T	ENST00000369020.3	-	6	1117	c.872G>A	c.(871-873)cGc>cAc	p.R291H	SCML4_ENST00000369021.3_Missense_Mutation_p.R262H|SCML4_ENST00000369022.2_Missense_Mutation_p.R233H|SCML4_ENST00000479803.1_5'UTR|SCML4_ENST00000369025.2_Missense_Mutation_p.R49H	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	291	SAM.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R262H(1)		endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		GGGGCTAGTGCGGGGACCACC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	6											48	55	53					6																	108042008		2203	4300	6503	108148701	SO:0001583	missense	256380				CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.872G>A	6.37:g.108042008C>T	ENSP00000358016:p.Arg291His		108148701	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	C	9.253	1.041281	0.19669	.	.	ENSG00000146285	ENST00000369022;ENST00000369025;ENST00000369020;ENST00000369021	T;T;T	0.52057	0.88;0.87;0.68	5.19	2.47	0.30058	.	0.622280	0.17209	N	0.182794	T	0.49029	0.1533	M	0.70275	2.135	0.09310	N	1	B;P;D	0.76494	0.004;0.602;0.999	B;B;D	0.67382	0.003;0.051;0.951	T	0.40887	-0.9539	10	0.48119	T	0.1	.	10.5252	0.44943	0.0:0.7892:0.0:0.2108	.	291;291;262	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	H	233;49;291;262	ENSP00000358018:R233H;ENSP00000358016:R291H;ENSP00000358017:R262H	ENSP00000358016:R291H	R	-	2	0	SCML4	108148701	0.589000	0.26807	0.001000	0.08648	0.127000	0.20565	0.944000	0.29043	0.355000	0.24131	0.650000	0.86243	CGC		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		T	108042008	C	T	108042008	3	4	70	1	0	0	0	0	1	0	0	0	13948	768	27	1	384	1	SCML4	6	108042008	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	18131060	108042008	63073059	34	21035										
CHST12	55501	broad.mit.edu	37	chr7	2472319	2472319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctgtggctggtgctggggtcGgtgttcatgatcctgctgat	16	8	1	2	rs577438892	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr7:2472319G>A	ENST00000258711.6	+	2	180	c.45G>A	c.(43-45)tcG>tcA	p.S15S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	15					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)	p.S15S(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		TGCTGGGGTCGGTGTTCATGA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	7											52	44	46					7																	2472319		2203	4300	6503	2438845	SO:0001819	synonymous_variant	55501			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.45G>A	7.37:g.2472319G>A			2438845	A4D1Z9|Q502W3|Q9NXY7	Silent	SNP	ENST00000258711.6	37	CCDS5333.1																																																																																				0.672	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		A	2472319	G	A	2472319	2	1	70	1	0	0	0	0	0	0	0	1	3406	1103	39	1		1	CHST12	7	2472319	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		2472319	156666344	35	21036										
MAGI2	9863	broad.mit.edu	37	chr7	77797326	77797326	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gacatagcggtgggttttgcCggctactggaatcccatcaa	12	10	1	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr7:77797326C>T	ENST00000354212.4	-	15	2756	c.2503G>A	c.(2503-2505)Ggc>Agc	p.G835S	MAGI2_ENST00000522391.1_Missense_Mutation_p.G835S|MAGI2_ENST00000419488.1_Missense_Mutation_p.G821S	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	835	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.G835S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGGGTTTTGCCGGCTACTGGA	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	7											164	148	153					7																	77797326		2203	4300	6503	77635262	SO:0001583	missense	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2503G>A	7.37:g.77797326C>T	ENSP00000346151:p.Gly835Ser		77635262	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	36	5.925043	0.97110	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.54071	0.59;0.74;0.74	5.96	5.96	0.96718	PDZ/DHR/GLGF (4);	0.000000	0.37261	U	0.002175	T	0.66597	0.2805	L	0.61036	1.89	0.80722	D	1	P;D;P	0.62365	0.691;0.991;0.881	B;P;B	0.54965	0.227;0.765;0.227	T	0.67348	-0.5693	10	0.66056	D	0.02	.	19.4074	0.94653	0.0:1.0:0.0:0.0	.	835;821;835	E7EWI0;Q86UL8-2;Q86UL8	.;.;MAGI2_HUMAN	S	821;835;835;835	ENSP00000405766:G821S;ENSP00000346151:G835S;ENSP00000428389:G835S	ENSP00000346151:G835S	G	-	1	0	MAGI2	77635262	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.818000	0.86416	2.831000	0.97527	0.650000	0.86243	GGC		0.537	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		T	77797326	C	T	77797326	3	4	70	1	0	0	0	0	1	0	0	0	9221	652	23	1	1896	1	MAGI2	7	77797326	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	75325007	77797326	81341337	36	21037										
GIMAP6	474344	broad.mit.edu	37	chr7	150325442	150325442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cccagcccactctcggctccGtctctgggaggtcttggtca	11	16	4	0	rs149376163		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr7:150325442G>A	ENST00000328902.5	-	3	460	c.244C>T	c.(244-246)Cgg>Tgg	p.R82W	GIMAP6_ENST00000493969.1_Intron	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	82	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)	p.R82W(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTCGGCTCCGTCTCTGGGAG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	TRP/ARG	0,4406		0,0,2203	136	140	139		244	3.4	0	7	dbSNP_134	139	1,8599	1.2+/-3.3	0,1,4299	no	missense	GIMAP6	NM_024711.5	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	82/293	150325442	1,13005	2203	4300	6503	149956375	SO:0001583	missense	474344			AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.244C>T	7.37:g.150325442G>A	ENSP00000330374:p.Arg82Trp		149956375	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572995	0.65765	0.0	1.16E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.34472	1.36	4.29	3.41	0.39046	AIG1 (1);	0.554035	0.18417	N	0.141867	T	0.48554	0.1506	L	0.54323	1.7	0.48511	D	0.999667	P	0.50272	0.933	P	0.58970	0.849	T	0.46911	-0.9157	10	0.72032	D	0.01	.	10.1908	0.43026	0.0:0.7973:0.2027:0.0	.	82	Q6P9H5	GIMA6_HUMAN	W	82;143	ENSP00000330374:R82W	ENSP00000330374:R82W	R	-	1	2	GIMAP6	149956375	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.246000	0.18160	1.048000	0.40298	-0.228000	0.12330	CGG		0.587	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		A	150325442	G	A	150325442	3	1	70	1	0	0	0	0	1	0	0	0	6403	1144	40	1	638	1	GIMAP6	7	150325442	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	72528116	150325442	8813221	37	21038										
CSMD1	64478	broad.mit.edu	37	chr8	3019722	3019722	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gcactggaaggagagcacgtCgttcaccatgtaccgatctc	11	12	2	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:3019722C>T	ENST00000520002.1	-	39	6361	c.5806G>A	c.(5806-5808)Gac>Aac	p.D1936N	CSMD1_ENST00000602557.1_Missense_Mutation_p.D1936N|CSMD1_ENST00000539096.1_Missense_Mutation_p.D1935N|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000537824.1_Missense_Mutation_p.D1935N|CSMD1_ENST00000602723.1_Missense_Mutation_p.D1936N|CSMD1_ENST00000400186.3_Missense_Mutation_p.D1936N|CSMD1_ENST00000542608.1_Missense_Mutation_p.D1935N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1936	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.D1664N(1)|p.D1935N(1)		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)		GAGAGCACGTCGTTCACCATG	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	8											89	93	92					8																	3019722		1977	4165	6142	3007129	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5806G>A	8.37:g.3019722C>T	ENSP00000430733:p.Asp1936Asn		3007129	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.143256|4.143256	0.77888|0.77888	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2;-0.2|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Complement control module (2);Sushi/SCR/CCP (3);|.	0.063724|.	0.64402|.	D|.	0.000008|.	T|T	0.69205|0.69205	0.3085|0.3085	L|L	0.47016|0.47016	1.485|1.485	0.80722|0.80722	D|D	1|1	D;B;D;P|.	0.89917|.	1.0;0.09;0.967;0.842|.	D;B;P;B|.	0.87578|.	0.998;0.376;0.652;0.41|.	T|T	0.64715|0.64715	-0.6342|-0.6342	10|5	0.21540|.	T|.	0.41|.	.|.	19.0734|19.0734	0.93150|0.93150	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1936;1936;1935;1936|.	E5RIG2;Q96PZ7;F5H2I8;Q96PZ7-4|.	.;CSMD1_HUMAN;.;.|.	N|Q	1936;1936;1797;1935;1935;1935|1415	ENSP00000383047:D1936N;ENSP00000430733:D1936N;ENSP00000441462:D1935N;ENSP00000446243:D1935N;ENSP00000441675:D1935N|.	ENSP00000320445:D1797N|.	D|R	-|-	1|2	0|0	CSMD1|CSMD1	3007129|3007129	1.000000|1.000000	0.71417|0.71417	0.898000|0.898000	0.35279|0.35279	0.529000|0.529000	0.34654|0.34654	5.328000|5.328000	0.65887|0.65887	2.664000|2.664000	0.90586|0.90586	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.512	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3019722	C	T	3019722	3	4	70	1	0	0	0	0	1	0	0	0	3950	884	31	1	5023	1	CSMD1	8	3019722	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		3019722	143344300	38	21039										
ANGPT1	284	broad.mit.edu	37	chr8	108359322	108359322	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gttttccacaatgtaattctCaagctgcaagagataaagaa	7	7	1	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:108359322C>T								ANGPT1 (10572 upstream) : RNA5SP275 (537399 downstream)														p.E101K(1)									ATGTAATTCTCAAGCTGCAAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	8											112	108	109					8																	108359322		2203	4300	6503	108428498	SO:0001628	intergenic_variant	284																															8.37:g.108359322C>T			108428498		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	33	5.238976	0.95240	.	.	ENSG00000154188	ENST00000517746;ENST00000297450	T;T	0.44083	0.93;0.93	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.67636	0.2914	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66590	-0.5885	10	0.54805	T	0.06	.	20.3501	0.98811	0.0:1.0:0.0:0.0	.	101;101	Q5HYA0;Q15389	.;ANGP1_HUMAN	K	101	ENSP00000428340:E101K;ENSP00000297450:E101K	ENSP00000297450:E101K	E	-	1	0	ANGPT1	108428498	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.995000	0.70631	2.807000	0.96579	0.650000	0.86243	GAG	0	0.433									T	108359322	C	T	108359322	1	4	70	0	1	0	0	0	0	0	0	0	610	835	29	3		3	ANGPT1	8	108359322	IGR	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	105339600	108359322	38004700	39	21040										
CSMD3	114788	broad.mit.edu	37	chr8	113529433	113529433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tcatggggacccctgggtcaCgacacgcagtggcaacagaa	13	12	2	1	rs138068999		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:113529433C>T	ENST00000297405.5	-	28	4830	c.4586G>A	c.(4585-4587)cGt>cAt	p.R1529H	CSMD3_ENST00000352409.3_Missense_Mutation_p.R1529H|CSMD3_ENST00000455883.2_Missense_Mutation_p.R1425H|CSMD3_ENST00000343508.3_Missense_Mutation_p.R1489H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1529	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1529H(2)|p.R1489H(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCCTGGGTCACGACACGCAGT	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	1	0.000199681	8e-04	0	5008	,	,		14260	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	kidney(2)|large_intestine(1)	8						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	55	49	51		4274,4586,4466	3.8	1	8	dbSNP_134	51	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	29,29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	1425/3539,1529/3708,1489/3668	113529433	2,13004	2203	4300	6503	113598609	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4586G>A	8.37:g.113529433C>T	ENSP00000297405:p.Arg1529His		113598609	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	21.3	4.129748	0.77549	0.0	2.33E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	4.7	3.81	0.43845	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.70098	0.3185	L	0.41632	1.29	0.33293	D	0.563809	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.76071	0.977;0.987;0.862	T	0.76661	-0.2877	10	0.39692	T	0.17	.	14.2188	0.65812	0.1506:0.8494:0.0:0.0	.	1425;1529;1489	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	H	1489;1529;869;1425;1529	ENSP00000345799:R1489H;ENSP00000297405:R1529H;ENSP00000341558:R869H;ENSP00000412263:R1425H;ENSP00000343124:R1529H	ENSP00000297405:R1529H	R	-	2	0	CSMD3	113598609	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.894000	0.56250	1.159000	0.42565	0.585000	0.79938	CGT		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113529433	C	T	113529433	3	4	70	1	0	0	0	0	1	0	0	0	3952	536	19	1	6713	1	CSMD3	8	113529433	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	5170111	113529433	32834589	40	21041										
FER1L6	654463	broad.mit.edu	37	chr8	125109516	125109516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tttttttcttaacaagggccGcctgcagatgtgggtggaca	12	8	1	1	rs190405294	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:125109516G>A	ENST00000522917.1	+	36	4906	c.4700G>A	c.(4699-4701)cGc>cAc	p.R1567H	FER1L6_ENST00000399018.1_Missense_Mutation_p.R1567H|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1567						integral component of membrane (GO:0016021)		p.R1567H(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AACAAGGGCCGCCTGCAGATG	0.463													G|||	9	0.00179712	0.0061	0	5008	,	,		15110	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						G	HIS/ARG	17,3809		0,17,1896	83	80	81		4700	5.8	1	8		81	1,8293		0,1,4146	yes	missense	FER1L6	NM_001039112.2	29	0,18,6042	AA,AG,GG		0.0121,0.4443,0.1485	benign	1567/1858	125109516	18,12102	1913	4147	6060	125178697	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4700G>A	8.37:g.125109516G>A	ENSP00000428280:p.Arg1567His		125178697		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.40	3.380225	0.61845	0.004443	1.21E-4	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.86297	-2.1;-2.1	5.85	5.85	0.93711	C2 calcium/lipid-binding domain, CaLB (1);	0.297938	0.30611	U	0.009249	D	0.85720	0.5762	L	0.54323	1.7	0.36042	D	0.840182	B	0.23058	0.079	B	0.17979	0.02	D	0.85092	0.0952	10	0.62326	D	0.03	-11.2725	18.4185	0.90579	0.0:0.0:1.0:0.0	.	1567	Q2WGJ9	FR1L6_HUMAN	H	1567	ENSP00000428280:R1567H;ENSP00000381982:R1567H	ENSP00000381982:R1567H	R	+	2	0	FER1L6	125178697	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	3.618000	0.54188	2.779000	0.95612	0.650000	0.86243	CGC		0.463	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125109516	G	A	125109516	3	1	70	1	0	0	0	0	1	0	0	0	5834	1087	38	1	4838	1	FER1L6	8	125109516	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	11580083	125109516	21254506	41	21042										
ASAP1	50807	broad.mit.edu	37	chr8	131070229	131070229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctggtcctcttcccctgtgaCgataatcacttctccctcga	6	16	3	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:131070229C>T	ENST00000518721.1	-	29	3513	c.3286G>A	c.(3286-3288)Gtc>Atc	p.V1096I	ASAP1_ENST00000357668.1_Missense_Mutation_p.V1096I	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	1096	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.V1096I(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TCCCCTGTGACGATAATCACT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											318	245	270					8																	131070229		2203	4300	6503	131139411	SO:0001583	missense	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.3286G>A	8.37:g.131070229C>T	ENSP00000429900:p.Val1096Ile		131139411	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	37	CCDS6362.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.026989|5.026989	0.93518|0.93518	.|.	.|.	ENSG00000153317|ENSG00000153317	ENST00000524124;ENST00000519483|ENST00000343135;ENST00000357668;ENST00000518721	.|T;T	.|0.57107	.|0.42;0.42	5.27|5.27	5.27|5.27	0.74061|0.74061	.|Src homology-3 domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63367|0.63367	0.2505|0.2505	L|L	0.31578|0.31578	0.945|0.945	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.79784	.|0.993;0.993;0.991	T|T	0.67397|0.67397	-0.5681|-0.5681	5|10	.|0.87932	.|D	.|0	.|.	17.8947|17.8947	0.88883|0.88883	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1096;1096;1099	.|B2RNV3;Q9ULH1;Q9ULH1-2	.|.;ASAP1_HUMAN;.	H|I	916;452|1099;1096;1096	.|ENSP00000350297:V1096I;ENSP00000429900:V1096I	.|ENSP00000344591:V1099I	R|V	-|-	2|1	0|0	ASAP1|ASAP1	131139411|131139411	1.000000|1.000000	0.71417|0.71417	0.931000|0.931000	0.37212|0.37212	0.777000|0.777000	0.43975|0.43975	7.696000|7.696000	0.84270|0.84270	2.436000|2.436000	0.82500|0.82500	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.498	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		T	131070229	C	T	131070229	3	4	70	1	0	0	0	0	1	0	0	0	1011	536	19	1	111	1	ASAP1	8	131070229	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	5960713	131070229	15293793	42	21043										
KCNQ3	3786	broad.mit.edu	37	chr8	133152333	133152333	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ggggcattacctgacggctcGgatggcggccttcagggtgg	18	10	1	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr8:133152333G>A	ENST00000388996.4	-	11	1978	c.1558C>T	c.(1558-1560)Cga>Tga	p.R520*	KCNQ3_ENST00000521134.1_Nonsense_Mutation_p.R400*|KCNQ3_ENST00000519445.1_Nonsense_Mutation_p.R520*	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	520					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R520*(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CTGACGGCTCGGATGGCGGCC	0.607																																																2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	8											59	63	62					8																	133152333		2203	4300	6503	133221515	SO:0001587	stop_gained	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1558C>T	8.37:g.133152333G>A	ENSP00000373648:p.Arg520*		133221515	A2VCT8|B4DJY4|E7EQ89	Nonsense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	G	37	6.046189	0.97231	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	.	.	.	6.03	4.08	0.47627	.	0.062532	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5201	15.7279	0.77777	0.0:0.0:0.6884:0.3116	.	.	.	.	X	520;400;520;509;399	.	ENSP00000373648:R520X	R	-	1	2	KCNQ3	133221515	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	0.726000	0.25984	1.555000	0.49500	-0.152000	0.13540	CGA		0.607	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133152333	G	A	133152333	4	1	70	1	0	0	0	0	0	1	0	0	8105	1124	39	1	1080	1	KCNQ3	8	133152333	Nonsense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	2082104	133152333	13211689	43	21044										
C9orf64	84267	broad.mit.edu	37	chr9	86559713	86559713	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	acttaaagttgcaaacctttGagaagcttcttcagtaggtc	8	8	2	1	rs36082863	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr9:86559713G>A	ENST00000376344.3	-	3	1005	c.789C>T	c.(787-789)ctC>ctT	p.L263L	C9orf64_ENST00000314700.1_Silent_p.L122L	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	263								p.L263L(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						GCAAACCTTTGAGAAGCTTCT	0.358													G|||	45	0.00898562	0.031	0.0029	5008	,	,		17977	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9						G		122,4284	90.6+/-129.3	1,120,2082	79	79	79		789	-4.8	0.5	9	dbSNP_126	79	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	C9orf64	NM_032307.3		1,122,6380	AA,AG,GG		0.0233,2.769,0.9534		263/342	86559713	124,12882	2203	4300	6503	85749533	SO:0001819	synonymous_variant	84267			AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.789C>T	9.37:g.86559713G>A			85749533	B2RPI6|Q8N2B1|Q9BT18	Silent	SNP	ENST00000376344.3	37	CCDS6666.2																																																																																				0.358	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307		A	86559713	G	A	86559713	2	1	70	1	0	0	0	0	0	0	0	1	2495	1277	45	3		3	C9orf64	9	86559713	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		86559713	54653718	44	21045										
TET1	80312	broad.mit.edu	37	chr10	70333380	70333380	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gtgggagtgttgtcccagacTtgcctgtcttccttcctgtt	11	11	1	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr10:70333380T>C	ENST00000373644.4	+	2	1494	c.1285T>C	c.(1285-1287)Ttg>Ctg	p.L429L		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	429					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.L429L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGTCCCAGACTTGCCTGTCTT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	10											139	127	131					10																	70333380		2203	4300	6503	70003386	SO:0001819	synonymous_variant	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1285T>C	10.37:g.70333380T>C			70003386	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Silent	SNP	ENST00000373644.4	37	CCDS7281.1																																																																																				0.468	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70333380	T	C	70333380	2	2	70	1	0	0	0	0	0	0	0	1	15808	1606	56	4		4	TET1	10	70333380	Silent	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09		70333380	65201367	45	21046										
ZNF408	79797	broad.mit.edu	37	chr11	46726469	46726469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgctgggccaccgtggggtgCggcccttcccctgtccacaa	13	16	0	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr11:46726469C>T	ENST00000311764.2	+	5	1449	c.1219C>T	c.(1219-1221)Cgg>Tgg	p.R407W		NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.R407W(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CCGTGGGGTGCGGCCCTTCCC	0.587																																					Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)											1	Substitution - Missense(1)	large_intestine(1)	11											62	61	61					11																	46726469		2201	4299	6500	46683045	SO:0001583	missense	79797			AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"Zinc fingers, C2H2-type"	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.1219C>T	11.37:g.46726469C>T	ENSP00000309606:p.Arg407Trp		46683045		Missense_Mutation	SNP	ENST00000311764.2	37	CCDS7923.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.718704	0.68844	.	.	ENSG00000175213	ENST00000311764	T	0.20332	2.08	5.57	4.67	0.58626	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40469	N	0.001097	T	0.40719	0.1128	M	0.93462	3.42	0.49130	D	0.999757	D;D	0.53151	0.958;0.958	P;P	0.45794	0.493;0.493	T	0.58375	-0.7647	10	0.87932	D	0	-30.0805	12.506	0.55981	0.0:0.861:0.0:0.139	.	399;407	B4DXY4;Q9H9D4	.;ZN408_HUMAN	W	407	ENSP00000309606:R407W	ENSP00000309606:R407W	R	+	1	2	ZNF408	46683045	0.976000	0.34144	0.982000	0.44146	0.945000	0.59286	0.478000	0.22212	1.492000	0.48499	0.563000	0.77884	CGG		0.587	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741		T	46726469	C	T	46726469	3	4	70	1	0	0	0	0	1	0	0	0	17927	759	27	1	1269	1	ZNF408	11	46726469	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		46726469	88280047	46	21047										
PPFIA1	8500	broad.mit.edu	37	chr11	70172850	70172850	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	atgtgacagaactggaagagGatctggacacggctagaaaa	13	6	1	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr11:70172850G>T	ENST00000253925.7	+	7	1071	c.856G>T	c.(856-858)Gat>Tat	p.D286Y	PPFIA1_ENST00000389547.3_Missense_Mutation_p.D286Y|CTA-797E19.2_ENST00000526017.1_RNA|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	286					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.D286Y(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			ACTGGAAGAGGATCTGGACAC	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	11											153	155	154					11																	70172850		2200	4294	6494	69850498	SO:0001583	missense	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.856G>T	11.37:g.70172850G>T	ENSP00000253925:p.Asp286Tyr		69850498	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083689	0.55861	.	.	ENSG00000131626	ENST00000253925;ENST00000389547	T;T	0.79141	-1.24;-1.24	4.68	4.68	0.58851	.	0.064286	0.64402	U	0.000015	D	0.86418	0.5928	M	0.73962	2.25	0.80722	D	1	D;D	0.62365	0.989;0.991	P;P	0.61592	0.88;0.891	D	0.88557	0.3120	10	0.87932	D	0	.	16.9973	0.86371	0.0:0.0:1.0:0.0	.	286;286	Q13136;Q13136-2	LIPA1_HUMAN;.	Y	286	ENSP00000253925:D286Y;ENSP00000374198:D286Y	ENSP00000253925:D286Y	D	+	1	0	PPFIA1	69850498	1.000000	0.71417	0.103000	0.21229	0.124000	0.20399	9.638000	0.98445	2.327000	0.79052	0.655000	0.94253	GAT		0.418	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		T	70172850	G	T	70172850	3	4	70	1	0	0	0	0	1	0	0	0	12340	1174	41	2	878	2	PPFIA1	11	70172850	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	23446381	70172850	64833666	47	21048										
ODZ4	26011	broad.mit.edu	37	chr11	78381535	78381535	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gcatcgtcacagaagagaggCggtcattcttgtcgaactca	11	10	4	2	rs140341040	byFrequency	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr11:78381535C>T	ENST00000278550.7	-	32	6317	c.5855G>A	c.(5854-5856)cGc>cAc	p.R1952H		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1952					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.R1952H(2)|p.R1952L(2)									AGAAGAGAGGCGGTCATTCTT	0.542													C|||	2	0.000399361	0	0	5008	,	,		21705	0.002		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(2)|lung(2)	11											72	75	74					11																	78381535		1997	4159	6156	78059183	SO:0001583	missense	26011			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5855G>A	11.37:g.78381535C>T	ENSP00000278550:p.Arg1952His		78059183	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	16.16	3.044927	0.55110	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90444	-2.67;0.72	4.93	3.08	0.35506	.	0.112900	0.64402	N	0.000008	D	0.94000	0.8078	M	0.75447	2.3	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	D	0.93007	0.6428	9	.	.	.	.	11.7033	0.51583	0.0:0.8566:0.0:0.1434	.	1952	Q6N022	TEN4_HUMAN	H	1952;416	ENSP00000278550:R1952H;ENSP00000431711:R416H	.	R	-	2	0	ODZ4	78059183	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	3.125000	0.50469	0.802000	0.34089	-0.126000	0.14955	CGC		0.542	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78381535	C	T	78381535	3	4	70	1	0	0	0	0	1	0	0	0	10868	768	27	1	2466	1	ODZ4	11	78381535	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	8208685	78381535	56624981	48	21049										
HTR3B	9177	broad.mit.edu	37	chr11	113816765	113816765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gtggctggtcctcctgtcccGctttgaccgactgctcttcc	10	16	1	1	rs200815025		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr11:113816765G>A	ENST00000260191.2	+	9	1489	c.1232G>A	c.(1231-1233)cGc>cAc	p.R411H	HTR3B_ENST00000537778.1_Missense_Mutation_p.R400H	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	411	HA-stretch.				cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)	p.R411H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	CTCCTGTCCCGCTTTGACCGA	0.557													G|||	1	0.000199681	0	0	5008	,	,		15084	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											81	73	76					11																	113816765		2201	4296	6497	113321975	SO:0001583	missense	9177			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.1232G>A	11.37:g.113816765G>A	ENSP00000260191:p.Arg411His		113321975	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	.	.	.	.	.	.	.	.	.	.	G	9.620	1.133594	0.21041	.	.	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.22539	1.95;1.95	5.48	2.57	0.30868	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.258863	0.37906	N	0.001883	T	0.16300	0.0392	L	0.35723	1.085	0.28872	N	0.894895	B;B	0.15141	0.012;0.01	B;B	0.10450	0.005;0.002	T	0.11792	-1.0573	10	0.59425	D	0.04	-4.0172	9.504	0.39035	0.2265:0.0:0.7735:0.0	.	400;411	O95264-2;O95264	.;5HT3B_HUMAN	H	411;400	ENSP00000260191:R411H;ENSP00000443118:R400H	ENSP00000260191:R411H	R	+	2	0	HTR3B	113321975	0.061000	0.20836	0.877000	0.34402	0.083000	0.17756	0.393000	0.20817	0.281000	0.22233	0.491000	0.48974	CGC		0.557	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		A	113816765	G	A	113816765	3	1	70	1	0	0	0	0	1	0	0	0	7466	1087	38	1	1266	1	HTR3B	11	113816765	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	35435230	113816765	21189751	49	21050										
PHLDB1	23187	broad.mit.edu	37	chr11	118498785	118498785	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ctccaggcagtgagcgggtgCtaacaaccagcccctcacgc	11	16	1	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr11:118498785C>G	ENST00000361417.2	+	7	1657	c.1246C>G	c.(1246-1248)Cta>Gta	p.L416V	PHLDB1_ENST00000356063.5_Missense_Mutation_p.L416V	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	416								p.L416V(1)		breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		TGAGCGGGTGCTAACAACCAG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											72	75	74					11																	118498785		2200	4295	6495	118003995	SO:0001583	missense	23187				CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.1246C>G	11.37:g.118498785C>G	ENSP00000354498:p.Leu416Val		118003995	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	C	5.064	0.197537	0.09652	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000356063	T;T	0.33654	1.4;1.41	4.79	-9.08	0.00720	.	0.462873	0.21680	N	0.070721	T	0.19805	0.0476	L	0.34521	1.04	0.09310	N	1	B;B;B	0.32573	0.084;0.376;0.001	B;B;B	0.31751	0.037;0.135;0.005	T	0.14309	-1.0477	10	0.14252	T	0.57	-11.9462	16.0443	0.80707	0.0913:0.7168:0.0:0.1919	.	416;416;416	Q86UU1-3;Q86UU1-2;Q86UU1	.;.;PHLB1_HUMAN	V	416;175;416	ENSP00000354498:L416V;ENSP00000348359:L416V	ENSP00000348359:L416V	L	+	1	2	PHLDB1	118003995	0.000000	0.05858	0.000000	0.03702	0.658000	0.38924	-0.172000	0.09868	-1.280000	0.02402	0.462000	0.41574	CTA		0.637	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		G	118498785	C	G	118498785	3	3	70	1	0	0	0	0	1	0	0	0	11882	796	28	5	1264	5	PHLDB1	11	118498785	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	4682020	118498785	16507731	50	21051										
ACVR1B	91	broad.mit.edu	37	chr12	52370257	52370257	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	agcgtgtctatcacaaccgcCagagactggacatggaagat	11	10	2	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr12:52370257C>T	ENST00000257963.4	+	3	555	c.478C>T	c.(478-480)Cag>Tag	p.Q160*	ACVR1B_ENST00000541224.1_Nonsense_Mutation_p.Q160*|ACVR1B_ENST00000426655.2_Nonsense_Mutation_p.Q160*|ACVR1B_ENST00000542485.1_Nonsense_Mutation_p.Q108*|ACVR1B_ENST00000415850.2_Nonsense_Mutation_p.Q160*	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	160					activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)	p.Q160*(2)		breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TCACAACCGCCAGAGACTGGA	0.512																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											178	164	169					12																	52370257		2203	4300	6503	50656524	SO:0001587	stop_gained	91				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.478C>T	12.37:g.52370257C>T	ENSP00000257963:p.Gln160*		50656524	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Nonsense_Mutation	SNP	ENST00000257963.4	37	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.577285	0.86645	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	19.35	0.94379	0.0:1.0:0.0:0.0	.	.	.	.	X	160;160;160;160;108	.	ENSP00000257963:Q160X	Q	+	1	0	ACVR1B	50656524	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.950000	0.70265	2.652000	0.90054	0.462000	0.41574	CAG		0.512	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		T	52370257	C	T	52370257	4	4	70	1	0	0	0	0	0	1	0	0	221	595	21	3	488	3	ACVR1B	12	52370257	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		52370257	81481638	51	21052										
ACVR1B	91	broad.mit.edu	37	chr12	52374974	52374974	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tccttggatttattgctgctGacaataaaggtaagggctgg	12	6	0	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr12:52374974G>A	ENST00000257963.4	+	4	879	c.802G>A	c.(802-804)Gac>Aac	p.D268N	ACVR1B_ENST00000541224.1_Missense_Mutation_p.D268N|ACVR1B_ENST00000426655.2_Missense_Mutation_p.D268N|ACVR1B_ENST00000542485.1_Missense_Mutation_p.D216N|ACVR1B_ENST00000415850.2_Missense_Mutation_p.D268N	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)	p.D268N(2)		breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TATTGCTGCTGACAATAAAGG	0.468											OREG0021829	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	12											89	87	88					12																	52374974		2203	4300	6503	50661241	SO:0001583	missense	91				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.802G>A	12.37:g.52374974G>A	ENSP00000257963:p.Asp268Asn	984	50661241	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	37	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261561	0.80358	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	D;D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2;-3.2	5.13	5.13	0.70059	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97188	0.9081	M	0.86420	2.815	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.999;0.999	D	0.97777	1.0230	10	0.87932	D	0	.	18.9833	0.92762	0.0:0.0:1.0:0.0	.	268;268;268;268	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	N	268;268;268;268;216	ENSP00000257963:D268N;ENSP00000442656:D268N;ENSP00000390477:D268N;ENSP00000397550:D268N;ENSP00000442885:D216N	ENSP00000257963:D268N	D	+	1	0	ACVR1B	50661241	1.000000	0.71417	0.995000	0.50966	0.289000	0.27227	9.869000	0.99810	2.567000	0.86603	0.655000	0.94253	GAC		0.468	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		A	52374974	G	A	52374974	3	1	70	1	0	0	0	0	1	0	0	0	221	1290	45	3	816	3	ACVR1B	12	52374974	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	4717	52374974	81476921	52	21053										
N6AMT2	221143	broad.mit.edu	37	chr13	21306020	21306020	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ccccgcgtcaggtacttgacGgtttccgatgtttttctgag	11	11	2	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr13:21306020G>A	ENST00000382758.1	-	4	515	c.468C>T	c.(466-468)acC>acT	p.T156T	N6AMT2_ENST00000382754.4_Silent_p.T156T			Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2 (putative)	156						extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)	p.T156T(1)		endometrium(1)|large_intestine(3)|lung(3)	7		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)		GGTACTTGACGGTTTCCGATG	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	13											126	119	122					13																	21306020		2203	4300	6503	20204020	SO:0001819	synonymous_variant	221143			AK055408	CCDS9293.1	13q12.11	2006-12-14			ENSG00000150456	ENSG00000150456			27351	protein-coding gene	gene with protein product						12477932	Standard	NM_174928		Approved		uc001uno.1	Q8WVE0	OTTHUMG00000016519	ENST00000382758.1:c.468C>T	13.37:g.21306020G>A			20204020	B5G4V1	Silent	SNP	ENST00000382758.1	37	CCDS9293.1																																																																																				0.463	N6AMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044083.1	NM_174928		A	21306020	G	A	21306020	2	1	70	1	0	0	0	0	0	0	0	1	10145	1103	39	1		1	N6AMT2	13	21306020	Silent	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		21306020	93863858	53	21054										
ZNF828	283489	broad.mit.edu	37	chr13	115089492	115089493	+	Missense_Mutation	DNP	GC	GC	TT													0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgatattttaccagaaaagtGcaaagttatttcactgccat							TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr13:115089492_115089493GC>TT	ENST00000361283.1	+	3	484_485	c.175_176GC>TT	c.(175-177)GCa>TTa	p.A59L		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	59					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A59>?(1)									CCAGAAAAGTGCAAAGTTATTT	0.376																																																1	Complex(1)	large_intestine(1)	13																																								114107595	SO:0001583	missense	283489			AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	Exception_encountered	13.37:g.115089492_115089493delinsTT	ENSP00000354730:p.Ala59Leu		114107594	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	DNP	ENST00000361283.1	37	CCDS9545.1																																																																																				0.376	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		TT	115089493	GC	TT	115089492	3	4	70	1	0	0	0	0	1	0	0	0	18220	1319	46	2	177	2	ZNF828	13	115089492	Missense_Mutation	DNP	GC	TCGA-AG-A01L-01A-01W-A00K-09	93783472	115089492	80386	54	21055										
MYH7	4625	broad.mit.edu	37	chr14	23902842	23902842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	aggcacgaagacatccttctTgaggtcaaaaggcctggtct	11	10	3	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr14:23902842T>C	ENST00000355349.3	-	3	262	c.100A>G	c.(100-102)Aag>Gag	p.K34E		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	34					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.K34E(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ACATCCTTCTTGAGGTCAAAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											110	96	101					14																	23902842		2203	4300	6503	22972682	SO:0001583	missense	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.100A>G	14.37:g.23902842T>C	ENSP00000347507:p.Lys34Glu		22972682	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.019730	0.75275	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.91521	-2.86	4.26	4.26	0.50523	Myosin, N-terminal, SH3-like (1);	.	.	.	.	D	0.94568	0.8250	H	0.94658	3.565	0.58432	D	0.999999	B	0.15473	0.013	B	0.38327	0.271	D	0.94225	0.7471	9	0.66056	D	0.02	.	13.3331	0.60500	0.0:0.0:0.0:1.0	.	34	P12883	MYH7_HUMAN	E	34	ENSP00000347507:K34E	ENSP00000347507:K34E	K	-	1	0	MYH7	22972682	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.684000	0.51022	0.454000	0.30748	AAG		0.562	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		C	23902842	T	C	23902842	3	2	70	1	0	0	0	0	1	0	0	0	10069	1821	63	4	5859	4	MYH7	14	23902842	Missense_Mutation	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09		23902842	83446698	55	21056										
FSCB	84075	broad.mit.edu	37	chr14	44975156	44975156	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	ggcagaatttcagccagaagCtctacagaaggagactcttc	10	10	3	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr14:44975156C>A	ENST00000340446.4	-	1	1326	c.1035G>T	c.(1033-1035)gaG>gaT	p.E345D	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	345	Pro-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.E345D(1)		breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CAGCCAGAAGCTCTACAGAAG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	81	77					14																	44975156		2203	4300	6503	44044906	SO:0001583	missense	84075			AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1035G>T	14.37:g.44975156C>A	ENSP00000344579:p.Glu345Asp		44044906	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412000	0.25465	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.14640	2.49	1.8	0.884	0.19182	.	.	.	.	.	T	0.16727	0.0402	N	0.24115	0.695	0.09310	N	1	D	0.64830	0.994	D	0.65987	0.94	T	0.23440	-1.0188	9	0.25106	T	0.35	.	6.3232	0.21229	0.0:0.8255:0.0:0.1745	.	345	Q5H9T9	FSCB_HUMAN	D	345	ENSP00000344579:E345D	ENSP00000344579:E345D	E	-	3	2	FSCB	44044906	0.000000	0.05858	0.007000	0.13788	0.018000	0.09664	-0.672000	0.05244	0.332000	0.23536	-0.451000	0.05528	GAG		0.498	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		A	44975156	C	A	44975156	3	1	70	1	0	0	0	0	1	0	0	0	6085	796	28	2	1446	2	FSCB	14	44975156	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	21072314	44975156	62374384	56	21057										
C14orf49	161176	broad.mit.edu	37	chr14	95921953	95921953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cctcatctcttccagttctcCggtgatcttctctgcaccca	5	17	5	1	rs112493785		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr14:95921953C>T	ENST00000334258.5	-	5	912	c.898G>A	c.(898-900)Gga>Aga	p.G300R	SYNE3_ENST00000554873.1_Missense_Mutation_p.G57R|SYNE3_ENST00000557275.1_Missense_Mutation_p.G300R|SYNE3_ENST00000553340.1_Missense_Mutation_p.G300R	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	300					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.G300R(2)		breast(1)|endometrium(2)|lung(25)	28						TCCAGTTCTCCGGTGATCTTC	0.617																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	14						C	ARG/GLY	0,4406		0,0,2203	107	113	111		898	-8.1	0	14	dbSNP_132	111	1,8599	1.2+/-3.3	0,1,4299	no	missense	C14orf49	NM_152592.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	300/976	95921953	1,13005	2203	4300	6503	94991706	SO:0001583	missense	161176			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.898G>A	14.37:g.95921953C>T	ENSP00000334308:p.Gly300Arg		94991706	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	1.626	-0.520327	0.04171	0.0	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.33654	3.67;1.4;3.67;3.1	4.99	-8.14	0.01069	.	1.670270	0.03928	N	0.284762	T	0.16685	0.0401	N	0.12182	0.205	0.09310	N	1	B;B;B	0.14012	0.003;0.009;0.002	B;B;B	0.09377	0.002;0.004;0.001	T	0.15665	-1.0429	10	0.17369	T	0.5	0.1359	8.4086	0.32629	0.0:0.1937:0.3622:0.4441	.	300;300;300	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	R	300;57;300;300	ENSP00000334308:G300R;ENSP00000452154:G57R;ENSP00000450562:G300R;ENSP00000450774:G300R	ENSP00000334308:G300R	G	-	1	0	C14orf49	94991706	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-0.522000	0.06237	-1.246000	0.02510	0.455000	0.32223	GGA		0.617	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95921953	C	T	95921953	3	4	70	1	0	0	0	0	1	0	0	0	1780	661	23	1	2081	1	C14orf49	14	95921953	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	50946797	95921953	11427587	57	21058										
NTRK3	4916	broad.mit.edu	37	chr15	88678541	88678541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cattgtgcagccagtgcagcGttggtggggggttgccacgc	17	10	0	0	rs145157285		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr15:88678541G>A	ENST00000360948.2	-	9	1156	c.995C>T	c.(994-996)aCg>aTg	p.T332M	NTRK3_ENST00000540489.2_Missense_Mutation_p.T332M|NTRK3_ENST00000394480.2_Missense_Mutation_p.T332M|NTRK3_ENST00000557856.1_Missense_Mutation_p.T332M|NTRK3_ENST00000355254.2_Missense_Mutation_p.T332M|NTRK3_ENST00000357724.2_Missense_Mutation_p.T332M|NTRK3_ENST00000558676.1_Missense_Mutation_p.T332M|NTRK3_ENST00000542733.2_Missense_Mutation_p.T234M|NTRK3_ENST00000317501.3_Missense_Mutation_p.T332M	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	332	Ig-like C2-type 2.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T332M(3)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCAGTGCAGCGTTGGTGGGGG	0.602			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)			G|||	1	0.000199681	0	0	5008	,	,		17971	0.001		0	False		,,,				2504	0						Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	3	Substitution - Missense(3)	large_intestine(3)	15						G	MET/THR,MET/THR,MET/THR	0,4402		0,0,2201	72	74	73		995,995,995	5.3	0.6	15	dbSNP_134	73	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense,missense	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	81,81,81	0,2,6498	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	332/613,332/840,332/826	88678541	2,12998	2201	4299	6500	86479545	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.995C>T	15.37:g.88678541G>A	ENSP00000354207:p.Thr332Met		86479545	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.48	2.249763	0.39797	0.0	2.33E-4	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.153551	0.56097	D	0.000027	D	0.82825	0.5121	M	0.90198	3.095	0.43819	D	0.996386	D;D;D;D;D;D	0.76494	0.998;0.999;0.998;0.998;0.999;0.999	P;D;D;P;D;D	0.67725	0.761;0.938;0.932;0.761;0.923;0.953	D	0.85907	0.1438	10	0.87932	D	0	.	11.3995	0.49862	0.0821:0.0:0.9179:0.0	.	234;332;332;332;332;332	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	M	332;332;332;332;234;332;332	ENSP00000377990:T332M;ENSP00000354207:T332M;ENSP00000350356:T332M;ENSP00000347397:T332M;ENSP00000437773:T234M;ENSP00000444673:T332M;ENSP00000318328:T332M	ENSP00000318328:T332M	T	-	2	0	NTRK3	86479545	0.678000	0.27586	0.632000	0.29296	0.219000	0.24729	2.064000	0.41432	2.454000	0.82982	0.563000	0.77884	ACG		0.602	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88678541	G	A	88678541	3	1	70	1	0	0	0	0	1	0	0	0	10739	1145	40	1	1830	1	NTRK3	15	88678541	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		88678541	13852851	58	21059										
SV2B	9899	broad.mit.edu	37	chr15	91795147	91795147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tcctcagcatgtctctggccGtcaatgcctccttcgcctcc	7	18	3	0	rs143979505		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr15:91795147G>A	ENST00000394232.1	+	3	1020	c.550G>A	c.(550-552)Gtc>Atc	p.V184I	SV2B_ENST00000545111.2_Missense_Mutation_p.V33I|SV2B_ENST00000557291.1_3'UTR|SV2B_ENST00000330276.4_Missense_Mutation_p.V184I	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	184					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.V184I(1)		NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GTCTCTGGCCGTCAATGCCTC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	ILE/VAL,ILE/VAL	0,4396		0,0,2198	147	118	128		97,550	-10.8	0.1	15	dbSNP_134	128	2,8594	2.2+/-6.3	0,2,4296	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	33/533,184/684	91795147	2,12990	2198	4298	6496	89596151	SO:0001583	missense	9899			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.550G>A	15.37:g.91795147G>A	ENSP00000377779:p.Val184Ile		89596151	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.804130	0.31869	0.0	2.33E-4	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.72167	-0.63;-0.63;-0.63	5.38	-10.8	0.00216	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.464311	0.26812	N	0.022373	T	0.31263	0.0791	N	0.02247	-0.625	0.18873	N	0.999983	B	0.06786	0.001	B	0.11329	0.006	T	0.41734	-0.9492	10	0.07813	T	0.8	-5.6354	12.5431	0.56184	0.6661:0.2445:0.0894:0.0	.	184	Q7L1I2	SV2B_HUMAN	I	33;184;184	ENSP00000443243:V33I;ENSP00000377779:V184I;ENSP00000332818:V184I	ENSP00000332818:V184I	V	+	1	0	SV2B	89596151	0.561000	0.26578	0.118000	0.21660	0.994000	0.84299	0.477000	0.22196	-2.034000	0.00924	-0.253000	0.11424	GTC		0.567	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91795147	G	A	91795147	3	1	70	1	0	0	0	0	1	0	0	0	15457	1145	40	1	556	1	SV2B	15	91795147	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09	3116606	91795147	10736245	59	21060										
CHD2	1106	broad.mit.edu	37	chr15	93545489	93545489	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	caaggagaaacaaatgagttCtaggaaagacaaagaagggg	13	4	1	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr15:93545489C>A	ENST00000394196.4	+	33	5288	c.4220C>A	c.(4219-4221)tCt>tAt	p.S1407Y	CHD2_ENST00000557381.1_Missense_Mutation_p.S1407Y	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1407					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.S1407Y(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			caaatgagttctaggaaagac	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											123	122	122					15																	93545489		2197	4298	6495	91346493	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4220C>A	15.37:g.93545489C>A	ENSP00000377747:p.Ser1407Tyr		91346493	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	C	13.02	2.112775	0.37242	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;T	0.02709	4.19;4.19	4.89	2.95	0.34219	.	0.000000	0.34110	U	0.004245	T	0.02767	0.0083	N	0.22421	0.69	0.80722	D	1	P;P	0.49447	0.875;0.924	B;P	0.44811	0.272;0.461	T	0.58869	-0.7560	10	0.66056	D	0.02	-5.0328	7.2564	0.26179	0.0:0.7363:0.1699:0.0939	.	1407;1407	O14647;O14647-2	CHD2_HUMAN;.	Y	1407	ENSP00000377747:S1407Y;ENSP00000451366:S1407Y	ENSP00000377747:S1407Y	S	+	2	0	CHD2	91346493	0.856000	0.29760	0.921000	0.36526	0.983000	0.72400	1.377000	0.34317	0.548000	0.28955	0.655000	0.94253	TCT		0.383	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		A	93545489	C	A	93545489	3	1	70	1	0	0	0	0	1	0	0	0	3331	913	32	2	4350	2	CHD2	15	93545489	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	1750342	93545489	8985903	60	21061										
PLD2	5338	broad.mit.edu	37	chr17	4719185	4719185	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gctgggatgacctgcactacCgactgactgaccttggagac	12	12	0	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr17:4719185C>T	ENST00000263088.6	+	14	1542	c.1411C>T	c.(1411-1413)Cga>Tga	p.R471*	PLD2_ENST00000572940.1_Nonsense_Mutation_p.R471*	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	471	Catalytic.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.R471*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	CCTGCACTACCGACTGACTGA	0.572											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Nonsense(1)	large_intestine(1)	17											193	158	170					17																	4719185		2203	4300	6503	4666151	SO:0001587	stop_gained	5338			AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1411C>T	17.37:g.4719185C>T	ENSP00000263088:p.Arg471*	621	4666151	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Nonsense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	C	39	7.392471	0.98255	.	.	ENSG00000129219	ENST00000263088	.	.	.	5.58	3.51	0.40186	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7731	11.6446	0.51253	0.4906:0.5094:0.0:0.0	.	.	.	.	X	471	.	ENSP00000263088:R471X	R	+	1	2	PLD2	4666151	0.048000	0.20356	1.000000	0.80357	0.999000	0.98932	0.122000	0.15687	0.639000	0.30564	0.655000	0.94253	CGA		0.572	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		T	4719185	C	T	4719185	4	4	70	1	0	0	0	0	0	1	0	0	12077	644	23	1	1461	1	PLD2	17	4719185	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		4719185	76476025	61	21062										
TP53	7157	broad.mit.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	70	1	0	0	0	0	1	0	0	0	16421	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	2858353	7577538	73617672	62	21063										
TCEB3B	51224	broad.mit.edu	37	chr18	44561290	44561290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgggctcctgggggccgtcgCgttttctgggaagccccagg	17	12	1	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr18:44561290C>T	ENST00000332567.4	-	1	698	c.346G>A	c.(346-348)Gcg>Acg	p.A116T	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	116					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A116T(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGGGCCGTCGCGTTTTCTGGG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	18											45	53	50					18																	44561290		2199	4296	6495	42815288	SO:0001583	missense	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.346G>A	18.37:g.44561290C>T	ENSP00000331302:p.Ala116Thr		42815288	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	C	5.944	0.358254	0.11239	.	.	ENSG00000206181	ENST00000332567	T	0.06687	3.27	2.61	-5.22	0.02806	.	1.448910	0.05242	U	0.512412	T	0.03477	0.0100	N	0.22421	0.69	0.09310	N	1	P	0.46020	0.871	B	0.33521	0.165	T	0.20806	-1.0264	10	0.22706	T	0.39	2.3089	1.5561	0.02585	0.1498:0.3783:0.2263:0.2456	.	116	Q8IYF1	ELOA2_HUMAN	T	116	ENSP00000331302:A116T	ENSP00000331302:A116T	A	-	1	0	TCEB3B	42815288	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.541000	0.06099	-2.991000	0.00279	-0.534000	0.04291	GCG		0.662	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44561290	C	T	44561290	3	4	70	1	0	0	0	0	1	0	0	0	15721	768	27	1	1919	1	TCEB3B	18	44561290	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		44561290	33515958	63	21064										
CCDC123	84902	broad.mit.edu	37	chr19	33372823	33372823	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gtgcaggtgccgcatctcctGccggtactgggctgtcttgc	14	13	2	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr19:33372823G>A	ENST00000305768.5	-	18	2150	c.2062C>T	c.(2062-2064)Cag>Tag	p.Q688*		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	688					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.Q688*(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CGCATCTCCTGCCGGTACTGG	0.652																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											38	28	31					19																	33372823		2203	4300	6503	38064663	SO:0001587	stop_gained	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2062C>T	19.37:g.33372823G>A	ENSP00000306105:p.Gln688*		38064663	B9EGA6|Q8N5J8	Nonsense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	g	26.3	4.725362	0.89298	.	.	ENSG00000121289	ENST00000305768	.	.	.	5.76	2.38	0.29361	.	0.631105	0.14995	N	0.286499	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-5.6234	8.691	0.34267	0.0722:0.0:0.6499:0.2779	.	.	.	.	X	688	.	ENSP00000306105:Q688X	Q	-	1	0	CEP89	38064663	1.000000	0.71417	0.962000	0.40283	0.178000	0.23041	1.332000	0.33805	0.315000	0.23110	0.556000	0.70494	CAG		0.652	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33372823	G	A	33372823	4	1	70	1	0	0	0	0	0	1	0	0	2765	1328	46	3	297	3	CCDC123	19	33372823	Nonsense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		33372823	25756160	64	21065										
ZNF793	390927	broad.mit.edu	37	chr19	38028005	38028005	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gtggaaagaatttgaaccatAatttagacttgattggtttt	9	3	0	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr19:38028005A>T	ENST00000587143.1	+	6	680	c.445A>T	c.(445-447)Aat>Tat	p.N149Y	ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000542455.1_Missense_Mutation_p.N149Y|ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000445217.1_Missense_Mutation_p.N149Y			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N149Y(1)		kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTGAACCATAATTTAGACTT	0.358																																					Melanoma(44;400 1431 1499 19093)											1	Substitution - Missense(1)	large_intestine(1)	19											44	42	43					19																	38028005		1814	4073	5887	42719845	SO:0001583	missense	390927			AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.445A>T	19.37:g.38028005A>T	ENSP00000468605:p.Asn149Tyr		42719845	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	37	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589798	0.46214	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.07800	3.16;3.16	4.15	1.89	0.25635	.	0.568533	0.14678	N	0.304928	T	0.05823	0.0152	L	0.45228	1.405	0.09310	N	1	P	0.35982	0.531	B	0.31191	0.125	T	0.38845	-0.9642	10	0.16896	T	0.51	.	5.6397	0.17557	0.6537:0.1766:0.0:0.1697	.	149	E9PGN4	.	Y	149;149;149;148	ENSP00000444355:N149Y;ENSP00000396402:N149Y	ENSP00000318811:N148Y	N	+	1	0	ZNF793	42719845	0.000000	0.05858	0.253000	0.24343	0.942000	0.58702	0.392000	0.20801	0.189000	0.20188	0.533000	0.62120	AAT		0.358	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		T	38028005	A	T	38028005	3	4	70	1	0	0	0	0	1	0	0	0	18204	362	13	5	459	5	ZNF793	19	38028005	Missense_Mutation	SNP	A	TCGA-AG-A01L-01A-01W-A00K-09	4655182	38028005	21100978	65	21066										
ARHGEF1	9138	broad.mit.edu	37	chr19	42396742	42396742	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgcaggaggtggtgcaaagcCagcaggtagccgtgggccgg	19	9	0	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr19:42396742C>T	ENST00000354532.3	+	7	584	c.436C>T	c.(436-438)Cag>Tag	p.Q146*	ARHGEF1_ENST00000378152.4_Nonsense_Mutation_p.Q128*|ARHGEF1_ENST00000599846.1_Nonsense_Mutation_p.Q146*|ARHGEF1_ENST00000337665.4_Nonsense_Mutation_p.Q161*|ARHGEF1_ENST00000347545.4_Nonsense_Mutation_p.Q113*	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	146	RGSL.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Q161*(1)		breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GGTGCAAAGCCAGCAGGTAGC	0.662																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											39	40	40					19																	42396742		2203	4300	6503	47088582	SO:0001587	stop_gained	9138			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"Rho guanine nucleotide exchange factors"	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.436C>T	19.37:g.42396742C>T	ENSP00000346532:p.Gln146*		47088582	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Nonsense_Mutation	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153113	0.78001	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000316079;ENST00000337665;ENST00000378152	.	.	.	4.32	4.32	0.51571	.	0.165430	0.39759	N	0.001273	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-23.0337	14.7275	0.69354	0.0:1.0:0.0:0.0	.	.	.	.	X	146;113;182;161;128	.	ENSP00000323044:Q182X	Q	+	1	0	ARHGEF1	47088582	0.995000	0.38212	0.986000	0.45419	0.457000	0.32468	3.640000	0.54350	2.157000	0.67596	0.306000	0.20318	CAG		0.662	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		T	42396742	C	T	42396742	4	4	70	1	0	0	0	0	0	1	0	0	893	595	21	3	507	3	ARHGEF1	19	42396742	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	4368737	42396742	16732241	66	21067										
BCAM	4059	broad.mit.edu	37	chr19	45322958	45322958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gcaaagggggcccctgctgcCgccagcggcgggagaagggg	20	12	0	1	rs376176106		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr19:45322958C>T	ENST00000270233.6	+	13	1760	c.1738C>T	c.(1738-1740)Cgc>Tgc	p.R580C	BCAM_ENST00000589651.1_Missense_Mutation_p.R580C	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	580					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)	p.R580C(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCCCTGCTGCCGCCAGCGGCG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19							CYS/ARG,CYS/ARG	0,4364		0,0,2182	16	19	18		1738,1738	3	1	19		18	2,8508		0,2,4253	no	missense,missense	BCAM	NM_001013257.1,NM_005581.3	180,180	0,2,6435	TT,TC,CC		0.0235,0.0,0.0155	benign,benign	580/589,580/629	45322958	2,12872	2182	4255	6437	50014798	SO:0001583	missense	4059			X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1738C>T	19.37:g.45322958C>T	ENSP00000270233:p.Arg580Cys		50014798	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	7.155	0.584470	0.13749	0.0	2.35E-4	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.60299	0.2;0.24	4.08	3.04	0.35103	.	.	.	.	.	T	0.30696	0.0773	N	0.03608	-0.345	0.31357	N	0.681868	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	9	0.45353	T	0.12	-23.0305	6.0449	0.19753	0.0:0.1279:0.0:0.8721	.	580	P50895	BCAM_HUMAN	C	580	ENSP00000270233:R580C;ENSP00000375817:R580C	ENSP00000270233:R580C	R	+	1	0	BCAM	50014798	1.000000	0.71417	0.999000	0.59377	0.015000	0.08874	1.530000	0.36007	0.576000	0.29452	-0.425000	0.05940	CGC		0.647	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322958	C	T	45322958	3	4	70	1	0	0	0	0	1	0	0	0	1345	652	23	1	1788	1	BCAM	19	45322958	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	2926216	45322958	13806025	67	21068										
KCNG1	3755	broad.mit.edu	37	chr20	49620944	49620944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gatgacgtagagcaggggcgCgaagagggcgatggccacgc	19	9	0	3			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr20:49620944C>T	ENST00000371571.4	-	3	1459	c.1174G>A	c.(1174-1176)Gcg>Acg	p.A392T	RP5-955M13.4_ENST00000424566.1_RNA|KCNG1_ENST00000506387.1_5'UTR	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	392					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.A392T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						AGCAGGGGCGCGAAGAGGGCG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	20											32	36	35					20																	49620944		2203	4300	6503	49054351	SO:0001583	missense	3755			AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.1174G>A	20.37:g.49620944C>T	ENSP00000360626:p.Ala392Thr		49054351	A8K3S4|O43528|Q5JXL5|Q9BRC1	Missense_Mutation	SNP	ENST00000371571.4	37	CCDS13436.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.903477	0.52333	.	.	ENSG00000026559	ENST00000371571	D	0.98400	-4.91	5.22	5.22	0.72569	Ion transport (1);	0.203246	0.52532	D	0.000072	D	0.97826	0.9286	M	0.63843	1.955	0.80722	D	1	D	0.56287	0.975	P	0.52424	0.698	D	0.97484	1.0049	9	.	.	.	.	14.4818	0.67587	0.1477:0.8523:0.0:0.0	.	392	Q9UIX4	KCNG1_HUMAN	T	392	ENSP00000360626:A392T	.	A	-	1	0	KCNG1	49054351	0.999000	0.42202	1.000000	0.80357	0.221000	0.24807	3.874000	0.56101	2.433000	0.82419	0.313000	0.20887	GCG		0.672	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		T	49620944	C	T	49620944	3	4	70	1	0	0	0	0	1	0	0	0	8048	768	27	1	371	1	KCNG1	20	49620944	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		49620944	13404576	68	21069										
KRTAP19-5	337972	broad.mit.edu	37	chr21	31874312	31874312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	accgccatagcccagtctgcGgaagctgccacatccacagc	9	17	1	0	rs142713888		TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	SOLID			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr21:31874312G>A	ENST00000334151.2	-	1	123	c.97C>T	c.(97-99)Cgc>Tgc	p.R33C		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	33						intermediate filament (GO:0005882)		p.R33C(1)		endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						CCCAGTCTGCGGAAGCTGCCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	21						G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	136	124	128		97	-9.4	0	21	dbSNP_134	128	0,8600		0,0,4300	no	missense	KRTAP19-5	NM_181611.1	180	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	33/73	31874312	3,13003	2203	4300	6503	30796183	SO:0001583	missense	337972			AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.97C>T	21.37:g.31874312G>A	ENSP00000334985:p.Arg33Cys		30796183	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	37	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	G	9.976	1.226806	0.22542	6.81E-4	0.0	ENSG00000186977	ENST00000334151	T	0.10477	2.87	4.71	-9.43	0.00607	.	.	.	.	.	T	0.06280	0.0162	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.39292	-0.9621	8	0.87932	D	0	.	4.6993	0.12820	0.2416:0.442:0.2274:0.089	.	33	Q3LI72	KR195_HUMAN	C	33	ENSP00000334985:R33C	ENSP00000334985:R33C	R	-	1	0	KRTAP19-5	30796183	0.000000	0.05858	0.000000	0.03702	0.238000	0.25445	-0.422000	0.07043	-2.657000	0.00421	-0.226000	0.12346	CGC		0.587	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			A	31874312	G	A	31874312	3	1	70	1	0	0	0	0	1	0	0	0	8553	1116	39	1	124	1	KRTAP19-5	21	31874312	Missense_Mutation	SNP	G	TCGA-AG-A01L-01A-01W-A00K-09		31874312	16255583	69	21070										
TNRC6B	23112	broad.mit.edu	37	chr22	40662788	40662788	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	caccacctccaggcaacgttCgaccttccaattccagctgg	7	17	0	0			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr22:40662788C>T	ENST00000454349.2	+	5	2765	c.2554C>T	c.(2554-2556)Cga>Tga	p.R852*	TNRC6B_ENST00000335727.9_Nonsense_Mutation_p.R852*|TNRC6B_ENST00000301923.9_Intron|TNRC6B_ENST00000402203.1_Intron	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	852	Interaction with argonaute proteins.|Pro-rich.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R866*(2)		breast(1)	1						AGGCAACGTTCGACCTTCCAA	0.617																																																2	Substitution - Nonsense(2)	large_intestine(2)	22											31	37	35					22																	40662788		2107	4216	6323	38992734	SO:0001587	stop_gained	23112			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.2554C>T	22.37:g.40662788C>T	ENSP00000401946:p.Arg852*		38992734	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Nonsense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	43	10.036531	0.99323	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	.	.	.	5.46	4.4	0.53042	.	0.062472	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-4.4001	12.7472	0.57287	0.4244:0.5756:0.0:0.0	.	.	.	.	X	852	.	ENSP00000338371:R852X	R	+	1	2	TNRC6B	38992734	1.000000	0.71417	0.936000	0.37596	0.986000	0.74619	2.771000	0.47670	1.230000	0.43646	0.561000	0.74099	CGA		0.617	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40662788	C	T	40662788	4	4	70	1	0	0	0	0	0	1	0	0	16380	876	31	1	2693	1	TNRC6B	22	40662788	Nonsense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09		40662788	10641778	70	21071										
EFCAB6	64800	broad.mit.edu	37	chr22	43926709	43926709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	gctcaccgtcctgaaatctgCgacgcttagcagccctgttc	9	15	2	1			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chr22:43926709C>T	ENST00000262726.7	-	31	4622	c.4369G>A	c.(4369-4371)Gca>Aca	p.A1457T	EFCAB6_ENST00000396231.2_Missense_Mutation_p.A1305T|EFCAB6-AS1_ENST00000431327.3_RNA|EFCAB6_ENST00000461800.1_5'UTR	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1457	EF-hand 16. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Interaction with AR.|Interaction with PARK7.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.A1457T(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				CTGAAATCTGCGACGCTTAGC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	22											78	68	72					22																	43926709		2203	4300	6503	42258042	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.4369G>A	22.37:g.43926709C>T	ENSP00000262726:p.Ala1457Thr		42258042	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.012689	0.35511	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.08102	3.13;3.13	4.56	3.54	0.40534	EF-hand-like domain (1);	0.521194	0.17829	N	0.160586	T	0.15176	0.0366	L	0.49571	1.57	0.09310	N	0.999991	D	0.76494	0.999	P	0.62560	0.904	T	0.10337	-1.0634	10	0.14656	T	0.56	-6.3559	7.4113	0.27019	0.0:0.7392:0.1689:0.0919	.	1457	Q5THR3	EFCB6_HUMAN	T	1305;1457	ENSP00000379533:A1305T;ENSP00000262726:A1457T	ENSP00000262726:A1457T	A	-	1	0	EFCAB6	42258042	0.021000	0.18746	0.312000	0.25196	0.015000	0.08874	0.512000	0.22755	1.129000	0.42072	0.655000	0.94253	GCA		0.592	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43926709	C	T	43926709	3	4	70	1	0	0	0	0	1	0	0	0	4950	768	27	1	144	1	EFCAB6	22	43926709	Missense_Mutation	SNP	C	TCGA-AG-A01L-01A-01W-A00K-09	3263921	43926709	7377857	71	21072										
SCML2	10389	broad.mit.edu	37	chrX	18348761	18348761	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tttctcttgattctccttctTgacatccatggaatctaata	4	10	4	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chrX:18348761T>A	ENST00000251900.4	-	3	196	c.37A>T	c.(37-39)Aag>Tag	p.K13*		NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	13					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K13*(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					TTCTCCTTCTTGACATCCATG	0.328																																					Esophageal Squamous(100;1252 1965 19021 35517)											1	Substitution - Nonsense(1)	large_intestine(1)	X											74	64	67					X																	18348761		2202	4298	6500	18258682	SO:0001587	stop_gained	10389			Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"Sterile alpha motif (SAM) domain containing"	10581	protein-coding gene	gene with protein product		300208	"sex comb on midleg (Drosophila)-like 2"			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.37A>T	X.37:g.18348761T>A	ENSP00000251900:p.Lys13*		18258682	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Nonsense_Mutation	SNP	ENST00000251900.4	37	CCDS14185.1	.	.	.	.	.	.	.	.	.	.	T	36	5.697012	0.96802	.	.	ENSG00000102098	ENST00000251900;ENST00000442000	.	.	.	4.15	2.98	0.34508	.	1.230160	0.06241	N	0.690364	.	.	.	.	.	.	0.38440	D	0.946687	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.7235	0.23342	0.0:0.1138:0.0:0.8862	.	.	.	.	X	13	.	ENSP00000251900:K13X	K	-	1	0	SCML2	18258682	0.955000	0.32602	0.118000	0.21660	0.957000	0.61999	1.424000	0.34848	0.743000	0.32719	0.412000	0.27726	AAG		0.328	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055941.1	NM_006089		A	18348761	T	A	18348761	4	1	70	1	0	0	0	0	0	1	0	0	13947	1821	63	5	2117	5	SCML2	23	18348761	Nonsense_Mutation	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09		18348761	136921799	72	21073										
ZXDA	7789	broad.mit.edu	37	chrX	57935200	57935200	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	tgtgcttggatgtgaagagtTtattacaagaggagatcggg	15	3	0	4			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chrX:57935200T>G	ENST00000358697.4	-	1	1867	c.1655A>C	c.(1654-1656)aAa>aCa	p.K552T		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	552	Required for interaction with ZXDC.				positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K552T(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						TGTGAAGAGTTTATTACAAGA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	X											50	46	48					X																	57935200		2201	4279	6480	57951925	SO:0001583	missense	7789			L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"Zinc fingers, C2H2-type"	13198	protein-coding gene	gene with protein product	"zinc finger protein 896"	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.1655A>C	X.37:g.57935200T>G	ENSP00000351530:p.Lys552Thr		57951925	Q9UJP7	Missense_Mutation	SNP	ENST00000358697.4	37	CCDS14376.1	.	.	.	.	.	.	.	.	.	.	.	15.46	2.839390	0.51057	.	.	ENSG00000198205	ENST00000358697	T	0.35421	1.31	3.15	3.15	0.36227	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.054870	0.64402	D	0.000001	T	0.45175	0.1329	M	0.62723	1.935	0.80722	D	1	P	0.41546	0.754	P	0.51945	0.685	T	0.33445	-0.9868	9	.	.	.	.	8.9853	0.35990	0.0:0.0:0.0:1.0	.	552	P98168	ZXDA_HUMAN	T	552	ENSP00000351530:K552T	.	K	-	2	0	ZXDA	57951925	1.000000	0.71417	0.996000	0.52242	0.904000	0.53231	6.818000	0.75257	1.471000	0.48121	0.339000	0.21740	AAA		0.483	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156		G	57935200	T	G	57935200	3	3	70	1	0	0	0	0	1	0	0	0	18289	1841	64	4	748	4	ZXDA	23	57935200	Missense_Mutation	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09	39586439	57935200	97335360	73	21074										
PLP1	5354	broad.mit.edu	37	chrX	103040643	103040643	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0675675675675676	5	1	0.707070707070707	0	0.719261581330547	0.0151515151515152	0.132034632034632	0	cctcactggcacagaaaagcTaattgagacctatttctcca	6	12	2	2			TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01L-01A-01W-A00K-09	TCGA-AG-A01L-10A-01W-A00L-09	g.chrX:103040643T>A	ENST00000303958.2	+	2	283	c.137T>A	c.(136-138)cTa>cAa	p.L46Q	PLP1_ENST00000361621.2_Missense_Mutation_p.L46Q|PLP1_ENST00000418604.1_Missense_Mutation_p.L46Q	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	46			L -> P (in HLD1/SPG2). {ECO:0000269|PubMed:15712223, ECO:0000269|PubMed:9934976}.|L -> R (in HLD1). {ECO:0000269|PubMed:9894878}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)	p.L46Q(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						ACAGAAAAGCTAATTGAGACC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	X	GRCh37	CM991053|CM993196	PLP1	M							204	182	190					X																	103040643		2203	4300	6503	102927299	SO:0001583	missense	5354			M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.137T>A	X.37:g.103040643T>A	ENSP00000305152:p.Leu46Gln		102927299	P04400|P06905|Q502Y1|Q6FHZ6	Missense_Mutation	SNP	ENST00000303958.2	37	CCDS14513.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.246937	0.80024	.	.	ENSG00000123560	ENST00000434483;ENST00000429977;ENST00000455268;ENST00000422393;ENST00000433491;ENST00000418604;ENST00000443502;ENST00000303958;ENST00000361621;ENST00000428755	D;D;D;D;D;D;D;D;D	0.99494	-6.01;-6.01;-6.01;-6.01;-6.01;-6.01;-6.01;-6.01;-6.01	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.99312	0.9759	M	0.68317	2.08	0.58432	D	0.99999	D;D;D	0.89917	0.999;1.0;0.99	D;D;P	0.91635	0.998;0.999;0.637	D	0.99143	1.0856	10	0.44086	T	0.13	0.2692	12.5455	0.56197	0.0:0.0:0.0:1.0	.	46;46;46	B1B1G6;P60201;P60201-2	.;MYPR_HUMAN;.	Q	46	ENSP00000403335:L46Q;ENSP00000399913:L46Q;ENSP00000409802:L46Q;ENSP00000413931:L46Q;ENSP00000393391:L46Q;ENSP00000405750:L46Q;ENSP00000391853:L46Q;ENSP00000305152:L46Q;ENSP00000354860:L46Q	ENSP00000305152:L46Q	L	+	2	0	PLP1	102927299	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	7.698000	0.84413	1.869000	0.54173	0.486000	0.48141	CTA		0.493	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			A	103040643	T	A	103040643	3	1	70	1	0	0	0	0	1	0	0	0	12135	1522	53	5	143	5	PLP1	23	103040643	Missense_Mutation	SNP	T	TCGA-AG-A01L-01A-01W-A00K-09	45105443	103040643	52229917	74	21075										
FAM54B	56181	broad.mit.edu	37	chr1	26156308	26156308	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aggactttcaccgaatgaaaCagagtcaagatctgtaagta	9	7	3	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:26156308C>T	ENST00000374301.3	+	6	1068	c.760C>T	c.(760-762)Cag>Tag	p.Q254*	RP1-317E23.7_ENST00000606617.1_RNA|MTFR1L_ENST00000469815.1_3'UTR|MTFR1L_ENST00000374307.5_Nonsense_Mutation_p.Q242*|MTFR1L_ENST00000374303.2_Nonsense_Mutation_p.Q254*|MTFR1L_ENST00000474295.1_3'UTR|MTFR1L_ENST00000466284.1_3'UTR|MTFR1L_ENST00000374300.3_Nonsense_Mutation_p.Q254*|MTFR1L_ENST00000526894.1_3'UTR|MTFR1L_ENST00000524618.1_Nonsense_Mutation_p.Q157*	NM_019557.5	NP_062457.3	Q9H019	MFR1L_HUMAN	mitochondrial fission regulator 1-like	254								p.Q254*(1)									CCGAATGAAACAGAGTCAAGA	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											31	29	30					1																	26156308		1921	4125	6046	26028895	SO:0001587	stop_gained	56181				CCDS41284.1, CCDS44089.1	1p36.11	2012-11-30	2012-11-29	2012-11-29	ENSG00000117640	ENSG00000117640			28836	protein-coding gene	gene with protein product			"family with sequence similarity 54, member B"	FAM54B		8619474, 9110174	Standard	NM_019557		Approved		uc001bkq.4	Q9H019	OTTHUMG00000007377	ENST00000374301.3:c.760C>T	1.37:g.26156308C>T	ENSP00000363419:p.Gln254*		26028895	A6NCB4|B7WNV5|D3DPJ4|Q63HP1|Q7Z2S7|Q9NUI7	Nonsense_Mutation	SNP	ENST00000374301.3	37	CCDS41284.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782905	0.90282	.	.	ENSG00000117640	ENST00000374303;ENST00000472643;ENST00000524618;ENST00000374307;ENST00000374301;ENST00000374300	.	.	.	5.95	5.95	0.96441	.	0.102064	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	0.0534	20.3932	0.98965	0.0:1.0:0.0:0.0	.	.	.	.	X	254;157;157;242;254;254	.	ENSP00000363418:Q254X	Q	+	1	0	FAM54B	26028895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.744000	0.68664	2.824000	0.97209	0.655000	0.94253	CAG		0.443	MTFR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019319.1	NM_019557		T	26156308	C	T	26156308	4	4	71	1	0	0	0	0	0	1	0	0	5602	479	17	3	778	3	FAM54B	1	26156308	Nonsense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		26156308	223094313	1	21076										
MUTYH	4595	broad.mit.edu	37	chr1	45799144	45799144	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccagcttagcaggctccctcGgaaggctgtgacttcagcta	11	13	1	1	rs138775799		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:45799144G>A	ENST00000372098.3	-	3	413	c.280C>T	c.(280-282)Cga>Tga	p.R94*	MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000372100.5_Nonsense_Mutation_p.R80*|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000354383.6_Nonsense_Mutation_p.R70*|MUTYH_ENST00000448481.1_Nonsense_Mutation_p.R80*|MUTYH_ENST00000372104.1_Nonsense_Mutation_p.R69*|MUTYH_ENST00000372110.3_Nonsense_Mutation_p.R84*|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000355498.2_Nonsense_Mutation_p.R69*|MUTYH_ENST00000372115.3_Nonsense_Mutation_p.R83*|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000456914.2_Nonsense_Mutation_p.R69*|MUTYH_ENST00000528013.2_Nonsense_Mutation_p.R83*|MUTYH_ENST00000450313.1_Nonsense_Mutation_p.R97*			Q9UIF7	MUTYH_HUMAN	mutY homolog	94					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)	p.R94*(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					AGGCTCCCTCGGAAGGCTGTG	0.612			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																													yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	1	Substitution - Nonsense(1)	large_intestine(1)	1	GRCh37	CM030378	MUTYH	M	rs138775799	G	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	101	86	91		247,208,205,205,289,280	4.4	0.9	1	dbSNP_134	91	0,8600		0,0,4300	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	MUTYH	NM_001048171.1,NM_001048172.1,NM_001048173.1,NM_001048174.1,NM_001128425.1,NM_012222.2	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	83/536,70/523,69/522,69/522,97/550,94/547	45799144	1,13005	2203	4300	6503	45571731	SO:0001587	stop_gained	4595	Familial Cancer Database	MAP, MYH-associated polyposis	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.280C>T	1.37:g.45799144G>A	ENSP00000361170:p.Arg94*		45571731	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Nonsense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.102628	0.76983	2.27E-4	0.0	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000435155;ENST00000528013;ENST00000483127	.	.	.	5.33	4.41	0.53225	.	0.055638	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.0325	15.4466	0.75235	0.0:0.0:0.86:0.14	.	.	.	.	X	69;80;69;70;69;94;84;83;97;80;80;83;75	.	ENSP00000346354:R70X	R	-	1	2	MUTYH	45571731	1.000000	0.71417	0.870000	0.34147	0.421000	0.31385	6.756000	0.74919	1.451000	0.47736	0.655000	0.94253	CGA		0.612	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		A	45799144	G	A	45799144	4	1	71	1	0	0	0	0	0	1	0	0	10023	1124	39	1	1416	1	MUTYH	1	45799144	Nonsense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	19642836	45799144	203451477	2	21077										
DENND2D	79961	broad.mit.edu	37	chr1	111737251	111737251	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tctccagcacggcagaggcaAagatctgaagtatctgttca	10	10	4	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:111737251A>G	ENST00000357640.4	-	7	972	c.743T>C	c.(742-744)tTt>tCt	p.F248S	DENND2D_ENST00000369752.5_Missense_Mutation_p.F245S|DENND2D_ENST00000473682.1_5'Flank	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	248	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.F248S(1)		breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		GGCAGAGGCAAAGATCTGAAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	68	67					1																	111737251		2203	4300	6503	111538774	SO:0001583	missense	79961				CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"DENN/MADD domain containing"	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.743T>C	1.37:g.111737251A>G	ENSP00000350266:p.Phe248Ser		111538774	Q5T5V6|Q9BSU0	Missense_Mutation	SNP	ENST00000357640.4	37	CCDS831.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.922484	0.92319	.	.	ENSG00000162777	ENST00000357640;ENST00000369752	T;T	0.15256	2.44;2.44	5.79	5.79	0.91817	DENN (3);	0.000000	0.85682	D	0.000000	T	0.41673	0.1169	M	0.90759	3.145	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.53373	-0.8448	10	0.87932	D	0	-16.1842	14.083	0.64937	1.0:0.0:0.0:0.0	.	245;248	Q9H6A0-2;Q9H6A0	.;DEN2D_HUMAN	S	248;245	ENSP00000350266:F248S;ENSP00000358767:F245S	ENSP00000350266:F248S	F	-	2	0	DENND2D	111538774	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.497000	0.81536	2.211000	0.71520	0.533000	0.62120	TTT		0.532	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		G	111737251	A	G	111737251	3	3	71	1	0	0	0	0	1	0	0	0	4442	14	1	4	696	4	DENND2D	1	111737251	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	65938107	111737251	137513370	3	21078										
SYT6	148281	broad.mit.edu	37	chr1	114680226	114680226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcatgtcatggcgggagaagCggtcaaagtcgaagacactg	14	8	3	2	rs549305784		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:114680226C>T	ENST00000610222.1	-	3	1108	c.962G>A	c.(961-963)cGc>cAc	p.R321H	SYT6_ENST00000393296.1_Missense_Mutation_p.R321H|SYT6_ENST00000609117.1_Missense_Mutation_p.R236H|SYT6_ENST00000607941.1_Missense_Mutation_p.R236H|SYT6_ENST00000369547.1_Missense_Mutation_p.R236H			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	321	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.R236H(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-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)		GCGGGAGAAGCGGTCAAAGTC	0.532													C|||	1	0.000199681	0	0	5008	,	,		17826	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											90	84	86					1																	114680226		2203	4300	6503	114481749	SO:0001583	missense	148281				CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.962G>A	1.37:g.114680226C>T	ENSP00000476396:p.Arg321His		114481749	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.293177	0.95546	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	5.45	5.45	0.79879	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.30448	0.0765	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.08764	-1.0706	10	0.87932	D	0	.	19.2901	0.94095	0.0:1.0:0.0:0.0	.	321	Q5T7P8	SYT6_HUMAN	H	236;321;236;321	ENSP00000358560:R236H;ENSP00000376974:R321H;ENSP00000358559:R236H;ENSP00000358558:R321H	ENSP00000358558:R321H	R	-	2	0	SYT6	114481749	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.815000	0.86186	2.567000	0.86603	0.650000	0.86243	CGC		0.532	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		T	114680226	C	T	114680226	3	4	71	1	0	0	0	0	1	0	0	0	15517	768	27	1	590	1	SYT6	1	114680226	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	2942975	114680226	134570395	4	21079										
FAM5C	339479	broad.mit.edu	37	chr1	190067930	190067930	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aatggcatggacttctattcGtctgtccgttttctgcagca	9	10	3	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:190067930G>A	ENST00000367462.3	-	8	1750	c.1519C>T	c.(1519-1521)Cga>Tga	p.R507*	BRINP3_ENST00000534846.1_Nonsense_Mutation_p.R405*	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	507					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.R507*(3)									ACTTCTATTCGTCTGTCCGTT	0.483																																																3	Substitution - Nonsense(3)	large_intestine(1)|kidney(1)|endometrium(1)	1											159	152	154					1																	190067930		2203	4300	6503	188334553	SO:0001587	stop_gained	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1519C>T	1.37:g.190067930G>A	ENSP00000356432:p.Arg507*		188334553	B3KVP1|B7Z260|O95726|Q2M330	Nonsense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028520	0.93518	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	.	.	.	5.75	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6238	0.45495	0.0:0.0:0.6879:0.3121	.	.	.	.	X	507;405	.	ENSP00000356432:R507X	R	-	1	2	FAM5C	188334553	0.819000	0.29175	0.368000	0.25939	0.962000	0.63368	1.147000	0.31602	2.712000	0.92718	0.591000	0.81541	CGA		0.483	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190067930	G	A	190067930	4	1	71	1	0	0	0	0	0	1	0	0	5613	1153	40	1	785	1	FAM5C	1	190067930	Nonsense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	75387704	190067930	59182691	5	21080										
KCNT2	343450	broad.mit.edu	37	chr1	196438126	196438126	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggttcttttaggacttactgAgataatgaagggaactgcat	11	5	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:196438126A>C	ENST00000294725.9	-	6	1372	c.457T>G	c.(457-459)Tca>Gca	p.S153A	KCNT2_ENST00000609185.1_Missense_Mutation_p.S153A|KCNT2_ENST00000367433.5_Missense_Mutation_p.S153A|KCNT2_ENST00000367431.4_Missense_Mutation_p.S153A|KCNT2_ENST00000451324.2_5'UTR			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	153					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.S153A(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GGACTTACTGAGATAATGAAG	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	1											41	42	41					1																	196438126		2200	4297	6497	194704749	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.457T>G	1.37:g.196438126A>C	ENSP00000294725:p.Ser153Ala		194704749	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.615017	0.46631	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.18016	2.24;2.26;2.52	5.41	5.41	0.78517	.	0.278962	0.26231	N	0.025561	T	0.11623	0.0283	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.19445	0.036;0.007;0.012;0.036	B;B;B;B	0.25506	0.01;0.016;0.061;0.01	T	0.17258	-1.0375	10	0.27082	T	0.32	-14.7458	8.5006	0.33156	0.7321:0.0:0.0:0.2679	.	153;153;153;153	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	A	153	ENSP00000356403:S153A;ENSP00000356401:S153A;ENSP00000294725:S153A	ENSP00000294725:S153A	S	-	1	0	KCNT2	194704749	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.720000	0.68470	2.269000	0.75478	0.455000	0.32223	TCA		0.289	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196438126	A	C	196438126	3	2	71	1	0	0	0	0	1	0	0	0	8113	304	11	4	3042	4	KCNT2	1	196438126	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	6370196	196438126	52812495	6	21081										
F13B	2165	broad.mit.edu	37	chr1	197009695	197009695	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	atattttaactgccctctgtCacattgcattctaagtatag	5	9	3	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:197009695C>A	ENST00000367412.1	-	11	1952	c.1909G>T	c.(1909-1911)Gac>Tac	p.D637Y	F13B_ENST00000490002.1_5'UTR	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	637	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)		p.D637Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						TGCCCTCTGTCACATTGCATT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											79	84	82					1																	197009695		2201	4293	6494	195276318	SO:0001583	missense	2165			M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1909G>T	1.37:g.197009695C>A	ENSP00000356382:p.Asp637Tyr		195276318	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	C	8.355	0.831881	0.16820	.	.	ENSG00000143278	ENST00000367412	D	0.82893	-1.66	5.77	1.62	0.23740	Complement control module (1);	0.471179	0.15845	N	0.241834	T	0.75547	0.3864	M	0.68317	2.08	0.29167	N	0.877365	P	0.47106	0.89	B	0.36719	0.231	T	0.70684	-0.4804	10	0.59425	D	0.04	.	5.9223	0.19088	0.0:0.5085:0.1876:0.3038	.	637	P05160	F13B_HUMAN	Y	637	ENSP00000356382:D637Y	ENSP00000356382:D637Y	D	-	1	0	F13B	195276318	0.862000	0.29867	0.995000	0.50966	0.172000	0.22775	-0.314000	0.08092	0.461000	0.27071	-0.140000	0.14226	GAC		0.308	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		A	197009695	C	A	197009695	3	1	71	1	0	0	0	0	1	0	0	0	5354	826	29	2	84	2	F13B	1	197009695	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	571569	197009695	52240926	7	21082										
IGFN1	91156	broad.mit.edu	37	chr1	201185880	201185880	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gagatattggtggctcctgaGggtgagagaaaaggctgggg	19	4	0	4	rs35601315		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:201185880G>T	ENST00000335211.4	+	16	9724	c.9594G>T	c.(9592-9594)gaG>gaT	p.E3198D	IGFN1_ENST00000295591.8_Splice_Site_p.E358D	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	741						nucleus (GO:0005634)|Z disc (GO:0030018)		p.E3198D(1)|p.E358D(1)		autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TGGCTCCTGAGGGTGAGAGAA	0.647																																																2	Substitution - Missense(2)	large_intestine(2)	1											26	32	30					1																	201185880		2203	4299	6502	199452503	SO:0001630	splice_region_variant	91156			AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.9595+1G>T	1.37:g.201185880G>T			199452503	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.30|14.30	2.495435|2.495435	0.44352|0.44352	.|.	.|.	ENSG00000163395|ENSG00000163395	ENST00000335211;ENST00000295591|ENST00000412892	D;D|.	0.82711|.	-1.64;-1.64|.	4.06|4.06	-0.682|-0.682	0.11339|0.11339	.|.	0.696719|.	0.13421|.	N|.	0.389167|.	T|T	0.38878|0.38878	0.1057|0.1057	M|M	0.61703|0.61703	1.905|1.905	0.29993|0.29993	N|N	0.816734|0.816734	B|.	0.29085|.	0.232|.	B|.	0.29267|.	0.1|.	T|T	0.43245|0.43245	-0.9403|-0.9403	10|5	0.54805|.	T|.	0.06|.	.|.	2.2373|2.2373	0.04011|0.04011	0.327:0.0:0.2717:0.4013|0.327:0.0:0.2717:0.4013	.|.	3198|.	F8WAI1|.	.|.	D|C	3198;358|616	ENSP00000334714:E3198D;ENSP00000295591:E358D|.	ENSP00000295591:E358D|.	E|G	+|+	3|1	2|0	IGFN1|IGFN1	199452503|199452503	0.983000|0.983000	0.35010|0.35010	0.998000|0.998000	0.56505|0.56505	0.858000|0.858000	0.48976|0.48976	0.215000|0.215000	0.17562|0.17562	0.010000|0.010000	0.14839|0.14839	0.561000|0.561000	0.74099|0.74099	GAG|GGC		0.647	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	Missense_Mutation	T	201185880	G	T	201185880	5	4	71	1	0	0	0	0	0	0	1	0	7611	1014	35	2	9652	2	IGFN1	1	201185880	Splice_Site	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	4176185	201185880	48064741	8	21083										
ETNK2	55224	broad.mit.edu	37	chr1	204115797	204115797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgatctcgttcttcacaagcGtgaaataattgtgcatcttg	8	8	4	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:204115797G>A	ENST00000367202.4	-	3	764	c.614C>T	c.(613-615)aCg>aTg	p.T205M	ETNK2_ENST00000367198.2_Missense_Mutation_p.T27M|ETNK2_ENST00000367199.2_Intron|ETNK2_ENST00000367201.3_Missense_Mutation_p.T205M	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	205					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)	p.T205M(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CTTCACAAGCGTGAAATAATT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											203	174	184					1																	204115797		2203	4300	6503	202382420	SO:0001583	missense	55224			AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.614C>T	1.37:g.204115797G>A	ENSP00000356170:p.Thr205Met		202382420	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932393	0.52866	.	.	ENSG00000143845	ENST00000367201;ENST00000367202;ENST00000455266;ENST00000367198;ENST00000422699;ENST00000452983	T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4	5.34	4.42	0.53409	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.396532	0.30473	N	0.009560	T	0.34513	0.0900	L	0.33245	0.995	0.36903	D	0.890482	P;P	0.39480	0.46;0.675	B;B	0.29862	0.108;0.094	T	0.44832	-0.9302	10	0.52906	T	0.07	-12.0424	7.9755	0.30153	0.0817:0.0:0.7597:0.1586	.	205;205	Q9NVF9;Q9NVF9-2	EKI2_HUMAN;.	M	205;205;71;27;71;62	ENSP00000356169:T205M;ENSP00000356170:T205M;ENSP00000356166:T27M;ENSP00000405497:T71M;ENSP00000398091:T62M	ENSP00000356166:T27M	T	-	2	0	ETNK2	202382420	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.809000	0.55606	1.478000	0.48253	0.655000	0.94253	ACG		0.502	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		A	204115797	G	A	204115797	3	1	71	1	0	0	0	0	1	0	0	0	5287	1145	40	1	570	1	ETNK2	1	204115797	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	2929917	204115797	45134824	9	21084										
RYR2	6262	broad.mit.edu	37	chr1	237872314	237872314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggacatgtcggaggcagaacTcctcatcctagatgagttca	11	10	2	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr1:237872314T>C	ENST00000366574.2	+	69	10375	c.10058T>C	c.(10057-10059)cTc>cCc	p.L3353P	RYR2_ENST00000360064.6_Missense_Mutation_p.L3351P|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.L3337P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3353					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.L3351P(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGGCAGAACTCCTCATCCTA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											83	83	83					1																	237872314		1923	4131	6054	235938937	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10058T>C	1.37:g.237872314T>C	ENSP00000355533:p.Leu3353Pro		235938937	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640415	0.47153	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.97161	-4.27;-4.24;-4.26	5.51	5.51	0.81932	.	0.000000	0.53938	D	0.000042	D	0.97813	0.9282	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.65010	0.931	D	0.98043	1.0383	10	0.59425	D	0.04	-12.0057	11.6029	0.51015	0.0:0.0:0.1487:0.8513	.	3353	Q92736	RYR2_HUMAN	P	3353;3351;3337;308	ENSP00000355533:L3353P;ENSP00000353174:L3351P;ENSP00000443798:L3337P	ENSP00000353174:L3351P	L	+	2	0	RYR2	235938937	1.000000	0.71417	0.399000	0.26333	0.235000	0.25334	5.028000	0.64115	2.093000	0.63338	0.533000	0.62120	CTC		0.478	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237872314	T	C	237872314	3	2	71	1	0	0	0	0	1	0	0	0	13806	1551	54	4	10332	4	RYR2	1	237872314	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	33756517	237872314	11378307	10	21085										
ERLEC1	27248	broad.mit.edu	37	chr2	54028753	54028753	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcttgtgcagtcatcctaaaTataggtaggatgtgcattta	9	6	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:54028753T>G	ENST00000185150.4	+	7	876	c.745T>G	c.(745-747)Tat>Gat	p.Y249D	ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ERLEC1_ENST00000378239.5_Missense_Mutation_p.Y249D|ASB3_ENST00000498475.2_Intron|ERLEC1_ENST00000405123.3_Missense_Mutation_p.Y249D	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	249					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)	p.Y249D(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TCATCCTAAATATAGGTAGGA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	2											55	51	52					2																	54028753		2203	4300	6503	53882257	SO:0001583	missense	27248			AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"erlectin 1"	611229	"chromosome 2 open reading frame 30"	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.745T>G	2.37:g.54028753T>G	ENSP00000185150:p.Tyr249Asp		53882257	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	37	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.330846	0.81690	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	T;T	0.53640	0.68;0.61	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.987;0.99	T	0.75513	-0.3291	9	0.87932	D	0	-16.1865	16.4323	0.83853	0.0:0.0:0.0:1.0	.	249;249;249	Q96DZ1-2;B5MC72;Q96DZ1	.;.;ERLEC_HUMAN	D	249	ENSP00000385629:Y249D;ENSP00000185150:Y249D	ENSP00000185150:Y249D	Y	+	1	0	ERLEC1	53882257	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.281000	0.76405	0.528000	0.53228	TAT		0.343	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701		G	54028753	T	G	54028753	3	3	71	1	0	0	0	0	1	0	0	0	5244	1406	49	4	771	4	ERLEC1	2	54028753	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10		54028753	189170620	11	21086										
KIAA1841	84542	broad.mit.edu	37	chr2	61324877	61324877	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cacattgtcaataccactcaGaaacagtggtttatcctact	5	11	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:61324877G>A	ENST00000402291.1	+	12	1496	c.1255G>A	c.(1255-1257)Gaa>Aaa	p.E419K	KIAA1841_ENST00000356719.2_Missense_Mutation_p.E419K|KIAA1841_ENST00000295031.5_Missense_Mutation_p.E419K|KIAA1841_ENST00000453873.1_Missense_Mutation_p.E419K	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	419								p.E419K(1)		breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			ATACCACTCAGAAACAGTGGT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											139	132	134					2																	61324877		2203	4300	6503	61178381	SO:0001583	missense	84542			BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.1255G>A	2.37:g.61324877G>A	ENSP00000385579:p.Glu419Lys		61178381	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	37	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.651111	0.67472	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.89	5.89	0.94794	.	0.289214	0.38164	N	0.001781	T	0.54334	0.1852	L	0.56769	1.78	0.47183	D	0.999347	B;P	0.35468	0.447;0.503	B;B	0.31101	0.108;0.124	T	0.58482	-0.7629	9	0.62326	D	0.03	-8.0847	16.0538	0.80779	0.0:0.1703:0.8297:0.0	.	419;419	Q6NSI8-2;Q6NSI8	.;K1841_HUMAN	K	419	.	ENSP00000295031:E419K	E	+	1	0	KIAA1841	61178381	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	6.829000	0.75314	2.799000	0.96334	0.579000	0.79373	GAA		0.353	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		A	61324877	G	A	61324877	3	1	71	1	0	0	0	0	1	0	0	0	8282	943	33	3	1293	3	KIAA1841	2	61324877	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	7296124	61324877	181874496	12	21087										
DPP10	57628	broad.mit.edu	37	chr2	116548883	116548883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aacttcctttacagttgtccCttcccaaagattttatggac	5	11	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:116548883C>T	ENST00000410059.1	+	19	2131	c.1651C>T	c.(1651-1653)Ctt>Ttt	p.L551F	DPP10_ENST00000393147.2_Missense_Mutation_p.L555F|DPP10_ENST00000310323.8_Missense_Mutation_p.L544F|DPP10_ENST00000409163.1_Missense_Mutation_p.L501F	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	551						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.L544F(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						ACAGTTGTCCCTTCCCAAAGA	0.294																																																1	Substitution - Missense(1)	large_intestine(1)	2											91	96	94					2																	116548883		2203	4299	6502	116265353	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1651C>T	2.37:g.116548883C>T	ENSP00000386565:p.Leu551Phe		116265353	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	C	4.609	0.113217	0.08831	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.54	1.7	0.24286	.	0.380667	0.29073	N	0.013225	T	0.19604	0.0471	N	0.02539	-0.55	0.25491	N	0.987645	B;B;B;B	0.09022	0.002;0.0;0.0;0.001	B;B;B;B	0.12156	0.007;0.0;0.002;0.003	T	0.16571	-1.0398	10	0.35671	T	0.21	-3.6091	7.4393	0.27174	0.0:0.3616:0.0:0.6384	.	544;555;547;551	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	F	551;501;555;544;501	ENSP00000386565:L551F;ENSP00000387038:L501F;ENSP00000376855:L555F;ENSP00000309066:L544F	ENSP00000309066:L544F	L	+	1	0	DPP10	116265353	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.376000	0.34306	0.176000	0.19873	-0.300000	0.09419	CTT		0.294	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116548883	C	T	116548883	3	4	71	1	0	0	0	0	1	0	0	0	4738	681	24	3	1896	3	DPP10	2	116548883	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	55224006	116548883	126650490	13	21088										
NEB	4703	broad.mit.edu	37	chr2	152506794	152506794	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgacgatatttcttctcacTgatgatttccgaagcccgct	7	12	2	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:152506794T>G	ENST00000172853.10	-	54	7474	c.7327A>C	c.(7327-7329)Agt>Cgt	p.S2443R	NEB_ENST00000604864.1_Missense_Mutation_p.S2443R|NEB_ENST00000427231.2_Missense_Mutation_p.S2443R|NEB_ENST00000603639.1_Missense_Mutation_p.S2443R|NEB_ENST00000409198.1_Missense_Mutation_p.S2443R|NEB_ENST00000397345.3_Missense_Mutation_p.S2443R			P20929	NEBU_HUMAN	nebulin	2443					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.S2443R(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCTTCTCACTGATGATTTCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	2											154	145	148					2																	152506794		1903	4123	6026	152215040	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7327A>C	2.37:g.152506794T>G	ENSP00000172853:p.Ser2443Arg		152215040	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	22.1	4.245785	0.80024	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.10382	2.88;2.91;2.9;2.97	5.37	5.37	0.77165	.	0.047237	0.85682	D	0.000000	T	0.37705	0.1013	M	0.87971	2.92	0.80722	D	1	D	0.71674	0.998	D	0.67900	0.954	T	0.40905	-0.9538	10	0.72032	D	0.01	.	15.3752	0.74598	0.0:0.0:0.0:1.0	.	2443	P20929	NEBU_HUMAN	R	2443	ENSP00000386259:S2443R;ENSP00000380505:S2443R;ENSP00000416578:S2443R;ENSP00000172853:S2443R	ENSP00000172853:S2443R	S	-	1	0	NEB	152215040	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.124000	0.64709	2.044000	0.60594	0.528000	0.53228	AGT		0.443	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152506794	T	G	152506794	3	3	71	1	0	0	0	0	1	0	0	0	10333	1580	55	4	18875	4	NEB	2	152506794	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	35957911	152506794	90692579	14	21089										
FIGN	55137	broad.mit.edu	37	chr2	164467927	164467927	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agagacatctgctggagggaGggctgaactgactccagctt	14	9	1	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:164467927G>T	ENST00000333129.3	-	3	729	c.415C>A	c.(415-417)Ctc>Atc	p.L139I	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'UTR	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	139					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)	p.L139I(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GCTGGAGGGAGGGCTGAACTG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	2											100	96	97					2																	164467927		1963	4159	6122	164176173	SO:0001583	missense	55137			AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.415C>A	2.37:g.164467927G>T	ENSP00000333836:p.Leu139Ile		164176173	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	G	14.74	2.625280	0.46840	.	.	ENSG00000182263	ENST00000333129	T	0.25250	1.81	6.07	6.07	0.98685	.	0.067362	0.64402	D	0.000009	T	0.23133	0.0559	L	0.34521	1.04	0.54753	D	0.999986	B	0.13145	0.007	B	0.10450	0.005	T	0.01613	-1.1312	10	0.56958	D	0.05	-8.5629	15.3849	0.74691	0.0:0.0:0.8607:0.1393	.	139	Q5HY92	FIGN_HUMAN	I	139	ENSP00000333836:L139I	ENSP00000333836:L139I	L	-	1	0	FIGN	164176173	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.496000	0.66918	2.885000	0.99019	0.655000	0.94253	CTC		0.507	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164467927	G	T	164467927	3	4	71	1	0	0	0	0	1	0	0	0	5910	1000	35	2	1868	2	FIGN	2	164467927	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	11961133	164467927	78731446	15	21090										
SCN9A	6335	broad.mit.edu	37	chr2	167084233	167084233	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cgtccatcccttaaaagttgCctttaagaataacattaata	4	9	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:167084233C>A	ENST00000409435.1	-	22	4206	c.4207G>T	c.(4207-4209)Gca>Tca	p.A1403S	SCN9A_ENST00000375387.4_Splice_Site_p.A1404S|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Splice_Site_p.A1404S|SCN9A_ENST00000409672.1_Splice_Site_p.A1392S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1403					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.A1392S(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTAAAAGTTGCCTTTAAGAAT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	2											49	45	47					2																	167084233		1788	4032	5820	166792479	SO:0001630	splice_region_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4207-1G>T	2.37:g.167084233C>A			166792479	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.322149	0.60634	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	D	0.98204	0.9406	L	0.42245	1.32	0.58432	D	0.999998	D	0.62365	0.991	D	0.71184	0.972	D	0.99349	1.0914	10	0.87932	D	0	.	15.6585	0.77162	0.1376:0.8624:0.0:0.0	.	1392	E7EUN6	.	S	1392;1404;1404;1403	ENSP00000386306:A1392S;ENSP00000364536:A1404S;ENSP00000304748:A1404S;ENSP00000386330:A1403S	ENSP00000304748:A1404S	A	-	1	0	SCN9A	166792479	1.000000	0.71417	1.000000	0.80357	0.136000	0.21042	4.777000	0.62361	2.571000	0.86741	0.467000	0.42956	GCA		0.274	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	Missense_Mutation	A	167084233	C	A	167084233	5	1	71	1	0	0	0	0	0	0	1	0	13962	753	26	2	1779	2	SCN9A	2	167084233	Splice_Site	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	2616306	167084233	76115140	16	21091										
TTN	7273	broad.mit.edu	37	chr2	179463494	179463494	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccaattggatctctagcagtCgctgggtctgatggcagact	12	10	2	2	rs370998052		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:179463494C>T	ENST00000591111.1	-	241	52244	c.52020G>A	c.(52018-52020)gcG>gcA	p.A17340A	TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Silent_p.A18981A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Silent_p.A10041A|TTN_ENST00000460472.2_Silent_p.A9916A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Silent_p.A16413A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.A10108A			Q8WZ42	TITIN_HUMAN	titin	17340	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A16411A(1)|p.A9916A(1)|p.A10108A(1)|p.A10041A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTAGCAGTCGCTGGGTCTG	0.418													C|||	1	0.000199681	0	0	5008	,	,		19712	0.001		0	False		,,,				2504	0															4	Substitution - coding silent(4)	large_intestine(4)	2						C	,,,	0,3730		0,0,1865	144	141	142		29748,49239,30123,30324	3.9	1	2		142	1,8169		0,1,4084	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,5949	TT,TC,CC		0.0122,0.0,0.0084	,,,	9916/26927,16413/33424,10041/27052,10108/27119	179463494	1,11899	1865	4085	5950	179171739	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.52020G>A	2.37:g.179463494C>T			179171739	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179463494	C	T	179463494	2	4	71	1	0	0	0	0	0	0	0	1	16775	871	31	1		1	TTN	2	179463494	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	12379261	179463494	63735879	17	21092										
WDR75	84128	broad.mit.edu	37	chr2	190313193	190313193	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tactgcatggacacagaaatCtggtgactggaatccagctt	10	9	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:190313193C>T	ENST00000314761.4	+	2	235	c.175C>T	c.(175-177)Ctg>Ttg	p.L59L		NM_032168.1	NP_115544.1	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	59						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L59L(1)		breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			ACACAGAAATCTGGTGACTGG	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	2											139	125	130					2																	190313193		2203	4300	6503	190021438	SO:0001819	synonymous_variant	84128			AK091546	CCDS2298.1	2q32.2	2013-01-09			ENSG00000115368	ENSG00000115368		"WD repeat domain containing"	25725	protein-coding gene	gene with protein product	"UTP17, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_032168		Approved	FLJ12519, NET16, UTP17	uc002uql.1	Q8IWA0	OTTHUMG00000132660	ENST00000314761.4:c.175C>T	2.37:g.190313193C>T			190021438	Q96J10|Q9H8U8|Q9H9U5|Q9H9V8|Q9UIX2	Silent	SNP	ENST00000314761.4	37	CCDS2298.1																																																																																				0.383	WDR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255913.1	NM_032168		T	190313193	C	T	190313193	2	4	71	1	0	0	0	0	0	0	0	1	17365	912	32	3		3	WDR75	2	190313193	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	10849699	190313193	52886180	18	21093										
ANKRD44	91526	broad.mit.edu	37	chr2	197990164	197990164	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgtcaaatgcattgatatttGcccctttggccaagagtaaa	8	8	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:197990164G>T	ENST00000328737.2	-	6	492	c.416C>A	c.(415-417)gCa>gAa	p.A139E	ANKRD44_ENST00000409919.1_Missense_Mutation_p.A164E|ANKRD44_ENST00000337207.5_Missense_Mutation_p.A139E|ANKRD44_ENST00000450567.1_Missense_Mutation_p.A139E|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A156E|ANKRD44_ENST00000409153.1_Missense_Mutation_p.A164E|ANKRD44_ENST00000539527.1_Missense_Mutation_p.A92E			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	164								p.A139E(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTGATATTTGCCCCTTTGGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	2											128	118	121					2																	197990164		2203	4300	6503	197698409	SO:0001583	missense	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.416C>A	2.37:g.197990164G>T	ENSP00000331516:p.Ala139Glu		197698409	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		.	.	.	.	.	.	.	.	.	.	G	24.0	4.486414	0.84854	.	.	ENSG00000065413	ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000409153;ENST00000539527;ENST00000409919	T;T;T;T;T;T;T	0.70631	1.68;-0.5;-0.5;1.75;1.75;1.33;-0.5	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.88209	0.6375	M	0.92970	3.365	0.80722	D	1	P;D	0.89917	0.687;1.0	P;D	0.91635	0.732;0.999	D	0.90909	0.4774	10	0.87932	D	0	.	18.6181	0.91310	0.0:0.0:1.0:0.0	.	92;164	F5H682;Q8N8A2-3	.;.	E	156;139;139;139;164;92;164	ENSP00000282272:A156E;ENSP00000331516:A139E;ENSP00000402420:A139E;ENSP00000338794:A139E;ENSP00000387141:A164E;ENSP00000437825:A92E;ENSP00000387233:A164E	ENSP00000282272:A156E	A	-	2	0	ANKRD44	197698409	1.000000	0.71417	1.000000	0.80357	0.491000	0.33493	9.601000	0.98297	2.612000	0.88384	0.655000	0.94253	GCA		0.448	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		T	197990164	G	T	197990164	3	4	71	1	0	0	0	0	1	0	0	0	672	1319	46	2	2427	2	ANKRD44	2	197990164	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	7676971	197990164	45209209	19	21094										
STRADB	55437	broad.mit.edu	37	chr2	202337735	202337735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	acggcatactcccacaggaaCactggtaactataaaaatta	6	10	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:202337735C>T	ENST00000194530.3	+	5	616	c.251C>T	c.(250-252)aCa>aTa	p.T84I	STRADB_ENST00000392249.2_Missense_Mutation_p.T84I	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	84	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.T84I(1)		breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						CCCACAGGAACACTGGTAACT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											120	118	119					2																	202337735		2203	4300	6503	202045980	SO:0001583	missense	55437			AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.251C>T	2.37:g.202337735C>T	ENSP00000194530:p.Thr84Ile		202045980	Q5BKY7|Q9P1L0	Missense_Mutation	SNP	ENST00000194530.3	37	CCDS2348.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476131	0.44044	.	.	ENSG00000082146	ENST00000458269;ENST00000194530;ENST00000539670;ENST00000392249	T;T;T	0.65732	-0.17;-0.17;-0.17	5.36	4.48	0.54585	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.162090	0.56097	D	0.000034	T	0.54647	0.1871	L	0.39566	1.225	0.37416	D	0.913455	P	0.34562	0.457	B	0.36989	0.238	T	0.63492	-0.6625	10	0.66056	D	0.02	.	11.5947	0.50966	0.0:0.807:0.1239:0.0691	.	84	Q9C0K7	STRAB_HUMAN	I	29;84;84;84	ENSP00000409552:T29I;ENSP00000194530:T84I;ENSP00000376080:T84I	ENSP00000194530:T84I	T	+	2	0	STRADB	202045980	0.371000	0.25056	1.000000	0.80357	0.849000	0.48306	0.872000	0.28037	1.385000	0.46445	0.563000	0.77884	ACA		0.378	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571		T	202337735	C	T	202337735	3	4	71	1	0	0	0	0	1	0	0	0	15364	478	17	3	265	3	STRADB	2	202337735	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	4347571	202337735	40861638	20	21095										
ZDBF2	57683	broad.mit.edu	37	chr2	207162065	207162065	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cgtttcttacaggatgtactGcagcaccacccatatcattg	7	12	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:207162065G>T	ENST00000374423.3	+	4	542	c.156G>T	c.(154-156)ctG>ctT	p.L52L		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	52							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L52L(2)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGGATGTACTGCAGCACCACC	0.388																																																2	Substitution - coding silent(2)	large_intestine(2)	2											145	138	140					2																	207162065		1926	4132	6058	206870310	SO:0001819	synonymous_variant	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.156G>T	2.37:g.207162065G>T			206870310	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																				0.388	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207162065	G	T	207162065	2	4	71	1	0	0	0	0	0	0	0	1	17638	1306	46	2		2	ZDBF2	2	207162065	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	4824330	207162065	36037308	21	21096										
C2orf57	165100	broad.mit.edu	37	chr2	232458831	232458831	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	caccccacgccaggcccaggCtgaccccaactatgattaga	8	17	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr2:232458831C>A	ENST00000313965.2	+	1	1257	c.1169C>A	c.(1168-1170)gCt>gAt	p.A390D		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	390								p.A390D(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		CAGGCCCAGGCTGACCCCAAC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	2											30	29	29					2																	232458831		2201	4300	6501	232167075	SO:0001583	missense	165100			BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.1169C>A	2.37:g.232458831C>A	ENSP00000315557:p.Ala390Asp		232167075	Q8N4F2	Missense_Mutation	SNP	ENST00000313965.2	37	CCDS2487.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027516	0.54683	.	.	ENSG00000177673	ENST00000313965	T	0.21361	2.01	4.92	4.92	0.64577	.	.	.	.	.	T	0.26268	0.0641	N	0.12182	0.205	0.09310	N	1	D	0.71674	0.998	D	0.69654	0.965	T	0.20240	-1.0281	9	0.26408	T	0.33	.	13.5084	0.61497	0.0:1.0:0.0:0.0	.	390	Q53QW1	CB057_HUMAN	D	390	ENSP00000315557:A390D	ENSP00000315557:A390D	A	+	2	0	C2orf57	232167075	0.000000	0.05858	0.005000	0.12908	0.119000	0.20118	0.666000	0.25097	2.569000	0.86673	0.557000	0.71058	GCT		0.657	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614		A	232458831	C	A	232458831	3	1	71	1	0	0	0	0	1	0	0	0	2184	797	28	2	1171	2	C2orf57	2	232458831	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	25296766	232458831	10740542	22	21097										
SCN10A	6336	broad.mit.edu	37	chr3	38753913	38753913	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttcatgatggatgggatggcGcccaccagggcatccaccac	12	13	1	1	rs375572917		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:38753913G>A	ENST00000449082.2	-	22	3827	c.3828C>T	c.(3826-3828)ggC>ggT	p.G1276G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1276					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G1276G(2)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	ATGGGATGGCGCCCACCAGGG	0.542																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	3						G		0,4406		0,0,2203	84	81	82		3828	-5.4	0.8	3		82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SCN10A	NM_006514.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1276/1957	38753913	1,13005	2203	4300	6503	38728917	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3828C>T	3.37:g.38753913G>A			38728917	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.542	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38753913	G	A	38753913	2	1	71	1	0	0	0	0	0	0	0	1	13949	1074	38	1		1	SCN10A	3	38753913	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		38753913	159268517	23	21098										
BSN	8927	broad.mit.edu	37	chr3	49699686	49699686	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcaaggggtacgaaagggaaCgggaggctgtggagcgactt	19	6	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:49699686C>T	ENST00000296452.4	+	6	10522	c.10408C>T	c.(10408-10410)Cgg>Tgg	p.R3470W		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3470					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.R3470W(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CGAAAGGGAACGGGAGGCTGT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	3											46	52	50					3																	49699686		2203	4300	6503	49674690	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.10408C>T	3.37:g.49699686C>T	ENSP00000296452:p.Arg3470Trp		49674690	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	5.724	0.318101	0.10845	.	.	ENSG00000164061	ENST00000296452	T	0.20069	2.1	5.81	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.37265	0.0997	L	0.40543	1.245	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.05533	-1.0879	10	0.72032	D	0.01	-22.2479	14.3088	0.66403	0.2636:0.7364:0.0:0.0	.	3470	Q9UPA5	BSN_HUMAN	W	3470	ENSP00000296452:R3470W	ENSP00000296452:R3470W	R	+	1	2	BSN	49674690	0.256000	0.24012	0.933000	0.37362	0.427000	0.31564	0.778000	0.26732	2.745000	0.94114	0.655000	0.94253	CGG		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49699686	C	T	49699686	3	4	71	1	0	0	0	0	1	0	0	0	1533	527	19	1	10430	1	BSN	3	49699686	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	10945773	49699686	148322744	24	21099										
ROBO2	6092	broad.mit.edu	37	chr3	77666710	77666710	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cattgccagtacaaacttacTtacaccaaggtctggaagat	7	10	1	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:77666710T>C	ENST00000461745.1	+	22	4240	c.3340T>C	c.(3340-3342)Tta>Cta	p.L1114L	ROBO2_ENST00000487694.3_Silent_p.L1130L|ROBO2_ENST00000332191.8_Silent_p.L1114L|ROBO2_ENST00000469233.1_3'UTR	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1114					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.L1114L(1)|p.L1130L(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ACAAACTTACTTACACCAAGG	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	3											129	118	121					3																	77666710		1983	4169	6152	77749400	SO:0001819	synonymous_variant	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3340T>C	3.37:g.77666710T>C			77749400	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	37	CCDS43109.1																																																																																				0.428	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77666710	T	C	77666710	2	2	71	1	0	0	0	0	0	0	0	1	13551	1606	56	4		4	ROBO2	3	77666710	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	27967024	77666710	120355720	25	21100										
CBLB	868	broad.mit.edu	37	chr3	105459353	105459353	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cttacaatccttccctgctgCcatcaatcagggcttgaaat	6	13	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:105459353C>A	ENST00000264122.4	-	7	1289	c.968G>T	c.(967-969)gGc>gTc	p.G323V	CBLB_ENST00000394027.3_Missense_Mutation_p.G345V|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000403724.1_Missense_Mutation_p.G323V|CBLB_ENST00000405772.1_Missense_Mutation_p.G323V	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	323	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G323V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TTCCCTGCTGCCATCAATCAG	0.418			Mis S		AML																																GBM(93;588 1337 9788 29341 43499)		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	1	Substitution - Missense(1)	large_intestine(1)	3											139	120	127					3																	105459353		2203	4300	6503	106942043	SO:0001583	missense	868			U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.968G>T	3.37:g.105459353C>A	ENSP00000264122:p.Gly323Val		106942043	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169737	0.78452	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	5.73	4.86	0.63082	Adaptor protein Cbl, PTB domain (1);SH2 motif (2);Adaptor protein Cbl, SH2-like (1);	0.000000	0.85682	D	0.000000	D	0.92522	0.7625	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93543	0.6879	10	0.87932	D	0	-15.3322	14.8526	0.70309	0.0:0.931:0.0:0.069	.	345;323;323	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	V	323;345;323;323	ENSP00000264122:G323V;ENSP00000377595:G345V;ENSP00000384816:G323V;ENSP00000384938:G323V	ENSP00000264122:G323V	G	-	2	0	CBLB	106942043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.479000	0.81095	1.423000	0.47198	0.650000	0.86243	GGC		0.418	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		A	105459353	C	A	105459353	3	1	71	1	0	0	0	0	1	0	0	0	2707	739	26	2	2032	2	CBLB	3	105459353	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	27792643	105459353	92563077	26	21101										
A4GNT	51146	broad.mit.edu	37	chr3	137849958	137849958	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aacacaatgccacgtctgtgGctcaggagggcttccagccc	11	14	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:137849958G>C	ENST00000236709.3	-	2	342	c.141C>G	c.(139-141)agC>agG	p.S47R		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	47					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)	p.S47R(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						CACGTCTGTGGCTCAGGAGGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											80	82	82					3																	137849958		2203	4300	6503	139332648	SO:0001583	missense	51146			AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.141C>G	3.37:g.137849958G>C	ENSP00000236709:p.Ser47Arg		139332648	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	ENST00000236709.3	37	CCDS3097.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.091886	0.00364	.	.	ENSG00000118017	ENST00000236709	T	0.80480	-1.38	5.42	0.853	0.19001	.	0.602435	0.15765	N	0.245754	T	0.50377	0.1612	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.38478	-0.9659	10	0.14656	T	0.56	-1.1079	5.3855	0.16216	0.07:0.2098:0.5078:0.2124	.	47	Q9UNA3	A4GCT_HUMAN	R	47	ENSP00000236709:S47R	ENSP00000236709:S47R	S	-	3	2	A4GNT	139332648	0.063000	0.20901	0.285000	0.24819	0.023000	0.10783	0.593000	0.23999	0.219000	0.20840	0.561000	0.74099	AGC		0.532	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161		C	137849958	G	C	137849958	3	2	71	1	0	0	0	0	1	0	0	0	7	1194	42	5	889	5	A4GNT	3	137849958	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	32390605	137849958	60172472	27	21102										
PLCH1	23007	broad.mit.edu	37	chr3	155200316	155200316	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aataagatgggaaattacacTctcctgcagaattgcagttg	9	7	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr3:155200316T>A	ENST00000340059.7	-	23	3522	c.3523A>T	c.(3523-3525)Agt>Tgt	p.S1175C	PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000334686.6_Missense_Mutation_p.S1137C|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000460012.1_Missense_Mutation_p.S1137C|PLCH1_ENST00000414191.1_Missense_Mutation_p.S1137C	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1175					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.S1137C(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GAAATTACACTCTCCTGCAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											72	72	72					3																	155200316		2203	4300	6503	156683010	SO:0001583	missense	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3523A>T	3.37:g.155200316T>A	ENSP00000345988:p.Ser1175Cys		156683010	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.339585	0.81911	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.57	4.37	0.52481	.	0.498534	0.22562	N	0.058458	T	0.49218	0.1544	L	0.32530	0.975	0.37343	D	0.91048	D;D	0.63046	0.988;0.992	P;P	0.54706	0.759;0.579	T	0.58999	-0.7536	10	0.87932	D	0	.	12.0085	0.53274	0.1291:0.0:0.0:0.8709	.	1137;1175	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	C	1137;1175;1137;1137	ENSP00000417502:S1137C;ENSP00000345988:S1175C;ENSP00000335469:S1137C;ENSP00000412977:S1137C	ENSP00000335469:S1137C	S	-	1	0	PLCH1	156683010	1.000000	0.71417	0.976000	0.42696	0.978000	0.69477	4.651000	0.61447	2.116000	0.64780	0.482000	0.46254	AGT		0.458	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		A	155200316	T	A	155200316	3	1	71	1	0	0	0	0	1	0	0	0	12068	1551	54	5	1562	5	PLCH1	3	155200316	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	17350358	155200316	42822114	28	21103										
CORIN	10699	broad.mit.edu	37	chr4	47676443	47676443	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	actgttgttcgggtcacagaGagagctaccaccacatgaat	10	10	1	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr4:47676443G>C	ENST00000273857.4	-	10	1323	c.1324C>G	c.(1324-1326)Ctc>Gtc	p.L442V	CORIN_ENST00000508498.1_Missense_Mutation_p.L303V|CORIN_ENST00000502252.1_Missense_Mutation_p.L375V|CORIN_ENST00000504584.1_Missense_Mutation_p.L405V|CORIN_ENST00000505909.1_Missense_Mutation_p.L405V	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	442					female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.L442V(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						GGGTCACAGAGAGAGCTACCA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	4											232	206	215					4																	47676443		2203	4300	6503	47371200	SO:0001583	missense	10699			AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.1324C>G	4.37:g.47676443G>C	ENSP00000273857:p.Leu442Val		47371200	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	37	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.568640	0.28003	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	D;D;D;D;D	0.92752	-2.63;-2.61;-2.61;-2.49;-3.1	4.83	3.98	0.46160	.	0.529435	0.19248	N	0.118994	D	0.87853	0.6282	M	0.63843	1.955	0.25417	N	0.988308	B;P;B;B	0.38922	0.146;0.651;0.022;0.172	B;B;B;B	0.30943	0.034;0.122;0.006;0.023	T	0.78380	-0.2226	10	0.24483	T	0.36	.	11.6759	0.51430	0.0824:0.0:0.9176:0.0	.	405;405;375;442	B7Z4R1;B4E2W9;B4E1Y7;Q9Y5Q5	.;.;.;CORIN_HUMAN	V	442;303;375;405;405	ENSP00000273857:L442V;ENSP00000425597:L303V;ENSP00000424212:L375V;ENSP00000425401:L405V;ENSP00000423216:L405V	ENSP00000273857:L442V	L	-	1	0	CORIN	47371200	0.002000	0.14202	0.701000	0.30321	0.966000	0.64601	0.600000	0.24104	1.381000	0.46364	0.650000	0.86243	CTC		0.448	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			C	47676443	G	C	47676443	3	2	71	1	0	0	0	0	1	0	0	0	3758	942	33	5	1856	5	CORIN	4	47676443	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		47676443	143477833	29	21104										
LPHN3	23284	broad.mit.edu	37	chr4	62758608	62758608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgtgaggctgtggaagcccGagaaatcatgtggtttaaga	14	6	1	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr4:62758608G>A	ENST00000514591.1	+	9	1840	c.1511G>A	c.(1510-1512)cGa>cAa	p.R504Q	LPHN3_ENST00000506700.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000509896.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000514157.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000506720.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000514996.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000507164.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000504896.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000508946.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000545650.1_Missense_Mutation_p.R504Q|LPHN3_ENST00000507625.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000508693.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000512091.2_Missense_Mutation_p.R504Q|LPHN3_ENST00000506746.1_Missense_Mutation_p.R572Q|LPHN3_ENST00000511324.1_Missense_Mutation_p.R572Q			Q9HAR2	LPHN3_HUMAN	latrophilin 3	504					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.R504Q(1)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GTGGAAGCCCGAGAAATCATG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4											62	60	61					4																	62758608		1947	4149	6096	62441203	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1511G>A	4.37:g.62758608G>A	ENSP00000422533:p.Arg504Gln		62441203	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.196024	0.78902	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.83	5.83	0.93111	.	0.608627	0.17519	N	0.171330	T	0.64011	0.2560	L	0.54965	1.715	0.45378	D	0.998368	P;P	0.52463	0.953;0.453	B;B	0.43052	0.406;0.05	T	0.69075	-0.5241	10	0.87932	D	0	.	19.1256	0.93382	0.0:0.0:1.0:0.0	.	504;504	E9PE04;Q9HAR2-2	.;.	Q	504;504;572;572;504;504;504;504;504;572;572;572;504;504;504;572;572;504	ENSP00000423388:R504Q;ENSP00000422533:R504Q;ENSP00000423787:R572Q;ENSP00000425033:R572Q;ENSP00000424120:R504Q;ENSP00000439831:R504Q;ENSP00000421476:R572Q;ENSP00000424030:R572Q;ENSP00000421372:R572Q;ENSP00000425201:R504Q;ENSP00000423434:R504Q;ENSP00000421627:R504Q;ENSP00000420931:R572Q;ENSP00000425884:R572Q;ENSP00000424258:R504Q	ENSP00000280009:R504Q	R	+	2	0	LPHN3	62441203	0.998000	0.40836	0.998000	0.56505	0.996000	0.88848	7.779000	0.85648	2.763000	0.94921	0.563000	0.77884	CGA		0.488	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62758608	G	A	62758608	3	1	71	1	0	0	0	0	1	0	0	0	8946	1058	37	1	1537	1	LPHN3	4	62758608	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	15082165	62758608	128395668	30	21105										
LPHN3	23284	broad.mit.edu	37	chr4	62775310	62775310	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gaaacagctgccaacattgcTagagagctggctgaacagac	11	10	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr4:62775310T>C	ENST00000514591.1	+	11	2045	c.1716T>C	c.(1714-1716)gcT>gcC	p.A572A	LPHN3_ENST00000506700.1_Silent_p.A572A|LPHN3_ENST00000509896.1_Silent_p.A640A|LPHN3_ENST00000514157.1_Silent_p.A572A|LPHN3_ENST00000506720.1_Silent_p.A640A|LPHN3_ENST00000514996.1_Silent_p.A572A|LPHN3_ENST00000507164.1_Silent_p.A640A|LPHN3_ENST00000504896.1_Silent_p.A572A|LPHN3_ENST00000508946.1_Silent_p.A572A|LPHN3_ENST00000545650.1_Silent_p.A572A|LPHN3_ENST00000507625.1_Silent_p.A640A|LPHN3_ENST00000508693.1_Silent_p.A640A|LPHN3_ENST00000512091.2_Silent_p.A572A|LPHN3_ENST00000506746.1_Silent_p.A640A|LPHN3_ENST00000511324.1_Silent_p.A640A			Q9HAR2	LPHN3_HUMAN	latrophilin 3	572					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.A572A(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CCAACATTGCTAGAGAGCTGG	0.423																																																3	Substitution - coding silent(3)	large_intestine(3)	4											43	43	43					4																	62775310		1897	4121	6018	62457905	SO:0001819	synonymous_variant	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1716T>C	4.37:g.62775310T>C			62457905	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.295617	0.23564	.	.	ENSG00000150471	ENST00000502815	.	.	.	5.33	-3.39	0.04868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.9337	0.03332	0.3:0.3647:0.1021:0.2332	.	.	.	.	Q	43	.	.	X	+	1	0	LPHN3	62457905	0.960000	0.32886	0.988000	0.46212	0.966000	0.64601	0.147000	0.16202	-0.395000	0.07715	-0.344000	0.07964	TAG		0.423	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			C	62775310	T	C	62775310	2	2	71	1	0	0	0	0	0	0	0	1	8946	1509	53	4		4	LPHN3	4	62775310	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	16702	62775310	128378966	31	21106										
GALNTL6	442117	broad.mit.edu	37	chr4	173873385	173873385	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aaatactaccctccagtggaGcccccgcctgctgcctgggg	11	16	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr4:173873385G>T	ENST00000506823.1	+	10	2004	c.1347G>T	c.(1345-1347)gaG>gaT	p.E449D	GALNTL6_ENST00000508122.1_Missense_Mutation_p.E432D	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	449					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.E449D(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						CTCCAGTGGAGCCCCCGCCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	4											44	41	42					4																	173873385		2203	4300	6503	174109960	SO:0001583	missense	442117				CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.1347G>T	4.37:g.173873385G>T	ENSP00000423313:p.Glu449Asp		174109960	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	37	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	g	16.06	3.014579	0.54468	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	T;T	0.76578	-1.03;-1.03	5.36	3.61	0.41365	Ricin B-related lectin (1);	0.000000	0.64402	D	0.000004	T	0.62950	0.2470	N	0.25647	0.755	0.58432	D	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.55970	-0.8056	10	0.17369	T	0.5	.	11.7217	0.51685	0.1439:0.0:0.8561:0.0	.	449	Q49A17	GLTL6_HUMAN	D	449;432	ENSP00000423313:E449D;ENSP00000423827:E432D	ENSP00000423313:E449D	E	+	3	2	GALNTL6	174109960	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.088000	0.57678	1.393000	0.46605	0.478000	0.44815	GAG		0.607	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		T	173873385	G	T	173873385	3	4	71	1	0	0	0	0	1	0	0	0	6245	962	34	2	1381	2	GALNTL6	4	173873385	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	111098075	173873385	17280891	32	21107										
GPR98	84059	broad.mit.edu	37	chr5	90040915	90040915	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gctctttactgctggaattcGgagcgtaatcaattctcttt	8	9	3	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr5:90040915G>A	ENST00000405460.2	+	51	10698	c.10602G>A	c.(10600-10602)tcG>tcA	p.S3534S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3534	Calx-beta 23. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.S3534S(2)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCTGGAATTCGGAGCGTAATC	0.388																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	5											359	342	347					5																	90040915		1877	4100	5977	90076671	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.10602G>A	5.37:g.90040915G>A			90076671	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.525	-0.860255	0.02610	.	.	ENSG00000164199	ENST00000509621	.	.	.	5.48	-0.422	0.12329	.	.	.	.	.	T	0.53883	0.1824	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40384	-0.9566	4	.	.	.	.	7.8713	0.29567	0.6872:0.1007:0.2121:0.0	.	.	.	.	Q	1100	.	.	R	+	2	0	GPR98	90076671	0.003000	0.15002	0.978000	0.43139	0.054000	0.15201	-1.361000	0.02597	-0.706000	0.05028	-1.847000	0.00572	CGG		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90040915	G	A	90040915	2	1	71	1	0	0	0	0	0	0	0	1	6742	1103	39	1		1	GPR98	5	90040915	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		90040915	90874345	33	21108										
APC	324	broad.mit.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	71	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	22133002	112173917	68741343	34	21109										
GFRA3	2676	broad.mit.edu	37	chr5	137593604	137593604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggtcacacttgtcattgagaGtacacagcatggcaaacttg	10	9	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr5:137593604G>A	ENST00000274721.3	-	4	755	c.509C>T	c.(508-510)aCt>aTt	p.T170I	GFRA3_ENST00000378362.3_Missense_Mutation_p.T139I	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3	170					nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)	p.T170I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GTCATTGAGAGTACACAGCAT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	5											35	38	37					5																	137593604		2203	4300	6503	137621503	SO:0001583	missense	2676			AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.509C>T	5.37:g.137593604G>A	ENSP00000274721:p.Thr170Ile		137621503	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Missense_Mutation	SNP	ENST00000274721.3	37	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.335719	0.24253	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	T;T	0.63913	-0.07;-0.07	5.12	3.32	0.38043	GDNF/GAS1 (2);	0.166361	0.52532	D	0.000069	T	0.61451	0.2348	L	0.55834	1.745	0.30314	N	0.788206	P;P	0.39404	0.611;0.672	P;P	0.47251	0.509;0.542	T	0.59674	-0.7410	10	0.36615	T	0.2	-3.2682	8.1463	0.31113	0.1898:0.0:0.8102:0.0	.	139;170	O60609-2;O60609	.;GFRA3_HUMAN	I	170;139	ENSP00000274721:T170I;ENSP00000367613:T139I	ENSP00000274721:T170I	T	-	2	0	GFRA3	137621503	0.957000	0.32711	0.280000	0.24747	0.014000	0.08584	0.907000	0.28531	0.549000	0.28973	-0.136000	0.14681	ACT		0.647	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496		A	137593604	G	A	137593604	3	1	71	1	0	0	0	0	1	0	0	0	6369	1029	36	3	713	3	GFRA3	5	137593604	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	25419687	137593604	43321656	35	21110										
PCDHB7	56129	broad.mit.edu	37	chr5	140553683	140553683	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agtacaacatcaccatcaccGtcaccgacttggggacaccc	7	16	3	0	rs369077920		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr5:140553683G>A	ENST00000231137.3	+	1	1441	c.1267G>A	c.(1267-1269)Gtc>Atc	p.V423I		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	423	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V423I(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACCATCACCGTCACCGACTT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	ILE/VAL	0,4406		0,0,2203	146	131	136		1267	3.6	0.2	5		136	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCDHB7	NM_018940.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	423/794	140553683	1,13005	2203	4300	6503	140533867	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1267G>A	5.37:g.140553683G>A	ENSP00000231137:p.Val423Ile		140533867	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536445	0.65085	0.0	1.16E-4	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.42900	0.96	4.48	3.58	0.41010	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.52661	0.1748	M	0.90145	3.09	0.37786	D	0.927197	P	0.36222	0.544	B	0.37780	0.258	T	0.67499	-0.5655	9	0.54805	T	0.06	.	13.2826	0.60224	0.0827:0.0:0.9173:0.0	.	423	Q9Y5E2	PCDB7_HUMAN	I	423;206	ENSP00000231137:V423I	ENSP00000231137:V423I	V	+	1	0	PCDHB7	140533867	1.000000	0.71417	0.175000	0.22980	0.983000	0.72400	4.636000	0.61339	2.174000	0.68829	0.557000	0.71058	GTC		0.517	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140553683	G	A	140553683	3	1	71	1	0	0	0	0	1	0	0	0	11578	1145	40	1	1269	1	PCDHB7	5	140553683	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	2960079	140553683	40361577	36	21111										
GFPT2	9945	broad.mit.edu	37	chr5	179740821	179740821	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcctaccttggtgctggccaCgccgatctccggccctgcgt	11	17	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr5:179740821C>G	ENST00000253778.8	-	14	1586	c.1417G>C	c.(1417-1419)Gtg>Ctg	p.V473L	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	473	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.V473L(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GTGCTGGCCACGCCGATCTCC	0.721																																																1	Substitution - Missense(1)	large_intestine(1)	5											11	13	13					5																	179740821		2177	4271	6448	179673427	SO:0001583	missense	9945			AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1417G>C	5.37:g.179740821C>G	ENSP00000253778:p.Val473Leu		179673427	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	37	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504995	0.96371	.	.	ENSG00000131459	ENST00000253778	T	0.73575	-0.76	5.8	5.8	0.92144	Sugar isomerase (SIS) (2);	0.000000	0.85682	D	0.000000	D	0.87180	0.6113	H	0.96111	3.77	0.80722	D	1	P	0.40970	0.734	P	0.45856	0.495	D	0.89808	0.3980	9	.	.	.	-30.0037	20.063	0.97692	0.0:1.0:0.0:0.0	.	473	O94808	GFPT2_HUMAN	L	473	ENSP00000253778:V473L	.	V	-	1	0	GFPT2	179673427	1.000000	0.71417	0.967000	0.41034	0.918000	0.54935	7.479000	0.81095	2.741000	0.93983	0.650000	0.86243	GTG		0.721	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		G	179740821	C	G	179740821	3	3	71	1	0	0	0	0	1	0	0	0	6366	536	19	5	655	5	GFPT2	5	179740821	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	39187138	179740821	1174439	37	21112										
FAM50B	26240	broad.mit.edu	37	chr6	3850928	3850928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	acgcgggcaaggtggtgctgCgcagctggtacgagaagaac	17	9	0	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:3850928C>T	ENST00000380274.1	+	1	1309	c.883C>T	c.(883-885)Cgc>Tgc	p.R295C	FAM50B_ENST00000380272.3_Missense_Mutation_p.R295C			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	295						nucleus (GO:0005634)		p.R295C(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				GGTGGTGCTGCGCAGCTGGTA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	64	68					6																	3850928		2203	4300	6503	3795927	SO:0001583	missense	26240			Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.883C>T	6.37:g.3850928C>T	ENSP00000369627:p.Arg295Cys		3795927	Q5T2L6	Missense_Mutation	SNP	ENST00000380274.1	37	CCDS4487.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392137	0.62066	.	.	ENSG00000145945	ENST00000380274;ENST00000380272	.	.	.	4.34	-0.0737	0.13734	.	0.000000	0.85682	D	0.000000	T	0.80160	0.4572	M	0.93462	3.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84188	0.0443	9	0.87932	D	0	-27.9147	12.8376	0.57782	0.6406:0.3594:0.0:0.0	.	295	Q9Y247	FA50B_HUMAN	C	295	.	ENSP00000369625:R295C	R	+	1	0	FAM50B	3795927	1.000000	0.71417	0.962000	0.40283	0.976000	0.68499	1.327000	0.33746	-0.139000	0.11414	-0.410000	0.06199	CGC		0.627	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1	NM_012135		T	3850928	C	T	3850928	3	4	71	1	0	0	0	0	1	0	0	0	5597	768	27	1	885	1	FAM50B	6	3850928	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		3850928	167264139	38	21113										
ZNF292	23036	broad.mit.edu	37	chr6	87967866	87967866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccagtacatttgagggtgccGaaatgctttctcatgtttca	9	9	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:87967866G>A	ENST00000369577.3	+	8	4562	c.4519G>A	c.(4519-4521)Gaa>Aaa	p.E1507K	ZNF292_ENST00000339907.4_Missense_Mutation_p.E1502K	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1507						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E1507K(1)|p.E1362K(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TGAGGGTGCCGAAATGCTTTC	0.433																																																2	Substitution - Missense(2)	large_intestine(2)	6											41	41	41					6																	87967866		1966	4141	6107	88024585	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4519G>A	6.37:g.87967866G>A	ENSP00000358590:p.Glu1507Lys		88024585	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	G	9.901	1.206837	0.22205	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07800	3.16;3.17	5.87	5.87	0.94306	.	0.420327	0.25089	N	0.033222	T	0.03305	0.0096	N	0.24115	0.695	0.43729	D	0.99621	B	0.29766	0.256	B	0.21546	0.035	T	0.47636	-0.9102	10	0.36615	T	0.2	.	18.3838	0.90459	0.0:0.0:1.0:0.0	.	1507	O60281	ZN292_HUMAN	K	1507;1502	ENSP00000358590:E1507K;ENSP00000342847:E1502K	ENSP00000342847:E1502K	E	+	1	0	ZNF292	88024585	0.999000	0.42202	0.794000	0.32065	0.171000	0.22731	3.124000	0.50461	2.779000	0.95612	0.655000	0.94253	GAA		0.433	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87967866	G	A	87967866	3	1	71	1	0	0	0	0	1	0	0	0	17865	1059	37	1	4549	1	ZNF292	6	87967866	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	84116938	87967866	83147201	39	21114										
SIM1	6492	broad.mit.edu	37	chr6	100841613	100841613	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tagcagagagagctgcggtcCgaaaactgtctgtaggcgca	14	9	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:100841613C>T	ENST00000369208.3	-	11	2102	c.1320G>A	c.(1318-1320)tcG>tcA	p.S440S	SIM1_ENST00000262901.4_Silent_p.S440S			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	440	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.S440S(2)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		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)		AGCTGCGGTCCGAAAACTGTC	0.622																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	6											84	79	81					6																	100841613		2203	4300	6503	100948334	SO:0001819	synonymous_variant	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1320G>A	6.37:g.100841613C>T			100948334	Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.622	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		T	100841613	C	T	100841613	2	4	71	1	0	0	0	0	0	0	0	1	14360	639	23	1		1	SIM1	6	100841613	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	12873747	100841613	70273454	40	21115										
GRIK2	2898	broad.mit.edu	37	chr6	102483372	102483372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccatcgagtttgttacccagCggaactgtaacctgacacag	9	12	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:102483372C>T	ENST00000421544.1	+	14	2732	c.2242C>T	c.(2242-2244)Cgg>Tgg	p.R748W	GRIK2_ENST00000369134.4_Missense_Mutation_p.R699W|GRIK2_ENST00000318991.6_Missense_Mutation_p.R748W|GRIK2_ENST00000369137.3_Missense_Mutation_p.R672W|GRIK2_ENST00000413795.1_Missense_Mutation_p.R748W|GRIK2_ENST00000369138.1_Missense_Mutation_p.R748W	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	748					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.R748W(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TGTTACCCAGCGGAACTGTAA	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	6											175	178	177					6																	102483372		2203	4300	6503	102590065	SO:0001583	missense	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2242C>T	6.37:g.102483372C>T	ENSP00000397026:p.Arg748Trp		102590065	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.959914	0.74016	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69;2.69	5.46	2.6	0.31112	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	M	0.90483	3.12	0.44254	D	0.997109	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.48703	-0.9012	10	0.87932	D	0	.	14.8939	0.70630	0.5112:0.4888:0.0:0.0	.	748;748;748	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	W	748;748;748;672;748;699;523	ENSP00000397026:R748W;ENSP00000405596:R748W;ENSP00000358134:R748W;ENSP00000358133:R672W;ENSP00000313276:R748W;ENSP00000358130:R699W	ENSP00000313276:R748W	R	+	1	2	GRIK2	102590065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.133000	0.42093	0.225000	0.20959	0.655000	0.94253	CGG		0.458	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			T	102483372	C	T	102483372	3	4	71	1	0	0	0	0	1	0	0	0	6795	759	27	1	2296	1	GRIK2	6	102483372	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1641759	102483372	68631695	41	21116										
SYNE1	23345	broad.mit.edu	37	chr6	152686149	152686149	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttttcctgtttgactgataaTagagcctgtgaaaacacata	7	7	0	4			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:152686149T>C	ENST00000367255.5	-	63	10579	c.9978A>G	c.(9976-9978)ctA>ctG	p.L3326L	SYNE1_ENST00000341594.5_Silent_p.L3365L|SYNE1_ENST00000448038.1_Silent_p.L3333L|SYNE1_ENST00000265368.4_Silent_p.L3326L|SYNE1_ENST00000423061.1_Silent_p.L3333L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3326					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L3326L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGACTGATAATAGAGCCTGTG	0.373										HNSCC(10;0.0054)																																						2	Substitution - coding silent(2)	large_intestine(2)	6											100	93	96					6																	152686149		2203	4300	6503	152727842	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9978A>G	6.37:g.152686149T>C			152727842	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152686149	T	C	152686149	2	2	71	1	0	0	0	0	0	0	0	1	15484	1393	49	4		4	SYNE1	6	152686149	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	50202777	152686149	18428918	42	21117										
RPS6KA2	6196	broad.mit.edu	37	chr6	166836801	166836801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	atgagcagcccgttccccgcGcgcagctgcttggcaaagcc	12	16	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:166836801G>A	ENST00000265678.4	-	17	1909	c.1686C>T	c.(1684-1686)cgC>cgT	p.R562R	RPS6KA2_ENST00000481261.2_Silent_p.R473R|RPS6KA2_ENST00000405189.3_Silent_p.R473R|RPS6KA2_ENST00000510118.1_Silent_p.R587R|RPS6KA2_ENST00000509742.1_5'UTR|RPS6KA2_ENST00000503859.1_Silent_p.R570R	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	562	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.R570R(1)|p.R562R(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		CGTTCCCCGCGCGCAGCTGCT	0.607																																																2	Substitution - coding silent(2)	large_intestine(2)	6											57	53	55					6																	166836801		2203	4300	6503	166756791	SO:0001819	synonymous_variant	6196			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.1686C>T	6.37:g.166836801G>A			166756791	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																				0.607	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		A	166836801	G	A	166836801	2	1	71	1	0	0	0	0	0	0	0	1	13688	1074	38	1		1	RPS6KA2	6	166836801	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	14150652	166836801	4278266	43	21118										
C6orf70	55780	broad.mit.edu	37	chr6	170159121	170159121	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gtctcaacctgcgtaacgtcTtatggcatgggtttgcgtca	11	10	3	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:170159121T>A	ENST00000366773.3	+	6	598	c.565T>A	c.(565-567)Tta>Ata	p.L189I	ERMARD_ENST00000392095.4_Missense_Mutation_p.L63I|ERMARD_ENST00000418781.3_Missense_Mutation_p.L189I|ERMARD_ENST00000366772.2_Missense_Mutation_p.L189I|ERMARD_ENST00000588451.1_Missense_Mutation_p.L63I	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	189					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.L189I(1)									GCGTAACGTCTTATGGCATGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	6											211	189	197					6																	170159121		2203	4300	6503	169901046	SO:0001583	missense	55780			AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.565T>A	6.37:g.170159121T>A	ENSP00000355735:p.Leu189Ile		169901046	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.079570	0.55753	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095	T;T	0.52754	0.69;0.65	5.47	-2.43	0.06522	.	0.000000	0.41712	D	0.000833	T	0.39759	0.1090	L	0.55103	1.725	0.26015	N	0.981936	D;D;D	0.89917	0.996;0.996;1.0	P;P;D	0.87578	0.885;0.885;0.998	T	0.39502	-0.9611	10	0.66056	D	0.02	.	6.3326	0.21279	0.1152:0.2574:0.0:0.6274	.	189;189;189	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	I	189;189;189;63	ENSP00000355735:L189I;ENSP00000375945:L63I	ENSP00000355734:L189I	L	+	1	2	C6orf70	169901046	0.860000	0.29831	0.061000	0.19648	0.312000	0.27988	0.073000	0.14640	-0.717000	0.04955	0.533000	0.62120	TTA		0.378	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		A	170159121	T	A	170159121	3	1	71	1	0	0	0	0	1	0	0	0	2376	1606	56	5	587	5	C6orf70	6	170159121	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	3322320	170159121	955946	44	21119										
C6orf70	55780	broad.mit.edu	37	chr6	170168258	170168258	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cttcctcttttccttggagaGcctgctatggtaagtattag	9	9	1	1	rs200693784		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr6:170168258G>C	ENST00000366773.3	+	11	1083	c.1050G>C	c.(1048-1050)gaG>gaC	p.E350D	ERMARD_ENST00000392095.4_Missense_Mutation_p.E224D|ERMARD_ENST00000418781.3_Missense_Mutation_p.E350D|ERMARD_ENST00000366772.2_Missense_Mutation_p.E350D|ERMARD_ENST00000588451.1_Missense_Mutation_p.E214D|RP1-266L20.9_ENST00000586101.1_RNA	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	350					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.E350D(1)									TCCTTGGAGAGCCTGCTATGG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	6											124	121	122					6																	170168258		2203	4300	6503	169910183	SO:0001583	missense	55780			AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1050G>C	6.37:g.170168258G>C	ENSP00000355735:p.Glu350Asp		169910183	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.477619	0.26511	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095	T;T	0.44083	0.93;0.94	5.1	0.117	0.14652	.	0.216928	0.31601	N	0.007371	T	0.20740	0.0499	L	0.48986	1.54	0.27597	N	0.94908	P;P;B	0.49559	0.925;0.72;0.007	P;B;B	0.47162	0.54;0.275;0.006	T	0.13072	-1.0523	10	0.34782	T	0.22	.	8.018	0.30393	0.7135:0.0:0.2865:0.0	.	350;350;350	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	D	350;350;350;224	ENSP00000355735:E350D;ENSP00000375945:E224D	ENSP00000355734:E350D	E	+	3	2	C6orf70	169910183	0.781000	0.28676	0.960000	0.40013	0.979000	0.70002	-0.403000	0.07214	0.144000	0.18951	0.655000	0.94253	GAG		0.338	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		C	170168258	G	C	170168258	3	2	71	1	0	0	0	0	1	0	0	0	2376	962	34	5	1092	5	C6orf70	6	170168258	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	9137	170168258	946809	45	21120										
EPDR1	54749	broad.mit.edu	37	chr7	37988628	37988628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	atcaccgtccaggagtggtcGgacagaaagtcagctagatc	12	10	2	2	rs200760284	byFrequency	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:37988628G>A	ENST00000199448.4	+	2	835	c.456G>A	c.(454-456)tcG>tcA	p.S152S	EPDR1_ENST00000425345.1_Silent_p.S91S|EPDR1_ENST00000476620.1_Silent_p.S50S|EPDR1_ENST00000423717.1_Intron|EPDR1_ENST00000559325.1_Silent_p.S272S	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	152					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)	p.S272S(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						AGGAGTGGTCGGACAGAAAGT	0.488													G|||	2	0.000399361	0.0015	0	5008	,	,		18199	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						G		0,4406		0,0,2203	66	67	67		816	-10.5	0	7		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EPDR1	NM_017549.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		272/345	37988628	1,13005	2203	4300	6503	37955153	SO:0001819	synonymous_variant	54749			BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.456G>A	7.37:g.37988628G>A			37955153	A8K4C0|C9JYS3|Q06BL0|Q99M77	Silent	SNP	ENST00000199448.4	37	CCDS5454.2																																																																																				0.488	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		A	37988628	G	A	37988628	2	1	71	1	0	0	0	0	0	0	0	1	5176	1103	39	1		1	EPDR1	7	37988628	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		37988628	121150035	46	21121										
PCLO	27445	broad.mit.edu	37	chr7	82582364	82582364	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gagatgtagaaggtctgttcTgaagaaattggaatttctac	11	4	3	4			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:82582364T>G	ENST00000333891.9	-	5	8242	c.7905A>C	c.(7903-7905)tcA>tcC	p.S2635S	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Silent_p.S2635S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S2635S(4)|p.S2566S(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGGTCTGTTCTGAAGAAATTG	0.463																																																6	Substitution - coding silent(6)	large_intestine(3)|lung(3)	7											90	87	88					7																	82582364		1870	4110	5980	82420300	SO:0001819	synonymous_variant	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7905A>C	7.37:g.82582364T>G			82420300		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.463	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82582364	T	G	82582364	2	3	71	1	0	0	0	0	0	0	0	1	11614	1567	55	4		4	PCLO	7	82582364	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	44593736	82582364	76556299	47	21122										
ZNF804B	219578	broad.mit.edu	37	chr7	88964180	88964180	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gatgaggacctatcttttccTtcctacatctctaggtttaa	6	10	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:88964180T>C	ENST00000333190.4	+	4	2493	c.1884T>C	c.(1882-1884)ccT>ccC	p.P628P		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	628							metal ion binding (GO:0046872)	p.P628P(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TATCTTTTCCTTCCTACATCT	0.388										HNSCC(36;0.09)																																						1	Substitution - coding silent(1)	large_intestine(1)	7											80	84	82					7																	88964180		2203	4300	6503	88802116	SO:0001819	synonymous_variant	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1884T>C	7.37:g.88964180T>C			88802116	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																				0.388	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88964180	T	C	88964180	2	2	71	1	0	0	0	0	0	0	0	1	18210	1596	56	4		4	ZNF804B	7	88964180	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	6381816	88964180	70174483	48	21123										
MUC17	140453	broad.mit.edu	37	chr7	100685938	100685938	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	accaccatgtctgtgtcaatGcccatggaaataagcaccct	7	13	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:100685938G>T	ENST00000306151.4	+	3	11305	c.11241G>T	c.(11239-11241)atG>atT	p.M3747I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3747	Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.M3747I(2)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGTGTCAATGCCCATGGAAA	0.473																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	7											231	219	223					7																	100685938		2203	4300	6503	100472658	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.11241G>T	7.37:g.100685938G>T	ENSP00000302716:p.Met3747Ile		100472658	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.015	-1.568913	0.00895	.	.	ENSG00000169876	ENST00000306151	T	0.01854	4.6	2.18	-4.37	0.03633	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.21546	0.035	T	0.44251	-0.9340	9	0.36615	T	0.2	.	1.8825	0.03231	0.2822:0.1252:0.4285:0.164	.	3747	Q685J3	MUC17_HUMAN	I	3747	ENSP00000302716:M3747I	ENSP00000302716:M3747I	M	+	3	0	MUC17	100472658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.017000	0.03630	-2.879000	0.00320	-2.111000	0.00353	ATG		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100685938	G	T	100685938	3	4	71	1	0	0	0	0	1	0	0	0	10004	1319	46	2	11251	2	MUC17	7	100685938	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	11721758	100685938	58452725	49	21124										
AKR1B15	441282	broad.mit.edu	37	chr7	134256405	134256405	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	taaaggtaatatgatcagtgGaaaaggaacgttcttggatg	12	3	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:134256405G>T	ENST00000457545.2	+	6	745	c.485G>T	c.(484-486)gGa>gTa	p.G162V	AKR1B15_ENST00000423958.1_Missense_Mutation_p.G134V	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	162							oxidoreductase activity (GO:0016491)	p.G134V(1)|p.G134E(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						ATGATCAGTGGAAAAGGAACG	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	7											165	172	170					7																	134256405		2203	4300	6503	133906945	SO:0001583	missense	441282				CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.485G>T	7.37:g.134256405G>T	ENSP00000389289:p.Gly162Val		133906945	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	-	10.08	1.252599	0.22880	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.16073	2.37;2.37	3.04	3.04	0.35103	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.09468	0.0233	N	0.04508	-0.205	0.28335	N	0.92159	B;B	0.25563	0.066;0.129	B;B	0.25987	0.039;0.065	T	0.19289	-1.0310	9	0.87932	D	0	.	11.9075	0.52721	0.0:0.0:1.0:0.0	.	134;162	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	V	162;134	ENSP00000389289:G162V;ENSP00000397009:G134V	ENSP00000397009:G134V	G	+	2	0	AKR1B15	133906945	0.026000	0.19158	0.006000	0.13384	0.068000	0.16541	2.016000	0.40971	1.685000	0.51034	0.405000	0.27470	GGA		0.418	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134256405	G	T	134256405	3	4	71	1	0	0	0	0	1	0	0	0	468	1174	41	2	499	2	AKR1B15	7	134256405	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	33570467	134256405	24882258	50	21125										
AGK	55750	broad.mit.edu	37	chr7	141333742	141333742	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tttgcaatgaccggccttcgAtggggatctttcagagatgc	12	9	2	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:141333742A>G	ENST00000355413.4	+	10	890	c.630A>G	c.(628-630)cgA>cgG	p.R210R	AGK_ENST00000473247.1_Silent_p.R182R|AGK_ENST00000535825.1_Silent_p.R207R	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	210					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.R210R(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					CCGGCCTTCGATGGGGATCTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	7											121	122	122					7																	141333742		2203	4300	6503	140980211	SO:0001819	synonymous_variant	55750			BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.630A>G	7.37:g.141333742A>G			140980211	Q75KN1|Q96GC3|Q9NP48	Silent	SNP	ENST00000355413.4	37	CCDS5865.1																																																																																				0.363	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		G	141333742	A	G	141333742	2	3	71	1	0	0	0	0	0	0	0	1	383	320	12	4		4	AGK	7	141333742	Silent	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	7077337	141333742	17804921	51	21126										
SSPO	23145	broad.mit.edu	37	chr7	149477053	149477053	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cgtcctttcctgcaggtttcCcctgctgagtaccacgaggc	10	15	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:149477053C>T	ENST00000378016.2	+	0	1230							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGCAGGTTTCCCCTGCTGAGT	0.587																																																0			7											46	46	46					7																	149477053		2038	4170	6208	149107986			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149477053C>T			149107986	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																					0.587	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149477053	C	T	149477053	1	4	71	0	1	0	0	0	0	0	0	0	15228	610	22	3		3	SSPO	7	149477053	RNA	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	8143311	149477053	9661610	52	21127										
WDR86	349136	broad.mit.edu	37	chr7	151093140	151093140	+	Frame_Shift_Del	DEL	C	C	-													0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcagggagtgctggggaggtCccacggggcagagtaggcta							TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr7:151093140delC	ENST00000334493.6	-	3	878	c.448delG	c.(448-450)gacfs	p.D150fs	WDR86_ENST00000477459.1_Frame_Shift_Del_p.D22fs|WDR86_ENST00000463000.1_5'Flank|WDR86_ENST00000469830.2_Frame_Shift_Del_p.D150fs	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	150								p.D22fs*18(1)		breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGGGGAGGTCCCACGGGGCA	0.706																																																1	Deletion - Frameshift(1)	large_intestine(1)	7											14	16	15					7																	151093140		2197	4293	6490	150724073	SO:0001589	frameshift_variant	349136			AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"WD repeat domain containing"	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.448delG	7.37:g.151093140delC	ENSP00000335522:p.Asp150fs		150724073	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Frame_Shift_Del	DEL	ENST00000334493.6	37	CCDS5925.2																																																																																				0.706	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285		-	151093140	C	-	151093140	7	5	71	1	0	1	0	1	0	0	0	0	17374	855	30	0	698	0	WDR86	7	151093140	Frame_Shift_Del	DEL	C	TCGA-AG-A01W-01A-21W-A096-10	1616087	151093140	8045523	53	21128										
MYOM2	9172	broad.mit.edu	37	chr8	1998942	1998942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcacttcgaccagtcctaccGtaatattcaaacacggtacc	6	14	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:1998942G>A	ENST00000262113.4	+	2	203	c.62G>A	c.(61-63)cGt>cAt	p.R21H	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	21					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R21H(1)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CAGTCCTACCGTAATATTCAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	8											120	92	101					8																	1998942		2203	4300	6503	1986349	SO:0001583	missense	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.62G>A	8.37:g.1998942G>A	ENSP00000262113:p.Arg21His		1986349	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451218	0.63290	.	.	ENSG00000036448	ENST00000262113	T	0.74209	-0.82	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000004	D	0.85669	0.5750	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84937	0.0863	10	0.48119	T	0.1	.	19.3732	0.94498	0.0:0.0:1.0:0.0	.	21	P54296	MYOM2_HUMAN	H	21	ENSP00000262113:R21H	ENSP00000262113:R21H	R	+	2	0	MYOM2	1986349	1.000000	0.71417	0.544000	0.28141	0.019000	0.09904	4.827000	0.62723	2.653000	0.90120	0.563000	0.77884	CGT		0.488	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		A	1998942	G	A	1998942	3	1	71	1	0	0	0	0	1	0	0	0	10122	1145	40	1	64	1	MYOM2	8	1998942	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		1998942	144365080	54	21129										
CSMD1	64478	broad.mit.edu	37	chr8	2823359	2823359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tacagcgaatagtggcggatGtgactgcttccatgacatag	12	8	0	2	rs375759183		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:2823359G>A	ENST00000520002.1	-	60	9776	c.9221C>T	c.(9220-9222)aCa>aTa	p.T3074I	CSMD1_ENST00000537824.1_Missense_Mutation_p.T3073I|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Missense_Mutation_p.T3074I			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3074	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.T3073I(1)|p.T2802I(1)		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)		AGTGGCGGATGTGACTGCTTC	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	8						G	ILE/THR	1,4129		0,1,2064	71	81	78		9218	2.4	0	8		78	0,8414		0,0,4207	no	missense	CSMD1	NM_033225.5	89	0,1,6271	AA,AG,GG		0.0,0.0242,0.0080	benign	3073/3565	2823359	1,12543	2065	4207	6272	2810766	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9221C>T	8.37:g.2823359G>A	ENSP00000430733:p.Thr3074Ile		2810766	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	1.379	-0.584083	0.03827	2.42E-4	0.0	ENSG00000183117	ENST00000520002;ENST00000318252;ENST00000537824	T;T	0.24908	1.83;1.83	5.42	2.38	0.29361	Complement control module (2);Sushi/SCR/CCP (3);	0.424541	0.22867	N	0.054666	T	0.15262	0.0368	L	0.34521	1.04	0.09310	N	0.999994	B;B	0.20164	0.042;0.0	B;B	0.18561	0.022;0.01	T	0.20240	-1.0281	10	0.16420	T	0.52	.	6.6554	0.22984	0.1811:0.4452:0.3737:0.0	.	3074;3074	E5RIG2;Q96PZ7	.;CSMD1_HUMAN	I	3074;2935;3073	ENSP00000430733:T3074I;ENSP00000441462:T3073I	ENSP00000320445:T2935I	T	-	2	0	CSMD1	2810766	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.678000	0.25277	1.219000	0.43474	0.655000	0.94253	ACA		0.483	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2823359	G	A	2823359	3	1	71	1	0	0	0	0	1	0	0	0	3950	1377	48	3	1524	3	CSMD1	8	2823359	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	824417	2823359	143540663	55	21130										
PDLIM2	64236	broad.mit.edu	37	chr8	22451342	22451342	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgaagatgcgcgggcacttCtgggtgggtgacgagctgta	17	8	1	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:22451342C>G	ENST00000397760.4	+	10	1378	c.978C>G	c.(976-978)ttC>ttG	p.F326L	PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000308354.7_Missense_Mutation_p.F576L|PDLIM2_ENST00000409417.1_Missense_Mutation_p.F326L|AC037459.4_ENST00000430850.2_Missense_Mutation_p.F120L|PDLIM2_ENST00000397761.2_Missense_Mutation_p.F326L|PDLIM2_ENST00000265810.4_Missense_Mutation_p.F326L|PDLIM2_ENST00000409141.1_3'UTR|PDLIM2_ENST00000339162.7_3'UTR			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	326	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.F326L(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		GCGGGCACTTCTGGGTGGGTG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	8											40	30	33					8																	22451342		2203	4297	6500	22507287	SO:0001583	missense	64236			AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.978C>G	8.37:g.22451342C>G	ENSP00000380867:p.Phe326Leu		22507287	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.101652	0.76983	.	.	ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000248235	ENST00000308354;ENST00000397760;ENST00000397761;ENST00000265810;ENST00000409417;ENST00000430850	D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	4.72	0.69	0.18039	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.92922	0.7748	M	0.88906	2.99	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.994	D	0.91345	0.5100	10	0.87932	D	0	-22.5603	10.1588	0.42838	0.0:0.8292:0.0:0.1708	.	326;326	Q96JY6-3;Q96JY6	.;PDLI2_HUMAN	L	576;326;326;326;326;120	ENSP00000312634:F576L;ENSP00000380867:F326L;ENSP00000380868:F326L;ENSP00000265810:F326L;ENSP00000387084:F326L;ENSP00000428700:F120L	ENSP00000428700:F120L	F	+	3	2	AC037459.4;PDLIM2	22507287	0.997000	0.39634	0.995000	0.50966	0.800000	0.45204	0.444000	0.21661	-0.182000	0.10602	0.491000	0.48974	TTC		0.672	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			G	22451342	C	G	22451342	3	3	71	1	0	0	0	0	1	0	0	0	11711	912	32	5	1012	5	PDLIM2	8	22451342	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	19627983	22451342	123912680	56	21131										
KIAA1429	25962	broad.mit.edu	37	chr8	95504925	95504925	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgtgcttcccaagtttgaatCctttagtagtcttggttctt	8	8	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:95504925C>A	ENST00000297591.5	-	21	4838	c.4763G>T	c.(4762-4764)gGa>gTa	p.G1588V	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1588					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.G1588V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			AAGTTTGAATCCTTTAGTAGT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	8											165	155	158					8																	95504925		2203	4300	6503	95574101	SO:0001583	missense	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.4763G>T	8.37:g.95504925C>A	ENSP00000297591:p.Gly1588Val		95574101	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910842	0.52439	.	.	ENSG00000164944	ENST00000297591	T	0.47869	0.83	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.63931	0.2553	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54984	-0.8211	10	0.14252	T	0.57	-16.8225	19.5445	0.95285	0.0:1.0:0.0:0.0	.	1588	Q69YN4	VIR_HUMAN	V	1588	ENSP00000297591:G1588V	ENSP00000297591:G1588V	G	-	2	0	KIAA1429	95574101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.614000	0.88457	0.585000	0.79938	GGA		0.368	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		A	95504925	C	A	95504925	3	1	71	1	0	0	0	0	1	0	0	0	8252	855	30	2	691	2	KIAA1429	8	95504925	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	73053583	95504925	50859097	57	21132										
TM7SF4	81501	broad.mit.edu	37	chr8	105361454	105361454	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agggctttcgctcgtcctgcTtggcactggcctcttcatga	11	13	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:105361454T>G	ENST00000297581.2	+	2	723	c.674T>G	c.(673-675)cTt>cGt	p.L225R	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.L225R|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	225					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)		p.L225R(1)									CTCGTCCTGCTTGGCACTGGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	8											100	92	95					8																	105361454		2203	4300	6503	105430630	SO:0001583	missense	81501			AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.674T>G	8.37:g.105361454T>G	ENSP00000297581:p.Leu225Arg		105430630	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.785544	0.49997	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.37752	1.18	5.52	4.32	0.51571	.	0.356779	0.29239	N	0.012724	T	0.39410	0.1077	L	0.47716	1.5	0.09310	N	1	D	0.54397	0.966	P	0.50440	0.641	T	0.21245	-1.0251	9	.	.	.	-12.6714	11.4999	0.50430	0.0:0.0:0.1492:0.8508	.	225	Q9H295	TM7S4_HUMAN	R	225	ENSP00000297581:L225R	.	L	+	2	0	TM7SF4	105430630	0.319000	0.24607	0.031000	0.17742	0.720000	0.41350	3.897000	0.56273	2.120000	0.65058	0.454000	0.30748	CTT		0.498	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		G	105361454	T	G	105361454	3	3	71	1	0	0	0	0	1	0	0	0	16015	1609	56	4	676	4	TM7SF4	8	105361454	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	9856529	105361454	41002568	58	21133										
CSMD3	114788	broad.mit.edu	37	chr8	113267618	113267618	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aaagcttttgccttctctttTtccttgggcaggtataccag	8	10	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:113267618T>G	ENST00000297405.5	-	62	10145	c.9901A>C	c.(9901-9903)Aaa>Caa	p.K3301Q	CSMD3_ENST00000352409.3_Missense_Mutation_p.K3231Q|CSMD3_ENST00000343508.3_Missense_Mutation_p.K3261Q|CSMD3_ENST00000455883.2_Missense_Mutation_p.K3132Q	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3301	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K3301Q(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCTTCTCTTTTTCCTTGGGCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											111	102	105					8																	113267618		2203	4299	6502	113336794	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9901A>C	8.37:g.113267618T>G	ENSP00000297405:p.Lys3301Gln		113336794	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571988	0.45798	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	4.99	4.99	0.66335	Complement control module (2);Sushi/SCR/CCP (3);	0.365631	0.25159	N	0.032687	T	0.45637	0.1352	N	0.20483	0.58	0.36140	D	0.846756	B;B;B	0.30634	0.009;0.004;0.288	B;B;B	0.25614	0.01;0.011;0.062	T	0.52888	-0.8515	10	0.25106	T	0.35	.	14.8704	0.70453	0.0:0.0:0.0:1.0	.	3132;3301;3261	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Q	3261;3301;2571;3132;3231	ENSP00000345799:K3261Q;ENSP00000297405:K3301Q;ENSP00000341558:K2571Q;ENSP00000412263:K3132Q;ENSP00000343124:K3231Q	ENSP00000297405:K3301Q	K	-	1	0	CSMD3	113336794	0.933000	0.31639	1.000000	0.80357	0.973000	0.67179	2.473000	0.45145	2.103000	0.63969	0.528000	0.53228	AAA		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113267618	T	G	113267618	3	3	71	1	0	0	0	0	1	0	0	0	3952	1850	64	4	1262	4	CSMD3	8	113267618	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	7906164	113267618	33096404	59	21134										
FLJ43860	389690	broad.mit.edu	37	chr8	142486077	142486077	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgggtccccagccctggtgcGtccagcctgcccgctcccga	12	19	0	0	rs372270658		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr8:142486077G>A	ENST00000430863.1	-	0	1696					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5									p.T539M(1)									GCCCTGGTGCGTCCAGCCTGC	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		18866	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						G	MET/THR	2,3990		0,2,1994	20	26	24		1616	-5.2	0	8		24	1,8313		0,1,4156	no	missense	FLJ43860	NM_207414.2	81	0,3,6150	AA,AG,GG		0.012,0.0501,0.0244	benign	539/1319	142486077	3,12303	1996	4157	6153	142555259			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142486077G>A			142555259		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																					0.612	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		A	142486077	G	A	142486077	1	1	71	0	1	0	0	0	0	0	0	0	5949	1145	40	1		1	FLJ43860	8	142486077	RNA	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	29218459	142486077	3877945	60	21135										
TAF1L	138474	broad.mit.edu	37	chr9	32635569	32635569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctcagcagcaaatcgcagccGggtcgcataaaccggaaata	10	12	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr9:32635569G>A	ENST00000242310.4	-	1	98	c.9C>T	c.(7-9)ccC>ccT	p.P3P	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	3					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.P3P(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		AATCGCAGCCGGGTCGCATAA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	9											47	45	46					9																	32635569		2203	4300	6503	32625569	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.9C>T	9.37:g.32635569G>A			32625569	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.552	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32635569	G	A	32635569	2	1	71	1	0	0	0	0	0	0	0	1	15562	1103	39	1		1	TAF1L	9	32635569	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		32635569	108577862	61	21136										
TLE4	7091	broad.mit.edu	37	chr9	82188608	82188608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tattgttgttcttcaggcacCgcatcagcctgctcaaccct	7	14	4	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr9:82188608C>A	ENST00000376552.2	+	2	1068	c.50C>A	c.(49-51)cCg>cAg	p.P17Q	TLE4_ENST00000265284.6_Missense_Mutation_p.P17Q|TLE4_ENST00000376544.3_Missense_Mutation_p.P17Q|TLE4_ENST00000376537.4_Missense_Mutation_p.P17Q|TLE4_ENST00000376520.4_Missense_Mutation_p.P17Q|TLE4_ENST00000376534.4_5'UTR	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	17	Gln-rich (Q domain).				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)	p.P17Q(2)|p.P17R(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						CTTCAGGCACCGCATCAGCCT	0.458																																																3	Substitution - Missense(3)	large_intestine(2)|prostate(1)	9											73	68	70					9																	82188608		1923	4132	6055	81378428	SO:0001583	missense	7091			M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.50C>A	9.37:g.82188608C>A	ENSP00000365735:p.Pro17Gln		81378428	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593257	0.66219	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000414465;ENST00000376537;ENST00000265284;ENST00000425506;ENST00000428713	T;T;T;T;T;T;T;T	0.63096	0.5;0.42;0.47;0.66;0.49;0.74;0.47;-0.02	4.33	3.43	0.39272	Groucho/TLE, N-terminal Q-rich domain (1);	0.062013	0.64402	D	0.000004	T	0.82153	0.4975	M	0.92459	3.31	0.80722	D	1	D;D;D	0.89917	0.962;1.0;0.983	P;D;D	0.87578	0.846;0.998;0.947	D	0.85088	0.0950	10	0.87932	D	0	-6.634	11.9792	0.53111	0.0:0.9133:0.0:0.0867	.	17;17;17	F8W6T6;Q04727-2;Q04727	.;.;TLE4_HUMAN	Q	17;17;17;17;17;17;17;17;15;2	ENSP00000365735:P17Q;ENSP00000365727:P17Q;ENSP00000365703:P17Q;ENSP00000415423:P17Q;ENSP00000365720:P17Q;ENSP00000265284:P17Q;ENSP00000412567:P15Q;ENSP00000409313:P2Q	ENSP00000265284:P17Q	P	+	2	0	TLE4	81378428	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.398000	0.79919	0.815000	0.34398	0.462000	0.41574	CCG		0.458	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		A	82188608	C	A	82188608	3	1	71	1	0	0	0	0	1	0	0	0	15980	652	23	2	56	2	TLE4	9	82188608	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	49553039	82188608	59024823	62	21137										
ZCCHC6	79670	broad.mit.edu	37	chr9	88938185	88938186	+	Frame_Shift_Del	DEL	AG	AG	-													0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgagtgggtaaagtggtttAgagagtcttctagttcctca							TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr9:88938185_88938186delAG	ENST00000375963.3	-	13	2651_2652	c.2479_2480delCT	c.(2479-2481)ctafs	p.L827fs	ZCCHC6_ENST00000277141.6_Frame_Shift_Del_p.L116fs|ZCCHC6_ENST00000375961.2_Frame_Shift_Del_p.L827fs|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375960.2_Frame_Shift_Del_p.L704fs	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	827	Glu-rich.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.L827fs*18(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						AAAGTGGTTTAGAGAGTCTTCT	0.46																																																1	Deletion - Frameshift(1)	large_intestine(1)	9																																								88128006	SO:0001589	frameshift_variant	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2479_2480delCT	9.37:g.88938189_88938190delAG	ENSP00000365130:p.Leu827fs		88128005	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Frame_Shift_Del	DEL	ENST00000375963.3	37	CCDS35057.1																																																																																				0.46	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		-	88938186	AG	-	88938185	7	5	71	1	0	1	0	1	0	0	0	0	17631	420	15	0	2067	0	ZCCHC6	9	88938185	Frame_Shift_Del	DEL	AG	TCGA-AG-A01W-01A-21W-A096-10	6749577	88938185	52275246	63	21138										
ZNF484	83744	broad.mit.edu	37	chr9	95609939	95609939	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agtgtttccctccagtatgaAtttttttatgtatattaagg	7	5	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr9:95609939A>T	ENST00000375495.3	-	5	1278	c.1130T>A	c.(1129-1131)aTt>aAt	p.I377N	ZNF484_ENST00000332591.6_Missense_Mutation_p.I341N|ZNF484_ENST00000395505.2_Missense_Mutation_p.I341N|ZNF484_ENST00000395506.3_Missense_Mutation_p.I379N|ANKRD19P_ENST00000473204.1_RNA	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I377N(1)		NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						TCCAGTATGAATTTTTTTATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	9											36	40	38					9																	95609939		2201	4284	6485	94649760	SO:0001583	missense	83744			AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"Zinc fingers, C2H2-type", "-"	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.1130T>A	9.37:g.95609939A>T	ENSP00000364645:p.Ile377Asn		94649760	B1AL89|B4DRI2	Missense_Mutation	SNP	ENST00000375495.3	37	CCDS35066.1	.	.	.	.	.	.	.	.	.	.	.	0.049	-1.255563	0.01457	.	.	ENSG00000127081	ENST00000395505;ENST00000395506;ENST00000375495;ENST00000332591	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	2.49	-4.98	0.03019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16685	0.0401	M	0.73319	2.225	0.09310	N	1	P;P	0.38677	0.642;0.642	B;B	0.40009	0.316;0.316	T	0.15492	-1.0435	9	0.72032	D	0.01	.	1.7796	0.03028	0.1241:0.3064:0.167:0.4025	.	379;377	B4DRI2;Q5JVG2	.;ZN484_HUMAN	N	341;379;377;341	ENSP00000378881:I341N;ENSP00000378882:I379N;ENSP00000364645:I377N;ENSP00000364646:I341N	ENSP00000364646:I341N	I	-	2	0	ZNF484	94649760	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.304000	0.08199	-4.745000	0.00034	-0.353000	0.07706	ATT		0.343	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861		T	95609939	A	T	95609939	3	4	71	1	0	0	0	0	1	0	0	0	17976	101	4	5	1432	5	ZNF484	9	95609939	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	6671754	95609939	45603492	64	21139										
RALGDS	5900	broad.mit.edu	37	chr9	135983678	135983678	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agctctgaacctggagctggTgttggagctggctctggctc	15	10	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr9:135983678T>G	ENST00000372050.3	-	6	915	c.894A>C	c.(892-894)acA>acC	p.T298T	RALGDS_ENST00000372062.3_Silent_p.T269T|RALGDS_ENST00000542690.1_Silent_p.T369T|RALGDS_ENST00000393160.3_Silent_p.T243T|RALGDS_ENST00000393157.3_Silent_p.T297T|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000372047.3_Silent_p.T286T	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	298					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)	p.T298T(1)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		ctggagctggtgttggagctg	0.627			T	CIITA	"PMBL, Hodgkin Lymphona, "																																Melanoma(189;762 2088 15384 21931 52515)		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	1	Substitution - coding silent(1)	large_intestine(1)	9											20	20	20					9																	135983678		2139	4200	6339	134973499	SO:0001819	synonymous_variant	5900			AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.894A>C	9.37:g.135983678T>G			134973499	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																				0.627	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		G	135983678	T	G	135983678	2	3	71	1	0	0	0	0	0	0	0	1	13053	1683	59	4		4	RALGDS	9	135983678	Silent	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	40373739	135983678	5229753	65	21140										
PLXDC2	84898	broad.mit.edu	37	chr10	20568697	20568697	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggacatcctgcctatgctgaAgttgaaccagttggagagaa	12	8	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:20568697A>C	ENST00000377252.4	+	14	2380	c.1539A>C	c.(1537-1539)gaA>gaC	p.E513D	PLXDC2_ENST00000377242.3_Missense_Mutation_p.E464D|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	513					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.E513D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						CCTATGCTGAAGTTGAACCAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	10											98	97	97					10																	20568697		2203	4300	6503	20608703	SO:0001583	missense	84898			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.1539A>C	10.37:g.20568697A>C	ENSP00000366460:p.Glu513Asp		20608703	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.630383	0.67015	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	T;T	0.37235	1.21;1.4	5.62	0.68	0.17980	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.77103	2.36	0.52099	D	0.999941	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.55811	-0.8082	10	0.54805	T	0.06	.	10.5624	0.45152	0.6789:0.0:0.3211:0.0	.	464;513	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	D	513;464;376;499	ENSP00000366460:E513D;ENSP00000366450:E464D	ENSP00000366446:E376D	E	+	3	2	PLXDC2	20608703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.666000	0.46799	0.147000	0.19030	0.528000	0.53228	GAA		0.423	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		C	20568697	A	C	20568697	3	2	71	1	0	0	0	0	1	0	0	0	12149	69	3	4	1593	4	PLXDC2	10	20568697	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10		20568697	114966050	66	21141										
C10orf113	387638	broad.mit.edu	37	chr10	21435316	21435316	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cagccacacaagaaaaaaatGactggttgattagtaaagca	8	7	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:21435316G>A	ENST00000534331.1	-	1	172	c.122C>T	c.(121-123)tCa>tTa	p.S41L	C10orf113_ENST00000377118.4_Missense_Mutation_p.S31L|NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000529198.1_Missense_Mutation_p.S41L	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	41								p.S31L(2)		endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						AGAAAAAAATGACTGGTTGAT	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	10											157	142	147					10																	21435316		2203	4300	6503	21475322	SO:0001583	missense	387638				CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.122C>T	10.37:g.21435316G>A	ENSP00000433646:p.Ser41Leu		21475322	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	37	CCDS31162.2	.	.	.	.	.	.	.	.	.	.	G	12.70	2.017387	0.35606	.	.	ENSG00000204683	ENST00000534331;ENST00000529198;ENST00000377118	T;T	0.38240	1.15;1.15	5.71	-7.51	0.01346	.	.	.	.	.	T	0.13030	0.0316	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24048	-1.0171	9	0.87932	D	0	.	0.7479	0.00985	0.261:0.3055:0.1201:0.3134	.	41	Q5VZT2	CJ113_HUMAN	L	41;41;31	ENSP00000433646:S41L;ENSP00000366322:S31L	ENSP00000366322:S31L	S	-	2	0	C10orf113	21475322	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.342000	0.00505	-1.246000	0.02510	-0.140000	0.14226	TCA		0.428	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896		A	21435316	G	A	21435316	3	1	71	1	0	0	0	0	1	0	0	0	1588	1294	45	3	388	3	C10orf113	10	21435316	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	866619	21435316	114099431	67	21142										
ANKRD30A	91074	broad.mit.edu	37	chr10	37505292	37505292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	acagttagagaaccaaaaagTtaaatgggaacaagagctct	9	6	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:37505292T>C	ENST00000602533.1	+	32	2984	c.2885T>C	c.(2884-2886)gTt>gCt	p.V962A	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.V1081A|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.V962A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1018					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V962A(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AACCAAAAAGTTAAATGGGAA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	10											77	78	78					10																	37505292		1831	4078	5909	37545298	SO:0001583	missense	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2885T>C	10.37:g.37505292T>C	ENSP00000473551:p.Val962Ala		37545298	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	t	1.865	-0.461580	0.04508	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05649	3.41;3.41	2.63	2.63	0.31362	.	.	.	.	.	T	0.05502	0.0145	N	0.11064	0.09	0.09310	N	1	D	0.61697	0.99	P	0.51516	0.672	T	0.43032	-0.9416	9	0.21540	T	0.41	.	8.4494	0.32862	0.0:0.0:0.0:1.0	.	1018	Q9BXX3	AN30A_HUMAN	A	962;1081	ENSP00000354432:V962A;ENSP00000363792:V1081A	ENSP00000354432:V962A	V	+	2	0	ANKRD30A	37545298	0.020000	0.18652	0.002000	0.10522	0.006000	0.05464	0.854000	0.27791	1.055000	0.40461	0.260000	0.18958	GTT		0.308	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		C	37505292	T	C	37505292	3	2	71	1	0	0	0	0	1	0	0	0	658	1725	60	4	3011	4	ANKRD30A	10	37505292	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10	16069976	37505292	98029455	68	21143										
RHOBTB1	9886	broad.mit.edu	37	chr10	62634763	62634763	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccgtcaatgcccacgccactCgtggcggctttggtcaactc	10	16	2	0	rs556718498		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:62634763C>T	ENST00000337910.5	-	9	2101	c.1764G>A	c.(1762-1764)acG>acA	p.T588T	RHOBTB1_ENST00000357917.4_Silent_p.T588T|RHOBTB1_ENST00000490827.1_5'UTR	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	588					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.T588T(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					CCACGCCACTCGTGGCGGCTT	0.507													C|||	1	0.000199681	0	0	5008	,	,		19492	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											92	89	90					10																	62634763		2203	4300	6503	62304769	SO:0001819	synonymous_variant	9886			AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1764G>A	10.37:g.62634763C>T			62304769		Silent	SNP	ENST00000337910.5	37	CCDS7261.1																																																																																				0.507	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			T	62634763	C	T	62634763	2	4	71	1	0	0	0	0	0	0	0	1	13370	871	31	1		1	RHOBTB1	10	62634763	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	25129471	62634763	72899984	69	21144										
DMBT1	1755	broad.mit.edu	37	chr10	124402857	124402857	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	taccaggaaaaggtggacgtCgtcctgggtcccatccagct	12	12	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:124402857C>T	ENST00000338354.3	+	53	7291	c.7185C>T	c.(7183-7185)gtC>gtT	p.V2395V	DMBT1_ENST00000330163.4_Silent_p.V1767V|DMBT1_ENST00000368955.3_Silent_p.V2385V|DMBT1_ENST00000359586.6_Silent_p.V1115V|DMBT1_ENST00000368909.3_Silent_p.V2395V|DMBT1_ENST00000368956.2_Silent_p.V1767V|DMBT1_ENST00000344338.3_Silent_p.V2385V			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2395					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)	p.V2395V(3)|p.V2524V(2)		breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AGGTGGACGTCGTCCTGGGTC	0.647																																					Ovarian(182;93 2026 18125 22222 38972)											5	Substitution - coding silent(5)	endometrium(3)|large_intestine(2)	10											65	67	66					10																	124402857		2029	4170	6199	124392847	SO:0001819	synonymous_variant	1755				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7185C>T	10.37:g.124402857C>T			124392847	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																					0.647	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124402857	C	T	124402857	2	4	71	1	0	0	0	0	0	0	0	1	4588	871	31	1		1	DMBT1	10	124402857	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	61768094	124402857	11131890	70	21145										
CHST15	51363	broad.mit.edu	37	chr10	125780804	125780804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gttgagggtgttgttgtagaCgcaggcgcgcagtgaataat	16	5	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr10:125780804C>T	ENST00000346248.5	-	6	1957	c.1315G>A	c.(1315-1317)Gtc>Atc	p.V439I	CHST15_ENST00000435907.1_Missense_Mutation_p.V439I|CHST15_ENST00000421115.1_Missense_Mutation_p.V439I	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	439					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)	p.V439I(1)		endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TTGTTGTAGACGCAGGCGCGC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											70	63	65					10																	125780804		2203	4300	6503	125770794	SO:0001583	missense	51363			AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"Sulfotransferases, membrane-bound"	18137	protein-coding gene	gene with protein product	"B cell RAG associated protein", "N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1315G>A	10.37:g.125780804C>T	ENSP00000333947:p.Val439Ile		125770794	O60338|O60474|Q86VM4	Missense_Mutation	SNP	ENST00000346248.5	37	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.514056	0.44763	.	.	ENSG00000182022	ENST00000346248;ENST00000435907;ENST00000546346;ENST00000421115	.	.	.	4.41	3.5	0.40072	Sulfotransferase domain (1);	0.225046	0.37012	N	0.002293	T	0.38161	0.1030	L	0.28192	0.835	0.33557	D	0.596824	B;B	0.18741	0.03;0.023	B;B	0.14023	0.007;0.01	T	0.44236	-0.9341	9	0.33940	T	0.23	-19.9862	12.0463	0.53480	0.0:0.9152:0.0:0.0848	.	439;439	Q7LFX5-2;Q7LFX5	.;CHSTF_HUMAN	I	439	.	ENSP00000333947:V439I	V	-	1	0	CHST15	125770794	0.985000	0.35326	0.983000	0.44433	0.989000	0.77384	2.574000	0.46016	0.841000	0.35020	0.467000	0.42956	GTC		0.532	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		T	125780804	C	T	125780804	3	4	71	1	0	0	0	0	1	0	0	0	3409	536	19	1	382	1	CHST15	10	125780804	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1377947	125780804	9753943	71	21146										
DLG2	1740	broad.mit.edu	37	chr11	83874536	83874536	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aatttcttcaaattcatattCaatttctgtcccattgacct	2	10	5	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr11:83874536C>T	ENST00000532653.1	-	4	579	c.277G>A	c.(277-279)Gaa>Aaa	p.E93K	DLG2_ENST00000280241.8_Missense_Mutation_p.E132K|DLG2_ENST00000531015.1_Missense_Mutation_p.E60K|DLG2_ENST00000398309.2_Missense_Mutation_p.E93K|DLG2_ENST00000543673.1_Missense_Mutation_p.E198K|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000524982.1_Missense_Mutation_p.E93K|DLG2_ENST00000330014.6_Missense_Mutation_p.E32K|DLG2_ENST00000418306.2_Missense_Mutation_p.E42K|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000398301.2_Missense_Mutation_p.E132K|DLG2_ENST00000376104.2_Missense_Mutation_p.E198K			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.E93K(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				AATTCATATTCAATTTCTGTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											82	78	79					11																	83874536		1787	4057	5844	83552184	SO:0001583	missense	1740			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.277G>A	11.37:g.83874536C>T	ENSP00000435849:p.Glu93Lys		83552184	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	C	19.35	3.810422	0.70797	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301;ENST00000398299	T;T;T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;2.21;0.81;0.81;0.81;0.81;0.81;0.81;0.81;2.21	5.32	5.32	0.75619	Membrane-associated guanylate kinase (MAGUK), PEST domain, N-terminal (1);PDZ/DHR/GLGF (1);	0.000000	0.64402	D	0.000002	T	0.61388	0.2343	M	0.63843	1.955	0.80722	D	1	P;B;P;D;P;D;B;P	0.61697	0.873;0.285;0.755;0.99;0.93;0.962;0.106;0.657	P;B;P;P;P;P;B;B	0.60173	0.566;0.191;0.752;0.87;0.636;0.6;0.145;0.431	T	0.59359	-0.7469	9	.	.	.	.	14.3785	0.66895	0.0:1.0:0.0:0.0	.	60;93;93;32;132;198;93;42	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	K	93;198;42;198;132;32;93;93;198;60;132;10	ENSP00000381355:E93K;ENSP00000365272:E198K;ENSP00000402275:E42K;ENSP00000441994:E198K;ENSP00000280241:E132K;ENSP00000381353:E32K;ENSP00000432894:E93K;ENSP00000435849:E93K;ENSP00000433848:E60K;ENSP00000381346:E132K;ENSP00000381344:E10K	.	E	-	1	0	DLG2	83552184	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.674000	0.61612	2.753000	0.94483	0.655000	0.94253	GAA		0.323	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		T	83874536	C	T	83874536	3	4	71	1	0	0	0	0	1	0	0	0	4566	835	29	3	2465	3	DLG2	11	83874536	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		83874536	51131980	72	21147										
DYNC2H1	79659	broad.mit.edu	37	chr11	103049785	103049785	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	atggataatctgtgatggtgAtattgaccctgaatggatag	12	4	1	4			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr11:103049785A>C	ENST00000375735.2	+	39	6314	c.6170A>C	c.(6169-6171)gAt>gCt	p.D2057A	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.D2057A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2057	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGTGATGGTGATATTGACCCT	0.353																																																0			11											124	115	117					11																	103049785		1856	4111	5967	102554995	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.6170A>C	11.37:g.103049785A>C	ENSP00000364887:p.Asp2057Ala		102554995	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.470834	0.84533	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	D;D	0.86497	-2.13;-2.13	5.27	5.27	0.74061	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	.	.	.	.	D	0.92685	0.7675	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93202	0.6592	9	0.59425	D	0.04	.	15.4843	0.75551	1.0:0.0:0.0:0.0	.	2057;2057	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	2057	ENSP00000364887:D2057A;ENSP00000381167:D2057A	ENSP00000364887:D2057A	D	+	2	0	DYNC2H1	102554995	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.287000	0.95975	2.129000	0.65627	0.477000	0.44152	GAT		0.353	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103049785	A	C	103049785	3	2	71	1	0	0	0	0	1	0	0	0	4857	333	12	4	6324	4	DYNC2H1	11	103049785	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	19175249	103049785	31956731	73	21148										
NCAM1	4684	broad.mit.edu	37	chr11	113076335	113076335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgatgtggtcagctccctccCaccaaccatcatctggaaac	7	15	3	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr11:113076335C>T	ENST00000533760.1	+	4	682	c.83C>T	c.(82-84)cCa>cTa	p.P28L	NCAM1_ENST00000401611.2_Missense_Mutation_p.P145L|NCAM1_ENST00000316851.7_Missense_Mutation_p.P136L|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	146	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.P136L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGCTCCCTCCCACCAACCATC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	11											153	151	152					11																	113076335		2024	4157	6181	112581545	SO:0001583	missense	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.83C>T	11.37:g.113076335C>T	ENSP00000473281:p.Pro28Leu		112581545	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	C	26.7	4.763943	0.89932	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.67171	-0.25;-0.25	5.73	5.73	0.89815	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	.	.	.	0.80722	D	1	D;D;D;D;D	0.67145	0.996;0.992;0.993;0.992;0.996	P;P;P;D;D	0.65773	0.898;0.898;0.881;0.921;0.938	D	0.83663	0.0162	9	0.72032	D	0.01	-32.1918	19.8991	0.96978	0.0:1.0:0.0:0.0	.	146;146;146;146;146	P13591-5;P13591-1;P13591;P13591-3;P13591-6	.;.;NCAM1_HUMAN;.;.	L	28;145;136	ENSP00000384055:P145L;ENSP00000318472:P136L	ENSP00000318472:P136L	P	+	2	0	NCAM1	112581545	1.000000	0.71417	0.990000	0.47175	0.866000	0.49608	5.838000	0.69388	2.708000	0.92522	0.655000	0.94253	CCA		0.527	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113076335	C	T	113076335	3	4	71	1	0	0	0	0	1	0	0	0	10233	594	21	3	452	3	NCAM1	11	113076335	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	10026550	113076335	21930181	74	21149										
KRAS	3845	broad.mit.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	71	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		25398281	108453614	75	21150										
ITPR2	3709	broad.mit.edu	37	chr12	26640015	26640015	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctttacctctcattcgtggaCcagatgtcatcaattcattg	6	11	4	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:26640015C>G	ENST00000381340.3	-	40	5956	c.5540G>C	c.(5539-5541)gGt>gCt	p.G1847A		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1847					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.G1847A(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CATTCGTGGACCAGATGTCAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	12											206	189	194					12																	26640015		1877	4114	5991	26531282	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5540G>C	12.37:g.26640015C>G	ENSP00000370744:p.Gly1847Ala		26531282	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	4.384	0.070883	0.08436	.	.	ENSG00000123104	ENST00000381340	D	0.89746	-2.56	4.39	4.39	0.52855	.	0.155778	0.39020	N	0.001492	T	0.76133	0.3945	N	0.19112	0.55	0.26056	N	0.981415	B	0.16603	0.018	B	0.14023	0.01	T	0.57539	-0.7794	10	0.08179	T	0.78	.	7.8191	0.29278	0.2266:0.6301:0.1433:0.0	.	1847	Q14571	ITPR2_HUMAN	A	1847	ENSP00000370744:G1847A	ENSP00000370744:G1847A	G	-	2	0	ITPR2	26531282	0.202000	0.23423	0.167000	0.22817	0.996000	0.88848	1.612000	0.36889	2.745000	0.94114	0.650000	0.86243	GGT		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26640015	C	G	26640015	3	3	71	1	0	0	0	0	1	0	0	0	7942	507	18	5	2637	5	ITPR2	12	26640015	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1241734	26640015	107211880	76	21151										
KRT75	9119	broad.mit.edu	37	chr12	52827639	52827639	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttgagggtcttgatctgctcGcgctcctcggcccgcacccg	12	16	2	2	rs138137930		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:52827639G>A	ENST00000252245.5	-	1	670	c.450C>T	c.(448-450)cgC>cgT	p.R150R		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	150	Coil 1A.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R150R(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGATCTGCTCGCGCTCCTCGG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	12											148	149	149					12																	52827639		2203	4300	6503	51113906	SO:0001819	synonymous_variant	9119			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.450C>T	12.37:g.52827639G>A			51113906	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																				0.562	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		A	52827639	G	A	52827639	2	1	71	1	0	0	0	0	0	0	0	1	8509	1074	38	1		1	KRT75	12	52827639	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	26187624	52827639	81024256	77	21152										
DNAH10	196385	broad.mit.edu	37	chr12	124293412	124293412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccacactgaaaccattctgaCggcacctgagatcatccttc	6	15	2	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:124293412C>T	ENST00000409039.3	+	18	2727	c.2702C>T	c.(2701-2703)aCg>aTg	p.T901M		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	901	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T719M(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ACCATTCTGACGGCACCTGAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											336	294	308					12																	124293412		2203	4300	6503	122859365	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2702C>T	12.37:g.124293412C>T	ENSP00000386770:p.Thr901Met		122859365	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	12.07	1.827686	0.32329	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.72	3.79	0.43588	.	0.562003	0.16078	N	0.230660	T	0.30665	0.0772	L	0.29908	0.895	0.27905	N	0.938843	D;D;P	0.63880	0.993;0.963;0.834	P;P;B	0.59221	0.854;0.696;0.238	T	0.14172	-1.0482	10	0.40728	T	0.16	.	16.1603	0.81700	0.0:0.7486:0.2514:0.0	.	901;776;901	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	M	901	ENSP00000386770:T901M	ENSP00000386770:T901M	T	+	2	0	DNAH10	122859365	0.983000	0.35010	0.330000	0.25442	0.173000	0.22820	2.571000	0.45990	1.383000	0.46405	0.655000	0.94253	ACG		0.468	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124293412	C	T	124293412	3	4	71	1	0	0	0	0	1	0	0	0	4609	536	19	1	2772	1	DNAH10	12	124293412	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	71465773	124293412	9558483	78	21153										
MMP17	4326	broad.mit.edu	37	chr12	132325289	132325289	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gccgaccataacgacggctaCcccttcgacggccccggcgg	12	18	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:132325289C>T	ENST00000360564.1	+	4	696	c.594C>T	c.(592-594)taC>taT	p.Y198Y	MMP17_ENST00000535182.1_3'UTR|MMP17_ENST00000535291.1_Silent_p.Y114Y	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	198					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y198Y(1)|p.N198N(1)		endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	ACGACGGCTACCCCTTCGACG	0.677																																																2	Substitution - coding silent(2)	large_intestine(2)	12											66	57	60					12																	132325289		2203	4300	6503	130891242	SO:0001819	synonymous_variant	4326			X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"matrix metalloproteinase 17 (membrane-inserted)"			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.594C>T	12.37:g.132325289C>T			130891242	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																				0.677	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		T	132325289	C	T	132325289	2	4	71	1	0	0	0	0	0	0	0	1	9686	518	18	3		3	MMP17	12	132325289	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	8031877	132325289	1526606	79	21154										
POLE	5426	broad.mit.edu	37	chr12	133209349	133209349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agcactgcgcctcagcccgtCcttcatgcagtggtacacgg	11	15	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr12:133209349C>T	ENST00000320574.5	-	44	6080	c.6037G>A	c.(6037-6039)Gac>Aac	p.D2013N	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Missense_Mutation_p.D1986N	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2013			D -> N. {ECO:0000269|PubMed:23263490}.		base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.D2013N(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CTCAGCCCGTCCTTCATGCAG	0.677								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	12											41	42	42					12																	133209349		2202	4299	6501	131719422	SO:0001583	missense	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.6037G>A	12.37:g.133209349C>T	ENSP00000322570:p.Asp2013Asn		131719422	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417824	0.42918	.	.	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000535270	T;T;T	0.46451	0.87;0.87;0.87	5.58	5.58	0.84498	.	0.323797	0.36066	N	0.002813	T	0.30166	0.0756	N	0.14661	0.345	0.34590	D	0.715395	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20706	-1.0267	10	0.24483	T	0.36	.	19.6185	0.95645	0.0:1.0:0.0:0.0	.	2013;223	Q07864;B3KS74	DPOE1_HUMAN;.	N	223;2013;2024;1986	ENSP00000322570:D2013N;ENSP00000406383:D2024N;ENSP00000445753:D1986N	ENSP00000322570:D2013N	D	-	1	0	POLE	131719422	1.000000	0.71417	0.997000	0.53966	0.230000	0.25150	4.714000	0.61902	2.644000	0.89710	0.478000	0.44815	GAC		0.677	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		T	133209349	C	T	133209349	3	4	71	1	0	0	0	0	1	0	0	0	12227	855	30	3	847	3	POLE	12	133209349	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	884060	133209349	642546	80	21155										
CCDC70	83446	broad.mit.edu	37	chr13	52439668	52439668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgcaggaggaaaaggcttttCgcgaagagatgaaaattttt	12	4	0	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr13:52439668C>T	ENST00000242819.4	+	2	450	c.154C>T	c.(154-156)Cgc>Tgc	p.R52C		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	52						extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.R52C(1)		breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		AAAGGCTTTTCGCGAAGAGAT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	13											67	69	68					13																	52439668		2203	4300	6503	51337669	SO:0001583	missense	83446				CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.154C>T	13.37:g.52439668C>T	ENSP00000242819:p.Arg52Cys		51337669	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	37	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.641014	0.29157	.	.	ENSG00000123171	ENST00000242819	T	0.22336	1.96	5.55	1.83	0.25207	.	0.233858	0.30134	N	0.010334	T	0.31702	0.0805	M	0.70595	2.14	0.09310	N	1	D	0.71674	0.998	P	0.56700	0.804	T	0.12553	-1.0543	10	0.87932	D	0	-3.7611	4.4143	0.11448	0.1466:0.5351:0.0:0.3183	.	52	Q6NSX1	CCD70_HUMAN	C	52	ENSP00000242819:R52C	ENSP00000242819:R52C	R	+	1	0	CCDC70	51337669	0.015000	0.18098	0.000000	0.03702	0.008000	0.06430	0.565000	0.23578	0.297000	0.22615	-0.251000	0.11542	CGC		0.517	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290		T	52439668	C	T	52439668	3	4	71	1	0	0	0	0	1	0	0	0	2849	884	31	1	156	1	CCDC70	13	52439668	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		52439668	62730210	81	21156										
PCDH9	5101	broad.mit.edu	37	chr13	67801643	67801643	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gacctctgaactgtaatcagCccagtagtattatttaaagc	7	9	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr13:67801643C>T	ENST00000377865.2	-	1	1064	c.930G>A	c.(928-930)ggG>ggA	p.G310G	PCDH9_ENST00000456367.1_Silent_p.G310G|PCDH9_ENST00000328454.5_Silent_p.G310G|PCDH9_ENST00000377861.3_Silent_p.G310G|PCDH9_ENST00000544246.1_Silent_p.G310G			Q9HC56	PCDH9_HUMAN	protocadherin 9	310	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G310G(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CTGTAATCAGCCCAGTAGTAT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	13											83	86	85					13																	67801643		2203	4300	6503	66699644	SO:0001819	synonymous_variant	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.930G>A	13.37:g.67801643C>T			66699644	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																				0.488	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67801643	C	T	67801643	2	4	71	1	0	0	0	0	0	0	0	1	11549	726	26	3		3	PCDH9	13	67801643	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	15361975	67801643	47368235	82	21157										
PCID2	55795	broad.mit.edu	37	chr13	113838679	113838679	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccttgcttaaaatcgctgtcAaacatagccttgcgtccaac	6	13	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr13:113838679A>C	ENST00000337344.4	-	9	742	c.666T>G	c.(664-666)ttT>ttG	p.F222L	PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000375477.1_Missense_Mutation_p.F222L|PCID2_ENST00000375479.2_Missense_Mutation_p.F222L|PCID2_ENST00000375459.1_Missense_Mutation_p.F220L|PCID2_ENST00000375457.2_Missense_Mutation_p.F220L|PCID2_ENST00000246505.5_Missense_Mutation_p.F276L	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	222					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)			p.F276L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	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)			AATCGCTGTCAAACATAGCCT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											242	211	222					13																	113838679		2203	4300	6503	112886680	SO:0001583	missense	55795			AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.666T>G	13.37:g.113838679A>C	ENSP00000337405:p.Phe222Leu		112886680	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	37	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	A	17.88	3.496757	0.64186	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	.	.	.	5.31	-4.49	0.03504	PCI/PINT associated module (1);	0.049040	0.85682	D	0.000000	T	0.50990	0.1648	L	0.37750	1.13	0.80722	D	1	P;D	0.55605	0.778;0.972	P;P	0.53518	0.498;0.728	T	0.59289	-0.7482	9	0.10636	T	0.68	-29.1013	16.0074	0.80372	0.9015:0.0:0.0985:0.0	.	276;222	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	L	222;222;222;276;220;220;199;222;199	.	ENSP00000246505:F276L	F	-	3	2	PCID2	112886680	1.000000	0.71417	0.547000	0.28179	0.548000	0.35241	1.031000	0.30165	-1.173000	0.02758	-0.290000	0.09829	TTT		0.358	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386		C	113838679	A	C	113838679	3	2	71	1	0	0	0	0	1	0	0	0	11610	127	5	4	557	4	PCID2	13	113838679	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	46037036	113838679	1331199	83	21158										
C14orf106	55320	broad.mit.edu	37	chr14	45693420	45693420	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttggtgtttcctgctttggtTttcttaacttcagctttcct	7	9	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr14:45693420T>A	ENST00000310806.4	-	11	2828	c.2370A>T	c.(2368-2370)aaA>aaT	p.K790N		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	790					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K790N(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						CTGCTTTGGTTTTCTTAACTT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	14											164	159	161					14																	45693420		2203	4300	6503	44763170	SO:0001583	missense	55320			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2370A>T	14.37:g.45693420T>A	ENSP00000309790:p.Lys790Asn		44763170	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307676	0.23821	.	.	ENSG00000129534	ENST00000310806	T	0.24723	1.84	5.72	4.56	0.56223	.	0.460721	0.23991	N	0.042572	T	0.31513	0.0799	L	0.59436	1.845	0.09310	N	1	D	0.59767	0.986	P	0.48304	0.573	T	0.17137	-1.0379	10	0.59425	D	0.04	-7.1591	10.1302	0.42674	0.0:0.0:0.1681:0.8319	.	790	Q6P0N0	M18BP_HUMAN	N	790	ENSP00000309790:K790N	ENSP00000309790:K790N	K	-	3	2	MIS18BP1	44763170	0.280000	0.24249	0.033000	0.17914	0.008000	0.06430	1.417000	0.34770	1.082000	0.41137	-0.316000	0.08728	AAA		0.368	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45693420	T	A	45693420	3	1	71	1	0	0	0	0	1	0	0	0	1742	1838	64	5	1056	5	C14orf106	14	45693420	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10		45693420	61656120	84	21159										
MDGA2	161357	broad.mit.edu	37	chr14	47426715	47426715	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aaattgacccgtccgtaataAtttattgcccaagcgccact	6	12	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr14:47426715A>C	ENST00000399232.2	-	9	2108	c.1744T>G	c.(1744-1746)Tta>Gta	p.L582V	MDGA2_ENST00000439988.3_Missense_Mutation_p.L651V|MDGA2_ENST00000426342.1_Missense_Mutation_p.L353V|MDGA2_ENST00000357362.3_Missense_Mutation_p.L353V|SNORA25_ENST00000515926.1_RNA	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	582	Ig-like 6.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.L353V(1)|p.L651V(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						GTCCGTAATAATTTATTGCCC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	14											96	97	96					14																	47426715		1947	4148	6095	46496465	SO:0001583	missense	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1744T>G	14.37:g.47426715A>C	ENSP00000382178:p.Leu582Val		46496465	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	A	16.75	3.210774	0.58343	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.54	3.2	0.36748	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40385	U	0.001110	T	0.18923	0.0454	L	0.60455	1.87	0.80722	D	1	P;P	0.41710	0.76;0.689	P;P	0.51657	0.622;0.676	T	0.10870	-1.0611	10	0.08837	T	0.75	.	7.6936	0.28581	0.7717:0.0:0.2283:0.0	.	353;582	F6W3S7;Q7Z553	.;MDGA2_HUMAN	V	582;353;651;353	ENSP00000400011:L582V;ENSP00000405456:L353V;ENSP00000382178:L651V;ENSP00000349925:L353V	ENSP00000349925:L353V	L	-	1	2	MDGA2	46496465	0.935000	0.31712	0.977000	0.42913	0.994000	0.84299	1.065000	0.30592	0.923000	0.37045	0.528000	0.53228	TTA		0.443	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		C	47426715	A	C	47426715	3	2	71	1	0	0	0	0	1	0	0	0	9437	98	4	4	1162	4	MDGA2	14	47426715	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	1733295	47426715	59922825	85	21160										
ZBTB1	22890	broad.mit.edu	37	chr14	64990173	64990173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcagaaaacatgaccatgtaCggcatatgatttctcattta	6	8	2	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr14:64990173C>T	ENST00000554015.1	+	4	2382	c.1951C>T	c.(1951-1953)Cgg>Tgg	p.R651W	ZBTB1_ENST00000358738.3_Intron|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Missense_Mutation_p.R651W			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	651					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R651W(1)		kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		TGACCATGTACGGCATATGAT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	14											186	142	155					14																	64990173		692	1591	2283	64059926	SO:0001583	missense	22890			AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1951C>T	14.37:g.64990173C>T	ENSP00000451000:p.Arg651Trp		64059926	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	37	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.121061	0.56613	.	.	ENSG00000126804	ENST00000554015;ENST00000394712	T;T	0.31510	1.49;1.49	5.47	4.57	0.56435	Zinc finger, C2H2-like (1);	1.514670	0.06157	U	0.675328	T	0.53270	0.1786	M	0.80332	2.49	0.58432	D	0.999991	D	0.76494	0.999	P	0.51918	0.684	T	0.45086	-0.9285	9	.	.	.	-8.9417	15.5226	0.75875	0.1392:0.8608:0.0:0.0	.	651	Q9Y2K1	ZBTB1_HUMAN	W	651	ENSP00000451000:R651W;ENSP00000378201:R651W	.	R	+	1	2	ZBTB1	64059926	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.699000	0.68310	1.272000	0.44329	0.650000	0.86243	CGG		0.428	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			T	64990173	C	T	64990173	3	4	71	1	0	0	0	0	1	0	0	0	17561	527	19	1	1953	1	ZBTB1	14	64990173	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	17563458	64990173	42359367	86	21161										
SERPINA3	12	broad.mit.edu	37	chr14	95081101	95081101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aggcctcaagttcaacctcaCggagacttctgaggcagaaa	10	11	4	3	rs375245228		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr14:95081101C>T	ENST00000467132.1	+	2	1471	c.323C>T	c.(322-324)aCg>aTg	p.T108M	SERPINA3_ENST00000482740.1_5'Flank|RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393078.3_Missense_Mutation_p.T108M|SERPINA3_ENST00000393080.4_Missense_Mutation_p.T108M			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	108					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T108M(1)		NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		TTCAACCTCACGGAGACTTCT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	14						C	MET/THR	0,4406		0,0,2203	64	66	65		323	3.1	0.7	14		65	4,8596	3.7+/-12.6	0,4,4296	no	missense	SERPINA3	NM_001085.4	81	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging	108/424	95081101	4,13002	2203	4300	6503	94150854	SO:0001583	missense	12			K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.323C>T	14.37:g.95081101C>T	ENSP00000450540:p.Thr108Met		94150854	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	37	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235029	0.39498	0.0	4.65E-4	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132	D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41	5.03	3.07	0.35406	Serpin domain (3);	0.164548	0.41396	N	0.000884	D	0.93086	0.7799	M	0.83692	2.655	0.28931	N	0.891554	D;P	0.63880	0.993;0.912	D;P	0.67548	0.952;0.542	D	0.87687	0.2551	10	0.87932	D	0	.	8.7412	0.34558	0.1496:0.7705:0.0:0.08	.	108;133	P01011;G3V5I3	AACT_HUMAN;.	M	133;108;108;108;108	ENSP00000452367:T133M;ENSP00000376793:T108M;ENSP00000376795:T108M;ENSP00000450540:T108M	ENSP00000376793:T108M	T	+	2	0	SERPINA3	94150854	0.051000	0.20477	0.696000	0.30242	0.124000	0.20399	1.399000	0.34566	1.235000	0.43724	0.561000	0.74099	ACG		0.552	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		T	95081101	C	T	95081101	3	4	71	1	0	0	0	0	1	0	0	0	14127	536	19	1	325	1	SERPINA3	14	95081101	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	30090928	95081101	12268439	87	21162										
AHNAK2	113146	broad.mit.edu	37	chr14	105418844	105418844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gtcggccagggacaggtcccCctccagccacgcaccatcca	10	19	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr14:105418844C>T	ENST00000333244.5	-	7	3063	c.2944G>A	c.(2944-2946)Ggg>Agg	p.G982R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	982						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.G982R(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GACAGGTCCCCCTCCAGCCAC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	14											211	238	229					14																	105418844		2043	4190	6233	104489889	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2944G>A	14.37:g.105418844C>T	ENSP00000353114:p.Gly982Arg		104489889	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	14.63	2.594017	0.46214	.	.	ENSG00000185567	ENST00000333244	T	0.01584	4.75	3.58	2.67	0.31697	.	.	.	.	.	T	0.07413	0.0187	M	0.73217	2.22	0.09310	N	1	D	0.71674	0.998	D	0.70935	0.971	T	0.26087	-1.0113	9	0.23302	T	0.38	.	10.6887	0.45858	0.0:0.8042:0.1958:0.0	.	982	Q8IVF2	AHNK2_HUMAN	R	982	ENSP00000353114:G982R	ENSP00000353114:G982R	G	-	1	0	AHNAK2	104489889	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	0.851000	0.27751	0.463000	0.27118	0.313000	0.20887	GGG		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105418844	C	T	105418844	3	4	71	1	0	0	0	0	1	0	0	0	415	623	22	3	14447	3	AHNAK2	14	105418844	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	10337743	105418844	1930696	88	21163										
ATP10A	57194	broad.mit.edu	37	chr15	25940178	25940178	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aggcagtggacgtggagggtGggcagagagaggagaacctc	20	6	0	3	rs571308575		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr15:25940178G>T	ENST00000356865.6	-	14	2987	c.2876C>A	c.(2875-2877)cCa>cAa	p.P959Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	959					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.P959Q(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CGTGGAGGGTGGGCAGAGAGA	0.592													G|||	1	0.000199681	0	0	5008	,	,		18070	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	15											123	112	116					15																	25940178		2203	4300	6503	23491271	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2876C>A	15.37:g.25940178G>T	ENSP00000349325:p.Pro959Gln		23491271	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641244	0.47153	.	.	ENSG00000206190	ENST00000356865	T	0.78595	-1.19	4.91	1.95	0.26073	HAD-like domain (1);	1.249030	0.05050	N	0.477913	D	0.83631	0.5296	M	0.71581	2.175	0.09310	N	1	P	0.45827	0.867	P	0.60609	0.877	T	0.62656	-0.6808	10	0.19147	T	0.46	-0.3615	4.3327	0.11071	0.2484:0.0:0.5922:0.1594	.	959	O60312	AT10A_HUMAN	Q	959	ENSP00000349325:P959Q	ENSP00000349325:P959Q	P	-	2	0	ATP10A	23491271	0.036000	0.19791	0.000000	0.03702	0.068000	0.16541	1.612000	0.36889	0.246000	0.21394	0.563000	0.77884	CCA		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25940178	G	T	25940178	3	4	71	1	0	0	0	0	1	0	0	0	1117	1348	47	2	1655	2	ATP10A	15	25940178	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		25940178	76591214	89	21164										
ANKDD1A	348094	broad.mit.edu	37	chr15	65239626	65239626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttgggatctgccccacaggaCcaccccagtgatccctctgg	10	16	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr15:65239626C>T	ENST00000380230.3	+	13	1193	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	ANKDD1A_ENST00000357698.3_Silent_p.D356D|ANKDD1A_ENST00000395720.1_Silent_p.D388D|ANKDD1A_ENST00000395723.1_Silent_p.D265D	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	388					signal transduction (GO:0007165)			p.D388D(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						CCCCACAGGACCACCCCAGTG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	15											42	41	42					15																	65239626		2202	4299	6501	63026679	SO:0001819	synonymous_variant	348094				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1164C>T	15.37:g.65239626C>T			63026679	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	37	CCDS10197.2																																																																																				0.612	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65239626	C	T	65239626	2	4	71	1	0	0	0	0	0	0	0	1	624	506	18	3		3	ANKDD1A	15	65239626	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	39299448	65239626	37291766	90	21165										
CSK	1445	broad.mit.edu	37	chr15	75094100	75094100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgcatcgagacctggctgccCgcaatgtgctggtgtctgag	14	11	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr15:75094100C>T	ENST00000220003.9	+	11	1681	c.952C>T	c.(952-954)Cgc>Tgc	p.R318C	CSK_ENST00000439220.2_Missense_Mutation_p.R318C|CSK_ENST00000567571.1_Missense_Mutation_p.R318C|CSK_ENST00000309470.9_Missense_Mutation_p.R318C	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)	p.R318C(1)		central_nervous_system(1)|lung(2)	3						CCTGGCTGCCCGCAATGTGCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											66	64	65					15																	75094100		2197	4296	6493	72881153	SO:0001583	missense	1445				CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"SH2 domain containing"	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.952C>T	15.37:g.75094100C>T	ENSP00000220003:p.Arg318Cys		72881153	Q2M3N2|Q6FGZ6	Missense_Mutation	SNP	ENST00000220003.9	37	CCDS10269.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406604	0.62399	.	.	ENSG00000103653	ENST00000220003;ENST00000439220;ENST00000451345;ENST00000309470	D;D;D	0.87966	-2.32;-2.32;-2.32	4.62	3.7	0.42460	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.052333	0.85682	D	0.000000	D	0.94788	0.8317	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93958	0.7238	10	0.54805	T	0.06	-20.437	8.2878	0.31939	0.1557:0.7596:0.0:0.0847	.	318	P41240	CSK_HUMAN	C	318;318;267;318	ENSP00000220003:R318C;ENSP00000414764:R318C;ENSP00000438808:R318C	ENSP00000220003:R318C	R	+	1	0	CSK	72881153	0.909000	0.30893	1.000000	0.80357	0.972000	0.66771	1.469000	0.35343	1.162000	0.42619	0.561000	0.74099	CGC		0.602	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383		T	75094100	C	T	75094100	3	4	71	1	0	0	0	0	1	0	0	0	3949	652	23	1	990	1	CSK	15	75094100	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	9854474	75094100	27437292	91	21166										
BNC1	646	broad.mit.edu	37	chr15	83935704	83935704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gtccagtaggatttttaggcGaacggggatggcctgggtcc	16	8	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr15:83935704G>A	ENST00000345382.2	-	3	404	c.319C>T	c.(319-321)Cgc>Tgc	p.R107C	BNC1_ENST00000569704.1_Missense_Mutation_p.R100C|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	107					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R107C(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						ATTTTTAGGCGAACGGGGATG	0.512																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	15											107	99	102					15																	83935704		2203	4300	6503	81726708	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.319C>T	15.37:g.83935704G>A	ENSP00000307041:p.Arg107Cys		81726708	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	G	32	5.136508	0.94517	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	D	0.86956	-2.19	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.93556	0.7943	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93593	0.6923	10	0.87932	D	0	-34.9268	19.614	0.95622	0.0:0.0:1.0:0.0	.	100;107	F5GY04;Q01954	.;BNC1_HUMAN	C	107;100	ENSP00000307041:R107C	ENSP00000307041:R107C	R	-	1	0	BNC1	81726708	1.000000	0.71417	0.997000	0.53966	0.919000	0.55068	9.554000	0.98121	2.873000	0.98535	0.561000	0.74099	CGC		0.512	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83935704	G	A	83935704	3	1	71	1	0	0	0	0	1	0	0	0	1475	1058	37	1	2677	1	BNC1	15	83935704	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	8841604	83935704	18595688	92	21167										
SPATA8	145946	broad.mit.edu	37	chr15	97327442	97327442	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgcggctggaggcctttcaAgggtggcccaggaggcctca	16	12	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr15:97327442A>C	ENST00000328504.3	+	2	416	c.149A>C	c.(148-150)aAg>aCg	p.K50T	SPATA8-AS1_ENST00000558722.1_RNA|SPATA8-AS1_ENST00000560888.1_RNA|SPATA8_ENST00000558553.1_Missense_Mutation_p.Q9H	NM_173499.3	NP_775770.1	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8	50								p.K50T(1)		large_intestine(4)|lung(8)|ovary(1)|skin(3)	16	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			AGGCCTTTCAAGGGTGGCCCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	15											66	64	65					15																	97327442		2197	4298	6495	95128446	SO:0001583	missense	145946			AY489187	CCDS10376.1	15q26	2008-02-05			ENSG00000185594	ENSG00000185594			28676	protein-coding gene	gene with protein product		613948					Standard	NM_173499		Approved	MGC44294	uc002bue.3	Q6RVD6	OTTHUMG00000149847	ENST00000328504.3:c.149A>C	15.37:g.97327442A>C	ENSP00000328149:p.Lys50Thr		95128446	Q2KJ07	Missense_Mutation	SNP	ENST00000328504.3	37	CCDS10376.1	.	.	.	.	.	.	.	.	.	.	A	9.113	1.007129	0.19199	.	.	ENSG00000185594	ENST00000328504	T	0.37915	1.17	2.75	-2.46	0.06461	.	.	.	.	.	T	0.17874	0.0429	N	0.08118	0	0.09310	N	1	P	0.45827	0.867	P	0.44477	0.451	T	0.12372	-1.0550	9	0.87932	D	0	.	3.1463	0.06473	0.5315:0.0:0.2496:0.2189	.	50	Q6RVD6	SPAT8_HUMAN	T	50	ENSP00000328149:K50T	ENSP00000328149:K50T	K	+	2	0	SPATA8	95128446	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.479000	0.02327	-0.556000	0.06134	-0.366000	0.07423	AAG		0.587	SPATA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313533.1	NM_173499		C	97327442	A	C	97327442	3	2	71	1	0	0	0	0	1	0	0	0	15054	72	3	4	155	4	SPATA8	15	97327442	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	13391738	97327442	5203950	93	21168										
TMEM8A	58986	broad.mit.edu	37	chr16	424063	424063	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tggtgacccagatggccgccCcggagcccaagaagtcgcag	14	14	0	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr16:424063C>A	ENST00000431232.2	-	11	2004	c.1844G>T	c.(1843-1845)gGg>gTg	p.G615V	TMEM8A_ENST00000250930.3_Missense_Mutation_p.G422V	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	615					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)		p.G615V(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GATGGCCGCCCCGGAGCCCAA	0.657											OREG0003702	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				1	Substitution - Missense(1)	large_intestine(1)	16											58	55	56					16																	424063		2198	4297	6495	364064	SO:0001583	missense	58986			AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1844G>T	16.37:g.424063C>A	ENSP00000401338:p.Gly615Val	588	364064	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.790|6.790	0.514691|0.514691	0.12944|0.12944	.|.	.|.	ENSG00000129925|ENSG00000129925	ENST00000431232;ENST00000250930;ENST00000382942;ENST00000448854|ENST00000424078	T;T;T|T	0.38240|0.43294	1.15;1.15;1.15|0.95	3.94|3.94	2.9|2.9	0.33743|0.33743	.|.	0.238534|0.238534	0.27668|0.27668	N|N	0.018354|0.018354	T|T	0.27063|0.27063	0.0663|0.0663	N|N	0.04880|0.04880	-0.145|-0.145	0.58432|0.58432	D|D	0.999996|0.999996	B|.	0.12013|.	0.005|.	B|.	0.19666|.	0.026|.	T|T	0.17961|0.17961	-1.0352|-1.0352	10|8	0.17369|0.66056	T|D	0.5|0.02	-15.2333|-15.2333	9.7205|9.7205	0.40300|0.40300	0.6135:0.3865:0.0:0.0|0.6135:0.3865:0.0:0.0	.|.	615|.	Q9HCN3|.	TMM8A_HUMAN|.	V|W	615;422;142;163|122	ENSP00000401338:G615V;ENSP00000250930:G422V;ENSP00000401931:G163V|ENSP00000397620:G122W	ENSP00000250930:G422V|ENSP00000397620:G122W	G|G	-|-	2|1	0|0	TMEM8A|TMEM8A	364064|364064	0.982000|0.982000	0.34865|0.34865	0.632000|0.632000	0.29296|0.29296	0.429000|0.429000	0.31625|0.31625	5.597000|5.597000	0.67577|0.67577	0.834000|0.834000	0.34852|0.34852	0.563000|0.563000	0.77884|0.77884	GGG|GGG		0.657	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		A	424063	C	A	424063	3	1	71	1	0	0	0	0	1	0	0	0	16253	623	22	2	483	2	TMEM8A	16	424063	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		424063	89930690	94	21169										
EDC4	23644	broad.mit.edu	37	chr16	67916939	67916939	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcgctcaaggagcagcaggcCgccgtcacctccagcatcat	11	16	3	0	rs144428519	byFrequency	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr16:67916939C>T	ENST00000358933.5	+	27	3947	c.3708C>T	c.(3706-3708)gcC>gcT	p.A1236A	NRN1L_ENST00000339176.3_5'Flank|NRN1L_ENST00000576147.1_5'Flank|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1236					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A1236A(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AGCAGCAGGCCGCCGTCACCT	0.612											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	16						C		0,4396		0,0,2198	73	63	67		3708	-11.4	0	16	dbSNP_134	67	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	EDC4	NM_014329.3		0,6,6492	TT,TC,CC		0.0698,0.0,0.0462		1236/1402	67916939	6,12990	2198	4300	6498	66474440	SO:0001819	synonymous_variant	23644			U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3708C>T	16.37:g.67916939C>T		1103	66474440	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	37	CCDS10849.1																																																																																				0.612	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		T	67916939	C	T	67916939	2	4	71	1	0	0	0	0	0	0	0	1	4919	639	23	1		1	EDC4	16	67916939	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	67492876	67916939	22437814	95	21170										
DHODH	1723	broad.mit.edu	37	chr16	72057435	72057435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aggacgcgctggagaagatcCgggcaggggcctccctggtg	18	11	0	2	rs201947120		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr16:72057435C>T	ENST00000219240.4	+	8	1057	c.1036C>T	c.(1036-1038)Cgg>Tgg	p.R346W	DHODH_ENST00000572887.1_Missense_Mutation_p.R344W	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	346			R -> W (in POADS). {ECO:0000269|PubMed:19915526}.		'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)	p.R346W(1)		breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	GGAGAAGATCCGGGCAGGGGC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	TRP/ARG	0,4052		0,0,2026	66	76	73		1036	5.5	1	16		73	2,8360		0,2,4179	yes	missense	DHODH	NM_001361.4	101	0,2,6205	TT,TC,CC		0.0239,0.0,0.0161	probably-damaging	346/396	72057435	2,12412	2026	4181	6207	70614936	SO:0001583	missense	1723				CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"dihydroorotate dehydrogenase"			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.1036C>T	16.37:g.72057435C>T	ENSP00000219240:p.Arg346Trp		70614936	A8K8C8|Q6P176	Missense_Mutation	SNP	ENST00000219240.4	37	CCDS42192.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.042565	0.93685	0.0	2.39E-4	ENSG00000102967	ENST00000219240	D	0.94417	-3.42	5.48	5.48	0.80851	Aldolase-type TIM barrel (1);Dihydroorotate dehydrogenase, conserved site (1);	0.161254	0.56097	D	0.000021	D	0.98128	0.9382	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.98842	1.0755	10	0.87932	D	0	-10.9133	19.7014	0.96054	0.0:1.0:0.0:0.0	.	346	Q02127	PYRD_HUMAN	W	346	ENSP00000219240:R346W	ENSP00000219240:R346W	R	+	1	2	DHODH	70614936	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.506000	0.60428	2.733000	0.93635	0.561000	0.74099	CGG		0.612	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361		T	72057435	C	T	72057435	3	4	71	1	0	0	0	0	1	0	0	0	4495	643	23	1	1066	1	DHODH	16	72057435	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	4140496	72057435	18297318	96	21171										
DERL2	51009	broad.mit.edu	37	chr17	5384619	5384619	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgtttgttgaaggatacggtCattaagaatccaccaaaaag	9	6	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr17:5384619C>T	ENST00000158771.4	-	4	379	c.324G>A	c.(322-324)atG>atA	p.M108I	DERL2_ENST00000572834.1_Intron|DERL2_ENST00000570848.1_Missense_Mutation_p.M108I|DERL2_ENST00000571968.1_5'Flank	NM_016041.3	NP_057125.2	Q9GZP9	DERL2_HUMAN	derlin 2	108					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|retrograde protein transport, ER to cytosol (GO:0030970)|suckling behavior (GO:0001967)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|late endosome (GO:0005770)|membrane (GO:0016020)		p.M108I(1)		large_intestine(3)	3						AGGATACGGTCATTAAGAATC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	17											123	113	117					17																	5384619		2203	4300	6503	5325343	SO:0001583	missense	51009			BC010890	CCDS11073.1	17p13.2	2012-02-01	2012-02-01		ENSG00000072849	ENSG00000072849			17943	protein-coding gene	gene with protein product		610304	"Der1-like domain family, member 2"			10810093, 11500051	Standard	NM_016041		Approved	F-LAN-1, FLANa, F-LANa, CGI-101, derlin-2	uc002gcc.1	Q9GZP9	OTTHUMG00000102040	ENST00000158771.4:c.324G>A	17.37:g.5384619C>T	ENSP00000158771:p.Met108Ile		5325343	Q9Y3A7	Missense_Mutation	SNP	ENST00000158771.4	37	CCDS11073.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939175	0.73557	.	.	ENSG00000072849	ENST00000158771	T	0.10668	2.85	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.15089	0.0364	L	0.56124	1.755	0.80722	D	1	B	0.17038	0.02	B	0.20384	0.029	T	0.06409	-1.0828	10	0.23891	T	0.37	-16.8784	19.609	0.95594	0.0:1.0:0.0:0.0	.	108	Q9GZP9	DERL2_HUMAN	I	108	ENSP00000158771:M108I	ENSP00000158771:M108I	M	-	3	0	DERL2	5325343	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.408000	0.80041	2.882000	0.98803	0.655000	0.94253	ATG		0.423	DERL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219825.1	NM_016041		T	5384619	C	T	5384619	3	4	71	1	0	0	0	0	1	0	0	0	4458	826	29	3	411	3	DERL2	17	5384619	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		5384619	75810591	97	21172										
TP53	7157	broad.mit.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	71	1	0	0	0	0	1	0	0	0	16421	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	2192920	7577539	73617671	98	21173										
C17orf104	284071	broad.mit.edu	37	chr17	42745338	42745338	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttcaacaacttggttcaaatGggtttcccctaagatccacc	6	12	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr17:42745338G>T	ENST00000409122.2	+	5	2201	c.2059G>T	c.(2059-2061)Ggg>Tgg	p.G687W	C17orf104_ENST00000409464.1_Missense_Mutation_p.G521W|C17orf104_ENST00000359945.3_Missense_Mutation_p.G687W	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	687								p.G687W(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						TGGTTCAAATGGGTTTCCCCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	17											86	79	81					17																	42745338		2203	4300	6503	40100864	SO:0001583	missense	284071				CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.2059G>T	17.37:g.42745338G>T	ENSP00000386452:p.Gly687Trp		40100864	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161171	0.38119	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000409464	T;T;T	0.33438	1.41;1.41;1.42	5.74	5.74	0.90152	.	0.312048	0.30949	N	0.008559	T	0.42245	0.1194	L	0.34521	1.04	0.32390	N	0.553414	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70487	0.969;0.969;0.969	T	0.52403	-0.8580	10	0.72032	D	0.01	-17.6866	11.3449	0.49554	0.07:0.128:0.8019:0.0	.	687;687;521	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	W	687;687;521	ENSP00000353028:G687W;ENSP00000386452:G687W;ENSP00000386586:G521W	ENSP00000353028:G687W	G	+	1	0	C17orf104	40100864	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.186000	0.42593	2.709000	0.92574	0.655000	0.94253	GGG		0.398	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42745338	G	T	42745338	3	4	71	1	0	0	0	0	1	0	0	0	1855	1348	47	2	2077	2	C17orf104	17	42745338	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	35167799	42745338	38449872	99	21174										
GPRC5C	55890	broad.mit.edu	37	chr17	72436604	72436604	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cttcctgggggcctggcccgCcctgtgtggccgctacaagc	14	16	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr17:72436604C>A	ENST00000392627.1	+	2	1950	c.824C>A	c.(823-825)gCc>gAc	p.A275D	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Missense_Mutation_p.A242D|GPRC5C_ENST00000481232.1_Intron	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	230					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)	p.A275D(1)		central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GCCTGGCCCGCCCTGTGTGGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											45	38	40					17																	72436604		2203	4300	6503	69948199	SO:0001583	missense	55890			AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"GPCR / Class C : Orphans"	13309	protein-coding gene	gene with protein product		605949	"G protein-coupled receptor, family C, group 5, member C"			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.824C>A	17.37:g.72436604C>A	ENSP00000376403:p.Ala275Asp		69948199	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	37	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	C	8.441	0.850801	0.17034	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000392629;ENST00000392628	T	0.19938	2.11	5.79	2.28	0.28536	GPCR, family 3, C-terminal (2);	0.590250	0.19646	N	0.109334	T	0.24851	0.0603	L	0.61218	1.895	0.34301	D	0.684311	B;B;B	0.26602	0.154;0.154;0.127	B;B;B	0.31337	0.128;0.128;0.078	T	0.39683	-0.9602	10	0.87932	D	0	-3.6418	11.8626	0.52476	0.0:0.7753:0.0:0.2247	.	230;230;242	A8MXZ4;Q9NQ84;Q9NQ84-2	.;GPC5C_HUMAN;.	D	230;275;242;230	ENSP00000376405:A242D	ENSP00000340595:A275D	A	+	2	0	GPRC5C	69948199	0.004000	0.15560	0.698000	0.30274	0.013000	0.08279	1.629000	0.37071	0.796000	0.33947	0.561000	0.74099	GCC		0.617	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2			A	72436604	C	A	72436604	3	1	71	1	0	0	0	0	1	0	0	0	6747	739	26	2	838	2	GPRC5C	17	72436604	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	29691266	72436604	8758606	100	21175										
USH1G	124590	broad.mit.edu	37	chr17	72915979	72915979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	actgctcaagtaatttctgcGgaacaccatggtgcccaggc	10	12	2	0	rs558361799		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr17:72915979G>A	ENST00000319642.1	-	2	1134	c.952C>T	c.(952-954)Cgc>Tgc	p.R318C		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	318					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)	p.R318C(1)	HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					TAATTTCTGCGGAACACCATG	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	17											58	71	67					17																	72915979		2203	4299	6502	70427574	SO:0001583	missense	124590			AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.952C>T	17.37:g.72915979G>A	ENSP00000320076:p.Arg318Cys		70427574	Q8N251	Missense_Mutation	SNP	ENST00000319642.1	37	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.436279	0.62955	.	.	ENSG00000182040	ENST00000319642	T	0.75477	-0.94	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	D	0.82879	0.5133	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	D	0.83718	0.0191	10	0.54805	T	0.06	-25.1404	11.2464	0.49000	0.0:0.0:0.685:0.315	.	318	Q495M9	USH1G_HUMAN	C	318	ENSP00000320076:R318C	ENSP00000320076:R318C	R	-	1	0	USH1G	70427574	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.420000	0.52735	2.275000	0.75901	0.555000	0.69702	CGC		0.701	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		A	72915979	G	A	72915979	3	1	71	1	0	0	0	0	1	0	0	0	17075	1116	39	1	441	1	USH1G	17	72915979	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	479375	72915979	8279231	101	21176										
C18orf34	374864	broad.mit.edu	37	chr18	30672801	30672801	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aataattgtccttttcttttAagaatgtaatctgtagctgt	6	5	2	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr18:30672801A>G	ENST00000383096.3	-	21	2494	c.2312T>C	c.(2311-2313)tTa>tCa	p.L771S	CCDC178_ENST00000403303.1_Missense_Mutation_p.L771S|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000300227.8_Missense_Mutation_p.L733S|CCDC178_ENST00000583930.1_Missense_Mutation_p.L771S|CCDC178_ENST00000581852.1_Intron|CCDC178_ENST00000402325.1_Intron|CCDC178_ENST00000579947.1_Missense_Mutation_p.L771S|CCDC178_ENST00000406524.2_Missense_Mutation_p.L771S			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	771								p.L733S(1)|p.L771S(1)									CTTTTCTTTTAAGAATGTAAT	0.264																																																2	Substitution - Missense(2)	large_intestine(2)	18											45	49	47					18																	30672801		2200	4282	6482	28926799	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2312T>C	18.37:g.30672801A>G	ENSP00000372576:p.Leu771Ser		28926799	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	A	6.475	0.455818	0.12283	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524	T;T;T;T	0.35236	1.39;1.39;1.49;1.32	5.84	5.84	0.93424	.	.	.	.	.	T	0.47746	0.1462	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76575	0.988;0.988;0.988;0.988	T	0.30327	-0.9982	9	0.09590	T	0.72	-2.3701	15.205	0.73173	1.0:0.0:0.0:0.0	.	771;771;733;771	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	S	771;771;733;771	ENSP00000385591:L771S;ENSP00000372576:L771S;ENSP00000300227:L733S;ENSP00000385867:L771S	ENSP00000300227:L733S	L	-	2	0	C18orf34	28926799	1.000000	0.71417	0.212000	0.23672	0.154000	0.21943	5.672000	0.68102	2.236000	0.73375	0.528000	0.53228	TTA		0.264	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		G	30672801	A	G	30672801	3	3	71	1	0	0	0	0	1	0	0	0	1908	372	13	4	303	4	C18orf34	18	30672801	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10		30672801	47404447	102	21177										
SMAD2	4087	broad.mit.edu	37	chr18	45394753	45394753	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agttagtgttttctggaatgGagtgagtatagtcatccaga	12	4	2	2	rs576952880		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr18:45394753G>C	ENST00000402690.2	-	5	990	c.596C>G	c.(595-597)tCc>tGc	p.S199C	SMAD2_ENST00000586040.1_Missense_Mutation_p.S169C|SMAD2_ENST00000262160.6_Missense_Mutation_p.S199C|SMAD2_ENST00000591214.1_Missense_Mutation_p.S169C|SMAD2_ENST00000587353.1_5'UTR|SMAD2_ENST00000356825.4_Missense_Mutation_p.S169C	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	199					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.S199C(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						TTCTGGAATGGAGTGAGTATA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	18											117	110	112					18																	45394753		2203	4300	6503	43648751	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.596C>G	18.37:g.45394753G>C	ENSP00000384449:p.Ser199Cys		43648751		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	G	33	5.233724	0.95207	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.94576	-3.46;-3.45;-3.46	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.97018	0.9026	M	0.77820	2.39	0.80722	D	1	D;B;B	0.71674	0.998;0.036;0.096	D;B;B	0.63033	0.91;0.046;0.062	D	0.97003	0.9730	10	0.66056	D	0.02	.	19.9474	0.97186	0.0:0.0:1.0:0.0	.	169;169;199	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	C	199;169;199	ENSP00000262160:S199C;ENSP00000349282:S169C;ENSP00000384449:S199C	ENSP00000262160:S199C	S	-	2	0	SMAD2	43648751	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.819000	0.86621	2.774000	0.95407	0.655000	0.94253	TCC		0.418	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		C	45394753	G	C	45394753	3	2	71	1	0	0	0	0	1	0	0	0	14795	1174	41	5	835	5	SMAD2	18	45394753	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	14721952	45394753	32682495	103	21178										
ZNF532	55205	broad.mit.edu	37	chr18	56586498	56586498	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcatcgacgggaccaaaaaaCcatccctgaagcaaccggat	8	13	1	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr18:56586498C>A	ENST00000336078.4	+	4	1755	c.979C>A	c.(979-981)Cca>Aca	p.P327T	ZNF532_ENST00000591083.1_Missense_Mutation_p.P327T|ZNF532_ENST00000591808.1_Missense_Mutation_p.P327T|ZNF532_ENST00000591230.1_Missense_Mutation_p.P327T|ZNF532_ENST00000589288.1_Missense_Mutation_p.P327T	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P327T(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GACCAAAAAACCATCCCTGAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	18											101	103	102					18																	56586498		2203	4300	6503	54737478	SO:0001583	missense	55205			AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.979C>A	18.37:g.56586498C>A	ENSP00000338217:p.Pro327Thr		54737478	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	0.009	-1.800533	0.00611	.	.	ENSG00000074657	ENST00000336078	T	0.01505	4.82	4.97	0.878	0.19150	.	0.887861	0.09989	N	0.729997	T	0.01905	0.0060	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47071	-0.9145	10	0.19147	T	0.46	-8.4553	7.648	0.28331	0.0718:0.3877:0.4393:0.1012	.	327	Q9HCE3	ZN532_HUMAN	T	327	ENSP00000338217:P327T	ENSP00000338217:P327T	P	+	1	0	ZNF532	54737478	0.000000	0.05858	0.010000	0.14722	0.040000	0.13550	0.364000	0.20325	0.508000	0.28173	-0.324000	0.08512	CCA		0.532	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		A	56586498	C	A	56586498	3	1	71	1	0	0	0	0	1	0	0	0	18011	507	18	2	981	2	ZNF532	18	56586498	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	11191745	56586498	21490750	104	21179										
C19orf26	255057	broad.mit.edu	37	chr19	1234738	1234738	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aagtccccctccgtcagtgtGtacctgcgacagcatctggc	10	15	2	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:1234738G>A	ENST00000382477.2	-	6	793	c.519C>T	c.(517-519)taC>taT	p.Y173Y	C19orf26_ENST00000590083.1_Silent_p.Y153Y|C19orf26_ENST00000215376.6_Silent_p.Y147Y			Q8N350	DOS_HUMAN	chromosome 19 open reading frame 26	173						integral component of membrane (GO:0016021)		p.Y147Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CCGTCAGTGTGTACCTGCGAC	0.662										HNSCC(14;0.022)																																						1	Substitution - coding silent(1)	large_intestine(1)	19											92	77	82					19																	1234738		2198	4299	6497	1185738	SO:0001819	synonymous_variant	255057			BC028156	CCDS12057.1, CCDS12057.2	19p13.3	2012-10-24			ENSG00000099625	ENSG00000099625			28617	protein-coding gene	gene with protein product	"downstream of STK11"					12477932	Standard	NM_152769		Approved	MGC40084, DOS	uc002lrm.3	Q8N350	OTTHUMG00000180141	ENST00000382477.2:c.519C>T	19.37:g.1234738G>A			1185738	O43385	Silent	SNP	ENST00000382477.2	37																																																																																					0.662	C19orf26-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_152769		A	1234738	G	A	1234738	2	1	71	1	0	0	0	0	0	0	0	1	1922	1372	48	3		3	C19orf26	19	1234738	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		1234738	57894245	105	21180										
ACSBG2	81616	broad.mit.edu	37	chr19	6183076	6183076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	taatactcccgtgagctaccGcatggctaagactctcgtgt	9	12	1	2	rs372123644		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:6183076G>A	ENST00000586696.1	+	10	1391	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H	ACSBG2_ENST00000588304.1_Missense_Mutation_p.R322H|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000591403.1_Missense_Mutation_p.R372H|ACSBG2_ENST00000252669.5_Missense_Mutation_p.R372H|ACSBG2_ENST00000588485.1_Missense_Mutation_p.R185H			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	372					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.R372H(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTGAGCTACCGCATGGCTAAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	103	97	99		1115	-1.4	0	19		99	0,8600		0,0,4300	no	missense	ACSBG2	NM_030924.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	372/667	6183076	1,13005	2203	4300	6503	6134076	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1115G>A	19.37:g.6183076G>A	ENSP00000465589:p.Arg372His		6134076	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	G	2.269	-0.367374	0.05069	2.27E-4	0.0	ENSG00000130377	ENST00000252669	T	0.17370	2.28	5.06	-1.41	0.08941	AMP-dependent synthetase/ligase (1);	0.371965	0.19898	N	0.103569	T	0.12902	0.0313	L	0.50333	1.59	0.20703	N	0.999863	B;B	0.24533	0.07;0.105	B;B	0.24269	0.052;0.051	T	0.36672	-0.9738	10	0.15066	T	0.55	-11.3548	10.2141	0.43158	0.498:0.0:0.502:0.0	.	372;372	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	H	372	ENSP00000252669:R372H	ENSP00000252669:R372H	R	+	2	0	ACSBG2	6134076	0.007000	0.16637	0.046000	0.18839	0.000000	0.00434	0.099000	0.15210	-0.045000	0.13468	-0.781000	0.03364	CGC		0.512	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		A	6183076	G	A	6183076	3	1	71	1	0	0	0	0	1	0	0	0	174	1087	38	1	1149	1	ACSBG2	19	6183076	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	4948338	6183076	52945907	106	21181										
DNM2	1785	broad.mit.edu	37	chr19	10887842	10887842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcttgacctgatggacgaggGcaccgacgccagggacgtct	15	12	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:10887842G>A	ENST00000355667.6	+	5	718	c.638G>A	c.(637-639)gGc>gAc	p.G213D	DNM2_ENST00000408974.4_Missense_Mutation_p.G213D|DNM2_ENST00000585892.1_Missense_Mutation_p.G213D|DNM2_ENST00000314646.5_Missense_Mutation_p.G213D|DNM2_ENST00000359692.6_Missense_Mutation_p.G213D|DNM2_ENST00000389253.4_Missense_Mutation_p.G213D|DNM2_ENST00000591819.1_3'UTR	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	213	Dynamin-type G.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.G213D(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			ATGGACGAGGGCACCGACGCC	0.592			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	1	Substitution - Missense(1)	large_intestine(1)	19											117	103	108					19																	10887842		2203	4300	6503	10748842	SO:0001583	missense	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.638G>A	19.37:g.10887842G>A	ENSP00000347890:p.Gly213Asp		10748842	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122474	0.94429	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78	4.94	4.94	0.65067	Dynamin, GTPase domain (1);	0.000000	0.85682	D	0.000000	D	0.98308	0.9439	M	0.93241	3.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	D	0.99694	1.1002	10	0.87932	D	0	-6.9168	16.9491	0.86239	0.0:0.0:1.0:0.0	.	213;213;213;213	A8K1B6;P50570-2;P50570;E9PEQ4	.;.;DYN2_HUMAN;.	D	202;213;213;213;213;213	ENSP00000386192:G213D;ENSP00000347890:G213D;ENSP00000352721:G213D;ENSP00000373905:G213D;ENSP00000313164:G213D	ENSP00000313164:G213D	G	+	2	0	DNM2	10748842	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	9.756000	0.98918	2.286000	0.76751	0.561000	0.74099	GGC		0.592	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		A	10887842	G	A	10887842	3	1	71	1	0	0	0	0	1	0	0	0	4683	1203	42	3	656	3	DNM2	19	10887842	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	4704766	10887842	48241141	107	21182										
CACNA1A	773	broad.mit.edu	37	chr19	13409402	13409402	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttgtcctccctccgcgcgtcCccctcgtacgtggctggagc	11	18	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:13409402C>A	ENST00000360228.5	-	19	3044	c.3045G>T	c.(3043-3045)ggG>ggT	p.G1015G	CACNA1A_ENST00000573710.2_Silent_p.G1016G	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1016			E -> K (in dbSNP:rs16024).		adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.G1016G(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCGCGCGTCCCCCTCGTACG	0.677																																																2	Substitution - coding silent(2)	large_intestine(2)	19											22	22	22					19																	13409402		1606	3083	4689	13270402	SO:0001819	synonymous_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3045G>T	19.37:g.13409402C>A			13270402	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																				0.677	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13409402	C	A	13409402	2	1	71	1	0	0	0	0	0	0	0	1	2544	610	22	2		2	CACNA1A	19	13409402	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	2521560	13409402	45719581	108	21183										
SLC1A6	6511	broad.mit.edu	37	chr19	15079274	15079274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccatgtagtacacagctgccCgcatccccatccgccccgtg	8	19	0	0	rs200538770		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:15079274C>T	ENST00000221742.3	-	3	396	c.389G>A	c.(388-390)cGg>cAg	p.R130Q	SLC1A6_ENST00000430939.2_Intron|SLC1A6_ENST00000598504.1_Missense_Mutation_p.R130Q|SLC1A6_ENST00000544886.2_Missense_Mutation_p.R130Q|SLC1A6_ENST00000600144.1_Missense_Mutation_p.R130Q	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	130					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.R130Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CACAGCTGCCCGCATCCCCAT	0.607													c|||	1	0.000199681	0	0	5008	,	,		15303	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19							GLN/ARG	0,4406		0,0,2203	105	74	84		389	4.4	0.2	19		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC1A6	NM_005071.1	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	130/565	15079274	1,13005	2203	4300	6503	14940274	SO:0001583	missense	6511				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.389G>A	19.37:g.15079274C>T	ENSP00000221742:p.Arg130Gln		14940274	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	19.09	3.760800	0.69763	0.0	1.16E-4	ENSG00000105143	ENST00000221742;ENST00000544886;ENST00000542610	T;T	0.61040	0.14;0.14	4.39	4.39	0.52855	.	0.129882	0.52532	D	0.000066	T	0.69450	0.3112	M	0.79475	2.455	0.52099	D	0.999948	P;D;P	0.61080	0.94;0.989;0.902	P;P;B	0.54210	0.473;0.745;0.135	T	0.75331	-0.3355	10	0.66056	D	0.02	-20.5818	14.5124	0.67797	0.0:1.0:0.0:0.0	.	130;131;130	Q8N753;Q59GB0;P48664	.;.;EAA4_HUMAN	Q	130;130;131	ENSP00000221742:R130Q;ENSP00000446175:R130Q	ENSP00000221742:R130Q	R	-	2	0	SLC1A6	14940274	1.000000	0.71417	0.203000	0.23512	0.987000	0.75469	5.720000	0.68470	2.276000	0.75962	0.450000	0.29827	CGG		0.607	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15079274	C	T	15079274	3	4	71	1	0	0	0	0	1	0	0	0	14473	652	23	1	1333	1	SLC1A6	19	15079274	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1669872	15079274	44049709	109	21184										
ZNF829	374899	broad.mit.edu	37	chr19	37382938	37382938	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gatgatcattaaggtttgagCaatacttaaaggcttttcca	8	6	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:37382938C>A	ENST00000391711.3	-	6	1119	c.755G>T	c.(754-756)tGc>tTc	p.C252F	ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron|ZNF829_ENST00000520965.1_Missense_Mutation_p.C333F	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C252F(1)		endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAGGTTTGAGCAATACTTAAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19											49	52	51					19																	37382938		2202	4297	6499	42074778	SO:0001583	missense	374899			BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.755G>T	19.37:g.37382938C>A	ENSP00000429266:p.Cys252Phe		42074778	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	37	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740026	0.30865	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.07327	3.2	3.41	-0.179	0.13299	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03220	0.0094	N	0.10874	0.06	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.47368	-0.9123	9	0.09084	T	0.74	.	3.8994	0.09154	0.3231:0.4794:0.0:0.1975	.	252	Q3KNS6	ZN829_HUMAN	F	252	ENSP00000429266:C252F	ENSP00000429266:C252F	C	-	2	0	ZNF829	42074778	0.000000	0.05858	0.956000	0.39512	0.984000	0.73092	-2.992000	0.00657	0.065000	0.16485	-0.157000	0.13467	TGC		0.348	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		A	37382938	C	A	37382938	3	1	71	1	0	0	0	0	1	0	0	0	18221	710	25	2	547	2	ZNF829	19	37382938	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	22303664	37382938	21746045	110	21185										
SIGLEC7	27036	broad.mit.edu	37	chr19	51645997	51645997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tgcggggagatacttctttcGtatggagaaaggaaatataa	12	4	1	2	rs368230574	byFrequency	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:51645997G>A	ENST00000317643.6	+	1	440	c.371G>A	c.(370-372)cGt>cAt	p.R124H	SIGLEC7_ENST00000305628.7_Missense_Mutation_p.R124H|SIGLEC7_ENST00000600577.1_Missense_Mutation_p.R124H	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	124					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R124H(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		TACTTCTTTCGTATGGAGAAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	89	89					19																	51645997		2203	4300	6503	56337809	SO:0001583	missense	27036			AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.371G>A	19.37:g.51645997G>A	ENSP00000323328:p.Arg124His		56337809	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Missense_Mutation	SNP	ENST00000317643.6	37	CCDS12826.1	.	.	.	.	.	.	.	.	.	.	.	13.82	2.351240	0.41700	.	.	ENSG00000168995	ENST00000317643;ENST00000305628;ENST00000536156	T;T;T	0.65916	-0.18;-0.18;-0.18	2.89	0.393	0.16294	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	1.072930	0.07459	N	0.900226	T	0.63046	0.2478	M	0.77103	2.36	0.09310	N	1	D;P;D	0.64830	0.994;0.877;0.973	P;B;B	0.46320	0.512;0.029;0.36	T	0.52215	-0.8605	10	0.38643	T	0.18	.	4.9449	0.13984	0.3527:0.0:0.6473:0.0	.	124;124;124	Q9Y286-4;Q9Y286-2;Q9Y286	.;.;SIGL7_HUMAN	H	124	ENSP00000323328:R124H;ENSP00000306757:R124H;ENSP00000437609:R124H	ENSP00000306757:R124H	R	+	2	0	SIGLEC7	56337809	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.391000	0.20784	0.040000	0.15660	0.530000	0.56133	CGT		0.478	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		A	51645997	G	A	51645997	3	1	71	1	0	0	0	0	1	0	0	0	14350	1145	40	1	373	1	SIGLEC7	19	51645997	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	14263059	51645997	7482986	111	21186										
CACNG7	59284	broad.mit.edu	37	chr19	54445395	54445395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cgcgtctcagcgactgctccGactactcgggccagttcctg	11	16	1	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:54445395G>A	ENST00000391767.1	+	6	888	c.676G>A	c.(676-678)Gac>Aac	p.D226N	CACNG7_ENST00000222212.2_Missense_Mutation_p.D226N			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	226				GAGVMSVYLFTKRYAEEEMYRPHPAFYRPRLSDCSDYSGQF LQPEAWRRGRSPSDISSDVSIQMTQNYPPAIKYPDHLHIST SPC -> VTSVGPRL (in Ref. 1; AAK20030). {ECO:0000305}.	calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.D226N(1)		NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		CGACTGCTCCGACTACTCGGG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	67	68					19																	54445395		2203	4300	6503	59137207	SO:0001583	missense	59284			AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.676G>A	19.37:g.54445395G>A	ENSP00000375647:p.Asp226Asn		59137207	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	35	5.438525	0.96168	.	.	ENSG00000105605	ENST00000391767;ENST00000222212	T;T	0.64618	-0.11;-0.11	4.18	4.18	0.49190	.	0.055619	0.64402	D	0.000002	T	0.67627	0.2913	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66176	-0.5989	10	0.33141	T	0.24	-32.3698	14.3911	0.66978	0.0:0.0:1.0:0.0	.	226	P62955	CCG7_HUMAN	N	226	ENSP00000375647:D226N;ENSP00000222212:D226N	ENSP00000222212:D226N	D	+	1	0	CACNG7	59137207	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.212000	0.77941	2.072000	0.62099	0.491000	0.48974	GAC		0.662	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			A	54445395	G	A	54445395	3	1	71	1	0	0	0	0	1	0	0	0	2568	1058	37	1	694	1	CACNG7	19	54445395	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	2799398	54445395	4683588	112	21187										
RPL28	6158	broad.mit.edu	37	chr19	55898013	55898013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcaagactgtgggcgtggagCcggcagccgacggcaaaggt	18	10	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:55898013C>T	ENST00000344063.2	+	3	786	c.157C>T	c.(157-159)Ccg>Tcg	p.P53S	RPL28_ENST00000558815.1_Missense_Mutation_p.P53S|RPL28_ENST00000558131.1_Missense_Mutation_p.P53S|RPL28_ENST00000560055.1_Missense_Mutation_p.P53S|TMEM238_ENST00000444469.3_5'Flank|RPL28_ENST00000458349.2_Missense_Mutation_p.P53S|RPL28_ENST00000560583.1_Missense_Mutation_p.P53S|RPL28_ENST00000431533.2_Missense_Mutation_p.P53S|RPL28_ENST00000559463.1_Missense_Mutation_p.P53S|RPL28_ENST00000428193.2_Missense_Mutation_p.P53S|RPL28_ENST00000558752.1_Missense_Mutation_p.P53S			P46779	RL28_HUMAN	ribosomal protein L28	53					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.P53S(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		GGGCGTGGAGCCGGCAGCCGA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											83	92	89					19																	55898013		2203	4300	6503	60589825	SO:0001583	missense	6158			U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107		"L ribosomal proteins"	10330	protein-coding gene	gene with protein product	"60S ribosomal protein L28"	603638				7772601, 9582194	Standard	NM_001136134		Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000344063.2:c.157C>T	19.37:g.55898013C>T	ENSP00000342787:p.Pro53Ser		60589825	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	Missense_Mutation	SNP	ENST00000344063.2	37	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419367	0.62622	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000428193;ENST00000431533;ENST00000458349	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	3.54	3.54	0.40534	.	0.131871	0.51477	D	0.000082	T	0.36054	0.0953	L	0.52126	1.63	0.58432	D	0.999999	P;B;B;B;B	0.37207	0.587;0.412;0.075;0.107;0.025	B;B;B;B;B	0.35039	0.194;0.114;0.065;0.067;0.026	T	0.34527	-0.9825	10	0.42905	T	0.14	.	13.3801	0.60762	0.0:1.0:0.0:0.0	.	53;53;53;53;53	B4DEP9;E9PB24;C9JB50;G5E9L2;P46779	.;.;.;.;RL28_HUMAN	S	53	ENSP00000342787:P53S;ENSP00000391665:P53S;ENSP00000400596:P53S;ENSP00000401450:P53S	ENSP00000342787:P53S	P	+	1	0	RPL28	60589825	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.841000	0.62824	2.289000	0.77006	0.561000	0.74099	CCG		0.602	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	NM_000991		T	55898013	C	T	55898013	3	4	71	1	0	0	0	0	1	0	0	0	13614	739	26	3	163	3	RPL28	19	55898013	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1452618	55898013	3230970	113	21188										
ZNF835	90485	broad.mit.edu	37	chr19	57175194	57175194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggtgctggatcaggtaggagCggttgctgaaggccttgccg	18	8	1	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:57175194C>T	ENST00000537055.2	-	2	1604	c.1373G>A	c.(1372-1374)cGc>cAc	p.R458H		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	458					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R480H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CAGGTAGGAGCGGTTGCTGAA	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	19											74	82	80					19																	57175194		2202	4300	6502	61867006	SO:0001583	missense	90485			AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1373G>A	19.37:g.57175194C>T	ENSP00000444747:p.Arg458His		61867006	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	C	9.050	0.991927	0.18966	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.36157	1.27	2.15	1.1	0.20463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21468	0.0517	L	0.43646	1.37	0.09310	N	1	P	0.38420	0.63	B	0.28465	0.09	T	0.11397	-1.0589	9	0.30854	T	0.27	.	4.2416	0.10650	0.0:0.6499:0.0:0.3501	.	480	Q9Y2P0	ZN835_HUMAN	H	480;458	ENSP00000444747:R458H	ENSP00000341756:R480H	R	-	2	0	ZNF835	61867006	0.000000	0.05858	0.001000	0.08648	0.081000	0.17604	-2.247000	0.01190	0.453000	0.26858	0.561000	0.74099	CGC		0.667	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175194	C	T	57175194	3	4	71	1	0	0	0	0	1	0	0	0	18225	768	27	1	242	1	ZNF835	19	57175194	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	1277181	57175194	1953789	114	21189										
PEG3	5178	broad.mit.edu	37	chr19	57326370	57326370	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gatactcgctgatggaatggGtgtgaattacagaatgtgtg	14	4	0	3	rs149202084		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr19:57326370G>C	ENST00000326441.9	-	10	3803	c.3440C>G	c.(3439-3441)aCc>aGc	p.T1147S	ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.T1023S|PEG3_ENST00000593695.1_Missense_Mutation_p.T1021S|PEG3_ENST00000423103.2_Missense_Mutation_p.T1147S|ZIM2_ENST00000221722.5_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1147					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.T1147S(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GATGGAATGGGTGTGAATTAC	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	19											177	159	165					19																	57326370		2203	4300	6503	62018182	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3440C>G	19.37:g.57326370G>C	ENSP00000326581:p.Thr1147Ser		62018182	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	G	1.113	-0.657466	0.03480	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02421	4.3;4.3	4.33	-3.43	0.04810	.	0.844748	0.10178	N	0.706226	T	0.02929	0.0087	N	0.19112	0.55	.	.	.	B;D;P	0.76494	0.013;0.999;0.847	B;D;B	0.65987	0.006;0.94;0.293	T	0.26916	-1.0089	9	0.02654	T	1	-1.1575	1.5298	0.02533	0.4074:0.1292:0.319:0.1444	.	1023;1147;1082	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	S	1147	ENSP00000326581:T1147S;ENSP00000403051:T1147S	ENSP00000326581:T1147S	T	-	2	0	ZIM2	62018182	0.000000	0.05858	0.000000	0.03702	0.906000	0.53458	-0.889000	0.04144	-0.452000	0.07087	0.655000	0.94253	ACC		0.468	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			C	57326370	G	C	57326370	3	2	71	1	0	0	0	0	1	0	0	0	11751	1261	44	5	1330	5	PEG3	19	57326370	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	151176	57326370	1802613	115	21190										
CHD6	84181	broad.mit.edu	37	chr20	40112024	40112024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	agatgagtactttgtggccaCctgcaatcagcttagggagt	12	8	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr20:40112024C>T	ENST00000373233.3	-	16	2570	c.2393G>A	c.(2392-2394)gGt>gAt	p.G798D	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	798	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.G798D(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TTTGTGGCCACCTGCAATCAG	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	20											124	112	116					20																	40112024		2203	4300	6503	39545438	SO:0001583	missense	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.2393G>A	20.37:g.40112024C>T	ENSP00000362330:p.Gly798Asp		39545438	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036935	0.93630	.	.	ENSG00000124177	ENST00000373233	T	0.75154	-0.91	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000005	T	0.70325	0.3211	N	0.11284	0.12	0.80722	D	1	P	0.45768	0.866	P	0.51101	0.659	T	0.74520	-0.3638	10	0.56958	D	0.05	-17.3927	20.3242	0.98691	0.0:1.0:0.0:0.0	.	798	Q8TD26	CHD6_HUMAN	D	798	ENSP00000362330:G798D	ENSP00000362330:G798D	G	-	2	0	CHD6	39545438	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	7.750000	0.85110	2.882000	0.98803	0.655000	0.94253	GGT		0.507	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			T	40112024	C	T	40112024	3	4	71	1	0	0	0	0	1	0	0	0	3335	507	18	3	5842	3	CHD6	20	40112024	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10		40112024	22913496	116	21191										
CASS4	57091	broad.mit.edu	37	chr20	55012468	55012468	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gaagctcctgccagctcagaGgagacctatcaggtgcccac	11	14	2	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr20:55012468G>A	ENST00000360314.3	+	3	510	c.285G>A	c.(283-285)gaG>gaA	p.E95E	CASS4_ENST00000371336.3_Silent_p.E95E|CASS4_ENST00000434344.1_Silent_p.E95E	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	95					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)	p.E95E(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						CCAGCTCAGAGGAGACCTATC	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	20											34	38	36					20																	55012468		2203	4300	6503	54445875	SO:0001819	synonymous_variant	57091			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.285G>A	20.37:g.55012468G>A			54445875	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																				0.662	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		A	55012468	G	A	55012468	2	1	71	1	0	0	0	0	0	0	0	1	2689	991	35	3		3	CASS4	20	55012468	Silent	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	14900444	55012468	8013052	117	21192										
XKR3	150165	broad.mit.edu	37	chr22	17264597	17264597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	tcagctgcttatttttattcTtttcagttttctcgatgttt	5	7	4	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr22:17264597T>C	ENST00000331428.5	-	4	1394	c.1292A>G	c.(1291-1293)aAg>aGg	p.K431R		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	431						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K431R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				ATTTTTATTCTTTTCAGTTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	22											15	15	15					22																	17264597		344	1095	1439	15644597	SO:0001583	missense	150165			AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.1292A>G	22.37:g.17264597T>C	ENSP00000331704:p.Lys431Arg		15644597	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	.	.	.	.	.	.	.	.	.	.	.	5.033	0.191713	0.09547	.	.	ENSG00000172967	ENST00000331428	T	0.61510	0.1	0.762	-0.49	0.12049	.	1.462770	0.04749	U	0.424173	T	0.30696	0.0773	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.06405	0.002	T	0.10382	-1.0632	10	0.12430	T	0.62	.	2.8139	0.05450	0.0:0.3684:0.0:0.6316	.	431	Q5GH77	XKR3_HUMAN	R	431	ENSP00000331704:K431R	ENSP00000331704:K431R	K	-	2	0	XKR3	15644597	0.785000	0.28726	0.022000	0.16811	0.341000	0.28922	0.167000	0.16602	-0.170000	0.10816	0.240000	0.17902	AAG		0.363	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		C	17264597	T	C	17264597	3	2	71	1	0	0	0	0	1	0	0	0	17472	1609	56	4	91	4	XKR3	22	17264597	Missense_Mutation	SNP	T	TCGA-AG-A01W-01A-21W-A096-10		17264597	34039969	118	21193										
SLC5A4	6527	broad.mit.edu	37	chr22	32625241	32625241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gcatcttggtgtagaggtcaAtggtgaagagggtgctggcg	18	5	2	3			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr22:32625241A>G	ENST00000266086.4	-	11	1231	c.1220T>C	c.(1219-1221)aTt>aCt	p.I407T	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	407					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.I407T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GTAGAGGTCAATGGTGAAGAG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	22											156	149	151					22																	32625241		2203	4300	6503	30955241	SO:0001583	missense	6527			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1220T>C	22.37:g.32625241A>G	ENSP00000266086:p.Ile407Thr		30955241	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.056650	0.36277	.	.	ENSG00000100191	ENST00000266086	D	0.87412	-2.25	4.55	3.51	0.40186	.	0.266926	0.52532	D	0.000072	D	0.89945	0.6862	M	0.72894	2.215	0.34742	D	0.730857	B	0.22276	0.067	P	0.45794	0.493	D	0.90898	0.4766	10	0.87932	D	0	.	8.4846	0.33063	0.9053:0.0:0.0947:0.0	.	407	Q9NY91	SC5A4_HUMAN	T	407	ENSP00000266086:I407T	ENSP00000266086:I407T	I	-	2	0	SLC5A4	30955241	1.000000	0.71417	0.581000	0.28614	0.093000	0.18481	7.206000	0.77891	0.872000	0.35775	0.533000	0.62120	ATT		0.572	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		G	32625241	A	G	32625241	3	3	71	1	0	0	0	0	1	0	0	0	14704	101	4	4	779	4	SLC5A4	22	32625241	Missense_Mutation	SNP	A	TCGA-AG-A01W-01A-21W-A096-10	15360644	32625241	18679325	119	21194										
ZC3H7B	23264	broad.mit.edu	37	chr22	41745210	41745210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cttccagttcgacgtgtgccGccatgaggtgcgctacggct	13	13	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chr22:41745210G>A	ENST00000352645.4	+	16	2110	c.1853G>A	c.(1852-1854)cGc>cAc	p.R618H	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.R618H	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	634					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R618H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GACGTGTGCCGCCATGAGGTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	22											112	75	88					22																	41745210		2202	4300	6502	40075156	SO:0001583	missense	23264				CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.1853G>A	22.37:g.41745210G>A	ENSP00000345793:p.Arg618His		40075156	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	37	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	G	35	5.528100	0.96446	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.15017	2.46;2.46	5.2	5.2	0.72013	.	0.050759	0.85682	D	0.000000	T	0.43765	0.1262	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.63877	0.919	T	0.45716	-0.9242	10	0.87932	D	0	-33.623	18.7452	0.91789	0.0:0.0:1.0:0.0	.	618	Q9UGR2-2	.	H	618	ENSP00000345793:R618H;ENSP00000263243:R618H	ENSP00000263243:R618H	R	+	2	0	ZC3H7B	40075156	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.790000	0.99075	2.435000	0.82474	0.514000	0.50259	CGC		0.637	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		A	41745210	G	A	41745210	3	1	71	1	0	0	0	0	1	0	0	0	17612	1087	38	1	1911	1	ZC3H7B	22	41745210	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	9119969	41745210	9559356	120	21195										
BMX	660	broad.mit.edu	37	chrX	15527456	15527456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ttgttttttaattcagaaaaGgggcagcagaaaaggatcca	10	5	1	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:15527456G>A	ENST00000357607.2	+	3	331	c.143G>A	c.(142-144)aGg>aAg	p.R48K	BMX_ENST00000463891.1_3'UTR|BMX_ENST00000342014.6_Missense_Mutation_p.R48K|BMX_ENST00000348343.6_Missense_Mutation_p.R48K			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	48	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)	p.R48K(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					ATTCAGAAAAGGGGCAGCAGA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	X											69	63	65					X																	15527456		2203	4300	6503	15437377	SO:0001583	missense	660			AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1079	protein-coding gene	gene with protein product	"BTK-like on X chromosome"	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.143G>A	X.37:g.15527456G>A	ENSP00000350224:p.Arg48Lys		15437377	A6NIH9|O60564|Q12871	Missense_Mutation	SNP	ENST00000357607.2	37	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	g	7.484	0.649333	0.14516	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.93076	-3.16;-3.16;-3.16	5.69	3.93	0.45458	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.080840	0.53938	N	0.000057	D	0.85344	0.5675	L	0.27053	0.805	0.23991	N	0.996249	B	0.18166	0.026	B	0.18561	0.022	T	0.67753	-0.5589	10	0.10111	T	0.7	.	7.9103	0.29787	0.1925:0.0:0.8075:0.0	.	48	P51813	BMX_HUMAN	K	48	ENSP00000350224:R48K;ENSP00000308774:R48K;ENSP00000340082:R48K	ENSP00000340082:R48K	R	+	2	0	BMX	15437377	1.000000	0.71417	0.995000	0.50966	0.901000	0.52897	1.515000	0.35845	0.572000	0.29383	0.597000	0.82753	AGG		0.413	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		A	15527456	G	A	15527456	3	1	71	1	0	0	0	0	1	0	0	0	1474	1000	35	3	149	3	BMX	23	15527456	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10		15527456	139743104	121	21196										
ZNF41	7592	broad.mit.edu	37	chrX	47308278	47308278	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	cttttgtcacattcacgggaCttttctccagcatgaattct	6	11	4	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:47308278C>T	ENST00000377065.4	-	5	1530	c.891G>A	c.(889-891)aaG>aaA	p.K297K	ZNF41_ENST00000313116.7_Silent_p.K297K|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000397050.2_Silent_p.K307K	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K297K(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				ATTCACGGGACTTTTCTCCAG	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	X											102	93	96					X																	47308278		2203	4300	6503	47193222	SO:0001819	synonymous_variant	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.891G>A	X.37:g.47308278C>T			47193222	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Silent	SNP	ENST00000377065.4	37	CCDS14279.1																																																																																				0.428	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		T	47308278	C	T	47308278	2	4	71	1	0	0	0	0	0	0	0	1	17928	564	20	3		3	ZNF41	23	47308278	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	31780822	47308278	107962282	122	21197										
MAGED2	10916	broad.mit.edu	37	chrX	54841852	54841852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ccgggccctgcaactgggacGaagctgatatcggaccctgg	14	13	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:54841852G>A	ENST00000375068.1	+	12	1791	c.1558G>A	c.(1558-1560)Gaa>Aaa	p.E520K	MAGED2_ENST00000347546.4_Missense_Mutation_p.E502K|MAGED2_ENST00000218439.4_Missense_Mutation_p.E520K|MAGED2_ENST00000375058.1_Missense_Mutation_p.E520K|MAGED2_ENST00000375062.4_Missense_Mutation_p.E435K|MAGED2_ENST00000396224.1_Missense_Mutation_p.E520K|MAGED2_ENST00000375053.2_Missense_Mutation_p.E520K|MAGED2_ENST00000375060.1_Missense_Mutation_p.E435K|SNORA11_ENST00000408789.1_RNA			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	520						membrane (GO:0016020)		p.E520K(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						CAACTGGGACGAAGCTGATAT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	X											24	24	24					X																	54841852		2203	4297	6500	54858577	SO:0001583	missense	10916			AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated protein", "breast cancer associated gene 1", "melanoma-associated antigen D2", "hepatocellular carcinoma-associated protein HCA10"	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1558G>A	X.37:g.54841852G>A	ENSP00000364209:p.Glu520Lys		54858577	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977337	0.74360	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.45668	3.8;3.8;3.86;3.82;0.89;3.8;3.8;0.89;3.8	4.73	3.85	0.44370	.	0.000000	0.47093	D	0.000242	T	0.36441	0.0967	N	0.22421	0.69	0.29893	N	0.825084	D;P	0.62365	0.991;0.951	P;B	0.52758	0.708;0.269	T	0.27905	-1.0060	10	0.72032	D	0.01	.	7.2845	0.26330	0.1226:0.0:0.8774:0.0	.	435;520	Q5H907;Q9UNF1	.;MAGD2_HUMAN	K	520;520;464;502;435;520;520;435;520	ENSP00000364209:E520K;ENSP00000364193:E520K;ENSP00000336962:E464K;ENSP00000340290:E502K;ENSP00000364202:E435K;ENSP00000218439:E520K;ENSP00000364198:E520K;ENSP00000364200:E435K;ENSP00000379526:E520K	ENSP00000218439:E520K	E	+	1	0	MAGED2	54858577	0.999000	0.42202	0.959000	0.39883	0.910000	0.53928	3.071000	0.50041	2.098000	0.63641	0.513000	0.50165	GAA		0.617	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		A	54841852	G	A	54841852	3	1	71	1	0	0	0	0	1	0	0	0	9214	1059	37	1	1600	1	MAGED2	23	54841852	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	7533574	54841852	100428708	123	21198										
FAM104B	90736	broad.mit.edu	37	chrX	55187583	55187583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	aacttaccgtacagggcagcCtcccatagtcctgccctcgg	9	16	0	0			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:55187583C>T	ENST00000358460.4	-	1	160	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	FAM104B_ENST00000425133.2_Missense_Mutation_p.G3S|FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000332132.4_Missense_Mutation_p.G3S|FAM104B_ENST00000489298.1_5'Flank|FAM104B_ENST00000477847.2_5'Flank|FAM104B_ENST00000472571.2_Missense_Mutation_p.G3S			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	3								p.G3S(1)		endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						ACAGGGCAGCCTCCCATAGTC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	X											39	28	31					X																	55187583		2200	4296	6496	55204308	SO:0001583	missense	90736			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"chromosome X open reading frame 44"	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.7G>A	X.37:g.55187583C>T	ENSP00000364101:p.Gly3Ser		55204308	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Missense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	c	14.96	2.691457	0.48097	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000472571	T;T;T	0.60548	0.27;0.18;0.57	1.79	0.911	0.19343	.	0.655352	0.11179	N	0.591174	T	0.53948	0.1828	N	0.14661	0.345	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.79108	0.992;0.992;0.992	T	0.40572	-0.9556	10	0.87932	D	0	.	3.9153	0.09220	0.0:0.7648:0.0:0.2352	.	3;3;3	Q5XKR9-3;Q5XKR9;Q5XKR9-2	.;F104B_HUMAN;.	S	3	ENSP00000364101:G3S;ENSP00000333394:G3S;ENSP00000397188:G3S	ENSP00000333394:G3S	G	-	1	0	FAM104B	55204308	0.000000	0.05858	0.005000	0.12908	0.692000	0.40212	-0.150000	0.10189	0.251000	0.21505	0.292000	0.19580	GGC		0.637	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362		T	55187583	C	T	55187583	3	4	71	1	0	0	0	0	1	0	0	0	5402	681	24	3	496	3	FAM104B	23	55187583	Missense_Mutation	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	345731	55187583	100082977	124	21199										
UTP14A	10813	broad.mit.edu	37	chrX	129060041	129060041	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ctgacactacctggctggggCgagtggggtggtgtgggcct	19	9	0	1			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:129060041C>T	ENST00000394422.3	+	13	1924	c.1896C>T	c.(1894-1896)ggC>ggT	p.G632G	UTP14A_ENST00000425117.2_Silent_p.G580G|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000371042.3_Silent_p.G464G|UTP14A_ENST00000371051.5_Silent_p.G578G	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	632					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.G632G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						CTGGCTGGGGCGAGTGGGGTG	0.562											OREG0019920	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	X											39	42	41					X																	129060041		2202	4298	6500	128887722	SO:0001819	synonymous_variant	10813			AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"serologically defined colon cancer antigen 16"	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.1896C>T	X.37:g.129060041C>T		1569	128887722	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Silent	SNP	ENST00000394422.3	37	CCDS14615.1																																																																																				0.562	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		T	129060041	C	T	129060041	2	4	71	1	0	0	0	0	0	0	0	1	17135	755	27	1		1	UTP14A	23	129060041	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	73872458	129060041	26210519	125	21200										
HMGB3	3149	broad.mit.edu	37	chrX	150155626	150155626	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	gattcttcctgttctgttcaGaattccgccccaagatcaaa	6	12	4	2			TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:150155626G>A	ENST00000325307.7	+	4	412	c.316G>A	c.(316-318)Gaa>Aaa	p.E106K	HMGB3_ENST00000448905.2_Missense_Mutation_p.E106K	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	106					DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.E106K(1)		endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					GTTCTGTTCAGAATTCCGCCC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	65	66					X																	150155626		2203	4300	6503	149906284	SO:0001583	missense	3149			AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"High-mobility group / Canonical"	5004	protein-coding gene	gene with protein product	"non-histone chromosomal protein"	300193	"high-mobility group (nonhistone chromosomal) protein 4", "high-mobility group box 3"	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.316G>A	X.37:g.150155626G>A	ENSP00000359393:p.Glu106Lys		149906284	O95556|Q6NS40	Missense_Mutation	SNP	ENST00000325307.7	37	CCDS35428.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.975789	0.74360	.	.	ENSG00000029993	ENST00000419110;ENST00000325307;ENST00000455596;ENST00000448905;ENST00000430118	D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91	4.95	4.95	0.65309	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.98175	0.9397	M	0.88842	2.985	0.58432	D	0.999996	B	0.31459	0.324	B	0.37198	0.243	D	0.99774	1.1025	10	0.66056	D	0.02	.	16.2551	0.82510	0.0:0.0:1.0:0.0	.	106	O15347	HMGB3_HUMAN	K	106	ENSP00000410354:E106K;ENSP00000359393:E106K;ENSP00000405601:E106K;ENSP00000442758:E106K;ENSP00000417027:E106K	ENSP00000359393:E106K	E	+	1	0	HMGB3	149906284	1.000000	0.71417	0.903000	0.35520	0.948000	0.59901	9.660000	0.98599	2.033000	0.60031	0.529000	0.55759	GAA		0.393	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		A	150155626	G	A	150155626	3	1	71	1	0	0	0	0	1	0	0	0	7248	943	33	3	326	3	HMGB3	23	150155626	Missense_Mutation	SNP	G	TCGA-AG-A01W-01A-21W-A096-10	21095585	150155626	5114934	126	21201										
MAGEA4	4103	broad.mit.edu	37	chrX	151092778	151092778	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062992125984252	8	1	0.792156862745098	1.93088235294118	0.662016806722689	0.153434800493624	0.584970176881942	0	ggcacaattgcaatggagggCgacagcgcctctgaggagga	16	9	1	1	rs376198310		TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01W-01A-21W-A096-10	TCGA-AG-A01W-11A-11W-A096-10	g.chrX:151092778C>T	ENST00000360243.2	+	3	909	c.642C>T	c.(640-642)ggC>ggT	p.G214G	MAGEA4_ENST00000370337.4_Silent_p.G214G|MAGEA4_ENST00000370335.1_Silent_p.G214G|MAGEA4_ENST00000276344.2_Silent_p.G214G|MAGEA4_ENST00000370340.3_Silent_p.G214G|MAGEA4_ENST00000393921.1_Silent_p.G214G|MAGEA4_ENST00000393920.1_Silent_p.G214G	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	214	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.G214G(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					CAATGGAGGGCGACAGCGCCT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	X						C	,,,	0,3835		0,0,0,1632,571	101	104	103		642,642,642,642	-3.2	0	X		103	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAGEA4	NM_001011548.1,NM_001011549.1,NM_001011550.1,NM_002362.4	,,,	0,0,1,4060,2442	TT,TC,T,CC,C		0.0149,0.0,0.0095	,,,	214/318,214/318,214/318,214/318	151092778	1,10562	2203	4300	6503	150843434	SO:0001819	synonymous_variant	4103				CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"melanoma-associated antigen 4", "cancer/testis antigen family 1, member 4"	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.642C>T	X.37:g.151092778C>T			150843434	Q14798	Silent	SNP	ENST00000360243.2	37	CCDS14702.1																																																																																				0.557	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		T	151092778	C	T	151092778	2	4	71	1	0	0	0	0	0	0	0	1	9198	755	27	1		1	MAGEA4	23	151092778	Silent	SNP	C	TCGA-AG-A01W-01A-21W-A096-10	937152	151092778	4177782	127	21202										
UBR4	23352	broad.mit.edu	37	chr1	19513100	19513100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agtattggagtcggtggaggCgctggcatcgctgctcatgg	17	8	1	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:19513100C>T	ENST00000375254.3	-	14	1711	c.1684G>A	c.(1684-1686)Gcc>Acc	p.A562T	UBR4_ENST00000375217.2_Missense_Mutation_p.A562T|UBR4_ENST00000375226.2_Missense_Mutation_p.A562T|UBR4_ENST00000375267.2_Missense_Mutation_p.A562T	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	562					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A562T(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TCGGTGGAGGCGCTGGCATCG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	58	59					1																	19513100		2203	4300	6503	19385687	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.1684G>A	1.37:g.19513100C>T	ENSP00000364403:p.Ala562Thr		19385687	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652147	0.88056	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	N	0.22421	0.69	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.24404	-1.0161	10	0.62326	D	0.03	.	17.7534	0.88441	0.0:1.0:0.0:0.0	.	562	Q5T4S7	UBR4_HUMAN	T	562	ENSP00000364403:A562T;ENSP00000364416:A562T;ENSP00000364365:A562T;ENSP00000364374:A562T	ENSP00000364365:A562T	A	-	1	0	UBR4	19385687	1.000000	0.71417	0.990000	0.47175	0.941000	0.58515	7.250000	0.78287	2.519000	0.84933	0.655000	0.94253	GCC		0.517	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19513100	C	T	19513100	3	4	72	1	0	0	0	0	1	0	0	0	16944	768	27	1	14239	1	UBR4	1	19513100	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		19513100	229737521	1	21203										
NCDN	23154	broad.mit.edu	37	chr1	36028080	36028080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ccgaggagacctcatccttgCgtaaggaggtgtgccagctg	14	11	1	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:36028080C>T	ENST00000373243.2	+	4	1614	c.1231C>T	c.(1231-1233)Cgt>Tgt	p.R411C	NCDN_ENST00000356090.4_Missense_Mutation_p.R411C|NCDN_ENST00000373253.3_Missense_Mutation_p.R394C	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	411					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.R394C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTCATCCTTGCGTAAGGAGGT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	1											149	126	134					1																	36028080		2203	4300	6503	35800667	SO:0001583	missense	23154			AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.1231C>T	1.37:g.36028080C>T	ENSP00000362340:p.Arg411Cys		35800667	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	37	CCDS392.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325098	0.81580	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243	T;T;T	0.73789	-0.78;-0.78;-0.78	4.8	4.8	0.61643	.	0.206493	0.40064	N	0.001197	T	0.74129	0.3676	L	0.29908	0.895	0.54753	D	0.99998	D	0.76494	0.999	P	0.58928	0.848	T	0.76493	-0.2939	10	0.87932	D	0	.	10.5618	0.45150	0.2069:0.7931:0.0:0.0	.	411	Q9UBB6	NCDN_HUMAN	C	394;411;411	ENSP00000362350:R394C;ENSP00000348394:R411C;ENSP00000362340:R411C	ENSP00000348394:R411C	R	+	1	0	NCDN	35800667	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.545000	0.67237	2.503000	0.84419	0.561000	0.74099	CGT		0.622	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		T	36028080	C	T	36028080	3	4	72	1	0	0	0	0	1	0	0	0	10245	768	27	1	1245	1	NCDN	1	36028080	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	16514980	36028080	213222541	2	21204										
COL24A1	255631	broad.mit.edu	37	chr1	86426943	86426943	+	Frame_Shift_Del	DEL	T	T	-													0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	taagcttactgtttcaccaaTttttccaatatttccttgat							TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:86426943delT	ENST00000370571.2	-	24	2917	c.2551delA	c.(2551-2553)attfs	p.I851fs	COL24A1_ENST00000436319.1_Frame_Shift_Del_p.I851fs	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	851	Collagen-like 5.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.I851fs*15(1)		NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		GTTTCACCAATTTTTCCAATA	0.294																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											99	97	97					1																	86426943		1801	4057	5858	86199531	SO:0001589	frameshift_variant	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.2551delA	1.37:g.86426943delT	ENSP00000359603:p.Ile851fs		86199531	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Frame_Shift_Del	DEL	ENST00000370571.2	37	CCDS41353.1																																																																																				0.294	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		-	86426943	T	-	86426943	7	5	72	1	0	1	0	1	0	0	0	0	3689	1493	52	0	2741	0	COL24A1	1	86426943	Frame_Shift_Del	DEL	T	TCGA-AG-A01Y-01A-41W-A096-10	50398863	86426943	162823678	3	21205										
VAV3	10451	broad.mit.edu	37	chr1	108293775	108293775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gcttgtctagagtggttattCgaatttcaccatctccctga	8	10	3	2	rs377138310		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:108293775C>T	ENST00000370056.4	-	13	1497	c.1223G>A	c.(1222-1224)cGa>cAa	p.R408Q	VAV3_ENST00000527011.1_Missense_Mutation_p.R408Q|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Missense_Mutation_p.R343Q	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	408	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.R408Q(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		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)		AGTGGTTATTCGAATTTCACC	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	0,4406		0,0,2203	119	114	116		1223	5.5	1	1		116	2,8598	2.2+/-6.3	0,2,4298	no	missense	VAV3	NM_006113.4	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	408/848	108293775	2,13004	2203	4300	6503	108095298	SO:0001583	missense	10451			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1223G>A	1.37:g.108293775C>T	ENSP00000359073:p.Arg408Gln		108095298	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.098467|5.098467	0.94197|0.94197	0.0|0.0	2.33E-4|2.33E-4	ENSG00000134215|ENSG00000134215	ENST00000490388|ENST00000370056;ENST00000527011;ENST00000371846	.|D;D;D	.|0.87571	.|-2.27;-2.27;-2.27	5.5|5.5	5.5|5.5	0.81552|0.81552	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.90099|0.90099	0.6907|0.6907	L|L	0.59436|0.59436	1.845|1.845	0.48087|0.48087	D|D	0.999586|0.999586	.|P;D;D;D	.|0.89917	.|0.901;1.0;0.957;0.957	.|P;D;P;P	.|0.91635	.|0.455;0.999;0.838;0.838	D|D	0.90942|0.90942	0.4798|0.4798	5|10	.|0.72032	.|D	.|0.01	.|.	12.6979|12.6979	0.57014|0.57014	0.0:0.9248:0.0:0.0752|0.0:0.9248:0.0:0.0752	.|.	.|408;408;343;408	.|B7ZLR1;E9PQ97;B4DHL6;Q9UKW4	.|.;.;.;VAV3_HUMAN	K|Q	403|408;408;343	.|ENSP00000359073:R408Q;ENSP00000432540:R408Q;ENSP00000360912:R343Q	.|ENSP00000359073:R408Q	E|R	-|-	1|2	0|0	VAV3|VAV3	108095298|108095298	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.696000|3.696000	0.54757|0.54757	2.591000|2.591000	0.87537|0.87537	0.563000|0.563000	0.77884|0.77884	GAA|CGA		0.318	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108293775	C	T	108293775	3	4	72	1	0	0	0	0	1	0	0	0	17173	884	31	1	1405	1	VAV3	1	108293775	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	21866832	108293775	140956846	4	21206										
CELSR2	1952	broad.mit.edu	37	chr1	109816155	109816155	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gggtcttcccggggctcctcCgctagtgagggcagccgggg	18	13	1	1	rs552633270		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:109816155C>T	ENST00000271332.3	+	33	8668	c.8607C>T	c.(8605-8607)tcC>tcT	p.S2869S	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2869					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.S2869S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GGGGCTCCTCCGCTAGTGAGG	0.672																																					NSCLC(158;1285 2011 34800 34852 42084)											1	Substitution - coding silent(1)	large_intestine(1)	1											11	15	13					1																	109816155		2110	4240	6350	109617678	SO:0001819	synonymous_variant	1952			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.8607C>T	1.37:g.109816155C>T			109617678	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																				0.672	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109816155	C	T	109816155	2	4	72	1	0	0	0	0	0	0	0	1	3228	639	23	1		1	CELSR2	1	109816155	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	1522380	109816155	139434466	5	21207										
KCNA2	3737	broad.mit.edu	37	chr1	111146917	111146917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cagacacaatagctataatcCtggcaggccctgagctctct	8	13	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:111146917C>T	ENST00000485317.1	-	3	1161	c.488G>A	c.(487-489)aGg>aAg	p.R163K	KCNA2_ENST00000440270.1_Missense_Mutation_p.R163K|KCNA2_ENST00000369770.3_Missense_Mutation_p.R163K|KCNA2_ENST00000316361.4_Missense_Mutation_p.R163K|KCNA2_ENST00000525120.1_Intron			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	163					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R163K(1)		endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	AGCTATAATCCTGGCAGGCCC	0.468																																					Pancreas(18;568 735 10587 23710 36357)											1	Substitution - Missense(1)	large_intestine(1)	1											76	79	78					1																	111146917		2203	4300	6503	110948440	SO:0001583	missense	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.488G>A	1.37:g.111146917C>T	ENSP00000433109:p.Arg163Lys		110948440	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974093	0.74246	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.74981	0.3788	L	0.53561	1.675	0.80722	D	1	P;D	0.58970	0.816;0.984	P;D	0.70716	0.66;0.97	T	0.70773	-0.4781	10	0.38643	T	0.18	.	20.0697	0.97716	0.0:1.0:0.0:0.0	.	163;163	Q86XG6;P16389	.;KCNA2_HUMAN	K	163	ENSP00000358785:R163K;ENSP00000433109:R163K;ENSP00000415257:R163K;ENSP00000314520:R163K	ENSP00000314520:R163K	R	-	2	0	KCNA2	110948440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.757000	0.85209	2.751000	0.94390	0.609000	0.83330	AGG		0.468	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		T	111146917	C	T	111146917	3	4	72	1	0	0	0	0	1	0	0	0	8024	681	24	3	1015	3	KCNA2	1	111146917	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	1330762	111146917	138103704	6	21208										
KCNA3	3738	broad.mit.edu	37	chr1	111216790	111216790	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cacacctggcgctggaagtcGcggcggggcaagggccgctc	17	14	0	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:111216790G>A	ENST00000369769.2	-	1	865	c.642C>T	c.(640-642)cgC>cgT	p.R214R		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	214					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)	p.R214R(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	GCTGGAAGTCGCGGCGGGGCA	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	1											36	44	41					1																	111216790		2200	4285	6485	111018313	SO:0001819	synonymous_variant	3738			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.642C>T	1.37:g.111216790G>A			111018313	Q5VWN2	Silent	SNP	ENST00000369769.2	37	CCDS828.2																																																																																				0.687	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		A	111216790	G	A	111216790	2	1	72	1	0	0	0	0	0	0	0	1	8025	1074	38	1		1	KCNA3	1	111216790	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	69873	111216790	138033831	7	21209										
HSD3B1	3283	broad.mit.edu	37	chr1	120054198	120054198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gccattcctgaagagagcctGccaggacgtctcggtcatca	11	13	3	2	rs541042731		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:120054198G>T	ENST00000369413.3	+	3	363	c.218G>T	c.(217-219)tGc>tTc	p.C73F	HSD3B1_ENST00000235547.6_Missense_Mutation_p.C75F|HSD3B1_ENST00000528909.1_Missense_Mutation_p.C73F			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	73					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.C73F(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	AAGAGAGCCTGCCAGGACGTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											104	97	99					1																	120054198		2203	4300	6503	119855721	SO:0001583	missense	3283			S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5217	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 1"	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.218G>T	1.37:g.120054198G>T	ENSP00000358421:p.Cys73Phe		119855721	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	37	CCDS903.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932653	0.34096	.	.	ENSG00000203857	ENST00000531340;ENST00000369413;ENST00000235547;ENST00000528909	D;D;D;D	0.86366	-1.87;-2.11;-2.11;-2.11	3.27	2.31	0.28768	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.82167	0.4978	L	0.42008	1.315	0.54753	D	0.999989	P;P	0.50066	0.931;0.524	P;P	0.56434	0.798;0.452	T	0.79790	-0.1655	10	0.37606	T	0.19	-5.4127	9.7699	0.40582	0.0:0.2135:0.7865:0.0	.	75;73	Q5TDG2;P14060	.;3BHS1_HUMAN	F	73;73;75;73	ENSP00000435999:C73F;ENSP00000358421:C73F;ENSP00000235547:C75F;ENSP00000432268:C73F	ENSP00000235547:C75F	C	+	2	0	HSD3B1	119855721	1.000000	0.71417	0.974000	0.42286	0.084000	0.17831	4.187000	0.58344	0.527000	0.28560	0.491000	0.48974	TGC		0.488	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		T	120054198	G	T	120054198	3	4	72	1	0	0	0	0	1	0	0	0	7411	1319	46	2	224	2	HSD3B1	1	120054198	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	8837408	120054198	129196423	8	21210										
SELENBP1	8991	broad.mit.edu	37	chr1	151337106	151337106	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aggggctccttcccgaagtcCaccaggaagttggggttcaa	13	11	1	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:151337106C>T	ENST00000368868.5	-	12	1423	c.1332G>A	c.(1330-1332)gtG>gtA	p.V444V	SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000435071.1_Silent_p.V380V|SELENBP1_ENST00000426705.2_Silent_p.V486V|SELENBP1_ENST00000447402.3_Silent_p.V382V	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	444					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)	p.V444V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCCCGAAGTCCACCAGGAAGT	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	1											128	131	130					1																	151337106		2203	4300	6503	149603730	SO:0001819	synonymous_variant	8991			U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.1332G>A	1.37:g.151337106C>T			149603730	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Silent	SNP	ENST00000368868.5	37	CCDS995.1																																																																																				0.557	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4			T	151337106	C	T	151337106	2	4	72	1	0	0	0	0	0	0	0	1	14051	581	21	3		3	SELENBP1	1	151337106	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	31282908	151337106	97913515	9	21211										
HRNR	388697	broad.mit.edu	37	chr1	152193163	152193163	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctggaggagtgccccgaaccGgacccatgtcggacgtggct	15	13	0	0	rs566382287	byFrequency	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:152193163G>A	ENST00000368801.2	-	3	1017	c.942C>T	c.(940-942)tcC>tcT	p.S314S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	314					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S314S(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCCCGAACCGGACCCATGTC	0.612													G|||	2	0.000399361	0	0	5008	,	,		19938	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	1											88	97	94					1																	152193163		2203	4300	6503	150459787	SO:0001819	synonymous_variant	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.942C>T	1.37:g.152193163G>A			150459787	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																				0.612	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152193163	G	A	152193163	2	1	72	1	0	0	0	0	0	0	0	1	7380	1103	39	1		1	HRNR	1	152193163	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	856057	152193163	97057458	10	21212										
CFHR5	81494	broad.mit.edu	37	chr1	196952176	196952176	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggactcgcataacatgcacaGaagaaggatggtcaccaaca	10	10	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:196952176G>A	ENST00000256785.4	+	2	329	c.220G>A	c.(220-222)Gaa>Aaa	p.E74K	CFHR5_ENST00000367414.5_Missense_Mutation_p.E98K			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	74	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)		p.E74K(1)		NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						AACATGCACAGAAGAAGGATG	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	106	111					1																	196952176		2203	4300	6503	195218799	SO:0001583	missense	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.220G>A	1.37:g.196952176G>A	ENSP00000256785:p.Glu74Lys		195218799	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	.	14.83	2.652513	0.47362	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.64803	-0.12;-0.12	2.45	2.45	0.29901	Complement control module (2);Sushi/SCR/CCP (2);	.	.	.	.	T	0.53190	0.1781	M	0.66297	2.02	0.09310	N	1	B	0.32968	0.392	B	0.33960	0.173	T	0.45877	-0.9231	9	0.06625	T	0.88	.	8.4585	0.32915	0.0:0.0:1.0:0.0	.	74	Q9BXR6	FHR5_HUMAN	K	98;74	ENSP00000356384:E98K;ENSP00000256785:E74K	ENSP00000256785:E74K	E	+	1	0	CFHR5	195218799	0.004000	0.15560	0.064000	0.19789	0.499000	0.33736	0.530000	0.23036	1.679000	0.50963	0.305000	0.20034	GAA		0.418	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		A	196952176	G	A	196952176	3	1	72	1	0	0	0	0	1	0	0	0	3294	943	33	3	226	3	CFHR5	1	196952176	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	44759013	196952176	52298445	11	21213										
ETNK2	55224	broad.mit.edu	37	chr1	204115853	204115853	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttgggcaggctgccgttggcGtggatagtatgaatctttgc	15	7	1	1	rs139650333		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:204115853G>A	ENST00000367202.4	-	3	708	c.558C>T	c.(556-558)caC>caT	p.H186H	ETNK2_ENST00000367201.3_Silent_p.H186H|ETNK2_ENST00000367199.2_Intron|ETNK2_ENST00000367198.2_Silent_p.H8H	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	186					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)	p.H186H(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TGCCGTTGGCGTGGATAGTAT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	151	129	136		558	-4.5	0.9	1	dbSNP_134	136	0,8600		0,0,4300	no	coding-synonymous	ETNK2	NM_018208.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		186/387	204115853	1,13005	2203	4300	6503	202382476	SO:0001819	synonymous_variant	55224			AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.558C>T	1.37:g.204115853G>A			202382476	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Silent	SNP	ENST00000367202.4	37	CCDS1442.2																																																																																				0.498	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		A	204115853	G	A	204115853	2	1	72	1	0	0	0	0	0	0	0	1	5287	1136	40	1		1	ETNK2	1	204115853	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	7163677	204115853	45134768	12	21214										
C4BPA	722	broad.mit.edu	37	chr1	207317197	207317197	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ccagaattagtgaatggaagGttgtctgtggataaggatca	13	4	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:207317197G>T	ENST00000367070.3	+	11	1673	c.1479G>T	c.(1477-1479)agG>agT	p.R493S		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	493	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.R493S(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TGAATGGAAGGTTGTCTGTGG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											228	201	210					1																	207317197		2203	4300	6503	205383820	SO:0001583	missense	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1479G>T	1.37:g.207317197G>T	ENSP00000356037:p.Arg493Ser		205383820	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899890	0.33535	.	.	ENSG00000123838	ENST00000367070	T	0.62941	-0.01	5.29	-1.65	0.08291	Complement control module (2);Sushi/SCR/CCP (3);	2.382820	0.01442	N	0.015128	T	0.50735	0.1633	L	0.33710	1.025	0.09310	N	1	B	0.30973	0.302	B	0.36608	0.229	T	0.22836	-1.0205	10	0.21540	T	0.41	.	4.2713	0.10787	0.2327:0.0:0.3896:0.3777	.	493	P04003	C4BPA_HUMAN	S	493	ENSP00000356037:R493S	ENSP00000356037:R493S	R	+	3	2	C4BPA	205383820	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.153000	0.10144	-0.218000	0.10018	-0.143000	0.13931	AGG		0.408	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207317197	G	T	207317197	3	4	72	1	0	0	0	0	1	0	0	0	2255	1252	44	2	1517	2	C4BPA	1	207317197	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	3201344	207317197	41933424	13	21215										
AIDA	64853	broad.mit.edu	37	chr1	222846664	222846664	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggattacaaacctttggttaAtttttcaacatgcttctgga	7	7	2	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:222846664A>G	ENST00000340020.6	-	8	903	c.697T>C	c.(697-699)Tta>Cta	p.L233L	AIDA_ENST00000355727.2_Intron|AIDA_ENST00000541237.1_Silent_p.L209L|AIDA_ENST00000474863.1_5'UTR	NM_022831.2	NP_073742.2	Q96BJ3	AIDA_HUMAN	axin interactor, dorsalization associated	233					dorsal/ventral pattern formation (GO:0009953)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|regulation of protein homodimerization activity (GO:0043496)	cytoplasm (GO:0005737)		p.L233L(1)		kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10						CCTTTGGTTAATTTTTCAACA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	1											66	64	65					1																	222846664		2203	4299	6502	220913287	SO:0001819	synonymous_variant	64853			BC043142	CCDS1533.1	1q41	2008-05-22	2008-05-22	2008-05-22	ENSG00000186063	ENSG00000186063			25761	protein-coding gene	gene with protein product	"axin interaction partner and dorsalization antagonist"	612375	"chromosome 1 open reading frame 80"	C1orf80		8619474, 9110174, 17681137	Standard	NM_022831		Approved	FLJ12806	uc001hnn.3	Q96BJ3	OTTHUMG00000037653	ENST00000340020.6:c.697T>C	1.37:g.222846664A>G			220913287	A8K1F0|Q49A81|Q5JRA4|Q658P1|Q9H9E8	Silent	SNP	ENST00000340020.6	37	CCDS1533.1																																																																																				0.348	AIDA-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091818.1	NM_022831		G	222846664	A	G	222846664	2	3	72	1	0	0	0	0	0	0	0	1	423	98	4	4		4	AIDA	1	222846664	Silent	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	15529467	222846664	26403957	14	21216										
AGT	183	broad.mit.edu	37	chr1	230841702	230841702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggagatagtttcttcatccaGttgagggagttttgctggaa	13	5	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:230841702G>A	ENST00000366667.4	-	3	1315	c.1101C>T	c.(1099-1101)aaC>aaT	p.N367N		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	367					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)	p.N367N(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TCTTCATCCAGTTGAGGGAGT	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											106	113	110					1																	230841702		2203	4300	6503	228908325	SO:0001819	synonymous_variant	183			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.1101C>T	1.37:g.230841702G>A			228908325	Q16358|Q16359|Q96F91	Silent	SNP	ENST00000366667.4	37	CCDS1585.1																																																																																				0.607	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		A	230841702	G	A	230841702	2	1	72	1	0	0	0	0	0	0	0	1	399	1020	36	3		3	AGT	1	230841702	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	7995038	230841702	18408919	15	21217										
MTR	4548	broad.mit.edu	37	chr1	237048499	237048499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aatatgaagatattagacagGaccattatgagtctctcaag	8	6	2	4			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr1:237048499G>A	ENST00000366577.5	+	26	3149	c.2755G>A	c.(2755-2757)Gac>Aac	p.D919N	MTR_ENST00000535889.1_Missense_Mutation_p.D868N	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	919			D -> G (may be associated with susceptibility to FS-NTD; dbSNP:rs1805087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9013615}.		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.D919N(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TATTAGACAGGACCATTATGA	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											93	97	95					1																	237048499		2203	4300	6503	235115122	SO:0001583	missense	4548			U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2755G>A	1.37:g.237048499G>A	ENSP00000355536:p.Asp919Asn		235115122	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	37	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.070688	0.55539	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.70986	-0.53;-0.53;-0.53	5.99	5.99	0.97316	Cobalamin (vitamin B12)-binding (2);	0.149441	0.64402	D	0.000017	T	0.66257	0.2771	L	0.28694	0.88	0.51233	D	0.999917	B;P;B	0.37176	0.159;0.586;0.159	B;B;B	0.39617	0.161;0.305;0.161	T	0.66464	-0.5917	10	0.52906	T	0.07	-19.2895	20.4777	0.99188	0.0:0.0:1.0:0.0	.	919;868;919	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	N	773;919;868;473	ENSP00000355536:D919N;ENSP00000441845:D868N;ENSP00000355535:D473N	ENSP00000355535:D473N	D	+	1	0	MTR	235115122	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.034000	0.93747	2.840000	0.97914	0.655000	0.94253	GAC		0.318	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		A	237048499	G	A	237048499	3	1	72	1	0	0	0	0	1	0	0	0	9988	1174	41	3	2857	3	MTR	1	237048499	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	6206797	237048499	12202122	16	21218										
HADHB	3032	broad.mit.edu	37	chr2	26502924	26502924	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cactggagcagatggccaaaCtaaaacctgcattcatcaag	8	11	2	1	rs534014691		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:26502924C>G	ENST00000317799.5	+	10	978	c.874C>G	c.(874-876)Cta>Gta	p.L292V	HADHB_ENST00000405867.3_Missense_Mutation_p.L169V|HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000545822.1_Missense_Mutation_p.L270V|HADHB_ENST00000537713.1_Missense_Mutation_p.L277V	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	292					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)	p.L292V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGGCCAAACTAAAACCTGC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											145	127	133					2																	26502924		2203	4300	6503	26356428	SO:0001583	missense	3032				CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.874C>G	2.37:g.26502924C>G	ENSP00000325136:p.Leu292Val		26356428	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	37	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.157725	0.57368	.	.	ENSG00000138029	ENST00000317799;ENST00000405867;ENST00000537713;ENST00000545822	D;D;D;D	0.96011	-3.28;-3.88;-3.28;-3.28	5.43	4.56	0.56223	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.98270	0.9427	H	0.95151	3.63	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.973;0.973;0.994;0.984	D	0.99107	1.0845	10	0.87932	D	0	-5.8155	13.2781	0.60198	0.0:0.9225:0.0:0.0775	.	277;270;169;292	F5GZQ3;B4E2W0;B5MD38;P55084	.;.;.;ECHB_HUMAN	V	292;169;277;270	ENSP00000325136:L292V;ENSP00000385411:L169V;ENSP00000444295:L277V;ENSP00000442665:L270V	ENSP00000325136:L292V	L	+	1	2	HADHB	26356428	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	3.804000	0.55568	1.424000	0.47217	-0.145000	0.13849	CTA		0.368	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		G	26502924	C	G	26502924	3	3	72	1	0	0	0	0	1	0	0	0	6965	564	20	5	908	5	HADHB	2	26502924	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		26502924	216696449	17	21219										
POTEF	728378	broad.mit.edu	37	chr2	130865631	130865631	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agcatctgtttttctttgtaGtcagaaagtaactggcaaat	8	6	3	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:130865631G>T	ENST00000409914.2	-	8	1476	c.1077C>A	c.(1075-1077)gaC>gaA	p.D359E	POTEF_ENST00000361163.4_Missense_Mutation_p.D369E|AC018804.3_ENST00000433507.1_RNA|POTEF_ENST00000357462.5_Missense_Mutation_p.D359E|POTEF_ENST00000360967.5_Missense_Mutation_p.D359E|RNU6-1049P_ENST00000516414.1_RNA	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	359					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.D359E(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TTTCTTTGTAGTCAGAAAGTA	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	2											2	2	2					2																	130865631		797	1803	2600	130582101	SO:0001583	missense	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.1077C>A	2.37:g.130865631G>T	ENSP00000386786:p.Asp359Glu		130582101	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	2.898	-0.228088	0.06022	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.61392	0.11;0.11;0.11;0.7	1.16	-2.32	0.06745	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.22820	0.0551	N	0.01289	-0.905	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.14448	-1.0472	9	0.87932	D	0	.	2.3024	0.04165	0.0:0.2419:0.3234:0.4348	.	359	A5A3E0	POTEF_HUMAN	E	359;359;359;369	ENSP00000350052:D359E;ENSP00000386786:D359E;ENSP00000354232:D359E;ENSP00000355012:D369E	ENSP00000350052:D359E	D	-	3	2	POTEF	130582101	0.010000	0.17322	0.005000	0.12908	0.123000	0.20343	-0.140000	0.10342	-0.610000	0.05716	0.175000	0.17021	GAC		0.279	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		T	130865631	G	T	130865631	3	4	72	1	0	0	0	0	1	0	0	0	12296	1020	36	2	2190	2	POTEF	2	130865631	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	104362707	130865631	112333742	18	21220										
FAM123C	205147	broad.mit.edu	37	chr2	131521631	131521631	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggcccctggaggccaggtcaCggaggtgacactctggatgc	16	12	2	1	rs142277390	byFrequency	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:131521631C>T	ENST00000423981.1	+	2	2096	c.1986C>T	c.(1984-1986)caC>caT	p.H662H	AMER3_ENST00000321420.4_Silent_p.H662H	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	662					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.H662H(1)									GGCCAGGTCACGGAGGTGACA	0.647													C|||	10	0.00199681	0	0	5008	,	,		17068	0		0	False		,,,				2504	0.0102															1	Substitution - coding silent(1)	large_intestine(1)	2						C	,,,	0,4402		0,0,2201	22	25	24		1986,1986,1986,1986	-4.9	0	2	dbSNP_134	24	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	,,,	0,7,6494	TT,TC,CC		0.0814,0.0,0.0538	,,,	662/862,662/862,662/862,662/862	131521631	7,12995	2201	4300	6501	131238101	SO:0001819	synonymous_variant	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1986C>T	2.37:g.131521631C>T			131238101	B7ZLH6	Silent	SNP	ENST00000423981.1	37	CCDS2164.1																																																																																				0.647	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		T	131521631	C	T	131521631	2	4	72	1	0	0	0	0	0	0	0	1	5440	535	19	1		1	FAM123C	2	131521631	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	656000	131521631	111677742	19	21221										
TTN	7273	broad.mit.edu	37	chr2	179582330	179582330	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tatactgccctatgtggctcTggtcagtttgtaaaatctga	9	8	3	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:179582330T>C	ENST00000591111.1	-	85	24544	c.24320A>G	c.(24319-24321)cAg>cGg	p.Q8107R	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.Q7180R|TTN_ENST00000589042.1_Missense_Mutation_p.Q8424R|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12298	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Q7180R(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATGTGGCTCTGGTCAGTTTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											75	77	76					2																	179582330		1881	4118	5999	179290575	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24320A>G	2.37:g.179582330T>C	ENSP00000465570:p.Gln8107Arg		179290575	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	7.923	0.739036	0.15642	.	.	ENSG00000155657	ENST00000342992	T	0.27557	1.66	5.51	4.34	0.51931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14313	0.0346	N	0.04043	-0.29	0.80722	D	1	B	0.16166	0.016	B	0.17722	0.019	T	0.05321	-1.0892	9	0.87932	D	0	.	6.3592	0.21419	0.2642:0.0:0.1197:0.6161	.	8107	Q8WZ42	TITIN_HUMAN	R	7180	ENSP00000343764:Q7180R	ENSP00000343764:Q7180R	Q	-	2	0	TTN	179290575	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.559000	0.45888	0.999000	0.39023	-0.316000	0.08728	CAG		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179582330	T	C	179582330	3	2	72	1	0	0	0	0	1	0	0	0	16775	1580	55	4	79362	4	TTN	2	179582330	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	48060699	179582330	63617043	20	21222										
ZNF385B	151126	broad.mit.edu	37	chr2	180348097	180348097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ccattttgggtttatttttcGttgcgtctagtgctttgacc	9	8	1	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:180348097G>A	ENST00000410066.1	-	6	1175	c.572C>T	c.(571-573)aCg>aTg	p.T191M	ZNF385B_ENST00000336917.5_Missense_Mutation_p.T89M|ZNF385B_ENST00000409343.1_Missense_Mutation_p.T115M|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409692.1_Missense_Mutation_p.T89M	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	191	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)	p.T191M(1)		breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TTTATTTTTCGTTGCGTCTAG	0.463																																					Colon(155;204 2491 32774 51842)											1	Substitution - Missense(1)	large_intestine(1)	2											364	304	324					2																	180348097		2203	4300	6503	180056342	SO:0001583	missense	151126			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.572C>T	2.37:g.180348097G>A	ENSP00000386845:p.Thr191Met		180056342	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.704858	0.48412	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692;ENST00000457304;ENST00000439340	T;T;T;T;T;T	0.45276	1.52;1.52;1.52;1.52;1.53;0.9	5.93	5.05	0.67936	.	0.259394	0.44688	N	0.000430	T	0.39517	0.1081	L	0.44542	1.39	0.45161	D	0.998174	P;P	0.52577	0.824;0.954	B;P	0.44597	0.197;0.454	T	0.14227	-1.0480	10	0.27785	T	0.31	-1.7463	15.2158	0.73264	0.0674:0.0:0.9326:0.0	.	191;115	Q569K4;Q569K4-2	Z385B_HUMAN;.	M	191;89;115;89;89;122	ENSP00000386845:T191M;ENSP00000338225:T89M;ENSP00000386379:T115M;ENSP00000386507:T89M;ENSP00000394038:T89M;ENSP00000399198:T122M	ENSP00000338225:T89M	T	-	2	0	ZNF385B	180056342	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.866000	0.69590	1.510000	0.48803	0.561000	0.74099	ACG		0.463	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		A	180348097	G	A	180348097	3	1	72	1	0	0	0	0	1	0	0	0	17916	1145	40	1	863	1	ZNF385B	2	180348097	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	765767	180348097	62851276	21	21223										
ALS2CR8	79800	broad.mit.edu	37	chr2	203826146	203826146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	atggaatcccatttgttaatGcaggtacttttttaaagaat	7	5	0	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr2:203826146G>A	ENST00000402905.3	+	8	1150	c.829G>A	c.(829-831)Gca>Aca	p.A277T	CARF_ENST00000434998.1_Missense_Mutation_p.A175T|CARF_ENST00000545262.1_Missense_Mutation_p.A201T|CARF_ENST00000438828.2_Missense_Mutation_p.A277T|CARF_ENST00000414439.1_Missense_Mutation_p.A175T|CARF_ENST00000456821.2_Intron|CARF_ENST00000428585.1_Missense_Mutation_p.A201T|CARF_ENST00000471271.1_Intron|CARF_ENST00000545253.1_Missense_Mutation_p.A189T|WDR12_ENST00000477723.1_Intron|CARF_ENST00000320443.8_Missense_Mutation_p.A277T|CARF_ENST00000444724.1_Missense_Mutation_p.A277T	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	277					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A277T(1)									ATTTGTTAATGCAGGTACTTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	54	54					2																	203826146		1849	4088	5937	203534391	SO:0001583	missense	79800			AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.829G>A	2.37:g.203826146G>A	ENSP00000384006:p.Ala277Thr		203534391	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.321452	0.60634	.	.	ENSG00000138380	ENST00000402905;ENST00000444724;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000434998;ENST00000320443;ENST00000438828	.	.	.	5.38	4.47	0.54385	.	0.078222	0.49916	D	0.000136	T	0.51975	0.1706	N	0.19112	0.55	0.49130	D	0.999751	B;B;B;D	0.58620	0.033;0.019;0.019;0.983	B;B;B;P	0.56865	0.06;0.033;0.033;0.808	T	0.52983	-0.8502	9	0.41790	T	0.15	-13.4459	14.2666	0.66123	0.0:0.0:0.8501:0.1499	.	189;201;277;277	B4DIA7;G3V1K7;Q8N187;F6SXV3	.;.;AL2S8_HUMAN;.	T	277;277;175;201;189;201;175;277;277	.	ENSP00000316224:A277T	A	+	1	0	ALS2CR8	203534391	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.750000	0.55157	1.186000	0.42985	0.563000	0.77884	GCA		0.398	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		A	203826146	G	A	203826146	3	1	72	1	0	0	0	0	1	0	0	0	555	1319	46	3	851	3	ALS2CR8	2	203826146	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	23478049	203826146	39373227	22	21224										
TMEM43	79188	broad.mit.edu	37	chr3	14180741	14180741	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctggggcctgcgggcagctgGctggatggccatgttcatgg	18	10	1	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr3:14180741G>C	ENST00000306077.4	+	11	1198	c.944G>C	c.(943-945)gGc>gCc	p.G315A	RP11-434D12.1_ENST00000608606.1_Missense_Mutation_p.W60C|RP11-434D12.1_ENST00000601399.1_3'UTR	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	315					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.G315A(1)		breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						CGGGCAGCTGGCTGGATGGCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	99	104					3																	14180741		2203	4300	6503	14155742	SO:0001583	missense	79188			BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.944G>C	3.37:g.14180741G>C	ENSP00000303992:p.Gly315Ala		14155742	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283815	0.80803	.	.	ENSG00000170876	ENST00000306077	T	0.62639	0.01	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.78704	0.4325	M	0.71871	2.18	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.77822	-0.2445	10	0.40728	T	0.16	-29.7745	18.8558	0.92251	0.0:0.0:1.0:0.0	.	315	Q9BTV4	TMM43_HUMAN	A	315	ENSP00000303992:G315A	ENSP00000303992:G315A	G	+	2	0	TMEM43	14155742	1.000000	0.71417	0.995000	0.50966	0.703000	0.40648	9.165000	0.94761	2.448000	0.82819	0.305000	0.20034	GGC		0.592	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		C	14180741	G	C	14180741	3	2	72	1	0	0	0	0	1	0	0	0	16206	1203	42	5	986	5	TMEM43	3	14180741	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		14180741	183841689	23	21225										
BFSP2	8419	broad.mit.edu	37	chr3	133167379	133167379	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aggcggcagaagaggaaattAactctctgtataaagtcatt	10	6	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr3:133167379A>C	ENST00000302334.2	+	3	708	c.619A>C	c.(619-621)Aac>Cac	p.N207H	BFSP2-AS1_ENST00000515542.1_RNA	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	207	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.N207H(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						AGAGGAAATTAACTCTCTGTA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	3											61	64	63					3																	133167379		2203	4300	6503	134650069	SO:0001583	missense	8419			U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"Intermediate filaments type VI, eye lens intermediate filaments"	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.619A>C	3.37:g.133167379A>C	ENSP00000304987:p.Asn207His		134650069	Q14D32|Q9HBW5	Missense_Mutation	SNP	ENST00000302334.2	37	CCDS33859.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.709173	0.30322	.	.	ENSG00000170819	ENST00000302334	D	0.89270	-2.49	5.17	5.17	0.71159	Filament (1);	0.400171	0.23310	N	0.049569	D	0.89100	0.6619	L	0.45051	1.395	0.32071	N	0.594417	P	0.48911	0.917	P	0.53988	0.739	D	0.90280	0.4314	10	0.51188	T	0.08	-3.6609	11.0678	0.47985	0.8448:0.1552:0.0:0.0	.	207	Q13515	BFSP2_HUMAN	H	207	ENSP00000304987:N207H	ENSP00000304987:N207H	N	+	1	0	BFSP2	134650069	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	3.711000	0.54868	1.960000	0.56953	0.454000	0.30748	AAC		0.363	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1			C	133167379	A	C	133167379	3	2	72	1	0	0	0	0	1	0	0	0	1417	362	13	4	629	4	BFSP2	3	133167379	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	118986638	133167379	64855051	24	21226										
EIF4A2	1974	broad.mit.edu	37	chr3	186506930	186506930	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	acagaattggcagagggggtCgatttgggaggaaaggtgtg	19	3	0	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr3:186506930C>G	ENST00000323963.5	+	11	1160	c.1096C>G	c.(1096-1098)Cga>Gga	p.R366G	SNORA63_ENST00000363548.1_RNA|SNORA63_ENST00000363450.1_RNA|SNORA81_ENST00000408493.2_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.R271G|SNORA4_ENST00000584302.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.R367G			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	366	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.R366G(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		CAGAGGGGGTCGATTTGGGAG	0.403			T	BCL6	NHL																																		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	1	Substitution - Missense(1)	large_intestine(1)	3											136	143	141					3																	186506930		2203	4300	6503	187989624	SO:0001583	missense	1974			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.1096C>G	3.37:g.186506930C>G	ENSP00000326381:p.Arg366Gly		187989624	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362544	0.61403	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	D;D;D	0.94793	-3.52;-3.52;-3.52	5.87	5.87	0.94306	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.98592	0.9529	H	0.98786	4.33	0.80722	D	1	D;D;D	0.89917	0.983;0.998;1.0	D;D;D	0.79784	0.929;0.989;0.993	D	0.99264	1.0891	10	0.87932	D	0	-26.5244	18.0718	0.89410	0.0:1.0:0.0:0.0	.	271;367;366	Q9NZE6;Q14240-2;Q14240	.;.;IF4A2_HUMAN	G	366;367;271	ENSP00000326381:R366G;ENSP00000398370:R367G;ENSP00000348925:R271G	ENSP00000326381:R366G	R	+	1	2	EIF4A2	187989624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.335000	0.79234	2.941000	0.99782	0.655000	0.94253	CGA		0.403	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		G	186506930	C	G	186506930	3	3	72	1	0	0	0	0	1	0	0	0	5038	876	31	5	1138	5	EIF4A2	3	186506930	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	53339551	186506930	11515500	25	21227										
STK32B	55351	broad.mit.edu	37	chr4	5469766	5469766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agcactgtttggagactgtcCgggaggaattcatcatattc	11	8	2	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:5469766C>T	ENST00000282908.5	+	11	1497	c.1075C>T	c.(1075-1077)Cgg>Tgg	p.R359W	STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000510398.1_Missense_Mutation_p.R312W|STK32B_ENST00000512636.1_Missense_Mutation_p.R282W	NM_018401.1	NP_060871.1			serine/threonine kinase 32B									p.R359W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GGAGACTGTCCGGGAGGAATT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	4											162	154	157					4																	5469766		2203	4300	6503	5520667	SO:0001583	missense	55351			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.1075C>T	4.37:g.5469766C>T	ENSP00000282908:p.Arg359Trp		5520667		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.638996	0.67130	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.68765	-0.28;0.03;-0.35	4.75	2.76	0.32466	.	0.163089	0.27027	U	0.021299	T	0.70159	0.3192	L	0.43152	1.355	0.46185	D	0.998913	D	0.76494	0.999	P	0.60949	0.881	T	0.71560	-0.4556	10	0.72032	D	0.01	.	10.3981	0.44214	0.5962:0.4038:0.0:0.0	.	359	Q9NY57	ST32B_HUMAN	W	359;282;312	ENSP00000282908:R359W;ENSP00000423209:R282W;ENSP00000420984:R312W	ENSP00000282908:R359W	R	+	1	2	STK32B	5520667	0.996000	0.38824	0.996000	0.52242	0.900000	0.52787	0.973000	0.29422	0.978000	0.38470	0.563000	0.77884	CGG		0.522	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		T	5469766	C	T	5469766	3	4	72	1	0	0	0	0	1	0	0	0	15337	643	23	1	1117	1	STK32B	4	5469766	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		5469766	185684510	26	21228										
MAN2B2	23324	broad.mit.edu	37	chr4	6610849	6610849	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgcagacagagtaaccgaacGgtgcgcgtgacccaggaatt	13	10	0	3	rs540141303		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:6610849G>A	ENST00000285599.3	+	12	1866	c.1830G>A	c.(1828-1830)acG>acA	p.T610T	MAN2B2_ENST00000504960.1_3'UTR|MAN2B2_ENST00000504248.1_Silent_p.T559T	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	610					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.T610T(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						GTAACCGAACGGTGCGCGTGA	0.567													g|||	1	0.000199681	0	0	5008	,	,		21816	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	4											77	67	70					4																	6610849		2203	4300	6503	6661750	SO:0001819	synonymous_variant	23324			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1830G>A	4.37:g.6610849G>A			6661750	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	G	3.456	-0.110909	0.06924	.	.	ENSG00000013288	ENST00000505907	.	.	.	4.26	-8.52	0.00920	.	.	.	.	.	T	0.35799	0.0944	.	.	.	0.58432	D	0.99999	.	.	.	.	.	.	T	0.46748	-0.9169	4	.	.	.	-12.0277	2.8578	0.05577	0.1738:0.311:0.3683:0.1469	.	.	.	.	Q	609	.	.	R	+	2	0	MAN2B2	6661750	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-2.857000	0.00728	-3.427000	0.00165	-1.797000	0.00622	CGG		0.567	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6610849	G	A	6610849	2	1	72	1	0	0	0	0	0	0	0	1	9247	1103	39	1		1	MAN2B2	4	6610849	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	1141083	6610849	184543427	27	21229										
SORCS2	57537	broad.mit.edu	37	chr4	7666085	7666085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gcctctctcctgtagattttCggtacgtcacctgcgcaatc	8	14	2	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:7666085C>T	ENST00000507866.2	+	7	1067	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W	SORCS2_ENST00000329016.9_Missense_Mutation_p.R148W	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	320					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.R170W(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGTAGATTTTCGGTACGTCAC	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	4											43	44	44					4																	7666085		2075	4192	6267	7716985	SO:0001583	missense	57537			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.958C>T	4.37:g.7666085C>T	ENSP00000422185:p.Arg320Trp		7716985	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.179406	0.38511	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.31247	1.5;1.5	4.79	2.02	0.26589	VPS10 (1);	0.414901	0.22480	N	0.059519	T	0.39200	0.1069	L	0.57536	1.79	0.35199	D	0.774082	D;D	0.76494	0.998;0.999	P;P	0.57152	0.714;0.814	T	0.48031	-0.9070	10	0.59425	D	0.04	.	5.9996	0.19513	0.1529:0.6789:0.0:0.1682	.	148;320	B5MED8;Q96PQ0	.;SORC2_HUMAN	W	320;148	ENSP00000422185:R320W;ENSP00000329124:R148W	ENSP00000329124:R148W	R	+	1	2	SORCS2	7716985	0.998000	0.40836	0.001000	0.08648	0.008000	0.06430	2.969000	0.49232	0.094000	0.17404	-0.142000	0.14014	CGG		0.597	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7666085	C	T	7666085	3	4	72	1	0	0	0	0	1	0	0	0	14968	875	31	1	984	1	SORCS2	4	7666085	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	1055236	7666085	183488191	28	21230										
FAM114A1	92689	broad.mit.edu	37	chr4	38942625	38942625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aggtccttaaccccatgatcAgtagtgtattgttagaggta	10	7	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:38942625A>G	ENST00000358869.2	+	14	1749	c.1573A>G	c.(1573-1575)Agt>Ggt	p.S525G	FAM114A1_ENST00000515037.1_Missense_Mutation_p.S318G	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	525						cytoplasm (GO:0005737)		p.S525G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCCCATGATCAGTAGTGTATT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											118	109	112					4																	38942625		2203	4300	6503	38619020	SO:0001583	missense	92689				CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1573A>G	4.37:g.38942625A>G	ENSP00000351740:p.Ser525Gly		38619020	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.491457	0.26774	.	.	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.24350	1.86;2.9	5.28	4.06	0.47325	.	0.311140	0.43110	D	0.000603	T	0.13670	0.0331	N	0.08118	0	0.23107	N	0.998283	B;B	0.16396	0.005;0.017	B;B	0.11329	0.004;0.006	T	0.19418	-1.0306	10	0.66056	D	0.02	-10.89	10.2754	0.43507	0.859:0.0:0.141:0.0	.	318;525	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	G	318;525;318	ENSP00000424115:S318G;ENSP00000351740:S525G	ENSP00000347569:S318G	S	+	1	0	FAM114A1	38619020	0.998000	0.40836	1.000000	0.80357	0.638000	0.38207	2.520000	0.45554	0.906000	0.36621	0.533000	0.62120	AGT		0.408	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		G	38942625	A	G	38942625	3	3	72	1	0	0	0	0	1	0	0	0	5419	188	7	4	1619	4	FAM114A1	4	38942625	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	31276540	38942625	152211651	29	21231										
COL25A1	84570	broad.mit.edu	37	chr4	109773434	109773434	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggtccaggaggtccagggggAccctaaatcaagaaaaagca	13	9	1	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:109773434A>G	ENST00000399132.1	-	26	1877	c.1347T>C	c.(1345-1347)ggT>ggC	p.G449G	COL25A1_ENST00000399127.1_Silent_p.G422G|COL25A1_ENST00000399126.1_Silent_p.G449G	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1									p.G449G(1)		NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		GTCCAGGGGGACCCTAAATCA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	4											73	70	71					4																	109773434		1820	4072	5892	109992883	SO:0001819	synonymous_variant	84570			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1347T>C	4.37:g.109773434A>G			109992883		Silent	SNP	ENST00000399132.1	37	CCDS43258.1																																																																																				0.358	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		G	109773434	A	G	109773434	2	3	72	1	0	0	0	0	0	0	0	1	3690	262	10	4		4	COL25A1	4	109773434	Silent	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	70830809	109773434	81380842	30	21232										
ALPK1	80216	broad.mit.edu	37	chr4	113353701	113353701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttcagagactagagaatacgGgggtttttaagcccagtcaa	11	7	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr4:113353701G>A	ENST00000458497.1	+	11	3277	c.2998G>A	c.(2998-3000)Ggg>Agg	p.G1000R	ALPK1_ENST00000504176.2_Missense_Mutation_p.G922R|ALPK1_ENST00000177648.9_Missense_Mutation_p.G1000R	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1000							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G1000R(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		AGAGAATACGGGGGTTTTTAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4											81	90	87					4																	113353701		2203	4300	6503	113573150	SO:0001583	missense	80216			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2998G>A	4.37:g.113353701G>A	ENSP00000398048:p.Gly1000Arg		113573150	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837907	0.50951	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.06528	3.29;3.29;3.29	5.08	5.08	0.68730	Protein kinase-like domain (1);	0.226724	0.41001	D	0.000963	T	0.26195	0.0639	M	0.72118	2.19	0.40224	D	0.977771	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.991	T	0.01532	-1.1331	10	0.66056	D	0.02	-23.4998	18.4932	0.90855	0.0:0.0:1.0:0.0	.	922;922;1000	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	R	1000;1000;922	ENSP00000398048:G1000R;ENSP00000177648:G1000R;ENSP00000426044:G922R	ENSP00000177648:G1000R	G	+	1	0	ALPK1	113573150	1.000000	0.71417	0.059000	0.19551	0.140000	0.21249	6.573000	0.74009	2.354000	0.79902	0.563000	0.77884	GGG		0.488	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113353701	G	A	113353701	3	1	72	1	0	0	0	0	1	0	0	0	544	1232	43	3	3032	3	ALPK1	4	113353701	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	3580267	113353701	77800575	31	21233										
NSUN2	54888	broad.mit.edu	37	chr5	6625682	6625682	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aagaaatcaacttacagattCtgtttcactaactagaaact	4	8	3	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:6625682C>T	ENST00000264670.6	-	4	771	c.460G>A	c.(460-462)Gaa>Aaa	p.E154K	NSUN2_ENST00000506139.1_Missense_Mutation_p.E119K|NSUN2_ENST00000539938.1_5'UTR|NSUN2_ENST00000505264.1_5'UTR	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	154					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.E154K(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTTACAGATTCTGTTTCACTA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5											98	98	98					5																	6625682		2203	4300	6503	6678682	SO:0001583	missense	54888			AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.460G>A	5.37:g.6625682C>T	ENSP00000264670:p.Glu154Lys		6678682	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918488	0.92249	.	.	ENSG00000037474	ENST00000264670;ENST00000506139	T;T	0.38560	1.13;1.16	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.56978	0.2022	L	0.45137	1.4	0.80722	D	1	D;P	0.71674	0.998;0.804	D;P	0.69479	0.964;0.665	T	0.50955	-0.8766	10	0.33940	T	0.23	-40.1552	19.1283	0.93394	0.0:1.0:0.0:0.0	.	119;154	B4DQW2;Q08J23	.;NSUN2_HUMAN	K	154;119	ENSP00000264670:E154K;ENSP00000420957:E119K	ENSP00000264670:E154K	E	-	1	0	NSUN2	6678682	1.000000	0.71417	0.850000	0.33497	0.747000	0.42532	6.969000	0.76092	2.584000	0.87258	0.563000	0.77884	GAA		0.358	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6625682	C	T	6625682	3	4	72	1	0	0	0	0	1	0	0	0	10709	922	32	3	1907	3	NSUN2	5	6625682	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		6625682	174289578	32	21234										
ZNF622	90441	broad.mit.edu	37	chr5	16463691	16463691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gccacattcttcatcagcgaGctggaatgatgggaacaaaa	10	9	3	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:16463691G>T	ENST00000308683.2	-	2	912	c.786C>A	c.(784-786)agC>agA	p.S262R		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	262					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S262R(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						TCATCAGCGAGCTGGAATGAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	5											161	160	160					5																	16463691		2203	4300	6503	16516691	SO:0001583	missense	90441			AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.786C>A	5.37:g.16463691G>T	ENSP00000310042:p.Ser262Arg		16516691		Missense_Mutation	SNP	ENST00000308683.2	37	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	G	7.687	0.690284	0.15039	.	.	ENSG00000173545	ENST00000308683	T	0.45276	0.9	5.75	5.75	0.90469	Zinc finger, C2H2-like (1);	0.204778	0.52532	D	0.000068	T	0.21801	0.0525	N	0.04245	-0.25	0.34188	D	0.67171	B	0.26147	0.143	B	0.32393	0.145	T	0.35475	-0.9787	10	0.18276	T	0.48	-9.243	9.5862	0.39517	0.0742:0.0:0.7735:0.1523	.	262	Q969S3	ZN622_HUMAN	R	262	ENSP00000310042:S262R	ENSP00000310042:S262R	S	-	3	2	ZNF622	16516691	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	1.995000	0.40767	2.706000	0.92434	0.561000	0.74099	AGC		0.458	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		T	16463691	G	T	16463691	3	4	72	1	0	0	0	0	1	0	0	0	18085	962	34	2	667	2	ZNF622	5	16463691	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	9838009	16463691	164451569	33	21235										
ADAMTS6	11174	broad.mit.edu	37	chr5	64511306	64511307	+	IGR	INS	-	-	T													0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tagtaatcatctccttcagaINSttttaaagctagaaaacaaa							TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:64511306_64511307insT								ADAMTS6 (16714 upstream) : ADAMTS6 (81727 downstream)														p.S761fs*2(1)									TCTCCTTCAGATTTTAAAGCTA	0.332																																																1	Insertion - Frameshift(1)	large_intestine(1)	5																																								64547063	SO:0001628	intergenic_variant	11174																															5.37:g.64511310_64511310dupT			64547062		Frame_Shift_Ins	INS		37																																																																																				0	0.332									T	64511307	-	T	64511306	6	5	72	0	1	1	1	0	0	0	0	0	270	333	12	0		0	ADAMTS6	5	64511306	IGR	INS	-	TCGA-AG-A01Y-01A-41W-A096-10	48047615	64511306	116403954	34	21236										
CMYA5	202333	broad.mit.edu	37	chr5	79025565	79025565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tcatgaagatcaaaagaaaaTttatgctgattctcccctaa	5	8	3	4			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:79025565T>C	ENST00000446378.2	+	2	1008	c.977T>C	c.(976-978)aTt>aCt	p.I326T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	326					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.I326T(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CAAAAGAAAATTTATGCTGAT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	5											65	61	62					5																	79025565		1926	4134	6060	79061321	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.977T>C	5.37:g.79025565T>C	ENSP00000394770:p.Ile326Thr		79061321	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	4.856	0.159040	0.09236	.	.	ENSG00000164309	ENST00000446378	T	0.39056	1.1	5.79	-9.28	0.00656	.	2.041440	0.02229	N	0.064680	T	0.21509	0.0518	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15378	-1.0439	10	0.35671	T	0.21	.	11.715	0.51647	0.0:0.5116:0.2574:0.231	.	326	Q8N3K9	CMYA5_HUMAN	T	326	ENSP00000394770:I326T	ENSP00000394770:I326T	I	+	2	0	CMYA5	79061321	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.984000	0.03755	-1.314000	0.02300	-0.242000	0.12053	ATT		0.438	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79025565	T	C	79025565	3	2	72	1	0	0	0	0	1	0	0	0	3596	1493	52	4	983	4	CMYA5	5	79025565	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	14514259	79025565	101889695	35	21237										
APC	324	broad.mit.edu	37	chr5	112175171	112175171	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	taggatgtaatcagacgacaCaggaagcagattctgctaat	10	7	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:112175171C>T	ENST00000457016.1	+	16	4260	c.3880C>T	c.(3880-3882)Cag>Tag	p.Q1294*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1294*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1294*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1294	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1294*(11)|p.T1293fs*2(1)|p.Q1294fs*6(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAGACGACACAGGAAGCAGA	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(11)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5	GRCh37	CM930027	APC	M							55	57	56					5																	112175171		2202	4300	6502	112203070	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3880C>T	5.37:g.112175171C>T	ENSP00000413133:p.Gln1294*		112203070	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.839479	0.97877	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	4.85	0.62838	.	0.122222	0.53938	D	0.000054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.559	13.8243	0.63342	0.2784:0.7216:0.0:0.0	.	.	.	.	X	1294	.	.	Q	+	1	0	APC	112203070	0.993000	0.37304	1.000000	0.80357	0.962000	0.63368	2.731000	0.47343	1.533000	0.49186	0.655000	0.94253	CAG		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175171	C	T	112175171	4	4	72	1	0	0	0	0	0	1	0	0	763	479	17	3	3938	3	APC	5	112175171	Nonsense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	33149606	112175171	68740089	36	21238										
HSPA4	3308	broad.mit.edu	37	chr5	132412484	132412484	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gtgcattattacgactctctCaggagtgtgagaaactcaag	10	8	3	1	rs199586152		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:132412484C>G	ENST00000304858.2	+	7	1091	c.802C>G	c.(802-804)Cag>Gag	p.Q268E	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	268					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.Q268E(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACGACTCTCTCAGGAGTGTGA	0.348																																					Colon(114;1299 1588 6063 12302 48757)											1	Substitution - Missense(1)	large_intestine(1)	5											118	118	118					5																	132412484		2203	4300	6503	132440383	SO:0001583	missense	3308			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.802C>G	5.37:g.132412484C>G	ENSP00000302961:p.Gln268Glu		132440383	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772707	0.90108	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.00824	5.65	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.01976	0.0062	N	0.10645	0.015	0.80722	D	1	D	0.57257	0.979	D	0.74023	0.982	T	0.82394	-0.0479	10	0.17832	T	0.49	-7.0661	19.8041	0.96521	0.0:1.0:0.0:0.0	.	268	P34932	HSP74_HUMAN	E	268	ENSP00000302961:Q268E	ENSP00000302961:Q268E	Q	+	1	0	HSPA4	132440383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.358000	0.79466	2.748000	0.94277	0.591000	0.81541	CAG		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		G	132412484	C	G	132412484	3	3	72	1	0	0	0	0	1	0	0	0	7433	827	29	5	828	5	HSPA4	5	132412484	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	20237313	132412484	48502776	37	21239										
KIF4B	285643	broad.mit.edu	37	chr5	154395879	154395879	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gattgtattacaaaacagatTgaaagcctagagactgaaat	8	5	0	4			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr5:154395879T>C	ENST00000435029.4	+	1	2620	c.2460T>C	c.(2458-2460)atT>atC	p.I820I		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	820	Interaction with PRC1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.I820I(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CAAAACAGATTGAAAGCCTAG	0.453																																																2	Substitution - coding silent(2)	large_intestine(2)	5											52	55	54					5																	154395879		2203	4300	6503	154376072	SO:0001819	synonymous_variant	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2460T>C	5.37:g.154395879T>C			154376072		Silent	SNP	ENST00000435029.4	37	CCDS47324.1																																																																																				0.453	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			C	154395879	T	C	154395879	2	2	72	1	0	0	0	0	0	0	0	1	8325	1800	63	4		4	KIF4B	5	154395879	Silent	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	21983395	154395879	26519381	38	21240										
MICB	4277	broad.mit.edu	37	chr6	31474096	31474096	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tggctatgaacgtcacaaatTtctggaaggaagatgccatg	11	7	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr6:31474096T>A	ENST00000252229.6	+	3	581	c.502T>A	c.(502-504)Ttc>Atc	p.F168I	MICB_ENST00000538442.1_Missense_Mutation_p.F136I|MICB_ENST00000399150.3_Missense_Mutation_p.F125I	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B									p.F168I(2)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CGTCACAAATTTCTGGAAGGA	0.522																																																2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	6											82	82	82					6																	31474096		1957	4148	6105	31582075	SO:0001583	missense	4277				CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"Immunoglobulin superfamily / C1-set domain containing"	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.502T>A	6.37:g.31474096T>A	ENSP00000252229:p.Phe168Ile		31582075		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	.	.	.	.	.	.	.	.	.	.	N	7.034	0.561202	0.13498	.	.	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.01584	5.84;4.75;5.84	1.43	-1.8	0.07907	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	3.344840	0.01465	U	0.016045	T	0.00815	0.0027	L	0.38175	1.15	0.09310	N	1	P;B;B	0.46064	0.872;0.048;0.074	P;B;B	0.46144	0.505;0.041;0.048	T	0.34329	-0.9833	10	0.52906	T	0.07	.	2.1699	0.03846	0.2898:0.0:0.294:0.4162	.	136;125;168	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	I	136;125;168	ENSP00000442345:F136I;ENSP00000382103:F125I;ENSP00000252229:F168I	ENSP00000252229:F168I	F	+	1	0	MICB	31582075	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.876000	0.00717	-0.483000	0.06772	-0.973000	0.02599	TTC		0.522	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931		A	31474096	T	A	31474096	3	1	72	1	0	0	0	0	1	0	0	0	9605	1841	64	5	512	5	MICB	6	31474096	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10		31474096	139640971	39	21241										
IL17A	3605	broad.mit.edu	37	chr6	52052534	52052534	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	caacctgaacatccataaccGgaataccaataccaatccca	3	15	0	1	rs201890924		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr6:52052534G>A	ENST00000340057.1	+	2	206	c.161G>A	c.(160-162)cGg>cAg	p.R54Q		NM_002190.2	NP_002181.1	Q16552	IL17_HUMAN	interleukin 17A	54					apoptotic process (GO:0006915)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|fibroblast activation (GO:0072537)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein glycosylation (GO:0006486)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)	p.R54L(1)|p.R54Q(1)		endometrium(3)|large_intestine(2)|lung(8)|prostate(3)|skin(1)	17	Lung NSC(77;0.116)					ATCCATAACCGGAATACCAAT	0.458																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											173	154	160					6																	52052534		2203	4300	6503	52160493	SO:0001583	missense	3605			U32659	CCDS4937.1	6p12	2011-07-14	2006-04-26	2006-04-26	ENSG00000112115	ENSG00000112115		"Interleukins and interleukin receptors"	5981	protein-coding gene	gene with protein product	"cytotoxic T-lymphocyte-associated protein 8"	603149	"interleukin 17 (cytotoxic T-lymphocyte-associated serine esterase 8)"	CTLA8, IL17		8390535	Standard	NM_002190		Approved	IL-17A, IL-17	uc003pak.1	Q16552	OTTHUMG00000014840	ENST00000340057.1:c.161G>A	6.37:g.52052534G>A	ENSP00000344192:p.Arg54Gln		52160493	Q5T2P0	Missense_Mutation	SNP	ENST00000340057.1	37	CCDS4937.1	.	.	.	.	.	.	.	.	.	.	G	8.928	0.962627	0.18583	.	.	ENSG00000112115	ENST00000340057	T	0.55234	0.53	5.58	-0.437	0.12272	.	1.269480	0.05223	N	0.508931	T	0.17195	0.0413	L	0.60455	1.87	0.09310	N	1	B	0.17852	0.024	B	0.04013	0.001	T	0.05699	-1.0869	10	0.09843	T	0.71	-2.6974	1.7392	0.02948	0.3627:0.2797:0.2457:0.1119	.	54	Q16552	IL17_HUMAN	Q	54	ENSP00000344192:R54Q	ENSP00000344192:R54Q	R	+	2	0	IL17A	52160493	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.077000	0.11394	-0.452000	0.07087	0.561000	0.74099	CGG		0.458	IL17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040892.1	NM_002190		A	52052534	G	A	52052534	3	1	72	1	0	0	0	0	1	0	0	0	7655	1116	39	1	167	1	IL17A	6	52052534	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	20578438	52052534	119062533	40	21242										
FAM135A	57579	broad.mit.edu	37	chr6	71212449	71212449	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctggaagttataacgctacaCgaagaactaagaatattatt	7	6	0	2	rs202084380		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr6:71212449C>G	ENST00000418814.2	+	12	1598	c.984C>G	c.(982-984)caC>caG	p.H328Q	FAM135A_ENST00000370479.3_Missense_Mutation_p.H311Q|FAM135A_ENST00000505769.1_Missense_Mutation_p.H328Q|FAM135A_ENST00000361499.3_Missense_Mutation_p.H328Q|FAM135A_ENST00000457062.2_Missense_Mutation_p.H311Q|FAM135A_ENST00000505868.1_Missense_Mutation_p.H328Q	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	328								p.H311Q(1)		breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						TAACGCTACACGAAGAACTAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	6											136	139	138					6																	71212449		2203	4300	6503	71269170	SO:0001583	missense	57579			AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.984C>G	6.37:g.71212449C>G	ENSP00000410768:p.His328Gln		71269170	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270017	0.23221	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000515323;ENST00000457062;ENST00000361499;ENST00000505868	D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.77	1.93	0.25924	.	0.154856	0.64402	D	0.000015	T	0.38983	0.1061	N	0.00707	-1.245	0.27406	N	0.954727	B;B;B;B;B;B	0.14805	0.004;0.011;0.001;0.011;0.004;0.007	B;B;B;B;B;B	0.15870	0.004;0.013;0.005;0.014;0.006;0.006	T	0.46275	-0.9203	10	0.21540	T	0.41	.	1.4293	0.02330	0.3316:0.09:0.1272:0.4512	.	85;328;328;328;328;311	Q5JXJ9;Q9P2D6-4;D6RC17;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;.;.;F135A_HUMAN;.;.	Q	328;311;328;328;311;328;328	ENSP00000410768:H328Q;ENSP00000359510:H311Q;ENSP00000423785:H328Q;ENSP00000422406:H328Q;ENSP00000409201:H311Q;ENSP00000354913:H328Q;ENSP00000423307:H328Q	ENSP00000354913:H328Q	H	+	3	2	FAM135A	71269170	0.999000	0.42202	1.000000	0.80357	0.942000	0.58702	0.535000	0.23114	1.011000	0.39340	-0.290000	0.09829	CAC		0.348	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71212449	C	G	71212449	3	3	72	1	0	0	0	0	1	0	0	0	5464	535	19	5	1100	5	FAM135A	6	71212449	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	19159915	71212449	99902618	41	21243										
AKAP7	9465	broad.mit.edu	37	chr6	131481239	131481239	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	aatttgaagagaagtcaagaAaatgaatgggtcaagagtga	12	2	2	6			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr6:131481239A>C	ENST00000431975.2	+	3	290	c.192A>C	c.(190-192)gaA>gaC	p.E64D	AKAP7_ENST00000541650.1_Missense_Mutation_p.E63D|AKAP7_ENST00000368123.4_Missense_Mutation_p.E42D|AKAP7_ENST00000366358.2_3'UTR	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	64						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)	p.E42D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		GAAGTCAAGAAAATGAATGGG	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											52	51	51					6																	131481239		2203	4296	6499	131522932	SO:0001583	missense	9465			AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"A-kinase anchor proteins"	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.192A>C	6.37:g.131481239A>C	ENSP00000405252:p.Glu64Asp		131522932	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	.	.	.	.	.	.	.	.	.	.	A	10.56	1.383596	0.25031	.	.	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.33865	1.41;1.39;1.42	5.32	4.14	0.48551	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.352423	0.29572	N	0.011763	T	0.16642	0.0400	L	0.57536	1.79	0.27318	N	0.957121	B	0.13145	0.007	B	0.12156	0.007	T	0.15694	-1.0428	10	0.46703	T	0.11	-9.5975	9.6537	0.39912	0.8249:0.1751:0.0:0.0	.	64	Q9P0M2	AKA7G_HUMAN	D	64;63;42	ENSP00000405252:E64D;ENSP00000441048:E63D;ENSP00000357105:E42D	ENSP00000357105:E42D	E	+	3	2	AKAP7	131522932	1.000000	0.71417	0.958000	0.39756	0.242000	0.25591	2.627000	0.46469	0.950000	0.37743	0.528000	0.53228	GAA		0.328	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842		C	131481239	A	C	131481239	3	2	72	1	0	0	0	0	1	0	0	0	456	11	1	4	132	4	AKAP7	6	131481239	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	60268790	131481239	39633828	42	21244										
SYNJ2	8871	broad.mit.edu	37	chr6	158495722	158495722	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gttaaacgccaagactggaaGaaacttctggaatttgatca	9	7	2	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr6:158495722G>A	ENST00000355585.4	+	16	2319	c.2244G>A	c.(2242-2244)aaG>aaA	p.K748K	SYNJ2_ENST00000367112.1_5'Flank|SYNJ2_ENST00000367122.2_Silent_p.K748K|SYNJ2_ENST00000367121.3_Silent_p.K748K	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	748					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.K748K(1)		biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		AAGACTGGAAGAAACTTCTGG	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	6											87	82	84					6																	158495722		2203	4300	6503	158415710	SO:0001819	synonymous_variant	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.2244G>A	6.37:g.158495722G>A			158415710	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1																																																																																				0.348	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			A	158495722	G	A	158495722	2	1	72	1	0	0	0	0	0	0	0	1	15492	933	33	3		3	SYNJ2	6	158495722	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	27014483	158495722	12619345	43	21245										
SVOPL	136306	broad.mit.edu	37	chr7	138312916	138312916	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cacttacaagcaatttcaccGatggtgctgatgatcatggt	9	9	2	2	rs374157361		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr7:138312916G>A	ENST00000419765.3	-	10	1089	c.1056C>T	c.(1054-1056)atC>atT	p.I352I	SNORA40_ENST00000516379.1_RNA|SVOPL_ENST00000463557.1_5'Flank|SVOPL_ENST00000436657.1_Silent_p.I200I|SVOPL_ENST00000288513.5_Silent_p.I200I|SVOPL_ENST00000421622.1_Silent_p.I232I	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	352						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.I352I(1)|p.I200I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						CAATTTCACCGATGGTGCTGA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	7						G	,	0,4406		0,0,2203	171	122	138		1056,600	-8.6	0	7		138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SVOPL	NM_001139456.1,NM_174959.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	352/493,200/341	138312916	1,13005	2203	4300	6503	137963456	SO:0001819	synonymous_variant	136306			BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"SV2 related protein homolog (rat)-like"				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1056C>T	7.37:g.138312916G>A			137963456		Silent	SNP	ENST00000419765.3	37	CCDS47721.1																																																																																				0.552	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959		A	138312916	G	A	138312916	2	1	72	1	0	0	0	0	0	0	0	1	15463	1048	37	1		1	SVOPL	7	138312916	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		138312916	20825747	44	21246										
MYBL1	4603	broad.mit.edu	37	chr8	67492524	67492524	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	taaaactcactagtgtgctcGtcaaggctatttagagtatt	8	7	2	1	rs565495156		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr8:67492524G>A	ENST00000522677.3	-	9	1355	c.945C>T	c.(943-945)gaC>gaT	p.D315D	MYBL1_ENST00000524176.2_Silent_p.D315D|MYBL1_ENST00000517885.1_Intron	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	315	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.D315D(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			TAGTGTGCTCGTCAAGGCTAT	0.433													G|||	1	0.000199681	0	0	5008	,	,		16978	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	8											70	68	69					8																	67492524		1902	4127	6029	67655078	SO:0001819	synonymous_variant	4603			X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.945C>T	8.37:g.67492524G>A			67655078	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	37	CCDS47867.1																																																																																				0.433	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67492524	G	A	67492524	2	1	72	1	0	0	0	0	0	0	0	1	10039	1136	40	1		1	MYBL1	8	67492524	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		67492524	78871498	45	21247										
KCNB2	9312	broad.mit.edu	37	chr8	73848703	73848703	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttcaccagtatccctgcatcAttttggtgggccaccatcac	7	14	3	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr8:73848703A>G	ENST00000523207.1	+	3	1701	c.1113A>G	c.(1111-1113)tcA>tcG	p.S371S		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	371					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.S371S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TCCCTGCATCATTTTGGTGGG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	8											112	113	113					8																	73848703		2203	4300	6503	74011257	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1113A>G	8.37:g.73848703A>G			74011257	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.438	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73848703	A	G	73848703	2	3	72	1	0	0	0	0	0	0	0	1	8034	204	8	4		4	KCNB2	8	73848703	Silent	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	6356179	73848703	72515319	46	21248										
RALYL	138046	broad.mit.edu	37	chr8	85762215	85762215	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttttttgtttccctctttagCggttatgtctttgactatga	7	7	2	2	rs182622234		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr8:85762215C>T	ENST00000521268.1	+	5	1471	c.366C>T	c.(364-366)ggC>ggT	p.G122G	RALYL_ENST00000523850.1_Splice_Site_p.G49G|RALYL_ENST00000518566.1_Splice_Site_p.S111S|RALYL_ENST00000517638.1_Splice_Site_p.G135G|RALYL_ENST00000522455.1_Splice_Site_p.G122G|RALYL_ENST00000521695.1_Splice_Site_p.G122G|RALYL_ENST00000521376.1_Intron	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	122							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G122G(2)		endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						CCCTCTTTAGCGGTTATGTCT	0.259													C|||	1	0.000199681	0	0	5008	,	,		12219	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	8											105	90	95					8																	85762215		1783	4039	5822	85924770	SO:0001630	splice_region_variant	138046				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.366-1C>T	8.37:g.85762215C>T			85924770	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Silent	SNP	ENST00000521268.1	37	CCDS55253.1																																																																																				0.259	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1		Silent	T	85762215	C	T	85762215	5	4	72	1	0	0	0	0	0	0	1	0	13057	782	27	1	423	1	RALYL	8	85762215	Splice_Site	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	11913512	85762215	60601807	47	21249										
POLR2K	5440	broad.mit.edu	37	chr8	101163632	101163632	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	caaagcagcaaccaatgataTatatctgtggaggtaagagt	10	6	1	2	rs200510163		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr8:101163632T>C	ENST00000353107.3	+	2	184	c.49T>C	c.(49-51)Tat>Cat	p.Y17H	POLR2K_ENST00000522439.1_Missense_Mutation_p.Y17H|POLR2K_ENST00000519765.1_3'UTR	NM_005034.3	NP_005025.1	P53803	RPAB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa	17					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|RNA splicing (GO:0008380)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.Y17H(1)		large_intestine(1)|lung(1)|prostate(1)	3	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.59e-09)|all cancers(13;1.74e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			ACCAATGATATATATCTGTGG	0.348													T|||	1	0.000199681	0	0.0014	5008	,	,		19496	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8											96	96	96					8																	101163632		2203	4300	6503	101232808	SO:0001583	missense	5440				CCDS6285.1	8q22	2013-01-21	2002-08-29		ENSG00000147669	ENSG00000147669		"RNA polymerase subunits"	9198	protein-coding gene	gene with protein product		606033	"polymerase (RNA) II (DNA directed) polypeptide K (7.0kD)"				Standard	NM_005034		Approved	RPB10alpha	uc003yjf.3	P53803	OTTHUMG00000164705	ENST00000353107.3:c.49T>C	8.37:g.101163632T>C	ENSP00000342889:p.Tyr17His		101232808	Q6IBD4	Missense_Mutation	SNP	ENST00000353107.3	37	CCDS6285.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	31	5.086820	0.94100	.	.	ENSG00000147669	ENST00000353107;ENST00000522439	.	.	.	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000001	T	0.57651	0.2068	.	.	.	0.80722	D	1	B	0.16396	0.017	B	0.18561	0.022	T	0.54931	-0.8219	8	0.62326	D	0.03	.	16.1099	0.81255	0.0:0.0:0.0:1.0	.	17	P53803	RPAB4_HUMAN	H	17	.	ENSP00000342889:Y17H	Y	+	1	0	POLR2K	101232808	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.009000	0.70745	2.285000	0.76669	0.533000	0.62120	TAT		0.348	POLR2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379849.1	NM_005034		C	101163632	T	C	101163632	3	2	72	1	0	0	0	0	1	0	0	0	12257	1406	49	4	51	4	POLR2K	8	101163632	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	15401417	101163632	45200390	48	21250										
COL22A1	169044	broad.mit.edu	37	chr8	139606408	139606408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgagatgacttcatgtacgcCgggggcatctgggccaggag	16	9	2	2	rs201934935		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr8:139606408C>T	ENST00000303045.6	-	63	4913	c.4467G>A	c.(4465-4467)ccG>ccA	p.P1489P	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Silent_p.P1469P	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1489	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.P1489P(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCATGTACGCCGGGGGCATCT	0.597										HNSCC(7;0.00092)			T|||	1	0.000199681	0	0	5008	,	,		17740	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8											37	42	41					8																	139606408		2203	4300	6503	139675590	SO:0001819	synonymous_variant	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4467G>A	8.37:g.139606408C>T			139675590	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																				0.597	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139606408	C	T	139606408	2	4	72	1	0	0	0	0	0	0	0	1	3687	639	23	1		1	COL22A1	8	139606408	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	38442776	139606408	6757614	49	21251										
C9orf129	445577	broad.mit.edu	37	chr9	96081434	96081434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tacatggtggtcagtggcacGgaatccccaatagattgtat	11	8	1	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr9:96081434G>A	ENST00000375419.1	-	4	751	c.388C>T	c.(388-390)Cgt>Tgt	p.R130C	WNK2_ENST00000349097.3_Intron|WNK2_ENST00000395477.2_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000395475.2_Intron	NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	130								p.R130C(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						TCAGTGGCACGGAATCCCCAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	9											90	92	92					9																	96081434		1938	4133	6071	95121255	SO:0001583	missense	445577				CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.388C>T	9.37:g.96081434G>A	ENSP00000364568:p.Arg130Cys		95121255		Missense_Mutation	SNP	ENST00000375419.1	37	CCDS43850.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032861	0.35893	.	.	ENSG00000204352	ENST00000375419	T	0.51071	0.72	5.41	0.86	0.19042	.	.	.	.	.	T	0.22475	0.0542	N	0.08118	0	0.31021	N	0.718168	B	0.10296	0.003	B	0.04013	0.001	T	0.16778	-1.0391	9	0.36615	T	0.2	.	3.551	0.07845	0.4948:0.0:0.3211:0.1841	.	130	Q5T035	CI129_HUMAN	C	130	ENSP00000364568:R130C	ENSP00000364568:R130C	R	-	1	0	C9orf129	95121255	0.052000	0.20516	0.424000	0.26647	0.743000	0.42351	-0.215000	0.09279	0.332000	0.23536	-0.218000	0.12543	CGT		0.468	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808		A	96081434	G	A	96081434	3	1	72	1	0	0	0	0	1	0	0	0	2462	1116	39	1	210	1	C9orf129	9	96081434	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		96081434	45131997	50	21252										
LRRC8A	56262	broad.mit.edu	37	chr9	131678382	131678382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tttttccctccagatcgagaCgctccctccggagctcttcc	7	17	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr9:131678382C>T	ENST00000259324.5	+	4	2688	c.2165C>T	c.(2164-2166)aCg>aTg	p.T722M	LRRC8A_ENST00000492784.1_3'UTR|LRRC8A_ENST00000372599.3_Missense_Mutation_p.T722M|LRRC8A_ENST00000372600.4_Missense_Mutation_p.T722M	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	722					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.T722M(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						CAGATCGAGACGCTCCCTCCG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	9											62	64	63					9																	131678382		2202	4294	6496	130718203	SO:0001583	missense	56262			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.2165C>T	9.37:g.131678382C>T	ENSP00000259324:p.Thr722Met		130718203	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	C	7.964	0.747524	0.15710	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.58210	0.35;0.35;0.35	5.16	3.26	0.37387	.	0.543746	0.20202	N	0.097074	T	0.40322	0.1112	L	0.53780	1.695	0.31804	N	0.627986	B	0.19331	0.035	B	0.17722	0.019	T	0.38929	-0.9638	10	0.30854	T	0.27	.	2.4837	0.04594	0.2505:0.3876:0.2663:0.0956	.	722	Q8IWT6	LRC8A_HUMAN	M	722	ENSP00000361682:T722M;ENSP00000361680:T722M;ENSP00000259324:T722M	ENSP00000259324:T722M	T	+	2	0	LRRC8A	130718203	0.242000	0.23868	0.995000	0.50966	0.816000	0.46133	0.758000	0.26447	1.176000	0.42840	0.462000	0.41574	ACG		0.642	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131678382	C	T	131678382	3	4	72	1	0	0	0	0	1	0	0	0	9050	536	19	1	2171	1	LRRC8A	9	131678382	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	35596948	131678382	9535049	51	21253										
SETX	23064	broad.mit.edu	37	chr9	135204359	135204359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gttttcatggaaagagaaaaTaactaattcttcattcttta	5	5	4	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr9:135204359T>C	ENST00000224140.5	-	10	2808	c.2626A>G	c.(2626-2628)Att>Gtt	p.I876V	SETX_ENST00000393220.1_Missense_Mutation_p.I876V|SETX_ENST00000372169.2_Missense_Mutation_p.I876V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	876					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.I876V(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AAAGAGAAAATAACTAATTCT	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	9	GRCh37	CD040620	SETX	D							38	38	38					9																	135204359		2201	4298	6499	134194180	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2626A>G	9.37:g.135204359T>C	ENSP00000224140:p.Ile876Val		134194180	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	1.511	-0.549545	0.03996	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.85955	-1.95;-2.05;-1.66	5.11	-10.2	0.00374	.	3.396890	0.00465	N	0.000103	T	0.64516	0.2605	N	0.24115	0.695	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.61787	-0.6991	10	0.02654	T	1	.	2.5543	0.04756	0.1462:0.1897:0.4299:0.2341	.	876;876;876	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	876	ENSP00000224140:I876V;ENSP00000361242:I876V;ENSP00000376913:I876V	ENSP00000224140:I876V	I	-	1	0	SETX	134194180	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.329000	0.07935	-1.361000	0.02169	-0.313000	0.08912	ATT		0.308	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135204359	T	C	135204359	3	2	72	1	0	0	0	0	1	0	0	0	14178	1406	49	4	5475	4	SETX	9	135204359	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	3525977	135204359	6009072	52	21254										
FAM190B	54462	broad.mit.edu	37	chr10	86132007	86132007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgtggatgacatttccttgtCgtctttgtcatcttctgata	8	8	4	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr10:86132007C>T	ENST00000224756.8	+	2	1384	c.1199C>T	c.(1198-1200)tCg>tTg	p.S400L	CCSER2_ENST00000359979.4_Missense_Mutation_p.S400L|CCSER2_ENST00000372088.2_Missense_Mutation_p.S400L	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	400					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)		p.S400L(1)									ATTTCCTTGTCGTCTTTGTCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	10											106	103	104					10																	86132007		2203	4300	6503	86121987	SO:0001583	missense	54462				CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1199C>T	10.37:g.86132007C>T	ENSP00000224756:p.Ser400Leu		86121987	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	37	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347906	0.61183	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.69306	-0.39;1.04;0.91	5.73	4.83	0.62350	.	0.165613	0.38720	N	0.001594	T	0.78509	0.4294	M	0.63843	1.955	0.80722	D	1	P;B;D	0.89917	0.58;0.427;1.0	B;B;D	0.83275	0.066;0.046;0.996	T	0.80462	-0.1372	10	0.87932	D	0	-11.184	12.2768	0.54739	0.0:0.9184:0.0:0.0816	.	400;400;400	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	L	400	ENSP00000353068:S400L;ENSP00000224756:S400L;ENSP00000361160:S400L	ENSP00000224756:S400L	S	+	2	0	FAM190B	86121987	1.000000	0.71417	0.911000	0.35937	0.935000	0.57460	6.705000	0.74644	1.431000	0.47355	0.655000	0.94253	TCG		0.333	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		T	86132007	C	T	86132007	3	4	72	1	0	0	0	0	1	0	0	0	5538	893	31	1	1201	1	FAM190B	10	86132007	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		86132007	49402740	53	21255										
TNKS2	80351	broad.mit.edu	37	chr10	93611010	93611010	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agttgagatggggcacaaggAgctgaaggagattggaatca	16	4	1	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr10:93611010A>C	ENST00000371627.4	+	21	3111	c.2732A>C	c.(2731-2733)gAg>gCg	p.E911A		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	911	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.E911A(1)		biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GGGCACAAGGAGCTGAAGGAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											127	129	129					10																	93611010		2203	4300	6503	93600990	SO:0001583	missense	80351			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2732A>C	10.37:g.93611010A>C	ENSP00000360689:p.Glu911Ala		93600990	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	37	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.940361	0.92526	.	.	ENSG00000107854	ENST00000371627	D	0.89196	-2.48	5.32	5.32	0.75619	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.64402	D	0.000018	D	0.90031	0.6887	M	0.76170	2.325	0.58432	D	0.999999	P	0.36712	0.566	B	0.40702	0.338	D	0.90686	0.4609	10	0.59425	D	0.04	.	15.5766	0.76397	1.0:0.0:0.0:0.0	.	911	Q9H2K2	TNKS2_HUMAN	A	911	ENSP00000360689:E911A	ENSP00000360689:E911A	E	+	2	0	TNKS2	93600990	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.287000	0.95975	2.138000	0.66242	0.533000	0.62120	GAG		0.363	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		C	93611010	A	C	93611010	3	2	72	1	0	0	0	0	1	0	0	0	16360	304	11	4	2814	4	TNKS2	10	93611010	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	7479003	93611010	41923737	54	21256										
ZNF518A	9849	broad.mit.edu	37	chr10	97920282	97920282	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctcctaaaacaacttatgatGatttttccaagaggcacaaa	5	9	0	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr10:97920282G>T	ENST00000534948.1	+	0	5058							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		AACTTATGATGATTTTTCCAA	0.294																																																0			10											69	68	68					10																	97920282		1799	4075	5874	97910272			9849			AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"Zinc fingers, C2H2-type"	29009	protein-coding gene	gene with protein product			"zinc finger protein 518"	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97920282G>T			97910272	A0PJI5|O15044|Q32MP4	Missense_Mutation	SNP	ENST00000534948.1	37																																																																																					0.294	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		T	97920282	G	T	97920282	1	4	72	0	1	0	0	0	0	0	0	0	18001	1290	45	2		2	ZNF518A	10	97920282	RNA	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	4309272	97920282	37614465	55	21257										
RRP8	23378	broad.mit.edu	37	chr11	6622595	6622595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gggctcgcaaagcccctgccCgagcctcatggctgtctgtc	12	16	2	0	rs527676627		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr11:6622595C>T	ENST00000254605.6	-	3	818	c.701G>A	c.(700-702)cGg>cAg	p.R234Q	ILK_ENST00000299421.4_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000537806.1_5'Flank|RRP8_ENST00000534343.1_Intron|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000420936.2_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	234					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.R234Q(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						AGCCCCTGCCCGAGCCTCATG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11											32	33	33					11																	6622595		2201	4296	6497	6579171	SO:0001583	missense	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.701G>A	11.37:g.6622595C>T	ENSP00000254605:p.Arg234Gln		6579171	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010133	0.75046	.	.	ENSG00000132275	ENST00000254605;ENST00000533907	T;T	0.46063	1.52;0.88	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	L	0.34521	1.04	0.80722	D	1	D	0.64830	0.994	P	0.50825	0.651	T	0.08126	-1.0737	10	0.23302	T	0.38	-17.6516	16.6393	0.85068	0.0:1.0:0.0:0.0	.	234	O43159	RRP8_HUMAN	Q	234	ENSP00000254605:R234Q;ENSP00000436246:R234Q	ENSP00000254605:R234Q	R	-	2	0	RRP8	6579171	0.837000	0.29446	0.637000	0.29366	0.726000	0.41606	1.442000	0.35046	2.702000	0.92279	0.650000	0.86243	CGG		0.622	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6622595	C	T	6622595	3	4	72	1	0	0	0	0	1	0	0	0	13727	652	23	1	689	1	RRP8	11	6622595	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		6622595	128383921	56	21258										
SAA2	6289	broad.mit.edu	37	chr11	18269473	18269473	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cttctgaagccttaccatcaAaagcctcgccaaggaacgaa	7	13	2	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr11:18269473A>C	ENST00000526900.1	-	2	269	c.86T>G	c.(85-87)tTt>tGt	p.F29C	SAA2_ENST00000528349.1_Missense_Mutation_p.F29C|SAA2_ENST00000256733.4_Missense_Mutation_p.F29C|SAA2_ENST00000529528.1_Missense_Mutation_p.F29C|RNA5SP333_ENST00000363466.1_RNA|SAA2_ENST00000414546.2_Missense_Mutation_p.F29C|SAA2_ENST00000530400.1_Missense_Mutation_p.F29C|SAA2-SAA4_ENST00000524555.1_RNA			P0DJI9	SAA2_HUMAN	serum amyloid A2	29					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)		p.F29C(1)		central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						CTTACCATCAAAAGCCTCGCC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											76	74	74					11																	18269473		2198	4288	6486	18226049	SO:0001583	missense	6289			M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.86T>G	11.37:g.18269473A>C	ENSP00000436126:p.Phe29Cys		18226049	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Missense_Mutation	SNP	ENST00000526900.1	37	CCDS7833.1	.	.	.	.	.	.	.	.	.	.	A	0.319	-0.962951	0.02249	.	.	ENSG00000134339	ENST00000414546;ENST00000530400;ENST00000528349;ENST00000256733;ENST00000529528;ENST00000526900	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	4.2	-8.41	0.00961	.	3.200260	0.01088	N	0.005124	T	0.17916	0.0430	.	.	.	0.37029	D	0.896572	P;P	0.49961	0.93;0.854	P;P	0.56343	0.627;0.796	T	0.60627	-0.7226	9	0.39692	T	0.17	.	2.4066	0.04414	0.437:0.2033:0.075:0.2847	.	29;29	G3XAK9;E9PR14	.;.	C	29	ENSP00000416716:F29C;ENSP00000432370:F29C;ENSP00000435659:F29C;ENSP00000256733:F29C;ENSP00000437162:F29C;ENSP00000436126:F29C	ENSP00000256733:F29C	F	-	2	0	SAA2	18226049	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.648000	0.00107	-5.527000	0.00013	-2.790000	0.00116	TTT		0.488	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754		C	18269473	A	C	18269473	3	2	72	1	0	0	0	0	1	0	0	0	13836	14	1	4	320	4	SAA2	11	18269473	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	11646878	18269473	116737043	57	21259										
DPF2	5977	broad.mit.edu	37	chr11	65119165	65119165	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tctctgcaggaagttggagcTgccacctgtgtctggacctg	13	11	2	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr11:65119165T>A	ENST00000528416.1	+	11	1244	c.1111T>A	c.(1111-1113)Tgc>Agc	p.C371S	DPF2_ENST00000415073.2_Missense_Mutation_p.C187S|DPF2_ENST00000252268.4_Missense_Mutation_p.C385S	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	371					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)	p.C371S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						AAGTTGGAGCTGCCACCTGTG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	11											154	145	148					11																	65119165		2201	4297	6498	64875741	SO:0001583	missense	5977			U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.1111T>A	11.37:g.65119165T>A	ENSP00000436901:p.Cys371Ser		64875741	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	37	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.252753	0.80135	.	.	ENSG00000133884	ENST00000528416;ENST00000415073;ENST00000252268;ENST00000531989	D;D;D;D	0.99950	-8.73;-8.73;-8.73;-8.73	5.06	5.06	0.68205	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.41194	D	0.000922	D	0.99966	0.9987	H	0.99820	4.81	0.80722	D	1	D;D	0.61697	0.968;0.99	D;D	0.91635	0.966;0.999	D	0.96364	0.9268	10	0.87932	D	0	-22.1382	12.7743	0.57439	0.0:0.0:0.0:1.0	.	187;371	B4DT58;Q92785	.;REQU_HUMAN	S	371;187;385;96	ENSP00000436901:C371S;ENSP00000399714:C187S;ENSP00000252268:C385S;ENSP00000435887:C96S	ENSP00000252268:C385S	C	+	1	0	DPF2	64875741	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.823000	0.86660	1.903000	0.55091	0.454000	0.30748	TGC		0.527	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		A	65119165	T	A	65119165	3	1	72	1	0	0	0	0	1	0	0	0	4728	1580	55	5	1153	5	DPF2	11	65119165	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	46849692	65119165	69887351	58	21260										
IGHMBP2	3508	broad.mit.edu	37	chr11	68707026	68707026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	atggctgcggtgagagggctCgcgcccatgcccggcagaga	17	12	0	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr11:68707026C>T	ENST00000255078.3	+	15	2920	c.2809C>T	c.(2809-2811)Cgc>Tgc	p.R937C	RP11-757G1.5_ENST00000542410.1_RNA	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	937					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)	p.R937C(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGAGAGGGCTCGCGCCCATGC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	11											28	33	31					11																	68707026		2200	4293	6493	68463602	SO:0001583	missense	3508			L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"Zinc fingers, AN1-type domain containing"	5542	protein-coding gene	gene with protein product	"cardiac transcription factor 1", "zinc finger, AN1-type domain 7"	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2809C>T	11.37:g.68707026C>T	ENSP00000255078:p.Arg937Cys		68463602	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230146	0.58777	.	.	ENSG00000132740	ENST00000255078	T	0.45276	0.9	4.54	4.54	0.55810	Zinc finger, AN1-type (4);	0.536223	0.20003	N	0.101289	T	0.57873	0.2083	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.60622	-0.7227	10	0.87932	D	0	-12.3199	10.1715	0.42913	0.3243:0.6756:0.0:0.0	.	937	P38935	SMBP2_HUMAN	C	937	ENSP00000255078:R937C	ENSP00000255078:R937C	R	+	1	0	IGHMBP2	68463602	0.995000	0.38212	0.373000	0.26003	0.582000	0.36321	4.743000	0.62110	2.054000	0.61138	0.491000	0.48974	CGC		0.637	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		T	68707026	C	T	68707026	3	4	72	1	0	0	0	0	1	0	0	0	7612	884	31	1	2867	1	IGHMBP2	11	68707026	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	3587861	68707026	66299490	59	21261										
CCDC81	60494	broad.mit.edu	37	chr11	86126222	86126222	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	atgagggtgaactgatggtgGaaaagcaaaagcgagaacaa	14	4	0	4			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr11:86126222G>T	ENST00000445632.2	+	13	1830	c.1558G>T	c.(1558-1560)Gaa>Taa	p.E520*	CCDC81_ENST00000354755.1_Nonsense_Mutation_p.E430*|CCDC81_ENST00000278487.3_Nonsense_Mutation_p.E255*|CCDC81_ENST00000528728.1_Nonsense_Mutation_p.E255*	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	520								p.E430*(1)		kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				ACTGATGGTGGAAAAGCAAAA	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											71	68	69					11																	86126222		2202	4299	6501	85803870	SO:0001587	stop_gained	60494			AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1558G>T	11.37:g.86126222G>T	ENSP00000415528:p.Glu520*		85803870	A0AVL7|Q53FW3|Q9H5E5	Nonsense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	G	46	12.113861	0.99637	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	.	.	.	5.59	4.67	0.58626	.	0.431103	0.23365	N	0.048962	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.3586	15.3419	0.74303	0.0:0.1408:0.8592:0.0	.	.	.	.	X	430;255;520;255	.	.	E	+	1	0	CCDC81	85803870	0.916000	0.31088	0.009000	0.14445	0.009000	0.06853	2.330000	0.43885	1.327000	0.45338	0.650000	0.86243	GAA		0.488	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		T	86126222	G	T	86126222	4	4	72	1	0	0	0	0	0	1	0	0	2861	1175	41	2	1608	2	CCDC81	11	86126222	Nonsense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	17419196	86126222	48880294	60	21262										
SLCO1C1	53919	broad.mit.edu	37	chr12	20870141	20870141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	attatgtgccaaactatatgTtgacattggctttgtaaacc	7	7	0	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:20870141T>C	ENST00000266509.2	+	7	1120	c.752T>C	c.(751-753)gTt>gCt	p.V251A	SLCO1C1_ENST00000540354.1_Missense_Mutation_p.V202A|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.V251A|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.V133A|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.V251A	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	251					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.V251A(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	AAACTATATGTTGACATTGGC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	12											189	171	177					12																	20870141		2203	4300	6503	20761408	SO:0001583	missense	53919			AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.752T>C	12.37:g.20870141T>C	ENSP00000266509:p.Val251Ala		20761408	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.755213	0.89843	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.76	5.76	0.90799	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	M	0.89785	3.06	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.91635	0.944;0.991;0.999;0.999	T	0.76937	-0.2774	10	0.54805	T	0.06	.	16.0645	0.80861	0.0:0.0:0.0:1.0	.	133;202;251;251	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	A	251;202;251;251;133	ENSP00000444149:V251A;ENSP00000438665:V202A;ENSP00000266509:V251A;ENSP00000370964:V251A;ENSP00000444527:V133A	ENSP00000266509:V251A	V	+	2	0	SLCO1C1	20761408	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.594000	0.82698	2.200000	0.70718	0.482000	0.46254	GTT		0.343	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		C	20870141	T	C	20870141	3	2	72	1	0	0	0	0	1	0	0	0	14762	1725	60	4	774	4	SLCO1C1	12	20870141	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10		20870141	112981754	61	21263										
NCKAP1L	3071	broad.mit.edu	37	chr12	54910030	54910030	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgtcaatcctcaggtatggcAagagagtggcagacataaag	12	7	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:54910030A>C	ENST00000293373.6	+	10	1028	c.949A>C	c.(949-951)Aag>Cag	p.K317Q	NCKAP1L_ENST00000552211.1_3'UTR|NCKAP1L_ENST00000545638.2_Missense_Mutation_p.K267Q	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	317					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)	p.K317Q(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CAGGTATGGCAAGAGAGTGGC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											273	195	221					12																	54910030		2203	4300	6503	53196297	SO:0001583	missense	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.949A>C	12.37:g.54910030A>C	ENSP00000293373:p.Lys317Gln		53196297	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653853	0.88056	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.54279	0.58;0.58	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.73249	0.3563	M	0.81802	2.56	0.53688	D	0.999975	D	0.76494	0.999	D	0.83275	0.996	T	0.77493	-0.2567	10	0.87932	D	0	-23.4779	13.5955	0.61987	1.0:0.0:0.0:0.0	.	317	P55160	NCKPL_HUMAN	Q	317;267	ENSP00000293373:K317Q;ENSP00000445596:K267Q	ENSP00000293373:K317Q	K	+	1	0	NCKAP1L	53196297	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.606000	0.82863	2.106000	0.64143	0.397000	0.26171	AAG		0.498	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		C	54910030	A	C	54910030	3	2	72	1	0	0	0	0	1	0	0	0	10253	131	5	4	987	4	NCKAP1L	12	54910030	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	34039889	54910030	78941865	62	21264										
CS	1431	broad.mit.edu	37	chr12	56668624	56668624	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tcatctgacacatctttgccAacttccttctgcagctgtgt	6	13	4	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:56668624A>G	ENST00000351328.3	-	9	1147	c.957T>C	c.(955-957)gtT>gtC	p.V319V	CS_ENST00000548567.1_Silent_p.V253V|CS_ENST00000542324.2_Silent_p.V306V	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	319					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)	p.V319V(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		CATCTTTGCCAACTTCCTTCT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	12											141	122	129					12																	56668624		2203	4300	6503	54954891	SO:0001819	synonymous_variant	1431				CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.957T>C	12.37:g.56668624A>G			54954891	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																				0.443	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		G	56668624	A	G	56668624	2	3	72	1	0	0	0	0	0	0	0	1	3930	117	5	4		4	CS	12	56668624	Silent	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	1758594	56668624	77183271	63	21265										
TBX3	6926	broad.mit.edu	37	chr12	115118830	115118830	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gtcggccttaccagccaccaTccaccgagaattgtgaaatt	8	13	0	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:115118830T>G	ENST00000257566.3	-	2	900	c.511A>C	c.(511-513)Atg>Ctg	p.M171L	TBX3_ENST00000349155.2_Missense_Mutation_p.M171L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	171					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M171L(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CCAGCCACCATCCACCGAGAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	12											112	112	112					12																	115118830		2203	4300	6503	113603213	SO:0001583	missense	6926			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.511A>C	12.37:g.115118830T>G	ENSP00000257566:p.Met171Leu		113603213	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.000418	0.93227	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.88741	-2.42;-2.42	5.81	5.81	0.92471	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.89553	0.6748	L	0.28344	0.845	0.80722	D	1	B;B;B	0.32188	0.012;0.293;0.359	B;B;P	0.50934	0.031;0.319;0.654	D	0.88569	0.3128	10	0.44086	T	0.13	.	15.352	0.74396	0.0:0.0:0.0:1.0	.	171;171;171	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	L	171	ENSP00000257567:M171L;ENSP00000257566:M171L	ENSP00000257566:M171L	M	-	1	0	TBX3	113603213	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.225000	0.72522	0.533000	0.62120	ATG		0.463	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		G	115118830	T	G	115118830	3	3	72	1	0	0	0	0	1	0	0	0	15698	1435	50	4	1748	4	TBX3	12	115118830	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	58450206	115118830	18733065	64	21266										
SRRM4	84530	broad.mit.edu	37	chr12	119583287	119583287	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tacgactcaggaaatgacacGtcctcgccaccctccacgca	7	17	1	1	rs367777055		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:119583287G>C	ENST00000267260.4	+	9	1261	c.873G>C	c.(871-873)acG>acC	p.T291T		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	291	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.T291T(2)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GAAATGACACGTCCTCGCCAC	0.632																																																2	Substitution - coding silent(2)	large_intestine(2)	12											32	37	35					12																	119583287		2003	4159	6162	118067670	SO:0001819	synonymous_variant	84530			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.873G>C	12.37:g.119583287G>C			118067670	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Silent	SNP	ENST00000267260.4	37	CCDS44994.1																																																																																				0.632	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		C	119583287	G	C	119583287	2	2	72	1	0	0	0	0	0	0	0	1	15210	1132	40	5		5	SRRM4	12	119583287	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	4464457	119583287	14268608	65	21267										
DNAH10	196385	broad.mit.edu	37	chr12	124289557	124289557	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	caaatactgggaaaagaaaaTttatgaggtcctgacaaagc	9	6	0	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr12:124289557T>A	ENST00000409039.3	+	17	2628	c.2603T>A	c.(2602-2604)aTt>aAt	p.I868N		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	868	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I686N(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAAAAGAAAATTTATGAGGTC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	12											67	70	69					12																	124289557		2203	4300	6503	122855510	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2603T>A	12.37:g.124289557T>A	ENSP00000386770:p.Ile868Asn		122855510	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	T	13.64	2.296712	0.40594	.	.	ENSG00000197653	ENST00000409039	T	0.25250	1.81	5.42	4.25	0.50352	.	0.494884	0.17038	N	0.189451	T	0.50394	0.1613	M	0.80183	2.485	0.35850	D	0.82668	D;D;D	0.76494	0.999;0.999;0.993	D;D;P	0.68353	0.957;0.954;0.895	T	0.60885	-0.7174	10	0.52906	T	0.07	.	11.5375	0.50645	0.1342:0.0:0.0:0.8657	.	868;743;868	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	N	868	ENSP00000386770:I868N	ENSP00000386770:I868N	I	+	2	0	DNAH10	122855510	1.000000	0.71417	0.003000	0.11579	0.177000	0.22998	7.977000	0.88081	0.861000	0.35504	0.448000	0.29417	ATT		0.443	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124289557	T	A	124289557	3	1	72	1	0	0	0	0	1	0	0	0	4609	1493	52	5	2669	5	DNAH10	12	124289557	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	4706270	124289557	9562338	66	21268										
KIAA0564	23078	broad.mit.edu	37	chr13	42465656	42465656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgttcaaaacaggcaaaacaTtcctctctgccttttccaaa	4	12	2	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr13:42465656T>C	ENST00000379310.3	-	5	619	c.551A>G	c.(550-552)aAt>aGt	p.N184S	VWA8_ENST00000281496.6_Missense_Mutation_p.N184S	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	184						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.N184S(1)									AGGCAAAACATTCCTCTCTGC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	13											130	120	123					13																	42465656		2203	4300	6503	41363656	SO:0001583	missense	23078			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.551A>G	13.37:g.42465656T>C	ENSP00000368612:p.Asn184Ser		41363656	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.956543	0.92726	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.52754	0.65;0.65	5.71	5.71	0.89125	ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68123	-0.5492	10	0.44086	T	0.13	.	16.2826	0.82703	0.0:0.0:0.0:1.0	.	184	A3KMH1	K0564_HUMAN	S	88;184;184;184	ENSP00000368612:N184S;ENSP00000281496:N184S	ENSP00000251030:N88S	N	-	2	0	KIAA0564	41363656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.750000	0.85110	2.307000	0.77673	0.528000	0.53228	AAT		0.443	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		C	42465656	T	C	42465656	3	2	72	1	0	0	0	0	1	0	0	0	8206	1493	52	4	5334	4	KIAA0564	13	42465656	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10		42465656	72704222	67	21269										
NEK5	341676	broad.mit.edu	37	chr13	52674003	52674003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cctggaatctcactttttgtAttttacactcttaattaacc	3	10	2	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr13:52674003A>G	ENST00000355568.4	-	12	1041	c.902T>C	c.(901-903)aTa>aCa	p.I301T		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	301					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.I358T(1)|p.I301T(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		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)		CACTTTTTGTATTTTACACTC	0.313																																																2	Substitution - Missense(2)	large_intestine(2)	13											117	107	110					13																	52674003		2203	4300	6503	51572004	SO:0001583	missense	341676			BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)-related kinase 5"			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.902T>C	13.37:g.52674003A>G	ENSP00000347767:p.Ile301Thr		51572004	Q5TAP5	Missense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	A	8.382	0.837805	0.16891	.	.	ENSG00000197168	ENST00000355568	T	0.71341	-0.56	5.52	4.27	0.50696	Protein kinase-like domain (1);	0.329050	0.25014	N	0.033806	T	0.51210	0.1661	L	0.29908	0.895	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.36407	-0.9749	10	0.09084	T	0.74	.	11.159	0.48505	0.8621:0.0:0.0:0.1379	.	301	Q6P3R8	NEK5_HUMAN	T	301	ENSP00000347767:I301T	ENSP00000347767:I301T	I	-	2	0	NEK5	51572004	0.222000	0.23652	0.350000	0.25708	0.434000	0.31775	2.161000	0.42358	2.105000	0.64084	0.528000	0.53228	ATA		0.313	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		G	52674003	A	G	52674003	3	3	72	1	0	0	0	0	1	0	0	0	10358	449	16	4	1268	4	NEK5	13	52674003	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	10208347	52674003	62495875	68	21270										
DIS3	22894	broad.mit.edu	37	chr13	73336150	73336150	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	attccagaacagaagtacacAgcttgcatcatacagcgagt	8	10	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr13:73336150A>G	ENST00000377767.4	-	17	2353	c.2253T>C	c.(2251-2253)gcT>gcC	p.A751A	DIS3_ENST00000545453.1_Silent_p.A589A|DIS3_ENST00000377780.4_Silent_p.A721A	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	751					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)	p.A751A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		AGAAGTACACAGCTTGCATCA	0.398										Multiple Myeloma(4;0.011)																																						1	Substitution - coding silent(1)	large_intestine(1)	13											97	93	95					13																	73336150		2203	4300	6503	72234151	SO:0001819	synonymous_variant	22894			AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.2253T>C	13.37:g.73336150A>G			72234151	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Silent	SNP	ENST00000377767.4	37	CCDS9447.1																																																																																				0.398	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		G	73336150	A	G	73336150	2	3	72	1	0	0	0	0	0	0	0	1	4546	175	7	4		4	DIS3	13	73336150	Silent	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	20662147	73336150	41833728	69	21271										
SEC23A	10484	broad.mit.edu	37	chr14	39524468	39524468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cctggtcaaaagatgcagcaAtgttttggatttgagtttga	11	5	1	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr14:39524468A>G	ENST00000307712.6	-	14	2055	c.1538T>C	c.(1537-1539)aTt>aCt	p.I513T	SEC23A_ENST00000536508.1_Missense_Mutation_p.I387T|SEC23A_ENST00000537403.1_Missense_Mutation_p.I311T|SEC23A_ENST00000545328.2_Missense_Mutation_p.I484T	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	513					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)	p.I513T(1)		kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		AGATGCAGCAATGTTTTGGAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	14											97	93	94					14																	39524468		2203	4300	6503	38594219	SO:0001583	missense	10484			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1538T>C	14.37:g.39524468A>G	ENSP00000306881:p.Ile513Thr		38594219	B2R5P4|B3KXI2|Q8NE16	Missense_Mutation	SNP	ENST00000307712.6	37	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862078	0.71949	.	.	ENSG00000100934	ENST00000537403;ENST00000307712;ENST00000536508;ENST00000545328	D;D;D;D	0.89939	-1.56;-2.04;-2.59;-2.04	5.81	5.81	0.92471	.	0.051004	0.85682	D	0.000000	D	0.94578	0.8253	M	0.92507	3.315	0.80722	D	1	P;P;P	0.51791	0.948;0.896;0.913	P;P;P	0.54270	0.747;0.66;0.459	D	0.95637	0.8695	10	0.87932	D	0	-22.5493	16.1603	0.81700	1.0:0.0:0.0:0.0	.	484;387;513	F5H365;F5H6C4;Q15436	.;.;SC23A_HUMAN	T	311;513;387;484	ENSP00000444193:I311T;ENSP00000306881:I513T;ENSP00000437715:I387T;ENSP00000445393:I484T	ENSP00000306881:I513T	I	-	2	0	SEC23A	38594219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.138000	0.94501	2.218000	0.71995	0.450000	0.29827	ATT		0.433	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			G	39524468	A	G	39524468	3	3	72	1	0	0	0	0	1	0	0	0	14028	101	4	4	787	4	SEC23A	14	39524468	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10		39524468	67825072	70	21272										
SPTB	6710	broad.mit.edu	37	chr14	65270368	65270368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agatgaggcccaggaccaggCggtggttgccatctacaatg	14	10	1	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr14:65270368C>T	ENST00000389721.5	-	3	463	c.431G>A	c.(430-432)cGc>cAc	p.R144H	SPTB_ENST00000556626.1_Missense_Mutation_p.R144H|SPTB_ENST00000542895.1_Missense_Mutation_p.R144H|SPTB_ENST00000389720.3_Missense_Mutation_p.R144H|SPTB_ENST00000389722.3_Missense_Mutation_p.R144H	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	144	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.R144H(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CAGGACCAGGCGGTGGTTGCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	14											112	101	105					14																	65270368		2203	4300	6503	64340121	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.431G>A	14.37:g.65270368C>T	ENSP00000374371:p.Arg144His		64340121	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425798	0.96131	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.59906	0.23;0.23;0.23;0.23;0.23	5.38	5.38	0.77491	Actinin-type, actin-binding, conserved site (1);Calponin homology domain (5);	0.053422	0.85682	D	0.000000	T	0.68833	0.3044	L	0.39020	1.185	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.72338	0.977;0.952	T	0.71286	-0.4638	10	0.87932	D	0	.	18.2717	0.90070	0.0:1.0:0.0:0.0	.	144;148	P11277;Q59FP5	SPTB1_HUMAN;.	H	148;144;144;144;144;144	ENSP00000374372:R144H;ENSP00000451752:R144H;ENSP00000374371:R144H;ENSP00000443882:R144H;ENSP00000374370:R144H	ENSP00000374370:R144H	R	-	2	0	SPTB	64340121	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	2.677000	0.91161	0.563000	0.77884	CGC		0.607	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65270368	C	T	65270368	3	4	72	1	0	0	0	0	1	0	0	0	15157	768	27	1	6756	1	SPTB	14	65270368	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	25745900	65270368	42079172	71	21273										
C15orf2	23742	broad.mit.edu	37	chr15	24922476	24922476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gaggctcttataattcagtcGtaggagcagcgcctctcact	10	11	3	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr15:24922476G>A	ENST00000329468.2	+	1	1936	c.1462G>A	c.(1462-1464)Gta>Ata	p.V488I		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	488	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.V488I(2)									TAATTCAGTCGTAGGAGCAGC	0.512																																																2	Substitution - Missense(2)	large_intestine(2)	15											188	198	195					15																	24922476		2203	4300	6503	22473569	SO:0001583	missense	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1462G>A	15.37:g.24922476G>A	ENSP00000333735:p.Val488Ile		22473569		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	8.200	0.798045	0.16327	.	.	ENSG00000185823	ENST00000329468	T	0.04917	3.53	2.07	-4.13	0.03904	.	6.428760	0.00447	N	0.000086	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	B	0.23854	0.092	B	0.13407	0.009	T	0.34875	-0.9811	10	0.15952	T	0.53	.	4.5352	0.12024	0.2848:0.2157:0.4995:0.0	.	488	Q9NZP6	CO002_HUMAN	I	488	ENSP00000333735:V488I	ENSP00000333735:V488I	V	+	1	0	C15orf2	22473569	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-2.612000	0.00884	-1.139000	0.02881	0.313000	0.20887	GTA		0.512	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24922476	G	A	24922476	3	1	72	1	0	0	0	0	1	0	0	0	1788	1145	40	1	1464	1	C15orf2	15	24922476	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		24922476	77608916	72	21274										
MYO9A	4649	broad.mit.edu	37	chr15	72311380	72311380	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	atttaggtacttgtactgacCggctcagagtcatagcaata	9	8	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr15:72311380C>T	ENST00000356056.5	-	6	1627	c.1155G>A	c.(1153-1155)ccG>ccA	p.P385P	MYO9A_ENST00000424560.1_Splice_Site_p.P385P|MYO9A_ENST00000564571.1_Splice_Site_p.P385P|RP11-390D11.1_ENST00000568391.1_RNA|MYO9A_ENST00000566885.1_Intron|MYO9A_ENST00000563542.1_Intron|MYO9A_ENST00000444904.1_Intron	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	385	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.P385P(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTGTACTGACCGGCTCAGAGT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	15											134	127	130					15																	72311380		2199	4297	6496	70098434	SO:0001630	splice_region_variant	4649			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.1155+1G>A	15.37:g.72311380C>T			70098434	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																				0.388	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	Silent	T	72311380	C	T	72311380	5	4	72	1	0	0	0	0	0	0	1	0	10114	666	23	1	6639	1	MYO9A	15	72311380	Splice_Site	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	47388904	72311380	30220012	73	21275										
STRA6	64220	broad.mit.edu	37	chr15	74483549	74483549	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agtgtctcaagcagacgcggGcccaggacaggaagccatgc	14	12	1	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr15:74483549G>C	ENST00000323940.5	-	10	1069	c.824C>G	c.(823-825)gCc>gGc	p.A275G	STRA6_ENST00000574278.1_Missense_Mutation_p.A290G|STRA6_ENST00000535552.1_Missense_Mutation_p.A312G|STRA6_ENST00000416286.3_Missense_Mutation_p.A267G|STRA6_ENST00000449139.2_Missense_Mutation_p.A275G|STRA6_ENST00000423167.2_Missense_Mutation_p.A266G|STRA6_ENST00000563965.1_Missense_Mutation_p.A314G|STRA6_ENST00000395105.4_Missense_Mutation_p.A275G|STRA6_ENST00000574439.1_5'UTR	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	275					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)	p.A275G(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						GCAGACGCGGGCCCAGGACAG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	15											89	75	80					15																	74483549		2198	4297	6495	72270602	SO:0001583	missense	64220			AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"retinol binding protein 4 receptor"	610745	"stimulated by retinoic acid gene 6 homolog (mouse)", "stimulated by retinoic acid 6 homolog (mouse)"			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.824C>G	15.37:g.74483549G>C	ENSP00000326085:p.Ala275Gly		72270602	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.519460	0.27211	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	4.67	2.34	0.29019	.	0.382752	0.29087	N	0.013199	T	0.72252	0.3437	M	0.63428	1.95	0.18873	N	0.999989	P;P;P;P;P;P	0.41848	0.763;0.763;0.763;0.763;0.763;0.493	B;B;B;B;B;B	0.39379	0.229;0.229;0.229;0.229;0.229;0.298	T	0.61840	-0.6980	10	0.32370	T	0.25	-6.3065	4.7741	0.13171	0.357:0.0:0.643:0.0	.	312;313;266;275;314;84	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	G	275;275;207;84;314;266;312;165	ENSP00000378537:A275G;ENSP00000326085:A275G;ENSP00000413012:A266G;ENSP00000440238:A312G	ENSP00000326085:A275G	A	-	2	0	STRA6	72270602	0.002000	0.14202	0.094000	0.20943	0.061000	0.15899	0.923000	0.28757	1.100000	0.41517	0.561000	0.74099	GCC		0.632	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1			C	74483549	G	C	74483549	3	2	72	1	0	0	0	0	1	0	0	0	15361	1203	42	5	1219	5	STRA6	15	74483549	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	2172169	74483549	28047843	74	21276										
SEMA4B	10509	broad.mit.edu	37	chr15	90760826	90760826	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gcttcctgccaggcggggagTaccaggaggtgagagatgtt	17	8	0	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr15:90760826T>A	ENST00000411539.2	+	2	573	c.313T>A	c.(313-315)Tac>Aac	p.Y105N	SEMA4B_ENST00000332496.6_Missense_Mutation_p.Y105N|SEMA4B_ENST00000379122.3_Missense_Mutation_p.Y100N	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	100	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)	p.Y105N(1)		NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			AGGCGGGGAGTACCAGGAGGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	15											54	55	55					15																	90760826		2033	4191	6224	88561830	SO:0001583	missense	10509			AB051532	CCDS45347.1	15q25	2008-07-18						"Semaphorins"	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.313T>A	15.37:g.90760826T>A	ENSP00000394720:p.Tyr105Asn		88561830	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Missense_Mutation	SNP	ENST00000411539.2	37	CCDS45347.1	.	.	.	.	.	.	.	.	.	.	T	10.12	1.264219	0.23136	.	.	ENSG00000185033	ENST00000332496;ENST00000379122;ENST00000411539	T;T;T	0.09630	2.96;2.96;2.96	5.62	4.5	0.54988	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.290343	0.33591	N	0.004752	T	0.11665	0.0284	L	0.28054	0.825	0.38175	D	0.939431	P;P	0.38978	0.652;0.652	P;P	0.50270	0.636;0.636	T	0.24119	-1.0169	10	0.27785	T	0.31	.	5.5329	0.16995	0.0:0.2302:0.0:0.7698	.	105;100	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	N	105;100;105	ENSP00000332204:Y105N;ENSP00000368417:Y100N;ENSP00000394720:Y105N	ENSP00000332204:Y105N	Y	+	1	0	SEMA4B	88561830	0.997000	0.39634	0.895000	0.35142	0.116000	0.19942	3.543000	0.53633	2.128000	0.65567	0.533000	0.62120	TAC		0.602	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925		A	90760826	T	A	90760826	3	1	72	1	0	0	0	0	1	0	0	0	14069	1638	57	5	319	5	SEMA4B	15	90760826	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10	16277277	90760826	11770566	75	21277										
GPR139	124274	broad.mit.edu	37	chr16	20043133	20043133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgatgcagtgtgagtttgccGgcgagatccaggggctactt	15	8	0	3			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr16:20043133G>A	ENST00000570682.1	-	2	1286	c.986C>T	c.(985-987)cCg>cTg	p.P329L		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	329					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)	p.P329L(1)		autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						TGAGTTTGCCGGCGAGATCCA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	16											168	161	163					16																	20043133		2203	4300	6503	19950634	SO:0001583	missense	124274			AY255545	CCDS32398.1	16p13.11	2012-08-21						"GPCR / Class A : Orphans"	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.986C>T	16.37:g.20043133G>A	ENSP00000458791:p.Pro329Leu		19950634	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	37	CCDS32398.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.975336	0.74360	.	.	ENSG00000180269	ENST00000326571	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.64659	0.2618	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.68465	-0.5401	9	0.59425	D	0.04	-17.9077	18.4466	0.90686	0.0:0.0:1.0:0.0	.	329	Q6DWJ6	GP139_HUMAN	L	329	.	ENSP00000370779:P329L	P	-	2	0	GPR139	19950634	1.000000	0.71417	0.229000	0.23960	0.939000	0.58152	9.471000	0.97696	2.581000	0.87130	0.655000	0.94253	CCG		0.473	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911		A	20043133	G	A	20043133	3	1	72	1	0	0	0	0	1	0	0	0	6668	1116	39	1	79	1	GPR139	16	20043133	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		20043133	70311620	76	21278										
TP53	7157	broad.mit.edu	37	chr17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttgtcctgcttgcttacctcGcttagtgctccctgggggca	11	13	0	0	rs121913344		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr17:7577022G>A	ENST00000269305.4	-	8	1105	c.916C>T	c.(916-918)Cga>Tga	p.R306*	TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	306	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCTTACCTCGCTTAGTGCTC	0.562	R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	147	Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(39)|breast(21)|upper_aerodigestive_tract(15)|ovary(11)|central_nervous_system(10)|oesophagus(10)|stomach(8)|lung(8)|endometrium(6)|bone(4)|pancreas(3)|haematopoietic_and_lymphoid_tissue(3)|biliary_tract(3)|kidney(2)|NS(2)|urinary_tract(1)|liver(1)	17	GRCh37	CM971506	TP53	M	rs121913344						120	106	110					17																	7577022		2203	4300	6503	7517747	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.916C>T	17.37:g.7577022G>A	ENSP00000269305:p.Arg306*		7517747	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782988	0.90282	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	3.21	0.36854	.	1.348720	0.05032	N	0.474808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4785	0.44678	0.0:0.0:0.6334:0.3666	.	.	.	.	X	306;306;306;306;306;295;174	.	ENSP00000269305:R306X	R	-	1	2	TP53	7517747	1.000000	0.71417	0.970000	0.41538	0.345000	0.29048	2.280000	0.43443	0.735000	0.32537	0.561000	0.74099	CGA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577022	G	A	7577022	4	1	72	1	0	0	0	0	0	1	0	0	16421	1095	38	1	370	1	TP53	17	7577022	Nonsense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		7577022	73618188	77	21279										
UBB	7314	broad.mit.edu	37	chr17	16285609	16285609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gcaagcagctggaagatggcCgcactctttctgactacaac	10	12	2	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr17:16285609C>T	ENST00000395837.1	+	2	569	c.388C>T	c.(388-390)Cgc>Tgc	p.R130C	UBB_ENST00000395839.1_Missense_Mutation_p.R130C|UBB_ENST00000578649.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Missense_Mutation_p.R130C|UBB_ENST00000535788.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	130	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.R130C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		GGAAGATGGCCGCACTCTTTC	0.542																																					Melanoma(163;1126 3406 34901)											1	Substitution - Missense(1)	large_intestine(1)	17											82	82	82					17																	16285609		2203	4300	6503	16226334	SO:0001583	missense	7314				CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"polyubiquitin B"	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.388C>T	17.37:g.16285609C>T	ENSP00000379178:p.Arg130Cys		16226334	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000395837.1	37	CCDS11177.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539141	0.45176	.	.	ENSG00000170315	ENST00000302182;ENST00000395839;ENST00000395837	T;T;T	0.74421	-0.84;-0.84;-0.84	4.13	4.13	0.48395	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.53938	U	0.000060	T	0.71804	0.3383	M	0.67700	2.07	0.80722	D	1	B	0.32338	0.365	B	0.27608	0.081	T	0.76825	-0.2816	10	0.87932	D	0	.	15.8221	0.78662	0.0:1.0:0.0:0.0	.	130	P0CG47	UBB_HUMAN	C	130	ENSP00000304697:R130C;ENSP00000379180:R130C;ENSP00000379178:R130C	ENSP00000304697:R130C	R	+	1	0	UBB	16226334	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	6.949000	0.75971	2.043000	0.60533	0.644000	0.83932	CGC		0.542	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955		T	16285609	C	T	16285609	3	4	72	1	0	0	0	0	1	0	0	0	16881	652	23	1	390	1	UBB	17	16285609	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	8708587	16285609	64909601	78	21280										
SREBF1	6720	broad.mit.edu	37	chr17	17720323	17720323	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgcctccagaagtacacggcGgggcctgagtggggccgtgt	17	11	0	2	rs142128892		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr17:17720323G>A	ENST00000261646.5	-	9	1918	c.1734C>T	c.(1732-1734)ccC>ccT	p.P578P	SREBF1_ENST00000395757.1_Silent_p.P324P|SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000338854.5_Silent_p.P578P|SREBF1_ENST00000355815.4_Silent_p.P608P	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	578					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)	p.P608P(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						AGTACACGGCGGGGCCTGAGT	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	17						G	,	1,4405	2.1+/-5.4	0,1,2202	50	58	55		1824,1734	-2.9	0.7	17	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SREBF1	NM_001005291.2,NM_004176.4	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	608/1178,578/1148	17720323	2,13004	2203	4300	6503	17661048	SO:0001819	synonymous_variant	6720			BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.1734C>T	17.37:g.17720323G>A			17661048	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Silent	SNP	ENST00000261646.5	37	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	G	5.034	0.191973	0.09547	2.27E-4	1.16E-4	ENSG00000072310	ENST00000395751	.	.	.	5.32	-2.94	0.05581	.	.	.	.	.	T	0.39226	0.1070	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27640	-1.0068	4	.	.	.	-24.5522	2.1224	0.03729	0.4653:0.1305:0.2784:0.1258	.	.	.	.	C	586	.	.	R	-	1	0	SREBF1	17661048	0.000000	0.05858	0.672000	0.29872	0.262000	0.26303	-4.486000	0.00226	-0.902000	0.03886	-0.258000	0.10820	CGC		0.662	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		A	17720323	G	A	17720323	2	1	72	1	0	0	0	0	0	0	0	1	15180	1103	39	1		1	SREBF1	17	17720323	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	1434714	17720323	63474887	79	21281										
CALCOCO2	10241	broad.mit.edu	37	chr17	46919164	46919164	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	taacagtgtggagaagttctAcatccctggaggggacgtca	13	8	2	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr17:46919164A>G	ENST00000258947.3	+	2	196	c.95A>G	c.(94-96)tAc>tGc	p.Y32C	CALCOCO2_ENST00000416445.2_Missense_Mutation_p.Y32C|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.Y32C|CALCOCO2_ENST00000508679.1_Intron|CALCOCO2_ENST00000509507.1_Missense_Mutation_p.Y32C	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	32					response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)	p.Y32C(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						GAGAAGTTCTACATCCCTGGA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	17											173	148	156					17																	46919164		2203	4300	6503	44274163	SO:0001583	missense	10241			BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.95A>G	17.37:g.46919164A>G	ENSP00000258947:p.Tyr32Cys		44274163	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.136745	0.56936	.	.	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000509415;ENST00000416445;ENST00000505071;ENST00000502761	T;T;T;T;T;T;T	0.37915	2.02;1.17;1.3;2.02;2.02;2.02;2.02	6.07	5.0	0.66597	.	0.111470	0.40728	N	0.001027	T	0.53351	0.1791	M	0.72894	2.215	0.80722	D	1	P;P;P;P	0.50156	0.589;0.77;0.922;0.932	B;P;P;P	0.57244	0.29;0.5;0.623;0.816	T	0.56571	-0.7957	10	0.87932	D	0	-13.5035	11.9689	0.53051	0.9319:0.0:0.0681:0.0	.	32;32;32;32	E7ETP5;B4DP36;E9PBE5;Q13137	.;.;.;CACO2_HUMAN	C	32	ENSP00000258947:Y32C;ENSP00000424352:Y32C;ENSP00000398523:Y32C;ENSP00000425692:Y32C;ENSP00000406974:Y32C;ENSP00000422697:Y32C;ENSP00000424889:Y32C	ENSP00000258947:Y32C	Y	+	2	0	CALCOCO2	44274163	0.999000	0.42202	0.813000	0.32504	0.982000	0.71751	4.244000	0.58728	1.114000	0.41781	0.533000	0.62120	TAC		0.468	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831		G	46919164	A	G	46919164	3	3	72	1	0	0	0	0	1	0	0	0	2584	391	14	4	97	4	CALCOCO2	17	46919164	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	29198841	46919164	34276046	80	21282										
CBX4	8535	broad.mit.edu	37	chr17	77808886	77808886	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctcttggcccccaggtccggGcaggtggggctgggcgcctc	17	15	1	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr17:77808886G>A	ENST00000269397.4	-	5	732	c.555C>T	c.(553-555)tgC>tgT	p.C185C	CBX4_ENST00000448310.1_3'UTR	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	185	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.C185C(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CCAGGTCCGGGCAGGTGGGGC	0.701											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	17											40	44	42					17																	77808886		2202	4298	6500	75423481	SO:0001819	synonymous_variant	8535			AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.555C>T	17.37:g.77808886G>A		1178	75423481	B1PJR7|Q6TPI8|Q96C04	Silent	SNP	ENST00000269397.4	37	CCDS32758.1																																																																																				0.701	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		A	77808886	G	A	77808886	2	1	72	1	0	0	0	0	0	0	0	1	2726	1195	42	3		3	CBX4	17	77808886	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	30889722	77808886	3386324	81	21283										
LRG1	116844	broad.mit.edu	37	chr19	4538669	4538669	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ggcactggccgcaggaattcGggcgagaggctttccagccc	15	13	0	1	rs567253168		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:4538669G>A	ENST00000306390.6	-	2	787	c.327C>T	c.(325-327)ccC>ccT	p.P109P	CTB-50L17.14_ENST00000586020.1_Intron|LRG1_ENST00000586883.1_5'UTR	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	109					brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.P109P(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGGAATTCGGGCGAGAGGC	0.637													G|||	1	0.000199681	0	0	5008	,	,		16411	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	19											24	27	26					19																	4538669		2202	4300	6502	4489669	SO:0001819	synonymous_variant	116844				CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"leucine rich alpha 2 glycoprotein"	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.327C>T	19.37:g.4538669G>A			4489669	Q8N4F5|Q96QZ4	Silent	SNP	ENST00000306390.6	37	CCDS12130.1																																																																																				0.637	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972		A	4538669	G	A	4538669	2	1	72	1	0	0	0	0	0	0	0	1	8971	1103	39	1		1	LRG1	19	4538669	Silent	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10		4538669	54590314	82	21284										
MUC16	94025	broad.mit.edu	37	chr19	9049680	9049680	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	agtgaccagtggggtcagtgCatctagttcactaggtgaga	14	7	3	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:9049680C>A	ENST00000397910.4	-	5	32154	c.31951G>T	c.(31951-31953)Gca>Tca	p.A10651S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10653	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A6284S(1)|p.A10651S(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGGTCAGTGCATCTAGTTCA	0.473																																																2	Substitution - Missense(2)	large_intestine(2)	19											137	122	127					19																	9049680		2015	4178	6193	8910680	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31951G>T	19.37:g.9049680C>A	ENSP00000381008:p.Ala10651Ser		8910680	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	5.841	0.339450	0.11069	.	.	ENSG00000181143	ENST00000397910	T	0.02631	4.22	2.33	-4.67	0.03319	.	.	.	.	.	T	0.02494	0.0076	N	0.22421	0.69	.	.	.	P	0.34977	0.478	B	0.38020	0.263	T	0.30534	-0.9975	8	0.87932	D	0	.	9.4227	0.38561	0.0:0.2699:0.0:0.7301	.	10651	B5ME49	.	S	10651	ENSP00000381008:A10651S	ENSP00000381008:A10651S	A	-	1	0	MUC16	8910680	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-7.255000	0.00040	-1.583000	0.01638	0.298000	0.19748	GCA		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9049680	C	A	9049680	3	1	72	1	0	0	0	0	1	0	0	0	10003	710	25	2	11892	2	MUC16	19	9049680	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	4511011	9049680	50079303	83	21285										
SYDE1	85360	broad.mit.edu	37	chr19	15221024	15221024	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gaggggggccggacttcctgCggctggaccacaccttccac	14	15	0	0			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:15221024C>A	ENST00000342784.2	+	3	971	c.940C>A	c.(940-942)Cgg>Agg	p.R314R	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Silent_p.R247R	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	314					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)	p.R314R(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						GGACTTCCTGCGGCTGGACCA	0.726																																																1	Substitution - coding silent(1)	large_intestine(1)	19											5	8	7					19																	15221024		1948	3801	5749	15082024	SO:0001819	synonymous_variant	85360			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.940C>A	19.37:g.15221024C>A			15082024	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	37	CCDS12324.1																																																																																				0.726	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		A	15221024	C	A	15221024	2	1	72	1	0	0	0	0	0	0	0	1	15474	759	27	2		2	SYDE1	19	15221024	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	6171344	15221024	43907959	84	21286										
PSMC4	5704	broad.mit.edu	37	chr19	40480525	40480525	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gagctcccgctcacgcatttCgagctctacaagcaggtgag	11	13	2	1	rs201936053	byFrequency	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:40480525C>T	ENST00000157812.2	+	5	762	c.564C>T	c.(562-564)ttC>ttT	p.F188F	PSMC4_ENST00000455878.2_Silent_p.F157F	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	188					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.F188F(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TCACGCATTTCGAGCTCTACA	0.622													C|||	2	0.000399361	0	0.0014	5008	,	,		18922	0		0.001	False		,,,				2504	0				Colon(105;1478 1543 4034 6132 38638)											1	Substitution - coding silent(1)	large_intestine(1)	19											51	56	54					19																	40480525		2203	4300	6503	45172365	SO:0001819	synonymous_variant	5704			U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.564C>T	19.37:g.40480525C>T			45172365	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																				0.622	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		T	40480525	C	T	40480525	2	4	72	1	0	0	0	0	0	0	0	1	12723	883	31	1		1	PSMC4	19	40480525	Silent	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	25259501	40480525	18648458	85	21287										
ZNF615	284370	broad.mit.edu	37	chr19	52496253	52496253	+	Frame_Shift_Del	DEL	T	T	-													0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tgatgaacattgagccctgaTtttgtagtgaaggctttccc							TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:52496253delT	ENST00000602063.1	-	6	2425	c.2076delA	c.(2074-2076)aaafs	p.K692fs	ZNF615_ENST00000391795.3_Frame_Shift_Del_p.K697fs|ZNF615_ENST00000598071.1_Frame_Shift_Del_p.K703fs|ZNF615_ENST00000376716.5_Frame_Shift_Del_p.K692fs|ZNF615_ENST00000594083.1_Frame_Shift_Del_p.K703fs			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	692					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K703fs*>40(1)|p.K692fs*>40(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TGAGCCCTGATTTTGTAGTGA	0.413																																																2	Deletion - Frameshift(2)	large_intestine(2)	19											167	164	165					19																	52496253		2203	4300	6503	57188065	SO:0001589	frameshift_variant	284370			AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.2076delA	19.37:g.52496253delT	ENSP00000473089:p.Lys692fs		57188065	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Frame_Shift_Del	DEL	ENST00000602063.1	37	CCDS12846.1																																																																																				0.413	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		-	52496253	T	-	52496253	7	5	72	1	0	1	0	1	0	0	0	0	18079	1490	52	0	123	0	ZNF615	19	52496253	Frame_Shift_Del	DEL	T	TCGA-AG-A01Y-01A-41W-A096-10	12015728	52496253	6632730	86	21288										
CACNG7	59284	broad.mit.edu	37	chr19	54418628	54418628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	cccctccccagagacagtgcGcacggccacccccttcccca	7	23	0	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:54418628G>A	ENST00000391767.1	+	4	505	c.293G>A	c.(292-294)cGc>cAc	p.R98H	CACNG7_ENST00000391766.1_Missense_Mutation_p.R98H|CACNG7_ENST00000222212.2_Missense_Mutation_p.R98H|CACNG7_ENST00000468076.1_3'UTR			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	98					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R98H(1)		NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		GAGACAGTGCGCACGGCCACC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											72	60	64					19																	54418628		2203	4300	6503	59110440	SO:0001583	missense	59284			AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.293G>A	19.37:g.54418628G>A	ENSP00000375647:p.Arg98His		59110440	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.729511	0.89390	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.89875	-2.58;-2.58;-2.58	3.9	3.9	0.45041	.	0.000000	0.85682	D	0.000000	D	0.93357	0.7882	M	0.84082	2.675	0.80722	D	1	D	0.69078	0.997	P	0.61070	0.883	D	0.93851	0.7145	10	0.59425	D	0.04	-22.6554	14.1939	0.65656	0.0:0.0:1.0:0.0	.	98	P62955	CCG7_HUMAN	H	98	ENSP00000375647:R98H;ENSP00000222212:R98H;ENSP00000375646:R98H	ENSP00000222212:R98H	R	+	2	0	CACNG7	59110440	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.081000	0.94049	2.451000	0.82905	0.655000	0.94253	CGC		0.627	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			A	54418628	G	A	54418628	3	1	72	1	0	0	0	0	1	0	0	0	2568	1087	38	1	303	1	CACNG7	19	54418628	Missense_Mutation	SNP	G	TCGA-AG-A01Y-01A-41W-A096-10	1922375	54418628	4710355	87	21289										
NLRP4	147945	broad.mit.edu	37	chr19	56369571	56369571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	gctgaggaagaagatgctccCggaggcctccctgctcatcg	13	13	1	3	rs147621156		TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr19:56369571C>T	ENST00000301295.6	+	3	1234	c.812C>T	c.(811-813)cCg>cTg	p.P271L	NLRP4_ENST00000587891.1_Missense_Mutation_p.P196L|NLRP4_ENST00000346986.5_Missense_Mutation_p.P271L	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	271	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.P271L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		AAGATGCTCCCGGAGGCCTCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	LEU/PRO	0,4406		0,0,2203	69	76	74		812	3.1	0.2	19	dbSNP_134	74	1,8599		0,1,4299	no	missense	NLRP4	NM_134444.4	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	271/995	56369571	1,13005	2203	4300	6503	61061383	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.812C>T	19.37:g.56369571C>T	ENSP00000301295:p.Pro271Leu		61061383	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235428	0.39498	0.0	1.16E-4	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.82803	-1.65;-1.65	4.1	3.06	0.35304	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.88179	0.6367	M	0.67517	2.055	0.45415	D	0.998397	D;D;D	0.76494	0.999;0.998;0.998	D;P;P	0.74023	0.982;0.761;0.846	D	0.87827	0.2642	9	0.72032	D	0.01	.	9.8202	0.40878	0.0:0.8973:0.0:0.1027	.	271;196;271	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	L	271	ENSP00000301295:P271L;ENSP00000344787:P271L	ENSP00000301295:P271L	P	+	2	0	NLRP4	61061383	0.027000	0.19231	0.156000	0.22583	0.107000	0.19398	0.783000	0.26802	1.075000	0.40932	-0.136000	0.14681	CCG		0.582	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369571	C	T	56369571	3	4	72	1	0	0	0	0	1	0	0	0	10510	652	23	1	818	1	NLRP4	19	56369571	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10	1950943	56369571	2759412	88	21290										
SYCP2	10388	broad.mit.edu	37	chr20	58489210	58489210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttttaaatgccttagcaataAaatccattgaaaaccactga	4	8	0	2			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr20:58489210A>G	ENST00000357552.3	-	11	956	c.731T>C	c.(730-732)tTt>tCt	p.F244S	SYCP2_ENST00000371001.2_Missense_Mutation_p.F244S			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	244					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.F244S(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CTTAGCAATAAAATCCATTGA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	20											81	79	80					20																	58489210		2201	4297	6498	57922605	SO:0001583	missense	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.731T>C	20.37:g.58489210A>G	ENSP00000350162:p.Phe244Ser		57922605	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.767541	0.69878	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.05139	3.49;3.49;3.49	5.1	5.1	0.69264	.	0.101712	0.44902	D	0.000405	T	0.21631	0.0521	L	0.56769	1.78	0.37068	D	0.898402	D;D	0.89917	0.999;1.0	D;D	0.76575	0.929;0.988	T	0.03103	-1.1072	10	0.72032	D	0.01	-16.6685	15.1945	0.73075	1.0:0.0:0.0:0.0	.	244;244	A2A341;Q9BX26	.;SYCP2_HUMAN	S	244	ENSP00000360040:F244S;ENSP00000350162:F244S;ENSP00000402456:F244S	ENSP00000350162:F244S	F	-	2	0	SYCP2	57922605	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.739000	0.62080	2.057000	0.61298	0.533000	0.62120	TTT		0.299	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		G	58489210	A	G	58489210	3	3	72	1	0	0	0	0	1	0	0	0	15471	14	1	4	4001	4	SYCP2	20	58489210	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10		58489210	4536310	89	21291										
SLC17A9	63910	broad.mit.edu	37	chr20	61597010	61597010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ttgctctgtgcctgggccacAcctccagcttctgtgagtct	10	14	3	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr20:61597010A>T	ENST00000370351.4	+	10	1125	c.994A>T	c.(994-996)Acc>Tcc	p.T332S	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Missense_Mutation_p.T326S	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	332					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.T332S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CCTGGGCCACACCTCCAGCTT	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	20											151	165	160					20																	61597010		2130	4241	6371	61067455	SO:0001583	missense	63910			AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.994A>T	20.37:g.61597010A>T	ENSP00000359376:p.Thr332Ser		61067455	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479545	0.26511	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.58797	0.31;0.31	4.8	4.8	0.61643	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.206521	0.48767	N	0.000163	T	0.52224	0.1721	L	0.50919	1.6	0.54753	D	0.999985	B;B;B	0.17038	0.02;0.011;0.009	B;B;B	0.24006	0.05;0.034;0.02	T	0.49615	-0.8921	10	0.34782	T	0.22	.	12.9271	0.58266	1.0:0.0:0.0:0.0	.	352;332;326	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	S	332;326	ENSP00000359376:T332S;ENSP00000359374:T326S	ENSP00000359374:T326S	T	+	1	0	SLC17A9	61067455	1.000000	0.71417	0.915000	0.36163	0.133000	0.20885	5.057000	0.64294	1.788000	0.52465	0.459000	0.35465	ACC		0.647	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		T	61597010	A	T	61597010	3	4	72	1	0	0	0	0	1	0	0	0	14461	159	6	5	1032	5	SLC17A9	20	61597010	Missense_Mutation	SNP	A	TCGA-AG-A01Y-01A-41W-A096-10	3107800	61597010	1428510	90	21292										
BRWD1	54014	broad.mit.edu	37	chr21	40610476	40610476	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	tcttctgaagaaccagaaccTtcactctgatcacaggaagt	7	11	5	4			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chr21:40610476T>G	ENST00000333229.2	-	22	2832	c.2505A>C	c.(2503-2505)gaA>gaC	p.E835D	BRWD1_ENST00000380800.3_Missense_Mutation_p.E835D|BRWD1_ENST00000342449.3_Missense_Mutation_p.E835D	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	835					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E835D(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AACCAGAACCTTCACTCTGAT	0.383																																					Melanoma(170;988 1986 4794 16843 39731)											2	Substitution - Missense(2)	large_intestine(2)	21											135	124	128					21																	40610476		2203	4300	6503	39532346	SO:0001583	missense	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2505A>C	21.37:g.40610476T>G	ENSP00000330753:p.Glu835Asp		39532346	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.074365	0.36566	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.59224	0.28;0.31;0.39	5.18	2.7	0.31948	.	0.259165	0.33813	N	0.004540	T	0.43656	0.1257	L	0.49126	1.545	0.80722	D	1	B;B;B	0.15141	0.012;0.003;0.007	B;B;B	0.12837	0.008;0.004;0.005	T	0.20638	-1.0269	10	0.20519	T	0.43	-15.0503	4.7199	0.12913	0.0:0.1431:0.206:0.6509	.	502;835;835	Q5R2U6;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	D	835	ENSP00000330753:E835D;ENSP00000344333:E835D;ENSP00000370178:E835D	ENSP00000330753:E835D	E	-	3	2	BRWD1	39532346	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	0.494000	0.22467	0.865000	0.35603	0.482000	0.46254	GAA		0.383	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		G	40610476	T	G	40610476	3	3	72	1	0	0	0	0	1	0	0	0	1528	1606	56	4	4780	4	BRWD1	21	40610476	Missense_Mutation	SNP	T	TCGA-AG-A01Y-01A-41W-A096-10		40610476	7519419	91	21293										
FAM47C	442444	broad.mit.edu	37	chrX	37027369	37027369	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	4	1	0.504055944055944	0.936103896103896	0.436848484848485	0.523809523809524	1	0	ctcgcgtatctcatctccatCgggagcctcctgagactgga	10	14	2	1			TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A01Y-01A-41W-A096-10	TCGA-AG-A01Y-11A-11W-A096-10	g.chrX:37027369C>T	ENST00000358047.3	+	1	938	c.886C>T	c.(886-888)Cgg>Tgg	p.R296W		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	296								p.R296W(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TCATCTCCATCGGGAGCCTCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	X											76	66	69					X																	37027369		2202	4300	6502	36937290	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.886C>T	X.37:g.37027369C>T	ENSP00000367913:p.Arg296Trp		36937290	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	c	8.010	0.757338	0.15846	.	.	ENSG00000198173	ENST00000358047	T	0.14144	2.53	0.998	-0.163	0.13363	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	P	0.38711	0.643	B	0.24541	0.054	T	0.33189	-0.9878	9	0.72032	D	0.01	.	4.4105	0.11431	0.0:0.6919:0.0:0.3081	.	296	Q5HY64	FA47C_HUMAN	W	296	ENSP00000367913:R296W	ENSP00000367913:R296W	R	+	1	2	FAM47C	36937290	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	1.346000	0.33964	0.275000	0.22094	0.279000	0.19357	CGG		0.597	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37027369	C	T	37027369	3	4	72	1	0	0	0	0	1	0	0	0	5590	875	31	1	888	1	FAM47C	23	37027369	Missense_Mutation	SNP	C	TCGA-AG-A01Y-01A-41W-A096-10		37027369	118243191	92	21294										
KIAA0467	81888	broad.mit.edu	37	chr1	43913916	43913916	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggcttattctagcgcctggaCcggctcctctgttcccacca	9	16	2	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:43913916C>T	ENST00000372425.4	-	0	1115				SZT2_ENST00000372442.1_Missense_Mutation_p.P2345S|SZT2_ENST00000562955.1_Missense_Mutation_p.P3187S|SZT2-AS1_ENST00000396885.2_RNA			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)								hydroxypyruvate isomerase activity (GO:0008903)	p.P2345S(2)		large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGCGCCTGGACCGGCTCCTCT	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	1											9	11	10					1																	43913916		2196	4291	6487	43686503	SO:0001628	intergenic_variant	23334				CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"hydroxypyruvate isomerase homolog (E. coli)"			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502		1.37:g.43913916C>T			43686503	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Missense_Mutation	SNP	ENST00000372425.4	37	CCDS53309.1	.	.	.	.	.	.	.	.	.	.	C	6.065	0.380342	0.11466	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.65	3.74	0.42951	.	0.190773	0.38058	N	0.001822	T	0.36054	0.0953	L	0.43152	1.355	0.09310	N	1	B;B	0.22683	0.001;0.073	B;B	0.21151	0.005;0.033	T	0.20107	-1.0285	9	0.14252	T	0.57	.	10.6749	0.45781	0.2667:0.6047:0.1286:0.0	.	3244;3187	Q5T011;Q5T011-5	SZT2_HUMAN;.	S	2345	.	ENSP00000361519:P2345S	P	+	1	0	SZT2	43686503	0.034000	0.19679	0.103000	0.21229	0.043000	0.13939	1.964000	0.40462	0.710000	0.31997	-0.311000	0.09066	CCG		0.687	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207		T	43913916	C	T	43913916	1	4	73	0	1	0	0	0	0	0	0	0	8199	507	18	3		3	KIAA0467	1	43913916	IGR	SNP	C	TCGA-AG-A020-01A-21W-A096-10		43913916	205336705	1	21295										
BRDT	676	broad.mit.edu	37	chr1	92445134	92445134	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ttttcattacaggatgttttCgaaacgcatttttcaaagat	6	6	2	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:92445134C>T	ENST00000362005.3	+	9	1525	c.1107C>T	c.(1105-1107)ttC>ttT	p.F369F	BRDT_ENST00000402388.1_Silent_p.F369F|BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000399546.2_Silent_p.F369F|BRDT_ENST00000370389.2_Silent_p.F296F|BRDT_ENST00000394530.3_Silent_p.F323F	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	369					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)	p.F369F(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AGGATGTTTTCGAAACGCATT	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	1											72	73	73					1																	92445134		2203	4300	6503	92217722	SO:0001819	synonymous_variant	676			AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1107C>T	1.37:g.92445134C>T			92217722	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Silent	SNP	ENST00000362005.3	37	CCDS735.1																																																																																				0.323	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		T	92445134	C	T	92445134	2	4	73	1	0	0	0	0	0	0	0	1	1511	883	31	1		1	BRDT	1	92445134	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	48531218	92445134	156805487	2	21296										
CSF1	1435	broad.mit.edu	37	chr1	110466663	110466663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccctgccccgttttaactccGttcctttgactgacacaggc	7	16	0	2	rs548942397		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:110466663G>A	ENST00000329608.6	+	6	1811	c.1420G>A	c.(1420-1422)Gtt>Att	p.V474I	CSF1_ENST00000369802.3_Missense_Mutation_p.V474I|CSF1_ENST00000369801.1_Intron|CSF1_ENST00000420111.2_Intron|CSF1_ENST00000344188.5_Intron	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	474					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)	p.V474I(1)		breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTTTAACTCCGTTCCTTTGAC	0.632													G|||	1	0.000199681	0	0	5008	,	,		17035	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											73	81	78					1																	110466663		2203	4300	6503	110268186	SO:0001583	missense	1435			BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1420G>A	1.37:g.110466663G>A	ENSP00000327513:p.Val474Ile		110268186	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Missense_Mutation	SNP	ENST00000329608.6	37	CCDS816.1	.	.	.	.	.	.	.	.	.	.	G	6.175	0.400558	0.11696	.	.	ENSG00000184371	ENST00000329608;ENST00000369802	T;T	0.11277	2.79;2.79	5.57	-1.29	0.09288	.	0.920311	0.09003	N	0.862624	T	0.00998	0.0033	N	0.10733	0.035	0.31008	N	0.719603	B	0.18610	0.029	B	0.12837	0.008	T	0.47674	-0.9099	10	0.08837	T	0.75	.	2.3246	0.04220	0.2426:0.2613:0.3864:0.1096	.	474	P09603	CSF1_HUMAN	I	474	ENSP00000327513:V474I;ENSP00000358817:V474I	ENSP00000327513:V474I	V	+	1	0	CSF1	110268186	0.012000	0.17670	0.781000	0.31783	0.976000	0.68499	-0.151000	0.10175	0.027000	0.15297	0.467000	0.42956	GTT		0.632	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757		A	110466663	G	A	110466663	3	1	73	1	0	0	0	0	1	0	0	0	3937	1145	40	1	1442	1	CSF1	1	110466663	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	18021529	110466663	138783958	3	21297										
SPTA1	6708	broad.mit.edu	37	chr1	158624492	158624492	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggaagtcatataaagccatgAccctttgttctccagcaact	7	11	2	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:158624492A>T	ENST00000368147.4	-	21	3125	c.2945T>A	c.(2944-2946)gTc>gAc	p.V982D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	982	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.V982D(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TAAAGCCATGACCCTTTGTTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	76	76					1																	158624492		1951	4160	6111	156891116	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2945T>A	1.37:g.158624492A>T	ENSP00000357129:p.Val982Asp		156891116	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.957783	0.73902	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.35605	1.3;1.3	5.31	5.31	0.75309	Src homology-3 domain (3);Spectrin alpha chain, SH3 domain (1);	0.000000	0.29684	N	0.011478	T	0.63010	0.2475	M	0.93808	3.46	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.73304	-0.4025	10	0.62326	D	0.03	.	14.2542	0.66040	1.0:0.0:0.0:0.0	.	982	P02549	SPTA1_HUMAN	D	982	ENSP00000357130:V982D;ENSP00000357129:V982D	ENSP00000357129:V982D	V	-	2	0	SPTA1	156891116	1.000000	0.71417	0.904000	0.35570	0.555000	0.35460	8.213000	0.89758	2.243000	0.73865	0.482000	0.46254	GTC		0.488	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158624492	A	T	158624492	3	4	73	1	0	0	0	0	1	0	0	0	15155	275	10	5	4442	5	SPTA1	1	158624492	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10	48157829	158624492	90626129	4	21298										
SELP	6403	broad.mit.edu	37	chr1	169572294	169572294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tggtggggagtctgtccagcGtcccgatcgagtacaatcca	13	11	1	0	rs144811959	byFrequency	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:169572294G>A	ENST00000263686.6	-	10	1712	c.1675C>T	c.(1675-1677)Cgc>Tgc	p.R559C	SELP_ENST00000367794.2_Missense_Mutation_p.R497C|SELP_ENST00000367788.2_Missense_Mutation_p.R497C|SELP_ENST00000367786.2_Missense_Mutation_p.R497C|SELP_ENST00000458599.2_Intron|SELP_ENST00000367792.2_Intron|SELP_ENST00000367791.2_Missense_Mutation_p.R435C|SELP_ENST00000367793.2_Missense_Mutation_p.R497C	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	559	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)	p.R559C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	TCTGTCCAGCGTCCCGATCGA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	0,4406		0,0,2203	105	97	100		1675	5	0.1	1	dbSNP_134	100	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SELP	NM_003005.3	180	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	possibly-damaging	559/831	169572294	4,13002	2203	4300	6503	167838918	SO:0001583	missense	6403			BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"CD molecules"	10721	protein-coding gene	gene with protein product		173610	"selectin P (granule membrane protein 140kD, antigen CD62)"	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.1675C>T	1.37:g.169572294G>A	ENSP00000263686:p.Arg559Cys		167838918	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222295	0.39300	0.0	4.65E-4	ENSG00000174175	ENST00000367795;ENST00000367790;ENST00000426706;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.9	4.98	0.66077	Complement control module (2);Sushi/SCR/CCP (3);	0.957439	0.08697	N	0.906990	T	0.56877	0.2015	L	0.58354	1.805	0.22728	N	0.998801	P;P;P	0.52061	0.928;0.928;0.95	P;P;P	0.51453	0.67;0.601;0.471	T	0.52419	-0.8578	10	0.54805	T	0.06	-0.7352	12.5811	0.56391	0.0:0.0:0.8346:0.1654	.	559;559;559	Q6NUL9;P16109;G3V1U2	.;LYAM3_HUMAN;.	C	435;559;558;559;559;497;497;435;497;497;482	ENSP00000263686:R559C;ENSP00000356767:R497C;ENSP00000356768:R497C;ENSP00000356765:R435C;ENSP00000356762:R497C;ENSP00000356760:R497C	ENSP00000263686:R559C	R	-	1	0	SELP	167838918	0.520000	0.26250	0.134000	0.22075	0.169000	0.22640	0.678000	0.25277	1.464000	0.47987	0.650000	0.86243	CGC		0.448	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005		A	169572294	G	A	169572294	3	1	73	1	0	0	0	0	1	0	0	0	14056	1145	40	1	845	1	SELP	1	169572294	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	10947802	169572294	79678327	5	21299										
DUSP10	11221	broad.mit.edu	37	chr1	221875849	221875849	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gaactctagcaactgccccaTgaagttaaggtttggggaga	12	8	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:221875849T>A	ENST00000366899.3	-	4	1592	c.1354A>T	c.(1354-1356)Atg>Ttg	p.M452L	DUSP10_ENST00000544095.1_Missense_Mutation_p.M110L|DUSP10_ENST00000323825.3_Missense_Mutation_p.M110L|DUSP10_ENST00000468085.1_5'UTR	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	452	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.M452L(1)		NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		AACTGCCCCATGAAGTTAAGG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											226	207	213					1																	221875849		2203	4300	6503	219942472	SO:0001583	missense	11221			AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.1354A>T	1.37:g.221875849T>A	ENSP00000355866:p.Met452Leu		219942472	D3DTB4|Q6GSI4|Q9H9Z5	Missense_Mutation	SNP	ENST00000366899.3	37	CCDS1528.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683432	0.88542	.	.	ENSG00000143507	ENST00000366899;ENST00000418487;ENST00000323825;ENST00000544095	T;T;T	0.57595	0.39;0.39;0.39	5.72	5.72	0.89469	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	T	0.62696	0.2449	L	0.35723	1.085	0.80722	D	1	D	0.63880	0.993	D	0.66084	0.941	T	0.62253	-0.6893	10	0.45353	T	0.12	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	452	Q9Y6W6	DUS10_HUMAN	L	452;397;110;110	ENSP00000355866:M452L;ENSP00000322015:M110L;ENSP00000441302:M110L	ENSP00000322015:M110L	M	-	1	0	DUSP10	219942472	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	ATG		0.468	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207		A	221875849	T	A	221875849	3	1	73	1	0	0	0	0	1	0	0	0	4821	1464	51	5	98	5	DUSP10	1	221875849	Missense_Mutation	SNP	T	TCGA-AG-A020-01A-21W-A096-10	52303555	221875849	27374772	6	21300										
OR2L8	391190	broad.mit.edu	37	chr1	248112888	248112888	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tatttgacctgcagcacccaCctcactgtagtaactttcta	5	13	2	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr1:248112888C>A	ENST00000357191.3	+	1	729	c.729C>A	c.(727-729)caC>caA	p.H243Q	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H243Q(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	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;0.0152)			GCAGCACCCACCTCACTGTAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1											165	118	134					1																	248112888		2203	4300	6503	246179511	SO:0001583	missense	391190			BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.729C>A	1.37:g.248112888C>A	ENSP00000349719:p.His243Gln		246179511	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	9.892	1.204532	0.22205	.	.	ENSG00000196936	ENST00000357191	T	0.00307	8.17	1.8	0.829	0.18847	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33040	U	0.005352	T	0.00784	0.0026	H	0.96048	3.76	0.27477	N	0.952695	D	0.89917	1.0	D	0.83275	0.996	T	0.31530	-0.9940	10	0.87932	D	0	.	5.1303	0.14907	0.0:0.6581:0.0:0.3419	.	243	Q8NGY9	OR2L8_HUMAN	Q	243	ENSP00000349719:H243Q	ENSP00000349719:H243Q	H	+	3	2	OR2L8	246179511	0.000000	0.05858	0.996000	0.52242	0.287000	0.27160	-1.351000	0.02622	1.010000	0.39314	0.485000	0.47835	CAC		0.458	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112888	C	A	248112888	3	1	73	1	0	0	0	0	1	0	0	0	11040	506	18	2	731	2	OR2L8	1	248112888	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	26237039	248112888	1137733	7	21301										
ZNF638	27332	broad.mit.edu	37	chr2	71607379	71607379	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aggtgaagaaaaagactttaGagtcaaagaaagtatctgca	10	4	2	5			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:71607379G>T	ENST00000409544.1	+	9	2923	c.2293G>T	c.(2293-2295)Gag>Tag	p.E765*	ZNF638_ENST00000355812.3_Nonsense_Mutation_p.E765*|RNU6-105P_ENST00000363909.1_RNA|ZNF638_ENST00000264447.4_Nonsense_Mutation_p.E765*|ZNF638_ENST00000377802.2_Nonsense_Mutation_p.E765*|ZNF638_ENST00000410075.1_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	765					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E765*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAAGACTTTAGAGTCAAAGAA	0.249																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											33	33	33					2																	71607379		2189	4244	6433	71460887	SO:0001587	stop_gained	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2293G>T	2.37:g.71607379G>T	ENSP00000386433:p.Glu765*		71460887	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Nonsense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	39	7.420577	0.98272	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000394137;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	.	.	.	4.58	4.58	0.56647	.	0.310564	0.28431	N	0.015365	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-9.6736	13.1824	0.59662	0.0:0.0:1.0:0.0	.	.	.	.	X	765;871;344;765;765;765;765	.	ENSP00000264447:E765X	E	+	1	0	ZNF638	71460887	0.991000	0.36638	0.973000	0.42090	0.150000	0.21749	2.648000	0.46647	2.835000	0.97688	0.591000	0.81541	GAG		0.249	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71607379	G	T	71607379	4	4	73	1	0	0	0	0	0	1	0	0	18094	943	33	2	2323	2	ZNF638	2	71607379	Nonsense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10		71607379	171591994	8	21302										
CNNM3	26505	broad.mit.edu	37	chr2	97493857	97493857	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gcagggttgaagtggagatcGggaaagagggtctgaagttt	18	3	1	4			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:97493857G>A	ENST00000305510.3	+	5	1739	c.1711G>A	c.(1711-1713)Ggg>Agg	p.G571R	CNNM3_ENST00000377060.3_Missense_Mutation_p.G523R|ANKRD23_ENST00000476975.1_Intron	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	571					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.G571R(1)		NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						AGTGGAGATCGGGAAAGAGGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	115	113					2																	97493857		2203	4300	6503	96857584	SO:0001583	missense	26505			AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"cyclin M3"	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.1711G>A	2.37:g.97493857G>A	ENSP00000305449:p.Gly571Arg		96857584	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Missense_Mutation	SNP	ENST00000305510.3	37	CCDS2025.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110384	0.94292	.	.	ENSG00000168763	ENST00000377060;ENST00000424641;ENST00000305510	T;T	0.58797	0.31;0.31	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.81361	0.4806	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.991	D	0.85680	0.1300	10	0.87932	D	0	-39.4218	17.2957	0.87170	0.0:0.0:1.0:0.0	.	523;571	Q8NE01-2;Q8NE01	.;CNNM3_HUMAN	R	523;523;571	ENSP00000366260:G523R;ENSP00000305449:G571R	ENSP00000305449:G571R	G	+	1	0	CNNM3	96857584	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	9.601000	0.98297	2.611000	0.88343	0.491000	0.48974	GGG		0.567	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623		A	97493857	G	A	97493857	3	1	73	1	0	0	0	0	1	0	0	0	3620	1116	39	1	1729	1	CNNM3	2	97493857	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	25886478	97493857	145705516	9	21303										
DPP10	57628	broad.mit.edu	37	chr2	116497365	116497365	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggtggtcaccagatggagaaAgacttgccttcctgatgata	12	8	1	5			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:116497365A>C	ENST00000410059.1	+	9	1228	c.748A>C	c.(748-750)Aga>Cga	p.R250R	DPP10_ENST00000393147.2_Silent_p.R254R|DPP10_ENST00000409163.1_Silent_p.R200R|DPP10_ENST00000310323.8_Silent_p.R243R	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	250						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.R243R(1)|p.R250R(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGATGGAGAAAGACTTGCCTT	0.468																																																2	Substitution - coding silent(2)	large_intestine(2)	2											203	174	184					2																	116497365		2203	4299	6502	116213835	SO:0001819	synonymous_variant	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.748A>C	2.37:g.116497365A>C			116213835	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																				0.468	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116497365	A	C	116497365	2	2	73	1	0	0	0	0	0	0	0	1	4738	64	3	4		4	DPP10	2	116497365	Silent	SNP	A	TCGA-AG-A020-01A-21W-A096-10	19003508	116497365	126702008	10	21304										
KYNU	8942	broad.mit.edu	37	chr2	143743579	143743579	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	catgaaaagcatgcccatacGattaaacctgcgtgagtacc	8	11	0	2	rs140758594		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:143743579G>A	ENST00000264170.4	+	10	1149	c.891G>A	c.(889-891)acG>acA	p.T297T	KYNU_ENST00000375773.2_Silent_p.T297T|KYNU_ENST00000409512.1_Silent_p.T297T	NM_003937.2	NP_003928.1			kynureninase									p.T297T(2)		large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		ATGCCCATACGATTAAACCTG	0.328																																																2	Substitution - coding silent(2)	large_intestine(2)	2						G	,,	1,4405	4.2+/-10.8	0,1,2202	75	75	75		891,891,891	-7.6	0	2	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	KYNU	NM_001032998.1,NM_001199241.1,NM_003937.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	297/308,297/466,297/466	143743579	1,13005	2203	4300	6503	143460049	SO:0001819	synonymous_variant	8942			U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.891G>A	2.37:g.143743579G>A			143460049		Silent	SNP	ENST00000264170.4	37	CCDS2183.1																																																																																				0.328	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998		A	143743579	G	A	143743579	2	1	73	1	0	0	0	0	0	0	0	1	8609	1045	37	1		1	KYNU	2	143743579	Silent	SNP	G	TCGA-AG-A020-01A-21W-A096-10	27246214	143743579	99455794	11	21305										
TTN	7273	broad.mit.edu	37	chr2	179604188	179604188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cctcagcttcctgtatctttActgtagcaacctcctcagta	5	14	3	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:179604188A>G	ENST00000591111.1	-	46	13045	c.12821T>C	c.(12820-12822)gTa>gCa	p.V4274A	TTN_ENST00000342175.6_Missense_Mutation_p.V4420A|TTN_ENST00000359218.5_Missense_Mutation_p.V4353A|TTN_ENST00000460472.2_Missense_Mutation_p.V4228A|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V4591A|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32487					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V4228A(1)|p.V4420A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGTATCTTTACTGTAGCAAC	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	2											126	118	121					2																	179604188		1930	4139	6069	179312433	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12821T>C	2.37:g.179604188A>G	ENSP00000465570:p.Val4274Ala		179312433	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	1.815	-0.473732	0.04414	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.61742	0.13;0.09;0.08	5.29	-10.6	0.00265	.	.	.	.	.	T	0.33059	0.0850	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34551	-0.9824	9	0.87932	D	0	.	1.4454	0.02363	0.1771:0.1576:0.2806:0.3847	.	4228;4353;4420	D3DPF9;E7EQE6;E7ET18	.;.;.	A	4228;4420;4353;4228	ENSP00000434586:V4228A;ENSP00000340554:V4420A;ENSP00000352154:V4353A	ENSP00000340554:V4420A	V	-	2	0	TTN	179312433	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.563000	0.05943	-2.822000	0.00343	-0.327000	0.08410	GTA		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179604188	A	G	179604188	3	3	73	1	0	0	0	0	1	0	0	0	16775	391	14	4	91017	4	TTN	2	179604188	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10	35860609	179604188	63595185	12	21306										
ALS2	57679	broad.mit.edu	37	chr2	202614457	202614457	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ttgcaagacgaggaactgttGttggaaaatcggaatgccca	12	7	0	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr2:202614457G>T	ENST00000264276.6	-	8	2165	c.1793C>A	c.(1792-1794)aCa>aAa	p.T598K		NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	598					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.T598K(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						AGGAACTGTTGTTGGAAAATC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	102	104					2																	202614457		1858	4089	5947	202322702	SO:0001583	missense	57679			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1793C>A	2.37:g.202614457G>T	ENSP00000264276:p.Thr598Lys		202322702	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784941	0.70222	.	.	ENSG00000003393	ENST00000264276	T	0.79845	-1.31	5.87	5.87	0.94306	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.047300	0.85682	D	0.000000	T	0.76040	0.3932	N	0.25060	0.705	0.80722	D	1	P;B;P	0.44478	0.836;0.437;0.629	B;B;B	0.44163	0.319;0.443;0.243	T	0.76386	-0.2978	10	0.46703	T	0.11	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	598;598;598	Q96Q42-3;Q6IQ41;Q96Q42	.;.;ALS2_HUMAN	K	598	ENSP00000264276:T598K	ENSP00000264276:T598K	T	-	2	0	ALS2	202322702	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.189000	0.58358	2.941000	0.99782	0.655000	0.94253	ACA		0.368	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		T	202614457	G	T	202614457	3	4	73	1	0	0	0	0	1	0	0	0	550	1377	48	2	3288	2	ALS2	2	202614457	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	23010269	202614457	40584916	13	21307										
FBLN2	2199	broad.mit.edu	37	chr3	13678033	13678033	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	agcttccgctgcctgcgcttCgagtgtcctcccaactatgt	9	15	0	0	rs17854691		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr3:13678033C>T	ENST00000295760.7	+	16	3231	c.3162C>T	c.(3160-3162)ttC>ttT	p.F1054F	FBLN2_ENST00000404922.3_Silent_p.F1101F|FBLN2_ENST00000492059.1_Silent_p.F1101F|FBLN2_ENST00000535798.1_Silent_p.F1080F	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	1054	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)	p.F520F(1)|p.F1101F(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GCCTGCGCTTCGAGTGTCCTC	0.592																																																2	Substitution - coding silent(2)	large_intestine(2)	3						C	,,	1,4363		0,1,2181	63	72	69		3303,3303,3162	-3.7	0.6	3	dbSNP_123	69	3,8567		0,3,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	0,4,6463	TT,TC,CC		0.035,0.0229,0.0309	,,	1101/1232,1101/1232,1054/1185	13678033	4,12930	2182	4285	6467	13653034	SO:0001819	synonymous_variant	2199			X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.3162C>T	3.37:g.13678033C>T			13653034	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1	.	.	.	.	.	.	.	.	.	.	C	6.708	0.499313	0.12762	2.29E-4	3.5E-4	ENSG00000163520	ENST00000295761;ENST00000421373	.	.	.	4.91	-3.65	0.04502	.	.	.	.	.	T	0.50871	0.1641	.	.	.	0.51482	D	0.99992	.	.	.	.	.	.	T	0.47182	-0.9137	4	.	.	.	.	7.9235	0.29861	0.0:0.2474:0.1181:0.6345	.	.	.	.	L	73;30	.	.	S	+	2	0	FBLN2	13653034	0.000000	0.05858	0.558000	0.28319	0.621000	0.37620	-1.542000	0.02196	-0.832000	0.04251	-1.080000	0.02220	TCG		0.592	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		T	13678033	C	T	13678033	2	4	73	1	0	0	0	0	0	0	0	1	5718	883	31	1		1	FBLN2	3	13678033	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10		13678033	184344397	14	21308										
CTNNB1	1499	broad.mit.edu	37	chr3	41274897	41274897	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gtcttgttcagaactgtcttTggactctcaggaatctttca	8	9	6	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr3:41274897T>G	ENST00000349496.5	+	8	1427	c.1147T>G	c.(1147-1149)Tgg>Ggg	p.W383G	CTNNB1_ENST00000405570.1_Missense_Mutation_p.W383G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.W383G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.W383G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.W376G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	383					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.W383G(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GAACTGTCTTTGGACTCTCAG	0.408		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	1	Substitution - Missense(1)	large_intestine(1)	3											105	96	99					3																	41274897		2203	4300	6503	41249901	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1147T>G	3.37:g.41274897T>G	ENSP00000344456:p.Trp383Gly		41249901	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.405136	0.83230	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85509	0.5713	M	0.87269	2.87	0.80722	D	1	P;D	0.89917	0.858;1.0	B;D	0.79784	0.386;0.993	D	0.85685	0.1303	10	0.34782	T	0.22	-7.7281	15.9983	0.80268	0.0:0.0:0.0:1.0	.	311;383	B4DSW9;P35222	.;CTNB1_HUMAN	G	383;383;383;376;383	ENSP00000385604:W383G;ENSP00000379486:W383G;ENSP00000344456:W383G;ENSP00000411226:W376G;ENSP00000379488:W383G	ENSP00000344456:W383G	W	+	1	0	CTNNB1	41249901	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.171000	0.68590	0.533000	0.62120	TGG		0.408	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41274897	T	G	41274897	3	3	73	1	0	0	0	0	1	0	0	0	4022	1812	63	4	1173	4	CTNNB1	3	41274897	Missense_Mutation	SNP	T	TCGA-AG-A020-01A-21W-A096-10	27596864	41274897	156747533	15	21309										
CACNA2D3	55799	broad.mit.edu	37	chr3	54603874	54603874	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	attgccttcgactgcaggaaCcgaaaatggtaggcagtggt	13	8	0	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr3:54603874C>T	ENST00000474759.1	+	7	777	c.729C>T	c.(727-729)aaC>aaT	p.N243N	CACNA2D3_ENST00000490478.1_Silent_p.N149N|CACNA2D3_ENST00000288197.5_Silent_p.N243N|CACNA2D3_ENST00000415676.2_Silent_p.N243N	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	243						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.N243N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	ACTGCAGGAACCGAAAATGGT	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	3											71	68	69					3																	54603874		1860	4106	5966	54578914	SO:0001819	synonymous_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.729C>T	3.37:g.54603874C>T			54578914	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																				0.378	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54603874	C	T	54603874	2	4	73	1	0	0	0	0	0	0	0	1	2556	506	18	3		3	CACNA2D3	3	54603874	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	13328977	54603874	143418556	16	21310										
CACNA2D3	55799	broad.mit.edu	37	chr3	55038848	55038848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	acaaggaaagcagcgatggcGcccatggcctcctggatgta	13	11	0	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr3:55038848G>A	ENST00000474759.1	+	32	2797	c.2749G>A	c.(2749-2751)Gcc>Acc	p.A917T	CACNA2D3_ENST00000490478.1_Missense_Mutation_p.A823T|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.A917T|CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.A917T	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	917						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.A917T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAGCGATGGCGCCCATGGCCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											113	109	110					3																	55038848		1956	4148	6104	55013888	SO:0001583	missense	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2749G>A	3.37:g.55038848G>A	ENSP00000419101:p.Ala917Thr		55013888	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	32	5.109610	0.94292	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	6.17	6.17	0.99709	.	0.244180	0.41938	D	0.000793	T	0.72526	0.3471	M	0.68952	2.095	0.48762	D	0.999701	P	0.35908	0.527	B	0.26770	0.073	T	0.74861	-0.3520	10	0.72032	D	0.01	.	19.0599	0.93085	0.0:0.0:1.0:0.0	.	917	Q8IZS8	CA2D3_HUMAN	T	917;917;917;823;823	ENSP00000389506:A917T;ENSP00000419101:A917T;ENSP00000288197:A917T;ENSP00000417279:A823T	ENSP00000288197:A917T	A	+	1	0	CACNA2D3	55013888	1.000000	0.71417	0.916000	0.36221	0.991000	0.79684	5.543000	0.67225	2.941000	0.99782	0.655000	0.94253	GCC		0.448	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	55038848	G	A	55038848	3	1	73	1	0	0	0	0	1	0	0	0	2556	1087	38	1	2875	1	CACNA2D3	3	55038848	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	434974	55038848	142983582	17	21311										
PIK3CA	5290	broad.mit.edu	37	chr3	178919287	178919287	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ttttaaaagtgtgtggatgtGatgaatacttcctagaaaaa	9	3	0	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr3:178919287G>A	ENST00000263967.3	+	4	929	c.772G>A	c.(772-774)Gat>Aat	p.D258N		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	258	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D258N(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTGTGGATGTGATGAATACTT	0.299		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	large_intestine(1)	3											50	49	49					3																	178919287		1807	4077	5884	180401981	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.772G>A	3.37:g.178919287G>A	ENSP00000263967:p.Asp258Asn		180401981	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.320599	0.60634	.	.	ENSG00000121879	ENST00000263967	T	0.46451	0.87	5.56	5.56	0.83823	Phosphoinositide 3-kinase, ras-binding (2);	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	L	0.37630	1.12	0.80722	D	1	B	0.22851	0.076	B	0.27170	0.077	T	0.10337	-1.0634	10	0.23302	T	0.38	-10.7335	19.9052	0.97004	0.0:0.0:1.0:0.0	.	258	P42336	PK3CA_HUMAN	N	258	ENSP00000263967:D258N	ENSP00000263967:D258N	D	+	1	0	PIK3CA	180401981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.358000	0.97109	2.776000	0.95493	0.655000	0.94253	GAT		0.299	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178919287	G	A	178919287	3	1	73	1	0	0	0	0	1	0	0	0	11944	1290	45	3	782	3	PIK3CA	3	178919287	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	123880439	178919287	19103143	18	21312										
GRXCR1	389207	broad.mit.edu	37	chr4	43032468	43032468	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggagcaagatgtccatgtttCgaaactgcttcacagactct	9	10	2	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr4:43032468C>T	ENST00000399770.2	+	4	784	c.784C>T	c.(784-786)Cga>Tga	p.R262*		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	262					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)	p.R262*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GTCCATGTTTCGAAACTGCTT	0.473																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											174	164	167					4																	43032468		1945	4152	6097	42727225	SO:0001587	stop_gained	389207				CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.784C>T	4.37:g.43032468C>T	ENSP00000382670:p.Arg262*		42727225		Nonsense_Mutation	SNP	ENST00000399770.2	37	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728299	0.89390	.	.	ENSG00000215203	ENST00000399770	.	.	.	5.64	5.64	0.86602	.	0.282108	0.28983	U	0.013518	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.3762	18.6692	0.91504	0.0:1.0:0.0:0.0	.	.	.	.	X	262	.	ENSP00000382670:R262X	R	+	1	2	GRXCR1	42727225	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	5.588000	0.67517	2.649000	0.89929	0.579000	0.79373	CGA		0.473	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		T	43032468	C	T	43032468	4	4	73	1	0	0	0	0	0	1	0	0	6833	876	31	1	798	1	GRXCR1	4	43032468	Nonsense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		43032468	148121808	19	21313										
FRYL	285527	broad.mit.edu	37	chr4	48569287	48569287	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggaacattctgaataatattCgccactaaggcactaaaatg	7	8	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr4:48569287C>T	ENST00000503238.1	-	25	3146	c.3147G>A	c.(3145-3147)gcG>gcA	p.A1049A	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Silent_p.A1049A|FRYL_ENST00000507711.1_Silent_p.A1049A|FRYL_ENST00000358350.4_Silent_p.A1049A			O94915	FRYL_HUMAN	FRY-like	1049					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.A1049A(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GAATAATATTCGCCACTAAGG	0.328																																																1	Substitution - coding silent(1)	large_intestine(1)	4											108	97	100					4																	48569287		1847	4109	5956	48264044	SO:0001819	synonymous_variant	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.3147G>A	4.37:g.48569287C>T			48264044	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1																																																																																				0.328	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48569287	C	T	48569287	2	4	73	1	0	0	0	0	0	0	0	1	6083	871	31	1		1	FRYL	4	48569287	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	5536819	48569287	142584989	20	21314										
APC	324	broad.mit.edu	37	chr5	112175021	112175022	+	Frame_Shift_Ins	INS	-	-	A													0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gagtagaagtggtcagcctcINSaaaaggctgccacttgcaaa					rs79122263		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:112175021_112175022insA	ENST00000457016.1	+	16	4110_4111	c.3730_3731insA	c.(3730-3732)caafs	p.Q1244fs	APC_ENST00000508376.2_Frame_Shift_Ins_p.Q1244fs|APC_ENST00000257430.4_Frame_Shift_Ins_p.Q1244fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1244	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.A1246fs*10(1)|p.Q1244*(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGTCAGCCTCAAAAGGCTGCC	0.396		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Substitution - Nonsense(1)|Unknown(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CM010756	APC	M	rs79122263																																			112202921	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3734dupA	5.37:g.112175025_112175025dupA	ENSP00000413133:p.Gln1244fs		112202920	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.396	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175022	-	A	112175021	7	5	73	1	0	1	1	0	0	0	0	0	763	827	29	0	3788	0	APC	5	112175021	Frame_Shift_Ins	INS	-	TCGA-AG-A020-01A-21W-A096-10		112175021	68740239	21	21315										
APC	324	broad.mit.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	73	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	618	112175639	68739621	22	21316										
HAND1	9421	broad.mit.edu	37	chr5	153857052	153857052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccttttccgcttgctctcacGgccgccatccgccttcttga	7	18	2	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:153857052G>A	ENST00000231121.2	-	1	772	c.517C>T	c.(517-519)Cgt>Tgt	p.R173C		NM_004821.2	NP_004812.1	O96004	HAND1_HUMAN	heart and neural crest derivatives expressed 1	173					angiogenesis (GO:0001525)|blastocyst development (GO:0001824)|cardiac left ventricle formation (GO:0003218)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cartilage morphogenesis (GO:0060536)|embryonic heart tube development (GO:0035050)|embryonic heart tube formation (GO:0003144)|heart development (GO:0007507)|heart looping (GO:0001947)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)|trophoblast giant cell differentiation (GO:0060707)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R173C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TTGCTCTCACGGCCGCCATCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	5											94	91	92					5																	153857052		2203	4300	6503	153837245	SO:0001583	missense	9421			AF061756	CCDS4327.1	5q33	2013-05-21			ENSG00000113196	ENSG00000113196		"Basic helix-loop-helix proteins"	4807	protein-coding gene	gene with protein product		602406				9337404, 9931445	Standard	NM_004821		Approved	eHand, Thing1, Hxt, bHLHa27	uc003lvn.3	O96004	OTTHUMG00000130193	ENST00000231121.2:c.517C>T	5.37:g.153857052G>A	ENSP00000231121:p.Arg173Cys		153837245		Missense_Mutation	SNP	ENST00000231121.2	37	CCDS4327.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.750396	0.69533	.	.	ENSG00000113196	ENST00000231121	D	0.95949	-3.86	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.95567	0.8559	L	0.38175	1.15	0.54753	D	0.999983	D	0.89917	1.0	P	0.62184	0.899	D	0.95684	0.8734	10	0.59425	D	0.04	-22.2536	14.3607	0.66768	0.0:0.0:1.0:0.0	.	173	O96004	HAND1_HUMAN	C	173	ENSP00000231121:R173C	ENSP00000231121:R173C	R	-	1	0	HAND1	153837245	0.859000	0.29813	0.998000	0.56505	0.920000	0.55202	0.477000	0.22196	2.448000	0.82819	0.462000	0.41574	CGT		0.622	HAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252511.1	NM_004821		A	153857052	G	A	153857052	3	1	73	1	0	0	0	0	1	0	0	0	6970	1116	39	1	138	1	HAND1	5	153857052	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	41681413	153857052	27058208	23	21317										
ODZ2	57451	broad.mit.edu	37	chr5	167674074	167674074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccgtcaccttcgggtatgacGagaccactggtgtcttgaag	12	11	2	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:167674074G>A	ENST00000518659.1	+	27	6169	c.6130G>A	c.(6130-6132)Gag>Aag	p.E2044K	TENM2_ENST00000519204.1_Missense_Mutation_p.E1923K|TENM2_ENST00000520394.1_Missense_Mutation_p.E1805K|TENM2_ENST00000545108.1_Missense_Mutation_p.E2043K|TENM2_ENST00000403607.2_Missense_Mutation_p.E1868K	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2044					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.E1877K(1)									CGGGTATGACGAGACCACTGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											80	79	80					5																	167674074		1934	4143	6077	167606652	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6130G>A	5.37:g.167674074G>A	ENSP00000429430:p.Glu2044Lys		167606652	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	23.2	4.390428	0.82902	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90620	-2.23;-2.22;-2.33;-2.65;-2.7	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	M	0.84433	2.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.999;0.998;0.98	D	0.96218	0.9158	10	0.72032	D	0.01	.	19.2461	0.93902	0.0:0.0:1.0:0.0	.	2043;2044;1805	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	K	2044;2043;1923;1805;1868	ENSP00000429430:E2044K;ENSP00000438635:E2043K;ENSP00000428964:E1923K;ENSP00000427874:E1805K;ENSP00000384905:E1868K	ENSP00000384905:E1868K	E	+	1	0	ODZ2	167606652	1.000000	0.71417	0.987000	0.45799	0.790000	0.44656	9.869000	0.99810	2.560000	0.86352	0.561000	0.74099	GAG		0.532	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167674074	G	A	167674074	3	1	73	1	0	0	0	0	1	0	0	0	10866	1059	37	1	6209	1	ODZ2	5	167674074	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	13817022	167674074	13241186	24	21318										
DOCK2	1794	broad.mit.edu	37	chr5	169461428	169461428	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tggaatgtgctgcagagcacCcaaccattgccaagtcggtg	12	11	0	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:169461428C>A	ENST00000256935.8	+	35	3573	c.3493C>A	c.(3493-3495)Cca>Aca	p.P1165T	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.P657T|DOCK2_ENST00000540750.1_Missense_Mutation_p.P226T	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1165	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.P1165T(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGCAGAGCACCCAACCATTGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											95	90	92					5																	169461428		2203	4300	6503	169394006	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3493C>A	5.37:g.169461428C>A	ENSP00000256935:p.Pro1165Thr		169394006	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	7.423	0.637176	0.14386	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.39997	1.05;1.05;1.05	5.63	5.63	0.86233	.	0.243081	0.41605	D	0.000857	T	0.34135	0.0887	L	0.39397	1.21	0.28165	N	0.928823	B;B	0.15473	0.0;0.013	B;B	0.06405	0.001;0.002	T	0.13415	-1.0510	10	0.31617	T	0.26	.	12.6264	0.56632	0.0:0.9237:0.0:0.0763	.	657;1165	E7ERW7;Q92608	.;DOCK2_HUMAN	T	1165;657;226	ENSP00000256935:P1165T;ENSP00000429283:P657T;ENSP00000438827:P226T	ENSP00000256935:P1165T	P	+	1	0	DOCK2	169394006	0.002000	0.14202	0.985000	0.45067	0.127000	0.20565	0.486000	0.22340	2.656000	0.90262	0.655000	0.94253	CCA		0.582	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169461428	C	A	169461428	3	1	73	1	0	0	0	0	1	0	0	0	4698	623	22	2	3631	2	DOCK2	5	169461428	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	1787354	169461428	11453832	25	21319										
GRM6	2916	broad.mit.edu	37	chr5	178413312	178413312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gcctgcgggcggcacagaccGcggccccaggctcagccacc	14	19	1	1	rs61733863	byFrequency	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr5:178413312G>A	ENST00000517717.1	-	9	1981	c.1943C>T	c.(1942-1944)gCg>gTg	p.A648V	GRM6_ENST00000231188.5_Missense_Mutation_p.A648V|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	648					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.A648V(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		GGCACAGACCGCGGCCCCAGG	0.642													g|||	3	0.000599042	0.0015	0	5008	,	,		17344	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	VAL/ALA	4,4402	8.1+/-20.4	0,4,2199	38	38	38		1943	2.3	0	5	dbSNP_129	38	3,8595	3.0+/-9.4	0,3,4296	yes	missense	GRM6	NM_000843.3	64	0,7,6495	AA,AG,GG		0.0349,0.0908,0.0538	benign	648/878	178413312	7,12997	2203	4299	6502	178345918	SO:0001583	missense	2916			U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1943C>T	5.37:g.178413312G>A	ENSP00000430767:p.Ala648Val		178345918		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	g	0.005	-2.201130	0.00296	9.08E-4	3.49E-4	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.88277	-2.36;-2.36	5.02	2.26	0.28386	GPCR, family 3, C-terminal (2);	.	.	.	.	T	0.78541	0.4299	N	0.13299	0.325	0.09310	N	1	P;B	0.42123	0.771;0.026	B;B	0.42555	0.391;0.025	T	0.65356	-0.6188	9	0.10377	T	0.69	.	9.5679	0.39409	0.1488:0.1203:0.7309:0.0	.	804;648	E7EX65;O15303	.;GRM6_HUMAN	V	804;648;648	ENSP00000231188:A648V;ENSP00000430767:A648V	ENSP00000231188:A648V	A	-	2	0	GRM6	178345918	0.083000	0.21467	0.000000	0.03702	0.004000	0.04260	1.437000	0.34991	0.016000	0.14998	-2.900000	0.00093	GCG		0.642	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			A	178413312	G	A	178413312	3	1	73	1	0	0	0	0	1	0	0	0	6822	1087	38	1	702	1	GRM6	5	178413312	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	8951884	178413312	2501948	26	21320										
DNAH8	1769	broad.mit.edu	37	chr6	38980051	38980051	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tgaacatatttcttagacaaGaaattgacagaatgcaaaga	7	5	1	6			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr6:38980051G>T	ENST00000359357.3	+	88	13035	c.12781G>T	c.(12781-12783)Gaa>Taa	p.E4261*	DNAH8_ENST00000441566.1_Nonsense_Mutation_p.E4225*			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4261					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E4261*(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TCTTAGACAAGAAATTGACAG	0.353																																																2	Substitution - Nonsense(2)	large_intestine(2)	6											112	108	109					6																	38980051		2203	4300	6503	39088029	SO:0001587	stop_gained	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12781G>T	6.37:g.38980051G>T	ENSP00000352312:p.Glu4261*		39088029	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Nonsense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	55	24.411429	0.99960	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	X	4466;4261;4225	.	ENSP00000333363:E4466X	E	+	1	0	DNAH8	39088029	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.830000	0.99415	2.937000	0.99478	0.650000	0.86243	GAA		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38980051	G	T	38980051	4	4	73	1	0	0	0	0	0	1	0	0	4618	943	33	2	13123	2	DNAH8	6	38980051	Nonsense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10		38980051	132135016	27	21321										
ZBTB24	9841	broad.mit.edu	37	chr6	109796613	109796613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gagttttacctgtgtgtgttCgcagatgtttctttagctga	11	6	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr6:109796613C>T	ENST00000230122.3	-	5	1444	c.1277G>A	c.(1276-1278)cGa>cAa	p.R426Q		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	426					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R426Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		TGTGTGTGTTCGCAGATGTTT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											229	184	199					6																	109796613		2203	4300	6503	109903306	SO:0001583	missense	9841			AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1277G>A	6.37:g.109796613C>T	ENSP00000230122:p.Arg426Gln		109903306	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	C	33	5.285572	0.95517	.	.	ENSG00000112365	ENST00000230122	T	0.02369	4.32	6.17	5.3	0.74995	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.050655	0.64402	D	0.000001	T	0.08313	0.0207	M	0.71581	2.175	0.42617	D	0.993337	D	0.89917	1.0	D	0.65140	0.932	T	0.02683	-1.1124	10	0.72032	D	0.01	-16.4091	16.944	0.86226	0.129:0.871:0.0:0.0	.	426	O43167	ZBT24_HUMAN	Q	426	ENSP00000230122:R426Q	ENSP00000230122:R426Q	R	-	2	0	ZBTB24	109903306	1.000000	0.71417	0.600000	0.28864	0.992000	0.81027	7.336000	0.79245	1.601000	0.50113	0.655000	0.94253	CGA		0.468	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		T	109796613	C	T	109796613	3	4	73	1	0	0	0	0	1	0	0	0	17570	884	31	1	828	1	ZBTB24	6	109796613	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	70816562	109796613	61318454	28	21322										
TRAF3IP2	10758	broad.mit.edu	37	chr6	111880737	111880737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tagacatgagtgttctgaagCcaggtgggcacatgctccta	12	9	1	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr6:111880737C>A	ENST00000340026.6	-	10	2190	c.1596G>T	c.(1594-1596)tgG>tgT	p.W532C	TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.W522C|TRAF3IP2-AS1_ENST00000442928.2_RNA|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.W523C|TRAF3IP2-AS1_ENST00000438298.2_RNA|TRAF3IP2_ENST00000368731.2_5'UTR|TRAF3IP2_ENST00000392556.4_Missense_Mutation_p.W111C|TRAF3IP2-AS1_ENST00000440395.1_RNA|TRAF3IP2-AS1_ENST00000449449.2_RNA|TRAF3IP2_ENST00000368735.1_Missense_Mutation_p.W67C|TRAF3IP2-AS1_ENST00000456352.2_RNA			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	532	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)			p.W532C(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		TGTTCTGAAGCCAGGTGGGCA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	6											110	109	109					6																	111880737		2203	4300	6503	111987430	SO:0001583	missense	10758			AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.1596G>T	6.37:g.111880737C>A	ENSP00000345984:p.Trp532Cys		111987430	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	C	22.5	4.300108	0.81136	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000392556;ENST00000340026;ENST00000359831;ENST00000368735	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	6.17	6.17	0.99709	.	0.114870	0.64402	D	0.000005	T	0.52500	0.1738	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.46456	-0.9190	10	0.56958	D	0.05	-22.3458	20.8794	0.99867	0.0:1.0:0.0:0.0	.	522	Q7Z6Q1	.	C	532;523;111;532;522;67	ENSP00000357750:W523C;ENSP00000376339:W111C;ENSP00000345984:W532C;ENSP00000352889:W522C;ENSP00000357724:W67C	ENSP00000345984:W532C	W	-	3	0	TRAF3IP2	111987430	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.676000	0.74498	2.941000	0.99782	0.655000	0.94253	TGG		0.522	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			A	111880737	C	A	111880737	3	1	73	1	0	0	0	0	1	0	0	0	16481	740	26	2	132	2	TRAF3IP2	6	111880737	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	2084124	111880737	59234330	29	21323										
LPA	4018	broad.mit.edu	37	chr6	161027610	161027610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gtgtcaggttgcagtactccCacctgacactgggatccctc	10	14	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr6:161027610C>A	ENST00000316300.5	-	17	2728	c.2684G>T	c.(2683-2685)tGg>tTg	p.W895L	LPA_ENST00000447678.1_Missense_Mutation_p.W895L			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3403	Kringle 8. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.W895L(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GCAGTACTCCCACCTGACACT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	6											120	126	124					6																	161027610		2126	4280	6406	160947600	SO:0001583	missense	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2684G>T	6.37:g.161027610C>A	ENSP00000321334:p.Trp895Leu		160947600	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	c	11.86	1.764728	0.31228	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.63096	-0.02;-0.02	2.18	2.18	0.27775	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.71888	0.3393	H	0.95539	3.685	0.23468	N	0.99762	P	0.49307	0.922	D	0.68621	0.959	T	0.64415	-0.6413	9	0.15952	T	0.53	.	7.8483	0.29440	0.0:1.0:0.0:0.0	.	3403	P08519	APOA_HUMAN	L	895	ENSP00000321334:W895L;ENSP00000395608:W895L	ENSP00000321334:W895L	W	-	2	0	LPA	160947600	1.000000	0.71417	0.816000	0.32577	0.236000	0.25371	3.370000	0.52372	1.215000	0.43411	0.184000	0.17185	TGG		0.512	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	161027610	C	A	161027610	3	1	73	1	0	0	0	0	1	0	0	0	8932	595	21	2	3530	2	LPA	6	161027610	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	49146873	161027610	10087457	30	21324										
SMOC2	64094	broad.mit.edu	37	chr6	168999590	168999590	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tccctgagtgtgcgcacggcGgcctctacaagccagtgcag	13	14	1	1	rs561879643		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr6:168999590G>A	ENST00000356284.2	+	8	950	c.730G>A	c.(730-732)Ggc>Agc	p.G244S	SMOC2_ENST00000354536.5_Missense_Mutation_p.G255S	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	244	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.G255S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		TGCGCACGGCGGCCTCTACAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	6											94	69	77					6																	168999590		2203	4299	6502	168741515	SO:0001583	missense	64094			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"EF-hand domain containing"	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.730G>A	6.37:g.168999590G>A	ENSP00000348630:p.Gly244Ser		168741515	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	G	34	5.335070	0.95758	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	D;D	0.94723	-3.5;-3.5	4.89	4.89	0.63831	Thyroglobulin type-1 (5);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.98305	0.9438	H	0.97732	4.065	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.99761	1.1021	10	0.72032	D	0.01	-21.8918	17.1175	0.86694	0.0:0.0:1.0:0.0	.	244;255	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	S	244;255;244	ENSP00000348630:G244S;ENSP00000346537:G255S	ENSP00000346537:G255S	G	+	1	0	SMOC2	168741515	1.000000	0.71417	0.862000	0.33874	0.926000	0.56050	8.993000	0.93524	2.268000	0.75426	0.386000	0.25728	GGC		0.627	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1			A	168999590	G	A	168999590	3	1	73	1	0	0	0	0	1	0	0	0	14839	1116	39	1	793	1	SMOC2	6	168999590	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	7971980	168999590	2115477	31	21325										
HECW1	23072	broad.mit.edu	37	chr7	43484411	43484411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cgagctggagacggtgatcgCgtcagcctgcggggaccccg	17	13	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr7:43484411C>T	ENST00000395891.2	+	11	2245	c.1640C>T	c.(1639-1641)gCg>gTg	p.A547V	HECW1_ENST00000453890.1_Missense_Mutation_p.A547V	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	547					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.A526V(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACGGTGATCGCGTCAGCCTGC	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	7											41	51	48					7																	43484411		2101	4215	6316	43450936	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1640C>T	7.37:g.43484411C>T	ENSP00000379228:p.Ala547Val		43450936	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849118	0.91277	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.53857	1.13;0.6	5.32	5.32	0.75619	.	0.277160	0.41194	D	0.000921	T	0.69305	0.3096	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.64939	-0.6289	10	0.29301	T	0.29	.	19.0047	0.92846	0.0:1.0:0.0:0.0	.	547;547	B4DH42;Q76N89	.;HECW1_HUMAN	V	547	ENSP00000379228:A547V;ENSP00000407774:A547V	ENSP00000265522:A547V	A	+	2	0	HECW1	43450936	1.000000	0.71417	0.944000	0.38274	0.735000	0.41995	7.680000	0.84062	2.475000	0.83589	0.655000	0.94253	GCG		0.687	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		T	43484411	C	T	43484411	3	4	73	1	0	0	0	0	1	0	0	0	7063	768	27	1	1674	1	HECW1	7	43484411	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		43484411	115654252	32	21326										
SAMD9	54809	broad.mit.edu	37	chr7	92732616	92732616	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cacactgtgatagtgaaatgGtggtatcaggcacatatgaa	11	6	1	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr7:92732616G>C	ENST00000379958.2	-	3	3064	c.2795C>G	c.(2794-2796)aCc>aGc	p.T932S		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	932						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.T932S(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TAGTGAAATGGTGGTATCAGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											55	55	55					7																	92732616		2172	4289	6461	92570552	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2795C>G	7.37:g.92732616G>C	ENSP00000369292:p.Thr932Ser		92570552	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.585368	0.28268	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.22134	1.97;2.77	4.68	1.74	0.24563	.	0.175400	0.35585	N	0.003113	T	0.16514	0.0397	L	0.59436	1.845	0.09310	N	1	B	0.22346	0.068	B	0.18561	0.022	T	0.21930	-1.0231	10	0.18710	T	0.47	-0.6752	6.4254	0.21766	0.1635:0.0:0.6908:0.1456	.	932	Q5K651	SAMD9_HUMAN	S	932	ENSP00000369292:T932S;ENSP00000414529:T932S	ENSP00000369292:T932S	T	-	2	0	SAMD9	92570552	0.923000	0.31300	0.456000	0.27044	0.861000	0.49209	1.861000	0.39438	0.600000	0.29862	-0.192000	0.12808	ACC		0.398	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92732616	G	C	92732616	3	2	73	1	0	0	0	0	1	0	0	0	13863	1261	44	5	1978	5	SAMD9	7	92732616	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	49248205	92732616	66406047	33	21327										
PEG10	23089	broad.mit.edu	37	chr7	94293392	94293392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	acgcaagatcagacgcctgcGccaaggcatggggtctgtca	13	12	3	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr7:94293392G>A	ENST00000482108.1	+	2	1003	c.524G>A	c.(523-525)cGc>cAc	p.R175H	PEG10_ENST00000488574.1_Missense_Mutation_p.R175H	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	175	Necessary for interaction with ALK1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R175H(1)|p.R175P(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	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)			AGACGCCTGCGCCAAGGCATG	0.527																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	7											140	146	144					7																	94293392		2020	4177	6197	94131328	SO:0001583	missense	23089			AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.524G>A	7.37:g.94293392G>A	ENSP00000417587:p.Arg175His		94131328	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	37	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154762	0.57259	.	.	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.14022	2.54;2.54	4.05	4.05	0.47172	Retrotransposon gag protein (1);	.	.	.	.	T	0.15522	0.0374	L	0.58510	1.815	0.24211	N	0.995479	P;P	0.39250	0.665;0.665	B;B	0.33799	0.108;0.17	T	0.11251	-1.0595	9	0.52906	T	0.07	.	14.1258	0.65219	0.0:0.0:1.0:0.0	.	251;175	B4DSP0;Q86TG7	.;PEG10_HUMAN	H	175	ENSP00000417587:R175H;ENSP00000418944:R175H	ENSP00000417587:R175H	R	+	2	0	PEG10	94131328	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	2.305000	0.43664	2.276000	0.75962	0.555000	0.69702	CGC		0.527	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		A	94293392	G	A	94293392	3	1	73	1	0	0	0	0	1	0	0	0	11750	1087	38	1	758	1	PEG10	7	94293392	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	1560776	94293392	64845271	34	21328										
LRWD1	222229	broad.mit.edu	37	chr7	102106371	102106371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	caaccacctggagacgctgcCggacaacctgggcctgtccc	11	17	0	1	rs371342787		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr7:102106371C>T	ENST00000292616.5	+	2	340	c.188C>T	c.(187-189)cCg>cTg	p.P63L	MIR5090_ENST00000582533.1_RNA|ALKBH4_ENST00000292566.3_5'Flank	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	63					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)	p.P63L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						GAGACGCTGCCGGACAACCTG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	LEU/PRO	0,4406		0,0,2203	48	49	49		188	5	0.6	7		49	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRWD1	NM_152892.1	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	63/648	102106371	1,13005	2203	4300	6503	101893376	SO:0001583	missense	222229			AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"WD repeat domain containing"	21769	protein-coding gene	gene with protein product	"origin recognition complex associated", "centromere protein 33"	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.188C>T	7.37:g.102106371C>T	ENSP00000292616:p.Pro63Leu		101893376	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	37	CCDS34715.1	.	.	.	.	.	.	.	.	.	.	C	33	5.218050	0.95104	0.0	1.16E-4	ENSG00000161036	ENST00000292616	T	0.28895	1.59	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.63343	0.2503	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71932	-0.4443	10	0.87932	D	0	-11.7684	17.3718	0.87380	0.0:1.0:0.0:0.0	.	63	Q9UFC0	LRWD1_HUMAN	L	63	ENSP00000292616:P63L	ENSP00000292616:P63L	P	+	2	0	LRWD1	101893376	1.000000	0.71417	0.551000	0.28230	0.937000	0.57800	6.846000	0.75399	2.349000	0.79799	0.561000	0.74099	CCG		0.622	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		T	102106371	C	T	102106371	3	4	73	1	0	0	0	0	1	0	0	0	9076	652	23	1	194	1	LRWD1	7	102106371	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	7812979	102106371	57032292	35	21329										
CSMD1	64478	broad.mit.edu	37	chr8	3263696	3263696	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aaacctgtcaccaaaacgtcGtccgtttataggaatgccag	8	11	1	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr8:3263696G>A	ENST00000520002.1	-	16	2677	c.2122C>T	c.(2122-2124)Cga>Tga	p.R708*	CSMD1_ENST00000602557.1_Nonsense_Mutation_p.R708*|CSMD1_ENST00000537824.1_Nonsense_Mutation_p.R707*|CSMD1_ENST00000539096.1_Nonsense_Mutation_p.R707*|CSMD1_ENST00000602723.1_Nonsense_Mutation_p.R708*|CSMD1_ENST00000400186.3_Nonsense_Mutation_p.R708*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.R707*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	708	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.R436*(1)|p.R707*(1)		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)		CCAAAACGTCGTCCGTTTATA	0.418																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											45	45	45					8																	3263696		1870	4108	5978	3251103	SO:0001587	stop_gained	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2122C>T	8.37:g.3263696G>A	ENSP00000430733:p.Arg708*		3251103	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.095341|8.095341	0.98651|0.98651	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	.|.	.|.	.|.	5.46|5.46	3.45|3.45	0.39498|0.39498	.|.	0.078833|.	0.52532|.	D|.	0.000073|.	.|T	.|0.55065	.|0.1897	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.64605	.|-0.6368	.|3	0.09590|.	T|.	0.72|.	.|.	11.8581|11.8581	0.52451|0.52451	0.0:0.0:0.4028:0.5972|0.0:0.0:0.4028:0.5972	.|.	.|.	.|.	.|.	X|M	708;708;570;707;707;707|187	.|.	ENSP00000320445:R570X|.	R|T	-|-	1|2	2|0	CSMD1|CSMD1	3251103|3251103	0.917000|0.917000	0.31117|0.31117	0.803000|0.803000	0.32268|0.32268	0.013000|0.013000	0.08279|0.08279	2.425000|2.425000	0.44723|0.44723	1.255000|1.255000	0.44051|0.44051	0.655000|0.655000	0.94253|0.94253	CGA|ACG		0.418	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3263696	G	A	3263696	4	1	73	1	0	0	0	0	0	1	0	0	3950	1153	40	1	8799	1	CSMD1	8	3263696	Nonsense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10		3263696	143100326	36	21330										
FZD3	7976	broad.mit.edu	37	chr8	28385090	28385090	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aatgcatccatccctgcacaAtataaggcttccacagtgac	6	13	0	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr8:28385090A>G	ENST00000240093.3	+	5	1291	c.813A>G	c.(811-813)caA>caG	p.Q271Q	RNA5SP259_ENST00000365541.1_RNA|FZD3_ENST00000537916.1_Silent_p.Q271Q	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	271					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q271Q(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TCCCTGCACAATATAAGGCTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	8											88	90	89					8																	28385090		2203	4299	6502	28441009	SO:0001819	synonymous_variant	7976			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.813A>G	8.37:g.28385090A>G			28441009	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																				0.383	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		G	28385090	A	G	28385090	2	3	73	1	0	0	0	0	0	0	0	1	6150	98	4	4		4	FZD3	8	28385090	Silent	SNP	A	TCGA-AG-A020-01A-21W-A096-10	25121394	28385090	117978932	37	21331										
CHRNB3	1142	broad.mit.edu	37	chr8	42587324	42587324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tcatcccatcgtcttccaaaGtcattcctctcattggagag	6	13	4	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr8:42587324G>A	ENST00000289957.2	+	5	1002	c.874G>A	c.(874-876)Gtc>Atc	p.V292I		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	292					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)	p.V292I(1)		endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	GTCTTCCAAAGTCATTCCTCT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											270	245	254					8																	42587324		2203	4300	6503	42706481	SO:0001583	missense	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.874G>A	8.37:g.42587324G>A	ENSP00000289957:p.Val292Ile		42706481	Q15827	Missense_Mutation	SNP	ENST00000289957.2	37	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	32	5.160200	0.94727	.	.	ENSG00000147432	ENST00000289957	D	0.88124	-2.34	5.85	5.85	0.93711	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95284	0.8470	M	0.91354	3.2	0.80722	D	1	D	0.71674	0.998	D	0.85130	0.997	D	0.95341	0.8438	10	0.66056	D	0.02	.	20.2225	0.98327	0.0:0.0:1.0:0.0	.	292	Q05901	ACHB3_HUMAN	I	292	ENSP00000289957:V292I	ENSP00000289957:V292I	V	+	1	0	CHRNB3	42706481	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	9.869000	0.99810	2.778000	0.95560	0.650000	0.86243	GTC		0.403	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			A	42587324	G	A	42587324	3	1	73	1	0	0	0	0	1	0	0	0	3398	1029	36	3	892	3	CHRNB3	8	42587324	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	14202234	42587324	103776698	38	21332										
CYP7B1	9420	broad.mit.edu	37	chr8	65528278	65528279	+	Missense_Mutation	DNP	AT	AT	TA													0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aaggtcctcgtgcacataatAtttctccaggacatcttgcc							TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr8:65528278_65528279AT>TA	ENST00000310193.3	-	3	992_993	c.819_820AT>TA	c.(817-822)aaATat>aaTAat	p.273_274KY>NN	CYP7B1_ENST00000523954.1_5'UTR	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	273					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)	p.K273>?(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TGCACATAATATTTCTCCAGGA	0.351																																																1	Complex(1)	large_intestine(1)	8																																								65690833	SO:0001583	missense	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.819_820delinsTA	8.37:g.65528278_65528279delinsTA	ENSP00000310721:p.K273_Y274delinsNN		65690832	B2RN07|Q9UNF5	Missense_Mutation	DNP	ENST00000310193.3	37	CCDS6180.1																																																																																				0.351	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			TA	65528279	AT	TA	65528278	3	4	73	1	0	0	0	0	1	0	0	0	4203	449	16	5	716	5	CYP7B1	8	65528278	Missense_Mutation	DNP	AT	TCGA-AG-A020-01A-21W-A096-10	22940954	65528278	80835744	39	21333										
RIMS2	9699	broad.mit.edu	37	chr8	104898096	104898096	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gaggctcagggaccaagttcTtatgcacaaaggaccacaaa	10	10	2	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr8:104898096T>G	ENST00000436393.2	+	2	844	c.603T>G	c.(601-603)tcT>tcG	p.S201S	RIMS2_ENST00000507740.1_Silent_p.S231S|RIMS2_ENST00000262231.10_Silent_p.S231S|RIMS2_ENST00000406091.3_Silent_p.S423S			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	454					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.S231S(3)|p.S459S(2)|p.S201S(2)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GACCAAGTTCTTATGCACAAA	0.478										HNSCC(12;0.0054)																																						7	Substitution - coding silent(7)	large_intestine(7)	8											85	80	81					8																	104898096		1935	4137	6072	104967272	SO:0001819	synonymous_variant	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.603T>G	8.37:g.104898096T>G			104967272	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																					0.478	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104898096	T	G	104898096	2	3	73	1	0	0	0	0	0	0	0	1	13405	1596	56	4		4	RIMS2	8	104898096	Silent	SNP	T	TCGA-AG-A020-01A-21W-A096-10	39369818	104898096	41465926	40	21334										
KIAA1958	158405	broad.mit.edu	37	chr9	115422301	115422301	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gagaacttcacctttgtctcGttcactcaggtctcccggag	9	13	5	1	rs552377099		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr9:115422301G>A	ENST00000337530.6	+	4	2399	c.2103G>A	c.(2101-2103)tcG>tcA	p.S701S	KIAA1958_ENST00000536272.1_Silent_p.S729S	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	701								p.S701S(1)		endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CCTTTGTCTCGTTCACTCAGG	0.612													G|||	1	0.000199681	0	0	5008	,	,		18847	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9											71	70	70					9																	115422301		2203	4300	6503	114462122	SO:0001819	synonymous_variant	158405			AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.2103G>A	9.37:g.115422301G>A			114462122	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	37	CCDS35108.1																																																																																				0.612	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		A	115422301	G	A	115422301	2	1	73	1	0	0	0	0	0	0	0	1	8285	1132	40	1		1	KIAA1958	9	115422301	Silent	SNP	G	TCGA-AG-A020-01A-21W-A096-10		115422301	25791130	41	21335										
PAPPA	5069	broad.mit.edu	37	chr9	119028244	119028244	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	atccatggaagtgggtactgTggcgatggcattatacaaaa	12	6	0	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr9:119028244T>C	ENST00000328252.3	+	8	3210	c.2841T>C	c.(2839-2841)tgT>tgC	p.C947C	PAPPA_ENST00000534838.1_5'UTR	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	947					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.C947C(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						GTGGGTACTGTGGCGATGGCA	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	9											94	87	89					9																	119028244		2203	4300	6503	118068065	SO:0001819	synonymous_variant	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2841T>C	9.37:g.119028244T>C			118068065	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																				0.438	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		C	119028244	T	C	119028244	2	2	73	1	0	0	0	0	0	0	0	1	11463	1702	59	4		4	PAPPA	9	119028244	Silent	SNP	T	TCGA-AG-A020-01A-21W-A096-10	3605943	119028244	22185187	42	21336										
TET1	80312	broad.mit.edu	37	chr10	70404538	70404538	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggtcatggggaagaacaaaaAttggaattgaacccacatac	10	7	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr10:70404538A>C	ENST00000373644.4	+	4	2261	c.2052A>C	c.(2050-2052)aaA>aaC	p.K684N		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	684					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.K684N(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AAGAACAAAAATTGGAATTGA	0.393																																																2	Substitution - Missense(2)	large_intestine(2)	10											65	61	62					10																	70404538		2203	4300	6503	70074544	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.2052A>C	10.37:g.70404538A>C	ENSP00000362748:p.Lys684Asn		70074544	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.200391	0.38905	.	.	ENSG00000138336	ENST00000373644	T	0.08546	3.08	5.93	2.29	0.28610	.	0.420483	0.23799	N	0.044445	T	0.03827	0.0108	N	0.14661	0.345	0.24774	N	0.99286	B	0.31125	0.309	B	0.23852	0.049	T	0.36648	-0.9739	10	0.72032	D	0.01	.	2.8236	0.05479	0.5125:0.0:0.29:0.1974	.	684	Q8NFU7	TET1_HUMAN	N	684	ENSP00000362748:K684N	ENSP00000362748:K684N	K	+	3	2	TET1	70074544	1.000000	0.71417	0.995000	0.50966	0.867000	0.49689	1.280000	0.33202	0.497000	0.27926	0.533000	0.62120	AAA		0.393	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70404538	A	C	70404538	3	2	73	1	0	0	0	0	1	0	0	0	15808	98	4	4	2062	4	TET1	10	70404538	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10		70404538	65130209	43	21337										
KIAA0913	23053	broad.mit.edu	37	chr10	75556556	75556556	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tagacaaactcttggaccgaGagagccagacacataagcca	9	11	1	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr10:75556556G>T	ENST00000605216.1	+	16	3260	c.3043G>T	c.(3043-3045)Gag>Tag	p.E1015*	ZSWIM8_ENST00000603114.1_Nonsense_Mutation_p.E982*|RP11-574K11.31_ENST00000603027.1_3'UTR|ZSWIM8_ENST00000604729.1_Nonsense_Mutation_p.E1020*|ZSWIM8_ENST00000604524.1_Nonsense_Mutation_p.E1015*|ZSWIM8_ENST00000398706.2_Nonsense_Mutation_p.E1020*|ZSWIM8-AS1_ENST00000456638.2_RNA	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1015							zinc ion binding (GO:0008270)	p.E1020*(1)									CTTGGACCGAGAGAGCCAGAC	0.527																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											51	55	54					10																	75556556		2032	4202	6234	75226562	SO:0001587	stop_gained	23053			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.3043G>T	10.37:g.75556556G>T	ENSP00000474748:p.Glu1015*		75226562	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Nonsense_Mutation	SNP	ENST00000605216.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	36|36|36	5.874733|5.874733|5.874733	0.97055|0.97055|0.97055	.|.|.	.|.|.	ENSG00000214655|ENSG00000214655|ENSG00000214655	ENST00000412198|ENST00000398706|ENST00000433366	.|.|.	.|.|.	.|.|.	5.3|5.3|5.3	5.3|5.3|5.3	0.74995|0.74995|0.74995	.|.|.	0.156200|0.156200|.	0.40728|0.40728|.	U|U|.	0.001029|0.001029|.	T|.|T	0.81475|.|0.81475	0.4830|.|0.4830	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	D|.|D	0.83921|.|0.83921	0.0301|.|0.0301	4|.|4	.|0.56958|0.87932	.|D|D	.|0.05|0	-8.3409|-8.3409|-8.3409	18.9581|18.9581|18.9581	0.92668|0.92668|0.92668	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	D|X|I	289|1020|730	.|.|.	.|ENSP00000381693:E1020X|ENSP00000387828:R730I	E|E|R	+|+|+	3|1|2	2|0|0	KIAA0913|KIAA0913|KIAA0913	75226562|75226562|75226562	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	9.649000|9.649000|9.649000	0.98487|0.98487|0.98487	2.482000|2.482000|2.482000	0.83794|0.83794|0.83794	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAG|GAG|AGA		0.527	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		T	75556556	G	T	75556556	4	4	73	1	0	0	0	0	0	1	0	0	8221	943	33	2	3120	2	KIAA0913	10	75556556	Nonsense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	5152018	75556556	59978191	44	21338										
OR10W1	81341	broad.mit.edu	37	chr11	58034657	58034657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aggtggagaaggcccggtggCggccagcagccgagtggatc	19	10	0	1	rs200070425		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr11:58034657C>T	ENST00000395079.2	-	1	1075	c.674G>A	c.(673-675)cGc>cAc	p.R225H		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R225H(1)		kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				GGCCCGGTGGCGGCCAGCAGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											76	75	75					11																	58034657		2201	4295	6496	57791233	SO:0001583	missense	81341			AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"GPCR / Class A : Olfactory receptors"	15139	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily W, member 1 pseudogene"	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.674G>A	11.37:g.58034657C>T	ENSP00000378516:p.Arg225His		57791233	A2RUD2|A8MTE1|Q6UXQ2	Missense_Mutation	SNP	ENST00000395079.2	37	CCDS7968.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614247	0.46631	.	.	ENSG00000172772	ENST00000395079	T	0.00333	8.07	6.01	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.128295	0.36167	N	0.002749	T	0.00468	0.0015	M	0.90019	3.08	0.09310	N	1	P	0.42337	0.776	B	0.36186	0.219	T	0.35025	-0.9805	10	0.87932	D	0	.	15.2235	0.73333	0.0:0.9318:0.0:0.0682	.	225	Q8NGF6	O10W1_HUMAN	H	225	ENSP00000378516:R225H	ENSP00000378516:R225H	R	-	2	0	OR10W1	57791233	0.000000	0.05858	0.907000	0.35723	0.837000	0.47467	0.291000	0.18994	1.548000	0.49413	0.655000	0.94253	CGC		0.587	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394704.1	NM_207374		T	58034657	C	T	58034657	3	4	73	1	0	0	0	0	1	0	0	0	10952	768	27	1	247	1	OR10W1	11	58034657	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		58034657	76971859	45	21339										
P2RY2	5029	broad.mit.edu	37	chr11	72945385	72945385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cgctctacatcttcttgtgcCgcctcaagacctggaatgcg	9	14	4	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr11:72945385C>T	ENST00000311131.2	+	3	648	c.181C>T	c.(181-183)Cgc>Tgc	p.R61C	P2RY2_ENST00000393597.2_Missense_Mutation_p.R61C|P2RY2_ENST00000393596.2_Missense_Mutation_p.R61C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	61					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)	p.R61C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CTTCTTGTGCCGCCTCAAGAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	11											225	185	199					11																	72945385		2200	4293	6493	72623033	SO:0001583	missense	5029			U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.181C>T	11.37:g.72945385C>T	ENSP00000310305:p.Arg61Cys		72623033	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532794	0.64972	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.72615	-0.67;-0.67;-0.67	5.28	4.37	0.52481	GPCR, rhodopsin-like superfamily (1);	0.056303	0.64402	N	0.000001	D	0.82416	0.5032	M	0.79805	2.47	0.58432	D	0.999992	D	0.89917	1.0	D	0.87578	0.998	T	0.83306	-0.0025	10	0.72032	D	0.01	.	8.9489	0.35776	0.1558:0.7643:0.0:0.0799	.	61	P41231	P2RY2_HUMAN	C	61	ENSP00000377222:R61C;ENSP00000310305:R61C;ENSP00000377221:R61C	ENSP00000310305:R61C	R	+	1	0	P2RY2	72623033	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.076000	0.50081	1.241000	0.43820	-0.194000	0.12790	CGC		0.582	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		T	72945385	C	T	72945385	3	4	73	1	0	0	0	0	1	0	0	0	11383	652	23	1	183	1	P2RY2	11	72945385	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	14910728	72945385	62061131	46	21340										
PAAF1	80227	broad.mit.edu	37	chr11	73610216	73610218	+	In_Frame_Del	DEL	GAG	GAG	-													0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	atgcctggacatttccagcaGaggaggtcttggtgtgtctt							TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	GAG	GAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr11:73610216_73610218delGAG	ENST00000310571.3	+	5	361_363	c.308_310delGAG	c.(307-312)agagga>aga	p.G105del	PAAF1_ENST00000543079.1_3'UTR|PAAF1_ENST00000541951.1_5'UTR|PAAF1_ENST00000376384.5_In_Frame_Del_p.G88del|PAAF1_ENST00000544909.1_In_Frame_Del_p.G106del|PAAF1_ENST00000535604.1_5'UTR|PAAF1_ENST00000536003.1_In_Frame_Del_p.G88del|PAAF1_ENST00000544552.1_In_Frame_Del_p.G88del	NM_025155.2	NP_079431.1	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	105					viral process (GO:0016032)	proteasome complex (GO:0000502)		p.G105delG(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					ATTTCCAGCAGAGGAGGTCTTGG	0.384																																																1	Deletion - In frame(1)	large_intestine(1)	11																																								73287866	SO:0001651	inframe_deletion	80227			BC006142	CCDS8226.1, CCDS58157.1, CCDS58158.1	11q13.4	2013-05-21	2007-08-16	2007-08-16	ENSG00000175575	ENSG00000175575		"WD repeat domain containing"	25687	protein-coding gene	gene with protein product			"WD repeat domain 71"	WDR71		15831487, 17317272, 17289585	Standard	NM_001267803		Approved	FLJ11848, Rpn14	uc001ouk.2	Q9BRP4	OTTHUMG00000168062	ENST00000310571.3:c.308_310delGAG	11.37:g.73610219_73610221delGAG	ENSP00000311665:p.Gly105del		73287864	A6NDR5|B4DPB0|B7ZAS9|Q4G165|Q53HS9|Q7Z500|Q8TBU6|Q9HAB6	In_Frame_Del	DEL	ENST00000310571.3	37	CCDS8226.1																																																																																				0.384	PAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397885.1	NM_025155		-	73610218	GAG	-	73610216	7	5	73	1	0	1	0	1	0	0	0	0	11393	942	33	0	326	0	PAAF1	11	73610216	In_Frame_Del	DEL	GAG	TCGA-AG-A020-01A-21W-A096-10	664831	73610216	61396300	47	21341										
KRAS	3845	broad.mit.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	73	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		25398284	108453611	48	21342										
KCNC2	3747	broad.mit.edu	37	chr12	75444461	75444461	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccatgtttgggggtacatatCcccataacccagggtagtca	10	11	1	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr12:75444461C>A	ENST00000549446.1	-	3	2004	c.1324G>T	c.(1324-1326)Gat>Tat	p.D442Y	KCNC2_ENST00000548513.1_Missense_Mutation_p.D442Y|KCNC2_ENST00000341669.3_Missense_Mutation_p.D442Y|KCNC2_ENST00000350228.2_Missense_Mutation_p.D442Y|KCNC2_ENST00000540018.1_Missense_Mutation_p.D442Y|KCNC2_ENST00000548243.1_5'UTR|KCNC2_ENST00000393288.2_Missense_Mutation_p.D442Y|KCNC2_ENST00000550433.1_Missense_Mutation_p.D442Y|KCNC2_ENST00000298972.1_Missense_Mutation_p.D442Y	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	442	Selectivity filter. {ECO:0000250}.				action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.D442Y(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GGGTACATATCCCCATAACCC	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	12											71	61	64					12																	75444461		2203	4300	6503	73730728	SO:0001583	missense	3747			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1324G>T	12.37:g.75444461C>A	ENSP00000449253:p.Asp442Tyr		73730728	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.020774	0.75275	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	D;D;D;D;D;D;D;D	0.99023	-5.34;-5.34;-5.34;-5.34;-5.34;-5.34;-5.34;-5.34	6.06	6.06	0.98353	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.99715	0.9890	H	0.99425	4.56	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	10	0.87932	D	0	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	442;442;442;442;442	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	Y	442	ENSP00000448301:D442Y;ENSP00000449941:D442Y;ENSP00000449253:D442Y;ENSP00000340121:D442Y;ENSP00000298972:D442Y;ENSP00000319877:D442Y;ENSP00000438423:D442Y;ENSP00000376966:D442Y	ENSP00000298972:D442Y	D	-	1	0	KCNC2	73730728	1.000000	0.71417	0.998000	0.56505	0.852000	0.48524	7.792000	0.85828	2.880000	0.98712	0.650000	0.86243	GAT		0.517	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75444461	C	A	75444461	3	1	73	1	0	0	0	0	1	0	0	0	8036	855	30	2	670	2	KCNC2	12	75444461	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	50046177	75444461	58407434	49	21343										
ULK1	8408	broad.mit.edu	37	chr12	132405904	132405904	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tgctgactggcatctgtgccTgacctttctggcctggctgg	13	12	2	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr12:132405904T>G	ENST00000321867.4	+	28	3502	c.3151T>G	c.(3151-3153)Tga>Gga	p.*1051G	ULK1_ENST00000540647.1_Nonstop_Mutation_p.*296G	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	0					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)	p.*1051G(1)		breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CATCTGTGCCTGACCTTTCTG	0.667																																																1	Nonstop extension(1)	large_intestine(1)	12											113	111	112					12																	132405904		2203	4300	6503	130971857	SO:0001578	stop_lost	8408			AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.3151T>G	12.37:g.132405904T>G	ENSP00000324560:p.*1051Glyext*36		130971857	Q9UQ28	Nonstop_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937694	0.52972	.	.	ENSG00000177169	ENST00000321867;ENST00000540647	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.205	0.65728	0.0:0.0:0.0:1.0	.	.	.	.	G	1051;296	.	.	X	+	1	0	ULK1	130971857	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	2.586000	0.46119	1.822000	0.53115	0.459000	0.35465	TGA		0.667	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			G	132405904	T	G	132405904	4	3	73	1	0	0	0	0	0	0	0	0	17015	1593	55	4	3261	4	ULK1	12	132405904	Nonstop_Mutation	SNP	T	TCGA-AG-A020-01A-21W-A096-10	56961443	132405904	1445991	50	21344										
PCCA	5095	broad.mit.edu	37	chr13	100909900	100909900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tggtggtgggaaaggcatgcGcattgcttgggatgatgaag	18	4	0	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr13:100909900G>A	ENST00000376285.1	+	9	727	c.689G>A	c.(688-690)cGc>cAc	p.R230H	PCCA_ENST00000376279.3_Missense_Mutation_p.R230H|PCCA_ENST00000376286.4_Missense_Mutation_p.R204H	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	230	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.R230H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	AAAGGCATGCGCATTGCTTGG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	13											131	111	117					13																	100909900		2203	4300	6503	99707901	SO:0001583	missense	5095			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.689G>A	13.37:g.100909900G>A	ENSP00000365462:p.Arg230His		99707901	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810635	0.90707	.	.	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285	D;D;D	0.97665	-4.48;-4.48;-4.48	4.82	4.82	0.62117	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.98899	0.9627	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.978;0.987	D	0.99737	1.1014	10	0.87932	D	0	.	17.8754	0.88824	0.0:0.0:1.0:0.0	.	230;204;230	C9JPQ8;P05165-2;P05165	.;.;PCCA_HUMAN	H	204;230;230	ENSP00000365463:R204H;ENSP00000365456:R230H;ENSP00000365462:R230H	ENSP00000365456:R230H	R	+	2	0	PCCA	99707901	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.208000	0.95075	2.212000	0.71576	0.563000	0.77884	CGC		0.443	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			A	100909900	G	A	100909900	3	1	73	1	0	0	0	0	1	0	0	0	11535	1087	38	1	723	1	PCCA	13	100909900	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10		100909900	14259978	51	21345										
OR4Q3	441669	broad.mit.edu	37	chr14	20215736	20215736	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ttgatagtggtaacagtgcaAgcccatgctcacctgctcca	9	12	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr14:20215736A>G	ENST00000331723.1	+	1	150	c.150A>G	c.(148-150)caA>caG	p.Q50Q		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q50Q(1)		NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TAACAGTGCAAGCCCATGCTC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	14											212	214	214					14																	20215736		2203	4300	6503	19285576	SO:0001819	synonymous_variant	441669			AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.150A>G	14.37:g.20215736A>G			19285576	Q6IEX4	Silent	SNP	ENST00000331723.1	37	CCDS32020.1																																																																																				0.398	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			G	20215736	A	G	20215736	2	3	73	1	0	0	0	0	0	0	0	1	11112	69	3	4		4	OR4Q3	14	20215736	Silent	SNP	A	TCGA-AG-A020-01A-21W-A096-10		20215736	87133804	52	21346										
C14orf149	112849	broad.mit.edu	37	chr14	59942587	59942587	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aagctaagggtgccacttacCctcacagctttccctgtgaa	8	13	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr14:59942587C>T	ENST00000247194.4	-	4	1052	c.939G>A	c.(937-939)agG>agA	p.R313R	L3HYPDH_ENST00000487285.1_Splice_Site_p.R142R|L3HYPDH_ENST00000543619.1_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	313					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)	p.R313R(1)								L-Proline(DB00172)	TGCCACTTACCCTCACAGCTT	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	14											83	82	82					14																	59942587		2203	4299	6502	59012340	SO:0001630	splice_region_variant	112849			AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"trans-L-3-hydroxyproline dehydratase"	614811	"chromosome 14 open reading frame 149"	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.939+1G>A	14.37:g.59942587C>T			59012340	Q96LJ5	Silent	SNP	ENST00000247194.4	37	CCDS9739.1																																																																																				0.448	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	Silent	T	59942587	C	T	59942587	5	4	73	1	0	0	0	0	0	0	1	0	1756	637	22	3	133	3	C14orf149	14	59942587	Splice_Site	SNP	C	TCGA-AG-A020-01A-21W-A096-10	39726851	59942587	47406953	53	21347										
RTN1	6252	broad.mit.edu	37	chr14	60212675	60212675	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tggagcaaatgtggattcttCcaataaatggtccttgatga	10	6	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr14:60212675C>G	ENST00000267484.5	-	2	1101	c.766G>C	c.(766-768)Gaa>Caa	p.E256Q		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	256					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)		p.E256Q(1)		central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GTGGATTCTTCCAATAAATGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	14											181	177	179					14																	60212675		2203	4300	6503	59282428	SO:0001583	missense	6252			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.766G>C	14.37:g.60212675C>G	ENSP00000267484:p.Glu256Gln		59282428	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	37	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047198	0.75846	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.30981	1.51	5.16	5.16	0.70880	.	0.380677	0.29328	N	0.012466	T	0.46190	0.1380	M	0.69823	2.125	0.38375	D	0.944966	D	0.67145	0.996	P	0.51657	0.676	T	0.48410	-0.9038	10	0.30078	T	0.28	.	18.6522	0.91433	0.0:1.0:0.0:0.0	.	256	Q16799	RTN1_HUMAN	Q	256;182	ENSP00000267484:E256Q	ENSP00000267484:E256Q	E	-	1	0	RTN1	59282428	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.323000	0.65858	2.399000	0.81585	0.557000	0.71058	GAA		0.438	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			G	60212675	C	G	60212675	3	3	73	1	0	0	0	0	1	0	0	0	13762	864	30	5	1661	5	RTN1	14	60212675	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	270088	60212675	47136865	54	21348										
SEL1L	6400	broad.mit.edu	37	chr14	81964374	81964374	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	actactgagcctcctgttagCgagatatcactagcaactga	8	11	1	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr14:81964374C>T	ENST00000336735.4	-	10	1106	c.990G>A	c.(988-990)tcG>tcA	p.S330S		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	330	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S330S(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CTCCTGTTAGCGAGATATCAC	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	14											72	66	68					14																	81964374		2203	4300	6503	81034127	SO:0001819	synonymous_variant	6400				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.990G>A	14.37:g.81964374C>T			81034127	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	37	CCDS9876.1																																																																																				0.403	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		T	81964374	C	T	81964374	2	4	73	1	0	0	0	0	0	0	0	1	14047	755	27	1		1	SEL1L	14	81964374	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	21751699	81964374	25385166	55	21349										
KIAA1409	57578	broad.mit.edu	37	chr14	94083506	94083506	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aacttgggaaaacaccttctCcccttagtggttcaggtgct	9	11	2	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr14:94083506C>G	ENST00000393151.2	+	28	4080	c.4080C>G	c.(4078-4080)ctC>ctG	p.L1360L	UNC79_ENST00000555664.1_Silent_p.L1360L|UNC79_ENST00000256339.4_Silent_p.L1183L|UNC79_ENST00000553484.1_Silent_p.L1382L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1360					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L1382L(1)|p.L1183L(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AACACCTTCTCCCCTTAGTGG	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	14											112	109	110					14																	94083506		2203	4300	6503	93153259	SO:0001819	synonymous_variant	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4080C>G	14.37:g.94083506C>G			93153259	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																					0.423	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94083506	C	G	94083506	2	3	73	1	0	0	0	0	0	0	0	1	8251	842	30	5		5	KIAA1409	14	94083506	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	12119132	94083506	13266034	56	21350										
GTF3C1	2975	broad.mit.edu	37	chr16	27549526	27549526	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	agcagtggtgtgaaggtctcGctggagctccccttgccacc	13	13	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr16:27549526G>A	ENST00000356183.4	-	3	598	c.583C>T	c.(583-585)Cga>Tga	p.R195*	GTF3C1_ENST00000561623.1_Nonsense_Mutation_p.R195*	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	195					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.R195*(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TGAAGGTCTCGCTGGAGCTCC	0.557																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											78	79	79					16																	27549526		2197	4300	6497	27457027	SO:0001587	stop_gained	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.583C>T	16.37:g.27549526G>A	ENSP00000348510:p.Arg195*		27457027	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Nonsense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	37	6.569659	0.97671	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	.	.	.	5.73	4.67	0.58626	.	0.126553	0.52532	D	0.000061	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.3041	11.5781	0.50875	0.0:0.0:0.6448:0.3552	.	.	.	.	X	195;193	.	ENSP00000348510:R195X	R	-	1	2	GTF3C1	27457027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.556000	0.53734	2.861000	0.98227	0.655000	0.94253	CGA		0.557	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		A	27549526	G	A	27549526	4	1	73	1	0	0	0	0	0	1	0	0	6893	1095	38	1	5886	1	GTF3C1	16	27549526	Nonsense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10		27549526	62805227	57	21351										
SPN	6693	broad.mit.edu	37	chr16	29676016	29676016	+	Frame_Shift_Del	DEL	G	G	-													0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cagtgaccgtgggagggtccGggggcgacaagggctctggg							TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr16:29676016delG	ENST00000360121.3	+	2	1059	c.967delG	c.(967-969)gggfs	p.G324fs	SPN_ENST00000395389.2_Frame_Shift_Del_p.G324fs	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G324fs*38(1)		central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						GGGAGGGTCCGGGGGCGACAA	0.697																																																1	Deletion - Frameshift(1)	large_intestine(1)	16											6	7	7					16																	29676016		2125	4210	6335	29583517	SO:0001589	frameshift_variant	6693			J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.967delG	16.37:g.29676016delG	ENSP00000353238:p.Gly324fs		29583517	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Frame_Shift_Del	DEL	ENST00000360121.3	37	CCDS10650.1																																																																																				0.697	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			-	29676016	G	-	29676016	7	5	73	1	0	1	0	1	0	0	0	0	15112	1116	39	0	969	0	SPN	16	29676016	Frame_Shift_Del	DEL	G	TCGA-AG-A020-01A-21W-A096-10	2126490	29676016	60678737	58	21352										
ITGAX	3687	broad.mit.edu	37	chr16	31383104	31383104	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	aaacttcaacctgctgctccCggtgcgtctgggcatgaacg	11	13	2	1	rs200637041	byFrequency	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr16:31383104C>T	ENST00000268296.4	+	17	2280	c.2159C>T	c.(2158-2160)cCg>cTg	p.P720L	ITGAX_ENST00000562522.1_Splice_Site_p.P720L	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	720					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.P720L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CTGCTGCTCCCGGTGCGTCTG	0.642													C|||	2	0.000399361	0	0.0014	5008	,	,		16934	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											49	43	45					16																	31383104		2197	4300	6497	31290605	SO:0001630	splice_region_variant	3687			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2160+1C>T	16.37:g.31383104C>T			31290605	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.03	2.711262	0.48517	.	.	ENSG00000140678	ENST00000268296	T	0.44881	0.91	5.4	-1.14	0.09741	Integrin alpha-2 (1);	.	.	.	.	T	0.21550	0.0519	L	0.39566	1.225	0.44492	D	0.997432	P	0.35174	0.488	B	0.25884	0.064	T	0.11203	-1.0597	9	0.31617	T	0.26	.	0.9333	0.01340	0.154:0.3642:0.1512:0.3306	.	720	P20702	ITAX_HUMAN	L	720	ENSP00000268296:P720L	ENSP00000268296:P720L	P	+	2	0	ITGAX	31290605	0.032000	0.19561	0.412000	0.26496	0.080000	0.17528	-0.167000	0.09940	-0.381000	0.07882	0.655000	0.94253	CCG		0.642	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	Missense_Mutation	T	31383104	C	T	31383104	5	4	73	1	0	0	0	0	0	0	1	0	7910	666	23	1	2225	1	ITGAX	16	31383104	Splice_Site	SNP	C	TCGA-AG-A020-01A-21W-A096-10	1707088	31383104	58971649	59	21353										
PLCG2	5336	broad.mit.edu	37	chr16	81927346	81927346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tgaccagctgcggagcgagtCgtccccagaagcttacatcc	11	14	0	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr16:81927346C>T	ENST00000359376.3	+	12	1233	c.1019C>T	c.(1018-1020)tCg>tTg	p.S340L		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	340	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S340L(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CGGAGCGAGTCGTCCCCAGAA	0.617																																																2	Substitution - Missense(2)	large_intestine(2)	16											63	66	65					16																	81927346		2171	4287	6458	80484847	SO:0001583	missense	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1019C>T	16.37:g.81927346C>T	ENSP00000352336:p.Ser340Leu		80484847	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251486	0.80135	.	.	ENSG00000197943	ENST00000359376	T	0.70045	-0.45	3.71	3.71	0.42584	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.123749	0.56097	D	0.000027	D	0.88676	0.6501	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.966	D	0.93600	0.6929	10	0.87932	D	0	.	16.357	0.83239	0.0:1.0:0.0:0.0	.	207;340	B4E3H3;P16885	.;PLCG2_HUMAN	L	340	ENSP00000352336:S340L	ENSP00000352336:S340L	S	+	2	0	PLCG2	80484847	1.000000	0.71417	0.944000	0.38274	0.500000	0.33767	7.625000	0.83145	2.034000	0.60081	0.467000	0.42956	TCG		0.617	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81927346	C	T	81927346	3	4	73	1	0	0	0	0	1	0	0	0	12067	893	31	1	1061	1	PLCG2	16	81927346	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	50544242	81927346	8427407	60	21354										
TP53	7157	broad.mit.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	73	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		7578406	73616804	61	21355										
TBX21	30009	broad.mit.edu	37	chr17	45822627	45822627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggagactctaagaggaggcgCgtgtccccctatccttccag	12	13	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr17:45822627C>T	ENST00000177694.1	+	6	1714	c.1503C>T	c.(1501-1503)cgC>cgT	p.R501R		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	501					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R501R(1)		NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						AGAGGAGGCGCGTGTCCCCCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	17											45	47	46					17																	45822627		2203	4300	6503	43177626	SO:0001819	synonymous_variant	30009			AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1503C>T	17.37:g.45822627C>T			43177626		Silent	SNP	ENST00000177694.1	37	CCDS11514.1																																																																																				0.567	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		T	45822627	C	T	45822627	2	4	73	1	0	0	0	0	0	0	0	1	15696	755	27	1		1	TBX21	17	45822627	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	38244221	45822627	35372583	62	21356										
SMAD4	4089	broad.mit.edu	37	chr18	48604788	48604788	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccgggccctccagctcctagAcgaagtacttcataccatgc	8	16	1	1	rs377767385		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr18:48604788A>G	ENST00000342988.3	+	12	2148	c.1610A>G	c.(1609-1611)gAc>gGc	p.D537G	SMAD4_ENST00000398417.2_Missense_Mutation_p.D537G|SMAD4_ENST00000588745.1_Missense_Mutation_p.D441G|SMAD4_ENST00000586253.1_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	537	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.D537G(1)|p.L536fs*11(1)|p.L536fs*14(1)|p.D537V(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CAGCTCCTAGACGAAGTACTT	0.483																																																42	Whole gene deletion(36)|Substitution - Missense(2)|Deletion - Frameshift(2)|Unknown(2)	pancreas(26)|large_intestine(6)|lung(3)|breast(3)|stomach(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											79	81	81					18																	48604788		2203	4300	6503	46858786	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1610A>G	18.37:g.48604788A>G	ENSP00000341551:p.Asp537Gly		46858786	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831347	0.71258	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98012	-4.66;-4.66	6.07	6.07	0.98685	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (1);	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99716	1.1008	10	0.87932	D	0	.	15.6232	0.76824	1.0:0.0:0.0:0.0	.	537	Q13485	SMAD4_HUMAN	G	537	ENSP00000341551:D537G;ENSP00000381452:D537G	ENSP00000341551:D537G	D	+	2	0	SMAD4	46858786	1.000000	0.71417	0.989000	0.46669	0.955000	0.61496	9.118000	0.94355	2.326000	0.78906	0.533000	0.62120	GAC		0.483	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48604788	A	G	48604788	3	3	73	1	0	0	0	0	1	0	0	0	14797	275	10	4	1652	4	SMAD4	18	48604788	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10		48604788	29472460	63	21357										
LILRB5	10990	broad.mit.edu	37	chr19	54756400	54756400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gccccgcagcccctgcaggaCggtagaaatgggctggacag	15	13	0	1	rs367690586		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr19:54756400C>T	ENST00000316219.5	-	10	1591	c.1484G>A	c.(1483-1485)cGt>cAt	p.R495H	LILRB5_ENST00000450632.1_Missense_Mutation_p.R487H|LILRB5_ENST00000449561.2_Missense_Mutation_p.R496H|LILRB5_ENST00000345866.6_Missense_Mutation_p.R396H|CTD-2337J16.1_ENST00000595133.1_lincRNA	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	495					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.R495H(2)|p.R487H(2)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCTGCAGGACGGTAGAAATG	0.597																																																4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	19						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	83	80	81		1487,1187,1484	-3.1	0	19		81	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	29,29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	496/592,396/492,495/591	54756400	2,13004	2203	4300	6503	59448212	SO:0001583	missense	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1484G>A	19.37:g.54756400C>T	ENSP00000320390:p.Arg495His		59448212	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	4.006	-0.001534	0.07819	0.0	2.33E-4	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00479	7.12;7.13;7.12;7.16	1.57	-3.14	0.05250	.	.	.	.	.	T	0.00178	0.0005	N	0.16790	0.44	0.09310	N	1	B;B;B;P	0.46784	0.032;0.013;0.099;0.884	B;B;B;B	0.38056	0.013;0.013;0.015;0.264	T	0.40346	-0.9568	9	0.07644	T	0.81	.	0.9829	0.01440	0.2361:0.3953:0.1794:0.1893	.	487;396;496;495	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	H	495;487;496;396	ENSP00000320390:R495H;ENSP00000414225:R487H;ENSP00000406478:R496H;ENSP00000263430:R396H	ENSP00000320390:R495H	R	-	2	0	LILRB5	59448212	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.670000	0.05256	-2.029000	0.00930	-0.745000	0.03516	CGT		0.597	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54756400	C	T	54756400	3	4	73	1	0	0	0	0	1	0	0	0	8817	536	19	1	304	1	LILRB5	19	54756400	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		54756400	4372583	64	21358										
ZIM3	114026	broad.mit.edu	37	chr19	57646816	57646816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tccagtgtgaacttttttatGttgaatgagggttgagttct	11	4	1	4			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr19:57646816G>A	ENST00000269834.1	-	5	1274	c.889C>T	c.(889-891)Cat>Tat	p.H297Y	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H297Y(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACTTTTTTATGTTGAATGAGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											114	113	114					19																	57646816		2203	4300	6503	62338628	SO:0001583	missense	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.889C>T	19.37:g.57646816G>A	ENSP00000269834:p.His297Tyr		62338628	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413521	0.25465	.	.	ENSG00000141946	ENST00000269834	D	0.86769	-2.17	2.53	2.53	0.30540	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94532	0.8239	M	0.94101	3.495	0.31567	N	0.656744	D	0.76494	0.999	D	0.85130	0.997	D	0.92854	0.6300	9	0.87932	D	0	.	12.1258	0.53917	0.0:0.0:1.0:0.0	.	297	Q96PE6	ZIM3_HUMAN	Y	297	ENSP00000269834:H297Y	ENSP00000269834:H297Y	H	-	1	0	ZIM3	62338628	1.000000	0.71417	0.579000	0.28588	0.238000	0.25445	7.542000	0.82095	1.392000	0.46585	0.313000	0.20887	CAT		0.373	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			A	57646816	G	A	57646816	3	1	73	1	0	0	0	0	1	0	0	0	17724	1377	48	3	533	3	ZIM3	19	57646816	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	2890416	57646816	1482167	65	21359										
GTPBP1	9567	broad.mit.edu	37	chr22	39124077	39124077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	acaaggccactgtacacttcCgcttcatcaagacccctgag	7	15	2	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chr22:39124077C>T	ENST00000216044.5	+	10	1860	c.1627C>T	c.(1627-1629)Cgc>Tgc	p.R543C		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	543					GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.R543C(1)		endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					TGTACACTTCCGCTTCATCAA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	22											149	97	114					22																	39124077		2203	4300	6503	37454023	SO:0001583	missense	9567			U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.1627C>T	22.37:g.39124077C>T	ENSP00000216044:p.Arg543Cys		37454023	Q6IC67	Missense_Mutation	SNP	ENST00000216044.5	37	CCDS13977.2	.	.	.	.	.	.	.	.	.	.	C	34	5.408272	0.96051	.	.	ENSG00000100226	ENST00000216044;ENST00000458073	T	0.37235	1.21	5.75	5.75	0.90469	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71213	0.3313	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77485	-0.2570	10	0.66056	D	0.02	.	19.9421	0.97168	0.0:1.0:0.0:0.0	.	543	O00178	GTPB1_HUMAN	C	543;121	ENSP00000216044:R543C	ENSP00000216044:R543C	R	+	1	0	GTPBP1	37454023	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.681000	0.84073	2.714000	0.92807	0.561000	0.74099	CGC		0.587	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286		T	39124077	C	T	39124077	3	4	73	1	0	0	0	0	1	0	0	0	6899	652	23	1	1665	1	GTPBP1	22	39124077	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10		39124077	12180489	66	21360										
FAM47C	442444	broad.mit.edu	37	chrX	37028940	37028940	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tgcccggagcctaccaagacCggagcgtcccatctaaaaga	10	14	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:37028940C>T	ENST00000358047.3	+	1	2509	c.2457C>T	c.(2455-2457)acC>acT	p.T819T		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	819								p.T819T(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						CTACCAAGACCGGAGCGTCCC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	X											58	58	58					X																	37028940		2202	4300	6502	36938861	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2457C>T	X.37:g.37028940C>T			36938861	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.547	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37028940	C	T	37028940	2	4	73	1	0	0	0	0	0	0	0	1	5590	639	23	1		1	FAM47C	23	37028940	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10		37028940	118241620	67	21361										
SRPX	8406	broad.mit.edu	37	chrX	38019445	38019445	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gcattgagtttgccacagcgTttgactgtagggacacaagt	12	8	0	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:38019445T>C	ENST00000378533.3	-	7	886	c.780A>G	c.(778-780)aaA>aaG	p.K260K	SRPX_ENST00000544439.1_Silent_p.K240K|SRPX_ENST00000479015.1_5'Flank|SRPX_ENST00000343800.6_Silent_p.K247K|SRPX_ENST00000538295.1_Silent_p.K260K|SRPX_ENST00000432886.2_Silent_p.K201K|TM4SF2_ENST00000465127.1_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	260	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.K260K(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						TGCCACAGCGTTTGACTGTAG	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	X											77	61	66					X																	38019445		2202	4300	6502	37904389	SO:0001819	synonymous_variant	8406			U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"sushi-repeat-containing protein, X chromosome", "sushi-repeat-containing protein, X-linked"			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.780A>G	X.37:g.38019445T>C			37904389	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Silent	SNP	ENST00000378533.3	37	CCDS14245.1																																																																																				0.527	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		C	38019445	T	C	38019445	2	2	73	1	0	0	0	0	0	0	0	1	15203	1722	60	4		4	SRPX	23	38019445	Silent	SNP	T	TCGA-AG-A020-01A-21W-A096-10	990505	38019445	117251115	68	21362										
RPGR	6103	broad.mit.edu	37	chrX	38145583	38145585	+	Intron	DEL	TCC	TCC	-													0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	cttctccctccccttctcctTcctcttctccctccccttct					rs199663434		TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	TCC	TCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:38145583_38145585delTCC	ENST00000339363.3	-	14	2688				RPGR_ENST00000338898.3_Intron|RPGR_ENST00000309513.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.889_890EE>E|RPGR_ENST00000318842.7_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)	p.E890delE(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cccttctccttcctcttctccct	0.591																																																1	Deletion - In frame(1)	large_intestine(1)	X							,	260,2646		30,169,31,1108,261					,		0.1			6	751,4006		117,346,171,1370,920	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	147,515,202,2478,1181	A1A1,A1R,A1,RR,R		15.7873,8.947,13.1933	,	,		1011,6652				38030529	SO:0001627	intron_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+761GGA>-	X.37:g.38145583_38145585delTCC			38030527	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																					0.591	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145585	TCC	-	38145583	6	5	73	0	1	1	0	1	0	0	0	0	13585	1783	62	0		0	RPGR	23	38145583	Intron	DEL	TCC	TCGA-AG-A020-01A-21W-A096-10	126138	38145583	117124977	69	21363										
HUWE1	10075	broad.mit.edu	37	chrX	53565406	53565406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggatctggtttaacacagtgCggtgagtctctgaggggaga	16	6	2	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:53565406C>T	ENST00000342160.3	-	76	12345	c.11888G>A	c.(11887-11889)cGc>cAc	p.R3963H	HUWE1_ENST00000262854.6_Missense_Mutation_p.R3963H			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3963					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.R3853H(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TAACACAGTGCGGTGAGTCTC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	X											144	91	109					X																	53565406		2203	4300	6503	53582131	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.11888G>A	X.37:g.53565406C>T	ENSP00000340648:p.Arg3963His		53582131	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275866	0.59649	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.49720	0.77;0.77	5.42	5.42	0.78866	.	0.412831	0.24332	N	0.039453	T	0.69324	0.3098	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.74674	0.977;0.964;0.984	T	0.73304	-0.4025	10	0.87932	D	0	.	16.9563	0.86260	0.0:1.0:0.0:0.0	.	785;3963;3947	Q5H935;Q7Z6Z7;Q7Z6Z7-2	.;HUWE1_HUMAN;.	H	3963	ENSP00000340648:R3963H;ENSP00000262854:R3963H	ENSP00000262854:R3963H	R	-	2	0	HUWE1	53582131	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.899000	0.75682	2.267000	0.75376	0.529000	0.55759	CGC		0.522	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53565406	C	T	53565406	3	4	73	1	0	0	0	0	1	0	0	0	7482	768	27	1	1268	1	HUWE1	23	53565406	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	15419823	53565406	101705154	70	21364										
PCDH19	57526	broad.mit.edu	37	chrX	99663337	99663337	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	gcacagcagatcacggtcaaTcttctgcttggtgaccagca	10	12	4	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:99663337T>A	ENST00000373034.4	-	1	1934	c.259A>T	c.(259-261)Att>Ttt	p.I87F	PCDH19_ENST00000420881.2_Missense_Mutation_p.I87F|PCDH19_ENST00000255531.7_Missense_Mutation_p.I87F	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	87	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I87F(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TCACGGTCAATCTTCTGCTTG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	X											73	68	70					X																	99663337		2088	4208	6296	99549993	SO:0001583	missense	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.259A>T	X.37:g.99663337T>A	ENSP00000362125:p.Ile87Phe		99549993	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	T	19.52	3.842273	0.71488	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.35048	1.33;1.33;1.33	5.7	5.7	0.88788	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.71247	0.3317	H	0.95187	3.635	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.988;0.993	T	0.80892	-0.1179	10	0.87932	D	0	.	14.5681	0.68194	0.0:0.0:0.0:1.0	.	87;87;87	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	F	87	ENSP00000400327:I87F;ENSP00000362125:I87F;ENSP00000255531:I87F	ENSP00000255531:I87F	I	-	1	0	PCDH19	99549993	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	6.186000	0.72026	1.906000	0.55180	0.441000	0.28932	ATT		0.572	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99663337	T	A	99663337	3	1	73	1	0	0	0	0	1	0	0	0	11545	1435	50	5	3211	5	PCDH19	23	99663337	Missense_Mutation	SNP	T	TCGA-AG-A020-01A-21W-A096-10	46097931	99663337	55607223	71	21365										
MUM1L1	139221	broad.mit.edu	37	chrX	105451154	105451154	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ttctggccattgtaaatggcAcaaaaggatccagatggctg	11	8	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:105451154A>C	ENST00000357175.2	+	4	2378	c.1729A>C	c.(1729-1731)Aca>Cca	p.T577P	MUM1L1_ENST00000337685.2_Missense_Mutation_p.T577P|MUM1L1_ENST00000372552.1_Missense_Mutation_p.T577P	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	577						extracellular vesicular exosome (GO:0070062)		p.T577P(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGTAAATGGCACAAAAGGATC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	X											46	41	42					X																	105451154		1871	4090	5961	105337810	SO:0001583	missense	139221			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1729A>C	X.37:g.105451154A>C	ENSP00000349699:p.Thr577Pro		105337810	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.265524	0.40095	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.44482	0.92;0.92;0.92	5.08	5.08	0.68730	.	0.367796	0.23243	N	0.050337	T	0.44222	0.1283	L	0.44542	1.39	0.27597	N	0.94909	P	0.52061	0.95	P	0.50708	0.648	T	0.42413	-0.9453	10	0.66056	D	0.02	-27.3014	10.1122	0.42570	1.0:0.0:0.0:0.0	.	577	Q5H9M0	MUML1_HUMAN	P	577	ENSP00000349699:T577P;ENSP00000338641:T577P;ENSP00000361632:T577P	ENSP00000338641:T577P	T	+	1	0	MUM1L1	105337810	0.918000	0.31147	0.625000	0.29200	0.471000	0.32888	2.214000	0.42853	1.992000	0.58205	0.486000	0.48141	ACA		0.448	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		C	105451154	A	C	105451154	3	2	73	1	0	0	0	0	1	0	0	0	10016	159	6	4	1731	4	MUM1L1	23	105451154	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10	5787817	105451154	49819406	72	21366										
GUCY2F	2986	broad.mit.edu	37	chrX	108619326	108619326	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	acccatctttgtccactggtGggggcacaggaaggggcttc	14	11	1	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:108619326G>T	ENST00000218006.2	-	18	3512	c.3221C>A	c.(3220-3222)cCa>cAa	p.P1074Q		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	1074					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.P1074Q(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GTCCACTGGTGGGGGCACAGG	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	X											183	172	176					X																	108619326		2203	4300	6503	108505982	SO:0001583	missense	2986			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.3221C>A	X.37:g.108619326G>T	ENSP00000218006:p.Pro1074Gln		108505982	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.063699	0.55432	.	.	ENSG00000101890	ENST00000218006	T	0.79845	-1.31	4.31	2.53	0.30540	.	0.193466	0.45361	D	0.000377	D	0.85035	0.5605	L	0.60455	1.87	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	T	0.83233	-0.0062	10	0.62326	D	0.03	.	7.925	0.29870	0.212:0.0:0.7879:0.0	.	1074	P51841	GUC2F_HUMAN	Q	1074	ENSP00000218006:P1074Q	ENSP00000218006:P1074Q	P	-	2	0	GUCY2F	108505982	1.000000	0.71417	0.921000	0.36526	0.921000	0.55340	3.485000	0.53208	0.571000	0.29365	0.600000	0.82982	CCA		0.438	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108619326	G	T	108619326	3	4	73	1	0	0	0	0	1	0	0	0	6919	1348	47	2	113	2	GUCY2F	23	108619326	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	3168172	108619326	46651234	73	21367										
GRIA3	2892	broad.mit.edu	37	chrX	122387324	122387324	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	agatgcgcccagccttgaagGgcgctattctgagtcttctg	12	11	3	3			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:122387324G>T	ENST00000371251.1	+	3	491	c.439G>T	c.(439-441)Ggc>Tgc	p.G147C	GRIA3_ENST00000264357.5_Missense_Mutation_p.G147C|GRIA3_ENST00000541091.1_Missense_Mutation_p.G131C|GRIA3_ENST00000479118.1_3'UTR|GRIA3_ENST00000371256.5_Missense_Mutation_p.G147C|GRIA3_ENST00000542149.1_Missense_Mutation_p.G147C			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	147					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)	p.G147C(2)		breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	AGCCTTGAAGGGCGCTATTCT	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	X											106	90	96					X																	122387324		2203	4300	6503	122215005	SO:0001583	missense	2892			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.439G>T	X.37:g.122387324G>T	ENSP00000360297:p.Gly147Cys		122215005	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344946	0.82022	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.63	5.63	0.86233	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89497	0.6732	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.987;1.0;0.999	D	0.90125	0.4202	10	0.72032	D	0.01	.	17.7593	0.88460	0.0:0.0:1.0:0.0	.	131;147;147	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	C	147;147;147;147;131	ENSP00000264357:G147C;ENSP00000446146:G147C;ENSP00000360302:G147C;ENSP00000360297:G147C;ENSP00000446440:G131C	ENSP00000264357:G147C	G	+	1	0	GRIA3	122215005	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.009000	0.88606	2.499000	0.84300	0.513000	0.50165	GGC		0.522	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		T	122387324	G	T	122387324	3	4	73	1	0	0	0	0	1	0	0	0	6790	1232	43	2	449	2	GRIA3	23	122387324	Missense_Mutation	SNP	G	TCGA-AG-A020-01A-21W-A096-10	13767998	122387324	32883236	74	21368										
ODZ1	10178	broad.mit.edu	37	chrX	123554302	123554302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	tgcttatagtcagccagtatActtgtccgccaggcaccaca	8	13	1	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:123554302A>G	ENST00000371130.3	-	24	4883	c.4820T>C	c.(4819-4821)gTa>gCa	p.V1607A	TENM1_ENST00000422452.2_Missense_Mutation_p.V1614A|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1607					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.V1609A(1)									CAGCCAGTATACTTGTCCGCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	X											75	56	63					X																	123554302		2203	4300	6503	123381983	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4820T>C	X.37:g.123554302A>G	ENSP00000360171:p.Val1607Ala		123381983	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	a	11.53	1.667096	0.29604	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86097	-2.07;-2.05	5.49	4.34	0.51931	Six-bladed beta-propeller, TolB-like (1);	0.065091	0.64402	D	0.000009	T	0.81302	0.4794	M	0.65975	2.015	0.42896	D	0.994213	B;B;B	0.28512	0.018;0.004;0.214	B;B;B	0.25759	0.008;0.005;0.063	T	0.78109	-0.2332	10	0.30854	T	0.27	.	9.9838	0.41830	0.9201:0.0:0.0798:0.0	.	1613;1614;1607	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	A	1607;1614	ENSP00000360171:V1607A;ENSP00000403954:V1614A	ENSP00000360171:V1607A	V	-	2	0	ODZ1	123381983	1.000000	0.71417	0.992000	0.48379	0.557000	0.35523	5.131000	0.64751	1.840000	0.53500	0.483000	0.47432	GTA		0.527	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	123554302	A	G	123554302	3	3	73	1	0	0	0	0	1	0	0	0	10865	391	14	4	3389	4	ODZ1	23	123554302	Missense_Mutation	SNP	A	TCGA-AG-A020-01A-21W-A096-10	1166978	123554302	31716258	75	21369										
SLITRK2	84631	broad.mit.edu	37	chrX	144903997	144903997	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	accgtggccgggatcttacaGacagagagtcgcaaaactgc	12	11	1	2			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:144903997G>A	ENST00000370490.1	+	1	4309	c.54G>A	c.(52-54)caG>caA	p.Q18Q	SLITRK2_ENST00000434188.2_Silent_p.Q18Q|SLITRK2_ENST00000413937.2_Silent_p.Q18Q|SLITRK2_ENST00000447897.2_Silent_p.Q18Q|SLITRK2_ENST00000428560.2_Silent_p.Q18Q			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	18					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.Q18Q(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGATCTTACAGACAGAGAGTC	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	X											69	63	65					X																	144903997		2203	4300	6503	144711689	SO:0001819	synonymous_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.54G>A	X.37:g.144903997G>A			144711689	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																				0.468	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144903997	G	A	144903997	2	1	73	1	0	0	0	0	0	0	0	1	14780	933	33	3		3	SLITRK2	23	144903997	Silent	SNP	G	TCGA-AG-A020-01A-21W-A096-10	21349695	144903997	10366563	76	21370										
MAMLD1	10046	broad.mit.edu	37	chrX	149638895	149638895	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ccatcaccacacccaccaccGctgccactgccaccaccacc	3	25	1	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:149638895G>A	ENST00000370401.2	+	4	1360	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	MAMLD1_ENST00000426613.2_Silent_p.P325P|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000432680.2_Silent_p.P325P|MAMLD1_ENST00000262858.5_Silent_p.P350P			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	350	Poly-Pro.				male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P277P(1)|p.P350P(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					acccaccaccgctgccactgc	0.627																																																2	Substitution - coding silent(2)	large_intestine(2)	X											80	56	64					X																	149638895		2202	4300	6502	149389553	SO:0001819	synonymous_variant	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1050G>A	X.37:g.149638895G>A			149389553	B2RCQ4|B4DG93|B9EGA5	Silent	SNP	ENST00000370401.2	37	CCDS14693.2																																																																																				0.627	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		A	149638895	G	A	149638895	2	1	73	1	0	0	0	0	0	0	0	1	9238	1074	38	1		1	MAMLD1	23	149638895	Silent	SNP	G	TCGA-AG-A020-01A-21W-A096-10	4734898	149638895	5631665	77	21371										
OPN1LW	5956	broad.mit.edu	37	chrX	153420184	153420184	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ctcgctatcatcatgctctgCtacctccaagtgtggctggc	9	14	3	0			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:153420184C>T	ENST00000369951.4	+	4	774	c.714C>T	c.(712-714)tgC>tgT	p.C238C	OPN1LW_ENST00000463296.1_Intron	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	238					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.C238C(2)		endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCATGCTCTGCTACCTCCAAG	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	X											281	206	231					X																	153420184		2189	4251	6440	153073378	SO:0001819	synonymous_variant	5956			Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"GPCR / Class A : Opsin receptors"	9936	protein-coding gene	gene with protein product	"cone dystrophy 5 (X-linked)"	300822	"color blindness, protan", "red cone photoreceptor pigment"	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.714C>T	X.37:g.153420184C>T			153073378		Silent	SNP	ENST00000369951.4	37	CCDS14742.1																																																																																				0.602	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061		T	153420184	C	T	153420184	2	4	73	1	0	0	0	0	0	0	0	1	10908	805	28	3		3	OPN1LW	23	153420184	Silent	SNP	C	TCGA-AG-A020-01A-21W-A096-10	3781289	153420184	1850376	78	21372										
FLNA	2316	broad.mit.edu	37	chrX	153590615	153590615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0253164556962025	2	1	0.328044508551411	0	0.350931334729417	0.444444444444444	1	0	ggtacctgtcctcaccagtgCgactgaggccagggccctcg	13	15	1	1			TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A020-01A-21W-A096-10	TCGA-AG-A020-11A-11W-A096-10	g.chrX:153590615C>T	ENST00000369850.3	-	18	2887	c.2651G>A	c.(2650-2652)cGc>cAc	p.R884H	FLNA_ENST00000344736.4_Missense_Mutation_p.R884H|FLNA_ENST00000360319.4_Missense_Mutation_p.R884H|FLNA_ENST00000422373.1_Missense_Mutation_p.R884H	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	884					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)	p.R884H(1)		breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTCACCAGTGCGACTGAGGCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	X											68	72	71					X																	153590615		2074	4178	6252	153243809	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.2651G>A	X.37:g.153590615C>T	ENSP00000358866:p.Arg884His		153243809	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.254805	0.59212	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.91	4.91	0.64330	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.88138	0.6356	L	0.42245	1.32	0.80722	D	1	D;D	0.76494	0.99;0.999	D;D	0.70487	0.923;0.969	D	0.88555	0.3119	10	0.62326	D	0.03	.	11.4197	0.49974	0.0:0.9016:0.0:0.0984	.	884;884	P21333-2;P21333	.;FLNA_HUMAN	H	884;857;884;884;884	ENSP00000353467:R884H;ENSP00000416926:R884H;ENSP00000358866:R884H;ENSP00000358863:R884H	ENSP00000358863:R884H	R	-	2	0	FLNA	153243809	0.065000	0.20965	0.948000	0.38648	0.709000	0.40893	1.181000	0.32017	2.156000	0.67533	0.529000	0.55759	CGC		0.652	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153590615	C	T	153590615	3	4	73	1	0	0	0	0	1	0	0	0	5952	768	27	1	5416	1	FLNA	23	153590615	Missense_Mutation	SNP	C	TCGA-AG-A020-01A-21W-A096-10	170431	153590615	1679945	79	21373										
ZNF593	51042	broad.mit.edu	37	chr1	26497149	26497149	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	atcctatgtgccccccaggcGgctggcagtgcccacggaag	13	15	0	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:26497149G>A	ENST00000374266.5	+	3	460	c.347G>A	c.(346-348)cGg>cAg	p.R116Q	RP11-96L14.7_ENST00000433939.1_RNA|RP11-96L14.7_ENST00000444682.1_RNA|ZNF593_ENST00000270812.5_Silent_p.A147A|RP11-96L14.7_ENST00000407889.2_RNA|RP11-96L14.7_ENST00000448923.1_RNA|RP11-96L14.7_ENST00000414762.1_RNA	NM_015871.4	NP_056955.2	O00488	ZN593_HUMAN	zinc finger protein 593	116					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.R116Q(1)		large_intestine(4)|prostate(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-26)|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;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		CCCCCCAGGCGGCTGGCAGTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											76	79	78					1																	26497149		2203	4300	6503	26369736	SO:0001583	missense	51042			D45213	CCDS275.2	1p35.3	2012-10-05			ENSG00000142684	ENSG00000142684			30943	protein-coding gene	gene with protein product						9115366	Standard	NM_015871		Approved	ZT86	uc001bll.4	O00488	OTTHUMG00000007538	ENST00000374266.5:c.347G>A	1.37:g.26497149G>A	ENSP00000363384:p.Arg116Gln		26369736	B2R4S0|Q5T2H7	Missense_Mutation	SNP	ENST00000374266.5	37	CCDS275.2	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862309	0.32884	.	.	ENSG00000142684	ENST00000374266	T	0.43688	0.94	5.27	3.27	0.37495	.	0.447922	0.24447	N	0.038441	T	0.28067	0.0692	L	0.38175	1.15	0.47819	D	0.999522	B	0.25105	0.118	B	0.20577	0.03	T	0.10222	-1.0639	10	0.39692	T	0.17	-16.4282	5.4111	0.16349	0.1121:0.0:0.5407:0.3472	.	116	O00488	ZN593_HUMAN	Q	116	ENSP00000363384:R116Q	ENSP00000363384:R116Q	R	+	2	0	ZNF593	26369736	0.231000	0.23751	0.760000	0.31359	0.036000	0.12997	1.871000	0.39539	1.354000	0.45846	-0.169000	0.13324	CGG		0.597	ZNF593-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019842.2	NM_015871		A	26497149	G	A	26497149	3	1	74	1	0	0	0	0	1	0	0	0	18062	1116	39	1	357	1	ZNF593	1	26497149	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		26497149	222753472	1	21374										
ARID1A	8289	broad.mit.edu	37	chr1	27105553	27105553	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccttgtagaatatttccgaCgatgcctgattgagatcttt	8	8	1	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:27105553C>T	ENST00000324856.7	+	20	5535	c.5164C>T	c.(5164-5166)Cga>Tga	p.R1722*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.R1505*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.R1339*|ARID1A_ENST00000540690.1_Nonsense_Mutation_p.R50*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1722					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R1722*(5)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		ATATTTCCGACGATGCCTGAT	0.443			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	5	Substitution - Nonsense(5)	large_intestine(2)|ovary(1)|stomach(1)|endometrium(1)	1											181	199	193					1																	27105553		2203	4300	6503	26978140	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5164C>T	1.37:g.27105553C>T	ENSP00000320485:p.Arg1722*		26978140	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.312365|9.312365	0.99133|0.99133	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690|ENST00000430799	.|.	.|.	.|.	4.71|4.71	2.75|2.75	0.32379|0.32379	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.68421	.|0.2999	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.66614	.|-0.5879	.|4	0.02654|.	T|.	1|.	-5.1918|-5.1918	13.8273|13.8273	0.63359|0.63359	0.2773:0.7227:0.0:0.0|0.2773:0.7227:0.0:0.0	.|.	.|.	.|.	.|.	X|M	1722;1505;1339;50|618	.|.	ENSP00000320485:R1722X|.	R|T	+|+	1|2	2|0	ARID1A|ARID1A	26978140|26978140	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.362000|4.362000	0.59467|0.59467	0.659000|0.659000	0.30945|0.30945	0.591000|0.591000	0.81541|0.81541	CGA|ACG		0.443	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27105553	C	T	27105553	4	4	74	1	0	0	0	0	0	1	0	0	913	528	19	1	5242	1	ARID1A	1	27105553	Nonsense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	608404	27105553	222145068	2	21375										
CSMD2	114784	broad.mit.edu	37	chr1	33999486	33999486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caggtagcctttttgacaacGgaagaggactgtgcttccaa	11	9	0	2	rs143597727		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:33999486G>A	ENST00000373381.4	-	63	10077	c.9901C>T	c.(9901-9903)Cgt>Tgt	p.R3301C		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R3157C(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTTTGACAACGGAAGAGGACT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	0,4406		0,0,2203	137	116	123		9469	4.4	1	1	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSMD2	NM_052896.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3157/3488	33999486	1,13005	2203	4300	6503	33772073	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9901C>T	1.37:g.33999486G>A	ENSP00000362479:p.Arg3301Cys		33772073	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	19.65	3.866564	0.72065	0.0	1.16E-4	ENSG00000121904	ENST00000373381	T	0.65916	-0.18	5.33	4.36	0.52297	Complement control module (2);Sushi/SCR/CCP (3);	0.324034	0.31010	N	0.008421	T	0.76905	0.4053	M	0.83012	2.62	0.80722	D	1	D;D	0.76494	0.994;0.999	P;D	0.67900	0.846;0.954	T	0.77419	-0.2595	10	0.42905	T	0.14	.	11.072	0.48008	0.0:0.0:0.664:0.336	.	3157;3301	Q7Z408;E7EUA6	CSMD2_HUMAN;.	C	3301	ENSP00000362479:R3301C	ENSP00000241312:R3157C	R	-	1	0	CSMD2	33772073	1.000000	0.71417	0.995000	0.50966	0.600000	0.36913	6.781000	0.75068	2.505000	0.84491	0.591000	0.81541	CGT		0.562	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	33999486	G	A	33999486	3	1	74	1	0	0	0	0	1	0	0	0	3951	1116	39	1	1026	1	CSMD2	1	33999486	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	6893933	33999486	215251135	3	21376										
KDM4A	9682	broad.mit.edu	37	chr1	44125982	44125982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caaaaaggtactgtaccccaCgctatagtgagtttgaagag	10	8	0	3	rs200705318		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:44125982C>T	ENST00000372396.3	+	4	462	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	KDM4A_ENST00000463151.1_3'UTR	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	110					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R110C(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						CTGTACCCCACGCTATAGTGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	85	85					1																	44125982		2203	4300	6503	43898569	SO:0001583	missense	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.328C>T	1.37:g.44125982C>T	ENSP00000361473:p.Arg110Cys		43898569	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	37	CCDS491.1	.	.	.	.	.	.	.	.	.	.	C	32	5.168471	0.94768	.	.	ENSG00000066135	ENST00000372396	T	0.50277	0.75	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.73892	0.3645	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.70716	0.792;0.97	T	0.75932	-0.3143	10	0.72032	D	0.01	-15.0475	20.5827	0.99408	0.0:1.0:0.0:0.0	.	110;110	B4DT38;O75164	.;KDM4A_HUMAN	C	110	ENSP00000361473:R110C	ENSP00000361473:R110C	R	+	1	0	KDM4A	43898569	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.423000	0.66458	2.941000	0.99782	0.655000	0.94253	CGC		0.378	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		T	44125982	C	T	44125982	3	4	74	1	0	0	0	0	1	0	0	0	8149	536	19	1	338	1	KDM4A	1	44125982	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	10126496	44125982	205124639	4	21377										
NSUN4	387338	broad.mit.edu	37	chr1	46810514	46810514	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cctgctgttcgactggctttGcagaattttgacatgactta	9	9	0	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:46810514G>C	ENST00000474844.1	+	2	785	c.135G>C	c.(133-135)ttG>ttC	p.L45F	NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_5'UTR|NSUN4_ENST00000536062.1_5'UTR	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	45					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)	p.L45F(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					GACTGGCTTTGCAGAATTTTG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	1											161	160	160					1																	46810514		2203	4300	6503	46583101	SO:0001583	missense	387338			AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"NOP2/Sun domain containing"	31802	protein-coding gene	gene with protein product	"sperm head and tail associated protein"	615394	"NOL1/NOP2/Sun domain family 4", "NOL1/NOP2/Sun domain family, member 4"				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.135G>C	1.37:g.46810514G>C	ENSP00000419740:p.Leu45Phe		46583101	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.750224	0.69533	.	.	ENSG00000117481	ENST00000474844	T	0.26067	1.76	5.45	1.18	0.20946	.	0.000000	0.64402	D	0.000001	T	0.47192	0.1432	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.43097	-0.9412	10	0.49607	T	0.09	-8.2124	6.9949	0.24777	0.2168:0.1247:0.6585:0.0	.	45	Q96CB9	NSUN4_HUMAN	F	45	ENSP00000419740:L45F	ENSP00000419740:L45F	L	+	3	2	NSUN4	46583101	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.748000	0.47483	0.680000	0.31366	0.563000	0.77884	TTG		0.483	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044		C	46810514	G	C	46810514	3	2	74	1	0	0	0	0	1	0	0	0	10711	1310	46	5	141	5	NSUN4	1	46810514	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	2684532	46810514	202440107	5	21378										
PRKAA2	5563	broad.mit.edu	37	chr1	57161768	57161768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aatatctcaatcgttctgtcGccactctcctgatgcatatg	6	12	3	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:57161768G>A	ENST00000371244.4	+	6	790	c.724G>A	c.(724-726)Gcc>Acc	p.A242T		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.A242T(1)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TCGTTCTGTCGCCACTCTCCT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											233	232	233					1																	57161768		2203	4300	6503	56934356	SO:0001583	missense	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.724G>A	1.37:g.57161768G>A	ENSP00000360290:p.Ala242Thr		56934356	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676777	0.67928	.	.	ENSG00000162409	ENST00000371244	T	0.65549	-0.16	5.98	5.98	0.97165	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51890	0.1701	N	0.20483	0.58	0.80722	D	1	B	0.28400	0.21	B	0.30316	0.114	T	0.42649	-0.9439	10	0.27082	T	0.32	-13.7548	20.4434	0.99119	0.0:0.0:1.0:0.0	.	242	P54646	AAPK2_HUMAN	T	242	ENSP00000360290:A242T	ENSP00000360290:A242T	A	+	1	0	PRKAA2	56934356	0.998000	0.40836	0.987000	0.45799	0.938000	0.57974	3.912000	0.56386	2.838000	0.97847	0.655000	0.94253	GCC		0.418	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		A	57161768	G	A	57161768	3	1	74	1	0	0	0	0	1	0	0	0	12528	1087	38	1	746	1	PRKAA2	1	57161768	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	10351254	57161768	192088853	6	21379										
DPYD	1806	broad.mit.edu	37	chr1	98039426	98039426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cagtttcatcttgctctgtcCgaacaaactgcatagcaaca	6	12	3	0	rs199646142		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:98039426C>T	ENST00000370192.3	-	11	1329	c.1229G>A	c.(1228-1230)cGg>cAg	p.R410Q		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	410					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.R410Q(2)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TTGCTCTGTCCGAACAAACTG	0.433																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	1						C	GLN/ARG	0,4406		0,0,2203	201	169	180		1229	5.8	1	1		180	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DPYD	NM_000110.3	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	410/1026	98039426	2,13004	2203	4300	6503	97812014	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1229G>A	1.37:g.98039426C>T	ENSP00000359211:p.Arg410Gln		97812014	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	33	5.233382	0.95207	0.0	2.33E-4	ENSG00000188641	ENST00000370192	D	0.94897	-3.55	5.81	5.81	0.92471	.	0.059399	0.64402	D	0.000001	D	0.95472	0.8529	M	0.81682	2.555	0.80722	D	1	D	0.71674	0.998	P	0.51742	0.678	D	0.95065	0.8199	10	0.52906	T	0.07	-12.6181	17.8525	0.88751	0.0:1.0:0.0:0.0	.	410	Q12882	DPYD_HUMAN	Q	410	ENSP00000359211:R410Q	ENSP00000359211:R410Q	R	-	2	0	DPYD	97812014	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.432000	0.80349	2.737000	0.93849	0.650000	0.86243	CGG		0.433	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	98039426	C	T	98039426	3	4	74	1	0	0	0	0	1	0	0	0	4756	652	23	1	1900	1	DPYD	1	98039426	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	40877658	98039426	151211195	7	21380										
RYR2	6262	broad.mit.edu	37	chr1	237774225	237774225	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tcgaataagtgaacgccaagGctggttggtgcagtgtttgg	15	6	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr1:237774225G>T	ENST00000366574.2	+	36	5164	c.4847G>T	c.(4846-4848)gGc>gTc	p.G1616V	RYR2_ENST00000542537.1_Missense_Mutation_p.G1600V|RYR2_ENST00000360064.6_Missense_Mutation_p.G1614V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1616	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.G1614V(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAACGCCAAGGCTGGTTGGTG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	1											73	73	73					1																	237774225		2002	4174	6176	235840848	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4847G>T	1.37:g.237774225G>T	ENSP00000355533:p.Gly1616Val		235840848	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747140	0.89663	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.98567	-5.0;-4.98;-4.99	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000019	D	0.99032	0.9669	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.99712	1.1007	10	0.87932	D	0	.	18.7848	0.91949	0.0:0.0:1.0:0.0	.	1616	Q92736	RYR2_HUMAN	V	1616;1614;1600	ENSP00000355533:G1616V;ENSP00000353174:G1614V;ENSP00000443798:G1600V	ENSP00000353174:G1614V	G	+	2	0	RYR2	235840848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.595000	0.98260	2.658000	0.90341	0.655000	0.94253	GGC		0.527	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237774225	G	T	237774225	3	4	74	1	0	0	0	0	1	0	0	0	13806	1203	42	2	4989	2	RYR2	1	237774225	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	139734799	237774225	11476396	8	21381										
PXDN	7837	broad.mit.edu	37	chr2	1667459	1667459	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cattcgtactggccctggtcGtggagggcaacaccagagat	13	11	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:1667459G>A	ENST00000252804.4	-	12	1535	c.1485C>T	c.(1483-1485)caC>caT	p.H495H	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	495	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.H495H(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGCCCTGGTCGTGGAGGGCAA	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	2											82	90	88					2																	1667459		2051	4171	6222	1646466	SO:0001819	synonymous_variant	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1485C>T	2.37:g.1667459G>A			1646466	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	2.695	-0.272295	0.05716	.	.	ENSG00000130508	ENST00000433670	.	.	.	5.79	-10.5	0.00291	.	.	.	.	.	T	0.72053	0.3413	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79296	-0.1862	4	.	.	.	-37.822	22.7105	0.99975	0.8558:0.0:0.1442:0.0	.	.	.	.	M	491	.	.	T	-	2	0	PXDN	1646466	0.489000	0.26004	0.089000	0.20774	0.333000	0.28666	-0.105000	0.10907	-2.393000	0.00584	-1.202000	0.01658	ACG		0.622	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1667459	G	A	1667459	2	1	74	1	0	0	0	0	0	0	0	1	12884	1136	40	1		1	PXDN	2	1667459	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		1667459	241531914	9	21382										
RSAD2	91543	broad.mit.edu	37	chr2	7030441	7030441	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gaagtgtcctgcttggtgccTgaatctaaccagaaggttgt	12	8	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:7030441T>C	ENST00000382040.3	+	4	1009	c.873T>C	c.(871-873)ccT>ccC	p.P291P	RSAD2_ENST00000541728.1_Silent_p.P184P	NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2									p.P291P(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		GCTTGGTGCCTGAATCTAACC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	2											91	88	89					2																	7030441		2203	4300	6503	6947892	SO:0001819	synonymous_variant	91543			AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321			30908	protein-coding gene	gene with protein product		607810				11752458	Standard	NM_080657		Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.873T>C	2.37:g.7030441T>C			6947892		Silent	SNP	ENST00000382040.3	37	CCDS1656.1																																																																																				0.413	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206724.2	NM_080657		C	7030441	T	C	7030441	2	2	74	1	0	0	0	0	0	0	0	1	13732	1567	55	4		4	RSAD2	2	7030441	Silent	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	5362982	7030441	236168932	10	21383										
BRE	9577	broad.mit.edu	37	chr2	28248112	28248112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gaatcttgcctcctggaatcCttcaaatcctgaatgtctct	6	12	3	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:28248112C>T	ENST00000342045.2	+	6	461	c.320C>T	c.(319-321)cCt>cTt	p.P107L	BRE_ENST00000344773.2_Missense_Mutation_p.P107L|BRE_ENST00000379632.2_Missense_Mutation_p.P107L|BRE_ENST00000379624.1_Missense_Mutation_p.P107L|BRE_ENST00000603461.1_3'UTR|BRE_ENST00000361704.2_Missense_Mutation_p.P107L	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)									p.P107L(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					TCCTGGAATCCTTCAAATCCT	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	2											103	114	111					2																	28248112		2202	4300	6502	28101616	SO:0001583	missense	9577			AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 4"	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.320C>T	2.37:g.28248112C>T	ENSP00000339371:p.Pro107Leu		28101616		Missense_Mutation	SNP	ENST00000342045.2	37	CCDS1763.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520412	0.64747	.	.	ENSG00000158019	ENST00000436924;ENST00000344773;ENST00000379624;ENST00000342045;ENST00000379632;ENST00000361704;ENST00000379629;ENST00000379623	.	.	.	5.7	5.7	0.88788	.	0.053968	0.85682	D	0.000000	T	0.56093	0.1962	L	0.41824	1.3	0.80722	D	1	P;B;P;B	0.47910	0.902;0.224;0.557;0.187	B;B;B;B	0.44133	0.442;0.096;0.125;0.058	T	0.55774	-0.8088	9	0.42905	T	0.14	-15.9175	19.8379	0.96666	0.0:1.0:0.0:0.0	.	107;107;107;107	Q9NXR7-1;Q9NXR7;Q9NXR7-4;Q9NXR7-3	.;BRE_HUMAN;.;.	L	107;107;107;107;107;107;107;9	.	ENSP00000339371:P107L	P	+	2	0	BRE	28101616	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.085000	0.76875	2.694000	0.91930	0.555000	0.69702	CCT		0.408	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1			T	28248112	C	T	28248112	3	4	74	1	0	0	0	0	1	0	0	0	1512	681	24	3	334	3	BRE	2	28248112	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	21217671	28248112	214951261	11	21384										
NRXN1	9378	broad.mit.edu	37	chr2	50699461	50699461	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	catcctctctcgatctgtccGttgcagaaaagagcatcgga	9	12	2	2	rs563089155		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:50699461G>A	ENST00000406316.2	-	16	4695	c.3219C>T	c.(3217-3219)aaC>aaT	p.N1073N	NRXN1_ENST00000406859.3_Silent_p.N1073N|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000404971.1_Silent_p.N1113N|NRXN1_ENST00000405472.3_Silent_p.N1065N|NRXN1_ENST00000401669.2_Silent_p.N1073N|NRXN1_ENST00000401710.1_Silent_p.N82N|NRXN1_ENST00000402717.3_Silent_p.N1065N	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1073	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.N1073N(1)|p.N1114N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CGATCTGTCCGTTGCAGAAAA	0.433													G|||	1	0.000199681	0	0	5008	,	,		16575	0.001		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	2											83	78	79					2																	50699461		1864	4114	5978	50552965	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3219C>T	2.37:g.50699461G>A			50552965	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50699461	G	A	50699461	2	1	74	1	0	0	0	0	0	0	0	1	10696	1136	40	1		1	NRXN1	2	50699461	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	22451349	50699461	192499912	12	21385										
GPR75	10936	broad.mit.edu	37	chr2	54080575	54080575	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cacaagcctggtccacaaatTtcttctgtggctttggagat	9	10	2	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:54080575T>G	ENST00000394705.2	-	2	1589	c.1319A>C	c.(1318-1320)aAa>aCa	p.K440T	ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	440					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)	p.K440T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GTCCACAAATTTCTTCTGTGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	2											118	114	115					2																	54080575		2203	4300	6503	53934079	SO:0001583	missense	10936			AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"GPCR / Class A : Orphans"	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.1319A>C	2.37:g.54080575T>G	ENSP00000378195:p.Lys440Thr		53934079	B2RC02|Q6NWR2	Missense_Mutation	SNP	ENST00000394705.2	37	CCDS1849.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.602255	0.46423	.	.	ENSG00000119737	ENST00000394705	T	0.27720	1.65	4.99	4.99	0.66335	.	0.049284	0.85682	D	0.000000	T	0.47838	0.1467	.	.	.	0.53688	D	0.999979	D	0.63880	0.993	P	0.56343	0.796	T	0.48969	-0.8987	9	0.52906	T	0.07	-9.698	15.1378	0.72583	0.0:0.0:0.0:1.0	.	440	O95800	GPR75_HUMAN	T	440	ENSP00000378195:K440T	ENSP00000378195:K440T	K	-	2	0	GPR75	53934079	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.840000	0.48215	2.224000	0.72417	0.459000	0.35465	AAA		0.473	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			G	54080575	T	G	54080575	3	3	74	1	0	0	0	0	1	0	0	0	6728	1841	64	4	307	4	GPR75	2	54080575	Missense_Mutation	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	3381114	54080575	189118798	13	21386										
BUB1	699	broad.mit.edu	37	chr2	111431795	111431795	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaattctcttctacccactgTatgtatctagaaaaatatgg	5	8	3	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:111431795T>C	ENST00000302759.6	-	3	211	c.93A>G	c.(91-93)atA>atG	p.I31M	BUB1_ENST00000409311.1_Missense_Mutation_p.I31M|BUB1_ENST00000535254.1_Missense_Mutation_p.I11M	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	31	BUB1 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00822}.|Necessary for kinetochore localization.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I31M(1)		breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		CTACCCACTGTATGTATCTAG	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	2											63	66	65					2																	111431795		2201	4300	6501	111148266	SO:0001583	missense	699			AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.93A>G	2.37:g.111431795T>C	ENSP00000302530:p.Ile31Met		111148266	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.387893	0.25031	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432;ENST00000447014;ENST00000420328;ENST00000436916	T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.43	-3.12	0.05282	Mad3/BUB1 homology region 1 (3);	0.470132	0.24323	N	0.039529	T	0.57888	0.2084	L	0.51422	1.61	0.25072	N	0.990982	B;B;B	0.15930	0.002;0.015;0.009	B;B;B	0.25759	0.008;0.04;0.063	T	0.50039	-0.8874	10	0.45353	T	0.12	-0.7592	7.1156	0.25414	0.1167:0.332:0.0:0.5513	.	11;31;31	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	M	11;31;31;31;22;22;22	ENSP00000441013:I11M;ENSP00000386701:I31M;ENSP00000302530:I31M;ENSP00000402883:I22M;ENSP00000409713:I22M;ENSP00000392219:I22M	ENSP00000302530:I31M	I	-	3	3	BUB1	111148266	0.001000	0.12720	0.362000	0.25862	0.930000	0.56654	-1.248000	0.02890	-0.509000	0.06532	-0.375000	0.07067	ATA		0.299	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		C	111431795	T	C	111431795	3	2	74	1	0	0	0	0	1	0	0	0	1573	1628	57	4	3256	4	BUB1	2	111431795	Missense_Mutation	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	57351220	111431795	131767578	14	21387										
TTN	7273	broad.mit.edu	37	chr2	179399547	179399548	+	Frame_Shift_Del	DEL	CT	CT	-													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caaagtgtccaatattatgaCtgtgtaaaaactgaagtgct							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:179399547_179399548delCT	ENST00000591111.1	-	308	97095_97096	c.96871_96872delAG	c.(96871-96873)agtfs	p.S32291fs	TTN_ENST00000589042.1_Frame_Shift_Del_p.S33932fs|TTN_ENST00000342992.6_Frame_Shift_Del_p.S31364fs|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.S25059fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.S24867fs|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.S24992fs|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32291	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.H24993fs*1(1)|p.H31363fs*1(1)|p.H25060fs*1(1)|p.H24868fs*1(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATATTATGACTGTGTAAAAAC	0.351																																																4	Deletion - Frameshift(4)	large_intestine(4)	2																																								179107794	SO:0001589	frameshift_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96871_96872delAG	2.37:g.179399547_179399548delCT	ENSP00000465570:p.Ser32291fs		179107793	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	37																																																																																					0.351	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179399548	CT	-	179399547	7	5	74	1	0	1	0	1	0	0	0	0	16775	565	20	0	6204	0	TTN	2	179399547	Frame_Shift_Del	DEL	CT	TCGA-AG-A025-01A-01W-A00E-09	67967752	179399547	63799826	15	21388										
TTN	7273	broad.mit.edu	37	chr2	179559340	179559340	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gtatacctttcacttcaataActtcttcctgtactggagtc	5	11	3	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:179559340A>T	ENST00000591111.1	-	115	30685	c.30461T>A	c.(30460-30462)gTt>gAt	p.V10154D	TTN_ENST00000589042.1_Missense_Mutation_p.V10471D|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9227D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V9227D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACTTCAATAACTTCTTCCTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	2											27	25	26					2																	179559340		1788	4038	5826	179267585	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30461T>A	2.37:g.179559340A>T	ENSP00000465570:p.Val10154Asp		179267585	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	16.57	3.158892	0.57368	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.71817	-0.6	6.07	4.93	0.64822	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.59418	0.2192	N	0.08118	0	0.80722	D	1	B;P	0.45212	0.145;0.853	B;P	0.49999	0.063;0.628	T	0.65274	-0.6208	9	0.87932	D	0	.	9.7816	0.40651	0.9218:0.0:0.0782:0.0	.	10154;10154	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	D	9227;349	ENSP00000343764:V9227D	ENSP00000343764:V9227D	V	-	2	0	TTN	179267585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.290000	0.51755	1.128000	0.42052	0.533000	0.62120	GTT		0.303	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179559340	A	T	179559340	3	4	74	1	0	0	0	0	1	0	0	0	16775	43	2	5	73101	5	TTN	2	179559340	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	159793	179559340	63640033	16	21389										
SESTD1	91404	broad.mit.edu	37	chr2	179982297	179982297	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	acatttaaacaactgcaccaTctgaagcatctttaaccttc	3	12	2	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:179982297T>G	ENST00000428443.3	-	14	1802	c.1486A>C	c.(1486-1488)Atg>Ctg	p.M496L		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	496							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.M496L(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AACTGCACCATCTGAAGCATC	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											190	163	173					2																	179982297		2203	4300	6503	179690542	SO:0001583	missense	91404			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1486A>C	2.37:g.179982297T>G	ENSP00000415332:p.Met496Leu		179690542	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447503	0.43429	.	.	ENSG00000187231	ENST00000428443	T	0.31769	1.48	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.19366	0.0465	N	0.14661	0.345	0.58432	D	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.07385	-1.0775	9	.	.	.	-21.3053	15.2453	0.73502	0.0:0.0:0.0:1.0	.	496	Q86VW0	SESD1_HUMAN	L	496	ENSP00000415332:M496L	.	M	-	1	0	SESTD1	179690542	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.345000	0.79337	2.080000	0.62538	0.477000	0.44152	ATG		0.338	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		G	179982297	T	G	179982297	3	3	74	1	0	0	0	0	1	0	0	0	14164	1435	50	4	624	4	SESTD1	2	179982297	Missense_Mutation	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	422957	179982297	63217076	17	21390										
SLC4A3	6508	broad.mit.edu	37	chr2	220502425	220502425	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	accgagggcccccccagcccGaggaaccagcccaatacggc	11	19	0	0	rs61753431	byFrequency	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr2:220502425G>A	ENST00000358055.3	+	17	3170	c.2658G>A	c.(2656-2658)ccG>ccA	p.P886P	SLC4A3_ENST00000373760.2_Silent_p.P886P|SLC4A3_ENST00000273063.6_Silent_p.P913P|SLC4A3_ENST00000317151.3_Silent_p.P886P|SLC4A3_ENST00000373762.3_Silent_p.P913P			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	886	Membrane (anion exchange).			SPR -> GPE (in Ref. 2; AAB05850). {ECO:0000305}.	bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.P913P(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCCCAGCCCGAGGAACCAGC	0.647													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		18214	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G	,	65,4341	60.5+/-97.4	0,65,2138	65	52	57		2658,2739	-9.1	0	2	dbSNP_129	57	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC4A3	NM_005070.3,NM_201574.2	,	0,65,6438	AA,AG,GG		0.0,1.4753,0.4998	,	886/1233,913/1260	220502425	65,12941	2203	4300	6503	220210669	SO:0001819	synonymous_variant	6508				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2658G>A	2.37:g.220502425G>A			220210669	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	37	CCDS2445.1																																																																																				0.647	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220502425	G	A	220502425	2	1	74	1	0	0	0	0	0	0	0	1	14692	1045	37	1		1	SLC4A3	2	220502425	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	40520128	220502425	22696948	18	21391										
OR5K2	402135	broad.mit.edu	37	chr3	98216888	98216888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tggcagcagtggcctatgacCgctatgtggccatctgcaac	12	12	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr3:98216888C>T	ENST00000427338.1	+	1	441	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	CLDND1_ENST00000502288.1_3'UTR	NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122C(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GGCCTATGACCGCTATGTGGC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											108	109	109					3																	98216888		2203	4300	6503	99699578	SO:0001583	missense	402135			AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"GPCR / Class A : Olfactory receptors"	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.364C>T	3.37:g.98216888C>T	ENSP00000393889:p.Arg122Cys		99699578	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	.	.	.	.	.	.	.	.	.	.	C	9.026	0.986140	0.18889	.	.	ENSG00000231861	ENST00000427338	T	0.77358	-1.09	2.65	1.76	0.24704	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43747	D	0.000530	T	0.74230	0.3689	M	0.87381	2.88	0.80722	D	1	P	0.35684	0.515	B	0.27715	0.082	T	0.74176	-0.3750	10	0.72032	D	0.01	-11.3127	7.6658	0.28430	0.0:0.8636:0.0:0.1364	.	122	Q8NHB8	OR5K2_HUMAN	C	122	ENSP00000393889:R122C	ENSP00000393889:R122C	R	+	1	0	OR5K2	99699578	0.367000	0.25023	0.995000	0.50966	0.650000	0.38633	0.689000	0.25437	0.677000	0.31305	0.298000	0.19748	CGC		0.478	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2			T	98216888	C	T	98216888	3	4	74	1	0	0	0	0	1	0	0	0	11198	652	23	1	366	1	OR5K2	3	98216888	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		98216888	99805542	19	21392										
PLCXD2	257068	broad.mit.edu	37	chr3	111564679	111564679	+	3'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tgtgtgcaggctggcactgaTcccagtttatcctttgagat	11	9	0	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr3:111564679T>A	ENST00000477665.1	+	0	1287				PHLDB2_ENST00000393923.3_5'UTR|PLCXD2_ENST00000393934.3_Missense_Mutation_p.I293N	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2						lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)	p.I293N(1)		endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						CTGGCACTGATCCCAGTTTAT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											185	168	174					3																	111564679		2203	4300	6503	113047369	SO:0001624	3_prime_UTR_variant	257068			AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.*45T>A	3.37:g.111564679T>A			113047369	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	37	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	T	4.359	0.066179	0.08388	.	.	ENSG00000240891	ENST00000393934	.	.	.	4.25	-0.815	0.10843	.	.	.	.	.	T	0.30916	0.0780	.	.	.	0.09310	N	1	B	0.21753	0.06	B	0.24006	0.05	T	0.33954	-0.9848	7	0.87932	D	0	.	7.334	0.26599	0.0:0.4427:0.0:0.5573	.	293	Q0VAA5-2	.	N	293	.	ENSP00000377511:I293N	I	+	2	0	PLCXD2	113047369	0.000000	0.05858	0.004000	0.12327	0.032000	0.12392	-0.247000	0.08866	-0.120000	0.11809	0.459000	0.35465	ATC		0.458	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111564679	T	A	111564679	1	1	74	0	1	0	0	0	0	0	0	0	12073	1435	50	5		5	PLCXD2	3	111564679	3'UTR	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	13347791	111564679	86457751	20	21393										
SEMA5B	54437	broad.mit.edu	37	chr3	122631753	122631753	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gcccacgcagggcaggccccCgttgcggggctccgggttag	17	15	0	0	rs78490011	byFrequency	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr3:122631753C>T	ENST00000357599.3	-	18	3048	c.2662G>A	c.(2662-2664)Ggg>Agg	p.G888R	SEMA5B_ENST00000195173.4_Missense_Mutation_p.G887R|SEMA5B_ENST00000451055.2_Missense_Mutation_p.G942R	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	888	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.G888R(1)|p.G942R(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GGCAGGCCCCCGTTGCGGGGC	0.692																																																2	Substitution - Missense(2)	large_intestine(2)	3											39	49	46					3																	122631753		2199	4300	6499	124114443	SO:0001583	missense	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2662G>A	3.37:g.122631753C>T	ENSP00000350215:p.Gly888Arg		124114443	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.126145	0.77549	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.2	5.2	0.72013	.	0.167915	0.52532	D	0.000079	D	0.83741	0.5320	M	0.93016	3.37	0.29631	N	0.845472	D;D	0.76494	0.998;0.999	D;D	0.70935	0.918;0.971	T	0.82623	-0.0366	10	0.72032	D	0.01	.	17.9141	0.88943	0.0:1.0:0.0:0.0	.	830;888	D3YTI7;Q9P283	.;SEM5B_HUMAN	R	888;887;830;942;888	ENSP00000350215:G888R;ENSP00000195173:G887R;ENSP00000389588:G942R;ENSP00000377208:G888R	ENSP00000195173:G887R	G	-	1	0	SEMA5B	124114443	0.318000	0.24598	0.997000	0.53966	0.996000	0.88848	2.374000	0.44274	2.722000	0.93159	0.655000	0.94253	GGG		0.692	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		T	122631753	C	T	122631753	3	4	74	1	0	0	0	0	1	0	0	0	14075	652	23	1	817	1	SEMA5B	3	122631753	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	11067074	122631753	75390677	21	21394										
VEPH1	79674	broad.mit.edu	37	chr3	157082169	157082169	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ctgatagagccaggggtattGctccctgcatttatcttgtc	10	10	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr3:157082169G>T	ENST00000362010.2	-	8	1567	c.1260C>A	c.(1258-1260)agC>agA	p.S420R	RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392832.2_Missense_Mutation_p.S420R|VEPH1_ENST00000392833.2_Missense_Mutation_p.S420R|VEPH1_ENST00000543418.1_Missense_Mutation_p.S420R	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	420						plasma membrane (GO:0005886)		p.S420R(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			CAGGGGTATTGCTCCCTGCAT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	3											143	138	139					3																	157082169		2203	4300	6503	158564863	SO:0001583	missense	79674			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1260C>A	3.37:g.157082169G>T	ENSP00000354919:p.Ser420Arg		158564863	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	G	1.812	-0.474314	0.04414	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	5.71	4.84	0.62591	.	0.763942	0.13061	N	0.416890	T	0.08133	0.0203	N	0.24115	0.695	0.58432	D	0.999996	B;B	0.20459	0.045;0.026	B;B	0.23275	0.045;0.021	T	0.26087	-1.0113	10	0.36615	T	0.2	-17.4684	14.6753	0.68975	0.0695:0.0:0.9305:0.0	.	420;420	Q14D04-2;Q14D04	.;MELT_HUMAN	R	420	ENSP00000376578:S420R;ENSP00000354919:S420R;ENSP00000446258:S420R;ENSP00000376577:S420R	ENSP00000354919:S420R	S	-	3	2	VEPH1	158564863	0.051000	0.20477	0.003000	0.11579	0.017000	0.09413	2.069000	0.41481	1.420000	0.47138	0.650000	0.86243	AGC		0.358	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		T	157082169	G	T	157082169	3	4	74	1	0	0	0	0	1	0	0	0	17194	1310	46	2	1269	2	VEPH1	3	157082169	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	34450416	157082169	40940261	22	21395										
HTT	3064	broad.mit.edu	37	chr4	3231640	3231640	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gtggtctcagacttgttcacCgagcgcaaccagtttgagct	11	11	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr4:3231640C>T	ENST00000355072.5	+	60	8281	c.8136C>T	c.(8134-8136)acC>acT	p.T2712T	HTT_ENST00000513806.1_3'UTR	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2712					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.T2712T(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ACTTGTTCACCGAGCGCAACC	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	4											106	112	110					4																	3231640		2170	4282	6452	3201438	SO:0001819	synonymous_variant	3064			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8136C>T	4.37:g.3231640C>T			3201438	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																				0.547	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3231640	C	T	3231640	2	4	74	1	0	0	0	0	0	0	0	1	7478	639	23	1		1	HTT	4	3231640	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		3231640	187922636	23	21396										
ENPEP	2028	broad.mit.edu	37	chr4	111412299	111412299	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caatttgactctgtaaagagAatatcaaatagtggaaaacc	7	6	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr4:111412299A>G	ENST00000265162.5	+	3	1239	c.897A>G	c.(895-897)agA>agG	p.R299R		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	299					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R299R(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		CTGTAAAGAGAATATCAAATA	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	4											79	82	81					4																	111412299		2203	4300	6503	111631748	SO:0001819	synonymous_variant	2028			L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.897A>G	4.37:g.111412299A>G			111631748	Q504U2	Silent	SNP	ENST00000265162.5	37	CCDS3691.1																																																																																				0.343	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			G	111412299	A	G	111412299	2	3	74	1	0	0	0	0	0	0	0	1	5141	243	9	4		4	ENPEP	4	111412299	Silent	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	108180659	111412299	79741977	24	21397										
ANK2	287	broad.mit.edu	37	chr4	114262919	114262919	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gtatacagagaaattatctgCgtaccttatatggccaaatt	7	7	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr4:114262919C>T	ENST00000357077.4	+	33	4022	c.3969C>T	c.(3967-3969)tgC>tgT	p.C1323C	ANK2_ENST00000394537.3_Silent_p.C1323C|ANK2_ENST00000509550.1_Silent_p.C499C|ANK2_ENST00000506722.1_Silent_p.C1314C|ANK2_ENST00000510275.2_5'Flank|ANK2_ENST00000504887.1_3'UTR|ANK2_ENST00000264366.6_Silent_p.C1290C	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1323	UPA domain.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.C1323C(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AAATTATCTGCGTACCTTATA	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	4											143	146	145					4																	114262919		2203	4300	6503	114482368	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.3969C>T	4.37:g.114262919C>T			114482368	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	9.925	1.213296	0.22289	.	.	ENSG00000145362	ENST00000514960;ENST00000504415	.	.	.	5.68	0.668	0.17912	.	.	.	.	.	T	0.55784	0.1942	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47923	-0.9079	4	.	.	.	.	9.095	0.36634	0.0:0.2871:0.0:0.7129	.	.	.	.	C	336;18	.	.	R	+	1	0	ANK2	114482368	0.991000	0.36638	0.998000	0.56505	0.985000	0.73830	0.224000	0.17738	0.109000	0.17891	-0.469000	0.05056	CGT		0.378	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114262919	C	T	114262919	2	4	74	1	0	0	0	0	0	0	0	1	621	776	27	1		1	ANK2	4	114262919	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	2850620	114262919	76891357	25	21398										
PHF17	79960	broad.mit.edu	37	chr4	129792844	129792844	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caacagaaaaatggtgtggtGatgccagaccatgggaaaag	13	6	0	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr4:129792844G>A	ENST00000226319.6	+	11	2236	c.1956G>A	c.(1954-1956)gtG>gtA	p.V652V	PHF17_ENST00000452328.2_Silent_p.V640V|PHF17_ENST00000512960.1_Silent_p.V652V	NM_199320.2	NP_955352.1												p.V652V(1)		NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						ATGGTGTGGTGATGCCAGACC	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	4											78	78	78					4																	129792844		2203	4300	6503	130012294	SO:0001819	synonymous_variant	79960																														ENST00000226319.6:c.1956G>A	4.37:g.129792844G>A			130012294		Silent	SNP	ENST00000226319.6	37	CCDS34062.1																																																																																				0.428	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			A	129792844	G	A	129792844	2	1	74	1	0	0	0	0	0	0	0	1	11859	1277	45	3		3	PHF17	4	129792844	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	15529925	129792844	61361432	26	21399										
RANBP3L	202151	broad.mit.edu	37	chr5	36269540	36269540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaaagtaaaagatgaagaccGtacacgctttgttggaaaac	9	6	0	3	rs146572714		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:36269540G>A	ENST00000296604.3	-	4	705	c.220C>T	c.(220-222)Cgg>Tgg	p.R74W	RANBP3L_ENST00000502994.1_Missense_Mutation_p.R74W|RANBP3L_ENST00000515759.1_Missense_Mutation_p.R74W	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	74					intracellular transport (GO:0046907)			p.R74W(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GATGAAGACCGTACACGCTTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	5						G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	107	104	105		220,220	1.1	0.8	5	dbSNP_134	105	2,8596	2.2+/-6.3	0,2,4297	no	missense,missense	RANBP3L	NM_001161429.1,NM_145000.3	101,101	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	74/491,74/466	36269540	2,13002	2203	4299	6502	36305297	SO:0001583	missense	202151			BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.220C>T	5.37:g.36269540G>A	ENSP00000296604:p.Arg74Trp		36305297	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	37	CCDS3918.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.202313	0.58234	0.0	2.33E-4	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759;ENST00000505865	T;T;T;T	0.73469	-0.69;0.08;-0.68;-0.75	4.66	1.13	0.20643	.	0.196194	0.34777	N	0.003696	D	0.82664	0.5086	M	0.75615	2.305	0.24072	N	0.995979	D;D	0.89917	1.0;1.0	D;D	0.72075	0.976;0.967	T	0.73509	-0.3960	10	0.87932	D	0	-1.3722	10.3751	0.44077	0.0:0.0:0.3576:0.6423	.	74;74	E9PGP9;Q86VV4	.;RNB3L_HUMAN	W	74	ENSP00000296604:R74W;ENSP00000421853:R74W;ENSP00000421149:R74W;ENSP00000427147:R74W	ENSP00000296604:R74W	R	-	1	2	RANBP3L	36305297	0.076000	0.21285	0.760000	0.31359	0.960000	0.62799	0.664000	0.25068	0.463000	0.27118	0.561000	0.74099	CGG		0.358	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		A	36269540	G	A	36269540	3	1	74	1	0	0	0	0	1	0	0	0	13067	1144	40	1	1300	1	RANBP3L	5	36269540	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		36269540	144645720	27	21400										
C5orf42	65250	broad.mit.edu	37	chr5	37167162	37167162	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gccttgcctttttttactgtCctttccttgtcttacttcag	5	12	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:37167162C>A	ENST00000508244.1	-	34	7480	c.7387G>T	c.(7387-7389)Gac>Tac	p.D2463Y	C5orf42_ENST00000425232.2_Missense_Mutation_p.D2463Y|C5orf42_ENST00000274258.7_Missense_Mutation_p.D1343Y			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2463						integral component of membrane (GO:0016021)		p.D2463Y(1)|p.D1343Y(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTTTTACTGTCCTTTCCTTGT	0.323																																																2	Substitution - Missense(2)	large_intestine(2)	5											177	165	169					5																	37167162		2203	4300	6503	37202919	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7387G>T	5.37:g.37167162C>A	ENSP00000421690:p.Asp2463Tyr		37202919	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069812	0.55539	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.27402	1.69;1.69;1.67;1.67	5.41	4.49	0.54785	.	0.883173	0.09576	N	0.783546	T	0.39436	0.1078	L	0.40543	1.245	0.29048	N	0.884689	D;D	0.65815	0.986;0.995	P;P	0.59288	0.855;0.834	T	0.27706	-1.0066	10	0.66056	D	0.02	.	5.2622	0.15580	0.0:0.6329:0.0:0.3671	.	2463;1343	E9PH94;Q9H799	.;CE042_HUMAN	Y	2463;2463;1343;1511;1343	ENSP00000421690:D2463Y;ENSP00000389014:D2463Y;ENSP00000274258:D1343Y;ENSP00000424223:D1511Y	ENSP00000274258:D1343Y	D	-	1	0	C5orf42	37202919	0.628000	0.27138	0.929000	0.37066	0.960000	0.62799	1.037000	0.30241	1.139000	0.42245	0.591000	0.81541	GAC		0.323	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37167162	C	A	37167162	3	1	74	1	0	0	0	0	1	0	0	0	2307	855	30	2	2278	2	C5orf42	5	37167162	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	897622	37167162	143748098	28	21401										
PIK3R1	5295	broad.mit.edu	37	chr5	67590446	67590446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	acagtgccagacccaagagcGgtacagcaaagaatacatag	10	10	0	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:67590446G>A	ENST00000521381.1	+	12	2124	c.1508G>A	c.(1507-1509)cGg>cAg	p.R503Q	PIK3R1_ENST00000274335.5_Missense_Mutation_p.R503Q|PIK3R1_ENST00000523872.1_Missense_Mutation_p.R140Q|PIK3R1_ENST00000320694.8_Missense_Mutation_p.R203Q|PIK3R1_ENST00000336483.5_Missense_Mutation_p.R233Q|PIK3R1_ENST00000521657.1_Missense_Mutation_p.R503Q|PIK3R1_ENST00000396611.1_Missense_Mutation_p.R503Q	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	503					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R503Q(2)|p.R203L(1)|p.0?(1)|p.?(1)|p.R503L(1)|p.R233Q(1)|p.R233L(1)|p.R203Q(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	ACCCAAGAGCGGTACAGCAAA	0.343			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	9	Substitution - Missense(7)|Whole gene deletion(1)|Unknown(1)	urinary_tract(3)|endometrium(3)|large_intestine(2)|lung(1)	5											72	73	73					5																	67590446		2203	4300	6503	67626202	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1508G>A	5.37:g.67590446G>A	ENSP00000428056:p.Arg503Gln		67626202	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870119	0.72065	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000519025;ENST00000523872	T;T;T;T;T;T;T;D	0.81908	-0.43;-0.43;-0.32;-0.43;-1.45;-1.45;0.36;-1.55	5.18	5.18	0.71444	.	0.054607	0.64402	D	0.000001	T	0.75280	0.3828	L	0.60455	1.87	0.80722	D	1	B;B;B;P	0.35807	0.017;0.061;0.006;0.522	B;B;B;B	0.19391	0.003;0.01;0.006;0.025	T	0.73145	-0.4075	10	0.27082	T	0.32	-16.1879	12.5699	0.56331	0.0758:0.0:0.9242:0.0	.	173;233;203;503	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	Q	503;503;503;503;203;233;176;140	ENSP00000428056:R503Q;ENSP00000429277:R503Q;ENSP00000379855:R503Q;ENSP00000274335:R503Q;ENSP00000323512:R203Q;ENSP00000338554:R233Q;ENSP00000429156:R176Q;ENSP00000430098:R140Q	ENSP00000274335:R503Q	R	+	2	0	PIK3R1	67626202	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.591000	0.74090	2.861000	0.98227	0.650000	0.86243	CGG		0.343	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		A	67590446	G	A	67590446	3	1	74	1	0	0	0	0	1	0	0	0	11949	1116	39	1	1680	1	PIK3R1	5	67590446	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	30423284	67590446	113324814	29	21402										
APC	324	broad.mit.edu	37	chr5	112175424	112175424	+	Frame_Shift_Del	DEL	A	A	-													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccacctgaacactatgttcAggagaccccactcatgttta							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:112175424delA	ENST00000457016.1	+	16	4513	c.4133delA	c.(4132-4134)cagfs	p.Q1378fs	APC_ENST00000257430.4_Frame_Shift_Del_p.Q1378fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Del_p.Q1378fs			P25054	APC_HUMAN	adenomatous polyposis coli	1378	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1378fs*7(2)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)|p.Y1376fs*1(1)|p.Q1378fs*37(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CACTATGTTCAGGAGACCCCA	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	9	Deletion - Frameshift(7)|Unknown(1)|Complex - frameshift(1)	large_intestine(7)|soft_tissue(1)|skin(1)	5											92	88	89					5																	112175424		2202	4300	6502	112203323	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4133delA	5.37:g.112175424delA	ENSP00000413133:p.Gln1378fs		112203323	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175424	A	-	112175424	7	5	74	1	0	1	0	1	0	0	0	0	763	188	7	0	4191	0	APC	5	112175424	Frame_Shift_Del	DEL	A	TCGA-AG-A025-01A-01W-A00E-09	44584978	112175424	68739836	30	21403										
LRRTM2	26045	broad.mit.edu	37	chr5	138209261	138209261	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tggagtgttcccaccgacctTggaaactgcccagccaggag	12	13	0	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:138209261T>A	ENST00000274711.6	-	2	1367	c.989A>T	c.(988-990)cAa>cTa	p.Q330L	CTNNA1_ENST00000520400.1_Intron|LRRTM2_ENST00000518785.1_3'UTR|CTNNA1_ENST00000518825.1_Intron|LRRTM2_ENST00000521094.2_Intron|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000540387.1_5'Flank|LRRTM2_ENST00000523537.1_5'Flank|CTNNA1_ENST00000302763.7_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	330	LRRCT.				long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.Q330L(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCACCGACCTTGGAAACTGCC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	5											91	91	91					5																	138209261		2017	4174	6191	138237160	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.989A>T	5.37:g.138209261T>A	ENSP00000274711:p.Gln330Leu		138237160	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.	.	.	.	.	.	.	.	.	.	T	10.82	1.458590	0.26248	.	.	ENSG00000146006	ENST00000274711	T	0.45668	0.89	5.3	5.3	0.74995	.	0.135329	0.49916	D	0.000135	T	0.34658	0.0905	L	0.44542	1.39	0.38661	D	0.952073	B;B	0.23735	0.003;0.09	B;B	0.19148	0.005;0.024	T	0.28808	-1.0032	10	0.52906	T	0.07	.	10.5452	0.45056	0.0:0.0769:0.0:0.9231	.	196;330	B7Z4G4;O43300	.;LRRT2_HUMAN	L	330	ENSP00000274711:Q330L	ENSP00000274711:Q330L	Q	-	2	0	LRRTM2	138237160	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.402000	0.52608	2.227000	0.72691	0.528000	0.53228	CAA		0.532	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			A	138209261	T	A	138209261	3	1	74	1	0	0	0	0	1	0	0	0	9069	1812	63	5	565	5	LRRTM2	5	138209261	Missense_Mutation	SNP	T	TCGA-AG-A025-01A-01W-A00E-09	26033837	138209261	42705999	31	21404										
PCDHA6	56142	broad.mit.edu	37	chr5	140209559	140209559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gtttcgcgtggggctgtacaCgggcgagatcagcaccactc	14	12	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:140209559C>T	ENST00000529310.1	+	1	1997	c.1883C>T	c.(1882-1884)aCg>aTg	p.T628M	PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	628	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.T628M(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCTGTACACGGGCGAGATC	0.667																																																2	Substitution - Missense(2)	large_intestine(2)	5											71	78	75					5																	140209559		2203	4300	6503	140189743	SO:0001583	missense	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1883C>T	5.37:g.140209559C>T	ENSP00000433378:p.Thr628Met		140189743	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.706462	0.30232	.	.	ENSG00000081842	ENST00000529310	T	0.58060	0.36	3.98	3.11	0.35812	Cadherin (4);Cadherin-like (1);	0.000000	0.37715	U	0.001966	T	0.74801	0.3764	H	0.97564	4.03	0.80722	D	1	D;D	0.76494	0.999;0.997	P;P	0.62491	0.903;0.871	T	0.74708	-0.3574	10	0.72032	D	0.01	.	3.3184	0.07041	0.1467:0.5329:0.2199:0.1005	.	628;628	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	M	628	ENSP00000433378:T628M	ENSP00000433378:T628M	T	+	2	0	PCDHA6	140189743	0.636000	0.27207	0.999000	0.59377	0.142000	0.21351	1.214000	0.32419	1.024000	0.39682	0.306000	0.20318	ACG		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		T	140209559	C	T	140209559	3	4	74	1	0	0	0	0	1	0	0	0	11559	536	19	1	1885	1	PCDHA6	5	140209559	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	2000298	140209559	40705701	32	21405										
PCDHB3	56132	broad.mit.edu	37	chr5	140482106	140482106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gggcgcacaatggcgaagtgCgcaccgccaggctgctgagc	16	13	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:140482106C>T	ENST00000231130.2	+	1	1873	c.1873C>T	c.(1873-1875)Cgc>Tgc	p.R625C	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	625	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R625C(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGCGAAGTGCGCACCGCCAG	0.706																																																1	Substitution - Missense(1)	large_intestine(1)	5											31	33	32					5																	140482106		2153	4172	6325	140462290	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1873C>T	5.37:g.140482106C>T	ENSP00000231130:p.Arg625Cys		140462290	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001096	0.54254	.	.	ENSG00000113205	ENST00000231130	T	0.52754	0.65	4.38	4.38	0.52667	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.79015	0.4375	H	0.98295	4.195	0.45995	D	0.9988	D	0.89917	1.0	D	0.87578	0.998	D	0.85404	0.1133	9	0.72032	D	0.01	.	11.1869	0.48662	0.3161:0.6839:0.0:0.0	.	625	Q9Y5E6	PCDB3_HUMAN	C	625	ENSP00000231130:R625C	ENSP00000231130:R625C	R	+	1	0	PCDHB3	140462290	0.973000	0.33851	1.000000	0.80357	0.992000	0.81027	0.709000	0.25734	2.143000	0.66587	0.556000	0.70494	CGC		0.706	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140482106	C	T	140482106	3	4	74	1	0	0	0	0	1	0	0	0	11574	768	27	1	1875	1	PCDHB3	5	140482106	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	272547	140482106	40433154	33	21406										
PCDHB12	56124	broad.mit.edu	37	chr5	140588873	140588873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	atataaatgatcactctcccGtcttcttggaaaaagaaatg	6	8	4	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:140588873G>A	ENST00000239450.2	+	1	583	c.394G>A	c.(394-396)Gtc>Atc	p.V132I	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	132	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.V132I(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCACTCTCCCGTCTTCTTGGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	5											101	110	107					5																	140588873		2202	4299	6501	140569057	SO:0001583	missense	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.394G>A	5.37:g.140588873G>A	ENSP00000239450:p.Val132Ile		140569057	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	2.721	-0.266481	0.05754	.	.	ENSG00000120328	ENST00000239450	T	0.21734	1.99	4.25	-0.996	0.10218	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.15565	0.0375	L	0.39633	1.23	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.22661	-1.0210	9	0.37606	T	0.19	.	8.035	0.30486	0.3308:0.1041:0.565:0.0	.	132	Q9Y5F1	PCDBC_HUMAN	I	132	ENSP00000239450:V132I	ENSP00000239450:V132I	V	+	1	0	PCDHB12	140569057	0.000000	0.05858	0.000000	0.03702	0.459000	0.32528	-4.600000	0.00210	-0.900000	0.03896	-1.134000	0.01955	GTC		0.408	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		A	140588873	G	A	140588873	3	1	74	1	0	0	0	0	1	0	0	0	11568	1145	40	1	396	1	PCDHB12	5	140588873	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	106767	140588873	40326387	34	21407										
LMAN2	10960	broad.mit.edu	37	chr5	176765564	176765564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cttcttccctgtgccgtggaCtttgaagtggacgtgcattt	11	10	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr5:176765564C>T	ENST00000303127.7	-	3	562	c.358G>A	c.(358-360)Gtc>Atc	p.V120I	LMAN2_ENST00000506310.1_5'UTR|LMAN2_ENST00000515209.1_Missense_Mutation_p.V120I|RN7SL562P_ENST00000582768.1_RNA	NM_006816.2	NP_006807.1	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2	120	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				positive regulation of phagocytosis (GO:0050766)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|heat shock protein binding (GO:0031072)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)	p.V120I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGCCGTGGACTTTGAAGTGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	5											283	228	247					5																	176765564		2203	4300	6503	176698170	SO:0001583	missense	10960			U10362	CCDS4417.1	5q35	2008-02-05		2003-07-04	ENSG00000169223	ENSG00000169223			16986	protein-coding gene	gene with protein product		609551	"chromosome 5 open reading frame 8"	C5orf8		12609988	Standard	NM_006816		Approved	GP36B, VIP36	uc003mge.3	Q12907	OTTHUMG00000130860	ENST00000303127.7:c.358G>A	5.37:g.176765564C>T	ENSP00000303366:p.Val120Ile		176698170	Q53HH1	Missense_Mutation	SNP	ENST00000303127.7	37	CCDS4417.1	.	.	.	.	.	.	.	.	.	.	C	6.429	0.447326	0.12223	.	.	ENSG00000169223	ENST00000303127;ENST00000539488;ENST00000515209;ENST00000514458;ENST00000502560;ENST00000513877	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.03	3.26	0.37387	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.239990	0.42821	N	0.000649	T	0.33498	0.0865	N	0.03084	-0.415	0.50313	D	0.999867	B;B	0.02656	0.0;0.0	B;B	0.12837	0.005;0.008	T	0.27020	-1.0086	10	0.02654	T	1	-32.5341	6.3583	0.21414	0.0:0.6058:0.0:0.3942	.	120;120	Q12907;D6RBV2	LMAN2_HUMAN;.	I	120;49;120;120;120;49	ENSP00000303366:V120I;ENSP00000423998:V120I;ENSP00000424132:V120I;ENSP00000425229:V120I;ENSP00000427377:V49I	ENSP00000303366:V120I	V	-	1	0	LMAN2	176698170	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	1.851000	0.39338	0.835000	0.34877	0.591000	0.81541	GTC		0.617	LMAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253434.1	NM_006816		T	176765564	C	T	176765564	3	4	74	1	0	0	0	0	1	0	0	0	8862	565	20	3	736	3	LMAN2	5	176765564	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	36176691	176765564	4149696	35	21408										
SCGN	10590	broad.mit.edu	37	chr6	25701470	25701470	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gtggaccttgataagttccgCgagattctcctgcgtcactg	11	11	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:25701470C>T	ENST00000377961.2	+	11	906	c.738C>T	c.(736-738)cgC>cgT	p.R246R	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	246	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.R246R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						ATAAGTTCCGCGAGATTCTCC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	6											118	100	106					6																	25701470		2203	4300	6503	25809449	SO:0001819	synonymous_variant	10590			BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.738C>T	6.37:g.25701470C>T			25809449	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Silent	SNP	ENST00000377961.2	37	CCDS4561.1																																																																																				0.498	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			T	25701470	C	T	25701470	2	4	74	1	0	0	0	0	0	0	0	1	13940	755	27	1		1	SCGN	6	25701470	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		25701470	145413597	36	21409										
ANKS1A	23294	broad.mit.edu	37	chr6	35048877	35048878	+	Missense_Mutation	DNP	GC	GC	CT													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aggggacacaggcaggaggcGccatgacagtctccatgacc							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:35048877_35048878GC>CT	ENST00000360359.3	+	17	2789_2790	c.2651_2652GC>CT	c.(2650-2652)cGC>cCT	p.R884P	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	884					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.R884>?(1)|p.R210>?(1)		cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GGCAGGAGGCGCCATGACAGTC	0.634																																																2	Complex(2)	large_intestine(2)	6																																								35156856	SO:0001583	missense	23294			D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	Exception_encountered	6.37:g.35048877_35048878delinsCT	ENSP00000353518:p.Arg884Pro		35156855	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	DNP	ENST00000360359.3	37	CCDS4798.1																																																																																				0.634	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		CT	35048878	GC	CT	35048877	3	2	74	1	0	0	0	0	1	0	0	0	688	1087	38	5	2717	5	ANKS1A	6	35048877	Missense_Mutation	DNP	GC	TCGA-AG-A025-01A-01W-A00E-09	9347407	35048877	136066190	37	21410										
BRPF3	27154	broad.mit.edu	37	chr6	36168861	36168861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tacatccctgagggccagtgGctatgccgctgctgcctgca	12	14	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:36168861G>T	ENST00000357641.6	+	2	1015	c.762G>T	c.(760-762)tgG>tgT	p.W254C	BRPF3_ENST00000443324.2_Missense_Mutation_p.W254C|BRPF3_ENST00000534694.1_Missense_Mutation_p.W254C|BRPF3_ENST00000543502.1_Missense_Mutation_p.W254C|BRPF3_ENST00000339717.7_Missense_Mutation_p.W254C|BRPF3_ENST00000534400.1_Missense_Mutation_p.W254C	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	254					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)	p.W254C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						AGGGCCAGTGGCTATGCCGCT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											87	78	81					6																	36168861		2203	4300	6503	36276839	SO:0001583	missense	27154			AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.762G>T	6.37:g.36168861G>T	ENSP00000350267:p.Trp254Cys		36276839	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	37	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818557	0.71028	.	.	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000534694;ENST00000543502;ENST00000443324;ENST00000534400	D;D;D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39;-3.39;-3.39	5.79	5.79	0.91817	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.98585	0.9527	H	0.99464	4.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.99568	1.0970	10	0.87932	D	0	.	20.0368	0.97565	0.0:0.0:1.0:0.0	.	254;254;254	B7ZLN5;Q17RB6;Q9ULD4	.;.;BRPF3_HUMAN	C	254	ENSP00000350267:W254C;ENSP00000345419:W254C;ENSP00000434501:W254C;ENSP00000445352:W254C;ENSP00000387368:W254C;ENSP00000436504:W254C	ENSP00000345419:W254C	W	+	3	0	BRPF3	36276839	1.000000	0.71417	0.971000	0.41717	0.987000	0.75469	9.414000	0.97362	2.735000	0.93741	0.563000	0.77884	TGG		0.552	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		T	36168861	G	T	36168861	3	4	74	1	0	0	0	0	1	0	0	0	1524	1212	42	2	764	2	BRPF3	6	36168861	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	1119984	36168861	134946206	38	21411										
PEX6	5190	broad.mit.edu	37	chr6	42933493	42933493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccagttcatcaaagaagatAatgcatggagctgcagccct	9	10	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:42933493A>G	ENST00000304611.8	-	13	2466	c.2397T>C	c.(2395-2397)atT>atC	p.I799I	PEX6_ENST00000244546.4_Missense_Mutation_p.L717S	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	799					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.I799I(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			CAAAGAAGATAATGCATGGAG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	6											108	120	116					6																	42933493		2203	4300	6503	43041471	SO:0001819	synonymous_variant	5190			U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"ATPases / AAA-type"	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2397T>C	6.37:g.42933493A>G			43041471	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Silent	SNP	ENST00000304611.8	37	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597925	0.28445	.	.	ENSG00000124587	ENST00000244546	D	0.95788	-3.81	5.86	-4.42	0.03579	.	.	.	.	.	D	0.90590	0.7050	.	.	.	0.22982	N	0.998473	.	.	.	.	.	.	D	0.87842	0.2652	6	0.87932	D	0	-8.186	9.786	0.40677	0.3778:0.0:0.5236:0.0986	.	.	.	.	S	717	ENSP00000244546:L717S	ENSP00000244546:L717S	L	-	2	0	PEX6	43041471	0.963000	0.33076	0.774000	0.31636	0.997000	0.91878	0.167000	0.16602	-0.678000	0.05224	0.460000	0.39030	TTA		0.567	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		G	42933493	A	G	42933493	2	3	74	1	0	0	0	0	0	0	0	1	11781	358	13	4		4	PEX6	6	42933493	Silent	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	6764632	42933493	128181574	39	21412										
FILIP1	27145	broad.mit.edu	37	chr6	76023702	76023702	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ggtgagctcagacccttttcGtgaccttcctcttgttattt	8	11	2	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:76023702G>A	ENST00000237172.7	-	5	2176	c.1846C>T	c.(1846-1848)Cga>Tga	p.R616*	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.R517*|FILIP1_ENST00000393004.2_Nonsense_Mutation_p.R616*	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	616								p.R616*(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GACCCTTTTCGTGACCTTCCT	0.398																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											264	273	270					6																	76023702		2203	4300	6503	76080422	SO:0001587	stop_gained	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1846C>T	6.37:g.76023702G>A	ENSP00000237172:p.Arg616*		76080422	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	37	6.036074	0.97221	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	6.11	4.29	0.51040	.	0.249082	0.40064	N	0.001184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-5.9393	8.1643	0.31217	0.076:0.0:0.4741:0.4499	.	.	.	.	X	616;616;517	.	ENSP00000237172:R616X	R	-	1	2	FILIP1	76080422	0.025000	0.19082	0.647000	0.29507	0.410000	0.31052	1.616000	0.36933	0.861000	0.35504	0.655000	0.94253	CGA		0.398	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023702	G	A	76023702	4	1	74	1	0	0	0	0	0	1	0	0	5913	1153	40	1	1803	1	FILIP1	6	76023702	Nonsense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	33090209	76023702	95091365	40	21413										
GRM1	2911	broad.mit.edu	37	chr6	146720759	146720759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ttgtccgcatgcatgttggcGatggcaagctgccctgccgc	13	13	0	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:146720759G>A	ENST00000282753.1	+	7	2819	c.2584G>A	c.(2584-2586)Gat>Aat	p.D862N	GRM1_ENST00000361719.2_Missense_Mutation_p.D862N|GRM1_ENST00000492807.2_Missense_Mutation_p.D862N|GRM1_ENST00000392299.2_Missense_Mutation_p.D862N|GRM1_ENST00000507907.1_Missense_Mutation_p.D862N|GRM1_ENST00000355289.4_Missense_Mutation_p.D862N			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	862					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.D862N(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCATGTTGGCGATGGCAAGCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	6											50	42	45					6																	146720759		2203	4299	6502	146762452	SO:0001583	missense	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2584G>A	6.37:g.146720759G>A	ENSP00000282753:p.Asp862Asn		146762452	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822644	0.90873	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.88431	-2.38;-2.33;-2.33;-2.38;-2.32;-2.33	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.94265	0.8158	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	0.961;1.0;0.961	B;D;B	0.77557	0.436;0.99;0.436	D	0.93572	0.6905	10	0.52906	T	0.07	.	19.7753	0.96389	0.0:0.0:1.0:0.0	.	862;862;862	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	N	862	ENSP00000354896:D862N;ENSP00000376119:D862N;ENSP00000424095:D862N;ENSP00000282753:D862N;ENSP00000347437:D862N;ENSP00000425599:D862N	ENSP00000282753:D862N	D	+	1	0	GRM1	146762452	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.686000	0.91538	0.585000	0.79938	GAT		0.517	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		A	146720759	G	A	146720759	3	1	74	1	0	0	0	0	1	0	0	0	6817	1058	37	1	2610	1	GRM1	6	146720759	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	70697057	146720759	24394308	41	21414										
SYNE1	23345	broad.mit.edu	37	chr6	152831401	152831401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gatcttggtggtcaccttccGtttacttggtgggctgggag	15	8	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:152831401G>A	ENST00000367255.5	-	8	1109	c.508C>T	c.(508-510)Cgg>Tgg	p.R170W	SYNE1_ENST00000423061.1_Missense_Mutation_p.R177W|SYNE1_ENST00000265368.4_Missense_Mutation_p.R170W|SYNE1_ENST00000341594.5_Missense_Mutation_p.R170W|SYNE1_ENST00000466159.2_Missense_Mutation_p.R170W|SYNE1_ENST00000448038.1_Missense_Mutation_p.R177W|SYNE1_ENST00000367248.3_Missense_Mutation_p.R177W|SYNE1_ENST00000367253.4_Missense_Mutation_p.R170W|SYNE1_ENST00000413186.2_Missense_Mutation_p.R170W	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	170	Actin-binding.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R170W(7)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTCACCTTCCGTTTACTTGGT	0.483										HNSCC(10;0.0054)																																						7	Substitution - Missense(7)	large_intestine(4)|prostate(3)	6											195	175	182					6																	152831401		2203	4300	6503	152873094	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.508C>T	6.37:g.152831401G>A	ENSP00000356224:p.Arg170Trp		152873094	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271820	0.59649	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	T;T;T;T;T;D;D;D;D;D	0.92348	0.32;0.31;0.22;0.31;0.47;-2.46;-2.58;-2.59;-2.83;-3.02	5.66	1.3	0.21679	Calponin homology domain (1);	0.118151	0.37219	N	0.002183	D	0.94889	0.8348	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.998;0.999;1.0	D	0.95353	0.8448	10	0.72032	D	0.01	.	14.8467	0.70264	0.0:0.0:0.52:0.4799	.	170;170;170;170;177	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	W	170;177;170;177;170;170;177;170;170;170	ENSP00000356224:R170W;ENSP00000396024:R177W;ENSP00000265368:R170W;ENSP00000390975:R177W;ENSP00000341887:R170W;ENSP00000356222:R170W;ENSP00000356217:R177W;ENSP00000414510:R170W;ENSP00000446021:R170W;ENSP00000441264:R170W	ENSP00000265368:R170W	R	-	1	2	SYNE1	152873094	0.978000	0.34361	0.672000	0.29872	0.750000	0.42670	1.413000	0.34725	0.686000	0.31488	-0.202000	0.12741	CGG		0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152831401	G	A	152831401	3	1	74	1	0	0	0	0	1	0	0	0	15484	1144	40	1	26514	1	SYNE1	6	152831401	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	6110642	152831401	18283666	42	21415										
THBS2	7058	broad.mit.edu	37	chr6	169622458	169622458	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccacatcaccacatagaagCggctgcttgactggtaacca	8	13	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr6:169622458C>T	ENST00000366787.3	-	20	3356	c.3107G>A	c.(3106-3108)cGc>cAc	p.R1036H	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1036	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R1036H(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		CACATAGAAGCGGCTGCTTGA	0.577																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Missense(1)	large_intestine(1)	6											69	61	64					6																	169622458		2203	4300	6503	169364383	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3107G>A	6.37:g.169622458C>T	ENSP00000355751:p.Arg1036His		169364383	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652566	0.47362	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.95447	-3.71	4.32	3.43	0.39272	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.41294	U	0.000901	D	0.87038	0.6078	L	0.38175	1.15	0.44316	D	0.997197	P	0.47962	0.903	B	0.36186	0.219	D	0.86173	0.1601	10	0.54805	T	0.06	-40.6879	13.2774	0.60194	0.1598:0.8402:0.0:0.0	.	1036	P35442	TSP2_HUMAN	H	1036;294	ENSP00000355751:R1036H	ENSP00000355751:R1036H	R	-	2	0	THBS2	169364383	1.000000	0.71417	0.997000	0.53966	0.609000	0.37215	7.276000	0.78559	0.758000	0.33059	0.297000	0.19635	CGC		0.577	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169622458	C	T	169622458	3	4	74	1	0	0	0	0	1	0	0	0	15893	768	27	1	427	1	THBS2	6	169622458	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	16791057	169622458	1492609	43	21416										
MIOS	54468	broad.mit.edu	37	chr7	7613282	7613282	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ttagaaaaagatatagcaacGaagatgcgtcttcgggcttt	10	6	1	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr7:7613282G>A	ENST00000340080.4	+	4	1597	c.1176G>A	c.(1174-1176)acG>acA	p.T392T	MIOS_ENST00000405785.1_Silent_p.T392T	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	392						lysosomal membrane (GO:0005765)		p.T392T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						ATATAGCAACGAAGATGCGTC	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	7											82	78	79					7																	7613282		1848	4095	5943	7579807	SO:0001819	synonymous_variant	54468				CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.1176G>A	7.37:g.7613282G>A			7579807	B2RTV6|O75216|Q7L551|Q9H092	Silent	SNP	ENST00000340080.4	37	CCDS43554.1																																																																																				0.408	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		A	7613282	G	A	7613282	2	1	74	1	0	0	0	0	0	0	0	1	9619	1045	37	1		1	MIOS	7	7613282	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		7613282	151525381	44	21417										
DNAJC2	27000	broad.mit.edu	37	chr7	102982334	102982335	+	Frame_Shift_Del	DEL	TC	TC	-													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tgaaaagaggcagaagcattTctgtttctcctcttaacaaa							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	TC	TC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr7:102982334_102982335delTC	ENST00000379263.3	-	2	381_382	c.131_132delGA	c.(130-132)agafs	p.R44fs	DNAJC2_ENST00000249270.7_Frame_Shift_Del_p.R44fs|DNAJC2_ENST00000412522.1_Frame_Shift_Del_p.R44fs	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	44					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)	p.R44fs*12(2)		endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						CAGAAGCATTTCTGTTTCTCCT	0.416																																																2	Deletion - Frameshift(2)	large_intestine(2)	7																																								102769571	SO:0001589	frameshift_variant	27000			X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.131_132delGA	7.37:g.102982334_102982335delTC	ENSP00000368565:p.Arg44fs		102769570	A4VCI0|Q9BVX1	Frame_Shift_Del	DEL	ENST00000379263.3	37	CCDS43628.1																																																																																				0.416	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			-	102982335	TC	-	102982334	7	5	74	1	0	1	0	1	0	0	0	0	4650	1780	62	0	1797	0	DNAJC2	7	102982334	Frame_Shift_Del	DEL	TC	TCGA-AG-A025-01A-01W-A00E-09	95369052	102982334	56156329	45	21418										
ST7	7982	broad.mit.edu	37	chr7	116810941	116810941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gaaggagttcccccttctgaGtatgttcaatatccatgaaa	8	9	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr7:116810941G>A	ENST00000393446.2	+	9	1223	c.920G>A	c.(919-921)aGt>aAt	p.S307N	ST7_ENST00000393449.1_Missense_Mutation_p.S330N|ST7_ENST00000432298.1_Missense_Mutation_p.S284N|ST7_ENST00000393451.3_Missense_Mutation_p.S307N|ST7_ENST00000393447.4_Missense_Mutation_p.S287N|ST7_ENST00000393443.1_Missense_Mutation_p.S257N|ST7_ENST00000393444.3_Missense_Mutation_p.S264N|ST7_ENST00000323984.3_Missense_Mutation_p.S330N|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000422922.1_Missense_Mutation_p.S261N|ST7_ENST00000265437.5_Missense_Mutation_p.S330N			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)	p.S330N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CCCCTTCTGAGTATGTTCAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	7											98	97	97					7																	116810941		2203	4300	6503	116598177	SO:0001583	missense	7982			AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.920G>A	7.37:g.116810941G>A	ENSP00000377092:p.Ser307Asn		116598177	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000393446.2	37		.	.	.	.	.	.	.	.	.	.	G	12.02	1.811220	0.32053	.	.	ENSG00000004866	ENST00000393446;ENST00000265437;ENST00000393451;ENST00000323984;ENST00000393449;ENST00000446490;ENST00000432298;ENST00000422922;ENST00000393443;ENST00000393447;ENST00000393444;ENST00000490039	T;T;T;T;T;T;T;T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.28	5.28	0.74379	Tetratricopeptide-like helical (1);	0.079027	0.85682	D	0.000000	T	0.30355	0.0762	N	0.25890	0.77	0.80722	D	1	D;B;B;B;B;B;B;B	0.64830	0.994;0.018;0.022;0.033;0.018;0.022;0.0;0.008	D;B;B;B;B;B;B;B	0.72338	0.977;0.042;0.018;0.036;0.031;0.068;0.002;0.029	T	0.01393	-1.1366	10	0.02654	T	1	-10.935	19.2638	0.93979	0.0:0.0:1.0:0.0	.	278;287;307;307;257;284;307;330	C9JU30;B7Z4L1;B7Z573;Q9NRC1-7;Q9NRC1-6;B7Z4U3;Q9NRC1-2;Q9NRC1	.;.;.;.;.;.;.;ST7_HUMAN	N	307;330;307;330;330;307;284;261;257;287;264;278	ENSP00000377092:S307N;ENSP00000265437:S330N;ENSP00000377097:S307N;ENSP00000325673:S330N;ENSP00000377095:S330N;ENSP00000402934:S307N;ENSP00000411118:S284N;ENSP00000414031:S261N;ENSP00000377089:S257N;ENSP00000377093:S287N;ENSP00000377090:S264N;ENSP00000419516:S278N	ENSP00000265437:S330N	S	+	2	0	ST7	116598177	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.420000	0.97426	2.629000	0.89072	0.557000	0.71058	AGT		0.333	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908		A	116810941	G	A	116810941	3	1	74	1	0	0	0	0	1	0	0	0	15268	1029	36	3	1027	3	ST7	7	116810941	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	13828607	116810941	42327722	46	21419										
NCAPG2	54892	broad.mit.edu	37	chr7	158482625	158482625	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaagcttgatggatacgccaAagccgacatacgtctgcacc	9	12	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr7:158482625A>T	ENST00000409423.1	-	7	730	c.558T>A	c.(556-558)ctT>ctA	p.L186L	NCAPG2_ENST00000409339.3_Silent_p.L186L|NCAPG2_ENST00000449727.2_Silent_p.L186L|NCAPG2_ENST00000275830.10_5'Flank|NCAPG2_ENST00000356309.3_Silent_p.L186L	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	186					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)	p.L186L(1)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		GGATACGCCAAAGCCGACATA	0.303																																																1	Substitution - coding silent(1)	large_intestine(1)	7											47	43	44					7																	158482625		1832	4087	5919	158175386	SO:0001819	synonymous_variant	54892			BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"leucine zipper protein 5"	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.558T>A	7.37:g.158482625A>T			158175386	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	De_novo_Start_OutOfFrame	SNP	ENST00000409423.1	37	CCDS43686.1																																																																																				0.303	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760		T	158482625	A	T	158482625	2	4	74	1	0	0	0	0	0	0	0	1	10239	1	1	5		5	NCAPG2	7	158482625	Silent	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	41671684	158482625	656038	47	21420										
PTDSS1	9791	broad.mit.edu	37	chr8	97311947	97311947	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cttcatgcatctcctccccaAttttgccgagtgctggtggg	10	13	2	0	rs375073869		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr8:97311947A>G	ENST00000517309.1	+	6	952	c.626A>G	c.(625-627)aAt>aGt	p.N209S	PTDSS1_ENST00000522072.1_Missense_Mutation_p.N6S|PTDSS1_ENST00000455950.2_Missense_Mutation_p.N63S|PTDSS1_ENST00000518776.1_3'UTR	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	209					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.N209S(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	CTCCTCCCCAATTTTGCCGAG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8						A	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	216	195	202		626	5.6	1	8		202	0,8600		0,0,4300	no	missense	PTDSS1	NM_014754.1	46	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	209/474	97311947	1,13005	2203	4300	6503	97381123	SO:0001583	missense	9791			D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.626A>G	8.37:g.97311947A>G	ENSP00000430548:p.Asn209Ser		97381123	E5RFC5|Q9BUQ5	Missense_Mutation	SNP	ENST00000517309.1	37	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.865371	0.91511	2.27E-4	0.0	ENSG00000156471	ENST00000517309;ENST00000455950;ENST00000522072	T;T;T	0.62105	0.05;0.24;0.17	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.83945	0.5364	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88169	0.2863	10	0.87932	D	0	-23.8644	14.4249	0.67207	1.0:0.0:0.0:0.0	.	209	P48651	PTSS1_HUMAN	S	209;63;6	ENSP00000430548:N209S;ENSP00000401248:N63S;ENSP00000430928:N6S	ENSP00000401248:N63S	N	+	2	0	PTDSS1	97381123	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	9.339000	0.96797	2.141000	0.66446	0.528000	0.53228	AAT		0.468	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2			G	97311947	A	G	97311947	3	3	74	1	0	0	0	0	1	0	0	0	12770	101	4	4	648	4	PTDSS1	8	97311947	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09		97311947	49052075	48	21421										
CTSL2	1515	broad.mit.edu	37	chr9	99799857	99799857	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tgtgcagttcaatcattttcAtattcttttcccacactgct	4	11	4	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr9:99799857A>C	ENST00000259470.5	-	3	416	c.167T>G	c.(166-168)aTg>aGg	p.M56R	CTSV_ENST00000538255.1_Missense_Mutation_p.M56R|CTSV_ENST00000479932.1_5'UTR	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V	56					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)	p.M56R(1)									AATCATTTTCATATTCTTTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	9											257	228	238					9																	99799857		2203	4300	6503	98839678	SO:0001583	missense	1515			Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"Cathepsins"	2538	protein-coding gene	gene with protein product		603308	"cathepsin L2"	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.167T>G	9.37:g.99799857A>C	ENSP00000259470:p.Met56Arg		98839678	O60233|Q2TB86|Q5T1U0	Missense_Mutation	SNP	ENST00000259470.5	37	CCDS6723.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.641257	0.29157	.	.	ENSG00000136943	ENST00000259470;ENST00000538255	D;D	0.85773	-2.03;-2.03	3.81	2.62	0.31277	Proteinase inhibitor I29, cathepsin propeptide (2);	0.242826	0.42548	D	0.000695	T	0.75925	0.3916	L	0.37561	1.115	0.45477	D	0.998445	B;B	0.18741	0.03;0.016	B;B	0.26094	0.044;0.066	T	0.65038	-0.6265	9	.	.	.	.	7.9995	0.30288	0.8175:0.0:0.0:0.1825	.	56;56	B2R717;O60911	.;CATL2_HUMAN	R	56	ENSP00000259470:M56R;ENSP00000445052:M56R	.	M	-	2	0	CTSL2	98839678	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	6.711000	0.74675	0.793000	0.33875	0.459000	0.35465	ATG		0.438	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053301.2	NM_001333		C	99799857	A	C	99799857	3	2	74	1	0	0	0	0	1	0	0	0	4045	217	8	4	861	4	CTSL2	9	99799857	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09		99799857	41413574	49	21422										
PAPPA	5069	broad.mit.edu	37	chr9	118950322	118950322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaccacacgctgacgggccaCgacggcggggattgccgcca	14	15	0	1	rs371022168		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr9:118950322C>T	ENST00000328252.3	+	2	1674	c.1305C>T	c.(1303-1305)caC>caT	p.H435H	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	435	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.H435H(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TGACGGGCCACGACGGCGGGG	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	9						C		0,4406		0,0,2203	64	51	55		1305	-5.5	0.3	9		55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PAPPA	NM_002581.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		435/1628	118950322	1,13005	2203	4300	6503	117990143	SO:0001819	synonymous_variant	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1305C>T	9.37:g.118950322C>T			117990143	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																				0.602	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118950322	C	T	118950322	2	4	74	1	0	0	0	0	0	0	0	1	11463	535	19	1		1	PAPPA	9	118950322	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	19150465	118950322	22263109	50	21423										
CACNA1B	774	broad.mit.edu	37	chr9	141010123	141010123	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccacctccctcagcaatggCggggccatgtgagtatccag	11	14	1	1	rs201682730		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr9:141010123C>T	ENST00000371372.1	+	42	5914	c.5769C>T	c.(5767-5769)ggC>ggT	p.G1923G	CACNA1B_ENST00000371357.1_Silent_p.G1922G|CACNA1B_ENST00000371355.4_Silent_p.G1924G|CACNA1B_ENST00000277549.5_Silent_p.G1117G|CACNA1B_ENST00000371363.1_Silent_p.G1921G|CACNA1B_ENST00000277551.2_Silent_p.G1923G	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1923					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.G1923G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCAGCAATGGCGGGGCCATGT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	9											58	60	60					9																	141010123		1969	4151	6120	140129944	SO:0001819	synonymous_variant	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.5769C>T	9.37:g.141010123C>T			140129944	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																				0.587	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	141010123	C	T	141010123	2	4	74	1	0	0	0	0	0	0	0	1	2545	755	27	1		1	CACNA1B	9	141010123	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	22059801	141010123	203308	51	21424										
GAD2	2572	broad.mit.edu	37	chr10	26518595	26518595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ttgctgtgcactttaggtggCgccatatctaacatgtatgc	10	9	1	0	rs149136572	byFrequency	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr10:26518595C>T	ENST00000376261.3	+	7	1232	c.729C>T	c.(727-729)ggC>ggT	p.G243G	GAD2_ENST00000259271.3_Silent_p.G243G	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	243					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.G243G(3)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTTTAGGTGGCGCCATATCTA	0.443													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		21933	0		0	False		,,,				2504	0															3	Substitution - coding silent(3)	large_intestine(2)|lung(1)	10						C	,	2,4404	4.2+/-10.8	0,2,2201	197	161	173		729,729	-0.5	1	10	dbSNP_134	173	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GAD2	NM_000818.2,NM_001134366.1	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	243/586,243/586	26518595	2,13004	2203	4300	6503	26558601	SO:0001819	synonymous_variant	2572			AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.729C>T	10.37:g.26518595C>T			26558601	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																				0.443	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26518595	C	T	26518595	2	4	74	1	0	0	0	0	0	0	0	1	6199	755	27	1		1	GAD2	10	26518595	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		26518595	109016152	52	21425										
KIF5B	3799	broad.mit.edu	37	chr10	32344784	32344784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ggggtcactcaccgcgatcaCgaccgtgtcttctccctgaa	10	15	5	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr10:32344784C>T	ENST00000302418.4	-	1	575	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	Y_RNA_ENST00000383933.1_RNA	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	40	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.V40M(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				ACCGCGATCACGACCGTGTCT	0.587			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	1	Substitution - Missense(1)	large_intestine(1)	10											68	54	58					10																	32344784		2203	4300	6503	32384790	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.118G>A	10.37:g.32344784C>T	ENSP00000307078:p.Val40Met		32384790	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659187	0.47467	.	.	ENSG00000170759	ENST00000302418	T	0.74315	-0.83	5.25	-1.67	0.08238	Kinesin, motor domain (4);	0.301676	0.36002	N	0.002841	T	0.68155	0.2970	L	0.37466	1.105	0.23210	N	0.998112	P	0.46020	0.871	P	0.51701	0.677	T	0.63497	-0.6624	10	0.39692	T	0.17	.	8.9751	0.35930	0.0:0.5792:0.1393:0.2815	.	40	P33176	KINH_HUMAN	M	40	ENSP00000307078:V40M	ENSP00000307078:V40M	V	-	1	0	KIF5B	32384790	0.003000	0.15002	0.491000	0.27477	0.986000	0.74619	0.003000	0.13083	-0.602000	0.05775	-0.345000	0.07892	GTG		0.587	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		T	32344784	C	T	32344784	3	4	74	1	0	0	0	0	1	0	0	0	8327	536	19	1	2873	1	KIF5B	10	32344784	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	5826189	32344784	103189963	53	21426										
CCKBR	887	broad.mit.edu	37	chr11	6291928	6291928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tcccgggtgtggttatggccGtggcctacgggcttatctct	14	11	1	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:6291928G>A	ENST00000334619.2	+	4	899	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	CCKBR_ENST00000532715.1_Missense_Mutation_p.V152M|CCKBR_ENST00000525462.1_Missense_Mutation_p.V236M	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	236					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)	p.V236M(3)		NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		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)	GGTTATGGCCGTGGCCTACGG	0.567																																																3	Substitution - Missense(3)	large_intestine(3)	11											192	135	154					11																	6291928		2201	4296	6497	6248504	SO:0001583	missense	887			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.706G>A	11.37:g.6291928G>A	ENSP00000335544:p.Val236Met		6248504	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513324	0.64522	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.41758	0.99;0.99;0.99	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.247555	0.41294	D	0.000901	T	0.67646	0.2915	M	0.83384	2.64	0.45962	D	0.998785	D;D;D	0.89917	1.0;0.987;0.989	D;P;P	0.79108	0.992;0.742;0.832	T	0.64334	-0.6432	10	0.27785	T	0.31	.	18.5901	0.91208	0.0:0.0:1.0:0.0	.	236;170;236	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	M	236;152;236	ENSP00000335544:V236M;ENSP00000432079:V152M;ENSP00000435534:V236M	ENSP00000335544:V236M	V	+	1	0	CCKBR	6248504	0.999000	0.42202	0.956000	0.39512	0.995000	0.86356	3.206000	0.51098	2.735000	0.93741	0.655000	0.94253	GTG		0.567	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		A	6291928	G	A	6291928	3	1	74	1	0	0	0	0	1	0	0	0	2887	1145	40	1	720	1	CCKBR	11	6291928	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		6291928	128714588	54	21427										
PTPN5	84867	broad.mit.edu	37	chr11	18762240	18762240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gaggcgctgagcaggtactcGcgggcggactcctcacgtgg	17	12	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:18762240G>A	ENST00000358540.2	-	8	1255	c.825C>T	c.(823-825)cgC>cgT	p.R275R	PTPN5_ENST00000396167.2_Silent_p.R243R|PTPN5_ENST00000396171.4_Silent_p.R275R|PTPN5_ENST00000396168.1_Silent_p.R251R|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000477854.1_Silent_p.R79R|PTPN5_ENST00000396170.1_Silent_p.R243R|PTPN5_ENST00000496201.2_5'Flank	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	275					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)	p.R275R(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GCAGGTACTCGCGGGCGGACT	0.602																																																2	Substitution - coding silent(2)	large_intestine(2)	11											61	59	60					11																	18762240		2199	4293	6492	18718816	SO:0001819	synonymous_variant	84867			BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.825C>T	11.37:g.18762240G>A			18718816	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Silent	SNP	ENST00000358540.2	37	CCDS7845.1																																																																																				0.602	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		A	18762240	G	A	18762240	2	1	74	1	0	0	0	0	0	0	0	1	12828	1074	38	1		1	PTPN5	11	18762240	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	12470312	18762240	116244276	55	21428										
FBXO3	26273	broad.mit.edu	37	chr11	33777486	33777486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cgtctaacaaatcttcagaaCgatagtgattagacagtgcc	8	9	3	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:33777486C>T	ENST00000265651.3	-	5	527	c.509G>A	c.(508-510)cGt>cAt	p.R170H	FBXO3_ENST00000534136.1_Missense_Mutation_p.R170H|FBXO3_ENST00000526785.1_Missense_Mutation_p.R57H|FBXO3_ENST00000448981.2_Missense_Mutation_p.R170H|FBXO3_ENST00000531080.1_5'Flank|FBXO3_ENST00000532057.1_5'Flank|FBXO3_ENST00000533103.1_5'Flank|FBXO3_ENST00000530401.1_Missense_Mutation_p.R165H	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	170					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.R170H(1)		NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		ATCTTCAGAACGATAGTGATT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	71	73					11																	33777486		2202	4298	6500	33734062	SO:0001583	missense	26273			AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.509G>A	11.37:g.33777486C>T	ENSP00000265651:p.Arg170His		33734062	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	37	CCDS7887.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.197355|5.197355	0.94960|0.94960	.|.	.|.	ENSG00000110429|ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000534136;ENST00000448981|ENST00000321458	T;T;T;T;T|.	0.45668|.	0.89;0.89;0.89;0.89;0.89|.	5.63|5.63	5.63|5.63	0.86233|0.86233	Cell wall assembly/cell proliferation coordinating protein, KNR4-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75347|0.75347	0.3837|0.3837	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;0.999|.	D;D;P|.	0.65010|.	0.909;0.931;0.869|.	T|T	0.75233|0.75233	-0.3390|-0.3390	10|6	0.62326|0.54805	D|T	0.03|0.06	-16.5187|-16.5187	19.6756|19.6756	0.95930|0.95930	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	165;170;170|.	Q9UK99-3;Q9UK99-2;Q9UK99|.	.;.;FBX3_HUMAN|.	H|I	57;170;165;170;170|168	ENSP00000435680:R57H;ENSP00000265651:R170H;ENSP00000433781:R165H;ENSP00000431745:R170H;ENSP00000408836:R170H|.	ENSP00000265651:R170H|ENSP00000315066:V168I	R|V	-|-	2|1	0|0	FBXO3|FBXO3	33734062|33734062	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.442000|7.442000	0.80503|0.80503	2.655000|2.655000	0.90218|0.90218	0.555000|0.555000	0.69702|0.69702	CGT|GTT		0.448	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		T	33777486	C	T	33777486	3	4	74	1	0	0	0	0	1	0	0	0	5758	536	19	1	943	1	FBXO3	11	33777486	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	15015246	33777486	101229030	56	21429										
OR8I2	120586	broad.mit.edu	37	chr11	55861577	55861577	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tttgcaacctgataacacatCatcgctgacccaggcgcagg	9	13	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:55861577C>A	ENST00000302124.2	+	1	825	c.794C>A	c.(793-795)tCa>tAa	p.S265*		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S265*(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GATAACACATCATCGCTGACC	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											114	110	111					11																	55861577		2201	4296	6497	55618153	SO:0001587	stop_gained	120586			AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.794C>A	11.37:g.55861577C>A	ENSP00000303864:p.Ser265*		55618153	B2RNN4|Q6IFC0|Q96RC5	Nonsense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	7.657	0.684072	0.14907	.	.	ENSG00000172154	ENST00000302124	.	.	.	4.33	-1.63	0.08345	.	0.749703	0.10943	U	0.616993	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-5.3404	4.4477	0.11606	0.265:0.4808:0.0:0.2543	.	.	.	.	X	265	.	ENSP00000303864:S265X	S	+	2	0	OR8I2	55618153	0.000000	0.05858	0.140000	0.22221	0.255000	0.26057	-3.092000	0.00608	0.041000	0.15688	0.440000	0.28878	TCA		0.468	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		A	55861577	C	A	55861577	4	1	74	1	0	0	0	0	0	1	0	0	11271	838	29	2	796	2	OR8I2	11	55861577	Nonsense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	22084091	55861577	79144939	57	21430										
TNKS1BP1	85456	broad.mit.edu	37	chr11	57069686	57069686	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ccgatacatggcactgtcgaGgatctcggtgtcctgcttgg	13	11	1	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:57069686G>A	ENST00000532437.1	-	7	5007	c.4696C>T	c.(4696-4698)Ctc>Ttc	p.L1566F	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.L1566F			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1566	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)	p.L1566F(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GCACTGTCGAGGATCTCGGTG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	11											38	35	36					11																	57069686		2201	4296	6497	56826262	SO:0001583	missense	85456			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4696C>T	11.37:g.57069686G>A	ENSP00000437271:p.Leu1566Phe		56826262	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294034	0.81025	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.56444	0.46;0.46	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000004	T	0.69043	0.3067	L	0.60455	1.87	0.50467	D	0.999877	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.998	T	0.71151	-0.4676	10	0.62326	D	0.03	-15.3738	15.6156	0.76764	0.0:0.0:1.0:0.0	.	1566;148	Q9C0C2;Q86TK2	TB182_HUMAN;.	F	1566	ENSP00000350990:L1566F;ENSP00000437271:L1566F	ENSP00000350990:L1566F	L	-	1	0	TNKS1BP1	56826262	1.000000	0.71417	0.979000	0.43373	0.899000	0.52679	5.831000	0.69330	2.422000	0.82143	0.561000	0.74099	CTC		0.657	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57069686	G	A	57069686	3	1	74	1	0	0	0	0	1	0	0	0	16359	1000	35	3	509	3	TNKS1BP1	11	57069686	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	1208109	57069686	77936830	58	21431										
CCDC87	55231	broad.mit.edu	37	chr11	66359383	66359383	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccagtggtgggtagcgagtCccctccaacttcatcttctt	9	13	3	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:66359383C>A	ENST00000333861.3	-	1	1171	c.1104G>T	c.(1102-1104)ggG>ggT	p.G368G	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	368					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)			p.G368G(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						GGTAGCGAGTCCCCTCCAACT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											50	54	53					11																	66359383		2200	4294	6494	66115959	SO:0001819	synonymous_variant	55231			BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1104G>T	11.37:g.66359383C>A			66115959	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																				0.582	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		A	66359383	C	A	66359383	2	1	74	1	0	0	0	0	0	0	0	1	2868	842	30	2		2	CCDC87	11	66359383	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	9289697	66359383	68647133	59	21432										
USP2	9099	broad.mit.edu	37	chr11	119230287	119230288	+	Missense_Mutation	DNP	GT	GT	TG													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gcattgctgccgtggtgcagGtcccgcatgtagagcctctg							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr11:119230287_119230288GT>TG	ENST00000260187.2	-	4	1202_1203	c.908_909AC>CA	c.(907-909)gAC>gCA	p.D303A	USP2_ENST00000525735.1_Missense_Mutation_p.D94A|USP2_ENST00000455332.2_Missense_Mutation_p.D60A	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	303	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.D303>?(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CGTGGTGCAGGTCCCGCATGTA	0.589																																																1	Complex(1)	large_intestine(1)	11																																								118735498	SO:0001583	missense	9099			AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.908_909delinsTG	11.37:g.119230287_119230288delinsTG	ENSP00000260187:p.Asp303Ala		118735497	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	DNP	ENST00000260187.2	37	CCDS8422.1																																																																																				0.589	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		TG	119230288	GT	TG	119230287	3	4	74	1	0	0	0	0	1	0	0	0	17091	1252	44	2	948	2	USP2	11	119230287	Missense_Mutation	DNP	GT	TCGA-AG-A025-01A-01W-A00E-09	52870904	119230287	15776229	60	21433										
CDKN1B	1027	broad.mit.edu	37	chr12	12870995	12870995	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaacccctagagggcaagtaCgagtggcaagaggtggagaa	15	7	0	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:12870995C>G	ENST00000228872.4	+	1	938	c.222C>G	c.(220-222)taC>taG	p.Y74*	CDKN1B_ENST00000477087.1_Intron|CDKN1B_ENST00000396340.1_Nonsense_Mutation_p.Y74*	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	74					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)	p.Y74*(1)		breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		AGGGCAAGTACGAGTGGCAAG	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											77	88	84					12																	12870995		2203	4300	6503	12762262	SO:0001587	stop_gained	1027			AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.222C>G	12.37:g.12870995C>G	ENSP00000228872:p.Tyr74*		12762262	Q16307|Q5U0H2|Q9BUS6	Nonsense_Mutation	SNP	ENST00000228872.4	37	CCDS8653.1	.	.	.	.	.	.	.	.	.	.	C	43	10.345728	0.99388	.	.	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000396340	.	.	.	5.4	2.14	0.27477	.	0.153716	0.44688	D	0.000431	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.0847	11.6909	0.51514	0.0:0.7682:0.0:0.2318	.	.	.	.	X	74;23;74	.	ENSP00000228872:Y74X	Y	+	3	2	CDKN1B	12762262	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	2.682000	0.46934	0.666000	0.31087	-0.145000	0.13849	TAC		0.592	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		G	12870995	C	G	12870995	4	3	74	1	0	0	0	0	0	1	0	0	3165	547	19	5	224	5	CDKN1B	12	12870995	Nonsense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		12870995	120980900	61	21434										
KRAS	3845	broad.mit.edu	37	chr12	25398255	25398255	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	aaaatgattctgaattagctGtatcgtcaaggcactcttgc	8	8	3	2	rs121913236		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:25398255G>T	ENST00000256078.4	-	2	127	c.64C>A	c.(64-66)Cag>Aag	p.Q22K	KRAS_ENST00000311936.3_Missense_Mutation_p.Q22K|KRAS_ENST00000556131.1_Missense_Mutation_p.Q22K|KRAS_ENST00000557334.1_Missense_Mutation_p.Q22K	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	22			Q -> E (in CFC2; exhibits an increase in intrinsic and guanine nucleotide exchange factor catalyzed nucleotide exchange in combination with an impaired GTPase- activating protein-stimulated GTP hydrolysis but functional in interaction with effectors). {ECO:0000269|PubMed:17056636}.|Q -> R (in NS3; impairs GTPase-activating protein stimulated GTP hydrolysis with unaffected intrinsic functions and a virtually functional effector interaction).		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q22K(8)|p.Q22*(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TGAATTAGCTGTATCGTCAAG	0.363		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	9	Substitution - Missense(8)|Substitution - Nonsense(1)	large_intestine(7)|haematopoietic_and_lymphoid_tissue(1)|small_intestine(1)	12	GRCh37	CM070964	KRAS	M	rs121913236						88	76	80					12																	25398255		2203	4300	6503	25289522	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.64C>A	12.37:g.25398255G>T	ENSP00000256078:p.Gln22Lys		25289522	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113031	0.94339	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79749	-1.3;-0.43;-0.43;-0.43	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90013	0.6882	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.976	D	0.90739	0.4648	10	0.87932	D	0	.	18.3719	0.90409	0.0:0.0:1.0:0.0	.	22;22	P01116-2;P01116	.;RASK_HUMAN	K	22	ENSP00000308495:Q22K;ENSP00000452512:Q22K;ENSP00000256078:Q22K;ENSP00000451856:Q22K	ENSP00000256078:Q22K	Q	-	1	0	KRAS	25289522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.770000	0.98971	2.668000	0.90789	0.563000	0.77884	CAG		0.363	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398255	G	T	25398255	3	4	74	1	0	0	0	0	1	0	0	0	8459	1386	48	2	642	2	KRAS	12	25398255	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	12527260	25398255	108453640	62	21435										
MLL2	8085	broad.mit.edu	37	chr12	49431873	49431874	+	Frame_Shift_Ins	INS	-	-	C													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gcccaagggtcctggctccaINSccccccgcagcagggcctcc							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:49431873_49431874insC	ENST00000301067.7	-	34	9264_9265	c.9265_9266insG	c.(9265-9267)gtgfs	p.V3089fs	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3089					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V2819fs*9(1)|p.V3089fs*9(1)									TCCTGGCTCCACCCCCCGCAGC	0.624																																																2	Insertion - Frameshift(2)	large_intestine(2)	12																																								47718141	SO:0001589	frameshift_variant	8085			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9266dupG	12.37:g.49431879_49431879dupC	ENSP00000301067:p.Val3089fs		47718140	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																				0.624	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49431874	-	C	49431873	7	5	74	1	0	1	1	0	0	0	0	0	9651	159	6	0	7431	0	MLL2	12	49431873	Frame_Shift_Ins	INS	-	TCGA-AG-A025-01A-01W-A00E-09	24033618	49431873	84420022	63	21436										
OR6C3	254786	broad.mit.edu	37	chr12	55725989	55725989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	agctggattactgtgcttccAacgtcattgatcactttgca	8	10	2	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:55725989A>G	ENST00000379667.1	+	1	505	c.505A>G	c.(505-507)Aac>Gac	p.N169D		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	169					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N169D(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						CTGTGCTTCCAACGTCATTGA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											282	253	263					12																	55725989		2203	4300	6503	54012256	SO:0001583	missense	254786			AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"GPCR / Class A : Olfactory receptors"	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.505A>G	12.37:g.55725989A>G	ENSP00000368989:p.Asn169Asp		54012256		Missense_Mutation	SNP	ENST00000379667.1	37	CCDS31819.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.808696	0.31961	.	.	ENSG00000205329	ENST00000379667	T	0.00241	8.46	5.28	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000050	T	0.00328	0.0010	M	0.83312	2.635	0.09310	N	1	P	0.49559	0.925	P	0.51516	0.672	T	0.39800	-0.9596	10	0.72032	D	0.01	.	5.0071	0.14293	0.5875:0.2496:0.1629:0.0	.	169	Q9NZP0	OR6C3_HUMAN	D	169	ENSP00000368989:N169D	ENSP00000368989:N169D	N	+	1	0	OR6C3	54012256	0.016000	0.18221	0.379000	0.26080	0.204000	0.24138	2.746000	0.47467	0.549000	0.28973	-0.250000	0.11733	AAC		0.438	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1			G	55725989	A	G	55725989	3	3	74	1	0	0	0	0	1	0	0	0	11223	130	5	4	507	4	OR6C3	12	55725989	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	6294116	55725989	78125906	64	21437										
TMCC3	57458	broad.mit.edu	37	chr12	94975538	94975538	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccaggatcacggcgagcttGccctggctgtccagtgtgct	13	13	1	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:94975538G>T	ENST00000261226.4	-	2	986	c.855C>A	c.(853-855)ggC>ggA	p.G285G	TMCC3_ENST00000551457.1_Silent_p.G254G	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	285						integral component of membrane (GO:0016021)		p.G285G(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						CGGCGAGCTTGCCCTGGCTGT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	12											96	94	94					12																	94975538		2203	4300	6503	93499669	SO:0001819	synonymous_variant	57458			AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.855C>A	12.37:g.94975538G>T			93499669	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																				0.567	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		T	94975538	G	T	94975538	2	4	74	1	0	0	0	0	0	0	0	1	16033	1306	46	2		2	TMCC3	12	94975538	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	39249549	94975538	38876357	65	21438										
C12orf51	283450	broad.mit.edu	37	chr12	112638547	112638547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tgtcaataggataccagtatCgcaccagcacaccttcactg	7	13	2	0	rs535700898		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr12:112638547C>T	ENST00000430131.2	-	54	8341	c.7196G>A	c.(7195-7197)cGa>cAa	p.R2399Q	HECTD4_ENST00000550722.1_Missense_Mutation_p.R2675Q|HECTD4_ENST00000377560.5_Missense_Mutation_p.R2649Q			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2399					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R2399Q(1)|p.R2649Q(1)									ATACCAGTATCGCACCAGCAC	0.478																																																2	Substitution - Missense(2)	large_intestine(2)	12											134	132	133					12																	112638547		2067	4222	6289	111122930	SO:0001583	missense	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.7196G>A	12.37:g.112638547C>T	ENSP00000404379:p.Arg2399Gln		111122930	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	C	37	6.323721	0.97476	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000548896	T;T;T	0.53423	0.62;0.63;0.62	5.86	5.86	0.93980	.	.	.	.	.	T	0.58004	0.2092	L	0.27053	0.805	0.53005	D	0.999966	D	0.64830	0.994	D	0.64042	0.921	T	0.59495	-0.7444	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	2399	Q9Y4D8	K0614_HUMAN	Q	2649;2399;2675;30	ENSP00000366783:R2649Q;ENSP00000404379:R2399Q;ENSP00000449784:R2675Q	ENSP00000366783:R2649Q	R	-	2	0	C12orf51	111122930	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	7.226000	0.78060	2.937000	0.99478	0.650000	0.86243	CGA		0.478	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112638547	C	T	112638547	3	4	74	1	0	0	0	0	1	0	0	0	1700	884	31	1	4882	1	C12orf51	12	112638547	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	17663009	112638547	21213348	66	21439										
TGM1	7051	broad.mit.edu	37	chr14	24724250	24724250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	actgacaccagtatagaaagTgactgagaggtagaggtgca	13	6	0	5			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr14:24724250T>C	ENST00000206765.6	-	12	1978	c.1855A>G	c.(1855-1857)Act>Gct	p.T619A	TGM1_ENST00000544573.1_Missense_Mutation_p.T177A	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	619					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T619A(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GTATAGAAAGTGACTGAGAGG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	14											70	62	65					14																	24724250		2203	4300	6503	23794090	SO:0001583	missense	7051			D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.1855A>G	14.37:g.24724250T>C	ENSP00000206765:p.Thr619Ala		23794090	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	37	CCDS9622.1	.	.	.	.	.	.	.	.	.	.	T	19.31	3.803364	0.70682	.	.	ENSG00000092295	ENST00000206765;ENST00000544573	T;T	0.68331	-0.32;-0.32	5.28	5.28	0.74379	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.044531	0.85682	D	0.000000	T	0.72431	0.3459	L	0.61218	1.895	0.37978	D	0.933514	P	0.48162	0.906	P	0.52343	0.696	T	0.74087	-0.3778	10	0.30854	T	0.27	-31.0938	14.3153	0.66446	0.0:0.0:0.0:1.0	.	619	P22735	TGM1_HUMAN	A	619;177	ENSP00000206765:T619A;ENSP00000439446:T177A	ENSP00000206765:T619A	T	-	1	0	TGM1	23794090	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	4.259000	0.58828	2.209000	0.71365	0.533000	0.62120	ACT		0.562	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		C	24724250	T	C	24724250	3	2	74	1	0	0	0	0	1	0	0	0	15868	1696	59	4	614	4	TGM1	14	24724250	Missense_Mutation	SNP	T	TCGA-AG-A025-01A-01W-A00E-09		24724250	82625290	67	21440										
AHNAK2	113146	broad.mit.edu	37	chr14	105412698	105412699	+	Missense_Mutation	DNP	GG	GG	AT													0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	acctccagttgggcagagggGggctcaatgctgatgtcagt							TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr14:105412698_105412699GG>AT	ENST00000333244.5	-	7	9208_9209	c.9089_9090CC>AT	c.(9088-9090)cCC>cAT	p.P3030H	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3030						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.P3030>?(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GGGCAGAGGGGGGCTCAATGCT	0.639																																																1	Complex(1)	large_intestine(1)	14																																								104483744	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9089_9090delinsAT	14.37:g.105412698_105412699delinsAT	ENSP00000353114:p.Pro3030His		104483743	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	DNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.639	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		AT	105412699	GG	AT	105412698	3	1	74	1	0	0	0	0	1	0	0	0	415	1219	43	3	8301	3	AHNAK2	14	105412698	Missense_Mutation	DNP	GG	TCGA-AG-A025-01A-01W-A00E-09	80688448	105412698	1936842	68	21441										
C15orf2	23742	broad.mit.edu	37	chr15	24921752	24921752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cccagcacacacagccaggcCggatgtgcccggcatcttgg	12	16	1	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr15:24921752C>T	ENST00000329468.2	+	1	1212	c.738C>T	c.(736-738)gcC>gcT	p.A246A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	246					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A246A(1)									ACAGCCAGGCCGGATGTGCCC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	15											32	35	34					15																	24921752		2203	4299	6502	22472845	SO:0001819	synonymous_variant	23742			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.738C>T	15.37:g.24921752C>T			22472845		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.622	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921752	C	T	24921752	2	4	74	1	0	0	0	0	0	0	0	1	1788	639	23	1		1	C15orf2	15	24921752	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		24921752	77609640	69	21442										
TMOD3	29766	broad.mit.edu	37	chr15	52161473	52161473	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	acatcaaagtccaccacaggGccatttgatagagagcatct	8	11	2	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr15:52161473G>A	ENST00000308580.7	+	3	467	c.186G>A	c.(184-186)ggG>ggA	p.G62G	TMOD3_ENST00000544199.1_Silent_p.G62G	NM_014547.4	NP_055362.1	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	62						striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)	p.G62G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14				all cancers(107;0.00194)		CCACCACAGGGCCATTTGATA	0.453																																					Colon(122;1837 2251 18387 22826)											1	Substitution - coding silent(1)	large_intestine(1)	15											93	92	92					15																	52161473		2195	4293	6488	49948765	SO:0001819	synonymous_variant	29766			AF177171	CCDS10145.1	15q21.1-q21.2	2008-05-14			ENSG00000138594	ENSG00000138594			11873	protein-coding gene	gene with protein product		605112				10662549	Standard	NM_014547		Approved	UTMOD	uc002abn.3	Q9NYL9	OTTHUMG00000131803	ENST00000308580.7:c.186G>A	15.37:g.52161473G>A			49948765	B2R6G7|Q9NT43|Q9NZR0	Silent	SNP	ENST00000308580.7	37	CCDS10145.1																																																																																				0.453	TMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254740.3			A	52161473	G	A	52161473	2	1	74	1	0	0	0	0	0	0	0	1	16274	1190	42	3		3	TMOD3	15	52161473	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	27239721	52161473	50369919	70	21443										
PRM2	5620	broad.mit.edu	37	chr16	11370148	11370148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gctcctcttggccgtggtgtCcttgctcttgcccatgcaac	10	15	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr16:11370148C>T	ENST00000241808.4	-	1	189	c.80G>A	c.(79-81)gGa>gAa	p.G27E	PRM2_ENST00000435245.2_Missense_Mutation_p.G27E|PRM3_ENST00000327157.2_5'Flank|SNORA48_ENST00000390926.1_RNA|RMI2_ENST00000572173.1_Intron	NM_002762.2	NP_002753.2	P04554	PRM2_HUMAN	protamine 2	27					cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G27E(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)	7						GCCGTGGTGTCCTTGCTCTTG	0.617																																																2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											83	90	88					16																	11370148		2180	4280	6460	11277649	SO:0001583	missense	5620				CCDS42118.1, CCDS66944.1	16p13.13	2013-10-17			ENSG00000122304	ENSG00000122304			9448	protein-coding gene	gene with protein product	"cancer/testis antigen family 94, member 2"	182890				16632464	Standard	NM_001286356		Approved	CT94.2	uc002dau.1	P04554	OTTHUMG00000172317	ENST00000241808.4:c.80G>A	16.37:g.11370148C>T	ENSP00000241808:p.Gly27Glu		11277649	Q6ZMM0	Missense_Mutation	SNP	ENST00000241808.4	37	CCDS42118.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.609466	0.46527	.	.	ENSG00000122304	ENST00000241808;ENST00000435245	.	.	.	3.13	-3.01	0.05463	.	0.515171	0.14626	N	0.308099	T	0.25382	0.0617	L	0.27053	0.805	0.09310	N	1	B;B	0.20887	0.049;0.008	B;B	0.17433	0.018;0.006	T	0.16778	-1.0391	9	0.87932	D	0	.	8.2431	0.31671	0.0:0.2168:0.0:0.7832	.	27;27	Q6ZMM0;P04554	.;PRM2_HUMAN	E	27	.	ENSP00000241808:G27E	G	-	2	0	PRM2	11277649	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.775000	0.04679	-0.603000	0.05767	0.491000	0.48974	GGA		0.617	PRM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417808.1			T	11370148	C	T	11370148	3	4	74	1	0	0	0	0	1	0	0	0	12567	855	30	3	236	3	PRM2	16	11370148	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		11370148	78984605	71	21444										
CHD9	80205	broad.mit.edu	37	chr16	53272320	53272320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tcaatcaattacattcctctAtgaaatccttctgactggta	4	10	4	2	rs370605180		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr16:53272320A>G	ENST00000398510.3	+	11	2786	c.2699A>G	c.(2698-2700)tAt>tGt	p.Y900C	CHD9_ENST00000566029.1_Missense_Mutation_p.Y900C|CHD9_ENST00000564845.1_Missense_Mutation_p.Y900C|CHD9_ENST00000447540.1_Missense_Mutation_p.Y900C			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	900	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Y900C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ACATTCCTCTATGAAATCCTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	16						A	CYS/TYR	0,3660		0,0,1830	121	113	115		2699	3.9	1	16		115	1,8173		0,1,4086	no	missense	CHD9	NM_025134.4	194	0,1,5916	GG,GA,AA		0.0122,0.0,0.0085	possibly-damaging	900/2882	53272320	1,11833	1830	4087	5917	51829821	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2699A>G	16.37:g.53272320A>G	ENSP00000381522:p.Tyr900Cys		51829821	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	A	15.97	2.988518	0.53934	0.0	1.22E-4	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.93488	-3.23;-3.23	5.02	3.9	0.45041	DEAD-like helicase (2);SNF2-related (1);	0.251083	0.28203	N	0.016209	D	0.92116	0.7501	L	0.28504	0.86	0.34407	D	0.695933	P;D;P;P	0.56287	0.491;0.975;0.512;0.456	P;P;B;B	0.61328	0.586;0.887;0.432;0.306	D	0.91857	0.5496	10	0.39692	T	0.17	-1.6142	7.6522	0.28354	0.7151:0.1456:0.0:0.1393	.	426;900;900;900	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	C	900;900;426	ENSP00000396345:Y900C;ENSP00000381522:Y900C	ENSP00000219084:Y426C	Y	+	2	0	CHD9	51829821	0.997000	0.39634	0.998000	0.56505	0.959000	0.62525	3.396000	0.52565	0.729000	0.32403	0.377000	0.23210	TAT		0.363	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53272320	A	G	53272320	3	3	74	1	0	0	0	0	1	0	0	0	3338	449	16	4	2741	4	CHD9	16	53272320	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	41902172	53272320	37082433	72	21445										
CLEC18C	283971	broad.mit.edu	37	chr16	70219844	70219844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cttcaactggaacaaccagcGctgcaaaacccgaaaccgtt	7	14	1	0	rs560740555	byFrequency	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr16:70219844G>A	ENST00000569347.2	+	11	1522	c.1268G>A	c.(1267-1269)cGc>cAc	p.R423H	CLEC18C_ENST00000541793.2_Missense_Mutation_p.R423H|CLEC18C_ENST00000536907.2_Missense_Mutation_p.R432H|CLEC18C_ENST00000314151.8_Missense_Mutation_p.R423H	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	423	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.R423H(2)		endometrium(3)|large_intestine(6)|lung(1)	10						AACAACCAGCGCTGCAAAACC	0.587													g|||	2	0.000399361	0	0	5008	,	,		17169	0		0.002	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	16											94	132	119					16																	70219844		2076	4297	6373	68777345	SO:0001583	missense	283971			AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"C-type lectin domain containing"	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.1268G>A	16.37:g.70219844G>A	ENSP00000455920:p.Arg423His		68777345	Q8IUW8	Missense_Mutation	SNP	ENST00000569347.2	37	CCDS32473.1	.	.	.	.	.	.	.	.	.	.	g	20.3	3.962318	0.74016	.	.	ENSG00000157335	ENST00000541793;ENST00000314151;ENST00000536907	T;T;T	0.55052	0.54;0.54;0.54	4.34	4.34	0.51931	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.069626	0.64402	D	0.000019	T	0.55000	0.1893	L	0.33339	1.005	0.48341	D	0.999634	D;D	0.61697	0.98;0.99	P;P	0.56823	0.807;0.707	T	0.57625	-0.7779	10	0.54805	T	0.06	.	12.7412	0.57253	0.0:0.0:1.0:0.0	.	423;432	Q8NCF0;F8W692	CL18C_HUMAN;.	H	423;423;432	ENSP00000444875:R423H;ENSP00000326538:R423H;ENSP00000444726:R432H	ENSP00000326538:R423H	R	+	2	0	CLEC18C	68777345	1.000000	0.71417	0.990000	0.47175	0.958000	0.62258	3.543000	0.53633	2.132000	0.65825	0.450000	0.29827	CGC		0.587	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619		A	70219844	G	A	70219844	3	1	74	1	0	0	0	0	1	0	0	0	3510	1087	38	1	1310	1	CLEC18C	16	70219844	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	16947524	70219844	20134909	73	21446										
EFNB3	1949	broad.mit.edu	37	chr17	7611424	7611424	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tagggggtgctcagggccggCgctgtgaggcaccccctgcc	17	14	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr17:7611424C>T	ENST00000226091.2	+	2	668	c.271C>T	c.(271-273)Cgc>Tgc	p.R91C		NM_001406.3	NP_001397.1	Q15768	EFNB3_HUMAN	ephrin-B3	91	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				adult walking behavior (GO:0007628)|axon choice point recognition (GO:0016198)|axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)	p.R91C(1)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	8		all_cancers(10;1.14e-06)|Prostate(122;0.081)				TCAGGGCCGGCGCTGTGAGGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	17											62	68	66					17																	7611424		2203	4300	6503	7552149	SO:0001583	missense	1949			U57001	CCDS11120.1	17p13.1	2011-03-09			ENSG00000108947	ENSG00000108947		"Ephrins"	3228	protein-coding gene	gene with protein product		602297		EPLG8		9126477	Standard	NM_001406		Approved	LERK-8	uc002gis.3	Q15768	OTTHUMG00000108161	ENST00000226091.2:c.271C>T	17.37:g.7611424C>T	ENSP00000226091:p.Arg91Cys		7552149	B2RBW2|D3DTQ6|O00680|Q8TBH7|Q92875	Missense_Mutation	SNP	ENST00000226091.2	37	CCDS11120.1	.	.	.	.	.	.	.	.	.	.	c	12.58	1.981039	0.34942	.	.	ENSG00000108947	ENST00000226091	D	0.93488	-3.23	4.98	4.98	0.66077	Cupredoxin (2);	0.067130	0.56097	D	0.000025	D	0.94463	0.8218	L	0.43152	1.355	0.46823	D	0.99921	D	0.89917	1.0	D	0.73708	0.981	D	0.94239	0.7483	10	0.62326	D	0.03	0.4507	12.2855	0.54789	0.1698:0.8302:0.0:0.0	.	91	Q15768	EFNB3_HUMAN	C	91	ENSP00000226091:R91C	ENSP00000226091:R91C	R	+	1	0	EFNB3	7552149	0.986000	0.35501	1.000000	0.80357	0.087000	0.18053	0.509000	0.22707	2.576000	0.86940	0.574000	0.79327	CGC		0.602	EFNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226965.1	NM_001406		T	7611424	C	T	7611424	3	4	74	1	0	0	0	0	1	0	0	0	4968	768	27	1	277	1	EFNB3	17	7611424	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		7611424	73583786	74	21447										
FZD2	2535	broad.mit.edu	37	chr17	42636400	42636400	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cgcaccatcatgaagcacgaCggcaccaagaccgaaaagct	9	14	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr17:42636400C>T	ENST00000315323.3	+	1	1476	c.1344C>T	c.(1342-1344)gaC>gaT	p.D448D		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	448					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.D448D(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TGAAGCACGACGGCACCAAGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	17											107	92	97					17																	42636400		2203	4300	6503	39991926	SO:0001819	synonymous_variant	2535			L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"GPCR / Class F : Frizzled receptors"	4040	protein-coding gene	gene with protein product		600667	"frizzled (Drosophila) homolog 2", "frizzled homolog 2 (Drosophila)", "frizzled 2, seven transmembrane spanning receptor", "frizzled family receptor 2"			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.1344C>T	17.37:g.42636400C>T			39991926	Q0VG82	Silent	SNP	ENST00000315323.3	37	CCDS11484.1																																																																																				0.607	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		T	42636400	C	T	42636400	2	4	74	1	0	0	0	0	0	0	0	1	6149	535	19	1		1	FZD2	17	42636400	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	35024976	42636400	38558810	75	21448										
NGFR	4804	broad.mit.edu	37	chr17	47587820	47587820	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tccacacccccagagggctcGgacagcacagcccccagcac	9	20	0	1	rs377669981		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr17:47587820G>A	ENST00000172229.3	+	4	740	c.615G>A	c.(613-615)tcG>tcA	p.S205S	NGFR_ENST00000504201.1_Silent_p.S111S|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	205	Ser/Thr-rich.		S -> L (in dbSNP:rs2072446).		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.S205S(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					CAGAGGGCTCGGACAGCACAG	0.617													G|||	1	0.000199681	8e-04	0	5008	,	,		18535	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17						G		1,4405	2.1+/-5.4	0,1,2202	78	78	78		615	-9.3	0	17		78	0,8600		0,0,4300	no	coding-synonymous	NGFR	NM_002507.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		205/428	47587820	1,13005	2203	4300	6503	44942819	SO:0001819	synonymous_variant	4804			M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.615G>A	17.37:g.47587820G>A			44942819	B2R961|B4E096	Silent	SNP	ENST00000172229.3	37	CCDS11549.1																																																																																				0.617	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			A	47587820	G	A	47587820	2	1	74	1	0	0	0	0	0	0	0	1	10427	1103	39	1		1	NGFR	17	47587820	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	4951420	47587820	33607390	76	21449										
SOX9	6662	broad.mit.edu	37	chr17	70120103	70120103	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cgcaggcggcgcccccacagCagccggcggcacccccgcag	14	21	0	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr17:70120103C>T	ENST00000245479.2	+	3	1477	c.1105C>T	c.(1105-1107)Cag>Tag	p.Q369*		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	369	Gln/Pro-rich.				astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q369*(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			gcccccacagcagccggcggc	0.771																																					Pancreas(42;83 1041 2320 35205 39456)											1	Substitution - Nonsense(1)	large_intestine(1)	17											8	11	10					17																	70120103		2143	4198	6341	67631698	SO:0001587	stop_gained	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.1105C>T	17.37:g.70120103C>T	ENSP00000245479:p.Gln369*		67631698	Q53Y80	Nonsense_Mutation	SNP	ENST00000245479.2	37	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	37	6.225287	0.97390	.	.	ENSG00000125398	ENST00000245479	.	.	.	3.84	2.83	0.33086	.	1.206400	0.06266	U	0.694773	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	10.8696	0.46875	0.0:0.8066:0.1934:0.0	.	.	.	.	X	369	.	ENSP00000245479:Q369X	Q	+	1	0	SOX9	67631698	0.013000	0.17824	0.197000	0.23402	0.224000	0.24922	0.000000	0.12993	0.558000	0.29135	0.462000	0.41574	CAG		0.771	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70120103	C	T	70120103	4	4	74	1	0	0	0	0	0	1	0	0	14995	711	25	3	1115	3	SOX9	17	70120103	Nonsense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	22532283	70120103	11075107	77	21450										
SLC14A1	6563	broad.mit.edu	37	chr18	43316498	43316498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caccctccctttcaacatggCgttgtcaatgtacctttcag	6	14	3	0	rs367901541		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr18:43316498C>T	ENST00000321925.4	+	6	780	c.548C>T	c.(547-549)gCg>gTg	p.A183V	RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000402943.2_Missense_Mutation_p.A78V|SLC14A1_ENST00000591541.1_5'Flank|SLC14A1_ENST00000535474.1_Missense_Mutation_p.A51V|SLC14A1_ENST00000436407.3_Missense_Mutation_p.A239V|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000415427.3_Missense_Mutation_p.A239V|SLC14A1_ENST00000586142.1_Missense_Mutation_p.A183V|SLC14A1_ENST00000591943.1_Intron|SLC14A1_ENST00000589700.1_Missense_Mutation_p.A183V|SLC14A1_ENST00000502059.2_Missense_Mutation_p.A75V	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	183					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)	p.A183V(2)|p.A239V(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						TTCAACATGGCGTTGTCAATG	0.443																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	18						C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	167	147	154		716,548,716,548	4.7	0.9	18		154	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	SLC14A1	NM_001128588.3,NM_001146036.2,NM_001146037.1,NM_015865.6	64,64,64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	239/446,183/390,239/446,183/390	43316498	1,13005	2203	4300	6503	41570496	SO:0001583	missense	6563			BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.548C>T	18.37:g.43316498C>T	ENSP00000318546:p.Ala183Val		41570496	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	37	CCDS11925.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482152	0.44147	0.0	1.16E-4	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000502059;ENST00000402943;ENST00000535474;ENST00000436407	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.51	4.65	0.58169	.	0.306075	0.32624	N	0.005848	T	0.39809	0.1092	M	0.66297	2.02	0.80722	D	1	B;B;P	0.46277	0.333;0.133;0.875	B;B;B	0.41332	0.061;0.03;0.354	T	0.36407	-0.9749	10	0.08381	T	0.77	-3.2679	14.4418	0.67323	0.0:0.9294:0.0:0.0706	.	239;75;183	Q13336-2;B3KXJ3;Q13336	.;.;UT1_HUMAN	V	183;239;75;78;51;239	ENSP00000318546:A183V;ENSP00000412309:A239V;ENSP00000442180:A75V;ENSP00000385320:A78V;ENSP00000441998:A51V;ENSP00000390637:A239V	ENSP00000318546:A183V	A	+	2	0	SLC14A1	41570496	0.999000	0.42202	0.869000	0.34112	0.894000	0.52154	3.996000	0.57009	1.344000	0.45657	0.650000	0.86243	GCG		0.443	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		T	43316498	C	T	43316498	3	4	74	1	0	0	0	0	1	0	0	0	14433	768	27	1	734	1	SLC14A1	18	43316498	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		43316498	34760750	78	21451										
DSEL	92126	broad.mit.edu	37	chr18	65181497	65181497	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gttaccataaatttcattccActtggcagcaaaatcagcat	5	10	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr18:65181497A>C	ENST00000310045.7	-	2	1852	c.379T>G	c.(379-381)Tgg>Ggg	p.W127G	RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	117					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.W127G(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				ATTTCATTCCACTTGGCAGCA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	18											114	101	106					18																	65181497		2203	4300	6503	63332477	SO:0001583	missense	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.379T>G	18.37:g.65181497A>C	ENSP00000310565:p.Trp127Gly		63332477	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386726	0.82902	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.23552	1.9	4.79	4.79	0.61399	.	0.000000	0.85682	U	0.000000	T	0.50922	0.1644	M	0.75777	2.31	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.56312	-0.8000	10	0.72032	D	0.01	-6.2316	14.6496	0.68786	1.0:0.0:0.0:0.0	.	117	Q8IZU8	DSEL_HUMAN	G	127;117	ENSP00000310565:W127G	ENSP00000310565:W127G	W	-	1	0	DSEL	63332477	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.057000	0.93889	1.937000	0.56155	0.459000	0.35465	TGG		0.398	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		C	65181497	A	C	65181497	3	2	74	1	0	0	0	0	1	0	0	0	4786	159	6	4	3293	4	DSEL	18	65181497	Missense_Mutation	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	21864999	65181497	12895751	79	21452										
ZNF561	93134	broad.mit.edu	37	chr19	9724724	9724724	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	atcccactgaatatttgattCttcaaaaaaccctgctgaag	5	10	2	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr19:9724724C>A	ENST00000302851.3	-	5	660	c.297G>T	c.(295-297)aaG>aaT	p.K99N	ZNF561_ENST00000326044.5_Intron|ZNF561_ENST00000424629.1_Missense_Mutation_p.K30N|ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000354661.4_Intron	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	99	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K30N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						ATATTTGATTCTTCAAAAAAC	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	19											129	128	128					19																	9724724		2203	4300	6503	9585724	SO:0001583	missense	93134			AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"Zinc fingers, C2H2-type", "-"	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.297G>T	19.37:g.9724724C>A	ENSP00000303915:p.Lys99Asn		9585724	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	37	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	C	6.619	0.482654	0.12581	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000444611	T;T;T	0.08720	3.06;3.16;3.77	1.69	-0.679	0.11350	Krueppel-associated box (2);	.	.	.	.	T	0.09642	0.0237	N	0.16708	0.43	0.09310	N	1	D	0.57899	0.981	D	0.67231	0.95	T	0.32534	-0.9903	9	0.21540	T	0.41	.	4.0789	0.09917	0.0:0.5732:0.0:0.4268	.	99	Q8N587	ZN561_HUMAN	N	30;99;105	ENSP00000393074:K30N;ENSP00000303915:K99N;ENSP00000392013:K105N	ENSP00000303915:K99N	K	-	3	2	ZNF561	9585724	0.000000	0.05858	0.000000	0.03702	0.235000	0.25334	-1.186000	0.03070	-0.107000	0.12088	0.313000	0.20887	AAG		0.333	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9724724	C	A	9724724	3	1	74	1	0	0	0	0	1	0	0	0	18031	912	32	2	1171	2	ZNF561	19	9724724	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		9724724	49404259	80	21453										
CYP2A13	1553	broad.mit.edu	37	chr19	41597792	41597792	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ccacgggacttcatcgactcCtttctcatccgcatgcagga	8	15	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr19:41597792C>G	ENST00000330436.3	+	5	810	c.810C>G	c.(808-810)tcC>tcG	p.S270S		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	270					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.S270S(1)		breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	TCATCGACTCCTTTCTCATCC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	19											139	108	119					19																	41597792		2203	4300	6503	46289632	SO:0001819	synonymous_variant	1553			U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.810C>G	19.37:g.41597792C>G			46289632	Q53YR8|Q6R569|Q6R570|Q9H2X2	Silent	SNP	ENST00000330436.3	37	CCDS12571.1																																																																																				0.592	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41597792	C	G	41597792	2	3	74	1	0	0	0	0	0	0	0	1	4167	668	24	5		5	CYP2A13	19	41597792	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	31873068	41597792	17531191	81	21454										
PAFAH1B3	5050	broad.mit.edu	37	chr19	42801507	42801507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ggttgggatgttggcctcgcGgaagcaggccctgagcagga	18	9	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr19:42801507G>A	ENST00000262890.3	-	5	680	c.419C>T	c.(418-420)cCg>cTg	p.P140L	PAFAH1B3_ENST00000538771.1_Missense_Mutation_p.P140L	NM_002573.3	NP_002564.1	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa)	140					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)	p.P140L(1)		breast(1)|large_intestine(2)|ovary(1)	4		Prostate(69;0.0704)				TTGGCCTCGCGGAAGCAGGCC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											61	57	58					19																	42801507		2203	4300	6503	47493347	SO:0001583	missense	5050			D63391	CCDS12602.1	19q13.1	2011-10-24	2010-02-10			ENSG00000079462			8576	protein-coding gene	gene with protein product	"PAF-AH1b alpha 1 subunit"	603074	"platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29kD)", "platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 3 (29kDa)"			7669037	Standard	NM_002573		Approved		uc010xwj.1	Q15102		ENST00000262890.3:c.419C>T	19.37:g.42801507G>A	ENSP00000262890:p.Pro140Leu		47493347	Q53X88	Missense_Mutation	SNP	ENST00000262890.3	37	CCDS12602.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.862764	0.71949	.	.	ENSG00000079462	ENST00000538771;ENST00000262890	T;T	0.56103	0.48;0.48	5.93	5.93	0.95920	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.054076	0.85682	N	0.000000	T	0.81602	0.4857	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86347	0.1708	10	0.87932	D	0	-14.1733	17.8376	0.88704	0.0:0.0:1.0:0.0	.	140	Q15102	PA1B3_HUMAN	L	140	ENSP00000444935:P140L;ENSP00000262890:P140L	ENSP00000262890:P140L	P	-	2	0	PAFAH1B3	47493347	1.000000	0.71417	0.981000	0.43875	0.112000	0.19704	9.460000	0.97641	2.815000	0.96918	0.561000	0.74099	CCG		0.582	PAFAH1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463726.1	NM_002573		A	42801507	G	A	42801507	3	1	74	1	0	0	0	0	1	0	0	0	11417	1116	39	1	280	1	PAFAH1B3	19	42801507	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09	1203715	42801507	16327476	82	21455										
PLEKHA4	57664	broad.mit.edu	37	chr19	49348687	49348687	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gggctggaagcccgggagacCctcggagacccaagacctgg	16	13	0	3			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr19:49348687C>G	ENST00000263265.6	-	16	2238	c.1683G>C	c.(1681-1683)agG>agC	p.R561S	PLEKHA4_ENST00000355496.5_Missense_Mutation_p.R536S	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	561						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)	p.R561S(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		CCCGGGAGACCCTCGGAGACC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19											87	92	90					19																	49348687		2203	4300	6503	54040499	SO:0001583	missense	57664			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1683G>C	19.37:g.49348687C>G	ENSP00000263265:p.Arg561Ser		54040499	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	c	11.73	1.724428	0.30593	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.25250	1.81;1.81	4.97	1.33	0.21861	.	0.889799	0.09388	N	0.808988	T	0.14787	0.0357	L	0.27053	0.805	0.09310	N	1	B;B	0.34290	0.447;0.003	B;B	0.33690	0.168;0.002	T	0.26189	-1.0110	10	0.22109	T	0.4	.	4.1996	0.10460	0.1811:0.6256:0.0:0.1933	.	536;561	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	S	561;536	ENSP00000263265:R561S;ENSP00000347683:R536S	ENSP00000263265:R561S	R	-	3	2	PLEKHA4	54040499	0.000000	0.05858	0.073000	0.20177	0.653000	0.38743	-0.433000	0.06948	0.746000	0.32786	0.544000	0.68410	AGG		0.577	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			G	49348687	C	G	49348687	3	3	74	1	0	0	0	0	1	0	0	0	12089	622	22	5	676	5	PLEKHA4	19	49348687	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	6547180	49348687	9780296	83	21456										
CACNG6	59285	broad.mit.edu	37	chr19	54515329	54515329	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	tactcctggtccctgggctgCggcgtgggggccggcctgat	17	13	0	1	rs199614002		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr19:54515329C>T	ENST00000252729.2	+	4	1259	c.669C>T	c.(667-669)tgC>tgT	p.C223C	CACNG6_ENST00000352529.1_Silent_p.C152C|CACNG6_ENST00000346968.2_Silent_p.C177C	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	223					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.C223C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	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;0.168)		CCCTGGGCTGCGGCGTGGGGG	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	19											23	28	26					19																	54515329		2195	4278	6473	59207141	SO:0001819	synonymous_variant	59285			AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"Calcium channel subunits"	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.669C>T	19.37:g.54515329C>T			59207141		Silent	SNP	ENST00000252729.2	37	CCDS12870.1																																																																																				0.706	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1			T	54515329	C	T	54515329	2	4	74	1	0	0	0	0	0	0	0	1	2567	776	27	1		1	CACNG6	19	54515329	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	5166642	54515329	4613654	84	21457										
CSTF1	1477	broad.mit.edu	37	chr20	54970683	54970683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	attagccagctgctatatgaCggctacatcagcatcgccaa	8	12	1	1	rs112830633	byFrequency	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr20:54970683C>T	ENST00000217109.4	+	2	427	c.75C>T	c.(73-75)gaC>gaT	p.D25D	CSTF1_ENST00000493039.1_3'UTR	NM_001033521.1|NM_001324.2	NP_001028693.1|NP_001315.1	Q05048	CSTF1_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa	25	Hydrophobic.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D25D(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	15			Colorectal(105;0.202)			TGCTATATGACGGCTACATCA	0.502													C|||	12	0.00239617	0.0083	0.0014	5008	,	,		19914	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	20						C	,,	14,4392	21.2+/-45.6	0,14,2189	109	87	94		75,75,75	-10	0.1	20	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CSTF1	NM_001033521.1,NM_001033522.1,NM_001324.2	,,	0,14,6489	TT,TC,CC		0.0,0.3177,0.1076	,,	25/432,25/432,25/432	54970683	14,12992	2203	4300	6503	54404090	SO:0001819	synonymous_variant	1477				CCDS13452.1	20q13.31	2013-01-10	2002-08-29		ENSG00000101138	ENSG00000101138		"WD repeat domain containing"	2483	protein-coding gene	gene with protein product		600369	"cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD"			1358884, 11257228	Standard	NM_001033521		Approved		uc002xxl.1	Q05048	OTTHUMG00000032791	ENST00000217109.4:c.75C>T	20.37:g.54970683C>T			54404090	Q5QPD8	De_novo_Start_OutOfFrame	SNP	ENST00000217109.4	37	CCDS13452.1																																																																																				0.502	CSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079794.2	NM_001033521		T	54970683	C	T	54970683	2	4	74	1	0	0	0	0	0	0	0	1	3989	535	19	1		1	CSTF1	20	54970683	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		54970683	8054837	85	21458										
TIAM1	7074	broad.mit.edu	37	chr21	32525074	32525074	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gttaaatttccaaaaagcacGtcaagctagaaataaaacag	6	7	1	1	rs151124534		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr21:32525074G>A	ENST00000286827.3	-	20	3717	c.3246C>T	c.(3244-3246)gaC>gaT	p.D1082D	TIAM1_ENST00000541036.1_Silent_p.D1022D	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1082	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D1082D(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAAAAAGCACGTCAAGCTAGA	0.323													G|||	1	0.000199681	0	0	5008	,	,		19631	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	21						G		0,4406		0,0,2203	51	52	52		3246	-1	1	21	dbSNP_134	52	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous	TIAM1	NM_003253.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		1082/1592	32525074	2,13004	2203	4300	6503	31446945	SO:0001819	synonymous_variant	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3246C>T	21.37:g.32525074G>A			31446945	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.323	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32525074	G	A	32525074	2	1	74	1	0	0	0	0	0	0	0	1	15929	1136	40	1		1	TIAM1	21	32525074	Silent	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		32525074	15604821	86	21459										
HLCS	3141	broad.mit.edu	37	chr21	38309487	38309487	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	cctcccctgtcactgtccccAgcaggctcactcccagaggc	8	20	2	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr21:38309487A>G	ENST00000399120.1	-	5	1488	c.258T>C	c.(256-258)gcT>gcC	p.A86A	HLCS_ENST00000336648.4_Silent_p.A86A	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	86					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)	p.A86A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CACTGTCCCCAGCAGGCTCAC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	21											80	71	74					21																	38309487		2203	4300	6503	37231357	SO:0001819	synonymous_variant	3141				CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.258T>C	21.37:g.38309487A>G			37231357	B2RAH1|D3DSG6|Q99451	Silent	SNP	ENST00000399120.1	37	CCDS13647.1																																																																																				0.557	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			G	38309487	A	G	38309487	2	3	74	1	0	0	0	0	0	0	0	1	7234	175	7	4		4	HLCS	21	38309487	Silent	SNP	A	TCGA-AG-A025-01A-01W-A00E-09	5784413	38309487	9820408	87	21460										
PI4KA	5297	broad.mit.edu	37	chr22	21115649	21115649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	gcagaacattacctggaagcGatcaggatctgttgaacgca	11	9	2	2	rs202070171		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr22:21115649G>A	ENST00000572273.1	-	23	2790	c.2560C>T	c.(2560-2562)Cgc>Tgc	p.R854C	PI4KA_ENST00000255882.6_Missense_Mutation_p.R912C|PI4KA_ENST00000466162.1_5'UTR			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	854					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.R854C(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ACCTGGAAGCGATCAGGATCT	0.378													G|||	1	0.000199681	0	0	5008	,	,		20116	0.001		0	False		,,,				2504	0				GBM(136;1332 1831 3115 23601 50806)											2	Substitution - Missense(2)	large_intestine(2)	22											102	92	95					22																	21115649		2203	4300	6503	19445649	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2560C>T	22.37:g.21115649G>A	ENSP00000458238:p.Arg854Cys		19445649	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.63	3.664681	0.67700	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.49047	0.1534	L	0.36672	1.1	0.80722	D	1	B	0.30824	0.296	B	0.20767	0.031	T	0.48281	-0.9049	9	0.48119	T	0.1	-25.0446	19.1301	0.93402	0.0:0.0:1.0:0.0	.	854	P42356	PI4KA_HUMAN	C	854	.	ENSP00000255882:R854C	R	-	1	0	PI4KA	19445649	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.593000	0.61034	2.767000	0.95098	0.655000	0.94253	CGC		0.378	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21115649	G	A	21115649	3	1	74	1	0	0	0	0	1	0	0	0	11904	1058	37	1	3706	1	PI4KA	22	21115649	Missense_Mutation	SNP	G	TCGA-AG-A025-01A-01W-A00E-09		21115649	30188917	88	21461										
MYO18B	84700	broad.mit.edu	37	chr22	26343729	26343729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	agaaggcggacctcctgaagCgcatcgatgaggaccaggat	14	10	0	3	rs368617132		TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr22:26343729C>T	ENST00000407587.2	+	36	5855	c.5686C>T	c.(5686-5688)Cgc>Tgc	p.R1896C	MYO18B_ENST00000335473.7_Missense_Mutation_p.R1895C|MYO18B_ENST00000536101.1_Missense_Mutation_p.R1895C			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1895	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1896C(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CCTCCTGAAGCGCATCGATGA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	22						C	CYS/ARG	1,4211		0,1,2105	67	69	69		5683	5.1	1	22		69	0,8466		0,0,4233	no	missense	MYO18B	NM_032608.5	180	0,1,6338	TT,TC,CC		0.0,0.0237,0.0079	probably-damaging	1895/2568	26343729	1,12677	2106	4233	6339	24673729	SO:0001583	missense	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5686C>T	22.37:g.26343729C>T	ENSP00000386096:p.Arg1896Cys		24673729	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	C	17.87	3.494010	0.64186	2.37E-4	0.0	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.88354	-2.34;-2.34;-2.37	5.06	5.06	0.68205	.	0.151245	0.42172	D	0.000759	D	0.93061	0.7791	M	0.76328	2.33	0.48975	D	0.999736	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;P;D;D	0.65874	0.917;0.87;0.917;0.939	D	0.93566	0.6899	10	0.87932	D	0	.	12.1623	0.54110	0.1711:0.8289:0.0:0.0	.	1408;1895;1896;1895	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	C	1895;1895;1896	ENSP00000441229:R1895C;ENSP00000334563:R1895C;ENSP00000386096:R1896C	ENSP00000334563:R1895C	R	+	1	0	MYO18B	24673729	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.123000	0.41996	2.360000	0.80028	0.655000	0.94253	CGC		0.557	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26343729	C	T	26343729	3	4	74	1	0	0	0	0	1	0	0	0	10096	768	27	1	5821	1	MYO18B	22	26343729	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	5228080	26343729	24960837	89	21462										
RNF215	200312	broad.mit.edu	37	chr22	30776099	30776099	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	accgcacaggtctcagcaccCggatctgggaggccctgcgc	13	16	2	0			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr22:30776099C>T	ENST00000382363.3	-	7	1034	c.960G>A	c.(958-960)ccG>ccA	p.P320P	RP1-130H16.16_ENST00000332468.4_RNA	NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	320						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.P320P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						TCTCAGCACCCGGATCTGGGA	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	22											64	73	70					22																	30776099		2203	4300	6503	29106099	SO:0001819	synonymous_variant	200312				CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999		"RING-type (C3HC4) zinc fingers"	33434	protein-coding gene	gene with protein product							Standard	NM_001017981		Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.960G>A	22.37:g.30776099C>T			29106099	A6NEL1	Silent	SNP	ENST00000382363.3	37	CCDS33633.1	.	.	.	.	.	.	.	.	.	.	C	0.074	-1.195768	0.01594	.	.	ENSG00000099999	ENST00000215798	.	.	.	3.71	-7.42	0.01388	.	.	.	.	.	T	0.52322	0.1727	.	.	.	0.42395	D	0.992543	.	.	.	.	.	.	T	0.58607	-0.7607	4	.	.	.	-23.0055	11.1364	0.48377	0.1549:0.5944:0.2507:0.0	.	.	.	.	R	258	.	.	G	-	1	0	RNF215	29106099	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-4.557000	0.00216	-2.128000	0.00818	-0.397000	0.06425	GGG		0.642	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320960.1	NM_001017981		T	30776099	C	T	30776099	2	4	74	1	0	0	0	0	0	0	0	1	13516	639	23	1		1	RNF215	22	30776099	Silent	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	4432370	30776099	20528467	90	21463										
L3MBTL2	83746	broad.mit.edu	37	chr22	41625556	41625556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	attcaaagggaaaagaatccCgcccactaagacgcgacccc	8	14	1	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chr22:41625556C>T	ENST00000216237.5	+	16	2059	c.1901C>T	c.(1900-1902)cCg>cTg	p.P634L	CHADL_ENST00000216241.9_3'UTR	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	634					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.P634L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AAAAGAATCCCGCCCACTAAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	22											46	48	48					22																	41625556		2203	4300	6503	39955502	SO:0001583	missense	83746			AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.1901C>T	22.37:g.41625556C>T	ENSP00000216237:p.Pro634Leu		39955502	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	37	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.817607	0.32145	.	.	ENSG00000100395	ENST00000216237	T	0.16897	2.31	4.41	2.33	0.28932	.	0.249318	0.34178	N	0.004200	T	0.07728	0.0194	N	0.24115	0.695	0.24165	N	0.995645	P	0.39782	0.688	B	0.27715	0.082	T	0.26950	-1.0088	10	0.48119	T	0.1	.	5.9839	0.19423	0.0:0.6807:0.0:0.3193	.	634	Q969R5	LMBL2_HUMAN	L	634	ENSP00000216237:P634L	ENSP00000216237:P634L	P	+	2	0	L3MBTL2	39955502	0.319000	0.24607	0.375000	0.26029	0.830000	0.47004	1.855000	0.39378	0.798000	0.33994	0.650000	0.86243	CCG		0.542	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		T	41625556	C	T	41625556	3	4	74	1	0	0	0	0	1	0	0	0	8614	652	23	1	1963	1	L3MBTL2	22	41625556	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	10849457	41625556	9679010	91	21464										
RPS4X	6191	broad.mit.edu	37	chrX	71493153	71493153	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ggcatctttcacgtgaaccaCgtcaaaagatccagggtgcc	10	12	3	2			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chrX:71493153C>T	ENST00000316084.6	-	6	723	c.619G>A	c.(619-621)Gtg>Atg	p.V207M	RPS4X_ENST00000486733.1_5'UTR	NM_001007.4	NP_000998.1	P62701	RS4X_HUMAN	ribosomal protein S4, X-linked	207					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.V207M(1)		NS(1)|large_intestine(1)	2	Renal(35;0.156)					ACGTGAACCACGTCAAAAGAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	X											62	49	53					X																	71493153		2203	4300	6503	71409878	SO:0001583	missense	6191				CCDS14418.1	Xq13.1	2011-04-05			ENSG00000198034	ENSG00000198034		"S ribosomal proteins"	10424	protein-coding gene	gene with protein product	"40S ribosomal protein S4, X isoform", "ribosomal protein S4X isoform", "single-copy abundant mRNA", "cell cycle gene 2"	312760				1795030, 8139551	Standard	NM_001007		Approved	DXS306, CCG2, SCAR, SCR10, FLJ40595, RPS4, S4	uc004ear.3	P62701	OTTHUMG00000021813	ENST00000316084.6:c.619G>A	X.37:g.71493153C>T	ENSP00000362744:p.Val207Met		71409878	P12631|P12750|P27576|P55831|Q14727|Q6IPY4	Missense_Mutation	SNP	ENST00000316084.6	37	CCDS14418.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.573230	0.45902	.	.	ENSG00000198034	ENST00000316084	T	0.27720	1.65	4.52	4.52	0.55395	KOW (1);	0.000000	0.64402	D	0.000003	T	0.20292	0.0488	N	0.12637	0.245	0.80722	D	1	B	0.26483	0.15	B	0.29785	0.107	T	0.07693	-1.0759	10	0.41790	T	0.15	.	14.0455	0.64702	0.0:1.0:0.0:0.0	.	207	P62701	RS4X_HUMAN	M	207	ENSP00000362744:V207M	ENSP00000362744:V207M	V	-	1	0	RPS4X	71409878	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	7.642000	0.83385	1.975000	0.57531	0.600000	0.82982	GTG		0.468	RPS4X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057188.1	NM_001007		T	71493153	C	T	71493153	3	4	74	1	0	0	0	0	1	0	0	0	13682	536	19	1	180	1	RPS4X	23	71493153	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09		71493153	83777407	92	21465										
NXF5	55998	broad.mit.edu	37	chrX	101096737	101096737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	caaagaagcatgcccgatttCggatgtagtggaactacagg	12	8	0	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chrX:101096737C>T	ENST00000361708.2	-	5	508	c.149G>A	c.(148-150)cGa>cAa	p.R50Q	NXF5_ENST00000473265.2_Missense_Mutation_p.R50Q|NXF5_ENST00000537026.1_Missense_Mutation_p.R50Q			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	50	RRM.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R50Q(2)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						TGCCCGATTTCGGATGTAGTG	0.507																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	X											163	135	145					X																	101096737		2203	4300	6503	100983393	SO:0001583	missense	55998			AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.149G>A	X.37:g.101096737C>T	ENSP00000355286:p.Arg50Gln		100983393	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Missense_Mutation	SNP	ENST00000361708.2	37		.	.	.	.	.	.	.	.	.	.	.	8.283	0.816095	0.16607	.	.	ENSG00000126952	ENST00000537026;ENST00000473265;ENST00000361708	T;T;T	0.45276	0.9;0.9;0.9	2.18	-0.423	0.12325	.	0.805437	0.11286	U	0.579766	T	0.24624	0.0597	N	0.22421	0.69	0.09310	N	1	B	0.15719	0.014	B	0.17722	0.019	T	0.19614	-1.0300	10	0.45353	T	0.12	.	4.2641	0.10754	0.0:0.3854:0.0:0.6146	.	50	A2RRM0	.	Q	50	ENSP00000442401:R50Q;ENSP00000426978:R50Q;ENSP00000355286:R50Q	ENSP00000263032:R50Q	R	-	2	0	NXF5	100983393	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.078000	0.11375	-0.130000	0.11599	-0.731000	0.03576	CGA		0.507	NXF5-201	KNOWN	basic	protein_coding	protein_coding				T	101096737	C	T	101096737	3	4	74	1	0	0	0	0	1	0	0	0	10817	884	31	1	996	1	NXF5	23	101096737	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	29603584	101096737	54173823	93	21466										
ARHGAP36	158763	broad.mit.edu	37	chrX	130220336	130220336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0106382978723404	1	1	0.134958297382801	0	0.144429055093875	1	1	0	ttcagaggcaggttgctaagCgcgtgtggaagtccagcccg	15	10	1	1			TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A025-01A-01W-A00E-09	TCGA-AG-A025-10A-01W-A00E-09	g.chrX:130220336C>T	ENST00000276211.5	+	10	1660	c.1315C>T	c.(1315-1317)Cgc>Tgc	p.R439C	ARHGAP36_ENST00000370922.1_Missense_Mutation_p.R427C|ARHGAP36_ENST00000370921.1_Missense_Mutation_p.R303C	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	439					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R439C(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GGTTGCTAAGCGCGTGTGGAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	91	94					X																	130220336		2203	4300	6503	130048017	SO:0001583	missense	158763				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.1315C>T	X.37:g.130220336C>T	ENSP00000276211:p.Arg439Cys		130048017	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662549	0.29515	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000412432;ENST00000370921	T;T;T;T	0.10860	2.83;2.83;2.84;2.86	4.69	2.74	0.32292	.	0.000000	0.45126	D	0.000397	T	0.12433	0.0302	N	0.08118	0	0.43430	D	0.995599	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.977;0.977;0.948	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.361	0.32359	0.4276:0.5724:0.0:0.0	.	408;427;439	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	C	439;427;408;303	ENSP00000276211:R439C;ENSP00000359960:R427C;ENSP00000408515:R408C;ENSP00000359959:R303C	ENSP00000276211:R439C	R	+	1	0	ARHGAP36	130048017	0.993000	0.37304	0.999000	0.59377	0.117000	0.20001	0.628000	0.24522	1.059000	0.40554	0.600000	0.82982	CGC		0.453	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130220336	C	T	130220336	3	4	74	1	0	0	0	0	1	0	0	0	883	768	27	1	1349	1	ARHGAP36	23	130220336	Missense_Mutation	SNP	C	TCGA-AG-A025-01A-01W-A00E-09	29123599	130220336	25050224	94	21467										
IGSF21	84966	broad.mit.edu	37	chr1	18692066	18692066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccgcaccccgagcagtgacgGcactgtggaagtacgtgccc	13	15	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:18692066G>A	ENST00000251296.1	+	6	1273	c.890G>A	c.(889-891)gGc>gAc	p.G297D		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	297						extracellular region (GO:0005576)		p.G297D(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		AGCAGTGACGGCACTGTGGAA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	97	103					1																	18692066		2203	4300	6503	18564653	SO:0001583	missense	84966			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.890G>A	1.37:g.18692066G>A	ENSP00000251296:p.Gly297Asp		18564653	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	37	CCDS184.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540785	0.85917	.	.	ENSG00000117154	ENST00000251296	T	0.63580	-0.05	4.28	4.28	0.50868	Immunoglobulin-like fold (1);	0.047421	0.85682	D	0.000000	T	0.68540	0.3012	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68040	-0.5514	10	0.37606	T	0.19	-6.8934	15.7859	0.78304	0.0:0.0:1.0:0.0	.	297	Q96ID5	IGS21_HUMAN	D	297	ENSP00000251296:G297D	ENSP00000251296:G297D	G	+	2	0	IGSF21	18564653	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.821000	0.92009	2.383000	0.81215	0.561000	0.74099	GGC		0.632	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		A	18692066	G	A	18692066	3	1	75	1	0	0	0	0	1	0	0	0	7620	1203	42	3	912	3	IGSF21	1	18692066	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		18692066	230558555	1	21468										
PLA2G2F	64600	broad.mit.edu	37	chr1	20474891	20474891	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccagcgccccccgcccctccCtagagcctctgaggtttgag	10	19	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:20474891C>A	ENST00000375102.3	+	5	735	c.633C>A	c.(631-633)ccC>ccA	p.P211P		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	168					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)	p.P211P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CCGCCCCTCCCTAGAGCCTCT	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	1											25	28	27					1																	20474891		2203	4300	6503	20347478	SO:0001819	synonymous_variant	64600			AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.633C>A	1.37:g.20474891C>A			20347478	Q5R385|Q8N217|Q9H506	Silent	SNP	ENST00000375102.3	37	CCDS204.2																																																																																				0.657	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		A	20474891	C	A	20474891	2	1	75	1	0	0	0	0	0	0	0	1	12030	668	24	2		2	PLA2G2F	1	20474891	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1782825	20474891	228775730	2	21469										
CLSPN	63967	broad.mit.edu	37	chr1	36228830	36228830	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gactcttcatcttccaatggAgagttattttcatcctccaa	5	11	4	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:36228830A>G	ENST00000318121.3	-	4	732	c.675T>C	c.(673-675)tcT>tcC	p.S225S	CLSPN_ENST00000520551.1_Silent_p.S225S|CLSPN_ENST00000373220.3_Silent_p.S225S|CLSPN_ENST00000251195.5_Silent_p.S225S	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	225					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.S225S(2)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTTCCAATGGAGAGTTATTTT	0.353																																																2	Substitution - coding silent(2)	large_intestine(2)	1											136	130	132					1																	36228830		2203	4299	6502	36001417	SO:0001819	synonymous_variant	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.675T>C	1.37:g.36228830A>G			36001417	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Silent	SNP	ENST00000318121.3	37	CCDS396.1																																																																																				0.353	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		G	36228830	A	G	36228830	2	3	75	1	0	0	0	0	0	0	0	1	3566	291	11	4		4	CLSPN	1	36228830	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	15753939	36228830	213021791	3	21470										
MAST2	23139	broad.mit.edu	37	chr1	46500589	46500589	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aaactggcagcagcacttgcCgcctctgagaagaagctagc	11	12	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:46500589C>T	ENST00000361297.2	+	29	4531	c.4248C>T	c.(4246-4248)gcC>gcT	p.A1416A	MAST2_ENST00000372009.2_Silent_p.A1226A	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2									p.A1416A(1)		breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CAGCACTTGCCGCCTCTGAGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	1											53	60	57					1																	46500589		2028	4189	6217	46273176	SO:0001819	synonymous_variant	23139			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4248C>T	1.37:g.46500589C>T			46273176		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																				0.607	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		T	46500589	C	T	46500589	2	4	75	1	0	0	0	0	0	0	0	1	9355	639	23	1		1	MAST2	1	46500589	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	10271759	46500589	202750032	4	21471										
PKN2	5586	broad.mit.edu	37	chr1	89271666	89271666	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcttggagaaatagatgaatCttctgaattaagagttttgg	10	3	3	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:89271666C>T	ENST00000370521.3	+	12	2128	c.1769C>T	c.(1768-1770)tCt>tTt	p.S590F	PKN2_ENST00000370513.5_Missense_Mutation_p.S542F|PKN2_ENST00000316005.7_3'UTR|PKN2_ENST00000370505.3_Missense_Mutation_p.S433F|PKN2_ENST00000544045.1_Missense_Mutation_p.S264F	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	590					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.S590F(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		ATAGATGAATCTTCTGAATTA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	63	64					1																	89271666		1821	4076	5897	89044254	SO:0001583	missense	5586			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1769C>T	1.37:g.89271666C>T	ENSP00000359552:p.Ser590Phe		89044254	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.497995	0.44455	.	.	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.72	4.8	0.61643	.	0.155083	0.29924	U	0.010849	T	0.20820	0.0501	L	0.50333	1.59	0.45342	D	0.99833	P;B;B	0.35208	0.49;0.148;0.257	B;B;B	0.29598	0.081;0.104;0.033	T	0.09975	-1.0650	10	0.59425	D	0.04	.	15.1111	0.72359	0.0:0.931:0.0:0.069	.	574;542;590	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	F	590;433;542;264	ENSP00000359552:S590F;ENSP00000359536:S433F;ENSP00000359544:S542F;ENSP00000439643:S264F	ENSP00000359536:S433F	S	+	2	0	PKN2	89044254	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	4.385000	0.59613	2.689000	0.91719	0.591000	0.81541	TCT		0.388	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		T	89271666	C	T	89271666	3	4	75	1	0	0	0	0	1	0	0	0	12011	913	32	3	1815	3	PKN2	1	89271666	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	42771077	89271666	159978955	5	21472										
DRAM2	128338	broad.mit.edu	37	chr1	111668891	111668891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cattgccccaaataagcattTttctggagctactgtaccag	7	11	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:111668891T>C	ENST00000286692.4	-	4	774	c.157A>G	c.(157-159)Aaa>Gaa	p.K53E	DRAM2_ENST00000539140.1_Missense_Mutation_p.K53E|DRAM2_ENST00000484310.1_5'UTR			Q6UX65	DRAM2_HUMAN	DNA-damage regulated autophagy modulator 2	53					apoptotic process (GO:0006915)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|microtubule cytoskeleton (GO:0015630)		p.K53E(1)		endometrium(1)|large_intestine(5)|lung(3)	9						AATAAGCATTTTTCTGGAGCT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	1											105	113	110					1																	111668891		2203	4296	6499	111470414	SO:0001583	missense	128338			AY336747	CCDS30801.1	1p13.3	2010-07-08	2009-06-12	2009-06-12	ENSG00000156171	ENSG00000156171			28769	protein-coding gene	gene with protein product		613360	"transmembrane protein 77"	TMEM77		12975309	Standard	NM_178454		Approved	MGC54289, PRO180, WWFQ154, RP5-1180E21.1	uc001ead.4	Q6UX65	OTTHUMG00000011911	ENST00000286692.4:c.157A>G	1.37:g.111668891T>C	ENSP00000286692:p.Lys53Glu		111470414	B3SUG9|Q4VWF6|Q86VD3|Q8NBQ4	Missense_Mutation	SNP	ENST00000286692.4	37	CCDS30801.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.647205	0.47258	.	.	ENSG00000156171	ENST00000286692;ENST00000539140	T;T	0.43294	0.95;0.95	5.53	5.53	0.82687	.	0.110120	0.64402	D	0.000007	T	0.22244	0.0536	L	0.43152	1.355	0.31554	N	0.658328	B	0.25390	0.125	B	0.30716	0.119	T	0.14364	-1.0475	10	0.42905	T	0.14	-4.2814	12.0642	0.53578	0.0:0.0:0.0:1.0	.	53	Q6UX65	DRAM2_HUMAN	E	53	ENSP00000286692:K53E;ENSP00000437718:K53E	ENSP00000286692:K53E	K	-	1	0	DRAM2	111470414	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.802000	0.55553	2.105000	0.64084	0.528000	0.53228	AAA		0.323	DRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032930.3	NM_178454		C	111668891	T	C	111668891	3	2	75	1	0	0	0	0	1	0	0	0	4765	1850	64	4	667	4	DRAM2	1	111668891	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	22397225	111668891	137581730	6	21473										
WDR77	79084	broad.mit.edu	37	chr1	111991767	111991767	+	Frame_Shift_Del	DEL	G	G	-													0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccgggccgccgggggcactaGggggggtggggtttccttcc							TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:111991767delG	ENST00000235090.5	-	1	231	c.25delC	c.(25-27)ctafs	p.L9fs	WDR77_ENST00000411751.2_Frame_Shift_Del_p.L9fs|ATP5F1_ENST00000483994.1_5'Flank|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'UTR|WDR77_ENST00000497278.1_5'Flank	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77	9					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA metabolic process (GO:0016070)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|methylosome (GO:0034709)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.L9fs*1(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGGGGCACTAGGGGGGGTGGG	0.672																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											5	6	6					1																	111991767		1724	3675	5399	111793290	SO:0001589	frameshift_variant	79084			BC016946	CCDS835.1	1p13.2	2013-01-09		2005-08-09	ENSG00000116455	ENSG00000116455		"WD repeat domain containing"	29652	protein-coding gene	gene with protein product		611734				11756452, 8619474	Standard	NM_024102		Approved	MEP50	uc001ebb.3	Q9BQA1	OTTHUMG00000011748	ENST00000235090.5:c.25delC	1.37:g.111991767delG	ENSP00000235090:p.Leu9fs		111793290	B3KMW6|B4DP38|Q3LID2|Q53FU2|Q6JZZ5|Q96GK4|Q9BWY3	Frame_Shift_Del	DEL	ENST00000235090.5	37	CCDS835.1																																																																																				0.672	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1	NM_024102		-	111991767	G	-	111991767	7	5	75	1	0	1	0	1	0	0	0	0	17367	991	35	0	1043	0	WDR77	1	111991767	Frame_Shift_Del	DEL	G	TCGA-AG-A026-01A-32W-A096-10	322876	111991767	137258854	7	21474										
DENND2C	163259	broad.mit.edu	37	chr1	115141935	115141935	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggagctgtggtaaggagcaaGacaggattccaataaggaat	14	5	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:115141935G>T	ENST00000393274.1	-	16	2868	c.2243C>A	c.(2242-2244)tCt>tAt	p.S748Y	DENND2C_ENST00000393277.1_Intron|DENND2C_ENST00000393276.3_Missense_Mutation_p.S691Y|DENND2C_ENST00000481894.1_5'UTR	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	748	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.S691Y(1)		NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-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)		TAAGGAGCAAGACAGGATTCC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											163	140	148					1																	115141935		2203	4300	6503	114943458	SO:0001583	missense	163259				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.2243C>A	1.37:g.115141935G>T	ENSP00000376955:p.Ser748Tyr		114943458	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037800	0.93630	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540	T;T	0.14391	2.51;2.51	5.81	5.81	0.92471	DENN (3);	0.251016	0.43747	D	0.000529	T	0.33876	0.0878	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.992;0.987	T	0.05733	-1.0867	10	0.87932	D	0	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	748;691	Q68D51;Q68D51-3	DEN2C_HUMAN;.	Y	691;748;748	ENSP00000376957:S691Y;ENSP00000376955:S748Y	ENSP00000358553:S748Y	S	-	2	0	DENND2C	114943458	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.337000	0.96545	2.769000	0.95229	0.644000	0.83932	TCT		0.443	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		T	115141935	G	T	115141935	3	4	75	1	0	0	0	0	1	0	0	0	4441	942	33	2	567	2	DENND2C	1	115141935	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	3150168	115141935	134108686	8	21475										
OTUD7B	56957	broad.mit.edu	37	chr1	149922060	149922060	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tatgggcctcctaagcacatGagcaaggacaaagacgtgaa	11	9	0	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:149922060G>A	ENST00000369135.4	-	8	1204	c.910C>T	c.(910-912)Cat>Tat	p.H304Y		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	304	Catalytic.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.H304Y(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CTAAGCACATGAGCAAGGACA	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	1											78	80	79					1																	149922060		2059	4205	6264	148188684	SO:0001583	missense	56957			AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.910C>T	1.37:g.149922060G>A	ENSP00000358131:p.His304Tyr		148188684	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866620	0.91511	.	.	ENSG00000163113	ENST00000369135;ENST00000543330;ENST00000417191	T;T	0.35421	1.31;1.31	5.03	5.03	0.67393	Ovarian tumour, otubain (2);	0.000000	0.85682	D	0.000000	T	0.57888	0.2084	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.61023	-0.7146	9	.	.	.	-1.6017	17.52	0.87784	0.0:0.0:1.0:0.0	.	304	Q6GQQ9	OTU7B_HUMAN	Y	304	ENSP00000358131:H304Y;ENSP00000408231:H304Y	.	H	-	1	0	OTUD7B	148188684	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.612000	0.88384	0.655000	0.94253	CAT		0.557	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		A	149922060	G	A	149922060	3	1	75	1	0	0	0	0	1	0	0	0	11350	1290	45	3	1641	3	OTUD7B	1	149922060	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	34780125	149922060	99328561	9	21476										
LCE1F	353137	broad.mit.edu	37	chr1	152749149	152749149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgctgcagccagccctcagCgggctccagctgctgcggag	14	16	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:152749149C>T	ENST00000334371.2	+	1	302	c.302C>T	c.(301-303)gCg>gTg	p.A101V		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	101					keratinization (GO:0031424)			p.A101V(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGCCCTCAGCGGGCTCCAGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	1											31	35	34					1																	152749149		2199	4294	6493	151015773	SO:0001583	missense	353137				CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.302C>T	1.37:g.152749149C>T	ENSP00000334187:p.Ala101Val		151015773		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.652520	0.29336	.	.	ENSG00000240386	ENST00000334371	T	0.03635	3.86	4.45	2.57	0.30868	.	0.707775	0.11673	N	0.540692	T	0.00906	0.0030	N	0.08118	0	0.20196	N	0.999921	B	0.14438	0.01	B	0.14578	0.011	T	0.49771	-0.8904	10	0.87932	D	0	.	10.7817	0.46382	0.0:0.1987:0.8013:0.0	.	101	Q5T754	LCE1F_HUMAN	V	101	ENSP00000334187:A101V	ENSP00000334187:A101V	A	+	2	0	LCE1F	151015773	0.991000	0.36638	0.998000	0.56505	0.740000	0.42216	2.108000	0.41854	1.200000	0.43188	-0.267000	0.10333	GCG		0.647	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		T	152749149	C	T	152749149	3	4	75	1	0	0	0	0	1	0	0	0	8686	768	27	1	304	1	LCE1F	1	152749149	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	2827089	152749149	96501472	10	21477										
UBAP2L	9898	broad.mit.edu	37	chr1	154224075	154224075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgattatgagtccacccccaCcacgagcgcctcttcaagcc	7	17	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:154224075C>T	ENST00000361546.2	+	13	1652	c.1610C>T	c.(1609-1611)aCc>aTc	p.T537I	UBAP2L_ENST00000428931.1_Missense_Mutation_p.T537I|UBAP2L_ENST00000271877.7_Missense_Mutation_p.T548I|AL590431.1_ENST00000517008.1_RNA|UBAP2L_ENST00000343815.6_Missense_Mutation_p.T537I			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	537					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.T537I(1)|p.T33I(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCCACCCCCACCACGAGCGCC	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	1											96	96	96					1																	154224075		2203	4300	6503	152490699	SO:0001583	missense	9898			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1610C>T	1.37:g.154224075C>T	ENSP00000355343:p.Thr537Ile		152490699	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606099	0.87157	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.12569	2.68;2.67;2.69;2.67	5.09	5.09	0.68999	.	0.106104	0.64402	D	0.000004	T	0.11495	0.0280	L	0.36672	1.1	0.50039	D	0.999841	P;P;P;P;P	0.43477	0.808;0.782;0.782;0.782;0.675	B;P;B;B;B	0.46172	0.228;0.506;0.404;0.404;0.309	T	0.01583	-1.1319	10	0.62326	D	0.03	-2.6015	18.0834	0.89449	0.0:1.0:0.0:0.0	.	451;548;530;537;537	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	I	537;537;33;33;548;537	ENSP00000345308:T537I;ENSP00000389445:T537I;ENSP00000271877:T548I;ENSP00000355343:T537I	ENSP00000271877:T548I	T	+	2	0	UBAP2L	152490699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.521000	0.67086	2.820000	0.97059	0.650000	0.86243	ACC		0.507	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154224075	C	T	154224075	3	4	75	1	0	0	0	0	1	0	0	0	16878	507	18	3	1660	3	UBAP2L	1	154224075	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1474926	154224075	95026546	11	21478										
YY1AP1	55249	broad.mit.edu	37	chr1	155629929	155629929	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tagggttaaccaagagggtgGcgatgggaatagtctgggga	18	4	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:155629929G>T	ENST00000295566.4	-	11	1933	c.1910C>A	c.(1909-1911)gCc>gAc	p.A637D	YY1AP1_ENST00000404643.1_Missense_Mutation_p.A571D|YY1AP1_ENST00000347088.5_Missense_Mutation_p.A591D|YY1AP1_ENST00000311573.5_Missense_Mutation_p.A560D|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000407221.1_Missense_Mutation_p.A560D|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000368339.5_Missense_Mutation_p.A729D|YY1AP1_ENST00000368340.5_Missense_Mutation_p.A709D|YY1AP1_ENST00000359205.5_Missense_Mutation_p.A580D|YY1AP1_ENST00000355499.4_Missense_Mutation_p.A591D|YY1AP1_ENST00000535662.1_Missense_Mutation_p.A437D|YY1AP1_ENST00000368330.2_Missense_Mutation_p.A591D|YY1AP1_ENST00000361831.5_Missense_Mutation_p.A580D	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	637					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A637D(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CAAGAGGGTGGCGATGGGAAT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	76	79					1																	155629929		2203	4300	6503	153896553	SO:0001583	missense	55249			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1910C>A	1.37:g.155629929G>T	ENSP00000295566:p.Ala637Asp		153896553	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	g	13.40	2.226173	0.39300	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662	T;T;T;T;T;T;T;T;T;T;T;T	0.24723	1.91;1.91;1.91;1.91;1.91;1.85;1.88;1.91;1.91;1.91;1.84;1.91	2.53	2.53	0.30540	.	0.303789	0.32357	N	0.006215	T	0.06096	0.0158	N	0.08118	0	0.80722	D	1	B;B;B;B;P	0.41848	0.092;0.119;0.275;0.116;0.763	B;B;B;B;B	0.35971	0.11;0.092;0.121;0.135;0.215	T	0.21109	-1.0255	10	0.87932	D	0	.	13.0809	0.59114	0.0:0.0:1.0:0.0	.	729;571;637;591;709	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	D	580;591;560;591;580;709;637;591;560;571;729;437	ENSP00000352134:A580D;ENSP00000347686:A591D;ENSP00000311138:A560D;ENSP00000316079:A591D;ENSP00000355298:A580D;ENSP00000357324:A709D;ENSP00000295566:A637D;ENSP00000357314:A591D;ENSP00000385791:A560D;ENSP00000385390:A571D;ENSP00000357323:A729D;ENSP00000437926:A437D	ENSP00000295566:A637D	A	-	2	0	YY1AP1	153896553	1.000000	0.71417	0.998000	0.56505	0.757000	0.42996	4.592000	0.61027	1.419000	0.47118	0.306000	0.20318	GCC		0.537	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155629929	G	T	155629929	3	4	75	1	0	0	0	0	1	0	0	0	17548	1203	42	2	484	2	YY1AP1	1	155629929	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	1405854	155629929	93620692	12	21479										
NES	10763	broad.mit.edu	37	chr1	156640422	156640422	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cccagggtctcagcagggaaCgcctcctctgctcccctggg	12	17	2	0	rs149557132	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:156640422C>T	ENST00000368223.3	-	4	3690	c.3558G>A	c.(3556-3558)gcG>gcA	p.A1186A		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1186	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)	p.A1186A(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGCAGGGAACGCCTCCTCTG	0.637													C|||	4	0.000798722	0.0015	0	5008	,	,		15258	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						C		2,4404	4.2+/-10.8	0,2,2201	77	78	77		3558	-3.4	0	1	dbSNP_134	77	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	NES	NM_006617.1		0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538		1186/1622	156640422	7,12999	2203	4300	6503	154907046	SO:0001819	synonymous_variant	10763			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3558G>A	1.37:g.156640422C>T			154907046	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																				0.637	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156640422	C	T	156640422	2	4	75	1	0	0	0	0	0	0	0	1	10368	523	19	1		1	NES	1	156640422	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1010493	156640422	92610199	13	21480										
FCRL3	115352	broad.mit.edu	37	chr1	157666049	157666049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tactgagcaaataaggaccaTattttctccttcaatcagct	5	10	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:157666049T>C	ENST00000368184.3	-	7	1204	c.913A>G	c.(913-915)Atg>Gtg	p.M305V	FCRL3_ENST00000368186.5_Missense_Mutation_p.M305V|FCRL3_ENST00000473231.1_5'UTR|RP11-367J7.3_ENST00000453692.1_RNA	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	305	Ig-like C2-type 4.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.M305V(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ATAAGGACCATATTTTCTCCT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	118	121					1																	157666049		2203	4300	6503	155932673	SO:0001583	missense	115352			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.913A>G	1.37:g.157666049T>C	ENSP00000357167:p.Met305Val		155932673	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	T	5.483	0.274196	0.10403	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.08458	3.09;3.09	5.22	0.972	0.19704	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.808279	0.10423	N	0.676504	T	0.00468	0.0015	N	0.00114	-2.085	0.09310	N	1	B;B;B	0.18013	0.025;0.012;0.02	B;B;B	0.22152	0.012;0.038;0.007	T	0.44251	-0.9340	10	0.22706	T	0.39	.	4.4373	0.11557	0.179:0.0:0.4753:0.3457	.	305;210;305	Q96P31;D3DVD1;Q96P31-6	FCRL3_HUMAN;.;.	V	305	ENSP00000357169:M305V;ENSP00000357167:M305V	ENSP00000292392:M305V	M	-	1	0	FCRL3	155932673	0.098000	0.21812	0.162000	0.22713	0.428000	0.31595	0.576000	0.23744	0.157000	0.19338	-1.275000	0.01399	ATG		0.517	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		C	157666049	T	C	157666049	3	2	75	1	0	0	0	0	1	0	0	0	5815	1406	49	4	1327	4	FCRL3	1	157666049	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	1025627	157666049	91584572	14	21481										
OR6K6	128371	broad.mit.edu	37	chr1	158725622	158725622	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cactatcagaagagggctggTtgggctgggaaatagataca	14	6	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:158725622T>G	ENST00000368144.2	+	1	1113	c.1017T>G	c.(1015-1017)ggT>ggG	p.G339G		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	339						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G339G(1)		endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					AGAGGGCTGGTTGGGCTGGGA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	1											72	77	75					1																	158725622		2203	4299	6502	156992246	SO:0001819	synonymous_variant	128371			BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.1017T>G	1.37:g.158725622T>G			156992246	B9EIM8|Q5VUU9|Q6IFR4	Silent	SNP	ENST00000368144.2	37	CCDS30904.1																																																																																				0.413	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		G	158725622	T	G	158725622	2	3	75	1	0	0	0	0	0	0	0	1	11235	1712	60	4		4	OR6K6	1	158725622	Silent	SNP	T	TCGA-AG-A026-01A-32W-A096-10	1059573	158725622	90524999	15	21482										
C1orf226	400793	broad.mit.edu	37	chr1	162351795	162351795	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cggctctgcccctctgggctCtggtgagcctggggggccag	17	14	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:162351795C>G	ENST00000458626.2	+	1	276	c.104C>G	c.(103-105)tCt>tGt	p.S35C	C1orf226_ENST00000426197.2_Missense_Mutation_p.S78C|RP11-565P22.6_ENST00000431696.1_Missense_Mutation_p.S144C	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	35								p.S78C(2)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						CCTCTGGGCTCTGGTGAGCCT	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	1											11	14	13					1																	162351795		1790	4006	5796	160618419	SO:0001583	missense	400793			AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.104C>G	1.37:g.162351795C>G	ENSP00000437071:p.Ser35Cys		160618419	B4DF31	Missense_Mutation	SNP	ENST00000458626.2	37	CCDS53422.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.570805	0.45798	.	.	ENSG00000254706;ENSG00000239887;ENSG00000239887;ENSG00000239887	ENST00000431696;ENST00000420220;ENST00000426197;ENST00000458626	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	T	0.45895	0.1365	L	0.27053	0.805	.	.	.	D;D	0.63046	0.992;0.992	P;P	0.55999	0.789;0.789	T	0.52320	-0.8591	7	0.59425	D	0.04	-1.1778	16.3966	0.83607	0.0:1.0:0.0:0.0	.	78;35	A1L170-2;A1L170	.;CA226_HUMAN	C	144;35;78;35	.	ENSP00000398035:S35C	S	+	2	0	C1orf226;RP11-565P22.6	160618419	0.049000	0.20398	0.043000	0.18650	0.206000	0.24218	3.681000	0.54648	2.447000	0.82792	0.655000	0.94253	TCT		0.627	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		G	162351795	C	G	162351795	3	3	75	1	0	0	0	0	1	0	0	0	2038	913	32	5	239	5	C1orf226	1	162351795	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3626173	162351795	86898826	16	21483										
CEP350	9857	broad.mit.edu	37	chr1	179983080	179983080	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgagaagtaaatctcggtctGaaaataatataaagaaacta	7	5	2	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:179983080G>C	ENST00000367607.3	+	10	1910	c.1492G>C	c.(1492-1494)Gaa>Caa	p.E498Q		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	498					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E498Q(1)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						ATCTCGGTCTGAAAATAATAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	1											49	52	51					1																	179983080		2203	4300	6503	178249703	SO:0001583	missense	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.1492G>C	1.37:g.179983080G>C	ENSP00000356579:p.Glu498Gln		178249703	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996044	0.74703	.	.	ENSG00000135837	ENST00000367607	D	0.90197	-2.63	5.78	5.78	0.91487	.	0.000000	0.49916	D	0.000130	D	0.94361	0.8187	M	0.70595	2.14	0.41659	D	0.989172	D;D	0.60575	0.988;0.988	P;D	0.63192	0.815;0.912	D	0.93787	0.7089	9	.	.	.	.	17.7934	0.88562	0.0:0.0:1.0:0.0	.	498;498	E7EU22;Q5VT06	.;CE350_HUMAN	Q	498	ENSP00000356579:E498Q	.	E	+	1	0	CEP350	178249703	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.564000	0.67359	2.729000	0.93468	0.650000	0.86243	GAA		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	179983080	G	C	179983080	3	2	75	1	0	0	0	0	1	0	0	0	3260	1291	45	5	1526	5	CEP350	1	179983080	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	17631285	179983080	69267541	17	21484										
GLT25D2	23127	broad.mit.edu	37	chr1	183942876	183942876	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttagtcaggaaattgtcaacAtctatgaactaggaaaagaa	8	5	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:183942876A>C	ENST00000361927.4	-	4	872	c.501T>G	c.(499-501)gaT>gaG	p.D167E	COLGALT2_ENST00000546159.1_Missense_Mutation_p.D167E	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	167					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.D167E(1)									AATTGTCAACATCTATGAACT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											99	107	104					1																	183942876		2203	4300	6503	182209499	SO:0001583	missense	23127			AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.501T>G	1.37:g.183942876A>C	ENSP00000354960:p.Asp167Glu		182209499	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	37	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.940209	0.73557	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.79554	-1.28;-1.28	5.23	4.11	0.48088	.	0.000000	0.85682	D	0.000000	D	0.91161	0.7216	M	0.93197	3.39	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.79784	0.972;0.993	D	0.91682	0.5359	10	0.87932	D	0	.	10.8469	0.46748	0.9259:0.0:0.0741:0.0	.	167;167	F5H3T5;Q8IYK4	.;GT252_HUMAN	E	167	ENSP00000439112:D167E;ENSP00000354960:D167E	ENSP00000354960:D167E	D	-	3	2	GLT25D2	182209499	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.622000	0.46427	0.836000	0.34901	0.477000	0.44152	GAT		0.413	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		C	183942876	A	C	183942876	3	2	75	1	0	0	0	0	1	0	0	0	6487	214	8	4	1415	4	GLT25D2	1	183942876	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	3959796	183942876	65307745	18	21485										
IVNS1ABP	10625	broad.mit.edu	37	chr1	185269187	185269187	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttacaggatcaaatacatcaCaatttttcagtcctttttga	4	8	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:185269187C>G	ENST00000367498.3	-	13	2067	c.1445G>C	c.(1444-1446)tGt>tCt	p.C482S	IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.C264S|IVNS1ABP_ENST00000459929.1_5'UTR	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	482					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)		p.C482S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						AAATACATCACAATTTTTCAG	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	1											103	96	99					1																	185269187		2203	4300	6503	183535810	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1445G>C	1.37:g.185269187C>G	ENSP00000356468:p.Cys482Ser		183535810	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573392	0.86542	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.78246	-1.16;-1.16	5.61	5.61	0.85477	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.86994	0.6067	L	0.58810	1.83	0.80722	D	1	D;D;D	0.89917	0.985;1.0;0.997	P;D;D	0.87578	0.71;0.998;0.945	D	0.87302	0.2306	10	0.87932	D	0	.	19.5968	0.95544	0.0:1.0:0.0:0.0	.	264;183;482	A8MVR0;Q6MZF3;Q9Y6Y0	.;.;NS1BP_HUMAN	S	482;264	ENSP00000356468:C482S;ENSP00000375864:C264S	ENSP00000356468:C482S	C	-	2	0	IVNS1ABP	183535810	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.420000	0.80191	2.793000	0.96121	0.655000	0.94253	TGT		0.338	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		G	185269187	C	G	185269187	3	3	75	1	0	0	0	0	1	0	0	0	7951	478	17	5	495	5	IVNS1ABP	1	185269187	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1326311	185269187	63981434	19	21486										
LYPLAL1	127018	broad.mit.edu	37	chr1	219352564	219352564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aacattccaacacataaaaaTtatttatccaacagctcctc	1	12	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:219352564T>C	ENST00000366928.5	+	2	214	c.167T>C	c.(166-168)aTt>aCt	p.I56T	LYPLAL1_ENST00000366927.3_Missense_Mutation_p.I56T|LYPLAL1_ENST00000483635.1_3'UTR	NM_138794.3	NP_620149	Q5VWZ2	LYPL1_HUMAN	lysophospholipase-like 1	56					negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|protein depalmitoylation (GO:0002084)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	lysophospholipase activity (GO:0004622)	p.I56T(1)		large_intestine(1)|lung(5)	6				GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116)		CACATAAAAATTATTTATCCA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	65	65					1																	219352564		2203	4297	6500	217419187	SO:0001583	missense	127018			BC016711	CCDS1522.1, CCDS73032.1	1q41	2008-02-05			ENSG00000143353	ENSG00000143353			20440	protein-coding gene	gene with protein product							Standard	XM_005273046		Approved	Q96AV0	uc001hlq.4	Q5VWZ2	OTTHUMG00000037141	ENST00000366928.5:c.167T>C	1.37:g.219352564T>C	ENSP00000355895:p.Ile56Thr		217419187	A8K677|Q5VWZ3|Q7Z4A3|Q96AV0	Missense_Mutation	SNP	ENST00000366928.5	37	CCDS1522.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.064560	0.76187	.	.	ENSG00000143353	ENST00000366928;ENST00000366927	T;T	0.23147	1.92;1.92	5.68	5.68	0.88126	Phospholipase/carboxylesterase/thioesterase (1);	0.163843	0.52532	D	0.000069	T	0.36744	0.0978	L	0.56280	1.765	0.43021	D	0.994576	P;P	0.46220	0.874;0.818	P;P	0.49301	0.606;0.514	T	0.14980	-1.0453	10	0.72032	D	0.01	.	15.2047	0.73169	0.0:0.0:0.0:1.0	.	56;56	Q5VWZ2-2;Q5VWZ2	.;LYPL1_HUMAN	T	56	ENSP00000355895:I56T;ENSP00000355894:I56T	ENSP00000355894:I56T	I	+	2	0	LYPLAL1	217419187	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.796000	0.62496	2.289000	0.77006	0.482000	0.46254	ATT		0.333	LYPLAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090208.1	NM_138794		C	219352564	T	C	219352564	3	2	75	1	0	0	0	0	1	0	0	0	9148	1493	52	4	173	4	LYPLAL1	1	219352564	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	34083377	219352564	29898057	20	21487										
OBSCN	84033	broad.mit.edu	37	chr1	228504566	228504566	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gccggatgacagcgactggaCtgtcaccgccgacggcagtc	14	14	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:228504566C>G	ENST00000422127.1	+	51	13486	c.13442C>G	c.(13441-13443)aCt>aGt	p.T4481S	OBSCN_ENST00000366709.4_Missense_Mutation_p.T1600S|OBSCN_ENST00000570156.2_Missense_Mutation_p.T5438S|OBSCN_ENST00000284548.11_Missense_Mutation_p.T4481S|OBSCN_ENST00000366707.4_Missense_Mutation_p.T2115S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4481	Ig-like 46.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.T5063S(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCGACTGGACTGTCACCGCC	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	1											11	17	15					1																	228504566		2147	4230	6377	226571189	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13442C>G	1.37:g.228504566C>G	ENSP00000409493:p.Thr4481Ser		226571189	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	c	12.20	1.866836	0.32977	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.75704	-0.96;-0.96;0.14;0.64	5.41	-3.46	0.04767	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.926528	0.09118	N	0.846142	T	0.49372	0.1553	N	0.24115	0.695	0.09310	N	1	B;P	0.34587	0.146;0.458	B;B	0.27796	0.039;0.083	T	0.34900	-0.9810	10	0.16896	T	0.51	.	5.6043	0.17371	0.3919:0.3729:0.0:0.2353	.	4481;4481	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	4481;4481;2115;1600	ENSP00000284548:T4481S;ENSP00000409493:T4481S;ENSP00000355668:T2115S;ENSP00000355670:T1600S	ENSP00000284548:T4481S	T	+	2	0	OBSCN	226571189	0.000000	0.05858	0.010000	0.14722	0.016000	0.09150	-0.445000	0.06845	-0.646000	0.05452	-0.333000	0.08304	ACT		0.697	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228504566	C	G	228504566	3	3	75	1	0	0	0	0	1	0	0	0	10843	565	20	5	13640	5	OBSCN	1	228504566	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9152002	228504566	20746055	21	21488										
PGBD5	79605	broad.mit.edu	37	chr1	230492810	230492810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catgacgagggcgaggctgcGgttgctgtagaagcctccgc	16	11	0	2	rs148878203		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:230492810G>A	ENST00000525115.1	-	2	405	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	PGBD5_ENST00000391860.1_Missense_Mutation_p.R82C|PGBD5_ENST00000321327.2_Missense_Mutation_p.R227C			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	128						integral component of membrane (GO:0016021)		p.R227C(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		GCGAGGCTGCGGTTGCTGTAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	CYS/ARG	1,4405		0,1,2202	98	80	86		382	-0.4	0.3	1	dbSNP_134	86	0,8600		0,0,4300	no	missense	PGBD5	NM_024554.3	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	128/456	230492810	1,13005	2203	4300	6503	228559433	SO:0001583	missense	79605			AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.382C>T	1.37:g.230492810G>A	ENSP00000431404:p.Arg128Cys		228559433	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	37		.	.	.	.	.	.	.	.	.	.	G	18.76	3.691947	0.68271	2.27E-4	0.0	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.17854	2.25;2.25;2.25	6.03	-0.444	0.12245	.	0.230823	0.43110	D	0.000606	T	0.18215	0.0437	N	0.24115	0.695	0.49213	D	0.999763	D	0.71674	0.998	P	0.54815	0.761	T	0.01084	-1.1457	10	0.51188	T	0.08	-24.9672	13.0813	0.59115	0.0:0.0783:0.1567:0.765	.	128	Q8N414	PGBD5_HUMAN	C	82;227;128	ENSP00000375733:R82C;ENSP00000322530:R227C;ENSP00000431404:R128C	ENSP00000322530:R227C	R	-	1	0	PGBD5	228559433	0.790000	0.28787	0.275000	0.24674	0.947000	0.59692	1.055000	0.30467	-0.001000	0.14495	0.655000	0.94253	CGC		0.617	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		A	230492810	G	A	230492810	3	1	75	1	0	0	0	0	1	0	0	0	11815	1116	39	1	1009	1	PGBD5	1	230492810	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	1988244	230492810	18757811	22	21489										
ZP4	57829	broad.mit.edu	37	chr1	238050711	238050711	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aggaagtaaatggaaactggAacagaacaaaagcttgtgtt	11	4	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:238050711A>T	ENST00000366570.4	-	5	862	c.704T>A	c.(703-705)tTc>tAc	p.F235Y	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	235	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)	p.F235Y(1)		breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TGGAAACTGGAACAGAACAAA	0.517																																					NSCLC(166;160 2029 11600 18754 19936)											1	Substitution - Missense(1)	large_intestine(1)	1											165	157	159					1																	238050711		2203	4300	6503	236117334	SO:0001583	missense	57829			U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.704T>A	1.37:g.238050711A>T	ENSP00000355529:p.Phe235Tyr		236117334	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446562	0.25987	.	.	ENSG00000116996	ENST00000366570	D	0.83837	-1.77	5.26	4.14	0.48551	Zona pellucida sperm-binding protein (3);	0.121953	0.56097	D	0.000039	D	0.86091	0.5850	L	0.58101	1.795	0.09310	N	0.999997	D	0.60160	0.987	D	0.63381	0.914	T	0.76361	-0.2987	10	0.33940	T	0.23	-27.1514	8.9958	0.36052	0.9117:0.0:0.0883:0.0	.	235	Q12836	ZP4_HUMAN	Y	235	ENSP00000355529:F235Y	ENSP00000355529:F235Y	F	-	2	0	ZP4	236117334	1.000000	0.71417	0.009000	0.14445	0.020000	0.10135	1.312000	0.33574	0.845000	0.35118	0.533000	0.62120	TTC		0.517	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238050711	A	T	238050711	3	4	75	1	0	0	0	0	1	0	0	0	18257	246	9	5	950	5	ZP4	1	238050711	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	7557901	238050711	11199910	23	21490										
FMN2	56776	broad.mit.edu	37	chr1	240371930	240371930	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attgccaagtggcttgtttgGattagggatgaatcaggaca	13	5	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:240371930G>T	ENST00000319653.9	+	5	4048	c.3818G>T	c.(3817-3819)gGa>gTa	p.G1273V		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1273					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1416V(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGCTTGTTTGGATTAGGGATG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	53	53					1																	240371930		2203	4300	6503	238438553	SO:0001583	missense	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3818G>T	1.37:g.240371930G>T	ENSP00000318884:p.Gly1273Val		238438553	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	g	11.25	1.582547	0.28180	.	.	ENSG00000155816	ENST00000319653	T	0.28895	1.59	4.6	3.62	0.41486	Actin-binding FH2 (1);Actin-binding FH2/DRF autoregulatory (1);	0.256475	0.25083	U	0.033278	T	0.32585	0.0834	L	0.53249	1.67	0.80722	D	1	P	0.35714	0.517	B	0.43728	0.429	T	0.05920	-1.0856	9	.	.	.	.	8.0504	0.30575	0.0:0.3652:0.4952:0.1396	.	1273	Q9NZ56	FMN2_HUMAN	V	1273	ENSP00000318884:G1273V	.	G	+	2	0	FMN2	238438553	0.953000	0.32496	1.000000	0.80357	0.855000	0.48748	1.677000	0.37576	2.099000	0.63709	0.472000	0.43445	GGA		0.493	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371930	G	T	240371930	3	4	75	1	0	0	0	0	1	0	0	0	5969	1174	41	2	3836	2	FMN2	1	240371930	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2321219	240371930	8878691	24	21491										
WDR64	128025	broad.mit.edu	37	chr1	241912880	241912880	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atctgggactttggcagtggGcaggagatgaaggtgttgcc	17	6	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:241912880G>C	ENST00000366552.2	+	13	1803	c.1596G>C	c.(1594-1596)ggG>ggC	p.G532G	WDR64_ENST00000437684.2_Silent_p.G532G	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	532								p.G252G(1)|p.G532G(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TTGGCAGTGGGCAGGAGATGA	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	1											126	129	128					1																	241912880		2203	4300	6503	239979503	SO:0001819	synonymous_variant	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1596G>C	1.37:g.241912880G>C			239979503	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	G	10.68	1.418109	0.25552	.	.	ENSG00000162843	ENST00000425826	T	0.36340	1.26	6.06	-1.65	0.08291	.	0.167159	0.42548	D	0.000700	T	0.35248	0.0925	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20472	-1.0274	7	0.87932	D	0	-9.1647	2.3982	0.04394	0.4072:0.1148:0.3605:0.1175	.	.	.	.	A	11	ENSP00000406342:G11A	ENSP00000406342:G11A	G	+	2	0	WDR64	239979503	0.163000	0.22920	0.973000	0.42090	0.992000	0.81027	-1.030000	0.03581	-0.289000	0.09038	0.655000	0.94253	GGC		0.498	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		C	241912880	G	C	241912880	2	2	75	1	0	0	0	0	0	0	0	1	17355	1190	42	5		5	WDR64	1	241912880	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	1540950	241912880	7337741	25	21492										
OR2L13	284521	broad.mit.edu	37	chr1	248262801	248262801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttctggcctcggtgggtaacTcggccatgattcacctcatc	10	13	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr1:248262801T>C	ENST00000358120.2	+	2	269	c.124T>C	c.(124-126)Tcg>Ccg	p.S42P	OR2L13_ENST00000366478.2_Missense_Mutation_p.S42P			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S42P(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			GGTGGGTAACTCGGCCATGAT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											212	202	205					1																	248262801		2203	4300	6503	246329424	SO:0001583	missense	284521			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.124T>C	1.37:g.248262801T>C	ENSP00000350836:p.Ser42Pro		246329424	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.700205	0.30142	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00446	7.39;7.39	4.07	0.26	0.15588	GPCR, rhodopsin-like superfamily (1);	0.222293	0.22983	N	0.053292	T	0.00300	0.0009	L	0.55990	1.75	0.09310	N	1	P	0.42123	0.771	B	0.36504	0.226	T	0.50491	-0.8822	10	0.38643	T	0.18	.	4.7748	0.13173	0.0:0.2509:0.288:0.4611	.	42	Q8N349	OR2LD_HUMAN	P	42	ENSP00000355434:S42P;ENSP00000350836:S42P	ENSP00000350836:S42P	S	+	1	0	OR2L13	246329424	0.000000	0.05858	0.023000	0.16930	0.013000	0.08279	-2.743000	0.00797	0.137000	0.18759	-0.263000	0.10527	TCG		0.468	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		C	248262801	T	C	248262801	3	2	75	1	0	0	0	0	1	0	0	0	11037	1551	54	4	126	4	OR2L13	1	248262801	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	6349921	248262801	987820	26	21493										
NTSR2	23620	broad.mit.edu	37	chr2	11798794	11798794	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggagtcacagctgagctgacGtagaaaagtgtgttggtcac	14	7	2	3	rs143067546	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:11798794G>A	ENST00000306928.5	-	4	1078	c.1044C>T	c.(1042-1044)taC>taT	p.Y348Y		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	348					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.Y348Y(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CTGAGCTGACGTAGAAAAGTG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		6,4400	11.4+/-27.6	0,6,2197	108	106	107		1044	-3.5	0	2	dbSNP_134	107	0,8600		0,0,4300	yes	coding-synonymous	NTSR2	NM_012344.3		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		348/411	11798794	6,13000	2203	4300	6503	11716245	SO:0001819	synonymous_variant	23620			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.1044C>T	2.37:g.11798794G>A			11716245	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	37	CCDS1681.1																																																																																				0.532	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			A	11798794	G	A	11798794	2	1	75	1	0	0	0	0	0	0	0	1	10742	1140	40	1		1	NTSR2	2	11798794	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10		11798794	231400579	27	21494										
CAD	790	broad.mit.edu	37	chr2	27458139	27458139	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cagttctccttctcccgcttGgcgggtgctgacgtggtgtt	13	12	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:27458139G>A	ENST00000403525.1	+	23	3768	c.3624G>A	c.(3622-3624)ttG>ttA	p.L1208L	CAD_ENST00000264705.4_Silent_p.L1271L			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.L1271L(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCCCGCTTGGCGGGTGCTG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	2											69	64	65					2																	27458139		2203	4300	6503	27311643	SO:0001819	synonymous_variant	790			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.3624G>A	2.37:g.27458139G>A			27311643	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37																																																																																					0.612	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27458139	G	A	27458139	2	1	75	1	0	0	0	0	0	0	0	1	2571	1339	47	3		3	CAD	2	27458139	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	15659345	27458139	215741234	28	21495										
PLB1	151056	broad.mit.edu	37	chr2	28826833	28826833	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcctccccctctttgtgcagCgttttgtgtaactgcgttct	9	13	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:28826833C>A	ENST00000327757.5	+	40	2819	c.2775C>A	c.(2773-2775)agC>agA	p.S925R	PLB1_ENST00000422425.2_Splice_Site_p.S914R|PLB1_ENST00000541605.1_Intron	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	925	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.S925R(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CTTTGTGCAGCGTTTTGTGTA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	73	76					2																	28826833		2203	4300	6503	28680337	SO:0001630	splice_region_variant	151056				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.2775-1C>A	2.37:g.28826833C>A			28680337	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.23|12.23	1.875854|1.875854	0.33162|0.33162	.|.	.|.	ENSG00000163803|ENSG00000163803	ENST00000404858|ENST00000327757;ENST00000422425	.|T;T	.|0.11712	.|2.75;2.77	5.43|5.43	-0.655|-0.655	0.11439|0.11439	.|Esterase, SGNH hydrolase-type (1);Lipase, GDSL (1);	.|0.302937	.|0.33732	.|N	.|0.004613	T|T	0.12050|0.12050	0.0293|0.0293	N|N	0.12569|0.12569	0.235|0.235	0.50313|0.50313	D|D	0.99986|0.99986	.|D;D	.|0.89917	.|0.996;1.0	.|D;D	.|0.78314	.|0.95;0.991	T|T	0.07966|0.07966	-1.0745|-1.0745	5|9	.|.	.|.	.|.	.|.	8.9404|8.9404	0.35727|0.35727	0.0:0.5059:0.0:0.4941|0.0:0.5059:0.0:0.4941	.|.	.|914;925	.|Q6P1J6-3;Q6P1J6	.|.;PLB1_HUMAN	E|R	913|925;914	.|ENSP00000330442:S925R;ENSP00000416440:S914R	.|.	A|S	+|+	2|3	0|2	PLB1|PLB1	28680337|28680337	0.003000|0.003000	0.15002|0.15002	0.014000|0.014000	0.15608|0.15608	0.344000|0.344000	0.29017|0.29017	-0.508000|-0.508000	0.06344|0.06344	-0.361000|-0.361000	0.08125|0.08125	-0.254000|-0.254000	0.11334|0.11334	GCG|AGC		0.622	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Missense_Mutation	A	28826833	C	A	28826833	5	1	75	1	0	0	0	0	0	0	1	0	12055	782	27	2	2966	2	PLB1	2	28826833	Splice_Site	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1368694	28826833	214372540	29	21496										
SOCS5	9655	broad.mit.edu	37	chr2	46987240	46987240	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcattataaacaaaaagttaGagttcgctggttggaacgag	10	5	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:46987240G>C	ENST00000306503.5	+	2	1743	c.1571G>C	c.(1570-1572)aGa>aCa	p.R524T	SOCS5_ENST00000394861.2_Missense_Mutation_p.R524T	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	524					cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)	p.R524T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			CAAAAAGTTAGAGTTCGCTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											45	45	45					2																	46987240		2203	4300	6503	46840744	SO:0001583	missense	9655			AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1571G>C	2.37:g.46987240G>C	ENSP00000305133:p.Arg524Thr		46840744	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	37	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203934	0.58234	.	.	ENSG00000171150	ENST00000306503;ENST00000394861	T;T	0.50277	0.75;0.75	5.43	5.43	0.79202	.	0.105219	0.64402	D	0.000004	T	0.70378	0.3217	M	0.76838	2.35	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.73186	-0.4062	10	0.87932	D	0	-12.6804	19.0206	0.92912	0.0:0.0:1.0:0.0	.	524	O75159	SOCS5_HUMAN	T	524	ENSP00000305133:R524T;ENSP00000378330:R524T	ENSP00000305133:R524T	R	+	2	0	SOCS5	46840744	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.615000	0.98356	2.824000	0.97209	0.655000	0.94253	AGA		0.428	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			C	46987240	G	C	46987240	3	2	75	1	0	0	0	0	1	0	0	0	14954	942	33	5	1573	5	SOCS5	2	46987240	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	18160407	46987240	196212133	30	21497										
USP34	9736	broad.mit.edu	37	chr2	61484423	61484423	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgttccccagtattcagaggCtgcttatccatggtgtatgt	10	9	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:61484423C>A	ENST00000398571.2	-	45	5983	c.5907G>T	c.(5905-5907)caG>caT	p.Q1969H		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1969	USP.				positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Q1969H(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TATTCAGAGGCTGCTTATCCA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											106	101	103					2																	61484423		1821	4084	5905	61337927	SO:0001583	missense	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5907G>T	2.37:g.61484423C>A	ENSP00000381577:p.Gln1969His		61337927	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.636972	0.67130	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.30182	1.54;1.54	5.96	2.74	0.32292	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);Armadillo-type fold (1);	0.054693	0.85682	N	0.000000	T	0.47097	0.1427	M	0.62209	1.925	0.51482	D	0.999924	D	0.57257	0.979	D	0.76575	0.988	T	0.41822	-0.9487	10	0.87932	D	0	.	7.3393	0.26627	0.1268:0.6665:0.0:0.2067	.	1969	Q70CQ2	UBP34_HUMAN	H	1817;1817;1969;247	ENSP00000381577:Q1969H;ENSP00000410559:Q247H	ENSP00000263989:Q1817H	Q	-	3	2	USP34	61337927	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.669000	0.37492	0.830000	0.34757	0.650000	0.86243	CAG		0.368	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61484423	C	A	61484423	3	1	75	1	0	0	0	0	1	0	0	0	17105	796	28	2	4877	2	USP34	2	61484423	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	14497183	61484423	181714950	31	21498										
VAX2	25806	broad.mit.edu	37	chr2	71160241	71160241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccgctcctggatctgcctgcCggctacgaactgggttcctc	11	16	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:71160241C>T	ENST00000234392.2	+	3	812	c.780C>T	c.(778-780)gcC>gcT	p.A260A	snoU13_ENST00000459218.1_RNA|ATP6V1B1_ENST00000234396.4_5'Flank|ATP6V1B1_ENST00000412314.1_5'Flank	NM_012476.2	NP_036608.1	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	260					axonogenesis (GO:0007409)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic eye morphogenesis (GO:0048048)|forebrain development (GO:0030900)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A260A(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	7						ATCTGCCTGCCGGCTACGAAC	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	2											21	23	23					2																	71160241		2203	4300	6503	71013749	SO:0001819	synonymous_variant	25806			Y17791	CCDS1911.1	2p13.3	2011-06-20			ENSG00000116035	ENSG00000116035		"Homeoboxes / ANTP class : NKL subclass"	12661	protein-coding gene	gene with protein product		604295				10485894	Standard	NM_012476		Approved	DRES93	uc002shh.3	Q9UIW0	OTTHUMG00000129714	ENST00000234392.2:c.780C>T	2.37:g.71160241C>T			71013749	Q53Y33	Silent	SNP	ENST00000234392.2	37	CCDS1911.1																																																																																				0.642	VAX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251923.1			T	71160241	C	T	71160241	2	4	75	1	0	0	0	0	0	0	0	1	17175	639	23	1		1	VAX2	2	71160241	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9675818	71160241	172039132	32	21499										
EXOC6B	23233	broad.mit.edu	37	chr2	72606983	72606983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgcaagctgacatacacgctGtctgggccacctttccctga	9	14	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:72606983G>A	ENST00000272427.6	-	19	2127	c.1997C>T	c.(1996-1998)aCa>aTa	p.T666I		NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	666					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)		p.T203I(1)		breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						CATACACGCTGTCTGGGCCAC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	68	69					2																	72606983		1990	4166	6156	72460491	SO:0001583	missense	23233			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1997C>T	2.37:g.72606983G>A	ENSP00000272427:p.Thr666Ile		72460491	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	37	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571946	0.86542	.	.	ENSG00000144036	ENST00000272427	T	0.28895	1.59	4.73	4.73	0.59995	.	.	.	.	.	T	0.57932	0.2087	M	0.84433	2.695	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	T	0.58008	-0.7712	9	0.21540	T	0.41	.	16.4984	0.84251	0.0:0.0:1.0:0.0	.	666	Q9Y2D4	EXC6B_HUMAN	I	666	ENSP00000272427:T666I	ENSP00000272427:T666I	T	-	2	0	EXOC6B	72460491	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.614000	0.98353	2.449000	0.82847	0.558000	0.71614	ACA		0.388	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		A	72606983	G	A	72606983	3	1	75	1	0	0	0	0	1	0	0	0	5322	1377	48	3	454	3	EXOC6B	2	72606983	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	1446742	72606983	170592390	33	21500										
POLR1A	25885	broad.mit.edu	37	chr2	86254602	86254602	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cccgcccctgacgaccttccCgaccacaaggcaggcagaag	10	18	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:86254602C>T	ENST00000263857.6	-	34	5485	c.5107G>A	c.(5107-5109)Ggg>Agg	p.G1703R	POLR1A_ENST00000409681.1_Missense_Mutation_p.G1642R			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1703					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.G1703R(1)|p.G1703W(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGACCTTCCCGACCACAAGG	0.577																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	2											84	90	88					2																	86254602		2081	4208	6289	86108113	SO:0001583	missense	25885			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.5107G>A	2.37:g.86254602C>T	ENSP00000263857:p.Gly1703Arg		86108113	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.471108	0.84533	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	D;D	0.90676	-2.71;-2.71	5.18	4.29	0.51040	.	0.000000	0.85682	D	0.000000	D	0.96306	0.8795	H	0.94222	3.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.96920	0.9673	10	0.87932	D	0	-28.0669	13.0751	0.59083	0.0:0.921:0.0:0.079	.	1703	O95602	RPA1_HUMAN	R	1703;1642	ENSP00000263857:G1703R;ENSP00000386300:G1642R	ENSP00000263857:G1703R	G	-	1	0	POLR1A	86108113	1.000000	0.71417	0.846000	0.33378	0.850000	0.48378	5.228000	0.65310	2.399000	0.81585	0.655000	0.94253	GGG		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		T	86254602	C	T	86254602	3	4	75	1	0	0	0	0	1	0	0	0	12240	652	23	1	59	1	POLR1A	2	86254602	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	13647619	86254602	156944771	34	21501										
KIAA1310	55683	broad.mit.edu	37	chr2	97268017	97268017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tggtacggacaatggtgctgGtgcccgtggtgatggcaccc	16	10	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:97268017G>A	ENST00000431828.1	-	19	2394	c.2318C>T	c.(2317-2319)aCc>aTc	p.T773I	KANSL3_ENST00000440133.1_Missense_Mutation_p.T593I|KANSL3_ENST00000599854.1_Missense_Mutation_p.T686I|KANSL3_ENST00000441706.2_Intron|KANSL3_ENST00000487070.1_Intron			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	799					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T773I(1)									AATGGTGCTGGTGCCCGTGGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											37	40	39					2																	97268017		2086	4219	6305	96631744	SO:0001583	missense	55683			BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.2318C>T	2.37:g.97268017G>A	ENSP00000396749:p.Thr773Ile		96631744	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	37	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.310086	0.60414	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000440133;ENST00000444759	T;T	0.54866	0.55;0.62	5.81	5.81	0.92471	.	0.203319	0.51477	N	0.000087	T	0.45276	0.1334	L	0.27053	0.805	0.80722	D	1	B;P;B;B;B	0.39216	0.232;0.664;0.126;0.13;0.343	B;B;B;B;B	0.39419	0.034;0.299;0.074;0.075;0.074	T	0.44205	-0.9343	10	0.51188	T	0.08	.	17.5664	0.87921	0.0:0.0:1.0:0.0	.	567;799;773;684;659	B4E1W4;Q9P2N6;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;K1310_HUMAN;.;.;.	I	686;659;773;593;567	ENSP00000396749:T773I;ENSP00000406207:T593I	ENSP00000346144:T686I	T	-	2	0	KIAA1310	96631744	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.319000	0.72871	2.738000	0.93877	0.655000	0.94253	ACC		0.617	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		A	97268017	G	A	97268017	3	1	75	1	0	0	0	0	1	0	0	0	8243	1261	44	3	330	3	KIAA1310	2	97268017	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	11013415	97268017	145931356	35	21502										
RANBP2	5903	broad.mit.edu	37	chr2	109384117	109384117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gttcgtatagtgatgagaagGgaccaagtattaaaactttg	11	4	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:109384117G>T	ENST00000283195.6	+	20	7248	c.7122G>T	c.(7120-7122)agG>agT	p.R2374S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2374	RanBD1 3. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R2374S(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGATGAGAAGGGACCAAGTAT	0.358																																																2	Substitution - Missense(2)	large_intestine(2)	2											62	74	70					2																	109384117		2061	3946	6007	108750549	SO:0001583	missense	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7122G>T	2.37:g.109384117G>T	ENSP00000283195:p.Arg2374Ser		108750549	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255960	0.39896	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.47869	0.83	5.47	-0.536	0.11876	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.67757	0.2927	M	0.79011	2.435	0.30436	N	0.776655	D	0.89917	1.0	D	0.97110	1.0	T	0.69939	-0.5009	9	0.87932	D	0	-26.7645	15.1017	0.72284	0.0967:0.0:0.9033:0.0	.	2374	P49792	RBP2_HUMAN	S	1398;2374	ENSP00000283195:R2374S	ENSP00000283195:R2374S	R	+	3	2	RANBP2	108750549	0.999000	0.42202	0.991000	0.47740	0.898000	0.52572	0.587000	0.23909	-0.324000	0.08589	-0.786000	0.03341	AGG		0.358	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109384117	G	T	109384117	3	4	75	1	0	0	0	0	1	0	0	0	13065	1223	43	2	7200	2	RANBP2	2	109384117	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	12116100	109384117	133815256	36	21503										
CCNT2	905	broad.mit.edu	37	chr2	135676566	135676566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccaacctcatccaggagatgGgacagcgtctcaatgtgtat	10	11	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:135676566G>A	ENST00000264157.5	+	1	172	c.142G>A	c.(142-144)Gga>Aga	p.G48R	CCNT2_ENST00000537343.1_5'UTR|AC016725.4_ENST00000392929.2_RNA|AC016725.4_ENST00000428857.1_RNA|CCNT2_ENST00000295238.6_Missense_Mutation_p.G48R|AC016725.4_ENST00000413962.1_RNA|AC016725.4_ENST00000537615.1_RNA	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	48					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.G48R(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CCAGGAGATGGGACAGCGTCT	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	2											52	55	54					2																	135676566		2203	4300	6503	135393036	SO:0001583	missense	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.142G>A	2.37:g.135676566G>A	ENSP00000264157:p.Gly48Arg		135393036	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	37	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	G	32	5.156953	0.94686	.	.	ENSG00000082258	ENST00000295238;ENST00000264157	T;T	0.51574	0.7;0.7	5.25	4.36	0.52297	Cyclin, N-terminal (1);Cyclin-like (3);	0.099937	0.64402	D	0.000002	T	0.75162	0.3812	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82649	-0.0353	10	0.87932	D	0	.	14.719	0.69291	0.0:0.0:0.8541:0.1459	.	48;48	O60583;O60583-2	CCNT2_HUMAN;.	R	48	ENSP00000295238:G48R;ENSP00000264157:G48R	ENSP00000264157:G48R	G	+	1	0	CCNT2	135393036	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.378000	0.79679	1.550000	0.49438	0.585000	0.79938	GGA		0.667	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		A	135676566	G	A	135676566	3	1	75	1	0	0	0	0	1	0	0	0	2941	1233	43	3	144	3	CCNT2	2	135676566	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	26292449	135676566	107522807	37	21504										
SCN3A	6328	broad.mit.edu	37	chr2	165986780	165986780	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agcatatttagtgtgggccaGgattttgccaacttgaaaac	10	7	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:165986780G>A	ENST00000360093.3	-	17	3083	c.2592C>T	c.(2590-2592)tcC>tcT	p.S864S	SCN3A_ENST00000409101.3_Silent_p.S815S|SCN3A_ENST00000283254.7_Silent_p.S864S	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	864					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.S864S(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTGTGGGCCAGGATTTTGCCA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	2											70	73	72					2																	165986780		2203	4300	6503	165695026	SO:0001819	synonymous_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2592C>T	2.37:g.165986780G>A			165695026	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																					0.363	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		A	165986780	G	A	165986780	2	1	75	1	0	0	0	0	0	0	0	1	13955	987	35	3		3	SCN3A	2	165986780	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	30310214	165986780	77212593	38	21505										
TTN	7273	broad.mit.edu	37	chr2	179451304	179451304	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tccaacagcatttctggccgCtactctaaatttgtatttct	5	11	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:179451304C>G	ENST00000591111.1	-	258	59625	c.59401G>C	c.(59401-59403)Gcg>Ccg	p.A19801P	TTN_ENST00000359218.5_Missense_Mutation_p.A12502P|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A12377P|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A21442P|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A12569P|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A18874P|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19801	Fibronectin type-III 43. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A18872P(1)|p.A12377P(1)|p.A12569P(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCTGGCCGCTACTCTAAAT	0.438																																																3	Substitution - Missense(3)	large_intestine(3)	2											104	106	105					2																	179451304		1997	4185	6182	179159550	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.59401G>C	2.37:g.179451304C>G	ENSP00000465570:p.Ala19801Pro		179159550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	21.9	4.221116	0.79464	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	6.07	6.07	0.98685	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79563	0.4467	M	0.85299	2.745	0.44373	D	0.997275	D;D;D;D	0.62365	0.991;0.991;0.991;0.991	P;P;P;D	0.64776	0.84;0.84;0.84;0.929	T	0.81026	-0.1119	9	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	12377;12502;12569;19801	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	18874;12377;12569;12502;12375	ENSP00000343764:A18874P;ENSP00000434586:A12377P;ENSP00000340554:A12569P;ENSP00000352154:A12502P	ENSP00000340554:A12569P	A	-	1	0	TTN	179159550	0.948000	0.32251	0.244000	0.24202	0.972000	0.66771	7.440000	0.80464	2.884000	0.98904	0.655000	0.94253	GCG		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179451304	C	G	179451304	3	3	75	1	0	0	0	0	1	0	0	0	16775	797	28	5	43875	5	TTN	2	179451304	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	13464524	179451304	63748069	39	21506										
TTN	7273	broad.mit.edu	37	chr2	179616598	179616598	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctaaaacatatttaaatgtaAgtttctgggtaaaagaaggc	8	4	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:179616598A>C	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.L3510R|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L3510R(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTAAATGTAAGTTTCTGGGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	102	99					2																	179616598		2203	4300	6503	179324843	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1252T>G	2.37:g.179616598A>C			179324843	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	16.74	3.206171	0.58343	.	.	ENSG00000155657	ENST00000360870;ENST00000446208	T	0.50548	0.74	5.86	5.86	0.93980	.	.	.	.	.	T	0.76314	0.3970	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82481	-0.0436	9	0.72032	D	0.01	.	15.9094	0.79461	1.0:0.0:0.0:0.0	.	3510	Q8WZ42-6	.	R	3510;115	ENSP00000354117:L3510R	ENSP00000354117:L3510R	L	-	2	0	TTN	179324843	1.000000	0.71417	0.980000	0.43619	0.942000	0.58702	9.277000	0.95755	2.241000	0.73720	0.533000	0.62120	CTT		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179616598	A	C	179616598	1	2	75	0	1	0	0	0	0	0	0	0	16775	72	3	4		4	TTN	2	179616598	Intron	SNP	A	TCGA-AG-A026-01A-32W-A096-10	165294	179616598	63582775	40	21507										
NEUROD1	4760	broad.mit.edu	37	chr2	182543516	182543516	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcctgagaactgagacactcGtctgtccagcttggaggacc	11	12	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:182543516G>A	ENST00000295108.3	-	2	529	c.72C>T	c.(70-72)gaC>gaT	p.D24D	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	24					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.D24D(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			TGAGACACTCGTCTGTCCAGC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	2											91	75	81					2																	182543516		2203	4300	6503	182251761	SO:0001819	synonymous_variant	4760			U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.72C>T	2.37:g.182543516G>A			182251761	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Silent	SNP	ENST00000295108.3	37	CCDS2283.1																																																																																				0.562	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		A	182543516	G	A	182543516	2	1	75	1	0	0	0	0	0	0	0	1	10379	1136	40	1		1	NEUROD1	2	182543516	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2926918	182543516	60655857	41	21508										
NCKAP1	10787	broad.mit.edu	37	chr2	183866720	183866720	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcttccatcatcttctttaaAgggttttcataatccacaat	3	10	5	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:183866720A>T	ENST00000361354.4	-	6	936	c.564T>A	c.(562-564)ccT>ccA	p.P188P	NCKAP1_ENST00000360982.2_Silent_p.P194P	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	188					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)	p.P194P(1)		breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TCTTCTTTAAAGGGTTTTCAT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	2											161	153	156					2																	183866720		2203	4300	6503	183574965	SO:0001819	synonymous_variant	10787			AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.564T>A	2.37:g.183866720A>T			183574965	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																				0.388	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		T	183866720	A	T	183866720	2	4	75	1	0	0	0	0	0	0	0	1	10252	59	3	5		5	NCKAP1	2	183866720	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	1323204	183866720	59332653	42	21509										
MARS2	92935	broad.mit.edu	37	chr2	198571812	198571812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctcgattctatggacatccAtgcccttttgaagggaggag	11	10	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:198571812A>G	ENST00000282276.6	+	1	1726	c.1683A>G	c.(1681-1683)ccA>ccG	p.P561P	AC011997.1_ENST00000409845.1_Intron	NM_138395.3	NP_612404.1	Q96GW9	SYMM_HUMAN	methionyl-tRNA synthetase 2, mitochondrial	561					cell death (GO:0008219)|gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)	p.P561P(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	22					L-Methionine(DB00134)	ATGGACATCCATGCCCTTTTG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	2											124	125	125					2																	198571812		2203	4300	6503	198280057	SO:0001819	synonymous_variant	92935			BC009115	CCDS33358.1	2q33.1	2014-01-30	2007-02-26		ENSG00000247626	ENSG00000247626	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	25133	protein-coding gene	gene with protein product	"methionine tRNA ligase 2, mitochondrial"	609728				15274629	Standard	NM_138395		Approved	mtMetRS, SPAX3	uc002uuq.3	Q96GW9	OTTHUMG00000154487	ENST00000282276.6:c.1683A>G	2.37:g.198571812A>G			198280057	A0AVC3|Q76E79|Q8IW62|Q8N7N4	Silent	SNP	ENST00000282276.6	37	CCDS33358.1																																																																																				0.547	MARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335477.1	NM_138395		G	198571812	A	G	198571812	2	3	75	1	0	0	0	0	0	0	0	1	9347	204	8	4		4	MARS2	2	198571812	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	14705092	198571812	44627561	43	21510										
MPP4	58538	broad.mit.edu	37	chr2	202546225	202546225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cagtaaattcttaccatctgCtggctattcacaggagggtc	9	10	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:202546225C>A	ENST00000409474.3	-	9	933	c.726G>T	c.(724-726)caG>caT	p.Q242H	MPP4_ENST00000428900.2_Missense_Mutation_p.Q242H|MPP4_ENST00000447335.2_Missense_Mutation_p.Q242H|MPP4_ENST00000409143.1_Missense_Mutation_p.Q215H|MPP4_ENST00000396886.3_Missense_Mutation_p.Q198H|MPP4_ENST00000315506.7_Missense_Mutation_p.Q242H|MPP4_ENST00000359962.5_Missense_Mutation_p.Q242H	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	242	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)		p.Q242H(1)		kidney(1)|lung(11)	12						TTACCATCTGCTGGCTATTCA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	2											101	93	96					2																	202546225		1941	4141	6082	202254470	SO:0001583	missense	58538			AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.726G>T	2.37:g.202546225C>A	ENSP00000387278:p.Gln242His		202254470	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Missense_Mutation	SNP	ENST00000409474.3	37	CCDS46491.1	.	.	.	.	.	.	.	.	.	.	C	9.351	1.065481	0.20067	.	.	ENSG00000082126	ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000374605;ENST00000428900;ENST00000409143;ENST00000447335	T;D;T;T;T;T	0.82433	3.45;-1.61;3.45;3.43;3.46;3.44	5.55	4.67	0.58626	Src homology-3 domain (2);	0.209202	0.43747	D	0.000529	T	0.76076	0.3937	L	0.45581	1.43	0.53688	D	0.999974	B;B;B;B;B;B;B;B;B;B	0.14012	0.002;0.001;0.001;0.001;0.002;0.001;0.004;0.009;0.001;0.002	B;B;B;B;B;B;B;B;B;B	0.20384	0.015;0.006;0.007;0.007;0.015;0.003;0.008;0.029;0.005;0.008	T	0.71520	-0.4568	10	0.45353	T	0.12	.	7.5358	0.27710	0.0:0.7061:0.1374:0.1565	.	215;198;242;242;242;242;198;255;242;198	F6Q0Y6;B4DUF3;E7ET46;B7ZM19;Q96JB8-2;E7EUL8;F8WC25;F8WBH8;Q96JB8;Q96JB8-4	.;.;.;.;.;.;.;.;MPP4_HUMAN;.	H	242;242;198;242;198;171;242;215;242	ENSP00000387278:Q242H;ENSP00000319363:Q242H;ENSP00000353047:Q242H;ENSP00000416781:Q242H;ENSP00000387293:Q215H;ENSP00000406160:Q242H	ENSP00000319363:Q242H	Q	-	3	2	MPP4	202254470	0.999000	0.42202	0.984000	0.44739	0.317000	0.28152	0.633000	0.24598	1.474000	0.48178	0.561000	0.74099	CAG		0.423	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			A	202546225	C	A	202546225	3	1	75	1	0	0	0	0	1	0	0	0	9766	796	28	2	1243	2	MPP4	2	202546225	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3974413	202546225	40653148	44	21511										
ALS2CR8	79800	broad.mit.edu	37	chr2	203836412	203836412	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tagcacataagattcaagaaTtagtatcacagggaatagaa	8	5	2	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:203836412T>A	ENST00000402905.3	+	11	1603	c.1282T>A	c.(1282-1284)Tta>Ata	p.L428I	CARF_ENST00000545253.1_Missense_Mutation_p.L340I|WDR12_ENST00000477723.1_Intron|CARF_ENST00000428585.1_Missense_Mutation_p.L352I|CARF_ENST00000545262.1_Missense_Mutation_p.L352I|CARF_ENST00000438828.2_Missense_Mutation_p.L428I|CARF_ENST00000320443.8_Missense_Mutation_p.L428I|CARF_ENST00000414439.1_Missense_Mutation_p.L326I	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	428					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L428I(1)									GATTCAAGAATTAGTATCACA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	86	88					2																	203836412		1906	4118	6024	203544657	SO:0001583	missense	79800			AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1282T>A	2.37:g.203836412T>A	ENSP00000384006:p.Leu428Ile		203544657	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.105158	0.77096	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	4.96	-0.378	0.12497	.	0.000000	0.56097	D	0.000024	T	0.68723	0.3032	M	0.71581	2.175	0.36290	D	0.856379	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79108	0.987;0.986;0.992	T	0.71196	-0.4664	9	0.52906	T	0.07	-9.5962	9.3062	0.37876	0.0:0.4905:0.0:0.5095	.	340;352;428	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	I	428;326;352;340;352;428;428	.	ENSP00000316224:L428I	L	+	1	2	ALS2CR8	203544657	0.981000	0.34729	0.996000	0.52242	0.994000	0.84299	0.931000	0.28871	0.012000	0.14892	0.374000	0.22700	TTA		0.368	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		A	203836412	T	A	203836412	3	1	75	1	0	0	0	0	1	0	0	0	555	1490	52	5	1316	5	ALS2CR8	2	203836412	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	1290187	203836412	39362961	45	21512										
WNT6	7475	broad.mit.edu	37	chr2	219735804	219735804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcatctgcaggaaggcacggCggctggccgggcggcaggcc	19	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:219735804C>T	ENST00000233948.3	+	2	353	c.136C>T	c.(136-138)Cgg>Tgg	p.R46W	WNT6_ENST00000486233.1_Intron	NM_006522.3	NP_006513.1	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family, member 6	46					axis specification (GO:0009798)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|epithelial-mesenchymal cell signaling (GO:0060684)|nephron tubule formation (GO:0072079)|neuron differentiation (GO:0030182)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of gene expression (GO:0010628)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription, DNA-templated (GO:0045893)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.R46W(1)		large_intestine(1)|ovary(2)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.53e-07)|all cancers(144;9.3e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAAGGCACGGCGGCTGGCCGG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	2											57	68	64					2																	219735804		2202	4299	6501	219444048	SO:0001583	missense	7475			AF079522	CCDS2425.1	2q35	2008-05-23			ENSG00000115596	ENSG00000115596		"Wingless-type MMTV integration sites"	12785	protein-coding gene	gene with protein product		604663				10343101, 11350055	Standard	NM_006522		Approved		uc002vjc.1	Q9Y6F9	OTTHUMG00000133082	ENST00000233948.3:c.136C>T	2.37:g.219735804C>T	ENSP00000233948:p.Arg46Trp		219444048	Q9H1J6|Q9H238	Missense_Mutation	SNP	ENST00000233948.3	37	CCDS2425.1	.	.	.	.	.	.	.	.	.	.	c	17.35	3.367545	0.61513	.	.	ENSG00000115596	ENST00000233948	T	0.76578	-1.03	5.17	2.17	0.27698	.	0.359822	0.28016	N	0.016926	D	0.82393	0.5027	L	0.45051	1.395	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.80890	-0.1180	10	0.56958	D	0.05	.	13.3694	0.60705	0.4444:0.5555:0.0:0.0	.	46	Q9Y6F9	WNT6_HUMAN	W	46	ENSP00000233948:R46W	ENSP00000233948:R46W	R	+	1	2	WNT6	219444048	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	1.510000	0.35790	0.108000	0.17862	0.586000	0.80456	CGG		0.652	WNT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256727.2	NM_006522		T	219735804	C	T	219735804	3	4	75	1	0	0	0	0	1	0	0	0	17433	759	27	1	142	1	WNT6	2	219735804	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	15899392	219735804	23463569	46	21513										
RHBDD1	84236	broad.mit.edu	37	chr2	227779017	227779017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cacgtacacagcaggactgaGtgaagaagaacagctcgaga	12	9	0	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:227779017G>A	ENST00000341329.3	+	6	1048	c.806G>A	c.(805-807)aGt>aAt	p.S269N	RHBDD1_ENST00000493526.1_3'UTR|RHBDD1_ENST00000409053.1_Missense_Mutation_p.S103N|RHBDD1_ENST00000392062.2_Missense_Mutation_p.S269N	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	269	Ubiquitin-binding domain (UBD). {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.S269N(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GCAGGACTGAGTGAAGAAGAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	107	108					2																	227779017		2203	4300	6503	227487261	SO:0001583	missense	84236			AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.806G>A	2.37:g.227779017G>A	ENSP00000344779:p.Ser269Asn		227487261	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Missense_Mutation	SNP	ENST00000341329.3	37	CCDS2464.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.020319	0.54576	.	.	ENSG00000144468	ENST00000341329;ENST00000392062;ENST00000409053	T;T	0.50277	0.75;0.75	6.06	5.15	0.70609	.	0.233125	0.52532	D	0.000078	T	0.65460	0.2693	M	0.71581	2.175	0.34667	D	0.723251	D;B	0.76494	0.999;0.166	D;B	0.71656	0.974;0.029	T	0.71626	-0.4536	10	0.39692	T	0.17	-23.2314	14.1894	0.65628	0.0:0.1622:0.8378:0.0	.	60;269	Q8TEB9-2;Q8TEB9	.;RHBD1_HUMAN	N	269;269;103	ENSP00000344779:S269N;ENSP00000375914:S269N	ENSP00000344779:S269N	S	+	2	0	RHBDD1	227487261	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.771000	0.47670	2.880000	0.98712	0.650000	0.86243	AGT		0.488	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			A	227779017	G	A	227779017	3	1	75	1	0	0	0	0	1	0	0	0	13353	1029	36	3	824	3	RHBDD1	2	227779017	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	8043213	227779017	15420356	47	21514										
COL6A3	1293	broad.mit.edu	37	chr2	238249316	238249316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctcctccagctgctgctccGgcacctcgcccgtcagcatc	8	21	1	0	rs115595706	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr2:238249316G>A	ENST00000295550.4	-	38	8695	c.8243C>T	c.(8242-8244)cCg>cTg	p.P2748L	COL6A3_ENST00000346358.4_Missense_Mutation_p.P2548L|COL6A3_ENST00000409809.1_Missense_Mutation_p.P2542L|COL6A3_ENST00000472056.1_Missense_Mutation_p.P2141L|COL6A3_ENST00000347401.3_Missense_Mutation_p.P2547L|COL6A3_ENST00000353578.4_Missense_Mutation_p.P2542L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2748	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P2748L(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		CTGCTGCTCCGGCACCTCGCC	0.547													G|||	2	0.000399361	8e-04	0.0014	5008	,	,		21749	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											80	79	80					2																	238249316		2203	4300	6503	237914055	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8243C>T	2.37:g.238249316G>A	ENSP00000295550:p.Pro2748Leu		237914055	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	8.002	0.755630	0.15846	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.44	-10.9	0.00192	von Willebrand factor, type A (3);	1.166690	0.06424	N	0.722924	T	0.77837	0.4190	L	0.36672	1.1	0.09310	N	1	B;B;D	0.62365	0.016;0.013;0.991	B;B;P	0.53760	0.01;0.006;0.734	T	0.78945	-0.2004	10	0.41790	T	0.15	.	9.562	0.39376	0.0:0.271:0.458:0.271	.	2141;2542;2748	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	L	2748;2547;2542;2141;2542;2548	ENSP00000295550:P2748L;ENSP00000315609:P2547L;ENSP00000315873:P2542L;ENSP00000418285:P2141L;ENSP00000386844:P2542L;ENSP00000295546:P2548L	ENSP00000295550:P2748L	P	-	2	0	COL6A3	237914055	0.000000	0.05858	0.000000	0.03702	0.475000	0.33008	-0.711000	0.05019	-2.866000	0.00325	-1.799000	0.00621	CCG		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238249316	G	A	238249316	3	1	75	1	0	0	0	0	1	0	0	0	3707	1116	39	1	1318	1	COL6A3	2	238249316	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	10470299	238249316	4950057	48	21515										
TMEM43	79188	broad.mit.edu	37	chr3	14176378	14176378	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tttctaccacagcgaaaatcCcaagtatccagaggtgtgcg	9	11	1	1	rs533275736		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:14176378C>G	ENST00000306077.4	+	8	946	c.692C>G	c.(691-693)cCc>cGc	p.P231R	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	231					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.P231R(1)		breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						AGCGAAAATCCCAAGTATCCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	3											86	86	86					3																	14176378		2203	4300	6503	14151379	SO:0001583	missense	79188			BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.692C>G	3.37:g.14176378C>G	ENSP00000303992:p.Pro231Arg		14151379	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240438	0.79912	.	.	ENSG00000170876	ENST00000306077	T	0.37235	1.21	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.54663	0.1872	L	0.48362	1.52	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.87578	0.998;0.905	T	0.50634	-0.8805	10	0.42905	T	0.14	-31.7777	18.0052	0.89207	0.0:1.0:0.0:0.0	.	161;231	Q8TEP9;Q9BTV4	.;TMM43_HUMAN	R	231	ENSP00000303992:P231R	ENSP00000303992:P231R	P	+	2	0	TMEM43	14151379	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	6.389000	0.73199	2.491000	0.84063	0.491000	0.48974	CCC		0.547	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		G	14176378	C	G	14176378	3	3	75	1	0	0	0	0	1	0	0	0	16206	623	22	5	722	5	TMEM43	3	14176378	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10		14176378	183846052	49	21516										
CCDC71	64925	broad.mit.edu	37	chr3	49200714	49200714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgctgccttggccttggcccGggccttagcagccttggcct	13	15	0	0	rs538826878|rs373036352	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:49200714G>A	ENST00000321895.6	-	2	1034	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	310								p.R310W(2)		endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		gccttgGCCCGGGCCTTAGCA	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		19237	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	3						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59	47	51		928	0.8	0	3		51	0,8600		0,0,4300	no	missense	CCDC71	NM_022903.3	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	310/468	49200714	1,13005	2203	4300	6503	49175718	SO:0001583	missense	64925			AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.928C>T	3.37:g.49200714G>A	ENSP00000319006:p.Arg310Trp		49175718	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	G	2.398	-0.338307	0.05243	2.27E-4	0.0	ENSG00000177352	ENST00000321895	T	0.37058	1.22	3.95	0.819	0.18785	.	0.506412	0.17017	N	0.190244	T	0.30916	0.0780	L	0.51422	1.61	0.09310	N	1	D	0.54772	0.968	B	0.43783	0.431	T	0.17137	-1.0379	10	0.72032	D	0.01	-19.6975	7.2435	0.26109	0.0:0.1389:0.2836:0.5774	.	310	Q8IV32	CCD71_HUMAN	W	310	ENSP00000319006:R310W	ENSP00000319006:R310W	R	-	1	2	CCDC71	49175718	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	0.092000	0.15066	0.145000	0.18977	0.313000	0.20887	CGG		0.612	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		A	49200714	G	A	49200714	3	1	75	1	0	0	0	0	1	0	0	0	2850	1115	39	1	479	1	CCDC71	3	49200714	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	35024336	49200714	148821716	50	21517										
TLR9	54106	broad.mit.edu	37	chr3	52257592	52257592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttccgcccacatcgagcacaCgcagggcggtcagattggcc	12	15	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:52257592C>T	ENST00000360658.2	-	2	1373	c.740G>A	c.(739-741)cGt>cAt	p.R247H	TLR9_ENST00000597542.1_Missense_Mutation_p.R271H|TLR9_ENST00000494383.1_Silent_p.A400A	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	247					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.R247H(1)		endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	ATCGAGCACACGCAGGGCGGT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3											38	29	32					3																	52257592		2203	4300	6503	52232632	SO:0001583	missense	54106			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.740G>A	3.37:g.52257592C>T	ENSP00000353874:p.Arg247His		52232632	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.239741	0.39598	.	.	ENSG00000239732	ENST00000360658	T	0.61158	0.13	5.38	0.394	0.16299	.	0.255193	0.19851	N	0.104633	T	0.59985	0.2234	M	0.65498	2.005	0.19300	N	0.999977	D;D	0.65815	0.986;0.995	P;P	0.55667	0.781;0.781	T	0.50775	-0.8788	10	0.52906	T	0.07	.	3.8964	0.09141	0.1626:0.4266:0.0:0.4109	.	344;247	B4E0A1;Q9NR96	.;TLR9_HUMAN	H	247	ENSP00000353874:R247H	ENSP00000353874:R247H	R	-	2	0	TLR9	52232632	0.000000	0.05858	0.065000	0.19835	0.113000	0.19764	0.241000	0.18065	0.239000	0.21243	0.655000	0.94253	CGT		0.627	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			T	52257592	C	T	52257592	3	4	75	1	0	0	0	0	1	0	0	0	15997	536	19	1	2362	1	TLR9	3	52257592	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3056878	52257592	145764838	51	21518										
SHQ1	55164	broad.mit.edu	37	chr3	72842105	72842105	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	acacagtagtctgagatgtaGagatcattcagtatgtacgc	10	7	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:72842105G>C	ENST00000325599.8	-	10	1282	c.1143C>G	c.(1141-1143)ctC>ctG	p.L381L	SHQ1_ENST00000468371.1_5'UTR|SHQ1_ENST00000463369.1_Silent_p.L353L	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	381					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.L381L(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		CTGAGATGTAGAGATCATTCA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	3											84	82	83					3																	72842105		2203	4299	6502	72924795	SO:0001819	synonymous_variant	55164			BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1143C>G	3.37:g.72842105G>C			72924795	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Silent	SNP	ENST00000325599.8	37	CCDS33788.1																																																																																				0.323	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		C	72842105	G	C	72842105	2	2	75	1	0	0	0	0	0	0	0	1	14329	929	33	5		5	SHQ1	3	72842105	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	20584513	72842105	125180325	52	21519										
CBLB	868	broad.mit.edu	37	chr3	105421116	105421116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcccaaacacatcccgagggCaccatgcttcaagaggcatt	8	14	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:105421116C>T	ENST00000264122.4	-	12	2102	c.1781G>A	c.(1780-1782)tGc>tAc	p.C594Y	CBLB_ENST00000394027.3_Missense_Mutation_p.C616Y|CBLB_ENST00000403724.1_Missense_Mutation_p.C594Y|CBLB_ENST00000405772.1_Missense_Mutation_p.C594Y	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	594	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C594Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						ATCCCGAGGGCACCATGCTTC	0.522			Mis S		AML																																GBM(93;588 1337 9788 29341 43499)		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	1	Substitution - Missense(1)	large_intestine(1)	3											116	105	109					3																	105421116		2203	4300	6503	106903806	SO:0001583	missense	868			U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1781G>A	3.37:g.105421116C>T	ENSP00000264122:p.Cys594Tyr		106903806	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	6.273	0.418552	0.11870	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772	D;D;D;D	0.83837	-1.75;-1.73;-1.76;-1.77	5.67	5.67	0.87782	.	0.188780	0.64402	D	0.000020	T	0.77226	0.4099	L	0.36672	1.1	0.80722	D	1	B;B;B	0.22983	0.019;0.078;0.047	B;B;B	0.21917	0.017;0.037;0.015	T	0.71009	-0.4716	9	.	.	.	-11.2839	17.9312	0.88998	0.0:1.0:0.0:0.0	.	616;594;594	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	Y	594;616;594;594	ENSP00000264122:C594Y;ENSP00000377595:C616Y;ENSP00000384816:C594Y;ENSP00000384938:C594Y	.	C	-	2	0	CBLB	106903806	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.037000	0.70956	2.663000	0.90544	0.536000	0.68110	TGC		0.522	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		T	105421116	C	T	105421116	3	4	75	1	0	0	0	0	1	0	0	0	2707	710	25	3	1199	3	CBLB	3	105421116	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	32579011	105421116	92601314	53	21520										
TF	7018	broad.mit.edu	37	chr3	133496021	133496021	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catgacagaaacacatatgaAaaatacttaggagaagaata	7	5	0	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:133496021A>G	ENST00000402696.3	+	16	2486	c.2001A>G	c.(1999-2001)gaA>gaG	p.E667E	TF_ENST00000264998.3_Silent_p.E540E	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	667	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.E667E(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	ACACATATGAAAAATACTTAG	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	3											78	74	76					3																	133496021		2203	4300	6503	134978711	SO:0001819	synonymous_variant	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.2001A>G	3.37:g.133496021A>G			134978711	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																				0.448	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		G	133496021	A	G	133496021	2	3	75	1	0	0	0	0	0	0	0	1	15824	11	1	4		4	TF	3	133496021	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	28074905	133496021	64526409	54	21521										
NCEH1	57552	broad.mit.edu	37	chr3	172363473	172363473	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgtacacagctcatcataaTacctgatttctaaaagacac	4	11	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:172363473T>C	ENST00000475381.1	-	3	610	c.377A>G	c.(376-378)tAt>tGt	p.Y126C	NCEH1_ENST00000543711.1_5'UTR|NCEH1_ENST00000538775.1_Missense_Mutation_p.Y166C|NCEH1_ENST00000273512.3_Missense_Mutation_p.Y158C			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	126					lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)	p.Y158C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						CTCATCATAATACCTGATTTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	3											132	142	139					3																	172363473		2203	4297	6500	173846167	SO:0001583	missense	57552			AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"arylacetamide deacetylase-like 1"	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.377A>G	3.37:g.172363473T>C	ENSP00000418571:p.Tyr126Cys		173846167	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.77|14.77	2.634963|2.634963	0.47049|0.47049	.|.	.|.	ENSG00000144959|ENSG00000144959	ENST00000424772|ENST00000475381;ENST00000538775;ENST00000273512	.|T;T;T	.|0.05025	.|3.65;3.51;3.66	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Alpha/beta hydrolase fold-3 (1);	.|0.273474	.|0.36338	.|N	.|0.002653	T|T	0.06325|0.06325	0.0163|0.0163	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D;P	.|0.56287	.|0.975;0.897	.|P;P	.|0.47102	.|0.525;0.537	T|T	0.38478|0.38478	-0.9659|-0.9659	6|10	0.24483|0.40728	T|T	0.36|0.16	-7.42|-7.42	7.0155|7.0155	0.24885|0.24885	0.1533:0.0:0.14:0.7067|0.1533:0.0:0.14:0.7067	.|.	.|166;126	.|F5H7K4;Q6PIU2	.|.;NCEH1_HUMAN	V|C	157|126;166;158	.|ENSP00000418571:Y126C;ENSP00000442464:Y166C;ENSP00000273512:Y158C	ENSP00000402196:I82V|ENSP00000273512:Y158C	I|Y	-|-	1|2	0|0	NCEH1|NCEH1	173846167|173846167	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.971000|0.971000	0.66376|0.66376	2.594000|2.594000	0.46189|0.46189	1.959000|1.959000	0.56917|0.56917	0.402000|0.402000	0.26972|0.26972	ATT|TAT		0.323	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792		C	172363473	T	C	172363473	3	2	75	1	0	0	0	0	1	0	0	0	10246	1406	49	4	861	4	NCEH1	3	172363473	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	38867452	172363473	25658957	55	21522										
ZDHHC19	131540	broad.mit.edu	37	chr3	195936249	195936249	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aggtagaggggcactcacctCcacacagatgttgcaccagg	12	12	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr3:195936249C>A	ENST00000296326.3	-	3	485	c.406G>T	c.(406-408)Gag>Tag	p.E136*	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	136						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.E136*(1)		breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GCACTCACCTCCACACAGATG	0.642																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											38	46	43					3																	195936249		2056	4189	6245	197420646	SO:0001587	stop_gained	131540			BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"Zinc fingers, DHHC-type"	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.406G>T	3.37:g.195936249C>A	ENSP00000296326:p.Glu136*		197420646	A8MSY6|B3KVI1	Nonsense_Mutation	SNP	ENST00000296326.3	37	CCDS43190.1	.	.	.	.	.	.	.	.	.	.	C	37	6.262302	0.97421	.	.	ENSG00000163958	ENST00000296326	.	.	.	5.81	5.81	0.92471	.	0.000000	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-35.6208	15.5735	0.76356	0.0:1.0:0.0:0.0	.	.	.	.	X	136	.	ENSP00000296326:E136X	E	-	1	0	ZDHHC19	197420646	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	5.673000	0.68109	2.751000	0.94390	0.555000	0.69702	GAG		0.642	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637		A	195936249	C	A	195936249	4	1	75	1	0	0	0	0	0	1	0	0	17648	864	30	2	543	2	ZDHHC19	3	195936249	Nonsense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	23572776	195936249	2086181	56	21523										
PPP2R2C	5522	broad.mit.edu	37	chr4	6331012	6331012	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcgctcccgttccaggcacaTtcaaacttgtcgaaaatgca	7	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:6331012T>C	ENST00000382599.4	-	8	1245	c.1029A>G	c.(1027-1029)gaA>gaG	p.E343E	PPP2R2C_ENST00000335585.5_Silent_p.E343E|PPP2R2C_ENST00000506140.1_Silent_p.E336E|PPP2R2C_ENST00000515571.1_Silent_p.E326E|PPP2R2C_ENST00000507294.1_Silent_p.E336E			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	343					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.E343E(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						TCCAGGCACATTCAAACTTGT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	4											175	140	152					4																	6331012		2203	4300	6503	6381913	SO:0001819	synonymous_variant	5522			AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.1029A>G	4.37:g.6331012T>C			6381913	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Silent	SNP	ENST00000382599.4	37																																																																																					0.582	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		C	6331012	T	C	6331012	2	2	75	1	0	0	0	0	0	0	0	1	12420	1490	52	4		4	PPP2R2C	4	6331012	Silent	SNP	T	TCGA-AG-A026-01A-32W-A096-10		6331012	184823264	57	21524										
DRD5	1816	broad.mit.edu	37	chr4	9783956	9783956	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atgccctggaaggcagtcgcCgaggtggccggttactggcc	16	12	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:9783956C>T	ENST00000304374.2	+	1	699	c.303C>T	c.(301-303)gcC>gcT	p.A101A		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	101					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.A101A(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	AGGCAGTCGCCGAGGTGGCCG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	4											51	48	49					4																	9783956		2203	4300	6503	9393054	SO:0001819	synonymous_variant	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.303C>T	4.37:g.9783956C>T			9393054	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																				0.617	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			T	9783956	C	T	9783956	2	4	75	1	0	0	0	0	0	0	0	1	4771	639	23	1		1	DRD5	4	9783956	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3452944	9783956	181370320	58	21525										
LPHN3	23284	broad.mit.edu	37	chr4	62849252	62849252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atacttttatctggtcggctAtgggatgcctgcactcattg	10	9	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:62849252A>G	ENST00000514591.1	+	18	3292	c.2963A>G	c.(2962-2964)tAt>tGt	p.Y988C	LPHN3_ENST00000507625.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000508946.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000506700.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000514996.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000504896.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000511324.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000506720.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000508693.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000512091.2_Missense_Mutation_p.Y988C|LPHN3_ENST00000506746.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000507164.1_Missense_Mutation_p.Y1056C|LPHN3_ENST00000514157.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000545650.1_Missense_Mutation_p.Y988C|LPHN3_ENST00000509896.1_Missense_Mutation_p.Y1056C			Q9HAR2	LPHN3_HUMAN	latrophilin 3	975					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.Y988C(1)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CTGGTCGGCTATGGGATGCCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	4											210	207	208					4																	62849252		1932	4153	6085	62531847	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2963A>G	4.37:g.62849252A>G	ENSP00000422533:p.Tyr988Cys		62531847	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.311740	0.81358	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59	5.72	5.72	0.89469	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.82070	0.4957	H	0.97186	3.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.88321	0.2962	10	0.87932	D	0	.	16.0129	0.80417	1.0:0.0:0.0:0.0	.	988;975;988	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	C	988;988;1056;1056;988;988;975;988;1056;1056;1056;988;988;988;1056;1056;988	ENSP00000423388:Y988C;ENSP00000422533:Y988C;ENSP00000423787:Y1056C;ENSP00000425033:Y1056C;ENSP00000424120:Y988C;ENSP00000439831:Y988C;ENSP00000421476:Y1056C;ENSP00000424030:Y1056C;ENSP00000421372:Y1056C;ENSP00000425201:Y988C;ENSP00000423434:Y988C;ENSP00000421627:Y988C;ENSP00000420931:Y1056C;ENSP00000425884:Y1056C;ENSP00000424258:Y988C	ENSP00000280009:Y988C	Y	+	2	0	LPHN3	62531847	1.000000	0.71417	0.941000	0.38009	0.981000	0.71138	9.339000	0.96797	2.184000	0.69523	0.482000	0.46254	TAT		0.423	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			G	62849252	A	G	62849252	3	3	75	1	0	0	0	0	1	0	0	0	8946	449	16	4	3025	4	LPHN3	4	62849252	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	53065296	62849252	128305024	59	21526										
UNC5C	8633	broad.mit.edu	37	chr4	96124004	96124004	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agccgctttggtggtggaatGtcctaccagggcgtaggtgc	16	9	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:96124004G>T	ENST00000453304.1	-	12	2362	c.2014C>A	c.(2014-2016)Cat>Aat	p.H672N		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	672					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)	p.H672N(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		GTGGTGGAATGTCCTACCAGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	4											132	126	128					4																	96124004		2203	4300	6503	96343027	SO:0001583	missense	8633			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.2014C>A	4.37:g.96124004G>T	ENSP00000406022:p.His672Asn		96343027	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589641	0.46214	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.55588	0.85;0.51	5.47	5.47	0.80525	.	0.114104	0.64402	D	0.000011	T	0.47581	0.1453	L	0.34521	1.04	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.12156	0.007;0.0	T	0.41378	-0.9512	10	0.87932	D	0	.	19.6995	0.96047	0.0:0.0:1.0:0.0	.	672;672	A8K385;O95185	.;UNC5C_HUMAN	N	672;631;691	ENSP00000406022:H672N;ENSP00000426924:H691N	ENSP00000328673:H631N	H	-	1	0	UNC5C	96343027	1.000000	0.71417	0.193000	0.23327	0.778000	0.44026	7.823000	0.86660	2.744000	0.94065	0.561000	0.74099	CAT		0.597	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96124004	G	T	96124004	3	4	75	1	0	0	0	0	1	0	0	0	17033	1377	48	2	801	2	UNC5C	4	96124004	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	33274752	96124004	95030272	60	21527										
ANK2	287	broad.mit.edu	37	chr4	114275608	114275608	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgtttcaccctccggaagaaCggacaagcaccaacctgtat	8	13	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:114275608C>T	ENST00000357077.4	+	38	5887	c.5834C>T	c.(5833-5835)aCg>aTg	p.T1945M	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.T1912M|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1945	Repeat-rich region.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.T1945M(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TCCGGAAGAACGGACAAGCAC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	4											74	72	72					4																	114275608		2203	4300	6503	114495057	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.5834C>T	4.37:g.114275608C>T	ENSP00000349588:p.Thr1945Met		114495057	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	3.918	-0.018766	0.07681	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.68025	-0.28;-0.3	5.65	0.422	0.16457	.	1.106060	0.06968	N	0.817639	T	0.51466	0.1676	L	0.28115	0.83	0.19300	N	0.99998	B;B	0.13145	0.007;0.004	B;B	0.11329	0.004;0.006	T	0.32508	-0.9904	9	.	.	.	.	9.1321	0.36852	0.0:0.6133:0.0:0.3867	.	1912;1945	Q01484;Q01484-4	ANK2_HUMAN;.	M	1945;1912	ENSP00000349588:T1945M;ENSP00000264366:T1912M	.	T	+	2	0	ANK2	114495057	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.458000	0.06737	0.077000	0.16863	-0.794000	0.03295	ACG		0.532	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114275608	C	T	114275608	3	4	75	1	0	0	0	0	1	0	0	0	621	536	19	1	6049	1	ANK2	4	114275608	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	18151604	114275608	76878668	61	21528										
ZNF330	27309	broad.mit.edu	37	chr4	142155045	142155045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aggaagaagatgaaggcagaAaggattcagatactgagtca	13	4	2	6			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:142155045A>G	ENST00000262990.4	+	10	1093	c.865A>G	c.(865-867)Aag>Gag	p.K289E	ZNF330_ENST00000421169.2_Missense_Mutation_p.K229E	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	289						chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.K289E(1)		kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					tgaagGCAGAAAGGATTCAGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	4											136	140	138					4																	142155045		2203	4300	6503	142374495	SO:0001583	missense	27309			AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"Zinc fingers, C2H2-type"	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.865A>G	4.37:g.142155045A>G	ENSP00000262990:p.Lys289Glu		142374495	B2RDA3	Missense_Mutation	SNP	ENST00000262990.4	37	CCDS3754.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124855	0.56613	.	.	ENSG00000109445	ENST00000262990;ENST00000421169	T;T	0.29655	1.56;1.56	6.17	4.98	0.66077	.	0.144293	0.64402	D	0.000007	T	0.11410	0.0278	N	0.00926	-1.1	0.51767	D	0.99993	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.13575	-1.0504	10	0.32370	T	0.25	-22.0031	12.6751	0.56889	0.935:0.0:0.065:0.0	.	229;289	E9PDK6;Q9Y3S2	.;ZN330_HUMAN	E	289;229	ENSP00000262990:K289E;ENSP00000397397:K229E	ENSP00000262990:K289E	K	+	1	0	ZNF330	142374495	1.000000	0.71417	0.993000	0.49108	0.956000	0.61745	4.197000	0.58413	2.371000	0.80710	0.533000	0.62120	AAG		0.418	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487		G	142155045	A	G	142155045	3	3	75	1	0	0	0	0	1	0	0	0	17887	15	1	4	899	4	ZNF330	4	142155045	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	27879437	142155045	48999231	62	21529										
MLF1IP	79682	broad.mit.edu	37	chr4	185623590	185623590	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tacaaactttagattctattCtttgtctgtagaggaattaa	6	5	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr4:185623590C>A	ENST00000281453.5	-	9	873	c.803G>T	c.(802-804)aGa>aTa	p.R268I	MLF1IP_ENST00000541971.1_Missense_Mutation_p.R268I|MLF1IP_ENST00000506535.1_5'UTR	NM_024629.3	NP_078905.2												p.R268I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		AGATTCTATTCTTTGTCTGTA	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4											85	88	87					4																	185623590		2203	4300	6503	185860584	SO:0001583	missense	79682																														ENST00000281453.5:c.803G>T	4.37:g.185623590C>A	ENSP00000281453:p.Arg268Ile		185860584		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	.	.	.	.	.	.	.	.	.	.	C	9.568	1.120287	0.20877	.	.	ENSG00000151725	ENST00000281453;ENST00000541665;ENST00000541971	T;T	0.24723	1.84;1.84	4.5	1.53	0.23141	.	0.858078	0.10389	N	0.680610	T	0.26085	0.0636	L	0.34521	1.04	0.21527	N	0.999658	P;P	0.48998	0.918;0.918	P;P	0.52267	0.694;0.694	T	0.12656	-1.0539	10	0.45353	T	0.12	-24.6861	4.938	0.13950	0.0:0.3942:0.0:0.6058	.	268;268	Q09GN1;Q71F23	.;CENPU_HUMAN	I	268	ENSP00000281453:R268I;ENSP00000445862:R268I	ENSP00000281453:R268I	R	-	2	0	MLF1IP	185860584	0.167000	0.22975	0.110000	0.21437	0.027000	0.11550	0.261000	0.18442	0.299000	0.22661	0.557000	0.71058	AGA		0.328	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2			A	185623590	C	A	185623590	3	1	75	1	0	0	0	0	1	0	0	0	9645	913	32	2	473	2	MLF1IP	4	185623590	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	43468545	185623590	5530686	63	21530										
PLEKHG4B	153478	broad.mit.edu	37	chr5	182162	182162	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcggtgtcctcctctgaccaCgccgcccccttcaagcgacc	9	20	2	1	rs115843378		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:182162C>T	ENST00000283426.6	+	18	3590	c.3540C>T	c.(3538-3540)caC>caT	p.H1180H		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1180	Ser-rich.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.H1180H(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CCTCTGACCACGCCGCCCCCT	0.617													c|||	1	0.000199681	8e-04	0	5008	,	,		20192	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5											111	101	104					5																	182162		2203	4300	6503	235162	SO:0001819	synonymous_variant	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3540C>T	5.37:g.182162C>T			235162		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																				0.617	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	182162	C	T	182162	2	4	75	1	0	0	0	0	0	0	0	1	12103	535	19	1		1	PLEKHG4B	5	182162	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10		182162	180733098	64	21531										
SDHA	6389	broad.mit.edu	37	chr5	228421	228421	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgggtccatccatcgcataaGagcaaagaacactgttgttg	10	10	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:228421G>C	ENST00000264932.6	+	6	858	c.743G>C	c.(742-744)aGa>aCa	p.R248T	SDHA_ENST00000504309.1_Missense_Mutation_p.R248T|SDHA_ENST00000510361.1_Missense_Mutation_p.R200T	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	248					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)	p.R248T(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CATCGCATAAGAGCAAAGAAC	0.383									Familial Paragangliomas																																							1	Substitution - Missense(1)	large_intestine(1)	5											102	93	96					5																	228421		2203	4300	6503	281421	SO:0001583	missense	6389	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.743G>C	5.37:g.228421G>C	ENSP00000264932:p.Arg248Thr		281421	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	g	20.7	4.037619	0.75617	.	.	ENSG00000073578	ENST00000264932;ENST00000504309;ENST00000510361	T;T;T	0.65178	-0.14;-0.14;-0.14	5.23	5.23	0.72850	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.66645	0.2810	M	0.79343	2.45	0.80722	D	1	B;B;B;B;B	0.33919	0.02;0.267;0.432;0.285;0.285	B;B;B;B;B	0.35312	0.056;0.123;0.086;0.2;0.2	T	0.71695	-0.4515	10	0.87932	D	0	.	16.7213	0.85410	0.0:0.0:1.0:0.0	.	200;248;248;248;254	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	T	248;248;200	ENSP00000264932:R248T;ENSP00000426514:R248T;ENSP00000427703:R200T	ENSP00000264932:R248T	R	+	2	0	SDHA	281421	1.000000	0.71417	0.939000	0.37840	0.996000	0.88848	7.518000	0.81795	2.633000	0.89246	0.644000	0.83932	AGA		0.383	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		C	228421	G	C	228421	3	2	75	1	0	0	0	0	1	0	0	0	14000	942	33	5	765	5	SDHA	5	228421	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	46259	228421	180686839	65	21532										
ADAMTS16	170690	broad.mit.edu	37	chr5	5146494	5146494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgcagactttaccgccagagGacttctgtttctatcaaggc	9	11	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:5146494G>A	ENST00000274181.7	+	3	565	c.427G>A	c.(427-429)Gac>Aac	p.D143N	CTD-2297D10.1_ENST00000514848.1_RNA|ADAMTS16_ENST00000511368.1_Missense_Mutation_p.D143N	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	143					branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D143N(2)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						ACCGCCAGAGGACTTCTGTTT	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	5											119	115	117					5																	5146494		1909	4137	6046	5199494	SO:0001583	missense	170690			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.427G>A	5.37:g.5146494G>A	ENSP00000274181:p.Asp143Asn		5199494	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005791	0.35415	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.06218	3.33;3.33	5.74	4.85	0.62838	Peptidase M12B, propeptide (1);	0.120606	0.52532	D	0.000066	T	0.14356	0.0347	L	0.53780	1.695	0.46749	D	0.99918	D;B;B	0.54601	0.967;0.397;0.452	P;B;B	0.54759	0.76;0.363;0.395	T	0.12785	-1.0534	10	0.18276	T	0.48	.	15.7901	0.78350	0.0:0.1369:0.8631:0.0	.	143;143;143	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	N	143	ENSP00000274181:D143N;ENSP00000421631:D143N	ENSP00000274181:D143N	D	+	1	0	ADAMTS16	5199494	1.000000	0.71417	0.380000	0.26093	0.054000	0.15201	4.651000	0.61447	1.507000	0.48752	0.563000	0.77884	GAC		0.527	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		A	5146494	G	A	5146494	3	1	75	1	0	0	0	0	1	0	0	0	261	1174	41	3	437	3	ADAMTS16	5	5146494	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4918073	5146494	175768766	66	21533										
MYO10	4651	broad.mit.edu	37	chr5	16703107	16703107	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttcttgctcccttttctctgCcagcaattgtctgtaaactc	5	13	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:16703107C>G	ENST00000513610.1	-	23	2891	c.2437G>C	c.(2437-2439)Gca>Cca	p.A813P	MYO10_ENST00000515803.1_Missense_Mutation_p.A152P|MYO10_ENST00000427430.2_Missense_Mutation_p.A170P|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000274203.9_Missense_Mutation_p.A170P|MYO10_ENST00000505695.1_Missense_Mutation_p.A152P	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	813	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.A813P(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						cttttctCTGCCAGCAATTGT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	5											55	50	51					5																	16703107		1768	3894	5662	16756107	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2437G>C	5.37:g.16703107C>G	ENSP00000421280:p.Ala813Pro		16756107	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946406	0.73672	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430;ENST00000513882	D;D;D;D;D;D	0.87887	-1.52;-1.52;-1.52;-1.52;-1.52;-2.31	5.61	5.61	0.85477	.	.	.	.	.	T	0.76083	0.3938	N	0.08118	0	0.45979	D	0.998797	B;P	0.37955	0.145;0.612	B;B	0.31547	0.093;0.132	T	0.79169	-0.1914	9	0.52906	T	0.07	.	19.2661	0.93985	0.0:1.0:0.0:0.0	.	454;813	Q69YP8;Q9HD67	.;MYO10_HUMAN	P	813;152;170;152;170;824	ENSP00000421280:A813P;ENSP00000425051:A152P;ENSP00000274203:A170P;ENSP00000421170:A152P;ENSP00000391106:A170P;ENSP00000421309:A824P	ENSP00000274203:A170P	A	-	1	0	MYO10	16756107	1.000000	0.71417	0.992000	0.48379	0.753000	0.42808	7.487000	0.81328	2.643000	0.89663	0.557000	0.71058	GCA		0.443	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		G	16703107	C	G	16703107	3	3	75	1	0	0	0	0	1	0	0	0	10092	739	26	5	3815	5	MYO10	5	16703107	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	11556613	16703107	164212153	67	21534										
CDH18	1016	broad.mit.edu	37	chr5	19571825	19571825	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcatctacatccccaacaatGatcttcagcatagtagcatc	4	13	4	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:19571825G>T	ENST00000507958.1	-	10	2106	c.1116C>A	c.(1114-1116)atC>atA	p.I372I	CDH18_ENST00000506372.1_Silent_p.I372I|CDH18_ENST00000274170.4_Silent_p.I372I|CDH18_ENST00000502796.1_Silent_p.I372I|CDH18_ENST00000511273.1_Silent_p.I372I|CDH18_ENST00000382275.1_Silent_p.I372I			Q13634	CAD18_HUMAN	cadherin 18, type 2	372	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I372I(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CCCCAACAATGATCTTCAGCA	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)	5											149	126	134					5																	19571825		2203	4300	6503	19607582	SO:0001819	synonymous_variant	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1116C>A	5.37:g.19571825G>T			19607582	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																				0.408	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19571825	G	T	19571825	2	4	75	1	0	0	0	0	0	0	0	1	3109	1280	45	2		2	CDH18	5	19571825	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2868718	19571825	161343435	68	21535										
ZFR	51663	broad.mit.edu	37	chr5	32395272	32395272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttaaagatattacctcatttCcattctccaacgctcctctt	2	13	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:32395272C>T	ENST00000265069.8	-	11	2074	c.1972G>A	c.(1972-1974)Gaa>Aaa	p.E658K	MIR579_ENST00000385221.1_RNA	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	658					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E658K(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		TACCTCATTTCCATTCTCCAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	5											233	213	220					5																	32395272		2203	4300	6503	32431029	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1972G>A	5.37:g.32395272C>T	ENSP00000265069:p.Glu658Lys		32431029	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930514	0.92389	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.09723	2.95	5.96	5.96	0.96718	.	0.087235	0.85682	D	0.000000	T	0.37517	0.1006	M	0.78456	2.415	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.02417	-1.1162	10	0.59425	D	0.04	.	20.4008	0.98991	0.0:1.0:0.0:0.0	.	658	Q96KR1	ZFR_HUMAN	K	658;636	ENSP00000265069:E658K	ENSP00000265069:E658K	E	-	1	0	ZFR	32431029	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.625000	0.83145	2.826000	0.97356	0.655000	0.94253	GAA		0.403	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			T	32395272	C	T	32395272	3	4	75	1	0	0	0	0	1	0	0	0	17698	864	30	3	1292	3	ZFR	5	32395272	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	12823447	32395272	148519988	69	21536										
APC	324	broad.mit.edu	37	chr5	112175101	112175101	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gtagaagatactccaatatgTttttcaagatgtagttcatt	7	5	2	3	rs587783033		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:112175101T>A	ENST00000457016.1	+	16	4190	c.3810T>A	c.(3808-3810)tgT>tgA	p.C1270*	APC_ENST00000257430.4_Nonsense_Mutation_p.C1270*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.C1270*			P25054	APC_HUMAN	adenomatous polyposis coli	1270	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1272fs*16(1)|p.K1192fs*3(1)|p.?(1)|p.C1270*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCCAATATGTTTTTCAAGAT	0.373		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(2)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CM000125|CX995213	APC	M|X							54	56	55					5																	112175101		2202	4300	6502	112203000	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3810T>A	5.37:g.112175101T>A	ENSP00000413133:p.Cys1270*		112203000	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	39	7.338126	0.98221	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	3.66	0.41972	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.4828	9.2249	0.37400	0.0:0.1981:0.0:0.8019	.	.	.	.	X	1270	.	.	C	+	3	2	APC	112203000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.618000	0.24373	1.094000	0.41399	0.533000	0.62120	TGT		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175101	T	A	112175101	4	1	75	1	0	0	0	0	0	1	0	0	763	1731	60	5	3868	5	APC	5	112175101	Nonsense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	79779829	112175101	68740159	70	21537										
AQPEP	206338	broad.mit.edu	37	chr5	115298564	115298564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agctagcggtgacgaccaccCcgagcaactggcgacccccg	12	17	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:115298564C>T	ENST00000357872.4	+	1	374	c.250C>T	c.(250-252)Ccg>Tcg	p.P84S	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		84						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P84S(1)									GACGACCACCCCGAGCAACTG	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	5											27	31	30					5																	115298564		2190	4286	6476	115326463	SO:0001583	missense	206338																														ENST00000357872.4:c.250C>T	5.37:g.115298564C>T	ENSP00000350541:p.Pro84Ser		115326463	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	8.798	0.932182	0.18131	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.01252	5.1	3.5	-0.411	0.12370	.	3.638010	0.00792	N	0.001348	T	0.01189	0.0039	N	0.14661	0.345	0.09310	N	0.999991	B	0.12013	0.005	B	0.08055	0.003	T	0.46610	-0.9179	10	0.33141	T	0.24	.	4.0863	0.09948	0.0:0.37:0.4186:0.2114	.	84	Q6Q4G3	AMPQ_HUMAN	S	84	ENSP00000350541:P84S	ENSP00000350541:P84S	P	+	1	0	AC010282.1	115326463	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.232000	0.09811	-0.951000	0.02657	CCG		0.692	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115298564	C	T	115298564	3	4	75	1	0	0	0	0	1	0	0	0	834	623	22	3	252	3	AQPEP	5	115298564	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3123463	115298564	65616696	71	21538										
PCDHA12	56137	broad.mit.edu	37	chr5	140256370	140256370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctcgccttcgctgtgggccaCggctagagtgtccgtggagg	16	12	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:140256370C>T	ENST00000398631.2	+	1	1313	c.1313C>T	c.(1312-1314)aCg>aTg	p.T438M	PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	438	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T438M(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTGGGCCACGGCTAGAGTG	0.662																																					Pancreas(113;759 1672 13322 24104 50104)											1	Substitution - Missense(1)	large_intestine(1)	5											125	130	128					5																	140256370		2203	4299	6502	140236554	SO:0001583	missense	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1313C>T	5.37:g.140256370C>T	ENSP00000381628:p.Thr438Met		140236554	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	C	9.981	1.228015	0.22542	.	.	ENSG00000251664	ENST00000398631	T	0.01854	4.6	4.92	4.92	0.64577	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.11965	0.0291	M	0.83953	2.67	0.09310	N	1	D;D	0.69078	0.997;0.997	P;D	0.66847	0.784;0.947	T	0.05649	-1.0872	9	0.66056	D	0.02	.	10.2762	0.43512	0.0:0.7861:0.1376:0.0763	.	438;438	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	M	438	ENSP00000381628:T438M	ENSP00000381628:T438M	T	+	2	0	PCDHA12	140236554	0.000000	0.05858	0.177000	0.23020	0.022000	0.10575	-0.074000	0.11450	2.452000	0.82932	0.650000	0.86243	ACG		0.662	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140256370	C	T	140256370	3	4	75	1	0	0	0	0	1	0	0	0	11553	536	19	1	1315	1	PCDHA12	5	140256370	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	24957806	140256370	40658890	72	21539										
PCDHGA2	56113	broad.mit.edu	37	chr5	140720096	140720096	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tactctatgcactgcgctccTttgattatgagcagttgcga	9	10	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:140720096T>A	ENST00000394576.2	+	1	1558	c.1558T>A	c.(1558-1560)Ttt>Att	p.F520I	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	520	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F520I(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGCGCTCCTTTGATTATGA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	129	128					5																	140720096		2203	4300	6503	140700280	SO:0001583	missense	56113			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1558T>A	5.37:g.140720096T>A	ENSP00000378077:p.Phe520Ile		140700280	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	16.59	3.164492	0.57476	.	.	ENSG00000081853	ENST00000394576	T	0.47528	0.84	5.21	5.21	0.72293	Cadherin (5);Cadherin-like (1);	0.000000	0.42294	U	0.000724	T	0.70020	0.3176	M	0.80616	2.505	0.38477	D	0.94762	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	T	0.77286	-0.2644	10	0.87932	D	0	.	15.0453	0.71822	0.0:0.0:0.0:1.0	.	520;520	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	I	520	ENSP00000378077:F520I	ENSP00000378077:F520I	F	+	1	0	PCDHGA2	140700280	0.966000	0.33281	0.997000	0.53966	0.018000	0.09664	1.689000	0.37700	2.094000	0.63399	0.482000	0.46254	TTT		0.507	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		A	140720096	T	A	140720096	3	1	75	1	0	0	0	0	1	0	0	0	11585	1609	56	5	1560	5	PCDHGA2	5	140720096	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	463726	140720096	40195164	73	21540										
PCDHGB5	56102	broad.mit.edu	37	chr5	140779318	140779318	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgcctgcgctcagcgcaaacGtgagcctgcgcgtgttggtg	15	13	1	1	rs564705346		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:140779318G>A	ENST00000576222.1	+	1	2546				PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCGCAAACGTGAGCCTGCG	0.672													.|||	1	0.000199681	0	0.0014	5008	,	,		17891	0		0	False		,,,				2504	0															0			5											26	33	31					5																	140779318		2046	4196	6242	140759502	SO:0001627	intron_variant	56101			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26942G>A	5.37:g.140779318G>A			140759502	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.672	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140779318	G	A	140779318	1	1	75	0	1	0	0	0	0	0	0	0	11597	1145	40	1		1	PCDHGB5	5	140779318	Intron	SNP	G	TCGA-AG-A026-01A-32W-A096-10	59222	140779318	40135942	74	21541										
PCDHGC4	56098	broad.mit.edu	37	chr5	140865911	140865911	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atgtgagcctccgcattcctGaccacttgccatttgccctc	7	16	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:140865911G>A	ENST00000306593.1	+	1	1171	c.1171G>A	c.(1171-1173)Gac>Aac	p.D391N	PCDHGA11_ENST00000398587.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGC3_ENST00000308177.3_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	391	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D391N(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCATTCCTGACCACTTGCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	5											120	97	104					5																	140865911		2203	4300	6503	140846095	SO:0001583	missense	56098			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.1171G>A	5.37:g.140865911G>A	ENSP00000306918:p.Asp391Asn		140846095	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	G	8.505	0.865206	0.17250	.	.	ENSG00000242419	ENST00000306593	T	0.02863	4.13	5.01	4.13	0.48395	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02688	0.0081	N	0.16790	0.44	0.09310	N	1	B;B	0.28880	0.226;0.022	B;B	0.29598	0.104;0.09	T	0.48269	-0.9050	9	0.22109	T	0.4	.	14.8606	0.70379	0.0:0.2709:0.7291:0.0	.	391;391	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	N	391	ENSP00000306918:D391N	ENSP00000306918:D391N	D	+	1	0	PCDHGC4	140846095	0.000000	0.05858	0.988000	0.46212	0.724000	0.41520	0.276000	0.18716	1.308000	0.44962	0.563000	0.77884	GAC		0.547	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		A	140865911	G	A	140865911	3	1	75	1	0	0	0	0	1	0	0	0	11601	1290	45	3	1173	3	PCDHGC4	5	140865911	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	86593	140865911	40049349	75	21542										
MSX2	4488	broad.mit.edu	37	chr5	174151701	174151701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggcaatgacttgttttcgccCgacgaggagggcccagcagt	14	11	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:174151701C>T	ENST00000239243.6	+	1	166	c.39C>T	c.(37-39)ccC>ccT	p.P13P	MSX2_ENST00000507785.1_Silent_p.P13P	NM_002449.4	NP_002440.2	P35548	MSX2_HUMAN	msh homeobox 2	13					activation of meiosis (GO:0090427)|anagen (GO:0042640)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone trabecula formation (GO:0060346)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte development (GO:0002063)|cranial suture morphogenesis (GO:0060363)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|enamel mineralization (GO:0070166)|endochondral bone growth (GO:0003416)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|frontal suture morphogenesis (GO:0060364)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of catagen (GO:0051795)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of osteoblast differentiation (GO:0045669)|signal transduction involved in regulation of gene expression (GO:0023019)|wound healing, spreading of epidermal cells (GO:0035313)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.P13P(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TGTTTTCGCCCGACGAGGAGG	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	5											6	8	7					5																	174151701		2139	4216	6355	174084307	SO:0001819	synonymous_variant	4488			D26145	CCDS4392.1	5q35.2	2011-06-20	2006-11-21		ENSG00000120149	ENSG00000120149		"Homeoboxes / ANTP class : NKL subclass"	7392	protein-coding gene	gene with protein product	"craniosynostosis, type 2"	123101	"msh (Drosophila) homeo box homolog 2", "parietal foramina 1", "msh homeobox homolog 2 (Drosophila)"	PFM1		8668339, 8786091	Standard	XM_006714868		Approved	CRS2, FPP, HOX8, MSH, PFM	uc003mcy.3	P35548	OTTHUMG00000130556	ENST00000239243.6:c.39C>T	5.37:g.174151701C>T			174084307	D3DQN1|Q53XM4|Q9UD60	Silent	SNP	ENST00000239243.6	37	CCDS4392.1																																																																																				0.706	MSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252981.3			T	174151701	C	T	174151701	2	4	75	1	0	0	0	0	0	0	0	1	9926	639	23	1		1	MSX2	5	174151701	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	33285790	174151701	6763559	76	21543										
GFPT2	9945	broad.mit.edu	37	chr5	179762829	179762829	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggggaagcatgccacataccGttgcctttgtctgagcgctg	13	11	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr5:179762829G>A	ENST00000253778.8	-	4	508	c.339C>T	c.(337-339)aaC>aaT	p.N113N		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	113	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.N113N(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GCCACATACCGTTGCCTTTGT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	5											107	125	119					5																	179762829		2108	4228	6336	179695435	SO:0001630	splice_region_variant	9945			AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.340+1C>T	5.37:g.179762829G>A			179695435	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	37	CCDS43411.1																																																																																				0.627	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	Silent	A	179762829	G	A	179762829	5	1	75	1	0	0	0	0	0	0	1	0	6366	1159	40	1	1773	1	GFPT2	5	179762829	Splice_Site	SNP	G	TCGA-AG-A026-01A-32W-A096-10	5611128	179762829	1152431	77	21544										
TJAP1	93643	broad.mit.edu	37	chr6	43469402	43469402	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cagagccgcgaggagctggaCaaatttaaggataagttccg	13	8	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:43469402C>G	ENST00000372445.5	+	6	643	c.267C>G	c.(265-267)gaC>gaG	p.D89E	TJAP1_ENST00000436109.2_Missense_Mutation_p.D89E|TJAP1_ENST00000372452.1_Missense_Mutation_p.D89E|TJAP1_ENST00000372449.1_Missense_Mutation_p.D89E|TJAP1_ENST00000259751.1_Missense_Mutation_p.D89E|TJAP1_ENST00000438588.2_Missense_Mutation_p.D89E|TJAP1_ENST00000372444.2_Missense_Mutation_p.D89E|TJAP1_ENST00000483640.1_3'UTR	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	89					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)		p.D89E(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AGGAGCTGGACAAATTTAAGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											28	29	28					6																	43469402		2203	4300	6503	43577380	SO:0001583	missense	93643			AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.267C>G	6.37:g.43469402C>G	ENSP00000361522:p.Asp89Glu		43577380	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.08|13.08	2.130078|2.130078	0.37630|0.37630	.|.	.|.	ENSG00000137221|ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588|ENST00000454762	T;T;T;T;T;T;T;T|.	0.78246|.	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16|.	4.91|4.91	3.11|3.11	0.35812|0.35812	.|.	0.062472|.	0.64402|.	D|.	0.000008|.	T|T	0.05960|0.05960	0.0155|0.0155	N|N	0.11560|0.11560	0.145|0.145	0.30291|0.30291	N|N	0.790397|0.790397	B;D;B|.	0.67145|.	0.006;0.996;0.197|.	B;D;B|.	0.77557|.	0.022;0.99;0.134|.	T|T	0.27468|0.27468	-1.0073|-1.0073	10|5	0.06494|.	T|.	0.89|.	-15.9062|-15.9062	2.4402|2.4402	0.04492|0.04492	0.1346:0.4898:0.2067:0.169|0.1346:0.4898:0.2067:0.169	.|.	89;89;89|.	E2QRK7;Q5JTD0;Q5JTD0-2|.	.;TJAP1_HUMAN;.|.	E|E	89|47	ENSP00000361521:D89E;ENSP00000361522:D89E;ENSP00000407080:D89E;ENSP00000390981:D89E;ENSP00000259751:D89E;ENSP00000361530:D89E;ENSP00000361527:D89E;ENSP00000408769:D89E|.	ENSP00000259751:D89E|.	D|Q	+|+	3|1	2|0	TJAP1|TJAP1	43577380|43577380	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.825000|0.825000	0.46686|0.46686	0.894000|0.894000	0.28350|0.28350	1.081000|1.081000	0.41110|0.41110	0.298000|0.298000	0.19748|0.19748	GAC|CAA		0.582	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		G	43469402	C	G	43469402	3	3	75	1	0	0	0	0	1	0	0	0	15967	477	17	5	277	5	TJAP1	6	43469402	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10		43469402	127645665	78	21545										
DOPEY1	23033	broad.mit.edu	37	chr6	83863236	83863236	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttatgttttcataggttttgGctcatcttttggatatggtt	9	4	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:83863236G>C	ENST00000349129.2	+	31	6396	c.6136G>C	c.(6136-6138)Gct>Cct	p.A2046P	DOPEY1_ENST00000237163.5_Missense_Mutation_p.A1976P|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.A2037P	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2046					protein transport (GO:0015031)			p.A2046P(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		ATAGGTTTTGGCTCATCTTTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											175	162	167					6																	83863236		2203	4297	6500	83919955	SO:0001583	missense	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6136G>C	6.37:g.83863236G>C	ENSP00000195654:p.Ala2046Pro		83919955	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546830	0.86022	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.28069	1.63;1.7	5.17	5.17	0.71159	.	0.153691	0.64402	D	0.000019	T	0.51227	0.1662	M	0.73430	2.235	0.80722	D	1	D;D;P	0.76494	0.999;0.999;0.934	D;D;P	0.79784	0.993;0.991;0.621	T	0.53690	-0.8403	10	0.66056	D	0.02	.	18.8557	0.92251	0.0:0.0:1.0:0.0	.	1937;2037;2046	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	P	2046;1976;1976	ENSP00000195654:A2046P;ENSP00000237163:A1976P	ENSP00000237163:A1976P	A	+	1	0	DOPEY1	83919955	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	7.412000	0.80091	2.688000	0.91661	0.650000	0.86243	GCT		0.343	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		C	83863236	G	C	83863236	3	2	75	1	0	0	0	0	1	0	0	0	4718	1203	42	5	6250	5	DOPEY1	6	83863236	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	40393834	83863236	87251831	79	21546										
CGA	1081	broad.mit.edu	37	chr6	87796017	87796017	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tggactctgaggtgacgttcTtttggaccaacatcgtcttc	10	10	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:87796017T>G	ENST00000369582.2	-	3	324	c.224A>C	c.(223-225)aAg>aCg	p.K75T	RN7SKP209_ENST00000516888.1_RNA	NM_000735.3	NP_000726.1	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide	75					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|cellular response to hormone stimulus (GO:0032870)|developmental growth (GO:0048589)|follicle-stimulating hormone secretion (GO:0046884)|gonad development (GO:0008406)|luteinizing hormone secretion (GO:0032275)|negative regulation of organ growth (GO:0046621)|peptide hormone processing (GO:0016486)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.K75T(1)		NS(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(1)	15		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)		GGTGACGTTCTTTTGGACCAA	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	6											197	193	194					6																	87796017		2203	4300	6503	87852736	SO:0001583	missense	1081			V00518	CCDS5007.1, CCDS75492.1	6q14-q21	2013-02-26			ENSG00000135346	ENSG00000135346		"Endogenous ligands"	1885	protein-coding gene	gene with protein product	"follicle-stimulating hormone alpha subunit", "chorionic gonadotropin, alpha polypeptide", "luteinizing hormone alpha chain", "lutropin alpha chain", "thyroid-stimulating hormone alpha chain", "glycoprotein hormones alpha chain"	118850				6286817	Standard	NM_000735		Approved	HCG, GPHa, GPHA1, FSHA, LHA, TSHA	uc021zci.1	P01215	OTTHUMG00000015161	ENST00000369582.2:c.224A>C	6.37:g.87796017T>G	ENSP00000358595:p.Lys75Thr		87852736		Missense_Mutation	SNP	ENST00000369582.2	37	CCDS5007.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.043093	0.55003	.	.	ENSG00000135346	ENST00000369582	.	.	.	5.62	5.62	0.85841	.	0.042815	0.85682	D	0.000000	T	0.73814	0.3635	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78130	-0.2324	9	0.87932	D	0	0.3063	15.8151	0.78595	0.0:0.0:0.0:1.0	.	75	P01215	GLHA_HUMAN	T	75	.	ENSP00000358595:K75T	K	-	2	0	CGA	87852736	1.000000	0.71417	0.606000	0.28943	0.001000	0.01503	7.404000	0.79996	2.136000	0.66102	0.477000	0.44152	AAG		0.483	CGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041425.1	NM_000735		G	87796017	T	G	87796017	3	3	75	1	0	0	0	0	1	0	0	0	3301	1609	56	4	134	4	CGA	6	87796017	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	3932781	87796017	83319050	80	21547										
CASP8AP2	9994	broad.mit.edu	37	chr6	90581012	90581012	+	RNA	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attttttcctcctcagaaatGatgaccgggaaattttattg	7	7	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:90581012G>C	ENST00000551025.1	+	0	7234									caspase 8 associated protein 2									p.D1933H(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		CCTCAGAAATGATGACCGGGA	0.353																																					Colon(187;1656 2025 17045 31481 39901)											1	Substitution - Missense(1)	large_intestine(1)	6											72	69	70					6																	90581012		1800	4069	5869	90637733			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90581012G>C			90637733		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.353	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90581012	G	C	90581012	1	2	75	0	1	0	0	0	0	0	0	0	2684	1290	45	5		5	CASP8AP2	6	90581012	RNA	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2784995	90581012	80534055	81	21548										
EPHA7	2045	broad.mit.edu	37	chr6	94068039	94068039	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catcttcacattcacatctgGaggagccttctttatcagaa	6	11	6	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:94068039G>T	ENST00000369303.4	-	4	1107	c.923C>A	c.(922-924)tCc>tAc	p.S308Y		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	308	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.S308Y(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TTCACATCTGGAGGAGCCTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	105	108					6																	94068039		2203	4300	6503	94124760	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.923C>A	6.37:g.94068039G>T	ENSP00000358309:p.Ser308Tyr		94124760	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.240205	0.58995	.	.	ENSG00000135333	ENST00000369303	T	0.29397	1.57	5.62	5.62	0.85841	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.371469	0.28431	N	0.015377	T	0.22244	0.0536	L	0.52126	1.63	0.80722	D	1	B;B;B	0.29909	0.078;0.261;0.086	B;B;B	0.28011	0.027;0.071;0.085	T	0.04664	-1.0935	10	0.66056	D	0.02	.	19.6472	0.95784	0.0:0.0:1.0:0.0	.	308;308;308	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	Y	308	ENSP00000358309:S308Y	ENSP00000358309:S308Y	S	-	2	0	EPHA7	94124760	1.000000	0.71417	0.987000	0.45799	0.991000	0.79684	7.324000	0.79115	2.652000	0.90054	0.655000	0.94253	TCC		0.463	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	94068039	G	T	94068039	3	4	75	1	0	0	0	0	1	0	0	0	5185	1174	41	2	2129	2	EPHA7	6	94068039	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	3487027	94068039	77047028	82	21549										
HACE1	57531	broad.mit.edu	37	chr6	105244595	105244595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgaaaaagcctcgggtgatAttgaattaatacttcacaag	8	7	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:105244595A>G	ENST00000262903.4	-	9	1027	c.751T>C	c.(751-753)Tat>Cat	p.Y251H	HACE1_ENST00000369125.2_Missense_Mutation_p.Y251H	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	251					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.Y251H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CTCGGGTGATATTGAATTAAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	6											76	76	76					6																	105244595		2202	4298	6500	105351288	SO:0001583	missense	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.751T>C	6.37:g.105244595A>G	ENSP00000262903:p.Tyr251His		105351288	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386488	0.25031	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645	T;T;T	0.62232	0.04;0.04;0.04	5.4	3.05	0.35203	Ankyrin repeat-containing domain (2);	0.183555	0.49305	N	0.000150	T	0.15392	0.0371	N	0.04508	-0.205	0.40010	D	0.975272	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08994	-1.0695	10	0.14252	T	0.57	.	7.4126	0.27025	0.6925:0.0:0.3075:0.0	.	251;251	E9PGP0;Q8IYU2	.;HACE1_HUMAN	H	251;251;207	ENSP00000262903:Y251H;ENSP00000358121:Y251H;ENSP00000429765:Y207H	ENSP00000262903:Y251H	Y	-	1	0	HACE1	105351288	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	5.436000	0.66538	0.890000	0.36211	0.477000	0.44152	TAT		0.328	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		G	105244595	A	G	105244595	3	3	75	1	0	0	0	0	1	0	0	0	6961	449	16	4	2042	4	HACE1	6	105244595	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	11176556	105244595	65870472	83	21550										
HECA	51696	broad.mit.edu	37	chr6	139487480	139487482	+	In_Frame_Del	DEL	GAC	GAC	-													0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggccggtggacctggagaagGacgactaccagaaggtggtg					rs142291743	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	GAC	GAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:139487480_139487482delGAC	ENST00000367658.2	+	2	616_618	c.331_333delGAC	c.(331-333)gacdel	p.D112del	RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	112					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.D111delD(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		CCTGGAGAAGGACGACTACCAGA	0.567																																																1	Deletion - In frame(1)	large_intestine(1)	6																																								139529175	SO:0001651	inframe_deletion	51696			AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.331_333delGAC	6.37:g.139487483_139487485delGAC	ENSP00000356630:p.Asp112del		139529173		In_Frame_Del	DEL	ENST00000367658.2	37	CCDS5194.1																																																																																				0.567	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		-	139487482	GAC	-	139487480	7	5	75	1	0	1	0	1	0	0	0	0	7059	1174	41	0	337	0	HECA	6	139487480	In_Frame_Del	DEL	GAC	TCGA-AG-A026-01A-32W-A096-10	34242885	139487480	31627587	84	21551										
PDE10A	10846	broad.mit.edu	37	chr6	165863797	165863797	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctcctgtgtccaaccgttgTtctatatagctgtttagttc	7	11	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr6:165863797T>A	ENST00000366882.1	-	5	403	c.249A>T	c.(247-249)gaA>gaT	p.E83D	PDE10A_ENST00000539869.2_Missense_Mutation_p.E93D|PDE10A_ENST00000354448.4_Missense_Mutation_p.E83D			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	83					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.E83D(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	CCAACCGTTGTTCTATATAGC	0.328																																					Esophageal Squamous(22;308 615 5753 12038 40624)											1	Substitution - Missense(1)	large_intestine(1)	6											169	154	159					6																	165863797		2203	4300	6503	165783787	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.249A>T	6.37:g.165863797T>A	ENSP00000355847:p.Glu83Asp		165783787	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	T	14.12	2.440470	0.43326	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.71341	-0.56;-0.56	4.7	-1.3	0.09259	.	0.099622	0.64402	D	0.000002	T	0.61664	0.2365	L	0.44542	1.39	0.41880	D	0.990315	D;P	0.58970	0.984;0.537	D;B	0.68192	0.956;0.134	T	0.62058	-0.6934	10	0.16896	T	0.51	.	12.3919	0.55362	0.0:0.6521:0.0:0.3479	.	93;83	Q9ULW9;Q9Y233	.;PDE10_HUMAN	D	83;111;93;83;82	ENSP00000355847:E83D;ENSP00000346435:E83D	ENSP00000341187:E93D	E	-	3	2	PDE10A	165783787	0.987000	0.35691	0.986000	0.45419	0.947000	0.59692	0.218000	0.17622	-0.406000	0.07588	-0.468000	0.05107	GAA		0.328	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			A	165863797	T	A	165863797	3	1	75	1	0	0	0	0	1	0	0	0	11661	1722	60	5	2166	5	PDE10A	6	165863797	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	26376317	165863797	5251270	85	21552										
IQCE	23288	broad.mit.edu	37	chr7	2617958	2617958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggaaaacagcaggaaggaccGgcagatagagcagctcctgg	15	9	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:2617958G>A	ENST00000402050.2	+	7	732	c.548G>A	c.(547-549)cGg>cAg	p.R183Q	IQCE_ENST00000325979.7_Missense_Mutation_p.R118Q|IQCE_ENST00000438376.2_Missense_Mutation_p.R167Q|IQCE_ENST00000404984.1_Missense_Mutation_p.R132Q	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	183						mitochondrion (GO:0005739)		p.R183Q(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		AGGAAGGACCGGCAGATAGAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	7											56	65	62					7																	2617958		2081	4211	6292	2584484	SO:0001583	missense	23288			AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.548G>A	7.37:g.2617958G>A	ENSP00000385597:p.Arg183Gln		2584484	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704091	0.88924	.	.	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000415271;ENST00000438376;ENST00000325979;ENST00000423395;ENST00000422276	T;T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19;3.19	5.5	5.5	0.81552	.	0.125660	0.51477	D	0.000091	T	0.26593	0.0650	M	0.71581	2.175	0.36221	D	0.851975	D;D;D;D;D;D	0.89917	0.997;0.987;1.0;0.997;0.987;1.0	P;P;D;P;P;D	0.83275	0.826;0.661;0.975;0.877;0.584;0.996	T	0.08310	-1.0728	10	0.49607	T	0.09	-33.4197	12.3018	0.54878	0.0819:0.0:0.9181:0.0	.	118;167;118;183;183;167	B4DXN1;B4DDX4;Q6IPM2-2;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;.;IQCE_HUMAN;.;.	Q	183;132;219;167;118;118;118	ENSP00000385597:R183Q;ENSP00000385945:R132Q;ENSP00000404643:R219Q;ENSP00000396178:R167Q;ENSP00000313772:R118Q;ENSP00000413570:R118Q	ENSP00000313772:R118Q	R	+	2	0	IQCE	2584484	0.998000	0.40836	1.000000	0.80357	0.963000	0.63663	2.027000	0.41078	2.572000	0.86782	0.563000	0.77884	CGG		0.627	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		A	2617958	G	A	2617958	3	1	75	1	0	0	0	0	1	0	0	0	7827	1116	39	1	574	1	IQCE	7	2617958	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		2617958	156520705	86	21553										
DNAH11	8701	broad.mit.edu	37	chr7	21583072	21583072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cggccgcctggcgatgatgcTggggttcacggaggagaaat	17	9	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:21583072T>C	ENST00000409508.3	+	1	240	c.209T>C	c.(208-210)cTg>cCg	p.L70P	DNAH11_ENST00000328843.6_Missense_Mutation_p.L70P	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	70	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L70P(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GCGATGATGCTGGGGTTCACG	0.642									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	7											22	26	25					7																	21583072		1927	4121	6048	21549597	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.209T>C	7.37:g.21583072T>C	ENSP00000475939:p.Leu70Pro		21549597	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	13.08	2.130458	0.37630	.	.	ENSG00000105877	ENST00000328843	T	0.26660	1.72	3.99	3.99	0.46301	.	3.606890	0.00682	N	0.000683	T	0.41696	0.1170	L	0.34521	1.04	0.44834	D	0.997844	D	0.71674	0.998	D	0.63488	0.915	T	0.15549	-1.0433	10	0.59425	D	0.04	.	9.4709	0.38842	0.0:0.0:0.0:1.0	.	70	Q96DT5	DYH11_HUMAN	P	70	ENSP00000330671:L70P	ENSP00000330671:L70P	L	+	2	0	DNAH11	21549597	0.981000	0.34729	0.630000	0.29268	0.105000	0.19272	2.298000	0.43602	1.821000	0.53095	0.460000	0.39030	CTG		0.642	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		C	21583072	T	C	21583072	3	2	75	1	0	0	0	0	1	0	0	0	4610	1580	55	4	211	4	DNAH11	7	21583072	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	18965114	21583072	137555591	87	21554										
SKAP2	8935	broad.mit.edu	37	chr7	26778460	26778460	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	accgttttactgagagcacaCcaccgtttctgccattcaaa	6	13	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:26778460C>A	ENST00000345317.2	-	6	736	c.423G>T	c.(421-423)tgG>tgT	p.W141C	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.W141C(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TGAGAGCACACCACCGTTTCT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	7											116	115	115					7																	26778460		2203	4300	6503	26744985	SO:0001583	missense	8935				CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.423G>T	7.37:g.26778460C>A	ENSP00000005587:p.Trp141Cys		26744985	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	37	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142534	0.77888	.	.	ENSG00000005020	ENST00000345317;ENST00000535331;ENST00000432747	T;T	0.27402	1.67;1.67	5.7	5.7	0.88788	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.69305	0.3096	H	0.96175	3.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79381	-0.1827	10	0.87932	D	0	-9.3935	16.7512	0.85487	0.0:1.0:0.0:0.0	.	126;141	B7Z5N4;O75563	.;SKAP2_HUMAN	C	141;126;126	ENSP00000005587:W141C;ENSP00000408163:W126C	ENSP00000005587:W141C	W	-	3	0	SKAP2	26744985	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.032000	0.70918	2.696000	0.92011	0.561000	0.74099	TGG		0.338	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			A	26778460	C	A	26778460	3	1	75	1	0	0	0	0	1	0	0	0	14393	508	18	2	684	2	SKAP2	7	26778460	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	5195388	26778460	132360203	88	21555										
RALA	5898	broad.mit.edu	37	chr7	39745751	39745751	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gatttaatgagagaaattcgAgcgagaaagatggaagacag	13	3	0	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:39745751A>T	ENST00000005257.2	+	5	908	c.528A>T	c.(526-528)cgA>cgT	p.R176R	AC004837.5_ENST00000435766.1_RNA|RALA_ENST00000468201.1_3'UTR	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	176					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R176R(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						GAGAAATTCGAGCGAGAAAGA	0.323																																																1	Substitution - coding silent(1)	large_intestine(1)	7											61	67	65					7																	39745751		2203	4298	6501	39712276	SO:0001819	synonymous_variant	5898				CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"RAS-like protein A", "Ras-related protein Ral-A", "Ras family small GTP binding protein RALA", "ras related GTP binding protein A"	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.528A>T	7.37:g.39745751A>T			39712276	A4D1W3	Silent	SNP	ENST00000005257.2	37	CCDS5460.1																																																																																				0.323	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402		T	39745751	A	T	39745751	2	4	75	1	0	0	0	0	0	0	0	1	13047	291	11	5		5	RALA	7	39745751	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	12967291	39745751	119392912	89	21556										
AEBP1	165	broad.mit.edu	37	chr7	44153252	44153252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agtaccgcgtgacagcccacGcggagggctacaccccgagc	13	16	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:44153252G>A	ENST00000223357.3	+	21	3174	c.2869G>A	c.(2869-2871)Gcg>Acg	p.A957T	AEBP1_ENST00000450684.2_Missense_Mutation_p.A532T|MIR4649_ENST00000582839.1_RNA	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	957	Interaction with PTEN. {ECO:0000250}.|Required for transcriptional repression. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A957T(1)		NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GACAGCCCACGCGGAGGGCTA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	7											68	70	69					7																	44153252		2203	4300	6503	44119777	SO:0001583	missense	165			D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.2869G>A	7.37:g.44153252G>A	ENSP00000223357:p.Ala957Thr		44119777	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	-	26.3	4.723323	0.89298	.	.	ENSG00000106624	ENST00000223357;ENST00000450684	T;T	0.51071	0.72;0.72	4.94	4.94	0.65067	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.000000	0.85682	D	0.000000	T	0.78168	0.4241	H	0.94264	3.515	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.85099	0.0956	10	0.87932	D	0	-26.7182	18.1495	0.89669	0.0:0.0:1.0:0.0	.	532;957	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	T	957;532	ENSP00000223357:A957T;ENSP00000398878:A532T	ENSP00000223357:A957T	A	+	1	0	AEBP1	44119777	1.000000	0.71417	0.915000	0.36163	0.722000	0.41435	7.895000	0.87343	2.473000	0.83533	0.645000	0.84053	GCG		0.622	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44153252	G	A	44153252	3	1	75	1	0	0	0	0	1	0	0	0	349	1087	38	1	2951	1	AEBP1	7	44153252	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4407501	44153252	114985411	90	21557										
LIMK1	3984	broad.mit.edu	37	chr7	73535496	73535496	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tttgtgaagctggaacactgGctggagaccctccgcatgca	12	11	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:73535496G>A	ENST00000336180.2	+	16	1860	c.1809G>A	c.(1807-1809)tgG>tgA	p.W603*	LIMK1_ENST00000418310.1_Nonsense_Mutation_p.W633*|LIMK1_ENST00000538333.3_Nonsense_Mutation_p.W569*	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.W603*(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	TGGAACACTGGCTGGAGACCC	0.677																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											58	54	56					7																	73535496		2203	4300	6503	73173432	SO:0001587	stop_gained	3984			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1809G>A	7.37:g.73535496G>A	ENSP00000336740:p.Trp603*		73173432	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Nonsense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	37	6.492174	0.97612	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	.	.	.	4.3	4.3	0.51218	.	0.063657	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.4637	14.7078	0.69203	0.0:0.0:1.0:0.0	.	.	.	.	X	633;603;603;569	.	ENSP00000336740:W603X	W	+	3	0	LIMK1	73173432	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	5.952000	0.70282	2.157000	0.67596	0.456000	0.33151	TGG		0.677	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73535496	G	A	73535496	4	1	75	1	0	0	0	0	0	1	0	0	8824	1212	42	3	1871	3	LIMK1	7	73535496	Nonsense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	29382244	73535496	85603167	91	21558										
GRM3	2913	broad.mit.edu	37	chr7	86394606	86394606	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggggcctgtttcctattaacGaaaaaggcactggaactgaa	11	8	0	1	rs267601603		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:86394606G>A	ENST00000361669.2	+	2	1244	c.145G>A	c.(145-147)Gaa>Aaa	p.E49K	GRM3_ENST00000394720.2_Missense_Mutation_p.E47K|GRM3_ENST00000536043.1_Intron|GRM3_ENST00000439827.1_Missense_Mutation_p.E49K|GRM3_ENST00000546348.1_Intron	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	49					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.E49K(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					TCCTATTAACGAAAAAGGCAC	0.408																																					GBM(52;969 1098 3139 52280)											1	Substitution - Missense(1)	large_intestine(1)	7											114	115	114					7																	86394606		2203	4300	6503	86232542	SO:0001583	missense	2913				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.145G>A	7.37:g.86394606G>A	ENSP00000355316:p.Glu49Lys		86232542	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.900098	0.72754	.	.	ENSG00000198822	ENST00000361669;ENST00000439827;ENST00000394720;ENST00000421579;ENST00000441140	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	L	0.58583	1.82	0.80722	D	1	D;P	0.53312	0.959;0.828	B;B	0.36378	0.223;0.219	T	0.75706	-0.3224	10	0.26408	T	0.33	.	17.9854	0.89154	0.0:0.0:1.0:0.0	.	49;49	G5E9K2;Q14832	.;GRM3_HUMAN	K	49;49;47;49;49	ENSP00000355316:E49K;ENSP00000398767:E49K;ENSP00000378209:E47K;ENSP00000390037:E49K;ENSP00000407490:E49K	ENSP00000355316:E49K	E	+	1	0	GRM3	86232542	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	2.732000	0.93576	0.655000	0.94253	GAA		0.408	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			A	86394606	G	A	86394606	3	1	75	1	0	0	0	0	1	0	0	0	6819	1059	37	1	147	1	GRM3	7	86394606	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	12859110	86394606	72744057	92	21559										
DYNC1I1	1780	broad.mit.edu	37	chr7	95665000	95665000	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gaatggctttcccaacgggaGacgtcaataacttcgtggtt	11	9	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:95665000G>C	ENST00000324972.6	+	13	1544	c.1351G>C	c.(1351-1353)Gac>Cac	p.D451H	DYNC1I1_ENST00000457059.1_Missense_Mutation_p.D434H|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.D414H|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.D431H|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.D434H|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.D414H	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	451					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)	p.D451H(1)		NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			CCCAACGGGAGACGTCAATAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	7											316	254	275					7																	95665000		2203	4300	6503	95502936	SO:0001583	missense	1780			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1351G>C	7.37:g.95665000G>C	ENSP00000320130:p.Asp451His		95502936	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096306	0.56075	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.90140	0.6919	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;1.0	D;D;D;D;D	0.77557	0.977;0.99;0.99;0.985;0.99	D	0.91353	0.5106	10	0.72032	D	0.01	-3.803	19.0933	0.93238	0.0:0.0:1.0:0.0	.	434;431;434;451;414	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	H	434;451;414;431;414;434	ENSP00000392337:D434H;ENSP00000320130:D451H;ENSP00000438377:D414H;ENSP00000398118:D431H;ENSP00000352348:D414H;ENSP00000412444:D434H	ENSP00000320130:D451H	D	+	1	0	DYNC1I1	95502936	1.000000	0.71417	0.999000	0.59377	0.024000	0.10985	9.657000	0.98554	2.830000	0.97506	0.585000	0.79938	GAC		0.468	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		C	95665000	G	C	95665000	3	2	75	1	0	0	0	0	1	0	0	0	4853	942	33	5	1397	5	DYNC1I1	7	95665000	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	9270394	95665000	63473663	93	21560										
NPTX2	4885	broad.mit.edu	37	chr7	98257841	98257841	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caactgctccacaaacatgcCgggcaacatcatcccgtggg	9	15	1	0	rs553029244		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:98257841C>G	ENST00000265634.3	+	5	1361	c.1196C>G	c.(1195-1197)cCg>cGg	p.P399R		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	399	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.P399R(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			ACAAACATGCCGGGCAACATC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	7											94	76	82					7																	98257841		2203	4300	6503	98095777	SO:0001583	missense	4885				CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1196C>G	7.37:g.98257841C>G	ENSP00000265634:p.Pro399Arg		98095777	A4D267|Q86XV7|Q96G70	Missense_Mutation	SNP	ENST00000265634.3	37	CCDS5657.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159711	0.78226	.	.	ENSG00000106236	ENST00000265634	T	0.06142	3.34	5.94	5.94	0.96194	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.192567	0.56097	D	0.000024	T	0.11324	0.0276	N	0.16368	0.405	0.80722	D	1	D	0.62365	0.991	D	0.64144	0.922	T	0.35151	-0.9800	10	0.08179	T	0.78	-16.6299	19.3514	0.94389	0.0:1.0:0.0:0.0	.	399	P47972	NPTX2_HUMAN	R	399	ENSP00000265634:P399R	ENSP00000265634:P399R	P	+	2	0	NPTX2	98095777	1.000000	0.71417	0.869000	0.34112	0.989000	0.77384	6.077000	0.71275	2.826000	0.97356	0.561000	0.74099	CCG		0.562	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		G	98257841	C	G	98257841	3	3	75	1	0	0	0	0	1	0	0	0	10634	652	23	5	1214	5	NPTX2	7	98257841	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	2592841	98257841	60880822	94	21561										
PMPCB	9512	broad.mit.edu	37	chr7	102940636	102940636	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tatttcaagggcaccaagaaGagatcccagttagatctgga	10	8	2	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:102940636G>C	ENST00000249269.4	+	4	377	c.339G>C	c.(337-339)aaG>aaC	p.K113N	PMPCB_ENST00000420236.2_Missense_Mutation_p.K8N|PMPCB_ENST00000428154.1_Missense_Mutation_p.K113N	NM_004279.2	NP_004270.2	O75439	MPPB_HUMAN	peptidase (mitochondrial processing) beta	113					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.K113N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(9)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCACCAAGAAGAGATCCCAGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	7											123	128	126					7																	102940636		2203	4300	6503	102727872	SO:0001583	missense	9512			AF054182	CCDS5730.1	7q22.1	2007-07-30			ENSG00000105819	ENSG00000105819			9119	protein-coding gene	gene with protein product		603131				9653160	Standard	XM_005250717		Approved	MPPB, MPPP52	uc003vbl.3	O75439	OTTHUMG00000157205	ENST00000249269.4:c.339G>C	7.37:g.102940636G>C	ENSP00000249269:p.Lys113Asn		102727872	O60416|Q96FV4	Missense_Mutation	SNP	ENST00000249269.4	37	CCDS5730.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533254	0.27387	.	.	ENSG00000105819	ENST00000249269;ENST00000428154;ENST00000420236	T;T;T	0.43688	0.94;0.94;0.94	5.5	2.27	0.28462	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.042367	0.85682	D	0.000000	T	0.26085	0.0636	N	0.25647	0.755	0.47778	D	0.99951	B;B;B;B;B;B;B	0.15141	0.006;0.002;0.012;0.012;0.007;0.012;0.004	B;B;B;B;B;B;B	0.17098	0.007;0.01;0.017;0.017;0.017;0.017;0.006	T	0.04930	-1.0917	10	0.26408	T	0.33	.	7.9055	0.29759	0.2201:0.1193:0.6605:0.0	.	8;8;113;113;104;113;113	E7ERZ4;B4DM90;A8K1E9;B3KM34;Q96CP5;O75439;G3V0E4	.;.;.;.;.;MPPB_HUMAN;.	N	113;113;8	ENSP00000249269:K113N;ENSP00000390035:K113N;ENSP00000410393:K8N	ENSP00000249269:K113N	K	+	3	2	PMPCB	102727872	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.495000	0.35627	0.698000	0.31739	0.644000	0.83932	AAG		0.373	PMPCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347913.1	NM_004279		C	102940636	G	C	102940636	3	2	75	1	0	0	0	0	1	0	0	0	12172	933	33	5	353	5	PMPCB	7	102940636	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4682795	102940636	56198027	95	21562										
ORC5L	5001	broad.mit.edu	37	chr7	103801610	103801610	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tctagtggaaatggttttggCccaaggagatgattgcttgt	13	5	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:103801610C>G	ENST00000297431.4	-	12	1201	c.1059G>C	c.(1057-1059)ggG>ggC	p.G353G	ORC5_ENST00000545943.1_Silent_p.G221G	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	353					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)	p.G353G(1)		kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						ATGGTTTTGGCCCAAGGAGAT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	7											120	123	122					7																	103801610		2203	4300	6503	103588846	SO:0001819	synonymous_variant	5001				CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 117"	602331	"origin recognition complex, subunit 5 (yeast homolog)-like", "origin recognition complex, subunit 5-like (yeast)", "origin recognition complex, subunit 5 homolog (yeast)"	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.1059G>C	7.37:g.103801610C>G			103588846	A4D0P8|O60590|O95268	Silent	SNP	ENST00000297431.4	37	CCDS5734.1																																																																																				0.363	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		G	103801610	C	G	103801610	2	3	75	1	0	0	0	0	0	0	0	1	11296	726	26	5		5	ORC5L	7	103801610	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	860974	103801610	55337053	96	21563										
DOCK4	9732	broad.mit.edu	37	chr7	111462470	111462470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctttggaaacatctccgggcGtatcaatattcggaacacag	9	10	2	0	rs186031092	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr7:111462470G>A	ENST00000437633.1	-	27	3134	c.2878C>T	c.(2878-2880)Cgc>Tgc	p.R960C	DOCK4_ENST00000428084.1_Missense_Mutation_p.R960C|DOCK4-AS1_ENST00000452714.1_RNA	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	960					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.R948C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATCTCCGGGCGTATCAATATT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	7											84	76	79					7																	111462470		1853	4091	5944	111249706	SO:0001583	missense	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2878C>T	7.37:g.111462470G>A	ENSP00000404179:p.Arg960Cys		111249706	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440123	0.83993	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.65916	-0.18;-0.18	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.73666	0.3616	M	0.69823	2.125	0.80722	D	1	D;D;D	0.71674	0.997;0.997;0.998	P;P;P	0.58520	0.776;0.696;0.84	T	0.76113	-0.3078	10	0.62326	D	0.03	.	13.3017	0.60328	0.0:0.0:0.8415:0.1585	.	996;960;960	Q149N5;Q8N1I0;Q8N1I0-2	.;DOCK4_HUMAN;.	C	948;960;960;948;959	ENSP00000410746:R960C;ENSP00000404179:R960C	ENSP00000345432:R948C	R	-	1	0	DOCK4	111249706	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.351000	0.59398	2.614000	0.88457	0.650000	0.86243	CGC		0.368	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111462470	G	A	111462470	3	1	75	1	0	0	0	0	1	0	0	0	4700	1145	40	1	3126	1	DOCK4	7	111462470	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	7660860	111462470	47676193	97	21564										
CSMD1	64478	broad.mit.edu	37	chr8	2808792	2808792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attgacgaaaaagacatctgAaggaactgtgggaagggggg	16	4	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:2808792A>G	ENST00000520002.1	-	67	10603	c.10048T>C	c.(10048-10050)Tca>Cca	p.S3350P	CSMD1_ENST00000602723.1_Missense_Mutation_p.S3173P|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3350P|CSMD1_ENST00000537824.1_Missense_Mutation_p.S3349P|CSMD1_ENST00000400186.3_Missense_Mutation_p.S3173P|CSMD1_ENST00000542608.1_Missense_Mutation_p.S3172P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3350						integral component of membrane (GO:0016021)		p.S3349P(1)|p.S3078P(1)		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)		AAGACATCTGAAGGAACTGTG	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	8											41	40	41					8																	2808792		1919	4120	6039	2796199	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10048T>C	8.37:g.2808792A>G	ENSP00000430733:p.Ser3350Pro		2796199	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.76|12.76	2.035145|2.035145	0.35893|0.35893	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.|T;T;T;T	.|0.26518	.|1.73;1.85;1.88;1.73	5.29|5.29	4.11|4.11	0.48088|0.48088	.|.	.|0.183579	.|0.37955	.|N	.|0.001865	T|T	0.34077|0.34077	0.0885|0.0885	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|P;B;P	.|0.49961	.|0.93;0.017;0.883	.|B;B;P	.|0.52909	.|0.36;0.01;0.713	T|T	0.02138|0.02138	-1.1207|-1.1207	5|10	.|0.31617	.|T	.|0.26	.|.	12.272|12.272	0.54712|0.54712	0.8577:0.1423:0.0:0.0|0.8577:0.1423:0.0:0.0	.|.	.|3350;3350;3172	.|E5RIG2;Q96PZ7;F5H2I8	.|.;CSMD1_HUMAN;.	S|P	2751|3173;3350;3211;3349;3172	.|ENSP00000383047:S3173P;ENSP00000430733:S3350P;ENSP00000441462:S3349P;ENSP00000446243:S3172P	.|ENSP00000320445:S3211P	F|S	-|-	2|1	0|0	CSMD1|CSMD1	2796199|2796199	0.987000|0.987000	0.35691|0.35691	0.998000|0.998000	0.56505|0.56505	0.253000|0.253000	0.25986|0.25986	3.342000|3.342000	0.52159|0.52159	0.810000|0.810000	0.34279|0.34279	0.523000|0.523000	0.50628|0.50628	TTC|TCA		0.418	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2808792	A	G	2808792	3	3	75	1	0	0	0	0	1	0	0	0	3950	246	9	4	669	4	CSMD1	8	2808792	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10		2808792	143555230	98	21565										
ADAMDEC1	27299	broad.mit.edu	37	chr8	24256410	24256410	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tataacaccatagatgttcaAgtggccttggtaggtatgga	11	6	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:24256410A>C	ENST00000256412.4	+	9	1006	c.786A>C	c.(784-786)caA>caC	p.Q262H	ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.Q183H|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.Q183H|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	262	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Q262H(1)		NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TAGATGTTCAAGTGGCCTTGG	0.428																																					Ovarian(147;687 1849 3699 25981 31337)											1	Substitution - Missense(1)	large_intestine(1)	8											108	105	106					8																	24256410		2203	4300	6503	24312355	SO:0001583	missense	27299			Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.786A>C	8.37:g.24256410A>C	ENSP00000256412:p.Gln262His		24312355	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.754524	0.00663	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.63417	-0.04;-0.04;-0.04	5.87	-6.32	0.01995	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.083810	0.06986	N	0.820787	T	0.25606	0.0623	N	0.04387	-0.21	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.32798	-0.9893	10	0.02654	T	1	-3.6408	2.6709	0.05067	0.2014:0.2128:0.0743:0.5116	.	262	O15204	ADEC1_HUMAN	H	262;183;183	ENSP00000256412:Q262H;ENSP00000442592:Q183H;ENSP00000428993:Q183H	ENSP00000256412:Q262H	Q	+	3	2	ADAMDEC1	24312355	0.023000	0.18921	0.002000	0.10522	0.287000	0.27160	-0.370000	0.07523	-0.741000	0.04797	-2.347000	0.00243	CAA		0.428	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		C	24256410	A	C	24256410	3	2	75	1	0	0	0	0	1	0	0	0	254	69	3	4	820	4	ADAMDEC1	8	24256410	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	21447618	24256410	122107612	99	21566										
DPYSL2	1808	broad.mit.edu	37	chr8	26505284	26505284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcatctgggaccccgacagcGttaaaaccatctctgccaag	8	14	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:26505284G>A	ENST00000311151.5	+	11	1661	c.1249G>A	c.(1249-1251)Gtt>Att	p.V417I	DPYSL2_ENST00000521913.1_Missense_Mutation_p.V381I|DPYSL2_ENST00000523027.1_Missense_Mutation_p.V381I	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	417					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)	p.V417I(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		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)		CCCCGACAGCGTTAAAACCAT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	8											80	73	75					8																	26505284		2203	4300	6503	26561201	SO:0001583	missense	1808			D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.1249G>A	8.37:g.26505284G>A	ENSP00000309539:p.Val417Ile		26561201	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	37	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152721	0.38021	.	.	ENSG00000092964	ENST00000545637;ENST00000521913;ENST00000311151;ENST00000522745;ENST00000523027	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	5.07	1.16	0.20824	Metal-dependent hydrolase, composite domain (1);	0.333575	0.32416	N	0.006131	T	0.58466	0.2124	N	0.25332	0.735	0.09310	N	0.999999	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.52268	-0.8598	10	0.62326	D	0.03	-9.3468	9.27	0.37666	0.3008:0.0:0.6992:0.0	.	417;473	Q16555;Q59GB4	DPYL2_HUMAN;.	I	56;381;417;417;381	ENSP00000427985:V381I;ENSP00000309539:V417I;ENSP00000428909:V417I;ENSP00000431117:V381I	ENSP00000309539:V417I	V	+	1	0	DPYSL2	26561201	0.853000	0.29707	0.002000	0.10522	0.846000	0.48090	1.555000	0.36277	0.094000	0.17404	0.563000	0.77884	GTT		0.542	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		A	26505284	G	A	26505284	3	1	75	1	0	0	0	0	1	0	0	0	4758	1145	40	1	1291	1	DPYSL2	8	26505284	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2248874	26505284	119858738	100	21567										
RNF122	79845	broad.mit.edu	37	chr8	33406959	33406959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggcgtgttggcacgggagcaCgcctaactcatccttcccct	11	15	1	0	rs115346711		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:33406959C>T	ENST00000256257.1	-	5	723	c.322G>A	c.(322-324)Gtg>Atg	p.V108M		NM_024787.2	NP_079063.2	Q9H9V4	RN122_HUMAN	ring finger protein 122	108						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.V108M(1)		endometrium(2)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)		CACGGGAGCACGCCTAACTCA	0.547													c|||	1	0.000199681	0	0	5008	,	,		17934	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	MET/VAL	0,4406		0,0,2203	135	104	114		322	4.1	0.7	8	dbSNP_132	114	2,8598	2.2+/-6.3	0,2,4298	yes	missense	RNF122	NM_024787.2	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	108/156	33406959	2,13004	2203	4300	6503	33526501	SO:0001583	missense	79845			AK022588	CCDS6091.1	8p12	2013-01-09			ENSG00000133874	ENSG00000133874		"RING-type (C3HC4) zinc fingers"	21147	protein-coding gene	gene with protein product							Standard	NM_024787		Approved	FLJ12526	uc003xjo.1	Q9H9V4	OTTHUMG00000163960	ENST00000256257.1:c.322G>A	8.37:g.33406959C>T	ENSP00000256257:p.Val108Met		33526501	Q52LK3	Missense_Mutation	SNP	ENST00000256257.1	37	CCDS6091.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.3	4.397100	0.83120	0.0	2.33E-4	ENSG00000133874	ENST00000256257	T	0.46063	0.88	5.96	4.05	0.47172	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.114001	0.64402	N	0.000013	T	0.53850	0.1822	L	0.49455	1.56	0.50632	D	0.999886	D	0.89917	1.0	D	0.77557	0.99	T	0.53408	-0.8443	10	0.87932	D	0	-10.3984	7.6049	0.28097	0.1613:0.7508:0.0:0.0878	.	108	Q9H9V4	RN122_HUMAN	M	108	ENSP00000256257:V108M	ENSP00000256257:V108M	V	-	1	0	RNF122	33526501	0.987000	0.35691	0.666000	0.29783	0.985000	0.73830	2.686000	0.46968	0.727000	0.32360	0.655000	0.94253	GTG		0.547	RNF122-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376562.1	NM_024787		T	33406959	C	T	33406959	3	4	75	1	0	0	0	0	1	0	0	0	13469	536	19	1	153	1	RNF122	8	33406959	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	6901675	33406959	112957063	101	21568										
RB1CC1	9821	broad.mit.edu	37	chr8	53558276	53558276	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	acagacctgttgttccgcaaTcaaagatgttcgaacatttt	7	9	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:53558276T>C	ENST00000025008.5	-	16	4496	c.3973A>G	c.(3973-3975)Att>Gtt	p.I1325V	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Missense_Mutation_p.I1325V|RB1CC1_ENST00000539297.1_Missense_Mutation_p.I1325V	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1325					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.I1325V(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TGTTCCGCAATCAAAGATGTT	0.323																																					GBM(180;1701 2102 13475 42023 52570)											1	Substitution - Missense(1)	large_intestine(1)	8											83	78	80					8																	53558276		2203	4300	6503	53720829	SO:0001583	missense	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3973A>G	8.37:g.53558276T>C	ENSP00000025008:p.Ile1325Val		53720829	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	T	6.851	0.526210	0.13066	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.15603	2.41;2.41;2.41	5.28	5.28	0.74379	.	0.060586	0.64402	D	0.000004	T	0.13970	0.0338	L	0.34521	1.04	0.46149	D	0.998895	B;B	0.32507	0.373;0.256	B;B	0.31495	0.131;0.062	T	0.09885	-1.0654	10	0.17832	T	0.49	-18.216	15.213	0.73241	0.0:0.0:0.0:1.0	.	1325;1325	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	V	1325	ENSP00000025008:I1325V;ENSP00000396067:I1325V;ENSP00000445960:I1325V	ENSP00000025008:I1325V	I	-	1	0	RB1CC1	53720829	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	6.485000	0.73625	2.002000	0.58637	0.533000	0.62120	ATT		0.323	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		C	53558276	T	C	53558276	3	2	75	1	0	0	0	0	1	0	0	0	13136	1435	50	4	847	4	RB1CC1	8	53558276	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	20151317	53558276	92805746	102	21569										
RP1	6101	broad.mit.edu	37	chr8	55539830	55539830	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attcatccactaatctccttCtagcttggctcttggtgcta	6	12	4	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:55539830C>G	ENST00000220676.1	+	4	3536	c.3388C>G	c.(3388-3390)Cta>Gta	p.L1130V		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1130					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.L1130V(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			TAATCTCCTTCTAGCTTGGCT	0.408																																					Colon(91;1014 1389 7634 14542 40420)											1	Substitution - Missense(1)	large_intestine(1)	8											82	74	76					8																	55539830		2203	4300	6503	55702383	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3388C>G	8.37:g.55539830C>G	ENSP00000220676:p.Leu1130Val		55702383		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.396353	0.62177	.	.	ENSG00000104237	ENST00000220676	T	0.56611	0.45	5.7	3.58	0.41010	.	0.000000	0.44285	D	0.000466	T	0.69061	0.3069	M	0.68952	2.095	0.32161	N	0.582955	D	0.89917	1.0	D	0.87578	0.998	T	0.77112	-0.2708	10	0.87932	D	0	.	13.5936	0.61975	0.0:0.8536:0.0:0.1464	.	1130	P56715	RP1_HUMAN	V	1130	ENSP00000220676:L1130V	ENSP00000220676:L1130V	L	+	1	2	RP1	55702383	1.000000	0.71417	0.998000	0.56505	0.923000	0.55619	0.741000	0.26202	1.403000	0.46800	0.563000	0.77884	CTA		0.408	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55539830	C	G	55539830	3	3	75	1	0	0	0	0	1	0	0	0	13569	912	32	5	3398	5	RP1	8	55539830	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1981554	55539830	90824192	103	21570										
KCNB2	9312	broad.mit.edu	37	chr8	73848793	73848793	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aaaattgtgggaggtctgtgCtgtattgctggggttctggt	16	4	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:73848793C>A	ENST00000523207.1	+	3	1791	c.1203C>A	c.(1201-1203)tgC>tgA	p.C401*		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	401					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.C401*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAGGTCTGTGCTGTATTGCTG	0.433																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											94	93	94					8																	73848793		2203	4300	6503	74011347	SO:0001587	stop_gained	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1203C>A	8.37:g.73848793C>A	ENSP00000430846:p.Cys401*		74011347	Q7Z7D0|Q9BXD3	Nonsense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	40	8.108011	0.98657	.	.	ENSG00000182674	ENST00000523207	.	.	.	5.74	4.87	0.63330	.	0.000000	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.1732	0.37096	0.0:0.7831:0.0:0.2169	.	.	.	.	X	401	.	ENSP00000430846:C401X	C	+	3	2	KCNB2	74011347	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.006000	0.29847	1.432000	0.47375	0.655000	0.94253	TGC		0.433	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73848793	C	A	73848793	4	1	75	1	0	0	0	0	0	1	0	0	8034	805	28	2	1209	2	KCNB2	8	73848793	Nonsense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	18308963	73848793	72515229	104	21571										
KCNB2	9312	broad.mit.edu	37	chr8	73849624	73849624	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gttgacataactgtgaacctCgatgccagtggctcccagtg	11	11	0	2	rs374713448		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:73849624C>T	ENST00000523207.1	+	3	2622	c.2034C>T	c.(2032-2034)ctC>ctT	p.L678L		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	678					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.L678L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CTGTGAACCTCGATGCCAGTG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	8						C		1,4405	2.1+/-5.4	0,1,2202	56	56	56		2034	-8.7	0	8		56	0,8600		0,0,4300	no	coding-synonymous	KCNB2	NM_004770.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		678/912	73849624	1,13005	2203	4300	6503	74012178	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2034C>T	8.37:g.73849624C>T			74012178	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.542	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73849624	C	T	73849624	2	4	75	1	0	0	0	0	0	0	0	1	8034	871	31	1		1	KCNB2	8	73849624	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	831	73849624	72514398	105	21572										
CPNE3	8895	broad.mit.edu	37	chr8	87570635	87570635	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gccacgaaacaacagaagcaGtgaccacttcaacagaattc	7	12	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:87570635G>T	ENST00000521271.1	+	17	1773	c.1611G>T	c.(1609-1611)caG>caT	p.Q537H	CPNE3_ENST00000198765.4_Missense_Mutation_p.Q537H	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	537					lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)	p.Q537H(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						AACAGAAGCAGTGACCACTTC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	8											117	108	111					8																	87570635		2203	4300	6503	87639751	SO:0001583	missense	8895			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.1611G>T	8.37:g.87570635G>T	ENSP00000430934:p.Gln537His		87639751	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.287236	0.40494	.	.	ENSG00000085719	ENST00000198765;ENST00000521271	T;T	0.05580	3.42;3.42	5.78	-5.28	0.02755	.	2.829760	0.01245	N	0.008732	T	0.03178	0.0093	N	0.08118	0	0.09310	N	0.999999	B	0.14438	0.01	B	0.06405	0.002	T	0.39722	-0.9600	10	0.72032	D	0.01	-19.5667	2.0571	0.03583	0.2118:0.3421:0.276:0.1701	.	537	O75131	CPNE3_HUMAN	H	537	ENSP00000198765:Q537H;ENSP00000430934:Q537H	ENSP00000198765:Q537H	Q	+	3	2	CPNE3	87639751	0.000000	0.05858	0.000000	0.03702	0.296000	0.27459	-0.276000	0.08514	-1.144000	0.02862	0.655000	0.94253	CAG		0.468	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1			T	87570635	G	T	87570635	3	4	75	1	0	0	0	0	1	0	0	0	3819	1020	36	2	1669	2	CPNE3	8	87570635	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	13721011	87570635	58793387	106	21573										
VPS13B	157680	broad.mit.edu	37	chr8	100520063	100520063	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctttcctgtactgacaagcTgaacagacgcaccttgttgg	9	12	0	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:100520063T>G	ENST00000358544.2	+	28	4334	c.4223T>G	c.(4222-4224)cTg>cGg	p.L1408R	VPS13B_ENST00000357162.2_Intron|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1408					protein transport (GO:0015031)			p.L1408R(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ACTGACAAGCTGAACAGACGC	0.458																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											205	174	184					8																	100520063		2203	4300	6503	100589239	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.4223T>G	8.37:g.100520063T>G	ENSP00000351346:p.Leu1408Arg		100589239	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.542809	0.65198	.	.	ENSG00000132549	ENST00000358544	T	0.54675	0.56	5.64	5.64	0.86602	.	0.171967	0.38436	N	0.001683	T	0.65544	0.2701	L	0.39898	1.24	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.68561	-0.5376	10	0.87932	D	0	.	15.8329	0.78773	0.0:0.0:0.0:1.0	.	1407;1408	Q7Z7G8-6;Q7Z7G8	.;VP13B_HUMAN	R	1408	ENSP00000351346:L1408R	ENSP00000351346:L1408R	L	+	2	0	VPS13B	100589239	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.780000	0.85658	2.149000	0.67028	0.482000	0.46254	CTG		0.458	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100520063	T	G	100520063	3	3	75	1	0	0	0	0	1	0	0	0	17230	1580	55	4	4523	4	VPS13B	8	100520063	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	12949428	100520063	45843959	107	21574										
DCAF13	25879	broad.mit.edu	37	chr8	104453843	104453843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catgaaagaagctcgtcgacGaaagtatgttttgaggcatt	11	6	0	3	rs139907413	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:104453843G>A	ENST00000297579.5	+	10	1980	c.1703G>A	c.(1702-1704)cGa>cAa	p.R568Q		NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	416					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.R568Q(1)		NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GCTCGTCGACGAAAGTATGTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	110	107	108		1703	5.4	0.3	8	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DCAF13	NM_015420.6	43	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	probably-damaging	568/598	104453843	4,13002	2203	4300	6503	104523019	SO:0001583	missense	25879			AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.1703G>A	8.37:g.104453843G>A	ENSP00000297579:p.Arg568Gln		104523019	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	G	35	5.567540	0.96540	2.27E-4	3.49E-4	ENSG00000164934	ENST00000297579	T	0.77620	-1.11	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.90752	0.7097	M	0.92833	3.35	0.80722	D	1	.	.	.	.	.	.	D	0.92716	0.6187	8	0.72032	D	0.01	-8.2276	17.4002	0.87458	0.0:0.0:1.0:0.0	.	.	.	.	Q	568	ENSP00000297579:R568Q	ENSP00000297579:R568Q	R	+	2	0	DCAF13	104523019	1.000000	0.71417	0.333000	0.25482	0.971000	0.66376	7.239000	0.78182	2.521000	0.84997	0.563000	0.77884	CGA		0.393	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		A	104453843	G	A	104453843	3	1	75	1	0	0	0	0	1	0	0	0	4272	1058	37	1	1741	1	DCAF13	8	104453843	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	3933780	104453843	41910179	108	21575										
RIMS2	9699	broad.mit.edu	37	chr8	104709326	104709326	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctctgcagaaaactgcatcaGcagtttgaaatgtataaaga	8	7	2	3	rs374844910	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:104709326G>A	ENST00000406091.3	+	2	189	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	94	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.Q99Q(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AACTGCATCAGCAGTTTGAAA	0.368										HNSCC(12;0.0054)			G|||	8	0.00159744	0.0061	0	5008	,	,		16531	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						G		10,3692		0,10,1841	56	55	55		189	3.3	1	8		55	0,8192		0,0,4096	no	coding-synonymous	RIMS2	NM_001100117.2		0,10,5937	AA,AG,GG		0.0,0.2701,0.0841		63/1350	104709326	10,11884	1851	4096	5947	104778502	SO:0001819	synonymous_variant	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.189G>A	8.37:g.104709326G>A			104778502	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																				0.368	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117		A	104709326	G	A	104709326	2	1	75	1	0	0	0	0	0	0	0	1	13405	962	34	3		3	RIMS2	8	104709326	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	255483	104709326	41654696	109	21576										
RSPO2	340419	broad.mit.edu	37	chr8	108973016	108973016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggtacaaaagtctttgctaaAgcaagaatcacagttttcta	7	7	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:108973016A>G	ENST00000276659.5	-	4	933	c.313T>C	c.(313-315)Ttt>Ctt	p.F105L	RSPO2_ENST00000517781.1_Missense_Mutation_p.F42L|RSPO2_ENST00000378439.2_Missense_Mutation_p.F42L|RSPO2_ENST00000517939.1_Missense_Mutation_p.F38L	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	105					bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.F105L(1)	EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			TCTTTGCTAAAGCAAGAATCA	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	8											66	63	64					8																	108973016		2203	4300	6503	109042192	SO:0001583	missense	340419			AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.313T>C	8.37:g.108973016A>G	ENSP00000276659:p.Phe105Leu		109042192	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	A	33	5.275490	0.95459	.	.	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502;ENST00000521757;ENST00000521956;ENST00000520026	D;D;D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.86	5.86	0.93980	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.87849	0.6281	L	0.37697	1.125	0.80722	D	1	D;P	0.56035	0.974;0.928	D;P	0.70487	0.969;0.718	D	0.84602	0.0673	10	0.17369	T	0.5	-11.451	16.261	0.82547	1.0:0.0:0.0:0.0	.	105;42	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	L	38;42;42;105;38;38;105;77	ENSP00000428940:F38L;ENSP00000427937:F42L;ENSP00000367698:F42L;ENSP00000276659:F105L;ENSP00000428614:F38L;ENSP00000430485:F38L;ENSP00000430010:F105L;ENSP00000429159:F77L	ENSP00000276659:F105L	F	-	1	0	RSPO2	109042192	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.279000	0.95777	2.246000	0.74042	0.445000	0.29226	TTT		0.308	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		G	108973016	A	G	108973016	3	3	75	1	0	0	0	0	1	0	0	0	13747	72	3	4	430	4	RSPO2	8	108973016	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	4263690	108973016	37391006	110	21577										
LY6K	54742	broad.mit.edu	37	chr8	143784537	143784537	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccacgttttttcatggttgcGaagcagtgctccgctggttg	12	10	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:143784537G>A	ENST00000292430.6	+	3	663	c.246G>A	c.(244-246)gcG>gcA	p.A82A	LY6K_ENST00000519390.1_3'UTR|CTD-2292P10.4_ENST00000520572.1_RNA|LY6K_ENST00000561179.1_Silent_p.A140A|LY6K_ENST00000519387.1_Intron|LY6K_ENST00000522591.1_3'UTR			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	82	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A140A(1)		NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCATGGTTGCGAAGCAGTGCT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	8											62	60	61					8																	143784537		2203	4300	6503	143781539	SO:0001819	synonymous_variant	54742			AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886			24225	protein-coding gene	gene with protein product	"cancer/testis antigen 97"	615093				12516096	Standard	NM_017527		Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000292430.6:c.246G>A	8.37:g.143784537G>A			143781539	G3V116|O15227|Q9BVD7	Silent	SNP	ENST00000292430.6	37	CCDS6385.2																																																																																				0.498	LY6K-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379893.2	NM_017527		A	143784537	G	A	143784537	2	1	75	1	0	0	0	0	0	0	0	1	9128	1045	37	1		1	LY6K	8	143784537	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	34811521	143784537	2579485	111	21578										
SPATC1	375686	broad.mit.edu	37	chr8	145096221	145096221	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tccagcatcttcccagagcgCgtacggctctacggcttcac	9	16	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr8:145096221C>T	ENST00000377470.3	+	4	1497	c.1395C>T	c.(1393-1395)cgC>cgT	p.R465R	SPATC1_ENST00000447830.2_Intron	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	465						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R465R(1)|p.R374R(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCCCAGAGCGCGTACGGCTCT	0.627																																																2	Substitution - coding silent(2)	large_intestine(2)	8											76	57	63					8																	145096221		2203	4300	6503	145168209	SO:0001819	synonymous_variant	375686			BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.1395C>T	8.37:g.145096221C>T			145168209	B4DWW9|Q5U5I8|Q7Z6L7	Silent	SNP	ENST00000377470.3	37	CCDS6413.2																																																																																				0.627	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572		T	145096221	C	T	145096221	2	4	75	1	0	0	0	0	0	0	0	1	15056	755	27	1		1	SPATC1	8	145096221	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1311684	145096221	1267801	112	21579										
ACO1	48	broad.mit.edu	37	chr9	32431754	32431755	+	Frame_Shift_Ins	INS	-	-	A													0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agcaggtatttctgaaagatINSatctggccgactagagacga							TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr9:32431754_32431755insA	ENST00000309951.6	+	15	1902_1903	c.1764_1765insA	c.(1765-1767)atcfs	p.I589fs	ACO1_ENST00000541043.1_Frame_Shift_Ins_p.I490fs|ACO1_ENST00000379923.1_Frame_Shift_Ins_p.I589fs	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	589					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.I589fs*5(2)		breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TTCTGAAAGATATCTGGCCGAC	0.411											OREG0019130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Insertion - Frameshift(2)	large_intestine(2)	9																																								32421755	SO:0001589	frameshift_variant	48			M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1765dupA	9.37:g.32431755_32431755dupA	ENSP00000309477:p.Ile589fs	832	32421754	D3DRK7|Q14652|Q5VZA7	Frame_Shift_Ins	INS	ENST00000309951.6	37	CCDS6525.1																																																																																				0.411	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		A	32431755	-	A	32431754	7	5	75	1	0	1	1	0	0	0	0	0	146	1403	49	0	1818	0	ACO1	9	32431754	Frame_Shift_Ins	INS	-	TCGA-AG-A026-01A-32W-A096-10		32431754	108781677	113	21580										
GKAP1	80318	broad.mit.edu	37	chr9	86403589	86403589	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgcttcaaacatttcagatGtcagctacaaaaaaaaagtt	5	8	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr9:86403589G>T	ENST00000376371.2	-	5	765	c.365C>A	c.(364-366)aCa>aAa	p.T122K	GKAP1_ENST00000376365.3_Missense_Mutation_p.T122K	NM_025211.3	NP_079487.2	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1	122					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)		p.T122K(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	14						CATTTCAGATGTCAGCTACAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	9											119	120	120					9																	86403589		2201	4292	6493	85593409	SO:0001583	missense	80318			BC014476	CCDS35049.1, CCDS47988.1	9q22.1	2008-02-05			ENSG00000165113	ENSG00000165113			17496	protein-coding gene	gene with protein product	"cGMP-dependent protein kinase anchoring protein 42kDa"	611356					Standard	NM_025211		Approved	GKAP42, FKSG21	uc004amy.3	Q5VSY0	OTTHUMG00000020106	ENST00000376371.2:c.365C>A	9.37:g.86403589G>T	ENSP00000365550:p.Thr122Lys		85593409	Q96LI0|Q9BYI1|Q9BYI2|Q9H225	Missense_Mutation	SNP	ENST00000376371.2	37	CCDS35049.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495548	0.85069	.	.	ENSG00000165113	ENST00000376371;ENST00000376365	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.77082	0.4078	M	0.76838	2.35	0.80722	D	1	P;D	0.58970	0.775;0.984	B;P	0.56700	0.436;0.804	T	0.79820	-0.1642	9	0.72032	D	0.01	-14.7711	19.1566	0.93514	0.0:0.0:1.0:0.0	.	122;122	Q5VSY0-2;Q5VSY0	.;GKAP1_HUMAN	K	122	.	ENSP00000365544:T122K	T	-	2	0	GKAP1	85593409	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.725000	0.74752	2.700000	0.92200	0.585000	0.79938	ACA		0.299	GKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052839.2	NM_025211		T	86403589	G	T	86403589	3	4	75	1	0	0	0	0	1	0	0	0	6443	1377	48	2	771	2	GKAP1	9	86403589	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	53971835	86403589	54809842	114	21581										
SSNA1	8636	broad.mit.edu	37	chr9	140083672	140083672	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgcaagattgcctctcgcaaCgagttcgaccggaccatcgc	10	15	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr9:140083672C>A	ENST00000322310.5	+	2	287	c.207C>A	c.(205-207)aaC>aaA	p.N69K	SSNA1_ENST00000459860.1_3'UTR|ANAPC2_ENST00000323927.2_5'Flank	NM_003731.2	NP_003722.2	O43805	SSNA1_HUMAN	Sjogren syndrome nuclear autoantigen 1	69					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport (GO:0042073)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|nucleus (GO:0005634)		p.N69K(1)		breast(2)|kidney(1)|large_intestine(1)|lung(2)	6	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.43e-05)|Epithelial(140;0.00087)		CCTCTCGCAACGAGTTCGACC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	9											54	42	46					9																	140083672		2203	4299	6502	139203493	SO:0001583	missense	8636			Z96932	CCDS7034.1	9q34.3	2008-02-05	2007-10-04		ENSG00000176101	ENSG00000176101			11321	protein-coding gene	gene with protein product		610882	"Sjogren's syndrome nuclear autoantigen 1"			9430706	Standard	NM_003731		Approved	NA14, N14	uc004cls.2	O43805	OTTHUMG00000020982	ENST00000322310.5:c.207C>A	9.37:g.140083672C>A	ENSP00000313752:p.Asn69Lys		139203493	Q5VSG0|Q6FG70|Q9BVW8	Missense_Mutation	SNP	ENST00000322310.5	37	CCDS7034.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.600636	0.28534	.	.	ENSG00000176101	ENST00000322310	D	0.82711	-1.64	4.07	2.16	0.27623	.	0.192916	0.45361	D	0.000379	T	0.80082	0.4558	M	0.84683	2.71	0.35541	D	0.803026	B	0.20164	0.042	B	0.15484	0.013	T	0.73382	-0.4000	10	0.12103	T	0.63	-28.6855	8.7668	0.34708	0.0:0.7902:0.0:0.2098	.	69	O43805	SSNA1_HUMAN	K	69	ENSP00000313752:N69K	ENSP00000313752:N69K	N	+	3	2	SSNA1	139203493	0.652000	0.27349	1.000000	0.80357	0.995000	0.86356	0.080000	0.14802	0.827000	0.34685	0.561000	0.74099	AAC		0.642	SSNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055311.1	NM_003731		A	140083672	C	A	140083672	3	1	75	1	0	0	0	0	1	0	0	0	15226	535	19	2	213	2	SSNA1	9	140083672	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	53680083	140083672	1129759	115	21582										
KLF6	1316	broad.mit.edu	37	chr10	3824117	3824117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccgagctgaccaaaacttcgCcaatggggtcggaggtaaac	12	11	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:3824117C>T	ENST00000497571.1	-	2	652	c.392G>A	c.(391-393)gGc>gAc	p.G131D	KLF6_ENST00000542957.1_Missense_Mutation_p.G131D|KLF6_ENST00000173785.4_5'UTR|KLF6_ENST00000469435.1_Missense_Mutation_p.G131D	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	131					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G131D(1)		breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		CAAAACTTCGCCAATGGGGTC	0.542											OREG0019980	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	10											95	99	98					10																	3824117		2203	4300	6503	3814117	SO:0001583	missense	1316			U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.392G>A	10.37:g.3824117C>T	ENSP00000419923:p.Gly131Asp	614	3814117	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Missense_Mutation	SNP	ENST00000497571.1	37	CCDS7060.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172016	0.38315	.	.	ENSG00000067082	ENST00000497571;ENST00000542957;ENST00000469435	T;T;T	0.52983	3.35;0.64;0.87	4.99	4.99	0.66335	.	0.549231	0.21711	N	0.070267	T	0.49575	0.1565	M	0.62723	1.935	0.27205	N	0.960058	B;B;P;P	0.49783	0.29;0.076;0.928;0.79	B;B;B;B	0.44085	0.17;0.246;0.44;0.343	T	0.49771	-0.8904	10	0.23302	T	0.38	.	17.2727	0.87106	0.0:1.0:0.0:0.0	.	131;131;131;131	D3GC14;F5H3M5;Q99612-2;Q99612	.;.;.;KLF6_HUMAN	D	131	ENSP00000419923:G131D;ENSP00000445301:G131D;ENSP00000419079:G131D	ENSP00000419079:G131D	G	-	2	0	KLF6	3814117	0.923000	0.31300	0.650000	0.29550	0.169000	0.22640	4.858000	0.62947	2.309000	0.77851	0.561000	0.74099	GGC		0.542	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			T	3824117	C	T	3824117	3	4	75	1	0	0	0	0	1	0	0	0	8371	739	26	3	471	3	KLF6	10	3824117	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10		3824117	131710630	116	21583										
DHTKD1	55526	broad.mit.edu	37	chr10	12131190	12131190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcgcggcaggcagcagtctcGccaagacggcgattactctc	12	14	2	1	rs17849603		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:12131190G>A	ENST00000263035.4	+	5	985	c.923G>A	c.(922-924)cGc>cAc	p.R308H	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	308			R -> L (in dbSNP:rs17849603). {ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R308H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CAGCAGTCTCGCCAAGACGGC	0.607													G|||	1	0.000199681	0	0	5008	,	,		17379	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						G	HIS/ARG	0,4406		0,0,2203	63	60	61		923	3.2	0	10	dbSNP_123	61	1,8597	1.2+/-3.3	0,1,4298	no	missense	DHTKD1	NM_018706.5	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	308/920	12131190	1,13003	2203	4299	6502	12171196	SO:0001583	missense	55526			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.923G>A	10.37:g.12131190G>A	ENSP00000263035:p.Arg308His		12171196	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.53	1.376683	0.24857	0.0	1.16E-4	ENSG00000181192	ENST00000263035;ENST00000437298;ENST00000415935	T;T;D	0.90732	2.49;2.49;-2.72	5.43	3.19	0.36642	Dehydrogenase, E1 component (1);	0.417546	0.25032	N	0.033677	D	0.86176	0.5870	L	0.38953	1.18	0.09310	N	1	P	0.44734	0.842	P	0.47645	0.553	T	0.76828	-0.2815	10	0.36615	T	0.2	-10.0499	5.9275	0.19120	0.178:0.0:0.5744:0.2475	.	308	Q96HY7	DHTK1_HUMAN	H	308;243;6	ENSP00000263035:R308H;ENSP00000388163:R243H;ENSP00000400625:R6H	ENSP00000263035:R308H	R	+	2	0	DHTKD1	12171196	0.012000	0.17670	0.020000	0.16555	0.024000	0.10985	1.915000	0.39976	1.259000	0.44117	0.563000	0.77884	CGC		0.607	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		A	12131190	G	A	12131190	3	1	75	1	0	0	0	0	1	0	0	0	4511	1087	38	1	941	1	DHTKD1	10	12131190	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	8307073	12131190	123403557	117	21584										
NEBL	10529	broad.mit.edu	37	chr10	21074816	21074816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aaaggagacctcgtcttcatCctgggcactgtaatcgtaca	9	11	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:21074816C>T	ENST00000377122.4	-	28	3301	c.2905G>A	c.(2905-2907)Gat>Aat	p.D969N	NEBL_ENST00000417816.2_Missense_Mutation_p.D225N|NEBL_ENST00000377159.4_Missense_Mutation_p.D191N	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	969	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.D969N(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TCGTCTTCATCCTGGGCACTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	10											134	113	120					10																	21074816		2203	4300	6503	21114822	SO:0001583	missense	10529			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.2905G>A	10.37:g.21074816C>T	ENSP00000366326:p.Asp969Asn		21114822	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	35	5.496545	0.96355	.	.	ENSG00000078114	ENST00000377122;ENST00000417816;ENST00000377159	T;T;T	0.52526	0.66;0.66;0.66	5.84	5.84	0.93424	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.71796	0.3382	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.97110	0.995;1.0	T	0.71293	-0.4636	9	0.51188	T	0.08	.	20.1379	0.98040	0.0:1.0:0.0:0.0	.	225;969	Q70I54;O76041	.;NEBL_HUMAN	N	969;225;191	ENSP00000366326:D969N;ENSP00000393896:D225N;ENSP00000366364:D191N	ENSP00000366326:D969N	D	-	1	0	NEBL	21114822	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.803000	0.85983	2.779000	0.95612	0.655000	0.94253	GAT		0.498	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		T	21074816	C	T	21074816	3	4	75	1	0	0	0	0	1	0	0	0	10334	855	30	3	143	3	NEBL	10	21074816	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	8943626	21074816	114459931	118	21585										
BMS1	9790	broad.mit.edu	37	chr10	43325738	43325738	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aggcaaaagaaacattttaaTtcactgcacattccaaaagc	5	9	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:43325738T>G	ENST00000374518.5	+	22	3549	c.3486T>G	c.(3484-3486)aaT>aaG	p.N1162K	RNU6-885P_ENST00000516607.1_RNA	NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	1162					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.N1162K(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AACATTTTAATTCACTGCACA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	10											60	64	63					10																	43325738		2203	4298	6501	42645744	SO:0001583	missense	9790			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.3486T>G	10.37:g.43325738T>G	ENSP00000363642:p.Asn1162Lys		42645744	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665222	0.47677	.	.	ENSG00000165733	ENST00000374518	T	0.23552	1.9	4.78	1.03	0.20045	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.71920	2.185	0.41412	D	0.987744	D	0.69078	0.997	D	0.75484	0.986	T	0.15321	-1.0441	10	0.33141	T	0.24	.	9.4841	0.38919	0.0:0.3756:0.0:0.6244	.	1162	Q14692	BMS1_HUMAN	K	1162	ENSP00000363642:N1162K	ENSP00000363642:N1162K	N	+	3	2	BMS1	42645744	0.994000	0.37717	0.998000	0.56505	0.985000	0.73830	0.312000	0.19397	-0.008000	0.14320	0.254000	0.18369	AAT		0.413	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		G	43325738	T	G	43325738	3	3	75	1	0	0	0	0	1	0	0	0	1473	1490	52	4	3568	4	BMS1	10	43325738	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	22250922	43325738	92209009	119	21586										
KIF20B	9585	broad.mit.edu	37	chr10	91498179	91498179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tttggaaaaggaatctatcaTcttaaagctagaaagaaatt	7	4	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:91498179T>C	ENST00000371728.3	+	20	3646	c.3581T>C	c.(3580-3582)aTc>aCc	p.I1194T	KIF20B_ENST00000416354.1_Missense_Mutation_p.I1224T|KIF20B_ENST00000394289.2_Missense_Mutation_p.I1194T|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.I1154T	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1194					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.I1154T(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GAATCTATCATCTTAAAGCTA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	10											52	57	55					10																	91498179		2203	4296	6499	91488159	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3581T>C	10.37:g.91498179T>C	ENSP00000360793:p.Ile1194Thr		91488159	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	T	9.276	1.046894	0.19748	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.72835	-0.61;-0.63;-0.69;-0.62	5.82	5.82	0.92795	.	0.000000	0.51477	D	0.000094	T	0.65037	0.2653	L	0.52364	1.645	0.31004	N	0.71997	P;P	0.40970	0.615;0.734	B;B	0.39503	0.158;0.301	T	0.73607	-0.3929	10	0.72032	D	0.01	-9.9549	10.5104	0.44857	0.0:0.0721:0.0:0.9279	.	1194;1154	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	T	1154;1224;1194;1194	ENSP00000260753:I1154T;ENSP00000411545:I1224T;ENSP00000377830:I1194T;ENSP00000360793:I1194T	ENSP00000260753:I1154T	I	+	2	0	KIF20B	91488159	1.000000	0.71417	0.747000	0.31113	0.126000	0.20510	3.285000	0.51716	2.222000	0.72286	0.383000	0.25322	ATC		0.313	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		C	91498179	T	C	91498179	3	2	75	1	0	0	0	0	1	0	0	0	8308	1435	50	4	3535	4	KIF20B	10	91498179	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	48172441	91498179	44036568	120	21587										
KIF11	3832	broad.mit.edu	37	chr10	94368853	94368853	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgataatggtactgaattttCagtcaaagtgtctctgttgg	10	5	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:94368853C>T	ENST00000260731.3	+	5	554	c.464C>T	c.(463-465)tCa>tTa	p.S155L		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	155	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)	p.S155L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACTGAATTTTCAGTCAAAGTG	0.348																																					Colon(47;212 1003 2764 4062 8431)											1	Substitution - Missense(1)	large_intestine(1)	10											80	81	81					10																	94368853		2203	4300	6503	94358833	SO:0001583	missense	3832			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.464C>T	10.37:g.94368853C>T	ENSP00000260731:p.Ser155Leu		94358833	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	37	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893988	0.91889	.	.	ENSG00000138160	ENST00000260731	T	0.64618	-0.11	5.54	5.54	0.83059	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.73001	0.3531	L	0.41079	1.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67110	-0.5753	10	0.29301	T	0.29	.	19.6745	0.95926	0.0:1.0:0.0:0.0	.	155	P52732	KIF11_HUMAN	L	155	ENSP00000260731:S155L	ENSP00000260731:S155L	S	+	2	0	KIF11	94358833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.872000	0.69636	2.880000	0.98712	0.650000	0.86243	TCA		0.348	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		T	94368853	C	T	94368853	3	4	75	1	0	0	0	0	1	0	0	0	8293	838	29	3	482	3	KIF11	10	94368853	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	2870674	94368853	41165894	121	21588										
GOLGA7B	401647	broad.mit.edu	37	chr10	99623796	99623796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gggctgcctggcctgcgccaCggcctacttcatcttcctct	10	17	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:99623796C>T	ENST00000370602.1	+	3	313	c.248C>T	c.(247-249)aCg>aTg	p.T83M		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	83				T -> M (in Ref. 2; AAI10811). {ECO:0000305}.		Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.T83M(1)		endometrium(1)|large_intestine(3)|prostate(1)	5						GCCTGCGCCACGGCCTACTTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10											49	51	51					10																	99623796		2203	4300	6503	99613786	SO:0001583	missense	401647			BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.248C>T	10.37:g.99623796C>T	ENSP00000359634:p.Thr83Met		99613786	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	37	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598387	0.66332	.	.	ENSG00000155265	ENST00000370602	.	.	.	5.31	5.31	0.75309	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	D	0.84465	0.5478	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86566	0.1844	9	0.72032	D	0.01	-30.2452	17.9131	0.88940	0.0:1.0:0.0:0.0	.	83	Q2TAP0	GOG7B_HUMAN	M	83	.	ENSP00000359634:T83M	T	+	2	0	GOLGA7B	99613786	1.000000	0.71417	0.956000	0.39512	0.010000	0.07245	7.651000	0.83577	2.779000	0.95612	0.655000	0.94253	ACG		0.607	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917		T	99623796	C	T	99623796	3	4	75	1	0	0	0	0	1	0	0	0	6582	536	19	1	258	1	GOLGA7B	10	99623796	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	5254943	99623796	35910951	122	21589										
ACTR1A	10121	broad.mit.edu	37	chr10	104243990	104243990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctccttacgcaggtagaggCgcaggaagcgagagacgtcc	14	12	0	2	rs368237331		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:104243990C>T	ENST00000369905.4	-	6	647	c.584G>A	c.(583-585)cGc>cAc	p.R195H	RP11-18I14.11_ENST00000608017.1_RNA|ACTR1A_ENST00000446605.2_Missense_Mutation_p.R148H|ACTR1A_ENST00000487599.1_Missense_Mutation_p.R195H|ACTR1A_ENST00000470322.1_5'Flank|ACTR1A_ENST00000545684.1_Missense_Mutation_p.R121H	NM_005736.3	NP_005727.1	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A, centractin alpha (yeast)	195					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|microtubule associated complex (GO:0005875)	ATP binding (GO:0005524)	p.R195H(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	13		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		CAGGTAGAGGCGCAGGAAGCG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10						C	HIS/ARG	0,4406		0,0,2203	97	90	92		584	5.7	1	10		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACTR1A	NM_005736.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	195/377	104243990	1,13005	2203	4300	6503	104233980	SO:0001583	missense	10121			X82206	CCDS7536.1	10q24	2008-07-08	2001-11-28		ENSG00000138107	ENSG00000138107			167	protein-coding gene	gene with protein product		605143	"ARP1 (actin-related protein 1, yeast) homolog A (centractin alpha)"			1528266	Standard	NM_005736		Approved	ARP1	uc001kvv.3	P61163	OTTHUMG00000018956	ENST00000369905.4:c.584G>A	10.37:g.104243990C>T	ENSP00000358921:p.Arg195His		104233980	B2R6B0|P42024	Missense_Mutation	SNP	ENST00000369905.4	37	CCDS7536.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605157	0.66445	0.0	1.16E-4	ENSG00000138107	ENST00000369905;ENST00000545684;ENST00000446605	T;T;T	0.08282	3.11;3.11;3.11	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.14743	0.0356	M	0.64170	1.965	0.80722	D	1	B	0.15719	0.014	B	0.18263	0.021	T	0.02184	-1.1199	10	0.87932	D	0	.	19.7891	0.96450	0.0:1.0:0.0:0.0	.	195	P61163	ACTZ_HUMAN	H	195;121;148	ENSP00000358921:R195H;ENSP00000438890:R121H;ENSP00000406028:R148H	ENSP00000358921:R195H	R	-	2	0	ACTR1A	104233980	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.738000	0.62073	2.692000	0.91855	0.561000	0.74099	CGC		0.577	ACTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050053.1			T	104243990	C	T	104243990	3	4	75	1	0	0	0	0	1	0	0	0	209	768	27	1	570	1	ACTR1A	10	104243990	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	4620194	104243990	31290757	123	21590										
ATRNL1	26033	broad.mit.edu	37	chr10	117061475	117061475	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgtggtgcagcagtacgaaaCgatgtgttgactctaatgcc	12	8	1	1	rs555650933		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:117061475C>T	ENST00000355044.3	+	17	2866	c.2740C>T	c.(2740-2742)Cga>Tga	p.R914*	ATRNL1_ENST00000423111.2_Nonsense_Mutation_p.R11*|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	914	PSI 4.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R914*(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CAGTACGAAACGATGTGTTGA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											292	214	241					10																	117061475		2203	4300	6503	117051465	SO:0001587	stop_gained	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2740C>T	10.37:g.117061475C>T	ENSP00000347152:p.Arg914*		117051465	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Nonsense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.247262|7.247262	0.98161|0.98161	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000355044;ENST00000423111|ENST00000526373	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76506	.|0.3997	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74630	.|-0.3601	.|4	0.02654|.	T|.	1|.	-5.4211|-5.4211	19.7031|19.7031	0.96063|0.96063	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|M	914;11|43	.|.	ENSP00000347152:R914X|.	R|T	+|+	1|2	2|0	ATRNL1|ATRNL1	117051465|117051465	1.000000|1.000000	0.71417|0.71417	0.142000|0.142000	0.22268|0.22268	0.861000|0.861000	0.49209|0.49209	7.730000|7.730000	0.84881|0.84881	2.664000|2.664000	0.90586|0.90586	0.591000|0.591000	0.81541|0.81541	CGA|ACG		0.453	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117061475	C	T	117061475	4	4	75	1	0	0	0	0	0	1	0	0	1208	528	19	1	2806	1	ATRNL1	10	117061475	Nonsense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	12817485	117061475	18473272	124	21591										
DOCK1	1793	broad.mit.edu	37	chr10	128824642	128824642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attcccatcgaggacgttaaCcgcagtcaccttcggtttac	8	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:128824642C>T	ENST00000280333.6	+	16	1624	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	RP11-223P11.3_ENST00000432554.2_RNA|RP11-223P11.3_ENST00000608350.1_RNA|RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000599979.1_RNA|RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.3_ENST00000594559.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA|RP11-223P11.2_ENST00000420941.2_RNA|RP11-223P11.3_ENST00000601826.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	505	DHR-1.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.N505N(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGGACGTTAACCGCAGTCACC	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	10											74	74	74					10																	128824642		1955	4144	6099	128714632	SO:0001819	synonymous_variant	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1515C>T	10.37:g.128824642C>T			128714632	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																					0.458	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	128824642	C	T	128824642	2	4	75	1	0	0	0	0	0	0	0	1	4695	506	18	3		3	DOCK1	10	128824642	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	11763167	128824642	6710105	125	21592										
FAM196A	642938	broad.mit.edu	37	chr10	128973764	128973764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccagggcagtttccgagggcGcctggagcccgttgagatgt	16	11	0	1	rs150869481		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr10:128973764G>A	ENST00000522781.1	-	4	1451	c.896C>T	c.(895-897)gCg>gTg	p.A299V	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.A299V	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	299								p.A299V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TTCCGAGGGCGCCTGGAGCCC	0.677													G|||	1	0.000199681	8e-04	0	5008	,	,		15789	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						G	VAL/ALA,	0,4406		0,0,2203	30	33	32		896,	-3.3	0	10	dbSNP_134	32	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	64,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,	299/480,	128973764	1,13005	2203	4300	6503	128863754	SO:0001583	missense	642938				CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 141"	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.896C>T	10.37:g.128973764G>A	ENSP00000429763:p.Ala299Val		128863754	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	37	CCDS31312.1	.	.	.	.	.	.	.	.	.	.	G	7.165	0.586482	0.13749	0.0	1.16E-4	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.44881	0.91;0.91	4.69	-3.33	0.04958	.	0.528179	0.21148	N	0.079380	T	0.27027	0.0662	L	0.35723	1.085	0.09310	N	1	B;B	0.18310	0.027;0.015	B;B	0.12837	0.008;0.007	T	0.16158	-1.0412	10	0.46703	T	0.11	.	9.3448	0.38102	0.1361:0.4551:0.4089:0.0	.	299;299	B7ZME7;Q6ZSG2	.;F196A_HUMAN	V	299	ENSP00000429763:A299V;ENSP00000428730:A299V	ENSP00000428730:A299V	A	-	2	0	FAM196A	128863754	0.192000	0.23301	0.014000	0.15608	0.025000	0.11179	0.594000	0.24014	-0.470000	0.06901	-0.214000	0.12660	GCG		0.677	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762		A	128973764	G	A	128973764	3	1	75	1	0	0	0	0	1	0	0	0	5544	1087	38	1	555	1	FAM196A	10	128973764	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	149122	128973764	6560983	126	21593										
BTBD10	84280	broad.mit.edu	37	chr11	13410492	13410492	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggatgcatgactaccagctgGtcctggggaatgtctgctgc	14	10	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:13410492G>C	ENST00000278174.5	-	9	1559	c.1314C>G	c.(1312-1314)gaC>gaG	p.D438E	BTBD10_ENST00000530907.1_Missense_Mutation_p.D446E|BTBD10_ENST00000528120.1_Missense_Mutation_p.D390E	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	438	Interaction with AKT family members. {ECO:0000250|UniProtKB:Q80X66}.					nucleus (GO:0005634)		p.D438E(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		CTACCAGCTGGTCCTGGGGAA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	11											137	121	126					11																	13410492		2200	4294	6494	13367068	SO:0001583	missense	84280			AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"BTB/POZ domain containing"	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.1314C>G	11.37:g.13410492G>C	ENSP00000278174:p.Asp438Glu		13367068	B7Z228|Q86WG1	Missense_Mutation	SNP	ENST00000278174.5	37	CCDS7811.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.223663	0.58668	.	.	ENSG00000148925	ENST00000278174;ENST00000530907;ENST00000528120	D;D;D	0.82433	-1.61;-1.61;-1.61	5.03	2.01	0.26516	.	0.000000	0.85682	D	0.000000	T	0.78679	0.4321	L	0.29908	0.895	0.58432	D	0.99999	D;D;D	0.58970	0.984;0.984;0.984	P;P;P	0.54238	0.746;0.679;0.679	T	0.72606	-0.4242	10	0.23302	T	0.38	.	9.8146	0.40844	0.238:0.0:0.762:0.0	.	446;438;438	B7Z228;D3DQW7;Q9BSF8	.;.;BTBDA_HUMAN	E	438;446;390	ENSP00000278174:D438E;ENSP00000431186:D446E;ENSP00000435257:D390E	ENSP00000278174:D438E	D	-	3	2	BTBD10	13367068	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.334000	0.52097	0.662000	0.31006	0.555000	0.69702	GAC		0.498	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320		C	13410492	G	C	13410492	3	2	75	1	0	0	0	0	1	0	0	0	1541	1252	44	5	117	5	BTBD10	11	13410492	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		13410492	121596024	127	21594										
CAT	847	broad.mit.edu	37	chr11	34489852	34489852	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caggtgcgggcattctatgtGaacgtgctgaatgaggaaca	14	7	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:34489852G>C	ENST00000241052.4	+	11	1433	c.1344G>C	c.(1342-1344)gtG>gtC	p.V448V		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	448					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.V448V(1)		breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	CATTCTATGTGAACGTGCTGA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	11											130	130	130					11																	34489852		2202	4298	6500	34446428	SO:0001819	synonymous_variant	847			AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.1344G>C	11.37:g.34489852G>C			34446428	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Silent	SNP	ENST00000241052.4	37	CCDS7891.1																																																																																				0.443	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		C	34489852	G	C	34489852	2	2	75	1	0	0	0	0	0	0	0	1	2692	1277	45	5		5	CAT	11	34489852	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	21079360	34489852	100516664	128	21595										
OR8K1	390157	broad.mit.edu	37	chr11	56113842	56113842	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atgccactcagctagcattcTttgagattttcatcatctct	5	11	5	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:56113842T>G	ENST00000279783.2	+	1	422	c.328T>G	c.(328-330)Ttt>Gtt	p.F110V		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F110V(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					GCTAGCATTCTTTGAGATTTT	0.408										HNSCC(65;0.19)																																						1	Substitution - Missense(1)	large_intestine(1)	11											180	181	181					11																	56113842		2201	4296	6497	55870418	SO:0001583	missense	390157			AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.328T>G	11.37:g.56113842T>G	ENSP00000279783:p.Phe110Val		55870418	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.092695	0.36952	.	.	ENSG00000150261	ENST00000279783	T	0.00377	7.69	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000079	T	0.00328	0.0010	M	0.63428	1.95	0.09310	N	1	P	0.45474	0.859	B	0.37833	0.259	T	0.52155	-0.8613	10	0.72032	D	0.01	-22.2381	9.2	0.37251	0.0:0.1335:0.0:0.8665	.	110	Q8NGG5	OR8K1_HUMAN	V	110	ENSP00000279783:F110V	ENSP00000279783:F110V	F	+	1	0	OR8K1	55870418	0.756000	0.28383	0.630000	0.29268	0.991000	0.79684	1.479000	0.35453	1.862000	0.54008	0.448000	0.29417	TTT		0.408	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		G	56113842	T	G	56113842	3	3	75	1	0	0	0	0	1	0	0	0	11274	1609	56	4	330	4	OR8K1	11	56113842	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	21623990	56113842	78892674	129	21596										
CCDC86	79080	broad.mit.edu	37	chr11	60615429	60615429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcttcaggacaagcccctgcGcacatcgtggcagcggaaga	13	13	1	1	rs376975583		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:60615429G>A	ENST00000227520.5	+	2	845	c.791G>A	c.(790-792)cGc>cAc	p.R264H	RP11-804A23.4_ENST00000538705.1_RNA|CCDC86_ENST00000545580.1_Missense_Mutation_p.R8H	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	264					viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R264H(1)		endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						AAGCCCCTGCGCACATCGTGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	110	104	106		791	1.3	1	11		106	0,8598		0,0,4299	no	missense	CCDC86	NM_024098.3	29	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	264/361	60615429	1,13003	2203	4299	6502	60372005	SO:0001583	missense	79080			AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.791G>A	11.37:g.60615429G>A	ENSP00000227520:p.Arg264His		60372005	B4DY99	Missense_Mutation	SNP	ENST00000227520.5	37	CCDS7993.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.801352	0.31869	2.27E-4	0.0	ENSG00000110104	ENST00000227520;ENST00000545580	T	0.50548	0.74	5.3	1.33	0.21861	.	0.203884	0.42548	N	0.000682	T	0.37461	0.1004	L	0.52206	1.635	0.38152	D	0.938767	B	0.10296	0.003	B	0.06405	0.002	T	0.21690	-1.0238	10	0.40728	T	0.16	-5.176	8.4444	0.32833	0.3236:0.0:0.6764:0.0	.	264	Q9H6F5	CCD86_HUMAN	H	264;8	ENSP00000227520:R264H	ENSP00000227520:R264H	R	+	2	0	CCDC86	60372005	0.648000	0.27313	0.983000	0.44433	0.747000	0.42532	0.419000	0.21247	0.243000	0.21327	-0.948000	0.02665	CGC		0.617	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098		A	60615429	G	A	60615429	3	1	75	1	0	0	0	0	1	0	0	0	2867	1087	38	1	797	1	CCDC86	11	60615429	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4501587	60615429	74391087	130	21597										
SYT7	9066	broad.mit.edu	37	chr11	61290608	61290608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgacagtgatgatgatggtcGtctccctcagcttctccgtg	11	11	3	4			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:61290608G>A	ENST00000263846.4	-	8	1373	c.1046C>T	c.(1045-1047)aCg>aTg	p.T349M	SYT7_ENST00000542836.1_Missense_Mutation_p.T393M|SYT7_ENST00000540831.1_5'Flank|SYT7_ENST00000535826.1_Missense_Mutation_p.T468M|SYT7_ENST00000539008.1_Missense_Mutation_p.T632M|SYT7_ENST00000540677.1_Missense_Mutation_p.T424M|SYT7_ENST00000542670.1_Missense_Mutation_p.T557M	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	349	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)	p.T349M(2)		kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GATGATGGTCGTCTCCCTCAG	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	11											290	226	248					11																	61290608		2202	4299	6501	61047184	SO:0001583	missense	9066			AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"Synaptotagmins"	11514	protein-coding gene	gene with protein product		604146	"prostate cancer associated protein 7"	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.1046C>T	11.37:g.61290608G>A	ENSP00000263846:p.Thr349Met		61047184	F5GZU9|Q08AH6	Missense_Mutation	SNP	ENST00000263846.4	37	CCDS31577.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126586	0.77549	.	.	ENSG00000011347	ENST00000263846;ENST00000540677;ENST00000539008;ENST00000542836;ENST00000542670;ENST00000535826	T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	4.64	4.64	0.57946	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.85682	D	0.000000	T	0.75989	0.3925	L	0.28608	0.87	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.67725	0.921;0.953	T	0.77213	-0.2670	10	0.48119	T	0.1	.	18.1087	0.89528	0.0:0.0:1.0:0.0	.	424;349	F5GZU9;O43581	.;SYT7_HUMAN	M	349;424;632;393;557;468	ENSP00000263846:T349M;ENSP00000444201:T424M;ENSP00000439694:T632M;ENSP00000444568:T393M;ENSP00000444019:T557M;ENSP00000437720:T468M	ENSP00000263846:T349M	T	-	2	0	SYT7	61047184	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	4.829000	0.62737	2.583000	0.87209	0.561000	0.74099	ACG		0.567	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		A	61290608	G	A	61290608	3	1	75	1	0	0	0	0	1	0	0	0	15518	1145	40	1	173	1	SYT7	11	61290608	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	675179	61290608	73715908	131	21598										
ALG8	79053	broad.mit.edu	37	chr11	77815451	77815451	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gaataatgtcctgttgtggtCagaatcagaaaaatcgaagc	10	6	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:77815451C>G	ENST00000299626.5	-	11	1298	c.1227G>C	c.(1225-1227)ctG>ctC	p.L409L	ALG8_ENST00000532552.2_5'UTR|ALG8_ENST00000376156.3_Silent_p.L409L	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	409					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)	p.L409L(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			CTGTTGTGGTCAGAATCAGAA	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	11											70	71	70					11																	77815451		2200	4292	6492	77493099	SO:0001819	synonymous_variant	79053			AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	608103	"asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1227G>C	11.37:g.77815451C>G			77493099	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	37	CCDS8258.1	.	.	.	.	.	.	.	.	.	.	C	8.594	0.885232	0.17540	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.3337	18.8103	0.92056	0.0:1.0:0.0:0.0	.	.	.	.	S	111;196	.	.	X	-	2	2	ALG8	77493099	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.842000	0.39250	2.507000	0.84556	0.655000	0.94253	TGA		0.358	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		G	77815451	C	G	77815451	2	3	75	1	0	0	0	0	0	0	0	1	523	813	29	5		5	ALG8	11	77815451	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	16524843	77815451	57191065	132	21599										
ME3	10873	broad.mit.edu	37	chr11	86158137	86158137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cggtagcacttctcagccgtGcactcggccttgctggtggg	14	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:86158137G>A	ENST00000393324.3	-	11	1603	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	ME3_ENST00000543262.1_Silent_p.C450C|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Silent_p.C450C	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	450					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.C450C(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				TCTCAGCCGTGCACTCGGCCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											68	60	63					11																	86158137		2202	4299	6501	85835785	SO:0001819	synonymous_variant	10873			X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1350C>T	11.37:g.86158137G>A			85835785	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																				0.582	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2			A	86158137	G	A	86158137	2	1	75	1	0	0	0	0	0	0	0	1	9449	1311	46	3		3	ME3	11	86158137	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	8342686	86158137	48848379	133	21600										
FAT3	120114	broad.mit.edu	37	chr11	92086535	92086535	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctggtgaggatgcagtgtaCtttaaaattaatcctcggtc	10	8	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:92086535C>T	ENST00000298047.6	+	1	1274	c.1257C>T	c.(1255-1257)taC>taT	p.Y419Y	FAT3_ENST00000409404.2_Silent_p.Y419Y|FAT3_ENST00000541502.1_Silent_p.Y419Y|FAT3_ENST00000525166.1_Silent_p.Y269Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	419	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y419Y(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATGCAGTGTACTTTAAAATTA	0.423										TCGA Ovarian(4;0.039)																																						2	Substitution - coding silent(2)	large_intestine(2)	11											65	61	62					11																	92086535		1855	4092	5947	91726183	SO:0001819	synonymous_variant	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1257C>T	11.37:g.92086535C>T			91726183	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.423	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92086535	C	T	92086535	2	4	75	1	0	0	0	0	0	0	0	1	5710	576	20	3		3	FAT3	11	92086535	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	5928398	92086535	42919981	134	21601										
OR6M1	390261	broad.mit.edu	37	chr11	123676334	123676334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggcaatggagacaacagtgaTgtgagaagcacaggtagaaa	14	5	0	4			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr11:123676334T>C	ENST00000309154.2	-	1	761	c.724A>G	c.(724-726)Atc>Gtc	p.I242V		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I242V(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		ACAACAGTGATGTGAGAAGCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	11											100	85	90					11																	123676334		2202	4299	6501	123181544	SO:0001583	missense	390261			AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.724A>G	11.37:g.123676334T>C	ENSP00000311038:p.Ile242Val		123181544	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	T	7.959	0.746509	0.15710	.	.	ENSG00000196099	ENST00000309154	T	0.37058	1.22	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33691	U	0.004659	T	0.22781	0.0550	N	0.21240	0.645	0.25205	N	0.990022	B	0.32968	0.392	B	0.33960	0.173	T	0.15321	-1.0441	10	0.62326	D	0.03	.	6.7148	0.23296	0.0:0.0:0.2428:0.7572	.	242	Q8NGM8	OR6M1_HUMAN	V	242	ENSP00000311038:I242V	ENSP00000311038:I242V	I	-	1	0	OR6M1	123181544	0.224000	0.23674	0.146000	0.22360	0.212000	0.24457	0.053000	0.14184	1.432000	0.47375	0.533000	0.62120	ATC		0.502	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		C	123676334	T	C	123676334	3	2	75	1	0	0	0	0	1	0	0	0	11236	1464	51	4	220	4	OR6M1	11	123676334	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	31589799	123676334	11330182	135	21602										
CACNA1C	775	broad.mit.edu	37	chr12	2705069	2705069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccagtgccaccgcattgtcaAtgacacgatcttcaccaacc	6	16	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:2705069A>G	ENST00000347598.4	+	20	2693	c.2693A>G	c.(2692-2694)aAt>aGt	p.N898S	CACNA1C_ENST00000402845.3_Missense_Mutation_p.N898S|CACNA1C_ENST00000399591.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399606.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399597.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399641.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000327702.7_Missense_Mutation_p.N898S|CACNA1C_ENST00000335762.5_Missense_Mutation_p.N923S|CACNA1C_ENST00000399638.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399617.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399649.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399634.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000344100.3_Missense_Mutation_p.N898S|CACNA1C_ENST00000399621.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000406454.3_Missense_Mutation_p.N898S|CACNA1C_ENST00000480911.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399603.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399595.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399601.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399629.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399644.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399655.1_Missense_Mutation_p.N898S|CACNA1C_ENST00000399637.1_Missense_Mutation_p.N898S	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	898					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.N928S(1)|p.N433S(1)|p.N898S(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGCATTGTCAATGACACGATC	0.567																																																3	Substitution - Missense(3)	large_intestine(3)	12											125	126	125					12																	2705069		2101	4222	6323	2575330	SO:0001583	missense	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.2693A>G	12.37:g.2705069A>G	ENSP00000266376:p.Asn898Ser		2575330	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306732	0.81247	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96334	-3.92;-3.92;-3.91;-3.91;-3.9;-3.93;-3.93;-3.83;-3.86;-3.92;-3.85;-3.86;-3.92;-3.95;-3.82;-3.76;-3.98;-3.93;-3.94;-3.94;-3.85;-3.94;-3.98	4.93	4.93	0.64822	.	0.045287	0.85682	D	0.000000	D	0.97545	0.9196	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.996;0.999;0.987;0.982;0.993;0.999;0.99;0.967;0.996;0.982;0.999;0.998;0.564;0.998;0.997;0.997;0.99;0.997;0.999;0.969;0.99;0.999;0.999;0.999;0.974;0.999	D;D;P;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;P;D;D;D;D;D;D	0.81914	0.99;0.994;0.858;0.952;0.99;0.994;0.96;0.969;0.937;0.918;0.994;0.987;0.406;0.995;0.97;0.989;0.979;0.938;0.994;0.845;0.979;0.994;0.994;0.991;0.969;0.99	D	0.98338	1.0537	10	0.87932	D	0	.	14.7299	0.69374	1.0:0.0:0.0:0.0	.	898;895;898;898;898;898;898;898;898;898;898;898;869;898;898;898;898;898;898;898;898;898;898;898;898;898	Q13936-14;Q13936-35;Q13936;E9PDI6;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	923;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;898;739	ENSP00000336982:N923S;ENSP00000382563:N898S;ENSP00000437936:N898S;ENSP00000382552:N898S;ENSP00000382547:N898S;ENSP00000382506:N898S;ENSP00000382530:N898S;ENSP00000382546:N898S;ENSP00000382500:N898S;ENSP00000382549:N898S;ENSP00000266376:N898S;ENSP00000382515:N898S;ENSP00000382510:N898S;ENSP00000341092:N898S;ENSP00000382537:N898S;ENSP00000329877:N898S;ENSP00000382557:N898S;ENSP00000385724:N898S;ENSP00000382512:N898S;ENSP00000382542:N898S;ENSP00000382526:N898S;ENSP00000385896:N898S;ENSP00000382504:N898S	ENSP00000323129:N739S	N	+	2	0	CACNA1C	2575330	1.000000	0.71417	0.987000	0.45799	0.738000	0.42128	9.053000	0.93860	2.074000	0.62210	0.455000	0.32223	AAT		0.567	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		G	2705069	A	G	2705069	3	3	75	1	0	0	0	0	1	0	0	0	2546	101	4	4	2879	4	CACNA1C	12	2705069	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10		2705069	131146826	136	21603										
VWF	7450	broad.mit.edu	37	chr12	6128449	6128449	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catcaggagcagggtgatgcGggaggcttcagggcggtcga	19	8	2	1	rs61750074		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:6128449G>A	ENST00000261405.5	-	28	4389	c.4135C>T	c.(4135-4137)Cgc>Tgc	p.R1379C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1379	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.R1379C(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	AGGGTGATGCGGGAGGCTTCA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12	GRCh37	CM011508	VWF	M	rs61750074						48	49	49					12																	6128449		2203	4300	6503	5998710	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4135C>T	12.37:g.6128449G>A	ENSP00000261405:p.Arg1379Cys		5998710	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	16.34	3.094678	0.56075	.	.	ENSG00000110799	ENST00000261405	D	0.84370	-1.84	4.98	4.98	0.66077	von Willebrand factor, type A (3);	0.328267	0.22298	N	0.061915	D	0.94571	0.8251	H	0.96970	3.915	0.49299	D	0.999777	D	0.89917	1.0	D	0.85130	0.997	D	0.95356	0.8451	10	0.72032	D	0.01	.	12.1622	0.54110	0.0:0.0:0.7174:0.2826	rs61750074	1379	P04275	VWF_HUMAN	C	1379	ENSP00000261405:R1379C	ENSP00000261405:R1379C	R	-	1	0	VWF	5998710	1.000000	0.71417	0.560000	0.28344	0.736000	0.42039	4.514000	0.60482	2.605000	0.88082	0.555000	0.69702	CGC		0.577	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6128449	G	A	6128449	3	1	75	1	0	0	0	0	1	0	0	0	17286	1116	39	1	4406	1	VWF	12	6128449	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	3423380	6128449	127723446	137	21604										
CLEC2B	9976	broad.mit.edu	37	chr12	10015151	10015151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caccaacaattataaaacacTttttatgtttggtcatcata	3	8	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:10015151T>C	ENST00000228438.2	-	2	953	c.20A>G	c.(19-21)aAg>aGg	p.K7R		NM_005127.2	NP_005118.2	Q92478	CLC2B_HUMAN	C-type lectin domain family 2, member B	7						integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.K7R(1)		endometrium(1)|large_intestine(3)|lung(1)	5						TATAAAACACTTTTTATGTTT	0.289																																																1	Substitution - Missense(1)	large_intestine(1)	12											23	25	24					12																	10015151		2179	4264	6443	9906418	SO:0001583	missense	9976			X96719	CCDS8605.1	12p13-p12	2005-02-09	2005-02-09	2005-02-09		ENSG00000110852		"C-type lectin domain containing"	2053	protein-coding gene	gene with protein product		603242	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 2 (activation-induced)"	CLECSF2		9038101	Standard	NM_005127		Approved	AICL, HP10085	uc001qwn.3	Q92478		ENST00000228438.2:c.20A>G	12.37:g.10015151T>C	ENSP00000228438:p.Lys7Arg		9906418	B2R9U1|Q8IZE9|Q9BS74|Q9UQB4	Missense_Mutation	SNP	ENST00000228438.2	37	CCDS8605.1	.	.	.	.	.	.	.	.	.	.	T	1.746	-0.490426	0.04322	.	.	ENSG00000110852	ENST00000228438	T	0.02050	4.48	1.39	-2.78	0.05859	.	.	.	.	.	T	0.01320	0.0043	L	0.36672	1.1	0.09310	N	1	P	0.37233	0.588	B	0.24541	0.054	T	0.46484	-0.9188	9	0.18276	T	0.48	.	2.6243	0.04925	0.49:0.0:0.218:0.2919	.	7	Q92478	CLC2B_HUMAN	R	7	ENSP00000228438:K7R	ENSP00000228438:K7R	K	-	2	0	CLEC2B	9906418	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.918000	0.00695	-1.242000	0.02523	0.402000	0.26972	AAG		0.289	CLEC2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399881.1	NM_005127		C	10015151	T	C	10015151	3	2	75	1	0	0	0	0	1	0	0	0	3513	1609	56	4	445	4	CLEC2B	12	10015151	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	3886702	10015151	123836744	138	21605										
TAS2R8	50836	broad.mit.edu	37	chr12	10959213	10959213	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caccatatcaattttccactTcagccagagaaaaagtggat	6	10	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:10959213T>G	ENST00000240615.2	-	1	679	c.367A>C	c.(367-369)Aag>Cag	p.K123Q		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	123					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.K123Q(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						ATTTTCCACTTCAGCCAGAGA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											78	75	76					12																	10959213		2203	4300	6503	10850480	SO:0001583	missense	50836			AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.367A>C	12.37:g.10959213T>G	ENSP00000240615:p.Lys123Gln		10850480	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	37	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.491878	0.44352	.	.	ENSG00000121314	ENST00000240615	T	0.01505	4.82	5.1	3.96	0.45880	GPCR, rhodopsin-like superfamily (1);	0.200108	0.29212	U	0.012815	T	0.12008	0.0292	M	0.90977	3.165	0.24839	N	0.992474	D	0.89917	1.0	D	0.87578	0.998	T	0.06391	-1.0829	10	0.87932	D	0	.	8.9116	0.35557	0.0:0.0904:0.0:0.9096	.	123	Q9NYW2	TA2R8_HUMAN	Q	123	ENSP00000240615:K123Q	ENSP00000240615:K123Q	K	-	1	0	TAS2R8	10850480	0.965000	0.33210	0.746000	0.31095	0.187000	0.23431	2.626000	0.46460	0.786000	0.33708	0.455000	0.32223	AAG		0.418	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1			G	10959213	T	G	10959213	3	3	75	1	0	0	0	0	1	0	0	0	15626	1792	62	4	565	4	TAS2R8	12	10959213	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	944062	10959213	122892682	139	21606										
ERP27	121506	broad.mit.edu	37	chr12	15067698	15067698	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cacctttggagtctttccttCtgattcacgattttctttct	5	11	5	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:15067698C>G	ENST00000266397.2	-	7	1366	c.793G>C	c.(793-795)Gaa>Caa	p.E265Q	ERP27_ENST00000544881.1_5'Flank|ERP27_ENST00000540097.1_Missense_Mutation_p.E164Q	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	265						endoplasmic reticulum (GO:0005783)		p.E265Q(1)		breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						GTCTTTCCTTCTGATTCACGA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											183	157	165					12																	15067698		2203	4300	6503	14958965	SO:0001583	missense	121506			AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"Protein disulfide isomerases"	26495	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 8"	610642	"chromosome 12 open reading frame 46", "endoplasmic reticulum protein 27 kDa"	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.793G>C	12.37:g.15067698C>G	ENSP00000266397:p.Glu265Gln		14958965		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	C	8.146	0.786238	0.16189	.	.	ENSG00000139055	ENST00000266397;ENST00000540097	T;T	0.53640	1.51;0.61	4.54	3.65	0.41850	Thioredoxin-like fold (1);	0.116253	0.56097	D	0.000024	T	0.40839	0.1133	L	0.55481	1.735	0.37780	D	0.926996	B	0.14438	0.01	B	0.18263	0.021	T	0.43556	-0.9384	10	0.45353	T	0.12	-0.1396	8.7204	0.34436	0.0:0.8988:0.0:0.1012	.	265	Q96DN0	ERP27_HUMAN	Q	265;164	ENSP00000266397:E265Q;ENSP00000440573:E164Q	ENSP00000266397:E265Q	E	-	1	0	ERP27	14958965	0.988000	0.35896	0.931000	0.37212	0.087000	0.18053	1.535000	0.36061	1.521000	0.48983	0.655000	0.94253	GAA		0.348	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321		G	15067698	C	G	15067698	3	3	75	1	0	0	0	0	1	0	0	0	5254	922	32	5	32	5	ERP27	12	15067698	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	4108485	15067698	118784197	140	21607										
LRMP	4033	broad.mit.edu	37	chr12	25232638	25232638	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttcttgtgaccttgacagaaActcgctctgtaagaaagagg	10	8	2	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:25232638A>T	ENST00000354454.3	+	8	1014	c.185A>T	c.(184-186)aAc>aTc	p.N62I	LRMP_ENST00000548766.1_Missense_Mutation_p.N62I|LRMP_ENST00000547044.1_Missense_Mutation_p.N62I	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	118					immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)		p.N62I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					CTTGACAGAAACTCGCTCTGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	12											110	109	109					12																	25232638		2203	4300	6503	25123905	SO:0001583	missense	4033				CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.185A>T	12.37:g.25232638A>T	ENSP00000346442:p.Asn62Ile		25123905	A0AVM2|B4E077|Q8N301	Missense_Mutation	SNP	ENST00000354454.3	37	CCDS8701.1	.	.	.	.	.	.	.	.	.	.	A	7.040	0.562318	0.13498	.	.	ENSG00000118308	ENST00000550945;ENST00000557489;ENST00000354454;ENST00000536173;ENST00000548766;ENST00000554942;ENST00000547044	T;T;T;T;T;T;T	0.15256	2.44;2.44;2.44;2.44;2.44;2.44;2.44	4.55	3.4	0.38934	.	0.258068	0.28724	N	0.014342	T	0.08802	0.0218	N	0.08118	0	0.09310	N	1	B	0.28082	0.2	B	0.32864	0.154	T	0.21075	-1.0256	10	0.62326	D	0.03	-13.5205	5.5966	0.17331	0.8612:0.0:0.1388:0.0	.	118	Q12912	LRMP_HUMAN	I	62;62;62;9;62;62;62	ENSP00000448534:N62I;ENSP00000452116:N62I;ENSP00000346442:N62I;ENSP00000444056:N9I;ENSP00000446496:N62I;ENSP00000450634:N62I;ENSP00000450246:N62I	ENSP00000346442:N62I	N	+	2	0	LRMP	25123905	0.008000	0.16893	0.037000	0.18230	0.002000	0.02628	1.148000	0.31614	0.877000	0.35895	0.491000	0.48974	AAC		0.378	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152		T	25232638	A	T	25232638	3	4	75	1	0	0	0	0	1	0	0	0	8979	43	2	5	199	5	LRMP	12	25232638	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	10164940	25232638	108619257	141	21608										
GXYLT1	283464	broad.mit.edu	37	chr12	42523599	42523599	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aagcagttcattccacaaacAtcagagggcagcatccaata	7	11	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:42523599A>T	ENST00000398675.3	-	2	508	c.276T>A	c.(274-276)gaT>gaA	p.D92E	GXYLT1_ENST00000280876.6_Intron	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	92					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.D92E(1)		kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						TTCCACAAACATCAGAGGGCA	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	12											112	102	105					12																	42523599		1856	4098	5954	40809866	SO:0001583	missense	283464			BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.276T>A	12.37:g.42523599A>T	ENSP00000381666:p.Asp92Glu		40809866	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	37	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.721613	0.48728	.	.	ENSG00000151233	ENST00000398675	.	.	.	5.41	5.41	0.78517	.	2.040290	0.02632	N	0.104471	T	0.54919	0.1888	N	0.24115	0.695	0.80722	D	1	B	0.21071	0.051	B	0.15052	0.012	T	0.01935	-1.1244	9	0.17832	T	0.49	-8.4982	15.7333	0.77822	1.0:0.0:0.0:0.0	.	92	Q4G148	GXLT1_HUMAN	E	92	.	ENSP00000381666:D92E	D	-	3	2	GXYLT1	40809866	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.218000	0.72224	2.186000	0.69663	0.482000	0.46254	GAT		0.373	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		T	42523599	A	T	42523599	3	4	75	1	0	0	0	0	1	0	0	0	6924	214	8	5	1074	5	GXYLT1	12	42523599	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	17290961	42523599	91328296	142	21609										
KRT73	319101	broad.mit.edu	37	chr12	53012010	53012010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctgatggatacccccgggcGggcacaacgacggacacacg	13	15	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:53012010G>A	ENST00000305748.3	-	1	333	c.299C>T	c.(298-300)cCg>cTg	p.P100L	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	100	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.P100L(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		ACCCCCGGGCGGGCACAACGA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	12											110	117	115					12																	53012010		2203	4300	6503	51298277	SO:0001583	missense	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.299C>T	12.37:g.53012010G>A	ENSP00000307014:p.Pro100Leu		51298277	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	G	4.896	0.166513	0.09339	.	.	ENSG00000186049	ENST00000305748	D	0.91351	-2.83	4.64	1.38	0.22167	.	0.617506	0.14424	N	0.320475	D	0.88228	0.6380	M	0.72576	2.205	0.09310	N	1	B	0.26147	0.143	B	0.21546	0.035	T	0.80077	-0.1533	10	0.72032	D	0.01	.	9.5273	0.39171	0.3028:0.0:0.6972:0.0	.	100	Q86Y46	K2C73_HUMAN	L	100	ENSP00000307014:P100L	ENSP00000307014:P100L	P	-	2	0	KRT73	51298277	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.638000	0.05452	0.135000	0.18707	0.655000	0.94253	CCG		0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		A	53012010	G	A	53012010	3	1	75	1	0	0	0	0	1	0	0	0	8507	1116	39	1	1359	1	KRT73	12	53012010	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	10488411	53012010	80839885	143	21610										
C12orf51	283450	broad.mit.edu	37	chr12	112617047	112617047	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aagaagaggtggaggaggttGcctggggtctgggagttgat	20	3	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:112617047G>C	ENST00000430131.2	-	62	11021	c.9876C>G	c.(9874-9876)ggC>ggG	p.G3292G	HECTD4_ENST00000550722.1_Silent_p.G3568G|HECTD4_ENST00000377560.5_Silent_p.G3542G			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3292					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.G3542G(1)|p.G3292G(1)									GGAGGAGGTTGCCTGGGGTCT	0.577																																																2	Substitution - coding silent(2)	large_intestine(2)	12											85	92	90					12																	112617047		2003	4166	6169	111101430	SO:0001819	synonymous_variant	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9876C>G	12.37:g.112617047G>C			111101430	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																					0.577	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112617047	G	C	112617047	2	2	75	1	0	0	0	0	0	0	0	1	1700	1306	46	5		5	C12orf51	12	112617047	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	59605037	112617047	21234848	144	21611										
NOS1	4842	broad.mit.edu	37	chr12	117728150	117728150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agtgagaaccacctcagtctCccagttcttgaccttgagga	9	12	3	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:117728150C>T	ENST00000338101.4	-	3	938	c.934G>A	c.(934-936)Gag>Aag	p.E312K	NOS1_ENST00000344089.3_Silent_p.G330G|NOS1_ENST00000317775.6_Missense_Mutation_p.E312K			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.E312K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		ACCTCAGTCTCCCAGTTCTTG	0.542																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - Missense(1)	large_intestine(1)	12											55	58	57					12																	117728150		2059	4208	6267	116212533	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.934G>A	12.37:g.117728150C>T	ENSP00000337459:p.Glu312Lys		116212533		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251908	0.59212	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.42131	0.98;0.98	5.13	5.13	0.70059	Nitric oxide synthase, oxygenase domain (1);	0.053609	0.85682	D	0.000000	T	0.51024	0.1650	M	0.67625	2.065	0.80722	D	1	D	0.55800	0.973	P	0.50378	0.639	T	0.43798	-0.9369	10	0.13108	T	0.6	-32.9204	18.7669	0.91876	0.0:1.0:0.0:0.0	.	312	P29475	NOS1_HUMAN	K	312	ENSP00000320758:E312K;ENSP00000337459:E312K	ENSP00000320758:E312K	E	-	1	0	NOS1	116212533	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.382000	0.79729	2.680000	0.91292	0.467000	0.42956	GAG		0.542	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117728150	C	T	117728150	3	4	75	1	0	0	0	0	1	0	0	0	10572	864	30	3	3474	3	NOS1	12	117728150	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	5111103	117728150	16123745	145	21612										
LRRC43	254050	broad.mit.edu	37	chr12	122670781	122670781	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgaaatttctaaagctggaGgagttggtactgagcgccaa	12	7	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr12:122670781G>A	ENST00000339777.4	+	3	484	c.456G>A	c.(454-456)gaG>gaA	p.E152E	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	152								p.E152E(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	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)		TAAAGCTGGAGGAGTTGGTAC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	12											58	59	59					12																	122670781		1913	4120	6033	121236734	SO:0001819	synonymous_variant	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.456G>A	12.37:g.122670781G>A			121236734	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																				0.562	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		A	122670781	G	A	122670781	2	1	75	1	0	0	0	0	0	0	0	1	9030	991	35	3		3	LRRC43	12	122670781	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4942631	122670781	11181114	146	21613										
C13orf23	80209	broad.mit.edu	37	chr13	39587547	39587547	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctttgaaggccgagggagtAggacttgtgggctcagtttt	15	7	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:39587547A>G	ENST00000352251.3	-	11	2675	c.1842T>C	c.(1840-1842)ccT>ccC	p.P614P	PROSER1_ENST00000350125.3_Silent_p.P592P|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	614	Ser-rich.							p.P614P(1)									CCGAGGGAGTAGGACTTGTGG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	13											155	164	161					13																	39587547		2203	4300	6503	38485547	SO:0001819	synonymous_variant	80209			AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1842T>C	13.37:g.39587547A>G			38485547	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																				0.502	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		G	39587547	A	G	39587547	2	3	75	1	0	0	0	0	0	0	0	1	1725	407	15	4		4	C13orf23	13	39587547	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10		39587547	75582331	147	21614										
COG6	57511	broad.mit.edu	37	chr13	40297544	40297544	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agggtaggcttgagttacatCtataacactgtacagcaaca	9	8	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:40297544C>G	ENST00000455146.3	+	16	1709	c.1659C>G	c.(1657-1659)atC>atG	p.I553M	COG6_ENST00000416691.1_Missense_Mutation_p.I553M	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	553					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.I553M(1)		NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		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)		TGAGTTACATCTATAACACTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											107	98	102					13																	40297544		2203	4300	6503	39195544	SO:0001583	missense	57511			AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1659C>G	13.37:g.40297544C>G	ENSP00000397441:p.Ile553Met		39195544	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	C	8.653	0.898622	0.17686	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	T;T	0.56444	0.46;0.46	5.66	3.95	0.45737	.	0.044756	0.85682	D	0.000000	T	0.46210	0.1381	M	0.61703	1.905	0.80722	D	1	P;B	0.38280	0.625;0.425	B;B	0.37508	0.252;0.192	T	0.39354	-0.9618	10	0.45353	T	0.12	-12.1367	6.1824	0.20478	0.1327:0.6519:0.0:0.2154	.	574;553	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	M	553;584;553	ENSP00000403733:I553M;ENSP00000397441:I553M	ENSP00000255468:I584M	I	+	3	3	COG6	39195544	1.000000	0.71417	0.998000	0.56505	0.186000	0.23388	1.037000	0.30241	0.755000	0.32990	-0.157000	0.13467	ATC		0.358	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40297544	C	G	40297544	3	3	75	1	0	0	0	0	1	0	0	0	3668	903	32	5	1721	5	COG6	13	40297544	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	709997	40297544	74872334	148	21615										
DIAPH3	81624	broad.mit.edu	37	chr13	60584789	60584789	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctcctctcctcactcataatTctttccaagccatactataa	1	15	4	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:60584789T>C	ENST00000400324.4	-	8	1006	c.786A>G	c.(784-786)agA>agG	p.R262R	DIAPH3_ENST00000267215.4_Silent_p.R262R|DIAPH3_ENST00000400330.1_Silent_p.R262R|DIAPH3-AS1_ENST00000432995.1_RNA|DIAPH3-AS1_ENST00000422052.1_RNA|DIAPH3_ENST00000400319.1_Silent_p.R192R|DIAPH3-AS1_ENST00000435636.1_RNA|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.R216R|DIAPH3_ENST00000377908.2_Silent_p.R251R	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	262	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R262R(1)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CACTCATAATTCTTTCCAAGC	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	13											46	48	48					13																	60584789		1820	4079	5899	59482790	SO:0001819	synonymous_variant	81624			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.786A>G	13.37:g.60584789T>C			59482790	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																				0.353	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		C	60584789	T	C	60584789	2	2	75	1	0	0	0	0	0	0	0	1	4531	1780	62	4		4	DIAPH3	13	60584789	Silent	SNP	T	TCGA-AG-A026-01A-32W-A096-10	20287245	60584789	54585089	149	21616										
PCDH9	5101	broad.mit.edu	37	chr13	66878816	66878816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gtgctccttaggactctcagTagcacctcctgcttgcttat	8	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:66878816T>C	ENST00000377865.2	-	4	3819	c.3685A>G	c.(3685-3687)Act>Gct	p.T1229A	PCDH9_ENST00000544246.1_Missense_Mutation_p.T1229A|PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000456367.1_Missense_Mutation_p.T1195A|PCDH9_ENST00000328454.5_Missense_Mutation_p.T1195A			Q9HC56	PCDH9_HUMAN	protocadherin 9	1229					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T1229A(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GGACTCTCAGTAGCACCTCCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	13											114	109	110					13																	66878816		2203	4300	6503	65776817	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3685A>G	13.37:g.66878816T>C	ENSP00000367096:p.Thr1229Ala		65776817	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.419100	0.25552	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.51817	0.76;0.76;0.69;0.69	6.05	2.52	0.30459	.	0.631198	0.14265	N	0.330555	T	0.22975	0.0555	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.19353	-1.0308	10	0.19590	T	0.45	.	5.9808	0.19405	0.0:0.4852:0.0:0.5148	.	1187;1195;1229	B7ZM79;Q9HC56-2;Q9HC56	.;.;PCDH9_HUMAN	A	1229;1229;1195;1195	ENSP00000442186:T1229A;ENSP00000367096:T1229A;ENSP00000401699:T1195A;ENSP00000332060:T1195A	ENSP00000332060:T1195A	T	-	1	0	PCDH9	65776817	0.147000	0.22687	0.132000	0.22025	0.965000	0.64279	1.604000	0.36804	0.543000	0.28864	0.528000	0.53228	ACT		0.428	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		C	66878816	T	C	66878816	3	2	75	1	0	0	0	0	1	0	0	0	11549	1638	57	4	32	4	PCDH9	13	66878816	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	6294027	66878816	48291062	150	21617										
TBC1D4	9882	broad.mit.edu	37	chr13	75873657	75873657	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caggaggttaaacagtgacaGctgtcctggcccaagctgta	12	10	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:75873657G>C	ENST00000377636.3	-	17	3311	c.2965C>G	c.(2965-2967)Ctg>Gtg	p.L989V	TBC1D4_ENST00000425511.1_Missense_Mutation_p.L153V|TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000377625.2_Missense_Mutation_p.L926V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.L981V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	989	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.L989V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		AACAGTGACAGCTGTCCTGGC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	13											53	55	54					13																	75873657		1893	4126	6019	74771658	SO:0001583	missense	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2965C>G	13.37:g.75873657G>C	ENSP00000366863:p.Leu989Val		74771658	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812391	0.70912	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.10763	2.84;2.84;2.84;2.84	5.45	4.59	0.56863	Rab-GAP/TBC domain (4);	0.259655	0.26311	N	0.025109	T	0.20455	0.0492	L	0.35414	1.06	0.53005	D	0.99996	B;P;D;D	0.63046	0.376;0.682;0.974;0.992	B;P;P;D	0.81914	0.276;0.74;0.902;0.995	T	0.00341	-1.1804	10	0.59425	D	0.04	-14.8351	10.7376	0.46135	0.1465:0.0:0.8535:0.0	.	153;926;981;989	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	989;981;926;153	ENSP00000366863:L989V;ENSP00000395986:L981V;ENSP00000366852:L926V;ENSP00000390654:L153V	ENSP00000366852:L926V	L	-	1	2	TBC1D4	74771658	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.778000	0.47726	2.539000	0.85634	0.591000	0.81541	CTG		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		C	75873657	G	C	75873657	3	2	75	1	0	0	0	0	1	0	0	0	15661	962	34	5	951	5	TBC1D4	13	75873657	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	8994841	75873657	39296221	151	21618										
SLITRK5	26050	broad.mit.edu	37	chr13	88330382	88330382	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggggacagcaggctacgggaAccggtgctctacagcccccc	14	15	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:88330382A>T	ENST00000325089.6	+	2	2958	c.2739A>T	c.(2737-2739)gaA>gaT	p.E913D	SLITRK5_ENST00000400028.3_Missense_Mutation_p.E672D	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	913					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)		p.E913D(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GGCTACGGGAACCGGTGCTCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	13											78	86	83					13																	88330382		2203	4300	6503	87128383	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.2739A>T	13.37:g.88330382A>T	ENSP00000366283:p.Glu913Asp		87128383	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531706	0.64972	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.64085	-0.08;0.26	5.77	5.77	0.91146	.	0.057952	0.64402	D	0.000003	T	0.62563	0.2438	L	0.59436	1.845	0.47862	D	0.99953	P;P	0.49185	0.852;0.92	B;P	0.45071	0.213;0.468	T	0.63941	-0.6523	9	.	.	.	-10.0643	14.0545	0.64759	1.0:0.0:0.0:0.0	.	672;913	B4DSH5;O94991	.;SLIK5_HUMAN	D	913;672	ENSP00000366283:E913D;ENSP00000442244:E672D	.	E	+	3	2	SLITRK5	87128383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.095000	0.50235	2.200000	0.70718	0.459000	0.35465	GAA		0.572	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			T	88330382	A	T	88330382	3	4	75	1	0	0	0	0	1	0	0	0	14783	40	2	5	2741	5	SLITRK5	13	88330382	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	12456725	88330382	26839496	152	21619										
DOCK9	23348	broad.mit.edu	37	chr13	99515280	99515280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catgcttacgtaccatgcccGcgttcacagggaagggtgac	12	12	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:99515280G>A	ENST00000376460.1	-	32	3652	c.3572C>T	c.(3571-3573)gCg>gTg	p.A1191V	DOCK9_ENST00000339416.2_Missense_Mutation_p.A1192V|DOCK9_ENST00000448493.2_Missense_Mutation_p.A1203V|DOCK9_ENST00000461998.1_5'UTR|DOCK9_ENST00000442173.1_Missense_Mutation_p.A1191V	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1192					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A1192V(1)|p.A1203V(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TACCATGCCCGCGTTCACAGG	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	13											52	50	50					13																	99515280		2033	4191	6224	98313281	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3572C>T	13.37:g.99515280G>A	ENSP00000365643:p.Ala1191Val		98313281	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	G	9.635	1.137461	0.21123	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	4.26	4.26	0.50523	.	0.352684	0.34025	N	0.004334	T	0.15262	0.0368	N	0.14661	0.345	0.21915	N	0.999471	B;B;B;B;B;B	0.20459	0.008;0.001;0.014;0.001;0.0;0.045	B;B;B;B;B;B	0.14023	0.002;0.0;0.004;0.001;0.001;0.01	T	0.13926	-1.0491	10	0.31617	T	0.26	.	12.8979	0.58109	0.0:0.0:1.0:0.0	.	1192;1191;1192;1191;1191;1192	A6H8Z6;E9PFM9;A8MWZ5;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;.;DOCK9_HUMAN	V	1191;1192;1192;1192;1191;122;1192;1203;1191	ENSP00000365643:A1191V;ENSP00000341086:A1192V;ENSP00000401958:A1203V;ENSP00000406883:A1191V	ENSP00000341086:A1192V	A	-	2	0	DOCK9	98313281	.	.	0.875000	0.34327	0.002000	0.02628	.	.	2.293000	0.77203	0.555000	0.69702	GCG		0.547	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		A	99515280	G	A	99515280	3	1	75	1	0	0	0	0	1	0	0	0	4705	1087	38	1	2795	1	DOCK9	13	99515280	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	11184898	99515280	15654598	153	21620										
GPR18	2841	broad.mit.edu	37	chr13	99908103	99908103	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgttaaaagggacaggttgAtcttgattgttcagggtgat	13	4	2	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr13:99908103A>T	ENST00000340807.3	-	3	580	c.24T>A	c.(22-24)gaT>gaA	p.D8E	GPR18_ENST00000397470.2_Missense_Mutation_p.D8E|UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397473.2_Missense_Mutation_p.D8E|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	8					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D8E(1)		endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	GGACAGGTTGATCTTGATTGT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	13											136	133	134					13																	99908103		2203	4300	6503	98706104	SO:0001583	missense	2841			L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.24T>A	13.37:g.99908103A>T	ENSP00000343428:p.Asp8Glu		98706104	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	37	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	A	8.601	0.886845	0.17540	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	T;T;T;T	0.63255	-0.03;-0.03;-0.03;1.38	5.47	0.867	0.19085	.	0.665170	0.14456	N	0.318474	T	0.35828	0.0945	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.09377	0.004	T	0.18147	-1.0346	9	.	.	.	0.0	8.5782	0.33612	0.612:0.0:0.388:0.0	.	8	Q14330	GPR18_HUMAN	E	8	ENSP00000380613:D8E;ENSP00000380610:D8E;ENSP00000343428:D8E;ENSP00000401611:D8E	.	D	-	3	2	GPR18	98706104	0.085000	0.21516	0.006000	0.13384	0.521000	0.34408	1.170000	0.31883	-0.065000	0.13021	0.460000	0.39030	GAT		0.328	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			T	99908103	A	T	99908103	3	4	75	1	0	0	0	0	1	0	0	0	6695	330	12	5	975	5	GPR18	13	99908103	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	392823	99908103	15261775	154	21621										
LRRC16B	90668	broad.mit.edu	37	chr14	24533523	24533523	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gatgaagggctggaggacttCttcagccgaagggtcctgga	16	8	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr14:24533523C>T	ENST00000342740.5	+	32	3202	c.3048C>T	c.(3046-3048)ttC>ttT	p.F1016F	LRRC16B_ENST00000334420.7_Silent_p.F112F	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1016						cytoplasm (GO:0005737)		p.F1016F(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TGGAGGACTTCTTCAGCCGAA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	14											69	57	61					14																	24533523		2203	4300	6503	23603363	SO:0001819	synonymous_variant	90668			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3048C>T	14.37:g.24533523C>T			23603363	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																				0.587	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24533523	C	T	24533523	2	4	75	1	0	0	0	0	0	0	0	1	9001	912	32	3		3	LRRC16B	14	24533523	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10		24533523	82816017	155	21622										
HDC	3067	broad.mit.edu	37	chr15	50555518	50555518	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	actctcaggcagctgggctcGcaggtagccaggctgcacgt	14	13	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:50555518G>A	ENST00000267845.3	-	2	520	c.118C>T	c.(118-120)Cga>Tga	p.R40*	HDC_ENST00000543581.1_Nonsense_Mutation_p.R40*	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0	Ala/Gly-rich.				respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.R40*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGCTGGGCTCGCAGGTAGCCA	0.572																																					GBM(95;1627 1936 6910 9570)											1	Substitution - Nonsense(1)	large_intestine(1)	15											112	102	106					15																	50555518		2196	4295	6491	48342810	SO:0001587	stop_gained	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.118C>T	15.37:g.50555518G>A	ENSP00000267845:p.Arg40*		48342810		Nonsense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	G	37	6.480361	0.97603	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	.	.	.	6.05	2.85	0.33270	.	0.341439	0.28921	N	0.013710	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6665	10.7951	0.46455	0.072:0.0:0.6337:0.2943	.	.	.	.	X	40	.	ENSP00000267845:R40X	R	-	1	2	HDC	48342810	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.957000	0.40392	0.877000	0.35895	0.650000	0.86243	CGA		0.572	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50555518	G	A	50555518	4	1	75	1	0	0	0	0	0	1	0	0	7036	1095	38	1	1914	1	HDC	15	50555518	Nonsense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		50555518	51975874	156	21623										
NPTN	27020	broad.mit.edu	37	chr15	73884391	73884391	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agctgtatgtaagggtgtgaGagctggaggtgaggttacac	17	4	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:73884391G>A	ENST00000345330.4	-	3	724	c.527C>T	c.(526-528)tCt>tTt	p.S176F	NPTN_ENST00000564551.1_5'UTR|NPTN_ENST00000287226.8_Missense_Mutation_p.S176F|NPTN_ENST00000563691.1_Missense_Mutation_p.S176F|NPTN_ENST00000351217.6_Missense_Mutation_p.S60F|NPTN_ENST00000542234.1_Intron|NPTN_ENST00000562924.1_Missense_Mutation_p.S60F|NPTN_ENST00000545878.1_Missense_Mutation_p.S176F	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	176	Ig-like 2.				homophilic cell adhesion (GO:0007156)|long-term synaptic potentiation (GO:0060291)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)	cell adhesion molecule binding (GO:0050839)|type 1 fibroblast growth factor receptor binding (GO:0005105)	p.S176F(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	13						AAGGGTGTGAGAGCTGGAGGT	0.507																																					Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)											1	Substitution - Missense(1)	large_intestine(1)	15											214	177	190					15																	73884391		2198	4297	6495	71671444	SO:0001583	missense	27020			AF035287	CCDS10249.1, CCDS10250.1, CCDS58379.1, CCDS58380.1	15q24.1	2013-01-29	2006-02-22	2006-02-22	ENSG00000156642	ENSG00000156642		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17867	protein-coding gene	gene with protein product		612820	"stromal cell derived factor receptor 1"	SDFR1		8619474, 9110174	Standard	NM_012428		Approved	SDR1, GP55, GP65, np65, np55	uc002avs.3	Q9Y639	OTTHUMG00000137586	ENST00000345330.4:c.527C>T	15.37:g.73884391G>A	ENSP00000290401:p.Ser176Phe		71671444	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Missense_Mutation	SNP	ENST00000345330.4	37	CCDS10249.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647527	0.67358	.	.	ENSG00000156642	ENST00000345330;ENST00000351217;ENST00000545878;ENST00000287226	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	6.07	5.15	0.70609	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.373692	0.33290	N	0.005063	T	0.19287	0.0463	L	0.50333	1.59	0.32220	N	0.575427	D;P;D;P	0.56035	0.967;0.93;0.974;0.947	B;P;P;P	0.50314	0.434;0.532;0.57;0.637	T	0.06391	-1.0829	10	0.54805	T	0.06	.	9.6878	0.40109	0.0698:0.0:0.7888:0.1414	.	176;60;176;60	Q9Y639-5;B2RAL7;Q9Y639;Q9Y639-3	.;.;NPTN_HUMAN;.	F	176;60;176;176	ENSP00000290401:S176F;ENSP00000342958:S60F;ENSP00000444548:S176F;ENSP00000287226:S176F	ENSP00000287226:S176F	S	-	2	0	NPTN	71671444	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.668000	0.61568	2.884000	0.98904	0.655000	0.94253	TCT		0.507	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428		A	73884391	G	A	73884391	3	1	75	1	0	0	0	0	1	0	0	0	10632	942	33	3	693	3	NPTN	15	73884391	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	23328873	73884391	28647001	157	21624										
ACSBG1	23205	broad.mit.edu	37	chr15	78475123	78475123	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttagatgtggcaactgtttcCagatctgcattgacaggaaa	10	7	1	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:78475123C>G	ENST00000258873.4	-	6	873	c.668G>C	c.(667-669)tGg>tCg	p.W223S	ACSBG1_ENST00000541759.1_5'UTR|ACSBG1_ENST00000560817.1_5'UTR	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	223					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.W223S(1)|p.W223*(1)		endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						CAACTGTTTCCAGATCTGCAT	0.463																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|liver(1)	15											101	93	96					15																	78475123		2196	4293	6489	76262178	SO:0001583	missense	23205			AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.668G>C	15.37:g.78475123C>G	ENSP00000258873:p.Trp223Ser		76262178	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	37	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.454380	0.26161	.	.	ENSG00000103740	ENST00000258873	T	0.09817	2.94	5.49	5.49	0.81192	AMP-dependent synthetase/ligase (1);	0.149009	0.48286	D	0.000196	T	0.09686	0.0238	L	0.36672	1.1	0.80722	D	1	B;B	0.26708	0.157;0.017	B;B	0.29663	0.105;0.065	T	0.23833	-1.0177	10	0.17832	T	0.49	-19.4471	11.7867	0.52047	0.0:0.9207:0.0:0.0793	.	219;223	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	S	223	ENSP00000258873:W223S	ENSP00000258873:W223S	W	-	2	0	ACSBG1	76262178	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	3.540000	0.53611	2.565000	0.86533	0.655000	0.94253	TGG		0.463	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162		G	78475123	C	G	78475123	3	3	75	1	0	0	0	0	1	0	0	0	173	595	21	5	1542	5	ACSBG1	15	78475123	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	4590732	78475123	24056269	158	21625										
SH3GL3	6457	broad.mit.edu	37	chr15	84237364	84237364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caggatacccgcagacggaaGgcttgctgggggactgtatg	16	9	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:84237364G>A	ENST00000427482.2	+	4	577	c.271G>A	c.(271-273)Ggc>Agc	p.G91S	SH3GL3_ENST00000434347.1_Missense_Mutation_p.G99S|SH3GL3_ENST00000324537.5_Missense_Mutation_p.G99S|SH3GL3_ENST00000535412.1_Missense_Mutation_p.G91S	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	91	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.G99S(2)		central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						GCAGACGGAAGGCTTGCTGGG	0.517																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	15											84	85	85					15																	84237364		2203	4300	6503	82028368	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.271G>A	15.37:g.84237364G>A	ENSP00000391372:p.Gly91Ser		82028368	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365073	0.82463	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	4.86	3.95	0.45737	BAR (3);	0.000000	0.85682	D	0.000000	T	0.77778	0.4181	M	0.79805	2.47	0.80722	D	1	D;P;P	0.89917	1.0;0.75;0.874	D;P;P	0.71870	0.975;0.77;0.742	T	0.79662	-0.1710	10	0.52906	T	0.07	-40.6955	12.7223	0.57149	0.0803:0.0:0.9197:0.0	.	91;91;99	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	S	91;91;99;99	ENSP00000391372:G91S;ENSP00000439239:G91S;ENSP00000320092:G99S;ENSP00000397871:G99S	ENSP00000320092:G99S	G	+	1	0	SH3GL3	82028368	1.000000	0.71417	0.975000	0.42487	0.969000	0.65631	7.431000	0.80335	1.171000	0.42768	0.544000	0.68410	GGC		0.517	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		A	84237364	G	A	84237364	3	1	75	1	0	0	0	0	1	0	0	0	14289	1000	35	3	285	3	SH3GL3	15	84237364	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	5762241	84237364	18294028	159	21626										
MESP2	145873	broad.mit.edu	37	chr15	90321388	90321388	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	agactgcagcctcagaccccCgggaggtgctggagccacag	14	14	1	2	rs370227491		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:90321388C>T	ENST00000341735.3	+	2	1017	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	MESP2_ENST00000560219.1_Silent_p.P41P|MESP2_ENST00000558723.1_3'UTR	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	339					mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P339P(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			CTCAGACCCCCGGGAGGTGCT	0.647													C|||	1	0.000199681	8e-04	0	5008	,	,		16737	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	15						C		2,3872		0,2,1935	30	34	33		1017	-0.3	0	15		33	0,8292		0,0,4146	no	coding-synonymous	MESP2	NM_001039958.1		0,2,6081	TT,TC,CC		0.0,0.0516,0.0164		339/398	90321388	2,12164	1937	4146	6083	88122392	SO:0001819	synonymous_variant	145873				CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"Basic helix-loop-helix proteins"	29659	protein-coding gene	gene with protein product		605195	"mesoderm posterior 2 homolog (mouse)"			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.1017C>T	15.37:g.90321388C>T			88122392	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																				0.647	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		T	90321388	C	T	90321388	2	4	75	1	0	0	0	0	0	0	0	1	9513	639	23	1		1	MESP2	15	90321388	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	6084024	90321388	12210004	160	21627										
LASS3	204219	broad.mit.edu	37	chr15	100996237	100996237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gatacataggcaagatcagcGtgcaatataaaatcctgaaa	8	7	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr15:100996237G>A	ENST00000394113.1	-	13	1550	c.860C>T	c.(859-861)aCg>aTg	p.T287M	CERS3_ENST00000538112.2_Missense_Mutation_p.T287M|CERS3_ENST00000284382.4_Missense_Mutation_p.T287M|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	287	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.T287M(1)									CAAGATCAGCGTGCAATATAA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	15											82	76	78					15																	100996237		2203	4300	6503	98813760	SO:0001583	missense	204219				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.860C>T	15.37:g.100996237G>A	ENSP00000377672:p.Thr287Met		98813760	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.667684	0.47677	.	.	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	D;D	0.85258	-1.96;-1.96	5.66	5.66	0.87406	TRAM/LAG1/CLN8 homology domain (3);	0.223476	0.45126	D	0.000389	D	0.93713	0.7991	M	0.91920	3.255	0.58432	D	0.999997	D	0.89917	1.0	D	0.75484	0.986	D	0.94651	0.7839	10	0.87932	D	0	-16.0042	15.244	0.73493	0.0:0.0:1.0:0.0	.	287	Q8IU89	CERS3_HUMAN	M	287;298;287	ENSP00000284382:T287M;ENSP00000437640:T287M	ENSP00000284382:T287M	T	-	2	0	CERS3	98813760	1.000000	0.71417	0.945000	0.38365	0.076000	0.17211	5.442000	0.66575	2.669000	0.90835	0.655000	0.94253	ACG		0.368	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		A	100996237	G	A	100996237	3	1	75	1	0	0	0	0	1	0	0	0	8662	1145	40	1	299	1	LASS3	15	100996237	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	10674849	100996237	1535155	161	21628										
ACSM2A	123876	broad.mit.edu	37	chr16	20497974	20497974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttcgagacaaggagtggaagAtgtccggaaaagcccgtgcg	15	8	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:20497974A>G	ENST00000573854.1	+	14	1822	c.1708A>G	c.(1708-1710)Atg>Gtg	p.M570V	ACSM2A_ENST00000219054.6_Missense_Mutation_p.M570V|ACSM2A_ENST00000575690.1_Missense_Mutation_p.M570V|ACSM2A_ENST00000417235.2_Missense_Mutation_p.M491V|AC137056.1_ENST00000593357.1_5'Flank|ACSM2A_ENST00000536134.1_Missense_Mutation_p.M342V|ACSM2A_ENST00000396104.2_Missense_Mutation_p.M570V	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	570					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.M570V(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GGAGTGGAAGATGTCCGGAAA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	16											200	190	193					16																	20497974		2203	4300	6503	20405475	SO:0001583	missense	123876			AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1708A>G	16.37:g.20497974A>G	ENSP00000459451:p.Met570Val		20405475	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	A	3.951	-0.012173	0.07727	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.43294	0.95;0.98;1.51;0.98	2.88	2.88	0.33553	.	2.011570	0.03264	U	0.183740	T	0.27933	0.0688	N	0.08118	0	0.38813	D	0.95546	B	0.06786	0.001	B	0.04013	0.001	T	0.15896	-1.0421	10	0.51188	T	0.08	-0.5111	9.1914	0.37202	1.0:0.0:0.0:0.0	.	570	Q08AH3	ACS2A_HUMAN	V	491;570;342;570	ENSP00000392169:M491V;ENSP00000219054:M570V;ENSP00000445082:M342V;ENSP00000379411:M570V	ENSP00000219054:M570V	M	+	1	0	ACSM2A	20405475	0.997000	0.39634	0.428000	0.26697	0.039000	0.13416	3.339000	0.52135	1.565000	0.49641	0.254000	0.18369	ATG		0.468	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		G	20497974	A	G	20497974	3	3	75	1	0	0	0	0	1	0	0	0	183	333	12	4	1758	4	ACSM2A	16	20497974	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10		20497974	69856779	162	21629										
HS3ST2	9956	broad.mit.edu	37	chr16	22826314	22826314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgtgaagaaggggggcacccGggccgtgctggagtttatcc	17	10	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:22826314G>T	ENST00000261374.3	+	1	817	c.383G>T	c.(382-384)cGg>cTg	p.R128L		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	128					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)	p.R128L(1)		breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		GGGGGCACCCGGGCCGTGCTG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	16											13	16	15					16																	22826314		2181	4278	6459	22733815	SO:0001583	missense	9956			AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.383G>T	16.37:g.22826314G>T	ENSP00000261374:p.Arg128Leu		22733815	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	37	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	32	5.118617	0.94385	.	.	ENSG00000122254	ENST00000261374;ENST00000540146	T	0.44881	0.91	5.02	5.02	0.67125	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.74504	0.3725	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83033	-0.0161	10	0.87932	D	0	.	16.9118	0.86142	0.0:0.0:1.0:0.0	.	128	Q9Y278	HS3S2_HUMAN	L	128;136	ENSP00000261374:R128L	ENSP00000261374:R128L	R	+	2	0	HS3ST2	22733815	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.240000	0.95396	2.315000	0.78130	0.655000	0.94253	CGG		0.652	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		T	22826314	G	T	22826314	3	4	75	1	0	0	0	0	1	0	0	0	7385	1116	39	2	385	2	HS3ST2	16	22826314	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2328340	22826314	67528439	163	21630										
SRCAP	10847	broad.mit.edu	37	chr16	30748499	30748499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggactggtggaggcacccacCggcgcagtaaaaaggccaaa	14	11	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:30748499C>T	ENST00000262518.4	+	34	7523	c.7138C>T	c.(7138-7140)Cgg>Tgg	p.R2380W	SRCAP_ENST00000344771.4_Missense_Mutation_p.R2222W|SRCAP_ENST00000395059.2_Missense_Mutation_p.R2318W	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2380					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.R2380W(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGGCACCCACCGGCGCAGTAA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	16											39	43	42					16																	30748499		2197	4300	6497	30656000	SO:0001583	missense	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7138C>T	16.37:g.30748499C>T	ENSP00000262518:p.Arg2380Trp		30656000	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697016	0.48202	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.93366	-3.13;-3.19;-3.21	4.8	4.8	0.61643	.	0.000000	0.42682	D	0.000670	D	0.92450	0.7603	N	0.08118	0	0.33581	D	0.599891	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.981	D	0.95121	0.8246	10	0.72032	D	0.01	-1.144	16.865	0.86027	0.0:1.0:0.0:0.0	.	2318;2380	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	W	2380;2318;2222	ENSP00000262518:R2380W;ENSP00000378499:R2318W;ENSP00000343042:R2222W	ENSP00000262518:R2380W	R	+	1	2	SRCAP	30656000	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.762000	0.47597	2.513000	0.84729	0.558000	0.71614	CGG		0.652	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30748499	C	T	30748499	3	4	75	1	0	0	0	0	1	0	0	0	15174	643	23	1	7264	1	SRCAP	16	30748499	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	7922185	30748499	59606254	164	21631										
CCDC113	29070	broad.mit.edu	37	chr16	58312466	58312466	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcaccacaggtgatgacttaCgtccgggagaagatcttaaa	11	9	1	4	rs571059899	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:58312466C>T	ENST00000219299.4	+	8	1051	c.972C>T	c.(970-972)taC>taT	p.Y324Y	CCDC113_ENST00000443128.2_Silent_p.Y270Y	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	324						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.Y324Y(1)		large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						TGATGACTTACGTCCGGGAGA	0.582													C|||	2	0.000399361	0	0	5008	,	,		16439	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											61	62	62					16																	58312466		2198	4300	6498	56869967	SO:0001819	synonymous_variant	29070			AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	ENST00000219299.4:c.972C>T	16.37:g.58312466C>T			56869967	B2RAQ7|B4DR20|Q9NZX2	Silent	SNP	ENST00000219299.4	37	CCDS10795.1																																																																																				0.582	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		T	58312466	C	T	58312466	2	4	75	1	0	0	0	0	0	0	0	1	2756	547	19	1		1	CCDC113	16	58312466	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	27563967	58312466	32042287	165	21632										
PRSS54	221191	broad.mit.edu	37	chr16	58325032	58325032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gaaaacggaagctttctggaCgccacaacctgcggagcagg	13	11	1	0	rs367701903		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:58325032C>T	ENST00000219301.4	-	4	488	c.94G>A	c.(94-96)Gtc>Atc	p.V32I	PRSS54_ENST00000543437.1_Intron|PRSS54_ENST00000567164.1_Missense_Mutation_p.V32I	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	32						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.V32I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCTTTCTGGACGCCACAACCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	ILE/VAL	0,4396		0,0,2198	54	46	49		94	0.8	1	16		49	1,8599	1.2+/-3.3	0,1,4299	no	missense	PRSS54	NM_001080492.1	29	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	benign	32/396	58325032	1,12995	2198	4300	6498	56882533	SO:0001583	missense	221191			AK058068	CCDS32463.1	16q21	2010-05-07			ENSG00000103023	ENSG00000103023		"Serine peptidases / Serine peptidases"	26336	protein-coding gene	gene with protein product	"cancer/testis antigen 67"					17521433	Standard	NM_001080492		Approved	FLJ25339, KLKBL4, CT67	uc002enf.3	Q6PEW0		ENST00000219301.4:c.94G>A	16.37:g.58325032C>T	ENSP00000219301:p.Val32Ile		56882533	Q96LN9|Q9NT77	Missense_Mutation	SNP	ENST00000219301.4	37	CCDS32463.1	.	.	.	.	.	.	.	.	.	.	C	0.946	-0.707839	0.03230	0.0	1.16E-4	ENSG00000103023	ENST00000219301	D	0.88975	-2.45	5.85	0.827	0.18835	Peptidase cysteine/serine, trypsin-like (1);	0.224009	0.30244	N	0.010078	T	0.62853	0.2462	N	0.03050	-0.425	0.21020	N	0.999801	B	0.17852	0.024	B	0.09377	0.004	T	0.55667	-0.8105	10	0.02654	T	1	-15.9758	1.2558	0.01991	0.1453:0.1673:0.151:0.5364	.	32	Q6PEW0	PRS54_HUMAN	I	32	ENSP00000219301:V32I	ENSP00000219301:V32I	V	-	1	0	PRSS54	56882533	0.983000	0.35010	1.000000	0.80357	0.034000	0.12701	-0.151000	0.10175	0.129000	0.18514	-0.302000	0.09304	GTC		0.617	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492		T	58325032	C	T	58325032	3	4	75	1	0	0	0	0	1	0	0	0	12667	536	19	1	1109	1	PRSS54	16	58325032	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	12566	58325032	32029721	166	21633										
CTCF	10664	broad.mit.edu	37	chr16	67644806	67644806	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	taaaggaaaggagagaaagaCttaccagagacgccgggaag	14	6	0	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:67644806C>G	ENST00000264010.4	+	3	515	c.71C>G	c.(70-72)aCt>aGt	p.T24S	CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	24					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.T24S(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GAGAGAAAGACTTACCAGAGA	0.522																																					Colon(175;1200 1966 6945 23069 27405)											1	Substitution - Missense(1)	large_intestine(1)	16											51	57	55					16																	67644806		2198	4300	6498	66202307	SO:0001583	missense	10664			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.71C>G	16.37:g.67644806C>G	ENSP00000264010:p.Thr24Ser		66202307	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	37	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569346	0.86439	.	.	ENSG00000102974	ENST00000264010	T	0.11712	2.75	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	T	0.09949	0.0244	N	0.24115	0.695	0.80722	D	1	B	0.29378	0.243	B	0.24541	0.054	T	0.13953	-1.0490	10	0.87932	D	0	-2.5955	18.8924	0.92410	0.0:1.0:0.0:0.0	.	24	P49711	CTCF_HUMAN	S	24	ENSP00000264010:T24S	ENSP00000264010:T24S	T	+	2	0	CTCF	66202307	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.646000	0.61411	2.696000	0.92011	0.655000	0.94253	ACT		0.522	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		G	67644806	C	G	67644806	3	3	75	1	0	0	0	0	1	0	0	0	4006	565	20	5	73	5	CTCF	16	67644806	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9319774	67644806	22709947	167	21634										
FTSJD1	55783	broad.mit.edu	37	chr16	71319233	71319233	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggaccaaagtaccaccagtgCaaggtatttgcaataagccg	10	10	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:71319233C>G	ENST00000338099.5	-	3	927	c.591G>C	c.(589-591)ttG>ttC	p.L197F	CMTR2_ENST00000434935.2_Missense_Mutation_p.L197F			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	197	Adrift-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00946}.				7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.L197F(1)									ACCACCAGTGCAAGGTATTTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	16											125	115	118					16																	71319233		2198	4300	6498	69876734	SO:0001583	missense	55783			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.591G>C	16.37:g.71319233C>G	ENSP00000337512:p.Leu197Phe		69876734	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428687	0.43122	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.37411	1.2;1.2	5.49	2.37	0.29283	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.154190	0.44483	D	0.000450	T	0.53449	0.1797	M	0.70903	2.155	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	T	0.47911	-0.9080	10	0.46703	T	0.11	-16.2939	8.5142	0.33235	0.0:0.5822:0.0:0.4178	.	197	Q8IYT2	FTSJ1_HUMAN	F	197	ENSP00000337512:L197F;ENSP00000411148:L197F	ENSP00000337512:L197F	L	-	3	2	FTSJD1	69876734	1.000000	0.71417	0.365000	0.25901	0.992000	0.81027	0.920000	0.28705	0.326000	0.23384	0.556000	0.70494	TTG		0.428	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		G	71319233	C	G	71319233	3	3	75	1	0	0	0	0	1	0	0	0	6109	709	25	5	1725	5	FTSJD1	16	71319233	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	3674427	71319233	19035520	168	21635										
ZNF23	7571	broad.mit.edu	37	chr16	71483092	71483092	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cacattccttgcactgatagGgcttctctcccgtatggatt	8	12	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:71483092G>C	ENST00000393539.2	-	6	1649	c.836C>G	c.(835-837)cCc>cGc	p.P279R	ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000357254.4_Missense_Mutation_p.P279R|ZNF23_ENST00000539742.1_5'UTR|ZNF23_ENST00000358700.2_3'UTR|ZNF23_ENST00000417828.1_Missense_Mutation_p.P279R|ZNF23_ENST00000564528.1_Missense_Mutation_p.P221R|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000428724.2_Missense_Mutation_p.P221R	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	279					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P279R(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		GCACTGATAGGGCTTCTCTCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	16											98	95	96					16																	71483092		2198	4300	6498	70040593	SO:0001583	missense	7571			X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.836C>G	16.37:g.71483092G>C	ENSP00000377171:p.Pro279Arg		70040593	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308714	0.60305	.	.	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742;ENST00000358700	T;T;T;T;T	0.34667	1.64;1.64;1.64;1.64;1.35	3.7	3.7	0.42460	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40908	D	0.000984	T	0.58595	0.2133	M	0.75447	2.3	0.53005	D	0.999969	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.962	T	0.63708	-0.6576	10	0.66056	D	0.02	-16.353	13.7712	0.63026	0.0:0.0:1.0:0.0	.	279;279	B3KR55;P17027	.;ZNF23_HUMAN	R	279;279;279;221;221;79	ENSP00000377171:P279R;ENSP00000349796:P279R;ENSP00000395712:P279R;ENSP00000387673:P221R;ENSP00000351535:P79R	ENSP00000349796:P279R	P	-	2	0	ZNF23	70040593	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.571000	0.82399	2.371000	0.80710	0.561000	0.74099	CCC		0.468	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		C	71483092	G	C	71483092	3	2	75	1	0	0	0	0	1	0	0	0	17822	1232	43	5	1099	5	ZNF23	16	71483092	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	163859	71483092	18871661	169	21636										
FBXO31	79791	broad.mit.edu	37	chr16	87369863	87369863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	attcctccctcagccacgtcCgaaactccttccaaaagaac	4	17	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:87369863C>T	ENST00000311635.7	-	6	752	c.740G>A	c.(739-741)cGg>cAg	p.R247Q	RP11-178L8.4_ENST00000568879.1_5'Flank	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	247					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)	p.R247Q(1)|p.R75Q(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		CAGCCACGTCCGAAACTCCTT	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	16											141	110	120					16																	87369863		2198	4300	6498	85927364	SO:0001583	missense	79791			BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"F-boxes /  "other""	16510	protein-coding gene	gene with protein product		609102	"F-box only protein 31"				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.740G>A	16.37:g.87369863C>T	ENSP00000310841:p.Arg247Gln		85927364	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Missense_Mutation	SNP	ENST00000311635.7	37	CCDS32501.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.418788	0.83559	.	.	ENSG00000103264	ENST00000311635	T	0.69306	-0.39	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.70002	0.3174	N	0.17082	0.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.72354	-0.4319	10	0.38643	T	0.18	-16.1671	17.4779	0.87666	0.0:1.0:0.0:0.0	.	247;139	Q5XUX0;Q5XUX0-2	FBX31_HUMAN;.	Q	247	ENSP00000310841:R247Q	ENSP00000310841:R247Q	R	-	2	0	FBXO31	85927364	1.000000	0.71417	0.998000	0.56505	0.823000	0.46562	7.565000	0.82337	2.208000	0.71279	0.561000	0.74099	CGG		0.547	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735		T	87369863	C	T	87369863	3	4	75	1	0	0	0	0	1	0	0	0	5760	652	23	1	895	1	FBXO31	16	87369863	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	15886771	87369863	2984890	170	21637										
TUBB3	10381	broad.mit.edu	37	chr16	90002152	90002152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	taccaggacgccacggccgaGgaagagggcgagatgtacga	16	10	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr16:90002152G>T	ENST00000315491.7	+	4	1416	c.1293G>T	c.(1291-1293)gaG>gaT	p.E431D	TUBB3_ENST00000555576.1_Intron|TUBB3_ENST00000556922.1_Missense_Mutation_p.E778D|TUBB3_ENST00000304984.5_Missense_Mutation_p.E359D|TUBB3_ENST00000554444.1_Missense_Mutation_p.E359D	NM_006086.3	NP_006077.2	Q13509	TBB3_HUMAN	tubulin, beta 3 class III	431					'de novo' posttranslational protein folding (GO:0051084)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.E431D(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Ixabepilone(DB04845)	CCACGGCCGAGGAAGAGGGCG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	16											77	73	74					16																	90002152		2198	4300	6498	88529653	SO:0001583	missense	10381			BC000748	CCDS10988.1, CCDS56012.1	16q24.3	2014-02-04	2011-10-10		ENSG00000198211	ENSG00000198211		"Tubulins"	20772	protein-coding gene	gene with protein product	"class III beta-tubulin"	602661	"tubulin, beta 3", "fibrosis of extraocular muscles, congenital, 3"	FEOM3		9473684, 8098743, 20074521	Standard	NM_006086		Approved	beta-4, CFEOM3, CFEOM3A	uc002fph.2	Q13509	OTTHUMG00000138985	ENST00000315491.7:c.1293G>T	16.37:g.90002152G>T	ENSP00000320295:p.Glu431Asp		88529653	A8K854|Q9BTZ0|Q9BW10	Missense_Mutation	SNP	ENST00000315491.7	37	CCDS10988.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.075822	0.36662	.	.	ENSG00000258947;ENSG00000258947;ENSG00000258947;ENSG00000198211;ENSG00000198211	ENST00000556922;ENST00000555399;ENST00000304984;ENST00000554444;ENST00000315491	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	4.66	4.66	0.58398	.	0.000000	0.56097	D	0.000022	T	0.51958	0.1705	N	0.03304	-0.355	0.47009	D	0.999287	B;B	0.15141	0.0;0.012	B;B	0.11329	0.0;0.006	T	0.49960	-0.8883	9	.	.	.	.	16.6871	0.85311	0.0:0.0:1.0:0.0	.	431;431	Q13509;B2RBD5	TBB3_HUMAN;.	D	778;431;359;359;431	ENSP00000451560:E778D;ENSP00000302777:E359D;ENSP00000451617:E359D;ENSP00000320295:E431D	.	E	+	3	2	RP11-566K11.2;TUBB3	88529653	0.999000	0.42202	1.000000	0.80357	0.937000	0.57800	0.386000	0.20702	2.313000	0.78055	0.561000	0.74099	GAG		0.652	TUBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272874.1	NM_006086		T	90002152	G	T	90002152	3	4	75	1	0	0	0	0	1	0	0	0	16797	991	35	2	1307	2	TUBB3	16	90002152	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	2632289	90002152	352601	171	21638										
ANKFY1	51479	broad.mit.edu	37	chr17	4098323	4098323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgccgcgctggatgagtctgGctgcaaagctgttctcatca	12	11	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:4098323G>C	ENST00000341657.4	-	10	1357	c.1322C>G	c.(1321-1323)gCc>gGc	p.A441G	ANKFY1_ENST00000433651.1_Missense_Mutation_p.A441G|ANKFY1_ENST00000574367.1_Missense_Mutation_p.A441G|ANKFY1_ENST00000570535.1_Missense_Mutation_p.A483G|Y_RNA_ENST00000384660.1_RNA	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	441					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.A441G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GATGAGTCTGGCTGCAAAGCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											51	54	53					17																	4098323		2108	4251	6359	4045072	SO:0001583	missense	51479			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1322C>G	17.37:g.4098323G>C	ENSP00000343362:p.Ala441Gly		4045072	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	29.1	4.977256	0.92982	.	.	ENSG00000185722	ENST00000341657;ENST00000535427;ENST00000433651	T;T	0.53206	0.63;0.69	5.58	5.58	0.84498	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.60843	0.2300	L	0.39020	1.185	0.80722	D	1	D;P;B;B;B	0.71674	0.998;0.867;0.41;0.204;0.342	D;P;B;B;B	0.80764	0.994;0.658;0.226;0.156;0.142	T	0.58440	-0.7636	10	0.44086	T	0.13	-15.9981	18.5599	0.91096	0.0:0.0:1.0:0.0	.	382;441;441;441;483	F5H754;Q9P2R3-3;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;.;ANFY1_HUMAN;.;.	G	441;382;441	ENSP00000343362:A441G;ENSP00000416005:A441G	ENSP00000343362:A441G	A	-	2	0	ANKFY1	4045072	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.771000	0.98977	2.644000	0.89710	0.655000	0.94253	GCC		0.587	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		C	4098323	G	C	4098323	3	2	75	1	0	0	0	0	1	0	0	0	626	1203	42	5	2346	5	ANKFY1	17	4098323	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		4098323	77096887	172	21639										
TP53	7157	broad.mit.edu	37	chr17	7579590	7579591	+	Splice_Site	INS	-	-	CT													0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcttgggacggcaagggggaINSctgtagatgggtgaaaagag							TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:7579590_7579591insCT	ENST00000269305.4	-	4	286	c.97_97insAG	c.(97-99)tcc>AGtcc	p.S33fs	TP53_ENST00000420246.2_Splice_Site_p.S33fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Splice_Site_p.S33fs|TP53_ENST00000359597.4_Splice_Site_p.S33fs|TP53_ENST00000455263.2_Splice_Site_p.S33fs|TP53_ENST00000445888.2_Splice_Site_p.S33fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	33	Interaction with HRMT1L2.|Transcription activation (acidic).		S -> T (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(8)|p.L35fs*10(3)|p.S33fs*23(1)|p.S33fs*11(1)|p.S33fs*10(1)|p.S33T(1)|p.P13fs*18(1)|p.S33fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCAAGGGGGACTGTAGATGGG	0.589		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	25	Unknown(11)|Whole gene deletion(8)|Deletion - Frameshift(4)|Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(4)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|lung(3)|pancreas(3)|stomach(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|ovary(1)	17	GRCh37	CS971912	TP53	S																																				7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1->AG	17.37:g.7579591_7579592dupCT			7520315	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.589	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Frame_Shift_Ins	CT	7579591	-	CT	7579590	8	5	75	1	0	1	1	0	0	0	1	0	16421	289	10	0	1205	0	TP53	17	7579590	Splice_Site	INS	-	TCGA-AG-A026-01A-32W-A096-10	3481267	7579590	73615620	173	21640										
ELAC2	60528	broad.mit.edu	37	chr17	12909266	12909266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gcccatctcctttgctttgaGcaccaagaagtttcctctct	6	14	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:12909266G>A	ENST00000338034.4	-	9	1008	c.769C>T	c.(769-771)Ctc>Ttc	p.L257F	ELAC2_ENST00000426905.3_Missense_Mutation_p.L217F|ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000395962.2_Missense_Mutation_p.L238F	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	257					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.L257F(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						TTTGCTTTGAGCACCAAGAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	17											137	128	131					17																	12909266		2203	4300	6503	12849991	SO:0001583	missense	60528			AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.769C>T	17.37:g.12909266G>A	ENSP00000337445:p.Leu257Phe		12849991	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	37	CCDS11164.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.511|8.511	0.866476|0.866476	0.17250|0.17250	.|.	.|.	ENSG00000006744|ENSG00000006744	ENST00000446899|ENST00000426905;ENST00000338034;ENST00000395962	.|T;T;T	.|0.55234	.|0.53;0.53;0.53	4.43|4.43	3.46|3.46	0.39613|0.39613	.|.	.|0.266144	.|0.35555	.|N	.|0.003130	T|T	0.63827|0.63827	0.2544|0.2544	M|M	0.72118|0.72118	2.19|2.19	0.40864|0.40864	D|D	0.983859|0.983859	.|D;D;D;P;D;D	.|0.65815	.|0.981;0.97;0.995;0.94;0.991;0.981	.|P;P;P;P;P;P	.|0.60068	.|0.779;0.608;0.868;0.454;0.779;0.606	T|T	0.66312|0.66312	-0.5955|-0.5955	5|10	.|0.56958	.|D	.|0.05	-27.5499|-27.5499	8.654|8.654	0.34051|0.34051	0.1053:0.0:0.8947:0.0|0.1053:0.0:0.8947:0.0	.|.	.|217;240;238;80;257;17	.|B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9	.|.;.;.;.;RNZ2_HUMAN;.	V|F	33|217;257;238	.|ENSP00000405223:L217F;ENSP00000337445:L257F;ENSP00000379291:L238F	.|ENSP00000337445:L257F	A|L	-|-	2|1	0|0	ELAC2|ELAC2	12849991|12849991	0.817000|0.817000	0.29147|0.29147	0.983000|0.983000	0.44433|0.44433	0.540000|0.540000	0.34992|0.34992	1.353000|1.353000	0.34045|0.34045	1.213000|1.213000	0.43380|0.43380	-0.244000|-0.244000	0.11960|0.11960	GCT|CTC		0.443	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			A	12909266	G	A	12909266	3	1	75	1	0	0	0	0	1	0	0	0	5060	971	34	3	1775	3	ELAC2	17	12909266	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	5329676	12909266	68285944	174	21641										
HS3ST3A1	9955	broad.mit.edu	37	chr17	13504318	13504318	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gacagggtctggcagcgctcGgccaggcagtagaagacgta	16	10	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:13504318G>A	ENST00000284110.1	-	1	926	c.129C>T	c.(127-129)gcC>gcT	p.A43A		NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	43					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)	p.A43A(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGCAGCGCTCGGCCAGGCAGT	0.716																																																1	Substitution - coding silent(1)	large_intestine(1)	17											28	25	26					17																	13504318		2181	4289	6470	13445043	SO:0001819	synonymous_variant	9955			AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"Sulfotransferases, membrane-bound"	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.129C>T	17.37:g.13504318G>A			13445043	A8K7N2	Silent	SNP	ENST00000284110.1	37	CCDS11165.1																																																																																				0.716	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042		A	13504318	G	A	13504318	2	1	75	1	0	0	0	0	0	0	0	1	7386	1103	39	1		1	HS3ST3A1	17	13504318	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	595052	13504318	67690892	175	21642										
ZNF287	57336	broad.mit.edu	37	chr17	16456605	16456605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	catcagtgtgaattttccagAagccaccttttcctcgcctc	6	14	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:16456605A>G	ENST00000395824.1	-	6	1468	c.851T>C	c.(850-852)tTc>tCc	p.F284S	ZNF287_ENST00000395825.3_Missense_Mutation_p.F284S			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	277					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F277S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		AATTTTCCAGAAGCCACCTTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	17											128	134	132					17																	16456605		2202	4299	6501	16397330	SO:0001583	missense	57336			AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"Zinc fingers, C2H2-type", "-", "-", "-"	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.851T>C	17.37:g.16456605A>G	ENSP00000379168:p.Phe284Ser		16397330	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	1.926	-0.447206	0.04572	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.05025	3.51;3.51	4.35	1.99	0.26369	.	0.128788	0.36409	N	0.002615	T	0.03305	0.0096	N	0.14661	0.345	0.09310	N	1	B	0.22604	0.072	B	0.23574	0.047	T	0.44952	-0.9294	10	0.21540	T	0.41	.	5.4067	0.16326	0.4702:0.3572:0.0:0.1726	.	277	Q9HBT7	ZN287_HUMAN	S	284	ENSP00000379169:F284S;ENSP00000379168:F284S	ENSP00000379168:F284S	F	-	2	0	ZNF287	16397330	0.001000	0.12720	0.019000	0.16419	0.085000	0.17905	0.207000	0.17395	0.387000	0.25024	0.477000	0.44152	TTC		0.363	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			G	16456605	A	G	16456605	3	3	75	1	0	0	0	0	1	0	0	0	17864	246	9	4	1438	4	ZNF287	17	16456605	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	2952287	16456605	64738605	176	21643										
CSH2	1443	broad.mit.edu	37	chr17	61950623	61950623	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aaaagcctggataacggaacGgtttggacggcaccagcctc	12	11	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:61950623G>T	ENST00000392886.2	-	2	238	c.87C>A	c.(85-87)acC>acA	p.T29T	CSH2_ENST00000336844.5_Silent_p.T29T|CSH2_ENST00000560142.1_Intron|CSH2_ENST00000345366.7_Silent_p.T29T	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	29						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.T29T(2)		endometrium(2)|large_intestine(1)|lung(3)	6						ATAACGGAACGGTTTGGACGG	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	17											105	103	104					17																	61950623		2203	4300	6503	59304355	SO:0001819	synonymous_variant	1443			V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"placental lactogen", "chorionic somatomammotropin B"	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.87C>A	17.37:g.61950623G>T			59304355	P01243|Q0VDB1|Q14407	Silent	SNP	ENST00000392886.2	37	CCDS42369.1																																																																																				0.597	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417657.1	NM_020991		T	61950623	G	T	61950623	2	4	75	1	0	0	0	0	0	0	0	1	3947	1103	39	2		2	CSH2	17	61950623	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	45494018	61950623	19244587	177	21644										
RGS9	8787	broad.mit.edu	37	chr17	63221156	63221156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctcccagcccccatctgaccGtgtacaccgggacctgcatg	9	18	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:63221156G>A	ENST00000262406.9	+	18	1511	c.1444G>A	c.(1444-1446)Gtg>Atg	p.V482M	RGS9_ENST00000449996.3_Missense_Mutation_p.V479M|RGS9_ENST00000443584.3_Missense_Mutation_p.V479M	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	482					dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.V482M(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						CCATCTGACCGTGTACACCGG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											104	121	115					17																	63221156		2061	4205	6266	60651618	SO:0001583	missense	8787			AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"Regulators of G-protein signaling"	10004	protein-coding gene	gene with protein product	"regulator of G protein signalling 9", "regulator of G protein signalling 9L", "regulator of G-protein signaling 9L"	604067	"regulator of G-protein signalling 9"			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1444G>A	17.37:g.63221156G>A	ENSP00000262406:p.Val482Met		60651618	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.605289	0.28623	.	.	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.38560	1.15;1.13	4.56	4.56	0.56223	.	0.228808	0.39407	N	0.001367	T	0.49440	0.1557	L	0.27053	0.805	0.39183	D	0.962824	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.962;0.962;0.983	T	0.54649	-0.8262	10	0.66056	D	0.02	.	12.756	0.57335	0.0845:0.0:0.9155:0.0	.	482;482;479	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	M	482;479	ENSP00000262406:V482M;ENSP00000396329:V479M	ENSP00000262406:V482M	V	+	1	0	RGS9	60651618	1.000000	0.71417	0.975000	0.42487	0.421000	0.31385	6.572000	0.74005	2.450000	0.82876	0.561000	0.74099	GTG		0.657	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835		A	63221156	G	A	63221156	3	1	75	1	0	0	0	0	1	0	0	0	13350	1145	40	1	1569	1	RGS9	17	63221156	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	1270533	63221156	17974054	178	21645										
TMEM104	54868	broad.mit.edu	37	chr17	72773474	72773474	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttcctcacttttggaaatggCgggtgaaattacagagaccg	11	8	1	2	rs147087919	byFrequency	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:72773474C>T	ENST00000335464.5	+	2	167	c.5C>T	c.(4-6)gCg>gTg	p.A2V	NAT9_ENST00000580301.1_5'Flank|TMEM104_ENST00000582773.1_Missense_Mutation_p.A2V|NAT9_ENST00000583476.1_5'Flank|NAT9_ENST00000580632.1_5'Flank|NAT9_ENST00000582524.1_5'Flank|NAT9_ENST00000582870.1_5'Flank|TMEM104_ENST00000417024.2_Missense_Mutation_p.A2V|NAT9_ENST00000581136.1_5'Flank|NAT9_ENST00000583757.1_5'Flank|NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000578822.1_5'Flank|NAT9_ENST00000357814.3_5'Flank|TMEM104_ENST00000582330.1_Missense_Mutation_p.A2V	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	2						integral component of membrane (GO:0016021)		p.A2V(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TTGGAAATGGCGGGTGAAATT	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	17											72	71	71					17																	72773474		2203	4300	6503	70285069	SO:0001583	missense	54868			AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.5C>T	17.37:g.72773474C>T	ENSP00000334849:p.Ala2Val		70285069	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	37	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	C	34	5.365410	0.95900	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	T;T	0.56776	1.15;0.44	4.81	4.81	0.61882	.	0.049194	0.85682	D	0.000000	T	0.71962	0.3402	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;P	0.77004	0.989;0.977;0.783	T	0.75875	-0.3163	10	0.72032	D	0.01	-36.5763	15.7722	0.78180	0.0:1.0:0.0:0.0	.	2;2;2	B4DKL7;Q8NE00-2;Q8NE00	.;.;TM104_HUMAN	V	2	ENSP00000334849:A2V;ENSP00000397676:A2V	ENSP00000334849:A2V	A	+	2	0	TMEM104	70285069	0.999000	0.42202	0.952000	0.39060	0.978000	0.69477	4.584000	0.60971	2.392000	0.81423	0.561000	0.74099	GCG		0.498	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		T	72773474	C	T	72773474	3	4	75	1	0	0	0	0	1	0	0	0	16057	768	27	1	7	1	TMEM104	17	72773474	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9552318	72773474	8421736	179	21646										
SGSH	6448	broad.mit.edu	37	chr17	78185900	78185900	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cacgtaggcctcgctgacttGgccccagcgttttgggtgct	13	13	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:78185900G>C	ENST00000326317.6	-	7	1005	c.919C>G	c.(919-921)Caa>Gaa	p.Q307E	SGSH_ENST00000534910.1_Missense_Mutation_p.Q104E|SGSH_ENST00000572208.1_5'Flank|SGSH_ENST00000570923.1_3'UTR	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	307			Q -> P (in MPS3A). {ECO:0000269|PubMed:15902564}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)	p.Q307E(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TCGCTGACTTGGCCCCAGCGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											74	61	65					17																	78185900		2203	4300	6503	75800495	SO:0001583	missense	6448			BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"sulfamidase", "mucopolysaccharidosis type IIIA"	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.919C>G	17.37:g.78185900G>C	ENSP00000314606:p.Gln307Glu		75800495	A8K5E2	Missense_Mutation	SNP	ENST00000326317.6	37	CCDS11770.1	.	.	.	.	.	.	.	.	.	.	G	4.927	0.172160	0.09391	.	.	ENSG00000181523	ENST00000326317;ENST00000534910	D;D	0.98531	-4.98;-4.98	4.62	4.62	0.57501	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.192486	0.45126	D	0.000381	D	0.93808	0.8020	N	0.13140	0.3	0.45541	D	0.998499	B	0.06786	0.001	B	0.15484	0.013	D	0.90487	0.4464	10	0.02654	T	1	-26.7145	17.0355	0.86474	0.0:0.0:1.0:0.0	.	307	P51688	SPHM_HUMAN	E	307;104	ENSP00000314606:Q307E;ENSP00000437778:Q104E	ENSP00000314606:Q307E	Q	-	1	0	SGSH	75800495	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	4.084000	0.57650	2.115000	0.64714	0.557000	0.71058	CAA		0.617	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		C	78185900	G	C	78185900	3	2	75	1	0	0	0	0	1	0	0	0	14258	1357	47	5	597	5	SGSH	17	78185900	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	5412426	78185900	3009310	180	21647										
SLC26A11	6448	broad.mit.edu	37	chr17	78195518	78195518	+	5'Flank	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tggctgaagatggatttcgtCgccggcctctcagttggcct	13	11	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr17:78195518C>A	ENST00000326317.6	-	0	0				SGSH_ENST00000534910.1_5'Flank|SLC26A11_ENST00000546047.2_Silent_p.V53V|SGSH_ENST00000572208.1_5'Flank|SLC26A11_ENST00000572725.1_Silent_p.V53V|SLC26A11_ENST00000571602.1_3'UTR|SLC26A11_ENST00000411502.3_Silent_p.V53V|SGSH_ENST00000570923.1_5'Flank|SLC26A11_ENST00000361193.3_Silent_p.V53V	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase						carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)	p.V53V(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TGGATTTCGTCGCCGGCCTCT	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	17											31	33	32					17																	78195518		2203	4300	6503	75810113	SO:0001631	upstream_gene_variant	284129			BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"sulfamidase", "mucopolysaccharidosis type IIIA"	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688			17.37:g.78195518C>A	Exception_encountered		75810113	A8K5E2	Silent	SNP	ENST00000326317.6	37	CCDS11770.1																																																																																				0.677	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		A	78195518	C	A	78195518	1	1	75	0	1	0	0	0	0	0	0	0	14553	871	31	2		2	SLC26A11	17	78195518	5'Flank	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9618	78195518	2999692	181	21648										
L3MBTL4	91133	broad.mit.edu	37	chr18	6263993	6263993	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gacagccttctgttctttcaAgtaccactcccaagaccatg	6	14	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr18:6263993A>C	ENST00000284898.6	-	5	372	c.172T>G	c.(172-174)Ttg>Gtg	p.L58V	L3MBTL4_ENST00000317931.7_Missense_Mutation_p.L58V|L3MBTL4_ENST00000400104.3_Missense_Mutation_p.L58V|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.L58V	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	58					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.L58V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				TGTTCTTTCAAGTACCACTCC	0.438																																					Esophageal Squamous(41;748 902 17366 28959 43175)											1	Substitution - Missense(1)	large_intestine(1)	18											88	90	90					18																	6263993		2203	4300	6503	6253993	SO:0001583	missense	91133			BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.172T>G	18.37:g.6263993A>C	ENSP00000284898:p.Leu58Val		6253993	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	37	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	A	10.71	1.428191	0.25726	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000400104	D;D;D;D	0.92199	-2.99;-2.99;-2.99;-2.99	5.04	-7.54	0.01332	.	0.000000	0.49305	D	0.000147	D	0.93288	0.7861	M	0.69185	2.1	0.47037	D	0.999297	D	0.89917	1.0	D	0.91635	0.999	D	0.92556	0.6054	10	0.87932	D	0	.	13.0768	0.59091	0.6629:0.0:0.3371:0.0	.	58	Q8NA19	LMBL4_HUMAN	V	58	ENSP00000382976:L58V;ENSP00000318543:L58V;ENSP00000284898:L58V;ENSP00000382975:L58V	ENSP00000284898:L58V	L	-	1	2	L3MBTL4	6253993	0.014000	0.17966	0.305000	0.25099	0.976000	0.68499	-0.754000	0.04787	-1.294000	0.02360	-0.256000	0.11100	TTG		0.438	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		C	6263993	A	C	6263993	3	2	75	1	0	0	0	0	1	0	0	0	8616	69	3	4	1763	4	L3MBTL4	18	6263993	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10		6263993	71813255	182	21649										
ZNF521	25925	broad.mit.edu	37	chr18	22805162	22805162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	caggtctgatgttgtggtctCggagctggtgattctgcagc	15	8	3	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr18:22805162C>T	ENST00000361524.3	-	4	2868	c.2720G>A	c.(2719-2721)cGa>cAa	p.R907Q	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.R687Q|ZNF521_ENST00000538137.2_Missense_Mutation_p.R907Q	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	907					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.R907Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GTTGTGGTCTCGGAGCTGGTG	0.498			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - Missense(1)	large_intestine(1)	18											119	114	116					18																	22805162		2203	4300	6503	21059160	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2720G>A	18.37:g.22805162C>T	ENSP00000354794:p.Arg907Gln		21059160	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532333	0.45073	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.09630	2.96;2.98	6.07	6.07	0.98685	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.36166	0.0957	M	0.81239	2.535	0.40226	D	0.977796	D	0.89917	1.0	D	0.70716	0.97	T	0.03077	-1.1075	10	0.20046	T	0.44	-18.5157	20.6439	0.99570	0.0:1.0:0.0:0.0	.	907	Q96K83	ZN521_HUMAN	Q	907;941;907	ENSP00000354794:R907Q;ENSP00000382352:R907Q	ENSP00000354794:R907Q	R	-	2	0	ZNF521	21059160	1.000000	0.71417	0.444000	0.26895	0.976000	0.68499	7.487000	0.81328	2.884000	0.98904	0.655000	0.94253	CGA		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22805162	C	T	22805162	3	4	75	1	0	0	0	0	1	0	0	0	18004	884	31	1	1235	1	ZNF521	18	22805162	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	16541169	22805162	55272086	183	21650										
C18orf34	374864	broad.mit.edu	37	chr18	30806811	30806811	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gtgagttttttcaggaattcTtctctaccctatatgttagg	8	7	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr18:30806811T>C	ENST00000383096.3	-	16	1784	c.1602A>G	c.(1600-1602)gaA>gaG	p.E534E	CCDC178_ENST00000583930.1_Silent_p.E534E|CCDC178_ENST00000402325.1_Silent_p.E534E|CCDC178_ENST00000403303.1_Silent_p.E534E|CCDC178_ENST00000300227.8_Silent_p.E534E|CCDC178_ENST00000406524.2_Silent_p.E534E|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000579947.1_Silent_p.E534E			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	534								p.E534E(2)									TCAGGAATTCTTCTCTACCCT	0.284																																																2	Substitution - coding silent(2)	large_intestine(2)	18											68	69	69					18																	30806811		2203	4300	6503	29060809	SO:0001819	synonymous_variant	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1602A>G	18.37:g.30806811T>C			29060809	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Silent	SNP	ENST00000383096.3	37	CCDS42424.1																																																																																				0.284	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30806811	T	C	30806811	2	2	75	1	0	0	0	0	0	0	0	1	1908	1606	56	4		4	C18orf34	18	30806811	Silent	SNP	T	TCGA-AG-A026-01A-32W-A096-10	8001649	30806811	47270437	184	21651										
FBXO15	201456	broad.mit.edu	37	chr18	71740902	71740902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgatctcaggcacaccggggAactgaaacaccaaaagggtt	11	11	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr18:71740902A>G	ENST00000419743.2	-	10	1406	c.1327T>C	c.(1327-1329)Tcc>Ccc	p.S443P	FBXO15_ENST00000269500.5_Missense_Mutation_p.S367P|FBXO15_ENST00000580806.1_5'UTR	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	443						SCF ubiquitin ligase complex (GO:0019005)		p.S367P(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		CACACCGGGGAACTGAAACAC	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	18											183	171	175					18																	71740902		2203	4300	6503	69891882	SO:0001583	missense	201456			AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1327T>C	18.37:g.71740902A>G	ENSP00000393154:p.Ser443Pro		69891882	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	a	19.20	3.781400	0.70222	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.44881	0.91;0.91	5.9	4.73	0.59995	.	0.159438	0.52532	D	0.000063	T	0.60843	0.2300	M	0.69823	2.125	0.30247	N	0.794404	D;D	0.76494	0.999;0.998	D;D	0.66196	0.942;0.915	T	0.65434	-0.6169	10	0.87932	D	0	-21.7078	12.6173	0.56584	0.5687:0.4313:0.0:0.0	.	443;367	B3KST3;Q8NCQ5	.;FBX15_HUMAN	P	367;443	ENSP00000269500:S367P;ENSP00000393154:S443P	ENSP00000269500:S367P	S	-	1	0	FBXO15	69891882	1.000000	0.71417	0.996000	0.52242	0.888000	0.51559	2.264000	0.43302	1.043000	0.40175	0.529000	0.55759	TCC		0.478	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		G	71740902	A	G	71740902	3	3	75	1	0	0	0	0	1	0	0	0	5747	246	9	4	209	4	FBXO15	18	71740902	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	40934091	71740902	6336346	185	21652										
MUC16	94025	broad.mit.edu	37	chr19	9082718	9082718	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttctttctcagtggataggcTtatgggagaggaactagaac	12	6	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:9082718T>A	ENST00000397910.4	-	1	9300	c.9097A>T	c.(9097-9099)Agc>Tgc	p.S3033C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3034	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S3033C(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGATAGGCTTATGGGAGAG	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	19											111	110	111					19																	9082718		2033	4196	6229	8943718	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9097A>T	19.37:g.9082718T>A	ENSP00000381008:p.Ser3033Cys		8943718	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.649	-0.282421	0.05642	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.541	0.541	0.17168	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	.	.	.	D	0.67145	0.996	D	0.65773	0.938	T	0.45659	-0.9246	7	0.87932	D	0	.	.	.	.	.	3033	B5ME49	.	C	3033	ENSP00000381008:S3033C	ENSP00000381008:S3033C	S	-	1	0	MUC16	8943718	0.002000	0.14202	0.116000	0.21606	0.082000	0.17680	0.084000	0.14891	0.441000	0.26529	0.260000	0.18958	AGC		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9082718	T	A	9082718	3	1	75	1	0	0	0	0	1	0	0	0	10003	1609	56	5	34762	5	MUC16	19	9082718	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10		9082718	50046265	186	21653										
ZNF266	10781	broad.mit.edu	37	chr19	9524696	9524696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aagatctagtgaaggctatcCcacattccttgcattcataa	6	10	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:9524696C>A	ENST00000592904.1	-	5	2981	c.905G>T	c.(904-906)gGg>gTg	p.G302V	ZNF266_ENST00000361451.2_Missense_Mutation_p.G302V|ZNF266_ENST00000361151.1_Missense_Mutation_p.G302V|ZNF266_ENST00000588221.1_Missense_Mutation_p.G302V|ZNF266_ENST00000592292.1_Missense_Mutation_p.G302V|ZNF266_ENST00000588933.1_Missense_Mutation_p.G302V|ZNF266_ENST00000590306.1_Missense_Mutation_p.G302V			Q14584	ZN266_HUMAN	zinc finger protein 266	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G302V(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						GAAGGCTATCCCACATTCCTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											110	108	109					19																	9524696		2203	4300	6503	9385696	SO:0001583	missense	10781			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.905G>T	19.37:g.9524696C>A	ENSP00000466714:p.Gly302Val		9385696	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.322015	0.60634	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.07567	3.18;3.18	2.53	2.53	0.30540	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36248	0.0960	H	0.94503	3.545	0.46564	D	0.999101	D	0.89917	1.0	D	0.87578	0.998	T	0.50074	-0.8870	9	0.72032	D	0.01	.	11.1769	0.48606	0.0:1.0:0.0:0.0	.	302	Q14584	ZN266_HUMAN	V	302	ENSP00000354680:G302V;ENSP00000355047:G302V	ENSP00000355047:G302V	G	-	2	0	ZNF266	9385696	0.026000	0.19158	0.506000	0.27664	0.244000	0.25665	0.208000	0.17415	1.727000	0.51537	0.555000	0.69702	GGG		0.378	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			A	9524696	C	A	9524696	3	1	75	1	0	0	0	0	1	0	0	0	17844	623	22	2	748	2	ZNF266	19	9524696	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	441978	9524696	49604287	187	21654										
DNASE2	1777	broad.mit.edu	37	chr19	12989212	12989212	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcaccatctccaaatttgctGaacttggcaaagctctggaa	7	11	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:12989212G>A	ENST00000222219.3	-	5	785	c.693C>T	c.(691-693)ttC>ttT	p.F231F	DNASE2_ENST00000538460.1_Silent_p.F176F|CTD-2265O21.7_ENST00000592400.1_RNA	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	231					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)	p.F231F(1)		breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						CAAATTTGCTGAACTTGGCAA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	19											99	112	107					19																	12989212		2203	4300	6503	12850212	SO:0001819	synonymous_variant	1777			AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.693C>T	19.37:g.12989212G>A			12850212	B2RD06|B7Z4K6|O43910	Silent	SNP	ENST00000222219.3	37	CCDS12284.1																																																																																				0.547	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			A	12989212	G	A	12989212	2	1	75	1	0	0	0	0	0	0	0	1	4675	1281	45	3		3	DNASE2	19	12989212	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	3464516	12989212	46139771	188	21655										
ZNF568	374900	broad.mit.edu	37	chr19	37440531	37440531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cattgaatgtaaaaaagttgCgaaaatatttcctctgagtt	7	5	1	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:37440531C>T	ENST00000333987.7	+	7	982	c.476C>T	c.(475-477)gCg>gTg	p.A159V	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.A95V	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	159					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A159V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAAAAGTTGCGAAAATATTT	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	19											76	70	72					19																	37440531		1825	4083	5908	42132371	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.476C>T	19.37:g.37440531C>T	ENSP00000334685:p.Ala159Val		42132371	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	C	9.086	1.000416	0.19121	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.07800	3.16;3.16	4.17	1.88	0.25563	.	0.995063	0.08135	N	0.992462	T	0.05960	0.0155	L	0.27053	0.805	0.09310	N	1	B	0.32781	0.384	B	0.21546	0.035	T	0.37753	-0.9692	10	0.66056	D	0.02	.	6.6885	0.23158	0.3643:0.4583:0.1774:0.0	.	159	Q3ZCX4	ZN568_HUMAN	V	159;95	ENSP00000334685:A159V;ENSP00000394514:A95V	ENSP00000334685:A159V	A	+	2	0	ZNF568	42132371	0.000000	0.05858	0.029000	0.17559	0.797000	0.45037	-0.560000	0.05964	0.442000	0.26555	0.655000	0.94253	GCG		0.348	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37440531	C	T	37440531	3	4	75	1	0	0	0	0	1	0	0	0	18038	768	27	1	494	1	ZNF568	19	37440531	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	24451319	37440531	21688452	189	21656										
ZNF570	148268	broad.mit.edu	37	chr19	37975202	37975202	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgtaatgactgtgaaaaagtCttcagccagagttcatccct	8	9	3	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:37975202C>G	ENST00000330173.1	+	5	1207	c.678C>G	c.(676-678)gtC>gtG	p.V226V	ZNF570_ENST00000388801.3_Silent_p.V23V|ZNF570_ENST00000586475.1_Silent_p.V282V	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V226V(1)		endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTGAAAAAGTCTTCAGCCAGA	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	19											111	129	123					19																	37975202		2203	4299	6502	42667042	SO:0001819	synonymous_variant	148268			AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.678C>G	19.37:g.37975202C>G			42667042	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																				0.363	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		G	37975202	C	G	37975202	2	3	75	1	0	0	0	0	0	0	0	1	18041	900	32	5		5	ZNF570	19	37975202	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10	534671	37975202	21153781	190	21657										
ZNF607	84775	broad.mit.edu	37	chr19	38190600	38190600	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aatgccttcctaaacttttcAcattgatcaggttcctcact	4	12	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:38190600A>C	ENST00000355202.4	-	5	1027	c.432T>G	c.(430-432)tgT>tgG	p.C144W	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.C143W	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C144W(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TAAACTTTTCACATTGATCAG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	19											148	146	147					19																	38190600		2203	4300	6503	42882440	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.432T>G	19.37:g.38190600A>C	ENSP00000347338:p.Cys144Trp		42882440	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	A	6.081	0.383188	0.11524	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.40225	1.04;1.04	2.1	2.1	0.27182	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71736	0.3375	H	0.97682	4.055	0.21822	N	0.999521	D;D	0.89917	0.993;1.0	P;D	0.91635	0.858;0.999	T	0.59327	-0.7475	9	0.87932	D	0	.	5.2394	0.15464	0.8403:0.0:0.1597:0.0	.	144;143	Q96SK3;F5H141	ZN607_HUMAN;.	W	144;143	ENSP00000347338:C144W;ENSP00000438015:C143W	ENSP00000347338:C144W	C	-	3	2	ZNF607	42882440	0.001000	0.12720	0.026000	0.17262	0.012000	0.07955	-0.124000	0.10595	0.952000	0.37798	0.459000	0.35465	TGT		0.373	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		C	38190600	A	C	38190600	3	2	75	1	0	0	0	0	1	0	0	0	18072	157	6	4	1662	4	ZNF607	19	38190600	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	215398	38190600	20938383	191	21658										
RYR1	6261	broad.mit.edu	37	chr19	38987109	38987109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcctctgctatttctgccgaAtcagccggcagaaccagcgc	9	15	3	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:38987109A>G	ENST00000359596.3	+	41	6724	c.6724A>G	c.(6724-6726)Atc>Gtc	p.I2242V	RYR1_ENST00000360985.3_Missense_Mutation_p.I2242V|RYR1_ENST00000355481.4_Missense_Mutation_p.I2242V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2242	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.I2242V(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TTTCTGCCGAATCAGCCGGCA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											49	52	51					19																	38987109		2203	4300	6503	43678949	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6724A>G	19.37:g.38987109A>G	ENSP00000352608:p.Ile2242Val		43678949	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.434978	0.43224	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.88818	-2.43;-2.43;-2.43	4.91	4.91	0.64330	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000002	D	0.92734	0.7690	L	0.56769	1.78	0.45172	D	0.998182	P;D	0.53151	0.948;0.958	D;D	0.70716	0.949;0.97	D	0.93328	0.6698	10	0.66056	D	0.02	.	14.3703	0.66836	1.0:0.0:0.0:0.0	.	2242;2242	P21817-2;P21817	.;RYR1_HUMAN	V	2242	ENSP00000352608:I2242V;ENSP00000347667:I2242V;ENSP00000354254:I2242V	ENSP00000347667:I2242V	I	+	1	0	RYR1	43678949	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.139000	0.94554	2.061000	0.61500	0.454000	0.30748	ATC		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38987109	A	G	38987109	3	3	75	1	0	0	0	0	1	0	0	0	13805	101	4	4	6886	4	RYR1	19	38987109	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	796509	38987109	20141874	192	21659										
CYP2A6	1548	broad.mit.edu	37	chr19	41355745	41355746	+	Nonsense_Mutation	DNP	GA	GA	TT													0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tagcctttgaagacccagtcGaaggtggcttgctcgcctcg							TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:41355745_41355746GA>TT	ENST00000301141.5	-	2	340_341	c.320_321TC>AA	c.(319-321)tTC>tAA	p.F107*	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	107					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.F107>?(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AGACCCAGTCGAAGGTGGCTTG	0.644																																																1	Complex(1)	large_intestine(1)	19																																								46047586	SO:0001587	stop_gained	1548			AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.320_321delinsTT	19.37:g.41355745_41355746delinsTT	ENSP00000301141:p.Phe107*		46047585	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Nonsense_Mutation	DNP	ENST00000301141.5	37	CCDS12568.1																																																																																				0.644	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		TT	41355746	GA	TT	41355745	4	4	75	1	0	0	0	0	0	1	0	0	4168	1049	37	2	1195	2	CYP2A6	19	41355745	Nonsense_Mutation	DNP	GA	TCGA-AG-A026-01A-32W-A096-10	2368636	41355745	17773238	193	21660										
ARHGAP35	2909	broad.mit.edu	37	chr19	47424699	47424699	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	acggaaggttcacaagcatcCcctgtagccaaccccagcat	8	15	1	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:47424699C>A	ENST00000404338.3	+	1	2767	c.2767C>A	c.(2767-2769)Ccc>Acc	p.P923T		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	923					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.P923T(1)									CACAAGCATCCCCTGTAGCCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	19											119	118	118					19																	47424699		1919	4136	6055	52116539	SO:0001583	missense	2909			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2767C>A	19.37:g.47424699C>A	ENSP00000385720:p.Pro923Thr		52116539	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	C	2.644	-0.283492	0.05642	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.06449	3.3	5.79	5.79	0.91817	.	0.237636	0.43110	D	0.000604	T	0.06508	0.0167	L	0.29908	0.895	0.39034	D	0.960002	B	0.28933	0.228	B	0.25614	0.062	T	0.45293	-0.9271	10	0.16896	T	0.51	-25.8602	18.8035	0.92028	0.0:1.0:0.0:0.0	.	923	Q9NRY4-2	.	T	923	ENSP00000385720:P923T	ENSP00000324820:P923T	P	+	1	0	ARHGAP35	52116539	0.081000	0.21417	1.000000	0.80357	0.995000	0.86356	0.875000	0.28079	2.743000	0.94032	0.655000	0.94253	CCC		0.433	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		A	47424699	C	A	47424699	3	1	75	1	0	0	0	0	1	0	0	0	6816	623	22	2	2769	2	ARHGAP35	19	47424699	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	6068954	47424699	11704284	194	21661										
GLTSCR1	29998	broad.mit.edu	37	chr19	48198221	48198221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgccgccccgcagacctccaCcagcctggggcccctcacca	9	22	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:48198221C>A	ENST00000396720.3	+	9	3154	c.2960C>A	c.(2959-2961)aCc>aAc	p.T987N	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	987								p.T987N(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CAGACCTCCACCAGCCTGGGG	0.726																																																1	Substitution - Missense(1)	large_intestine(1)	19											9	11	11					19																	48198221		1810	4044	5854	52890033	SO:0001583	missense	29998			AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.2960C>A	19.37:g.48198221C>A	ENSP00000379946:p.Thr987Asn		52890033	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	C	3.975	-0.007611	0.07773	.	.	ENSG00000063169	ENST00000396720	T	0.35605	1.3	3.43	1.21	0.21127	.	.	.	.	.	T	0.19446	0.0467	N	0.14661	0.345	0.09310	N	1	B	0.29716	0.255	B	0.31812	0.136	T	0.26643	-1.0097	9	0.25106	T	0.35	.	5.8355	0.18605	0.0:0.732:0.0:0.268	.	987	Q9NZM4	GSCR1_HUMAN	N	987	ENSP00000379946:T987N	ENSP00000379946:T987N	T	+	2	0	GLTSCR1	52890033	0.031000	0.19500	0.790000	0.31976	0.020000	0.10135	1.131000	0.31406	0.111000	0.17947	0.313000	0.20887	ACC		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		A	48198221	C	A	48198221	3	1	75	1	0	0	0	0	1	0	0	0	6494	507	18	2	2986	2	GLTSCR1	19	48198221	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	773522	48198221	10930762	195	21662										
TPRX1	284355	broad.mit.edu	37	chr19	48305873	48305873	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ttgggcctgggattggggctGggatcgggcttgggatctga	20	6	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:48305873G>T	ENST00000322175.3	-	2	550	c.395C>A	c.(394-396)cCa>cAa	p.P132Q	TPRX1_ENST00000543508.1_Missense_Mutation_p.P132Q|TPRX1_ENST00000535759.1_Missense_Mutation_p.P229Q	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	132	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P132Q(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gattggggctgggatcgggct	0.652																																					Esophageal Squamous(123;175 2281 3051 32395)											1	Substitution - Missense(1)	large_intestine(1)	19											19	17	18					19																	48305873		2078	4084	6162	52997685	SO:0001583	missense	284355				CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.395C>A	19.37:g.48305873G>T	ENSP00000323455:p.Pro132Gln		52997685	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	g	0.306	-0.970557	0.02232	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.59364	0.27;0.27;0.27	0.383	-0.766	0.11020	.	.	.	.	.	T	0.31327	0.0793	N	0.19112	0.55	0.09310	N	1	B	0.30361	0.277	B	0.20955	0.032	T	0.09400	-1.0676	8	0.42905	T	0.14	.	.	.	.	.	132	Q8N7U7	TPRX1_HUMAN	Q	132;229;132	ENSP00000323455:P132Q;ENSP00000438832:P229Q;ENSP00000438712:P132Q	ENSP00000323455:P132Q	P	-	2	0	TPRX1	52997685	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.540000	0.06106	-1.947000	0.01034	-2.005000	0.00442	CCA		0.652	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		T	48305873	G	T	48305873	3	4	75	1	0	0	0	0	1	0	0	0	16462	1348	47	2	844	2	TPRX1	19	48305873	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	107652	48305873	10823110	196	21663										
ZNF528	84436	broad.mit.edu	37	chr19	52919663	52919663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	aaattcatacaggagaaaagCcttacaaatgtaatcaatgt	6	6	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:52919663C>T	ENST00000360465.3	+	7	1984	c.1558C>T	c.(1558-1560)Cct>Tct	p.P520S	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	520					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P520S(1)		breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AGGAGAAAAGCCTTACAAATG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	19											58	56	57					19																	52919663		2203	4300	6503	57611475	SO:0001583	missense	84436			AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.1558C>T	19.37:g.52919663C>T	ENSP00000353652:p.Pro520Ser		57611475	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.248455	0.22880	.	.	ENSG00000167555	ENST00000360465	T	0.28454	1.61	1.83	1.83	0.25207	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38692	0.1050	L	0.60455	1.87	0.23906	N	0.996502	D	0.54047	0.964	P	0.50659	0.647	T	0.19647	-1.0299	9	0.66056	D	0.02	.	10.6285	0.45521	0.0:1.0:0.0:0.0	.	520	Q3MIS6	ZN528_HUMAN	S	520	ENSP00000353652:P520S	ENSP00000353652:P520S	P	+	1	0	ZNF528	57611475	0.720000	0.27996	0.389000	0.26208	0.041000	0.13682	3.121000	0.50438	0.986000	0.38683	0.557000	0.71058	CCT		0.388	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		T	52919663	C	T	52919663	3	4	75	1	0	0	0	0	1	0	0	0	18008	739	26	3	1572	3	ZNF528	19	52919663	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	4613790	52919663	6209320	197	21664										
LILRB5	10990	broad.mit.edu	37	chr19	54758749	54758749	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctataagactggtactttgaCtttagacacagcgggggatg	12	7	0	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:54758749C>A	ENST00000316219.5	-	6	1211	c.1104G>T	c.(1102-1104)aaG>aaT	p.K368N	LILRB5_ENST00000345866.6_Missense_Mutation_p.K268N|LILRB5_ENST00000449561.2_Missense_Mutation_p.K368N|LILRB5_ENST00000450632.1_Missense_Mutation_p.K359N	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	368	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.K359N(1)|p.K368N(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTACTTTGACTTTAGACACA	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	19											85	81	83					19																	54758749		2203	4300	6503	59450561	SO:0001583	missense	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1104G>T	19.37:g.54758749C>A	ENSP00000320390:p.Lys368Asn		59450561	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.601172	0.28534	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.02916	4.11;4.11;4.11;4.11	3.08	-5.73	0.02398	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.716310	0.01649	N	0.024453	T	0.04363	0.0120	L	0.31526	0.94	0.09310	N	1	B;P;P;B;B	0.50443	0.1;0.888;0.935;0.01;0.033	B;P;P;B;B	0.53954	0.06;0.698;0.738;0.015;0.026	T	0.29792	-1.0000	10	0.87932	D	0	.	2.2052	0.03934	0.1853:0.4592:0.1554:0.2002	.	359;259;268;368;368	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	N	368;359;368;268	ENSP00000320390:K368N;ENSP00000414225:K359N;ENSP00000406478:K368N;ENSP00000263430:K268N	ENSP00000320390:K368N	K	-	3	2	LILRB5	59450561	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.210000	0.00273	-1.341000	0.02225	-0.510000	0.04470	AAG		0.532	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			A	54758749	C	A	54758749	3	1	75	1	0	0	0	0	1	0	0	0	8817	564	20	2	703	2	LILRB5	19	54758749	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1839086	54758749	4370234	198	21665										
EPN1	29924	broad.mit.edu	37	chr19	56204103	56204103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgatccctggacaccggcccCggccttctcagatccctggg	11	18	1	1	rs370785243		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:56204103C>T	ENST00000270460.6	+	8	1429	c.1118C>T	c.(1117-1119)cCg>cTg	p.P373L	EPN1_ENST00000085079.7_Missense_Mutation_p.P348L|AC010525.4_ENST00000585559.1_RNA|EPN1_ENST00000411543.2_Missense_Mutation_p.P459L	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	373	8 X 3 AA repeats of [ED]-P-W.|Ala/Gly/Pro-rich.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.P459L(1)		endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		ACACCGGCCCCGGCCTTCTCA	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	LEU/PRO,LEU/PRO,LEU/PRO	0,3824		0,0,1912	12	15	14		1376,1118,1043	2.2	0.1	19		14	1,8225		0,1,4112	no	missense,missense,missense	EPN1	NM_001130071.1,NM_001130072.1,NM_013333.3	98,98,98	0,1,6024	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging	459/663,373/577,348/551	56204103	1,12049	1912	4113	6025	60895915	SO:0001583	missense	29924			AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.1118C>T	19.37:g.56204103C>T	ENSP00000270460:p.Pro373Leu		60895915	Q86ST3|Q9HA18	Missense_Mutation	SNP	ENST00000270460.6	37	CCDS46199.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320881	0.23994	0.0	1.22E-4	ENSG00000063245	ENST00000270460;ENST00000085079;ENST00000544375;ENST00000411543	T;T;T	0.15952	2.45;2.4;2.38	3.3	2.22	0.28083	.	0.259012	0.31784	N	0.007065	T	0.13884	0.0336	L	0.48642	1.525	0.37982	D	0.933632	B;P;B;D	0.54047	0.249;0.876;0.249;0.964	B;B;B;B	0.40825	0.019;0.124;0.019;0.341	T	0.17899	-1.0354	10	0.25106	T	0.35	-17.6055	10.8229	0.46614	0.1914:0.8086:0.0:0.0	.	334;459;373;348	B4DU91;Q9Y6I3-1;Q9Y6I3;Q9Y6I3-3	.;.;EPN1_HUMAN;.	L	373;348;334;459	ENSP00000270460:P373L;ENSP00000085079:P348L;ENSP00000406209:P459L	ENSP00000085079:P348L	P	+	2	0	EPN1	60895915	0.157000	0.22836	0.121000	0.21740	0.002000	0.02628	3.220000	0.51207	0.710000	0.31997	-0.521000	0.04368	CCG		0.662	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333		T	56204103	C	T	56204103	3	4	75	1	0	0	0	0	1	0	0	0	5198	652	23	1	1485	1	EPN1	19	56204103	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	1445354	56204103	2924880	199	21666										
ZNF582	147948	broad.mit.edu	37	chr19	56896345	56896345	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tggtcaaaagtgggcatttcTtcatgtctgatgatcatctg	10	7	6	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:56896345T>G	ENST00000301310.4	-	5	599	c.441A>C	c.(439-441)gaA>gaC	p.E147D	ZNF582_ENST00000586929.1_Missense_Mutation_p.E147D|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	147					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E147D(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		TGGGCATTTCTTCATGTCTGA	0.368																																					Ovarian(183;1887 2032 4349 30507 51343)											1	Substitution - Missense(1)	large_intestine(1)	19											150	148	149					19																	56896345		2203	4300	6503	61588157	SO:0001583	missense	147948			AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.441A>C	19.37:g.56896345T>G	ENSP00000301310:p.Glu147Asp		61588157	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.281391	0.40394	.	.	ENSG00000018869	ENST00000301310	T	0.06142	3.34	4.23	3.21	0.36854	.	0.218000	0.23298	N	0.049714	T	0.07548	0.0190	L	0.48642	1.525	0.09310	N	1	P;P	0.47409	0.895;0.895	P;P	0.44518	0.452;0.452	T	0.19582	-1.0301	10	0.54805	T	0.06	.	6.7391	0.23424	0.0:0.106:0.0:0.894	.	147;178	Q96NG8;B4DQZ9	ZN582_HUMAN;.	D	147	ENSP00000301310:E147D	ENSP00000301310:E147D	E	-	3	2	ZNF582	61588157	0.724000	0.28038	0.007000	0.13788	0.254000	0.26022	0.054000	0.14205	0.941000	0.37499	0.482000	0.46254	GAA		0.368	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		G	56896345	T	G	56896345	3	3	75	1	0	0	0	0	1	0	0	0	18053	1606	56	4	1116	4	ZNF582	19	56896345	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	692242	56896345	2232638	200	21667										
ZIM3	114026	broad.mit.edu	37	chr19	57646504	57646504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	atgaaggtttgacttctgaaAgaaggcttttccacatctgt	9	7	2	4			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr19:57646504A>G	ENST00000269834.1	-	5	1586	c.1201T>C	c.(1201-1203)Ttt>Ctt	p.F401L	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	401					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F401L(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GACTTCTGAAAGAAGGCTTTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											142	145	144					19																	57646504		2203	4300	6503	62338316	SO:0001583	missense	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1201T>C	19.37:g.57646504A>G	ENSP00000269834:p.Phe401Leu		62338316	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	A	0.088	-1.171461	0.01660	.	.	ENSG00000141946	ENST00000269834	T	0.32023	1.47	2.71	-5.43	0.02632	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09468	0.0233	N	0.03029	-0.43	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.20874	-1.0262	9	0.62326	D	0.03	.	0.8516	0.01173	0.3547:0.1318:0.1194:0.3941	.	401	Q96PE6	ZIM3_HUMAN	L	401	ENSP00000269834:F401L	ENSP00000269834:F401L	F	-	1	0	ZIM3	62338316	0.000000	0.05858	0.004000	0.12327	0.090000	0.18270	-6.358000	0.00069	-1.173000	0.02758	-0.696000	0.03686	TTT		0.378	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			G	57646504	A	G	57646504	3	3	75	1	0	0	0	0	1	0	0	0	17724	72	3	4	221	4	ZIM3	19	57646504	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	750159	57646504	1482479	201	21668										
RASSF2	9770	broad.mit.edu	37	chr20	4776522	4776522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ggatggagggggtcgaatgcGttcgttgtcatcctgcatct	15	8	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr20:4776522G>A	ENST00000379400.3	-	5	421	c.226C>T	c.(226-228)Cgc>Tgc	p.R76C	RASSF2_ENST00000379376.2_Missense_Mutation_p.R76C|RASSF2_ENST00000478553.1_5'Flank	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	76					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R76C(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						GGTCGAATGCGTTCGTTGTCA	0.617																																					Melanoma(158;1891 3343 50738)											1	Substitution - Missense(1)	large_intestine(1)	20											133	123	127					20																	4776522		2203	4300	6503	4724522	SO:0001583	missense	9770			D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"centromere protein 34"	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.226C>T	20.37:g.4776522G>A	ENSP00000368710:p.Arg76Cys		4724522	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Missense_Mutation	SNP	ENST00000379400.3	37	CCDS13083.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545666	0.65198	.	.	ENSG00000101265	ENST00000379400;ENST00000379376	T;T	0.10960	2.82;2.82	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	P	0.62885	0.908	T	0.01500	-1.1339	10	0.35671	T	0.21	.	12.4217	0.55524	0.0:0.0:0.8321:0.1678	.	76	P50749	RASF2_HUMAN	C	76	ENSP00000368710:R76C;ENSP00000368684:R76C	ENSP00000368684:R76C	R	-	1	0	RASSF2	4724522	1.000000	0.71417	0.997000	0.53966	0.489000	0.33432	5.022000	0.64078	2.665000	0.90641	0.563000	0.77884	CGC		0.617	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		A	4776522	G	A	4776522	3	1	75	1	0	0	0	0	1	0	0	0	13123	1145	40	1	786	1	RASSF2	20	4776522	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		4776522	58248998	202	21669										
C20orf117	140710	broad.mit.edu	37	chr20	35431473	35431473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctgccttccagtcgggccctGcccgctccccggcccccttc	9	23	0	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr20:35431473G>A	ENST00000357779.3	-	11	2737	c.2411C>T	c.(2410-2412)gCa>gTa	p.A804V	SOGA1_ENST00000456801.2_Missense_Mutation_p.A645V|SOGA1_ENST00000279034.6_Missense_Mutation_p.A804V|SOGA1_ENST00000237536.4_Missense_Mutation_p.A1042V			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	804					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.A804V(1)		endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GTCGGGCCCTGCCCGCTCCCC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	20											17	20	19					20																	35431473		2135	4248	6383	34864887	SO:0001583	missense	140710			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2411C>T	20.37:g.35431473G>A	ENSP00000350424:p.Ala804Val		34864887	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	G	9.893	1.204711	0.22205	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.18174	2.23;2.23;2.24;2.24	5.58	4.63	0.57726	.	0.861437	0.10477	N	0.670105	T	0.13543	0.0328	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23904	-1.0175	10	0.33940	T	0.23	3.1044	13.6715	0.62427	0.076:0.0:0.924:0.0	.	804	O94964-4	.	V	1042;804;645;804	ENSP00000237536:A1042V;ENSP00000279034:A804V;ENSP00000413886:A645V;ENSP00000350424:A804V	ENSP00000237536:A1042V	A	-	2	0	KIAA0889	34864887	0.100000	0.21855	0.008000	0.14137	0.232000	0.25224	2.735000	0.47377	1.357000	0.45904	0.563000	0.77884	GCA		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		A	35431473	G	A	35431473	3	1	75	1	0	0	0	0	1	0	0	0	2089	1319	46	3	1942	3	C20orf117	20	35431473	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	30654951	35431473	27594047	203	21670										
SEMG2	6407	broad.mit.edu	37	chr20	43851702	43851702	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cttcaagtacagaagaaagaCgactcaactatggaggaaag	10	7	2	3	rs546357756		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr20:43851702C>T	ENST00000372769.3	+	2	1519	c.1429C>T	c.(1429-1431)Cga>Tga	p.R477*		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	477	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.R477*(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				AGAAGAAAGACGACTCAACTA	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		23707	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	large_intestine(1)	20											80	80	80					20																	43851702		2203	4300	6503	43285116	SO:0001587	stop_gained	6407				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1429C>T	20.37:g.43851702C>T	ENSP00000361855:p.Arg477*		43285116	Q53ZU2|Q6X2M5|Q6X2M6	Nonsense_Mutation	SNP	ENST00000372769.3	37	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686047	0.47991	.	.	ENSG00000124157	ENST00000372769	.	.	.	1.38	-2.06	0.07298	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	1.7879	0.03045	0.2797:0.3394:0.0:0.3808	.	.	.	.	X	477	.	ENSP00000361855:R477X	R	+	1	2	SEMG2	43285116	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.664000	0.05292	-0.689000	0.05149	-0.182000	0.12963	CGA		0.393	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		T	43851702	C	T	43851702	4	4	75	1	0	0	0	0	0	1	0	0	14082	528	19	1	1435	1	SEMG2	20	43851702	Nonsense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	8420229	43851702	19173818	204	21671										
HUNK	30811	broad.mit.edu	37	chr21	33331199	33331199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gaccgggacgctgcctttcaCggtggagcctttcagcctga	13	13	2	1	rs576162040		TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr21:33331199C>T	ENST00000270112.2	+	5	1151	c.791C>T	c.(790-792)aCg>aTg	p.T264M		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	264	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T264M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CTGCCTTTCACGGTGGAGCCT	0.537													C|||	1	0.000199681	0	0	5008	,	,		19682	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21											152	136	141					21																	33331199		2203	4300	6503	32253070	SO:0001583	missense	30811			AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.791C>T	21.37:g.33331199C>T	ENSP00000270112:p.Thr264Met		32253070		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607871	0.87258	.	.	ENSG00000142149	ENST00000270112	T	0.65916	-0.18	4.87	4.87	0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73877	0.3643	L	0.45422	1.42	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.76753	-0.2843	10	0.87932	D	0	-10.7685	18.2097	0.89866	0.0:1.0:0.0:0.0	.	264	P57058	HUNK_HUMAN	M	264	ENSP00000270112:T264M	ENSP00000270112:T264M	T	+	2	0	HUNK	32253070	1.000000	0.71417	0.951000	0.38953	0.937000	0.57800	7.104000	0.77024	2.525000	0.85131	0.655000	0.94253	ACG		0.537	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33331199	C	T	33331199	3	4	75	1	0	0	0	0	1	0	0	0	7479	536	19	1	809	1	HUNK	21	33331199	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10		33331199	14798696	205	21672										
CECR1	51816	broad.mit.edu	37	chr22	17672656	17672656	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gctacttcctggtaagtcttCactgaccactcttcgtcatg	7	13	4	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr22:17672656C>T	ENST00000399839.1	-	5	1068	c.798G>A	c.(796-798)gtG>gtA	p.V266V	CECR1_ENST00000262607.3_Silent_p.V266V|CECR1_ENST00000480276.1_5'UTR|CECR1_ENST00000399837.2_Silent_p.V266V|CECR1_ENST00000449907.2_Silent_p.V224V|CECR1_ENST00000330232.4_Silent_p.V25V	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	266					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.V266V(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GGTAAGTCTTCACTGACCACT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	22											153	146	148					22																	17672656		2203	4300	6503	16052656	SO:0001819	synonymous_variant	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.798G>A	22.37:g.17672656C>T			16052656	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																				0.488	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			T	17672656	C	T	17672656	2	4	75	1	0	0	0	0	0	0	0	1	3211	813	29	3		3	CECR1	22	17672656	Silent	SNP	C	TCGA-AG-A026-01A-32W-A096-10		17672656	33631910	206	21673										
MMP11	4320	broad.mit.edu	37	chr22	24122836	24122836	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tggcccatgccttcttccccAagactcaccgagaaggggat	10	14	2	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chr22:24122836A>G	ENST00000215743.3	+	4	602	c.550A>G	c.(550-552)Aag>Gag	p.K184E	MMP11_ENST00000477567.1_3'UTR	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	184					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K184E(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	CTTCTTCCCCAAGACTCACCG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	22											67	65	66					22																	24122836		2203	4300	6503	22452836	SO:0001583	missense	4320				CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.550A>G	22.37:g.24122836A>G	ENSP00000215743:p.Lys184Glu		22452836	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313137	0.81358	.	.	ENSG00000099953	ENST00000215743	T	0.13657	2.57	4.33	4.33	0.51752	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.092863	0.64402	D	0.000001	T	0.08358	0.0208	N	0.05510	-0.035	0.58432	D	0.999992	P	0.48640	0.913	B	0.41174	0.349	T	0.22906	-1.0203	10	0.72032	D	0.01	.	13.7466	0.62879	1.0:0.0:0.0:0.0	.	184	P24347	MMP11_HUMAN	E	184	ENSP00000215743:K184E	ENSP00000215743:K184E	K	+	1	0	MMP11	22452836	0.999000	0.42202	0.999000	0.59377	0.976000	0.68499	4.209000	0.58493	2.193000	0.70182	0.529000	0.55759	AAG		0.612	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		G	24122836	A	G	24122836	3	3	75	1	0	0	0	0	1	0	0	0	9680	131	5	4	564	4	MMP11	22	24122836	Missense_Mutation	SNP	A	TCGA-AG-A026-01A-32W-A096-10	6450180	24122836	27181730	207	21674										
MAGEB18	286514	broad.mit.edu	37	chrX	26157245	26157245	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ctatcttctctttggtgacaGaccccagaatttgcctgctg	8	12	2	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:26157245G>T	ENST00000325250.1	+	2	330	c.143G>T	c.(142-144)aGa>aTa	p.R48I		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	48						cytoplasm (GO:0005737)		p.R48I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						TTTGGTGACAGACCCCAGAAT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	X											51	45	47					X																	26157245		2202	4300	6502	26067166	SO:0001583	missense	286514			AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.143G>T	X.37:g.26157245G>T	ENSP00000314543:p.Arg48Ile		26067166		Missense_Mutation	SNP	ENST00000325250.1	37	CCDS14216.1	.	.	.	.	.	.	.	.	.	.	G	8.124	0.781586	0.16120	.	.	ENSG00000176774	ENST00000325250	T	0.04049	3.72	3.78	-5.13	0.02884	Melanoma associated antigen, MAGE, N-terminal (1);	2.685990	0.01163	N	0.006694	T	0.04815	0.0130	L	0.51422	1.61	0.09310	N	1	B	0.10296	0.003	B	0.16722	0.016	T	0.36986	-0.9725	10	0.33940	T	0.23	.	0.2163	0.00162	0.283:0.2734:0.1934:0.2502	.	48	Q96M61	MAGBI_HUMAN	I	48	ENSP00000314543:R48I	ENSP00000314543:R48I	R	+	2	0	MAGEB18	26067166	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.838000	0.04372	-1.534000	0.01743	0.600000	0.82982	AGA		0.562	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699		T	26157245	G	T	26157245	3	4	75	1	0	0	0	0	1	0	0	0	9205	942	33	2	145	2	MAGEB18	23	26157245	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10		26157245	129113315	208	21675										
DMD	1756	broad.mit.edu	37	chrX	32381009	32381009	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gtcaccgcggtttgccatcaAgtttgctgcttggtcacgtg	12	11	3	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:32381009A>G	ENST00000357033.4	-	37	5427	c.5221T>C	c.(5221-5223)Ttg>Ctg	p.L1741L	DMD_ENST00000378677.2_Silent_p.L1737L	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1741	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L1737L(1)|p.L400L(1)|p.L1736L(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				TTTGCCATCAAGTTTGCTGCT	0.463																																																3	Substitution - coding silent(3)	large_intestine(3)	X											202	154	170					X																	32381009		2202	4300	6502	32290930	SO:0001819	synonymous_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5221T>C	X.37:g.32381009A>G			32290930	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																				0.463	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	32381009	A	G	32381009	2	3	75	1	0	0	0	0	0	0	0	1	4591	69	3	4		4	DMD	23	32381009	Silent	SNP	A	TCGA-AG-A026-01A-32W-A096-10	6223764	32381009	122889551	209	21676										
USP9X	8239	broad.mit.edu	37	chrX	41007672	41007672	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cgtgaaaagctacttgagctGatacgtcgtcttgcagaaga	11	8	1	5			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:41007672G>A	ENST00000324545.8	+	12	2103	c.1470G>A	c.(1468-1470)ctG>ctA	p.L490L	USP9X_ENST00000378308.2_Silent_p.L490L	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	490					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.L483L(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TACTTGAGCTGATACGTCGTC	0.403																																					Ovarian(172;1807 2695 35459 49286)											1	Substitution - coding silent(1)	large_intestine(1)	X											194	169	177					X																	41007672		2203	4300	6503	40892616	SO:0001819	synonymous_variant	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1470G>A	X.37:g.41007672G>A			40892616	O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	37	CCDS43930.1																																																																																				0.403	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	41007672	G	A	41007672	2	1	75	1	0	0	0	0	0	0	0	1	17130	1277	45	3		3	USP9X	23	41007672	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	8626663	41007672	114262888	210	21677										
PAGE5	90737	broad.mit.edu	37	chrX	55247041	55247041	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	ccccaggtcctgatgcaggcGccatgggccggtaatcgtgg	15	13	0	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:55247041G>A	ENST00000289619.5	+	1	254	c.9G>A	c.(7-9)gcG>gcA	p.A3A	PAGE5_ENST00000374955.3_Intron|PAGE5_ENST00000374952.1_Intron	NM_130467.3	NP_569734.2	Q96GU1	PAGE5_HUMAN	P antigen family, member 5 (prostate associated)	3								p.A3A(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8						TGATGCAGGCGCCATGGGCCG	0.667																																																2	Substitution - coding silent(2)	large_intestine(2)	X											33	24	27					X																	55247041		2202	4298	6500	55263766	SO:0001819	synonymous_variant	90737			AJ344352	CCDS14368.1, CCDS35306.1	Xp11.22	2009-08-18			ENSG00000158639	ENSG00000158639			29992	protein-coding gene	gene with protein product	"cancer/testis antigen family 16, member 1", "cancer/testis antigen family 16, member 2"					11920606, 11992404	Standard	XM_006724613		Approved	PAGE-5, CT16.1, CT16.2	uc004duk.3	Q96GU1	OTTHUMG00000021650	ENST00000289619.5:c.9G>A	X.37:g.55247041G>A			55263766	Q2NL97|Q5JUL0|Q8WWL9	Silent	SNP	ENST00000289619.5	37	CCDS14368.1																																																																																				0.667	PAGE5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056861.1	NM_130467		A	55247041	G	A	55247041	2	1	75	1	0	0	0	0	0	0	0	1	11424	1074	38	1		1	PAGE5	23	55247041	Silent	SNP	G	TCGA-AG-A026-01A-32W-A096-10	14239369	55247041	100023519	211	21678										
SLC7A3	84889	broad.mit.edu	37	chrX	70148454	70148454	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	gaacactttggtaaccagggCcgactcactagccccgagag	11	13	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:70148454C>G	ENST00000374299.3	-	4	703	c.559G>C	c.(559-561)Gcc>Ccc	p.A187P	SLC7A3_ENST00000298085.4_Missense_Mutation_p.A187P			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	187					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)	p.A187P(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GTAACCAGGGCCGACTCACTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	X											44	38	40					X																	70148454		2203	4300	6503	70065179	SO:0001583	missense	84889			AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"Solute carriers"	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.559G>C	X.37:g.70148454C>G	ENSP00000363417:p.Ala187Pro		70065179	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397094	0.62177	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.91407	-2.84;-2.84	5.21	4.35	0.52113	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.92545	0.7632	M	0.90369	3.11	0.58432	D	0.999999	B	0.19445	0.036	B	0.30316	0.114	D	0.90920	0.4782	10	0.62326	D	0.03	.	13.4069	0.60919	0.1578:0.8422:0.0:0.0	.	187	Q8WY07	CTR3_HUMAN	P	187	ENSP00000363417:A187P;ENSP00000298085:A187P	ENSP00000298085:A187P	A	-	1	0	SLC7A3	70065179	1.000000	0.71417	0.837000	0.33122	0.981000	0.71138	5.786000	0.69006	1.175000	0.42826	0.436000	0.28706	GCC		0.522	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803		G	70148454	C	G	70148454	3	3	75	1	0	0	0	0	1	0	0	0	14735	739	26	5	1336	5	SLC7A3	23	70148454	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	14901413	70148454	85122106	212	21679										
P2RY10	27334	broad.mit.edu	37	chrX	78216666	78216666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cagtgatcatcatcgcatggTgtacctggaaaactactata	8	9	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:78216666T>A	ENST00000171757.2	+	4	929	c.649T>A	c.(649-651)Tgt>Agt	p.C217S	P2RY10_ENST00000544091.1_Missense_Mutation_p.C217S	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.C217S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						CATCGCATGGTGTACCTGGAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											153	118	130					X																	78216666		2203	4300	6503	78103322	SO:0001583	missense	27334			AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.649T>A	X.37:g.78216666T>A	ENSP00000171757:p.Cys217Ser		78103322	D3DTE5|Q4VBN7|Q86V16	Missense_Mutation	SNP	ENST00000171757.2	37	CCDS14442.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.948726	0.53186	.	.	ENSG00000078589	ENST00000544091;ENST00000171757	T;T	0.35048	1.33;1.33	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.052083	0.85682	D	0.000000	T	0.49695	0.1572	L	0.60455	1.87	0.51767	D	0.999931	P	0.52061	0.95	P	0.58266	0.836	T	0.46569	-0.9182	10	0.41790	T	0.15	.	12.3133	0.54940	0.0:0.0:0.0:1.0	.	217	O00398	P2Y10_HUMAN	S	217	ENSP00000443138:C217S;ENSP00000171757:C217S	ENSP00000171757:C217S	C	+	1	0	P2RY10	78103322	0.999000	0.42202	1.000000	0.80357	0.897000	0.52465	2.342000	0.43992	1.788000	0.52465	0.438000	0.28831	TGT		0.478	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			A	78216666	T	A	78216666	3	1	75	1	0	0	0	0	1	0	0	0	11378	1696	59	5	651	5	P2RY10	23	78216666	Missense_Mutation	SNP	T	TCGA-AG-A026-01A-32W-A096-10	8068212	78216666	77053894	213	21680										
PCDH11X	27328	broad.mit.edu	37	chrX	91873510	91873510	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cctccagtgacacagaccatCgcattgtgccacagcccacc	7	18	0	2			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:91873510C>G	ENST00000373094.1	+	7	4460	c.3615C>G	c.(3613-3615)atC>atG	p.I1205M	PCDH11X_ENST00000361655.2_Missense_Mutation_p.I1187M|PCDH11X_ENST00000373088.1_Missense_Mutation_p.I1168M|PCDH11X_ENST00000406881.1_Missense_Mutation_p.I1197M|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000298274.8_Missense_Mutation_p.I1168M|PCDH11X_ENST00000373097.1_Missense_Mutation_p.I1195M	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1205					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I1205M(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CACAGACCATCGCATTGTGCC	0.597																																					NSCLC(38;925 1092 2571 38200 45895)											1	Substitution - Missense(1)	large_intestine(1)	X											205	155	172					X																	91873510		2203	4300	6503	91760166	SO:0001583	missense	27328			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3615C>G	X.37:g.91873510C>G	ENSP00000362186:p.Ile1205Met		91760166	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	5.553	0.286912	0.10513	.	.	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000373088;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T	0.54071	0.61;0.62;0.59;0.6;0.62;0.59	3.93	-7.85	0.01192	.	.	.	.	.	T	0.42337	0.1198	N	0.24115	0.695	0.09310	N	1	D;D;D;D;P	0.55172	0.97;0.97;0.97;0.97;0.949	P;P;P;P;P	0.51550	0.601;0.673;0.673;0.673;0.473	T	0.60541	-0.7243	9	0.52906	T	0.07	.	10.5534	0.45103	0.1071:0.169:0.0:0.7239	.	1168;1187;1197;1195;1205	Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7	.;.;.;.;PC11X_HUMAN	M	1205;1195;1168;1187;1197;1205;1168	ENSP00000362186:I1205M;ENSP00000362189:I1195M;ENSP00000362180:I1168M;ENSP00000355105:I1187M;ENSP00000384758:I1197M;ENSP00000298274:I1168M	ENSP00000298274:I1168M	I	+	3	3	PCDH11X	91760166	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.751000	0.01821	-2.856000	0.00329	-0.537000	0.04273	ATC		0.597	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		G	91873510	C	G	91873510	3	3	75	1	0	0	0	0	1	0	0	0	11539	874	31	5	3763	5	PCDH11X	23	91873510	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	13656844	91873510	63397050	214	21681										
SLC6A14	11254	broad.mit.edu	37	chrX	115584286	115584286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tgcttttaactttgggtctcGattctcagtttgcttcgatt	8	8	2	0			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:115584286G>A	ENST00000371900.4	+	9	1352	c.1264G>A	c.(1264-1266)Gat>Aat	p.D422N		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	422					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)	p.D422N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TTTGGGTCTCGATTCTCAGTT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											164	139	148					X																	115584286		2203	4300	6503	115498314	SO:0001583	missense	11254			AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.1264G>A	X.37:g.115584286G>A	ENSP00000360967:p.Asp422Asn		115498314	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	37	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	32	5.182937	0.94885	.	.	ENSG00000087916	ENST00000371900	T	0.75367	-0.93	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.86083	0.5848	M	0.82132	2.575	0.51233	D	0.999916	D	0.89917	1.0	D	0.66351	0.943	D	0.87734	0.2581	10	0.72032	D	0.01	.	16.2172	0.82238	0.0:0.0:1.0:0.0	.	422	Q9UN76	S6A14_HUMAN	N	422	ENSP00000360967:D422N	ENSP00000360967:D422N	D	+	1	0	SLC6A14	115498314	1.000000	0.71417	0.947000	0.38551	0.964000	0.63967	9.444000	0.97578	2.433000	0.82419	0.591000	0.81541	GAT		0.378	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			A	115584286	G	A	115584286	3	1	75	1	0	0	0	0	1	0	0	0	14714	1058	37	1	1298	1	SLC6A14	23	115584286	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	23710776	115584286	39686274	215	21682										
DCAF12L2	340578	broad.mit.edu	37	chrX	125298991	125298991	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	tcaggcacacattctctcggCagtagggcagcctgatggac	12	12	2	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	C	C	A	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:125298991C>A	ENST00000360028.2	-	1	943	c.917G>T	c.(916-918)tGc>tTc	p.C306F	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.C306F			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	306								p.C306F(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						ATTCTCTCGGCAGTAGGGCAG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	X											100	103	102					X																	125298991		2203	4300	6503	125126672	SO:0001583	missense	340578			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.917G>T	X.37:g.125298991C>A	ENSP00000353128:p.Cys306Phe		125126672	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	C	9.547	1.114827	0.20795	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.62498	0.02;0.02	4.71	2.68	0.31781	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.408519	0.18317	N	0.144933	T	0.40791	0.1131	L	0.31664	0.95	0.39443	D	0.967278	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	10	0.07644	T	0.81	.	5.8276	0.18562	0.2435:0.5578:0.1987:0.0	.	306	Q5VW00	DC122_HUMAN	F	306	ENSP00000441489:C306F;ENSP00000353128:C306F	ENSP00000353128:C306F	C	-	2	0	DCAF12L2	125126672	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	2.965000	0.49200	1.003000	0.39130	0.544000	0.68410	TGC		0.607	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		A	125298991	C	A	125298991	3	1	75	1	0	0	0	0	1	0	0	0	4271	710	25	2	478	2	DCAF12L2	23	125298991	Missense_Mutation	SNP	C	TCGA-AG-A026-01A-32W-A096-10	9714705	125298991	29971569	216	21683										
ZNF280C	55609	broad.mit.edu	37	chrX	129364600	129364600	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	taaaactcattgactaacatGatcaactttcctgtctctga	4	10	3	3			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:129364600G>C	ENST00000370978.4	-	9	1026	c.873C>G	c.(871-873)atC>atG	p.I291M		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I291M(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TGACTAACATGATCAACTTTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	X											165	153	157					X																	129364600		2203	4300	6503	129192281	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.873C>G	X.37:g.129364600G>C	ENSP00000360017:p.Ile291Met		129192281	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	g	13.25	2.182559	0.38511	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.08807	3.97;3.05	3.4	0.411	0.16392	.	.	.	.	.	T	0.24890	0.0604	M	0.80746	2.51	0.26757	N	0.970087	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.05354	-1.0890	9	0.52906	T	0.07	.	6.33	0.21264	0.5629:0.0:0.4371:0.0	.	291;291	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	M	291	ENSP00000360017:I291M;ENSP00000408521:I291M	ENSP00000066465:I291M	I	-	3	3	ZNF280C	129192281	0.998000	0.40836	0.995000	0.50966	0.688000	0.40055	0.397000	0.20883	-0.151000	0.11176	0.458000	0.33432	ATC		0.368	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		C	129364600	G	C	129364600	3	2	75	1	0	0	0	0	1	0	0	0	17855	1280	45	5	1384	5	ZNF280C	23	129364600	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	4065609	129364600	25905960	217	21684										
GPR112	139378	broad.mit.edu	37	chrX	135427196	135427196	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.110091743119266	24	1	1.3381229903537	2.89323889806205	0.705823115790961	0.176476338697089	0.633238627089555	0	cattgaatctacagctgccgGaactgtaccttggtttacag	9	10	1	1			TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A026-01A-32W-A096-10	TCGA-AG-A026-10A-01W-A096-10	g.chrX:135427196G>C	ENST00000394143.1	+	6	1622	c.1331G>C	c.(1330-1332)gGa>gCa	p.G444A	GPR112_ENST00000370652.1_Missense_Mutation_p.G444A|GPR112_ENST00000412101.1_Missense_Mutation_p.G239A|GPR112_ENST00000287534.4_Missense_Mutation_p.G381A|GPR112_ENST00000394141.1_Missense_Mutation_p.G239A	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	444					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G444A(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ACAGCTGCCGGAACTGTACCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X											80	73	75					X																	135427196		2203	4299	6502	135254862	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1331G>C	X.37:g.135427196G>C	ENSP00000377699:p.Gly444Ala		135254862	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	0.315	-0.965197	0.02249	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.31510	1.53;1.53;1.49;1.62;1.49	3.57	0.481	0.16809	.	.	.	.	.	T	0.16385	0.0394	N	0.19112	0.55	0.09310	N	1	B;B;B	0.23591	0.03;0.008;0.088	B;B;B	0.21917	0.037;0.023;0.037	T	0.28933	-1.0028	9	0.25751	T	0.34	.	5.0833	0.14668	0.2356:0.0:0.5995:0.1649	.	381;239;444	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	A	444;444;239;381;239	ENSP00000377699:G444A;ENSP00000359686:G444A;ENSP00000416526:G239A;ENSP00000287534:G381A;ENSP00000377697:G239A	ENSP00000287534:G381A	G	+	2	0	GPR112	135254862	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.117000	0.15583	-0.496000	0.06650	-1.687000	0.00730	GGA		0.478	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135427196	G	C	135427196	3	2	75	1	0	0	0	0	1	0	0	0	6649	1174	41	5	1341	5	GPR112	23	135427196	Missense_Mutation	SNP	G	TCGA-AG-A026-01A-32W-A096-10	6062596	135427196	19843364	218	21685										
LEPROT	54741	broad.mit.edu	37	chr1	65895720	65895720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gatttcctgttattcttgctCgtgtggctgtggtaagtttt	11	6	1	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr1:65895720C>T	ENST00000371065.4	+	3	406	c.268C>T	c.(268-270)Cgt>Tgt	p.R90C	LEPR_ENST00000371059.3_Intron|LEPR_ENST00000349533.6_Intron|LEPR_ENST00000406510.3_Intron|LEPROT_ENST00000484243.1_3'UTR|LEPR_ENST00000371060.3_Intron|LEPR_ENST00000344610.8_Intron	NM_001198681.1|NM_017526.4	NP_001185610.1|NP_059996.1	O15243	OBRG_HUMAN	leptin receptor overlapping transcript	90					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.R90C(1)		kidney(1)|large_intestine(1)|lung(5)	7				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TATTCTTGCTCGTGTGGCTGT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	1											351	338	342					1																	65895720		2203	4300	6503	65668308	SO:0001583	missense	54741			Y12670	CCDS630.1, CCDS72801.1	1p31.2	2008-02-05			ENSG00000213625	ENSG00000213625			29477	protein-coding gene	gene with protein product	"leptin receptor gene related protein"	613461				9207021	Standard	NM_001198681		Approved	OBRGRP, OB-RGRP, VPS55, FLJ90360	uc001dcf.3	O15243	OTTHUMG00000009065	ENST00000371065.4:c.268C>T	1.37:g.65895720C>T	ENSP00000360104:p.Arg90Cys		65668308	Q6FHL5	Missense_Mutation	SNP	ENST00000371065.4	37	CCDS630.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349349	0.82132	.	.	ENSG00000213625	ENST00000371065	.	.	.	5.89	4.91	0.64330	.	0.000000	0.85682	U	0.000000	T	0.58409	0.2120	M	0.85462	2.755	0.80722	D	1	P	0.37141	0.584	B	0.35312	0.2	T	0.69749	-0.5061	9	0.87932	D	0	-11.4278	15.8532	0.78952	0.2227:0.7773:0.0:0.0	.	90	O15243	OBRG_HUMAN	C	90	.	ENSP00000360104:R90C	R	+	1	0	LEPROT	65668308	0.971000	0.33674	0.996000	0.52242	0.996000	0.88848	2.268000	0.43338	2.782000	0.95742	0.557000	0.71058	CGT		0.438	LEPROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025132.4	NM_017526		T	65895720	C	T	65895720	3	4	76	1	0	0	0	0	1	0	0	0	8754	884	31	1	278	1	LEPROT	1	65895720	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		65895720	183354901	1	21686										
CD1C	911	broad.mit.edu	37	chr1	158262062	158262062	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tcaatcatcagtatgaaggcGtcacagaaacagtgtataat	8	7	4	2	rs146158051		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr1:158262062G>A	ENST00000368170.3	+	3	796	c.517G>A	c.(517-519)Gtc>Atc	p.V173I		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	173					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)	p.V173I(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					GTATGAAGGCGTCACAGAAAC	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ILE/VAL	0,4406		0,0,2203	279	278	279		517	0.8	0	1	dbSNP_134	279	2,8598		0,2,4298	yes	missense	CD1C	NM_001765.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	173/334	158262062	2,13004	2203	4300	6503	156528686	SO:0001583	missense	911			M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.517G>A	1.37:g.158262062G>A	ENSP00000357152:p.Val173Ile		156528686	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	37	CCDS1175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.017|0.017	-1.493131|-1.493131	0.01009|0.01009	0.0|0.0	2.33E-4|2.33E-4	ENSG00000158481|ENSG00000158481	ENST00000443761|ENST00000368169;ENST00000368170	.|T	.|0.06142	.|3.34	3.36|3.36	0.761|0.761	0.18448|0.18448	.|MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.438795	.|0.16866	.|N	.|0.196303	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.00197|0.00197	-1.87|-1.87	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.39583|0.39583	-0.9607|-0.9607	5|10	.|0.02654	.|T	.|1	.|.	5.213|5.213	0.15327|0.15327	0.7447:0.0:0.2553:0.0|0.7447:0.0:0.2553:0.0	.|.	.|173	.|P29017	.|CD1C_HUMAN	H|I	107|173	.|ENSP00000357152:V173I	.|ENSP00000357151:V173I	R|V	+|+	2|1	0|0	CD1C|CD1C	156528686|156528686	0.001000|0.001000	0.12720|0.12720	0.005000|0.005000	0.12908|0.12908	0.031000|0.031000	0.12232|0.12232	0.004000|0.004000	0.13106|0.13106	0.189000|0.189000	0.20188|0.20188	-0.313000|-0.313000	0.08912|0.08912	CGT|GTC		0.458	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		A	158262062	G	A	158262062	3	1	76	1	0	0	0	0	1	0	0	0	2982	1145	40	1	527	1	CD1C	1	158262062	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	92366342	158262062	90988559	2	21687										
OR2T4	127074	broad.mit.edu	37	chr1	248525726	248525726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cccacctgactgtggtcatcCtcttctatggggctgccatc	9	15	3	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr1:248525726C>A	ENST00000366475.1	+	1	844	c.844C>A	c.(844-846)Ctc>Atc	p.L282I		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L282I(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTGGTCATCCTCTTCTATGG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	1											155	149	151					1																	248525726		2203	4300	6503	246592349	SO:0001583	missense	127074			BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.844C>A	1.37:g.248525726C>A	ENSP00000355431:p.Leu282Ile		246592349	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	7.441	0.640658	0.14386	.	.	ENSG00000196944	ENST00000366475	T	0.00256	8.42	3.0	-0.398	0.12418	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38217	N	0.001765	T	0.00144	0.0004	L	0.45470	1.425	0.09310	N	1	B	0.33826	0.427	B	0.37888	0.26	T	0.37337	-0.9710	10	0.49607	T	0.09	.	3.0637	0.06207	0.3112:0.3852:0.0:0.3036	.	282	Q8NH00	OR2T4_HUMAN	I	282	ENSP00000355431:L282I	ENSP00000355431:L282I	L	+	1	0	OR2T4	246592349	0.000000	0.05858	0.934000	0.37439	0.080000	0.17528	-1.822000	0.01711	0.045000	0.15804	0.585000	0.79938	CTC		0.542	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248525726	C	A	248525726	3	1	76	1	0	0	0	0	1	0	0	0	11058	681	24	2	846	2	OR2T4	1	248525726	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	90263664	248525726	724895	3	21688										
GPR113	165082	broad.mit.edu	37	chr2	26534355	26534356	+	Missense_Mutation	DNP	GC	GC	AT													0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gcagtgaggtgctggcagagGcactgagcagtggggctggc							TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:26534355_26534356GC>AT	ENST00000311519.1	-	11	2239_2240	c.2240_2241GC>AT	c.(2239-2241)tGC>tAT	p.C747Y	GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000333478.6_Missense_Mutation_p.C548Y|GPR113_ENST00000421160.2_Missense_Mutation_p.C678Y|GPR113_ENST00000541401.1_Missense_Mutation_p.C350Y	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	747	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.C548>?(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGGCAGAGGCACTGAGCAGT	0.619																																																1	Complex(1)	large_intestine(1)	2																																								26387860	SO:0001583	missense	165082			AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"-", "GPCR / Class B : Orphans"	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.2240_2241delinsAT	2.37:g.26534355_26534356delinsAT	ENSP00000307831:p.Cys747Tyr		26387859	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	DNP	ENST00000311519.1	37	CCDS46239.1																																																																																				0.619	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		AT	26534356	GC	AT	26534355	3	1	76	1	0	0	0	0	1	0	0	0	6650	1195	42	3	1099	3	GPR113	2	26534355	Missense_Mutation	DNP	GC	TCGA-AG-A02G-01A-01W-A00E-09		26534355	216665018	4	21689										
SOCS5	9655	broad.mit.edu	37	chr2	46987060	46987060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	acattataaagatcccagttCgtgcatgttttttgaaccat	6	8	0	2	rs149307689		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:46987060C>T	ENST00000306503.5	+	2	1563	c.1391C>T	c.(1390-1392)tCg>tTg	p.S464L	SOCS5_ENST00000394861.2_Missense_Mutation_p.S464L	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	464	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)	p.S464L(3)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			GATCCCAGTTCGTGCATGTTT	0.438																																																3	Substitution - Missense(3)	large_intestine(2)|lung(1)	2						C	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	111	106	107		1391,1391	4.6	1	2	dbSNP_134	107	0,8600		0,0,4300	no	missense,missense	SOCS5	NM_014011.4,NM_144949.2	145,145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	464/537,464/537	46987060	1,13005	2203	4300	6503	46840564	SO:0001583	missense	9655			AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1391C>T	2.37:g.46987060C>T	ENSP00000305133:p.Ser464Leu		46840564	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	37	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.781752	0.70222	2.27E-4	0.0	ENSG00000171150	ENST00000306503;ENST00000394861	T;T	0.32272	1.46;1.46	5.43	4.55	0.56014	SH2 motif (3);	0.055880	0.64402	D	0.000001	T	0.13072	0.0317	N	0.01352	-0.895	0.53005	D	0.999961	B	0.19583	0.037	B	0.12837	0.008	T	0.07252	-1.0782	10	0.41790	T	0.15	-20.7869	15.4335	0.75125	0.1399:0.8601:0.0:0.0	.	464	O75159	SOCS5_HUMAN	L	464	ENSP00000305133:S464L;ENSP00000378330:S464L	ENSP00000305133:S464L	S	+	2	0	SOCS5	46840564	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.651000	0.83577	1.514000	0.48869	0.655000	0.94253	TCG		0.438	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			T	46987060	C	T	46987060	3	4	76	1	0	0	0	0	1	0	0	0	14954	893	31	1	1393	1	SOCS5	2	46987060	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	20452705	46987060	196212313	5	21690										
BIN1	274	broad.mit.edu	37	chr2	127806139	127806139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tgaagttctcggggaagacgCcacggcacttctccagctcc	11	14	2	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:127806139C>A	ENST00000316724.5	-	19	2156	c.1745G>T	c.(1744-1746)gGc>gTc	p.G582V	BIN1_ENST00000409400.1_Missense_Mutation_p.G428V|BIN1_ENST00000351659.3_Missense_Mutation_p.G495V|BIN1_ENST00000376113.2_Missense_Mutation_p.G413V|BIN1_ENST00000346226.3_Missense_Mutation_p.G507V|BIN1_ENST00000393040.3_Missense_Mutation_p.G471V|BIN1_ENST00000348750.4_Missense_Mutation_p.G398V|BIN1_ENST00000259238.4_Missense_Mutation_p.G486V|BIN1_ENST00000357970.3_Missense_Mutation_p.G539V|BIN1_ENST00000466111.1_5'Flank|BIN1_ENST00000393041.3_Missense_Mutation_p.G464V|BIN1_ENST00000352848.3_Missense_Mutation_p.G443V	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	582	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)	p.G582V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GGGGAAGACGCCACGGCACTT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	2											96	92	93					2																	127806139		2203	4300	6503	127522609	SO:0001583	missense	274			U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1745G>T	2.37:g.127806139C>A	ENSP00000316779:p.Gly582Val		127522609	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.242176	0.58995	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	4.88	4.88	0.63580	Src homology-3 domain (4);Variant SH3 (1);	0.000000	0.85682	D	0.000000	D	0.92932	0.7751	H	0.98866	4.355	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.95460	0.8542	10	0.87932	D	0	-33.5637	15.6379	0.76970	0.0:1.0:0.0:0.0	.	459;374;464;428;471;507;495;443;486;539;413;398;582	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	V	413;539;471;398;486;507;464;495;443;582;428	ENSP00000365281:G413V;ENSP00000350654:G539V;ENSP00000376760:G471V;ENSP00000259237:G398V;ENSP00000259238:G486V;ENSP00000315411:G507V;ENSP00000376761:G464V;ENSP00000315388:G495V;ENSP00000315284:G443V;ENSP00000316779:G582V;ENSP00000386797:G428V	ENSP00000259238:G486V	G	-	2	0	BIN1	127522609	1.000000	0.71417	0.995000	0.50966	0.130000	0.20726	6.071000	0.71229	2.565000	0.86533	0.555000	0.69702	GGC		0.627	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		A	127806139	C	A	127806139	3	1	76	1	0	0	0	0	1	0	0	0	1433	739	26	2	40	2	BIN1	2	127806139	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	80819079	127806139	115393234	6	21691										
THSD7B	80731	broad.mit.edu	37	chr2	137872782	137872782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	actggcatgtgacgggacccGtgtgtggcggtgggatccag	18	9	0	1	rs375232957		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:137872782G>A	ENST00000409968.1	+	5	1466	c.1288G>A	c.(1288-1290)Gtg>Atg	p.V430M	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Missense_Mutation_p.V399M|THSD7B_ENST00000272643.3_Missense_Mutation_p.V430M			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	430	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.V430M(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		GACGGGACCCGTGTGTGGCGG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2						G	MET/VAL	1,3929		0,1,1964	46	51	50		1195	-1	0	2		50	0,8316		0,0,4158	no	missense	THSD7B	NM_001080427.1	21	0,1,6122	AA,AG,GG		0.0,0.0254,0.0082	possibly-damaging	399/1578	137872782	1,12245	1965	4158	6123	137589252	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1288G>A	2.37:g.137872782G>A	ENSP00000387145:p.Val430Met		137589252		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	G	10.92	1.487096	0.26686	2.54E-4	0.0	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.60920	0.15;0.15;0.15	4.88	-1.02	0.10135	.	0.351936	0.30085	N	0.010447	T	0.35451	0.0932	L	0.29908	0.895	0.20638	N	0.999879	P;P	0.46987	0.888;0.888	B;B	0.39503	0.301;0.283	T	0.31110	-0.9955	10	0.44086	T	0.13	.	4.9514	0.14015	0.4264:0.2418:0.3318:0.0	.	430;399	Q9C0I4;C9JKN6	THS7B_HUMAN;.	M	430;430;399	ENSP00000387145:V430M;ENSP00000272643:V430M;ENSP00000413841:V399M	ENSP00000272643:V430M	V	+	1	0	THSD7B	137589252	0.014000	0.17966	0.028000	0.17463	0.577000	0.36160	0.205000	0.17356	-0.030000	0.13804	0.655000	0.94253	GTG		0.597	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		A	137872782	G	A	137872782	3	1	76	1	0	0	0	0	1	0	0	0	15919	1145	40	1	1209	1	THSD7B	2	137872782	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	10066643	137872782	105326591	7	21692										
LRP2	4036	broad.mit.edu	37	chr2	170022537	170022537	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gattgttgtcacaccggaaaCggtttggtgaattacaggga	13	6	1	1	rs77686710	byFrequency	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:170022537C>T	ENST00000263816.3	-	62	11948	c.11663G>A	c.(11662-11664)cGt>cAt	p.R3888H		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3888	LDL-receptor class A 35. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R3888H(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	ACACCGGAAACGGTTTGGTGA	0.398													C|||	16	0.00319489	0.0091	0.0043	5008	,	,		22500	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						C	HIS/ARG	43,4363	45.3+/-79.5	0,43,2160	172	159	164		11663	6.1	1	2	dbSNP_131	164	3,8597	3.0+/-9.4	0,3,4297	yes	missense	LRP2	NM_004525.2	29	0,46,6457	TT,TC,CC		0.0349,0.9759,0.3537	probably-damaging	3888/4656	170022537	46,12960	2203	4300	6503	169730783	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11663G>A	2.37:g.170022537C>T	ENSP00000263816:p.Arg3888His		169730783	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	5|5	0.0022893772893772895|0.0022893772893772895	3|3	0.006097560975609756|0.006097560975609756	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	36|36	5.765429|5.765429	0.96906|0.96906	0.009759|0.009759	3.49E-4|3.49E-4	ENSG00000081479|ENSG00000081479	ENST00000263816|ENST00000536293	D|.	0.95412|.	-3.7|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64316|0.64316	0.2587|0.2587	L|L	0.42529|0.42529	1.33|1.33	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.66504|0.66504	-0.5907|-0.5907	10|6	0.59425|0.54805	D|T	0.04|0.06	.|.	20.6397|20.6397	0.99537|0.99537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3888|.	P98164|.	LRP2_HUMAN|.	H|I	3888|553	ENSP00000263816:R3888H|.	ENSP00000263816:R3888H|ENSP00000438157:V553I	R|V	-|-	2|1	0|0	LRP2|LRP2	169730783|169730783	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.974000|0.974000	0.67602|0.67602	6.093000|6.093000	0.71422|0.71422	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	CGT|GTT		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170022537	C	T	170022537	3	4	76	1	0	0	0	0	1	0	0	0	8985	536	19	1	2376	1	LRP2	2	170022537	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	32149755	170022537	73176836	8	21693										
ITGAV	3685	broad.mit.edu	37	chr2	187540408	187540408	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ggaaagagtgcaatcttgtaCgtaaagtcattactgtggac	11	6	2	1	rs199793723	byFrequency	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr2:187540408C>A	ENST00000261023.3	+	27	3058	c.2784C>A	c.(2782-2784)taC>taA	p.Y928*	AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000433736.2_Nonsense_Mutation_p.Y882*|ITGAV_ENST00000374907.3_Nonsense_Mutation_p.Y892*	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	928					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.Y928fs*1(1)|p.Y928*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CAATCTTGTACGTAAAGTCAT	0.393																																					Melanoma(58;108 1995 6081)											2	Substitution - Nonsense(1)|Deletion - Frameshift(1)	large_intestine(1)|stomach(1)	2											126	119	121					2																	187540408		2203	4300	6503	187248653	SO:0001587	stop_gained	3685				CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2784C>A	2.37:g.187540408C>A	ENSP00000261023:p.Tyr928*		187248653	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Nonsense_Mutation	SNP	ENST00000261023.3	37	CCDS2292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.510260|5.510260	0.96386|0.96386	.|.	.|.	ENSG00000138448|ENSG00000138448	ENST00000430709|ENST00000261023;ENST00000374907;ENST00000433736	.|.	.|.	.|.	5.4|5.4	-4.85|-4.85	0.03142|0.03142	.|.	.|0.060791	.|0.64402	.|D	.|0.000002	T|.	0.35422|.	0.0931|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.44128|.	-0.9348|.	3|.	.|0.10636	.|T	.|0.68	.|.	13.0029|13.0029	0.58687|0.58687	0.0:0.5285:0.0:0.4715|0.0:0.5285:0.0:0.4715	.|.	.|.	.|.	.|.	K|X	79|928;892;882	.|.	.|ENSP00000261023:Y928X	T|Y	+|+	2|3	0|2	ITGAV|ITGAV	187248653|187248653	0.837000|0.837000	0.29446|0.29446	0.097000|0.097000	0.21041|0.21041	0.258000|0.258000	0.26162|0.26162	-0.285000|-0.285000	0.08410|0.08410	-0.977000|-0.977000	0.03537|0.03537	-0.440000|-0.440000	0.05779|0.05779	ACG|TAC		0.393	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		A	187540408	C	A	187540408	4	1	76	1	0	0	0	0	0	1	0	0	7909	547	19	2	2941	2	ITGAV	2	187540408	Nonsense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	17517871	187540408	55658965	9	21694										
DZIP1L	199221	broad.mit.edu	37	chr3	137786448	137786448	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gtcccagtcatccttgggccGgggcaccatcctggaaggaa	13	13	1	0	rs150921263	byFrequency	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr3:137786448G>A	ENST00000327532.2	-	14	2289	c.1927C>T	c.(1927-1929)Cgg>Tgg	p.R643W	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	643					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)	p.R643W(2)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TCCTTGGGCCGGGGCACCATC	0.622													G|||	7	0.00139776	0.003	0.0043	5008	,	,		15974	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	3						G	TRP/ARG	2,4404	2.1+/-5.4	0,2,2201	57	57	57		1927	-0.9	0	3	dbSNP_134	57	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DZIP1L	NM_173543.2	101	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	possibly-damaging	643/768	137786448	4,13002	2203	4300	6503	139269138	SO:0001583	missense	199221			AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1927C>T	3.37:g.137786448G>A	ENSP00000332148:p.Arg643Trp		139269138	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	3|3	0.0013736263736263737|0.0013736263736263737	1|1	0.0020325203252032522|0.0020325203252032522	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	12.56|12.56	1.975595|1.975595	0.34848|0.34848	4.54E-4|4.54E-4	2.33E-4|2.33E-4	ENSG00000158163|ENSG00000158163	ENST00000486487|ENST00000327532	T|T	0.47177|0.39229	0.85|1.09	4.45|4.45	-0.889|-0.889	0.10580|0.10580	.|.	.|1.282800	.|0.05751	.|N	.|0.603121	T|T	0.28928|0.28928	0.0718|0.0718	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	.|B	.|0.15719	.|0.014	.|B	.|0.09377	.|0.004	T|T	0.44421|0.44421	-0.9329|-0.9329	7|10	0.66056|0.72032	D|D	0.02|0.01	-2.0392|-2.0392	12.3472|12.3472	0.55128|0.55128	0.0:0.0:0.3111:0.6889|0.0:0.0:0.3111:0.6889	.|.	.|643	.|Q8IYY4	.|DZI1L_HUMAN	L|W	12|643	ENSP00000417228:P12L|ENSP00000332148:R643W	ENSP00000417228:P12L|ENSP00000332148:R643W	P|R	-|-	2|1	0|2	DZIP1L|DZIP1L	139269138|139269138	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.005000|0.005000	0.04900|0.04900	-0.001000|-0.001000	0.12947|0.12947	-0.012000|-0.012000	0.14223|0.14223	0.561000|0.561000	0.74099|0.74099	CCG|CGG		0.622	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		A	137786448	G	A	137786448	3	1	76	1	0	0	0	0	1	0	0	0	4875	1115	39	1	388	1	DZIP1L	3	137786448	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		137786448	60235982	10	21695										
RUFY3	22902	broad.mit.edu	37	chr4	71634260	71634260	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ggatttctcttacagtgaatTctacgaacccaatgccctca	6	12	3	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr4:71634260T>G	ENST00000226328.4	+	5	1141	c.578T>G	c.(577-579)tTc>tGc	p.F193C	RUFY3_ENST00000381006.3_Missense_Mutation_p.F193C|RUFY3_ENST00000417478.2_Missense_Mutation_p.F253C|RUFY3_ENST00000502653.1_Missense_Mutation_p.F140C|RUFY3_ENST00000536664.1_Missense_Mutation_p.F177C	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	193	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)		p.F193C(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TACAGTGAATTCTACGAACCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	4											146	143	144					4																	71634260		2203	4300	6503	71853124	SO:0001583	missense	22902			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.578T>G	4.37:g.71634260T>G	ENSP00000226328:p.Phe193Cys		71853124	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.696620	0.88830	.	.	ENSG00000018189	ENST00000503876;ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2;1.2	5.73	5.73	0.89815	RUN (3);	0.000000	0.85682	D	0.000000	T	0.64483	0.2602	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.987	D;D;D;D	0.91635	0.999;0.997;0.998;0.93	T	0.70174	-0.4944	10	0.87932	D	0	-15.8519	16.017	0.80445	0.0:0.0:0.0:1.0	.	177;193;193;253	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	C	129;253;193;193;177;129;140	ENSP00000426734:F129C;ENSP00000399771:F253C;ENSP00000370394:F193C;ENSP00000226328:F193C;ENSP00000443652:F177C;ENSP00000425574:F129C;ENSP00000425400:F140C	ENSP00000226328:F193C	F	+	2	0	RUFY3	71853124	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.874000	0.87199	2.182000	0.69389	0.455000	0.32223	TTC		0.383	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		G	71634260	T	G	71634260	3	3	76	1	0	0	0	0	1	0	0	0	13777	1783	62	4	958	4	RUFY3	4	71634260	Missense_Mutation	SNP	T	TCGA-AG-A02G-01A-01W-A00E-09		71634260	119520016	11	21696										
NR3C2	4306	broad.mit.edu	37	chr4	149181259	149181259	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agatccagtagaaacacttcGtaaagtagagctggggaaag	12	6	0	3			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr4:149181259G>A	ENST00000358102.3	-	3	2130	c.1768C>T	c.(1768-1770)Cga>Tga	p.R590*	NR3C2_ENST00000511528.1_Nonsense_Mutation_p.R590*|NR3C2_ENST00000512865.1_Nonsense_Mutation_p.R590*|NR3C2_ENST00000355292.3_Nonsense_Mutation_p.R590*|NR3C2_ENST00000344721.4_Nonsense_Mutation_p.R590*	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	590	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R590*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	GAAACACTTCGTAAAGTAGAG	0.408																																					Melanoma(27;428 957 40335 51025 51111)											1	Substitution - Nonsense(1)	large_intestine(1)	4	GRCh37	CM066154	NR3C2	M							85	82	83					4																	149181259		2203	4300	6503	149400709	SO:0001587	stop_gained	4306			M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.1768C>T	4.37:g.149181259G>A	ENSP00000350815:p.Arg590*		149400709	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Nonsense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	39	7.873960	0.98537	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	.	.	.	5.98	5.98	0.97165	.	0.065195	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.077	0.72084	0.0:0.0:0.8252:0.1748	.	.	.	.	X	590	.	.	R	-	1	2	NR3C2	149400709	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.787000	0.62432	2.838000	0.97847	0.591000	0.81541	CGA		0.408	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149181259	G	A	149181259	4	1	76	1	0	0	0	0	0	1	0	0	10662	1153	40	1	1214	1	NR3C2	4	149181259	Nonsense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	77546999	149181259	41973017	12	21697										
APC	324	broad.mit.edu	37	chr5	112116592	112116592	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cctgccaggatatggaaaaaCgagcacaggtaagttacttg	11	8	0	0	rs587781392		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr5:112116592C>T	ENST00000457016.1	+	6	1017	c.637C>T	c.(637-639)Cga>Tga	p.R213*	RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000257430.4_Nonsense_Mutation_p.R213*|APC_ENST00000508376.2_Nonsense_Mutation_p.R213*			P25054	APC_HUMAN	adenomatous polyposis coli	213	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R213*(20)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATGGAAAAACGAGCACAGGT	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(20)	large_intestine(19)|lung(1)	5	GRCh37	CM920027	APC	M							58	57	58					5																	112116592		2202	4300	6502	112144491	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.637C>T	5.37:g.112116592C>T	ENSP00000413133:p.Arg213*		112144491	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.046788	0.97231	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0079	14.2561	0.66053	0.4075:0.5925:0.0:0.0	.	.	.	.	X	213;223;213;213;213	.	ENSP00000257430:R213X	R	+	1	2	APC	112144491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.672000	0.46850	0.659000	0.30945	0.655000	0.94253	CGA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112116592	C	T	112116592	4	4	76	1	0	0	0	0	0	1	0	0	763	528	19	1	655	1	APC	5	112116592	Nonsense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		112116592	68798668	13	21698										
NRG2	9542	broad.mit.edu	37	chr5	139267060	139267060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gcttctcacccacctgtcccGtctggctcttcatcttcttc	5	18	6	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr5:139267060G>A	ENST00000361474.1	-	2	961	c.737C>T	c.(736-738)aCg>aTg	p.T246M	NRG2_ENST00000340391.3_Missense_Mutation_p.T43M|NRG2_ENST00000394770.1_Missense_Mutation_p.T246M|NRG2_ENST00000518130.1_5'UTR|NRG2_ENST00000289422.7_Missense_Mutation_p.T246M|NRG2_ENST00000541337.1_Missense_Mutation_p.T246M|NRG2_ENST00000545385.1_Missense_Mutation_p.T246M|NRG2_ENST00000358522.3_Missense_Mutation_p.T246M|NRG2_ENST00000289409.4_Missense_Mutation_p.T246M	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	246	Ig-like C2-type.				embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.T154M(2)|p.T246M(2)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCTGTCCCGTCTGGCTCTT	0.582																																																4	Substitution - Missense(4)	large_intestine(4)	5											96	81	86					5																	139267060		2203	4300	6503	139247244	SO:0001583	missense	9542				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.737C>T	5.37:g.139267060G>A	ENSP00000354910:p.Thr246Met		139247244		Missense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.491233	0.64074	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000340391;ENST00000289409;ENST00000358522;ENST00000544729;ENST00000378238	T;T;T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.29	4.36	0.52297	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.349244	0.26616	N	0.023382	T	0.66327	0.2778	M	0.68317	2.08	0.37234	D	0.905809	P;P;P;P	0.47253	0.868;0.725;0.868;0.892	B;B;B;P	0.45232	0.294;0.37;0.294;0.474	T	0.74269	-0.3720	10	0.59425	D	0.04	-8.1125	10.3883	0.44154	0.0:0.0:0.7124:0.2876	.	246;246;246;246	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	M	246;246;246;246;246;246;43;246;246;154;246	ENSP00000444235:T246M;ENSP00000289422:T246M;ENSP00000354910:T246M;ENSP00000438753:T246M;ENSP00000378251:T246M;ENSP00000342660:T43M;ENSP00000289409:T246M;ENSP00000351323:T246M;ENSP00000367483:T246M	ENSP00000289409:T246M	T	-	2	0	NRG2	139247244	0.990000	0.36364	0.969000	0.41365	0.991000	0.79684	2.167000	0.42415	2.473000	0.83533	0.462000	0.41574	ACG		0.582	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		A	139267060	G	A	139267060	3	1	76	1	0	0	0	0	1	0	0	0	10679	1145	40	1	1942	1	NRG2	5	139267060	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	27150468	139267060	41648200	14	21699										
PCDHA3	56145	broad.mit.edu	37	chr5	140181074	140181074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	accgcgaggaactgtgcgggCggagcgcggagtgcagcatc	18	11	0	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr5:140181074C>T	ENST00000522353.2	+	1	292	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.R98W|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	98	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R98W(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGTGCGGGCGGAGCGCGGA	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	5											127	142	137					5																	140181074		2203	4300	6503	140161258	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.292C>T	5.37:g.140181074C>T	ENSP00000429808:p.Arg98Trp		140161258	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	N	3.113	-0.182174	0.06340	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.28666	1.6;1.6	4.51	1.59	0.23543	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.38005	U	0.001845	T	0.27594	0.0678	M	0.66378	2.025	0.09310	N	1	P;B	0.35226	0.491;0.091	B;B	0.35039	0.194;0.106	T	0.18335	-1.0340	10	0.59425	D	0.04	.	5.4105	0.16346	0.3787:0.4499:0.0978:0.0737	.	98;98	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	W	98	ENSP00000429808:R98W;ENSP00000434086:R98W	ENSP00000429808:R98W	R	+	1	2	PCDHA3	140161258	0.000000	0.05858	0.664000	0.29753	0.048000	0.14542	-1.633000	0.02022	-0.140000	0.11394	-1.595000	0.00837	CGG		0.567	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		T	140181074	C	T	140181074	3	4	76	1	0	0	0	0	1	0	0	0	11556	759	27	1	294	1	PCDHA3	5	140181074	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	914014	140181074	40734186	15	21700										
GPLD1	2822	broad.mit.edu	37	chr6	24437388	24437388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agtgcagaacgccaccaaatCgggagaagcggcggtctccg	14	12	1	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr6:24437388C>T	ENST00000230036.1	-	21	2260	c.2150G>A	c.(2149-2151)cGa>cAa	p.R717Q		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	717					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)	p.R717Q(2)		breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						GCCACCAAATCGGGAGAAGCG	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	6											108	97	101					6																	24437388		2203	4300	6503	24545367	SO:0001583	missense	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.2150G>A	6.37:g.24437388C>T	ENSP00000230036:p.Arg717Gln		24545367	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.336492	0.60963	.	.	ENSG00000112293	ENST00000230036	T	0.73681	-0.77	4.69	3.82	0.43975	.	0.103103	0.42548	D	0.000695	T	0.79281	0.4419	M	0.84846	2.72	0.33389	D	0.575862	D	0.89917	1.0	P	0.62491	0.903	T	0.79834	-0.1636	10	0.41790	T	0.15	-15.3974	10.9809	0.47494	0.0:0.9122:0.0:0.0878	.	717	P80108	PHLD_HUMAN	Q	717	ENSP00000230036:R717Q	ENSP00000230036:R717Q	R	-	2	0	GPLD1	24545367	0.958000	0.32768	0.011000	0.14972	0.522000	0.34438	2.889000	0.48601	1.328000	0.45358	0.563000	0.77884	CGA		0.572	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24437388	C	T	24437388	3	4	76	1	0	0	0	0	1	0	0	0	6634	884	31	1	392	1	GPLD1	6	24437388	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		24437388	146677679	16	21701										
TULP1	7287	broad.mit.edu	37	chr6	35473905	35473905	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	aggccggagcacaaactcccGgggttcgtccacctccacgg	12	16	0	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr6:35473905G>T	ENST00000229771.6	-	10	953	c.874C>A	c.(874-876)Cgg>Agg	p.R292R	TULP1_ENST00000322263.4_Silent_p.R239R	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	292					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R292R(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						ACAAACTCCCGGGGTTCGTCC	0.687																																					GBM(55;1027 1091 11115 23439)											1	Substitution - coding silent(1)	large_intestine(1)	6											29	35	33					6																	35473905		2201	4296	6497	35581883	SO:0001819	synonymous_variant	7287			U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.874C>A	6.37:g.35473905G>T			35581883	O43536|Q5TGM5|Q8N571	Silent	SNP	ENST00000229771.6	37	CCDS4807.1																																																																																				0.687	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			T	35473905	G	T	35473905	2	4	76	1	0	0	0	0	0	0	0	1	16813	1115	39	2		2	TULP1	6	35473905	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	11036517	35473905	135641162	17	21702										
ASL	435	broad.mit.edu	37	chr7	65557632	65557633	+	Missense_Mutation	DNP	AG	AG	CA													0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cctcaaccagctgtcactgcAggagctgcagaccatcaggt					rs202182043		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr7:65557632_65557633AG>CA	ENST00000304874.9	+	16	1334_1335	c.1232_1233AG>CA	c.(1231-1233)cAG>cCA	p.Q411P	AC068533.7_ENST00000450043.1_Missense_Mutation_p.G180R|ASL_ENST00000395332.3_Missense_Mutation_p.Q411P|ASL_ENST00000395331.3_Missense_Mutation_p.Q391P|ASL_ENST00000464970.1_3'UTR|ASL_ENST00000380839.4_Missense_Mutation_p.Q385P	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	411					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)	p.Q411>?(1)		breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	CTGTCACTGCAGGAGCTGCAGA	0.673																																																1	Complex(1)	large_intestine(1)	7																																								65195068	SO:0001583	missense	435				CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	Exception_encountered	7.37:g.65557632_65557633delinsCA	ENSP00000307188:p.Gln411Pro		65195067	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Missense_Mutation	DNP	ENST00000304874.9	37	CCDS5531.1																																																																																				0.673	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048		CA	65557633	AG	CA	65557632	3	2	76	1	0	0	0	0	1	0	0	0	1045	188	7	4	1290	4	ASL	7	65557632	Missense_Mutation	DNP	AG	TCGA-AG-A02G-01A-01W-A00E-09		65557632	93581031	18	21703										
AKAP9	10142	broad.mit.edu	37	chr7	91718761	91718761	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gatagaaggagtttgttatcTgaaattcaggcactgcatgc	11	6	2	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr7:91718761T>G	ENST00000359028.2	+	38	9513	c.9288T>G	c.(9286-9288)tcT>tcG	p.S3096S	AKAP9_ENST00000356239.3_Silent_p.S3092S|AKAP9_ENST00000358100.2_Silent_p.S3042S			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3096					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.S3092S(1)|p.S3096S(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GTTTGTTATCTGAAATTCAGG	0.393			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - coding silent(2)	large_intestine(2)	7											122	117	119					7																	91718761		2203	4300	6503	91556697	SO:0001819	synonymous_variant	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9288T>G	7.37:g.91718761T>G			91556697	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	T	10.07	1.250218	0.22880	.	.	ENSG00000127914	ENST00000435423	.	.	.	4.81	2.17	0.27698	.	.	.	.	.	T	0.52158	0.1717	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44590	-0.9318	4	.	.	.	.	5.0105	0.14310	0.2511:0.0:0.3171:0.4318	.	.	.	.	R	237	.	.	L	+	2	0	AKAP9	91556697	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.393000	0.34497	0.931000	0.37242	0.482000	0.46254	CTG		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91718761	T	G	91718761	2	3	76	1	0	0	0	0	0	0	0	1	459	1567	55	4		4	AKAP9	7	91718761	Silent	SNP	T	TCGA-AG-A02G-01A-01W-A00E-09	26161129	91718761	67419902	19	21704										
PREX2	80243	broad.mit.edu	37	chr8	69009298	69009298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gccatcattgatgggaagaaGgagcatgtgagtctgacagt	14	6	2	4			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr8:69009298G>A	ENST00000288368.4	+	22	2692	c.2415G>A	c.(2413-2415)aaG>aaA	p.K805K	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	805					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.K805K(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ATGGGAAGAAGGAGCATGTGA	0.428																																																2	Substitution - coding silent(2)	large_intestine(2)	8											173	152	159					8																	69009298		2203	4300	6503	69171852	SO:0001819	synonymous_variant	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2415G>A	8.37:g.69009298G>A			69171852	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																				0.428	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69009298	G	A	69009298	2	1	76	1	0	0	0	0	0	0	0	1	12511	991	35	3		3	PREX2	8	69009298	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		69009298	77354724	20	21705										
KIAA2026	158358	broad.mit.edu	37	chr9	6007467	6007468	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cctcctccgcggtggcaacgINSccccccaagggctgcagaaa							TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr9:6007467_6007468insC	ENST00000399933.3	-	1	319_320	c.320_321insG	c.(319-321)ggcfs	p.G107fs	MIR4665_ENST00000581132.1_RNA|KIAA2026_ENST00000381461.2_Frame_Shift_Ins_p.G107fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	107								p.V108fs*104(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CGGTGGCAACGCCCCCCAAGGG	0.723																																																1	Insertion - Frameshift(1)	large_intestine(1)	9																																								5997468	SO:0001589	frameshift_variant	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.321dupG	9.37:g.6007473_6007473dupC	ENSP00000382815:p.Gly107fs		5997467	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Ins	INS	ENST00000399933.3	37																																																																																					0.723	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	6007468	-	C	6007467	7	5	76	1	0	1	1	0	0	0	0	0	8291	1074	38	0	6022	0	KIAA2026	9	6007467	Frame_Shift_Ins	INS	-	TCGA-AG-A02G-01A-01W-A00E-09		6007467	135205964	21	21706										
ZNF462	58499	broad.mit.edu	37	chr9	109694777	109694777	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gccctggccatgtttacccgCgaggacaagtacagctgcca	11	14	0	0	rs376720857		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr9:109694777C>T	ENST00000277225.5	+	5	6352	c.6063C>T	c.(6061-6063)cgC>cgT	p.R2021R	ZNF462_ENST00000441147.2_Silent_p.R927R|ZNF462_ENST00000542028.1_5'Flank|ZNF462_ENST00000457913.1_Silent_p.R2081R|ZNF462_ENST00000497489.1_3'UTR			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2021					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R2021R(2)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TGTTTACCCGCGAGGACAAGT	0.537													C|||	1	0.000199681	8e-04	0	5008	,	,		18931	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|breast(1)	9						C		1,4405	2.1+/-5.4	0,1,2202	145	105	119		6063	-5	1	9		119	0,8600		0,0,4300	no	coding-synonymous	ZNF462	NM_021224.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		2021/2507	109694777	1,13005	2203	4300	6503	108734598	SO:0001819	synonymous_variant	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.6063C>T	9.37:g.109694777C>T			108734598	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																				0.537	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109694777	C	T	109694777	2	4	76	1	0	0	0	0	0	0	0	1	17965	755	27	1		1	ZNF462	9	109694777	Silent	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	103687310	109694777	31518654	22	21707										
LRRC8A	56262	broad.mit.edu	37	chr9	131671018	131671018	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gaggagctgcacctgacgggCaacctgagcgcggagaacaa	15	11	0	3			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr9:131671018C>G	ENST00000259324.5	+	3	2098	c.1575C>G	c.(1573-1575)ggC>ggG	p.G525G	LRRC8A_ENST00000372600.4_Silent_p.G525G|LRRC8A_ENST00000372599.3_Silent_p.G525G	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	525					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G525G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						ACCTGACGGGCAACCTGAGCG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	9											47	42	44					9																	131671018		2203	4300	6503	130710839	SO:0001819	synonymous_variant	56262			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1575C>G	9.37:g.131671018C>G			130710839	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																				0.592	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		G	131671018	C	G	131671018	2	3	76	1	0	0	0	0	0	0	0	1	9050	697	25	5		5	LRRC8A	9	131671018	Silent	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	21976241	131671018	9542413	23	21708										
ERCC6	2074	broad.mit.edu	37	chr10	50678590	50678590	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tttcatcaccagatggcataGaagttttgcctgttcctgaa	8	9	2	3			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr10:50678590G>A	ENST00000355832.5	-	18	3494	c.3416C>T	c.(3415-3417)tCt>tTt	p.S1139F	RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank|ERCC6_ENST00000542458.1_Missense_Mutation_p.S509F	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1139					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.S1139F(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AGATGGCATAGAAGTTTTGCC	0.408								Direct reversal of damage;Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	10											119	110	113					10																	50678590		2203	4300	6503	50348596	SO:0001583	missense	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3416C>T	10.37:g.50678590G>A	ENSP00000348089:p.Ser1139Phe		50348596	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434193	0.25813	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.82984	-1.67;-1.41	5.65	-4.25	0.03766	.	.	.	.	.	T	0.64538	0.2607	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.51276	-0.8726	9	0.52906	T	0.07	11.5364	5.9236	0.19096	0.0774:0.2384:0.5085:0.1757	.	1139;516	Q03468;Q59FF6	ERCC6_HUMAN;.	F	1139;516;509	ENSP00000348089:S1139F;ENSP00000445134:S509F	ENSP00000348089:S1139F	S	-	2	0	ERCC6	50348596	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.216000	0.01221	-0.506000	0.06558	0.655000	0.94253	TCT		0.408	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		A	50678590	G	A	50678590	3	1	76	1	0	0	0	0	1	0	0	0	5230	942	33	3	1081	3	ERCC6	10	50678590	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		50678590	84856157	24	21709										
TET1	80312	broad.mit.edu	37	chr10	70451231	70451231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ggttttgattgagtgtgcccGgcgagagctgcacgctacca	14	10	0	3			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr10:70451231G>A	ENST00000373644.4	+	12	6280	c.6071G>A	c.(6070-6072)cGg>cAg	p.R2024Q		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	2024					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.R2024Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GAGTGTGCCCGGCGAGAGCTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	10											96	90	92					10																	70451231		2203	4300	6503	70121237	SO:0001583	missense	80312			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.6071G>A	10.37:g.70451231G>A	ENSP00000362748:p.Arg2024Gln		70121237	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053723	0.75960	.	.	ENSG00000138336	ENST00000373644	T	0.12465	2.68	5.6	5.6	0.85130	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	0.296167	0.30781	N	0.008893	T	0.35828	0.0945	M	0.72894	2.215	0.32793	N	0.500866	D	0.76494	0.999	D	0.79108	0.992	T	0.45702	-0.9243	10	0.72032	D	0.01	.	13.2315	0.59947	0.0729:0.0:0.9271:0.0	.	2024	Q8NFU7	TET1_HUMAN	Q	2024	ENSP00000362748:R2024Q	ENSP00000362748:R2024Q	R	+	2	0	TET1	70121237	1.000000	0.71417	0.950000	0.38849	0.329000	0.28539	7.596000	0.82721	2.806000	0.96561	0.655000	0.94253	CGG		0.522	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70451231	G	A	70451231	3	1	76	1	0	0	0	0	1	0	0	0	15808	1116	39	1	6113	1	TET1	10	70451231	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	19772641	70451231	65083516	25	21710										
NT5C2	22978	broad.mit.edu	37	chr10	104850701	104850701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ccatttggataccttaatacGtctctggatggaactgatgt	9	8	1	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr10:104850701G>A	ENST00000404739.3	-	15	1287	c.1264C>T	c.(1264-1266)Cgt>Tgt	p.R422C	NT5C2_ENST00000343289.5_Missense_Mutation_p.R422C|NT5C2_ENST00000369857.4_5'UTR|NT5C2_ENST00000423468.2_Missense_Mutation_p.R393C			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	422					cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)	p.R422C(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		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)	ACCTTAATACGTCTCTGGATG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											87	88	88					10																	104850701		2203	4300	6503	104840691	SO:0001583	missense	22978			D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"purine 5' nucleotidase"	600417	"5'-nucleotidase (purine), cytosolic type B"	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1264C>T	10.37:g.104850701G>A	ENSP00000383960:p.Arg422Cys		104840691	B7Z382|D3DR91|Q5JUV5	Missense_Mutation	SNP	ENST00000404739.3	37	CCDS7544.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416477	0.42918	.	.	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000423468;ENST00000421281	T;T;T;T	0.24350	1.9;1.9;1.9;1.86	5.95	5.95	0.96441	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40297	0.1111	L	0.46614	1.455	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.997	P;P;P	0.55087	0.668;0.768;0.668	T	0.01228	-1.1412	10	0.35671	T	0.21	-13.1343	20.3854	0.98941	0.0:0.0:1.0:0.0	.	393;269;422	B7Z382;B3KXN5;P49902	.;.;5NTC_HUMAN	C	422;422;393;122	ENSP00000339479:R422C;ENSP00000383960:R422C;ENSP00000392236:R393C;ENSP00000408112:R122C	ENSP00000339479:R422C	R	-	1	0	NT5C2	104840691	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	5.656000	0.67988	2.825000	0.97269	0.655000	0.94253	CGT		0.363	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229		A	104850701	G	A	104850701	3	1	76	1	0	0	0	0	1	0	0	0	10718	1145	40	1	433	1	NT5C2	10	104850701	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	34399470	104850701	30684046	26	21711										
PRPF19	27339	broad.mit.edu	37	chr11	60670225	60670225	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gctgcaccttctcgggcagcAgtgacttccttggtgagacg	13	12	1	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr11:60670225A>G	ENST00000227524.4	-	4	580	c.375T>C	c.(373-375)acT>acC	p.T125T		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19									p.T125T(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						CTCGGGCAGCAGTGACTTCCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											64	57	59					11																	60670225		2203	4299	6502	60426801	SO:0001819	synonymous_variant	27339			BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.375T>C	11.37:g.60670225A>G			60426801		Silent	SNP	ENST00000227524.4	37	CCDS7995.1																																																																																				0.582	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		G	60670225	A	G	60670225	2	3	76	1	0	0	0	0	0	0	0	1	12598	175	7	4		4	PRPF19	11	60670225	Silent	SNP	A	TCGA-AG-A02G-01A-01W-A00E-09		60670225	74336291	27	21712										
SLC22A8	9376	broad.mit.edu	37	chr11	62782410	62782410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cccatgcttcccacacggtcCaggatctccgagaaggtcat	9	15	2	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr11:62782410C>T	ENST00000336232.2	-	2	156	c.21G>A	c.(19-21)ctG>ctA	p.L7L	SLC22A8_ENST00000311438.8_Silent_p.L7L|SLC22A8_ENST00000545207.1_Intron|SLC22A8_ENST00000430500.2_Silent_p.L7L|SLC22A8_ENST00000535878.1_Intron	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	7					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)	p.L7L(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCACACGGTCCAGGATCTCCG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	11											113	99	104					11																	62782410		2201	4298	6499	62538986	SO:0001819	synonymous_variant	9376			AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.21G>A	11.37:g.62782410C>T			62538986	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Silent	SNP	ENST00000336232.2	37	CCDS8042.1																																																																																				0.582	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		T	62782410	C	T	62782410	2	4	76	1	0	0	0	0	0	0	0	1	14497	581	21	3		3	SLC22A8	11	62782410	Silent	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	2112185	62782410	72224106	28	21713										
GRM5	2915	broad.mit.edu	37	chr11	88337888	88337888	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agaattgtaacacaatacctTcctggagagtctccattctc	6	11	2	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr11:88337888T>C	ENST00000305447.4	-	4	1541	c.1392A>G	c.(1390-1392)ggA>ggG	p.G464G	GRM5_ENST00000418177.2_Silent_p.G464G|GRM5_ENST00000305432.5_Silent_p.G464G|GRM5_ENST00000393297.1_Silent_p.G464G|GRM5_ENST00000455756.2_Silent_p.G464G	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	464					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.G464G(2)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	CACAATACCTTCCTGGAGAGT	0.418																																																2	Substitution - coding silent(2)	large_intestine(2)	11											47	50	49					11																	88337888		2201	4299	6500	87977536	SO:0001819	synonymous_variant	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1392A>G	11.37:g.88337888T>C			87977536	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																				0.418	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		C	88337888	T	C	88337888	2	2	76	1	0	0	0	0	0	0	0	1	6821	1770	62	4		4	GRM5	11	88337888	Silent	SNP	T	TCGA-AG-A02G-01A-01W-A00E-09	25555478	88337888	46668628	29	21714										
FAM113B	91523	broad.mit.edu	37	chr12	47629178	47629178	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	catcttgaaagagctgcagtCgggcgagcacgcccccgacc	12	15	1	2	rs146595577		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr12:47629178C>G	ENST00000546455.1	+	4	1063	c.332C>G	c.(331-333)tCg>tGg	p.S111W	PCED1B_ENST00000432328.1_Missense_Mutation_p.S111W|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	111							hydrolase activity (GO:0016787)	p.S111W(1)									GAGCTGCAGTCGGGCGAGCAC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	12											105	117	113					12																	47629178		2203	4300	6503	45915445	SO:0001583	missense	91523			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.332C>G	12.37:g.47629178C>G	ENSP00000446688:p.Ser111Trp		45915445	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	C	7.334	0.619559	0.14193	.	.	ENSG00000179715	ENST00000546455;ENST00000432328;ENST00000549500;ENST00000549630	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	4.19	1.29	0.21616	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	1.794230	0.03374	N	0.199407	T	0.32315	0.0825	L	0.29908	0.895	0.09310	N	0.999999	D	0.76494	0.999	D	0.71414	0.973	T	0.20371	-1.0277	10	0.37606	T	0.19	-0.5229	6.2747	0.20973	0.0:0.5348:0.364:0.1012	.	111	Q96HM7	F113B_HUMAN	W	111	ENSP00000446688:S111W;ENSP00000396040:S111W;ENSP00000449680:S111W;ENSP00000448000:S111W	ENSP00000396040:S111W	S	+	2	0	FAM113B	45915445	0.001000	0.12720	0.000000	0.03702	0.104000	0.19210	1.387000	0.34430	0.286000	0.22352	0.655000	0.94253	TCG		0.577	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		G	47629178	C	G	47629178	3	3	76	1	0	0	0	0	1	0	0	0	5418	893	31	5	334	5	FAM113B	12	47629178	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		47629178	86222717	30	21715										
PA2G4	5036	broad.mit.edu	37	chr12	56505062	56505062	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cgagcctgacctctacaagtCtgagatggaggtccaggatg	13	10	2	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr12:56505062C>T	ENST00000303305.6	+	11	1453	c.1034C>T	c.(1033-1035)tCt>tTt	p.S345F	RP11-603J24.17_ENST00000548595.1_RNA|PA2G4_ENST00000552766.1_Intron	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa	345	Necessary for nucleolar localization.				cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)	p.S345F(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			CTCTACAAGTCTGAGATGGAG	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	12											82	73	76					12																	56505062		2203	4300	6503	54791329	SO:0001583	missense	5036			U59435, BC007561	CCDS8902.1	12q13.2	2008-09-05	2002-08-29		ENSG00000170515	ENSG00000170515			8550	protein-coding gene	gene with protein product		602145	"proliferation-associated 2G4, 38kD"			9345902	Standard	NM_006191		Approved		uc001sjm.3	Q9UQ80	OTTHUMG00000170173	ENST00000303305.6:c.1034C>T	12.37:g.56505062C>T	ENSP00000302886:p.Ser345Phe		54791329	O43846|Q9UM59	Missense_Mutation	SNP	ENST00000303305.6	37	CCDS8902.1	.	.	.	.	.	.	.	.	.	.	C	33	5.206015	0.95033	.	.	ENSG00000170515	ENST00000303305;ENST00000417031;ENST00000546435	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.85474	0.5705	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.87545	0.2461	9	0.66056	D	0.02	.	18.1683	0.89736	0.0:1.0:0.0:0.0	.	345;345	F8VTY8;Q9UQ80	.;PA2G4_HUMAN	F	345;374;345	.	ENSP00000302886:S345F	S	+	2	0	PA2G4	54791329	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.567000	0.82357	2.824000	0.97209	0.655000	0.94253	TCT		0.483	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191		T	56505062	C	T	56505062	3	4	76	1	0	0	0	0	1	0	0	0	11392	913	32	3	1076	3	PA2G4	12	56505062	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	8875884	56505062	77346833	31	21716										
CSRP2	1466	broad.mit.edu	37	chr12	77256987	77256987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gatgcccagcctctcgccacGgtccatgttaagcgtgccag	11	15	1	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr12:77256987G>A	ENST00000311083.5	-	3	373	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	CSRP2_ENST00000552330.1_Missense_Mutation_p.R84C|CSRP2_ENST00000547435.1_Missense_Mutation_p.R84C|CSRP2_ENST00000546966.1_Missense_Mutation_p.R84C	NM_001321.1	NP_001312.1	Q16527	CSRP2_HUMAN	cysteine and glycine-rich protein 2	84					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R84C(1)		kidney(1)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)	8						CTCTCGCCACGGTCCATGTTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	12											109	94	99					12																	77256987		2203	4300	6503	75781118	SO:0001583	missense	1466			BC000992	CCDS9015.1	12q21.1	2005-10-30				ENSG00000175183			2470	protein-coding gene	gene with protein product		601871				7499425, 9286703	Standard	XM_006719258		Approved	SmLIM, CRP2, LMO5	uc001syl.1	Q16527		ENST00000311083.5:c.250C>T	12.37:g.77256987G>A	ENSP00000310901:p.Arg84Cys		75781118	Q93030	Missense_Mutation	SNP	ENST00000311083.5	37	CCDS9015.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.754994	0.49362	.	.	ENSG00000175183	ENST00000311083;ENST00000552330;ENST00000546966;ENST00000547435	T;T;T;T	0.64618	-0.03;-0.01;-0.03;-0.11	5.72	4.78	0.61160	.	0.104904	0.64402	D	0.000008	T	0.57272	0.2042	L	0.44542	1.39	0.58432	D	0.999999	D	0.54397	0.966	P	0.44860	0.462	T	0.61048	-0.7141	10	0.54805	T	0.06	-1.5829	13.7683	0.63008	0.0:0.0:0.7367:0.2633	.	84	Q16527	CSRP2_HUMAN	C	84	ENSP00000310901:R84C;ENSP00000449824:R84C;ENSP00000450056:R84C;ENSP00000450143:R84C	ENSP00000310901:R84C	R	-	1	0	CSRP2	75781118	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.229000	0.42990	2.878000	0.98634	0.650000	0.86243	CGT		0.522	CSRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406572.1	NM_001321		A	77256987	G	A	77256987	3	1	76	1	0	0	0	0	1	0	0	0	3973	1116	39	1	347	1	CSRP2	12	77256987	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	20751925	77256987	56594908	32	21717										
PPFIA2	8499	broad.mit.edu	37	chr12	81693091	81693091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ttctcttacctctagccatgCgaccacagttggcccatccc	6	17	2	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr12:81693091C>T	ENST00000549396.1	-	23	2873	c.2713G>A	c.(2713-2715)Gca>Aca	p.A905T	PPFIA2_ENST00000407050.4_Missense_Mutation_p.A831T|PPFIA2_ENST00000552948.1_Missense_Mutation_p.A905T|PPFIA2_ENST00000541017.1_Missense_Mutation_p.A122T|RP11-121G22.3_ENST00000549161.1_lincRNA|PPFIA2_ENST00000550584.2_Missense_Mutation_p.A905T|PPFIA2_ENST00000541570.2_Missense_Mutation_p.A472T|PPFIA2_ENST00000333447.7_Missense_Mutation_p.A890T|PPFIA2_ENST00000549325.1_Missense_Mutation_p.A890T|PPFIA2_ENST00000550359.2_Missense_Mutation_p.A752T|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000548586.1_Missense_Mutation_p.A905T|PPFIA2_ENST00000443686.3_Missense_Mutation_p.A806T	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	905	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.A905T(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TCTAGCCATGCGACCACAGTT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	12											71	69	69					12																	81693091		1840	4105	5945	80217222	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2713G>A	12.37:g.81693091C>T	ENSP00000450337:p.Ala905Thr		80217222	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.0|28.0	4.881334|4.881334	0.91740|0.91740	.|.	.|.	ENSG00000139220|ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000541017;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948|ENST00000551147	T;T;T;T;T;T;T;T;T|.	0.49432|.	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72045|0.72045	0.3412|0.3412	L|L	0.52206|0.52206	1.635|1.635	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.65833|0.65833	-0.6072|-0.6072	10|5	0.45353|.	T|.	0.12|.	-16.922|-16.922	20.6397|20.6397	0.99537|0.99537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	905|.	O75334|.	LIPA2_HUMAN|.	T|H	905;890;472;122;831;916;890;905;806;905|70	ENSP00000450337:A905T;ENSP00000450298:A890T;ENSP00000438337:A472T;ENSP00000445532:A122T;ENSP00000385093:A831T;ENSP00000327416:A890T;ENSP00000449338:A905T;ENSP00000388373:A806T;ENSP00000447868:A905T|.	ENSP00000327416:A890T|.	A|R	-|-	1|2	0|0	PPFIA2|PPFIA2	80217222|80217222	1.000000|1.000000	0.71417|0.71417	0.280000|0.280000	0.24747|0.24747	0.997000|0.997000	0.91878|0.91878	6.019000|6.019000	0.70818|0.70818	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	GCA|CGC		0.423	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81693091	C	T	81693091	3	4	76	1	0	0	0	0	1	0	0	0	12341	768	27	1	1100	1	PPFIA2	12	81693091	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	4436104	81693091	52158804	33	21718										
FLT1	2321	broad.mit.edu	37	chr13	28903789	28903789	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gctcccagcaggttaaccacGttcagatggtggccaatgtg	12	11	1	1	rs550669773		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr13:28903789G>A	ENST00000282397.4	-	19	2921	c.2670C>T	c.(2668-2670)aaC>aaT	p.N890N	FLT1_ENST00000540678.1_Silent_p.N108N	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.N890N(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGTTAACCACGTTCAGATGGT	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		17705	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13											156	132	140					13																	28903789		2203	4300	6503	27801789	SO:0001819	synonymous_variant	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2670C>T	13.37:g.28903789G>A			27801789	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																				0.572	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28903789	G	A	28903789	2	1	76	1	0	0	0	0	0	0	0	1	5960	1136	40	1		1	FLT1	13	28903789	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		28903789	86266089	34	21719										
INTS6	26512	broad.mit.edu	37	chr13	51961664	51961664	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	atccaaaaggccttgatataTctggctgcccatctatagca	7	11	2	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr13:51961664T>A	ENST00000311234.4	-	7	1224	c.752A>T	c.(751-753)gAt>gTt	p.D251V	INTS6_ENST00000425000.1_5'UTR|INTS6_ENST00000490542.1_5'Flank|INTS6_ENST00000497989.1_Missense_Mutation_p.D73V|INTS6_ENST00000420668.2_3'UTR|INTS6_ENST00000398119.2_Missense_Mutation_p.D238V|INTS6_ENST00000463928.1_Missense_Mutation_p.D251V	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	251					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.D251V(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		CCTTGATATATCTGGCTGCCC	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	13											58	54	56					13																	51961664		2203	4300	6503	50859665	SO:0001583	missense	26512			AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"DEAD-boxes"	14879	protein-coding gene	gene with protein product		604331	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.752A>T	13.37:g.51961664T>A	ENSP00000310260:p.Asp251Val		50859665	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	37	CCDS9428.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723288	0.48728	.	.	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989	.	.	.	4.81	4.81	0.61882	.	0.435447	0.27433	N	0.019392	T	0.63331	0.2502	M	0.63428	1.95	0.80722	D	1	B	0.26935	0.164	B	0.34590	0.186	T	0.63567	-0.6608	9	0.44086	T	0.13	-14.4311	13.825	0.63346	0.0:0.0:0.0:1.0	.	251	Q9UL03	INT6_HUMAN	V	251;238;73	.	ENSP00000310260:D251V	D	-	2	0	INTS6	50859665	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.688000	0.68227	1.909000	0.55274	0.459000	0.35465	GAT		0.358	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		A	51961664	T	A	51961664	3	1	76	1	0	0	0	0	1	0	0	0	7803	1435	50	5	1959	5	INTS6	13	51961664	Missense_Mutation	SNP	T	TCGA-AG-A02G-01A-01W-A00E-09	23057875	51961664	63208214	35	21720										
NALCN	259232	broad.mit.edu	37	chr13	102029174	102029174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	cactccatatttgttctcccGatcgcctagagaaacaaaag	6	12	1	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr13:102029174G>A	ENST00000251127.6	-	6	602	c.521C>T	c.(520-522)tCg>tTg	p.S174L	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376200.5_Missense_Mutation_p.S174L|NALCN_ENST00000376196.3_Missense_Mutation_p.S174L	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	174					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.S174L(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTGTTCTCCCGATCGCCTAGA	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	13											104	116	112					13																	102029174		2202	4300	6502	100827175	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.521C>T	13.37:g.102029174G>A	ENSP00000251127:p.Ser174Leu		100827175	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.400129	0.83120	.	.	ENSG00000102452	ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582	D;D;D	0.98889	-5.21;-5.21;-5.21	4.92	4.92	0.64577	Ion transport (1);	0.066807	0.64402	D	0.000006	D	0.99093	0.9688	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.975;0.991	D	0.99814	1.1043	10	0.87932	D	0	.	17.7591	0.88459	0.0:0.0:1.0:0.0	.	174;174	F2Z323;Q8IZF0	.;NALCN_HUMAN	L	174	ENSP00000251127:S174L;ENSP00000365367:S174L;ENSP00000365373:S174L	ENSP00000251127:S174L	S	-	2	0	NALCN	100827175	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	9.460000	0.97641	2.283000	0.76528	0.650000	0.86243	TCG		0.313	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		A	102029174	G	A	102029174	3	1	76	1	0	0	0	0	1	0	0	0	10178	1059	37	1	4851	1	NALCN	13	102029174	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	50067510	102029174	13140704	36	21721										
GALNTL1	57452	broad.mit.edu	37	chr14	69814672	69814672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ccaccttaatgtcctcccctGgatccccagtcatactgcag	6	17	1	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr14:69814672G>A	ENST00000337827.4	+	14	1819	c.1492G>A	c.(1492-1494)Gga>Aga	p.G498R	GALNT16_ENST00000553669.1_Missense_Mutation_p.G498R|GALNT16_ENST00000448469.3_Missense_Mutation_p.G498R	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	498	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.G498R(1)									GTCCTCCCCTGGATCCCCAGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14											135	105	115					14																	69814672		2203	4300	6503	68884425	SO:0001583	missense	57452			AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23233	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 16"	615132	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.1492G>A	14.37:g.69814672G>A	ENSP00000336729:p.Gly498Arg		68884425	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.613117	0.66672	.	.	ENSG00000100626	ENST00000337827;ENST00000536652;ENST00000448469;ENST00000553669	T;T;T	0.40476	1.03;1.03;1.03	5.76	5.76	0.90799	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.69214	0.3086	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76071	0.957;0.987	T	0.73560	-0.3944	10	0.87932	D	0	.	17.1265	0.86715	0.0:0.0:1.0:0.0	.	498;498	Q8N428;Q58A55	GLTL1_HUMAN;.	R	498;124;498;498	ENSP00000336729:G498R;ENSP00000402970:G498R;ENSP00000451200:G498R	ENSP00000336729:G498R	G	+	1	0	GALNTL1	68884425	1.000000	0.71417	0.512000	0.27736	0.065000	0.16274	7.536000	0.82023	2.728000	0.93425	0.655000	0.94253	GGA		0.612	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		A	69814672	G	A	69814672	3	1	76	1	0	0	0	0	1	0	0	0	6241	1349	47	3	1546	3	GALNTL1	14	69814672	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		69814672	37534868	37	21722										
DPF3	8110	broad.mit.edu	37	chr14	73137953	73137953	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	caaagccgtggaaagttgacGtgtcactttctgacgtggaa	12	8	2	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr14:73137953G>A	ENST00000556509.1	-	8	871				DPF3_ENST00000541685.1_Missense_Mutation_p.T322M|DPF3_ENST00000546183.1_Missense_Mutation_p.T332M|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)	p.T322M(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GAAAGTTGACGTGTCACTTTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	14											82	88	86					14																	73137953		2196	4296	6492	72207706	SO:0001627	intron_variant	8110			U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.871+2994C>T	14.37:g.73137953G>A			72207706	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	G	22.5	4.293994	0.81025	.	.	ENSG00000205683	ENST00000541685;ENST00000546183	T;T	0.68479	-0.31;-0.33	5.79	5.79	0.91817	.	.	.	.	.	T	0.69468	0.3114	N	0.19112	0.55	0.34409	D	0.696135	D;D	0.71674	0.998;0.994	P;P	0.58077	0.832;0.738	T	0.77273	-0.2649	9	0.66056	D	0.02	.	20.04	0.97581	0.0:0.0:1.0:0.0	.	332;322	F5H575;Q92784-2	.;.	M	322;332	ENSP00000441640:T322M;ENSP00000444662:T332M	ENSP00000381791:T377M	T	-	2	0	DPF3	72207706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.152000	0.77419	2.733000	0.93635	0.655000	0.94253	ACG		0.577	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			A	73137953	G	A	73137953	1	1	76	0	1	0	0	0	0	0	0	0	4729	1145	40	1		1	DPF3	14	73137953	Intron	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	3323281	73137953	34211587	38	21723										
THBS1	7057	broad.mit.edu	37	chr15	39886364	39886364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tttcaccgcctacagatggcGtctcagccacaggccaaaga	9	14	2	2	rs370392120		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr15:39886364G>A	ENST00000260356.5	+	20	3497	c.3332G>A	c.(3331-3333)cGt>cAt	p.R1111H	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1111	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.R1111H(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TACAGATGGCGTCTCAGCCAC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	HIS/ARG	0,4400		0,0,2200	68	66	67		3332	4.9	1	15		67	1,8593	1.2+/-3.3	0,1,4296	no	missense	THBS1	NM_003246.2	29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	1111/1171	39886364	1,12993	2200	4297	6497	37673656	SO:0001583	missense	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3332G>A	15.37:g.39886364G>A	ENSP00000260356:p.Arg1111His		37673656	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.182340	0.57800	0.0	1.16E-4	ENSG00000137801	ENST00000260356	D	0.95238	-3.65	5.83	4.92	0.64577	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.214223	0.23811	N	0.044321	T	0.77232	0.4100	N	0.00403	-1.54	0.48762	D	0.999706	B;B	0.14438	0.007;0.01	B;B	0.06405	0.001;0.002	T	0.75519	-0.3289	10	0.02654	T	1	-12.1599	11.0787	0.48047	0.1417:0.0:0.8583:0.0	.	1026;1111	B4E3J7;P07996	.;TSP1_HUMAN	H	1111	ENSP00000260356:R1111H	ENSP00000260356:R1111H	R	+	2	0	THBS1	37673656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.284000	0.72652	1.468000	0.48064	0.655000	0.94253	CGT		0.463	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39886364	G	A	39886364	3	1	76	1	0	0	0	0	1	0	0	0	15892	1145	40	1	3406	1	THBS1	15	39886364	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		39886364	62645028	39	21724										
CYP11A1	1583	broad.mit.edu	37	chr15	74631641	74631641	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agatatctctgcagggtcacGgagatggggtgaagtctgcg	16	7	3	3			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr15:74631641G>A	ENST00000268053.6	-	7	1327	c.1173C>T	c.(1171-1173)tcC>tcT	p.S391S	CYP11A1_ENST00000358632.4_Silent_p.S233S|CYP11A1_ENST00000419019.2_Silent_p.S233S	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	391					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.S391S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	GCAGGGTCACGGAGATGGGGT	0.582																																					Esophageal Squamous(87;818 1337 4093 9268 37314)											1	Substitution - coding silent(1)	large_intestine(1)	15																																								72418694	SO:0001819	synonymous_variant	1583			AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.1173C>T	15.37:g.74631641G>A			72418694	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Silent	SNP	ENST00000268053.6	37	CCDS32291.1																																																																																				0.582	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			A	74631641	G	A	74631641	2	1	76	1	0	0	0	0	0	0	0	1	4150	1103	39	1		1	CYP11A1	15	74631641	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	34745277	74631641	27899751	40	21725										
ACAN	176	broad.mit.edu	37	chr15	89382193	89382193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ccttggaagtccagagcctgCgctccaatgactctggggtc	12	13	1	2	rs201105250		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr15:89382193C>T	ENST00000561243.1	+	2	370	c.370C>T	c.(370-372)Cgc>Tgc	p.R124C	ACAN_ENST00000559004.1_Missense_Mutation_p.R124C|ACAN_ENST00000352105.7_Missense_Mutation_p.R124C|ACAN_ENST00000558207.1_Missense_Mutation_p.R124C|ACAN_ENST00000439576.2_Missense_Mutation_p.R124C			P16112	PGCA_HUMAN	aggrecan	124	G1-A.|Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.R124C(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCAGAGCCTGCGCTCCAATGA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	15											116	133	127					15																	89382193		2138	4255	6393	87183197	SO:0001583	missense	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.370C>T	15.37:g.89382193C>T	ENSP00000453342:p.Arg124Cys		87183197	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250194	0.59212	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.68765	-0.35;-0.35	5.36	4.45	0.53987	.	.	.	.	.	T	0.82079	0.4959	M	0.86343	2.81	0.48040	D	0.999574	P;P;D	0.89917	0.697;0.697;1.0	B;B;D	0.83275	0.178;0.178;0.996	D	0.84230	0.0466	9	0.87932	D	0	-12.5448	10.1001	0.42499	0.1361:0.7904:0.0:0.0735	.	124;124;124	E7ENV9;E7EX88;Q6PID9	.;.;.	C	124	ENSP00000387356:R124C;ENSP00000341615:R124C	ENSP00000268134:R124C	R	+	1	0	ACAN	87183197	0.992000	0.36948	1.000000	0.80357	0.985000	0.73830	2.067000	0.41461	1.410000	0.46936	0.591000	0.81541	CGC		0.617	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89382193	C	T	89382193	3	4	76	1	0	0	0	0	1	0	0	0	117	768	27	1	376	1	ACAN	15	89382193	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	14750552	89382193	13149199	41	21726										
RNF40	9810	broad.mit.edu	37	chr16	30780286	30780286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gcagatagaacacctgcagcGcaagctgggtgccaccaagc	12	13	0	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr16:30780286G>A	ENST00000324685.6	+	15	2660	c.2225G>A	c.(2224-2226)cGc>cAc	p.R742H	RNF40_ENST00000357890.5_Missense_Mutation_p.R642H|RNF40_ENST00000402121.3_Missense_Mutation_p.R434H|RNF40_ENST00000563683.1_Missense_Mutation_p.R702H	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	742					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R742H(1)		central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			CACCTGCAGCGCAAGCTGGGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	16											44	44	44					16																	30780286		2197	4300	6497	30687787	SO:0001583	missense	9810			AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2225G>A	16.37:g.30780286G>A	ENSP00000325677:p.Arg742His		30687787	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114195	0.77210	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121;ENST00000538323	T;T;T	0.32272	1.46;1.46;1.47	5.87	4.86	0.63082	.	0.056954	0.64402	D	0.000003	T	0.43875	0.1267	L	0.50333	1.59	0.44995	D	0.998017	D;D;D;D;D	0.76494	0.98;0.996;0.999;0.994;0.994	P;P;D;P;P	0.65323	0.725;0.852;0.934;0.655;0.655	T	0.31613	-0.9937	10	0.87932	D	0	-19.3507	8.7875	0.34830	0.078:0.0:0.7693:0.1526	.	74;434;642;742;742	F6SYU7;F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;.;BRE1B_HUMAN	H	742;642;434;74	ENSP00000325677:R742H;ENSP00000350563:R642H;ENSP00000384942:R434H	ENSP00000325677:R742H	R	+	2	0	RNF40	30687787	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.808000	0.47963	2.779000	0.95612	0.655000	0.94253	CGC		0.617	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		A	30780286	G	A	30780286	3	1	76	1	0	0	0	0	1	0	0	0	13530	1087	38	1	2279	1	RNF40	16	30780286	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		30780286	59574467	42	21727										
OR1A1	8383	broad.mit.edu	37	chr17	3119791	3119791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tcatctacagtctgagaaatCgggacatgaaggctgccctg	11	10	3	2	rs371610534		TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr17:3119791C>T	ENST00000304094.1	+	1	877	c.877C>T	c.(877-879)Cgg>Tgg	p.R293W		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R293W(2)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						TCTGAGAAATCGGGACATGAA	0.468																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	17						C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	109	104	106		877	1.9	0.1	17		106	0,8600		0,0,4300	no	missense	OR1A1	NM_014565.2	101	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	293/310	3119791	3,13003	2203	4300	6503	3066541	SO:0001583	missense	8383			AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.877C>T	17.37:g.3119791C>T	ENSP00000305207:p.Arg293Trp		3066541	A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	37	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	C	6.227	0.409970	0.11812	6.81E-4	0.0	ENSG00000172146	ENST00000304094	T	0.39997	1.05	5.05	1.9	0.25705	.	0.547245	0.15536	N	0.257203	T	0.44953	0.1318	M	0.78637	2.42	0.09310	N	1	B	0.21753	0.06	B	0.11329	0.006	T	0.46596	-0.9180	10	0.87932	D	0	.	13.0249	0.58808	0.552:0.448:0.0:0.0	.	293	Q9P1Q5	OR1A1_HUMAN	W	293	ENSP00000305207:R293W	ENSP00000305207:R293W	R	+	1	2	OR1A1	3066541	0.000000	0.05858	0.135000	0.22099	0.303000	0.27691	-1.829000	0.01701	0.287000	0.22375	-0.428000	0.05917	CGG		0.468	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		T	3119791	C	T	3119791	3	4	76	1	0	0	0	0	1	0	0	0	10980	875	31	1	879	1	OR1A1	17	3119791	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		3119791	78075419	43	21728										
SRP68	6730	broad.mit.edu	37	chr17	74068472	74068472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	tttctttattttcttcccctCcggcaccacgtccaccgccg	5	18	2	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr17:74068472C>T	ENST00000307877.2	-	1	262	c.101G>A	c.(100-102)gGa>gAa	p.G34E	GALR2_ENST00000329003.3_5'Flank|SRP68_ENST00000539137.1_Missense_Mutation_p.G34E|SRP68_ENST00000355113.5_5'UTR	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	34					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.G34E(1)		NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						TTCTTCCCCTCCGGCACCACG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											79	83	82					17																	74068472		2203	4300	6503	71580067	SO:0001583	missense	6730			AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"signal recognition particle 68kD"			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.101G>A	17.37:g.74068472C>T	ENSP00000312066:p.Gly34Glu		71580067	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.915549	0.52546	.	.	ENSG00000167881	ENST00000539137;ENST00000540937;ENST00000307877;ENST00000304220	D;D	0.86497	-2.13;-2.13	4.58	3.58	0.41010	.	0.493028	0.21464	N	0.074115	T	0.79435	0.4445	L	0.44542	1.39	0.80722	D	1	B;B	0.17038	0.02;0.02	B;B	0.18871	0.023;0.023	T	0.70324	-0.4903	10	0.21540	T	0.41	-13.9185	6.9515	0.24548	0.0:0.5658:0.3424:0.0918	.	34;34	G3V1U4;Q9UHB9	.;SRP68_HUMAN	E	34	ENSP00000446136:G34E;ENSP00000312066:G34E	ENSP00000307756:G34E	G	-	2	0	SRP68	71580067	0.991000	0.36638	1.000000	0.80357	0.854000	0.48673	1.758000	0.38410	1.243000	0.43853	0.542000	0.68232	GGA		0.627	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		T	74068472	C	T	74068472	3	4	76	1	0	0	0	0	1	0	0	0	15195	855	30	3	1846	3	SRP68	17	74068472	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09	70948681	74068472	7126738	44	21729										
USP36	57602	broad.mit.edu	37	chr17	76803074	76803074	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agggccagttttttggctggTggaggagacatggtgcttgc	17	6	0	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr17:76803074T>C	ENST00000542802.3	-	14	2495	c.2052A>G	c.(2050-2052)ccA>ccG	p.P684P	USP36_ENST00000588467.1_5'Flank|USP36_ENST00000312010.6_Silent_p.P684P|USP36_ENST00000449938.2_Silent_p.P384P			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	684					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.P684P(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			TTTTGGCTGGTGGAGGAGACA	0.562																																																2	Substitution - coding silent(2)	large_intestine(2)	17											120	105	110					17																	76803074		2203	4300	6503	74314669	SO:0001819	synonymous_variant	57602			AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2052A>G	17.37:g.76803074T>C			74314669	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																				0.562	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		C	76803074	T	C	76803074	2	2	76	1	0	0	0	0	0	0	0	1	17107	1683	59	4		4	USP36	17	76803074	Silent	SNP	T	TCGA-AG-A02G-01A-01W-A00E-09	2734602	76803074	4392136	45	21730										
SALL3	27164	broad.mit.edu	37	chr18	76757273	76757273	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ctcagaaacagcagccagccGcccattcacgcggtttatcg	9	15	2	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr18:76757273G>A	ENST00000537592.2	+	3	3854	c.3854G>A	c.(3853-3855)cGc>cAc	p.R1285H	SALL3_ENST00000536229.3_Missense_Mutation_p.R1080H|SALL3_ENST00000575389.2_Missense_Mutation_p.R1213H	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1285					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1285H(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GCAGCCAGCCGCCCATTCACG	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	18											128	130	130					18																	76757273		2203	4300	6503	74858261	SO:0001583	missense	27164			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3854G>A	18.37:g.76757273G>A	ENSP00000441823:p.Arg1285His		74858261	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	G	9.711	1.157041	0.21454	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.41400	1.0	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000035	T	0.23886	0.0578	N	0.03238	-0.38	0.51012	D	0.999904	B;B	0.31054	0.037;0.306	B;B	0.25291	0.007;0.059	T	0.10154	-1.0642	10	0.37606	T	0.19	-58.0545	19.4741	0.94979	0.0:0.0:1.0:0.0	.	945;1285	F5GXY4;Q9BXA9	.;SALL3_HUMAN	H	1285;1213;945	ENSP00000441823:R1285H	ENSP00000299466:R1285H	R	+	2	0	SALL3	74858261	1.000000	0.71417	0.992000	0.48379	0.369000	0.29798	5.659000	0.68010	2.595000	0.87683	0.655000	0.94253	CGC		0.572	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76757273	G	A	76757273	3	1	76	1	0	0	0	0	1	0	0	0	13849	1087	38	1	3864	1	SALL3	18	76757273	Missense_Mutation	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09		76757273	1319975	46	21731										
DTD1	92675	broad.mit.edu	37	chr20	18576871	18576871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gctgcgtaaaacatacaggcCggagcttatcaaaggtaagc	11	9	1	0			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr20:18576871C>T	ENST00000377452.3	+	3	536	c.356C>T	c.(355-357)cCg>cTg	p.P119L	DTD1_ENST00000494921.1_3'UTR	NM_080820.4	NP_543010.3	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1	119					D-amino acid catabolic process (GO:0019478)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)	p.P119L(1)		large_intestine(4)|lung(1)|ovary(2)	7						ACATACAGGCCGGAGCTTATC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	20											44	43	43					20																	18576871		2203	4300	6503	18524871	SO:0001583	missense	92675			AF332356	CCDS13138.1	20p11.23	2012-09-25	2012-09-25	2007-02-23	ENSG00000125821	ENSG00000125821			16219	protein-coding gene	gene with protein product		610996	"chromosome 20 open reading frame 88", "D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae)"	C20orf88, HARS2			Standard	NM_080820		Approved	DUEB, MGC119131, MGC41905, bA379J5.3, bA555E18.1, pqn-68	uc002wrf.4	Q8TEA8	OTTHUMG00000031980	ENST00000377452.3:c.356C>T	20.37:g.18576871C>T	ENSP00000366672:p.Pro119Leu		18524871	A8K5X5|D3DW37|Q496D1|Q5W184|Q8WXU8|Q9BW67|Q9H464|Q9H474	Missense_Mutation	SNP	ENST00000377452.3	37	CCDS13138.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380566	0.61845	.	.	ENSG00000125821	ENST00000377452	.	.	.	5.83	5.83	0.93111	D-Tyr tRNAtyr deacylase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77961	0.4209	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.78809	-0.2058	9	0.72032	D	0.01	-9.0054	19.0993	0.93268	0.0:1.0:0.0:0.0	.	119	Q8TEA8	DTD1_HUMAN	L	119	.	ENSP00000366672:P119L	P	+	2	0	DTD1	18524871	1.000000	0.71417	0.971000	0.41717	0.030000	0.12068	7.792000	0.85828	2.741000	0.93983	0.655000	0.94253	CCG		0.527	DTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078189.3	NM_080820		T	18576871	C	T	18576871	3	4	76	1	0	0	0	0	1	0	0	0	4797	652	23	1	366	1	DTD1	20	18576871	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		18576871	44448649	47	21732										
DNTTIP1	116092	broad.mit.edu	37	chr20	44424049	44424049	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gaggtggacgcagagcagctGatccaggaagcctgtcggag	17	9	0	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chr20:44424049G>A	ENST00000372622.3	+	4	407	c.339G>A	c.(337-339)ctG>ctA	p.L113L		NM_052951.2	NP_443183.1	Q9H147	TDIF1_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 1	113						nucleolus (GO:0005730)|nucleus (GO:0005634)		p.L113L(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9		Myeloproliferative disorder(115;0.0122)				CAGAGCAGCTGATCCAGGAAG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	20											48	33	38					20																	44424049		2203	4300	6503	43857456	SO:0001819	synonymous_variant	116092			AB035676	CCDS13369.1	20q13.12	2003-09-10	2003-09-10	2003-09-12	ENSG00000101457	ENSG00000101457			16160	protein-coding gene	gene with protein product	"novel protein similar to synaptotagmin 1 (SYT1, P65) (isoform 1)", "TdT binding protein"	611388	"chromosome 20 open reading frame 167"	C20orf167		11473582	Standard	NM_052951		Approved	dJ447F3.4, Tdif1	uc002xpk.3	Q9H147	OTTHUMG00000032610	ENST00000372622.3:c.339G>A	20.37:g.44424049G>A			43857456	B2RA18|Q96DE3|Q9BQP2|Q9H148	Silent	SNP	ENST00000372622.3	37	CCDS13369.1																																																																																				0.562	DNTTIP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079502.1	NM_052951		A	44424049	G	A	44424049	2	1	76	1	0	0	0	0	0	0	0	1	4692	1277	45	3		3	DNTTIP1	20	44424049	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	25847178	44424049	18601471	48	21733										
DMD	1756	broad.mit.edu	37	chrX	31986498	31986498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	gtttgcagacctcctgccacCgcagattcaggcttcccaat	8	15	1	2			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chrX:31986498C>T	ENST00000357033.4	-	45	6778	c.6572G>A	c.(6571-6573)cGg>cAg	p.R2191Q	DMD_ENST00000474231.1_5'UTR|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000378677.2_Missense_Mutation_p.R2187Q|DMD_ENST00000343523.2_5'UTR|DMD_ENST00000359836.1_5'UTR|DMD_ENST00000541735.1_5'UTR	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2191			R -> W. {ECO:0000269|PubMed:7849724}.		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R2187Q(1)|p.R2186Q(1)|p.R850Q(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CTCCTGCCACCGCAGATTCAG	0.408																																																3	Substitution - Missense(3)	large_intestine(3)	X											121	115	117					X																	31986498		2202	4300	6502	31896419	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6572G>A	X.37:g.31986498C>T	ENSP00000354923:p.Arg2191Gln		31896419	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254825	0.80135	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.38077	1.16;1.16	5.37	4.51	0.55191	.	0.000000	0.32258	U	0.006351	T	0.59514	0.2199	M	0.77486	2.375	0.80722	D	1	D;B;D;B;D;D	0.89917	1.0;0.006;0.962;0.007;0.999;0.998	D;B;B;B;P;D	0.77004	0.989;0.004;0.297;0.007;0.908;0.988	T	0.61182	-0.7114	10	0.45353	T	0.12	.	13.2846	0.60235	0.0:0.9217:0.0:0.0783	.	850;2183;2191;2187;850;847	P11532-2;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;.;DMD_HUMAN;.;.;.	Q	2183;850;847;2187;2191;2191;2068	ENSP00000367948:R2187Q;ENSP00000354923:R2191Q	ENSP00000354923:R2191Q	R	-	2	0	DMD	31896419	1.000000	0.71417	0.999000	0.59377	0.850000	0.48378	4.078000	0.57606	1.050000	0.40346	0.538000	0.68166	CGG		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	31986498	C	T	31986498	3	4	76	1	0	0	0	0	1	0	0	0	4591	652	23	1	4773	1	DMD	23	31986498	Missense_Mutation	SNP	C	TCGA-AG-A02G-01A-01W-A00E-09		31986498	123284062	49	21734										
FAM123B	139285	broad.mit.edu	37	chrX	63411961	63411961	+	Frame_Shift_Del	DEL	T	T	-													0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	agatattctaagtcatcatcTtcttcctcctccttaacctc							TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chrX:63411961delT	ENST00000330258.3	-	2	1478	c.1206delA	c.(1204-1206)gaafs	p.E402fs	AMER1_ENST00000403336.1_Frame_Shift_Del_p.E402fs|AMER1_ENST00000374869.3_Frame_Shift_Del_p.E402fs	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	402	Glu-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.D403fs*4(2)									AGTCATCAtcttcttcctcct	0.517																																																69	Whole gene deletion(67)|Deletion - Frameshift(2)	kidney(65)|large_intestine(3)|ovary(1)	X											232	221	225					X																	63411961		2203	4300	6503	63328686	SO:0001589	frameshift_variant	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1206delA	X.37:g.63411961delT	ENSP00000329117:p.Glu402fs		63328686	A2IB86|Q8N885	Frame_Shift_Del	DEL	ENST00000330258.3	37	CCDS14377.2																																																																																				0.517	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		-	63411961	T	-	63411961	7	5	76	1	0	1	0	1	0	0	0	0	5439	1606	56	0	2205	0	FAM123B	23	63411961	Frame_Shift_Del	DEL	T	TCGA-AG-A02G-01A-01W-A00E-09	31425463	63411961	91858599	50	21735										
ELF4	2000	broad.mit.edu	37	chrX	129200876	129200876	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	0.654305468258957	0	0.691694352159468	0.1	0.466258722490609	0	ggggtcagcccaacagtgggGcggctgggaggagacaaagt	19	8	1	1			TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02G-01A-01W-A00E-09	TCGA-AG-A02G-10A-01W-A00E-09	g.chrX:129200876G>A	ENST00000308167.5	-	9	2191	c.1812C>T	c.(1810-1812)cgC>cgT	p.R604R	ELF4_ENST00000335997.7_Silent_p.R604R	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)									p.R604R(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CAACAGTGGGGCGGCTGGGAG	0.597			T	ERG	AML																																		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	1	Substitution - coding silent(1)	large_intestine(1)	X											80	87	85					X																	129200876		2203	4300	6503	129028557	SO:0001819	synonymous_variant	2000			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1812C>T	X.37:g.129200876G>A			129028557		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																				0.597	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		A	129200876	G	A	129200876	2	1	76	1	0	0	0	0	0	0	0	1	5069	1190	42	3		3	ELF4	23	129200876	Silent	SNP	G	TCGA-AG-A02G-01A-01W-A00E-09	65788915	129200876	26069684	51	21736										
ATAD3B	83858	broad.mit.edu	37	chr1	1421166	1421166	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttcccctccggcaggtcaGccggcggctcctcagtcgac	11	19	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:1421166G>A	ENST00000308647.7	+	9	1027	c.911G>A	c.(910-912)aGc>aAc	p.S304N		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	304						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)	p.S304N(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CGGCAGGTCAGCCGGCGGCTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	1											47	46	46					1																	1421166		2203	4295	6498	1411029	SO:0001583	missense	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.911G>A	1.37:g.1421166G>A	ENSP00000311766:p.Ser304Asn		1411029	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	10.99	1.507710	0.27036	.	.	ENSG00000160072	ENST00000360489;ENST00000378737;ENST00000308647	D	0.93811	-3.29	2.26	2.26	0.28386	.	0.684600	0.16100	N	0.229603	D	0.90140	0.6919	L	0.47716	1.5	0.80722	D	1	P;B	0.36909	0.573;0.437	B;B	0.40134	0.32;0.171	D	0.86489	0.1796	10	0.27785	T	0.31	.	11.3553	0.49613	0.0:0.0:1.0:0.0	.	258;304	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	N	199;119;304	ENSP00000311766:S304N	ENSP00000311766:S304N	S	+	2	0	ATAD3B	1411029	0.588000	0.26799	0.938000	0.37757	0.021000	0.10359	2.060000	0.41394	1.253000	0.44018	0.205000	0.17691	AGC		0.647	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		A	1421166	G	A	1421166	3	1	77	1	0	0	0	0	1	0	0	0	1075	971	34	3	945	3	ATAD3B	1	1421166	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		1421166	247829455	1	21737										
CDK11B	8510	broad.mit.edu	37	chr1	1572825	1572825	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcttgaggtcgtgctccacAtagttcatcacgatgtagat	9	10	3	2	rs375978633	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:1572825A>G	ENST00000356026.5	+	0	1326				CDK11B_ENST00000341832.6_Silent_p.Y461Y|CDK11B_ENST00000340677.5_Silent_p.Y495Y|CDK11B_ENST00000407249.3_Silent_p.Y508Y|CDK11B_ENST00000317673.7_Silent_p.Y506Y			O75900	MMP23_HUMAN	matrix metallopeptidase 23B						proteolysis (GO:0006508)|reproduction (GO:0000003)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y508Y(1)		large_intestine(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	Marimastat(DB00786)	CGTGCTCCACATAGTTCATCA	0.617													.|||	7	0.00139776	0	0	5008	,	,		22598	0.006		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						A	,,,,,	0,4256		0,0,2128	149	140	143		1260,747,1149,1158,1278,1251	-4.9	0.9	1		143	4,8458		0,4,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDK11B	NM_033486.1,NM_033487.1,NM_033488.1,NM_033489.1,NM_033492.1,NM_033493.1	,,,,,	0,4,6355	GG,GA,AA		0.0473,0.0,0.0315	,,,,,	420/698,249/527,383/661,386/664,426/704,417/695	1572825	4,12714	2128	4231	6359	1562688	SO:0001628	intergenic_variant	984				CCDS30559.1	1p36.3	2013-01-11	2005-08-08		ENSG00000189409	ENSG00000189409		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7171	protein-coding gene	gene with protein product	"matrix metalloproteinase 22", "femalysin", "matrix metalloproteinase in the female reproductive tract"	603321	"matrix metalloproteinase 23B"	MMP22		9740677, 9750192	Standard	XM_005244810		Approved	MIFR, MIFR-1	uc001agp.3	O75900	OTTHUMG00000074713		1.37:g.1572825A>G			1562688	A2AGN0|A2AGN1|O75894|O75895|Q5QPQ8|Q76P96|Q7LDM6|Q7LDM7|Q9UBR9|Q9UJK8	Silent	SNP	ENST00000356026.5	37	CCDS30559.1																																																																																				0.617	MMP23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158492.2	NM_006983		G	1572825	A	G	1572825	1	3	77	0	1	0	0	0	0	0	0	0	3133	224	8	4		4	CDK11B	1	1572825	IGR	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	151659	1572825	247677796	2	21738										
NADK	65220	broad.mit.edu	37	chr1	1685603	1685603	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatcatggaggccccggccgCggccgcatacgccgtgctgc	15	16	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:1685603C>T	ENST00000341426.5	-	10	1209	c.988G>A	c.(988-990)Gcg>Acg	p.A330T	NADK_ENST00000341991.3_Missense_Mutation_p.A330T|NADK_ENST00000344463.4_Missense_Mutation_p.A475T|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.A475T|NADK_ENST00000342348.5_Missense_Mutation_p.A298T	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	330	Poly-Ala.				ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.A330T(1)		NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		GCCCCGGCCGCGGCCGCATAC	0.716																																																1	Substitution - Missense(1)	large_intestine(1)	1											35	45	42					1																	1685603		2203	4296	6499	1675463	SO:0001583	missense	65220			BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.988G>A	1.37:g.1685603C>T	ENSP00000341679:p.Ala330Thr		1675463	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	37	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.811492	0.70797	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.57	4.66	0.58398	ATP-NAD kinase, PpnK-type, all-beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.71634	0.3363	H	0.94222	3.51	0.58432	D	0.999996	D;D;D	0.89917	0.999;0.995;1.0	D;D;D	0.67900	0.953;0.949;0.954	T	0.80246	-0.1462	10	0.87932	D	0	-26.7725	13.1765	0.59630	0.0:0.9222:0.0:0.0778	.	298;475;330	F5GXR5;Q5QPS4;O95544	.;.;NADK_HUMAN	T	330;330;475;475;298	ENSP00000341679:A330T;ENSP00000344340:A330T;ENSP00000367890:A475T;ENSP00000340925:A475T;ENSP00000339727:A298T	ENSP00000341679:A330T	A	-	1	0	NADK	1675463	1.000000	0.71417	0.019000	0.16419	0.853000	0.48598	7.329000	0.79170	1.360000	0.45960	0.561000	0.74099	GCG		0.716	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		T	1685603	C	T	1685603	3	4	77	1	0	0	0	0	1	0	0	0	10167	768	27	1	364	1	NADK	1	1685603	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	112778	1685603	247565018	3	21739										
MEGF6	1953	broad.mit.edu	37	chr1	3519090	3519090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggccttccacaccggcaccGtgtggcttaaggcctgcacg	12	16	0	0	rs373558942		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:3519090G>A	ENST00000356575.4	-	2	432	c.206C>T	c.(205-207)aCg>aTg	p.T69M		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	69	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T69M(1)		cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CACCGGCACCGTGTGGCTTAA	0.682																																					Ovarian(73;978 3658)											1	Substitution - Missense(1)	large_intestine(1)	1						G	MET/THR	0,4256		0,0,2128	22	29	27		206	-8.9	0	1		27	2,8438		0,2,4218	no	missense	MEGF6	NM_001409.3	81	0,2,6346	AA,AG,GG		0.0237,0.0,0.0158	benign	69/1542	3519090	2,12694	2128	4220	6348	3508950	SO:0001583	missense	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.206C>T	1.37:g.3519090G>A	ENSP00000348982:p.Thr69Met		3508950	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	3.032	-0.199504	0.06219	0.0	2.37E-4	ENSG00000162591	ENST00000356575	D	0.84730	-1.89	4.44	-8.88	0.00789	EMI domain (1);	0.603848	0.13551	N	0.379512	T	0.67373	0.2886	N	0.12569	0.235	0.09310	N	1	B	0.15719	0.014	B	0.06405	0.002	T	0.40079	-0.9582	10	0.31617	T	0.26	4.4674	15.3134	0.74053	0.8531:0.0:0.1469:0.0	.	69	O75095	MEGF6_HUMAN	M	69	ENSP00000348982:T69M	ENSP00000348982:T69M	T	-	2	0	MEGF6	3508950	0.070000	0.21116	0.000000	0.03702	0.062000	0.15995	1.588000	0.36633	-2.156000	0.00790	-1.907000	0.00523	ACG		0.682	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3519090	G	A	3519090	3	1	77	1	0	0	0	0	1	0	0	0	9492	1145	40	1	4563	1	MEGF6	1	3519090	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1833487	3519090	245731531	4	21740										
KIAA0562	9731	broad.mit.edu	37	chr1	3753195	3753195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatttccggctccaccactGcctccccataatgcttacga	5	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:3753195G>A	ENST00000378230.3	-	10	1505	c.1181C>T	c.(1180-1182)gCa>gTa	p.A394V	CEP104_ENST00000460038.1_Intron	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	394						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.A394V(1)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						CTCCACCACTGCCTCCCCATA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	1											96	87	90					1																	3753195		2203	4300	6503	3743055	SO:0001583	missense	9731			AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1181C>T	1.37:g.3753195G>A	ENSP00000367476:p.Ala394Val		3743055	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.060007	0.36373	.	.	ENSG00000116198	ENST00000378230;ENST00000443466	T;T	0.48836	1.44;0.8	5.68	2.79	0.32731	.	0.456739	0.23265	N	0.050089	T	0.32194	0.0821	L	0.28192	0.835	0.38919	D	0.957699	B;B	0.09022	0.001;0.002	B;B	0.09377	0.002;0.004	T	0.10965	-1.0607	10	0.28530	T	0.3	.	10.7231	0.46052	0.2099:0.0:0.7901:0.0	.	394;394	O60308-3;O60308	.;CE104_HUMAN	V	394;88	ENSP00000367476:A394V;ENSP00000411927:A88V	ENSP00000367476:A394V	A	-	2	0	CEP104	3743055	0.000000	0.05858	0.012000	0.15200	0.025000	0.11179	0.270000	0.18607	0.758000	0.33059	0.650000	0.86243	GCA		0.567	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3753195	G	A	3753195	3	1	77	1	0	0	0	0	1	0	0	0	8205	1319	46	3	1648	3	KIAA0562	1	3753195	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	234105	3753195	245497426	5	21741										
CHD5	26038	broad.mit.edu	37	chr1	6184050	6184050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caggaggtgggcagggctggCgggcactggtgtgttggggt	23	6	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:6184050C>T	ENST00000262450.3	-	31	4756	c.4657G>A	c.(4657-4659)Gcc>Acc	p.A1553T	CHD5_ENST00000378021.1_Missense_Mutation_p.A410T	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A1553T(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGGGCTGGCGGGCACTGGT	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	1											17	22	20					1																	6184050		2203	4299	6502	6106637	SO:0001583	missense	26038			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.4657G>A	1.37:g.6184050C>T	ENSP00000262450:p.Ala1553Thr		6106637	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	c	13.78	2.339016	0.41398	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000378021;ENST00000536802;ENST00000538279;ENST00000377999	D;T	0.90788	-2.73;2.22	4.63	3.72	0.42706	.	0.077310	0.51477	D	0.000094	T	0.79263	0.4416	N	0.24115	0.695	0.48185	D	0.999602	B;P	0.40083	0.342;0.702	B;B	0.29663	0.045;0.105	T	0.77319	-0.2632	10	0.07813	T	0.8	-23.7896	14.4564	0.67418	0.1485:0.8515:0.0:0.0	.	1553;410	Q8TDI0;Q5TG85	CHD5_HUMAN;.	T	1553;1069;410;961;961;410	ENSP00000262450:A1553T;ENSP00000367260:A410T	ENSP00000262450:A1553T	A	-	1	0	CHD5	6106637	0.396000	0.25262	0.791000	0.31998	0.684000	0.39900	1.443000	0.35057	1.064000	0.40671	-0.268000	0.10319	GCC		0.682	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6184050	C	T	6184050	3	4	77	1	0	0	0	0	1	0	0	0	3334	768	27	1	1251	1	CHD5	1	6184050	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2430855	6184050	243066571	6	21742										
CHD5	26038	broad.mit.edu	37	chr1	6202309	6202309	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaccacgtagaagtcgggcGcccacatctcaaactcgcgt	10	14	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:6202309G>A	ENST00000262450.3	-	15	2414	c.2315C>T	c.(2314-2316)gCg>gTg	p.A772V	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A772V(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GAAGTCGGGCGCCCACATCTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	95	96					1																	6202309		2203	4300	6503	6124896	SO:0001583	missense	26038			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2315C>T	1.37:g.6202309G>A	ENSP00000262450:p.Ala772Val		6124896	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086309	0.94100	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.93604	-3.25	4.07	4.07	0.47477	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000001	D	0.95623	0.8577	L	0.58302	1.8	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95855	0.8878	10	0.54805	T	0.06	-21.7301	16.6218	0.84932	0.0:0.0:1.0:0.0	.	772	Q8TDI0	CHD5_HUMAN	V	772;288;180;180	ENSP00000262450:A772V	ENSP00000262450:A772V	A	-	2	0	CHD5	6124896	1.000000	0.71417	0.912000	0.35992	0.986000	0.74619	9.702000	0.98712	1.977000	0.57605	0.561000	0.74099	GCG		0.607	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6202309	G	A	6202309	3	1	77	1	0	0	0	0	1	0	0	0	3334	1087	38	1	3657	1	CHD5	1	6202309	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	18259	6202309	243048312	7	21743										
PHF13	148479	broad.mit.edu	37	chr1	6679925	6679925	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctggtaccattgacagcgaCggctgggacgcgggtttctc	15	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:6679925C>T	ENST00000377648.4	+	3	586	c.204C>T	c.(202-204)gaC>gaT	p.D68D	PHF13_ENST00000495385.1_Intron	NM_153812.2	NP_722519.2	Q86YI8	PHF13_HUMAN	PHD finger protein 13	68					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.D68D(1)		endometrium(3)|large_intestine(1)|lung(3)	7	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;1.46e-33)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0642)		TTGACAGCGACGGCTGGGACG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	1											58	61	60					1																	6679925		2203	4299	6502	6602512	SO:0001819	synonymous_variant	148479			AK027492	CCDS85.1	1p36.23	2013-01-28			ENSG00000116273	ENSG00000116273		"Zinc fingers, PHD-type"	22983	protein-coding gene	gene with protein product							Standard	NM_153812		Approved	MGC43399	uc001aob.4	Q86YI8	OTTHUMG00000001439	ENST00000377648.4:c.204C>T	1.37:g.6679925C>T			6602512	B3KUQ7|Q59FB6|Q5TH65|Q8N551|Q9UJP2	Silent	SNP	ENST00000377648.4	37	CCDS85.1																																																																																				0.567	PHF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004201.1	NM_153812		T	6679925	C	T	6679925	2	4	77	1	0	0	0	0	0	0	0	1	11855	535	19	1		1	PHF13	1	6679925	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	477616	6679925	242570696	8	21744										
DNAJC11	55735	broad.mit.edu	37	chr1	6700010	6700010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgatgatcagacggtgcatgGcaaagtagaccactagaggc	13	8	1	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:6700010G>A	ENST00000377577.5	-	11	1328	c.1205C>T	c.(1204-1206)gCc>gTc	p.A402V	DNAJC11_ENST00000294401.7_Intron|DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000542246.1_Missense_Mutation_p.A364V|DNAJC11_ENST00000377573.5_Missense_Mutation_p.A312V	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	402						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.A402V(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		ACGGTGCATGGCAAAGTAGAC	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	88	91					1																	6700010		2203	4300	6503	6622597	SO:0001583	missense	55735			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.1205C>T	1.37:g.6700010G>A	ENSP00000366800:p.Ala402Val		6622597	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.856018	0.32791	.	.	ENSG00000007923	ENST00000377577;ENST00000542246;ENST00000377573	T;T;T	0.26067	2.37;2.13;1.76	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.21468	0.0517	L	0.39245	1.2	0.80722	D	1	B;B	0.29188	0.236;0.014	B;B	0.24848	0.056;0.026	T	0.05716	-1.0868	10	0.05959	T	0.93	-28.4508	19.4017	0.94632	0.0:0.0:1.0:0.0	.	312;402	B4DGD5;Q9NVH1	.;DJC11_HUMAN	V	402;364;312	ENSP00000366800:A402V;ENSP00000444020:A364V;ENSP00000366796:A312V	ENSP00000366796:A312V	A	-	2	0	DNAJC11	6622597	1.000000	0.71417	0.354000	0.25760	0.991000	0.79684	9.158000	0.94723	2.835000	0.97688	0.591000	0.81541	GCC		0.537	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		A	6700010	G	A	6700010	3	1	77	1	0	0	0	0	1	0	0	0	4641	1203	42	3	498	3	DNAJC11	1	6700010	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	20085	6700010	242550611	9	21745										
DNAJC11	55735	broad.mit.edu	37	chr1	6706019	6706020	+	Frame_Shift_Del	DEL	CA	CA	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgggatgaaaactgcagagCacagtttgttgtcacaaagc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:6706019_6706020delCA	ENST00000377577.5	-	8	846_847	c.723_724delTG	c.(721-726)tgtgctfs	p.A242fs	DNAJC11_ENST00000294401.7_Frame_Shift_Del_p.A242fs|DNAJC11_ENST00000465508.1_5'Flank|DNAJC11_ENST00000349363.6_Frame_Shift_Del_p.A204fs|DNAJC11_ENST00000542246.1_Frame_Shift_Del_p.A204fs|DNAJC11_ENST00000377573.5_Frame_Shift_Del_p.A152fs	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	242						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.A242fs*41(1)|p.A272fs*41(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		AACTGCAGAGCACAGTTTGTTG	0.545																																																2	Deletion - Frameshift(2)	large_intestine(2)	1																																								6628607	SO:0001589	frameshift_variant	55735			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.723_724delTG	1.37:g.6706021_6706022delCA	ENSP00000366800:p.Ala242fs		6628606	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Frame_Shift_Del	DEL	ENST00000377577.5	37	CCDS87.1																																																																																				0.545	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		-	6706020	CA	-	6706019	7	5	77	1	0	1	0	1	0	0	0	0	4641	710	25	0	991	0	DNAJC11	1	6706019	Frame_Shift_Del	DEL	CA	TCGA-AG-A02N-01A-11W-A096-10	6009	6706019	242544602	10	21746										
SLC2A7	155184	broad.mit.edu	37	chr1	9063541	9063541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgcagtgaggaggcagattcCggcaaagatgatgaaactgt	14	7	0	5	rs200269396	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:9063541C>T	ENST00000400906.1	-	12	1356	c.1357G>A	c.(1357-1359)Gga>Aga	p.G453R		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	453					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.G453R(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		AGGCAGATTCCGGCAAAGATG	0.498													C|||	5	0.000998403	0	0	5008	,	,		22829	0		0	False		,,,				2504	0.0051															1	Substitution - Missense(1)	large_intestine(1)	1						C	ARG/GLY	0,4406		0,0,2203	83	75	78		1357	4.6	0.2	1		78	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC2A7	NM_207420.2	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	453/513	9063541	1,13005	2203	4300	6503	8986128	SO:0001583	missense	155184			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.1357G>A	1.37:g.9063541C>T	ENSP00000383698:p.Gly453Arg		8986128	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471525	0.43942	0.0	1.16E-4	ENSG00000197241	ENST00000400906	T	0.60920	0.15	4.64	4.64	0.57946	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.403647	0.24107	N	0.041491	T	0.74053	0.3666	M	0.82132	2.575	0.09310	N	1	D	0.64830	0.994	P	0.59357	0.856	T	0.68765	-0.5322	10	0.62326	D	0.03	.	16.2406	0.82405	0.0:1.0:0.0:0.0	.	453	Q6PXP3	GTR7_HUMAN	R	453	ENSP00000383698:G453R	ENSP00000383698:G453R	G	-	1	0	SLC2A7	8986128	0.000000	0.05858	0.204000	0.23530	0.845000	0.48019	0.870000	0.28010	2.403000	0.81681	0.561000	0.74099	GGA		0.498	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		T	9063541	C	T	9063541	3	4	77	1	0	0	0	0	1	0	0	0	14587	661	23	1	185	1	SLC2A7	1	9063541	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2357522	9063541	240187080	11	21747										
PIK3CD	5293	broad.mit.edu	37	chr1	9770571	9770571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaaggaggagaatcagagcGttgtggttgacttcctgctg	14	8	1	3	rs143116020	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:9770571G>A	ENST00000377346.4	+	3	253	c.58G>A	c.(58-60)Gtt>Att	p.V20I	PIK3CD_ENST00000536656.1_Missense_Mutation_p.V20I|PIK3CD_ENST00000361110.2_Missense_Mutation_p.V20I	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	20	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.V20I(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	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)	Caffeine(DB00201)	GAATCAGAGCGTTGTGGTTGA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	185	162	170		58	4.5	0.8	1	dbSNP_134	170	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PIK3CD	NM_005026.3	29	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	benign	20/1045	9770571	4,13002	2203	4300	6503	9693158	SO:0001583	missense	5293				CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.58G>A	1.37:g.9770571G>A	ENSP00000366563:p.Val20Ile		9693158	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	8.754	0.922006	0.17982	4.54E-4	2.33E-4	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.67345	-0.26;-0.23;-0.26	5.42	4.51	0.55191	.	0.423880	0.26366	N	0.024797	T	0.39253	0.1071	N	0.08118	0	0.80722	D	1	B;B;B	0.22983	0.043;0.078;0.043	B;B;B	0.18263	0.021;0.014;0.01	T	0.21655	-1.0239	10	0.08837	T	0.75	-38.5491	7.8426	0.29408	0.2228:0.0:0.7772:0.0	.	20;20;20	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	I	20	ENSP00000446444:V20I;ENSP00000366563:V20I;ENSP00000354410:V20I	ENSP00000353766:V20I	V	+	1	0	PIK3CD	9693158	1.000000	0.71417	0.798000	0.32154	0.923000	0.55619	4.700000	0.61803	1.424000	0.47217	0.563000	0.77884	GTT		0.552	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		A	9770571	G	A	9770571	3	1	77	1	0	0	0	0	1	0	0	0	11946	1145	40	1	60	1	PIK3CD	1	9770571	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	707030	9770571	239480050	12	21748										
CLSTN1	22883	broad.mit.edu	37	chr1	9795567	9795567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctgcgaattccgggcgtgGggaactgccgggagttcagg	18	9	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:9795567G>T	ENST00000377298.4	-	13	2633	c.1841C>A	c.(1840-1842)cCc>cAc	p.P614H	CLSTN1_ENST00000361311.4_Missense_Mutation_p.P604H|CLSTN1_ENST00000477264.1_5'Flank|CLSTN1_ENST00000377288.3_Missense_Mutation_p.P595H	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	614					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.P614H(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-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;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TCCGGGCGTGGGGAACTGCCG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											180	178	179					1																	9795567		2203	4300	6503	9718154	SO:0001583	missense	22883			AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1841C>A	1.37:g.9795567G>T	ENSP00000366513:p.Pro614His		9718154	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	37	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095721	0.94197	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63651	0.2529	M	0.84585	2.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.67110	-0.5753	10	0.87932	D	0	-37.6211	20.2985	0.98592	0.0:0.0:1.0:0.0	.	595;604;614	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	H	614;604;415;595;595	ENSP00000366513:P614H;ENSP00000354997:P604H;ENSP00000401934:P415H;ENSP00000366502:P595H	ENSP00000354997:P604H	P	-	2	0	CLSTN1	9718154	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	CCC		0.517	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			T	9795567	G	T	9795567	3	4	77	1	0	0	0	0	1	0	0	0	3567	1232	43	2	1132	2	CLSTN1	1	9795567	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	24996	9795567	239455054	13	21749										
VPS13D	55187	broad.mit.edu	37	chr1	12320804	12320804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgaggaattgaagattttgCgtgaactggttcatgatcga	12	4	1	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:12320804C>T	ENST00000358136.3	+	11	1295	c.1165C>T	c.(1165-1167)Cgt>Tgt	p.R389C	VPS13D_ENST00000356315.4_Missense_Mutation_p.R389C	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.R389C(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GAAGATTTTGCGTGAACTGGT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	94	94					1																	12320804		2203	4300	6503	12243391	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.1165C>T	1.37:g.12320804C>T	ENSP00000350854:p.Arg389Cys		12243391		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.924947	0.52759	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.47177	0.85;0.85	5.66	5.66	0.87406	.	0.289408	0.34828	N	0.003659	T	0.39733	0.1089	L	0.38175	1.15	0.80722	D	1	B;B	0.15930	0.015;0.004	B;B	0.10450	0.005;0.002	T	0.24941	-1.0146	10	0.72032	D	0.01	.	12.6903	0.56970	0.0:0.9204:0.0:0.0796	.	389;389	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	C	389	ENSP00000348666:R389C;ENSP00000350854:R389C	ENSP00000348666:R389C	R	+	1	0	VPS13D	12243391	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.466000	0.35310	2.657000	0.90304	0.655000	0.94253	CGT		0.413	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12320804	C	T	12320804	3	4	77	1	0	0	0	0	1	0	0	0	17232	768	27	1	1203	1	VPS13D	1	12320804	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2525237	12320804	236929817	14	21750										
AADACL4	343066	broad.mit.edu	37	chr1	12726163	12726163	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcagatcagatcttccccGgatccgggctcaggttctga	13	12	4	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:12726163G>A	ENST00000376221.1	+	4	641	c.641G>A	c.(640-642)cGg>cAg	p.R214Q		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	214						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.R214Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		GATCTTCCCCGGATCCGGGCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	1											84	87	86					1																	12726163		2203	4300	6503	12648750	SO:0001583	missense	343066				CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.641G>A	1.37:g.12726163G>A	ENSP00000365395:p.Arg214Gln		12648750		Missense_Mutation	SNP	ENST00000376221.1	37	CCDS30590.1	.	.	.	.	.	.	.	.	.	.	G	9.728	1.161463	0.21538	.	.	ENSG00000204518	ENST00000376221	T	0.58506	0.33	4.23	-5.82	0.02333	Alpha/beta hydrolase fold-3 (1);	0.915226	0.09312	N	0.819496	T	0.36082	0.0954	N	0.11845	0.185	0.09310	N	0.999996	B	0.27416	0.178	B	0.28784	0.094	T	0.21211	-1.0252	10	0.37606	T	0.19	-2.5952	13.5302	0.61617	0.6569:0.0:0.3431:0.0	.	214	Q5VUY2	ADCL4_HUMAN	Q	214	ENSP00000365395:R214Q	ENSP00000365395:R214Q	R	+	2	0	AADACL4	12648750	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.843000	0.04350	-1.181000	0.02730	-0.136000	0.14681	CGG		0.572	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630		A	12726163	G	A	12726163	3	1	77	1	0	0	0	0	1	0	0	0	13	1116	39	1	655	1	AADACL4	1	12726163	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	405359	12726163	236524458	15	21751										
AGMAT	79814	broad.mit.edu	37	chr1	15901300	15901300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacaagatcacagcccatcaCgttcaggccttgacaacccc	7	16	3	2	rs199886325		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:15901300C>T	ENST00000375826.3	-	6	1079	c.937G>A	c.(937-939)Gtg>Atg	p.V313M	DNAJC16_ENST00000375849.1_3'UTR|DNAJC16_ENST00000483270.1_3'UTR	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	313					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)	p.V313M(2)		endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCCCATCACGTTCAGGCCT	0.463													C|||	1	0.000199681	0	0	5008	,	,		21008	0.001		0	False		,,,				2504	0				NSCLC(126;1678 1780 25805 43508 49531)											2	Substitution - Missense(2)	large_intestine(2)	1											126	106	113					1																	15901300		2203	4300	6503	15773887	SO:0001583	missense	79814			AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.937G>A	1.37:g.15901300C>T	ENSP00000364986:p.Val313Met		15773887	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	15.23	2.771109	0.49680	.	.	ENSG00000116771	ENST00000375826	D	0.86366	-2.11	5.93	3.02	0.34903	Ureohydrolase domain (1);	0.245141	0.41605	D	0.000852	D	0.86814	0.6023	M	0.81179	2.53	0.39136	D	0.961941	B	0.25521	0.128	B	0.35770	0.21	D	0.83799	0.0235	10	0.54805	T	0.06	-21.7355	5.5346	0.17003	0.1508:0.6384:0.0:0.2109	.	313	Q9BSE5	SPEB_HUMAN	M	313	ENSP00000364986:V313M	ENSP00000364986:V313M	V	-	1	0	AGMAT	15773887	0.866000	0.29940	0.974000	0.42286	0.954000	0.61252	0.971000	0.29396	0.822000	0.34565	0.603000	0.83216	GTG		0.463	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		T	15901300	C	T	15901300	3	4	77	1	0	0	0	0	1	0	0	0	385	536	19	1	129	1	AGMAT	1	15901300	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3175137	15901300	233349321	16	21752										
UQCRHL	0	broad.mit.edu	37	chr1	16134130	16134130	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcggtaagcatcttttgctcGtcctccagtcccatgtctgg	9	13	2	0	rs373188682		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:16134130G>A								FBLIM1 (21041 upstream) : RP11-169K16.9 (26429 downstream)																							TCTTTTGCTCGTCCTCCAGTC	0.488													G|||	1	0.000199681	0	0	5008	,	,		18502	0		0	False		,,,				2504	0.001															0			1						G		0,4406		0,0,2203	72	69	70		15	-3.3	0	1		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UQCRHL	NM_001089591.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		5/92	16134130	1,13005	2203	4300	6503	16006717	SO:0001628	intergenic_variant	440567																															1.37:g.16134130G>A			16006717		Silent	SNP		37																																																																																				0	0.488									A	16134130	G	A	16134130	1	1	77	0	1	0	0	0	0	0	0	0	17063	1136	40	1		1	UQCRHL	1	16134130	IGR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	232830	16134130	233116491	17	21753										
SPEN	23013	broad.mit.edu	37	chr1	16260808	16260808	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acccctgctgggcccgtgaaCgtcctgaaagggcctgtgaa	13	13	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:16260808C>T	ENST00000375759.3	+	11	8277	c.8073C>T	c.(8071-8073)aaC>aaT	p.N2691N		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2691	RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.N2691N(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		GGCCCGTGAACGTCCTGAAAG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	1											73	77	76					1																	16260808		2203	4300	6503	16133395	SO:0001819	synonymous_variant	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.8073C>T	1.37:g.16260808C>T			16133395	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																				0.597	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16260808	C	T	16260808	2	4	77	1	0	0	0	0	0	0	0	1	15077	535	19	1		1	SPEN	1	16260808	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	126678	16260808	232989813	18	21754										
ZBTB17	7709	broad.mit.edu	37	chr1	16273537	16273537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgcatttggaggaaagtgGccacggccagcacatcatcc	11	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:16273537G>A	ENST00000375743.4	-	4	519	c.287C>T	c.(286-288)gCc>gTc	p.A96V	ZBTB17_ENST00000537142.1_Missense_Mutation_p.P7S|ZBTB17_ENST00000448462.2_Intron|ZBTB17_ENST00000479282.1_5'UTR|ZBTB17_ENST00000375733.2_Missense_Mutation_p.A96V	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	96	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A96V(1)		breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|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;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAAAGTGGCCACGGCCAG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	81	83					1																	16273537		2203	4300	6503	16146124	SO:0001583	missense	7709			U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12936	protein-coding gene	gene with protein product		604084	"zinc finger protein 151 (pHZ-67)", "zinc finger protein 60"	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.287C>T	1.37:g.16273537G>A	ENSP00000364895:p.Ala96Val		16146124	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	37	CCDS165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.540517|5.540517	0.96474|0.96474	.|.	.|.	ENSG00000116809|ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000444654|ENST00000537142	T;T|T	0.58940|0.09255	0.3;0.3|3.0	5.48|5.48	5.48|5.48	0.80851|0.80851	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.24736|0.24736	0.0600|0.0600	M|M	0.94063|0.94063	3.49|3.49	0.80722|0.80722	D|D	1|1	D;B;D;D|P	0.89917|0.41848	1.0;0.018;1.0;1.0|0.763	D;B;D;D|B	0.87578|0.33960	0.998;0.038;0.997;0.994|0.173	T|T	0.45963|0.45963	-0.9225|-0.9225	10|9	0.87932|0.87932	D|D	0|0	.|.	19.3344|19.3344	0.94309|0.94309	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	96;20;96;96|7	B4DGV6;B4DYU5;Q13105-2;Q13105|F5H411	.;.;.;ZBT17_HUMAN|.	V|S	96|7	ENSP00000364895:A96V;ENSP00000364885:A96V|ENSP00000438529:P7S	ENSP00000364885:A96V|ENSP00000438529:P7S	A|P	-|-	2|1	0|0	ZBTB17|ZBTB17	16146124|16146124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	9.414000|9.414000	0.97362|0.97362	2.572000|2.572000	0.86782|0.86782	0.561000|0.561000	0.74099|0.74099	GCC|CCA		0.612	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443		A	16273537	G	A	16273537	3	1	77	1	0	0	0	0	1	0	0	0	17566	1203	42	3	2176	3	ZBTB17	1	16273537	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	12729	16273537	232977084	19	21755										
PADI6	353238	broad.mit.edu	37	chr1	17714914	17714914	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgagttggtgctggggcccGaccagcacgcctataccttg	13	12	0	1	rs529584194		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:17714914G>A	ENST00000434762.2	+	0	768							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.D240N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GCTGGGGCCCGACCAGCACGC	0.527													G|||	1	0.000199681	0	0.0014	5008	,	,		18604	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											57	55	56					1																	17714914		1868	4103	5971	17587501			353238			AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17714914G>A			17587501	Q330K5|Q70SX3	Missense_Mutation	SNP	ENST00000434762.2	37																																																																																					0.527	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		A	17714914	G	A	17714914	1	1	77	0	1	0	0	0	0	0	0	0	11412	1058	37	1		1	PADI6	1	17714914	RNA	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1441377	17714914	231535707	20	21756										
PADI6	353238	broad.mit.edu	37	chr1	17720552	17720552	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacctcaggccgccgatctcGatgagttccccatgaagtac	9	15	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:17720552G>A	ENST00000434762.2	+	0	1207							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.D385N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CGCCGATCTCGATGAGTTCCC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	1											98	105	103					1																	17720552		1991	4158	6149	17593139			353238			AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17720552G>A			17593139	Q330K5|Q70SX3	Missense_Mutation	SNP	ENST00000434762.2	37																																																																																					0.547	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		A	17720552	G	A	17720552	1	1	77	0	1	0	0	0	0	0	0	0	11412	1058	37	1		1	PADI6	1	17720552	RNA	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5638	17720552	231530069	21	21757										
RCC2	55920	broad.mit.edu	37	chr1	17749225	17749225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caaggccaaggtgtggttccGcccacatgctgcagacacaa	11	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:17749225G>A	ENST00000375436.4	-	5	818	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	RCC2_ENST00000375433.3_Missense_Mutation_p.R211W	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	211					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)	p.R211W(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		GTGTGGTTCCGCCCACATGCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	1											110	89	96					1																	17749225		2203	4300	6503	17621812	SO:0001583	missense	55920				CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.631C>T	1.37:g.17749225G>A	ENSP00000364585:p.Arg211Trp		17621812	Q8IVL9|Q9BSN6|Q9NPV8	Missense_Mutation	SNP	ENST00000375436.4	37	CCDS181.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.078040	0.55753	.	.	ENSG00000179051	ENST00000375436;ENST00000375433	D;D	0.84944	-1.92;-1.92	5.1	3.08	0.35506	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.87010	0.6071	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87987	0.2747	10	0.66056	D	0.02	-32.4312	13.3867	0.60799	0.0:0.0:0.718:0.282	.	211	Q9P258	RCC2_HUMAN	W	211	ENSP00000364585:R211W;ENSP00000364582:R211W	ENSP00000364582:R211W	R	-	1	2	RCC2	17621812	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.403000	0.66338	1.273000	0.44346	0.555000	0.69702	CGG		0.592	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007144.1	NM_018715		A	17749225	G	A	17749225	3	1	77	1	0	0	0	0	1	0	0	0	13211	1086	38	1	973	1	RCC2	1	17749225	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	28673	17749225	231501396	22	21758										
UBR4	23352	broad.mit.edu	37	chr1	19536655	19536655	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caggggccgcacagccacctCccagcccggggtcgtgtccg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:19536655delC	ENST00000375254.3	-	1	115	c.88delG	c.(88-90)gagfs	p.E30fs	UBR4_ENST00000375217.2_Frame_Shift_Del_p.E30fs|UBR4_ENST00000375267.2_Frame_Shift_Del_p.E30fs|RP1-43E13.2_ENST00000437898.1_RNA|UBR4_ENST00000375226.2_Frame_Shift_Del_p.E30fs	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	30					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E30fs*17(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ACAGCCACCTCCCAGCCCGGG	0.726																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											7	8	8					1																	19536655		2152	4230	6382	19409242	SO:0001589	frameshift_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.88delG	1.37:g.19536655delC	ENSP00000364403:p.Glu30fs		19409242	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Frame_Shift_Del	DEL	ENST00000375254.3	37	CCDS189.1																																																																																				0.726	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		-	19536655	C	-	19536655	7	5	77	1	0	1	0	1	0	0	0	0	16944	864	30	0	15887	0	UBR4	1	19536655	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	1787430	19536655	229713966	23	21759										
DDOST	1650	broad.mit.edu	37	chr1	20981191	20981191	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accaaagggttatcaggatcGgccaccatcctgcagcagga	11	12	1	0	rs550450324		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:20981191G>A	ENST00000375048.3	-	6	717	c.612C>T	c.(610-612)gcC>gcT	p.A204A	DDOST_ENST00000415136.2_Silent_p.A167A|DDOST_ENST00000602624.2_Silent_p.A187A|PINK1-AS_ENST00000451424.1_RNA	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	204					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.A204A(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TATCAGGATCGGCCACCATCC	0.582													G|||	1	0.000199681	0	0	5008	,	,		16402	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											37	36	36					1																	20981191		2194	4279	6473	20853778	SO:0001819	synonymous_variant	1650			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"oligosaccharyltransferase subunit 48"	602202	"dolichyl-diphosphooligosaccharide-protein glycosyltransferase", "dolichyl-diphosphooligosaccharide--protein glycosyltransferase"			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.612C>T	1.37:g.20981191G>A			20853778	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.582	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216		A	20981191	G	A	20981191	2	1	77	1	0	0	0	0	0	0	0	1	4341	1103	39	1		1	DDOST	1	20981191	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1444536	20981191	228269430	24	21760										
EIF4G3	8672	broad.mit.edu	37	chr1	21268770	21268770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttctctccactgaggactaGcctaaggactggggaaggag	13	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:21268770G>A	ENST00000264211.8	-	8	903	c.709C>T	c.(709-711)Cta>Tta	p.L237L	EIF4G3_ENST00000400422.1_Silent_p.L237L|EIF4G3_ENST00000356916.3_Silent_p.L248L|EIF4G3_ENST00000374933.3_5'Flank|EIF4G3_ENST00000536266.1_5'UTR|EIF4G3_ENST00000374937.3_Silent_p.L243L|EIF4G3_ENST00000602326.1_Silent_p.L243L|EIF4G3_ENST00000374927.4_Silent_p.L237L|EIF4G3_ENST00000544689.1_5'Flank|EIF4G3_ENST00000374935.3_Intron	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	237					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.L237L(1)|p.L243L(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CTGAGGACTAGCCTAAGGACT	0.438																																																2	Substitution - coding silent(2)	large_intestine(2)	1											121	130	127					1																	21268770		2203	4300	6503	21141357	SO:0001819	synonymous_variant	8672			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.709C>T	1.37:g.21268770G>A			21141357	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Silent	SNP	ENST00000264211.8	37	CCDS214.1																																																																																				0.438	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		A	21268770	G	A	21268770	2	1	77	1	0	0	0	0	0	0	0	1	5051	962	34	3		3	EIF4G3	1	21268770	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	287579	21268770	227981851	25	21761										
EIF4G3	8672	broad.mit.edu	37	chr1	21299535	21299535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggaggcggctgttgctgcGtaggcactatgataggtgct	16	8	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:21299535G>A	ENST00000264211.8	-	5	577	c.383C>T	c.(382-384)aCg>aTg	p.T128M	EIF4G3_ENST00000400422.1_Missense_Mutation_p.T128M|EIF4G3_ENST00000356916.3_Missense_Mutation_p.T139M|EIF4G3_ENST00000536266.1_5'Flank|EIF4G3_ENST00000374937.3_Missense_Mutation_p.T135M|EIF4G3_ENST00000602326.1_Missense_Mutation_p.T135M|EIF4G3_ENST00000374927.4_Missense_Mutation_p.T128M|EIF4G3_ENST00000374935.3_Missense_Mutation_p.T128M	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	128					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.T128M(1)|p.T135M(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CTGTTGCTGCGTAGGCACTAT	0.353																																																2	Substitution - Missense(2)	large_intestine(2)	1											52	55	54					1																	21299535		2203	4300	6503	21172122	SO:0001583	missense	8672			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.383C>T	1.37:g.21299535G>A	ENSP00000264211:p.Thr128Met		21172122	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	G	32	5.133725	0.94517	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000356916;ENST00000374927;ENST00000537059;ENST00000438975;ENST00000411888	T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9	6.05	6.05	0.98169	.	0.096440	0.64402	D	0.000001	T	0.41073	0.1143	N	0.22421	0.69	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.997;0.996;0.998;0.997;0.997	T	0.16482	-1.0401	10	0.52906	T	0.07	-11.6556	20.1963	0.98243	0.0:0.0:1.0:0.0	.	128;324;128;254;135;128	B4DXR2;Q59GJ0;Q504Z1;B1AN89;B9EGQ7;O43432	.;.;.;.;.;IF4G3_HUMAN	M	128;325;128;128;135;254;128;139;128;166	ENSP00000264211:T128M;ENSP00000383274:T128M;ENSP00000364071:T128M;ENSP00000364073:T135M;ENSP00000364062:T128M;ENSP00000395381:T128M;ENSP00000396083:T166M	ENSP00000264211:T128M	T	-	2	0	EIF4G3	21172122	1.000000	0.71417	0.994000	0.49952	0.972000	0.66771	8.753000	0.91637	2.878000	0.98634	0.650000	0.86243	ACG		0.353	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		A	21299535	G	A	21299535	3	1	77	1	0	0	0	0	1	0	0	0	5051	1145	40	1	4482	1	EIF4G3	1	21299535	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	30765	21299535	227951086	26	21762										
HSPG2	3339	broad.mit.edu	37	chr1	22206927	22206927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtggtatccatggcgatgtcGctaagtcccacgctggccat	12	12	0	0	rs139220302		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:22206927G>A	ENST00000374695.3	-	16	2203	c.2124C>T	c.(2122-2124)agC>agT	p.S708S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	708	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.S708S(2)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGCGATGTCGCTAAGTCCCA	0.662																																																2	Substitution - coding silent(2)	large_intestine(2)	1						G		1,4405	2.1+/-5.4	0,1,2202	86	69	75		2124	-6.1	0.9	1	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous	HSPG2	NM_005529.5		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		708/4392	22206927	1,13005	2203	4300	6503	22079514	SO:0001819	synonymous_variant	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.2124C>T	1.37:g.22206927G>A			22079514	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																				0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22206927	G	A	22206927	2	1	77	1	0	0	0	0	0	0	0	1	7451	1078	38	1		1	HSPG2	1	22206927	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	907392	22206927	227043694	27	21763										
TCEB3	6924	broad.mit.edu	37	chr1	24078022	24078024	+	In_Frame_Del	DEL	GAA	GAA	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacagagagggcagcagcctGaagaagaagtgtttgcctcc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	GAA	GAA	GAA	-	GAA	GAA	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:24078022_24078024delGAA	ENST00000418390.2	+	4	1276_1278	c.1005_1007delGAA	c.(1003-1008)ctgaag>ctg	p.K338del	TCEB3_ENST00000609199.1_In_Frame_Del_p.K312del	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	338					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.K312delK(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		GCAGCAGCCTGAAGAAGAAGTGT	0.527											OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Deletion - In frame(1)	large_intestine(1)	1																																								23950611	SO:0001651	inframe_deletion	6924			L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1005_1007delGAA	1.37:g.24078028_24078030delGAA	ENSP00000395574:p.Lys338del	768	23950609	B2R7Q8|Q8IXH1	In_Frame_Del	DEL	ENST00000418390.2	37	CCDS239.2																																																																																				0.527	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		-	24078024	GAA	-	24078022	7	5	77	1	0	1	0	1	0	0	0	0	15720	1277	45	0	1019	0	TCEB3	1	24078022	In_Frame_Del	DEL	GAA	TCGA-AG-A02N-01A-11W-A096-10	1871095	24078022	225172599	28	21764										
UBXN11	91544	broad.mit.edu	37	chr1	26612372	26612372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgaacatcatgatgccattcCggtagagcttcagcgggatg	12	10	2	2	rs372332532		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:26612372C>T	ENST00000374222.1	-	10	1180	c.716G>A	c.(715-717)cGg>cAg	p.R239Q	UBXN11_ENST00000374217.2_Missense_Mutation_p.R206Q|UBXN11_ENST00000436301.2_Missense_Mutation_p.R164Q|UBXN11_ENST00000374221.3_Missense_Mutation_p.R239Q|UBXN11_ENST00000357089.4_Missense_Mutation_p.R206Q|UBXN11_ENST00000535108.1_Missense_Mutation_p.R81Q|UBXN11_ENST00000374223.1_5'UTR|UBXN11_ENST00000314675.7_Missense_Mutation_p.R119Q			Q5T124	UBX11_HUMAN	UBX domain protein 11	239	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R239Q(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						GATGCCATTCCGGTAGAGCTT	0.632											OREG0013265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG,GLN/ARG,GLN/ARG	1,4111		0,1,2055	60	67	65		716,617,356	2	1	1		65	0,8370		0,0,4185	no	missense,missense,missense	UBXN11	NM_183008.2,NM_145345.2,NM_001077262.1	43,43,43	0,1,6240	TT,TC,CC		0.0,0.0243,0.0080	benign,benign,benign	239/521,206/488,119/401	26612372	1,12481	2056	4185	6241	26484959	SO:0001583	missense	91544			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.716G>A	1.37:g.26612372C>T	ENSP00000363339:p.Arg239Gln	788	26484959	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127636	0.56721	2.43E-4	0.0	ENSG00000158062	ENST00000314675;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217;ENST00000535108;ENST00000436301;ENST00000374215;ENST00000452980	T;T;T;T;T;T;T;T;T	0.44482	2.27;2.53;2.54;2.54;2.53;0.94;0.96;0.96;0.92	5.51	2.03	0.26663	SEP domain (3);	0.365309	0.26119	N	0.026238	T	0.25791	0.0628	L	0.39020	1.185	0.25873	N	0.983687	B;B;B;B;B;B	0.33000	0.318;0.393;0.179;0.196;0.196;0.393	B;B;B;B;B;B	0.27608	0.081;0.071;0.024;0.011;0.011;0.05	T	0.10177	-1.0641	10	0.37606	T	0.19	-22.7099	5.6016	0.17357	0.1458:0.5677:0.0:0.2865	.	81;164;206;201;119;239	B7Z1T8;B7Z3N8;Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;.;.;UBX11_HUMAN	Q	119;206;239;239;206;81;164;201;206	ENSP00000324721:R119Q;ENSP00000349601:R206Q;ENSP00000363338:R239Q;ENSP00000363339:R239Q;ENSP00000363334:R206Q;ENSP00000446034:R81Q;ENSP00000393858:R164Q;ENSP00000363332:R201Q;ENSP00000410357:R206Q	ENSP00000324721:R119Q	R	-	2	0	UBXN11	26484959	0.999000	0.42202	1.000000	0.80357	0.917000	0.54804	1.207000	0.32333	0.647000	0.30713	0.591000	0.81541	CGG		0.632	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		T	26612372	C	T	26612372	3	4	77	1	0	0	0	0	1	0	0	0	16953	652	23	1	874	1	UBXN11	1	26612372	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2534350	26612372	222638249	29	21765										
SESN2	83667	broad.mit.edu	37	chr1	28605651	28605651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggtgaaccagctcctggagCggaacctcaaggtctatatc	11	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:28605651C>T	ENST00000253063.3	+	9	1576	c.1255C>T	c.(1255-1257)Cgg>Tgg	p.R419W		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	419					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R419W(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCCTGGAGCGGAACCTCAA	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											94	88	90					1																	28605651		2203	4300	6503	28478238	SO:0001583	missense	83667			AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.1255C>T	1.37:g.28605651C>T	ENSP00000253063:p.Arg419Trp		28478238	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	37	CCDS321.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357993	0.82243	.	.	ENSG00000130766	ENST00000253063	T	0.35236	1.32	4.87	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.60547	0.2277	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65755	-0.6091	10	0.87932	D	0	-32.4088	11.7871	0.52049	0.2975:0.7025:0.0:0.0	.	419	P58004	SESN2_HUMAN	W	419	ENSP00000253063:R419W	ENSP00000253063:R419W	R	+	1	2	SESN2	28478238	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.065000	0.41442	2.533000	0.85409	0.561000	0.74099	CGG		0.512	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1			T	28605651	C	T	28605651	3	4	77	1	0	0	0	0	1	0	0	0	14162	759	27	1	1289	1	SESN2	1	28605651	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1993279	28605651	220644970	30	21766										
PTPRU	10076	broad.mit.edu	37	chr1	29609216	29609216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggtgattgtggaggaggagCgggcgcggaggctgcggcgg	24	6	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:29609216C>T	ENST00000345512.3	+	12	2026	c.1897C>T	c.(1897-1899)Cgg>Tgg	p.R633W	PTPRU_ENST00000428026.2_Missense_Mutation_p.R633W|PTPRU_ENST00000460170.2_Missense_Mutation_p.R633W|PTPRU_ENST00000323874.8_Missense_Mutation_p.R633W|PTPRU_ENST00000373779.3_Missense_Mutation_p.R633W|PTPRU_ENST00000356870.3_Missense_Mutation_p.R633W|PTPRU_ENST00000415600.2_3'UTR	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	633	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R633W(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GGAGGAGGAGCGGGCGCGGAG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	1											46	41	43					1																	29609216		2202	4299	6501	29481803	SO:0001583	missense	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.1897C>T	1.37:g.29609216C>T	ENSP00000334941:p.Arg633Trp		29481803	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106433	0.77096	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.35048	1.38;1.39;1.39;1.39;1.33;1.39	5.52	3.49	0.39957	.	0.562203	0.17418	N	0.174932	T	0.51483	0.1677	M	0.68317	2.08	0.34708	D	0.727426	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	P;P;P;P;P	0.59221	0.854;0.854;0.854;0.719;0.719	T	0.64478	-0.6398	9	.	.	.	.	12.356	0.55176	0.4321:0.5679:0.0:0.0	.	633;633;633;633;633	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	W	633	ENSP00000334941:R633W;ENSP00000362884:R633W;ENSP00000349333:R633W;ENSP00000314987:R633W;ENSP00000392332:R633W;ENSP00000432906:R633W	.	R	+	1	2	PTPRU	29481803	0.952000	0.32445	0.997000	0.53966	0.701000	0.40568	0.911000	0.28584	1.291000	0.44653	0.549000	0.68633	CGG		0.657	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			T	29609216	C	T	29609216	3	4	77	1	0	0	0	0	1	0	0	0	12850	759	27	1	1943	1	PTPRU	1	29609216	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1003565	29609216	219641405	31	21767										
MATN1	4146	broad.mit.edu	37	chr1	31188935	31188935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctccatgtaggacatattcCgcacagccgccttgatgtcc	8	14	1	1	rs143893133	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:31188935C>T	ENST00000373765.4	-	5	1063	c.1028G>A	c.(1027-1029)cGg>cAg	p.R343Q	MATN1-AS1_ENST00000414532.2_RNA|MATN1_ENST00000477320.1_5'UTR|MATN1-AS1_ENST00000414763.1_RNA|MATN1-AS1_ENST00000454613.1_RNA	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	343	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.R343Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		GGACATATTCCGCACAGCCGC	0.592													C|||	2	0.000399361	0	0.0029	5008	,	,		20400	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	107	116	113		1028	3.2	1	1	dbSNP_134	113	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MATN1	NM_002379.3	43	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	possibly-damaging	343/497	31188935	13,12993	2203	4300	6503	30961522	SO:0001583	missense	4146			M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.1028G>A	1.37:g.31188935C>T	ENSP00000362870:p.Arg343Gln		30961522	B2R7E3|Q5TBB9	Missense_Mutation	SNP	ENST00000373765.4	37	CCDS336.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.871701	0.51695	4.54E-4	0.001279	ENSG00000162510	ENST00000373765	T	0.78595	-1.19	5.34	3.23	0.37069	von Willebrand factor, type A (3);	.	.	.	.	T	0.60521	0.2275	L	0.28192	0.835	0.33648	D	0.608127	P;D	0.55385	0.95;0.971	B;B	0.41571	0.36;0.36	T	0.63829	-0.6548	9	0.21540	T	0.41	-22.2694	6.1139	0.20116	0.0:0.6079:0.0:0.3921	.	327;343	A3KMG0;P21941	.;MATN1_HUMAN	Q	343	ENSP00000362870:R343Q	ENSP00000362870:R343Q	R	-	2	0	MATN1	30961522	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.318000	0.43779	1.254000	0.44035	0.650000	0.86243	CGG		0.592	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1	NM_002379		T	31188935	C	T	31188935	3	4	77	1	0	0	0	0	1	0	0	0	9363	652	23	1	478	1	MATN1	1	31188935	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1579719	31188935	218061686	32	21768										
SDC3	9672	broad.mit.edu	37	chr1	31349842	31349842	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgggacttctgtcaccaccaGggggctggtggctggctcca							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:31349842delG	ENST00000339394.6	-	3	601	c.427delC	c.(427-429)ctgfs	p.L143fs	SDC3_ENST00000471567.1_5'UTR|SDC3_ENST00000336798.7_Frame_Shift_Del_p.L85fs	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	143	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L143fs*3(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GTCACCACCAGGGGGCTGGTG	0.647																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											26	30	29					1																	31349842		2201	4299	6500	31122429	SO:0001589	frameshift_variant	9672			AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"Proteoglycans / Cell Surface : Syndecans"	10660	protein-coding gene	gene with protein product	"syndecan proteoglycan 3"	186357	"syndecan 3 (N-syndecan)"			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.427delC	1.37:g.31349842delG	ENSP00000344468:p.Leu143fs		31122429	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Frame_Shift_Del	DEL	ENST00000339394.6	37	CCDS30661.1																																																																																				0.647	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		-	31349842	G	-	31349842	7	5	77	1	0	1	0	1	0	0	0	0	13990	991	35	0	913	0	SDC3	1	31349842	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	160907	31349842	217900779	33	21769										
PUM1	9698	broad.mit.edu	37	chr1	31426613	31426613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatatgtccagcaatctcccGcagttgtaaattggggtacc	9	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:31426613G>A	ENST00000257075.5	-	15	2632	c.2539C>T	c.(2539-2541)Cgg>Tgg	p.R847W	PUM1_ENST00000373747.3_Missense_Mutation_p.R848W|PUM1_ENST00000423018.2_Missense_Mutation_p.R703W|PUM1_ENST00000424085.2_Missense_Mutation_p.R605W|PUM1_ENST00000373741.4_Missense_Mutation_p.R883W|PUM1_ENST00000373742.2_Missense_Mutation_p.R788W|PUM1_ENST00000426105.2_Missense_Mutation_p.R847W|PUM1_ENST00000440538.2_Missense_Mutation_p.R821W	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	847	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)	p.R847W(1)		breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		GCAATCTCCCGCAGTTGTAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	1											151	164	160					1																	31426613		2203	4300	6503	31199200	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2539C>T	1.37:g.31426613G>A	ENSP00000257075:p.Arg847Trp		31199200	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.943632|3.943632	0.73672|0.73672	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000525843;ENST00000498419|ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	.|T;T;T;T;T;T;T;T	.|0.15603	.|2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41	5.78|5.78	5.78|5.78	0.91487|0.91487	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.44244|0.44244	0.1284|0.1284	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D	.|0.75020	.|0.967;0.93;0.967;0.985;0.967;0.967;0.967;0.967	T|T	0.38950|0.38950	-0.9637|-0.9637	5|10	.|0.87932	.|D	.|0	-12.0396|-12.0396	14.438|14.438	0.67296|0.67296	0.0:0.0:0.8159:0.1841|0.0:0.0:0.8159:0.1841	.|.	.|788;703;883;821;847;847;848;847	.|B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.|.;.;.;.;PUM1_HUMAN;.;.;.	V|W	785;558|605;847;848;585;847;821;883;703;788	.|ENSP00000400141:R605W;ENSP00000257075:R847W;ENSP00000362852:R848W;ENSP00000391723:R847W;ENSP00000401777:R821W;ENSP00000362846:R883W;ENSP00000399440:R703W;ENSP00000362847:R788W	.|ENSP00000257075:R847W	A|R	-|-	2|1	0|2	PUM1|PUM1	31199200|31199200	0.952000|0.952000	0.32445|0.32445	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.432000|1.432000	0.34936|0.34936	2.738000|2.738000	0.93877|0.93877	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.463	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			A	31426613	G	A	31426613	3	1	77	1	0	0	0	0	1	0	0	0	12862	1086	38	1	1059	1	PUM1	1	31426613	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	76771	31426613	217824008	34	21770										
KHDRBS1	10657	broad.mit.edu	37	chr1	32508135	32508135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttttccccacaggccaggaCgactggaatgggaccaggcc	13	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:32508135C>T	ENST00000327300.7	+	9	1409	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D	KHDRBS1_ENST00000492989.1_Silent_p.D375D|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1									p.D414D(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CAGGCCAGGACGACTGGAATG	0.488																																					Ovarian(173;401 1982 12359 31110 42403)											1	Substitution - coding silent(1)	large_intestine(1)	1											57	52	54					1																	32508135		2203	4300	6503	32280722	SO:0001819	synonymous_variant	10657			U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"GAP-associated tyrosine phosphoprotein p62 (Sam68)"	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.1242C>T	1.37:g.32508135C>T			32280722		Silent	SNP	ENST00000327300.7	37	CCDS350.1																																																																																				0.488	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		T	32508135	C	T	32508135	2	4	77	1	0	0	0	0	0	0	0	1	8167	535	19	1		1	KHDRBS1	1	32508135	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1081522	32508135	216742486	35	21771										
CSF3R	1441	broad.mit.edu	37	chr1	36935421	36935421	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agggtctcgggccatggcatGgagtctggtcagagctgggc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:36935421delG	ENST00000373106.1	-	11	1853	c.1306delC	c.(1306-1308)catfs	p.H436fs	CSF3R_ENST00000361632.4_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000373103.1_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000331941.5_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000440588.2_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000418048.2_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000338937.5_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000373104.1_Frame_Shift_Del_p.H436fs|CSF3R_ENST00000487540.2_5'UTR	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	436	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.H436fs*12(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GCCATGGCATGGAGTCTGGTC	0.612																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											24	26	26					1																	36935421		2203	4298	6501	36708008	SO:0001589	frameshift_variant	1441			M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"CD molecules", "Fibronectin type III domain containing"	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1306delC	1.37:g.36935421delG	ENSP00000362198:p.His436fs		36708008		Frame_Shift_Del	DEL	ENST00000373106.1	37	CCDS413.1																																																																																				0.612	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		-	36935421	G	-	36935421	7	5	77	1	0	1	0	1	0	0	0	0	3943	1348	47	0	1422	0	CSF3R	1	36935421	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	4427286	36935421	212315200	36	21772										
GRIK3	2899	broad.mit.edu	37	chr1	37346245	37346245	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccacccacctgtactgtcGtcatagaccacggtggctga	11	14	1	2	rs377438243		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:37346245G>A	ENST00000373091.3	-	3	556	c.540C>T	c.(538-540)gaC>gaT	p.D180D	GRIK3_ENST00000373093.4_Silent_p.D180D	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	180					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.D180D(2)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CTGTACTGTCGTCATAGACCA	0.612																																																2	Substitution - coding silent(2)	large_intestine(2)	1											259	247	251					1																	37346245		2203	4300	6503	37118832	SO:0001819	synonymous_variant	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.540C>T	1.37:g.37346245G>A			37118832	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																				0.612	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37346245	G	A	37346245	2	1	77	1	0	0	0	0	0	0	0	1	6796	1136	40	1		1	GRIK3	1	37346245	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	410824	37346245	211904376	37	21773										
MACF1	23499	broad.mit.edu	37	chr1	39852998	39852998	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atttctgcaaaattggagcgGctacagtctcagctacagga	10	9	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:39852998G>A	ENST00000372915.3	+	57	14586	c.14499G>A	c.(14497-14499)cgG>cgA	p.R4833R	MACF1_ENST00000564288.1_Silent_p.R4828R|MACF1_ENST00000317713.7_Silent_p.R2766R|MACF1_ENST00000289893.4_Silent_p.R3268R|MACF1_ENST00000545844.1_Silent_p.R2766R|MACF1_ENST00000361689.2_Silent_p.R2766R|MACF1_ENST00000567887.1_Silent_p.R4865R|MACF1_ENST00000539005.1_Silent_p.R2745R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4833					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.R2766R(1)|p.R3268R(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			AATTGGAGCGGCTACAGTCTC	0.448																																																2	Substitution - coding silent(2)	large_intestine(2)	1											125	142	136					1																	39852998		2203	4300	6503	39625585	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.14499G>A	1.37:g.39852998G>A			39625585	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	G	0.005	-2.192980	0.00302	.	.	ENSG00000127603	ENST00000372925	.	.	.	6.06	-0.678	0.11353	.	.	.	.	.	T	0.35128	0.0921	.	.	.	0.20074	N	0.999938	.	.	.	.	.	.	T	0.32587	-0.9901	4	.	.	.	.	10.6296	0.45527	0.4051:0.0:0.5949:0.0	.	.	.	.	T	1879	.	.	A	+	1	0	MACF1	39625585	0.000000	0.05858	0.008000	0.14137	0.101000	0.19017	-0.038000	0.12144	-0.390000	0.07774	-0.150000	0.13652	GCT		0.448	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39852998	G	A	39852998	2	1	77	1	0	0	0	0	0	0	0	1	9174	1190	42	3		3	MACF1	1	39852998	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2506753	39852998	209397623	38	21774										
MACF1	23499	broad.mit.edu	37	chr1	39951334	39951334	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagacgcagtctgcttgttcCgacacttcagaaagcagcgc	11	12	2	2	rs377022334		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:39951334C>T	ENST00000372915.3	+	97	22122	c.22035C>T	c.(22033-22035)tcC>tcT	p.S7345S	MACF1_ENST00000564288.1_Silent_p.S7512S|MACF1_ENST00000317713.7_Silent_p.S5387S|MACF1_ENST00000289893.4_Silent_p.S5895S|MACF1_ENST00000545844.1_Silent_p.S5387S|MACF1_ENST00000361689.2_Silent_p.S5387S|MACF1_ENST00000567887.1_Silent_p.S7549S|MACF1_ENST00000539005.1_Silent_p.S5257S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	7345	C-terminal tail. {ECO:0000250}.|Ser-rich.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S5387S(1)|p.S5895S(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			CTGCTTGTTCCGACACTTCAG	0.577																																																2	Substitution - coding silent(2)	large_intestine(2)	1						C	,	0,4406		0,0,2203	77	83	81		16161,17685	-3.8	1	1		81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	5387/5431,5895/5939	39951334	1,13005	2203	4300	6503	39723921	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.22035C>T	1.37:g.39951334C>T			39723921	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.625|2.625	-0.287770|-0.287770	0.05605|0.05605	0.0|0.0	1.16E-4|1.16E-4	ENSG00000127603|ENSG00000127603	ENST00000360115;ENST00000442046|ENST00000372925;ENST00000446276	.|.	.|.	.|.	5.58|5.58	-3.85|-3.85	0.04243|0.04243	.|.	.|.	.|.	.|.	.|.	T|.	0.37705|.	0.1013|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34527|.	-0.9825|.	4|.	.|.	.|.	.|.	.|.	1.1651|1.1651	0.01813|0.01813	0.2259:0.351:0.1631:0.26|0.2259:0.351:0.1631:0.26	.|.	.|.	.|.	.|.	L|X	500;325|4391;412	.|.	.|.	P|R	+|+	2|1	0|2	MACF1|MACF1	39723921|39723921	0.007000|0.007000	0.16637|0.16637	0.971000|0.971000	0.41717|0.41717	0.950000|0.950000	0.60333|0.60333	-0.928000|-0.928000	0.03980|0.03980	-0.770000|-0.770000	0.04614|0.04614	-2.276000|-2.276000	0.00273|0.00273	CCG|CGA		0.577	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39951334	C	T	39951334	2	4	77	1	0	0	0	0	0	0	0	1	9174	639	23	1		1	MACF1	1	39951334	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	98336	39951334	209299287	39	21775										
CTPS	1503	broad.mit.edu	37	chr1	41475218	41475218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctcctggcctctgtggggCggctctcacattacctccag	10	16	2	0	rs552737439		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:41475218C>T	ENST00000372621.4	+	17	2156	c.1648C>T	c.(1648-1650)Cgg>Tgg	p.R550W	CTPS1_ENST00000541520.1_Missense_Mutation_p.R319W|CTPS1_ENST00000372616.1_Missense_Mutation_p.R550W	NM_001905.2	NP_001896.2			CTP synthase 1									p.R550W(1)		endometrium(3)|lung(10)	13						CTCTGTGGGGCGGCTCTCACA	0.542													C|||	1	0.000199681	0	0.0014	5008	,	,		17542	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											116	115	116					1																	41475218		2203	4300	6503	41247805	SO:0001583	missense	1503			BC009408	CCDS459.1	1p34.1	2012-05-02	2012-05-02	2012-05-02	ENSG00000171793	ENSG00000171793	6.3.4.2		2519	protein-coding gene	gene with protein product		123860	"CTP synthase"	CTPS		1783378	Standard	XM_005270536		Approved		uc001cgk.4	P17812	OTTHUMG00000005712	ENST00000372621.4:c.1648C>T	1.37:g.41475218C>T	ENSP00000361704:p.Arg550Trp		41247805		Missense_Mutation	SNP	ENST00000372621.4	37	CCDS459.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038074	0.75617	.	.	ENSG00000171793	ENST00000372621;ENST00000541520;ENST00000372616	T;T;T	0.46819	0.88;0.86;0.88	5.38	-2.76	0.05896	Glutamine amidotransferase type 1 (1);	0.159006	0.51477	D	0.000086	T	0.46073	0.1374	L	0.55990	1.75	0.51012	D	0.9999	P;D	0.62365	0.952;0.991	P;P	0.46144	0.505;0.462	T	0.59354	-0.7470	10	0.66056	D	0.02	.	17.1978	0.86898	0.34:0.66:0.0:0.0	.	319;550	B4DR64;P17812	.;PYRG1_HUMAN	W	550;319;550	ENSP00000361704:R550W;ENSP00000442646:R319W;ENSP00000361699:R550W	ENSP00000361699:R550W	R	+	1	2	CTPS	41247805	0.856000	0.29760	0.964000	0.40570	0.917000	0.54804	1.174000	0.31932	-0.394000	0.07727	0.655000	0.94253	CGG		0.542	CTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015629.1	NM_001905		T	41475218	C	T	41475218	3	4	77	1	0	0	0	0	1	0	0	0	4028	759	27	1	1710	1	CTPS	1	41475218	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1523884	41475218	207775403	40	21776										
KIAA0467	23334	broad.mit.edu	37	chr1	43893291	43893291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcttcccagacagagagtgCggatgggccccggacccggt	16	13	0	2	rs553638915		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:43893291C>T	ENST00000562955.1	+	25	3518	c.3518C>T	c.(3517-3519)gCg>gTg	p.A1173V	SZT2_ENST00000372442.1_Missense_Mutation_p.A331V	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1230					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.A331V(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						ACAGAGAGTGCGGATGGGCCC	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	1											84	88	87					1																	43893291		2203	4300	6503	43665878	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.3518C>T	1.37:g.43893291C>T	ENSP00000457168:p.Ala1173Val		43665878	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450099	0.26074	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.26	3.33	0.38152	.	1.032190	0.07650	N	0.931731	T	0.32315	0.0825	L	0.34521	1.04	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.17745	-1.0359	9	0.34782	T	0.22	.	7.5181	0.27612	0.0:0.6416:0.2622:0.0962	.	1173	Q5T011-5	.	V	331	.	ENSP00000361519:A331V	A	+	2	0	SZT2	43665878	0.085000	0.21516	0.063000	0.19743	0.328000	0.28507	2.461000	0.45040	1.457000	0.47850	0.655000	0.94253	GCG		0.582	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43893291	C	T	43893291	3	4	77	1	0	0	0	0	1	0	0	0	8199	768	27	1	1026	1	KIAA0467	1	43893291	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2418073	43893291	205357330	41	21777										
KIAA0467	23334	broad.mit.edu	37	chr1	43909277	43909277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tactctcatagcggcgccatCgccctgagtcagggtctggg	13	13	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:43909277C>T	ENST00000562955.1	+	61	8464	c.8464C>T	c.(8464-8466)Cgc>Tgc	p.R2822C	SZT2_ENST00000372442.1_Missense_Mutation_p.R1980C	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2879					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.R1980C(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						GCGGCGCCATCGCCCTGAGTC	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	1											59	61	61					1																	43909277		2203	4300	6503	43681864	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.8464C>T	1.37:g.43909277C>T	ENSP00000457168:p.Arg2822Cys		43681864	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195023	0.58017	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.36	4.43	0.53597	.	0.256104	0.39615	N	0.001313	T	0.48822	0.1521	L	0.43152	1.355	0.34504	D	0.706374	B	0.15930	0.015	B	0.12156	0.007	T	0.57946	-0.7723	9	0.59425	D	0.04	.	10.7108	0.45982	0.0:0.8514:0.0:0.1486	.	2822	Q5T011-5	.	C	1980	.	ENSP00000361519:R1980C	R	+	1	0	SZT2	43681864	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	4.845000	0.62853	1.233000	0.43693	0.650000	0.86243	CGC		0.612	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43909277	C	T	43909277	3	4	77	1	0	0	0	0	1	0	0	0	8199	884	31	1	6116	1	KIAA0467	1	43909277	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	15986	43909277	205341344	42	21778										
PTCH2	8643	broad.mit.edu	37	chr1	45294213	45294213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgcagcgcagggatgggaaCgagggcagccatgaggaagg	19	8	0	1	rs113543298		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:45294213C>T	ENST00000372192.3	-	12	1685	c.1555G>A	c.(1555-1557)Gtt>Att	p.V519I	PTCH2_ENST00000447098.2_Missense_Mutation_p.V519I	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	519	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)	p.V519I(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGGATGGGAACGAGGGCAGCC	0.642									Basal Cell Nevus syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	1											89	67	75					1																	45294213		2202	4299	6501	45066800	SO:0001583	missense	8643	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.1555G>A	1.37:g.45294213C>T	ENSP00000361266:p.Val519Ile		45066800	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	6.938	0.542858	0.13250	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.95482	-3.72;-3.72	5.2	4.28	0.50868	Sterol-sensing domain (1);	0.083770	0.48286	D	0.000199	D	0.85762	0.5772	N	0.03324	-0.35	0.52501	D	0.999955	B;B	0.10296	0.0;0.003	B;B	0.12837	0.001;0.008	T	0.79957	-0.1584	10	0.02654	T	1	-22.9206	13.7667	0.62999	0.0:0.9241:0.0:0.0759	.	519;519	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	I	519	ENSP00000389703:V519I;ENSP00000361266:V519I	ENSP00000361266:V519I	V	-	1	0	PTCH2	45066800	0.985000	0.35326	0.722000	0.30670	0.887000	0.51463	2.701000	0.47094	1.181000	0.42912	0.462000	0.41574	GTT		0.642	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		T	45294213	C	T	45294213	3	4	77	1	0	0	0	0	1	0	0	0	12765	536	19	1	2120	1	PTCH2	1	45294213	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1384936	45294213	203956408	43	21779										
MUTYH	4595	broad.mit.edu	37	chr1	45798466	45798466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcctgcagccgccggccaCgagaatagtagcccaggcca	11	17	0	1	rs143353451		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:45798466C>T	ENST00000372098.3	-	7	669	c.536G>A	c.(535-537)cGt>cAt	p.R179H	MUTYH_ENST00000456914.2_Missense_Mutation_p.R154H|MUTYH_ENST00000354383.6_Missense_Mutation_p.R155H|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000450313.1_Missense_Mutation_p.R182H|MUTYH_ENST00000528332.2_Silent_p.S66S|MUTYH_ENST00000372104.1_Missense_Mutation_p.R154H|MUTYH_ENST00000528013.2_Missense_Mutation_p.R168H|MUTYH_ENST00000355498.2_Missense_Mutation_p.R154H|MUTYH_ENST00000448481.1_Missense_Mutation_p.R165H|MUTYH_ENST00000372110.3_Missense_Mutation_p.R169H|MUTYH_ENST00000372100.5_Missense_Mutation_p.R165H|MUTYH_ENST00000529984.1_Silent_p.S52S|MUTYH_ENST00000372115.3_Missense_Mutation_p.R168H|MUTYH_ENST00000488731.2_Silent_p.S52S			Q9UIF7	MUTYH_HUMAN	mutY homolog	179			R -> C (in FAP2). {ECO:0000269|PubMed:18091433}.|R -> H (in FAP2). {ECO:0000269|PubMed:15366000}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)	p.R179H(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					CCGCCGGCCACGAGAATAGTA	0.552			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																													yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	1	Substitution - Missense(1)	large_intestine(1)	1	GRCh37	CM042753	MUTYH	M	rs143353451						87	100	96					1																	45798466		2203	4300	6503	45571053	SO:0001583	missense	4595	Familial Cancer Database	MAP, MYH-associated polyposis	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.536G>A	1.37:g.45798466C>T	ENSP00000361170:p.Arg179His		45571053	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.591105	0.86851	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971;ENST00000435155;ENST00000528013	D;D;D;D;D;D;D;D;D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65	4.99	4.99	0.66335	HhH-GPD domain (2);DNA glycosylase (2);	0.000000	0.85682	D	0.000000	D	0.97670	0.9236	H	0.99325	4.515	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.99686	1.1000	10	0.87932	D	0	-9.2585	18.6358	0.91378	0.0:1.0:0.0:0.0	.	182;169;179;168;62;155	E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;MUTYH_HUMAN;.;.;.	H	154;165;154;155;154;179;169;168;182;165;26;26;165;168	ENSP00000361176:R154H;ENSP00000409718:R165H;ENSP00000407590:R154H;ENSP00000346354:R155H;ENSP00000347685:R154H;ENSP00000361170:R179H;ENSP00000361182:R169H;ENSP00000361187:R168H;ENSP00000408176:R182H;ENSP00000361172:R165H;ENSP00000410263:R26H;ENSP00000403655:R165H;ENSP00000433130:R168H	ENSP00000346354:R155H	R	-	2	0	MUTYH	45571053	0.999000	0.42202	1.000000	0.80357	0.749000	0.42624	7.103000	0.77014	2.458000	0.83093	0.549000	0.68633	CGT		0.552	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		T	45798466	C	T	45798466	3	4	77	1	0	0	0	0	1	0	0	0	10023	536	19	1	1144	1	MUTYH	1	45798466	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	504253	45798466	203452155	44	21780										
LRRC41	10489	broad.mit.edu	37	chr1	46745170	46745170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctggcccccacccaggcGgttccctggcagccggaggc	15	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:46745170G>A	ENST00000343304.6	-	8	2422	c.2137C>T	c.(2137-2139)Cgc>Tgc	p.R713C	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	713					protein ubiquitination (GO:0016567)	membrane (GO:0016020)		p.R713C(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					CCACCCAGGCGGTTCCCTGGC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	1											77	91	87					1																	46745170		2203	4300	6503	46517757	SO:0001583	missense	10489			AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.2137C>T	1.37:g.46745170G>A	ENSP00000343298:p.Arg713Cys		46517757	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Missense_Mutation	SNP	ENST00000343304.6	37	CCDS533.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.729736	0.48833	.	.	ENSG00000132128	ENST00000343304	T	0.55052	0.54	4.57	3.65	0.41850	.	0.166822	0.42548	D	0.000696	T	0.56352	0.1979	N	0.19112	0.55	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.60342	-0.7282	10	0.59425	D	0.04	-8.9559	12.7442	0.57270	0.0:0.0:0.7026:0.2974	.	713;713	Q15345-3;Q15345	.;LRC41_HUMAN	C	713	ENSP00000343298:R713C	ENSP00000343298:R713C	R	-	1	0	LRRC41	46517757	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.428000	0.52792	1.129000	0.42072	0.561000	0.74099	CGC		0.587	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369		A	46745170	G	A	46745170	3	1	77	1	0	0	0	0	1	0	0	0	9028	1116	39	1	313	1	LRRC41	1	46745170	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	946704	46745170	202505451	45	21781										
SLC5A9	200010	broad.mit.edu	37	chr1	48694605	48694605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggctgccggaggccttgcCgtaggtggcttcgagtggaa	19	9	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:48694605C>T	ENST00000438567.2	+	3	370	c.318C>T	c.(316-318)gcC>gcT	p.A106A	SLC5A9_ENST00000533824.1_Silent_p.A106A|SLC5A9_ENST00000420136.2_Silent_p.A99A|SLC5A9_ENST00000236495.5_Silent_p.A106A|RP5-1024N4.4_ENST00000606809.1_RNA	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	106					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.A99A(1)		breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GAGGCCTTGCCGTAGGTGGCT	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	1											82	80	80					1																	48694605		2203	4300	6503	48467192	SO:0001819	synonymous_variant	200010			BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.318C>T	1.37:g.48694605C>T			48467192	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Silent	SNP	ENST00000438567.2	37	CCDS30709.2																																																																																				0.577	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48694605	C	T	48694605	2	4	77	1	0	0	0	0	0	0	0	1	14709	639	23	1		1	SLC5A9	1	48694605	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1949435	48694605	200556016	46	21782										
CC2D1B	200014	broad.mit.edu	37	chr1	52826104	52826104	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcccgactcaccttcaggcCgcgctcgcagcgcctggctt	11	18	2	0	rs149964496	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:52826104C>T	ENST00000371586.2	-	6	733	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Missense_Mutation_p.G199S|CC2D1B_ENST00000438831.1_5'UTR	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	199						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.G199S(1)		breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						ACCTTCAGGCCGCGCTCGCAG	0.662													C|||	9	0.00179712	0.0053	0	5008	,	,		15992	0		0.002	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	SER/GLY	17,4385		0,17,2184	20	22	22		595	5.6	1	1	dbSNP_134	22	17,8573		0,17,4278	no	missense	CC2D1B	NM_032449.2	56	0,34,6462	TT,TC,CC		0.1979,0.3862,0.2617	probably-damaging	199/859	52826104	34,12958	2201	4295	6496	52598692	SO:0001583	missense	200014			AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.595G>A	1.37:g.52826104C>T	ENSP00000360642:p.Gly199Ser		52598692	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	6	0.0027472527472527475	4	0.008130081300813009	0	0.0	0	0.0	2	0.002638522427440633	C	23.3	4.403101	0.83230	0.003862	0.001979	ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371573	D;D	0.91295	-2.82;-2.82	5.57	5.57	0.84162	Domain of unknown function DM14 (1);	0.112580	0.64402	D	0.000013	D	0.93664	0.7976	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92965	0.6392	10	0.42905	T	0.14	-15.9576	17.0407	0.86488	0.0:1.0:0.0:0.0	.	199	Q5T0F9	C2D1B_HUMAN	S	199;199;113	ENSP00000360642:G199S;ENSP00000284376:G199S	ENSP00000284376:G199S	G	-	1	0	CC2D1B	52598692	1.000000	0.71417	0.962000	0.40283	0.368000	0.29767	6.596000	0.74113	2.619000	0.88677	0.561000	0.74099	GGC		0.662	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		T	52826104	C	T	52826104	3	4	77	1	0	0	0	0	1	0	0	0	2733	652	23	1	2057	1	CC2D1B	1	52826104	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4131499	52826104	196424517	47	21783										
PRPF38A	84950	broad.mit.edu	37	chr1	52878292	52878292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaggaagaagaggaggatgAgaaggtctggcacctgagac	17	5	1	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:52878292A>G	ENST00000257181.9	+	5	791	c.605A>G	c.(604-606)gAg>gGg	p.E202G	PRPF38A_ENST00000474048.1_3'UTR|snoU13_ENST00000458879.1_RNA	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	202					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.E202G(1)		cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						GAGGAGGATGAGAAGGTCTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	99	95					1																	52878292		2203	4300	6503	52650880	SO:0001583	missense	84950			AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.605A>G	1.37:g.52878292A>G	ENSP00000257181:p.Glu202Gly		52650880	Q96JW1|Q9BVZ8	Missense_Mutation	SNP	ENST00000257181.9	37	CCDS567.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614681	0.87359	.	.	ENSG00000134748	ENST00000257181	T	0.40225	1.04	5.43	5.43	0.79202	Pre-mRNA-splicing factor 38, C-terminal (1);	0.043415	0.85682	D	0.000000	T	0.45776	0.1359	L	0.34521	1.04	0.80722	D	1	P	0.51449	0.945	P	0.54460	0.753	T	0.21690	-1.0238	10	0.23302	T	0.38	-22.6093	15.7879	0.78322	1.0:0.0:0.0:0.0	.	202	Q8NAV1	PR38A_HUMAN	G	202	ENSP00000257181:E202G	ENSP00000257181:E202G	E	+	2	0	PRPF38A	52650880	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	8.526000	0.90588	2.189000	0.69895	0.528000	0.53228	GAG		0.428	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		G	52878292	A	G	52878292	3	3	77	1	0	0	0	0	1	0	0	0	12601	304	11	4	623	4	PRPF38A	1	52878292	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	52188	52878292	196372329	48	21784										
MRPL37	51253	broad.mit.edu	37	chr1	54681863	54681863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtggtgcagagcgtgggcaCggatggacgtgtcttccatt	17	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:54681863C>T	ENST00000360840.5	+	6	1117	c.1040C>T	c.(1039-1041)aCg>aTg	p.T347M	MRPL37_ENST00000605337.1_Missense_Mutation_p.T347M|MRPL37_ENST00000336230.6_Missense_Mutation_p.T216M	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	347					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T347M(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						AGCGTGGGCACGGATGGACGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	1											179	156	164					1																	54681863		2203	4300	6503	54454451	SO:0001583	missense	51253			AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"Mitochondrial ribosomal proteins / large subunits"	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1040C>T	1.37:g.54681863C>T	ENSP00000354086:p.Thr347Met		54454451	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	37	CCDS589.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.71|16.71	3.199769|3.199769	0.58126|0.58126	.|.	.|.	ENSG00000116221|ENSG00000116221	ENST00000398219|ENST00000360840;ENST00000329505;ENST00000336230	.|T;T	.|0.32753	.|1.44;1.44	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	.|0.046251	.|0.85682	.|D	.|0.000000	T|T	0.57140|0.57140	0.2033|0.2033	M|M	0.76574|0.76574	2.34|2.34	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;D;D	.|0.68483	.|0.945;0.958;0.923	T|T	0.60811|0.60811	-0.7189|-0.7189	5|10	.|0.62326	.|D	.|0.03	-1.1871|-1.1871	18.7983|18.7983	0.92005|0.92005	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|216;284;347	.|A6NHR2;E9PB99;Q9BZE1	.|.;.;RM37_HUMAN	W|M	132|347;284;216	.|ENSP00000354086:T347M;ENSP00000338526:T216M	.|ENSP00000328799:T284M	R|T	+|+	1|2	2|0	MRPL37|MRPL37	54454451|54454451	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.163000|0.163000	0.22366|0.22366	7.440000|7.440000	0.80464|0.80464	2.433000|2.433000	0.82419|0.82419	0.455000|0.455000	0.32223|0.32223	CGG|ACG		0.517	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491		T	54681863	C	T	54681863	3	4	77	1	0	0	0	0	1	0	0	0	9830	536	19	1	1062	1	MRPL37	1	54681863	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1803571	54681863	194568758	49	21785										
C1orf168	199920	broad.mit.edu	37	chr1	57257862	57257862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaagagggatcttcagagacGttatgtaatattttgggggc	13	4	2	2	rs202073337		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:57257862G>A	ENST00000343433.6	-	2	704	c.624C>T	c.(622-624)aaC>aaT	p.N208N	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	208								p.N208N(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						CTTCAGAGACGTTATGTAATA	0.512																																																1	Substitution - coding silent(1)	large_intestine(1)	1											93	100	97					1																	57257862		2203	4300	6503	57030450	SO:0001819	synonymous_variant	199920			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.624C>T	1.37:g.57257862G>A			57030450	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																				0.512	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		A	57257862	G	A	57257862	2	1	77	1	0	0	0	0	0	0	0	1	2018	1136	40	1		1	C1orf168	1	57257862	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2575999	57257862	191992759	50	21786										
JAK1	3716	broad.mit.edu	37	chr1	65321241	65321241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcatgaagctgatgttatcCgtgcgcaggatctgcttctt	11	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:65321241C>T	ENST00000342505.4	-	11	1847	c.1599G>A	c.(1597-1599)acG>acA	p.T533T		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	533	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.T533T(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGATGTTATCCGTGCGCAGGA	0.587			Mis		ALL																																		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	1	Substitution - coding silent(1)	large_intestine(1)	1											65	69	68					1																	65321241		2123	4234	6357	65093829	SO:0001819	synonymous_variant	3716			M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1599G>A	1.37:g.65321241C>T			65093829	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																				0.587	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65321241	C	T	65321241	2	4	77	1	0	0	0	0	0	0	0	1	7958	639	23	1		1	JAK1	1	65321241	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8063379	65321241	183929380	51	21787										
SERBP1	26135	broad.mit.edu	37	chr1	67890848	67890848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcggcccattccacgtccacGgccccctcgacctcttccaa	6	21	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:67890848G>A	ENST00000370995.2	-	3	608	c.523C>T	c.(523-525)Cgt>Tgt	p.R175C	SERBP1_ENST00000370994.4_Missense_Mutation_p.R175C|SERBP1_ENST00000361219.6_Missense_Mutation_p.R175C|SERBP1_ENST00000370990.5_Missense_Mutation_p.R175C|SERBP1_ENST00000484880.1_5'Flank			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	175					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)	p.R175C(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						CCACGTCCACGGCCCCCTCGA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	1											42	43	43					1																	67890848		2203	4294	6497	67663436	SO:0001583	missense	26135			AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.523C>T	1.37:g.67890848G>A	ENSP00000360034:p.Arg175Cys		67663436	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868362	0.72065	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	5.15	5.15	0.70609	.	0.118368	0.64402	D	0.000018	T	0.80099	0.4561	M	0.81802	2.56	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76575	0.985;0.988;0.911;0.95	T	0.80379	-0.1407	9	0.48119	T	0.1	-27.9479	18.5865	0.91191	0.0:0.0:1.0:0.0	.	238;238;175;175	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	C	175	.	ENSP00000354591:R175C	R	-	1	0	SERBP1	67663436	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.168000	0.71908	2.559000	0.86315	0.462000	0.41574	CGT		0.443	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		A	67890848	G	A	67890848	3	1	77	1	0	0	0	0	1	0	0	0	14112	1116	39	1	727	1	SERBP1	1	67890848	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2569607	67890848	181359773	52	21788										
LHX8	431707	broad.mit.edu	37	chr1	75626560	75626560	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taccccattcaatgacacaaCtgccaataagtcatacctaa	3	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:75626560C>A	ENST00000294638.5	+	10	1715	c.1051C>A	c.(1051-1053)Ctg>Atg	p.L351M	LHX8_ENST00000356261.3_Missense_Mutation_p.L341M	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	351					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.L351M(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						AATGACACAACTGCCAATAAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	1											134	131	132					1																	75626560		2203	4299	6502	75399148	SO:0001583	missense	431707			AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.1051C>A	1.37:g.75626560C>A	ENSP00000294638:p.Leu351Met		75399148	E9PGE3	Missense_Mutation	SNP	ENST00000294638.5	37	CCDS30756.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343804	0.61073	.	.	ENSG00000162624	ENST00000294638;ENST00000356261	D;D	0.87491	-2.26;-2.24	5.73	4.82	0.62117	.	1.222560	0.05957	N	0.639865	D	0.89068	0.6610	L	0.46157	1.445	0.46298	D	0.998977	D	0.71674	0.998	D	0.80764	0.994	T	0.81136	-0.1070	10	0.30854	T	0.27	.	14.6004	0.68438	0.0:0.9299:0.0:0.0701	.	351	Q68G74	LHX8_HUMAN	M	351;341	ENSP00000294638:L351M;ENSP00000348597:L341M	ENSP00000294638:L351M	L	+	1	2	LHX8	75399148	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.253000	0.58791	1.409000	0.46915	0.655000	0.94253	CTG		0.333	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		A	75626560	C	A	75626560	3	1	77	1	0	0	0	0	1	0	0	0	8799	564	20	2	1085	2	LHX8	1	75626560	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	7735712	75626560	173624061	53	21789										
LPAR3	23566	broad.mit.edu	37	chr1	85331691	85331691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaataaacaggcagaaaaacGtcccaacacacaaaacaatc	4	11	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:85331691G>A	ENST00000440886.1	-	1	151	c.113C>T	c.(112-114)aCg>aTg	p.T38M	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Missense_Mutation_p.T38M			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	38					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.T38M(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						GCAGAAAAACGTCCCAACACA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	115	113					1																	85331691		2203	4300	6503	85104279	SO:0001583	missense	23566			AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	14298	protein-coding gene	gene with protein product		605106	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.113C>T	1.37:g.85331691G>A	ENSP00000395389:p.Thr38Met		85104279	A0AVA3	Missense_Mutation	SNP	ENST00000440886.1	37	CCDS700.1	.	.	.	.	.	.	.	.	.	.	G	8.439	0.850425	0.17034	.	.	ENSG00000171517	ENST00000440886;ENST00000370611	T;T	0.37752	1.18;1.18	5.58	5.58	0.84498	.	0.328747	0.37304	N	0.002150	T	0.24470	0.0593	L	0.51422	1.61	0.09310	N	0.999999	P	0.46656	0.882	B	0.39660	0.306	T	0.16808	-1.0390	10	0.62326	D	0.03	.	19.5777	0.95452	0.0:0.0:1.0:0.0	.	38	Q9UBY5	LPAR3_HUMAN	M	38	ENSP00000395389:T38M;ENSP00000359643:T38M	ENSP00000359643:T38M	T	-	2	0	LPAR3	85104279	1.000000	0.71417	0.074000	0.20217	0.226000	0.24999	5.687000	0.68219	2.621000	0.88768	0.467000	0.42956	ACG		0.383	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152		A	85331691	G	A	85331691	3	1	77	1	0	0	0	0	1	0	0	0	8935	1145	40	1	956	1	LPAR3	1	85331691	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	9705131	85331691	163918930	54	21790										
SYDE2	84144	broad.mit.edu	37	chr1	85656319	85656319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actctgatatagccaattgcGtttctttgaaacagtgatgc	8	8	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:85656319G>A	ENST00000341460.5	-	2	911	c.862C>T	c.(862-864)Cgc>Tgc	p.R288C		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	288					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.R288C(1)|p.R210C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AGCCAATTGCGTTTCTTTGAA	0.388																																																2	Substitution - Missense(2)	large_intestine(2)	1											161	151	154					1																	85656319		1847	4112	5959	85428907	SO:0001583	missense	84144			AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.862C>T	1.37:g.85656319G>A	ENSP00000340594:p.Arg288Cys		85428907	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.138349	0.77775	.	.	ENSG00000097096	ENST00000341460	T	0.18657	2.2	6.17	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.13030	0.0316	M	0.76002	2.32	0.80722	D	1	B;P	0.43024	0.445;0.798	B;B	0.32980	0.044;0.156	T	0.07271	-1.0781	10	0.87932	D	0	.	13.2347	0.59963	0.1297:0.0:0.8703:0.0	.	288;288	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	C	288	ENSP00000340594:R288C	ENSP00000340594:R288C	R	-	1	0	SYDE2	85428907	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.105000	0.71505	1.620000	0.50308	0.655000	0.94253	CGC		0.388	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			A	85656319	G	A	85656319	3	1	77	1	0	0	0	0	1	0	0	0	15475	1145	40	1	2746	1	SYDE2	1	85656319	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	324628	85656319	163594302	55	21791										
HS2ST1	9653	broad.mit.edu	37	chr1	87538643	87538643	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctattgcaagacacgaagtcCgagaaattgagcagcgacat	10	9	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:87538643C>T	ENST00000370550.5	+	2	514	c.151C>T	c.(151-153)Cga>Tga	p.R51*	HS2ST1_ENST00000356813.4_Nonsense_Mutation_p.R25*|HS2ST1_ENST00000370551.4_Nonsense_Mutation_p.R51*|RP5-1052I5.2_ENST00000370548.2_Nonsense_Mutation_p.R25*	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	51					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)	p.R51*(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		ACACGAAGTCCGAGAAATTGA	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											75	69	71					1																	87538643		2203	4300	6503	87311231	SO:0001587	stop_gained	9653			AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.151C>T	1.37:g.87538643C>T	ENSP00000359581:p.Arg51*		87311231	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Nonsense_Mutation	SNP	ENST00000370550.5	37	CCDS711.1	.	.	.	.	.	.	.	.	.	.	C	38	7.235221	0.98154	.	.	ENSG00000153936	ENST00000370551;ENST00000370550;ENST00000370548;ENST00000356813	.	.	.	5.09	4.17	0.49024	.	0.066689	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4279	13.7197	0.62719	0.2938:0.7062:0.0:0.0	.	.	.	.	X	51;51;25;25	.	ENSP00000349268:R25X	R	+	1	2	HS2ST1	87311231	0.475000	0.25894	0.921000	0.36526	0.993000	0.82548	1.116000	0.31221	1.334000	0.45468	0.563000	0.77884	CGA		0.418	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		T	87538643	C	T	87538643	4	4	77	1	0	0	0	0	0	1	0	0	7383	644	23	1	157	1	HS2ST1	1	87538643	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1882324	87538643	161711978	56	21792										
GLMN	11146	broad.mit.edu	37	chr1	92735333	92735333	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aactgcaaaaggtacaatggGctaaaatagaaacaaaacaa	7	6	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:92735333G>A	ENST00000370360.3	-	9	1005	c.924C>T	c.(922-924)agC>agT	p.S308S	GLMN_ENST00000534881.1_Splice_Site_p.S308S	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	308					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)	p.S308S(1)		endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		GGTACAATGGGCTAAAATAGA	0.308									Multiple Glomus Tumors (of the Skin), Familial																																							1	Substitution - coding silent(1)	large_intestine(1)	1											64	64	64					1																	92735333		2203	4298	6501	92507921	SO:0001630	splice_region_variant	11146	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.924-1C>T	1.37:g.92735333G>A			92507921	Q5VVC3|Q9BVE8	Silent	SNP	ENST00000370360.3	37	CCDS738.1																																																																																				0.308	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070	Silent	A	92735333	G	A	92735333	5	1	77	1	0	0	0	0	0	0	1	0	6468	1217	42	3	904	3	GLMN	1	92735333	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5196690	92735333	156515288	57	21793										
RPAP2	79871	broad.mit.edu	37	chr1	92801972	92801972	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacacaacttaaaaatcttgTtcgaactttcaggttagtgt	6	8	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:92801972T>A	ENST00000610020.1	+	10	1716	c.1607T>A	c.(1606-1608)gTt>gAt	p.V536D		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	536					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)	p.V536D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		AAAAATCTTGTTCGAACTTTC	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											72	76	75					1																	92801972		2203	4297	6500	92574560	SO:0001583	missense	79871			AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1607T>A	1.37:g.92801972T>A	ENSP00000476948:p.Val536Asp		92574560	C9JKB5|Q49AS7|Q9H8Y2	Missense_Mutation	SNP	ENST00000610020.1	37	CCDS740.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.729093	0.69074	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	5.74	5.74	0.90152	.	0.284721	0.39341	N	0.001385	T	0.63462	0.2513	M	0.70275	2.135	0.33819	D	0.628877	D	0.67145	0.996	P	0.58721	0.844	T	0.71787	-0.4487	8	0.87932	D	0	-1.3603	13.4234	0.61011	0.0:0.0:0.0:1.0	.	536	Q8IXW5	RPAP2_HUMAN	D	536	.	ENSP00000359368:V536D	V	+	2	0	RPAP2	92574560	0.824000	0.29247	0.387000	0.26183	0.990000	0.78478	4.777000	0.62361	2.197000	0.70478	0.528000	0.53228	GTT		0.308	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		A	92801972	T	A	92801972	3	1	77	1	0	0	0	0	1	0	0	0	13579	1725	60	5	1645	5	RPAP2	1	92801972	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	66639	92801972	156448649	58	21794										
BCAR3	8412	broad.mit.edu	37	chr1	94140314	94140314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacaggaccttatgggaggaGgaccttttttcttccgtgga	12	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:94140314G>T	ENST00000370244.1	-	4	461	c.173C>A	c.(172-174)cCt>cAt	p.P58H	BCAR3_ENST00000370243.1_Missense_Mutation_p.P58H|BCAR3_ENST00000260502.6_Missense_Mutation_p.P58H	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	58					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)	p.P58H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		TATGGGAGGAGGACCTTTTTT	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											81	70	74					1																	94140314		2203	4300	6503	93912902	SO:0001583	missense	8412			U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.173C>A	1.37:g.94140314G>T	ENSP00000359264:p.Pro58His		93912902	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.841286	0.51057	.	.	ENSG00000137936	ENST00000260502;ENST00000370244;ENST00000370243	T;T;T	0.23950	1.88;1.88;1.88	5.83	4.92	0.64577	.	0.289155	0.29814	N	0.011132	T	0.11750	0.0286	N	0.24115	0.695	0.80722	D	1	D	0.60575	0.988	P	0.46975	0.533	T	0.03166	-1.1065	10	0.56958	D	0.05	-0.7107	10.4793	0.44684	0.0697:0.1333:0.797:0.0	.	58	O75815	BCAR3_HUMAN	H	58	ENSP00000260502:P58H;ENSP00000359264:P58H;ENSP00000359263:P58H	ENSP00000260502:P58H	P	-	2	0	BCAR3	93912902	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.250000	0.58772	1.481000	0.48307	0.655000	0.94253	CCT		0.562	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			T	94140314	G	T	94140314	3	4	77	1	0	0	0	0	1	0	0	0	1350	1000	35	2	2348	2	BCAR3	1	94140314	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1338342	94140314	155110307	59	21795										
ABCD3	5825	broad.mit.edu	37	chr1	94943853	94943853	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgtatatctttaagttaacGagtgcaattggagctcaggt	10	5	2	0	rs145275743		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:94943853G>A	ENST00000370214.4	+	8	690	c.666G>A	c.(664-666)acG>acA	p.T222T	ABCD3_ENST00000536817.1_Silent_p.T149T|ABCD3_ENST00000454898.2_Silent_p.T246T|ABCD3_ENST00000315713.5_Silent_p.T222T|ABCD3_ENST00000394233.2_Silent_p.T222T	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	222	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.T222T(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TTAAGTTAACGAGTGCAATTG	0.274																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,	1,4401	2.1+/-5.4	0,1,2200	70	72	71		666,666	-5	0.9	1	dbSNP_134	71	0,8578		0,0,4289	no	coding-synonymous,coding-synonymous	ABCD3	NM_001122674.1,NM_002858.3	,	0,1,6489	AA,AG,GG		0.0,0.0227,0.0077	,	222/237,222/660	94943853	1,12979	2201	4289	6490	94716441	SO:0001819	synonymous_variant	5825			M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"ATP binding cassette transporters / subfamily D"	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.666G>A	1.37:g.94943853G>A			94716441	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Silent	SNP	ENST00000370214.4	37	CCDS749.1																																																																																				0.274	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858		A	94943853	G	A	94943853	2	1	77	1	0	0	0	0	0	0	0	1	62	1045	37	1		1	ABCD3	1	94943853	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	803539	94943853	154306768	60	21796										
SLC25A24	29957	broad.mit.edu	37	chr1	108703824	108703824	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtagaatgtttccagaaacGgataatttcctcaatgtctg	8	7	2	2	rs151259113	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:108703824G>T	ENST00000565488.1	-	4	709	c.490C>A	c.(490-492)Cgt>Agt	p.R164S	SLC25A24_ENST00000370041.4_Missense_Mutation_p.R145S	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	164					ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)	p.R145S(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TTCCAGAAACGGATAATTTCC	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	1											100	99	100					1																	108703824		2203	4300	6503	108505347	SO:0001583	missense	29957			AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"Solute carriers", "EF-hand domain containing"	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.490C>A	1.37:g.108703824G>T	ENSP00000457733:p.Arg164Ser		108505347	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Missense_Mutation	SNP	ENST00000565488.1	37	CCDS41361.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629440	0.28978	.	.	ENSG00000085491	ENST00000264128;ENST00000370041	T	0.43294	0.95	5.53	3.65	0.41850	EF-hand-like domain (1);	0.369578	0.34200	N	0.004174	T	0.13030	0.0316	L	0.45698	1.435	0.80722	D	1	B;B	0.24920	0.114;0.052	B;B	0.22753	0.02;0.041	T	0.07309	-1.0779	10	0.07990	T	0.79	-2.6807	6.5836	0.22609	0.1506:0.0:0.7069:0.1425	.	164;145	Q6NUK1;Q6NUK1-2	SCMC1_HUMAN;.	S	164;145	ENSP00000359058:R145S	ENSP00000264128:R164S	R	-	1	0	SLC25A24	108505347	1.000000	0.71417	0.954000	0.39281	0.995000	0.86356	4.048000	0.57390	1.333000	0.45449	0.591000	0.81541	CGT		0.348	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386		T	108703824	G	T	108703824	3	4	77	1	0	0	0	0	1	0	0	0	14524	1116	39	2	971	2	SLC25A24	1	108703824	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	13759971	108703824	140546797	61	21797										
AHCYL1	10768	broad.mit.edu	37	chr1	110555558	110555558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgccctgggggctcagtgcCgctggtctgcttgtaacatc	14	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:110555558C>T	ENST00000369799.5	+	5	884	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	AHCYL1_ENST00000393614.4_Missense_Mutation_p.R126C|AHCYL1_ENST00000359172.3_Missense_Mutation_p.R126C|AHCYL1_ENST00000475081.1_3'UTR	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	173					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)	p.R173C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		GGCTCAGTGCCGCTGGTCTGC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											95	83	87					1																	110555558		2203	4300	6503	110357081	SO:0001583	missense	10768			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.517C>T	1.37:g.110555558C>T	ENSP00000358814:p.Arg173Cys		110357081	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	C	36	5.600752	0.96614	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	T;T;T	0.80480	-1.38;-1.38;-1.38	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94149	0.8123	H	0.97962	4.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95123	0.8248	10	0.87932	D	0	-19.8836	20.8794	0.99867	0.0:1.0:0.0:0.0	.	173	O43865	SAHH2_HUMAN	C	173;126;126	ENSP00000358814:R173C;ENSP00000352092:R126C;ENSP00000377238:R126C	ENSP00000352092:R126C	R	+	1	0	AHCYL1	110357081	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.710000	0.61873	2.941000	0.99782	0.655000	0.94253	CGC		0.522	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			T	110555558	C	T	110555558	3	4	77	1	0	0	0	0	1	0	0	0	410	652	23	1	535	1	AHCYL1	1	110555558	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1851734	110555558	138695063	62	21798										
SLC16A1	6566	broad.mit.edu	37	chr1	113460504	113460504	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagaattagaaagcttcctCtccatccaaagataccgaag	6	11	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:113460504C>T	ENST00000538576.1	-	4	1355	c.524G>A	c.(523-525)aGa>aAa	p.R175K	SLC16A1_ENST00000433570.4_Missense_Mutation_p.R175K|SLC16A1_ENST00000369626.3_Missense_Mutation_p.R175K	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	175					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.R175K(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	AAAGCTTCCTCTCCATCCAAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											53	55	54					1																	113460504		2203	4300	6503	113262027	SO:0001583	missense	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.524G>A	1.37:g.113460504C>T	ENSP00000441065:p.Arg175Lys		113262027	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731520	0.89390	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570;ENST00000443580;ENST00000429288	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.74	5.74	0.90152	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	L	0.43646	1.37	0.80722	D	1	P;P	0.40578	0.722;0.722	B;P	0.44359	0.371;0.447	T	0.04752	-1.0929	10	0.40728	T	0.16	.	19.8931	0.96937	0.0:1.0:0.0:0.0	.	175;175	Q49A45;P53985	.;MOT1_HUMAN	K	175	ENSP00000358640:R175K;ENSP00000441065:R175K;ENSP00000416167:R175K;ENSP00000445061:R175K;ENSP00000399104:R175K;ENSP00000397106:R175K	ENSP00000358640:R175K	R	-	2	0	SLC16A1	113262027	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.767000	0.85331	2.873000	0.98535	0.563000	0.77884	AGA		0.552	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		T	113460504	C	T	113460504	3	4	77	1	0	0	0	0	1	0	0	0	14439	913	32	3	986	3	SLC16A1	1	113460504	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2904946	113460504	135790117	63	21799										
SYCP1	6847	broad.mit.edu	37	chr1	115537402	115537402	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catctttgtgtcaaaacaccAaaaaaggtagcttttaaatt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:115537402delA	ENST00000369522.3	+	31	3027	c.2787delA	c.(2785-2787)ccafs	p.P929fs	SYCP1_ENST00000369518.1_Frame_Shift_Del_p.P929fs|SYCP1_ENST00000477590.1_3'UTR	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	929					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)	p.K931fs*6(1)	RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		TCAAAACACCAAAAAAGGTAG	0.274																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											30	33	32					1																	115537402		2194	4284	6478	115338925	SO:0001589	frameshift_variant	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2787delA	1.37:g.115537402delA	ENSP00000358535:p.Pro929fs		115338925	O14963|Q5VXJ6	Frame_Shift_Del	DEL	ENST00000369522.3	37	CCDS879.1																																																																																				0.274	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		-	115537402	A	-	115537402	7	5	77	1	0	1	0	1	0	0	0	0	15470	117	5	0	2905	0	SYCP1	1	115537402	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	2076898	115537402	133713219	64	21800										
VTCN1	79679	broad.mit.edu	37	chr1	117699344	117699344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcagcaaacactgctgtccgGcctctgaacatttcatcctg	7	14	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:117699344G>A	ENST00000369458.3	-	3	375	c.297C>T	c.(295-297)ggC>ggT	p.G99G	VTCN1_ENST00000539893.1_Silent_p.G4G|VTCN1_ENST00000359008.4_Silent_p.G102G|VTCN1_ENST00000328189.3_Intron|VTCN1_ENST00000463461.1_5'UTR	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1									p.G99G(1)		large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	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)		CTGCTGTCCGGCCTCTGAACA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											113	104	107					1																	117699344		2203	4300	6503	117500867	SO:0001819	synonymous_variant	79679			BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28873	protein-coding gene	gene with protein product	"B7 family member, H4", "B7 superfamily member 1"	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.297C>T	1.37:g.117699344G>A			117500867		Silent	SNP	ENST00000369458.3	37	CCDS894.1																																																																																				0.458	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626		A	117699344	G	A	117699344	2	1	77	1	0	0	0	0	0	0	0	1	17274	1190	42	3		3	VTCN1	1	117699344	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2161942	117699344	131551277	65	21801										
ADAM30	11085	broad.mit.edu	37	chr1	120438357	120438357	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcaattccaagtactttggGtgtttataggatccaggaaa	9	6	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:120438357G>A	ENST00000369400.1	-	1	761	c.603C>T	c.(601-603)caC>caT	p.H201H		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	201					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.H201H(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		AGTACTTTGGGTGTTTATAGG	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	1											102	102	102					1																	120438357		2203	4300	6503	120239880	SO:0001819	synonymous_variant	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.603C>T	1.37:g.120438357G>A			120239880	A8K8W8|Q5T3X6|Q9UKF1	Silent	SNP	ENST00000369400.1	37	CCDS907.1																																																																																				0.403	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		A	120438357	G	A	120438357	2	1	77	1	0	0	0	0	0	0	0	1	248	1252	44	3		3	ADAM30	1	120438357	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2739013	120438357	128812264	66	21802										
NOTCH2	4853	broad.mit.edu	37	chr1	120468218	120468218	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagagttcacagcggctaccCgagaatggtggggcacactg	14	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:120468218C>T	ENST00000256646.2	-	25	4440	c.4221G>A	c.(4219-4221)tcG>tcA	p.S1407S	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1407	EGF-like 35. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.S1407S(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCGGCTACCCGAGAATGGTG	0.642			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - coding silent(1)	large_intestine(1)	1											41	43	43					1																	120468218		2202	4292	6494	120269741	SO:0001819	synonymous_variant	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4221G>A	1.37:g.120468218C>T			120269741	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																				0.642	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120468218	C	T	120468218	2	4	77	1	0	0	0	0	0	0	0	1	10579	639	23	1		1	NOTCH2	1	120468218	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	29861	120468218	128782403	67	21803										
POLR3C	10623	broad.mit.edu	37	chr1	145608605	145608605	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccaccacaccacgtttgtGcacttgataactcaccaggt	6	15	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:145608605G>A	ENST00000334163.3	-	3	362	c.202C>T	c.(202-204)Cac>Tac	p.H68Y	RNF115_ENST00000369291.5_5'Flank|POLR3C_ENST00000471254.1_Intron|POLR3C_ENST00000369294.1_Missense_Mutation_p.H68Y	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	68					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.H68Y(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			CCACGTTTGTGCACTTGATAA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	1											123	112	116					1																	145608605		2203	4300	6503	144319962	SO:0001583	missense	10623			AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.202C>T	1.37:g.145608605G>A	ENSP00000334564:p.His68Tyr		144319962	O15317|Q9Y3R6	Missense_Mutation	SNP	ENST00000334163.3	37	CCDS921.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.438724	0.43326	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.45276	0.9;0.9	4.76	4.76	0.60689	.	0.512588	0.23834	N	0.044102	T	0.11239	0.0274	L	0.29908	0.895	0.36192	D	0.850129	B;B;B	0.19073	0.033;0.033;0.022	B;B;B	0.11329	0.006;0.006;0.004	T	0.04481	-1.0948	10	0.02654	T	1	-15.064	10.36	0.43987	0.0:0.0:0.8043:0.1956	.	68;68;68	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	Y	68	ENSP00000334564:H68Y;ENSP00000358300:H68Y	ENSP00000334564:H68Y	H	-	1	0	POLR3C	144319962	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.264000	0.58859	2.461000	0.83175	0.563000	0.77884	CAC		0.453	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		A	145608605	G	A	145608605	3	1	77	1	0	0	0	0	1	0	0	0	12261	1319	46	3	1454	3	POLR3C	1	145608605	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	25140387	145608605	103642016	68	21804										
FMO5	2330	broad.mit.edu	37	chr1	146687385	146687385	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acatcctgaaatactccaggAcctgggcattatgcatgaag	9	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:146687385A>C	ENST00000254090.4	-	3	651	c.263T>G	c.(262-264)gTc>gGc	p.V88G	FMO5_ENST00000369272.3_Missense_Mutation_p.V88G|RP11-337C18.10_ENST00000606856.1_RNA|FMO5_ENST00000465173.1_5'UTR|FMO5_ENST00000441068.2_Missense_Mutation_p.V88G	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5	88						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.V88G(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	25	all_hematologic(923;0.0487)					ATACTCCAGGACCTGGGCATT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	1											131	127	129					1																	146687385		2203	4300	6503	145154009	SO:0001583	missense	2330			Z47553	CCDS926.1, CCDS44209.1, CCDS44210.1	1q21.1	2011-08-04			ENSG00000131781	ENSG00000131781			3773	protein-coding gene	gene with protein product		603957				8786146, 9119381	Standard	NM_001461		Approved		uc001epi.2	P49326	OTTHUMG00000014607	ENST00000254090.4:c.263T>G	1.37:g.146687385A>C	ENSP00000254090:p.Val88Gly		145154009	B2RBG1|C9JJD1|Q8IV22	Missense_Mutation	SNP	ENST00000254090.4	37	CCDS926.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.801915	0.90538	.	.	ENSG00000131781	ENST00000441068;ENST00000254090;ENST00000369272;ENST00000533174;ENST00000533848	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15	6.14	6.14	0.99180	.	0.248545	0.46145	D	0.000301	T	0.77772	0.4180	M	0.92923	3.36	0.80722	D	1	P;D;P;D	0.59357	0.931;0.974;0.933;0.985	P;D;P;D	0.71184	0.857;0.972;0.799;0.972	D	0.83552	0.0102	10	0.87932	D	0	-10.9799	14.758	0.69583	1.0:0.0:0.0:0.0	.	88;88;88;88	Q9HA79;Q8IV22;P49326;C9JJD1	.;.;FMO5_HUMAN;.	G	88	ENSP00000416011:V88G;ENSP00000254090:V88G;ENSP00000358277:V88G;ENSP00000436429:V88G;ENSP00000432569:V88G	ENSP00000254090:V88G	V	-	2	0	FMO5	145154009	1.000000	0.71417	0.865000	0.33974	0.857000	0.48899	8.858000	0.92256	2.367000	0.80283	0.529000	0.55759	GTC		0.358	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	NM_001461		C	146687385	A	C	146687385	3	2	77	1	0	0	0	0	1	0	0	0	5977	275	10	4	1509	4	FMO5	1	146687385	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1078780	146687385	102563236	69	21805										
GJA8	2703	broad.mit.edu	37	chr1	147380239	147380239	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggatgagcaatccgacttcGtgtgcaacacccagcagcct	11	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:147380239G>A	ENST00000369235.1	+	1	157	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	GJA8_ENST00000240986.4_Missense_Mutation_p.V53M			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	53					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)	p.V53M(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					ATCCGACTTCGTGTGCAACAC	0.592																																					Melanoma(76;1255 1795 8195 52096)											1	Substitution - Missense(1)	large_intestine(1)	1											134	108	117					1																	147380239		2203	4300	6503	145846863	SO:0001583	missense	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.157G>A	1.37:g.147380239G>A	ENSP00000358238:p.Val53Met		145846863	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	37	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	g	18.65	3.669626	0.67814	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.99167	-5.51;-5.51	5.0	5.0	0.66597	Connexin, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98950	0.9643	L	0.56340	1.77	0.53688	D	0.999977	D	0.89917	1.0	D	0.97110	1.0	D	0.99912	1.1204	10	0.62326	D	0.03	.	18.262	0.90039	0.0:0.0:1.0:0.0	.	53	P48165	CXA8_HUMAN	M	53	ENSP00000240986:V53M;ENSP00000358238:V53M	ENSP00000240986:V53M	V	+	1	0	GJA8	145846863	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.797000	0.85911	2.297000	0.77311	0.491000	0.48974	GTG		0.592	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		A	147380239	G	A	147380239	3	1	77	1	0	0	0	0	1	0	0	0	6425	1145	40	1	159	1	GJA8	1	147380239	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	692854	147380239	101870382	70	21806										
PLEKHO1	51177	broad.mit.edu	37	chr1	150131323	150131323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggaggagatcctatctcagCgggatgctgcctctgcccgc	13	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:150131323C>T	ENST00000369124.4	+	6	1113	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.R245W|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.R96W	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	279	Interaction with ATM, CKIP, IFP35 and NMI.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R279W(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTATCTCAGCGGGATGCTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	1											26	31	29					1																	150131323		2202	4297	6499	148397947	SO:0001583	missense	51177			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.835C>T	1.37:g.150131323C>T	ENSP00000358120:p.Arg279Trp		148397947	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	37	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764378	0.69878	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T	0.54675	0.56;0.65	4.97	4.04	0.47022	.	0.351400	0.28790	N	0.014129	T	0.46580	0.1400	L	0.54323	1.7	0.45046	D	0.998061	D	0.69078	0.997	P	0.56434	0.798	T	0.53436	-0.8439	10	0.72032	D	0.01	-31.1806	7.277	0.26290	0.1763:0.7389:0.0:0.0847	.	279	Q53GL0	PKHO1_HUMAN	W	96;245;279;159	ENSP00000025469:R245W;ENSP00000358120:R279W	ENSP00000025469:R245W	R	+	1	2	PLEKHO1	148397947	0.995000	0.38212	1.000000	0.80357	0.892000	0.51952	0.771000	0.26633	1.253000	0.44018	0.655000	0.94253	CGG		0.657	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		T	150131323	C	T	150131323	3	4	77	1	0	0	0	0	1	0	0	0	12115	759	27	1	857	1	PLEKHO1	1	150131323	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2751084	150131323	99119298	71	21807										
RPRD2	23248	broad.mit.edu	37	chr1	150432768	150432768	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcagttccatccttagcagTttaacatcagtcatgaaaaa	5	9	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:150432768T>C	ENST00000369068.4	+	9	1390	c.1386T>C	c.(1384-1386)agT>agC	p.S462S	RPRD2_ENST00000539519.1_Silent_p.S436S|RPRD2_ENST00000401000.4_Silent_p.S436S|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	462	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.S462S(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TCCTTAGCAGTTTAACATCAG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	1											51	48	49					1																	150432768		1854	4112	5966	148699392	SO:0001819	synonymous_variant	23248			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.1386T>C	1.37:g.150432768T>C			148699392	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Silent	SNP	ENST00000369068.4	37	CCDS44216.1																																																																																				0.388	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150432768	T	C	150432768	2	2	77	1	0	0	0	0	0	0	0	1	13654	1722	60	4		4	RPRD2	1	150432768	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	301445	150432768	98817853	72	21808										
CGN	57530	broad.mit.edu	37	chr1	151491863	151491863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgcacaggaccccaccatgCtgcaggtcagacccagcccc	10	18	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:151491863C>A	ENST00000271636.7	+	2	1001	c.868C>A	c.(868-870)Ctg>Atg	p.L290M		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	284	Head.|Interacts with ZO-2.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)	p.L290M(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCCCACCATGCTGCAGGTCAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											30	31	30					1																	151491863		2203	4298	6501	149758487	SO:0001583	missense	57530			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.868C>A	1.37:g.151491863C>A	ENSP00000271636:p.Leu290Met		149758487	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.15|16.15	3.042715|3.042715	0.55003|0.55003	.|.	.|.	ENSG00000143375|ENSG00000143375	ENST00000416743|ENST00000427934;ENST00000271636	.|T;T	.|0.65549	.|0.66;-0.16	5.18|5.18	0.927|0.927	0.19437|0.19437	.|.	.|0.747724	.|0.12483	.|N	.|0.465000	.|T	.|0.30885	.|0.0779	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	N|N	0.999995|0.999995	.|P	.|0.43477	.|0.808	.|B	.|0.41088	.|0.347	.|T	.|0.16070	.|-1.0415	.|10	.|0.44086	.|T	.|0.13	-9.3081|-9.3081	1.6422|1.6422	0.02755|0.02755	0.1643:0.4794:0.1716:0.1848|0.1643:0.4794:0.1716:0.1848	.|.	.|284	.|Q9P2M7	.|CING_HUMAN	X|M	6|290	.|ENSP00000410836:L290M;ENSP00000271636:L290M	.|ENSP00000271636:L290M	C|L	+|+	3|1	2|2	CGN|CGN	149758487|149758487	0.140000|0.140000	0.22579|0.22579	0.920000|0.920000	0.36463|0.36463	0.864000|0.864000	0.49448|0.49448	0.016000|0.016000	0.13377|0.13377	0.427000|0.427000	0.26145|0.26145	0.561000|0.561000	0.74099|0.74099	TGC|CTG		0.562	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		A	151491863	C	A	151491863	3	1	77	1	0	0	0	0	1	0	0	0	3309	796	28	2	870	2	CGN	1	151491863	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1059095	151491863	97758758	73	21809										
TCHH	7062	broad.mit.edu	37	chr1	152082765	152082765	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgccttctcttctccggttcCtctcccagcagctgctcttc	6	19	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:152082765C>A	ENST00000368804.1	-	2	2927	c.2928G>T	c.(2926-2928)gaG>gaT	p.E976D		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	976	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E976D(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			tctccggttcctctcccagca	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											135	139	138					1																	152082765		1894	4119	6013	150349389	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2928G>T	1.37:g.152082765C>A	ENSP00000357794:p.Glu976Asp		150349389	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	9.321	1.058097	0.19987	.	.	ENSG00000159450	ENST00000368804	T	0.12774	2.65	3.35	-0.131	0.13494	.	.	.	.	.	T	0.05135	0.0137	N	0.24115	0.695	0.09310	N	1	D	0.67145	0.996	P	0.57679	0.825	T	0.30534	-0.9975	9	0.16420	T	0.52	.	6.7601	0.23536	0.0:0.4415:0.0:0.5585	.	976	Q07283	TRHY_HUMAN	D	976	ENSP00000357794:E976D	ENSP00000357794:E976D	E	-	3	2	TCHH	150349389	0.000000	0.05858	0.024000	0.17045	0.110000	0.19582	-0.293000	0.08320	-0.063000	0.13065	0.462000	0.41574	GAG		0.562	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152082765	C	A	152082765	3	1	77	1	0	0	0	0	1	0	0	0	15739	680	24	2	2907	2	TCHH	1	152082765	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	590902	152082765	97167856	74	21810										
KPRP	448834	broad.mit.edu	37	chr1	152733122	152733122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gattcctcccatcagacgccGctcccagagctgtggcccgc	10	18	1	2	rs199539090	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:152733122G>A	ENST00000606109.1	+	1	1086	c.1058G>A	c.(1057-1059)cGc>cAc	p.R353H	KPRP_ENST00000368773.1_Missense_Mutation_p.R353H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	353	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.R353H(1)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATCAGACGCCGCTCCCAGAGC	0.657													G|||	2	0.000399361	0	0	5008	,	,		14836	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											46	49	48					1																	152733122		2203	4300	6503	150999746	SO:0001583	missense	448834			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1058G>A	1.37:g.152733122G>A	ENSP00000475216:p.Arg353His		150999746		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	15.28	2.786217	0.49997	.	.	ENSG00000203786	ENST00000368773	T	0.13778	2.56	5.3	1.85	0.25348	.	0.679913	0.13632	N	0.373657	T	0.04634	0.0126	N	0.24115	0.695	0.09310	N	1	D	0.56521	0.976	P	0.44696	0.458	T	0.32402	-0.9908	10	0.44086	T	0.13	-0.7834	12.9913	0.58620	0.0:0.5794:0.4206:0.0	.	353	Q5T749	KPRP_HUMAN	H	353	ENSP00000357762:R353H	ENSP00000357762:R353H	R	+	2	0	KPRP	150999746	0.006000	0.16342	0.564000	0.28396	0.611000	0.37282	1.323000	0.33701	0.656000	0.30886	0.462000	0.41574	CGC		0.657	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152733122	G	A	152733122	3	1	77	1	0	0	0	0	1	0	0	0	8457	1087	38	1	1060	1	KPRP	1	152733122	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	650357	152733122	96517499	75	21811										
FAM189B	10712	broad.mit.edu	37	chr1	155221578	155221578	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgggggatagtagggcggtGggggcacaggcgggacaaat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:155221578delG	ENST00000361361.2	-	6	1249	c.740delC	c.(739-741)ccafs	p.P249fs	FAM189B_ENST00000472550.1_5'UTR|FAM189B_ENST00000350210.2_Frame_Shift_Del_p.P153fs|FAM189B_ENST00000368368.3_Frame_Shift_Del_p.P231fs	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	249	Poly-Pro.					integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)	p.P247fs*74(1)		breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						GTAGGGCGGTGGGGGCACAGG	0.632																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											13	14	14					1																	155221578		2198	4298	6496	153488202	SO:0001589	frameshift_variant	10712			AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 2"	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.740delC	1.37:g.155221578delG	ENSP00000354958:p.Pro249fs		153488202	B1AVS5|Q8IXL3|Q9BR66	Frame_Shift_Del	DEL	ENST00000361361.2	37	CCDS1103.1																																																																																				0.632	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		-	155221578	G	-	155221578	7	5	77	1	0	1	0	1	0	0	0	0	5533	1348	47	0	1294	0	FAM189B	1	155221578	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	2488456	155221578	94029043	76	21812										
HCN3	57657	broad.mit.edu	37	chr1	155258121	155258121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggcgatggctctcctgggcGtaagggatcaggaagtgagc	17	8	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:155258121G>A	ENST00000368358.3	+	8	2200	c.2192G>A	c.(2191-2193)cGt>cAt	p.R731H	HCN3_ENST00000496230.1_3'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	731	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.R731H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	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)			TCTCCTGGGCGTAAGGGATCA	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	1											29	32	31					1																	155258121		2203	4300	6503	153524745	SO:0001583	missense	57657			AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.2192G>A	1.37:g.155258121G>A	ENSP00000357342:p.Arg731His		153524745	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Missense_Mutation	SNP	ENST00000368358.3	37	CCDS1108.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.966949	0.34659	.	.	ENSG00000143630	ENST00000368358	D	0.98192	-4.78	5.01	5.01	0.66863	.	0.000000	0.49305	D	0.000153	D	0.91751	0.7391	N	0.08118	0	0.28128	N	0.930337	D;P	0.60575	0.988;0.928	P;B	0.46543	0.52;0.288	D	0.88039	0.2780	10	0.44086	T	0.13	.	9.5441	0.39271	0.0939:0.0:0.9061:0.0	.	426;731	B7Z5R8;Q9P1Z3	.;HCN3_HUMAN	H	731	ENSP00000357342:R731H	ENSP00000357342:R731H	R	+	2	0	HCN3	153524745	0.788000	0.28762	0.944000	0.38274	0.956000	0.61745	1.416000	0.34759	2.764000	0.94973	0.557000	0.71058	CGT		0.687	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		A	155258121	G	A	155258121	3	1	77	1	0	0	0	0	1	0	0	0	7019	1145	40	1	2222	1	HCN3	1	155258121	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	36543	155258121	93992500	77	21813										
ASH1L	55870	broad.mit.edu	37	chr1	155408564	155408566	+	In_Frame_Del	DEL	ATG	ATG	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccactacacttctcttgatAtgatggggggaacagctgct							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	ATG	ATG	ATG	-	ATG	ATG	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:155408564_155408566delATG	ENST00000368346.3	-	5	6019_6021	c.5380_5382delCAT	c.(5380-5382)catdel	p.H1794del	ASH1L_ENST00000392403.3_In_Frame_Del_p.H1794del			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1794					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.H1794delH(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTCTCTTGATATGATGGGGGGAA	0.429																																																1	Deletion - In frame(1)	large_intestine(1)	1																																								153675190	SO:0001651	inframe_deletion	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5380_5382delCAT	1.37:g.155408567_155408569delATG	ENSP00000357330:p.His1794del		153675188	Q59GP1|Q5T714|Q5T715|Q9P2C7	In_Frame_Del	DEL	ENST00000368346.3	37																																																																																					0.429	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		-	155408566	ATG	-	155408564	7	5	77	1	0	1	0	1	0	0	0	0	1042	446	16	0	3608	0	ASH1L	1	155408564	In_Frame_Del	DEL	ATG	TCGA-AG-A02N-01A-11W-A096-10	150443	155408564	93842057	78	21814										
ASH1L	55870	broad.mit.edu	37	chr1	155491150	155491150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagcttcgatgtttctttctCgattccgtttgcgaaggtcc	9	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:155491150C>T	ENST00000368346.3	-	2	800	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	ASH1L_ENST00000392403.3_Missense_Mutation_p.R54Q|ASH1L_ENST00000548830.1_Missense_Mutation_p.R54Q			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	54					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R54Q(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GTTTCTTTCTCGATTCCGTTT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	1											309	310	310					1																	155491150		2203	4300	6503	153757774	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.161G>A	1.37:g.155491150C>T	ENSP00000357330:p.Arg54Gln		153757774	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	18.85	3.712305	0.68730	.	.	ENSG00000116539	ENST00000368346;ENST00000392403;ENST00000548830	D;D	0.88896	-2.44;-2.44	6.03	4.17	0.49024	.	0.498508	0.20108	N	0.099074	T	0.60702	0.2289	N	0.08118	0	0.29807	N	0.83194	B;B	0.28584	0.138;0.216	B;B	0.15870	0.006;0.014	T	0.52268	-0.8598	10	0.38643	T	0.18	.	11.1503	0.48455	0.1288:0.8048:0.0:0.0664	.	54;54	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	Q	54	ENSP00000357330:R54Q;ENSP00000376204:R54Q	ENSP00000357330:R54Q	R	-	2	0	ASH1L	153757774	0.999000	0.42202	0.947000	0.38551	0.915000	0.54546	2.681000	0.46926	0.883000	0.36040	0.557000	0.71058	CGA		0.408	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155491150	C	T	155491150	3	4	77	1	0	0	0	0	1	0	0	0	1042	884	31	1	8841	1	ASH1L	1	155491150	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	82586	155491150	93759471	79	21815										
TMEM79	84283	broad.mit.edu	37	chr1	156255627	156255627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctaagggctgtggcctccGtgggagccgcactcattctc	14	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:156255627G>A	ENST00000405535.2	+	2	781	c.610G>A	c.(610-612)Gtg>Atg	p.V204M	TMEM79_ENST00000357501.2_Intron|TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Missense_Mutation_p.V204M	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	204					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)		p.V204M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TGTGGCCTCCGTGGGAGCCGC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	64	63					1																	156255627		2203	4300	6503	154522251	SO:0001583	missense	84283			BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.610G>A	1.37:g.156255627G>A	ENSP00000384748:p.Val204Met		154522251	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	37	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	G	8.497	0.863318	0.17250	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.54071	0.59;0.59	5.66	2.02	0.26589	.	0.758888	0.12021	N	0.506986	T	0.08758	0.0217	N	0.03608	-0.345	0.09310	N	1	B	0.21905	0.062	B	0.19148	0.024	T	0.34279	-0.9835	10	0.20519	T	0.43	-14.6089	5.0847	0.14676	0.2205:0.0:0.5571:0.2224	.	204	Q9BSE2	TMM79_HUMAN	M	204	ENSP00000295694:V204M;ENSP00000384748:V204M	ENSP00000295694:V204M	V	+	1	0	TMEM79	154522251	0.050000	0.20438	0.470000	0.27216	0.822000	0.46500	0.138000	0.16016	0.554000	0.29061	0.555000	0.69702	GTG		0.632	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		A	156255627	G	A	156255627	3	1	77	1	0	0	0	0	1	0	0	0	16242	1145	40	1	612	1	TMEM79	1	156255627	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	764477	156255627	92994994	80	21816										
PEAR1	375033	broad.mit.edu	37	chr1	156875168	156875168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaagacggaccaccgccagCgcctgcagtgctgccatggc	13	15	0	2	rs150236151		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:156875168C>T	ENST00000338302.3	+	5	484	c.259C>T	c.(259-261)Cgc>Tgc	p.R87C	PEAR1_ENST00000292357.7_Missense_Mutation_p.R87C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	87	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.R87C(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCACCGCCAGCGCCTGCAGTG	0.652													C|||	1	0.000199681	0	0	5008	,	,		16796	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											64	57	59					1																	156875168		2203	4300	6503	155141792	SO:0001583	missense	375033			AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.259C>T	1.37:g.156875168C>T	ENSP00000344465:p.Arg87Cys		155141792	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	16.83	3.232393	0.58777	.	.	ENSG00000187800	ENST00000338302;ENST00000455314;ENST00000292357	D;D;D	0.89552	-2.53;-1.77;-2.53	4.02	3.09	0.35607	EMI domain (1);	0.000000	0.41605	D	0.000845	D	0.89466	0.6723	L	0.58101	1.795	0.45108	D	0.99812	D	0.89917	1.0	D	0.81914	0.995	D	0.89373	0.3676	10	0.66056	D	0.02	.	8.8991	0.35484	0.4055:0.5945:0.0:0.0	.	87	Q5VY43	PEAR1_HUMAN	C	87	ENSP00000344465:R87C;ENSP00000389742:R87C;ENSP00000292357:R87C	ENSP00000292357:R87C	R	+	1	0	PEAR1	155141792	1.000000	0.71417	0.835000	0.33067	0.961000	0.63080	1.211000	0.32382	0.874000	0.35823	0.655000	0.94253	CGC		0.652	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156875168	C	T	156875168	3	4	77	1	0	0	0	0	1	0	0	0	11743	768	27	1	269	1	PEAR1	1	156875168	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	619541	156875168	92375453	81	21817										
ARHGEF11	9826	broad.mit.edu	37	chr1	156918167	156918167	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtgcaggcgagtagcctcCgcagcagcatccatgtcaac	12	13	1	0	rs375267004	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:156918167C>T	ENST00000361409.2	-	22	2671	c.1929G>A	c.(1927-1929)gcG>gcA	p.A643A	ARHGEF11_ENST00000368194.3_Silent_p.A683A|ARHGEF11_ENST00000487682.1_5'Flank|ARHGEF11_ENST00000315174.8_Silent_p.A59A	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	643					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A683A(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GAGTAGCCTCCGCAGCAGCAT	0.617													C|||	3	0.000599042	0.0023	0	5008	,	,		19619	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						C	,	3,4403	6.2+/-15.9	0,3,2200	94	80	85		1929,2049	-11.8	0	1		85	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGEF11	NM_014784.2,NM_198236.1	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	643/1523,683/1563	156918167	3,13003	2203	4300	6503	155184791	SO:0001819	synonymous_variant	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.1929G>A	1.37:g.156918167C>T			155184791	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	37	CCDS1162.1																																																																																				0.617	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156918167	C	T	156918167	2	4	77	1	0	0	0	0	0	0	0	1	896	639	23	1		1	ARHGEF11	1	156918167	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	42999	156918167	92332454	82	21818										
MNDA	4332	broad.mit.edu	37	chr1	158811985	158811985	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attcttttgctgaaaggattTgagctcatggatgattatca	9	5	3	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:158811985T>G	ENST00000368141.4	+	2	303	c.42T>G	c.(40-42)ttT>ttG	p.F14L	MNDA_ENST00000491210.1_3'UTR	NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	14	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F14L(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TGAAAGGATTTGAGCTCATGG	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	66	67					1																	158811985		2203	4300	6503	157078609	SO:0001583	missense	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.42T>G	1.37:g.158811985T>G	ENSP00000357123:p.Phe14Leu		157078609		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.223778	0.00283	.	.	ENSG00000163563	ENST00000368141	T	0.10573	2.86	3.51	-7.02	0.01589	Pyrin (2);	.	.	.	.	T	0.00328	0.0010	N	0.00325	-1.645	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35400	-0.9790	9	0.02654	T	1	-0.0047	2.5485	0.04742	0.1409:0.106:0.328:0.4252	.	14	P41218	MNDA_HUMAN	L	14	ENSP00000357123:F14L	ENSP00000357123:F14L	F	+	3	2	MNDA	157078609	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.081000	0.00613	-4.118000	0.00072	-2.848000	0.00103	TTT		0.313	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		G	158811985	T	G	158811985	3	3	77	1	0	0	0	0	1	0	0	0	9706	1809	63	4	44	4	MNDA	1	158811985	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1893818	158811985	90438636	83	21819										
IGSF8	93185	broad.mit.edu	37	chr1	160062744	160062744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacatgtacagggagaggccGggaacgggcactggctgctt	16	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:160062744G>A	ENST00000368086.1	-	4	1498	c.1282C>T	c.(1282-1284)Cgg>Tgg	p.R428W	IGSF8_ENST00000314485.7_Missense_Mutation_p.R428W|IGSF8_ENST00000460351.1_5'Flank			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	428					cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R428W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	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)			GGGAGAGGCCGGGAACGGGCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	1											33	39	37					1																	160062744		2203	4300	6503	158329368	SO:0001583	missense	93185			AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1282C>T	1.37:g.160062744G>A	ENSP00000357065:p.Arg428Trp		158329368	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	37	CCDS1195.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490309	0.44249	.	.	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475	T;T	0.05258	3.47;3.47	3.17	3.17	0.36434	Immunoglobulin subtype (1);	0.245363	0.27841	U	0.017633	T	0.05960	0.0155	L	0.36672	1.1	0.27780	N	0.943204	D	0.89917	1.0	D	0.64144	0.922	T	0.12041	-1.0563	10	0.66056	D	0.02	-12.104	8.1705	0.31252	0.0:0.2491:0.7509:0.0	.	428	Q969P0	IGSF8_HUMAN	W	428	ENSP00000316664:R428W;ENSP00000357065:R428W	ENSP00000316664:R428W	R	-	1	2	IGSF8	158329368	0.997000	0.39634	1.000000	0.80357	0.938000	0.57974	2.094000	0.41719	1.589000	0.49982	0.313000	0.20887	CGG		0.642	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		A	160062744	G	A	160062744	3	1	77	1	0	0	0	0	1	0	0	0	7625	1115	39	1	571	1	IGSF8	1	160062744	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1250759	160062744	89187877	84	21820										
ADAMTS4	9507	broad.mit.edu	37	chr1	161168328	161168328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccacaccagccaggagagCggcacaatggggagcaggag	16	11	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:161168328C>T	ENST00000367996.5	-	1	518	c.90G>A	c.(88-90)ccG>ccA	p.P30P	ADAMTS4_ENST00000367995.3_Silent_p.P30P|NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	30					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)	p.P30P(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GCCAGGAGAGCGGCACAATGG	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	1											19	12	14					1																	161168328		2157	4248	6405	159434952	SO:0001819	synonymous_variant	9507			AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.90G>A	1.37:g.161168328C>T			159434952	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Silent	SNP	ENST00000367996.5	37	CCDS1223.1																																																																																				0.687	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		T	161168328	C	T	161168328	2	4	77	1	0	0	0	0	0	0	0	1	268	755	27	1		1	ADAMTS4	1	161168328	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1105584	161168328	88082293	85	21821										
RCSD1	92241	broad.mit.edu	37	chr1	167653147	167653147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catttgccaggaaagaccggCagagaccaatgccaatgtgg	12	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:167653147C>T	ENST00000367854.3	+	2	348	c.17C>T	c.(16-18)gCa>gTa	p.A6V	RCSD1_ENST00000537350.1_Missense_Mutation_p.A6V	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	6					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)	p.A6V(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					GAAAGACCGGCAGAGACCAAT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	1											153	162	159					1																	167653147		2203	4300	6503	165919771	SO:0001583	missense	92241			BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.17C>T	1.37:g.167653147C>T	ENSP00000356828:p.Ala6Val		165919771	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	37	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.753309	0.31046	.	.	ENSG00000198771	ENST00000367854;ENST00000361496;ENST00000537350	T;T	0.55588	0.51;0.61	5.25	4.34	0.51931	.	0.721132	0.13078	N	0.415545	T	0.26557	0.0649	L	0.36672	1.1	0.23640	N	0.99723	B;B	0.30851	0.297;0.191	B;B	0.31390	0.129;0.09	T	0.08472	-1.0720	9	0.39692	T	0.17	-3.6409	11.4774	0.50306	0.0:0.9163:0.0:0.0837	.	6;6	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	V	6	ENSP00000356828:A6V;ENSP00000439409:A6V	ENSP00000355291:A6V	A	+	2	0	RCSD1	165919771	0.689000	0.27690	0.174000	0.22961	0.086000	0.17979	2.760000	0.47581	1.195000	0.43115	0.655000	0.94253	GCA		0.577	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		T	167653147	C	T	167653147	3	4	77	1	0	0	0	0	1	0	0	0	13222	710	25	3	23	3	RCSD1	1	167653147	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6484819	167653147	81597474	86	21822										
BAT2L2	23215	broad.mit.edu	37	chr1	171501621	171501621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcagcagtagaacgtgctcGtaaacggcgtgaagaggaag	15	7	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:171501621G>A	ENST00000338920.4	+	12	1625	c.1388G>A	c.(1387-1389)cGt>cAt	p.R463H	PRRC2C_ENST00000426496.2_Missense_Mutation_p.R463H|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R465H|PRRC2C_ENST00000392078.3_Missense_Mutation_p.R465H	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	463					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.R465H(1)									GAACGTGCTCGTAAACGGCGT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	1											74	66	69					1																	171501621		2203	4300	6503	169768245	SO:0001583	missense	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.1388G>A	1.37:g.171501621G>A	ENSP00000343629:p.Arg463His		169768245	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591013	0.66219	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	6.02	6.02	0.97574	.	0.000000	0.44285	D	0.000469	T	0.39545	0.1082	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.13602	-1.0503	10	0.72032	D	0.01	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	463;465	Q9Y520-4;E7EPN9	.;.	H	465;463;463;465;463;219;221	ENSP00000375928:R465H;ENSP00000410219:R463H;ENSP00000356716:R465H;ENSP00000343629:R463H	ENSP00000343629:R463H	R	+	2	0	PRRC2C	169768245	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.244000	0.95423	2.857000	0.98124	0.650000	0.86243	CGT		0.473	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		A	171501621	G	A	171501621	3	1	77	1	0	0	0	0	1	0	0	0	1322	1145	40	1	1430	1	BAT2L2	1	171501621	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3848474	171501621	77749000	87	21823										
RABGAP1L	9910	broad.mit.edu	37	chr1	174340165	174340165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggtgatgtgtctaaggattGtcctgagaagatcctgtatt	12	5	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:174340165G>A	ENST00000251507.4	+	12	1688	c.1514G>A	c.(1513-1515)tGt>tAt	p.C505Y	RABGAP1L_ENST00000367689.3_Missense_Mutation_p.C152Y|RABGAP1L_ENST00000357444.6_Missense_Mutation_p.C468Y	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0								p.C505Y(1)		NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						TCTAAGGATTGTCCTGAGAAG	0.318																																																1	Substitution - Missense(1)	large_intestine(1)	1											112	112	112					1																	174340165		2203	4300	6503	172606788	SO:0001583	missense	9910			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.1514G>A	1.37:g.174340165G>A	ENSP00000251507:p.Cys505Tyr		172606788	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	37	CCDS1314.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.329714	0.81690	.	.	ENSG00000152061	ENST00000357444;ENST00000367689;ENST00000251507;ENST00000457696;ENST00000367692	D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.95076	0.8405	M	0.83384	2.64	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.996;0.991;0.995;0.995;0.998	D	0.94982	0.8126	10	0.66056	D	0.02	.	19.5364	0.95255	0.0:0.0:1.0:0.0	.	517;152;505;505;468	B7WPG6;Q5JZA9;F1LJ00;Q5R372;Q5R372-2	.;.;.;RBG1L_HUMAN;.	Y	468;152;505;517;517	ENSP00000350027:C468Y;ENSP00000356662:C152Y;ENSP00000251507:C505Y;ENSP00000403136:C517Y	ENSP00000251507:C505Y	C	+	2	0	RABGAP1L	172606788	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.143000	0.94623	2.789000	0.95967	0.655000	0.94253	TGT		0.318	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765		A	174340165	G	A	174340165	3	1	77	1	0	0	0	0	1	0	0	0	13002	1377	48	3	1556	3	RABGAP1L	1	174340165	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2838544	174340165	74910456	88	21824										
TDRD5	163589	broad.mit.edu	37	chr1	179660017	179660017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgccttaggtgctgccgcacGgttagctacatccaggagcc	12	13	0	0	rs188949880		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:179660017G>A	ENST00000367614.1	+	17	3244	c.2885G>A	c.(2884-2886)cGg>cAg	p.R962Q	TDRD5_ENST00000444136.1_Missense_Mutation_p.R1016Q|TDRD5_ENST00000294848.8_Missense_Mutation_p.R962Q	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	962					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)		p.R962Q(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						GCTGCCGCACGGTTAGCTACA	0.522													G|||	1	0.000199681	0	0.0014	5008	,	,		19171	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1											48	50	49					1																	179660017		2203	4300	6503	177926640	SO:0001583	missense	163589			AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2885G>A	1.37:g.179660017G>A	ENSP00000356586:p.Arg962Gln		177926640	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	22.1	4.244320	0.79912	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.60920	1.08;1.08;1.19;0.15	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000001	T	0.73776	0.3630	M	0.68952	2.095	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.67237	-0.5721	10	0.87932	D	0	-28.0338	14.7519	0.69533	0.0:0.0:1.0:0.0	.	1016;962	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	Q	962;962;1016;472	ENSP00000356586:R962Q;ENSP00000294848:R962Q;ENSP00000406052:R1016Q;ENSP00000410744:R472Q	ENSP00000294848:R962Q	R	+	2	0	TDRD5	177926640	0.325000	0.24660	0.023000	0.16930	0.897000	0.52465	3.276000	0.51646	2.614000	0.88457	0.655000	0.94253	CGG		0.522	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		A	179660017	G	A	179660017	3	1	77	1	0	0	0	0	1	0	0	0	15772	1116	39	1	2947	1	TDRD5	1	179660017	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5319852	179660017	69590604	89	21825										
NPL	80896	broad.mit.edu	37	chr1	182783968	182783968	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcatcgctgtcattgcaccGttcttcctcaagccatggac	9	14	3	0	rs150521146		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:182783968G>A	ENST00000367553.1	+	6	383	c.339G>A	c.(337-339)ccG>ccA	p.P113P	NPL_ENST00000367555.1_Silent_p.P113P|NPL_ENST00000463899.1_3'UTR|NPL_ENST00000258317.2_Silent_p.P113P|NPL_ENST00000367554.3_Silent_p.P94P|NPL_ENST00000367552.2_Silent_p.P113P	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	113					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)	p.P113P(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						TCATTGCACCGTTCTTCCTCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,,,,	1,4405	2.1+/-5.4	0,1,2202	151	124	133		282,339,339,339,339	0	1	1	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	94/302,113/241,113/231,113/285,113/321	182783968	1,13005	2203	4300	6503	181050591	SO:0001819	synonymous_variant	80896			AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 1 (E. coli)"	611412	"chromosome 1 open reading frame 13"	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.339G>A	1.37:g.182783968G>A			181050591	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1																																																																																				0.433	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		A	182783968	G	A	182783968	2	1	77	1	0	0	0	0	0	0	0	1	10616	1132	40	1		1	NPL	1	182783968	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3123951	182783968	66466653	90	21826										
DHX9	1660	broad.mit.edu	37	chr1	182852428	182852428	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcgtaatgcacttatccaCaaatcatctgttaattgtcc	7	10	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:182852428C>T	ENST00000367549.3	+	25	3179	c.3069C>T	c.(3067-3069)caC>caT	p.H1023H	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1023					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)	p.H1023H(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CACTTATCCACAAATCATCTG	0.398																																					Colon(69;210 1162 3697 13559 39565)											1	Substitution - coding silent(1)	large_intestine(1)	1											123	104	110					1																	182852428		1900	4119	6019	181119051	SO:0001819	synonymous_variant	1660			L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3069C>T	1.37:g.182852428C>T			181119051	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																				0.398	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182852428	C	T	182852428	2	4	77	1	0	0	0	0	0	0	0	1	4527	477	17	3		3	DHX9	1	182852428	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	68460	182852428	66398193	91	21827										
HMCN1	83872	broad.mit.edu	37	chr1	186043907	186043907	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgatcatgttaatattgctgCgaatggacacacacttcaaa	7	8	2	1	rs138928800	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:186043907C>T	ENST00000271588.4	+	53	8403	c.8174C>T	c.(8173-8175)gCg>gTg	p.A2725V	HMCN1_ENST00000367492.2_Missense_Mutation_p.A2725V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2725	Ig-like C2-type 25.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.A2725V(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AATATTGCTGCGAATGGACAC	0.383													C|||	8	0.00159744	0	0	5008	,	,		14913	0.003		0.005	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						C	VAL/ALA	0,4406		0,0,2203	120	115	117		8174	2.2	0.5	1	dbSNP_134	117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	HMCN1	NM_031935.2	64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	2725/5636	186043907	2,13004	2203	4300	6503	184310530	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8174C>T	1.37:g.186043907C>T	ENSP00000271588:p.Ala2725Val		184310530	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	14.07	2.424994	0.43020	0.0	2.33E-4	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66280	-0.2;-0.2	5.47	2.16	0.27623	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.219005	0.47093	D	0.000242	T	0.36552	0.0971	N	0.16602	0.42	0.44123	D	0.996904	D	0.56521	0.976	P	0.50270	0.636	T	0.26849	-1.0091	10	0.24483	T	0.36	.	2.7623	0.05310	0.1341:0.4973:0.132:0.2367	.	2725	Q96RW7	HMCN1_HUMAN	V	2725	ENSP00000271588:A2725V;ENSP00000356462:A2725V	ENSP00000271588:A2725V	A	+	2	0	HMCN1	184310530	0.956000	0.32656	0.476000	0.27291	0.988000	0.76386	2.173000	0.42472	0.660000	0.30964	0.491000	0.48974	GCG		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186043907	C	T	186043907	3	4	77	1	0	0	0	0	1	0	0	0	7241	768	27	1	8384	1	HMCN1	1	186043907	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3191479	186043907	63206714	92	21828										
ASPM	259266	broad.mit.edu	37	chr1	197091052	197091052	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attctaggagtacctgatggCgtttgagatctgtttttagt	11	5	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:197091052C>T	ENST00000367409.4	-	16	4119	c.3863G>A	c.(3862-3864)cGc>cAc	p.R1288H	ASPM_ENST00000367408.1_Missense_Mutation_p.R538H|ASPM_ENST00000294732.7_Missense_Mutation_p.R1288H	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1288					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.R1288H(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TACCTGATGGCGTTTGAGATC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	1											116	117	117					1																	197091052		2203	4299	6502	195357675	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3863G>A	1.37:g.197091052C>T	ENSP00000356379:p.Arg1288His		195357675	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.953953	0.34471	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	D;T;T	0.81579	-1.51;-0.58;-0.58	5.84	-2.21	0.06973	.	1.103920	0.06881	N	0.802515	T	0.59918	0.2229	N	0.17474	0.49	0.09310	N	1	B;B	0.22683	0.008;0.073	B;B	0.17722	0.001;0.019	T	0.43065	-0.9414	10	0.11182	T	0.66	.	5.0673	0.14589	0.4247:0.1856:0.0:0.3897	.	1288;1288	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	H	1288;1288;538	ENSP00000356379:R1288H;ENSP00000294732:R1288H;ENSP00000356378:R538H	ENSP00000294732:R1288H	R	-	2	0	ASPM	195357675	0.050000	0.20438	0.004000	0.12327	0.979000	0.70002	0.474000	0.22148	-0.203000	0.10251	0.655000	0.94253	CGC		0.313	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197091052	C	T	197091052	3	4	77	1	0	0	0	0	1	0	0	0	1057	768	27	1	6622	1	ASPM	1	197091052	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	11047145	197091052	52159569	93	21829										
PTPRC	5788	broad.mit.edu	37	chr1	198665864	198665864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgactacagcaaagatgcccAgtgttccactttcaagtgac	8	11	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:198665864A>G	ENST00000367376.2	+	4	289	c.118A>G	c.(118-120)Agt>Ggt	p.S40G	PTPRC_ENST00000352140.3_Missense_Mutation_p.S40G|PTPRC_ENST00000348564.6_Intron|PTPRC_ENST00000442510.2_Missense_Mutation_p.S42G|PTPRC_ENST00000391970.3_Intron|PTPRC_ENST00000594404.1_Intron	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	40					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S40G(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AAAGATGCCCAGTGTTCCACT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	146	147					1																	198665864		2203	4300	6503	196932487	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.118A>G	1.37:g.198665864A>G	ENSP00000356346:p.Ser40Gly		196932487	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	A	16.73	3.204021	0.58234	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000535566;ENST00000271610;ENST00000442510;ENST00000418674	T	0.03035	4.07	5.33	-4.33	0.03677	Protein tyrosine phosphatase, receptor type, N terminal (1);	1.225800	0.05834	N	0.618022	T	0.06005	0.0156	L	0.47716	1.5	0.09310	N	1	P;P;P	0.52170	0.901;0.946;0.951	P;P;P	0.52758	0.607;0.671;0.708	T	0.33317	-0.9873	10	0.51188	T	0.08	.	2.2181	0.03965	0.3111:0.3687:0.0794:0.2408	.	81;40;40	Q6Q1P2;E9PC28;P08575	.;.;PTPRC_HUMAN	G	42;40;40;81;40;40	ENSP00000193532:S40G	ENSP00000271610:S81G	S	+	1	0	PTPRC	196932487	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.364000	0.07583	-0.324000	0.08589	0.533000	0.62120	AGT		0.418	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				G	198665864	A	G	198665864	3	3	77	1	0	0	0	0	1	0	0	0	12834	188	7	4	139	4	PTPRC	1	198665864	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1574812	198665864	50584757	94	21830										
PTPRC	5788	broad.mit.edu	37	chr1	198685924	198685924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acatcattgcaaaagtgcaaCgtaatggaagtgctgcaatg	10	7	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:198685924C>T	ENST00000367376.2	+	13	1570	c.1399C>T	c.(1399-1401)Cgt>Tgt	p.R467C	PTPRC_ENST00000352140.3_Missense_Mutation_p.R419C|PTPRC_ENST00000348564.6_Missense_Mutation_p.R308C|PTPRC_ENST00000442510.2_Missense_Mutation_p.R469C|PTPRC_ENST00000594404.1_Missense_Mutation_p.R306C	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	467	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R467C(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AAAAGTGCAACGTAATGGAAG	0.308																																																1	Substitution - Missense(1)	large_intestine(1)	1											86	89	88					1																	198685924		2202	4300	6502	196952547	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1399C>T	1.37:g.198685924C>T	ENSP00000356346:p.Arg467Cys		196952547	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	14.86	2.662255	0.47572	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.54071	0.59	4.43	3.5	0.40072	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000151	T	0.65207	0.2669	M	0.64404	1.975	0.18873	N	0.999988	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.70016	0.967;0.964;0.927;0.951;0.964	T	0.55101	-0.8193	10	0.51188	T	0.08	.	10.1512	0.42794	0.1974:0.8026:0.0:0.0	.	403;403;308;419;467	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	C	469;403;419;419;353;467;401;306	ENSP00000193532:R419C	ENSP00000306782:R306C	R	+	1	0	PTPRC	196952547	0.350000	0.24878	0.049000	0.19019	0.002000	0.02628	1.667000	0.37471	1.426000	0.47256	0.650000	0.86243	CGT		0.308	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198685924	C	T	198685924	3	4	77	1	0	0	0	0	1	0	0	0	12834	536	19	1	1456	1	PTPRC	1	198685924	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	20060	198685924	50564697	95	21831										
MYBPH	4608	broad.mit.edu	37	chr1	203143635	203143635	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaactcactgcagacacgCgcaggaggaacttgtctccc	10	14	2	2	rs146696842		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:203143635C>T	ENST00000255416.4	-	3	488	c.431G>A	c.(430-432)cGc>cAc	p.R144H		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	144	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R144H(1)		endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		TGCAGACACGCGCAGGAGGAA	0.632													C|||	1	0.000199681	0	0	5008	,	,		16196	0		0	False		,,,				2504	0.001				NSCLC(32;174 1025 14462 23899 42933)											1	Substitution - Missense(1)	large_intestine(1)	1						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	49	50	50		431	5.7	1	1	dbSNP_134	50	0,8600		0,0,4300	no	missense	MYBPH	NM_004997.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	144/478	203143635	1,13005	2203	4300	6503	201410258	SO:0001583	missense	4608			BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7552	protein-coding gene	gene with protein product		160795	"myosin-binding protein H"			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.431G>A	1.37:g.203143635C>T	ENSP00000255416:p.Arg144His		201410258	Q16886|Q86YC5	Missense_Mutation	SNP	ENST00000255416.4	37	CCDS30975.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.895692	0.72639	2.27E-4	0.0	ENSG00000133055	ENST00000255416	T	0.60920	0.15	5.67	5.67	0.87782	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000087	T	0.82075	0.4958	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86063	0.1533	10	0.87932	D	0	.	17.2606	0.87068	0.0:1.0:0.0:0.0	.	144	Q13203	MYBPH_HUMAN	H	144	ENSP00000255416:R144H	ENSP00000255416:R144H	R	-	2	0	MYBPH	201410258	1.000000	0.71417	0.952000	0.39060	0.030000	0.12068	6.598000	0.74122	2.681000	0.91329	0.655000	0.94253	CGC		0.632	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997		T	203143635	C	T	203143635	3	4	77	1	0	0	0	0	1	0	0	0	10044	768	27	1	1034	1	MYBPH	1	203143635	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4457711	203143635	46106986	96	21832										
CHIT1	1118	broad.mit.edu	37	chr1	203186148	203186149	+	Frame_Shift_Ins	INS	-	-	T													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgggatagagcccatcagcINStttgccctggcagaacgtgt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:203186148_203186149insT	ENST00000367229.1	-	11	1303_1304	c.1269_1270insA	c.(1267-1272)aaagctfs	p.A424fs	CHIT1_ENST00000484834.1_Intron|CHIT1_ENST00000535569.1_Frame_Shift_Ins_p.A415fs|CHIT1_ENST00000255427.3_Frame_Shift_Ins_p.A405fs	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	424	Chitin-binding type-2. {ECO:0000255|PROSITE-ProRule:PRU00144}.				chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)	p.A424fs*2(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						AGCCCATCAGCTTTGCCCTGGC	0.604											OREG0014113	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Insertion - Frameshift(1)	large_intestine(1)	1																																								201452772	SO:0001589	frameshift_variant	1118			U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.1270dupA	1.37:g.203186151_203186151dupT	ENSP00000356198:p.Ala424fs	2135	201452771	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Frame_Shift_Ins	INS	ENST00000367229.1	37	CCDS1436.1																																																																																				0.604	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465		T	203186149	-	T	203186148	7	5	77	1	0	1	1	0	0	0	0	0	3352	797	28	0	134	0	CHIT1	1	203186148	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	42513	203186148	46064473	97	21833										
PLEKHA6	22874	broad.mit.edu	37	chr1	204234135	204234135	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctacccggaagctcaggaGggggatgctgcccaggatac							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:204234135delG	ENST00000272203.3	-	6	632	c.316delC	c.(316-318)ctcfs	p.L107fs	PLEKHA6_ENST00000485632.1_5'Flank|PLEKHA6_ENST00000414478.1_Frame_Shift_Del_p.L107fs	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	107	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.							p.L106fs*2(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			AAGCTCAGGAGGGGGATGCTG	0.597																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											155	138	144					1																	204234135		2203	4300	6503	202500758	SO:0001589	frameshift_variant	22874			AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.316delC	1.37:g.204234135delG	ENSP00000272203:p.Leu107fs		202500758	A7MD51|Q5VTI6	Frame_Shift_Del	DEL	ENST00000272203.3	37	CCDS1444.1																																																																																				0.597	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		-	204234135	G	-	204234135	7	5	77	1	0	1	0	1	0	0	0	0	12091	1000	35	0	2898	0	PLEKHA6	1	204234135	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1047987	204234135	45016486	98	21834										
TMCC2	9911	broad.mit.edu	37	chr1	205210827	205210827	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagatgcatcgcgtctcctaCgccatgtccctgcacgacct	9	16	1	1	rs77588763		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:205210827C>T	ENST00000358024.3	+	2	791	c.402C>T	c.(400-402)taC>taT	p.Y134Y	TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000545499.1_Silent_p.Y56Y	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	134						integral component of membrane (GO:0016021)		p.Y134Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GCGTCTCCTACGCCATGTCCC	0.667													C|||	1	0.000199681	0	0	5008	,	,		16235	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1											75	60	65					1																	205210827		2203	4300	6503	203477450	SO:0001819	synonymous_variant	9911			AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"Transmembrane and coiled-coil domain containing"	24239	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 2"			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.402C>T	1.37:g.205210827C>T			203477450	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																				0.667	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		T	205210827	C	T	205210827	2	4	77	1	0	0	0	0	0	0	0	1	16032	547	19	1		1	TMCC2	1	205210827	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	976692	205210827	44039794	99	21835										
PIGR	5284	broad.mit.edu	37	chr1	207106479	207106479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caccttctcatcaggagcagCgtctgccttcgctaggctga	10	14	3	1	rs529407537	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:207106479C>T	ENST00000356495.4	-	7	1921	c.1738G>A	c.(1738-1740)Gct>Act	p.A580T	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	580			A -> V (in dbSNP:rs291102).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.A580T(2)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TCAGGAGCAGCGTCTGCCTTC	0.542													C|||	2	0.000399361	0.0015	0	5008	,	,		21107	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	1											66	65	66					1																	207106479		2203	4300	6503	205173102	SO:0001583	missense	5284				CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1738G>A	1.37:g.207106479C>T	ENSP00000348888:p.Ala580Thr		205173102	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	7.714	0.695788	0.15106	.	.	ENSG00000162896	ENST00000356495	T	0.16457	2.34	2.02	1.02	0.19986	.	1.246790	0.05490	N	0.556394	T	0.09862	0.0242	L	0.27053	0.805	0.09310	N	1	P	0.38440	0.631	B	0.24394	0.053	T	0.29610	-1.0006	10	0.40728	T	0.16	-32.5565	6.2298	0.20728	0.0:0.6814:0.3186:0.0	.	580	P01833	PIGR_HUMAN	T	580	ENSP00000348888:A580T	ENSP00000348888:A580T	A	-	1	0	PIGR	205173102	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	0.011000	0.13264	0.384000	0.24942	0.555000	0.69702	GCT		0.542	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		T	207106479	C	T	207106479	3	4	77	1	0	0	0	0	1	0	0	0	11928	768	27	1	576	1	PIGR	1	207106479	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1895652	207106479	42144142	100	21836										
PLXNA2	5362	broad.mit.edu	37	chr1	208315787	208315787	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcgtactggaccccaccatGggggggaccgtcggcccgaa					rs200374067	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:208315787delG	ENST00000367033.3	-	4	2150	c.1393delC	c.(1393-1395)catfs	p.H465fs		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	465	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.H465fs*57(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		ACCCCACCATGGGGGGGACCG	0.592																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											98	99	99					1																	208315787		2203	4300	6503	206382410	SO:0001589	frameshift_variant	5362			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1393delC	1.37:g.208315787delG	ENSP00000356000:p.His465fs		206382410	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Frame_Shift_Del	DEL	ENST00000367033.3	37	CCDS31013.1																																																																																				0.592	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		-	208315787	G	-	208315787	7	5	77	1	0	1	0	1	0	0	0	0	12151	1348	47	0	4407	0	PLXNA2	1	208315787	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1209308	208315787	40934834	101	21837										
ANGEL2	90806	broad.mit.edu	37	chr1	213186456	213186456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggtgttttcttcgttttgAtgaaggctcatctccctcag	9	9	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:213186456A>G	ENST00000366962.3	-	2	518	c.364T>C	c.(364-366)Tca>Cca	p.S122P	ANGEL2_ENST00000360506.2_Intron|ANGEL2_ENST00000535388.1_Intron|ANGEL2_ENST00000544555.1_Intron|ANGEL2_ENST00000540642.1_Intron	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	122								p.S122P(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CTTCGTTTTGATGAAGGCTCA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											126	125	125					1																	213186456		2203	4299	6502	211253079	SO:0001583	missense	90806			AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.364T>C	1.37:g.213186456A>G	ENSP00000355929:p.Ser122Pro		211253079	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Missense_Mutation	SNP	ENST00000366962.3	37	CCDS1512.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.163657	0.38217	.	.	ENSG00000174606	ENST00000366962;ENST00000310246	T	0.24350	1.86	5.45	5.45	0.79879	.	0.259393	0.32533	N	0.005975	T	0.11793	0.0287	N	0.11560	0.145	0.80722	D	1	B;B	0.25441	0.126;0.003	B;B	0.22152	0.038;0.003	T	0.20773	-1.0265	10	0.21540	T	0.41	-7.7786	6.2539	0.20864	0.7719:0.0:0.0767:0.1515	.	100;122	Q96AL9;Q5VTE6	.;ANGE2_HUMAN	P	122;100	ENSP00000355929:S122P	ENSP00000309755:S100P	S	-	1	0	ANGEL2	211253079	1.000000	0.71417	0.953000	0.39169	0.997000	0.91878	3.100000	0.50275	2.181000	0.69327	0.460000	0.39030	TCA		0.383	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		G	213186456	A	G	213186456	3	3	77	1	0	0	0	0	1	0	0	0	609	333	12	4	1302	4	ANGEL2	1	213186456	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	4870669	213186456	36064165	102	21838										
TGFB2	7042	broad.mit.edu	37	chr1	218536744	218536744	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctccagacagtcccaggtgCtctgtgggtaccttggtgag	14	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:218536744C>T	ENST00000366930.4	+	1	813				TGFB2_ENST00000366929.4_Missense_Mutation_p.L139F	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2						activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.L139F(1)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GTCCCAGGTGCTCTGTGGGTA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	1											170	148	155					1																	218536744		1568	3582	5150	216603367	SO:0001627	intron_variant	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.346+16355C>T	1.37:g.218536744C>T			216603367	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	C	5.681	0.310284	0.10733	.	.	ENSG00000092969	ENST00000366929	T	0.75367	-0.93	4.55	3.64	0.41730	.	0.278277	0.30347	N	0.009824	T	0.69196	0.3084	N	0.19112	0.55	0.24700	N	0.993266	P;B	0.47106	0.89;0.01	D;B	0.66351	0.943;0.019	T	0.59478	-0.7447	10	0.06099	T	0.92	.	8.7359	0.34528	0.0:0.8996:0.0:0.1004	.	139;140	P61812-2;Q59EG9	.;.	F	139	ENSP00000355896:L139F	ENSP00000355896:L139F	L	+	1	0	TGFB2	216603367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.563000	0.23547	1.536000	0.49237	0.655000	0.94253	CTC		0.468	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		T	218536744	C	T	218536744	1	4	77	0	1	0	0	0	0	0	0	0	15857	797	28	3		3	TGFB2	1	218536744	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5350288	218536744	30713877	103	21839										
RAB3GAP2	25782	broad.mit.edu	37	chr1	220364618	220364618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatccatccaatttgtgcgtCgcggtacccttagagacaga	9	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:220364618C>T	ENST00000358951.2	-	14	1395	c.1279G>A	c.(1279-1281)Gac>Aac	p.D427N		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	427					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)	p.D427N(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		ATTTGTGCGTCGCGGTACCCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											39	37	37					1																	220364618		2203	4300	6503	218431241	SO:0001583	missense	25782			AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.1279G>A	1.37:g.220364618C>T	ENSP00000351832:p.Asp427Asn		218431241	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.117820	0.77323	.	.	ENSG00000118873	ENST00000358951	T	0.58506	0.33	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.69433	0.3110	L	0.41492	1.28	0.80722	D	1	D	0.89917	1.0	D	0.68483	0.958	T	0.67003	-0.5780	10	0.42905	T	0.14	.	19.7949	0.96477	0.0:1.0:0.0:0.0	.	427	Q9H2M9	RBGPR_HUMAN	N	427	ENSP00000351832:D427N	ENSP00000351832:D427N	D	-	1	0	RAB3GAP2	218431241	1.000000	0.71417	0.994000	0.49952	0.213000	0.24496	7.190000	0.77755	2.691000	0.91804	0.591000	0.81541	GAC		0.478	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		T	220364618	C	T	220364618	3	4	77	1	0	0	0	0	1	0	0	0	12973	884	31	1	2990	1	RAB3GAP2	1	220364618	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1827874	220364618	28886003	104	21840										
MARK1	4139	broad.mit.edu	37	chr1	220825398	220825398	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctctgctgtcccctcagcaCgaccccgccaccagaagtcc	7	21	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:220825398C>T	ENST00000366917.4	+	15	1908	c.1642C>T	c.(1642-1644)Cga>Tga	p.R548*	MARK1_ENST00000366918.4_Nonsense_Mutation_p.R526*|MARK1_ENST00000402574.1_Nonsense_Mutation_p.R413*					MAP/microtubule affinity-regulating kinase 1									p.R548*(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		CCCCTCAGCACGACCCCGCCA	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											104	96	99					1																	220825398		2203	4300	6503	218892021	SO:0001587	stop_gained	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1642C>T	1.37:g.220825398C>T	ENSP00000355884:p.Arg548*		218892021		Nonsense_Mutation	SNP	ENST00000366917.4	37	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	C	44	11.149198	0.99522	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	.	.	.	5.95	5.03	0.67393	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5565	0.76200	0.0:0.9329:0.0:0.0671	.	.	.	.	X	413;526;548	.	ENSP00000355884:R548X	R	+	1	2	MARK1	218892021	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.856000	0.69518	2.817000	0.96982	0.563000	0.77884	CGA		0.512	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220825398	C	T	220825398	4	4	77	1	0	0	0	0	0	1	0	0	9342	528	19	1	1700	1	MARK1	1	220825398	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	460780	220825398	28425223	105	21841										
GALNT2	2590	broad.mit.edu	37	chr1	230415129	230415129	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacagtcgcacggccaagagCgggggcctaagcgtggaggt	18	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:230415129C>T	ENST00000366672.4	+	16	1713	c.1641C>T	c.(1639-1641)agC>agT	p.S547S	RP5-956O18.3_ENST00000414640.1_RNA|GALNT2_ENST00000543760.1_Silent_p.S509S|GALNT2_ENST00000485438.1_3'UTR	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	547	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.S547S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CGGCCAAGAGCGGGGGCCTAA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	1											68	62	64					1																	230415129		2203	4300	6503	228481752	SO:0001819	synonymous_variant	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.1641C>T	1.37:g.230415129C>T			228481752	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1																																																																																				0.637	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		T	230415129	C	T	230415129	2	4	77	1	0	0	0	0	0	0	0	1	6233	767	27	1		1	GALNT2	1	230415129	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	9589731	230415129	18835492	106	21842										
PGBD5	79605	broad.mit.edu	37	chr1	230472933	230472933	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgtagttcttgcctgccgcGttccggcacaggctcctggc	12	14	1	0	rs370784342	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:230472933G>A	ENST00000525115.1	-	4	812	c.789C>T	c.(787-789)aaC>aaT	p.N263N	PGBD5_ENST00000530424.1_5'Flank|PGBD5_ENST00000391860.1_Silent_p.N217N|PGBD5_ENST00000321327.2_Silent_p.N362N			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	263						integral component of membrane (GO:0016021)		p.N362N(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		TGCCTGCCGCGTTCCGGCACA	0.572													G|||	2	0.000399361	8e-04	0.0014	5008	,	,		20696	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		1,4405	2.1+/-5.4	0,1,2202	82	72	76		789	-6.7	0	1		76	0,8600		0,0,4300	no	coding-synonymous	PGBD5	NM_024554.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		263/456	230472933	1,13005	2203	4300	6503	228539556	SO:0001819	synonymous_variant	79605			AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.789C>T	1.37:g.230472933G>A			228539556	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Silent	SNP	ENST00000525115.1	37																																																																																					0.572	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		A	230472933	G	A	230472933	2	1	77	1	0	0	0	0	0	0	0	1	11815	1136	40	1		1	PGBD5	1	230472933	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	57804	230472933	18777688	107	21843										
GNPAT	8443	broad.mit.edu	37	chr1	231408093	231408094	+	Frame_Shift_Ins	INS	-	-	T													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttcgcttcctacgtgatgINStttttgcagatgagttcatc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:231408093_231408094insT	ENST00000366647.4	+	11	1727_1728	c.1558_1559insT	c.(1558-1560)gttfs	p.V520fs	GNPAT_ENST00000366646.3_Frame_Shift_Ins_p.V459fs	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	520					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)	p.A522fs*3(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				CCTACGTGATGTTTTTGCAGAT	0.376																																																1	Insertion - Frameshift(1)	large_intestine(1)	1																																								229474717	SO:0001589	frameshift_variant	8443			AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1563dupT	1.37:g.231408098_231408098dupT	ENSP00000355607:p.Val520fs		229474716	B4DNM9|Q5TBH7|Q9BWC2	Frame_Shift_Ins	INS	ENST00000366647.4	37	CCDS1592.1																																																																																				0.376	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			T	231408094	-	T	231408093	7	5	77	1	0	1	1	0	0	0	0	0	6561	1377	48	0	1600	0	GNPAT	1	231408093	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	935160	231408093	17842528	108	21844										
KIAA1804	84451	broad.mit.edu	37	chr1	233489620	233489620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggcattgatggcctcgccGtggcttatggggtagcagtc	17	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:233489620G>A	ENST00000366624.3	+	3	1315	c.1054G>A	c.(1054-1056)Gtg>Atg	p.V352M	MLK4_ENST00000366623.3_Missense_Mutation_p.V352M	NM_032435.2	NP_115811.2												p.V352M(1)									TGGCCTCGCCGTGGCTTATGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	113	117					1																	233489620		2203	4300	6503	231556243	SO:0001583	missense	84451																														ENST00000366624.3:c.1054G>A	1.37:g.233489620G>A	ENSP00000355583:p.Val352Met		231556243		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.104267	0.76983	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.84298	-1.83;-1.83	4.91	4.91	0.64330	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.90212	0.6940	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.91207	0.4996	10	0.87932	D	0	.	18.301	0.90163	0.0:0.0:1.0:0.0	.	352;352	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	M	352	ENSP00000355582:V352M;ENSP00000355583:V352M	ENSP00000355582:V352M	V	+	1	0	RP5-862P8.2	231556243	1.000000	0.71417	0.956000	0.39512	0.430000	0.31655	9.648000	0.98483	2.538000	0.85594	0.563000	0.77884	GTG		0.522	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			A	233489620	G	A	233489620	3	1	77	1	0	0	0	0	1	0	0	0	8280	1145	40	1	1064	1	KIAA1804	1	233489620	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2081527	233489620	15761001	109	21845										
KIAA1804	84451	broad.mit.edu	37	chr1	233497907	233497907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcagagcgcgagatcgacGtgctggagcgggaacttaac	16	9	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:233497907G>A	ENST00000366624.3	+	5	1681	c.1420G>A	c.(1420-1422)Gtg>Atg	p.V474M	MLK4_ENST00000366623.3_Missense_Mutation_p.V474M	NM_032435.2	NP_115811.2												p.V474M(2)									CGAGATCGACGTGCTGGAGCG	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	1											59	58	58					1																	233497907		2203	4300	6503	231564530	SO:0001583	missense	84451																														ENST00000366624.3:c.1420G>A	1.37:g.233497907G>A	ENSP00000355583:p.Val474Met		231564530		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720169	0.68844	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.76060	-0.87;-0.99	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000002	T	0.81093	0.4751	M	0.65975	2.015	0.80722	D	1	D;D	0.63880	0.975;0.993	P;P	0.61003	0.636;0.882	T	0.79482	-0.1785	10	0.35671	T	0.21	.	11.6727	0.51411	0.0808:0.0:0.9192:0.0	.	474;474	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	M	474	ENSP00000355582:V474M;ENSP00000355583:V474M	ENSP00000355582:V474M	V	+	1	0	RP5-862P8.2	231564530	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.610000	0.74178	2.525000	0.85131	0.655000	0.94253	GTG		0.542	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			A	233497907	G	A	233497907	3	1	77	1	0	0	0	0	1	0	0	0	8280	1145	40	1	1438	1	KIAA1804	1	233497907	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8287	233497907	15752714	110	21846										
TARBP1	6894	broad.mit.edu	37	chr1	234565409	234565409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccatccttgggaagatgacGattcttccaaaacactgaaa	7	11	1	3	rs374573385		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:234565409G>A	ENST00000040877.1	-	16	2623	c.2624C>T	c.(2623-2625)tCg>tTg	p.S875L		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	875					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)	p.S875L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GGAAGATGACGATTCTTCCAA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	LEU/SER	0,4406		0,0,2203	74	75	75		2624	4.3	0.1	1		75	1,8599	1.2+/-3.3	0,1,4299	no	missense	TARBP1	NM_005646.3	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	875/1622	234565409	1,13005	2203	4300	6503	232632032	SO:0001583	missense	6894				CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2624C>T	1.37:g.234565409G>A	ENSP00000040877:p.Ser875Leu		232632032	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.522072	0.44866	0.0	1.16E-4	ENSG00000059588	ENST00000040877	T	0.33865	1.39	5.18	4.26	0.50523	.	0.622689	0.15906	N	0.238845	T	0.38348	0.1037	M	0.67953	2.075	0.31488	N	0.666281	B	0.15473	0.013	B	0.09377	0.004	T	0.45731	-0.9241	10	0.59425	D	0.04	-18.0552	12.3558	0.55174	0.0789:0.0:0.9211:0.0	.	875	Q13395	TARB1_HUMAN	L	875	ENSP00000040877:S875L	ENSP00000040877:S875L	S	-	2	0	TARBP1	232632032	0.027000	0.19231	0.091000	0.20842	0.506000	0.33950	2.137000	0.42130	1.314000	0.45095	-0.140000	0.14226	TCG		0.388	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234565409	G	A	234565409	3	1	77	1	0	0	0	0	1	0	0	0	15594	1059	37	1	2301	1	TARBP1	1	234565409	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1067502	234565409	14685212	111	21847										
RBM34	23029	broad.mit.edu	37	chr1	235295057	235295057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttctctgtttcttagggcGtccacttttcttctgtcctt	6	11	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:235295057G>A	ENST00000408888.3	-	11	1494	c.1264C>T	c.(1264-1266)Cgc>Tgc	p.R422C	TOMM20_ENST00000366607.4_5'Flank|RBM34_ENST00000366606.3_Missense_Mutation_p.R417C|RBM34_ENST00000495224.1_5'UTR			P42696	RBM34_HUMAN	RNA binding motif protein 34	422						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R422C(1)		central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			TTCTTAGGGCGTCCACTTTTC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	115	116					1																	235295057		1837	4093	5930	233361680	SO:0001583	missense	23029				CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.1264C>T	1.37:g.235295057G>A	ENSP00000386226:p.Arg422Cys		233361680	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	37	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	G	2.451	-0.326435	0.05350	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000447801	T;T;T	0.15952	2.38;2.39;2.52	5.71	1.3	0.21679	.	1.538070	0.03650	N	0.240865	T	0.10423	0.0255	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	10	0.37606	T	0.19	3.6436	8.3649	0.32380	0.1644:0.0:0.6995:0.1362	.	422	P42696	RBM34_HUMAN	C	422;417;400	ENSP00000386226:R422C;ENSP00000355565:R417C;ENSP00000400000:R400C	ENSP00000355565:R417C	R	-	1	0	RBM34	233361680	0.001000	0.12720	0.037000	0.18230	0.001000	0.01503	0.547000	0.23299	0.358000	0.24211	-1.305000	0.01319	CGC		0.368	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235295057	G	A	235295057	3	1	77	1	0	0	0	0	1	0	0	0	13168	1145	40	1	32	1	RBM34	1	235295057	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	729648	235295057	13955564	112	21848										
CEP170	9859	broad.mit.edu	37	chr1	243362374	243362374	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttttacctgatgttccagCttcatggtttttttcttcag	6	8	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:243362374C>G	ENST00000366542.1	-	7	670	c.619G>C	c.(619-621)Gct>Cct	p.A207P	CEP170_ENST00000366543.1_Missense_Mutation_p.A207P|CEP170_ENST00000366544.1_Missense_Mutation_p.A207P	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	207						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.A207P(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GATGTTCCAGCTTCATGGTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	1											88	73	78					1																	243362374		1822	4080	5902	241428997	SO:0001583	missense	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.619G>C	1.37:g.243362374C>G	ENSP00000355500:p.Ala207Pro		241428997	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.729|2.729	-0.264827|-0.264827	0.05754|0.05754	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081|ENST00000336415	T;T;T|.	0.30714|.	1.52;1.52;1.52|.	5.05|5.05	-0.0734|-0.0734	0.13735|0.13735	.|.	0.447731|.	0.25089|.	N|.	0.033237|.	T|T	0.10895|0.10895	0.0266|0.0266	N|N	0.01705|0.01705	-0.755|-0.755	0.30306|0.30306	N|N	0.789017|0.789017	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.06405|.	0.002;0.002;0.001|.	T|T	0.33317|0.33317	-0.9873|-0.9873	10|5	0.28530|.	T|.	0.3|.	-1.3374|-1.3374	5.3867|5.3867	0.16222|0.16222	0.0:0.3025:0.262:0.4355|0.0:0.3025:0.262:0.4355	.|.	207;207;207|.	Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;CE170_HUMAN|.	P|N	207;207;207;105|108	ENSP00000355500:A207P;ENSP00000355502:A207P;ENSP00000355501:A207P|.	ENSP00000355500:A207P|.	A|K	-|-	1|3	0|2	CEP170|CEP170	241428997|241428997	0.132000|0.132000	0.22450|0.22450	0.068000|0.068000	0.19968|0.19968	0.200000|0.200000	0.23975|0.23975	0.011000|0.011000	0.13264|0.13264	-0.006000|-0.006000	0.14370|0.14370	-0.391000|-0.391000	0.06502|0.06502	GCT|AAG		0.403	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		G	243362374	C	G	243362374	3	3	77	1	0	0	0	0	1	0	0	0	3256	797	28	5	4221	5	CEP170	1	243362374	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8067317	243362374	5888247	113	21849										
KIF26B	55083	broad.mit.edu	37	chr1	245530624	245530624	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caccagtacctggatggcacCtggtccctgtcgagaaccaa	10	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:245530624C>A	ENST00000407071.2	+	3	1394	c.954C>A	c.(952-954)acC>acA	p.T318T	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	318					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.T318T(1)|p.T118T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TGGATGGCACCTGGTCCCTGT	0.597																																																2	Substitution - coding silent(2)	large_intestine(2)	1											21	27	25					1																	245530624		2120	4230	6350	243597247	SO:0001819	synonymous_variant	55083			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.954C>A	1.37:g.245530624C>A			243597247	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																				0.597	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245530624	C	A	245530624	2	1	77	1	0	0	0	0	0	0	0	1	8316	668	24	2		2	KIF26B	1	245530624	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2168250	245530624	3719997	114	21850										
KIF26B	55083	broad.mit.edu	37	chr1	245847548	245847548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggcagagagagcaagctcGccatgttgctgcgggagtct	15	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:245847548G>A	ENST00000407071.2	+	11	2712	c.2272G>A	c.(2272-2274)Gcc>Acc	p.A758T	KIF26B_ENST00000366518.4_Missense_Mutation_p.A377T	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	758	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.A758T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GAGCAAGCTCGCCATGTTGCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											67	74	71					1																	245847548		2085	4195	6280	243914171	SO:0001583	missense	55083			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2272G>A	1.37:g.245847548G>A	ENSP00000385545:p.Ala758Thr		243914171	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	8.722	0.914672	0.17907	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.03580	3.88;3.88	5.74	2.17	0.27698	Kinesin, motor domain (4);	.	.	.	.	T	0.00524	0.0017	N	0.00004	-3.37	0.27352	N	0.956227	B;B	0.09022	0.001;0.002	B;B	0.08055	0.001;0.003	T	0.42241	-0.9463	9	0.02654	T	1	.	9.4028	0.38442	0.8001:0.0:0.1999:0.0	.	377;758	B7WPD9;Q2KJY2	.;KI26B_HUMAN	T	758;377;374	ENSP00000385545:A758T;ENSP00000355475:A377T	ENSP00000355475:A377T	A	+	1	0	KIF26B	243914171	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	6.195000	0.72088	0.113000	0.18004	-0.793000	0.03317	GCC		0.612	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245847548	G	A	245847548	3	1	77	1	0	0	0	0	1	0	0	0	8316	1087	38	1	2314	1	KIF26B	1	245847548	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	316924	245847548	3403073	115	21851										
OR2L13	284521	broad.mit.edu	37	chr1	248263047	248263047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcctacgaccgttatttgGccatctgccactctctctat	7	14	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:248263047G>A	ENST00000358120.2	+	2	515	c.370G>A	c.(370-372)Gcc>Acc	p.A124T	OR2L13_ENST00000366478.2_Missense_Mutation_p.A124T			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A124T(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			CCGTTATTTGGCCATCTGCCA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											212	201	205					1																	248263047		2203	4300	6503	246329670	SO:0001583	missense	284521			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.370G>A	1.37:g.248263047G>A	ENSP00000350836:p.Ala124Thr		246329670	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405363	0.62288	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00912	5.55;5.55	4.13	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000377	T	0.05410	0.0143	H	0.94582	3.555	0.32534	N	0.534599	D	0.53745	0.962	P	0.49597	0.616	T	0.08868	-1.0701	10	0.87932	D	0	.	16.1615	0.81721	0.0:0.0:1.0:0.0	.	124	Q8N349	OR2LD_HUMAN	T	124	ENSP00000355434:A124T;ENSP00000350836:A124T	ENSP00000350836:A124T	A	+	1	0	OR2L13	246329670	1.000000	0.71417	0.921000	0.36526	0.324000	0.28378	4.405000	0.59741	2.091000	0.63221	0.650000	0.86243	GCC		0.502	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		A	248263047	G	A	248263047	3	1	77	1	0	0	0	0	1	0	0	0	11037	1203	42	3	372	3	OR2L13	1	248263047	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2415499	248263047	987574	116	21852										
OR2T27	403239	broad.mit.edu	37	chr1	248814155	248814155	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caaacccagaaggataaagtCggcatacacggaataattgc	9	9	0	1	rs543746159	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr1:248814155C>T	ENST00000344889.3	-	1	30	c.31G>A	c.(31-33)Gac>Aac	p.D11N		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D11Y(2)|p.D11N(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGGATAAAGTCGGCATACACG	0.443													C|||	2	0.000399361	0.0015	0	5008	,	,		28258	0		0	False		,,,				2504	0															3	Substitution - Missense(3)	lung(2)|large_intestine(1)	1																																								246880778	SO:0001583	missense	403239				CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"GPCR / Class A : Olfactory receptors"	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.31G>A	1.37:g.248814155C>T	ENSP00000342008:p.Asp11Asn		246880778		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	4.302	0.055400	0.08291	.	.	ENSG00000187701	ENST00000344889	T	0.03094	4.05	3.3	2.37	0.29283	.	0.000000	0.41938	D	0.000792	T	0.05593	0.0147	M	0.67397	2.05	0.09310	N	1	B	0.27559	0.181	B	0.26969	0.075	T	0.21449	-1.0245	10	0.52906	T	0.07	.	9.6882	0.40111	0.0:0.8903:0.0:0.1097	.	11	Q8NH04	O2T27_HUMAN	N	11	ENSP00000342008:D11N	ENSP00000342008:D11N	D	-	1	0	OR2T27	246880778	0.012000	0.17670	0.076000	0.20297	0.033000	0.12548	1.381000	0.34362	0.724000	0.32296	0.194000	0.17425	GAC		0.443	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		T	248814155	C	T	248814155	3	4	77	1	0	0	0	0	1	0	0	0	11052	884	31	1	925	1	OR2T27	1	248814155	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	551108	248814155	436466	117	21853										
PXDN	7837	broad.mit.edu	37	chr2	1667493	1667493	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagagattctaagtgttcccGatgacaggaccaggtgccgc	12	11	1	2	rs548513750		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:1667493G>A	ENST00000252804.4	-	12	1501	c.1451C>T	c.(1450-1452)tCg>tTg	p.S484L	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	484	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.S484L(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AAGTGTTCCCGATGACAGGAC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											67	75	73					2																	1667493		2041	4166	6207	1646500	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1451C>T	2.37:g.1667493G>A	ENSP00000252804:p.Ser484Leu		1646500	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.79|16.79	3.220621|3.220621	0.58560|0.58560	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000433670|ENST00000252804	.|T	.|0.68181	.|-0.31	5.79|5.79	5.79|5.79	0.91817|0.91817	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.141323	.|0.48767	.|D	.|0.000161	T|T	0.76550|0.76550	0.4003|0.4003	L|L	0.55481|0.55481	1.735|1.735	0.50039|0.50039	D|D	0.999842|0.999842	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.63033	.|0.91;0.909	T|T	0.76713|0.76713	-0.2858|-0.2858	5|10	.|0.54805	.|T	.|0.06	-25.0738|-25.0738	15.5016|15.5016	0.75703|0.75703	0.0:0.1377:0.8623:0.0|0.0:0.1377:0.8623:0.0	.|.	.|484;484	.|Q92626-2;Q92626	.|.;PXDN_HUMAN	W|L	480|484	.|ENSP00000252804:S484L	.|ENSP00000252804:S484L	R|S	-|-	1|2	2|0	PXDN|PXDN	1646500|1646500	0.997000|0.997000	0.39634|0.39634	0.132000|0.132000	0.22025|0.22025	0.115000|0.115000	0.19883|0.19883	6.166000|6.166000	0.71896|0.71896	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.617	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1667493	G	A	1667493	3	1	77	1	0	0	0	0	1	0	0	0	12884	1059	37	1	3036	1	PXDN	2	1667493	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		1667493	241531880	118	21854										
MYT1L	23040	broad.mit.edu	37	chr2	1914027	1914027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtacctgagcacgcggtccGaggcctggctggacttggac	16	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:1914027G>A	ENST00000399161.2	-	13	2549	c.1802C>T	c.(1801-1803)tCg>tTg	p.S601L	MYT1L_ENST00000428368.2_Missense_Mutation_p.S599L	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	601					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S601L(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CACGCGGTCCGAGGCCTGGCT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											54	63	60					2																	1914027		2095	4209	6304	1893034	SO:0001583	missense	23040			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1802C>T	2.37:g.1914027G>A	ENSP00000382114:p.Ser601Leu		1893034	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	G	36	5.735631	0.96865	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.50001	0.76;0.76	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.63488	0.915;0.79	T	0.64795	-0.6323	10	0.59425	D	0.04	-13.8321	19.1056	0.93293	0.0:0.0:1.0:0.0	.	601;599	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	L	601;547;599	ENSP00000382114:S601L;ENSP00000396103:S599L	ENSP00000295067:S547L	S	-	2	0	MYT1L	1893034	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	9.464000	0.97655	2.600000	0.87896	0.655000	0.94253	TCG		0.632	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1914027	G	A	1914027	3	1	77	1	0	0	0	0	1	0	0	0	10137	1059	37	1	1810	1	MYT1L	2	1914027	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	246534	1914027	241285346	119	21855										
COLEC11	78989	broad.mit.edu	37	chr2	3691412	3691412	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgtcctgccagggccgcGggggcacgctgagcatgccc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:3691412delG	ENST00000349077.4	+	7	623	c.520delG	c.(520-522)gggfs	p.G175fs	COLEC11_ENST00000402794.1_Frame_Shift_Del_p.G125fs|COLEC11_ENST00000236693.7_Frame_Shift_Del_p.G172fs|COLEC11_ENST00000382062.2_Frame_Shift_Del_p.G151fs|COLEC11_ENST00000404205.1_Frame_Shift_Del_p.G101fs|COLEC11_ENST00000402922.1_Frame_Shift_Del_p.G125fs|COLEC11_ENST00000418971.2_Frame_Shift_Del_p.G189fs|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_Frame_Shift_Del_p.G149fs	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	175	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.G189fs*3(1)|p.G172fs*3(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		CCAGGGCCGCGGGGGCACGCT	0.667																																																2	Deletion - Frameshift(2)	large_intestine(2)	2											32	34	33					2																	3691412		2201	4298	6499	3669287	SO:0001589	frameshift_variant	78989			BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"Collectins"	17213	protein-coding gene	gene with protein product	"Collectin K1"	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.520delG	2.37:g.3691412delG	ENSP00000339168:p.Gly175fs		3669287	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Frame_Shift_Del	DEL	ENST00000349077.4	37	CCDS1649.1																																																																																				0.667	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		-	3691412	G	-	3691412	7	5	77	1	0	1	0	1	0	0	0	0	3717	1116	39	0	625	0	COLEC11	2	3691412	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1777385	3691412	239507961	120	21856										
ODC1	4953	broad.mit.edu	37	chr2	10582260	10582260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctcactccagagtctgacGgaaagtatttgtccaacgct	8	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:10582260G>A	ENST00000234111.4	-	9	1301	c.791C>T	c.(790-792)cCg>cTg	p.P264L	ODC1_ENST00000446285.1_5'Flank|ODC1_ENST00000405333.1_Missense_Mutation_p.P264L	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	264					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)	p.P264L(1)		NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	AGAGTCTGACGGAAAGTATTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											71	73	72					2																	10582260		2203	4300	6503	10499711	SO:0001583	missense	4953				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.791C>T	2.37:g.10582260G>A	ENSP00000234111:p.Pro264Leu		10499711	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	37	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933360	0.73442	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000537630	T;T	0.52057	0.68;0.68	5.95	5.95	0.96441	Orn/DAP/Arg decarboxylase 2, N-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (1);	0.049431	0.85682	D	0.000000	T	0.68229	0.2978	M	0.87758	2.905	0.80722	D	1	D	0.55605	0.972	P	0.52189	0.692	T	0.73477	-0.3970	10	0.72032	D	0.01	.	20.3747	0.98911	0.0:0.0:1.0:0.0	.	264	P11926	DCOR_HUMAN	L	264;264;135	ENSP00000234111:P264L;ENSP00000385333:P264L	ENSP00000234111:P264L	P	-	2	0	ODC1	10499711	1.000000	0.71417	0.391000	0.26233	0.141000	0.21300	9.807000	0.99171	2.817000	0.96982	0.563000	0.77884	CCG		0.438	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			A	10582260	G	A	10582260	3	1	77	1	0	0	0	0	1	0	0	0	10856	1116	39	1	610	1	ODC1	2	10582260	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6890848	10582260	232617113	121	21857										
WDR35	57539	broad.mit.edu	37	chr2	20169327	20169327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acctccttcccaagatagtgCagatatttcctttccaggaa	6	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:20169327C>T	ENST00000345530.3	-	9	1037	c.922G>A	c.(922-924)Gca>Aca	p.A308T	WDR35_ENST00000416055.2_5'UTR|WDR35_ENST00000281405.4_Missense_Mutation_p.A308T	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	308					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.A308T(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAGATAGTGCAGATATTTCC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	80	79					2																	20169327		2203	4300	6503	20032808	SO:0001583	missense	57539			AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.922G>A	2.37:g.20169327C>T	ENSP00000314444:p.Ala308Thr		20032808	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100893	0.56183	.	.	ENSG00000118965	ENST00000345530;ENST00000281405	T;T	0.63096	-0.02;-0.02	4.58	3.67	0.42095	.	0.116795	0.56097	D	0.000027	T	0.59418	0.2192	M	0.69823	2.125	0.80722	D	1	B;B	0.26483	0.15;0.034	B;B	0.34779	0.189;0.081	T	0.51466	-0.8702	10	0.06494	T	0.89	-8.2294	12.0686	0.53603	0.3201:0.6799:0.0:0.0	.	308;308	Q9P2L0-2;Q9P2L0	.;WDR35_HUMAN	T	308	ENSP00000314444:A308T;ENSP00000281405:A308T	ENSP00000281405:A308T	A	-	1	0	WDR35	20032808	1.000000	0.71417	0.963000	0.40424	0.976000	0.68499	4.954000	0.63631	0.846000	0.35142	0.460000	0.39030	GCA		0.323	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		T	20169327	C	T	20169327	3	4	77	1	0	0	0	0	1	0	0	0	17329	710	25	3	2703	3	WDR35	2	20169327	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	9587067	20169327	223030046	122	21858										
APOB	338	broad.mit.edu	37	chr2	21256233	21256233	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatcactgaggcctctcagCtcagtaaccagcttattgaa	7	12	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:21256233C>A	ENST00000233242.1	-	9	1189	c.1062G>T	c.(1060-1062)gaG>gaT	p.E354D	APOB_ENST00000399256.4_Missense_Mutation_p.E354D	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	354	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.E354D(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCTCTCAGCTCAGTAACCA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	2											122	115	118					2																	21256233		2203	4300	6503	21109738	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1062G>T	2.37:g.21256233C>A	ENSP00000233242:p.Glu354Asp		21109738	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	9.636	1.137710	0.21123	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.40756	1.02;1.02	5.53	-0.818	0.10833	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.323197	0.26369	N	0.024766	T	0.37732	0.1014	M	0.67953	2.075	0.28494	N	0.914355	P	0.43578	0.811	P	0.45660	0.489	T	0.36040	-0.9764	10	0.16420	T	0.52	.	6.8045	0.23770	0.0:0.3966:0.2954:0.3081	.	354	P04114	APOB_HUMAN	D	354	ENSP00000233242:E354D;ENSP00000382200:E354D	ENSP00000233242:E354D	E	-	3	2	APOB	21109738	0.118000	0.22208	0.853000	0.33588	0.163000	0.22366	-0.598000	0.05706	0.100000	0.17581	-0.137000	0.14449	GAG		0.428	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21256233	C	A	21256233	3	1	77	1	0	0	0	0	1	0	0	0	785	796	28	2	12713	2	APOB	2	21256233	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1086906	21256233	221943140	123	21859										
C2orf44	80304	broad.mit.edu	37	chr2	24261373	24261373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggaatagtgacttttctcGtcatggtaactgccttctta	8	9	3	1	rs201871067	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:24261373G>A	ENST00000295148.4	-	2	1049	c.992C>T	c.(991-993)aCg>aTg	p.T331M	C2orf44_ENST00000406895.3_Missense_Mutation_p.T331M	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	331								p.T331M(1)	C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACTTTTCTCGTCATGGTAAC	0.393			T	ALK	NSCLC								G|||	3	0.000599042	8e-04	0	5008	,	,		22453	0		0	False		,,,				2504	0.002						Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	1	Substitution - Missense(1)	large_intestine(1)	2											62	58	59					2																	24261373		2203	4300	6503	24114877	SO:0001583	missense	80304			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.992C>T	2.37:g.24261373G>A	ENSP00000295148:p.Thr331Met		24114877	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	13.55	2.270051	0.40194	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.52057	0.68;0.68	5.38	2.54	0.30619	WD40/YVTN repeat-like-containing domain (1);	0.241522	0.48286	D	0.000193	T	0.59715	0.2214	M	0.68593	2.085	0.47621	D	0.999472	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.58053	-0.7704	10	0.87932	D	0	-4.0166	6.861	0.24067	0.0696:0.1291:0.6675:0.1338	.	331;331	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	M	331	ENSP00000295148:T331M;ENSP00000385816:T331M	ENSP00000295148:T331M	T	-	2	0	C2orf44	24114877	1.000000	0.71417	0.002000	0.10522	0.183000	0.23260	3.731000	0.55013	0.321000	0.23259	-0.211000	0.12701	ACG		0.393	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		A	24261373	G	A	24261373	3	1	77	1	0	0	0	0	1	0	0	0	2174	1145	40	1	1185	1	C2orf44	2	24261373	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3005140	24261373	218938000	124	21860										
ADCY3	109	broad.mit.edu	37	chr2	25141365	25141365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagcccaccgtgtcactagcCgcgtgggcacgcgcgaagtt	13	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:25141365C>T	ENST00000260600.5	-	1	1343	c.492G>A	c.(490-492)gcG>gcA	p.A164A		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	164					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.A164A(1)		NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TGTCACTAGCCGCGTGGGCAC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	2											75	81	79					2																	25141365		2203	4300	6503	24994869	SO:0001819	synonymous_variant	109			AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.492G>A	2.37:g.25141365C>T			24994869	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																				0.622	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			T	25141365	C	T	25141365	2	4	77	1	0	0	0	0	0	0	0	1	295	639	23	1		1	ADCY3	2	25141365	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	879992	25141365	218058008	125	21861										
DNMT3A	1788	broad.mit.edu	37	chr2	25497823	25497823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcctcacctcccttttccagCgtgccagccactcgtcccgc	7	21	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:25497823C>T	ENST00000264709.3	-	6	963	c.626G>A	c.(625-627)cGc>cAc	p.R209H	DNMT3A_ENST00000321117.5_Missense_Mutation_p.R209H	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	209	Interaction with DNMT1 and DNMT3B.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R209H(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTTTTCCAGCGTGCCAGCCA	0.642			"Mis, F, N, S"		AML																																		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Missense(1)	large_intestine(1)	2											44	43	43					2																	25497823		2203	4300	6503	25351327	SO:0001583	missense	1788				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.626G>A	2.37:g.25497823C>T	ENSP00000264709:p.Arg209His		25351327	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.441027	0.83993	.	.	ENSG00000119772	ENST00000321117;ENST00000264709	D;D	0.93247	-3.19;-3.19	5.19	5.19	0.71726	.	0.202505	0.30781	N	0.008889	D	0.89712	0.6794	N	0.24115	0.695	0.80722	D	1	D	0.61080	0.989	P	0.45343	0.477	D	0.91157	0.4958	10	0.59425	D	0.04	-8.3274	16.2234	0.82274	0.0:1.0:0.0:0.0	.	209	Q9Y6K1	DNM3A_HUMAN	H	209	ENSP00000324375:R209H;ENSP00000264709:R209H	ENSP00000264709:R209H	R	-	2	0	DNMT3A	25351327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.943000	0.56621	2.428000	0.82296	0.561000	0.74099	CGC		0.642	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25497823	C	T	25497823	3	4	77	1	0	0	0	0	1	0	0	0	4687	768	27	1	2264	1	DNMT3A	2	25497823	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	356458	25497823	217701550	126	21862										
CAD	790	broad.mit.edu	37	chr2	27445107	27445107	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagttgcgggaacaggggtCtctgctggggaagctggtcc	18	8	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:27445107C>A	ENST00000403525.1	+	4	542	c.398C>A	c.(397-399)tCt>tAt	p.S133Y	CAD_ENST00000264705.4_Missense_Mutation_p.S133Y			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.S133Y(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAACAGGGGTCTCTGCTGGGG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	2											78	74	75					2																	27445107		2203	4300	6503	27298611	SO:0001583	missense	790			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.398C>A	2.37:g.27445107C>A	ENSP00000384510:p.Ser133Tyr		27298611	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	C	24.2	4.510612	0.85389	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.94537	-3.45;-3.45	5.0	5.0	0.66597	Carbamoyl-phosphate synthase, small subunit, N-terminal (3);	0.068089	0.64402	D	0.000013	D	0.96784	0.8950	M	0.81682	2.555	0.48762	D	0.9997	D;P	0.57571	0.98;0.938	P;B	0.61592	0.891;0.382	D	0.97335	0.9953	10	0.87932	D	0	-13.3657	16.124	0.81380	0.0:1.0:0.0:0.0	.	133;133	F8VPD4;P27708	.;PYR1_HUMAN	Y	133	ENSP00000264705:S133Y;ENSP00000384510:S133Y	ENSP00000264705:S133Y	S	+	2	0	CAD	27298611	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.073000	0.76784	2.480000	0.83734	0.491000	0.48974	TCT		0.527	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27445107	C	A	27445107	3	1	77	1	0	0	0	0	1	0	0	0	2571	913	32	2	412	2	CAD	2	27445107	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1947284	27445107	215754266	127	21863										
EHD3	30845	broad.mit.edu	37	chr2	31489460	31489460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atggcatgctggacgacgacGagtttgcactggccaaccac	12	12	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:31489460G>A	ENST00000322054.5	+	6	1783	c.1498G>A	c.(1498-1500)Gag>Aag	p.E500K	EHD3_ENST00000541626.1_3'UTR	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	500	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.E500K(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GGACGACGACGAGTTTGCACT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	2											108	97	101					2																	31489460		2203	4300	6503	31342964	SO:0001583	missense	30845			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"EF-hand domain containing"	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.1498G>A	2.37:g.31489460G>A	ENSP00000327116:p.Glu500Lys		31342964	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	33	5.261563	0.95368	.	.	ENSG00000013016	ENST00000322054	T	0.60040	0.22	5.55	5.55	0.83447	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.86422	0.5929	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91538	0.5247	10	0.87932	D	0	-47.3755	19.4915	0.95052	0.0:0.0:1.0:0.0	.	500	Q9NZN3	EHD3_HUMAN	K	500	ENSP00000327116:E500K	ENSP00000327116:E500K	E	+	1	0	EHD3	31342964	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	9.869000	0.99810	2.619000	0.88677	0.462000	0.41574	GAG		0.597	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600		A	31489460	G	A	31489460	3	1	77	1	0	0	0	0	1	0	0	0	4990	1059	37	1	1520	1	EHD3	2	31489460	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4044353	31489460	211709913	128	21864										
CDC42EP3	10602	broad.mit.edu	37	chr2	37873218	37873218	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagaaccgctggagccccaCgaggtgtctccctggtggac	14	14	1	1	rs544069972	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:37873218C>T	ENST00000295324.3	-	2	1513	c.513G>A	c.(511-513)tcG>tcA	p.S171S	AC006369.2_ENST00000419425.1_RNA	NM_001270436.1|NM_001270437.1|NM_001270438.1|NM_006449.4	NP_001257365.1|NP_001257366.1|NP_001257367.1|NP_006440.2	Q9UKI2	BORG2_HUMAN	CDC42 effector protein (Rho GTPase binding) 3	171					regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	cytoskeletal regulatory protein binding (GO:0005519)	p.S171S(1)		endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	11		all_hematologic(82;0.172)				TGGAGCCCCACGAGGTGTCTC	0.597													c|||	2	0.000399361	0.0015	0	5008	,	,		17336	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											72	78	76					2																	37873218		2203	4300	6503	37726722	SO:0001819	synonymous_variant	10602			AF094521	CCDS1791.1	2p21	2008-05-21			ENSG00000163171	ENSG00000163171			16943	protein-coding gene	gene with protein product		606133				9535835, 11035016	Standard	NM_001270436		Approved	CEP3, UB1, BORG2	uc031rnz.1	Q9UKI2	OTTHUMG00000100971	ENST00000295324.3:c.513G>A	2.37:g.37873218C>T			37726722	B2R8S0|O95353|Q9UQJ0	Silent	SNP	ENST00000295324.3	37	CCDS1791.1																																																																																				0.597	CDC42EP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218581.3	NM_006449		T	37873218	C	T	37873218	2	4	77	1	0	0	0	0	0	0	0	1	3083	523	19	1		1	CDC42EP3	2	37873218	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6383758	37873218	205326155	129	21865										
NRXN1	9378	broad.mit.edu	37	chr2	50724784	50724784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggacagaagaaagataccGtcgttctgtgatgatgccag	14	7	1	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:50724784G>A	ENST00000406316.2	-	14	4042	c.2566C>T	c.(2566-2568)Cgg>Tgg	p.R856W	NRXN1_ENST00000406859.3_Missense_Mutation_p.R856W|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000404971.1_Missense_Mutation_p.R896W|NRXN1_ENST00000402717.3_Missense_Mutation_p.R848W|NRXN1_ENST00000401710.1_5'Flank|NRXN1_ENST00000405472.3_Missense_Mutation_p.R848W|NRXN1_ENST00000401669.2_Missense_Mutation_p.R856W	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	856	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.R856W(1)|p.R897W(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GAAAGATACCGTCGTTCTGTG	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	2											92	85	87					2																	50724784		1943	4141	6084	50578288	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2566C>T	2.37:g.50724784G>A	ENSP00000384311:p.Arg856Trp		50578288	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358195	0.82243	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.97	4.13	0.48395	.	0.000000	0.85682	D	0.000000	D	0.88437	0.6436	M	0.83012	2.62	0.45097	D	0.998113	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.995	D	0.89273	0.3606	10	0.59425	D	0.04	.	15.3392	0.74282	0.0:0.0:0.7447:0.2553	.	896;856;848	Q9ULB1-3;F8WB18;A7E294	.;.;.	W	896;856;848;856;897;848;856	ENSP00000385142:R896W;ENSP00000384311:R856W;ENSP00000434015:R848W;ENSP00000385017:R856W;ENSP00000385434:R848W;ENSP00000385681:R856W	ENSP00000385017:R856W	R	-	1	2	NRXN1	50578288	1.000000	0.71417	0.079000	0.20413	0.990000	0.78478	6.400000	0.73252	0.813000	0.34350	0.561000	0.74099	CGG		0.403	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50724784	G	A	50724784	3	1	77	1	0	0	0	0	1	0	0	0	10696	1144	40	1	2260	1	NRXN1	2	50724784	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	12851566	50724784	192474589	130	21866										
PSME4	23198	broad.mit.edu	37	chr2	54159016	54159016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aattcaggtctcatgagtgcAagattctgcaaagcctgggc	11	9	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:54159016A>G	ENST00000404125.1	-	10	1327	c.1272T>C	c.(1270-1272)ctT>ctC	p.L424L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	424					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.L310L(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TCATGAGTGCAAGATTCTGCA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											83	80	81					2																	54159016		2203	4300	6503	54012520	SO:0001819	synonymous_variant	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.1272T>C	2.37:g.54159016A>G			54012520	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																				0.443	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54159016	A	G	54159016	2	3	77	1	0	0	0	0	0	0	0	1	12743	117	5	4		4	PSME4	2	54159016	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	3434232	54159016	189040357	131	21867										
SMEK2	57223	broad.mit.edu	37	chr2	55825686	55825686	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taccctgtaagtctgatgtaTtttttgccttagttcagagt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:55825686delT	ENST00000345102.5	-	4	1088	c.787delA	c.(787-789)atafs	p.I263fs	SMEK2_ENST00000407823.3_Frame_Shift_Del_p.I263fs|SMEK2_ENST00000272313.5_Frame_Shift_Del_p.I263fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	263					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)		p.I263fs*40(1)		kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GTCTGATGTATTTTTTGCCTT	0.368																																																1	Deletion - Frameshift(1)	large_intestine(1)	2											104	102	103					2																	55825686		2203	4300	6503	55679190	SO:0001589	frameshift_variant	57223			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.787delA	2.37:g.55825686delT	ENSP00000339769:p.Ile263fs		55679190	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	37	CCDS46289.1																																																																																				0.368	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		-	55825686	T	-	55825686	7	5	77	1	0	1	0	1	0	0	0	0	14831	1493	52	0	1818	0	SMEK2	2	55825686	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	1666670	55825686	187373687	132	21868										
PAPOLG	64895	broad.mit.edu	37	chr2	60987381	60987381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acacacagaaattaattgacGccatgaaaccatttggagtg	8	8	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:60987381G>A	ENST00000238714.3	+	2	379	c.130G>A	c.(130-132)Gcc>Acc	p.A44T		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	44					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.A44T(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			ATTAATTGACGCCATGAAACC	0.348																																					GBM(183;1497 2932 21839 46797)											2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	2											88	86	87					2																	60987381		2203	4300	6503	60840885	SO:0001583	missense	64895			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.130G>A	2.37:g.60987381G>A	ENSP00000238714:p.Ala44Thr		60840885	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413785	0.25465	.	.	ENSG00000115421	ENST00000238714	.	.	.	5.74	5.74	0.90152	Poly(A) polymerase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.36853	0.0982	N	0.05467	-0.045	0.80722	D	1	B	0.23650	0.089	B	0.23150	0.044	T	0.36578	-0.9742	9	0.02654	T	1	-0.8582	19.5165	0.95167	0.0:0.0:1.0:0.0	.	44	Q9BWT3	PAPOG_HUMAN	T	44	.	ENSP00000238714:A44T	A	+	1	0	PAPOLG	60840885	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.605000	0.74155	2.716000	0.92895	0.563000	0.77884	GCC		0.348	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		A	60987381	G	A	60987381	3	1	77	1	0	0	0	0	1	0	0	0	11462	1087	38	1	136	1	PAPOLG	2	60987381	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5161695	60987381	182211992	133	21869										
AFTPH	54812	broad.mit.edu	37	chr2	64819127	64819127	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgttgatgttcccagccacGttaacaccttccacaagctc	7	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:64819127G>A	ENST00000422803.1	+	10	3086	c.2772G>A	c.(2770-2772)acG>acA	p.T924T	AFTPH_ENST00000409933.1_Silent_p.T923T|AFTPH_ENST00000238856.4_Silent_p.T896T|AFTPH_ENST00000409183.1_Silent_p.T555T|AFTPH_ENST00000238855.7_Silent_p.T923T			Q6ULP2	AFTIN_HUMAN	aftiphilin	924					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)	p.T896T(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						TCCCAGCCACGTTAACACCTT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	2											187	166	173					2																	64819127		2203	4300	6503	64672631	SO:0001819	synonymous_variant	54812			AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2772G>A	2.37:g.64819127G>A			64672631	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Silent	SNP	ENST00000422803.1	37																																																																																					0.443	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		A	64819127	G	A	64819127	2	1	77	1	0	0	0	0	0	0	0	1	364	1132	40	1		1	AFTPH	2	64819127	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3831746	64819127	178380246	134	21870										
SERTAD2	9792	broad.mit.edu	37	chr2	64863308	64863308	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgtcaggaaacccgtggacGtcgttatttcaaaattccca	8	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:64863308G>A	ENST00000313349.3	-	2	995	c.698C>T	c.(697-699)aCg>aTg	p.T233M	SERTAD2_ENST00000476805.2_5'Flank	NM_014755.2	NP_055570.1	Q14140	SRTD2_HUMAN	SERTA domain containing 2	233					negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.T233M(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|skin(1)	12						ACCCGTGGACGTCGTTATTTC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											97	92	94					2																	64863308		2203	4300	6503	64716812	SO:0001583	missense	9792			D50917	CCDS33210.1	2p15	2007-05-01			ENSG00000179833	ENSG00000179833			30784	protein-coding gene	gene with protein product	"transcriptional regulator interacting with the PHS-bromodomain 2"					8590280, 11331592	Standard	NM_014755		Approved	TRIP-Br2, KIAA0127, Sei-2	uc002sde.2	Q14140	OTTHUMG00000152678	ENST00000313349.3:c.698C>T	2.37:g.64863308G>A	ENSP00000326933:p.Thr233Met		64716812	Q53TS2	Missense_Mutation	SNP	ENST00000313349.3	37	CCDS33210.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145917	0.57044	.	.	ENSG00000179833	ENST00000313349	.	.	.	6.08	6.08	0.98989	.	0.095705	0.64402	D	0.000001	T	0.64692	0.2621	L	0.48642	1.525	0.58432	D	0.999996	D	0.63046	0.992	P	0.50791	0.65	T	0.65903	-0.6055	9	0.87932	D	0	-12.262	20.6634	0.99662	0.0:0.0:1.0:0.0	.	233	Q14140	SRTD2_HUMAN	M	233	.	ENSP00000326933:T233M	T	-	2	0	SERTAD2	64716812	1.000000	0.71417	0.860000	0.33809	0.347000	0.29111	6.628000	0.74262	2.894000	0.99253	0.655000	0.94253	ACG		0.517	SERTAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327322.2	NM_014755		A	64863308	G	A	64863308	3	1	77	1	0	0	0	0	1	0	0	0	14158	1145	40	1	250	1	SERTAD2	2	64863308	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	44181	64863308	178336065	135	21871										
SLC1A4	6509	broad.mit.edu	37	chr2	65243772	65243772	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agattcctcctgggcctcctCgccccatttgcgacagcatt	8	16	0	1	rs189823702	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:65243772C>T	ENST00000234256.3	+	5	1242	c.999C>T	c.(997-999)ctC>ctT	p.L333L	SLC1A4_ENST00000531327.1_Intron	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	333					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)	p.L333L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	TGGGCCTCCTCGCCCCATTTG	0.473													C|||	2	0.000399361	0	0.0014	5008	,	,		19640	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						C	,	1,4405	2.1+/-5.4	0,1,2202	92	92	92		,999	1	0.9	2		92	3,8597	2.2+/-6.3	0,3,4297	no	intron,coding-synonymous	SLC1A4	NM_001193493.1,NM_003038.4	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	,333/533	65243772	4,13002	2203	4300	6503	65097276	SO:0001819	synonymous_variant	6509				CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"Solute carriers"	10942	protein-coding gene	gene with protein product	"alanine/serine/cysteine/threonine transporter"	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.999C>T	2.37:g.65243772C>T			65097276	B7Z3C0|D6W5F0	Silent	SNP	ENST00000234256.3	37	CCDS1879.1																																																																																				0.473	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038		T	65243772	C	T	65243772	2	4	77	1	0	0	0	0	0	0	0	1	14471	871	31	1		1	SLC1A4	2	65243772	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	380464	65243772	177955601	136	21872										
ANTXR1	84168	broad.mit.edu	37	chr2	69300171	69300171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagggtacaggacagccagcGtcatcattgctttgactgat	11	10	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:69300171G>A	ENST00000303714.4	+	6	752	c.430G>A	c.(430-432)Gtc>Atc	p.V144I	ANTXR1_ENST00000409829.3_Missense_Mutation_p.V144I|ANTXR1_ENST00000409349.3_Missense_Mutation_p.V144I	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	144	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)	p.V144I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						GACAGCCAGCGTCATCATTGC	0.483									Familial Infantile Hemangioma																																							1	Substitution - Missense(1)	large_intestine(1)	2											245	223	231					2																	69300171		2203	4300	6503	69153675	SO:0001583	missense	84168	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.430G>A	2.37:g.69300171G>A	ENSP00000301945:p.Val144Ile		69153675	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Missense_Mutation	SNP	ENST00000303714.4	37	CCDS1892.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920933	0.52653	.	.	ENSG00000169604	ENST00000303714;ENST00000409829;ENST00000409349	D;D;D	0.85339	-1.97;-1.97;-1.97	6.06	6.06	0.98353	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	L	0.53780	1.695	0.51767	D	0.99993	D;B;D;D	0.89917	1.0;0.09;0.983;1.0	D;B;P;D	0.91635	0.999;0.17;0.882;0.996	D	0.85384	0.1121	10	0.14656	T	0.56	-32.7014	18.1147	0.89549	0.0:0.0:1.0:0.0	.	144;144;144;144	Q9H6X2;Q9H6X2-2;Q9H6X2-4;Q9H6X2-3	ANTR1_HUMAN;.;.;.	I	144	ENSP00000301945:V144I;ENSP00000387058:V144I;ENSP00000386494:V144I	ENSP00000301945:V144I	V	+	1	0	ANTXR1	69153675	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.175000	0.89684	2.882000	0.98803	0.655000	0.94253	GTC		0.483	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		A	69300171	G	A	69300171	3	1	77	1	0	0	0	0	1	0	0	0	711	1145	40	1	452	1	ANTXR1	2	69300171	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4056399	69300171	173899202	137	21873										
SNRNP27	11017	broad.mit.edu	37	chr2	70122329	70122329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggagccgctcgcgatccccGcaccgaagacgctcccggta	12	17	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:70122329G>A	ENST00000244227.3	+	2	563	c.138G>A	c.(136-138)ccG>ccA	p.P46P	SNRNP27_ENST00000409116.1_Silent_p.P46P	NM_006857.2	NP_006848.1	Q8WVK2	SNR27_HUMAN	small nuclear ribonucleoprotein 27kDa (U4/U6.U5)	46	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.P46P(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	11						CGCGATCCCCGCACCGAAGAC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	2											33	38	36					2																	70122329		2203	4300	6503	69975833	SO:0001819	synonymous_variant	11017			X76302	CCDS33219.1	2p14	2011-10-11			ENSG00000124380	ENSG00000124380			30240	protein-coding gene	gene with protein product	"nucleic acid binding protein RY 1"					7931148	Standard	NM_006857		Approved	RY1	uc002sfw.3	Q8WVK2	OTTHUMG00000152689	ENST00000244227.3:c.138G>A	2.37:g.70122329G>A			69975833	Q15410	Silent	SNP	ENST00000244227.3	37	CCDS33219.1																																																																																				0.557	SNRNP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327369.1	NM_006857		A	70122329	G	A	70122329	2	1	77	1	0	0	0	0	0	0	0	1	14891	1074	38	1		1	SNRNP27	2	70122329	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	822158	70122329	173077044	138	21874										
ADD2	119	broad.mit.edu	37	chr2	70923459	70923459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgatcttgcaccgcatgagcCgctcccctttggccaggttc	10	15	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:70923459C>T	ENST00000264436.4	-	5	836	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	ADD2_ENST00000355733.3_Missense_Mutation_p.R131Q|ADD2_ENST00000407644.2_Missense_Mutation_p.R131Q|ADD2_ENST00000413157.2_Missense_Mutation_p.R131Q|ADD2_ENST00000430656.1_Missense_Mutation_p.R147Q	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	131					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)	p.R131Q(1)		autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CCGCATGAGCCGCTCCCCTTT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	2											103	81	89					2																	70923459		2203	4300	6503	70776967	SO:0001583	missense	119			X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.392G>A	2.37:g.70923459C>T	ENSP00000264436:p.Arg131Gln		70776967	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479243	0.96307	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976	T;T;T;T;T;T;T;T	0.36699	1.97;1.97;1.97;1.83;1.97;1.97;1.97;1.24	5.12	4.25	0.50352	Class II aldolase/adducin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.56834	0.2012	M	0.72118	2.19	0.45554	D	0.998503	D;D;D;D;P;D	0.89917	0.995;0.971;0.999;1.0;0.945;0.999	P;P;D;D;B;D	0.79784	0.838;0.508;0.984;0.941;0.413;0.993	T	0.61292	-0.7092	10	0.87932	D	0	-23.7286	11.6733	0.51415	0.0:0.9139:0.0:0.0861	.	147;131;131;131;131;131	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	Q	131;131;131;131;131;131;131;131;147;131;131	ENSP00000264436:R131Q;ENSP00000384677:R131Q;ENSP00000347972:R131Q;ENSP00000430243:R131Q;ENSP00000388072:R131Q;ENSP00000398112:R147Q;ENSP00000412357:R131Q;ENSP00000412681:R131Q	ENSP00000264436:R131Q	R	-	2	0	ADD2	70776967	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.476000	0.45171	1.531000	0.49152	0.650000	0.86243	CGG		0.587	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		T	70923459	C	T	70923459	3	4	77	1	0	0	0	0	1	0	0	0	305	652	23	1	2017	1	ADD2	2	70923459	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	801130	70923459	172275914	139	21875										
CLEC4F	165530	broad.mit.edu	37	chr2	71036419	71036419	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctcttagttactgaggatcCagggacagggaggggtgtct	16	7	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:71036419C>A	ENST00000272367.2	-	7	1830	c.1754G>T	c.(1753-1755)tGg>tTg	p.W585L	CLEC4F_ENST00000426626.1_Intron	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	585	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.W585L(1)		endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						ACTGAGGATCCAGGGACAGGG	0.547																																					Colon(107;10 2157 6841 26035)											1	Substitution - Missense(1)	large_intestine(1)	2											70	66	67					2																	71036419		2203	4300	6503	70889927	SO:0001583	missense	165530			AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1754G>T	2.37:g.71036419C>A	ENSP00000272367:p.Trp585Leu		70889927	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.244901	0.22796	.	.	ENSG00000152672	ENST00000272367	T	0.01745	4.66	3.23	-3.32	0.04973	C-type lectin (2);	.	.	.	.	T	0.02156	0.0067	M	0.75777	2.31	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.46707	-0.9172	9	0.33940	T	0.23	.	0.495	0.00570	0.3919:0.2316:0.1647:0.2118	.	585	Q8N1N0	CLC4F_HUMAN	L	585	ENSP00000272367:W585L	ENSP00000272367:W585L	W	-	2	0	CLEC4F	70889927	0.000000	0.05858	0.000000	0.03702	0.717000	0.41224	-0.762000	0.04745	-0.878000	0.04007	0.305000	0.20034	TGG		0.547	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71036419	C	A	71036419	3	1	77	1	0	0	0	0	1	0	0	0	3522	595	21	2	19	2	CLEC4F	2	71036419	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	112960	71036419	172162954	140	21876										
CLEC4F	165530	broad.mit.edu	37	chr2	71043359	71043359	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctgtatctctctgctggcaTttttcatatgaccatttaag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:71043359delT	ENST00000272367.2	-	4	1230	c.1154delA	c.(1153-1155)aatfs	p.N385fs	CLEC4F_ENST00000426626.1_Frame_Shift_Del_p.N385fs	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	385					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.N385fs*9(1)		endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TCTGCTGGCATTTTTCATATG	0.423																																					Colon(107;10 2157 6841 26035)											1	Deletion - Frameshift(1)	large_intestine(1)	2											121	121	121					2																	71043359		2203	4300	6503	70896867	SO:0001589	frameshift_variant	165530			AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1154delA	2.37:g.71043359delT	ENSP00000272367:p.Asn385fs		70896867	A4QPA5	Frame_Shift_Del	DEL	ENST00000272367.2	37	CCDS1910.1																																																																																				0.423	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		-	71043359	T	-	71043359	7	5	77	1	0	1	0	1	0	0	0	0	3522	1493	52	0	631	0	CLEC4F	2	71043359	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	6940	71043359	172156014	141	21877										
DYSF	8291	broad.mit.edu	37	chr2	71797751	71797751	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggagtatagcatcaccatCcccccggagcggaagccgaa					rs368033221		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:71797751delC	ENST00000258104.3	+	29	3331	c.3054delC	c.(3052-3054)atcfs	p.I1018fs	DYSF_ENST00000410041.1_Frame_Shift_Del_p.I1036fs|DYSF_ENST00000409762.1_Frame_Shift_Del_p.I1035fs|DYSF_ENST00000429174.2_Frame_Shift_Del_p.I1018fs|DYSF_ENST00000413539.2_Frame_Shift_Del_p.I1049fs|DYSF_ENST00000409651.1_Frame_Shift_Del_p.I1050fs|DYSF_ENST00000409582.3_Frame_Shift_Del_p.I1035fs|DYSF_ENST00000394120.2_Frame_Shift_Del_p.I1019fs|DYSF_ENST00000410020.3_Frame_Shift_Del_p.I1036fs|DYSF_ENST00000409366.1_Frame_Shift_Del_p.I1019fs|DYSF_ENST00000409744.1_Frame_Shift_Del_p.I1005fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1018					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.P1020fs*37(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCATCACCATCCCCCCGGAGC	0.632																																																1	Deletion - Frameshift(1)	large_intestine(1)	2											45	46	46					2																	71797751		2201	4300	6501	71651259	SO:0001589	frameshift_variant	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3054delC	2.37:g.71797751delC	ENSP00000258104:p.Ile1018fs		71651259	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Frame_Shift_Del	DEL	ENST00000258104.3	37	CCDS1918.1																																																																																				0.632	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		-	71797751	C	-	71797751	7	5	77	1	0	1	0	1	0	0	0	0	4870	845	30	0	3360	0	DYSF	2	71797751	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	754392	71797751	171401622	142	21878										
TET3	200424	broad.mit.edu	37	chr2	74328943	74328943	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgggagctgcacgccaccacGccgcttaagaagcccaaccg	11	17	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:74328943G>A	ENST00000409262.3	+	9	4623	c.4623G>A	c.(4621-4623)acG>acA	p.T1541T		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1541					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.T1541T(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACGCCACCACGCCGCTTAAGA	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	2											26	31	29					2																	74328943		2070	4194	6264	74182451	SO:0001819	synonymous_variant	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.4623G>A	2.37:g.74328943G>A			74182451	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																				0.662	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			A	74328943	G	A	74328943	2	1	77	1	0	0	0	0	0	0	0	1	15810	1074	38	1		1	TET3	2	74328943	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2531192	74328943	168870430	143	21879										
CTNNA2	1496	broad.mit.edu	37	chr2	80801397	80801397	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatgcctctcgcctggtgtaTgatggcgttcgggacatcag	14	10	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:80801397T>C	ENST00000402739.4	+	12	1856	c.1851T>C	c.(1849-1851)taT>taC	p.Y617Y	CTNNA2_ENST00000466387.1_Silent_p.Y617Y|CTNNA2_ENST00000541047.1_Silent_p.Y617Y|AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000496558.1_Silent_p.Y617Y|CTNNA2_ENST00000343114.3_Silent_p.Y296Y|CTNNA2_ENST00000361291.4_Silent_p.Y651Y|CTNNA2_ENST00000540488.1_Silent_p.Y617Y|AC008067.2_ENST00000609950.1_RNA	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	617					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.D618D(1)|p.Y617Y(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GCCTGGTGTATGATGGCGTTC	0.512																																																2	Substitution - coding silent(2)	large_intestine(2)	2											173	165	168					2																	80801397		2145	4278	6423	80654908	SO:0001819	synonymous_variant	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1851T>C	2.37:g.80801397T>C			80654908	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																					0.512	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		C	80801397	T	C	80801397	2	2	77	1	0	0	0	0	0	0	0	1	4019	1471	51	4		4	CTNNA2	2	80801397	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	6472454	80801397	162397976	144	21880										
GGCX	2677	broad.mit.edu	37	chr2	85780434	85780434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggcagctcccagctgatggCgcagccctggcttctggcca	13	15	1	1	rs200774203		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:85780434C>T	ENST00000233838.4	-	8	1156	c.1076G>A	c.(1075-1077)cGc>cAc	p.R359H	GGCX_ENST00000473665.1_5'UTR|GGCX_ENST00000430215.3_Missense_Mutation_p.R302H	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	359					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)	p.R359H(1)		endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	CAGCTGATGGCGCAGCCCTGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	2											72	79	77					2																	85780434		2203	4300	6503	85633945	SO:0001583	missense	2677				CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1076G>A	2.37:g.85780434C>T	ENSP00000233838:p.Arg359His		85633945	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.961787	0.74016	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.92199	-2.99;-2.99	5.64	5.64	0.86602	.	0.233816	0.45606	D	0.000354	D	0.94722	0.8297	L	0.57536	1.79	0.41494	D	0.988243	D;D;D	0.76494	0.998;0.999;0.991	P;D;P	0.63877	0.883;0.919;0.86	D	0.94982	0.8126	10	0.66056	D	0.02	-9.4469	17.1941	0.86887	0.0:1.0:0.0:0.0	.	302;198;359	E9PEE1;B4DQW4;P38435	.;.;VKGC_HUMAN	H	359;302	ENSP00000233838:R359H;ENSP00000408045:R302H	ENSP00000233838:R359H	R	-	2	0	GGCX	85633945	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.176000	0.58269	2.657000	0.90304	0.655000	0.94253	CGC		0.577	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85780434	C	T	85780434	3	4	77	1	0	0	0	0	1	0	0	0	6376	768	27	1	1232	1	GGCX	2	85780434	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4979037	85780434	157418939	145	21881										
POLR1A	25885	broad.mit.edu	37	chr2	86302212	86302212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtcagaagctgcttggccaCggcctctcgctgggtcatgt	14	12	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:86302212C>T	ENST00000263857.6	-	12	1930	c.1552G>A	c.(1552-1554)Gtg>Atg	p.V518M	POLR1A_ENST00000409681.1_Missense_Mutation_p.V518M			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	518					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.V518M(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TGCTTGGCCACGGCCTCTCGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	2											32	36	35					2																	86302212		2034	4178	6212	86155723	SO:0001583	missense	25885			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1552G>A	2.37:g.86302212C>T	ENSP00000263857:p.Val518Met		86155723	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	14.50	2.554307	0.45487	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.78816	-1.21;-1.21	5.01	5.01	0.66863	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.056432	0.64402	D	0.000001	T	0.81819	0.4903	L	0.47016	1.485	0.53005	D	0.999962	D	0.76494	0.999	D	0.70016	0.967	T	0.80427	-0.1387	10	0.42905	T	0.14	-28.6344	9.8735	0.41189	0.0:0.8726:0.0:0.1274	.	518	O95602	RPA1_HUMAN	M	518	ENSP00000263857:V518M;ENSP00000386300:V518M	ENSP00000263857:V518M	V	-	1	0	POLR1A	86155723	0.993000	0.37304	0.994000	0.49952	0.782000	0.44232	2.797000	0.47877	2.606000	0.88127	0.655000	0.94253	GTG		0.622	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		T	86302212	C	T	86302212	3	4	77	1	0	0	0	0	1	0	0	0	12240	536	19	1	3702	1	POLR1A	2	86302212	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	521778	86302212	156897161	146	21882										
IMMT	10989	broad.mit.edu	37	chr2	86389194	86389194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cactgagcagatttcttctcGcctgcaatctaaacaaaaaa	5	11	3	2	rs189100508	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:86389194G>A	ENST00000410111.3	-	8	1188	c.801C>T	c.(799-801)ggC>ggT	p.G267G	IMMT_ENST00000254636.5_Silent_p.G168G|Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000449247.2_Silent_p.G256G|IMMT_ENST00000442664.2_Silent_p.G266G|IMMT_ENST00000409051.2_Silent_p.G220G|IMMT_ENST00000490238.1_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	267					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.G267G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ATTTCTTCTCGCCTGCAATCT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	2											34	32	32					2																	86389194		1876	4115	5991	86242705	SO:0001819	synonymous_variant	10989			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.801C>T	2.37:g.86389194G>A			86242705	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	G	3.936	-0.015264	0.07681	.	.	ENSG00000132305	ENST00000419070	.	.	.	5.24	1.45	0.22620	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.1395	6.092	0.19999	0.607:0.2527:0.1403:0.0	.	.	.	.	X	122	.	.	R	-	1	2	IMMT	86242705	0.817000	0.29147	0.997000	0.53966	0.552000	0.35366	-0.129000	0.10515	0.013000	0.14918	-1.650000	0.00758	CGA		0.388	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86389194	G	A	86389194	2	1	77	1	0	0	0	0	0	0	0	1	7739	1074	38	1		1	IMMT	2	86389194	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	86982	86389194	156810179	147	21883										
RNF103	7844	broad.mit.edu	37	chr2	86849812	86849814	+	In_Frame_Del	DEL	CTT	CTT	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccaccagctcccggacatcCttcttctcgggcaaccctga							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CTT	CTT	CTT	-	CTT	CTT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:86849812_86849814delCTT	ENST00000237455.4	-	1	1164_1166	c.196_198delAAG	c.(196-198)aagdel	p.K66del	RNF103-CHMP3_ENST00000604011.1_Intron|CHMP3_ENST00000439940.2_Intron|RNF103_ENST00000477307.1_5'UTR	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	66					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K66delK(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						CCCGGACATCCTTCTTCTCGGGC	0.616																																																1	Deletion - In frame(1)	large_intestine(1)	2																																								86703325	SO:0001651	inframe_deletion	7844			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.196_198delAAG	2.37:g.86849815_86849817delCTT	ENSP00000237455:p.Lys66del		86703323	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	In_Frame_Del	DEL	ENST00000237455.4	37	CCDS33237.1																																																																																				0.616	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		-	86849814	CTT	-	86849812	7	5	77	1	0	1	0	1	0	0	0	0	13460	680	24	0	1875	0	RNF103	2	86849812	In_Frame_Del	DEL	CTT	TCGA-AG-A02N-01A-11W-A096-10	460618	86849812	156349561	148	21884										
SNRNP200	23020	broad.mit.edu	37	chr2	96952566	96952566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catggtgcagaatcacctcgCtgtccacatcctccaccaga	7	16	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:96952566C>A	ENST00000323853.5	-	28	3766	c.3689G>T	c.(3688-3690)aGc>aTc	p.S1230I	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1230	SEC63 1.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.S1230I(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						AATCACCTCGCTGTCCACATC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	2											123	125	125					2																	96952566		2203	4300	6503	96316293	SO:0001583	missense	23020			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.3689G>T	2.37:g.96952566C>A	ENSP00000317123:p.Ser1230Ile		96316293	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.287038	0.80803	.	.	ENSG00000144028	ENST00000323853	T	0.61980	0.06	4.75	4.75	0.60458	Sec63 domain (3);	0.000000	0.85682	D	0.000000	T	0.78078	0.4227	M	0.88775	2.98	0.80722	D	1	P	0.48230	0.907	P	0.53266	0.722	D	0.83503	0.0076	10	0.87932	D	0	-13.2815	16.6715	0.85268	0.0:1.0:0.0:0.0	.	1230	O75643	U520_HUMAN	I	1230	ENSP00000317123:S1230I	ENSP00000317123:S1230I	S	-	2	0	SNRNP200	96316293	1.000000	0.71417	0.963000	0.40424	0.929000	0.56500	5.796000	0.69080	2.477000	0.83638	0.455000	0.32223	AGC		0.517	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		A	96952566	C	A	96952566	3	1	77	1	0	0	0	0	1	0	0	0	14889	797	28	2	2793	2	SNRNP200	2	96952566	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	10102754	96952566	146246807	149	21885										
ACTR1B	10120	broad.mit.edu	37	chr2	98275431	98275431	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccttctcccggttcttactCgggttgagcggggcctccgt	13	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:98275431C>T	ENST00000289228.5	-	5	567	c.351G>A	c.(349-351)ccG>ccA	p.P117P		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	117					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.P117P(1)		endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						GGTTCTTACTCGGGTTGAGCG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	2											104	114	111					2																	98275431		2203	4300	6503	97641863	SO:0001819	synonymous_variant	10120			X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.351G>A	2.37:g.98275431C>T			97641863	D3DVH2|Q53SK5|Q9BRB7	Silent	SNP	ENST00000289228.5	37	CCDS2033.1																																																																																				0.587	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		T	98275431	C	T	98275431	2	4	77	1	0	0	0	0	0	0	0	1	210	871	31	1		1	ACTR1B	2	98275431	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1322865	98275431	144923942	150	21886										
TGFBRAP1	9392	broad.mit.edu	37	chr2	105897177	105897177	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcccggacatcaagctggccGcttctgcaattacagtgtca	9	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:105897177G>A	ENST00000393359.2	-	6	1551	c.1125C>T	c.(1123-1125)agC>agT	p.S375S	TGFBRAP1_ENST00000258449.1_Silent_p.S375S			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	375					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)	p.S375S(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CAAGCTGGCCGCTTCTGCAAT	0.542																																					Esophageal Squamous(183;794 2019 9730 21801 48859)											1	Substitution - coding silent(1)	large_intestine(1)	2											61	61	61					2																	105897177		2203	4300	6503	105263609	SO:0001819	synonymous_variant	9392			AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1125C>T	2.37:g.105897177G>A			105263609	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																				0.542	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105897177	G	A	105897177	2	1	77	1	0	0	0	0	0	0	0	1	15863	1078	38	1		1	TGFBRAP1	2	105897177	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7621746	105897177	137302196	151	21887										
EDAR	10913	broad.mit.edu	37	chr2	109529181	109529181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggtgctgctgcccgaggtgCcagggaagttggcagaagct	18	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:109529181C>T	ENST00000258443.2	-	6	912	c.482G>A	c.(481-483)gGc>gAc	p.G161D	EDAR_ENST00000409271.1_Missense_Mutation_p.G161D|EDAR_ENST00000376651.1_Missense_Mutation_p.G161D	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	161					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.G161D(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						GCCCGAGGTGCCAGGGAAGTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	2											52	48	49					2																	109529181		2203	4299	6502	108895613	SO:0001583	missense	10913			AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"Tumor necrosis factor receptor superfamily"	2895	protein-coding gene	gene with protein product		604095	"ectodysplasin 1, anhidrotic receptor"	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.482G>A	2.37:g.109529181C>T	ENSP00000258443:p.Gly161Asp		108895613	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Missense_Mutation	SNP	ENST00000258443.2	37	CCDS2081.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.688453	0.48097	.	.	ENSG00000135960	ENST00000409271;ENST00000258443;ENST00000376651	D;D;D	0.90069	-2.61;-2.59;-2.61	5.26	5.26	0.73747	.	0.430453	0.28016	N	0.016930	D	0.82815	0.5119	N	0.22421	0.69	0.33307	D	0.565556	B;B	0.23058	0.079;0.012	B;B	0.18871	0.023;0.01	T	0.81378	-0.0960	10	0.28530	T	0.3	-12.1006	18.8621	0.92276	0.0:1.0:0.0:0.0	.	161;161	E9PC98;Q9UNE0	.;EDAR_HUMAN	D	161	ENSP00000386371:G161D;ENSP00000258443:G161D;ENSP00000365839:G161D	ENSP00000258443:G161D	G	-	2	0	EDAR	108895613	1.000000	0.71417	0.919000	0.36401	0.008000	0.06430	5.758000	0.68776	2.437000	0.82529	0.655000	0.94253	GGC		0.567	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			T	109529181	C	T	109529181	3	4	77	1	0	0	0	0	1	0	0	0	4916	739	26	3	892	3	EDAR	2	109529181	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3632004	109529181	133670192	152	21888										
SH3RF3	344558	broad.mit.edu	37	chr2	110065656	110065656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcagcccaggctcaggaccGgccaactgccaccgtgtcac	11	17	2	0	rs376984287	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:110065656G>A	ENST00000309415.6	+	8	1859	c.1859G>A	c.(1858-1860)cGg>cAg	p.R620Q		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	620							zinc ion binding (GO:0008270)	p.R620Q(1)		endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GCTCAGGACCGGCCAACTGCC	0.652													G|||	2	0.000399361	0	0	5008	,	,		15538	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2						G	GLN/ARG	0,4328		0,0,2164	19	26	24		1859	4.3	0.2	2		24	1,8509		0,1,4254	no	missense	SH3RF3	NM_001099289.1	43	0,1,6418	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging	620/883	110065656	1,12837	2164	4255	6419	109432088	SO:0001583	missense	344558			AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1859G>A	2.37:g.110065656G>A	ENSP00000309186:p.Arg620Gln		109432088	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	G	15.07	2.723127	0.48728	0.0	1.18E-4	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.59638	0.25;1.99	5.15	4.28	0.50868	.	0.062791	0.64402	D	0.000007	T	0.68723	0.3032	.	.	.	0.47214	D	0.999354	D	0.65815	0.995	P	0.56088	0.791	T	0.72701	-0.4214	9	0.56958	D	0.05	-21.7545	13.7407	0.62847	0.0736:0.0:0.9264:0.0	.	620	Q8TEJ3	SH3R3_HUMAN	Q	620	ENSP00000414997:R620Q;ENSP00000309186:R620Q	ENSP00000309186:R620Q	R	+	2	0	SH3RF3	109432088	1.000000	0.71417	0.166000	0.22797	0.013000	0.08279	4.991000	0.63883	1.412000	0.46977	-0.136000	0.14681	CGG		0.652	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		A	110065656	G	A	110065656	3	1	77	1	0	0	0	0	1	0	0	0	14297	1116	39	1	1889	1	SH3RF3	2	110065656	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	536475	110065656	133133717	153	21889										
BUB1	699	broad.mit.edu	37	chr2	111406833	111406833	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aattgaaattcagtcttgggCttgatggctggaagtttaca	11	5	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:111406833C>T	ENST00000302759.6	-	19	2443	c.2325G>A	c.(2323-2325)aaG>aaA	p.K775K	BUB1_ENST00000535254.1_Silent_p.K755K|BUB1_ENST00000409311.1_Silent_p.K775K	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	775					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K775K(1)		breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		CAGTCTTGGGCTTGATGGCTG	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	2											95	98	97					2																	111406833		2203	4300	6503	111123305	SO:0001819	synonymous_variant	699			AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2325G>A	2.37:g.111406833C>T			111123305	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Silent	SNP	ENST00000302759.6	37	CCDS33273.1																																																																																				0.353	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		T	111406833	C	T	111406833	2	4	77	1	0	0	0	0	0	0	0	1	1573	796	28	3		3	BUB1	2	111406833	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1341177	111406833	131792540	154	21890										
FBLN7	129804	broad.mit.edu	37	chr2	112944926	112944926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggccactttgtgatgcagcGttcagaccggcagactgggg	15	11	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:112944926G>A	ENST00000331203.2	+	8	1434	c.1163G>A	c.(1162-1164)cGt>cAt	p.R388H	FBLN7_ENST00000409450.3_Missense_Mutation_p.R342H|FBLN7_ENST00000409903.1_Intron|FBLN7_ENST00000409667.3_Missense_Mutation_p.R254H	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	388					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R388H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GTGATGCAGCGTTCAGACCGG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	93	93					2																	112944926		2203	4300	6503	112661397	SO:0001583	missense	129804				CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.1163G>A	2.37:g.112944926G>A	ENSP00000331411:p.Arg388His		112661397	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	37	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	G	35	5.479192	0.96307	.	.	ENSG00000144152	ENST00000331203;ENST00000409667;ENST00000409450;ENST00000272559	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.72833	-0.4173	10	0.87932	D	0	-35.5253	19.2064	0.93732	0.0:0.0:1.0:0.0	.	254;342;388	Q53RD9-4;Q53RD9-2;Q53RD9	.;.;FBLN7_HUMAN	H	388;254;342;210	ENSP00000331411:R388H;ENSP00000386822:R254H;ENSP00000387000:R342H;ENSP00000272559:R210H	ENSP00000272559:R210H	R	+	2	0	FBLN7	112661397	1.000000	0.71417	0.995000	0.50966	0.960000	0.62799	9.368000	0.97152	2.542000	0.85734	0.555000	0.69702	CGT		0.647	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		A	112944926	G	A	112944926	3	1	77	1	0	0	0	0	1	0	0	0	5720	1145	40	1	1193	1	FBLN7	2	112944926	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1538093	112944926	130254447	155	21891										
WDR33	55339	broad.mit.edu	37	chr2	128520690	128520690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcccagattctaacagtgcCgtcatcagagcatgtagcaa	9	11	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:128520690C>T	ENST00000322313.4	-	7	828	c.670G>A	c.(670-672)Ggc>Agc	p.G224S	WDR33_ENST00000409658.3_3'UTR|WDR33_ENST00000393006.1_Missense_Mutation_p.G224S	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	224					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.G224S(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTAACAGTGCCGTCATCAGAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	117	120					2																	128520690		2203	4300	6503	128237160	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.670G>A	2.37:g.128520690C>T	ENSP00000325377:p.Gly224Ser		128237160	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270626	0.40194	.	.	ENSG00000136709	ENST00000322313;ENST00000436787;ENST00000393006	T;T;T	0.64618	-0.11;-0.11;-0.11	5.91	5.91	0.95273	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73613	0.3609	L	0.39514	1.22	0.80722	D	1	B;D	0.89917	0.358;1.0	B;D	0.91635	0.091;0.999	T	0.67741	-0.5592	10	0.30078	T	0.28	-7.0305	20.3552	0.98837	0.0:1.0:0.0:0.0	.	224;224	Q6NUQ0;Q9C0J8	.;WDR33_HUMAN	S	224;146;224	ENSP00000325377:G224S;ENSP00000397547:G146S;ENSP00000376730:G224S	ENSP00000325377:G224S	G	-	1	0	WDR33	128237160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.815000	0.86186	2.812000	0.96745	0.558000	0.71614	GGC		0.408	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128520690	C	T	128520690	3	4	77	1	0	0	0	0	1	0	0	0	17327	652	23	1	3458	1	WDR33	2	128520690	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	15575764	128520690	114678683	156	21892										
UGGT1	56886	broad.mit.edu	37	chr2	128903422	128903422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggagttggacctctgcccGttgtgctgttcaatggaatg	13	9	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:128903422G>A	ENST00000259253.6	+	18	1944	c.1897G>A	c.(1897-1899)Gtt>Att	p.V633I	UGGT1_ENST00000375990.3_Missense_Mutation_p.V609I	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	633					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.V633I(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ACCTCTGCCCGTTGTGCTGTT	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											155	141	146					2																	128903422		2203	4300	6503	128619892	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1897G>A	2.37:g.128903422G>A	ENSP00000259253:p.Val633Ile		128619892	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462511	0.26248	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.35236	1.32;1.32	5.62	4.73	0.59995	.	0.053440	0.85682	D	0.000000	T	0.33731	0.0873	M	0.62723	1.935	0.54753	D	0.999986	B;B	0.13145	0.005;0.007	B;B	0.12837	0.008;0.003	T	0.08554	-1.0716	10	0.22706	T	0.39	.	11.2711	0.49140	0.1398:0.0:0.8602:0.0	.	609;633	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	I	609;633	ENSP00000365158:V609I;ENSP00000259253:V633I	ENSP00000259253:V633I	V	+	1	0	UGGT1	128619892	0.999000	0.42202	0.775000	0.31657	0.417000	0.31264	2.934000	0.48956	2.638000	0.89438	0.585000	0.79938	GTT		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		A	128903422	G	A	128903422	3	1	77	1	0	0	0	0	1	0	0	0	16981	1145	40	1	1967	1	UGGT1	2	128903422	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	382732	128903422	114295951	157	21893										
GPR39	2863	broad.mit.edu	37	chr2	133175300	133175300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagcatcttcggcgccttcGtggtctacctcgtggtcctg	11	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:133175300G>A	ENST00000329321.3	+	1	1154	c.685G>A	c.(685-687)Gtg>Atg	p.V229M		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	229					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)	p.V229M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CGGCGCCTTCGTGGTCTACCT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	78	80					2																	133175300		2203	4300	6503	132891770	SO:0001583	missense	2863			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"GPCR / Class A : Orphans"	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.685G>A	2.37:g.133175300G>A	ENSP00000327417:p.Val229Met		132891770	B2RC12|B6V9G4|Q08AS2|Q53R01	Missense_Mutation	SNP	ENST00000329321.3	37	CCDS2170.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886496	0.33348	.	.	ENSG00000183840	ENST00000329321	T	0.74737	-0.87	4.93	8.5E-4	0.14044	GPCR, rhodopsin-like superfamily (1);	0.931444	0.09118	N	0.846117	T	0.78368	0.4272	L	0.57536	1.79	0.09310	N	1	D	0.54601	0.967	P	0.56042	0.79	T	0.66724	-0.5851	10	0.56958	D	0.05	.	9.4743	0.38862	0.5846:0.0:0.4154:0.0	.	229	O43194	GPR39_HUMAN	M	229	ENSP00000327417:V229M	ENSP00000327417:V229M	V	+	1	0	GPR39	132891770	0.000000	0.05858	0.018000	0.16275	0.479000	0.33129	0.090000	0.15025	0.101000	0.17610	0.585000	0.79938	GTG		0.617	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			A	133175300	G	A	133175300	3	1	77	1	0	0	0	0	1	0	0	0	6713	1145	40	1	687	1	GPR39	2	133175300	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4271878	133175300	110024073	158	21894										
ZRANB3	84083	broad.mit.edu	37	chr2	135985518	135985518	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atagtttgaacctttttggaGgtgtctttctgagaatcatc	9	6	3	2	rs568807221	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:135985518G>T	ENST00000264159.6	-	14	2138	c.2022C>A	c.(2020-2022)acC>acA	p.T674T	ZRANB3_ENST00000401392.1_Silent_p.T674T|ZRANB3_ENST00000536680.1_Silent_p.T674T|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	674					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)	p.T139T(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CCTTTTTGGAGGTGTCTTTCT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	2											101	84	89					2																	135985518		1818	4040	5858	135701988	SO:0001819	synonymous_variant	84083			AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2022C>A	2.37:g.135985518G>T			135701988	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Silent	SNP	ENST00000264159.6	37	CCDS46419.1																																																																																				0.363	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		T	135985518	G	T	135985518	2	4	77	1	0	0	0	0	0	0	0	1	18263	987	35	2		2	ZRANB3	2	135985518	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2810218	135985518	107213855	159	21895										
LCT	3938	broad.mit.edu	37	chr2	136575285	136575285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtacacctgagcccggaggcCgcaaagcagggcgacgtcag	15	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:136575285C>T	ENST00000264162.2	-	6	1343	c.1333G>A	c.(1333-1335)Ggc>Agc	p.G445S	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	445	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.G445S(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCCCGGAGGCCGCAAAGCAGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	2											69	65	66					2																	136575285		2203	4300	6503	136291755	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1333G>A	2.37:g.136575285C>T	ENSP00000264162:p.Gly445Ser		136291755	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	33	5.271003	0.95429	.	.	ENSG00000115850	ENST00000264162	T	0.49432	0.78	5.77	5.77	0.91146	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.052557	0.85682	D	0.000000	T	0.56247	0.1972	N	0.21508	0.67	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.47114	-0.9142	10	0.23302	T	0.38	-15.8411	20.3627	0.98863	0.0:1.0:0.0:0.0	.	445	P09848	LPH_HUMAN	S	445	ENSP00000264162:G445S	ENSP00000264162:G445S	G	-	1	0	LCT	136291755	1.000000	0.71417	0.832000	0.32986	0.988000	0.76386	6.053000	0.71089	2.885000	0.99019	0.655000	0.94253	GGC		0.642	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136575285	C	T	136575285	3	4	77	1	0	0	0	0	1	0	0	0	8715	652	23	1	4498	1	LCT	2	136575285	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	589767	136575285	106624088	160	21896										
THSD7B	80731	broad.mit.edu	37	chr2	138413226	138413226	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagctgtgttctgtgccttgCccaggtatgcaatgctagtg	12	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:138413226C>T	ENST00000409968.1	+	22	4279	c.4101C>T	c.(4099-4101)tgC>tgT	p.C1367C	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Silent_p.C1339C|THSD7B_ENST00000272643.3_Silent_p.C1370C			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1369	TSP type-1 17. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.C1370C(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CTGTGCCTTGCCCAGGTATGC	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	2											59	58	58					2																	138413226		2034	4197	6231	138129696	SO:0001819	synonymous_variant	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.4101C>T	2.37:g.138413226C>T			138129696		Silent	SNP	ENST00000409968.1	37																																																																																					0.463	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	138413226	C	T	138413226	2	4	77	1	0	0	0	0	0	0	0	1	15919	747	26	3		3	THSD7B	2	138413226	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1837941	138413226	104786147	161	21897										
MBD5	55777	broad.mit.edu	37	chr2	149248058	149248058	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaaggacgttcaatgttggCgacttggtctggggccaaat	13	9	2	0	rs543329958		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:149248058C>T	ENST00000407073.1	+	12	5155	c.4158C>T	c.(4156-4158)ggC>ggT	p.G1386G	MBD5_ENST00000404807.1_Silent_p.G1619G	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1386	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.G1386G(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		TCAATGTTGGCGACTTGGTCT	0.448													C|||	1	0.000199681	0	0	5008	,	,		18682	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2											77	77	77					2																	149248058		2203	4300	6503	148964528	SO:0001819	synonymous_variant	55777			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.4158C>T	2.37:g.149248058C>T			148964528	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Silent	SNP	ENST00000407073.1	37	CCDS33302.1																																																																																				0.448	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			T	149248058	C	T	149248058	2	4	77	1	0	0	0	0	0	0	0	1	9377	755	27	1		1	MBD5	2	149248058	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	10834832	149248058	93951315	162	21898										
CACNB4	785	broad.mit.edu	37	chr2	152727085	152727085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccccactaacaccaccggaCgcattgacggtacaacatcg	8	16	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:152727085C>T	ENST00000539935.1	-	8	726	c.659G>A	c.(658-660)cGt>cAt	p.R220H	CACNB4_ENST00000397327.2_Missense_Mutation_p.R173H|CACNB4_ENST00000534999.1_Missense_Mutation_p.R186H|CACNB4_ENST00000427385.1_Missense_Mutation_p.R202H|CACNB4_ENST00000201943.5_Missense_Mutation_p.R220H|CACNB4_ENST00000360283.6_Missense_Mutation_p.R187H	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	220					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R220H(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CACCACCGGACGCATTGACGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	2											85	86	86					2																	152727085		2101	4215	6316	152435331	SO:0001583	missense	785			AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.659G>A	2.37:g.152727085C>T	ENSP00000438949:p.Arg220His		152435331	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	C	36	5.720892	0.96839	.	.	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.91	5.91	0.95273	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.000000	0.85682	D	0.000000	T	0.80297	0.4597	M	0.92026	3.265	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.999;0.997;0.999;0.995	D	0.83531	0.0091	10	0.87932	D	0	-11.1915	20.2983	0.98569	0.0:1.0:0.0:0.0	.	220;186;220;202;186	A7BJ74;E7DBM8;O00305;B4DG40;O00305-2	.;.;CACB4_HUMAN;.;.	H	220;187;177;215;186;173;202;220;221	ENSP00000438949:R220H;ENSP00000353425:R187H;ENSP00000390161:R215H;ENSP00000443893:R186H;ENSP00000380490:R173H;ENSP00000410978:R202H;ENSP00000201943:R220H	ENSP00000201943:R220H	R	-	2	0	CACNB4	152435331	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.746000	0.85057	2.802000	0.96397	0.655000	0.94253	CGT		0.498	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		T	152727085	C	T	152727085	3	4	77	1	0	0	0	0	1	0	0	0	2561	536	19	1	931	1	CACNB4	2	152727085	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3479027	152727085	90472288	163	21899										
SCN2A	6326	broad.mit.edu	37	chr2	166152376	166152376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgccaggacctgacagcttcCgcttctttaccagggaatcc	9	15	1	1	rs551347418		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:166152376C>T	ENST00000375437.2	+	2	333	c.43C>T	c.(43-45)Cgc>Tgc	p.R15C	SCN2A_ENST00000375427.2_Missense_Mutation_p.R15C|SCN2A_ENST00000283256.6_Missense_Mutation_p.R15C|SCN2A_ENST00000357398.3_Missense_Mutation_p.R15C	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	15					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R15C(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGACAGCTTCCGCTTCTTTAC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	2											82	75	77					2																	166152376		2203	4300	6503	165860622	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.43C>T	2.37:g.166152376C>T	ENSP00000364586:p.Arg15Cys		165860622	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241071	0.58995	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.97114	-4.22;-4.24;-4.25;-4.24;-4.25	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000002	D	0.97579	0.9207	M	0.92970	3.365	0.80722	D	1	B;B	0.14805	0.011;0.006	B;B	0.12837	0.008;0.006	D	0.95688	0.8738	10	0.72032	D	0.01	.	19.5116	0.95144	0.0:1.0:0.0:0.0	.	15;15	Q99250-2;Q99250	.;SCN2A_HUMAN	C	15	ENSP00000406454:R15C;ENSP00000364586:R15C;ENSP00000349973:R15C;ENSP00000283256:R15C;ENSP00000364576:R15C	ENSP00000283256:R15C	R	+	1	0	SCN2A	165860622	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.976000	0.56867	2.619000	0.88677	0.655000	0.94253	CGC		0.468	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166152376	C	T	166152376	3	4	77	1	0	0	0	0	1	0	0	0	13953	652	23	1	45	1	SCN2A	2	166152376	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	13425291	166152376	77046997	164	21900										
XIRP2	129446	broad.mit.edu	37	chr2	168106624	168106624	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaagggcatacaagagaaaCaagtcttctctaatactaaa	6	8	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:168106624C>T	ENST00000409195.1	+	9	8811	c.8722C>T	c.(8722-8724)Caa>Taa	p.Q2908*	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Nonsense_Mutation_p.Q2908*|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Nonsense_Mutation_p.Q2686*|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2733					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.Q2908*(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACAAGAGAAACAAGTCTTCTC	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											78	73	75					2																	168106624		1824	4083	5907	167814870	SO:0001587	stop_gained	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8722C>T	2.37:g.168106624C>T	ENSP00000386840:p.Gln2908*		167814870	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Nonsense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	c	49	15.745629	0.99844	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	.	.	.	6.02	4.23	0.50019	.	0.821127	0.11531	N	0.554655	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-2.9008	10.2958	0.43623	0.143:0.581:0.276:0.0	.	.	.	.	X	2908;2908;2686;322	.	ENSP00000295237:Q2908X	Q	+	1	0	XIRP2	167814870	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	1.189000	0.32114	0.876000	0.35872	-0.121000	0.15023	CAA		0.393	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168106624	C	T	168106624	4	4	77	1	0	0	0	0	0	1	0	0	17470	479	17	3	8752	3	XIRP2	2	168106624	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1954248	168106624	75092749	165	21901										
SPC25	57405	broad.mit.edu	37	chr2	169746018	169746018	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttatcgaaaagtgccagttcGtcctctaccattatgtagga	8	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:169746018G>A	ENST00000282074.2	-	2	153	c.12C>T	c.(10-12)gaC>gaT	p.D4D	SPC25_ENST00000472216.2_5'UTR	NM_020675.3	NP_065726.1	Q9HBM1	SPC25_HUMAN	SPC25, NDC80 kinetochore complex component	4	Interaction with the N-terminus of SPBC24.|Interaction with the NDC80-NUF2 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	condensed chromosome kinetochore (GO:0000777)|cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.D4D(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	9						GTGCCAGTTCGTCCTCTACCA	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	2											52	49	50					2																	169746018		2203	4300	6503	169454264	SO:0001819	synonymous_variant	57405			AF225416	CCDS2229.1	2q31.1	2013-06-05	2013-06-05	2007-03-02	ENSG00000152253	ENSG00000152253			24031	protein-coding gene	gene with protein product		609395	"spindle pole body component 25 homolog (S. cerevisiae)", "SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	SPBC25		12477932	Standard	NM_020675		Approved	MGC22228, AD024	uc002uel.3	Q9HBM1	OTTHUMG00000132181	ENST00000282074.2:c.12C>T	2.37:g.169746018G>A			169454264	A8K4X8|D3DPC0	Silent	SNP	ENST00000282074.2	37	CCDS2229.1																																																																																				0.368	SPC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255233.2	NM_020675		A	169746018	G	A	169746018	2	1	77	1	0	0	0	0	0	0	0	1	15061	1136	40	1		1	SPC25	2	169746018	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1639394	169746018	73453355	166	21902										
UBR3	130507	broad.mit.edu	37	chr2	170937148	170937148	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcaccgcttctgcctctggGgttccgtgtatttggatgct	12	11	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:170937148G>T	ENST00000272793.5	+	38	5553	c.5503G>T	c.(5503-5505)Ggt>Tgt	p.G1835C	UBR3_ENST00000418381.1_Missense_Mutation_p.G1835C|UBR3_ENST00000392631.1_Missense_Mutation_p.G656C			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1835					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G1835C(1)|p.G688C(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CTGCCTCTGGGGTTCCGTGTA	0.423																																																2	Substitution - Missense(2)	large_intestine(2)	2											154	143	147					2																	170937148		2203	4300	6503	170645394	SO:0001583	missense	130507			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.5503G>T	2.37:g.170937148G>T	ENSP00000272793:p.Gly1835Cys		170645394	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.955556	0.92726	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.65544	0.2701	M	0.70903	2.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.997	T	0.62469	-0.6848	10	0.37606	T	0.19	.	19.5215	0.95187	0.0:0.0:1.0:0.0	.	1835;656;1864	Q6ZT12;Q6ZT12-2;E7EVK3	UBR3_HUMAN;.;.	C	1835;1864;1835;656;535	ENSP00000272793:G1835C;ENSP00000396068:G1835C;ENSP00000376408:G656C;ENSP00000389097:G535C	ENSP00000272793:G1835C	G	+	1	0	UBR3	170645394	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.471000	0.97696	2.585000	0.87301	0.650000	0.86243	GGT		0.423	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		T	170937148	G	T	170937148	3	4	77	1	0	0	0	0	1	0	0	0	16943	1232	43	2	5653	2	UBR3	2	170937148	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1191130	170937148	72262225	167	21903										
AGPS	8540	broad.mit.edu	37	chr2	178357914	178357914	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attcgcctcatggacaacaaGcagtttcagtttggtaagta	9	8	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:178357914G>A	ENST00000264167.4	+	12	1418	c.1272G>A	c.(1270-1272)aaG>aaA	p.K424K	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	424					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)	p.K424K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TGGACAACAAGCAGTTTCAGT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	2											106	107	107					2																	178357914		2203	4300	6503	178066160	SO:0001819	synonymous_variant	8540			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1272G>A	2.37:g.178357914G>A			178066160	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																				0.363	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			A	178357914	G	A	178357914	2	1	77	1	0	0	0	0	0	0	0	1	394	962	34	3		3	AGPS	2	178357914	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7420766	178357914	64841459	168	21904										
TTC30B	150737	broad.mit.edu	37	chr2	178416321	178416321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacttgtatggtaagtttccGgaggacctcagtcagcatcc	10	10	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:178416321G>A	ENST00000408939.3	-	1	1421	c.1171C>T	c.(1171-1173)Cgg>Tgg	p.R391W		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	391					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.R391W(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			GTAAGTTTCCGGAGGACCTCA	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	2											199	203	202					2																	178416321		2203	4300	6503	178124567	SO:0001583	missense	150737			AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	26425	protein-coding gene	gene with protein product						12477932	Standard	NM_152517		Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.1171C>T	2.37:g.178416321G>A	ENSP00000386181:p.Arg391Trp		178124567	Q63HQ1|Q96NE6	Missense_Mutation	SNP	ENST00000408939.3	37	CCDS42784.1	.	.	.	.	.	.	.	.	.	.	G	8.698	0.909108	0.17833	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	T	0.29397	1.57	4.77	1.75	0.24633	.	0.000000	0.85682	D	0.000000	T	0.57946	0.2088	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61973	-0.6952	10	0.87932	D	0	.	8.2721	0.31851	0.0813:0.0:0.5315:0.3872	.	391	Q8N4P2	TT30B_HUMAN	W	344;391	ENSP00000386181:R391W	ENSP00000386181:R391W	R	-	1	2	TTC30B	178124567	1.000000	0.71417	0.999000	0.59377	0.078000	0.17371	0.719000	0.25881	0.707000	0.31934	-0.136000	0.14681	CGG		0.438	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334193.2	NM_152517		A	178416321	G	A	178416321	3	1	77	1	0	0	0	0	1	0	0	0	16739	1115	39	1	830	1	TTC30B	2	178416321	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	58407	178416321	64783052	169	21905										
RBM45	129831	broad.mit.edu	37	chr2	178977395	178977395	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtacacacctgagtcggtgcTgagggagcgcttctcgcctt	13	12	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:178977395T>G	ENST00000286070.5	+	1	214	c.122T>G	c.(121-123)cTg>cGg	p.L41R		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	41	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.L41R(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			GAGTCGGTGCTGAGGGAGCGC	0.627											OREG0015102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											80	73	75					2																	178977395		2203	4300	6503	178685641	SO:0001583	missense	129831			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"RNA binding motif (RRM) containing"	24468	protein-coding gene	gene with protein product	"developmentally regulated RNA binding protein 1"	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.122T>G	2.37:g.178977395T>G	ENSP00000286070:p.Leu41Arg	1950	178685641	Q6NYL0|Q8NFC9	Missense_Mutation	SNP	ENST00000286070.5	37	CCDS33335.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380828	0.82792	.	.	ENSG00000155636	ENST00000286070	T	0.46819	0.86	5.16	2.57	0.30868	.	0.159614	0.41823	D	0.000818	T	0.73651	0.3614	H	0.98027	4.13	0.43368	D	0.995458	D	0.61697	0.99	P	0.61201	0.885	T	0.76857	-0.2804	10	0.87932	D	0	-2.4125	7.2427	0.26106	0.0:0.0777:0.1453:0.7771	.	41	Q8IUH3-3	.	R	41	ENSP00000286070:L41R	ENSP00000286070:L41R	L	+	2	0	RBM45	178685641	1.000000	0.71417	0.637000	0.29366	0.970000	0.65996	5.684000	0.68197	0.901000	0.36495	0.460000	0.39030	CTG		0.627	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		G	178977395	T	G	178977395	3	3	77	1	0	0	0	0	1	0	0	0	13176	1580	55	4	124	4	RBM45	2	178977395	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	561074	178977395	64221978	170	21906										
NEUROD1	4760	broad.mit.edu	37	chr2	182542935	182542935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caggcgactggtaggagtagGggtgtacagggaaggaagcg	20	5	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:182542935G>T	ENST00000295108.3	-	2	1110	c.653C>A	c.(652-654)cCc>cAc	p.P218H	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	218					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.P218H(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GTAGGAGTAGGGGTGTACAGG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	2											56	65	62					2																	182542935		2203	4300	6503	182251180	SO:0001583	missense	4760			U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.653C>A	2.37:g.182542935G>T	ENSP00000295108:p.Pro218His		182251180	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409454	0.25378	.	.	ENSG00000162992	ENST00000295108	T	0.65916	-0.18	6.02	6.02	0.97574	Neurogenic differentiation factor, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.61986	0.2391	L	0.50333	1.59	0.51482	D	0.999923	B	0.17038	0.02	B	0.23018	0.043	T	0.57740	-0.7759	10	0.72032	D	0.01	-19.5201	19.1109	0.93315	0.0:0.0:1.0:0.0	.	218	Q13562	NDF1_HUMAN	H	218	ENSP00000295108:P218H	ENSP00000295108:P218H	P	-	2	0	NEUROD1	182251180	0.997000	0.39634	1.000000	0.80357	0.972000	0.66771	2.992000	0.49417	2.850000	0.98022	0.650000	0.86243	CCC		0.637	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		T	182542935	G	T	182542935	3	4	77	1	0	0	0	0	1	0	0	0	10379	1232	43	2	421	2	NEUROD1	2	182542935	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3565540	182542935	60656438	171	21907										
FRZB	2487	broad.mit.edu	37	chr2	183707268	183707268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taataggcttacatttacagCgttctgaaaaacacatttta	5	7	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:183707268C>T	ENST00000295113.4	-	3	1139	c.530G>A	c.(529-531)cGc>cAc	p.R177H		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	177					brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R177H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			ACATTTACAGCGTTCTGAAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	2											188	181	184					2																	183707268		2203	4300	6503	183415513	SO:0001583	missense	2487			U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"Secreted frizzled-related proteins"	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.530G>A	2.37:g.183707268C>T	ENSP00000295113:p.Arg177His		183415513	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	37	CCDS2286.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.226605	0.58668	.	.	ENSG00000162998	ENST00000295113	T	0.73469	-0.75	5.92	5.04	0.67666	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.108195	0.64402	D	0.000004	T	0.61451	0.2348	L	0.41236	1.265	0.80722	D	1	B	0.18310	0.027	B	0.12837	0.008	T	0.53521	-0.8427	10	0.13853	T	0.58	.	9.8643	0.41134	0.0:0.8505:0.0:0.1495	.	177	Q92765	SFRP3_HUMAN	H	177	ENSP00000295113:R177H	ENSP00000295113:R177H	R	-	2	0	FRZB	183415513	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.388000	0.59633	2.818000	0.97014	0.655000	0.94253	CGC		0.338	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463		T	183707268	C	T	183707268	3	4	77	1	0	0	0	0	1	0	0	0	6084	768	27	1	463	1	FRZB	2	183707268	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1164333	183707268	59492105	172	21908										
COL5A2	1290	broad.mit.edu	37	chr2	189923247	189923247	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctttccccaggatttcctcGttctccctagcacaaaattg	5	14	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:189923247G>A	ENST00000374866.3	-	33	2411	c.2137C>T	c.(2137-2139)Cga>Tga	p.R713*		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	713					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.R713*(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GGATTTCCTCGTTCTCCCTAG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											99	93	95					2																	189923247		2203	4300	6503	189631492	SO:0001587	stop_gained	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.2137C>T	2.37:g.189923247G>A	ENSP00000364000:p.Arg713*		189631492	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Nonsense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	G	42	9.502324	0.99189	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	.	.	.	5.52	3.65	0.41850	.	0.000000	0.49305	D	0.000143	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7674	0.69648	0.0:0.0:0.7378:0.2622	.	.	.	.	X	713;353	.	.	R	-	1	2	COL5A2	189631492	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.532000	0.67154	0.746000	0.32786	0.558000	0.71614	CGA		0.438	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		A	189923247	G	A	189923247	4	1	77	1	0	0	0	0	0	1	0	0	3703	1153	40	1	2450	1	COL5A2	2	189923247	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6215979	189923247	53276126	173	21909										
MYO1B	4430	broad.mit.edu	37	chr2	192214912	192214912	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatatatggatattgaatttGactttaaaggcgatccacta	7	5	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:192214912G>T	ENST00000392318.3	+	7	770	c.523G>T	c.(523-525)Gac>Tac	p.D175Y	MYO1B_ENST00000304164.4_Missense_Mutation_p.D175Y|MYO1B_ENST00000392316.1_Missense_Mutation_p.D175Y|MYO1B_ENST00000339514.4_Missense_Mutation_p.D175Y	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	175	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.D175Y(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			TATTGAATTTGACTTTAAAGG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											87	91	90					2																	192214912		2203	4298	6501	191923157	SO:0001583	missense	4430			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.523G>T	2.37:g.192214912G>T	ENSP00000376132:p.Asp175Tyr		191923157	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.968350	0.74131	.	.	ENSG00000128641	ENST00000339514;ENST00000439452;ENST00000392318;ENST00000304164;ENST00000451437;ENST00000392316	T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85	5.05	3.22	0.36961	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.88168	0.6364	H	0.94964	3.605	0.80722	D	1	D;D	0.65815	0.995;0.989	D;D	0.70935	0.971;0.964	D	0.89936	0.4069	10	0.87932	D	0	.	10.7846	0.46398	0.1567:0.0:0.8433:0.0	.	175;175	O43795;O43795-2	MYO1B_HUMAN;.	Y	175	ENSP00000341903:D175Y;ENSP00000376132:D175Y;ENSP00000306382:D175Y;ENSP00000388140:D175Y;ENSP00000376130:D175Y	ENSP00000306382:D175Y	D	+	1	0	MYO1B	191923157	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.338000	0.72963	1.266000	0.44231	0.561000	0.74099	GAC		0.323	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		T	192214912	G	T	192214912	3	4	77	1	0	0	0	0	1	0	0	0	10099	1290	45	2	545	2	MYO1B	2	192214912	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2291665	192214912	50984461	174	21910										
DNAH7	56171	broad.mit.edu	37	chr2	196729378	196729378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctactaggagagcatggctgCgaggctgcttcaggatcctg	14	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:196729378C>T	ENST00000312428.6	-	41	7101	c.7001G>A	c.(7000-7002)cGc>cAc	p.R2334H		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2334	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.R2334H(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGCATGGCTGCGAGGCTGCTT	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	2											92	92	92					2																	196729378		1954	4172	6126	196437623	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.7001G>A	2.37:g.196729378C>T	ENSP00000311273:p.Arg2334His		196437623	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561832	0.45590	.	.	ENSG00000118997	ENST00000312428	T	0.57273	0.41	4.7	4.7	0.59300	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.80003	0.4544	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84076	0.0382	10	0.41790	T	0.15	.	17.4131	0.87492	0.0:1.0:0.0:0.0	.	2334	Q8WXX0	DYH7_HUMAN	H	2334	ENSP00000311273:R2334H	ENSP00000311273:R2334H	R	-	2	0	DNAH7	196437623	0.912000	0.30974	0.970000	0.41538	0.188000	0.23474	3.900000	0.56295	2.452000	0.82932	0.460000	0.39030	CGC		0.458	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196729378	C	T	196729378	3	4	77	1	0	0	0	0	1	0	0	0	4617	768	27	1	5173	1	DNAH7	2	196729378	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4514466	196729378	46469995	175	21911										
ERBB4	2066	broad.mit.edu	37	chr2	212989544	212989544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggttgcccatgacaacctcaCagttttcatagtacttgcgc	8	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:212989544C>T	ENST00000342788.4	-	2	477	c.167G>A	c.(166-168)tGt>tAt	p.C56Y	ERBB4_ENST00000436443.1_Missense_Mutation_p.C56Y|ERBB4_ENST00000402597.1_Missense_Mutation_p.C56Y	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	56					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.C56Y(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GACAACCTCACAGTTTTCATA	0.498										TSP Lung(8;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	2											143	125	131					2																	212989544		2203	4300	6503	212697789	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.167G>A	2.37:g.212989544C>T	ENSP00000342235:p.Cys56Tyr		212697789	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.7|27.7	4.856759|4.856759	0.91433|0.91433	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	D;D;D|.	0.99755|.	-6.64;-6.64;-6.64|.	5.28|5.28	5.28|5.28	0.74379|0.74379	EGF receptor, L domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88551|0.88551	0.6467|0.6467	H|H	0.97023|0.97023	3.925|3.925	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.999;1.0;0.999;1.0|.	D|D	0.92387|0.92387	0.5918|0.5918	10|5	0.87932|.	D|.	0|.	.|.	18.918|18.918	0.92513|0.92513	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	56;56;56;56|.	Q15303-4;Q15303-2;Q15303-3;Q15303|.	.;.;.;ERBB4_HUMAN|.	Y|M	56|56	ENSP00000342235:C56Y;ENSP00000403204:C56Y;ENSP00000385565:C56Y|.	ENSP00000342235:C56Y|.	C|V	-|-	2|1	0|0	ERBB4|ERBB4	212697789|212697789	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.769000|7.769000	0.85360|0.85360	2.467000|2.467000	0.83353|0.83353	0.655000|0.655000	0.94253|0.94253	TGT|GTG		0.498	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212989544	C	T	212989544	3	4	77	1	0	0	0	0	1	0	0	0	5222	478	17	3	3867	3	ERBB4	2	212989544	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	16260166	212989544	30209829	176	21912										
SPAG16	79582	broad.mit.edu	37	chr2	214174838	214174838	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acctgaagtaatagaagactTtctctgcaatttcttgatca	6	8	3	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:214174838T>G	ENST00000331683.5	+	4	430	c.335T>G	c.(334-336)tTt>tGt	p.F112C	SPAG16_ENST00000447990.1_Missense_Mutation_p.F112C|SPAG16_ENST00000272898.7_Missense_Mutation_p.F112C|SPAG16_ENST00000374309.3_Intron|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000432529.2_Missense_Mutation_p.F112C|SPAG16_ENST00000413312.1_Missense_Mutation_p.F81C	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	112					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.F112C(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		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)		ATAGAAGACTTTCTCTGCAAT	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											125	133	130					2																	214174838		2203	4299	6502	213883083	SO:0001583	missense	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.335T>G	2.37:g.214174838T>G	ENSP00000332592:p.Phe112Cys		213883083	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964613	0.74131	.	.	ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000413312;ENST00000272898;ENST00000447990	T	0.76839	-1.05	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.88089	0.6343	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.999;0.998;0.993;0.999	D	0.89556	0.3803	10	0.87932	D	0	.	12.4805	0.55839	0.0:0.0:0.0:1.0	.	81;52;112;112	Q8N0X2-3;Q4G1A2;Q8N0X2;Q8N0X2-4	.;.;SPG16_HUMAN;.	C	112;112;81;112;112	ENSP00000332592:F112C	ENSP00000272898:F112C	F	+	2	0	SPAG16	213883083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.793000	0.62474	2.261000	0.74972	0.533000	0.62120	TTT		0.323	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		G	214174838	T	G	214174838	3	3	77	1	0	0	0	0	1	0	0	0	15017	1841	64	4	349	4	SPAG16	2	214174838	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1185294	214174838	29024535	177	21913										
XRCC5	7520	broad.mit.edu	37	chr2	217026709	217026709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtatattttaggttggaaGtgtgaatcctgctgaaaact	11	4	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:217026709G>A	ENST00000392133.3	+	18	2233	c.1772G>A	c.(1771-1773)aGt>aAt	p.S591N	XRCC5_ENST00000392132.2_Missense_Mutation_p.S591N			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	591					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.S591N(1)		endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		TAGGTTGGAAGTGTGAATCCT	0.408								Non-homologous end-joining																																								1	Substitution - Missense(1)	large_intestine(1)	2											161	156	158					2																	217026709		2203	4300	6503	216734954	SO:0001583	missense	7520			AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.1772G>A	2.37:g.217026709G>A	ENSP00000375978:p.Ser591Asn		216734954	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	37	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032677	0.75504	.	.	ENSG00000079246	ENST00000392133;ENST00000392132	T;T	0.36520	1.25;1.25	5.52	5.52	0.82312	Ku, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.52709	0.1751	M	0.83012	2.62	0.58432	D	0.999998	P	0.38767	0.646	P	0.46718	0.525	T	0.49113	-0.8973	10	0.32370	T	0.25	.	16.3144	0.82913	0.0:0.0:1.0:0.0	.	591	P13010	XRCC5_HUMAN	N	591	ENSP00000375978:S591N;ENSP00000375977:S591N	ENSP00000375977:S591N	S	+	2	0	XRCC5	216734954	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.136000	0.71703	2.866000	0.98385	0.650000	0.86243	AGT		0.408	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		A	217026709	G	A	217026709	3	1	77	1	0	0	0	0	1	0	0	0	17496	1029	36	3	1834	3	XRCC5	2	217026709	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2851871	217026709	26172664	178	21914										
MARCH4	57574	broad.mit.edu	37	chr2	217234552	217234552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccagtgagtagcgatcctcGgtcttctccttacagaagtc	9	13	2	2	rs374936017		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:217234552G>A	ENST00000273067.4	-	1	2198	c.432C>T	c.(430-432)acC>acT	p.T144T		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	144						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T144T(2)		breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		AGCGATCCTCGGTCTTCTCCT	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	2											72	63	66					2																	217234552		2203	4300	6503	216942797	SO:0001819	synonymous_variant	57574			AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.432C>T	2.37:g.217234552G>A			216942797	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																				0.587	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		A	217234552	G	A	217234552	2	1	77	1	0	0	0	0	0	0	0	1	9333	1103	39	1		1	MARCH4	2	217234552	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	207843	217234552	25964821	179	21915										
ATG9A	79065	broad.mit.edu	37	chr2	220088465	220088465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggtgtgacaatggggctcaGcaactcttccaaaatgaaca	11	9	2	2	rs190418139	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:220088465G>T	ENST00000409618.1	-	10	1880	c.1441C>A	c.(1441-1443)Ctg>Atg	p.L481M	AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000409422.1_Missense_Mutation_p.L420M|ATG9A_ENST00000396761.2_Missense_Mutation_p.L481M|ATG9A_ENST00000361242.4_Missense_Mutation_p.L481M			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	481					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)		p.L481M(1)		endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGGGGCTCAGCAACTCTTCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	2											58	67	64					2																	220088465		2031	4204	6235	219796709	SO:0001583	missense	79065			AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1441C>A	2.37:g.220088465G>T	ENSP00000386710:p.Leu481Met		219796709	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.385903	0.61956	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000429920	T;T;T;T;T	0.38887	1.56;1.56;1.56;1.16;1.11	5.78	5.78	0.91487	.	0.071120	0.56097	D	0.000024	T	0.63827	0.2544	M	0.74389	2.26	0.49798	D	0.999821	D	0.63046	0.992	P	0.60415	0.874	T	0.62525	-0.6836	10	0.46703	T	0.11	-7.1277	20.0204	0.97499	0.0:0.0:1.0:0.0	.	481	Q7Z3C6	ATG9A_HUMAN	M	481;481;481;420;40	ENSP00000379983:L481M;ENSP00000386710:L481M;ENSP00000355173:L481M;ENSP00000386535:L420M;ENSP00000400234:L40M	ENSP00000355173:L481M	L	-	1	2	ATG9A	219796709	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.771000	0.55318	2.729000	0.93468	0.650000	0.86243	CTG		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		T	220088465	G	T	220088465	3	4	77	1	0	0	0	0	1	0	0	0	1103	962	34	2	1106	2	ATG9A	2	220088465	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2853913	220088465	23110908	180	21916										
PAX3	5077	broad.mit.edu	37	chr2	223161816	223161816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgcgagatgacgcagggccGgatgccgtggtgggccatct	18	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:223161816G>A	ENST00000350526.4	-	2	338	c.202C>T	c.(202-204)Cgg>Tgg	p.R68W	PAX3_ENST00000392069.2_Missense_Mutation_p.R68W|PAX3_ENST00000336840.6_Missense_Mutation_p.R68W|CCDC140_ENST00000295226.1_5'Flank|PAX3_ENST00000409551.3_Missense_Mutation_p.R68W|PAX3_ENST00000344493.4_Missense_Mutation_p.R68W|PAX3_ENST00000409828.3_Missense_Mutation_p.R68W|PAX3_ENST00000392070.2_Missense_Mutation_p.R68W|PAX3_ENST00000258387.5_Missense_Mutation_p.R68W	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	68	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R68W(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACGCAGGGCCGGATGCCGTGG	0.647			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																Dom	yes		2	2q35	5077	paired box gene 3	yes	M	1	Substitution - Missense(1)	large_intestine(1)	2	GRCh37	CD920899	PAX3	D							36	34	35					2																	223161816		2203	4298	6501	222870060	SO:0001583	missense	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.202C>T	2.37:g.223161816G>A	ENSP00000343052:p.Arg68Trp		222870060	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	37	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.072190	0.76415	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000409828;ENST00000258387	D;D;D;D;D;D;D;D	0.99680	-6.38;-6.38;-6.38;-6.38;-6.38;-6.38;-6.38;-6.38	5.24	5.24	0.73138	Paired box protein, N-terminal (5);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99819	0.9920	H	0.97540	4.025	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.997;1.0;0.999;1.0;0.998	D	0.96939	0.9686	10	0.87932	D	0	.	13.0806	0.59112	0.0:0.0:0.7172:0.2828	.	68;68;68;68;68;68;68	P23760;P23760-2;P23760-3;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.;.;.	W	68	ENSP00000375921:R68W;ENSP00000342092:R68W;ENSP00000343052:R68W;ENSP00000375922:R68W;ENSP00000338767:R68W;ENSP00000386750:R68W;ENSP00000386817:R68W;ENSP00000258387:R68W	ENSP00000258387:R68W	R	-	1	2	PAX3	222870060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.745000	0.26259	2.426000	0.82243	0.655000	0.94253	CGG		0.647	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			A	223161816	G	A	223161816	3	1	77	1	0	0	0	0	1	0	0	0	11511	1115	39	1	1480	1	PAX3	2	223161816	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3073351	223161816	20037557	181	21917										
IRS1	3667	broad.mit.edu	37	chr2	227662755	227662755	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacctgcatccagaactcccCgggccccgtcacggcagaac	9	19	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:227662755C>T	ENST00000305123.5	-	1	1720	c.700G>A	c.(700-702)Ggg>Agg	p.G234R	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	234	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.G234R(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		CAGAACTCCCCGGGCCCCGTC	0.627											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	2											80	89	86					2																	227662755		2203	4300	6503	227370999	SO:0001583	missense	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.700G>A	2.37:g.227662755C>T	ENSP00000304895:p.Gly234Arg	2321	227370999		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423628	0.83559	.	.	ENSG00000169047	ENST00000305123	D	0.95518	-3.73	5.79	5.79	0.91817	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.000000	0.85682	D	0.000000	D	0.98115	0.9378	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98532	1.0628	10	0.87932	D	0	-35.7946	20.0212	0.97504	0.0:1.0:0.0:0.0	.	234	P35568	IRS1_HUMAN	R	234	ENSP00000304895:G234R	ENSP00000304895:G234R	G	-	1	0	IRS1	227370999	1.000000	0.71417	0.963000	0.40424	0.814000	0.46013	7.818000	0.86416	2.735000	0.93741	0.561000	0.74099	GGG		0.627	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		T	227662755	C	T	227662755	3	4	77	1	0	0	0	0	1	0	0	0	7861	652	23	1	3032	1	IRS1	2	227662755	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4500939	227662755	15536618	182	21918										
MFF	56947	broad.mit.edu	37	chr2	228197247	228197247	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtgtacttacgctgagtgaAagaccactagattttctgga	10	8	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:228197247A>G	ENST00000353339.3	+	5	813	c.372A>G	c.(370-372)gaA>gaG	p.E124E	MFF_ENST00000304593.9_Silent_p.E98E|MFF_ENST00000349901.7_Silent_p.E98E|MFF_ENST00000354503.6_Silent_p.E98E|MFF_ENST00000392059.1_Silent_p.E124E|MFF_ENST00000337110.7_Silent_p.E98E|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000524634.1_5'UTR|MFF_ENST00000409616.1_Silent_p.E98E|MFF_ENST00000409565.1_Silent_p.E98E	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	124					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.E124E(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						CGCTGAGTGAAAGACCACTAG	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	2											256	253	254					2																	228197247		2203	4300	6503	227905491	SO:0001819	synonymous_variant	56947			AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"chromosome 2 open reading frame 33"	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.372A>G	2.37:g.228197247A>G			227905491	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																				0.393	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194		G	228197247	A	G	228197247	2	3	77	1	0	0	0	0	0	0	0	1	9549	11	1	4		4	MFF	2	228197247	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	534492	228197247	15002126	183	21919										
DNER	92737	broad.mit.edu	37	chr2	230271991	230271991	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacgtgccattcaggccgtcGctgtcacaggtggctccgtt	12	14	2	0	rs200801433	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:230271991G>A	ENST00000341772.4	-	10	1814	c.1680C>T	c.(1678-1680)agC>agT	p.S560S		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	560	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Follistatin-like.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.S560S(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		TCAGGCCGTCGCTGTCACAGG	0.512													G|||	3	0.000599042	0	0	5008	,	,		19446	0		0	False		,,,				2504	0.0031															1	Substitution - coding silent(1)	large_intestine(1)	2											140	125	130					2																	230271991		2203	4300	6503	229980235	SO:0001819	synonymous_variant	92737			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1680C>T	2.37:g.230271991G>A			229980235	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Silent	SNP	ENST00000341772.4	37	CCDS33390.1																																																																																				0.512	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		A	230271991	G	A	230271991	2	1	77	1	0	0	0	0	0	0	0	1	4678	1078	38	1		1	DNER	2	230271991	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2074744	230271991	12927382	184	21920										
DNER	92737	broad.mit.edu	37	chr2	230456430	230456430	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggaacaggctgaagctgtcGgggtgccatggattcggtcc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:230456430delG	ENST00000341772.4	-	2	585	c.451delC	c.(451-453)cgafs	p.R151fs		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	151					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.R151fs*23(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		TGAAGCTGTCGGGGTGCCATG	0.572																																																1	Deletion - Frameshift(1)	large_intestine(1)	2											78	64	69					2																	230456430		2203	4300	6503	230164674	SO:0001589	frameshift_variant	92737			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.451delC	2.37:g.230456430delG	ENSP00000345229:p.Arg151fs		230164674	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Frame_Shift_Del	DEL	ENST00000341772.4	37	CCDS33390.1																																																																																				0.572	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		-	230456430	G	-	230456430	7	5	77	1	0	1	0	1	0	0	0	0	4678	1124	39	0	1810	0	DNER	2	230456430	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	184439	230456430	12742943	185	21921										
NCL	4691	broad.mit.edu	37	chr2	232320742	232320742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttggaggacccagtttccCggtcagtaactatccttgcc	9	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:232320742C>T	ENST00000322723.4	-	12	2051	c.1811G>A	c.(1810-1812)cGg>cAg	p.R604Q	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	604	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.R604Q(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CCCAGTTTCCCGGTCAGTAAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											74	72	72					2																	232320742		2203	4300	6503	232028986	SO:0001583	missense	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1811G>A	2.37:g.232320742C>T	ENSP00000318195:p.Arg604Gln		232028986	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	37	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.730421	0.69074	.	.	ENSG00000115053	ENST00000322723;ENST00000392033;ENST00000322732;ENST00000356936	D;D	0.85629	-1.71;-2.01	5.82	5.82	0.92795	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.095731	0.64402	N	0.000002	D	0.82935	0.5145	L	0.27053	0.805	0.58432	D	0.999991	P	0.52692	0.955	P	0.47786	0.557	D	0.84098	0.0394	10	0.52906	T	0.07	1.4296	19.1392	0.93441	0.0:1.0:0.0:0.0	.	604	P19338	NUCL_HUMAN	Q	604;496;376;229	ENSP00000318195:R604Q;ENSP00000349410:R229Q	ENSP00000318195:R604Q	R	-	2	0	NCL	232028986	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.543000	0.53633	2.766000	0.95052	0.551000	0.68910	CGG		0.488	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232320742	C	T	232320742	3	4	77	1	0	0	0	0	1	0	0	0	10257	652	23	1	333	1	NCL	2	232320742	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1864312	232320742	10878631	186	21922										
EFHD1	80303	broad.mit.edu	37	chr2	233537103	233537103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcaaagctttctgagatcGatgtggccctggagggtgtc	15	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:233537103G>A	ENST00000264059.3	+	3	1012	c.535G>A	c.(535-537)Gat>Aat	p.D179N	EFHD1_ENST00000409708.1_Missense_Mutation_p.D67N|EFHD1_ENST00000410095.1_Missense_Mutation_p.D67N|EFHD1_ENST00000409613.1_Missense_Mutation_p.D83N	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	179					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)	p.D179N(1)		NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		TTCTGAGATCGATGTGGCCCT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	129	130					2																	233537103		2203	4300	6503	233245347	SO:0001583	missense	80303				CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"EF-hand domain containing"	29556	protein-coding gene	gene with protein product	"swiprosin-2"	611617	"EF hand domain containing 1"			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.535G>A	2.37:g.233537103G>A	ENSP00000264059:p.Asp179Asn		233245347	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Missense_Mutation	SNP	ENST00000264059.3	37	CCDS2497.1	.	.	.	.	.	.	.	.	.	.	G	5.651	0.304747	0.10678	.	.	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000427698;ENST00000410095	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	4.96	-2.98	0.05513	.	0.274240	0.40385	N	0.001120	T	0.36744	0.0978	L	0.38692	1.165	0.41501	D	0.988287	B;B	0.32101	0.015;0.356	B;B	0.29785	0.003;0.107	T	0.03433	-1.1037	10	0.32370	T	0.25	-3.7005	13.2399	0.59992	0.4315:0.0:0.5685:0.0	.	83;179	E9PFH3;Q9BUP0	.;EFHD1_HUMAN	N	83;179;82;67;67;67	ENSP00000386556:D83N;ENSP00000264059:D179N;ENSP00000386243:D67N;ENSP00000401073:D67N;ENSP00000386685:D67N	ENSP00000264059:D179N	D	+	1	0	EFHD1	233245347	0.922000	0.31269	0.000000	0.03702	0.017000	0.09413	1.437000	0.34991	-1.128000	0.02922	-1.134000	0.01955	GAT		0.557	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		A	233537103	G	A	233537103	3	1	77	1	0	0	0	0	1	0	0	0	4959	1058	37	1	545	1	EFHD1	2	233537103	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1216361	233537103	9662270	187	21923										
INPP5D	3635	broad.mit.edu	37	chr2	234072413	234072413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccaaggggcagggaaagaCgcgggacgactctgcggact	16	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr2:234072413C>T	ENST00000359570.5	+	14	1265	c.1265C>T	c.(1264-1266)aCg>aTg	p.T422M	INPP5D_ENST00000538935.1_Missense_Mutation_p.T421M|INPP5D_ENST00000450745.1_Missense_Mutation_p.T186M|INPP5D_ENST00000455936.2_Missense_Mutation_p.T186M			Q92835	SHIP1_HUMAN	inositol polyphosphate-5-phosphatase, 145kDa	434					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|determination of adult lifespan (GO:0008340)|immunoglobulin mediated immune response (GO:0016064)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of bone resorption (GO:0045779)|negative regulation of immune response (GO:0050777)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of neutrophil differentiation (GO:0045659)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of signal transduction (GO:0009968)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of erythrocyte differentiation (GO:0045648)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|membrane (GO:0016020)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)	p.T434M(1)		central_nervous_system(1)|ovary(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CAGGGAAAGACGCGGGACGAC	0.562																																					NSCLC(82;1215 1426 16163 20348 41018)											1	Substitution - Missense(1)	large_intestine(1)	2											145	151	149					2																	234072413		2048	4176	6224	233736485	SO:0001583	missense	3635			U57650	CCDS74672.1	2q37.1	2013-02-14	2002-08-29		ENSG00000168918	ENSG00000168918		"SH2 domain containing"	6079	protein-coding gene	gene with protein product		601582	"inositol polyphosphate-5-phosphatase, 145kD"			8643691, 8874179	Standard	NM_001017915		Approved	SHIP, hp51CN	uc010zmp.2	Q92835	OTTHUMG00000133688	ENST00000359570.5:c.1265C>T	2.37:g.234072413C>T	ENSP00000352575:p.Thr422Met		233736485	O00145|Q13544|Q13545|Q6P5A4|Q92656|Q9UE80	Missense_Mutation	SNP	ENST00000359570.5	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.632814	0.87660	.	.	ENSG00000168918	ENST00000359570;ENST00000538935;ENST00000450745;ENST00000455936;ENST00000435188;ENST00000415617;ENST00000445964	D;D;D;D;D;D;D	0.97114	-4.23;-4.15;-4.25;-4.25;-4.22;-4.22;-4.22	5.08	5.08	0.68730	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.090226	0.64402	D	0.000002	D	0.98504	0.9501	.	.	.	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.989	D	0.99529	1.0960	9	0.87932	D	0	.	18.6649	0.91486	0.0:1.0:0.0:0.0	.	433;434	Q92835-2;Q92835	.;SHIP1_HUMAN	M	422;421;186;186;55;55;55	ENSP00000352575:T422M;ENSP00000441010:T421M;ENSP00000407916:T186M;ENSP00000404610:T186M;ENSP00000400151:T55M;ENSP00000397421:T55M;ENSP00000405338:T55M	ENSP00000352575:T422M	T	+	2	0	INPP5D	233736485	1.000000	0.71417	0.982000	0.44146	0.860000	0.49131	7.275000	0.78548	2.652000	0.90054	0.655000	0.94253	ACG		0.562	INPP5D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001017915		T	234072413	C	T	234072413	3	4	77	1	0	0	0	0	1	0	0	0	7777	536	19	1	855	1	INPP5D	2	234072413	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	535310	234072413	9126960	188	21924										
TATDN2	9797	broad.mit.edu	37	chr3	10312487	10312487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctctgacttctgtgatcccCgcaccctgacagattgccta	7	15	2	4	rs576056241		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:10312487C>T	ENST00000287652.4	+	4	2672	c.1621C>T	c.(1621-1623)Cgc>Tgc	p.R541C	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.R541C	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	541					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.R541C(1)|p.R541S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CTGTGATCCCCGCACCCTGAC	0.493																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	3											100	106	104					3																	10312487		2203	4300	6503	10287487	SO:0001583	missense	9797			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.1621C>T	3.37:g.10312487C>T	ENSP00000287652:p.Arg541Cys		10287487	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593791	0.46214	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.27402	1.67;1.67	5.0	1.95	0.26073	.	0.098253	0.38217	N	0.001774	T	0.40570	0.1122	L	0.43152	1.355	0.09310	N	0.999999	D	0.76494	0.999	D	0.65443	0.935	T	0.17258	-1.0375	10	0.87932	D	0	-13.1926	8.3749	0.32436	0.4944:0.3701:0.1355:0.0	.	541	Q93075	TATD2_HUMAN	C	541	ENSP00000287652:R541C;ENSP00000408736:R541C	ENSP00000287652:R541C	R	+	1	0	TATDN2	10287487	0.028000	0.19301	0.830000	0.32933	0.870000	0.49936	0.238000	0.18004	0.138000	0.18790	0.644000	0.83932	CGC		0.493	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10312487	C	T	10312487	3	4	77	1	0	0	0	0	1	0	0	0	15631	652	23	1	1631	1	TATDN2	3	10312487	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		10312487	187709943	189	21925										
TMEM40	55287	broad.mit.edu	37	chr3	12785415	12785415	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctaccgggtgagccgttcccGtgggggtatccagcccccag	14	15	0	1	rs374102262	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:12785415G>A	ENST00000314124.7	-	4	641	c.285C>T	c.(283-285)caC>caT	p.H95H	TMEM40_ENST00000264728.8_Silent_p.H95H|TMEM40_ENST00000435218.2_Intron|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000431022.2_Silent_p.H111H|TMEM40_ENST00000476331.1_5'Flank	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	95						integral component of membrane (GO:0016021)		p.H95H(1)		breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						AGCCGTTCCCGTGGGGGTATC	0.542													G|||	2	0.000399361	0	0	5008	,	,		19446	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											81	79	80					3																	12785415		2203	4300	6503	12760415	SO:0001819	synonymous_variant	55287			BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726			25620	protein-coding gene	gene with protein product						12477932	Standard	NM_018306		Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.285C>T	3.37:g.12785415G>A			12760415	C9JID5|Q8NAL4|Q9NUZ4	Silent	SNP	ENST00000314124.7	37	CCDS2613.1																																																																																				0.542	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252029.2	NM_018306		A	12785415	G	A	12785415	2	1	77	1	0	0	0	0	0	0	0	1	16202	1136	40	1		1	TMEM40	3	12785415	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2472928	12785415	185237015	190	21926										
CAND2	23066	broad.mit.edu	37	chr3	12845082	12845082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtggtgaagatgctgctccGgctcctggaggacaagaacg	16	9	0	3	rs530014195	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:12845082G>A	ENST00000456430.2	+	2	205	c.164G>A	c.(163-165)cGg>cAg	p.R55Q	CAND2_ENST00000295989.5_Missense_Mutation_p.R55Q	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	55					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.R55Q(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ATGCTGCTCCGGCTCCTGGAG	0.612													G|||	2	0.000399361	0	0.0014	5008	,	,		6133	0		0.001	False		,,,				2504	0				GBM(43;676 868 1633 6395 37496)											1	Substitution - Missense(1)	large_intestine(1)	3											55	62	59					3																	12845082		2201	4300	6501	12820082	SO:0001583	missense	23066				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.164G>A	3.37:g.12845082G>A	ENSP00000387641:p.Arg55Gln		12820082	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.316136	0.40996	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.06849	3.25;3.25	4.66	-0.118	0.13547	Armadillo-like helical (1);Armadillo-type fold (1);	0.314499	0.27504	N	0.019074	T	0.04998	0.0134	L	0.33093	0.98	0.47778	D	0.999511	B;B	0.29253	0.155;0.239	B;B	0.23018	0.043;0.021	T	0.46707	-0.9172	10	0.18710	T	0.47	-15.3241	7.6699	0.28453	0.579:0.0:0.421:0.0	.	55;55	O75155;O75155-2	CAND2_HUMAN;.	Q	55	ENSP00000295989:R55Q;ENSP00000387641:R55Q	ENSP00000295989:R55Q	R	+	2	0	CAND2	12820082	0.998000	0.40836	0.096000	0.21009	0.905000	0.53344	2.351000	0.44071	0.047000	0.15862	-0.136000	0.14681	CGG		0.612	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		A	12845082	G	A	12845082	3	1	77	1	0	0	0	0	1	0	0	0	2622	1116	39	1	170	1	CAND2	3	12845082	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	59667	12845082	185177348	191	21927										
GRIP2	80852	broad.mit.edu	37	chr3	14536472	14536472	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgctgaaaccaaagtcatgcCgcatggggtccttgtgcagg	13	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:14536472C>T	ENST00000273083.3	-	0	2913							Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2						synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.R951Q(1)		endometrium(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	25						AAAGTCATGCCGCATGGGGTC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											102	108	106					3																	14536472		2092	4208	6300	14511476			80852			AB051506		3p24-p23	2012-02-08			ENSG00000144596	ENSG00000144596			23841	protein-coding gene	gene with protein product							Standard	NM_001080423		Approved	KIAA1719	uc021wtn.1	Q9C0E4	OTTHUMG00000155544		3.37:g.14536472C>T			14511476	Q8TEH9|Q9H7H3	Missense_Mutation	SNP	ENST00000273083.3	37																																																																																					0.597	GRIP2-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000340582.2	NM_001080423		T	14536472	C	T	14536472	1	4	77	0	1	0	0	0	0	0	0	0	6809	652	23	1		1	GRIP2	3	14536472	RNA	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1691390	14536472	183485958	192	21928										
NGLY1	55768	broad.mit.edu	37	chr3	25761041	25761041	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgggtgtgttgccaagcGacatcaccatctcctctgct	10	13	3	0	rs117889176	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:25761041G>A	ENST00000280700.5	-	12	2035	c.1875C>T	c.(1873-1875)gtC>gtT	p.V625V	NGLY1_ENST00000428257.1_Silent_p.V607V|NGLY1_ENST00000396649.3_3'UTR|NGLY1_ENST00000417874.2_Silent_p.V583V|NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000467224.1_5'UTR	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	625	PAW. {ECO:0000255|PROSITE- ProRule:PRU00731}.				glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)	p.V625V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						GTTGCCAAGCGACATCACCAT	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	3											106	108	107					3																	25761041		2203	4300	6503	25736045	SO:0001819	synonymous_variant	55768			AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1875C>T	3.37:g.25761041G>A			25736045	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Silent	SNP	ENST00000280700.5	37	CCDS33719.1																																																																																				0.388	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			A	25761041	G	A	25761041	2	1	77	1	0	0	0	0	0	0	0	1	10429	1045	37	1		1	NGLY1	3	25761041	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11224569	25761041	172261389	193	21929										
MLH1	4292	broad.mit.edu	37	chr3	37070324	37070324	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaatggtggaagatgattccCgaaaggaaatgactgcagct	12	6	0	3	rs63749795|rs587778919		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:37070324C>T	ENST00000231790.2	+	13	1675	c.1459C>T	c.(1459-1461)Cga>Tga	p.R487*	MLH1_ENST00000455445.2_Nonsense_Mutation_p.R246*|MLH1_ENST00000435176.1_Nonsense_Mutation_p.R389*|MLH1_ENST00000458205.2_Nonsense_Mutation_p.R246*|MLH1_ENST00000539477.1_Nonsense_Mutation_p.R246*|MLH1_ENST00000536378.1_Nonsense_Mutation_p.R246*	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	487	Interaction with EXO1.				ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.R487*(1)|p.R487R(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						AGATGATTCCCGAAAGGAAAT	0.418		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	3	Substitution - Nonsense(1)|Whole gene deletion(1)|Substitution - coding silent(1)	ovary(1)|lung(1)|large_intestine(1)	3	GRCh37	CM000177	MLH1	M	rs63749795						207	211	210					3																	37070324		2203	4300	6503	37045328	SO:0001587	stop_gained	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1459C>T	3.37:g.37070324C>T	ENSP00000231790:p.Arg487*		37045328	B4DI13|B4DQ11|E9PCU2	Nonsense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	C	40	8.097178	0.98651	.	.	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000421440;ENST00000396438;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378;ENST00000450420;ENST00000413740	.	.	.	5.72	1.29	0.21616	.	1.288720	0.05174	N	0.500017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-2.0E-4	9.3531	0.38151	0.3865:0.2478:0.3657:0.0	rs63749795	.	.	.	X	487;351;30;30;246;246;246;389;246;28;28	.	ENSP00000231790:R487X	R	+	1	2	MLH1	37045328	0.000000	0.05858	0.416000	0.26546	0.962000	0.63368	0.280000	0.18790	0.308000	0.22923	0.563000	0.77884	CGA		0.418	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		T	37070324	C	T	37070324	4	4	77	1	0	0	0	0	0	1	0	0	9647	644	23	1	1509	1	MLH1	3	37070324	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	11309283	37070324	160952106	194	21930										
ACAA1	30	broad.mit.edu	37	chr3	38168131	38168131	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgcccttgtcatcatggacCgtggtggtcacaggcacaat	12	11	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:38168131C>T	ENST00000333167.8	-	8	859	c.687G>A	c.(685-687)acG>acA	p.T229T	ACAA1_ENST00000450296.1_Silent_p.T188T|ACAA1_ENST00000301810.7_Silent_p.T196T|ACAA1_ENST00000444607.2_3'UTR|Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000544624.1_Silent_p.T77T|ACAA1_ENST00000480865.1_5'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	229					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)	p.T229T(1)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CATCATGGACCGTGGTGGTCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	3											173	139	151					3																	38168131		2203	4300	6503	38143135	SO:0001819	synonymous_variant	30			X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.687G>A	3.37:g.38168131C>T			38143135	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	37	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	C	4.992	0.184215	0.09495	.	.	ENSG00000060971	ENST00000452171;ENST00000421218	.	.	.	5.46	-5.41	0.02648	.	.	.	.	.	T	0.18759	0.0450	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	T	0.29058	-1.0024	4	.	.	.	-14.2767	3.7997	0.08753	0.1485:0.2792:0.3858:0.1864	.	.	.	.	Q	102;119	.	.	R	-	2	0	ACAA1	38143135	0.000000	0.05858	0.004000	0.12327	0.738000	0.42128	-0.850000	0.04317	-0.885000	0.03971	-0.882000	0.02950	CGG		0.602	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		T	38168131	C	T	38168131	2	4	77	1	0	0	0	0	0	0	0	1	104	639	23	1		1	ACAA1	3	38168131	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1097807	38168131	159854299	195	21931										
MYRIP	25924	broad.mit.edu	37	chr3	40085626	40085626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgtggagcactgctgcatgCgctgctgctcgcccttcacc	11	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:40085626C>T	ENST00000302541.6	+	3	538	c.196C>T	c.(196-198)Cgc>Tgc	p.R66C	MYRIP_ENST00000396217.3_Silent_p.C22C|MYRIP_ENST00000444716.1_Missense_Mutation_p.R66C|MYRIP_ENST00000425621.1_Missense_Mutation_p.R66C	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	66	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)	p.R66C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		CTGCTGCATGCGCTGCTGCTC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	3											99	77	85					3																	40085626		2203	4300	6503	40060630	SO:0001583	missense	25924			AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.196C>T	3.37:g.40085626C>T	ENSP00000301972:p.Arg66Cys		40060630	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	C	31	5.065203	0.93898	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621	T;T;T	0.78246	-1.16;-1.16;-1.16	5.51	5.51	0.81932	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89553	0.6748	M	0.87827	2.91	0.80722	D	1	P;D;D	0.89917	0.929;0.958;1.0	P;P;D	0.83275	0.457;0.659;0.996	D	0.90512	0.4482	9	.	.	.	.	16.9147	0.86148	0.0:1.0:0.0:0.0	.	66;66;66	B3KWW4;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	C	66	ENSP00000398665:R66C;ENSP00000301972:R66C;ENSP00000389323:R66C	.	R	+	1	0	MYRIP	40060630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.080000	0.71299	2.582000	0.87167	0.563000	0.77884	CGC		0.552	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		T	40085626	C	T	40085626	3	4	77	1	0	0	0	0	1	0	0	0	10130	768	27	1	202	1	MYRIP	3	40085626	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1917495	40085626	157936804	196	21932										
TRAK1	22906	broad.mit.edu	37	chr3	42251393	42251393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgaagtgtactgccttaacGactttgaagaagatgacaca	9	8	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:42251393G>A	ENST00000327628.5	+	14	2279	c.1879G>A	c.(1879-1881)Gac>Aac	p.D627N	TRAK1_ENST00000341421.3_Missense_Mutation_p.D569N|TRAK1_ENST00000396175.1_Missense_Mutation_p.D569N|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	627					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.D569N(4)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CTGCCTTAACGACTTTGAAGA	0.587																																					GBM(44;195 884 22595 31865 41850)											4	Substitution - Missense(4)	large_intestine(4)	3											138	123	128					3																	42251393		2203	4300	6503	42226397	SO:0001583	missense	22906				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1879G>A	3.37:g.42251393G>A	ENSP00000328998:p.Asp627Asn		42226397	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595021	0.86953	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175;ENST00000341421	T;T;T	0.21031	2.17;2.13;2.03	5.31	5.31	0.75309	.	0.113159	0.56097	D	0.000026	T	0.30916	0.0780	M	0.70595	2.14	0.58432	D	0.999996	D;D;D;D;D	0.62365	0.968;0.984;0.968;0.991;0.975	B;B;B;B;B	0.43754	0.248;0.248;0.248;0.43;0.335	T	0.25152	-1.0140	10	0.87932	D	0	.	17.9657	0.89099	0.0:0.0:1.0:0.0	.	553;569;627;569;627	B7Z218;C9JC32;B7Z347;Q9UPV9-2;Q9UPV9	.;.;.;.;TRAK1_HUMAN	N	627;627;569;569	ENSP00000328998:D627N;ENSP00000379478:D569N;ENSP00000340702:D569N	ENSP00000328998:D627N	D	+	1	0	TRAK1	42226397	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.471000	0.80985	2.468000	0.83385	0.655000	0.94253	GAC		0.587	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		A	42251393	G	A	42251393	3	1	77	1	0	0	0	0	1	0	0	0	16489	1058	37	1	2049	1	TRAK1	3	42251393	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2165767	42251393	155771037	197	21933										
ABHD5	51099	broad.mit.edu	37	chr3	43744000	43744000	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagagtggagatgtgccctaGgattggacaaaatgatcttg	13	5	1	3	rs374480855		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:43744000G>T	ENST00000458276.2	+	3	550	c.427G>T	c.(427-429)Gga>Tga	p.G143*		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	143					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)	p.G143*(1)		kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		ATGTGCCCTAGGATTGGACAA	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											241	231	235					3																	43744000		2203	4300	6503	43719004	SO:0001587	stop_gained	51099			AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"Abhydrolase domain containing"	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.427G>T	3.37:g.43744000G>T	ENSP00000390849:p.Gly143*		43719004	B2R9K0|Q9Y369	Nonsense_Mutation	SNP	ENST00000458276.2	37	CCDS2711.1	.	.	.	.	.	.	.	.	.	.	G	37	6.277214	0.97435	.	.	ENSG00000011198	ENST00000456453;ENST00000458276	.	.	.	5.66	2.81	0.32909	.	0.154543	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-24.5331	9.9641	0.41715	0.2295:0.0:0.7705:0.0	.	.	.	.	X	102;143	.	ENSP00000391582:G102X	G	+	1	0	ABHD5	43719004	1.000000	0.71417	0.008000	0.14137	0.780000	0.44128	5.434000	0.66526	0.284000	0.22305	-0.244000	0.11960	GGA		0.468	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		T	43744000	G	T	43744000	4	4	77	1	0	0	0	0	0	1	0	0	85	1001	35	2	437	2	ABHD5	3	43744000	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1492607	43744000	154278430	198	21934										
LARS2	23395	broad.mit.edu	37	chr3	45500311	45500311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaacatggctgttcatggcGttctggagcaaaggtggaac	14	7	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:45500311G>A	ENST00000415258.1	+	7	824	c.683G>A	c.(682-684)cGt>cAt	p.R228H	LARS2_ENST00000265537.3_Missense_Mutation_p.R228H|LARS2_ENST00000414984.1_Missense_Mutation_p.R185H			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	228					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.R228H(1)		endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	TGTTCATGGCGTTCTGGAGCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	3											133	122	126					3																	45500311		2203	4300	6503	45475315	SO:0001583	missense	23395			AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	17095	protein-coding gene	gene with protein product	"leucine tRNA ligase 2, mitochondrial"	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.683G>A	3.37:g.45500311G>A	ENSP00000408576:p.Arg228His		45475315		Missense_Mutation	SNP	ENST00000415258.1	37	CCDS2728.1	.	.	.	.	.	.	.	.	.	.	G	35	5.497919	0.96355	.	.	ENSG00000011376	ENST00000265537;ENST00000415258;ENST00000414984	D;D;D	0.82167	-1.58;-1.58;-1.58	5.41	5.41	0.78517	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	D	0.94003	0.8079	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95149	0.8271	10	0.87932	D	0	-19.5389	19.5567	0.95351	0.0:0.0:1.0:0.0	.	185;228	E9PHM2;Q15031	.;SYLM_HUMAN	H	228;228;185	ENSP00000265537:R228H;ENSP00000408576:R228H;ENSP00000412893:R185H	ENSP00000265537:R228H	R	+	2	0	LARS2	45475315	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	9.420000	0.97426	2.711000	0.92665	0.563000	0.77884	CGT		0.478	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340		A	45500311	G	A	45500311	3	1	77	1	0	0	0	0	1	0	0	0	8657	1145	40	1	705	1	LARS2	3	45500311	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1756311	45500311	152522119	199	21935										
XCR1	2829	broad.mit.edu	37	chr3	46062775	46062775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgaagatgagcttgaccgtgCggtggcgccgcttggagcgt	17	10	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:46062775C>T	ENST00000309285.3	-	2	1021	c.665G>A	c.(664-666)cGc>cAc	p.R222H	XCR1_ENST00000542109.1_Missense_Mutation_p.R222H	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	222					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)	p.R222H(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CTTGACCGTGCGGTGGCGCCG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	3											68	61	64					3																	46062775		2203	4300	6503	46037779	SO:0001583	missense	2829				CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"GPCR / Class A : Chemokine receptors : X-C motif"	1625	protein-coding gene	gene with protein product		600552	"chemokine (C motif) XC receptor 1"	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.665G>A	3.37:g.46062775C>T	ENSP00000310405:p.Arg222His		46037779		Missense_Mutation	SNP	ENST00000309285.3	37	CCDS2736.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.905715	0.72868	.	.	ENSG00000173578	ENST00000309285;ENST00000542109	T;T	0.43688	0.94;0.94	5.72	5.72	0.89469	GPCR, rhodopsin-like superfamily (1);	0.191393	0.39544	N	0.001325	T	0.65739	0.2720	M	0.80746	2.51	0.37263	D	0.907054	D	0.89917	1.0	D	0.85130	0.997	T	0.73366	-0.4005	10	0.87932	D	0	.	13.1218	0.59331	0.0:0.927:0.0:0.0729	.	222	P46094	XCR1_HUMAN	H	222	ENSP00000310405:R222H;ENSP00000438119:R222H	ENSP00000310405:R222H	R	-	2	0	XCR1	46037779	1.000000	0.71417	0.956000	0.39512	0.677000	0.39632	2.051000	0.41307	2.696000	0.92011	0.650000	0.86243	CGC		0.587	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2			T	46062775	C	T	46062775	3	4	77	1	0	0	0	0	1	0	0	0	17465	768	27	1	340	1	XCR1	3	46062775	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	562464	46062775	151959655	200	21936										
NBEAL2	23218	broad.mit.edu	37	chr3	47042866	47042866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcaagcgctttggctgctgCgtctgctgcaggacttcctg	13	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:47042866C>T	ENST00000450053.3	+	29	4761	c.4582C>T	c.(4582-4584)Cgt>Tgt	p.R1528C	NBEAL2_ENST00000292309.5_Missense_Mutation_p.R1344C|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1528					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R905C(1)|p.R1528C(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TTGGCTGCTGCGTCTGCTGCA	0.612																																																2	Substitution - Missense(2)	large_intestine(2)	3											36	42	40					3																	47042866		2121	4248	6369	47017870	SO:0001583	missense	23218			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4582C>T	3.37:g.47042866C>T	ENSP00000415034:p.Arg1528Cys		47017870	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.852868	0.71719	.	.	ENSG00000160796	ENST00000292309;ENST00000450053	T;T	0.60424	0.22;0.19	4.87	4.87	0.63330	.	0.070544	0.64402	D	0.000017	T	0.71804	0.3383	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.74811	-0.3538	10	0.72032	D	0.01	.	15.544	0.76081	0.0:1.0:0.0:0.0	.	1528	Q6ZNJ1	NBEL2_HUMAN	C	1344;1528	ENSP00000292309:R1344C;ENSP00000415034:R1528C	ENSP00000292309:R1344C	R	+	1	0	NBEAL2	47017870	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.814000	0.38972	2.517000	0.84864	0.563000	0.77884	CGT		0.612	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47042866	C	T	47042866	3	4	77	1	0	0	0	0	1	0	0	0	10219	768	27	1	4696	1	NBEAL2	3	47042866	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	980091	47042866	150979564	201	21937										
PTPN23	25930	broad.mit.edu	37	chr3	47452321	47452322	+	Frame_Shift_Ins	INS	-	-	C													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggtcctggggcagccgccaINSccccccctacacacccagct					rs374554596		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:47452321_47452322insC	ENST00000265562.4	+	20	3110_3111	c.3033_3034insC	c.(3034-3036)cccfs	p.P1012fs	PTPN23_ENST00000431726.1_Frame_Shift_Ins_p.P886fs	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1012	His.|Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.L1014fs*68(1)		breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGCAGCCGCCACCCCCCCTACA	0.688																																																1	Insertion - Frameshift(1)	large_intestine(1)	3																																								47427326	SO:0001589	frameshift_variant	25930			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3040dupC	3.37:g.47452328_47452328dupC	ENSP00000265562:p.Pro1012fs		47427325	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Frame_Shift_Ins	INS	ENST00000265562.4	37	CCDS2754.1																																																																																				0.688	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		C	47452322	-	C	47452321	7	5	77	1	0	1	1	0	0	0	0	0	12825	146	6	0	3111	0	PTPN23	3	47452321	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	409455	47452321	150570109	202	21938										
PLXNB1	5364	broad.mit.edu	37	chr3	48463566	48463566	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtccctgtgagcaaggcaagAtgcacagtccaggtgctgag	14	10	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:48463566A>G	ENST00000358536.4	-	6	1737	c.1468T>C	c.(1468-1470)Tct>Cct	p.S490P	PLXNB1_ENST00000358459.4_Missense_Mutation_p.S490P|PLXNB1_ENST00000296440.6_Missense_Mutation_p.S490P|PLXNB1_ENST00000456774.1_Missense_Mutation_p.S490P|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	490					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.S490P(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCAAGGCAAGATGCACAGTCC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	3											82	73	76					3																	48463566		2203	4300	6503	48438570	SO:0001583	missense	5364			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.1468T>C	3.37:g.48463566A>G	ENSP00000351338:p.Ser490Pro		48438570	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	a	22.7	4.324822	0.81580	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	5.45	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	M	0.88906	2.99	0.80722	D	1	D;P	0.76494	0.999;0.674	D;P	0.76575	0.988;0.518	T	0.56282	-0.8005	10	0.59425	D	0.04	.	11.7561	0.51875	0.8524:0.1476:0.0:0.0	.	490;490	O43157;O43157-2	PLXB1_HUMAN;.	P	490	ENSP00000296440:S490P;ENSP00000351242:S490P;ENSP00000351338:S490P;ENSP00000414199:S490P	ENSP00000296440:S490P	S	-	1	0	PLXNB1	48438570	1.000000	0.71417	0.733000	0.30861	0.977000	0.68977	9.044000	0.93805	0.869000	0.35703	0.524000	0.50904	TCT		0.577	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		G	48463566	A	G	48463566	3	3	77	1	0	0	0	0	1	0	0	0	12154	333	12	4	5071	4	PLXNB1	3	48463566	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1011245	48463566	149558864	203	21939										
P4HTM	54681	broad.mit.edu	37	chr3	49039998	49039998	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagagcattcaggagatgtaCgccgcgatcaaggctgaccc	13	11	2	3	rs558724306	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:49039998C>T	ENST00000383729.4	+	4	1064	c.693C>T	c.(691-693)taC>taT	p.Y231Y	P4HTM_ENST00000343546.4_Silent_p.Y231Y	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	231	EF-hand 2.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)	p.Y231Y(1)		NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	AGGAGATGTACGCCGCGATCA	0.577													C|||	3	0.000599042	0	0	5008	,	,		19678	0		0	False		,,,				2504	0.0031															1	Substitution - coding silent(1)	large_intestine(1)	3											201	180	187					3																	49039998		2203	4300	6503	49015002	SO:0001819	synonymous_variant	54681				CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"Prolyl hydroxlase domain-containing 4", "hypoxia inducible factor prolyl 4 hydroxylase"	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.693C>T	3.37:g.49039998C>T			49015002	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Silent	SNP	ENST00000383729.4	37	CCDS43089.1	.	.	.	.	.	.	.	.	.	.	C	5.737	0.320365	0.10845	.	.	ENSG00000178467	ENST00000444213	.	.	.	5.76	3.98	0.46160	.	.	.	.	.	T	0.58694	0.2140	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54111	-0.8342	4	.	.	.	-23.819	8.63	0.33913	0.0:0.7134:0.0:0.2866	.	.	.	.	C	161	.	.	R	+	1	0	P4HTM	49015002	0.808000	0.29022	0.842000	0.33263	0.629000	0.37895	0.678000	0.25277	0.793000	0.33875	-0.253000	0.11424	CGC		0.577	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938		T	49039998	C	T	49039998	2	4	77	1	0	0	0	0	0	0	0	1	11391	547	19	1		1	P4HTM	3	49039998	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	576432	49039998	148982432	204	21940										
NICN1	84276	broad.mit.edu	37	chr3	49463813	49463813	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaggtgtactgacggacacGgatgctcaaaaaagctgtgt	13	7	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:49463813G>T	ENST00000273598.3	-	2	267	c.181C>A	c.(181-183)Cgt>Agt	p.R61S	NICN1_ENST00000422593.1_5'UTR|NICN1_ENST00000436744.2_Missense_Mutation_p.R61S|NICN1-AS1_ENST00000424915.1_RNA	NM_032316.3	NP_115692.1	Q9BSH3	NICN1_HUMAN	nicolin 1	61						microtubule (GO:0005874)|nucleus (GO:0005634)		p.R61S(1)		kidney(1)|large_intestine(3)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGACGGACACGGATGCTCAAA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	3											96	82	86					3																	49463813		2203	4300	6503	49438817	SO:0001583	missense	84276			AJ299740	CCDS2798.1	3p21.31	2008-07-18			ENSG00000145029	ENSG00000145029			18317	protein-coding gene	gene with protein product		611516				12392556	Standard	NM_032316		Approved	MGC12936	uc003cwz.1	Q9BSH3	OTTHUMG00000156848	ENST00000273598.3:c.181C>A	3.37:g.49463813G>T	ENSP00000273598:p.Arg61Ser		49438817	Q8IZQ2	Missense_Mutation	SNP	ENST00000273598.3	37	CCDS2798.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.655985	0.67586	.	.	ENSG00000145029	ENST00000273598;ENST00000430622;ENST00000436744	T;T	0.23754	1.89;1.89	5.15	5.15	0.70609	.	0.063063	0.64402	D	0.000009	T	0.35799	0.0944	L	0.48642	1.525	0.49389	D	0.999788	D;D	0.56287	0.975;0.975	P;P	0.55577	0.7;0.779	T	0.07751	-1.0756	10	0.72032	D	0.01	-5.8005	11.2404	0.48966	0.0:0.0:0.817:0.1829	.	61;61	B4DX77;Q9BSH3	.;NICN1_HUMAN	S	61	ENSP00000273598:R61S;ENSP00000402335:R61S	ENSP00000273598:R61S	R	-	1	0	NICN1	49438817	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.396000	0.73234	2.417000	0.82017	0.655000	0.94253	CGT		0.532	NICN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346224.3	NM_032316		T	49463813	G	T	49463813	3	4	77	1	0	0	0	0	1	0	0	0	10444	1116	39	2	480	2	NICN1	3	49463813	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	423815	49463813	148558617	205	21941										
MST1R	4486	broad.mit.edu	37	chr3	49933239	49933239	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcagcaggataccaaggagCgtgctctgtgggaccccatc	14	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:49933239C>T	ENST00000296474.3	-	12	2898	c.2871G>A	c.(2869-2871)acG>acA	p.T957T	MST1R_ENST00000344206.4_Silent_p.T908T	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	957					cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)	p.T957T(2)		cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		TACCAAGGAGCGTGCTCTGTG	0.607																																																2	Substitution - coding silent(2)	large_intestine(2)	3											62	62	62					3																	49933239		2203	4300	6503	49908243	SO:0001819	synonymous_variant	4486			X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.2871G>A	3.37:g.49933239C>T			49908243	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	37	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	C	6.656	0.489541	0.12641	.	.	ENSG00000164078	ENST00000434765	.	.	.	5.43	-10.9	0.00192	.	.	.	.	.	T	0.21468	0.0517	.	.	.	0.09310	N	0.99999	.	.	.	.	.	.	T	0.14755	-1.0461	4	.	.	.	2.0586	6.3956	0.21611	0.0905:0.1811:0.0901:0.6383	.	.	.	.	H	4	.	.	R	-	2	0	MST1R	49908243	0.000000	0.05858	0.001000	0.08648	0.178000	0.23041	-1.751000	0.01821	-1.597000	0.01609	-0.333000	0.08304	CGC		0.607	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			T	49933239	C	T	49933239	2	4	77	1	0	0	0	0	0	0	0	1	9921	755	27	1		1	MST1R	3	49933239	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	469426	49933239	148089191	206	21942										
CACNA2D2	9254	broad.mit.edu	37	chr3	50416556	50416556	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caattgtacttctcaaagacGtcctgcacgcggtcctcacc	7	15	2	1	rs150031515		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:50416556G>A	ENST00000479441.1	-	12	1226	c.1227C>T	c.(1225-1227)gaC>gaT	p.D409D	CACNA2D2_ENST00000266039.3_Silent_p.D409D|CACNA2D2_ENST00000360963.3_Silent_p.D340D|CACNA2D2_ENST00000395083.1_Silent_p.D409D|CACNA2D2_ENST00000429770.1_Silent_p.D409D|CACNA2D2_ENST00000435965.1_Silent_p.D409D|CACNA2D2_ENST00000423994.2_Silent_p.D409D|CACNA2D2_ENST00000424201.2_Silent_p.D409D			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	409	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.D409D(1)		breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TCTCAAAGACGTCCTGCACGC	0.597													G|||	1	0.000199681	8e-04	0	5008	,	,		21945	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3						G	,,	9,4397	16.8+/-37.8	0,9,2194	156	121	133		1227,1227,1227	-9.3	0.6	3	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA2D2	NM_001005505.1,NM_001174051.1,NM_006030.2	,,	0,10,6493	AA,AG,GG		0.0116,0.2043,0.0769	,,	409/1146,409/1151,409/1144	50416556	10,12996	2203	4300	6503	50391560	SO:0001819	synonymous_variant	9254			AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.1227C>T	3.37:g.50416556G>A			50391560	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Silent	SNP	ENST00000479441.1	37	CCDS54588.1																																																																																				0.597	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		A	50416556	G	A	50416556	2	1	77	1	0	0	0	0	0	0	0	1	2555	1136	40	1		1	CACNA2D2	3	50416556	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	483317	50416556	147605874	207	21943										
RBM15B	29890	broad.mit.edu	37	chr3	51430451	51430451	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacaccttctgtactcagacCgagaccggacttttttggaa	8	12	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:51430451C>T	ENST00000323686.4	+	1	1721	c.1621C>T	c.(1621-1623)Cga>Tga	p.R541*		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	541					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R541R(1)|p.R541*(1)		endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTACTCAGACCGAGACCGGAC	0.607																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(2)	3											37	43	41					3																	51430451		2203	4300	6503	51405491	SO:0001587	stop_gained	29890			AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.1621C>T	3.37:g.51430451C>T	ENSP00000313890:p.Arg541*		51405491	A4QPG7|Q6QE19|Q9BV96	Nonsense_Mutation	SNP	ENST00000323686.4	37	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	C	36	5.746616	0.96882	.	.	ENSG00000179837	ENST00000323686;ENST00000541145	.	.	.	5.55	2.58	0.30949	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4592	14.3491	0.66688	0.5025:0.4975:0.0:0.0	.	.	.	.	X	541;214	.	ENSP00000313890:R541X	R	+	1	2	RBM15B	51405491	0.937000	0.31787	0.998000	0.56505	0.998000	0.95712	0.821000	0.27338	0.676000	0.31285	0.655000	0.94253	CGA		0.607	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		T	51430451	C	T	51430451	4	4	77	1	0	0	0	0	0	1	0	0	13154	644	23	1	1623	1	RBM15B	3	51430451	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1013895	51430451	146591979	208	21944										
GPR62	118442	broad.mit.edu	37	chr3	51989779	51989779	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcaacggcgcgctgctggtCgtggtgctgcgcacgccggg	19	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:51989779C>T	ENST00000322241.4	+	1	450	c.111C>T	c.(109-111)gtC>gtT	p.V37V		NM_080865.3	NP_543141.3	Q9BZJ7	GPR62_HUMAN	G protein-coupled receptor 62	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.V37V(1)		endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CGCTGCTGGTCGTGGTGCTGC	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	3											36	29	31					3																	51989779		2196	4298	6494	51964819	SO:0001819	synonymous_variant	118442			AF317653	CCDS2838.1	3p21.1	2012-08-21			ENSG00000180929	ENSG00000180929		"GPCR / Class A : Orphans"	13301	protein-coding gene	gene with protein product		606917				11165367	Standard	NM_080865		Approved		uc003dca.4	Q9BZJ7	OTTHUMG00000157367	ENST00000322241.4:c.111C>T	3.37:g.51989779C>T			51964819	F1DAM4|Q5KU27	Silent	SNP	ENST00000322241.4	37	CCDS2838.1																																																																																				0.706	GPR62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348611.1			T	51989779	C	T	51989779	2	4	77	1	0	0	0	0	0	0	0	1	6723	871	31	1		1	GPR62	3	51989779	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	559328	51989779	146032651	209	21945										
ALAS1	211	broad.mit.edu	37	chr3	52242218	52242218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaggcggagggattggggatCgggatggagtcatgccaaaa	19	5	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52242218C>T	ENST00000394965.2	+	9	1645	c.1285C>T	c.(1285-1287)Cgg>Tgg	p.R429W	ALAS1_ENST00000469224.1_Missense_Mutation_p.R429W|ALAS1_ENST00000310271.2_Missense_Mutation_p.R429W|ALAS1_ENST00000484952.1_Missense_Mutation_p.R429W	NM_000688.5	NP_000679.1	P13196	HEM1_HUMAN	aminolevulinate, delta-, synthase 1	429					cellular lipid metabolic process (GO:0044255)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5-aminolevulinate synthase activity (GO:0003870)|pyridoxal phosphate binding (GO:0030170)	p.R429W(2)		endometrium(3)|kidney(3)|large_intestine(7)|liver(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)	GATTGGGGATCGGGATGGAGT	0.478																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	3											137	126	130					3																	52242218		2203	4300	6503	52217258	SO:0001583	missense	211			X56351	CCDS2847.1	3p21	2004-11-18			ENSG00000023330	ENSG00000023330	2.3.1.37		396	protein-coding gene	gene with protein product		125290		ALAS3, ALAS			Standard	NM_000688		Approved		uc003dcz.2	P13196	OTTHUMG00000158108	ENST00000394965.2:c.1285C>T	3.37:g.52242218C>T	ENSP00000378416:p.Arg429Trp		52217258		Missense_Mutation	SNP	ENST00000394965.2	37	CCDS2847.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313335	0.81358	.	.	ENSG00000023330	ENST00000469224;ENST00000394965;ENST00000310271;ENST00000484952	D;D;D;D	0.91740	-2.9;-2.9;-2.9;-2.9	5.11	5.11	0.69529	Aminotransferase, class I/classII (1);Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.97343	0.9131	H	0.96996	3.92	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98354	1.0545	10	0.87932	D	0	-13.6701	13.9625	0.64191	0.1524:0.8476:0.0:0.0	.	446;429	B4DVA0;P13196	.;HEM1_HUMAN	W	429	ENSP00000417719:R429W;ENSP00000378416:R429W;ENSP00000309259:R429W;ENSP00000418779:R429W	ENSP00000309259:R429W	R	+	1	2	ALAS1	52217258	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	2.966000	0.49208	2.372000	0.80975	0.655000	0.94253	CGG		0.478	ALAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350207.1			T	52242218	C	T	52242218	3	4	77	1	0	0	0	0	1	0	0	0	484	875	31	1	1311	1	ALAS1	3	52242218	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	252439	52242218	145780212	210	21946										
GLYCTK	132158	broad.mit.edu	37	chr3	52326835	52326835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggctcgggcaggggtggccGgaaccaggaactggccctgc	19	12	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52326835G>A	ENST00000436784.2	+	5	1325	c.1265G>A	c.(1264-1266)cGg>cAg	p.R422Q	MIR135A1_ENST00000385191.1_RNA|GLYCTK_ENST00000305690.8_Intron|GLYCTK_ENST00000471180.1_Intron|GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000473032.1_Intron|GLYCTK_ENST00000354773.4_3'UTR|GLYCTK_ENST00000461183.1_Intron|GLYCTK_ENST00000477382.1_3'UTR			Q8IVS8	GLCTK_HUMAN	glycerate kinase	422					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)	p.R422Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		AGGGGTGGCCGGAACCAGGAA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	3											65	64	64					3																	52326835		2203	4300	6503	52301875	SO:0001583	missense	132158				CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380	ENST00000436784.2:c.1265G>A	3.37:g.52326835G>A	ENSP00000389175:p.Arg422Gln		52301875	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	Missense_Mutation	SNP	ENST00000436784.2	37	CCDS2852.1	.	.	.	.	.	.	.	.	.	.	G	36	5.891426	0.97074	.	.	ENSG00000168237	ENST00000436784;ENST00000411757	T	0.63096	-0.02	5.98	5.98	0.97165	MOFRL domain (2);	0.000000	0.85682	D	0.000000	D	0.87374	0.6161	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90560	0.4515	9	.	.	.	-32.0588	20.4293	0.99080	0.0:0.0:1.0:0.0	.	422	Q8IVS8	GLCTK_HUMAN	Q	422;356	ENSP00000389175:R422Q	.	R	+	2	0	GLYCTK	52301875	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.609000	0.98334	2.833000	0.97629	0.655000	0.94253	CGG		0.652	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1	NM_145262		A	52326835	G	A	52326835	3	1	77	1	0	0	0	0	1	0	0	0	6502	1116	39	1	1279	1	GLYCTK	3	52326835	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	84617	52326835	145695595	211	21947										
DNAH1	25981	broad.mit.edu	37	chr3	52407054	52407054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggaccacggcggctggtacGaccgcaagatcattggtgag	15	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52407054G>A	ENST00000420323.2	+	44	7231	c.6970G>A	c.(6970-6972)Gac>Aac	p.D2324N		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2324	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D2324N(3)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		CGGCTGGTACGACCGCAAGAT	0.622																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	3											37	42	40					3																	52407054		2069	4198	6267	52382094	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.6970G>A	3.37:g.52407054G>A	ENSP00000401514:p.Asp2324Asn		52382094	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	34	5.322378	0.95708	.	.	ENSG00000114841	ENST00000420323	T	0.51071	0.72	4.5	4.5	0.54988	.	0.120071	0.36932	N	0.002337	T	0.65450	0.2692	M	0.78916	2.43	0.80722	D	1	D	0.65815	0.995	P	0.58077	0.832	T	0.68292	-0.5447	10	0.44086	T	0.13	.	17.7428	0.88411	0.0:0.0:1.0:0.0	.	2324	C9JXH6	.	N	2324	ENSP00000401514:D2324N	ENSP00000401514:D2324N	D	+	1	0	DNAH1	52382094	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	9.383000	0.97214	2.501000	0.84356	0.655000	0.94253	GAC		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52407054	G	A	52407054	3	1	77	1	0	0	0	0	1	0	0	0	4608	1058	37	1	7140	1	DNAH1	3	52407054	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	80219	52407054	145615376	212	21948										
STAB1	23166	broad.mit.edu	37	chr3	52538507	52538507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgggaaatccttaccacagCgggccctttcaccgtgctgg	11	15	1	0	rs147636423		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52538507C>T	ENST00000321725.6	+	11	1257	c.1181C>T	c.(1180-1182)gCg>gTg	p.A394V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	394	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)	p.A394V(1)		breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTTACCACAGCGGGCCCTTTC	0.632													C|||	1	0.000199681	0	0	5008	,	,		17541	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	98	95	96		1181	4.5	0.3	3	dbSNP_134	96	4,8596	3.7+/-12.6	0,4,4296	yes	missense	STAB1	NM_015136.2	64	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	benign	394/2571	52538507	5,13001	2203	4300	6503	52513547	SO:0001583	missense	23166			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.1181C>T	3.37:g.52538507C>T	ENSP00000312946:p.Ala394Val		52513547	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.886	0.532961	0.13188	2.27E-4	4.65E-4	ENSG00000010327	ENST00000321725	T	0.08370	3.1	4.47	4.47	0.54385	FAS1 domain (3);	0.399722	0.23922	N	0.043226	T	0.05502	0.0145	L	0.29908	0.895	0.20074	N	0.999938	P;P	0.39601	0.506;0.68	B;B	0.30716	0.084;0.119	T	0.39722	-0.9600	10	0.15952	T	0.53	.	13.0001	0.58670	0.0:1.0:0.0:0.0	.	394;394	Q9NY15;Q9NY15-2	STAB1_HUMAN;.	V	394	ENSP00000312946:A394V	ENSP00000312946:A394V	A	+	2	0	STAB1	52513547	0.002000	0.14202	0.302000	0.25058	0.120000	0.20174	1.592000	0.36676	2.214000	0.71695	0.462000	0.41574	GCG		0.632	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52538507	C	T	52538507	3	4	77	1	0	0	0	0	1	0	0	0	15276	768	27	1	1223	1	STAB1	3	52538507	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	131453	52538507	145483923	213	21949										
STAB1	23166	broad.mit.edu	37	chr3	52540233	52540233	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtcggatcctcaccatggcGaaccaggtcctggctgtgaa	13	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52540233G>A	ENST00000321725.6	+	17	1873	c.1797G>A	c.(1795-1797)gcG>gcA	p.A599A		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	599	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)	p.A599A(1)		breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCACCATGGCGAACCAGGTCC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	3											96	76	83					3																	52540233		2202	4300	6502	52515273	SO:0001819	synonymous_variant	23166			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.1797G>A	3.37:g.52540233G>A			52515273	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																				0.622	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52540233	G	A	52540233	2	1	77	1	0	0	0	0	0	0	0	1	15276	1045	37	1		1	STAB1	3	52540233	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1726	52540233	145482197	214	21950										
STAB1	23166	broad.mit.edu	37	chr3	52557260	52557260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctattgggctatgccaatgCcacccagcggggtctcgact	12	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52557260C>T	ENST00000321725.6	+	64	7119	c.7043C>T	c.(7042-7044)gCc>gTc	p.A2348V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2348	FAS1 7. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)	p.A2348V(1)		breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TATGCCAATGCCACCCAGCGG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	3											104	99	101					3																	52557260		2203	4300	6503	52532300	SO:0001583	missense	23166			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.7043C>T	3.37:g.52557260C>T	ENSP00000312946:p.Ala2348Val		52532300	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.483718	0.63962	.	.	ENSG00000010327	ENST00000321725	D	0.91237	-2.81	5.74	4.86	0.63082	FAS1 domain (3);	0.506468	0.19990	N	0.101592	D	0.83487	0.5265	L	0.41236	1.265	0.33626	D	0.605458	P;P	0.37612	0.602;0.543	B;B	0.31946	0.138;0.095	D	0.86094	0.1552	10	0.42905	T	0.14	.	8.292	0.31963	0.1568:0.7632:0.0:0.08	.	235;2348	B3KSK0;Q9NY15	.;STAB1_HUMAN	V	2348	ENSP00000312946:A2348V	ENSP00000312946:A2348V	A	+	2	0	STAB1	52532300	0.604000	0.26932	1.000000	0.80357	0.974000	0.67602	1.549000	0.36212	2.712000	0.92718	0.561000	0.74099	GCC		0.577	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52557260	C	T	52557260	3	4	77	1	0	0	0	0	1	0	0	0	15276	739	26	3	7297	3	STAB1	3	52557260	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	17027	52557260	145465170	215	21951										
ITIH1	3697	broad.mit.edu	37	chr3	52821017	52821017	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcccaggccctgcagatgtCgctggactatgggtttgtga	13	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52821017C>T	ENST00000273283.2	+	14	1814	c.1790C>T	c.(1789-1791)tCg>tTg	p.S597L	ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Missense_Mutation_p.S309L|ITIH1_ENST00000540715.1_Missense_Mutation_p.S455L|ITIH1_ENST00000542827.1_Missense_Mutation_p.S597L	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	597	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S597L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		CTGCAGATGTCGCTGGACTAT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	84	86					3																	52821017		2203	4300	6503	52796057	SO:0001583	missense	3697				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1790C>T	3.37:g.52821017C>T	ENSP00000273283:p.Ser597Leu		52796057	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670272	0.67814	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.44	5.44	0.79542	.	0.059907	0.64402	D	0.000001	T	0.78052	0.4223	M	0.90814	3.15	0.50467	D	0.999872	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.994;0.946;0.932	T	0.82110	-0.0619	10	0.87932	D	0	-9.7388	17.2341	0.86994	0.0:1.0:0.0:0.0	.	455;198;597	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	L	597;597;455;309;150	ENSP00000442584:S597L;ENSP00000273283:S597L;ENSP00000443973:S455L;ENSP00000443847:S309L;ENSP00000395836:S150L	ENSP00000273283:S597L	S	+	2	0	ITIH1	52796057	1.000000	0.71417	0.966000	0.40874	0.005000	0.04900	4.926000	0.63433	2.837000	0.97791	0.655000	0.94253	TCG		0.617	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		T	52821017	C	T	52821017	3	4	77	1	0	0	0	0	1	0	0	0	7924	893	31	1	1844	1	ITIH1	3	52821017	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	263757	52821017	145201413	216	21952										
ITIH3	3699	broad.mit.edu	37	chr3	52835122	52835122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagaaccatgggtttgcccGgcgcatttatgaggactctg	14	9	1	2	rs199816198	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:52835122G>T	ENST00000449956.2	+	11	1349	c.1343G>T	c.(1342-1344)cGg>cTg	p.R448L	ITIH3_ENST00000416872.2_Missense_Mutation_p.R448L	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	448	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R448L(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		GGGTTTGCCCGGCGCATTTAT	0.522																																																2	Substitution - Missense(2)	large_intestine(2)	3											65	68	67					3																	52835122		1949	4127	6076	52810162	SO:0001583	missense	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.1343G>T	3.37:g.52835122G>T	ENSP00000415769:p.Arg448Leu		52810162	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119987	0.94385	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	D;D	0.82984	-1.67;-1.67	5.33	5.33	0.75918	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.92008	0.7468	M	0.86740	2.835	0.53688	D	0.99997	D;D	0.71674	0.993;0.998	P;D	0.71414	0.86;0.973	D	0.92250	0.5808	10	0.52906	T	0.07	-14.4835	17.9616	0.89087	0.0:0.0:1.0:0.0	.	448;448	E7ET33;Q06033	.;ITIH3_HUMAN	L	448;436;443;448;448	ENSP00000413922:R448L;ENSP00000415769:R448L	ENSP00000273291:R443L	R	+	2	0	ITIH3	52810162	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.012000	0.76366	2.775000	0.95449	0.655000	0.94253	CGG		0.522	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52835122	G	T	52835122	3	4	77	1	0	0	0	0	1	0	0	0	7926	1116	39	2	1385	2	ITIH3	3	52835122	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	14105	52835122	145187308	217	21953										
CACNA1D	776	broad.mit.edu	37	chr3	53845190	53845190	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaagggacccaaaatttgtGtcagcaacaaaacacgaaat	8	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:53845190G>A	ENST00000350061.5	+	48	6754	c.6243G>A	c.(6241-6243)gtG>gtA	p.V2081V	CACNA1D_ENST00000422281.2_Silent_p.V2057V|CACNA1D_ENST00000288139.4_Silent_p.V2101V|CACNA1D_ENST00000544977.1_3'UTR	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2081					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.V2101V(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CAAAATTTGTGTCAGCAACAA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	3											114	105	108					3																	53845190		2203	4300	6503	53820230	SO:0001819	synonymous_variant	776			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6243G>A	3.37:g.53845190G>A			53820230	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1																																																																																				0.527	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53845190	G	A	53845190	2	1	77	1	0	0	0	0	0	0	0	1	2547	1364	48	3		3	CACNA1D	3	53845190	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1010068	53845190	144177240	218	21954										
CHDH	55349	broad.mit.edu	37	chr3	53856621	53856621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcggccttgaggttggtgCggctcagtgctgggtgcagg	18	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:53856621C>T	ENST00000315251.6	-	4	1189	c.752G>A	c.(751-753)cGc>cAc	p.R251H		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	251					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)	p.R251H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GAGGTTGGTGCGGCTCAGTGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	73	79					3																	53856621		2203	4300	6503	53831661	SO:0001583	missense	55349			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.752G>A	3.37:g.53856621C>T	ENSP00000319851:p.Arg251His		53831661	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346508	0.95807	.	.	ENSG00000016391	ENST00000315251	T	0.51817	0.69	5.65	4.78	0.61160	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.74574	0.3734	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81602	-0.0858	10	0.87932	D	0	-38.7829	14.5778	0.68262	0.0:0.9297:0.0:0.0703	.	251	Q8NE62	CHDH_HUMAN	H	251	ENSP00000319851:R251H	ENSP00000319851:R251H	R	-	2	0	CHDH	53831661	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.888000	0.75622	1.626000	0.50381	0.655000	0.94253	CGC		0.647	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		T	53856621	C	T	53856621	3	4	77	1	0	0	0	0	1	0	0	0	3339	768	27	1	1056	1	CHDH	3	53856621	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	11431	53856621	144165809	219	21955										
MAGI1	9223	broad.mit.edu	37	chr3	65342585	65342585	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccgctgtcgggtttcctcGaagtcccattccaggtgtgg	12	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:65342585G>A	ENST00000402939.2	-	23	3856	c.3857C>T	c.(3856-3858)tCg>tTg	p.S1286L	MAGI1_ENST00000330909.8_3'UTR|RP11-88H12.2_ENST00000602316.1_RNA	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1315					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.S1286L(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		GGGTTTCCTCGAAGTCCCATT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	3											123	117	119					3																	65342585		2203	4300	6503	65317625	SO:0001583	missense	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000402939.2:c.3857C>T	3.37:g.65342585G>A	ENSP00000385450:p.Ser1286Leu		65317625	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000402939.2	37	CCDS33780.1	.	.	.	.	.	.	.	.	.	.	G	6.411	0.443971	0.12164	.	.	ENSG00000151276	ENST00000402939	T	0.12879	2.64	4.7	3.79	0.43588	.	0.833032	0.10977	N	0.613142	T	0.12135	0.0295	L	0.29908	0.895	0.80722	D	1	B	0.22604	0.072	B	0.16722	0.016	T	0.08534	-1.0717	10	0.25106	T	0.35	-1.3914	14.4224	0.67193	0.0:0.2797:0.7202:0.0	.	1286	Q96QZ7-2	.	L	1286	ENSP00000385450:S1286L	ENSP00000385450:S1286L	S	-	2	0	MAGI1	65317625	1.000000	0.71417	0.815000	0.32552	0.013000	0.08279	2.867000	0.48428	0.906000	0.36621	0.561000	0.74099	TCG		0.652	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742		A	65342585	G	A	65342585	3	1	77	1	0	0	0	0	1	0	0	0	9220	1059	37	1	535	1	MAGI1	3	65342585	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11485964	65342585	132679845	220	21956										
MAGI1	9223	broad.mit.edu	37	chr3	65376821	65376821	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaggatgctactcacgtcgGttttcatacatgctcctgga	9	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:65376821G>A	ENST00000497477.2	-	14	2411	c.2412C>T	c.(2410-2412)aaC>aaT	p.N804N	MAGI1_ENST00000402939.2_Silent_p.N804N|MAGI1_ENST00000483466.1_Silent_p.N804N|MAGI1_ENST00000330909.8_Silent_p.N804N			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	804					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.N804N(2)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		ACTCACGTCGGTTTTCATACA	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	3											79	80	80					3																	65376821		2203	4300	6503	65351861	SO:0001819	synonymous_variant	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.2412C>T	3.37:g.65376821G>A			65351861	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	G	8.913	0.959096	0.18507	.	.	ENSG00000151276	ENST00000460329	.	.	.	5.84	4.97	0.65823	.	.	.	.	.	T	0.70780	0.3263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70200	-0.4937	4	.	.	.	-17.9764	14.9732	0.71249	0.0682:0.0:0.9318:0.0	.	.	.	.	I	685	.	.	T	-	2	0	MAGI1	65351861	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.795000	0.69074	1.482000	0.48325	0.655000	0.94253	ACC		0.498	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		A	65376821	G	A	65376821	2	1	77	1	0	0	0	0	0	0	0	1	9220	1252	44	3		3	MAGI1	3	65376821	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	34236	65376821	132645609	221	21957										
MITF	4286	broad.mit.edu	37	chr3	70014356	70014356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcttccaaaacaagcagccGgaggagcagtatgagcatgg	13	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:70014356G>A	ENST00000448226.2	+	10	1665	c.1538G>A	c.(1537-1539)cGg>cAg	p.R513Q	MITF_ENST00000314589.5_Missense_Mutation_p.R491Q|MITF_ENST00000531774.1_Missense_Mutation_p.R344Q|MITF_ENST00000394355.2_Missense_Mutation_p.R482Q|MITF_ENST00000352241.4_Missense_Mutation_p.R507Q|MITF_ENST00000394351.3_Missense_Mutation_p.R406Q|MITF_ENST00000314557.6_Missense_Mutation_p.R400Q|MITF_ENST00000328528.6_Missense_Mutation_p.R506Q|MITF_ENST00000472437.1_Missense_Mutation_p.R455Q			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	513					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.R406Q(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		ACAAGCAGCCGGAGGAGCAGT	0.517			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	1	Substitution - Missense(1)	large_intestine(1)	3											93	97	96					3																	70014356		2203	4300	6503	70097046	SO:0001583	missense	4286				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.1538G>A	3.37:g.70014356G>A	ENSP00000391803:p.Arg513Gln		70097046	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	G	26.6	4.753800	0.89753	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000472437;ENST00000328528;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	T;T;T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	6.04	6.04	0.98038	.	0.051855	0.85682	D	0.000000	D	0.85309	0.5667	M	0.79123	2.44	0.43608	D	0.995977	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.999;0.999	D;D;D;D;D;D;D	0.75484	0.986;0.975;0.975;0.975;0.975;0.975;0.975	D	0.83925	0.0303	9	.	.	.	.	20.5792	0.99380	0.0:0.0:1.0:0.0	.	455;406;400;482;491;506;507	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	Q	507;513;455;506;491;482;400;406;344	ENSP00000295600:R507Q;ENSP00000391803:R513Q;ENSP00000418845:R455Q;ENSP00000327867:R506Q;ENSP00000324443:R491Q;ENSP00000377884:R482Q;ENSP00000324246:R400Q;ENSP00000377880:R406Q;ENSP00000435909:R344Q	.	R	+	2	0	MITF	70097046	1.000000	0.71417	0.986000	0.45419	0.971000	0.66376	6.890000	0.75633	2.873000	0.98535	0.561000	0.74099	CGG		0.517	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		A	70014356	G	A	70014356	3	1	77	1	0	0	0	0	1	0	0	0	9626	1116	39	1	1797	1	MITF	3	70014356	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4637535	70014356	128008074	222	21958										
GXYLT2	727936	broad.mit.edu	37	chr3	73016726	73016726	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatgtattcccctgccagtgGaactaccgtcccgatcactg	8	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:73016726G>A	ENST00000389617.4	+	6	1166	c.1005G>A	c.(1003-1005)tgG>tgA	p.W335*		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	335					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.W335*(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						CCTGCCAGTGGAACTACCGTC	0.502																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											82	81	81					3																	73016726		2022	4190	6212	73099416	SO:0001587	stop_gained	727936			AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"Glycosyltransferase family 8 domain containing"	33383	protein-coding gene	gene with protein product		613322	"glycosyltransferase 8 domain containing 4"	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.1005G>A	3.37:g.73016726G>A	ENSP00000374268:p.Trp335*		73099416		Nonsense_Mutation	SNP	ENST00000389617.4	37	CCDS46870.1	.	.	.	.	.	.	.	.	.	.	G	35	5.592330	0.96590	.	.	ENSG00000172986	ENST00000389617;ENST00000491839	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.7923	0.96464	0.0:0.0:1.0:0.0	.	.	.	.	X	335;96	.	ENSP00000374268:W335X	W	+	3	0	GXYLT2	73099416	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.565000	0.98154	2.752000	0.94435	0.557000	0.71058	TGG		0.502	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393		A	73016726	G	A	73016726	4	1	77	1	0	0	0	0	0	1	0	0	6925	1183	41	3	1027	3	GXYLT2	3	73016726	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3002370	73016726	125005704	223	21959										
EBLN2	55096	broad.mit.edu	37	chr3	73111422	73111422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagcagcccaggagatgacGcaatggacaggagtgggctc	15	11	0	2	rs376896494		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:73111422G>A	ENST00000533473.1	+	1	613	c.190G>A	c.(190-192)Gca>Aca	p.A64T	PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	64								p.A64T(1)		endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						AGGAGATGACGCAATGGACAG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	THR/ALA,	0,3948		0,0,1974	33	34	34		190,	0.2	0	3		34	1,8323		0,1,4161	no	missense,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	58,	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign,	64/273,	73111422	1,12271	1974	4162	6136	73194112	SO:0001583	missense	55096				CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.190G>A	3.37:g.73111422G>A	ENSP00000432104:p.Ala64Thr		73194112	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	G	3.622	-0.077416	0.07184	0.0	1.2E-4	ENSG00000255423	ENST00000533473	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	1	B	0.20550	0.046	B	0.09377	0.004	T	0.20605	-1.0270	7	0.33141	T	0.24	.	.	.	.	.	64	Q6P2I7	EBLN2_HUMAN	T	64	.	ENSP00000432104:A64T	A	+	1	0	EBLN2	73194112	0.006000	0.16342	0.006000	0.13384	0.006000	0.05464	0.364000	0.20325	0.300000	0.22699	0.305000	0.20034	GCA		0.453	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		A	73111422	G	A	73111422	3	1	77	1	0	0	0	0	1	0	0	0	4895	1087	38	1	192	1	EBLN2	3	73111422	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	94696	73111422	124911008	224	21960										
PDZRN3	23024	broad.mit.edu	37	chr3	73432828	73432828	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccatcttcatctcgctcacCgcgtcgtcgtcggtggtcat	9	16	5	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:73432828C>T	ENST00000263666.4	-	10	3003	c.2889G>A	c.(2887-2889)gcG>gcA	p.A963A	PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Silent_p.A620A|PDZRN3_ENST00000535920.1_Silent_p.A685A|PDZRN3_ENST00000466780.1_Silent_p.A620A|PDZRN3_ENST00000479530.1_Silent_p.A680A	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	963					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A963A(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCTCGCTCACCGCGTCGTCGT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	3											75	72	73					3																	73432828		2203	4300	6503	73515518	SO:0001819	synonymous_variant	23024			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2889G>A	3.37:g.73432828C>T			73515518	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.192|5.192	0.220967|0.220967	0.09863|0.09863	.|.	.|.	ENSG00000121440|ENSG00000121440	ENST00000416926|ENST00000494559	.|.	.|.	.|.	5.21|5.21	-1.55|-1.55	0.08558|0.08558	.|.	.|.	.|.	.|.	.|.	T|T	0.80149|0.80149	0.4570|0.4570	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.78157|0.78157	-0.2313|-0.2313	5|4	0.09590|.	T|.	0.72|.	.|.	25.5553|25.5553	0.99994|0.99994	0.0:0.1209:0.8791:0.0|0.0:0.1209:0.8791:0.0	.|.	.|.	.|.	.|.	S|Q	683|279	.|.	ENSP00000392657:G683S|.	G|R	-|-	1|2	0|0	PDZRN3|PDZRN3	73515518|73515518	0.370000|0.370000	0.25047|0.25047	0.008000|0.008000	0.14137|0.14137	0.813000|0.813000	0.45954|0.45954	-0.257000|-0.257000	0.08745|0.08745	-0.749000|-0.749000	0.04747|0.04747	0.563000|0.563000	0.77884|0.77884	GGT|CGG		0.672	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73432828	C	T	73432828	2	4	77	1	0	0	0	0	0	0	0	1	11740	639	23	1		1	PDZRN3	3	73432828	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	321406	73432828	124589602	225	21961										
ROBO2	6092	broad.mit.edu	37	chr3	77147435	77147435	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaaggaagctacgtttgtgTtgcgaggaactatcttggtg	14	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:77147435T>A	ENST00000461745.1	+	2	1232	c.332T>A	c.(331-333)gTt>gAt	p.V111D	ROBO2_ENST00000487694.3_Missense_Mutation_p.V127D|ROBO2_ENST00000332191.8_Missense_Mutation_p.V111D	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	111	Ig-like C2-type 1.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.V111D(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TACGTTTGTGTTGCGAGGAAC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	3											106	108	107					3																	77147435		2051	4205	6256	77230125	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.332T>A	3.37:g.77147435T>A	ENSP00000417164:p.Val111Asp		77230125	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915242	0.52546	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191	T;T;T	0.68181	-0.31;-0.31;-0.31	5.59	4.43	0.53597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.216400	0.21861	U	0.068026	T	0.81230	0.4779	M	0.81112	2.525	0.45502	D	0.998465	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	D	0.86081	0.1544	9	0.72032	D	0.01	.	11.6544	0.51309	0.0:0.0696:0.0:0.9304	.	127;111;111	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	D	127;127;127;111;111	ENSP00000417335:V127D;ENSP00000417164:V111D;ENSP00000327536:V111D	ENSP00000327536:V111D	V	+	2	0	ROBO2	77230125	1.000000	0.71417	0.990000	0.47175	0.011000	0.07611	6.305000	0.72805	0.948000	0.37687	-0.264000	0.10439	GTT		0.488	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77147435	T	A	77147435	3	1	77	1	0	0	0	0	1	0	0	0	13551	1734	60	5	340	5	ROBO2	3	77147435	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	3714607	77147435	120874995	226	21962										
ROBO1	6091	broad.mit.edu	37	chr3	78663874	78663874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctggttttctgcattacGgcggcactcatgttgctgtc	12	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:78663874G>A	ENST00000464233.1	-	28	4472	c.4359C>T	c.(4357-4359)gcC>gcT	p.A1453A	ROBO1_ENST00000495273.1_Silent_p.A1408A|ROBO1_ENST00000467549.1_Silent_p.A1353A|ROBO1_ENST00000436010.2_Silent_p.A1414A	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1453					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.A1430A(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCTGCATTACGGCGGCACTCA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	3											109	113	112					3																	78663874		1977	4151	6128	78746564	SO:0001819	synonymous_variant	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4359C>T	3.37:g.78663874G>A			78746564	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																				0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78663874	G	A	78663874	2	1	77	1	0	0	0	0	0	0	0	1	13550	1103	39	1		1	ROBO1	3	78663874	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1516439	78663874	119358556	227	21963										
ABI3BP	25890	broad.mit.edu	37	chr3	100569567	100569567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggatagaatccagaatacGatcacttgttgctgttggaa	11	6	1	2	rs377450718		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:100569567G>A	ENST00000284322.5	-	14	1346	c.1237C>T	c.(1237-1239)Cgt>Tgt	p.R413C	ABI3BP_ENST00000471714.1_Missense_Mutation_p.R462C|ABI3BP_ENST00000495063.1_Missense_Mutation_p.R462C	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	413					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.R413C(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						TCCAGAATACGATCACTTGTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	CYS/ARG	0,3622		0,0,1811	129	127	127		1237	1.4	0.7	3		127	1,8133		0,1,4066	no	missense	ABI3BP	NM_015429.3	180	0,1,5877	AA,AG,GG		0.0123,0.0,0.0085	possibly-damaging	413/1076	100569567	1,11755	1811	4067	5878	102052257	SO:0001583	missense	25890			AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1237C>T	3.37:g.100569567G>A	ENSP00000284322:p.Arg413Cys		102052257	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.35|14.35	2.510692|2.510692	0.44660|0.44660	0.0|0.0	1.23E-4|1.23E-4	ENSG00000154175|ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000495063|ENST00000459682	T;T;T|.	0.57436|.	0.4;0.4;0.4|.	5.86|5.86	1.4|1.4	0.22301|0.22301	.|.	0.777035|.	0.12965|.	N|.	0.424639|.	T|T	0.36799|0.36799	0.0980|0.0980	N|N	0.22421|0.22421	0.69|0.69	0.53688|0.53688	D|D	0.99997|0.99997	P;P|.	0.47350|.	0.894;0.876|.	B;B|.	0.41723|.	0.365;0.183|.	T|T	0.06409|0.06409	-1.0828|-1.0828	10|5	0.66056|.	D|.	0.02|.	0.076|0.076	4.999|4.999	0.14255|0.14255	0.3437:0.1561:0.5002:0.0|0.3437:0.1561:0.5002:0.0	.|.	462;413|.	Q5JPC9;Q7Z7G0|.	.;TARSH_HUMAN|.	C|L	462;413;462|38	ENSP00000420524:R462C;ENSP00000284322:R413C;ENSP00000433993:R462C|.	ENSP00000284322:R413C|.	R|S	-|-	1|2	0|0	ABI3BP|ABI3BP	102052257|102052257	0.998000|0.998000	0.40836|0.40836	0.688000|0.688000	0.30117|0.30117	0.889000|0.889000	0.51656|0.51656	1.030000|1.030000	0.30153|0.30153	0.438000|0.438000	0.26450|0.26450	-0.182000|-0.182000	0.12963|0.12963	CGT|TCG		0.343	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			A	100569567	G	A	100569567	3	1	77	1	0	0	0	0	1	0	0	0	91	1058	37	1	2078	1	ABI3BP	3	100569567	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	21905693	100569567	97452863	228	21964										
CEP97	79598	broad.mit.edu	37	chr3	101481366	101481366	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgaagaacgtattaaaaaaTttgtacaagaagaagctttc	7	4	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:101481366T>A	ENST00000341893.3	+	10	2607	c.1855T>A	c.(1855-1857)Ttt>Att	p.F619I	CEP97_ENST00000494050.1_Missense_Mutation_p.F560I|CEP97_ENST00000327230.4_Missense_Mutation_p.F619I			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	619	CCP110-binding.				cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)		p.F619I(1)		cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						TATTAAAAAATTTGTACAAGA	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	3											75	79	77					3																	101481366		2203	4297	6500	102964056	SO:0001583	missense	79598			AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.1855T>A	3.37:g.101481366T>A	ENSP00000342510:p.Phe619Ile		102964056	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	ENST00000341893.3	37	CCDS2944.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.935430	0.52866	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.49720	0.86;0.81;0.77	5.56	-2.14	0.07123	.	0.301981	0.37136	N	0.002226	T	0.31857	0.0810	L	0.57536	1.79	0.28846	N	0.896345	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.09596	-1.0667	10	0.34782	T	0.22	-0.8876	0.957	0.01387	0.367:0.1601:0.3182:0.1548	.	560;619	E9PG22;Q8IW35	.;CEP97_HUMAN	I	619;619;560	ENSP00000342510:F619I;ENSP00000325881:F619I;ENSP00000418185:F560I	ENSP00000325881:F619I	F	+	1	0	CEP97	102964056	0.983000	0.35010	0.643000	0.29450	0.989000	0.77384	0.369000	0.20416	-0.252000	0.09528	0.477000	0.44152	TTT		0.333	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		A	101481366	T	A	101481366	3	1	77	1	0	0	0	0	1	0	0	0	3269	1493	52	5	1893	5	CEP97	3	101481366	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	911799	101481366	96541064	229	21965										
WDR52	55779	broad.mit.edu	37	chr3	113115475	113115475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcatccaaaattttcttccGtcccgcaaaaatcgtgagcc	6	13	1	1	rs113101974		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:113115475G>A	ENST00000295868.2	-	14	1831	c.1669C>T	c.(1669-1671)Cgg>Tgg	p.R557W	WDR52_ENST00000393845.2_Missense_Mutation_p.R557W|WDR52_ENST00000475568.1_5'UTR	NM_018338.3	NP_060808.2												p.R557W(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						ATTTTCTTCCGTCCCGCAAAA	0.393													G|||	1	0.000199681	0	0	5008	,	,		17386	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	3											102	103	103					3																	113115475		2203	4300	6503	114598165	SO:0001583	missense	55779																														ENST00000295868.2:c.1669C>T	3.37:g.113115475G>A	ENSP00000295868:p.Arg557Trp		114598165		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.372657	0.42003	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.65916	-0.18;0.65	5.39	2.38	0.29361	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.70448	0.3225	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.73052	-0.4104	9	0.66056	D	0.02	.	14.534	0.67947	0.0:0.0:0.6229:0.3771	.	557	Q96MT7	WDR52_HUMAN	W	557	ENSP00000377428:R557W;ENSP00000295868:R557W	ENSP00000295868:R557W	R	-	1	2	WDR52	114598165	0.999000	0.42202	1.000000	0.80357	0.067000	0.16453	2.011000	0.40922	0.725000	0.32318	0.655000	0.94253	CGG		0.393	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113115475	G	A	113115475	3	1	77	1	0	0	0	0	1	0	0	0	17344	1144	40	1	3998	1	WDR52	3	113115475	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11634109	113115475	84906955	230	21966										
KIAA1407	57577	broad.mit.edu	37	chr3	113724766	113724766	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gactgagcatacaaccactgCttcccaagggaggcttttcc	9	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:113724766C>A	ENST00000295878.3	-	10	1603	c.1457G>T	c.(1456-1458)aGc>aTc	p.S486I	KIAA1407_ENST00000545063.1_Missense_Mutation_p.S317I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	486								p.S486I(1)		endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						ACAACCACTGCTTCCCAAGGG	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	3											102	105	104					3																	113724766		2203	4300	6503	115207456	SO:0001583	missense	57577			AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1457G>T	3.37:g.113724766C>A	ENSP00000295878:p.Ser486Ile		115207456	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469506	0.43839	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.47528	1.42;0.84;0.85	5.23	-0.947	0.10382	.	0.979750	0.08452	N	0.943838	T	0.41858	0.1177	M	0.63428	1.95	0.09310	N	1	P;P;P	0.45078	0.85;0.85;0.85	B;B;B	0.43575	0.424;0.424;0.424	T	0.31223	-0.9951	10	0.46703	T	0.11	.	1.9504	0.03365	0.1153:0.2612:0.3391:0.2845	.	473;362;486	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	486;317;473	ENSP00000295878:S486I;ENSP00000446381:S317I;ENSP00000418099:S473I	ENSP00000295878:S486I	S	-	2	0	KIAA1407	115207456	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-1.069000	0.03444	-0.399000	0.07668	0.655000	0.94253	AGC		0.493	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113724766	C	A	113724766	3	1	77	1	0	0	0	0	1	0	0	0	8250	797	28	2	1385	2	KIAA1407	3	113724766	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	609291	113724766	84297664	231	21967										
ZBTB20	26137	broad.mit.edu	37	chr3	114069920	114069920	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcccgtagtagtcgtaatcGtcctccatctcctgcttgat	8	13	1	1	rs367805942		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:114069920G>A	ENST00000474710.1	-	4	1183	c.1005C>T	c.(1003-1005)gaC>gaT	p.D335D	ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000464560.1_Silent_p.D262D|ZBTB20_ENST00000471418.1_Silent_p.D262D|ZBTB20_ENST00000357258.3_Silent_p.D262D|ZBTB20_ENST00000481632.1_Silent_p.D262D|ZBTB20_ENST00000393785.2_Silent_p.D262D|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000462705.1_Silent_p.D262D	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	335						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.D262D(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		AGTCGTAATCGTCCTCCATCT	0.617																																					NSCLC(69;748 1344 9802 11203 30933)											1	Substitution - coding silent(1)	large_intestine(1)	3						G	,,,,,,	0,4406		0,0,2203	146	113	125		1005,786,786,786,786,786,786	0.6	1	3		125	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZBTB20	NM_001164342.1,NM_001164343.1,NM_001164344.1,NM_001164345.1,NM_001164346.1,NM_001164347.1,NM_015642.4	,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,	335/742,262/669,262/669,262/669,262/669,262/669,262/669	114069920	1,13005	2203	4300	6503	115552610	SO:0001819	synonymous_variant	26137			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.1005C>T	3.37:g.114069920G>A			115552610	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	37	CCDS54626.1																																																																																				0.617	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		A	114069920	G	A	114069920	2	1	77	1	0	0	0	0	0	0	0	1	17568	1136	40	1		1	ZBTB20	3	114069920	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	345154	114069920	83952510	232	21968										
CASR	846	broad.mit.edu	37	chr3	121981046	121981046	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacaggtttagcaacagctcGacagccttccgacccctctg	9	15	1	0	rs200898785	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:121981046G>A	ENST00000490131.1	+	4	1536	c.1164G>A	c.(1162-1164)tcG>tcA	p.S388S	CASR_ENST00000296154.5_Silent_p.S388S|CASR_ENST00000498619.1_Silent_p.S388S	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	388					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.S388S(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GCAACAGCTCGACAGCCTTCC	0.488													G|||	4	0.000798722	0	0	5008	,	,		21880	0		0	False		,,,				2504	0.0041															1	Substitution - coding silent(1)	large_intestine(1)	3											106	96	99					3																	121981046		2203	4300	6503	123463736	SO:0001819	synonymous_variant	846			U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1164G>A	3.37:g.121981046G>A			123463736	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Silent	SNP	ENST00000490131.1	37	CCDS3010.1																																																																																				0.488	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		A	121981046	G	A	121981046	2	1	77	1	0	0	0	0	0	0	0	1	2688	1045	37	1		1	CASR	3	121981046	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7911126	121981046	76041384	233	21969										
ADCY5	111	broad.mit.edu	37	chr3	123038662	123038662	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggttcgcactctcctgggcGttcctggggagcagaaggca	16	11	1	1	rs150253262	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:123038662G>A	ENST00000462833.1	-	10	3327	c.2115C>T	c.(2113-2115)aaC>aaT	p.N705N	ADCY5_ENST00000491190.1_Silent_p.N338N|ADCY5_ENST00000309879.5_Silent_p.N355N	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	705					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.N705N(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		TCTCCTGGGCGTTCCTGGGGA	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G	,	1,4405	2.1+/-5.4	0,1,2202	74	59	65		1065,2115	-3.6	0.9	3	dbSNP_134	65	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ADCY5	NM_001199642.1,NM_183357.2	,	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,	355/912,705/1262	123038662	3,13003	2203	4300	6503	124521352	SO:0001819	synonymous_variant	111			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.2115C>T	3.37:g.123038662G>A			124521352	B7Z8A6|Q7RTV7|Q8NFM3	Silent	SNP	ENST00000462833.1	37	CCDS3022.1																																																																																				0.632	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		A	123038662	G	A	123038662	2	1	77	1	0	0	0	0	0	0	0	1	297	1136	40	1		1	ADCY5	3	123038662	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1057616	123038662	74983768	234	21970										
SLC41A3	54946	broad.mit.edu	37	chr3	125731529	125731529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggcaggacgccaggtgcaCtccacatgtgcaggtaggtt	16	10	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:125731529C>T	ENST00000315891.6	-	9	1272	c.1034G>A	c.(1033-1035)aGt>aAt	p.S345N	SLC41A3_ENST00000360370.4_Missense_Mutation_p.S345N|SLC41A3_ENST00000346785.5_Missense_Mutation_p.S309N|SLC41A3_ENST00000383598.2_Missense_Mutation_p.S319N|SLC41A3_ENST00000508835.1_Missense_Mutation_p.S228N	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	345						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.S319N(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		GCCAGGTGCACTCCACATGTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	3											158	148	151					3																	125731529		2203	4300	6503	127214219	SO:0001583	missense	54946				CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"Solute carriers"	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1034G>A	3.37:g.125731529C>T	ENSP00000326070:p.Ser345Asn		127214219	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.471295	0.63625	.	.	ENSG00000114544	ENST00000360370;ENST00000346785;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000508835	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.43	5.43	0.79202	MgtE magnesium transporter, integral membrane (1);	0.113256	0.85682	D	0.000000	T	0.57636	0.2067	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.999;1.0;0.999;0.998	D;D;D;D;D	0.74348	0.957;0.975;0.983;0.982;0.928	T	0.55724	-0.8096	10	0.25106	T	0.35	-0.001	16.7188	0.85405	0.0:1.0:0.0:0.0	.	228;345;309;345;319	B7Z4Y2;E7ENY4;Q96GZ6-3;Q96GZ6;Q96GZ6-7	.;.;.;S41A3_HUMAN;.	N	345;309;319;336;345;228	ENSP00000353533:S345N;ENSP00000264471:S309N;ENSP00000373092:S319N;ENSP00000326070:S345N;ENSP00000427409:S228N	ENSP00000326070:S345N	S	-	2	0	SLC41A3	127214219	1.000000	0.71417	0.994000	0.49952	0.044000	0.14063	6.827000	0.75303	2.541000	0.85698	0.591000	0.81541	AGT		0.517	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		T	125731529	C	T	125731529	3	4	77	1	0	0	0	0	1	0	0	0	14668	565	20	3	603	3	SLC41A3	3	125731529	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2692867	125731529	72290901	235	21971										
CCDC37	348807	broad.mit.edu	37	chr3	126137555	126137555	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagaaatccctggagaaggaCgccgccttgttcgacgagtt	13	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:126137555C>T	ENST00000352312.1	+	7	687	c.588C>T	c.(586-588)gaC>gaT	p.D196D	CCDC37_ENST00000505024.1_Silent_p.D197D|CCDC37_ENST00000393425.1_Silent_p.D197D	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	196								p.D196D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		TGGAGAAGGACGCCGCCTTGT	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	3											47	51	49					3																	126137555		2197	4296	6493	127620245	SO:0001819	synonymous_variant	348807			AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.588C>T	3.37:g.126137555C>T			127620245	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																				0.652	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		T	126137555	C	T	126137555	2	4	77	1	0	0	0	0	0	0	0	1	2815	535	19	1		1	CCDC37	3	126137555	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	406026	126137555	71884875	236	21972										
PLXND1	23129	broad.mit.edu	37	chr3	129281777	129281777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccacagccctggaaggacaCgttcaggttctgcaggggga	15	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:129281777C>T	ENST00000324093.4	-	27	4856	c.4678G>A	c.(4678-4680)Gtg>Atg	p.V1560M	PLXND1_ENST00000393239.1_Missense_Mutation_p.V1560M	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1560					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.V1560M(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						TGGAAGGACACGTTCAGGTTC	0.602																																					Ovarian(97;366 1484 3738 22084 39045)											1	Substitution - Missense(1)	large_intestine(1)	3											71	59	63					3																	129281777		2203	4300	6503	130764467	SO:0001583	missense	23129			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4678G>A	3.37:g.129281777C>T	ENSP00000317128:p.Val1560Met		130764467	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.994504	0.93167	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.14516	2.5;2.5	5.38	5.38	0.77491	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.232708	0.36034	N	0.002828	T	0.45094	0.1325	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.50659	-0.8802	10	0.87932	D	0	.	19.1508	0.93487	0.0:1.0:0.0:0.0	.	155;1560	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	M	1560	ENSP00000317128:V1560M;ENSP00000376931:V1560M	ENSP00000317128:V1560M	V	-	1	0	PLXND1	130764467	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.779000	0.85648	2.524000	0.85096	0.561000	0.74099	GTG		0.602	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129281777	C	T	129281777	3	4	77	1	0	0	0	0	1	0	0	0	12158	536	19	1	1139	1	PLXND1	3	129281777	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3144222	129281777	68740653	237	21973										
CPNE4	131034	broad.mit.edu	37	chr3	131261532	131261532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcagcgttccctactcccaCgatgatgactgacatgggga	11	12	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:131261532C>T	ENST00000512055.1	-	19	3534	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M	CPNE4_ENST00000429747.1_Missense_Mutation_p.V470M|CPNE4_ENST00000502818.1_Missense_Mutation_p.V488M|CPNE4_ENST00000511604.1_Missense_Mutation_p.V470M|CPNE4_ENST00000512332.1_Missense_Mutation_p.V488M			Q96A23	CPNE4_HUMAN	copine IV	470	VWFA.					extracellular vesicular exosome (GO:0070062)		p.V470M(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CCTACTCCCACGATGATGACT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	3											169	142	151					3																	131261532		2203	4300	6503	132744222	SO:0001583	missense	131034			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1408G>A	3.37:g.131261532C>T	ENSP00000421705:p.Val470Met		132744222	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.951986	0.92660	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	5.54	5.54	0.83059	von Willebrand factor, type A (1);Copine (1);	0.000000	0.85682	D	0.000000	T	0.69024	0.3065	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.78386	-0.2224	10	0.87932	D	0	-21.4172	19.563	0.95380	0.0:1.0:0.0:0.0	.	488;470	Q96A23-2;Q96A23	.;CPNE4_HUMAN	M	470;470;488;470;488	ENSP00000421705:V470M;ENSP00000411904:V470M;ENSP00000424853:V488M;ENSP00000423811:V470M;ENSP00000421646:V488M	ENSP00000411904:V470M	V	-	1	0	CPNE4	132744222	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.783000	0.85696	2.619000	0.88677	0.650000	0.86243	GTG		0.552	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		T	131261532	C	T	131261532	3	4	77	1	0	0	0	0	1	0	0	0	3820	536	19	1	273	1	CPNE4	3	131261532	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1979755	131261532	66760898	238	21974										
DNAJC13	23317	broad.mit.edu	37	chr3	132172153	132172153	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttgtgcagcatttatttgcGtcagagcaaagagaagagat	11	5	1	3	rs528705790	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:132172153G>A	ENST00000260818.6	+	7	797	c.549G>A	c.(547-549)gcG>gcA	p.A183A	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	183					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.A183A(2)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ATTTATTTGCGTCAGAGCAAA	0.348													G|||	2	0.000399361	8e-04	0	5008	,	,		17341	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	3											36	37	37					3																	132172153		2201	4300	6501	133654843	SO:0001819	synonymous_variant	23317			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.549G>A	3.37:g.132172153G>A			133654843	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																				0.348	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		A	132172153	G	A	132172153	2	1	77	1	0	0	0	0	0	0	0	1	4643	1132	40	1		1	DNAJC13	3	132172153	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	910621	132172153	65850277	239	21975										
C3orf36	80111	broad.mit.edu	37	chr3	133647307	133647307	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctccctgagagggcgcagAgtgggtggttccccccaggt	15	13	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:133647307A>C	ENST00000408895.2	-	1	1349	c.341T>G	c.(340-342)cTc>cGc	p.L114R		NM_025041.2	NP_079317.2	Q3SXR2	CC036_HUMAN	chromosome 3 open reading frame 36	114								p.L114R(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6						GAGGGCGCAGAGTGGGTGGTT	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	3											30	33	32					3																	133647307		2203	4300	6503	135129997	SO:0001583	missense	80111			AK025826	CCDS3083.1	3q22.1	2011-09-30			ENSG00000221972	ENSG00000221972			26170	protein-coding gene	gene with protein product						12477932	Standard	NM_025041		Approved	FLJ22173	uc003epz.1	Q3SXR2		ENST00000408895.2:c.341T>G	3.37:g.133647307A>C	ENSP00000386219:p.Leu114Arg		135129997	Q3SXR3|Q9H6K8	Missense_Mutation	SNP	ENST00000408895.2	37	CCDS3083.1	.	.	.	.	.	.	.	.	.	.	A	9.916	1.210807	0.22289	.	.	ENSG00000221972	ENST00000408895	.	.	.	2.06	-0.313	0.12754	.	.	.	.	.	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	P	0.46020	0.871	B	0.34346	0.18	T	0.18871	-1.0323	8	0.87932	D	0	.	3.4456	0.07480	0.4026:0.3871:0.2103:0.0	.	114	Q3SXR2	CC036_HUMAN	R	114	.	ENSP00000386219:L114R	L	-	2	0	C3orf36	135129997	0.000000	0.05858	0.003000	0.11579	0.072000	0.16883	-0.623000	0.05546	-0.080000	0.12685	0.260000	0.18958	CTC		0.657	C3orf36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025041		C	133647307	A	C	133647307	3	2	77	1	0	0	0	0	1	0	0	0	2232	304	11	4	160	4	C3orf36	3	133647307	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1475154	133647307	64375123	240	21976										
PLS1	5357	broad.mit.edu	37	chr3	142389951	142389951	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atttccagtgagggcacacaGcattcttattcaggtaactg	9	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:142389951G>A	ENST00000337777.3	+	4	564	c.351G>A	c.(349-351)caG>caA	p.Q117Q	PLS1_ENST00000497002.1_Silent_p.Q117Q|RN7SKP25_ENST00000362449.1_RNA|PLS1_ENST00000457734.2_Silent_p.Q117Q	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	117	Actin-binding 1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.Q117Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						AGGGCACACAGCATTCTTATT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	3											191	183	186					3																	142389951		2203	4299	6502	143872641	SO:0001819	synonymous_variant	5357			L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.351G>A	3.37:g.142389951G>A			143872641	A8K2Q1|D3DNG3|Q8NEG6	Silent	SNP	ENST00000337777.3	37	CCDS3125.1																																																																																				0.353	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		A	142389951	G	A	142389951	2	1	77	1	0	0	0	0	0	0	0	1	12138	962	34	3		3	PLS1	3	142389951	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8742644	142389951	55632479	241	21977										
TM4SF4	7104	broad.mit.edu	37	chr3	149216547	149216547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccttatggaacaagtgccGagagcctctcaatgtggttc	12	10	1	1	rs367773065		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:149216547G>A	ENST00000305354.4	+	4	1344	c.440G>A	c.(439-441)cGa>cAa	p.R147Q		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	147					tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)		p.R147Q(2)		large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			AACAAGTGCCGAGAGCCTCTC	0.483																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	3						G	GLN/ARG	0,3854		0,0,1927	92	93	92		440	-11.8	0	3		92	1,8263		0,1,4131	no	missense	TM4SF4	NM_004617.3	43	0,1,6058	AA,AG,GG		0.0121,0.0,0.0083	benign	147/203	149216547	1,12117	1927	4132	6059	150699237	SO:0001583	missense	7104				CCDS46932.1	3q25	2005-03-21	2005-03-21		ENSG00000169903	ENSG00000169903			11856	protein-coding gene	gene with protein product		606567	"transmembrane 4 superfamily member 4"			7665614	Standard	NM_004617		Approved	il-TMP	uc003exd.2	P48230	OTTHUMG00000159619	ENST00000305354.4:c.440G>A	3.37:g.149216547G>A	ENSP00000305852:p.Arg147Gln		150699237	B2RDA4	Missense_Mutation	SNP	ENST00000305354.4	37	CCDS46932.1	.	.	.	.	.	.	.	.	.	.	G	4.644	0.119685	0.08881	0.0	1.21E-4	ENSG00000169903	ENST00000305354	T	0.29655	1.56	5.9	-11.8	0.00035	.	4.093850	0.00166	N	0.000008	T	0.07638	0.0192	N	0.01505	-0.83	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21042	-1.0257	10	0.12103	T	0.63	-6.939	2.8524	0.05562	0.1187:0.2483:0.1436:0.4894	.	147	P48230	T4S4_HUMAN	Q	147	ENSP00000305852:R147Q	ENSP00000305852:R147Q	R	+	2	0	TM4SF4	150699237	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-6.430000	0.00066	-4.682000	0.00036	-0.295000	0.09555	CGA		0.483	TM4SF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356528.1			A	149216547	G	A	149216547	3	1	77	1	0	0	0	0	1	0	0	0	16009	1058	37	1	454	1	TM4SF4	3	149216547	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6826596	149216547	48805883	242	21978										
P2RY12	64805	broad.mit.edu	37	chr3	151056087	151056087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatttcatgccagactagacCgaactctgatttaaggaaag	8	8	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:151056087C>T	ENST00000302632.3	-	3	846	c.547G>A	c.(547-549)Ggt>Agt	p.G183S	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	183					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.G183S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	CAGACTAGACCGAACTCTGAT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											101	98	99					3																	151056087		2203	4300	6503	152538777	SO:0001583	missense	64805			AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.547G>A	3.37:g.151056087C>T	ENSP00000307259:p.Gly183Ser		152538777	D3DNJ5|Q546J7	Missense_Mutation	SNP	ENST00000302632.3	37	CCDS3159.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033469	0.93575	.	.	ENSG00000169313	ENST00000302632	T	0.35973	1.28	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.048000	0.85682	D	0.000000	T	0.55862	0.1947	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.42258	-0.9462	10	0.14656	T	0.56	-15.7289	19.6002	0.95559	0.0:1.0:0.0:0.0	.	183	Q9H244	P2Y12_HUMAN	S	183	ENSP00000307259:G183S	ENSP00000307259:G183S	G	-	1	0	P2RY12	152538777	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.445000	0.80570	2.691000	0.91804	0.655000	0.94253	GGT		0.353	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1			T	151056087	C	T	151056087	3	4	77	1	0	0	0	0	1	0	0	0	11380	652	23	1	485	1	P2RY12	3	151056087	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1839540	151056087	46966343	243	21979										
P2RY1	5028	broad.mit.edu	37	chr3	152554449	152554449	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccggcttgattttcagacccCagcaatgtgtgctttcaatg	9	11	2	2	rs145570287		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:152554449C>A	ENST00000305097.3	+	1	1714	c.878C>A	c.(877-879)cCa>cAa	p.P293Q	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	293					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.P293Q(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TTTCAGACCCCAGCAATGTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	3											110	112	111					3																	152554449		2203	4300	6503	154037139	SO:0001583	missense	5028			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.878C>A	3.37:g.152554449C>A	ENSP00000304767:p.Pro293Gln		154037139		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.531249	0.45073	.	.	ENSG00000169860	ENST00000305097	T	0.69685	-0.42	5.58	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.061993	0.64402	D	0.000003	T	0.56848	0.2013	L	0.31752	0.955	0.80722	D	1	B	0.30406	0.278	B	0.36504	0.226	T	0.50346	-0.8839	10	0.12430	T	0.62	.	15.3449	0.74327	0.0:0.8599:0.1401:0.0	.	293	P47900	P2RY1_HUMAN	Q	293	ENSP00000304767:P293Q	ENSP00000304767:P293Q	P	+	2	0	P2RY1	154037139	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	4.856000	0.62932	1.311000	0.45024	0.563000	0.77884	CCA		0.448	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		A	152554449	C	A	152554449	3	1	77	1	0	0	0	0	1	0	0	0	11377	594	21	2	880	2	P2RY1	3	152554449	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1498362	152554449	45467981	244	21980										
DHX36	170506	broad.mit.edu	37	chr3	154027489	154027489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtacaaactattctgcaagCagatccttttcctctttcaa	4	11	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:154027489C>T	ENST00000496811.1	-	5	846	c.766G>A	c.(766-768)Gct>Act	p.A256T	DHX36_ENST00000544526.1_Missense_Mutation_p.A256T|DHX36_ENST00000308361.6_Missense_Mutation_p.A256T|DHX36_ENST00000329463.5_Missense_Mutation_p.A256T	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	256	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)	p.A256T(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATTCTGCAAGCAGATCCTTTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	3											91	90	91					3																	154027489		2202	4299	6501	155510183	SO:0001583	missense	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.766G>A	3.37:g.154027489C>T	ENSP00000417078:p.Ala256Thr		155510183	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	C	8.732	0.916807	0.17907	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;4.13	5.26	2.35	0.29111	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.646123	0.16327	N	0.219289	T	0.03783	0.0107	N	0.04090	-0.28	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.11329	0.004;0.004;0.006	T	0.45614	-0.9249	10	0.08381	T	0.77	.	5.7753	0.18275	0.5043:0.3458:0.0:0.1499	.	256;256;256	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	T	256;256;256;256;170	ENSP00000417078:A256T;ENSP00000309296:A256T;ENSP00000444247:A256T;ENSP00000330113:A256T;ENSP00000419862:A170T	ENSP00000309296:A256T	A	-	1	0	DHX36	155510183	0.041000	0.20044	0.891000	0.34965	0.962000	0.63368	0.397000	0.20883	0.591000	0.29711	-0.188000	0.12872	GCT		0.338	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		T	154027489	C	T	154027489	3	4	77	1	0	0	0	0	1	0	0	0	4520	710	25	3	2344	3	DHX36	3	154027489	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1473040	154027489	43994941	245	21981										
DHX36	170506	broad.mit.edu	37	chr3	154042165	154042165	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccaccggagctgcggggaCccccatcacggccccagttc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:154042165delC	ENST00000496811.1	-	1	121	c.41delG	c.(40-42)ggtfs	p.G14fs	DHX36_ENST00000544526.1_Frame_Shift_Del_p.G14fs|DHX36_ENST00000308361.6_Frame_Shift_Del_p.G14fs|DHX36_ENST00000329463.5_Frame_Shift_Del_p.G14fs	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	14	Gly-rich.|RNA-binding; sufficient and required for recruitment to cytoplasmic stress granules.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)	p.G14fs*44(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GCTGCGGGGACCCCCATCACG	0.672																																																1	Deletion - Frameshift(1)	large_intestine(1)	3											12	16	15					3																	154042165		2200	4295	6495	155524859	SO:0001589	frameshift_variant	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.41delG	3.37:g.154042165delC	ENSP00000417078:p.Gly14fs		155524859	B2RB00|Q70JU3|Q8IYE5|Q9P240	Frame_Shift_Del	DEL	ENST00000496811.1	37	CCDS3171.1																																																																																				0.672	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		-	154042165	C	-	154042165	7	5	77	1	0	1	0	1	0	0	0	0	4520	507	18	0	3085	0	DHX36	3	154042165	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	14676	154042165	43980265	246	21982										
TNIK	23043	broad.mit.edu	37	chr3	170843805	170843805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtgggatctgagttctggcGtggcatctccacgcggtggg	18	9	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:170843805G>A	ENST00000436636.2	-	17	2253	c.1909C>T	c.(1909-1911)Cgc>Tgc	p.R637C	TNIK_ENST00000369326.5_Missense_Mutation_p.R608C|TNIK_ENST00000475336.1_Missense_Mutation_p.R553C|TNIK_ENST00000284483.8_Missense_Mutation_p.R637C|TNIK_ENST00000470834.1_Missense_Mutation_p.R608C|TNIK_ENST00000357327.5_Missense_Mutation_p.R608C|TNIK_ENST00000538048.1_Missense_Mutation_p.R582C|TNIK_ENST00000341852.6_Missense_Mutation_p.R553C|TNIK_ENST00000460047.1_Missense_Mutation_p.R582C|TNIK_ENST00000488470.1_Missense_Mutation_p.R582C	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	637	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R637C(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GAGTTCTGGCGTGGCATCTCC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	3											85	87	87					3																	170843805		1923	4135	6058	172326499	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.1909C>T	3.37:g.170843805G>A	ENSP00000399511:p.Arg637Cys		172326499	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504781	0.85176	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.74947	0.88;0.88;-0.85;-0.82;0.88;-0.86;0.88;-0.89;-0.84;0.88	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.82733	0.5101	L	0.55481	1.735	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.79108	0.992;0.975;0.992;0.992;0.988;0.975;0.992;0.972	T	0.82575	-0.0389	10	0.52906	T	0.07	.	14.6057	0.68478	0.0:0.0:0.8199:0.1801	.	553;608;582;553;637;608;582;637	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	C	637;608;582;553;637;553;608;582;582;608	ENSP00000399511:R637C;ENSP00000358332:R608C;ENSP00000443278:R582C;ENSP00000345352:R553C;ENSP00000284483:R637C;ENSP00000418156:R553C;ENSP00000349880:R608C;ENSP00000418916:R582C;ENSP00000418378:R582C;ENSP00000419990:R608C	ENSP00000284483:R637C	R	-	1	0	TNIK	172326499	1.000000	0.71417	0.979000	0.43373	0.973000	0.67179	7.040000	0.76551	2.761000	0.94854	0.655000	0.94253	CGC		0.572	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170843805	G	A	170843805	3	1	77	1	0	0	0	0	1	0	0	0	16352	1145	40	1	2241	1	TNIK	3	170843805	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	16801640	170843805	27178625	247	21983										
FNDC3B	64778	broad.mit.edu	37	chr3	171969255	171969255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaagtggcggaggcggcagCggtagtggtcccggaattaa	19	7	0	0	rs151151218		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:171969255C>T	ENST00000336824.4	+	6	813	c.714C>T	c.(712-714)agC>agT	p.S238S	FNDC3B_ENST00000416957.1_Silent_p.S238S|FNDC3B_ENST00000415807.2_Silent_p.S238S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	238	Poly-Gly.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S238S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GAGGCGGCAGCGGTAGTGGTC	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	3											71	73	72					3																	171969255		2203	4300	6503	173451949	SO:0001819	synonymous_variant	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.714C>T	3.37:g.171969255C>T			173451949	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																				0.498	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	171969255	C	T	171969255	2	4	77	1	0	0	0	0	0	0	0	1	5989	767	27	1		1	FNDC3B	3	171969255	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1125450	171969255	26053175	248	21984										
PIK3CA	5290	broad.mit.edu	37	chr3	178948079	178948079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatttggttataaacgagaaCgtgtgccatttgttttgaca	9	5	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:178948079C>T	ENST00000263967.3	+	20	3008	c.2851C>T	c.(2851-2853)Cgt>Tgt	p.R951C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	951	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R951C(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TAAACGAGAACGTGTGCCATT	0.328		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	large_intestine(1)	3											81	79	80					3																	178948079		1811	4074	5885	180430773	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2851C>T	3.37:g.178948079C>T	ENSP00000263967:p.Arg951Cys		180430773	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178810	0.78564	.	.	ENSG00000121879	ENST00000263967	T	0.76968	-1.06	4.99	4.99	0.66335	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.90424	0.7002	M	0.93150	3.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92390	0.5920	10	0.72032	D	0.01	-12.5645	13.5798	0.61896	0.1556:0.8444:0.0:0.0	.	951	P42336	PK3CA_HUMAN	C	951	ENSP00000263967:R951C	ENSP00000263967:R951C	R	+	1	0	PIK3CA	180430773	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.502000	0.66956	2.459000	0.83118	0.585000	0.79938	CGT		0.328	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178948079	C	T	178948079	3	4	77	1	0	0	0	0	1	0	0	0	11944	536	19	1	2925	1	PIK3CA	3	178948079	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6978824	178948079	19074351	249	21985										
MCF2L2	23101	broad.mit.edu	37	chr3	182994664	182994664	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggatgtgcagtcttacctgcGgggggaaaggtctccgagcc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:182994664delG	ENST00000328913.3	-	15	2155	c.1858delC	c.(1858-1860)cgcfs	p.R622fs	MCF2L2_ENST00000447025.2_Frame_Shift_Del_p.R622fs|MCF2L2_ENST00000473233.1_Frame_Shift_Del_p.R622fs|MCF2L2_ENST00000414362.2_Frame_Shift_Del_p.R621fs	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	622	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R620fs*16(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TCTTACCTGCGGGGGGAAAGG	0.567																																																1	Deletion - Frameshift(1)	large_intestine(1)	3											23	23	23					3																	182994664		2203	4300	6503	184477358	SO:0001589	frameshift_variant	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1858delC	3.37:g.182994664delG	ENSP00000328118:p.Arg622fs		184477358	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Frame_Shift_Del	DEL	ENST00000328913.3	37	CCDS3243.1																																																																																				0.567	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		-	182994664	G	-	182994664	7	5	77	1	0	1	0	1	0	0	0	0	9410	1116	39	0	1550	0	MCF2L2	3	182994664	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	4046585	182994664	15027766	250	21986										
MCF2L2	23101	broad.mit.edu	37	chr3	183097194	183097194	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggggcgccatcctcccctcGgcctcctgcaacaaaaacag	10	17	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:183097194G>A	ENST00000328913.3	-	3	463	c.166C>T	c.(166-168)Cga>Tga	p.R56*	MCF2L2_ENST00000447025.2_Nonsense_Mutation_p.R56*|MCF2L2_ENST00000473233.1_Nonsense_Mutation_p.R56*|MCF2L2_ENST00000414362.2_Nonsense_Mutation_p.R56*	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	56	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R56*(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TCCTCCCCTCGGCCTCCTGCA	0.498																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											69	62	64					3																	183097194		2203	4300	6503	184579888	SO:0001587	stop_gained	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.166C>T	3.37:g.183097194G>A	ENSP00000328118:p.Arg56*		184579888	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Nonsense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535641	0.45176	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362;ENST00000482017	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5619	0.50782	0.0:0.0:0.7144:0.2855	.	.	.	.	X	56;56;56;56;28	.	ENSP00000328118:R56X	R	-	1	2	MCF2L2	184579888	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	3.266000	0.51569	2.580000	0.87095	0.655000	0.94253	CGA		0.498	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		A	183097194	G	A	183097194	4	1	77	1	0	0	0	0	0	1	0	0	9410	1124	39	1	3290	1	MCF2L2	3	183097194	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	102530	183097194	14925236	251	21987										
DVL3	1857	broad.mit.edu	37	chr3	183882366	183882366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcccagcgagagcggccacGccggagggatggcccagagc	17	14	0	2	rs146812695	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:183882366G>A	ENST00000313143.3	+	4	688	c.440G>A	c.(439-441)cGc>cAc	p.R147H	DVL3_ENST00000431765.1_Missense_Mutation_p.R147H|DVL3_ENST00000462665.1_3'UTR|EIF2B5_ENST00000444495.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	147					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)	p.R147H(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			GAGCGGCCACGCCGGAGGGAT	0.607													G|||	2	0.000399361	0.0015	0	5008	,	,		18772	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	HIS/ARG	0,4406		0,0,2203	37	37	37		440	4.6	1	3	dbSNP_134	37	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DVL3	NM_004423.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	147/717	183882366	1,13005	2203	4300	6503	185365060	SO:0001583	missense	1857			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.440G>A	3.37:g.183882366G>A	ENSP00000316054:p.Arg147His		185365060	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Missense_Mutation	SNP	ENST00000313143.3	37	CCDS3253.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	12.97	2.096874	0.37048	0.0	1.16E-4	ENSG00000161202	ENST00000313143;ENST00000415612;ENST00000431765;ENST00000423300	T;T;T	0.06933	3.67;3.66;3.24	4.58	4.58	0.56647	Dishevelled protein domain (1);	0.102804	0.64402	D	0.000005	T	0.24967	0.0606	L	0.55481	1.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00536	-1.1683	10	0.37606	T	0.19	-17.5236	17.9371	0.89015	0.0:0.0:1.0:0.0	.	147;147	B4E3E5;Q92997	.;DVL3_HUMAN	H	147;147;147;45	ENSP00000316054:R147H;ENSP00000405885:R147H;ENSP00000393849:R45H	ENSP00000316054:R147H	R	+	2	0	DVL3	185365060	1.000000	0.71417	0.997000	0.53966	0.059000	0.15707	7.244000	0.78228	2.542000	0.85734	0.650000	0.86243	CGC		0.607	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		A	183882366	G	A	183882366	3	1	77	1	0	0	0	0	1	0	0	0	4848	1087	38	1	454	1	DVL3	3	183882366	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	785172	183882366	14140064	252	21988										
CLCN2	1181	broad.mit.edu	37	chr3	184075230	184075230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaagccccgccagtagttcCgcactgcaaagaaggtggag	13	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:184075230C>T	ENST00000265593.4	-	8	989	c.818G>A	c.(817-819)cGg>cAg	p.R273Q	CLCN2_ENST00000434054.2_Missense_Mutation_p.R229Q|CLCN2_ENST00000475279.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000457512.1_Missense_Mutation_p.R273Q|CLCN2_ENST00000344937.7_Missense_Mutation_p.R273Q	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	273					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)	p.R273Q(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	CCAGTAGTTCCGCACTGCAAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	3											90	100	97					3																	184075230		2203	4300	6503	185557924	SO:0001583	missense	1181			S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.818G>A	3.37:g.184075230C>T	ENSP00000265593:p.Arg273Gln		185557924	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	37	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	c	25.3	4.624806	0.87560	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51	5.53	4.64	0.57946	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.96744	0.8937	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.987;1.0;0.993	D;D;P;D;D	0.91635	0.998;0.999;0.858;0.985;0.925	D	0.97155	0.9834	10	0.87932	D	0	-10.7105	15.1004	0.72269	0.0:0.8573:0.1427:0.0	.	273;229;273;273;273	B4DYE3;E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;.;CLCN2_HUMAN	Q	273;273;229;273	ENSP00000265593:R273Q;ENSP00000345056:R273Q;ENSP00000400425:R229Q;ENSP00000391928:R273Q	ENSP00000265593:R273Q	R	-	2	0	CLCN2	185557924	1.000000	0.71417	0.145000	0.22337	0.831000	0.47069	6.070000	0.71220	1.293000	0.44690	0.561000	0.74099	CGG		0.627	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			T	184075230	C	T	184075230	3	4	77	1	0	0	0	0	1	0	0	0	3469	652	23	1	1946	1	CLCN2	3	184075230	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	192864	184075230	13947200	253	21989										
ETV5	2119	broad.mit.edu	37	chr3	185797801	185797801	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggcagagttgcctgaggtGggggaaataggggattctga					rs537105512		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:185797801delG	ENST00000306376.5	-	7	701	c.455delC	c.(454-456)ccafs	p.P153fs	ETV5_ENST00000434744.1_Frame_Shift_Del_p.P153fs|ETV5_ENST00000537818.1_Frame_Shift_Del_p.P195fs|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	153					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.P152fs*55(1)		breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TGCCTGAGGTGGGGGAAATAG	0.617			T	"TMPRSS2, SCL45A3"	Prostate																																		Dom	yes		3	3q28	2119	ets variant gene 5		E	1	Deletion - Frameshift(1)	large_intestine(1)	3																																								187280495	SO:0001589	frameshift_variant	2119			BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.455delC	3.37:g.185797801delG	ENSP00000306894:p.Pro153fs		187280495	A6NH46|B7Z7D7|Q6IBN5	Frame_Shift_Del	DEL	ENST00000306376.5	37	CCDS33906.1																																																																																				0.617	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		-	185797801	G	-	185797801	7	5	77	1	0	1	0	1	0	0	0	0	5295	1348	47	0	1105	0	ETV5	3	185797801	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1722571	185797801	12224629	254	21990										
BCL6	604	broad.mit.edu	37	chr3	187446270	187446270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccgcaggacgtgcacttcGgggggtgcatgtagagtggt	18	8	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:187446270G>A	ENST00000406870.2	-	6	1784	c.1418C>T	c.(1417-1419)cCg>cTg	p.P473L	RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000450123.2_Missense_Mutation_p.P473L|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Missense_Mutation_p.P473L	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	473					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P473L(1)|p.K474fs*26(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CGTGCACTTCGGGGGGTGCAT	0.627			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(2)	3											63	56	58					3																	187446270		2203	4300	6503	188928964	SO:0001583	missense	604				CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1418C>T	3.37:g.187446270G>A	ENSP00000384371:p.Pro473Leu		188928964	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.456922	0.26161	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.09817	3.12;3.12;2.94	5.09	5.09	0.68999	.	0.114333	0.64402	D	0.000009	T	0.03564	0.0102	N	0.00926	-1.1	0.49299	D	0.999775	B;P	0.46020	0.0;0.871	B;B	0.33521	0.001;0.165	T	0.56872	-0.7907	10	0.26408	T	0.33	.	18.3699	0.90403	0.0:0.0:1.0:0.0	.	473;473	B8PSA7;P41182	.;BCL6_HUMAN	L	473	ENSP00000384371:P473L;ENSP00000232014:P473L;ENSP00000413122:P473L	ENSP00000232014:P473L	P	-	2	0	BCL6	188928964	1.000000	0.71417	0.985000	0.45067	0.894000	0.52154	6.735000	0.74806	2.756000	0.94617	0.561000	0.74099	CCG		0.627	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187446270	G	A	187446270	3	1	77	1	0	0	0	0	1	0	0	0	1377	1116	39	1	722	1	BCL6	3	187446270	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1648469	187446270	10576160	255	21991										
C3orf59	151963	broad.mit.edu	37	chr3	192516726	192516726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctttgcaggcctgataggCctgcatgaggctgctggaga	16	9	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:192516726C>T	ENST00000392452.2	-	2	1245	c.925G>A	c.(925-927)Gcc>Acc	p.A309T		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	309							protein complex binding (GO:0032403)	p.A307T(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GCCTGATAGGCCTGCATGAGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	3											34	34	34					3																	192516726		2203	4300	6503	193999420	SO:0001583	missense	151963			AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.925G>A	3.37:g.192516726C>T	ENSP00000376246:p.Ala309Thr		193999420	Q86VD8	Missense_Mutation	SNP	ENST00000392452.2	37	CCDS3302.2	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294427	0.60086	.	.	ENSG00000180611	ENST00000392452	T	0.08008	3.14	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.09291	0.0229	L	0.39397	1.21	0.80722	D	1	B	0.33883	0.43	B	0.30572	0.117	T	0.24799	-1.0150	10	0.27785	T	0.31	.	18.2403	0.89966	0.0:1.0:0.0:0.0	.	309	Q8IYB1	M21D2_HUMAN	T	309	ENSP00000376246:A309T	ENSP00000376246:A309T	A	-	1	0	MB21D2	193999420	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.542000	0.85734	0.655000	0.94253	GCC		0.557	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		T	192516726	C	T	192516726	3	4	77	1	0	0	0	0	1	0	0	0	2243	739	26	3	554	3	C3orf59	3	192516726	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5070456	192516726	5505704	256	21992										
HRASLS	57110	broad.mit.edu	37	chr3	192980824	192980824	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtaaggccctggtgaaaatgCagctcttgaaggatgttgtg	14	6	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:192980824C>T	ENST00000602513.1	+	3	614	c.205C>T	c.(205-207)Cag>Tag	p.Q69*	HRASLS_ENST00000264735.2_Nonsense_Mutation_p.Q174*			Q9HDD0	HRSL1_HUMAN	HRAS-like suppressor	69					ether lipid metabolic process (GO:0046485)|lipid catabolic process (GO:0016042)|peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|nuclear envelope lumen (GO:0005641)|peroxisome (GO:0005777)	phospholipase activity (GO:0004620)|transferase activity (GO:0016740)	p.Q69*(1)		breast(1)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	10	all_cancers(143;9.1e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000159)		GGTGAAAATGCAGCTCTTGAA	0.428																																																1	Substitution - Nonsense(1)	large_intestine(1)	3											164	171	169					3																	192980824		2203	4300	6503	194463518	SO:0001587	stop_gained	57110			AB030816	CCDS3303.1, CCDS3303.2	3q29	2008-05-15			ENSG00000127252	ENSG00000127252			14922	protein-coding gene	gene with protein product		606487					Standard	NM_020386		Approved	H-REV107, HRASLS1	uc003fta.4	Q9HDD0	OTTHUMG00000156104	ENST00000602513.1:c.205C>T	3.37:g.192980824C>T	ENSP00000473258:p.Gln69*		194463518	D2KX19	Nonsense_Mutation	SNP	ENST00000602513.1	37		.	.	.	.	.	.	.	.	.	.	C	42	9.215668	0.99103	.	.	ENSG00000127252	ENST00000264735	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	4.6886	19.8676	0.96824	0.0:1.0:0.0:0.0	.	.	.	.	X	69	.	ENSP00000264735:Q69X	Q	+	1	0	HRASLS	194463518	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.739000	0.55075	2.941000	0.99782	0.655000	0.94253	CAG		0.428	HRASLS-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	192980824	C	T	192980824	4	4	77	1	0	0	0	0	0	1	0	0	7370	711	25	3	211	3	HRASLS	3	192980824	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	464098	192980824	5041606	257	21993										
LRRC15	131578	broad.mit.edu	37	chr3	194080363	194080363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggacgcttggaacagcaacGttgacattgatgataatgag	12	6	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:194080363G>A	ENST00000347624.3	-	2	1495	c.1410C>T	c.(1408-1410)aaC>aaT	p.N470N	LRRC15_ENST00000439944.2_Silent_p.N476N|LRRC15_ENST00000428839.1_Silent_p.N476N	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	470	LRRCT.				negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)	p.N470N(1)		biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GAACAGCAACGTTGACATTGA	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	3											145	126	132					3																	194080363		2203	4300	6503	195561658	SO:0001819	synonymous_variant	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1410C>T	3.37:g.194080363G>A			195561658	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																				0.547	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			A	194080363	G	A	194080363	2	1	77	1	0	0	0	0	0	0	0	1	8999	1136	40	1		1	LRRC15	3	194080363	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1099539	194080363	3942067	258	21994										
SENP5	205564	broad.mit.edu	37	chr3	196612055	196612056	+	Start_Codon_Ins	INS	-	-	A													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cattatgcatcagaaaaatgINSaaaaaacagaggaaaattct							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr3:196612055_196612056insA	ENST00000323460.5	+	0	252_253				SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Start_Codon_Ins	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5						cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.Q4fs*16(1)		NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TCAGAAAAATGAAAAAACAGAG	0.332																																					Ovarian(47;891 1095 11174 13858 51271)											1	Insertion - Frameshift(1)	large_intestine(1)	3																																								198096453	SO:0001582	initiator_codon_variant	205564			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.9dupA	3.37:g.196612061_196612061dupA			198096452	B4DY82|Q96SA5	Frame_Shift_Ins	INS	ENST00000323460.5	37	CCDS3322.1																																																																																				0.332	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		A	196612056	-	A	196612055	7	5	77	1	0	1	1	0	0	0	0	0	14086	1290	45	0	5	0	SENP5	3	196612055	Start_Codon_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	2531692	196612055	1410375	259	21995										
ZNF595	152687	broad.mit.edu	37	chr4	87034	87034	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgtggcaaagcctttactcGgtccacagccctgaatgaac	9	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:87034G>A	ENST00000339368.6	+	0	1843							Q8IYB9	ZN595_HUMAN	zinc finger protein 595						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GCCTTTACTCGGTCCACAGCC	0.393																																																0			4											54	61	59					4																	87034		2073	4241	6314	77034	SO:0001624	3_prime_UTR_variant	152687			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000339368.6:c.*1840G>A	4.37:g.87034G>A			77034		Missense_Mutation	SNP	ENST00000339368.6	37																																																																																					0.393	ZNF595-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000357814.2	NM_182524		A	87034	G	A	87034	1	1	77	0	1	0	0	0	0	0	0	0	18064	1116	39	1		1	ZNF595	4	87034	3'UTR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		87034	191067242	260	21996										
WHSC2	7469	broad.mit.edu	37	chr4	1988081	1988081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggggctgaagacgctgggcGccgtggggcttctgaagggc	20	9	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:1988081G>A	ENST00000411638.2	-	5	698	c.683C>T	c.(682-684)gCg>gTg	p.A228V	NELFA_ENST00000382882.3_Missense_Mutation_p.A239V|MIR943_ENST00000401286.1_RNA|NELFA_ENST00000542778.1_Missense_Mutation_p.A93V	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	228	HDAg-like.				gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.A228V(1)									GACGCTGGGCGCCGTGGGGCT	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	4											24	27	26					4																	1988081		2192	4299	6491	1957879	SO:0001583	missense	7469			AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"Wolf-Hirschhorn syndrome candidate 2"	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.683C>T	4.37:g.1988081G>A	ENSP00000399165:p.Ala228Val		1957879	A2A2T1|O95392	Missense_Mutation	SNP	ENST00000411638.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.03|15.03	2.710899|2.710899	0.48517|0.48517	.|.	.|.	ENSG00000185049|ENSG00000185049	ENST00000382882;ENST00000416258;ENST00000542778;ENST00000411638;ENST00000431323;ENST00000455762|ENST00000453740	T;T;T;T;T;T|.	0.52754|.	0.65;0.65;0.65;0.65;0.65;0.65|.	4.76|4.76	3.89|3.89	0.44902|0.44902	.|.	0.330372|.	0.36591|.	N|.	0.002520|.	T|T	0.48960|0.48960	0.1529|0.1529	L|L	0.29908|0.29908	0.895|0.895	0.34954|0.34954	D|D	0.751505|0.751505	B|.	0.24483|.	0.104|.	B|.	0.21708|.	0.036|.	T|T	0.57376|0.57376	-0.7822|-0.7822	10|5	0.11485|.	T|.	0.65|.	-6.9287|-6.9287	14.9894|14.9894	0.71374|0.71374	0.0:0.1437:0.8562:0.0|0.0:0.1437:0.8562:0.0	.|.	228|.	Q9H3P2|.	NELFA_HUMAN|.	V|C	239;232;93;228;244;158|129	ENSP00000372335:A239V;ENSP00000387647:A232V;ENSP00000445757:A93V;ENSP00000399165:A228V;ENSP00000395761:A244V;ENSP00000410154:A158V|.	ENSP00000372335:A239V|.	A|R	-|-	2|1	0|0	WHSC2|WHSC2	1957879|1957879	0.990000|0.990000	0.36364|0.36364	0.132000|0.132000	0.22025|0.22025	0.831000|0.831000	0.47069|0.47069	5.035000|5.035000	0.64158|0.64158	1.087000|1.087000	0.41251|0.41251	0.462000|0.462000	0.41574|0.41574	GCG|CGC		0.682	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663		A	1988081	G	A	1988081	3	1	77	1	0	0	0	0	1	0	0	0	17404	1087	38	1	931	1	WHSC2	4	1988081	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1901047	1988081	189166195	261	21997										
SH3BP2	6452	broad.mit.edu	37	chr4	2826421	2826421	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcagcaagaagcaccgcacGtggttcttctcggcctcctc	9	15	3	1	rs140178337		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:2826421G>A	ENST00000356331.5	+	4	582	c.321G>A	c.(319-321)acG>acA	p.T107T	SH3BP2_ENST00000503393.2_Silent_p.T164T|SH3BP2_ENST00000435136.2_Silent_p.T107T|SH3BP2_ENST00000442312.2_Silent_p.T135T|SH3BP2_ENST00000452765.2_Silent_p.T107T|SH3BP2_ENST00000511747.1_Silent_p.T107T|SH3BP2_ENST00000515183.1_3'UTR	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	107	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.T107T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		AGCACCGCACGTGGTTCTTCT	0.637									Cherubism																																							1	Substitution - coding silent(1)	large_intestine(1)	4						G	,,,	0,4406		0,0,2203	84	79	81		321,405,492,321	-9.7	0.7	4	dbSNP_134	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,	107/562,135/590,164/619,107/562	2826421	2,13004	2203	4300	6503	2796219	SO:0001819	synonymous_variant	6452	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.321G>A	4.37:g.2826421G>A			2796219	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																				0.637	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		A	2826421	G	A	2826421	2	1	77	1	0	0	0	0	0	0	0	1	14282	1132	40	1		1	SH3BP2	4	2826421	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	838340	2826421	188327855	262	21998										
CRMP1	1400	broad.mit.edu	37	chr4	5823521	5823521	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgatgttggagcggccaccaGggggcgccacgatgcggtgg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:5823521delG	ENST00000397890.2	-	14	1899	c.1685delC	c.(1684-1686)cctfs	p.P562fs	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Frame_Shift_Del_p.P560fs|CRMP1_ENST00000324989.7_Frame_Shift_Del_p.P676fs|EVC_ENST00000382674.2_Intron	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	562					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.P676fs*>11(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		GCGGCCACCAGGGGGCGCCAC	0.592											OREG0016065	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Deletion - Frameshift(1)	large_intestine(1)	4											38	37	37					4																	5823521		2201	4300	6501	5874422	SO:0001589	frameshift_variant	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1685delC	4.37:g.5823521delG	ENSP00000380987:p.Pro562fs	629	5874422	A0EJG6|Q13024|Q4W5F1|Q96TC8	Frame_Shift_Del	DEL	ENST00000397890.2	37	CCDS43207.1																																																																																				0.592	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		-	5823521	G	-	5823521	7	5	77	1	0	1	0	1	0	0	0	0	3896	1000	35	0	37	0	CRMP1	4	5823521	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	2997100	5823521	185330755	263	21999										
ACOX3	8310	broad.mit.edu	37	chr4	8417629	8417629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actcgaagatccgcttgcatCgaaggaagttcagctcgcga	11	11	1	1	rs199723449		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:8417629C>T	ENST00000356406.5	-	3	319	c.242G>A	c.(241-243)cGa>cAa	p.R81Q	ACOX3_ENST00000503233.1_Missense_Mutation_p.R81Q|ACOX3_ENST00000413009.2_Missense_Mutation_p.R81Q	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	81					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)	p.R81Q(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CCGCTTGCATCGAAGGAAGTT	0.517													C|||	1	0.000199681	0	0.0014	5008	,	,		18779	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	87	80	83		242,242	5.4	0.3	4		83	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ACOX3	NM_001101667.1,NM_003501.2	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	81/625,81/701	8417629	1,13005	2203	4300	6503	8468529	SO:0001583	missense	8310			Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.242G>A	4.37:g.8417629C>T	ENSP00000348775:p.Arg81Gln		8468529	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010784	0.75046	0.0	1.16E-4	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.57595	0.39;0.39;0.39	5.39	5.39	0.77823	Acyl-CoA dehydrogenase/oxidase (1);	0.000000	0.85682	D	0.000000	T	0.53738	0.1815	M	0.62154	1.92	0.58432	D	0.999999	P;P	0.48640	0.913;0.858	B;B	0.43916	0.436;0.252	T	0.51164	-0.8740	10	0.15952	T	0.53	-30.946	17.9729	0.89118	0.0:1.0:0.0:0.0	.	81;81	O15254-2;O15254	.;ACOX3_HUMAN	Q	81	ENSP00000413994:R81Q;ENSP00000348775:R81Q;ENSP00000421625:R81Q	ENSP00000348775:R81Q	R	-	2	0	ACOX3	8468529	1.000000	0.71417	0.290000	0.24890	0.046000	0.14306	3.825000	0.55730	2.546000	0.85860	0.650000	0.86243	CGA		0.517	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			T	8417629	C	T	8417629	3	4	77	1	0	0	0	0	1	0	0	0	160	884	31	1	1924	1	ACOX3	4	8417629	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2594108	8417629	182736647	264	22000										
CPZ	8532	broad.mit.edu	37	chr4	8608581	8608581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcggagacccgcggcgcaCgcagcgaccacatccccatc	12	18	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:8608581C>T	ENST00000360986.4	+	6	1198	c.1024C>T	c.(1024-1026)Cgc>Tgc	p.R342C	CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000382480.2_Missense_Mutation_p.R205C|CPZ_ENST00000315782.6_Missense_Mutation_p.R331C	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	342					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R342C(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCGCGGCGCACGCAGCGACCA	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	4											38	37	37					4																	8608581		2200	4300	6500	8659481	SO:0001583	missense	8532			U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1024C>T	4.37:g.8608581C>T	ENSP00000354255:p.Arg342Cys		8659481	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	c	21.1	4.093053	0.76756	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	T;T;T	0.03468	3.92;3.92;3.92	3.46	3.46	0.39613	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	U	0.000000	T	0.20659	0.0497	M	0.86420	2.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.07520	-1.0768	10	0.52906	T	0.07	-40.844	15.1455	0.72647	0.0:1.0:0.0:0.0	.	331;342	Q66K79-2;Q66K79	.;CBPZ_HUMAN	C	342;205;331	ENSP00000354255:R342C;ENSP00000371920:R205C;ENSP00000315074:R331C	ENSP00000315074:R331C	R	+	1	0	CPZ	8659481	1.000000	0.71417	0.037000	0.18230	0.619000	0.37552	6.808000	0.75206	1.761000	0.52028	0.450000	0.29827	CGC		0.652	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8608581	C	T	8608581	3	4	77	1	0	0	0	0	1	0	0	0	3845	536	19	1	1046	1	CPZ	4	8608581	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	190952	8608581	182545695	265	22001										
DRD5	1816	broad.mit.edu	37	chr4	9784146	9784146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtcatggtcggcctggcaTggaccttgtccatcctcatc	11	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:9784146T>C	ENST00000304374.2	+	1	889	c.493T>C	c.(493-495)Tgg>Cgg	p.W165R		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	165					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.W165R(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CGGCCTGGCATGGACCTTGTC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	4											37	36	36					4																	9784146		2203	4300	6503	9393244	SO:0001583	missense	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.493T>C	4.37:g.9784146T>C	ENSP00000306129:p.Trp165Arg		9393244	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	t	17.84	3.487452	0.63962	.	.	ENSG00000169676	ENST00000304374	D	0.88896	-2.44	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97167	0.9074	H	0.99847	4.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98128	1.0429	10	0.87932	D	0	.	13.2146	0.59851	0.0:0.0:0.0:1.0	.	165	P21918	DRD5_HUMAN	R	165	ENSP00000306129:W165R	ENSP00000306129:W165R	W	+	1	0	DRD5	9393244	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	7.493000	0.81493	1.906000	0.55180	0.254000	0.18369	TGG		0.627	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			C	9784146	T	C	9784146	3	2	77	1	0	0	0	0	1	0	0	0	4771	1464	51	4	495	4	DRD5	4	9784146	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1175565	9784146	181370130	266	22002										
CC2D2A	57545	broad.mit.edu	37	chr4	15517559	15517559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagatgaaggcctttacaccGgggtaagaccagaggtggca	14	8	0	4	rs188018643	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:15517559G>A	ENST00000503292.1	+	11	1129	c.949G>A	c.(949-951)Ggg>Agg	p.G317R	CC2D2A_ENST00000389652.5_Missense_Mutation_p.G268R|CC2D2A_ENST00000424120.1_Missense_Mutation_p.G317R|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Missense_Mutation_p.G317R	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	317					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.G268R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						CCTTTACACCGGGGTAAGACC	0.458													G|||	2	0.000399361	0	0	5008	,	,		16764	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											45	45	45					4																	15517559		1906	4111	6017	15126657	SO:0001583	missense	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.949G>A	4.37:g.15517559G>A	ENSP00000421809:p.Gly317Arg		15126657	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	17.26	3.344994	0.61073	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000512702;ENST00000503292;ENST00000389652	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	6.17	6.17	0.99709	.	0.054227	0.85682	D	0.000000	T	0.55065	0.1897	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.48031	-0.9070	10	0.45353	T	0.12	.	19.6509	0.95805	0.0:0.0:1.0:0.0	.	317;268	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	R	317;317;268;268;317;317;268	ENSP00000403465:G317R;ENSP00000398391:G317R;ENSP00000422875:G317R;ENSP00000421809:G317R;ENSP00000374303:G268R	ENSP00000374303:G268R	G	+	1	0	CC2D2A	15126657	1.000000	0.71417	0.264000	0.24511	0.031000	0.12232	8.051000	0.89446	2.941000	0.99782	0.655000	0.94253	GGG		0.458	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		A	15517559	G	A	15517559	3	1	77	1	0	0	0	0	1	0	0	0	2734	1116	39	1	1186	1	CC2D2A	4	15517559	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5733413	15517559	175636717	267	22003										
GPR125	166647	broad.mit.edu	37	chr4	22444396	22444396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtcctgatcaatatatgaaGccatgcactggaaaggaagg	11	7	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:22444396G>A	ENST00000334304.5	-	7	1066	c.797C>T	c.(796-798)gCt>gTt	p.A266V	GPR125_ENST00000502482.1_Missense_Mutation_p.A266V|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Missense_Mutation_p.A40V	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	266	Ig-like.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.A266V(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				AATATATGAAGCCATGCACTG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											60	58	59					4																	22444396		2202	4279	6481	22053494	SO:0001583	missense	166647			AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.797C>T	4.37:g.22444396G>A	ENSP00000334952:p.Ala266Val		22053494	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	34	5.327214	0.95708	.	.	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482;ENST00000514129	T;T;T	0.58652	0.32;0.32;0.32	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.76521	0.3999	M	0.67397	2.05	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;0.996;0.895	D;D;D;P	0.91635	0.999;0.998;0.99;0.658	T	0.77397	-0.2603	10	0.87932	D	0	-24.2358	20.0027	0.97425	0.0:0.0:1.0:0.0	.	141;266;40;266	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	V	266;40;266;2	ENSP00000334952:A266V;ENSP00000422606:A40V;ENSP00000421006:A266V	ENSP00000334952:A266V	A	-	2	0	GPR125	22053494	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	9.414000	0.97362	2.733000	0.93635	0.655000	0.94253	GCT		0.428	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			A	22444396	G	A	22444396	3	1	77	1	0	0	0	0	1	0	0	0	6659	971	34	3	3220	3	GPR125	4	22444396	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6926837	22444396	168709880	268	22004										
KLHL5	51088	broad.mit.edu	37	chr4	39098493	39098493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agttgggggaatggattcaaCaaaaggtatcaaataatctt	10	4	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:39098493C>T	ENST00000504108.1	+	6	1716	c.1433C>T	c.(1432-1434)aCa>aTa	p.T478I	KLHL5_ENST00000508137.2_Missense_Mutation_p.T291I|KLHL5_ENST00000359687.2_Missense_Mutation_p.T478I|KLHL5_ENST00000381930.3_Missense_Mutation_p.T478I|KLHL5_ENST00000261425.3_Missense_Mutation_p.T432I|KLHL5_ENST00000261426.5_Missense_Mutation_p.T417I	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	478						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.T478R(1)|p.T478I(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						ATGGATTCAACAAAAGGTATC	0.378																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	4											75	69	71					4																	39098493		2203	4300	6503	38774888	SO:0001583	missense	51088			AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"Kelch-like", "BTB/POZ domain containing"	6356	protein-coding gene	gene with protein product		608064	"kelch (Drosophila)-like 5", "kelch-like 5 (Drosophila)"			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.1433C>T	4.37:g.39098493C>T	ENSP00000423897:p.Thr478Ile		38774888	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Missense_Mutation	SNP	ENST00000504108.1	37	CCDS33974.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039883	0.55003	.	.	ENSG00000109790	ENST00000544221;ENST00000261425;ENST00000508137;ENST00000504108;ENST00000359687;ENST00000381930;ENST00000261426;ENST00000546147	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.36	5.36	0.76844	Galactose oxidase, beta-propeller (1);	0.045781	0.85682	D	0.000000	T	0.67757	0.2927	L	0.46741	1.465	0.80722	D	1	P;P;P	0.43352	0.479;0.804;0.611	B;P;P	0.46419	0.219;0.516;0.511	T	0.62506	-0.6840	10	0.22706	T	0.39	.	19.4686	0.94952	0.0:1.0:0.0:0.0	.	417;478;478	F8WAE7;Q96PQ7;Q96PQ7-2	.;KLHL5_HUMAN;.	I	512;432;291;478;478;478;417;72	ENSP00000261425:T432I;ENSP00000423080:T291I;ENSP00000423897:T478I;ENSP00000352716:T478I;ENSP00000371355:T478I;ENSP00000261426:T417I	ENSP00000261425:T432I	T	+	2	0	KLHL5	38774888	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.784000	0.85713	2.668000	0.90789	0.650000	0.86243	ACA		0.378	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1			T	39098493	C	T	39098493	3	4	77	1	0	0	0	0	1	0	0	0	8413	478	17	3	1455	3	KLHL5	4	39098493	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	16654097	39098493	152055783	269	22005										
PHOX2B	8929	broad.mit.edu	37	chr4	41749524	41749524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgcgcttctcgttgaggcCgccgtggtccgtgaagagtt	14	11	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:41749524C>T	ENST00000226382.2	-	2	630	c.271G>A	c.(271-273)Ggc>Agc	p.G91S	RP11-227F19.2_ENST00000510602.1_lincRNA|RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	91					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	p.G91S(1)		autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						TCGTTGAGGCCGCCGTGGTCC	0.577			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	1	Substitution - Missense(1)	large_intestine(1)	4											70	71	71					4																	41749524		2203	4300	6503	41444281	SO:0001583	missense	8929	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.271G>A	4.37:g.41749524C>T	ENSP00000226382:p.Gly91Ser		41444281	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	37	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188181	0.57909	.	.	ENSG00000109132	ENST00000226382	D	0.90955	-2.76	5.4	5.4	0.78164	Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.93396	0.7894	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	P	0.56960	0.81	D	0.92722	0.6192	10	0.46703	T	0.11	.	19.366	0.94461	0.0:1.0:0.0:0.0	.	91	Q99453	PHX2B_HUMAN	S	91	ENSP00000226382:G91S	ENSP00000226382:G91S	G	-	1	0	PHOX2B	41444281	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.245000	0.78237	2.797000	0.96272	0.655000	0.94253	GGC		0.577	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			T	41749524	C	T	41749524	3	4	77	1	0	0	0	0	1	0	0	0	11890	652	23	1	681	1	PHOX2B	4	41749524	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2651031	41749524	149404752	270	22006										
FIP1L1	81608	broad.mit.edu	37	chr4	54308840	54308840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttttcctcctccaccaggcGctccacctccatctcttata	4	18	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:54308840G>A	ENST00000337488.6	+	14	1389	c.1195G>A	c.(1195-1197)Gct>Act	p.A399T	FIP1L1_ENST00000358575.5_Missense_Mutation_p.A393T|FIP1L1_ENST00000306932.6_Missense_Mutation_p.A325T|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	399	Pro-rich.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A399T(1)		large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCCACCAGGCGCTCCACCTCC	0.358			T	PDGFRA	idiopathic hypereosinophilic syndrome																																		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	1	Substitution - Missense(1)	large_intestine(1)	4											116	114	114					4																	54308840		2203	4300	6503	54003597	SO:0001583	missense	81608			AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1195G>A	4.37:g.54308840G>A	ENSP00000336752:p.Ala399Thr		54003597	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498056	0.64186	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	T;T;T;T	0.47869	2.97;0.83;1.97;0.83	5.52	5.52	0.82312	.	0.081721	0.49916	D	0.000138	T	0.36331	0.0963	L	0.29908	0.895	0.80722	D	1	P;P;P;P	0.51240	0.943;0.715;0.902;0.905	B;B;B;B	0.37731	0.257;0.08;0.257;0.131	T	0.19778	-1.0295	10	0.38643	T	0.18	-28.5405	17.5668	0.87922	0.0:0.0:1.0:0.0	.	393;393;325;399	G3XAD6;B4DIR3;Q6UN15-3;Q6UN15	.;.;.;FIP1_HUMAN	T	399;393;325;56	ENSP00000336752:A399T;ENSP00000351383:A393T;ENSP00000302993:A325T;ENSP00000421691:A56T	ENSP00000302993:A325T	A	+	1	0	FIP1L1	54003597	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	5.907000	0.69908	2.755000	0.94549	0.591000	0.81541	GCT		0.358	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		A	54308840	G	A	54308840	3	1	77	1	0	0	0	0	1	0	0	0	5915	1087	38	1	1280	1	FIP1L1	4	54308840	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	12559316	54308840	136845436	271	22007										
KDR	3791	broad.mit.edu	37	chr4	55964922	55964922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaagaacatggcaatcaccGccgtgcctactagaataatg	9	10	1	3	rs199982402		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:55964922G>A	ENST00000263923.4	-	16	2610	c.2315C>T	c.(2314-2316)gCg>gTg	p.A772V		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	772				A -> T (in Ref. 7; AAA59459/CAA43837). {ECO:0000305}.	angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.A772V(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGCAATCACCGCCGTGCCTAC	0.418			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - Missense(1)	large_intestine(1)	4											114	114	114					4																	55964922		2203	4300	6503	55659679	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2315C>T	4.37:g.55964922G>A	ENSP00000263923:p.Ala772Val		55659679	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	G	7.367	0.626070	0.14257	.	.	ENSG00000128052	ENST00000263923	T	0.77229	-1.08	5.97	5.97	0.96955	.	0.116782	0.64402	D	0.000018	T	0.48978	0.1530	N	0.04508	-0.205	0.44880	D	0.99789	P	0.41313	0.745	B	0.26310	0.068	T	0.62487	-0.6844	10	0.05959	T	0.93	.	15.841	0.78845	0.0:0.135:0.8649:0.0	.	772	P35968	VGFR2_HUMAN	V	772	ENSP00000263923:A772V	ENSP00000263923:A772V	A	-	2	0	KDR	55659679	0.999000	0.42202	0.235000	0.24058	0.063000	0.16089	3.413000	0.52686	2.831000	0.97527	0.655000	0.94253	GCG		0.418	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55964922	G	A	55964922	3	1	77	1	0	0	0	0	1	0	0	0	8160	1087	38	1	1815	1	KDR	4	55964922	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1656082	55964922	135189354	272	22008										
EPHA5	2044	broad.mit.edu	37	chr4	66361110	66361110	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgtgggtttccttacttgtGcatgccattgtgggtggatc	13	9	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:66361110G>A	ENST00000273854.3	-	4	1662	c.1062C>T	c.(1060-1062)tgC>tgT	p.C354C	EPHA5_ENST00000511294.1_Silent_p.C354C|EPHA5_ENST00000432638.2_Intron|EPHA5_ENST00000354839.4_Silent_p.C354C	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	354	Cys-rich.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.C354C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CCTTACTTGTGCATGCCATTG	0.438										TSP Lung(17;0.13)																																						1	Substitution - coding silent(1)	large_intestine(1)	4											159	156	157					4																	66361110		2203	4300	6503	66043705	SO:0001819	synonymous_variant	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1062C>T	4.37:g.66361110G>A			66043705	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																				0.438	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66361110	G	A	66361110	2	1	77	1	0	0	0	0	0	0	0	1	5183	1311	46	3		3	EPHA5	4	66361110	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	10396188	66361110	124793166	273	22009										
GK2	2712	broad.mit.edu	37	chr4	80329149	80329149	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagtttctcacacgttctcGctatacactcgtagacagac	6	13	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:80329149G>A	ENST00000358842.3	-	1	223	c.206C>T	c.(205-207)gCg>gTg	p.A69V		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	226					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.A69V(1)		autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						ACACGTTCTCGCTATACACTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											179	176	177					4																	80329149		2203	4300	6503	80548173	SO:0001583	missense	2712			BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"Glycerol kinases"	4291	protein-coding gene	gene with protein product		600148	"glycerol kinase pseudogene 2"	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.206C>T	4.37:g.80329149G>A	ENSP00000351706:p.Ala69Val		80548173	Q7Z4Q4	Missense_Mutation	SNP	ENST00000358842.3	37	CCDS3585.1	.	.	.	.	.	.	.	.	.	.	G	4.561	0.104146	0.08731	.	.	ENSG00000196475	ENST00000358842	T	0.48836	0.8	3.92	-0.592	0.11671	Carbohydrate kinase, FGGY, N-terminal (1);	0.219686	0.45867	D	0.000337	T	0.31009	0.0783	N	0.20357	0.565	0.28350	N	0.920962	P	0.39060	0.657	B	0.38500	0.275	T	0.25117	-1.0141	10	0.39692	T	0.17	-4.2477	13.4607	0.61225	0.0:0.0:0.1806:0.8193	.	69	Q14410	GLPK2_HUMAN	V	69	ENSP00000351706:A69V	ENSP00000351706:A69V	A	-	2	0	GK2	80548173	0.971000	0.33674	0.092000	0.20876	0.015000	0.08874	0.786000	0.26844	-0.116000	0.11893	-1.350000	0.01237	GCG		0.408	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214		A	80329149	G	A	80329149	3	1	77	1	0	0	0	0	1	0	0	0	6441	1087	38	1	1459	1	GK2	4	80329149	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	13968039	80329149	110825127	274	22010										
ANTXR2	118429	broad.mit.edu	37	chr4	80992751	80992751	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agatacctcacaaatctctcCgcaagttgctgtacgaaatt	6	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:80992751C>T	ENST00000307333.7	-	2	212	c.210G>A	c.(208-210)gcG>gcA	p.A70A	ANTXR2_ENST00000403729.2_Silent_p.A70A|ANTXR2_ENST00000346652.6_Silent_p.A70A|ANTXR2_ENST00000404191.1_5'UTR|ANTXR2_ENST00000295465.4_Silent_p.A70A	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	70	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.A70A(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						CAAATCTCTCCGCAAGTTGCT	0.363									Juvenile Hyaline Fibromatosis																																							1	Substitution - coding silent(1)	large_intestine(1)	4											89	88	89					4																	80992751		1828	4092	5920	81211775	SO:0001819	synonymous_variant	118429	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.210G>A	4.37:g.80992751C>T			81211775	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Silent	SNP	ENST00000307333.7	37	CCDS47086.1																																																																																				0.363	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		T	80992751	C	T	80992751	2	4	77	1	0	0	0	0	0	0	0	1	712	639	23	1		1	ANTXR2	4	80992751	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	663602	80992751	110161525	275	22011										
FGF5	2250	broad.mit.edu	37	chr4	81188243	81188243	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcccctcggggcgccggaccGgcagcctctactgcagagtg	15	16	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:81188243G>A	ENST00000312465.7	+	1	491	c.265G>A	c.(265-267)Ggc>Agc	p.G89S	FGF5_ENST00000456523.3_Missense_Mutation_p.G89S	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	89					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)	p.G89S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						GCGCCGGACCGGCAGCCTCTA	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	4											46	54	51					4																	81188243		2201	4293	6494	81407267	SO:0001583	missense	2250			M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"Endogenous ligands"	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.265G>A	4.37:g.81188243G>A	ENSP00000311697:p.Gly89Ser		81407267	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	37	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630205	0.87660	.	.	ENSG00000138675	ENST00000312465;ENST00000456523	T;T	0.81247	-0.2;-1.47	5.41	5.41	0.78517	.	0.052247	0.85682	D	0.000000	D	0.85669	0.5750	L	0.41710	1.295	0.58432	D	0.999998	D;D	0.89917	1.0;0.993	D;P	0.83275	0.996;0.773	T	0.81961	-0.0693	10	0.25751	T	0.34	.	19.0018	0.92837	0.0:0.0:1.0:0.0	.	89;89	P12034-2;P12034	.;FGF5_HUMAN	S	89	ENSP00000311697:G89S;ENSP00000398353:G89S	ENSP00000311697:G89S	G	+	1	0	FGF5	81407267	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.456000	0.73501	2.816000	0.96949	0.561000	0.74099	GGC		0.577	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			A	81188243	G	A	81188243	3	1	77	1	0	0	0	0	1	0	0	0	5874	1116	39	1	267	1	FGF5	4	81188243	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	195492	81188243	109966033	276	22012										
AFF1	4299	broad.mit.edu	37	chr4	88036412	88036412	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagcacagctctgagaagagGagctcagacagctcaagcaa	11	10	3	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:88036412G>T	ENST00000307808.6	+	11	2826	c.2406G>T	c.(2404-2406)agG>agT	p.R802S	AFF1_ENST00000544085.1_Missense_Mutation_p.R440S|AFF1_ENST00000395146.4_Missense_Mutation_p.R809S	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	802					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R809S(1)		breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		CTGAGAAGAGGAGCTCAGACA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	4											34	41	38					4																	88036412		2201	4299	6500	88255436	SO:0001583	missense	4299			L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.2406G>T	4.37:g.88036412G>T	ENSP00000305689:p.Arg802Ser		88255436	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	37	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	10.64	1.406304	0.25378	.	.	ENSG00000172493	ENST00000395146;ENST00000541943;ENST00000307808;ENST00000544085	T;T;T	0.63096	-0.02;-0.02;-0.02	5.93	-2.55	0.06288	.	0.370825	0.29342	N	0.012422	T	0.49236	0.1545	M	0.62723	1.935	0.09310	N	1	B;B;B	0.30763	0.294;0.19;0.19	B;B;B	0.29942	0.109;0.109;0.109	T	0.41502	-0.9505	10	0.19590	T	0.45	-5.5249	7.9685	0.30113	0.4818:0.114:0.4042:0.0	.	809;802;802	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	S	809;461;802;440	ENSP00000378578:R809S;ENSP00000305689:R802S;ENSP00000440843:R440S	ENSP00000305689:R802S	R	+	3	2	AFF1	88255436	0.000000	0.05858	0.002000	0.10522	0.091000	0.18340	0.030000	0.13688	-0.673000	0.05259	-0.218000	0.12543	AGG		0.592	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88036412	G	T	88036412	3	4	77	1	0	0	0	0	1	0	0	0	356	1165	41	2	2490	2	AFF1	4	88036412	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6848169	88036412	103117864	277	22013										
HERC6	55008	broad.mit.edu	37	chr4	89334236	89334236	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atttttaccacagataactaCgtgtctcgaggatgatctgc	8	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:89334236C>T	ENST00000264346.7	+	12	1435	c.1376C>T	c.(1375-1377)aCg>aTg	p.T459M	HERC6_ENST00000380265.5_Missense_Mutation_p.T459M	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	459					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.T459M(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		CAGATAACTACGTGTCTCGAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	4											215	206	209					4																	89334236		1920	4150	6070	89553259	SO:0001583	missense	55008			AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1376C>T	4.37:g.89334236C>T	ENSP00000264346:p.Thr459Met		89553259	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	De_novo_Start_OutOfFrame	SNP	ENST00000264346.7	37	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474851	0.26511	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.39997	1.05;1.08	4.76	-1.71	0.08133	.	1.440270	0.04266	N	0.341279	T	0.51991	0.1707	M	0.66939	2.045	0.09310	N	1	D;D	0.76494	0.999;0.999	P;P	0.59703	0.862;0.732	T	0.39921	-0.9590	10	0.54805	T	0.06	.	1.1796	0.01842	0.3773:0.2162:0.2472:0.1593	.	459;459	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	M	459	ENSP00000369617:T459M;ENSP00000264346:T459M	ENSP00000264346:T459M	T	+	2	0	HERC6	89553259	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.630000	0.05502	-0.683000	0.05190	-0.302000	0.09304	ACG		0.443	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			T	89334236	C	T	89334236	3	4	77	1	0	0	0	0	1	0	0	0	7083	536	19	1	1219	1	HERC6	4	89334236	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1297824	89334236	101820040	278	22014										
MTTP	4547	broad.mit.edu	37	chr4	100512428	100512428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attgtaaagtgacctaccagGctcatcaagacaaagtgatc	8	9	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:100512428G>A	ENST00000265517.5	+	5	741	c.538G>A	c.(538-540)Gct>Act	p.A180T	MTTP_ENST00000511045.1_Missense_Mutation_p.A207T|MTTP_ENST00000457717.1_Missense_Mutation_p.A180T			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	180	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.A180T(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GACCTACCAGGCTCATCAAGA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	4											106	103	104					4																	100512428		2203	4300	6503	100731451	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.538G>A	4.37:g.100512428G>A	ENSP00000265517:p.Ala180Thr		100731451	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.746393	0.49257	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.39787	1.06;1.06;1.06	5.9	4.2	0.49525	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.254140	0.45361	D	0.000363	T	0.31888	0.0811	L	0.37561	1.115	0.30562	N	0.764426	B;B	0.16166	0.016;0.007	B;B	0.20767	0.031;0.009	T	0.24012	-1.0172	9	.	.	.	-14.3896	11.0278	0.47755	0.1455:0.0:0.8545:0.0	.	207;180	E9PBP6;P55157	.;MTP_HUMAN	T	207;180;180;180	ENSP00000427679:A207T;ENSP00000400821:A180T;ENSP00000265517:A180T	.	A	+	1	0	MTTP	100731451	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.895000	0.69814	0.857000	0.35407	-0.136000	0.14681	GCT		0.408	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100512428	G	A	100512428	3	1	77	1	0	0	0	0	1	0	0	0	9994	1203	42	3	556	3	MTTP	4	100512428	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11178192	100512428	90641848	279	22015										
MANBA	4126	broad.mit.edu	37	chr4	103644049	103644049	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccgaacaaagttgacatgGcattcacccttctgcacaag	7	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:103644049G>A	ENST00000226578.4	-	4	627	c.528C>T	c.(526-528)tgC>tgT	p.C176C	MANBA_ENST00000505239.1_Intron	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	176					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)	p.C176C(1)		cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		AGTTGACATGGCATTCACCCT	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	4											132	119	123					4																	103644049		2203	4300	6503	103863095	SO:0001819	synonymous_variant	4126				CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.528C>T	4.37:g.103644049G>A			103863095	Q96BC3|Q9NYX9	Silent	SNP	ENST00000226578.4	37	CCDS3658.1																																																																																				0.498	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			A	103644049	G	A	103644049	2	1	77	1	0	0	0	0	0	0	0	1	9249	1195	42	3		3	MANBA	4	103644049	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3131621	103644049	87510227	280	22016										
ANK2	287	broad.mit.edu	37	chr4	114275187	114275187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caaaaaagaccacccacaggCcacatccagctgcgtcaccc	6	18	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:114275187C>T	ENST00000357077.4	+	38	5466	c.5413C>T	c.(5413-5415)Cca>Tca	p.P1805S	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P1772S	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1805					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.P1805S(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CACCCACAGGCCACATCCAGC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	4											98	109	106					4																	114275187		2203	4300	6503	114494636	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.5413C>T	4.37:g.114275187C>T	ENSP00000349588:p.Pro1805Ser		114494636	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	c	6.809	0.518265	0.13005	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.65178	-0.14;-0.14	5.44	-7.86	0.01187	.	1.471000	0.04246	N	0.337827	T	0.34600	0.0903	N	0.08118	0	0.37069	D	0.898453	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.09975	-1.0650	9	.	.	.	.	8.5765	0.33601	0.1273:0.5952:0.1964:0.0811	.	1772;1805	Q01484;Q01484-4	ANK2_HUMAN;.	S	1805;1772	ENSP00000349588:P1805S;ENSP00000264366:P1772S	.	P	+	1	0	ANK2	114494636	0.000000	0.05858	0.012000	0.15200	0.016000	0.09150	-0.765000	0.04730	-1.036000	0.03287	-0.994000	0.02522	CCA		0.532	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114275187	C	T	114275187	3	4	77	1	0	0	0	0	1	0	0	0	621	739	26	3	5628	3	ANK2	4	114275187	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	10631138	114275187	76879089	281	22017										
ANKRD50	57182	broad.mit.edu	37	chr4	125590911	125590911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgacagtgatgacttctgcCggtcaactgtagaatctgga	11	8	3	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:125590911C>T	ENST00000504087.1	-	4	4558	c.3521G>A	c.(3520-3522)cGg>cAg	p.R1174Q	ANKRD50_ENST00000515641.1_Missense_Mutation_p.R995Q	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1174	Ser-rich.							p.R1174Q(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TGACTTCTGCCGGTCAACTGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	4											90	92	91					4																	125590911		2203	4298	6501	125810361	SO:0001583	missense	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3521G>A	4.37:g.125590911C>T	ENSP00000425658:p.Arg1174Gln		125810361	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500149	0.64298	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.69561	-0.4;-0.41	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.47507	0.1449	N	0.14661	0.345	0.44388	D	0.997293	P	0.47253	0.892	B	0.32677	0.15	T	0.54820	-0.8236	10	0.40728	T	0.16	.	19.1278	0.93393	0.0:1.0:0.0:0.0	.	1174	Q9ULJ7	ANR50_HUMAN	Q	1174;995	ENSP00000425658:R1174Q;ENSP00000425355:R995Q	ENSP00000425658:R1174Q	R	-	2	0	ANKRD50	125810361	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	5.461000	0.66699	2.756000	0.94617	0.561000	0.74099	CGG		0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		T	125590911	C	T	125590911	3	4	77	1	0	0	0	0	1	0	0	0	677	652	23	1	772	1	ANKRD50	4	125590911	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	11315724	125590911	65563365	282	22018										
SLC25A31	83447	broad.mit.edu	37	chr4	128651748	128651748	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagaaaagcggctgtttgaCgcctcatccttcgggaagga	13	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:128651748C>T	ENST00000281154.4	+	1	216	c.48C>T	c.(46-48)gaC>gaT	p.D16D		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	16					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.D16D(1)		NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						GGCTGTTTGACGCCTCATCCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	4											62	57	58					4																	128651748		2203	4300	6503	128871198	SO:0001819	synonymous_variant	83447			AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.48C>T	4.37:g.128651748C>T			128871198		Silent	SNP	ENST00000281154.4	37	CCDS3733.1																																																																																				0.582	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		T	128651748	C	T	128651748	2	4	77	1	0	0	0	0	0	0	0	1	14532	535	19	1		1	SLC25A31	4	128651748	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3060837	128651748	62502528	283	22019										
MFSD8	256471	broad.mit.edu	37	chr4	128841858	128841858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccactcccaggagggtgatgGtgagcactattattccacac	10	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:128841858G>A	ENST00000296468.3	-	13	1611	c.1484C>T	c.(1483-1485)aCc>aTc	p.T495I	MFSD8_ENST00000513559.1_Missense_Mutation_p.T450I|MFSD8_ENST00000515130.1_5'UTR	NM_152778.2	NP_689991.1	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing 8	495					cell death (GO:0008219)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)		p.T495I(1)		cervix(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)	23						GAGGGTGATGGTGAGCACTAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	4											97	92	93					4																	128841858		2203	4300	6503	129061308	SO:0001583	missense	256471			AK074564	CCDS3736.1	4q28.2	2014-09-17			ENSG00000164073	ENSG00000164073			28486	protein-coding gene	gene with protein product		611124	"ceroid-lipofuscinosis, neuronal 7, late infantile, variant"	CLN7		17564970	Standard	NM_152778		Approved	MGC33302	uc003ifp.3	Q8NHS3	OTTHUMG00000133303	ENST00000296468.3:c.1484C>T	4.37:g.128841858G>A	ENSP00000296468:p.Thr495Ile		129061308	B2RDM1|B7Z205|Q8N2P3	Missense_Mutation	SNP	ENST00000296468.3	37	CCDS3736.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.587815	0.28268	.	.	ENSG00000164073	ENST00000296468;ENST00000513559	T;T	0.80480	-1.38;-1.38	4.15	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.341251	0.31210	N	0.008056	T	0.72526	0.3471	L	0.42686	1.345	0.80722	D	1	B	0.33583	0.418	B	0.29785	0.107	T	0.70568	-0.4836	10	0.19590	T	0.45	-0.8738	16.6403	0.85070	0.0:0.0:1.0:0.0	.	495	Q8NHS3	MFSD8_HUMAN	I	495;450	ENSP00000296468:T495I;ENSP00000425000:T450I	ENSP00000296468:T495I	T	-	2	0	MFSD8	129061308	1.000000	0.71417	0.802000	0.32245	0.463000	0.32649	5.738000	0.68613	2.151000	0.67156	0.561000	0.74099	ACC		0.478	MFSD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257097.1	NM_152778		A	128841858	G	A	128841858	3	1	77	1	0	0	0	0	1	0	0	0	9568	1261	44	3	76	3	MFSD8	4	128841858	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	190110	128841858	62312418	284	22020										
UCP1	7350	broad.mit.edu	37	chr4	141483523	141483523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacaccaagtggcaggggacGtcatctaaaatggatcgatg	13	8	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:141483523G>A	ENST00000262999.3	-	5	708	c.633C>T	c.(631-633)gaC>gaT	p.D211D		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	211					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)	p.D211D(1)		NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					GGCAGGGGACGTCATCTAAAA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	4											63	58	59					4																	141483523		2203	4300	6503	141702973	SO:0001819	synonymous_variant	7350			X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.633C>T	4.37:g.141483523G>A			141702973	Q13218|Q4KMZ3|Q68G66	Silent	SNP	ENST00000262999.3	37	CCDS3753.1																																																																																				0.423	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1			A	141483523	G	A	141483523	2	1	77	1	0	0	0	0	0	0	0	1	16970	1136	40	1		1	UCP1	4	141483523	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	12641665	141483523	49670753	285	22021										
TBC1D9	23158	broad.mit.edu	37	chr4	141543834	141543834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggctcaacagactccaccaCgtaaggctggcctggccctt	11	15	1	1	rs545624117		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:141543834C>T	ENST00000442267.2	-	21	3390	c.3316G>A	c.(3316-3318)Gtg>Atg	p.V1106M		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1106							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.V1106M(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GACTCCACCACGTAAGGCTGG	0.662													C|||	1	0.000199681	8e-04	0	5008	,	,		17378	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											31	37	35					4																	141543834		2036	4160	6196	141763284	SO:0001583	missense	23158			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.3316G>A	4.37:g.141543834C>T	ENSP00000411197:p.Val1106Met		141763284	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	C	2.597	-0.293834	0.05568	.	.	ENSG00000109436	ENST00000442267	T	0.45668	0.89	5.35	1.12	0.20585	.	.	.	.	.	T	0.25606	0.0623	N	0.22421	0.69	0.09310	N	1	B	0.28208	0.203	B	0.32465	0.146	T	0.27468	-1.0073	9	0.46703	T	0.11	.	1.5453	0.02563	0.1755:0.3203:0.3228:0.1814	.	1106	Q6ZT07	TBCD9_HUMAN	M	1106	ENSP00000411197:V1106M	ENSP00000411197:V1106M	V	-	1	0	TBC1D9	141763284	0.001000	0.12720	0.001000	0.08648	0.168000	0.22595	-0.058000	0.11750	0.235000	0.21160	-0.136000	0.14681	GTG		0.662	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		T	141543834	C	T	141543834	3	4	77	1	0	0	0	0	1	0	0	0	15666	536	19	1	488	1	TBC1D9	4	141543834	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	60311	141543834	49610442	286	22022										
OTUD4	54726	broad.mit.edu	37	chr4	146092862	146092862	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttaaatattcttcaaatgatCcttctataaactgcaaaaaa	2	7	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:146092862C>G	ENST00000447906.2	-	3	441	c.254G>C	c.(253-255)gGa>gCa	p.G85A	OTUD4_ENST00000296579.6_Missense_Mutation_p.G20A|OTUD4_ENST00000454497.2_Missense_Mutation_p.G20A|OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000509620.2_Missense_Mutation_p.G20A			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	85	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.G20A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					TTCAAATGATCCTTCTATAAA	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	4											36	41	39					4																	146092862		2196	4284	6480	146312312	SO:0001583	missense	54726				CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"OTU domain containing"	24949	protein-coding gene	gene with protein product		611744	"OTU domain containing 4"			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.254G>C	4.37:g.146092862C>G	ENSP00000395487:p.Gly85Ala		146312312	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	C	25.5	4.640082	0.87760	.	.	ENSG00000164164	ENST00000454497;ENST00000447906;ENST00000514973;ENST00000509620;ENST00000296579;ENST00000504501	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	5.8	5.8	0.92144	Ovarian tumour, otubain (2);	0.000000	0.51477	D	0.000082	T	0.70736	0.3258	M	0.77820	2.39	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72472	-0.4283	10	0.62326	D	0.03	-16.0813	17.5525	0.87880	0.0:1.0:0.0:0.0	.	85;85	G3V0I6;Q01804	.;OTUD4_HUMAN	A	20;85;20;20;20;20	ENSP00000409279:G20A;ENSP00000395487:G85A;ENSP00000425972:G20A;ENSP00000424192:G20A;ENSP00000296579:G20A;ENSP00000423453:G20A	ENSP00000296579:G20A	G	-	2	0	OTUD4	146312312	1.000000	0.71417	0.988000	0.46212	0.979000	0.70002	5.597000	0.67577	2.741000	0.93983	0.650000	0.86243	GGA		0.279	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		G	146092862	C	G	146092862	3	3	77	1	0	0	0	0	1	0	0	0	11345	855	30	5	3170	5	OTUD4	4	146092862	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4549028	146092862	45061414	287	22023										
FBXW7	55294	broad.mit.edu	37	chr4	153249385	153249385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcatgaagatgcatacaacGcacagtggaagtatgcccat	9	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:153249385G>A	ENST00000281708.4	-	9	2622	c.1393C>T	c.(1393-1395)Cgt>Tgt	p.R465C	FBXW7_ENST00000603841.1_Missense_Mutation_p.R465C|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347C|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385C|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465C|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289C	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465C(71)|p.R226C(11)|p.R385C(11)|p.R347C(3)|p.R465Y(2)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGCATACAACGCACAGTGGAA	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	99	Substitution - Missense(98)|Unknown(1)	haematopoietic_and_lymphoid_tissue(41)|large_intestine(27)|endometrium(20)|stomach(6)|biliary_tract(4)|pancreas(1)	4											260	223	235					4																	153249385		2203	4300	6503	153468835	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1393C>T	4.37:g.153249385G>A	ENSP00000281708:p.Arg465Cys		153468835	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909959	0.92107	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67287	0.2877	M	0.71206	2.165	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67130	-0.5748	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:0.0:1.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	C	465;347;385;289	ENSP00000281708:R465C;ENSP00000296555:R347C;ENSP00000263981:R385C;ENSP00000377528:R289C	ENSP00000263981:R385C	R	-	1	0	FBXW7	153468835	1.000000	0.71417	0.959000	0.39883	0.996000	0.88848	9.869000	0.99810	2.878000	0.98634	0.650000	0.86243	CGT		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249385	G	A	153249385	3	1	77	1	0	0	0	0	1	0	0	0	5788	1087	38	1	746	1	FBXW7	4	153249385	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7156523	153249385	37904891	288	22024										
LRAT	9227	broad.mit.edu	37	chr4	155670222	155670222	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggcgtctatagtctgtacGggcttggtatcatacactac	10	9	3	0	rs146717374	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:155670222G>A	ENST00000336356.3	+	3	880	c.627G>A	c.(625-627)acG>acA	p.T209T	LRAT_ENST00000507827.1_Silent_p.T209T	NM_004744.3	NP_004735.2	O95237	LRAT_HUMAN	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	209					phototransduction, visible light (GO:0007603)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)	phosphatidylcholine-retinol O-acyltransferase activity (GO:0047173)|retinoic acid binding (GO:0001972)|retinol binding (GO:0019841)|transferase activity, transferring acyl groups (GO:0016746)	p.T209T(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)	16	all_hematologic(180;0.215)	Renal(120;0.0458)			Vitamin A(DB00162)	TAGTCTGTACGGGCTTGGTAT	0.408													G|||	32	0.00638978	0.0234	0.0014	5008	,	,		18395	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	4						G		66,4340	61.1+/-98.1	0,66,2137	257	226	237		627	0.7	0.2	4	dbSNP_134	237	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LRAT	NM_004744.3		0,67,6436	AA,AG,GG		0.0116,1.498,0.5151		209/231	155670222	67,12939	2203	4300	6503	155889672	SO:0001819	synonymous_variant	9227			AF071510	CCDS3789.1	4q32.1	2014-01-28			ENSG00000121207	ENSG00000121207	2.3.1.135		6685	protein-coding gene	gene with protein product		604863				9920938	Standard	XM_006714412		Approved	LCA14	uc003ion.1	O95237	OTTHUMG00000161418	ENST00000336356.3:c.627G>A	4.37:g.155670222G>A			155889672	A8K983|Q8N716	Silent	SNP	ENST00000336356.3	37	CCDS3789.1																																																																																				0.408	LRAT-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365246.1	NM_004744		A	155670222	G	A	155670222	2	1	77	1	0	0	0	0	0	0	0	1	8959	1103	39	1		1	LRAT	4	155670222	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2420837	155670222	35484054	289	22025										
TKTL2	84076	broad.mit.edu	37	chr4	164393142	164393142	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaacaaggatatcaggctccCtggagacagctgcacaaaca	10	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:164393142C>A	ENST00000280605.3	-	1	1905	c.1745G>T	c.(1744-1746)aGg>aTg	p.R582M		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	582						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.R582M(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ATCAGGCTCCCTGGAGACAGC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	4											97	85	89					4																	164393142		2203	4300	6503	164612592	SO:0001583	missense	84076			BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.1745G>T	4.37:g.164393142C>A	ENSP00000280605:p.Arg582Met		164612592	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	6.649	0.488227	0.12641	.	.	ENSG00000151005	ENST00000280605	D	0.91124	-2.79	5.06	3.32	0.38043	Transketolase, C-terminal (1);Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.872164	0.10070	N	0.719840	T	0.80701	0.4673	N	0.11064	0.09	0.24248	N	0.995334	B	0.10296	0.003	B	0.15052	0.012	T	0.67055	-0.5767	10	0.30078	T	0.28	-0.1567	8.8681	0.35298	0.0:0.7654:0.1512:0.0835	.	582	Q9H0I9	TKTL2_HUMAN	M	582	ENSP00000280605:R582M	ENSP00000280605:R582M	R	-	2	0	TKTL2	164612592	0.000000	0.05858	0.575000	0.28536	0.700000	0.40528	0.718000	0.25866	0.830000	0.34757	-0.172000	0.13284	AGG		0.502	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		A	164393142	C	A	164393142	3	1	77	1	0	0	0	0	1	0	0	0	15975	681	24	2	139	2	TKTL2	4	164393142	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8722920	164393142	26761134	290	22026										
CBR4	84869	broad.mit.edu	37	chr4	169927953	169927953	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttgaatcatagtcctcatgGcagctttacaggtcagcatg	10	9	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:169927953G>A	ENST00000306193.3	-	3	521	c.353C>T	c.(352-354)gCc>gTc	p.A118V	CBR4_ENST00000509108.1_5'Flank|RNY4P17_ENST00000364948.1_RNA|CBR4_ENST00000504480.1_Missense_Mutation_p.A118V	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4	118					daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)	p.A118V(1)		kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		AGTCCTCATGGCAGCTTTACA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	4											178	178	178					4																	169927953		2203	4300	6503	170164528	SO:0001583	missense	84869			BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	25891	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 45C, member 1"					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.353C>T	4.37:g.169927953G>A	ENSP00000303525:p.Ala118Val		170164528	Q8WTW8|Q96K93	Missense_Mutation	SNP	ENST00000306193.3	37	CCDS3812.1	.	.	.	.	.	.	.	.	.	.	G	8.796	0.931747	0.18131	.	.	ENSG00000145439	ENST00000306193;ENST00000504480;ENST00000504561	D;D;D	0.86956	-2.19;-2.19;-2.19	5.35	5.35	0.76521	NAD(P)-binding domain (1);	0.047823	0.85682	D	0.000000	T	0.80934	0.4719	N	0.22421	0.69	0.80722	D	1	B	0.30406	0.278	B	0.31390	0.129	T	0.76479	-0.2944	9	.	.	.	.	19.4162	0.94700	0.0:0.0:1.0:0.0	.	118	Q8N4T8	CBR4_HUMAN	V	118;118;115	ENSP00000303525:A118V;ENSP00000427615:A118V;ENSP00000423128:A115V	.	A	-	2	0	CBR4	170164528	1.000000	0.71417	0.969000	0.41365	0.432000	0.31715	8.580000	0.90784	2.658000	0.90341	0.650000	0.86243	GCC		0.378	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783		A	169927953	G	A	169927953	3	1	77	1	0	0	0	0	1	0	0	0	2716	1203	42	3	372	3	CBR4	4	169927953	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5534811	169927953	21226323	291	22027										
GALNTL6	442117	broad.mit.edu	37	chr4	173734792	173734792	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagctggggatgccatgcgaGgagccttcgactgggaaatg	16	8	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:173734792G>T	ENST00000506823.1	+	7	1498	c.841G>T	c.(841-843)Gga>Tga	p.G281*	GALNTL6_ENST00000508122.1_Nonsense_Mutation_p.G264*	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	281					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.G281*(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TGCCATGCGAGGAGCCTTCGA	0.522																																																1	Substitution - Nonsense(1)	large_intestine(1)	4											106	97	100					4																	173734792		2203	4300	6503	173971367	SO:0001587	stop_gained	442117				CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.841G>T	4.37:g.173734792G>T	ENSP00000423313:p.Gly281*		173971367	Q2L4S6	Nonsense_Mutation	SNP	ENST00000506823.1	37	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	G	37	6.223492	0.97390	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	.	.	.	5.97	5.14	0.70334	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.2089	0.73202	0.0672:0.0:0.9328:0.0	.	.	.	.	X	281;264	.	ENSP00000423313:G281X	G	+	1	0	GALNTL6	173971367	1.000000	0.71417	0.978000	0.43139	0.997000	0.91878	9.830000	0.99415	1.537000	0.49254	0.655000	0.94253	GGA		0.522	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		T	173734792	G	T	173734792	4	4	77	1	0	0	0	0	0	1	0	0	6245	1001	35	2	863	2	GALNTL6	4	173734792	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3806839	173734792	17419484	292	22028										
CCDC110	256309	broad.mit.edu	37	chr4	186382305	186382305	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaatatttcactgatttcCgactgtacctttaaaagata	4	8	2	2	rs141194686	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:186382305C>T	ENST00000307588.3	-	5	321	c.246G>A	c.(244-246)tcG>tcA	p.S82S	CCDC110_ENST00000393540.3_Intron|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000510617.1_Silent_p.S82S	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	82						nucleus (GO:0005634)		p.S82S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		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)		CACTGATTTCCGACTGTACCT	0.289													C|||	3	0.000599042	8e-04	0	5008	,	,		16668	0		0.001	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	4						C	,	1,4405	2.1+/-5.4	0,1,2202	90	89	89		,246	3.5	1	4	dbSNP_134	89	10,8582	7.1+/-27.0	0,10,4286	no	intron,coding-synonymous	CCDC110	NM_001145411.1,NM_152775.3	,	0,11,6488	TT,TC,CC		0.1164,0.0227,0.0846	,	,82/834	186382305	11,12987	2203	4296	6499	186619299	SO:0001819	synonymous_variant	256309			AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.246G>A	4.37:g.186382305C>T			186619299	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	37	CCDS3843.1																																																																																				0.289	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		T	186382305	C	T	186382305	2	4	77	1	0	0	0	0	0	0	0	1	2753	639	23	1		1	CCDC110	4	186382305	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	12647513	186382305	4771971	293	22029										
TRIML2	205860	broad.mit.edu	37	chr4	189020189	189020189	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctttttcccagcatcttacCttgagcaatgccaaggtgcc	7	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr4:189020189C>A	ENST00000512729.1	-	4	845	c.471G>T	c.(469-471)aaG>aaT	p.K157N	TRIML2_ENST00000326754.3_Splice_Site_p.K157N|TRIML2_ENST00000536972.1_Missense_Mutation_p.K207N	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	157					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.K157N(2)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		AGCATCTTACCTTGAGCAATG	0.453																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	4											73	69	70					4																	189020189		2203	4300	6503	189257183	SO:0001630	splice_region_variant	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.471+1G>T	4.37:g.189020189C>A			189257183	B7Z6J6	De_novo_Start_OutOfFrame	SNP	ENST00000512729.1	37	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382954	0.25031	.	.	ENSG00000179046	ENST00000512729;ENST00000326754;ENST00000536972	T;T;T	0.58797	3.53;0.31;3.73	4.56	3.71	0.42584	.	0.974842	0.08369	N	0.956422	T	0.45418	0.1341	L	0.27053	0.805	0.28562	N	0.911094	P;P;B	0.35328	0.48;0.495;0.276	B;B;B	0.31614	0.133;0.09;0.062	T	0.43734	-0.9373	10	0.87932	D	0	.	10.8458	0.46743	0.0:0.8094:0.1906:0.0	.	207;157;157	B7Z6J6;B7ZLC3;Q8N7C3	.;.;TRIMM_HUMAN	N	157;157;207	ENSP00000422581:K157N;ENSP00000317498:K157N;ENSP00000441236:K207N	ENSP00000317498:K157N	K	-	3	2	TRIML2	189257183	1.000000	0.71417	0.997000	0.53966	0.268000	0.26511	0.685000	0.25378	1.262000	0.44165	0.650000	0.86243	AAG		0.453	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	Missense_Mutation	A	189020189	C	A	189020189	5	1	77	1	0	0	0	0	0	0	1	0	16591	695	24	2	708	2	TRIML2	4	189020189	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2637884	189020189	2134087	294	22030										
PLEKHG4B	153478	broad.mit.edu	37	chr5	156250	156250	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtcctggaagacccactgcTtgtgtctctcaggctggagg	13	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:156250T>G	ENST00000283426.6	+	8	1255	c.1205T>G	c.(1204-1206)cTt>cGt	p.L402R		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	402							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L402R(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GACCCACTGCTTGTGTCTCTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											100	94	96					5																	156250		2203	4300	6503	209250	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1205T>G	5.37:g.156250T>G	ENSP00000283426:p.Leu402Arg		209250		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.679712	0.29783	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.45276	0.9;2.49	3.65	3.65	0.41850	.	.	.	.	.	T	0.62183	0.2407	M	0.78916	2.43	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.50398	-0.8833	9	0.59425	D	0.04	.	8.7019	0.34332	0.0:0.0:0.0:1.0	.	402	Q96PX9	PKH4B_HUMAN	R	402;316	ENSP00000283426:L402R;ENSP00000422493:L316R	ENSP00000283426:L402R	L	+	2	0	PLEKHG4B	209250	0.995000	0.38212	0.008000	0.14137	0.115000	0.19883	4.170000	0.58229	1.291000	0.44653	0.383000	0.25322	CTT		0.587	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		G	156250	T	G	156250	3	3	77	1	0	0	0	0	1	0	0	0	12103	1609	56	4	1235	4	PLEKHG4B	5	156250	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10		156250	180759010	295	22031										
SLC6A3	6531	broad.mit.edu	37	chr5	1443096	1443096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtccacagcaaagccaatgaCggacaggagaaagtcgatct	11	10	1	2	rs150576860		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:1443096C>T	ENST00000270349.9	-	2	344	c.217G>A	c.(217-219)Gtc>Atc	p.V73I	SLC6A3_ENST00000453492.2_Missense_Mutation_p.V73I	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	73					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)	p.V73I(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	AAGCCAATGACGGACAGGAGA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	5						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	111	99	103		217	4.8	0.3	5	dbSNP_134	103	0,8600		0,0,4300	no	missense	SLC6A3	NM_001044.4	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	73/621	1443096	1,13005	2203	4300	6503	1496096	SO:0001583	missense	6531				CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.217G>A	5.37:g.1443096C>T	ENSP00000270349:p.Val73Ile		1496096	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	37	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608607	0.66558	2.27E-4	0.0	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.74842	-0.88;-0.88	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.75324	0.3834	L	0.38531	1.155	0.58432	D	0.999998	D	0.54601	0.967	P	0.54270	0.747	T	0.76405	-0.2971	10	0.45353	T	0.12	.	15.2518	0.73552	0.0:1.0:0.0:0.0	.	73	Q01959	SC6A3_HUMAN	I	73	ENSP00000270349:V73I;ENSP00000399806:V73I	ENSP00000270349:V73I	V	-	1	0	SLC6A3	1496096	1.000000	0.71417	0.283000	0.24790	0.813000	0.45954	5.562000	0.67346	2.202000	0.70862	0.561000	0.74099	GTC		0.612	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1443096	C	T	1443096	3	4	77	1	0	0	0	0	1	0	0	0	14722	536	19	1	1701	1	SLC6A3	5	1443096	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1286846	1443096	179472164	296	22032										
SEMA5A	9037	broad.mit.edu	37	chr5	9054218	9054218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgggcagggctgcgtgttGcagagtgcctcttctgtgtg	16	10	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:9054218G>A	ENST00000382496.5	-	19	3335	c.2670C>T	c.(2668-2670)tgC>tgT	p.C890C	MIR4636_ENST00000582271.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	890	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.C890C(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCTGCGTGTTGCAGAGTGCCT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	5											78	74	75					5																	9054218		2203	4300	6503	9107218	SO:0001819	synonymous_variant	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2670C>T	5.37:g.9054218G>A			9107218	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																				0.552	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			A	9054218	G	A	9054218	2	1	77	1	0	0	0	0	0	0	0	1	14074	1311	46	3		3	SEMA5A	5	9054218	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7611122	9054218	171861042	297	22033										
CTNND2	1501	broad.mit.edu	37	chr5	11346700	11346700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccgtgctggctgcctgtgCgctgcaaggggacggagtcg	19	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:11346700C>T	ENST00000304623.8	-	9	1601	c.1412G>A	c.(1411-1413)cGc>cAc	p.R471H	CTNND2_ENST00000511377.1_Missense_Mutation_p.R380H|CTNND2_ENST00000359640.2_Missense_Mutation_p.R471H|CTNND2_ENST00000503622.1_Missense_Mutation_p.R134H|CTNND2_ENST00000458100.2_Missense_Mutation_p.R38H|CTNND2_ENST00000495388.2_5'UTR	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	471					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R471H(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GCTGCCTGTGCGCTGCAAGGG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	5											34	38	37					5																	11346700		2203	4300	6503	11399700	SO:0001583	missense	1501			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.1412G>A	5.37:g.11346700C>T	ENSP00000307134:p.Arg471His		11399700	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568157	0.86439	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000458100;ENST00000503622	D;D;D;D;D	0.82984	-1.58;-1.67;-1.58;-1.5;-1.51	5.79	5.79	0.91817	.	0.220193	0.30686	N	0.009093	D	0.83764	0.5325	L	0.57536	1.79	0.80722	D	1	D;P;B	0.52996	0.957;0.606;0.086	B;B;B	0.44044	0.439;0.143;0.013	D	0.85665	0.1291	10	0.72032	D	0.01	-14.6061	20.0943	0.97832	0.0:1.0:0.0:0.0	.	134;38;471	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	H	471;471;380;38;134	ENSP00000307134:R471H;ENSP00000352661:R471H;ENSP00000426510:R380H;ENSP00000391155:R38H;ENSP00000426887:R134H	ENSP00000307134:R471H	R	-	2	0	CTNND2	11399700	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.758000	0.94735	0.579000	0.79373	CGC		0.607	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11346700	C	T	11346700	3	4	77	1	0	0	0	0	1	0	0	0	4026	768	27	1	2321	1	CTNND2	5	11346700	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2292482	11346700	169568560	298	22034										
DNAH5	1767	broad.mit.edu	37	chr5	13717543	13717543	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accgaacttgcgcctctcctGgacagtggagtgcaggaaag	13	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:13717543G>T	ENST00000265104.4	-	73	12690	c.12586C>A	c.(12586-12588)Cag>Aag	p.Q4196K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4196	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Q4196K(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CGCCTCTCCTGGACAGTGGAG	0.552									Kartagener syndrome																																							1	Substitution - Missense(1)	large_intestine(1)	5											67	60	62					5																	13717543		2203	4300	6503	13770543	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12586C>A	5.37:g.13717543G>T	ENSP00000265104:p.Gln4196Lys		13770543	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571457	0.86542	.	.	ENSG00000039139	ENST00000265104	T	0.09630	2.96	5.45	5.45	0.79879	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.54208	0.1844	H	0.98769	4.325	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	T	0.74893	-0.3509	10	0.72032	D	0.01	.	19.2888	0.94090	0.0:0.0:1.0:0.0	.	4196	Q8TE73	DYH5_HUMAN	K	4196	ENSP00000265104:Q4196K	ENSP00000265104:Q4196K	Q	-	1	0	DNAH5	13770543	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	9.843000	0.99491	2.557000	0.86248	0.655000	0.94253	CAG		0.552	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13717543	G	T	13717543	3	4	77	1	0	0	0	0	1	0	0	0	4615	1357	47	2	1316	2	DNAH5	5	13717543	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2370843	13717543	167197717	299	22035										
MYO10	4651	broad.mit.edu	37	chr5	16681496	16681496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagggtccccagtttgagcgCgttcttctctgaactcttgt	10	12	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:16681496C>T	ENST00000513610.1	-	32	4760	c.4306G>A	c.(4306-4308)Gcg>Acg	p.A1436T	MYO10_ENST00000505695.1_Missense_Mutation_p.A775T|MYO10_ENST00000274203.9_Missense_Mutation_p.A793T|MYO10_ENST00000427430.2_Missense_Mutation_p.A793T|MYO10_ENST00000515803.1_Missense_Mutation_p.A775T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1436	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.A1436T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGTTTGAGCGCGTTCTTCTCT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	5											126	129	128					5																	16681496		1893	4101	5994	16734496	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4306G>A	5.37:g.16681496C>T	ENSP00000421280:p.Ala1436Thr		16734496	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.189357	0.57909	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.93076	-3.16;-3.16;-3.16;-3.16;-3.16	5.45	4.56	0.56223	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.94228	0.8147	M	0.64170	1.965	0.80722	D	1	P;P;P	0.51240	0.814;0.929;0.943	B;P;P	0.51999	0.266;0.508;0.687	D	0.94037	0.7306	9	0.51188	T	0.08	.	15.717	0.77674	0.1379:0.8621:0.0:0.0	.	315;1076;1436	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	T	1436;775;793;775;793	ENSP00000421280:A1436T;ENSP00000425051:A775T;ENSP00000274203:A793T;ENSP00000421170:A775T;ENSP00000391106:A793T	ENSP00000274203:A793T	A	-	1	0	MYO10	16734496	1.000000	0.71417	0.336000	0.25522	0.126000	0.20510	4.998000	0.63927	1.403000	0.46800	0.555000	0.69702	GCG		0.502	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16681496	C	T	16681496	3	4	77	1	0	0	0	0	1	0	0	0	10092	768	27	1	1910	1	MYO10	5	16681496	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2963953	16681496	164233764	300	22036										
MYO10	4651	broad.mit.edu	37	chr5	16766264	16766264	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggtcaaagcatctgtgagCtgtgttgggtccagcccaag	14	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:16766264C>A	ENST00000513610.1	-	11	1558	c.1104G>T	c.(1102-1104)caG>caT	p.Q368H		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	368	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.Q368H(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CATCTGTGAGCTGTGTTGGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	5											124	121	122					5																	16766264		1960	4165	6125	16819264	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1104G>T	5.37:g.16766264C>A	ENSP00000421280:p.Gln368His		16819264	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042602	0.75732	.	.	ENSG00000145555	ENST00000513610;ENST00000513882	D;D	0.87491	-2.26;-2.26	5.05	5.05	0.67936	Myosin head, motor domain (2);	.	.	.	.	D	0.92169	0.7517	M	0.74467	2.265	0.80722	D	1	D	0.69078	0.997	D	0.68483	0.958	D	0.92606	0.6095	9	0.62326	D	0.03	.	12.8243	0.57710	0.0:0.9216:0.0:0.0784	.	368	Q9HD67	MYO10_HUMAN	H	368;379	ENSP00000421280:Q368H;ENSP00000421309:Q379H	ENSP00000421280:Q368H	Q	-	3	2	MYO10	16819264	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.633000	0.46519	2.344000	0.79699	0.591000	0.81541	CAG		0.517	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16766264	C	A	16766264	3	1	77	1	0	0	0	0	1	0	0	0	10092	796	28	2	5196	2	MYO10	5	16766264	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	84768	16766264	164148996	301	22037										
CDH18	1016	broad.mit.edu	37	chr5	19473789	19473789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaatgatcaagggctcttttTtgctgcgcctcagggtgata	11	8	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:19473789T>C	ENST00000507958.1	-	15	2909	c.1919A>G	c.(1918-1920)aAa>aGa	p.K640R	CDH18_ENST00000506372.1_3'UTR|CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000502796.1_3'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.K640R|CDH18_ENST00000274170.4_Missense_Mutation_p.K640R			Q13634	CAD18_HUMAN	cadherin 18, type 2	640					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K640R(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GGGCTCTTTTTTGCTGCGCCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	5											145	153	150					5																	19473789		2203	4300	6503	19509546	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1919A>G	5.37:g.19473789T>C	ENSP00000425093:p.Lys640Arg		19509546	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126184	0.77549	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.77489	-1.1;-1.1;-1.1	6.16	6.16	0.99307	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.63070	0.2480	N	0.11698	0.16	0.54753	D	0.99998	B	0.14805	0.011	B	0.22601	0.04	T	0.59053	-0.7526	9	.	.	.	.	15.6301	0.76899	0.0:0.0:0.0:1.0	.	640	Q13634	CAD18_HUMAN	R	640	ENSP00000371710:K640R;ENSP00000425093:K640R;ENSP00000274170:K640R	.	K	-	2	0	CDH18	19509546	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.285000	0.72658	2.367000	0.80283	0.528000	0.53228	AAA		0.428	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		C	19473789	T	C	19473789	3	2	77	1	0	0	0	0	1	0	0	0	3109	1841	64	4	457	4	CDH18	5	19473789	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	2707525	19473789	161441471	302	22038										
PRDM9	56979	broad.mit.edu	37	chr5	23509200	23509200	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagacacagagagaacagagCggaagcccatggtgagaagt	14	7	0	5	rs184600328	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:23509200C>T	ENST00000296682.3	+	2	240	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	20					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R20W(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GAGAACAGAGCGGAAGCCCAT	0.572										HNSCC(3;0.000094)			C|||	4	0.000798722	0	0	5008	,	,		18158	0		0.004	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5						C	TRP/ARG	0,3952		0,0,1976	81	91	87		58	-1	0.1	5		87	15,8287		0,15,4136	no	missense	PRDM9	NM_020227.2	101	0,15,6112	TT,TC,CC		0.1807,0.0,0.1224	benign	20/895	23509200	15,12239	1976	4151	6127	23544957	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.58C>T	5.37:g.23509200C>T	ENSP00000296682:p.Arg20Trp		23544957	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	6.582	0.475653	0.12521	0.0	0.001807	ENSG00000164256	ENST00000502755;ENST00000296682	T;T	0.10382	2.88;2.98	1.77	-0.976	0.10286	Krueppel-associated box (1);	.	.	.	.	T	0.02610	0.0079	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	9	0.02654	T	1	.	4.0249	0.09683	0.0:0.2217:0.0:0.7783	.	20	Q9NQV7	PRDM9_HUMAN	W	20	ENSP00000425471:R20W;ENSP00000296682:R20W	ENSP00000296682:R20W	R	+	1	2	PRDM9	23544957	0.000000	0.05858	0.076000	0.20297	0.003000	0.03518	-2.009000	0.01455	0.045000	0.15804	-0.901000	0.02856	CGG		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23509200	C	T	23509200	3	4	77	1	0	0	0	0	1	0	0	0	12497	759	27	1	60	1	PRDM9	5	23509200	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4035411	23509200	157406060	303	22039										
RNASEN	29102	broad.mit.edu	37	chr5	31464406	31464406	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctacttagctccaccgttacTtctcgtctcattgtattctt	4	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:31464406T>C	ENST00000511367.2	-	19	2755	c.2511A>G	c.(2509-2511)gaA>gaG	p.E837E	DROSHA_ENST00000513349.1_Silent_p.E800E|DROSHA_ENST00000344624.3_Silent_p.E837E|DROSHA_ENST00000442743.1_Silent_p.E800E	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	837	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.E837E(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						CCACCGTTACTTCTCGTCTCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	5											111	105	106					5																	31464406		1873	4118	5991	31500163	SO:0001819	synonymous_variant	29102			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.2511A>G	5.37:g.31464406T>C			31500163	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1																																																																																				0.433	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		C	31464406	T	C	31464406	2	2	77	1	0	0	0	0	0	0	0	1	13454	1606	56	4		4	RNASEN	5	31464406	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	7955206	31464406	149450854	304	22040										
PDZD2	23037	broad.mit.edu	37	chr5	32061110	32061110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctgttgccctccctagccGcggggatcaaatcctggaag	11	13	2	0	rs556048029		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:32061110G>A	ENST00000438447.1	+	14	2709	c.2321G>A	c.(2320-2322)cGc>cAc	p.R774H	PDZD2_ENST00000282493.3_Missense_Mutation_p.R774H			O15018	PDZD2_HUMAN	PDZ domain containing 2	774	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.R774H(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTCCCTAGCCGCGGGGATCAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	5											88	75	79					5																	32061110		2203	4300	6503	32096867	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2321G>A	5.37:g.32061110G>A	ENSP00000402033:p.Arg774His		32096867	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075225	0.76415	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.27256	1.68;1.68	5.76	5.76	0.90799	PDZ/DHR/GLGF (4);	0.224065	0.26038	N	0.026701	T	0.56366	0.1980	M	0.83012	2.62	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.58803	-0.7572	10	0.59425	D	0.04	.	17.4556	0.87606	0.0:0.0:1.0:0.0	.	600;774	B4E3P2;O15018	.;PDZD2_HUMAN	H	774;593;774	ENSP00000402033:R774H;ENSP00000282493:R774H	ENSP00000282493:R774H	R	+	2	0	PDZD2	32096867	1.000000	0.71417	0.953000	0.39169	0.440000	0.31957	6.194000	0.72082	2.722000	0.93159	0.650000	0.86243	CGC		0.488	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32061110	G	A	32061110	3	1	77	1	0	0	0	0	1	0	0	0	11732	1087	38	1	2371	1	PDZD2	5	32061110	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	596704	32061110	148854150	305	22041										
PDZD2	23037	broad.mit.edu	37	chr5	32074112	32074112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaaggtaggctgctacgatgCcaacgatgccagtgatgagg	15	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:32074112C>T	ENST00000438447.1	+	18	3288	c.2900C>T	c.(2899-2901)gCc>gTc	p.A967V	PDZD2_ENST00000282493.3_Missense_Mutation_p.A967V			O15018	PDZD2_HUMAN	PDZ domain containing 2	967					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.A967V(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TGCTACGATGCCAACGATGCC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	5											66	70	68					5																	32074112		2203	4300	6503	32109869	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2900C>T	5.37:g.32074112C>T	ENSP00000402033:p.Ala967Val		32109869	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467185	0.43839	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.07444	3.19;3.19	5.16	3.28	0.37604	.	0.909484	0.09133	N	0.844048	T	0.06462	0.0166	N	0.19112	0.55	0.09310	N	1	B;B	0.34103	0.08;0.437	B;B	0.32864	0.027;0.154	T	0.40942	-0.9536	10	0.48119	T	0.1	.	8.4159	0.32670	0.1612:0.5034:0.3354:0.0	.	793;967	B4E3P2;O15018	.;PDZD2_HUMAN	V	967;769;967	ENSP00000402033:A967V;ENSP00000282493:A967V	ENSP00000282493:A967V	A	+	2	0	PDZD2	32109869	0.001000	0.12720	0.000000	0.03702	0.987000	0.75469	0.083000	0.14871	0.506000	0.28125	0.551000	0.68910	GCC		0.602	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074112	C	T	32074112	3	4	77	1	0	0	0	0	1	0	0	0	11732	739	26	3	2966	3	PDZD2	5	32074112	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	13002	32074112	148841148	306	22042										
BRIX1	55299	broad.mit.edu	37	chr5	34923288	34923288	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccaaccatttgtggaccaCgtgtttactttcaccatttt	6	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:34923288C>T	ENST00000336767.5	+	8	975	c.612C>T	c.(610-612)caC>caT	p.H204H	BRIX1_ENST00000506023.1_3'UTR	NM_018321.3	NP_060791.3	Q8TDN6	BRX1_HUMAN	BRX1, biogenesis of ribosomes, homolog (S. cerevisiae)	204	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				ribosome biogenesis (GO:0042254)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.H204H(1)		central_nervous_system(1)|large_intestine(2)|lung(1)	4						TTGTGGACCACGTGTTTACTT	0.313																																																1	Substitution - coding silent(1)	large_intestine(1)	5											127	127	127					5																	34923288		2203	4300	6503	34959045	SO:0001819	synonymous_variant	55299				CCDS34143.1	5p13.2	2009-09-25	2009-09-25	2009-09-25	ENSG00000113460	ENSG00000113460			24170	protein-coding gene	gene with protein product			"brix domain containing 2"	BXDC2		12477932	Standard	NM_018321		Approved	BRIX, FLJ11100	uc003jja.3	Q8TDN6	OTTHUMG00000162021	ENST00000336767.5:c.612C>T	5.37:g.34923288C>T			34959045	A8K0P5|Q3ZTT4|Q8N453|Q96DH1	Silent	SNP	ENST00000336767.5	37	CCDS34143.1																																																																																				0.313	BRIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366826.2	NM_018321		T	34923288	C	T	34923288	2	4	77	1	0	0	0	0	0	0	0	1	1518	535	19	1		1	BRIX1	5	34923288	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2849176	34923288	145991972	307	22043										
HEATR7B2	133558	broad.mit.edu	37	chr5	41000448	41000448	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaccatcaagacatcacgGcaagcctggaaaacagagtt	9	11	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:41000448G>A	ENST00000399564.4	-	39	4806	c.4356C>T	c.(4354-4356)tgC>tgT	p.C1452C	MROH2B_ENST00000506092.2_Silent_p.C1007C	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1452								p.C1452C(1)									AGACATCACGGCAAGCCTGGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	5											48	47	48					5																	41000448		1913	4119	6032	41036205	SO:0001819	synonymous_variant	133558				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.4356C>T	5.37:g.41000448G>A			41036205	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																				0.478	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		A	41000448	G	A	41000448	2	1	77	1	0	0	0	0	0	0	0	1	7056	1195	42	3		3	HEATR7B2	5	41000448	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6077160	41000448	139914812	308	22044										
HCN1	348980	broad.mit.edu	37	chr5	45262468	45262468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgtggctgagtctgcggcGgctgggactgctgtacctgc	17	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:45262468G>A	ENST00000303230.4	-	8	2285	c.2228C>T	c.(2227-2229)cCg>cTg	p.P743L		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	743	Gln-rich.				apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.P743L(1)|p.P743Q(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						agtctgcggcggctgggactg	0.637																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	5											30	32	32					5																	45262468		2203	4299	6502	45298225	SO:0001583	missense	348980			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2228C>T	5.37:g.45262468G>A	ENSP00000307342:p.Pro743Leu		45298225		Missense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	9.169	1.020576	0.19433	.	.	ENSG00000164588	ENST00000303230	T	0.74842	-0.88	4.49	2.52	0.30459	.	0.449943	0.18476	N	0.140075	T	0.55705	0.1937	L	0.29908	0.895	0.25562	N	0.986987	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	10	0.33940	T	0.23	.	3.3166	0.07035	0.2156:0.0:0.506:0.2784	.	743	O60741	HCN1_HUMAN	L	743	ENSP00000307342:P743L	ENSP00000307342:P743L	P	-	2	0	HCN1	45298225	0.208000	0.23494	0.560000	0.28344	0.776000	0.43924	-0.200000	0.09478	1.215000	0.43411	0.655000	0.94253	CCG		0.637	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45262468	G	A	45262468	3	1	77	1	0	0	0	0	1	0	0	0	7017	1116	39	1	448	1	HCN1	5	45262468	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4262020	45262468	135652792	309	22045										
MAST4	375449	broad.mit.edu	37	chr5	66461412	66461412	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catcccagcagcatccctccGccccctctgacggccaaaga	7	20	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:66461412G>A	ENST00000403625.2	+	29	6700	c.6405G>A	c.(6403-6405)ccG>ccA	p.P2135P	MAST4_ENST00000403666.1_Silent_p.P1946P|MAST4_ENST00000405643.1_Silent_p.P1956P|MAST4_ENST00000404260.3_Silent_p.P2138P|MAST4_ENST00000261569.7_Silent_p.P1941P	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2138	Pro-rich.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.P2138P(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCATCCCTCCGCCCCCTCTGA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	5											29	39	35					5																	66461412		2075	4189	6264	66497168	SO:0001819	synonymous_variant	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6405G>A	5.37:g.66461412G>A			66497168	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	3.909	-0.020537	0.07634	.	.	ENSG00000069020	ENST00000443808	.	.	.	5.2	0.399	0.16325	.	.	.	.	.	T	0.35335	0.0928	.	.	.	0.23946	N	0.996388	.	.	.	.	.	.	T	0.29212	-1.0019	4	.	.	.	-8.7172	10.1001	0.42499	0.5396:0.0:0.4604:0.0	.	.	.	.	T	1192	.	.	A	+	1	0	MAST4	66497168	0.288000	0.24324	0.142000	0.22268	0.001000	0.01503	1.981000	0.40628	-0.116000	0.11893	-0.794000	0.03295	GCC		0.602	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66461412	G	A	66461412	2	1	77	1	0	0	0	0	0	0	0	1	9357	1074	38	1		1	MAST4	5	66461412	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	21198944	66461412	114453848	310	22046										
TAF9	6880	broad.mit.edu	37	chr5	68661290	68661290	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttgccttgcaatatctaatAaaaaatctcttgggggagga							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:68661290delA	ENST00000328663.4	-	3	741	c.275delT	c.(274-276)ttafs	p.L93fs	TAF9_ENST00000512561.1_Intron|TAF9_ENST00000380818.3_Intron|TAF9_ENST00000502819.1_Intron|TAF9_ENST00000217893.5_Frame_Shift_Del_p.L93fs|TAF9_ENST00000380822.4_Intron|TAF9_ENST00000506736.1_Frame_Shift_Del_p.L93fs	NM_001015892.1	NP_001015892.1	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa	93					cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cell growth (GO:0030307)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|response to interleukin-1 (GO:0070555)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|pre-snoRNP complex (GO:0070761)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	activating transcription factor binding (GO:0033613)|C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.L92fs*2(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	8		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		AATATCTAATAAAAAATCTCT	0.448																																																1	Deletion - Frameshift(1)	large_intestine(1)	5											83	85	85					5																	68661290		2203	4300	6503	68697046	SO:0001589	frameshift_variant	6880			U21858	CCDS4001.1, CCDS4002.1, CCDS43324.1	5q13.2	2013-09-26	2002-08-29	2001-12-07	ENSG00000085231	ENSG00000085231			11542	protein-coding gene	gene with protein product		600822	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, G, 32kD"	TAF2G		10191103, 15630091, 16079131	Standard	NM_001015892		Approved	TAFII31, TAFII32, TAFIID32, MGC5067, CGI-137, MGC1603, MGC3647, AD-004	uc003jwa.3	Q16594	OTTHUMG00000099359	ENST00000328663.4:c.275delT	5.37:g.68661290delA	ENSP00000370193:p.Leu93fs		68697046	D3DWA3|Q5U0D1|Q9BTS1	Frame_Shift_Del	DEL	ENST00000328663.4	37	CCDS4002.1																																																																																				0.448	TAF9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216803.1	NM_003187		-	68661290	A	-	68661290	7	5	77	1	0	1	0	1	0	0	0	0	15574	372	13	0	933	0	TAF9	5	68661290	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	2199878	68661290	112253970	311	22047										
MAP1B	4131	broad.mit.edu	37	chr5	71490040	71490040	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaatatgctcatcaatggCggatcagagagaaaatcctg	9	8	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:71490040C>T	ENST00000296755.7	+	5	1156	c.858C>T	c.(856-858)ggC>ggT	p.G286G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	286					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.G286G(3)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		TCATCAATGGCGGATCAGAGA	0.488																																					Melanoma(17;367 822 11631 31730 47712)											3	Substitution - coding silent(3)	large_intestine(2)|ovary(1)	5											81	86	84					5																	71490040		2203	4300	6503	71525796	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.858C>T	5.37:g.71490040C>T			71525796	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.488	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71490040	C	T	71490040	2	4	77	1	0	0	0	0	0	0	0	1	9258	755	27	1		1	MAP1B	5	71490040	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2828750	71490040	109425220	312	22048										
MAP1B	4131	broad.mit.edu	37	chr5	71492953	71492953	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcagcccatcgaagagcccGtccctgagtccatctccacc	8	18	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:71492953G>A	ENST00000296755.7	+	5	4069	c.3771G>A	c.(3769-3771)ccG>ccA	p.P1257P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1257					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.P1257P(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		CGAAGAGCCCGTCCCTGAGTC	0.498																																					Melanoma(17;367 822 11631 31730 47712)											2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	5											87	85	86					5																	71492953		2203	4300	6503	71528709	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3771G>A	5.37:g.71492953G>A			71528709	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.498	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71492953	G	A	71492953	2	1	77	1	0	0	0	0	0	0	0	1	9258	1132	40	1		1	MAP1B	5	71492953	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2913	71492953	109422307	313	22049										
BTF3	689	broad.mit.edu	37	chr5	72798924	72798924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctagtttaaggagactggccGaagctctgcccaaacaatgt	10	10	1	1	rs186931485	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:72798924G>A	ENST00000335895.8	+	4	518	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	BTF3_ENST00000514505.2_3'UTR|BTF3_ENST00000380591.3_Missense_Mutation_p.E167K	NM_001207.4	NP_001198.2	O00478	BT3A3_HUMAN	basic transcription factor 3	325	Ig-like V-type 1.				T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.E167K(1)		endometrium(1)|large_intestine(2)|lung(2)	5		Lung NSC(167;0.00405)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;2.73e-54)		GAGACTGGCCGAAGCTCTGCC	0.453													G|||	2	0.000399361	0	0	5008	,	,		17438	0.001		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											61	60	61					5																	72798924		2203	4300	6503	72834680	SO:0001583	missense	689			M90352	CCDS4019.1, CCDS34185.1	5q13.3	2010-06-17			ENSG00000145741	ENSG00000145741			1125	protein-coding gene	gene with protein product		602542	"nascent-polypeptide-associated complex beta polypeptide"	NACB		2320128, 1386332, 15716105	Standard	NM_001207		Approved	BTF3a, BTF3b	uc003kcr.1	P20290	OTTHUMG00000102031	ENST00000335895.8:c.367G>A	5.37:g.72798924G>A	ENSP00000338516:p.Glu123Lys		72834680	B4DWI7|E9PCP5	Missense_Mutation	SNP	ENST00000335895.8	37	CCDS4019.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.7	4.190218	0.78789	.	.	ENSG00000145741	ENST00000335895;ENST00000380591;ENST00000507081;ENST00000509708	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	U	0.000000	T	0.64416	0.2596	M	0.79693	2.465	0.80722	D	1	B	0.31752	0.338	B	0.19946	0.027	T	0.65825	-0.6074	9	0.38643	T	0.18	-19.6762	19.2707	0.94008	0.0:0.0:1.0:0.0	.	167	P20290	BTF3_HUMAN	K	123;167;85;65	.	ENSP00000338516:E123K	E	+	1	0	BTF3	72834680	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.289000	0.96061	2.620000	0.88729	0.650000	0.86243	GAA		0.453	BTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219815.2	NM_001207		A	72798924	G	A	72798924	3	1	77	1	0	0	0	0	1	0	0	0	1554	1059	37	1	513	1	BTF3	5	72798924	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1305971	72798924	108116336	314	22050										
THBS4	7060	broad.mit.edu	37	chr5	79354543	79354543	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctacaggggactttaaccGgcagttcttgggtcaaatga	11	9	2	1	rs553602331		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:79354543G>A	ENST00000350881.2	+	5	852	c.662G>A	c.(661-663)cGg>cAg	p.R221Q	THBS4_ENST00000511733.1_Missense_Mutation_p.R130Q|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	221					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.R221Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GACTTTAACCGGCAGTTCTTG	0.443													G|||	1	0.000199681	0	0	5008	,	,		17229	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	5											66	67	67					5																	79354543		2203	4300	6503	79390299	SO:0001583	missense	7060				CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.662G>A	5.37:g.79354543G>A	ENSP00000339730:p.Arg221Gln		79390299	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.893489	0.72639	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	T;T	0.30182	1.54;1.54	5.75	5.75	0.90469	Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain (1);	0.108147	0.64402	D	0.000009	T	0.27134	0.0665	L	0.44542	1.39	0.43885	D	0.996509	P	0.46142	0.873	B	0.37015	0.239	T	0.02958	-1.1089	10	0.21540	T	0.41	-22.2693	18.936	0.92586	0.0:0.0:1.0:0.0	.	221	P35443	TSP4_HUMAN	Q	221;130	ENSP00000339730:R221Q;ENSP00000422298:R130Q	ENSP00000339730:R221Q	R	+	2	0	THBS4	79390299	1.000000	0.71417	0.986000	0.45419	0.991000	0.79684	5.437000	0.66544	2.712000	0.92718	0.591000	0.81541	CGG		0.443	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			A	79354543	G	A	79354543	3	1	77	1	0	0	0	0	1	0	0	0	15895	1116	39	1	680	1	THBS4	5	79354543	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6555619	79354543	101560717	315	22051										
ANKRD34B	340120	broad.mit.edu	37	chr5	79855107	79855107	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcttgacccagggtggagcGtgggggagcttgggcccctt	17	11	1	1	rs369753277		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:79855107G>A	ENST00000338682.3	-	5	1404	c.732C>T	c.(730-732)caC>caT	p.H244H		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	244						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.H244H(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		AGGGTGGAGCGTGGGGGAGCT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G		1,4405		0,1,2202	40	46	44		732	0.4	0.2	5		44	0,8598		0,0,4299	no	coding-synonymous	ANKRD34B	NM_001004441.2		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		244/515	79855107	1,13003	2203	4299	6502	79890863	SO:0001819	synonymous_variant	340120				CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"Ankyrin repeat domain containing"	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.732C>T	5.37:g.79855107G>A			79890863	B2RPH1|Q68D79	Silent	SNP	ENST00000338682.3	37	CCDS34194.1																																																																																				0.522	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		A	79855107	G	A	79855107	2	1	77	1	0	0	0	0	0	0	0	1	663	1136	40	1		1	ANKRD34B	5	79855107	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	500564	79855107	101060153	316	22052										
POU5F2	134187	broad.mit.edu	37	chr5	93076585	93076585	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcttagggcaccgctggaAgaatttctccaggctgtttc	13	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:93076585A>G	ENST00000510627.4	-	1	758	c.685T>C	c.(685-687)Ttc>Ctc	p.F229L	RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000395965.3_Intron|POU5F2_ENST00000606183.1_5'UTR|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000509163.1_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	229				F -> L (in Ref. 3; CAE46012). {ECO:0000305}.	transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-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;0.0415)|all cancers(79;2.03e-19)		CACCGCTGGAAGAATTTCTCC	0.542																																																0			5											74	72	72					5																	93076585		1973	4182	6155	93102341	SO:0001583	missense	134187				CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.685T>C	5.37:g.93076585A>G	ENSP00000464890:p.Phe229Leu		93102341	Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	37	CCDS59489.1																																																																																				0.542	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		G	93076585	A	G	93076585	3	3	77	1	0	0	0	0	1	0	0	0	12314	72	3	4	305	4	POU5F2	5	93076585	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	13221478	93076585	87838675	317	22053										
SPATA9	83890	broad.mit.edu	37	chr5	94999697	94999697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgaagcatatattatgctaGttaaagcagtctttgctgga	9	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:94999697G>A	ENST00000274432.8	-	4	575	c.434C>T	c.(433-435)aCt>aTt	p.T145I	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	145					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T145I(1)		large_intestine(3)|lung(4)	7		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)		TATTATGCTAGTTAAAGCAGT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	5											32	33	32					5																	94999697		2202	4285	6487	95025453	SO:0001583	missense	83890			AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.434C>T	5.37:g.94999697G>A	ENSP00000274432:p.Thr145Ile		95025453	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.346350	0.41599	.	.	ENSG00000145757	ENST00000274432	T	0.32272	1.46	5.57	4.7	0.59300	.	0.343904	0.25341	N	0.031366	T	0.22003	0.0530	N	0.24115	0.695	0.80722	D	1	B	0.12630	0.006	B	0.13407	0.009	T	0.03374	-1.1043	10	0.52906	T	0.07	-11.3968	11.6104	0.51055	0.0836:0.0:0.9164:0.0	.	145	Q9BWV2	SPAT9_HUMAN	I	145	ENSP00000274432:T145I	ENSP00000274432:T145I	T	-	2	0	SPATA9	95025453	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.980000	0.49321	1.377000	0.46286	0.655000	0.94253	ACT		0.274	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		A	94999697	G	A	94999697	3	1	77	1	0	0	0	0	1	0	0	0	15055	1029	36	3	338	3	SPATA9	5	94999697	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1923112	94999697	85915563	318	22054										
PCSK1	5122	broad.mit.edu	37	chr5	95728864	95728864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcagcttttccagggcttcGtagaagttttcataagggat	10	7	2	1	rs149384979	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:95728864G>A	ENST00000311106.3	-	14	2340	c.2103C>T	c.(2101-2103)taC>taT	p.Y701Y	PCSK1_ENST00000508626.1_Silent_p.Y654Y|PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	701					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.Y701Y(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CCAGGGCTTCGTAGAAGTTTT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	5						G	,,	0,4406		0,0,2203	116	122	120		2103,1962,1173	-8.7	0.2	5	dbSNP_134	120	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	,,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,,	701/754,654/707,391/444	95728864	3,13003	2203	4300	6503	95754620	SO:0001819	synonymous_variant	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.2103C>T	5.37:g.95728864G>A			95754620	B7Z8T7|E9PHA1|P78478|Q92532	Silent	SNP	ENST00000311106.3	37	CCDS4081.1																																																																																				0.408	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		A	95728864	G	A	95728864	2	1	77	1	0	0	0	0	0	0	0	1	11631	1140	40	1		1	PCSK1	5	95728864	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	729167	95728864	85186396	319	22055										
EFNA5	1946	broad.mit.edu	37	chr5	106763002	106763002	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaatttttcagagaacttcaGcggtccatttggagagtgag	12	6	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:106763002G>A	ENST00000333274.6	-	2	615	c.334C>T	c.(334-336)Ctg>Ttg	p.L112L	EFNA5_ENST00000509503.1_Silent_p.L112L	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	112	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)	p.L112L(1)		large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		GAGAACTTCAGCGGTCCATTT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	5											81	81	81					5																	106763002		2202	4300	6502	106790901	SO:0001819	synonymous_variant	1946			U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.334C>T	5.37:g.106763002G>A			106790901		Silent	SNP	ENST00000333274.6	37	CCDS4097.1																																																																																				0.458	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		A	106763002	G	A	106763002	2	1	77	1	0	0	0	0	0	0	0	1	4965	962	34	3		3	EFNA5	5	106763002	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11034138	106763002	74152258	320	22056										
PJA2	9867	broad.mit.edu	37	chr5	108714666	108714666	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agatggtcattatcttctccAtgtttgccatctggatcata	7	9	5	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:108714666A>G	ENST00000361189.2	-	4	761	c.522T>C	c.(520-522)caT>caC	p.H174H	PJA2_ENST00000511624.1_5'Flank|PJA2_ENST00000361557.3_Silent_p.H174H	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	174					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H174H(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		TATCTTCTCCATGTTTGCCAT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	5											151	139	143					5																	108714666		2202	4300	6502	108742565	SO:0001819	synonymous_variant	9867			AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.522T>C	5.37:g.108714666A>G			108742565	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Silent	SNP	ENST00000361189.2	37	CCDS4099.1																																																																																				0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		G	108714666	A	G	108714666	2	3	77	1	0	0	0	0	0	0	0	1	11993	214	8	4		4	PJA2	5	108714666	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1951664	108714666	72200594	321	22057										
WDR36	134430	broad.mit.edu	37	chr5	110440033	110440033	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccacttcttgtcacaaatggCgctgacaatgctcttagggt	9	11	3	1	rs139303905	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:110440033C>T	ENST00000513710.2	+	8	1060	c.1056C>T	c.(1054-1056)ggC>ggT	p.G352G	WDR36_ENST00000505303.1_Silent_p.G296G|WDR36_ENST00000506538.2_Silent_p.G352G			Q8NI36	WDR36_HUMAN	WD repeat domain 36	352					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.G352G(1)		cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TCACAAATGGCGCTGACAATG	0.378													C|||	6	0.00119808	0.0045	0	5008	,	,		18902	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	5						C		5,4399	9.9+/-24.2	0,5,2197	155	154	154		1056	-4.2	0.9	5	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	WDR36	NM_139281.2		0,5,6497	TT,TC,CC		0.0,0.1135,0.0384		352/952	110440033	5,12999	2202	4300	6502	110467932	SO:0001819	synonymous_variant	134430			AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1056C>T	5.37:g.110440033C>T			110467932	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																				0.378	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110440033	C	T	110440033	2	4	77	1	0	0	0	0	0	0	0	1	17330	755	27	1		1	WDR36	5	110440033	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1725367	110440033	70475227	322	22058										
APC	324	broad.mit.edu	37	chr5	112128191	112128191	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaaggacatacttcgtataCgacagcttttacagtcccaa	6	10	0	0	rs397515734		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:112128191C>T	ENST00000457016.1	+	7	1074	c.694C>T	c.(694-696)Cga>Tga	p.R232*	APC_ENST00000508376.2_Nonsense_Mutation_p.R232*|APC_ENST00000257430.4_Nonsense_Mutation_p.R232*			P25054	APC_HUMAN	adenomatous polyposis coli	232	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R232*(13)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACTTCGTATACGACAGCTTTT	0.308		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	13	Substitution - Nonsense(13)	large_intestine(13)	5	GRCh37	CM920029	APC	M							82	79	80					5																	112128191		2202	4300	6502	112156090	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.694C>T	5.37:g.112128191C>T	ENSP00000413133:p.Arg232*		112156090	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.033640	0.98621	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	4.32	0.51571	.	0.206644	0.42682	D	0.000664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.475	13.9715	0.64242	0.2757:0.7243:0.0:0.0	.	.	.	.	X	232	.	ENSP00000257430:R232X	R	+	1	2	APC	112156090	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.535000	0.36061	1.304000	0.44892	-0.158000	0.13435	CGA		0.308	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112128191	C	T	112128191	4	4	77	1	0	0	0	0	0	1	0	0	763	528	19	1	716	1	APC	5	112128191	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1688158	112128191	68787069	323	22059										
APC	324	broad.mit.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	77	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	47448	112175639	68739621	324	22060										
DCP2	167227	broad.mit.edu	37	chr5	112337151	112337151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acctaacaaattttttatggCcattccctttatcaggtgtg	6	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:112337151C>T	ENST00000389063.2	+	6	881	c.683C>T	c.(682-684)gCc>gTc	p.A228V	DCP2_ENST00000543319.1_Missense_Mutation_p.A17V|DCP2_ENST00000515408.1_Missense_Mutation_p.A228V	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	228					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)	p.A228V(1)		endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		TTTTTTATGGCCATTCCCTTT	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	5											106	114	111					5																	112337151		2202	4300	6502	112365050	SO:0001583	missense	167227			AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"Nudix motif containing"	24452	protein-coding gene	gene with protein product	"nudix (nucleoside diphosphate linked moiety X)-type motif 20", "M(7)GpppN-mRNA hydrolase"	609844	"DCP2 decapping enzyme homolog (S. cerevisiae)"			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.683C>T	5.37:g.112337151C>T	ENSP00000373715:p.Ala228Val		112365050	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Missense_Mutation	SNP	ENST00000389063.2	37	CCDS34210.1	.	.	.	.	.	.	.	.	.	.	C	7.318	0.616459	0.14129	.	.	ENSG00000172795	ENST00000515408;ENST00000389063;ENST00000543319	T;T	0.33654	1.47;1.4	5.56	5.56	0.83823	.	0.095001	0.64402	D	0.000001	T	0.20210	0.0486	N	0.17082	0.46	0.54753	D	0.999986	B;B	0.20550	0.046;0.027	B;B	0.19946	0.027;0.021	T	0.06144	-1.0843	10	0.02654	T	1	-13.6601	12.8195	0.57685	0.0:0.9254:0.0:0.0746	.	228;228	Q8IU60-2;Q8IU60	.;DCP2_HUMAN	V	228;228;17	ENSP00000425770:A228V;ENSP00000373715:A228V	ENSP00000373715:A228V	A	+	2	0	DCP2	112365050	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.654000	0.61469	2.628000	0.89032	0.453000	0.30009	GCC		0.353	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624		T	112337151	C	T	112337151	3	4	77	1	0	0	0	0	1	0	0	0	4306	739	26	3	705	3	DCP2	5	112337151	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	161512	112337151	68578109	325	22061										
AP3S1	1176	broad.mit.edu	37	chr5	115205726	115205726	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatttagattaattggaggAtctgacaacaaactgattta	7	5	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:115205726A>T	ENST00000316788.7	+	3	731	c.174A>T	c.(172-174)ggA>ggT	p.G58G		NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	58					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.G58G(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		TAATTGGAGGATCTGACAACA	0.294																																																1	Substitution - coding silent(1)	large_intestine(1)	5											109	107	107					5																	115205726		2202	4294	6496	115233625	SO:0001819	synonymous_variant	1176			D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.174A>T	5.37:g.115205726A>T			115233625	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Silent	SNP	ENST00000316788.7	37	CCDS4123.1																																																																																				0.294	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2			T	115205726	A	T	115205726	2	4	77	1	0	0	0	0	0	0	0	1	749	320	12	5		5	AP3S1	5	115205726	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	2868575	115205726	65709534	326	22062										
ALDH7A1	501	broad.mit.edu	37	chr5	125911134	125911134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgacagccacactaatgaGggaagtggttggagctcctt	13	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:125911134G>A	ENST00000409134.3	-	7	892	c.673C>T	c.(673-675)Ctc>Ttc	p.L225F	ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000447989.2_Missense_Mutation_p.L252F|ALDH7A1_ENST00000553117.1_Missense_Mutation_p.L225F	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	225					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)	p.L197F(1)		endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		ACACTAATGAGGGAAGTGGTT	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	5											64	62	63					5																	125911134		2203	4300	6503	125939033	SO:0001583	missense	501			S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"Aldehyde dehydrogenases"	877	protein-coding gene	gene with protein product	"antiquitin 1", "26g turgor protein homolog", "alpha-aminoadipic semialdehyde dehydrogenase", "alpha-AASA dehydrogenase", "delta1-piperideine-6-carboxylate dehydrogenease", "P6c dehydrogenase"	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.673C>T	5.37:g.125911134G>A	ENSP00000387123:p.Leu225Phe		125939033	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Missense_Mutation	SNP	ENST00000409134.3	37	CCDS4137.2	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903392	0.92035	.	.	ENSG00000164904	ENST00000409134;ENST00000553117;ENST00000447989;ENST00000437170;ENST00000510111	T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3	5.09	5.09	0.68999	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.90868	0.7131	M	0.86740	2.835	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.92004	0.5613	10	0.87932	D	0	.	16.8052	0.85625	0.0:0.0:1.0:0.0	.	252;252;225	E7EPT3;B4DMA0;P49419	.;.;AL7A1_HUMAN	F	225;225;252;33;196	ENSP00000387123:L225F;ENSP00000448593:L225F;ENSP00000414132:L252F;ENSP00000447388:L196F	ENSP00000387123:L225F	L	-	1	0	ALDH7A1	125939033	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.492000	0.90471	2.809000	0.96659	0.557000	0.71058	CTC		0.343	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		A	125911134	G	A	125911134	3	1	77	1	0	0	0	0	1	0	0	0	504	1000	35	3	994	3	ALDH7A1	5	125911134	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	10705408	125911134	55004126	327	22063										
FBN2	2201	broad.mit.edu	37	chr5	127671687	127671687	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctccccttacctgtacaGccctggcggtctggcgtagc	12	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:127671687G>A	ENST00000508053.1	-	34	4691	c.3717C>T	c.(3715-3717)ggC>ggT	p.G1239G	FBN2_ENST00000507835.1_Silent_p.G89G|FBN2_ENST00000508989.1_Silent_p.G1206G|FBN2_ENST00000262464.4_Silent_p.G1239G			P35556	FBN2_HUMAN	fibrillin 2	1239	EGF-like 18; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.G1239G(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TACCTGTACAGCCCTGGCGGT	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	5											72	64	66					5																	127671687		2203	4300	6503	127699586	SO:0001819	synonymous_variant	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3717C>T	5.37:g.127671687G>A			127699586	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																				0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127671687	G	A	127671687	2	1	77	1	0	0	0	0	0	0	0	1	5722	958	34	3		3	FBN2	5	127671687	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1760553	127671687	53243573	328	22064										
RAPGEF6	51735	broad.mit.edu	37	chr5	130782243	130782243	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctcatctgtctctacatcGagactggaaagatactgctt	7	11	3	2	rs151303165		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:130782243G>A	ENST00000509018.1	-	22	3559	c.3354C>T	c.(3352-3354)ctC>ctT	p.L1118L	RAPGEF6_ENST00000507093.1_Silent_p.L1126L|RAPGEF6_ENST00000308008.6_Silent_p.L1118L|RAPGEF6_ENST00000307984.5_Silent_p.L1131L|RAPGEF6_ENST00000296859.6_Silent_p.L1126L|RAPGEF6_ENST00000512052.1_Silent_p.L841L|CTC-432M15.3_ENST00000514667.1_Silent_p.L1168L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1118					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.L1168L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCTCTACATCGAGACTGGAAA	0.453													G|||	1	0.000199681	8e-04	0	5008	,	,		19303	0		0	False		,,,				2504	0				Melanoma(168;435 1955 13113 13877 23213)											1	Substitution - coding silent(1)	large_intestine(1)	5						G	,,,,	3,4403	6.2+/-15.9	0,3,2200	225	200	208		3378,3393,3378,3354,3354	0.2	1	5	dbSNP_134	208	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAPGEF6	NM_001164386.1,NM_001164387.1,NM_001164388.1,NM_001164389.1,NM_016340.5	,,,,	0,10,6493	AA,AG,GG		0.0814,0.0681,0.0769	,,,,	1126/1610,1131/1510,1126/1505,1118/1392,1118/1602	130782243	10,12996	2203	4300	6503	130810142	SO:0001819	synonymous_variant	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3354C>T	5.37:g.130782243G>A			130810142	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	37	CCDS34225.1																																																																																				0.453	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		A	130782243	G	A	130782243	2	1	77	1	0	0	0	0	0	0	0	1	13085	1045	37	1		1	RAPGEF6	5	130782243	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3110556	130782243	50133017	329	22065										
TRPC7	57113	broad.mit.edu	37	chr5	135692632	135692632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgtaggcatagaagtcgtcGtcgcgcagctcctgttccag	12	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:135692632G>A	ENST00000513104.1	-	2	726	c.444C>T	c.(442-444)gaC>gaT	p.D148D	TRPC7_ENST00000426057.2_Silent_p.D148D|TRPC7_ENST00000355180.3_Silent_p.D148D	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	148					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.D148D(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGAAGTCGTCGTCGCGCAGCT	0.652																																																2	Substitution - coding silent(2)	large_intestine(2)	5											97	105	102					5																	135692632		2202	4299	6501	135720531	SO:0001819	synonymous_variant	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.444C>T	5.37:g.135692632G>A			135720531	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	De_novo_Start_OutOfFrame	SNP	ENST00000513104.1	37	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	2.029	-0.422814	0.04734	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	5.27	-3.68	0.04463	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.9109	8.8472	0.35177	0.7143:0.0:0.1594:0.1263	.	.	.	.	X	148	.	.	R	-	1	2	TRPC7	135720531	0.168000	0.22989	0.320000	0.25306	0.348000	0.29142	-0.290000	0.08354	-0.651000	0.05415	-1.816000	0.00601	CGA		0.652	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692632	G	A	135692632	2	1	77	1	0	0	0	0	0	0	0	1	16624	1136	40	1		1	TRPC7	5	135692632	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4910389	135692632	45222628	330	22066										
CDC25C	995	broad.mit.edu	37	chr5	137622891	137622891	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccagatactcatatggataGcgacaatcaatgacataaaa	6	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:137622891G>A	ENST00000323760.6	-	11	1271	c.993C>T	c.(991-993)cgC>cgT	p.R331R	CDC25C_ENST00000356505.3_Silent_p.R301R|CDC25C_ENST00000514555.1_Silent_p.R301R|CDC25C_ENST00000357274.3_Silent_p.R288R|CDC25C_ENST00000348983.3_Silent_p.R258R|CDC25C_ENST00000513970.1_Silent_p.R331R|CDC25C_ENST00000415130.2_Silent_p.R258R	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	331	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)	p.R331R(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CATATGGATAGCGACAATCAA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	5											123	116	118					5																	137622891		2203	4300	6503	137650790	SO:0001819	synonymous_variant	995			M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"Protein tyrosine phosphatases / Class III Cys-based PTPs", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1727	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 60"	157680	"cell division cycle 25C", "cell division cycle 25 homolog C (S. cerevisiae)", "cell division cycle 25 homolog C (S. pombe)"	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.993C>T	5.37:g.137622891G>A			137650790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Silent	SNP	ENST00000323760.6	37	CCDS4202.1																																																																																				0.463	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			A	137622891	G	A	137622891	2	1	77	1	0	0	0	0	0	0	0	1	3070	958	34	3		3	CDC25C	5	137622891	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1930259	137622891	43292369	331	22067										
EGR1	1958	broad.mit.edu	37	chr5	137803261	137803261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccagtgccgcatctgcatgCgcaacttcagccgcagcgac	10	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:137803261C>T	ENST00000239938.4	+	2	1395	c.1123C>T	c.(1123-1125)Cgc>Tgc	p.R375C		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	375					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R375C(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CATCTGCATGCGCAACTTCAG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	82	83					5																	137803261		2203	4300	6503	137831160	SO:0001583	missense	1958			M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"Zinc fingers, C2H2-type"	3238	protein-coding gene	gene with protein product	"nerve growth factor-induced protein A", "transcription factor ETR103", "zinc finger protein 225", "early growth response protein 1"	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.1123C>T	5.37:g.137803261C>T	ENSP00000239938:p.Arg375Cys		137831160		Missense_Mutation	SNP	ENST00000239938.4	37	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.806753	0.50421	.	.	ENSG00000120738	ENST00000239938	T	0.68765	-0.35	4.2	4.2	0.49525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.76040	0.3932	L	0.52823	1.66	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78033	-0.2362	10	0.87932	D	0	-16.5076	11.0361	0.47802	0.1856:0.8144:0.0:0.0	.	375	P18146	EGR1_HUMAN	C	375	ENSP00000239938:R375C	ENSP00000239938:R375C	R	+	1	0	EGR1	137831160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.333000	0.43912	2.177000	0.69029	0.563000	0.77884	CGC		0.622	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		T	137803261	C	T	137803261	3	4	77	1	0	0	0	0	1	0	0	0	4982	768	27	1	1129	1	EGR1	5	137803261	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	180370	137803261	43111999	332	22068										
PCDHA2	56146	broad.mit.edu	37	chr5	140176479	140176479	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagacgaggctgactcccctCgacaccgcctactcgtgctg	10	16	0	2	rs143944331		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:140176479C>T	ENST00000526136.1	+	1	1930	c.1930C>T	c.(1930-1932)Cga>Tga	p.R644*	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Nonsense_Mutation_p.R644*|PCDHA2_ENST00000378132.1_Nonsense_Mutation_p.R644*|PCDHA1_ENST00000504120.2_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	644	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R644*(2)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTCCCCTCGACACCGCCT	0.632																																																2	Substitution - Nonsense(2)	large_intestine(2)	5											82	80	81					5																	140176479		2203	4300	6503	140156663	SO:0001587	stop_gained	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1930C>T	5.37:g.140176479C>T	ENSP00000431748:p.Arg644*		140156663	O75287|Q9BTV3	Nonsense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	c	13.95	2.389561	0.42410	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	.	.	.	3.91	1.94	0.25998	.	0.790188	0.10028	U	0.725113	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8347	0.23929	0.292:0.6209:0.0:0.0871	.	.	.	.	X	644	.	ENSP00000367372:R644X	R	+	1	2	PCDHA2	140156663	0.000000	0.05858	0.083000	0.20561	0.001000	0.01503	-0.167000	0.09940	0.780000	0.33566	-0.274000	0.10170	CGA		0.632	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140176479	C	T	140176479	4	4	77	1	0	0	0	0	0	1	0	0	11555	876	31	1	1932	1	PCDHA2	5	140176479	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2373218	140176479	40738781	333	22069										
PCDHA3	56145	broad.mit.edu	37	chr5	140181890	140181890	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccacttagcacagtcatcGctctgatcagcgtgtccgac	8	15	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:140181890G>A	ENST00000522353.2	+	1	1108	c.1108G>A	c.(1108-1110)Gct>Act	p.A370T	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.A370T|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A370T(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACAGTCATCGCTCTGATCAG	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	5											123	119	120					5																	140181890		2203	4300	6503	140162074	SO:0001583	missense	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1108G>A	5.37:g.140181890G>A	ENSP00000429808:p.Ala370Thr		140162074	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	15.19	2.760474	0.49468	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52754	0.65;0.65	4.79	4.79	0.61399	Cadherin (3);Cadherin-like (1);	0.000000	0.41500	U	0.000870	T	0.65852	0.2731	M	0.70787	2.145	0.34566	D	0.712864	D;D	0.69078	0.997;0.979	P;P	0.60609	0.799;0.877	T	0.76865	-0.2801	10	0.59425	D	0.04	.	18.1862	0.89793	0.0:0.0:1.0:0.0	.	370;370	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	T	370	ENSP00000429808:A370T;ENSP00000434086:A370T	ENSP00000429808:A370T	A	+	1	0	PCDHA3	140162074	1.000000	0.71417	0.945000	0.38365	0.119000	0.20118	7.981000	0.88123	2.378000	0.81104	0.467000	0.42956	GCT		0.483	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140181890	G	A	140181890	3	1	77	1	0	0	0	0	1	0	0	0	11556	1087	38	1	1110	1	PCDHA3	5	140181890	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5411	140181890	40733370	334	22070										
PCDHA5	56143	broad.mit.edu	37	chr5	140201827	140201827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcggtttccgctagagggcgCgtcggatttggatattggag	17	7	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:140201827C>T	ENST00000529859.1	+	1	467	c.467C>T	c.(466-468)gCg>gTg	p.A156V	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A156V|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.A156V|PCDHA3_ENST00000522353.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	156	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A156V(4)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTAGAGGGCGCGTCGGATTTG	0.398																																																4	Substitution - Missense(4)	large_intestine(4)	5											50	55	54					5																	140201827		2203	4300	6503	140182011	SO:0001583	missense	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.467C>T	5.37:g.140201827C>T	ENSP00000436557:p.Ala156Val		140182011	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472423	0.84533	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.59364	0.27;0.27;0.27	4.02	4.02	0.46733	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.82815	0.5119	H	0.95079	3.62	0.42748	D	0.993768	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.89364	0.3670	9	0.87932	D	0	.	16.5119	0.84288	0.0:1.0:0.0:0.0	.	156;156;156	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	V	156	ENSP00000433416:A156V;ENSP00000436557:A156V;ENSP00000367366:A156V	ENSP00000367366:A156V	A	+	2	0	PCDHA5	140182011	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.815000	0.86186	1.946000	0.56461	0.591000	0.81541	GCG		0.398	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140201827	C	T	140201827	3	4	77	1	0	0	0	0	1	0	0	0	11558	768	27	1	469	1	PCDHA5	5	140201827	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	19937	140201827	40713433	335	22071										
PCDHGB3	56102	broad.mit.edu	37	chr5	140751522	140751522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgttcgcgcagcgagccttcGaccacgagcagctgcgtgcc	13	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:140751522G>A	ENST00000576222.1	+	1	1692	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	521	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGAGCCTTCGACCACGAGCA	0.682																																																0			5											41	47	45					5																	140751522		2119	4234	6353	140731706	SO:0001583	missense	56102			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1561G>A	5.37:g.140751522G>A	ENSP00000461862:p.Asp521Asn		140731706	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.682	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751522	G	A	140751522	3	1	77	1	0	0	0	0	1	0	0	0	11595	1058	37	1	1563	1	PCDHGB3	5	140751522	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	549695	140751522	40163738	336	22072										
ARAP3	64411	broad.mit.edu	37	chr5	141033860	141033860	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggttctctggcttcactgtcCactcccgtgtggtggagaag	13	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:141033860C>A	ENST00000239440.4	-	33	4357	c.4292G>T	c.(4291-4293)tGg>tTg	p.W1431L	ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000522783.1_5'Flank|ARAP3_ENST00000513878.1_Missense_Mutation_p.W1080L|ARAP3_ENST00000508305.1_Missense_Mutation_p.W1262L|FCHSD1_ENST00000519800.1_5'Flank|FCHSD1_ENST00000435817.2_5'Flank	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1431					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.W1431L(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CTTCACTGTCCACTCCCGTGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	5											117	115	115					5																	141033860		2203	4300	6503	141014044	SO:0001583	missense	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4292G>T	5.37:g.141033860C>A	ENSP00000239440:p.Trp1431Leu		141014044	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	1.608	-0.524839	0.04141	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.41400	1.0;1.0;1.0	4.6	2.75	0.32379	.	1.111220	0.06885	N	0.803285	T	0.24967	0.0606	N	0.12182	0.205	0.09310	N	1	B;B;B	0.18310	0.004;0.027;0.016	B;B;B	0.14023	0.004;0.01;0.007	T	0.23119	-1.0197	10	0.39692	T	0.17	.	5.1978	0.15246	0.1604:0.6598:0.0:0.1798	.	1080;1262;1431	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	L	1262;1431;1080	ENSP00000421826:W1262L;ENSP00000239440:W1431L;ENSP00000421468:W1080L	ENSP00000239440:W1431L	W	-	2	0	ARAP3	141014044	0.011000	0.17503	0.048000	0.18961	0.039000	0.13416	0.216000	0.17585	0.494000	0.27859	0.655000	0.94253	TGG		0.572	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141033860	C	A	141033860	3	1	77	1	0	0	0	0	1	0	0	0	840	595	21	2	346	2	ARAP3	5	141033860	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	282338	141033860	39881400	337	22073										
ARAP3	64411	broad.mit.edu	37	chr5	141059990	141059990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgccgtcggaacgtgtctgCatactgctccaggtgcaccg	12	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:141059990C>T	ENST00000239440.4	-	2	129	c.64G>A	c.(64-66)Gca>Aca	p.A22T	ARAP3_ENST00000508305.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	22	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.A22T(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						AACGTGTCTGCATACTGCTCC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	5											41	40	40					5																	141059990		2203	4299	6502	141040174	SO:0001583	missense	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.64G>A	5.37:g.141059990C>T	ENSP00000239440:p.Ala22Thr		141040174	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.782285	0.49891	.	.	ENSG00000120318	ENST00000239440;ENST00000504448	D;T	0.84589	-1.87;-0.02	4.39	4.39	0.52855	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.451841	0.20449	N	0.092126	T	0.80706	0.4674	L	0.41961	1.31	0.80722	D	1	P	0.51791	0.948	P	0.48627	0.584	T	0.75844	-0.3174	10	0.08837	T	0.75	.	10.3573	0.43972	0.0:0.8004:0.1996:0.0	.	22	Q8WWN8	ARAP3_HUMAN	T	22	ENSP00000239440:A22T;ENSP00000421148:A22T	ENSP00000239440:A22T	A	-	1	0	ARAP3	141040174	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.898000	0.48672	2.272000	0.75746	0.462000	0.41574	GCA		0.682	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		T	141059990	C	T	141059990	3	4	77	1	0	0	0	0	1	0	0	0	840	710	25	3	4698	3	ARAP3	5	141059990	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	26130	141059990	39855270	338	22074										
SPRY4	81848	broad.mit.edu	37	chr5	141693948	141693948	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcaggcagggcagcaccacGgagagagcacccatgaagga	15	11	0	2	rs145360326	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:141693948G>A	ENST00000434127.2	-	2	969	c.726C>T	c.(724-726)tcC>tcT	p.S242S	SPRY4_ENST00000503582.1_5'Flank|SPRY4_ENST00000344120.4_Silent_p.S265S	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	242	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.S265S(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCACCACGGAGAGAGCAC	0.682									Testicular Cancer, Familial Clustering of																																							3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	5						G	,	2,4404	4.2+/-10.8	0,2,2201	60	60	60		726,795	0.7	1	5	dbSNP_134	60	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPRY4	NM_001127496.1,NM_030964.3	,	0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538	,	242/300,265/323	141693948	7,12999	2203	4300	6503	141674132	SO:0001819	synonymous_variant	81848	Familial Cancer Database		AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.726C>T	5.37:g.141693948G>A			141674132	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Silent	SNP	ENST00000434127.2	37	CCDS47296.1																																																																																				0.682	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1			A	141693948	G	A	141693948	2	1	77	1	0	0	0	0	0	0	0	1	15147	1103	39	1		1	SPRY4	5	141693948	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	633958	141693948	39221312	339	22075										
RBM27	54439	broad.mit.edu	37	chr5	145609404	145609404	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtaagagtcggagtaagagtCgaggcctgagtcgcagtaga	16	6	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:145609404C>T	ENST00000265271.5	+	5	686	c.520C>T	c.(520-522)Cga>Tga	p.R174*	RBM27_ENST00000506502.1_Nonsense_Mutation_p.R174*	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	174	Arg-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R174*(2)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gagtaagagtcgAGGCCTGAG	0.507																																																2	Substitution - Nonsense(2)	large_intestine(1)|pancreas(1)	5											132	128	129					5																	145609404		1568	3582	5150	145589597	SO:0001587	stop_gained	54439			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.520C>T	5.37:g.145609404C>T	ENSP00000265271:p.Arg174*		145589597	Q8IYW9	Nonsense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	C	38	6.662337	0.97743	.	.	ENSG00000091009	ENST00000265271	.	.	.	5.74	4.8	0.61643	.	0.086456	0.47093	D	0.000249	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6106	15.8716	0.79122	0.1812:0.8188:0.0:0.0	.	.	.	.	X	174	.	ENSP00000265271:R174X	R	+	1	2	RBM27	145589597	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.902000	0.39848	2.695000	0.91970	0.655000	0.94253	CGA		0.507	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		T	145609404	C	T	145609404	4	4	77	1	0	0	0	0	0	1	0	0	13164	876	31	1	538	1	RBM27	5	145609404	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3915456	145609404	35305856	340	22076										
SYNPO	11346	broad.mit.edu	37	chr5	150029718	150029718	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgggcctctacacctccccCggccaggacagcctgcagcc	10	21	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:150029718C>T	ENST00000394243.1	+	3	2987	c.2613C>T	c.(2611-2613)ccC>ccT	p.P871P	SYNPO_ENST00000522122.1_Silent_p.P871P|SYNPO_ENST00000519664.1_Silent_p.P627P|SYNPO_ENST00000307662.4_Silent_p.P627P	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	871	Pro-rich.				positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)	p.P627P(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACACCTCCCCCGGCCAGGACA	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	5											53	59	57					5																	150029718		2203	4299	6502	150009911	SO:0001819	synonymous_variant	11346			AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.2613C>T	5.37:g.150029718C>T			150009911	A5PKZ8|D3DQG8|O15271|Q9UPX1	Silent	SNP	ENST00000394243.1	37	CCDS54937.1																																																																																				0.706	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		T	150029718	C	T	150029718	2	4	77	1	0	0	0	0	0	0	0	1	15495	639	23	1		1	SYNPO	5	150029718	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4420314	150029718	30885542	341	22077										
MYOZ3	91977	broad.mit.edu	37	chr5	150050156	150050156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcttccagaagaggcagcgcCgtgtgcagaagttcactttc	11	11	2	3	rs201088365		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:150050156C>T	ENST00000297130.4	+	3	371	c.172C>T	c.(172-174)Cgt>Tgt	p.R58C	MYOZ3_ENST00000517768.1_Missense_Mutation_p.R58C|CTC-345K18.2_ENST00000511626.2_RNA|MYOZ3_ENST00000520112.1_5'Flank	NM_001122853.2|NM_133371.4	NP_001116325.1|NP_588612.2			myozenin 3									p.R58C(1)		large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGGCAGCGCCGTGTGCAGAA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	5											54	43	47					5																	150050156		2203	4300	6503	150030349	SO:0001583	missense	91977			AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"calsarcin 3", "FATZ related protein 3"	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000297130.4:c.172C>T	5.37:g.150050156C>T	ENSP00000297130:p.Arg58Cys		150030349		Missense_Mutation	SNP	ENST00000297130.4	37	CCDS4309.1	.	.	.	.	.	.	.	.	.	.	C	19.51	3.840716	0.71488	.	.	ENSG00000164591	ENST00000517768;ENST00000297130	D;D	0.82619	-1.63;-1.63	4.89	2.93	0.34026	.	0.000000	0.51477	D	0.000094	D	0.90549	0.7038	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91144	0.4948	10	0.87932	D	0	-17.4299	11.1552	0.48484	0.4147:0.5852:0.0:0.0	.	58	Q8TDC0	MYOZ3_HUMAN	C	58	ENSP00000428815:R58C;ENSP00000297130:R58C	ENSP00000297130:R58C	R	+	1	0	MYOZ3	150030349	0.404000	0.25328	0.986000	0.45419	0.977000	0.68977	0.213000	0.17521	1.141000	0.42275	0.555000	0.69702	CGT		0.587	MYOZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252369.1	NM_001122853		T	150050156	C	T	150050156	3	4	77	1	0	0	0	0	1	0	0	0	10127	652	23	1	178	1	MYOZ3	5	150050156	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	20438	150050156	30865104	342	22078										
GPX3	10318	broad.mit.edu	37	chr5	150407576	150407576	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttgagaagttcctggtggGgccagatggtatacccatca	12	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:150407576G>T	ENST00000389378.2	-	0	3268				GPX3_ENST00000517973.1_3'UTR|GPX3_ENST00000388825.4_Missense_Mutation_p.G189V	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1						defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)	p.G189V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCCTGGTGGGGCCAGATGGT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											43	47	46					5																	150407576		2062	4222	6284	150387769	SO:0001628	intergenic_variant	2878			AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025			5.37:g.150407576G>T			150387769	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514721	0.85389	.	.	ENSG00000211445	ENST00000388825	T	0.04502	3.61	5.33	5.33	0.75918	Thioredoxin-like fold (2);	0.055100	0.64402	D	0.000001	T	0.29093	0.0723	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.12837	-1.0532	10	0.87932	D	0	-6.2534	19.0343	0.92971	0.0:0.0:1.0:0.0	.	189	P22352	GPX3_HUMAN	V	189	ENSP00000373477:G189V	ENSP00000373477:G189V	G	+	2	0	GPX3	150387769	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.208000	0.77907	2.478000	0.83669	0.655000	0.94253	GGG		0.597	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		T	150407576	G	T	150407576	1	4	77	0	1	0	0	0	0	0	0	0	6762	1232	43	2		2	GPX3	5	150407576	IGR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	357420	150407576	30507684	343	22079										
NMUR2	56923	broad.mit.edu	37	chr5	151784173	151784173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagaagccccagacgatgcCgaggatcctgagggcccggc	16	13	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:151784173C>T	ENST00000255262.3	-	1	667	c.502G>A	c.(502-504)Ggc>Agc	p.G168S	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	168					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.G168S(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CAGACGATGCCGAGGATCCTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	5											56	63	60					5																	151784173		2203	4300	6503	151764366	SO:0001583	missense	56923			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.502G>A	5.37:g.151784173C>T	ENSP00000255262:p.Gly168Ser		151764366	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	5.835	0.338269	0.11069	.	.	ENSG00000132911	ENST00000255262	T	0.37584	1.19	5.44	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.685869	0.13990	N	0.348883	T	0.21267	0.0512	L	0.35644	1.08	0.09310	N	1	B	0.22346	0.068	B	0.10450	0.005	T	0.19257	-1.0311	10	0.21540	T	0.41	-1.8093	2.5006	0.04632	0.1314:0.514:0.1279:0.2267	.	168	Q9GZQ4	NMUR2_HUMAN	S	168	ENSP00000255262:G168S	ENSP00000255262:G168S	G	-	1	0	NMUR2	151764366	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	0.209000	0.17435	0.231000	0.21079	0.585000	0.79938	GGC		0.637	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151784173	C	T	151784173	3	4	77	1	0	0	0	0	1	0	0	0	10538	652	23	1	761	1	NMUR2	5	151784173	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1376597	151784173	29131087	344	22080										
GRIA1	2890	broad.mit.edu	37	chr5	153182028	153182028	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgagttctgctacaaatcccGtagtgaatccaagcggatga	10	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:153182028G>A	ENST00000285900.5	+	15	2841	c.2498G>A	c.(2497-2499)cGt>cAt	p.R833H	GRIA1_ENST00000518783.1_Missense_Mutation_p.R843H|GRIA1_ENST00000340592.5_Missense_Mutation_p.R833H|GRIA1_ENST00000518142.1_Missense_Mutation_p.R753H|GRIA1_ENST00000521843.2_Missense_Mutation_p.R764H|GRIA1_ENST00000448073.4_Missense_Mutation_p.R843H	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	833					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)	p.R833H(1)		NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	TACAAATCCCGTAGTGAATCC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											245	226	233					5																	153182028		2203	4300	6503	153162221	SO:0001583	missense	2890				CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2498G>A	5.37:g.153182028G>A	ENSP00000285900:p.Arg833His		153162221	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	32	5.148440	0.94603	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.75184	0.3815	M	0.70275	2.135	0.80722	D	1	D;D;B;D;P	0.67145	0.994;0.994;0.143;0.996;0.51	P;P;B;P;B	0.57152	0.656;0.656;0.03;0.814;0.117	T	0.78125	-0.2326	10	0.66056	D	0.02	.	18.1053	0.89518	0.0:0.0:1.0:0.0	.	843;843;753;833;833	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	H	833;833;753;833;766;764;843;843	ENSP00000285900:R833H;ENSP00000427920:R753H;ENSP00000339343:R833H;ENSP00000427864:R766H;ENSP00000442108:R764H;ENSP00000428994:R843H;ENSP00000415569:R843H	ENSP00000285900:R833H	R	+	2	0	GRIA1	153162221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.581000	0.98210	2.516000	0.84829	0.655000	0.94253	CGT		0.527	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			A	153182028	G	A	153182028	3	1	77	1	0	0	0	0	1	0	0	0	6788	1145	40	1	2675	1	GRIA1	5	153182028	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1397855	153182028	27733232	345	22081										
GEMIN5	25929	broad.mit.edu	37	chr5	154311118	154311118	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttgtgctacagcattcccGttggtaatttcagcttcttc	8	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:154311118G>A	ENST00000285873.7	-	5	756	c.681C>T	c.(679-681)aaC>aaT	p.N227N		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	227					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)	p.N227N(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CAGCATTCCCGTTGGTAATTT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	5											136	121	126					5																	154311118		2203	4300	6503	154291311	SO:0001819	synonymous_variant	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.681C>T	5.37:g.154311118G>A			154291311	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																				0.383	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			A	154311118	G	A	154311118	2	1	77	1	0	0	0	0	0	0	0	1	6351	1136	40	1		1	GEMIN5	5	154311118	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1129090	154311118	26604142	346	22082										
FAM71B	153745	broad.mit.edu	37	chr5	156589823	156589823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgccccttacgttgctgtAccctttttcttttttgtcat	5	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:156589823A>G	ENST00000302938.4	-	2	1548	c.1453T>C	c.(1453-1455)Tac>Cac	p.Y485H		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	485						nucleus (GO:0005634)		p.Y485H(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACGTTGCTGTACCCTTTTTCT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	5											235	224	227					5																	156589823		2203	4300	6503	156522401	SO:0001583	missense	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1453T>C	5.37:g.156589823A>G	ENSP00000305596:p.Tyr485His		156522401	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	2.162	-0.392034	0.04932	.	.	ENSG00000170613	ENST00000302938	T	0.18657	2.2	4.52	2.67	0.31697	.	1.878220	0.02837	N	0.127535	T	0.06690	0.0171	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34254	-0.9836	10	0.10636	T	0.68	1.3145	3.7576	0.08592	0.0932:0.1634:0.5745:0.1689	.	485	Q8TC56	FA71B_HUMAN	H	485	ENSP00000305596:Y485H	ENSP00000305596:Y485H	Y	-	1	0	FAM71B	156522401	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.256000	0.18351	0.202000	0.20498	-0.825000	0.03093	TAC		0.527	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		G	156589823	A	G	156589823	3	3	77	1	0	0	0	0	1	0	0	0	5627	391	14	4	368	4	FAM71B	5	156589823	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	2278705	156589823	24325437	347	22083										
SLIT3	6586	broad.mit.edu	37	chr5	168111081	168111081	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctttgtagagaaggatgccGttgtccttgtcagtggccac	12	10	1	1	rs369562472		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:168111081G>A	ENST00000519560.1	-	32	3995	c.3576C>T	c.(3574-3576)aaC>aaT	p.N1192N	SLIT3_ENST00000332966.8_Silent_p.N1199N|SLIT3_ENST00000404867.3_Silent_p.N1192N	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1192	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.N1192N(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAAGGATGCCGTTGTCCTTGT	0.582																																					Ovarian(29;311 847 10864 17279 24903)											1	Substitution - coding silent(1)	large_intestine(1)	5						A		0,4406		0,0,2203	107	100	102		3576	-6.3	1	5		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLIT3	NM_003062.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1192/1524	168111081	1,13005	2203	4300	6503	168043659	SO:0001819	synonymous_variant	6586			AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3576C>T	5.37:g.168111081G>A			168043659	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																				0.582	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168111081	G	A	168111081	2	1	77	1	0	0	0	0	0	0	0	1	14778	1136	40	1		1	SLIT3	5	168111081	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11521258	168111081	12804179	348	22084										
DOCK2	1794	broad.mit.edu	37	chr5	169483737	169483737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccactactcccggcccgtgCgcagggggaccgtagaccca	12	17	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:169483737C>T	ENST00000256935.8	+	43	4425	c.4345C>T	c.(4345-4347)Cgc>Tgc	p.R1449C	DOCK2_ENST00000540750.1_Missense_Mutation_p.R510C|DOCK2_ENST00000520908.1_Missense_Mutation_p.R941C|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1449	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R1449C(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCGGCCCGTGCGCAGGGGGAC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											110	91	97					5																	169483737		2203	4300	6503	169416315	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4345C>T	5.37:g.169483737C>T	ENSP00000256935:p.Arg1449Cys		169416315	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991926	0.74703	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.17528	2.27;2.27;2.27	5.27	4.34	0.51931	.	0.133600	0.50627	D	0.000115	T	0.45935	0.1367	M	0.90650	3.135	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;P	0.66196	0.942;0.853	T	0.54227	-0.8325	10	0.56958	D	0.05	.	13.2004	0.59765	0.2398:0.7602:0.0:0.0	.	941;1449	E7ERW7;Q92608	.;DOCK2_HUMAN	C	1449;941;510	ENSP00000256935:R1449C;ENSP00000429283:R941C;ENSP00000438827:R510C	ENSP00000256935:R1449C	R	+	1	0	DOCK2	169416315	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.860000	0.48372	2.449000	0.82847	0.650000	0.86243	CGC		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169483737	C	T	169483737	3	4	77	1	0	0	0	0	1	0	0	0	4698	768	27	1	4515	1	DOCK2	5	169483737	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1372656	169483737	11431523	349	22085										
GABRP	2568	broad.mit.edu	37	chr5	170222236	170222236	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acacagccaccatatacctcCgacagcgctggatggaccag	9	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:170222236C>T	ENST00000518525.1	+	6	729	c.265C>T	c.(265-267)Cga>Tga	p.R89*	GABRP_ENST00000519598.1_Nonsense_Mutation_p.R89*|GABRP_ENST00000265294.4_Nonsense_Mutation_p.R89*|GABRP_ENST00000519385.1_Nonsense_Mutation_p.R89*			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	89					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R89*(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATATACCTCCGACAGCGCTG	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											142	146	145					5																	170222236		2203	4300	6503	170154814	SO:0001587	stop_gained	2568			U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4089	protein-coding gene	gene with protein product	"GABA(A) receptor, pi"	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.265C>T	5.37:g.170222236C>T	ENSP00000430100:p.Arg89*		170154814	A8KA36|D3DQL2|Q32MJ1	Nonsense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891228	0.91889	.	.	ENSG00000094755	ENST00000521481;ENST00000521009;ENST00000522868;ENST00000518525;ENST00000539175;ENST00000265294;ENST00000519385;ENST00000519598	.	.	.	5.59	3.4	0.38934	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.5153	0.67816	0.3671:0.6329:0.0:0.0	.	.	.	.	X	89;89;89;89;10;89;89;89	.	ENSP00000265294:R89X	R	+	1	2	GABRP	170154814	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.575000	0.46025	1.352000	0.45808	0.643000	0.83706	CGA		0.562	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		T	170222236	C	T	170222236	4	4	77	1	0	0	0	0	0	1	0	0	6193	644	23	1	279	1	GABRP	5	170222236	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	738499	170222236	10693024	350	22086										
CDHR2	54825	broad.mit.edu	37	chr5	176016163	176016163	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcacctcctccgaggccgaCgtgttcgctgggagcattca	11	14	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:176016163C>T	ENST00000510636.1	+	22	3262	c.2988C>T	c.(2986-2988)gaC>gaT	p.D996D	CDHR2_ENST00000506348.1_Silent_p.D996D|CDHR2_ENST00000261944.5_Silent_p.D996D	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	996	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D996D(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CCGAGGCCGACGTGTTCGCTG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	5											148	149	149					5																	176016163		2203	4300	6503	175948769	SO:0001819	synonymous_variant	54825			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2988C>T	5.37:g.176016163C>T			175948769	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																				0.617	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	176016163	C	T	176016163	2	4	77	1	0	0	0	0	0	0	0	1	3125	535	19	1		1	CDHR2	5	176016163	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5793927	176016163	4899097	351	22087										
HK3	3101	broad.mit.edu	37	chr5	176315425	176315425	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggaggcaggagagaacagcGgccagggcggcagcacagag	19	9	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:176315425G>A	ENST00000292432.5	-	10	1303	c.1212C>T	c.(1210-1212)gcC>gcT	p.A404A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	404	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)	p.A404A(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			AGAGAACAGCGGCCAGGGCGG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	5											23	22	22					5																	176315425		2174	4258	6432	176248031	SO:0001819	synonymous_variant	3101				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1212C>T	5.37:g.176315425G>A			176248031	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																				0.662	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			A	176315425	G	A	176315425	2	1	77	1	0	0	0	0	0	0	0	1	7213	1103	39	1		1	HK3	5	176315425	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	299262	176315425	4599835	352	22088										
LMAN2	10960	broad.mit.edu	37	chr5	176761352	176761352	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgatgctctcctcgtcgggCgtgtgctccaccatcagctg	11	15	2	0	rs367812402		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:176761352C>T	ENST00000303127.7	-	7	1047	c.843G>A	c.(841-843)acG>acA	p.T281T	LMAN2_ENST00000515209.1_Silent_p.T281T	NM_006816.2	NP_006807.1	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2	281					positive regulation of phagocytosis (GO:0050766)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|heat shock protein binding (GO:0031072)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)	p.T281T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTCGTCGGGCGTGTGCTCCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	110	84	93		843	-11.1	0	5		93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LMAN2	NM_006816.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		281/357	176761352	1,13005	2203	4300	6503	176693958	SO:0001819	synonymous_variant	10960			U10362	CCDS4417.1	5q35	2008-02-05		2003-07-04	ENSG00000169223	ENSG00000169223			16986	protein-coding gene	gene with protein product		609551	"chromosome 5 open reading frame 8"	C5orf8		12609988	Standard	NM_006816		Approved	GP36B, VIP36	uc003mge.3	Q12907	OTTHUMG00000130860	ENST00000303127.7:c.843G>A	5.37:g.176761352C>T			176693958	Q53HH1	Silent	SNP	ENST00000303127.7	37	CCDS4417.1																																																																																				0.592	LMAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253434.1	NM_006816		T	176761352	C	T	176761352	2	4	77	1	0	0	0	0	0	0	0	1	8862	755	27	1		1	LMAN2	5	176761352	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	445927	176761352	4153908	353	22089										
GRM6	2916	broad.mit.edu	37	chr5	178419043	178419043	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagtcatagcgtgtggagtcGctgagctccggggctgtgga	17	8	1	1	rs200220261		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:178419043G>A	ENST00000517717.1	-	3	584	c.546C>T	c.(544-546)agC>agT	p.S182S	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.S182S			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	182					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.S182S(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		GTGTGGAGTCGCTGAGCTCCG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	5											44	44	44					5																	178419043		2203	4300	6503	178351649	SO:0001819	synonymous_variant	2916			U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.546C>T	5.37:g.178419043G>A			178351649		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																				0.607	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			A	178419043	G	A	178419043	2	1	77	1	0	0	0	0	0	0	0	1	6822	1078	38	1		1	GRM6	5	178419043	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1657691	178419043	2496217	354	22090										
ADAMTS2	9509	broad.mit.edu	37	chr5	178541106	178541106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggggtgcttggtgatggcCgcacctccatggctacagtg	17	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:178541106C>T	ENST00000251582.7	-	22	3499	c.3398G>A	c.(3397-3399)cGg>cAg	p.R1133Q		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1133					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1133Q(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TGGTGATGGCCGCACCTCCAT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	5											177	156	163					5																	178541106		2203	4300	6503	178473712	SO:0001583	missense	9509			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3398G>A	5.37:g.178541106C>T	ENSP00000251582:p.Arg1133Gln		178473712		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.252696	0.00268	.	.	ENSG00000087116	ENST00000251582	T	0.58060	0.36	5.05	-0.641	0.11490	.	0.828579	0.10123	N	0.713134	T	0.18383	0.0441	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22103	-1.0226	10	0.11485	T	0.65	.	2.372	0.04333	0.1227:0.2188:0.4194:0.239	.	1133	O95450	ATS2_HUMAN	Q	1133	ENSP00000251582:R1133Q	ENSP00000251582:R1133Q	R	-	2	0	ADAMTS2	178473712	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.844000	0.04345	-0.046000	0.13446	-1.762000	0.00668	CGG		0.582	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178541106	C	T	178541106	3	4	77	1	0	0	0	0	1	0	0	0	265	652	23	1	241	1	ADAMTS2	5	178541106	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	122063	178541106	2374154	355	22091										
MGAT4B	11282	broad.mit.edu	37	chr5	179229097	179229097	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgacatctgttcttgtgccTgccacacgtgacatagctgg	10	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:179229097T>G	ENST00000292591.7	-	2	448				MGAT4B_ENST00000337755.5_Silent_p.A5A|MGAT4B_ENST00000521305.1_Intron	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B						cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.A5A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCTTGTGCCTGCCACACGTG	0.557											OREG0017110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(13;414 434 4098 22176 23230)											1	Substitution - coding silent(1)	large_intestine(1)	5											71	79	76					5																	179229097		2193	4289	6482	179161703	SO:0001627	intron_variant	11282			AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7048	protein-coding gene	gene with protein product		604561	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.98-128A>C	5.37:g.179229097T>G		1952	179161703	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Silent	SNP	ENST00000292591.7	37	CCDS4448.1																																																																																				0.557	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275		G	179229097	T	G	179229097	1	3	77	0	1	0	0	0	0	0	0	0	9576	1567	55	4		4	MGAT4B	5	179229097	Intron	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	687991	179229097	1686163	356	22092										
C5orf45	51149	broad.mit.edu	37	chr5	179264844	179264844	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagttctcctggaggcagggGctgctgccttgtttcacctt	13	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr5:179264844G>A	ENST00000292586.6	-	7	669	c.579C>T	c.(577-579)agC>agT	p.S193S	C5orf45_ENST00000518219.1_3'UTR|C5orf45_ENST00000518235.1_Silent_p.S193S|SQSTM1_ENST00000389805.4_3'UTR|C5orf45_ENST00000520698.1_Silent_p.S138S|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000376931.2_Silent_p.S138S|C5orf45_ENST00000521333.1_Intron|C5orf45_ENST00000523267.1_5'UTR|C5orf45_ENST00000403396.2_Silent_p.S235S|C5orf45_ENST00000523084.1_Silent_p.S59S	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	193								p.S193S(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAGGCAGGGGCTGCTGCCTT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5											34	38	37					5																	179264844		2203	4300	6503	179197450	SO:0001819	synonymous_variant	51149				CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"truncated calcium binding protein"						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.579C>T	5.37:g.179264844G>A			179197450	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Silent	SNP	ENST00000292586.6	37	CCDS34319.1																																																																																				0.592	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		A	179264844	G	A	179264844	2	1	77	1	0	0	0	0	0	0	0	1	2310	1194	42	3		3	C5orf45	5	179264844	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	35747	179264844	1650416	357	22093										
NQO2	4835	broad.mit.edu	37	chr6	3012826	3012826	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttatggagtggaaacccacgAagcctacaagcaaaggtctc	10	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:3012826A>G	ENST00000338130.2	+	7	933	c.221A>G	c.(220-222)gAa>gGa	p.E74G	NQO2_ENST00000380455.4_Missense_Mutation_p.E74G|NQO2_ENST00000380441.1_Missense_Mutation_p.E74G|NQO2_ENST00000380454.4_Missense_Mutation_p.E74G|NQO2_ENST00000380430.1_Missense_Mutation_p.E74G			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	74					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)	p.E74G(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	GAAACCCACGAAGCCTACAAG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											123	120	121					6																	3012826		2203	4300	6503	2957825	SO:0001583	missense	4835			U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"NAD(P)H menadione oxidoreductase 2, dioxin-inducible"	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.221A>G	6.37:g.3012826A>G	ENSP00000337773:p.Glu74Gly		2957825	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	37	CCDS4481.1	.	.	.	.	.	.	.	.	.	.	A	9.343	1.063484	0.20067	.	.	ENSG00000124588	ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T	0.09911	2.93;2.93;3.13;3.13;3.13;3.13;3.13	5.65	4.44	0.53790	Flavodoxin-like fold (1);	0.611219	0.18193	N	0.148752	T	0.14917	0.0360	M	0.67569	2.06	0.09310	N	1	B;D	0.64830	0.194;0.994	B;P	0.61328	0.18;0.887	T	0.02610	-1.1134	9	.	.	.	-26.746	10.8835	0.46953	0.8606:0.0:0.0:0.1394	.	74;121	P16083;Q59EN2	NQO2_HUMAN;.	G	74;121;74;74;74;74;74;74	ENSP00000369839:E74G;ENSP00000380829:E74G;ENSP00000337773:E74G;ENSP00000369806:E74G;ENSP00000369822:E74G;ENSP00000369821:E74G;ENSP00000369795:E74G	.	E	+	2	0	NQO2	2957825	0.000000	0.05858	0.961000	0.40146	0.286000	0.27126	0.457000	0.21875	2.149000	0.67028	0.533000	0.62120	GAA		0.473	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1			G	3012826	A	G	3012826	3	3	77	1	0	0	0	0	1	0	0	0	10643	246	9	4	231	4	NQO2	6	3012826	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10		3012826	168102241	358	22094										
TUBB2A	7280	broad.mit.edu	37	chr6	3154186	3154186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggtactcggacaccaggtCgttcatgttgctctcggcct	11	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:3154186C>T	ENST00000333628.3	-	4	1311	c.1249G>A	c.(1249-1251)Gac>Aac	p.D417N	TUBB2A_ENST00000489942.1_5'Flank|RP1-40E16.11_ENST00000447644.1_RNA	NM_001069.2	NP_001060.1	Q13885	TBB2A_HUMAN	tubulin, beta 2A class IIa	417					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.D417N(1)		endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				GACACCAGGTCGTTCATGTTG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											75	63	68					6																	3154186		2202	4279	6481	3099185	SO:0001583	missense	7280			AY159127	CCDS4484.1	6p25.2	2012-10-02	2011-10-10	2005-11-03	ENSG00000137267	ENSG00000137267		"Tubulins"	12412	protein-coding gene	gene with protein product	"class IIa beta-tubulin"	615101	"tubulin, beta polypeptide", "tubulin, beta 2", "tubulin, beta 2A"	TUBB, TUBB2		14574404	Standard	NM_001069		Approved	dJ40E16.7	uc003mvc.3	Q13885	OTTHUMG00000014135	ENST00000333628.3:c.1249G>A	6.37:g.3154186C>T	ENSP00000369703:p.Asp417Asn		3099185	Q6FGZ8|Q8IWR2	Missense_Mutation	SNP	ENST00000333628.3	37	CCDS4484.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.687240	0.68157	.	.	ENSG00000137267	ENST00000333628;ENST00000392362	T	0.72835	-0.69	4.96	4.96	0.65561	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.56097	U	0.000024	D	0.83128	0.5187	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	P;D;D	0.87578	0.744;0.998;0.998	D	0.85570	0.1233	10	0.87932	D	0	.	18.563	0.91107	0.0:1.0:0.0:0.0	.	417;417;417	B2R6L0;Q13885;Q8N6N5	.;TBB2A_HUMAN;.	N	417;327	ENSP00000369703:D417N	ENSP00000369703:D417N	D	-	1	0	TUBB2A	3099185	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.662000	0.83803	2.468000	0.83385	0.555000	0.69702	GAC		0.612	TUBB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039662.1	NM_001069		T	3154186	C	T	3154186	3	4	77	1	0	0	0	0	1	0	0	0	16794	884	31	1	92	1	TUBB2A	6	3154186	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	141360	3154186	167960881	359	22095										
FAM50B	26240	broad.mit.edu	37	chr6	3850707	3850707	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaaggcgctgcaggggctgcGcaaggacttcctggagctgc	17	11	0	0	rs369953711		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:3850707G>A	ENST00000380274.1	+	1	1088	c.662G>A	c.(661-663)cGc>cAc	p.R221H	FAM50B_ENST00000380272.3_Missense_Mutation_p.R221H			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	221						nucleus (GO:0005634)		p.R221H(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				CAGGGGCTGCGCAAGGACTTC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	HIS/ARG	0,4406		0,0,2203	42	43	43		662	4.9	1	6		43	1,8597	1.2+/-3.3	0,1,4298	no	missense	FAM50B	NM_012135.1	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	221/326	3850707	1,13003	2203	4299	6502	3795706	SO:0001583	missense	26240			Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.662G>A	6.37:g.3850707G>A	ENSP00000369627:p.Arg221His		3795706	Q5T2L6	Missense_Mutation	SNP	ENST00000380274.1	37	CCDS4487.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153547	0.94645	0.0	1.16E-4	ENSG00000145945	ENST00000380274;ENST00000380272	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.76162	0.3949	M	0.84219	2.685	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.77273	-0.2649	9	0.44086	T	0.13	-24.3921	15.9418	0.79758	0.0:0.0:1.0:0.0	.	221	Q9Y247	FA50B_HUMAN	H	221	.	ENSP00000369625:R221H	R	+	2	0	FAM50B	3795706	1.000000	0.71417	0.980000	0.43619	0.995000	0.86356	4.327000	0.59247	2.430000	0.82344	0.555000	0.69702	CGC		0.642	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1	NM_012135		A	3850707	G	A	3850707	3	1	77	1	0	0	0	0	1	0	0	0	5597	1087	38	1	664	1	FAM50B	6	3850707	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	696521	3850707	167264360	360	22096										
GMPR	2766	broad.mit.edu	37	chr6	16286037	16286037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgaaggatggaggctgtaCgtgtccaggggatgtcgcca	17	7	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:16286037C>T	ENST00000259727.4	+	7	782	c.668C>T	c.(667-669)aCg>aTg	p.T223M		NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	223					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)	p.T223R(1)|p.T223M(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				GGAGGCTGTACGTGTCCAGGG	0.612											OREG0017214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											91	66	74					6																	16286037		2203	4300	6503	16394016	SO:0001583	missense	2766				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.668C>T	6.37:g.16286037C>T	ENSP00000259727:p.Thr223Met	709	16394016	Q96HQ6	Missense_Mutation	SNP	ENST00000259727.4	37	CCDS4537.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.907475	0.52333	.	.	ENSG00000137198	ENST00000259727	T	0.79033	-1.23	4.9	4.9	0.64082	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.087292	0.85682	D	0.000000	D	0.86280	0.5895	M	0.91920	3.255	0.42701	D	0.993615	D	0.71674	0.998	P	0.60415	0.874	D	0.88813	0.3293	10	0.72032	D	0.01	-2.5393	12.5921	0.56449	0.0:0.6937:0.3063:0.0	.	223	P36959	GMPR1_HUMAN	M	223	ENSP00000259727:T223M	ENSP00000259727:T223M	T	+	2	0	GMPR	16394016	0.993000	0.37304	0.968000	0.41197	0.581000	0.36288	2.425000	0.44723	2.547000	0.85894	0.655000	0.94253	ACG		0.612	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2			T	16286037	C	T	16286037	3	4	77	1	0	0	0	0	1	0	0	0	6516	536	19	1	694	1	GMPR	6	16286037	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	12435330	16286037	154829030	361	22097										
ATXN1	6310	broad.mit.edu	37	chr6	16327059	16327059	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgcttccatgtcagtgctgcCgaccgggatgagcaggggct	15	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:16327059C>T	ENST00000244769.4	-	8	2419	c.1483G>A	c.(1483-1485)Ggc>Agc	p.G495S	ATXN1_ENST00000436367.1_Missense_Mutation_p.G495S	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	495	Self-association.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.G495S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				TCAGTGCTGCCGACCGGGATG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	6											73	87	82					6																	16327059		2203	4300	6503	16435038	SO:0001583	missense	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1483G>A	6.37:g.16327059C>T	ENSP00000244769:p.Gly495Ser		16435038	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.413395	0.25465	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.73363	-0.74;-0.74	4.86	4.86	0.63082	.	0.044341	0.85682	D	0.000000	T	0.65417	0.2689	N	0.08118	0	0.49915	D	0.999831	D	0.89917	1.0	D	0.91635	0.999	T	0.68051	-0.5511	10	0.21014	T	0.42	-21.5975	17.9977	0.89189	0.0:1.0:0.0:0.0	.	495	P54253	ATX1_HUMAN	S	495	ENSP00000244769:G495S;ENSP00000416360:G495S	ENSP00000244769:G495S	G	-	1	0	ATXN1	16435038	1.000000	0.71417	0.467000	0.27180	0.766000	0.43426	5.639000	0.67868	2.241000	0.73720	0.561000	0.74099	GGC		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		T	16327059	C	T	16327059	3	4	77	1	0	0	0	0	1	0	0	0	1210	652	23	1	972	1	ATXN1	6	16327059	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	41022	16327059	154788008	362	22098										
ATXN1	6310	broad.mit.edu	37	chr6	16327462	16327462	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggctcgggtggaccaccacGtgcctggactcgtacgggtg	17	12	0	0	rs199716501		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:16327462G>A	ENST00000244769.4	-	8	2016	c.1080C>T	c.(1078-1080)caC>caT	p.H360H	ATXN1_ENST00000436367.1_Silent_p.H360H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	360					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H360H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GGACCACCACGTGCCTGGACT	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	0,4406		0,0,2203	76	86	82		1080,1080	-1.2	1	6		82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATXN1	NM_000332.3,NM_001128164.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	360/816,360/816	16327462	1,13005	2203	4300	6503	16435441	SO:0001819	synonymous_variant	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1080C>T	6.37:g.16327462G>A			16435441	Q17S02|Q9UJG2|Q9Y4J1	Silent	SNP	ENST00000244769.4	37	CCDS34342.1																																																																																				0.677	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327462	G	A	16327462	2	1	77	1	0	0	0	0	0	0	0	1	1210	1136	40	1		1	ATXN1	6	16327462	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	403	16327462	154787605	363	22099										
KIF13A	63971	broad.mit.edu	37	chr6	17834270	17834270	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcagcttttcagactcttcGagcttctccttcagttcagg	7	12	6	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:17834270G>A	ENST00000259711.6	-	12	1293	c.1188C>T	c.(1186-1188)ctC>ctT	p.L396L	KIF13A_ENST00000378826.2_Silent_p.L396L|KIF13A_ENST00000378843.2_Silent_p.L396L|KIF13A_ENST00000378816.5_Silent_p.L396L|KIF13A_ENST00000378814.5_Silent_p.L396L	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	396					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L396L(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CAGACTCTTCGAGCTTCTCCT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	6											113	101	104					6																	17834270		1822	4077	5899	17942249	SO:0001819	synonymous_variant	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1188C>T	6.37:g.17834270G>A			17942249	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																				0.383	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17834270	G	A	17834270	2	1	77	1	0	0	0	0	0	0	0	1	8295	1045	37	1		1	KIF13A	6	17834270	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1506808	17834270	153280797	364	22100										
BTN3A1	11119	broad.mit.edu	37	chr6	26409843	26409843	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgctgcttcttgggggagcCggttacttcctgtggcaaca	13	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:26409843C>T	ENST00000289361.6	+	5	1166	c.798C>T	c.(796-798)gcC>gcT	p.A266A	BTN3A1_ENST00000425234.2_Silent_p.A266A|BTN3A1_ENST00000414912.2_Silent_p.A214A|BTN3A1_ENST00000476549.2_Silent_p.A266A	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	266					activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A266A(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						TTGGGGGAGCCGGTTACTTCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	6											63	70	68					6																	26409843		2203	4300	6503	26517822	SO:0001819	synonymous_variant	11119			U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.798C>T	6.37:g.26409843C>T			26517822	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Silent	SNP	ENST00000289361.6	37	CCDS4608.1																																																																																				0.552	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			T	26409843	C	T	26409843	2	4	77	1	0	0	0	0	0	0	0	1	1565	639	23	1		1	BTN3A1	6	26409843	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8575573	26409843	144705224	365	22101										
C6orf134	79969	broad.mit.edu	37	chr6	30610756	30610757	+	Frame_Shift_Ins	INS	-	-	G													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctgttggctgctgaccctINSgggggcagcccagctcaacg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:30610756_30610757insG	ENST00000376485.4	+	10	966_967	c.936_937insG	c.(937-939)gggfs	p.G313fs	ATAT1_ENST00000468713.1_Intron|ATAT1_ENST00000330083.5_Frame_Shift_Ins_p.G301fs|ATAT1_ENST00000376483.4_Frame_Shift_Ins_p.G313fs|ATAT1_ENST00000318999.7_Frame_Shift_Ins_p.G290fs|ATAT1_ENST00000319027.5_Frame_Shift_Ins_p.G290fs|ATAT1_ENST00000329992.8_Frame_Shift_Ins_p.G313fs|ATAT1_ENST00000376478.2_Frame_Shift_Ins_p.G290fs					alpha tubulin acetyltransferase 1									p.S315fs*>10(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	9						CTGCTGACCCTGGGGGCAGCCC	0.604																																																1	Insertion - Frameshift(1)	large_intestine(1)	6																																								30718736	SO:0001589	frameshift_variant	79969			AK023220	CCDS4683.2, CCDS54978.1, CCDS59002.1	6p21.32	2014-06-17	2010-10-11	2010-10-11	ENSG00000137343	ENSG00000137343	2.3.1.108		21186	protein-coding gene	gene with protein product	"alpha-tubulin N-acetyltransferase"	615556	"chromosome 6 open reading frame 134"	C6orf134		20829795	Standard	NM_024909		Approved	FLJ13158, Em:AB023049.7, MEC17	uc003nqv.3	Q5SQI0	OTTHUMG00000031219	ENST00000376485.4:c.941dupG	6.37:g.30610761_30610761dupG	ENSP00000365668:p.Gly313fs		30718735		Frame_Shift_Ins	INS	ENST00000376485.4	37																																																																																					0.604	ATAT1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076449.2	NM_024909		G	30610757	-	G	30610756	7	5	77	1	0	1	1	0	0	0	0	0	2336	1567	55	0	974	0	C6orf134	6	30610756	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	4200913	30610756	140504311	366	22102										
TUBB	203068	broad.mit.edu	37	chr6	30691451	30691451	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagacctattgcattgacaaCgaggccctctatgatatctg	9	10	2	3	rs141142574		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:30691451C>T	ENST00000327892.8	+	4	918	c.612C>T	c.(610-612)aaC>aaT	p.N204N	TUBB_ENST00000330914.3_Silent_p.N132N|TUBB_ENST00000396389.1_Silent_p.N186N|XXbac-BPG252P9.9_ENST00000607476.1_RNA|TUBB_ENST00000396384.1_Silent_p.N132N|TUBB_ENST00000435534.1_Intron	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	204					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.N204N(1)		breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	GCATTGACAACGAGGCCCTCT	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	6						C		2,4404	4.2+/-10.8	0,2,2201	98	88	92		612	-1.1	1	6	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TUBB	NM_178014.2		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		204/445	30691451	3,13003	2203	4300	6503	30799430	SO:0001819	synonymous_variant	203068			AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"Tubulins"	20778	protein-coding gene	gene with protein product	"class I beta-tubulin", "beta1-tubulin"	191130	"tubulin, beta polypeptide", "tubulin, beta"			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.612C>T	6.37:g.30691451C>T			30799430	P05218|Q8WUC1|Q9CY33	Silent	SNP	ENST00000327892.8	37	CCDS4687.1																																																																																				0.527	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014		T	30691451	C	T	30691451	2	4	77	1	0	0	0	0	0	0	0	1	16792	535	19	1		1	TUBB	6	30691451	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	80695	30691451	140423616	367	22103										
BAT5	7920	broad.mit.edu	37	chr6	31655018	31655018	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagggcatctggaagttctGggctgggagtggggtgcagt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:31655018delG	ENST00000395952.3	-	20	1810	c.1648delC	c.(1648-1650)cagfs	p.Q550fs	XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000375842.4_Frame_Shift_Del_p.Q331fs|ABHD16A_ENST00000471644.1_5'Flank|ABHD16A_ENST00000440843.2_Frame_Shift_Del_p.Q517fs	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	550						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.Q550fs*>9(1)		endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						TGGAAGTTCTGGGCTGGGAGT	0.547																																																1	Deletion - Frameshift(1)	large_intestine(1)	6											91	62	72					6																	31655018		1511	2709	4220	31762997	SO:0001589	frameshift_variant	7920			AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1648delC	6.37:g.31655018delG	ENSP00000379282:p.Gln550fs		31762997	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Frame_Shift_Del	DEL	ENST00000395952.3	37	CCDS4713.1																																																																																				0.547	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			-	31655018	G	-	31655018	7	5	77	1	0	1	0	1	0	0	0	0	1325	1357	47	0	32	0	BAT5	6	31655018	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	963567	31655018	139460049	368	22104										
EHMT2	10919	broad.mit.edu	37	chr6	31854575	31854575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctatagacacagccaccacGctgcaccatgtaacgggcta	9	14	0	1	rs144112397		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:31854575G>A	ENST00000375537.4	-	17	2224	c.2218C>T	c.(2218-2220)Cgt>Tgt	p.R740C	EHMT2_ENST00000375530.4_Missense_Mutation_p.R706C|EHMT2_ENST00000395728.3_Missense_Mutation_p.R797C|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Missense_Mutation_p.R763C|EHMT2-AS1_ENST00000434689.1_RNA	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	740					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)	p.R740C(1)		central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						CAGCCACCACGCTGCACCATG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	6						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	137	122	127		2218,2116	4.5	1	6	dbSNP_134	127	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EHMT2	NM_006709.3,NM_025256.5	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	740/1211,706/1177	31854575	1,13005	2203	4300	6503	31962554	SO:0001583	missense	10919			AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.2218C>T	6.37:g.31854575G>A	ENSP00000364687:p.Arg740Cys		31962554	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.74|11.74	1.727740|1.727740	0.30593|0.30593	0.0|0.0	1.16E-4|1.16E-4	ENSG00000204371|ENSG00000204371	ENST00000436026|ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	.|T;T;T;T	.|0.65732	.|-0.17;-0.17;-0.17;-0.17	5.36|5.36	4.48|4.48	0.54585|0.54585	.|Ankyrin repeat-containing domain (3);	.|0.323123	.|0.33477	.|N	.|0.004877	T|T	0.24890|0.24890	0.0604|0.0604	N|N	0.20328|0.20328	0.56|0.56	0.37446|0.37446	D|D	0.914631|0.914631	.|B;B;B;B	.|0.25441	.|0.126;0.026;0.003;0.001	.|B;B;B;B	.|0.26517	.|0.07;0.042;0.009;0.005	T|T	0.10086|0.10086	-1.0645|-1.0645	5|10	.|0.33940	.|T	.|0.23	.|.	5.5415|5.5415	0.17041|0.17041	0.166:0.0:0.6748:0.1591|0.166:0.0:0.6748:0.1591	.|.	.|763;706;740;554	.|A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.|.;.;EHMT2_HUMAN;.	V|C	57|797;763;706;740;554	.|ENSP00000379078:R797C;ENSP00000364678:R763C;ENSP00000364680:R706C;ENSP00000364687:R740C	.|ENSP00000364678:R763C	A|R	-|-	2|1	0|0	EHMT2|EHMT2	31962554|31962554	0.322000|0.322000	0.24634|0.24634	0.953000|0.953000	0.39169|0.39169	0.932000|0.932000	0.56968|0.56968	0.869000|0.869000	0.27996|0.27996	1.209000|1.209000	0.43321|0.43321	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.617	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31854575	G	A	31854575	3	1	77	1	0	0	0	0	1	0	0	0	4995	1087	38	1	1462	1	EHMT2	6	31854575	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	199557	31854575	139260492	369	22105										
HLA-DQB1	3119	broad.mit.edu	37	chr6	32629870	32629870	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagtcaccattcctaataaGgggggtggacacaacgccgg					rs9273971		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:32629870delG	ENST00000399082.3	-	2	309	c.265delC	c.(265-267)cttfs	p.L89fs	HLA-DQB1_ENST00000434651.2_Frame_Shift_Del_p.L179fs|HLA-DQB1_ENST00000399084.1_Frame_Shift_Del_p.L179fs|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000374943.4_Frame_Shift_Del_p.L179fs|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000399079.3_Frame_Shift_Del_p.L179fs			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	179	Beta-1.		D -> A (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:04, allele DQB1*03:05, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:14, allele DQB1*03:18 and allele DQB1*06:29; dbSNP:rs1071637).|D -> S (in allele DQB1*05:02, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:10 and allele DQB1*06:25; requires 2 nucleotide substitutions).|D -> V (in allele DQB1*05:01, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:27, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:38 and allele DQB1*06:39).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.I180fs*12(1)		breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""Insulin(DB00071)"	TTCCTAATAAGGGGGGTGGAC	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												Esophageal Squamous(151;720 1825 15000 40336 43415)											1	Deletion - Frameshift(1)	large_intestine(1)	6											52	56	55					6																	32629870		2197	4299	6496	32737848	SO:0001589	frameshift_variant	3119	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.265delC	6.37:g.32629870delG	ENSP00000382032:p.Leu89fs		32737848	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Frame_Shift_Del	DEL	ENST00000399082.3	37																																																																																					0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123		-	32629870	G	-	32629870	7	5	77	1	0	1	0	1	0	0	0	0	7227	1000	35	0	262	0	HLA-DQB1	6	32629870	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	775295	32629870	138485197	370	22106										
SLC39A7	7922	broad.mit.edu	37	chr6	33171324	33171324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttctgcccatcaggcgatgCgtctgcaactactgacagca	9	13	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:33171324C>T	ENST00000374677.3	+	7	1517	c.1144C>T	c.(1144-1146)Cgt>Tgt	p.R382C	RXRB_ENST00000413614.2_5'Flank|SLC39A7_ENST00000463972.1_3'UTR|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000374685.4_5'Flank|HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.R382C|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	382					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)	p.R382C(2)		NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TCAGGCGATGCGTCTGCAACT	0.527																																																2	Substitution - Missense(2)	large_intestine(2)	6											65	64	64					6																	33171324		1986	4149	6135	33279302	SO:0001583	missense	7922			AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1144C>T	6.37:g.33171324C>T	ENSP00000363809:p.Arg382Cys		33279302	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	37	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.462329	0.26248	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.48522	0.81;0.81	4.96	4.09	0.47781	.	0.319926	0.31290	N	0.007919	T	0.13157	0.0319	N	0.16166	0.38	0.45066	D	0.998087	B;B	0.18863	0.031;0.03	B;B	0.18561	0.022;0.004	T	0.06023	-1.0850	10	0.38643	T	0.18	-8.6378	6.23	0.20730	0.1829:0.7239:0.0:0.0932	.	363;382	B4DVK8;Q92504	.;S39A7_HUMAN	C	382;363;287;382	ENSP00000363807:R382C;ENSP00000363809:R382C	ENSP00000363807:R382C	R	+	1	0	SLC39A7	33279302	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	1.272000	0.33109	1.316000	0.45131	0.549000	0.68633	CGT		0.527	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		T	33171324	C	T	33171324	3	4	77	1	0	0	0	0	1	0	0	0	14660	768	27	1	1170	1	SLC39A7	6	33171324	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	541454	33171324	137943743	371	22107										
ITPR3	3710	broad.mit.edu	37	chr6	33657104	33657104	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaccaagcgctacagcatcCgccccctcatcgtggcgctc	8	19	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:33657104C>T	ENST00000374316.5	+	51	7844	c.6784C>T	c.(6784-6786)Cgc>Tgc	p.R2262C	ITPR3_ENST00000605930.1_Missense_Mutation_p.R2262C			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2262					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.R2262C(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTACAGCATCCGCCCCCTCAT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	6											140	118	125					6																	33657104		2203	4300	6503	33765082	SO:0001583	missense	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6784C>T	6.37:g.33657104C>T	ENSP00000363435:p.Arg2262Cys		33765082	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320049	0.81469	.	.	ENSG00000096433	ENST00000374316	D	0.92348	-3.02	5.31	5.31	0.75309	.	0.107756	0.64402	D	0.000005	D	0.94984	0.8377	M	0.82517	2.595	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;P	0.67725	0.953;0.88	D	0.95094	0.8224	10	0.87932	D	0	-28.6017	11.873	0.52531	0.2908:0.7092:0.0:0.0	.	2262;1932	Q14573;Q59ES2	ITPR3_HUMAN;.	C	2262	ENSP00000363435:R2262C	ENSP00000363435:R2262C	R	+	1	0	ITPR3	33765082	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.611000	0.54132	2.768000	0.95171	0.561000	0.74099	CGC		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33657104	C	T	33657104	3	4	77	1	0	0	0	0	1	0	0	0	7943	652	23	1	6982	1	ITPR3	6	33657104	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	485780	33657104	137457963	372	22108										
PACSIN1	29993	broad.mit.edu	37	chr6	34496557	34496557	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagaactggcagaaggacgCctatcacaagcagatcatgg	12	9	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:34496557C>T	ENST00000538621.1	+	4	604	c.359C>T	c.(358-360)gCc>gTc	p.A120V	PACSIN1_ENST00000374043.2_Missense_Mutation_p.A78V|PACSIN1_ENST00000486120.1_3'UTR|PACSIN1_ENST00000244458.2_Missense_Mutation_p.A120V	NM_001199583.2	NP_001186512.1	Q9BY11	PACN1_HUMAN	protein kinase C and casein kinase substrate in neurons 1	120	F-BAR domain.				actin filament organization (GO:0007015)|establishment of protein localization to plasma membrane (GO:0090002)|membrane tubulation (GO:0097320)|neuron projection morphogenesis (GO:0048812)|positive regulation of dendrite development (GO:1900006)|protein localization to membrane (GO:0072657)|synaptic vesicle endocytosis (GO:0048488)	axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	phospholipid binding (GO:0005543)	p.A120V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	13						CAGAAGGACGCCTATCACAAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	6											178	160	166					6																	34496557		2203	4300	6503	34604535	SO:0001583	missense	29993			AB037800	CCDS4793.1	6p21.3	2008-02-05			ENSG00000124507	ENSG00000124507			8570	protein-coding gene	gene with protein product	"syndapin I"	606512				11179684	Standard	NM_020804		Approved	SDPI	uc003ojp.4	Q9BY11	OTTHUMG00000014547	ENST00000538621.1:c.359C>T	6.37:g.34496557C>T	ENSP00000439639:p.Ala120Val		34604535	Q9P2G8	Missense_Mutation	SNP	ENST00000538621.1	37	CCDS4793.1	.	.	.	.	.	.	.	.	.	.	c	17.62	3.435513	0.62955	.	.	ENSG00000124507	ENST00000244458;ENST00000374043;ENST00000436831;ENST00000538621	T;T;T	0.54866	0.73;0.55;0.73	4.05	4.05	0.47172	.	0.464724	0.22716	N	0.056510	T	0.29914	0.0748	M	0.82630	2.6	0.58432	D	0.999999	P	0.46457	0.878	B	0.25405	0.06	T	0.33445	-0.9868	10	0.15952	T	0.53	-7.2376	12.3349	0.55060	0.0:0.8292:0.1708:0.0	.	120	Q9BY11	PACN1_HUMAN	V	120;78;120;120	ENSP00000244458:A120V;ENSP00000363155:A78V;ENSP00000439639:A120V	ENSP00000244458:A120V	A	+	2	0	PACSIN1	34604535	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	4.743000	0.62110	2.253000	0.74438	0.450000	0.29827	GCC		0.537	PACSIN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040236.1			T	34496557	C	T	34496557	3	4	77	1	0	0	0	0	1	0	0	0	11405	739	26	3	369	3	PACSIN1	6	34496557	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	839453	34496557	136618510	373	22109										
SRPK1	6732	broad.mit.edu	37	chr6	35837473	35837473	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgctgtctccattttgggaGcttaggaaactagattcctg	10	9	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:35837473G>T	ENST00000373825.2	-	11	1482	c.1197C>A	c.(1195-1197)agC>agA	p.S399R	SRPK1_ENST00000373822.1_Missense_Mutation_p.S292R|SRPK1_ENST00000423325.2_Missense_Mutation_p.S383R					SRSF protein kinase 1									p.S399R(1)		endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CATTTTGGGAGCTTAGGAAAC	0.403																																					NSCLC(31;67 978 16289 24856 26454)											1	Substitution - Missense(1)	large_intestine(1)	6											149	141	143					6																	35837473		1947	4137	6084	35945451	SO:0001583	missense	6732			U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"SR protein kinase 1", "serine/arginine-rich splicing factor kinase 1"	601939	"SFRS protein kinase 1"			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1197C>A	6.37:g.35837473G>T	ENSP00000362931:p.Ser399Arg		35945451		Missense_Mutation	SNP	ENST00000373825.2	37	CCDS47415.1	.	.	.	.	.	.	.	.	.	.	G	8.950	0.967959	0.18659	.	.	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822;ENST00000510290	T;T;T;T	0.27890	1.64;1.64;1.64;1.69	5.66	2.89	0.33648	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.08891	0.0220	L	0.32530	0.975	0.37236	D	0.905891	B;B	0.17667	0.0;0.023	B;B	0.20767	0.003;0.031	T	0.11227	-1.0596	9	0.21014	T	0.42	0.0022	8.9517	0.35792	0.306:0.0:0.694:0.0	.	383;399	B4DS61;Q96SB4	.;SRPK1_HUMAN	R	399;415;383;292;137	ENSP00000362931:S399R;ENSP00000354674:S415R;ENSP00000391069:S383R;ENSP00000362928:S292R	ENSP00000354674:S415R	S	-	3	2	SRPK1	35945451	0.552000	0.26505	0.905000	0.35620	0.986000	0.74619	0.581000	0.23819	0.408000	0.25621	-0.140000	0.14226	AGC		0.403	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137		T	35837473	G	T	35837473	3	4	77	1	0	0	0	0	1	0	0	0	15198	962	34	2	794	2	SRPK1	6	35837473	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1340916	35837473	135277594	374	22110										
KCTD20	222658	broad.mit.edu	37	chr6	36452576	36452576	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgttaaaggaacggggcctAaaaaacattcgcattggaat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:36452576delA	ENST00000373731.2	+	7	1333	c.942delA	c.(940-942)ctafs	p.L314fs	KCTD20_ENST00000449081.2_Frame_Shift_Del_p.L148fs|KCTD20_ENST00000544295.1_Frame_Shift_Del_p.L68fs|KCTD20_ENST00000536244.1_Frame_Shift_Del_p.L169fs|KCTD20_ENST00000474988.1_3'UTR	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	314					protein homooligomerization (GO:0051260)			p.N316fs*64(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						AACGGGGCCTAAAAAACATTC	0.343																																																2	Deletion - Frameshift(2)	large_intestine(2)	6											103	115	111					6																	36452576		2203	4300	6503	36560554	SO:0001589	frameshift_variant	222658			BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.942delA	6.37:g.36452576delA	ENSP00000362836:p.Leu314fs		36560554	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Frame_Shift_Del	DEL	ENST00000373731.2	37	CCDS4821.1																																																																																				0.343	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		-	36452576	A	-	36452576	7	5	77	1	0	1	0	1	0	0	0	0	8129	349	13	0	964	0	KCTD20	6	36452576	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	615103	36452576	134662491	375	22111										
PGC	5225	broad.mit.edu	37	chr6	41712186	41712186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacccacaagttggaggagcCggtgtcaaaaaggaccagga	13	10	1	0	rs531970409		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:41712186C>T	ENST00000373025.3	-	3	339	c.277G>A	c.(277-279)Ggc>Agc	p.G93S	PGC_ENST00000425343.2_Missense_Mutation_p.G93S	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	93					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)	p.G93S(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TTGGAGGAGCCGGTGTCAAAA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	71	71					6																	41712186		2203	4300	6503	41820164	SO:0001583	missense	5225				CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.277G>A	6.37:g.41712186C>T	ENSP00000362116:p.Gly93Ser		41820164	B4DVZ3|Q5T3D7|Q5T3D8	Missense_Mutation	SNP	ENST00000373025.3	37	CCDS4859.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.032606	0.75504	.	.	ENSG00000096088	ENST00000373025;ENST00000394278;ENST00000425343	D;D	0.85861	-2.04;-2.04	4.79	4.79	0.61399	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.95645	0.8584	H	0.98849	4.35	0.58432	D	0.999993	D	0.89917	1.0	D	0.91635	0.999	D	0.97473	1.0042	10	0.87932	D	0	.	17.6692	0.88212	0.0:1.0:0.0:0.0	.	93	P20142	PEPC_HUMAN	S	93	ENSP00000362116:G93S;ENSP00000405094:G93S	ENSP00000362116:G93S	G	-	1	0	PGC	41820164	1.000000	0.71417	0.908000	0.35775	0.127000	0.20565	5.365000	0.66116	2.523000	0.85059	0.585000	0.79938	GGC		0.607	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			T	41712186	C	T	41712186	3	4	77	1	0	0	0	0	1	0	0	0	11816	652	23	1	1226	1	PGC	6	41712186	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5259610	41712186	129402881	376	22112										
GUCA1B	2979	broad.mit.edu	37	chr6	42152642	42152642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcatcacccacttgtcccGacgggcaccttcaacaaact	5	17	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:42152642G>A	ENST00000230361.3	-	4	609	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	172	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.R172W(1)		large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			CACTTGTCCCGACGGGCACCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	100	104					6																	42152642		2203	4300	6503	42260620	SO:0001583	missense	2979			AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"EF-hand domain containing"	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.514C>T	6.37:g.42152642G>A	ENSP00000230361:p.Arg172Trp		42260620	Q9NU15	Missense_Mutation	SNP	ENST00000230361.3	37	CCDS4865.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.351930	0.61183	.	.	ENSG00000112599	ENST00000230361;ENST00000372949	T	0.56611	0.45	4.12	4.12	0.48240	EF-hand-like domain (1);	0.100234	0.64402	D	0.000008	T	0.60248	0.2254	M	0.78049	2.395	0.30353	N	0.784584	D	0.89917	1.0	D	0.68621	0.959	T	0.59225	-0.7494	10	0.87932	D	0	.	9.9683	0.41738	0.0:0.0:0.7968:0.2032	.	172	Q9UMX6	GUC1B_HUMAN	W	172;164	ENSP00000230361:R172W	ENSP00000230361:R172W	R	-	1	2	GUCA1B	42260620	1.000000	0.71417	0.889000	0.34880	0.979000	0.70002	2.904000	0.48719	2.243000	0.73865	0.655000	0.94253	CGG		0.582	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098		A	42152642	G	A	42152642	3	1	77	1	0	0	0	0	1	0	0	0	6910	1057	37	1	92	1	GUCA1B	6	42152642	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	440456	42152642	128962425	377	22113										
CUL9	23113	broad.mit.edu	37	chr6	43184152	43184152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accaggctcaggctgtacccGtacggcctgaccactgcccc	10	18	1	1	rs375119455		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:43184152G>A	ENST00000252050.4	+	31	6277	c.6193G>A	c.(6193-6195)Gta>Ata	p.V2065I	CUL9_ENST00000372647.2_Missense_Mutation_p.V2037I|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Missense_Mutation_p.V1955I	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2065					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.V2065I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGCTGTACCCGTACGGCCTGA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	80	82					6																	43184152		2203	4300	6503	43292130	SO:0001583	missense	23113			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.6193G>A	6.37:g.43184152G>A	ENSP00000252050:p.Val2065Ile		43292130	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	9.279	1.047766	0.19827	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.03860	3.78;3.78;3.78	5.7	-11.4	0.00090	.	1.039970	0.07498	N	0.906760	T	0.00936	0.0031	N	0.24115	0.695	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.06405	0.002;0.001;0.001	T	0.49570	-0.8926	10	0.51188	T	0.08	4.3901	10.6312	0.45538	0.1403:0.1175:0.664:0.0782	.	1955;2037;2065	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	I	2065;1955;2037	ENSP00000252050:V2065I;ENSP00000346490:V1955I;ENSP00000361730:V2037I	ENSP00000252050:V2065I	V	+	1	0	CUL9	43292130	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.244000	0.02902	-2.105000	0.00842	-0.302000	0.09304	GTA		0.642	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43184152	G	A	43184152	3	1	77	1	0	0	0	0	1	0	0	0	4067	1145	40	1	6311	1	CUL9	6	43184152	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1031510	43184152	127930915	378	22114										
CLIC5	53405	broad.mit.edu	37	chr6	45870842	45870842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgctcaggatcggctgaggcGtttggcgacatcagcgtagg	16	9	2	1	rs202022202		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:45870842G>A	ENST00000185206.6	-	6	1368	c.1216C>T	c.(1216-1218)Cgc>Tgc	p.R406C	CLIC5_ENST00000339561.6_Missense_Mutation_p.R247C	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	406					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)	p.R247C(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						CGGCTGAGGCGTTTGGCGACA	0.562													G|||	1	0.000199681	8e-04	0	5008	,	,		18634	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	6											130	100	111					6																	45870842		2203	4300	6503	45978820	SO:0001583	missense	53405			AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"Ion channels / Chloride channels : Intracellular"	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.1216C>T	6.37:g.45870842G>A	ENSP00000185206:p.Arg406Cys		45978820	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Missense_Mutation	SNP	ENST00000185206.6	37	CCDS47438.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858920	0.71834	.	.	ENSG00000112782	ENST00000185206;ENST00000339561	D;D	0.94184	-3.37;-3.37	5.78	4.88	0.63580	Glutathione S-transferase, C-terminal-like (2);	0.000000	0.85682	D	0.000000	D	0.96482	0.8852	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.72982	0.979;0.62	D	0.96630	0.9466	10	0.87932	D	0	.	14.0814	0.64925	0.0:0.0:0.6247:0.3753	.	406;247	Q9NZA1;Q53G01	CLIC5_HUMAN;.	C	406;247	ENSP00000185206:R406C;ENSP00000344165:R247C	ENSP00000185206:R406C	R	-	1	0	CLIC5	45978820	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.802000	0.55553	2.731000	0.93534	0.637000	0.83480	CGC		0.562	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1			A	45870842	G	A	45870842	3	1	77	1	0	0	0	0	1	0	0	0	3535	1145	40	1	20	1	CLIC5	6	45870842	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2686690	45870842	125244225	379	22115										
TDRD6	221400	broad.mit.edu	37	chr6	46657764	46657764	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaagaattagtcatccatatTcttgataaacaggatcatca	5	7	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:46657764T>C	ENST00000316081.6	+	1	1899	c.1899T>C	c.(1897-1899)atT>atC	p.I633I	TDRD6_ENST00000544460.1_Silent_p.I633I|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	633					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)		p.I633I(1)		NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TCATCCATATTCTTGATAAAC	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	6											51	52	52					6																	46657764		2203	4300	6503	46765723	SO:0001819	synonymous_variant	221400			AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.1899T>C	6.37:g.46657764T>C			46765723	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Silent	SNP	ENST00000316081.6	37	CCDS34470.1																																																																																				0.398	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		C	46657764	T	C	46657764	2	2	77	1	0	0	0	0	0	0	0	1	15773	1771	62	4		4	TDRD6	6	46657764	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	786922	46657764	124457303	380	22116										
BAI3	577	broad.mit.edu	37	chr6	69665996	69665996	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggactcagcagagaagccggCagtgcactgcagctgcccat	13	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:69665996C>A	ENST00000370598.1	+	7	2097	c.1276C>A	c.(1276-1278)Cag>Aag	p.Q426K		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	426	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Q426K(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GAGAAGCCGGCAGTGCACTGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											79	71	73					6																	69665996		2203	4300	6503	69722717	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1276C>A	6.37:g.69665996C>A	ENSP00000359630:p.Gln426Lys		69722717	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.357995	0.24598	.	.	ENSG00000135298	ENST00000370598	T	0.51325	0.71	5.71	5.71	0.89125	.	0.062767	0.64402	D	0.000004	T	0.08935	0.0221	N	0.01789	-0.72	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23940	-1.0174	10	0.06236	T	0.91	.	15.3429	0.74311	0.0:0.8609:0.1391:0.0	.	426	O60242	BAI3_HUMAN	K	426	ENSP00000359630:Q426K	ENSP00000359630:Q426K	Q	+	1	0	BAI3	69722717	1.000000	0.71417	0.996000	0.52242	0.681000	0.39784	4.817000	0.62650	2.701000	0.92244	0.591000	0.81541	CAG		0.542	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69665996	C	A	69665996	3	1	77	1	0	0	0	0	1	0	0	0	1301	711	25	2	1294	2	BAI3	6	69665996	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	23008232	69665996	101449071	381	22117										
RIMS1	22999	broad.mit.edu	37	chr6	73000420	73000420	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctagaaggggacacgcagCcccaagagcaactgatcagc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:73000420delC	ENST00000521978.1	+	25	3593	c.3593delC	c.(3592-3594)gccfs	p.A1198fs	RIMS1_ENST00000425662.2_Intron|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000491071.2_Intron|RIMS1_ENST00000538414.1_Intron|RIMS1_ENST00000348717.5_Intron|RIMS1_ENST00000517960.1_Intron|RIMS1_ENST00000264839.7_Intron|RIMS1_ENST00000401910.3_Intron|RIMS1_ENST00000523963.1_Intron|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000522291.1_Intron	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1198					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.P1199fs*46(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GGACACGCAGCCCCAAGAGCA	0.468																																																1	Deletion - Frameshift(1)	large_intestine(1)	6											77	77	77					6																	73000420		1999	4184	6183	73057141	SO:0001589	frameshift_variant	22999			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3593delC	6.37:g.73000420delC	ENSP00000428417:p.Ala1198fs		73057141	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Frame_Shift_Del	DEL	ENST00000521978.1	37	CCDS47449.1																																																																																				0.468	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			-	73000420	C	-	73000420	7	5	77	1	0	1	0	1	0	0	0	0	13404	739	26	0	3854	0	RIMS1	6	73000420	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	3334424	73000420	98114647	382	22118										
C6orf221	154288	broad.mit.edu	37	chr6	74073442	74073442	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcgggacacagggttctccGgtggaggtgcaggaggccgg	20	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:74073442G>A	ENST00000370367.3	+	3	566	c.513G>A	c.(511-513)ccG>ccA	p.P171P		NM_001017361.2	NP_001017361.1	Q587J8	KHD3L_HUMAN	KH domain containing 3-like, subcortical maternal complex member	171							RNA binding (GO:0003723)	p.P171P(1)									AGGGTTCTCCGGTGGAGGTGC	0.687																																																1	Substitution - coding silent(1)	large_intestine(1)	6											31	34	33					6																	74073442		2203	4300	6503	74130163	SO:0001819	synonymous_variant	154288			AB211062	CCDS34484.1	6q13	2012-06-25	2012-06-25	2012-06-25	ENSG00000203908	ENSG00000203908			33699	protein-coding gene	gene with protein product	"ES cell associated transcript 1"	611687	"chromosome 6 open reading frame 221"	C6orf221		21885028	Standard	NM_001017361		Approved	ECAT1	uc003pgt.4	Q587J8	OTTHUMG00000015024	ENST00000370367.3:c.513G>A	6.37:g.74073442G>A			74130163	B2RNW7	Silent	SNP	ENST00000370367.3	37	CCDS34484.1																																																																																				0.687	KHDC3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041202.3	NM_001017361		A	74073442	G	A	74073442	2	1	77	1	0	0	0	0	0	0	0	1	2361	1103	39	1		1	C6orf221	6	74073442	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1073022	74073442	97041625	383	22119										
COL12A1	1303	broad.mit.edu	37	chr6	75875407	75875407	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccatgagaccctgtaaccGcgaaccattcctggagcaga	9	13	0	2	rs372499120		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:75875407G>A	ENST00000322507.8	-	14	3108	c.2799C>T	c.(2797-2799)cgC>cgT	p.R933R	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.R933R|COL12A1_ENST00000483888.2_Silent_p.R933R	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	933	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.R933R(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCCTGTAACCGCGAACCATTC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	0,3756		0,0,1878	122	114	116		2799,	-10.6	0.5	6		116	1,8209		0,1,4104	no	coding-synonymous,intron	COL12A1	NM_004370.5,NM_080645.2	,	0,1,5982	AA,AG,GG		0.0122,0.0,0.0084	,	933/3064,	75875407	1,11965	1878	4105	5983	75932127	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2799C>T	6.37:g.75875407G>A			75932127	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.413	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75875407	G	A	75875407	2	1	77	1	0	0	0	0	0	0	0	1	3675	1074	38	1		1	COL12A1	6	75875407	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1801965	75875407	95239660	384	22120										
FILIP1	27145	broad.mit.edu	37	chr6	76022318	76022318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacctgaagtcccaggggacCgtttaaactgagaccctaag	10	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:76022318C>T	ENST00000237172.7	-	5	3560	c.3230G>A	c.(3229-3231)cGg>cAg	p.R1077Q	FILIP1_ENST00000393004.2_Missense_Mutation_p.R1077Q|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Missense_Mutation_p.R978Q	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1077								p.R1077Q(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						CCCAGGGGACCGTTTAAACTG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											221	192	202					6																	76022318		2203	4300	6503	76079038	SO:0001583	missense	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3230G>A	6.37:g.76022318C>T	ENSP00000237172:p.Arg1077Gln		76079038	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	C	2.901	-0.227476	0.06022	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.16196	2.36;2.37;2.38	5.63	5.63	0.86233	.	0.125908	0.53938	D	0.000058	T	0.07683	0.0193	L	0.33485	1.01	0.41867	D	0.990252	D;B;B	0.57571	0.98;0.112;0.097	P;B;B	0.45119	0.47;0.028;0.034	T	0.03008	-1.1083	10	0.02654	T	1	-9.426	19.7021	0.96059	0.0:1.0:0.0:0.0	.	1077;1077;1077	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	Q	1077;1077;978	ENSP00000376728:R1077Q;ENSP00000237172:R1077Q;ENSP00000359037:R978Q	ENSP00000237172:R1077Q	R	-	2	0	FILIP1	76079038	1.000000	0.71417	0.999000	0.59377	0.075000	0.17131	4.793000	0.62474	2.661000	0.90470	0.655000	0.94253	CGG		0.473	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		T	76022318	C	T	76022318	3	4	77	1	0	0	0	0	1	0	0	0	5913	652	23	1	419	1	FILIP1	6	76022318	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	146911	76022318	95092749	385	22121										
MYO6	4646	broad.mit.edu	37	chr6	76596648	76596648	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgttgaaagatggaaaaccCgagatgaataaacagatcaa	10	5	1	5	rs150876010	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:76596648C>T	ENST00000369977.3	+	25	2734	c.2595C>T	c.(2593-2595)ccC>ccT	p.P865P	MYO6_ENST00000369981.3_Silent_p.P865P|MYO6_ENST00000369975.1_Silent_p.P865P|MYO6_ENST00000369985.4_Silent_p.P865P	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	865					actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.P865P(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		ATGGAAAACCCGAGATGAATA	0.333													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		16126	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						C		14,4392	21.2+/-45.6	0,14,2189	81	84	83		2595	-6.5	0.2	6	dbSNP_134	83	0,8598		0,0,4299	no	coding-synonymous	MYO6	NM_004999.3		0,14,6488	TT,TC,CC		0.0,0.3177,0.1077		865/1286	76596648	14,12990	2203	4299	6502	76653368	SO:0001819	synonymous_variant	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2595C>T	6.37:g.76596648C>T			76653368	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																				0.333	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		T	76596648	C	T	76596648	2	4	77	1	0	0	0	0	0	0	0	1	10111	639	23	1		1	MYO6	6	76596648	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	574330	76596648	94518419	386	22122										
PHIP	55023	broad.mit.edu	37	chr6	79707220	79707220	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctatttcacttcttggtgcGttgctgtgcatttgccgtac	10	10	2	0	rs144262648	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:79707220G>A	ENST00000275034.4	-	19	2279	c.2112C>T	c.(2110-2112)aaC>aaT	p.N704N		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	704					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.N704N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTCTTGGTGCGTTGCTGTGCA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	6						G		8,4398	14.3+/-33.2	0,8,2195	254	218	230		2112	-4.9	1	6	dbSNP_134	230	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	PHIP	NM_017934.5		0,8,6495	AA,AG,GG		0.0,0.1816,0.0615		704/1822	79707220	8,12998	2203	4300	6503	79763939	SO:0001819	synonymous_variant	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2112C>T	6.37:g.79707220G>A			79763939	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																				0.498	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79707220	G	A	79707220	2	1	77	1	0	0	0	0	0	0	0	1	11873	1136	40	1		1	PHIP	6	79707220	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3110572	79707220	91407847	387	22123										
TPBG	7162	broad.mit.edu	37	chr6	83075281	83075281	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcgagggcatggtggtggcGgccctgctggcgggccgtgc	20	11	0	0	rs142377093	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:83075281G>A	ENST00000369750.3	+	2	1220	c.603G>A	c.(601-603)gcG>gcA	p.A201A	TPBG_ENST00000543496.1_Silent_p.A201A|TPBG_ENST00000535040.1_Silent_p.A201A			Q13641	TPBG_HUMAN	trophoblast glycoprotein	201					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)		p.A201A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		TGGTGGTGGCGGCCCTGCTGG	0.672													G|||	3	0.000599042	0.0023	0	5008	,	,		14145	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						G	,	1,4405	2.1+/-5.4	0,1,2202	58	66	63		603,603	-5.3	0	6	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TPBG	NM_001166392.1,NM_006670.4	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	201/421,201/421	83075281	1,13005	2203	4300	6503	83132000	SO:0001819	synonymous_variant	7162			AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.603G>A	6.37:g.83075281G>A			83132000	A8K555	Silent	SNP	ENST00000369750.3	37	CCDS4995.1																																																																																				0.672	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1			A	83075281	G	A	83075281	2	1	77	1	0	0	0	0	0	0	0	1	16434	1103	39	1		1	TPBG	6	83075281	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3368061	83075281	88039786	388	22124										
C6orf165	154313	broad.mit.edu	37	chr6	88170751	88170751	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttctttagatgagagatgcTgacaaacattatataaaacc	6	7	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:88170751T>C	ENST00000507897.1	+	12	1589	c.1506T>C	c.(1504-1506)gcT>gcC	p.A502A	C6ORF165_ENST00000369562.4_Silent_p.A502A|C6orf165_ENST00000506888.1_3'UTR			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	502								p.A502A(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		TGAGAGATGCTGACAAACATT	0.308																																																1	Substitution - coding silent(1)	large_intestine(1)	6											62	57	58					6																	88170751		2203	4298	6501	88227470	SO:0001819	synonymous_variant	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1506T>C	6.37:g.88170751T>C			88227470	A8K969|E1P507|Q8N9U4	Silent	SNP	ENST00000507897.1	37	CCDS34498.1																																																																																				0.308	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		C	88170751	T	C	88170751	2	2	77	1	0	0	0	0	0	0	0	1	2347	1567	55	4		4	C6orf165	6	88170751	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	5095470	88170751	82944316	389	22125										
BACH2	60468	broad.mit.edu	37	chr6	90718449	90718449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctctccacgatcaaagtcaCgtcacagagaatatcctttt	5	13	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:90718449C>T	ENST00000257749.4	-	6	822	c.115G>A	c.(115-117)Gtg>Atg	p.V39M	BACH2_ENST00000537989.1_Missense_Mutation_p.V39M|BACH2_ENST00000343122.3_Missense_Mutation_p.V39M	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	39	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.V39M(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		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)		ATCAAAGTCACGTCACAGAGA	0.537																																																2	Substitution - Missense(2)	large_intestine(2)	6											161	152	155					6																	90718449		2203	4300	6503	90775170	SO:0001583	missense	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.115G>A	6.37:g.90718449C>T	ENSP00000257749:p.Val39Met		90775170	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	37	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.216033	0.79352	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122;ENST00000406998;ENST00000453877	T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82	5.33	5.33	0.75918	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.062988	0.64402	D	0.000006	D	0.87386	0.6164	M	0.88241	2.94	0.46774	D	0.999198	D	0.89917	1.0	D	0.77557	0.99	D	0.89463	0.3738	10	0.87932	D	0	-0.0182	19.0228	0.92921	0.0:1.0:0.0:0.0	.	39	Q9BYV9	BACH2_HUMAN	M	39	ENSP00000257749:V39M;ENSP00000437473:V39M;ENSP00000345642:V39M;ENSP00000384145:V39M;ENSP00000397668:V39M	ENSP00000257749:V39M	V	-	1	0	BACH2	90775170	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.643000	0.67895	2.507000	0.84556	0.591000	0.81541	GTG		0.537	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		T	90718449	C	T	90718449	3	4	77	1	0	0	0	0	1	0	0	0	1285	536	19	1	2426	1	BACH2	6	90718449	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2547698	90718449	80396618	390	22126										
FUT9	10690	broad.mit.edu	37	chr6	96651507	96651507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taacctgactctgacttaccGccgtgattcagatatccaag	7	12	2	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:96651507G>A	ENST00000302103.5	+	3	802	c.476G>A	c.(475-477)cGc>cAc	p.R159H		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	159					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.R159H(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		CTGACTTACCGCCGTGATTCA	0.458																																					Melanoma(98;1369 1476 6592 22940 26587)											1	Substitution - Missense(1)	large_intestine(1)	6											69	65	66					6																	96651507		2203	4300	6503	96758228	SO:0001583	missense	10690			AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.476G>A	6.37:g.96651507G>A	ENSP00000302599:p.Arg159His		96758228	Q5T0W4	Missense_Mutation	SNP	ENST00000302103.5	37	CCDS5033.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.152686	0.57259	.	.	ENSG00000172461	ENST00000302103	T	0.39997	1.05	5.3	5.3	0.74995	.	0.050188	0.85682	D	0.000000	T	0.57257	0.2041	M	0.72624	2.21	0.54753	D	0.999988	D	0.67145	0.996	D	0.66602	0.945	T	0.59757	-0.7394	10	0.62326	D	0.03	-11.0367	18.3049	0.90177	0.0:0.0:1.0:0.0	.	159	Q9Y231	FUT9_HUMAN	H	159	ENSP00000302599:R159H	ENSP00000302599:R159H	R	+	2	0	FUT9	96758228	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	7.499000	0.81566	2.643000	0.89663	0.655000	0.94253	CGC		0.458	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		A	96651507	G	A	96651507	3	1	77	1	0	0	0	0	1	0	0	0	6130	1087	38	1	478	1	FUT9	6	96651507	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5933058	96651507	74463560	391	22127										
AIM1	202	broad.mit.edu	37	chr6	106968762	106968762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgacaaagagaacagggacGtcacaaatggtggcattaag	12	6	1	2	rs368874479	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:106968762G>A	ENST00000369066.3	+	2	2942	c.2455G>A	c.(2455-2457)Gtc>Atc	p.V819I		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.V819I(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GAACAGGGACGTCACAAATGG	0.438													G|||	8	0.00159744	0	0	5008	,	,		21650	0		0	False		,,,				2504	0.0082															1	Substitution - Missense(1)	large_intestine(1)	6						G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	90	85	87		2455	-11	0	6		87	0,8600		0,0,4300	no	missense	AIM1	NM_001624.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	819/1724	106968762	1,13005	2203	4300	6503	107075455	SO:0001583	missense	202			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2455G>A	6.37:g.106968762G>A	ENSP00000358062:p.Val819Ile		107075455	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	0.034	-1.316384	0.01331	2.27E-4	0.0	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71222	-0.55	5.97	-11.0	0.00169	.	1.351790	0.04395	N	0.363074	T	0.17195	0.0413	N	0.11064	0.09	0.18873	N	0.999987	B	0.06786	0.001	B	0.01281	0.0	T	0.07654	-1.0761	10	0.05721	T	0.95	.	10.5951	0.45331	0.2858:0.0:0.5051:0.2091	.	819	Q9Y4K1	AIM1_HUMAN	I	1227;819	ENSP00000358062:V819I	ENSP00000285105:V1227I	V	+	1	0	AIM1	107075455	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.359000	0.02602	-1.773000	0.01290	-2.869000	0.00099	GTC		0.438	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106968762	G	A	106968762	3	1	77	1	0	0	0	0	1	0	0	0	430	1145	40	1	2461	1	AIM1	6	106968762	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	10317255	106968762	64146305	392	22128										
C6orf203	51250	broad.mit.edu	37	chr6	107361043	107361043	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggactctggggtgttctcCgagggacaccttcatcatac	11	11	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:107361043C>T	ENST00000405204.2	+	2	686	c.79C>T	c.(79-81)Cga>Tga	p.R27*	C6orf203_ENST00000443043.1_Nonsense_Mutation_p.R32*|C6orf203_ENST00000311381.5_Nonsense_Mutation_p.R27*	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	27						mitochondrion (GO:0005739)		p.R27*(1)		large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		GGGTGTTCTCCGAGGGACACC	0.408																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											92	94	93					6																	107361043		2203	4300	6503	107467736	SO:0001587	stop_gained	51250			AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.79C>T	6.37:g.107361043C>T	ENSP00000384867:p.Arg27*		107467736	B3KRG9	Nonsense_Mutation	SNP	ENST00000405204.2	37	CCDS5058.1	.	.	.	.	.	.	.	.	.	.	C	31	5.074783	0.94000	.	.	ENSG00000130349	ENST00000443043;ENST00000405204;ENST00000311381	.	.	.	5.56	4.62	0.57501	.	0.639657	0.13930	N	0.352966	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2162	6.7392	0.23426	0.0:0.8202:0.0:0.1798	.	.	.	.	X	32;27;27	.	ENSP00000310951:R27X	R	+	1	2	C6orf203	107467736	0.312000	0.24545	0.016000	0.15963	0.834000	0.47266	1.083000	0.30815	2.890000	0.99128	0.655000	0.94253	CGA		0.408	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487		T	107361043	C	T	107361043	4	4	77	1	0	0	0	0	0	1	0	0	2358	644	23	1	100	1	C6orf203	6	107361043	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	392281	107361043	63754024	393	22129										
FOXO3	2309	broad.mit.edu	37	chr6	108984785	108984785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggaaaagccccccggcggcGggctgtctccatggacaata	13	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:108984785G>A	ENST00000343882.6	+	3	1053	c.749G>A	c.(748-750)cGg>cAg	p.R250Q	FOXO3_ENST00000540898.1_Missense_Mutation_p.R30Q|FOXO3_ENST00000406360.1_Missense_Mutation_p.R250Q	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	250					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R250Q(1)		central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		CCCCGGCGGCGGGCTGTCTCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	6											14	17	16					6																	108984785		2193	4271	6464	109091478	SO:0001583	missense	2309			AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"Forkhead boxes"	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.749G>A	6.37:g.108984785G>A	ENSP00000339527:p.Arg250Gln		109091478	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Missense_Mutation	SNP	ENST00000343882.6	37	CCDS5068.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465291	0.84425	.	.	ENSG00000118689	ENST00000343882;ENST00000406360;ENST00000540258;ENST00000540898	D;D	0.94417	-3.42;-3.42	5.74	5.74	0.90152	Transcription factor, fork head (1);	0.000000	0.85682	D	0.000000	D	0.97420	0.9156	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96614	0.9454	10	0.46703	T	0.11	-5.5525	19.9077	0.97014	0.0:0.0:1.0:0.0	.	250	O43524	FOXO3_HUMAN	Q	250;250;30;30	ENSP00000339527:R250Q;ENSP00000385824:R250Q	ENSP00000339527:R250Q	R	+	2	0	FOXO3	109091478	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	9.448000	0.97600	2.712000	0.92718	0.561000	0.74099	CGG		0.592	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2			A	108984785	G	A	108984785	3	1	77	1	0	0	0	0	1	0	0	0	6043	1116	39	1	755	1	FOXO3	6	108984785	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1623742	108984785	62130282	394	22130										
FOXO3	2309	broad.mit.edu	37	chr6	108985678	108985678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agggcgctcttggtggcagcCgtgccttgtcgaattctgtc	14	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:108985678C>T	ENST00000343882.6	+	3	1946	c.1642C>T	c.(1642-1644)Cgt>Tgt	p.R548C	FOXO3_ENST00000540898.1_Missense_Mutation_p.R328C|FOXO3_ENST00000406360.1_Missense_Mutation_p.R548C	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	548					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R548C(1)		central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TGGTGGCAGCCGTGCCTTGTC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	6											32	33	33					6																	108985678		2201	4295	6496	109092371	SO:0001583	missense	2309			AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"Forkhead boxes"	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.1642C>T	6.37:g.108985678C>T	ENSP00000339527:p.Arg548Cys		109092371	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Missense_Mutation	SNP	ENST00000343882.6	37	CCDS5068.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.839955	0.71488	.	.	ENSG00000118689	ENST00000343882;ENST00000406360;ENST00000540258;ENST00000540898	D;D	0.91011	-2.77;-2.77	5.8	5.8	0.92144	.	0.213542	0.50627	D	0.000103	D	0.93413	0.7899	M	0.63843	1.955	0.58432	D	0.999999	D	0.76494	0.999	P	0.62298	0.9	D	0.92493	0.6002	10	0.51188	T	0.08	-1.2629	20.0693	0.97712	0.0:1.0:0.0:0.0	.	548	O43524	FOXO3_HUMAN	C	548;548;328;328	ENSP00000339527:R548C;ENSP00000385824:R548C	ENSP00000339527:R548C	R	+	1	0	FOXO3	109092371	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.326000	0.52037	2.758000	0.94735	0.563000	0.77884	CGT		0.562	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2			T	108985678	C	T	108985678	3	4	77	1	0	0	0	0	1	0	0	0	6043	652	23	1	1648	1	FOXO3	6	108985678	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	893	108985678	62129389	395	22131										
HEY2	23493	broad.mit.edu	37	chr6	126080335	126080335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agagtgcctaacagaagttgCgcggtacctgagctccgtgg	14	10	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:126080335C>T	ENST00000368364.3	+	5	598	c.401C>T	c.(400-402)gCg>gTg	p.A134V	HEY2_ENST00000368365.1_Missense_Mutation_p.A88V	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	134	Orange. {ECO:0000255|PROSITE- ProRule:PRU00380}.				anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.A134V(2)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		ACAGAAGTTGCGCGGTACCTG	0.587																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	6											132	118	123					6																	126080335		2203	4300	6503	126122028	SO:0001583	missense	23493			AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"Basic helix-loop-helix proteins"	4881	protein-coding gene	gene with protein product		604674	"hairy/enhancer-of-split related with YRPW motif 2"			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.401C>T	6.37:g.126080335C>T	ENSP00000357348:p.Ala134Val		126122028		Missense_Mutation	SNP	ENST00000368364.3	37	CCDS5131.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731357	0.69189	.	.	ENSG00000135547	ENST00000368365;ENST00000368364	T;T	0.54071	0.59;0.59	5.54	5.54	0.83059	Orange subgroup (1);Orange (2);	0.066854	0.64402	D	0.000019	T	0.49575	0.1565	L	0.38838	1.175	0.80722	D	1	D	0.60160	0.987	P	0.56788	0.806	T	0.30794	-0.9966	10	0.25751	T	0.34	-8.5007	19.4671	0.94946	0.0:1.0:0.0:0.0	.	134	Q9UBP5	HEY2_HUMAN	V	88;134	ENSP00000357349:A88V;ENSP00000357348:A134V	ENSP00000357348:A134V	A	+	2	0	HEY2	126122028	1.000000	0.71417	0.959000	0.39883	0.214000	0.24535	7.736000	0.84948	2.606000	0.88127	0.561000	0.74099	GCG		0.587	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1			T	126080335	C	T	126080335	3	4	77	1	0	0	0	0	1	0	0	0	7100	768	27	1	419	1	HEY2	6	126080335	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	17094657	126080335	45034732	396	22132										
HEY2	23493	broad.mit.edu	37	chr6	126080782	126080782	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagcttccctctgtccttcgCgggggcattccccatgcttc	9	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:126080782C>T	ENST00000368364.3	+	5	1045	c.848C>T	c.(847-849)gCg>gTg	p.A283V	HEY2_ENST00000368365.1_Missense_Mutation_p.A237V	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	283	Ala-rich.				anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.A283V(1)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		CTGTCCTTCGCGGGGGCATTC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	6											108	115	113					6																	126080782		2203	4299	6502	126122475	SO:0001583	missense	23493			AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"Basic helix-loop-helix proteins"	4881	protein-coding gene	gene with protein product		604674	"hairy/enhancer-of-split related with YRPW motif 2"			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.848C>T	6.37:g.126080782C>T	ENSP00000357348:p.Ala283Val		126122475		Missense_Mutation	SNP	ENST00000368364.3	37	CCDS5131.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150205	0.37923	.	.	ENSG00000135547	ENST00000368365;ENST00000368364	T;T	0.58797	0.31;0.31	5.24	5.24	0.73138	.	0.444772	0.22338	N	0.061380	T	0.26195	0.0639	N	0.22421	0.69	0.09310	N	1	B	0.25390	0.125	B	0.16289	0.015	T	0.05146	-1.0903	10	0.30078	T	0.28	-19.5146	15.8869	0.79258	0.0:0.8647:0.1353:0.0	.	283	Q9UBP5	HEY2_HUMAN	V	237;283	ENSP00000357349:A237V;ENSP00000357348:A283V	ENSP00000357348:A283V	A	+	2	0	HEY2	126122475	0.367000	0.25023	0.423000	0.26634	0.960000	0.62799	2.187000	0.42602	2.431000	0.82371	0.561000	0.74099	GCG		0.667	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1			T	126080782	C	T	126080782	3	4	77	1	0	0	0	0	1	0	0	0	7100	768	27	1	866	1	HEY2	6	126080782	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	447	126080782	45034285	397	22133										
RSPO3	84870	broad.mit.edu	37	chr6	127469957	127469957	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagtggatattatggaactCgatatccagatataaataag	8	5	0	1	rs200509277		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:127469957C>T	ENST00000356698.4	+	2	851	c.262C>T	c.(262-264)Cga>Tga	p.R88*	RSPO3_ENST00000368317.3_Nonsense_Mutation_p.R88*|RSPO3_ENST00000485757.1_3'UTR	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	88					branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.R88*(1)	PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		TTATGGAACTCGATATCCAGA	0.363																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											129	123	125					6																	127469957		2203	4300	6503	127511650	SO:0001587	stop_gained	84870			BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"Endogenous ligands"	20866	protein-coding gene	gene with protein product		610574	"thrombospondin, type I, domain containing 2", "R-spondin 3 homolog (Xenopus laevis)"	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.262C>T	6.37:g.127469957C>T	ENSP00000349131:p.Arg88*		127511650	B2RC27|Q5VTV4|Q96K87	Nonsense_Mutation	SNP	ENST00000356698.4	37	CCDS5135.1	.	.	.	.	.	.	.	.	.	.	C	37	6.183353	0.97357	.	.	ENSG00000146374	ENST00000356698;ENST00000368317	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.5343	19.9155	0.97058	0.0:1.0:0.0:0.0	.	.	.	.	X	88	.	ENSP00000349131:R88X	R	+	1	2	RSPO3	127511650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.526000	0.60566	2.699000	0.92147	0.650000	0.86243	CGA		0.363	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784		T	127469957	C	T	127469957	4	4	77	1	0	0	0	0	0	1	0	0	13748	876	31	1	268	1	RSPO3	6	127469957	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1389175	127469957	43645110	398	22134										
PTPRK	5796	broad.mit.edu	37	chr6	128388755	128388755	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccttggtaggtccgattgTcacccacagtgaacggggca	13	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:128388755T>A	ENST00000368215.3	-	12	2065	c.2066A>T	c.(2065-2067)gAc>gTc	p.D689V	RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368213.5_Missense_Mutation_p.D689V|PTPRK_ENST00000368227.3_Missense_Mutation_p.D689V|PTPRK_ENST00000532331.1_Missense_Mutation_p.D689V|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Missense_Mutation_p.D689V|PTPRK_ENST00000368226.4_Missense_Mutation_p.D689V|PTPRK_ENST00000368207.3_Missense_Mutation_p.D689V			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	689					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D689V(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GGTCCGATTGTCACCCACAGT	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	6											101	99	99					6																	128388755		2203	4300	6503	128430448	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2066A>T	6.37:g.128388755T>A	ENSP00000357198:p.Asp689Val		128430448	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	T	23.5	4.428218	0.83667	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.14893	2.51;2.47;2.49;2.51;2.47;2.58;2.53	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.33847	0.0877	M	0.71871	2.18	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.999;0.998;1.0;0.998;0.999	D;D;D;D;D;D	0.83275	0.994;0.959;0.969;0.993;0.991;0.996	T	0.14254	-1.0479	10	0.87932	D	0	.	16.0183	0.80460	0.0:0.0:0.0:1.0	.	689;689;689;546;689;689	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	V	689;689;689;689;689;689;689;546	ENSP00000357209:D689V;ENSP00000357210:D689V;ENSP00000432973:D689V;ENSP00000357196:D689V;ENSP00000357193:D689V;ENSP00000357198:D689V;ENSP00000357190:D689V	ENSP00000357190:D689V	D	-	2	0	PTPRK	128430448	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	8.040000	0.89188	2.187000	0.69744	0.533000	0.62120	GAC		0.542	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128388755	T	A	128388755	3	1	77	1	0	0	0	0	1	0	0	0	12842	1667	58	5	2354	5	PTPRK	6	128388755	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	918798	128388755	42726312	399	22135										
LAMA2	3908	broad.mit.edu	37	chr6	129722399	129722399	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggctgttgaaagcggcaaaCgacaaattgagaacacttta	10	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:129722399C>T	ENST00000421865.2	+	38	5525	c.5476C>T	c.(5476-5478)Cga>Tga	p.R1826*		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1826	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R1826*(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AAGCGGCAAACGACAAATTGA	0.393																																																1	Substitution - Nonsense(1)	large_intestine(1)	6	GRCh37	CM983961	LAMA2	M							142	141	141					6																	129722399		2203	4300	6503	129764092	SO:0001587	stop_gained	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5476C>T	6.37:g.129722399C>T	ENSP00000400365:p.Arg1826*		129764092	Q14736|Q5VUM2|Q93022	Nonsense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	44	10.545815	0.99425	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	.	.	.	4.82	1.95	0.26073	.	0.445606	0.21181	N	0.078818	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	13.5952	0.61984	0.5421:0.4579:0.0:0.0	.	.	.	.	X	1826	.	ENSP00000346769:R1826X	R	+	1	2	LAMA2	129764092	0.026000	0.19158	0.048000	0.18961	0.488000	0.33401	1.030000	0.30153	0.150000	0.19136	-0.182000	0.12963	CGA		0.393	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129722399	C	T	129722399	4	4	77	1	0	0	0	0	0	1	0	0	8628	528	19	1	5626	1	LAMA2	6	129722399	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1333644	129722399	41392668	400	22136										
LAMA2	3908	broad.mit.edu	37	chr6	129813184	129813184	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccactcagaaatattcctccTtttgaaggctgcatatggaa	7	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:129813184T>C	ENST00000421865.2	+	57	8086	c.8037T>C	c.(8035-8037)ccT>ccC	p.P2679P	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2679	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.P2679P(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATATTCCTCCTTTTGAAGGCT	0.383																																																1	Substitution - coding silent(1)	large_intestine(1)	6											75	80	78					6																	129813184		2203	4300	6503	129854877	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8037T>C	6.37:g.129813184T>C			129854877	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.383	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129813184	T	C	129813184	2	2	77	1	0	0	0	0	0	0	0	1	8628	1596	56	4		4	LAMA2	6	129813184	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	90785	129813184	41301883	401	22137										
MYB	4602	broad.mit.edu	37	chr6	135518401	135518401	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctccttcatatttgctgaCgtcagcagttcaactcccaa	6	13	3	1	rs150884969	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:135518401C>T	ENST00000367814.4	+	9	1389				MYB_ENST00000534121.1_Silent_p.D486D|MYB_ENST00000531845.1_Intron|MYB_ENST00000533624.1_Intron|MYB_ENST00000534044.1_Intron|MYB_ENST00000527615.1_Intron|MYB_ENST00000316528.8_Intron|MYB_ENST00000525369.1_Intron|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000442647.2_Intron|MYB_ENST00000341911.5_Silent_p.D502D|MYB_ENST00000528774.1_Silent_p.D499D	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.D502D(2)		breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		TATTTGCTGACGTCAGCAGTT	0.512			T	NFIB	adenoid cystic carcinoma								C|||	2	0.000399361	8e-04	0	5008	,	,		20044	0.001		0	False		,,,				2504	0						Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	2	Substitution - coding silent(2)	large_intestine(2)	6						C	,,,,,,,	1,3135		0,1,1567	77	72	74		,1506,1497,,1458,,,	4	1	6	dbSNP_134	74	0,7164		0,0,3582	no	intron,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,intron,intron	MYB	NM_001130172.1,NM_001130173.1,NM_001161656.1,NM_001161657.1,NM_001161658.1,NM_001161659.1,NM_001161660.1,NM_005375.2	,,,,,,,	0,1,5149	TT,TC,CC		0.0,0.0319,0.0097	,,,,,,,	,502/762,499/759,,486/746,,,	135518401	1,10299	1568	3582	5150	135560094	SO:0001627	intron_variant	4602				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1261C>T	6.37:g.135518401C>T			135560094	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Silent	SNP	ENST00000367814.4	37	CCDS5174.1																																																																																				0.512	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			T	135518401	C	T	135518401	1	4	77	0	1	0	0	0	0	0	0	0	10037	535	19	1		1	MYB	6	135518401	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5705217	135518401	35596666	402	22138										
AHI1	54806	broad.mit.edu	37	chr6	135644405	135644405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaacactcggataatgtctcCgcgatggatggttagttcat	10	8	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:135644405C>T	ENST00000367800.4	-	23	3439	c.3223G>A	c.(3223-3225)Gga>Aga	p.G1075R	AHI1_ENST00000417892.2_Missense_Mutation_p.G429R|AHI1_ENST00000457866.2_Missense_Mutation_p.G1075R	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1075	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)		p.G1075R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATAATGTCTCCGCGATGGATG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											114	104	107					6																	135644405		1913	4128	6041	135686098	SO:0001583	missense	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3223G>A	6.37:g.135644405C>T	ENSP00000356774:p.Gly1075Arg		135686098	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733531	0.69189	.	.	ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	6.06	5.02	0.67125	Src homology-3 domain (5);	0.108387	0.64402	D	0.000004	D	0.83275	0.5219	H	0.98664	4.295	0.80722	D	1	D;D	0.61697	0.99;0.98	P;P	0.56960	0.81;0.626	D	0.85619	0.1263	10	0.44086	T	0.13	-22.1267	7.0422	0.25027	0.0:0.7687:0.0:0.2312	.	1075;1075	Q8N157;Q4FD35	AHI1_HUMAN;.	R	1075;1075;429;1075	ENSP00000356774:G1075R;ENSP00000388650:G1075R;ENSP00000416867:G429R;ENSP00000265602:G1075R	ENSP00000265602:G1075R	G	-	1	0	AHI1	135686098	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.754000	0.55189	2.882000	0.98803	0.655000	0.94253	GGA		0.433	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		T	135644405	C	T	135644405	3	4	77	1	0	0	0	0	1	0	0	0	413	661	23	1	387	1	AHI1	6	135644405	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	126004	135644405	35470662	403	22139										
GPR126	57211	broad.mit.edu	37	chr6	142704975	142704975	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taacagaatcgataaacaaaGgaatggtaagaaatcattac	7	5	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:142704975G>T	ENST00000230173.6	+	6	1693	c.1217G>T	c.(1216-1218)aGg>aTg	p.R406M	GPR126_ENST00000367609.3_Missense_Mutation_p.R406M|GPR126_ENST00000367608.2_Intron|GPR126_ENST00000296932.8_Intron	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	406					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R406M(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GATAAACAAAGGAATGGTAAG	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	6											129	116	120					6																	142704975		1845	4102	5947	142746668	SO:0001583	missense	57211			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.1217G>T	6.37:g.142704975G>T	ENSP00000230173:p.Arg406Met		142746668	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369387	0.24771	.	.	ENSG00000112414	ENST00000230173;ENST00000367609	T;T	0.37058	1.22;1.22	5.55	-10.1	0.00402	.	1.263790	0.05160	N	0.497636	T	0.06325	0.0163	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.09596	-1.0667	10	0.39692	T	0.17	.	0.8789	0.01230	0.3091:0.1643:0.1189:0.4077	.	406;406	Q86SQ4-3;Q86SQ4	.;GP126_HUMAN	M	406	ENSP00000230173:R406M;ENSP00000356581:R406M	ENSP00000230173:R406M	R	+	2	0	GPR126	142746668	0.008000	0.16893	0.140000	0.22221	0.955000	0.61496	-0.375000	0.07475	-2.429000	0.00558	-1.359000	0.01217	AGG		0.323	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142704975	G	T	142704975	3	4	77	1	0	0	0	0	1	0	0	0	6660	1000	35	2	1239	2	GPR126	6	142704975	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7060570	142704975	28410092	404	22140										
HIVEP2	3097	broad.mit.edu	37	chr6	143090995	143090995	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgctggaaatctgccatgtcCgtgagaagaagagttgagtc	13	7	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:143090995C>T	ENST00000367604.1	-	4	5520	c.4881G>A	c.(4879-4881)acG>acA	p.T1627T	HIVEP2_ENST00000012134.2_Silent_p.T1627T|HIVEP2_ENST00000367603.2_Silent_p.T1627T			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1627					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T1627T(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CTGCCATGTCCGTGAGAAGAA	0.532																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - coding silent(1)	large_intestine(1)	6											49	53	52					6																	143090995		2098	4230	6328	143132688	SO:0001819	synonymous_variant	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.4881G>A	6.37:g.143090995C>T			143132688	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																				0.532	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143090995	C	T	143090995	2	4	77	1	0	0	0	0	0	0	0	1	7208	639	23	1		1	HIVEP2	6	143090995	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	386020	143090995	28024072	405	22141										
HIVEP2	3097	broad.mit.edu	37	chr6	143095361	143095361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcttgtgagcctcttctgccTgttcaatacttttctgggag	9	10	5	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:143095361T>C	ENST00000367604.1	-	4	1154	c.515A>G	c.(514-516)cAg>cGg	p.Q172R	HIVEP2_ENST00000012134.2_Missense_Mutation_p.Q172R|HIVEP2_ENST00000367603.2_Missense_Mutation_p.Q172R			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q172R(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CTCTTCTGCCTGTTCAATACT	0.438																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											1	Substitution - Missense(1)	large_intestine(1)	6											138	132	134					6																	143095361		1867	4110	5977	143137054	SO:0001583	missense	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.515A>G	6.37:g.143095361T>C	ENSP00000356576:p.Gln172Arg		143137054	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.341485	0.41498	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02579	4.24;4.24;4.24	5.79	3.29	0.37713	.	0.117281	0.64402	D	0.000013	T	0.00936	0.0031	L	0.56769	1.78	0.28877	N	0.894601	B	0.27068	0.167	B	0.28553	0.091	T	0.47699	-0.9097	10	0.07175	T	0.84	-9.1507	7.9716	0.30130	0.1285:0.0:0.2685:0.6031	.	172	P31629	ZEP2_HUMAN	R	172	ENSP00000356576:Q172R;ENSP00000356575:Q172R;ENSP00000012134:Q172R	ENSP00000012134:Q172R	Q	-	2	0	HIVEP2	143137054	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	3.191000	0.50981	0.404000	0.25506	0.533000	0.62120	CAG		0.438	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143095361	T	C	143095361	3	2	77	1	0	0	0	0	1	0	0	0	7208	1580	55	4	6849	4	HIVEP2	6	143095361	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	4366	143095361	28019706	406	22142										
STX11	8676	broad.mit.edu	37	chr6	144508243	144508243	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgcgacaactgcaagatccGcatccagcgccagctggaga	12	14	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:144508243G>A	ENST00000367568.4	+	2	662	c.479G>A	c.(478-480)cGc>cAc	p.R160H		NM_003764.3	NP_003755.2	O75558	STX11_HUMAN	syntaxin 11	160					cytotoxic T cell degranulation (GO:0043316)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|natural killer cell degranulation (GO:0043320)|neutrophil degranulation (GO:0043312)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	SNAP receptor activity (GO:0005484)	p.R160H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	12				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		TGCAAGATCCGCATCCAGCGC	0.592									Familial Hemophagocytic Lymphohistiocytosis																																							1	Substitution - Missense(1)	large_intestine(1)	6											50	49	49					6																	144508243		2203	4300	6503	144549936	SO:0001583	missense	8676	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AF044309	CCDS5205.1	6q24.1	2014-09-17			ENSG00000135604	ENSG00000135604			11429	protein-coding gene	gene with protein product		605014				9553086	Standard	NM_003764		Approved		uc003qks.4	O75558	OTTHUMG00000015739	ENST00000367568.4:c.479G>A	6.37:g.144508243G>A	ENSP00000356540:p.Arg160His		144549936	E1P598|O75378|O95148|Q5TCL6	Missense_Mutation	SNP	ENST00000367568.4	37	CCDS5205.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578019	0.86645	.	.	ENSG00000135604	ENST00000367568	T	0.23950	1.88	5.61	5.61	0.85477	t-SNARE (1);	0.000000	0.85682	D	0.000000	T	0.29126	0.0724	M	0.80982	2.52	0.80722	D	1	P	0.51351	0.944	B	0.43680	0.427	T	0.20874	-1.0262	10	0.49607	T	0.09	-21.5685	19.2487	0.93913	0.0:0.0:1.0:0.0	.	160	O75558	STX11_HUMAN	H	160	ENSP00000356540:R160H	ENSP00000356540:R160H	R	+	2	0	STX11	144549936	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.799000	0.99117	2.631000	0.89168	0.655000	0.94253	CGC		0.592	STX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042544.1			A	144508243	G	A	144508243	3	1	77	1	0	0	0	0	1	0	0	0	15376	1087	38	1	481	1	STX11	6	144508243	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1412882	144508243	26606824	407	22143										
KATNA1	11104	broad.mit.edu	37	chr6	149922871	149922871	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcttccccgtgccaggtggGccgaccatcagtactccctg	11	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:149922871G>A	ENST00000335647.5	-	6	791	c.747C>T	c.(745-747)ggC>ggT	p.G249G	KATNA1_ENST00000494504.1_5'UTR|KATNA1_ENST00000335643.8_Silent_p.G173G|KATNA1_ENST00000367411.2_Silent_p.G249G					katanin p60 (ATPase containing) subunit A 1									p.G249G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		TGCCAGGTGGGCCGACCATCA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	6											89	82	84					6																	149922871		2203	4300	6503	149964564	SO:0001819	synonymous_variant	11104			AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.747C>T	6.37:g.149922871G>A			149964564		Silent	SNP	ENST00000335647.5	37	CCDS5217.1																																																																																				0.418	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		A	149922871	G	A	149922871	2	1	77	1	0	0	0	0	0	0	0	1	8005	1190	42	3		3	KATNA1	6	149922871	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5414628	149922871	21192196	408	22144										
RAET1G	353091	broad.mit.edu	37	chr6	150240885	150240885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatccacctggccttgaacCgcacaccaccgtggtccagg	9	17	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:150240885C>T	ENST00000367360.2	-	2	220	c.153G>A	c.(151-153)gcG>gcA	p.A51A	RAET1E-AS1_ENST00000446954.2_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000605899.1_RNA|RAET1G_ENST00000479265.1_Silent_p.A51A	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G									p.A51A(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		GGCCTTGAACCGCACACCACC	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	6											101	102	102					6																	150240885		2203	4297	6500	150282578	SO:0001819	synonymous_variant	353091			AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"retinoic acid early transcript 1G pseudogene"			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.153G>A	6.37:g.150240885C>T			150282578		Silent	SNP	ENST00000367360.2	37	CCDS43514.1																																																																																				0.532	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2			T	150240885	C	T	150240885	2	4	77	1	0	0	0	0	0	0	0	1	13037	639	23	1		1	RAET1G	6	150240885	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	318014	150240885	20874182	409	22145										
SYNE1	23345	broad.mit.edu	37	chr6	152532698	152532698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgagtgcaaaatctgctgaCgactgaacatctcggcttga	10	9	2	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:152532698C>T	ENST00000367255.5	-	124	23121	c.22520G>A	c.(22519-22521)cGt>cAt	p.R7507H	SYNE1_ENST00000356820.4_Missense_Mutation_p.R2031H|SYNE1_ENST00000448038.1_Missense_Mutation_p.R7436H|SYNE1_ENST00000341594.5_Missense_Mutation_p.R7119H|SYNE1_ENST00000265368.4_Missense_Mutation_p.R7507H|SYNE1_ENST00000423061.1_Missense_Mutation_p.R7436H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7507					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R7507H(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AATCTGCTGACGACTGAACAT	0.333										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											85	83	84					6																	152532698		2203	4300	6503	152574391	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.22520G>A	6.37:g.152532698C>T	ENSP00000356224:p.Arg7507His		152574391	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	29.0	4.968388	0.92855	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000009	T	0.51176	0.1659	M	0.70595	2.14	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	T	0.46735	-0.9170	10	0.52906	T	0.07	.	20.0274	0.97527	0.0:1.0:0.0:0.0	.	7507;7507;7436;7436	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	H	7507;153;7436;7507;7436;7119;2031;429	ENSP00000356224:R7507H;ENSP00000356226:R153H;ENSP00000396024:R7436H;ENSP00000265368:R7507H;ENSP00000390975:R7436H;ENSP00000341887:R7119H;ENSP00000349276:R2031H;ENSP00000356220:R429H	ENSP00000265368:R7507H	R	-	2	0	SYNE1	152574391	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.721000	0.84768	2.798000	0.96311	0.557000	0.71058	CGT		0.333	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152532698	C	T	152532698	3	4	77	1	0	0	0	0	1	0	0	0	15484	536	19	1	4038	1	SYNE1	6	152532698	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2291813	152532698	18582369	410	22146										
TIAM2	26230	broad.mit.edu	37	chr6	155450636	155450636	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaggtgttgcctactccacGcacaggacaaatgccccagg	11	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:155450636G>A	ENST00000461783.3	+	6	1552	c.279G>A	c.(277-279)acG>acA	p.T93T	TIAM2_ENST00000318981.5_Silent_p.T93T|TIAM2_ENST00000456144.1_Silent_p.T93T|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000529824.2_Silent_p.T93T|TIAM2_ENST00000360366.4_Silent_p.T93T			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	93					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T93T(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CCTACTCCACGCACAGGACAA	0.552																																																2	Substitution - coding silent(2)	large_intestine(2)	6											70	64	66					6																	155450636		2203	4300	6503	155492328	SO:0001819	synonymous_variant	26230				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.279G>A	6.37:g.155450636G>A			155492328	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																				0.552	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		A	155450636	G	A	155450636	2	1	77	1	0	0	0	0	0	0	0	1	15930	1074	38	1		1	TIAM2	6	155450636	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2917938	155450636	15664431	411	22147										
TAGAP	117289	broad.mit.edu	37	chr6	159456924	159456924	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaccggctggctacatcgtcGcacgagacagtcccgcttat	11	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:159456924G>A	ENST00000367066.3	-	10	2462	c.2131C>T	c.(2131-2133)Cga>Tga	p.R711*	RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000326965.6_Nonsense_Mutation_p.R533*|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	711					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R711*(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTACATCGTCGCACGAGACAG	0.572																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											68	62	64					6																	159456924		2203	4300	6503	159376912	SO:0001587	stop_gained	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.2131C>T	6.37:g.159456924G>A	ENSP00000356033:p.Arg711*		159376912	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Nonsense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	41	8.771134	0.98948	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	.	.	.	5.82	-5.39	0.02664	.	0.573271	0.16820	N	0.198182	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1856	6.9636	0.24611	0.0564:0.1573:0.2893:0.497	.	.	.	.	X	711;533	.	ENSP00000322650:R533X	R	-	1	2	TAGAP	159376912	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.397000	0.20883	-0.505000	0.06568	-0.309000	0.09137	CGA		0.572	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159456924	G	A	159456924	4	1	77	1	0	0	0	0	0	1	0	0	15576	1095	38	1	68	1	TAGAP	6	159456924	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4006288	159456924	11658143	412	22148										
TAGAP	117289	broad.mit.edu	37	chr6	159457699	159457699	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctttgagaaccagtgcccgCgggagcaccgaacccggggc	15	14	0	1	rs560834483		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:159457699C>T	ENST00000367066.3	-	10	1687	c.1356G>A	c.(1354-1356)ccG>ccA	p.P452P	RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000326965.6_Silent_p.P274P|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	452					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.P452P(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CCAGTGCCCGCGGGAGCACCG	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		14974	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6											75	84	81					6																	159457699		2203	4300	6503	159377687	SO:0001819	synonymous_variant	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1356G>A	6.37:g.159457699C>T			159377687	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Silent	SNP	ENST00000367066.3	37	CCDS5261.1																																																																																				0.577	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159457699	C	T	159457699	2	4	77	1	0	0	0	0	0	0	0	1	15576	755	27	1		1	TAGAP	6	159457699	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	775	159457699	11657368	413	22149										
IGF2R	3482	broad.mit.edu	37	chr6	160494305	160494305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caacaagaggctgagatacgTggaccaggtcctgcagctgg	14	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:160494305T>C	ENST00000356956.1	+	34	4899	c.4751T>C	c.(4750-4752)gTg>gCg	p.V1584A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1584					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.V1584A(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CTGAGATACGTGGACCAGGTC	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	6											178	142	154					6																	160494305		2203	4300	6503	160414295	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4751T>C	6.37:g.160494305T>C	ENSP00000349437:p.Val1584Ala		160414295	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	0.395	-0.921422	0.02396	.	.	ENSG00000197081	ENST00000356956	T	0.01981	4.52	5.3	-3.54	0.04653	Mannose-6-phosphate receptor, binding (1);	0.780830	0.12177	N	0.492462	T	0.00496	0.0016	L	0.45581	1.43	0.25361	N	0.988787	B	0.02656	0.0	B	0.06405	0.002	T	0.49031	-0.8981	10	0.06494	T	0.89	-9.5889	4.7369	0.12993	0.3743:0.2751:0.0:0.3506	.	1584	P11717	MPRI_HUMAN	A	1584	ENSP00000349437:V1584A	ENSP00000349437:V1584A	V	+	2	0	IGF2R	160414295	0.975000	0.34042	0.989000	0.46669	0.161000	0.22273	0.440000	0.21592	-0.812000	0.04363	-0.441000	0.05720	GTG		0.557	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160494305	T	C	160494305	3	2	77	1	0	0	0	0	1	0	0	0	7597	1696	59	4	4885	4	IGF2R	6	160494305	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1036606	160494305	10620762	414	22150										
MAP3K4	4216	broad.mit.edu	37	chr6	161469968	161469968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggactgactgtccagcagatCgtttaaagttttttgaaact	9	7	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:161469968C>T	ENST00000392142.4	+	3	812	c.664C>T	c.(664-666)Cgt>Tgt	p.R222C	MAP3K4_ENST00000348824.7_Missense_Mutation_p.R222C|MAP3K4_ENST00000366920.2_Missense_Mutation_p.R222C|MAP3K4_ENST00000366919.2_Missense_Mutation_p.R222C	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	222					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.R222C(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TCCAGCAGATCGTTTAAAGTT	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	6											40	39	39					6																	161469968		2203	4300	6503	161389958	SO:0001583	missense	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.664C>T	6.37:g.161469968C>T	ENSP00000375986:p.Arg222Cys		161389958	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466143	0.84425	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	D;D;D;D	0.93366	-3.1;-3.21;-3.17;-3.07	6.14	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.95953	0.8682	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.96658	0.9487	10	0.87932	D	0	-24.2205	17.0824	0.86602	0.1277:0.8722:0.0:0.0	.	222;222	Q9Y6R4-2;Q9Y6R4	.;M3K4_HUMAN	C	222	ENSP00000355886:R222C;ENSP00000375986:R222C;ENSP00000355887:R222C;ENSP00000297332:R222C	ENSP00000297332:R222C	R	+	1	0	MAP3K4	161389958	1.000000	0.71417	0.966000	0.40874	0.962000	0.63368	4.524000	0.60552	1.606000	0.50161	0.637000	0.83480	CGT		0.448	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161469968	C	T	161469968	3	4	77	1	0	0	0	0	1	0	0	0	9282	884	31	1	674	1	MAP3K4	6	161469968	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	975663	161469968	9645099	415	22151										
AGPAT4	56895	broad.mit.edu	37	chr6	161587297	161587297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacccctaacagcccaaagcGttcggacaggctccagccac	8	17	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:161587297G>A	ENST00000320285.4	-	3	543	c.331C>T	c.(331-333)Cgc>Tgc	p.R111C	AGPAT4_ENST00000366908.5_Missense_Mutation_p.R111C|AGPAT4_ENST00000366911.5_Intron|AGPAT4_ENST00000457520.2_Intron|AGPAT4_ENST00000366906.5_Missense_Mutation_p.R49C|AGPAT4_ENST00000366905.3_Missense_Mutation_p.R111C	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	111					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R111C(1)		endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		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)		AGCCCAAAGCGTTCGGACAGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	6											67	56	60					6																	161587297		2203	4300	6503	161507287	SO:0001583	missense	56895			AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20885	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, delta"	614795	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.331C>T	6.37:g.161587297G>A	ENSP00000314036:p.Arg111Cys		161507287	B4DSF9|Q5TEF0	Missense_Mutation	SNP	ENST00000320285.4	37	CCDS5280.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879557	0.51801	.	.	ENSG00000026652	ENST00000320285;ENST00000366908;ENST00000366906;ENST00000366905	D;D	0.92397	-3.03;-3.03	4.74	4.74	0.60224	Phospholipid/glycerol acyltransferase (2);	0.103621	0.64402	D	0.000008	D	0.95765	0.8622	M	0.89968	3.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.954	D	0.96013	0.9003	10	0.87932	D	0	-22.862	10.9335	0.47233	0.0:0.0:0.6775:0.3225	.	111;111	B4DHC0;Q9NRZ5	.;PLCD_HUMAN	C	111;111;49;111	ENSP00000314036:R111C;ENSP00000355873:R49C	ENSP00000314036:R111C	R	-	1	0	AGPAT4	161507287	1.000000	0.71417	0.961000	0.40146	0.532000	0.34746	3.578000	0.53892	2.466000	0.83321	0.650000	0.86243	CGC		0.522	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133		A	161587297	G	A	161587297	3	1	77	1	0	0	0	0	1	0	0	0	389	1145	40	1	833	1	AGPAT4	6	161587297	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	117329	161587297	9527770	416	22152										
PACRG	135138	broad.mit.edu	37	chr6	163149278	163149279	+	Frame_Shift_Del	DEL	AA	AA	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctaggaagatggtggcagAaaaagagaccctgagcttaa							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	AA	AA	AA	-	AA	AA	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:163149278_163149279delAA	ENST00000337019.3	+	2	235_236	c.11_12delAA	c.(10-12)gaafs	p.E4fs	PARK2_ENST00000366897.1_5'Flank|PARK2_ENST00000366896.1_5'Flank|PACRG_ENST00000542669.1_3'UTR|PARK2_ENST00000366894.1_5'Flank|PARK2_ENST00000338468.3_5'Flank|PACRG_ENST00000366888.2_Frame_Shift_Del_p.E4fs|PACRG_ENST00000366889.2_Frame_Shift_Del_p.E4fs|PARK2_ENST00000366898.1_5'Flank|PARK2_ENST00000366892.1_5'Flank	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	4					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)		p.K5fs*35(1)		endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		ATGGTGGCAGAAAAAGAGACCC	0.475																																																1	Deletion - Frameshift(1)	large_intestine(1)	6																																								163069269	SO:0001589	frameshift_variant	135138			AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.11_12delAA	6.37:g.163149280_163149281delAA	ENSP00000337946:p.Glu4fs		163069268	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Frame_Shift_Del	DEL	ENST00000337019.3	37	CCDS5284.1																																																																																				0.475	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410		-	163149279	AA	-	163149278	7	5	77	1	0	1	0	1	0	0	0	0	11401	246	9	0	13	0	PACRG	6	163149278	Frame_Shift_Del	DEL	AA	TCGA-AG-A02N-01A-11W-A096-10	1561981	163149278	7965789	417	22153										
FRMD1	79981	broad.mit.edu	37	chr6	168462502	168462502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccaccttctgcctcctcccGctgccgcagctgttgcagag	9	19	1	1	rs372041975		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:168462502G>A	ENST00000283309.6	-	8	1094	c.1030C>T	c.(1030-1032)Cgg>Tgg	p.R344W	FRMD1_ENST00000537786.1_Missense_Mutation_p.R115W|FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.R276W	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	344	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)		p.R344W(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCCTCCTCCCGCTGCCGCAGC	0.711																																					GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)											1	Substitution - Missense(1)	large_intestine(1)	6						G	TRP/ARG,TRP/ARG	1,4367		0,1,2183	10	12	11		826,1030	2.2	0.6	6		11	0,8556		0,0,4278	no	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	101,101	0,1,6461	AA,AG,GG		0.0,0.0229,0.0077	probably-damaging,probably-damaging	276/482,344/550	168462502	1,12923	2184	4278	6462	168205351	SO:0001583	missense	79981				CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1030C>T	6.37:g.168462502G>A	ENSP00000283309:p.Arg344Trp		168205351	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847246	0.32606	2.29E-4	0.0	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	D;D;D	0.82081	-1.57;-1.57;-1.57	2.23	2.23	0.28157	FERM domain (1);	0.327137	0.20311	U	0.094830	T	0.80297	0.4597	L	0.52573	1.65	0.29197	N	0.875455	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	P;D;D;P	0.67103	0.889;0.937;0.949;0.889	T	0.71576	-0.4551	10	0.66056	D	0.02	.	7.7936	0.29135	0.0:0.0:0.7521:0.2479	.	279;344;276;239	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	W	344;276;115	ENSP00000283309:R344W;ENSP00000414115:R276W;ENSP00000440078:R115W	ENSP00000283309:R344W	R	-	1	2	FRMD1	168205351	0.996000	0.38824	0.638000	0.29380	0.055000	0.15305	2.457000	0.45005	1.254000	0.44035	0.313000	0.20887	CGG		0.711	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		A	168462502	G	A	168462502	3	1	77	1	0	0	0	0	1	0	0	0	6068	1086	38	1	635	1	FRMD1	6	168462502	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5313224	168462502	2652565	418	22154										
DLL1	28514	broad.mit.edu	37	chr6	170592829	170592829	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaggaactggcagttgggaCccccgtagcctcgggcacac							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:170592829delC	ENST00000366756.3	-	9	1871	c.1538delG	c.(1537-1539)ggtfs	p.G513fs		NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	513	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.G513fs*24(1)		NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		GCAGTTGGGACCCCCGTAGCC	0.706																																																1	Deletion - Frameshift(1)	large_intestine(1)	6											14	16	15					6																	170592829		2165	4257	6422	170434754	SO:0001589	frameshift_variant	28514			AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.1538delG	6.37:g.170592829delC	ENSP00000355718:p.Gly513fs		170434754	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Frame_Shift_Del	DEL	ENST00000366756.3	37	CCDS5313.1																																																																																				0.706	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			-	170592829	C	-	170592829	7	5	77	1	0	1	0	1	0	0	0	0	4577	507	18	0	645	0	DLL1	6	170592829	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	2130327	170592829	522238	419	22155										
DLL1	28514	broad.mit.edu	37	chr6	170597495	170597495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagtacttgaggtccgtgcGgccgctgctgtgcaggtcct	16	11	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:170597495G>A	ENST00000366756.3	-	4	835	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C	FAM120B_ENST00000540480.1_5'Flank	NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	168					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.R168C(1)		NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		AGGTCCGTGCGGCCGCTGCTG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	6											66	54	58					6																	170597495		2203	4300	6503	170439420	SO:0001583	missense	28514			AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.502C>T	6.37:g.170597495G>A	ENSP00000355718:p.Arg168Cys		170439420	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	37	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690194	0.68271	.	.	ENSG00000198719	ENST00000366756	D	0.96300	-3.97	4.48	4.48	0.54585	Delta/Serrate/lag-2 (DSL) protein (2);	0.000000	0.85682	D	0.000000	D	0.96691	0.8920	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.65874	0.877;0.939	D	0.95484	0.8563	10	0.31617	T	0.26	.	17.3763	0.87392	0.0:0.0:1.0:0.0	.	168;168	B5M0B3;O00548	.;DLL1_HUMAN	C	168	ENSP00000355718:R168C	ENSP00000355718:R168C	R	-	1	0	DLL1	170439420	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	4.271000	0.58902	2.328000	0.79073	0.563000	0.77884	CGC		0.632	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			A	170597495	G	A	170597495	3	1	77	1	0	0	0	0	1	0	0	0	4577	1116	39	1	1701	1	DLL1	6	170597495	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4666	170597495	517572	420	22156										
FAM120B	84498	broad.mit.edu	37	chr6	170667354	170667354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggatttgcatgcgtttattgCgcaggccttgtgcctccaag	12	10	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr6:170667354C>T	ENST00000476287.1	+	6	2339	c.2231C>T	c.(2230-2232)gCg>gTg	p.A744V	FAM120B_ENST00000540480.1_Missense_Mutation_p.A756V|FAM120B_ENST00000252510.9_Missense_Mutation_p.A76V|FAM120B_ENST00000537664.1_Missense_Mutation_p.A767V	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	744					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.A744V(2)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GCGTTTATTGCGCAGGCCTTG	0.478																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6											103	78	87					6																	170667354		2203	4300	6503	170509279	SO:0001583	missense	84498			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2231C>T	6.37:g.170667354C>T	ENSP00000417970:p.Ala744Val		170509279	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.221779	0.58560	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287;ENST00000252510	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.5	4.5	0.54988	.	0.233076	0.43110	D	0.000608	T	0.57607	0.2065	L	0.61387	1.9	0.41855	D	0.990194	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.60850	-0.7181	10	0.54805	T	0.06	-8.8033	14.4596	0.67440	0.0:1.0:0.0:0.0	.	744;744	Q96EK7;F2Z2E1	F120B_HUMAN;.	V	756;767;744;76	ENSP00000444125:A756V;ENSP00000440125:A767V;ENSP00000417970:A744V;ENSP00000252510:A76V	ENSP00000252510:A76V	A	+	2	0	FAM120B	170509279	0.994000	0.37717	0.090000	0.20809	0.230000	0.25150	3.953000	0.56699	2.216000	0.71823	0.655000	0.94253	GCG		0.478	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		T	170667354	C	T	170667354	3	4	77	1	0	0	0	0	1	0	0	0	5433	768	27	1	2249	1	FAM120B	6	170667354	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	69859	170667354	447713	421	22157										
SUN1	23353	broad.mit.edu	37	chr7	883126	883126	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcggcccccgggcccgtgtcGagagtttattctagggacag	15	12	1	1	rs370251394		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:883126G>A	ENST00000405266.1	+	5	651	c.627G>A	c.(625-627)tcG>tcA	p.S209S	SUN1_ENST00000425407.2_Silent_p.S159S|SUN1_ENST00000401592.1_Silent_p.S209S|SUN1_ENST00000403868.1_Silent_p.S209S|SUN1_ENST00000389574.3_Silent_p.S159S|SUN1_ENST00000456758.2_Silent_p.S267S|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000457378.2_Silent_p.S230S			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	209	SYNE2-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)		p.S159S(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGCCCGTGTCGAGAGTTTATT	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	7						G	,,,,	0,3756		0,0,1878	90	104	100		627,,690,627,477	-8.8	0	7		100	1,8193		0,1,4096	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	,,,,	0,1,5974	AA,AG,GG		0.0122,0.0,0.0084	,,,,	209/786,,230/279,209/258,159/703	883126	1,11949	1878	4097	5975	849652	SO:0001819	synonymous_variant	23353			AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.627G>A	7.37:g.883126G>A			849652	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		.	.	.	.	.	.	.	.	.	.	G	4.232	0.041992	0.08196	0.0	1.22E-4	ENSG00000164828	ENST00000419312	.	.	.	4.4	-8.8	0.00817	.	.	.	.	.	T	0.34978	0.0916	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.51957	-0.8639	4	.	.	.	-5.5543	12.2413	0.54544	0.6045:0.3114:0.0842:0.0	.	.	.	.	Q	50	.	.	R	+	2	0	SUN1	849652	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.451000	0.00121	-5.250000	0.00018	-1.366000	0.01203	CGA		0.522	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		A	883126	G	A	883126	2	1	77	1	0	0	0	0	0	0	0	1	15430	1045	37	1		1	SUN1	7	883126	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		883126	158255537	422	22158										
GPR146	115330	broad.mit.edu	37	chr7	1097946	1097946	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcatctcgcgagggaagccCgtggacgcacactacctggg	13	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:1097946C>T	ENST00000397095.1	+	2	1018	c.795C>T	c.(793-795)ccC>ccT	p.P265P	C7orf50_ENST00000397100.2_Intron|GPR146_ENST00000297468.3_Silent_p.P265P|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|RP11-449P15.1_ENST00000549241.1_RNA			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P265P(1)		autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GAGGGAAGCCCGTGGACGCAC	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	7											98	84	89					7																	1097946		2203	4300	6503	1064472	SO:0001819	synonymous_variant	115330			BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"GPCR / Class A : Orphans"	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.795C>T	7.37:g.1097946C>T			1064472	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																				0.582	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445		T	1097946	C	T	1097946	2	4	77	1	0	0	0	0	0	0	0	1	6672	639	23	1		1	GPR146	7	1097946	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	214820	1097946	158040717	423	22159										
INTS1	26173	broad.mit.edu	37	chr7	1526651	1526651	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcatcgtgcagcaggaactcGcacagacactgcacgggcag	13	13	0	1	rs200150900	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:1526651G>A	ENST00000404767.3	-	21	2818	c.2733C>T	c.(2731-2733)tgC>tgT	p.C911C	INTS1_ENST00000389470.4_Silent_p.C1054C	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	911					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.C1054C(1)		autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCAGGAACTCGCACAGACACT	0.667													G|||	2	0.000399361	8e-04	0	5008	,	,		13354	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											47	50	49					7																	1526651		2183	4264	6447	1493177	SO:0001819	synonymous_variant	26173			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.2733C>T	7.37:g.1526651G>A			1493177	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																				0.667	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1526651	G	A	1526651	2	1	77	1	0	0	0	0	0	0	0	1	7796	1079	38	1		1	INTS1	7	1526651	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	428705	1526651	157612012	424	22160										
INTS1	26173	broad.mit.edu	37	chr7	1539938	1539938	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccccgcacagcacgccctcGatcctgtcatcgttgccctc	8	20	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:1539938G>A	ENST00000404767.3	-	4	499	c.414C>T	c.(412-414)atC>atT	p.I138I	INTS1_ENST00000493531.1_5'UTR|INTS1_ENST00000389470.4_Silent_p.I266I	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	138					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.I266I(1)		autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCACGCCCTCGATCCTGTCAT	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	7											43	49	47					7																	1539938		2171	4259	6430	1506464	SO:0001819	synonymous_variant	26173			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.414C>T	7.37:g.1539938G>A			1506464	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																				0.662	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1539938	G	A	1539938	2	1	77	1	0	0	0	0	0	0	0	1	7796	1048	37	1		1	INTS1	7	1539938	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	13287	1539938	157598725	425	22161										
TTYH3	80727	broad.mit.edu	37	chr7	2689210	2689210	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctgccccagggtctgcctGctgggagtcctggccctggt	14	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:2689210G>A	ENST00000258796.7	+	6	937	c.732G>A	c.(730-732)ctG>ctA	p.L244L	TTYH3_ENST00000477439.1_3'UTR|TTYH3_ENST00000403167.1_Silent_p.L73L|TTYH3_ENST00000407643.1_Silent_p.L212L	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	244					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)	p.L244L(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GGGTCTGCCTGCTGGGAGTCC	0.711																																																1	Substitution - coding silent(1)	large_intestine(1)	7											23	20	21					7																	2689210		2194	4291	6485	2655736	SO:0001819	synonymous_variant	80727				CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.732G>A	7.37:g.2689210G>A			2655736	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Silent	SNP	ENST00000258796.7	37	CCDS34588.1																																																																																				0.711	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		A	2689210	G	A	2689210	2	1	77	1	0	0	0	0	0	0	0	1	16781	1306	46	3		3	TTYH3	7	2689210	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1149272	2689210	156449453	426	22162										
CARD11	84433	broad.mit.edu	37	chr7	2976744	2976744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgacgatgcaggcctcccgcCgcaccatctcgatcctcatc	8	18	2	1	rs577877958		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:2976744C>T	ENST00000396946.4	-	9	1671	c.1268G>A	c.(1267-1269)cGg>cAg	p.R423Q		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	423					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.R416Q(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GGCCTCCCGCCGCACCATCTC	0.607			Mis		DLBCL								C|||	1	0.000199681	0	0	5008	,	,		20627	0		0	False		,,,				2504	0.001						Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	2	Substitution - Missense(2)	large_intestine(2)	7											146	117	127					7																	2976744		2203	4300	6503	2943270	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1268G>A	7.37:g.2976744C>T	ENSP00000380150:p.Arg423Gln		2943270	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	36	5.697925	0.96802	.	.	ENSG00000198286	ENST00000396946	T	0.33654	1.4	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.27278	0.0669	N	0.16307	0.4	0.58432	D	0.999999	P	0.51933	0.949	B	0.43809	0.432	T	0.03112	-1.1071	10	0.20519	T	0.43	-34.3605	17.7576	0.88453	0.0:1.0:0.0:0.0	.	423	Q9BXL7	CAR11_HUMAN	Q	423	ENSP00000380150:R423Q	ENSP00000380150:R423Q	R	-	2	0	CARD11	2943270	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.869000	0.69613	2.447000	0.82792	0.561000	0.74099	CGG		0.607	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2976744	C	T	2976744	3	4	77	1	0	0	0	0	1	0	0	0	2651	652	23	1	2264	1	CARD11	7	2976744	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	287534	2976744	156161919	427	22163										
SLC29A4	222962	broad.mit.edu	37	chr7	5330812	5330814	+	In_Frame_Del	DEL	TCC	TCC	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttggtggcactggcagctgTcctcctgaacaacgtcctgg					rs567644235|rs371767928		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	TCC	TCC	TCC	-	TCC	TCC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:5330812_5330814delTCC	ENST00000396872.3	+	4	520_522	c.359_361delTCC	c.(358-363)gtcctc>gtc	p.L122del	SLC29A4_ENST00000297195.4_In_Frame_Del_p.L122del|SLC29A4_ENST00000406453.3_In_Frame_Del_p.L122del			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	122					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)	p.L122delL(1)		breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	CTGGCAGCTGTCCTCCTGAACAA	0.635																																																1	Deletion - In frame(1)	large_intestine(1)	7																																								5297340	SO:0001651	inframe_deletion	222962			AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"Solute carriers"	23097	protein-coding gene	gene with protein product		609149	"solute carrier family 29 (nucleoside transporters), member 4"			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.359_361delTCC	7.37:g.5330815_5330817delTCC	ENSP00000380081:p.Leu122del		5297338	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	In_Frame_Del	DEL	ENST00000396872.3	37	CCDS5340.1																																																																																				0.635	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247		-	5330814	TCC	-	5330812	7	5	77	1	0	1	0	1	0	0	0	0	14574	1667	58	0	369	0	SLC29A4	7	5330812	In_Frame_Del	DEL	TCC	TCGA-AG-A02N-01A-11W-A096-10	2354068	5330812	153807851	428	22164										
GLCCI1	113263	broad.mit.edu	37	chr7	8062168	8062168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaggtcacatcagcgttctgCgtcatgggggagtgctgatc	15	9	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:8062168C>T	ENST00000223145.5	+	3	1222	c.665C>T	c.(664-666)gCg>gTg	p.A222V	GLCCI1_ENST00000474269.1_3'UTR	NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	222						cytoplasm (GO:0005737)		p.A222V(1)		endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		CAGCGTTCTGCGTCATGGGGG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											179	166	170					7																	8062168		2203	4300	6503	8028693	SO:0001583	missense	113263			BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.665C>T	7.37:g.8062168C>T	ENSP00000223145:p.Ala222Val		8028693	A4D103|Q96FD0	Missense_Mutation	SNP	ENST00000223145.5	37	CCDS34601.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755850	0.89843	.	.	ENSG00000106415	ENST00000223145;ENST00000430798	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.78355	0.4270	M	0.74647	2.275	0.58432	D	0.99999	D	0.76494	0.999	D	0.78314	0.991	T	0.80160	-0.1498	9	0.66056	D	0.02	-27.082	15.5927	0.76550	0.0:1.0:0.0:0.0	.	222	Q86VQ1	GLCI1_HUMAN	V	222;110	.	ENSP00000223145:A222V	A	+	2	0	GLCCI1	8028693	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	4.781000	0.62389	2.734000	0.93682	0.650000	0.86243	GCG		0.363	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426		T	8062168	C	T	8062168	3	4	77	1	0	0	0	0	1	0	0	0	6451	768	27	1	675	1	GLCCI1	7	8062168	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2731356	8062168	151076495	429	22165										
TMEM106B	54664	broad.mit.edu	37	chr7	12269442	12269442	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attggtccacttgatatgaaAcaagtaagaatcaatcatga	7	6	2	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:12269442A>G	ENST00000396667.3	+	6	901	c.579A>G	c.(577-579)aaA>aaG	p.K193K	TMEM106B_ENST00000396668.3_Silent_p.K193K	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	193					cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.K193K(1)		NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		TTGATATGAAACAAGTAAGAA	0.333																																																1	Substitution - coding silent(1)	large_intestine(1)	7											59	60	60					7																	12269442		2203	4297	6500	12235967	SO:0001819	synonymous_variant	54664			BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.579A>G	7.37:g.12269442A>G			12235967	A4D108|Q53FL9|Q8N4L0	Silent	SNP	ENST00000396667.3	37	CCDS5358.1																																																																																				0.333	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374		G	12269442	A	G	12269442	2	3	77	1	0	0	0	0	0	0	0	1	16060	40	2	4		4	TMEM106B	7	12269442	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	4207274	12269442	146869221	430	22166										
ANKMY2	57037	broad.mit.edu	37	chr7	16650266	16650266	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgtaatgcatcttcatagcCaatacttcattcatgtctct	4	10	5	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:16650266C>A	ENST00000306999.2	-	6	897	c.654G>T	c.(652-654)ttG>ttT	p.L218F		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	218						cilium (GO:0005929)	metal ion binding (GO:0046872)	p.L218F(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TCTTCATAGCCAATACTTCAT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7											153	138	143					7																	16650266		2203	4300	6503	16616791	SO:0001583	missense	57037			AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.654G>T	7.37:g.16650266C>A	ENSP00000303570:p.Leu218Phe		16616791	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	37	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731057	0.69074	.	.	ENSG00000106524	ENST00000306999	D	0.83673	-1.75	5.78	1.75	0.24633	.	0.000000	0.85682	D	0.000000	D	0.87830	0.6276	M	0.82056	2.57	0.54753	D	0.99998	D	0.89917	1.0	D	0.77004	0.989	D	0.84284	0.0496	10	0.39692	T	0.17	-28.3613	4.6555	0.12615	0.113:0.5909:0.1005:0.1956	.	218	Q8IV38	ANKY2_HUMAN	F	218	ENSP00000303570:L218F	ENSP00000303570:L218F	L	-	3	2	ANKMY2	16616791	1.000000	0.71417	0.983000	0.44433	0.993000	0.82548	1.914000	0.39966	0.775000	0.33450	0.655000	0.94253	TTG		0.363	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		A	16650266	C	A	16650266	3	1	77	1	0	0	0	0	1	0	0	0	635	593	21	2	691	2	ANKMY2	7	16650266	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4380824	16650266	142488397	431	22167										
AHR	196	broad.mit.edu	37	chr7	17378642	17378642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aacagagcatttacgaaaacGaaatacgaagttgcctttta	7	7	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:17378642G>A	ENST00000242057.4	+	10	1836	c.1193G>A	c.(1192-1194)cGa>cAa	p.R398Q	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	398					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R398Q(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTACGAAAACGAAATACGAAG	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	7											121	125	124					7																	17378642		2203	4300	6503	17345167	SO:0001583	missense	196			L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1193G>A	7.37:g.17378642G>A	ENSP00000242057:p.Arg398Gln		17345167	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.950388	0.73787	.	.	ENSG00000106546	ENST00000242057	T	0.08458	3.09	6.07	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.37544	0.1007	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.50372	-0.8836	10	0.87932	D	0	.	15.381	0.74654	0.0664:0.0:0.9336:0.0	.	398	P35869	AHR_HUMAN	Q	398	ENSP00000242057:R398Q	ENSP00000242057:R398Q	R	+	2	0	AHR	17345167	1.000000	0.71417	0.724000	0.30704	0.200000	0.23975	9.779000	0.99018	1.583000	0.49898	0.655000	0.94253	CGA		0.333	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		A	17378642	G	A	17378642	3	1	77	1	0	0	0	0	1	0	0	0	416	1058	37	1	1231	1	AHR	7	17378642	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	728376	17378642	141760021	432	22168										
HDAC9	9734	broad.mit.edu	37	chr7	18801810	18801810	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcgaaaagccagcctggagGaaatacagcttgttcattct	10	9	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:18801810G>T	ENST00000432645.2	+	14	2065	c.2065G>T	c.(2065-2067)Gaa>Taa	p.E689*	HDAC9_ENST00000401921.1_Nonsense_Mutation_p.E648*|HDAC9_ENST00000441542.2_Nonsense_Mutation_p.E692*|HDAC9_ENST00000406451.4_Nonsense_Mutation_p.E689*	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	689	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.E692*(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CAGCCTGGAGGAAATACAGCT	0.483																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											72	72	72					7																	18801810		1932	4130	6062	18768335	SO:0001587	stop_gained	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2065G>T	7.37:g.18801810G>T	ENSP00000410337:p.Glu689*		18768335	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Nonsense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	39	7.616022	0.98390	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	.	.	.	5.56	4.69	0.59074	.	0.084642	0.51477	D	0.000095	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-37.7813	13.0689	0.59048	0.0746:0.0:0.9254:0.0	.	.	.	.	X	689;648;689;692;601	.	ENSP00000339165:E601X	E	+	1	0	HDAC9	18768335	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.990000	0.88215	1.485000	0.48380	0.655000	0.94253	GAA		0.483	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18801810	G	T	18801810	4	4	77	1	0	0	0	0	0	1	0	0	7035	1175	41	2	2179	2	HDAC9	7	18801810	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1423168	18801810	140336853	433	22169										
DNAH11	8701	broad.mit.edu	37	chr7	21856162	21856162	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaattgccgcctggaataaCgaaggactgcccagtgacag	11	11	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:21856162C>T	ENST00000409508.3	+	64	10441	c.10410C>T	c.(10408-10410)aaC>aaT	p.N3470N	DNAH11_ENST00000328843.6_Silent_p.N3477N	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3477	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.N3477N(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						CCTGGAATAACGAAGGACTGC	0.483									Kartagener syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	7											88	84	85					7																	21856162		1991	4149	6140	21822687	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10410C>T	7.37:g.21856162C>T			21822687	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.483	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21856162	C	T	21856162	2	4	77	1	0	0	0	0	0	0	0	1	4610	535	19	1		1	DNAH11	7	21856162	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3054352	21856162	137282501	434	22170										
CDCA7L	55536	broad.mit.edu	37	chr7	21942715	21942715	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caattgcagatcccacgacaGgggggacacacccaatccta					rs201829504		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:21942715delG	ENST00000406877.3	-	9	1494	c.1215delC	c.(1213-1215)cccfs	p.P405fs	CDCA7L_ENST00000356195.5_Frame_Shift_Del_p.P371fs|CDCA7L_ENST00000373934.4_Frame_Shift_Del_p.P359fs|CDCA7L_ENST00000465490.1_5'Flank	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	405					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.C406fs*46(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						TCCCACGACAGGGGGGACACA	0.517																																																2	Deletion - Frameshift(2)	large_intestine(2)	7											53	49	50					7																	21942715		2203	4300	6503	21909240	SO:0001589	frameshift_variant	55536				CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.1215delC	7.37:g.21942715delG	ENSP00000383986:p.Pro405fs		21909240	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Frame_Shift_Del	DEL	ENST00000406877.3	37	CCDS5374.1																																																																																				0.517	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719		-	21942715	G	-	21942715	7	5	77	1	0	1	0	1	0	0	0	0	3097	987	35	0	157	0	CDCA7L	7	21942715	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	86553	21942715	137195948	435	22171										
STK31	56164	broad.mit.edu	37	chr7	23809351	23809351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagactgagtcaagtgtctgCaaagagctggagatagctct	12	7	3	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:23809351C>T	ENST00000355870.3	+	13	1808	c.1689C>T	c.(1687-1689)tgC>tgT	p.C563C	STK31_ENST00000354639.3_Silent_p.C540C|STK31_ENST00000428484.1_Silent_p.C540C|STK31_ENST00000433467.2_Silent_p.C563C|STK31_ENST00000405627.3_3'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	563						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)	p.C563C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CAAGTGTCTGCAAAGAGCTGG	0.388																																																1	Substitution - coding silent(1)	large_intestine(1)	7											202	198	199					7																	23809351		2203	4300	6503	23775876	SO:0001819	synonymous_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1689C>T	7.37:g.23809351C>T			23775876	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				0.388	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		T	23809351	C	T	23809351	2	4	77	1	0	0	0	0	0	0	0	1	15335	718	25	3		3	STK31	7	23809351	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1866636	23809351	135329312	436	22172										
HOXA6	3203	broad.mit.edu	37	chr7	27186987	27186987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctcgtgtacttccggtcggCgccttcgtcatggagtgctt	13	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:27186987C>T	ENST00000222728.3	-	1	406	c.382G>A	c.(382-384)Gcc>Acc	p.A128T	HOXA6_ENST00000521478.1_5'UTR|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000524304.1_RNA	NM_024014.3	NP_076919.1	P31267	HXA6_HUMAN	homeobox A6	128					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A128T(1)		central_nervous_system(1)|large_intestine(5)|lung(3)|ovary(1)	10						TTCCGGTCGGCGCCTTCGTCA	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	7											84	81	82					7																	27186987		2203	4300	6503	27153512	SO:0001583	missense	3203				CCDS5407.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106006	ENSG00000106006		"Homeoboxes / ANTP class : HOXL subclass"	5107	protein-coding gene	gene with protein product		142951	"homeo box A6"	HOX1B, HOX1		1973146, 1358459	Standard	NM_024014		Approved		uc003syo.2	P31267	OTTHUMG00000023216	ENST00000222728.3:c.382G>A	7.37:g.27186987C>T	ENSP00000222728:p.Ala128Thr		27153512	A4D192|Q2M3G3|Q9UPM0	Missense_Mutation	SNP	ENST00000222728.3	37	CCDS5407.1	.	.	.	.	.	.	.	.	.	.	c	9.271	1.045556	0.19748	.	.	ENSG00000106006	ENST00000222728	D	0.90955	-2.76	5.07	1.34	0.21922	.	1.281110	0.05599	N	0.576036	T	0.72187	0.3429	N	0.00926	-1.1	0.24446	N	0.994508	B	0.02656	0.0	B	0.01281	0.0	T	0.62015	-0.6943	10	0.10636	T	0.68	.	7.0815	0.25234	0.1323:0.0832:0.0:0.7845	.	128	P31267	HXA6_HUMAN	T	128	ENSP00000222728:A128T	ENSP00000222728:A128T	A	-	1	0	HOXA6	27153512	0.624000	0.27102	0.999000	0.59377	0.994000	0.84299	0.398000	0.20899	-0.034000	0.13713	-0.142000	0.14014	GCC		0.612	HOXA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358697.1			T	27186987	C	T	27186987	3	4	77	1	0	0	0	0	1	0	0	0	7317	768	27	1	327	1	HOXA6	7	27186987	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3377636	27186987	131951676	437	22173										
FKBP14	55033	broad.mit.edu	37	chr7	30065965	30065965	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccgtccttttctaagtagcCttcatagtggaccaacatca	7	12	3	0	rs150170721		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:30065965C>A	ENST00000222803.5	-	1	335	c.160G>T	c.(160-162)Ggc>Tgc	p.G54C	AC007285.6_ENST00000422239.1_RNA|AC007285.6_ENST00000419103.1_RNA|PLEKHA8_ENST00000396259.1_5'Flank|PLEKHA8_ENST00000449726.1_5'Flank|PLEKHA8_ENST00000396257.2_5'Flank|PLEKHA8_ENST00000258679.7_5'Flank	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	54	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.G54C(1)		breast(1)|large_intestine(2)|lung(2)	5						TCTAAGTAGCCTTCATAGTGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											151	152	152					7																	30065965		2203	4300	6503	30032490	SO:0001583	missense	55033			AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"EF-hand domain containing"	18625	protein-coding gene	gene with protein product		614505	"FK506 binding protein 14 (22 kDa)"			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.160G>T	7.37:g.30065965C>A	ENSP00000222803:p.Gly54Cys		30032490		Missense_Mutation	SNP	ENST00000222803.5	37	CCDS5423.1	.	.	.	.	.	.	.	.	.	.	C	34	5.358229	0.95854	.	.	ENSG00000106080	ENST00000222803	T	0.61859	0.07	6.08	6.08	0.98989	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.044157	0.85682	D	0.000000	D	0.82379	0.5024	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83223	-0.0067	10	0.42905	T	0.14	-32.7721	19.2359	0.93858	0.0:1.0:0.0:0.0	.	54	Q9NWM8	FKB14_HUMAN	C	54	ENSP00000222803:G54C	ENSP00000222803:G54C	G	-	1	0	FKBP14	30032490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.894000	0.99253	0.591000	0.81541	GGC		0.433	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946		A	30065965	C	A	30065965	3	1	77	1	0	0	0	0	1	0	0	0	5923	681	24	2	491	2	FKBP14	7	30065965	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2878978	30065965	129072698	438	22174										
ADCYAP1R1	117	broad.mit.edu	37	chr7	31104495	31104495	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaagaaggagcaagccatgTgcctggagaagatccagagg	14	8	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:31104495T>C	ENST00000304166.4	+	3	389	c.100T>C	c.(100-102)Tgc>Cgc	p.C34R	ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.C34R|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.C34R|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.C34R	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	34					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.C34R(1)		endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						GCAAGCCATGTGCCTGGAGAA	0.592																																					Ovarian(44;225 1186 2158 11092)											1	Substitution - Missense(1)	large_intestine(1)	7											83	69	74					7																	31104495		2203	4300	6503	31071020	SO:0001583	missense	117				CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.100T>C	7.37:g.31104495T>C	ENSP00000306620:p.Cys34Arg		31071020	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.930057	0.73327	.	.	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000431811;ENST00000396211;ENST00000409489	T;T;T;T;T	0.56776	0.67;0.92;0.44;0.67;0.67	5.58	5.58	0.84498	GPCR, family 2, extracellular hormone receptor domain (1);	0.000000	0.85682	D	0.000000	T	0.67776	0.2929	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.89917	0.986;1.0;1.0;1.0;1.0	P;D;D;D;D	0.97110	0.864;0.954;0.999;1.0;0.997	T	0.70799	-0.4774	10	0.87932	D	0	.	12.1376	0.53981	0.0:0.0:0.0:1.0	.	34;34;34;34;34	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	R	34	ENSP00000306620:C34R;ENSP00000387335:C34R;ENSP00000400893:C34R;ENSP00000379514:C34R;ENSP00000386395:C34R	ENSP00000306620:C34R	C	+	1	0	ADCYAP1R1	31071020	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	4.240000	0.58701	2.115000	0.64714	0.460000	0.39030	TGC		0.592	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		C	31104495	T	C	31104495	3	2	77	1	0	0	0	0	1	0	0	0	303	1696	59	4	106	4	ADCYAP1R1	7	31104495	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1038530	31104495	128034168	439	22175										
AVL9	23080	broad.mit.edu	37	chr7	32593350	32593350	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acattgtaggtctgtcacctCgagatcttgtccttcatttt	7	10	4	1	rs149731136		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:32593350C>T	ENST00000318709.4	+	7	762	c.541C>T	c.(541-543)Cga>Tga	p.R181*	AVL9_ENST00000409301.1_Nonsense_Mutation_p.R181*|AVL9_ENST00000404479.1_Nonsense_Mutation_p.R181*	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	181					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)		p.R181*(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTGTCACCTCGAGATCTTGT	0.363																																																2	Substitution - Nonsense(2)	large_intestine(2)	7						C	stop/ARG	0,4406		0,0,2203	175	152	160		541	5.9	1	7	dbSNP_134	160	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	AVL9	NM_015060.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		181/649	32593350	1,13005	2203	4300	6503	32559875	SO:0001587	stop_gained	23080			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.541C>T	7.37:g.32593350C>T	ENSP00000315568:p.Arg181*		32559875	Q92573	Nonsense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	C	40	7.918173	0.98560	0.0	1.16E-4	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.3575	14.9745	0.71261	0.1426:0.8574:0.0:0.0	.	.	.	.	X	181;181;181;181;112	.	ENSP00000315568:R181X	R	+	1	2	AVL9	32559875	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.652000	0.46682	2.776000	0.95493	0.650000	0.86243	CGA		0.363	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		T	32593350	C	T	32593350	4	4	77	1	0	0	0	0	0	1	0	0	1229	876	31	1	567	1	AVL9	7	32593350	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1488855	32593350	126545313	440	22176										
NPSR1	387129	broad.mit.edu	37	chr7	34874019	34874019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catgtatggcattgtgatccGaactatttggattaaaagca	9	6	0	1	rs116249859	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:34874019G>A	ENST00000360581.1	+	6	832	c.704G>A	c.(703-705)cGa>cAa	p.R235Q	NPSR1_ENST00000359791.1_Missense_Mutation_p.R235Q|NPSR1_ENST00000381542.1_Missense_Mutation_p.R169Q|NPSR1_ENST00000531252.1_Missense_Mutation_p.R224Q|NPSR1_ENST00000381539.3_Missense_Mutation_p.R235Q	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	235						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)	p.R235Q(4)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	ATTGTGATCCGAACTATTTGG	0.438													G|||	4	0.000798722	0	0	5008	,	,		21671	0.004		0	False		,,,				2504	0															4	Substitution - Missense(4)	large_intestine(4)	7											197	169	179					7																	34874019		2203	4300	6503	34840544	SO:0001583	missense	387129			AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.704G>A	7.37:g.34874019G>A	ENSP00000353788:p.Arg235Gln		34840544	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	21.6	4.168595	0.78339	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	4.75	3.87	0.44632	GPCR, rhodopsin-like superfamily (1);	0.193094	0.29260	N	0.012678	T	0.56572	0.1994	M	0.64080	1.96	0.40488	D	0.980513	D;D;D;P;D;P	0.89917	1.0;1.0;1.0;0.892;1.0;0.911	D;P;D;P;P;P	0.66716	0.946;0.801;0.91;0.474;0.801;0.541	T	0.55405	-0.8146	10	0.31617	T	0.26	-5.4177	11.8755	0.52544	0.0859:0.0:0.9141:0.0	.	169;224;169;235;235;235	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	Q	235;169;235;224;235	ENSP00000353788:R235Q;ENSP00000370953:R169Q;ENSP00000352839:R235Q;ENSP00000433258:R224Q;ENSP00000370950:R235Q	ENSP00000352839:R235Q	R	+	2	0	NPSR1	34840544	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.383000	0.44354	1.212000	0.43366	0.555000	0.69702	CGA		0.438	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		A	34874019	G	A	34874019	3	1	77	1	0	0	0	0	1	0	0	0	10631	1058	37	1	726	1	NPSR1	7	34874019	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2280669	34874019	124264644	441	22177										
AMPH	273	broad.mit.edu	37	chr7	38502589	38502589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctacctgtgaaggtgaccGaggccgtgctggtgcgggag	17	10	0	2	rs151055033		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:38502589G>A	ENST00000356264.2	-	10	1089	c.874C>T	c.(874-876)Cgg>Tgg	p.R292W	AMPH_ENST00000428293.2_Missense_Mutation_p.R292W|AMPH_ENST00000325590.5_Missense_Mutation_p.R292W	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	292					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.R292W(2)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GAAGGTGACCGAGGCCGTGCT	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		18709	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	7											135	128	130					7																	38502589		2203	4300	6503	38469114	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.874C>T	7.37:g.38502589G>A	ENSP00000348602:p.Arg292Trp		38469114	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.47|18.47	3.631699|3.631699	0.67015|0.67015	.|.	.|.	ENSG00000078053|ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242;ENST00000544070|ENST00000441628	T;T;T|.	0.49432|.	0.78;0.78;0.78|.	6.17|6.17	-0.324|-0.324	0.12706|0.12706	.|.	0.238754|.	0.47455|.	D|.	0.000224|.	T|T	0.31071|0.31071	0.0785|0.0785	N|N	0.08118|0.08118	0|0	0.31913|0.31913	N|N	0.614416|0.614416	D;D;D|.	0.76494|.	0.999;0.999;0.999|.	D;P;P|.	0.65140|.	0.932;0.895;0.893|.	T|T	0.28038|0.28038	-1.0056|-1.0056	10|5	0.87932|.	D|.	0|.	-14.774|-14.774	16.7578|16.7578	0.85504|0.85504	0.0:0.0:0.443:0.557|0.0:0.0:0.443:0.557	.|.	292;292;48|.	P49418-2;P49418;Q8NFL4|.	.;AMPH_HUMAN;.|.	W|L	292;292;292;62;295|42	ENSP00000317441:R292W;ENSP00000348602:R292W;ENSP00000390734:R292W|.	ENSP00000317441:R292W|.	R|S	-|-	1|2	2|0	AMPH|AMPH	38469114|38469114	1.000000|1.000000	0.71417|0.71417	0.700000|0.700000	0.30305|0.30305	0.621000|0.621000	0.37620|0.37620	1.893000|1.893000	0.39758|0.39758	-0.265000|-0.265000	0.09352|0.09352	-0.262000|-0.262000	0.10625|0.10625	CGG|TCG		0.567	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38502589	G	A	38502589	3	1	77	1	0	0	0	0	1	0	0	0	588	1057	37	1	1261	1	AMPH	7	38502589	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3628570	38502589	120636074	442	22178										
POLM	27434	broad.mit.edu	37	chr7	44113770	44113770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcactctaggcagcagccccGcctcctgaccctccttgggg	10	18	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:44113770G>A	ENST00000242248.5	-	8	1132	c.1031C>T	c.(1030-1032)gCg>gTg	p.A344V	POLM_ENST00000395831.3_Intron|POLM_ENST00000492971.1_5'UTR|POLM_ENST00000335195.6_Intron	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	344					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.A344V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						CAGCAGCCCCGCCTCCTGACC	0.657								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	large_intestine(1)	7											42	36	38					7																	44113770		2203	4300	6503	44080295	SO:0001583	missense	27434			AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"DNA polymerases"	9185	protein-coding gene	gene with protein product	"Pol iota"	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.1031C>T	7.37:g.44113770G>A	ENSP00000242248:p.Ala344Val		44080295	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.498211	0.26861	.	.	ENSG00000122678	ENST00000242248	T	0.30182	1.54	5.67	0.965	0.19661	DNA-directed DNA polymerase X (1);	.	.	.	.	T	0.16085	0.0387	N	0.16903	0.455	0.80722	D	1	B	0.15719	0.014	B	0.04013	0.001	T	0.08827	-1.0703	9	0.28530	T	0.3	.	7.5611	0.27851	0.467:0.0:0.533:0.0	.	344	Q9NP87	DPOLM_HUMAN	V	344	ENSP00000242248:A344V	ENSP00000242248:A344V	A	-	2	0	POLM	44080295	0.000000	0.05858	0.537000	0.28052	0.522000	0.34438	-1.232000	0.02936	-0.103000	0.12175	-0.156000	0.13503	GCG		0.657	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		A	44113770	G	A	44113770	3	1	77	1	0	0	0	0	1	0	0	0	12237	1087	38	1	469	1	POLM	7	44113770	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5611181	44113770	115024893	443	22179										
ADCY1	107	broad.mit.edu	37	chr7	45717783	45717783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtaccaccagcttcaggacGagtatttcaccagcgccgtt	9	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:45717783G>A	ENST00000297323.7	+	10	1841	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	607					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.E607K(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCTTCAGGACGAGTATTTCAC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	7											221	203	209					7																	45717783		2203	4300	6503	45684308	SO:0001583	missense	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1819G>A	7.37:g.45717783G>A	ENSP00000297323:p.Glu607Lys		45684308	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	37	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.194024	0.58017	.	.	ENSG00000164742	ENST00000297323;ENST00000545300	T	0.59638	0.25	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.42653	0.1212	L	0.43152	1.355	0.80722	D	1	P	0.38788	0.647	B	0.26310	0.068	T	0.42258	-0.9462	10	0.09590	T	0.72	.	16.1939	0.82011	0.0:0.0:1.0:0.0	.	607	Q08828	ADCY1_HUMAN	K	607	ENSP00000297323:E607K	ENSP00000297323:E607K	E	+	1	0	ADCY1	45684308	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.205000	0.95048	2.482000	0.83794	0.655000	0.94253	GAG		0.532	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		A	45717783	G	A	45717783	3	1	77	1	0	0	0	0	1	0	0	0	292	1059	37	1	1857	1	ADCY1	7	45717783	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1604013	45717783	113420880	444	22180										
GRB10	2887	broad.mit.edu	37	chr7	50672999	50672999	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccttaccctccaggcgtgGccctcctccagggctgcgct	12	18	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:50672999G>A	ENST00000401949.1	-	15	1846	c.1377C>T	c.(1375-1377)ggC>ggT	p.G459G	GRB10_ENST00000406641.1_Silent_p.G401G|GRB10_ENST00000402497.1_Silent_p.G401G|GRB10_ENST00000398812.2_Silent_p.G459G|GRB10_ENST00000398810.2_Silent_p.G401G|GRB10_ENST00000402578.1_Silent_p.G401G|GRB10_ENST00000335866.3_Silent_p.G401G|GRB10_ENST00000403097.1_Silent_p.G453G|GRB10_ENST00000407526.1_Silent_p.G401G|GRB10_ENST00000439599.1_Silent_p.G453G|GRB10_ENST00000357271.5_Silent_p.G413G			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	459					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)	p.G453G(1)|p.G459G(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TCCAGGCGTGGCCCTCCTCCA	0.637									Russell-Silver syndrome																																							2	Substitution - coding silent(2)	large_intestine(2)	7											39	40	40					7																	50672999		1888	4102	5990	50640493	SO:0001819	synonymous_variant	2887	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1377C>T	7.37:g.50672999G>A			50640493	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																				0.637	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			A	50672999	G	A	50672999	2	1	77	1	0	0	0	0	0	0	0	1	6777	1190	42	3		3	GRB10	7	50672999	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4955216	50672999	108465664	445	22181										
ASL	435	broad.mit.edu	37	chr7	65548152	65548152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cattaggaccatggtggatcGggcagaggcgtgagtcctac	15	9	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:65548152G>A	ENST00000304874.9	+	6	539	c.437G>A	c.(436-438)cGg>cAg	p.R146Q	ASL_ENST00000380839.4_Missense_Mutation_p.R146Q|ASL_ENST00000395331.3_Missense_Mutation_p.R146Q|ASL_ENST00000395332.3_Missense_Mutation_p.R146Q	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	146					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)	p.R146Q(1)		breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	ATGGTGGATCGGGCAGAGGCG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	7											40	38	38					7																	65548152		2203	4300	6503	65185587	SO:0001583	missense	435				CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.437G>A	7.37:g.65548152G>A	ENSP00000307188:p.Arg146Gln		65185587	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Missense_Mutation	SNP	ENST00000304874.9	37	CCDS5531.1	.	.	.	.	.	.	.	.	.	.	g	20.3	3.974000	0.74246	.	.	ENSG00000126522	ENST00000304874;ENST00000380839;ENST00000395332;ENST00000362000;ENST00000395331	D;D;D;D;D	0.99429	-5.89;-5.89;-5.89;-5.89;-5.89	4.62	4.62	0.57501	Lyase 1, N-terminal (1);L-Aspartase-like (1);	0.000000	0.85682	D	0.000000	D	0.98988	0.9655	L	0.39467	1.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.991;0.999;0.916;0.999	D	0.99844	1.1064	10	0.10377	T	0.69	.	16.6169	0.84918	0.0:0.0:1.0:0.0	.	146;146;146;146	B4DU69;E9PE48;E7EMI0;P04424	.;.;.;ARLY_HUMAN	Q	146;146;146;81;146	ENSP00000307188:R146Q;ENSP00000370219:R146Q;ENSP00000378741:R146Q;ENSP00000354710:R81Q;ENSP00000378740:R146Q	ENSP00000307188:R146Q	R	+	2	0	ASL	65185587	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	6.771000	0.74996	2.401000	0.81631	0.407000	0.27541	CGG		0.637	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048		A	65548152	G	A	65548152	3	1	77	1	0	0	0	0	1	0	0	0	1045	1116	39	1	455	1	ASL	7	65548152	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	14875153	65548152	93590511	446	22182										
C7orf42	55069	broad.mit.edu	37	chr7	66418325	66418325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcagacctagcaaattgcGtcagagcaatcctgaatttt	10	9	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:66418325G>A	ENST00000341567.4	+	6	1148	c.893G>A	c.(892-894)cGt>cAt	p.R298H		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	298						integral component of membrane (GO:0016021)		p.R298H(1)									AGCAAATTGCGTCAGAGCAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	7											180	169	173					7																	66418325		2203	4300	6503	66055760	SO:0001583	missense	55069				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.893G>A	7.37:g.66418325G>A	ENSP00000340668:p.Arg298His		66055760	Q53H07|Q96FR2	Missense_Mutation	SNP	ENST00000341567.4	37	CCDS5536.1	.	.	.	.	.	.	.	.	.	.	G	35	5.523703	0.96431	.	.	ENSG00000106609	ENST00000341567	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.70288	-0.4913	9	0.72032	D	0.01	-0.5093	18.9796	0.92751	0.0:0.0:1.0:0.0	.	298	Q9NWD8	CG042_HUMAN	H	298	.	ENSP00000340668:R298H	R	+	2	0	C7orf42	66055760	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.394000	0.97261	2.723000	0.93209	0.655000	0.94253	CGT		0.443	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		A	66418325	G	A	66418325	3	1	77	1	0	0	0	0	1	0	0	0	2398	1145	40	1	911	1	C7orf42	7	66418325	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	870173	66418325	92720338	447	22183										
NSUN5	55695	broad.mit.edu	37	chr7	72718372	72718372	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcgtggccatggatgccagCcgcttggcatccaggtcaaa	13	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:72718372C>T	ENST00000252594.6	-	7	804	c.789G>A	c.(787-789)cgG>cgA	p.R263R	NSUN5_ENST00000310326.8_Silent_p.R263R|NSUN5_ENST00000438747.2_Silent_p.R263R|NSUN5_ENST00000428206.1_Silent_p.R225R			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	263					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.R263R(2)		breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				TGGATGCCAGCCGCTTGGCAT	0.622																																																2	Substitution - coding silent(2)	large_intestine(2)	7											31	33	32					7																	72718372		2203	4300	6503	72356308	SO:0001819	synonymous_variant	55695			AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"NOP2/Sun domain containing"	16385	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 5A"	615732	"Williams Beuren syndrome chromosome region 20A", "NOL1/NOP2/Sun domain family, member 5"	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.789G>A	7.37:g.72718372C>T			72356308	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																				0.622	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956		T	72718372	C	T	72718372	2	4	77	1	0	0	0	0	0	0	0	1	10712	726	26	3		3	NSUN5	7	72718372	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6300047	72718372	86420291	448	22184										
GTF2IRD1	9569	broad.mit.edu	37	chr7	73933929	73933929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcacggcgctccccaaccacGccatccgagagctcaagcag	10	18	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:73933929G>A	ENST00000265755.3	+	6	1189	c.796G>A	c.(796-798)Gcc>Acc	p.A266T	GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A266T|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.A266T|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A298T	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	266					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A266T(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCCCAACCACGCCATCCGAGA	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	7											56	49	51					7																	73933929		2203	4300	6503	73571865	SO:0001583	missense	9569			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.796G>A	7.37:g.73933929G>A	ENSP00000265755:p.Ala266Thr		73571865	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	G	7.496	0.651605	0.14516	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.30448	1.54;1.53;1.54;1.53	5.13	-10.3	0.00346	.	0.666459	0.15396	N	0.264577	T	0.09730	0.0239	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.06405	0.0;0.001;0.002;0.002	T	0.18903	-1.0322	10	0.10377	T	0.69	-3.9035	10.9195	0.47156	0.6142:0.1858:0.2:0.0	.	298;266;266;266	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	T	266;298;266;266	ENSP00000265755:A266T;ENSP00000397566:A298T;ENSP00000408477:A266T;ENSP00000418383:A266T	ENSP00000265755:A266T	A	+	1	0	GTF2IRD1	73571865	0.000000	0.05858	0.000000	0.03702	0.929000	0.56500	-1.324000	0.02690	-2.716000	0.00391	-0.258000	0.10820	GCC		0.697	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		A	73933929	G	A	73933929	3	1	77	1	0	0	0	0	1	0	0	0	6889	1087	38	1	814	1	GTF2IRD1	7	73933929	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1215557	73933929	85204734	449	22185										
GTF2IRD2	84163	broad.mit.edu	37	chr7	74212435	74212435	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccatatactggtcataatgCttgctgtgattggtttgata	9	6	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:74212435C>T	ENST00000405086.2	-	16	1605	c.1416G>A	c.(1414-1416)aaG>aaA	p.K472K	GTF2IRD2_ENST00000451013.2_Silent_p.K19K	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K472K(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						ggtcataatgcttgctgtgat	0.423																																					NSCLC(40;560 1096 7501 40315 49546)											1	Substitution - coding silent(1)	large_intestine(1)	7											214	190	198					7																	74212435		2203	4300	6503	73850371	SO:0001819	synonymous_variant	84163			BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"transcription factor GTF2IRD2"	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1416G>A	7.37:g.74212435C>T			73850371	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Silent	SNP	ENST00000405086.2	37	CCDS5576.1																																																																																				0.423	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537		T	74212435	C	T	74212435	2	4	77	1	0	0	0	0	0	0	0	1	6890	796	28	3		3	GTF2IRD2	7	74212435	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	278506	74212435	84926228	450	22186										
FZD1	8321	broad.mit.edu	37	chr7	90895546	90895546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacagtattttcacctggccGcctgggctgtgccggccatc	11	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:90895546G>A	ENST00000287934.2	+	1	1764	c.1351G>A	c.(1351-1353)Gcc>Acc	p.A451T		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	451					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A451T(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			TCACCTGGCCGCCTGGGCTGT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	7											85	82	83					7																	90895546		2203	4300	6503	90733482	SO:0001583	missense	8321			AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1351G>A	7.37:g.90895546G>A	ENSP00000287934:p.Ala451Thr		90733482	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483778	0.84854	.	.	ENSG00000157240	ENST00000287934	D	0.85861	-2.04	4.52	4.52	0.55395	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000006	D	0.92103	0.7497	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.67900	0.954	D	0.93218	0.6606	10	0.66056	D	0.02	.	17.4373	0.87555	0.0:0.0:1.0:0.0	.	451	Q9UP38	FZD1_HUMAN	T	451	ENSP00000287934:A451T	ENSP00000287934:A451T	A	+	1	0	FZD1	90733482	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.657000	0.98554	2.352000	0.79861	0.462000	0.41574	GCC		0.622	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		A	90895546	G	A	90895546	3	1	77	1	0	0	0	0	1	0	0	0	6147	1087	38	1	1353	1	FZD1	7	90895546	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	16683111	90895546	68243117	451	22187										
AKAP9	10142	broad.mit.edu	37	chr7	91707148	91707148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accaattaaatgaacaagttAcgaaactccagcagcaactt	5	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:91707148A>G	ENST00000359028.2	+	31	7165	c.6940A>G	c.(6940-6942)Acg>Gcg	p.T2314A	AKAP9_ENST00000356239.3_Missense_Mutation_p.T2302A|AKAP9_ENST00000358100.2_Missense_Mutation_p.T2314A			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2314	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.T2302A(1)|p.T2314A(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAACAAGTTACGAAACTCCA	0.313			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - Missense(2)	large_intestine(2)	7											72	71	71					7																	91707148		2203	4300	6503	91545084	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.6940A>G	7.37:g.91707148A>G	ENSP00000351922:p.Thr2314Ala		91545084	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	1.504	-0.551204	0.03996	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03413	4.03;4.03;4.02;3.94	5.53	-0.74	0.11115	.	1.447210	0.04714	N	0.418175	T	0.01976	0.0062	N	0.04880	-0.145	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.45145	-0.9281	10	0.08837	T	0.75	.	7.1213	0.25446	0.3284:0.0:0.5274:0.1441	.	2306;2314;2302;2294	Q99996-6;Q99996;Q99996-2;Q99996-3	.;AKAP9_HUMAN;.;.	A	2302;2314;2314;2306;148	ENSP00000348573:T2302A;ENSP00000351922:T2314A;ENSP00000350813:T2314A;ENSP00000378042:T148A	ENSP00000348573:T2302A	T	+	1	0	AKAP9	91545084	0.001000	0.12720	0.080000	0.20451	0.018000	0.09664	0.043000	0.13971	-0.063000	0.13065	-0.462000	0.05337	ACG		0.313	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91707148	A	G	91707148	3	3	77	1	0	0	0	0	1	0	0	0	459	391	14	4	7022	4	AKAP9	7	91707148	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	811602	91707148	67431515	452	22188										
DLX5	1749	broad.mit.edu	37	chr7	96653798	96653798	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccccgtagggctgtagtaGtcagaatcggtagctgaaga	13	10	1	3	rs370973096		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:96653798G>A	ENST00000222598.4	-	1	611	c.138C>T	c.(136-138)gaC>gaT	p.D46D	DLX5_ENST00000486603.2_Silent_p.D46D|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	46					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.D46D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGCTGTAGTAGTCAGAATCGG	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	7											51	56	54					7																	96653798		2203	4300	6503	96491734	SO:0001819	synonymous_variant	1749				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.138C>T	7.37:g.96653798G>A			96491734	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																				0.587	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			A	96653798	G	A	96653798	2	1	77	1	0	0	0	0	0	0	0	1	4585	1020	36	3		3	DLX5	7	96653798	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4946650	96653798	62484865	453	22189										
TRRAP	8295	broad.mit.edu	37	chr7	98490132	98490132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacaaaaaatgttttgtctgTgatgtttcgctttttagagg	9	5	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:98490132T>C	ENST00000359863.4	+	5	556	c.347T>C	c.(346-348)gTg>gCg	p.V116A	TRRAP_ENST00000446306.3_Missense_Mutation_p.V116A|TRRAP_ENST00000355540.3_Missense_Mutation_p.V116A	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	116					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.V116A(2)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTTTTGTCTGTGATGTTTCGC	0.338																																																2	Substitution - Missense(2)	large_intestine(2)	7											110	111	111					7																	98490132		2203	4300	6503	98328068	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.347T>C	7.37:g.98490132T>C	ENSP00000352925:p.Val116Ala		98328068	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.749041	0.69533	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.63580	3.55;-0.05	5.97	5.97	0.96955	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.50394	0.1613	N	0.20986	0.625	0.80722	D	1	P;B	0.35872	0.525;0.39	B;B	0.35353	0.201;0.099	T	0.50841	-0.8780	10	0.36615	T	0.2	.	16.4383	0.83889	0.0:0.0:0.0:1.0	.	116;116	Q9Y4A5-2;Q9Y4A5	.;TRRAP_HUMAN	A	116	ENSP00000352925:V116A;ENSP00000347733:V116A	ENSP00000347733:V116A	V	+	2	0	TRRAP	98328068	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.958000	0.87877	2.287000	0.76781	0.482000	0.46254	GTG		0.338	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		C	98490132	T	C	98490132	3	2	77	1	0	0	0	0	1	0	0	0	16641	1696	59	4	361	4	TRRAP	7	98490132	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1836334	98490132	60648531	454	22190										
TRRAP	8295	broad.mit.edu	37	chr7	98533291	98533291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcgtacctttacgaattgcGgcattaagtaagttaatgaa	8	7	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:98533291G>A	ENST00000359863.4	+	28	4313	c.4104G>A	c.(4102-4104)gcG>gcA	p.A1368A	TRRAP_ENST00000446306.3_Silent_p.A1367A|TRRAP_ENST00000355540.3_Silent_p.A1368A	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1368					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.A1368A(2)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TACGAATTGCGGCATTAAGTA	0.393																																																2	Substitution - coding silent(2)	large_intestine(2)	7											62	57	59					7																	98533291		2203	4300	6503	98371227	SO:0001819	synonymous_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4104G>A	7.37:g.98533291G>A			98371227	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	4.225	0.040625	0.08196	.	.	ENSG00000196367	ENST00000456197	.	.	.	6.17	-0.455	0.12193	.	.	.	.	.	T	0.39708	0.1088	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21348	-1.0248	4	.	.	.	.	1.0201	0.01516	0.4513:0.0995:0.1776:0.2716	.	.	.	.	Q	1083	.	.	R	+	2	0	TRRAP	98371227	0.040000	0.19996	0.977000	0.42913	0.385000	0.30292	-0.577000	0.05847	-0.279000	0.09167	-2.272000	0.00274	CGG		0.393	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98533291	G	A	98533291	2	1	77	1	0	0	0	0	0	0	0	1	16641	1103	39	1		1	TRRAP	7	98533291	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	43159	98533291	60605372	455	22191										
ZKSCAN5	23660	broad.mit.edu	37	chr7	99129114	99129114	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatgtgggaaaagctacaacCaacgcgtgcacctaactcag	9	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:99129114C>A	ENST00000394170.2	+	7	2013	c.1762C>A	c.(1762-1764)Caa>Aaa	p.Q588K	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.Q588K|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.Q588K	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	588					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q588K(2)		breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AAGCTACAACCAACGCGTGCA	0.493																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	7											99	93	95					7																	99129114		2203	4300	6503	98967050	SO:0001583	missense	23660			AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.1762C>A	7.37:g.99129114C>A	ENSP00000377725:p.Gln588Lys		98967050	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600986	0.46423	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.35421	1.31;1.31;1.31	5.22	5.22	0.72569	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000064	T	0.44540	0.1298	L	0.39898	1.24	0.21220	N	0.999758	D;D	0.71674	0.993;0.998	P;P	0.55824	0.711;0.785	T	0.27226	-1.0080	10	0.30854	T	0.27	.	16.6795	0.85288	0.0:1.0:0.0:0.0	.	588;588	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	K	588	ENSP00000322872:Q588K;ENSP00000392104:Q588K;ENSP00000377725:Q588K	ENSP00000322872:Q588K	Q	+	1	0	ZKSCAN5	98967050	0.000000	0.05858	0.729000	0.30791	0.870000	0.49936	-0.339000	0.07832	2.890000	0.99128	0.585000	0.79938	CAA		0.493	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		A	99129114	C	A	99129114	3	1	77	1	0	0	0	0	1	0	0	0	17729	595	21	2	1784	2	ZKSCAN5	7	99129114	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	595823	99129114	60009549	456	22192										
ZSCAN21	7589	broad.mit.edu	37	chr7	99661734	99661734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acactggggagaaaccttacGtgtgcaccaagtgtgggaaa	13	8	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:99661734G>A	ENST00000292450.4	+	4	1080	c.916G>A	c.(916-918)Gtg>Atg	p.V306M	ZSCAN21_ENST00000456748.2_Silent_p.T271T|ZSCAN21_ENST00000543588.1_Silent_p.T271T|ZNF3_ENST00000413658.2_3'UTR|ZSCAN21_ENST00000477297.1_3'UTR	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	306					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V306M(1)		breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GAAACCTTACGTGTGCACCAA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	7											72	70	71					7																	99661734		2203	4300	6503	99499670	SO:0001583	missense	7589			AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.916G>A	7.37:g.99661734G>A	ENSP00000292450:p.Val306Met		99499670	A4D2A6|D6W5T9|Q9H0B5	Missense_Mutation	SNP	ENST00000292450.4	37	CCDS5681.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.103387	0.37145	.	.	ENSG00000166529	ENST00000292450;ENST00000379635	T	0.34472	1.36	4.08	2.2	0.27929	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.227404	0.23123	N	0.051667	T	0.35480	0.0933	L	0.33753	1.03	0.09310	N	1	D	0.60575	0.988	P	0.53224	0.721	T	0.10753	-1.0616	10	0.56958	D	0.05	.	8.8278	0.35065	0.1675:0.0:0.8325:0.0	.	306	Q9Y5A6	ZSC21_HUMAN	M	306;281	ENSP00000292450:V306M	ENSP00000292450:V306M	V	+	1	0	ZSCAN21	99499670	0.000000	0.05858	0.154000	0.22540	0.887000	0.51463	-0.481000	0.06552	0.638000	0.30545	0.655000	0.94253	GTG		0.478	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		A	99661734	G	A	99661734	3	1	77	1	0	0	0	0	1	0	0	0	18272	1145	40	1	926	1	ZSCAN21	7	99661734	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	532620	99661734	59476929	457	22193										
ZAN	7455	broad.mit.edu	37	chr7	100361686	100361686	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgaaggccgcttccttcttCgacagctgcatgcttgatat	10	11	1	2	rs377380617		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:100361686C>T	ENST00000348028.3	+	0	4299				ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000349350.6_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F1378F(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CTTCCTTCTTCGACAGCTGCA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	7						C	,	1,4307		0,1,2153	64	63	63		4134,4134	-4.9	0	7		63	0,8508		0,0,4254	no	coding-synonymous,coding-synonymous	ZAN	NM_003386.1,NM_173059.1	,	0,1,6407	TT,TC,CC		0.0,0.0232,0.0078	,	1378/2813,1378/2722	100361686	1,12815	2154	4254	6408	100199622			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100361686C>T			100199622	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Silent	SNP	ENST00000348028.3	37																																																																																					0.612	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100361686	C	T	100361686	1	4	77	0	1	0	0	0	0	0	0	0	17553	883	31	1		1	ZAN	7	100361686	RNA	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	699952	100361686	58776977	458	22194										
EPHB4	2050	broad.mit.edu	37	chr7	100405106	100405106	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttgcgagcagccaggtctcGgtggacgtagctcatctcgg	15	11	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:100405106G>A	ENST00000358173.3	-	13	2683	c.2215C>T	c.(2215-2217)Cga>Tga	p.R739*	EPHB4_ENST00000360620.3_Nonsense_Mutation_p.R739*	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	739	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R739*(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCCAGGTCTCGGTGGACGTAG	0.582																																					GBM(200;2113 3072 25865 52728)											1	Substitution - Nonsense(1)	large_intestine(1)	7											174	132	146					7																	100405106		2203	4300	6503	100243042	SO:0001587	stop_gained	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.2215C>T	7.37:g.100405106G>A	ENSP00000350896:p.Arg739*		100243042	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Nonsense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	G	44	10.739601	0.99460	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	.	.	.	4.65	4.65	0.58169	.	0.000000	0.40302	N	0.001137	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0272	0.71680	0.0:0.0:1.0:0.0	.	.	.	.	X	739	.	ENSP00000350896:R739X	R	-	1	2	EPHB4	100243042	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.503000	0.73699	2.124000	0.65301	0.313000	0.20887	CGA		0.582	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100405106	G	A	100405106	4	1	77	1	0	0	0	0	0	1	0	0	5190	1124	39	1	768	1	EPHB4	7	100405106	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	43420	100405106	58733557	459	22195										
TRIM56	81844	broad.mit.edu	37	chr7	100731313	100731313	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggagggtggagaaggaggcGctagcccggctgcgggagca	21	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:100731313G>A	ENST00000306085.6	+	3	1017	c.720G>A	c.(718-720)gcG>gcA	p.A240A		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	240					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A240A(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					AGAAGGAGGCGCTAGCCCGGC	0.726																																					Ovarian(89;1092 1379 22756 38989 39611)											1	Substitution - coding silent(1)	large_intestine(1)	7											7	10	9					7																	100731313		2093	4193	6286	100518033	SO:0001819	synonymous_variant	81844			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.720G>A	7.37:g.100731313G>A			100518033	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																				0.726	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		A	100731313	G	A	100731313	2	1	77	1	0	0	0	0	0	0	0	1	16570	1074	38	1		1	TRIM56	7	100731313	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	326207	100731313	58407350	460	22196										
PLOD3	8985	broad.mit.edu	37	chr7	100855927	100855927	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaacacggccagaaacacccGggggggaggctggaagatgc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:100855927delG	ENST00000223127.3	-	9	1287	c.889delC	c.(889-891)cggfs	p.R297fs		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	297					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)	p.R297fs*61(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	AGAAACACCCGGGGGGGAGGC	0.642																																																2	Deletion - Frameshift(2)	large_intestine(2)	7											28	35	33					7																	100855927		2202	4297	6499	100642647	SO:0001589	frameshift_variant	8985			AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"lysyl hydroxlase 3"	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.889delC	7.37:g.100855927delG	ENSP00000223127:p.Arg297fs		100642647	B2R6W6|Q540C3	Frame_Shift_Del	DEL	ENST00000223127.3	37	CCDS5715.1																																																																																				0.642	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1			-	100855927	G	-	100855927	7	5	77	1	0	1	0	1	0	0	0	0	12134	1115	39	0	1371	0	PLOD3	7	100855927	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	124614	100855927	58282736	461	22197										
FIS1	51024	broad.mit.edu	37	chr7	100883435	100883435	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgtcacctttcttcatggCcttgtcaatgagccgctcca	8	14	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:100883435C>A	ENST00000223136.4	-	4	429	c.349G>T	c.(349-351)Gcc>Tcc	p.A117S	FIS1_ENST00000442303.1_3'UTR|CLDN15_ENST00000401528.1_5'Flank|CLDN15_ENST00000433422.1_5'Flank|FIS1_ENST00000474120.1_3'UTR|FIS1_ENST00000482199.1_5'UTR|CLDN15_ENST00000308344.5_5'Flank	NM_016068.2	NP_057152.2	Q9Y3D6	FIS1_HUMAN	fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)	117					calcium-mediated signaling using intracellular calcium source (GO:0035584)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|mitochondrion morphogenesis (GO:0070584)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|peroxisome fission (GO:0016559)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|release of cytochrome c from mitochondria (GO:0001836)	integral component of mitochondrial outer membrane (GO:0031307)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|protein complex (GO:0043234)	receptor binding (GO:0005102)	p.A117S(1)		kidney(1)|large_intestine(2)|lung(1)	4	Lung NSC(181;0.168)|all_lung(186;0.215)					TTCTTCATGGCCTTGTCAATG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7											139	142	141					7																	100883435		2052	4187	6239	100670155	SO:0001583	missense	51024			AF151893	CCDS43626.1	7q22.1	2012-10-01	2006-04-04	2006-01-24	ENSG00000214253	ENSG00000214253			21689	protein-coding gene	gene with protein product	"CGI-135 protein"	609003	"tetratricopeptide repeat domain 11", "fission 1 (mitochondrial outer membrane) homolog (yeast)"	TTC11		14996942, 16010987	Standard	NM_016068		Approved	CGI-135, H_NH0132A01.6, Fis1	uc003uyj.4	Q9Y3D6	OTTHUMG00000157106	ENST00000223136.4:c.349G>T	7.37:g.100883435C>A	ENSP00000223136:p.Ala117Ser		100670155	Q9BTP3	Missense_Mutation	SNP	ENST00000223136.4	37	CCDS43626.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.649166	0.67358	.	.	ENSG00000214253	ENST00000223136	.	.	.	5.1	4.19	0.49359	Tetratricopeptide-like helical (1);	0.000000	0.64402	U	0.000019	T	0.76343	0.3974	M	0.77103	2.36	0.51233	D	0.999917	B	0.27416	0.178	P	0.45829	0.494	T	0.73889	-0.3840	9	0.35671	T	0.21	.	13.1066	0.59252	0.0:0.8374:0.1626:0.0	.	117	Q9Y3D6	FIS1_HUMAN	S	117	.	ENSP00000223136:A117S	A	-	1	0	FIS1	100670155	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.572000	0.74005	1.111000	0.41721	0.561000	0.74099	GCC		0.587	FIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347449.1	NM_016068		A	100883435	C	A	100883435	3	1	77	1	0	0	0	0	1	0	0	0	5916	739	26	2	117	2	FIS1	7	100883435	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	27508	100883435	58255228	462	22198										
CUX1	1523	broad.mit.edu	37	chr7	101845304	101845304	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcgagacaccacagaacagCcccctgccatcctccccgat					rs137933356		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:101845304delC	ENST00000292535.7	+	18	2765	c.2727delC	c.(2725-2727)agcfs	p.S909fs	CUX1_ENST00000550008.2_Frame_Shift_Del_p.S853fs|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Frame_Shift_Del_p.S807fs|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000549414.2_Frame_Shift_Del_p.S887fs|CUX1_ENST00000360264.3_Frame_Shift_Del_p.S920fs|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Frame_Shift_Del_p.S751fs|CUX1_ENST00000393824.3_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	909					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.L911fs*20(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CACAGAACAGCCCCCTGCCAT	0.652																																																1	Deletion - Frameshift(1)	large_intestine(1)	7											120	114	116					7																	101845304		2203	4300	6503	101632024	SO:0001589	frameshift_variant	1523			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2727delC	7.37:g.101845304delC	ENSP00000292535:p.Ser909fs		101632024	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Frame_Shift_Del	DEL	ENST00000292535.7	37	CCDS5721.1																																																																																				0.652	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		-	101845304	C	-	101845304	7	5	77	1	0	1	0	1	0	0	0	0	4070	738	26	0	2864	0	CUX1	7	101845304	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	961869	101845304	57293359	463	22199										
CDHR3	222256	broad.mit.edu	37	chr7	105641916	105641916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctctgttccagcccgacacGagtgtacacagtcctggagg	11	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:105641916G>A	ENST00000317716.9	+	7	802	c.722G>A	c.(721-723)cGa>cAa	p.R241Q	CDHR3_ENST00000478080.1_Missense_Mutation_p.R153Q|CDHR3_ENST00000542731.1_Missense_Mutation_p.R241Q|CDHR3_ENST00000541203.1_Missense_Mutation_p.E142K|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	241	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R241Q(1)		breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AGCCCGACACGAGTGTACACA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	7											117	115	116					7																	105641916		1991	4157	6148	105429152	SO:0001583	missense	222256			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.722G>A	7.37:g.105641916G>A	ENSP00000325954:p.Arg241Gln		105429152	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.65|13.65	2.300659|2.300659	0.40694|0.40694	.|.	.|.	ENSG00000128536|ENSG00000128536	ENST00000541203|ENST00000542731;ENST00000317716;ENST00000478080	T|T;T;T	0.29917|0.37752	1.55|1.18;1.18;1.18	5.38|5.38	2.15|2.15	0.27550|0.27550	.|Cadherin (2);Cadherin-like (1);	.|0.673417	.|0.13301	.|N	.|0.398224	T|T	0.44912|0.44912	0.1316|0.1316	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	0.999998|0.999998	.|D;D	.|0.69078	.|0.988;0.997	.|P;P	.|0.57468	.|0.632;0.821	T|T	0.21724|0.21724	-1.0237|-1.0237	7|10	0.87932|0.72032	D|D	0|0.01	-0.795|-0.795	5.541|5.541	0.17038|0.17038	0.1925:0.2627:0.5448:0.0|0.1925:0.2627:0.5448:0.0	.|.	.|228;241	.|B3KYA0;Q6ZTQ4	.|.;CDHR3_HUMAN	K|Q	142|241;241;153	ENSP00000443733:E142K|ENSP00000439766:R241Q;ENSP00000325954:R241Q;ENSP00000417771:R153Q	ENSP00000419593:E54K|ENSP00000325954:R241Q	E|R	+|+	1|2	0|0	CDHR3|CDHR3	105429152|105429152	0.004000|0.004000	0.15560|0.15560	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	0.562000|0.562000	0.23531|0.23531	1.141000|1.141000	0.42275|0.42275	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.507	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		A	105641916	G	A	105641916	3	1	77	1	0	0	0	0	1	0	0	0	3126	1058	37	1	748	1	CDHR3	7	105641916	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3796612	105641916	53496747	464	22200										
CDHR3	222256	broad.mit.edu	37	chr7	105653318	105653318	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaccagcattatggtgccGgaaagaacagccaaggggac	12	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:105653318G>T	ENST00000317716.9	+	9	1145	c.1065G>T	c.(1063-1065)ccG>ccT	p.P355P	CDHR3_ENST00000478080.1_Silent_p.P267P|CDHR3_ENST00000542731.1_Silent_p.P355P|CDHR3_ENST00000541203.1_3'UTR|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000343407.5_Silent_p.P72P	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	355	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P355P(1)		breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						TTATGGTGCCGGAAAGAACAG	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	7											250	235	240					7																	105653318		1981	4175	6156	105440554	SO:0001819	synonymous_variant	222256			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1065G>T	7.37:g.105653318G>T			105440554	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																				0.468	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		T	105653318	G	T	105653318	2	4	77	1	0	0	0	0	0	0	0	1	3126	1103	39	2		2	CDHR3	7	105653318	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11402	105653318	53485345	465	22201										
DLD	1738	broad.mit.edu	37	chr7	107556141	107556141	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agatggaaaaattgatgtttCgtaagtatacatcatttgtt	8	3	1	2	rs201652869		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:107556141C>T	ENST00000205402.5	+	9	1156	c.875C>T	c.(874-876)tCt>tTt	p.S292F	DLD_ENST00000437604.2_Splice_Site_p.S244F|DLD_ENST00000440410.1_Splice_Site_p.S269F|DLD_ENST00000537148.1_Splice_Site_p.S193F	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	292					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)	p.S292F(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	ATTGATGTTTCGTAAGTATAC	0.313																																																1	Substitution - Missense(1)	large_intestine(1)	7						C	PHE/SER	0,4406		0,0,2203	48	49	49		875	3.5	1	7		49	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	DLD	NM_000108.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	292/510	107556141	1,13005	2203	4300	6503	107343377	SO:0001630	splice_region_variant	1738			AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.875+1C>T	7.37:g.107556141C>T			107343377	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	37	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.910567	0.72983	0.0	1.16E-4	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000537148;ENST00000440410;ENST00000437604;ENST00000539590	T;T;T;T;T	0.66460	-0.21;-0.21;0.34;-0.21;0.34	5.3	3.51	0.40186	Pyridine nucleotide-disulphide oxidoreductase, NAD-binding domain (1);Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.208574	0.49916	N	0.000138	T	0.76681	0.4021	M	0.82056	2.57	0.58432	D	0.999999	P;P;D	0.63880	0.879;0.513;0.993	P;B;P	0.55455	0.544;0.329;0.776	T	0.79240	-0.1885	10	0.72032	D	0.01	-1.8583	11.8398	0.52346	0.0:0.8586:0.0:0.1414	.	269;244;292	E9PEX6;B4DT69;P09622	.;.;DLDH_HUMAN	F	292;292;193;269;244;242	ENSP00000205402:S292F;ENSP00000390667:S292F;ENSP00000442399:S193F;ENSP00000417016:S269F;ENSP00000387542:S244F	ENSP00000205402:S292F	S	+	2	0	DLD	107343377	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.247000	0.51422	0.812000	0.34326	0.591000	0.81541	TCT		0.313	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108	Missense_Mutation	T	107556141	C	T	107556141	5	4	77	1	0	0	0	0	0	0	1	0	4562	898	31	1	909	1	DLD	7	107556141	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1902823	107556141	51582522	466	22202										
LAMB4	22798	broad.mit.edu	37	chr7	107671367	107671367	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaaagtccatcctccagccCtgatcgctgctttgctaact	8	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:107671367C>A	ENST00000388781.3	-	32	4959	c.4876G>T	c.(4876-4878)Ggg>Tgg	p.G1626W	LAMB4_ENST00000483484.1_Intron|LAMB4_ENST00000388780.3_Missense_Mutation_p.G1626W|LAMB4_ENST00000205386.4_Missense_Mutation_p.G1626W	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1626	Domain I.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.G1626W(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TCCTCCAGCCCTGATCGCTGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	7											203	155	171					7																	107671367		2203	4300	6503	107458603	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.4876G>T	7.37:g.107671367C>A	ENSP00000373433:p.Gly1626Trp		107458603	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	7.968	0.748549	0.15710	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.79141	1.43;1.43;-1.24;1.45	5.01	0.858	0.19030	.	3.052940	0.01089	N	0.005155	T	0.57154	0.2034	N	0.08118	0	0.09310	N	1	P;P	0.50066	0.931;0.574	B;B	0.35240	0.198;0.176	T	0.58399	-0.7643	10	0.72032	D	0.01	.	6.6246	0.22823	0.0:0.5834:0.0:0.4166	.	1626;1626	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	W	1626;1626;652;1626	ENSP00000205386:G1626W;ENSP00000373433:G1626W;ENSP00000416562:G652W;ENSP00000373432:G1626W	ENSP00000205386:G1626W	G	-	1	0	LAMB4	107458603	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	0.058000	0.14301	0.293000	0.22520	0.585000	0.79938	GGG		0.473	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107671367	C	A	107671367	3	1	77	1	0	0	0	0	1	0	0	0	8635	681	24	2	421	2	LAMB4	7	107671367	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	115226	107671367	51467296	467	22203										
LAMB4	22798	broad.mit.edu	37	chr7	107746459	107746459	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtaaagtttatcctcaggtTtgtcaatgtcacaaggtcta	9	7	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:107746459T>C	ENST00000388781.3	-	8	756	c.673A>G	c.(673-675)Aac>Gac	p.N225D	LAMB4_ENST00000414450.2_Missense_Mutation_p.N225D|LAMB4_ENST00000418464.1_Missense_Mutation_p.N225D|LAMB4_ENST00000388780.3_Missense_Mutation_p.N225D|LAMB4_ENST00000205386.4_Missense_Mutation_p.N225D	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	225	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.N225D(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ATCCTCAGGTTTGTCAATGTC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	84	86					7																	107746459		2203	4300	6503	107533695	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.673A>G	7.37:g.107746459T>C	ENSP00000373433:p.Asn225Asp		107533695	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640723	0.87859	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	4.73	4.73	0.59995	Laminin, N-terminal (3);	0.000000	0.53938	D	0.000059	D	0.83339	0.5233	L	0.60957	1.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85396	0.1128	10	0.87932	D	0	.	14.3948	0.67003	0.0:0.0:0.0:1.0	.	225	A4D0S4	LAMB4_HUMAN	D	225	ENSP00000205386:N225D;ENSP00000373433:N225D;ENSP00000373432:N225D;ENSP00000402353:N225D;ENSP00000402265:N225D	ENSP00000205386:N225D	N	-	1	0	LAMB4	107533695	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.170000	0.77587	1.981000	0.57761	0.533000	0.62120	AAC		0.388	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		C	107746459	T	C	107746459	3	2	77	1	0	0	0	0	1	0	0	0	8635	1841	64	4	4720	4	LAMB4	7	107746459	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	75092	107746459	51392204	468	22204										
TMEM168	64418	broad.mit.edu	37	chr7	112424705	112424706	+	Frame_Shift_Ins	INS	-	-	T													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caaaattaaggaatttgctgINSttttttcccatcttacgtat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:112424705_112424706insT	ENST00000312814.6	-	2	735_736	c.175_176insA	c.(175-177)acafs	p.T59fs	TMEM168_ENST00000454074.1_Frame_Shift_Ins_p.T59fs	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	59						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.T59fs*52(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						GGAATTTGCTGTTTTTTCCCAT	0.342																																																1	Insertion - Frameshift(1)	large_intestine(1)	7																																								112211942	SO:0001589	frameshift_variant	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.176dupA	7.37:g.112424711_112424711dupT	ENSP00000323068:p.Thr59fs		112211941	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Frame_Shift_Ins	INS	ENST00000312814.6	37	CCDS5757.1																																																																																				0.342	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		T	112424706	-	T	112424705	7	5	77	1	0	1	1	0	0	0	0	0	16122	1377	48	0	1933	0	TMEM168	7	112424705	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	4678246	112424705	46713958	469	22205										
TFEC	22797	broad.mit.edu	37	chr7	115582087	115582087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatggttcctttgttccagcGcatatcactgtagaatggag	10	8	1	1	rs376001735		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:115582087G>A	ENST00000265440.7	-	7	703	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C	TFEC_ENST00000484212.1_Missense_Mutation_p.R265C|TFEC_ENST00000393485.1_Missense_Mutation_p.R146C|TFEC_ENST00000457268.1_Missense_Mutation_p.R108C|TFEC_ENST00000320239.7_Missense_Mutation_p.R146C	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	175	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.R175C(1)		NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			TTGTTCCAGCGCATATCACTG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	7						G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	182	172	175		436,523	5.6	1	7		175	0,8600		0,0,4300	no	missense,missense	TFEC	NM_001018058.2,NM_012252.3	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	146/319,175/348	115582087	1,13005	2203	4300	6503	115369323	SO:0001583	missense	22797			D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"Basic helix-loop-helix proteins"	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.523C>T	7.37:g.115582087G>A	ENSP00000265440:p.Arg175Cys		115369323	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Missense_Mutation	SNP	ENST00000265440.7	37	CCDS5762.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494825	0.85069	2.27E-4	0.0	ENSG00000105967	ENST00000265440;ENST00000457268;ENST00000320239;ENST00000393485;ENST00000484212	D;D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78;-4.78	5.57	5.57	0.84162	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99180	0.9716	M	0.89715	3.055	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.959;0.959;0.986	D	0.99461	1.0943	10	0.87932	D	0	-8.3726	19.5508	0.95319	0.0:0.0:1.0:0.0	.	265;146;146;175	B7Z757;O14948-3;O14948-2;O14948	.;.;.;TFEC_HUMAN	C	175;108;146;146;265	ENSP00000265440:R175C;ENSP00000387650:R108C;ENSP00000318676:R146C;ENSP00000377125:R146C;ENSP00000417432:R265C	ENSP00000265440:R175C	R	-	1	0	TFEC	115369323	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.830000	0.99415	2.617000	0.88574	0.655000	0.94253	CGC		0.363	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252		A	115582087	G	A	115582087	3	1	77	1	0	0	0	0	1	0	0	0	15841	1087	38	1	528	1	TFEC	7	115582087	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3157382	115582087	43556576	470	22206										
CFTR	1080	broad.mit.edu	37	chr7	117267579	117267579	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgttatttttatttcagatgCgatctgtgagccgagtcttt	9	6	3	2	rs79850223		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:117267579C>T	ENST00000003084.6	+	22	3604	c.3472C>T	c.(3472-3474)Cga>Tga	p.R1158*	AC000111.6_ENST00000456270.1_RNA|CFTR_ENST00000454343.1_Nonsense_Mutation_p.R1097*	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1158					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.R1158*(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	ATTTCAGATGCGATCTGTGAG	0.343									Cystic Fibrosis																																							1	Substitution - Nonsense(1)	large_intestine(1)	7	GRCh37	CM920180	CFTR	M	rs79850223						66	61	63					7																	117267579		2203	4299	6502	117054815	SO:0001587	stop_gained	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.3472C>T	7.37:g.117267579C>T	ENSP00000003084:p.Arg1158*		117054815	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Nonsense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	C	40	8.166875	0.98686	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	.	.	.	5.77	3.92	0.45320	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-12.7034	15.4107	0.74917	0.2538:0.7462:0.0:0.0	.	.	.	.	X	1158;1097;1128	.	ENSP00000003084:R1158X	R	+	1	2	CFTR	117054815	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.969000	0.49232	0.855000	0.35359	0.585000	0.79938	CGA		0.343	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117267579	C	T	117267579	4	4	77	1	0	0	0	0	0	1	0	0	3300	760	27	1	3558	1	CFTR	7	117267579	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1685492	117267579	41871084	471	22207										
KCND2	3751	broad.mit.edu	37	chr7	119915142	119915142	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagcgcctgcaggacgacgcGgataccgacaccgctgggga	16	13	0	0	rs116322872	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:119915142G>A	ENST00000331113.4	+	1	1421	c.456G>A	c.(454-456)gcG>gcA	p.A152A		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	152					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.A152A(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AGGACGACGCGGATACCGACA	0.632													G|||	30	0.00599042	0.0227	0	5008	,	,		17065	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7						G		97,4309	79.3+/-117.8	0,97,2106	75	77	76		456	-11.4	0	7	dbSNP_132	76	1,8599		0,1,4299	no	coding-synonymous	KCND2	NM_012281.2		0,98,6405	AA,AG,GG		0.0116,2.2015,0.7535		152/631	119915142	98,12908	2203	4300	6503	119702378	SO:0001819	synonymous_variant	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.456G>A	7.37:g.119915142G>A			119702378	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Silent	SNP	ENST00000331113.4	37	CCDS5776.1																																																																																				0.632	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		A	119915142	G	A	119915142	2	1	77	1	0	0	0	0	0	0	0	1	8040	1103	39	1		1	KCND2	7	119915142	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2647563	119915142	39223521	472	22208										
AASS	10157	broad.mit.edu	37	chr7	121773616	121773616	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaaggctgtatcaagaccttGtatcccagattggtgatgcc	11	9	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:121773616G>A	ENST00000393376.1	-	1	260	c.165C>T	c.(163-165)taC>taT	p.Y55Y	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Silent_p.Y55Y			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	55	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.Y55Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TCAAGACCTTGTATCCCAGAT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	7											110	95	100					7																	121773616		2203	4300	6503	121560852	SO:0001819	synonymous_variant	10157			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.165C>T	7.37:g.121773616G>A			121560852	O95462	Silent	SNP	ENST00000393376.1	37	CCDS5783.1																																																																																				0.473	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		A	121773616	G	A	121773616	2	1	77	1	0	0	0	0	0	0	0	1	24	1372	48	3		3	AASS	7	121773616	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1858474	121773616	37365047	473	22209										
ASB15	142685	broad.mit.edu	37	chr7	123267185	123267185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtgatgtgcttgctttggCggatgatggggcgtcggtgc	19	6	0	2	rs564570457|rs138215101	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:123267185C>T	ENST00000451558.1	+	11	1240	c.719C>T	c.(718-720)gCg>gTg	p.A240V	ASB15_ENST00000540573.1_Missense_Mutation_p.A240V|RP11-390E23.3_ENST00000451016.1_RNA|ASB15_ENST00000434204.1_Missense_Mutation_p.A240V|RP11-390E23.3_ENST00000418409.1_RNA|RP11-390E23.3_ENST00000422401.1_RNA|ASB15_ENST00000451215.1_Missense_Mutation_p.A240V|RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000275699.3_Missense_Mutation_p.A240V|RP11-390E23.3_ENST00000440504.1_RNA			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	240					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.A240V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						CTTGCTTTGGCGGATGATGGG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											176	141	153					7																	123267185		2203	4300	6503	123054421	SO:0001583	missense	142685			AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"Ankyrin repeat domain containing"	19767	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 15"			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.719C>T	7.37:g.123267185C>T	ENSP00000397655:p.Ala240Val		123054421	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.771686	0.90108	.	.	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000447789;ENST00000275699	T;T;T;T;T;T	0.72835	2.33;2.33;2.33;2.33;-0.69;2.33	5.58	5.58	0.84498	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000002	T	0.81908	0.4922	L	0.49350	1.555	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	T	0.82544	-0.0404	10	0.66056	D	0.02	-4.0069	19.5733	0.95430	0.0:1.0:0.0:0.0	.	240	Q8WXK1	ASB15_HUMAN	V	240;240;240;240;29;240;240	ENSP00000397655:A240V;ENSP00000390963:A240V;ENSP00000416433:A240V;ENSP00000438643:A240V;ENSP00000401166:A240V;ENSP00000275699:A240V	ENSP00000275699:A240V	A	+	2	0	ASB15	123054421	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	7.456000	0.80751	2.618000	0.88619	0.563000	0.77884	GCG		0.498	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			T	123267185	C	T	123267185	3	4	77	1	0	0	0	0	1	0	0	0	1020	768	27	1	741	1	ASB15	7	123267185	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1493569	123267185	35871478	474	22210										
FLNC	2318	broad.mit.edu	37	chr7	128488083	128488083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccactgacgggccctacaCggtagccgtcaagtatgctg	12	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:128488083C>T	ENST00000325888.8	+	26	4802	c.4541C>T	c.(4540-4542)aCg>aTg	p.T1514M	FLNC_ENST00000346177.6_Missense_Mutation_p.T1514M|RP11-309L24.2_ENST00000469965.1_RNA	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1514					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.T1514M(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGGCCCTACACGGTAGCCGTC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	7											26	34	32					7																	128488083		2146	4237	6383	128275319	SO:0001583	missense	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4541C>T	7.37:g.128488083C>T	ENSP00000327145:p.Thr1514Met		128275319	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.006306	0.35415	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85556	-2.0;-2.0	5.12	5.12	0.69794	Immunoglobulin E-set (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.88786	0.6531	L	0.53249	1.67	0.53688	D	0.99997	D;B	0.89917	1.0;0.381	D;B	0.70487	0.969;0.103	D	0.85794	0.1369	10	0.23891	T	0.37	.	12.7724	0.57429	0.0:0.9136:0.0:0.0864	.	1514;1514	Q14315-2;Q14315	.;FLNC_HUMAN	M	1514	ENSP00000327145:T1514M;ENSP00000344002:T1514M	ENSP00000327145:T1514M	T	+	2	0	FLNC	128275319	0.724000	0.28038	0.959000	0.39883	0.729000	0.41735	1.492000	0.35594	2.543000	0.85770	0.561000	0.74099	ACG		0.662	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128488083	C	T	128488083	3	4	77	1	0	0	0	0	1	0	0	0	5954	536	19	1	4643	1	FLNC	7	128488083	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5220898	128488083	30650580	475	22211										
SMO	6608	broad.mit.edu	37	chr7	128852004	128852004	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgccgccccctgagcttcaCccccctgcccctgcccccag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:128852004delC	ENST00000249373.3	+	12	2356	c.2076delC	c.(2074-2076)cacfs	p.H692fs	RP11-286H14.8_ENST00000466717.1_RNA	NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	692					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.P694fs*82(1)		biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTGAGCTTCACCCCCCTGCCC	0.667			Mis		skin basal cell																																		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	1	Deletion - Frameshift(1)	large_intestine(1)	7											11	12	11					7																	128852004		2143	4193	6336	128639240	SO:0001589	frameshift_variant	6608			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.2076delC	7.37:g.128852004delC	ENSP00000249373:p.His692fs		128639240	A4D1K5	Frame_Shift_Del	DEL	ENST00000249373.3	37	CCDS5811.1																																																																																				0.667	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		-	128852004	C	-	128852004	7	5	77	1	0	1	0	1	0	0	0	0	14837	506	18	0	2122	0	SMO	7	128852004	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	363921	128852004	30286659	476	22212										
KLF14	136259	broad.mit.edu	37	chr7	130418544	130418545	+	Frame_Shift_Ins	INS	-	-	C													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggacgaggcgcgtggagcttINScccccgagttctcccaggag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:130418544_130418545insC	ENST00000310992.4	-	1	343_344	c.316_317insG	c.(316-318)gaafs	p.E106fs		NM_138693.2	NP_619638.2	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E106fs*117(1)		large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(18;0.0435)					GCGTGGAGCTTCCCCCGAGTTC	0.767																																																1	Insertion - Frameshift(1)	large_intestine(1)	7																																								130069085	SO:0001589	frameshift_variant	136259			AF490374	CCDS5825.1	7q32.3	2014-05-06			ENSG00000174595	ENSG00000266265		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	23025	protein-coding gene	gene with protein product		609393				17480121	Standard	NM_138693		Approved	BTEB5	uc003vqk.2	Q8TD94	OTTHUMG00000188298	ENST00000310992.4:c.317dupG	7.37:g.130418549_130418549dupC	ENSP00000310878:p.Glu106fs		130069084	Q19A42|Q19A43	Frame_Shift_Ins	INS	ENST00000310992.4	37	CCDS5825.1																																																																																				0.767	KLF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338013.1	NM_138693		C	130418545	-	C	130418544	7	5	77	1	0	1	1	0	0	0	0	0	8363	1783	62	0	658	0	KLF14	7	130418544	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	1566540	130418544	28720119	477	22213										
EPHA1	2041	broad.mit.edu	37	chr7	143098433	143098433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaccttctggaacaagggcCgtcggagctgaatgcccaca	12	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:143098433C>T	ENST00000275815.3	-	3	502	c.416G>A	c.(415-417)cGg>cAg	p.R139Q		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	139	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.R139Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GAACAAGGGCCGTCGGAGCTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	7											90	93	92					7																	143098433		2203	4300	6503	142808555	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.416G>A	7.37:g.143098433C>T	ENSP00000275815:p.Arg139Gln		142808555	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.492843	0.84962	.	.	ENSG00000146904	ENST00000275815	T	0.09350	2.99	4.63	4.63	0.57726	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.49305	D	0.000149	T	0.29817	0.0745	L	0.56769	1.78	0.38759	D	0.954287	D	0.89917	1.0	D	0.87578	0.998	T	0.05386	-1.0888	10	0.66056	D	0.02	.	15.8453	0.78883	0.0:1.0:0.0:0.0	.	139	P21709	EPHA1_HUMAN	Q	139	ENSP00000275815:R139Q	ENSP00000275815:R139Q	R	-	2	0	EPHA1	142808555	0.915000	0.31059	0.990000	0.47175	0.995000	0.86356	3.980000	0.56895	2.402000	0.81655	0.655000	0.94253	CGG		0.587	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			T	143098433	C	T	143098433	3	4	77	1	0	0	0	0	1	0	0	0	5178	652	23	1	2578	1	EPHA1	7	143098433	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	12679889	143098433	16040230	478	22214										
CUL1	8454	broad.mit.edu	37	chr7	148496426	148496426	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaacaccagcagttacttggCgaggtcctcactcagctgtc	9	13	2	0	rs565504382	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:148496426C>T	ENST00000325222.4	+	21	2475	c.2196C>T	c.(2194-2196)ggC>ggT	p.G732G	CUL1_ENST00000602748.1_Silent_p.G732G|CUL1_ENST00000409469.1_Silent_p.G732G	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	732					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)		p.G732G(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AGTTACTTGGCGAGGTCCTCA	0.453													c|||	2	0.000399361	8e-04	0	5008	,	,		18578	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	7											153	115	128					7																	148496426		2203	4300	6503	148127359	SO:0001819	synonymous_variant	8454			U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.2196C>T	7.37:g.148496426C>T			148127359	D3DWG3|O60719|Q08AL6|Q8IYW1	Silent	SNP	ENST00000325222.4	37	CCDS34772.1																																																																																				0.453	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		T	148496426	C	T	148496426	2	4	77	1	0	0	0	0	0	0	0	1	4060	755	27	1		1	CUL1	7	148496426	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5397993	148496426	10642237	479	22215										
ZNF746	155061	broad.mit.edu	37	chr7	149171510	149171510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcggtgggtcccaggacgcTgaggccacaagtccagtcgg	15	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:149171510T>C	ENST00000340622.3	-	7	2180	c.1900A>G	c.(1900-1902)Agc>Ggc	p.S634G	ZNF746_ENST00000458143.2_Missense_Mutation_p.S635G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	634					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.S634G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CCCAGGACGCTGAGGCCACAA	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	7											30	28	29					7																	149171510		2201	4298	6499	148802443	SO:0001583	missense	155061			AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"Zinc fingers, C2H2-type", "-"	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.1900A>G	7.37:g.149171510T>C	ENSP00000345140:p.Ser634Gly		148802443	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	37	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	T	15.30	2.792927	0.50102	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.08546	3.11;3.08	5.36	1.76	0.24704	.	0.257847	0.27577	N	0.018760	T	0.05273	0.0140	N	0.19112	0.55	0.20196	N	0.999929	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33574	-0.9863	10	0.52906	T	0.07	-2.3554	7.4907	0.27460	0.0:0.2612:0.0:0.7388	.	635;634	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	G	634;635	ENSP00000345140:S634G;ENSP00000395007:S635G	ENSP00000345140:S634G	S	-	1	0	ZNF746	148802443	.	.	0.734000	0.30879	0.889000	0.51656	.	.	0.358000	0.24211	0.379000	0.24179	AGC		0.667	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		C	149171510	T	C	149171510	3	2	77	1	0	0	0	0	1	0	0	0	18168	1580	55	4	38	4	ZNF746	7	149171510	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	675084	149171510	9967153	480	22216										
NUB1	51667	broad.mit.edu	37	chr7	151065947	151065947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgggaacgtggatcatgcgGccactcatattaccaaccgc	10	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:151065947G>A	ENST00000355851.4	+	11	1299	c.1222G>A	c.(1222-1224)Gcc>Acc	p.A408T	NUB1_ENST00000413040.2_Missense_Mutation_p.A432T|NUB1_ENST00000566856.1_Missense_Mutation_p.A408T|NUB1_ENST00000568733.1_Missense_Mutation_p.A432T	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	408	UBA 1. {ECO:0000255|PROSITE- ProRule:PRU00212}.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.A408T(1)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGATCATGCGGCCACTCATAT	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	7											62	63	63					7																	151065947		1943	4136	6079	150696880	SO:0001583	missense	51667			AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"NEDD8 ultimate buster-1"	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1222G>A	7.37:g.151065947G>A	ENSP00000348110:p.Ala408Thr		150696880	O95422|Q75MR9|Q8IX22|Q9BXR2	Missense_Mutation	SNP	ENST00000355851.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.5|23.5	4.426472|4.426472	0.83667|0.83667	.|.	.|.	ENSG00000013374|ENSG00000013374	ENST00000413040;ENST00000355851|ENST00000480714	T|.	0.23950|.	1.88|.	5.49|5.49	5.49|5.49	0.81192|0.81192	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);|.	0.053035|.	0.85682|.	D|.	0.000000|.	T|T	0.67420|0.67420	0.2891|0.2891	L|L	0.42008|0.42008	1.315|1.315	0.80722|0.80722	D|D	1|1	P;P|.	0.40398|.	0.716;0.669|.	B;B|.	0.43052|.	0.406;0.376|.	T|T	0.62932|0.62932	-0.6749|-0.6749	10|5	0.34782|.	T|.	0.22|.	-14.2908|-14.2908	18.3594|18.3594	0.90370|0.90370	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	408;408|.	Q9Y5A7;Q9Y5A7-2|.	NUB1_HUMAN;.|.	T|D	408|11	ENSP00000348110:A408T|.	ENSP00000348110:A408T|.	A|G	+|+	1|2	0|0	NUB1|NUB1	150696880|150696880	1.000000|1.000000	0.71417|0.71417	0.919000|0.919000	0.36401|0.36401	0.973000|0.973000	0.67179|0.67179	5.859000|5.859000	0.69539|0.69539	2.564000|2.564000	0.86499|0.86499	0.650000|0.650000	0.86243|0.86243	GCC|GGC		0.483	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118		A	151065947	G	A	151065947	3	1	77	1	0	0	0	0	1	0	0	0	10745	1203	42	3	1260	3	NUB1	7	151065947	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1894437	151065947	8072716	481	22217										
PAXIP1	22976	broad.mit.edu	37	chr7	154760135	154760135	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccactgctggatcatgtccAaaaagctgatgctgctgagg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr7:154760135delA	ENST00000404141.1	-	7	1930	c.1776delT	c.(1774-1776)tttfs	p.F592fs	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Frame_Shift_Del_p.F592fs			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	592	Gln-rich.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)		p.F558fs*41(1)		NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GATCATGTCCAAAAAGCTGAT	0.512																																																1	Deletion - Frameshift(1)	large_intestine(1)	7											42	46	45					7																	154760135		1927	3628	5555	154391068	SO:0001589	frameshift_variant	22976			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1776delT	7.37:g.154760135delA	ENSP00000384048:p.Phe592fs		154391068	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Frame_Shift_Del	DEL	ENST00000404141.1	37	CCDS47753.1																																																																																				0.512	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		-	154760135	A	-	154760135	7	5	77	1	0	1	0	1	0	0	0	0	11518	127	5	0	1493	0	PAXIP1	7	154760135	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	3694188	154760135	4378528	482	22218										
MYOM2	9172	broad.mit.edu	37	chr8	2017571	2017571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttgctgtcttgcagggttcCggggagacgaggaaccattc	14	9	1	1	rs375889597		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:2017571C>T	ENST00000262113.4	+	8	889	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	250					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R250W(1)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TGCAGGGTTCCGGGGAGACGA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	166	164	164		748	3.5	0.2	8		164	0,8600		0,0,4300	no	missense	MYOM2	NM_003970.2	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	250/1466	2017571	1,13005	2203	4300	6503	2004978	SO:0001583	missense	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.748C>T	8.37:g.2017571C>T	ENSP00000262113:p.Arg250Trp		2004978	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.722725	0.48728	2.27E-4	0.0	ENSG00000036448	ENST00000262113	T	0.52295	0.67	5.48	3.46	0.39613	.	0.577300	0.15998	N	0.234498	T	0.46658	0.1404	L	0.46157	1.445	0.80722	D	1	D	0.63046	0.992	P	0.46339	0.513	T	0.49331	-0.8951	10	0.51188	T	0.08	.	13.7247	0.62750	0.4269:0.5731:0.0:0.0	.	250	P54296	MYOM2_HUMAN	W	250	ENSP00000262113:R250W	ENSP00000262113:R250W	R	+	1	2	MYOM2	2004978	1.000000	0.71417	0.245000	0.24217	0.538000	0.34931	1.959000	0.40412	1.232000	0.43678	0.655000	0.94253	CGG		0.532	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2017571	C	T	2017571	3	4	77	1	0	0	0	0	1	0	0	0	10122	643	23	1	774	1	MYOM2	8	2017571	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		2017571	144346451	483	22219										
RP1L1	94137	broad.mit.edu	37	chr8	10470414	10470414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacttgggccctggctgcccGcctcggccaaagacttccct	10	17	0	1	rs368122675		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:10470414G>A	ENST00000382483.3	-	4	1417	c.1194C>T	c.(1192-1194)ggC>ggT	p.G398G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	398					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.G398G(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTGGCTGCCCGCCTCGGCCAA	0.657													G|||	1	0.000199681	8e-04	0	5008	,	,		16386	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						G		6,3846		0,6,1920	43	50	48		1194	-1.1	0	8		48	1,8227		0,1,4113	no	coding-synonymous	RP1L1	NM_178857.5		0,7,6033	AA,AG,GG		0.0122,0.1558,0.0579		398/2401	10470414	7,12073	1926	4114	6040	10507824	SO:0001819	synonymous_variant	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1194C>T	8.37:g.10470414G>A			10507824	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10470414	G	A	10470414	2	1	77	1	0	0	0	0	0	0	0	1	13570	1074	38	1		1	RP1L1	8	10470414	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8452843	10470414	135893608	484	22220										
PINX1	54984	broad.mit.edu	37	chr8	10623424	10623424	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagtggagggactggcatcGccctatggtgggcagaagag	19	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:10623424G>A	ENST00000314787.3	-	7	593	c.474C>T	c.(472-474)ggC>ggT	p.G158G	SOX7_ENST00000553390.1_Intron|PINX1_ENST00000519088.1_Nonsense_Mutation_p.R133*|PINX1_ENST00000426190.2_Nonsense_Mutation_p.R131*|SOX7_ENST00000554914.1_Intron|CTD-2135J3.3_ENST00000506149.2_RNA|CTD-2135J3.3_ENST00000519568.1_RNA	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	158					mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)	p.G158G(1)		kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		GACTGGCATCGCCCTATGGTG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	8											113	120	118					8																	10623424		2101	4219	6320	10660834	SO:0001819	synonymous_variant	54984			AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"G patch domain containing"	30046	protein-coding gene	gene with protein product	"PIN2 interacting protein 1", "liver-related putative tumor suppressor"	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.474C>T	8.37:g.10623424G>A			10660834	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Nonsense_Mutation	SNP	ENST00000314787.3	37	CCDS47801.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.712113	0.30322	.	.	ENSG00000254093	ENST00000426190;ENST00000519088	.	.	.	5.7	-7.92	0.01160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	2.8142	0.05451	0.2043:0.3359:0.3394:0.1204	.	.	.	.	X	131;133	.	ENSP00000411396:R131X	R	-	1	2	PINX1	10660834	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.004000	0.03678	-0.884000	0.03976	-0.302000	0.09304	CGA		0.582	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884		A	10623424	G	A	10623424	2	1	77	1	0	0	0	0	0	0	0	1	11964	1074	38	1		1	PINX1	8	10623424	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	153010	10623424	135740598	485	22221										
XKR6	286046	broad.mit.edu	37	chr8	10782208	10782208	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtagcaccagttggggcgcGctctccaggaaggtctccag	14	12	2	0	rs149808365		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:10782208G>A	ENST00000416569.2	-	2	923	c.897C>T	c.(895-897)agC>agT	p.S299S	XKR6_ENST00000304437.2_Silent_p.S20S	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	299						integral component of membrane (GO:0016021)		p.S299S(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GTTGGGGCGCGCTCTCCAGGA	0.642													g|||	1	0.000199681	8e-04	0	5008	,	,		15690	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8								2,4404	4.2+/-10.8	0,2,2201	94	89	91		897	3.8	1	8	dbSNP_134	91	0,8600		0,0,4300	no	coding-synonymous	XKR6	NM_173683.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		299/642	10782208	2,13004	2203	4300	6503	10819618	SO:0001819	synonymous_variant	286046			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.897C>T	8.37:g.10782208G>A			10819618	Q8TBA0	Silent	SNP	ENST00000416569.2	37	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	g	10.46	1.355552	0.24598	4.54E-4	0.0	ENSG00000171044	ENST00000382461	.	.	.	4.84	3.85	0.44370	.	.	.	.	.	T	0.62792	0.2457	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59685	-0.7408	4	.	.	.	0.0916	11.933	0.52857	0.0929:0.0:0.9071:0.0	.	.	.	.	V	76	.	.	A	-	2	0	XKR6	10819618	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.452000	0.60054	0.835000	0.34877	0.457000	0.33378	GCG		0.642	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		A	10782208	G	A	10782208	2	1	77	1	0	0	0	0	0	0	0	1	17475	1078	38	1		1	XKR6	8	10782208	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	158784	10782208	135581814	486	22222										
DLC1	10395	broad.mit.edu	37	chr8	12943905	12943905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcacacccaccacaggtgCgcgatcgtgatccacagagg	10	16	1	2	rs367679746		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:12943905C>T	ENST00000276297.4	-	17	4769	c.4360G>A	c.(4360-4362)Gca>Aca	p.A1454T	DLC1_ENST00000520226.1_Missense_Mutation_p.A943T|DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000358919.2_Missense_Mutation_p.A1017T|DLC1_ENST00000512044.2_Missense_Mutation_p.A1051T	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1454	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.A1454T(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						ACCACAGGTGCGCGATCGTGA	0.488													C|||	1	0.000199681	0	0	5008	,	,		19593	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	8						C	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	124	120	122		2827,3049,4360	5	1	8		122	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	58,58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	943/1018,1017/1092,1454/1529	12943905	1,13005	2203	4300	6503	12988276	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.4360G>A	8.37:g.12943905C>T	ENSP00000276297:p.Ala1454Thr		12988276	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160845	0.78226	0.0	1.16E-4	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000510318;ENST00000512044;ENST00000520226	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.99	4.99	0.66335	Lipid-binding START (3);START-like domain (1);	0.113489	0.64402	D	0.000018	T	0.40645	0.1125	L	0.48642	1.525	0.80722	D	1	P;D;D	0.64830	0.918;0.973;0.994	B;P;P	0.50934	0.439;0.585;0.654	T	0.26052	-1.0114	10	0.62326	D	0.03	.	18.8379	0.92169	0.0:1.0:0.0:0.0	.	1454;1051;1017	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	T	1454;1017;393;1051;943	ENSP00000276297:A1454T;ENSP00000351797:A1017T;ENSP00000422595:A1051T;ENSP00000428028:A943T	ENSP00000276297:A1454T	A	-	1	0	DLC1	12988276	1.000000	0.71417	0.994000	0.49952	0.233000	0.25261	3.681000	0.54648	2.767000	0.95098	0.561000	0.74099	GCA		0.488	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	12943905	C	T	12943905	3	4	77	1	0	0	0	0	1	0	0	0	4561	768	27	1	234	1	DLC1	8	12943905	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2161697	12943905	133420117	487	22223										
DLC1	10395	broad.mit.edu	37	chr8	13357260	13357260	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctcatcagaaacatgcacTagtgtttctgtgctggcttc	8	11	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:13357260T>C	ENST00000276297.4	-	2	730	c.321A>G	c.(319-321)ctA>ctG	p.L107L	DLC1_ENST00000511869.1_Silent_p.L107L|DLC1_ENST00000316609.5_Silent_p.L107L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	107					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.L107L(2)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AAACATGCACTAGTGTTTCTG	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	8											220	221	221					8																	13357260		2203	4300	6503	13401631	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.321A>G	8.37:g.13357260T>C			13401631	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.423	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13357260	T	C	13357260	2	2	77	1	0	0	0	0	0	0	0	1	4561	1509	53	4		4	DLC1	8	13357260	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	413355	13357260	133006762	488	22224										
MTUS1	57509	broad.mit.edu	37	chr8	17579278	17579278	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaaaggctgtacgatcccaCgaccagcagtgtcaataagg	10	11	1	0	rs201491467	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:17579278C>T	ENST00000262102.6	-	4	2674				MTUS1_ENST00000381869.3_Intron|MTUS1_ENST00000381861.3_Missense_Mutation_p.V45M|MTUS1_ENST00000544260.1_Intron|MTUS1_ENST00000519263.1_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1						cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V45M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TACGATCCCACGACCAGCAGT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	8											83	81	82					8																	17579278		1912	4110	6022	17623558	SO:0001627	intron_variant	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2449+1902G>A	8.37:g.17579278C>T			17623558	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.022207	0.54683	.	.	ENSG00000129422	ENST00000381861	T	0.17854	2.25	5.56	2.63	0.31362	.	.	.	.	.	T	0.23688	0.0573	.	.	.	0.80722	D	1	P	0.51147	0.942	P	0.44673	0.457	T	0.24119	-1.0169	8	0.72032	D	0.01	.	16.9767	0.86315	0.0:0.5633:0.4367:0.0	.	45	Q9ULD2-6	.	M	45	ENSP00000371285:V45M	ENSP00000371285:V45M	V	-	1	0	MTUS1	17623558	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.930000	0.40124	0.817000	0.34445	0.655000	0.94253	GTG		0.408	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17579278	C	T	17579278	1	4	77	0	1	0	0	0	0	0	0	0	9995	536	19	1		1	MTUS1	8	17579278	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4222018	17579278	128784744	489	22225										
PHYHIP	9796	broad.mit.edu	37	chr8	22079140	22079140	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccccagggagcctttgggcGccagcaccaggatggcgtag	15	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:22079140G>A	ENST00000321613.3	-	6	1175	c.719C>T	c.(718-720)gCg>gTg	p.A240V	PHYHIP_ENST00000454243.2_Missense_Mutation_p.A240V	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	240								p.A240V(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		GCCTTTGGGCGCCAGCACCAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	8											22	31	28					8																	22079140		2068	4180	6248	22135085	SO:0001583	missense	9796			D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"phytanoyl-CoA hydroxylase interacting protein", "DYRK1A interacting protein 3"	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.719C>T	8.37:g.22079140G>A	ENSP00000320017:p.Ala240Val		22135085	D3DSR1|Q8N4I9	Missense_Mutation	SNP	ENST00000321613.3	37	CCDS43723.1	.	.	.	.	.	.	.	.	.	.	G	33	5.258573	0.95368	.	.	ENSG00000168490	ENST00000321613;ENST00000454243;ENST00000456132;ENST00000523252	T;T	0.36520	1.25;1.25	5.48	5.48	0.80851	.	0.056164	0.64402	D	0.000001	T	0.59018	0.2163	M	0.67953	2.075	0.52099	D	0.999949	D	0.76494	0.999	D	0.67103	0.949	T	0.60449	-0.7261	10	0.62326	D	0.03	-30.1201	18.1109	0.89536	0.0:0.0:1.0:0.0	.	240	Q92561	PHYIP_HUMAN	V	240;240;147;192	ENSP00000320017:A240V;ENSP00000415491:A240V	ENSP00000320017:A240V	A	-	2	0	PHYHIP	22135085	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.862000	0.99564	2.580000	0.87095	0.555000	0.69702	GCG		0.617	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759		A	22079140	G	A	22079140	3	1	77	1	0	0	0	0	1	0	0	0	11897	1087	38	1	277	1	PHYHIP	8	22079140	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4499862	22079140	124284882	490	22226										
PIWIL2	55124	broad.mit.edu	37	chr8	22165564	22165564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actgatgcgttgggggctccGtctgcaaaaggatgtacata	13	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:22165564G>A	ENST00000454009.2	+	14	2173	c.1664G>A	c.(1663-1665)cGt>cAt	p.R555H	PIWIL2_ENST00000356766.6_Missense_Mutation_p.R555H|PIWIL2_ENST00000521356.1_Missense_Mutation_p.R555H	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	555					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.R555H(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		TGGGGGCTCCGTCTGCAAAAG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											61	54	56					8																	22165564		2203	4300	6503	22221509	SO:0001583	missense	55124			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.1664G>A	8.37:g.22165564G>A	ENSP00000406956:p.Arg555His		22221509	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	G	9.474	1.096355	0.20552	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.05855	3.38;3.38;3.38	5.99	0.885	0.19188	Ribonuclease H-like (1);	0.654084	0.17860	N	0.159574	T	0.03053	0.0090	N	0.14661	0.345	0.21762	N	0.999556	B;B	0.14012	0.009;0.004	B;B	0.08055	0.003;0.003	T	0.40739	-0.9547	10	0.44086	T	0.13	-1.5601	1.42	0.02310	0.2139:0.1187:0.4229:0.2444	.	555;555	E7ECA4;Q8TC59	.;PIWL2_HUMAN	H	555	ENSP00000349208:R555H;ENSP00000428267:R555H;ENSP00000406956:R555H	ENSP00000349208:R555H	R	+	2	0	PIWIL2	22221509	0.012000	0.17670	0.973000	0.42090	0.427000	0.31564	0.022000	0.13511	-0.114000	0.11936	-0.355000	0.07637	CGT		0.443	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			A	22165564	G	A	22165564	3	1	77	1	0	0	0	0	1	0	0	0	11989	1145	40	1	1714	1	PIWIL2	8	22165564	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	86424	22165564	124198458	491	22227										
LOXL2	4017	broad.mit.edu	37	chr8	23191123	23191123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagtagcgctgcttcctccGtgaggcaaacattctgcaga	10	13	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:23191123G>A	ENST00000389131.3	-	5	1126	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	LOXL2_ENST00000518472.1_5'Flank|RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	253	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)	p.R253W(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		TGCTTCCTCCGTGAGGCAAAC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	8											52	42	45					8																	23191123		2203	4300	6503	23247068	SO:0001583	missense	4017			U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.757C>T	8.37:g.23191123G>A	ENSP00000373783:p.Arg253Trp		23247068	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	37	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	g	19.98	3.927535	0.73327	.	.	ENSG00000134013	ENST00000389131	T	0.36157	1.27	5.78	2.87	0.33458	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.167097	0.49916	D	0.000126	T	0.51160	0.1658	M	0.80183	2.485	0.46044	D	0.99883	D	0.60160	0.987	P	0.51453	0.67	T	0.59032	-0.7530	10	0.66056	D	0.02	.	14.3468	0.66672	0.0:0.0:0.4652:0.5348	.	253	Q9Y4K0	LOXL2_HUMAN	W	253	ENSP00000373783:R253W	ENSP00000373783:R253W	R	-	1	2	LOXL2	23247068	0.956000	0.32656	0.470000	0.27216	0.951000	0.60555	2.125000	0.42016	0.288000	0.22398	0.645000	0.84053	CGG		0.607	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			A	23191123	G	A	23191123	3	1	77	1	0	0	0	0	1	0	0	0	8929	1144	40	1	1607	1	LOXL2	8	23191123	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1025559	23191123	123172899	492	22228										
CDCA2	157313	broad.mit.edu	37	chr8	25364643	25364643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aacccatggaaagtagcagtGttgtgagttgcagagacagg	14	6	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:25364643G>A	ENST00000330560.3	+	15	2938	c.2461G>A	c.(2461-2463)Gtt>Att	p.V821I	CDCA2_ENST00000521098.2_3'UTR|CDCA2_ENST00000380665.3_Missense_Mutation_p.V806I	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	821					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V821I(1)		breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		AAGTAGCAGTGTTGTGAGTTG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	8											80	77	78					8																	25364643		2203	4300	6503	25420560	SO:0001583	missense	157313			BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 81"					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2461G>A	8.37:g.25364643G>A	ENSP00000328228:p.Val821Ile		25420560	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	G	3.860	-0.030015	0.07543	.	.	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.31769	1.49;1.48	5.71	-3.51	0.04696	.	1.684560	0.03157	N	0.168748	T	0.20210	0.0486	N	0.22421	0.69	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.005	T	0.31024	-0.9958	10	0.48119	T	0.1	0.2772	6.2553	0.20870	0.3546:0.3289:0.3166:0.0	.	806;821	E9PEI0;Q69YH5	.;CDCA2_HUMAN	I	821;806;220	ENSP00000328228:V821I;ENSP00000370040:V806I	ENSP00000328228:V821I	V	+	1	0	CDCA2	25420560	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.454000	0.06770	-0.382000	0.07870	-0.291000	0.09656	GTT		0.378	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562		A	25364643	G	A	25364643	3	1	77	1	0	0	0	0	1	0	0	0	3092	1377	48	3	2515	3	CDCA2	8	25364643	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2173520	25364643	120999379	493	22229										
CHRNA2	1135	broad.mit.edu	37	chr8	27324847	27324847	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccagcgcagtttgtagtcGctccactcctgtgtgtgggg	13	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:27324847G>A	ENST00000520933.2	-	4	501	c.348C>T	c.(346-348)agC>agT	p.S116S	CHRNA2_ENST00000240132.2_Silent_p.S101S|CHRNA2_ENST00000407991.1_Silent_p.S116S			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	116					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.S116S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GTTTGTAGTCGCTCCACTCCT	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	8											95	94	95					8																	27324847		2203	4300	6503	27380764	SO:0001819	synonymous_variant	1135			U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.348C>T	8.37:g.27324847G>A			27380764	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	37	CCDS6059.1																																																																																				0.552	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			A	27324847	G	A	27324847	2	1	77	1	0	0	0	0	0	0	0	1	3389	1078	38	1		1	CHRNA2	8	27324847	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1960204	27324847	119039175	494	22230										
EXTL3	2137	broad.mit.edu	37	chr8	28573811	28573811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgtgcgaggtgaagcacGtgctggatctgtgccgcatc	15	10	1	1	rs374083446		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:28573811G>A	ENST00000220562.4	+	3	1137	c.235G>A	c.(235-237)Gtg>Atg	p.V79M	EXTL3_ENST00000523149.1_Intron|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	79					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.V79M(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		GGTGAAGCACGTGCTGGATCT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	8						G	MET/VAL	0,4406		0,0,2203	92	87	89		235	5.5	1	8		89	1,8599	1.2+/-3.3	0,1,4299	no	missense	EXTL3	NM_001440.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	79/920	28573811	1,13005	2203	4300	6503	28629730	SO:0001583	missense	2137			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.235G>A	8.37:g.28573811G>A	ENSP00000220562:p.Val79Met		28629730	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	37	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036224	0.75617	0.0	1.16E-4	ENSG00000012232	ENST00000220562	D	0.95980	-3.87	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.95623	0.8577	L	0.43152	1.355	0.80722	D	1	D	0.71674	0.998	P	0.54965	0.765	D	0.94645	0.7834	9	.	.	.	-22.8024	19.4523	0.94872	0.0:0.0:1.0:0.0	.	79	O43909	EXTL3_HUMAN	M	79	ENSP00000220562:V79M	.	V	+	1	0	EXTL3	28629730	1.000000	0.71417	0.994000	0.49952	0.929000	0.56500	9.869000	0.99810	2.600000	0.87896	0.491000	0.48974	GTG		0.597	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		A	28573811	G	A	28573811	3	1	77	1	0	0	0	0	1	0	0	0	5340	1145	40	1	237	1	EXTL3	8	28573811	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1248964	28573811	117790211	495	22231										
EXTL3	2137	broad.mit.edu	37	chr8	28574617	28574617	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatctcttcaccttccagggCgagaagattgagtctctgag	10	10	3	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:28574617C>T	ENST00000220562.4	+	3	1943	c.1041C>T	c.(1039-1041)ggC>ggT	p.G347G	EXTL3_ENST00000523149.1_Intron|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	347					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.G347G(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CCTTCCAGGGCGAGAAGATTG	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	8											81	73	76					8																	28574617		2203	4300	6503	28630536	SO:0001819	synonymous_variant	2137			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1041C>T	8.37:g.28574617C>T			28630536	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	37	CCDS6070.1																																																																																				0.567	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28574617	C	T	28574617	2	4	77	1	0	0	0	0	0	0	0	1	5340	755	27	1		1	EXTL3	8	28574617	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	806	28574617	117789405	496	22232										
TEX15	56154	broad.mit.edu	37	chr8	30700458	30700458	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attatccatgttattatcttGtagcatctgaaagtattttt	5	5	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:30700458G>A	ENST00000256246.2	-	1	6150	c.6076C>T	c.(6076-6078)Caa>Taa	p.Q2026*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2026					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.Q2026*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TTATTATCTTGTAGCATCTGA	0.323																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											19	21	20					8																	30700458		2176	4275	6451	30820000	SO:0001587	stop_gained	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.6076C>T	8.37:g.30700458G>A	ENSP00000256246:p.Gln2026*		30820000		Nonsense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	46	12.151148	0.99640	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.62	5.62	0.85841	.	0.000000	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.412	0.90555	0.0:0.0:1.0:0.0	.	.	.	.	X	2026	.	ENSP00000256246:Q2026X	Q	-	1	0	TEX15	30820000	1.000000	0.71417	0.971000	0.41717	0.846000	0.48090	4.494000	0.60347	2.653000	0.90120	0.585000	0.79938	CAA		0.323	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30700458	G	A	30700458	4	1	77	1	0	0	0	0	0	1	0	0	15818	1386	48	3	2309	3	TEX15	8	30700458	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2125841	30700458	115663564	497	22233										
FGFR1	2260	broad.mit.edu	37	chr8	38287255	38287255	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccgaggggctgctggttacGcaagcatagaggccggagtc	16	11	0	1	rs142638017	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:38287255G>A	ENST00000447712.2	-	3	1244	c.303C>T	c.(301-303)tgC>tgT	p.C101C	FGFR1_ENST00000341462.5_Silent_p.C101C|FGFR1_ENST00000397103.1_Intron|FGFR1_ENST00000397091.5_Silent_p.C101C|FGFR1_ENST00000356207.5_Intron|FGFR1_ENST00000425967.3_Silent_p.C134C|FGFR1_ENST00000335922.5_Silent_p.C93C|FGFR1_ENST00000397108.4_Silent_p.C101C|FGFR1_ENST00000326324.6_Intron|FGFR1_ENST00000397113.2_Silent_p.C101C|FGFR1_ENST00000532791.1_Silent_p.C101C	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	101	Ig-like C2-type 1.		C -> F (in HH2). {ECO:0000269|PubMed:17154279}.		angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.C101C(2)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TGCTGGTTACGCAAGCATAGA	0.652		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"						G|||	2	0.000399361	0	0.0014	5008	,	,		15456	0.001		0	False		,,,				2504	0				Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	2	Substitution - coding silent(2)	large_intestine(2)	8						G	,,,,,,,,	2,4396		0,2,2197	71	59	63		303,279,303,,402,303,,,303	-2.8	0.9	8	dbSNP_134	63	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	FGFR1	NM_001174063.1,NM_001174064.1,NM_001174065.1,NM_001174066.1,NM_001174067.1,NM_015850.3,NM_023105.2,NM_023106.2,NM_023110.2	,,,,,,,,	0,2,6496	AA,AG,GG		0.0,0.0455,0.0154	,,,,,,,,	101/821,93/813,101/821,,134/854,101/821,,,101/823	38287255	2,12994	2199	4299	6498	38406412	SO:0001819	synonymous_variant	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.303C>T	8.37:g.38287255G>A			38406412	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	37	CCDS6107.2																																																																																				0.652	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	38287255	G	A	38287255	2	1	77	1	0	0	0	0	0	0	0	1	5882	1079	38	1		1	FGFR1	8	38287255	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7586797	38287255	108076767	498	22234										
FGFR1	2260	broad.mit.edu	37	chr8	38287381	38287381	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagttgatgctctgcacatcGtcccgcagccgacagcgaag	11	14	1	1	rs367880371		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:38287381G>A	ENST00000447712.2	-	3	1118	c.177C>T	c.(175-177)gaC>gaT	p.D59D	FGFR1_ENST00000341462.5_Silent_p.D59D|FGFR1_ENST00000397103.1_Intron|FGFR1_ENST00000397091.5_Silent_p.D59D|FGFR1_ENST00000356207.5_Intron|FGFR1_ENST00000425967.3_Silent_p.D92D|FGFR1_ENST00000335922.5_Silent_p.D51D|FGFR1_ENST00000397108.4_Silent_p.D59D|FGFR1_ENST00000326324.6_Intron|FGFR1_ENST00000397113.2_Silent_p.D59D|FGFR1_ENST00000532791.1_Silent_p.D59D	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	59	Ig-like C2-type 1.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.D59D(2)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCTGCACATCGTCCCGCAGCC	0.682		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	2	Substitution - coding silent(2)	large_intestine(2)	8						G	,,,,,,,,	0,4406		0,0,2203	34	31	32		177,153,177,,276,177,,,177	1.3	1	8		32	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	FGFR1	NM_001174063.1,NM_001174064.1,NM_001174065.1,NM_001174066.1,NM_001174067.1,NM_015850.3,NM_023105.2,NM_023106.2,NM_023110.2	,,,,,,,,	0,3,6499	AA,AG,GG		0.0349,0.0,0.0231	,,,,,,,,	59/821,51/813,59/821,,92/854,59/821,,,59/823	38287381	3,13001	2203	4299	6502	38406538	SO:0001819	synonymous_variant	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.177C>T	8.37:g.38287381G>A			38406538	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	37	CCDS6107.2																																																																																				0.682	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	38287381	G	A	38287381	2	1	77	1	0	0	0	0	0	0	0	1	5882	1136	40	1		1	FGFR1	8	38287381	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	126	38287381	108076641	499	22235										
ADAM18	8749	broad.mit.edu	37	chr8	39494820	39494820	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaaatgatggctgtaacacAaaaaattgtccaggttattg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:39494820delA	ENST00000265707.5	+	8	671	c.626delA	c.(625-627)caafs	p.Q209fs	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	209	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.I211fs*17(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			GCTGTAACACAAAAAATTGTC	0.274																																																1	Deletion - Frameshift(1)	large_intestine(1)	8											75	81	79					8																	39494820		2203	4294	6497	39613977	SO:0001589	frameshift_variant	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.626delA	8.37:g.39494820delA	ENSP00000265707:p.Gln209fs		39613977	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Frame_Shift_Del	DEL	ENST00000265707.5	37	CCDS6113.1																																																																																				0.274	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		-	39494820	A	-	39494820	7	5	77	1	0	1	0	1	0	0	0	0	239	130	5	0	656	0	ADAM18	8	39494820	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	1207439	39494820	106869202	500	22236										
MYST3	7994	broad.mit.edu	37	chr8	41834819	41834819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taccccttccagggccagttCgaactttgctgaagggacct	10	13	0	1	rs372273756		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:41834819C>T	ENST00000396930.3	-	8	1613	c.1070G>A	c.(1069-1071)cGa>cAa	p.R357Q	KAT6A_ENST00000485568.1_Missense_Mutation_p.R357Q|KAT6A_ENST00000406337.1_Missense_Mutation_p.R357Q|KAT6A_ENST00000265713.2_Missense_Mutation_p.R357Q	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	357	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R357Q(1)									AGGGCCAGTTCGAACTTTGCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	91	84	86		1070,1070,1070	4.5	1	8		86	1,8599		0,1,4299	no	missense,missense,missense	KAT6A	NM_006766.3,NM_001099413.1,NM_001099412.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	357/2005,357/2005,357/2005	41834819	1,13005	2203	4300	6503	41953976	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1070G>A	8.37:g.41834819C>T	ENSP00000380136:p.Arg357Gln		41953976	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612978	0.46631	0.0	1.16E-4	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.84223	0.23;0.23;0.23;-1.82	5.37	4.49	0.54785	.	0.337782	0.24506	N	0.037937	T	0.77239	0.4101	L	0.38175	1.15	0.28857	N	0.895756	B;B	0.11235	0.003;0.004	B;B	0.04013	0.001;0.001	T	0.65796	-0.6081	10	0.26408	T	0.33	-1.6842	11.0597	0.47940	0.0:0.851:0.0:0.149	.	357;357	A5PLL3;Q92794	.;KAT6A_HUMAN	Q	357	ENSP00000265713:R357Q;ENSP00000385888:R357Q;ENSP00000380136:R357Q;ENSP00000430606:R357Q	ENSP00000265713:R357Q	R	-	2	0	KAT6A	41953976	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.552000	0.53705	1.258000	0.44101	0.650000	0.86243	CGA		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		T	41834819	C	T	41834819	3	4	77	1	0	0	0	0	1	0	0	0	10134	884	31	1	4988	1	MYST3	8	41834819	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2339999	41834819	104529203	501	22237										
IKBKB	3551	broad.mit.edu	37	chr8	42166485	42166485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actggagcttcggcaccctgGcctttgagtgcatcacgggc	13	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:42166485G>A	ENST00000520810.1	+	8	820	c.634G>A	c.(634-636)Gcc>Acc	p.A212T	IKBKB_ENST00000379708.3_Intron|IKBKB_ENST00000416505.2_Missense_Mutation_p.A153T|IKBKB_ENST00000519735.1_Missense_Mutation_p.A212T|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.A210T	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	212	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)	p.A212T(1)		breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CGGCACCCTGGCCTTTGAGTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	8											148	132	137					8																	42166485		2203	4300	6503	42285642	SO:0001583	missense	3551			AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.634G>A	8.37:g.42166485G>A	ENSP00000430684:p.Ala212Thr		42285642	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918562	0.92249	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000519735;ENST00000520835	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055732	0.64402	D	0.000001	T	0.45975	0.1369	N	0.25957	0.775	0.80722	D	1	D;P;B;P;P	0.53619	0.961;0.753;0.425;0.792;0.932	P;B;B;P;P	0.53224	0.721;0.406;0.42;0.643;0.514	T	0.49881	-0.8892	10	0.66056	D	0.02	.	18.4904	0.90844	0.0:0.0:1.0:0.0	.	153;210;163;212;212	B4E0U4;O14920-2;Q59GL9;O14920;Q32ND9	.;.;.;IKKB_HUMAN;.	T	212;153;212;210	ENSP00000430684:A212T;ENSP00000404920:A153T;ENSP00000430483:A212T;ENSP00000430868:A210T	ENSP00000404920:A153T	A	+	1	0	IKBKB	42285642	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.636000	0.74299	2.437000	0.82529	0.563000	0.77884	GCC		0.647	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42166485	G	A	42166485	3	1	77	1	0	0	0	0	1	0	0	0	7632	1203	42	3	660	3	IKBKB	8	42166485	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	331666	42166485	104197537	502	22238										
DKK4	27121	broad.mit.edu	37	chr8	42231685	42231685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gattgctggtcaattggcttCgacacagtagtccagggcca	12	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:42231685C>T	ENST00000220812.2	-	4	794	c.608G>A	c.(607-609)cGa>cAa	p.R203Q		NM_014420.2	NP_055235.1	Q9UBT3	DKK4_HUMAN	dickkopf WNT signaling pathway inhibitor 4	203	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)		p.R203Q(2)		NS(1)|endometrium(1)|large_intestine(7)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|Lung(22;0.00597)|LUSC - Lung squamous cell carcinoma(45;0.024)			CAATTGGCTTCGACACAGTAG	0.443																																																2	Substitution - Missense(2)	large_intestine(2)	8											92	93	92					8																	42231685		2203	4300	6503	42350842	SO:0001583	missense	27121			AF177397	CCDS6130.1	8p11.2-p11.1	2013-05-15	2013-05-15		ENSG00000104371	ENSG00000104371			2894	protein-coding gene	gene with protein product		605417	"dickkopf (Xenopus laevis) homolog 4", "dickkopf homolog 4 (Xenopus laevis)"			10570958, 11701963	Standard	NM_014420		Approved		uc003xpb.3	Q9UBT3	OTTHUMG00000164167	ENST00000220812.2:c.608G>A	8.37:g.42231685C>T	ENSP00000220812:p.Arg203Gln		42350842	Q3KNX0|Q9Y4C3	Missense_Mutation	SNP	ENST00000220812.2	37	CCDS6130.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.217661	0.39201	.	.	ENSG00000104371	ENST00000220812	D	0.84146	-1.81	6.03	4.25	0.50352	Prokineticin domain (1);	0.272637	0.26535	N	0.023835	T	0.73776	0.3630	L	0.31664	0.95	0.34135	D	0.665696	B	0.33000	0.393	B	0.27608	0.081	T	0.74006	-0.3803	10	0.21540	T	0.41	-1.0608	10.8868	0.46972	0.0:0.8479:0.0:0.1521	.	203	Q9UBT3	DKK4_HUMAN	Q	203	ENSP00000220812:R203Q	ENSP00000220812:R203Q	R	-	2	0	DKK4	42350842	0.690000	0.27699	0.287000	0.24848	0.039000	0.13416	1.250000	0.32850	0.883000	0.36040	0.655000	0.94253	CGA		0.443	DKK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377563.1			T	42231685	C	T	42231685	3	4	77	1	0	0	0	0	1	0	0	0	4558	884	31	1	70	1	DKK4	8	42231685	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	65200	42231685	104132337	503	22239										
SLC20A2	6575	broad.mit.edu	37	chr8	42294520	42294520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacccacctcacgtcattgcCgccgtgagcaaaggacccga	9	17	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:42294520C>T	ENST00000342228.3	-	8	1879	c.1510G>A	c.(1510-1512)Ggc>Agc	p.G504S	SLC20A2_ENST00000520179.1_Missense_Mutation_p.G504S|SLC20A2_ENST00000520262.1_Missense_Mutation_p.G504S	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	504					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)	p.G504S(1)		breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ACGTCATTGCCGCCGTGAGCA	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	47	54					8																	42294520		2203	4300	6503	42413677	SO:0001583	missense	6575				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"Solute carriers"	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1510G>A	8.37:g.42294520C>T	ENSP00000340465:p.Gly504Ser		42413677		Missense_Mutation	SNP	ENST00000342228.3	37	CCDS6132.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236646	0.95240	.	.	ENSG00000168575	ENST00000342228;ENST00000520262;ENST00000520179	D;D;D	0.89343	-2.5;-2.5;-2.5	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.80391	0.4614	N	0.21583	0.68	0.80722	D	1	P	0.49447	0.924	B	0.37601	0.254	T	0.79412	-0.1814	10	0.17369	T	0.5	-28.992	17.1672	0.86819	0.0:1.0:0.0:0.0	.	504	Q08357	S20A2_HUMAN	S	504	ENSP00000340465:G504S;ENSP00000429754:G504S;ENSP00000429712:G504S	ENSP00000340465:G504S	G	-	1	0	SLC20A2	42413677	1.000000	0.71417	0.988000	0.46212	0.806000	0.45545	7.792000	0.85828	2.657000	0.90304	0.585000	0.79938	GGC		0.602	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			T	42294520	C	T	42294520	3	4	77	1	0	0	0	0	1	0	0	0	14476	652	23	1	464	1	SLC20A2	8	42294520	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	62835	42294520	104069502	504	22240										
PRKDC	5591	broad.mit.edu	37	chr8	48713536	48713536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttgcttaagtagcttgacaCgttgttctcatctgttggat	9	7	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:48713536C>T	ENST00000314191.2	-	72	9987	c.9931G>A	c.(9931-9933)Gtg>Atg	p.V3311M	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Missense_Mutation_p.V3311M	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	3312	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.V3312M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TAGCTTGACACGTTGTTCTCA	0.353								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											1	Substitution - Missense(1)	large_intestine(1)	8											67	61	63					8																	48713536		1855	4106	5961	48876089	SO:0001583	missense	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.9931G>A	8.37:g.48713536C>T	ENSP00000313420:p.Val3311Met		48876089	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	C	0.086	-1.174604	0.01646	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.71934	-0.61;-0.61	2.21	-0.342	0.12635	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.930749	0.09077	N	0.851897	T	0.43077	0.1231	N	0.08118	0	0.09310	N	1	B;B	0.26876	0.162;0.162	B;B	0.21546	0.035;0.021	T	0.22871	-1.0204	10	0.31617	T	0.26	.	2.4536	0.04524	0.0:0.1917:0.2945:0.5139	.	3311;3312	E7EUY0;P78527	.;PRKDC_HUMAN	M	3311	ENSP00000313420:V3311M;ENSP00000345182:V3311M	ENSP00000313420:V3311M	V	-	1	0	PRKDC	48876089	0.001000	0.12720	0.026000	0.17262	0.171000	0.22731	0.083000	0.14871	-0.075000	0.12798	-1.092000	0.02172	GTG		0.353	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		T	48713536	C	T	48713536	3	4	77	1	0	0	0	0	1	0	0	0	12555	536	19	1	2516	1	PRKDC	8	48713536	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6419016	48713536	97650486	505	22241										
PRKDC	5591	broad.mit.edu	37	chr8	48801169	48801169	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcctgctcctgtccacttgCgcgtcagggccatacaagtt	10	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:48801169C>T	ENST00000314191.2	-	35	4376	c.4320G>A	c.(4318-4320)gcG>gcA	p.A1440A	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Silent_p.A1440A|AC103686.1_ENST00000390136.2_RNA	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	1441					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.A1441A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TGTCCACTTGCGCGTCAGGGC	0.468								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											1	Substitution - coding silent(1)	large_intestine(1)	8											30	32	31					8																	48801169		2000	4183	6183	48963722	SO:0001819	synonymous_variant	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.4320G>A	8.37:g.48801169C>T			48963722	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Silent	SNP	ENST00000314191.2	37																																																																																					0.468	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		T	48801169	C	T	48801169	2	4	77	1	0	0	0	0	0	0	0	1	12555	755	27	1		1	PRKDC	8	48801169	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	87633	48801169	97562853	506	22242										
ST18	9705	broad.mit.edu	37	chr8	53028962	53028962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctctatcgtctttaagttgCtctccatagatgtgatctac	6	11	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:53028962C>T	ENST00000276480.7	-	25	3559	c.2876G>A	c.(2875-2877)aGc>aAc	p.S959N		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	959					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S959N(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CTTTAAGTTGCTCTCCATAGA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	8											184	138	154					8																	53028962		2203	4300	6503	53191515	SO:0001583	missense	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2876G>A	8.37:g.53028962C>T	ENSP00000276480:p.Ser959Asn		53191515	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685735	0.47991	.	.	ENSG00000147488	ENST00000276480	T	0.45276	0.9	5.63	4.74	0.60224	.	0.190654	0.56097	D	0.000023	T	0.28400	0.0702	N	0.24115	0.695	0.27424	N	0.954203	P	0.36616	0.561	B	0.29942	0.109	T	0.08006	-1.0743	10	0.33940	T	0.23	-17.5125	15.8047	0.78483	0.0:0.6201:0.3799:0.0	.	959	O60284	ST18_HUMAN	N	959	ENSP00000276480:S959N	ENSP00000276480:S959N	S	-	2	0	ST18	53191515	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.653000	0.46691	1.348000	0.45733	0.655000	0.94253	AGC		0.423	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028962	C	T	53028962	3	4	77	1	0	0	0	0	1	0	0	0	15251	797	28	3	275	3	ST18	8	53028962	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4227793	53028962	93335060	507	22243										
NSMAF	8439	broad.mit.edu	37	chr8	59522172	59522172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctacacaccgggtagccGttgaggggctgaaaatacag	14	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:59522172G>A	ENST00000038176.3	-	10	890	c.678C>T	c.(676-678)aaC>aaT	p.N226N	NSMAF_ENST00000427130.2_Silent_p.N257N|NSMAF_ENST00000519858.1_5'UTR	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	226	GRAM.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.N226N(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CCGGGTAGCCGTTGAGGGGCT	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	8											92	85	87					8																	59522172		2203	4300	6503	59684726	SO:0001819	synonymous_variant	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.678C>T	8.37:g.59522172G>A			59684726	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																				0.532	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		A	59522172	G	A	59522172	2	1	77	1	0	0	0	0	0	0	0	1	10705	1136	40	1		1	NSMAF	8	59522172	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6493210	59522172	86841850	508	22244										
CYP7B1	9420	broad.mit.edu	37	chr8	65528436	65528436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atactaaatatgcaaacttgTcatcaaattttaaaaaatca	2	6	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:65528436T>C	ENST00000310193.3	-	3	835	c.662A>G	c.(661-663)gAc>gGc	p.D221G	CYP7B1_ENST00000523954.1_5'Flank	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	221					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)	p.D221G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TGCAAACTTGTCATCAAATTT	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	8											68	69	69					8																	65528436		2202	4300	6502	65690990	SO:0001583	missense	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.662A>G	8.37:g.65528436T>C	ENSP00000310721:p.Asp221Gly		65690990	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	.	.	.	.	.	.	.	.	.	.	T	2.403	-0.337215	0.05278	.	.	ENSG00000172817	ENST00000310193	T	0.70749	-0.51	5.62	-3.28	0.05033	.	0.624237	0.18438	N	0.141231	T	0.51415	0.1673	L	0.38838	1.175	0.28686	N	0.904845	B	0.09022	0.002	B	0.15052	0.012	T	0.37244	-0.9714	9	.	.	.	-1.1329	7.6935	0.28581	0.0:0.2936:0.3771:0.3293	.	221	O75881	CP7B1_HUMAN	G	221	ENSP00000310721:D221G	.	D	-	2	0	CYP7B1	65690990	0.915000	0.31059	0.485000	0.27403	0.416000	0.31233	0.150000	0.16263	-0.151000	0.11176	-0.256000	0.11100	GAC		0.274	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			C	65528436	T	C	65528436	3	2	77	1	0	0	0	0	1	0	0	0	4203	1667	58	4	874	4	CYP7B1	8	65528436	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	6006264	65528436	80835586	509	22245										
MYBL1	4603	broad.mit.edu	37	chr8	67507952	67507952	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcctgttccacttttcttcGcatagtagaattccaatgat	5	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:67507952G>A	ENST00000522677.3	-	6	963	c.553C>T	c.(553-555)Cga>Tga	p.R185*	MYBL1_ENST00000517885.1_Intron|MYBL1_ENST00000524176.2_Nonsense_Mutation_p.R185*	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	185	HTH myb-type 3. {ECO:0000255|PROSITE- ProRule:PRU00625}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R185*(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			ACTTTTCTTCGCATAGTAGAA	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											136	121	125					8																	67507952		1822	4069	5891	67670506	SO:0001587	stop_gained	4603			X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.553C>T	8.37:g.67507952G>A	ENSP00000429633:p.Arg185*		67670506	E7EW29|Q495F9	Nonsense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	G	39	7.615818	0.98390	.	.	ENSG00000185697	ENST00000522677;ENST00000524176	.	.	.	5.51	3.65	0.41850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2225	14.0399	0.64669	0.0:0.0:0.4854:0.5146	.	.	.	.	X	185	.	ENSP00000429633:R185X	R	-	1	2	MYBL1	67670506	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.254000	0.32897	0.747000	0.32809	0.655000	0.94253	CGA		0.338	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67507952	G	A	67507952	4	1	77	1	0	0	0	0	0	1	0	0	10039	1095	38	1	1749	1	MYBL1	8	67507952	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1979516	67507952	78856070	510	22246										
SULF1	23213	broad.mit.edu	37	chr8	70540067	70540067	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgagaggacatctgaagagaAggaagcctgaggaatgtagc	15	5	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:70540067A>G	ENST00000260128.4	+	17	2725	c.2008A>G	c.(2008-2010)Agg>Ggg	p.R670G	SULF1_ENST00000458141.2_Missense_Mutation_p.R670G|SULF1_ENST00000419716.3_Missense_Mutation_p.R670G|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Missense_Mutation_p.R670G	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	670					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.R670G(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TCTGAAGAGAAGGAAGCCTGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	8											130	150	143					8																	70540067		2203	4300	6503	70702621	SO:0001583	missense	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2008A>G	8.37:g.70540067A>G	ENSP00000260128:p.Arg670Gly		70702621	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.129429	0.77549	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	D;D;D;D	0.98947	-5.26;-5.26;-5.26;-5.26	4.92	4.92	0.64577	Extracellular sulfatase, C-terminal (1);Alkaline-phosphatase-like, core domain (1);	0.088138	0.85682	D	0.000000	D	0.98698	0.9563	M	0.72118	2.19	0.51012	D	0.999903	D	0.56746	0.977	P	0.61722	0.893	D	0.99167	1.0863	10	0.52906	T	0.07	.	14.2115	0.65767	1.0:0.0:0.0:0.0	.	670	Q8IWU6	SULF1_HUMAN	G	670	ENSP00000403040:R670G;ENSP00000260128:R670G;ENSP00000385704:R670G;ENSP00000390315:R670G	ENSP00000260128:R670G	R	+	1	2	SULF1	70702621	1.000000	0.71417	0.951000	0.38953	0.809000	0.45718	4.229000	0.58625	1.837000	0.53436	0.379000	0.24179	AGG		0.403	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		G	70540067	A	G	70540067	3	3	77	1	0	0	0	0	1	0	0	0	15409	63	3	4	2058	4	SULF1	8	70540067	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	3032115	70540067	75823955	511	22247										
NCOA2	10499	broad.mit.edu	37	chr8	71074996	71074996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagattctccttcatgctgcGcatggaacttctgaatacac	7	12	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:71074996G>A	ENST00000452400.2	-	9	1107	c.926C>T	c.(925-927)gCg>gTg	p.A309V		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	309					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)	p.A309V(1)	PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TTCATGCTGCGCATGGAACTT	0.448			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	1	Substitution - Missense(1)	large_intestine(1)	8											142	139	140					8																	71074996		1966	4161	6127	71237550	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.926C>T	8.37:g.71074996G>A	ENSP00000399968:p.Ala309Val		71237550	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502251	0.44455	.	.	ENSG00000140396	ENST00000452400	T	0.16457	2.34	6.16	6.16	0.99307	.	0.267246	0.39687	N	0.001293	T	0.14485	0.0350	N	0.22421	0.69	0.80722	D	1	B	0.23185	0.081	B	0.18561	0.022	T	0.14755	-1.0461	10	0.17832	T	0.49	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	309	Q15596	NCOA2_HUMAN	V	309	ENSP00000399968:A309V	ENSP00000399968:A309V	A	-	2	0	NCOA2	71237550	0.778000	0.28640	0.163000	0.22734	0.981000	0.71138	4.503000	0.60407	2.937000	0.99478	0.650000	0.86243	GCG		0.448	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71074996	G	A	71074996	3	1	77	1	0	0	0	0	1	0	0	0	10260	1087	38	1	3528	1	NCOA2	8	71074996	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	534929	71074996	75289026	512	22248										
KCNB2	9312	broad.mit.edu	37	chr8	73848316	73848316	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtggaggctgtgtgtattgcAtggtttaccatggagtacct	14	6	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:73848316A>G	ENST00000523207.1	+	3	1314	c.726A>G	c.(724-726)gcA>gcG	p.A242A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	242					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.A242A(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TGTGTATTGCATGGTTTACCA	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	8											202	173	182					8																	73848316		2203	4300	6503	74010870	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.726A>G	8.37:g.73848316A>G			74010870	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73848316	A	G	73848316	2	3	77	1	0	0	0	0	0	0	0	1	8034	204	8	4		4	KCNB2	8	73848316	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	2773320	73848316	72515706	513	22249										
STAU2	27067	broad.mit.edu	37	chr8	74528000	74528000	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctttgtcatcatccacatcCtttcctgattcaccattcta	2	14	5	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:74528000C>T	ENST00000524300.1	-	8	938	c.588G>A	c.(586-588)aaG>aaA	p.K196K	STAU2_ENST00000519961.1_Silent_p.K196K|STAU2_ENST00000521727.1_Silent_p.K176K|STAU2_ENST00000355780.5_Silent_p.K164K|STAU2_ENST00000523558.1_Silent_p.K24K|STAU2_ENST00000517542.1_Silent_p.K158K|STAU2_ENST00000521451.1_5'UTR|STAU2_ENST00000521210.1_Silent_p.K92K|STAU2_ENST00000522695.1_Silent_p.K164K|STAU2_ENST00000522509.1_Silent_p.K164K	NM_001164380.1|NM_001164381.1	NP_001157852.1|NP_001157853.1	Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	196					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.K164K(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			CATCCACATCCTTTCCTGATT	0.343																																																1	Substitution - coding silent(1)	large_intestine(1)	8											153	136	142					8																	74528000		2203	4300	6503	74690554	SO:0001819	synonymous_variant	27067			Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"staufen (Drosophila, RNA-binding protein) homolog 2", "staufen, RNA binding protein, homolog 2 (Drosophila)"			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000524300.1:c.588G>A	8.37:g.74528000C>T			74690554	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000524300.1	37	CCDS55247.1																																																																																				0.343	STAU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379000.2	NM_001164380		T	74528000	C	T	74528000	2	4	77	1	0	0	0	0	0	0	0	1	15312	680	24	3		3	STAU2	8	74528000	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	679684	74528000	71836022	514	22250										
ZFHX4	79776	broad.mit.edu	37	chr8	77761900	77761900	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catctccaactgcatctgacGcatttgcacagtgtgtctcc	7	14	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:77761900G>A	ENST00000521891.2	+	8	4246	c.3798G>A	c.(3796-3798)acG>acA	p.T1266T	ZFHX4_ENST00000050961.6_Silent_p.T1221T|ZFHX4_ENST00000518282.1_Silent_p.T1240T|ZFHX4_ENST00000455469.2_Silent_p.T1221T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.T1266T(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGCATCTGACGCATTTGCACA	0.478										HNSCC(33;0.089)																																						1	Substitution - coding silent(1)	large_intestine(1)	8											89	84	86					8																	77761900		2055	4213	6268	77924455	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3798G>A	8.37:g.77761900G>A			77924455	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.478	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77761900	G	A	77761900	2	1	77	1	0	0	0	0	0	0	0	1	17674	1074	38	1		1	ZFHX4	8	77761900	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3233900	77761900	68602122	515	22251										
TSPYL5	85453	broad.mit.edu	37	chr8	98289373	98289373	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgctccaagtgctgcagtcGcaactgcccaaacttcctgg	10	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:98289373G>A	ENST00000322128.3	-	1	803	c.700C>T	c.(700-702)Cga>Tga	p.R234*		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	234					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)		p.R234*(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					TGCTGCAGTCGCAACTGCCCA	0.567																																																1	Substitution - Nonsense(1)	large_intestine(1)	8											64	64	64					8																	98289373		2203	4300	6503	98358549	SO:0001587	stop_gained	85453			AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.700C>T	8.37:g.98289373G>A	ENSP00000322802:p.Arg234*		98358549	B3KRF0|Q9C0B3	Nonsense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	.	.	.	.	.	.	.	.	.	.	G	37	6.597208	0.97692	.	.	ENSG00000180543	ENST00000322128	.	.	.	4.4	4.4	0.53042	.	0.000000	0.31381	N	0.007750	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9987	12.7896	0.57526	0.0:0.0:1.0:0.0	.	.	.	.	X	234	.	ENSP00000322802:R234X	R	-	1	2	TSPYL5	98358549	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.896000	0.48656	2.739000	0.93911	0.563000	0.77884	CGA		0.567	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		A	98289373	G	A	98289373	4	1	77	1	0	0	0	0	0	1	0	0	16702	1095	38	1	557	1	TSPYL5	8	98289373	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	20527473	98289373	48074649	516	22252										
MATN2	4147	broad.mit.edu	37	chr8	98943420	98943420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcgtgctgtcaagaggatgCggcatctgtccacgggcacc	14	12	2	1	rs377009254		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:98943420C>T	ENST00000520016.1	+	2	506	c.382C>T	c.(382-384)Cgg>Tgg	p.R128W	MATN2_ENST00000524308.1_Missense_Mutation_p.R128W|MATN2_ENST00000521689.1_Missense_Mutation_p.R128W|MATN2_ENST00000254898.5_Missense_Mutation_p.R128W|MATN2_ENST00000522025.2_Intron			O00339	MATN2_HUMAN	matrilin 2	128	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.R128W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			CAAGAGGATGCGGCATCTGTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	8						C	TRP/ARG,TRP/ARG	1,4261		0,1,2130	55	60	59		382,382	0.8	1	8		59	0,8508		0,0,4254	no	missense,missense	MATN2	NM_002380.3,NM_030583.2	101,101	0,1,6384	TT,TC,CC		0.0,0.0235,0.0078	probably-damaging,probably-damaging	128/957,128/938	98943420	1,12769	2131	4254	6385	99012596	SO:0001583	missense	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.382C>T	8.37:g.98943420C>T	ENSP00000430487:p.Arg128Trp		99012596	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827179	0.71143	2.35E-4	0.0	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000520016	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	5.97	0.813	0.18749	von Willebrand factor, type A (3);	0.081678	0.51477	D	0.000095	D	0.83594	0.5288	L	0.59436	1.845	0.31865	N	0.620505	D;D;D;D	0.89917	0.999;0.998;1.0;0.999	D;D;D;P	0.64877	0.93;0.921;0.91;0.873	D	0.85514	0.1199	10	0.59425	D	0.04	-22.3411	15.5484	0.76126	0.4575:0.5425:0.0:0.0	.	128;128;128;128	E9PF03;O00339-2;O00339;Q8N2G3	.;.;MATN2_HUMAN;.	W	128	ENSP00000429977:R128W;ENSP00000254898:R128W;ENSP00000430221:R128W;ENSP00000430487:R128W	ENSP00000254898:R128W	R	+	1	2	MATN2	99012596	0.996000	0.38824	0.998000	0.56505	0.997000	0.91878	0.484000	0.22308	-0.083000	0.12618	0.655000	0.94253	CGG		0.587	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	98943420	C	T	98943420	3	4	77	1	0	0	0	0	1	0	0	0	9364	759	27	1	388	1	MATN2	8	98943420	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	654047	98943420	47420602	517	22253										
MATN2	4147	broad.mit.edu	37	chr8	99019771	99019771	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgtcaacatggacagatcCtttgcctgtcagtgtcctga	10	10	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:99019771C>A	ENST00000520016.1	+	9	1639	c.1515C>A	c.(1513-1515)tcC>tcA	p.S505S	MATN2_ENST00000254898.5_Silent_p.S505S|MATN2_ENST00000524308.1_Silent_p.S464S|MATN2_ENST00000522025.2_Silent_p.S221S|MATN2_ENST00000521689.1_Silent_p.S505S			O00339	MATN2_HUMAN	matrilin 2	505	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S505S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGGACAGATCCTTTGCCTGTC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	8											149	147	148					8																	99019771		2123	4235	6358	99088947	SO:0001819	synonymous_variant	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1515C>A	8.37:g.99019771C>A			99088947	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	2.203	-0.382450	0.04966	.	.	ENSG00000132561	ENST00000518154	.	.	.	5.65	1.9	0.25705	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47433	-0.9118	4	.	.	.	-29.3922	8.0953	0.30824	0.0:0.6744:0.0:0.3256	.	.	.	.	I	288	.	.	L	+	1	0	MATN2	99088947	0.992000	0.36948	0.997000	0.53966	0.134000	0.20937	0.179000	0.16840	0.351000	0.24027	-0.140000	0.14226	CTT		0.537	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			A	99019771	C	A	99019771	2	1	77	1	0	0	0	0	0	0	0	1	9364	668	24	2		2	MATN2	8	99019771	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	76351	99019771	47344251	518	22254										
MATN2	4147	broad.mit.edu	37	chr8	99030335	99030335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctcgctgaggatgggaaaCgctgccgaagtaagtagcct	15	9	0	1	rs367737640		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:99030335C>T	ENST00000520016.1	+	11	1934	c.1810C>T	c.(1810-1812)Cgc>Tgc	p.R604C	MATN2_ENST00000254898.5_Missense_Mutation_p.R604C|MATN2_ENST00000524308.1_Missense_Mutation_p.R563C|MATN2_ENST00000522025.2_Missense_Mutation_p.R320C|MATN2_ENST00000521689.1_Missense_Mutation_p.R604C			O00339	MATN2_HUMAN	matrilin 2	604	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.R604C(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GGATGGGAAACGCTGCCGAAG	0.473													C|||	1	0.000199681	0	0	5008	,	,		21932	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	8						C	CYS/ARG,CYS/ARG	0,4146		0,0,2073	159	166	164		1810,1810	4.3	0.3	8		164	1,8419		0,1,4209	no	missense,missense	MATN2	NM_002380.3,NM_030583.2	180,180	0,1,6282	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging,probably-damaging	604/957,604/938	99030335	1,12565	2073	4210	6283	99099511	SO:0001583	missense	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1810C>T	8.37:g.99030335C>T	ENSP00000430487:p.Arg604Cys		99099511	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.33|14.33	2.502927|2.502927	0.44558|0.44558	0.0|0.0	1.19E-4|1.19E-4	ENSG00000132561|ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016|ENST00000518154;ENST00000517321	D;D;D;D;D|.	0.96427|.	-4.01;-4.01;-4.01;-4.01;-4.01|.	5.2|5.2	4.28|4.28	0.50868|0.50868	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);|.	0.643455|.	0.14765|.	N|.	0.299748|.	T|T	0.65481|0.65481	0.2695|0.2695	M|M	0.64997|0.64997	1.995|1.995	0.36236|0.36236	D|D	0.852989|0.852989	B;D;D;D|.	0.54207|.	0.025;0.958;0.965;0.958|.	B;P;B;P|.	0.47941|.	0.007;0.562;0.345;0.562|.	T|T	0.70073|0.70073	-0.4972|-0.4972	10|5	0.62326|.	D|.	0.03|.	-13.8728|-13.8728	12.5972|12.5972	0.56476|0.56476	0.3278:0.6722:0.0:0.0|0.3278:0.6722:0.0:0.0	.|.	563;604;604;604|.	C9JH87;E9PF03;O00339-2;O00339|.	.;.;.;MATN2_HUMAN|.	C|M	604;604;563;563;320;604|386;78	ENSP00000429977:R604C;ENSP00000254898:R604C;ENSP00000430221:R563C;ENSP00000429010:R320C;ENSP00000430487:R604C|.	ENSP00000254898:R604C|.	R|T	+|+	1|2	0|0	MATN2|MATN2	99099511|99099511	0.574000|0.574000	0.26684|0.26684	0.294000|0.294000	0.24946|0.24946	0.005000|0.005000	0.04900|0.04900	3.637000|3.637000	0.54324|0.54324	2.691000|2.691000	0.91804|0.91804	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.473	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99030335	C	T	99030335	3	4	77	1	0	0	0	0	1	0	0	0	9364	536	19	1	1852	1	MATN2	8	99030335	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	10564	99030335	47333687	519	22255										
VPS13B	157680	broad.mit.edu	37	chr8	100830682	100830682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgctatttcatgtgcaggtgCcatcttcaaacagttccatt	7	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:100830682C>T	ENST00000358544.2	+	46	8551	c.8440C>T	c.(8440-8442)Cca>Tca	p.P2814S	VPS13B_ENST00000357162.2_Missense_Mutation_p.P2789S|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2814					protein transport (GO:0015031)			p.P2814S(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TGTGCAGGTGCCATCTTCAAA	0.373																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	large_intestine(1)	8											138	127	131					8																	100830682		2203	4300	6503	100899858	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.8440C>T	8.37:g.100830682C>T	ENSP00000351346:p.Pro2814Ser		100899858	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562322	0.65538	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.73258	-0.73;-0.73	5.38	5.38	0.77491	.	0.127115	0.52532	N	0.000070	T	0.71169	0.3308	N	0.17082	0.46	0.80722	D	1	P;D	0.65815	0.927;0.995	P;P	0.57425	0.508;0.82	T	0.75110	-0.3433	10	0.54805	T	0.06	.	19.1314	0.93408	0.0:1.0:0.0:0.0	.	2789;2814	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	S	2789;2814	ENSP00000349685:P2789S;ENSP00000351346:P2814S	ENSP00000349685:P2789S	P	+	1	0	VPS13B	100899858	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.662000	0.68032	2.523000	0.85059	0.650000	0.86243	CCA		0.373	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100830682	C	T	100830682	3	4	77	1	0	0	0	0	1	0	0	0	17230	739	26	3	8812	3	VPS13B	8	100830682	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1800347	100830682	45533340	520	22256										
UBR5	51366	broad.mit.edu	37	chr8	103291365	103291365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaatgtcatggagtctgaacGtcggaaaaatggatggtttt	13	4	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:103291365G>A	ENST00000520539.1	-	43	6679	c.6073C>T	c.(6073-6075)Cgt>Tgt	p.R2025C	UBR5_ENST00000220959.4_Missense_Mutation_p.R2025C|UBR5_ENST00000521922.1_Missense_Mutation_p.R2019C	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2025					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.R2025C(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			GAGTCTGAACGTCGGAAAAAT	0.433																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	large_intestine(1)	8											109	109	109					8																	103291365		2203	4300	6503	103360541	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.6073C>T	8.37:g.103291365G>A	ENSP00000429084:p.Arg2025Cys		103360541	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901649	0.92035	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.80033	-1.33;-1.33;-1.33	5.87	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.88581	0.6475	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	D	0.89114	0.3498	10	0.87932	D	0	.	16.165	0.81747	0.0:0.0:0.8661:0.1338	.	2019;2025	E7EMW7;O95071	.;UBR5_HUMAN	C	2025;2025;2019	ENSP00000429084:R2025C;ENSP00000220959:R2025C;ENSP00000427819:R2019C	ENSP00000220959:R2025C	R	-	1	0	UBR5	103360541	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.502000	0.81614	2.941000	0.99782	0.655000	0.94253	CGT		0.433	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		A	103291365	G	A	103291365	3	1	77	1	0	0	0	0	1	0	0	0	16945	1145	40	1	2394	1	UBR5	8	103291365	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2460683	103291365	43072657	521	22257										
TMEM74	157753	broad.mit.edu	37	chr8	109796787	109796787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtgaccaagaacaagatggCgctgatgaaaccatagtcta	10	8	1	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:109796787C>T	ENST00000297459.3	-	2	719	c.541G>A	c.(541-543)Gcc>Acc	p.A181T	TMEM74_ENST00000518838.1_Intron	NM_153015.1	NP_694560.1	Q96NL1	TMM74_HUMAN	transmembrane protein 74	181					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.A181T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			AACAAGATGGCGCTGATGAAA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	8											108	100	103					8																	109796787		2203	4300	6503	109865963	SO:0001583	missense	157753			AK055230	CCDS6310.1	8q23.1	2009-11-06				ENSG00000164841			26409	protein-coding gene	gene with protein product		613935				12477932	Standard	NM_153015		Approved	FLJ30668, NET36	uc003ymy.1	Q96NL1		ENST00000297459.3:c.541G>A	8.37:g.109796787C>T	ENSP00000297459:p.Ala181Thr		109865963		Missense_Mutation	SNP	ENST00000297459.3	37	CCDS6310.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539933	0.85917	.	.	ENSG00000164841	ENST00000297459	T	0.18502	2.21	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.22906	-1.0203	10	0.87932	D	0	-17.0454	19.416	0.94700	0.0:1.0:0.0:0.0	.	181	Q96NL1	TMM74_HUMAN	T	181	ENSP00000297459:A181T	ENSP00000297459:A181T	A	-	1	0	TMEM74	109865963	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.762000	0.68809	2.821000	0.97095	0.650000	0.86243	GCC		0.507	TMEM74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380755.1	NM_153015		T	109796787	C	T	109796787	3	4	77	1	0	0	0	0	1	0	0	0	16241	768	27	1	380	1	TMEM74	8	109796787	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6505422	109796787	36567235	522	22258										
CSMD3	114788	broad.mit.edu	37	chr8	114290926	114290926	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggaggtggcagatggaatcCtgttaacctaaaacaaaatg	11	6	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:114290926C>A	ENST00000297405.5	-	3	653	c.409G>T	c.(409-411)Gga>Tga	p.G137*	CSMD3_ENST00000343508.3_Nonsense_Mutation_p.G97*|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.G137*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.G137*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	137	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G137*(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGATGGAATCCTGTTAACCTA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Nonsense(1)	large_intestine(1)	8											98	90	93					8																	114290926		2203	4299	6502	114360102	SO:0001587	stop_gained	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.409G>T	8.37:g.114290926C>A	ENSP00000297405:p.Gly137*		114360102	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	38	7.168368	0.98111	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	.	.	.	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.5442	0.84410	0.0:1.0:0.0:0.0	.	.	.	.	X	97;137;137;137	.	ENSP00000297405:G137X	G	-	1	0	CSMD3	114360102	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.250000	0.78287	2.561000	0.86390	0.543000	0.68304	GGA		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	114290926	C	A	114290926	4	1	77	1	0	0	0	0	0	1	0	0	3952	690	24	2	10990	2	CSMD3	8	114290926	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4494139	114290926	32073096	523	22259										
TRPS1	7227	broad.mit.edu	37	chr8	116427045	116427045	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggctgaccaggactggctGctgagcagaatggcttttag	14	8	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:116427045G>A	ENST00000220888.5	-	6	3211	c.3052C>T	c.(3052-3054)Cag>Tag	p.Q1018*	TRPS1_ENST00000519076.1_Nonsense_Mutation_p.Q772*|TRPS1_ENST00000395715.3_Nonsense_Mutation_p.Q1031*|TRPS1_ENST00000520276.1_Nonsense_Mutation_p.Q1022*			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1018	Mediates interaction with RNF4. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q1018*(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			AGGACTGGCTGCTGAGCAGAA	0.443									Langer-Giedion syndrome																																							1	Substitution - Nonsense(1)	large_intestine(1)	8											125	120	122					8																	116427045		1907	4129	6036	116496221	SO:0001587	stop_gained	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3052C>T	8.37:g.116427045G>A	ENSP00000220888:p.Gln1018*		116496221	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Nonsense_Mutation	SNP	ENST00000220888.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.270278|7.270278	0.98179|0.98179	.|.	.|.	ENSG00000104447|ENSG00000104447	ENST00000518018|ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	.|.	.|.	.|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.79100|.	0.4389|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.80903|.	-0.1174|.	4|.	.|0.72032	.|D	.|0.01	.|.	19.6491|19.6491	0.95794|0.95794	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	142|1031;1018;772;1022	.|.	.|ENSP00000220888:Q1018X	A|Q	-|-	2|1	0|0	TRPS1|TRPS1	116496221|116496221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.288000|9.288000	0.96055|0.96055	2.638000|2.638000	0.89438|0.89438	0.655000|0.655000	0.94253|0.94253	GCA|CAG		0.443	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116427045	G	A	116427045	4	1	77	1	0	0	0	0	0	1	0	0	16633	1328	46	3	797	3	TRPS1	8	116427045	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2136119	116427045	29936977	524	22260										
TNFRSF11B	4982	broad.mit.edu	37	chr8	119945384	119945384	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagtggtcagggcaaggggcGcacacggtcttccactttgc	14	11	2	0	rs142201380	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:119945384G>A	ENST00000297350.4	-	2	564	c.186C>T	c.(184-186)tgC>tgT	p.C62C		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	62					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)	p.C62C(1)		breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GGCAAGGGGCGCACACGGTCT	0.517													G|||	15	0.00299521	0.0113	0	5008	,	,		20846	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						G		46,4360	48.2+/-83.0	1,44,2158	290	258	269		186	-6.6	0	8	dbSNP_134	269	0,8600		0,0,4300	no	coding-synonymous	TNFRSF11B	NM_002546.3		1,44,6458	AA,AG,GG		0.0,1.044,0.3537		62/402	119945384	46,12960	2203	4300	6503	120014565	SO:0001819	synonymous_variant	4982			U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.186C>T	8.37:g.119945384G>A			120014565	B2R9A8|O60236|Q53FX6|Q9UHP4	Silent	SNP	ENST00000297350.4	37	CCDS6326.1																																																																																				0.517	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			A	119945384	G	A	119945384	2	1	77	1	0	0	0	0	0	0	0	1	16324	1079	38	1		1	TNFRSF11B	8	119945384	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3518339	119945384	26418638	525	22261										
TG	7038	broad.mit.edu	37	chr8	133995595	133995595	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gactgctttttccttttcagTtgctcaaaataatgctccca	5	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:133995595T>A	ENST00000220616.4	+	35	6240	c.6200T>A	c.(6199-6201)aTt>aAt	p.I2067N	TG_ENST00000522523.1_3'UTR|TG_ENST00000377869.1_Splice_Site_p.I2010N|TG_ENST00000519543.1_Intron|TG_ENST00000542445.1_Splice_Site_p.I437N	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2067					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.I2067N(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		TCCTTTTCAGTTGCTCAAAAT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	8											273	255	261					8																	133995595		2203	4300	6503	134064777	SO:0001630	splice_region_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.6200-1T>A	8.37:g.133995595T>A			134064777	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.24|10.24	1.294985|1.294985	0.23564|0.23564	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445	.|T;T;T	.|0.66995	.|-0.03;-0.03;-0.24	4.6|4.6	-0.385|-0.385	0.12470|0.12470	.|.	.|1.186100	.|0.06029	.|N	.|0.652677	T|T	0.46795|0.46795	0.1411|0.1411	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.09022	.|0.001;0.002	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.18713|0.18713	-1.0328|-1.0328	5|9	.|.	.|.	.|.	.|.	3.1262|3.1262	0.06408|0.06408	0.1802:0.3052:0.0:0.5146|0.1802:0.3052:0.0:0.5146	.|.	.|437;2067	.|F5GWW5;P01266	.|.;THYG_HUMAN	Q|N	522|2010;873;2067;437	.|ENSP00000367100:I2010N;ENSP00000220616:I2067N;ENSP00000441693:I437N	.|.	H|I	+|+	3|2	2|0	TG|TG	134064777|134064777	0.002000|0.002000	0.14202|0.14202	0.073000|0.073000	0.20177|0.20177	0.087000|0.087000	0.18053|0.18053	-0.781000|-0.781000	0.04648|0.04648	-0.057000|-0.057000	0.13199|0.13199	0.533000|0.533000	0.62120|0.62120	CAT|ATT		0.378	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Missense_Mutation	A	133995595	T	A	133995595	5	1	77	1	0	0	0	0	0	0	1	0	15852	1739	60	5	6338	5	TG	8	133995595	Splice_Site	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	14050211	133995595	12368427	526	22262										
ST3GAL1	6482	broad.mit.edu	37	chr8	134472163	134472163	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccctttgctgtctgccccGaagccgtacaagtccacctg	8	16	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:134472163G>A	ENST00000319914.5	-	9	1894	c.867C>T	c.(865-867)ttC>ttT	p.F289F	ST3GAL1_ENST00000399640.2_Silent_p.F289F|ST3GAL1_ENST00000522652.1_Silent_p.F289F|ST3GAL1_ENST00000521180.1_Silent_p.F289F			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	289					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)	p.F289F(1)		endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			TGTCTGCCCCGAAGCCGTACA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	8											115	118	117					8																	134472163		2203	4300	6503	134541345	SO:0001819	synonymous_variant	6482			L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"Sialyltransferases"	10862	protein-coding gene	gene with protein product	"ST3Gal I"	607187	"sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.867C>T	8.37:g.134472163G>A			134541345	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																				0.577	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033		A	134472163	G	A	134472163	2	1	77	1	0	0	0	0	0	0	0	1	15253	1049	37	1		1	ST3GAL1	8	134472163	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	476568	134472163	11891859	527	22263										
FAM135B	51059	broad.mit.edu	37	chr8	139380194	139380194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taaaatttatgtagctctacCgaaaactcaaccgttccttg	5	10	2	0	rs376994267		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:139380194C>T	ENST00000395297.1	-	2	203	c.33G>A	c.(31-33)tcG>tcA	p.S11S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	11								p.S11S(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GTAGCTCTACCGAAAACTCAA	0.368										HNSCC(54;0.14)																																						2	Substitution - coding silent(2)	large_intestine(2)	8						C		0,3736		0,0,1868	152	145	147		33	-0.1	1	8		147	1,8203		0,1,4101	no	coding-synonymous	FAM135B	NM_015912.3		0,1,5969	TT,TC,CC		0.0122,0.0,0.0084		11/1407	139380194	1,11939	1868	4102	5970	139449376	SO:0001819	synonymous_variant	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.33G>A	8.37:g.139380194C>T			139449376	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																				0.368	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139380194	C	T	139380194	2	4	77	1	0	0	0	0	0	0	0	1	5465	639	23	1		1	FAM135B	8	139380194	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4908031	139380194	6983828	528	22264										
DENND3	22898	broad.mit.edu	37	chr8	142161746	142161746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgcatcctgacggaacagcGgatcgtcttcttctcctcgg	10	13	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:142161746G>A	ENST00000262585.2	+	7	922	c.644G>A	c.(643-645)cGg>cAg	p.R215Q	DENND3_ENST00000519811.1_Missense_Mutation_p.R295Q|DENND3_ENST00000424248.1_Missense_Mutation_p.R215Q	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	215	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R215Q(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	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)			ACGGAACAGCGGATCGTCTTC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	8											145	117	127					8																	142161746		2203	4300	6503	142230928	SO:0001583	missense	22898			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.644G>A	8.37:g.142161746G>A	ENSP00000262585:p.Arg215Gln		142230928	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529763	0.45073	.	.	ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.38	5.38	0.77491	DENN (3);	0.165227	0.49916	D	0.000132	T	0.29850	0.0746	L	0.42245	1.32	0.53005	D	0.999969	D;D	0.89917	1.0;0.998	D;D	0.70227	0.968;0.915	T	0.01136	-1.1440	10	0.49607	T	0.09	-27.7175	9.2328	0.37448	0.203:0.0:0.797:0.0	.	295;215	E9PF32;A2RUS2	.;DEND3_HUMAN	Q	215;215;295;217	ENSP00000262585:R215Q;ENSP00000410594:R215Q;ENSP00000428714:R295Q;ENSP00000429780:R217Q	ENSP00000262585:R215Q	R	+	2	0	DENND3	142230928	0.993000	0.37304	0.968000	0.41197	0.169000	0.22640	1.946000	0.40283	2.506000	0.84524	0.563000	0.77884	CGG		0.547	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142161746	G	A	142161746	3	1	77	1	0	0	0	0	1	0	0	0	4443	1116	39	1	666	1	DENND3	8	142161746	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2781552	142161746	4202276	529	22265										
CYP11B1	1584	broad.mit.edu	37	chr8	143955812	143955812	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttgatggctctgaaggtgaGgagggggaacatgctgggcc	19	6	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:143955812G>T	ENST00000292427.4	-	9	1521	c.1489C>A	c.(1489-1491)Ctc>Atc	p.L497I	CYP11B1_ENST00000517471.1_Missense_Mutation_p.L431I|CYP11B1_ENST00000377675.3_Missense_Mutation_p.L568I	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	497					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.L497I(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CTGAAGGTGAGGAGGGGGAAC	0.562									Familial Hyperaldosteronism type I																																							1	Substitution - Missense(1)	large_intestine(1)	8											217	176	189					8																	143955812		2203	4300	6503	143952814	SO:0001583	missense	1584	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1489C>A	8.37:g.143955812G>T	ENSP00000292427:p.Leu497Ile		143952814	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	13.05	2.122584	0.37436	.	.	ENSG00000160882	ENST00000519285;ENST00000292427;ENST00000517471;ENST00000377675	T;T;D;T	0.86956	-0.88;-1.03;-2.19;-0.97	4.01	-0.203	0.13204	.	0.538701	0.15539	N	0.257066	D	0.87370	0.6160	M	0.62016	1.91	0.20926	N	0.999821	P;P;B;D;B	0.54047	0.593;0.483;0.2;0.964;0.2	B;B;B;P;B	0.57846	0.402;0.225;0.037;0.828;0.037	T	0.76503	-0.2935	10	0.27785	T	0.31	.	5.3401	0.15979	0.298:0.1531:0.5488:0.0	.	568;497;431;497;147	Q4VAR0;Q8TDD0;Q4VAQ9;P15538;Q8N9P8	.;.;.;C11B1_HUMAN;.	I	175;497;431;568	ENSP00000430144:L175I;ENSP00000292427:L497I;ENSP00000428043:L431I;ENSP00000366903:L568I	ENSP00000292427:L497I	L	-	1	0	CYP11B1	143952814	0.982000	0.34865	0.030000	0.17652	0.552000	0.35366	0.981000	0.29526	-0.022000	0.13986	0.655000	0.94253	CTC		0.562	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143955812	G	T	143955812	3	4	77	1	0	0	0	0	1	0	0	0	4151	1000	35	2	26	2	CYP11B1	8	143955812	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1794066	143955812	2408210	530	22266										
SCRIB	23513	broad.mit.edu	37	chr8	144886021	144886021	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcactgactgcttcttggtgCgtggcatcccgcacgtcttg	12	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:144886021C>T	ENST00000320476.3	-	23	3216	c.3210G>A	c.(3208-3210)acG>acA	p.T1070T	SCRIB_ENST00000377533.3_Silent_p.T989T|SCRIB_ENST00000356994.2_Silent_p.T1070T	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1070	Interaction with ARHGEF7.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)		p.T1070T(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CTTCTTGGTGCGTGGCATCCC	0.716																																					Pancreas(51;966 1133 10533 14576 29674)											1	Substitution - coding silent(1)	large_intestine(1)	8											23	24	24					8																	144886021		2190	4292	6482	144958009	SO:0001819	synonymous_variant	23513			AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3210G>A	8.37:g.144886021C>T			144958009	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	C	4.727	0.135262	0.09032	.	.	ENSG00000180900	ENST00000526832	.	.	.	4.52	-9.05	0.00730	.	.	.	.	.	T	0.42245	0.1194	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47724	-0.9095	4	.	.	.	.	4.7074	0.12856	0.0847:0.1957:0.1804:0.5392	.	.	.	.	T	66	.	.	A	-	1	0	SCRIB	144958009	0.000000	0.05858	0.403000	0.26384	0.494000	0.33585	-5.849000	0.00094	-2.568000	0.00469	-0.390000	0.06520	GCA		0.716	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144886021	C	T	144886021	2	4	77	1	0	0	0	0	0	0	0	1	13974	755	27	1		1	SCRIB	8	144886021	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	930209	144886021	1478001	531	22267										
CPSF1	29894	broad.mit.edu	37	chr8	145620510	145620510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctcaaactccttctcctCgccagtcatgcgtgggatgc	10	14	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr8:145620510C>T	ENST00000349769.3	-	28	3251	c.3157G>A	c.(3157-3159)Gag>Aag	p.E1053K	CPSF1_ENST00000531727.1_5'Flank|MIR939_ENST00000401314.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1053					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)	p.E1053K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TCCTTCTCCTCGCCAGTCATG	0.612																																					NSCLC(133;1088 1848 27708 34777 35269)											1	Substitution - Missense(1)	large_intestine(1)	8											60	57	58					8																	145620510		2202	4300	6502	145591318	SO:0001583	missense	29894			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3157G>A	8.37:g.145620510C>T	ENSP00000339353:p.Glu1053Lys		145591318	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.598705	0.87055	.	.	ENSG00000071894	ENST00000349769	T	0.51325	0.71	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	T	0.72789	-0.4187	10	0.72032	D	0.01	-13.1137	14.8037	0.69935	0.0:1.0:0.0:0.0	.	1053	Q10570	CPSF1_HUMAN	K	1053	ENSP00000339353:E1053K	ENSP00000339353:E1053K	E	-	1	0	CPSF1	145591318	1.000000	0.71417	0.963000	0.40424	0.805000	0.45488	5.264000	0.65513	2.358000	0.79984	0.561000	0.74099	GAG		0.612	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		T	145620510	C	T	145620510	3	4	77	1	0	0	0	0	1	0	0	0	3830	893	31	1	1218	1	CPSF1	8	145620510	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	734489	145620510	743512	532	22268										
KCNV2	169522	broad.mit.edu	37	chr9	2718017	2718017	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgagggccccagcgaccctcCggccctgctgtccacgctga	12	19	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:2718017C>T	ENST00000382082.3	+	1	516	c.278C>T	c.(277-279)cCg>cTg	p.P93L		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	93					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.P93L(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		AGCGACCCTCCGGCCCTGCTG	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	9											61	45	51					9																	2718017		2202	4295	6497	2708017	SO:0001583	missense	169522			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.278C>T	9.37:g.2718017C>T	ENSP00000371514:p.Pro93Leu		2708017	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	C	2.529	-0.309051	0.05458	.	.	ENSG00000168263	ENST00000423608;ENST00000382082	D	0.96491	-4.03	4.53	1.51	0.23008	.	0.365106	0.28371	N	0.015599	D	0.90027	0.6886	N	0.19112	0.55	0.09310	N	0.999999	B	0.12630	0.006	B	0.06405	0.002	T	0.81690	-0.0818	10	0.41790	T	0.15	.	7.6292	0.28230	0.0:0.7115:0.1345:0.154	.	93	Q8TDN2	KCNV2_HUMAN	L	93	ENSP00000371514:P93L	ENSP00000371514:P93L	P	+	2	0	KCNV2	2708017	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	0.275000	0.18698	0.483000	0.27608	0.467000	0.42956	CCG		0.682	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718017	C	T	2718017	3	4	77	1	0	0	0	0	1	0	0	0	8116	652	23	1	280	1	KCNV2	9	2718017	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		2718017	138495414	533	22269										
GLIS3	169792	broad.mit.edu	37	chr9	3829457	3829457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctctgggaatcggggtagtGtgggggacagaacttctgca	16	7	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:3829457G>A	ENST00000324333.10	-	9	2237	c.2044C>T	c.(2044-2046)Cac>Tac	p.H682Y	GLIS3_ENST00000381971.3_Missense_Mutation_p.H837Y|GLIS3_ENST00000461870.1_5'UTR	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	682					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.H682Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TCGGGGTAGTGTGGGGGACAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	9											93	76	82					9																	3829457		2203	4300	6503	3819457	SO:0001583	missense	169792			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.2044C>T	9.37:g.3829457G>A	ENSP00000325494:p.His682Tyr		3819457	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	g	16.53	3.148375	0.57151	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.12361	2.7;2.69	5.93	3.08	0.35506	.	0.114081	0.36409	N	0.002603	T	0.14874	0.0359	L	0.29908	0.895	0.30470	N	0.773403	P;P;B	0.48764	0.915;0.857;0.001	P;B;B	0.49829	0.623;0.439;0.002	T	0.03103	-1.1072	10	0.66056	D	0.02	.	9.9257	0.41492	0.0651:0.0:0.6858:0.2491	.	277;837;682	Q59FQ6;Q8NEA6-2;Q8NEA6	.;.;GLIS3_HUMAN	Y	682;837	ENSP00000325494:H682Y;ENSP00000371398:H837Y	ENSP00000325494:H682Y	H	-	1	0	GLIS3	3819457	0.979000	0.34478	0.054000	0.19295	0.602000	0.36980	2.695000	0.47043	0.394000	0.25230	0.563000	0.77884	CAC		0.542	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		A	3829457	G	A	3829457	3	1	77	1	0	0	0	0	1	0	0	0	6467	1377	48	3	291	3	GLIS3	9	3829457	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1111440	3829457	137383974	534	22270										
SLC1A1	6505	broad.mit.edu	37	chr9	4561493	4561493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatccggaaaaattggtctgCgcgctgtcgtgtattatttc	10	8	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:4561493C>T	ENST00000262352.3	+	3	513	c.277C>T	c.(277-279)Cgc>Tgc	p.R93C	SLC1A1_ENST00000490167.1_3'UTR	NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	93					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.R93C(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	AATTGGTCTGCGCGCTGTCGT	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											340	320	327					9																	4561493		2203	4300	6503	4551493	SO:0001583	missense	6505				CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.277C>T	9.37:g.4561493C>T	ENSP00000262352:p.Arg93Cys		4551493	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	37	CCDS6452.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949503	0.53186	.	.	ENSG00000106688	ENST00000262352	T	0.61627	0.09	5.67	5.67	0.87782	.	0.100416	0.64402	D	0.000001	T	0.72740	0.3498	H	0.95224	3.64	0.80722	D	1	B	0.31383	0.321	B	0.31337	0.128	T	0.78031	-0.2363	10	0.72032	D	0.01	.	19.3557	0.94412	0.0:1.0:0.0:0.0	.	93	P43005	EAA3_HUMAN	C	93	ENSP00000262352:R93C	ENSP00000262352:R93C	R	+	1	0	SLC1A1	4551493	1.000000	0.71417	0.933000	0.37362	0.408000	0.30992	3.758000	0.55220	2.673000	0.90976	0.563000	0.77884	CGC		0.373	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			T	4561493	C	T	4561493	3	4	77	1	0	0	0	0	1	0	0	0	14468	768	27	1	287	1	SLC1A1	9	4561493	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	732036	4561493	136651938	535	22271										
SLC1A1	6505	broad.mit.edu	37	chr9	4583132	4583132	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgagtgccgtgggcctgcccGccgaggatgtcaccctgatc	14	14	1	2	rs199857691		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:4583132G>A	ENST00000262352.3	+	11	1524	c.1288G>A	c.(1288-1290)Gcc>Acc	p.A430T		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	430					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.A430T(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	GGGCCTGCCCGCCGAGGATGT	0.617													G|||	1	0.000199681	0	0	5008	,	,		19896	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	9											141	121	128					9																	4583132		2203	4300	6503	4573132	SO:0001583	missense	6505				CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1288G>A	9.37:g.4583132G>A	ENSP00000262352:p.Ala430Thr		4573132	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	37	CCDS6452.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.38	1.620661	0.28889	.	.	ENSG00000106688	ENST00000262352	T	0.59772	0.24	5.49	3.53	0.40419	.	0.147549	0.64402	N	0.000010	T	0.29389	0.0732	N	0.03194	-0.395	0.80722	D	1	B	0.16396	0.017	B	0.24974	0.057	T	0.20405	-1.0276	10	0.02654	T	1	.	11.308	0.49347	0.1575:0.0:0.8425:0.0	.	430	P43005	EAA3_HUMAN	T	430	ENSP00000262352:A430T	ENSP00000262352:A430T	A	+	1	0	SLC1A1	4573132	1.000000	0.71417	0.061000	0.19648	0.800000	0.45204	4.884000	0.63135	0.700000	0.31782	0.655000	0.94253	GCC		0.617	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			A	4583132	G	A	4583132	3	1	77	1	0	0	0	0	1	0	0	0	14468	1087	38	1	1330	1	SLC1A1	9	4583132	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	21639	4583132	136630299	536	22272										
RLN2	6019	broad.mit.edu	37	chr9	5304494	5304494	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgcataatttaataacttcCtccatccatgagtccgcgac	5	14	0	1	rs201648853	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:5304494C>G	ENST00000381627.3	-	1	475	c.87G>C	c.(85-87)gaG>gaC	p.E29D	RLN2_ENST00000308420.3_Missense_Mutation_p.E29D	NM_134441.2	NP_604390.1	P04090	REL2_HUMAN	relaxin 2	29					female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.E29D(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	11	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)		TAATAACTTCCTCCATCCATG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	9											78	80	79					9																	5304494		2203	4300	6503	5294494	SO:0001583	missense	6019				CCDS6460.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107014	ENSG00000107014		"Endogenous ligands"	10027	protein-coding gene	gene with protein product	"relaxin H2", "prorelaxin H2", "relaxin, ovarian, of pregnancy"	179740	"relaxin 2 (H2)"			6548703, 6548702	Standard	NM_134441		Approved	H2, RLXH2, bA12D24.1.1, bA12D24.1.2	uc003zja.2	P04090	OTTHUMG00000019496	ENST00000381627.3:c.87G>C	9.37:g.5304494C>G	ENSP00000371040:p.Glu29Asp		5294494	A0AVM0|Q99936|Q9UCX3|Q9UQJ2	Missense_Mutation	SNP	ENST00000381627.3	37	CCDS6460.1	.	.	.	.	.	.	.	.	.	.	G	0.093	-1.164388	0.01673	.	.	ENSG00000107014	ENST00000381627;ENST00000308420	D;D	0.84516	-1.86;-1.84	3.08	-2.65	0.06095	Insulin-like (1);	1.112660	0.07194	N	0.856292	T	0.46132	0.1377	N	0.00289	-1.7	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50206	-0.8855	10	0.02654	T	1	.	2.2803	0.04112	0.2026:0.4343:0.216:0.1472	.	29;29	P04090;P04090-2	REL2_HUMAN;.	D	29	ENSP00000371040:E29D;ENSP00000308018:E29D	ENSP00000308018:E29D	E	-	3	2	RLN2	5294494	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.543000	0.02194	-1.046000	0.03246	-0.357000	0.07601	GAG		0.512	RLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051619.1	NM_134441		G	5304494	C	G	5304494	3	3	77	1	0	0	0	0	1	0	0	0	13429	680	24	5	583	5	RLN2	9	5304494	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	721362	5304494	135908937	537	22273										
NFIB	4781	broad.mit.edu	37	chr9	14307164	14307164	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaccatgactagatccagaCgccagactttgtctgcctgt	8	13	2	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:14307164C>T	ENST00000380959.3	-	2	859	c.386G>A	c.(385-387)cGt>cAt	p.R129H	NFIB_ENST00000397579.2_Missense_Mutation_p.R129H|NFIB_ENST00000397575.3_Missense_Mutation_p.R129H|NFIB_ENST00000380934.4_Missense_Mutation_p.R155H|NFIB_ENST00000380921.3_Missense_Mutation_p.R129H|NFIB_ENST00000397581.2_Missense_Mutation_p.R129H|NFIB_ENST00000380953.1_Missense_Mutation_p.R129H	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	129					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R129H(2)		central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		TAGATCCAGACGCCAGACTTT	0.522			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																Esophageal Squamous(132;921 1730 14828 40753 46471)		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	2	Substitution - Missense(2)	large_intestine(2)	9											113	117	116					9																	14307164		2203	4300	6503	14297164	SO:0001583	missense	4781			U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.386G>A	9.37:g.14307164C>T	ENSP00000370346:p.Arg129His		14297164	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608781	0.87258	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000380921	D;D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	5.71	5.71	0.89125	MAD homology 1, Dwarfin-type (2);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.91888	0.7432	M	0.81802	2.56	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.991;0.994;0.991	D	0.92289	0.5840	10	0.87932	D	0	.	19.8773	0.96884	0.0:1.0:0.0:0.0	.	129;129;129	Q5VW27;Q5VW29;O00712	.;.;NFIB_HUMAN	H	155;129;129;129;129;129;129	ENSP00000370321:R155H;ENSP00000370346:R129H;ENSP00000370340:R129H;ENSP00000380705:R129H;ENSP00000380711:R129H;ENSP00000380709:R129H;ENSP00000370308:R129H	ENSP00000370308:R129H	R	-	2	0	NFIB	14297164	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.686000	0.91538	0.650000	0.86243	CGT		0.522	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		T	14307164	C	T	14307164	3	4	77	1	0	0	0	0	1	0	0	0	10402	536	19	1	908	1	NFIB	9	14307164	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	9002670	14307164	126906267	538	22274										
C9orf11	54586	broad.mit.edu	37	chr9	27297005	27297005	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtaggcttcaaagtgctacTttttaaggaaaaaactccag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:27297005delT	ENST00000380032.3	-	1	132	c.49delA	c.(49-51)agtfs	p.S18fs	EQTN_ENST00000537675.1_Frame_Shift_Del_p.S18fs|EQTN_ENST00000380031.1_Frame_Shift_Del_p.S18fs|EQTN_ENST00000484994.1_5'Flank	NM_020641.2	NP_065692.2	Q9NQ60	EQTN_HUMAN	equatorin, sperm acrosome associated	18					acrosomal vesicle exocytosis (GO:0060478)|endocytosis (GO:0006897)|fusion of sperm to egg plasma membrane (GO:0007342)	early endosome (GO:0005769)|inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|outer acrosomal membrane (GO:0002081)|plasma membrane (GO:0005886)		p.S17fs*4(1)									AAAGTGCTACTTTTTAAGGAA	0.318																																																1	Deletion - Frameshift(1)	large_intestine(1)	9											26	27	27					9																	27297005		2187	4291	6478	27287005	SO:0001589	frameshift_variant	54586			AJ278482	CCDS35001.1, CCDS55300.1	9p21	2012-09-20	2012-09-20	2012-09-20	ENSG00000120160	ENSG00000120160			1359	protein-coding gene	gene with protein product	"Acr formation associated factor", "Acrosome formation associated factor", "sperm acrosome associated 8"		"chromosome 9 open reading frame 11", "equatorin"	C9orf11			Standard	NM_020641		Approved	AFAF, SPACA8, equatorin	uc003zql.3	Q9NQ60	OTTHUMG00000021033	ENST00000380032.3:c.49delA	9.37:g.27297005delT	ENSP00000369371:p.Ser18fs		27287005	B2RPB3|B7ZMK1|Q5TCU1|Q96L22	Frame_Shift_Del	DEL	ENST00000380032.3	37	CCDS35001.1																																																																																				0.318	EQTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055499.1	NM_020641		-	27297005	T	-	27297005	7	5	77	1	0	1	0	1	0	0	0	0	2454	1609	56	0	867	0	C9orf11	9	27297005	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	12989841	27297005	113916426	539	22275										
TLN1	7094	broad.mit.edu	37	chr9	35706487	35706487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcagcccgggcagcattgGccagcggctcaatgagatgg	14	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:35706487G>A	ENST00000314888.9	-	39	5503	c.5150C>T	c.(5149-5151)gCc>gTc	p.A1717V	TLN1_ENST00000540444.1_Missense_Mutation_p.A1701V|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1717	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.A1717V(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GGCAGCATTGGCCAGCGGCTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	9											44	44	44					9																	35706487		2203	4300	6503	35696487	SO:0001583	missense	7094			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5150C>T	9.37:g.35706487G>A	ENSP00000316029:p.Ala1717Val		35696487	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.047218	0.55110	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.11277	2.79;2.79	5.38	5.38	0.77491	.	0.052934	0.85682	D	0.000000	T	0.12817	0.0311	L	0.48642	1.525	0.80722	D	1	B	0.24618	0.107	B	0.19946	0.027	T	0.08207	-1.0733	10	0.24483	T	0.36	-13.8324	18.736	0.91755	0.0:0.0:1.0:0.0	.	1717	Q9Y490	TLN1_HUMAN	V	1717;1701	ENSP00000316029:A1717V;ENSP00000442981:A1701V	ENSP00000316029:A1717V	A	-	2	0	TLN1	35696487	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.864000	0.99589	2.512000	0.84698	0.555000	0.69702	GCC		0.592	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35706487	G	A	35706487	3	1	77	1	0	0	0	0	1	0	0	0	15986	1203	42	3	2551	3	TLN1	9	35706487	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8409482	35706487	105506944	540	22276										
TMEM8B	51754	broad.mit.edu	37	chr9	35847067	35847067	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acagtctgtatttccaccacGttctccgagggtttgggaat	10	10	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:35847067G>A	ENST00000377991.4	+	11	1834				TMEM8B_ENST00000439587.2_Silent_p.T298T|TMEM8B_ENST00000377996.1_Silent_p.T298T|TMEM8B_ENST00000377988.2_Intron	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B						cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T298T(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						TTTCCACCACGTTCTCCGAGG	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	9											193	136	155					9																	35847067		2203	4300	6503	35837067	SO:0001627	intron_variant	51754			BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma expressed 6"		"chromosome 9 open reading frame 127"	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.819+75G>A	9.37:g.35847067G>A			35837067	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Missense_Mutation	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																				0.488	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446		A	35847067	G	A	35847067	1	1	77	0	1	0	0	0	0	0	0	0	16254	1132	40	1		1	TMEM8B	9	35847067	Intron	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	140580	35847067	105366364	541	22277										
FBXO10	26267	broad.mit.edu	37	chr9	37537831	37537831	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcacgttgtgcaggaagataTgggtgtttttgaaggtacag	15	4	0	2	rs375383268		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:37537831T>C	ENST00000432825.2	-	3	743	c.695A>G	c.(694-696)cAt>cGt	p.H232R	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron|FBXO10_ENST00000543968.1_5'Flank	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	232					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.H232R(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CAGGAAGATATGGGTGTTTTT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	9						T	ARG/HIS	1,3911		0,1,1955	81	81	81		695	4	1	9		81	0,8268		0,0,4134	no	missense	FBXO10	NM_012166.2	29	0,1,6089	CC,CT,TT		0.0,0.0256,0.0082	benign	232/957	37537831	1,12179	1956	4134	6090	37527831	SO:0001583	missense	26267			AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.695A>G	9.37:g.37537831T>C	ENSP00000403802:p.His232Arg		37527831	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	T	10.77	1.444861	0.25987	2.56E-4	0.0	ENSG00000147912	ENST00000432825	T	0.40756	1.02	5.3	3.99	0.46301	Pectin lyase fold/virulence factor (1);	0.267886	0.38111	N	0.001802	T	0.18800	0.0451	N	0.14661	0.345	0.80722	D	1	B	0.29432	0.244	B	0.20767	0.031	T	0.08659	-1.0711	10	0.20046	T	0.44	-9.1982	4.0673	0.09866	0.0:0.2907:0.0:0.7093	.	232	Q9UK96	FBX10_HUMAN	R	232	ENSP00000403802:H232R	ENSP00000276960:H232R	H	-	2	0	FBXO10	37527831	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	4.684000	0.61686	2.126000	0.65437	0.533000	0.62120	CAT		0.502	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			C	37537831	T	C	37537831	3	2	77	1	0	0	0	0	1	0	0	0	5745	1464	51	4	2211	4	FBXO10	9	37537831	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1690764	37537831	103675600	542	22278										
FRMPD1	22844	broad.mit.edu	37	chr9	37740286	37740286	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgacagacagtgccgagtcCgaggcgtccgactcagccaa	12	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:37740286C>T	ENST00000539465.1	+	15	2354	c.1761C>T	c.(1759-1761)tcC>tcT	p.S587S	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000536622.1_Silent_p.S409S|FRMPD1_ENST00000377765.3_Silent_p.S587S|FRMPD1_ENST00000541302.1_Silent_p.S456S			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	587						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.S587S(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GTGCCGAGTCCGAGGCGTCCG	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	9											32	35	34					9																	37740286		2203	4300	6503	37730286	SO:0001819	synonymous_variant	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1761C>T	9.37:g.37740286C>T			37730286	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																				0.637	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37740286	C	T	37740286	2	4	77	1	0	0	0	0	0	0	0	1	6076	639	23	1		1	FRMPD1	9	37740286	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	202455	37740286	103473145	543	22279										
ALDH1B1	219	broad.mit.edu	37	chr9	38396925	38396925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcggagagcgtttcggggagCgtggtttcttcatcaagcct	15	9	3	1	rs201118307	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:38396925C>T	ENST00000377698.3	+	2	1333	c.1180C>T	c.(1180-1182)Cgt>Tgt	p.R394C		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	394					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)	p.R394C(1)		NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		TTTCGGGGAGCGTGGTTTCTT	0.542													C|||	2	0.000399361	0	0	5008	,	,		19496	0.001		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	9											106	86	93					9																	38396925		2203	4300	6503	38386925	SO:0001583	missense	219			M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1180C>T	9.37:g.38396925C>T	ENSP00000366927:p.Arg394Cys		38386925	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	10.83	1.461412	0.26248	.	.	ENSG00000137124	ENST00000377698;ENST00000540055	T	0.77098	-1.07	5.81	3.8	0.43715	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.587759	0.15205	N	0.274791	T	0.77294	0.4109	M	0.83223	2.63	0.09310	N	0.999999	B	0.18968	0.032	B	0.14578	0.011	T	0.71474	-0.4582	10	0.87932	D	0	.	8.2225	0.31549	0.2201:0.6952:0.0:0.0847	.	394	P30837	AL1B1_HUMAN	C	394;95	ENSP00000366927:R394C	ENSP00000366927:R394C	R	+	1	0	ALDH1B1	38386925	0.004000	0.15560	0.003000	0.11579	0.989000	0.77384	1.580000	0.36547	1.479000	0.48272	0.655000	0.94253	CGT		0.542	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			T	38396925	C	T	38396925	3	4	77	1	0	0	0	0	1	0	0	0	493	768	27	1	1182	1	ALDH1B1	9	38396925	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	656639	38396925	102816506	544	22280										
PRKACG	5568	broad.mit.edu	37	chr9	71628906	71628906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgagctggcggtgttttgagCggggtttccccatctgtaga	15	9	1	2	rs138280963	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:71628906C>T	ENST00000377276.2	-	1	133	c.103G>A	c.(103-105)Gct>Act	p.A35T		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	35					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.A35T(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GTGTTTTGAGCGGGGTTTCCC	0.632																																					Esophageal Squamous(110;2236 2623 32146)											1	Substitution - Missense(1)	large_intestine(1)	9						C	THR/ALA	7,4399	12.9+/-30.5	0,7,2196	73	75	75		103	-0.6	0	9	dbSNP_134	75	0,8600		0,0,4300	yes	missense	PRKACG	NM_002732.3	58	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	benign	35/352	71628906	7,12999	2203	4300	6503	70818726	SO:0001583	missense	5568			M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.103G>A	9.37:g.71628906C>T	ENSP00000366488:p.Ala35Thr		70818726	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	37	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	C	2.832	-0.242500	0.05906	0.001589	0.0	ENSG00000165059	ENST00000377276	T	0.07908	3.15	1.03	-0.614	0.11590	Protein kinase-like domain (1);	1.402030	0.05983	U	0.644664	T	0.05181	0.0138	L	0.33753	1.03	0.21256	N	0.999746	B	0.02656	0.0	B	0.06405	0.002	T	0.40831	-0.9542	10	0.02654	T	1	.	4.1425	0.10200	0.0:0.5491:0.4509:0.0	.	35	P22612	KAPCG_HUMAN	T	35	ENSP00000366488:A35T	ENSP00000366488:A35T	A	-	1	0	PRKACG	70818726	0.381000	0.25140	0.005000	0.12908	0.005000	0.04900	-2.437000	0.01018	0.458000	0.26988	0.467000	0.42956	GCT		0.632	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			T	71628906	C	T	71628906	3	4	77	1	0	0	0	0	1	0	0	0	12533	768	27	1	956	1	PRKACG	9	71628906	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	33231981	71628906	69584525	545	22281										
FAM189A2	9413	broad.mit.edu	37	chr9	72003331	72003331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatctgatgaggagcacatgGaggaagccatcacaagtgcc	12	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:72003331G>A	ENST00000257515.8	+	10	1534	c.1114G>A	c.(1114-1116)Gag>Aag	p.E372K	FAM189A2_ENST00000455972.1_Missense_Mutation_p.E372K|FAM189A2_ENST00000469179.1_3'UTR|FAM189A2_ENST00000377216.3_Missense_Mutation_p.E159K|FAM189A2_ENST00000303068.7_Missense_Mutation_p.E207K	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2	372						integral component of membrane (GO:0016021)		p.E159K(1)|p.E372K(1)		endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GGAGCACATGGAGGAAGCCAT	0.418																																																2	Substitution - Missense(2)	large_intestine(2)	9											41	38	39					9																	72003331		2203	4300	6503	71193151	SO:0001583	missense	9413			L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"chromosome 9 open reading frame 61"	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.1114G>A	9.37:g.72003331G>A	ENSP00000257515:p.Glu372Lys		71193151	Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Missense_Mutation	SNP	ENST00000257515.8	37	CCDS6629.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624856	0.96660	.	.	ENSG00000135063	ENST00000455972;ENST00000257515;ENST00000303068;ENST00000377225;ENST00000377216	T;T;T	0.42513	2.07;2.07;0.97	5.8	5.8	0.92144	.	0.057165	0.64402	D	0.000002	T	0.52435	0.1734	M	0.73217	2.22	0.58432	D	0.999999	P	0.52316	0.952	P	0.45829	0.494	T	0.57406	-0.7817	10	0.62326	D	0.03	-25.6262	20.063	0.97692	0.0:0.0:1.0:0.0	.	372	Q15884	F1892_HUMAN	K	372;372;207;371;159	ENSP00000395675:E372K;ENSP00000257515:E372K;ENSP00000304435:E207K	ENSP00000257515:E372K	E	+	1	0	FAM189A2	71193151	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.731000	0.98807	2.735000	0.93741	0.655000	0.94253	GAG		0.418	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816		A	72003331	G	A	72003331	3	1	77	1	0	0	0	0	1	0	0	0	5532	1175	41	3	1148	3	FAM189A2	9	72003331	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	374425	72003331	69210100	546	22282										
TRPM6	140803	broad.mit.edu	37	chr9	77377530	77377530	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctgctgaaaaaggaactcGctttagattagaggggacca	11	7	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:77377530G>A	ENST00000360774.1	-	26	4294	c.4057C>T	c.(4057-4059)Cga>Tga	p.R1353*	TRPM6_ENST00000449912.2_Nonsense_Mutation_p.R1348*|TRPM6_ENST00000451710.3_Nonsense_Mutation_p.R1353*|TRPM6_ENST00000376864.4_Nonsense_Mutation_p.R1353*|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Nonsense_Mutation_p.R1348*	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1353					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R1353*(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AAAGGAACTCGCTTTAGATTA	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											153	160	158					9																	77377530		2203	4300	6503	76567350	SO:0001587	stop_gained	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.4057C>T	9.37:g.77377530G>A	ENSP00000354006:p.Arg1353*		76567350	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Nonsense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	43	9.868141	0.99284	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	.	.	.	6.02	2.81	0.32909	.	1.247560	0.05078	N	0.482954	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9039	0.24299	0.0733:0.3558:0.4707:0.1002	.	.	.	.	X	1353;1353;1348;1348;1353;1016;1016	.	ENSP00000309693:R1016X	R	-	1	2	TRPM6	76567350	0.002000	0.14202	0.952000	0.39060	0.751000	0.42716	0.956000	0.29202	1.500000	0.48636	0.655000	0.94253	CGA		0.478	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77377530	G	A	77377530	4	1	77	1	0	0	0	0	0	1	0	0	16630	1095	38	1	2067	1	TRPM6	9	77377530	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5374199	77377530	63835901	547	22283										
TRPM6	140803	broad.mit.edu	37	chr9	77397705	77397705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggcgaaaggatggccttgCgtgccactccaaagctcagc	12	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:77397705C>T	ENST00000360774.1	-	22	3221	c.2984G>A	c.(2983-2985)cGc>cAc	p.R995H	TRPM6_ENST00000449912.2_Missense_Mutation_p.R990H|TRPM6_ENST00000451710.3_Missense_Mutation_p.R995H|TRPM6_ENST00000376864.4_Missense_Mutation_p.R995H|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.R990H	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	995					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R995H(2)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GATGGCCTTGCGTGCCACTCC	0.448																																																2	Substitution - Missense(2)	large_intestine(2)	9											124	105	111					9																	77397705		2203	4300	6503	76587525	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2984G>A	9.37:g.77397705C>T	ENSP00000354006:p.Arg995His		76587525	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	34	5.348060	0.95807	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77	5.71	5.71	0.89125	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	M	0.91612	3.225	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.997;0.998;0.914	T	0.54516	-0.8282	10	0.87932	D	0	.	19.8632	0.96793	0.0:1.0:0.0:0.0	.	658;995;990	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	H	995;995;990;990;995;658;658	ENSP00000354006:R995H;ENSP00000407341:R995H;ENSP00000396672:R990H;ENSP00000354962:R990H;ENSP00000366060:R995H	ENSP00000309693:R658H	R	-	2	0	TRPM6	76587525	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.771000	0.85420	2.704000	0.92352	0.561000	0.74099	CGC		0.448	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77397705	C	T	77397705	3	4	77	1	0	0	0	0	1	0	0	0	16630	768	27	1	3156	1	TRPM6	9	77397705	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	20175	77397705	63815726	548	22284										
TRPM6	140803	broad.mit.edu	37	chr9	77448951	77448951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctctggttctcaatgacaCcccaaggagggattccaact	8	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:77448951C>T	ENST00000360774.1	-	6	869	c.632G>A	c.(631-633)gGt>gAt	p.G211D	TRPM6_ENST00000359047.2_Missense_Mutation_p.G211D|TRPM6_ENST00000449912.2_Missense_Mutation_p.G206D|TRPM6_ENST00000451710.3_Missense_Mutation_p.G211D|TRPM6_ENST00000376864.4_Missense_Mutation_p.G211D|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000376871.3_Missense_Mutation_p.G211D|TRPM6_ENST00000376872.3_Missense_Mutation_p.G211D|TRPM6_ENST00000361255.3_Missense_Mutation_p.G206D	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	211					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.G211N(1)|p.G211D(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CTCAATGACACCCCAAGGAGG	0.428																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	9											163	150	155					9																	77448951		2203	4300	6503	76638771	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.632G>A	9.37:g.77448951C>T	ENSP00000354006:p.Gly211Asp		76638771	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	34	5.295869	0.95574	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.57577	0.2063	H	0.94925	3.6	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.992;0.996	T	0.68135	-0.5489	10	0.87932	D	0	.	20.4366	0.99092	0.0:1.0:0.0:0.0	.	211;211;211;211;211;206	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	D	211;211;211;211;206;206;210;211;211	ENSP00000354006:G211D;ENSP00000407341:G211D;ENSP00000366068:G211D;ENSP00000366067:G211D;ENSP00000396672:G206D;ENSP00000354962:G206D;ENSP00000366060:G211D;ENSP00000351942:G211D	ENSP00000351942:G211D	G	-	2	0	TRPM6	76638771	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.730000	0.84881	2.837000	0.97791	0.591000	0.81541	GGT		0.428	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77448951	C	T	77448951	3	4	77	1	0	0	0	0	1	0	0	0	16630	507	18	3	5572	3	TRPM6	9	77448951	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	51246	77448951	63764480	549	22285										
PCSK5	5125	broad.mit.edu	37	chr9	78789974	78789974	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaccaaccaatgaatttcCgaaagtggaacggttccgct	8	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:78789974C>T	ENST00000545128.1	+	14	2367	c.1829C>T	c.(1828-1830)cCg>cTg	p.P610L	PCSK5_ENST00000376767.3_Missense_Mutation_p.P610L|PCSK5_ENST00000376752.4_Missense_Mutation_p.P610L	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	610					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)	p.P610L(3)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						AATGAATTTCCGAAAGTGGAA	0.478																																																3	Substitution - Missense(3)	large_intestine(3)	9											126	118	121					9																	78789974		2203	4300	6503	77979794	SO:0001583	missense	5125				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1829C>T	9.37:g.78789974C>T	ENSP00000446280:p.Pro610Leu		77979794	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291869	0.80914	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	T;T;T;T	0.69435	0.73;-0.4;0.58;1.58	5.74	5.74	0.90152	.	0.218247	0.49305	D	0.000160	T	0.63498	0.2516	M	0.78049	2.395	0.53688	D	0.999971	P;B	0.40681	0.727;0.022	B;B	0.32393	0.145;0.011	T	0.66316	-0.5954	10	0.07030	T	0.85	-14.496	19.9326	0.97124	0.0:1.0:0.0:0.0	.	610;610	Q92824-2;B1AMG5	.;.	L	610;313;610;610;610;283	ENSP00000446280:P610L;ENSP00000365958:P610L;ENSP00000365943:P610L;ENSP00000411654:P283L	ENSP00000365943:P610L	P	+	2	0	PCSK5	77979794	0.973000	0.33851	0.998000	0.56505	0.915000	0.54546	2.280000	0.43443	2.720000	0.93068	0.650000	0.86243	CCG		0.478	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	78789974	C	T	78789974	3	4	77	1	0	0	0	0	1	0	0	0	11634	652	23	1	1883	1	PCSK5	9	78789974	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1341023	78789974	62423457	550	22286										
PRUNE2	158471	broad.mit.edu	37	chr9	79270373	79270373	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagcactgggactcagcacGccctcttcaaaggggatgtc	12	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:79270373G>A	ENST00000376718.3	-	10	8445	c.8322C>T	c.(8320-8322)ggC>ggT	p.G2774G	PRUNE2_ENST00000428286.1_Silent_p.G2415G|PRUNE2_ENST00000223609.6_Silent_p.G38G|PRUNE2_ENST00000443509.2_Silent_p.G23G|PRUNE2_ENST00000466266.2_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2774					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.G2774G(2)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GACTCAGCACGCCCTCTTCAA	0.458																																																2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	9											75	67	69					9																	79270373		1568	3582	5150	78460193	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8322C>T	9.37:g.79270373G>A			78460193	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	8.310	0.821925	0.16678	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.74	-1.01	0.10169	.	.	.	.	.	T	0.39358	0.1075	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25572	-1.0128	4	.	.	.	-27.9261	0.7209	0.00940	0.1527:0.2162:0.2224:0.4087	.	.	.	.	C	2096	.	.	R	-	1	0	PRUNE2	78460193	0.016000	0.18221	0.838000	0.33150	0.781000	0.44180	-0.091000	0.11146	-0.312000	0.08741	-1.463000	0.01021	CGT		0.458	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79270373	G	A	79270373	2	1	77	1	0	0	0	0	0	0	0	1	12675	1074	38	1		1	PRUNE2	9	79270373	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	480399	79270373	61943058	551	22287										
SYK	6850	broad.mit.edu	37	chr9	93607788	93607789	+	Frame_Shift_Ins	INS	-	-	A													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatcgctaccacagcccatgINSaaaaaatgccttggttccat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:93607788_93607789insA	ENST00000375754.4	+	3	638_639	c.490_491insA	c.(490-492)gaafs	p.E164fs	SYK_ENST00000375746.1_Frame_Shift_Ins_p.E164fs|SYK_ENST00000375747.1_Frame_Shift_Ins_p.E164fs|SYK_ENST00000375751.4_Frame_Shift_Ins_p.E164fs	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	164	Interdomain A.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.M166fs*14(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CACAGCCCATGAAAAAATGCCT	0.485			T	"ETV6, ITK"	"MDS, peripheral T-cell lymphoma"																																		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	1	Insertion - Frameshift(1)	large_intestine(1)	9																																								92647610	SO:0001589	frameshift_variant	6850			L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"SH2 domain containing"	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.496dupA	9.37:g.93607794_93607794dupA	ENSP00000364907:p.Glu164fs		92647609		Frame_Shift_Ins	INS	ENST00000375754.4	37	CCDS6688.1																																																																																				0.485	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			A	93607789	-	A	93607788	7	5	77	1	0	1	1	0	0	0	0	0	15477	1291	45	0	496	0	SYK	9	93607788	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	14337415	93607788	47605643	552	22288										
OMD	4958	broad.mit.edu	37	chr9	95177558	95177558	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catcatcatctggaaatctcCtgaaaacttgtgtctttagt	6	9	5	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:95177558C>A	ENST00000375550.4	-	3	1417	c.1142G>T	c.(1141-1143)aGg>aTg	p.R381M	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	381					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.R381M(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TGGAAATCTCCTGAAAACTTG	0.398			T	USP6	aneurysmal bone cysts																																		Dom	yes		9	9q22.31	4958	osteomodulin		M	1	Substitution - Missense(1)	large_intestine(1)	9											221	204	210					9																	95177558		2203	4300	6503	94217379	SO:0001583	missense	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.1142G>T	9.37:g.95177558C>A	ENSP00000364700:p.Arg381Met		94217379	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	37	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765847	0.69878	.	.	ENSG00000127083	ENST00000375550	T	0.48201	0.82	5.44	4.54	0.55810	.	0.326406	0.27966	N	0.017121	T	0.54647	0.1871	M	0.63428	1.95	0.33731	D	0.61821	D	0.59767	0.986	P	0.49708	0.62	T	0.71988	-0.4426	10	0.87932	D	0	-1.4285	14.4467	0.67356	0.0:0.9288:0.0:0.0712	.	381	Q99983	OMD_HUMAN	M	381	ENSP00000364700:R381M	ENSP00000364700:R381M	R	-	2	0	OMD	94217379	0.023000	0.18921	0.812000	0.32479	0.894000	0.52154	0.993000	0.29680	1.429000	0.47314	0.555000	0.69702	AGG		0.398	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		A	95177558	C	A	95177558	3	1	77	1	0	0	0	0	1	0	0	0	10896	681	24	2	127	2	OMD	9	95177558	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1569770	95177558	46035873	553	22289										
NCBP1	4686	broad.mit.edu	37	chr9	100410309	100410309	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtatttagattgcctgtgggCccagattcagaaattgaaaa	10	6	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:100410309C>T	ENST00000375147.3	+	8	957	c.701C>T	c.(700-702)gCc>gTc	p.A234V		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	234	MIF4G.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)	p.A234V(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TGCCTGTGGGCCCAGATTCAG	0.358																																					Ovarian(36;879 898 2893 44212 50307)											1	Substitution - Missense(1)	large_intestine(1)	9											51	47	48					9																	100410309		2203	4300	6503	99450130	SO:0001583	missense	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.701C>T	9.37:g.100410309C>T	ENSP00000364289:p.Ala234Val		99450130	B2R718|Q59G76|Q5T1V0|Q5T7X2	Missense_Mutation	SNP	ENST00000375147.3	37	CCDS6728.1	.	.	.	.	.	.	.	.	.	.	C	31	5.078288	0.94000	.	.	ENSG00000136937	ENST00000375147	T	0.20598	2.06	5.55	5.55	0.83447	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.054189	0.64402	D	0.000001	T	0.43678	0.1258	M	0.84585	2.705	0.80722	D	1	B	0.27166	0.17	B	0.41946	0.371	T	0.33904	-0.9850	10	0.38643	T	0.18	-7.9335	19.55	0.95314	0.0:1.0:0.0:0.0	.	234	Q09161	NCBP1_HUMAN	V	234	ENSP00000364289:A234V	ENSP00000364289:A234V	A	+	2	0	NCBP1	99450130	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.593000	0.67550	2.799000	0.96334	0.586000	0.80456	GCC		0.358	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		T	100410309	C	T	100410309	3	4	77	1	0	0	0	0	1	0	0	0	10242	739	26	3	731	3	NCBP1	9	100410309	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5232751	100410309	40803122	554	22290										
GABBR2	9568	broad.mit.edu	37	chr9	101216264	101216264	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagaggcatgggactgaccGtgaccccgaagaagttggtc	14	11	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:101216264G>A	ENST00000259455.2	-	7	1694	c.1235C>T	c.(1234-1236)aCg>aTg	p.T412M		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	412					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.T412M(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GGGACTGACCGTGACCCCGAA	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	9											172	152	159					9																	101216264		2203	4300	6503	100256085	SO:0001630	splice_region_variant	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1236+1C>T	9.37:g.101216264G>A			100256085	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948118	0.92593	.	.	ENSG00000136928	ENST00000259455	D	0.86097	-2.07	5.79	5.79	0.91817	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.92492	0.7616	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92893	0.6333	10	0.87932	D	0	.	17.5351	0.87827	0.0:0.0:1.0:0.0	.	412	O75899	GABR2_HUMAN	M	412	ENSP00000259455:T412M	ENSP00000259455:T412M	T	-	2	0	GABBR2	100256085	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.869000	0.99810	2.751000	0.94390	0.650000	0.86243	ACG		0.517	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		Missense_Mutation	A	101216264	G	A	101216264	5	1	77	1	0	0	0	0	0	0	1	0	6175	1159	40	1	1642	1	GABBR2	9	101216264	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	805955	101216264	39997167	555	22291										
GABBR2	9568	broad.mit.edu	37	chr9	101304306	101304306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcttatcggctagaacaggcGtggttgcagcaaaagaaagc	12	8	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:101304306G>A	ENST00000259455.2	-	3	938	c.479C>T	c.(478-480)aCg>aTg	p.T160M	GABBR2_ENST00000477471.1_5'UTR	NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	160					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.T160M(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TAGAACAGGCGTGGTTGCAGC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	9											55	51	52					9																	101304306		2203	4300	6503	100344127	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.479C>T	9.37:g.101304306G>A	ENSP00000259455:p.Thr160Met		100344127	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522906	0.85600	.	.	ENSG00000136928	ENST00000259455	D	0.82803	-1.65	5.39	5.39	0.77823	Extracellular ligand-binding receptor (1);	0.109676	0.64402	D	0.000009	D	0.88108	0.6348	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88720	0.3229	10	0.62326	D	0.03	.	16.6427	0.85130	0.0:0.0:1.0:0.0	.	160	O75899	GABR2_HUMAN	M	160	ENSP00000259455:T160M	ENSP00000259455:T160M	T	-	2	0	GABBR2	100344127	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	7.841000	0.86834	2.538000	0.85594	0.655000	0.94253	ACG		0.448	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101304306	G	A	101304306	3	1	77	1	0	0	0	0	1	0	0	0	6175	1145	40	1	2414	1	GABBR2	9	101304306	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	88042	101304306	39909125	556	22292										
ANKS6	203286	broad.mit.edu	37	chr9	101552642	101552642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agacgcaccacggcctcgtgCccgtgctggatggcagccat	13	15	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:101552642C>T	ENST00000353234.4	-	2	653	c.606G>A	c.(604-606)ggG>ggA	p.G202G	ANKS6_ENST00000540940.1_Silent_p.G7G|ANKS6_ENST00000375019.2_Intron|ANKS6_ENST00000375018.1_Silent_p.G202G|ANKS6_ENST00000471846.1_5'UTR			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	202						cilium (GO:0005929)|cytoplasm (GO:0005737)		p.G202G(1)		endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				CGGCCTCGTGCCCGTGCTGGA	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	9											31	36	34					9																	101552642		2100	4200	6300	100592463	SO:0001819	synonymous_variant	203286			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.606G>A	9.37:g.101552642C>T			100592463	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Silent	SNP	ENST00000353234.4	37	CCDS43856.1																																																																																				0.672	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		T	101552642	C	T	101552642	2	4	77	1	0	0	0	0	0	0	0	1	692	726	26	3		3	ANKS6	9	101552642	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	248336	101552642	39660789	557	22293										
TGFBR1	7046	broad.mit.edu	37	chr9	101894949	101894949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagaggacccttcattagatCgcccttttatttcagagggt	9	9	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:101894949C>T	ENST00000374994.4	+	3	619	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C	TGFBR1_ENST00000552516.1_Missense_Mutation_p.R172C|TGFBR1_ENST00000374990.2_Intron|TGFBR1_ENST00000550253.1_Missense_Mutation_p.R99C	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	168					activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R168C(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TTCATTAGATCGCCCTTTTAT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	9											141	121	128					9																	101894949		2203	4300	6503	100934770	SO:0001583	missense	7046				CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.502C>T	9.37:g.101894949C>T	ENSP00000364133:p.Arg168Cys		100934770	Q6IR47|Q706C0|Q706C1	Missense_Mutation	SNP	ENST00000374994.4	37	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.774791	0.70107	.	.	ENSG00000106799	ENST00000547314;ENST00000552573;ENST00000374994;ENST00000540092;ENST00000552516;ENST00000548365;ENST00000550253;ENST00000546584	T;T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07;0.07	6.02	6.02	0.97574	.	0.090608	0.85682	D	0.000000	T	0.46718	0.1407	N	0.19112	0.55	0.80722	D	1	B	0.12630	0.006	B	0.01281	0.0	T	0.25012	-1.0144	10	0.38643	T	0.18	.	19.3122	0.94192	0.0:1.0:0.0:0.0	.	168	P36897	TGFR1_HUMAN	C	99;103;168;168;172;103;99;165	ENSP00000449934:R99C;ENSP00000447182:R103C;ENSP00000364133:R168C;ENSP00000447297:R172C;ENSP00000448518:R103C;ENSP00000450052:R99C;ENSP00000447707:R165C	ENSP00000364133:R168C	R	+	1	0	TGFBR1	100934770	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.059000	0.71133	2.865000	0.98341	0.655000	0.94253	CGC		0.423	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			T	101894949	C	T	101894949	3	4	77	1	0	0	0	0	1	0	0	0	15860	884	31	1	512	1	TGFBR1	9	101894949	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	342307	101894949	39318482	558	22294										
TEX10	54881	broad.mit.edu	37	chr9	103102585	103102585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttggttatttcttttaagaCatatggaaaacgactcataa	6	6	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:103102585C>T	ENST00000374902.4	-	5	1380	c.1204G>A	c.(1204-1206)Gtc>Atc	p.V402I	TEX10_ENST00000535814.1_Missense_Mutation_p.V405I|TEX10_ENST00000537512.1_Missense_Mutation_p.V337I	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	402						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)		p.V402I(1)		NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TCTTTTAAGACATATGGAAAA	0.299																																																1	Substitution - Missense(1)	large_intestine(1)	9											172	188	183					9																	103102585		2203	4297	6500	102142406	SO:0001583	missense	54881			AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1204G>A	9.37:g.103102585C>T	ENSP00000364037:p.Val402Ile		102142406	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	37	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.542697	0.45280	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730;ENST00000429235;ENST00000537512	T;T;T	0.63580	-0.05;-0.05;-0.05	5.45	0.962	0.19643	Armadillo-type fold (1);	0.614083	0.17975	N	0.155732	T	0.34832	0.0911	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.13145	0.003;0.0;0.007;0.007;0.0	B;B;B;B;B	0.09377	0.004;0.0;0.001;0.002;0.0	T	0.19484	-1.0304	10	0.54805	T	0.06	0.7652	4.3783	0.11281	0.4751:0.3357:0.0:0.1892	.	337;405;270;270;402	B7Z9D5;B4DYV2;E7ERG2;B4DQR0;Q9NXF1	.;.;.;.;TEX10_HUMAN	I	405;402;270;47;337	ENSP00000444555:V405I;ENSP00000364037:V402I;ENSP00000438120:V337I	ENSP00000364037:V402I	V	-	1	0	TEX10	102142406	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.874000	0.39568	0.633000	0.30452	0.591000	0.81541	GTC		0.299	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		T	103102585	C	T	103102585	3	4	77	1	0	0	0	0	1	0	0	0	15811	478	17	3	1629	3	TEX10	9	103102585	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1207636	103102585	38110846	559	22295										
MURC	347273	broad.mit.edu	37	chr9	103340481	103340481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatccaccagaatcgcctgtCgagtgttacagaagatgaag	10	9	0	4	rs375508129		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:103340481C>T	ENST00000307584.5	+	1	121	c.56C>T	c.(55-57)tCg>tTg	p.S19L	RN7SKP87_ENST00000364096.1_RNA	NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	19					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)		p.S19L(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				AATCGCCTGTCGAGTGTTACA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	115	106	109		56	5.4	0.8	9		109	0,8600		0,0,4300	no	missense	MURC	NM_001018116.1	145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	19/365	103340481	1,13005	2203	4300	6503	102380302	SO:0001583	missense	347273			BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"muscle-restricted coiled-coil protein"					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.56C>T	9.37:g.103340481C>T	ENSP00000418668:p.Ser19Leu		102380302	B1PRL3|B4DT88	Missense_Mutation	SNP	ENST00000307584.5	37	CCDS35083.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277212	0.59758	2.27E-4	0.0	ENSG00000170681	ENST00000307584	T	0.69306	-0.39	5.39	5.39	0.77823	.	0.206543	0.33253	N	0.005111	T	0.77418	0.4127	L	0.47716	1.5	0.44227	D	0.997065	D	0.89917	1.0	D	0.81914	0.995	T	0.79060	-0.1958	10	0.72032	D	0.01	-4.5535	16.6642	0.85248	0.0:1.0:0.0:0.0	.	19	Q5BKX8	MURC_HUMAN	L	19	ENSP00000418668:S19L	ENSP00000418668:S19L	S	+	2	0	MURC	102380302	1.000000	0.71417	0.810000	0.32431	0.786000	0.44442	6.162000	0.71874	2.532000	0.85374	0.655000	0.94253	TCG		0.443	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116		T	103340481	C	T	103340481	3	4	77	1	0	0	0	0	1	0	0	0	10017	893	31	1	58	1	MURC	9	103340481	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	237896	103340481	37872950	560	22296										
GRIN3A	116443	broad.mit.edu	37	chr9	104375771	104375771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gattagctcggatatgttggCggtcaatggagagttgggtg	17	4	1	1	rs372945887		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:104375771C>T	ENST00000361820.3	-	6	3253	c.2653G>A	c.(2653-2655)Gcc>Acc	p.A885T	GRIN3A_ENST00000479772.1_5'UTR	NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	885					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)	p.A885T(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	GATATGTTGGCGGTCAATGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											185	151	162					9																	104375771		2203	4300	6503	103415592	SO:0001583	missense	116443				CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2653G>A	9.37:g.104375771C>T	ENSP00000355155:p.Ala885Thr		103415592	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.860851	0.91433	.	.	ENSG00000198785	ENST00000361820	T	0.50548	0.74	5.14	5.14	0.70334	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.28267	0.0698	N	0.05124	-0.11	0.20638	N	0.999872	B	0.16603	0.018	B	0.17098	0.017	T	0.17319	-1.0373	10	0.41790	T	0.15	.	12.5244	0.56077	0.8602:0.1398:0.0:0.0	.	885	Q8TCU5	NMD3A_HUMAN	T	885	ENSP00000355155:A885T	ENSP00000355155:A885T	A	-	1	0	GRIN3A	103415592	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.869000	0.69613	0.898000	0.36418	-0.256000	0.11100	GCC		0.463	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104375771	C	T	104375771	3	4	77	1	0	0	0	0	1	0	0	0	6804	768	27	1	710	1	GRIN3A	9	104375771	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1035290	104375771	36837660	561	22297										
OR13F1	138805	broad.mit.edu	37	chr9	107267447	107267447	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagaggtgaaagtggccttgAaaaaattgctgattagaaat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:107267447delA	ENST00000334726.2	+	1	993	c.904delA	c.(904-906)aaafs	p.K303fs		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K303fs*3(1)		endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AGTGGCCTTGAAAAAATTGCT	0.363																																																1	Deletion - Frameshift(1)	large_intestine(1)	9											41	44	43					9																	107267447		2203	4300	6503	106307268	SO:0001589	frameshift_variant	138805				CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"GPCR / Class A : Olfactory receptors"	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.904delA	9.37:g.107267447delA	ENSP00000334452:p.Lys303fs		106307268	Q6IF50	Frame_Shift_Del	DEL	ENST00000334726.2	37	CCDS35087.1																																																																																				0.363	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1			-	107267447	A	-	107267447	7	5	77	1	0	1	0	1	0	0	0	0	10972	247	9	0	906	0	OR13F1	9	107267447	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	2891676	107267447	33945984	562	22298										
OR13C3	138803	broad.mit.edu	37	chr9	107298552	107298552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acagctgaatttattccaccGgacagccaggacacagaagc	9	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:107298552G>A	ENST00000374781.2	-	1	585	c.543C>T	c.(541-543)tcC>tcT	p.S181S		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S181S(1)		endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						TTATTCCACCGGACAGCCAGG	0.448																																					GBM(86;1248 1274 14222 15028 46219)											1	Substitution - coding silent(1)	large_intestine(1)	9											156	153	154					9																	107298552		2203	4300	6503	106338373	SO:0001819	synonymous_variant	138803				CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"GPCR / Class A : Olfactory receptors"	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.543C>T	9.37:g.107298552G>A			106338373	Q5VVG1|Q6IF52	Silent	SNP	ENST00000374781.2	37	CCDS35089.1																																																																																				0.448	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			A	107298552	G	A	107298552	2	1	77	1	0	0	0	0	0	0	0	1	10966	1103	39	1		1	OR13C3	9	107298552	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	31105	107298552	33914879	563	22299										
ABCA1	19	broad.mit.edu	37	chr9	107581921	107581921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgcgggagtaagggtccaCaccagctgtgggttcatcca	13	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:107581921C>T	ENST00000374736.3	-	22	3581	c.3187G>A	c.(3187-3189)Gtg>Atg	p.V1063M		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1063	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.V1063M(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TAAGGGTCCACACCAGCTGTG	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	9											112	115	114					9																	107581921		2203	4300	6503	106621742	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.3187G>A	9.37:g.107581921C>T	ENSP00000363868:p.Val1063Met		106621742	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	33	5.235792	0.95240	.	.	ENSG00000165029	ENST00000374736	T	0.80393	-1.37	6.03	6.03	0.97812	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.81992	0.4940	N	0.11154	0.105	0.80722	D	1	D	0.71674	0.998	D	0.69307	0.963	D	0.85292	0.1068	10	0.87932	D	0	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	1063	O95477	ABCA1_HUMAN	M	1063	ENSP00000363868:V1063M	ENSP00000363868:V1063M	V	-	1	0	ABCA1	106621742	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GTG		0.498	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107581921	C	T	107581921	3	4	77	1	0	0	0	0	1	0	0	0	28	478	17	3	3714	3	ABCA1	9	107581921	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	283369	107581921	33631510	564	22300										
SVEP1	79987	broad.mit.edu	37	chr9	113251998	113251998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagttgccgtgtatacgataGcaacatctccaattgggaaa	9	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:113251998G>A	ENST00000401783.2	-	9	2198	c.1862C>T	c.(1861-1863)gCt>gTt	p.A621V	SVEP1_ENST00000302728.8_Missense_Mutation_p.A621V|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Missense_Mutation_p.A598V|SVEP1_ENST00000374469.1_Missense_Mutation_p.A598V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	621	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.A621V(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTATACGATAGCAACATCTCC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	9											141	137	139					9																	113251998		1944	4149	6093	112291819	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1862C>T	9.37:g.113251998G>A	ENSP00000384917:p.Ala621Val		112291819	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	5.504	0.277970	0.10403	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.20738	2.05;2.05;2.05;2.05	4.85	2.99	0.34606	Hyalin (2);	0.346678	0.31834	N	0.006986	T	0.10766	0.0263	N	0.13140	0.3	0.26413	N	0.976226	B;B;B	0.20550	0.046;0.012;0.01	B;B;B	0.23275	0.045;0.016;0.011	T	0.22173	-1.0224	10	0.27785	T	0.31	.	6.9413	0.24494	0.1548:0.0:0.7042:0.141	.	621;621;621	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	V	621;598;621;598	ENSP00000384917:A621V;ENSP00000363593:A598V;ENSP00000304118:A621V;ENSP00000363585:A598V	ENSP00000304118:A621V	A	-	2	0	SVEP1	112291819	0.974000	0.33945	0.985000	0.45067	0.840000	0.47671	1.805000	0.38883	1.048000	0.40298	0.563000	0.77884	GCT		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113251998	G	A	113251998	3	1	77	1	0	0	0	0	1	0	0	0	15459	971	34	3	9013	3	SVEP1	9	113251998	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5670077	113251998	27961433	565	22301										
MUSK	4593	broad.mit.edu	37	chr9	113496569	113496569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggctcctgaatcccacaatGtcacctttggctcctttgtg	9	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:113496569G>A	ENST00000374448.4	+	6	801	c.667G>A	c.(667-669)Gtc>Atc	p.V223I	MUSK_ENST00000189978.5_Missense_Mutation_p.V223I|MUSK_ENST00000416899.2_Missense_Mutation_p.V223I	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	223	Ig-like 3.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V223I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						ATCCCACAATGTCACCTTTGG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											102	95	98					9																	113496569		2010	4182	6192	112536390	SO:0001583	missense	4593			AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.667G>A	9.37:g.113496569G>A	ENSP00000363571:p.Val223Ile		112536390	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.942621	0.34283	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.14391	2.51	5.18	5.18	0.71444	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.193381	0.44902	D	0.000407	T	0.18923	0.0454	L	0.58302	1.8	0.80722	D	1	B;B	0.31435	0.001;0.323	B;B	0.38056	0.014;0.264	T	0.03795	-1.1003	10	0.15066	T	0.55	.	16.5633	0.84572	0.0:0.0:1.0:0.0	.	223;233	O15146;F5H6T2	MUSK_HUMAN;.	I	223;223;223;233;233;223	ENSP00000363571:V223I	ENSP00000189978:V223I	V	+	1	0	MUSK	112536390	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.206000	0.58473	2.576000	0.86940	0.655000	0.94253	GTC		0.522	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	113496569	G	A	113496569	3	1	77	1	0	0	0	0	1	0	0	0	10019	1377	48	3	723	3	MUSK	9	113496569	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	244571	113496569	27716862	566	22302										
ALAD	210	broad.mit.edu	37	chr9	116152053	116152053	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccctgcccacccctgctcacCggaaagggccatagaaacag	9	17	1	1	rs201127458		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:116152053C>T	ENST00000409155.3	-	8	822	c.626G>A	c.(625-627)cGg>cAg	p.R209Q	ALAD_ENST00000277315.5_Splice_Site_p.R192Q|ALAD_ENST00000482001.1_5'Flank	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	209					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)	p.R238Q(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	CCCTGCTCACCGGAAAGGGCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	9											78	65	70					9																	116152053		2203	4300	6503	115191874	SO:0001630	splice_region_variant	210			M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.626+1G>A	9.37:g.116152053C>T			115191874	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	37	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	C	34	5.308064	0.95629	.	.	ENSG00000148218	ENST00000409155;ENST00000277315	D;D	0.92348	-3.02;-3.02	5.41	5.41	0.78517	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.97929	0.9319	H	0.99058	4.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.987;0.988	D	0.99624	1.0984	9	.	.	.	-8.4921	17.7737	0.88501	0.0:1.0:0.0:0.0	.	209;192;238	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	Q	209;192	ENSP00000386284:R209Q;ENSP00000277315:R192Q	.	R	-	2	0	ALAD	115191874	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	5.667000	0.68067	2.524000	0.85096	0.655000	0.94253	CGG		0.562	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	Missense_Mutation	T	116152053	C	T	116152053	5	4	77	1	0	0	0	0	0	0	1	0	483	666	23	1	386	1	ALAD	9	116152053	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2655484	116152053	25061378	567	22303										
PAPPA	5069	broad.mit.edu	37	chr9	118989819	118989819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catcaggacactggagccctCgtgaagcagaaggtaagcca	12	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:118989819C>T	ENST00000328252.3	+	6	2590	c.2221C>T	c.(2221-2223)Cgt>Tgt	p.R741C	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	741					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R741C(1)		NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CTGGAGCCCTCGTGAAGCAGA	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	9											83	70	74					9																	118989819		2203	4300	6503	118029640	SO:0001583	missense	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2221C>T	9.37:g.118989819C>T	ENSP00000330658:p.Arg741Cys		118029640	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106222	0.77096	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.02032	4.49	5.85	4.93	0.64822	.	0.055211	0.64402	D	0.000001	T	0.09949	0.0244	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.61940	0.896;0.863	T	0.00088	-1.2091	10	0.87932	D	0	-22.9407	14.0767	0.64893	0.2702:0.7298:0.0:0.0	.	185;741	E7EMD3;Q13219	.;PAPP1_HUMAN	C	741;185	ENSP00000330658:R741C	ENSP00000330658:R741C	R	+	1	0	PAPPA	118029640	0.903000	0.30736	1.000000	0.80357	0.956000	0.61745	1.815000	0.38981	2.764000	0.94973	0.591000	0.81541	CGT		0.493	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118989819	C	T	118989819	3	4	77	1	0	0	0	0	1	0	0	0	11463	884	31	1	2243	1	PAPPA	9	118989819	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2837766	118989819	22223612	568	22304										
ASTN2	23245	broad.mit.edu	37	chr9	119413828	119413828	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctttgtgccattgtcttgGatgagggtataaagtggcac	12	7	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:119413828G>A	ENST00000313400.4	-	17	3151	c.3051C>T	c.(3049-3051)atC>atT	p.I1017I	ASTN2_ENST00000288520.5_Silent_p.I118I|ASTN2_ENST00000341734.4_Silent_p.I69I|ASTN2_ENST00000361209.2_Silent_p.I966I|ASTN2_ENST00000373996.3_Silent_p.I1013I|ASTN2_ENST00000358637.4_Silent_p.I69I|ASTN2_ENST00000361477.3_Silent_p.I69I			O75129	ASTN2_HUMAN	astrotactin 2	1017					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.I966I(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						CATTGTCTTGGATGAGGGTAT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9											75	61	66					9																	119413828		2203	4300	6503	118453649	SO:0001819	synonymous_variant	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3051C>T	9.37:g.119413828G>A			118453649	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																					0.582	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119413828	G	A	119413828	2	1	77	1	0	0	0	0	0	0	0	1	1066	1164	41	3		3	ASTN2	9	119413828	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	424009	119413828	21799603	569	22305										
PHF19	26147	broad.mit.edu	37	chr9	123632078	123632080	+	Intron	DEL	GGA	GGA	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtctctggtctgccccactGgaggaggcaggagaggcagg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	GGA	GGA	GGA	-	GGA	GGA	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:123632078_123632080delGGA	ENST00000373896.3	-	5	718				PHF19_ENST00000487555.1_5'Flank|PHF19_ENST00000312189.6_In_Frame_Del_p.S171del|PHF19_ENST00000419155.1_5'Flank	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19						chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.S170delS(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTGCCCCACTGGAGGAGGCAGGA	0.626																																																1	Deletion - In frame(1)	large_intestine(1)	9																																								122671901	SO:0001627	intron_variant	26147			BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"Tudor domain containing", "Zinc fingers, PHD-type"	24566	protein-coding gene	gene with protein product	"polycomb-like 3", "tudor domain containing 19B"	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.465+42TCC>-	9.37:g.123632081_123632083delGGA			122671899	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	In_Frame_Del	DEL	ENST00000373896.3	37	CCDS35116.1																																																																																				0.626	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		-	123632080	GGA	-	123632078	6	5	77	0	1	1	0	1	0	0	0	0	11860	1335	47	0		0	PHF19	9	123632078	Intron	DEL	GGA	TCGA-AG-A02N-01A-11W-A096-10	4218250	123632078	17581353	570	22306										
OR5C1	392391	broad.mit.edu	37	chr9	125551916	125551916	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgatccacatgcgctcggtCgagggcagtcggcgagcagc	16	12	0	1	rs374636365		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:125551916C>T	ENST00000373680.2	+	1	767	c.705C>T	c.(703-705)gtC>gtT	p.V235V		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V235V(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						TGCGCTCGGTCGAGGGCAGTC	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	9						C		0,4406		0,0,2203	73	68	69		705	-10.9	0	9		69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR5C1	NM_001001923.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		235/321	125551916	1,13005	2203	4300	6503	124591737	SO:0001819	synonymous_variant	392391			AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"GPCR / Class A : Olfactory receptors"	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.705C>T	9.37:g.125551916C>T			124591737	B2RN54|B9EGT0|Q96RC4	Silent	SNP	ENST00000373680.2	37	CCDS35131.1																																																																																				0.592	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			T	125551916	C	T	125551916	2	4	77	1	0	0	0	0	0	0	0	1	11184	871	31	1		1	OR5C1	9	125551916	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1919838	125551916	15661515	571	22307										
DENND1A	57706	broad.mit.edu	37	chr9	126143789	126143789	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agggccggactcgggctcacGtcttgcttggttttctgtaa	13	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:126143789G>A	ENST00000373624.2	-	22	3153	c.2952C>T	c.(2950-2952)gaC>gaT	p.D984D	DENND1A_ENST00000542603.1_Silent_p.D769D|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Silent_p.D995D	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	984	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.D984D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						TCGGGCTCACGTCTTGCTTGG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	9											44	55	52					9																	126143789		2203	4300	6503	125183610	SO:0001819	synonymous_variant	57706			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.2952C>T	9.37:g.126143789G>A			125183610	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																				0.647	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126143789	G	A	126143789	2	1	77	1	0	0	0	0	0	0	0	1	4437	1136	40	1		1	DENND1A	9	126143789	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	591873	126143789	15069642	572	22308										
OLFML2A	169611	broad.mit.edu	37	chr9	127549371	127549371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagtgcgcagtgggcgggcaCgcgtggaggacttctacacg	18	10	1	0	rs371169223		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:127549371C>T	ENST00000373580.3	+	2	208	c.208C>T	c.(208-210)Cgc>Tgc	p.R70C		NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	70					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.R70C(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						TGGGCGGGCACGCGTGGAGGA	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	9						C	CYS/ARG	0,4340		0,0,2170	51	58	56		208	2.5	0.5	9		56	1,8545		0,1,4272	no	missense	OLFML2A	NM_182487.2	180	0,1,6442	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	70/653	127549371	1,12885	2170	4273	6443	126589192	SO:0001583	missense	169611			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.208C>T	9.37:g.127549371C>T	ENSP00000362682:p.Arg70Cys		126589192	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	37	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198759	0.58126	0.0	1.17E-4	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580	T;T	0.43294	0.95;0.95	5.73	2.51	0.30379	.	0.000000	0.85682	D	0.000000	T	0.62392	0.2424	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.961	T	0.68565	-0.5375	10	0.87932	D	0	.	14.635	0.68682	0.41:0.59:0.0:0.0	.	70;70	Q5JTM7;Q68BL7	.;OLM2A_HUMAN	C	70	ENSP00000336425:R70C;ENSP00000362682:R70C	ENSP00000336425:R70C	R	+	1	0	OLFML2A	126589192	0.251000	0.23961	0.509000	0.27700	0.384000	0.30261	1.002000	0.29796	0.715000	0.32103	0.655000	0.94253	CGC		0.647	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		T	127549371	C	T	127549371	3	4	77	1	0	0	0	0	1	0	0	0	10888	536	19	1	214	1	OLFML2A	9	127549371	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1405582	127549371	13664060	573	22309										
SLC2A8	29988	broad.mit.edu	37	chr9	130167206	130167206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcggcgcctgtctctgcacaGcctgttgatgccagcgtggg	14	13	1	1	rs374084827		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:130167206G>T	ENST00000373371.3	+	8	1175	c.1086G>T	c.(1084-1086)caG>caT	p.Q362H	SLC2A8_ENST00000485806.1_3'UTR|SLC2A8_ENST00000373352.1_Missense_Mutation_p.Q99H|SLC2A8_ENST00000373360.3_Missense_Mutation_p.Q362H	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	362					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)	p.Q362H(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						TCTCTGCACAGCCTGTTGATG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	9											65	63	64					9																	130167206		2203	4299	6502	129207027	SO:0001583	missense	29988			AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"Solute carriers"	13812	protein-coding gene	gene with protein product		605245	"solute carrier family 2 (facilitated glucose transporter) member 8"			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.1086G>T	9.37:g.130167206G>T	ENSP00000362469:p.Gln362His		129207027	Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	37	CCDS6870.1	.	.	.	.	.	.	.	.	.	.	G	9.510	1.105526	0.20632	.	.	ENSG00000136856	ENST00000373371;ENST00000451404;ENST00000373352;ENST00000373360;ENST00000439597;ENST00000423934;ENST00000373350;ENST00000430147	D;T;D;T;D;T;T	0.88664	-1.65;-1.46;-2.41;0.3;-2.37;-1.35;-1.29	5.43	1.51	0.23008	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.123265	0.35040	N	0.003481	T	0.79329	0.4427	N	0.24115	0.695	0.09310	N	1	B;P	0.34815	0.291;0.47	B;B	0.38428	0.087;0.273	T	0.68857	-0.5298	10	0.42905	T	0.14	.	5.3497	0.16028	0.3134:0.1387:0.548:0.0	.	362;362	Q5VVV9;Q9NY64	.;GTR8_HUMAN	H	362;199;99;362;201;227;227;201	ENSP00000362469:Q362H;ENSP00000392434:Q199H;ENSP00000362450:Q99H;ENSP00000362458:Q362H;ENSP00000404893:Q201H;ENSP00000389070:Q227H;ENSP00000391213:Q201H	ENSP00000362448:Q227H	Q	+	3	2	SLC2A8	129207027	0.131000	0.22433	0.037000	0.18230	0.010000	0.07245	0.926000	0.28804	0.359000	0.24239	-0.136000	0.14681	CAG		0.672	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		T	130167206	G	T	130167206	3	4	77	1	0	0	0	0	1	0	0	0	14588	962	34	2	1116	2	SLC2A8	9	130167206	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2617835	130167206	11046225	574	22310										
STXBP1	6812	broad.mit.edu	37	chr9	130427603	130427603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taaagctgatgatccaacaaTgggggaggtaagtctggctt	13	6	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:130427603T>C	ENST00000373299.1	+	8	771	c.656T>C	c.(655-657)aTg>aCg	p.M219T	STXBP1_ENST00000373302.3_Missense_Mutation_p.M219T	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	219					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)	p.M219T(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						GATCCAACAATGGGGGAGGTA	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	9											174	136	149					9																	130427603		2203	4300	6503	129467424	SO:0001583	missense	6812			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.656T>C	9.37:g.130427603T>C	ENSP00000362396:p.Met219Thr		129467424	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	37	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.712786	0.68730	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000373299	T;T	0.79940	-1.32;-1.32	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.89928	0.6857	M	0.87758	2.905	0.80722	D	1	D;D	0.64830	0.994;0.993	D;D	0.66979	0.948;0.913	D	0.91594	0.5289	10	0.87932	D	0	-12.8952	13.2805	0.60212	0.0:0.0:0.0:1.0	.	219;219	P61764;P61764-2	STXB1_HUMAN;.	T	173;219;219	ENSP00000362399:M219T;ENSP00000362396:M219T	ENSP00000362396:M219T	M	+	2	0	STXBP1	129467424	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	7.491000	0.81471	2.031000	0.59945	0.459000	0.35465	ATG		0.522	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		C	130427603	T	C	130427603	3	2	77	1	0	0	0	0	1	0	0	0	15391	1464	51	4	686	4	STXBP1	9	130427603	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	260397	130427603	10785828	575	22311										
NAIF1	203245	broad.mit.edu	37	chr9	130825918	130825918	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgcacttcctgggagcggCggatcatctgcagtaggtcg	14	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:130825918C>T	ENST00000373078.4	-	2	992	c.773G>A	c.(772-774)cGc>cAc	p.R258H	NAIF1_ENST00000488519.1_5'UTR	NM_197956.3	NP_931045.1	Q69YI7	NAIF1_HUMAN	nuclear apoptosis inducing factor 1	258					negative regulation of cell growth (GO:0030308)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R258H(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CTGGGAGCGGCGGATCATCTG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	9											98	86	90					9																	130825918		2203	4300	6503	129865739	SO:0001583	missense	203245			AK122729	CCDS6889.1	9q34.11	2008-04-10	2008-04-10	2008-04-10	ENSG00000171169	ENSG00000171169			25446	protein-coding gene	gene with protein product	"nuclear apoptosis-inducing factor 1"	610673	"chromosome 9 open reading frame 90"	C9orf90		14702039, 16378748	Standard	NM_197956		Approved	DKFZp762G199, bA379C10.2	uc004bta.3	Q69YI7	OTTHUMG00000020727	ENST00000373078.4:c.773G>A	9.37:g.130825918C>T	ENSP00000362170:p.Arg258His		129865739	B3KV81|Q8WU12	Missense_Mutation	SNP	ENST00000373078.4	37	CCDS6889.1	.	.	.	.	.	.	.	.	.	.	C	35	5.484791	0.96323	.	.	ENSG00000171169	ENST00000373078	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66992	0.2846	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.70949	-0.4733	9	0.87932	D	0	-2.6944	17.8545	0.88759	0.0:1.0:0.0:0.0	.	258	Q69YI7	NAIF1_HUMAN	H	258	.	ENSP00000362170:R258H	R	-	2	0	NAIF1	129865739	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.298000	0.78815	2.452000	0.82932	0.563000	0.77884	CGC		0.637	NAIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054330.1	NM_197956		T	130825918	C	T	130825918	3	4	77	1	0	0	0	0	1	0	0	0	10176	768	27	1	214	1	NAIF1	9	130825918	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	398315	130825918	10387513	576	22312										
TRUB2	26995	broad.mit.edu	37	chr9	131083986	131083986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgaacacgctgtttaggagCgggaggcttcctggcattga	15	9	0	1	rs545026119	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:131083986C>T	ENST00000372890.4	-	2	466	c.133G>A	c.(133-135)Gct>Act	p.A45T	COQ4_ENST00000608951.1_5'Flank|COQ4_ENST00000609948.1_5'Flank|TRUB2_ENST00000546104.1_5'UTR|COQ4_ENST00000300452.3_5'Flank|TRUB2_ENST00000460320.1_5'UTR|COQ4_ENST00000372875.3_5'Flank	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	45					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)	p.A45T(1)		kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						TGTTTAGGAGCGGGAGGCTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											87	71	77					9																	131083986		2203	4300	6503	130123807	SO:0001583	missense	26995			AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"TruB pseudouridine (psi) synthase homolog 2 (E. coli)"			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.133G>A	9.37:g.131083986C>T	ENSP00000361982:p.Ala45Thr		130123807	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	37	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471734	0.43942	.	.	ENSG00000167112	ENST00000372890	T	0.18174	2.23	5.83	3.68	0.42216	Pseudouridine synthase, catalytic domain (1);	0.313958	0.34959	N	0.003545	T	0.13670	0.0331	L	0.49455	1.56	0.25881	N	0.983598	B	0.26902	0.163	B	0.16289	0.015	T	0.13764	-1.0497	10	0.46703	T	0.11	-12.2338	6.4321	0.21803	0.0:0.6629:0.156:0.1811	.	45	O95900	TRUB2_HUMAN	T	45	ENSP00000361982:A45T	ENSP00000361982:A45T	A	-	1	0	TRUB2	130123807	0.368000	0.25031	0.688000	0.30117	0.932000	0.56968	0.175000	0.16762	1.477000	0.48234	0.563000	0.77884	GCT		0.463	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679		T	131083986	C	T	131083986	3	4	77	1	0	0	0	0	1	0	0	0	16643	768	27	1	890	1	TRUB2	9	131083986	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	258068	131083986	10129445	577	22313										
LRRC8A	56262	broad.mit.edu	37	chr9	131678487	131678487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcgagctgaccaacctgaCgcagatcgagctgcggggca	16	12	0	3	rs557710052	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:131678487C>T	ENST00000259324.5	+	4	2793	c.2270C>T	c.(2269-2271)aCg>aTg	p.T757M	LRRC8A_ENST00000372599.3_Missense_Mutation_p.T757M|LRRC8A_ENST00000492784.1_3'UTR|LRRC8A_ENST00000372600.4_Missense_Mutation_p.T757M	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	757					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.T757M(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						ACCAACCTGACGCAGATCGAG	0.682													C|||	2	0.000399361	0	0	5008	,	,		17392	0		0	False		,,,				2504	0.002															1	Substitution - Missense(1)	large_intestine(1)	9											49	49	49					9																	131678487		2203	4300	6503	130718308	SO:0001583	missense	56262			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.2270C>T	9.37:g.131678487C>T	ENSP00000259324:p.Thr757Met		130718308	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641464	0.67244	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.59638	0.25;0.25;0.25	5.03	5.03	0.67393	.	0.157893	0.56097	D	0.000027	T	0.61652	0.2364	L	0.42744	1.35	0.51767	D	0.999932	P	0.41848	0.763	P	0.48425	0.577	T	0.65496	-0.6154	10	0.66056	D	0.02	.	17.3366	0.87283	0.0:1.0:0.0:0.0	.	757	Q8IWT6	LRC8A_HUMAN	M	757	ENSP00000361682:T757M;ENSP00000361680:T757M;ENSP00000259324:T757M	ENSP00000259324:T757M	T	+	2	0	LRRC8A	130718308	0.999000	0.42202	1.000000	0.80357	0.530000	0.34684	3.744000	0.55112	2.337000	0.79520	0.313000	0.20887	ACG		0.682	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131678487	C	T	131678487	3	4	77	1	0	0	0	0	1	0	0	0	9050	536	19	1	2276	1	LRRC8A	9	131678487	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	594501	131678487	9534944	578	22314										
DOLK	22845	broad.mit.edu	37	chr9	131708156	131708156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgcaaatatagatgtcatgGtcccctcaaaagtctttttg	8	9	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:131708156G>A	ENST00000372586.3	-	1	1742	c.1427C>T	c.(1426-1428)aCc>aTc	p.T476I	NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	476					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)	p.T476I(1)		breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						AGATGTCATGGTCCCCTCAAA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	9											110	107	108					9																	131708156		2203	4300	6503	130747977	SO:0001583	missense	22845			AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"dolichol kinase 1"	610746	"transmembrane protein 15"	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.1427C>T	9.37:g.131708156G>A	ENSP00000361667:p.Thr476Ile		130747977	Q5SRE6	Missense_Mutation	SNP	ENST00000372586.3	37	CCDS6915.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094101	0.76870	.	.	ENSG00000175283	ENST00000372586	T	0.69435	-0.4	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.85164	0.5634	M	0.88570	2.965	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87814	0.2633	10	0.87932	D	0	-25.4778	18.2839	0.90107	0.0:0.0:1.0:0.0	.	476	Q9UPQ8	DOLK_HUMAN	I	476	ENSP00000361667:T476I	ENSP00000361667:T476I	T	-	2	0	DOLK	130747977	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.864000	0.99589	2.548000	0.85928	0.561000	0.74099	ACC		0.498	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		A	131708156	G	A	131708156	3	1	77	1	0	0	0	0	1	0	0	0	4714	1261	44	3	193	3	DOLK	9	131708156	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	29669	131708156	9505275	579	22315										
BAT2L1	84726	broad.mit.edu	37	chr9	134358191	134358191	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaaagggctcggagggggCcgagcggctgcaaggggctg	21	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:134358191C>T	ENST00000357304.4	+	21	5325	c.5270C>T	c.(5269-5271)gCc>gTc	p.A1757V	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.A1063V|PRRC2B_ENST00000405995.1_Missense_Mutation_p.A1063V|SNORD62A_ENST00000428514.1_RNA	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1757							poly(A) RNA binding (GO:0044822)	p.A1757V(1)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						TCGGAGGGGGCCGAGCGGCTG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	9											19	24	22					9																	134358191		1905	4114	6019	133348012	SO:0001583	missense	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5270C>T	9.37:g.134358191C>T	ENSP00000349856:p.Ala1757Val		133348012	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812594	0.32053	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.02472	4.28;4.6;4.28	5.03	4.08	0.47627	.	0.372166	0.18713	U	0.133234	T	0.02193	0.0068	N	0.08118	0	0.58432	D	0.999999	B;B	0.23442	0.063;0.085	B;B	0.21151	0.033;0.022	T	0.61501	-0.7050	10	0.27785	T	0.31	-25.381	16.167	0.81768	0.0:0.8546:0.1454:0.0	.	489;1757	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	V	1063;1757;1063	ENSP00000384606:A1063V;ENSP00000349856:A1757V;ENSP00000398853:A1063V	ENSP00000349856:A1757V	A	+	2	0	PRRC2B	133348012	0.968000	0.33430	0.997000	0.53966	0.507000	0.33981	2.435000	0.44811	2.333000	0.79357	0.561000	0.74099	GCC		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	134358191	C	T	134358191	3	4	77	1	0	0	0	0	1	0	0	0	1321	739	26	3	5352	3	BAT2L1	9	134358191	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2650035	134358191	6855240	580	22316										
C9orf98	158067	broad.mit.edu	37	chr9	135753607	135753607	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccccgtactggggcatctcGggggggatacggtgcggggc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:135753607delG	ENST00000298545.3	-	1	557	c.36delC	c.(34-36)cccfs	p.P12fs	AK8_ENST00000477396.1_5'UTR|C9orf9_ENST00000356311.5_5'Flank|C9orf9_ENST00000372136.3_5'UTR|C9orf9_ENST00000350499.6_5'Flank	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	12					nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)	p.E13fs*14(2)|p.E13fs*40(2)		NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						GGGGCATCTCGGGGGGGATAC	0.697																																																4	Deletion - Frameshift(2)|Insertion - Frameshift(2)	large_intestine(2)|pancreas(2)	9											41	35	37					9																	135753607		2203	4298	6501	134743428	SO:0001589	frameshift_variant	158067			AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.36delC	9.37:g.135753607delG	ENSP00000298545:p.Pro12fs		134743428	A8K821|Q8N9W9	Frame_Shift_Del	DEL	ENST00000298545.3	37	CCDS6954.1																																																																																				0.697	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		-	135753607	G	-	135753607	7	5	77	1	0	1	0	1	0	0	0	0	2515	1103	39	0	1455	0	C9orf98	9	135753607	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1395416	135753607	5459824	581	22317										
VAV2	7410	broad.mit.edu	37	chr9	136642532	136642532	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttccatccacagggcagggCttcacagatgagctggggaa	13	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:136642532C>A	ENST00000371850.3	-	23	1975	c.1944G>T	c.(1942-1944)aaG>aaT	p.K648N	VAV2_ENST00000371851.1_Missense_Mutation_p.K638N|VAV2_ENST00000406606.3_Missense_Mutation_p.K638N	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	648	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K638N(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		CAGGGCAGGGCTTCACAGATG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	9											143	137	139					9																	136642532		2203	4300	6503	135632353	SO:0001583	missense	7410				CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12658	protein-coding gene	gene with protein product		600428	"vav 2 oncogene"			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.1944G>T	9.37:g.136642532C>A	ENSP00000360916:p.Lys648Asn		135632353	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604194	0.66445	.	.	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;T	0.16457	2.34;2.34;2.34	4.43	3.51	0.40186	Src homology-3 domain (3);Variant SH3 (1);	0.103138	0.64402	D	0.000004	T	0.25901	0.0631	L	0.61218	1.895	0.49130	D	0.999759	B;D;B	0.53462	0.215;0.96;0.215	B;P;B	0.52031	0.135;0.688;0.135	T	0.00912	-1.1517	10	0.42905	T	0.14	.	9.909	0.41394	0.0:0.8375:0.0:0.1625	.	638;648;638	P52735-2;P52735;P52735-3	.;VAV2_HUMAN;.	N	648;638;638;638	ENSP00000360916:K648N;ENSP00000360917:K638N;ENSP00000385362:K638N	ENSP00000317258:K638N	K	-	3	2	VAV2	135632353	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.000000	0.29770	2.288000	0.76882	0.655000	0.94253	AAG		0.597	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1			A	136642532	C	A	136642532	3	1	77	1	0	0	0	0	1	0	0	0	17172	796	28	2	724	2	VAV2	9	136642532	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	888925	136642532	4570899	582	22318										
OBP2A	29991	broad.mit.edu	37	chr9	138438641	138438641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagatcacagggacctggtaCgtgaaggccatggtggtcga	15	9	1	2	rs371191828		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:138438641C>T	ENST00000539850.1	+	2	116	c.90C>T	c.(88-90)taC>taT	p.Y30Y	OBP2A_ENST00000371776.1_Silent_p.Y30Y|OBP2A_ENST00000340780.3_Silent_p.Y30Y|OBP2A_ENST00000342114.4_Intron			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	30					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)	p.Y30Y(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GGACCTGGTACGTGAAGGCCA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	9						C		0,4394		0,0,2197	15	17	17		90	-3.9	0	9		17	1,8547		0,1,4273	no	coding-synonymous	OBP2A	NM_014582.2		0,1,6470	TT,TC,CC		0.0117,0.0,0.0077		30/171	138438641	1,12941	2197	4274	6471	137578462	SO:0001819	synonymous_variant	29991			AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"Lipocalins"	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.90C>T	9.37:g.138438641C>T			137578462	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Silent	SNP	ENST00000539850.1	37	CCDS6992.1																																																																																				0.612	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582		T	138438641	C	T	138438641	2	4	77	1	0	0	0	0	0	0	0	1	10841	547	19	1		1	OBP2A	9	138438641	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1796109	138438641	2774790	583	22319										
KCNT1	57582	broad.mit.edu	37	chr9	138662819	138662821	+	In_Frame_Del	DEL	AGG	AGG	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttctacatcaacatcaccaAggaggagaactcggccttca					rs531712032		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	AGG	AGG	AGG	-	AGG	AGG	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:138662819_138662821delAGG	ENST00000263604.3	+	18	1829_1831	c.1829_1831delAGG	c.(1828-1833)aaggag>aag	p.E612del	KCNT1_ENST00000298480.5_In_Frame_Del_p.E631del|KCNT1_ENST00000486577.2_In_Frame_Del_p.E592del|KCNT1_ENST00000490355.2_In_Frame_Del_p.E612del|KCNT1_ENST00000371757.2_In_Frame_Del_p.E631del|KCNT1_ENST00000491806.2_In_Frame_Del_p.E598del|KCNT1_ENST00000488444.2_In_Frame_Del_p.E612del|KCNT1_ENST00000487664.1_In_Frame_Del_p.E586del			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	612					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.E631delE(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AACATCACCAAGGAGGAGAACTC	0.635																																																1	Deletion - In frame(1)	large_intestine(1)	9																																								137802642	SO:0001651	inframe_deletion	57582			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1829_1831delAGG	9.37:g.138662822_138662824delAGG	ENSP00000263604:p.Glu612del		137802640	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	In_Frame_Del	DEL	ENST00000263604.3	37																																																																																					0.635	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		-	138662821	AGG	-	138662819	7	5	77	1	0	1	0	1	0	0	0	0	8112	72	3	0	1956	0	KCNT1	9	138662819	In_Frame_Del	DEL	AGG	TCGA-AG-A02N-01A-11W-A096-10	224178	138662819	2550612	584	22320										
TRAF2	7186	broad.mit.edu	37	chr9	139818362	139818362	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtatctacctgaacggcgaCggcaccgggcgaggaacaca	13	13	1	1	rs202188895		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:139818362C>T	ENST00000247668.2	+	10	1249	c.1197C>T	c.(1195-1197)gaC>gaT	p.D399D	TRAF2_ENST00000536468.1_Silent_p.D399D|TRAF2_ENST00000359662.3_Silent_p.D451D	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	399	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D399D(1)		breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	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)		TGAACGGCGACGGCACCGGGC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	9											117	93	101					9																	139818362		2203	4300	6503	138938183	SO:0001819	synonymous_variant	7186			U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"RING-type (C3HC4) zinc fingers"	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.1197C>T	9.37:g.139818362C>T			138938183	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																				0.612	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		T	139818362	C	T	139818362	2	4	77	1	0	0	0	0	0	0	0	1	16478	535	19	1		1	TRAF2	9	139818362	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1155543	139818362	1395069	585	22321										
FBXW5	54461	broad.mit.edu	37	chr9	139837342	139837342	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggtgtagctccagttgtaGggccgcatgtccgcgctgtg	16	10	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr9:139837342G>T	ENST00000325285.3	-	4	484	c.405C>A	c.(403-405)ccC>ccA	p.P135P	FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	135					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)	p.P135P(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		TCCAGTTGTAGGGCCGCATGT	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	9											121	118	119					9																	139837342		2203	4300	6503	138957163	SO:0001819	synonymous_variant	54461			BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.405C>A	9.37:g.139837342G>T			138957163	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	37	CCDS7014.1																																																																																				0.647	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		T	139837342	G	T	139837342	2	4	77	1	0	0	0	0	0	0	0	1	5787	987	35	2		2	FBXW5	9	139837342	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	18980	139837342	1376089	586	22322										
PFKP	5214	broad.mit.edu	37	chr10	3155602	3155602	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcatcaacgtgggggcaccCgcggctgggatgaacgcagc	16	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:3155602C>T	ENST00000381125.4	+	13	1339	c.1263C>T	c.(1261-1263)ccC>ccT	p.P421P	PFKP_ENST00000381075.2_Silent_p.P413P	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	421	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)	p.P421P(1)		breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TGGGGGCACCCGCGGCTGGGA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	10											42	38	40					10																	3155602		2203	4300	6503	3145602	SO:0001819	synonymous_variant	5214			AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1263C>T	10.37:g.3155602C>T			3145602	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																				0.607	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		T	3155602	C	T	3155602	2	4	77	1	0	0	0	0	0	0	0	1	11797	639	23	1		1	PFKP	10	3155602	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		3155602	132379145	587	22323										
TAF3	83860	broad.mit.edu	37	chr10	8006792	8006792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcccaaagcttccacttccgCgaacaatttcacaaagtcag	5	14	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:8006792C>T	ENST00000344293.5	+	3	1525	c.1319C>T	c.(1318-1320)gCg>gTg	p.A440V		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	440					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)	p.A440V(1)		NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						TCCACTTCCGCGAACAATTTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	10											79	80	80					10																	8006792		1911	4129	6040	8046798	SO:0001583	missense	83860			AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1319C>T	10.37:g.8006792C>T	ENSP00000340271:p.Ala440Val		8046798	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	C	3.898	-0.022613	0.07634	.	.	ENSG00000165632	ENST00000344293	T	0.17854	2.25	5.51	3.67	0.42095	.	0.858259	0.10226	N	0.700245	T	0.11367	0.0277	N	0.22421	0.69	0.09310	N	1	B	0.20780	0.048	B	0.09377	0.004	T	0.33240	-0.9876	10	0.29301	T	0.29	-6.1066	7.5875	0.28002	0.0:0.7204:0.1354:0.1442	.	440	Q5VWG9	TAF3_HUMAN	V	440	ENSP00000340271:A440V	ENSP00000340271:A440V	A	+	2	0	TAF3	8046798	0.074000	0.21230	0.021000	0.16686	0.109000	0.19521	2.032000	0.41127	0.701000	0.31803	0.650000	0.86243	GCG		0.463	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		T	8006792	C	T	8006792	3	4	77	1	0	0	0	0	1	0	0	0	15564	768	27	1	1329	1	TAF3	10	8006792	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4851190	8006792	127527955	588	22324										
DHTKD1	55526	broad.mit.edu	37	chr10	12131131	12131131	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaatgttgcccaatccctcGcacctggaggccgtcaaccc	8	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:12131131G>A	ENST00000263035.4	+	5	926	c.864G>A	c.(862-864)tcG>tcA	p.S288S	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	288					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.S288S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CCAATCCCTCGCACCTGGAGG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	10											106	90	95					10																	12131131		2203	4300	6503	12171137	SO:0001819	synonymous_variant	55526			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.864G>A	10.37:g.12131131G>A			12171137	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	37	CCDS7087.1																																																																																				0.622	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		A	12131131	G	A	12131131	2	1	77	1	0	0	0	0	0	0	0	1	4511	1074	38	1		1	DHTKD1	10	12131131	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4124339	12131131	123403616	589	22325										
DCLRE1C	64421	broad.mit.edu	37	chr10	14964984	14964984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accagtgactactcacatttCgacaactttatccatagttg	5	11	1	1	rs541855040		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:14964984C>T	ENST00000378278.2	-	12	1094	c.1057G>A	c.(1057-1059)Gaa>Aaa	p.E353K	DCLRE1C_ENST00000492201.1_5'UTR|DCLRE1C_ENST00000378254.1_Missense_Mutation_p.E233K|DCLRE1C_ENST00000378242.1_Missense_Mutation_p.E6K|DCLRE1C_ENST00000396817.2_Missense_Mutation_p.E233K|DCLRE1C_ENST00000378258.1_Missense_Mutation_p.E233K|DCLRE1C_ENST00000378246.2_Missense_Mutation_p.E238K|DCLRE1C_ENST00000378255.1_Missense_Mutation_p.E233K|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.E353K|DCLRE1C_ENST00000453695.2_Missense_Mutation_p.E233K|DCLRE1C_ENST00000378249.1_Missense_Mutation_p.E238K|DCLRE1C_ENST00000357717.2_Missense_Mutation_p.E238K			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	353					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.E238K(1)|p.E353K(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						ACTCACATTTCGACAACTTTA	0.423								Non-homologous end-joining																																								2	Substitution - Missense(2)	large_intestine(2)	10											129	110	116					10																	14964984		2203	4300	6503	15004990	SO:0001583	missense	64421			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.1057G>A	10.37:g.14964984C>T	ENSP00000367527:p.Glu353Lys		15004990	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997465	0.54147	.	.	ENSG00000152457	ENST00000378289;ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000378242	T;T;T;T;T;T;T;T;T;T	0.76448	-0.94;-0.46;-0.47;-0.47;-0.47;-0.46;-0.46;-0.46;-1.02;-0.46	5.47	5.47	0.80525	.	0.269558	0.42420	D	0.000705	T	0.68586	0.3017	L	0.54323	1.7	0.40449	D	0.980121	B;P;B	0.36249	0.021;0.545;0.106	B;B;B	0.23716	0.011;0.048;0.007	T	0.70160	-0.4948	10	0.37606	T	0.19	.	12.6387	0.56696	0.0:0.9232:0.0:0.0768	.	353;238;353	Q96SD1-4;Q96SD1-3;Q96SD1	.;.;DCR1C_HUMAN	K	353;233;238;238;238;233;233;233;353;233;6	ENSP00000367538:E353K;ENSP00000400529:E233K;ENSP00000367492:E238K;ENSP00000350349:E238K;ENSP00000367496:E238K;ENSP00000380030:E233K;ENSP00000367503:E233K;ENSP00000367502:E233K;ENSP00000367527:E353K;ENSP00000367506:E233K	ENSP00000350349:E238K	E	-	1	0	DCLRE1C	15004990	0.986000	0.35501	0.961000	0.40146	0.911000	0.54048	2.512000	0.45485	2.726000	0.93360	0.655000	0.94253	GAA		0.423	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		T	14964984	C	T	14964984	3	4	77	1	0	0	0	0	1	0	0	0	4302	893	31	1	1033	1	DCLRE1C	10	14964984	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2833853	14964984	120569763	590	22326										
CUBN	8029	broad.mit.edu	37	chr10	16975162	16975162	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaaagaatgttgagttccacGgtagagtcgggagcctggat	15	6	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:16975162G>A	ENST00000377833.4	-	40	6113	c.6048C>T	c.(6046-6048)acC>acT	p.T2016T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2016	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.T2016T(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGAGTTCCACGGTAGAGTCGG	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	10											133	116	122					10																	16975162		2203	4300	6503	17015168	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6048C>T	10.37:g.16975162G>A			17015168	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.507	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16975162	G	A	16975162	2	1	77	1	0	0	0	0	0	0	0	1	4057	1103	39	1		1	CUBN	10	16975162	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2010178	16975162	118559585	591	22327										
TRDMT1	1787	broad.mit.edu	37	chr10	17191103	17191103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgagactatttccaagtaggCgataacgctgtttcactgtt	9	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:17191103C>T	ENST00000377799.3	-	11	1159	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H	TRDMT1_ENST00000358282.7_3'UTR|TRDMT1_ENST00000412821.3_Missense_Mutation_p.R347H|TRDMT1_ENST00000377766.5_3'UTR|TRDMT1_ENST00000457442.2_Missense_Mutation_p.R290H|TRDMT1_ENST00000351358.4_Missense_Mutation_p.R325H|TRDMT1_ENST00000452380.2_5'Flank	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	371	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)	p.R371H(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	TCCAAGTAGGCGATAACGCTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	10											67	67	67					10																	17191103		2202	4297	6499	17231109	SO:0001583	missense	1787			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"DNA (cytosine-5-)-methyltransferase 2"	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.1112G>A	10.37:g.17191103C>T	ENSP00000367030:p.Arg371His		17231109	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Missense_Mutation	SNP	ENST00000377799.3	37	CCDS7114.1	.	.	.	.	.	.	.	.	.	.	C	32	5.141730	0.94560	.	.	ENSG00000107614	ENST00000377799;ENST00000412821;ENST00000351358;ENST00000457442	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.63	5.63	0.86233	.	0.051406	0.85682	D	0.000000	D	0.92648	0.7664	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;P;P	0.77557	0.99;0.983;0.718;0.815	D	0.91985	0.5598	10	0.51188	T	0.08	-5.7722	20.0499	0.97621	0.0:1.0:0.0:0.0	.	290;325;347;371	E7EMI8;O14717-3;O14717-2;O14717	.;.;.;TRDMT_HUMAN	H	371;347;325;290	ENSP00000367030:R371H;ENSP00000409354:R347H;ENSP00000324328:R325H;ENSP00000412256:R290H	ENSP00000324328:R325H	R	-	2	0	TRDMT1	17231109	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.169000	0.64984	2.798000	0.96311	0.655000	0.94253	CGC		0.303	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412		T	17191103	C	T	17191103	3	4	77	1	0	0	0	0	1	0	0	0	16507	768	27	1	67	1	TRDMT1	10	17191103	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	215941	17191103	118343644	592	22328										
NEBL	10529	broad.mit.edu	37	chr10	21124510	21124510	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcagtgccagcttgcattcCtttccctttaattattgact	6	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:21124510C>A	ENST00000377122.4	-	14	1777	c.1381G>T	c.(1381-1383)Gga>Tga	p.G461*	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	461					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.G461*(2)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GCTTGCATTCCTTTCCCTTTA	0.448																																																2	Substitution - Nonsense(2)	large_intestine(1)|kidney(1)	10											259	236	244					10																	21124510		2203	4300	6503	21164516	SO:0001587	stop_gained	10529			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1381G>T	10.37:g.21124510C>A	ENSP00000366326:p.Gly461*		21164516	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Nonsense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	42	9.599904	0.99216	.	.	ENSG00000078114	ENST00000377122	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	18.0946	0.89485	0.0:1.0:0.0:0.0	.	.	.	.	X	461	.	ENSP00000366326:G461X	G	-	1	0	NEBL	21164516	1.000000	0.71417	0.997000	0.53966	0.848000	0.48234	5.828000	0.69307	2.380000	0.81148	0.505000	0.49811	GGA		0.448	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		A	21124510	C	A	21124510	4	1	77	1	0	0	0	0	0	1	0	0	10334	690	24	2	1723	2	NEBL	10	21124510	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3933407	21124510	114410237	593	22329										
PTCHD3	374308	broad.mit.edu	37	chr10	27703118	27703118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcggcccggtggcagagtccGgtttggtgagcttgggcttc	18	10	0	2	rs115676272	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:27703118G>A	ENST00000438700.3	-	1	179	c.62C>T	c.(61-63)cCg>cTg	p.P21L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	21					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)	p.P21L(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GGCAGAGTCCGGTTTGGTGAG	0.652																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	10											56	68	64					10																	27703118		2203	4300	6503	27743124	SO:0001583	missense	374308			AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.62C>T	10.37:g.27703118G>A	ENSP00000417658:p.Pro21Leu		27743124	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648307	0.29336	.	.	ENSG00000182077	ENST00000438700	D	0.89939	-2.59	2.12	-4.23	0.03789	.	.	.	.	.	T	0.71367	0.3331	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47898	-0.9081	9	0.39692	T	0.17	.	2.405	0.04410	0.1221:0.2341:0.4353:0.2085	.	21	Q3KNS1	PTHD3_HUMAN	L	21	ENSP00000417658:P21L	ENSP00000417658:P21L	P	-	2	0	PTCHD3	27743124	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	-0.914000	0.04038	-3.544000	0.00144	-2.875000	0.00098	CCG		0.652	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		A	27703118	G	A	27703118	3	1	77	1	0	0	0	0	1	0	0	0	12768	1116	39	1	2257	1	PTCHD3	10	27703118	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6578608	27703118	107831629	594	22330										
SVIL	6840	broad.mit.edu	37	chr10	29782301	29782301	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgccggtgacagtgagcacCgtttcgtgcatcccgccaac	11	14	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:29782301C>T	ENST00000355867.4	-	21	4613	c.3861G>A	c.(3859-3861)acG>acA	p.T1287T	SVIL_ENST00000535393.1_Silent_p.T201T|SVIL_ENST00000375398.2_Silent_p.T1287T|SVIL_ENST00000375400.3_Silent_p.T861T|SVIL_ENST00000538146.1_Silent_p.T79T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1287					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.T1287T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CAGTGAGCACCGTTTCGTGCA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	10											87	81	83					10																	29782301		2203	4300	6503	29822307	SO:0001819	synonymous_variant	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3861G>A	10.37:g.29782301C>T			29822307	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.393	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29782301	C	T	29782301	2	4	77	1	0	0	0	0	0	0	0	1	15460	639	23	1		1	SVIL	10	29782301	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2079183	29782301	105752446	595	22331										
KIAA1462	57608	broad.mit.edu	37	chr10	30318177	30318177	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcccctagactgctggtgCgagctgtaagatgggggctt	14	11	0	2	rs372892398		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:30318177C>T	ENST00000375377.1	-	3	1001	c.900G>A	c.(898-900)tcG>tcA	p.S300S		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	300	Pro-rich.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.S300S(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						ACTGCTGGTGCGAGCTGTAAG	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	10						C		1,4037		0,1,2018	70	73	72		900	-9.5	0	10		72	0,8338		0,0,4169	no	coding-synonymous	KIAA1462	NM_020848.2		0,1,6187	TT,TC,CC		0.0,0.0248,0.0081		300/1360	30318177	1,12375	2019	4169	6188	30358183	SO:0001819	synonymous_variant	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.900G>A	10.37:g.30318177C>T			30358183	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																				0.592	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30318177	C	T	30318177	2	4	77	1	0	0	0	0	0	0	0	1	8255	755	27	1		1	KIAA1462	10	30318177	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	535876	30318177	105216570	596	22332										
ZEB1	6935	broad.mit.edu	37	chr10	31815861	31815861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgagcacgtgggtgccagggCgtctccctcacagggcgact	15	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:31815861C>T	ENST00000320985.10	+	9	3154	c.3044C>T	c.(3043-3045)gCg>gTg	p.A1015V	ZEB1_ENST00000542815.3_Missense_Mutation_p.A948V|ZEB1_ENST00000361642.5_Missense_Mutation_p.A1016V|ZEB1_ENST00000560721.2_Missense_Mutation_p.A995V|ZEB1_ENST00000446923.2_Missense_Mutation_p.A999V			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	1015	Glu-rich (acidic).				cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A1015V(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GGTGCCAGGGCGTCTCCCTCA	0.537																																					Ovarian(40;423 959 14296 36701 49589)											1	Substitution - Missense(1)	large_intestine(1)	10											71	65	67					10																	31815861		2203	4300	6503	31855867	SO:0001583	missense	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.3044C>T	10.37:g.31815861C>T	ENSP00000319248:p.Ala1015Val		31855867	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	C	0.091	-1.167596	0.01660	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.12774	2.96;2.65;2.7;2.65;2.69	4.57	0.395	0.16304	.	1.576300	0.04093	N	0.311636	T	0.07593	0.0191	N	0.13043	0.29	0.20196	N	0.999926	B;B;B;B;B	0.14805	0.011;0.004;0.003;0.004;0.002	B;B;B;B;B	0.15484	0.013;0.002;0.002;0.001;0.001	T	0.33954	-0.9848	10	0.25106	T	0.35	-1.54	2.0609	0.03592	0.2708:0.4436:0.1368:0.1488	.	948;999;995;1016;1015	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	V	797;1015;1016;1010;948;1015;995;906;999	ENSP00000444282:A797V;ENSP00000354487:A1016V;ENSP00000444891:A948V;ENSP00000319248:A1015V;ENSP00000391612:A999V	ENSP00000319248:A1015V	A	+	2	0	ZEB1	31855867	0.648000	0.27313	0.035000	0.18076	0.019000	0.09904	1.334000	0.33827	0.033000	0.15463	-0.474000	0.04947	GCG		0.537	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31815861	C	T	31815861	3	4	77	1	0	0	0	0	1	0	0	0	17662	768	27	1	3092	1	ZEB1	10	31815861	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1497684	31815861	103718886	597	22333										
CCNY	219771	broad.mit.edu	37	chr10	35772401	35772401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attcctcagtaaatctcagaCggacggtaggtccttaattt	8	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:35772401C>T	ENST00000374704.4	+	2	404	c.224C>T	c.(223-225)aCg>aTg	p.T75M	CCNY_ENST00000492478.1_3'UTR|CCNY_ENST00000374706.1_Missense_Mutation_p.T21M|CCNY_ENST00000339497.5_Intron|CCNY_ENST00000265375.9_Missense_Mutation_p.T21M	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	75					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)	p.T21M(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						AAATCTCAGACGGACGGTAGG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	10											86	82	84					10																	35772401		2203	4300	6503	35812407	SO:0001583	missense	219771			AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100			23354	protein-coding gene	gene with protein product		612786	"chromosome 10 open reading frame 9"	C10orf9		20441050	Standard	XM_005252388		Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.224C>T	10.37:g.35772401C>T	ENSP00000363836:p.Thr75Met		35812407	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	Missense_Mutation	SNP	ENST00000374704.4	37	CCDS7189.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.589431	0.46214	.	.	ENSG00000108100	ENST00000374706;ENST00000537547;ENST00000374704;ENST00000265375	T;T;T	0.32988	1.44;1.43;1.44	5.84	5.84	0.93424	.	0.046365	0.85682	D	0.000000	T	0.44932	0.1317	L	0.41824	1.3	0.80722	D	1	D	0.89917	1.0	D	0.65010	0.931	T	0.05550	-1.0878	10	0.17369	T	0.5	-0.7518	18.9061	0.92462	0.0:1.0:0.0:0.0	.	75	Q8ND76	CCNY_HUMAN	M	21;75;75;21	ENSP00000363838:T21M;ENSP00000363836:T75M;ENSP00000265375:T21M	ENSP00000265375:T21M	T	+	2	0	CCNY	35812407	1.000000	0.71417	0.966000	0.40874	0.602000	0.36980	4.795000	0.62489	2.765000	0.95021	0.655000	0.94253	ACG		0.343	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047568.2	NM_181698		T	35772401	C	T	35772401	3	4	77	1	0	0	0	0	1	0	0	0	2942	536	19	1	230	1	CCNY	10	35772401	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3956540	35772401	99762346	598	22334										
ANKRD30A	91074	broad.mit.edu	37	chr10	37430724	37430724	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacagctgaaagcttggtggAaaaaacacctgatgaggctg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:37430724delA	ENST00000602533.1	+	7	830	c.731delA	c.(730-732)gaafs	p.E244fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.E244fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.E244fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	300					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E244G(1)|p.T246fs*95(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AGCTTGGTGGAAAAAACACCT	0.512																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|endometrium(1)	10											43	45	44					10																	37430724		1870	4099	5969	37470730	SO:0001589	frameshift_variant	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.731delA	10.37:g.37430724delA	ENSP00000473551:p.Glu244fs		37470730	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	37																																																																																					0.512	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37430724	A	-	37430724	7	5	77	1	0	1	0	1	0	0	0	0	658	246	9	0	757	0	ANKRD30A	10	37430724	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	1658323	37430724	98104023	599	22335										
ZNF33A	7581	broad.mit.edu	37	chr10	38305877	38305877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggaggagtggcagcacctgGaccctagtcagagggctctg	16	10	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:38305877G>A	ENST00000458705.2	+	3	246	c.88G>A	c.(88-90)Gac>Aac	p.D30N	ZNF33A_ENST00000476504.1_3'UTR|ZNF33A_ENST00000307441.9_Missense_Mutation_p.D30N|ZNF33A_ENST00000432900.2_Missense_Mutation_p.D37N|ZNF33A_ENST00000374618.3_Missense_Mutation_p.D30N|ZNF33A_ENST00000469037.2_Missense_Mutation_p.D30N			Q06730	ZN33A_HUMAN	zinc finger protein 33A	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D30N(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						GCAGCACCTGGACCCTAGTCA	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	10											64	65	65					10																	38305877		2203	4297	6500	38345883	SO:0001583	missense	7581			D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.88G>A	10.37:g.38305877G>A	ENSP00000387713:p.Asp30Asn		38345883	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330764	0.41297	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000277672;ENST00000307441	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	3.64	3.64	0.41730	Krueppel-associated box (4);	.	.	.	.	T	0.61837	0.2379	L	0.54863	1.705	0.09310	N	1	D;D;D;D	0.76494	0.996;0.965;0.999;0.999	D;P;D;D	0.79784	0.993;0.896;0.958;0.967	T	0.49818	-0.8899	9	0.72032	D	0.01	.	11.0139	0.47677	0.0:0.0:1.0:0.0	.	37;30;30;30	F6TH33;Q9H5I4;Q06730;F8WAJ5	.;.;ZN33A_HUMAN;.	N	30;37;30;30;30	ENSP00000363747:D30N;ENSP00000402467:D37N;ENSP00000387713:D30N;ENSP00000304268:D30N	ENSP00000277672:D30N	D	+	1	0	ZNF33A	38345883	0.979000	0.34478	0.227000	0.23927	0.739000	0.42172	2.764000	0.47613	2.047000	0.60756	0.462000	0.41574	GAC		0.468	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		A	38305877	G	A	38305877	3	1	77	1	0	0	0	0	1	0	0	0	17893	1174	41	3	94	3	ZNF33A	10	38305877	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	875153	38305877	97228870	600	22336										
RASGEF1A	221002	broad.mit.edu	37	chr10	43695125	43695125	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctgccatgggcacttaccCggcacacctcagtggccacc	10	17	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:43695125C>T	ENST00000395809.1	-	7	3354	c.848G>A	c.(847-849)cGg>cAg	p.R283Q	RASGEF1A_ENST00000374459.1_Splice_Site_p.R291Q|RASGEF1A_ENST00000395810.1_Splice_Site_p.R283Q|RASGEF1A_ENST00000472864.1_5'Flank			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	283	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.R230Q(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						GGCACTTACCCGGCACACCTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10											84	62	69					10																	43695125		2203	4300	6503	43015131	SO:0001630	splice_region_variant	221002			AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.849+1G>A	10.37:g.43695125C>T			43015131	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	37	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043826	0.55110	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.29917	1.55;1.55;1.55	5.1	5.1	0.69264	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.080882	0.49916	D	0.000127	T	0.20210	0.0486	N	0.12422	0.21	0.48341	D	0.999638	B;P	0.49253	0.428;0.921	B;P	0.45913	0.117;0.497	T	0.01874	-1.1256	10	0.34782	T	0.22	.	9.3278	0.38003	0.0:0.8397:0.0:0.1603	.	283;291	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	Q	291;283;283	ENSP00000363583:R291Q;ENSP00000379155:R283Q;ENSP00000379154:R283Q	ENSP00000363583:R291Q	R	-	2	0	RASGEF1A	43015131	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.806000	0.55583	2.352000	0.79861	0.655000	0.94253	CGG		0.577	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313	Missense_Mutation	T	43695125	C	T	43695125	5	4	77	1	0	0	0	0	0	0	1	0	13106	666	23	1	625	1	RASGEF1A	10	43695125	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5389248	43695125	91839622	601	22337										
RBP3	5949	broad.mit.edu	37	chr10	48385873	48385873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgatgatcatggcatccgtGtgcatgatcttcttccagat	9	10	3	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:48385873G>A	ENST00000224600.4	-	2	3332	c.3219C>T	c.(3217-3219)caC>caT	p.H1073H	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	1073	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)	p.H1073H(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	TGGCATCCGTGTGCATGATCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	10											116	97	104					10																	48385873		2203	4300	6503	48005879	SO:0001819	synonymous_variant	5949			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.3219C>T	10.37:g.48385873G>A			48005879	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																				0.567	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		A	48385873	G	A	48385873	2	1	77	1	0	0	0	0	0	0	0	1	13194	1368	48	3		3	RBP3	10	48385873	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4690748	48385873	87148874	602	22338										
MAPK8	5599	broad.mit.edu	37	chr10	49609719	49609719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccatcatgagcagaagcaagCgtgacaacaatttttatagt	8	8	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:49609719C>T	ENST00000374189.1	+	2	197	c.16C>T	c.(16-18)Cgt>Tgt	p.R6C	MAPK8_ENST00000360332.3_Missense_Mutation_p.R6C|MAPK8_ENST00000374174.1_Missense_Mutation_p.R6C|MAPK8_ENST00000374182.3_Missense_Mutation_p.R6C|MAPK8_ENST00000395611.3_Missense_Mutation_p.R6C			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	6					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.R6C(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		CAGAAGCAAGCGTGACAACAA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	10											84	82	83					10																	49609719		2203	4300	6503	49279725	SO:0001583	missense	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.16C>T	10.37:g.49609719C>T	ENSP00000363304:p.Arg6Cys		49279725	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067947	0.36470	.	.	ENSG00000107643	ENST00000432379;ENST00000374189;ENST00000426557;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000374174;ENST00000395611	T;T;T;T;T;T;T;T;T	0.76060	3.04;-0.98;3.04;-0.96;-0.96;-0.98;-0.99;-0.9;-0.81	5.65	3.81	0.43845	.	0.055094	0.64402	D	0.000001	T	0.60444	0.2269	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B	0.12630	0.0;0.002;0.004;0.004;0.006	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.002;0.002	T	0.56032	-0.8046	10	0.48119	T	0.1	.	12.0415	0.53456	0.0:0.8626:0.0:0.1374	.	6;6;6;6;6	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	C	6	ENSP00000387936:R6C;ENSP00000363304:R6C;ENSP00000397729:R6C;ENSP00000363297:R6C;ENSP00000363294:R6C;ENSP00000353483:R6C;ENSP00000363291:R6C;ENSP00000363289:R6C;ENSP00000378974:R6C	ENSP00000353483:R6C	R	+	1	0	MAPK8	49279725	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	2.322000	0.43814	0.944000	0.37579	0.655000	0.94253	CGT		0.363	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			T	49609719	C	T	49609719	3	4	77	1	0	0	0	0	1	0	0	0	9313	768	27	1	18	1	MAPK8	10	49609719	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1223846	49609719	85925028	603	22339										
ARHGAP22	58504	broad.mit.edu	37	chr10	49659110	49659110	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgcggggaggtgggcccttcCgggaccggtgccgtgaagag	20	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:49659110C>T	ENST00000249601.4	-	9	1358	c.1062G>A	c.(1060-1062)ccG>ccA	p.P354P	ARHGAP22_ENST00000477708.2_Silent_p.P187P|ARHGAP22_ENST00000374170.1_Silent_p.P195P|ARHGAP22_ENST00000374172.1_Silent_p.P245P|ARHGAP22_ENST00000417912.2_Silent_p.P370P|ARHGAP22_ENST00000435790.2_Silent_p.P360P|ARHGAP22_ENST00000417247.2_Silent_p.P264P	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	354					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.P354P(1)		endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGGGCCCTTCCGGGACCGGTG	0.711																																																1	Substitution - coding silent(1)	large_intestine(1)	10											12	15	14					10																	49659110		2057	4120	6177	49329116	SO:0001819	synonymous_variant	58504			AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1062G>A	10.37:g.49659110C>T			49329116	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Silent	SNP	ENST00000249601.4	37	CCDS7227.1																																																																																				0.711	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49659110	C	T	49659110	2	4	77	1	0	0	0	0	0	0	0	1	872	639	23	1		1	ARHGAP22	10	49659110	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	49391	49659110	85875637	604	22340										
ARID5B	84159	broad.mit.edu	37	chr10	63852161	63852161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagatcaggaaaacctcaccAtgtgagactggagaatttca	9	8	3	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:63852161A>G	ENST00000279873.7	+	10	3349	c.2939A>G	c.(2938-2940)cAt>cGt	p.H980R	ARID5B_ENST00000309334.5_Missense_Mutation_p.H737R	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	980					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)	p.H980R(1)		NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					AAACCTCACCATGTGAGACTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	10											71	77	75					10																	63852161		2203	4300	6503	63522167	SO:0001583	missense	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.2939A>G	10.37:g.63852161A>G	ENSP00000279873:p.His980Arg		63522167	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	37	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	A	9.965	1.223933	0.22457	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.42513	0.97;0.97	5.59	4.45	0.53987	.	0.644721	0.16294	N	0.220759	T	0.35653	0.0939	L	0.44542	1.39	0.22562	N	0.998987	B	0.17038	0.02	B	0.11329	0.006	T	0.25676	-1.0125	10	0.49607	T	0.09	-7.75	10.5207	0.44918	0.6407:0.3593:0.0:0.0	.	980	Q14865	ARI5B_HUMAN	R	980;737	ENSP00000279873:H980R;ENSP00000308862:H737R	ENSP00000279873:H980R	H	+	2	0	ARID5B	63522167	0.889000	0.30405	0.969000	0.41365	0.992000	0.81027	1.743000	0.38258	0.954000	0.37851	0.460000	0.39030	CAT		0.532	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63852161	A	G	63852161	3	3	77	1	0	0	0	0	1	0	0	0	922	217	8	4	2977	4	ARID5B	10	63852161	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	14193051	63852161	71682586	605	22341										
EGR2	1959	broad.mit.edu	37	chr10	64573428	64573428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggtctgttggggtacttgcGaggcctcagaatgggccgca	17	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:64573428G>A	ENST00000242480.3	-	2	1295	c.970C>T	c.(970-972)Cgc>Tgc	p.R324C	EGR2_ENST00000439032.1_Missense_Mutation_p.R324C|EGR2_ENST00000411732.1_Missense_Mutation_p.R274C|EGR2_ENST00000493899.2_5'Flank	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	324					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.R324C(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					GGGTACTTGCGAGGCCTCAGA	0.692																																																1	Substitution - Missense(1)	large_intestine(1)	10											31	35	34					10																	64573428		2203	4300	6503	64243434	SO:0001583	missense	1959			BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"Zinc fingers, C2H2-type"	3239	protein-coding gene	gene with protein product	"Krox-20 homolog, Drosophila"	129010	"early growth response 2 (Krox-20 homolog, Drosophila)"	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.970C>T	10.37:g.64573428G>A	ENSP00000242480:p.Arg324Cys		64243434	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245572	0.59103	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000411732	T;T;T	0.14893	2.47;2.47;2.53	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.40886	0.1135	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	T	0.25152	-1.0140	10	0.87932	D	0	-19.114	12.2484	0.54585	0.0:0.0:0.8299:0.1701	.	274;324	P11161-2;P11161	.;EGR2_HUMAN	C	324;324;274	ENSP00000242480:R324C;ENSP00000402040:R324C;ENSP00000387634:R274C	ENSP00000242480:R324C	R	-	1	0	EGR2	64243434	0.880000	0.30214	1.000000	0.80357	0.999000	0.98932	0.738000	0.26158	2.570000	0.86706	0.655000	0.94253	CGC		0.692	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		A	64573428	G	A	64573428	3	1	77	1	0	0	0	0	1	0	0	0	4983	1058	37	1	464	1	EGR2	10	64573428	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	721267	64573428	70961319	606	22342										
CCAR1	55749	broad.mit.edu	37	chr10	70525679	70525679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgtcaagaggaaatagaacGccagcgtcgagaaagaagat	12	7	1	5	rs561113593		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:70525679G>A	ENST00000265872.6	+	17	2260	c.2141G>A	c.(2140-2142)cGc>cAc	p.R714H	CCAR1_ENST00000543719.1_Missense_Mutation_p.R699H|CCAR1_ENST00000535016.1_Missense_Mutation_p.R699H	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	714	Glu-rich.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)	p.R714H(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						GAAATAGAACGCCAGCGTCGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	10											93	84	87					10																	70525679		2203	4300	6503	70195685	SO:0001583	missense	55749			AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.2141G>A	10.37:g.70525679G>A	ENSP00000265872:p.Arg714His		70195685	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	37	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.105888	0.56291	.	.	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15;2.15	5.2	3.33	0.38152	.	0.000000	0.85682	D	0.000000	T	0.23330	0.0564	M	0.66939	2.045	0.49130	D	0.999755	B;B;B	0.13145	0.007;0.0;0.001	B;B;B	0.08055	0.003;0.001;0.003	T	0.04454	-1.0950	10	0.72032	D	0.01	-4.0512	10.5262	0.44950	0.0727:0.1343:0.793:0.0	.	699;714;688	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	H	714;699;699;699;688;519	ENSP00000265872:R714H;ENSP00000441820:R699H;ENSP00000445254:R699H;ENSP00000439252:R699H;ENSP00000438610:R688H;ENSP00000439642:R519H	ENSP00000265872:R714H	R	+	2	0	CCAR1	70195685	1.000000	0.71417	0.995000	0.50966	0.625000	0.37756	9.668000	0.98619	0.564000	0.29238	-0.175000	0.13238	CGC		0.383	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		A	70525679	G	A	70525679	3	1	77	1	0	0	0	0	1	0	0	0	2736	1087	38	1	2203	1	CCAR1	10	70525679	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5952251	70525679	65009068	607	22343										
DDX50	79009	broad.mit.edu	37	chr10	70706228	70706228	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagtggctggtcaagtggtCgatcaggccggtcaggccgg	19	9	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:70706228C>T	ENST00000373585.3	+	15	2163	c.2056C>T	c.(2056-2058)Cga>Tga	p.R686*	DDX50_ENST00000466265.1_3'UTR	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	686	Arg-rich.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.R686*(1)		breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						GTCAAGTGGTCGATCAGGCCG	0.512																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											37	38	37					10																	70706228		2203	4300	6503	70376234	SO:0001587	stop_gained	79009			AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.2056C>T	10.37:g.70706228C>T	ENSP00000362687:p.Arg686*		70376234	Q5VX37|Q8WV76|Q9BWI8	Nonsense_Mutation	SNP	ENST00000373585.3	37	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.835370	0.91117	.	.	ENSG00000107625	ENST00000373585	.	.	.	4.16	2.09	0.27110	.	0.567803	0.19309	N	0.117435	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.796	8.6244	0.33881	0.5313:0.4687:0.0:0.0	.	.	.	.	X	686	.	ENSP00000362687:R686X	R	+	1	2	DDX50	70376234	0.992000	0.36948	0.115000	0.21578	0.960000	0.62799	2.190000	0.42630	0.400000	0.25396	0.467000	0.42956	CGA		0.512	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70706228	C	T	70706228	4	4	77	1	0	0	0	0	0	1	0	0	4374	876	31	1	2114	1	DDX50	10	70706228	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	180549	70706228	64828519	608	22344										
ADAMTS14	140766	broad.mit.edu	37	chr10	72517806	72517806	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgggcattgcgagggggataGgccagacactgtccaggtct	16	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:72517806G>T	ENST00000373207.1	+	20	3026	c.3026G>T	c.(3025-3027)aGg>aTg	p.R1009M	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.R1012M	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1009	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R1012M(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GAGGGGGATAGGCCAGACACT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	10											44	42	42					10																	72517806		2203	4300	6503	72187812	SO:0001583	missense	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3026G>T	10.37:g.72517806G>T	ENSP00000362303:p.Arg1009Met		72187812	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.343540	0.41498	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.53423	0.62;0.62	4.34	0.74	0.18330	.	0.274613	0.33670	N	0.004665	T	0.53786	0.1818	M	0.64997	1.995	0.30840	N	0.735752	P;P	0.42556	0.783;0.783	P;P	0.53450	0.726;0.726	T	0.57929	-0.7726	10	0.87932	D	0	.	7.8439	0.29414	0.7396:0.0:0.2604:0.0	.	1009;1012	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	M	1012;1009	ENSP00000362304:R1012M;ENSP00000362303:R1009M	ENSP00000362303:R1009M	R	+	2	0	ADAMTS14	72187812	1.000000	0.71417	0.104000	0.21259	0.205000	0.24178	5.198000	0.65147	-0.033000	0.13736	-0.367000	0.07326	AGG		0.652	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72517806	G	T	72517806	3	4	77	1	0	0	0	0	1	0	0	0	259	1000	35	2	3113	2	ADAMTS14	10	72517806	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1811578	72517806	63016941	609	22345										
ADAMTS14	140766	broad.mit.edu	37	chr10	72520415	72520415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagctctggatacaagctccCcagggacccagcatcccttt	9	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:72520415C>A	ENST00000373207.1	+	22	3478	c.3478C>A	c.(3478-3480)Cca>Aca	p.P1160T	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.P1163T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1160	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P1163T(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						TACAAGCTCCCCAGGGACCCA	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	10											60	59	60					10																	72520415		2203	4300	6503	72190421	SO:0001583	missense	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3478C>A	10.37:g.72520415C>A	ENSP00000362303:p.Pro1160Thr		72190421	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	C	3.790	-0.043897	0.07452	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61158	0.13;0.16	4.44	0.853	0.19001	.	1.374990	0.05540	N	0.565643	T	0.41789	0.1174	L	0.29908	0.895	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.21917	0.037;0.037	T	0.19031	-1.0318	10	0.20046	T	0.44	.	4.6786	0.12724	0.0:0.5116:0.187:0.3014	.	1160;1163	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	T	1163;1160	ENSP00000362304:P1163T;ENSP00000362303:P1160T	ENSP00000362303:P1160T	P	+	1	0	ADAMTS14	72190421	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.116000	0.10724	0.051000	0.15978	0.655000	0.94253	CCA		0.637	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		A	72520415	C	A	72520415	3	1	77	1	0	0	0	0	1	0	0	0	259	623	22	2	3573	2	ADAMTS14	10	72520415	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2609	72520415	63014332	610	22346										
CDH23	414152	broad.mit.edu	37	chr10	73491943	73491943	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctacatcactctgctcaaCgagctggacgaggccgtgca	11	13	4	0	rs568924674		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:73491943C>T	ENST00000398786.2	-	1	97				CDH23_ENST00000224721.6_Silent_p.N1310N	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)		p.N1310N(2)									CTCTGCTCAACGAGCTGGACG	0.577																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	10											66	68	67					10																	73491943		2075	4209	6284	73161949	SO:0001627	intron_variant	64072			AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.4+5541G>A	10.37:g.73491943C>T			73161949		Silent	SNP	ENST00000398786.2	37	CCDS44430.1																																																																																				0.577	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375		T	73491943	C	T	73491943	1	4	77	0	1	0	0	0	0	0	0	0	3114	535	19	1		1	CDH23	10	73491943	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	971528	73491943	62042804	611	22347										
MYOZ1	58529	broad.mit.edu	37	chr10	75393754	75393754	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgggggtcaacccccatgGctcgctcccatggggaaata	13	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:75393754G>T	ENST00000359322.4	-	5	936	c.572C>A	c.(571-573)gCc>gAc	p.A191D	RP11-464F9.22_ENST00000609434.1_lincRNA	NM_021245.3	NP_067068.1			myozenin 1									p.A191D(1)		central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					AACCCCCATGGCTCGCTCCCA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	10											97	94	95					10																	75393754		2203	4300	6503	75063760	SO:0001583	missense	58529			AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"calsarcin-2"	605603	"myozenin"	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.572C>A	10.37:g.75393754G>T	ENSP00000352272:p.Ala191Asp		75063760		Missense_Mutation	SNP	ENST00000359322.4	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	35	5.515292	0.96402	.	.	ENSG00000177791	ENST00000359322	T	0.70399	-0.48	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.86451	0.5936	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85168	0.0996	10	0.49607	T	0.09	-15.1364	20.8794	0.99867	0.0:0.0:1.0:0.0	.	191	Q9NP98	MYOZ1_HUMAN	D	191	ENSP00000352272:A191D	ENSP00000352272:A191D	A	-	2	0	MYOZ1	75063760	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.325000	0.72901	2.941000	0.99782	0.655000	0.94253	GCC		0.498	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1			T	75393754	G	T	75393754	3	4	77	1	0	0	0	0	1	0	0	0	10125	1203	42	2	335	2	MYOZ1	10	75393754	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1901811	75393754	60140993	612	22348										
POLR3A	11128	broad.mit.edu	37	chr10	79741243	79741243	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcctgtcgatgctcatgccGtggttcaccatggtgtactg	11	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:79741243G>A	ENST00000372371.3	-	29	3971	c.3834C>T	c.(3832-3834)caC>caT	p.H1278H		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1278					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)	p.H1278H(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TGCTCATGCCGTGGTTCACCA	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	10											334	297	309					10																	79741243		2203	4300	6503	79411249	SO:0001819	synonymous_variant	11128			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3834C>T	10.37:g.79741243G>A			79411249	Q8IW34|Q8TCW5	Silent	SNP	ENST00000372371.3	37	CCDS7354.1																																																																																				0.572	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		A	79741243	G	A	79741243	2	1	77	1	0	0	0	0	0	0	0	1	12259	1136	40	1		1	POLR3A	10	79741243	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4347489	79741243	55793504	613	22349										
LRIT1	26103	broad.mit.edu	37	chr10	85992437	85992437	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaccagcttgttgttgtaaGcagcagcttcccctccgcca	8	16	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:85992437G>A	ENST00000372105.3	-	4	1139	c.1118C>T	c.(1117-1119)gCt>gTt	p.A373V		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	373						integral component of endoplasmic reticulum membrane (GO:0030176)		p.A373V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						GTTGTTGTAAGCAGCAGCTTC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	10											70	51	58					10																	85992437		2203	4300	6503	85982417	SO:0001583	missense	26103			AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1118C>T	10.37:g.85992437G>A	ENSP00000361177:p.Ala373Val		85982417	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	g	9.488	1.100016	0.20552	.	.	ENSG00000148602	ENST00000372105	T	0.36699	1.24	5.8	3.97	0.46021	.	0.156037	0.56097	N	0.000022	T	0.22044	0.0531	L	0.34521	1.04	0.39230	D	0.963651	B	0.31241	0.315	B	0.25759	0.063	T	0.08513	-1.0718	10	0.22109	T	0.4	.	6.9792	0.24694	0.1466:0.0:0.7139:0.1395	.	373	Q9P2V4	LRIT1_HUMAN	V	373	ENSP00000361177:A373V	ENSP00000361177:A373V	A	-	2	0	LRIT1	85982417	0.977000	0.34250	0.037000	0.18230	0.034000	0.12701	3.164000	0.50770	0.822000	0.34565	-0.766000	0.03442	GCT		0.592	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		A	85992437	G	A	85992437	3	1	77	1	0	0	0	0	1	0	0	0	8976	971	34	3	757	3	LRIT1	10	85992437	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6251194	85992437	49542310	614	22350										
FAM35A	54537	broad.mit.edu	37	chr10	88911830	88911830	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttaaaatatcaactgataCagaatttctcagtataatta	3	7	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:88911830C>A	ENST00000298784.1	+	3	833	c.719C>A	c.(718-720)aCa>aAa	p.T240K	FAM35A_ENST00000298786.4_Missense_Mutation_p.T240K|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	240								p.T240K(2)		endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						TCAACTGATACAGAATTTCTC	0.388																																					Ovarian(175;703 2004 25460 32514 43441)											2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	10											30	30	30					10																	88911830		2203	4295	6498	88901810	SO:0001583	missense	54537			BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.719C>A	10.37:g.88911830C>A	ENSP00000298784:p.Thr240Lys		88901810	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	c	16.25	3.071539	0.55646	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.27104	1.7;1.69;1.69	4.09	3.09	0.35607	.	0.289768	0.25801	N	0.028214	T	0.45716	0.1356	.	.	.	0.34044	D	0.655393	D	0.63046	0.992	D	0.65573	0.936	T	0.61700	-0.7009	9	0.59425	D	0.04	-9.6069	12.3445	0.55114	0.0:0.9021:0.0:0.0979	.	240	Q86V20	FA35A_HUMAN	K	240	ENSP00000298786:T240K;ENSP00000298784:T240K;ENSP00000351064:T240K	ENSP00000298784:T240K	T	+	2	0	FAM35A	88901810	1.000000	0.71417	0.665000	0.29768	0.884000	0.51177	2.667000	0.46808	2.134000	0.65973	0.537000	0.68136	ACA		0.388	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		A	88911830	C	A	88911830	3	1	77	1	0	0	0	0	1	0	0	0	5572	478	17	2	721	2	FAM35A	10	88911830	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2919393	88911830	46622917	615	22351										
KIF20B	9585	broad.mit.edu	37	chr10	91514321	91514321	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagaaagaaatggttagaagAaaaaatgatgcttatcactc					rs375746203		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:91514321delA	ENST00000371728.3	+	26	4459	c.4394delA	c.(4393-4395)gaafs	p.E1465fs	KIF20B_ENST00000416354.1_Frame_Shift_Del_p.E1495fs|KIF20B_ENST00000394289.2_Frame_Shift_Del_p.E1465fs|KIF20B_ENST00000260753.4_Frame_Shift_Del_p.E1425fs|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1465					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.M1427fs*1(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TGGTTAGAAGAAAAAATGATG	0.328																																																1	Deletion - Frameshift(1)	large_intestine(1)	10											66	67	67					10																	91514321		2203	4299	6502	91504301	SO:0001589	frameshift_variant	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4394delA	10.37:g.91514321delA	ENSP00000360793:p.Glu1465fs		91504301	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Frame_Shift_Del	DEL	ENST00000371728.3	37																																																																																					0.328	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		-	91514321	A	-	91514321	7	5	77	1	0	1	0	1	0	0	0	0	8308	246	9	0	4372	0	KIF20B	10	91514321	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	2602491	91514321	44020426	616	22352										
EXOC6	54536	broad.mit.edu	37	chr10	94675520	94675520	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctcttcaaaataggcacaGcatcagaaaaccttcagtgt	6	11	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:94675520G>A	ENST00000260762.6	+	7	683	c.669G>A	c.(667-669)caG>caA	p.Q223Q	EXOC6_ENST00000497262.1_3'UTR|EXOC6_ENST00000443748.2_Silent_p.Q223Q|EXOC6_ENST00000371547.4_Silent_p.Q239Q|EXOC6_ENST00000371552.4_Silent_p.Q218Q	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	223					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)		p.Q223Q(1)|p.Q218Q(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				AATAGGCACAGCATCAGAAAA	0.279																																																2	Substitution - coding silent(2)	large_intestine(2)	10											47	52	50					10																	94675520		2197	4293	6490	94665500	SO:0001819	synonymous_variant	54536			BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"SEC15-like 1 (S. cerevisiae)"	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.669G>A	10.37:g.94675520G>A			94665500	E9PHI3|Q5VXH8|Q9NZ24	Silent	SNP	ENST00000260762.6	37	CCDS7424.2																																																																																				0.279	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053		A	94675520	G	A	94675520	2	1	77	1	0	0	0	0	0	0	0	1	5321	962	34	3		3	EXOC6	10	94675520	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3161199	94675520	40859227	617	22353										
SORBS1	10580	broad.mit.edu	37	chr10	97096451	97096451	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtactcaggcacctgaccaCgtctgaaggcttcaagcagc	10	13	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:97096451C>T	ENST00000361941.3	-	28	3492	c.3466G>A	c.(3466-3468)Gtg>Atg	p.V1156M	SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000277982.5_Missense_Mutation_p.V1015M|SORBS1_ENST00000371247.2_Missense_Mutation_p.V1156M|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371246.2_Missense_Mutation_p.V1015M|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371227.4_Missense_Mutation_p.V1110M|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000354106.3_Intron	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.V1156M(2)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CACCTGACCACGTCTGAAGGC	0.567																																																2	Substitution - Missense(2)	large_intestine(2)	10											97	99	98					10																	97096451		2203	4300	6503	97086441	SO:0001583	missense	10580			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.3466G>A	10.37:g.97096451C>T	ENSP00000355136:p.Val1156Met		97086441		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.224189	0.39300	.	.	ENSG00000095637	ENST00000371247;ENST00000371227;ENST00000371246;ENST00000361941;ENST00000277982	T;T;T;T;T	0.08282	3.11;3.11;3.41;3.11;3.41	5.58	4.65	0.58169	.	0.000000	0.38217	N	0.001770	T	0.04137	0.0115	N	0.14661	0.345	0.80722	D	1	P;B;P	0.36974	0.576;0.44;0.576	B;B;B	0.30251	0.113;0.053;0.113	T	0.46498	-0.9187	10	0.37606	T	0.19	-9.1639	7.4193	0.27063	0.0:0.6365:0.266:0.0975	.	1110;1156;1015	Q9BX66-11;Q9BX66;Q9BX66-2	.;SRBS1_HUMAN;.	M	1156;1110;1015;1156;1015	ENSP00000360293:V1156M;ENSP00000360271:V1110M;ENSP00000360292:V1015M;ENSP00000355136:V1156M;ENSP00000277982:V1015M	ENSP00000277982:V1015M	V	-	1	0	SORBS1	97086441	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.528000	0.35985	2.641000	0.89580	0.561000	0.74099	GTG		0.567	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			T	97096451	C	T	97096451	3	4	77	1	0	0	0	0	1	0	0	0	14964	536	19	1	492	1	SORBS1	10	97096451	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2420931	97096451	38438296	618	22354										
FAM178A	55719	broad.mit.edu	37	chr10	102676714	102676714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagaatgatagagatcgagGcaaaaccaatgcagactcca	10	8	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:102676714G>A	ENST00000238961.4	+	3	1114	c.572G>A	c.(571-573)gGc>gAc	p.G191D	FAM178A_ENST00000370269.3_Missense_Mutation_p.G191D|FAM178A_ENST00000370271.3_Missense_Mutation_p.G191D	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	191						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.G191D(1)									AGAGATCGAGGCAAAACCAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	10											53	53	53					10																	102676714		2203	4300	6503	102666704	SO:0001583	missense	55719			AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.572G>A	10.37:g.102676714G>A	ENSP00000238961:p.Gly191Asp		102666704	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	G	1.913	-0.450348	0.04572	.	.	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	T;T;T	0.43294	0.95;1.59;1.58	5.84	-0.535	0.11879	.	0.492323	0.19173	N	0.120892	T	0.15089	0.0364	N	0.08118	0	0.19775	N	0.999954	B;B;B	0.17268	0.0;0.0;0.021	B;B;B	0.16722	0.001;0.001;0.016	T	0.26189	-1.0110	10	0.06891	T	0.86	2.9504	4.6005	0.12350	0.4844:0.0:0.3668:0.1488	.	191;191;191	Q8IX21;B1AL17;B1AL16	F178A_HUMAN;.;.	D	191	ENSP00000359294:G191D;ENSP00000238961:G191D;ENSP00000359292:G191D	ENSP00000238961:G191D	G	+	2	0	FAM178A	102666704	0.162000	0.22906	0.947000	0.38551	0.106000	0.19336	0.289000	0.18957	0.029000	0.15352	0.655000	0.94253	GGC		0.443	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			A	102676714	G	A	102676714	3	1	77	1	0	0	0	0	1	0	0	0	5519	1203	42	3	582	3	FAM178A	10	102676714	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5580263	102676714	32858033	619	22355										
FAM178A	55719	broad.mit.edu	37	chr10	102683864	102683864	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagcgtcctgatggaccacAtcagaaagaaaaatttataa	8	7	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:102683864A>T	ENST00000238961.4	+	5	1648	c.1106A>T	c.(1105-1107)cAt>cTt	p.H369L	FAM178A_ENST00000370269.3_Missense_Mutation_p.H369L|FAM178A_ENST00000370271.3_Missense_Mutation_p.H369L	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	369						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.H369L(1)									GATGGACCACATCAGAAAGAA	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	10											64	66	65					10																	102683864		2203	4300	6503	102673854	SO:0001583	missense	55719			AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.1106A>T	10.37:g.102683864A>T	ENSP00000238961:p.His369Leu		102673854	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.867900	0.32977	.	.	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	T;T;T	0.52526	0.66;1.29;1.28	5.16	3.99	0.46301	.	0.112011	0.41194	D	0.000933	T	0.46210	0.1381	L	0.27053	0.805	0.33854	D	0.633023	D;P;P;P	0.61697	0.99;0.557;0.557;0.763	P;B;B;B	0.57152	0.814;0.167;0.167;0.229	T	0.57940	-0.7724	10	0.42905	T	0.14	-3.1157	9.3547	0.38159	0.8193:0.1807:0.0:0.0	.	18;369;369;369	Q96LW0;Q8IX21;B1AL17;B1AL16	.;F178A_HUMAN;.;.	L	369	ENSP00000359294:H369L;ENSP00000238961:H369L;ENSP00000359292:H369L	ENSP00000238961:H369L	H	+	2	0	FAM178A	102673854	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.174000	0.31932	1.022000	0.39626	0.528000	0.53228	CAT		0.408	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102683864	A	T	102683864	3	4	77	1	0	0	0	0	1	0	0	0	5519	217	8	5	1124	5	FAM178A	10	102683864	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	7150	102683864	32850883	620	22356										
SEMA4G	57715	broad.mit.edu	37	chr10	102739898	102739898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgtatcacagattcattgcGcagccaaggctacaattcat	8	10	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:102739898G>A	ENST00000370250.4	+	10	1521	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	MRPL43_ENST00000370242.4_Intron|SEMA4G_ENST00000517724.1_Missense_Mutation_p.R383H|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000210633.3_Missense_Mutation_p.R383H|MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000370241.3_Intron	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	383	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R383H(1)		breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		GATTCATTGCGCAGCCAAGGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	10											131	96	108					10																	102739898		2203	4300	6503	102729888	SO:0001583	missense	57715			AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.1148G>A	10.37:g.102739898G>A	ENSP00000359270:p.Arg383His		102729888	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	G	25.3	4.627181	0.87560	.	.	ENSG00000095539	ENST00000519649;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.61627	0.2362	M	0.84511	2.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.998	T	0.68667	-0.5348	10	0.87932	D	0	.	17.5741	0.87943	0.0:0.0:1.0:0.0	.	383;383;383	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	H	383	ENSP00000428896:R383H;ENSP00000359270:R383H;ENSP00000430175:R383H;ENSP00000210633:R383H	ENSP00000210633:R383H	R	+	2	0	SEMA4G	102729888	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.314000	0.96306	2.405000	0.81733	0.484000	0.47621	CGC		0.582	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			A	102739898	G	A	102739898	3	1	77	1	0	0	0	0	1	0	0	0	14073	1087	38	1	1186	1	SEMA4G	10	102739898	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	56034	102739898	32794849	621	22357										
PDZD7	79955	broad.mit.edu	37	chr10	102782092	102782092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttctgagctggtgtcggagGgtgttgaaccgcacttctcc	13	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:102782092G>T	ENST00000370215.3	-	5	818	c.593C>A	c.(592-594)cCc>cAc	p.P198H		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	198						cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.P198H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		GGTGTCGGAGGGTGTTGAACC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	10											133	119	124					10																	102782092		2203	4300	6503	102772082	SO:0001583	missense	79955			AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.593C>A	10.37:g.102782092G>T	ENSP00000359234:p.Pro198His		102772082	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.154152	0.38021	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.15372	2.43	5.29	3.38	0.38709	.	0.130552	0.51477	D	0.000094	T	0.31918	0.0812	L	0.53249	1.67	0.51767	D	0.99993	D;D	0.89917	1.0;0.992	D;P	0.69142	0.962;0.863	T	0.00958	-1.1500	10	0.37606	T	0.19	.	10.6327	0.45547	0.0724:0.133:0.7946:0.0	.	198;198	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	H	198	ENSP00000359234:P198H	ENSP00000359234:P198H	P	-	2	0	PDZD7	102772082	1.000000	0.71417	0.002000	0.10522	0.002000	0.02628	5.387000	0.66243	0.579000	0.29504	-0.379000	0.06801	CCC		0.617	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		T	102782092	G	T	102782092	3	4	77	1	0	0	0	0	1	0	0	0	11735	1232	43	2	984	2	PDZD7	10	102782092	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	42194	102782092	32752655	622	22358										
LDB1	8861	broad.mit.edu	37	chr10	103869241	103869241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcgtgacatgagctcttgCatgggctcgagtatcacaca	12	10	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:103869241C>T	ENST00000425280.1	-	9	1098	c.756G>A	c.(754-756)atG>atA	p.M252I	LDB1_ENST00000361198.5_Missense_Mutation_p.M216I|LDB1_ENST00000490751.1_5'Flank	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	252					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)	p.M216I(1)		breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		TGAGCTCTTGCATGGGCTCGA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	10											115	105	109					10																	103869241		2203	4300	6503	103859231	SO:0001583	missense	8861			AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.756G>A	10.37:g.103869241C>T	ENSP00000392466:p.Met252Ile		103859231	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	37	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	C	35	5.591595	0.96590	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.84737	0.5538	M	0.85945	2.785	0.80722	D	1	P;D	0.61080	0.705;0.989	P;D	0.75484	0.785;0.986	D	0.86146	0.1584	9	0.87932	D	0	-21.3774	20.0341	0.97551	0.0:1.0:0.0:0.0	.	252;216	Q86U70;Q86U70-3	LDB1_HUMAN;.	I	216;252	.	ENSP00000354616:M216I	M	-	3	0	LDB1	103859231	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.753000	0.94483	0.555000	0.69702	ATG		0.587	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		T	103869241	C	T	103869241	3	4	77	1	0	0	0	0	1	0	0	0	8717	710	25	3	491	3	LDB1	10	103869241	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1087149	103869241	31665506	623	22359										
COL17A1	1308	broad.mit.edu	37	chr10	105794081	105794081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggccaacaatgaagctgcGcacatcaggacctgcagggt	14	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:105794081G>A	ENST00000353479.5	-	52	4068	c.3778C>T	c.(3778-3780)Cgc>Tgc	p.R1260C	COL17A1_ENST00000369733.3_Missense_Mutation_p.R1178C	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1260	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R1260C(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ATGAAGCTGCGCACATCAGGA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	10											6	7	6					10																	105794081		2161	4233	6394	105784071	SO:0001583	missense	1308			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.3778C>T	10.37:g.105794081G>A	ENSP00000340937:p.Arg1260Cys		105784071	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.819495	0.90873	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.95342	-3.68;-3.38	5.07	5.07	0.68467	.	0.142074	0.32301	N	0.006292	D	0.97046	0.9035	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.97337	0.9954	10	0.56958	D	0.05	-14.8414	16.6199	0.84927	0.0:0.0:1.0:0.0	.	1260	Q9UMD9	COHA1_HUMAN	C	1260;1178	ENSP00000340937:R1260C;ENSP00000358748:R1178C	ENSP00000340937:R1260C	R	-	1	0	COL17A1	105784071	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	5.030000	0.64128	2.357000	0.79964	0.561000	0.74099	CGC		0.632	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		A	105794081	G	A	105794081	3	1	77	1	0	0	0	0	1	0	0	0	3680	1087	38	1	735	1	COL17A1	10	105794081	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1924840	105794081	29740666	624	22360										
COL17A1	1308	broad.mit.edu	37	chr10	105799260	105799260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtggtccctgaaggttgaGtccgaaagaactggaccctg	14	9	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:105799260G>T	ENST00000353479.5	-	43	3129	c.2839C>A	c.(2839-2841)Ctc>Atc	p.L947I	COL17A1_ENST00000369733.3_Intron	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	947	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.L947I(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TGAAGGTTGAGTCCGAAAGAA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	10											84	87	86					10																	105799260		2203	4300	6503	105789250	SO:0001583	missense	1308			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.2839C>A	10.37:g.105799260G>T	ENSP00000340937:p.Leu947Ile		105789250	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.291078	0.40494	.	.	ENSG00000065618	ENST00000353479	D	0.90900	-2.75	4.97	-5.65	0.02459	.	1.162690	0.06808	N	0.789875	T	0.74581	0.3735	N	0.08118	0	0.25886	N	0.98354	B	0.10296	0.003	B	0.06405	0.002	T	0.60188	-0.7312	10	0.38643	T	0.18	-0.5211	2.3576	0.04300	0.457:0.2619:0.1713:0.1098	.	947	Q9UMD9	COHA1_HUMAN	I	947	ENSP00000340937:L947I	ENSP00000340937:L947I	L	-	1	0	COL17A1	105789250	0.238000	0.23825	0.080000	0.20451	0.888000	0.51559	-1.088000	0.03379	-0.748000	0.04753	0.491000	0.48974	CTC		0.607	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		T	105799260	G	T	105799260	3	4	77	1	0	0	0	0	1	0	0	0	3680	1029	36	2	1710	2	COL17A1	10	105799260	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5179	105799260	29735487	625	22361										
C10orf79	80217	broad.mit.edu	37	chr10	105903248	105903248	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gattccagaccaaagggtccAagccttctggcatgttacta	9	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:105903248A>C	ENST00000357060.3	-	32	4209	c.4094T>G	c.(4093-4095)tTg>tGg	p.L1365W	WDR96_ENST00000428666.1_Missense_Mutation_p.L1337W|WDR96_ENST00000479392.1_5'Flank	NM_025145.5	NP_079421.5												p.L1365W(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CAAAGGGTCCAAGCCTTCTGG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											134	126	128					10																	105903248		2203	4300	6503	105893238	SO:0001583	missense	80217																														ENST00000357060.3:c.4094T>G	10.37:g.105903248A>C	ENSP00000349568:p.Leu1365Trp		105893238		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.094892|4.094892	0.76870|0.76870	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666|ENST00000457071;ENST00000434629	T;T|.	0.19532|.	2.14;2.21|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.151092|.	0.46758|.	D|.	0.000267|.	T|T	0.75384|0.75384	0.3842|0.3842	M|M	0.74881|0.74881	2.28|2.28	0.50039|0.50039	D|D	0.99984|0.99984	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|T	0.75744|0.75744	-0.3210|-0.3210	10|5	0.66056|.	D|.	0.02|.	.|.	15.9576|15.9576	0.79898|0.79898	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1337;1365|.	G5E9L1;Q8NDM7|.	.;WDR96_HUMAN|.	W|G	1365;1337|214;697	ENSP00000349568:L1365W;ENSP00000400289:L1337W|.	ENSP00000349568:L1365W|.	L|W	-|-	2|1	0|0	WDR96|WDR96	105893238|105893238	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.684000|0.684000	0.39900|0.39900	7.668000|7.668000	0.83897|0.83897	2.250000|2.250000	0.74265|0.74265	0.454000|0.454000	0.30748|0.30748	TTG|TGG		0.373	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	105903248	A	C	105903248	3	2	77	1	0	0	0	0	1	0	0	0	1622	131	5	4	931	4	C10orf79	10	105903248	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	103988	105903248	29631499	626	22362										
ADRB1	153	broad.mit.edu	37	chr10	115804529	115804529	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgccgctgctacaacgaccCcaagtgctgcgacttcgtca	10	16	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:115804529C>A	ENST00000369295.2	+	1	724	c.638C>A	c.(637-639)cCc>cAc	p.P213H		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	213					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)	p.P213H(1)		large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	TACAACGACCCCAAGTGCTGC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	10											62	50	54					10																	115804529		2203	4300	6503	115794519	SO:0001583	missense	153			J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"GPCR / Class A : Adrenoceptors : beta"	285	protein-coding gene	gene with protein product		109630	"adrenergic, beta-1-, receptor"	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.638C>A	10.37:g.115804529C>A	ENSP00000358301:p.Pro213His		115794519	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Missense_Mutation	SNP	ENST00000369295.2	37	CCDS7586.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678628	0.68042	.	.	ENSG00000043591	ENST00000369295	T	0.39406	1.08	4.46	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.66963	0.2843	M	0.83692	2.655	0.53005	D	0.999966	D	0.71674	0.998	D	0.68943	0.961	T	0.74166	-0.3753	10	0.66056	D	0.02	.	17.1083	0.86669	0.0:1.0:0.0:0.0	.	213	P08588	ADRB1_HUMAN	H	213	ENSP00000358301:P213H	ENSP00000358301:P213H	P	+	2	0	ADRB1	115794519	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.704000	0.61831	2.024000	0.59613	0.555000	0.69702	CCC		0.657	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1			A	115804529	C	A	115804529	3	1	77	1	0	0	0	0	1	0	0	0	340	623	22	2	640	2	ADRB1	10	115804529	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	9901281	115804529	19730218	627	22363										
VWA2	340706	broad.mit.edu	37	chr10	116045710	116045710	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccgcagccctgaagctgaGcctggaatgcagggtcgacc	13	15	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:116045710G>T	ENST00000392982.3	+	11	1260	c.1010G>T	c.(1009-1011)aGc>aTc	p.S337I	VWA2_ENST00000603594.1_Missense_Mutation_p.S337I			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	337					calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.S337I(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CTGAAGCTGAGCCTGGAATGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	10											60	51	54					10																	116045710		2203	4300	6503	116035700	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1010G>T	10.37:g.116045710G>T	ENSP00000376708:p.Ser337Ile		116035700	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	G	16.97	3.269501	0.59540	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.77620	-1.11	5.8	3.97	0.46021	.	0.111909	0.64402	D	0.000003	T	0.81847	0.4909	L	0.39566	1.225	0.27961	N	0.936787	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.74657	-0.3592	10	0.40728	T	0.16	.	12.2134	0.54391	0.139:0.0:0.861:0.0	.	33;337;337	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	I	337	ENSP00000376708:S337I	ENSP00000298715:S337I	S	+	2	0	VWA2	116035700	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	4.102000	0.57776	0.811000	0.34303	-0.259000	0.10710	AGC		0.617	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		T	116045710	G	T	116045710	3	4	77	1	0	0	0	0	1	0	0	0	17279	971	34	2	1048	2	VWA2	10	116045710	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	241181	116045710	19489037	628	22364										
GFRA1	2674	broad.mit.edu	37	chr10	117825111	117825111	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atacagaggtgtgtattgccCgacacattggatttcagctt	10	8	1	1	rs374656900		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:117825111C>T	ENST00000355422.6	-	10	1774	c.1224G>A	c.(1222-1224)tcG>tcA	p.S408S	GFRA1_ENST00000439649.3_Silent_p.S403S|GFRA1_ENST00000369236.1_Silent_p.S403S|GFRA1_ENST00000544592.1_Silent_p.S287S	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	408					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.S403S(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		GTGTATTGCCCGACACATTGG	0.433																																					Ovarian(128;329 1725 45498 46808 50759)											1	Substitution - coding silent(1)	large_intestine(1)	10						C	,,	1,4405	2.1+/-5.4	0,1,2202	95	86	89		1209,1224,1209	-5.9	0.6	10		89	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GFRA1	NM_001145453.1,NM_005264.4,NM_145793.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	403/461,408/466,403/461	117825111	1,13005	2203	4300	6503	117815101	SO:0001819	synonymous_variant	2674			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.1224G>A	10.37:g.117825111C>T			117815101	A8KA21|O15507|O43912	Silent	SNP	ENST00000355422.6	37	CCDS44481.1																																																																																				0.433	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		T	117825111	C	T	117825111	2	4	77	1	0	0	0	0	0	0	0	1	6367	639	23	1		1	GFRA1	10	117825111	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1779401	117825111	17709636	629	22365										
FAM45A	404636	broad.mit.edu	37	chr10	120877150	120877150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagtaaggattttgatgcccGaaaggcctacctggctggct	12	9	0	1	rs146864091	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:120877150G>A	ENST00000361432.2	+	4	478	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	FAM45A_ENST00000544016.1_Intron|FAM45A_ENST00000535029.1_Missense_Mutation_p.R151Q|FAM45A_ENST00000489988.1_3'UTR	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	151								p.R151Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		TTTGATGCCCGAAAGGCCTAC	0.493													G|||	3	0.000599042	0.0023	0	5008	,	,		19518	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	10						G	GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	84	87	86		452	5	1	10	dbSNP_134	86	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FAM45A	NM_207009.2	43	0,6,6497	AA,AG,GG		0.0233,0.0908,0.0461	probably-damaging	151/358	120877150	6,13000	2203	4300	6503	120867140	SO:0001583	missense	404636			AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.452G>A	10.37:g.120877150G>A	ENSP00000354688:p.Arg151Gln		120867140	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Missense_Mutation	SNP	ENST00000361432.2	37	CCDS7609.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	26.3	4.727550	0.89390	9.08E-4	2.33E-4	ENSG00000119979	ENST00000535029;ENST00000546291;ENST00000361432	.	.	.	5.87	4.97	0.65823	.	0.061593	0.64402	N	0.000004	T	0.75072	0.3800	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	P;D;P	0.65684	0.866;0.937;0.866	T	0.77289	-0.2643	9	0.59425	D	0.04	.	13.1923	0.59717	0.0735:0.0:0.9265:0.0	.	78;143;151	B4DNL9;Q8TCE6-2;Q8TCE6	.;.;FA45A_HUMAN	Q	151	.	ENSP00000354688:R151Q	R	+	2	0	FAM45A	120867140	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	5.917000	0.69989	1.482000	0.48325	0.591000	0.81541	CGA		0.493	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009		A	120877150	G	A	120877150	3	1	77	1	0	0	0	0	1	0	0	0	5583	1058	37	1	466	1	FAM45A	10	120877150	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3052039	120877150	14657597	630	22366										
BTBD16	118663	broad.mit.edu	37	chr10	124094441	124094441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgctctatatggattcttcTttaagataaagggactcaaa	7	6	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:124094441T>C	ENST00000260723.4	+	14	1461	c.1210T>C	c.(1210-1212)Ttt>Ctt	p.F404L	BTBD16_ENST00000368994.2_Missense_Mutation_p.F405L|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	404								p.F404L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TGGATTCTTCTTTAAGATAAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											123	124	123					10																	124094441		2202	4299	6501	124084431	SO:0001583	missense	118663			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1210T>C	10.37:g.124094441T>C	ENSP00000260723:p.Phe404Leu		124084431	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.003775	0.74932	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.21543	2.0;2.0	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000004	T	0.34774	0.0909	L	0.36672	1.1	0.42148	D	0.991543	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.05566	-1.0877	10	0.42905	T	0.14	-17.1063	12.0596	0.53555	0.0:0.0:0.0:1.0	.	405;404	Q32M84-2;Q32M84	.;BTBDG_HUMAN	L	404;405	ENSP00000260723:F404L;ENSP00000357990:F405L	ENSP00000260723:F404L	F	+	1	0	BTBD16	124084431	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	3.938000	0.56583	2.108000	0.64289	0.533000	0.62120	TTT		0.338	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		C	124094441	T	C	124094441	3	2	77	1	0	0	0	0	1	0	0	0	1544	1609	56	4	1260	4	BTBD16	10	124094441	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	3217291	124094441	11440306	631	22367										
CPXM2	119587	broad.mit.edu	37	chr10	125602003	125602003	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatcattttcattaatgcccGcctagaaagaaagaaagcgg	8	8	2	3	rs200954130		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:125602003G>A	ENST00000241305.3	-	4	669	c.515C>T	c.(514-516)gCg>gTg	p.A172V	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	172	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.A172V(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		ATTAATGCCCGCCTAGAAAGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	10											40	39	39					10																	125602003		2203	4300	6503	125591993	SO:0001630	splice_region_variant	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.514-1C>T	10.37:g.125602003G>A			125591993	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708436	0.68615	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	D	0.97328	-4.34	5.24	4.34	0.51931	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97250	0.9101	L	0.51422	1.61	0.80722	D	1	D	0.67145	0.996	D	0.63877	0.919	D	0.96961	0.9701	10	0.49607	T	0.09	-24.1902	13.783	0.63093	0.0738:0.0:0.9262:0.0	.	172	Q8N436	CPXM2_HUMAN	V	172;5;172	ENSP00000241305:A172V	ENSP00000241305:A172V	A	-	2	0	CPXM2	125591993	1.000000	0.71417	0.968000	0.41197	0.569000	0.35902	9.403000	0.97302	1.204000	0.43247	-0.237000	0.12165	GCG		0.458	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	Missense_Mutation	A	125602003	G	A	125602003	5	1	77	1	0	0	0	0	0	0	1	0	3844	1101	38	1	1799	1	CPXM2	10	125602003	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1507562	125602003	9932744	632	22368										
ADAM12	8038	broad.mit.edu	37	chr10	127724815	127724815	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagcactcgctgagttgacTggggctgagggacattcagg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:127724815delT	ENST00000368679.4	-	21	2747	c.2438delA	c.(2437-2439)cagfs	p.Q813fs		NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	813					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.Q813fs*>97(2)		biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CTGAGTTGACTGGGGCTGAGG	0.587																																																2	Deletion - Frameshift(2)	large_intestine(2)	10											104	102	102					10																	127724815		2203	4300	6503	127714805	SO:0001589	frameshift_variant	8038			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.2438delA	10.37:g.127724815delT	ENSP00000357668:p.Gln813fs		127714805	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Frame_Shift_Del	DEL	ENST00000368679.4	37	CCDS7653.1																																																																																				0.587	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			-	127724815	T	-	127724815	7	5	77	1	0	1	0	1	0	0	0	0	236	1580	55	0	303	0	ADAM12	10	127724815	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	2122812	127724815	7809932	633	22369										
C10orf90	118611	broad.mit.edu	37	chr10	128193236	128193236	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcgccattggccagagccGggggcgcctggaacagtgtg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:128193236delG	ENST00000284694.7	-	3	653	c.533delC	c.(532-534)ccgfs	p.P178fs	C10orf90_ENST00000356858.3_Frame_Shift_Del_p.P131fs|C10orf90_ENST00000392694.1_Frame_Shift_Del_p.P131fs|C10orf90_ENST00000454341.1_Frame_Shift_Del_p.P178fs|C10orf90_ENST00000544758.1_Frame_Shift_Del_p.P275fs|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	178	Required for interaction with HDAC1. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.P178fs*30(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GGCCAGAGCCGGGGGCGCCTG	0.662											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Deletion - Frameshift(1)	large_intestine(1)	10											46	54	51					10																	128193236		2202	4300	6502	128183226	SO:0001589	frameshift_variant	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.533delC	10.37:g.128193236delG	ENSP00000284694:p.Pro178fs	1563	128183226	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Frame_Shift_Del	DEL	ENST00000284694.7	37	CCDS31310.1																																																																																				0.662	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		-	128193236	G	-	128193236	7	5	77	1	0	1	0	1	0	0	0	0	1627	1116	39	0	1594	0	C10orf90	10	128193236	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	468421	128193236	7341511	634	22370										
MKI67	4288	broad.mit.edu	37	chr10	129904387	129904387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacctactgctgctttaggcGtgtgcatggctttgcctgct	11	12	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:129904387G>A	ENST00000368654.3	-	13	6092	c.5717C>T	c.(5716-5718)aCg>aTg	p.T1906M	MKI67_ENST00000368653.3_Missense_Mutation_p.T1546M	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1906	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.T1906M(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGCTTTAGGCGTGTGCATGGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	10											266	260	262					10																	129904387		2203	4300	6503	129794377	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5717C>T	10.37:g.129904387G>A	ENSP00000357643:p.Thr1906Met		129794377	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972398	0.34848	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03301	3.98;3.98	2.96	1.02	0.19986	.	1.106030	0.07176	U	0.853270	T	0.12475	0.0303	M	0.67397	2.05	0.09310	N	1	D;D;D	0.89917	0.972;1.0;1.0	B;D;D	0.78314	0.365;0.991;0.989	T	0.22452	-1.0216	10	0.52906	T	0.07	.	2.4661	0.04553	0.2632:0.0:0.4978:0.239	.	1905;1546;1906	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	M	1906;1546;1905	ENSP00000357643:T1906M;ENSP00000357642:T1546M	ENSP00000357642:T1546M	T	-	2	0	MKI67	129794377	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.151000	0.16283	0.274000	0.22072	0.561000	0.74099	ACG		0.473	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129904387	G	A	129904387	3	1	77	1	0	0	0	0	1	0	0	0	9628	1145	40	1	4065	1	MKI67	10	129904387	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1711151	129904387	5630360	635	22371										
MGMT	4255	broad.mit.edu	37	chr10	131334603	131334603	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggttgtgagcagggtctgcaCgaaataaagctcctgggcaa	14	8	1	1	rs572781091		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:131334603C>T	ENST00000306010.7	+	2	212	c.180C>T	c.(178-180)caC>caT	p.H60H		NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	29					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)	p.H29H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		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)	L-Cysteine(DB00151)	AGGGTCTGCACGAAATAAAGC	0.512								Direct reversal of damage					C|||	1	0.000199681	8e-04	0	5008	,	,		18383	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	10											102	88	92					10																	131334603		2203	4300	6503	131224593	SO:0001819	synonymous_variant	4255			M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.180C>T	10.37:g.131334603C>T			131224593	Q5VY78	Silent	SNP	ENST00000306010.7	37	CCDS7660.2																																																																																				0.512	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412		T	131334603	C	T	131334603	2	4	77	1	0	0	0	0	0	0	0	1	9587	535	19	1		1	MGMT	10	131334603	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1430216	131334603	4200144	636	22372										
EBF3	253738	broad.mit.edu	37	chr10	131666125	131666125	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caattatgatgacggtggcaCcccccgtggtccagccttca							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:131666125delC	ENST00000355311.5	-	9	905	c.833delG	c.(832-834)ggtfs	p.G278fs	EBF3_ENST00000368648.3_Frame_Shift_Del_p.G269fs			Q9H4W6	COE3_HUMAN	early B-cell factor 3	278	IPT/TIG.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G269fs*6(2)|p.G278fs*6(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		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)		GACGGTGGCACCCCCCGTGGT	0.577																																																3	Deletion - Frameshift(3)	large_intestine(3)	10											119	95	103					10																	131666125		2203	4300	6503	131556115	SO:0001589	frameshift_variant	253738				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.833delG	10.37:g.131666125delC	ENSP00000347463:p.Gly278fs		131556115	A0AUY1|Q5T6H9|Q9H4W5	Frame_Shift_Del	DEL	ENST00000355311.5	37																																																																																					0.577	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		-	131666125	C	-	131666125	7	5	77	1	0	1	0	1	0	0	0	0	4893	507	18	0	881	0	EBF3	10	131666125	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	331522	131666125	3868622	637	22373										
GLRX3	10539	broad.mit.edu	37	chr10	131959258	131959258	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaactcctcaagaaccacgcTgtggtaagaagctgccttta	9	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:131959258T>C	ENST00000368644.1	+	4	497	c.475T>C	c.(475-477)Tgt>Cgt	p.C159R	GLRX3_ENST00000331244.5_Missense_Mutation_p.C159R	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	159	Glutaredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)	p.C159R(2)		endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		AGAACCACGCTGTGGTAAGAA	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	10											60	58	59					10																	131959258		2203	4300	6503	131849248	SO:0001583	missense	10539			AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"glutaredoxin 4"	612754	"thioredoxin-like 2"	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.475T>C	10.37:g.131959258T>C	ENSP00000357633:p.Cys159Arg		131849248	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.279077	0.59758	.	.	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.73681	-0.77;-0.77	4.39	4.39	0.52855	Glutaredoxin (2);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.87732	0.6251	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90149	0.4219	10	0.87932	D	0	-4.8758	12.9885	0.58606	0.0:0.0:0.0:1.0	.	159	O76003	GLRX3_HUMAN	R	159	ENSP00000330836:C159R;ENSP00000357633:C159R	ENSP00000330836:C159R	C	+	1	0	GLRX3	131849248	1.000000	0.71417	0.978000	0.43139	0.472000	0.32918	7.395000	0.79876	1.854000	0.53819	0.533000	0.62120	TGT		0.428	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541		C	131959258	T	C	131959258	3	2	77	1	0	0	0	0	1	0	0	0	6481	1580	55	4	489	4	GLRX3	10	131959258	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	293133	131959258	3575489	638	22374										
PPP2R2D	55844	broad.mit.edu	37	chr10	133757518	133757518	+	5'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatggtagaagcgagtccacGgcgaatttttgcaaatgctc	11	8	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:133757518G>A	ENST00000422256.2	+	0	328				PPP2R2D_ENST00000470416.1_Intron			Q66LE6	2ABD_HUMAN	protein phosphatase 2, regulatory subunit B, delta						exit from mitosis (GO:0010458)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.R144Q(2)		endometrium(3)|large_intestine(3)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)		GCGAGTCCACGGCGAATTTTT	0.348																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	10											121	105	110					10																	133757518		1852	4092	5944	133607508	SO:0001623	5_prime_UTR_variant	55844			AF220046	CCDS73224.1	10q26.3	2013-01-10	2010-06-18		ENSG00000175470	ENSG00000175470		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	23732	protein-coding gene	gene with protein product	"PP2A subunit B isoform delta"	613992	"protein phosphatase 2, regulatory subunit B, delta isoform"			10819331	Standard	XM_005277927		Approved	MDS026	uc001lks.3	Q66LE6	OTTHUMG00000019277	ENST00000422256.2:c.-158G>A	10.37:g.133757518G>A			133607508	A8KAK0|Q5SQJ2|Q9P1Y7	Missense_Mutation	SNP	ENST00000422256.2	37		.	.	.	.	.	.	.	.	.	.	G	34	5.298683	0.95574	.	.	ENSG00000175470	ENST00000455566	T	0.36340	1.26	3.78	3.78	0.43462	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.52354	0.1729	.	.	.	0.80722	D	1	D	0.71674	0.998	P	0.54965	0.765	T	0.62407	-0.6861	9	0.87932	D	0	-13.7349	16.2203	0.82255	0.0:0.0:1.0:0.0	.	175	Q66LE6	2ABD_HUMAN	Q	144	ENSP00000399970:R144Q	ENSP00000399970:R144Q	R	+	2	0	PPP2R2D	133607508	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	6.762000	0.74950	2.126000	0.65437	0.655000	0.94253	CGG		0.348	PPP2R2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_018461		A	133757518	G	A	133757518	1	1	77	0	1	0	0	0	0	0	0	0	12421	1116	39	1		1	PPP2R2D	10	133757518	5'UTR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1798260	133757518	1777229	639	22375										
JAKMIP3	282973	broad.mit.edu	37	chr10	133931058	133931058	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccgcatcaagaaggagtgcGagcgggagatccgcaggctg	16	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:133931058G>A	ENST00000298622.4	+	2	751	c.613G>A	c.(613-615)Gag>Aag	p.E205K		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	205						Golgi apparatus (GO:0005794)		p.E205K(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GAAggagtgcgagcgggagat	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	10											13	15	14					10																	133931058		2032	4153	6185	133781048	SO:0001583	missense	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.613G>A	10.37:g.133931058G>A	ENSP00000298622:p.Glu205Lys		133781048	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351282	0.95830	.	.	ENSG00000188385	ENST00000298622	T	0.12255	2.7	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	M	0.67700	2.07	0.53688	D	0.999976	D	0.89917	1.0	D	0.80764	0.994	T	0.04400	-1.0954	10	0.38643	T	0.18	-42.5123	17.7631	0.88470	0.0:0.0:1.0:0.0	.	205	Q5VZ66	JKIP3_HUMAN	K	205	ENSP00000298622:E205K	ENSP00000298622:E205K	E	+	1	0	JAKMIP3	133781048	1.000000	0.71417	0.987000	0.45799	0.914000	0.54420	9.079000	0.94032	2.419000	0.82065	0.591000	0.81541	GAG		0.697	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		A	133931058	G	A	133931058	3	1	77	1	0	0	0	0	1	0	0	0	7963	1059	37	1	619	1	JAKMIP3	10	133931058	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	173540	133931058	1603689	640	22376										
JAKMIP3	282973	broad.mit.edu	37	chr10	133946947	133946947	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagctgtcccaggtccgagaGgccgaccggcacccgggcag	15	16	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:133946947G>T	ENST00000298622.4	+	3	903	c.765G>T	c.(763-765)gaG>gaT	p.E255D		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	255						Golgi apparatus (GO:0005794)		p.E255D(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AGGTCCGAGAGGCCGACCGGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	10											24	28	26					10																	133946947		1956	4138	6094	133796937	SO:0001583	missense	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.765G>T	10.37:g.133946947G>T	ENSP00000298622:p.Glu255Asp		133796937	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806613	0.70682	.	.	ENSG00000188385	ENST00000298622	T	0.50813	0.73	4.5	4.5	0.54988	.	0.056837	0.64402	D	0.000001	T	0.42063	0.1186	L	0.46157	1.445	0.33225	D	0.555222	B	0.29115	0.233	B	0.25987	0.065	T	0.52185	-0.8609	10	0.24483	T	0.36	-32.8063	17.3619	0.87353	0.0:0.0:1.0:0.0	.	255	Q5VZ66	JKIP3_HUMAN	D	255	ENSP00000298622:E255D	ENSP00000298622:E255D	E	+	3	2	JAKMIP3	133796937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.112000	0.77086	2.328000	0.79073	0.563000	0.77884	GAG		0.617	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		T	133946947	G	T	133946947	3	4	77	1	0	0	0	0	1	0	0	0	7963	991	35	2	775	2	JAKMIP3	10	133946947	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	15889	133946947	1587800	641	22377										
LRRC27	80313	broad.mit.edu	37	chr10	134151131	134151131	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatttctttcagttgcttccGaacctgacttggctggacct	9	11	2	1	rs116451295	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr10:134151131G>A	ENST00000368614.3	+	3	378	c.273G>A	c.(271-273)ccG>ccA	p.P91P	LRRC27_ENST00000368613.4_Silent_p.P91P|LRRC27_ENST00000432555.2_5'UTR|LRRC27_ENST00000392638.2_Silent_p.P91P|LRRC27_ENST00000356571.4_Silent_p.P91P|LRRC27_ENST00000368615.3_Silent_p.P91P|LRRC27_ENST00000368612.1_Silent_p.P29P|LRRC27_ENST00000344079.5_Silent_p.P91P|LRRC27_ENST00000368610.3_Silent_p.P29P	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	91								p.P91P(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	18		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		AGTTGCTTCCGAACCTGACTT	0.408																																																2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	10											105	99	101					10																	134151131		2203	4300	6503	134001121	SO:0001819	synonymous_variant	80313			AB051461	CCDS31316.1, CCDS44496.1	10q26.3	2013-09-20			ENSG00000148814	ENSG00000148814			29346	protein-coding gene	gene with protein product						11214970	Standard	NM_030626		Approved	KIAA1674	uc010quw.1	Q9C0I9	OTTHUMG00000019284	ENST00000368614.3:c.273G>A	10.37:g.134151131G>A			134001121	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Silent	SNP	ENST00000368614.3	37	CCDS31316.1	.	.	.	.	.	.	.	.	.	.	G	0.093	-1.164734	0.01673	.	.	ENSG00000148814	ENST00000450442	.	.	.	4.73	-9.47	0.00594	.	.	.	.	.	T	0.44871	0.1314	.	.	.	0.52501	D	0.999954	.	.	.	.	.	.	T	0.61153	-0.7120	4	.	.	.	-20.1907	6.1334	0.20217	0.2244:0.4943:0.2025:0.0788	.	.	.	.	Q	43	.	.	R	+	2	0	LRRC27	134001121	0.957000	0.32711	0.005000	0.12908	0.040000	0.13550	-0.274000	0.08537	-4.666000	0.00037	-1.623000	0.00790	CGA		0.408	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462		A	134151131	G	A	134151131	2	1	77	1	0	0	0	0	0	0	0	1	9010	1045	37	1		1	LRRC27	10	134151131	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	204184	134151131	1383616	642	22378										
MUC5B	727897	broad.mit.edu	37	chr11	1273619	1273619	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgagccggctgccatttctaCgcagtgtgcaatcagcactg	11	13	2	0	rs369818141		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:1273619C>T	ENST00000529681.1	+	32	14968	c.14910C>T	c.(14908-14910)taC>taT	p.Y4970Y	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.Y4973Y	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4970					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.Y4925Y(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		GCCATTTCTACGCAGTGTGCA	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C		1,4191		0,1,2095	82	99	93		14910	-8.8	0.2	11		93	0,8418		0,0,4209	no	coding-synonymous	MUC5B	NM_002458.2		0,1,6304	TT,TC,CC		0.0,0.0239,0.0079		4970/5763	1273619	1,12609	2096	4209	6305	1230195	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14910C>T	11.37:g.1273619C>T			1230195	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.587	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1273619	C	T	1273619	2	4	77	1	0	0	0	0	0	0	0	1	10009	547	19	1		1	MUC5B	11	1273619	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		1273619	133732897	643	22379										
OSBPL5	114879	broad.mit.edu	37	chr11	3123491	3123491	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggtctcccccaggatgggGttgtacggcttcttgattcc	12	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:3123491G>A	ENST00000263650.7	-	12	1506	c.1347C>T	c.(1345-1347)aaC>aaT	p.N449N	OSBPL5_ENST00000542243.1_Silent_p.N80N|OSBPL5_ENST00000389989.3_Silent_p.N381N|OSBPL5_ENST00000525498.1_Silent_p.N360N|OSBPL5_ENST00000348039.5_Silent_p.N381N	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	449					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)	p.N449N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		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)		CCAGGATGGGGTTGTACGGCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	11											59	51	53					11																	3123491		2201	4298	6499	3080067	SO:0001819	synonymous_variant	114879			AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.1347C>T	11.37:g.3123491G>A			3080067	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																				0.587	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			A	3123491	G	A	3123491	2	1	77	1	0	0	0	0	0	0	0	1	11311	1252	44	3		3	OSBPL5	11	3123491	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1849872	3123491	131883025	644	22380										
ZNF195	7748	broad.mit.edu	37	chr11	3380754	3380754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgttgccacattcttcacacGtgtagggtttttcttcagaa	8	9	4	1	rs559329436		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:3380754G>A	ENST00000399602.4	-	6	1610	c.1484C>T	c.(1483-1485)aCg>aTg	p.T495M	ZNF195_ENST00000354599.6_Missense_Mutation_p.T423M|ZNF195_ENST00000343338.7_Missense_Mutation_p.T427M|ZNF195_ENST00000429541.2_Missense_Mutation_p.T427M|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000005082.9_Missense_Mutation_p.T472M|ZNF195_ENST00000526601.1_Missense_Mutation_p.T476M	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	495					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.T423M(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		TTCTTCACACGTGTAGGGTTT	0.423													g|||	1	0.000199681	8e-04	0	5008	,	,		23265	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											152	152	152					11																	3380754		2024	4213	6237	3337330	SO:0001583	missense	7748				CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.1484C>T	11.37:g.3380754G>A	ENSP00000382511:p.Thr495Met		3337330	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	.	.	.	.	.	.	.	.	.	.	g	15.18	2.758286	0.49468	.	.	ENSG00000005801	ENST00000354599;ENST00000399602;ENST00000343338;ENST00000429541;ENST00000005082;ENST00000526601	T;T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16;3.16	1.27	-2.53	0.06326	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13841	0.0335	L	0.39692	1.235	0.09310	N	1	D;D;D;D;D;D	0.76494	0.994;0.994;0.998;0.993;0.999;0.993	D;P;P;B;D;B	0.72625	0.978;0.501;0.865;0.368;0.917;0.368	T	0.13045	-1.0524	9	0.62326	D	0.03	.	3.1338	0.06433	0.1966:0.0:0.4297:0.3736	.	476;354;472;427;495;423	O14628-6;Q59EZ7;O14628-5;O14628-7;O14628;O14628-4	.;.;.;.;ZN195_HUMAN;.	M	423;495;427;427;472;476	ENSP00000346613:T423M;ENSP00000382511:T495M;ENSP00000344483:T427M;ENSP00000387998:T427M;ENSP00000005082:T472M;ENSP00000435828:T476M	ENSP00000005082:T472M	T	-	2	0	ZNF195	3337330	0.000000	0.05858	0.000000	0.03702	0.916000	0.54674	-1.025000	0.03600	-0.985000	0.03503	0.305000	0.20034	ACG		0.423	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			A	3380754	G	A	3380754	3	1	77	1	0	0	0	0	1	0	0	0	17797	1145	40	1	409	1	ZNF195	11	3380754	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	257263	3380754	131625762	645	22381										
PGAP2	27315	broad.mit.edu	37	chr11	3845167	3845167	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcggcggggaggtgccccagCgctacgtgtggcgtttctgc	17	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:3845167C>T	ENST00000463452.2	+	3	303	c.220C>T	c.(220-222)Cgc>Tgc	p.R74C	PGAP2_ENST00000278243.4_Missense_Mutation_p.R135C|PGAP2_ENST00000496834.2_5'UTR|PGAP2_ENST00000396993.4_Missense_Mutation_p.A27V|PGAP2_ENST00000532017.1_3'UTR|PGAP2_ENST00000396986.2_Missense_Mutation_p.R131C|AC090587.2_ENST00000507938.1_RNA|PGAP2_ENST00000465307.2_Missense_Mutation_p.A77V|PGAP2_ENST00000300730.6_Missense_Mutation_p.R131C|PGAP2_ENST00000493547.2_Missense_Mutation_p.R74C|PGAP2_ENST00000396991.2_Missense_Mutation_p.R135C|PGAP2_ENST00000479072.1_5'UTR	NM_001256240.1	NP_001243169.1	Q9UHJ9	PGAP2_HUMAN	post-GPI attachment to proteins 2	74					GPI anchor biosynthetic process (GO:0006506)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|signal transduction in response to DNA damage (GO:0042770)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.R135C(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11						GGTGCCCCAGCGCTACGTGTG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											72	71	71					11																	3845167		2201	4298	6499	3801743	SO:0001583	missense	27315			AF159615	CCDS7747.1, CCDS44523.1, CCDS58112.1, CCDS58113.1, CCDS73244.1, CCDS73245.1	11p15.4	2014-01-31			ENSG00000148985	ENSG00000148985			17893	protein-coding gene	gene with protein product	"FGF receptor activating protein 1", "cell wall biogenesis 43 N-terminal homolog (S. cerevisiae)"	615187	"mental retardation, non-syndromic, autosomal recessive, 21"	MRT21		10585768, 16407401, 23561846	Standard	NM_014489		Approved	FRAG1, CWH43-N	uc010qxw.3	Q9UHJ9	OTTHUMG00000012238	ENST00000463452.2:c.220C>T	11.37:g.3845167C>T	ENSP00000435223:p.Arg74Cys		3801743	E9PJG5|H7BXL9|Q6UC77|Q96G66|Q9UF01|Q9Y4N1	Missense_Mutation	SNP	ENST00000463452.2	37	CCDS58112.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.99|14.99	2.698868|2.698868	0.48307|0.48307	.|.	.|.	ENSG00000148985|ENSG00000148985	ENST00000396993;ENST00000532523;ENST00000465307|ENST00000396986;ENST00000300730;ENST00000396991;ENST00000464261;ENST00000493547;ENST00000278243;ENST00000463452;ENST00000469307	.|T;T;T;T;T;T;T;T	.|0.48836	.|0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.86|5.86	4.92|4.92	0.64577|0.64577	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65026|0.65026	0.2652|0.2652	M|M	0.71206|0.71206	2.165|2.165	0.80722|0.80722	D|D	1|1	D;P|P;P;B;D;P	0.56521|0.89917	0.976;0.783|0.566;0.501;0.424;1.0;0.501	B;B|B;B;B;D;B	0.42319|0.69307	0.383;0.134|0.099;0.086;0.099;0.963;0.086	T|T	0.67469|0.67469	-0.5663|-0.5663	8|10	0.87932|0.87932	D|D	0|0	-15.3272|-15.3272	12.419|12.419	0.55510|0.55510	0.1667:0.8332:0.0:0.0|0.1667:0.8332:0.0:0.0	.|.	77;27|131;74;135;74;74	B7Z2X5;A8MZF5|A8MYS5;Q9UHJ9-3;Q9UHJ9;E9PJG5;Q9UHJ9-2	.;.|.;.;PGAP2_HUMAN;.;.	V|C	27;92;77|131;131;135;104;74;135;74;74	.|ENSP00000380183:R131C;ENSP00000300730:R131C;ENSP00000380188:R135C;ENSP00000434088:R104C;ENSP00000431851:R74C;ENSP00000278243:R135C;ENSP00000435223:R74C;ENSP00000434507:R74C	ENSP00000380190:A27V|ENSP00000278243:R135C	A|R	+|+	2|1	0|0	PGAP2|PGAP2	3801743|3801743	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	2.540000|2.540000	0.45727|0.45727	2.766000|2.766000	0.95052|0.95052	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.647	PGAP2-049	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383260.1			T	3845167	C	T	3845167	3	4	77	1	0	0	0	0	1	0	0	0	11809	768	27	1	592	1	PGAP2	11	3845167	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	464413	3845167	131161349	646	22382										
OR51S1	119692	broad.mit.edu	37	chr11	4870128	4870128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaccatctgtagaaggcagGctgaggcagggacagtgtga	15	7	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:4870128G>A	ENST00000322101.2	-	1	386	c.311C>T	c.(310-312)gCc>gTc	p.A104V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A104V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TAGAAGGCAGGCTGAGGCAGG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	11											108	95	99					11																	4870128		2201	4298	6499	4826704	SO:0001583	missense	119692			AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.311C>T	11.37:g.4870128G>A	ENSP00000322754:p.Ala104Val		4826704	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.664490	0.47572	.	.	ENSG00000176922	ENST00000322101	T	0.03124	4.04	4.65	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.179400	0.26883	N	0.022004	T	0.05090	0.0136	L	0.58354	1.805	0.22591	N	0.998951	B	0.18968	0.032	B	0.21917	0.037	T	0.28427	-1.0044	10	0.62326	D	0.03	-4.9591	7.4092	0.27007	0.1982:0.0:0.8018:0.0	.	104	Q8NGJ8	O51S1_HUMAN	V	104	ENSP00000322754:A104V	ENSP00000322754:A104V	A	-	2	0	OR51S1	4826704	0.001000	0.12720	0.985000	0.45067	0.897000	0.52465	0.114000	0.15520	0.582000	0.29556	-0.222000	0.12452	GCC		0.537	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		A	4870128	G	A	4870128	3	1	77	1	0	0	0	0	1	0	0	0	11136	1203	42	3	663	3	OR51S1	11	4870128	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1024961	4870128	130136388	647	22383										
OR51G2	81282	broad.mit.edu	37	chr11	4936383	4936383	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggggagccacaataggggaAtcttttgagcataaaaggta	13	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:4936383A>C	ENST00000322013.3	-	1	539	c.511T>G	c.(511-513)Ttc>Gtc	p.F171V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F171V(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAATAGGGGAATCTTTTGAGC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	11											83	85	85					11																	4936383		2201	4298	6499	4892959	SO:0001583	missense	81282			AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.511T>G	11.37:g.4936383A>C	ENSP00000322593:p.Phe171Val		4892959	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.156392	0.57259	.	.	ENSG00000176893	ENST00000322013	T	0.00231	8.49	5.58	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.123056	0.37304	N	0.002141	T	0.00271	0.0008	L	0.33245	0.995	0.21762	N	0.999552	D	0.89917	1.0	D	0.91635	0.999	T	0.53201	-0.8472	10	0.66056	D	0.02	.	4.0603	0.09836	0.6838:0.0:0.1643:0.1519	.	171	Q8NGK0	O51G2_HUMAN	V	171	ENSP00000322593:F171V	ENSP00000322593:F171V	F	-	1	0	OR51G2	4892959	0.004000	0.15560	0.783000	0.31826	0.949000	0.60115	0.225000	0.17757	1.129000	0.42072	0.533000	0.62120	TTC		0.468	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		C	4936383	A	C	4936383	3	2	77	1	0	0	0	0	1	0	0	0	11130	101	4	4	437	4	OR51G2	11	4936383	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	66255	4936383	130070133	648	22384										
UBQLN3	50613	broad.mit.edu	37	chr11	5530484	5530484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagggacagaggcagctgggCactcattgcccatggcacgg	15	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:5530484C>T	ENST00000311659.4	-	2	452	c.305G>A	c.(304-306)tGc>tAc	p.C102Y	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	102								p.C102Y(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCAGCTGGGCACTCATTGCC	0.592																																					Ovarian(72;684 1260 12332 41642 52180)											1	Substitution - Missense(1)	large_intestine(1)	11											72	68	69					11																	5530484		2201	4297	6498	5487060	SO:0001583	missense	50613			AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.305G>A	11.37:g.5530484C>T	ENSP00000347997:p.Cys102Tyr		5487060	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351755	0.24512	.	.	ENSG00000175520	ENST00000311659;ENST00000445998	T;T	0.51325	1.28;0.71	5.3	3.39	0.38822	.	0.554792	0.16540	N	0.209966	T	0.49881	0.1583	M	0.68317	2.08	0.09310	N	0.999997	B	0.33198	0.401	B	0.38428	0.273	T	0.42749	-0.9433	10	0.44086	T	0.13	-34.3468	12.4819	0.55847	0.0:0.6776:0.3224:0.0	.	102	Q9H347	UBQL3_HUMAN	Y	102	ENSP00000347997:C102Y;ENSP00000412561:C102Y	ENSP00000347997:C102Y	C	-	2	0	UBQLN3	5487060	0.001000	0.12720	0.749000	0.31150	0.838000	0.47535	-0.025000	0.12413	0.700000	0.31782	0.484000	0.47621	TGC		0.592	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		T	5530484	C	T	5530484	3	4	77	1	0	0	0	0	1	0	0	0	16938	710	25	3	1666	3	UBQLN3	11	5530484	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	594101	5530484	129476032	649	22385										
DNHD1	144132	broad.mit.edu	37	chr11	6591491	6591491	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcagcttcagttttctacGggggtcctctgggggacact							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:6591491delG	ENST00000527990.2	+	39	12970	c.12970delG	c.(12970-12972)gggfs	p.G4325fs	DNHD1_ENST00000254579.6_Frame_Shift_Del_p.G4325fs			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4325					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.G4325fs*12(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGTTTTCTACGGGGGTCCTCT	0.562																																																1	Deletion - Frameshift(1)	large_intestine(1)	11											27	30	29					11																	6591491		1896	4106	6002	6548067	SO:0001589	frameshift_variant	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.12970delG	11.37:g.6591491delG	ENSP00000436180:p.Gly4325fs		6548067	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Frame_Shift_Del	DEL	ENST00000527990.2	37	CCDS44532.1																																																																																				0.562	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		-	6591491	G	-	6591491	7	5	77	1	0	1	0	1	0	0	0	0	4679	1116	39	0	13133	0	DNHD1	11	6591491	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1061007	6591491	128415025	650	22386										
DCHS1	8642	broad.mit.edu	37	chr11	6644734	6644734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gattgcatgcagagtggtcaCgagagtgcctggaggctgat	16	7	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:6644734C>T	ENST00000299441.3	-	21	8584	c.8173G>A	c.(8173-8175)Gtg>Atg	p.V2725M	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2725	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2725M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGAGTGGTCACGAGAGTGCCT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	11											46	41	43					11																	6644734		2200	4296	6496	6601310	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8173G>A	11.37:g.6644734C>T	ENSP00000299441:p.Val2725Met		6601310	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803217	0.50315	.	.	ENSG00000166341	ENST00000299441	T	0.59772	0.24	5.41	4.49	0.54785	Cadherin (3);Cadherin-like (1);	0.000000	0.35739	N	0.003019	T	0.69984	0.3172	M	0.75085	2.285	0.46725	D	0.999174	D	0.69078	0.997	D	0.63113	0.911	T	0.72414	-0.4301	10	0.62326	D	0.03	.	8.5815	0.33632	0.0:0.7654:0.1538:0.0808	.	2725	Q96JQ0	PCD16_HUMAN	M	2725	ENSP00000299441:V2725M	ENSP00000299441:V2725M	V	-	1	0	DCHS1	6601310	0.954000	0.32549	0.998000	0.56505	0.924000	0.55760	2.068000	0.41471	1.521000	0.48983	0.655000	0.94253	GTG		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6644734	C	T	6644734	3	4	77	1	0	0	0	0	1	0	0	0	4293	536	19	1	1727	1	DCHS1	11	6644734	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	53243	6644734	128361782	651	22387										
OR10A2	341276	broad.mit.edu	37	chr11	6891618	6891618	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatactcacattgctgctgcCatcctcaagatcccatcagc	5	15	3	1	rs61737577		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:6891618C>T	ENST00000307322.4	+	1	695	c.633C>T	c.(631-633)gcC>gcT	p.A211A		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A211A(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TTGCTGCTGCCATCCTCAAGA	0.448																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	11											277	220	239					11																	6891618		2201	4296	6497	6848194	SO:0001819	synonymous_variant	341276			BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.633C>T	11.37:g.6891618C>T			6848194	B2RNL9|Q6IFG9	Silent	SNP	ENST00000307322.4	37	CCDS31415.1																																																																																				0.448	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891618	C	T	6891618	2	4	77	1	0	0	0	0	0	0	0	1	10921	581	21	3		3	OR10A2	11	6891618	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	246884	6891618	128114898	652	22388										
BTBD10	84280	broad.mit.edu	37	chr11	13466592	13466592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgaatgtttataaagtttaCgaggtctactatgcaatttc	7	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:13466592C>T	ENST00000278174.5	-	2	325	c.80G>A	c.(79-81)cGt>cAt	p.R27H	BTBD10_ENST00000528120.1_Intron	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	27						nucleus (GO:0005634)		p.R27H(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		ATAAAGTTTACGAGGTCTACT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	11											157	160	159					11																	13466592		2200	4294	6494	13423168	SO:0001583	missense	84280			AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"BTB/POZ domain containing"	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.80G>A	11.37:g.13466592C>T	ENSP00000278174:p.Arg27His		13423168	B7Z228|Q86WG1	Missense_Mutation	SNP	ENST00000278174.5	37	CCDS7811.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010398	0.75046	.	.	ENSG00000148925	ENST00000278174;ENST00000529708;ENST00000526841	T	0.37058	1.22	5.57	5.57	0.84162	.	0.640975	0.15759	N	0.246022	T	0.48714	0.1515	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.52961	-0.8505	10	0.72032	D	0.01	1.1724	19.1455	0.93463	0.0:1.0:0.0:0.0	.	27	Q9BSF8	BTBDA_HUMAN	H	27	ENSP00000278174:R27H	ENSP00000278174:R27H	R	-	2	0	BTBD10	13423168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.504000	0.73704	2.612000	0.88384	0.655000	0.94253	CGT		0.408	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320		T	13466592	C	T	13466592	3	4	77	1	0	0	0	0	1	0	0	0	1541	536	19	1	1379	1	BTBD10	11	13466592	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6574974	13466592	121539924	653	22389										
FAR1	84188	broad.mit.edu	37	chr11	13733357	13733357	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagtggtctctttattgcggTaagtaaaccttttgatttat	8	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:13733357T>C	ENST00000354817.3	+	6	912		c.e6+2		FAR1_ENST00000527202.1_Splice_Site	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)	p.?(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						TTTATTGCGGTAAGTAAACCT	0.279																																																1	Unknown(1)	large_intestine(1)	11											62	68	66					11																	13733357		2200	4287	6487	13689933	SO:0001630	splice_region_variant	84188			AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	26222	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 1"		"male sterility domain containing 2"	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.768+2T>C	11.37:g.13733357T>C			13689933	D3DQW8|Q5CZA3	Splice_Site	SNP	ENST00000354817.3	37	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.053376	0.75960	.	.	ENSG00000197601	ENST00000354817;ENST00000532701;ENST00000355107	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2629	0.73637	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAR1	13689933	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.967000	0.87967	2.080000	0.62538	0.482000	0.46254	.		0.279	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228	Intron	C	13733357	T	C	13733357	5	2	77	1	0	0	0	0	0	0	1	0	5693	1652	57	4	788	4	FAR1	11	13733357	Splice_Site	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	266765	13733357	121273159	654	22390										
MRGPRX2	117194	broad.mit.edu	37	chr11	19076975	19076975	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctacaccagactgcttctCgacatctccggggtgccctg	9	16	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:19076975C>T	ENST00000329773.2	-	2	1062	c.975G>A	c.(973-975)tcG>tcA	p.S325S		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	325					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.S325S(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						GACTGCTTCTCGACATCTCCG	0.532																																					GBM(198;1966 2199 4849 37227 49954)											1	Substitution - coding silent(1)	large_intestine(1)	11											60	61	61					11																	19076975		2199	4293	6492	19033551	SO:0001819	synonymous_variant	117194				CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"GPCR / Class A : Orphans"	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.975G>A	11.37:g.19076975C>T			19033551	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Silent	SNP	ENST00000329773.2	37	CCDS7847.1																																																																																				0.532	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030		T	19076975	C	T	19076975	2	4	77	1	0	0	0	0	0	0	0	1	9797	871	31	1		1	MRGPRX2	11	19076975	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5343618	19076975	115929541	655	22391										
PAX6	5080	broad.mit.edu	37	chr11	31823109	31823109	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatgttctcaatgaacttacGcttggtatgttatcgttggt	10	6	1	1	rs121907928		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:31823109G>A	ENST00000379132.3	-	5	637	c.357C>T	c.(355-357)agC>agT	p.S119S	PAX6_ENST00000379107.2_Splice_Site_p.S133S|PAX6_ENST00000379123.5_Splice_Site_p.S119S|PAX6_ENST00000533156.1_5'Flank|PAX6_ENST00000379129.2_Splice_Site_p.S133S|PAX6_ENST00000419022.1_Splice_Site_p.S133S|PAX6_ENST00000241001.8_Splice_Site_p.S119S|PAX6_ENST00000379115.4_Splice_Site_p.S133S|PAX6_ENST00000379111.2_Splice_Site_p.S119S			P26367	PAX6_HUMAN	paired box 6	119	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.		S -> R (in AN). {ECO:0000269|PubMed:11553050, ECO:0000269|Ref.25}.		astrocyte differentiation (GO:0048708)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|cerebral cortex regionalization (GO:0021796)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|cornea development in camera-type eye (GO:0061303)|dorsal/ventral axis specification (GO:0009950)|embryonic camera-type eye morphogenesis (GO:0048596)|eye development (GO:0001654)|eye photoreceptor cell development (GO:0042462)|forebrain anterior/posterior pattern specification (GO:0021797)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain-midbrain boundary formation (GO:0021905)|glucose homeostasis (GO:0042593)|hindbrain development (GO:0030902)|iris morphogenesis (GO:0061072)|keratinocyte differentiation (GO:0030216)|lacrimal gland development (GO:0032808)|lens development in camera-type eye (GO:0002088)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|neuron migration (GO:0001764)|oligodendrocyte cell fate specification (GO:0021778)|organ morphogenesis (GO:0009887)|pancreatic A cell development (GO:0003322)|pituitary gland development (GO:0021983)|positive regulation of cell fate specification (GO:0042660)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of gene expression (GO:0010628)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to organelle (GO:0033365)|protein ubiquitination (GO:0016567)|regulation of cell migration (GO:0030334)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment (GO:0021918)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|salivary gland morphogenesis (GO:0007435)|signal transduction involved in regulation of gene expression (GO:0023019)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell differentiation (GO:0003309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.S133S(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)	35	Lung SC(675;0.225)					ATGAACTTACGCTTGGTATGT	0.512									Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation																																							1	Substitution - coding silent(1)	large_intestine(1)	11	GRCh37	CD082176|CI992573|CM013024|CM993965	PAX6	D|I|M	rs121907928						72	69	70					11																	31823109		2202	4299	6501	31779685	SO:0001630	splice_region_variant	5080	Familial Cancer Database	WAGR syndrome	AY707088	CCDS31451.1, CCDS31452.1	11p13	2014-09-17	2007-07-12		ENSG00000007372	ENSG00000007372		"Paired boxes", "Homeoboxes / PRD class"	8620	protein-coding gene	gene with protein product	"aniridia, keratitis"	607108	"paired box gene 6 (aniridia, keratitis)"	AN2		1302030	Standard	NM_001127612		Approved	D11S812E, AN, WAGR	uc021qfm.1	P26367	OTTHUMG00000041447	ENST00000379132.3:c.357+1C>T	11.37:g.31823109G>A			31779685	Q6N006|Q99413	Silent	SNP	ENST00000379132.3	37	CCDS31451.1																																																																																				0.512	PAX6-008	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000099293.4	NM_001604	Silent	A	31823109	G	A	31823109	5	1	77	1	0	0	0	0	0	0	1	0	11514	1101	38	1	943	1	PAX6	11	31823109	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	12746134	31823109	103183407	656	22392										
WT1	7490	broad.mit.edu	37	chr11	32450156	32450156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgtcccgtcgaaggtgaccGtgctgtaacctgcgggagcg	16	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:32450156G>A	ENST00000379079.2	-	2	293	c.20C>T	c.(19-21)aCg>aTg	p.T7M	WT1_ENST00000530998.1_Missense_Mutation_p.T7M|WT1_ENST00000332351.3_Missense_Mutation_p.T219M|WT1_ENST00000448076.3_Missense_Mutation_p.T219M	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	151					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.T151M(1)|p.?(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GAAGGTGACCGTGCTGTAACC	0.662			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|kidney(1)	11											72	55	61					11																	32450156		2202	4299	6501	32406732	SO:0001583	missense	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.20C>T	11.37:g.32450156G>A	ENSP00000368370:p.Thr7Met		32406732	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	37	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.459260	0.84317	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076	D;D;D;D;D	0.86030	-2.06;-2.06;-2.06;-2.06;-2.06	5.45	5.45	0.79879	Wilm&apos (1);s tumour protein, N-terminal (1);	0.078421	0.49305	U	0.000144	D	0.86598	0.5971	L	0.34521	1.04	0.44432	D	0.997352	D;P;D;D;D	0.64830	0.994;0.868;0.989;0.961;0.988	P;P;P;P;P	0.57283	0.763;0.696;0.763;0.751;0.817	D	0.87789	0.2617	10	0.72032	D	0.01	.	16.6448	0.85174	0.0:0.1296:0.8704:0.0	.	224;151;224;7;7	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	M	7;219;7;219;219	ENSP00000368370:T7M;ENSP00000331327:T219M;ENSP00000435307:T7M;ENSP00000415516:T219M;ENSP00000413452:T219M	ENSP00000331327:T219M	T	-	2	0	WT1	32406732	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.130000	0.77235	2.744000	0.94065	0.561000	0.74099	ACG		0.662	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		A	32450156	G	A	32450156	3	1	77	1	0	0	0	0	1	0	0	0	17448	1145	40	1	933	1	WT1	11	32450156	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	627047	32450156	102556360	657	22393										
LDLRAD3	143458	broad.mit.edu	37	chr11	36057709	36057709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtgcaacataccaggcaacTtcatgtgcagcaatggacgg	11	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:36057709T>C	ENST00000315571.5	+	2	124	c.103T>C	c.(103-105)Ttc>Ctc	p.F35L	LDLRAD3_ENST00000528989.1_Intron|LDLRAD3_ENST00000524419.1_Intron	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	35	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.F35L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				ACCAGGCAACTTCATGTGCAG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	11											108	96	100					11																	36057709		2202	4298	6500	36014285	SO:0001583	missense	143458			AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.103T>C	11.37:g.36057709T>C	ENSP00000318607:p.Phe35Leu		36014285	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	37	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.013228	0.93346	.	.	ENSG00000179241	ENST00000545142;ENST00000315571	D	0.98889	-5.21	5.1	5.1	0.69264	.	0.055518	0.64402	D	0.000001	D	0.98915	0.9632	M	0.75150	2.29	0.58432	D	0.999996	D	0.57257	0.979	D	0.74023	0.982	D	0.99787	1.1030	10	0.72032	D	0.01	.	14.3685	0.66823	0.0:0.0:0.0:1.0	.	35	Q86YD5	LRAD3_HUMAN	L	35	ENSP00000318607:F35L	ENSP00000318607:F35L	F	+	1	0	LDLRAD3	36014285	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.352000	0.79404	2.052000	0.61016	0.533000	0.62120	TTC		0.597	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		C	36057709	T	C	36057709	3	2	77	1	0	0	0	0	1	0	0	0	8729	1609	56	4	109	4	LDLRAD3	11	36057709	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	3607553	36057709	98948807	658	22394										
PRR5L	79899	broad.mit.edu	37	chr11	36484051	36484051	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcagcgtgcggcggcacaCggtggccaatgcccactcgg	16	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:36484051C>T	ENST00000378867.3	+	10	1227	c.872C>T	c.(871-873)aCg>aTg	p.T291M	PRR5L_ENST00000311599.5_Missense_Mutation_p.T218M|PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000530639.1_Missense_Mutation_p.T291M	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	291					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)	p.T291M(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						CGGCGGCACACGGTGGCCAAT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											37	36	36					11																	36484051		2202	4298	6500	36440627	SO:0001583	missense	79899				CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"protein observed with Rictor-2"	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.872C>T	11.37:g.36484051C>T	ENSP00000368144:p.Thr291Met		36440627	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	37	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825070	0.90955	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867	D;D;D	0.89270	-2.49;-2.49;-2.49	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.93983	0.8073	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.94483	0.7695	10	0.87932	D	0	-12.0987	18.8377	0.92169	0.0:1.0:0.0:0.0	.	163;291	Q6MZQ0-3;Q6MZQ0	.;PRR5L_HUMAN	M	291;218;291	ENSP00000435050:T291M;ENSP00000310103:T218M;ENSP00000368144:T291M	ENSP00000310103:T218M	T	+	2	0	PRR5L	36440627	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	7.142000	0.77339	2.451000	0.82905	0.555000	0.69702	ACG		0.642	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841		T	36484051	C	T	36484051	3	4	77	1	0	0	0	0	1	0	0	0	12636	536	19	1	908	1	PRR5L	11	36484051	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	426342	36484051	98522465	659	22395										
LRRC4C	57689	broad.mit.edu	37	chr11	40136090	40136090	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcgatagcaggcatgggcaGgtggctttccatgggtgtgt	16	8	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:40136090G>T	ENST00000278198.2	-	2	3716	c.1753C>A	c.(1753-1755)Ctg>Atg	p.L585M	LRRC4C_ENST00000527150.1_Missense_Mutation_p.L585M|LRRC4C_ENST00000528697.1_Missense_Mutation_p.L585M|LRRC4C_ENST00000530763.1_Missense_Mutation_p.L585M			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	585					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.L585M(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				GGCATGGGCAGGTGGCTTTCC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	11											226	219	221					11																	40136090		2203	4300	6503	40092666	SO:0001583	missense	57689			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1753C>A	11.37:g.40136090G>T	ENSP00000278198:p.Leu585Met		40092666	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	G	8.229	0.804314	0.16467	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	6.17	5.17	0.71159	.	0.000000	0.64402	D	0.000003	T	0.16642	0.0400	L	0.34521	1.04	0.46521	D	0.999088	P	0.38048	0.616	B	0.29598	0.104	T	0.03175	-1.1064	10	0.33141	T	0.24	.	4.7468	0.13042	0.2538:0.0:0.7462:0.0	.	585	Q9HCJ2	LRC4C_HUMAN	M	585	ENSP00000278198:L585M;ENSP00000436976:L585M;ENSP00000437132:L585M;ENSP00000434761:L585M	ENSP00000278198:L585M	L	-	1	2	LRRC4C	40092666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.457000	0.60088	2.941000	0.99782	0.655000	0.94253	CTG		0.438	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		T	40136090	G	T	40136090	3	4	77	1	0	0	0	0	1	0	0	0	9037	991	35	2	173	2	LRRC4C	11	40136090	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3652039	40136090	94870426	660	22396										
DGKZ	8525	broad.mit.edu	37	chr11	46393076	46393076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttcatgctgcagcagatcGaggagccgtgctcgctgggg	16	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:46393076G>A	ENST00000454345.1	+	9	1371	c.1246G>A	c.(1246-1248)Gag>Aag	p.E416K	DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Missense_Mutation_p.E232K|DGKZ_ENST00000343674.6_Missense_Mutation_p.E244K|DGKZ_ENST00000527911.1_Missense_Mutation_p.E228K|DGKZ_ENST00000421244.2_Missense_Mutation_p.E228K|DGKZ_ENST00000395574.3_Missense_Mutation_p.E194K|DGKZ_ENST00000456247.2_Missense_Mutation_p.E227K|DGKZ_ENST00000528615.1_Missense_Mutation_p.E6K|DGKZ_ENST00000318201.8_Missense_Mutation_p.E205K	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	416					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)	p.E244K(1)|p.E416K(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GCAGCAGATCGAGGAGCCGTG	0.672																																																2	Substitution - Missense(2)	large_intestine(2)	11											26	31	29					11																	46393076		2202	4299	6501	46349652	SO:0001583	missense	8525			U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1246G>A	11.37:g.46393076G>A	ENSP00000412178:p.Glu416Lys		46349652	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	.	.	.	.	.	.	.	.	.	.	G	35	5.414306	0.96092	.	.	ENSG00000149091	ENST00000343674;ENST00000528615;ENST00000395574;ENST00000532868;ENST00000527911;ENST00000456247;ENST00000421244;ENST00000318201;ENST00000454345	D;T;D;D;D;D;D;T;D	0.93307	-3.2;2.54;-3.2;-3.2;-3.2;-3.2;-3.2;2.67;-3.2	5.07	5.07	0.68467	Protein kinase C-like, phorbol ester/diacylglycerol binding (2);	0.000000	0.85682	D	0.000000	D	0.95382	0.8501	L	0.52759	1.655	0.80722	D	1	P;D;D;D;D;D;D;D;P	0.89917	0.955;0.979;0.998;0.999;0.978;0.985;1.0;0.994;0.956	B;P;D;D;P;P;D;P;P	0.72338	0.284;0.663;0.92;0.971;0.832;0.63;0.977;0.876;0.663	D	0.94182	0.7433	10	0.33141	T	0.24	.	18.8612	0.92273	0.0:0.0:1.0:0.0	.	205;193;171;228;416;227;228;194;244	B7Z2M9;B7Z6M3;B7Z8F6;E9PPW4;Q13574;Q13574-2;G3V0F6;A8MVN1;Q6ZVG7	.;.;.;.;DGKZ_HUMAN;.;.;.;.	K	244;6;194;193;228;227;228;205;416	ENSP00000343065:E244K;ENSP00000434719:E6K;ENSP00000378941:E194K;ENSP00000436273:E193K;ENSP00000436291:E228K;ENSP00000395684:E227K;ENSP00000391021:E228K;ENSP00000320340:E205K;ENSP00000412178:E416K	ENSP00000320340:E205K	E	+	1	0	DGKZ	46349652	1.000000	0.71417	0.955000	0.39395	0.723000	0.41478	9.863000	0.99569	2.536000	0.85505	0.561000	0.74099	GAG		0.672	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		A	46393076	G	A	46393076	3	1	77	1	0	0	0	0	1	0	0	0	4485	1059	37	1	1723	1	DGKZ	11	46393076	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6256986	46393076	88613440	661	22397										
MYBPC3	4607	broad.mit.edu	37	chr11	47372961	47372961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actgcctccgcgctgccagcGcaccttcactcctgcccgct	8	21	1	0	rs373638535		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:47372961G>A	ENST00000545968.1	-	2	175	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	MYBPC3_ENST00000399249.2_Missense_Mutation_p.R41C|MYBPC3_ENST00000256993.4_Missense_Mutation_p.R41C	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	41					cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.R41C(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		CGCTGCCAGCGCACCTTCACT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	11											33	37	36					11																	47372961		2188	4279	6467	47329537	SO:0001583	missense	4607			X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7551	protein-coding gene	gene with protein product		600958	"myosin-binding protein C, cardiac"	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.121C>T	11.37:g.47372961G>A	ENSP00000442795:p.Arg41Cys		47329537	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.780744	0.70222	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.68025	-0.3;-0.3;-0.3	4.27	4.27	0.50696	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71358	0.3330	M	0.63428	1.95	0.48975	D	0.999731	D	0.65815	0.995	P	0.54210	0.745	T	0.74559	-0.3625	9	0.72032	D	0.01	.	10.1606	0.42849	0.0:0.0:0.6467:0.3533	.	41	Q14896	MYPC3_HUMAN	C	41	ENSP00000442795:R41C;ENSP00000382193:R41C;ENSP00000256993:R41C	ENSP00000256993:R41C	R	-	1	0	MYBPC3	47329537	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	5.285000	0.65633	2.218000	0.71995	0.467000	0.42956	CGC		0.642	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			A	47372961	G	A	47372961	3	1	77	1	0	0	0	0	1	0	0	0	10043	1087	38	1	3828	1	MYBPC3	11	47372961	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	979885	47372961	87633555	662	22398										
SPI1	6688	broad.mit.edu	37	chr11	47381437	47381437	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgggatggggtggcaccatGggggtatcgaggacgtgcat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:47381437delG	ENST00000378538.3	-	3	519	c.297delC	c.(295-297)cccfs	p.P99fs	SPI1_ENST00000227163.4_Frame_Shift_Del_p.P100fs|SPI1_ENST00000533968.1_Frame_Shift_Del_p.P99fs|SPI1_ENST00000533030.1_Intron	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	99					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M94fs*86(1)		central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GTGGCACCATGGGGGTATCGA	0.672																																																1	Deletion - Frameshift(1)	large_intestine(1)	11											71	62	65					11																	47381437		2201	4298	6499	47338013	SO:0001589	frameshift_variant	6688			X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.297delC	11.37:g.47381437delG	ENSP00000367799:p.Pro99fs		47338013		Frame_Shift_Del	DEL	ENST00000378538.3	37	CCDS7933.2																																																																																				0.672	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		-	47381437	G	-	47381437	7	5	77	1	0	1	0	1	0	0	0	0	15088	1335	47	0	527	0	SPI1	11	47381437	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	8476	47381437	87625079	663	22399										
OR5M10	390167	broad.mit.edu	37	chr11	56344660	56344660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catgataagaggaggatcagCgcagtagaaatgattgattt	12	4	1	5	rs566095437		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:56344660C>T	ENST00000526812.2	-	1	603	c.538G>A	c.(538-540)Gct>Act	p.A180T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	180						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A180T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						GGAGGATCAGCGCAGTAGAAA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	11											80	78	79					11																	56344660		1951	4122	6073	56101236	SO:0001583	missense	390167			BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.538G>A	11.37:g.56344660C>T	ENSP00000436004:p.Ala180Thr		56101236	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.825281	0.50739	.	.	ENSG00000254834	ENST00000526812	T	0.00099	8.73	4.04	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00241	0.0007	L	0.54323	1.7	0.33657	D	0.609201	D	0.54047	0.964	P	0.48921	0.595	T	0.72981	-0.4126	9	0.72032	D	0.01	.	10.9012	0.47054	0.0:0.9054:0.0:0.0946	.	180	Q6IEU7	OR5MA_HUMAN	T	180	ENSP00000436004:A180T	ENSP00000436004:A180T	A	-	1	0	OR5M10	56101236	1.000000	0.71417	0.852000	0.33557	0.172000	0.22775	2.640000	0.46579	1.041000	0.40125	0.632000	0.83419	GCT		0.463	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		T	56344660	C	T	56344660	3	4	77	1	0	0	0	0	1	0	0	0	11204	768	27	1	413	1	OR5M10	11	56344660	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8963223	56344660	78661856	664	22400										
OR6Q1	219952	broad.mit.edu	37	chr11	57799254	57799254	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccatcaacttcaacaaggTggtatctgtcttctactctg	6	12	6	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:57799254T>A	ENST00000302622.3	+	1	853	c.830T>A	c.(829-831)gTg>gAg	p.V277E	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V277E(1)		biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				TTCAACAAGGTGGTATCTGTC	0.483																																																1	Substitution - Missense(1)	large_intestine(1)	11											153	142	146					11																	57799254		2201	4296	6497	57555830	SO:0001583	missense	219952			AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"GPCR / Class A : Olfactory receptors"	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.830T>A	11.37:g.57799254T>A	ENSP00000307734:p.Val277Glu		57555830	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.609470	0.66558	.	.	ENSG00000172381	ENST00000302622	T	0.00289	8.28	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34802	N	0.003661	T	0.00784	0.0026	M	0.88906	2.99	0.20926	N	0.99982	D	0.67145	0.996	D	0.71184	0.972	T	0.27839	-1.0062	10	0.87932	D	0	.	13.6468	0.62286	0.0:0.0:0.0:1.0	.	277	Q8NGQ2	OR6Q1_HUMAN	E	277	ENSP00000307734:V277E	ENSP00000307734:V277E	V	+	2	0	OR6Q1	57555830	0.527000	0.26306	1.000000	0.80357	0.957000	0.61999	4.358000	0.59442	1.860000	0.53959	0.533000	0.62120	GTG		0.483	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186		A	57799254	T	A	57799254	3	1	77	1	0	0	0	0	1	0	0	0	11239	1696	59	5	832	5	OR6Q1	11	57799254	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1454594	57799254	77207262	665	22401										
MS4A14	84689	broad.mit.edu	37	chr11	60182929	60182929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggttctgtttttcttgccttCggatgttactcaaaatagtg	9	7	3	0	rs550060785		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:60182929C>T	ENST00000300187.6	+	5	765	c.488C>T	c.(487-489)tCg>tTg	p.S163L	MS4A14_ENST00000531783.1_Missense_Mutation_p.S196L|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.S51L|MS4A14_ENST00000395005.2_Missense_Mutation_p.S146L	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	163						integral component of membrane (GO:0016021)		p.S163L(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						TTCTTGCCTTCGGATGTTACT	0.323													C|||	1	0.000199681	8e-04	0	5008	,	,		19155	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											92	91	92					11																	60182929		2202	4299	6501	59939505	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.488C>T	11.37:g.60182929C>T	ENSP00000300187:p.Ser163Leu		59939505	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.973452	0.53614	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.33438	1.43;2.61;1.41;2.96	3.73	-0.343	0.12632	.	7.709870	0.00357	N	0.000029	T	0.28333	0.0700	M	0.69823	2.125	0.39608	D	0.969837	P;P	0.45428	0.828;0.858	B;B	0.33339	0.1;0.162	T	0.45071	-0.9286	10	0.87932	D	0	-0.6102	2.9607	0.05891	0.1947:0.4764:0.0:0.3289	.	146;163	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	L	51;163;146;196	ENSP00000437222:S51L;ENSP00000300187:S163L;ENSP00000378453:S146L;ENSP00000433761:S196L	ENSP00000300187:S163L	S	+	2	0	MS4A14	59939505	0.089000	0.21612	0.612000	0.29024	0.714000	0.41099	0.121000	0.15667	-0.053000	0.13289	0.650000	0.86243	TCG		0.323	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			T	60182929	C	T	60182929	3	4	77	1	0	0	0	0	1	0	0	0	9888	893	31	1	506	1	MS4A14	11	60182929	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2383675	60182929	74823587	666	22402										
DDB1	1642	broad.mit.edu	37	chr11	61070162	61070162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaaaagacattgacaaactCgcccaggtggaaaagaccaa	9	10	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:61070162C>T	ENST00000301764.7	-	24	3401	c.3004G>A	c.(3004-3006)Gag>Aag	p.E1002K	DDB1_ENST00000451943.2_5'UTR|DDB1_ENST00000450997.2_Missense_Mutation_p.E313K|DDB1_ENST00000538470.1_Missense_Mutation_p.E49K	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	1002	Interaction with CDT1 and CUL4A.|WD repeat beta-propeller C.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.E1002K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						TTGACAAACTCGCCCAGGTGG	0.567								Nucleotide excision repair (NER)																																								1	Substitution - Missense(1)	large_intestine(1)	11											113	116	115					11																	61070162		2203	4299	6502	60826738	SO:0001583	missense	1642			AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.3004G>A	11.37:g.61070162C>T	ENSP00000301764:p.Glu1002Lys		60826738	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	37	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	C	36	5.649581	0.96714	.	.	ENSG00000167986	ENST00000301764;ENST00000450997;ENST00000538470;ENST00000539332	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.03	5.03	0.67393	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71434	0.3339	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.986	T	0.76271	-0.3020	10	0.72032	D	0.01	-20.5081	18.3488	0.90330	0.0:1.0:0.0:0.0	.	313;1002	B4DG00;Q16531	.;DDB1_HUMAN	K	1002;313;49;168	ENSP00000301764:E1002K;ENSP00000388705:E313K;ENSP00000441522:E49K;ENSP00000439787:E168K	ENSP00000301764:E1002K	E	-	1	0	DDB1	60826738	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.772000	0.85439	2.336000	0.79503	0.561000	0.74099	GAG		0.567	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		T	61070162	C	T	61070162	3	4	77	1	0	0	0	0	1	0	0	0	4329	893	31	1	434	1	DDB1	11	61070162	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	887233	61070162	73936354	667	22403										
DAK	26007	broad.mit.edu	37	chr11	61111695	61111695	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acacctgaatgccctggaccGggctgctggtgacggcgact	14	13	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:61111695G>A	ENST00000394900.3	+	13	1419	c.1190G>A	c.(1189-1191)cGg>cAg	p.R397Q		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	397	DhaL. {ECO:0000255|PROSITE- ProRule:PRU00813}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)	p.R397Q(1)		NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTGGACCGGGCTGCTGGT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	11											58	56	57					11																	61111695		2203	4299	6502	60868271	SO:0001583	missense	26007				CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1190G>A	11.37:g.61111695G>A	ENSP00000378360:p.Arg397Gln		60868271	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	37	CCDS8003.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.023043	0.93462	.	.	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.29917	1.56;1.55	6.08	6.08	0.98989	Dak phosphatase (2);	0.050022	0.85682	D	0.000000	T	0.48768	0.1518	L	0.42581	1.335	0.80722	D	1	D;P	0.89917	1.0;0.522	D;B	0.69307	0.963;0.056	T	0.17837	-1.0356	10	0.42905	T	0.14	-21.2664	18.4365	0.90648	0.0:0.0:1.0:0.0	.	397;397	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	Q	397;396	ENSP00000378360:R397Q;ENSP00000432539:R396Q	ENSP00000378360:R397Q	R	+	2	0	DAK	60868271	1.000000	0.71417	0.997000	0.53966	0.344000	0.29017	9.045000	0.93812	2.894000	0.99253	0.655000	0.94253	CGG		0.632	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		A	61111695	G	A	61111695	3	1	77	1	0	0	0	0	1	0	0	0	4234	1116	39	1	1236	1	DAK	11	61111695	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	41533	61111695	73894821	668	22404										
CPSF7	79869	broad.mit.edu	37	chr11	61188903	61188903	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aacggcagctcgtctattacGcaggccactgtaggtataca	10	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:61188903G>A	ENST00000394888.4	-	3	404	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	CPSF7_ENST00000448745.1_Missense_Mutation_p.R78C|CPSF7_ENST00000340437.4_Missense_Mutation_p.R121C|CPSF7_ENST00000439958.3_Missense_Mutation_p.R78C|CPSF7_ENST00000541963.1_Missense_Mutation_p.R78C	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	78					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R78C(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						CGTCTATTACGCAGGCCACTG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	11											146	125	132					11																	61188903		2202	4299	6501	60945479	SO:0001583	missense	79869				CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.232C>T	11.37:g.61188903G>A	ENSP00000378352:p.Arg78Cys		60945479	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	37	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464946	0.63513	.	.	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000477890;ENST00000539952;ENST00000544585;ENST00000413232;ENST00000541963;ENST00000450000;ENST00000449811;ENST00000413184	T;T;T	0.43688	0.94;0.94;0.94	5.68	4.75	0.60458	Nucleotide-binding, alpha-beta plait (1);	0.141721	0.50627	D	0.000116	T	0.56381	0.1981	L	0.43152	1.355	0.54753	D	0.999983	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;P;D;D	0.83275	0.996;0.875;0.994;0.994	T	0.54589	-0.8271	10	0.38643	T	0.18	.	15.5245	0.75890	0.0:0.0:0.8606:0.1394	.	78;78;121;78	F5H1W4;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	C	121;78;78;78;78;78;78;78;78;78;78;78	ENSP00000391359:R78C;ENSP00000392400:R78C;ENSP00000414295:R78C	ENSP00000345412:R121C	R	-	1	0	CPSF7	60945479	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	5.329000	0.65892	1.360000	0.45960	0.650000	0.86243	CGT		0.562	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		A	61188903	G	A	61188903	3	1	77	1	0	0	0	0	1	0	0	0	3836	1087	38	1	1211	1	CPSF7	11	61188903	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	77208	61188903	73817613	669	22405										
C11orf9	745	broad.mit.edu	37	chr11	61539074	61539074	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcaaacaggagcctgggacCgtgacagccctgcctctgca	11	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:61539074C>T	ENST00000278836.5	+	6	939	c.843C>T	c.(841-843)acC>acT	p.T281T	MYRF_ENST00000327797.1_5'Flank|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Silent_p.T272T	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	281	Pro-rich.				central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T272T(1)									AGCCTGGGACCGTGACAGCCC	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	11											88	100	96					11																	61539074		2202	4299	6501	61295650	SO:0001819	synonymous_variant	745				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.843C>T	11.37:g.61539074C>T			61295650	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																				0.632	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		T	61539074	C	T	61539074	2	4	77	1	0	0	0	0	0	0	0	1	1675	639	23	1		1	C11orf9	11	61539074	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	350171	61539074	73467442	670	22406										
FADS3	3995	broad.mit.edu	37	chr11	61643644	61643644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtgaaaagtgagggctccaCgttgcaggtggctgccagct	16	9	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:61643644C>T	ENST00000278829.2	-	10	1251	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	FADS3_ENST00000525588.1_Missense_Mutation_p.V339M|FADS3_ENST00000527697.1_Missense_Mutation_p.V243M|FADS3_ENST00000540820.1_3'UTR	NM_021727.3	NP_068373.1	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	367					unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717)	p.V367M(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GAGGGCTCCACGTTGCAGGTG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	11											32	31	31					11																	61643644		2199	4295	6494	61400220	SO:0001583	missense	3995				CCDS8013.1	11q12-q13.1	2013-01-25			ENSG00000221968	ENSG00000221968	1.14.19.3	"Fatty acid desaturases"	3576	protein-coding gene	gene with protein product	"delta-9-desaturase"	606150		LLCDL3			Standard	NM_021727		Approved	CYB5RP	uc001nsm.3	Q9Y5Q0	OTTHUMG00000167500	ENST00000278829.2:c.1099G>A	11.37:g.61643644C>T	ENSP00000278829:p.Val367Met		61400220	O60426	Missense_Mutation	SNP	ENST00000278829.2	37	CCDS8013.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.91|16.91	3.252988|3.252988	0.59212|0.59212	.|.	.|.	ENSG00000221968|ENSG00000221968	ENST00000525094|ENST00000527697;ENST00000278829;ENST00000525588	.|T;T;T	.|0.18502	.|2.21;2.21;2.21	5.22|5.22	5.22|5.22	0.72569|0.72569	.|Fatty acid desaturase, type 1 (1);	.|.	.|.	.|.	.|.	T|T	0.41419|0.41419	0.1158|0.1158	M|M	0.80422|0.80422	2.495|2.495	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.74674	.|0.979;0.984	T|T	0.30387|0.30387	-0.9980|-0.9980	5|9	.|0.56958	.|D	.|0.05	-8.6162|-8.6162	10.941|10.941	0.47273|0.47273	0.0:0.9139:0.0:0.0861|0.0:0.9139:0.0:0.0861	.|.	.|243;367	.|E9PKP8;Q9Y5Q0	.|.;FADS3_HUMAN	H|M	37|243;367;339	.|ENSP00000431533:V243M;ENSP00000278829:V367M;ENSP00000432206:V339M	.|ENSP00000278829:V367M	R|V	-|-	2|1	0|0	FADS3|FADS3	61400220|61400220	0.843000|0.843000	0.29541|0.29541	1.000000|1.000000	0.80357|0.80357	0.513000|0.513000	0.34164|0.34164	0.870000|0.870000	0.28010|0.28010	2.442000|2.442000	0.82660|0.82660	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.667	FADS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394836.1			T	61643644	C	T	61643644	3	4	77	1	0	0	0	0	1	0	0	0	5383	536	19	1	250	1	FADS3	11	61643644	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	104570	61643644	73362872	671	22407										
INTS5	80789	broad.mit.edu	37	chr11	62414874	62414874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtgggtcgtgtcagggtggCgagaggcttcccaatggccc	17	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:62414874C>T	ENST00000330574.2	-	2	2730	c.2678G>A	c.(2677-2679)cGc>cAc	p.R893H	GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000346178.4_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	893					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.R893H(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						GTCAGGGTGGCGAGAGGCTTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											64	68	67					11																	62414874		2202	4299	6501	62171450	SO:0001583	missense	80789			AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"KIAA1698"	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.2678G>A	11.37:g.62414874C>T	ENSP00000327889:p.Arg893His		62171450	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.326968	0.81690	.	.	ENSG00000185085	ENST00000330574	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	L	0.50333	1.59	0.49130	D	0.99975	D	0.89917	1.0	D	0.76071	0.987	T	0.76366	-0.2985	9	0.87932	D	0	.	17.8981	0.88895	0.0:1.0:0.0:0.0	.	893	Q6P9B9	INT5_HUMAN	H	893	.	ENSP00000327889:R893H	R	-	2	0	INTS5	62171450	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	7.430000	0.80321	2.823000	0.97156	0.650000	0.86243	CGC		0.647	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		T	62414874	C	T	62414874	3	4	77	1	0	0	0	0	1	0	0	0	7802	768	27	1	385	1	INTS5	11	62414874	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	771230	62414874	72591642	672	22408										
SLC22A6	9356	broad.mit.edu	37	chr11	62748503	62748503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtggcggagggtggggcagcGcagcagctccatggccgatg	20	10	0	0	rs150409056	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:62748503G>A	ENST00000377871.3	-	6	1257	c.991C>T	c.(991-993)Cgc>Tgc	p.R331C	SLC22A6_ENST00000458333.2_Missense_Mutation_p.R331C|SLC22A6_ENST00000421062.2_Missense_Mutation_p.R331C|SLC22A6_ENST00000360421.4_Missense_Mutation_p.R331C|SLC22A6_ENST00000537349.1_5'UTR	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	331					alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R331C(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GTGGGGCAGCGCAGCAGCTCC	0.652													G|||	3	0.000599042	8e-04	0	5008	,	,		16537	0		0	False		,,,				2504	0.002															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	11											52	47	49					11																	62748503		2201	4298	6499	62505079	SO:0001583	missense	9356			AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901		"Solute carriers"	10970	protein-coding gene	gene with protein product		607582				9762842, 9950961	Standard	NM_004790		Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000377871.3:c.991C>T	11.37:g.62748503G>A	ENSP00000367102:p.Arg331Cys		62505079	A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	Missense_Mutation	SNP	ENST00000377871.3	37	CCDS31591.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293500	0.80914	.	.	ENSG00000197901	ENST00000360421;ENST00000394651;ENST00000377871;ENST00000458333;ENST00000421062	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.01	5.01	0.66863	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.056000	0.64402	D	0.000002	T	0.80237	0.4586	M	0.84511	2.7	0.58432	D	0.999991	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.998	T	0.82337	-0.0507	10	0.56958	D	0.05	.	13.6808	0.62484	0.0:0.0:1.0:0.0	.	331;331;331;331	Q4U2R8-4;Q4U2R8-3;Q4U2R8;Q4U2R8-2	.;.;S22A6_HUMAN;.	C	331;310;331;331;331	ENSP00000353597:R331C;ENSP00000367102:R331C;ENSP00000396401:R331C;ENSP00000404441:R331C	ENSP00000353597:R331C	R	-	1	0	SLC22A6	62505079	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.061000	0.71148	2.584000	0.87258	0.467000	0.42956	CGC		0.652	SLC22A6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396186.1	NM_004790		A	62748503	G	A	62748503	3	1	77	1	0	0	0	0	1	0	0	0	14495	1087	38	1	720	1	SLC22A6	11	62748503	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	333629	62748503	72258013	673	22409										
SLC22A10	387775	broad.mit.edu	37	chr11	63065156	63065156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagactggcaaaccctgcacGtggtggcgtctgtacctttc	12	12	1	1	rs200940829	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:63065156G>A	ENST00000332793.6	+	4	789	c.787G>A	c.(787-789)Gtg>Atg	p.V263M	SLC22A10_ENST00000544661.1_Missense_Mutation_p.V108M|SLC22A10_ENST00000535888.1_Missense_Mutation_p.V53M|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000525620.1_3'UTR	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	263						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.V263M(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	AACCCTGCACGTGGTGGCGTC	0.458													G|||	17	0.00339457	0.0098	0.0014	5008	,	,		17597	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	11						G	MET/VAL	31,3873		0,31,1921	163	154	157		787	1	0.1	11		157	1,8265		0,1,4132	yes	missense	SLC22A10	NM_001039752.3	21	0,32,6053	AA,AG,GG		0.0121,0.7941,0.2629	possibly-damaging	263/542	63065156	32,12138	1952	4133	6085	62821732	SO:0001583	missense	387775			AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.787G>A	11.37:g.63065156G>A	ENSP00000327569:p.Val263Met		62821732	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.30	1.897059	0.33535	0.007941	1.21E-4	ENSG00000184999	ENST00000535888;ENST00000544661;ENST00000332793	T;T;T	0.59502	0.26;0.26;0.26	3.0	1.02	0.19986	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.208186	0.32147	U	0.006506	T	0.35799	0.0944	L	0.39514	1.22	0.24426	N	0.994593	P	0.51147	0.942	B	0.42462	0.388	T	0.34527	-0.9825	10	0.62326	D	0.03	.	6.986	0.24729	0.1879:0.6096:0.2025:0.0	.	263	Q63ZE4	S22AA_HUMAN	M	53;108;263	ENSP00000444602:V53M;ENSP00000445667:V108M;ENSP00000327569:V263M	ENSP00000327569:V263M	V	+	1	0	SLC22A10	62821732	0.996000	0.38824	0.058000	0.19502	0.215000	0.24574	0.470000	0.22084	0.154000	0.19237	-0.576000	0.04144	GTG		0.458	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		A	63065156	G	A	63065156	3	1	77	1	0	0	0	0	1	0	0	0	14478	1145	40	1	801	1	SLC22A10	11	63065156	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	316653	63065156	71941360	674	22410										
FLRT1	28992	broad.mit.edu	37	chr11	63883856	63883856	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gactggctgttcctctgctaCgggctcatcgccttcctgac	10	15	2	1	rs146061545	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:63883856C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Silent_p.Y39Y|RP11-21A7A.3_ENST00000543817.1_RNA	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.Y39Y(1)		breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TCCTCTGCTACGGGCTCATCG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	11						C	,	0,4402		0,0,2201	125	69	88		117,	0.4	1	11	dbSNP_134	88	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	,	39/675,	63883856	2,12994	2201	4297	6498	63640432	SO:0001627	intron_variant	23769			AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34854G>A	11.37:g.63883856C>T			63640432	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																				0.652	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		T	63883856	C	T	63883856	1	4	77	0	1	0	0	0	0	0	0	0	5957	547	19	1		1	FLRT1	11	63883856	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	818700	63883856	71122660	675	22411										
ATG2A	23130	broad.mit.edu	37	chr11	64678613	64678613	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcatcaaactcggtgaaaaAgtgcgtggcgaggtcaggtg	16	7	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:64678613A>G	ENST00000377264.3	-	10	1475	c.1363T>C	c.(1363-1365)Ttt>Ctt	p.F455L	ATG2A_ENST00000421419.2_Missense_Mutation_p.F455L	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	455					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.F455L(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						TCGGTGAAAAAGTGCGTGGCG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											113	104	107					11																	64678613		2201	4297	6498	64435189	SO:0001583	missense	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1363T>C	11.37:g.64678613A>G	ENSP00000366475:p.Phe455Leu		64435189	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	29.7|29.7	5.028134|5.028134	0.93518|0.93518	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000421419;ENST00000377264|ENST00000418259	T;T|.	0.20738|.	2.05;2.05|.	4.82|4.82	4.82|4.82	0.62117|0.62117	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64371|0.64371	0.2592|0.2592	L|L	0.59436|0.59436	1.845|1.845	0.51482|0.51482	D|D	0.999928|0.999928	D|.	0.69078|.	0.997|.	D|.	0.70716|.	0.97|.	T|T	0.63314|0.63314	-0.6665|-0.6665	10|5	0.87932|.	D|.	0|.	.|.	12.677|12.677	0.56899|0.56899	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	455|.	Q2TAZ0|.	ATG2A_HUMAN|.	L|P	455|256	ENSP00000410522:F455L;ENSP00000366475:F455L|.	ENSP00000366475:F455L|.	F|L	-|-	1|2	0|0	ATG2A|ATG2A	64435189|64435189	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.923000|0.923000	0.55619|0.55619	7.056000|7.056000	0.76662|0.76662	2.163000|2.163000	0.67991|0.67991	0.459000|0.459000	0.35465|0.35465	TTT|CTT		0.602	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		G	64678613	A	G	64678613	3	3	77	1	0	0	0	0	1	0	0	0	1094	72	3	4	4581	4	ATG2A	11	64678613	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	794757	64678613	70327903	676	22412										
FAM89B	23625	broad.mit.edu	37	chr11	65340985	65340985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagctcctacccaccggatgCgggcctgtctgacgacgagg	13	15	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:65340985C>T	ENST00000530349.1	+	2	585	c.443C>T	c.(442-444)gCg>gTg	p.A148V	FAM89B_ENST00000316409.2_Missense_Mutation_p.A135V|FAM89B_ENST00000449319.2_Silent_p.C151C|EHBP1L1_ENST00000309295.4_5'Flank			Q8N5H3	FA89B_HUMAN	family with sequence similarity 89, member B	148					negative regulation of SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)	transcription corepressor binding (GO:0001222)	p.A135V(1)		large_intestine(1)|urinary_tract(2)	3						CCACCGGATGCGGGCCTGTCT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11											78	67	71					11																	65340985		2201	4297	6498	65097561	SO:0001583	missense	23625			AF052151	CCDS8105.1, CCDS44648.1, CCDS53662.1	11q23	2007-12-04				ENSG00000176973			16708	protein-coding gene	gene with protein product						9525630, 10512749	Standard	NM_152832		Approved		uc001oel.2	Q8N5H3		ENST00000530349.1:c.443C>T	11.37:g.65340985C>T	ENSP00000431459:p.Ala148Val		65097561	E9PB01|E9PL72|Q6PJ27	Missense_Mutation	SNP	ENST00000530349.1	37	CCDS53662.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402365	0.42613	.	.	ENSG00000173465;ENSG00000176973;ENSG00000176973;ENSG00000176973	ENST00000526433;ENST00000316409;ENST00000530349;ENST00000377088	.	.	.	4.78	3.84	0.44239	.	0.232511	0.22244	N	0.062653	T	0.37544	0.1007	N	0.22421	0.69	0.33896	D	0.637977	B;B	0.22604	0.072;0.072	B;B	0.19666	0.026;0.026	T	0.48422	-0.9037	9	0.48119	T	0.1	0.2229	10.6505	0.45645	0.0:0.806:0.194:0.0	.	135;148	Q8N5H3;E9PL72	FA89B_HUMAN;.	V	104;135;148;121	.	ENSP00000314829:A135V	A	+	2	0	SSSCA1;FAM89B	65097561	0.975000	0.34042	0.986000	0.45419	0.516000	0.34256	1.928000	0.40104	1.203000	0.43233	0.561000	0.74099	GCG		0.622	FAM89B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390095.1	NM_152832		T	65340985	C	T	65340985	3	4	77	1	0	0	0	0	1	0	0	0	5667	777	27	1	459	1	FAM89B	11	65340985	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	662372	65340985	69665531	677	22413										
CNIH2	254263	broad.mit.edu	37	chr11	66050206	66050206	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttccttcccccaacagcgCgagcgtttaaaaaacatcga	6	13	0	0	rs374304001		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66050206C>T	ENST00000311445.6	+	3	411	c.153C>T	c.(151-153)cgC>cgT	p.R51R	YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000530519.1_3'UTR|CNIH2_ENST00000528852.1_Silent_p.R51R	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	51					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.R51R(1)		endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						CCCAACAGCGCGAGCGTTTAA	0.652											OREG0021100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	11						C		0,4400		0,0,2200	31	31	31		153	0.3	1	11		31	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous	CNIH2	NM_182553.1		0,1,6493	TT,TC,CC		0.0116,0.0,0.0077		51/161	66050206	1,12987	2200	4294	6494	65806782	SO:0001819	synonymous_variant	254263			BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.153C>T	11.37:g.66050206C>T		1088	65806782		Silent	SNP	ENST00000311445.6	37	CCDS8131.1																																																																																				0.652	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		T	66050206	C	T	66050206	2	4	77	1	0	0	0	0	0	0	0	1	3609	755	27	1		1	CNIH2	11	66050206	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	709221	66050206	68956310	678	22414										
NPAS4	266743	broad.mit.edu	37	chr11	66188763	66188763	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcggacaaggtccggctgtCctacctgcacatcatgagcc	11	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66188763C>T	ENST00000311034.2	+	1	289	c.113C>T	c.(112-114)tCc>tTc	p.S38F		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	38	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.S38F(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GTCCGGCTGTCCTACCTGCAC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											79	63	68					11																	66188763		2200	4295	6495	65945339	SO:0001583	missense	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.113C>T	11.37:g.66188763C>T	ENSP00000311196:p.Ser38Phe		65945339	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584763	0.86748	.	.	ENSG00000174576	ENST00000311034	T	0.51325	0.71	5.19	5.19	0.71726	Helix-loop-helix DNA-binding (1);	0.257683	0.28527	N	0.015030	T	0.35913	0.0948	N	0.08118	0	0.80722	D	1	P	0.36990	0.577	B	0.42112	0.376	T	0.40608	-0.9554	10	0.56958	D	0.05	-21.2056	16.2538	0.82501	0.0:1.0:0.0:0.0	.	38	Q8IUM7	NPAS4_HUMAN	F	38	ENSP00000311196:S38F	ENSP00000311196:S38F	S	+	2	0	NPAS4	65945339	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.181000	0.77682	2.691000	0.91804	0.563000	0.77884	TCC		0.647	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		T	66188763	C	T	66188763	3	4	77	1	0	0	0	0	1	0	0	0	10596	855	30	3	115	3	NPAS4	11	66188763	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	138557	66188763	68817753	679	22415										
BBS1	582	broad.mit.edu	37	chr11	66298370	66298370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaccctctccataggttcaGggccttggccccacctttaa	7	17	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66298370G>T	ENST00000318312.7	+	15	1530	c.1479G>T	c.(1477-1479)caG>caT	p.Q493H	BBS1_ENST00000393994.2_Missense_Mutation_p.Q364H|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.Q530H|BBS1_ENST00000455748.2_Missense_Mutation_p.Q396H|ZDHHC24_ENST00000526986.1_Intron	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	493					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)	p.Q493H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						CATAGGTTCAGGGCCTTGGCC	0.597									Bardet-Biedl syndrome																												GBM(152;173 2612 9770 10137)											1	Substitution - Missense(1)	large_intestine(1)	11											178	151	160					11																	66298370		2200	4295	6495	66054946	SO:0001583	missense	582	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1479G>T	11.37:g.66298370G>T	ENSP00000317469:p.Gln493His		66054946	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399952	0.62177	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748;ENST00000393994	D;D;D;D	0.97209	-4.22;-4.29;-4.09;-4.06	4.59	1.68	0.24146	.	.	.	.	.	D	0.97682	0.9240	M	0.76838	2.35	0.80722	D	1	D;D;P;D;D;D	0.89917	0.962;1.0;0.544;1.0;1.0;1.0	P;D;B;D;D;D	0.76575	0.517;0.98;0.434;0.987;0.988;0.988	D	0.96246	0.9179	9	0.72032	D	0.01	.	7.5269	0.27660	0.2945:0.0:0.7055:0.0	.	168;396;364;381;493;530	B4DH75;E7EQH1;Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;.;.;BBS1_HUMAN;.	H	530;493;396;364	ENSP00000398526:Q530H;ENSP00000317469:Q493H;ENSP00000405764:Q396H;ENSP00000377563:Q364H	ENSP00000317469:Q493H	Q	+	3	2	BBS1;CTD-3074O7.11	66054946	1.000000	0.71417	0.997000	0.53966	0.953000	0.61014	3.690000	0.54713	0.187000	0.20147	0.650000	0.86243	CAG		0.597	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			T	66298370	G	T	66298370	3	4	77	1	0	0	0	0	1	0	0	0	1336	991	35	2	1537	2	BBS1	11	66298370	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	109607	66298370	68708146	680	22416										
CTSF	8722	broad.mit.edu	37	chr11	66332098	66332098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagaggggccggagagggcGggagatcccgtggcggtaaa	21	8	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66332098G>A	ENST00000310325.5	-	11	1361	c.1252C>T	c.(1252-1254)Cgc>Tgc	p.R418C	ACTN3_ENST00000502692.1_RNA|CTSF_ENST00000533168.1_5'Flank|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	418					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)	p.R418C(1)		endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CGGAGAGGGCGGGAGATCCCG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											25	29	27					11																	66332098		2200	4293	6493	66088674	SO:0001583	missense	8722			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1252C>T	11.37:g.66332098G>A	ENSP00000310832:p.Arg418Cys		66088674	B2R964|O95240|Q9NSU4|Q9UKQ5	Missense_Mutation	SNP	ENST00000310325.5	37	CCDS8144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.54|19.54	3.847269|3.847269	0.71603|0.71603	.|.	.|.	ENSG00000174080|ENSG00000174080	ENST00000524994|ENST00000310325	.|D	.|0.87412	.|-2.25	4.32|4.32	4.32|4.32	0.51571|0.51571	.|Peptidase C1A, papain C-terminal (2);	.|0.053861	.|0.64402	.|D	.|0.000001	D|D	0.83385|0.83385	0.5243|0.5243	N|N	0.05230|0.05230	-0.09|-0.09	0.42665|0.42665	D|D	0.993497|0.993497	.|D	.|0.69078	.|0.997	.|P	.|0.60068	.|0.868	D|D	0.85687|0.85687	0.1304|0.1304	5|10	.|0.42905	.|T	.|0.14	.|.	14.3648|14.3648	0.66799|0.66799	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|418	.|Q9UBX1	.|CATF_HUMAN	L|C	265|418	.|ENSP00000310832:R418C	.|ENSP00000310832:R418C	P|R	-|-	2|1	0|0	CTSF|CTSF	66088674|66088674	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.770000|7.770000	0.85390|0.85390	2.247000|2.247000	0.74100|0.74100	0.462000|0.462000	0.41574|0.41574	CCG|CGC		0.627	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		A	66332098	G	A	66332098	3	1	77	1	0	0	0	0	1	0	0	0	4040	1116	39	1	214	1	CTSF	11	66332098	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	33728	66332098	68674418	681	22417										
SPTBN2	6712	broad.mit.edu	37	chr11	66458979	66458979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagcaggtcagcccaggcctCgttgagactgtccttccact	10	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66458979C>T	ENST00000533211.1	-	27	5672	c.5341G>A	c.(5341-5343)Gag>Aag	p.E1781K	SPTBN2_ENST00000529997.1_Missense_Mutation_p.E1781K|SPTBN2_ENST00000309996.2_Missense_Mutation_p.E1781K			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1781					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.E1781K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCCCAGGCCTCGTTGAGACTG	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	11											52	41	45					11																	66458979		2200	4295	6495	66215555	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.5341G>A	11.37:g.66458979C>T	ENSP00000432568:p.Glu1781Lys		66215555	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	36	5.636449	0.96693	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.67865	-0.29;-0.29;-0.29	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	D	0.84710	0.5532	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.85906	0.1437	10	0.36615	T	0.2	.	16.7391	0.85454	0.0:1.0:0.0:0.0	.	1781	O15020	SPTN2_HUMAN	K	1781	ENSP00000432568:E1781K;ENSP00000311489:E1781K;ENSP00000433593:E1781K	ENSP00000311489:E1781K	E	-	1	0	SPTBN2	66215555	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.591000	0.82666	2.480000	0.83734	0.655000	0.94253	GAG		0.672	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66458979	C	T	66458979	3	4	77	1	0	0	0	0	1	0	0	0	15159	893	31	1	1879	1	SPTBN2	11	66458979	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	126881	66458979	68547537	682	22418										
SPTBN2	6712	broad.mit.edu	37	chr11	66466466	66466466	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccccagggagcctcacctcGtgacaatcttgcaggaaatg	11	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66466466G>A	ENST00000533211.1	-	19	4195	c.3864C>T	c.(3862-3864)caC>caT	p.H1288H	SPTBN2_ENST00000529997.1_Silent_p.H1288H|SPTBN2_ENST00000309996.2_Silent_p.H1288H			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1288					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.H1288H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCCTCACCTCGTGACAATCTT	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	11											69	68	68					11																	66466466		2200	4295	6495	66223042	SO:0001819	synonymous_variant	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.3864C>T	11.37:g.66466466G>A			66223042	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																				0.572	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66466466	G	A	66466466	2	1	77	1	0	0	0	0	0	0	0	1	15159	1136	40	1		1	SPTBN2	11	66466466	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7487	66466466	68540050	683	22419										
PC	5091	broad.mit.edu	37	chr11	66617300	66617300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agggagggaggctccaggccGcccctccacccttggcaggt	15	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66617300G>A	ENST00000393958.2	-	20	3022	c.2929C>T	c.(2929-2931)Cgg>Tgg	p.R977W	PC_ENST00000393960.1_Missense_Mutation_p.R977W|PC_ENST00000528224.1_5'UTR|PC_ENST00000393955.2_Missense_Mutation_p.R977W|PC_ENST00000529047.1_Missense_Mutation_p.R97W	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	977					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.R977W(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GCTCCAGGCCGCCCCTCCACC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											60	56	57					11																	66617300		2200	4295	6495	66373876	SO:0001583	missense	5091			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.2929C>T	11.37:g.66617300G>A	ENSP00000377530:p.Arg977Trp		66373876	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.898591	0.52227	.	.	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	D;D;D;D	0.97598	-2.21;-4.45;-4.45;-4.45	5.01	3.09	0.35607	Carboxylase, conserved domain (1);	0.060430	0.64402	D	0.000004	D	0.99007	0.9661	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98406	1.0570	10	0.87932	D	0	-22.3326	11.1786	0.48614	0.0:0.0:0.5196:0.4804	.	977	P11498	PYC_HUMAN	W	97;977;977;977	ENSP00000435905:R97W;ENSP00000377527:R977W;ENSP00000377530:R977W;ENSP00000377532:R977W	ENSP00000377527:R977W	R	-	1	2	PC	66373876	0.996000	0.38824	1.000000	0.80357	0.639000	0.38242	2.192000	0.42649	0.657000	0.30906	0.462000	0.41574	CGG		0.647	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		A	66617300	G	A	66617300	3	1	77	1	0	0	0	0	1	0	0	0	11528	1086	38	1	619	1	PC	11	66617300	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	150834	66617300	68389216	684	22420										
PC	5091	broad.mit.edu	37	chr11	66620250	66620250	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagggacaacggggtccgtgGggctggggctggccttgacg	20	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66620250G>T	ENST00000393958.2	-	13	1664	c.1571C>A	c.(1570-1572)cCc>cAc	p.P524H	PC_ENST00000393960.1_Missense_Mutation_p.P524H|PC_ENST00000528224.1_5'Flank|PC_ENST00000393955.2_Missense_Mutation_p.P524H|PC_ENST00000529047.1_5'Flank	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	524					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.P524H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GGGGTCCGTGGGGCTGGGGCT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											76	74	75					11																	66620250		2200	4295	6495	66376826	SO:0001583	missense	5091			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.1571C>A	11.37:g.66620250G>T	ENSP00000377530:p.Pro524His		66376826	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.825178	0.32237	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960	D;D;D	0.95724	-3.79;-3.79;-3.79	5.53	5.53	0.82687	.	0.233244	0.45361	D	0.000370	D	0.92496	0.7617	L	0.43152	1.355	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	D	0.88826	0.3302	10	0.17832	T	0.49	-18.3137	16.9874	0.86344	0.0:0.0:1.0:0.0	.	524	P11498	PYC_HUMAN	H	524	ENSP00000377527:P524H;ENSP00000377530:P524H;ENSP00000377532:P524H	ENSP00000377527:P524H	P	-	2	0	PC	66376826	1.000000	0.71417	0.959000	0.39883	0.978000	0.69477	5.575000	0.67430	2.605000	0.88082	0.655000	0.94253	CCC		0.627	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66620250	G	T	66620250	3	4	77	1	0	0	0	0	1	0	0	0	11528	1232	43	2	2005	2	PC	11	66620250	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2950	66620250	68386266	685	22421										
PC	5091	broad.mit.edu	37	chr11	66638919	66638919	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctcgctcagagaggaacccGtagccagggtgcactgcatc	13	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:66638919G>A	ENST00000393958.2	-	5	447	c.354C>T	c.(352-354)taC>taT	p.Y118Y	PC_ENST00000524491.1_Silent_p.Y78Y|PC_ENST00000393960.1_Silent_p.Y118Y|PC_ENST00000393955.2_Silent_p.Y118Y|PC_ENST00000355677.3_Silent_p.Y118Y	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	118	Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.Y118Y(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AGAGGAACCCGTAGCCAGGGT	0.627																																																1	Substitution - coding silent(1)	large_intestine(1)	11											84	89	88					11																	66638919		2200	4295	6495	66395495	SO:0001819	synonymous_variant	5091			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.354C>T	11.37:g.66638919G>A			66395495	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	37	CCDS8152.1																																																																																				0.627	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		A	66638919	G	A	66638919	2	1	77	1	0	0	0	0	0	0	0	1	11528	1140	40	1		1	PC	11	66638919	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	18669	66638919	68367597	686	22422										
ANKRD13D	338692	broad.mit.edu	37	chr11	67059112	67059112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgcccaagcgatgtgtacCgcgtgtggaagcggggtgag	18	8	0	1	rs377577130		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:67059112C>T	ENST00000447274.2	+	5	1350	c.175C>T	c.(175-177)Cgc>Tgc	p.R59C	ANKRD13D_ENST00000511455.2_Missense_Mutation_p.R146C|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.R59C|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.R59C			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	59						endosome (GO:0005768)|plasma membrane (GO:0005886)		p.R59C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CGATGTGTACCGCGTGTGGAA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	CYS/ARG	1,4399	2.1+/-5.4	0,1,2199	73	76	75		436	3	0.9	11		75	0,8590		0,0,4295	no	missense	ANKRD13D	NM_207354.2	180	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	146/606	67059112	1,12989	2200	4295	6495	66815688	SO:0001583	missense	338692			AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.175C>T	11.37:g.67059112C>T	ENSP00000402616:p.Arg59Cys		66815688	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	37		.	.	.	.	.	.	.	.	.	.	C	19.16	3.774176	0.69992	2.27E-4	0.0	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.35605	1.3;1.49;1.3;1.3	3.95	3.03	0.35002	.	0.081744	0.48767	N	0.000177	T	0.51432	0.1674	M	0.69523	2.12	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.67900	0.954;0.899	T	0.52102	-0.8620	10	0.87932	D	0	-8.8452	6.2149	0.20649	0.1837:0.7172:0.0:0.0991	.	146;59	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	C	59;146;59;59	ENSP00000402616:R59C;ENSP00000427130:R146C;ENSP00000310874:R59C;ENSP00000444404:R59C	ENSP00000310874:R59C	R	+	1	0	ANKRD13D	66815688	0.998000	0.40836	0.927000	0.36925	0.949000	0.60115	1.103000	0.31062	1.020000	0.39573	0.561000	0.74099	CGC		0.622	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		T	67059112	C	T	67059112	3	4	77	1	0	0	0	0	1	0	0	0	644	652	23	1	454	1	ANKRD13D	11	67059112	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	420193	67059112	67947404	687	22423										
SSH3	54961	broad.mit.edu	37	chr11	67076975	67076975	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagtcggcccagctgctgcCgcactggaaggagacgcacc	15	14	0	1	rs145193470	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:67076975C>A	ENST00000308127.4	+	11	1347	c.1169C>A	c.(1168-1170)cCg>cAg	p.P390Q	SSH3_ENST00000532181.1_3'UTR|SSH3_ENST00000308298.7_Intron|SSH3_ENST00000376757.5_Missense_Mutation_p.P390Q	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	390	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.P390Q(1)		NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CAGCTGCTGCCGCACTGGAAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											74	66	69					11																	67076975		2200	4295	6495	66833551	SO:0001583	missense	54961			AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30581	protein-coding gene	gene with protein product		606780	"slingshot homolog 3 (Drosophila)"			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.1169C>A	11.37:g.67076975C>A	ENSP00000312081:p.Pro390Gln		66833551	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Missense_Mutation	SNP	ENST00000308127.4	37	CCDS8157.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.274014	0.59649	.	.	ENSG00000172830	ENST00000308127;ENST00000376757	D;D	0.85171	-1.95;-1.95	4.18	4.18	0.49190	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.64402	D	0.000009	T	0.73040	0.3536	N	0.10972	0.075	0.41260	D	0.986773	P;B	0.47841	0.901;0.44	B;B	0.43413	0.419;0.398	T	0.72510	-0.4271	10	0.15499	T	0.54	-26.3929	15.8042	0.78481	0.0:1.0:0.0:0.0	.	244;390	Q8TE77-3;Q8TE77	.;SSH3_HUMAN	Q	390	ENSP00000312081:P390Q;ENSP00000365948:P390Q	ENSP00000312081:P390Q	P	+	2	0	SSH3	66833551	0.608000	0.26966	0.997000	0.53966	0.701000	0.40568	2.231000	0.43009	2.351000	0.79841	0.462000	0.41574	CCG		0.617	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276		A	67076975	C	A	67076975	3	1	77	1	0	0	0	0	1	0	0	0	15225	652	23	2	1211	2	SSH3	11	67076975	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	17863	67076975	67929541	688	22424										
CHKA	1119	broad.mit.edu	37	chr11	67842289	67842289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgctctccagaaccatggcCtcagccccctaaaacagatg	7	16	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:67842289C>A	ENST00000265689.4	-	4	551	c.525G>T	c.(523-525)gaG>gaT	p.E175D	CHKA_ENST00000356135.5_Missense_Mutation_p.E157D	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	175					CDP-choline pathway (GO:0006657)|choline metabolic process (GO:0019695)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline binding (GO:0033265)|choline kinase activity (GO:0004103)|cholinesterase activity (GO:0004104)|drug binding (GO:0008144)|ethanolamine kinase activity (GO:0004305)|signal transducer activity (GO:0004871)	p.E175D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13					Choline(DB00122)	GAACCATGGCCTCAGCCCCCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	11											93	83	86					11																	67842289		2200	4294	6494	67598865	SO:0001583	missense	1119			D10704	CCDS8178.1, CCDS8179.1	11q13.1	2008-02-05	2004-04-19	2004-04-21	ENSG00000110721	ENSG00000110721	2.7.1.32		1937	protein-coding gene	gene with protein product		118491	"choline kinase"	CHK		1618328, 15003397	Standard	NM_001277		Approved	CKI	uc001onj.3	P35790	OTTHUMG00000167424	ENST00000265689.4:c.525G>T	11.37:g.67842289C>A	ENSP00000265689:p.Glu175Asp		67598865	Q8NE29	Missense_Mutation	SNP	ENST00000265689.4	37	CCDS8178.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581396	0.28180	.	.	ENSG00000110721	ENST00000265689;ENST00000356135;ENST00000531341	T;T;T	0.58797	0.31;0.31;0.31	4.97	2.06	0.26882	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.123855	0.53938	D	0.000051	T	0.29028	0.0721	N	0.04508	-0.205	0.58432	D	0.999994	B;B	0.11235	0.0;0.004	B;B	0.16289	0.001;0.015	T	0.03587	-1.1022	10	0.15952	T	0.53	-23.2848	8.1948	0.31389	0.0:0.6136:0.0:0.3864	.	157;175	P35790-2;P35790	.;CHKA_HUMAN	D	175;157;53	ENSP00000265689:E175D;ENSP00000348454:E157D;ENSP00000435032:E53D	ENSP00000265689:E175D	E	-	3	2	CHKA	67598865	0.985000	0.35326	1.000000	0.80357	0.924000	0.55760	0.219000	0.17641	0.273000	0.22049	0.563000	0.77884	GAG		0.507	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277		A	67842289	C	A	67842289	3	1	77	1	0	0	0	0	1	0	0	0	3353	680	24	2	884	2	CHKA	11	67842289	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	765314	67842289	67164227	689	22425										
C11orf24	53838	broad.mit.edu	37	chr11	68030061	68030061	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttgtactggaggctgcagtCgtgggagcactggaggccac	17	9	0	0	rs148354708	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:68030061C>T	ENST00000304271.6	-	4	804	c.402G>A	c.(400-402)acG>acA	p.T134T	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'UTR	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	134						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T134T(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AGGCTGCAGTCGTGGGAGCAC	0.622													C|||	2	0.000399361	8e-04	0	5008	,	,		17045	0.001		0	False		,,,				2504	0				NSCLC(21;855 905 4198 36694)											1	Substitution - coding silent(1)	large_intestine(1)	11						C		2,4398	4.2+/-10.8	0,2,2198	50	42	45		402	-1	0	11	dbSNP_134	45	0,8588		0,0,4294	no	coding-synonymous	C11orf24	NM_022338.3		0,2,6492	TT,TC,CC		0.0,0.0455,0.0154		134/450	68030061	2,12986	2200	4294	6494	67786637	SO:0001819	synonymous_variant	53838			AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.402G>A	11.37:g.68030061C>T			67786637	Q9H2K4	Silent	SNP	ENST00000304271.6	37	CCDS8180.1																																																																																				0.622	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		T	68030061	C	T	68030061	2	4	77	1	0	0	0	0	0	0	0	1	1639	871	31	1		1	C11orf24	11	68030061	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	187772	68030061	66976455	690	22426										
LRP5	4041	broad.mit.edu	37	chr11	68191157	68191157	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agggccatcgtcgtcaacgcGgagcgagggtaggaggccaa	17	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:68191157G>A	ENST00000294304.7	+	14	3334	c.3228G>A	c.(3226-3228)gcG>gcA	p.A1076A		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1076	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A1076A(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCGTCAACGCGGAGCGAGGGT	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	11											49	47	48					11																	68191157		2200	4293	6493	67947733	SO:0001819	synonymous_variant	4041			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3228G>A	11.37:g.68191157G>A			67947733	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																				0.682	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		A	68191157	G	A	68191157	2	1	77	1	0	0	0	0	0	0	0	1	8989	1103	39	1		1	LRP5	11	68191157	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	161096	68191157	66815359	691	22427										
ORAOV1	220064	broad.mit.edu	37	chr11	69482347	69482347	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctggctgaacattgagtaaCgaacaaaactgaaaacacaa	7	8	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:69482347C>T	ENST00000535657.1	-	5	435	c.354G>A	c.(352-354)tcG>tcA	p.S118S	ORAOV1_ENST00000279147.4_Silent_p.S118S|ORAOV1_ENST00000539414.1_3'UTR|ORAOV1_ENST00000536870.1_Silent_p.S59S			Q8WV07	ORAV1_HUMAN	oral cancer overexpressed 1	118								p.S118S(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;5.64e-57)|all cancers(3;5.98e-51)|BRCA - Breast invasive adenocarcinoma(2;5.49e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			CATTGAGTAACGAACAAAACT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	11											89	93	91					11																	69482347		2200	4294	6494	69191528	SO:0001819	synonymous_variant	220064				CCDS8192.1	11q13.2	2010-11-23			ENSG00000149716	ENSG00000149716			17589	protein-coding gene	gene with protein product	"oral cancer overexpressed protein 1-A"	607224				12172009	Standard	NM_153451		Approved	TAOS1	uc001opc.3	Q8WV07		ENST00000535657.1:c.354G>A	11.37:g.69482347C>T			69191528	B2R4R2|Q8NFK0	Silent	SNP	ENST00000535657.1	37	CCDS8192.1																																																																																				0.368	ORAOV1-009	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000396821.1	NM_153451		T	69482347	C	T	69482347	2	4	77	1	0	0	0	0	0	0	0	1	11291	523	19	1		1	ORAOV1	11	69482347	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1291190	69482347	65524169	692	22428										
ANO1	55107	broad.mit.edu	37	chr11	70017144	70017144	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgtcagagccaaagacatCggtgagtgaccccacgggcc	13	13	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:70017144C>T	ENST00000355303.5	+	22	2654	c.2349C>T	c.(2347-2349)atC>atT	p.I783I	ANO1_ENST00000531349.1_Splice_Site_p.I492I|ANO1_ENST00000538023.1_Splice_Site_p.I783I|ANO1_ENST00000525494.1_3'UTR|ANO1_ENST00000398543.2_Splice_Site_p.I637I|ANO1_ENST00000530676.1_Splice_Site_p.I637I	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	783					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.I783I(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CCAAAGACATCGGTGAGTGAC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	11											34	35	35					11																	70017144		1986	4169	6155	69694792	SO:0001630	splice_region_variant	55107			BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2350+1C>T	11.37:g.70017144C>T			69694792	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																				0.602	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	Silent	T	70017144	C	T	70017144	5	4	77	1	0	0	0	0	0	0	1	0	695	898	31	1	2435	1	ANO1	11	70017144	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	534797	70017144	64989372	693	22429										
IL18BP	10068	broad.mit.edu	37	chr11	71712286	71712286	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgtgtggcctgcagccgctTccccaacttcagcatcctct	8	17	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:71712286T>C	ENST00000393703.4	+	4	812	c.275T>C	c.(274-276)tTc>tCc	p.F92S	IL18BP_ENST00000404792.1_Missense_Mutation_p.F92S|IL18BP_ENST00000393707.4_Intron|IL18BP_ENST00000260049.5_Missense_Mutation_p.F92S|IL18BP_ENST00000531053.1_Missense_Mutation_p.F92S|IL18BP_ENST00000337131.5_Missense_Mutation_p.F92S|IL18BP_ENST00000393705.4_Missense_Mutation_p.F92S|IL18BP_ENST00000497194.2_Missense_Mutation_p.F92S	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	92	Ig-like C2-type.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)	p.F92S(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						TGCAGCCGCTTCCCCAACTTC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	11											53	56	55					11																	71712286		2105	4218	6323	71389934	SO:0001583	missense	10068			AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5987	protein-coding gene	gene with protein product	"MC51L-53L-54L homolog gene product"	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.275T>C	11.37:g.71712286T>C	ENSP00000377306:p.Phe92Ser		71389934	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	T	9.756	1.168886	0.21621	.	.	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	4.64	3.51	0.40186	Immunoglobulin-like (1);	0.462022	0.20609	N	0.089006	T	0.21387	0.0515	L	0.41027	1.25	0.09310	N	1	P;B	0.37731	0.607;0.379	B;B	0.34652	0.187;0.11	T	0.14090	-1.0485	10	0.52906	T	0.07	-15.4615	5.7806	0.18304	0.0:0.0891:0.1684:0.7425	.	92;92	G3V1C5;O95998	.;I18BP_HUMAN	S	92	ENSP00000377306:F92S;ENSP00000434717:F92S;ENSP00000377308:F92S;ENSP00000338723:F92S;ENSP00000434835:F92S;ENSP00000384212:F92S;ENSP00000260049:F92S	ENSP00000260049:F92S	F	+	2	0	IL18BP	71389934	0.018000	0.18449	0.151000	0.22473	0.662000	0.39071	1.005000	0.29834	0.801000	0.34066	0.459000	0.35465	TTC		0.602	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		C	71712286	T	C	71712286	3	2	77	1	0	0	0	0	1	0	0	0	7667	1783	62	4	285	4	IL18BP	11	71712286	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1695142	71712286	63294230	694	22430										
ARHGEF17	9828	broad.mit.edu	37	chr11	73073162	73073162	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctgcaacagcgacggctaCgtgggccaggtgtgcctgct	15	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:73073162C>T	ENST00000263674.3	+	13	4922	c.4572C>T	c.(4570-4572)taC>taT	p.Y1524Y		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1524					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Y1524Y(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						GCGACGGCTACGTGGGCCAGG	0.697																																																1	Substitution - coding silent(1)	large_intestine(1)	11											29	30	29					11																	73073162		2199	4293	6492	72750810	SO:0001819	synonymous_variant	9828			AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.4572C>T	11.37:g.73073162C>T			72750810	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																				0.697	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73073162	C	T	73073162	2	4	77	1	0	0	0	0	0	0	0	1	900	547	19	1		1	ARHGEF17	11	73073162	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1360876	73073162	61933354	695	22431										
C2CD3	26005	broad.mit.edu	37	chr11	73850697	73850697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgctaactcttttccatcAattttgatggtatgtatgtc	7	8	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:73850697A>G	ENST00000334126.7	-	4	886	c.660T>C	c.(658-660)atT>atC	p.I220I	C2CD3_ENST00000313663.7_Silent_p.I220I|C2CD3_ENST00000539061.1_Silent_p.I220I			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	220					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.I220I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					CTTTTCCATCAATTTTGATGG	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	11											288	285	286					11																	73850697		2200	4293	6493	73528345	SO:0001819	synonymous_variant	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.660T>C	11.37:g.73850697A>G			73528345	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																					0.433	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73850697	A	G	73850697	2	3	77	1	0	0	0	0	0	0	0	1	2160	126	5	4		4	C2CD3	11	73850697	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	777535	73850697	61155819	696	22432										
OMP	4975	broad.mit.edu	37	chr11	76814196	76814196	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagctgctggaccccactgCcatcttctggcgcaaggagg	12	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:76814196C>A	ENST00000529803.1	+	1	311	c.311C>A	c.(310-312)gCc>gAc	p.A104D	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Intron|CAPN5_ENST00000456580.2_Intron|CAPN5_ENST00000278559.3_Intron	NM_006189.1	NP_006180.1	P47874	OMP_HUMAN	olfactory marker protein	104					neurogenesis (GO:0022008)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A104D(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						GACCCCACTGCCATCTTCTGG	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	11											49	57	55					11																	76814196		2141	4232	6373	76491844	SO:0001583	missense	4975			U01212	CCDS53682.1	11q14-q21	2008-07-21				ENSG00000254550			8136	protein-coding gene	gene with protein product		164340				8499899	Standard	NM_006189		Approved		uc010rsk.2	P47874		ENST00000529803.1:c.311C>A	11.37:g.76814196C>A	ENSP00000436376:p.Ala104Asp		76491844	Q562G2	Missense_Mutation	SNP	ENST00000529803.1	37	CCDS53682.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.774950	0.70107	.	.	ENSG00000254550	ENST00000529803	T	0.34859	1.34	5.29	5.29	0.74685	.	.	.	.	.	T	0.47303	0.1438	L	0.27053	0.805	0.36754	D	0.882941	D	0.67145	0.996	D	0.83275	0.996	T	0.55244	-0.8171	9	0.87932	D	0	.	14.3849	0.66938	0.0:0.8406:0.1594:0.0	.	104	P47874	OMP_HUMAN	D	104	ENSP00000436376:A104D	ENSP00000436376:A104D	A	+	2	0	OMP	76491844	1.000000	0.71417	0.991000	0.47740	0.980000	0.70556	3.695000	0.54749	2.757000	0.94681	0.462000	0.41574	GCC		0.622	OMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382570.1	NM_006189		A	76814196	C	A	76814196	3	1	77	1	0	0	0	0	1	0	0	0	10898	739	26	2	313	2	OMP	11	76814196	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2963499	76814196	58192320	697	22433										
MYO7A	4647	broad.mit.edu	37	chr11	76912561	76912561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctggaccatgacacgggcGagcaggtcatgaactcgggc	14	12	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:76912561G>A	ENST00000409709.3	+	36	5193	c.4921G>A	c.(4921-4923)Gag>Aag	p.E1641K	MYO7A_ENST00000409619.2_Missense_Mutation_p.E1592K|MYO7A_ENST00000458637.2_Missense_Mutation_p.E1603K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1641	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)	p.E1641K(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGACACGGGCGAGCAGGTCAT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	11											65	72	70					11																	76912561		2169	4251	6420	76590209	SO:0001583	missense	4647			U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.4921G>A	11.37:g.76912561G>A	ENSP00000386331:p.Glu1641Lys		76590209	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	32	5.131426	0.94473	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	4.58	4.58	0.56647	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	T	0.72724	0.3496	M	0.66506	2.035	0.80722	D	1	D;P;P	0.55605	0.972;0.723;0.9	P;B;P	0.46452	0.517;0.203;0.449	T	0.72564	-0.4255	10	0.26408	T	0.33	.	17.5911	0.87997	0.0:0.0:1.0:0.0	.	1592;1603;1641	B9A011;F8VUN5;Q13402	.;.;MYO7A_HUMAN	K	1641;1603;1592;814;1640;1610;1517;783;256	ENSP00000386331:E1641K;ENSP00000392185:E1603K;ENSP00000386635:E1592K;ENSP00000417017:E783K	ENSP00000345075:E1517K	E	+	1	0	MYO7A	76590209	1.000000	0.71417	0.922000	0.36590	0.951000	0.60555	9.222000	0.95196	2.375000	0.81037	0.561000	0.74099	GAG		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76912561	G	A	76912561	3	1	77	1	0	0	0	0	1	0	0	0	10112	1059	37	1	5093	1	MYO7A	11	76912561	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	98365	76912561	58093955	698	22434										
NARS2	79731	broad.mit.edu	37	chr11	78147846	78147846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtggcacagatccaaatcgaCgaaggtccagatacctgttt	10	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:78147846C>T	ENST00000281038.5	-	14	1679	c.1304G>A	c.(1303-1305)cGt>cAt	p.R435H	NARS2_ENST00000528850.1_Missense_Mutation_p.R208H|RP11-452H21.1_ENST00000534168.1_RNA	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	435					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.R435H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TCCAAATCGACGAAGGTCCAG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	11											178	179	179					11																	78147846		2200	4292	6492	77825494	SO:0001583	missense	79731			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1304G>A	11.37:g.78147846C>T	ENSP00000281038:p.Arg435His		77825494	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	C	34	5.404005	0.96051	.	.	ENSG00000137513	ENST00000281038;ENST00000528850	D;D	0.85258	-1.96;-1.96	5.78	5.78	0.91487	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.048793	0.85682	D	0.000000	D	0.96009	0.8700	H	0.98426	4.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97255	0.9900	10	0.87932	D	0	-14.5891	19.994	0.97377	0.0:1.0:0.0:0.0	.	435	Q96I59	SYNM_HUMAN	H	435;208	ENSP00000281038:R435H;ENSP00000432635:R208H	ENSP00000281038:R435H	R	-	2	0	NARS2	77825494	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.716000	0.92895	0.591000	0.81541	CGT		0.358	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		T	78147846	C	T	78147846	3	4	77	1	0	0	0	0	1	0	0	0	10201	536	19	1	133	1	NARS2	11	78147846	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1235285	78147846	56858670	699	22435										
NARS2	79731	broad.mit.edu	37	chr11	78204194	78204194	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtgcctccggctctgagaaTtttcagctcggaaggtcgga	14	10	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:78204194T>A	ENST00000281038.5	-	7	1112	c.737A>T	c.(736-738)aAt>aTt	p.N246I	NARS2_ENST00000528850.1_Missense_Mutation_p.N19I	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	246					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.N246I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GCTCTGAGAATTTTCAGCTCG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											66	70	68					11																	78204194		2200	4292	6492	77881842	SO:0001583	missense	79731			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.737A>T	11.37:g.78204194T>A	ENSP00000281038:p.Asn246Ile		77881842	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.973687	0.92919	.	.	ENSG00000137513	ENST00000281038;ENST00000528850	D;D	0.85088	-1.94;-1.94	5.67	5.67	0.87782	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.000000	0.85682	D	0.000000	D	0.92756	0.7697	M	0.92970	3.365	0.80722	D	1	D	0.56287	0.975	P	0.58454	0.839	D	0.94198	0.7447	10	0.87932	D	0	-16.8714	13.427	0.61030	0.0:0.0:0.0:1.0	.	246	Q96I59	SYNM_HUMAN	I	246;19	ENSP00000281038:N246I;ENSP00000432635:N19I	ENSP00000281038:N246I	N	-	2	0	NARS2	77881842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.121000	0.77160	2.157000	0.67596	0.528000	0.53228	AAT		0.388	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		A	78204194	T	A	78204194	3	1	77	1	0	0	0	0	1	0	0	0	10201	1493	52	5	728	5	NARS2	11	78204194	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	56348	78204194	56802322	700	22436										
CREBZF	58487	broad.mit.edu	37	chr11	85375242	85375244	+	In_Frame_Del	DEL	CTT	CTT	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccagccccatcacgtactcCttcttcttcagtcgattaag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CTT	CTT	CTT	-	CTT	CTT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:85375242_85375244delCTT	ENST00000527447.1	-	1	902_904	c.676_678delAAG	c.(676-678)aagdel	p.K226del	CREBZF_ENST00000534224.1_Intron|CREBZF_ENST00000398294.2_In_Frame_Del_p.K144del|CREBZF_ENST00000531515.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	226	Basic motif. {ECO:0000250}.|bZIP.				negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K226delK(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				TCACGTACTCCTTCTTCTTCAGT	0.665											OREG0021274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									NSCLC(172;674 2044 9050 18334 41735)											1	Deletion - In frame(1)	large_intestine(1)	11								5,3619		2,1,1809						4.9	1			62	8,7784		3,2,3891	no	coding	CREBZF	NM_001039618.2		5,3,5700	A1A1,A1R,RR		0.1027,0.138,0.1139				13,11403				85052892	SO:0001651	inframe_deletion	58487			AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.676_678delAAG	11.37:g.85375248_85375250delCTT	ENSP00000433459:p.Lys226del	1236	85052890	B2R8Q9|Q0P5U9|Q52LT3	In_Frame_Del	DEL	ENST00000527447.1	37	CCDS41697.1																																																																																				0.665	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		-	85375244	CTT	-	85375242	7	5	77	1	0	1	0	1	0	0	0	0	3869	680	24	0	390	0	CREBZF	11	85375242	In_Frame_Del	DEL	CTT	TCGA-AG-A02N-01A-11W-A096-10	7171048	85375242	49631274	701	22437										
SESN3	143686	broad.mit.edu	37	chr11	94918604	94918604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatgtgccaggaggaccacaGcatgtaccagttcaggcaga	12	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:94918604G>A	ENST00000536441.1	-	5	914	c.578C>T	c.(577-579)gCt>gTt	p.A193V	SESN3_ENST00000393234.1_Missense_Mutation_p.A193V|RP11-712B9.2_ENST00000534864.1_RNA|RP11-712B9.2_ENST00000534891.1_RNA|SESN3_ENST00000416495.2_Missense_Mutation_p.A193V|SESN3_ENST00000278499.2_Missense_Mutation_p.A54V	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	193					glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)		p.A193V(1)		endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		GAGGACCACAGCATGTACCAG	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	11											102	102	102					11																	94918604		2201	4297	6498	94558252	SO:0001583	missense	143686			AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212			23060	protein-coding gene	gene with protein product		607768				12607115	Standard	NM_144665		Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.578C>T	11.37:g.94918604G>A	ENSP00000441927:p.Ala193Val		94558252	B7Z7P9|Q96AD1	Missense_Mutation	SNP	ENST00000536441.1	37	CCDS8303.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475659	0.84640	.	.	ENSG00000149212	ENST00000536441;ENST00000278499;ENST00000393234;ENST00000416495	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.70133	0.3189	M	0.86028	2.79	0.80722	D	1	D;P;P	0.69078	0.997;0.869;0.474	D;B;B	0.79108	0.992;0.38;0.285	T	0.74553	-0.3627	10	0.72032	D	0.01	-11.9922	19.4864	0.95030	0.0:0.0:1.0:0.0	.	54;193;193	B7Z7P9;P58005-3;P58005	.;.;SESN3_HUMAN	V	193;54;193;193	ENSP00000441927:A193V;ENSP00000278499:A54V;ENSP00000376926:A193V;ENSP00000407008:A193V	ENSP00000278499:A54V	A	-	2	0	SESN3	94558252	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	8.895000	0.92512	2.687000	0.91594	0.561000	0.74099	GCT		0.388	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396475.3	NM_144665		A	94918604	G	A	94918604	3	1	77	1	0	0	0	0	1	0	0	0	14163	971	34	3	924	3	SESN3	11	94918604	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	9543362	94918604	40087912	702	22438										
BIRC3	330	broad.mit.edu	37	chr11	102206715	102206715	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agatgatttattattaatccGgaagaatagaatggcacttt	8	4	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:102206715G>A	ENST00000263464.3	+	7	4093	c.1343G>A	c.(1342-1344)cGg>cAg	p.R448Q	BIRC3_ENST00000532808.1_Missense_Mutation_p.R448Q	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	448	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R448Q(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TTATTAATCCGGAAGAATAGA	0.318			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	1	Substitution - Missense(1)	large_intestine(1)	11											68	74	72					11																	102206715		2202	4299	6501	101711925	SO:0001583	missense	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1343G>A	11.37:g.102206715G>A	ENSP00000263464:p.Arg448Gln		101711925	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688835	0.48097	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	T;T	0.21191	2.02;2.02	5.27	4.29	0.51040	DEATH-like (2);Caspase Recruitment (3);	0.051514	0.85682	D	0.000000	T	0.23330	0.0564	L	0.60455	1.87	0.42943	D	0.994357	B	0.29909	0.261	B	0.30943	0.122	T	0.04870	-1.0921	10	0.52906	T	0.07	.	13.2776	0.60196	0.1282:0.0:0.8718:0.0	.	448	Q13489	BIRC3_HUMAN	Q	448;448;216	ENSP00000263464:R448Q;ENSP00000432907:R448Q	ENSP00000263464:R448Q	R	+	2	0	BIRC3	101711925	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.196000	0.42686	2.751000	0.94390	0.650000	0.86243	CGG		0.318	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		A	102206715	G	A	102206715	3	1	77	1	0	0	0	0	1	0	0	0	1437	1116	39	1	1365	1	BIRC3	11	102206715	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7288111	102206715	32799801	703	22439										
BIRC3	330	broad.mit.edu	37	chr11	102206835	102206835	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tattaaacagaagacacagaCgtctttacaagcaagagaac	7	8	1	4	rs200008391		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:102206835C>T	ENST00000263464.3	+	7	4213	c.1463C>T	c.(1462-1464)aCg>aTg	p.T488M	BIRC3_ENST00000532808.1_Missense_Mutation_p.T488M	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	488	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T488M(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		AAGACACAGACGTCTTTACAA	0.353			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	1	Substitution - Missense(1)	large_intestine(1)	11											115	118	117					11																	102206835		2203	4299	6502	101712045	SO:0001583	missense	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1463C>T	11.37:g.102206835C>T	ENSP00000263464:p.Thr488Met		101712045	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.611429	0.28712	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	T;T	0.21543	2.0;2.0	4.89	1.8	0.24995	DEATH-like (2);Caspase Recruitment (3);	0.238168	0.51477	N	0.000094	T	0.30135	0.0755	M	0.80183	2.485	0.09310	N	1	B	0.26672	0.156	B	0.36378	0.223	T	0.30446	-0.9978	10	0.52906	T	0.07	.	10.7241	0.46057	0.0:0.6941:0.0:0.3059	.	488	Q13489	BIRC3_HUMAN	M	488;488;256	ENSP00000263464:T488M;ENSP00000432907:T488M	ENSP00000263464:T488M	T	+	2	0	BIRC3	101712045	0.004000	0.15560	0.685000	0.30070	0.989000	0.77384	0.331000	0.19733	0.671000	0.31185	0.655000	0.94253	ACG		0.353	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102206835	C	T	102206835	3	4	77	1	0	0	0	0	1	0	0	0	1437	536	19	1	1485	1	BIRC3	11	102206835	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	120	102206835	32799681	704	22440										
MMP7	4316	broad.mit.edu	37	chr11	102398591	102398591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttctgcattatttctatgaCgcgggagtttaacattccag	8	9	2	1	rs145006821		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:102398591C>T	ENST00000260227.4	-	2	284	c.232G>A	c.(232-234)Gtc>Atc	p.V78I		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	78					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.V78I(1)		large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	ATTTCTATGACGCGGGAGTTT	0.408													C|||	1	0.000199681	0	0	5008	,	,		18024	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						C	ILE/VAL	0,4406		0,0,2203	94	102	99		232	-8	0	11	dbSNP_134	99	1,8597	1.2+/-3.3	0,1,4298	no	missense	MMP7	NM_002423.3	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	78/268	102398591	1,13003	2203	4299	6502	101903801	SO:0001583	missense	4316			Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"matrix metalloproteinase 7 (matrilysin, uterine)"	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.232G>A	11.37:g.102398591C>T	ENSP00000260227:p.Val78Ile		101903801	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	37	CCDS8317.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.355	0.831875	0.16820	0.0	1.16E-4	ENSG00000137673	ENST00000260227	T	0.36340	1.26	5.39	-8.02	0.01118	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	1.131920	0.06679	N	0.767584	T	0.11580	0.0282	N	0.01668	-0.77	0.09310	N	1	B;B;B	0.15141	0.012;0.001;0.001	B;B;B	0.15052	0.012;0.002;0.003	T	0.37197	-0.9716	10	0.39692	T	0.17	-0.1407	7.6475	0.28329	0.0:0.3793:0.2089:0.4119	.	78;78;78	B4DDW4;Q53GF1;P09237	.;.;MMP7_HUMAN	I	78	ENSP00000260227:V78I	ENSP00000260227:V78I	V	-	1	0	MMP7	101903801	0.002000	0.14202	0.000000	0.03702	0.062000	0.15995	0.628000	0.24522	-1.955000	0.01023	-1.384000	0.01168	GTC		0.408	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2			T	102398591	C	T	102398591	3	4	77	1	0	0	0	0	1	0	0	0	9697	536	19	1	591	1	MMP7	11	102398591	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	191756	102398591	32607925	705	22441										
CUL5	8065	broad.mit.edu	37	chr11	107925641	107925641	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagaagaaaaacgagcactaCgttatttagaaacaagacga	8	6	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:107925641C>T	ENST00000393094.2	+	7	1355	c.739C>T	c.(739-741)Cgt>Tgt	p.R247C		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	247					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)	p.R247C(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		ACGAGCACTACGTTATTTAGA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	11											73	71	71					11																	107925641		2201	4295	6496	107430851	SO:0001583	missense	8065			X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.739C>T	11.37:g.107925641C>T	ENSP00000376808:p.Arg247Cys		107430851	A8K960|O14766|Q9BZC6	Missense_Mutation	SNP	ENST00000393094.2	37	CCDS31668.1	.	.	.	.	.	.	.	.	.	.	C	33	5.237331	0.95240	.	.	ENSG00000166266	ENST00000393094	T	0.74526	-0.85	6.02	6.02	0.97574	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.86184	0.5872	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	D	0.85856	0.1407	10	0.66056	D	0.02	-8.6771	20.5407	0.99260	0.0:1.0:0.0:0.0	.	247	Q93034	CUL5_HUMAN	C	247	ENSP00000376808:R247C	ENSP00000376808:R247C	R	+	1	0	CUL5	107430851	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.014000	0.57145	2.865000	0.98341	0.655000	0.94253	CGT		0.323	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			T	107925641	C	T	107925641	3	4	77	1	0	0	0	0	1	0	0	0	4065	536	19	1	765	1	CUL5	11	107925641	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5527050	107925641	27080875	706	22442										
KDELC2	143888	broad.mit.edu	37	chr11	108361840	108361840	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggtttagggacatgtatcCggaccaactctttaggtgaa	11	7	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:108361840C>T	ENST00000323468.5	-	2	322	c.257G>A	c.(256-258)cGg>cAg	p.R86Q	KDELC2_ENST00000434945.2_Missense_Mutation_p.R30Q|KDELC2_ENST00000375648.1_Missense_Mutation_p.R30Q	NM_153705.4	NP_714916.3	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2	86						endoplasmic reticulum (GO:0005783)		p.R86Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)		GACATGTATCCGGACCAACTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	11											85	79	81					11																	108361840		1872	4094	5966	107867050	SO:0001583	missense	143888			AF533708	CCDS41711.1	11q32	2010-11-18			ENSG00000178202	ENSG00000178202			28496	protein-coding gene	gene with protein product						12975309	Standard	NM_153705		Approved	MGC33424	uc001pkj.2	Q7Z4H8	OTTHUMG00000166535	ENST00000323468.5:c.257G>A	11.37:g.108361840C>T	ENSP00000315386:p.Arg86Gln		107867050	Q6UWW2|Q6ZUM9|Q8N7L8|Q8NE24	Missense_Mutation	SNP	ENST00000323468.5	37	CCDS41711.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.717876	0.68844	.	.	ENSG00000178202	ENST00000323468;ENST00000434945;ENST00000375648	D;T;T	0.84442	-1.85;1.6;1.87	5.34	4.36	0.52297	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.051096	0.85682	D	0.000000	D	0.86020	0.5833	M	0.76328	2.33	0.53005	D	0.999968	P;P	0.52842	0.729;0.956	B;P	0.47118	0.337;0.538	D	0.86355	0.1713	10	0.49607	T	0.09	-15.0416	12.0366	0.53429	0.0:0.8671:0.0:0.1329	.	86;30	Q7Z4H8;Q7Z4H8-2	KDEL2_HUMAN;.	Q	86;30;30	ENSP00000315386:R86Q;ENSP00000413429:R30Q;ENSP00000364799:R30Q	ENSP00000315386:R86Q	R	-	2	0	KDELC2	107867050	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.490000	0.60319	2.785000	0.95823	0.655000	0.94253	CGG		0.378	KDELC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390273.1	NM_153705		T	108361840	C	T	108361840	3	4	77	1	0	0	0	0	1	0	0	0	8139	652	23	1	1294	1	KDELC2	11	108361840	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	436199	108361840	26644676	707	22443										
LAYN	143903	broad.mit.edu	37	chr11	111428283	111428283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaagctgccttgaatctgGcctacatcctaatccccagc	7	15	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:111428283G>A	ENST00000375615.3	+	7	885	c.700G>A	c.(700-702)Gcc>Acc	p.A234T	LAYN_ENST00000525126.1_Missense_Mutation_p.A234T|LAYN_ENST00000528924.1_3'UTR|LAYN_ENST00000436913.2_Missense_Mutation_p.A81T|LAYN_ENST00000533265.1_Missense_Mutation_p.A226T|LAYN_ENST00000375614.2_Missense_Mutation_p.A226T	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	234						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.A226T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	CTTGAATCTGGCCTACATCCT	0.423																																					Ovarian(17;551 586 12136 22082 22900)											1	Substitution - Missense(1)	large_intestine(1)	11											373	344	353					11																	111428283		2201	4297	6498	110933493	SO:0001583	missense	143903				CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.700G>A	11.37:g.111428283G>A	ENSP00000364765:p.Ala234Thr		110933493	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Missense_Mutation	SNP	ENST00000375615.3	37	CCDS58178.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512652	0.44660	.	.	ENSG00000204381	ENST00000375614;ENST00000375615;ENST00000525126;ENST00000436913;ENST00000533265;ENST00000541011;ENST00000530962	T;T;T;T	0.05996	3.87;3.47;3.36;4.06	5.81	4.84	0.62591	.	1.051460	0.07339	N	0.880480	T	0.16257	0.0391	M	0.65975	2.015	0.34404	D	0.69559	D;P;P;P;P	0.53745	0.962;0.839;0.682;0.839;0.868	P;B;B;B;B	0.50082	0.63;0.298;0.154;0.298;0.439	T	0.05971	-1.0853	10	0.28530	T	0.3	-7.6633	14.0271	0.64592	0.0:0.2529:0.7471:0.0	.	81;226;234;234;226	B4DJU0;E9PMI0;Q6UX15;E9PQU7;Q6UX15-2	.;.;LAYN_HUMAN;.;.	T	226;234;234;81;226;189;82	ENSP00000364764:A226T;ENSP00000364765:A234T;ENSP00000434328:A234T;ENSP00000434972:A226T	ENSP00000364764:A226T	A	+	1	0	LAYN	110933493	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	3.159000	0.50731	2.763000	0.94921	0.650000	0.86243	GCC		0.423	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834		A	111428283	G	A	111428283	3	1	77	1	0	0	0	0	1	0	0	0	8671	1203	42	3	698	3	LAYN	11	111428283	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3066443	111428283	23578233	708	22444										
USP28	57646	broad.mit.edu	37	chr11	113679081	113679081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggctgtgtttgcaatagccTgggcagtttgctcctttaca	12	9	0	0	rs36042945		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:113679081T>C	ENST00000003302.4	-	18	2311	c.2243A>G	c.(2242-2244)cAg>cGg	p.Q748R	USP28_ENST00000544967.1_Missense_Mutation_p.Q456R|USP28_ENST00000545540.1_Missense_Mutation_p.Q623R|USP28_ENST00000260188.5_Missense_Mutation_p.Q748R	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	748					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Q748R(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TGCAATAGCCTGGGCAGTTTG	0.522																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											1	Substitution - Missense(1)	large_intestine(1)	11											155	144	148					11																	113679081		2201	4296	6497	113184291	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2243A>G	11.37:g.113679081T>C	ENSP00000003302:p.Gln748Arg		113184291	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.513518	0.27123	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	T;T;T;T	0.41400	1.54;1.58;1.0;1.59	5.36	5.36	0.76844	.	0.735735	0.13907	N	0.354539	T	0.23688	0.0573	N	0.12569	0.235	0.25424	N	0.988242	B;B;B	0.20887	0.001;0.049;0.034	B;B;B	0.18871	0.001;0.01;0.023	T	0.15178	-1.0446	10	0.15066	T	0.55	-10.986	9.5986	0.39589	0.2649:0.0:0.0:0.7351	.	623;748;456	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	R	748;748;456;623	ENSP00000003302:Q748R;ENSP00000260188:Q748R;ENSP00000442431:Q456R;ENSP00000444991:Q623R	ENSP00000003302:Q748R	Q	-	2	0	USP28	113184291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.854000	0.48325	2.254000	0.74563	0.533000	0.62120	CAG		0.522	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			C	113679081	T	C	113679081	3	2	77	1	0	0	0	0	1	0	0	0	17098	1580	55	4	1022	4	USP28	11	113679081	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	2250798	113679081	21327435	709	22445										
SIDT2	51092	broad.mit.edu	37	chr11	117058364	117058364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaatgtttctggatctaccGatggtctggttgacagcgct	12	8	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:117058364G>A	ENST00000324225.4	+	12	1639	c.1108G>A	c.(1108-1110)Gat>Aat	p.D370N	SIDT2_ENST00000431081.2_Missense_Mutation_p.D374N	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	370					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)	p.D370N(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		TGGATCTACCGATGGTCTGGT	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	11											129	109	116					11																	117058364		2201	4296	6497	116563574	SO:0001583	missense	51092			AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1108G>A	11.37:g.117058364G>A	ENSP00000314023:p.Asp370Asn		116563574	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.235725	0.58886	.	.	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081	T;T;T	0.17528	2.28;2.27;2.27	4.54	4.54	0.55810	.	0.464892	0.21515	N	0.073302	T	0.11452	0.0279	N	0.24115	0.695	0.38677	D	0.95244	P;P;P;P	0.51791	0.617;0.948;0.781;0.482	B;B;B;B	0.36244	0.14;0.176;0.22;0.067	T	0.14559	-1.0468	10	0.49607	T	0.09	-7.7506	15.6416	0.77009	0.0:0.0:1.0:0.0	.	370;374;370;370	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	N	370;370;374	ENSP00000314023:D370N;ENSP00000278951:D370N;ENSP00000399635:D374N	ENSP00000278951:D370N	D	+	1	0	SIDT2	116563574	1.000000	0.71417	0.361000	0.25849	0.052000	0.14988	5.377000	0.66184	2.357000	0.79964	0.462000	0.41574	GAT		0.617	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		A	117058364	G	A	117058364	3	1	77	1	0	0	0	0	1	0	0	0	14340	1058	37	1	1154	1	SIDT2	11	117058364	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3379283	117058364	17948152	710	22446										
UBE4A	9354	broad.mit.edu	37	chr11	118252107	118252107	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaatattttctttttcagaAttttttgcagataacctggg	7	5	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:118252107A>T	ENST00000431736.2	+	12	1971	c.1899A>T	c.(1897-1899)gaA>gaT	p.E633D	UBE4A_ENST00000252108.3_Splice_Site_p.E626D|UBE4A_ENST00000545354.1_Splice_Site_p.E98D					ubiquitination factor E4A									p.E633D(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	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;3.28e-05)		CTTTTTCAGAATTTTTTGCAG	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	11											138	138	138					11																	118252107		2200	4296	6496	117757317	SO:0001630	splice_region_variant	9354			D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1898-1A>T	11.37:g.118252107A>T			117757317		Missense_Mutation	SNP	ENST00000431736.2	37	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.096083	0.76870	.	.	ENSG00000110344	ENST00000252108;ENST00000431736;ENST00000545354	T;T;T	0.53206	0.63;0.63;0.63	6.08	3.78	0.43462	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.66771	0.2823	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.66646	-0.5871	10	0.62326	D	0.03	.	9.2467	0.37529	0.798:0.0:0.202:0.0	.	626;633	Q14139;Q14139-2	UBE4A_HUMAN;.	D	626;633;98	ENSP00000252108:E626D;ENSP00000387362:E633D;ENSP00000438918:E98D	ENSP00000252108:E626D	E	+	3	2	UBE4A	117757317	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.766000	0.38491	0.543000	0.28864	0.482000	0.46254	GAA		0.363	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	Missense_Mutation	T	118252107	A	T	118252107	5	4	77	1	0	0	0	0	0	0	1	0	16922	115	4	5	1941	5	UBE4A	11	118252107	Splice_Site	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1193743	118252107	16754409	711	22447										
MLL	4297	broad.mit.edu	37	chr11	118373690	118373690	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgaaccctcttcagtgtcGttttcttctaaagaggccct	8	12	4	2	rs192173056		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:118373690G>A	ENST00000389506.5	+	27	7074	c.7074G>A	c.(7072-7074)tcG>tcA	p.S2358S	KMT2A_ENST00000534358.1_Silent_p.S2361S|KMT2A_ENST00000354520.4_Silent_p.S2320S			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2358					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.S2358S(1)									CTTCAGTGTCGTTTTCTTCTA	0.463													G|||	1	0.000199681	0	0.0014	5008	,	,		19524	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	11											101	110	107					11																	118373690		2200	4296	6496	117878900	SO:0001819	synonymous_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7074G>A	11.37:g.118373690G>A			117878900	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.463	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118373690	G	A	118373690	2	1	77	1	0	0	0	0	0	0	0	1	9650	1132	40	1		1	MLL	11	118373690	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	121583	118373690	16632826	712	22448										
BCL9L	283149	broad.mit.edu	37	chr11	118779311	118779311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcaggggggcaatgaccgCggggggacagcggcgggctc	23	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:118779311C>T	ENST00000334801.3	-	2	1044	c.80G>A	c.(79-81)cGc>cAc	p.R27H	MIR4492_ENST00000581627.1_RNA|BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	27					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.R27H(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GCAATGACCGCGGGGGGACAG	0.597																																																2	Substitution - Missense(2)	large_intestine(2)	11											36	44	41					11																	118779311		2145	4257	6402	118284521	SO:0001583	missense	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.80G>A	11.37:g.118779311C>T	ENSP00000335320:p.Arg27His		118284521	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646990	0.87958	.	.	ENSG00000186174	ENST00000334801;ENST00000392849;ENST00000431085;ENST00000532899	T;T	0.65178	-0.14;-0.14	5.69	4.74	0.60224	.	0.225948	0.22897	N	0.054304	T	0.53110	0.1776	N	0.08118	0	0.29840	N	0.829294	D;D	0.60575	0.988;0.979	P;P	0.50896	0.653;0.451	T	0.59579	-0.7428	10	0.87932	D	0	-5.5948	16.7019	0.85351	0.0:0.8709:0.1291:0.0	.	22;27	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	H	27	ENSP00000335320:R27H;ENSP00000432804:R27H	ENSP00000335320:R27H	R	-	2	0	BCL9L	118284521	0.994000	0.37717	0.947000	0.38551	0.975000	0.68041	1.396000	0.34531	2.688000	0.91661	0.561000	0.74099	CGC		0.597	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118779311	C	T	118779311	3	4	77	1	0	0	0	0	1	0	0	0	1383	768	27	1	4447	1	BCL9L	11	118779311	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	405621	118779311	16227205	713	22449										
PDZD3	79849	broad.mit.edu	37	chr11	119059247	119059247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtcgaccctgaggcggaccGcttcttcagcatggtgcgtg	14	13	2	1	rs137900666	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:119059247G>A	ENST00000531114.1	+	6	1793	c.1244G>A	c.(1243-1245)cGc>cAc	p.R415H	PDZD3_ENST00000355547.5_Missense_Mutation_p.R349H|PDZD3_ENST00000525131.1_Missense_Mutation_p.R336H|PDZD3_ENST00000392817.2_Missense_Mutation_p.R415H|PDZD3_ENST00000322712.4_Missense_Mutation_p.R335H			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	415					cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)	p.R335H(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		GAGGCGGACCGCTTCTTCAGC	0.657													G|||	7	0.00139776	0.0053	0	5008	,	,		15240	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						G	HIS/ARG,HIS/ARG	6,4394	11.4+/-27.6	0,6,2194	34	32	33		1046,1004	3.7	1	11	dbSNP_134	33	0,8590		0,0,4295	yes	missense,missense	PDZD3	NM_001168468.1,NM_024791.3	29,29	0,6,6489	AA,AG,GG		0.0,0.1364,0.0462	benign,benign	349/506,335/492	119059247	6,12984	2200	4295	6495	118564457	SO:0001583	missense	79849			AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"PDZ domain containing 2"	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1244G>A	11.37:g.119059247G>A	ENSP00000431164:p.Arg415His		118564457	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		.	.	.	.	.	.	.	.	.	.	G	11.48	1.652343	0.29336	0.001364	0.0	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.66	3.74	0.42951	PDZ/DHR/GLGF (1);	0.551038	0.19296	N	0.117778	T	0.16171	0.0389	L	0.32530	0.975	0.33118	D	0.541443	B;P;B;B	0.42078	0.397;0.77;0.38;0.387	B;B;B;B	0.24974	0.053;0.057;0.031;0.014	T	0.26360	-1.0105	10	0.42905	T	0.14	-11.2701	7.5178	0.27610	0.1494:0.2546:0.5961:0.0	.	336;415;349;335	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	H	336;415;349;335;349;415	ENSP00000434559:R336H;ENSP00000431164:R415H;ENSP00000347742:R349H;ENSP00000327107:R335H;ENSP00000376564:R415H	ENSP00000327107:R335H	R	+	2	0	PDZD3	118564457	0.999000	0.42202	1.000000	0.80357	0.255000	0.26057	1.417000	0.34770	1.369000	0.46134	0.609000	0.83330	CGC		0.657	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791		A	119059247	G	A	119059247	3	1	77	1	0	0	0	0	1	0	0	0	11733	1087	38	1	1076	1	PDZD3	11	119059247	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	279936	119059247	15947269	714	22450										
THY1	7070	broad.mit.edu	37	chr11	119291056	119291056	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctggtccactaggcaggcCgttaggctggtcaccttctg	12	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:119291056C>T	ENST00000284240.5	-	3	1117	c.78G>A	c.(76-78)acG>acA	p.T26T	THY1_ENST00000580275.1_Intron|USP2-AS1_ENST00000530002.1_RNA|USP2-AS1_ENST00000498979.2_RNA|USP2-AS1_ENST00000578923.1_RNA|USP2-AS1_ENST00000500970.1_RNA|RP11-334E6.12_ENST00000578216.1_RNA|THY1_ENST00000528522.1_Silent_p.T26T|THY1_ENST00000527590.1_5'UTR	NM_006288.3	NP_006279.2	P04216	THY1_HUMAN	Thy-1 cell surface antigen	26	Ig-like V-type.				angiogenesis (GO:0001525)|cytoskeleton organization (GO:0007010)|focal adhesion assembly (GO:0048041)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of GTPase activity (GO:0043547)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell activation (GO:0050870)|retinal cone cell development (GO:0046549)|single organismal cell-cell adhesion (GO:0016337)|T cell receptor signaling pathway (GO:0050852)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|integrin binding (GO:0005178)|Rho GTPase activator activity (GO:0005100)	p.T26T(1)		breast(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.83e-05)		CTAGGCAGGCCGTTAGGCTGG	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	11											84	78	80					11																	119291056		2199	4295	6494	118796266	SO:0001819	synonymous_variant	7070			M11749	CCDS8424.1	11q23.3	2013-01-14				ENSG00000154096		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11801	protein-coding gene	gene with protein product		188230				2864690	Standard	NM_006288		Approved	CD90	uc001pwr.3	P04216		ENST00000284240.5:c.78G>A	11.37:g.119291056C>T			118796266	Q16008|Q9NSP1	Silent	SNP	ENST00000284240.5	37	CCDS8424.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.729531	0.30684	.	.	ENSG00000154096	ENST00000527590	.	.	.	5.13	-9.74	0.00509	.	.	.	.	.	T	0.42921	0.1224	.	.	.	0.53688	D	0.999977	.	.	.	.	.	.	T	0.50110	-0.8866	4	.	.	.	-5.4845	5.7504	0.18144	0.1146:0.2139:0.0792:0.5922	.	.	.	.	Q	34	.	.	R	-	2	0	THY1	118796266	0.005000	0.15991	0.729000	0.30791	0.832000	0.47134	-2.287000	0.01151	-1.620000	0.01564	-1.303000	0.01326	CGG		0.617	THY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388370.2	NM_006288		T	119291056	C	T	119291056	2	4	77	1	0	0	0	0	0	0	0	1	15924	639	23	1		1	THY1	11	119291056	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	231809	119291056	15715460	715	22451										
PVRL1	5818	broad.mit.edu	37	chr11	119535968	119535968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgtgggcaccggcccggcgCgccgcccatgttcgggagga	17	16	0	0	rs148045547	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:119535968C>T	ENST00000264025.3	-	6	1573	c.1043G>A	c.(1042-1044)cGc>cAc	p.R348H	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	348					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.R348H(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CGGCCCGGCGCGCCGCCCATG	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG,	3,4393		0,3,2195	22	26	25		1043,	4.3	1	11	dbSNP_134	25	0,8584		0,0,4292	no	missense,intron	PVRL1	NM_002855.4,NM_203285.1	29,	0,3,6487	TT,TC,CC		0.0,0.0682,0.0231	possibly-damaging,	348/518,	119535968	3,12977	2198	4292	6490	119041178	SO:0001583	missense	5818			X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9706	protein-coding gene	gene with protein product	"nectin"	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.1043G>A	11.37:g.119535968C>T	ENSP00000264025:p.Arg348His		119041178	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	.	.	.	.	.	.	.	.	.	.	-	19.16	3.773299	0.69992	6.82E-4	0.0	ENSG00000110400	ENST00000264025	T	0.75938	-0.98	4.32	4.32	0.51571	.	0.331525	0.28072	N	0.016707	T	0.69251	0.3090	L	0.52011	1.625	0.80722	D	1	D	0.61080	0.989	B	0.42087	0.375	T	0.71170	-0.4671	10	0.33141	T	0.24	.	16.1855	0.81948	0.0:1.0:0.0:0.0	.	348	Q15223	PVRL1_HUMAN	H	348	ENSP00000264025:R348H	ENSP00000264025:R348H	R	-	2	0	PVRL1	119041178	1.000000	0.71417	0.974000	0.42286	0.986000	0.74619	3.522000	0.53480	2.108000	0.64289	0.479000	0.44913	CGC		0.677	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			T	119535968	C	T	119535968	3	4	77	1	0	0	0	0	1	0	0	0	12876	768	27	1	900	1	PVRL1	11	119535968	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	244912	119535968	15470548	716	22452										
C11orf63	79864	broad.mit.edu	37	chr11	122795675	122795675	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaaatggaaaatgctgccaTcgatcctgaagataaatggc	11	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:122795675T>A	ENST00000531316.1	+	3	1027	c.935T>A	c.(934-936)aTc>aAc	p.I312N	C11orf63_ENST00000227349.2_Missense_Mutation_p.I312N|RNU4-23P_ENST00000362839.1_RNA			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	312					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.I312N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		AATGCTGCCATCGATCCTGAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											186	155	165					11																	122795675		2202	4299	6501	122300885	SO:0001583	missense	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.935T>A	11.37:g.122795675T>A	ENSP00000431669:p.Ile312Asn		122300885	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.368618	0.61624	.	.	ENSG00000109944	ENST00000227349;ENST00000531316	T;T	0.47528	0.84;0.84	5.98	2.4	0.29515	.	0.621973	0.15694	N	0.249267	T	0.49779	0.1577	M	0.63428	1.95	0.09310	N	1	P	0.49090	0.919	P	0.48627	0.584	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.5844	8.1297	0.31020	0.0:0.232:0.0:0.768	.	312	Q6NUN7	CK063_HUMAN	N	312	ENSP00000227349:I312N;ENSP00000431669:I312N	ENSP00000227349:I312N	I	+	2	0	C11orf63	122300885	0.000000	0.05858	0.161000	0.22692	0.986000	0.74619	0.250000	0.18235	0.519000	0.28406	0.460000	0.39030	ATC		0.403	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		A	122795675	T	A	122795675	3	1	77	1	0	0	0	0	1	0	0	0	1658	1435	50	5	1009	5	C11orf63	11	122795675	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	3259707	122795675	12210841	717	22453										
VWA5A	4013	broad.mit.edu	37	chr11	124005694	124005694	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggtattgcccgggcatcaGggggcacctcagaatttatc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:124005694delG	ENST00000456829.2	+	12	1563	c.1312delG	c.(1312-1314)gggfs	p.G439fs	VWA5A_ENST00000392748.1_Frame_Shift_Del_p.G439fs|VWA5A_ENST00000360334.4_Intron	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	439	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.							p.G439fs*20(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						CCGGGCATCAGGGGGCACCTC	0.502																																																1	Deletion - Frameshift(1)	large_intestine(1)	11											85	77	79					11																	124005694		2201	4299	6500	123510904	SO:0001589	frameshift_variant	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1312delG	11.37:g.124005694delG	ENSP00000407726:p.Gly439fs		123510904	Q6UN19|Q6UN20|Q9BVF8	Frame_Shift_Del	DEL	ENST00000456829.2	37	CCDS8444.1																																																																																				0.502	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		-	124005694	G	-	124005694	7	5	77	1	0	1	0	1	0	0	0	0	17282	1000	35	0	1354	0	VWA5A	11	124005694	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1210019	124005694	11000822	718	22454										
SIAE	54414	broad.mit.edu	37	chr11	124517286	124517286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagtccaaatgggaagaaaCgctccgtctgcccctgggaa	11	12	1	1	rs147649509	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:124517286C>T	ENST00000263593.3	-	7	1113	c.941G>A	c.(940-942)cGt>cAt	p.R314H	SIAE_ENST00000545756.1_Missense_Mutation_p.R279H			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	314			R -> H (defective enzyme secretion and activity). {ECO:0000269|PubMed:20555325}.		carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)	p.R314H(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		TGGGAAGAAACGCTCCGTCTG	0.478													C|||	5	0.000998403	0.0015	0	5008	,	,		18286	0		0	False		,,,				2504	0.0031															1	Substitution - Missense(1)	large_intestine(1)	11						C	HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	157	126	136		836,941	2.3	0	11	dbSNP_134	136	0,8598		0,0,4299	yes	missense,missense	SIAE	NM_001199922.1,NM_170601.4	29,29	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	279/489,314/524	124517286	1,12999	2201	4299	6500	124022496	SO:0001583	missense	54414			AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"sialic acid-specific acetylesterase II"	610079	"Ysg2 homolog (mouse)"	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.941G>A	11.37:g.124517286C>T	ENSP00000263593:p.Arg314His		124022496	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Missense_Mutation	SNP	ENST00000263593.3	37	CCDS8449.1	.	.	.	.	.	.	.	.	.	.	C	6.337	0.430194	0.12045	2.27E-4	0.0	ENSG00000110013	ENST00000263593;ENST00000545756	D;D	0.94793	-3.52;-3.52	5.44	2.35	0.29111	Esterase, SGNH hydrolase-type (1);	0.489617	0.21668	N	0.070918	D	0.91236	0.7238	M	0.77820	2.39	0.09310	N	1	B	0.22683	0.073	B	0.19946	0.027	T	0.77552	-0.2545	10	0.15066	T	0.55	-12.3651	5.0126	0.14321	0.2581:0.5417:0.1258:0.0745	.	314	Q9HAT2	SIAE_HUMAN	H	314;279	ENSP00000263593:R314H;ENSP00000437877:R279H	ENSP00000263593:R314H	R	-	2	0	SIAE	124022496	0.561000	0.26578	0.047000	0.18901	0.055000	0.15305	0.871000	0.28023	0.776000	0.33473	-0.917000	0.02746	CGT		0.478	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601		T	124517286	C	T	124517286	3	4	77	1	0	0	0	0	1	0	0	0	14335	536	19	1	646	1	SIAE	11	124517286	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	511592	124517286	10489230	719	22455										
SLC37A2	219855	broad.mit.edu	37	chr11	124952225	124952225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgcccctctacatcgccaAtgtgggtaagtccaagagaa	10	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:124952225A>G	ENST00000403796.2	+	10	1272	c.971A>G	c.(970-972)aAt>aGt	p.N324S	SLC37A2_ENST00000308074.4_Missense_Mutation_p.N324S|SLC37A2_ENST00000298280.5_Missense_Mutation_p.N324S|SLC37A2_ENST00000407458.1_Missense_Mutation_p.N324S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	324					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.N324S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TACATCGCCAATGTGGGTAAG	0.577																																					Melanoma(11;373 620 21213 26083 47768)											1	Substitution - Missense(1)	large_intestine(1)	11											127	109	115					11																	124952225		2201	4299	6500	124457435	SO:0001583	missense	219855			AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"Solute carriers"	20644	protein-coding gene	gene with protein product			"solute carrier family 37 (glycerol-3-phosphate transporter), member 2"				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.971A>G	11.37:g.124952225A>G	ENSP00000384407:p.Asn324Ser		124457435	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.652278	0.29336	.	.	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.046569	0.85682	D	0.000000	T	0.46386	0.1390	L	0.45137	1.4	0.52099	D	0.999944	B;B	0.21753	0.049;0.06	B;B	0.25987	0.061;0.065	T	0.36553	-0.9743	10	0.26408	T	0.33	-17.7921	14.5002	0.67716	1.0:0.0:0.0:0.0	.	324;324	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	S	324	ENSP00000384407:N324S;ENSP00000385126:N324S;ENSP00000298280:N324S;ENSP00000311833:N324S	ENSP00000298280:N324S	N	+	2	0	SLC37A2	124457435	1.000000	0.71417	1.000000	0.80357	0.444000	0.32077	8.761000	0.91691	2.098000	0.63641	0.459000	0.35465	AAT		0.577	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		G	124952225	A	G	124952225	3	3	77	1	0	0	0	0	1	0	0	0	14635	101	4	4	1009	4	SLC37A2	11	124952225	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	434939	124952225	10054291	720	22456										
PKNOX2	63876	broad.mit.edu	37	chr11	125237794	125237794	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaggctgtccacatctctgCcccctcagctgctgccagca							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:125237794delC	ENST00000298282.9	+	5	411	c.140delC	c.(139-141)gccfs	p.A47fs	PKNOX2_ENST00000530517.1_3'UTR|PKNOX2_ENST00000542175.1_Intron	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	47					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)	p.S49fs*35(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		CACATCTCTGCCCCCTCAGCT	0.637																																																1	Deletion - Frameshift(1)	large_intestine(1)	11											56	68	64					11																	125237794		2089	4208	6297	124743004	SO:0001589	frameshift_variant	63876			AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.140delC	11.37:g.125237794delC	ENSP00000298282:p.Ala47fs		124743004	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Frame_Shift_Del	DEL	ENST00000298282.9	37	CCDS41730.1																																																																																				0.637	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			-	125237794	C	-	125237794	7	5	77	1	0	1	0	1	0	0	0	0	12014	739	26	0	146	0	PKNOX2	11	125237794	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	285569	125237794	9768722	721	22457										
SRPR	6734	broad.mit.edu	37	chr11	126137205	126137205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcatggtagtgggagcacGgatcttactgctctcctctg	11	11	4	0	rs558045090		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:126137205G>A	ENST00000332118.6	-	4	545	c.391C>T	c.(391-393)Cgt>Tgt	p.R131C	FOXRED1_ENST00000442061.2_5'Flank|SRPR_ENST00000532259.1_Missense_Mutation_p.R103C|SRPR_ENST00000530680.1_5'Flank|FOXRED1_ENST00000263578.5_5'Flank|FOXRED1_ENST00000532125.1_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	131					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.R131C(1)		endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		GTGGGAGCACGGATCTTACTG	0.448													G|||	1	0.000199681	0	0	5008	,	,		19003	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11											137	134	135					11																	126137205		2201	4298	6499	125642415	SO:0001583	missense	6734			BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"signal recognition particle receptor ('docking protein')"			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.391C>T	11.37:g.126137205G>A	ENSP00000328023:p.Arg131Cys		125642415	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.395232	0.42512	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	4.92	4.92	0.64577	Signal recognition particle receptor, alpha subunit, N-terminal (1);	0.054376	0.64402	D	0.000001	T	0.67449	0.2894	M	0.67953	2.075	0.80722	D	1	B;B	0.25850	0.125;0.136	B;B	0.24269	0.052;0.052	T	0.69075	-0.5241	9	0.72032	D	0.01	-7.5361	18.3148	0.90217	0.0:0.0:1.0:0.0	.	103;131	E9PJS4;P08240	.;SRPR_HUMAN	C	131;103	.	ENSP00000328023:R131C	R	-	1	0	SRPR	125642415	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	4.960000	0.63673	2.546000	0.85860	0.305000	0.20034	CGT		0.448	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		A	126137205	G	A	126137205	3	1	77	1	0	0	0	0	1	0	0	0	15201	1116	39	1	1569	1	SRPR	11	126137205	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	899411	126137205	8869311	722	22458										
ARHGAP32	9743	broad.mit.edu	37	chr11	128840469	128840469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccacatatgtgttataacGaagacccatggaggctggtg	13	8	0	1	rs142674734		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:128840469G>A	ENST00000310343.9	-	22	4596	c.4597C>T	c.(4597-4599)Cgt>Tgt	p.R1533C	ARHGAP32_ENST00000392657.3_Missense_Mutation_p.R1184C|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.R1184C|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1533	Interaction with GAB2.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)	p.R1184C(1)|p.R1533C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GTGTTATAACGAAGACCCATG	0.542													G|||	1	0.000199681	0	0	5008	,	,		19697	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	11						G	CYS/ARG,CYS/ARG	0,4402		0,0,2201	81	73	75		4597,3550	5.8	0.5	11	dbSNP_134	75	2,8592	2.2+/-6.3	0,2,4295	no	missense,missense	ARHGAP32	NM_001142685.1,NM_014715.3	180,180	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	1533/2088,1184/1739	128840469	2,12994	2201	4297	6498	128345679	SO:0001583	missense	9743			AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.4597C>T	11.37:g.128840469G>A	ENSP00000310561:p.Arg1533Cys		128345679	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.569346	0.45798	0.0	2.33E-4	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.15952	2.42;2.38;2.38	5.75	5.75	0.90469	.	0.187703	0.47455	D	0.000228	T	0.33469	0.0864	M	0.66939	2.045	0.19575	N	0.999967	D	0.89917	1.0	P	0.60609	0.877	T	0.30592	-0.9973	10	0.87932	D	0	.	9.0189	0.36186	0.0732:0.0:0.7784:0.1484	.	1533	A7KAX9	RHG32_HUMAN	C	1533;1184;1184	ENSP00000310561:R1533C;ENSP00000376425:R1184C;ENSP00000432862:R1184C	ENSP00000310561:R1533C	R	-	1	0	ARHGAP32	128345679	0.996000	0.38824	0.547000	0.28179	0.942000	0.58702	3.756000	0.55205	2.719000	0.93026	0.655000	0.94253	CGT		0.542	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		A	128840469	G	A	128840469	3	1	77	1	0	0	0	0	1	0	0	0	881	1058	37	1	1670	1	ARHGAP32	11	128840469	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2703264	128840469	6166047	723	22459										
PRDM10	56980	broad.mit.edu	37	chr11	129787028	129787028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatttcccttttaccttatcGcaatactgacaaaagtaatc	3	10	0	1	rs141324100		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr11:129787028G>A	ENST00000360871.3	-	15	2550	c.2319C>T	c.(2317-2319)tgC>tgT	p.C773C	PRDM10_ENST00000526082.1_Silent_p.C691C|PRDM10_ENST00000423662.2_Silent_p.C691C|PRDM10_ENST00000528746.1_Silent_p.C747C|PRDM10_ENST00000358825.5_Silent_p.C777C|PRDM10_ENST00000304538.6_Silent_p.C687C	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	777					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.C773C(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TTACCTTATCGCAATACTGAC	0.378																																																1	Substitution - coding silent(1)	large_intestine(1)	11						G	,,,	1,4401	2.1+/-5.4	0,1,2200	179	162	168		2331,2319,2073,2061	0.8	1	11	dbSNP_134	168	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,,,	777/1161,773/1157,691/1062,687/1024	129787028	1,12995	2201	4297	6498	129292238	SO:0001819	synonymous_variant	56980			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2319C>T	11.37:g.129787028G>A			129292238	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																				0.378	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129787028	G	A	129787028	2	1	77	1	0	0	0	0	0	0	0	1	12485	1079	38	1		1	PRDM10	11	129787028	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	946559	129787028	5219488	724	22460										
TULP3	7289	broad.mit.edu	37	chr12	3040268	3040268	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aacctcctgggagacatagaCgacctggaggactttgtgta	12	9	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:3040268C>T	ENST00000448120.2	+	6	609	c.558C>T	c.(556-558)gaC>gaT	p.D186D	RNU7-166P_ENST00000459397.1_RNA|TULP3_ENST00000397132.2_Silent_p.D186D	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	186					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)	p.D186D(1)		endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GAGACATAGACGACCTGGAGG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	12											119	116	117					12																	3040268		2203	4300	6503	2910529	SO:0001819	synonymous_variant	7289			AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"Intraflagellar transport homologs"	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.558C>T	12.37:g.3040268C>T			2910529	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	De_novo_Start_InFrame	SNP	ENST00000448120.2	37	CCDS8519.1																																																																																				0.532	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		T	3040268	C	T	3040268	2	4	77	1	0	0	0	0	0	0	0	1	16815	535	19	1		1	TULP3	12	3040268	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		3040268	130811627	725	22461										
PRMT8	56341	broad.mit.edu	37	chr12	3692311	3692311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcgcaacgactacgtccacGccctggtcacctattttaat	7	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:3692311G>A	ENST00000382622.3	+	8	1306	c.916G>A	c.(916-918)Gcc>Acc	p.A306T	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Missense_Mutation_p.A297T	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	306	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.A306T(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			CTACGTCCACGCCCTGGTCAC	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	12											96	77	84					12																	3692311		2203	4300	6503	3562572	SO:0001583	missense	56341			AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.916G>A	12.37:g.3692311G>A	ENSP00000372067:p.Ala306Thr		3562572	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	26.0	4.692116	0.88735	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	T;T	0.78595	-1.19;-1.19	5.55	5.55	0.83447	.	0.047145	0.85682	D	0.000000	D	0.90469	0.7015	H	0.95850	3.73	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.57425	0.82;0.67	D	0.93312	0.6685	10	0.87932	D	0	.	17.0578	0.86539	0.0:0.0:1.0:0.0	.	297;306	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	T	297;306	ENSP00000414507:A297T;ENSP00000372067:A306T	ENSP00000372067:A306T	A	+	1	0	PRMT8	3562572	1.000000	0.71417	0.996000	0.52242	0.520000	0.34377	9.869000	0.99810	2.625000	0.88918	0.650000	0.86243	GCC		0.498	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		A	3692311	G	A	3692311	3	1	77	1	0	0	0	0	1	0	0	0	12576	1087	38	1	946	1	PRMT8	12	3692311	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	652043	3692311	130159584	726	22462										
VWF	7450	broad.mit.edu	37	chr12	6103073	6103073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aacgcagaccccgttggtccGacagaggtgggcataagagg	15	10	0	3	rs569962285		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:6103073G>A	ENST00000261405.5	-	37	6807	c.6553C>T	c.(6553-6555)Cgg>Tgg	p.R2185W		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2185			R -> Q (in dbSNP:rs2229446).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.R2185W(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCGTTGGTCCGACAGAGGTGG	0.557													G|||	1	0.000199681	0	0	5008	,	,		17412	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	12											72	60	64					12																	6103073		2203	4300	6503	5973334	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6553C>T	12.37:g.6103073G>A	ENSP00000261405:p.Arg2185Trp		5973334	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616046	0.87359	.	.	ENSG00000110799	ENST00000261405	T	0.77620	-1.11	5.3	5.3	0.74995	Uncharacterised domain, cysteine-rich (2);	0.000000	0.40385	N	0.001115	D	0.90154	0.6923	M	0.93507	3.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91849	0.5490	10	0.72032	D	0.01	.	11.7774	0.51993	0.0:0.0:0.7203:0.2797	.	2185	P04275	VWF_HUMAN	W	2185	ENSP00000261405:R2185W	ENSP00000261405:R2185W	R	-	1	2	VWF	5973334	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	2.942000	0.49018	2.482000	0.83794	0.655000	0.94253	CGG		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6103073	G	A	6103073	3	1	77	1	0	0	0	0	1	0	0	0	17286	1057	37	1	1952	1	VWF	12	6103073	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2410762	6103073	127748822	727	22463										
CHD4	1108	broad.mit.edu	37	chr12	6696613	6696613	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagctcaaatattcattcatGccctgcaattctgtgtcttc	6	11	5	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:6696613G>A	ENST00000357008.2	-	25	3979	c.3816C>T	c.(3814-3816)ggC>ggT	p.G1272G	CHD4_ENST00000540960.1_5'UTR|RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000544040.1_Silent_p.G1265G|CHD4_ENST00000544484.1_Silent_p.G1269G|CHD4_ENST00000309577.6_Silent_p.G1272G	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1272					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.G1272G(1)		central_nervous_system(2)	2						ATTCATTCATGCCCTGCAATT	0.458																																					Colon(32;586 792 4568 16848 45314)											1	Substitution - coding silent(1)	large_intestine(1)	12											228	191	203					12																	6696613		2203	4300	6503	6566874	SO:0001819	synonymous_variant	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.3816C>T	12.37:g.6696613G>A			6566874	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																				0.458	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6696613	G	A	6696613	2	1	77	1	0	0	0	0	0	0	0	1	3333	1306	46	3		3	CHD4	12	6696613	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	593540	6696613	127155282	728	22464										
MLF2	8079	broad.mit.edu	37	chr12	6858070	6858070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagcccctgaggactcaagcCgccgaaactccaggggacgc	12	16	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:6858070C>T	ENST00000203630.5	-	8	1282	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	MLF2_ENST00000542154.1_Missense_Mutation_p.R213Q|MLF2_ENST00000435120.1_Missense_Mutation_p.R213Q|MLF2_ENST00000539187.1_Missense_Mutation_p.R213Q|MLF2_ENST00000564181.1_5'Flank			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	213					defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R213Q(1)		kidney(2)|large_intestine(3)|lung(4)	9						GGACTCAAGCCGCCGAAACTC	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	12											16	18	17					12																	6858070		2186	4286	6472	6728331	SO:0001583	missense	8079			U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.638G>A	12.37:g.6858070C>T	ENSP00000203630:p.Arg213Gln		6728331		Missense_Mutation	SNP	ENST00000203630.5	37	CCDS8559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.98|17.98	3.520830|3.520830	0.64747|0.64747	.|.	.|.	ENSG00000089693|ENSG00000089693	ENST00000537126|ENST00000435120;ENST00000203630;ENST00000542154;ENST00000539187	.|.	.|.	.|.	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.054096	.|0.64402	.|D	.|0.000001	T|T	0.33876|0.33876	0.0878|0.0878	L|L	0.27053|0.27053	0.805|0.805	0.37331|0.37331	D|D	0.909998|0.909998	.|P	.|0.52692	.|0.955	.|B	.|0.38562	.|0.276	T|T	0.31024|0.31024	-0.9958|-0.9958	6|9	0.87932|0.23891	D|T	0|0.37	.|.	16.6666|16.6666	0.85254|0.85254	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|213	.|Q15773	.|MLF2_HUMAN	S|Q	224|213	.|.	ENSP00000439789:G224S|ENSP00000203630:R213Q	G|R	-|-	1|2	0|0	MLF2|MLF2	6728331|6728331	0.606000|0.606000	0.26949|0.26949	0.906000|0.906000	0.35671|0.35671	0.023000|0.023000	0.10783|0.10783	6.266000|6.266000	0.72540|0.72540	2.365000|2.365000	0.80145|0.80145	0.491000|0.491000	0.48974|0.48974	GGC|CGG		0.682	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2			T	6858070	C	T	6858070	3	4	77	1	0	0	0	0	1	0	0	0	9646	652	23	1	112	1	MLF2	12	6858070	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	161457	6858070	126993825	729	22465										
C1S	716	broad.mit.edu	37	chr12	7174393	7174393	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acttgtcaaagcaatggaaaGtggagtaattccaaactgaa	9	6	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:7174393G>T	ENST00000406697.1	+	12	1666	c.1038G>T	c.(1036-1038)aaG>aaT	p.K346N	C1S_ENST00000328916.3_Missense_Mutation_p.K346N|C1S_ENST00000402681.3_Missense_Mutation_p.K179N|C1S_ENST00000360817.5_Missense_Mutation_p.K346N			P09871	C1S_HUMAN	complement component 1, s subcomponent	346	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)	p.K346N(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GCAATGGAAAGTGGAGTAATT	0.373																																					GBM(156;750 1943 12971 24779 31015)											1	Substitution - Missense(1)	large_intestine(1)	12											144	132	136					12																	7174393		2203	4300	6503	7044654	SO:0001583	missense	716				CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1038G>T	12.37:g.7174393G>T	ENSP00000385035:p.Lys346Asn		7044654	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.704619	0.68615	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.74	5.74	0.90152	Complement control module (2);Sushi/SCR/CCP (3);	0.334156	0.21912	N	0.067300	T	0.56455	0.1986	L	0.41906	1.305	0.34113	D	0.663167	B	0.22346	0.068	B	0.28553	0.091	T	0.61955	-0.6956	10	0.33940	T	0.23	.	15.4279	0.75069	0.0:0.0:1.0:0.0	.	346	P09871	C1S_HUMAN	N	346;346;346;334;179	ENSP00000385035:K346N;ENSP00000328173:K346N;ENSP00000354057:K346N;ENSP00000384171:K179N	ENSP00000328173:K346N	K	+	3	2	C1S	7044654	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.924000	0.56476	2.710000	0.92621	0.561000	0.74099	AAG		0.373	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		T	7174393	G	T	7174393	3	4	77	1	0	0	0	0	1	0	0	0	1980	1020	36	2	1068	2	C1S	12	7174393	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	316323	7174393	126677502	730	22466										
CD163L1	283316	broad.mit.edu	37	chr12	7527308	7527308	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgatagatctctactctccCggcacagcggctgtccccat	9	15	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:7527308C>A	ENST00000313599.3	-	13	3196	c.3139G>T	c.(3139-3141)Ggg>Tgg	p.G1047W	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Missense_Mutation_p.G1057W|CD163L1_ENST00000396630.1_Missense_Mutation_p.G1047W			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1047	SRCR 10. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.G1047W(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TCTACTCTCCCGGCACAGCGG	0.552											OREG0021653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											45	41	43					12																	7527308		2203	4300	6503	7418575	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3139G>T	12.37:g.7527308C>A	ENSP00000315945:p.Gly1047Trp	642	7418575	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967138	0.74131	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	D;D;D	0.84298	-1.83;-1.83;-1.83	2.52	2.52	0.30459	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.000000	0.50627	U	0.000111	D	0.95755	0.8619	H	0.99919	4.95	0.41522	D	0.988401	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95772	0.8809	10	0.87932	D	0	.	11.1201	0.48284	0.0:1.0:0.0:0.0	.	1057;1047	E7EVK4;Q9NR16	.;C163B_HUMAN	W	1047;1057;1047	ENSP00000315945:G1047W;ENSP00000393474:G1057W;ENSP00000379871:G1047W	ENSP00000315945:G1047W	G	-	1	0	CD163L1	7418575	0.999000	0.42202	0.680000	0.29994	0.386000	0.30323	4.521000	0.60532	1.694000	0.51137	0.462000	0.41574	GGG		0.552	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7527308	C	A	7527308	3	1	77	1	0	0	0	0	1	0	0	0	2974	652	23	2	1250	2	CD163L1	12	7527308	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	352915	7527308	126324587	731	22467										
SLC2A14	144195	broad.mit.edu	37	chr12	7970444	7970444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacagcagcagaggggaagaGcaatccgactaggaagttgg	15	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:7970444G>A	ENST00000543909.1	-	15	2086	c.1327C>T	c.(1327-1329)Ctc>Ttc	p.L443F	SLC2A14_ENST00000535295.1_Missense_Mutation_p.L334F|SLC2A14_ENST00000542505.1_Missense_Mutation_p.L84F|SLC2A14_ENST00000396589.2_Missense_Mutation_p.L443F|SLC2A14_ENST00000539924.1_Missense_Mutation_p.L458F|SLC2A14_ENST00000542546.1_Missense_Mutation_p.L334F|SLC2A14_ENST00000431042.2_Missense_Mutation_p.L420F|SLC2A14_ENST00000340749.5_Missense_Mutation_p.L420F			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	443					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)	p.L443F(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GAGGGGAAGAGCAATCCGACT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	12											50	51	51					12																	7970444		2203	4300	6503	7861711	SO:0001583	missense	144195			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1327C>T	12.37:g.7970444G>A	ENSP00000440480:p.Leu443Phe		7861711	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	G	1.840	-0.467623	0.04476	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	T;T;T;T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96;-0.96;-0.96;-0.96	3.31	1.29	0.21616	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.589505	0.18568	N	0.137403	T	0.56062	0.1960	L	0.33792	1.035	0.34203	D	0.673365	B;B;B;B	0.17038	0.02;0.011;0.009;0.02	B;B;B;B	0.21151	0.033;0.022;0.013;0.033	T	0.49808	-0.8900	10	0.11182	T	0.66	.	6.31	0.21159	0.3762:0.0:0.6238:0.0	.	458;334;420;443	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	F	420;443;420;84;443;334;334;458	ENSP00000340450:L420F;ENSP00000440480:L443F;ENSP00000407287:L420F;ENSP00000438484:L84F;ENSP00000379834:L443F;ENSP00000440492:L334F;ENSP00000443903:L334F;ENSP00000445929:L458F	ENSP00000340450:L420F	L	-	1	0	SLC2A14	7861711	0.996000	0.38824	0.944000	0.38274	0.761000	0.43186	0.603000	0.24149	0.457000	0.26962	0.195000	0.17529	CTC		0.473	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		A	7970444	G	A	7970444	3	1	77	1	0	0	0	0	1	0	0	0	14580	971	34	3	243	3	SLC2A14	12	7970444	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	443136	7970444	125881451	732	22468										
FOXJ2	55810	broad.mit.edu	37	chr12	8200750	8200750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgggcctccccctgtaatgGccatgcatccacccccgctg	9	18	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:8200750G>A	ENST00000162391.3	+	7	2235	c.1090G>A	c.(1090-1092)Gcc>Acc	p.A364T	FOXJ2_ENST00000428177.2_Missense_Mutation_p.A364T	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	364					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.A364T(1)		autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		CCCTGTAATGGCCATGCATCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											57	49	51					12																	8200750		2203	4300	6503	8092017	SO:0001583	missense	55810			AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"Forkhead boxes"	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.1090G>A	12.37:g.8200750G>A	ENSP00000162391:p.Ala364Thr		8092017	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Missense_Mutation	SNP	ENST00000162391.3	37	CCDS8587.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624475	0.28889	.	.	ENSG00000065970	ENST00000162391;ENST00000428177	D;D	0.94966	-3.4;-3.57	5.61	4.72	0.59763	.	0.536026	0.17910	N	0.157863	D	0.88603	0.6481	L	0.44542	1.39	0.32741	N	0.50764	P;B	0.35155	0.487;0.0	B;B	0.31101	0.124;0.002	D	0.85083	0.0947	10	0.02654	T	1	.	10.6197	0.45472	0.0887:0.0:0.9113:0.0	.	364;364	Q9P0K8;Q9P0K8-2	FOXJ2_HUMAN;.	T	364	ENSP00000162391:A364T;ENSP00000403411:A364T	ENSP00000162391:A364T	A	+	1	0	FOXJ2	8092017	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.381000	0.44336	1.376000	0.46267	0.491000	0.48974	GCC		0.652	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		A	8200750	G	A	8200750	3	1	77	1	0	0	0	0	1	0	0	0	6031	1203	42	3	1112	3	FOXJ2	12	8200750	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	230306	8200750	125651145	733	22469										
C3AR1	719	broad.mit.edu	37	chr12	8211804	8211804	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggggtgttggcacttgatcGtcatctgtgaattggcctaa	13	7	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:8211804G>A	ENST00000307637.4	-	2	1181	c.978C>T	c.(976-978)gaC>gaT	p.D326D		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	326					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.D326D(1)		breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		GCACTTGATCGTCATCTGTGA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	12											164	157	159					12																	8211804		2203	4300	6503	8103071	SO:0001819	synonymous_variant	719			U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.978C>T	12.37:g.8211804G>A			8103071	O43771|Q92868	Silent	SNP	ENST00000307637.4	37	CCDS8588.1																																																																																				0.458	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			A	8211804	G	A	8211804	2	1	77	1	0	0	0	0	0	0	0	1	2211	1136	40	1		1	C3AR1	12	8211804	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11054	8211804	125640091	734	22470										
TAS2R14	50840	broad.mit.edu	37	chr12	11091497	11091497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgagaaaataaaaagtacCgaggcctgtagctaaccaga	9	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:11091497C>T	ENST00000537503.1	-	1	365	c.310G>A	c.(310-312)Ggt>Agt	p.G104S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	104					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.G104S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						TAAAAAGTACCGAGGCCTGTA	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											48	49	49					12																	11091497		2202	4300	6502	10982764	SO:0001583	missense	50840			AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.310G>A	12.37:g.11091497C>T	ENSP00000441949:p.Gly104Ser		10982764	Q645X3	Missense_Mutation	SNP	ENST00000537503.1	37	CCDS8637.1	.	.	.	.	.	.	.	.	.	.	C	0.037	-1.299966	0.01364	.	.	ENSG00000212127	ENST00000537503	T	0.26223	1.75	4.03	1.62	0.23740	.	0.407670	0.21546	N	0.072804	T	0.04998	0.0134	N	0.01081	-1.03	0.09310	N	1	B	0.31730	0.337	B	0.22152	0.038	T	0.39014	-0.9634	10	0.02654	T	1	.	5.5135	0.16894	0.0:0.2407:0.0:0.7593	.	104	Q9NYV8	T2R14_HUMAN	S	104	ENSP00000441949:G104S	ENSP00000375094:G104S	G	-	1	0	TAS2R14	10982764	0.901000	0.30685	0.003000	0.11579	0.004000	0.04260	1.247000	0.32815	0.225000	0.20959	-0.320000	0.08662	GGT		0.368	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922		T	11091497	C	T	11091497	3	4	77	1	0	0	0	0	1	0	0	0	15607	652	23	1	646	1	TAS2R14	12	11091497	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2879693	11091497	122760398	735	22471										
STRAP	11171	broad.mit.edu	37	chr12	16043574	16043574	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggacaggataaactgttacGcatatatgacttgaacaaac	9	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:16043574G>A	ENST00000419869.2	+	4	687	c.374G>A	c.(373-375)cGc>cAc	p.R125H	STRAP_ENST00000538352.1_Missense_Mutation_p.R31H|STRAP_ENST00000025399.6_Missense_Mutation_p.R138H	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	125					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)	p.R125H(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				AAACTGTTACGCATATATGAC	0.274																																																1	Substitution - Missense(1)	large_intestine(1)	12											75	78	77					12																	16043574		2203	4300	6503	15934841	SO:0001583	missense	11171			AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"WD repeat domain containing"	30796	protein-coding gene	gene with protein product	"Unr-interacting protein"	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.374G>A	12.37:g.16043574G>A	ENSP00000392270:p.Arg125His		15934841	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Missense_Mutation	SNP	ENST00000419869.2	37	CCDS8676.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400396	0.62177	.	.	ENSG00000023734	ENST00000538352;ENST00000025399;ENST00000419869	T;T;T	0.67523	-0.27;-0.27;-0.27	4.81	3.92	0.45320	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.098289	0.64402	D	0.000001	T	0.65606	0.2707	M	0.76727	2.345	0.58432	D	0.999999	P;P	0.45569	0.861;0.856	B;B	0.39562	0.303;0.303	T	0.72141	-0.4380	10	0.87932	D	0	-7.6984	13.0515	0.58958	0.0777:0.0:0.9223:0.0	.	138;125	B4DNJ6;Q9Y3F4	.;STRAP_HUMAN	H	31;138;125	ENSP00000439761:R31H;ENSP00000025399:R138H;ENSP00000392270:R125H	ENSP00000025399:R138H	R	+	2	0	STRAP	15934841	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.585000	0.90802	1.251000	0.43983	0.585000	0.79938	CGC		0.274	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178		A	16043574	G	A	16043574	3	1	77	1	0	0	0	0	1	0	0	0	15365	1087	38	1	388	1	STRAP	12	16043574	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4952077	16043574	117808321	736	22472										
ABCC9	10060	broad.mit.edu	37	chr12	21995261	21995261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacttacttagaggcaacccGaaagtatttctggataaaat	7	7	1	1	rs387907208		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:21995261G>A	ENST00000261201.4	-	27	3459	c.3460C>T	c.(3460-3462)Cgg>Tgg	p.R1154W	ABCC9_ENST00000261200.4_Missense_Mutation_p.R1154W|ABCC9_ENST00000345162.2_Missense_Mutation_p.R1118W|RP11-729I10.2_ENST00000539874.1_RNA	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1154	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		R -> Q (in HTOCD; mutant channels show reduced ATP sensitivity). {ECO:0000269|PubMed:22608503, ECO:0000269|PubMed:22610116}.|R -> W (in HTOCD). {ECO:0000269|PubMed:22608503, ECO:0000269|PubMed:22610116}.		defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.R1154W(1)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	GAGGCAACCCGAAAGTATTTC	0.438																																																1	Substitution - Missense(1)	large_intestine(1)	12											81	75	77					12																	21995261		2203	4300	6503	21886528	SO:0001583	missense	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.3460C>T	12.37:g.21995261G>A	ENSP00000261201:p.Arg1154Trp		21886528	O60707	Missense_Mutation	SNP	ENST00000261201.4	37	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.283716	0.59867	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56	5.0	4.1	0.47936	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	H	0.94423	3.535	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.968	D	0.96178	0.9128	10	0.72032	D	0.01	-9.0031	12.8165	0.57669	0.0:0.0:0.5866:0.4134	.	1154;1154	O60706;O60706-2	ABCC9_HUMAN;.	W	1154;781;1154;1118	ENSP00000261200:R1154W;ENSP00000440521:R781W;ENSP00000261201:R1154W;ENSP00000261202:R1118W	ENSP00000261200:R1154W	R	-	1	2	ABCC9	21886528	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.824000	0.48088	1.312000	0.45043	-0.309000	0.09137	CGG		0.438	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	21995261	G	A	21995261	3	1	77	1	0	0	0	0	1	0	0	0	59	1057	37	1	1379	1	ABCC9	12	21995261	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5951687	21995261	111856634	737	22473										
KRAS	3845	broad.mit.edu	37	chr12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acttacctgtcttgtctttgCtgatgtttcaataaaaggaa	7	7	3	1	rs121913527		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	12											207	188	195					12																	25378562		2203	4300	6503	25269829	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr		25269829	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA		0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25378562	C	T	25378562	3	4	77	1	0	0	0	0	1	0	0	0	8459	797	28	3	262	3	KRAS	12	25378562	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3383301	25378562	108473333	738	22474										
DDX11	1663	broad.mit.edu	37	chr12	31243006	31243006	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgtccctattacgggagccGccttgccatccctgcagccc	9	18	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:31243006G>A	ENST00000407793.2	+	9	1318	c.1067G>A	c.(1066-1068)cGc>cAc	p.R356H	DDX11_ENST00000542838.1_Missense_Mutation_p.R356H|DDX11_ENST00000228264.6_Missense_Mutation_p.R330H|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000545668.1_Missense_Mutation_p.R356H|DDX11_ENST00000350437.4_Missense_Mutation_p.R356H	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	356	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.R356H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TACGGGAGCCGCCTTGCCATC	0.647										Multiple Myeloma(12;0.14)																																						1	Substitution - Missense(1)	large_intestine(1)	12											2	3	3					12																	31243006		1496	3128	4624	31134273	SO:0001583	missense	1663			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1067G>A	12.37:g.31243006G>A	ENSP00000384703:p.Arg356His		31134273	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.270949	0.80469	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23	3.98	3.98	0.46160	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.056546	0.64402	D	0.000001	D	0.90868	0.7131	H	0.95712	3.71	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;0.999	D	0.93340	0.6709	10	0.87932	D	0	.	13.634	0.62213	0.0:0.0:1.0:0.0	.	81;330;356;356;356	Q93000;Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;.;DDX11_HUMAN;.;.	H	356;356;81;330;356;356	ENSP00000443426:R356H;ENSP00000384703:R356H;ENSP00000228264:R330H;ENSP00000440402:R356H;ENSP00000309965:R356H	ENSP00000228264:R330H	R	+	2	0	DDX11	31134273	1.000000	0.71417	0.833000	0.33012	0.717000	0.41224	8.776000	0.91776	2.038000	0.60285	0.505000	0.49811	CGC		0.647	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		A	31243006	G	A	31243006	3	1	77	1	0	0	0	0	1	0	0	0	4349	1087	38	1	1097	1	DDX11	12	31243006	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5864444	31243006	102608889	739	22475										
PKP2	5318	broad.mit.edu	37	chr12	33003756	33003756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttcagcacctggagcagcCgaggtaccccatttagttca	10	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:33003756C>T	ENST00000070846.6	-	5	1346	c.1322G>A	c.(1321-1323)cGg>cAg	p.R441Q	PKP2_ENST00000340811.4_Missense_Mutation_p.R441Q	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	441					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.R441Q(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CTGGAGCAGCCGAGGTACCCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	12											124	123	123					12																	33003756		2203	4300	6503	32895023	SO:0001583	missense	5318			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1322G>A	12.37:g.33003756C>T	ENSP00000070846:p.Arg441Gln		32895023	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.493494	0.26774	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.69175	-0.38;0.79	4.7	3.81	0.43845	Armadillo-like helical (1);Armadillo-type fold (1);	0.591033	0.16475	N	0.212795	T	0.46983	0.1421	L	0.38175	1.15	0.30039	N	0.812779	B;B;P	0.36162	0.338;0.39;0.54	B;B;B	0.20767	0.018;0.031;0.013	T	0.42241	-0.9463	10	0.21540	T	0.41	-21.8214	8.369	0.32404	0.191:0.7242:0.0:0.0848	.	441;441;441	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	Q	441	ENSP00000342800:R441Q;ENSP00000070846:R441Q	ENSP00000070846:R441Q	R	-	2	0	PKP2	32895023	0.555000	0.26530	0.999000	0.59377	0.897000	0.52465	1.270000	0.33086	1.109000	0.41680	0.462000	0.41574	CGG		0.448	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		T	33003756	C	T	33003756	3	4	77	1	0	0	0	0	1	0	0	0	12016	652	23	1	1363	1	PKP2	12	33003756	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1760750	33003756	100848139	740	22476										
LRRK2	120892	broad.mit.edu	37	chr12	40707885	40707885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgaatttcccgtaattgacCggaaacgattattacaacta	6	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:40707885C>T	ENST00000298910.7	+	32	4706	c.4648C>T	c.(4648-4650)Cgg>Tgg	p.R1550W	LRRK2_ENST00000481256.1_3'UTR	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1550			R -> Q (in an ovarian mucinous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.R1550W(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CGTAATTGACCGGAAACGATT	0.378																																																2	Substitution - Missense(2)	large_intestine(2)	12											82	77	78					12																	40707885		2203	4299	6502	38994152	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4648C>T	12.37:g.40707885C>T	ENSP00000298910:p.Arg1550Trp		38994152	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423663	0.83559	.	.	ENSG00000188906	ENST00000298910	T	0.71222	-0.55	5.83	3.86	0.44501	.	0.257637	0.39544	N	0.001339	T	0.57213	0.2038	N	0.12182	0.205	0.35881	D	0.828972	D;D	0.63046	0.983;0.992	B;P	0.46339	0.427;0.513	T	0.67925	-0.5544	10	0.40728	T	0.16	.	14.5714	0.68213	0.266:0.734:0.0:0.0	.	1550;1550	Q17RV3;Q5S007	.;LRRK2_HUMAN	W	1550	ENSP00000298910:R1550W	ENSP00000298910:R1550W	R	+	1	2	LRRK2	38994152	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.422000	0.52749	1.422000	0.47177	0.585000	0.79938	CGG		0.378	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40707885	C	T	40707885	3	4	77	1	0	0	0	0	1	0	0	0	9062	643	23	1	4774	1	LRRK2	12	40707885	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	7704129	40707885	93144010	741	22477										
FAM113B	91523	broad.mit.edu	37	chr12	47629772	47629772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttgggttcccaccccagcGcttgccgctgctcccgctcc	10	20	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:47629772G>A	ENST00000546455.1	+	4	1657	c.926G>A	c.(925-927)cGc>cAc	p.R309H	PCED1B_ENST00000432328.1_Missense_Mutation_p.R309H|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	309	Pro-rich.						hydrolase activity (GO:0016787)	p.R309H(1)									ccaccccagcgcttgccgctg	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											51	55	53					12																	47629772		2203	4300	6503	45916039	SO:0001583	missense	91523			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.926G>A	12.37:g.47629772G>A	ENSP00000446688:p.Arg309His		45916039	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.465077	0.26335	.	.	ENSG00000179715	ENST00000546455;ENST00000432328;ENST00000548348	T;T	0.31247	1.5;1.5	4.28	-4.27	0.03744	.	1.657320	0.04115	N	0.315272	T	0.12390	0.0301	N	0.08118	0	0.09310	N	1	B	0.33904	0.431	B	0.26202	0.067	T	0.11792	-1.0573	10	0.29301	T	0.29	.	5.4039	0.16310	0.1001:0.172:0.5577:0.1702	.	309	Q96HM7	F113B_HUMAN	H	309;309;189	ENSP00000446688:R309H;ENSP00000396040:R309H	ENSP00000396040:R309H	R	+	2	0	FAM113B	45916039	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.241000	0.02911	-0.866000	0.04068	-0.835000	0.03068	CGC		0.652	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47629772	G	A	47629772	3	1	77	1	0	0	0	0	1	0	0	0	5418	1087	38	1	928	1	FAM113B	12	47629772	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6921887	47629772	86222123	742	22478										
OR8S1	341568	broad.mit.edu	37	chr12	48921793	48921793	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accgaaggccgcagggagccCggacacccggagctgagcat	15	14	0	1	rs375054614		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:48921793C>T	ENST00000310194.1	+	2	987	c.987C>T	c.(985-987)ccC>ccT	p.P329P	OR8S1_ENST00000551654.1_3'UTR	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P329P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						GCAGGGAGCCCGGACACCCGG	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	12						C		0,4406		0,0,2203	22	25	24		987	-0.3	0	12		24	1,8599		0,1,4299	no	coding-synonymous	OR8S1	NM_001005203.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		329/360	48921793	1,13005	2203	4300	6503	47208060	SO:0001819	synonymous_variant	341568				CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"GPCR / Class A : Olfactory receptors"	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.987C>T	12.37:g.48921793C>T			47208060		Silent	SNP	ENST00000310194.1	37	CCDS31789.1																																																																																				0.677	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1			T	48921793	C	T	48921793	2	4	77	1	0	0	0	0	0	0	0	1	11277	639	23	1		1	OR8S1	12	48921793	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1292021	48921793	84930102	743	22479										
FKBP11	51303	broad.mit.edu	37	chr12	49315858	49315858	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctgtataggtgatacccaAtgaggcccaggagggctggc	14	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:49315858A>T	ENST00000550765.1	-	6	913	c.515T>A	c.(514-516)aTt>aAt	p.I172N	RP11-302B13.5_ENST00000398092.4_Intron|FKBP11_ENST00000444214.2_Missense_Mutation_p.I70N|AC073610.5_ENST00000537495.1_3'UTR|CCDC65_ENST00000266984.5_Intron	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	172					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.I172N(1)		kidney(1)|large_intestine(3)|lung(1)	5						GTGATACCCAATGAGGCCCAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	12											88	92	91					12																	49315858		2203	4300	6503	47602125	SO:0001583	missense	51303			AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"FK506 binding protein 11 (19 kDa)"			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.515T>A	12.37:g.49315858A>T	ENSP00000449751:p.Ile172Asn		47602125	B4DWB7	Missense_Mutation	SNP	ENST00000550765.1	37	CCDS8773.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810156	0.90707	.	.	ENSG00000134285	ENST00000444214;ENST00000550765	T;T	0.67523	-0.27;0.27	5.85	5.85	0.93711	.	0.065662	0.64402	D	0.000007	T	0.68421	0.2999	N	0.14661	0.345	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.74343	-0.3696	10	0.87932	D	0	-5.8454	15.5289	0.75936	1.0:0.0:0.0:0.0	.	172	Q9NYL4	FKB11_HUMAN	N	70;172	ENSP00000412403:I70N;ENSP00000449751:I172N	ENSP00000412403:I70N	I	-	2	0	FKBP11	47602125	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.151000	0.89636	2.371000	0.80710	0.533000	0.62120	ATT		0.458	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		T	49315858	A	T	49315858	3	4	77	1	0	0	0	0	1	0	0	0	5922	101	4	5	94	5	FKBP11	12	49315858	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	394065	49315858	84536037	744	22480										
MLL2	8085	broad.mit.edu	37	chr12	49434492	49434492	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggtgccaaagcctgggcaGggggtggctcctggggcctt					rs572022239	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:49434492delG	ENST00000301067.7	-	31	7060	c.7061delC	c.(7060-7062)cctfs	p.P2354fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2354	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P2084fs*30(1)									AGCCTGGGCAGGGGGTGGCTC	0.622																																																1	Deletion - Frameshift(1)	large_intestine(1)	12											25	31	29					12																	49434492		1901	4079	5980	47720759	SO:0001589	frameshift_variant	8085			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7061delC	12.37:g.49434492delG	ENSP00000301067:p.Pro2354fs		47720759	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																				0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49434492	G	-	49434492	7	5	77	1	0	1	0	1	0	0	0	0	9651	1000	35	0	9648	0	MLL2	12	49434492	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	118634	49434492	84417403	745	22481										
PRPH	5630	broad.mit.edu	37	chr12	49690017	49690017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcacaacctcgtgctcttccGcaaggtgagtccgagcccct	10	16	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:49690017G>A	ENST00000257860.4	+	2	2101	c.602G>A	c.(601-603)cGc>cAc	p.R201H	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.R201H(1)		kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GTGCTCTTCCGCAAGGTGAGT	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	12											36	38	37					12																	49690017		2203	4300	6503	47976284	SO:0001583	missense	5630				CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.602G>A	12.37:g.49690017G>A	ENSP00000257860:p.Arg201His		47976284	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	37	CCDS8783.1	.	.	.	.	.	.	.	.	.	.	G	37	6.337828	0.97485	.	.	ENSG00000135406	ENST00000257860;ENST00000451891	D	0.92397	-3.03	5.27	5.27	0.74061	Filament (1);	0.000000	0.39909	N	0.001234	D	0.96420	0.8832	M	0.92880	3.355	0.80722	D	1	D	0.59357	0.985	P	0.57371	0.819	D	0.97354	0.9965	10	0.87932	D	0	.	17.7005	0.88293	0.0:0.0:1.0:0.0	.	201	P41219	PERI_HUMAN	H	201;88	ENSP00000257860:R201H	ENSP00000257860:R201H	R	+	2	0	PRPH	47976284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.488000	0.73637	2.474000	0.83562	0.650000	0.86243	CGC		0.672	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		A	49690017	G	A	49690017	3	1	77	1	0	0	0	0	1	0	0	0	12610	1087	38	1	608	1	PRPH	12	49690017	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	255525	49690017	84161878	746	22482										
PRPF40B	25766	broad.mit.edu	37	chr12	50028964	50028964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggaggagaaggaggaggccCggctaagggccaaagaggcc	19	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:50028964C>T	ENST00000380281.1	+	12	1082	c.1018C>T	c.(1018-1020)Cgg>Tgg	p.R340W	PRPF40B_ENST00000261897.1_Missense_Mutation_p.R334W|PRPF40B_ENST00000548825.2_Missense_Mutation_p.R362W|FMNL3_ENST00000550668.1_5'Flank			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	340	FF 2.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)		p.R340R(1)|p.R340W(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						GGAGGAGGCCCGGCTAAGGGC	0.597																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	12											50	49	49					12																	50028964		2203	4300	6503	48315231	SO:0001583	missense	25766			AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"Huntingtin interacting protein C"		"PRP40 pre-mRNA processing factor 40 homolog B (yeast)"			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.1018C>T	12.37:g.50028964C>T	ENSP00000369634:p.Arg340Trp		48315231	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	37		.	.	.	.	.	.	.	.	.	.	C	19.90	3.912815	0.72983	.	.	ENSG00000110844	ENST00000261897;ENST00000380281	T;T	0.30448	1.53;1.55	5.13	5.13	0.70059	.	0.000000	0.56097	D	0.000033	T	0.58264	0.2110	M	0.84683	2.71	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.61004	-0.7150	9	.	.	.	-22.3182	12.9	0.58121	0.1628:0.8372:0.0:0.0	.	340;334;340	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	W	334;340	ENSP00000261897:R334W;ENSP00000369634:R340W	.	R	+	1	2	PRPF40B	48315231	0.978000	0.34361	1.000000	0.80357	0.975000	0.68041	1.448000	0.35112	2.843000	0.97960	0.655000	0.94253	CGG		0.597	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		T	50028964	C	T	50028964	3	4	77	1	0	0	0	0	1	0	0	0	12606	643	23	1	1064	1	PRPF40B	12	50028964	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	338947	50028964	83822931	747	22483										
FMNL3	91010	broad.mit.edu	37	chr12	50044574	50044574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgctggcagctttttgcgCtgtcttgtttttggagcaga	12	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:50044574C>T	ENST00000293590.5	-	17	2118	c.1885G>A	c.(1885-1887)Gcg>Acg	p.A629T	FMNL3_ENST00000352151.5_Missense_Mutation_p.A578T|FMNL3_ENST00000335154.5_Missense_Mutation_p.A629T|FMNL3_ENST00000550488.1_Missense_Mutation_p.A629T			Q8IVF7	FMNL3_HUMAN	formin-like 3	629	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)	p.A629T(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GCTTTTTGCGCTGTCTTGTTT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	12											129	121	124					12																	50044574		2003	4166	6169	48330841	SO:0001583	missense	91010			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.1885G>A	12.37:g.50044574C>T	ENSP00000293590:p.Ala629Thr		48330841	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	ENST00000293590.5	37		.	.	.	.	.	.	.	.	.	.	C	12.73	2.026335	0.35701	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.54	4.54	0.55810	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.113641	0.64402	D	0.000012	T	0.41351	0.1155	N	0.12182	0.205	0.38228	D	0.940945	B;B;B	0.27594	0.182;0.073;0.037	B;B;B	0.31245	0.126;0.059;0.042	T	0.35151	-0.9800	10	0.13108	T	0.6	.	11.0342	0.47791	0.3403:0.6597:0.0:0.0	.	578;629;629	Q8IVF7-2;Q8IVF7-3;Q8IVF7	.;.;FMNL3_HUMAN	T	629;629;578;629	ENSP00000335655:A629T;ENSP00000447479:A629T;ENSP00000344311:A578T;ENSP00000293590:A629T	ENSP00000293590:A629T	A	-	1	0	FMNL3	48330841	0.000000	0.05858	1.000000	0.80357	0.961000	0.63080	0.009000	0.13219	2.776000	0.95493	0.650000	0.86243	GCG		0.527	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		T	50044574	C	T	50044574	3	4	77	1	0	0	0	0	1	0	0	0	5972	797	28	3	1238	3	FMNL3	12	50044574	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	15610	50044574	83807321	748	22484										
KRT74	121391	broad.mit.edu	37	chr12	52966448	52966448	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttctgctgctctaggaagcGtacctggaacccaaatcaac	9	12	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:52966448G>A	ENST00000305620.2	-	2	522	c.475C>T	c.(475-477)Cgc>Tgc	p.R159C	KRT74_ENST00000549343.1_Missense_Mutation_p.R159C	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	159	Coil 1A.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)	p.R159C(1)		kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		TCTAGGAAGCGTACCTGGAAC	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											80	71	74					12																	52966448		2203	4300	6503	51252715	SO:0001583	missense	121391			BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"-", "Intermediate filaments type II, keratins (basic)"	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.475C>T	12.37:g.52966448G>A	ENSP00000307240:p.Arg159Cys		51252715	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	.	.	.	.	.	.	.	.	.	.	G	10.13	1.266065	0.23136	.	.	ENSG00000170484	ENST00000549343;ENST00000305620	D;D	0.92595	-3.07;-3.07	4.71	-0.404	0.12396	Filament (1);	0.321298	0.17789	N	0.161958	D	0.94192	0.8136	H	0.98754	4.32	0.53688	D	0.999971	P	0.36633	0.562	B	0.37888	0.26	D	0.89621	0.3848	10	0.87932	D	0	.	6.0537	0.19799	0.1922:0.0:0.4866:0.3212	.	159	Q7RTS7	K2C74_HUMAN	C	159	ENSP00000447447:R159C;ENSP00000307240:R159C	ENSP00000307240:R159C	R	-	1	0	KRT74	51252715	0.939000	0.31865	0.922000	0.36590	0.189000	0.23516	1.533000	0.36040	-0.450000	0.07107	-0.824000	0.03097	CGC		0.532	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053		A	52966448	G	A	52966448	3	1	77	1	0	0	0	0	1	0	0	0	8508	1145	40	1	1146	1	KRT74	12	52966448	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2921874	52966448	80885447	749	22485										
CBX5	23468	broad.mit.edu	37	chr12	54651350	54651350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacttgtcccttaaccacgcGcctgtctagcaccttctcca	5	18	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:54651350G>A	ENST00000439541.2	-	2	210	c.85C>T	c.(85-87)Cgc>Tgc	p.R29C	RN7SL390P_ENST00000470634.2_RNA|CBX5_ENST00000550411.1_Missense_Mutation_p.R29C|CBX5_ENST00000209875.4_Missense_Mutation_p.R29C	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	29	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)	p.R29C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						TTAACCACGCGCCTGTCTAGC	0.483																																					Colon(153;588 2459 18334 48613)											1	Substitution - Missense(1)	large_intestine(1)	12											177	153	161					12																	54651350		2203	4300	6503	52937617	SO:0001583	missense	23468			U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"HP1 alpha homolog (Drosophila)"	604478	"chromobox homolog 5 (Drosophila HP1 alpha)", "chromobox homolog 5 (HP1 alpha homolog, Drosophila)"			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.85C>T	12.37:g.54651350G>A	ENSP00000401009:p.Arg29Cys		52937617	B2R8T9	Missense_Mutation	SNP	ENST00000439541.2	37	CCDS8875.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051027	0.75960	.	.	ENSG00000094916	ENST00000209875;ENST00000439541;ENST00000550489;ENST00000550411;ENST00000552562	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	5.65	5.65	0.86999	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.098342	0.64402	D	0.000003	D	0.89206	0.6649	M	0.90542	3.125	0.80722	D	1	D;P	0.76494	0.999;0.884	D;P	0.76575	0.988;0.662	D	0.90266	0.4304	10	0.87932	D	0	-4.8608	12.0477	0.53489	0.0:0.0:0.8284:0.1716	.	29;29	G3V1X9;P45973	.;CBX5_HUMAN	C	29	ENSP00000209875:R29C;ENSP00000401009:R29C;ENSP00000449207:R29C;ENSP00000450190:R29C	ENSP00000209875:R29C	R	-	1	0	CBX5	52937617	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	4.634000	0.61325	2.941000	0.99782	0.655000	0.94253	CGC		0.483	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117		A	54651350	G	A	54651350	3	1	77	1	0	0	0	0	1	0	0	0	2727	1087	38	1	506	1	CBX5	12	54651350	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1684902	54651350	79200545	750	22486										
OR10P1	121130	broad.mit.edu	37	chr12	56031567	56031567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acacccttcggaacaaggacGtgaggagggccctgcgacac	13	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:56031567G>A	ENST00000309675.2	+	1	924	c.892G>A	c.(892-894)Gtg>Atg	p.V298M	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V298M(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						GAACAAGGACGTGAGGAGGGC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											54	47	49					12																	56031567		2203	4300	6503	54317834	SO:0001583	missense	121130			BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"GPCR / Class A : Olfactory receptors"	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.892G>A	12.37:g.56031567G>A	ENSP00000308082:p.Val298Met		54317834	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.964947	0.34659	.	.	ENSG00000175398	ENST00000309675	T	0.39229	1.09	4.31	4.31	0.51392	.	0.000000	0.39834	N	0.001250	T	0.57388	0.2050	L	0.60012	1.86	0.33554	D	0.596497	D	0.89917	1.0	D	0.71184	0.972	T	0.67852	-0.5563	10	0.51188	T	0.08	.	12.4825	0.55852	0.0:0.0:1.0:0.0	.	298	Q8NGE3	O10P1_HUMAN	M	298	ENSP00000308082:V298M	ENSP00000308082:V298M	V	+	1	0	OR10P1	54317834	0.607000	0.26958	0.952000	0.39060	0.003000	0.03518	1.334000	0.33827	2.412000	0.81896	0.561000	0.74099	GTG		0.582	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1			A	56031567	G	A	56031567	3	1	77	1	0	0	0	0	1	0	0	0	10946	1145	40	1	894	1	OR10P1	12	56031567	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1380217	56031567	77820328	751	22487										
ERBB3	2065	broad.mit.edu	37	chr12	56478854	56478854	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taccattgcccaacctccgcGtggtgcgagggacccaggtc	12	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:56478854G>A	ENST00000267101.3	+	3	750	c.310G>A	c.(310-312)Gtg>Atg	p.V104M	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Missense_Mutation_p.V45M|ERBB3_ENST00000411731.2_Missense_Mutation_p.V104M	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	104			V -> M (in an ovarian mucinous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)	p.V104M(7)|p.V104L(2)		central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CAACCTCCGCGTGGTGCGAGG	0.517																																																9	Substitution - Missense(9)	large_intestine(5)|endometrium(2)|ovary(1)|NS(1)	12											186	159	168					12																	56478854		2203	4300	6503	54765121	SO:0001583	missense	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.310G>A	12.37:g.56478854G>A	ENSP00000267101:p.Val104Met		54765121	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.103691	0.56291	.	.	ENSG00000065361	ENST00000549282;ENST00000549061;ENST00000267101;ENST00000394099;ENST00000411731;ENST00000549672;ENST00000415288	T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	5.82	4.93	0.64822	EGF receptor, L domain (1);	0.096412	0.43416	D	0.000573	D	0.87438	0.6177	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.59221	0.698;0.854	D	0.88227	0.2901	10	0.59425	D	0.04	.	10.6531	0.45659	0.1547:0.0:0.8453:0.0	.	104;104	P21860;P21860-2	ERBB3_HUMAN;.	M	104;45;104;104;104;45;45	ENSP00000448636:V104M;ENSP00000449138:V45M;ENSP00000267101:V104M;ENSP00000415753:V104M;ENSP00000449713:V45M;ENSP00000408340:V45M	ENSP00000267101:V104M	V	+	1	0	ERBB3	54765121	1.000000	0.71417	0.892000	0.35008	0.052000	0.14988	4.300000	0.59079	1.450000	0.47717	0.655000	0.94253	GTG		0.517	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			A	56478854	G	A	56478854	3	1	77	1	0	0	0	0	1	0	0	0	5221	1145	40	1	320	1	ERBB3	12	56478854	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	447287	56478854	77373041	752	22488										
INHBE	83729	broad.mit.edu	37	chr12	57850588	57850588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taatggcaatgtggtcaagaCggatgtgccagatatggtgg	15	5	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:57850588C>T	ENST00000266646.2	+	2	1226	c.1010C>T	c.(1009-1011)aCg>aTg	p.T337M	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	337					growth (GO:0040007)	extracellular region (GO:0005576)		p.T337M(1)		breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						GTGGTCAAGACGGATGTGCCA	0.562											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(191;1808 2166 15720 36624 50371)											1	Substitution - Missense(1)	large_intestine(1)	12											99	84	89					12																	57850588		2203	4300	6503	56136855	SO:0001583	missense	83729				CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.1010C>T	12.37:g.57850588C>T	ENSP00000266646:p.Thr337Met	1026	56136855		Missense_Mutation	SNP	ENST00000266646.2	37	CCDS8939.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225799	0.58668	.	.	ENSG00000139269	ENST00000266646	D	0.84223	-1.82	4.65	3.76	0.43208	Transforming growth factor-beta, C-terminal (3);	0.054984	0.64402	D	0.000001	D	0.90242	0.6949	M	0.69358	2.11	0.50313	D	0.999866	D	0.76494	0.999	D	0.79784	0.993	D	0.90403	0.4404	10	0.59425	D	0.04	-17.61	11.9677	0.53044	0.0:0.9138:0.0:0.0862	.	337	P58166	INHBE_HUMAN	M	337	ENSP00000266646:T337M	ENSP00000266646:T337M	T	+	2	0	INHBE	56136855	0.894000	0.30519	1.000000	0.80357	0.996000	0.88848	1.806000	0.38892	1.306000	0.44926	0.655000	0.94253	ACG		0.562	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		T	57850588	C	T	57850588	3	4	77	1	0	0	0	0	1	0	0	0	7765	536	19	1	1016	1	INHBE	12	57850588	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1371734	57850588	76001307	753	22489										
ARHGAP9	64333	broad.mit.edu	37	chr12	57869692	57869692	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtccgactgcagcaggaacTcgtggccagggatcgtgcgg	17	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:57869692T>G	ENST00000356411.2	-	10	1373	c.1235A>C	c.(1234-1236)gAg>gCg	p.E412A	ARHGAP9_ENST00000550288.1_Missense_Mutation_p.E491A|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000430041.2_Missense_Mutation_p.E228A|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.E483A|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.E412A|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.E412A			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	412	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)	p.E412A(1)		endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			CAGCAGGAACTCGTGGCCAGG	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											28	31	30					12																	57869692		2200	4297	6497	56155959	SO:0001583	missense	64333			AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1235A>C	12.37:g.57869692T>G	ENSP00000348782:p.Glu412Ala		56155959	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	T	28.7	4.939706	0.92526	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139	T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	3.97	3.97	0.46021	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.140509	0.46442	D	0.000298	D	0.85353	0.5677	M	0.83774	2.66	0.54753	D	0.999984	D;D;D;D;P	0.89917	0.999;0.999;0.999;1.0;0.922	D;D;D;D;D	0.97110	0.996;0.996;0.992;1.0;0.91	D	0.87026	0.2132	10	0.87932	D	0	.	10.8084	0.46531	0.0:0.0:0.0:1.0	.	491;412;412;412;228	Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	.;RHG09_HUMAN;.;.;.	A	412;412;82;412;483;461;228;228	ENSP00000377380:E412A;ENSP00000348782:E412A;ENSP00000394307:E412A;ENSP00000377386:E483A;ENSP00000397950:E228A;ENSP00000449829:E228A	ENSP00000344852:E461A	E	-	2	0	ARHGAP9	56155959	1.000000	0.71417	0.986000	0.45419	0.978000	0.69477	4.030000	0.57260	1.815000	0.52974	0.459000	0.35465	GAG		0.652	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		G	57869692	T	G	57869692	3	3	77	1	0	0	0	0	1	0	0	0	889	1551	54	4	996	4	ARHGAP9	12	57869692	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	19104	57869692	75982203	754	22490										
GEFT	115557	broad.mit.edu	37	chr12	58009799	58009799	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccaacgggacttcctcaaCggtgaagctctcatcctttc	8	14	2	1	rs114895142	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:58009799C>T	ENST00000286494.4	+	13	1879	c.1419C>T	c.(1417-1419)aaC>aaT	p.N473N	AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000356672.3_RNA|ARHGEF25_ENST00000333972.7_Splice_Site_p.N512N	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	473	Sufficient to bind activated GNAQ.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N473N(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						ACTTCCTCAACGGTGAAGCTC	0.567													C|||	86	0.0171725	0.0598	0.0101	5008	,	,		20618	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	12						C	,	194,4212		2,190,2011	124	123	123		1536,1419	-0.2	1	12	dbSNP_132	123	6,8594		0,6,4294	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ARHGEF25	NM_001111270.1,NM_182947.2	,	2,196,6305	TT,TC,CC		0.0698,4.4031,1.5378	,	512/620,473/581	58009799	200,12806	2203	4300	6503	56296066	SO:0001630	splice_region_variant	115557				CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1420+1C>T	12.37:g.58009799C>T			56296066	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Silent	SNP	ENST00000286494.4	37	CCDS8947.1																																																																																				0.567	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	Silent	T	58009799	C	T	58009799	5	4	77	1	0	0	0	0	0	0	1	0	6348	550	19	1	1691	1	GEFT	12	58009799	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	140107	58009799	75842096	755	22491										
B4GALNT1	2583	broad.mit.edu	37	chr12	58022927	58022927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgtccctcggtggagaaccGgactgggaagaaaggacatg	15	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:58022927G>A	ENST00000341156.4	-	7	1299	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	B4GALNT1_ENST00000418555.2_Missense_Mutation_p.R184W|B4GALNT1_ENST00000449184.3_Intron|B4GALNT1_ENST00000550943.1_5'Flank	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	239					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)	p.R239W(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GTGGAGAACCGGACTGGGAAG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	12											59	55	56					12																	58022927		2203	4300	6503	56309194	SO:0001583	missense	2583			M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	4117	protein-coding gene	gene with protein product	"GD2 synthase, GM2 synthase"	601873	"UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)", "UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1", "spastic paraplegia 26"	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.715C>T	12.37:g.58022927G>A	ENSP00000341562:p.Arg239Trp		56309194	B4DE26|Q8N636	Missense_Mutation	SNP	ENST00000341156.4	37	CCDS8950.1	.	.	.	.	.	.	.	.	.	.	.	13.88	2.369290	0.42003	.	.	ENSG00000135454	ENST00000341156;ENST00000418555	T;T	0.19394	2.15;2.18	5.34	4.45	0.53987	.	0.210000	0.41097	D	0.000952	T	0.29783	0.0744	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.62014	0.897;0.875	T	0.01596	-1.1316	10	0.72032	D	0.01	-3.0107	10.5813	0.45257	0.0903:0.0:0.9097:0.0	.	184;239	B4DE26;Q00973	.;B4GN1_HUMAN	W	239;184	ENSP00000341562:R239W;ENSP00000401601:R184W	ENSP00000341562:R239W	R	-	1	2	B4GALNT1	56309194	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	3.601000	0.54059	2.522000	0.85027	0.655000	0.94253	CGG		0.532	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478		A	58022927	G	A	58022927	3	1	77	1	0	0	0	0	1	0	0	0	1267	1115	39	1	906	1	B4GALNT1	12	58022927	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	13128	58022927	75828968	756	22492										
AGAP2	116986	broad.mit.edu	37	chr12	58121195	58121195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgcgtgtcgctttcccacaCgcggttggccgtgtcgttgc	13	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:58121195C>T	ENST00000547588.1	-	17	3027	c.3028G>A	c.(3028-3030)Gtg>Atg	p.V1010M	RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000257897.3_Missense_Mutation_p.V654M|AGAP2-AS1_ENST00000542466.2_Silent_p.H140H	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	1010	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)	p.V654M(1)		breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CTTTCCCACACGCGGTTGGCC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	12											55	46	49					12																	58121195		2203	4300	6503	56407462	SO:0001583	missense	116986			AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.3028G>A	12.37:g.58121195C>T	ENSP00000449241:p.Val1010Met		56407462	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	37	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.52|15.52	2.857236|2.857236	0.51376|0.51376	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000328568|ENST00000257897;ENST00000547588	T|T;T	0.44881|0.46451	0.91|0.87;0.87	5.0|5.0	3.13|3.13	0.36017|0.36017	.|.	.|0.263595	.|0.35207	.|N	.|0.003365	T|T	0.58177|0.58177	0.2104|0.2104	M|M	0.80332|0.80332	2.49|2.49	0.42086|0.42086	D|D	0.99127|0.99127	.|P;D;D	.|0.71674	.|0.587;0.994;0.998	.|B;P;P	.|0.60173	.|0.339;0.704;0.87	T|T	0.63296|0.63296	-0.6669|-0.6669	7|10	0.59425|0.87932	D|D	0.04|0	.|.	8.8582|8.8582	0.35240|0.35240	0.0:0.7477:0.0:0.2523|0.0:0.7477:0.0:0.2523	.|.	.|654;1010;1010	.|Q99490-2;F8VVT9;Q99490	.|.;.;AGAP2_HUMAN	H|M	853|654;1010	ENSP00000328160:R853H|ENSP00000257897:V654M;ENSP00000449241:V1010M	ENSP00000328160:R853H|ENSP00000257897:V654M	R|V	-|-	2|1	0|0	AGAP2|AGAP2	56407462|56407462	0.913000|0.913000	0.31002|0.31002	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.408000|0.408000	0.21065|0.21065	1.235000|1.235000	0.43724|0.43724	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.672	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58121195	C	T	58121195	3	4	77	1	0	0	0	0	1	0	0	0	368	536	19	1	562	1	AGAP2	12	58121195	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	98268	58121195	75730700	757	22493										
CDK4	1019	broad.mit.edu	37	chr12	58143021	58143021	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taccaccgactgcactgggcGgggccctctggggggaaagg	17	12	1	0	rs587778188		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:58143021G>A	ENST00000257904.6	-	7	1128	c.763C>T	c.(763-765)Cgc>Tgc	p.R255C	CDK4_ENST00000312990.6_3'UTR|CDK4_ENST00000549606.1_5'UTR|TSPAN31_ENST00000547992.1_3'UTR|CDK4_ENST00000540325.1_Missense_Mutation_p.R135C|CDK4_ENST00000551888.1_5'UTR	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R255C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			TGCACTGGGCGGGGCCCTCTG	0.622			Mis			melanoma			Hereditary Melanoma																													yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	1	Substitution - Missense(1)	large_intestine(1)	12											59	66	64					12																	58143021		2203	4300	6503	56429288	SO:0001583	missense	1019	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446		"Cyclin-dependent kinases"	1773	protein-coding gene	gene with protein product		123829				8275715	Standard	NM_000075		Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.763C>T	12.37:g.58143021G>A	ENSP00000257904:p.Arg255Cys		56429288	B2R9A0|B4DNF9|O00576|Q6FG61	Missense_Mutation	SNP	ENST00000257904.6	37	CCDS8953.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369960	0.42003	.	.	ENSG00000135446	ENST00000257904;ENST00000540325;ENST00000546489;ENST00000547281	T;T;T;T	0.77358	0.9;0.9;0.9;-1.09	4.59	2.78	0.32641	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110120	0.64402	D	0.000007	T	0.66470	0.2792	L	0.37850	1.14	0.80722	D	1	B	0.14012	0.009	B	0.14023	0.01	T	0.63786	-0.6558	10	0.72032	D	0.01	.	8.9131	0.35565	0.1797:0.0:0.8203:0.0	.	255	P11802	CDK4_HUMAN	C	255;135;181;181	ENSP00000257904:R255C;ENSP00000439076:R135C;ENSP00000447779:R181C;ENSP00000447274:R181C	ENSP00000257904:R255C	R	-	1	0	CDK4	56429288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.561000	0.60809	0.877000	0.35895	0.655000	0.94253	CGC		0.622	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408790.2	NM_000075		A	58143021	G	A	58143021	3	1	77	1	0	0	0	0	1	0	0	0	3147	1116	39	1	156	1	CDK4	12	58143021	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	21826	58143021	75708874	758	22494										
MON2	23041	broad.mit.edu	37	chr12	62887758	62887758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggttgtggaaccaaggaacCgaagatcactcagctatgtt	12	8	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:62887758C>T	ENST00000393632.2	+	3	630	c.239C>T	c.(238-240)cCg>cTg	p.P80L	MON2_ENST00000393630.3_Missense_Mutation_p.P80L|MON2_ENST00000280379.6_Missense_Mutation_p.P80L|MON2_ENST00000549378.1_Intron|MON2_ENST00000552115.1_Missense_Mutation_p.P80L|MON2_ENST00000546600.1_Missense_Mutation_p.P80L|MON2_ENST00000393629.2_Missense_Mutation_p.P80L|MON2_ENST00000552738.1_Missense_Mutation_p.P80L	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	80					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P80L(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		ACCAAGGAACCGAAGATCACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	12											95	83	87					12																	62887758		2203	4300	6503	61174025	SO:0001583	missense	23041				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.239C>T	12.37:g.62887758C>T	ENSP00000377252:p.Pro80Leu		61174025	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934088	0.52866	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000261188;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.70986	-0.36;-0.53;-0.53;-0.36;-0.36;-0.53;1.3	5.66	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	N	0.17631	0.505	0.80722	D	1	B;B;B;B	0.15473	0.005;0.003;0.013;0.005	B;B;B;B	0.09377	0.001;0.004;0.002;0.003	T	0.49466	-0.8937	9	.	.	.	-9.7937	15.9559	0.79886	0.136:0.864:0.0:0.0	.	80;80;80;80	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	L	80;80;80;80;8;80;80;80	ENSP00000377252:P80L;ENSP00000377250:P80L;ENSP00000280379:P80L;ENSP00000447407:P80L;ENSP00000449215:P80L;ENSP00000377249:P80L;ENSP00000446635:P80L	.	P	+	2	0	MON2	61174025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.090000	0.71397	1.370000	0.46153	0.591000	0.81541	CCG		0.368	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62887758	C	T	62887758	3	4	77	1	0	0	0	0	1	0	0	0	9730	652	23	1	249	1	MON2	12	62887758	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4744737	62887758	70964137	759	22495										
GNS	2799	broad.mit.edu	37	chr12	65115435	65115435	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgacattgtcctcacacaGgcataggtattgttataagc	9	9	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:65115435G>T	ENST00000258145.3	-	12	1529	c.1359C>A	c.(1357-1359)gcC>gcA	p.A453A	GNS_ENST00000543646.1_Silent_p.A485A|GNS_ENST00000542058.1_Silent_p.A433A|GNS_ENST00000418919.2_Silent_p.A397A	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	453					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)	p.A453A(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		TCCTCACACAGGCATAGGTAT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	12											189	154	166					12																	65115435		2203	4300	6503	63401702	SO:0001819	synonymous_variant	2799				CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.1359C>A	12.37:g.65115435G>T			63401702	B4DYH8|Q53F05	Silent	SNP	ENST00000258145.3	37	CCDS8970.1	.	.	.	.	.	.	.	.	.	.	G	9.171	1.021204	0.19433	.	.	ENSG00000135677	ENST00000540196	.	.	.	5.71	-6.83	0.01693	.	.	.	.	.	T	0.47192	0.1432	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50783	-0.8787	4	.	.	.	-22.3648	7.1927	0.25834	0.158:0.0903:0.5717:0.18	.	.	.	.	M	239	.	.	L	-	1	2	GNS	63401702	0.971000	0.33674	0.782000	0.31804	0.804000	0.45430	0.209000	0.17435	-1.116000	0.02969	-0.367000	0.07326	CTG		0.433	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			T	65115435	G	T	65115435	2	4	77	1	0	0	0	0	0	0	0	1	6570	987	35	2		2	GNS	12	65115435	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2227677	65115435	68736460	760	22496										
ZFC3H1	196441	broad.mit.edu	37	chr12	72008478	72008478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tattatttgcaaagacaagaTaactgccaaaagaaaaatat	5	5	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:72008478T>C	ENST00000378743.3	-	30	5721	c.5363A>G	c.(5362-5364)tAt>tGt	p.Y1788C		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1788					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Y1788C(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AAAGACAAGATAACTGCCAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	12											73	73	73					12																	72008478		1808	4064	5872	70294745	SO:0001583	missense	196441			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5363A>G	12.37:g.72008478T>C	ENSP00000368017:p.Tyr1788Cys		70294745	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.201948	0.58234	.	.	ENSG00000133858	ENST00000378743	T	0.39787	1.06	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57985	-0.7716	10	0.87932	D	0	.	15.0819	0.72122	0.0:0.0:0.0:1.0	.	1788	O60293	ZC3H1_HUMAN	C	1788	ENSP00000368017:Y1788C	ENSP00000368017:Y1788C	Y	-	2	0	ZFC3H1	70294745	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.332000	0.72934	2.019000	0.59389	0.455000	0.32223	TAT		0.353	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		C	72008478	T	C	72008478	3	2	77	1	0	0	0	0	1	0	0	0	17672	1406	49	4	630	4	ZFC3H1	12	72008478	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	6893043	72008478	61843417	761	22497										
NAV3	89795	broad.mit.edu	37	chr12	78510558	78510558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtcttgcctttagctgggaTgacagcagttcagtgagcag	13	8	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:78510558T>C	ENST00000397909.2	+	13	2816	c.2643T>C	c.(2641-2643)gaT>gaC	p.D881D	NAV3_ENST00000228327.6_Silent_p.D881D|NAV3_ENST00000536525.2_Silent_p.D881D|NAV3_ENST00000266692.7_Silent_p.D881D			Q8IVL0	NAV3_HUMAN	neuron navigator 3	881						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.D881D(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TTAGCTGGGATGACAGCAGTT	0.438										HNSCC(70;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	12											128	119	122					12																	78510558		2080	4242	6322	77034689	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.2643T>C	12.37:g.78510558T>C			77034689	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																					0.438	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		C	78510558	T	C	78510558	2	2	77	1	0	0	0	0	0	0	0	1	10215	1461	51	4		4	NAV3	12	78510558	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	6502080	78510558	55341337	762	22498										
MYF5	4617	broad.mit.edu	37	chr12	81111120	81111120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcagccactatgcgcgagcGgaggcgcctgaagaaggtca	16	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:81111120G>A	ENST00000228644.3	+	1	430	c.278G>A	c.(277-279)cGg>cAg	p.R93Q		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	93	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.R93Q(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						ATGCGCGAGCGGAGGCGCCTG	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	12											49	44	46					12																	81111120		2203	4300	6503	79635251	SO:0001583	missense	4617				CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.278G>A	12.37:g.81111120G>A	ENSP00000228644:p.Arg93Gln		79635251	Q6ISR9	Missense_Mutation	SNP	ENST00000228644.3	37	CCDS9020.1	.	.	.	.	.	.	.	.	.	.	G	36	5.701055	0.96812	.	.	ENSG00000111049	ENST00000228644	D	0.98958	-5.27	6.06	6.06	0.98353	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99603	0.9856	H	0.98769	4.325	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97729	1.0201	10	0.87932	D	0	-6.2748	20.6208	0.99490	0.0:0.0:1.0:0.0	.	93	P13349	MYF5_HUMAN	Q	93	ENSP00000228644:R93Q	ENSP00000228644:R93Q	R	+	2	0	MYF5	79635251	1.000000	0.71417	0.991000	0.47740	0.971000	0.66376	9.476000	0.97823	2.882000	0.98803	0.655000	0.94253	CGG		0.607	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		A	81111120	G	A	81111120	3	1	77	1	0	0	0	0	1	0	0	0	10057	1116	39	1	280	1	MYF5	12	81111120	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2600562	81111120	52740775	763	22499										
NTN4	59277	broad.mit.edu	37	chr12	96059708	96059708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttaatcttcacattgaccTcaacatgagtacctttatca	3	10	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:96059708T>C	ENST00000343702.4	-	9	2076	c.1628A>G	c.(1627-1629)gAg>gGg	p.E543G	NTN4_ENST00000538383.1_Missense_Mutation_p.E506G|NTN4_ENST00000344911.4_Missense_Mutation_p.E506G|PGAM1P5_ENST00000552554.1_RNA|NTN4_ENST00000553059.1_Missense_Mutation_p.E520G	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	543	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)		p.E543G(1)		NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CACATTGACCTCAACATGAGT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	12											103	96	98					12																	96059708		2203	4300	6503	94583839	SO:0001583	missense	59277			AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"Netrins"	13658	protein-coding gene	gene with protein product	"beta-netrin", "Netrin-4"	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.1628A>G	12.37:g.96059708T>C	ENSP00000340998:p.Glu543Gly		94583839	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935209	0.73442	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.91	5.91	0.95273	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.000000	0.85682	D	0.000000	T	0.51770	0.1694	M	0.70275	2.135	0.52501	D	0.999955	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.981	T	0.52223	-0.8604	10	0.56958	D	0.05	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	520;543	Q9HB63-2;Q9HB63	.;NET4_HUMAN	G	543;506;506;520	ENSP00000340998:E543G;ENSP00000339436:E506G;ENSP00000444432:E506G;ENSP00000447292:E520G	ENSP00000340998:E543G	E	-	2	0	NTN4	94583839	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.424000	0.66464	2.261000	0.74972	0.533000	0.62120	GAG		0.333	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229		C	96059708	T	C	96059708	3	2	77	1	0	0	0	0	1	0	0	0	10733	1551	54	4	266	4	NTN4	12	96059708	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	14948588	96059708	37792187	764	22500										
HAL	3034	broad.mit.edu	37	chr12	96371738	96371738	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttaccttgctccacatgctcGatgaccctgagggctttcct	8	14	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:96371738G>A	ENST00000261208.3	-	18	2006	c.1638C>T	c.(1636-1638)atC>atT	p.I546I	HAL_ENST00000541929.1_Silent_p.I338I|HAL_ENST00000538703.1_Silent_p.I546I	NM_002108.3	NP_002099.1	P42357	HUTH_HUMAN	histidine ammonia-lyase	546					biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	histidine ammonia-lyase activity (GO:0004397)	p.I546I(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	34					L-Histidine(DB00117)	CCACATGCTCGATGACCCTGA	0.607																																					NSCLC(169;943 2815 23563 30031)											1	Substitution - coding silent(1)	large_intestine(1)	12											139	97	111					12																	96371738		2203	4300	6503	94895869	SO:0001819	synonymous_variant	3034				CCDS9058.1, CCDS58264.1, CCDS58265.1	12q22-q24.1	1991-07-12				ENSG00000084110	4.3.1.3		4806	protein-coding gene	gene with protein product		609457		HIS			Standard	NM_002108		Approved		uc001tem.2	P42357	OTTHUMG00000170354	ENST00000261208.3:c.1638C>T	12.37:g.96371738G>A			94895869	B4DQC1|B4E0V8|F5GXF2|F5H1U5|Q4VB92|Q4VB93	Silent	SNP	ENST00000261208.3	37	CCDS9058.1	.	.	.	.	.	.	.	.	.	.	G	1.388	-0.581627	0.03854	.	.	ENSG00000084110	ENST00000548808	.	.	.	5.73	-3.69	0.04450	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3251	6.7173	0.23310	0.4764:0.3824:0.1412:0.0	.	.	.	.	X	78	.	.	R	-	1	2	HAL	94895869	0.986000	0.35501	0.935000	0.37517	0.077000	0.17291	0.249000	0.18216	-0.508000	0.06540	-1.474000	0.01003	CGA		0.607	HAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408644.1			A	96371738	G	A	96371738	2	1	77	1	0	0	0	0	0	0	0	1	6968	1048	37	1		1	HAL	12	96371738	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	312030	96371738	37480157	765	22501										
STAB2	55576	broad.mit.edu	37	chr12	104083732	104083732	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgagaaaagcttctggttgTcacagagcaatattccagcc	9	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:104083732T>A	ENST00000388887.2	+	29	3358	c.3154T>A	c.(3154-3156)Tca>Aca	p.S1052T		NM_017564.9	NP_060034.9			stabilin 2									p.S1052T(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CTTCTGGTTGTCACAGAGCAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	12											177	159	165					12																	104083732		2203	4300	6503	102607862	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3154T>A	12.37:g.104083732T>A	ENSP00000373539:p.Ser1052Thr		102607862		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	T	8.043	0.764201	0.15914	.	.	ENSG00000136011	ENST00000388887	D	0.92048	-2.96	5.75	4.6	0.57074	FAS1 domain (5);Growth factor, receptor (1);	0.345452	0.29396	N	0.012270	D	0.83055	0.5171	N	0.17312	0.475	0.32144	N	0.585089	B	0.12630	0.006	B	0.20184	0.028	T	0.75703	-0.3225	10	0.11485	T	0.65	.	10.1342	0.42697	0.4053:0.0:0.0:0.5947	.	1052	Q8WWQ8	STAB2_HUMAN	T	1052	ENSP00000373539:S1052T	ENSP00000373539:S1052T	S	+	1	0	STAB2	102607862	1.000000	0.71417	0.999000	0.59377	0.915000	0.54546	0.508000	0.22692	1.100000	0.41517	0.528000	0.53228	TCA		0.428	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104083732	T	A	104083732	3	1	77	1	0	0	0	0	1	0	0	0	15277	1667	58	5	3268	5	STAB2	12	104083732	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	7711994	104083732	29768163	766	22502										
RFX4	5992	broad.mit.edu	37	chr12	106995106	106995106	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaggcgacaggaccaggcctCgacggcgccgttccactggt	15	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:106995106C>T	ENST00000392842.1	+	2	457				RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Nonsense_Mutation_p.R18*	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)						cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R18*(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						GACCAGGCCTCGACGGCGCCG	0.667																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											40	32	35					12																	106995106		2200	4293	6493	105519236	SO:0001627	intron_variant	5992			AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.44-7469C>T	12.37:g.106995106C>T			105519236	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Nonsense_Mutation	SNP	ENST00000392842.1	37	CCDS9106.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064702	0.76187	.	.	ENSG00000111783	ENST00000357881;ENST00000266774	.	.	.	3.87	-6.87	0.01671	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	21.3108	7.2008	0.25879	0.0:0.1539:0.2427:0.6034	.	.	.	.	X	18	.	ENSP00000266774:R18X	R	+	1	2	RFX4	105519236	0.000000	0.05858	0.000000	0.03702	0.153000	0.21895	-3.822000	0.00357	-1.650000	0.01506	0.609000	0.83330	CGA		0.667	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		T	106995106	C	T	106995106	1	4	77	0	1	0	0	0	0	0	0	0	13302	876	31	1		1	RFX4	12	106995106	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2911374	106995106	26856789	767	22503										
CRY1	1407	broad.mit.edu	37	chr12	107486655	107486655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtagacgcagcggatggtgtCggcgccctgaatgcactcct	14	12	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:107486655C>T	ENST00000008527.5	-	1	952	c.85G>A	c.(85-87)Gac>Aac	p.D29N	RP11-797M17.1_ENST00000547679.1_RNA|CRY1_ENST00000550633.1_5'UTR	NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	29	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.D29N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						CGGATGGTGTCGGCGCCCTGA	0.667											OREG0022082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	12											30	27	28					12																	107486655		2202	4299	6501	106010785	SO:0001583	missense	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.85G>A	12.37:g.107486655C>T	ENSP00000008527:p.Asp29Asn	1405	106010785		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179480	0.57800	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.71	4.8	0.61643	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.047445	0.85682	D	0.000000	T	0.66257	0.2771	M	0.70903	2.155	0.58432	D	0.999997	B	0.13594	0.008	B	0.13407	0.009	T	0.62562	-0.6828	9	0.27785	T	0.31	3.9771	16.2645	0.82568	0.0:0.8671:0.1329:0.0	.	29	Q16526	CRY1_HUMAN	N	29	.	ENSP00000008527:D29N	D	-	1	0	CRY1	106010785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.764000	0.68826	1.372000	0.46190	0.561000	0.74099	GAC		0.667	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		T	107486655	C	T	107486655	3	4	77	1	0	0	0	0	1	0	0	0	3909	884	31	1	1723	1	CRY1	12	107486655	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	491549	107486655	26365240	768	22504										
WSCD2	9671	broad.mit.edu	37	chr12	108603967	108603967	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacaagatccaggcgacgaaCgtgagcgaggcagagtgcga	15	10	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:108603967C>T	ENST00000332082.4	+	5	1385	c.567C>T	c.(565-567)aaC>aaT	p.N189N	WSCD2_ENST00000261400.3_Silent_p.N189N|WSCD2_ENST00000547525.1_Silent_p.N189N|WSCD2_ENST00000549903.1_Silent_p.N189N			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	189	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)		p.N189N(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						AGGCGACGAACGTGAGCGAGG	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	12											33	40	37					12																	108603967		2202	4295	6497	107128097	SO:0001819	synonymous_variant	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.567C>T	12.37:g.108603967C>T			107128097	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	37	CCDS41828.1																																																																																				0.672	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108603967	C	T	108603967	2	4	77	1	0	0	0	0	0	0	0	1	17447	535	19	1		1	WSCD2	12	108603967	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1117312	108603967	25247928	769	22505										
SSH1	54434	broad.mit.edu	37	chr12	109182258	109182258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccttccaatgaagcgggggCggcctctgacttctcatcac	10	14	3	2	rs190071016		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:109182258C>T	ENST00000326495.5	-	15	2749	c.2656G>A	c.(2656-2658)Gcc>Acc	p.A886T	SSH1_ENST00000360239.3_Missense_Mutation_p.A574T	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	886					actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A886T(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAGCGGGGGCGGCCTCTGAC	0.612													C|||	1	0.000199681	0	0	5008	,	,		16529	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	12						C	THR/ALA	0,4396		0,0,2198	23	27	26		2656	-2.1	0	12		26	2,8594		0,2,4296	no	missense	SSH1	NM_018984.3	58	0,2,6494	TT,TC,CC		0.0233,0.0,0.0154	benign	886/1050	109182258	2,12990	2198	4298	6496	107706387	SO:0001583	missense	54434			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.2656G>A	12.37:g.109182258C>T	ENSP00000315713:p.Ala886Thr		107706387	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.741	-0.053624	0.07362	0.0	2.33E-4	ENSG00000084112	ENST00000360239;ENST00000326495	T;T	0.10573	3.08;2.86	4.43	-2.11	0.07187	.	2.805710	0.01412	N	0.014030	T	0.04497	0.0123	N	0.08118	0	0.09310	N	1	B;B	0.21381	0.004;0.055	B;B	0.10450	0.001;0.005	T	0.23904	-1.0175	10	0.13470	T	0.59	0.5507	1.0252	0.01526	0.1369:0.2524:0.2683:0.3423	.	886;574	Q8WYL5;Q8WYL5-4	SSH1_HUMAN;.	T	574;886	ENSP00000353374:A574T;ENSP00000315713:A886T	ENSP00000315713:A886T	A	-	1	0	SSH1	107706387	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.441000	0.01015	-0.712000	0.04988	-0.882000	0.02950	GCC		0.612	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		T	109182258	C	T	109182258	3	4	77	1	0	0	0	0	1	0	0	0	15223	768	27	1	497	1	SSH1	12	109182258	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	578291	109182258	24669637	770	22506										
DAO	1610	broad.mit.edu	37	chr12	109293196	109293196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aactggcttccggccagtacGcccccagattcggctagaaa	10	14	0	2	rs566264618		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:109293196G>A	ENST00000228476.3	+	10	1061	c.857G>A	c.(856-858)cGc>cAc	p.R286H	DAO_ENST00000551281.1_Missense_Mutation_p.R220H	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	286					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)	p.R286H(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	CGGCCAGTACGCCCCCAGATT	0.468													g|||	1	0.000199681	0	0	5008	,	,		23561	0		0	False		,,,				2504	0.001															2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	12											43	36	38					12																	109293196		2203	4300	6503	107817325	SO:0001583	missense	1610			D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.857G>A	12.37:g.109293196G>A	ENSP00000228476:p.Arg286His		107817325	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	g	16.65	3.180959	0.57800	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	D;D;D	0.81499	-1.5;-1.5;-1.5	4.88	4.88	0.63580	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.92977	0.7765	H	0.96970	3.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.95251	0.8360	10	0.87932	D	0	-18.7759	15.5113	0.75786	0.0:0.0:1.0:0.0	.	286;269	P14920;Q7Z312	OXDA_HUMAN;.	H	220;286;163	ENSP00000446853:R220H;ENSP00000228476:R286H;ENSP00000449967:R163H	ENSP00000228476:R286H	R	+	2	0	DAO	107817325	1.000000	0.71417	0.476000	0.27291	0.090000	0.18270	7.514000	0.81750	2.258000	0.74832	0.542000	0.68232	CGC		0.468	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			A	109293196	G	A	109293196	3	1	77	1	0	0	0	0	1	0	0	0	4237	1087	38	1	891	1	DAO	12	109293196	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	110938	109293196	24558699	771	22507										
FOXN4	121643	broad.mit.edu	37	chr12	109719496	109719496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agacagccaggcagccatgcGccacggccactgtggtggcg	15	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:109719496G>A	ENST00000299162.5	-	9	1114	c.1010C>T	c.(1009-1011)gCg>gTg	p.A337V	FOXN4_ENST00000355216.1_Missense_Mutation_p.A157V	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	337					amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A157V(1)|p.A337V(1)		large_intestine(5)|lung(9)|ovary(2)	16						GCAGCCATGCGCCACGGCCAC	0.687																																																2	Substitution - Missense(2)	large_intestine(2)	12											24	17	19					12																	109719496		2192	4292	6484	108203879	SO:0001583	missense	121643			AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"Forkhead boxes"	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.1010C>T	12.37:g.109719496G>A	ENSP00000299162:p.Ala337Val		108203879	Q6ZMR4|Q96NZ0	Missense_Mutation	SNP	ENST00000299162.5	37	CCDS9126.2	.	.	.	.	.	.	.	.	.	.	G	10.58	1.389550	0.25118	.	.	ENSG00000139445	ENST00000355216;ENST00000299162	D;D	0.95069	-3.6;-3.18	5.1	3.09	0.35607	.	1.822880	0.02849	N	0.128887	D	0.91991	0.7463	L	0.44542	1.39	0.36604	D	0.874844	B;B	0.23650	0.089;0.089	B;B	0.15484	0.013;0.009	T	0.81293	-0.0998	10	0.52906	T	0.07	3.0028	8.642	0.33983	0.0:0.1468:0.5512:0.302	.	337;337	A6H901;Q96NZ1	.;FOXN4_HUMAN	V	157;337	ENSP00000347354:A157V;ENSP00000299162:A337V	ENSP00000299162:A337V	A	-	2	0	FOXN4	108203879	1.000000	0.71417	0.813000	0.32504	0.125000	0.20455	3.202000	0.51067	1.240000	0.43803	0.555000	0.69702	GCG		0.687	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735		A	109719496	G	A	109719496	3	1	77	1	0	0	0	0	1	0	0	0	6041	1087	38	1	551	1	FOXN4	12	109719496	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	426300	109719496	24132399	772	22508										
IFT81	28981	broad.mit.edu	37	chr12	110600740	110600740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaggcatctatcatttcccGtaaaaaagaagccaaagctg	7	10	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:110600740G>A	ENST00000242591.5	+	11	1564	c.1058G>A	c.(1057-1059)cGt>cAt	p.R353H	IFT81_ENST00000361948.4_Missense_Mutation_p.R353H|IFT81_ENST00000552912.1_Missense_Mutation_p.R353H|IFT81_ENST00000549009.1_3'UTR	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	353					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)	p.R353H(1)		endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						ATCATTTCCCGTAAAAAAGAA	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											72	69	70					12																	110600740		2203	4300	6503	109085123	SO:0001583	missense	28981			AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"Intraflagellar transport homologs"	14313	protein-coding gene	gene with protein product		605489	"carnitine deficiency-associated, expressed in ventricle 1", "intraflagellar transport 81 homolog (Chlamydomonas)"	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.1058G>A	12.37:g.110600740G>A	ENSP00000242591:p.Arg353His		109085123	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711966	0.48517	.	.	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T	0.37058	1.22	5.42	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.34687	0.0906	L	0.54323	1.7	0.80722	D	1	B;B	0.20887	0.049;0.035	B;B	0.20577	0.03;0.016	T	0.12400	-1.0549	10	0.44086	T	0.13	-5.5965	12.6712	0.56868	0.0765:0.0:0.9235:0.0	.	353;353	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	H	353;353;353;323	ENSP00000355372:R353H	ENSP00000242591:R353H	R	+	2	0	IFT81	109085123	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.287000	0.59001	1.303000	0.44873	-0.137000	0.14449	CGT		0.348	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		A	110600740	G	A	110600740	3	1	77	1	0	0	0	0	1	0	0	0	7586	1145	40	1	1096	1	IFT81	12	110600740	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	881244	110600740	23251155	773	22509										
HVCN1	84329	broad.mit.edu	37	chr12	111093101	111093101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtccaggatgagctcagcaaGcaccaggagggcatccagaa	13	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:111093101G>A	ENST00000356742.5	-	4	1102	c.349C>T	c.(349-351)Ctt>Ttt	p.L117F	HVCN1_ENST00000548312.1_Missense_Mutation_p.L117F|HVCN1_ENST00000439744.2_Missense_Mutation_p.L97F|HVCN1_ENST00000242607.8_Missense_Mutation_p.L117F			Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	117					cellular response to pH (GO:0071467)|cellular response to zinc ion (GO:0071294)|multicellular organism reproduction (GO:0032504)|proton transport (GO:0015992)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	voltage-gated cation channel activity (GO:0022843)|voltage-gated proton channel activity (GO:0030171)	p.L117F(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	19						AGCTCAGCAAGCACCAGGAGG	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	12											157	126	137					12																	111093101		2203	4300	6503	109577484	SO:0001583	missense	84329			BC007277	CCDS31900.1, CCDS58278.1	12q24.11	2011-12-09	2006-03-24	2006-03-24	ENSG00000122986	ENSG00000122986		"Voltage-gated ion channels / Hydrogen voltage-gated channel"	28240	protein-coding gene	gene with protein product	"voltage sensor domain-only protein"	611227				20961760, 16556803, 18356202, 22020278	Standard	NM_032369		Approved	MGC15619, Hv1, VSOP	uc001trs.2	Q96D96		ENST00000356742.5:c.349C>T	12.37:g.111093101G>A	ENSP00000349181:p.Leu117Phe		109577484	A8MQ37|B4DEB3|F8WCH5|Q6UW11|Q96IS5	Missense_Mutation	SNP	ENST00000356742.5	37	CCDS31900.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.821104	0.71028	.	.	ENSG00000122986	ENST00000548312;ENST00000242607;ENST00000356742;ENST00000439744	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.98369	0.9458	M	0.79475	2.455	0.58432	D	0.999999	P;D	0.89917	0.911;1.0	B;D	0.79108	0.311;0.992	D	0.99478	1.0947	10	0.72032	D	0.01	-29.633	18.7697	0.91887	0.0:0.0:1.0:0.0	.	117;117	Q96D96;Q96D96-3	HVCN1_HUMAN;.	F	117;117;117;97	ENSP00000449601:L117F;ENSP00000242607:L117F;ENSP00000349181:L117F;ENSP00000412052:L97F	ENSP00000242607:L117F	L	-	1	0	HVCN1	109577484	1.000000	0.71417	0.997000	0.53966	0.888000	0.51559	5.568000	0.67385	2.443000	0.82685	0.462000	0.41574	CTT		0.557	HVCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404653.1	NM_032369		A	111093101	G	A	111093101	3	1	77	1	0	0	0	0	1	0	0	0	7483	971	34	3	488	3	HVCN1	12	111093101	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	492361	111093101	22758794	774	22510										
LHX5	64211	broad.mit.edu	37	chr12	113901145	113901145	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgcccggcaggcctggctcGgggctcggtgtgtccgggtg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:113901145delG	ENST00000261731.3	-	5	1632	c.1059delC	c.(1057-1059)cccfs	p.P353fs		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	353					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.E354fs*26(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						GGCCTGGCTCGGGGCTCGGTG	0.741																																																1	Deletion - Frameshift(1)	large_intestine(1)	12											8	11	10					12																	113901145		2020	3970	5990	112385528	SO:0001589	frameshift_variant	64211			AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"Homeoboxes / LIM class"	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.1059delC	12.37:g.113901145delG	ENSP00000261731:p.Pro353fs		112385528	Q32MA4	Frame_Shift_Del	DEL	ENST00000261731.3	37	CCDS9171.1																																																																																				0.741	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		-	113901145	G	-	113901145	7	5	77	1	0	1	0	1	0	0	0	0	8797	1103	39	0	153	0	LHX5	12	113901145	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	2808044	113901145	19950750	775	22511										
NOS1	4842	broad.mit.edu	37	chr12	117715878	117715878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catcgaagcggcctctaggcGgtttccagccctgctgtatg	12	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:117715878G>A	ENST00000338101.4	-	8	1554	c.1550C>T	c.(1549-1551)cCg>cTg	p.P517L	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.P517L			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.P517L(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCCTCTAGGCGGTTTCCAGCC	0.582																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - Missense(1)	large_intestine(1)	12											46	52	50					12																	117715878		1945	4141	6086	116200261	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1550C>T	12.37:g.117715878G>A	ENSP00000337459:p.Pro517Leu		116200261		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946314	0.73672	.	.	ENSG00000089250	ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.46819	0.86;0.86	5.27	5.27	0.74061	Nitric oxide synthase, oxygenase domain (2);	0.152968	0.56097	D	0.000021	T	0.63850	0.2546	M	0.85373	2.75	0.80722	D	1	P	0.36587	0.559	B	0.44133	0.442	T	0.69146	-0.5222	10	0.72032	D	0.01	-20.2874	19.1369	0.93431	0.0:0.0:1.0:0.0	.	517	P29475	NOS1_HUMAN	L	517	ENSP00000320758:P517L;ENSP00000337459:P517L	ENSP00000320758:P517L	P	-	2	0	NOS1	116200261	1.000000	0.71417	0.988000	0.46212	0.312000	0.27988	9.529000	0.98049	2.759000	0.94783	0.555000	0.69702	CCG		0.582	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117715878	G	A	117715878	3	1	77	1	0	0	0	0	1	0	0	0	10572	1116	39	1	2838	1	NOS1	12	117715878	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3814733	117715878	16136017	776	22512										
NOS1	4842	broad.mit.edu	37	chr12	117723955	117723955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccacacagcgcgaggcattcCgccaggcgtgcttggcccca	12	17	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:117723955C>T	ENST00000338101.4	-	5	1248	c.1244G>A	c.(1243-1245)cGg>cAg	p.R415Q	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.R415Q			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.R415Q(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CGAGGCATTCCGCCAGGCGTG	0.547																																					Esophageal Squamous(162;1748 2599 51982 52956)											1	Substitution - Missense(1)	large_intestine(1)	12											144	145	144					12																	117723955		2166	4296	6462	116208338	SO:0001583	missense	4842				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1244G>A	12.37:g.117723955C>T	ENSP00000337459:p.Arg415Gln		116208338		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	C	36	5.694354	0.96793	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.61859	0.07;0.07	4.93	4.93	0.64822	Nitric oxide synthase, oxygenase domain (3);	0.000000	0.85682	D	0.000000	D	0.83783	0.5329	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.89256	0.3594	10	0.87932	D	0	-24.7757	18.3299	0.90264	0.0:1.0:0.0:0.0	.	415	P29475	NOS1_HUMAN	Q	415	ENSP00000320758:R415Q;ENSP00000337459:R415Q	ENSP00000320758:R415Q	R	-	2	0	NOS1	116208338	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.562000	0.82300	2.559000	0.86315	0.591000	0.81541	CGG		0.547	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117723955	C	T	117723955	3	4	77	1	0	0	0	0	1	0	0	0	10572	652	23	1	3156	1	NOS1	12	117723955	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8077	117723955	16127940	777	22513										
CIT	11113	broad.mit.edu	37	chr12	120150414	120150414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acctgctttggctgtatttgCgagttcggaagcaccaacgg	12	10	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:120150414C>T	ENST00000261833.7	-	35	4592	c.4540G>A	c.(4540-4542)Gca>Aca	p.A1514T	CIT_ENST00000392521.2_Missense_Mutation_p.A1556T|MIR1178_ENST00000408396.1_RNA|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1514	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.A1542T(1)|p.A1514T(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCTGTATTTGCGAGTTCGGAA	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	12											65	64	64					12																	120150414		2203	4300	6503	118634797	SO:0001583	missense	11113			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.4540G>A	12.37:g.120150414C>T	ENSP00000261833:p.Ala1514Thr		118634797	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539968	0.27563	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.63580	-0.03;-0.05	5.92	5.92	0.95590	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.366802	0.28754	N	0.014248	T	0.38746	0.1052	N	0.08118	0	0.25649	N	0.986114	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.14755	-1.0461	10	0.24483	T	0.36	.	9.2144	0.37337	0.1482:0.7733:0.0:0.0784	.	1556;1514;1032	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	T	1556;1514	ENSP00000376306:A1556T;ENSP00000261833:A1514T	ENSP00000261833:A1514T	A	-	1	0	CIT	118634797	0.018000	0.18449	1.000000	0.80357	0.987000	0.75469	0.222000	0.17699	2.795000	0.96236	0.655000	0.94253	GCA		0.602	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120150414	C	T	120150414	3	4	77	1	0	0	0	0	1	0	0	0	3444	768	27	1	1595	1	CIT	12	120150414	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2426459	120150414	13701481	778	22514										
CIT	11113	broad.mit.edu	37	chr12	120172014	120172014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttctctgcagctctcgaaccCgacactcaaactgggatttc	7	14	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:120172014C>T	ENST00000261833.7	-	25	3231	c.3179G>A	c.(3178-3180)cGg>cAg	p.R1060Q	CIT_ENST00000392521.2_Missense_Mutation_p.R1102Q|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1060					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R1103Q(1)|p.R1060Q(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTCTCGAACCCGACACTCAAA	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	12											125	105	112					12																	120172014		2203	4300	6503	118656397	SO:0001583	missense	11113			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3179G>A	12.37:g.120172014C>T	ENSP00000261833:p.Arg1060Gln		118656397	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.490276|5.490276	0.96339|0.96339	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833;ENST00000546026	.|T;T;T	.|0.65178	.|-0.12;-0.14;1.74	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.71117|0.71117	0.3302|0.3302	L|L	0.29908|0.29908	0.895|0.895	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D	.|0.89917	.|1.0;0.997;0.997	.|D;D;P	.|0.79108	.|0.992;0.968;0.811	T|T	0.72574|0.72574	-0.4252|-0.4252	5|10	.|0.51188	.|T	.|0.08	.|.	19.0703|19.0703	0.93130|0.93130	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1102;1060;593	.|Q2M5E1;O14578;O14578-3	.|.;CTRO_HUMAN;.	R|Q	688|1102;1060;102	.|ENSP00000376306:R1102Q;ENSP00000261833:R1060Q;ENSP00000446105:R102Q	.|ENSP00000261833:R1060Q	G|R	-|-	1|2	0|0	CIT|CIT	118656397|118656397	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.953000|0.953000	0.61014|0.61014	7.818000|7.818000	0.86416|0.86416	2.508000|2.508000	0.84585|0.84585	0.467000|0.467000	0.42956|0.42956	GGG|CGG		0.557	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120172014	C	T	120172014	3	4	77	1	0	0	0	0	1	0	0	0	3444	652	23	1	2996	1	CIT	12	120172014	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	21600	120172014	13679881	779	22515										
SNRNP35	11066	broad.mit.edu	37	chr12	123950499	123950499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctcaaagggtggatccctCggcgacttggaggcggtctt	14	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:123950499C>T	ENST00000526639.2	+	2	991	c.412C>T	c.(412-414)Cgg>Tgg	p.R138W	SNRNP35_ENST00000350887.5_Missense_Mutation_p.R138W|SNRNP35_ENST00000527158.2_Intron|SNRNP35_ENST00000412157.2_Missense_Mutation_p.R143W	NM_022717.3	NP_073208.1	Q16560	U1SBP_HUMAN	small nuclear ribonucleoprotein 35kDa (U11/U12)	138					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R138W(1)		NS(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GTGGATCCCTCGGCGACTTGG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											87	94	92					12																	123950499		2203	4300	6503	122516452	SO:0001583	missense	11066			BC054034	CCDS9249.1, CCDS45005.1	12q24.31	2013-02-12				ENSG00000184209		"RNA binding motif (RRM) containing"	30852	protein-coding gene	gene with protein product	"U1 snRNP binding protein homolog"					10520751, 8889548	Standard	XM_005253545		Approved	U1SNRNPBP	uc001ufb.1	Q16560		ENST00000526639.2:c.412C>T	12.37:g.123950499C>T	ENSP00000432595:p.Arg138Trp		122516452	A8K262|Q5XKN9	Missense_Mutation	SNP	ENST00000526639.2	37	CCDS9249.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477646	0.84640	.	.	ENSG00000184209	ENST00000526639;ENST00000412157;ENST00000350887	T;T;T	0.76186	-1.0;-1.0;-1.0	5.66	3.73	0.42828	Nucleotide-binding, alpha-beta plait (1);	0.060946	0.64402	D	0.000003	D	0.86108	0.5854	M	0.87097	2.86	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87541	0.2459	10	0.87932	D	0	-20.8623	10.4268	0.44383	0.1338:0.7967:0.0:0.0695	.	143;138	Q16560-2;Q16560	.;U1SBP_HUMAN	W	138;143;138	ENSP00000432595:R138W;ENSP00000403310:R143W;ENSP00000340774:R138W	ENSP00000340774:R138W	R	+	1	2	SNRNP35	122516452	0.997000	0.39634	0.983000	0.44433	0.998000	0.95712	3.572000	0.53849	1.420000	0.47138	0.555000	0.69702	CGG		0.517	SNRNP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395197.2	NM_007020		T	123950499	C	T	123950499	3	4	77	1	0	0	0	0	1	0	0	0	14892	875	31	1	433	1	SNRNP35	12	123950499	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3778485	123950499	9901396	780	22516										
TMED2	10959	broad.mit.edu	37	chr12	124069314	124069314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacctcgggcaccaagatggGcctcatcttcgaggtggcgg	14	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:124069314G>A	ENST00000262225.3	+	1	237	c.131G>A	c.(130-132)gGc>gAc	p.G44D	TMED2_ENST00000509052.2_5'Flank|RP11-486O12.2_ENST00000498967.2_lincRNA	NM_006815.3	NP_006806.1	Q15363	TMED2_HUMAN	transmembrane emp24 domain trafficking protein 2	44	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.|Interaction with F2RL1.				cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPII vesicle coating (GO:0048208)|embryonic morphogenesis (GO:0048598)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|maternal placenta development (GO:0001893)|negative regulation of GTPase activity (GO:0034260)|protein targeting to plasma membrane (GO:0072661)	COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|zymogen granule membrane (GO:0042589)		p.G44D(1)		kidney(1)|large_intestine(4)|lung(1)|prostate(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		ACCAAGATGGGCCTCATCTTC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	12											64	61	62					12																	124069314		2203	4300	6503	122635267	SO:0001583	missense	10959			X92098	CCDS9250.1	12q24.31	2006-03-27			ENSG00000086598	ENSG00000086598			16996	protein-coding gene	gene with protein product						8663407	Standard	NM_006815		Approved	RNP24, P24A	uc001ufg.3	Q15363	OTTHUMG00000168694	ENST00000262225.3:c.131G>A	12.37:g.124069314G>A	ENSP00000262225:p.Gly44Asp		122635267		Missense_Mutation	SNP	ENST00000262225.3	37	CCDS9250.1	.	.	.	.	.	.	.	.	.	.	G	36	5.717731	0.96839	.	.	ENSG00000086598	ENST00000262225;ENST00000438031;ENST00000541504	T;T	0.16457	2.34;2.34	4.29	4.29	0.51040	GOLD (3);	0.057598	0.64402	D	0.000001	T	0.47377	0.1442	M	0.94021	3.485	0.80722	D	1	D	0.53151	0.958	P	0.60541	0.876	T	0.58014	-0.7711	10	0.17369	T	0.5	-17.5601	17.2745	0.87111	0.0:0.0:1.0:0.0	.	44	Q15363	TMED2_HUMAN	D	44	ENSP00000262225:G44D;ENSP00000405845:G44D	ENSP00000262225:G44D	G	+	2	0	TMED2	122635267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.599000	0.74127	2.371000	0.80710	0.591000	0.81541	GGC		0.652	TMED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400606.1	NM_006815		A	124069314	G	A	124069314	3	1	77	1	0	0	0	0	1	0	0	0	16043	1203	42	3	133	3	TMED2	12	124069314	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	118815	124069314	9782581	781	22517										
DDX55	57696	broad.mit.edu	37	chr12	124093312	124093312	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggatctggccagctgtgtgCgatccctggatgtcctggtg	15	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:124093312C>T	ENST00000238146.4	+	6	537	c.487C>T	c.(487-489)Cga>Tga	p.R163*	DDX55_ENST00000538744.1_Nonsense_Mutation_p.R163*	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	163	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.R163*(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		CAGCTGTGTGCGATCCCTGGA	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											148	136	140					12																	124093312		2203	4300	6503	122659265	SO:0001587	stop_gained	57696			AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"DEAD-boxes"	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.487C>T	12.37:g.124093312C>T	ENSP00000238146:p.Arg163*		122659265	Q658L6|Q8IYH0|Q9HCH7	Nonsense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.702496	0.68501	.	.	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	.	.	.	5.45	-1.68	0.08212	.	0.253789	0.42964	D	0.000628	.	.	.	.	.	.	0.52501	D	0.999958	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-22.6613	16.5664	0.84599	0.371:0.629:0.0:0.0	.	.	.	.	X	163	.	ENSP00000238146:R163X	R	+	1	2	DDX55	122659265	0.967000	0.33354	0.022000	0.16811	0.987000	0.75469	2.461000	0.45040	-0.550000	0.06183	0.563000	0.77884	CGA		0.552	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2			T	124093312	C	T	124093312	4	4	77	1	0	0	0	0	0	1	0	0	4379	760	27	1	509	1	DDX55	12	124093312	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	23998	124093312	9758583	782	22518										
NCOR2	9612	broad.mit.edu	37	chr12	124840068	124840068	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggagatggtgggtgggcgCggcaggacgggccgggcagt	23	7	0	1	rs368708782		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:124840068C>T	ENST00000405201.1	-	24	3291	c.3291G>A	c.(3289-3291)ccG>ccA	p.P1097P	NCOR2_ENST00000397355.1_Silent_p.P1088P|NCOR2_ENST00000404621.1_Silent_p.P1087P|NCOR2_ENST00000356219.3_Silent_p.P1104P|NCOR2_ENST00000404121.2_Silent_p.P658P|NCOR2_ENST00000429285.2_Silent_p.P1087P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1105					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.P1104P(1)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TGGGTGGGCGCGGCAGGACGG	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	12						T	,,	1,4237		0,1,2118	47	68	61		3261,3261,3291	-9.9	0	12		61	0,8398		0,0,4199	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,1,6317	TT,TC,CC		0.0,0.0236,0.0079	,,	1087/2459,1087/2505,1097/2515	124840068	1,12635	2119	4199	6318	123406021	SO:0001819	synonymous_variant	9612			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3291G>A	12.37:g.124840068C>T			123406021	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																				0.652	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124840068	C	T	124840068	2	4	77	1	0	0	0	0	0	0	0	1	10267	755	27	1		1	NCOR2	12	124840068	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	746756	124840068	9011827	783	22519										
AACS	65985	broad.mit.edu	37	chr12	125621309	125621309	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgaagatggcctccgggcacGccttccagcctgacttggtt	12	13	0	3	rs200966429		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:125621309G>A	ENST00000316519.6	+	17	1986	c.1780G>A	c.(1780-1782)Gcc>Acc	p.A594T	AACS_ENST00000261686.6_Intron|AACS_ENST00000545511.1_Intron|AACS_ENST00000543665.1_Intron|AACS_ENST00000316543.10_Missense_Mutation_p.A192T	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	594					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)	p.A594T(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	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)		CTCCGGGCACGCCTTCCAGCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	12											127	104	112					12																	125621309		2203	4300	6503	124187262	SO:0001583	missense	65985			AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"Acyl-CoA synthetase family"	21298	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 1"	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.1780G>A	12.37:g.125621309G>A	ENSP00000324842:p.Ala594Thr		124187262	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	ENST00000316519.6	37	CCDS9263.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.737495	0.00681	.	.	ENSG00000081760	ENST00000316519;ENST00000316543;ENST00000539251;ENST00000536118	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	5.3	-10.6	0.00265	.	1.482540	0.03526	N	0.221799	T	0.04679	0.0127	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18524	-1.0334	10	0.12766	T	0.61	.	8.0298	0.30459	0.1175:0.0666:0.4847:0.3313	.	594	Q86V21	AACS_HUMAN	T	594;192;59;149	ENSP00000324842:A594T;ENSP00000324929:A192T;ENSP00000439151:A59T;ENSP00000441331:A149T	ENSP00000324842:A594T	A	+	1	0	AACS	124187262	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.459000	0.02370	-4.807000	0.00031	-1.288000	0.01363	GCC		0.597	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928		A	125621309	G	A	125621309	3	1	77	1	0	0	0	0	1	0	0	0	9	1087	38	1	1846	1	AACS	12	125621309	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	781241	125621309	8230586	784	22520										
TMEM132D	121256	broad.mit.edu	37	chr12	130184847	130184847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagcttctccccggcgctgCggtcgtcccagtctctgccc	11	19	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:130184847C>T	ENST00000422113.2	-	2	802	c.476G>A	c.(475-477)cGc>cAc	p.R159H	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	159					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.R159H(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		CCCGGCGCTGCGGTCGTCCCA	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	12											23	24	24					12																	130184847		2203	4300	6503	128750800	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.476G>A	12.37:g.130184847C>T	ENSP00000408581:p.Arg159His		128750800	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	3.410	-0.120411	0.06838	.	.	ENSG00000151952	ENST00000422113	T	0.11604	2.76	5.33	-8.28	0.01013	.	0.947996	0.08798	N	0.892180	T	0.02156	0.0067	N	0.00729	-1.24	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.47774	-0.9091	9	.	.	.	-2.6295	8.7331	0.34512	0.0:0.3706:0.3162:0.3132	.	159	Q14C87	T132D_HUMAN	H	159	ENSP00000408581:R159H	.	R	-	2	0	TMEM132D	128750800	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.175000	0.16762	-2.000000	0.00965	-0.378000	0.06908	CGC		0.632	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130184847	C	T	130184847	3	4	77	1	0	0	0	0	1	0	0	0	16086	768	27	1	2855	1	TMEM132D	12	130184847	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4563538	130184847	3667048	785	22521										
PGAM5	192111	broad.mit.edu	37	chr12	133291539	133291539	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaccactacaaagccaaggCcacgcggcacatcttcctca	8	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr12:133291539C>A	ENST00000498926.2	+	2	345	c.287C>A	c.(286-288)gCc>gAc	p.A96D	PGAM5_ENST00000317555.2_Missense_Mutation_p.A96D|PXMP2_ENST00000545677.1_Silent_p.G135G|PGAM5_ENST00000454808.2_5'UTR|PGAM5_ENST00000543955.1_5'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	96					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)	p.A96D(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		AAAGCCAAGGCCACGCGGCAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	12											158	108	125					12																	133291539		2203	4300	6503	131801612	SO:0001583	missense	192111			BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.287C>A	12.37:g.133291539C>A	ENSP00000438465:p.Ala96Asp		131801612	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922047	0.92319	.	.	ENSG00000247077	ENST00000317555;ENST00000498926	.	.	.	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.78886	0.4354	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.74348	0.961;0.983	T	0.81938	-0.0704	9	0.62326	D	0.03	0.3053	17.5103	0.87758	0.0:1.0:0.0:0.0	.	96;96	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	D	96	.	ENSP00000321503:A96D	A	+	2	0	PGAM5	131801612	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.448000	0.80631	2.136000	0.66102	0.462000	0.41574	GCC		0.582	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		A	133291539	C	A	133291539	3	1	77	1	0	0	0	0	1	0	0	0	11807	739	26	2	293	2	PGAM5	12	133291539	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3106692	133291539	560356	786	22522										
FAM123A	219287	broad.mit.edu	37	chr13	25744736	25744736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctggggcggcgggcgccCggccgctgccgccttcggag	20	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:25744736C>T	ENST00000515384.1	-	1	1689	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000357816.2_Intron|AMER2_ENST00000381853.3_Intron			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	341					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R341Q(1)									ggcgggcgcccggccgcTGCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	13											15	19	18					13																	25744736		997	2107	3104	24642736	SO:0001583	missense	219287			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1022G>A	13.37:g.25744736C>T	ENSP00000426528:p.Arg341Gln		24642736	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	37	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	C	7.300	0.612843	0.14066	.	.	ENSG00000165566	ENST00000515384	T	0.21543	2.0	3.32	-0.549	0.11829	.	.	.	.	.	T	0.06690	0.0171	N	0.04508	-0.205	0.80722	D	1	B	0.25441	0.126	B	0.12156	0.007	T	0.36866	-0.9730	9	0.13470	T	0.59	.	5.4178	0.16384	0.0:0.1989:0.4851:0.316	.	341	Q8N7J2	F123A_HUMAN	Q	341	ENSP00000426528:R341Q	ENSP00000426528:R341Q	R	-	2	0	FAM123A	24642736	0.937000	0.31787	0.543000	0.28128	0.813000	0.45954	0.767000	0.26575	-0.158000	0.11040	0.462000	0.41574	CGG		0.662	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25744736	C	T	25744736	3	4	77	1	0	0	0	0	1	0	0	0	5438	652	23	1	997	1	FAM123A	13	25744736	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		25744736	89425142	787	22523										
WASF3	10810	broad.mit.edu	37	chr13	27255349	27255349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtaccggcccccatctgcctCggcgaggcacatggccctca	11	18	2	0	rs547630336		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:27255349C>T	ENST00000335327.5	+	8	1053	c.875C>T	c.(874-876)tCg>tTg	p.S292L	WASF3_ENST00000361042.4_Missense_Mutation_p.S289L	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	292					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)		p.S292L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CCATCTGCCTCGGCGAGGCAC	0.701													C|||	1	0.000199681	0	0	5008	,	,		13009	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	13											46	53	51					13																	27255349		2203	4300	6503	26153349	SO:0001583	missense	10810			AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.875C>T	13.37:g.27255349C>T	ENSP00000335055:p.Ser292Leu		26153349	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.650335	0.47362	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.47528	0.84;0.87	5.94	5.94	0.96194	.	0.307523	0.36893	N	0.002356	T	0.38719	0.1051	L	0.33485	1.01	0.43394	D	0.99551	B;B	0.34061	0.313;0.436	B;B	0.25140	0.058;0.054	T	0.12167	-1.0558	10	0.32370	T	0.25	-23.4102	20.345	0.98787	0.0:1.0:0.0:0.0	.	289;292	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	L	289;292	ENSP00000354325:S289L;ENSP00000335055:S292L	ENSP00000335055:S292L	S	+	2	0	WASF3	26153349	0.980000	0.34600	0.972000	0.41901	0.416000	0.31233	2.983000	0.49345	2.817000	0.96982	0.555000	0.69702	TCG		0.701	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			T	27255349	C	T	27255349	3	4	77	1	0	0	0	0	1	0	0	0	17294	893	31	1	897	1	WASF3	13	27255349	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1510613	27255349	87914529	788	22524										
PAN3	255967	broad.mit.edu	37	chr13	28830471	28830471	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcccctcttcattcccccaAgattactccacatacttctc	1	18	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:28830471A>G	ENST00000380958.3	+	7	1195	c.1043A>G	c.(1042-1044)aAg>aGg	p.K348R	PAN3_ENST00000483842.1_3'UTR|PAN3_ENST00000399613.1_Missense_Mutation_p.K148R|PAN3_ENST00000282391.5_Missense_Mutation_p.K36R	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit									p.K148R(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	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)		CATTCCCCCAAGATTACTCCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	13											210	202	205					13																	28830471		2203	4300	6503	27728471	SO:0001583	missense	255967			AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.1043A>G	13.37:g.28830471A>G	ENSP00000370345:p.Lys348Arg		27728471		Missense_Mutation	SNP	ENST00000380958.3	37	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424847	0.83667	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.45276	0.9;0.92;0.93	5.8	5.8	0.92144	.	0.086330	0.85682	D	0.000000	T	0.47710	0.1460	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.57899	0.981;0.981;0.974;0.974	P;P;D;D	0.67725	0.727;0.73;0.953;0.953	T	0.38478	-0.9659	10	0.22109	T	0.4	-15.4314	16.1455	0.81563	1.0:0.0:0.0:0.0	.	348;348;36;294	Q58A45-4;Q58A45;Q58A45-2;Q58A45-3	.;PAN3_HUMAN;.;.	R	348;148;36	ENSP00000370345:K348R;ENSP00000382522:K148R;ENSP00000282391:K36R	ENSP00000282391:K36R	K	+	2	0	PAN3	27728471	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.938000	0.92943	2.206000	0.71126	0.528000	0.53228	AAG		0.413	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		G	28830471	A	G	28830471	3	3	77	1	0	0	0	0	1	0	0	0	11446	72	3	4	1069	4	PAN3	13	28830471	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1575122	28830471	86339407	789	22525										
USPL1	10208	broad.mit.edu	37	chr13	31232744	31232744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcacagctgcccacccacatGctcatgctgcttcagaagtt	8	15	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:31232744G>A	ENST00000255304.4	+	9	2872	c.2530G>A	c.(2530-2532)Gct>Act	p.A844T		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	844					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)	p.A844T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		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)		CCACCCACATGCTCATGCTGC	0.498																																					Ovarian(60;318 1180 1554 28110 31601)											1	Substitution - Missense(1)	large_intestine(1)	13											82	80	80					13																	31232744		2203	4300	6503	30130744	SO:0001583	missense	10208			X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2530G>A	13.37:g.31232744G>A	ENSP00000255304:p.Ala844Thr		30130744	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	G	7.283	0.609450	0.14066	.	.	ENSG00000132952	ENST00000255304	T	0.13538	2.58	5.4	1.75	0.24633	.	1.573510	0.03711	N	0.250154	T	0.09818	0.0241	N	0.22421	0.69	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.34279	-0.9835	10	0.02654	T	1	-0.2421	10.4734	0.44650	0.3312:0.0:0.6688:0.0	.	844	Q5W0Q7	USPL1_HUMAN	T	844	ENSP00000255304:A844T	ENSP00000255304:A844T	A	+	1	0	USPL1	30130744	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.084000	0.11268	0.019000	0.15079	-0.258000	0.10820	GCT		0.498	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		A	31232744	G	A	31232744	3	1	77	1	0	0	0	0	1	0	0	0	17132	1319	46	3	2560	3	USPL1	13	31232744	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2402273	31232744	83937134	790	22526										
DCLK1	9201	broad.mit.edu	37	chr13	36686075	36686075	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgatggcatcggtgatatcGgtgaggacctgctcaaagga	14	7	1	3	rs137961229		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:36686075G>A	ENST00000360631.3	-	3	865	c.654C>T	c.(652-654)acC>acT	p.T218T	DCLK1_ENST00000379892.4_Silent_p.T218T|DCLK1_ENST00000255448.4_Silent_p.T218T			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	218	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.T218T(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CGGTGATATCGGTGAGGACCT	0.502													G|||	1	0.000199681	8e-04	0	5008	,	,		18504	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	13						G		2,4404	4.2+/-10.8	0,2,2201	171	142	152		654	-9.4	0.6	13	dbSNP_134	152	0,8600		0,0,4300	no	coding-synonymous	DCLK1	NM_004734.4		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		218/730	36686075	2,13004	2203	4300	6503	35584075	SO:0001819	synonymous_variant	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.654C>T	13.37:g.36686075G>A			35584075	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																					0.502	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36686075	G	A	36686075	2	1	77	1	0	0	0	0	0	0	0	1	4297	1103	39	1		1	DCLK1	13	36686075	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5453331	36686075	78483803	791	22527										
SOHLH2	54937	broad.mit.edu	37	chr13	36748974	36748974	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttacatacggcaagagagtaCgcagctgctcacagcaatat	9	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:36748974C>T	ENST00000379881.3	-	7	762	c.674G>A	c.(673-675)cGt>cAt	p.R225H	CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.R302H|SOHLH2_ENST00000554962.1_Missense_Mutation_p.R302H	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	225	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R225H(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		CAAGAGAGTACGCAGCTGCTC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	13											78	75	76					13																	36748974		2203	4300	6503	35646974	SO:0001583	missense	54937			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.674G>A	13.37:g.36748974C>T	ENSP00000369210:p.Arg225His		35646974	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	37	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362183	0.61403	.	.	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	D;D;D	0.98717	-5.09;-5.09;-5.09	5.11	5.11	0.69529	Helix-loop-helix DNA-binding (5);	0.096082	0.46758	N	0.000265	D	0.99055	0.9676	M	0.82323	2.585	0.37305	D	0.908875	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99949	1.1511	10	0.87932	D	0	-8.7694	14.041	0.64674	0.0:1.0:0.0:0.0	.	302;225	B4DX90;Q9NX45	.;SOLH2_HUMAN	H	225;302;302	ENSP00000369210:R225H;ENSP00000451542:R302H;ENSP00000421868:R302H	ENSP00000421868:R302H	R	-	2	0	CCDC169-SOHLH2;SOHLH2	35646974	0.988000	0.35896	0.942000	0.38095	0.250000	0.25880	3.639000	0.54339	2.392000	0.81423	0.650000	0.86243	CGT		0.393	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		T	36748974	C	T	36748974	3	4	77	1	0	0	0	0	1	0	0	0	14961	536	19	1	623	1	SOHLH2	13	36748974	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	62899	36748974	78420904	792	22528										
SPERT	220082	broad.mit.edu	37	chr13	46287514	46287514	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggagctggactacaacccGccgcgggtgcagctcagcga	14	14	1	0	rs184200267		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:46287514G>A	ENST00000310521.1	+	3	434	c.354G>A	c.(352-354)ccG>ccA	p.P118P	SPERT_ENST00000378966.3_Silent_p.P82P	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	118						cytoplasmic membrane-bounded vesicle (GO:0016023)		p.P118P(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		ACTACAACCCGCCGCGGGTGC	0.632													G|||	1	0.000199681	0	0	5008	,	,		17081	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	13											61	67	65					13																	46287514		2203	4299	6502	45185515	SO:0001819	synonymous_variant	220082			AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.354G>A	13.37:g.46287514G>A			45185515	A8K8I5|Q8NHV2	Silent	SNP	ENST00000310521.1	37	CCDS9399.1																																																																																				0.632	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46287514	G	A	46287514	2	1	77	1	0	0	0	0	0	0	0	1	15078	1074	38	1		1	SPERT	13	46287514	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	9538540	46287514	68882364	793	22529										
ZC3H13	23091	broad.mit.edu	37	chr13	46559477	46559477	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccctacttcggcccattcGgtcatttctaatttcacttc	4	16	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:46559477G>A	ENST00000242848.4	-	10	2023	c.1675C>T	c.(1675-1677)Cga>Tga	p.R559*	ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.R559*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	559	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R559*(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		CGGCCCATTCGGTCATTTCTA	0.403																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											1	Substitution - Nonsense(1)	large_intestine(1)	13											87	89	88					13																	46559477		2203	4300	6503	45457478	SO:0001587	stop_gained	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1675C>T	13.37:g.46559477G>A	ENSP00000242848:p.Arg559*		45457478	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	41	9.109765	0.99068	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	.	.	.	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000030	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6379	0.76970	0.0:0.0:0.8624:0.1376	.	.	.	.	X	559;559;375	.	ENSP00000242848:R559X	R	-	1	2	ZC3H13	45457478	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.228000	0.51270	2.861000	0.98227	0.655000	0.94253	CGA		0.403	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46559477	G	A	46559477	4	1	77	1	0	0	0	0	0	1	0	0	17604	1124	39	1	3051	1	ZC3H13	13	46559477	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	271963	46559477	68610401	794	22530										
SETDB2	83852	broad.mit.edu	37	chr13	50055135	50055135	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcgacaattgtgtcaaaacCgagttgtccaacatggtcct	8	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:50055135C>T	ENST00000317257.8	+	9	1900	c.1075C>T	c.(1075-1077)Cga>Tga	p.R359*	SETDB2_ENST00000258672.5_Nonsense_Mutation_p.R347*|SETDB2_ENST00000354234.4_Nonsense_Mutation_p.R347*	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	359	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)	p.R359*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		GTGTCAAAACCGAGTTGTCCA	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	13											174	148	157					13																	50055135		2203	4300	6503	48953136	SO:0001587	stop_gained	83852			AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"Chromatin-modifying enzymes / K-methyltransferases"	20263	protein-coding gene	gene with protein product		607865	"chromosome 13 open reading frame 4"	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.1075C>T	13.37:g.50055135C>T	ENSP00000326477:p.Arg359*		48953136	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Nonsense_Mutation	SNP	ENST00000317257.8	37	CCDS9417.1	.	.	.	.	.	.	.	.	.	.	C	39	7.772225	0.98480	.	.	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	.	.	.	5.61	4.69	0.59074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2042	0.59787	0.2404:0.7596:0.0:0.0	.	.	.	.	X	347;359;347	.	ENSP00000258672:R347X	R	+	1	2	SETDB2	48953136	1.000000	0.71417	0.998000	0.56505	0.726000	0.41606	2.560000	0.45896	2.653000	0.90120	0.655000	0.94253	CGA		0.413	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915		T	50055135	C	T	50055135	4	4	77	1	0	0	0	0	0	1	0	0	14176	644	23	1	1105	1	SETDB2	13	50055135	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3495658	50055135	65114743	795	22531										
ALG11	440138	broad.mit.edu	37	chr13	52593173	52593173	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaaattagtgtcaactagcAaaaatgggaaaaatcaaatg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:52593173delA	ENST00000521508.1	+	2	174	c.169delA	c.(169-171)aaafs	p.K57fs	ALG11_ENST00000523764.1_Intron	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	57					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)	p.N58fs*7(1)		endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		GTCAACTAGCAAAAATGGGAA	0.403																																																1	Deletion - Frameshift(1)	large_intestine(1)	13											120	115	117					13																	52593173		2203	4300	6503	51491174	SO:0001589	frameshift_variant	9724			AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"Glycosyltransferase group 1 domain containing"	32456	protein-coding gene	gene with protein product	"GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"	613666	"asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)", "asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.169delA	13.37:g.52593173delA	ENSP00000430236:p.Lys57fs		51491174	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Frame_Shift_Del	DEL	ENST00000521508.1	37	CCDS31977.1																																																																																				0.403	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127		-	52593173	A	-	52593173	7	5	77	1	0	1	0	1	0	0	0	0	513	131	5	0	175	0	ALG11	13	52593173	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	2538038	52593173	62576705	796	22532										
PCDH20	64881	broad.mit.edu	37	chr13	61987546	61987546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccacagcaggatgctctatgGccagtcgggtgtttacaggt	13	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:61987546G>A	ENST00000409186.1	-	5	2791	c.686C>T	c.(685-687)gCc>gTc	p.A229V	PCDH20_ENST00000409204.4_Missense_Mutation_p.A229V			Q8N6Y1	PCD20_HUMAN	protocadherin 20	229	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.A202V(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		ATGCTCTATGGCCAGTCGGGT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	13											106	94	98					13																	61987546		2203	4300	6503	60885547	SO:0001583	missense	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.686C>T	13.37:g.61987546G>A	ENSP00000386653:p.Ala229Val		60885547	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	g	13.98	2.399968	0.42613	.	.	ENSG00000197991	ENST00000409204;ENST00000409186	T;T	0.51574	0.7;0.7	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000006	T	0.44074	0.1276	L	0.52011	1.625	0.54753	D	0.999989	B	0.24426	0.103	B	0.25614	0.062	T	0.31943	-0.9925	10	0.46703	T	0.11	.	13.2045	0.59787	0.0726:0.0:0.9274:0.0	.	229	A8K1K9	.	V	229	ENSP00000387250:A229V;ENSP00000386653:A229V	ENSP00000386653:A229V	A	-	2	0	PCDH20	60885547	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.999000	0.88496	2.722000	0.93159	0.651000	0.88453	GCC		0.537	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		A	61987546	G	A	61987546	3	1	77	1	0	0	0	0	1	0	0	0	11546	1203	42	3	2173	3	PCDH20	13	61987546	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	9394373	61987546	53182332	797	22533										
PCDH9	5101	broad.mit.edu	37	chr13	67800906	67800906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaacagtaacaatcacagccGcttggctttggaggggaggg	15	8	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:67800906G>A	ENST00000377865.2	-	1	1801	c.1667C>T	c.(1666-1668)gCg>gTg	p.A556V	PCDH9_ENST00000544246.1_Missense_Mutation_p.A556V|PCDH9_ENST00000377861.3_Missense_Mutation_p.A556V|PCDH9_ENST00000328454.5_Missense_Mutation_p.A556V|PCDH9_ENST00000456367.1_Missense_Mutation_p.A556V			Q9HC56	PCDH9_HUMAN	protocadherin 9	556	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A556E(1)|p.A556V(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AATCACAGCCGCTTGGCTTTG	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	13											85	90	88					13																	67800906		2203	4300	6503	66698907	SO:0001583	missense	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1667C>T	13.37:g.67800906G>A	ENSP00000367096:p.Ala556Val		66698907	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.240178	0.39598	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.78	5.78	0.91487	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.51805	0.1696	L	0.31476	0.935	0.80722	D	1	D;P;P;P	0.59767	0.986;0.841;0.895;0.914	P;B;B;P	0.51229	0.663;0.28;0.296;0.572	T	0.31998	-0.9923	10	0.13470	T	0.59	.	20.3668	0.98882	0.0:0.0:1.0:0.0	.	556;556;556;556	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	V	556	ENSP00000442186:A556V;ENSP00000367096:A556V;ENSP00000401699:A556V;ENSP00000332060:A556V;ENSP00000367092:A556V	ENSP00000332060:A556V	A	-	2	0	PCDH9	66698907	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.894000	0.99253	0.655000	0.94253	GCG		0.418	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67800906	G	A	67800906	3	1	77	1	0	0	0	0	1	0	0	0	11549	1087	38	1	2062	1	PCDH9	13	67800906	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5813360	67800906	47368972	798	22534										
DIS3	22894	broad.mit.edu	37	chr13	73335611	73335611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatggcattctttcttacaaAtaaaatataggcttcttcac	4	8	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:73335611A>G	ENST00000377767.4	-	19	2660	c.2560T>C	c.(2560-2562)Ttt>Ctt	p.F854L	DIS3_ENST00000377780.4_Missense_Mutation_p.F824L|DIS3_ENST00000545453.1_Missense_Mutation_p.F692L	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	854					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)	p.F854L(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		TTTCTTACAAATAAAATATAG	0.269										Multiple Myeloma(4;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	13											70	79	76					13																	73335611		2203	4300	6503	72233612	SO:0001583	missense	22894			AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.2560T>C	13.37:g.73335611A>G	ENSP00000366997:p.Phe854Leu		72233612	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461668	0.63513	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.21734	1.99;1.99;1.99	5.86	5.86	0.93980	.	0.195592	0.64402	D	0.000016	T	0.28962	0.0719	M	0.76574	2.34	0.80722	D	1	B;B	0.32203	0.36;0.032	B;B	0.34652	0.187;0.038	T	0.04930	-1.0917	10	0.21014	T	0.42	.	16.2668	0.82588	1.0:0.0:0.0:0.0	.	824;854	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	L	854;824;692	ENSP00000366997:F854L;ENSP00000367011:F824L;ENSP00000440058:F692L	ENSP00000366997:F854L	F	-	1	0	DIS3	72233612	1.000000	0.71417	0.932000	0.37286	0.992000	0.81027	7.188000	0.77739	2.240000	0.73641	0.533000	0.62120	TTT		0.269	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		G	73335611	A	G	73335611	3	3	77	1	0	0	0	0	1	0	0	0	4546	101	4	4	328	4	DIS3	13	73335611	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	5534705	73335611	41834267	799	22535										
DZIP1	22873	broad.mit.edu	37	chr13	96239830	96239830	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatcagtgtcctcgatttcGcttccctcggtcccgtccgc	8	17	2	0	rs371016866		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:96239830G>A	ENST00000376829.2	-	20	3032	c.2181C>T	c.(2179-2181)agC>agT	p.S727S	DZIP1_ENST00000361396.2_Silent_p.S708S|DZIP1_ENST00000347108.3_Silent_p.S727S|DZIP1_ENST00000361156.3_Silent_p.S708S	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	727					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.S708S(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CCTCGATTTCGCTTCCCTCGG	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	13						G	,	0,4406		0,0,2203	184	156	165		2124,2181	-4	0	13		165	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DZIP1	NM_014934.3,NM_198968.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	708/849,727/868	96239830	1,13005	2203	4300	6503	95037831	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2181C>T	13.37:g.96239830G>A			95037831	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.547	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		A	96239830	G	A	96239830	2	1	77	1	0	0	0	0	0	0	0	1	4874	1078	38	1		1	DZIP1	13	96239830	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	22904219	96239830	18930048	800	22536										
RNF113B	140432	broad.mit.edu	37	chr13	98828976	98828976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacgtatggggcccttcctcGccatccccgaggaggagttg	13	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:98828976G>A	ENST00000267291.6	-	1	543	c.515C>T	c.(514-516)gCg>gTg	p.A172V	FARP1_ENST00000319562.6_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Intron|FARP1_ENST00000376586.2_Intron	NM_178861.4	NP_849192.1	Q8IZP6	R113B_HUMAN	ring finger protein 113B	172							zinc ion binding (GO:0008270)	p.A172V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)			GCCCTTCCTCGCCATCCCCGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	13											80	68	72					13																	98828976		2203	4300	6503	97626977	SO:0001583	missense	140432			AF539427	CCDS9486.1	13q32.2	2006-08-22	2005-03-22	2005-03-22	ENSG00000139797	ENSG00000139797		"RING-type (C3HC4) zinc fingers"	17267	protein-coding gene	gene with protein product			"zinc finger protein 183-like 1"	ZNF183L1			Standard	NM_178861		Approved	RNF161	uc001vnk.3	Q8IZP6	OTTHUMG00000017245	ENST00000267291.6:c.515C>T	13.37:g.98828976G>A	ENSP00000267291:p.Ala172Val		97626977	Q8WWF9|Q96QY9	Missense_Mutation	SNP	ENST00000267291.6	37	CCDS9486.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.172681	0.00315	.	.	ENSG00000139797	ENST00000267291	T	0.27890	1.64	1.16	-0.143	0.13444	.	0.074349	0.53938	N	0.000060	T	0.04497	0.0123	N	0.00254	-1.765	0.22648	N	0.998891	B	0.09022	0.002	B	0.09377	0.004	T	0.36625	-0.9740	10	0.02654	T	1	.	3.0076	0.06033	0.6569:0.0:0.3431:0.0	.	172	Q8IZP6	R113B_HUMAN	V	172	ENSP00000267291:A172V	ENSP00000267291:A172V	A	-	2	0	RNF113B	97626977	1.000000	0.71417	0.976000	0.42696	0.243000	0.25628	2.097000	0.41748	-0.045000	0.13468	-0.350000	0.07774	GCG		0.622	RNF113B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045536.3	NM_178861		A	98828976	G	A	98828976	3	1	77	1	0	0	0	0	1	0	0	0	13465	1087	38	1	461	1	RNF113B	13	98828976	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2589146	98828976	16340902	801	22537										
NALCN	259232	broad.mit.edu	37	chr13	101736093	101736093	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaagatgaagaggctgtgcGatcttcagtcggctcttcag	14	8	4	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:101736093G>A	ENST00000251127.6	-	31	3633	c.3552C>T	c.(3550-3552)atC>atT	p.I1184I		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1184					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.I1184I(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GAGGCTGTGCGATCTTCAGTC	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	13											73	72	72					13																	101736093		2203	4300	6503	100534094	SO:0001819	synonymous_variant	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3552C>T	13.37:g.101736093G>A			100534094	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																				0.507	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		A	101736093	G	A	101736093	2	1	77	1	0	0	0	0	0	0	0	1	10178	1048	37	1		1	NALCN	13	101736093	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2907117	101736093	13433785	802	22538										
ITGBL1	9358	broad.mit.edu	37	chr13	102366833	102366833	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgttctgctgaagagtggtAtatttctggggagttctgtg	14	4	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:102366833A>T	ENST00000376180.3	+	10	1544	c.1325A>T	c.(1324-1326)tAt>tTt	p.Y442F	RP11-397O8.7_ENST00000606869.1_lincRNA|ITGBL1_ENST00000376162.3_Missense_Mutation_p.Y349F|ITGBL1_ENST00000545560.2_Missense_Mutation_p.Y301F	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	442	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)		p.Y442F(1)		breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GAAGAGTGGTATATTTCTGGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	13											425	394	404					13																	102366833		2203	4300	6503	101164834	SO:0001583	missense	9358			AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.1325A>T	13.37:g.102366833A>T	ENSP00000365351:p.Tyr442Phe		101164834	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Missense_Mutation	SNP	ENST00000376180.3	37	CCDS9499.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.125351	0.56721	.	.	ENSG00000198542	ENST00000376180;ENST00000537118;ENST00000539955;ENST00000545560;ENST00000376162	D;D;D	0.89939	-2.59;-2.59;-2.59	6.16	4.97	0.65823	.	0.114545	0.64402	D	0.000006	D	0.83248	0.5213	L	0.32530	0.975	0.45066	D	0.99808	P;P	0.42203	0.651;0.773	B;B	0.38106	0.112;0.265	D	0.83665	0.0163	10	0.72032	D	0.01	.	12.8826	0.58026	0.8779:0.0:0.0:0.1221	.	301;442	B3KTP1;O95965	.;ITGBL_HUMAN	F	442;350;301;301;349	ENSP00000365351:Y442F;ENSP00000439903:Y301F;ENSP00000365332:Y349F	ENSP00000365332:Y349F	Y	+	2	0	ITGBL1	101164834	1.000000	0.71417	0.891000	0.34965	0.525000	0.34531	6.967000	0.76079	1.129000	0.42072	0.528000	0.53228	TAT		0.398	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		T	102366833	A	T	102366833	3	4	77	1	0	0	0	0	1	0	0	0	7923	449	16	5	1363	5	ITGBL1	13	102366833	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	630740	102366833	12803045	803	22539										
FAM155A	728215	broad.mit.edu	37	chr13	107863000	107863000	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgggcaatataaatggacacCtcgtctgaacctccaaacag	8	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:107863000C>A	ENST00000375915.2	-	2	1157	c.1019G>T	c.(1018-1020)aGg>aTg	p.R340M		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	340						integral component of membrane (GO:0016021)		p.R340M(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						AAATGGACACCTCGTCTGAAC	0.468											OREG0022506	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	13											109	102	104					13																	107863000		2203	4300	6503	106661001	SO:0001583	missense	728215			L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1019G>T	13.37:g.107863000C>A	ENSP00000365080:p.Arg340Met	1407	106661001	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	37	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746723	0.89663	.	.	ENSG00000204442	ENST00000375915	T	0.13196	2.61	5.6	5.6	0.85130	.	0.051915	0.64402	D	0.000001	T	0.33990	0.0882	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.01557	-1.1325	10	0.87932	D	0	.	18.5812	0.91171	0.0:1.0:0.0:0.0	.	340	B1AL88	F155A_HUMAN	M	340	ENSP00000365080:R340M	ENSP00000365080:R340M	R	-	2	0	FAM155A	106661001	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.484000	0.81180	2.609000	0.88269	0.650000	0.86243	AGG		0.468	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		A	107863000	C	A	107863000	3	1	77	1	0	0	0	0	1	0	0	0	5481	681	24	2	365	2	FAM155A	13	107863000	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5496167	107863000	7306878	804	22540										
COL4A2	1284	broad.mit.edu	37	chr13	111125481	111125481	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccttcccggagacagaggCccccctggattcagaggtga							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:111125481delC	ENST00000360467.5	+	29	2715	c.2409delC	c.(2407-2409)ggcfs	p.G803fs		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	803	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)	p.P805fs*15(1)		NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GAGACAGAGGCCCCCCTGGAT	0.682																																																1	Deletion - Frameshift(1)	large_intestine(1)	13											10	13	12					13																	111125481		1900	4065	5965	109923482	SO:0001589	frameshift_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2409delC	13.37:g.111125481delC	ENSP00000353654:p.Gly803fs		109923482	Q14052|Q548C3|Q5VZA9|Q66K23	Frame_Shift_Del	DEL	ENST00000360467.5	37	CCDS41907.1																																																																																				0.682	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		-	111125481	C	-	111125481	7	5	77	1	0	1	0	1	0	0	0	0	3696	726	26	0	2519	0	COL4A2	13	111125481	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	3262481	111125481	4044397	805	22541										
ANKRD10	55608	broad.mit.edu	37	chr13	111567095	111567095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccgaaatgcgcggcccagtGcacgggcgtccagccataga	14	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:111567095G>A	ENST00000267339.2	-	1	321	c.187C>T	c.(187-189)Cac>Tac	p.H63Y	ANKRD10_ENST00000310847.4_Missense_Mutation_p.H63Y|ANKRD10_ENST00000375758.5_Missense_Mutation_p.H63Y	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	63								p.H63Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			GCGGCCCAGTGCACGGGCGTC	0.677																																																1	Substitution - Missense(1)	large_intestine(1)	13											16	18	18					13																	111567095		2180	4290	6470	110365096	SO:0001583	missense	55608			AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.187C>T	13.37:g.111567095G>A	ENSP00000267339:p.His63Tyr		110365096	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852089	0.71719	.	.	ENSG00000088448	ENST00000267339;ENST00000375758;ENST00000310847	T;T;T	0.71103	-0.54;-0.48;-0.48	3.99	3.99	0.46301	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.83445	0.5256	M	0.81614	2.55	0.58432	D	0.999997	D;P;D	0.62365	0.991;0.844;0.983	D;P;P	0.76575	0.988;0.482;0.862	D	0.84723	0.0741	10	0.44086	T	0.13	-8.4603	14.6237	0.68605	0.0:0.0:1.0:0.0	.	63;63;63	Q8IUW1;Q9NXR5-2;Q9NXR5	.;.;ANR10_HUMAN	Y	63	ENSP00000267339:H63Y;ENSP00000364911:H63Y;ENSP00000312534:H63Y	ENSP00000267339:H63Y	H	-	1	0	ANKRD10	110365096	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.322000	0.72886	1.752000	0.51891	0.491000	0.48974	CAC		0.677	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			A	111567095	G	A	111567095	3	1	77	1	0	0	0	0	1	0	0	0	638	1319	46	3	1099	3	ANKRD10	13	111567095	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	441614	111567095	3602783	806	22542										
PROZ	8858	broad.mit.edu	37	chr13	113826163	113826163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgggcaactcgctgaccaCgcggcctgtcacacttgtgg	12	15	1	1	rs200473651	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr13:113826163C>T	ENST00000375547.2	+	8	954	c.947C>T	c.(946-948)aCg>aTg	p.T316M	PROZ_ENST00000342783.4_Missense_Mutation_p.T338M	NM_003891.2	NP_003882.1	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma glycoprotein	316	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.T316M(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2)	16	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_lung(25;0.216)	all cancers(43;0.104)		Menadione(DB00170)	TCGCTGACCACGCGGCCTGTC	0.637													C|||	2	0.000399361	0	0	5008	,	,		16841	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	13											49	46	47					13																	113826163		2203	4300	6503	112874164	SO:0001583	missense	8858			M55670	CCDS9531.1, CCDS58300.1	13q34	2008-07-18			ENSG00000126231	ENSG00000126231			9460	protein-coding gene	gene with protein product		176895				2244898, 2403355	Standard	NM_001256134		Approved	PZ	uc010agr.2	P22891	OTTHUMG00000017376	ENST00000375547.2:c.947C>T	13.37:g.113826163C>T	ENSP00000364697:p.Thr316Met		112874164	A6NMB4|Q15213|Q5JVF5|Q5JVF6	Missense_Mutation	SNP	ENST00000375547.2	37	CCDS9531.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.435	-0.901309	0.02453	.	.	ENSG00000126231	ENST00000375547;ENST00000342783	D;D	0.88896	-2.44;-2.44	4.16	-8.32	0.00996	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.936100	0.01708	N	0.027570	T	0.68851	0.3046	N	0.01705	-0.755	0.09310	N	1	B;B	0.22480	0.011;0.07	B;B	0.18871	0.018;0.023	T	0.63769	-0.6562	10	0.87932	D	0	.	1.8959	0.03257	0.1173:0.2147:0.1925:0.4755	.	338;316	P22891-2;P22891	.;PROZ_HUMAN	M	316;338	ENSP00000364697:T316M;ENSP00000344458:T338M	ENSP00000344458:T338M	T	+	2	0	PROZ	112874164	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.751000	0.04803	-5.088000	0.00022	-1.800000	0.00619	ACG		0.637	PROZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045845.1	NM_003891		T	113826163	C	T	113826163	3	4	77	1	0	0	0	0	1	0	0	0	12596	536	19	1	977	1	PROZ	13	113826163	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2259068	113826163	1343715	807	22543										
FLJ10357	55701	broad.mit.edu	37	chr14	21549050	21549050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggagcgcctggcccaggcaCgggaggccctggctctggag	18	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:21549050C>T	ENST00000298694.4	+	13	2642	c.2515C>T	c.(2515-2517)Cgg>Tgg	p.R839W	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.R839W			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	839						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R839W(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GGCCCAGGCACGGGAGGCCCT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	14											59	60	60					14																	21549050		2203	4300	6503	20618890	SO:0001583	missense	55701				CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.2515C>T	14.37:g.21549050C>T	ENSP00000298694:p.Arg839Trp		20618890	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	De_novo_Start_OutOfFrame	SNP	ENST00000298694.4	37	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.439550	0.63067	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02916	4.17;4.11	5.52	2.39	0.29439	.	0.290182	0.24463	N	0.038316	T	0.06142	0.0159	N	0.19112	0.55	0.25955	N	0.9827	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.982	T	0.20638	-1.0269	10	0.56958	D	0.05	.	10.9969	0.47582	0.5259:0.4741:0.0:0.0	.	839;839	Q8TER5-4;Q8TER5	.;ARH40_HUMAN	W	839	ENSP00000298694:R839W;ENSP00000298693:R839W	ENSP00000298693:R839W	R	+	1	2	ARHGEF40	20618890	0.047000	0.20315	0.945000	0.38365	0.958000	0.62258	0.140000	0.16056	0.601000	0.29879	0.555000	0.69702	CGG		0.652	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			T	21549050	C	T	21549050	3	4	77	1	0	0	0	0	1	0	0	0	5945	527	19	1	2565	1	FLJ10357	14	21549050	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		21549050	85800490	808	22544										
LRP10	26020	broad.mit.edu	37	chr14	23346661	23346661	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggccctggaagatgaggaCgatgtgctactggtgccact	14	10	0	2	rs144502939		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:23346661C>T	ENST00000359591.4	+	7	2758	c.2067C>T	c.(2065-2067)gaC>gaT	p.D689D	LRP10_ENST00000546834.1_Intron|LRP10_ENST00000470660.1_3'UTR	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	689					endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.D689D(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		AAGATGAGGACGATGTGCTAC	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	14						T		0,4406		0,0,2203	30	33	32		2067	-9.9	0.4	14	dbSNP_134	32	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	LRP10	NM_014045.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		689/714	23346661	1,13003	2203	4299	6502	22416501	SO:0001819	synonymous_variant	26020			AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.2067C>T	14.37:g.23346661C>T			22416501	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Silent	SNP	ENST00000359591.4	37	CCDS9578.1																																																																																				0.682	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			T	23346661	C	T	23346661	2	4	77	1	0	0	0	0	0	0	0	1	8981	535	19	1		1	LRP10	14	23346661	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1797611	23346661	84002879	809	22545										
MYH6	4624	broad.mit.edu	37	chr14	23851697	23851697	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acctgggactcagcgatgtcCgcccgctcctctgcctcatc	9	18	3	0	rs150277296		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:23851697C>T	ENST00000356287.3	-	37	5765	c.5736G>A	c.(5734-5736)gcG>gcA	p.A1912A	MYH6_ENST00000405093.3_Silent_p.A1912A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1912					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.A1912A(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CAGCGATGTCCGCCCGCTCCT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	14						C		1,4405	2.1+/-5.4	0,1,2202	179	157	165		5736	-8.1	0.1	14	dbSNP_134	165	0,8600		0,0,4300	no	coding-synonymous	MYH6	NM_002471.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1912/1940	23851697	1,13005	2203	4300	6503	22921537	SO:0001819	synonymous_variant	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5736G>A	14.37:g.23851697C>T			22921537	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																				0.597	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23851697	C	T	23851697	2	4	77	1	0	0	0	0	0	0	0	1	10068	639	23	1		1	MYH6	14	23851697	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	505036	23851697	83497843	810	22546										
MYH6	4624	broad.mit.edu	37	chr14	23855205	23855205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccgccagcttccgggaccGctctgtctgctccaccacgg	10	19	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:23855205G>A	ENST00000356287.3	-	33	5124	c.5095C>T	c.(5095-5097)Cgg>Tgg	p.R1699W	MYH6_ENST00000405093.3_Missense_Mutation_p.R1699W|MIR208A_ENST00000362287.1_RNA			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1699					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.R1699W(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TTCCGGGACCGCTCTGTCTGC	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	14											61	55	57					14																	23855205		2203	4300	6503	22925045	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5095C>T	14.37:g.23855205G>A	ENSP00000348634:p.Arg1699Trp		22925045	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	g	18.29	3.590975	0.66219	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.85013	-1.93;-1.93	4.26	0.371	0.16168	Myosin tail (1);	.	.	.	.	D	0.94515	0.8234	H	0.97635	4.045	0.49213	D	0.99976	D	0.89917	1.0	D	0.97110	1.0	D	0.95315	0.8415	9	0.87932	D	0	.	14.0632	0.64812	0.0:0.0:0.4524:0.5476	.	1699	P13533	MYH6_HUMAN	W	1699	ENSP00000386041:R1699W;ENSP00000348634:R1699W	ENSP00000348634:R1699W	R	-	1	2	MYH6	22925045	0.954000	0.32549	0.994000	0.49952	0.967000	0.64934	0.138000	0.16016	0.307000	0.22880	0.561000	0.74099	CGG		0.642	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23855205	G	A	23855205	3	1	77	1	0	0	0	0	1	0	0	0	10068	1086	38	1	748	1	MYH6	14	23855205	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3508	23855205	83494335	811	22547										
MYH7	4625	broad.mit.edu	37	chr14	23886115	23886115	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgactgcagctccatcttctCggcctccagctgctttcgga	9	15	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:23886115C>T	ENST00000355349.3	-	33	4768	c.4606G>A	c.(4606-4608)Gag>Aag	p.E1536K	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1536					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.E1536K(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCATCTTCTCGGCCTCCAGC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	14											107	88	94					14																	23886115		2203	4300	6503	22955955	SO:0001583	missense	4625			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4606G>A	14.37:g.23886115C>T	ENSP00000347507:p.Glu1536Lys		22955955	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331894	0.95733	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.86627	-2.15	4.99	4.99	0.66335	Myosin tail (1);	.	.	.	.	D	0.93677	0.7980	H	0.95504	3.68	0.80722	D	1	D	0.52996	0.957	P	0.50440	0.641	D	0.95564	0.8632	9	0.87932	D	0	.	18.4802	0.90808	0.0:1.0:0.0:0.0	.	1536	P12883	MYH7_HUMAN	K	1536;1541	ENSP00000347507:E1536K	ENSP00000347507:E1536K	E	-	1	0	MYH7	22955955	1.000000	0.71417	0.955000	0.39395	0.800000	0.45204	7.310000	0.78947	2.586000	0.87340	0.655000	0.94253	GAG		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886115	C	T	23886115	3	4	77	1	0	0	0	0	1	0	0	0	10069	893	31	1	1233	1	MYH7	14	23886115	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	30910	23886115	83463425	812	22548										
LRRC16B	90668	broad.mit.edu	37	chr14	24528539	24528539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcgcaccagcatcctcatcAatgccctgggcagcaacacc	7	17	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:24528539A>G	ENST00000342740.5	+	21	1841	c.1687A>G	c.(1687-1689)Aat>Gat	p.N563D	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	563						cytoplasm (GO:0005737)		p.N563D(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CATCCTCATCAATGCCCTGGG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	14											69	59	62					14																	24528539		2203	4300	6503	23598379	SO:0001583	missense	90668			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1687A>G	14.37:g.24528539A>G	ENSP00000340467:p.Asn563Asp		23598379	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368824	0.42003	.	.	ENSG00000186648	ENST00000342740	T	0.52754	0.65	5.27	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	L	0.48935	1.535	0.80722	D	1	D	0.55172	0.97	P	0.51833	0.681	T	0.31613	-0.9937	10	0.16896	T	0.51	-11.6153	10.5843	0.45273	0.838:0.162:0.0:0.0	.	563	Q8ND23	LR16B_HUMAN	D	563	ENSP00000340467:N563D	ENSP00000340467:N563D	N	+	1	0	LRRC16B	23598379	1.000000	0.71417	0.994000	0.49952	0.176000	0.22953	9.137000	0.94496	1.002000	0.39104	-0.323000	0.08544	AAT		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		G	24528539	A	G	24528539	3	3	77	1	0	0	0	0	1	0	0	0	9001	130	5	4	1769	4	LRRC16B	14	24528539	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	642424	24528539	82821001	813	22549										
AKAP6	9472	broad.mit.edu	37	chr14	33147592	33147592	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccctcaagctgtacagcgagCagtataccagcagcagcaag	10	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:33147592C>T	ENST00000280979.4	+	8	2976	c.2806C>T	c.(2806-2808)Cag>Tag	p.Q936*	AKAP6_ENST00000557272.1_Nonsense_Mutation_p.Q936*|AKAP6_ENST00000557354.1_Nonsense_Mutation_p.Q936*	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	936					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.Q936*(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTACAGCGAGCAGTATACCAG	0.433																																					Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Nonsense(1)	large_intestine(1)	14											166	149	155					14																	33147592		2203	4300	6503	32217343	SO:0001587	stop_gained	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2806C>T	14.37:g.33147592C>T	ENSP00000280979:p.Gln936*		32217343	A7E242|A7E2D4|O15028	Nonsense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	42	9.706841	0.99244	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	.	.	.	5.3	5.3	0.74995	.	0.079753	0.53938	D	0.000051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-9.1012	17.1295	0.86723	0.0:1.0:0.0:0.0	.	.	.	.	X	936	.	ENSP00000280979:Q936X	Q	+	1	0	AKAP6	32217343	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.356000	0.66052	2.480000	0.83734	0.585000	0.79938	CAG		0.433	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33147592	C	T	33147592	4	4	77	1	0	0	0	0	0	1	0	0	455	711	25	3	2832	3	AKAP6	14	33147592	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8619053	33147592	74201948	814	22550										
SRP54	6729	broad.mit.edu	37	chr14	35492189	35492189	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caaagagtagcaagaggatcGggtgtatcaacaagagatgt	13	5	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:35492189G>A	ENST00000556994.1	+	15	1627	c.1230G>A	c.(1228-1230)tcG>tcA	p.S410S	SRP54_ENST00000555557.1_Silent_p.S346S|SRP54_ENST00000216774.6_Silent_p.S410S|SRP54_ENST00000546080.1_Silent_p.S361S			P61011	SRP54_HUMAN	signal recognition particle 54kDa	410	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)	p.S410S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		CAAGAGGATCGGGTGTATCAA	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	14											106	98	101					14																	35492189		2203	4300	6503	34561940	SO:0001819	synonymous_variant	6729			X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1230G>A	14.37:g.35492189G>A			34561940	B2R759|B4DUW6|P13624	Silent	SNP	ENST00000556994.1	37	CCDS9652.1																																																																																				0.393	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		A	35492189	G	A	35492189	2	1	77	1	0	0	0	0	0	0	0	1	15194	1103	39	1		1	SRP54	14	35492189	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2344597	35492189	71857351	815	22551										
SIP1	8487	broad.mit.edu	37	chr14	39583642	39583642	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggtttcgatccctcggtaCccccgaggacgcctcaggaa							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:39583642delC	ENST00000308317.6	+	1	216	c.133delC	c.(133-135)cccfs	p.P46fs	GEMIN2_ENST00000250379.8_Frame_Shift_Del_p.P46fs|GEMIN2_ENST00000396249.2_Frame_Shift_Del_p.P46fs	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	46					gene expression (GO:0010467)|mRNA processing (GO:0006397)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)		p.P46fs*8(1)									TCCCTCGGTACCCCCGAGGAC	0.642																																																1	Deletion - Frameshift(1)	large_intestine(1)	14											43	42	42					14																	39583642		2203	4300	6503	38653393	SO:0001589	frameshift_variant	8487			AF027150	CCDS9669.1, CCDS32068.1, CCDS41946.1	14q21.1	2011-08-04	2011-08-04	2011-08-04	ENSG00000092208	ENSG00000092208			10884	protein-coding gene	gene with protein product		602595	"survival of motor neuron protein interacting protein 1"	SIP1		9323130, 9323129, 11121410	Standard	NM_003616		Approved		uc001wuq.3	O14893	OTTHUMG00000028816	ENST00000308317.6:c.133delC	14.37:g.39583642delC	ENSP00000308533:p.Pro46fs		38653393	B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	Frame_Shift_Del	DEL	ENST00000308317.6	37	CCDS9669.1																																																																																				0.642	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276730.2			-	39583642	C	-	39583642	7	5	77	1	0	1	0	1	0	0	0	0	14364	507	18	0	135	0	SIP1	14	39583642	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	4091453	39583642	67765898	816	22552										
TRIM9	114088	broad.mit.edu	37	chr14	51561006	51561006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgtgggctcagcctccggcTcacacgaccctgggccgggg	16	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:51561006T>G	ENST00000298355.3	-	1	1773	c.652A>C	c.(652-654)Agc>Cgc	p.S218R	TRIM9_ENST00000338969.5_Missense_Mutation_p.S218R|TRIM9_ENST00000360392.4_Missense_Mutation_p.S218R|RP11-1140I5.1_ENST00000554475.1_RNA	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	218					negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S218R(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					AGCCTCCGGCTCACACGACCC	0.672																																																2	Substitution - Missense(2)	large_intestine(2)	14											43	37	39					14																	51561006		2203	4300	6503	50630756	SO:0001583	missense	114088			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16288	protein-coding gene	gene with protein product		606555	"tripartite motif-containing 9"			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.652A>C	14.37:g.51561006T>G	ENSP00000298355:p.Ser218Arg		50630756	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.642723	0.47153	.	.	ENSG00000100505	ENST00000298355;ENST00000338969;ENST00000360392	T;T;T	0.72835	-0.54;-0.69;0.37	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.54806	0.1881	N	0.19112	0.55	0.47183	D	0.999345	P;P;B	0.42375	0.762;0.778;0.394	B;B;B	0.40901	0.255;0.343;0.05	T	0.52771	-0.8531	10	0.16420	T	0.52	.	12.6409	0.56709	0.0:0.0:0.0:1.0	.	218;218;218	Q9C026-5;Q9C026-4;Q9C026	.;.;TRIM9_HUMAN	R	218	ENSP00000298355:S218R;ENSP00000342970:S218R;ENSP00000353561:S218R	ENSP00000298355:S218R	S	-	1	0	TRIM9	50630756	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.981000	0.63819	1.865000	0.54081	0.459000	0.35465	AGC		0.672	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163		G	51561006	T	G	51561006	3	3	77	1	0	0	0	0	1	0	0	0	16589	1551	54	4	1570	4	TRIM9	14	51561006	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	11977364	51561006	55788534	817	22553										
SAMD4A	23034	broad.mit.edu	37	chr14	55251328	55251328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcctcagtatgaccgaacaCgccctgggaggtgagtgtgt	14	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:55251328C>T	ENST00000554335.1	+	12	2781	c.2118C>T	c.(2116-2118)caC>caT	p.H706H	SAMD4A_ENST00000392067.3_Silent_p.H706H|SAMD4A_ENST00000555192.1_Silent_p.H333H|SAMD4A_ENST00000251091.5_Silent_p.H618H|SAMD4A_ENST00000357634.3_Silent_p.H705H			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	706					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.H705H(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TGACCGAACACGCCCTGGGAG	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	14											245	186	206					14																	55251328		2203	4300	6503	54321078	SO:0001819	synonymous_variant	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.2118C>T	14.37:g.55251328C>T			54321078	A8MPZ5|Q0VA96|Q6PEW4	Silent	SNP	ENST00000554335.1	37	CCDS32084.2																																																																																				0.552	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55251328	C	T	55251328	2	4	77	1	0	0	0	0	0	0	0	1	13858	535	19	1		1	SAMD4A	14	55251328	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3690322	55251328	52098212	818	22554										
ARID4A	5926	broad.mit.edu	37	chr14	58832898	58832898	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agagaaagataaacacagagAaaaacatccgaattcatccc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:58832898delA	ENST00000355431.3	+	22	3846	c.3473delA	c.(3472-3474)gaafs	p.E1158fs	ARID4A_ENST00000348476.3_Intron|ARID4A_ENST00000431317.2_Intron|ARID4A_ENST00000395168.3_Intron	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1158					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K1159fs*19(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AAACACAGAGAAAAACATCCG	0.383																																																1	Deletion - Frameshift(1)	large_intestine(1)	14											116	123	121					14																	58832898		2202	4300	6502	57902651	SO:0001589	frameshift_variant	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.3473delA	14.37:g.58832898delA	ENSP00000347602:p.Glu1158fs		57902651	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	37	CCDS9732.1																																																																																				0.383	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		-	58832898	A	-	58832898	7	5	77	1	0	1	0	1	0	0	0	0	919	246	9	0	3555	0	ARID4A	14	58832898	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	3581570	58832898	48516642	819	22555										
SYNE2	23224	broad.mit.edu	37	chr14	64604534	64604534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaaacattggtggaaaacaCgcccggctttaccaaactct	8	11	1	1	rs375987275		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:64604534C>T	ENST00000344113.4	+	79	14888	c.14676C>T	c.(14674-14676)caC>caT	p.H4892H	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000394768.2_Silent_p.H1277H|SYNE2_ENST00000357395.3_Silent_p.H1277H|SYNE2_ENST00000554584.1_Silent_p.H4809H|SYNE2_ENST00000358025.3_Silent_p.H4892H|SYNE2_ENST00000555002.1_Silent_p.H1526H	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4892					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.H4892H(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GTGGAAAACACGCCCGGCTTT	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	14											75	73	73					14																	64604534		2203	4300	6503	63674287	SO:0001819	synonymous_variant	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.14676C>T	14.37:g.64604534C>T			63674287	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																				0.403	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64604534	C	T	64604534	2	4	77	1	0	0	0	0	0	0	0	1	15485	535	19	1		1	SYNE2	14	64604534	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5771636	64604534	42745006	820	22556										
PLEKHG3	26030	broad.mit.edu	37	chr14	65208193	65208193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagcgagaagggcctggcccGgcatggcagtgccacagact	15	13	0	2	rs377488568		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:65208193G>A	ENST00000394691.1	+	16	2105	c.1958G>A	c.(1957-1959)cGg>cAg	p.R653Q	PLEKHG3_ENST00000471182.2_Missense_Mutation_p.R186Q|PLEKHG3_ENST00000484731.2_Missense_Mutation_p.R158Q|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.R597Q			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	653							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R597Q(1)		endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GGCCTGGCCCGGCATGGCAGT	0.652													G|||	1	0.000199681	8e-04	0	5008	,	,		16501	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	32	37	36		1790	-0.6	0	14		36	0,8600		0,0,4300	no	missense	PLEKHG3	NM_015549.1	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	597/1164	65208193	1,13005	2203	4300	6503	64277946	SO:0001583	missense	26030			AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1958G>A	14.37:g.65208193G>A	ENSP00000378183:p.Arg653Gln		64277946	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Missense_Mutation	SNP	ENST00000394691.1	37		.	.	.	.	.	.	.	.	.	.	G	3.951	-0.012261	0.07727	2.27E-4	0.0	ENSG00000126822	ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.78	-0.579	0.11720	.	1.057360	0.07363	N	0.884397	T	0.75451	0.3851	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.23316	0.043;0.043;0.05;0.083	B;B;B;B	0.14578	0.008;0.005;0.005;0.011	T	0.55490	-0.8133	10	0.10902	T	0.67	.	1.3829	0.02234	0.1961:0.1879:0.397:0.219	.	186;158;653;597	A1L390-2;G3V311;A1L390;A1L390-3	.;.;PKHG3_HUMAN;.	Q	597;653;186;158	ENSP00000247226:R597Q;ENSP00000378183:R653Q;ENSP00000450945:R186Q;ENSP00000450973:R158Q	ENSP00000247226:R597Q	R	+	2	0	PLEKHG3	64277946	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.082000	0.03400	-0.066000	0.12998	0.655000	0.94253	CGG		0.652	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		A	65208193	G	A	65208193	3	1	77	1	0	0	0	0	1	0	0	0	12101	1116	39	1	1840	1	PLEKHG3	14	65208193	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	603659	65208193	42141347	821	22557										
SPTB	6710	broad.mit.edu	37	chr14	65216131	65216131	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caggctctgcgccttgacgcGgatgctctgggactcgttga	14	12	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:65216131G>A	ENST00000556626.1	-	36	7022	c.6880C>T	c.(6880-6882)Cgc>Tgc	p.R2294C	SPTB_ENST00000342835.4_5'UTR|SPTB_ENST00000389722.3_Missense_Mutation_p.R2294C			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	0					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.R2294C(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCCTTGACGCGGATGCTCTGG	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	14											54	49	51					14																	65216131		2203	4300	6503	64285884	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000556626.1:c.6880C>T	14.37:g.65216131G>A	ENSP00000451752:p.Arg2294Cys		64285884	Q15510|Q15519	Missense_Mutation	SNP	ENST00000556626.1	37	CCDS32099.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107232	0.56291	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626	T;T;T	0.71817	-0.6;0.21;-0.6	4.75	4.75	0.60458	.	0.307216	0.30410	N	0.009689	T	0.62974	0.2472	L	0.34521	1.04	0.80722	D	1	D;P	0.53462	0.96;0.93	P;B	0.46339	0.513;0.39	T	0.66408	-0.5931	10	0.56958	D	0.05	.	10.5274	0.44957	0.0:0.0:0.686:0.314	.	1113;2298	E7EV95;Q59FP5	.;.	C	2298;2294;1113;994;2294	ENSP00000374372:R2294C;ENSP00000451324:R994C;ENSP00000451752:R2294C	ENSP00000334218:R1113C	R	-	1	0	SPTB	64285884	0.999000	0.42202	0.999000	0.59377	0.930000	0.56654	2.012000	0.40932	2.183000	0.69458	0.511000	0.50034	CGC		0.642	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414076.1			A	65216131	G	A	65216131	3	1	77	1	0	0	0	0	1	0	0	0	15157	1116	39	1	110	1	SPTB	14	65216131	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7938	65216131	42133409	822	22558										
ACTN1	87	broad.mit.edu	37	chr14	69356871	69356871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcaccgtcagtccaggcctCgtggatggaggccttctgcc	12	15	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:69356871C>T	ENST00000193403.6	-	11	1602	c.1219G>A	c.(1219-1221)Gag>Aag	p.E407K	ACTN1_ENST00000394419.4_Missense_Mutation_p.E407K|ACTN1_ENST00000376839.3_Missense_Mutation_p.E342K|ACTN1_ENST00000538545.2_Missense_Mutation_p.E407K|ACTN1_ENST00000438964.2_Missense_Mutation_p.E407K	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	407	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)	p.E407K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GTCCAGGCCTCGTGGATGGAG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	14											53	43	46					14																	69356871		2203	4300	6503	68426624	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1219G>A	14.37:g.69356871C>T	ENSP00000193403:p.Glu407Lys		68426624	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	C	34	5.347647	0.95807	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.77718	0.4172	M	0.88704	2.975	0.80722	D	1	D;D;D;P	0.89917	0.999;1.0;0.997;0.91	D;D;P;P	0.83275	0.975;0.996;0.847;0.775	T	0.82841	-0.0258	10	0.87932	D	0	.	18.1072	0.89524	0.0:1.0:0.0:0.0	.	407;407;407;407	B7TY16;P12814-2;Q1HE25;P12814	.;.;.;ACTN1_HUMAN	K	407;407;407;342;407	ENSP00000193403:E407K;ENSP00000377941:E407K;ENSP00000414272:E407K;ENSP00000366035:E342K;ENSP00000439828:E407K	ENSP00000193403:E407K	E	-	1	0	ACTN1	68426624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	2.492000	0.84095	0.655000	0.94253	GAG		0.612	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		T	69356871	C	T	69356871	3	4	77	1	0	0	0	0	1	0	0	0	204	893	31	1	1573	1	ACTN1	14	69356871	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4140740	69356871	37992669	823	22559										
SLC8A3	6547	broad.mit.edu	37	chr14	70633744	70633744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcgtcatcaattatgcccaCggagaactccttctgggtct	9	12	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:70633744C>T	ENST00000381269.2	-	2	2149	c.1396G>A	c.(1396-1398)Gtg>Atg	p.V466M	SLC8A3_ENST00000528359.1_Missense_Mutation_p.V466M|SLC8A3_ENST00000534137.1_Missense_Mutation_p.V466M|SLC8A3_ENST00000356921.2_Missense_Mutation_p.V466M|SLC8A3_ENST00000357887.3_Missense_Mutation_p.V466M	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	466	Calx-beta 1.				blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)	p.V466M(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		ATTATGCCCACGGAGAACTCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	14											166	166	166					14																	70633744		2203	4300	6503	69703497	SO:0001583	missense	6547			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1396G>A	14.37:g.70633744C>T	ENSP00000370669:p.Val466Met		69703497	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	C	9.906	1.208242	0.22205	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	5.53	5.53	0.82687	Na-Ca exchanger/integrin-beta4 (2);	0.137463	0.49916	D	0.000136	T	0.72574	0.3477	M	0.93678	3.445	0.58432	D	0.999996	D;D;D;D	0.64830	0.958;0.984;0.994;0.984	P;P;P;P	0.59643	0.674;0.832;0.861;0.861	T	0.79581	-0.1744	10	0.62326	D	0.03	.	13.7206	0.62725	0.0:0.9264:0.0:0.0736	.	466;466;466;466	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	M	466	ENSP00000349392:V466M;ENSP00000370669:V466M;ENSP00000350560:V466M;ENSP00000436688:V466M;ENSP00000433531:V466M	ENSP00000349392:V466M	V	-	1	0	SLC8A3	69703497	0.984000	0.35163	0.986000	0.45419	0.198000	0.23893	2.546000	0.45778	2.587000	0.87381	0.643000	0.83706	GTG		0.517	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70633744	C	T	70633744	3	4	77	1	0	0	0	0	1	0	0	0	14745	536	19	1	1526	1	SLC8A3	14	70633744	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1276873	70633744	36715796	824	22560										
NUMB	8650	broad.mit.edu	37	chr14	73753996	73753996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaacaggctgcaaaagcacaGcctactgcatggctcaacct	8	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:73753996G>A	ENST00000355058.3	-	9	755	c.477C>T	c.(475-477)ggC>ggT	p.G159G	NUMB_ENST00000557597.1_Silent_p.G148G|NUMB_ENST00000544991.3_Silent_p.G159G|NUMB_ENST00000559312.1_Silent_p.G159G|NUMB_ENST00000554521.2_Silent_p.G148G|NUMB_ENST00000560335.1_Silent_p.G159G|NUMB_ENST00000356296.4_Silent_p.G159G|NUMB_ENST00000555394.1_Silent_p.G159G|NUMB_ENST00000555738.2_Silent_p.G148G|NUMB_ENST00000554546.1_Silent_p.G148G|NUMB_ENST00000454166.4_Silent_p.G159G|NUMB_ENST00000556772.1_Silent_p.G15G|NUMB_ENST00000535282.1_Silent_p.G148G|NUMB_ENST00000555238.1_Silent_p.G159G|NUMB_ENST00000359560.3_Silent_p.G148G			P49757	NUMB_HUMAN	numb homolog (Drosophila)	159	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G159G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		CAAAAGCACAGCCTACTGCAT	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	14											77	66	70					14																	73753996		2203	4300	6503	72823749	SO:0001819	synonymous_variant	8650			L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.477C>T	14.37:g.73753996G>A			72823749	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Silent	SNP	ENST00000355058.3	37	CCDS32116.1																																																																																				0.413	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			A	73753996	G	A	73753996	2	1	77	1	0	0	0	0	0	0	0	1	10782	958	34	3		3	NUMB	14	73753996	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3120252	73753996	33595544	825	22561										
PGF	5228	broad.mit.edu	37	chr14	75416217	75416217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaccagcctctccagcgccCggcagtagctgcggccccac	10	21	1	0	rs559671641		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:75416217C>T	ENST00000405431.2	-	3	157	c.158G>A	c.(157-159)cGg>cAg	p.R53Q	PGF_ENST00000238607.6_Missense_Mutation_p.R52Q|PGF_ENST00000553716.1_Missense_Mutation_p.R53Q|PGF_ENST00000555567.1_Missense_Mutation_p.R53Q			P49763	PLGF_HUMAN	placental growth factor	53					branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of morphogenesis of a branching structure (GO:0060688)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.R53Q(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.00668)	Aflibercept(DB08885)	CTCCAGCGCCCGGCAGTAGCT	0.657																																					GBM(127;389 2301 5452 48547)											1	Substitution - Missense(1)	large_intestine(1)	14											31	29	29					14																	75416217		2202	4295	6497	74485970	SO:0001583	missense	5228			S72960	CCDS9835.1, CCDS55932.1, CCDS73664.1	14q24.3	2013-02-18	2008-03-20		ENSG00000119630	ENSG00000119630			8893	protein-coding gene	gene with protein product	"placenta growth factor"	601121	"placental growth factor-like", "placental growth factor, vascular endothelial growth factor-related protein"	PGFL		7681160	Standard	NM_002632		Approved	PLGF, PlGF-2, PlGF, SHGC-10760, D12S1900	uc001xqz.3	P49763	OTTHUMG00000171496	ENST00000405431.2:c.158G>A	14.37:g.75416217C>T	ENSP00000385365:p.Arg53Gln		74485970	Q07101|Q9BV78|Q9Y6S8	Missense_Mutation	SNP	ENST00000405431.2	37	CCDS9835.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058307	0.76074	.	.	ENSG00000119630	ENST00000555567;ENST00000553716;ENST00000238607;ENST00000405431	.	.	.	4.33	4.33	0.51752	Platelet-derived growth factor (PDGF) (3);	0.000000	0.85682	D	0.000000	T	0.44808	0.1311	L	0.31752	0.955	0.35342	D	0.786612	P;D;D;P	0.71674	0.771;0.998;0.994;0.805	B;P;P;B	0.55087	0.366;0.768;0.549;0.238	T	0.54351	-0.8307	9	0.42905	T	0.14	.	7.9104	0.29787	0.0:0.8169:0.0:0.1831	.	53;53;52;53	P49763;P49763-2;G3XA84;Q53XY6	PLGF_HUMAN;.;.;.	Q	53;53;52;53	.	ENSP00000238607:R53Q	R	-	2	0	PGF	74485970	0.999000	0.42202	0.994000	0.49952	0.998000	0.95712	3.245000	0.51407	2.241000	0.73720	0.561000	0.74099	CGG		0.657	PGF-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414064.1	NM_002632		T	75416217	C	T	75416217	3	4	77	1	0	0	0	0	1	0	0	0	11819	652	23	1	374	1	PGF	14	75416217	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1662221	75416217	31933323	826	22562										
ZC3H14	79882	broad.mit.edu	37	chr14	89041146	89041146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agatgatgattacgggtctcGaacaggaagcatctccagca	11	9	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:89041146G>A	ENST00000251038.5	+	7	1196	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	ZC3H14_ENST00000557605.1_3'UTR|ZC3H14_ENST00000555755.1_Missense_Mutation_p.R324Q|ZC3H14_ENST00000556945.1_Missense_Mutation_p.R324Q|ZC3H14_ENST00000302216.8_Missense_Mutation_p.R324Q|ZC3H14_ENST00000393514.5_Missense_Mutation_p.R324Q|ZC3H14_ENST00000336693.4_Missense_Mutation_p.R290Q|ZC3H14_ENST00000557607.1_Missense_Mutation_p.R169Q|ZC3H14_ENST00000359301.3_Missense_Mutation_p.R290Q	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	324						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R324Q(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						TACGGGTCTCGAACAGGAAGC	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	14											82	77	78					14																	89041146		2203	4300	6503	88110899	SO:0001583	missense	79882			AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.971G>A	14.37:g.89041146G>A	ENSP00000251038:p.Arg324Gln		88110899	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	37	CCDS32133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.041328|4.041328	0.75732|0.75732	.|.	.|.	ENSG00000100722|ENSG00000100722	ENST00000556000|ENST00000251038;ENST00000393530;ENST00000353091;ENST00000359301;ENST00000302216;ENST00000380684;ENST00000556945;ENST00000557607;ENST00000555755;ENST00000393514;ENST00000336693	.|.	.|.	.|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.183367	.|0.49916	.|D	.|0.000121	T|T	0.73931|0.73931	0.3650|0.3650	M|M	0.68952|0.68952	2.095|2.095	0.47698|0.47698	D|D	0.999496|0.999496	.|B;D;D;D;D;D	.|0.69078	.|0.043;0.997;0.991;0.967;0.997;0.967	.|B;P;P;B;P;P	.|0.54590	.|0.005;0.756;0.539;0.435;0.756;0.458	T|T	0.73839|0.73839	-0.3856|-0.3856	5|9	.|0.48119	.|T	.|0.1	-6.9583|-6.9583	19.9093|19.9093	0.97021|0.97021	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|324;305;324;324;324;324	.|G3V256;F8W848;G3V5R4;Q6PJT7-2;Q6PJT7-3;Q6PJT7	.|.;.;.;.;.;ZC3HE_HUMAN	K|Q	240|324;324;324;290;324;305;324;169;324;324;290	.|.	.|ENSP00000251038:R324Q	E|R	+|+	1|2	0|0	ZC3H14|ZC3H14	88110899|88110899	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.812000|0.812000	0.45895|0.45895	8.260000|8.260000	0.89857|0.89857	2.713000|2.713000	0.92767|0.92767	0.655000|0.655000	0.94253|0.94253	GAA|CGA		0.428	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		A	89041146	G	A	89041146	3	1	77	1	0	0	0	0	1	0	0	0	17605	1058	37	1	997	1	ZC3H14	14	89041146	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	13624929	89041146	18308394	827	22563										
ASB2	51676	broad.mit.edu	37	chr14	94420823	94420823	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atggcctttatcaaggggtcCgcaggcctgtgagaggaagg	16	8	1	1	rs201823942		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:94420823C>T	ENST00000315988.4	-	2	662	c.174G>A	c.(172-174)gcG>gcA	p.A58A	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Silent_p.A106A	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	58					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)	p.A58A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		TCAAGGGGTCCGCAGGCCTGT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	14											72	64	66					14																	94420823		2203	4300	6503	93490576	SO:0001819	synonymous_variant	51676			AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"Ankyrin repeat domain containing"	16012	protein-coding gene	gene with protein product		605759	"ankyrin repeat and SOCS box-containing 2"				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.174G>A	14.37:g.94420823C>T			93490576	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																				0.597	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			T	94420823	C	T	94420823	2	4	77	1	0	0	0	0	0	0	0	1	1024	639	23	1		1	ASB2	14	94420823	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5379677	94420823	12928717	828	22564										
PPP4R4	57718	broad.mit.edu	37	chr14	94712822	94712822	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgccacatgtcatatcaagCgatcagatttattaccgttt	6	10	3	1	rs577099284		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:94712822C>T	ENST00000304338.3	+	14	1711	c.1557C>T	c.(1555-1557)agC>agT	p.S519S		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	519					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)	p.S519S(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						TCATATCAAGCGATCAGATTT	0.408													C|||	1	0.000199681	0	0	5008	,	,		18895	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	14											120	117	118					14																	94712822		2203	4300	6503	93782575	SO:0001819	synonymous_variant	57718			AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1557C>T	14.37:g.94712822C>T			93782575	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	37	CCDS9921.1																																																																																				0.408	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		T	94712822	C	T	94712822	2	4	77	1	0	0	0	0	0	0	0	1	12439	767	27	1		1	PPP4R4	14	94712822	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	291999	94712822	12636718	829	22565										
SERPINA12	145264	broad.mit.edu	37	chr14	94964255	94964255	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagttggtaaggatggtttcGgcactgtaaaagttcttggc	13	5	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:94964255G>A	ENST00000341228.2	-	3	1275	c.480C>T	c.(478-480)gcC>gcT	p.A160A	SERPINA12_ENST00000556881.1_Silent_p.A160A	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	160					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A160A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		GGATGGTTTCGGCACTGTAAA	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	14											113	109	110					14																	94964255		2203	4300	6503	94034008	SO:0001819	synonymous_variant	145264			AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.480C>T	14.37:g.94964255G>A			94034008		Silent	SNP	ENST00000341228.2	37	CCDS9926.1																																																																																				0.443	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		A	94964255	G	A	94964255	2	1	77	1	0	0	0	0	0	0	0	1	14126	1103	39	1		1	SERPINA12	14	94964255	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	251433	94964255	12385285	830	22566										
TECPR2	9895	broad.mit.edu	37	chr14	102891387	102891387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctaaccttgtatgcgtcacGgcccgggctccggctatgga	12	13	2	0	rs551413559		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:102891387G>A	ENST00000359520.7	+	6	936	c.710G>A	c.(709-711)cGg>cAg	p.R237Q	TECPR2_ENST00000558678.1_Missense_Mutation_p.R237Q|TECPR2_ENST00000561228.1_3'UTR	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	237					autophagy (GO:0006914)|cell death (GO:0008219)			p.R237Q(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						TATGCGTCACGGCCCGGGCTC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	14											95	101	99					14																	102891387		2203	4300	6503	101961140	SO:0001583	missense	9895			AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.710G>A	14.37:g.102891387G>A	ENSP00000352510:p.Arg237Gln		101961140	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	g	21.5	4.155605	0.78114	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.24723	1.84	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.45357	0.1338	M	0.86268	2.805	0.37982	D	0.933628	D;D	0.64830	0.994;0.973	P;P	0.48114	0.553;0.567	T	0.61850	-0.6978	10	0.87932	D	0	.	18.9389	0.92597	0.0:0.0:1.0:0.0	.	237;237	A5PKY3;O15040	.;TCPR2_HUMAN	Q	237	ENSP00000352510:R237Q	ENSP00000352510:R237Q	R	+	2	0	TECPR2	101961140	1.000000	0.71417	0.913000	0.36048	0.108000	0.19459	8.524000	0.90579	2.476000	0.83614	0.552000	0.68991	CGG		0.453	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		A	102891387	G	A	102891387	3	1	77	1	0	0	0	0	1	0	0	0	15783	1116	39	1	728	1	TECPR2	14	102891387	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7927132	102891387	4458153	831	22567										
KIF26A	26153	broad.mit.edu	37	chr14	104633326	104633326	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgtggccgcccccggcgCccccctgcctgctcagggcc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:104633326delC	ENST00000423312.2	+	5	1054	c.1054delC	c.(1054-1056)cccfs	p.P353fs	KIF26A_ENST00000315264.7_Frame_Shift_Del_p.P214fs	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	353					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)	p.C354fs*19(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GCCCCCGGCGCCCCCCTGCCT	0.731																																																1	Deletion - Frameshift(1)	large_intestine(1)	14											8	12	11					14																	104633326		1855	4024	5879	103703079	SO:0001589	frameshift_variant	26153			AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1054delC	14.37:g.104633326delC	ENSP00000388241:p.Pro353fs		103703079	Q8TAZ7|Q96GK3|Q9UFL3	Frame_Shift_Del	DEL	ENST00000423312.2	37	CCDS45171.1																																																																																				0.731	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			-	104633326	C	-	104633326	7	5	77	1	0	1	0	1	0	0	0	0	8315	739	26	0	1072	0	KIF26A	14	104633326	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	1741939	104633326	2716214	832	22568										
INF2	64423	broad.mit.edu	37	chr14	105169745	105169745	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcaacgccgtcatcttgggCcccgaggacctgcgcgcgcg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:105169745delC	ENST00000392634.4	+	4	733	c.621delC	c.(619-621)ggcfs	p.G207fs	INF2_ENST00000398337.4_Frame_Shift_Del_p.G207fs|INF2_ENST00000330634.7_Frame_Shift_Del_p.G207fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	207	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.E209fs*>26(1)|p.E209fs*34(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		TCATCTTGGGCCCCGAGGACC	0.647																																																2	Deletion - Frameshift(2)	large_intestine(2)	14											70	76	74					14																	105169745		2145	4250	6395	104240790	SO:0001589	frameshift_variant	64423			AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.621delC	14.37:g.105169745delC	ENSP00000376410:p.Gly207fs		104240790	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Del	DEL	ENST00000392634.4	37	CCDS9989.2																																																																																				0.647	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		-	105169745	C	-	105169745	7	5	77	1	0	1	0	1	0	0	0	0	7755	726	26	0	631	0	INF2	14	105169745	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	536419	105169745	2179795	833	22569										
AHNAK2	113146	broad.mit.edu	37	chr14	105405244	105405244	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttaataaggaaaatccgtacGaaggtgtttgaatctctgac	9	6	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:105405244G>A	ENST00000333244.5	-	7	16663	c.16544C>T	c.(16543-16545)tCg>tTg	p.S5515L	AHNAK2_ENST00000557457.1_Missense_Mutation_p.S513L	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5515						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.S485L(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			AAATCCGTACGAAGGTGTTTG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											54	50	51					14																	105405244		1871	4100	5971	104476289	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.16544C>T	14.37:g.105405244G>A	ENSP00000353114:p.Ser5515Leu		104476289	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607943	0.66558	.	.	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.01068	5.38;5.38	5.55	5.55	0.83447	.	0.342975	0.20801	U	0.085431	T	0.05914	0.0154	L	0.59436	1.845	0.19945	N	0.999948	D	0.89917	1.0	D	0.72338	0.977	T	0.32481	-0.9905	10	0.34782	T	0.22	.	19.5026	0.95103	0.0:0.0:1.0:0.0	.	5515	Q8IVF2	AHNK2_HUMAN	L	513;5515	ENSP00000450998:S513L;ENSP00000353114:S5515L	ENSP00000353114:S5515L	S	-	2	0	AHNAK2	104476289	0.854000	0.29725	0.011000	0.14972	0.046000	0.14306	5.055000	0.64282	2.612000	0.88384	0.655000	0.94253	TCG		0.468	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105405244	G	A	105405244	3	1	77	1	0	0	0	0	1	0	0	0	415	1059	37	1	847	1	AHNAK2	14	105405244	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	235499	105405244	1944296	834	22570										
BRF1	2972	broad.mit.edu	37	chr14	105693010	105693010	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctgcccagctgtgtacgaGggggggtcgcactcctcctc					rs369618475		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr14:105693010delG	ENST00000546474.1	-	8	15835	c.876delC	c.(874-876)cccfs	p.P292fs	BRF1_ENST00000551787.1_Frame_Shift_Del_p.P88fs|BRF1_ENST00000440513.3_Frame_Shift_Del_p.P177fs|BRF1_ENST00000379937.2_Frame_Shift_Del_p.P265fs|BRF1_ENST00000327359.3_Frame_Shift_Del_p.P177fs|BRF1_ENST00000392557.4_Frame_Shift_Del_p.P88fs|BRF1_ENST00000446501.2_Frame_Shift_Del_p.P54fs|BRF1_ENST00000379932.4_Frame_Shift_Del_p.P88fs	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	292					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)	p.S293fs*11(1)		NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		CTGTGTACGAGGGGGGGTCGC	0.582																																																1	Deletion - Frameshift(1)	large_intestine(1)	14											63	65	64					14																	105693010		2203	4300	6503	104764055	SO:0001589	frameshift_variant	2972			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"General transcription factors"	11551	protein-coding gene	gene with protein product		604902	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2", "BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.876delC	14.37:g.105693010delG	ENSP00000448323:p.Pro292fs		104764055	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Frame_Shift_Del	DEL	ENST00000546474.1	37	CCDS10001.1																																																																																				0.582	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519		-	105693010	G	-	105693010	7	5	77	1	0	1	0	1	0	0	0	0	1513	987	35	0	1201	0	BRF1	14	105693010	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	287766	105693010	1656530	835	22571										
GABRB3	2562	broad.mit.edu	37	chr15	26812790	26812790	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggacacccacgacagaatcGttatcagtatagagggcata	10	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:26812790G>A	ENST00000311550.5	-	7	884	c.773C>T	c.(772-774)aCg>aTg	p.T258M	GABRB3_ENST00000545868.1_Missense_Mutation_p.T173M|GABRB3_ENST00000299267.4_Missense_Mutation_p.T258M|GABRB3_ENST00000400188.3_Missense_Mutation_p.T187M|GABRB3_ENST00000541819.2_Missense_Mutation_p.T314M	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	258					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.T258M(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGACAGAATCGTTATCAGTAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	15											131	111	118					15																	26812790		2203	4300	6503	24363883	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.773C>T	15.37:g.26812790G>A	ENSP00000308725:p.Thr258Met		24363883	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271652	0.59649	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.86030	-2.06;-2.06;-2.06;-2.06;-2.06	6.06	6.06	0.98353	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.93083	0.7798	M	0.80746	2.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.993;0.993;0.998	D	0.93036	0.6453	10	0.87932	D	0	.	19.6125	0.95613	0.0:0.0:1.0:0.0	.	314;258;258	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	M	258;314;258;187;173	ENSP00000308725:T258M;ENSP00000442408:T314M;ENSP00000299267:T258M;ENSP00000383049:T187M;ENSP00000439169:T173M	ENSP00000299267:T258M	T	-	2	0	GABRB3	24363883	1.000000	0.71417	0.288000	0.24862	0.033000	0.12548	9.724000	0.98775	2.879000	0.98667	0.650000	0.86243	ACG		0.408	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26812790	G	A	26812790	3	1	77	1	0	0	0	0	1	0	0	0	6187	1145	40	1	660	1	GABRB3	15	26812790	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		26812790	75718602	836	22572										
MTMR10	54893	broad.mit.edu	37	chr15	31233773	31233773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcttcgtctgcacagattcCctacaggagaaaatggaaat	9	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:31233773C>T	ENST00000435680.1	-	16	2331	c.2234G>A	c.(2233-2235)gGg>gAg	p.G745E	FAN1_ENST00000362065.4_3'UTR|MTMR10_ENST00000314404.8_Intron|MTMR10_ENST00000425768.1_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	745							phosphatase activity (GO:0016791)	p.G745E(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		GCACAGATTCCCTACAGGAGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	15											36	32	34					15																	31233773		1901	4126	6027	29021065	SO:0001583	missense	54893			AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.2234G>A	15.37:g.31233773C>T	ENSP00000402537:p.Gly745Glu		29021065	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712119	0.89112	.	.	ENSG00000166912	ENST00000435680	D	0.94931	-3.56	5.48	5.48	0.80851	.	.	.	.	.	D	0.95433	0.8517	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95192	0.8309	9	0.42905	T	0.14	.	19.3713	0.94488	0.0:1.0:0.0:0.0	.	745	Q9NXD2	MTMRA_HUMAN	E	745	ENSP00000402537:G745E	ENSP00000402537:G745E	G	-	2	0	MTMR10	29021065	1.000000	0.71417	0.632000	0.29296	0.990000	0.78478	7.487000	0.81328	2.575000	0.86900	0.655000	0.94253	GGG		0.478	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		T	31233773	C	T	31233773	3	4	77	1	0	0	0	0	1	0	0	0	9969	623	22	3	103	3	MTMR10	15	31233773	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4420983	31233773	71297619	837	22573										
TRPM1	4308	broad.mit.edu	37	chr15	31330248	31330248	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtcaagtgtgtcactgaccGtattttcctcttctttttct	7	10	5	1	rs377044822		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:31330248G>A	ENST00000256552.6	-	19	2585	c.2438C>T	c.(2437-2439)aCg>aTg	p.T813M	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Splice_Site_p.T830M|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000397795.2_Splice_Site_p.T791M	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1									p.T791M(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GTCACTGACCGTATTTTCCTC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15						G	MET/THR	1,3731		0,1,1865	126	115	119		2372	-1.1	0.2	15		119	0,8214		0,0,4107	no	missense-near-splice	TRPM1	NM_002420.4	81	0,1,5972	AA,AG,GG		0.0,0.0268,0.0084	benign	791/1604	31330248	1,11945	1866	4107	5973	29117540	SO:0001630	splice_region_variant	4308			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2439+1C>T	15.37:g.31330248G>A			29117540		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	G	2.684	-0.274616	0.05679	2.68E-4	0.0	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.66815	-0.23;-0.23;-0.23	5.33	-1.09	0.09904	.	0.364959	0.32533	N	0.005973	T	0.30510	0.0767	N	0.01352	-0.895	0.19300	N	0.999979	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.002	T	0.31641	-0.9936	10	0.10377	T	0.69	-9.349	11.8919	0.52635	0.5428:0.0:0.4572:0.0	.	785;791	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	M	791;830;813;791	ENSP00000380897:T791M;ENSP00000437849:T830M;ENSP00000256552:T813M	ENSP00000256552:T813M	T	-	2	0	TRPM1	29117540	0.005000	0.15991	0.151000	0.22473	0.064000	0.16182	0.030000	0.13688	-0.118000	0.11851	-0.982000	0.02568	ACG		0.378	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	Missense_Mutation	A	31330248	G	A	31330248	5	1	77	1	0	0	0	0	0	0	1	0	16625	1159	40	1	2479	1	TRPM1	15	31330248	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	96475	31330248	71201144	838	22574										
RYR3	6263	broad.mit.edu	37	chr15	33936603	33936603	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaagttttataccatgtgCggtctccaagagggctttga	10	8	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:33936603C>T	ENST00000389232.4	+	28	3718	c.3648C>T	c.(3646-3648)tgC>tgT	p.C1216C	RYR3_ENST00000415757.3_Silent_p.C1216C	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1216	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.C1216C(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ATACCATGTGCGGTCTCCAAG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	15											76	76	76					15																	33936603		1936	4144	6080	31723895	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3648C>T	15.37:g.33936603C>T			31723895	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.522	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33936603	C	T	33936603	2	4	77	1	0	0	0	0	0	0	0	1	13807	776	27	1		1	RYR3	15	33936603	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2606355	33936603	68594789	839	22575										
PGBD4	161779	broad.mit.edu	37	chr15	34394752	34394752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatgtcaaatcctagaaaacGtagcattcctatgcgtgata	7	8	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:34394752G>A	ENST00000397766.2	+	1	479	c.20G>A	c.(19-21)cGt>cAt	p.R7H	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	7								p.R7H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		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)		cctagaaaacgtagcattcct	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	15											19	20	20					15																	34394752		2190	4284	6474	32182044	SO:0001583	missense	161779			AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.20G>A	15.37:g.34394752G>A	ENSP00000380872:p.Arg7His		32182044	A1L487|A8K0C6|Q8N9E8	Missense_Mutation	SNP	ENST00000397766.2	37	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.303653	0.23736	.	.	ENSG00000182405	ENST00000397766	T	0.20738	2.05	0.793	0.793	0.18632	.	414.909000	0.03327	U	0.192847	T	0.15739	0.0379	N	0.08118	0	0.09310	N	1	D	0.60160	0.987	P	0.49799	0.622	T	0.18053	-1.0349	10	0.44086	T	0.13	.	4.869	0.13622	0.0:0.0:1.0:0.0	.	7	Q96DM1	PGBD4_HUMAN	H	7	ENSP00000380872:R7H	ENSP00000380872:R7H	R	+	2	0	PGBD4	32182044	0.127000	0.22367	0.228000	0.23943	0.264000	0.26372	0.563000	0.23547	0.726000	0.32339	0.305000	0.20034	CGT		0.343	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			A	34394752	G	A	34394752	3	1	77	1	0	0	0	0	1	0	0	0	11814	1145	40	1	22	1	PGBD4	15	34394752	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	458149	34394752	68136640	840	22576										
BAHD1	22893	broad.mit.edu	37	chr15	40751340	40751340	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggagctacccctgcggctgcCtcgtgcccatgcagaagtag	13	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:40751340C>A	ENST00000416165.1	+	2	748	c.677C>A	c.(676-678)cCt>cAt	p.P226H	BAHD1_ENST00000560846.1_Missense_Mutation_p.P226H|BAHD1_ENST00000561234.1_Missense_Mutation_p.P226H	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	226					heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)	p.P226H(1)		NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		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)		CTGCGGCTGCCTCGTGCCCAT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	15											27	32	30					15																	40751340		2203	4300	6503	38538632	SO:0001583	missense	22893			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.677C>A	15.37:g.40751340C>A	ENSP00000396976:p.Pro226His		38538632	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	37	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702712	0.30232	.	.	ENSG00000140320	ENST00000416165	T	0.18502	2.21	5.0	5.0	0.66597	.	0.404525	0.24585	N	0.037275	T	0.12050	0.0293	N	0.08118	0	0.24198	N	0.995529	P;B;P	0.36315	0.547;0.412;0.547	B;B;B	0.41036	0.346;0.188;0.346	T	0.20405	-1.0276	10	0.56958	D	0.05	-5.5308	13.0663	0.59036	0.0:0.712:0.288:0.0	.	226;226;226	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	H	226	ENSP00000396976:P226H	ENSP00000396976:P226H	P	+	2	0	BAHD1	38538632	0.996000	0.38824	0.992000	0.48379	0.498000	0.33706	2.180000	0.42537	2.750000	0.94351	0.655000	0.94253	CCT		0.627	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40751340	C	A	40751340	3	1	77	1	0	0	0	0	1	0	0	0	1298	681	24	2	679	2	BAHD1	15	40751340	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6356588	40751340	61780052	841	22577										
DLL4	54567	broad.mit.edu	37	chr15	41229055	41229055	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggccccagggcccctggggCgggggaccatgccaggaaag	18	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:41229055C>T	ENST00000249749.5	+	9	2146	c.1870C>T	c.(1870-1872)Cgg>Tgg	p.R624W		NM_019074.3	NP_061947.1	Q9NR61	DLL4_HUMAN	delta-like 4 (Drosophila)	624					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac atrium morphogenesis (GO:0003209)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|dorsal aorta morphogenesis (GO:0035912)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of neural precursor cell proliferation (GO:2000179)|regulation of neural retina development (GO:0061074)|regulation of neurogenesis (GO:0050767)|signal transduction (GO:0007165)|ventral spinal cord interneuron fate commitment (GO:0060579)|ventricular trabecula myocardium morphogenesis (GO:0003222)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.R624W(1)		breast(3)|large_intestine(1)	4		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GCCCCTGGGGCGGGGGACCAT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	15											26	29	28					15																	41229055		1882	4092	5974	39016347	SO:0001583	missense	54567			AF253468	CCDS45232.1	15q14	2008-07-03	2001-12-03			ENSG00000128917			2910	protein-coding gene	gene with protein product		605185	"delta-like 4 homolog (Drosophila)"			10837024	Standard	NM_019074		Approved		uc001zng.2	Q9NR61		ENST00000249749.5:c.1870C>T	15.37:g.41229055C>T	ENSP00000249749:p.Arg624Trp		39016347	Q3KP23|Q9NQT9	Missense_Mutation	SNP	ENST00000249749.5	37	CCDS45232.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827998	0.50845	.	.	ENSG00000128917	ENST00000249749	D	0.88201	-2.35	5.53	3.63	0.41609	.	0.311695	0.36444	N	0.002598	T	0.81983	0.4938	L	0.36672	1.1	0.33679	D	0.611883	B	0.06786	0.001	B	0.06405	0.002	T	0.80603	-0.1309	10	0.72032	D	0.01	.	7.5302	0.27679	0.4453:0.4761:0.0:0.0785	.	624	Q9NR61	DLL4_HUMAN	W	624	ENSP00000249749:R624W	ENSP00000249749:R624W	R	+	1	2	DLL4	39016347	0.173000	0.23056	0.997000	0.53966	0.986000	0.74619	0.242000	0.18087	0.861000	0.35504	0.650000	0.86243	CGG		0.587	DLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418859.1			T	41229055	C	T	41229055	3	4	77	1	0	0	0	0	1	0	0	0	4579	759	27	1	1904	1	DLL4	15	41229055	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	477715	41229055	61302337	842	22578										
SPTBN5	51332	broad.mit.edu	37	chr15	42147078	42147078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atagcgcctgggtgcaccccGctccagggtgcctgccaact	12	16	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:42147078G>A	ENST00000320955.6	-	56	9747	c.9520C>T	c.(9520-9522)Cgg>Tgg	p.R3174W	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3174					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.R3174W(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GGTGCACCCCGCTCCAGGGTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	15											59	61	60					15																	42147078		1917	4131	6048	39934370	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9520C>T	15.37:g.42147078G>A	ENSP00000317790:p.Arg3174Trp		39934370		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	12.73	2.024926	0.35701	.	.	ENSG00000137877	ENST00000320955	T	0.50548	0.74	5.2	0.63	0.17693	.	0.667620	0.13784	N	0.363007	T	0.59404	0.2191	M	0.65975	2.015	0.09310	N	1	D	0.89917	1.0	D	0.69654	0.965	T	0.48758	-0.9007	10	0.72032	D	0.01	.	5.9484	0.19232	0.0714:0.0923:0.48:0.3563	.	3174	Q9NRC6	SPTN5_HUMAN	W	3174	ENSP00000317790:R3174W	ENSP00000317790:R3174W	R	-	1	2	SPTBN5	39934370	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	0.789000	0.26886	-0.180000	0.10637	-0.150000	0.13652	CGG		0.592	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42147078	G	A	42147078	3	1	77	1	0	0	0	0	1	0	0	0	15161	1086	38	1	1556	1	SPTBN5	15	42147078	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	918023	42147078	60384314	843	22579										
CAPN3	825	broad.mit.edu	37	chr15	42689037	42689037	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtggacaaagatgagaaggcCcgtctgcagcaccaggtcac	13	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:42689037C>T	ENST00000397163.3	+	9	1374	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A	CAPN3_ENST00000357568.3_Silent_p.A385A|CAPN3_ENST00000349748.3_Silent_p.A337A|CAPN3_ENST00000356316.3_Silent_p.A298A|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000318023.7_Silent_p.A385A	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	385	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.A385A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		ATGAGAAGGCCCGTCTGCAGC	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	15											94	85	88					15																	42689037		2203	4299	6502	40476329	SO:0001819	synonymous_variant	825			X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1155C>T	15.37:g.42689037C>T			40476329	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																				0.537	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			T	42689037	C	T	42689037	2	4	77	1	0	0	0	0	0	0	0	1	2634	610	22	3		3	CAPN3	15	42689037	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	541959	42689037	59842355	844	22580										
ELL3	80237	broad.mit.edu	37	chr15	44068281	44068281	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccaagctaccaccagcgccCtcctgacaacactgggacac	7	18	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:44068281C>A	ENST00000319359.3	-	3	878	c.237G>T	c.(235-237)gaG>gaT	p.E79D	SERF2_ENST00000381359.1_5'Flank|RP11-296A16.1_ENST00000417761.2_3'UTR|ELL3_ENST00000497465.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	79					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)	p.E79D(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		CACCAGCGCCCTCCTGACAAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	15											104	92	96					15																	44068281		2198	4298	6496	41855573	SO:0001583	missense	80237			AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.237G>T	15.37:g.44068281C>A	ENSP00000320346:p.Glu79Asp		41855573	B3KQ66|B3KX08|Q6I9Z7|Q9H634	De_novo_Start_OutOfFrame	SNP	ENST00000319359.3	37	CCDS10102.1	.	.	.	.	.	.	.	.	.	.	C	9.452	1.090914	0.20471	.	.	ENSG00000128886	ENST00000319359;ENST00000433927	T;T	0.27720	1.65;1.65	5.67	-6.18	0.02085	.	0.307172	0.28067	N	0.016729	T	0.09818	0.0241	L	0.27053	0.805	0.23581	N	0.99737	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.009	T	0.40869	-0.9540	10	0.02654	T	1	-8.3588	0.0486	0.00011	0.3278:0.1901:0.2007:0.2813	.	79;33	Q9HB65;B3KQ66	ELL3_HUMAN;.	D	79;109	ENSP00000320346:E79D;ENSP00000404209:E109D	ENSP00000320346:E79D	E	-	3	2	ELL3	41855573	0.004000	0.15560	0.423000	0.26634	0.930000	0.56654	-1.046000	0.03525	-0.759000	0.04684	-0.136000	0.14681	GAG		0.582	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165		A	44068281	C	A	44068281	3	1	77	1	0	0	0	0	1	0	0	0	5077	680	24	2	992	2	ELL3	15	44068281	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1379244	44068281	58463111	845	22581										
B2M	567	broad.mit.edu	37	chr15	45003781	45003782	+	Frame_Shift_Del	DEL	CT	CT	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttagctgtgctcgcgctaCtctctctttctggcctggag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:45003781_45003782delCT	ENST00000558401.1	+	1	107_108	c.37_38delCT	c.(37-39)ctcfs	p.L13fs	B2M_ENST00000559916.1_Frame_Shift_Del_p.L13fs|PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000544417.1_Frame_Shift_Del_p.L13fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	13					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L15fs*41(4)|p.A11fs*42(1)|p.L13F(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCTCGCGCTACTCTCTCTTTCT	0.614																																																6	Deletion - Frameshift(5)|Substitution - Missense(1)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|skin(1)	15																																								42791074	SO:0001589	frameshift_variant	567			AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.37_38delCT	15.37:g.45003787_45003788delCT	ENSP00000452780:p.Leu13fs		42791073	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																				0.614	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45003782	CT	-	45003781	7	5	77	1	0	1	0	1	0	0	0	0	1245	565	20	0	39	0	B2M	15	45003781	Frame_Shift_Del	DEL	CT	TCGA-AG-A02N-01A-11W-A096-10	935500	45003781	57527611	846	22582										
B2M	567	broad.mit.edu	37	chr15	45007753	45007753	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagaatggagagagaattgAaaaagtggagcattcagact							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:45007753delA	ENST00000558401.1	+	2	270	c.200delA	c.(199-201)gaafs	p.E67fs	B2M_ENST00000559916.1_Frame_Shift_Del_p.E67fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.E67fs|B2M_ENST00000559220.1_Intron	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	67	Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.V69fs*34(1)|p.K61_L74del(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GAGAGAATTGAAAAAGTGGAG	0.418																																																2	Deletion - Frameshift(1)|Deletion - In frame(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	15											197	203	201					15																	45007753		2198	4298	6496	42795045	SO:0001589	frameshift_variant	567			AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.200delA	15.37:g.45007753delA	ENSP00000452780:p.Glu67fs		42795045	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																				0.418	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45007753	A	-	45007753	7	5	77	1	0	1	0	1	0	0	0	0	1245	246	9	0	206	0	B2M	15	45007753	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	3972	45007753	57523639	847	22583										
DUOX1	53905	broad.mit.edu	37	chr15	45433500	45433502	+	In_Frame_Del	DEL	AAG	AAG	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccaacttaggctgttctccAagaaggagattgaagaaatc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	AAG	AAG	AAG	-	AAG	AAG	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:45433500_45433502delAAG	ENST00000321429.4	+	15	1983_1985	c.1576_1578delAAG	c.(1576-1578)aagdel	p.K527del	DUOX1_ENST00000389037.3_In_Frame_Del_p.K527del|DUOX1_ENST00000561166.1_In_Frame_Del_p.K173del	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	527	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.K526delK(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GCTGTTCTCCAAGAAGGAGATTG	0.532																																																1	Deletion - In frame(1)	large_intestine(1)	15																																								43220794	SO:0001651	inframe_deletion	53905			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.1576_1578delAAG	15.37:g.45433503_45433505delAAG	ENSP00000317997:p.Lys527del		43220792	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	In_Frame_Del	DEL	ENST00000321429.4	37	CCDS32221.1																																																																																				0.532	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		-	45433502	AAG	-	45433500	7	5	77	1	0	1	0	1	0	0	0	0	4811	131	5	0	1626	0	DUOX1	15	45433500	In_Frame_Del	DEL	AAG	TCGA-AG-A02N-01A-11W-A096-10	425747	45433500	57097892	848	22584										
DTWD1	56986	broad.mit.edu	37	chr15	49917518	49917518	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagttcttcaaaaagctcagCaaagtgggagatcaaaatgt	9	6	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:49917518C>T	ENST00000251250.6	+	3	361	c.154C>T	c.(154-156)Caa>Taa	p.Q52*	DTWD1_ENST00000559223.1_3'UTR|DTWD1_ENST00000329873.5_Nonsense_Mutation_p.Q52*|DTWD1_ENST00000558653.1_Nonsense_Mutation_p.Q52*|DTWD1_ENST00000403028.3_Nonsense_Mutation_p.Q52*	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	52								p.Q52*(1)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		AAAAGCTCAGCAAAGTGGGAG	0.368																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											79	75	77					15																	49917518		2196	4292	6488	47704810	SO:0001587	stop_gained	56986			BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.154C>T	15.37:g.49917518C>T	ENSP00000251250:p.Gln52*		47704810	Q567Q3|Q8WVG9|Q9NRU6	Nonsense_Mutation	SNP	ENST00000251250.6	37	CCDS10132.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.798444	0.70567	.	.	ENSG00000104047	ENST00000403028;ENST00000329873;ENST00000251250	.	.	.	5.09	3.04	0.35103	.	0.482752	0.25086	N	0.033248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.9528	8.4535	0.32884	0.4605:0.4185:0.121:0.0	.	.	.	.	X	52	.	.	Q	+	1	0	DTWD1	47704810	1.000000	0.71417	0.989000	0.46669	0.984000	0.73092	2.239000	0.43079	1.234000	0.43709	0.591000	0.81541	CAA		0.368	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234		T	49917518	C	T	49917518	4	4	77	1	0	0	0	0	0	1	0	0	4802	711	25	3	156	3	DTWD1	15	49917518	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4484018	49917518	52613874	849	22585										
ATP8B4	79895	broad.mit.edu	37	chr15	50271892	50271892	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttaagaatccggagaacacaGagctcttctctccttcattc	6	12	3	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:50271892G>A	ENST00000284509.6	-	12	1097	c.956C>T	c.(955-957)tCt>tTt	p.S319F	ATP8B4_ENST00000558959.1_5'UTR|ATP8B4_ENST00000559829.1_Missense_Mutation_p.S319F|RNA5SP394_ENST00000364216.1_RNA	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	319						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.S319F(1)		breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		GGAGAACACAGAGCTCTTCTC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											111	121	117					15																	50271892		2196	4295	6491	48059184	SO:0001583	missense	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.956C>T	15.37:g.50271892G>A	ENSP00000284509:p.Ser319Phe		48059184	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	9.018	0.984085	0.18889	.	.	ENSG00000104043	ENST00000284509	D	0.91068	-2.78	5.68	2.63	0.31362	ATPase, P-type, ATPase-associated domain (1);	0.526462	0.21818	N	0.068665	D	0.86272	0.5893	L	0.52011	1.625	0.09310	N	1	B	0.06786	0.001	B	0.18263	0.021	T	0.75499	-0.3296	10	0.45353	T	0.12	.	9.3157	0.37932	0.254:0.0:0.746:0.0	.	319	Q8TF62	AT8B4_HUMAN	F	319	ENSP00000284509:S319F	ENSP00000284509:S319F	S	-	2	0	ATP8B4	48059184	0.434000	0.25570	0.034000	0.17996	0.934000	0.57294	3.377000	0.52425	0.280000	0.22209	-0.355000	0.07637	TCT		0.363	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		A	50271892	G	A	50271892	3	1	77	1	0	0	0	0	1	0	0	0	1198	942	33	3	2690	3	ATP8B4	15	50271892	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	354374	50271892	52259500	850	22586										
HDC	3067	broad.mit.edu	37	chr15	50535201	50535201	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttctgtgagacaattaggAccctgtttgaaaaataaagg	9	5	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:50535201A>G	ENST00000267845.3	-	12	1647	c.1245T>C	c.(1243-1245)ggT>ggC	p.G415G	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Silent_p.G382G	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.G415G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		GACAATTAGGACCCTGTTTGA	0.483																																					GBM(95;1627 1936 6910 9570)											1	Substitution - coding silent(1)	large_intestine(1)	15											36	40	38					15																	50535201		2194	4294	6488	48322493	SO:0001819	synonymous_variant	3067				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1245T>C	15.37:g.50535201A>G			48322493		Silent	SNP	ENST00000267845.3	37	CCDS10134.1																																																																																				0.483	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			G	50535201	A	G	50535201	2	3	77	1	0	0	0	0	0	0	0	1	7036	262	10	4		4	HDC	15	50535201	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	263309	50535201	51996191	851	22587										
DMXL2	23312	broad.mit.edu	37	chr15	51795011	51795011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagtgaccttacctgctgaaGgcgttgctcttattacttca	8	10	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:51795011G>T	ENST00000251076.5	-	17	3271	c.2984C>A	c.(2983-2985)cCt>cAt	p.P995H	DMXL2_ENST00000543779.2_Missense_Mutation_p.P995H|DMXL2_ENST00000449909.3_Intron	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	995						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.P995H(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ACCTGCTGAAGGCGTTGCTCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	15											103	100	101					15																	51795011		2195	4293	6488	49582303	SO:0001583	missense	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2984C>A	15.37:g.51795011G>T	ENSP00000251076:p.Pro995His		49582303	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.562454	0.86335	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.56103	0.48;0.48	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.76219	0.3957	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.80153	-0.1501	10	0.87932	D	0	.	18.9501	0.92638	0.0:0.0:1.0:0.0	.	995;995	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	H	995	ENSP00000251076:P995H;ENSP00000441858:P995H	ENSP00000251076:P995H	P	-	2	0	DMXL2	49582303	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.151000	0.94674	2.459000	0.83118	0.644000	0.83932	CCT		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51795011	G	T	51795011	3	4	77	1	0	0	0	0	1	0	0	0	4606	1000	35	2	6237	2	DMXL2	15	51795011	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1259810	51795011	50736381	852	22588										
UNC13C	440279	broad.mit.edu	37	chr15	54306438	54306438	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaatcaagaagaacaattgGcagtcacctgatgacagtga	9	7	2	5			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:54306438G>A	ENST00000260323.11	+	1	1338	c.1338G>A	c.(1336-1338)tgG>tgA	p.W446*	UNC13C_ENST00000545554.1_Nonsense_Mutation_p.W446*|UNC13C_ENST00000537900.1_Nonsense_Mutation_p.W446*	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	446					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.W446*(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AGAACAATTGGCAGTCACCTG	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											110	107	108					15																	54306438		1900	4114	6014	52093730	SO:0001587	stop_gained	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1338G>A	15.37:g.54306438G>A	ENSP00000260323:p.Trp446*		52093730	Q0P613|Q8ND48|Q96NP3	Nonsense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	38	7.230885	0.98150	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.7181	0.88343	0.0:0.0:1.0:0.0	.	.	.	.	X	446	.	ENSP00000260323:W446X	W	+	3	0	UNC13C	52093730	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	9.259000	0.95561	2.665000	0.90641	0.655000	0.94253	TGG		0.413	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54306438	G	A	54306438	4	1	77	1	0	0	0	0	0	1	0	0	17026	1212	42	3	1340	3	UNC13C	15	54306438	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2511427	54306438	48224954	853	22589										
TCF12	6938	broad.mit.edu	37	chr15	57565319	57565319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaatgccagagaacgcttaCgcgtgcgggatattaatgaa	11	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:57565319C>T	ENST00000267811.5	+	18	2069	c.1765C>T	c.(1765-1767)Cgc>Tgc	p.R589C	TCF12_ENST00000559703.1_Missense_Mutation_p.R246C|TCF12_ENST00000559710.1_Missense_Mutation_p.R223C|TCF12_ENST00000438423.2_Missense_Mutation_p.R613C|TCF12_ENST00000557843.1_Missense_Mutation_p.R589C|TCF12_ENST00000537840.1_Missense_Mutation_p.R353C|TCF12_ENST00000333725.5_Missense_Mutation_p.R613C|TCF12_ENST00000343827.3_Missense_Mutation_p.R419C|TCF12_ENST00000452095.2_Missense_Mutation_p.R609C|TCF12_ENST00000543579.1_Missense_Mutation_p.R443C	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	589	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.R609C(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AGAACGCTTACGCGTGCGGGA	0.428			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	1	Substitution - Missense(1)	large_intestine(1)	15											98	105	102					15																	57565319		2192	4292	6484	55352611	SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1765C>T	15.37:g.57565319C>T	ENSP00000267811:p.Arg589Cys		55352611	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568168	0.86439	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827;ENST00000543417	D;D;D;D;D;D;D	0.99722	-6.53;-6.53;-6.53;-6.53;-6.53;-6.53;-6.53	4.72	4.72	0.59763	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99778	0.9908	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.995;0.999;1.0;0.992;0.999;0.998;0.996;0.996;0.994	D	0.96981	0.9715	10	0.87932	D	0	-14.1354	18.0262	0.89270	0.0:1.0:0.0:0.0	.	609;223;443;353;609;641;443;419;589;613	B4DGI9;B4DZP2;B4DH96;B4E1W1;E9PGY0;F5H6Z6;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;.;.;.;HTF4_HUMAN;.	C	641;589;613;609;613;443;353;419;201	ENSP00000267811:R589C;ENSP00000388940:R613C;ENSP00000396881:R609C;ENSP00000331057:R613C;ENSP00000440017:R443C;ENSP00000444696:R353C;ENSP00000342459:R419C	ENSP00000267811:R589C	R	+	1	0	TCF12	55352611	1.000000	0.71417	0.993000	0.49108	0.954000	0.61252	6.026000	0.70873	2.329000	0.79093	0.655000	0.94253	CGC		0.428	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		T	57565319	C	T	57565319	3	4	77	1	0	0	0	0	1	0	0	0	15726	536	19	1	1980	1	TCF12	15	57565319	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3258881	57565319	44966073	854	22590										
GCOM1	100820829	broad.mit.edu	37	chr15	57913837	57913837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tttggaaaaggtgagaaagcGaatgtatggagactatgatg	14	2	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:57913837G>A	ENST00000267853.5	+	4	444	c.350G>A	c.(349-351)cGa>cAa	p.R117Q	GCOM1_ENST00000380561.2_Intron|GCOM1_ENST00000380569.2_Missense_Mutation_p.R117Q|GCOM1_ENST00000587652.1_Missense_Mutation_p.R117Q|GCOM1_ENST00000380560.2_Intron|POLR2M_ENST00000380563.2_Intron|GCOM1_ENST00000380568.3_Missense_Mutation_p.R117Q|MYZAP_ENST00000380565.4_Missense_Mutation_p.R117Q|GCOM1_ENST00000574161.1_Missense_Mutation_p.R117Q|GCOM1_ENST00000396180.1_Intron|GCOM1_ENST00000572390.1_Missense_Mutation_p.R117Q			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	117					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)		p.R117Q(1)									GTGAGAAAGCGAATGTATGGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	15											143	134	137					15																	57913837		2192	4292	6484	55701129	SO:0001583	missense	145781			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.350G>A	15.37:g.57913837G>A	ENSP00000267853:p.Arg117Gln		55701129	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.063082	0.55432	.	.	ENSG00000137878	ENST00000380569;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.66	4.73	0.59995	.	0.180261	0.46145	D	0.000316	T	0.19604	0.0471	N	0.25647	0.755	0.80722	D	1	B;B;B;B	0.26708	0.016;0.069;0.04;0.157	B;B;B;B	0.17098	0.003;0.008;0.004;0.017	T	0.06356	-1.0831	10	0.08599	T	0.76	-2.7833	8.1191	0.30961	0.2123:0.0:0.7877:0.0	.	117;117;117;117	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	Q	117	ENSP00000369943:R117Q;ENSP00000267853:R117Q;ENSP00000369939:R117Q;ENSP00000369942:R117Q	ENSP00000267853:R117Q	R	+	2	0	GCOM1	55701129	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.641000	0.46587	2.827000	0.97445	0.643000	0.83706	CGA		0.403	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		A	57913837	G	A	57913837	3	1	77	1	0	0	0	0	1	0	0	0	6324	1058	37	1	364	1	GCOM1	15	57913837	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	348518	57913837	44617555	855	22591										
GCNT3	9245	broad.mit.edu	37	chr15	59910945	59910945	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgtggatgagaagtccccaGaaactttcaaagaggcggtc	12	8	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:59910945G>T	ENST00000396065.1	+	3	956	c.508G>T	c.(508-510)Gaa>Taa	p.E170*	GCNT3_ENST00000560585.1_Nonsense_Mutation_p.E170*	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	170					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.E170*(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GAAGTCCCCAGAAACTTTCAA	0.453																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											101	99	100					15																	59910945		2190	4290	6480	57698237	SO:0001587	stop_gained	9245			AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.508G>T	15.37:g.59910945G>T	ENSP00000379377:p.Glu170*		57698237		Nonsense_Mutation	SNP	ENST00000396065.1	37	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	G	40	8.425545	0.98806	.	.	ENSG00000140297	ENST00000396065	.	.	.	6.16	6.16	0.99307	.	0.528716	0.20798	N	0.085492	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	17.0356	0.86474	0.0:0.1268:0.8732:0.0	.	.	.	.	X	170	.	ENSP00000379377:E170X	E	+	1	0	GCNT3	57698237	0.006000	0.16342	0.998000	0.56505	0.954000	0.61252	1.213000	0.32407	2.937000	0.99478	0.650000	0.86243	GAA		0.453	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		T	59910945	G	T	59910945	4	4	77	1	0	0	0	0	0	1	0	0	6322	943	33	2	510	2	GCNT3	15	59910945	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1997108	59910945	42620447	856	22592										
VPS13C	54832	broad.mit.edu	37	chr15	62155675	62155675	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggattgtcttcttgcttccaGgaatagcacagtggtatcgg	12	8	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:62155675G>T	ENST00000261517.5	-	82	10989	c.10916C>A	c.(10915-10917)cCt>cAt	p.P3639H	VPS13C_ENST00000249837.3_Missense_Mutation_p.P3596H	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.P3639H(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CTTGCTTCCAGGAATAGCACA	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	15											167	145	153					15																	62155675		2203	4300	6503	59942967	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10916C>A	15.37:g.62155675G>T	ENSP00000261517:p.Pro3639His		59942967		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782553	0.31502	.	.	ENSG00000129003	ENST00000249837;ENST00000261517	T;T	0.50277	0.75;0.75	5.68	2.83	0.33086	.	0.546215	0.19185	N	0.120573	T	0.40272	0.1110	L	0.52905	1.665	0.09310	N	0.999996	B;B	0.15719	0.014;0.004	B;B	0.22386	0.039;0.007	T	0.36456	-0.9747	10	0.51188	T	0.08	.	6.2282	0.20720	0.2028:0.0:0.6676:0.1295	.	3596;3639	Q709C8-3;Q709C8	.;VP13C_HUMAN	H	3596;3639	ENSP00000249837:P3596H;ENSP00000261517:P3639H	ENSP00000249837:P3596H	P	-	2	0	VPS13C	59942967	1.000000	0.71417	0.005000	0.12908	0.769000	0.43574	3.497000	0.53295	0.444000	0.26612	-0.229000	0.12294	CCT		0.363	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62155675	G	T	62155675	3	4	77	1	0	0	0	0	1	0	0	0	17231	1000	35	2	361	2	VPS13C	15	62155675	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2244730	62155675	40375717	857	22593										
SNX1	6642	broad.mit.edu	37	chr15	64410318	64410318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atatcaacttcattttagatGccacagtggagctatccttg	7	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:64410318G>A	ENST00000559844.1	+	3	288	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	SNX1_ENST00000560829.1_5'UTR|SNX1_ENST00000353874.4_Missense_Mutation_p.A92T|SNX1_ENST00000561026.1_Intron|SNX1_ENST00000261889.5_Missense_Mutation_p.A92T			Q13596	SNX1_HUMAN	sorting nexin 1	92					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.A92T(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						CATTTTAGATGCCACAGTGGA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	15											74	73	73					15																	64410318		2203	4300	6503	62197371	SO:0001583	missense	6642			BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.274G>A	15.37:g.64410318G>A	ENSP00000453785:p.Ala92Thr		62197371	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Missense_Mutation	SNP	ENST00000559844.1	37	CCDS32266.1	.	.	.	.	.	.	.	.	.	.	G	33	5.264701	0.95399	.	.	ENSG00000028528	ENST00000380285;ENST00000353874	T	0.63417	-0.04	5.87	5.87	0.94306	.	0.159208	0.56097	D	0.000028	T	0.73659	0.3615	L	0.50333	1.59	0.80722	D	1	D;P;D	0.63046	0.992;0.955;0.992	D;P;D	0.67900	0.954;0.763;0.954	T	0.68150	-0.5485	10	0.32370	T	0.25	-4.6913	17.7375	0.88397	0.0:0.0:1.0:0.0	.	92;92;92	Q6ZRJ8;A6NKH4;Q13596	.;.;SNX1_HUMAN	T	92	ENSP00000326668:A92T	ENSP00000326668:A92T	A	+	1	0	SNX1	62197371	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	8.661000	0.91125	2.941000	0.99782	0.655000	0.94253	GCC		0.383	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		A	64410318	G	A	64410318	3	1	77	1	0	0	0	0	1	0	0	0	14917	1319	46	3	284	3	SNX1	15	64410318	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2254643	64410318	38121074	858	22594										
SPG21	51324	broad.mit.edu	37	chr15	65261617	65261617	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taatagttacaggtatgtccCgaattttatgaggttccaca	8	7	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:65261617C>T	ENST00000204566.2	-	7	939	c.644G>A	c.(643-645)cGg>cAg	p.R215Q	SPG21_ENST00000433215.2_Missense_Mutation_p.R215Q|SPG21_ENST00000416889.2_Missense_Mutation_p.R188Q|SPG21_ENST00000559199.1_Missense_Mutation_p.R61Q	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	215					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)	p.R215Q(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						AGGTATGTCCCGAATTTTATG	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	15											99	104	102					15																	65261617		2202	4299	6501	63048670	SO:0001583	missense	51324			AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.644G>A	15.37:g.65261617C>T	ENSP00000204566:p.Arg215Gln		63048670	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	37	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622602	0.28889	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T;T	0.67865	-0.29;-0.29;-0.29	5.96	5.05	0.67936	.	0.103897	0.64402	D	0.000003	T	0.35278	0.0926	N	0.01109	-1.01	0.46849	D	0.999223	B;B	0.17465	0.022;0.003	B;B	0.11329	0.003;0.006	T	0.29822	-0.9999	10	0.12103	T	0.63	-13.4849	13.8851	0.63704	0.0:0.9266:0.0:0.0734	.	188;215	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	Q	215;188;215	ENSP00000204566:R215Q;ENSP00000394846:R188Q;ENSP00000404111:R215Q	ENSP00000204566:R215Q	R	-	2	0	SPG21	63048670	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.370000	0.66144	1.527000	0.49086	-0.142000	0.14014	CGG		0.343	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		T	65261617	C	T	65261617	3	4	77	1	0	0	0	0	1	0	0	0	15082	652	23	1	294	1	SPG21	15	65261617	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	851299	65261617	37269775	859	22595										
DPP8	54878	broad.mit.edu	37	chr15	65771245	65771245	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggcagcccaccactggatcGtttatatttgctttccttta	7	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:65771245G>A	ENST00000341861.5	-	11	3057	c.1477C>T	c.(1477-1479)Cga>Tga	p.R493*	DPP8_ENST00000559233.1_Nonsense_Mutation_p.R493*|DPP8_ENST00000321147.6_Nonsense_Mutation_p.R493*|DPP8_ENST00000358939.4_Nonsense_Mutation_p.R477*|DPP8_ENST00000300141.6_Nonsense_Mutation_p.R477*|DPP8_ENST00000321118.7_Nonsense_Mutation_p.R493*|DPP8_ENST00000339244.5_Intron	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	493					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)	p.R477*(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCACTGGATCGTTTATATTTG	0.358																																																1	Substitution - Nonsense(1)	large_intestine(1)	15											58	59	58					15																	65771245		2201	4299	6500	63558298	SO:0001587	stop_gained	54878			AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.1477C>T	15.37:g.65771245G>A	ENSP00000339208:p.Arg493*		63558298	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Nonsense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	G	39	7.469539	0.98302	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000395652	.	.	.	5.55	4.58	0.56647	.	0.099543	0.41194	D	0.000940	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-10.6631	15.198	0.73108	0.0:0.0:0.8585:0.1415	.	.	.	.	X	493;477;477;493;493;493	.	ENSP00000300141:R477X	R	-	1	2	DPP8	63558298	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.239000	0.51360	2.605000	0.88082	0.557000	0.71058	CGA		0.358	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		A	65771245	G	A	65771245	4	1	77	1	0	0	0	0	0	1	0	0	4743	1153	40	1	1259	1	DPP8	15	65771245	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	509628	65771245	36760147	860	22596										
C15orf44	81556	broad.mit.edu	37	chr15	65899641	65899641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggctgctaggtgcttacgCtggtattcctcggacccctc	12	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:65899641C>T	ENST00000395644.4	-	2	413	c.78G>A	c.(76-78)caG>caA	p.Q26Q	VWA9_ENST00000313182.2_Silent_p.Q26Q|VWA9_ENST00000431261.2_5'UTR|VWA9_ENST00000420799.2_Intron|VWA9_ENST00000442903.3_Silent_p.Q26Q|VWA9_ENST00000567744.1_Silent_p.Q62Q|VWA9_ENST00000569491.1_Splice_Site_p.Q26Q			Q96SY0	VWA9_HUMAN	von Willebrand factor A domain containing 9	26	VWFA.							p.Q26Q(1)									GGTGCTTACGCTGGTATTCCT	0.463																																																1	Substitution - coding silent(1)	large_intestine(1)	15											126	104	111					15																	65899641		2201	4299	6500	63686694	SO:0001819	synonymous_variant	81556			AL136662	CCDS55969.1, CCDS45283.1	15q22.31	2012-09-27	2012-09-27	2012-09-27	ENSG00000138614	ENSG00000138614			25372	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 44"	C15orf44		11230166	Standard	NM_001136043		Approved	DKFZP564O1664	uc010uja.2	Q96SY0	OTTHUMG00000133159	ENST00000395644.4:c.78G>A	15.37:g.65899641C>T			63686694	B4DDI6|B4DVD5|Q49AH8|Q96HX5|Q9H0S5	Silent	SNP	ENST00000395644.4	37																																																																																					0.463	VWA9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420604.3	NM_030800		T	65899641	C	T	65899641	2	4	77	1	0	0	0	0	0	0	0	1	1802	811	28	3		3	C15orf44	15	65899641	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	128396	65899641	36631751	861	22597										
KIF23	9493	broad.mit.edu	37	chr15	69718690	69718690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctaggccagaaaaagagacGtattgctaatacccatttga	8	9	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:69718690G>A	ENST00000260363.4	+	9	980	c.863G>A	c.(862-864)cGt>cAt	p.R288H	KIF23_ENST00000395392.2_Missense_Mutation_p.R288H|KIF23_ENST00000352331.4_Missense_Mutation_p.R288H|KIF23_ENST00000558585.1_Missense_Mutation_p.R105H|KIF23_ENST00000537891.1_Missense_Mutation_p.R105H|KIF23_ENST00000559279.1_Missense_Mutation_p.R288H	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	288	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)	p.R288H(2)		central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						AAAAAGAGACGTATTGCTAAT	0.398																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	15											238	230	233					15																	69718690		2199	4298	6497	67505744	SO:0001583	missense	9493			X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"Kinesins"	6392	protein-coding gene	gene with protein product		605064	"kinesin-like 5 (mitotic kinesin-like protein 1)"	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.863G>A	15.37:g.69718690G>A	ENSP00000260363:p.Arg288His		67505744	Q8WVP0	Missense_Mutation	SNP	ENST00000260363.4	37	CCDS32278.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.885857	0.91814	.	.	ENSG00000137807	ENST00000260363;ENST00000352331;ENST00000395392;ENST00000537891	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.63	5.63	0.86233	Kinesin, motor domain (4);	0.099034	0.64402	D	0.000003	T	0.81226	0.4778	L	0.33710	1.025	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	P;D;D	0.83275	0.719;0.996;0.995	T	0.81653	-0.0835	10	0.52906	T	0.07	.	18.6586	0.91463	0.0:0.0:1.0:0.0	.	105;288;288	B4E1K0;Q02241-2;Q02241	.;.;KIF23_HUMAN	H	288;288;288;105	ENSP00000260363:R288H;ENSP00000304978:R288H;ENSP00000378790:R288H;ENSP00000442969:R105H	ENSP00000260363:R288H	R	+	2	0	KIF23	67505744	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.659000	0.68010	2.635000	0.89317	0.655000	0.94253	CGT		0.398	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	69718690	G	A	69718690	3	1	77	1	0	0	0	0	1	0	0	0	8312	1145	40	1	897	1	KIF23	15	69718690	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3819049	69718690	32812702	862	22598										
THSD4	79875	broad.mit.edu	37	chr15	72069651	72069651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctacaactactacaagaccGcctgctgtgcctcctgcacc	6	17	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:72069651G>A	ENST00000355327.3	+	18	3129	c.2995G>A	c.(2995-2997)Gcc>Acc	p.A999T	THSD4_ENST00000261862.6_Missense_Mutation_p.A999T|THSD4_ENST00000357769.4_Missense_Mutation_p.A639T			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	999	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)	p.A999T(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CTACAAGACCGCCTGCTGTGC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	15											81	84	83					15																	72069651		2100	4216	6316	69856705	SO:0001583	missense	79875			AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2995G>A	15.37:g.72069651G>A	ENSP00000347484:p.Ala999Thr		69856705	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	37	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	7.362	0.625008	0.14257	.	.	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.45668	0.89;0.89;0.89	4.85	4.85	0.62838	PLAC (2);	.	.	.	.	T	0.24353	0.0590	N	0.24115	0.695	0.42035	D	0.991043	B;P	0.39665	0.268;0.682	B;B	0.32805	0.089;0.153	T	0.10132	-1.0643	9	0.06625	T	0.88	.	15.4645	0.75387	0.0:0.0:1.0:0.0	.	639;999	B4DR13;Q6ZMP0	.;THSD4_HUMAN	T	999;999;639	ENSP00000347484:A999T;ENSP00000261862:A999T;ENSP00000350413:A639T	ENSP00000261862:A999T	A	+	1	0	THSD4	69856705	1.000000	0.71417	0.931000	0.37212	0.835000	0.47333	5.251000	0.65438	2.238000	0.73509	0.655000	0.94253	GCC		0.547	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		A	72069651	G	A	72069651	3	1	77	1	0	0	0	0	1	0	0	0	15917	1087	38	1	3061	1	THSD4	15	72069651	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2350961	72069651	30461741	863	22599										
NR2E3	10002	broad.mit.edu	37	chr15	72104309	72104309	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccagccgtgcagaacgagCgccagccgcgaagcacagcc	12	18	0	1	rs527236086		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:72104309C>T	ENST00000398840.2	+	0	554							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R122C(1)		breast(1)|endometrium(1)|lung(1)	3						GCAGAACGAGCGCCAGCCGCG	0.716																																																1	Substitution - Missense(1)	large_intestine(1)	15											11	19	16					15																	72104309		2035	4048	6083	69891363			10002				CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"Nuclear hormone receptors"	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72104309C>T			69891363	B6ZGU0|Q9UHM4	Missense_Mutation	SNP	ENST00000398840.2	37		.	.	.	.	.	.	.	.	.	.	C	9.558	1.117638	0.20877	.	.	ENSG00000031544	ENST00000326995;ENST00000398840	.	.	.	4.45	4.45	0.53987	Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);	0.234168	0.44902	D	0.000407	T	0.78528	0.4297	M	0.72353	2.195	0.48762	D	0.999700	D	0.89917	1.0	D	0.87578	0.998	T	0.82784	-0.0286	8	0.87932	D	0	.	17.1308	0.86726	0.0:1.0:0.0:0.0	.	122	Q9Y5X4	NR2E3_HUMAN	C	34;122	.	ENSP00000317199:R34C	R	+	1	0	NR2E3	69891363	1.000000	0.71417	1.000000	0.80357	0.232000	0.25224	7.533000	0.81994	2.033000	0.60031	0.485000	0.47835	CGC		0.716	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		T	72104309	C	T	72104309	1	4	77	0	1	0	0	0	0	0	0	0	10657	768	27	1		1	NR2E3	15	72104309	RNA	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	34658	72104309	30427083	864	22600										
HCN4	10021	broad.mit.edu	37	chr15	73622056	73622056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acatgcccacgggcgcctgcCgcccgtagccgatgcacagc	12	18	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:73622056C>T	ENST00000261917.3	-	4	2441	c.1448G>A	c.(1447-1449)cGg>cAg	p.R483Q		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	483					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.R483Q(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GGGCGCCTGCCGCCCGTAGCC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	15											75	71	72					15																	73622056		2198	4297	6495	71409109	SO:0001583	missense	10021			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1448G>A	15.37:g.73622056C>T	ENSP00000261917:p.Arg483Gln		71409109	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.934891	0.34189	.	.	ENSG00000138622	ENST00000261917	D	0.97378	-4.36	4.16	1.78	0.24846	Ion transport (1);	.	.	.	.	D	0.90724	0.7089	N	0.20986	0.625	0.40603	D	0.981607	B	0.06786	0.001	B	0.01281	0.0	T	0.82788	-0.0284	9	0.16420	T	0.52	.	4.3053	0.10944	0.0:0.4374:0.0:0.5626	.	483	Q9Y3Q4	HCN4_HUMAN	Q	483	ENSP00000261917:R483Q	ENSP00000261917:R483Q	R	-	2	0	HCN4	71409109	1.000000	0.71417	0.850000	0.33497	0.566000	0.35808	4.178000	0.58284	0.865000	0.35603	0.561000	0.74099	CGG		0.632	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73622056	C	T	73622056	3	4	77	1	0	0	0	0	1	0	0	0	7020	652	23	1	2183	1	HCN4	15	73622056	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1517747	73622056	28909336	865	22601										
ISLR2	57611	broad.mit.edu	37	chr15	74427136	74427136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggagggccttgatgaagacGcggagcagggagacccaagt	18	8	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:74427136G>A	ENST00000361742.3	+	4	2810	c.2041G>A	c.(2041-2043)Gcg>Acg	p.A681T	ISLR2_ENST00000435464.1_Missense_Mutation_p.A681T|ISLR2_ENST00000453268.2_Missense_Mutation_p.A681T|ISLR2_ENST00000419208.1_Missense_Mutation_p.A681T|ISLR2_ENST00000445793.1_Missense_Mutation_p.A681T|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Missense_Mutation_p.A681T|ISLR2_ENST00000565540.1_Missense_Mutation_p.A681T	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	681					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A681T(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						TGATGAAGACGCGGAGCAGGG	0.662											OREG0023277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	15											43	49	47					15																	74427136		2198	4297	6495	72214189	SO:0001583	missense	57611				CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.2041G>A	15.37:g.74427136G>A	ENSP00000355402:p.Ala681Thr	1152	72214189	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	37	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	G	5.475	0.272741	0.10349	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000395121;ENST00000419208	T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5	4.69	2.67	0.31697	.	.	.	.	.	T	0.31482	0.0798	N	0.14661	0.345	0.09310	N	1	B	0.31519	0.327	B	0.17433	0.018	T	0.07083	-1.0791	9	0.35671	T	0.21	.	10.8706	0.46881	0.0:0.3705:0.6295:0.0	.	681	Q6UXK2	ISLR2_HUMAN	T	681;681;681;681;270;681	ENSP00000403244:A681T;ENSP00000355402:A681T;ENSP00000411443:A681T;ENSP00000411834:A681T;ENSP00000408872:A681T	ENSP00000355402:A681T	A	+	1	0	ISLR2	72214189	1.000000	0.71417	0.564000	0.28396	0.203000	0.24098	2.264000	0.43302	0.332000	0.23536	0.313000	0.20887	GCG		0.662	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		A	74427136	G	A	74427136	3	1	77	1	0	0	0	0	1	0	0	0	7880	1087	38	1	2043	1	ISLR2	15	74427136	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	805080	74427136	28104256	866	22602										
CYP1A1	1543	broad.mit.edu	37	chr15	75014700	75014700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtccttgaaggcattcagggAagggttgggtaggtagcgaa	17	5	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:75014700A>G	ENST00000379727.3	-	2	937	c.739T>C	c.(739-741)Tcc>Ccc	p.S247P	CYP1A1_ENST00000395049.4_Missense_Mutation_p.S247P|CYP1A1_ENST00000567032.1_Missense_Mutation_p.S247P|CYP1A1_ENST00000395048.2_Missense_Mutation_p.S247P|CYP1A1_ENST00000564596.1_5'UTR			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	247					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)	p.S247P(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	GCATTCAGGGAAGGGTTGGGT	0.478									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																																							1	Substitution - Missense(1)	large_intestine(1)	15											89	85	86					15																	75014700		2197	4296	6493	72801753	SO:0001583	missense	1543	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"Cytochrome P450s"	2595	protein-coding gene	gene with protein product		108330	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.739T>C	15.37:g.75014700A>G	ENSP00000369050:p.Ser247Pro		72801753	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	37	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	A	3.788	-0.044213	0.07452	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049	T;T;T	0.68624	-0.34;-0.34;-0.34	5.0	-8.65	0.00870	.	1.030670	0.07631	N	0.928630	T	0.46308	0.1386	L	0.31845	0.965	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.008	T	0.23297	-1.0192	10	0.23891	T	0.37	.	7.938	0.29941	0.1754:0.4:0.0:0.4246	.	247;247	E7EMT5;P04798	.;CP1A1_HUMAN	P	247	ENSP00000369050:S247P;ENSP00000378488:S247P;ENSP00000378489:S247P	ENSP00000369050:S247P	S	-	1	0	CYP1A1	72801753	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.278000	0.01159	-1.925000	0.01063	-0.406000	0.06334	TCC		0.478	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499		G	75014700	A	G	75014700	3	3	77	1	0	0	0	0	1	0	0	0	4155	246	9	4	823	4	CYP1A1	15	75014700	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	587564	75014700	27516692	867	22603										
SIN3A	25942	broad.mit.edu	37	chr15	75702219	75702219	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtaggatgtctgcggatctgGcagccattctggctgggcct	15	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:75702219G>A	ENST00000394947.3	-	8	1589	c.1275C>T	c.(1273-1275)tgC>tgT	p.C425C	SIN3A_ENST00000394949.4_Silent_p.C425C|SIN3A_ENST00000360439.4_Silent_p.C425C	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.C425C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						TGCGGATCTGGCAGCCATTCT	0.507																																																1	Substitution - coding silent(1)	large_intestine(1)	15											134	134	134					15																	75702219		2197	4294	6491	73489272	SO:0001819	synonymous_variant	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1275C>T	15.37:g.75702219G>A			73489272		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																				0.507	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75702219	G	A	75702219	2	1	77	1	0	0	0	0	0	0	0	1	14362	1195	42	3		3	SIN3A	15	75702219	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	687519	75702219	26829173	868	22604										
FAH	2184	broad.mit.edu	37	chr15	80473405	80473405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccagaaaacttcggctccAtgttggaactgtcgtggaag	12	9	0	1	rs371659518		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:80473405A>G	ENST00000407106.1	+	14	1239	c.1084A>G	c.(1084-1086)Atg>Gtg	p.M362V	FAH_ENST00000539156.1_Missense_Mutation_p.M292V|FAH_ENST00000561421.1_Missense_Mutation_p.M362V|FAH_ENST00000261755.5_Missense_Mutation_p.M362V			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	362					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)	p.M362V(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTTCGGCTCCATGTTGGAACT	0.498									Tyrosinemia, type 1																																							1	Substitution - Missense(1)	large_intestine(1)	15						A	VAL/MET	0,4406		0,0,2203	133	124	127		1084	-2.4	0.9	15		127	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAH	NM_000137.2	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging	362/420	80473405	1,13005	2203	4300	6503	78260460	SO:0001583	missense	2184	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.1084A>G	15.37:g.80473405A>G	ENSP00000385080:p.Met362Val		78260460	B2R9X1|D3DW95|Q53XA7	Missense_Mutation	SNP	ENST00000407106.1	37	CCDS10314.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.446847	0.63178	0.0	1.16E-4	ENSG00000103876	ENST00000407106;ENST00000261755;ENST00000539156	D;D;D	0.96491	-4.03;-4.03;-4.03	5.31	-2.39	0.06602	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.088488	0.85682	D	0.000000	D	0.96953	0.9005	M	0.85041	2.73	0.52501	D	0.999952	D	0.59767	0.986	P	0.60415	0.874	D	0.95282	0.8387	10	0.87932	D	0	-16.7592	9.4154	0.38519	0.3778:0.5009:0.0:0.1213	.	362	P16930	FAAA_HUMAN	V	362;362;292	ENSP00000385080:M362V;ENSP00000261755:M362V;ENSP00000454271:M292V	ENSP00000261755:M362V	M	+	1	0	FAH	78260460	0.996000	0.38824	0.942000	0.38095	0.729000	0.41735	0.859000	0.27858	-0.325000	0.08577	0.533000	0.62120	ATG		0.498	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2			G	80473405	A	G	80473405	3	3	77	1	0	0	0	0	1	0	0	0	5387	217	8	4	1134	4	FAH	15	80473405	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	4771186	80473405	22057987	869	22605										
BTBD1	53339	broad.mit.edu	37	chr15	83710510	83710510	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcctcaattgtcatcagtgGgaaccggattaaggaaagtg	11	7	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:83710510G>A	ENST00000261721.4	-	4	1034	c.832C>T	c.(832-834)Cca>Tca	p.P278S	RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.6_ENST00000568441.1_RNA|RP11-382A20.7_ENST00000570202.1_RNA|BTBD1_ENST00000560015.1_5'UTR|BTBD1_ENST00000379403.2_Missense_Mutation_p.P278S	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	278					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)		p.P278S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		GTCATCAGTGGGAACCGGATT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	15											108	109	109					15																	83710510		2203	4300	6503	81501514	SO:0001583	missense	53339			AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.832C>T	15.37:g.83710510G>A	ENSP00000261721:p.Pro278Ser		81501514	A6NMI8|Q9BX71|Q9NWN4	Missense_Mutation	SNP	ENST00000261721.4	37	CCDS10322.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984693	0.93044	.	.	ENSG00000064726	ENST00000261721;ENST00000379403	T;T	0.70045	-0.45;-0.45	5.62	5.62	0.85841	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.85133	0.5627	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.989	D	0.87095	0.2175	10	0.87932	D	0	-17.5533	19.6517	0.95819	0.0:0.0:1.0:0.0	.	278;278	A6NMI8;Q9H0C5	.;BTBD1_HUMAN	S	278	ENSP00000261721:P278S;ENSP00000368713:P278S	ENSP00000261721:P278S	P	-	1	0	BTBD1	81501514	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.618000	0.98365	2.662000	0.90505	0.655000	0.94253	CCA		0.418	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			A	83710510	G	A	83710510	3	1	77	1	0	0	0	0	1	0	0	0	1540	1232	43	3	636	3	BTBD1	15	83710510	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3237105	83710510	18820882	870	22606										
AGBL1	123624	broad.mit.edu	37	chr15	86940645	86940645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgagttcatccaggagagaGcaatgccagttgggtgatga	14	7	1	3	rs140873349	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:86940645G>A	ENST00000441037.2	+	17	2380	c.2285G>A	c.(2284-2286)aGc>aAc	p.S762N	AGBL1_ENST00000421325.2_Missense_Mutation_p.S762N|AGBL1_ENST00000389298.3_Missense_Mutation_p.S493N	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	762					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.S762N(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CCAGGAGAGAGCAATGCCAGT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	15											132	128	130					15																	86940645		1983	4157	6140	84741649	SO:0001583	missense	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2285G>A	15.37:g.86940645G>A	ENSP00000413001:p.Ser762Asn		84741649	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967748	0.74131	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10668	2.85;2.85	5.49	5.49	0.81192	Peptidase M14, carboxypeptidase A (1);	0.133888	0.50627	D	0.000107	T	0.35008	0.0917	M	0.81497	2.545	0.29376	N	0.863674	D	0.89917	1.0	D	0.79784	0.993	T	0.21930	-1.0231	10	0.87932	D	0	-20.8066	14.3551	0.66733	0.0:0.1478:0.8522:0.0	.	762	Q96MI9	CBPC4_HUMAN	N	791;762;493	ENSP00000397173:S762N;ENSP00000373949:S493N	ENSP00000373949:S493N	S	+	2	0	AGBL1	84741649	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.134000	0.50538	2.733000	0.93635	0.655000	0.94253	AGC		0.453	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	86940645	G	A	86940645	3	1	77	1	0	0	0	0	1	0	0	0	375	971	34	3	2347	3	AGBL1	15	86940645	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3230135	86940645	15590747	871	22607										
RLBP1	6017	broad.mit.edu	37	chr15	89760482	89760482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcccccgaggccgcctgcGcctgcaccatctcctgcagc	9	22	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:89760482G>A	ENST00000268125.5	-	5	654	c.215C>T	c.(214-216)gCg>gTg	p.A72V		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	72					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.A72V(2)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	GGCCGCCTGCGCCTGCACCAT	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	15											66	66	66					15																	89760482		2200	4299	6499	87561486	SO:0001583	missense	6017			BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.215C>T	15.37:g.89760482G>A	ENSP00000268125:p.Ala72Val		87561486	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.424948	0.43020	.	.	ENSG00000140522	ENST00000268125	D	0.88818	-2.43	5.03	-3.3	0.05003	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.357463	0.32120	N	0.006555	T	0.79782	0.4505	L	0.31157	0.91	0.32085	N	0.592676	B	0.27166	0.17	B	0.20955	0.032	T	0.66476	-0.5914	10	0.52906	T	0.07	-12.9063	13.9826	0.64315	0.0:0.0762:0.1304:0.7935	.	72	P12271	RLBP1_HUMAN	V	72	ENSP00000268125:A72V	ENSP00000268125:A72V	A	-	2	0	RLBP1	87561486	1.000000	0.71417	0.177000	0.23020	0.793000	0.44817	1.783000	0.38664	-0.854000	0.04131	-1.431000	0.01090	GCG		0.652	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		A	89760482	G	A	89760482	3	1	77	1	0	0	0	0	1	0	0	0	13425	1087	38	1	758	1	RLBP1	15	89760482	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2819837	89760482	12770910	872	22608										
RHCG	51458	broad.mit.edu	37	chr15	90021158	90021158	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgagcatcatctcagcagcGgtacccacggccacccctcc	8	18	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:90021158G>A	ENST00000268122.4	-	6	953	c.885C>T	c.(883-885)acC>acT	p.T295T	RHCG_ENST00000544600.1_Silent_p.T295T	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	295					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.T295T(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					TCTCAGCAGCGGTACCCACGG	0.617																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	15											63	60	61					15																	90021158		2200	4299	6499	87822162	SO:0001819	synonymous_variant	51458			AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.885C>T	15.37:g.90021158G>A			87822162	A8K4D4|Q6X3Y4	Silent	SNP	ENST00000268122.4	37	CCDS10351.1																																																																																				0.617	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		A	90021158	G	A	90021158	2	1	77	1	0	0	0	0	0	0	0	1	13363	1103	39	1		1	RHCG	15	90021158	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	260676	90021158	12510234	873	22609										
ZNF710	374655	broad.mit.edu	37	chr15	90611710	90611710	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacaagtccttccactaccgCagccagttgcagaaccacat	7	15	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:90611710C>T	ENST00000268154.4	+	2	1592	c.1341C>T	c.(1339-1341)cgC>cgT	p.R447R		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	447					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R447R(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			TCCACTACCGCAGCCAGTTGC	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	15											145	124	131					15																	90611710		2200	4298	6498	88412714	SO:0001819	synonymous_variant	374655			AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"Zinc fingers, C2H2-type"	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.1341C>T	15.37:g.90611710C>T			88412714	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																				0.602	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526		T	90611710	C	T	90611710	2	4	77	1	0	0	0	0	0	0	0	1	18154	697	25	3		3	ZNF710	15	90611710	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	590552	90611710	11919682	874	22610										
NGRN	51335	broad.mit.edu	37	chr15	90809018	90809018	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgctgtgggttcgcgacccGgggggtggcgggcccaggcc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:90809018delG	ENST00000379095.3	+	1	82	c.74delG	c.(73-75)cggfs	p.R25fs	RP11-697E2.6_ENST00000561573.1_Intron|NGRN_ENST00000331497.3_3'UTR	NM_001033088.1	NP_001028260.2	Q9NPE2	NGRN_HUMAN	neugrin, neurite outgrowth associated	25					neuron differentiation (GO:0030182)	extracellular region (GO:0005576)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.V27fs*31(1)		kidney(2)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			TTCGCGACCCGGGGGGTGGCG	0.692																																																1	Deletion - Frameshift(1)	large_intestine(1)	15											12	16	15					15																	90809018		2161	4252	6413	88610022	SO:0001589	frameshift_variant	51335			AB029315	CCDS32329.1	15q26.1	2008-02-05			ENSG00000182768	ENSG00000182768			18077	protein-coding gene	gene with protein product						11118320	Standard	NR_028052		Approved	DSC92	uc002bpf.1	Q9NPE2	OTTHUMG00000149807	ENST00000379095.3:c.74delG	15.37:g.90809018delG	ENSP00000368389:p.Arg25fs		88610022	B2R6M8|Q4V9L7|Q9HBL4	Frame_Shift_Del	DEL	ENST00000379095.3	37	CCDS32329.1																																																																																				0.692	NGRN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313418.1			-	90809018	G	-	90809018	7	5	77	1	0	1	0	1	0	0	0	0	10430	1116	39	0	76	0	NGRN	15	90809018	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	197308	90809018	11722374	875	22611										
IGF1R	3480	broad.mit.edu	37	chr15	99459970	99459970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtcacagagaaccccaagaCtgaggtgtgtggtggggaga	17	7	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:99459970C>T	ENST00000268035.6	+	10	2677	c.2066C>T	c.(2065-2067)aCt>aTt	p.T689I	IGF1R_ENST00000558762.1_Missense_Mutation_p.T689I	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	689	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.T689I(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	AACCCCAAGACTGAGGTGTGT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	15											78	79	79					15																	99459970		2197	4297	6494	97277493	SO:0001583	missense	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2066C>T	15.37:g.99459970C>T	ENSP00000268035:p.Thr689Ile		97277493	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737510	0.49045	.	.	ENSG00000140443	ENST00000268035	T	0.69306	-0.39	5.07	5.07	0.68467	Fibronectin, type III (3);	0.104565	0.40728	N	0.001040	T	0.49695	0.1572	N	0.08118	0	0.47698	D	0.999495	B;B	0.22983	0.078;0.011	B;B	0.19946	0.021;0.027	T	0.46034	-0.9220	10	0.40728	T	0.16	.	18.6358	0.91378	0.0:1.0:0.0:0.0	.	689;689	C9J5X1;P08069	.;IGF1R_HUMAN	I	689	ENSP00000268035:T689I	ENSP00000268035:T689I	T	+	2	0	IGF1R	97277493	1.000000	0.71417	0.940000	0.37924	0.437000	0.31866	4.715000	0.61909	2.631000	0.89168	0.655000	0.94253	ACT		0.532	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		T	99459970	C	T	99459970	3	4	77	1	0	0	0	0	1	0	0	0	7592	565	20	3	2104	3	IGF1R	15	99459970	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	8650952	99459970	3071422	876	22612										
LRRC28	123355	broad.mit.edu	37	chr15	99828112	99828112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtcgtctgagagctttacGtcatcttcgattagctaata	9	8	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:99828112G>A	ENST00000301981.3	+	5	581	c.341G>A	c.(340-342)cGt>cAt	p.R114H	LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000422500.2_Missense_Mutation_p.R114H|LRRC28_ENST00000447360.2_Missense_Mutation_p.R114H|LRRC28_ENST00000442993.2_Missense_Mutation_p.R114H|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000559399.1_3'UTR	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	114								p.R114H(1)		endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			AGAGCTTTACGTCATCTTCGA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	15											158	153	155					15																	99828112		2197	4297	6494	97645635	SO:0001583	missense	123355			AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.341G>A	15.37:g.99828112G>A	ENSP00000304923:p.Arg114His		97645635	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	37	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982676	0.74474	.	.	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500;ENST00000442993	T;T;T;T	0.65178	-0.14;-0.14;1.3;1.86	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.75125	0.3807	L	0.47016	1.485	0.80722	D	1	B;B;D	0.89917	0.017;0.013;1.0	B;B;D	0.81914	0.008;0.004;0.995	T	0.75124	-0.3428	10	0.59425	D	0.04	.	18.6354	0.91376	0.0:0.0:1.0:0.0	.	114;114;114	B4DHL3;Q86X40-2;Q86X40	.;.;LRC28_HUMAN	H	114	ENSP00000304923:R114H;ENSP00000404520:R114H;ENSP00000398606:R114H;ENSP00000404206:R114H	ENSP00000304923:R114H	R	+	2	0	LRRC28	97645635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.957000	0.93082	2.741000	0.93983	0.585000	0.79938	CGT		0.378	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		A	99828112	G	A	99828112	3	1	77	1	0	0	0	0	1	0	0	0	9011	1145	40	1	355	1	LRRC28	15	99828112	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	368142	99828112	2703280	877	22613										
LRRK1	79705	broad.mit.edu	37	chr15	101597218	101597218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagttccggcgactgcaggCgctcatgatggagtgctggg	17	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr15:101597218C>T	ENST00000388948.3	+	28	4849	c.4490C>T	c.(4489-4491)gCg>gTg	p.A1497V	LRRK1_ENST00000284395.5_Missense_Mutation_p.A1494V|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.A1509V(1)|p.A1497V(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	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)			CGACTGCAGGCGCTCATGATG	0.637																																																2	Substitution - Missense(2)	large_intestine(2)	15											63	73	70					15																	101597218		2011	4174	6185	99414741	SO:0001583	missense	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4490C>T	15.37:g.101597218C>T	ENSP00000373600:p.Ala1497Val		99414741		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	c	9.587	1.125200	0.20959	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	D;D	0.93659	-3.26;-3.26	5.05	4.13	0.48395	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.571183	0.19347	N	0.116506	D	0.88980	0.6585	L	0.48877	1.53	0.31140	N	0.706712	B	0.11235	0.004	B	0.08055	0.003	D	0.84873	0.0826	10	0.42905	T	0.14	.	8.018	0.30393	0.1591:0.7601:0.0:0.0808	.	1497	Q38SD2	LRRK1_HUMAN	V	1497;1494;188;51	ENSP00000373600:A1497V;ENSP00000284395:A1494V	ENSP00000284395:A1494V	A	+	2	0	LRRK1	99414741	0.187000	0.23238	0.788000	0.31933	0.190000	0.23558	0.715000	0.25822	2.351000	0.79841	0.486000	0.48141	GCG		0.637	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101597218	C	T	101597218	3	4	77	1	0	0	0	0	1	0	0	0	9061	768	27	1	4596	1	LRRK1	15	101597218	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1769106	101597218	934174	878	22614										
TMEM8A	58986	broad.mit.edu	37	chr16	426265	426265	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccaggggctggaagtgcacCgacaccacgtccatgtcctc	11	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:426265C>A	ENST00000431232.2	-	6	1255	c.1095G>T	c.(1093-1095)tcG>tcT	p.S365S	TMEM8A_ENST00000476735.1_5'Flank|TMEM8A_ENST00000250930.3_Silent_p.S172S	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	365					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)		p.S365S(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GGAAGTGCACCGACACCACGT	0.672																																																1	Substitution - coding silent(1)	large_intestine(1)	16											100	78	85					16																	426265		2201	4300	6501	366266	SO:0001819	synonymous_variant	58986			AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1095G>T	16.37:g.426265C>A			366266	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																				0.672	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		A	426265	C	A	426265	2	1	77	1	0	0	0	0	0	0	0	1	16253	639	23	2		2	TMEM8A	16	426265	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		426265	89928488	879	22615										
UNKL	64718	broad.mit.edu	37	chr16	1453205	1453205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcggccgcaggtccagggggCcgtgcgcgaaggcacagtgc	19	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:1453205C>T	ENST00000389221.4	-	3	427	c.428G>A	c.(427-429)gGc>gAc	p.G143D	UNKL_ENST00000301712.5_Missense_Mutation_p.G143D|UNKL_ENST00000397462.1_Missense_Mutation_p.G230D|UNKL_ENST00000508903.2_Missense_Mutation_p.G143D|UNKL_ENST00000503648.1_5'UTR	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	143					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.G143D(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				GTCCAGGGGGCCGTGCGCGAA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	16											168	113	132					16																	1453205		2199	4300	6499	1393206	SO:0001583	missense	64718			BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.428G>A	16.37:g.1453205C>T	ENSP00000373873:p.Gly143Asp		1393206	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	37	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721840	0.89298	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.75260	-0.92	3.81	3.81	0.43845	.	0.109124	0.64402	D	0.000007	D	0.85944	0.5815	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.87998	0.2754	10	0.66056	D	0.02	.	13.5612	0.61790	0.0:1.0:0.0:0.0	.	143	Q9H9P5-5	.	D	143;143;230;143	ENSP00000373873:G143D	ENSP00000301712:G143D	G	-	2	0	UNKL	1393206	1.000000	0.71417	0.944000	0.38274	0.900000	0.52787	7.286000	0.78671	2.118000	0.64928	0.462000	0.41574	GGC		0.627	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		T	1453205	C	T	1453205	3	4	77	1	0	0	0	0	1	0	0	0	17041	739	26	3	1136	3	UNKL	16	1453205	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1026940	1453205	88901548	880	22616										
CLCN7	1186	broad.mit.edu	37	chr16	1505228	1505228	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaacaaaattcagggtgaaCgtggagatcatggaagcaaa	12	5	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:1505228C>T	ENST00000382745.4	-	12	1610	c.1005G>A	c.(1003-1005)acG>acA	p.T335T	CLCN7_ENST00000262318.8_Silent_p.T311T|CLCN7_ENST00000448525.1_Silent_p.T311T|LA16c-390E6.4_ENST00000563610.1_RNA	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	335					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.T335T(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				TCAGGGTGAACGTGGAGATCA	0.577																																																1	Substitution - coding silent(1)	large_intestine(1)	16											157	142	147					16																	1505228		2199	4300	6499	1445229	SO:0001819	synonymous_variant	1186			Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive"	2025	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 63"	602727	"chloride channel 7"			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1005G>A	16.37:g.1505228C>T			1445229	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																				0.577	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1505228	C	T	1505228	2	4	77	1	0	0	0	0	0	0	0	1	3474	523	19	1		1	CLCN7	16	1505228	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	52023	1505228	88849525	881	22617										
IFT140	9742	broad.mit.edu	37	chr16	1568241	1568241	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtattcctccttccgcacGtagtgctccaccaggaagcc	9	15	0	0	rs111494974	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:1568241G>A	ENST00000426508.2	-	30	4521	c.4158C>T	c.(4156-4158)taC>taT	p.Y1386Y	IFT140_ENST00000361339.5_Silent_p.Y580Y	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1386					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.Y1386Y(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CCTTCCGCACGTAGTGCTCCA	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G		1,4397	2.1+/-5.4	0,1,2198	96	70	79		4158	1.6	0.2	16	dbSNP_132	79	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	IFT140	NM_014714.3		0,2,6497	AA,AG,GG		0.0116,0.0227,0.0154		1386/1463	1568241	2,12996	2199	4300	6499	1508242	SO:0001819	synonymous_variant	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.4158C>T	16.37:g.1568241G>A			1508242	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				0.582	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1568241	G	A	1568241	2	1	77	1	0	0	0	0	0	0	0	1	7577	1140	40	1		1	IFT140	16	1568241	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	63013	1568241	88786512	882	22618										
IFT140	9742	broad.mit.edu	37	chr16	1573848	1573848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttgtggtacagcatgaccGccctgtccatctgcacgccc	9	17	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:1573848G>A	ENST00000426508.2	-	25	3614	c.3251C>T	c.(3250-3252)gCg>gTg	p.A1084V	IFT140_ENST00000361339.5_Missense_Mutation_p.A278V	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1084					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.A1084E(1)|p.A1084V(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CAGCATGACCGCCCTGTCCAT	0.672																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	16											75	57	63					16																	1573848		2199	4300	6499	1513849	SO:0001583	missense	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.3251C>T	16.37:g.1573848G>A	ENSP00000406012:p.Ala1084Val		1513849	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511808	0.85389	.	.	ENSG00000187535	ENST00000397417;ENST00000361339;ENST00000426508	T;T	0.54866	0.55;0.55	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.79246	0.4413	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.991	T	0.82665	-0.0345	10	0.72032	D	0.01	.	19.8599	0.96779	0.0:0.0:1.0:0.0	.	1084;771	Q96RY7;B4DR58	IF140_HUMAN;.	V	1084;278;1084	ENSP00000354895:A278V;ENSP00000406012:A1084V	ENSP00000354895:A278V	A	-	2	0	IFT140	1513849	1.000000	0.71417	0.960000	0.40013	0.257000	0.26127	9.787000	0.99055	2.710000	0.92621	0.655000	0.94253	GCG		0.672	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1573848	G	A	1573848	3	1	77	1	0	0	0	0	1	0	0	0	7577	1087	38	1	1165	1	IFT140	16	1573848	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5607	1573848	88780905	883	22619										
MAPK8IP3	23162	broad.mit.edu	37	chr16	1812463	1812463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggagctgcaggaggctgtgCggtggactgagatgatcagg	19	6	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:1812463C>T	ENST00000250894.4	+	14	1805	c.1648C>T	c.(1648-1650)Cgg>Tgg	p.R550W	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.R544W	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	550					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)	p.R550W(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GGAGGCTGTGCGGTGGACTGA	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	16											56	69	64					16																	1812463		2169	4274	6443	1752464	SO:0001583	missense	23162			AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1648C>T	16.37:g.1812463C>T	ENSP00000250894:p.Arg550Trp		1752464	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	37	CCDS10442.2	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485164	0.84854	.	.	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.18960	2.18;2.18	5.72	-2.13	0.07144	.	0.055013	0.64402	D	0.000001	T	0.44932	0.1317	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.57476	-0.7805	10	0.87932	D	0	-34.2967	17.0589	0.86541	0.6741:0.3259:0.0:0.0	.	551;544;550	B7ZMF3;E9PFH7;Q9UPT6	.;.;JIP3_HUMAN	W	550;544	ENSP00000250894:R550W;ENSP00000348290:R544W	ENSP00000250894:R550W	R	+	1	2	MAPK8IP3	1752464	0.991000	0.36638	0.997000	0.53966	0.996000	0.88848	1.113000	0.31184	-0.149000	0.11215	0.655000	0.94253	CGG		0.672	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		T	1812463	C	T	1812463	3	4	77	1	0	0	0	0	1	0	0	0	9316	759	27	1	1718	1	MAPK8IP3	16	1812463	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	238615	1812463	88542290	884	22620										
TSC2	7249	broad.mit.edu	37	chr16	2100432	2100432	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaatgtggcctcaacaatcGcatccggatgatagggcaga	13	9	1	2	rs397515042|rs397514949		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:2100432G>A	ENST00000219476.3	+	3	800	c.170G>A	c.(169-171)cGc>cAc	p.R57H	NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000568454.1_Missense_Mutation_p.R68H|TSC2_ENST00000401874.2_Missense_Mutation_p.R57H|TSC2_ENST00000439673.2_Missense_Mutation_p.R57H|TSC2_ENST00000382538.6_Missense_Mutation_p.R8H|TSC2_ENST00000350773.4_Missense_Mutation_p.R57H|TSC2_ENST00000353929.4_Missense_Mutation_p.R57H	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	57	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)	p.R57H(2)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CTCAACAATCGCATCCGGATG	0.468			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																													yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	2	Substitution - Missense(2)	large_intestine(2)	16											90	87	88					16																	2100432		2198	4300	6498	2040433	SO:0001583	missense	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.170G>A	16.37:g.2100432G>A	ENSP00000219476:p.Arg57His		2040433	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802152	0.90538	.	.	ENSG00000103197	ENST00000219476;ENST00000432909;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773;ENST00000445113	D;D;D;T;D;D	0.89196	-2.48;-2.48;-2.48;-0.14;-2.48;-2.48	4.78	4.78	0.61160	Armadillo-type fold (1);Tuberin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94427	0.8207	M	0.77486	2.375	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.917;1.0;0.998;0.996	D	0.95241	0.8351	10	0.87932	D	0	-21.1781	17.808	0.88607	0.0:0.0:1.0:0.0	.	8;57;57;57;57;57	B4DIL8;P49815-6;B7Z2B8;P49815-4;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	H	57;8;57;57;57;8;57;68	ENSP00000219476:R57H;ENSP00000384468:R57H;ENSP00000248099:R57H;ENSP00000399232:R57H;ENSP00000371978:R8H;ENSP00000344383:R57H	ENSP00000219476:R57H	R	+	2	0	TSC2	2040433	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	8.804000	0.91921	2.195000	0.70347	0.407000	0.27541	CGC		0.468	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2100432	G	A	2100432	3	1	77	1	0	0	0	0	1	0	0	0	16646	1087	38	1	176	1	TSC2	16	2100432	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	287969	2100432	88254321	885	22621										
ABCA3	21	broad.mit.edu	37	chr16	2347505	2347505	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atggccctcctggagatggcGtccatgcccgaggtgggctc	15	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:2347505G>A	ENST00000301732.5	-	17	2788	c.2088C>T	c.(2086-2088)gaC>gaT	p.D696D	ABCA3_ENST00000382381.3_Silent_p.D638D	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	696	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.D696D(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	TGGAGATGGCGTCCATGCCCG	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	16											130	100	110					16																	2347505		2198	4300	6498	2287506	SO:0001819	synonymous_variant	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2088C>T	16.37:g.2347505G>A			2287506	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																				0.637	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2347505	G	A	2347505	2	1	77	1	0	0	0	0	0	0	0	1	33	1136	40	1		1	ABCA3	16	2347505	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	247073	2347505	88007248	886	22622										
CREBBP	1387	broad.mit.edu	37	chr16	3778018	3778018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggacaggggctggagaccGcacctggttactaagggacg	16	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:3778018G>A	ENST00000262367.5	-	31	7839	c.7030C>T	c.(7030-7032)Cgg>Tgg	p.R2344W	CREBBP_ENST00000382070.3_Missense_Mutation_p.R2306W	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2344					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R2344W(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GCTGGAGACCGCACCTGGTTA	0.652			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - Missense(1)	large_intestine(1)	16											87	85	86					16																	3778018		2197	4300	6497	3718019	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7030C>T	16.37:g.3778018G>A	ENSP00000262367:p.Arg2344Trp		3718019	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	10.65	1.410180	0.25465	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.86432	-2.12;-2.06	5.35	4.39	0.52855	.	0.249697	0.35067	N	0.003479	D	0.87309	0.6145	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.58970	0.719;0.849	D	0.88682	0.3203	10	0.62326	D	0.03	-13.798	14.8448	0.70251	0.0:0.0:0.8552:0.1448	.	2374;2344	Q4LE28;Q92793	.;CBP_HUMAN	W	2344;2374;2306;879	ENSP00000262367:R2344W;ENSP00000371502:R2306W	ENSP00000262367:R2344W	R	-	1	2	CREBBP	3718019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.584000	0.74057	1.369000	0.46134	0.655000	0.94253	CGG		0.652	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3778018	G	A	3778018	3	1	77	1	0	0	0	0	1	0	0	0	3867	1086	38	1	302	1	CREBBP	16	3778018	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1430513	3778018	86576735	887	22623										
CREBBP	1387	broad.mit.edu	37	chr16	3820703	3820703	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggctgctgcctggactgtAggggtgctctgggtttgggt	19	7	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:3820703A>G	ENST00000262367.5	-	14	3557	c.2748T>C	c.(2746-2748)ccT>ccC	p.P916P	CREBBP_ENST00000382070.3_Silent_p.P878P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	916					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.P916P(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCTGGACTGTAGGGGTGCTCT	0.647			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - coding silent(1)	large_intestine(1)	16											64	69	67					16																	3820703		2197	4300	6497	3760704	SO:0001819	synonymous_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.2748T>C	16.37:g.3820703A>G			3760704	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.647	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3820703	A	G	3820703	2	3	77	1	0	0	0	0	0	0	0	1	3867	407	15	4		4	CREBBP	16	3820703	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	42685	3820703	86534050	888	22624										
CREBBP	1387	broad.mit.edu	37	chr16	3828111	3828111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatgccttgtttatgtaaacGcgacctccgtttttcttcta	7	10	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:3828111G>A	ENST00000262367.5	-	10	2823	c.2014C>T	c.(2014-2016)Cgt>Tgt	p.R672C	CREBBP_ENST00000382070.3_Missense_Mutation_p.R634C	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	672					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R672C(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTATGTAAACGCGACCTCCGT	0.433			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - Missense(1)	large_intestine(1)	16											117	135	129					16																	3828111		2197	4300	6497	3768112	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.2014C>T	16.37:g.3828111G>A	ENSP00000262367:p.Arg672Cys		3768112	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665632	0.67700	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.87571	-2.27;-2.19	5.73	5.73	0.89815	Coactivator CBP, KIX (1);	0.000000	0.85682	D	0.000000	D	0.93462	0.7914	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.96;1.0	D	0.93310	0.6684	10	0.87932	D	0	-12.1168	20.2786	0.98501	0.0:0.0:1.0:0.0	.	702;672	Q4LE28;Q92793	.;CBP_HUMAN	C	672;702;634	ENSP00000262367:R672C;ENSP00000371502:R634C	ENSP00000262367:R672C	R	-	1	0	CREBBP	3768112	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.840000	0.86819	2.868000	0.98415	0.557000	0.71058	CGT		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3828111	G	A	3828111	3	1	77	1	0	0	0	0	1	0	0	0	3867	1087	38	1	5402	1	CREBBP	16	3828111	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7408	3828111	86526642	889	22625										
DNAJA3	9093	broad.mit.edu	37	chr16	4492299	4492299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agttgacattcaatcaagctGcaaagggggtcaacaaggag	12	7	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:4492299G>A	ENST00000262375.6	+	5	738	c.661G>A	c.(661-663)Gca>Aca	p.A221T	DNAJA3_ENST00000431375.2_Missense_Mutation_p.A68T|DNAJA3_ENST00000355296.4_Missense_Mutation_p.A221T	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	221					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)	p.A221T(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						CAATCAAGCTGCAAAGGGGGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	16											112	103	106					16																	4492299		2197	4300	6497	4432300	SO:0001583	missense	9093			AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"Heat shock proteins / DNAJ (HSP40)"	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.661G>A	16.37:g.4492299G>A	ENSP00000262375:p.Ala221Thr		4432300	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Missense_Mutation	SNP	ENST00000262375.6	37	CCDS10515.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.995188	0.93167	.	.	ENSG00000103423	ENST00000262375;ENST00000355296;ENST00000431375	T;T;T	0.66280	-0.2;-0.19;0.77	5.43	4.46	0.54185	HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.79741	0.4498	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	0.991;1.0;0.999	P;D;D	0.74023	0.873;0.982;0.919	T	0.82678	-0.0338	10	0.66056	D	0.02	-17.128	13.681	0.62484	0.0758:0.0:0.9242:0.0	.	68;221;221	E7ES32;Q96EY1-2;Q96EY1	.;.;DNJA3_HUMAN	T	221;221;68	ENSP00000262375:A221T;ENSP00000347445:A221T;ENSP00000393970:A68T	ENSP00000262375:A221T	A	+	1	0	DNAJA3	4432300	1.000000	0.71417	0.990000	0.47175	0.758000	0.43043	9.749000	0.98871	2.549000	0.85964	0.467000	0.42956	GCA		0.517	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1			A	4492299	G	A	4492299	3	1	77	1	0	0	0	0	1	0	0	0	4624	1319	46	3	679	3	DNAJA3	16	4492299	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	664188	4492299	85862454	890	22626										
ABCC6	368	broad.mit.edu	37	chr16	16248815	16248815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgatccagatcccaccctcaGctgcctcctggagccgcagc	9	19	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:16248815G>A	ENST00000205557.7	-	28	3985	c.3956C>T	c.(3955-3957)gCt>gTt	p.A1319V		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1319	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.A1319V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCCACCCTCAGCTGCCTCCTG	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	16											21	19	19					16																	16248815		2197	4295	6492	16156316	SO:0001583	missense	368			AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3956C>T	16.37:g.16248815G>A	ENSP00000205557:p.Ala1319Val		16156316	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231190	0.58777	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.94000	-3.33	4.53	3.55	0.40652	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.300521	0.23032	U	0.052730	D	0.91938	0.7447	N	0.12746	0.255	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66979	0.948;0.948	D	0.92172	0.5744	10	0.66056	D	0.02	.	12.6145	0.56569	0.0838:0.0:0.9162:0.0	.	1319;1319	O95255;A8Y988	MRP6_HUMAN;.	V	1319;257	ENSP00000205557:A1319V	ENSP00000205557:A1319V	A	-	2	0	ABCC6	16156316	1.000000	0.71417	0.072000	0.20136	0.266000	0.26442	7.952000	0.87827	0.868000	0.35678	0.465000	0.42564	GCT		0.682	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			A	16248815	G	A	16248815	3	1	77	1	0	0	0	0	1	0	0	0	57	971	34	3	571	3	ABCC6	16	16248815	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	11756516	16248815	74105938	891	22627										
ABCC6	368	broad.mit.edu	37	chr16	16291966	16291966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgctctcggtcagccgctgcAcgtccacggacaccagattg	11	16	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:16291966A>G	ENST00000205557.7	-	10	1279	c.1250T>C	c.(1249-1251)gTg>gCg	p.V417A	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	417	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		V -> M. {ECO:0000269|PubMed:19339160}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.V417A(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CAGCCGCTGCACGTCCACGGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	16											72	50	57					16																	16291966		2197	4299	6496	16199467	SO:0001583	missense	368			AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1250T>C	16.37:g.16291966A>G	ENSP00000205557:p.Val417Ala		16199467	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	A	1.179	-0.638665	0.03557	.	.	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	D;D	0.91011	-2.77;-2.77	4.4	4.4	0.53042	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.168636	0.26948	U	0.021698	D	0.82609	0.5074	N	0.19112	0.55	0.80722	D	1	B;P	0.48294	0.295;0.908	B;P	0.46253	0.132;0.509	T	0.81102	-0.1085	10	0.02654	T	1	.	11.4469	0.50129	1.0:0.0:0.0:0.0	.	429;417	F5GWQ0;O95255	.;MRP6_HUMAN	A	417;417;429	ENSP00000205557:V417A;ENSP00000405002:V417A	ENSP00000205557:V417A	V	-	2	0	ABCC6	16199467	0.995000	0.38212	0.986000	0.45419	0.213000	0.24496	4.975000	0.63777	1.746000	0.51805	0.459000	0.35465	GTG		0.622	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			G	16291966	A	G	16291966	3	3	77	1	0	0	0	0	1	0	0	0	57	159	6	4	3349	4	ABCC6	16	16291966	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	43151	16291966	74062787	892	22628										
SMG1	23049	broad.mit.edu	37	chr16	18869532	18869532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgattctggtacatagtataCcttaatgcctgcatccatgg	8	9	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:18869532C>T	ENST00000446231.2	-	29	4606	c.4194G>A	c.(4192-4194)agG>agA	p.R1398R	SMG1_ENST00000389467.3_Silent_p.R1398R			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1398	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R1394R(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACATAGTATACCTTAATGCCT	0.353																																																1	Substitution - coding silent(1)	large_intestine(1)	16											43	40	41					16																	18869532		1825	4073	5898	18777033	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4194G>A	16.37:g.18869532C>T			18777033	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.353	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18869532	C	T	18869532	2	4	77	1	0	0	0	0	0	0	0	1	14832	506	18	3		3	SMG1	16	18869532	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2577566	18869532	71485221	893	22629										
GPRC5B	51704	broad.mit.edu	37	chr16	19873271	19873271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctttttcccaagctgccgTtgggaaatcctgctgttcgg	11	11	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:19873271T>C	ENST00000300571.2	-	3	1246	c.1055A>G	c.(1054-1056)aAc>aGc	p.N352S	GPRC5B_ENST00000537135.1_Missense_Mutation_p.N378S|GPRC5B_ENST00000569847.1_Missense_Mutation_p.N352S|GPRC5B_ENST00000569479.1_Missense_Mutation_p.N352S|GPRC5B_ENST00000535671.1_Missense_Mutation_p.N352S	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	352					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)	p.N352S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						CAAGCTGCCGTTGGGAAATCC	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	16											59	54	56					16																	19873271		2197	4300	6497	19780772	SO:0001583	missense	51704			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"GPCR / Class C : Orphans"	13308	protein-coding gene	gene with protein product		605948	"G protein-coupled receptor, family C, group 1, member B", "G protein-coupled receptor, family C, group 5, member B"			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.1055A>G	16.37:g.19873271T>C	ENSP00000300571:p.Asn352Ser		19780772	D2DFB0|O75205|Q8NBZ8	Missense_Mutation	SNP	ENST00000300571.2	37	CCDS10581.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821700	0.32237	.	.	ENSG00000167191	ENST00000300571;ENST00000535671;ENST00000538074;ENST00000537135	T;T;T	0.25085	1.84;1.83;1.82	5.38	5.38	0.77491	.	0.465288	0.24375	N	0.039073	T	0.19127	0.0459	L	0.33485	1.01	0.39712	D	0.971342	P;P	0.41313	0.745;0.612	B;B	0.34931	0.192;0.138	T	0.05818	-1.0862	9	.	.	.	.	14.5802	0.68282	0.0:0.0:0.0:1.0	.	378;352	B7Z831;Q9NZH0	.;GPC5B_HUMAN	S	352;352;201;378	ENSP00000300571:N352S;ENSP00000442858:N352S;ENSP00000441775:N378S	.	N	-	2	0	GPRC5B	19780772	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.824000	0.62701	2.038000	0.60285	0.533000	0.62120	AAC		0.517	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			C	19873271	T	C	19873271	3	2	77	1	0	0	0	0	1	0	0	0	6746	1725	60	4	164	4	GPRC5B	16	19873271	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1003739	19873271	70481482	894	22630										
OTOA	146183	broad.mit.edu	37	chr16	21737882	21737882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtcccagcctcccagtgtgTgccctttctgatcagcctgg	10	15	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:21737882T>C	ENST00000286149.4	+	18	1962	c.1961T>C	c.(1960-1962)gTg>gCg	p.V654A	OTOA_ENST00000388958.3_Missense_Mutation_p.V640A|OTOA_ENST00000388957.3_Missense_Mutation_p.V316A|OTOA_ENST00000388956.4_Missense_Mutation_p.V561A			Q7RTW8	OTOAN_HUMAN	otoancorin	654					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)		p.V640A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		TCCCAGTGTGTGCCCTTTCTG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	16											119	115	116					16																	21737882		2198	4300	6498	21645383	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1961T>C	16.37:g.21737882T>C	ENSP00000286149:p.Val654Ala		21645383	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	T	10.47	1.357974	0.24598	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957;ENST00000338456	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	5.06	0.273	0.15650	.	0.476160	0.18816	N	0.130376	T	0.73853	0.3640	L	0.59436	1.845	0.28973	N	0.889092	B;B;B;B	0.18310	0.027;0.027;0.012;0.027	B;B;B;B	0.17722	0.018;0.019;0.009;0.012	T	0.57510	-0.7799	10	0.11794	T	0.64	-6.8404	7.507	0.27551	0.0:0.375:0.0:0.625	.	654;561;316;640	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	A	640;654;561;316;49	ENSP00000373610:V640A;ENSP00000286149:V654A;ENSP00000373608:V561A;ENSP00000373609:V316A	ENSP00000286149:V654A	V	+	2	0	OTOA	21645383	0.994000	0.37717	0.971000	0.41717	0.935000	0.57460	0.270000	0.18607	-0.155000	0.11098	0.533000	0.62120	GTG		0.547	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			C	21737882	T	C	21737882	3	2	77	1	0	0	0	0	1	0	0	0	11333	1696	59	4	2035	4	OTOA	16	21737882	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1864611	21737882	68616871	895	22631										
VWA3A	146177	broad.mit.edu	37	chr16	22163838	22163838	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcccttccttccagagcggcGgttgagttcctgagaaagct	11	12	0	3	rs369659498		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:22163838G>A	ENST00000389398.5	+	31	3384	c.3288G>A	c.(3286-3288)gcG>gcA	p.A1096A	VWA3A_ENST00000563755.1_Silent_p.A198A|VWA3A_ENST00000389397.4_Silent_p.A198A	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	1096	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)		p.A292A(1)|p.A1096A(1)|p.A198A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CCAGAGCGGCGGTTGAGTTCC	0.587																																																3	Substitution - coding silent(3)	large_intestine(3)	16						G		0,4046		0,0,2023	33	36	35		3288	-3.4	0	16		35	2,8372		0,2,4185	no	coding-synonymous	VWA3A	NM_173615.3		0,2,6208	AA,AG,GG		0.0239,0.0,0.0161		1096/1185	22163838	2,12418	2023	4187	6210	22071339	SO:0001819	synonymous_variant	146177			AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.3288G>A	16.37:g.22163838G>A			22071339	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	37	CCDS45441.1																																																																																				0.587	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22163838	G	A	22163838	2	1	77	1	0	0	0	0	0	0	0	1	17280	1103	39	1		1	VWA3A	16	22163838	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	425956	22163838	68190915	896	22632										
POLR3E	55718	broad.mit.edu	37	chr16	22337150	22337150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaaggcccagcagaaccacGcgttgctggagcgggagctg	15	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:22337150G>A	ENST00000299853.5	+	18	1584	c.1417G>A	c.(1417-1419)Gcg>Acg	p.A473T	POLR3E_ENST00000418581.2_Missense_Mutation_p.A437T|POLR3E_ENST00000359210.4_Missense_Mutation_p.A473T|POLR3E_ENST00000564209.1_Missense_Mutation_p.A473T	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	473					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)	p.A473T(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		GCAGAACCACGCGTTGCTGGA	0.701																																																1	Substitution - Missense(1)	large_intestine(1)	16											25	24	24					16																	22337150		2196	4297	6493	22244651	SO:0001583	missense	55718			AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.1417G>A	16.37:g.22337150G>A	ENSP00000299853:p.Ala473Thr		22244651	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	37	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.567604	0.28003	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	T;T;T	0.43294	0.95;0.95;0.95	5.27	0.271	0.15640	.	0.636877	0.16035	N	0.232686	T	0.35828	0.0945	L	0.59436	1.845	0.09310	N	1	B;B;B;B;B;B	0.16603	0.011;0.001;0.001;0.002;0.001;0.018	B;B;B;B;B;B	0.14023	0.004;0.002;0.003;0.002;0.002;0.01	T	0.37291	-0.9712	10	0.87932	D	0	-4.0025	8.0988	0.30844	0.2411:0.123:0.6359:0.0	.	417;437;473;473;473;473	B4DDR0;B4DL24;B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;.;.;RPC5_HUMAN;.	T	473;473;437	ENSP00000299853:A473T;ENSP00000352140:A473T;ENSP00000399254:A437T	ENSP00000299853:A473T	A	+	1	0	POLR3E	22244651	0.000000	0.05858	0.007000	0.13788	0.949000	0.60115	0.253000	0.18296	0.164000	0.19529	0.462000	0.41574	GCG		0.701	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		A	22337150	G	A	22337150	3	1	77	1	0	0	0	0	1	0	0	0	12263	1087	38	1	1483	1	POLR3E	16	22337150	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	173312	22337150	68017603	897	22633										
USP31	57478	broad.mit.edu	37	chr16	23085170	23085170	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgctgtcatcgaagcagtaCcagaggccgtccacagagtt	11	12	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:23085170C>T	ENST00000219689.7	-	14	2207	c.2208G>A	c.(2206-2208)tgG>tgA	p.W736*	USP31_ENST00000567975.1_5'Flank	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	366	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.W736*(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CGAAGCAGTACCAGAGGCCGT	0.582																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											69	60	63					16																	23085170		2197	4300	6497	22992671	SO:0001587	stop_gained	57478			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2208G>A	16.37:g.23085170C>T	ENSP00000219689:p.Trp736*		22992671	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Nonsense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	C	40	8.345304	0.98769	.	.	ENSG00000103404	ENST00000219689;ENST00000381162	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.2368	19.2867	0.94077	0.0:1.0:0.0:0.0	.	.	.	.	X	736;39	.	ENSP00000219689:W736X	W	-	3	0	USP31	22992671	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.453000	0.80700	2.793000	0.96121	0.655000	0.94253	TGG		0.582	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		T	23085170	C	T	23085170	4	4	77	1	0	0	0	0	0	1	0	0	17102	508	18	3	1862	3	USP31	16	23085170	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	748020	23085170	67269583	898	22634										
COG7	91949	broad.mit.edu	37	chr16	23436214	23436214	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggcagcgagggcatgagggCccccagggtctgaatcagca							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:23436214delC	ENST00000307149.5	-	7	1050	c.865delG	c.(865-867)gccfs	p.A289fs		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	289					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.A289fs*54(1)		breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GGCATGAGGGCCCCCAGGGTC	0.627																																																1	Deletion - Frameshift(1)	large_intestine(1)	16											45	40	42					16																	23436214		2197	4300	6497	23343715	SO:0001589	frameshift_variant	91949			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.865delG	16.37:g.23436214delC	ENSP00000305442:p.Ala289fs		23343715	Q6UWU7	Frame_Shift_Del	DEL	ENST00000307149.5	37	CCDS10610.1																																																																																				0.627	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			-	23436214	C	-	23436214	7	5	77	1	0	1	0	1	0	0	0	0	3669	739	26	0	1491	0	COG7	16	23436214	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	351044	23436214	66918539	899	22635										
AQP8	343	broad.mit.edu	37	chr16	25232875	25232875	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actgggtctcacagctgctcGgggggatgctcggggctgcc					rs141164855	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:25232875delG	ENST00000219660.5	+	3	483	c.358delG	c.(358-360)gggfs	p.G121fs	AQP8_ENST00000566125.1_Frame_Shift_Del_p.G115fs	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	121					canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)	p.M122fs*10(2)		NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		ACAGCTGCTCGGGGGGATGCT	0.632																																																2	Deletion - Frameshift(2)	large_intestine(2)	16								0,4264		0,0,2132	76	73	74			-4.2	0.9	16		77	1,8253		0,1,4126	no	frameshift	AQP8	NM_001169.2		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080			25232875	1,12517	2197	4300	6497	25140376	SO:0001589	frameshift_variant	343			BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"Ion channels / Aquaporins"	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.358delG	16.37:g.25232875delG	ENSP00000219660:p.Gly121fs		25140376	Q8IUU3|Q9UIA4	Frame_Shift_Del	DEL	ENST00000219660.5	37	CCDS10626.1																																																																																				0.632	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169		-	25232875	G	-	25232875	7	5	77	1	0	1	0	1	0	0	0	0	832	1116	39	0	368	0	AQP8	16	25232875	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1796661	25232875	65121878	900	22636										
IL21R	50615	broad.mit.edu	37	chr16	27460065	27460065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgacagcccagaactcggggGgctcagcttacagtgaggag	15	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:27460065G>A	ENST00000337929.3	+	9	1551	c.1078G>A	c.(1078-1080)Ggc>Agc	p.G360S	IL21R_ENST00000395755.1_Missense_Mutation_p.G360S|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395754.4_Missense_Mutation_p.G360S|IL21R_ENST00000564089.1_Missense_Mutation_p.G360S	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	360					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)	p.G360S(1)		breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GAACTCGGGGGGCTCAGCTTA	0.617			T	BCL6	NHL																																		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	1	Substitution - Missense(1)	large_intestine(1)	16											58	57	57					16																	27460065		2197	4300	6497	27367566	SO:0001583	missense	50615			AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1078G>A	16.37:g.27460065G>A	ENSP00000338010:p.Gly360Ser		27367566	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	8.424	0.847169	0.17034	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.35048	1.33;1.33;1.33	5.19	0.659	0.17861	.	1.518340	0.03464	N	0.212721	T	0.23532	0.0569	N	0.25144	0.715	0.09310	N	1	B	0.13594	0.008	B	0.17722	0.019	T	0.16571	-1.0398	10	0.08179	T	0.78	-9.2395	7.0854	0.25254	0.4391:0.0:0.5609:0.0	.	360	Q9HBE5	IL21R_HUMAN	S	360	ENSP00000338010:G360S;ENSP00000379104:G360S;ENSP00000379103:G360S	ENSP00000338010:G360S	G	+	1	0	IL21R	27367566	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.195000	0.09546	-0.109000	0.12044	0.561000	0.74099	GGC		0.617	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		A	27460065	G	A	27460065	3	1	77	1	0	0	0	0	1	0	0	0	7692	1232	43	3	1108	3	IL21R	16	27460065	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2227190	27460065	62894688	901	22637										
KIAA0556	23247	broad.mit.edu	37	chr16	27720169	27720169	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacacaaagctttatgtgtcGccccacgatgtggatatccg	10	11	0	0	rs533574674	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:27720169G>A	ENST00000261588.4	+	13	1552	c.1533G>A	c.(1531-1533)tcG>tcA	p.S511S	CTD-2049O4.1_ENST00000564893.1_RNA|KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000563052.1_RNA|CTD-2049O4.1_ENST00000568831.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	511						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S511S(4)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TTTATGTGTCGCCCCACGATG	0.557													G|||	2	0.000399361	0.0015	0	5008	,	,		18123	0		0	False		,,,				2504	0															4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	16											91	80	84					16																	27720169		2197	4300	6497	27627670	SO:0001819	synonymous_variant	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1533G>A	16.37:g.27720169G>A			27627670	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																				0.557	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27720169	G	A	27720169	2	1	77	1	0	0	0	0	0	0	0	1	8204	1074	38	1		1	KIAA0556	16	27720169	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	260104	27720169	62634584	902	22638										
XPO6	23214	broad.mit.edu	37	chr16	28109919	28109919	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtctgtagtagcgcaggtcGttgaccagcctgtgcacatt	12	10	1	1	rs552706253		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:28109919G>A	ENST00000304658.5	-	24	3818	c.3318C>T	c.(3316-3318)aaC>aaT	p.N1106N	XPO6_ENST00000565698.1_Silent_p.N1092N	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	1106					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.N1106N(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						AGCGCAGGTCGTTGACCAGCC	0.612																																																2	Substitution - coding silent(2)	large_intestine(2)	16											71	86	81					16																	28109919		2150	4266	6416	28017420	SO:0001819	synonymous_variant	23214			AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.3318C>T	16.37:g.28109919G>A			28017420	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Silent	SNP	ENST00000304658.5	37	CCDS42135.1																																																																																				0.612	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28109919	G	A	28109919	2	1	77	1	0	0	0	0	0	0	0	1	17488	1136	40	1		1	XPO6	16	28109919	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	389750	28109919	62244834	903	22639										
LAT	27040	broad.mit.edu	37	chr16	28997749	28997749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccaccggacgccatcttccCggcgggattctgatggtggt	13	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:28997749C>T	ENST00000360872.5	+	5	370	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	LAT_ENST00000564277.1_Missense_Mutation_p.R97W|LAT_ENST00000563964.1_3'UTR|LAT_ENST00000395461.3_Missense_Mutation_p.R134W|LAT_ENST00000566177.1_Missense_Mutation_p.R97W|LAT_ENST00000354453.4_Splice_Site|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000454369.2_Missense_Mutation_p.R97W|LAT_ENST00000395456.2_Missense_Mutation_p.R98W|RP11-264B17.5_ENST00000561471.1_RNA			O43561	LAT_HUMAN	linker for activation of T cells	98					blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)	p.R98W(1)		large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				GCCATCTTCCCGGCGGGATTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	16											35	43	40					16																	28997749		2194	4298	6492	28905250	SO:0001583	missense	27040			AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761	ENST00000360872.5:c.292C>T	16.37:g.28997749C>T	ENSP00000354119:p.Arg98Trp		28905250	B7WPI0|C7C5T6|G5E9K3|O43919	Missense_Mutation	SNP	ENST00000360872.5	37	CCDS10647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.386|3.386	-0.125309|-0.125309	0.06795|0.06795	.|.	.|.	ENSG00000213658|ENSG00000213658	ENST00000354453|ENST00000395461;ENST00000395456;ENST00000454369;ENST00000360872	.|.	.|.	.|.	4.85|4.85	2.82|2.82	0.32997|0.32997	.|.	.|.	.|.	.|.	.|.	.|T	.|0.64494	.|0.2603	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0;0.999	.|D;D;D;D;P	.|0.76071	.|0.987;0.915;0.949;0.987;0.83	.|T	.|0.64206	.|-0.6462	.|8	.|0.87932	.|D	.|0	.|-3.1856	12.5872|12.5872	0.56424|0.56424	0.2972:0.7028:0.0:0.0|0.2972:0.7028:0.0:0.0	.|.	.|97;98;134;98;97	.|C7C5T6;O43561-2;B7WPI0;O43561;G5E9K3	.|.;.;.;LAT_HUMAN;.	.|W	-1|134;98;97;98	.|.	.|ENSP00000354119:R98W	.|R	+|+	.|1	.|2	LAT|LAT	28905250|28905250	0.487000|0.487000	0.25988|0.25988	0.978000|0.978000	0.43139|0.43139	0.107000|0.107000	0.19398|0.19398	0.876000|0.876000	0.28092|0.28092	0.175000|0.175000	0.19841|0.19841	-2.048000|-2.048000	0.00412|0.00412	.|CGG		0.647	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			T	28997749	C	T	28997749	3	4	77	1	0	0	0	0	1	0	0	0	8666	643	23	1	422	1	LAT	16	28997749	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	887830	28997749	61357004	904	22640										
SEZ6L2	26470	broad.mit.edu	37	chr16	29897009	29897009	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagaccccgctcggggacatCgtccatgtccgaatcataga	11	13	1	2	rs547134098		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:29897009C>T	ENST00000308713.5	-	8	1797	c.1270G>A	c.(1270-1272)Gat>Aat	p.D424N	SEZ6L2_ENST00000346932.5_Missense_Mutation_p.D310N|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.D380N|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.D354N|SEZ6L2_ENST00000562159.1_5'Flank	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	424	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.D424N(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCGGGGACATCGTCCATGTCC	0.592													c|||	1	0.000199681	0	0	5008	,	,		17068	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16											72	66	68					16																	29897009		2197	4300	6497	29804510	SO:0001583	missense	26470			AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1270G>A	16.37:g.29897009C>T	ENSP00000312550:p.Asp424Asn		29804510	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	c	26.9	4.777729	0.90195	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.85	5.85	0.93711	CUB (4);	0.000000	0.56097	D	0.000026	T	0.51398	0.1672	L	0.41710	1.295	0.52501	D	0.999952	P;D;D;D;D;D	0.61080	0.744;0.981;0.981;0.989;0.981;0.989	B;P;P;P;P;P	0.53035	0.115;0.468;0.524;0.668;0.468;0.716	T	0.30909	-0.9962	10	0.22109	T	0.4	.	17.1439	0.86761	0.0:1.0:0.0:0.0	.	380;424;310;354;424;354	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	N	354;424;310;380	ENSP00000310206:D354N;ENSP00000312550:D424N;ENSP00000319215:D310N;ENSP00000439412:D380N	ENSP00000312550:D424N	D	-	1	0	SEZ6L2	29804510	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.730000	0.62015	2.785000	0.95823	0.645000	0.84053	GAT		0.592	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		T	29897009	C	T	29897009	3	4	77	1	0	0	0	0	1	0	0	0	14181	884	31	1	1545	1	SEZ6L2	16	29897009	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	899260	29897009	60457744	905	22641										
TAOK2	9344	broad.mit.edu	37	chr16	29993015	29993015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accgctctttaacatgaatgCgatgagtgccttataccaca	7	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:29993015C>T	ENST00000308893.4	+	9	1732	c.689C>T	c.(688-690)gCg>gTg	p.A230V	TAOK2_ENST00000279394.3_Missense_Mutation_p.A230V|TAOK2_ENST00000543033.1_Missense_Mutation_p.A230V|TAOK2_ENST00000416441.2_Missense_Mutation_p.A57V	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)	p.A230V(1)		breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						AACATGAATGCGATGAGTGCC	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	16											165	141	149					16																	29993015		2197	4300	6497	29900516	SO:0001583	missense	9344			AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.689C>T	16.37:g.29993015C>T	ENSP00000310094:p.Ala230Val		29900516	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	37	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	C	34	5.332234	0.95733	.	.	ENSG00000149930	ENST00000416441;ENST00000308893;ENST00000543033;ENST00000279394	D;D;D	0.85339	-1.97;-1.97;-1.97	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85191	0.5640	N	0.11427	0.14	0.80722	D	1	D;D;P;P;P	0.89917	0.986;1.0;0.653;0.834;0.931	B;D;B;B;B	0.73708	0.235;0.981;0.076;0.228;0.235	D	0.84401	0.0560	9	.	.	.	.	19.0726	0.93145	0.0:1.0:0.0:0.0	.	414;57;230;230;230	Q86V37;Q9UL54-3;Q9UL54-2;A0PJ48;Q9UL54	.;.;.;.;TAOK2_HUMAN	V	230	ENSP00000310094:A230V;ENSP00000440336:A230V;ENSP00000279394:A230V	.	A	+	2	0	TAOK2	29900516	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.809000	0.96659	0.555000	0.69702	GCG		0.522	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29993015	C	T	29993015	3	4	77	1	0	0	0	0	1	0	0	0	15587	768	27	1	719	1	TAOK2	16	29993015	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	96006	29993015	60361738	906	22642										
ZNF768	79724	broad.mit.edu	37	chr16	30537159	30537159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgattcagggcttctgggtGcaaactcagggcttgggggc	16	9	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:30537159G>A	ENST00000380412.5	-	2	477	c.302C>T	c.(301-303)gCa>gTa	p.A101V	ZNF768_ENST00000562803.1_Missense_Mutation_p.A70V	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	101	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A101V(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						GCTTCTGGGTGCAAACTCAGG	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	16											34	41	39					16																	30537159		2164	4283	6447	30444660	SO:0001583	missense	79724			BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"Zinc fingers, C2H2-type"	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.302C>T	16.37:g.30537159G>A	ENSP00000369777:p.Ala101Val		30444660	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	37	CCDS10681.2	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113674	0.56398	.	.	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.06933	3.24	4.23	2.19	0.27852	.	0.000000	0.47093	D	0.000253	T	0.04137	0.0115	N	0.08118	0	0.28669	N	0.905747	B	0.15930	0.015	B	0.17098	0.017	T	0.33954	-0.9848	10	0.30854	T	0.27	-6.5435	8.7478	0.34598	0.0:0.144:0.5605:0.2955	.	101	Q9H5H4	ZN768_HUMAN	V	101;70	ENSP00000369777:A101V	ENSP00000369777:A101V	A	-	2	0	ZNF768	30444660	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	3.416000	0.52707	0.682000	0.31407	0.561000	0.74099	GCA		0.582	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671		A	30537159	G	A	30537159	3	1	77	1	0	0	0	0	1	0	0	0	18180	1319	46	3	1324	3	ZNF768	16	30537159	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	544144	30537159	59817594	907	22643										
ZNF668	79759	broad.mit.edu	37	chr16	31073319	31073319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagtccttgccgcacttctcGcagtggtatggcttcacccc	9	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:31073319G>A	ENST00000538906.1	-	3	1714	c.930C>T	c.(928-930)tgC>tgT	p.C310C	ZNF668_ENST00000535577.1_Silent_p.C310C|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000300849.4_Silent_p.C310C|ZNF668_ENST00000426488.2_Silent_p.C333C|ZNF668_ENST00000394983.2_Silent_p.C310C|ZNF668_ENST00000539836.3_Silent_p.C333C|ZNF668_ENST00000417110.2_Silent_p.S169S	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C310C(1)		breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGCACTTCTCGCAGTGGTATG	0.662																																					Colon(181;1111 1980 5060 10512 25785)											1	Substitution - coding silent(1)	large_intestine(1)	16											30	28	29					16																	31073319		2194	4293	6487	30980820	SO:0001819	synonymous_variant	79759				CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.930C>T	16.37:g.31073319G>A			30980820	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																				0.662	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		A	31073319	G	A	31073319	2	1	77	1	0	0	0	0	0	0	0	1	18114	1079	38	1		1	ZNF668	16	31073319	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	536160	31073319	59281434	908	22644										
BCKDK	10295	broad.mit.edu	37	chr16	31120887	31120887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgctggccgctctcaggacgGcagccaccttctggtaagat	12	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:31120887G>A	ENST00000394951.1	+	4	874	c.251G>A	c.(250-252)gGc>gAc	p.G84D	BCKDK_ENST00000287507.3_Missense_Mutation_p.G84D|BCKDK_ENST00000219794.6_Missense_Mutation_p.G84D|AC135050.1_ENST00000517000.2_RNA|BCKDK_ENST00000394950.3_Missense_Mutation_p.G84D			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	84					branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)	p.G84D(2)		breast(1)|stomach(1)	2						TCTCAGGACGGCAGCCACCTT	0.592																																																2	Substitution - Missense(2)	large_intestine(1)|breast(1)	16											59	55	57					16																	31120887		2197	4300	6497	31028388	SO:0001583	missense	10295			AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.251G>A	16.37:g.31120887G>A	ENSP00000378405:p.Gly84Asp		31028388	A8MY43|Q6FGL4|Q96G95|Q96IN5	Missense_Mutation	SNP	ENST00000394951.1	37	CCDS10705.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265827	0.80358	.	.	ENSG00000103507	ENST00000394951;ENST00000219794;ENST00000394950;ENST00000287507	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.54	5.54	0.83059	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	L	0.31420	0.93	0.80722	D	1	D;D	0.56746	0.977;0.977	P;P	0.55871	0.786;0.666	T	0.02751	-1.1115	10	0.25106	T	0.35	-21.05	18.2514	0.90005	0.0:0.0:1.0:0.0	.	84;84	Q96G95;O14874	.;BCKD_HUMAN	D	84	ENSP00000378405:G84D;ENSP00000219794:G84D;ENSP00000378404:G84D;ENSP00000287507:G84D	ENSP00000219794:G84D	G	+	2	0	BCKDK	31028388	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.232000	0.89796	2.597000	0.87782	0.655000	0.94253	GGC		0.592	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881		A	31120887	G	A	31120887	3	1	77	1	0	0	0	0	1	0	0	0	1362	1203	42	3	257	3	BCKDK	16	31120887	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	47568	31120887	59233866	909	22645										
PRSS36	146547	broad.mit.edu	37	chr16	31151647	31151647	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctcctgcccctctgcatacaGgacacagagggttccagggg	12	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:31151647G>A	ENST00000268281.4	-	14	2315	c.2257C>T	c.(2257-2259)Ctg>Ttg	p.L753L	PRSS36_ENST00000569305.1_Silent_p.L748L|PRSS36_ENST00000418068.2_Intron	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	753	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)	p.L753L(1)		kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						TCTGCATACAGGACACAGAGG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	16											67	64	65					16																	31151647		2197	4300	6497	31059148	SO:0001819	synonymous_variant	146547			AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2257C>T	16.37:g.31151647G>A			31059148	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Silent	SNP	ENST00000268281.4	37	CCDS32436.1																																																																																				0.597	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		A	31151647	G	A	31151647	2	1	77	1	0	0	0	0	0	0	0	1	12659	991	35	3		3	PRSS36	16	31151647	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	30760	31151647	59203106	910	22646										
ITGAM	3684	broad.mit.edu	37	chr16	31308909	31308909	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcaccgacctggtcctcatCggggccccccattactacga	9	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:31308909C>T	ENST00000287497.8	+	13	1506	c.1431C>T	c.(1429-1431)atC>atT	p.I477I	ITGAM_ENST00000544665.3_Silent_p.I477I			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	477					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.I477I(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TGGTCCTCATCGGGGCCCCCC	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	16											73	82	79					16																	31308909		2192	4296	6488	31216410	SO:0001819	synonymous_variant	3684			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1431C>T	16.37:g.31308909C>T			31216410	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1																																																																																				0.667	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31308909	C	T	31308909	2	4	77	1	0	0	0	0	0	0	0	1	7908	874	31	1		1	ITGAM	16	31308909	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	157262	31308909	59045844	911	22647										
SLC5A2	6524	broad.mit.edu	37	chr16	31496148	31496151	+	Frame_Shift_Del	DEL	CTCT	CTCT	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggccacccaggttggggcCtctctcttcgccagcaacat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CTCT	CTCT	CTCT	-	CTCT	CTCT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:31496148_31496151delCTCT	ENST00000330498.3	+	3	226_229	c.207_210delCTCT	c.(205-210)gcctctfs	p.AS69fs	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	69					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)	p.L71fs*47(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	AGGTTGGGGCCTCTCTCTTCGCCA	0.657																																																1	Deletion - Frameshift(1)	large_intestine(1)	16																																								31403652	SO:0001589	frameshift_variant	6524				CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"Solute carriers"	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.207_210delCTCT	16.37:g.31496152_31496155delCTCT	ENSP00000327943:p.Ala69fs		31403649	A2RRD2	Frame_Shift_Del	DEL	ENST00000330498.3	37	CCDS10714.1																																																																																				0.657	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2			-	31496151	CTCT	-	31496148	7	5	77	1	0	1	0	1	0	0	0	0	14702	668	24	0	217	0	SLC5A2	16	31496148	Frame_Shift_Del	DEL	CTCT	TCGA-AG-A02N-01A-11W-A096-10	187239	31496148	58858605	912	22648										
ITFG1	81533	broad.mit.edu	37	chr16	47196467	47196467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcactttttctccagatggaCggggaataccaacgtagaga	10	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:47196467C>T	ENST00000320640.6	-	15	1790	c.1562G>A	c.(1561-1563)cGt>cAt	p.R521H	RP11-329J18.2_ENST00000565694.1_RNA|ITFG1_ENST00000568047.1_5'UTR|ITFG1_ENST00000544001.2_Missense_Mutation_p.R408H|RP11-329J18.2_ENST00000564705.1_RNA	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	521						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R521H(1)		breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				TCCAGATGGACGGGGAATACC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	16											87	90	89					16																	47196467		2202	4300	6502	45753968	SO:0001583	missense	81533			AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"T cell immunomodulatory protein"	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.1562G>A	16.37:g.47196467C>T	ENSP00000319918:p.Arg521His		45753968	Q96SR4|Q9BRE2|Q9H2V9	Missense_Mutation	SNP	ENST00000320640.6	37	CCDS10728.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731647	0.89390	.	.	ENSG00000129636	ENST00000320640;ENST00000537184;ENST00000542691;ENST00000544001	T;T	0.63096	-0.02;-0.02	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.75170	0.3813	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.966;0.982	T	0.68172	-0.5479	10	0.15499	T	0.54	-25.9559	19.4863	0.95030	0.0:1.0:0.0:0.0	.	408;521	F5GXC5;Q8TB96	.;TIP_HUMAN	H	521;181;266;408	ENSP00000319918:R521H;ENSP00000441062:R408H	ENSP00000319918:R521H	R	-	2	0	ITFG1	45753968	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	6.832000	0.75329	2.618000	0.88619	0.591000	0.81541	CGT		0.343	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		T	47196467	C	T	47196467	3	4	77	1	0	0	0	0	1	0	0	0	7890	536	19	1	292	1	ITFG1	16	47196467	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	15700319	47196467	43158286	913	22649										
ZNF423	23090	broad.mit.edu	37	chr16	49671152	49671152	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagttggagaacttgaggtcGcattgattgcaaggatactc	12	6	0	3	rs144950533		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:49671152G>A	ENST00000561648.1	-	4	1964	c.1911C>T	c.(1909-1911)tgC>tgT	p.C637C	ZNF423_ENST00000562871.1_Silent_p.C577C|ZNF423_ENST00000535559.1_Silent_p.C520C|ZNF423_ENST00000567169.1_Silent_p.C520C|ZNF423_ENST00000562520.1_Silent_p.C577C|ZNF423_ENST00000563137.2_Silent_p.C577C|ZNF423_ENST00000262383.2_Silent_p.C637C	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	637					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C637C(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ACTTGAGGTCGCATTGATTGC	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	16						G		0,4396		0,0,2198	69	67	68		1911	-4.7	1	16	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF423	NM_015069.2		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		637/1285	49671152	1,12995	2198	4300	6498	48228653	SO:0001819	synonymous_variant	23090			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1911C>T	16.37:g.49671152G>A			48228653	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	37	CCDS32445.1																																																																																				0.587	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49671152	G	A	49671152	2	1	77	1	0	0	0	0	0	0	0	1	17937	1079	38	1		1	ZNF423	16	49671152	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2474685	49671152	40683601	914	22650										
IRX3	79191	broad.mit.edu	37	chr16	54319087	54319087	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccccccgtgtcctcctcctCccccccgagctcctcctcct							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:54319087delC	ENST00000329734.3	-	2	1418	c.706delG	c.(706-708)gagfs	p.E238fs		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	238	Asp/Glu-rich (acidic).				mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.E236fs*24(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						tcctcctcctcccccccgagc	0.657																																					GBM(143;1830 1866 4487 4646 37383)											1	Deletion - Frameshift(1)	large_intestine(1)	16											53	32	39					16																	54319087		2193	4298	6491	52876588	SO:0001589	frameshift_variant	79191			U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"Homeoboxes / TALE class"	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.706delG	16.37:g.54319087delC	ENSP00000331608:p.Glu238fs		52876588	Q7Z4A4|Q7Z4A5|Q8IVC6	Frame_Shift_Del	DEL	ENST00000329734.3	37	CCDS10750.1																																																																																				0.657	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2			-	54319087	C	-	54319087	7	5	77	1	0	1	0	1	0	0	0	0	7866	864	30	0	811	0	IRX3	16	54319087	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	4647935	54319087	36035666	915	22651										
IRX6	79190	broad.mit.edu	37	chr16	55362817	55362817	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgattggagcgcagggagtgCggcctggctgcgccccgctt	17	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:55362817C>T	ENST00000290552.7	+	5	2259	c.927C>T	c.(925-927)tgC>tgT	p.C309C	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	309					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.C309C(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						GCAGGGAGTGCGGCCTGGCTG	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	16											45	49	47					16																	55362817		2195	4294	6489	53920318	SO:0001819	synonymous_variant	79190			AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.927C>T	16.37:g.55362817C>T			53920318	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																				0.657	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		T	55362817	C	T	55362817	2	4	77	1	0	0	0	0	0	0	0	1	7869	776	27	1		1	IRX6	16	55362817	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1043730	55362817	34991936	916	22652										
CES7	221223	broad.mit.edu	37	chr16	55883680	55883680	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atagaagtagacaggtgcacCagcatctgacaaaaggtcag	11	8	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:55883680C>T	ENST00000290567.9	-	11	1400	c.1279G>A	c.(1279-1281)Ggt>Agt	p.G427S	CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000319165.9_Intron|CES5A_ENST00000520435.1_Missense_Mutation_p.G397S|CES5A_ENST00000521992.1_Missense_Mutation_p.G456S|CES5A_ENST00000518005.1_Missense_Mutation_p.G321S	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	427						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)	p.G456S(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						ACAGGTGCACCAGCATCTGAC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16											70	61	64					16																	55883680		1568	3582	5150	54441181	SO:0001583	missense	221223			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1279G>A	16.37:g.55883680C>T	ENSP00000290567:p.Gly427Ser		54441181	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	.	17.77	3.471612	0.63737	.	.	ENSG00000159398	ENST00000521992;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T	0.16196	2.36;2.36;2.36;2.36	5.03	5.03	0.67393	Carboxylesterase, type B (1);	0.529435	0.15964	N	0.236085	T	0.41766	0.1173	M	0.69463	2.115	0.42118	D	0.991417	D	0.76494	0.999	D	0.75020	0.985	T	0.15292	-1.0442	10	0.62326	D	0.03	.	16.6465	0.85178	0.0:1.0:0.0:0.0	.	427	Q6NT32	EST5A_HUMAN	S	456;321;427;397;207	ENSP00000428864:G456S;ENSP00000428571:G321S;ENSP00000290567:G427S;ENSP00000428887:G397S	ENSP00000290567:G427S	G	-	1	0	CES5A	54441181	0.989000	0.36119	0.655000	0.29622	0.423000	0.31445	4.408000	0.59761	2.718000	0.92993	0.462000	0.41574	GGT		0.552	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		T	55883680	C	T	55883680	3	4	77	1	0	0	0	0	1	0	0	0	3278	594	21	3	460	3	CES7	16	55883680	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	520863	55883680	34471073	917	22653										
CETP	1071	broad.mit.edu	37	chr16	57003380	57003380	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgatgtctccattcagaacGtgtctgtggtcttcaagggg	12	8	5	2	rs371258270		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:57003380G>A	ENST00000566128.1	+	3	388	c.121G>A	c.(121-123)Gtg>Atg	p.V41M	CETP_ENST00000569082.1_3'UTR|CETP_ENST00000200676.3_Missense_Mutation_p.V106M|CETP_ENST00000379780.2_Missense_Mutation_p.V106M					cholesteryl ester transfer protein, plasma									p.V106M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CATTCAGAACGTGTCTGTGGT	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		20708	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	16						G	MET/VAL	1,4395	2.1+/-5.4	0,1,2197	199	177	185		316	-1.9	0	16		185	0,8600		0,0,4300	no	missense	CETP	NM_000078.2	21	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	106/494	57003380	1,12995	2198	4300	6498	55560881	SO:0001583	missense	1071			M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"BPI fold containing"	1869	protein-coding gene	gene with protein product	"BPI fold containing family F"	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.121G>A	16.37:g.57003380G>A	ENSP00000456276:p.Val41Met		55560881		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	G	10.38	1.333031	0.24167	2.27E-4	0.0	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.05925	3.37;3.37	3.87	-1.86	0.07760	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.255835	0.31624	U	0.007328	T	0.11281	0.0275	L	0.36672	1.1	0.18873	N	0.999986	D;D	0.89917	0.994;1.0	P;D	0.70716	0.579;0.97	T	0.07712	-1.0758	10	0.59425	D	0.04	-0.476	7.7852	0.29087	0.48:0.0:0.52:0.0	.	106;106	P11597-2;P11597	.;CETP_HUMAN	M	106	ENSP00000200676:V106M;ENSP00000369106:V106M	ENSP00000200676:V106M	V	+	1	0	CETP	55560881	0.086000	0.21541	0.001000	0.08648	0.181000	0.23173	1.282000	0.33226	-0.859000	0.04105	-0.469000	0.05056	GTG		0.567	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		A	57003380	G	A	57003380	3	1	77	1	0	0	0	0	1	0	0	0	3283	1145	40	1	326	1	CETP	16	57003380	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1119700	57003380	33351373	918	22654										
GPR114	221188	broad.mit.edu	37	chr16	57601915	57601915	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggccgctgccctgcactaCgcgctgctcagctgcctcac	10	19	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:57601915C>T	ENST00000340339.4	+	9	1492	c.969C>T	c.(967-969)taC>taT	p.Y323Y	GPR114_ENST00000349457.3_Silent_p.Y323Y|GPR114_ENST00000394361.4_3'UTR	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	323					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Y323Y(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CCCTGCACTACGCGCTGCTCA	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	16											104	81	89					16																	57601915		2198	4300	6498	56159416	SO:0001819	synonymous_variant	221188			AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"-", "GPCR / Class B : Orphans"	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.969C>T	16.37:g.57601915C>T			56159416	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Silent	SNP	ENST00000340339.4	37	CCDS10785.1																																																																																				0.612	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837		T	57601915	C	T	57601915	2	4	77	1	0	0	0	0	0	0	0	1	6651	547	19	1		1	GPR114	16	57601915	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	598535	57601915	32752838	919	22655										
GOT2	2806	broad.mit.edu	37	chr16	58752151	58752151	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccggacgcgggtccactccCgtgggattgtgggcgcaggc	17	13	0	0	rs181076765		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:58752151C>T	ENST00000245206.5	-	6	779	c.651G>A	c.(649-651)acG>acA	p.T217T	GOT2_ENST00000434819.2_Silent_p.T174T|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	217					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.T217T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	GGTCCACTCCCGTGGGATTGT	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	16											118	106	110					16																	58752151		2198	4300	6498	57309652	SO:0001819	synonymous_variant	2806				CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"kynurenine aminotransferase IV", "aspartate aminotransferase 2", "aspartate transaminase 2"	138150	"glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.651G>A	16.37:g.58752151C>T			57309652	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	9.175	1.022238	0.19433	.	.	ENSG00000125166	ENST00000425685	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	T	0.44371	0.1290	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58498	-0.7626	4	.	.	.	-4.826	7.7397	0.28835	0.1922:0.4884:0.0649:0.2545	.	.	.	.	Q	178	.	.	R	-	2	0	GOT2	57309652	0.000000	0.05858	0.026000	0.17262	0.972000	0.66771	-6.289000	0.00072	-3.381000	0.00175	-1.163000	0.01768	CGG		0.493	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3			T	58752151	C	T	58752151	2	4	77	1	0	0	0	0	0	0	0	1	6601	639	23	1		1	GOT2	16	58752151	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1150236	58752151	31602602	920	22656										
KCTD19	146212	broad.mit.edu	37	chr16	67333309	67333309	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attccctgtgatgtacagtcGgcttccgtctagcgtgctct	10	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:67333309G>A	ENST00000304372.5	-	6	998	c.943C>T	c.(943-945)Cga>Tga	p.R315*	KCTD19_ENST00000562860.1_5'UTR	NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	315					protein homooligomerization (GO:0051260)			p.R315*(1)		endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		ATGTACAGTCGGCTTCCGTCT	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											89	94	93					16																	67333309		2119	4232	6351	65890810	SO:0001587	stop_gained	146212			AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.943C>T	16.37:g.67333309G>A	ENSP00000305702:p.Arg315*		65890810	B4DZ49|Q8N804	Nonsense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	G	9.633	1.136863	0.21123	.	.	ENSG00000168676	ENST00000304372	.	.	.	5.77	-0.972	0.10300	.	0.225469	0.28889	N	0.013816	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.962	17.7919	0.88555	0.0:0.0:0.7283:0.2717	.	.	.	.	X	315	.	ENSP00000305702:R315X	R	-	1	2	KCTD19	65890810	0.665000	0.27466	0.150000	0.22450	0.390000	0.30446	0.182000	0.16900	-0.368000	0.08040	-1.014000	0.02459	CGA		0.597	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		A	67333309	G	A	67333309	4	1	77	1	0	0	0	0	0	1	0	0	8127	1124	39	1	1881	1	KCTD19	16	67333309	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8581158	67333309	23021444	921	22657										
PARD6A	50855	broad.mit.edu	37	chr16	67696050	67696050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagatggcatgagcgtgcgtGtggctccccagggcctggag	18	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:67696050G>A	ENST00000219255.3	+	3	621	c.541G>A	c.(541-543)Gtg>Atg	p.V181M	PARD6A_ENST00000602551.1_Missense_Mutation_p.V151M|ACD_ENST00000393919.4_5'Flank|ENKD1_ENST00000602409.1_5'Flank|ACD_ENST00000219251.8_5'Flank|PARD6A_ENST00000458121.2_Missense_Mutation_p.V180M			Q9NPB6	PAR6A_HUMAN	par-6 family cell polarity regulator alpha	181	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction maintenance (GO:0045217)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	GTP-dependent protein binding (GO:0030742)|Rho GTPase binding (GO:0017048)|transcription factor binding (GO:0008134)	p.V181M(1)		central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	6		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)		GAGCGTGCGTGTGGCTCCCCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	16											75	78	77					16																	67696050		2198	4300	6498	66253551	SO:0001583	missense	50855				CCDS10843.1, CCDS45514.1	16q22.1-q22.3	2013-08-28	2013-08-28		ENSG00000102981	ENSG00000102981			15943	protein-coding gene	gene with protein product		607484	"par-6 (partitioning defective 6, C.elegans) homolog alpha", "par-6 partitioning defective 6 homolog alpha (C. elegans)"			9482110, 11260256	Standard	XM_005255977		Approved	PAR-6, PAR-6A, TAX40, PAR6alpha, TIP-40	uc002ett.3	Q9NPB6	OTTHUMG00000137534	ENST00000219255.3:c.541G>A	16.37:g.67696050G>A	ENSP00000219255:p.Val181Met		66253551	O14911|Q9NPJ7	Missense_Mutation	SNP	ENST00000219255.3	37	CCDS10843.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401858	0.83120	.	.	ENSG00000102981	ENST00000458121;ENST00000219255	T;T	0.47177	0.86;0.85	5.39	5.39	0.77823	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	L	0.56340	1.77	0.80722	D	1	P;P	0.48162	0.813;0.906	P;P	0.57468	0.821;0.81	T	0.62586	-0.6823	10	0.56958	D	0.05	-11.871	18.7537	0.91825	0.0:0.0:1.0:0.0	.	181;180	Q9NPB6;Q9NPB6-2	PAR6A_HUMAN;.	M	180;181	ENSP00000392388:V180M;ENSP00000219255:V181M	ENSP00000219255:V181M	V	+	1	0	PARD6A	66253551	1.000000	0.71417	0.949000	0.38748	0.934000	0.57294	7.647000	0.83462	2.509000	0.84616	0.563000	0.77884	GTG		0.642	PARD6A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268863.2	NM_016948		A	67696050	G	A	67696050	3	1	77	1	0	0	0	0	1	0	0	0	11476	1377	48	3	551	3	PARD6A	16	67696050	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	362741	67696050	22658703	922	22658										
EDC4	23644	broad.mit.edu	37	chr16	67911201	67911201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctcaagggcttcacaggcaGtgtggctgatctggctttcg	14	10	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:67911201G>A	ENST00000358933.5	+	5	772	c.533G>A	c.(532-534)aGt>aAt	p.S178N	AC040162.1_ENST00000408599.1_RNA|EDC4_ENST00000574770.1_3'UTR	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	178					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S178N(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		TTCACAGGCAGTGTGGCTGAT	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											109	94	99					16																	67911201		2198	4300	6498	66468702	SO:0001583	missense	23644			U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.533G>A	16.37:g.67911201G>A	ENSP00000351811:p.Ser178Asn		66468702	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	De_novo_Start_OutOfFrame	SNP	ENST00000358933.5	37	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177749	0.38413	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	T	0.41400	1.0	5.71	5.71	0.89125	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.114155	0.64402	D	0.000007	T	0.35799	0.0944	L	0.36672	1.1	0.40792	D	0.983264	B;P	0.34462	0.327;0.454	B;B	0.32677	0.067;0.15	T	0.10382	-1.0632	10	0.19147	T	0.46	-11.5849	19.4549	0.94884	0.0:0.0:1.0:0.0	.	110;178	B7Z7V8;Q6P2E9	.;EDC4_HUMAN	N	178;110	ENSP00000351811:S178N	ENSP00000351811:S178N	S	+	2	0	EDC4	66468702	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.282000	0.78630	2.710000	0.92621	0.655000	0.94253	AGT		0.597	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67911201	G	A	67911201	3	1	77	1	0	0	0	0	1	0	0	0	4919	1029	36	3	551	3	EDC4	16	67911201	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	215151	67911201	22443552	923	22659										
ESRP2	80004	broad.mit.edu	37	chr16	68265749	68265749	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccggaagagttcaatgtatcGcttacccagcatgcccttgt	9	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:68265749G>A	ENST00000565858.1	-	10	1371	c.1285C>T	c.(1285-1287)Cga>Tga	p.R429*	ESRP2_ENST00000473183.2_Nonsense_Mutation_p.R419*|RP11-96D1.11_ENST00000571197.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	429	RRM 2.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R419*(2)		NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						TCAATGTATCGCTTACCCAGC	0.627																																																2	Substitution - Nonsense(2)	large_intestine(2)	16											52	48	49					16																	68265749		2198	4300	6498	66823250	SO:0001587	stop_gained	80004			AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.1285C>T	16.37:g.68265749G>A	ENSP00000454554:p.Arg429*		66823250	Q8N6H8|Q8WZ15|Q9H6I4	Nonsense_Mutation	SNP	ENST00000565858.1	37		.	.	.	.	.	.	.	.	.	.	G	41	8.870955	0.98984	.	.	ENSG00000103067	ENST00000473183	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.023	20.1278	0.97990	0.0:0.0:1.0:0.0	.	.	.	.	X	419	.	ENSP00000418748:R419X	R	-	1	2	ESRP2	66823250	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.902000	0.63266	2.768000	0.95171	0.561000	0.74099	CGA		0.627	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		A	68265749	G	A	68265749	4	1	77	1	0	0	0	0	0	1	0	0	5272	1095	38	1	922	1	ESRP2	16	68265749	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	354548	68265749	22089004	924	22660										
HAS3	54921	broad.mit.edu	37	chr16	69152319	69152319	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgcccaggtcagagctaCggaagcatggtccgttcacc	12	13	2	1	rs113161750	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:69152319C>T	ENST00000448552.2	-	0	2496				CHTF8_ENST00000306585.6_3'UTR|HAS3_ENST00000219322.3_Missense_Mutation_p.T267M|CHTF8_ENST00000518041.1_3'UTR|CHTF8_ENST00000523421.1_3'UTR	NM_001039690.3|NM_001040146.3	NP_001034779.1|NP_001035236.1	P0CG13	CTF8_HUMAN	CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)						cell cycle (GO:0007049)|DNA replication (GO:0006260)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T267M(1)									GTCAGAGCTACGGAAGCATGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	16						C	,,MET/THR	4,4392	8.1+/-20.4	0,4,2194	128	99	109		,,800	-0.1	0.4	16	dbSNP_132	109	0,8600		0,0,4300	no	utr-3,utr-3,missense	HAS3,CHTF8	NM_001039690.3,NM_001040146.3,NM_138612.2	,,81	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,	,,267/282	69152319	4,12992	2198	4300	6498	67709820	SO:0001624	3_prime_UTR_variant	3038				CCDS42185.1	16q22.1	2009-01-14				ENSG00000168802			24353	protein-coding gene	gene with protein product		613202				12766176	Standard	NM_001039690		Approved	FLJ20400, CTF8, DERPC	uc002ewo.2	P0CG12		ENST00000448552.2:c.*2009G>A	16.37:g.69152319C>T			67709820	A8MYX8|Q71E72|Q8NDH8|Q8WV66|Q9NX73	Missense_Mutation	SNP	ENST00000448552.2	37	CCDS42185.1	.	.	.	.	.	.	.	.	.	.	C	9.814	1.183824	0.21870	9.1E-4	0.0	ENSG00000103044	ENST00000219322	T	0.48201	0.82	5.56	-0.0605	0.13788	.	.	.	.	.	T	0.31420	0.0796	.	.	.	0.27229	N	0.959463	B	0.30021	0.265	B	0.26864	0.074	T	0.29212	-1.0019	8	0.87932	D	0	.	3.2121	0.06686	0.3159:0.4247:0.0:0.2594	.	267	O00219-2	.	M	267	ENSP00000219322:T267M	ENSP00000219322:T267M	T	+	2	0	HAS3	67709820	0.091000	0.21658	0.422000	0.26621	0.782000	0.44232	-0.275000	0.08525	0.044000	0.15775	-0.137000	0.14449	ACG		0.552	CHTF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376352.2	NM_017804		T	69152319	C	T	69152319	1	4	77	0	1	0	0	0	0	0	0	0	6984	536	19	1		1	HAS3	16	69152319	3'UTR	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	886570	69152319	21202434	925	22661										
PDPR	55066	broad.mit.edu	37	chr16	70162687	70162687	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggctcatttttcttacagGttacacaaggacaggctcaa	9	9	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:70162687G>A	ENST00000288050.4	+	5	1319	c.362G>A	c.(361-363)gGt>gAt	p.G121D	PDPR_ENST00000398122.3_Splice_Site_p.G21D|PDPR_ENST00000568530.1_Splice_Site_p.G121D	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	121					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.G121D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		TTTCTTACAGGTTACACAAGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	16											36	38	37					16																	70162687		1850	4107	5957	68720188	SO:0001630	splice_region_variant	55066				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.362-1G>A	16.37:g.70162687G>A			68720188	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709258	0.89018	.	.	ENSG00000090857	ENST00000288050;ENST00000398122	T;T	0.80994	-1.44;-1.44	4.5	4.5	0.54988	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.89938	0.6860	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91088	0.4904	9	.	.	.	.	14.3298	0.66548	0.0:0.0:1.0:0.0	.	121	Q8NCN5	PDPR_HUMAN	D	121;21	ENSP00000288050:G121D;ENSP00000381190:G21D	.	G	+	2	0	PDPR	68720188	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.187000	0.77730	2.042000	0.60477	0.555000	0.69702	GGT		0.458	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	Missense_Mutation	A	70162687	G	A	70162687	5	1	77	1	0	0	0	0	0	0	1	0	11720	1275	44	3	372	3	PDPR	16	70162687	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1010368	70162687	20192066	926	22662										
FUK	197258	broad.mit.edu	37	chr16	70513117	70513117	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgggccagtgcctgacctcGtactgggagcagaagaagct	14	11	0	3	rs201537001		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:70513117G>A	ENST00000288078.6	+	23	3196	c.2964G>A	c.(2962-2964)tcG>tcA	p.S988S	FUK_ENST00000571514.1_Silent_p.S479S|FUK_ENST00000378912.2_Silent_p.S994S	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	988						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)	p.S988S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				GCCTGACCTCGTACTGGGAGC	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	16						A		0,4198		0,0,2099	36	40	38		2964	-9.1	0.1	16		38	12,8404		0,12,4196	no	coding-synonymous	FUK	NM_145059.2		0,12,6295	AA,AG,GG		0.1426,0.0,0.0951		988/1085	70513117	12,12602	2099	4208	6307	69070618	SO:0001819	synonymous_variant	197258				CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"L-fucose kinase"	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.2964G>A	16.37:g.70513117G>A			69070618	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																				0.632	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		A	70513117	G	A	70513117	2	1	77	1	0	0	0	0	0	0	0	1	6115	1132	40	1		1	FUK	16	70513117	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	350430	70513117	19841636	927	22663										
CALB2	794	broad.mit.edu	37	chr16	71423724	71423724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaggcagggaagctctacCgcaaggacctggagattgtg	15	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:71423724C>T	ENST00000302628.4	+	11	849	c.772C>T	c.(772-774)Cgc>Tgc	p.R258C	CALB2_ENST00000349553.5_3'UTR	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	258	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R258C(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				GAAGCTCTACCGCAAGGACCT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	16											109	101	104					16																	71423724		2198	4300	6498	69981225	SO:0001583	missense	794			X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"EF-hand domain containing"	1435	protein-coding gene	gene with protein product	"calretinin"	114051	"calbindin 2, 29kDa (calretinin)"			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.772C>T	16.37:g.71423724C>T	ENSP00000307508:p.Arg258Cys		69981225	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	ENST00000302628.4	37	CCDS10899.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999484	0.74818	.	.	ENSG00000172137	ENST00000302628	D	0.83992	-1.79	5.35	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.88529	0.6461	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89028	0.3440	10	0.87932	D	0	-11.6433	12.2168	0.54410	0.1771:0.8229:0.0:0.0	.	258	P22676	CALB2_HUMAN	C	258	ENSP00000307508:R258C	ENSP00000307508:R258C	R	+	1	0	CALB2	69981225	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.170000	0.50816	1.190000	0.43042	0.455000	0.32223	CGC		0.557	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740		T	71423724	C	T	71423724	3	4	77	1	0	0	0	0	1	0	0	0	2580	652	23	1	814	1	CALB2	16	71423724	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	910607	71423724	18931029	928	22664										
ZNF23	7571	broad.mit.edu	37	chr16	71482621	71482621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgaattctcagatgctgcCgaaattgggagttacatctg	11	7	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:71482621C>T	ENST00000393539.2	-	6	2120	c.1307G>A	c.(1306-1308)cGg>cAg	p.R436Q	AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000428724.2_Missense_Mutation_p.R378Q|ZNF23_ENST00000539742.1_5'UTR|ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000357254.4_Missense_Mutation_p.R436Q|ZNF23_ENST00000417828.1_Missense_Mutation_p.R436Q|ZNF23_ENST00000358700.2_3'UTR|ZNF23_ENST00000564528.1_Missense_Mutation_p.R378Q	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	436					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R436Q(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		CAGATGCTGCCGAAATTGGGA	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	16											58	58	58					16																	71482621		2198	4300	6498	70040122	SO:0001583	missense	7571			X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.1307G>A	16.37:g.71482621C>T	ENSP00000377171:p.Arg436Gln		70040122	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231342	0.39399	.	.	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742;ENST00000358700	T;T;T;T	0.04275	3.66;3.66;3.66;3.66	4.27	3.32	0.38043	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.184730	0.26784	N	0.022515	T	0.07369	0.0186	N	0.16833	0.445	0.09310	N	1	D;D	0.89917	0.999;1.0	P;D	0.65323	0.82;0.934	T	0.28650	-1.0037	10	0.33940	T	0.23	-10.1157	7.8823	0.29629	0.0:0.8903:0.0:0.1097	.	436;436	B3KR55;P17027	.;ZNF23_HUMAN	Q	436;436;436;378;378;208	ENSP00000377171:R436Q;ENSP00000349796:R436Q;ENSP00000395712:R436Q;ENSP00000387673:R378Q	ENSP00000349796:R436Q	R	-	2	0	ZNF23	70040122	0.000000	0.05858	0.999000	0.59377	0.691000	0.40173	-0.130000	0.10498	1.388000	0.46506	0.561000	0.74099	CGG		0.458	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		T	71482621	C	T	71482621	3	4	77	1	0	0	0	0	1	0	0	0	17822	652	23	1	628	1	ZNF23	16	71482621	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	58897	71482621	18872132	929	22665										
MARVELD3	91862	broad.mit.edu	37	chr16	71674883	71674883	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaggcagccgagaacagcccGgaagttacagtgatgcaccg	13	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:71674883G>A	ENST00000299952.4	+	3	1229	c.1186G>A	c.(1186-1188)Gga>Aga	p.G396R	MARVELD3_ENST00000561682.1_Intron|MARVELD3_ENST00000565261.1_3'UTR|PHLPP2_ENST00000540628.1_3'UTR	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	0					cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)		p.G396R(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				AGAACAGCCCGGAAGTTACAG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	16											49	42	44					16																	71674883		2198	4300	6498	70232384	SO:0001583	missense	91862			BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.1186G>A	16.37:g.71674883G>A	ENSP00000299952:p.Gly396Arg		70232384	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000299952.4	37	CCDS32478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	12.10|12.10	1.837668|1.837668	0.32513|0.32513	.|.	.|.	ENSG00000140832|ENSG00000040199	ENST00000299952|ENST00000299971	T|.	0.37752|.	1.18|.	5.67|5.67	-2.35|-2.35	0.06684|0.06684	.|.	0.693312|.	0.15616|.	N|.	0.253144|.	T|T	0.52565|0.52565	0.1742|0.1742	.|.	.|.	.|.	0.34892|0.34892	D|D	0.745627|0.745627	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.57705|0.57705	-0.7765|-0.7765	9|5	0.11182|0.59425	T|D	0.66|0.04	-11.9522|-11.9522	7.6496|7.6496	0.28340|0.28340	0.5537:0.306:0.1403:0.0|0.5537:0.306:0.1403:0.0	.|.	396|.	Q96A59-2|.	.|.	R|W	396|767	ENSP00000299952:G396R|.	ENSP00000299952:G396R|ENSP00000299971:R767W	G|R	+|-	1|1	0|2	MARVELD3|PHLPP2	70232384|70232384	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.554000|-0.554000	0.06006|0.06006	-1.235000|-1.235000	0.02545|0.02545	-3.712000|-3.712000	0.00023|0.00023	GGA|CGG		0.512	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858		A	71674883	G	A	71674883	3	1	77	1	0	0	0	0	1	0	0	0	9349	1117	39	1	1811	1	MARVELD3	16	71674883	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	192262	71674883	18679870	930	22666										
HPR	3250	broad.mit.edu	37	chr16	72110265	72110265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgggtggacacctggatgCcaaaggcagctttccctggc	13	13	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:72110265C>T	ENST00000540303.2	+	5	364	c.332C>T	c.(331-333)gCc>gTc	p.A111V	HPR_ENST00000356967.5_Missense_Mutation_p.A111V|HPR_ENST00000561690.1_Intron|HPR_ENST00000228226.8_Missense_Mutation_p.A148V	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	111	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)	p.A111V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CACCTGGATGCCAAAGGCAGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	16											33	23	27					16																	72110265		1933	4121	6054	70667766	SO:0001583	missense	3250			BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.332C>T	16.37:g.72110265C>T	ENSP00000441828:p.Ala111Val		70667766	Q7LE20|Q92658|Q92659|Q9ULB0	Missense_Mutation	SNP	ENST00000540303.2	37	CCDS42193.1	.	.	.	.	.	.	.	.	.	.	.	12.50	1.957839	0.34565	.	.	ENSG00000257017	ENST00000356967;ENST00000540303;ENST00000228226	D;D;D	0.89123	-2.47;-2.47;-2.47	2.46	2.46	0.29980	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.068639	0.64402	D	0.000013	D	0.90584	0.7048	L	0.48218	1.51	0.39527	D	0.968611	D	0.89917	1.0	D	0.77004	0.989	D	0.89086	0.3479	10	0.36615	T	0.2	.	10.6658	0.45731	0.0:1.0:0.0:0.0	.	111	P00739	HPTR_HUMAN	V	111;111;148	ENSP00000349451:A111V;ENSP00000441828:A111V;ENSP00000228226:A148V	ENSP00000228226:A148V	A	+	2	0	HP	70667766	0.961000	0.32948	0.973000	0.42090	0.213000	0.24496	0.921000	0.28718	1.381000	0.46364	0.194000	0.17425	GCC		0.542	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		T	72110265	C	T	72110265	3	4	77	1	0	0	0	0	1	0	0	0	7358	739	26	3	350	3	HPR	16	72110265	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	435382	72110265	18244488	931	22667										
DHX38	9785	broad.mit.edu	37	chr16	72137514	72137514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgtagagacaacagcatcGtgatcgtggttggggagacg	15	7	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:72137514G>A	ENST00000268482.3	+	13	2160	c.1651G>A	c.(1651-1653)Gtg>Atg	p.V551M	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	551	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.V551M(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CAACAGCATCGTGATCGTGGT	0.547																																					Melanoma(97;711 1442 7855 13832 28836)											1	Substitution - Missense(1)	large_intestine(1)	16											116	91	100					16																	72137514		2198	4300	6498	70695015	SO:0001583	missense	9785			AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1651G>A	16.37:g.72137514G>A	ENSP00000268482:p.Val551Met		70695015	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661756	0.88154	.	.	ENSG00000140829	ENST00000268482	T	0.03635	3.86	5.8	5.8	0.92144	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.17238	0.0414	M	0.75447	2.3	0.80722	D	1	D	0.67145	0.996	P	0.59643	0.861	T	0.00022	-1.2340	10	0.62326	D	0.03	.	20.063	0.97692	0.0:0.0:1.0:0.0	.	551	Q92620	PRP16_HUMAN	M	551	ENSP00000268482:V551M	ENSP00000268482:V551M	V	+	1	0	DHX38	70695015	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.519000	0.73768	2.735000	0.93741	0.655000	0.94253	GTG		0.547	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72137514	G	A	72137514	3	1	77	1	0	0	0	0	1	0	0	0	4522	1145	40	1	1697	1	DHX38	16	72137514	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	27249	72137514	18217239	932	22668										
DHX38	9785	broad.mit.edu	37	chr16	72138441	72138441	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acatcagccacgatggatgcGgagaagtttgctgccttttt	11	9	1	1	rs199994362	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:72138441G>A	ENST00000268482.3	+	15	2576	c.2067G>A	c.(2065-2067)gcG>gcA	p.A689A	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	689	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.A689A(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CGATGGATGCGGAGAAGTTTG	0.572													G|||	5	0.000998403	0	0	5008	,	,		17099	0		0	False		,,,				2504	0.0051				Melanoma(97;711 1442 7855 13832 28836)											1	Substitution - coding silent(1)	large_intestine(1)	16						G		0,4396		0,0,2198	242	177	199		2067	-0.1	1	16		199	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DHX38	NM_014003.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		689/1228	72138441	1,12995	2198	4300	6498	70695942	SO:0001819	synonymous_variant	9785			AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.2067G>A	16.37:g.72138441G>A			70695942	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																				0.572	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72138441	G	A	72138441	2	1	77	1	0	0	0	0	0	0	0	1	4522	1103	39	1		1	DHX38	16	72138441	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	927	72138441	18216312	933	22669										
ZFHX3	463	broad.mit.edu	37	chr16	72993586	72993586	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccactcccacaggcgcccccGccctgggtcagctggctcag	11	20	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:72993586G>A	ENST00000268489.5	-	2	1131	c.459C>T	c.(457-459)ggC>ggT	p.G153G	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	153					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G153G(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AGGCGCCCCCGCCCTGGGTCA	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	16											30	35	33					16																	72993586		2198	4300	6498	71551087	SO:0001819	synonymous_variant	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.459C>T	16.37:g.72993586G>A			71551087	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																				0.677	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		A	72993586	G	A	72993586	2	1	77	1	0	0	0	0	0	0	0	1	17673	1074	38	1		1	ZFHX3	16	72993586	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	855145	72993586	17361167	934	22670										
ADAMTS18	170692	broad.mit.edu	37	chr16	77401380	77401380	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgctgcttttgcaaccttcGatggtgatactctgtctctc	8	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:77401380G>A	ENST00000282849.5	-	4	1154	c.736C>T	c.(736-738)Cga>Tga	p.R246*	ADAMTS18_ENST00000567121.1_5'UTR	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	246					eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R246*(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TGCAACCTTCGATGGTGATAC	0.488																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											88	83	85					16																	77401380		2198	4300	6498	75958881	SO:0001587	stop_gained	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.736C>T	16.37:g.77401380G>A	ENSP00000282849:p.Arg246*		75958881	Q6P4R5|Q6ZWJ9	Nonsense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	36	5.785162	0.96937	.	.	ENSG00000140873	ENST00000282849;ENST00000449265	.	.	.	4.57	2.56	0.30785	.	1.112010	0.06744	N	0.778858	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	13.2947	0.60290	0.0:0.5446:0.4554:0.0	.	.	.	.	X	246	.	ENSP00000282849:R246X	R	-	1	2	ADAMTS18	75958881	0.977000	0.34250	0.453000	0.27007	0.911000	0.54048	2.131000	0.42074	0.522000	0.28464	-0.314000	0.08810	CGA		0.488	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77401380	G	A	77401380	4	1	77	1	0	0	0	0	0	1	0	0	263	1066	37	1	3009	1	ADAMTS18	16	77401380	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4407794	77401380	12953373	935	22671										
CLEC3A	10143	broad.mit.edu	37	chr16	78064512	78064512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctatggtaaaaggagcctgcCaggtgtcaatgacttttggc	12	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:78064512C>T	ENST00000575655.1	+	3	449	c.368C>T	c.(367-369)cCa>cTa	p.P123L	CLEC3A_ENST00000299642.4_Missense_Mutation_p.P132L|RP11-281J9.2_ENST00000563114.1_RNA|CLEC3A_ENST00000565808.1_3'UTR	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	123	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.P123L(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						AGGAGCCTGCCAGGTGTCAAT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	16											92	78	83					16																	78064512		2198	4300	6498	76622013	SO:0001583	missense	10143			AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"C-type lectin domain containing"	2052	protein-coding gene	gene with protein product		613588	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.368C>T	16.37:g.78064512C>T	ENSP00000460682:p.Pro123Leu		76622013	B2R8C4|Q3SX91|Q6UXF5	Missense_Mutation	SNP	ENST00000575655.1	37		.	.	.	.	.	.	.	.	.	.	C	19.02	3.745334	0.69418	.	.	ENSG00000166509	ENST00000299642	.	.	.	5.76	4.81	0.61882	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.096180	0.64402	D	0.000001	T	0.60183	0.2249	L	0.58428	1.81	0.80722	D	1	P	0.42518	0.782	P	0.45276	0.475	T	0.61637	-0.7022	9	0.41790	T	0.15	-10.2239	15.2132	0.73241	0.0:0.7336:0.2664:0.0	.	123	O75596	CLC3A_HUMAN	L	123	.	ENSP00000299642:P123L	P	+	2	0	CLEC3A	76622013	1.000000	0.71417	0.906000	0.35671	0.938000	0.57974	5.460000	0.66691	1.559000	0.49555	0.650000	0.86243	CCA		0.507	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752		T	78064512	C	T	78064512	3	4	77	1	0	0	0	0	1	0	0	0	3516	594	21	3	378	3	CLEC3A	16	78064512	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	663132	78064512	12290241	936	22672										
WWOX	51741	broad.mit.edu	37	chr16	78149016	78149016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggccgggatttcactggcaAagtggttgtggtcactggag	17	7	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:78149016A>G	ENST00000566780.1	+	4	740	c.374A>G	c.(373-375)aAa>aGa	p.K125R	WWOX_ENST00000402655.2_Missense_Mutation_p.K125R|WWOX_ENST00000355860.3_Missense_Mutation_p.K125R|WWOX_ENST00000539474.2_Missense_Mutation_p.K125R|WWOX_ENST00000408984.3_Missense_Mutation_p.K125R|WWOX_ENST00000406884.2_Missense_Mutation_p.K125R	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	125	Interaction with MAPT. {ECO:0000250}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)	p.K125R(2)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TTCACTGGCAAAGTGGTTGTG	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	16											94	94	94					16																	78149016		1857	4095	5952	76706517	SO:0001583	missense	51741			AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	12799	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 41C, member 1"	605131	"WW domain-containing oxidoreductase"			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.374A>G	16.37:g.78149016A>G	ENSP00000457230:p.Lys125Arg		76706517	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.233136	0.39498	.	.	ENSG00000186153	ENST00000408984;ENST00000355860;ENST00000402655;ENST00000406884;ENST00000539474	T;T;T;T;T	0.58940	1.62;0.3;0.3;0.3;0.3	5.6	4.5	0.54988	NAD(P)-binding domain (1);	0.051016	0.85682	D	0.000000	T	0.47210	0.1433	L	0.48260	1.515	0.46954	D	0.999263	B;B;B;P	0.39181	0.176;0.095;0.001;0.663	B;B;B;B	0.37943	0.132;0.09;0.015;0.261	T	0.37056	-0.9722	10	0.17369	T	0.5	.	11.243	0.48980	0.9287:0.0:0.0713:0.0	.	125;125;125;125	Q9NZC7-6;Q9NZC7-5;Q9NZC7;Q9NZC7-3	.;.;WWOX_HUMAN;.	R	125	ENSP00000386161:K125R;ENSP00000348119:K125R;ENSP00000384238:K125R;ENSP00000384495:K125R;ENSP00000445210:K125R	ENSP00000348119:K125R	K	+	2	0	WWOX	76706517	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	3.350000	0.52224	2.251000	0.74343	0.528000	0.53228	AAA		0.468	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			G	78149016	A	G	78149016	3	3	77	1	0	0	0	0	1	0	0	0	17454	14	1	4	392	4	WWOX	16	78149016	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	84504	78149016	12205737	937	22673										
WWOX	51741	broad.mit.edu	37	chr16	78420807	78420807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacctcgctctgctccgtagCgtgcagcattttgctgaagc	11	13	1	1	rs201593515		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:78420807C>T	ENST00000566780.1	+	6	933	c.567C>T	c.(565-567)agC>agT	p.S189S	WWOX_ENST00000402655.2_Intron|WWOX_ENST00000539474.2_Intron|WWOX_ENST00000408984.3_Silent_p.S189S|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	189	Interaction with MAPT. {ECO:0000250}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)	p.S189S(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TGCTCCGTAGCGTGCAGCATT	0.398													C|||	1	0.000199681	0	0.0014	5008	,	,		18039	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											120	117	118					16																	78420807		1959	4145	6104	76978308	SO:0001819	synonymous_variant	51741			AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	12799	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 41C, member 1"	605131	"WW domain-containing oxidoreductase"			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.567C>T	16.37:g.78420807C>T			76978308	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Silent	SNP	ENST00000566780.1	37	CCDS42196.1																																																																																				0.398	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			T	78420807	C	T	78420807	2	4	77	1	0	0	0	0	0	0	0	1	17454	767	27	1		1	WWOX	16	78420807	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	271791	78420807	11933946	938	22674										
CMIP	80790	broad.mit.edu	37	chr16	81703766	81703766	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggactttgggaagtgcccgcGactgaggctgtttactcagg	15	9	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:81703766G>A	ENST00000537098.3	+	8	917	c.845G>A	c.(844-846)cGa>cAa	p.R282Q	CMIP_ENST00000539778.2_Missense_Mutation_p.R188Q|CMIP_ENST00000566513.1_3'UTR|CMIP_ENST00000398040.4_Missense_Mutation_p.R129Q	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	282						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R187Q(1)		endometrium(5)|kidney(1)|lung(7)	13						AAGTGCCCGCGACTGAGGCTG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	16											49	52	51					16																	81703766		2027	4177	6204	80261267	SO:0001583	missense	80790			AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.845G>A	16.37:g.81703766G>A	ENSP00000446100:p.Arg282Gln		80261267	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055493	0.75960	.	.	ENSG00000153815	ENST00000537098;ENST00000539778;ENST00000398040;ENST00000542097	T;T	0.10099	2.91;2.91	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.19886	0.0478	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.71674	0.997;0.997;0.998	D;D;D	0.66847	0.947;0.947;0.945	T	0.07347	-1.0777	10	0.26408	T	0.33	.	18.6513	0.91431	0.0:0.0:1.0:0.0	.	129;188;282	Q8IY22-3;Q8IY22-2;Q8IY22	.;.;CMIP_HUMAN	Q	282;188;188;95	ENSP00000446100:R282Q;ENSP00000440401:R188Q	ENSP00000381120:R188Q	R	+	2	0	CMIP	80261267	1.000000	0.71417	0.890000	0.34922	0.983000	0.72400	9.222000	0.95196	2.402000	0.81655	0.467000	0.42956	CGA		0.597	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		A	81703766	G	A	81703766	3	1	77	1	0	0	0	0	1	0	0	0	3584	1058	37	1	897	1	CMIP	16	81703766	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3282959	81703766	8650987	939	22675										
MBTPS1	8720	broad.mit.edu	37	chr16	84125349	84125349	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccacaaaccttgtcaacaaaCggatgatccatgaagtccgg	8	12	1	2	rs532832756		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:84125349C>T	ENST00000343411.3	-	7	1446	c.951G>A	c.(949-951)ccG>ccA	p.P317P	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	317	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.P317P(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TGTCAACAAACGGATGATCCA	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		17087	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	16											89	76	81					16																	84125349		2200	4300	6500	82682850	SO:0001819	synonymous_variant	8720			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.951G>A	16.37:g.84125349C>T			82682850	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																				0.493	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		T	84125349	C	T	84125349	2	4	77	1	0	0	0	0	0	0	0	1	9391	523	19	1		1	MBTPS1	16	84125349	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2421583	84125349	6229404	940	22676										
KCNG4	93107	broad.mit.edu	37	chr16	84256456	84256456	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctcctcagacaccgccagCgacacgtagtatggggagat	13	12	1	2	rs149847719		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:84256456C>T	ENST00000308251.4	-	3	995	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	309					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.S309S(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						ACACCGCCAGCGACACGTAGT	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	16						C		0,4400		0,0,2200	55	59	58		927	-11.2	0	16	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KCNG4	NM_172347.2		0,1,6499	TT,TC,CC		0.0116,0.0,0.0077		309/520	84256456	1,12999	2200	4300	6500	82813957	SO:0001819	synonymous_variant	93107			AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.927G>A	16.37:g.84256456C>T			82813957	Q96H24	Silent	SNP	ENST00000308251.4	37	CCDS10945.1																																																																																				0.642	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347		T	84256456	C	T	84256456	2	4	77	1	0	0	0	0	0	0	0	1	8051	755	27	1		1	KCNG4	16	84256456	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	131107	84256456	6098297	941	22677										
KIAA1609	57707	broad.mit.edu	37	chr16	84529436	84529436	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acgttctcactgggtcccttCgccttccctgtcaggtcgac	9	16	2	0	rs374570802		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:84529436C>T	ENST00000343629.6	-	3	419	c.237G>A	c.(235-237)gcG>gcA	p.A79A	TLDC1_ENST00000561807.1_5'UTR|RP11-517C16.4_ENST00000568771.1_RNA|TLDC1_ENST00000535580.1_Silent_p.A52A	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	79						lysosomal membrane (GO:0005765)		p.A79A(1)									TGGGTCCCTTCGCCTTCCCTG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	16						C		0,4400		0,0,2200	158	122	134		237	-10	0	16		134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1609	NM_020947.3		0,1,6499	TT,TC,CC		0.0116,0.0,0.0077		79/457	84529436	1,12999	2200	4300	6500	83086937	SO:0001819	synonymous_variant	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.237G>A	16.37:g.84529436C>T			83086937	Q8IZ64|Q9HCG3|Q9NTE8	Silent	SNP	ENST00000343629.6	37	CCDS32498.1																																																																																				0.562	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		T	84529436	C	T	84529436	2	4	77	1	0	0	0	0	0	0	0	1	8268	871	31	1		1	KIAA1609	16	84529436	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	272980	84529436	5825317	942	22678										
ZCCHC14	23174	broad.mit.edu	37	chr16	87445272	87445272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctggtacacccctgctgTccctgccatgaagttctgca	10	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:87445272T>A	ENST00000268616.4	-	12	2861	c.2644A>T	c.(2644-2646)Aca>Tca	p.T882S		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	882							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.T882S(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		ACCCCTGCTGTCCCTGCCATG	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	16											67	55	59					16																	87445272		2198	4300	6498	86002773	SO:0001583	missense	23174			AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2644A>T	16.37:g.87445272T>A	ENSP00000268616:p.Thr882Ser		86002773	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	T	4.657	0.122157	0.08931	.	.	ENSG00000140948	ENST00000268616	T	0.17854	2.25	5.28	0.0753	0.14399	.	0.395617	0.26314	N	0.025084	T	0.07098	0.0180	N	0.24115	0.695	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.12156	0.007;0.002	T	0.27054	-1.0085	10	0.15499	T	0.54	-2.1641	0.259	0.00216	0.2829:0.2183:0.1382:0.3607	.	882;882	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	S	882	ENSP00000268616:T882S	ENSP00000268616:T882S	T	-	1	0	ZCCHC14	86002773	0.186000	0.23225	0.212000	0.23672	0.389000	0.30415	0.031000	0.13710	0.107000	0.17824	0.533000	0.62120	ACA		0.602	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445272	T	A	87445272	3	1	77	1	0	0	0	0	1	0	0	0	17622	1667	58	5	213	5	ZCCHC14	16	87445272	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	2915836	87445272	2909481	943	22679										
ZC3H18	124245	broad.mit.edu	37	chr16	88690402	88690402	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgtccccgtccccgtccccAacaccttccccacatagacc	4	23	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:88690402A>G	ENST00000301011.5	+	11	2030	c.1830A>G	c.(1828-1830)ccA>ccG	p.P610P	ZC3H18_ENST00000452588.2_Silent_p.P634P	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	610	Ser-rich.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P610P(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CCCCGTCCCCAACACCTTCCC	0.652																																					Ovarian(121;375 2276 20373 38669)											1	Substitution - coding silent(1)	large_intestine(1)	16											98	94	95					16																	88690402		2198	4300	6498	87217903	SO:0001819	synonymous_variant	124245			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1830A>G	16.37:g.88690402A>G			87217903	Q96DG4|Q96MP7	Silent	SNP	ENST00000301011.5	37	CCDS10967.1																																																																																				0.652	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		G	88690402	A	G	88690402	2	3	77	1	0	0	0	0	0	0	0	1	17607	117	5	4		4	ZC3H18	16	88690402	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1245130	88690402	1664351	944	22680										
ZC3H18	124245	broad.mit.edu	37	chr16	88694459	88694459	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcgacaccccagcaggcaCcccccgggcagccccagcag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:88694459delC	ENST00000301011.5	+	15	2601	c.2401delC	c.(2401-2403)cccfs	p.P802fs	ZC3H18_ENST00000452588.2_Frame_Shift_Del_p.P826fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	802						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q804fs*15(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CCAGCAGGCACCCCCCGGGCA	0.612																																					Ovarian(121;375 2276 20373 38669)											1	Deletion - Frameshift(1)	large_intestine(1)	16											59	77	70					16																	88694459		2198	4300	6498	87221960	SO:0001589	frameshift_variant	124245			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.2401delC	16.37:g.88694459delC	ENSP00000301011:p.Pro802fs		87221960	Q96DG4|Q96MP7	Frame_Shift_Del	DEL	ENST00000301011.5	37	CCDS10967.1																																																																																				0.612	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		-	88694459	C	-	88694459	7	5	77	1	0	1	0	1	0	0	0	0	17607	507	18	0	2455	0	ZC3H18	16	88694459	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	4057	88694459	1660294	945	22681										
ANKRD11	29123	broad.mit.edu	37	chr16	89347487	89347487	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagggtggcatgggagagtcGtagctggaggcagcaggaac	20	6	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:89347487G>A	ENST00000301030.4	-	9	5923	c.5463C>T	c.(5461-5463)taC>taT	p.Y1821Y	ANKRD11_ENST00000378330.2_Silent_p.Y1821Y	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1821					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Y1821Y(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TGGGAGAGTCGTAGCTGGAGG	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	16											34	37	36					16																	89347487		2198	4299	6497	87874988	SO:0001819	synonymous_variant	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.5463C>T	16.37:g.89347487G>A			87874988	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																				0.622	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89347487	G	A	89347487	2	1	77	1	0	0	0	0	0	0	0	1	639	1140	40	1		1	ANKRD11	16	89347487	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	653028	89347487	1007266	946	22682										
DBNDD1	79007	broad.mit.edu	37	chr16	90075815	90075815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacgcccagcgcagcctgcgGcacctcagcctccttaacga	10	18	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr16:90075815G>A	ENST00000002501.6	-	2	186	c.55C>T	c.(55-57)Ccg>Tcg	p.P19S	DBNDD1_ENST00000392973.3_Missense_Mutation_p.P25S|DBNDD1_ENST00000568838.1_Missense_Mutation_p.P139S|DBNDD1_ENST00000304733.3_Missense_Mutation_p.P39S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	19						cytoplasm (GO:0005737)		p.P19S(1)		kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		GCAGCCTGCGGCACCTCAGCC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	16											79	92	88					16																	90075815		2075	4207	6282	88603316	SO:0001583	missense	79007			AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.55C>T	16.37:g.90075815G>A	ENSP00000002501:p.Pro19Ser		88603316	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.389682	0.25118	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.40756	1.02;1.02	4.71	2.43	0.29744	.	0.576204	0.16872	N	0.196073	T	0.30135	0.0755	L	0.42245	1.32	0.09310	N	1	B;B	0.17268	0.021;0.003	B;B	0.17722	0.019;0.012	T	0.07158	-1.0787	9	.	.	.	-12.6188	6.6968	0.23203	0.1127:0.1871:0.7002:0.0	.	19;39	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	S	39;19;139	ENSP00000306407:P39S;ENSP00000002501:P19S	.	P	-	1	0	DBNDD1	88603316	0.880000	0.30214	0.142000	0.22268	0.036000	0.12997	1.834000	0.39171	2.170000	0.68504	0.563000	0.77884	CCG		0.662	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		A	90075815	G	A	90075815	3	1	77	1	0	0	0	0	1	0	0	0	4259	1203	42	3	433	3	DBNDD1	16	90075815	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	728328	90075815	278938	947	22683										
RPH3AL	9501	broad.mit.edu	37	chr17	169336	169336	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtctccagccgctccaccaGccgcctgcagcacaggacac	10	19	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:169336G>A	ENST00000331302.7	-	5	533	c.226C>T	c.(226-228)Ctg>Ttg	p.L76L	RPH3AL_ENST00000536489.2_Silent_p.L76L|RP11-1260E13.1_ENST00000572998.1_RNA|RPH3AL_ENST00000576001.1_5'Flank|RP11-1260E13.1_ENST00000570501.1_RNA|RPH3AL_ENST00000323434.8_Silent_p.L76L	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	76	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)	p.L76L(1)		NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CGCTCCACCAGCCGCCTGCAG	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	17											75	61	66					17																	169336		2200	4296	6496	169336	SO:0001819	synonymous_variant	9501				CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"Synaptotagmins"	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.226C>T	17.37:g.169336G>A			169336	D3DTG7|Q9BSB3	Silent	SNP	ENST00000331302.7	37	CCDS10994.1																																																																																				0.642	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987		A	169336	G	A	169336	2	1	77	1	0	0	0	0	0	0	0	1	13589	962	34	3		3	RPH3AL	17	169336	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		169336	81025874	948	22684										
TIMM22	29928	broad.mit.edu	37	chr17	900503	900503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgacaagcgtcagccccggCtcctggagcctgggagcctg	15	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:900503C>T	ENST00000327158.4	+	1	147	c.121C>T	c.(121-123)Ctc>Ttc	p.L41F		NM_013337.2	NP_037469.2	Q9Y584	TIM22_HUMAN	translocase of inner mitochondrial membrane 22 homolog (yeast)	41					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial inner membrane (GO:0045039)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	protein channel activity (GO:0015266)	p.L41F(1)		breast(2)|endometrium(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	7				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCAGCCCCGGCTCCTGGAGCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											29	33	32					17																	900503		2203	4300	6503	847253	SO:0001583	missense	29928			AF155330	CCDS32521.1	17p13	2008-02-05	2003-07-22			ENSG00000177370			17317	protein-coding gene	gene with protein product		607251	"testis-expressed sequence 4"	TEX4			Standard	NM_013337		Approved		uc002fsc.3	Q9Y584		ENST00000327158.4:c.121C>T	17.37:g.900503C>T	ENSP00000320236:p.Leu41Phe		847253	Q9NWI8	Missense_Mutation	SNP	ENST00000327158.4	37	CCDS32521.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.994251	0.54041	.	.	ENSG00000177370	ENST00000327158	T	0.44482	0.92	5.42	3.35	0.38373	.	0.569846	0.19102	N	0.122675	T	0.27027	0.0662	N	0.22421	0.69	0.28146	N	0.929582	B	0.25169	0.119	B	0.21151	0.033	T	0.16837	-1.0389	10	0.56958	D	0.05	-4.6282	7.9484	0.29999	0.2967:0.4578:0.2455:0.0	.	41	Q9Y584	TIM22_HUMAN	F	41	ENSP00000320236:L41F	ENSP00000320236:L41F	L	+	1	0	TIMM22	847253	0.986000	0.35501	1.000000	0.80357	0.940000	0.58332	1.512000	0.35812	0.569000	0.29329	0.485000	0.47835	CTC		0.647	TIMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450107.2	NM_013337		T	900503	C	T	900503	3	4	77	1	0	0	0	0	1	0	0	0	15949	797	28	3	123	3	TIMM22	17	900503	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	731167	900503	80294707	949	22685										
TUSC5	286753	broad.mit.edu	37	chr17	1198899	1198899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgtcattatcatggtggccGtgaccgtcaacttcacaggt	10	11	4	1	rs372589098		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:1198899G>A	ENST00000333813.3	+	2	841	c.502G>A	c.(502-504)Gtg>Atg	p.V168M		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	168					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)		p.V168M(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CATGGTGGCCGTGACCGTCAA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	17											88	98	95					17																	1198899		2148	4242	6390	1145649	SO:0001583	missense	286753			AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"located at seventeen p thirteen point three 1", "interferon induced transmembrane protein domain containing 3"	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.502G>A	17.37:g.1198899G>A	ENSP00000329548:p.Val168Met		1145649	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	37	CCDS42225.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.732983	0.30684	.	.	ENSG00000184811	ENST00000333813	T	0.74526	-0.85	5.34	0.82	0.18793	.	0.698644	0.12270	U	0.483931	T	0.62478	0.2431	M	0.68317	2.08	0.09310	N	1	P	0.40398	0.716	B	0.28638	0.092	T	0.55909	-0.8066	10	0.59425	D	0.04	-7.2288	4.8394	0.13483	0.1622:0.0:0.5418:0.296	.	168	Q8IXB3	TUSC5_HUMAN	M	168	ENSP00000329548:V168M	ENSP00000329548:V168M	V	+	1	0	TUSC5	1145649	0.001000	0.12720	0.054000	0.19295	0.273000	0.26683	0.242000	0.18087	0.246000	0.21394	-0.243000	0.11985	GTG		0.622	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367		A	1198899	G	A	1198899	3	1	77	1	0	0	0	0	1	0	0	0	16819	1145	40	1	508	1	TUSC5	17	1198899	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	298396	1198899	79996311	950	22686										
YWHAE	7531	broad.mit.edu	37	chr17	1264466	1264466	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agacctaagcgaataggatgCgttggtggaagttctgtcat	13	6	2	1	rs146808095	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:1264466C>T	ENST00000264335.8	-	4	765	c.498G>A	c.(496-498)acG>acA	p.T166T	YWHAE_ENST00000575977.1_Intron|YWHAE_ENST00000573026.1_Intron|YWHAE_ENST00000571732.1_Silent_p.T144T	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon	166					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)	p.T166T(2)		kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		GAATAGGATGCGTTGGTGGAA	0.463			T	"FAM22a, FAM22B"	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome																																Dom	yes		17	17p13.3	7531	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)"	yes	M	2	Substitution - coding silent(2)	large_intestine(2)	17						C		3,4403	6.2+/-15.9	0,3,2200	133	125	127		498	-1.5	1	17	dbSNP_134	127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	YWHAE	NM_006761.4		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		166/256	1264466	4,13002	2203	4300	6503	1211216	SO:0001819	synonymous_variant	7531			U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953			12851	protein-coding gene	gene with protein product	"14-3-3 epsilon"	605066	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"			9371399	Standard	NM_006761		Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.498G>A	17.37:g.1264466C>T			1211216	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	Silent	SNP	ENST00000264335.8	37	CCDS11001.1																																																																																				0.463	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259354.3	NM_006761		T	1264466	C	T	1264466	2	4	77	1	0	0	0	0	0	0	0	1	17542	755	27	1		1	YWHAE	17	1264466	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	65567	1264466	79930744	951	22687										
PRPF8	10594	broad.mit.edu	37	chr17	1584923	1584924	+	Frame_Shift_Del	DEL	AG	AG	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagctgattagccaggcggtAgagagtcgacatcataggta							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:1584923_1584924delAG	ENST00000572621.1	-	5	979_980	c.714_715delCT	c.(712-717)ctctacfs	p.Y239fs	PRPF8_ENST00000304992.6_Frame_Shift_Del_p.Y239fs			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	239					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.Y239fs*4(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GCCAGGCGGTAGAGAGTCGACA	0.47																																																1	Deletion - Frameshift(1)	large_intestine(1)	17																																								1531674	SO:0001589	frameshift_variant	10594			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.714_715delCT	17.37:g.1584927_1584928delAG	ENSP00000460348:p.Tyr239fs		1531673	O14547|O75965	Frame_Shift_Del	DEL	ENST00000572621.1	37	CCDS11010.1																																																																																				0.47	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			-	1584924	AG	-	1584923	7	5	77	1	0	1	0	1	0	0	0	0	12609	420	15	0	6444	0	PRPF8	17	1584923	Frame_Shift_Del	DEL	AG	TCGA-AG-A02N-01A-11W-A096-10	320457	1584923	79610287	952	22688										
MNT	4335	broad.mit.edu	37	chr17	2290266	2290266	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacagggttgagcacggtctGgcccaccagctgggggtggt	17	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:2290266G>A	ENST00000174618.4	-	6	2083	c.1678C>T	c.(1678-1680)Cag>Tag	p.Q560*	MNT_ENST00000575374.1_5'Flank|RP1-59D14.1_ENST00000571775.1_RNA	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	560					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.Q560*(1)		endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		AGCACGGTCTGGCCCACCAGC	0.677																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											28	25	26					17																	2290266		2190	4291	6481	2237016	SO:0001587	stop_gained	4335			Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7188	protein-coding gene	gene with protein product	"myc antagonist", "Max-interacting protein"	603039	"MAX binding protein", "MNT, MAX dimerization protein"			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1678C>T	17.37:g.2290266G>A	ENSP00000174618:p.Gln560*		2237016	A8K6D1|D3DTI7|Q1ED38	Nonsense_Mutation	SNP	ENST00000174618.4	37	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	G	41	9.086166	0.99061	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	.	.	.	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-13.3413	17.0679	0.86564	0.0:0.0:1.0:0.0	.	.	.	.	X	560	.	ENSP00000174618:Q560X	Q	-	1	0	MNT	2237016	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.636000	0.98440	2.274000	0.75844	0.591000	0.81541	CAG		0.677	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310		A	2290266	G	A	2290266	4	1	77	1	0	0	0	0	0	1	0	0	9708	1357	47	3	74	3	MNT	17	2290266	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	705343	2290266	78904944	953	22689										
METT10D	79066	broad.mit.edu	37	chr17	2324125	2324125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttgagggataattccttcAtcacggacgccagcaccacg	9	13	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:2324125A>G	ENST00000263092.6	-	9	1089	c.962T>C	c.(961-963)aTg>aCg	p.M321T	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.M103T	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	321							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.M321T(2)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						TAATTCCTTCATCACGGACGC	0.453																																																2	Substitution - Missense(2)	large_intestine(2)	17											249	232	238					17																	2324125		1926	4152	6078	2270875	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.962T>C	17.37:g.2324125A>G	ENSP00000263092:p.Met321Thr		2270875	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.456423	0.26161	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.43688	0.97;0.94	6.06	6.06	0.98353	.	0.326036	0.40640	N	0.001043	T	0.42607	0.1210	L	0.57536	1.79	0.43275	D	0.995232	B	0.21753	0.06	B	0.18263	0.021	T	0.31530	-0.9940	10	0.66056	D	0.02	-6.5643	14.5675	0.68188	1.0:0.0:0.0:0.0	.	321	Q86W50	MET16_HUMAN	T	321;1;103	ENSP00000263092:M321T;ENSP00000443633:M103T	ENSP00000263092:M321T	M	-	2	0	METTL16	2270875	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	6.667000	0.74451	2.315000	0.78130	0.533000	0.62120	ATG		0.453	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		G	2324125	A	G	2324125	3	3	77	1	0	0	0	0	1	0	0	0	9520	217	8	4	734	4	METT10D	17	2324125	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	33859	2324125	78871085	954	22690										
METT10D	79066	broad.mit.edu	37	chr17	2381160	2381160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtcagagctctgactgcttCggggtctttaaaattaaggc	11	9	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:2381160C>T	ENST00000263092.6	-	3	275	c.148G>A	c.(148-150)Gaa>Aaa	p.E50K	METTL16_ENST00000538844.1_5'UTR|METTL16_ENST00000571669.2_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	50							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.E50K(2)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						CTGACTGCTTCGGGGTCTTTA	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	17											94	90	91					17																	2381160		1839	4081	5920	2327910	SO:0001583	missense	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.148G>A	17.37:g.2381160C>T	ENSP00000263092:p.Glu50Lys		2327910	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724193	0.68959	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.17370	2.28	6.07	6.07	0.98685	.	0.151027	0.64402	D	0.000007	T	0.11196	0.0273	N	0.25245	0.725	0.80722	D	1	B;B	0.32829	0.076;0.386	B;B	0.29598	0.021;0.104	T	0.23332	-1.0191	10	0.17832	T	0.49	-14.3847	13.0052	0.58701	0.1611:0.8389:0.0:0.0	.	50;50	Q86W50-2;Q86W50	.;MET16_HUMAN	K	50	ENSP00000263092:E50K	ENSP00000263092:E50K	E	-	1	0	METTL16	2327910	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	4.780000	0.62382	2.890000	0.99128	0.650000	0.86243	GAA		0.408	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		T	2381160	C	T	2381160	3	4	77	1	0	0	0	0	1	0	0	0	9520	893	31	1	1572	1	METT10D	17	2381160	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	57035	2381160	78814050	955	22691										
ZZEF1	23140	broad.mit.edu	37	chr17	3917692	3917692	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agacccgctgaagctgtgtcGgtcttgctggaagtcactgc	13	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:3917692G>A	ENST00000381638.2	-	50	8387	c.8263C>T	c.(8263-8265)Cga>Tga	p.R2755*		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2755							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R2755*(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						AAGCTGTGTCGGTCTTGCTGG	0.478																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											142	128	133					17																	3917692		2203	4300	6503	3864441	SO:0001587	stop_gained	23140			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8263C>T	17.37:g.3917692G>A	ENSP00000371051:p.Arg2755*		3864441	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Nonsense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	49	15.526175	0.99836	.	.	ENSG00000074755	ENST00000381638	.	.	.	5.17	5.17	0.71159	.	0.233606	0.37955	N	0.001867	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.938	18.8737	0.92327	0.0:0.0:1.0:0.0	.	.	.	.	X	2755	.	ENSP00000371051:R2755X	R	-	1	2	ZZEF1	3864441	1.000000	0.71417	0.993000	0.49108	0.896000	0.52359	3.398000	0.52579	2.703000	0.92315	0.655000	0.94253	CGA		0.478	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		A	3917692	G	A	3917692	4	1	77	1	0	0	0	0	0	1	0	0	18294	1124	39	1	646	1	ZZEF1	17	3917692	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1536532	3917692	77277518	956	22692										
MYBBP1A	10514	broad.mit.edu	37	chr17	4442902	4442902	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaggttccgtgggggacccGggagctccattcacctggga	16	12	1	0	rs201681236		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:4442902G>A	ENST00000254718.4	-	26	4101	c.3795C>T	c.(3793-3795)ccC>ccT	p.P1265P	MYBBP1A_ENST00000381556.2_Silent_p.P1265P			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1265	Required for nuclear and nucleolar localization. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)	p.P1265P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGGGGGACCCGGGAGCTCCAT	0.617													G|||	1	0.000199681	0	0	5008	,	,		13469	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17						G	,,	0,4406		0,0,2203	115	127	123		3795,,3795	-3.4	0	17		123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,utr-3,coding-synonymous	MYBBP1A,SPNS2	NM_001105538.1,NM_001124758.1,NM_014520.3	,,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,,	1265/1333,,1265/1329	4442902	3,13003	2203	4300	6503	4389651	SO:0001819	synonymous_variant	10514			AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3795C>T	17.37:g.4442902G>A			4389651	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																				0.617	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		A	4442902	G	A	4442902	2	1	77	1	0	0	0	0	0	0	0	1	10038	1103	39	1		1	MYBBP1A	17	4442902	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	525210	4442902	76752308	957	22693										
KIAA0753	9851	broad.mit.edu	37	chr17	6513474	6513474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctacctctttcagctttgcGgagtccctgtgagagataag	10	10	3	2	rs370311617		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:6513474G>A	ENST00000361413.3	-	9	1910	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	KIAA0753_ENST00000589033.1_5'UTR|KIAA0753_ENST00000542606.1_Missense_Mutation_p.R219C|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R219C	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	518						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R518C(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TCAGCTTTGCGGAGTCCCTGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	17						A	CYS/ARG	0,3802		0,0,1901	149	142	144		1552	3.2	0	17		144	1,8241		0,1,4120	no	missense	KIAA0753	NM_014804.2	180	0,1,6021	AA,AG,GG		0.0121,0.0,0.0083	possibly-damaging	518/968	6513474	1,12043	1901	4121	6022	6454198	SO:0001583	missense	9851				CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1552C>T	17.37:g.6513474G>A	ENSP00000355250:p.Arg518Cys		6454198	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	g	14.04	2.417355	0.42918	0.0	1.21E-4	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86164	-2.08;-2.08	5.14	3.16	0.36331	.	1.014290	0.07860	N	0.966163	T	0.81616	0.4860	L	0.40543	1.245	0.80722	D	1	P	0.47106	0.89	B	0.40101	0.319	T	0.71738	-0.4502	10	0.39692	T	0.17	0.9102	8.3041	0.32032	0.1836:0.0:0.8164:0.0	.	518	Q2KHM9	K0753_HUMAN	C	518;219	ENSP00000355250:R518C;ENSP00000444634:R219C	ENSP00000355250:R518C	R	-	1	0	KIAA0753	6454198	0.005000	0.15991	0.001000	0.08648	0.050000	0.14768	1.525000	0.35953	0.698000	0.31739	-0.127000	0.14921	CGC		0.428	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		A	6513474	G	A	6513474	3	1	77	1	0	0	0	0	1	0	0	0	8212	1116	39	1	1395	1	KIAA0753	17	6513474	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2070572	6513474	74681736	958	22694										
TEKT1	83659	broad.mit.edu	37	chr17	6704119	6704119	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcattagcctatattgtgcGacatcacgacacagctccac	6	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:6704119G>A	ENST00000338694.2	-	7	1125	c.996C>T	c.(994-996)gtC>gtT	p.V332V	TEKT1_ENST00000535086.1_Silent_p.V186V	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	332			V -> I (in dbSNP:rs2271233).			cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.V332V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TATATTGTGCGACATCACGAC	0.557											OREG0024124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - coding silent(1)	large_intestine(1)	17											231	207	215					17																	6704119		2203	4300	6503	6644843	SO:0001819	synonymous_variant	83659				CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.996C>T	17.37:g.6704119G>A		636	6644843	D3DTM7	Silent	SNP	ENST00000338694.2	37	CCDS11083.1																																																																																				0.557	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		A	6704119	G	A	6704119	2	1	77	1	0	0	0	0	0	0	0	1	15791	1045	37	1		1	TEKT1	17	6704119	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	190645	6704119	74491091	959	22695										
NLGN2	57555	broad.mit.edu	37	chr17	7319114	7319114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtacacagactgggccgaccGggacaatggcgaaatgcgcc	14	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:7319114G>A	ENST00000302926.2	+	6	1395	c.1322G>A	c.(1321-1323)cGg>cAg	p.R441Q	NLGN2_ENST00000575301.1_Missense_Mutation_p.R441Q	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	441					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.R441Q(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				TGGGCCGACCGGGACAATGGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											91	88	89					17																	7319114		2203	4300	6503	7259838	SO:0001583	missense	57555			AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1322G>A	17.37:g.7319114G>A	ENSP00000305288:p.Arg441Gln		7259838	Q9P2I1	Missense_Mutation	SNP	ENST00000302926.2	37	CCDS11103.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852812	0.91355	.	.	ENSG00000169992	ENST00000302926	T	0.67171	-0.25	5.41	5.41	0.78517	Carboxylesterase, type B (1);	0.129093	0.50627	D	0.000112	T	0.60625	0.2283	L	0.41356	1.27	0.80722	D	1	P	0.51240	0.943	B	0.42319	0.383	T	0.63251	-0.6679	10	0.45353	T	0.12	.	16.7464	0.85473	0.0:0.0:1.0:0.0	.	441	Q8NFZ4	NLGN2_HUMAN	Q	441	ENSP00000305288:R441Q	ENSP00000305288:R441Q	R	+	2	0	NLGN2	7259838	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.791000	0.85805	2.826000	0.97356	0.561000	0.74099	CGG		0.567	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		A	7319114	G	A	7319114	3	1	77	1	0	0	0	0	1	0	0	0	10493	1116	39	1	1344	1	NLGN2	17	7319114	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	614995	7319114	73876096	960	22696										
TP53	7157	broad.mit.edu	37	chr17	7579313	7579313	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcccctcagggcaactgaccGtgcaagtcacagacttggct	11	14	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:7579313G>A	ENST00000269305.4	-	4	563	c.374C>T	c.(373-375)aCg>aTg	p.T125M	TP53_ENST00000413465.2_Splice_Site_p.T125M|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site_p.T125M|TP53_ENST00000359597.4_Splice_Site_p.T125M|TP53_ENST00000445888.2_Splice_Site_p.T125M|TP53_ENST00000455263.2_Splice_Site_p.T125M	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	125	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in a sporadic cancer; somatic mutation).|T -> K (in sporadic cancers; somatic mutation).|T -> M (in sporadic cancers; somatic mutation).|T -> P (in a sporadic cancer; somatic mutation).|T -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.T125M(16)|p.0?(8)|p.T125K(6)|p.T125R(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y126fs*11(1)|p.Y107fs*44(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAACTGACCGTGCAAGTCAC	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	42	Substitution - Missense(25)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(1)	large_intestine(8)|upper_aerodigestive_tract(7)|lung(6)|haematopoietic_and_lymphoid_tissue(5)|bone(4)|central_nervous_system(3)|urinary_tract(3)|breast(2)|stomach(1)|liver(1)|pancreas(1)|prostate(1)	17											66	62	63					17																	7579313		2203	4300	6503	7520038	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.375+1C>T	17.37:g.7579313G>A			7520038	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430623	0.83776	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99850	-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99743	0.9898	M	0.70787	2.145	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.994;1.0;0.997;1.0	D;D;D;P;D;D;D	0.97110	1.0;0.956;0.986;0.868;0.985;0.981;1.0	D	0.96893	0.9654	10	0.87932	D	0	-16.188	15.6419	0.77012	0.0:0.0:1.0:0.0	.	86;125;125;125;125;125;125	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	M	125;125;125;125;125;125;114;125;125	ENSP00000410739:T125M;ENSP00000352610:T125M;ENSP00000269305:T125M;ENSP00000398846:T125M;ENSP00000391127:T125M;ENSP00000391478:T125M;ENSP00000424104:T125M;ENSP00000426252:T125M	ENSP00000269305:T125M	T	-	2	0	TP53	7520038	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.798000	0.85924	2.630000	0.89119	0.655000	0.94253	ACG		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Missense_Mutation	A	7579313	G	A	7579313	5	1	77	1	0	0	0	0	0	0	1	0	16421	1159	40	1	928	1	TP53	17	7579313	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	260199	7579313	73615897	961	22697										
DNAH2	146754	broad.mit.edu	37	chr17	7636490	7636490	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcaactgtgcagtttgggaCggtgcggggcccctatatcc	15	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:7636490C>T	ENST00000572933.1	+	5	1945	c.485C>T	c.(484-486)aCg>aTg	p.T162M	DNAH2_ENST00000082259.3_Missense_Mutation_p.T162M|DNAH2_ENST00000570791.1_Missense_Mutation_p.T162M|DNAH2_ENST00000389173.2_Missense_Mutation_p.T162M			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	162	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T162M(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CAGTTTGGGACGGTGCGGGGC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											100	96	97					17																	7636490		2203	4300	6503	7577215	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.485C>T	17.37:g.7636490C>T	ENSP00000458355:p.Thr162Met		7577215	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.884298	0.51908	.	.	ENSG00000183914	ENST00000360606;ENST00000389173;ENST00000082259	T;T	0.57907	0.37;0.37	5.56	3.59	0.41128	.	0.873352	0.09861	N	0.746182	T	0.56411	0.1983	N	0.16368	0.405	0.32614	N	0.524236	D;D	0.76494	0.999;0.999	P;D	0.71870	0.826;0.975	T	0.59215	-0.7496	10	0.48119	T	0.1	.	11.2974	0.49286	0.0:0.8496:0.0:0.1504	.	162;162	Q9P225;Q9P225-3	DYH2_HUMAN;.	M	162	ENSP00000373825:T162M;ENSP00000082259:T162M	ENSP00000082259:T162M	T	+	2	0	DNAH2	7577215	0.992000	0.36948	0.765000	0.31456	0.510000	0.34073	3.005000	0.49521	0.735000	0.32537	-0.126000	0.14955	ACG		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7636490	C	T	7636490	3	4	77	1	0	0	0	0	1	0	0	0	4613	536	19	1	499	1	DNAH2	17	7636490	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	57177	7636490	73558720	962	22698										
GUCY2D	3000	broad.mit.edu	37	chr17	7915606	7915606	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctctcttcaggacctcctcGctcagagagaaataaagctg	9	12	3	2	rs567708710		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:7915606G>A	ENST00000254854.4	+	9	2044	c.1894G>A	c.(1894-1896)Gct>Act	p.A632T		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	632	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.A632T(1)		skin(1)	1		Prostate(122;0.157)				GGACCTCCTCGCTCAGAGAGA	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	17											64	65	65					17																	7915606		2203	4300	6503	7856331	SO:0001583	missense	3000			L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1894G>A	17.37:g.7915606G>A	ENSP00000254854:p.Ala632Thr		7856331	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	2.568	-0.300401	0.05532	.	.	ENSG00000132518	ENST00000254854	D	0.82433	-1.61	5.44	3.35	0.38373	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.415630	0.20658	N	0.088068	T	0.67730	0.2924	N	0.26130	0.795	0.09310	N	1	B	0.21071	0.051	B	0.18561	0.022	T	0.52837	-0.8522	10	0.33940	T	0.23	.	3.5752	0.07932	0.0899:0.2847:0.4664:0.1591	.	632	Q02846	GUC2D_HUMAN	T	632	ENSP00000254854:A632T	ENSP00000254854:A632T	A	+	1	0	GUCY2D	7856331	0.000000	0.05858	0.926000	0.36857	0.378000	0.30076	0.214000	0.17541	1.545000	0.49373	-0.133000	0.14855	GCT		0.622	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7915606	G	A	7915606	3	1	77	1	0	0	0	0	1	0	0	0	6918	1087	38	1	1924	1	GUCY2D	17	7915606	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	279116	7915606	73279604	963	22699										
GUCY2D	3000	broad.mit.edu	37	chr17	7917215	7917215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaagtggtgcagagggtgCggagcccccctccactgtgt	15	12	0	2	rs200637525		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:7917215C>T	ENST00000254854.4	+	12	2431	c.2281C>T	c.(2281-2283)Cgg>Tgg	p.R761W		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	761	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.R761W(1)		skin(1)	1		Prostate(122;0.157)				GCAGAGGGTGCGGAGCCCCCC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	TRP/ARG	0,4406		0,0,2203	74	77	76		2281	3.3	0.5	17		76	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GUCY2D	NM_000180.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	761/1104	7917215	1,13005	2203	4300	6503	7857940	SO:0001583	missense	3000			L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2281C>T	17.37:g.7917215C>T	ENSP00000254854:p.Arg761Trp		7857940	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.519992	0.64634	0.0	1.16E-4	ENSG00000132518	ENST00000254854	D	0.83506	-1.73	5.44	3.34	0.38264	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.898770	0.09283	N	0.823427	D	0.89972	0.6870	M	0.88310	2.945	0.09310	N	1	D	0.67145	0.996	P	0.55303	0.773	T	0.79502	-0.1777	10	0.72032	D	0.01	.	11.0092	0.47652	0.1282:0.6448:0.2271:0.0	.	761	Q02846	GUC2D_HUMAN	W	761	ENSP00000254854:R761W	ENSP00000254854:R761W	R	+	1	2	GUCY2D	7857940	0.000000	0.05858	0.522000	0.27862	0.975000	0.68041	0.388000	0.20735	1.510000	0.48803	0.655000	0.94253	CGG		0.622	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			T	7917215	C	T	7917215	3	4	77	1	0	0	0	0	1	0	0	0	6918	759	27	1	2323	1	GUCY2D	17	7917215	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1609	7917215	73277995	964	22700										
GLP2R	9340	broad.mit.edu	37	chr17	9792936	9792936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggaccatgcacgctggcccCggggcagcagcctgtccgag	15	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:9792936C>T	ENST00000262441.5	+	13	2089	c.1576C>T	c.(1576-1578)Cgg>Tgg	p.R526W	GLP2R_ENST00000574745.1_Missense_Mutation_p.R346W	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	526					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)	p.R526W(1)		endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	ACGCTGGCCCCGGGGCAGCAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	17											27	25	26					17																	9792936		2203	4300	6503	9733661	SO:0001583	missense	9340			AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1576C>T	17.37:g.9792936C>T	ENSP00000262441:p.Arg526Trp		9733661	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	37	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	C	7.367	0.625983	0.14257	.	.	ENSG00000065325	ENST00000396206;ENST00000262441	T	0.57107	0.42	5.73	1.02	0.19986	.	0.217078	0.23600	N	0.046441	T	0.41719	0.1171	L	0.55990	1.75	0.23882	N	0.996578	B	0.15141	0.012	B	0.11329	0.006	T	0.40887	-0.9539	10	0.72032	D	0.01	.	5.0187	0.14350	0.3784:0.4473:0.0:0.1742	.	526	O95838	GLP2R_HUMAN	W	526	ENSP00000262441:R526W	ENSP00000262441:R526W	R	+	1	2	GLP2R	9733661	0.020000	0.18652	0.999000	0.59377	0.123000	0.20343	0.068000	0.14531	0.666000	0.31087	0.655000	0.94253	CGG		0.627	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			T	9792936	C	T	9792936	3	4	77	1	0	0	0	0	1	0	0	0	6473	643	23	1	1626	1	GLP2R	17	9792936	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1875721	9792936	71402274	965	22701										
RICH2	9912	broad.mit.edu	37	chr17	12887969	12887969	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccaccccgcccagcaccccGtcaccctatggactgagcta	7	21	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:12887969G>A	ENST00000379672.5	+	20	2361	c.2061G>A	c.(2059-2061)ccG>ccA	p.P687P	ARHGAP44_ENST00000340825.3_Silent_p.P681P|ARHGAP44_ENST00000262444.9_Silent_p.P687P	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	687					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)	p.P687P(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CCAGCACCCCGTCACCCTATG	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	17											22	26	24					17																	12887969		1891	4104	5995	12828694	SO:0001819	synonymous_variant	9912				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.2061G>A	17.37:g.12887969G>A			12828694	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																				0.667	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12887969	G	A	12887969	2	1	77	1	0	0	0	0	0	0	0	1	13394	1132	40	1		1	RICH2	17	12887969	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3095033	12887969	68307241	966	22702										
COPS3	8533	broad.mit.edu	37	chr17	17165397	17165397	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccaacatgatatgactgacCgccatggcaggagtagttat	10	9	0	3	rs374574802		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:17165397C>T	ENST00000268717.5	-	7	751	c.645G>A	c.(643-645)gcG>gcA	p.A215A	COPS3_ENST00000539941.2_Silent_p.A195A|COPS3_ENST00000439936.2_Silent_p.A195A	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	215	PCI.				cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.A215A(1)		NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TATGACTGACCGCCATGGCAG	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	17											59	58	59					17																	17165397		2203	4299	6502	17106122	SO:0001819	synonymous_variant	8533			AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3", "COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.645G>A	17.37:g.17165397C>T			17106122	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000268717.5	37	CCDS11183.1																																																																																				0.358	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			T	17165397	C	T	17165397	2	4	77	1	0	0	0	0	0	0	0	1	3740	639	23	1		1	COPS3	17	17165397	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4277428	17165397	64029813	967	22703										
MYO15A	51168	broad.mit.edu	37	chr17	18082115	18082115	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtcgtgtggtggccgtgcaCgtggagaacctgctcagtgc	16	10	1	1	rs375839184		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:18082115C>T	ENST00000205890.5	+	66	10862	c.10524C>T	c.(10522-10524)caC>caT	p.H3508H	MYO15A_ENST00000418233.3_Missense_Mutation_p.R790C|RP11-258F1.1_ENST00000577847.1_RNA|MYO15A_ENST00000451725.2_3'UTR|RP11-258F1.1_ENST00000583062.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3508	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.H3508H(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TGGCCGTGCACGTGGAGAACC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		0,4304		0,0,2152	129	144	139		10524	-11	0.3	17		139	2,8532		0,2,4265	no	coding-synonymous	MYO15A	NM_016239.3		0,2,6417	TT,TC,CC		0.0234,0.0,0.0156		3508/3531	18082115	2,12836	2152	4267	6419	18022840	SO:0001819	synonymous_variant	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10524C>T	17.37:g.18082115C>T			18022840	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18082115	C	T	18082115	2	4	77	1	0	0	0	0	0	0	0	1	10093	535	19	1		1	MYO15A	17	18082115	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	916718	18082115	63113095	968	22704										
PRPSAP2	5636	broad.mit.edu	37	chr17	18770596	18770596	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccctttctcttctctaggCggctaggggtggagatgggc	14	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:18770596C>T	ENST00000268835.2	+	4	404	c.121C>T	c.(121-123)Cgg>Tgg	p.R41W	PRPSAP2_ENST00000419071.2_Intron|PRPSAP2_ENST00000542013.1_Splice_Site_p.R41W|PRPSAP2_ENST00000536323.1_Intron	NM_002767.3	NP_002758.1	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 2	41					bone development (GO:0060348)|negative regulation of catalytic activity (GO:0043086)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)	p.R41W(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						CTTCTCTAGGCGGCTAGGGGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	17											108	107	107					17																	18770596		2203	4300	6503	18711321	SO:0001630	splice_region_variant	5636			AB007851	CCDS11200.1, CCDS58525.1, CCDS58526.1, CCDS58527.1	17p12-p11.2	2008-05-14			ENSG00000141127	ENSG00000141127			9467	protein-coding gene	gene with protein product		603762				9806849	Standard	NM_002767		Approved	PAP41	uc002gup.2	O60256	OTTHUMG00000059406	ENST00000268835.2:c.120-1C>T	17.37:g.18770596C>T			18711321	B4E1M8|B4E329|B7ZKZ1|E7EMY2|Q6IAS2	Missense_Mutation	SNP	ENST00000268835.2	37	CCDS11200.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153985	0.78114	.	.	ENSG00000141127	ENST00000441887;ENST00000395656;ENST00000414602;ENST00000432893;ENST00000431320;ENST00000455992;ENST00000412418;ENST00000419284;ENST00000268835;ENST00000422237;ENST00000542013	D;D;D;D;D;D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.1	4.06	0.47325	.	0.126993	0.53938	D	0.000041	D	0.96153	0.8746	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.96428	0.9317	10	0.72032	D	0.01	-2.0379	14.2934	0.66295	0.1494:0.8506:0.0:0.0	.	41;41	B7ZKZ1;O60256	.;KPRB_HUMAN	W	41	ENSP00000395127:R41W;ENSP00000416964:R41W;ENSP00000399625:R41W;ENSP00000416021:R41W;ENSP00000402612:R41W;ENSP00000415446:R41W;ENSP00000268835:R41W;ENSP00000401144:R41W;ENSP00000439129:R41W	ENSP00000268835:R41W	R	+	1	2	PRPSAP2	18711321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.164000	0.50770	2.524000	0.85096	0.655000	0.94253	CGG		0.418	PRPSAP2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132112.3	NM_002767	Missense_Mutation	T	18770596	C	T	18770596	5	4	77	1	0	0	0	0	0	0	1	0	12616	782	27	1	127	1	PRPSAP2	17	18770596	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	688481	18770596	62424614	969	22705										
EPN2	22905	broad.mit.edu	37	chr17	19232062	19232062	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccattgacccatggggggtgCccactggagccaccgtacaa	12	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:19232062C>T	ENST00000314728.5	+	8	1670	c.1186C>T	c.(1186-1188)Ccc>Tcc	p.P396S	EPN2_ENST00000395618.3_Missense_Mutation_p.P111S|EPN2_ENST00000395620.2_Missense_Mutation_p.P339S|EPN2_ENST00000571254.1_Missense_Mutation_p.P332S|EPN2_ENST00000575595.1_Missense_Mutation_p.P104S|EPN2_ENST00000395626.1_Missense_Mutation_p.P396S|EPN2_ENST00000347697.2_Missense_Mutation_p.P339S	NM_014964.4	NP_055779.2	O95208	EPN2_HUMAN	epsin 2	396	6 X 3 AA repeats of [DE]-P-W.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|in utero embryonic development (GO:0001701)|Notch signaling pathway (GO:0007219)	clathrin coat of endocytic vesicle (GO:0030128)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	lipid binding (GO:0008289)	p.P396S(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	19	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					ATGGGGGGTGCCCACTGGAGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											58	53	55					17																	19232062		2203	4300	6503	19172655	SO:0001583	missense	22905			AB028988	CCDS11203.1, CCDS11204.1, CCDS42277.1	17p11.2	2012-11-19			ENSG00000072134	ENSG00000072134			18639	protein-coding gene	gene with protein product	"Eps15 binding protein"	607263				10567358	Standard	NM_014964		Approved	KIAA1065, EHB21	uc002gvd.4	O95208	OTTHUMG00000178447	ENST00000314728.5:c.1186C>T	17.37:g.19232062C>T	ENSP00000320543:p.Pro396Ser		19172655	A8MTV8|B3KRX8|E9PBC2|O95207|Q52LD0|Q9H7Z2|Q9UPT7	Missense_Mutation	SNP	ENST00000314728.5	37	CCDS11203.1	.	.	.	.	.	.	.	.	.	.	C	6.672	0.492516	0.12702	.	.	ENSG00000072134	ENST00000347697;ENST00000395618;ENST00000314728;ENST00000395628;ENST00000395620;ENST00000395626	T;T;T;T;T;T	0.36699	2.39;2.09;2.25;1.41;2.39;1.24	5.14	4.14	0.48551	.	4.198420	0.00589	N	0.000356	T	0.42426	0.1202	M	0.68317	2.08	0.23848	N	0.996679	B;B;B;B;B;B;B	0.26672	0.021;0.156;0.063;0.063;0.038;0.021;0.038	B;B;B;B;B;B;B	0.29077	0.007;0.043;0.098;0.098;0.01;0.007;0.01	T	0.41627	-0.9498	10	0.15066	T	0.55	-8.5582	10.7528	0.46219	0.1481:0.7092:0.1427:0.0	.	339;332;104;111;396;339;396	Q52LD0;B7ZKM5;B7Z3A5;A8MTV8;E9PBC1;E9PBC2;O95208	.;.;.;.;.;.;EPN2_HUMAN	S	339;111;396;339;339;396	ENSP00000261495:P339S;ENSP00000378980:P111S;ENSP00000320543:P396S;ENSP00000378990:P339S;ENSP00000378982:P339S;ENSP00000378988:P396S	ENSP00000320543:P396S	P	+	1	0	EPN2	19172655	0.295000	0.24389	0.022000	0.16811	0.032000	0.12392	1.666000	0.37460	1.229000	0.43630	0.561000	0.74099	CCC		0.617	EPN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132283.3	NM_014964		T	19232062	C	T	19232062	3	4	77	1	0	0	0	0	1	0	0	0	5199	739	26	3	1208	3	EPN2	17	19232062	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	461466	19232062	61963148	970	22706										
VTN	7448	broad.mit.edu	37	chr17	26694894	26694894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccggcgggagttctggttgCggccacggctgtggcctcgt	18	12	1	0	rs150566083		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:26694894C>T	ENST00000226218.4	-	7	1784	c.1166G>A	c.(1165-1167)cGc>cAc	p.R389H	CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.R47H|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000438614.1_5'UTR|VTN_ENST00000431468.1_5'Flank|VTN_ENST00000536498.1_5'UTR|SARM1_ENST00000379061.4_Intron	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	389	Heparin-binding.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.R389H(1)		kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GTTCTGGTTGCGGCCACGGCT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	HIS/ARG	0,4406		0,0,2203	50	46	48		1166	2.7	0	17	dbSNP_134	48	2,8598	2.2+/-6.3	0,2,4298	yes	missense	VTN	NM_000638.3	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	389/479	26694894	2,13004	2203	4300	6503	23719021	SO:0001583	missense	7448			BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"Endogenous ligands"	12724	protein-coding gene	gene with protein product	"serum spreading factor", "somatomedin B", "complement S-protein"	193190	"vitronectin (serum spreading factor, somatomedin B, complement S-protein)"			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.1166G>A	17.37:g.26694894C>T	ENSP00000226218:p.Arg389His		23719021	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790566	0.31685	0.0	2.33E-4	ENSG00000255604	ENST00000226218	T	0.05081	3.5	4.65	2.68	0.31781	Hemopexin/matrixin (1);	0.318929	0.30930	N	0.008597	T	0.04634	0.0126	N	0.20986	0.625	0.20403	N	0.999906	B	0.13145	0.007	B	0.08055	0.003	T	0.34750	-0.9816	10	0.62326	D	0.03	-6.7317	7.8715	0.29569	0.0:0.743:0.0:0.257	.	389	P04004	VTNC_HUMAN	H	389	ENSP00000226218:R389H	ENSP00000226218:R389H	R	-	2	0	AC002094.1	23719021	0.001000	0.12720	0.015000	0.15790	0.005000	0.04900	0.216000	0.17585	0.595000	0.29777	-0.244000	0.11960	CGC		0.592	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638		T	26694894	C	T	26694894	3	4	77	1	0	0	0	0	1	0	0	0	17277	768	27	1	278	1	VTN	17	26694894	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	7462832	26694894	54500316	971	22707										
PROCA1	6830	broad.mit.edu	37	chr17	27030847	27030847	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggctcacgtctggcggggaaGgctccaatttaaccgggctt	14	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:27030847G>T	ENST00000314616.6	+	0	6518				PROCA1_ENST00000301039.2_Missense_Mutation_p.P247H|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Missense_Mutation_p.P249H|PROCA1_ENST00000579650.1_5'Flank	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P247H(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TGGCGGGGAAGGCTCCAATTT	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	17											106	111	109					17																	27030847		2203	4300	6503	24054974	SO:0001628	intergenic_variant	147011			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27030847G>T			24054974	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.963329	0.34659	.	.	ENSG00000167525	ENST00000301039;ENST00000439862;ENST00000415329	T;T	0.04758	3.56;3.56	5.27	3.21	0.36854	.	1.031230	0.07685	N	0.937708	T	0.04407	0.0121	N	0.08118	0	0.09310	N	1	P;P;P	0.49447	0.875;0.924;0.924	P;P;P	0.47941	0.459;0.562;0.562	T	0.44636	-0.9315	10	0.49607	T	0.09	-0.756	6.685	0.23140	0.0957:0.1826:0.7217:0.0	.	275;249;247	Q8NCQ7;G5E9R8;Q8NCQ7-2	PRCA1_HUMAN;.;.	H	247;249;275	ENSP00000301039:P247H;ENSP00000411400:P249H	ENSP00000301039:P247H	P	-	2	0	PROCA1	24054974	0.146000	0.22672	0.983000	0.44433	0.124000	0.20399	1.773000	0.38563	1.294000	0.44707	0.655000	0.94253	CCT		0.522	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27030847	G	T	27030847	1	4	77	0	1	0	0	0	0	0	0	0	12580	1000	35	2		2	PROCA1	17	27030847	IGR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	335953	27030847	54164363	972	22708										
NEK8	284086	broad.mit.edu	37	chr17	27061963	27061963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgacaaacaccgcatggtcGtcaagatcggtgatttcggc	11	10	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:27061963G>A	ENST00000268766.6	+	3	461	c.427G>A	c.(427-429)Gtc>Atc	p.V143I	NEK8_ENST00000593261.1_3'UTR|AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.V143I(1)		breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					CCGCATGGTCGTCAAGATCGG	0.557																																					NSCLC(6;19 293 14866 25253 49845)											1	Substitution - Missense(1)	large_intestine(1)	17											222	180	194					17																	27061963		2203	4300	6503	24086090	SO:0001583	missense	284086			AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.427G>A	17.37:g.27061963G>A	ENSP00000268766:p.Val143Ile		24086090	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	37	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.743417	0.69418	.	.	ENSG00000160602	ENST00000543014;ENST00000268766	T;T	0.26373	1.74;1.74	5.73	5.73	0.89815	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28234	0.0697	L	0.31926	0.97	0.80722	D	1	P	0.51449	0.945	P	0.46940	0.532	T	0.00653	-1.1625	10	0.29301	T	0.29	.	18.8738	0.92327	0.0:0.0:1.0:0.0	.	143	Q86SG6	NEK8_HUMAN	I	143	ENSP00000465859:V143I;ENSP00000268766:V143I	ENSP00000268766:V143I	V	+	1	0	NEK8	24086090	1.000000	0.71417	0.913000	0.36048	0.567000	0.35839	9.449000	0.97603	2.709000	0.92574	0.491000	0.48974	GTC		0.557	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			A	27061963	G	A	27061963	3	1	77	1	0	0	0	0	1	0	0	0	10361	1145	40	1	437	1	NEK8	17	27061963	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	31116	27061963	54133247	973	22709										
LRRC37B	114659	broad.mit.edu	37	chr17	30348649	30348649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcaaactacagatctagatCgggctgcaggtcatcaggca	10	10	4	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:30348649C>T	ENST00000341671.7	+	1	489	c.484C>T	c.(484-486)Cgg>Tgg	p.R162W	LRRC37B_ENST00000327564.7_Missense_Mutation_p.R189W|LRRC37B_ENST00000584368.1_Missense_Mutation_p.R174W|LRRC37B_ENST00000394713.3_Missense_Mutation_p.R162W|LRRC37B_ENST00000543378.2_Missense_Mutation_p.R80W	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	162						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R162W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AGATCTAGATCGGGCTGCAGG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											54	53	54					17																	30348649		2203	4300	6503	27372762	SO:0001583	missense	114659			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.484C>T	17.37:g.30348649C>T	ENSP00000340519:p.Arg162Trp		27372762	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	13.01	2.110729	0.37242	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.66995	-0.18;-0.24;0.87;-0.23	2.05	1.01	0.19927	.	.	.	.	.	T	0.42381	0.1200	N	0.22421	0.69	0.09310	N	1	D;D	0.63880	0.993;0.993	B;B	0.35278	0.199;0.199	T	0.27297	-1.0078	9	0.37606	T	0.19	.	6.3829	0.21544	0.0:0.6881:0.3119:0.0	.	162;162	Q17RC9;Q96QE4	.;LR37B_HUMAN	W	80;189;162;162	ENSP00000443345:R80W;ENSP00000332536:R189W;ENSP00000378202:R162W;ENSP00000340519:R162W	ENSP00000332536:R189W	R	+	1	2	LRRC37B	27372762	0.004000	0.15560	0.010000	0.14722	0.051000	0.14879	0.010000	0.13242	0.388000	0.25054	0.299000	0.19835	CGG		0.488	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		T	30348649	C	T	30348649	3	4	77	1	0	0	0	0	1	0	0	0	9023	875	31	1	486	1	LRRC37B	17	30348649	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3286686	30348649	50846561	974	22710										
NLE1	54475	broad.mit.edu	37	chr17	33460366	33460366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggttggccctacctcatccgCgtggccgggcaggtccatgg	15	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:33460366C>T	ENST00000442241.4	-	11	1405	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	NLE1_ENST00000586869.1_Missense_Mutation_p.A164T|NLE1_ENST00000360831.5_Missense_Mutation_p.A414T	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	456					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)		p.A456T(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				ACCTCATCCGCGTGGCCGGGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17											81	78	79					17																	33460366		2203	4300	6503	30484479	SO:0001583	missense	54475				CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1366G>A	17.37:g.33460366C>T	ENSP00000413572:p.Ala456Thr		30484479	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522641	0.64747	.	.	ENSG00000073536	ENST00000442241;ENST00000360831;ENST00000537697	T	0.54279	0.58	5.41	5.41	0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	N	0.00811	-1.165	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.941;0.999	T	0.64618	-0.6365	10	0.36615	T	0.2	-23.3494	16.7269	0.85424	0.0:1.0:0.0:0.0	.	432;456	B4E074;Q9NVX2	.;NLE1_HUMAN	T	456;164;432	ENSP00000413572:A456T	ENSP00000354075:A164T	A	-	1	0	NLE1	30484479	1.000000	0.71417	0.035000	0.18076	0.177000	0.22998	7.087000	0.76893	2.802000	0.96397	0.563000	0.77884	GCG		0.647	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		T	33460366	C	T	33460366	3	4	77	1	0	0	0	0	1	0	0	0	10491	768	27	1	103	1	NLE1	17	33460366	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3111717	33460366	47734844	975	22711										
ACACA	31	broad.mit.edu	37	chr17	35609842	35609842	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctgctatcagtctgtccagCcagccagtatcaattctgtt	7	12	5	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:35609842C>T	ENST00000394406.2	-	15	2026	c.1836G>A	c.(1834-1836)tgG>tgA	p.W612*	ACACA_ENST00000353139.5_Nonsense_Mutation_p.W649*|ACACA_ENST00000335166.5_Nonsense_Mutation_p.W534*|ACACA_ENST00000360679.3_Nonsense_Mutation_p.W554*	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	612	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.W554*(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GTCTGTCCAGCCAGCCAGTAT	0.423																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											1	Substitution - Nonsense(1)	large_intestine(1)	17											170	172	171					17																	35609842		2203	4300	6503	32683955	SO:0001587	stop_gained	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1836G>A	17.37:g.35609842C>T	ENSP00000377928:p.Trp612*		32683955	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Nonsense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	44	10.686466	0.99450	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3109	19.5674	0.95401	0.0:1.0:0.0:0.0	.	.	.	.	X	649;554;612;636;534	.	ENSP00000335323:W534X	W	-	3	0	ACACA	32683955	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.873000	0.98535	0.561000	0.74099	TGG		0.423	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35609842	C	T	35609842	4	4	77	1	0	0	0	0	0	1	0	0	106	740	26	3	5372	3	ACACA	17	35609842	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2149476	35609842	45585368	976	22712										
FBXO47	494188	broad.mit.edu	37	chr17	37118156	37118156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atctgtagtgctccagtataGcagagtcttgtctcctgtca	9	10	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:37118156G>A	ENST00000378079.2	-	3	525	c.326C>T	c.(325-327)gCt>gTt	p.A109V		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	109								p.A109V(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						CTCCAGTATAGCAGAGTCTTG	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	17											165	154	158					17																	37118156		2203	4300	6503	34371682	SO:0001583	missense	494188				CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.326C>T	17.37:g.37118156G>A	ENSP00000367319:p.Ala109Val		34371682	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	37	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.426281	0.25726	.	.	ENSG00000204952	ENST00000378079	T	0.69306	-0.39	5.59	-1.86	0.07760	.	1.082310	0.06882	N	0.802676	T	0.49406	0.1555	L	0.40543	1.245	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.28776	-1.0033	10	0.27082	T	0.32	0.2948	1.4144	0.02299	0.1587:0.3129:0.2276:0.3008	.	109	Q5MNV8	FBX47_HUMAN	V	109	ENSP00000367319:A109V	ENSP00000367319:A109V	A	-	2	0	FBXO47	34371682	0.000000	0.05858	0.001000	0.08648	0.953000	0.61014	-1.413000	0.02473	0.026000	0.15269	0.462000	0.41574	GCT		0.358	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		A	37118156	G	A	37118156	3	1	77	1	0	0	0	0	1	0	0	0	5775	971	34	3	1068	3	FBXO47	17	37118156	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1508314	37118156	44077054	977	22713										
CDK12	51755	broad.mit.edu	37	chr17	37673767	37673767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctacttcaacaccatgaaacCgaagaagcaatatcgaaggc	7	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:37673767C>T	ENST00000447079.4	+	10	2954	c.2921C>T	c.(2920-2922)cCg>cTg	p.P974L	CDK12_ENST00000430627.2_Missense_Mutation_p.P974L	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	974	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.P974L(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						ACCATGAAACCGAAGAAGCAA	0.463			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	1	Substitution - Missense(1)	large_intestine(1)	17											205	181	189					17																	37673767		2203	4300	6503	34927293	SO:0001583	missense	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2921C>T	17.37:g.37673767C>T	ENSP00000398880:p.Pro974Leu		34927293	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.147627	0.77888	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.39406	1.08;1.08	5.04	5.04	0.67666	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43416	D	0.000578	T	0.56891	0.2016	L	0.37697	1.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.58177	-0.7682	10	0.54805	T	0.06	-7.2995	18.749	0.91806	0.0:1.0:0.0:0.0	.	973;974;974	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	L	974	ENSP00000407720:P974L;ENSP00000398880:P974L	ENSP00000407720:P974L	P	+	2	0	CDK12	34927293	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.754000	0.85163	2.497000	0.84241	0.563000	0.77884	CCG		0.463	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37673767	C	T	37673767	3	4	77	1	0	0	0	0	1	0	0	0	3134	652	23	1	2959	1	CDK12	17	37673767	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	555611	37673767	43521443	978	22714										
KRT26	353288	broad.mit.edu	37	chr17	38922815	38922815	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctactgtaatgttgcttatTttagaggacttttcttcaac	6	7	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:38922815T>C	ENST00000335552.4	-	8	1407	c.1359A>G	c.(1357-1359)aaA>aaG	p.K453K		NM_181539.4	NP_853517.2			keratin 26									p.K453K(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TGTTGCTTATTTTAGAGGACT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)	17											169	166	167					17																	38922815		2203	4300	6503	36176341	SO:0001819	synonymous_variant	353288			AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.1359A>G	17.37:g.38922815T>C			36176341		Silent	SNP	ENST00000335552.4	37	CCDS11374.1																																																																																				0.368	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		C	38922815	T	C	38922815	2	2	77	1	0	0	0	0	0	0	0	1	8484	1838	64	4		4	KRT26	17	38922815	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	1249048	38922815	42272395	979	22715										
KRTAP3-2	83897	broad.mit.edu	37	chr17	39156085	39156085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagtggggacactgcagctGcgagaggcacagcaatccat	13	12	0	1	rs386797022|rs548322379	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:39156085G>A	ENST00000391587.1	-	1	53	c.21C>T	c.(19-21)cgC>cgT	p.R7R		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	7	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R7R(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				CACTGCAGCTGCGAGAGGCAC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	17											65	75	72					17																	39156085		2203	4296	6499	36409611	SO:0001819	synonymous_variant	83897			AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"Keratin associated proteins"	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.21C>T	17.37:g.39156085G>A			36409611		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																				0.552	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1			A	39156085	G	A	39156085	2	1	77	1	0	0	0	0	0	0	0	1	8568	1306	46	3		3	KRTAP3-2	17	39156085	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	233270	39156085	42039125	980	22716										
KRT38	8687	broad.mit.edu	37	chr17	39596806	39596806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cattctcctgctccagctggCgcaccttctccaggtagttg	9	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:39596806C>T	ENST00000246646.3	-	1	367	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	123	Coil 1A.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R123H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				CTCCAGCTGGCGCACCTTCTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											127	111	117					17																	39596806		2203	4300	6503	36850332	SO:0001583	missense	8687			Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.368G>A	17.37:g.39596806C>T	ENSP00000246646:p.Arg123His		36850332	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429455	0.43122	.	.	ENSG00000171360	ENST00000246646	D	0.91843	-2.92	4.45	2.4	0.29515	Filament (1);	0.000000	0.49305	D	0.000141	D	0.90290	0.6963	M	0.84511	2.7	0.09310	N	1	P	0.51537	0.946	B	0.41571	0.36	D	0.84438	0.0581	10	0.66056	D	0.02	.	4.7923	0.13254	0.1725:0.6503:0.0:0.1772	.	123	O76015	KRT38_HUMAN	H	123	ENSP00000246646:R123H	ENSP00000246646:R123H	R	-	2	0	KRT38	36850332	0.000000	0.05858	0.181000	0.23098	0.989000	0.77384	0.024000	0.13555	0.479000	0.27511	0.650000	0.86243	CGC		0.587	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		T	39596806	C	T	39596806	3	4	77	1	0	0	0	0	1	0	0	0	8496	768	27	1	1030	1	KRT38	17	39596806	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	440721	39596806	41598404	981	22717										
KRT19	3880	broad.mit.edu	37	chr17	39681203	39681203	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tccagcaccctgcgcaggccGttgatgtcggcctccacgct	11	17	0	1	rs267607655		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:39681203G>A	ENST00000361566.3	-	3	612	c.552C>T	c.(550-552)aaC>aaT	p.N184N	KRT15_ENST00000254043.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	184	Coil 1B.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.N184N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				TGCGCAGGCCGTTGATGTCGG	0.577													G|||	1	0.000199681	0	0	5008	,	,		19601	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17						G		0,4406		0,0,2203	107	112	110		552	-5.3	0.9	17		110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT19	NM_002276.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		184/401	39681203	1,13005	2203	4300	6503	36934729	SO:0001819	synonymous_variant	3880				CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"-", "Intermediate filaments type I, keratins (acidic)"	6436	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 19", "keratin, type I, 40-kd", "cytokeratin 19", "40-kDa keratin intermediate filament"	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.552C>T	17.37:g.39681203G>A			36934729	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Silent	SNP	ENST00000361566.3	37	CCDS11399.1																																																																																				0.577	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276		A	39681203	G	A	39681203	2	1	77	1	0	0	0	0	0	0	0	1	8477	1136	40	1		1	KRT19	17	39681203	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	84397	39681203	41514007	982	22718										
NT5C3L	115024	broad.mit.edu	37	chr17	39983803	39983803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccctcaagttgctggaagtAaccagagttctcacacgcag	10	12	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:39983803A>G	ENST00000435506.2	-	8	712	c.643T>C	c.(643-645)Tac>Cac	p.Y215H	NT5C3B_ENST00000269534.8_Missense_Mutation_p.Y207H|NT5C3B_ENST00000521789.1_Intron			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	215					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.Y207H(1)									TGCTGGAAGTAACCAGAGTTC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	17											180	173	175					17																	39983803		2203	4300	6503	37237329	SO:0001583	missense	115024				CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic III-like"	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.643T>C	17.37:g.39983803A>G	ENSP00000389948:p.Tyr215His		37237329	A8MWB9|C9JKC4|Q7L3B7	Missense_Mutation	SNP	ENST00000435506.2	37	CCDS11410.2	.	.	.	.	.	.	.	.	.	.	A	12.98	2.100660	0.37048	.	.	ENSG00000141698	ENST00000269534;ENST00000393911;ENST00000435506;ENST00000415460	D;D;D	0.83506	-1.73;-1.73;-1.73	5.07	3.99	0.46301	HAD-like domain (2);	0.057938	0.64402	D	0.000001	T	0.80808	0.4694	M	0.71206	2.165	0.48135	D	0.999593	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.005	T	0.75451	-0.3313	10	0.35671	T	0.21	-1.4575	11.8632	0.52478	0.8534:0.1466:0.0:0.0	.	215;207	C9JKC4;Q969T7	.;5NT3L_HUMAN	H	207;249;215;185	ENSP00000269534:Y207H;ENSP00000389948:Y215H;ENSP00000397742:Y185H	ENSP00000269534:Y207H	Y	-	1	0	NT5C3L	37237329	0.678000	0.27586	0.759000	0.31340	0.833000	0.47200	1.382000	0.34374	0.940000	0.37473	0.379000	0.24179	TAC		0.488	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935		G	39983803	A	G	39983803	3	3	77	1	0	0	0	0	1	0	0	0	10720	362	13	4	267	4	NT5C3L	17	39983803	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	302600	39983803	41211407	983	22719										
CNTNAP1	8506	broad.mit.edu	37	chr17	40843519	40843519	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcctgaggcctctgcgctgCtatggcgatcgtgagtggca	14	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:40843519C>T	ENST00000264638.4	+	15	2551	c.2334C>T	c.(2332-2334)tgC>tgT	p.C778C	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	778	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.C778C(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		CTCTGCGCTGCTATGGCGATC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	17											108	97	101					17																	40843519		2203	4300	6503	38097045	SO:0001819	synonymous_variant	8506			U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"neurexin 4"	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.2334C>T	17.37:g.40843519C>T			38097045		Silent	SNP	ENST00000264638.4	37	CCDS11436.1																																																																																				0.562	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		T	40843519	C	T	40843519	2	4	77	1	0	0	0	0	0	0	0	1	3652	805	28	3		3	CNTNAP1	17	40843519	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	859716	40843519	40351691	984	22720										
CD300LG	146894	broad.mit.edu	37	chr17	41934500	41934500	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccacggagacacagaggaaCgagaagttctgcctctcacg	12	12	2	3	rs142790995	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:41934500C>T	ENST00000317310.4	+	6	902	c.861C>T	c.(859-861)aaC>aaT	p.N287N	CD300LG_ENST00000539718.1_Silent_p.N287N|CD300LG_ENST00000586233.1_Silent_p.N202N|CD300LG_ENST00000293396.8_Silent_p.N202N|CD300LG_ENST00000377203.4_Silent_p.N253N	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	287					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.N287N(1)		central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CACAGAGGAACGAGAAGTTCT	0.567																																																1	Substitution - coding silent(1)	large_intestine(1)	17											127	94	105					17																	41934500		2203	4300	6503	39290026	SO:0001819	synonymous_variant	146894			BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"Immunoglobulin superfamily / V-set domain containing"	30455	protein-coding gene	gene with protein product	"nepmucin"	610520	"CD300 antigen like family member G"			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.861C>T	17.37:g.41934500C>T			39290026	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	37	CCDS11470.1																																																																																				0.567	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273		T	41934500	C	T	41934500	2	4	77	1	0	0	0	0	0	0	0	1	3008	535	19	1		1	CD300LG	17	41934500	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1090981	41934500	39260710	985	22721										
ITGA2B	3674	broad.mit.edu	37	chr17	42457802	42457802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggacacagctcttcacagcaGgattcagtgaatcttgcacc	9	12	4	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:42457802G>T	ENST00000262407.5	-	15	1527	c.1496C>A	c.(1495-1497)cCt>cAt	p.P499H	ITGA2B_ENST00000377068.3_3'UTR|ITGA2B_ENST00000353281.4_Missense_Mutation_p.P499H	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	499					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.P499H(1)		biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CTTCACAGCAGGATTCAGTGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											87	71	76					17																	42457802		2203	4300	6503	39813328	SO:0001583	missense	3674				CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1496C>A	17.37:g.42457802G>T	ENSP00000262407:p.Pro499His		39813328	B2RCY8|O95366|Q14443|Q17R67	De_novo_Start_OutOfFrame	SNP	ENST00000262407.5	37	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.678748	0.68042	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.48201	0.82;0.82	4.78	4.78	0.61160	Integrin alpha-2 (1);	0.000000	0.34932	N	0.003579	T	0.73783	0.3631	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79732	-0.1680	10	0.72032	D	0.01	.	16.7441	0.85467	0.0:0.0:1.0:0.0	.	499	P08514	ITA2B_HUMAN	H	499	ENSP00000262407:P499H;ENSP00000340536:P499H	ENSP00000262407:P499H	P	-	2	0	ITGA2B	39813328	1.000000	0.71417	0.990000	0.47175	0.881000	0.50899	3.207000	0.51106	2.486000	0.83907	0.561000	0.74099	CCT		0.562	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42457802	G	T	42457802	3	4	77	1	0	0	0	0	1	0	0	0	7897	1000	35	2	1687	2	ITGA2B	17	42457802	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	523302	42457802	38737408	986	22722										
EFTUD2	9343	broad.mit.edu	37	chr17	42964104	42964104	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctcctacgtcatcgtcgtcGtcatcatcatccatctgaaa	5	14	6	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:42964104G>A	ENST00000426333.2	-	3	417	c.120C>T	c.(118-120)gaC>gaT	p.D40D	EFTUD2_ENST00000591382.1_Silent_p.D40D|EFTUD2_ENST00000589211.1_5'UTR|EFTUD2_ENST00000592576.1_Silent_p.D40D|EFTUD2_ENST00000402521.3_Silent_p.D5D|RN7SL405P_ENST00000582502.1_RNA	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	40					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.D40D(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				catcgtcgtcgtcatcatcat	0.517																																					Ovarian(10;65 485 10258 29980 30707)											1	Substitution - coding silent(1)	large_intestine(1)	17											125	81	96					17																	42964104		2203	4300	6503	40319630	SO:0001819	synonymous_variant	9343			D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.120C>T	17.37:g.42964104G>A			40319630	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	37	CCDS11489.1																																																																																				0.517	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		A	42964104	G	A	42964104	2	1	77	1	0	0	0	0	0	0	0	1	4972	1136	40	1		1	EFTUD2	17	42964104	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	506302	42964104	38231106	987	22723										
HEXIM2	124790	broad.mit.edu	37	chr17	43246422	43246422	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccccaaacaccccctgagcGtcatgactctggtggttccc	8	18	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:43246422G>A	ENST00000307275.3	+	4	543	c.107G>A	c.(106-108)cGt>cAt	p.R36H	RP13-890H12.2_ENST00000589451.1_RNA|HEXIM2_ENST00000592695.1_Missense_Mutation_p.R36H|RP13-890H12.2_ENST00000589796.1_RNA|HEXIM2_ENST00000591576.1_Missense_Mutation_p.R36H	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	36					negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)	p.R36H(1)		endometrium(1)|large_intestine(3)|lung(1)	5						CCCCCTGAGCGTCATGACTCT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	17											145	163	157					17																	43246422		2203	4300	6503	40602205	SO:0001583	missense	124790			AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.107G>A	17.37:g.43246422G>A	ENSP00000302276:p.Arg36His		40602205	D3DX66	Missense_Mutation	SNP	ENST00000307275.3	37	CCDS11496.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301833	0.40694	.	.	ENSG00000168517	ENST00000307275	.	.	.	5.24	4.27	0.50696	.	0.629831	0.16141	N	0.227737	T	0.16085	0.0387	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16689	-1.0394	9	0.37606	T	0.19	-0.1951	12.0705	0.53613	0.0:0.8259:0.1741:0.0	.	36	Q96MH2	HEXI2_HUMAN	H	36	.	ENSP00000302276:R36H	R	+	2	0	HEXIM2	40602205	0.279000	0.24239	0.009000	0.14445	0.221000	0.24807	1.488000	0.35551	1.214000	0.43395	-0.228000	0.12330	CGT		0.612	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608		A	43246422	G	A	43246422	3	1	77	1	0	0	0	0	1	0	0	0	7098	1145	40	1	113	1	HEXIM2	17	43246422	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	282318	43246422	37948788	988	22724										
IMP5	162540	broad.mit.edu	37	chr17	43923369	43923369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgcctgttcgtcctgcaccGtgtgcggctgcccactctca	10	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:43923369G>A	ENST00000329196.5	+	1	1114	c.1097G>A	c.(1096-1098)cGt>cAt	p.R366H	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	366						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.R366H(1)									GTCCTGCACCGTGTGCGGCTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17											61	58	59					17																	43923369		2203	4300	6503	41279149	SO:0001583	missense	162540				CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"intramembrane protease 5"	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1097G>A	17.37:g.43923369G>A	ENSP00000332488:p.Arg366His		41279149	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917611	0.33815	.	.	ENSG00000185294	ENST00000329196	T	0.17691	2.26	5.57	4.6	0.57074	.	0.000000	0.44483	D	0.000448	T	0.28995	0.0720	L	0.59436	1.845	0.20196	N	0.999927	D	0.59357	0.985	P	0.56788	0.806	T	0.06679	-1.0813	10	0.62326	D	0.03	-5.1293	9.3733	0.38268	0.0947:0.0:0.9053:0.0	.	366	Q8IUH8	IMP5_HUMAN	H	366	ENSP00000332488:R366H	ENSP00000332488:R366H	R	+	2	0	AC217771.1	41279149	0.148000	0.22702	0.261000	0.24466	0.003000	0.03518	1.036000	0.30228	2.619000	0.88677	0.561000	0.74099	CGT		0.587	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882		A	43923369	G	A	43923369	3	1	77	1	0	0	0	0	1	0	0	0	7742	1145	40	1	1099	1	IMP5	17	43923369	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	676947	43923369	37271841	989	22725										
HOXB5	3215	broad.mit.edu	37	chr17	46670754	46670754	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggtgcagggcagggactcGggcgaggacagggagcagct	20	8	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:46670754G>A	ENST00000239151.5	-	1	569	c.291C>T	c.(289-291)ccC>ccT	p.P97P	HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000474324.1_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	97					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)	p.P97P(1)		large_intestine(1)|lung(2)	3						GCAGGGACTCGGGCGAGGACA	0.716																																																1	Substitution - coding silent(1)	large_intestine(1)	17											17	21	19					17																	46670754		2200	4297	6497	44025753	SO:0001819	synonymous_variant	3215				CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"Homeoboxes / ANTP class : HOXL subclass"	5116	protein-coding gene	gene with protein product		142960	"homeo box B5"	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.291C>T	17.37:g.46670754G>A			44025753	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	37	CCDS11530.1																																																																																				0.716	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			A	46670754	G	A	46670754	2	1	77	1	0	0	0	0	0	0	0	1	7325	1103	39	1		1	HOXB5	17	46670754	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2747385	46670754	34524456	990	22726										
HOXB6	3216	broad.mit.edu	37	chr17	46673911	46673911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgtcaggcacagggcgtgcGcgatctcgatgcgccgccgc	15	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:46673911G>A	ENST00000484302.2	-	3	1161	c.539C>T	c.(538-540)gCg>gTg	p.A180V	HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB5_ENST00000239151.5_5'Flank|HOXB6_ENST00000225648.3_Missense_Mutation_p.A180V|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000474324.1_RNA			P17509	HXB6_HUMAN	homeobox B6	180					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A180V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CAGGGCGTGCGCGATCTCGAT	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17											148	135	139					17																	46673911		2203	4300	6503	44028910	SO:0001583	missense	3216				CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"Homeoboxes / ANTP class : HOXL subclass"	5117	protein-coding gene	gene with protein product		142961	"homeo box B6"	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.539C>T	17.37:g.46673911G>A	ENSP00000420009:p.Ala180Val		44028910	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Missense_Mutation	SNP	ENST00000484302.2	37	CCDS11531.1	.	.	.	.	.	.	.	.	.	.	G	35	5.597398	0.96602	.	.	ENSG00000108511	ENST00000484302;ENST00000225648	D;D	0.98362	-4.89;-4.89	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.063724	0.64402	D	0.000009	D	0.99217	0.9728	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.99097	1.0842	10	0.87932	D	0	.	17.7415	0.88408	0.0:0.0:1.0:0.0	.	180	P17509	HXB6_HUMAN	V	180	ENSP00000420009:A180V;ENSP00000225648:A180V	ENSP00000225648:A180V	A	-	2	0	HOXB6	44028910	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.552000	0.98115	2.520000	0.84964	0.563000	0.77884	GCG		0.592	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2			A	46673911	G	A	46673911	3	1	77	1	0	0	0	0	1	0	0	0	7326	1087	38	1	139	1	HOXB6	17	46673911	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3157	46673911	34521299	991	22727										
HOXB7	3217	broad.mit.edu	37	chr17	46685369	46685369	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atctcgatgcgccgccgccgCgtcaggtagcgattgtagtg	14	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:46685369C>T	ENST00000239165.7	-	2	587	c.489G>A	c.(487-489)acG>acA	p.T163T	HOXB-AS3_ENST00000491264.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000494420.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB7_ENST00000567101.2_5'UTR	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	163					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T163T(2)		NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GCCGCCGCCGCGTCAGGTAGC	0.557																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	17											96	97	97					17																	46685369		2203	4300	6503	44040368	SO:0001819	synonymous_variant	3217				CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.489G>A	17.37:g.46685369C>T			44040368	A8K3N8|Q15957|Q53FN3|Q96BQ6	Silent	SNP	ENST00000239165.7	37	CCDS11532.1																																																																																				0.557	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			T	46685369	C	T	46685369	2	4	77	1	0	0	0	0	0	0	0	1	7327	755	27	1		1	HOXB7	17	46685369	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	11458	46685369	34509841	992	22728										
HOXB9	3219	broad.mit.edu	37	chr17	46703219	46703219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccctgcccgccgaagtttccAaactgtactcgggcgtgccc	10	17	0	0	rs200221711		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:46703219A>G	ENST00000311177.5	-	1	620	c.413T>C	c.(412-414)tTg>tCg	p.L138S	HOXB9_ENST00000550387.1_Intron|HOXB-AS4_ENST00000480386.1_RNA|HOXB7_ENST00000567101.2_Intron	NM_024017.4	NP_076922.1	P17482	HXB9_HUMAN	homeobox B9	138					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|embryonic skeletal system development (GO:0048706)|mammary gland development (GO:0030879)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.L138S(1)		breast(2)|endometrium(1)|large_intestine(1)|liver(1)|lung(6)|prostate(1)	12						CGAAGTTTCCAAACTGTACTC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	17											30	34	33					17																	46703219		2203	4300	6503	44058218	SO:0001583	missense	3219				CCDS11534.1	17q21.32	2011-06-20	2005-12-22		ENSG00000170689	ENSG00000170689		"Homeoboxes / ANTP class : HOXL subclass"	5120	protein-coding gene	gene with protein product		142964	"homeo box B9"	HOX2E, HOX2		1973146, 1358459	Standard	NM_024017		Approved		uc002inx.3	P17482	OTTHUMG00000159907	ENST00000311177.5:c.413T>C	17.37:g.46703219A>G	ENSP00000309439:p.Leu138Ser		44058218	B2RDB7|Q9H1I1	Missense_Mutation	SNP	ENST00000311177.5	37	CCDS11534.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.887606	0.52014	.	.	ENSG00000170689	ENST00000311177	D	0.93811	-3.29	4.84	4.84	0.62591	Hox9, N-terminal activation domain (1);	0.180985	0.36268	N	0.002686	D	0.89100	0.6619	L	0.43923	1.385	0.80722	D	1	P	0.37914	0.611	B	0.37888	0.26	D	0.86306	0.1683	10	0.20519	T	0.43	.	11.1217	0.48293	0.8619:0.0:0.0:0.1381	.	138	P17482	HXB9_HUMAN	S	138	ENSP00000309439:L138S	ENSP00000309439:L138S	L	-	2	0	HOXB9	44058218	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.698000	0.68302	1.920000	0.55613	0.454000	0.30748	TTG		0.652	HOXB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358101.2			G	46703219	A	G	46703219	3	3	77	1	0	0	0	0	1	0	0	0	7329	131	5	4	347	4	HOXB9	17	46703219	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	17850	46703219	34491991	993	22729										
LRRC59	55379	broad.mit.edu	37	chr17	48460470	48460470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctgctgctgcagctctgtcAcccgacaagcaaccagccct	9	17	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:48460470A>T	ENST00000225972.7	-	7	1038	c.803T>A	c.(802-804)gTg>gAg	p.V268E		NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	268						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.V268E(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CAGCTCTGTCACCCGACAAGC	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	17											41	32	36					17																	48460470		2203	4295	6498	45815469	SO:0001583	missense	55379			AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829			28817	protein-coding gene	gene with protein product		614854				12477932	Standard	NM_018509		Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.803T>A	17.37:g.48460470A>T	ENSP00000225972:p.Val268Glu		45815469	B2RE83|D3DTX8|Q9P189	Missense_Mutation	SNP	ENST00000225972.7	37	CCDS11566.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.899734	0.52227	.	.	ENSG00000108829	ENST00000225972	T	0.46819	0.86	5.77	4.63	0.57726	.	0.258981	0.39146	N	0.001450	T	0.39145	0.1067	L	0.40543	1.245	0.80722	D	1	B	0.22604	0.072	B	0.19666	0.026	T	0.35699	-0.9778	10	0.66056	D	0.02	.	11.4163	0.49954	0.8494:0.1506:0.0:0.0	.	268	Q96AG4	LRC59_HUMAN	E	268	ENSP00000225972:V268E	ENSP00000225972:V268E	V	-	2	0	LRRC59	45815469	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.624000	0.61254	2.214000	0.71695	0.372000	0.22366	GTG		0.617	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367117.2	NM_018509		T	48460470	A	T	48460470	3	4	77	1	0	0	0	0	1	0	0	0	9044	159	6	5	124	5	LRRC59	17	48460470	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	1757251	48460470	32734740	994	22730										
SPATA20	64847	broad.mit.edu	37	chr17	48627594	48627594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcaccgctactccacagaccGccagtggcacgtccctcact	7	19	2	1	rs368022155		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:48627594G>A	ENST00000356488.4	+	8	1054	c.971G>A	c.(970-972)cGc>cAc	p.R324H	SPATA20_ENST00000393244.3_Missense_Mutation_p.R280H|SPATA20_ENST00000006658.6_Missense_Mutation_p.R340H|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	324					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)	p.R340H(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TCCACAGACCGCCAGTGGCAC	0.632											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	8e-04	0	5008	,	,		16305	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	17						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	76	77	77		1019	4.8	1	17		77	0,8600		0,0,4300	no	missense	SPATA20	NM_022827.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	340/803	48627594	1,13005	2203	4300	6503	45982593	SO:0001583	missense	64847				CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.971G>A	17.37:g.48627594G>A	ENSP00000348878:p.Arg324His	119	45982593	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154287	0.57259	2.27E-4	0.0	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.30448	1.53;1.53;1.53	5.81	4.84	0.62591	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.308916	0.37219	N	0.002182	T	0.25568	0.0622	L	0.56396	1.775	0.27804	N	0.942362	P;P	0.45011	0.848;0.681	B;B	0.36808	0.233;0.15	T	0.35822	-0.9773	10	0.48119	T	0.1	-6.1238	8.2134	0.31496	0.2451:0.0:0.7549:0.0	.	324;340	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	H	340;324;280	ENSP00000006658:R340H;ENSP00000348878:R324H;ENSP00000376935:R280H	ENSP00000006658:R340H	R	+	2	0	SPATA20	45982593	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.245000	0.51407	2.746000	0.94184	0.655000	0.94253	CGC		0.632	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48627594	G	A	48627594	3	1	77	1	0	0	0	0	1	0	0	0	15045	1087	38	1	1053	1	SPATA20	17	48627594	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	167124	48627594	32567616	995	22731										
WFIKKN2	124857	broad.mit.edu	37	chr17	48917620	48917620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccaatggcacggctttccCggcggccgagtgcctgaagc	13	16	0	1	rs141860715		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:48917620C>T	ENST00000311378.4	+	2	1499	c.971C>T	c.(970-972)cCg>cTg	p.P324L	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Missense_Mutation_p.P231L	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	324					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.P324L(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			ACGGCTTTCCCGGCGGCCGAG	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	48	44	45		971	5.4	0.9	17	dbSNP_134	45	1,8599		0,1,4299	yes	missense	WFIKKN2	NM_175575.5	98	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	benign	324/577	48917620	4,13002	2203	4300	6503	46272619	SO:0001583	missense	124857			AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30916	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20B"	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.971C>T	17.37:g.48917620C>T	ENSP00000311184:p.Pro324Leu		46272619	Q6UXZ9	Missense_Mutation	SNP	ENST00000311378.4	37	CCDS11575.1	.	.	.	.	.	.	.	.	.	.	C	9.861	1.196203	0.22037	6.81E-4	1.16E-4	ENSG00000173714	ENST00000426127;ENST00000311378	T;T	0.56275	0.47;0.47	5.45	5.45	0.79879	Proteinase inhibitor I2, Kunitz metazoa (1);	0.000000	0.85682	D	0.000000	T	0.47192	0.1432	L	0.45581	1.43	0.80722	D	1	B	0.25521	0.128	B	0.14578	0.011	T	0.37337	-0.9710	10	0.19590	T	0.45	.	19.2734	0.94019	0.0:1.0:0.0:0.0	.	324	Q8TEU8	WFKN2_HUMAN	L	231;324	ENSP00000405889:P231L;ENSP00000311184:P324L	ENSP00000311184:P324L	P	+	2	0	WFIKKN2	46272619	0.996000	0.38824	0.945000	0.38365	0.009000	0.06853	3.954000	0.56708	2.537000	0.85549	0.655000	0.94253	CCG		0.647	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		T	48917620	C	T	48917620	3	4	77	1	0	0	0	0	1	0	0	0	17399	652	23	1	977	1	WFIKKN2	17	48917620	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	290026	48917620	32277590	996	22732										
CUEDC1	404093	broad.mit.edu	37	chr17	55950157	55950157	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcctggtctccgggccctggCccagccatggcaggtggaca	14	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:55950157C>T	ENST00000577830.1	-	5	1064	c.651G>A	c.(649-651)ggG>ggA	p.G217G	CUEDC1_ENST00000577840.1_Silent_p.G80G|CUEDC1_ENST00000360238.2_Silent_p.G217G|CUEDC1_ENST00000578357.1_5'Flank|CUEDC1_ENST00000407144.2_Silent_p.G217G	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	217								p.G217G(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						CGGGCCCTGGCCCAGCCATGG	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	17											70	65	67					17																	55950157		2203	4300	6503	53305156	SO:0001819	synonymous_variant	404093			AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.651G>A	17.37:g.55950157C>T			53305156	D3DTZ2|Q9NWD0	Silent	SNP	ENST00000577830.1	37	CCDS11599.1																																																																																				0.612	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949		T	55950157	C	T	55950157	2	4	77	1	0	0	0	0	0	0	0	1	4058	726	26	3		3	CUEDC1	17	55950157	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	7032537	55950157	25245053	997	22733										
EPX	8288	broad.mit.edu	37	chr17	56271143	56271143	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgctctccgggaccaggccGagcgctgcagcgacaagtac	14	14	1	0	rs369339605		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:56271143G>A	ENST00000225371.5	+	4	525	c.415G>A	c.(415-417)Gag>Aag	p.E139K		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	139					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.E139K(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GGACCAGGCCGAGCGCTGCAG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17						G	LYS/GLU	2,4404	2.1+/-5.4	0,2,2201	37	33	34		415	4.6	0.8	17		34	0,8600		0,0,4300	no	missense	EPX	NM_000502.4	56	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	139/716	56271143	2,13004	2203	4300	6503	53626142	SO:0001583	missense	8288			M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.415G>A	17.37:g.56271143G>A	ENSP00000225371:p.Glu139Lys		53626142	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	G	9.801	1.180569	0.21787	4.54E-4	0.0	ENSG00000121053	ENST00000225371	T	0.70399	-0.48	4.6	4.6	0.57074	.	0.309988	0.34959	N	0.003557	T	0.59197	0.2176	M	0.63428	1.95	0.09310	N	1	P	0.37612	0.602	B	0.27796	0.083	T	0.54043	-0.8352	10	0.24483	T	0.36	-26.4847	9.0188	0.36186	0.1029:0.0:0.8971:0.0	.	139	P11678	PERE_HUMAN	K	139	ENSP00000225371:E139K	ENSP00000225371:E139K	E	+	1	0	EPX	53626142	0.459000	0.25768	0.822000	0.32727	0.017000	0.09413	3.558000	0.53749	2.263000	0.75096	0.442000	0.29010	GAG		0.657	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		A	56271143	G	A	56271143	3	1	77	1	0	0	0	0	1	0	0	0	5213	1059	37	1	429	1	EPX	17	56271143	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	320986	56271143	24924067	998	22734										
MPO	4353	broad.mit.edu	37	chr17	56349219	56349219	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcccacagtttcaggctgCgggagcccacagaagcgcct	13	14	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:56349219C>T	ENST00000225275.3	-	11	2003	c.1827G>A	c.(1825-1827)ccG>ccA	p.P609P	MPO_ENST00000340482.3_Silent_p.P641P	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	609					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.P609P(2)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	TTTCAGGCTGCGGGAGCCCAC	0.597																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	17											89	74	79					17																	56349219		2203	4300	6503	53704218	SO:0001819	synonymous_variant	4353				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1827G>A	17.37:g.56349219C>T			53704218	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Silent	SNP	ENST00000225275.3	37	CCDS11604.1																																																																																				0.597	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56349219	C	T	56349219	2	4	77	1	0	0	0	0	0	0	0	1	9762	755	27	1		1	MPO	17	56349219	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	78076	56349219	24845991	999	22735										
SEPT4	5414	broad.mit.edu	37	chr17	56603076	56603076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcagcaccaagaagtttcCggtcccggtacagatcagtg	10	12	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:56603076C>T	ENST00000317268.3	-	4	694	c.518G>A	c.(517-519)cGg>cAg	p.R173Q	SEPT4_ENST00000412945.3_Missense_Mutation_p.R165Q|SEPT4_ENST00000580809.1_Missense_Mutation_p.R55Q|SEPT4_ENST00000426861.1_Missense_Mutation_p.R154Q|SEPT4_ENST00000317256.6_Missense_Mutation_p.R154Q|SEPT4_ENST00000579371.1_Missense_Mutation_p.R74Q|RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000580844.1_Missense_Mutation_p.R74Q|SEPT4_ENST00000393086.1_Missense_Mutation_p.R154Q|SEPT4_ENST00000580791.1_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_Missense_Mutation_p.R188Q|SEPT4_ENST00000583114.1_Missense_Mutation_p.R26Q|RP11-112H10.4_ENST00000578022.1_RNA	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	173	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.R173Q(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGAAGTTTCCGGTCCCGGTA	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	17											110	96	100					17																	56603076		2203	4300	6503	53958075	SO:0001583	missense	5414			AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.518G>A	17.37:g.56603076C>T	ENSP00000321674:p.Arg173Gln		53958075	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972483	0.53614	.	.	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086;ENST00000426861	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.94	4.94	0.65067	.	0.058893	0.64402	D	0.000003	T	0.60830	0.2299	L	0.39147	1.195	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.99;0.994;1.0;0.998;1.0	D;D;P;P;D;D;D	0.91635	0.999;0.993;0.838;0.886;0.999;0.965;0.999	T	0.62950	-0.6745	10	0.87932	D	0	.	16.0453	0.80717	0.0:1.0:0.0:0.0	.	165;188;26;154;154;26;173	O43236-3;O43236-4;B3KR63;O43236-6;O43236-2;O43236-5;O43236	.;.;.;.;.;.;SEPT4_HUMAN	Q	165;187;154;173;154;154	ENSP00000414779:R165Q;ENSP00000321071:R154Q;ENSP00000321674:R173Q;ENSP00000376801:R154Q;ENSP00000402348:R154Q	ENSP00000321071:R154Q	R	-	2	0	SEPT4	53958075	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.933000	0.70130	2.726000	0.93360	0.655000	0.94253	CGG		0.527	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		T	56603076	C	T	56603076	3	4	77	1	0	0	0	0	1	0	0	0	14103	652	23	1	1039	1	SEPT4	17	56603076	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	253857	56603076	24592134	1000	22736										
MED13	9969	broad.mit.edu	37	chr17	60042367	60042367	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcagtatttttaaaggtacCtttcagacacatcaggatgc	7	8	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:60042367C>A	ENST00000397786.2	-	20	4920	c.4844G>T	c.(4843-4845)aGc>aTc	p.S1615I		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1615					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.S1615I(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTAAAGGTACCTTTCAGACAC	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	17											50	49	49					17																	60042367		1866	4102	5968	57397149	SO:0001630	splice_region_variant	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4844+1G>T	17.37:g.60042367C>A			57397149	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767384	0.90020	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.78364	-1.17	5.95	5.95	0.96441	.	0.109206	0.85682	D	0.000000	D	0.87684	0.6239	M	0.66939	2.045	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	D	0.85593	0.1247	9	.	.	.	-19.4576	20.4024	0.99000	0.0:1.0:0.0:0.0	.	1615	Q9UHV7	MED13_HUMAN	I	1615;1614	ENSP00000380888:S1615I	.	S	-	2	0	MED13	57397149	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.178000	0.71968	2.827000	0.97445	0.650000	0.86243	AGC		0.423	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	Missense_Mutation	A	60042367	C	A	60042367	5	1	77	1	0	0	0	0	0	0	1	0	9460	695	24	2	1724	2	MED13	17	60042367	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3439291	60042367	21152843	1001	22737										
MED13	9969	broad.mit.edu	37	chr17	60062172	60062172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcattggggaaaatcccataAtatgttgttccaatgatggt	9	6	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:60062172A>G	ENST00000397786.2	-	14	2607	c.2531T>C	c.(2530-2532)aTt>aCt	p.I844T		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	844					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.I844T(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AAATCCCATAATATGTTGTTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	17											69	63	65					17																	60062172		1812	4066	5878	57416954	SO:0001583	missense	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.2531T>C	17.37:g.60062172A>G	ENSP00000380888:p.Ile844Thr		57416954	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	A	18.87	3.715144	0.68844	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.73681	-0.77	6.16	6.16	0.99307	.	0.048330	0.85682	D	0.000000	T	0.67297	0.2878	L	0.36672	1.1	0.53688	D	0.999972	P	0.47106	0.89	B	0.43413	0.419	T	0.64437	-0.6408	10	0.11794	T	0.64	-15.6346	16.8061	0.85666	1.0:0.0:0.0:0.0	.	844	Q9UHV7	MED13_HUMAN	T	844;843	ENSP00000380888:I844T	ENSP00000262436:I843T	I	-	2	0	MED13	57416954	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	ATT		0.323	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60062172	A	G	60062172	3	3	77	1	0	0	0	0	1	0	0	0	9460	101	4	4	4061	4	MED13	17	60062172	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	19805	60062172	21133038	1002	22738										
SCN4A	6329	broad.mit.edu	37	chr17	62049725	62049725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggatatgcatggatgagcaCcttgatggccccgcgcctga	13	11	0	3	rs369830835		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:62049725C>T	ENST00000435607.1	-	2	455	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	SCN4A_ENST00000578147.1_Missense_Mutation_p.V127M|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	127					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V127M(1)|p.V127L(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGATGAGCACCTTGATGGCC	0.617																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	17						C	MET/VAL	0,4298		0,0,2149	59	63	62		379	3.2	1	17		62	1,8511		0,1,4255	no	missense	SCN4A	NM_000334.4	21	0,1,6404	TT,TC,CC		0.0117,0.0,0.0078	possibly-damaging	127/1837	62049725	1,12809	2149	4256	6405	59403457	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.379G>A	17.37:g.62049725C>T	ENSP00000396320:p.Val127Met		59403457	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.795753	0.31777	0.0	1.17E-4	ENSG00000007314	ENST00000435607	D	0.96522	-4.04	4.23	3.22	0.36961	.	1.043120	0.07526	N	0.911422	D	0.95392	0.8504	M	0.78049	2.395	0.27148	N	0.961473	B	0.33494	0.414	B	0.28916	0.096	D	0.90850	0.4730	10	0.62326	D	0.03	.	11.6221	0.51124	0.0:0.9101:0.0:0.0899	.	127	P35499	SCN4A_HUMAN	M	127	ENSP00000396320:V127M	ENSP00000396320:V127M	V	-	1	0	SCN4A	59403457	0.286000	0.24305	1.000000	0.80357	0.329000	0.28539	0.241000	0.18065	2.188000	0.69820	0.313000	0.20887	GTG		0.617	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62049725	C	T	62049725	3	4	77	1	0	0	0	0	1	0	0	0	13957	507	18	3	5223	3	SCN4A	17	62049725	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1987553	62049725	19145485	1003	22739										
GNA13	10672	broad.mit.edu	37	chr17	63010573	63010573	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagcagtggggatccccttcAaattctaggaaatagtcttt	9	8	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:63010573A>G	ENST00000439174.2	-	4	1181	c.936T>C	c.(934-936)ttT>ttC	p.F312F	GNA13_ENST00000541118.1_Silent_p.F217F	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	312					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)	p.F312F(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						GATCCCCTTCAAATTCTAGGA	0.448																																																1	Substitution - coding silent(1)	large_intestine(1)	17											93	91	92					17																	63010573		2203	4300	6503	60441035	SO:0001819	synonymous_variant	10672			L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.936T>C	17.37:g.63010573A>G			60441035	B2R977|B7Z7R0|F5H1G8|Q8TD70	Silent	SNP	ENST00000439174.2	37	CCDS11661.1																																																																																				0.448	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		G	63010573	A	G	63010573	2	3	77	1	0	0	0	0	0	0	0	1	6521	127	5	4		4	GNA13	17	63010573	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	960848	63010573	18184637	1004	22740										
AXIN2	8313	broad.mit.edu	37	chr17	63545763	63545763	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgataaggattaacaggatcGctcctcttgaaggacctatg	10	8	1	2	rs186951572	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:63545763G>A	ENST00000375702.5	-	2	939	c.831C>T	c.(829-831)agC>agT	p.S277S	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Silent_p.S277S			Q9Y2T1	AXIN2_HUMAN	axin 2	277					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.S277S(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						TAACAGGATCGCTCCTCTTGA	0.507									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	2	0.000399361	0	0	5008	,	,		23231	0.002		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	17											117	86	96					17																	63545763		2203	4298	6501	60976225	SO:0001819	synonymous_variant	8313	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.831C>T	17.37:g.63545763G>A			60976225	Q3MJ88|Q9H3M6|Q9UH84	Silent	SNP	ENST00000375702.5	37																																																																																					0.507	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		A	63545763	G	A	63545763	2	1	77	1	0	0	0	0	0	0	0	1	1238	1078	38	1		1	AXIN2	17	63545763	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	535190	63545763	17649447	1005	22741										
ABCA9	10350	broad.mit.edu	37	chr17	66982383	66982383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccaggtgctgcctcactgtcAggttgggccacagcgcattc	12	14	2	0	rs137862082		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:66982383A>G	ENST00000340001.4	-	32	4341	c.4130T>C	c.(4129-4131)cTg>cCg	p.L1377P	ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000453985.2_Missense_Mutation_p.L1339P|ABCA9_ENST00000370732.2_Missense_Mutation_p.L1377P	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1377	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L1377P(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					CCTCACTGTCAGGTTGGGCCA	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	17						A	PRO/LEU	1,4405	2.1+/-5.4	0,1,2202	134	108	117		4130	4.9	0.9	17	dbSNP_134	117	0,8600		0,0,4300	no	missense	ABCA9	NM_080283.3	98	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	1377/1625	66982383	1,13005	2203	4300	6503	64493978	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4130T>C	17.37:g.66982383A>G	ENSP00000342216:p.Leu1377Pro		64493978	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179428	0.57800	2.27E-4	0.0	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732	T;T	0.17213	2.29;2.29	4.87	4.87	0.63330	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.187524	0.25566	N	0.029797	T	0.53045	0.1772	H	0.94264	3.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.67300	-0.5705	10	0.87932	D	0	.	13.9762	0.64275	1.0:0.0:0.0:0.0	.	1377;1377	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	P	1377;1322;1377	ENSP00000342216:L1377P;ENSP00000359767:L1377P	ENSP00000342216:L1377P	L	-	2	0	ABCA9	64493978	0.971000	0.33674	0.852000	0.33557	0.145000	0.21501	8.435000	0.90297	1.964000	0.57103	0.533000	0.62120	CTG		0.582	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		G	66982383	A	G	66982383	3	3	77	1	0	0	0	0	1	0	0	0	39	188	7	4	776	4	ABCA9	17	66982383	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	3436620	66982383	14212827	1006	22742										
C17orf80	55028	broad.mit.edu	37	chr17	71231873	71231873	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aattctaagttggtggtggaCaaaccagaacagacagtgaa	11	6	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:71231873C>T	ENST00000535032.2	+	2	365	c.252C>T	c.(250-252)gaC>gaT	p.D84D	C17orf80_ENST00000359042.2_Silent_p.D84D|C17orf80_ENST00000582793.1_Intron|FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000426147.2_Silent_p.D84D|C17orf80_ENST00000577615.1_Silent_p.D84D|C17orf80_ENST00000268942.8_Silent_p.D84D|C17orf80_ENST00000255557.4_Silent_p.D84D			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	84						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D84D(1)		kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			TGGTGGTGGACAAACCAGAAC	0.393																																																1	Substitution - coding silent(1)	large_intestine(1)	17											64	58	60					17																	71231873		2203	4300	6503	68743468	SO:0001819	synonymous_variant	55028			AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.252C>T	17.37:g.71231873C>T			68743468	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Silent	SNP	ENST00000535032.2	37	CCDS11694.1																																																																																				0.393	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		T	71231873	C	T	71231873	2	4	77	1	0	0	0	0	0	0	0	1	1890	477	17	3		3	C17orf80	17	71231873	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4249490	71231873	9963337	1007	22743										
CD300E	342510	broad.mit.edu	37	chr17	72610104	72610104	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccccggtgctgaggtttcGcccagggttcaccaccagga	12	15	1	1	rs61748965	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:72610104G>A	ENST00000328630.3	-	3	497	c.457C>T	c.(457-459)Cga>Tga	p.R153*	CD300E_ENST00000426295.2_Nonsense_Mutation_p.R194*|CD300E_ENST00000392619.1_Nonsense_Mutation_p.R180*			Q496F6	CLM2_HUMAN	CD300e molecule	153					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R153*(1)		breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						CTGAGGTTTCGCCCAGGGTTC	0.587																																																1	Substitution - Nonsense(1)	large_intestine(1)	17						G	stop/ARG	4,4402	9.9+/-24.2	0,4,2199	134	106	116		457	2.1	0	17	dbSNP_129	116	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	CD300E	NM_181449.2		0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384		153/206	72610104	5,13001	2203	4300	6503	70121699	SO:0001587	stop_gained	342510			BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	28874	protein-coding gene	gene with protein product		609801	"CD300 antigen like family member E", "CD300e antigen"	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.457C>T	17.37:g.72610104G>A	ENSP00000329942:p.Arg153*		70121699	B4DNS1|Q7Z7I3	Nonsense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.153735	0.38021	9.08E-4	1.16E-4	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630	.	.	.	3.07	2.07	0.26955	.	1.788950	0.04014	U	0.298664	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	0.194	6.3899	0.21581	0.1409:0.0:0.8591:0.0	.	.	.	.	X	180;194;153	.	ENSP00000329942:R153X	R	-	1	2	CD300E	70121699	0.037000	0.19845	0.002000	0.10522	0.007000	0.05969	0.444000	0.21661	0.842000	0.35045	0.411000	0.27672	CGA		0.587	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449		A	72610104	G	A	72610104	4	1	77	1	0	0	0	0	0	1	0	0	3004	1095	38	1	168	1	CD300E	17	72610104	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1378231	72610104	8585106	1008	22744										
RAB37	326624	broad.mit.edu	37	chr17	72725504	72725504	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cactgtgggcatcggattcaCggtaagcactggccggcact	13	12	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:72725504C>T	ENST00000340415.3	+	2	1191	c.182C>T	c.(181-183)aCg>aTg	p.T61M	RAB37_ENST00000402449.4_Splice_Site_p.T61M	NM_175738.4	NP_783865.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	68					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)	p.T61M(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						ATCGGATTCACGGTAAGCACT	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	17											129	108	115					17																	72725504		2203	4300	6503	70237099	SO:0001630	splice_region_variant	326624			BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"RAB, member RAS oncogene"	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000340415.3:c.183+1C>T	17.37:g.72725504C>T			70237099	A8MXF5|A8MYT0|Q8IWA7	Missense_Mutation	SNP	ENST00000340415.3	37		.	.	.	.	.	.	.	.	.	.	c	17.52	3.410980	0.62399	.	.	ENSG00000172794	ENST00000340415;ENST00000402449;ENST00000469248;ENST00000392617	T;T	0.80214	-1.35;-1.35	5.27	5.27	0.74061	.	.	.	.	.	T	0.79667	0.4485	N	0.10916	0.065	0.80722	D	1	B;B;D	0.69078	0.056;0.069;0.997	B;B;D	0.62955	0.044;0.045;0.909	D	0.84284	0.0496	9	0.87932	D	0	.	16.752	0.85488	0.0:1.0:0.0:0.0	.	61;61;61	Q96AX2-2;A8MSP2;A8MUU7	.;.;.	M	61	ENSP00000341354:T61M;ENSP00000383934:T61M	ENSP00000341354:T61M	T	+	2	0	RAB37	70237099	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.372000	0.66156	2.503000	0.84419	0.639000	0.83563	ACG		0.602	RAB37-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000258876.2	NM_175738	Missense_Mutation	T	72725504	C	T	72725504	5	4	77	1	0	0	0	0	0	0	1	0	12964	550	19	1	188	1	RAB37	17	72725504	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	115400	72725504	8469706	1009	22745										
USH1G	124590	broad.mit.edu	37	chr17	72916632	72916632	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggcagccatgtccagcggcGtgtggtagtcgttgtctagg	16	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:72916632G>A	ENST00000319642.1	-	2	481	c.299C>T	c.(298-300)aCg>aTg	p.T100M		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	100					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)	p.T100M(1)	HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					GTCCAGCGGCGTGTGGTAGTC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											120	97	105					17																	72916632		2203	4300	6503	70428227	SO:0001583	missense	124590			AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.299C>T	17.37:g.72916632G>A	ENSP00000320076:p.Thr100Met		70428227	Q8N251	Missense_Mutation	SNP	ENST00000319642.1	37	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977882	0.74360	.	.	ENSG00000182040	ENST00000319642	T	0.75154	-0.91	3.8	3.8	0.43715	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	H	0.96805	3.885	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.93998	0.7273	10	0.87932	D	0	-17.941	16.2003	0.82067	0.0:0.0:1.0:0.0	.	100	Q495M9	USH1G_HUMAN	M	100	ENSP00000320076:T100M	ENSP00000320076:T100M	T	-	2	0	USH1G	70428227	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.535000	0.98064	2.118000	0.64928	0.313000	0.20887	ACG		0.607	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		A	72916632	G	A	72916632	3	1	77	1	0	0	0	0	1	0	0	0	17075	1145	40	1	1094	1	USH1G	17	72916632	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	191128	72916632	8278578	1010	22746										
SRP68	6730	broad.mit.edu	37	chr17	74060169	74060169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ataacaagtgaaaccgttttCggggttcagtgttggcttcc	11	8	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:74060169C>T	ENST00000307877.2	-	4	610	c.449G>A	c.(448-450)cGa>cAa	p.R150Q	SRP68_ENST00000539137.1_Missense_Mutation_p.R112Q|SRP68_ENST00000355113.5_Missense_Mutation_p.R49Q	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	150					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.R150Q(1)		NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						AAACCGTTTTCGGGGTTCAGT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	17											189	161	170					17																	74060169		2203	4300	6503	71571764	SO:0001583	missense	6730			AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"signal recognition particle 68kD"			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.449G>A	17.37:g.74060169C>T	ENSP00000312066:p.Arg150Gln		71571764	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	.	.	.	.	.	.	.	.	.	.	C	36	5.730427	0.96856	.	.	ENSG00000167881	ENST00000539137;ENST00000540937;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.77922	0.4203	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.998;0.999	D;P	0.75484	0.986;0.797	T	0.78319	-0.2250	9	0.59425	D	0.04	-19.2274	19.1447	0.93459	0.0:1.0:0.0:0.0	.	112;150	G3V1U4;Q9UHB9	.;SRP68_HUMAN	Q	112;150;150;150;49	.	ENSP00000307756:R150Q	R	-	2	0	SRP68	71571764	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.564000	0.82326	2.753000	0.94483	0.585000	0.79938	CGA		0.502	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		T	74060169	C	T	74060169	3	4	77	1	0	0	0	0	1	0	0	0	15195	884	31	1	1486	1	SRP68	17	74060169	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1143537	74060169	7135041	1011	22747										
FOXJ1	2302	broad.mit.edu	37	chr17	74136147	74136147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttggtggcgtagtccacgtcGtcggggggtggggcctgcag	20	9	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:74136147G>A	ENST00000322957.6	-	2	684	c.330C>T	c.(328-330)gaC>gaT	p.D110D	RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000585542.1_RNA|RNF157_ENST00000589912.1_5'Flank	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	110					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.D110D(1)		large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			AGTCCACGTCGTCGGGGGGTG	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	17											41	35	37					17																	74136147		2203	4300	6503	71647742	SO:0001819	synonymous_variant	2302			X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"Forkhead boxes"	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.330C>T	17.37:g.74136147G>A			71647742	O00630	Silent	SNP	ENST00000322957.6	37	CCDS32739.1																																																																																				0.706	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454		A	74136147	G	A	74136147	2	1	77	1	0	0	0	0	0	0	0	1	6030	1136	40	1		1	FOXJ1	17	74136147	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	75978	74136147	7059063	1012	22748										
ST6GALNAC1	55808	broad.mit.edu	37	chr17	74639698	74639698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgccttggctcaggtgcctgCatctccacaggcaggacctc	11	16	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:74639698C>T	ENST00000156626.7	-	1	222	c.23G>A	c.(22-24)tGc>tAc	p.C8Y	ST6GALNAC1_ENST00000589992.1_Missense_Mutation_p.C8Y|ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	8					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)	p.C8Y(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						CAGGTGCCTGCATCTCCACAG	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	17											80	70	73					17																	74639698		2203	4300	6503	72151293	SO:0001583	missense	55808			Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"Sialyltransferases"	23614	protein-coding gene	gene with protein product		610138	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.23G>A	17.37:g.74639698C>T	ENSP00000156626:p.Cys8Tyr		72151293	Q6UW90|Q9NSC6	Missense_Mutation	SNP	ENST00000156626.7	37	CCDS11748.1	.	.	.	.	.	.	.	.	.	.	C	9.084	1.000016	0.19121	.	.	ENSG00000070526	ENST00000156626;ENST00000359088	T;T	0.25749	1.79;1.78	3.05	-2.36	0.06663	.	3.719150	0.00639	N	0.000512	T	0.20941	0.0504	L	0.38175	1.15	0.09310	N	1	B	0.30361	0.277	B	0.28139	0.086	T	0.29181	-1.0020	10	0.66056	D	0.02	-1.6619	6.5202	0.22271	0.2869:0.5929:0.1202:0.0	.	8	Q9NSC7	SIA7A_HUMAN	Y	8	ENSP00000156626:C8Y;ENSP00000351991:C8Y	ENSP00000156626:C8Y	C	-	2	0	ST6GALNAC1	72151293	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.767000	0.04720	-0.530000	0.06349	-0.397000	0.06425	TGC		0.562	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414		T	74639698	C	T	74639698	3	4	77	1	0	0	0	0	1	0	0	0	15262	710	25	3	1815	3	ST6GALNAC1	17	74639698	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	503551	74639698	6555512	1013	22749										
MXRA7	439921	broad.mit.edu	37	chr17	74673728	74673728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtcggacatctcgccaaacGtctccttgttgtctttcatg	8	13	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:74673728G>A	ENST00000355797.3	-	4	565	c.557C>T	c.(556-558)aCg>aTg	p.T186M		NM_001008528.1	NP_001008528.1	P84157	MXRA7_HUMAN	matrix-remodelling associated 7	186						integral component of membrane (GO:0016021)		p.T186M(1)		kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						CTCGCCAAACGTCTCCTTGTT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											150	128	136					17																	74673728		2203	4300	6503	72185323	SO:0001583	missense	439921			BC053983	CCDS32745.1, CCDS32746.1, CCDS45786.1	17q25.1	2007-08-01				ENSG00000182534			7541	protein-coding gene	gene with protein product							Standard	XM_005257382		Approved	FLJ46603, TMAP1, PS1TP1	uc002jsk.1	P84157		ENST00000355797.3:c.557C>T	17.37:g.74673728G>A	ENSP00000348050:p.Thr186Met		72185323	Q0P5W3	Missense_Mutation	SNP	ENST00000355797.3	37	CCDS32745.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705928	0.68615	.	.	ENSG00000182534	ENST00000355797	T	0.37058	1.22	5.54	5.54	0.83059	.	.	.	.	.	T	0.57844	0.2081	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58912	-0.7552	9	0.87932	D	0	.	18.2683	0.90059	0.0:0.0:1.0:0.0	.	186	P84157	MXRA7_HUMAN	M	186	ENSP00000348050:T186M	ENSP00000348050:T186M	T	-	2	0	MXRA7	72185323	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	8.375000	0.90135	2.611000	0.88343	0.643000	0.83706	ACG		0.567	MXRA7-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450983.1	NM_001008529		A	74673728	G	A	74673728	3	1	77	1	0	0	0	0	1	0	0	0	10034	1145	40	1	61	1	MXRA7	17	74673728	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	34030	74673728	6521482	1014	22750										
AFMID	125061	broad.mit.edu	37	chr17	76200772	76200772	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttcatggtccacccgctgaCggcacagggagtggccgtgg	15	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:76200772C>T	ENST00000327898.5	+	5	353	c.344C>T	c.(343-345)aCg>aTg	p.T115M	AFMID_ENST00000588800.1_Intron|AFMID_ENST00000589664.1_Intron|AFMID_ENST00000409257.5_Missense_Mutation_p.T115M|AFMID_ENST00000591952.1_Intron					arylformamidase									p.T115M(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)	19			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)			CACCCGCTGACGGCACAGGGA	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	17											97	69	78					17																	76200772		2203	4300	6503	73712367	SO:0001583	missense	125061			BX648442	CCDS32750.2, CCDS45801.1	17q25.3	2005-11-09			ENSG00000183077	ENSG00000183077	3.5.1.9		20910	protein-coding gene	gene with protein product							Standard	NR_027083		Approved	DKFZp686F03259, KF	uc002juz.3	Q63HM1	OTTHUMG00000153957	ENST00000327898.5:c.344C>T	17.37:g.76200772C>T	ENSP00000328938:p.Thr115Met		73712367		Missense_Mutation	SNP	ENST00000327898.5	37	CCDS45801.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.251235	0.39797	.	.	ENSG00000183077	ENST00000409257;ENST00000327898	T;T	0.11821	2.74;2.74	4.89	4.89	0.63831	Alpha/beta hydrolase fold-3 (1);	0.275715	0.35179	N	0.003387	T	0.32255	0.0823	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.65773	0.938;0.897	T	0.03807	-1.1002	10	0.62326	D	0.03	-22.9163	7.4995	0.27509	0.0:0.8539:0.0:0.1461	.	115;115	Q63HM1;Q63HM1-2	AFMID_HUMAN;.	M	115	ENSP00000386890:T115M;ENSP00000328938:T115M	ENSP00000328938:T115M	T	+	2	0	AFMID	73712367	0.999000	0.42202	0.892000	0.35008	0.071000	0.16799	3.755000	0.55197	2.521000	0.84997	0.655000	0.94253	ACG		0.592	AFMID-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333203.1	XM_058889		T	76200772	C	T	76200772	3	4	77	1	0	0	0	0	1	0	0	0	362	536	19	1	362	1	AFMID	17	76200772	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1527044	76200772	4994438	1015	22751										
ENGASE	64772	broad.mit.edu	37	chr17	77076344	77076344	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctctgtgaagccttcctggcCggggatgagcgctcgtacca	13	13	1	2	rs199791449		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:77076344C>T	ENST00000579016.1	+	5	621	c.621C>T	c.(619-621)gcC>gcT	p.A207A	ENGASE_ENST00000539857.2_Silent_p.A21A	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	207						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)	p.A207A(1)		breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CCTTCCTGGCCGGGGATGAGC	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C		0,3958		0,0,1979	59	65	63		621	-9.2	0.6	17		63	1,8303		0,1,4151	no	coding-synonymous	ENGASE	NM_001042573.1		0,1,6130	TT,TC,CC		0.012,0.0,0.0082		207/744	77076344	1,12261	1979	4152	6131	74587939	SO:0001819	synonymous_variant	64772			AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.621C>T	17.37:g.77076344C>T			74587939	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																				0.542	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		T	77076344	C	T	77076344	2	4	77	1	0	0	0	0	0	0	0	1	5131	639	23	1		1	ENGASE	17	77076344	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	875572	77076344	4118866	1016	22752										
CBX2	84733	broad.mit.edu	37	chr17	77757738	77757738	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccatccggaagaagcggggaCgaaagcccctgcccccagag	13	15	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:77757738C>T	ENST00000310942.4	+	5	600	c.496C>T	c.(496-498)Cga>Tga	p.R166*		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	166					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R166*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GAAGCGGGGACGAAAGCCCCT	0.677																																																1	Substitution - Nonsense(1)	large_intestine(1)	17											44	48	47					17																	77757738		2199	4300	6499	75372333	SO:0001587	stop_gained	84733			BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"Pc class homolog (Drosophila)"	602770	"chromobox homolog 2 (Drosophila Pc class)", "cell division cycle associated 6"	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.496C>T	17.37:g.77757738C>T	ENSP00000308750:p.Arg166*		75372333	Q0VDA5|Q9BTB1	Nonsense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.763335	0.69763	.	.	ENSG00000173894	ENST00000310942	.	.	.	5.47	4.46	0.54185	.	0.343245	0.29846	N	0.011056	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.7258	13.3656	0.60682	0.2834:0.7166:0.0:0.0	.	.	.	.	X	166	.	ENSP00000308750:R166X	R	+	1	2	CBX2	75372333	0.994000	0.37717	0.998000	0.56505	0.150000	0.21749	2.959000	0.49153	2.577000	0.86979	0.655000	0.94253	CGA		0.677	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647		T	77757738	C	T	77757738	4	4	77	1	0	0	0	0	0	1	0	0	2724	528	19	1	862	1	CBX2	17	77757738	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	681394	77757738	3437472	1017	22753										
RPTOR	57521	broad.mit.edu	37	chr17	78858821	78858821	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgcaggtccgctgcgcagCggtcttcgcccttggcacgt	13	15	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:78858821C>T	ENST00000306801.3	+	17	2218	c.1856C>T	c.(1855-1857)gCg>gTg	p.A619V	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Intron	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	619					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.A619V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CGCTGCGCAGCGGTCTTCGCC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											47	35	39					17																	78858821		2200	4299	6499	76473416	SO:0001583	missense	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1856C>T	17.37:g.78858821C>T	ENSP00000307272:p.Ala619Val		76473416	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559898	0.45590	.	.	ENSG00000141564	ENST00000306801	T	0.49720	0.77	4.78	4.78	0.61160	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.52266	1.64	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.52540	-0.8562	10	0.18276	T	0.48	.	17.8063	0.88602	0.0:1.0:0.0:0.0	.	619	Q8N122	RPTOR_HUMAN	V	619	ENSP00000307272:A619V	ENSP00000307272:A619V	A	+	2	0	RPTOR	76473416	1.000000	0.71417	0.094000	0.20943	0.010000	0.07245	7.323000	0.79105	2.209000	0.71365	0.462000	0.41574	GCG		0.657	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78858821	C	T	78858821	3	4	77	1	0	0	0	0	1	0	0	0	13702	768	27	1	1922	1	RPTOR	17	78858821	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1101083	78858821	2336389	1018	22754										
RPTOR	57521	broad.mit.edu	37	chr17	78935210	78935210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acagccgcgtcatgacgtacCgggagcacacagcctgggtg	14	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:78935210C>T	ENST00000306801.3	+	31	3984	c.3622C>T	c.(3622-3624)Cgg>Tgg	p.R1208W	RPTOR_ENST00000575542.1_3'UTR|CTD-2561B21.3_ENST00000571591.1_RNA|RPTOR_ENST00000544334.2_Missense_Mutation_p.R1050W	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1208					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R1208W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CATGACGTACCGGGAGCACAC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	17											80	46	58					17																	78935210		2168	4207	6375	76549805	SO:0001583	missense	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3622C>T	17.37:g.78935210C>T	ENSP00000307272:p.Arg1208Trp		76549805	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059378	0.55325	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.29917	1.55;1.55	4.27	4.27	0.50696	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.58552	0.2130	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.76575	0.988;0.854	T	0.66432	-0.5925	10	0.87932	D	0	.	17.2361	0.86999	0.0:1.0:0.0:0.0	.	1050;1208	F5H7J5;Q8N122	.;RPTOR_HUMAN	W	1208;1050	ENSP00000307272:R1208W;ENSP00000442479:R1050W	ENSP00000307272:R1208W	R	+	1	2	RPTOR	76549805	1.000000	0.71417	0.984000	0.44739	0.281000	0.26958	2.518000	0.45537	2.371000	0.80710	0.591000	0.81541	CGG		0.667	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78935210	C	T	78935210	3	4	77	1	0	0	0	0	1	0	0	0	13702	643	23	1	3744	1	RPTOR	17	78935210	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	76389	78935210	2260000	1019	22755										
ZNF750	79755	broad.mit.edu	37	chr17	80788076	80788076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggccgtgtcctgcagcttcGccttcttagctccttgctgg	11	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:80788076G>A	ENST00000269394.3	-	3	2947	c.2114C>T	c.(2113-2115)gCg>gTg	p.A705V	TBCD_ENST00000397466.2_Intron|ZNF750_ENST00000572562.1_Missense_Mutation_p.A306V|TBCD_ENST00000539345.2_Intron|TBCD_ENST00000355528.4_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	705					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A705V(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	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)			CTGCAGCTTCGCCTTCTTAGC	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	17											122	101	108					17																	80788076		2203	4300	6503	78381365	SO:0001583	missense	79755			AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.2114C>T	17.37:g.80788076G>A	ENSP00000269394:p.Ala705Val		78381365	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	G	2.983	-0.209835	0.06140	.	.	ENSG00000141579	ENST00000269394;ENST00000543850	T	0.11604	2.76	5.28	-0.647	0.11468	.	1.559540	0.03792	N	0.263027	T	0.06690	0.0171	L	0.27053	0.805	0.09310	N	1	B	0.24132	0.098	B	0.14578	0.011	T	0.33599	-0.9862	9	.	.	.	0.0083	1.0216	0.01519	0.3312:0.2658:0.2669:0.136	.	705	Q32MQ0	ZN750_HUMAN	V	705;298	ENSP00000269394:A705V	.	A	-	2	0	ZNF750	78381365	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	-0.130000	0.10498	-0.019000	0.14055	-0.339000	0.08088	GCG		0.567	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		A	80788076	G	A	80788076	3	1	77	1	0	0	0	0	1	0	0	0	18171	1087	38	1	61	1	ZNF750	17	80788076	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1852866	80788076	407134	1020	22756										
TBCD	6904	broad.mit.edu	37	chr17	80887119	80887119	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccatcccccacgtgccccacCgaggagaactggaaaagctg	10	16	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr17:80887119C>T	ENST00000355528.4	+	31	2954	c.2824C>T	c.(2824-2826)Cga>Tga	p.R942*	TBCD_ENST00000539345.2_Nonsense_Mutation_p.R942*	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	942					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)	p.R942*(2)				Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CGTGCCCCACCGAGGAGAACT	0.642																																																2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	17											61	66	64					17																	80887119		2074	4216	6290	78480408	SO:0001587	stop_gained	6904			BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2824C>T	17.37:g.80887119C>T	ENSP00000347719:p.Arg942*		78480408	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Nonsense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	C	35	5.485111	0.96323	.	.	ENSG00000141556	ENST00000355528;ENST00000334614	.	.	.	5.13	2.97	0.34412	.	0.076937	0.50627	D	0.000104	.	.	.	.	.	.	0.38567	D	0.94984	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5401	0.50661	0.3712:0.6288:0.0:0.0	.	.	.	.	X	942;693	.	.	R	+	1	2	TBCD	78480408	1.000000	0.71417	0.909000	0.35828	0.012000	0.07955	0.774000	0.26675	1.129000	0.42072	0.655000	0.94253	CGA		0.642	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		T	80887119	C	T	80887119	4	4	77	1	0	0	0	0	0	1	0	0	15672	644	23	1	2946	1	TBCD	17	80887119	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	99043	80887119	308091	1021	22757										
PTPRM	5797	broad.mit.edu	37	chr18	7774263	7774263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgacttctgatccatggatgCcatcaggtttgcttttagtt	9	9	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:7774263C>T	ENST00000332175.8	+	2	1227	c.190C>T	c.(190-192)Cca>Tca	p.P64S	PTPRM_ENST00000400053.4_Missense_Mutation_p.P2S|PTPRM_ENST00000400060.4_Missense_Mutation_p.P64S|PTPRM_ENST00000580170.1_Missense_Mutation_p.P64S	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	64	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P64S(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TCCATGGATGCCATCAGGTTT	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	18											182	162	169					18																	7774263		2203	4300	6503	7764263	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.190C>T	18.37:g.7774263C>T	ENSP00000331418:p.Pro64Ser		7764263	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261326	0.80246	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.02085	4.46;4.46;4.54	5.62	5.62	0.85841	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.064020	0.64402	D	0.000008	T	0.09642	0.0237	L	0.48362	1.52	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.71870	0.975;0.975	T	0.01675	-1.1298	10	0.56958	D	0.05	.	18.7818	0.91937	0.0:1.0:0.0:0.0	.	64;64	A7MBN1;P28827	.;PTPRM_HUMAN	S	64;64;2	ENSP00000331418:P64S;ENSP00000382933:P64S;ENSP00000382927:P2S	ENSP00000331418:P64S	P	+	1	0	PTPRM	7764263	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.852000	0.69488	2.795000	0.96236	0.655000	0.94253	CCA		0.393	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7774263	C	T	7774263	3	4	77	1	0	0	0	0	1	0	0	0	12843	739	26	3	196	3	PTPRM	18	7774263	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		7774263	70302985	1022	22758										
PTPRM	5797	broad.mit.edu	37	chr18	8113645	8113645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcagacagcctccaagctgCgcagccttttacaattggtg	10	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:8113645C>T	ENST00000332175.8	+	12	3055	c.2018C>T	c.(2017-2019)gCg>gTg	p.A673V	PTPRM_ENST00000400053.4_Missense_Mutation_p.A611V|PTPRM_ENST00000444013.1_Missense_Mutation_p.A460V|PTPRM_ENST00000400060.4_Missense_Mutation_p.A673V|PTPRM_ENST00000580170.1_Missense_Mutation_p.A673V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	673					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A673V(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CTCCAAGCTGCGCAGCCTTTT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	18											106	104	105					18																	8113645		2203	4300	6503	8103645	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2018C>T	18.37:g.8113645C>T	ENSP00000331418:p.Ala673Val		8103645	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.851033	0.71719	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.46063	1.21;1.2;1.03;0.88	5.95	5.95	0.96441	Fibronectin, type III (1);	0.165983	0.53938	D	0.000041	T	0.35393	0.0930	L	0.38175	1.15	0.51767	D	0.999932	B;P;P	0.36438	0.002;0.553;0.553	B;B;B	0.28305	0.006;0.088;0.088	T	0.10132	-1.0643	10	0.41790	T	0.15	.	20.3748	0.98911	0.0:1.0:0.0:0.0	.	460;673;673	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	V	673;673;611;460	ENSP00000331418:A673V;ENSP00000382933:A673V;ENSP00000382927:A611V;ENSP00000387608:A460V	ENSP00000331418:A673V	A	+	2	0	PTPRM	8103645	1.000000	0.71417	0.970000	0.41538	0.988000	0.76386	7.487000	0.81328	2.817000	0.96982	0.563000	0.77884	GCG		0.428	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8113645	C	T	8113645	3	4	77	1	0	0	0	0	1	0	0	0	12843	768	27	1	2064	1	PTPRM	18	8113645	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	339382	8113645	69963603	1023	22759										
ANKRD12	23253	broad.mit.edu	37	chr18	9255261	9255261	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agagggaaaaagaaaagcatAaaaaagaaattgaaggtgaa							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:9255261delA	ENST00000262126.4	+	9	2236	c.1996delA	c.(1996-1998)aaafs	p.K667fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.K644fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.K644fs	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	667						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E668fs*44(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						agaaaagcataaaaaagaaat	0.294																																																1	Deletion - Frameshift(1)	large_intestine(1)	18											44	49	47					18																	9255261		2192	4278	6470	9245261	SO:0001589	frameshift_variant	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1996delA	18.37:g.9255261delA	ENSP00000262126:p.Lys667fs		9245261	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	37	CCDS11843.1																																																																																				0.294	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		-	9255261	A	-	9255261	7	5	77	1	0	1	0	1	0	0	0	0	640	363	13	0	2026	0	ANKRD12	18	9255261	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	1141616	9255261	68821987	1024	22760										
RALBP1	10928	broad.mit.edu	37	chr18	9513167	9513167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctactaagtttcctggattgTaccgcactggcgagccctca	9	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:9513167T>C	ENST00000019317.4	+	2	347	c.124T>C	c.(124-126)Tac>Cac	p.Y42H	RALBP1_ENST00000383432.3_Missense_Mutation_p.Y42H			Q15311	RBP1_HUMAN	ralA binding protein 1	42					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)	p.Y42H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	TCCTGGATTGTACCGCACTGG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	18											61	60	61					18																	9513167		2203	4300	6503	9503167	SO:0001583	missense	10928			L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.124T>C	18.37:g.9513167T>C	ENSP00000019317:p.Tyr42His		9503167	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.591699	0.86953	.	.	ENSG00000017797	ENST00000019317;ENST00000383432;ENST00000458039	T;T	0.21734	1.99;1.99	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.43456	0.1248	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.37314	-0.9711	10	0.72032	D	0.01	-0.0647	15.1696	0.72862	0.0:0.0:0.0:1.0	.	42	Q15311	RBP1_HUMAN	H	42	ENSP00000019317:Y42H;ENSP00000372924:Y42H	ENSP00000019317:Y42H	Y	+	1	0	RALBP1	9503167	1.000000	0.71417	0.996000	0.52242	0.889000	0.51656	7.751000	0.85126	2.038000	0.60285	0.379000	0.24179	TAC		0.552	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		C	9513167	T	C	9513167	3	2	77	1	0	0	0	0	1	0	0	0	13049	1638	57	4	126	4	RALBP1	18	9513167	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	257906	9513167	68564081	1025	22761										
CEP192	55125	broad.mit.edu	37	chr18	13095600	13095600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcttctctcacgggcggctcGcccgcctctggatcagctgg	12	16	5	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:13095600G>A	ENST00000325971.8	+	33	6158	c.4565G>A	c.(4564-4566)cGc>cAc	p.R1522H	CEP192_ENST00000430049.2_Missense_Mutation_p.R1643H|CEP192_ENST00000540847.2_3'UTR|CEP192_ENST00000506447.1_Missense_Mutation_p.R2118H			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1522					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.R2118H(1)|p.R1522H(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGGGCGGCTCGCCCGCCTCTG	0.557																																																2	Substitution - Missense(2)	large_intestine(2)	18											77	77	77					18																	13095600		2203	4300	6503	13085600	SO:0001583	missense	55125			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.4565G>A	18.37:g.13095600G>A	ENSP00000317156:p.Arg1522His		13085600	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	G	13.91	2.376858	0.42105	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.30448	1.53;1.53;1.53	5.91	-11.8	0.00035	.	0.882696	0.09974	N	0.731835	T	0.10723	0.0262	N	0.04880	-0.145	0.09310	N	1	B;B;B;B	0.13594	0.001;0.008;0.001;0.001	B;B;B;B	0.09377	0.001;0.004;0.001;0.001	T	0.32241	-0.9914	10	0.29301	T	0.29	6.8547	11.4159	0.49951	0.25:0.533:0.217:0.0	.	1643;2118;122;720	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	H	2118;1522;1522;1643;122	ENSP00000427550:R2118H;ENSP00000317156:R1522H;ENSP00000389190:R1643H	ENSP00000317156:R1522H	R	+	2	0	CEP192	13085600	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.446000	0.21694	-2.678000	0.00410	-1.058000	0.02302	CGC		0.557	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		A	13095600	G	A	13095600	3	1	77	1	0	0	0	0	1	0	0	0	3257	1087	38	1	6487	1	CEP192	18	13095600	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3582433	13095600	64981648	1026	22762										
CDH2	1000	broad.mit.edu	37	chr18	25565021	25565021	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcaccggtgccaagccccgCacccacaatcctgtccacat	8	19	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:25565021C>T	ENST00000269141.3	-	13	2575	c.2152G>A	c.(2152-2154)Gcg>Acg	p.A718T	CDH2_ENST00000399380.3_Missense_Mutation_p.A687T	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	718					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.A718T(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CCAAGCCCCGCACCCACAATC	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	18											95	87	90					18																	25565021		2203	4300	6503	23819019	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2152G>A	18.37:g.25565021C>T	ENSP00000269141:p.Ala718Thr		23819019	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.144655	0.57044	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.60299	0.24;0.2	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.54111	0.1838	L	0.52126	1.63	0.80722	D	1	B;B	0.31859	0.343;0.153	B;B	0.34873	0.191;0.045	T	0.51012	-0.8759	10	0.38643	T	0.18	.	13.8	0.63194	0.0:0.9304:0.0:0.0696	.	687;718	A8MWK3;P19022	.;CADH2_HUMAN	T	718;687	ENSP00000269141:A718T;ENSP00000382312:A687T	ENSP00000269141:A718T	A	-	1	0	CDH2	23819019	0.998000	0.40836	0.646000	0.29493	0.981000	0.71138	3.788000	0.55446	2.890000	0.99128	0.585000	0.79938	GCG		0.488	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25565021	C	T	25565021	3	4	77	1	0	0	0	0	1	0	0	0	3111	710	25	3	584	3	CDH2	18	25565021	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	12469421	25565021	52512227	1027	22763										
FHOD3	80206	broad.mit.edu	37	chr18	34205516	34205516	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgatgagaccacggagccaCcccccagtgggtgccgggac							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:34205516delC	ENST00000359247.4	+	10	1000	c.1000delC	c.(1000-1002)cccfs	p.P335fs	FHOD3_ENST00000257209.4_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000591635.1_Frame_Shift_Del_p.H8fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.P335fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	335	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.S336fs*138(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CACGGAGCCACCCCCCAGTGG	0.677																																																1	Deletion - Frameshift(1)	large_intestine(1)	18											40	44	43					18																	34205516		2203	4299	6502	32459514	SO:0001589	frameshift_variant	80206			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1000delC	18.37:g.34205516delC	ENSP00000352186:p.Pro335fs		32459514	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	37																																																																																					0.677	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		-	34205516	C	-	34205516	7	5	77	1	0	1	0	1	0	0	0	0	5902	507	18	0	1038	0	FHOD3	18	34205516	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	8640495	34205516	43871732	1028	22764										
ATP5A1	498	broad.mit.edu	37	chr18	43667341	43667341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtcatagatgatcaaagcaTgtttgccattgtctctaaaa	7	8	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:43667341T>C	ENST00000398752.6	-	7	1038	c.917A>G	c.(916-918)cAt>cGt	p.H306R	ATP5A1_ENST00000593152.2_Missense_Mutation_p.H256R|ATP5A1_ENST00000282050.2_Missense_Mutation_p.H306R|ATP5A1_ENST00000590665.1_Missense_Mutation_p.H284R	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	306					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.H306R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						GATCAAAGCATGTTTGCCATT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	18											75	76	76					18																	43667341		2203	4300	6503	41921339	SO:0001583	missense	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.917A>G	18.37:g.43667341T>C	ENSP00000381736:p.His306Arg		41921339	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.167157	0.78339	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.81659	-1.52;-1.52	4.68	4.68	0.58851	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90400	0.6995	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92167	0.5740	10	0.87932	D	0	-21.9803	14.1589	0.65434	0.0:0.0:0.0:1.0	.	306	P25705	ATPA_HUMAN	R	306;306;256	ENSP00000282050:H306R;ENSP00000381736:H306R	ENSP00000282050:H306R	H	-	2	0	ATP5A1	41921339	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.953000	0.87836	1.749000	0.51849	0.460000	0.39030	CAT		0.413	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		C	43667341	T	C	43667341	3	2	77	1	0	0	0	0	1	0	0	0	1148	1464	51	4	768	4	ATP5A1	18	43667341	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	9461825	43667341	34409907	1029	22765										
TCF4	6925	broad.mit.edu	37	chr18	53254277	53254277	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccaccgttctttcttaccGcactgaaatccagtaaatca	4	13	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:53254277G>A	ENST00000356073.4	-	2	682	c.71C>T	c.(70-72)gCg>gTg	p.A24V	TCF4_ENST00000565018.2_Splice_Site_p.A24V|TCF4_ENST00000566286.1_Intron|TCF4_ENST00000564999.1_Splice_Site_p.A24V|TCF4_ENST00000398339.1_Splice_Site_p.A126V|TCF4_ENST00000566279.1_Splice_Site_p.A24V|TCF4_ENST00000540999.1_5'Flank|TCF4_ENST00000568740.1_Intron|TCF4_ENST00000567880.1_Splice_Site_p.A24V|TCF4_ENST00000537578.1_Intron|TCF4_ENST00000354452.3_Splice_Site_p.A24V|TCF4_ENST00000568673.1_5'Flank|TCF4_ENST00000564403.2_Splice_Site_p.A24V	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	24	Essential for MYOD1 inhibition. {ECO:0000250}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)	p.A24V(1)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		CTTTCTTACCGCACTGAAATC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	18											104	88	94					18																	53254277		2203	4300	6503	51405275	SO:0001630	splice_region_variant	6925			M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.72+1C>T	18.37:g.53254277G>A			51405275	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	37	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843330	0.91197	.	.	ENSG00000196628	ENST00000354452;ENST00000356073;ENST00000398339	T;T;T	0.31247	1.5;1.5;1.5	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000033	T	0.47340	0.1440	L	0.47190	1.495	0.53688	D	0.999971	D;D;D	0.89917	1.0;0.958;0.99	D;B;P	0.71656	0.974;0.27;0.551	T	0.12400	-1.0549	10	0.26408	T	0.33	-5.5357	16.1307	0.81436	0.0:0.1338:0.8662:0.0	.	24;126;24	G0LNT9;E9PH57;P15884	.;.;ITF2_HUMAN	V	24;24;126	ENSP00000346440:A24V;ENSP00000348374:A24V;ENSP00000381382:A126V	ENSP00000346440:A24V	A	-	2	0	TCF4	51405275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.456000	0.97628	2.711000	0.92665	0.655000	0.94253	GCG		0.403	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	Missense_Mutation	A	53254277	G	A	53254277	5	1	77	1	0	0	0	0	0	0	1	0	15734	1101	38	1	2016	1	TCF4	18	53254277	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	9586936	53254277	24822971	1030	22766										
NEDD4L	23327	broad.mit.edu	37	chr18	56057896	56057896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggctgtgctactcatggacGccgaaaagcgtatccggtta	12	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:56057896G>A	ENST00000400345.3	+	29	2957	c.2674G>A	c.(2674-2676)Gcc>Acc	p.A892T	NEDD4L_ENST00000456173.2_Missense_Mutation_p.A751T|NEDD4L_ENST00000589054.1_Missense_Mutation_p.A23T|NEDD4L_ENST00000456986.1_Missense_Mutation_p.A771T|NEDD4L_ENST00000356462.6_Missense_Mutation_p.A828T|NEDD4L_ENST00000256830.9_Missense_Mutation_p.A788T|NEDD4L_ENST00000431212.2_Missense_Mutation_p.A771T|NEDD4L_ENST00000256832.7_Missense_Mutation_p.A752T|NEDD4L_ENST00000586263.1_Missense_Mutation_p.A864T|NEDD4L_ENST00000382850.4_Missense_Mutation_p.A872T|NEDD4L_ENST00000357895.5_Missense_Mutation_p.A884T|NEDD4L_ENST00000435432.2_Missense_Mutation_p.A751T	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	892	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)	p.A872T(1)		breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						ACTCATGGACGCCGAAAAGCG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	18											83	80	81					18																	56057896		2039	4190	6229	54208876	SO:0001583	missense	23327			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.2674G>A	18.37:g.56057896G>A	ENSP00000383199:p.Ala892Thr		54208876	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	37	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.098376	0.56183	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.66	5.66	0.87406	HECT (4);	0.047041	0.85682	D	0.000000	T	0.42653	0.1212	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B;B	0.23128	0.015;0.009;0.005;0.08;0.019;0.015	B;B;B;B;B;B	0.21546	0.012;0.006;0.007;0.017;0.035;0.021	T	0.18681	-1.0329	10	0.24483	T	0.36	.	19.7559	0.96291	0.0:0.0:1.0:0.0	.	864;884;751;828;892;872	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	T	892;872;828;788;752;771;884;751;751;771	ENSP00000383199:A892T;ENSP00000372301:A872T;ENSP00000348847:A828T;ENSP00000256830:A788T;ENSP00000256832:A752T;ENSP00000411947:A771T;ENSP00000350569:A884T;ENSP00000393395:A751T;ENSP00000405440:A751T;ENSP00000389406:A771T	ENSP00000256830:A788T	A	+	1	0	NEDD4L	54208876	1.000000	0.71417	0.995000	0.50966	0.843000	0.47879	7.907000	0.87430	2.656000	0.90262	0.655000	0.94253	GCC		0.502	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			A	56057896	G	A	56057896	3	1	77	1	0	0	0	0	1	0	0	0	10342	1087	38	1	2816	1	NEDD4L	18	56057896	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2803619	56057896	22019352	1031	22767										
CDH19	28513	broad.mit.edu	37	chr18	64235800	64235800	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctattacctgggctcttaAgatgtagagggatcgctcct	11	9	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:64235800A>C	ENST00000540086.1	-	3	589	c.343T>G	c.(343-345)Tta>Gta	p.L115V	CDH19_ENST00000262150.2_Missense_Mutation_p.L115V	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	223	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L115V(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TGGGCTCTTAAGATGTAGAGG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	18											139	134	135					18																	64235800		2203	4299	6502	62386780	SO:0001583	missense	28513			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.343T>G	18.37:g.64235800A>C	ENSP00000439593:p.Leu115Val		62386780	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.514126	0.27123	.	.	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.72167	-0.63;-0.63	5.87	4.06	0.47325	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000001	T	0.81254	0.4784	M	0.77103	2.36	0.40968	D	0.98467	D;P	0.69078	0.997;0.832	D;P	0.69142	0.962;0.658	T	0.81662	-0.0831	10	0.66056	D	0.02	.	8.9152	0.35576	0.2319:0.0:0.7681:0.0	.	115;115	F5H1K0;Q9H159	.;CAD19_HUMAN	V	115;115;60	ENSP00000262150:L115V;ENSP00000439593:L115V	ENSP00000262150:L115V	L	-	1	2	CDH19	62386780	0.993000	0.37304	0.234000	0.24042	0.957000	0.61999	2.184000	0.42575	0.790000	0.33803	-0.462000	0.05337	TTA		0.423	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		C	64235800	A	C	64235800	3	2	77	1	0	0	0	0	1	0	0	0	3110	69	3	4	2015	4	CDH19	18	64235800	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	8177904	64235800	13841448	1032	22768										
FBXO15	201456	broad.mit.edu	37	chr18	71740947	71740947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgttcatccaaaagagttaCgtccatcatggaacaactct	6	10	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:71740947C>T	ENST00000419743.2	-	10	1361	c.1282G>A	c.(1282-1284)Gta>Ata	p.V428I	FBXO15_ENST00000580806.1_5'UTR|FBXO15_ENST00000269500.5_Missense_Mutation_p.V352I	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	428						SCF ubiquitin ligase complex (GO:0019005)		p.V352I(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		AAAAGAGTTACGTCCATCATG	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	18											144	136	139					18																	71740947		2203	4300	6503	69891927	SO:0001583	missense	201456			AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1282G>A	18.37:g.71740947C>T	ENSP00000393154:p.Val428Ile		69891927	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	c	9.789	1.177400	0.21787	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.44881	0.91;0.91	5.9	-9.48	0.00591	.	1.198800	0.05694	N	0.592719	T	0.27731	0.0682	L	0.35723	1.085	0.09310	N	1	B;B	0.18968	0.032;0.01	B;B	0.09377	0.004;0.002	T	0.23190	-1.0195	10	0.45353	T	0.12	-12.5595	9.1899	0.37193	0.0:0.3665:0.2234:0.4101	.	428;352	B3KST3;Q8NCQ5	.;FBX15_HUMAN	I	352;428	ENSP00000269500:V352I;ENSP00000393154:V428I	ENSP00000269500:V352I	V	-	1	0	FBXO15	69891927	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-3.445000	0.00468	-2.728000	0.00385	-1.812000	0.00611	GTA		0.453	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		T	71740947	C	T	71740947	3	4	77	1	0	0	0	0	1	0	0	0	5747	536	19	1	254	1	FBXO15	18	71740947	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	7505147	71740947	6336301	1033	22769										
CNDP2	55748	broad.mit.edu	37	chr18	72180811	72180812	+	Frame_Shift_Ins	INS	-	-	G													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggctctttggtggacaagaINSgggggaacatcctgatcccc					rs144608297		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr18:72180811_72180812insG	ENST00000324262.4	+	8	1076_1077	c.760_761insG	c.(760-762)aggfs	p.R254fs	CNDP2_ENST00000579847.1_Frame_Shift_Ins_p.R254fs|CNDP2_ENST00000324301.8_Frame_Shift_Ins_p.R170fs	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	254					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.N256fs*8(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GGTGGACAAGAGGGGGAACATC	0.599																																																1	Insertion - Frameshift(1)	large_intestine(1)	18																																								70331792	SO:0001589	frameshift_variant	55748			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.765dupG	18.37:g.72180816_72180816dupG	ENSP00000325548:p.Arg254fs		70331791	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Frame_Shift_Ins	INS	ENST00000324262.4	37	CCDS12006.1																																																																																				0.599	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		G	72180812	-	G	72180811	7	5	77	1	0	1	1	0	0	0	0	0	3600	295	11	0	786	0	CNDP2	18	72180811	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	439864	72180811	5896437	1034	22770										
SHC2	25759	broad.mit.edu	37	chr19	436639	436639	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctggcctcaccgtgtctccGcctgacgcgaaggagatgga	13	14	2	2	rs182383668		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:436639G>A	ENST00000264554.6	-	5	764	c.765C>T	c.(763-765)ggC>ggT	p.G255G		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	255	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)		p.G616G(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|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)		CCGTGTCTCCGCCTGACGCGA	0.706													G|||	1	0.000199681	8e-04	0	5008	,	,		15644	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						G		1,4287		0,1,2143	27	35	32		765	-9.2	0	19		32	0,8488		0,0,4244	no	coding-synonymous	SHC2	NM_012435.2		0,1,6387	AA,AG,GG		0.0,0.0233,0.0078		255/583	436639	1,12775	2144	4244	6388	387639	SO:0001819	synonymous_variant	25759			AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.765C>T	19.37:g.436639G>A			387639	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	37	CCDS45891.1																																																																																				0.706	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			A	436639	G	A	436639	2	1	77	1	0	0	0	0	0	0	0	1	14308	1074	38	1		1	SHC2	19	436639	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10		436639	58692344	1035	22771										
GZMM	3004	broad.mit.edu	37	chr19	544110	544110	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcactgctggtgctggccctGggggccctgtcagtaggtga							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:544110delG	ENST00000264553.3	+	1	77	c.39delG	c.(37-39)ctgfs	p.L13fs		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	13					apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A15fs*4(1)		endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|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)		TGCTGGCCCTGGGGGCCCTGT	0.726																																																1	Deletion - Frameshift(1)	large_intestine(1)	19											12	10	10					19																	544110		2132	4165	6297	495110	SO:0001589	frameshift_variant	3004				CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"lymphocyte met-ase 1"	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.39delG	19.37:g.544110delG	ENSP00000264553:p.Leu13fs		495110		Frame_Shift_Del	DEL	ENST00000264553.3	37	CCDS12031.1																																																																																				0.726	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317		-	544110	G	-	544110	7	5	77	1	0	1	0	1	0	0	0	0	6940	1335	47	0	41	0	GZMM	19	544110	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	107471	544110	58584873	1036	22772										
CNN2	1265	broad.mit.edu	37	chr19	1036152	1036152	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagactaaggggctgcagagCggggtggacattggcgtcaa	17	7	1	2	rs146615344		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:1036152C>T	ENST00000263097.4	+	5	777	c.414C>T	c.(412-414)agC>agT	p.S138S	CNN2_ENST00000565096.2_Silent_p.S127S|CNN2_ENST00000562958.2_Silent_p.S159S|AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000348419.3_Intron|CNN2_ENST00000606983.1_Intron	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	138					actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)	p.S138S(1)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		GGCTGCAGAGCGGGGTGGACA	0.647													C|||	1	0.000199681	8e-04	0	5008	,	,		16848	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C	,	5,4401	9.9+/-24.2	0,5,2198	35	33	34		414,	-7.3	0	19	dbSNP_134	34	0,8600		0,0,4300	no	coding-synonymous,intron	CNN2	NM_004368.2,NM_201277.1	,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,	138/310,	1036152	5,13001	2203	4300	6503	987152	SO:0001819	synonymous_variant	1265			D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.414C>T	19.37:g.1036152C>T			987152	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																				0.647	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368		T	1036152	C	T	1036152	2	4	77	1	0	0	0	0	0	0	0	1	3616	767	27	1		1	CNN2	19	1036152	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	492042	1036152	58092831	1037	22773										
CIRBP	1153	broad.mit.edu	37	chr19	1270937	1270937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctgccacaggccgccatggCatcagatgaaggcaaacttt	10	12	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:1270937C>T	ENST00000588030.1	+	2	265	c.5C>T	c.(4-6)gCa>gTa	p.A2V	CIRBP_ENST00000588230.1_Missense_Mutation_p.A2V|CIRBP_ENST00000586472.1_Missense_Mutation_p.A2V|CIRBP-AS1_ENST00000585832.1_RNA|CIRBP-AS1_ENST00000600215.1_RNA|CIRBP_ENST00000589710.1_Missense_Mutation_p.A2V|CIRBP_ENST00000587896.1_Missense_Mutation_p.A2V|CIRBP_ENST00000585630.1_Missense_Mutation_p.A2V|CIRBP_ENST00000591935.1_Missense_Mutation_p.A2V|CIRBP_ENST00000589235.1_Missense_Mutation_p.A2V|CIRBP_ENST00000320936.5_Missense_Mutation_p.A2V|CIRBP_ENST00000588090.1_Missense_Mutation_p.A2V|CIRBP_ENST00000444172.2_5'UTR|CIRBP_ENST00000589686.1_Missense_Mutation_p.A2V|CIRBP_ENST00000413636.2_Missense_Mutation_p.A2V|CIRBP_ENST00000587323.1_Missense_Mutation_p.A2V|CIRBP_ENST00000589660.1_Missense_Mutation_p.A2V|CIRBP_ENST00000586773.1_Missense_Mutation_p.A2V			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	2					mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)	p.A2V(1)		endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		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)		gccgccatggcatcagatgaa	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	19											169	176	174					19																	1270937		2203	4300	6503	1221937	SO:0001583	missense	1153			D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"RNA binding motif (RRM) containing"	1982	protein-coding gene	gene with protein product	"Cold-inducible RNA-binding protein", "glycine-rich RNA binding protein"	602649	"cold inducible RNA-binding protein"			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.5C>T	19.37:g.1270937C>T	ENSP00000468788:p.Ala2Val		1221937	B3KT17|B4E2X2	Missense_Mutation	SNP	ENST00000588030.1	37	CCDS12059.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754755	0.49362	.	.	ENSG00000099622	ENST00000320936;ENST00000413636	T;T	0.70282	0.18;-0.47	4.6	3.57	0.40892	.	0.218004	0.38326	U	0.001722	T	0.66906	0.2837	L	0.44542	1.39	0.80722	D	1	P;P;P	0.48998	0.863;0.918;0.846	P;P;B	0.46758	0.526;0.526;0.283	T	0.69390	-0.5158	10	0.87932	D	0	-8.6916	11.3577	0.49625	0.0:0.9098:0.0:0.0902	.	2;2;2	B4E2X2;D6W5Y5;Q14011	.;.;CIRBP_HUMAN	V	2	ENSP00000322887:A2V;ENSP00000412831:A2V	ENSP00000322887:A2V	A	+	2	0	CIRBP	1221937	1.000000	0.71417	0.859000	0.33776	0.090000	0.18270	4.957000	0.63652	0.937000	0.37394	-0.251000	0.11542	GCA		0.478	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		T	1270937	C	T	1270937	3	4	77	1	0	0	0	0	1	0	0	0	3439	710	25	3	7	3	CIRBP	19	1270937	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	234785	1270937	57858046	1038	22774										
LMNB2	84823	broad.mit.edu	37	chr19	2431784	2431784	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagccacacacacccacctcGccatccgcgttaaccaggac	6	19	0	0	rs372581793		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:2431784G>A	ENST00000582871.1	-	10	1733	c.1647C>T	c.(1645-1647)ggC>ggT	p.G549G	LMNB2_ENST00000475819.1_5'UTR|LMNB2_ENST00000325327.3_Silent_p.G569G	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	549	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)	p.G549G(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		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)		CACCCACCTCGCCATCCGCGT	0.726																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		1,4403	2.1+/-5.4	0,1,2201	73	65	68		1647	-4.2	0.3	19		68	0,8594		0,0,4297	no	coding-synonymous	LMNB2	NM_032737.2		0,1,6498	AA,AG,GG		0.0,0.0227,0.0077		549/601	2431784	1,12997	2202	4297	6499	2382784	SO:0001819	synonymous_variant	84823			M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"Intermediate filaments type V, lamins"	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1647C>T	19.37:g.2431784G>A			2382784	O75292|Q14734|Q96DF6	Silent	SNP	ENST00000582871.1	37																																																																																					0.726	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		A	2431784	G	A	2431784	2	1	77	1	0	0	0	0	0	0	0	1	8874	1074	38	1		1	LMNB2	19	2431784	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1160847	2431784	56697199	1039	22775										
ATCAY	85300	broad.mit.edu	37	chr19	3913846	3913846	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacgtccagatcccagactgCgtcctgcagtgagtggcccc	11	16	0	3	rs370680121		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:3913846C>T	ENST00000450849.2	+	9	1424	c.957C>T	c.(955-957)tgC>tgT	p.C319C	ATCAY_ENST00000301260.6_Silent_p.C319C|ATCAY_ENST00000398448.3_Silent_p.C325C|ATCAY_ENST00000600960.1_Silent_p.C319C	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	319	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.C319C(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		TCCCAGACTGCGTCCTGCAGT	0.537													C|||	1	0.000199681	0	0.0014	5008	,	,		12433	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		0,4086		0,0,2043	72	77	75		957	-2.7	0.8	19		75	1,8345		0,1,4172	no	coding-synonymous	ATCAY	NM_033064.4		0,1,6215	TT,TC,CC		0.012,0.0,0.0080		319/372	3913846	1,12431	2043	4173	6216	3864846	SO:0001819	synonymous_variant	85300				CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.957C>T	19.37:g.3913846C>T			3864846	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Silent	SNP	ENST00000450849.2	37	CCDS45923.1																																																																																				0.537	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			T	3913846	C	T	3913846	2	4	77	1	0	0	0	0	0	0	0	1	1078	776	27	1		1	ATCAY	19	3913846	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1482062	3913846	55215137	1040	22776										
DAPK3	1613	broad.mit.edu	37	chr19	3961142	3961142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttggtctcgcccaggaacGgggatgcaccgctcaggctg	15	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:3961142G>A	ENST00000545797.2	-	7	890	c.647C>T	c.(646-648)cCg>cTg	p.P216L	DAPK3_ENST00000301264.3_Missense_Mutation_p.P216L|MIR637_ENST00000385000.1_RNA			O43293	DAPK3_HUMAN	death-associated protein kinase 3	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> S (in a lung neuroendocrine carcinoma sample; somatic mutation; greatly reduces kinase acivity, increases cell proliferation, cell adhesion and cell survival). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21487036}.		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)	p.P216L(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCAGGAACGGGGATGCACC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											84	64	71					19																	3961142		2203	4299	6502	3912142	SO:0001583	missense	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.647C>T	19.37:g.3961142G>A	ENSP00000442973:p.Pro216Leu		3912142	A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	37	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.927978	0.92389	.	.	ENSG00000167657	ENST00000301264;ENST00000545797;ENST00000442766	T;T	0.56611	0.45;0.45	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80231	-0.1468	10	0.87932	D	0	.	18.1265	0.89587	0.0:0.0:1.0:0.0	.	216	O43293	DAPK3_HUMAN	L	216;216;71	ENSP00000301264:P216L;ENSP00000442973:P216L	ENSP00000301264:P216L	P	-	2	0	DAPK3	3912142	1.000000	0.71417	0.965000	0.40720	0.690000	0.40134	9.535000	0.98064	2.627000	0.88993	0.555000	0.69702	CCG		0.672	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		A	3961142	G	A	3961142	3	1	77	1	0	0	0	0	1	0	0	0	4243	1116	39	1	729	1	DAPK3	19	3961142	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	47296	3961142	55167841	1041	22777										
ZBTB7A	51341	broad.mit.edu	37	chr19	4054676	4054676	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcggacgccccaaaggcggaCcacgggaagctggcagcggc	16	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:4054676C>T	ENST00000322357.4	-	2	833	c.555G>A	c.(553-555)tgG>tgA	p.W185*	ZBTB7A_ENST00000601588.1_Nonsense_Mutation_p.W185*	NM_015898.2	NP_056982.1	O95365	ZBT7A_HUMAN	zinc finger and BTB domain containing 7A	185	Ala-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)	p.W185*(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.014)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAAGGCGGACCACGGGAAGC	0.701																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											10	11	11					19																	4054676		2157	4210	6367	4005676	SO:0001587	stop_gained	51341			AF000561	CCDS12119.1	19p13.3	2013-01-08		2005-04-07		ENSG00000178951		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18078	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 7A, HIV-1 inducer of short transcripts binding protein", "lymphoma related factor"	605878	"zinc finger and BTB domain containing 7"	ZBTB7		9973611, 9927193	Standard	NM_015898		Approved	FBI-1, LRF, DKFZp547O146, pokemon, ZNF857A	uc002lzi.3	O95365		ENST00000322357.4:c.555G>A	19.37:g.4054676C>T	ENSP00000323670:p.Trp185*		4005676	D6W619|O00456|Q14D41|Q5XG86	Nonsense_Mutation	SNP	ENST00000322357.4	37	CCDS12119.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343778	0.61073	.	.	ENSG00000178951	ENST00000322357	.	.	.	5.02	3.95	0.45737	.	0.743675	0.11029	U	0.607501	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	7.4715	0.27351	0.167:0.7484:0.0:0.0846	.	.	.	.	X	185	.	ENSP00000323670:W185X	W	-	3	0	ZBTB7A	4005676	1.000000	0.71417	0.831000	0.32960	0.027000	0.11550	5.209000	0.65208	1.050000	0.40346	0.462000	0.41574	TGG		0.701	ZBTB7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457621.2	NM_015898		T	4054676	C	T	4054676	4	4	77	1	0	0	0	0	0	1	0	0	17592	508	18	3	1207	3	ZBTB7A	19	4054676	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	93534	4054676	55074307	1042	22778										
MAP2K2	5605	broad.mit.edu	37	chr19	4110646	4110646	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggccggcttgatctcaaggTggatcagctgcaaggggaga	16	8	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:4110646T>C	ENST00000262948.5	-	3	564	c.311A>G	c.(310-312)cAc>cGc	p.H104R	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_Missense_Mutation_p.H7R	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)	p.H104R(1)					Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	GATCTCAAGGTGGATCAGCTG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	19											58	48	52					19																	4110646		2203	4300	6503	4061646	SO:0001583	missense	5605			L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.311A>G	19.37:g.4110646T>C	ENSP00000262948:p.His104Arg		4061646		Missense_Mutation	SNP	ENST00000262948.5	37	CCDS12120.1	.	.	.	.	.	.	.	.	.	.	t	15.99	2.994761	0.54041	.	.	ENSG00000126934	ENST00000262948;ENST00000394867	D;D	0.91686	-2.89;-2.89	5.3	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84005	0.5377	N	0.11341	0.13	0.80722	D	1	B	0.14805	0.011	B	0.20384	0.029	T	0.79463	-0.1793	10	0.31617	T	0.26	-43.0156	14.0565	0.64772	0.0:0.0:0.0:1.0	.	104	P36507	MP2K2_HUMAN	R	104;7	ENSP00000262948:H104R;ENSP00000378336:H7R	ENSP00000262948:H104R	H	-	2	0	MAP2K2	4061646	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.935000	0.87658	1.999000	0.58509	0.459000	0.35465	CAC		0.617	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			C	4110646	T	C	4110646	3	2	77	1	0	0	0	0	1	0	0	0	9267	1696	59	4	927	4	MAP2K2	19	4110646	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	55970	4110646	55018337	1043	22779										
GTF2F1	2962	broad.mit.edu	37	chr19	6380372	6380372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgaggatctgggccaacaCgttcactgtctgctcgctgc	11	13	3	1	rs199893553		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:6380372C>T	ENST00000394456.5	-	13	1938	c.1474G>A	c.(1474-1476)Gtg>Atg	p.V492M	GTF2F1_ENST00000429701.2_Missense_Mutation_p.V407M|PSPN_ENST00000597721.1_5'Flank	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	492					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.V492M(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						TGGGCCAACACGTTCACTGTC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	19											247	226	233					19																	6380372		2203	4300	6503	6331372	SO:0001583	missense	2962				CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"General transcription factors"	4652	protein-coding gene	gene with protein product		189968	"general transcription factor IIF, polypeptide 1 (74kD subunit)"			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.1474G>A	19.37:g.6380372C>T	ENSP00000377969:p.Val492Met		6331372	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045800	0.75846	.	.	ENSG00000125651	ENST00000394456;ENST00000429701	T;T	0.45668	0.89;0.89	4.62	4.62	0.57501	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.64402	D	0.000001	T	0.61223	0.2330	M	0.62723	1.935	0.58432	D	0.999995	P;D;D	0.89917	0.926;1.0;0.999	B;D;D	0.74674	0.185;0.984;0.971	T	0.60667	-0.7218	10	0.44086	T	0.13	-54.9666	16.7748	0.85548	0.0:1.0:0.0:0.0	.	407;390;492	E7EUG6;B4DDB5;P35269	.;.;T2FA_HUMAN	M	492;407	ENSP00000377969:V492M;ENSP00000392107:V407M	ENSP00000377969:V492M	V	-	1	0	GTF2F1	6331372	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	4.263000	0.58853	2.566000	0.86566	0.655000	0.94253	GTG		0.552	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		T	6380372	C	T	6380372	3	4	77	1	0	0	0	0	1	0	0	0	6879	536	19	1	83	1	GTF2F1	19	6380372	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2269726	6380372	52748611	1044	22780										
DENND1C	79958	broad.mit.edu	37	chr19	6467848	6467848	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttttcctgggctgtagaatcTtcagctgccttgtgggaagg	13	8	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:6467848T>C	ENST00000381480.2	-	23	2185	c.2073A>G	c.(2071-2073)gaA>gaG	p.E691E	DENND1C_ENST00000543576.1_Silent_p.E647E	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	691					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.E691E(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CTGTAGAATCTTCAGCTGCCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	19											29	30	30					19																	6467848		1900	4116	6016	6418848	SO:0001819	synonymous_variant	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.2073A>G	19.37:g.6467848T>C			6418848	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Silent	SNP	ENST00000381480.2	37	CCDS45938.1																																																																																				0.587	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		C	6467848	T	C	6467848	2	2	77	1	0	0	0	0	0	0	0	1	4439	1606	56	4		4	DENND1C	19	6467848	Silent	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	87476	6467848	52661135	1045	22781										
TUBB4	10382	broad.mit.edu	37	chr19	6495458	6495458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgggatgtcgcacacggccGtcttcacgttgttggggatc	15	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:6495458G>A	ENST00000264071.2	-	4	1423	c.1052C>T	c.(1051-1053)aCg>aTg	p.T351M	CTD-2396E7.9_ENST00000599292.1_RNA|CTD-2396E7.10_ENST00000596027.1_RNA|TUBB4A_ENST00000540257.1_Missense_Mutation_p.T351M			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	351					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.T351M(1)									GCACACGGCCGTCTTCACGTT	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	19											180	149	159					19																	6495458		2203	4300	6503	6446458	SO:0001583	missense	10382			AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1052C>T	19.37:g.6495458G>A	ENSP00000264071:p.Thr351Met		6446458	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582079	0.46006	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.81821	-1.54;-1.54	3.43	3.43	0.39272	.	0.000000	0.64402	U	0.000002	D	0.91064	0.7188	H	0.96430	3.82	0.53688	D	0.999972	D	0.56521	0.976	P	0.58660	0.843	D	0.93732	0.7042	10	0.87932	D	0	.	13.6752	0.62449	0.0:0.0:1.0:0.0	.	351	P04350	TBB4A_HUMAN	M	351;351;269	ENSP00000264071:T351M;ENSP00000443590:T351M	ENSP00000264071:T351M	T	-	2	0	TUBB4	6446458	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.620000	0.74224	1.473000	0.48159	0.306000	0.20318	ACG		0.627	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		A	6495458	G	A	6495458	3	1	77	1	0	0	0	0	1	0	0	0	16798	1145	40	1	286	1	TUBB4	19	6495458	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	27610	6495458	52633525	1046	22782										
INSR	3643	broad.mit.edu	37	chr19	7117191	7117191	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcgaggaccctccatcccggCcccccgcctcctccctctga							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:7117191delC	ENST00000302850.5	-	22	4167	c.4025delG	c.(4024-4026)ggcfs	p.G1342fs	INSR_ENST00000341500.5_Frame_Shift_Del_p.G1330fs	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1342					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.G1342fs*23(1)		breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	TCCATCCCGGCCCCCCGCCTC	0.592																																																1	Deletion - Frameshift(1)	large_intestine(1)	19											78	70	73					19																	7117191		2203	4300	6503	7068191	SO:0001589	frameshift_variant	3643			M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.4025delG	19.37:g.7117191delC	ENSP00000303830:p.Gly1342fs		7068191	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Frame_Shift_Del	DEL	ENST00000302850.5	37	CCDS12176.1																																																																																				0.592	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			-	7117191	C	-	7117191	7	5	77	1	0	1	0	1	0	0	0	0	7794	739	26	0	127	0	INSR	19	7117191	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	621733	7117191	52011792	1047	22783										
MCOLN1	57192	broad.mit.edu	37	chr19	7591677	7591677	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcctgacgtgtcactgggcCggtatgcgtatgtccgtggt	15	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:7591677C>A	ENST00000264079.6	+	4	561	c.436C>A	c.(436-438)Cgg>Agg	p.R146R		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	146					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)	p.R146R(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTCACTGGGCCGGTATGCGTA	0.667																																																1	Substitution - coding silent(1)	large_intestine(1)	19											119	82	95					19																	7591677		2203	4300	6503	7497677	SO:0001819	synonymous_variant	57192			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"Voltage-gated ion channels / Transient receptor potential cation channels"	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.436C>A	19.37:g.7591677C>A			7497677	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Silent	SNP	ENST00000264079.6	37	CCDS12180.1																																																																																				0.667	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533		A	7591677	C	A	7591677	2	1	77	1	0	0	0	0	0	0	0	1	9425	643	23	2		2	MCOLN1	19	7591677	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	474486	7591677	51537306	1048	22784										
KIAA1543	57662	broad.mit.edu	37	chr19	7670119	7670119	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatgcccccacagagcacgtGcccccggagctgtgggagcc	13	16	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:7670119G>A	ENST00000160298.4	+	2	257	c.156G>A	c.(154-156)gtG>gtA	p.V52V	CAMSAP3_ENST00000446248.2_Silent_p.V52V	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	52					epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)	p.V52V(1)		cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						CAGAGCACGTGCCCCCGGAGC	0.612																																																1	Substitution - coding silent(1)	large_intestine(1)	19											107	117	114					19																	7670119		2015	4181	6196	7576119	SO:0001819	synonymous_variant	57662			AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 80"	612685	"KIAA1543"	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.156G>A	19.37:g.7670119G>A			7576119	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																				0.612	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		A	7670119	G	A	7670119	2	1	77	1	0	0	0	0	0	0	0	1	8264	1306	46	3		3	KIAA1543	19	7670119	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	78442	7670119	51458864	1049	22785										
CD209	30835	broad.mit.edu	37	chr19	7809880	7809880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcccccacttctttgcaggCggtgatggagtcgtgccagt	14	12	1	1	rs139712001		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:7809880C>T	ENST00000315599.7	-	5	869	c.847G>A	c.(847-849)Gcc>Acc	p.A283T	CD209_ENST00000601951.1_Missense_Mutation_p.A259T|CD209_ENST00000204801.8_Missense_Mutation_p.A239T|CD209_ENST00000354397.6_Missense_Mutation_p.A283T|CD209_ENST00000602261.1_Missense_Mutation_p.A191T|CD209_ENST00000601256.1_Missense_Mutation_p.A259T|CD209_ENST00000593660.1_Missense_Mutation_p.A213T|CD209_ENST00000593821.1_Missense_Mutation_p.A147T|CD209_ENST00000315591.8_Missense_Mutation_p.A259T|CD209_ENST00000301357.8_Missense_Mutation_p.A147T|CD209_ENST00000394173.4_Missense_Mutation_p.A122T|CD209_ENST00000394161.5_Intron	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	283	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)	p.A283T(1)		endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TCTTTGCAGGCGGTGATGGAG	0.582													c|||	1	0.000199681	8e-04	0	5008	,	,		17657	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	4,4402	9.9+/-24.2	0,4,2199	85	81	82		439,715,571,775,847,364,847	-0.1	0	19	dbSNP_134	82	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense,missense,missense,missense	CD209	NM_001144893.1,NM_001144894.1,NM_001144895.1,NM_001144896.1,NM_001144897.1,NM_001144899.1,NM_021155.3	58,58,58,58,58,58,58	0,8,6495	TT,TC,CC		0.0465,0.0908,0.0615	benign,benign,benign,benign,benign,benign,benign	147/269,239/361,191/313,259/381,283/399,122/244,283/405	7809880	8,12998	2203	4300	6503	7715880	SO:0001583	missense	30835			M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659		"C-type lectin domain containing", "CD molecules"	1641	protein-coding gene	gene with protein product		604672	"CD209 antigen"			1518869	Standard	NM_021155		Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.847G>A	19.37:g.7809880C>T	ENSP00000315477:p.Ala283Thr		7715880	A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	Missense_Mutation	SNP	ENST00000315599.7	37	CCDS12186.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.007084	0.35415	9.08E-4	4.65E-4	ENSG00000090659	ENST00000315599;ENST00000354397;ENST00000315591;ENST00000204801;ENST00000394173;ENST00000301357;ENST00000540789	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	3.29	-0.0555	0.13809	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.27169	0.0666	L	0.45581	1.43	0.09310	N	1	D;D;P;D;P;P;D;D;D;P;D	0.89917	1.0;1.0;0.955;0.998;0.909;0.918;0.98;1.0;0.999;0.956;1.0	D;D;P;D;B;P;B;D;D;B;D	0.97110	0.955;0.967;0.799;0.964;0.234;0.522;0.421;1.0;0.951;0.345;0.996	T	0.13176	-1.0519	9	0.87932	D	0	.	2.7211	0.05201	0.2253:0.5221:0.0:0.2526	.	283;283;259;239;147;259;191;283;213;259;283	B2R907;Q9NNX6-2;Q9NNX6-12;Q9NNX6-7;Q9NNX6-8;Q9NNX6-6;G5E9C4;Q9NNX6;Q9NNX6-11;Q9NNX6-10;Q9NNX6-5	.;.;.;.;.;.;.;CD209_HUMAN;.;.;.	T	283;283;259;239;191;147;267	ENSP00000315477:A283T;ENSP00000346373:A283T;ENSP00000315407:A259T;ENSP00000204801:A239T;ENSP00000301357:A147T	ENSP00000204801:A239T	A	-	1	0	CD209	7715880	0.006000	0.16342	0.007000	0.13788	0.027000	0.11550	-0.132000	0.10467	0.085000	0.17107	0.455000	0.32223	GCC		0.582	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462241.1	NM_021155		T	7809880	C	T	7809880	3	4	77	1	0	0	0	0	1	0	0	0	2990	768	27	1	379	1	CD209	19	7809880	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	139761	7809880	51319103	1050	22786										
FBN3	84467	broad.mit.edu	37	chr19	8181654	8181654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcagtggccttggtcacaaaCgcgggggttctcttcacact	12	12	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:8181654C>T	ENST00000600128.1	-	29	4030	c.3616G>A	c.(3616-3618)Gtt>Att	p.V1206I	FBN3_ENST00000270509.2_Missense_Mutation_p.V1206I|FBN3_ENST00000601739.1_Missense_Mutation_p.V1206I			Q75N90	FBN3_HUMAN	fibrillin 3	1206	EGF-like 17. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.V1206I(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGGTCACAAACGCGGGGGTTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	19											100	84	89					19																	8181654		2203	4300	6503	8087654	SO:0001583	missense	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3616G>A	19.37:g.8181654C>T	ENSP00000470498:p.Val1206Ile		8087654	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.453056	0.00175	.	.	ENSG00000142449	ENST00000270509	D	0.92299	-3.01	3.98	-0.737	0.11129	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.198206	0.43110	N	0.000615	T	0.70046	0.3179	N	0.00985	-1.075	0.20563	N	0.999889	B	0.06786	0.001	B	0.04013	0.001	T	0.63972	-0.6516	10	0.02654	T	1	.	9.8398	0.40991	0.0:0.3421:0.0:0.6579	.	1206	Q75N90	FBN3_HUMAN	I	1206	ENSP00000270509:V1206I	ENSP00000270509:V1206I	V	-	1	0	FBN3	8087654	0.765000	0.28485	0.017000	0.16124	0.001000	0.01503	1.040000	0.30278	-0.463000	0.06973	-1.336000	0.01259	GTT		0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8181654	C	T	8181654	3	4	77	1	0	0	0	0	1	0	0	0	5723	536	19	1	4957	1	FBN3	19	8181654	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	371774	8181654	50947329	1051	22787										
ZNF558	148156	broad.mit.edu	37	chr19	8931929	8931929	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttgggcagggtccagcaaCgcccactcctcctgggtgaa	12	14	0	1	rs373869285		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:8931929C>T	ENST00000601372.1	-	7	885	c.174G>A	c.(172-174)gcG>gcA	p.A58A	CTD-2529P6.3_ENST00000594006.1_RNA|ZNF558_ENST00000599938.1_5'Flank|ZNF558_ENST00000444186.2_5'UTR|ZNF558_ENST00000301475.1_Silent_p.A58A			Q96NG5	ZN558_HUMAN	zinc finger protein 558	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A58A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						GGTCCAGCAACGCCCACTCCT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C		2,4404	4.2+/-10.8	0,2,2201	162	138	146		174	-6.1	0.3	19		146	0,8600		0,0,4300	no	coding-synonymous	ZNF558	NM_144693.1		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		58/403	8931929	2,13004	2203	4300	6503	8792929	SO:0001819	synonymous_variant	148156			AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.174G>A	19.37:g.8931929C>T			8792929	A8K5F0|B7Z798	Silent	SNP	ENST00000601372.1	37	CCDS12208.1																																																																																				0.547	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		T	8931929	C	T	8931929	2	4	77	1	0	0	0	0	0	0	0	1	18028	523	19	1		1	ZNF558	19	8931929	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	750275	8931929	50197054	1052	22788										
MUC16	94025	broad.mit.edu	37	chr19	9056821	9056821	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggccagtctggggatgatgTttttgcagaagaggtgaaat							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:9056821delT	ENST00000397910.4	-	3	30828	c.30625delA	c.(30625-30627)acafs	p.T10209fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10211	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T10209fs*19(1)|p.T5842fs*19(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGGATGATGTTTTTGCAGAA	0.478																																																2	Deletion - Frameshift(2)	large_intestine(2)	19											132	130	131					19																	9056821		1952	4161	6113	8917821	SO:0001589	frameshift_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30625delA	19.37:g.9056821delT	ENSP00000381008:p.Thr10209fs		8917821	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	37	CCDS54212.1																																																																																				0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		-	9056821	T	-	9056821	7	5	77	1	0	1	0	1	0	0	0	0	10003	1725	60	0	13226	0	MUC16	19	9056821	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	124892	9056821	50072162	1053	22789										
ZNF317	57693	broad.mit.edu	37	chr19	9266712	9266712	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatggcagctctgtcccccaCatttggtaagttcttgggtc	11	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:9266712C>T	ENST00000247956.6	+	2	325	c.20C>T	c.(19-21)aCa>aTa	p.T7I	ZNF317_ENST00000360385.3_Missense_Mutation_p.T7I	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	7					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T7I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						CTGTCCCCCACATTTGGTAAG	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19											115	93	100					19																	9266712		2203	4300	6503	9127712	SO:0001583	missense	57693			AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.20C>T	19.37:g.9266712C>T	ENSP00000247956:p.Thr7Ile		9127712	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	37	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	C	7.158	0.585216	0.13749	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.07800	3.49;3.16	2.95	1.9	0.25705	.	.	.	.	.	T	0.03695	0.0105	N	0.08118	0	0.09310	N	1	P;B	0.36909	0.573;0.437	B;B	0.30646	0.118;0.055	T	0.38156	-0.9674	9	0.62326	D	0.03	-0.5395	5.827	0.18558	0.0:0.8507:0.0:0.1493	.	7;7	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	I	7	ENSP00000247956:T7I;ENSP00000353554:T7I	ENSP00000247956:T7I	T	+	2	0	ZNF317	9127712	0.010000	0.17322	0.244000	0.24202	0.353000	0.29299	0.196000	0.17176	0.813000	0.34350	0.460000	0.39030	ACA		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		T	9266712	C	T	9266712	3	4	77	1	0	0	0	0	1	0	0	0	17874	478	17	3	22	3	ZNF317	19	9266712	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	209891	9266712	49862271	1054	22790										
OLFM2	93145	broad.mit.edu	37	chr19	9971411	9971411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccgtgcagatgcatttcccGtcaggggcctgggctgaggt	16	11	1	2	rs201897414	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:9971411G>A	ENST00000264833.4	-	2	308	c.123C>T	c.(121-123)gaC>gaT	p.D41D	OLFM2_ENST00000590841.1_5'Flank	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	41					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)		p.D41D(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						TGCATTTCCCGTCAGGGGCCT	0.607													G|||	2	0.000399361	0	0.0014	5008	,	,		18185	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											33	30	31					19																	9971411		2203	4300	6503	9832411	SO:0001819	synonymous_variant	93145			AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.123C>T	19.37:g.9971411G>A			9832411	Q6IMJ3|Q96FC2	Silent	SNP	ENST00000264833.4	37	CCDS12221.1																																																																																				0.607	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			A	9971411	G	A	9971411	2	1	77	1	0	0	0	0	0	0	0	1	10884	1136	40	1		1	OLFM2	19	9971411	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	704699	9971411	49157572	1055	22791										
DNMT1	1786	broad.mit.edu	37	chr19	10248650	10248650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaggtcggacatcgtgtctCgcaccgtgatggtccggaaa	14	11	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:10248650C>T	ENST00000340748.4	-	35	4338	c.4103G>A	c.(4102-4104)cGa>cAa	p.R1368Q	DNMT1_ENST00000359526.4_Missense_Mutation_p.R1384Q|DNMT1_ENST00000540357.1_Missense_Mutation_p.R1368Q|DNMT1_ENST00000589538.1_5'Flank			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1368	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R1368Q(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CATCGTGTCTCGCACCGTGAT	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	19											45	36	39					19																	10248650		2203	4300	6503	10109650	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4103G>A	19.37:g.10248650C>T	ENSP00000345739:p.Arg1368Gln		10109650	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.787654	0.90367	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	D;D;D	0.84223	-1.82;-1.82;-1.82	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.90652	0.7068	M	0.76328	2.33	0.80722	D	1	D;D;D	0.57571	0.975;0.975;0.98	P;P;P	0.58077	0.742;0.742;0.832	D	0.90854	0.4733	10	0.49607	T	0.09	-26.3197	17.6482	0.88154	0.0:1.0:0.0:0.0	.	1368;1384;1368	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	Q	1384;1368;1368;1236	ENSP00000352516:R1384Q;ENSP00000440457:R1368Q;ENSP00000345739:R1368Q	ENSP00000345739:R1368Q	R	-	2	0	DNMT1	10109650	1.000000	0.71417	0.995000	0.50966	0.338000	0.28826	7.475000	0.81041	2.446000	0.82766	0.655000	0.94253	CGA		0.622	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		T	10248650	C	T	10248650	3	4	77	1	0	0	0	0	1	0	0	0	4686	884	31	1	771	1	DNMT1	19	10248650	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	277239	10248650	48880333	1056	22792										
DNMT1	1786	broad.mit.edu	37	chr19	10291064	10291064	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acttgctcctcctgggcgtgCgaggtttggaaaggggtttg	16	8	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:10291064C>T	ENST00000340748.4	-	4	642	c.407G>A	c.(406-408)cGc>cAc	p.R136H	DNMT1_ENST00000359526.4_Missense_Mutation_p.R136H|DNMT1_ENST00000540357.1_Missense_Mutation_p.R136H			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	136	Interaction with DNMT3A.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R136H(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CCTGGGCGTGCGAGGTTTGGA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	81	81					19																	10291064		2203	4300	6503	10152064	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.407G>A	19.37:g.10291064C>T	ENSP00000345739:p.Arg136His		10152064	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	c	16.04	3.009397	0.54361	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748	T;T;T	0.29917	1.84;1.55;1.55	5.33	1.97	0.26223	.	0.578486	0.16795	N	0.199240	T	0.16214	0.0390	L	0.34521	1.04	0.09310	N	1	P;P;P	0.42123	0.771;0.771;0.661	B;B;B	0.34038	0.174;0.174;0.084	T	0.16778	-1.0391	10	0.12766	T	0.61	.	7.8565	0.29485	0.0:0.7169:0.1333:0.1498	.	136;136;136	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	H	136	ENSP00000352516:R136H;ENSP00000440457:R136H;ENSP00000345739:R136H	ENSP00000345739:R136H	R	-	2	0	DNMT1	10152064	0.000000	0.05858	0.001000	0.08648	0.536000	0.34869	0.476000	0.22180	0.237000	0.21200	0.650000	0.86243	CGC		0.502	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		T	10291064	C	T	10291064	3	4	77	1	0	0	0	0	1	0	0	0	4686	768	27	1	4643	1	DNMT1	19	10291064	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	42414	10291064	48837919	1057	22793										
ICAM4	3386	broad.mit.edu	37	chr19	10397719	10397719	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgttccctctgtcgctgctgTtttttttggcggccgcctac							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:10397719delT	ENST00000380770.3	+	1	77	c.31delT	c.(31-33)tttfs	p.F12fs	ICAM4_ENST00000393717.2_Frame_Shift_Del_p.F12fs|ICAM5_ENST00000221980.4_5'Flank|ICAM4_ENST00000340992.4_Frame_Shift_Del_p.F12fs|CTD-2369P2.8_ENST00000589379.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA	NM_001544.4	NP_001535.1	Q14773	ICAM4_HUMAN	intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)	12					extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)	p.L13fs*40(1)		breast(1)|large_intestine(3)|lung(2)|pancreas(1)	7			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			GTCGCTGCTGTTTTTTTTGGC	0.677																																																1	Deletion - Frameshift(1)	large_intestine(1)	19							,,	86,37,3567		4,0,78,6,25,1732	7	11	9		,,	-0.8	0	19	dbSNP_129	10	136,75,7175		4,1,127,2,70,3489	no	codingComplex,codingComplex,codingComplex	ICAM4	NM_022377.3,NM_001544.4,NM_001039132.2	,,	8,1,205,8,95,5221	A1A1,A1A2,A1R,A2A2,A2R,RR		2.8568,3.3333,3.0155	,,	,,	10397719	222,112,10742	1977	3930	5907	10258719	SO:0001589	frameshift_variant	3386			X93093	CCDS12232.1, CCDS32904.1, CCDS42500.1	19p13.2	2014-07-19	2006-02-23		ENSG00000105371	ENSG00000105371		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5347	protein-coding gene	gene with protein product		614088	"intercellular adhesion molecule 4, Landsteiner-Wiener blood group", "Landsteiner-Wiener blood group", "intercellular adhesion molecule 4 (LW blood group)"	LW		8639917, 6431896	Standard	NM_001039132		Approved	CD242	uc002mnr.2	Q14773	OTTHUMG00000180405	ENST00000380770.3:c.31delT	19.37:g.10397719delT	ENSP00000370147:p.Phe12fs		10258719	A0M8X2|Q14771|Q14772|Q16375|Q9BWR0	Frame_Shift_Del	DEL	ENST00000380770.3	37	CCDS12232.1																																																																																				0.677	ICAM4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451214.1	NM_001544		-	10397719	T	-	10397719	7	5	77	1	0	1	0	1	0	0	0	0	7503	1725	60	0	33	0	ICAM4	19	10397719	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	106655	10397719	48731264	1058	22794										
ICAM5	7087	broad.mit.edu	37	chr19	10404764	10404764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccagcaattggacatgggTggaaggatctgggcgcctgt	15	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:10404764T>C	ENST00000221980.4	+	8	1823	c.1760T>C	c.(1759-1761)gTg>gCg	p.V587A		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	587	Ig-like C2-type 7.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V587A(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			TGGACATGGGTGGAAGGATCT	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	61	59					19																	10404764		2191	4269	6460	10265764	SO:0001583	missense	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1760T>C	19.37:g.10404764T>C	ENSP00000221980:p.Val587Ala		10265764	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.523969	0.27299	.	.	ENSG00000105376	ENST00000221980	T	0.74315	-0.83	4.69	4.69	0.59074	Immunoglobulin-like fold (1);	0.000000	0.43110	D	0.000605	T	0.63319	0.2501	L	0.49350	1.555	0.34208	D	0.673962	B	0.30406	0.278	B	0.30179	0.112	T	0.63510	-0.6621	10	0.07175	T	0.84	-16.5938	10.4509	0.44522	0.0:0.0:0.0:1.0	.	587	Q9UMF0	ICAM5_HUMAN	A	587	ENSP00000221980:V587A	ENSP00000221980:V587A	V	+	2	0	ICAM5	10265764	1.000000	0.71417	0.997000	0.53966	0.311000	0.27955	2.442000	0.44873	1.968000	0.57251	0.448000	0.29417	GTG		0.652	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		C	10404764	T	C	10404764	3	2	77	1	0	0	0	0	1	0	0	0	7504	1696	59	4	1790	4	ICAM5	19	10404764	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	7045	10404764	48724219	1059	22795										
SMARCA4	6597	broad.mit.edu	37	chr19	11114031	11114031	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctaggtatgaagtagctccGaggtctgatagtgaagaaag	13	5	2	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:11114031G>A	ENST00000429416.3	+	14	2240	c.1959G>A	c.(1957-1959)ccG>ccA	p.P653P	SMARCA4_ENST00000344626.4_Silent_p.P653P|SMARCA4_ENST00000444061.3_Silent_p.P653P|SMARCA4_ENST00000589677.1_Silent_p.P653P|SMARCA4_ENST00000541122.2_Silent_p.P653P|SMARCA4_ENST00000590574.1_Silent_p.P653P|SMARCA4_ENST00000450717.3_Silent_p.P653P|SMARCA4_ENST00000413806.3_Silent_p.P653P|SMARCA4_ENST00000358026.2_Silent_p.P653P	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	653					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.P653P(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AAGTAGCTCCGAGGTCTGATA	0.468			"F, N, Mis"		NSCLC																																		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	19											146	142	143					19																	11114031		2203	4300	6503	10975031	SO:0001819	synonymous_variant	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1959G>A	19.37:g.11114031G>A			10975031	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																				0.468	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11114031	G	A	11114031	2	1	77	1	0	0	0	0	0	0	0	1	14807	1045	37	1		1	SMARCA4	19	11114031	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	709267	11114031	48014952	1060	22796										
DOCK6	57572	broad.mit.edu	37	chr19	11326115	11326115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtgacgctcttccgccagcGcacattctccggattcccaa	8	16	2	1	rs550858597		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:11326115G>A	ENST00000294618.7	-	32	4065	c.4054C>T	c.(4054-4056)Cgc>Tgc	p.R1352C	CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Missense_Mutation_p.R691C	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1352					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R1352C(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						TTCCGCCAGCGCACATTCTCC	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	53	53					19																	11326115		2036	4181	6217	11187115	SO:0001583	missense	57572				CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4054C>T	19.37:g.11326115G>A	ENSP00000294618:p.Arg1352Cys		11187115	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803212	0.70682	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.54479	0.57;0.57	5.68	4.57	0.56435	.	0.000000	0.64402	D	0.000001	T	0.74635	0.3742	M	0.84683	2.71	0.80722	D	1	D;D	0.71674	0.998;0.994	D;P	0.70935	0.971;0.762	T	0.79472	-0.1789	10	0.87932	D	0	-12.6499	16.3511	0.83208	0.0:0.0:0.859:0.141	.	691;1352	C9IZV6;Q96HP0	.;DOCK6_HUMAN	C	1352;691	ENSP00000294618:R1352C;ENSP00000321556:R691C	ENSP00000294618:R1352C	R	-	1	0	DOCK6	11187115	1.000000	0.71417	0.955000	0.39395	0.597000	0.36814	3.301000	0.51842	2.683000	0.91414	0.591000	0.81541	CGC		0.562	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11326115	G	A	11326115	3	1	77	1	0	0	0	0	1	0	0	0	4702	1087	38	1	2157	1	DOCK6	19	11326115	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	212084	11326115	47802868	1061	22797										
C19orf39	126074	broad.mit.edu	37	chr19	11486276	11486276	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccggggccagccccctccCttctgctgctcgacggccta	10	21	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:11486276C>A	ENST00000312423.2	+	2	333	c.274C>A	c.(274-276)Ctt>Att	p.L92I	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	92					ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)	p.L92I(1)									AGCCCCCTCCCTTCTGCTGCT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											70	82	78					19																	11486276		2203	4300	6503	11347276	SO:0001583	missense	126074			AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"zinc finger, SWIM-type containing 7 associated protein 1", "SWS1-associated protein 1"	614536	"chromosome 19 open reading frame 39"	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.274C>A	19.37:g.11486276C>A	ENSP00000310008:p.Leu92Ile		11347276	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565383	0.86439	.	.	ENSG00000173928	ENST00000312423	D	0.86497	-2.13	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000005	D	0.92899	0.7741	M	0.76002	2.32	0.44816	D	0.997825	D	0.76494	0.999	D	0.87578	0.998	D	0.93298	0.6674	10	0.59425	D	0.04	-8.0825	15.6006	0.76623	0.0:1.0:0.0:0.0	.	92	Q6NVH7	CS039_HUMAN	I	92	ENSP00000310008:L92I	ENSP00000310008:L92I	L	+	1	0	C19orf39	11347276	1.000000	0.71417	0.588000	0.28705	0.983000	0.72400	4.473000	0.60196	2.419000	0.82065	0.655000	0.94253	CTT		0.602	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871		A	11486276	C	A	11486276	3	1	77	1	0	0	0	0	1	0	0	0	1928	681	24	2	280	2	C19orf39	19	11486276	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	160161	11486276	47642707	1062	22798										
ZNF44	51710	broad.mit.edu	37	chr19	12384634	12384634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ataacttaagcctttcccacActgcttatgtgtatatgact	5	10	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:12384634A>G	ENST00000356109.5	-	5	698	c.580T>C	c.(580-582)Tgt>Cgt	p.C194R	ZNF44_ENST00000355684.5_Missense_Mutation_p.C146R	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C146R(1)		ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CCTTTCCCACACTGCTTATGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	19											123	123	123					19																	12384634		2198	4294	6492	12245634	SO:0001583	missense	51710			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.580T>C	19.37:g.12384634A>G	ENSP00000348419:p.Cys194Arg		12245634	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	37	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	A	6.160	0.397803	0.11696	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.59224	0.28;0.28;3.96	0.724	-0.498	0.12019	Zinc finger, C2H2 (1);	.	.	.	.	T	0.53206	0.1782	M	0.79475	2.455	.	.	.	B;B	0.15141	0.005;0.012	B;B	0.15484	0.009;0.013	T	0.53351	-0.8451	8	0.59425	D	0.04	.	5.7514	0.18148	0.7264:0.2736:0.0:0.0	.	194;146	P15621;F8W7T7	ZNF44_HUMAN;.	R	194;194;146;146	ENSP00000377008:C194R;ENSP00000348419:C194R;ENSP00000347910:C146R	ENSP00000347910:C146R	C	-	1	0	ZNF44	12245634	0.935000	0.31712	0.016000	0.15963	0.048000	0.14542	2.714000	0.47202	-0.297000	0.08934	-0.940000	0.02684	TGT		0.423	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		G	12384634	A	G	12384634	3	3	77	1	0	0	0	0	1	0	0	0	17951	159	6	4	1415	4	ZNF44	19	12384634	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	898358	12384634	46744349	1063	22799										
ZNF564	163050	broad.mit.edu	37	chr19	12637528	12637528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tatgagttctttcatgtgttCggacagaactaggacagtca	10	7	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:12637528C>T	ENST00000339282.7	-	4	1590	c.1394G>A	c.(1393-1395)cGa>cAa	p.R465Q	CTD-2192J16.20_ENST00000593682.1_3'UTR|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R465Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						TTCATGTGTTCGGACAGAACT	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	19											157	162	160					19																	12637528		2193	4297	6490	12498528	SO:0001583	missense	163050			BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.1394G>A	19.37:g.12637528C>T	ENSP00000340004:p.Arg465Gln		12498528	B9EGT4|Q6P1K6	Missense_Mutation	SNP	ENST00000339282.7	37	CCDS42505.1	.	.	.	.	.	.	.	.	.	.	C	8.036	0.762765	0.15914	.	.	ENSG00000249709	ENST00000339282	T	0.04275	3.66	1.71	-3.07	0.05363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02970	0.0088	N	0.25647	0.755	0.09310	N	1	P	0.48294	0.908	B	0.38954	0.286	T	0.43734	-0.9373	9	0.21540	T	0.41	.	7.795	0.29141	0.0:0.563:0.0:0.437	.	465	Q8TBZ8	ZN564_HUMAN	Q	465	ENSP00000340004:R465Q	ENSP00000340004:R465Q	R	-	2	0	ZNF564	12498528	0.000000	0.05858	0.000000	0.03702	0.965000	0.64279	-1.025000	0.03600	-0.891000	0.03940	0.643000	0.83706	CGA		0.368	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		T	12637528	C	T	12637528	3	4	77	1	0	0	0	0	1	0	0	0	18034	884	31	1	271	1	ZNF564	19	12637528	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	252894	12637528	46491455	1064	22800										
RNASEH2A	10535	broad.mit.edu	37	chr19	12918306	12918306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtatgcattggaccagggcGtgaacgtcacccaggtgagt	14	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:12918306G>A	ENST00000221486.4	+	4	491	c.397G>A	c.(397-399)Gtg>Atg	p.V133M		NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A	133					DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)	p.V133M(1)		breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						GGACCAGGGCGTGAACGTCAC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											130	113	119					19																	12918306		2203	4300	6503	12779306	SO:0001583	missense	10535			Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"ribonuclease H2, large subunit", "Aicardi-Goutieres syndrome 4"			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.397G>A	19.37:g.12918306G>A	ENSP00000221486:p.Val133Met		12779306	B2RCY1|Q96F11	Missense_Mutation	SNP	ENST00000221486.4	37	CCDS12282.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396399	0.83011	.	.	ENSG00000104889	ENST00000221486	D	0.87887	-2.31	4.8	4.8	0.61643	Ribonuclease HII/HIII domain (1);Ribonuclease H-like (1);	0.067299	0.64402	D	0.000018	D	0.93148	0.7818	M	0.86864	2.845	0.80722	D	1	D	0.63880	0.993	P	0.60886	0.88	D	0.94013	0.7286	10	0.56958	D	0.05	-15.5002	15.3366	0.74260	0.0:0.0:1.0:0.0	.	133	O75792	RNH2A_HUMAN	M	133	ENSP00000221486:V133M	ENSP00000221486:V133M	V	+	1	0	RNASEH2A	12779306	1.000000	0.71417	0.983000	0.44433	0.927000	0.56198	8.500000	0.90498	2.194000	0.70268	0.505000	0.49811	GTG		0.493	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397		A	12918306	G	A	12918306	3	1	77	1	0	0	0	0	1	0	0	0	13449	1145	40	1	411	1	RNASEH2A	19	12918306	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	280778	12918306	46210677	1065	22801										
MAST1	22983	broad.mit.edu	37	chr19	12978684	12978684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgaggatgaggcccggctgcGcaggcctccccggcccagct	15	17	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:12978684G>A	ENST00000251472.4	+	20	2498	c.2459G>A	c.(2458-2460)cGc>cAc	p.R820H		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1									p.R820H(1)		NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						GCCCGGCTGCGCAGGCCTCCC	0.736																																																1	Substitution - Missense(1)	large_intestine(1)	19											10	13	12					19																	12978684		2158	4244	6402	12839684	SO:0001583	missense	22983			AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2459G>A	19.37:g.12978684G>A	ENSP00000251472:p.Arg820His		12839684		Missense_Mutation	SNP	ENST00000251472.4	37	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.718773	0.68844	.	.	ENSG00000105613	ENST00000251472	T	0.66099	-0.19	4.13	4.13	0.48395	.	0.343569	0.22190	N	0.063388	T	0.63604	0.2525	L	0.42245	1.32	0.40590	D	0.981473	D	0.67145	0.996	P	0.53689	0.732	T	0.65290	-0.6204	10	0.44086	T	0.13	-26.8141	12.2539	0.54613	0.0:0.0:1.0:0.0	.	820	Q9Y2H9	MAST1_HUMAN	H	820	ENSP00000251472:R820H	ENSP00000251472:R820H	R	+	2	0	MAST1	12839684	0.991000	0.36638	1.000000	0.80357	0.944000	0.59088	2.389000	0.44407	2.031000	0.59945	0.549000	0.68633	CGC		0.736	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		A	12978684	G	A	12978684	3	1	77	1	0	0	0	0	1	0	0	0	9354	1087	38	1	2537	1	MAST1	19	12978684	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	60378	12978684	46150299	1066	22802										
MAST1	22983	broad.mit.edu	37	chr19	12980054	12980054	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtatggcttcacactgcgtgCcatccgtgtctacatgggtg	12	11	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:12980054C>T	ENST00000251472.4	+	22	2987	c.2948C>T	c.(2947-2949)gCc>gTc	p.A983V		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1									p.A983V(1)		NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						ACACTGCGTGCCATCCGTGTC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	19											71	60	64					19																	12980054		2203	4300	6503	12841054	SO:0001583	missense	22983			AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2948C>T	19.37:g.12980054C>T	ENSP00000251472:p.Ala983Val		12841054		Missense_Mutation	SNP	ENST00000251472.4	37	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	C	33	5.228749	0.95173	.	.	ENSG00000105613	ENST00000251472	T	0.26660	1.72	4.71	4.71	0.59529	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.36248	0.0960	N	0.20685	0.6	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.32561	-0.9902	10	0.87932	D	0	-31.3311	15.5036	0.75719	0.0:1.0:0.0:0.0	.	983	Q9Y2H9	MAST1_HUMAN	V	983	ENSP00000251472:A983V	ENSP00000251472:A983V	A	+	2	0	MAST1	12841054	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.715000	0.84713	2.327000	0.79052	0.462000	0.41574	GCC		0.582	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		T	12980054	C	T	12980054	3	4	77	1	0	0	0	0	1	0	0	0	9354	739	26	3	3034	3	MAST1	19	12980054	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1370	12980054	46148929	1067	22803										
IL27RA	9466	broad.mit.edu	37	chr19	14159807	14159807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	actcagggaatttcactgtcGgggtcccctatcgaatcact	9	12	3	0	rs370071884		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:14159807G>A	ENST00000263379.2	+	9	1281	c.1156G>A	c.(1156-1158)Ggg>Agg	p.G386R		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	386	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)	p.G386R(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						TTTCACTGTCGGGGTCCCCTA	0.532											OREG0025303	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(164;1849 1896 4443 37792 47834)											1	Substitution - Missense(1)	large_intestine(1)	19						G	ARG/GLY	0,4406		0,0,2203	115	113	114		1156	4	0.9	19		114	1,8599	1.2+/-3.3	0,1,4299	no	missense	IL27RA	NM_004843.2	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	386/637	14159807	1,13005	2203	4300	6503	14020807	SO:0001583	missense	9466			AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1156G>A	19.37:g.14159807G>A	ENSP00000263379:p.Gly386Arg	693	14020807	A0N0L1|O60624	Missense_Mutation	SNP	ENST00000263379.2	37	CCDS12303.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.673693	0.29693	0.0	1.16E-4	ENSG00000104998	ENST00000263379	T	0.62639	0.01	3.95	3.95	0.45737	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.43110	D	0.000602	T	0.73969	0.3655	M	0.70595	2.14	0.38511	D	0.948483	D	0.89917	1.0	D	0.77004	0.989	T	0.73017	-0.4115	10	0.23891	T	0.37	-6.2299	11.6998	0.51564	0.0:0.0:1.0:0.0	.	386	Q6UWB1	I27RA_HUMAN	R	386	ENSP00000263379:G386R	ENSP00000263379:G386R	G	+	1	0	IL27RA	14020807	0.998000	0.40836	0.909000	0.35828	0.004000	0.04260	4.167000	0.58209	2.209000	0.71365	0.448000	0.29417	GGG		0.532	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		A	14159807	G	A	14159807	3	1	77	1	0	0	0	0	1	0	0	0	7702	1116	39	1	1190	1	IL27RA	19	14159807	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1179753	14159807	44969176	1068	22804										
CD97	976	broad.mit.edu	37	chr19	14515305	14515305	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caggtgctgggcagcaagaaCggcagcaccacctgccaatg	13	13	0	1	rs373067809		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:14515305C>T	ENST00000242786.5	+	13	1640	c.1560C>T	c.(1558-1560)aaC>aaT	p.N520N	CD97_ENST00000357355.3_Silent_p.N471N|CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000358600.3_Silent_p.N427N	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	520	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.N520N(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GCAGCAAGAACGGCAGCACCA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	19						C	,,	1,4405	2.1+/-5.4	0,1,2202	62	55	58		1413,1281,1560	-7	0	19		58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CD97	NM_001025160.2,NM_001784.4,NM_078481.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	471/787,427/743,520/836	14515305	1,13005	2203	4300	6503	14376305	SO:0001819	synonymous_variant	976				CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1560C>T	19.37:g.14515305C>T			14376305	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	37	CCDS32929.1																																																																																				0.617	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14515305	C	T	14515305	2	4	77	1	0	0	0	0	0	0	0	1	3055	535	19	1		1	CD97	19	14515305	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	355498	14515305	44613678	1069	22805										
OR7A17	26333	broad.mit.edu	37	chr19	14991800	14991800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaggatgacagatggccacaAaccgatcataggccatcaca	10	11	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:14991800A>G	ENST00000327462.2	-	1	464	c.368T>C	c.(367-369)tTt>tCt	p.F123S		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F123S(1)		breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					GATGGCCACAAACCGATCATA	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	19											126	116	119					19																	14991800		2203	4300	6503	14852800	SO:0001583	missense	26333			X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.368T>C	19.37:g.14991800A>G	ENSP00000328144:p.Phe123Ser		14852800	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	37	CCDS12319.1	.	.	.	.	.	.	.	.	.	.	a	9.914	1.210219	0.22289	.	.	ENSG00000185385	ENST00000327462	T	0.01347	4.99	2.74	-4.68	0.03309	GPCR, rhodopsin-like superfamily (1);	0.829194	0.09815	U	0.752231	T	0.08313	0.0207	M	0.90542	3.125	0.09310	N	1	D	0.58620	0.983	D	0.68943	0.961	T	0.00209	-1.1917	10	0.87932	D	0	.	10.7349	0.46120	0.1961:0.0:0.0:0.8039	.	123	O14581	OR7AH_HUMAN	S	123	ENSP00000328144:F123S	ENSP00000328144:F123S	F	-	2	0	OR7A17	14852800	0.000000	0.05858	0.093000	0.20910	0.193000	0.23685	-0.316000	0.08071	-1.095000	0.03050	0.324000	0.21423	TTT		0.507	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		G	14991800	A	G	14991800	3	3	77	1	0	0	0	0	1	0	0	0	11246	14	1	4	563	4	OR7A17	19	14991800	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	476495	14991800	44137183	1070	22806										
NOTCH3	4854	broad.mit.edu	37	chr19	15289906	15289906	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggcagtcccgggtgtgtgcCgcgtggcaggcacctgagcg	18	12	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:15289906C>T	ENST00000263388.2	-	22	3723	c.3648G>A	c.(3646-3648)gcG>gcA	p.A1216A		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1216	EGF-like 31. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.A1216A(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GGGTGTGTGCCGCGTGGCAGG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	19											32	37	35					19																	15289906		2203	4300	6503	15150906	SO:0001819	synonymous_variant	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3648G>A	19.37:g.15289906C>T			15150906	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																				0.632	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15289906	C	T	15289906	2	4	77	1	0	0	0	0	0	0	0	1	10581	639	23	1		1	NOTCH3	19	15289906	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	298106	15289906	43839077	1071	22807										
EPHX3	79852	broad.mit.edu	37	chr19	15338334	15338334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatccaatgccctatgcctgGcaggatgtgggcctccaagc	12	13	0	0	rs147382956	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:15338334G>A	ENST00000221730.3	-	7	1217	c.997C>T	c.(997-999)Cca>Tca	p.P333S	EPHX3_ENST00000602233.1_Missense_Mutation_p.P333S|EPHX3_ENST00000435261.1_Missense_Mutation_p.P333S	NM_024794.2	NP_079070.1	Q9H6B9	EPHX3_HUMAN	epoxide hydrolase 3	333						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)	p.P333S(1)		endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	7						CCTATGCCTGGCAGGATGTGG	0.612													G|||	4	0.000798722	0	0	5008	,	,		18316	0		0.004	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						G	SER/PRO,SER/PRO	3,4403	9.9+/-24.2	0,3,2200	72	66	68		997,997	4.6	1	19	dbSNP_134	68	15,8585	10.5+/-38.8	0,15,4285	yes	missense,missense	EPHX3	NM_001142886.1,NM_024794.2	74,74	0,18,6485	AA,AG,GG		0.1744,0.0681,0.1384	benign,benign	333/361,333/361	15338334	18,12988	2203	4300	6503	15199334	SO:0001583	missense	79852			AK026061	CCDS12327.1	19p13.13	2011-10-05	2009-04-06	2009-04-06	ENSG00000105131	ENSG00000105131		"Abhydrolase domain containing"	23760	protein-coding gene	gene with protein product			"abhydrolase domain containing 9"	ABHD9			Standard	NM_024794		Approved	FLJ22408	uc002nap.3	Q9H6B9		ENST00000221730.3:c.997C>T	19.37:g.15338334G>A	ENSP00000221730:p.Pro333Ser		15199334	A3KMR3	Missense_Mutation	SNP	ENST00000221730.3	37	CCDS12327.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	7.342	0.621126	0.14193	6.81E-4	0.001744	ENSG00000105131	ENST00000221730;ENST00000435261	T;T	0.72394	-0.65;-0.65	4.63	4.63	0.57726	.	0.105878	0.40222	N	0.001141	T	0.64227	0.2579	M	0.72576	2.205	0.43698	D	0.996155	B	0.32382	0.368	B	0.39152	0.292	T	0.65425	-0.6171	10	0.23891	T	0.37	-7.0738	12.9142	0.58197	0.0:0.0:1.0:0.0	.	333	Q9H6B9	EPHX3_HUMAN	S	333	ENSP00000221730:P333S;ENSP00000410323:P333S	ENSP00000221730:P333S	P	-	1	0	EPHX3	15199334	1.000000	0.71417	0.965000	0.40720	0.509000	0.34042	4.273000	0.58914	2.417000	0.82017	0.549000	0.68633	CCA		0.612	EPHX3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465797.1	NM_024794		A	15338334	G	A	15338334	3	1	77	1	0	0	0	0	1	0	0	0	5194	1203	42	3	89	3	EPHX3	19	15338334	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	48428	15338334	43790649	1072	22808										
CYP4F3	4051	broad.mit.edu	37	chr19	15752323	15752323	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcctcctggctcctggcccGcatcctggcctggacctata	11	17	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:15752323G>A	ENST00000221307.8	+	2	145	c.98G>A	c.(97-99)cGc>cAc	p.R33H	CYP4F3_ENST00000585846.1_Missense_Mutation_p.R33H|CYP4F3_ENST00000591058.1_Missense_Mutation_p.R33H|CYP4F3_ENST00000586182.2_Missense_Mutation_p.R33H	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	33					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)	p.R33H(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						CTCCTGGCCCGCATCCTGGCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	19											58	61	60					19																	15752323		2203	4300	6503	15613323	SO:0001583	missense	4051			AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.98G>A	19.37:g.15752323G>A	ENSP00000221307:p.Arg33His		15613323	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	37	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	9.998	1.232799	0.22626	.	.	ENSG00000186529	ENST00000221307	D	0.91945	-2.94	3.9	0.0887	0.14455	.	0.676293	0.12536	U	0.460330	D	0.86485	0.5944	L	0.45581	1.43	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.14578	0.011;0.011	T	0.74121	-0.3767	10	0.35671	T	0.21	.	6.5297	0.22320	0.3854:0.0:0.6146:0.0	.	33;33	B7Z8Z3;Q08477	.;CP4F3_HUMAN	H	33	ENSP00000221307:R33H	ENSP00000221307:R33H	R	+	2	0	CYP4F3	15613323	0.000000	0.05858	0.014000	0.15608	0.003000	0.03518	0.526000	0.22971	0.165000	0.19558	-0.474000	0.04947	CGC		0.637	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		A	15752323	G	A	15752323	3	1	77	1	0	0	0	0	1	0	0	0	4196	1087	38	1	100	1	CYP4F3	19	15752323	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	413989	15752323	43376660	1073	22809										
TPM4	7171	broad.mit.edu	37	chr19	16192749	16192749	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggtgatgtggccgccctcaaCcgacgcatccagctcgttga	12	14	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:16192749C>T	ENST00000300933.4	+	2	419	c.159C>T	c.(157-159)aaC>aaT	p.N53N	TPM4_ENST00000538887.1_Silent_p.N89N|TPM4_ENST00000344824.6_Silent_p.N89N	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	53					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.N53N(1)|p.N89N(1)	TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CCGCCCTCAACCGACGCATCC	0.612			T	ALK	ALCL																																		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	2	Substitution - coding silent(2)	large_intestine(2)	19											46	47	47					19																	16192749		2203	4300	6503	16053749	SO:0001819	synonymous_variant	7171				CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.159C>T	19.37:g.16192749C>T			16053749	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Silent	SNP	ENST00000300933.4	37	CCDS12338.1																																																																																				0.612	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		T	16192749	C	T	16192749	2	4	77	1	0	0	0	0	0	0	0	1	16448	506	18	3		3	TPM4	19	16192749	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	440426	16192749	42936234	1074	22810										
HSH2D	84941	broad.mit.edu	37	chr19	16268434	16268434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	accaggaaggccgagaggtcGgtcagctgcattgaggtgac	16	9	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:16268434G>A	ENST00000253680.6	+	9	1419	c.888G>A	c.(886-888)tcG>tcA	p.S296S	HSH2D_ENST00000588246.1_Missense_Mutation_p.G297S|HSH2D_ENST00000397372.4_Silent_p.S206S|HSH2D_ENST00000593154.2_Missense_Mutation_p.G297S			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	296					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S296S(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)	4						CCGAGAGGTCGGTCAGCTGCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	19											44	49	47					19																	16268434		2025	4176	6201	16129434	SO:0001819	synonymous_variant	84941			AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"SH2 domain containing"	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.888G>A	19.37:g.16268434G>A			16129434	B5ME72|Q6ZNG7	Missense_Mutation	SNP	ENST00000253680.6	37																																																																																					0.602	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855		A	16268434	G	A	16268434	2	1	77	1	0	0	0	0	0	0	0	1	7421	1116	39	1		1	HSH2D	19	16268434	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	75685	16268434	42860549	1075	22811										
C19orf44	84167	broad.mit.edu	37	chr19	16612246	16612246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgattctccagacagtgacGaagaagaaatgaaagtattg	10	5	1	6			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:16612246G>A	ENST00000221671.3	+	2	799	c.643G>A	c.(643-645)Gaa>Aaa	p.E215K	C19orf44_ENST00000594035.1_Missense_Mutation_p.E215K|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	215								p.E215K(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						AGACAGTGACGAAGAAGAAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	19											79	84	82					19																	16612246		2203	4299	6502	16473246	SO:0001583	missense	84167			AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.643G>A	19.37:g.16612246G>A	ENSP00000221671:p.Glu215Lys		16473246	Q8N6Y7	Missense_Mutation	SNP	ENST00000221671.3	37	CCDS12345.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.241962	0.39598	.	.	ENSG00000105072	ENST00000221671	.	.	.	5.16	2.98	0.34508	.	0.069380	0.56097	N	0.000039	T	0.52403	0.1732	M	0.74258	2.255	0.41451	D	0.987982	P;P	0.49961	0.868;0.93	B;B	0.43680	0.179;0.427	T	0.56098	-0.8035	9	0.87932	D	0	-15.5564	8.4551	0.32895	0.0841:0.1527:0.7632:0.0	.	215;215	Q9H6X5;Q9H6X5-2	CS044_HUMAN;.	K	215	.	ENSP00000221671:E215K	E	+	1	0	C19orf44	16473246	0.998000	0.40836	0.906000	0.35671	0.428000	0.31595	2.404000	0.44539	0.542000	0.28846	0.655000	0.94253	GAA		0.443	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		A	16612246	G	A	16612246	3	1	77	1	0	0	0	0	1	0	0	0	1933	1059	37	1	645	1	C19orf44	19	16612246	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	343812	16612246	42516737	1076	22812										
JAK3	3718	broad.mit.edu	37	chr19	17955112	17955112	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaggagaaagataggcgctGggggggcccggggccccgag							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:17955112delG	ENST00000527670.1	-	1	144	c.115delC	c.(115-117)cagfs	p.Q39fs	JAK3_ENST00000534444.1_Frame_Shift_Del_p.Q39fs|JAK3_ENST00000458235.1_Frame_Shift_Del_p.Q39fs|JAK3_ENST00000526008.1_5'UTR			P52333	JAK3_HUMAN	Janus kinase 3	39	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.Q39fs*108(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GATAGGCGCTGGGGGGGCCCG	0.662		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	1	Deletion - Frameshift(1)	large_intestine(1)	19											13	15	14					19																	17955112		2197	4293	6490	17816112	SO:0001589	frameshift_variant	3718			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.115delC	19.37:g.17955112delG	ENSP00000432511:p.Gln39fs		17816112	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Frame_Shift_Del	DEL	ENST00000527670.1	37	CCDS12366.1																																																																																				0.662	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		-	17955112	G	-	17955112	7	5	77	1	0	1	0	1	0	0	0	0	7960	1357	47	0	3351	0	JAK3	19	17955112	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1342866	17955112	41173871	1077	22813										
ZNF493	284443	broad.mit.edu	37	chr19	21607517	21607517	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atactgaagagaaaccctacAaatgtgaaaaatgtggcaaa	8	6	0	3	rs200019691		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:21607517A>G	ENST00000355504.4	+	2	1938	c.1672A>G	c.(1672-1674)Aaa>Gaa	p.K558E	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.K686E	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	558					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K558E(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GAAACCCTACAAATGTGAAAA	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	19											32	36	35					19																	21607517		2201	4298	6499	21399357	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1672A>G	19.37:g.21607517A>G	ENSP00000347691:p.Lys558Glu		21399357	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.423	-0.907411	0.02434	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.57752	2.36;0.38	1.06	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47116	0.1428	N	0.25201	0.72	0.09310	N	1	D;P	0.63880	0.993;0.908	D;B	0.68765	0.96;0.151	T	0.38329	-0.9666	9	0.07482	T	0.82	.	5.0349	0.14428	0.6956:0.3043:0.0:0.0	.	558;686	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	686;558	ENSP00000376110:K686E;ENSP00000347691:K558E	ENSP00000347691:K558E	K	+	1	0	ZNF493	21399357	0.000000	0.05858	0.039000	0.18376	0.039000	0.13416	-2.599000	0.00893	0.388000	0.25054	0.383000	0.25322	AAA		0.343	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21607517	A	G	21607517	3	3	77	1	0	0	0	0	1	0	0	0	17983	131	5	4	2133	4	ZNF493	19	21607517	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	3652405	21607517	37521466	1078	22814										
ZNF675	171392	broad.mit.edu	37	chr19	23845960	23845960	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atccctaaatgtcaacagtcCctgaaaaacacatacacaca	3	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:23845960C>A	ENST00000359788.4	-	2	172	c.4G>T	c.(4-6)Gga>Tga	p.G2*	ZNF675_ENST00000601935.1_Splice_Site_p.G2*|ZNF675_ENST00000601010.1_Splice_Site_p.G2*|ZNF675_ENST00000599168.1_Splice_Site_p.G2*|ZNF675_ENST00000596211.1_Splice_Site_p.G2*|ZNF675_ENST00000600313.1_Splice_Site_p.G2*	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	2					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G2*(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GTCAACAGTCCCTGAAAAACA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											81	88	86					19																	23845960		2202	4300	6502	23637800	SO:0001630	splice_region_variant	171392				CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.4-1G>T	19.37:g.23845960C>A			23637800	Q8N211	Nonsense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	15.14	2.744229	0.49151	.	.	ENSG00000197372	ENST00000359788	.	.	.	0.926	0.926	0.19430	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	4.9893	0.14205	0.0:1.0:0.0:0.0	.	.	.	.	X	2	.	ENSP00000352836:G2X	G	-	1	0	ZNF675	23637800	0.742000	0.28228	0.155000	0.22561	0.156000	0.22039	2.584000	0.46102	0.308000	0.22923	0.313000	0.20887	GGA		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	Nonsense_Mutation	A	23845960	C	A	23845960	5	1	77	1	0	0	0	0	0	0	1	0	18121	637	22	2	1714	2	ZNF675	19	23845960	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2238443	23845960	35283023	1079	22815										
ZNF536	9745	broad.mit.edu	37	chr19	30934614	30934614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctcagccatgccttccccGagctccatccccggcccaac	7	21	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:30934614G>A	ENST00000355537.3	+	2	292	c.145G>A	c.(145-147)Gag>Aag	p.E49K		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	49					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.E49K(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TGCCTTCCCCGAGCTCCATCC	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	19											67	68	68					19																	30934614		2203	4300	6503	35626454	SO:0001583	missense	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.145G>A	19.37:g.30934614G>A	ENSP00000347730:p.Glu49Lys		35626454	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629857	0.46944	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.37	4.32	0.51571	.	0.160306	0.56097	D	0.000036	T	0.15652	0.0377	L	0.32530	0.975	0.50313	D	0.999861	P;D	0.69078	0.952;0.997	B;P	0.53954	0.278;0.738	T	0.08146	-1.0736	10	0.18710	T	0.47	-33.2908	16.3674	0.83338	0.0:0.1321:0.8679:0.0	.	49;49	A7E228;O15090	.;ZN536_HUMAN	K	49	ENSP00000347730:E49K	ENSP00000347730:E49K	E	+	1	0	ZNF536	35626454	1.000000	0.71417	0.966000	0.40874	0.941000	0.58515	7.788000	0.85771	1.382000	0.46385	0.462000	0.41574	GAG		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30934614	G	A	30934614	3	1	77	1	0	0	0	0	1	0	0	0	18013	1059	37	1	147	1	ZNF536	19	30934614	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7088654	30934614	28194369	1080	22816										
ZNF536	9745	broad.mit.edu	37	chr19	30935424	30935424	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggaggagctcatcagccacGtggagaaggcacacatcacg	13	11	3	1	rs142265762		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:30935424G>A	ENST00000355537.3	+	2	1102	c.955G>A	c.(955-957)Gtg>Atg	p.V319M		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	319					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.V319L(1)|p.V319M(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CATCAGCCACGTGGAGAAGGC	0.667																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	19						G	MET/VAL	0,4406		0,0,2203	88	98	95		955	5.6	1	19	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF536	NM_014717.1	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	319/1301	30935424	1,13005	2203	4300	6503	35627264	SO:0001583	missense	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.955G>A	19.37:g.30935424G>A	ENSP00000347730:p.Val319Met		35627264	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.882687	0.33255	0.0	1.16E-4	ENSG00000198597	ENST00000355537	T	0.27720	1.65	5.59	5.59	0.84812	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	N	0.04787	-0.16	0.51482	D	0.999927	D;D	0.89917	0.999;1.0	D;D	0.97110	0.963;1.0	T	0.36237	-0.9756	10	0.18710	T	0.47	-33.4233	19.5661	0.95393	0.0:0.0:1.0:0.0	.	319;319	A7E228;O15090	.;ZN536_HUMAN	M	319	ENSP00000347730:V319M	ENSP00000347730:V319M	V	+	1	0	ZNF536	35627264	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.024000	0.88770	2.631000	0.89168	0.491000	0.48974	GTG		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30935424	G	A	30935424	3	1	77	1	0	0	0	0	1	0	0	0	18013	1145	40	1	957	1	ZNF536	19	30935424	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	810	30935424	28193559	1081	22817										
SLC7A9	11136	broad.mit.edu	37	chr19	33350770	33350770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agccaccgcctgggactgcaGgagttcggtggcagtcatca	14	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:33350770G>A	ENST00000023064.4	-	8	1041	c.850C>T	c.(850-852)Ctg>Ttg	p.L284L	SLC7A9_ENST00000587772.1_Silent_p.L284L|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_Silent_p.L284L	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	284					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)	p.L284L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	TGGGACTGCAGGAGTTCGGTG	0.617																																					GBM(181;1335 2108 9644 44178 46689)											1	Substitution - coding silent(1)	large_intestine(1)	19											74	65	68					19																	33350770		2203	4300	6503	38042610	SO:0001819	synonymous_variant	11136			AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.850C>T	19.37:g.33350770G>A			38042610	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																				0.617	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			A	33350770	G	A	33350770	2	1	77	1	0	0	0	0	0	0	0	1	14742	991	35	3		3	SLC7A9	19	33350770	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2415346	33350770	25778213	1082	22818										
ATP4A	495	broad.mit.edu	37	chr19	36050919	36050919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacccccgacgccagcgatgCgatgcgcccaatgatggtgc	12	16	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:36050919C>T	ENST00000262623.3	-	7	872	c.844G>A	c.(844-846)Gca>Aca	p.A282T		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	282					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)	p.A282T(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GCCAGCGATGCGATGCGCCCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19											95	73	80					19																	36050919		2203	4300	6503	40742759	SO:0001583	missense	495				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.844G>A	19.37:g.36050919C>T	ENSP00000262623:p.Ala282Thr		40742759	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490498	0.64074	.	.	ENSG00000105675	ENST00000262623	D	0.92199	-2.99	3.94	3.94	0.45596	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.077790	0.48767	N	0.000178	D	0.95484	0.8533	M	0.84156	2.68	0.58432	D	0.999999	D	0.69078	0.997	D	0.64595	0.927	D	0.95985	0.8981	10	0.87932	D	0	.	13.8309	0.63380	0.0:1.0:0.0:0.0	.	282	P20648	ATP4A_HUMAN	T	282	ENSP00000262623:A282T	ENSP00000262623:A282T	A	-	1	0	ATP4A	40742759	1.000000	0.71417	0.291000	0.24904	0.060000	0.15804	7.608000	0.82898	2.203000	0.70933	0.561000	0.74099	GCA		0.642	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36050919	C	T	36050919	3	4	77	1	0	0	0	0	1	0	0	0	1146	768	27	1	2327	1	ATP4A	19	36050919	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2700149	36050919	23078064	1083	22819										
MLL4	9757	broad.mit.edu	37	chr19	36215969	36215969	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtctcccgatggtgtgcaccGcgtccgtgtggattttaagg	14	10	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:36215969G>A	ENST00000222270.7	+	10	3509	c.3509G>A	c.(3508-3510)cGc>cAc	p.R1170H	KMT2B_ENST00000420124.1_Missense_Mutation_p.R1170H|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1170					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1172H(1)									GGTGTGCACCGCGTCCGTGTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											65	71	69					19																	36215969		2018	4185	6203	40907809	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3509G>A	19.37:g.36215969G>A	ENSP00000222270:p.Arg1170His		40907809	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216456	0.58452	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	T;T	0.65916	-0.18;-0.18	5.28	5.28	0.74379	.	0.000000	0.40385	N	0.001109	T	0.75466	0.3853	L	0.49126	1.545	0.53005	D	0.999968	D	0.89917	1.0	D	0.83275	0.996	T	0.76252	-0.3027	10	0.62326	D	0.03	.	17.8487	0.88738	0.0:0.0:1.0:0.0	.	1170	Q9UMN6	MLL4_HUMAN	H	1170	ENSP00000222270:R1170H;ENSP00000398837:R1170H	ENSP00000222270:R1170H	R	+	2	0	AD000671.1	40907809	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	5.697000	0.68295	2.742000	0.94016	0.650000	0.86243	CGC		0.567	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36215969	G	A	36215969	3	1	77	1	0	0	0	0	1	0	0	0	9653	1087	38	1	3547	1	MLL4	19	36215969	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	165050	36215969	22913014	1084	22820										
ZNF461	92283	broad.mit.edu	37	chr19	37147386	37147386	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgtctcttccctcacaaccaTccagggctccttcccttgct	5	18	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:37147386T>C	ENST00000588268.1	-	4	423	c.196A>G	c.(196-198)Atg>Gtg	p.M66V	ZNF461_ENST00000360357.4_Missense_Mutation_p.M66V	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M66V(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CTCACAACCATCCAGGGCTCC	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	84	83					19																	37147386		2106	4256	6362	41839226	SO:0001583	missense	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.196A>G	19.37:g.37147386T>C	ENSP00000467931:p.Met66Val		41839226	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	8.756	0.922453	0.17982	.	.	ENSG00000197808	ENST00000396893;ENST00000360357;ENST00000396892	T	0.05649	3.41	3.27	2.12	0.27331	Krueppel-associated box (2);	.	.	.	.	T	0.04724	0.0128	L	0.31420	0.93	0.21579	N	0.999636	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.35351	-0.9792	9	0.33141	T	0.24	.	5.1859	0.15184	0.2598:0.0:0.0:0.7402	.	66;66	B4DRP8;Q8TAF7	.;ZN461_HUMAN	V	66;66;1	ENSP00000353515:M66V	ENSP00000353515:M66V	M	-	1	0	ZNF461	41839226	0.770000	0.28543	0.936000	0.37596	0.990000	0.78478	0.452000	0.21795	1.495000	0.48549	0.477000	0.44152	ATG		0.493	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		C	37147386	T	C	37147386	3	2	77	1	0	0	0	0	1	0	0	0	17964	1435	50	4	1507	4	ZNF461	19	37147386	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	931417	37147386	21981597	1085	22821										
SIPA1L3	23094	broad.mit.edu	37	chr19	38572495	38572495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggaggccctgagagagcacaGcaacccaagcccctcccagg	12	16	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:38572495G>A	ENST00000222345.6	+	3	799	c.290G>A	c.(289-291)aGc>aAc	p.S97N		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	97					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)	p.S97N(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGAGAGCACAGCAACCCAAGC	0.672																																																1	Substitution - Missense(1)	large_intestine(1)	19											54	61	58					19																	38572495		2203	4299	6502	43264335	SO:0001583	missense	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.290G>A	19.37:g.38572495G>A	ENSP00000222345:p.Ser97Asn		43264335	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	G	9.907	1.208388	0.22205	.	.	ENSG00000105738	ENST00000222345	T	0.76316	-1.01	4.99	-7.7	0.01259	.	0.812660	0.11552	N	0.552684	T	0.50069	0.1594	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.34625	-0.9821	10	0.44086	T	0.13	-10.6967	7.8378	0.29380	0.1186:0.0996:0.6904:0.0915	.	97	O60292	SI1L3_HUMAN	N	97	ENSP00000222345:S97N	ENSP00000222345:S97N	S	+	2	0	SIPA1L3	43264335	0.000000	0.05858	0.904000	0.35570	0.927000	0.56198	-0.836000	0.04382	-0.889000	0.03950	0.557000	0.71058	AGC		0.672	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		A	38572495	G	A	38572495	3	1	77	1	0	0	0	0	1	0	0	0	14368	971	34	3	292	3	SIPA1L3	19	38572495	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1425109	38572495	20556488	1086	22822										
YIF1B	90522	broad.mit.edu	37	chr19	38798117	38798117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agcccagcaccaggtagtagCcaatcttcccgaagagcagg	11	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:38798117C>T	ENST00000339413.6	-	7	785	c.740G>A	c.(739-741)gGc>gAc	p.G247D	YIF1B_ENST00000591755.1_Missense_Mutation_p.G244D|YIF1B_ENST00000329420.8_Missense_Mutation_p.G232D|YIF1B_ENST00000587361.1_5'Flank|YIF1B_ENST00000392124.3_Missense_Mutation_p.G216D|YIF1B_ENST00000592246.1_Missense_Mutation_p.G181D|YIF1B_ENST00000592694.1_Missense_Mutation_p.G216D|YIF1B_ENST00000337679.8_Missense_Mutation_p.G244D|YIF1B_ENST00000591784.1_Missense_Mutation_p.G216D	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	247						integral component of membrane (GO:0016021)		p.G216D(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGGTAGTAGCCAATCTTCCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											82	75	78					19																	38798117		2203	4300	6503	43489957	SO:0001583	missense	90522			AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.740G>A	19.37:g.38798117C>T	ENSP00000343435:p.Gly247Asp		43489957	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Missense_Mutation	SNP	ENST00000339413.6	37	CCDS33010.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.268960	0.80469	.	.	ENSG00000167645	ENST00000339413;ENST00000329420;ENST00000392124;ENST00000337679	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.66	5.66	0.87406	.	0.056263	0.64402	D	0.000002	D	0.94663	0.8279	M	0.91406	3.205	0.58432	D	0.999999	D;D;D;D;D	0.76494	0.996;0.997;0.999;0.997;0.999	D;D;D;D;D	0.76575	0.944;0.975;0.956;0.968;0.988	D	0.94065	0.7330	10	0.36615	T	0.2	-14.4652	17.2371	0.87002	0.0:1.0:0.0:0.0	.	216;244;244;247;244	Q5BJH7-2;Q5BJH7-5;Q5BJH7-4;Q5BJH7;Q5BJH7-3	.;.;.;YIF1B_HUMAN;.	D	247;232;216;244	ENSP00000343435:G247D;ENSP00000329559:G232D;ENSP00000375971:G216D;ENSP00000337411:G244D	ENSP00000329559:G232D	G	-	2	0	YIF1B	43489957	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	4.613000	0.61176	2.662000	0.90505	0.555000	0.69702	GGC		0.647	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557		T	38798117	C	T	38798117	3	4	77	1	0	0	0	0	1	0	0	0	17516	739	26	3	293	3	YIF1B	19	38798117	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	225622	38798117	20330866	1087	22823										
FAM98C	147965	broad.mit.edu	37	chr19	38896061	38896061	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgctagatgcacccagatgGgtaagactgtgtgcgactga	13	9	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:38896061G>T	ENST00000252530.5	+	5	652	c.633G>T	c.(631-633)tgG>tgT	p.W211C	FAM98C_ENST00000343358.7_Intron|FAM98C_ENST00000588262.1_Intron	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	211								p.W211C(1)		endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CACCCAGATGGGTAAGACTGT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											89	89	89					19																	38896061		2138	4258	6396	43587901	SO:0001630	splice_region_variant	147965				CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.633+1G>T	19.37:g.38896061G>T			43587901	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478053	0.63849	.	.	ENSG00000130244	ENST00000252530	T	0.54479	0.57	4.73	4.73	0.59995	.	0.163691	0.29522	N	0.011908	T	0.74794	0.3763	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79266	-0.1874	10	0.62326	D	0.03	-16.036	13.2635	0.60120	0.0:0.0:1.0:0.0	.	211	Q17RN3	FA98C_HUMAN	C	211	ENSP00000252530:W211C	ENSP00000252530:W211C	W	+	3	0	FAM98C	43587901	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.406000	0.52637	2.159000	0.67721	0.558000	0.71614	TGG		0.572	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	Missense_Mutation	T	38896061	G	T	38896061	5	4	77	1	0	0	0	0	0	0	1	0	5677	1246	43	2	651	2	FAM98C	19	38896061	Splice_Site	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	97944	38896061	20232922	1088	22824										
RYR1	6261	broad.mit.edu	37	chr19	38934889	38934889	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atccttgtcagtgtctcctcCgagcgctacctggtgagcca	10	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:38934889C>T	ENST00000359596.3	+	6	525	c.525C>T	c.(523-525)tcC>tcT	p.S175S	RYR1_ENST00000355481.4_Silent_p.S175S|RYR1_ENST00000360985.3_Silent_p.S175S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	175	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.S175S(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTGTCTCCTCCGAGCGCTACC	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	19											97	78	84					19																	38934889		2203	4300	6503	43626729	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.525C>T	19.37:g.38934889C>T			43626729	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38934889	C	T	38934889	2	4	77	1	0	0	0	0	0	0	0	1	13805	639	23	1		1	RYR1	19	38934889	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	38828	38934889	20194094	1089	22825										
SIRT2	22933	broad.mit.edu	37	chr19	39374330	39374330	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacgcagtgtgatgtgtagaAggtgccgtgcgcctccacca	14	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:39374330A>C	ENST00000249396.7	-	9	869	c.568T>G	c.(568-570)Ttc>Gtc	p.F190V	SIRT2_ENST00000358931.5_Missense_Mutation_p.F190V|SIRT2_ENST00000392081.2_Missense_Mutation_p.F153V	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	190	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.F190V(1)		endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			GATGTGTAGAAGGTGCCGTGC	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											91	72	78					19																	39374330		2203	4300	6503	44066170	SO:0001583	missense	22933			AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2", "sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.568T>G	19.37:g.39374330A>C	ENSP00000249396:p.Phe190Val		44066170	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	37	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784515	0.70222	.	.	ENSG00000068903	ENST00000249396;ENST00000392081;ENST00000358931;ENST00000456703;ENST00000414941;ENST00000407552	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.61489	0.2351	M	0.67953	2.075	0.80722	D	1	D;D;P;D	0.89917	1.0;1.0;0.906;1.0	D;D;D;D	0.91635	0.992;0.996;0.944;0.999	T	0.65837	-0.6071	10	0.87932	D	0	-10.6488	13.1972	0.59745	1.0:0.0:0.0:0.0	.	190;153;190;170	Q8IXJ6-4;Q8IXJ6-2;Q8IXJ6;Q8IXJ6-3	.;.;SIRT2_HUMAN;.	V	190;153;190;175;153;153	ENSP00000249396:F190V;ENSP00000375931:F153V;ENSP00000351809:F190V;ENSP00000404309:F153V;ENSP00000385146:F153V	ENSP00000249396:F190V	F	-	1	0	SIRT2	44066170	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	8.210000	0.89753	2.027000	0.59764	0.402000	0.26972	TTC		0.602	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1			C	39374330	A	C	39374330	3	2	77	1	0	0	0	0	1	0	0	0	14375	72	3	4	633	4	SIRT2	19	39374330	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	439441	39374330	19754653	1090	22826										
PAF1	55095	broad.mit.edu	37	chr19	39877397	39877397	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaagcagggcgttggtgccTgactgaaccccagccttggc	13	13	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:39877397T>C	ENST00000314471.6	+	0	4519				PAF1_ENST00000221266.7_Silent_p.S310S|PAF1_ENST00000221265.3_Silent_p.S343S|PAF1_ENST00000595564.1_Silent_p.S333S	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S343S(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CGTTGGTGCCTGACTGAACCC	0.572																																																1	Substitution - coding silent(1)	large_intestine(1)	19											123	104	111					19																	39877397		2203	4300	6503	44569237	SO:0001628	intergenic_variant	54623				CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"Sterile alpha motif (SAM) domain containing"	25492	protein-coding gene	gene with protein product	"smaug homolog B (Drosophila)"					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9			19.37:g.39877397T>C			44569237	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1																																																																																				0.572	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		C	39877397	T	C	39877397	1	2	77	0	1	0	0	0	0	0	0	0	11414	1567	55	4		4	PAF1	19	39877397	IGR	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	503067	39877397	19251586	1091	22827										
FCGBP	8857	broad.mit.edu	37	chr19	40389762	40389762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	catggcacgtgcactgctgcCgacagttgtcaatgaggact	12	11	1	1	rs587722177		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:40389762C>T	ENST00000221347.6	-	18	8427	c.8420G>A	c.(8419-8421)cGg>cAg	p.R2807Q		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2807	Cys-rich.					extracellular vesicular exosome (GO:0070062)		p.R2807Q(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			GCACTGCTGCCGACAGTTGTC	0.632													c|||	1	0.000199681	0	0.0014	5008	,	,		19954	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											10	9	9					19																	40389762		1990	3585	5575	45081602	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8420G>A	19.37:g.40389762C>T	ENSP00000221347:p.Arg2807Gln		45081602	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	c	7.620	0.676573	0.14841	.	.	ENSG00000090920	ENST00000221347	T	0.04654	3.58	2.94	-2.68	0.06041	von Willebrand factor, type C (1);	3.108090	0.01209	N	0.007781	T	0.01627	0.0052	N	0.02973	-0.45	0.18873	N	0.999988	P	0.42248	0.774	B	0.31495	0.131	T	0.37197	-0.9716	10	0.13470	T	0.59	.	4.2188	0.10547	0.0:0.456:0.2174:0.3265	.	2807	Q9Y6R7	FCGBP_HUMAN	Q	2807	ENSP00000221347:R2807Q	ENSP00000221347:R2807Q	R	-	2	0	FCGBP	45081602	0.958000	0.32768	0.946000	0.38457	0.073000	0.16967	-0.358000	0.07641	-0.365000	0.08076	0.313000	0.20887	CGG		0.632	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40389762	C	T	40389762	3	4	77	1	0	0	0	0	1	0	0	0	5797	652	23	1	7873	1	FCGBP	19	40389762	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	512365	40389762	18739221	1092	22828										
PRX	57716	broad.mit.edu	37	chr19	40900407	40900407	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tactcggcatggttgcccccGgatggcgagagctccacgtc	13	14	0	1	rs567324732	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:40900407G>A	ENST00000324001.7	-	7	4122	c.3852C>T	c.(3850-3852)tcC>tcT	p.S1284S	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	1284					axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S1284S(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGTTGCCCCCGGATGGCGAGA	0.701													G|||	2	0.000399361	0	0	5008	,	,		15432	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	19											12	12	12					19																	40900407		2194	4291	6485	45592247	SO:0001819	synonymous_variant	57716			AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.3852C>T	19.37:g.40900407G>A			45592247	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																				0.701	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		A	40900407	G	A	40900407	2	1	77	1	0	0	0	0	0	0	0	1	12676	1103	39	1		1	PRX	19	40900407	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	510645	40900407	18228576	1093	22829										
SNRPA	6626	broad.mit.edu	37	chr19	41263356	41263356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcttcaaggaggtcagcagcGccaccaacgccctgcgctcc	10	17	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:41263356G>A	ENST00000243563.3	+	2	743	c.193G>A	c.(193-195)Gcc>Acc	p.A65T	SNRPA_ENST00000599570.1_3'UTR	NM_004596.4	NP_004587.1	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	65	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snRNA binding (GO:0017069)	p.A65T(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GGTCAGCAGCGCCACCAACGC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	83	85					19																	41263356		2203	4300	6503	45955196	SO:0001583	missense	6626			X06347	CCDS12565.1	19q13.1	2013-02-12				ENSG00000077312		"RNA binding motif (RRM) containing"	11151	protein-coding gene	gene with protein product		182285				1701111	Standard	NM_004596		Approved	U1A, U1-A, Mud1	uc002ooz.3	P09012		ENST00000243563.3:c.193G>A	19.37:g.41263356G>A	ENSP00000243563:p.Ala65Thr		45955196		Missense_Mutation	SNP	ENST00000243563.3	37	CCDS12565.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519356	0.64634	.	.	ENSG00000077312	ENST00000243563	T	0.30714	1.52	5.97	4.94	0.65067	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.103999	0.64402	D	0.000003	T	0.52125	0.1715	H	0.96604	3.85	0.58432	D	0.999999	B	0.19817	0.039	B	0.32465	0.146	T	0.59852	-0.7376	10	0.72032	D	0.01	-35.8883	9.6557	0.39925	0.0739:0.0:0.7848:0.1412	.	65	P09012	SNRPA_HUMAN	T	65	ENSP00000243563:A65T	ENSP00000243563:A65T	A	+	1	0	SNRPA	45955196	1.000000	0.71417	0.973000	0.42090	0.714000	0.41099	6.474000	0.73578	1.546000	0.49388	-0.136000	0.14681	GCC		0.542	SNRPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463118.2	NM_004596		A	41263356	G	A	41263356	3	1	77	1	0	0	0	0	1	0	0	0	14896	1087	38	1	199	1	SNRPA	19	41263356	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	362949	41263356	17865627	1094	22830										
PAFAH1B3	5050	broad.mit.edu	37	chr19	42804150	42804150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caacccgggcctggggctgtCgctcattcaccagttgcaca	11	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:42804150C>T	ENST00000262890.3	-	4	641	c.380G>A	c.(379-381)cGa>cAa	p.R127Q	PAFAH1B3_ENST00000538771.1_Missense_Mutation_p.R127Q|PRR19_ENST00000341747.3_5'Flank|PRR19_ENST00000598490.1_5'Flank	NM_002573.3	NP_002564.1	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa)	127					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)	p.R127Q(1)		breast(1)|large_intestine(2)|ovary(1)	4		Prostate(69;0.0704)				CTGGGGCTGTCGCTCATTCAC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											138	128	131					19																	42804150		2203	4300	6503	47495990	SO:0001583	missense	5050			D63391	CCDS12602.1	19q13.1	2011-10-24	2010-02-10			ENSG00000079462			8576	protein-coding gene	gene with protein product	"PAF-AH1b alpha 1 subunit"	603074	"platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29kD)", "platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 3 (29kDa)"			7669037	Standard	NM_002573		Approved		uc010xwj.1	Q15102		ENST00000262890.3:c.380G>A	19.37:g.42804150C>T	ENSP00000262890:p.Arg127Gln		47495990	Q53X88	Missense_Mutation	SNP	ENST00000262890.3	37	CCDS12602.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141666	0.57044	.	.	ENSG00000079462	ENST00000538771;ENST00000262890	T;T	0.44881	0.91;0.91	5.46	4.4	0.53042	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.110134	0.64402	D	0.000018	T	0.31136	0.0787	L	0.58810	1.83	0.30795	N	0.740455	P	0.45176	0.852	B	0.29353	0.101	T	0.36648	-0.9739	10	0.18710	T	0.47	-15.8119	12.9396	0.58335	0.1691:0.8309:0.0:0.0	.	127	Q15102	PA1B3_HUMAN	Q	127	ENSP00000444935:R127Q;ENSP00000262890:R127Q	ENSP00000262890:R127Q	R	-	2	0	PAFAH1B3	47495990	0.049000	0.20398	1.000000	0.80357	0.943000	0.58893	1.004000	0.29822	1.237000	0.43756	0.467000	0.42956	CGA		0.592	PAFAH1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463726.1	NM_002573		T	42804150	C	T	42804150	3	4	77	1	0	0	0	0	1	0	0	0	11417	884	31	1	323	1	PAFAH1B3	19	42804150	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1540794	42804150	16324833	1095	22831										
MEGF8	1954	broad.mit.edu	37	chr19	42847783	42847783	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttccaggcacctgcccctgaCgtgagcactggggtgacagg	14	13	0	3	rs370015031		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:42847783C>T	ENST00000251268.6	+	9	1668	c.1668C>T	c.(1666-1668)gaC>gaT	p.D556D	MEGF8_ENST00000334370.4_Splice_Site_p.D556D	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	556					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.D97D(1)|p.D556D(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CTGCCCCTGACGTGAGCACTG	0.662																																																2	Substitution - coding silent(2)	large_intestine(2)	19						C		3,4403	6.2+/-15.9	0,3,2200	24	21	22		1668	-10.2	0.1	19		22	0,8600		0,0,4300	no	coding-synonymous-near-splice	MEGF8	NM_001410.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		556/2779	42847783	3,13003	2203	4300	6503	47539623	SO:0001630	splice_region_variant	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.1668+1C>T	19.37:g.42847783C>T			47539623	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																					0.662	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	Silent	T	42847783	C	T	42847783	5	4	77	1	0	0	0	0	0	0	1	0	9493	550	19	1	1702	1	MEGF8	19	42847783	Splice_Site	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	43633	42847783	16281200	1096	22832										
ZNF233	353355	broad.mit.edu	37	chr19	44778460	44778460	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagggctttagtcagagttcGcatctccaagaccatcagca	9	11	3	2	rs146745646		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:44778460G>A	ENST00000391958.2	+	5	1774	c.1647G>A	c.(1645-1647)tcG>tcA	p.S549S	ZNF233_ENST00000334152.1_Silent_p.S531S|ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	549					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S549S(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				GTCAGAGTTCGCATCTCCAAG	0.468													G|||	1	0.000199681	0	0	5008	,	,		22360	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19											103	93	97					19																	44778460		2203	4300	6503	49470300	SO:0001819	synonymous_variant	353355			AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"Zinc fingers, C2H2-type", "-"	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1647G>A	19.37:g.44778460G>A			49470300	B2RN78|B2RN79|Q86WL8	Silent	SNP	ENST00000391958.2	37	CCDS33047.1																																																																																				0.468	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756		A	44778460	G	A	44778460	2	1	77	1	0	0	0	0	0	0	0	1	17825	1074	38	1		1	ZNF233	19	44778460	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1930677	44778460	14350523	1097	22833										
ZFP112	7771	broad.mit.edu	37	chr19	44832206	44832206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacactctgatgactctgaaGgtatgatctctgactgaaac	9	9	3	6			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:44832206G>T	ENST00000337401.4	-	5	2210	c.2122C>A	c.(2122-2124)Ctt>Att	p.L708I	ZNF112_ENST00000354340.4_Missense_Mutation_p.L702I|ZNF112_ENST00000536500.1_Missense_Mutation_p.L725I	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	708					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L702I(1)									TGACTCTGAAGGTATGATCTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	19											137	116	123					19																	44832206		2203	4300	6503	49524046	SO:0001583	missense	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2122C>A	19.37:g.44832206G>T	ENSP00000337081:p.Leu708Ile		49524046	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882003	0.72294	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.53857	0.6;0.6;0.6	5.21	5.21	0.72293	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.30762	N	0.008926	T	0.79082	0.4386	M	0.92026	3.265	0.37653	D	0.922486	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.97110	0.999;1.0;0.999	D	0.85624	0.1266	10	0.72032	D	0.01	-11.5415	17.8963	0.88890	0.0:0.0:1.0:0.0	.	707;725;708	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	I	708;708;702;725;707	ENSP00000337081:L708I;ENSP00000346305:L702I;ENSP00000441990:L725I	ENSP00000253426:L707I	L	-	1	0	ZNF285	49524046	0.926000	0.31397	1.000000	0.80357	0.987000	0.75469	1.412000	0.34714	2.593000	0.87608	0.655000	0.94253	CTT		0.463	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		T	44832206	G	T	44832206	3	4	77	1	0	0	0	0	1	0	0	0	17677	1000	35	2	623	2	ZFP112	19	44832206	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	53746	44832206	14296777	1098	22834										
ZNF285	26974	broad.mit.edu	37	chr19	44891987	44891987	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggggtaagaacctgtgtcagGctttgccatgctgtgatatc	13	8	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:44891987G>A	ENST00000330997.4	-	4	484	c.420C>T	c.(418-420)agC>agT	p.S140S	ZNF285_ENST00000544719.2_Silent_p.S140S|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Silent_p.S147S	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S140S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						CCTGTGTCAGGCTTTGCCATG	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	19											90	89	89					19																	44891987		2203	4300	6503	49583827	SO:0001819	synonymous_variant	26974			AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.420C>T	19.37:g.44891987G>A			49583827	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																				0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		A	44891987	G	A	44891987	2	1	77	1	0	0	0	0	0	0	0	1	17861	1194	42	3		3	ZNF285	19	44891987	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	59781	44891987	14236996	1099	22835										
PVRL2	5819	broad.mit.edu	37	chr19	45375322	45375322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttggtgccctcgggccgaGcagatggtgtcacggtcacc	14	14	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:45375322G>A	ENST00000252483.5	+	3	691	c.691G>A	c.(691-693)Gca>Aca	p.A231T	PVRL2_ENST00000252485.4_Missense_Mutation_p.A231T	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	231	Ig-like C2-type 1.				acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)	p.A231T(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CTCGGGCCGAGCAGATGGTGT	0.602																																																1	Substitution - Missense(1)	large_intestine(1)	19											137	105	116					19																	45375322		2203	4300	6503	50067162	SO:0001583	missense	5819			X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.691G>A	19.37:g.45375322G>A	ENSP00000252483:p.Ala231Thr		50067162	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.313861	0.23908	.	.	ENSG00000130202	ENST00000252483;ENST00000252485	T;T	0.77229	-1.08;-1.08	4.25	1.58	0.23477	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.546453	0.16539	N	0.210023	T	0.69187	0.3083	L	0.58354	1.805	0.09310	N	1	B;B	0.27068	0.167;0.03	B;B	0.24974	0.057;0.03	T	0.58418	-0.7640	10	0.44086	T	0.13	.	6.1103	0.20097	0.2661:0.0:0.7339:0.0	.	231;231	Q92692;Q92692-2	PVRL2_HUMAN;.	T	231	ENSP00000252483:A231T;ENSP00000252485:A231T	ENSP00000252483:A231T	A	+	1	0	PVRL2	50067162	0.025000	0.19082	0.000000	0.03702	0.891000	0.51852	2.408000	0.44574	0.142000	0.18901	0.561000	0.74099	GCA		0.602	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		A	45375322	G	A	45375322	3	1	77	1	0	0	0	0	1	0	0	0	12877	971	34	3	701	3	PVRL2	19	45375322	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	483335	45375322	13753661	1100	22836										
APOC1	341	broad.mit.edu	37	chr19	45419513	45419514	+	Frame_Shift_Del	DEL	AC	AC	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	taagctgaaggagtttggaaAcacactggaggacaaggctc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	AC	AC	AC	-	AC	AC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:45419513_45419514delAC	ENST00000588750.1	+	4	450_451	c.125_126delAC	c.(124-126)aacfs	p.N42fs	APOC1_ENST00000252491.4_Frame_Shift_Del_p.N42fs|APOC1_ENST00000592885.1_Frame_Shift_Del_p.N42fs|APOC1_ENST00000589781.1_Intron|APOC1_ENST00000588802.1_Frame_Shift_Del_p.N42fs|APOC1_ENST00000586638.1_Frame_Shift_Del_p.N42fs			P02654	APOC1_HUMAN	apolipoprotein C-I	42					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phosphatidylcholine catabolic process (GO:0010900)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|plasma lipoprotein particle remodeling (GO:0034369)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cholesterol esterification (GO:0010873)|regulation of cholesterol transport (GO:0032374)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)|very-low-density lipoprotein particle clearance (GO:0034447)	chylomicron (GO:0042627)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	fatty acid binding (GO:0005504)|lipase inhibitor activity (GO:0055102)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipase inhibitor activity (GO:0004859)	p.L44fs*15(1)		cervix(1)|large_intestine(1)|lung(2)	4	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		GAGTTTGGAAACACACTGGAGG	0.569																																																1	Deletion - Frameshift(1)	large_intestine(1)	19																																								50111354	SO:0001589	frameshift_variant	341			X00570	CCDS12648.1	19q13.2	2013-01-24				ENSG00000130208		"Apolipoproteins"	607	protein-coding gene	gene with protein product		107710					Standard	NM_001645		Approved		uc002pae.1	P02654		ENST00000588750.1:c.125_126delAC	19.37:g.45419517_45419518delAC	ENSP00000465356:p.Asn42fs		50111353	B2R526|Q6IB97	Frame_Shift_Del	DEL	ENST00000588750.1	37	CCDS12648.1																																																																																				0.569	APOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453245.1			-	45419514	AC	-	45419513	7	5	77	1	0	1	0	1	0	0	0	0	797	43	2	0	131	0	APOC1	19	45419513	Frame_Shift_Del	DEL	AC	TCGA-AG-A02N-01A-11W-A096-10	44191	45419513	13709470	1101	22837										
CLPTM1	1209	broad.mit.edu	37	chr19	45489815	45489815	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtgggtgaagggcagtgtgCcccctcccctggatcaatgt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:45489815delC	ENST00000337392.5	+	7	925	c.775delC	c.(775-777)cccfs	p.P261fs	CLPTM1_ENST00000589158.1_3'UTR|CLPTM1_ENST00000541297.2_Frame_Shift_Del_p.P247fs|CLPTM1_ENST00000546079.1_Frame_Shift_Del_p.P159fs	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	261					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.P260fs*7(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		GGGCAGTGTGCCCCCTCCCCT	0.617																																																2	Deletion - Frameshift(2)	large_intestine(2)	19											124	97	106					19																	45489815		2203	4300	6503	50181655	SO:0001589	frameshift_variant	1209			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.775delC	19.37:g.45489815delC	ENSP00000336994:p.Pro261fs		50181655	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Frame_Shift_Del	DEL	ENST00000337392.5	37	CCDS12651.1																																																																																				0.617	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		-	45489815	C	-	45489815	7	5	77	1	0	1	0	1	0	0	0	0	3560	739	26	0	801	0	CLPTM1	19	45489815	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	70302	45489815	13639168	1102	22838										
RTN2	6253	broad.mit.edu	37	chr19	45998165	45998165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtaggagaaggtcagctcccGgggggtgccccagtcctgcg	17	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:45998165G>A	ENST00000245923.4	-	3	413	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	PPM1N_ENST00000396737.2_5'Flank|RTN2_ENST00000589384.1_5'UTR|PPM1N_ENST00000456399.2_5'Flank|RTN2_ENST00000590526.1_5'UTR|RTN2_ENST00000430715.2_5'Flank|RTN2_ENST00000344680.4_Missense_Mutation_p.R60W|PPM1N_ENST00000401705.1_Intron	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	60					cell death (GO:0008219)|intracellular protein transmembrane transport (GO:0065002)|regulation of glucose import (GO:0046324)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)		p.R60W(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(4)|skin(1)|urinary_tract(1)	20		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		GTCAGCTCCCGGGGGGTGCCC	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	19											29	32	31					19																	45998165		2203	4300	6503	50690005	SO:0001583	missense	6253			AF038540	CCDS12665.1, CCDS12666.1, CCDS46114.1	19q13.2-q13.3	2012-03-30				ENSG00000125744			10468	protein-coding gene	gene with protein product	"NSP-like protein 1", "Neuroendocrine-specific protein-like 1"	603183	"spastic paraplegia 12 (autosomal dominant)"	SPG12		8812484, 9530622, 22232211	Standard	NM_005619		Approved	NSP2, NSPL1	uc002pcb.4	O75298		ENST00000245923.4:c.178C>T	19.37:g.45998165G>A	ENSP00000245923:p.Arg60Trp		50690005	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Missense_Mutation	SNP	ENST00000245923.4	37	CCDS12665.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537400	0.65085	.	.	ENSG00000125744	ENST00000344680;ENST00000245923	T;T	0.58358	0.38;0.34	5.44	1.82	0.25136	.	0.138626	0.31797	N	0.007051	T	0.57636	0.2067	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58668	-0.7596	10	0.66056	D	0.02	-24.8057	11.2618	0.49087	0.0:0.0:0.5145:0.4854	.	60;60	O75298-2;O75298	.;RTN2_HUMAN	W	60	ENSP00000345127:R60W;ENSP00000245923:R60W	ENSP00000245923:R60W	R	-	1	2	RTN2	50690005	0.525000	0.26290	0.895000	0.35142	0.629000	0.37895	0.550000	0.23345	0.591000	0.29711	0.462000	0.41574	CGG		0.657	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619		A	45998165	G	A	45998165	3	1	77	1	0	0	0	0	1	0	0	0	13763	1115	39	1	1495	1	RTN2	19	45998165	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	508350	45998165	13130818	1103	22839										
EML2	24139	broad.mit.edu	37	chr19	46116874	46116874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagccagcaacttcccatcAtgagagcgggccacagcgtt	11	13	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:46116874A>G	ENST00000245925.3	-	18	1799	c.1749T>C	c.(1747-1749)caT>caC	p.H583H	EML2_ENST00000589876.1_Silent_p.H583H|EML2_ENST00000587152.1_Silent_p.H784H|EML2_ENST00000536630.1_Silent_p.H730H	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	583	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.H583H(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		ACTTCCCATCATGAGAGCGGG	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19											144	119	128					19																	46116874		2203	4300	6503	50808714	SO:0001819	synonymous_variant	24139			AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"WD repeat domain containing"	18035	protein-coding gene	gene with protein product	"echinoderm MT-associated protein (EMAP)-like protein 70", "microtubule-associated protein like echinoderm EMAP"					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.1749T>C	19.37:g.46116874A>G			50808714	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																				0.562	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		G	46116874	A	G	46116874	2	3	77	1	0	0	0	0	0	0	0	1	5110	214	8	4		4	EML2	19	46116874	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	118709	46116874	13012109	1104	22840										
NOVA2	4858	broad.mit.edu	37	chr19	46443211	46443211	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgagcggcttgcgtggccgcGgggctgcccgtgatggtgac	19	11	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:46443211G>A	ENST00000263257.5	-	4	1583	c.1389C>T	c.(1387-1389)ccC>ccT	p.P463P		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	463	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P463P(1)		endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		GCGTGGCCGCGGGGCTGCCCG	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	19											50	55	53					19																	46443211		2203	4300	6503	51135051	SO:0001819	synonymous_variant	4858			U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.1389C>T	19.37:g.46443211G>A			51135051	O43267|Q9UEA1	Silent	SNP	ENST00000263257.5	37	CCDS12679.1																																																																																				0.647	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		A	46443211	G	A	46443211	2	1	77	1	0	0	0	0	0	0	0	1	10586	1103	39	1		1	NOVA2	19	46443211	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	326337	46443211	12685772	1105	22841										
MEIS3	56917	broad.mit.edu	37	chr19	47910191	47910191	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcgtctcggtatagcccccGatgggctggccctctgggct	14	14	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:47910191G>A	ENST00000558555.1	-	11	1219	c.1032C>T	c.(1030-1032)atC>atT	p.I344I	MEIS3_ENST00000331559.5_Silent_p.I373I|MEIS3_ENST00000561293.1_Silent_p.I390I|MEIS3_ENST00000441740.2_Silent_p.I327I|MEIS3_ENST00000560253.1_5'UTR|MEIS3_ENST00000559524.1_Silent_p.I390I|MEIS3_ENST00000561096.1_Silent_p.I432I			Q99687	MEIS3_HUMAN	Meis homeobox 3	344					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.I390I(1)		breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		TATAGCCCCCGATGGGCTGGC	0.706																																																1	Substitution - coding silent(1)	large_intestine(1)	19											39	21	27					19																	47910191		2192	4289	6481	52602003	SO:0001819	synonymous_variant	56917			BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"Homeoboxes / TALE class"	29537	protein-coding gene	gene with protein product			"Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.1032C>T	19.37:g.47910191G>A			52602003	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	37																																																																																					0.706	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929		A	47910191	G	A	47910191	2	1	77	1	0	0	0	0	0	0	0	1	9499	1048	37	1		1	MEIS3	19	47910191	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1466980	47910191	11218792	1106	22842										
PLA2G4C	8605	broad.mit.edu	37	chr19	48608677	48608677	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gccttttcttctttctggagCccaggaattatggaaacttc	8	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:48608677C>T	ENST00000599921.1	-	3	390	c.33G>A	c.(31-33)ggG>ggA	p.G11G	PLA2G4C_ENST00000354276.3_Silent_p.G11G|PLA2G4C_ENST00000599111.1_Intron|PLA2G4C_ENST00000413144.2_Silent_p.G11G			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	11	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)	p.G11G(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		CTTTCTGGAGCCCAGGAATTA	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	19											78	91	86					19																	48608677		2203	4300	6503	53300489	SO:0001819	synonymous_variant	8605			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.33G>A	19.37:g.48608677C>T			53300489	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																				0.453	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			T	48608677	C	T	48608677	2	4	77	1	0	0	0	0	0	0	0	1	12034	726	26	3		3	PLA2G4C	19	48608677	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	698486	48608677	10520306	1107	22843										
IZUMO1	284359	broad.mit.edu	37	chr19	49247763	49247763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aggtttccttttgcaagtgcAacatccaaaatagctccttc	6	11	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:49247763A>G	ENST00000332955.2	-	4	891	c.344T>C	c.(343-345)tTg>tCg	p.L115S		NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	115					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.L115S(1)		endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTGCAAGTGCAACATCCAAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	19											121	108	112					19																	49247763		2203	4300	6503	53939575	SO:0001583	missense	284359			BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"-"	28539	protein-coding gene	gene with protein product	"oocyte binding/fusion factor"	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.344T>C	19.37:g.49247763A>G	ENSP00000327786:p.Leu115Ser		53939575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287258	0.59867	.	.	ENSG00000182264	ENST00000332955	T	0.24350	1.86	5.21	5.21	0.72293	.	0.297589	0.21337	N	0.076197	T	0.45538	0.1347	L	0.58101	1.795	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.34354	-0.9832	10	0.87932	D	0	-17.0681	11.7745	0.51977	1.0:0.0:0.0:0.0	.	115	Q8IYV9	IZUM1_HUMAN	S	115	ENSP00000327786:L115S	ENSP00000327786:L115S	L	-	2	0	IZUMO1	53939575	0.037000	0.19845	0.077000	0.20336	0.060000	0.15804	4.180000	0.58296	2.094000	0.63399	0.459000	0.35465	TTG		0.502	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		G	49247763	A	G	49247763	3	3	77	1	0	0	0	0	1	0	0	0	7954	131	5	4	736	4	IZUMO1	19	49247763	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	639086	49247763	9881220	1108	22844										
PPP1R15A	23645	broad.mit.edu	37	chr19	49377231	49377231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaggagccaggaagacctcCgtgtccccccgatcttcagg	11	14	2	1	rs141730546	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:49377231C>T	ENST00000200453.5	+	2	1010	c.741C>T	c.(739-741)tcC>tcT	p.S247S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	247	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)	p.S247S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GGAAGACCTCCGTGTCCCCCC	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	19											61	73	69					19																	49377231		2203	4300	6503	54069043	SO:0001819	synonymous_variant	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.741C>T	19.37:g.49377231C>T			54069043	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																				0.557	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		T	49377231	C	T	49377231	2	4	77	1	0	0	0	0	0	0	0	1	12397	639	23	1		1	PPP1R15A	19	49377231	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	129468	49377231	9751752	1109	22845										
TULP2	7288	broad.mit.edu	37	chr19	49391412	49391412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcctcatatggtcgctgtccGtgccaccctcgcctttcagg	10	16	2	0	rs139008587	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:49391412G>A	ENST00000221399.3	-	8	887	c.743C>T	c.(742-744)aCg>aTg	p.T248M		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	248					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.T248M(1)		NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GTCGCTGTCCGTGCCACCCTC	0.607													G|||	2	0.000399361	8e-04	0	5008	,	,		19309	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	97	64	75		743	-2.5	0	19	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TULP2	NM_003323.2	81	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	248/521	49391412	2,13004	2203	4300	6503	54083224	SO:0001583	missense	7288			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.743C>T	19.37:g.49391412G>A	ENSP00000221399:p.Thr248Met		54083224	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	12.56	1.973841	0.34848	2.27E-4	1.16E-4	ENSG00000104804	ENST00000221399;ENST00000518572	D;T	0.83506	-1.73;2.17	4.03	-2.54	0.06307	.	9.154460	0.00166	N	0.000007	T	0.69324	0.3098	N	0.14661	0.345	0.09310	N	1	D	0.60160	0.987	P	0.46049	0.502	T	0.62062	-0.6933	10	0.45353	T	0.12	7.382	0.3462	0.00341	0.3113:0.1505:0.3112:0.227	.	248	O00295	TULP2_HUMAN	M	248;202	ENSP00000221399:T248M;ENSP00000428420:T202M	ENSP00000221399:T248M	T	-	2	0	TULP2	54083224	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.236000	0.09003	-0.325000	0.08577	-0.261000	0.10672	ACG		0.607	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		A	49391412	G	A	49391412	3	1	77	1	0	0	0	0	1	0	0	0	16814	1145	40	1	843	1	TULP2	19	49391412	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	14181	49391412	9737571	1110	22846										
IRF3	3661	broad.mit.edu	37	chr19	50166695	50166695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttgcggttgagggcagagCggaaattcctcttccaggtt	13	9	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50166695C>T	ENST00000597198.1	-	3	623	c.242G>A	c.(241-243)cGc>cAc	p.R81H	IRF3_ENST00000596765.1_Intron|IRF3_ENST00000309877.7_Missense_Mutation_p.R81H|BCL2L12_ENST00000441864.2_5'Flank|IRF3_ENST00000600911.1_Missense_Mutation_p.R81H|IRF3_ENST00000596822.1_5'UTR|IRF3_ENST00000599680.1_5'Flank|IRF3_ENST00000599223.1_Missense_Mutation_p.R81H|IRF3_ENST00000598808.1_5'UTR|IRF3_ENST00000377135.4_Missense_Mutation_p.R81H|IRF3_ENST00000593922.1_5'UTR|BCL2L12_ENST00000246785.3_5'Flank|IRF3_ENST00000601291.1_Missense_Mutation_p.R81H|IRF3_ENST00000377139.3_Missense_Mutation_p.R81H|IRF3_ENST00000599144.1_Intron|IRF3_ENST00000600022.1_5'UTR|IRF3_ENST00000442265.2_Intron|BCL2L12_ENST00000246784.3_5'Flank			Q14653	IRF3_HUMAN	interferon regulatory factor 3	81					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dsRNA (GO:0071359)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage apoptotic process (GO:0071888)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of interferon-beta biosynthetic process (GO:0045358)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|programmed necrotic cell death (GO:0097300)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.R81H(1)		breast(1)|large_intestine(2)|lung(4)|ovary(2)|stomach(1)	10		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)		GAGGGCAGAGCGGAAATTCCT	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	19											65	58	61					19																	50166695		2203	4300	6503	54858507	SO:0001583	missense	3661				CCDS12775.1, CCDS56099.1, CCDS59407.1, CCDS59408.1, CCDS59409.1	19q13.3-q13.4	2008-07-16				ENSG00000126456			6118	protein-coding gene	gene with protein product		603734				8524823	Standard	NM_001571		Approved		uc002pow.3	Q14653		ENST00000597198.1:c.242G>A	19.37:g.50166695C>T	ENSP00000469113:p.Arg81His		54858507	A8K7L2|B2RAZ3|Q5FBY1|Q5FBY2|Q5FBY4|Q7Z5G6	Missense_Mutation	SNP	ENST00000597198.1	37	CCDS12775.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453716	0.84209	.	.	ENSG00000126456	ENST00000377139;ENST00000309877;ENST00000377135	D;D;D	0.98585	-5.01;-5.01;-5.01	4.92	4.92	0.64577	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.99155	0.9708	M	0.92784	3.345	0.80722	D	1	D;D;D;P;D	0.89917	0.987;0.994;0.994;0.953;1.0	P;P;P;B;D	0.91635	0.551;0.47;0.47;0.215;0.999	D	0.99239	1.0884	10	0.87932	D	0	-26.1128	15.961	0.79930	0.0:1.0:0.0:0.0	.	81;81;81;81;81	B2RAZ3;Q96GL3;Q7Z5G6;Q14653;Q5FBY1	.;.;.;IRF3_HUMAN;.	H	81	ENSP00000366344:R81H;ENSP00000310127:R81H;ENSP00000366339:R81H	ENSP00000310127:R81H	R	-	2	0	IRF3	54858507	1.000000	0.71417	0.853000	0.33588	0.543000	0.35085	4.269000	0.58890	2.451000	0.82905	0.655000	0.94253	CGC		0.567	IRF3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465962.1	NM_001571		T	50166695	C	T	50166695	3	4	77	1	0	0	0	0	1	0	0	0	7852	768	27	1	1065	1	IRF3	19	50166695	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	775283	50166695	8962288	1111	22847										
BCL2L12	83596	broad.mit.edu	37	chr19	50170355	50170356	+	Frame_Shift_Ins	INS	-	-	C													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctccctggggcgaggagcagINSccccctctgagtcccctcgg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50170355_50170356insC	ENST00000246785.3	+	3	697_698	c.439_440insC	c.(439-441)gccfs	p.A147fs	IRF3_ENST00000596765.1_5'Flank|IRF3_ENST00000309877.7_5'Flank|BCL2L12_ENST00000441864.2_Frame_Shift_Ins_p.A146fs|IRF3_ENST00000600911.1_5'Flank|IRF3_ENST00000596822.1_5'Flank|IRF3_ENST00000599223.1_5'Flank|IRF3_ENST00000598808.1_5'Flank|IRF3_ENST00000377135.4_5'Flank|IRF3_ENST00000593922.1_5'Flank|IRF3_ENST00000601291.1_5'Flank|IRF3_ENST00000377139.3_5'Flank|IRF3_ENST00000599144.1_5'Flank|IRF3_ENST00000600022.1_5'Flank|IRF3_ENST00000597198.1_5'Flank|IRF3_ENST00000442265.2_5'Flank|BCL2L12_ENST00000246784.3_Intron	NM_001040668.1|NM_138639.1	NP_001035758.1|NP_619580.1	Q9HB09	B2L12_HUMAN	BCL2-like 12 (proline rich)	147					inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)		p.S149fs*2(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	8		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)		GCGAGGAGCAGCCCCCTCTGAG	0.584																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								54862168	SO:0001589	frameshift_variant	83596			AF289220	CCDS12776.1, CCDS46144.1, CCDS74424.1, CCDS74423.1	19q13.3	2014-03-07				ENSG00000126453			13787	protein-coding gene	gene with protein product		610837					Standard	NM_001040668		Approved		uc002ppa.3	Q9HB09		ENST00000246785.3:c.444dupC	19.37:g.50170360_50170360dupC	ENSP00000246785:p.Ala147fs		54862167	Q3SY11|Q3SY13|Q96I96|Q9HB08	Frame_Shift_Ins	INS	ENST00000246785.3	37	CCDS12776.1																																																																																				0.584	BCL2L12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465770.1	NM_052842		C	50170356	-	C	50170355	7	5	77	1	0	1	1	0	0	0	0	0	1371	971	34	0	449	0	BCL2L12	19	50170355	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	3660	50170355	8958628	1112	22848										
PNKP	11284	broad.mit.edu	37	chr19	50365835	50365835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtctttcttcttccgccccGgggcccagttggccgggcgt	13	15	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50365835G>A	ENST00000322344.3	-	10	1005	c.896C>T	c.(895-897)cCg>cTg	p.P299L	PNKP_ENST00000596014.1_Missense_Mutation_p.P299L|PNKP_ENST00000600573.1_Missense_Mutation_p.P299L|AC018766.4_ENST00000596624.1_RNA|PNKP_ENST00000600910.1_Missense_Mutation_p.P299L	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	299	Phosphatase. {ECO:0000250}.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)	p.P299L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		CTTCCGCCCCGGGGCCCAGTT	0.716								Other BER factors																																								1	Substitution - Missense(1)	large_intestine(1)	19											16	19	18					19																	50365835		2197	4290	6487	55057647	SO:0001583	missense	11284			AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.896C>T	19.37:g.50365835G>A	ENSP00000323511:p.Pro299Leu		55057647	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	37	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	G	35	5.529552	0.96446	.	.	ENSG00000039650	ENST00000322344	T	0.63913	-0.07	5.15	5.15	0.70609	HAD-like domain (2);Polynucleotide kinase 3 phosphatase, central region (1);	0.138776	0.48767	D	0.000165	T	0.78413	0.4279	M	0.85859	2.78	0.80722	D	1	D;D	0.69078	0.97;0.997	P;P	0.61328	0.458;0.887	T	0.81373	-0.0962	10	0.54805	T	0.06	-16.1878	14.1076	0.65101	0.0:0.0:1.0:0.0	.	260;299	Q9BUL2;Q96T60	.;PNKP_HUMAN	L	299	ENSP00000323511:P299L	ENSP00000323511:P299L	P	-	2	0	PNKP	55057647	1.000000	0.71417	0.941000	0.38009	0.917000	0.54804	6.156000	0.71840	2.395000	0.81488	0.561000	0.74099	CCG		0.716	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		A	50365835	G	A	50365835	3	1	77	1	0	0	0	0	1	0	0	0	12178	1116	39	1	701	1	PNKP	19	50365835	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	195480	50365835	8763148	1113	22849										
IL4I1	259307	broad.mit.edu	37	chr19	50394348	50394349	+	Frame_Shift_Ins	INS	-	-	C													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggccggctcaggttcccctINSccccgagaagatattcctgc							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50394348_50394349insC	ENST00000391826.2	-	7	794_795	c.652_653insG	c.(652-654)gagfs	p.E218fs	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Frame_Shift_Ins_p.E240fs|IL4I1_ENST00000341114.3_Frame_Shift_Ins_p.E240fs	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	218						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)	p.E240fs*153(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	CAGGTTCCCCTCCCCGAGAAGA	0.673																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								55086161	SO:0001589	frameshift_variant	259307			AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.653dupG	19.37:g.50394352_50394352dupC	ENSP00000375702:p.Glu218fs		55086160	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Frame_Shift_Ins	INS	ENST00000391826.2	37	CCDS12787.1																																																																																				0.673	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			C	50394349	-	C	50394348	7	5	77	1	0	1	1	0	0	0	0	0	7718	1551	54	0	1058	0	IL4I1	19	50394348	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	28513	50394348	8734635	1114	22850										
MYH14	79784	broad.mit.edu	37	chr19	50758572	50758572	+	Intron	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctctgctatttctccgccaGggggtgggtgtctctgtgca					rs75915336	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50758572delG	ENST00000596571.1	+	15	1921				MYH14_ENST00000440075.2_Frame_Shift_Del_p.G681fs|MYH14_ENST00000262269.8_Frame_Shift_Del_p.G681fs|MYH14_ENST00000425460.1_Intron|MYH14_ENST00000376970.2_Frame_Shift_Del_p.G673fs|MYH14_ENST00000601313.1_Frame_Shift_Del_p.G681fs|MYH14_ENST00000598205.1_Intron			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle						actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.V682fs*10(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TTCTCCGCCAGGGGGTGGGTG	0.607																																																1	Deletion - Frameshift(1)	large_intestine(1)	19											55	51	52					19																	50758572		692	1591	2283	55450384	SO:0001627	intron_variant	79784			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.1922-1984G>-	19.37:g.50758572delG			55450384	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Frame_Shift_Del	DEL	ENST00000596571.1	37	CCDS59411.1																																																																																				0.607	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		-	50758572	G	-	50758572	6	5	77	0	1	1	0	1	0	0	0	0	10063	1000	35	0		0	MYH14	19	50758572	Intron	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	364224	50758572	8370411	1115	22851										
SPIB	6689	broad.mit.edu	37	chr19	50926876	50926876	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgcagaccctggttcccccGgcatatgccccgtaccccag	9	20	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:50926876G>A	ENST00000595883.1	+	5	379	c.354G>A	c.(352-354)ccG>ccA	p.P118P	SPIB_ENST00000596074.1_Missense_Mutation_p.G47S|SPIB_ENST00000597855.1_Intron|SPIB_ENST00000270632.7_Silent_p.P118P|CTD-2545M3.6_ENST00000599632.1_Missense_Mutation_p.G253S|SPIB_ENST00000439922.2_Silent_p.P27P	NM_001243999.1|NM_001244000.1|NM_003121.4	NP_001230928.1|NP_001230929.1|NP_003112.2	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	118					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P118P(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)	14		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		TGGTTCCCCCGGCATATGCCC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	19											59	49	53					19																	50926876		2203	4300	6503	55618688	SO:0001819	synonymous_variant	6689				CCDS33080.1, CCDS58674.1, CCDS59412.1	19q13.3-q13.4	2008-07-22				ENSG00000269404			11242	protein-coding gene	gene with protein product		606802				1406622	Standard	NM_003121		Approved	SPI-B	uc002psd.3	Q01892		ENST00000595883.1:c.354G>A	19.37:g.50926876G>A			55618688	A8K9C9|B4DUG6|Q15359	Silent	SNP	ENST00000595883.1	37	CCDS33080.1																																																																																				0.647	SPIB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464744.1	NM_003121		A	50926876	G	A	50926876	2	1	77	1	0	0	0	0	0	0	0	1	15089	1103	39	1		1	SPIB	19	50926876	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	168304	50926876	8202107	1116	22852										
SYT3	84258	broad.mit.edu	37	chr19	51128548	51128548	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgatcacctcgttgtgcccGatgctgggggttggggtcag	16	11	2	0	rs533895555		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:51128548G>A	ENST00000338916.4	-	7	2211	c.1578C>T	c.(1576-1578)atC>atT	p.I526I	SYT3_ENST00000593901.1_Silent_p.I526I|SYT3_ENST00000544769.1_Silent_p.I526I|SYT3_ENST00000600079.1_Silent_p.I526I	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	526	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.I526I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		CGTTGTGCCCGATGCTGGGGG	0.736													G|||	1	0.000199681	0	0	5008	,	,		11965	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	19											11	11	11					19																	51128548		2151	4160	6311	55820360	SO:0001819	synonymous_variant	84258			AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1578C>T	19.37:g.51128548G>A			55820360	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																				0.736	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51128548	G	A	51128548	2	1	77	1	0	0	0	0	0	0	0	1	15514	1048	37	1		1	SYT3	19	51128548	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	201672	51128548	8000435	1117	22853										
SHANK1	50944	broad.mit.edu	37	chr19	51175305	51175305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttgccggagcatcaacccagGtcctggaggcaggaaagaag	14	10	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:51175305G>A	ENST00000293441.1	-	21	2662	c.2644C>T	c.(2644-2646)Cct>Tct	p.P882S	SHANK1_ENST00000391814.1_Missense_Mutation_p.P890S|SHANK1_ENST00000391813.1_Missense_Mutation_p.P269S|SHANK1_ENST00000359082.3_Missense_Mutation_p.P873S	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	882					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)	p.P882S(1)		breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		ATCAACCCAGGTCCTGGAGGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	91	97					19																	51175305		2203	4300	6503	55867117	SO:0001583	missense	50944			AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.2644C>T	19.37:g.51175305G>A	ENSP00000293441:p.Pro882Ser		55867117	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181707	0.57800	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.38722	1.24;1.64;1.22;1.12	3.87	3.87	0.44632	.	1.972760	0.04376	N	0.359926	T	0.43322	0.1242	L	0.47190	1.495	0.39149	D	0.962181	P;P	0.47253	0.507;0.892	B;B	0.44224	0.116;0.444	T	0.48833	-0.9000	10	0.08381	T	0.77	-2.5979	15.1098	0.72346	0.0:0.0:1.0:0.0	.	882;269	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	S	882;269;873;890	ENSP00000293441:P882S;ENSP00000375689:P269S;ENSP00000351984:P873S;ENSP00000375690:P890S	ENSP00000293441:P882S	P	-	1	0	SHANK1	55867117	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.752000	0.55172	2.161000	0.67846	0.491000	0.48974	CCT		0.577	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51175305	G	A	51175305	3	1	77	1	0	0	0	0	1	0	0	0	14301	1261	44	3	3853	3	SHANK1	19	51175305	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	46757	51175305	7953678	1118	22854										
SIGLEC10	89790	broad.mit.edu	37	chr19	51919928	51919928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccacactcacaggccacaCggagtcggacggtcctctgt	12	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:51919928C>T	ENST00000339313.5	-	3	814	c.698G>A	c.(697-699)cGt>cAt	p.R233H	SIGLEC10_ENST00000356298.5_Missense_Mutation_p.R233H|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.R233H|SIGLEC10_ENST00000442846.3_Missense_Mutation_p.R175H|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.R150H|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.R175H|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.R233H|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.R175H|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.R185H|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	233					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R233H(1)|p.R175H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		ACAGGCCACACGGAGTCGGAC	0.662																																																2	Substitution - Missense(2)	large_intestine(2)	19											91	74	80					19																	51919928		2203	4300	6503	56611740	SO:0001583	missense	89790			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.698G>A	19.37:g.51919928C>T	ENSP00000345243:p.Arg233His		56611740	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	12.22	1.872762	0.33069	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;D;T;D;T;D;D;T;D	0.86230	1.05;2.18;-2.09;0.9;-2.09;1.91;-2.09;-2.09;0.9;-2.09	4.69	-2.31	0.06765	Immunoglobulin-like fold (1);	1.498280	0.03589	N	0.231483	T	0.77219	0.4098	L	0.28192	0.835	0.09310	N	1	B;B;B;B;B;B;B	0.33494	0.035;0.414;0.099;0.103;0.058;0.028;0.036	B;B;B;B;B;B;B	0.25405	0.016;0.034;0.031;0.035;0.06;0.013;0.011	T	0.65401	-0.6177	10	0.41790	T	0.15	.	8.438	0.32799	0.0:0.3321:0.0:0.6679	.	185;233;175;233;175;175;233	C9JM10;E9PL79;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	H	233;150;175;233;175;233;175;185;233;47	ENSP00000342389:R233H;ENSP00000396742:R150H;ENSP00000395475:R175H;ENSP00000348646:R233H;ENSP00000408387:R175H;ENSP00000431444:R233H;ENSP00000389132:R175H;ENSP00000414324:R185H;ENSP00000345243:R233H;ENSP00000435281:R47H	ENSP00000345243:R233H	R	-	2	0	SIGLEC10	56611740	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.683000	0.05179	-0.268000	0.09312	-0.657000	0.03884	CGT		0.662	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		T	51919928	C	T	51919928	3	4	77	1	0	0	0	0	1	0	0	0	14343	536	19	1	1431	1	SIGLEC10	19	51919928	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	744623	51919928	7209055	1119	22855										
ZNF528	84436	broad.mit.edu	37	chr19	52919045	52919045	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atcaaattgcacaccttgtaCgacatcaaaaaattcatact	3	10	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:52919045C>T	ENST00000360465.3	+	7	1366	c.940C>T	c.(940-942)Cga>Tga	p.R314*	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R314*(1)		breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		ACACCTTGTACGACATCAAAA	0.378																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											54	57	56					19																	52919045		2203	4300	6503	57610857	SO:0001587	stop_gained	84436			AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.940C>T	19.37:g.52919045C>T	ENSP00000353652:p.Arg314*		57610857	B3KPN4|Q86T88|Q96JK0	Nonsense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208671	0.95069	.	.	ENSG00000167555	ENST00000360465	.	.	.	1.85	-0.971	0.10303	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	3.5391	0.07804	0.4448:0.2597:0.2955:0.0	.	.	.	.	X	314	.	ENSP00000353652:R314X	R	+	1	2	ZNF528	57610857	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-2.828000	0.00745	-0.086000	0.12550	0.491000	0.48974	CGA		0.378	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		T	52919045	C	T	52919045	4	4	77	1	0	0	0	0	0	1	0	0	18008	528	19	1	954	1	ZNF528	19	52919045	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	999117	52919045	6209938	1120	22856										
ZNF468	90333	broad.mit.edu	37	chr19	53344762	53344762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctcaccagtgtgacatctaCgatggcaggcaaggtatcgc	11	11	2	1	rs372954739		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:53344762C>T	ENST00000595646.1	-	4	905	c.785G>A	c.(784-786)cGt>cAt	p.R262H	ZNF468_ENST00000390651.4_Missense_Mutation_p.R209H|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Missense_Mutation_p.R209H			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R262H(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		GTGACATCTACGATGGCAGGC	0.393																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	127	113	117		785,626	0.6	0	19		117	1,8599	818.7+/-406.8	0,1,4299	no	missense,missense	ZNF468	NM_001008801.1,NM_199132.1	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	262/523,209/470	53344762	1,13005	2203	4300	6503	58036574	SO:0001583	missense	90333			AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"Zinc fingers, C2H2-type", "-"	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.785G>A	19.37:g.53344762C>T	ENSP00000470381:p.Arg262His		58036574	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	t	7.001	0.554846	0.13436	0.0	1.16E-4	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651;ENST00000393865	T;T	0.07688	3.17;3.17	1.94	0.647	0.17796	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06005	0.0156	L	0.41415	1.275	0.09310	N	1	B	0.24882	0.113	B	0.10450	0.005	T	0.39354	-0.9618	9	0.36615	T	0.2	.	2.6819	0.05096	0.0:0.2445:0.2537:0.5018	.	262	Q5VIY5	ZN468_HUMAN	H	262;209;209;12	ENSP00000379690:R209H;ENSP00000445669:R209H	ENSP00000243639:R262H	R	-	2	0	ZNF468	58036574	0.000000	0.05858	0.004000	0.12327	0.288000	0.27193	-0.984000	0.03755	-0.038000	0.13624	0.174000	0.16983	CGT		0.393	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		T	53344762	C	T	53344762	3	4	77	1	0	0	0	0	1	0	0	0	17967	536	19	1	787	1	ZNF468	19	53344762	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	425717	53344762	5784221	1121	22857										
ZNF321	399669	broad.mit.edu	37	chr19	53432625	53432625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcacttctgtattgccttgcGctgtggatgagaactccttc	9	11	2	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:53432625G>A	ENST00000391777.3	-	4	354	c.233C>T	c.(232-234)gCg>gTg	p.A78V	ZNF816_ENST00000549216.1_Missense_Mutation_p.A9V|ZNF816-ZNF321P_ENST00000313956.4_RNA|ZNF816_ENST00000434371.2_Missense_Mutation_p.A78V			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	9								p.A9G(1)|p.A9V(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						ATTGCCTTGCGCTGTGGATGA	0.353																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	19											117	124	121					19																	53432625		2202	4298	6500	58124437	SO:0001583	missense	399669			AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.233C>T	19.37:g.53432625G>A	ENSP00000375656:p.Ala78Val		58124437	B7ZB38|Q68DZ0|Q86SS5	Missense_Mutation	SNP	ENST00000391777.3	37	CCDS56101.1	.	.	.	.	.	.	.	.	.	.	c	14.81	2.645407	0.47258	.	.	ENSG00000180257;ENSG00000180257;ENSG00000221874	ENST00000549216;ENST00000434371;ENST00000391777	T;T;T	0.01838	4.61;5.77;5.77	1.5	-3.01	0.05463	.	.	.	.	.	T	0.01661	0.0053	N	0.24115	0.695	0.09310	N	1	P	0.41597	0.756	B	0.43194	0.411	T	0.25916	-1.0118	9	0.30078	T	0.28	.	1.2856	0.02049	0.1543:0.3353:0.3112:0.1991	.	9	Q8N8H1	ZN321_HUMAN	V	9;78;78	ENSP00000449832:A9V;ENSP00000438519:A78V;ENSP00000375656:A78V	ENSP00000375656:A78V	A	-	2	0	ZNF321P;ZNF816	58124437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.687000	0.05156	-2.078000	0.00872	-1.824000	0.00597	GCG		0.353	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		A	53432625	G	A	53432625	3	1	77	1	0	0	0	0	1	0	0	0	17879	1087	38	1	472	1	ZNF321	19	53432625	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	87863	53432625	5696358	1122	22858										
ZNF665	79788	broad.mit.edu	37	chr19	53668755	53668755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgggtagtcaggcttgagcGaacactaaaggctttgccac	12	9	1	1	rs370811178		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:53668755G>A	ENST00000600412.1	-	2	908	c.793C>T	c.(793-795)Cgc>Tgc	p.R265C	ZNF665_ENST00000396424.3_Missense_Mutation_p.R330C|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R265C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		AGGCTTGAGCGAACACTAAAG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	CYS/ARG	0,4406		0,0,2203	118	123	121		988	-4.5	0	19		121	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF665	NM_024733.3	180	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	330/679	53668755	1,13003	2203	4299	6502	58360567	SO:0001583	missense	79788				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.793C>T	19.37:g.53668755G>A	ENSP00000469154:p.Arg265Cys		58360567	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	G	8.649	0.897719	0.17686	0.0	1.16E-4	ENSG00000197497	ENST00000396424	T	0.01034	5.42	2.26	-4.52	0.03472	.	.	.	.	.	T	0.01940	0.0061	L	0.45051	1.395	0.09310	N	1	D	0.89917	1.0	D	0.65140	0.932	T	0.05801	-1.0863	9	0.35671	T	0.21	.	5.02	0.14356	0.1154:0.0925:0.5855:0.2067	.	330	Q9H7R5-2	.	C	330	ENSP00000379702:R330C	ENSP00000379702:R330C	R	-	1	0	ZNF665	58360567	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.287000	0.00072	-3.532000	0.00145	-0.694000	0.03704	CGC		0.428	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53668755	G	A	53668755	3	1	77	1	0	0	0	0	1	0	0	0	18112	1058	37	1	1052	1	ZNF665	19	53668755	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	236130	53668755	5460228	1123	22859										
NLRP12	91662	broad.mit.edu	37	chr19	54313911	54313911	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgatgagcaaagatagctcAgggagcagcttcttccgaat	12	8	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:54313911A>G	ENST00000324134.6	-	3	1170	c.1002T>C	c.(1000-1002)ccT>ccC	p.P334P	NLRP12_ENST00000345770.5_Silent_p.P334P|NLRP12_ENST00000391773.1_Silent_p.P334P|NLRP12_ENST00000535162.1_Silent_p.P334P|NLRP12_ENST00000391772.1_Silent_p.P334P|NLRP12_ENST00000354278.3_Silent_p.P334P|NLRP12_ENST00000351894.4_Silent_p.P334P|NLRP12_ENST00000391775.3_Silent_p.P334P	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	334	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.P334P(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AAGATAGCTCAGGGAGCAGCT	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	19											65	69	68					19																	54313911		2203	4300	6503	59005723	SO:0001819	synonymous_variant	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.1002T>C	19.37:g.54313911A>G			59005723	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																				0.582	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		G	54313911	A	G	54313911	2	3	77	1	0	0	0	0	0	0	0	1	10505	175	7	4		4	NLRP12	19	54313911	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	645156	54313911	4815072	1124	22860										
PRKCG	5582	broad.mit.edu	37	chr19	54401305	54401305	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcttcggggcgagtccaggAcgcctgcacatctccgactt	11	14	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:54401305A>G	ENST00000263431.3	+	10	1314	c.1032A>G	c.(1030-1032)ggA>ggG	p.G344G	PRKCG_ENST00000536044.1_Missense_Mutation_p.D315G|PRKCG_ENST00000542049.1_Silent_p.G231G|PRKCG_ENST00000540413.1_Silent_p.G344G	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	344					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.G344G(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CGAGTCCAGGACGCCTGCACA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	19											53	52	52					19																	54401305		2203	4300	6503	59093117	SO:0001819	synonymous_variant	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1032A>G	19.37:g.54401305A>G			59093117	B7Z8Q0	Silent	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.769767	0.49680	.	.	ENSG00000126583	ENST00000536044	T	0.78003	-1.14	5.14	-1.92	0.07618	.	.	.	.	.	T	0.57198	0.2037	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30851	-0.9964	7	.	.	.	.	5.1236	0.14873	0.3411:0.3738:0.2851:0.0	.	315	B7Z870	.	G	315	ENSP00000440541:D315G	.	D	+	2	0	PRKCG	59093117	0.817000	0.29147	0.976000	0.42696	0.778000	0.44026	0.041000	0.13927	-0.174000	0.10743	0.397000	0.26171	GAC		0.607	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		G	54401305	A	G	54401305	2	3	77	1	0	0	0	0	0	0	0	1	12546	262	10	4		4	PRKCG	19	54401305	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	87394	54401305	4727678	1125	22861										
TTYH1	57348	broad.mit.edu	37	chr19	54930463	54930463	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtcacctggagctgcattgtCgcccttctcgccggctggta	12	14	2	0	rs142265106	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:54930463C>T	ENST00000376530.3	+	2	391	c.288C>T	c.(286-288)gtC>gtT	p.V96V	TTYH1_ENST00000376531.3_Silent_p.V96V|TTYH1_ENST00000391739.3_Silent_p.V145V|TTYH1_ENST00000301194.4_Silent_p.V96V	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	96					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.V96V(3)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		GCTGCATTGTCGCCCTTCTCG	0.711																																																3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	19											18	22	21					19																	54930463		2196	4289	6485	59622275	SO:0001819	synonymous_variant	57348			AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.288C>T	19.37:g.54930463C>T			59622275	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Silent	SNP	ENST00000376530.3	37	CCDS12893.1																																																																																				0.711	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			T	54930463	C	T	54930463	2	4	77	1	0	0	0	0	0	0	0	1	16779	871	31	1		1	TTYH1	19	54930463	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	529158	54930463	4198520	1126	22862										
CCDC106	29903	broad.mit.edu	37	chr19	56160579	56160579	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctcctctccagtgaaggacGatgagaccttcgagatctcc	9	13	3	3	rs374002589		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:56160579G>A	ENST00000586790.1	+	2	944	c.40G>A	c.(40-42)Gat>Aat	p.D14N	CCDC106_ENST00000588740.1_Missense_Mutation_p.D14N|CCDC106_ENST00000591241.1_Intron|CCDC106_ENST00000591578.1_Missense_Mutation_p.D14N|CCDC106_ENST00000308964.3_Missense_Mutation_p.D14N			Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106	14						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.D14N(1)		endometrium(2)|large_intestine(3)|lung(5)|skin(1)	11		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		AGTGAAGGACGATGAGACCTT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19						G	ASN/ASP	0,4406		0,0,2203	95	96	96		40	-0.1	0.7	19		96	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCDC106	NM_013301.2	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	14/281	56160579	1,13005	2203	4300	6503	60852391	SO:0001583	missense	29903			AF054984	CCDS33118.1	19q13.42	2013-09-20			ENSG00000173581	ENSG00000173581			30181	protein-coding gene	gene with protein product		613478				8619474, 9110174	Standard	XM_005258827		Approved	HSU79303	uc002qlr.3	Q9BWC9	OTTHUMG00000180907	ENST00000586790.1:c.40G>A	19.37:g.56160579G>A	ENSP00000465757:p.Asp14Asn		60852391	B3KUF9|D3K183|Q99786	Missense_Mutation	SNP	ENST00000586790.1	37	CCDS33118.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853734	0.32791	0.0	1.16E-4	ENSG00000173581	ENST00000308964	.	.	.	3.5	-0.12	0.13539	.	0.581171	0.16520	N	0.210853	T	0.23572	0.0570	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04454	-1.0950	9	0.22109	T	0.4	-28.613	2.9816	0.05955	0.2406:0.0:0.5473:0.2122	.	14	Q9BWC9	CC106_HUMAN	N	14	.	ENSP00000309681:D14N	D	+	1	0	CCDC106	60852391	1.000000	0.71417	0.739000	0.30968	0.912000	0.54170	2.893000	0.48633	-0.019000	0.14055	0.561000	0.74099	GAT		0.612	CCDC106-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453593.1	NM_013301		A	56160579	G	A	56160579	3	1	77	1	0	0	0	0	1	0	0	0	2747	1058	37	1	46	1	CCDC106	19	56160579	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1230116	56160579	2968404	1127	22863										
NLRP4	147945	broad.mit.edu	37	chr19	56369923	56369923	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgagggtgccgagggcccGactccgcaaacccagcacca	12	17	0	1	rs370158529		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:56369923G>A	ENST00000301295.6	+	3	1586	c.1164G>A	c.(1162-1164)ccG>ccA	p.P388P	NLRP4_ENST00000346986.5_Silent_p.P388P|NLRP4_ENST00000587891.1_Silent_p.P313P	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	388	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.P388P(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CCGAGGGCCCGACTCCGCAAA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	59	58	58		1164	-6.8	0	19		58	1,8599		0,1,4299	no	coding-synonymous	NLRP4	NM_134444.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		388/995	56369923	1,13005	2203	4300	6503	61061735	SO:0001819	synonymous_variant	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1164G>A	19.37:g.56369923G>A			61061735	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																				0.562	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		A	56369923	G	A	56369923	2	1	77	1	0	0	0	0	0	0	0	1	10510	1045	37	1		1	NLRP4	19	56369923	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	209344	56369923	2759060	1128	22864										
ZNF8	7554	broad.mit.edu	37	chr19	58805993	58805993	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaccataacgcacacctcacCgtgcacaagaggattcatac	6	14	2	1	rs142154798		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:58805993C>T	ENST00000196548.5	+	4	950	c.819C>T	c.(817-819)acC>acT	p.T273T	AC010642.1_ENST00000591325.1_3'UTR|ZNF8_ENST00000608843.1_Silent_p.T273T			P17098	ZNF8_HUMAN	zinc finger protein 8	273					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.T273T(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		CACACCTCACCGTGCACAAGA	0.502													C|||	1	0.000199681	0	0	5008	,	,		22312	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	19						C		3,4403	6.2+/-15.9	0,3,2200	88	83	85		819	-8	0.5	19	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	ZNF8	NM_021089.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		273/576	58805993	3,13003	2203	4300	6503	63497805	SO:0001819	synonymous_variant	7554			M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"Zinc fingers, C2H2-type", "-"	13154	protein-coding gene	gene with protein product		194532	"zinc finger protein 8 (clone HF.18)"			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.819C>T	19.37:g.58805993C>T			63497805	Q6PI99	Silent	SNP	ENST00000196548.5	37	CCDS12974.1																																																																																				0.502	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089		T	58805993	C	T	58805993	2	4	77	1	0	0	0	0	0	0	0	1	18206	639	23	1		1	ZNF8	19	58805993	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2436070	58805993	322990	1129	22865										
TRIM28	10155	broad.mit.edu	37	chr19	59061325	59061325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aatgtttgtagaaatgtgagCgtgtactgctggccctattc	11	7	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr19:59061325C>T	ENST00000253024.5	+	15	2405	c.2116C>T	c.(2116-2118)Cgt>Tgt	p.R706C	TRIM28_ENST00000341753.6_Missense_Mutation_p.R624C	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	706	Bromo.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R706C(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAAATGTGAGCGTGTACTGCT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	19											100	88	92					19																	59061325		2203	4300	6503	63753137	SO:0001583	missense	10155				CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.2116C>T	19.37:g.59061325C>T	ENSP00000253024:p.Arg706Cys		63753137	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	37	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730688	0.48939	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.44881	0.91;0.91	4.75	4.75	0.60458	Bromodomain (2);	0.182580	0.35320	N	0.003281	T	0.57036	0.2026	L	0.43923	1.385	0.49582	D	0.999808	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.972;0.986	T	0.59364	-0.7468	10	0.87932	D	0	-17.2325	15.6482	0.77070	0.0:1.0:0.0:0.0	.	624;706;706	Q13263-2;B2R8R5;Q13263	.;.;TIF1B_HUMAN	C	706;624	ENSP00000253024:R706C;ENSP00000342232:R624C	ENSP00000253024:R706C	R	+	1	0	TRIM28	63753137	0.998000	0.40836	1.000000	0.80357	0.251000	0.25915	1.833000	0.39161	2.643000	0.89663	0.443000	0.29094	CGT		0.572	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		T	59061325	C	T	59061325	3	4	77	1	0	0	0	0	1	0	0	0	16542	768	27	1	2174	1	TRIM28	19	59061325	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	255332	59061325	67658	1130	22866										
SIGLEC1	6614	broad.mit.edu	37	chr20	3677788	3677788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caccagcctcagtcaggatgCggcaggcgtaaagggcagca	14	12	2	0	rs564843501		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:3677788C>T	ENST00000344754.4	-	9	2323	c.2324G>A	c.(2323-2325)cGc>cAc	p.R775H	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.R775H	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	775	Ig-like C2-type 7.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R775H(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						AGTCAGGATGCGGCAGGCGTA	0.642													C|||	1	0.000199681	0	0.0014	5008	,	,		14324	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											62	61	61					20																	3677788		2203	4300	6503	3625788	SO:0001583	missense	6614			AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.2324G>A	20.37:g.3677788C>T	ENSP00000341141:p.Arg775His		3625788	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	C	6.241	0.412619	0.11812	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.14766	2.48;2.48	5.31	0.794	0.18638	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.831670	0.10192	N	0.704543	T	0.17577	0.0422	M	0.79475	2.455	0.09310	N	0.999992	B;B	0.14805	0.011;0.003	B;B	0.12156	0.007;0.003	T	0.24368	-1.0162	10	0.46703	T	0.11	.	7.7175	0.28712	0.0:0.6184:0.0:0.3816	.	775;775	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	H	775	ENSP00000341141:R775H;ENSP00000202578:R775H	ENSP00000202578:R775H	R	-	2	0	SIGLEC1	3625788	0.000000	0.05858	0.234000	0.24042	0.025000	0.11179	-1.231000	0.02939	0.298000	0.22638	-0.258000	0.10820	CGC		0.642	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3677788	C	T	3677788	3	4	77	1	0	0	0	0	1	0	0	0	14342	768	27	1	2857	1	SIGLEC1	20	3677788	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		3677788	59347732	1131	22867										
SIGLEC1	6614	broad.mit.edu	37	chr20	3684491	3684491	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgaagatgtggaggctgatGgggggtgagaccaaagagcc	18	6	0	5	rs373178169		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:3684491G>A	ENST00000344754.4	-	4	953	c.954C>T	c.(952-954)ccC>ccT	p.P318P	SIGLEC1_ENST00000202578.4_Silent_p.P318P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	318	Ig-like C2-type 2.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.P318P(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						GGAGGCTGATGGGGGGTGAGA	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	20						G		0,4406		0,0,2203	51	43	46		954	-10.5	0	20		46	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SIGLEC1	NM_023068.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		318/1710	3684491	1,13005	2203	4300	6503	3632491	SO:0001819	synonymous_variant	6614			AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.954C>T	20.37:g.3684491G>A			3632491	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																				0.617	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3684491	G	A	3684491	2	1	77	1	0	0	0	0	0	0	0	1	14342	1335	47	3		3	SIGLEC1	20	3684491	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	6703	3684491	59341029	1132	22868										
PROKR2	128674	broad.mit.edu	37	chr20	5282914	5282914	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagaaggcagtgaggtagtgCttttccttcacgaacacagt	11	8	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:5282914C>T	ENST00000217270.3	-	2	926	c.927G>A	c.(925-927)aaG>aaA	p.K309K	PROKR2_ENST00000546004.1_Silent_p.K309K	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	309					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.K309K(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						TGAGGTAGTGCTTTTCCTTCA	0.522										HNSCC(71;0.22)																																						1	Substitution - coding silent(1)	large_intestine(1)	20											222	163	183					20																	5282914		2203	4300	6503	5230914	SO:0001819	synonymous_variant	128674			AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"GPCR / Class A : Prokineticin receptors"	15836	protein-coding gene	gene with protein product		607123	"G protein-coupled receptor 73-like 1", "Kallmann syndrome 3 (autosomal dominant)"	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.927G>A	20.37:g.5282914C>T			5230914	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Silent	SNP	ENST00000217270.3	37	CCDS13089.1																																																																																				0.522	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		T	5282914	C	T	5282914	2	4	77	1	0	0	0	0	0	0	0	1	12587	796	28	3		3	PROKR2	20	5282914	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1598423	5282914	57742606	1133	22869										
PAK7	57144	broad.mit.edu	37	chr20	9546574	9546574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gttctcgtctctgttgcttcCggaggtccattttcttcact	8	12	4	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:9546574C>T	ENST00000378429.3	-	6	1994	c.1448G>A	c.(1447-1449)cGg>cAg	p.R483Q	PAK7_ENST00000378423.1_Missense_Mutation_p.R483Q|PAK7_ENST00000353224.5_Missense_Mutation_p.R483Q	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	483	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R483Q(2)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			CTGTTGCTTCCGGAGGTCCAT	0.438																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	20											267	248	255					20																	9546574		2203	4300	6503	9494574	SO:0001583	missense	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1448G>A	20.37:g.9546574C>T	ENSP00000367686:p.Arg483Gln		9494574	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	C	34	5.345104	0.95807	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.65916	-0.18;-0.18;-0.18	5.29	5.29	0.74685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	N	0.25485	0.75	0.80722	D	1	D;D	0.56035	0.974;0.974	P;P	0.51135	0.66;0.66	T	0.58470	-0.7631	9	.	.	.	.	18.9233	0.92534	0.0:1.0:0.0:0.0	.	483;483	B0AZM9;Q9P286	.;PAK7_HUMAN	Q	483;483;483;431	ENSP00000367686:R483Q;ENSP00000322957:R483Q;ENSP00000367679:R483Q	.	R	-	2	0	PAK7	9494574	1.000000	0.71417	0.997000	0.53966	0.955000	0.61496	7.818000	0.86416	2.452000	0.82932	0.460000	0.39030	CGG		0.438	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			T	9546574	C	T	9546574	3	4	77	1	0	0	0	0	1	0	0	0	11436	652	23	1	735	1	PAK7	20	9546574	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4263660	9546574	53478946	1134	22870										
ISM1	140862	broad.mit.edu	37	chr20	13260508	13260508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgggaccatacagccccaggCcaccggacttttgaaaccaa	9	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:13260508C>T	ENST00000262487.4	+	3	612	c.606C>T	c.(604-606)ggC>ggT	p.G202G	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	202						extracellular region (GO:0005576)		p.G202G(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						CAGCCCCAGGCCACCGGACTT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	20											41	46	45					20																	13260508		1884	4112	5996	13208508	SO:0001819	synonymous_variant	140862			AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"chromosome 20 open reading frame 82", "isthmin 1 homolog (zebrafish)"	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.606C>T	20.37:g.13260508C>T			13208508	Q8WVH9	Silent	SNP	ENST00000262487.4	37	CCDS46579.1																																																																																				0.517	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2			T	13260508	C	T	13260508	2	4	77	1	0	0	0	0	0	0	0	1	7881	726	26	3		3	ISM1	20	13260508	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3713934	13260508	49765012	1135	22871										
ESF1	51575	broad.mit.edu	37	chr20	13763275	13763275	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctgtagtatgttgaacaatgTtttttttctctttcttattt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:13763275delT	ENST00000202816.1	-	2	619	c.512delA	c.(511-513)aacfs	p.N171fs	NDUFAF5_ENST00000378106.5_5'Flank|NDUFAF5_ENST00000463598.1_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.N171fs*18(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						TTGAACAATGTTTTTTTTCTC	0.318																																																1	Deletion - Frameshift(1)	large_intestine(1)	20								16,4244		6,4,2120	44	45	45			-6.7	0	20		46	15,8227		6,3,4112	no	frameshift	ESF1	NM_016649.3		12,7,6232	A1A1,A1R,RR		0.182,0.3756,0.248			13763275	31,12471	2201	4297	6498	13711275	SO:0001589	frameshift_variant	51575				CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.512delA	20.37:g.13763275delT	ENSP00000202816:p.Asn171fs		13711275	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Del	DEL	ENST00000202816.1	37	CCDS13117.1																																																																																				0.318	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		-	13763275	T	-	13763275	7	5	77	1	0	1	0	1	0	0	0	0	5264	1725	60	0	2095	0	ESF1	20	13763275	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	502767	13763275	49262245	1136	22872										
KIF16B	55614	broad.mit.edu	37	chr20	16337027	16337027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttgcccgcagaggacgtagCgtgggatactaattttaatt	11	8	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:16337027C>T	ENST00000354981.2	-	23	3726	c.3569G>A	c.(3568-3570)cGc>cAc	p.R1190H	KIF16B_ENST00000378003.2_Intron|KIF16B_ENST00000355755.3_Missense_Mutation_p.R1190H	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1190	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.R1190H(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GAGGACGTAGCGTGGGATACT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	20											130	104	112					20																	16337027		2203	4300	6503	16285027	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3569G>A	20.37:g.16337027C>T	ENSP00000347076:p.Arg1190His		16285027	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	C	31	5.093901	0.94149	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997	T;T	0.30448	1.53;1.53	5.6	5.6	0.85130	Phox homologous domain (4);	.	.	.	.	T	0.53222	0.1783	L	0.49513	1.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.50363	-0.8837	9	0.66056	D	0.02	.	19.984	0.97341	0.0:1.0:0.0:0.0	.	1190	Q96L93	KI16B_HUMAN	H	1190;1190;1034	ENSP00000347076:R1190H;ENSP00000347995:R1190H	ENSP00000347076:R1190H	R	-	2	0	KIF16B	16285027	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.109000	0.77062	2.795000	0.96236	0.643000	0.83706	CGC		0.493	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		T	16337027	C	T	16337027	3	4	77	1	0	0	0	0	1	0	0	0	8299	768	27	1	400	1	KIF16B	20	16337027	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2573752	16337027	46688493	1137	22873										
C20orf26	26074	broad.mit.edu	37	chr20	20257861	20257861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacttacaccaccgtggagaCgctcttaaaccttggcgtga	9	12	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:20257861C>T	ENST00000245957.5	+	22	2631	c.2555C>T	c.(2554-2556)aCg>aTg	p.T852M	C20orf26_ENST00000377309.2_Missense_Mutation_p.T208M	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		852								p.T852M(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		ACCGTGGAGACGCTCTTAAAC	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	20											45	53	50					20																	20257861		2203	4300	6503	20205861	SO:0001583	missense	26074																														ENST00000245957.5:c.2555C>T	20.37:g.20257861C>T	ENSP00000245957:p.Thr852Met		20205861	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.370315	0.42003	.	.	ENSG00000089101	ENST00000343997;ENST00000377309;ENST00000389655;ENST00000245957	T;T	0.37411	1.2;1.2	4.93	1.93	0.25924	.	0.304797	0.34777	N	0.003694	T	0.30293	0.0760	L	0.55834	1.745	0.22266	N	0.999242	D;B	0.54772	0.968;0.291	B;B	0.40677	0.337;0.049	T	0.16217	-1.0410	10	0.45353	T	0.12	.	9.8582	0.41098	0.0:0.7751:0.0:0.2249	.	832;852	F8W6K4;Q8NHU2	.;CT026_HUMAN	M	792;208;832;852	ENSP00000366524:T208M;ENSP00000245957:T852M	ENSP00000245957:T852M	T	+	2	0	C20orf26	20205861	0.562000	0.26586	0.001000	0.08648	0.016000	0.09150	1.754000	0.38369	0.145000	0.18977	0.460000	0.39030	ACG		0.512	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20257861	C	T	20257861	3	4	77	1	0	0	0	0	1	0	0	0	2112	536	19	1	2669	1	C20orf26	20	20257861	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3920834	20257861	42767659	1138	22874										
TMEM90B	79953	broad.mit.edu	37	chr20	24565507	24565507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcagagcgactactcaagcGacacagagagtgaggacaat	12	9	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:24565507G>A	ENST00000376862.3	+	3	1129	c.496G>A	c.(496-498)Gac>Aac	p.D166N		NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN	synapse differentiation inducing 1	166					intracellular protein transport (GO:0006886)|positive regulation of synapse assembly (GO:0051965)|response to biotic stimulus (GO:0009607)|synaptic vesicle clustering (GO:0097091)	cell body (GO:0044297)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	glutamate receptor binding (GO:0035254)|protein homodimerization activity (GO:0042803)	p.D166N(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						CTACTCAAGCGACACAGAGAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											137	130	132					20																	24565507		2203	4300	6503	24513507	SO:0001583	missense	79953			AK024282	CCDS13164.1	20p11.21	2011-06-30	2011-06-30	2011-06-30	ENSG00000101463	ENSG00000101463			15885	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 5", "synapse differentiation induced gene 1"	614311	"chromosome 20 open reading frame 39", "transmembrane protein 90B"	C20orf39, TMEM90B		20152115	Standard	NM_024893		Approved	FLJ14220, IFITMD5, SynDIG1	uc002wtw.1	Q9H7V2	OTTHUMG00000032104	ENST00000376862.3:c.496G>A	20.37:g.24565507G>A	ENSP00000366058:p.Asp166Asn		24513507	Q6IA30|Q9H514	Missense_Mutation	SNP	ENST00000376862.3	37	CCDS13164.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720442	0.68959	.	.	ENSG00000101463	ENST00000376862	D	0.92545	-3.06	5.1	5.1	0.69264	.	0.149453	0.44285	D	0.000462	D	0.94268	0.8159	M	0.67397	2.05	0.52099	D	0.999948	D	0.76494	0.999	D	0.64144	0.922	D	0.94040	0.7308	10	0.56958	D	0.05	-43.9252	11.1641	0.48533	0.0:0.0:0.8161:0.1839	.	166	Q9H7V2	SYNG1_HUMAN	N	166	ENSP00000366058:D166N	ENSP00000366058:D166N	D	+	1	0	SYNDIG1	24513507	1.000000	0.71417	0.937000	0.37676	0.466000	0.32739	6.506000	0.73712	2.382000	0.81193	0.561000	0.74099	GAC		0.567	SYNDIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078376.1	NM_024893		A	24565507	G	A	24565507	3	1	77	1	0	0	0	0	1	0	0	0	16258	1058	37	1	502	1	TMEM90B	20	24565507	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4307646	24565507	38460013	1139	22875										
NINL	22981	broad.mit.edu	37	chr20	25493496	25493496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gctctccagagacgctgagcGccagaggtgacttttcaggc	13	12	2	4	rs139869636		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:25493496G>A	ENST00000278886.6	-	4	497	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C	NINL_ENST00000422516.1_Missense_Mutation_p.R142C	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	142					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.R142C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GACGCTGAGCGCCAGAGGTGA	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		20285	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20						G	CYS/ARG	2,4404	2.1+/-5.4	0,2,2201	41	45	44		424	3.2	0	20	dbSNP_134	44	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NINL	NM_025176.4	180	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	142/1383	25493496	3,13003	2203	4300	6503	25441496	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.424C>T	20.37:g.25493496G>A	ENSP00000278886:p.Arg142Cys		25441496	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827469	0.50845	4.54E-4	1.16E-4	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.25579	1.79;1.79	5.17	3.16	0.36331	.	0.210963	0.40640	N	0.001052	T	0.41581	0.1165	M	0.71581	2.175	0.09310	N	0.999993	D;D	0.89917	0.999;1.0	P;P	0.61722	0.804;0.893	T	0.20075	-1.0286	10	0.72032	D	0.01	-2.1027	7.2984	0.26405	0.0794:0.0:0.6229:0.2977	.	142;142	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	C	142	ENSP00000278886:R142C;ENSP00000410431:R142C	ENSP00000278886:R142C	R	-	1	0	NINL	25441496	0.004000	0.15560	0.001000	0.08648	0.008000	0.06430	0.962000	0.29280	0.706000	0.31912	0.650000	0.86243	CGC		0.612	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		A	25493496	G	A	25493496	3	1	77	1	0	0	0	0	1	0	0	0	10451	1087	38	1	3808	1	NINL	20	25493496	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	927989	25493496	37532024	1140	22876										
HCK	3055	broad.mit.edu	37	chr20	30662502	30662502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagcaactatgtcgcccgcGttgactctctggagacagag	11	12	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:30662502G>A	ENST00000520553.1	+	5	589	c.343G>A	c.(343-345)Gtt>Att	p.V115I	HCK_ENST00000375852.2_Missense_Mutation_p.V136I|HCK_ENST00000518730.1_Missense_Mutation_p.V114I|HCK_ENST00000538448.1_Missense_Mutation_p.V115I|HCK_ENST00000534862.1_Missense_Mutation_p.V116I|HCK_ENST00000375862.2_Missense_Mutation_p.V135I	NM_001172129.1|NM_001172130.1|NM_001172131.1|NM_002110.3	NP_001165600.1|NP_001165601.1|NP_001165602.1|NP_002101.2	P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	136	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.V115I(1)		NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	TGTCGCCCGCGTTGACTCTCT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	20											99	95	96					20																	30662502		2203	4300	6503	30126163	SO:0001583	missense	3055			AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"SH2 domain containing"	4840	protein-coding gene	gene with protein product		142370	"hemopoietic cell kinase"			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000520553.1:c.343G>A	20.37:g.30662502G>A	ENSP00000429848:p.Val115Ile		30126163	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Missense_Mutation	SNP	ENST00000520553.1	37	CCDS54455.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.917841	0.52546	.	.	ENSG00000101336	ENST00000534862;ENST00000538448;ENST00000375862;ENST00000520553;ENST00000518730;ENST00000375852	T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02	4.98	4.01	0.46588	Src homology-3 domain (3);	0.137326	0.32918	N	0.005493	T	0.10594	0.0259	N	0.04320	-0.23	0.29713	N	0.839261	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.08126	-1.0737	10	0.46703	T	0.11	.	13.034	0.58859	0.0798:0.0:0.9202:0.0	.	114;136	P08631-3;P08631	.;HCK_HUMAN	I	116;115;135;115;114;136	ENSP00000444986:V116I;ENSP00000441169:V115I;ENSP00000365022:V135I;ENSP00000429848:V115I;ENSP00000427757:V114I;ENSP00000365012:V136I	ENSP00000365012:V136I	V	+	1	0	HCK	30126163	0.997000	0.39634	0.832000	0.32986	0.705000	0.40729	4.483000	0.60264	2.584000	0.87258	0.563000	0.77884	GTT		0.552	HCK-006	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000375751.1			A	30662502	G	A	30662502	3	1	77	1	0	0	0	0	1	0	0	0	7015	1145	40	1	430	1	HCK	20	30662502	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5169006	30662502	32363018	1141	22877										
TM9SF4	9777	broad.mit.edu	37	chr20	30729320	30729320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gagaggtgctgagaggggacCggattgtcaacacccctttc	14	10	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:30729320C>T	ENST00000398022.2	+	4	485	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	TM9SF4_ENST00000217315.5_Missense_Mutation_p.R67W	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	84						integral component of membrane (GO:0016021)		p.R67W(1)		central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GAGAGGGGACCGGATTGTCAA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	20											79	77	78					20																	30729320		2203	4300	6503	30192981	SO:0001583	missense	9777			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.250C>T	20.37:g.30729320C>T	ENSP00000381104:p.Arg84Trp		30192981	B0QYT7|Q9NUA3	Missense_Mutation	SNP	ENST00000398022.2	37	CCDS13196.2	.	.	.	.	.	.	.	.	.	.	.	27.7	4.851987	0.91355	.	.	ENSG00000101337	ENST00000398022;ENST00000217315	T;T	0.55413	0.52;0.52	5.51	5.51	0.81932	.	0.131624	0.53938	D	0.000051	T	0.81621	0.4861	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87410	0.2375	10	0.87932	D	0	-18.6304	15.0704	0.72030	0.1425:0.8575:0.0:0.0	.	84	Q92544	TM9S4_HUMAN	W	84;67	ENSP00000381104:R84W;ENSP00000217315:R67W	ENSP00000217315:R67W	R	+	1	2	TM9SF4	30192981	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.567000	0.67378	2.586000	0.87340	0.563000	0.77884	CGG		0.547	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30729320	C	T	30729320	3	4	77	1	0	0	0	0	1	0	0	0	16019	643	23	1	264	1	TM9SF4	20	30729320	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	66818	30729320	32296200	1142	22878										
C20orf112	140688	broad.mit.edu	37	chr20	31040747	31040747	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcctttcttgtctcgctctcAcaggcagctgccaggatgtt	10	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:31040747A>G	ENST00000359676.5	-	6	970	c.828T>C	c.(826-828)tgT>tgC	p.C276C	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		276						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.C276C(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						TCTCGCTCTCACAGGCAGCTG	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	20											88	86	86					20																	31040747		2203	4300	6503	30504408	SO:0001819	synonymous_variant	140688																														ENST00000359676.5:c.828T>C	20.37:g.31040747A>G			30504408	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	37	CCDS13202.1																																																																																				0.632	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2			G	31040747	A	G	31040747	2	3	77	1	0	0	0	0	0	0	0	1	2087	157	6	4		4	C20orf112	20	31040747	Silent	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	311427	31040747	31984773	1143	22879										
DNMT3B	1789	broad.mit.edu	37	chr20	31367940	31367940	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acatggaaccaagtcctgagCctccaagcttggtgaggggg	14	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:31367940C>A	ENST00000328111.2	+	2	315				DNMT3B_ENST00000375623.4_Intron|DNMT3B_ENST00000348286.2_Intron|DNMT3B_ENST00000344505.4_Intron|DNMT3B_ENST00000443239.3_Intron|DNMT3B_ENST00000353855.2_Intron|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000201963.3_Missense_Mutation_p.P7T	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.P7T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AAGTCCTGAGCCTCCAAGCTT	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	20											20	22	21					20																	31367940		2200	4299	6499	30831601	SO:0001627	intron_variant	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.-6-184C>A	20.37:g.31367940C>A			30831601	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527560	0.27299	.	.	ENSG00000088305	ENST00000201963	D	0.97114	-4.25	4.33	4.33	0.51752	.	.	.	.	.	D	0.97888	0.9306	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.97180	0.9850	8	0.39692	T	0.17	.	12.5161	0.56034	0.0:1.0:0.0:0.0	.	7	Q9UBC3-6	.	T	7	ENSP00000201963:P7T	ENSP00000201963:P7T	P	+	1	0	DNMT3B	30831601	0.284000	0.24287	1.000000	0.80357	0.883000	0.51084	1.511000	0.35801	2.415000	0.81967	0.561000	0.74099	CCT		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31367940	C	A	31367940	1	1	77	0	1	0	0	0	0	0	0	0	4688	739	26	2		2	DNMT3B	20	31367940	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	327193	31367940	31657580	1144	22880										
MAPRE1	22919	broad.mit.edu	37	chr20	31413838	31413838	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagttgaatctgacaaagatCgaacagttgtgctcaggtaa	10	7	2	3	rs565248642		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:31413838C>T	ENST00000375571.5	+	2	244	c.105C>T	c.(103-105)atC>atT	p.I35I		NM_012325.2	NP_036457.1	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family, member 1	35	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of microtubule plus-end binding (GO:1903033)|protein localization to microtubule (GO:0035372)	cell projection membrane (GO:0031253)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule plus-end (GO:0035371)	microtubule plus-end binding (GO:0051010)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I35I(1)		endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8						TGACAAAGATCGAACAGTTGT	0.448													C|||	1	0.000199681	0	0	5008	,	,		15424	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	20											162	141	148					20																	31413838		2203	4300	6503	30877499	SO:0001819	synonymous_variant	22919			U24166	CCDS13208.1	20q11.1-q11.3	2013-01-17			ENSG00000101367	ENSG00000101367			6890	protein-coding gene	gene with protein product	"adenomatous polyposis coli-binding protein EB1"	603108				7606712, 9724749, 11470413	Standard	NM_012325		Approved	EB1	uc002wyh.3	Q15691	OTTHUMG00000032228	ENST00000375571.5:c.105C>T	20.37:g.31413838C>T			30877499	B2R6I7|E1P5M8|Q3KQS8	Silent	SNP	ENST00000375571.5	37	CCDS13208.1																																																																																				0.448	MAPRE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078647.2	NM_012325		T	31413838	C	T	31413838	2	4	77	1	0	0	0	0	0	0	0	1	9324	874	31	1		1	MAPRE1	20	31413838	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	45898	31413838	31611682	1145	22881										
EPB41L1	2036	broad.mit.edu	37	chr20	34810266	34810266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgctggtaaccaaagctgtcGtatacagagaaacagaccca	9	10	0	2	rs371978327		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:34810266G>A	ENST00000338074.2	+	21	2748	c.2587G>A	c.(2587-2589)Gta>Ata	p.V863I	EPB41L1_ENST00000373946.3_Missense_Mutation_p.V683I|EPB41L1_ENST00000373941.1_Missense_Mutation_p.V862I|EPB41L1_ENST00000441639.1_Missense_Mutation_p.V761I|EPB41L1_ENST00000373950.2_Missense_Mutation_p.V754I|EPB41L1_ENST00000202028.5_Missense_Mutation_p.V761I	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	863	C-terminal (CTD).				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.V863I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CAAAGCTGTCGTATACAGAGA	0.542													G|||	1	0.000199681	0	0	5008	,	,		19242	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20						G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	115	107	110		2587,2281	4.6	1	20		110	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPB41L1	NM_012156.2,NM_177996.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	863/882,761/780	34810266	1,13005	2203	4300	6503	34273680	SO:0001583	missense	2036			AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.2587G>A	20.37:g.34810266G>A	ENSP00000337168:p.Val863Ile		34273680	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	37	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416844	0.83449	0.0	1.16E-4	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000338074;ENST00000373941	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	4.61	4.61	0.57282	Band 4.1, C-terminal (1);	.	.	.	.	D	0.87962	0.6310	L	0.42686	1.345	0.53688	D	0.999972	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.994;0.999	D;D;D;D;D	0.85130	0.997;0.972;0.993;0.972;0.991	D	0.89351	0.3661	9	0.87932	D	0	.	16.6051	0.84826	0.0:0.0:1.0:0.0	.	863;683;754;754;761	Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	E41L1_HUMAN;.;.;.;.	I	761;754;754;761;683;863;862	ENSP00000202028:V761I;ENSP00000363061:V754I;ENSP00000399214:V761I;ENSP00000363057:V683I;ENSP00000337168:V863I;ENSP00000363052:V862I	ENSP00000202028:V761I	V	+	1	0	EPB41L1	34273680	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.263000	0.95617	2.401000	0.81631	0.462000	0.41574	GTA		0.542	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		A	34810266	G	A	34810266	3	1	77	1	0	0	0	0	1	0	0	0	5165	1145	40	1	2665	1	EPB41L1	20	34810266	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3396428	34810266	28215254	1146	22882										
DLGAP4	22839	broad.mit.edu	37	chr20	35125141	35125141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtggcgtataagaagacccCgccaccggtccctccacgca	10	16	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:35125141C>T	ENST00000373907.2	+	7	1881	c.1682C>T	c.(1681-1683)cCg>cTg	p.P561L	DLGAP4_ENST00000401952.2_Missense_Mutation_p.P561L|DLGAP4_ENST00000340491.4_Missense_Mutation_p.P22L|DLGAP4_ENST00000475894.1_3'UTR|DLGAP4_ENST00000373913.3_Missense_Mutation_p.P561L|DLGAP4_ENST00000339266.5_Missense_Mutation_p.P561L			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	561					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)		p.P561L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				AAGAAGACCCCGCCACCGGTC	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	20											74	74	74					20																	35125141		2203	4300	6503	34558555	SO:0001583	missense	22839			AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.1682C>T	20.37:g.35125141C>T	ENSP00000363014:p.Pro561Leu		34558555	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	37		.	.	.	.	.	.	.	.	.	.	C	28.5	4.923129	0.92319	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266;ENST00000340491	T;T;T;T;T	0.28895	1.59;1.59;2.23;2.23;1.59	5.49	5.49	0.81192	.	0.044692	0.85682	N	0.000000	T	0.61502	0.2352	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.979;1.0	T	0.65825	-0.6074	10	0.87932	D	0	.	18.7174	0.91680	0.0:1.0:0.0:0.0	.	22;561	Q9Y2H0-3;Q9Y2H0-1	.;.	L	561;561;561;561;22	ENSP00000363023:P561L;ENSP00000384954:P561L;ENSP00000363014:P561L;ENSP00000341633:P561L;ENSP00000345700:P22L	ENSP00000341633:P561L	P	+	2	0	DLGAP4	34558555	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.776000	0.85560	2.735000	0.93741	0.655000	0.94253	CCG		0.587	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		T	35125141	C	T	35125141	3	4	77	1	0	0	0	0	1	0	0	0	4573	652	23	1	1739	1	DLGAP4	20	35125141	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	314875	35125141	27900379	1147	22883										
MYL9	10398	broad.mit.edu	37	chr20	35173327	35173327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aagccaagaccaccaagaagCggccacagcgggccacatcc	10	16	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:35173327C>T	ENST00000279022.2	+	2	144	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W	MYL9_ENST00000346786.2_Missense_Mutation_p.R14W|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	14					axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.R14W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				CACCAAGAAGCGGCCACAGCG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	20											98	83	88					20																	35173327		2203	4300	6503	34606741	SO:0001583	missense	10398			J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"Myosins / Light chain", "EF-hand domain containing"	15754	protein-coding gene	gene with protein product	"myosin regulatory light chain 2, smooth muscle isoform", "myosin regulatory light chain 1"	609905	"myosin, light polypeptide 9, regulatory"			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.40C>T	20.37:g.35173327C>T	ENSP00000279022:p.Arg14Trp		34606741	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Missense_Mutation	SNP	ENST00000279022.2	37	CCDS13276.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741288	0.49151	.	.	ENSG00000101335	ENST00000279022;ENST00000346786	T;T	0.76186	-1.0;-0.69	4.67	-0.00696	0.14011	.	0.000000	0.85682	D	0.000000	T	0.78742	0.4331	M	0.91818	3.245	0.80722	D	1	P;D	0.52996	0.857;0.957	B;P	0.46026	0.037;0.501	T	0.79303	-0.1859	10	0.87932	D	0	.	9.4712	0.38844	0.442:0.434:0.124:0.0	.	14;14	Q9BUF9;P24844	.;MYL9_HUMAN	W	14	ENSP00000279022:R14W;ENSP00000217313:R14W	ENSP00000279022:R14W	R	+	1	2	MYL9	34606741	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	2.596000	0.46205	-0.177000	0.10690	-0.976000	0.02587	CGG		0.577	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		T	35173327	C	T	35173327	3	4	77	1	0	0	0	0	1	0	0	0	10084	759	27	1	42	1	MYL9	20	35173327	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	48186	35173327	27852193	1148	22884										
BLCAP	10904	broad.mit.edu	37	chr20	36147459	36147459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaaattgtgcaaggcttccGttccaggaggaagctgagca	12	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:36147459G>A	ENST00000373537.2	-	2	432	c.118C>T	c.(118-120)Cgg>Tgg	p.R40W	NNAT_ENST00000062104.2_5'Flank|BLCAP_ENST00000397137.1_Missense_Mutation_p.R40W|BLCAP_ENST00000397134.1_Missense_Mutation_p.R40W|BLCAP_ENST00000397135.1_Missense_Mutation_p.R40W|NNAT_ENST00000346199.2_5'Flank|BLCAP_ENST00000397131.1_Missense_Mutation_p.R40W|BLCAP_ENST00000414542.2_Missense_Mutation_p.R40W	NM_001167823.1|NM_006698.3	NP_001161295.1|NP_006689.1	P62952	BLCAP_HUMAN	bladder cancer associated protein	40					apoptotic nuclear changes (GO:0030262)|cell cycle (GO:0007049)	integral component of membrane (GO:0016021)		p.R40W(1)		breast(1)|large_intestine(1)|lung(2)|stomach(1)	5		Myeloproliferative disorder(115;0.00878)				CAAGGCTTCCGTTCCAGGAGG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	20											59	58	58					20																	36147459		2203	4300	6503	35580873	SO:0001583	missense	10904			AF053470	CCDS13295.1	20q11.23	2006-01-29			ENSG00000166619	ENSG00000166619			1055	protein-coding gene	gene with protein product		613110				10197429	Standard	NM_006698		Approved	BC10	uc021wdf.1	P62952	OTTHUMG00000032419	ENST00000373537.2:c.118C>T	20.37:g.36147459G>A	ENSP00000362637:p.Arg40Trp		35580873	A2A2K7|O60629|Q9D3B5	Missense_Mutation	SNP	ENST00000373537.2	37	CCDS13295.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.131962	0.56828	.	.	ENSG00000166619	ENST00000373537;ENST00000397137;ENST00000414542;ENST00000397135;ENST00000397134;ENST00000397131;ENST00000432507;ENST00000445723;ENST00000414080	.	.	.	5.16	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.76912	0.4054	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.79227	-0.1890	8	0.87932	D	0	-11.6846	10.4953	0.44775	0.0:0.0:0.6465:0.3535	.	40	P62952	BLCAP_HUMAN	W	40	.	ENSP00000362637:R40W	R	-	1	2	BLCAP	35580873	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	3.852000	0.55934	1.361000	0.45981	0.585000	0.79938	CGG		0.567	BLCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079113.2	NM_006698		A	36147459	G	A	36147459	3	1	77	1	0	0	0	0	1	0	0	0	1443	1144	40	1	149	1	BLCAP	20	36147459	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	974132	36147459	26878061	1149	22885										
FAM83D	81610	broad.mit.edu	37	chr20	37581028	37581028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcgctggtatcaggtcccgGctcaaccacatgctggctat	10	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:37581028G>A	ENST00000217429.4	+	4	1754	c.1713G>A	c.(1711-1713)cgG>cgA	p.R571R		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	541					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R571R(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				TCAGGTCCCGGCTCAACCACA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	20											83	88	87					20																	37581028		1970	4156	6126	37014442	SO:0001819	synonymous_variant	81610			AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.1713G>A	20.37:g.37581028G>A			37014442	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Silent	SNP	ENST00000217429.4	37	CCDS42872.1																																																																																				0.493	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			A	37581028	G	A	37581028	2	1	77	1	0	0	0	0	0	0	0	1	5655	1190	42	3		3	FAM83D	20	37581028	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1433569	37581028	25444492	1150	22886										
LPIN3	64900	broad.mit.edu	37	chr20	39974622	39974622	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caagctgggcgtcctgcggtCgcgggagaaggtggtgagtg	20	8	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:39974622C>T	ENST00000373257.3	+	2	270	c.179C>T	c.(178-180)tCg>tTg	p.S60L		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	60	N-LIP.				fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.S60L(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				GTCCTGCGGTCGCGGGAGAAG	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	20											66	59	61					20																	39974622		2203	4300	6503	39408036	SO:0001583	missense	64900			AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"lipin 3-like"	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.179C>T	20.37:g.39974622C>T	ENSP00000362354:p.Ser60Leu		39408036	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934822	0.92458	.	.	ENSG00000132793	ENST00000373257	T	0.77358	-1.09	5.59	5.59	0.84812	Lipin, N-terminal (1);	0.140991	0.48286	D	0.000187	D	0.90198	0.6936	M	0.90542	3.125	0.53688	D	0.999973	D;D	0.89917	0.998;1.0	D;D	0.67231	0.95;0.934	D	0.91462	0.5190	9	.	.	.	-9.6255	19.1895	0.93658	0.0:1.0:0.0:0.0	.	60;60	Q9BQK8-2;Q9BQK8	.;LPIN3_HUMAN	L	60	ENSP00000362354:S60L	.	S	+	2	0	LPIN3	39408036	1.000000	0.71417	0.942000	0.38095	0.460000	0.32559	7.455000	0.80726	2.624000	0.88883	0.511000	0.50034	TCG		0.637	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		T	39974622	C	T	39974622	3	4	77	1	0	0	0	0	1	0	0	0	8949	893	31	1	181	1	LPIN3	20	39974622	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2393594	39974622	23050898	1151	22887										
CHD6	84181	broad.mit.edu	37	chr20	40033809	40033809	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atctggggcacagcagccatGcctggcagcatcatgggcag	14	12	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:40033809G>A	ENST00000373233.3	-	37	7749	c.7572C>T	c.(7570-7572)ggC>ggT	p.G2524G	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2524					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.G2524G(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CAGCAGCCATGCCTGGCAGCA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	20											79	69	72					20																	40033809		2203	4300	6503	39467223	SO:0001819	synonymous_variant	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.7572C>T	20.37:g.40033809G>A			39467223	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																				0.592	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40033809	G	A	40033809	2	1	77	1	0	0	0	0	0	0	0	1	3335	1306	46	3		3	CHD6	20	40033809	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	59187	40033809	22991711	1152	22888										
CHD6	84181	broad.mit.edu	37	chr20	40081514	40081514	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctgaaaactccatgagctcGtcttcctcaaacgagttgta	7	11	3	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:40081514G>A	ENST00000373233.3	-	21	3366	c.3189C>T	c.(3187-3189)gaC>gaT	p.D1063D	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1063					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.D1063D(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCATGAGCTCGTCTTCCTCAA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	20											149	117	128					20																	40081514		2203	4300	6503	39514928	SO:0001819	synonymous_variant	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3189C>T	20.37:g.40081514G>A			39514928	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																				0.522	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40081514	G	A	40081514	2	1	77	1	0	0	0	0	0	0	0	1	3335	1136	40	1		1	CHD6	20	40081514	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	47705	40081514	22944006	1153	22889										
PTPRT	11122	broad.mit.edu	37	chr20	41419930	41419930	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attccacacagggttcccttGggggccaccattcaccttca							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:41419930delG	ENST00000373187.1	-	3	390	c.391delC	c.(391-393)caafs	p.Q131fs	PTPRT_ENST00000373190.1_Frame_Shift_Del_p.Q131fs|PTPRT_ENST00000373201.1_Frame_Shift_Del_p.Q131fs|PTPRT_ENST00000373198.4_Frame_Shift_Del_p.Q131fs|PTPRT_ENST00000373193.3_Frame_Shift_Del_p.Q131fs|PTPRT_ENST00000356100.2_Frame_Shift_Del_p.Q131fs|PTPRT_ENST00000373184.1_Frame_Shift_Del_p.Q131fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	131	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.Q131fs*17(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GGGTTCCCTTGGGGGCCACCA	0.567																																																1	Deletion - Frameshift(1)	large_intestine(1)	20											78	81	80					20																	41419930		1973	4169	6142	40853344	SO:0001589	frameshift_variant	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.391delC	20.37:g.41419930delG	ENSP00000362283:p.Gln131fs		40853344	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Del	DEL	ENST00000373187.1	37	CCDS42874.1																																																																																				0.567	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			-	41419930	G	-	41419930	7	5	77	1	0	1	0	1	0	0	0	0	12849	1357	47	0	4111	0	PTPRT	20	41419930	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	1338416	41419930	21605590	1154	22890										
SGK2	10110	broad.mit.edu	37	chr20	42196324	42196324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgcccagcccacggacttcGacttcctcaaagtcatcggc	9	16	2	0	rs200530019		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:42196324G>A	ENST00000341458.4	+	3	505	c.286G>A	c.(286-288)Gac>Aac	p.D96N	SGK2_ENST00000373077.1_Missense_Mutation_p.D36N|SGK2_ENST00000426287.1_Missense_Mutation_p.D62N|SGK2_ENST00000373092.3_Missense_Mutation_p.D36N|SGK2_ENST00000423407.3_Missense_Mutation_p.D36N|SGK2_ENST00000373100.1_Missense_Mutation_p.D36N	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.D96N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CACGGACTTCGACTTCCTCAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	20						G	ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	72	69	70		106,286,106	4.9	1	20		70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SGK2	NM_001199264.1,NM_016276.3,NM_170693.2	23,23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	36/368,96/428,36/368	42196324	1,13005	2203	4300	6503	41629738	SO:0001583	missense	10110			AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.286G>A	20.37:g.42196324G>A	ENSP00000340608:p.Asp96Asn		41629738	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.646979	0.67358	0.0	1.16E-4	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43678	0.1258	N	0.05554	-0.025	0.80722	D	1	B;B;B	0.29671	0.06;0.254;0.011	B;B;B	0.21546	0.033;0.035;0.005	T	0.49762	-0.8905	10	0.66056	D	0.02	.	17.3058	0.87194	0.0:0.0:1.0:0.0	.	62;96;36	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	N	36;36;36;36;36;96;62	ENSP00000362192:D36N;ENSP00000362184:D36N;ENSP00000362168:D36N;ENSP00000396222:D36N;ENSP00000392795:D36N;ENSP00000340608:D96N;ENSP00000412214:D62N	ENSP00000340608:D96N	D	+	1	0	SGK2	41629738	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.503000	0.66962	2.448000	0.82819	0.655000	0.94253	GAC		0.552	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			A	42196324	G	A	42196324	3	1	77	1	0	0	0	0	1	0	0	0	14246	1058	37	1	296	1	SGK2	20	42196324	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	776394	42196324	20829196	1155	22891										
JPH2	57158	broad.mit.edu	37	chr20	42788479	42788479	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgcaggttgtccagccactcGccctcgtagcggaggccact	12	16	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:42788479G>A	ENST00000372980.3	-	2	1820	c.948C>T	c.(946-948)ggC>ggT	p.G316G		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	316					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.G316G(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CCAGCCACTCGCCCTCGTAGC	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	20											58	49	52					20																	42788479		2203	4300	6503	42221893	SO:0001819	synonymous_variant	57158			AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.948C>T	20.37:g.42788479G>A			42221893	E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	CCDS13325.1																																																																																				0.662	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			A	42788479	G	A	42788479	2	1	77	1	0	0	0	0	0	0	0	1	7982	1074	38	1		1	JPH2	20	42788479	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	592155	42788479	20237041	1156	22892										
HNF4A	3172	broad.mit.edu	37	chr20	43034730	43034730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagaaggcaccaacctcaacGcgcccaacagcctgggtgtc	10	16	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:43034730G>A	ENST00000316099.4	+	2	237	c.148G>A	c.(148-150)Gcg>Acg	p.A50T	HNF4A_ENST00000415691.2_Missense_Mutation_p.A50T|HNF4A_ENST00000457232.1_Missense_Mutation_p.A28T|HNF4A_ENST00000443598.2_Missense_Mutation_p.A50T|HNF4A_ENST00000316673.4_Missense_Mutation_p.A28T|HNF4A_ENST00000609795.1_Missense_Mutation_p.A28T|MIR3646_ENST00000578301.1_RNA	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	50					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A28T(1)|p.A50T(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CAACCTCAACGCGCCCAACAG	0.622																																					Colon(79;2 1269 8820 14841 52347)											2	Substitution - Missense(2)	large_intestine(2)	20											140	139	139					20																	43034730		2203	4300	6503	42468144	SO:0001583	missense	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.148G>A	20.37:g.43034730G>A	ENSP00000312987:p.Ala50Thr		42468144	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	37	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	g	12.01	1.809641	0.31961	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.92699	-2.99;-2.98;-3.01;-3.09;-3.0	5.17	2.07	0.26955	.	1.112910	0.06695	N	0.770408	D	0.83018	0.5163	N	0.16903	0.455	0.29303	N	0.868584	B;B;B;B;B;B;B	0.16396	0.003;0.007;0.007;0.009;0.003;0.012;0.017	B;B;B;B;B;B;B	0.12837	0.002;0.002;0.002;0.005;0.004;0.008;0.006	T	0.69756	-0.5059	10	0.20046	T	0.44	.	4.2891	0.10869	0.2376:0.0:0.4855:0.277	.	43;50;50;50;28;28;28	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	T	28;28;50;50;80;50	ENSP00000315180:A28T;ENSP00000396216:A28T;ENSP00000312987:A50T;ENSP00000410911:A50T;ENSP00000412111:A50T	ENSP00000312987:A50T	A	+	1	0	HNF4A	42468144	0.747000	0.28283	0.773000	0.31616	0.993000	0.82548	1.422000	0.34826	0.170000	0.19704	0.645000	0.84053	GCG		0.622	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			A	43034730	G	A	43034730	3	1	77	1	0	0	0	0	1	0	0	0	7274	1087	38	1	207	1	HNF4A	20	43034730	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	246251	43034730	19990790	1157	22893										
HNF4A	3172	broad.mit.edu	37	chr20	43058195	43058195	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccacagccctcaccgccaGgtggctcagggtctgagccc	11	19	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:43058195G>T	ENST00000316099.4	+	10	1404	c.1315G>T	c.(1315-1317)Ggt>Tgt	p.G439C	HNF4A_ENST00000415691.2_Missense_Mutation_p.G429C|HNF4A_ENST00000457232.1_Missense_Mutation_p.G407C|HNF4A_ENST00000316673.4_Missense_Mutation_p.G417C	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	439					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G439C(1)|p.G417C(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CTCACCGCCAGGTGGCTCAGG	0.607																																					Colon(79;2 1269 8820 14841 52347)											2	Substitution - Missense(2)	large_intestine(2)	20											87	94	92					20																	43058195		2203	4300	6503	42491609	SO:0001583	missense	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.1315G>T	20.37:g.43058195G>T	ENSP00000312987:p.Gly439Cys		42491609	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	37	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.870816	0.51695	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000338692;ENST00000415691	T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58	5.23	4.27	0.50696	.	0.826695	0.10452	N	0.673001	T	0.56292	0.1975	N	0.08118	0	0.38281	D	0.942439	P;P;B;P;P	0.46020	0.871;0.726;0.422;0.726;0.82	B;B;B;B;B	0.43331	0.237;0.156;0.219;0.319;0.416	T	0.58668	-0.7596	10	0.49607	T	0.09	.	13.0226	0.58796	0.0786:0.0:0.9214:0.0	.	432;439;429;417;407	Q5QPB7;P41235;F1D8S2;F1D8T0;P41235-6	.;HNF4A_HUMAN;.;.;.	C	417;407;439;469;429	ENSP00000315180:G417C;ENSP00000396216:G407C;ENSP00000312987:G439C;ENSP00000412111:G429C	ENSP00000312987:G439C	G	+	1	0	HNF4A	42491609	0.999000	0.42202	0.999000	0.59377	0.943000	0.58893	2.991000	0.49409	1.408000	0.46895	0.561000	0.74099	GGT		0.607	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43058195	G	T	43058195	3	4	77	1	0	0	0	0	1	0	0	0	7274	1000	35	2	1531	2	HNF4A	20	43058195	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	23465	43058195	19967325	1158	22894										
PABPC1L	80336	broad.mit.edu	37	chr20	43559194	43559194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgtgacagagatgaacgggCgcatcgtgggcaccaagcca	14	12	0	3	rs199499305		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:43559194C>T	ENST00000217073.2	+	8	1066	c.1066C>T	c.(1066-1068)Cgc>Tgc	p.R356C	PABPC1L_ENST00000490798.1_3'UTR|PABPC1L_ENST00000372824.1_5'Flank|PABPC1L_ENST00000372819.1_5'Flank|PABPC1L_ENST00000217074.4_3'UTR|PABPC1L_ENST00000217075.2_5'Flank|PABPC1L_ENST00000255136.3_Missense_Mutation_p.R356C|PABPC1L_ENST00000537323.1_3'UTR			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	356	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R356C(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						GATGAACGGGCGCATCGTGGG	0.577													C|||	1	0.000199681	0	0.0014	5008	,	,		17933	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20						C	CYS/ARG	0,3136		0,0,1568	177	170	172		1066	1.5	1	20		172	1,7163		0,1,3581	no	missense	PABPC1L	NM_001124756.1	180	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	possibly-damaging	356/615	43559194	1,10299	1568	3582	5150	42992608	SO:0001583	missense	80336			AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1066C>T	20.37:g.43559194C>T	ENSP00000217073:p.Arg356Cys		42992608	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	37	CCDS42878.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.68	3.448583	0.63178	0.0	1.4E-4	ENSG00000101104	ENST00000255136;ENST00000217073	T;T	0.17691	2.26;2.26	5.63	1.54	0.23209	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.148667	0.64402	N	0.000020	T	0.16385	0.0394	L	0.46947	1.48	0.80722	D	1	P	0.47191	0.891	P	0.46510	0.519	T	0.02713	-1.1120	10	0.87932	D	0	.	4.2747	0.10802	0.2364:0.4887:0.0:0.2749	.	356	Q4VXU2	PAP1L_HUMAN	C	356	ENSP00000255136:R356C;ENSP00000217073:R356C	ENSP00000217073:R356C	R	+	1	0	PABPC1L	42992608	1.000000	0.71417	0.973000	0.42090	0.764000	0.43329	1.188000	0.32102	0.334000	0.23590	0.655000	0.94253	CGC		0.577	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			T	43559194	C	T	43559194	3	4	77	1	0	0	0	0	1	0	0	0	11395	768	27	1	1096	1	PABPC1L	20	43559194	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	500999	43559194	19466326	1159	22895										
WFDC6	57119	broad.mit.edu	37	chr20	44166705	44166705	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggtctatttcttccacttcGcattccactttgattttggg	7	10	2	1	rs374760516		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:44166705G>A	ENST00000354280.4	-	0	1987				EPPIN-WFDC6_ENST00000504988.1_Silent_p.C140C|WFDC6_ENST00000372670.3_Silent_p.C40C|EPPIN_ENST00000555685.1_Silent_p.C140C|WFDC6_ENST00000600168.1_Silent_p.C40C	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor						defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.C40C(2)									CTTCCACTTCGCATTCCACTT	0.498																																																2	Substitution - coding silent(2)	large_intestine(2)	20											211	195	201					20																	44166705		2203	4300	6503	43600119	SO:0001628	intergenic_variant	140870			AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"WAP four-disulfide core domain containing"	15932	protein-coding gene	gene with protein product	"epididymal protease inhibitor", "cancer/testis antigen 72"	609031	"serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)", "serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588		20.37:g.44166705G>A			43600119	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	37	CCDS13359.1																																																																																				0.498	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4			A	44166705	G	A	44166705	1	1	77	0	1	0	0	0	0	0	0	0	17395	1079	38	1		1	WFDC6	20	44166705	IGR	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	607511	44166705	18858815	1160	22896										
MMP9	4318	broad.mit.edu	37	chr20	44639920	44639920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagtaccacggccaactacgAcaccgacgaccggtttggct	10	15	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:44639920A>G	ENST00000372330.3	+	5	807	c.788A>G	c.(787-789)gAc>gGc	p.D263G	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	263	Fibronectin type-II 1. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D263G(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	GCCAACTACGACACCGACGAC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	20											59	61	61					20																	44639920		2203	4300	6503	44073327	SO:0001583	missense	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.788A>G	20.37:g.44639920A>G	ENSP00000361405:p.Asp263Gly		44073327	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.628059	0.46944	.	.	ENSG00000100985	ENST00000372330	T	0.57595	0.39	4.56	4.56	0.56223	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.091688	0.64402	D	0.000001	T	0.73110	0.3545	M	0.83223	2.63	0.58432	D	0.999998	D	0.71674	0.998	D	0.87578	0.998	T	0.76708	-0.2860	10	0.52906	T	0.07	.	13.5392	0.61664	1.0:0.0:0.0:0.0	.	263	P14780	MMP9_HUMAN	G	263	ENSP00000361405:D263G	ENSP00000361405:D263G	D	+	2	0	MMP9	44073327	1.000000	0.71417	0.602000	0.28890	0.091000	0.18340	7.046000	0.76592	2.034000	0.60081	0.528000	0.53228	GAC		0.652	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			G	44639920	A	G	44639920	3	3	77	1	0	0	0	0	1	0	0	0	9699	275	10	4	806	4	MMP9	20	44639920	Missense_Mutation	SNP	A	TCGA-AG-A02N-01A-11W-A096-10	473215	44639920	18385600	1161	22897										
MMP9	4318	broad.mit.edu	37	chr20	44641101	44641101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcgtggcggcgcatgagttcGgccacgcgctgggcttagat	16	11	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:44641101G>A	ENST00000372330.3	+	8	1229	c.1210G>A	c.(1210-1212)Ggc>Agc	p.G404S	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	404					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G404S(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	GCATGAGTTCGGCCACGCGCT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	20											65	61	63					20																	44641101		2203	4300	6503	44074508	SO:0001583	missense	4318				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1210G>A	20.37:g.44641101G>A	ENSP00000361405:p.Gly404Ser		44074508	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.814290	0.90790	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.76968	-1.06	4.99	4.99	0.66335	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91143	0.7211	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93268	0.6649	10	0.87932	D	0	.	17.4497	0.87588	0.0:0.0:1.0:0.0	.	404	P14780	MMP9_HUMAN	S	404;49	ENSP00000361405:G404S	ENSP00000361405:G404S	G	+	1	0	MMP9	44074508	1.000000	0.71417	0.958000	0.39756	0.398000	0.30690	9.519000	0.98025	2.606000	0.88127	0.561000	0.74099	GGC		0.642	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			A	44641101	G	A	44641101	3	1	77	1	0	0	0	0	1	0	0	0	9699	1116	39	1	1240	1	MMP9	20	44641101	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1181	44641101	18384419	1162	22898										
SLC2A10	81031	broad.mit.edu	37	chr20	45354683	45354683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctggctgtgcccaatgccacCgggcagacaggcctccctgg	13	16	0	1	rs370173604	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:45354683C>T	ENST00000359271.2	+	2	1258	c.1008C>T	c.(1006-1008)acC>acT	p.T336T		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	336					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)	p.T336T(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				CCAATGCCACCGGGCAGACAG	0.617													c|||	6	0.00119808	0	0	5008	,	,		19145	0.004		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	20											56	52	53					20																	45354683		2203	4300	6503	44788090	SO:0001819	synonymous_variant	81031			AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.1008C>T	20.37:g.45354683C>T			44788090	A8K4J6|Q3MIX5|Q9H4I6	Silent	SNP	ENST00000359271.2	37	CCDS13402.1																																																																																				0.617	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			T	45354683	C	T	45354683	2	4	77	1	0	0	0	0	0	0	0	1	14576	639	23	1		1	SLC2A10	20	45354683	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	713582	45354683	17670837	1163	22899										
PREX1	57580	broad.mit.edu	37	chr20	47242442	47242442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ttcagaggtccccatccaccGgcggctggcagaggcggtag	15	13	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:47242442G>A	ENST00000371941.3	-	40	4983	c.4961C>T	c.(4960-4962)cCg>cTg	p.P1654L	PREX1_ENST00000396220.1_3'UTR	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1654					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P1654L(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCCATCCACCGGCGGCTGGCA	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	20											16	18	17					20																	47242442		2196	4294	6490	46675849	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.4961C>T	20.37:g.47242442G>A	ENSP00000361009:p.Pro1654Leu		46675849	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267149	0.80469	.	.	ENSG00000124126	ENST00000371941	T	0.77098	-1.07	4.09	4.09	0.47781	.	0.000000	0.51477	U	0.000097	D	0.85535	0.5719	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87315	0.2314	10	0.87932	D	0	.	13.8056	0.63230	0.0:0.0:1.0:0.0	.	1654;951	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	L	1654	ENSP00000361009:P1654L	ENSP00000361009:P1654L	P	-	2	0	PREX1	46675849	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	5.898000	0.69838	1.837000	0.53436	0.385000	0.25706	CCG		0.617	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47242442	G	A	47242442	3	1	77	1	0	0	0	0	1	0	0	0	12510	1116	39	1	22	1	PREX1	20	47242442	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1887759	47242442	15783078	1164	22900										
BMP7	655	broad.mit.edu	37	chr20	55758841	55758841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cttggagcggttctggctgcGctgtttgctccccgtggacc	14	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:55758841G>A	ENST00000395863.3	-	4	1400	c.895C>T	c.(895-897)Cgc>Tgc	p.R299C	BMP7_ENST00000460817.1_5'UTR|BMP7_ENST00000450594.2_Missense_Mutation_p.R299C|BMP7_ENST00000395864.3_Intron	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	299					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)	p.R299C(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			TTCTGGCTGCGCTGTTTGCTC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	20											85	74	78					20																	55758841		2203	4300	6503	55192248	SO:0001583	missense	655				CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.895C>T	20.37:g.55758841G>A	ENSP00000379204:p.Arg299Cys		55192248	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	37	CCDS13455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.9|23.9	4.469338|4.469338	0.84533|0.84533	.|.	.|.	ENSG00000101144|ENSG00000101144	ENST00000433911|ENST00000395863;ENST00000450594	.|T;D	.|0.82893	.|-1.18;-1.66	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88901|0.88901	0.6563|0.6563	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.85130	.|0.997;0.95	D|D	0.89521|0.89521	0.3778|0.3778	5|10	.|0.72032	.|D	.|0.01	.|.	15.1003|15.1003	0.72269|0.72269	0.0:0.0:0.8496:0.1504|0.0:0.0:0.8496:0.1504	.|.	.|299;299	.|P18075;B1AL00	.|BMP7_HUMAN;.	V|C	220|299	.|ENSP00000379204:R299C;ENSP00000398687:R299C	.|ENSP00000379204:R299C	A|R	-|-	2|1	0|0	BMP7|BMP7	55192248|55192248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.111000|5.111000	0.64628|0.64628	2.559000|2.559000	0.86315|0.86315	0.643000|0.643000	0.83706|0.83706	GCG|CGC		0.632	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			A	55758841	G	A	55758841	3	1	77	1	0	0	0	0	1	0	0	0	1466	1087	38	1	416	1	BMP7	20	55758841	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	8516399	55758841	7266679	1165	22901										
CDH4	1002	broad.mit.edu	37	chr20	60427897	60427897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tcatcgacatgaatgacaacCgccctgagttcatcaaccag	7	13	3	3	rs555725508		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:60427897C>T	ENST00000360469.5	+	6	908	c.820C>T	c.(820-822)Cgc>Tgc	p.R274C	CDH4_ENST00000543233.1_Missense_Mutation_p.R200C	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	274	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.			R -> H (in Ref. 1; AAA35627). {ECO:0000305}.	adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R274C(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GAATGACAACCGCCCTGAGTT	0.567													C|||	1	0.000199681	0	0	5008	,	,		19902	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	20											215	168	184					20																	60427897		2203	4300	6503	59861292	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.820C>T	20.37:g.60427897C>T	ENSP00000353656:p.Arg274Cys		59861292	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886122	0.51908	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.61627	0.09;0.09	4.76	3.74	0.42951	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.050159	0.85682	D	0.000000	T	0.74809	0.3765	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	P	0.60415	0.874	T	0.80167	-0.1495	9	.	.	.	.	14.0449	0.64700	0.206:0.794:0.0:0.0	.	274	P55283	CADH4_HUMAN	C	274;182;200	ENSP00000353656:R274C;ENSP00000443301:R200C	.	R	+	1	0	CDH4	59861292	1.000000	0.71417	0.995000	0.50966	0.580000	0.36256	2.065000	0.41442	2.202000	0.70862	0.561000	0.74099	CGC		0.567	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60427897	C	T	60427897	3	4	77	1	0	0	0	0	1	0	0	0	3118	652	23	1	842	1	CDH4	20	60427897	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	4669056	60427897	2597623	1166	22902										
CDH4	1002	broad.mit.edu	37	chr20	60469978	60469978	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttccagaaagttcagcagTacacagtcatcgttcaggcc	8	13	3	1	rs207477702		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:60469978T>G	ENST00000360469.5	+	8	1151	c.1063T>G	c.(1063-1065)Tac>Gac	p.Y355D	CDH4_ENST00000543233.1_Missense_Mutation_p.Y281D	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	355	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y355D(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			AGTTCAGCAGTACACAGTCAT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	20											166	146	153					20																	60469978		2203	4300	6503	59903373	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1063T>G	20.37:g.60469978T>G	ENSP00000353656:p.Tyr355Asp		59903373	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891543	0.72524	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.70164	-0.46;-0.46	4.6	4.6	0.57074	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.89458	0.6721	H	0.99368	4.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93612	0.6940	9	.	.	.	.	13.9657	0.64207	0.0:0.0:0.0:1.0	.	355	P55283	CADH4_HUMAN	D	355;263;281	ENSP00000353656:Y355D;ENSP00000443301:Y281D	.	Y	+	1	0	CDH4	59903373	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.394000	0.79862	1.712000	0.51347	0.477000	0.44152	TAC		0.433	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		G	60469978	T	G	60469978	3	3	77	1	0	0	0	0	1	0	0	0	3118	1638	57	4	1093	4	CDH4	20	60469978	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	42081	60469978	2555542	1167	22903										
CDH4	1002	broad.mit.edu	37	chr20	60503417	60503417	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaccccaacatcggcccctaCgtcttcgagctgccctttgt	8	17	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:60503417C>T	ENST00000360469.5	+	12	2029	c.1941C>T	c.(1939-1941)taC>taT	p.Y647Y	CDH4_ENST00000543233.1_Silent_p.Y573Y	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	647	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y647Y(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TCGGCCCCTACGTCTTCGAGC	0.652																																																1	Substitution - coding silent(1)	large_intestine(1)	20											80	81	81					20																	60503417		2203	4300	6503	59936812	SO:0001819	synonymous_variant	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1941C>T	20.37:g.60503417C>T			59936812	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																				0.652	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60503417	C	T	60503417	2	4	77	1	0	0	0	0	0	0	0	1	3118	547	19	1		1	CDH4	20	60503417	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	33439	60503417	2522103	1168	22904										
ZNF512B	57473	broad.mit.edu	37	chr20	62598771	62598771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctggttctcggcttttggcCgcccctttttcttcccttct	7	16	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr20:62598771C>T	ENST00000450537.1	-	3	287	c.227G>A	c.(226-228)cGg>cAg	p.R76Q	ZNF512B_ENST00000217130.3_Missense_Mutation_p.R76Q|ZNF512B_ENST00000369888.1_Missense_Mutation_p.R76Q			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R76Q(1)		NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GGCTTTTGGCCGCCCCTTTTT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	20											139	135	136					20																	62598771		2203	4300	6503	62069215	SO:0001583	missense	57473			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.227G>A	20.37:g.62598771C>T	ENSP00000393795:p.Arg76Gln		62069215	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255525	0.95336	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.56444	0.46;0.46;0.46	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.60996	0.2312	L	0.29908	0.895	0.38883	D	0.956947	D	0.89917	1.0	D	0.63957	0.92	T	0.66380	-0.5938	10	0.72032	D	0.01	-18.7485	17.2884	0.87149	0.0:1.0:0.0:0.0	.	76	Q96KM6	Z512B_HUMAN	Q	76	ENSP00000358904:R76Q;ENSP00000393795:R76Q;ENSP00000217130:R76Q	ENSP00000217130:R76Q	R	-	2	0	ZNF512B	62069215	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	6.698000	0.74608	2.513000	0.84729	0.561000	0.74099	CGG		0.637	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		T	62598771	C	T	62598771	3	4	77	1	0	0	0	0	1	0	0	0	17996	652	23	1	2511	1	ZNF512B	20	62598771	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2095354	62598771	426749	1169	22905										
C21orf91	54149	broad.mit.edu	37	chr21	19168965	19168966	+	Frame_Shift_Ins	INS	-	-	T													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggactagagattgtctcttcINSttttttctgtgcctggttgt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:19168965_19168966insT	ENST00000400558.3	-	3	687_688	c.597_598insA	c.(595-600)aaagaafs	p.E200fs	C21orf91_ENST00000493464.1_5'Flank|C21orf91_ENST00000284881.4_Frame_Shift_Ins_p.E200fs|C21orf91_ENST00000400559.3_Frame_Shift_Ins_p.E200fs|AL109761.5_ENST00000428689.1_RNA	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91									p.E200fs*6(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		ATTGTCTCTTCTTTTTTCTGTG	0.411																																																1	Insertion - Frameshift(1)	large_intestine(1)	21																																								18090837	SO:0001589	frameshift_variant	54149			AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"cold sore susceptibility gene 1", "early undifferentiated retina and lens"		"chromosome 21 open reading frame 38"	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.598dupA	21.37:g.19168971_19168971dupT	ENSP00000383403:p.Glu200fs		18090836		Frame_Shift_Ins	INS	ENST00000400558.3	37	CCDS42909.1																																																																																				0.411	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447		T	19168966	-	T	19168965	7	5	77	1	0	1	1	0	0	0	0	0	2140	922	32	0	307	0	C21orf91	21	19168965	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10		19168965	28960930	1170	22906										
TMPRSS15	5651	broad.mit.edu	37	chr21	19770613	19770613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggatgttattttaaatgtcGctctggcttcatgactctgt	9	8	3	1	rs199751836		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:19770613G>A	ENST00000284885.3	-	2	212	c.179C>T	c.(178-180)gCg>gTg	p.A60V		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	60	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.A60V(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TTTAAATGTCGCTCTGGCTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	21											78	79	78					21																	19770613		2203	4300	6503	18692484	SO:0001583	missense	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.179C>T	21.37:g.19770613G>A	ENSP00000284885:p.Ala60Val		18692484	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	24.8	4.567927	0.86439	.	.	ENSG00000154646	ENST00000284885;ENST00000422787	T;T	0.37915	1.17;1.17	5.23	5.23	0.72850	SEA (3);	0.204191	0.40385	N	0.001101	T	0.18215	0.0437	N	0.08118	0	0.19775	N	0.99996	B	0.29270	0.24	B	0.24541	0.054	T	0.15093	-1.0449	9	.	.	.	.	11.9071	0.52719	0.0:0.8251:0.1749:0.0	.	60	P98073	ENTK_HUMAN	V	60;15	ENSP00000284885:A60V;ENSP00000398253:A15V	.	A	-	2	0	TMPRSS15	18692484	1.000000	0.71417	0.999000	0.59377	0.575000	0.36095	2.935000	0.48963	1.461000	0.47929	-0.132000	0.14878	GCG		0.353	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19770613	G	A	19770613	3	1	77	1	0	0	0	0	1	0	0	0	16285	1087	38	1	2976	1	TMPRSS15	21	19770613	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	601648	19770613	28359282	1171	22907										
TIAM1	7074	broad.mit.edu	37	chr21	32537376	32537376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgccctgctcgctgcaaaggCtgtgccctgtcagatgaaat	11	12	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:32537376C>T	ENST00000286827.3	-	17	3365	c.2894G>A	c.(2893-2895)aGc>aAc	p.S965N	TIAM1_ENST00000541036.1_Missense_Mutation_p.S905N	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	965					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S965N(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GCTGCAAAGGCTGTGCCCTGT	0.542																																																2	Substitution - Missense(2)	large_intestine(2)	21											61	58	59					21																	32537376		2203	4300	6503	31459247	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.2894G>A	21.37:g.32537376C>T	ENSP00000286827:p.Ser965Asn		31459247	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	7.312	0.615148	0.14129	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.41758	0.99;1.02	4.53	4.53	0.55603	.	1.186820	0.05631	N	0.581799	T	0.36826	0.0981	L	0.44542	1.39	0.23325	N	0.997907	B;B;B	0.28128	0.018;0.01;0.201	B;B;B	0.26770	0.021;0.009;0.073	T	0.17531	-1.0366	10	0.30854	T	0.27	.	7.8479	0.29437	0.1805:0.645:0.1745:0.0	.	905;905;965	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	N	965;806;905	ENSP00000286827:S965N;ENSP00000441570:S905N	ENSP00000286827:S965N	S	-	2	0	TIAM1	31459247	0.393000	0.25237	0.982000	0.44146	0.420000	0.31355	0.451000	0.21779	2.342000	0.79632	0.655000	0.94253	AGC		0.542	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32537376	C	T	32537376	3	4	77	1	0	0	0	0	1	0	0	0	15929	797	28	3	1933	3	TIAM1	21	32537376	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	12766763	32537376	15592519	1172	22908										
C2CD2	25966	broad.mit.edu	37	chr21	43327884	43327884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccagaggaactgtcgccgtcGccagcagacctgaaaagata	11	12	0	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:43327884G>A	ENST00000380486.3	-	9	1269	c.1028C>T	c.(1027-1029)gCg>gTg	p.A343V	C2CD2_ENST00000329623.7_Missense_Mutation_p.A188V	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	343	C2.					cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.A343V(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						TGTCGCCGTCGCCAGCAGACC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	21											32	36	35					21																	43327884		2203	4300	6503	42200953	SO:0001583	missense	25966			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1028C>T	21.37:g.43327884G>A	ENSP00000369853:p.Ala343Val		42200953	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368923	0.42003	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.71579	-0.58;-0.58	5.51	4.62	0.57501	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.120658	0.56097	D	0.000022	T	0.79381	0.4436	L	0.55990	1.75	0.29555	N	0.851037	D;D	0.89917	1.0;0.999	D;P	0.66351	0.943;0.904	T	0.77378	-0.2610	10	0.87932	D	0	-23.5782	13.7259	0.62759	0.0:0.3043:0.6957:0.0	.	188;343	Q6P6D1;Q9Y426	.;CU025_HUMAN	V	188;343	ENSP00000329302:A188V;ENSP00000369853:A343V	ENSP00000329302:A188V	A	-	2	0	C2CD2	42200953	0.998000	0.40836	0.180000	0.23079	0.042000	0.13812	3.090000	0.50191	1.288000	0.44600	0.650000	0.86243	GCG		0.622	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		A	43327884	G	A	43327884	3	1	77	1	0	0	0	0	1	0	0	0	2158	1087	38	1	1086	1	C2CD2	21	43327884	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	10790508	43327884	4802011	1173	22909										
CRYAA	1409	broad.mit.edu	37	chr21	44592183	44592183	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgcccccaccctctccaggaCgaccacggctacatttcccg	7	21	1	0	rs374245405		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:44592183C>T	ENST00000291554.2	+	3	407	c.315C>T	c.(313-315)gaC>gaT	p.D105D	CRYAA_ENST00000482775.1_3'UTR|CRYAA_ENST00000398132.1_Silent_p.D68D|CRYAA_ENST00000398133.1_Silent_p.D85D	NM_000394.2	NP_000385.1	P02489	CRYAA_HUMAN	crystallin, alpha A	105			D -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of apoptotic process (GO:0043066)|negative regulation of intracellular transport (GO:0032387)|protein homooligomerization (GO:0051260)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural constituent of eye lens (GO:0005212)|unfolded protein binding (GO:0051082)	p.D105D(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						CTCTCCAGGACGACCACGGCT	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	21						T		3,4403	821.5+/-416.4	0,3,2200	62	53	56		315	-0.8	1	21		56	0,8600		0,0,4300	no	coding-synonymous	CRYAA	NM_000394.2		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		105/174	44592183	3,13003	2203	4300	6503	43465252	SO:0001819	synonymous_variant	1409				CCDS13695.1	21q22.3	2011-09-05			ENSG00000160202	ENSG00000160202		"Heat shock proteins / HSPB"	2388	protein-coding gene	gene with protein product		123580		CRYA1			Standard	XM_005261093		Approved	HSPB4	uc002zdd.1	P02489	OTTHUMG00000086842	ENST00000291554.2:c.315C>T	21.37:g.44592183C>T			43465252	Q53X53	Silent	SNP	ENST00000291554.2	37	CCDS13695.1																																																																																				0.677	CRYAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195562.1			T	44592183	C	T	44592183	2	4	77	1	0	0	0	0	0	0	0	1	3911	535	19	1		1	CRYAA	21	44592183	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1264299	44592183	3537712	1174	22910										
TRAPPC10	7109	broad.mit.edu	37	chr21	45483618	45483618	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgtgggaggtggcccagcgCgccctagagctgctgcacaa	15	14	0	1	rs146263531		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr21:45483618C>T	ENST00000291574.4	+	7	1165	c.990C>T	c.(988-990)cgC>cgT	p.R330R		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	330					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.R330R(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						TGGCCCAGCGCGCCCTAGAGC	0.557													C|||	1	0.000199681	0	0	5008	,	,		18648	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	21						C		5,4401	9.9+/-24.2	0,5,2198	85	83	84		990	-1.3	1	21	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAPPC10	NM_003274.4		0,6,6497	TT,TC,CC		0.0116,0.1135,0.0461		330/1260	45483618	6,13000	2203	4300	6503	44308046	SO:0001819	synonymous_variant	7109			U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.990C>T	21.37:g.45483618C>T			44308046	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																				0.557	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		T	45483618	C	T	45483618	2	4	77	1	0	0	0	0	0	0	0	1	16497	755	27	1		1	TRAPPC10	21	45483618	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	891435	45483618	2646277	1175	22911										
IL17RA	23765	broad.mit.edu	37	chr22	17590338	17590338	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgacctccttccagaggaCgtgagggagcacctcgaagg	13	13	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:17590338C>T	ENST00000319363.6	+	13	2362	c.2229C>T	c.(2227-2229)gaC>gaT	p.D743D		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	743					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)	p.D743D(1)		endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		TTCCAGAGGACGTGAGGGAGC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	22											25	25	25					22																	17590338		2202	4299	6501	15970338	SO:0001819	synonymous_variant	23765			U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.2229C>T	22.37:g.17590338C>T			15970338	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	37	CCDS13739.1																																																																																				0.657	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		T	17590338	C	T	17590338	2	4	77	1	0	0	0	0	0	0	0	1	7660	535	19	1		1	IL17RA	22	17590338	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		17590338	33714228	1176	22912										
MICAL3	57553	broad.mit.edu	37	chr22	18363979	18363979	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agagaggatcacctgctggcCgccatgtgcccgacagggag	15	12	1	1	rs375394721		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:18363979C>T	ENST00000441493.2	-	16	2594				MICAL3_ENST00000383094.3_Intron|MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000429452.1_Missense_Mutation_p.G778S|MICAL3_ENST00000400561.2_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000585038.1_Missense_Mutation_p.G778S	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.G778S(1)		large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		ACCTGCTGGCCGCCATGTGCC	0.557													C|||	1	0.000199681	0	0	5008	,	,		19004	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											116	120	118					22																	18363979		1568	3582	5150	16743979	SO:0001627	intron_variant	57553			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2241+4664G>A	22.37:g.18363979C>T			16743979	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	4.619	0.115003	0.08831	.	.	ENSG00000093100	ENST00000429452	T	0.64085	-0.08	5.56	-11.1	0.00147	.	.	.	.	.	T	0.36799	0.0980	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33059	-0.9883	8	0.13108	T	0.6	.	13.2472	0.60029	0.0:0.5625:0.2749:0.1626	.	778	B2RXJ5	.	S	778	ENSP00000414846:G778S	ENSP00000414846:G778S	G	-	1	0	XXbac-B461K10.4	16743979	0.000000	0.05858	0.000000	0.03702	0.234000	0.25298	-1.526000	0.02229	-3.357000	0.00180	-1.004000	0.02495	GGC		0.557	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18363979	C	T	18363979	1	4	77	0	1	0	0	0	0	0	0	0	9601	652	23	1		1	MICAL3	22	18363979	Intron	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	773641	18363979	32940587	1177	22913										
ZNF74	7625	broad.mit.edu	37	chr22	20759894	20759894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccctcttcgcccagcaacgcGttcccgaggggggacccttg	12	17	1	0	rs372712683		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:20759894G>A	ENST00000400451.2	+	5	1085	c.571G>A	c.(571-573)Gtt>Att	p.V191I	ZNF74_ENST00000356671.5_Missense_Mutation_p.V191I|ZNF74_ENST00000405993.1_Missense_Mutation_p.V159I|ZNF74_ENST00000403682.3_Missense_Mutation_p.R162H|ZNF74_ENST00000357502.5_Missense_Mutation_p.R196H	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	191					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V191I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	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)			CCAGCAACGCGTTCCCGAGGG	0.667																																																1	Substitution - Missense(1)	large_intestine(1)	22						G	ILE/VAL	1,3939		0,1,1969	30	36	34		571	-3	0	22		34	0,8286		0,0,4143	no	missense	ZNF74	NM_003426.2	29	0,1,6112	AA,AG,GG		0.0,0.0254,0.0082	benign	191/645	20759894	1,12225	1970	4143	6113	19089894	SO:0001583	missense	7625			X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"Zinc fingers, C2H2-type", "-"	13144	protein-coding gene	gene with protein product		194548	"zinc finger protein 74 (Cos52)"			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.571G>A	22.37:g.20759894G>A	ENSP00000383301:p.Val191Ile		19089894	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	37	CCDS42982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.084|9.084	1.000152|1.000152	0.19121|0.19121	2.54E-4|2.54E-4	0.0|0.0	ENSG00000185252|ENSG00000185252	ENST00000403682;ENST00000357502|ENST00000400451;ENST00000356671;ENST00000405993	.|T;T;T	.|0.05513	.|3.55;3.55;3.43	3.85|3.85	-3.05|-3.05	0.05396|0.05396	.|.	.|1.938800	.|0.02813	.|N	.|0.124630	T|T	0.02380|0.02380	0.0073|0.0073	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.37865|0.37865	-0.9687|-0.9687	6|10	0.87932|0.02654	D|T	0|1	-0.7992|-0.7992	5.3392|5.3392	0.15974|0.15974	0.512:0.2716:0.2164:0.0|0.512:0.2716:0.2164:0.0	.|.	.|191	.|Q16587	.|ZNF74_HUMAN	H|I	162;196|191;191;159	.|ENSP00000383301:V191I;ENSP00000349098:V191I;ENSP00000385855:V159I	ENSP00000350101:R196H|ENSP00000349098:V191I	R|V	+|+	2|1	0|0	ZNF74|ZNF74	19089894|19089894	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.135000|-0.135000	0.10420|0.10420	-0.695000|-0.695000	0.05105|0.05105	-0.878000|-0.878000	0.02970|0.02970	CGT|GTT		0.667	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426		A	20759894	G	A	20759894	3	1	77	1	0	0	0	0	1	0	0	0	18166	1145	40	1	589	1	ZNF74	22	20759894	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2395915	20759894	30544672	1178	22914										
BCR	613	broad.mit.edu	37	chr22	23626224	23626224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tggagggggcccgcaagctgCgccacgtcttcctgttcacc	13	15	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:23626224C>T	ENST00000305877.8	+	9	2927	c.2176C>T	c.(2176-2178)Cgc>Tgc	p.R726C	BCR_ENST00000359540.3_Missense_Mutation_p.R726C	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	726	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R726C(1)	BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CCGCAAGCTGCGCCACGTCTT	0.652			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	1	Substitution - Missense(1)	large_intestine(1)	22											37	34	35					22																	23626224		2202	4299	6501	21956224	SO:0001583	missense	613				CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.2176C>T	22.37:g.23626224C>T	ENSP00000303507:p.Arg726Cys		21956224	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	37	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.391746	0.62066	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149;ENST00000427791	T;T;T	0.47528	0.84;0.84;1.68	5.64	4.63	0.57726	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.71143	0.3305	M	0.84683	2.71	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.77101	-0.2712	10	0.87932	D	0	.	13.9834	0.64319	0.0:0.9273:0.0:0.0727	.	315;391;344;726;726	B4E065;Q12843;Q12844;P11274-2;P11274	.;.;.;.;BCR_HUMAN	C	726;726;391;210	ENSP00000303507:R726C;ENSP00000352535:R726C;ENSP00000396531:R210C	ENSP00000303507:R726C	R	+	1	0	BCR	21956224	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	7.562000	0.82300	1.546000	0.49388	-0.136000	0.14681	CGC		0.652	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		T	23626224	C	T	23626224	3	4	77	1	0	0	0	0	1	0	0	0	1389	768	27	1	2210	1	BCR	22	23626224	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2866330	23626224	27678342	1179	22915										
CABIN1	23523	broad.mit.edu	37	chr22	24561508	24561508	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	atgaccgcaggaagtatctgCgagatgctgaccgccaggtc	13	11	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:24561508C>T	ENST00000398319.2	+	31	5306	c.4921C>T	c.(4921-4923)Cga>Tga	p.R1641*	CABIN1_ENST00000337989.7_Nonsense_Mutation_p.R66*|CABIN1_ENST00000263119.5_Nonsense_Mutation_p.R1641*|CABIN1_ENST00000405822.2_Nonsense_Mutation_p.R1562*	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1641					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.R1641*(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GAAGTATCTGCGAGATGCTGA	0.612																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											83	59	67					22																	24561508		2201	4300	6501	22891508	SO:0001587	stop_gained	23523			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.4921C>T	22.37:g.24561508C>T	ENSP00000381364:p.Arg1641*		22891508	G5E9F3|Q6PHY0|Q9Y460	Nonsense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	38	7.186191	0.98121	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319;ENST00000337989;ENST00000403176	.	.	.	4.47	4.47	0.54385	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5994	0.84807	0.0:1.0:0.0:0.0	.	.	.	.	X	1641;1562;1641;66;66	.	ENSP00000263119:R1641X	R	+	1	2	CABIN1	22891508	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.701000	0.61810	2.240000	0.73641	0.650000	0.86243	CGA		0.612	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24561508	C	T	24561508	4	4	77	1	0	0	0	0	0	1	0	0	2534	760	27	1	5039	1	CABIN1	22	24561508	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	935284	24561508	26743058	1180	22916										
TRIOBP	11078	broad.mit.edu	37	chr22	38109265	38109265	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagagggtcccacagctgcCcccaggagcaggagccggga	16	13	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:38109265C>A	ENST00000406386.3	+	5	558	c.303C>A	c.(301-303)gcC>gcA	p.A101A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	101					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.A101A(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CCACAGCTGCCCCCAGGAGCA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	22											40	48	46					22																	38109265		1913	4134	6047	36439211	SO:0001819	synonymous_variant	11078			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.303C>A	22.37:g.38109265C>A			36439211	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																				0.637	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			A	38109265	C	A	38109265	2	1	77	1	0	0	0	0	0	0	0	1	16593	610	22	2		2	TRIOBP	22	38109265	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	13547757	38109265	13195301	1181	22917										
MICALL1	85377	broad.mit.edu	37	chr22	38308394	38308394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agaaggagctggggatccccGctctcctggaccccaatgac	12	14	1	2	rs114708609	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:38308394G>A	ENST00000215957.6	+	3	358	c.232G>A	c.(232-234)Gct>Act	p.A78T		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	78	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)	p.A78T(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GGGGATCCCCGCTCTCCTGGA	0.592													G|||	6	0.00119808	0.0038	0	5008	,	,		17461	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22						G	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	80	71	74		232	4.7	1	22	dbSNP_132	74	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MICALL1	NM_033386.3	58	0,7,6496	AA,AG,GG		0.0116,0.1362,0.0538	probably-damaging	78/864	38308394	7,12999	2203	4300	6503	36638340	SO:0001583	missense	85377			BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.232G>A	22.37:g.38308394G>A	ENSP00000215957:p.Ala78Thr		36638340	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	35	5.488600	0.96323	0.001362	1.16E-4	ENSG00000100139	ENST00000215957	D	0.94793	-3.52	4.69	4.69	0.59074	Calponin homology domain (5);	0.310182	0.22740	N	0.056202	D	0.96935	0.8999	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97262	0.9905	10	0.66056	D	0.02	.	18.2487	0.89996	0.0:0.0:1.0:0.0	.	78	Q8N3F8	MILK1_HUMAN	T	78	ENSP00000215957:A78T	ENSP00000215957:A78T	A	+	1	0	MICALL1	36638340	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	7.604000	0.82830	2.609000	0.88269	0.632000	0.83419	GCT		0.592	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		A	38308394	G	A	38308394	3	1	77	1	0	0	0	0	1	0	0	0	9603	1087	38	1	242	1	MICALL1	22	38308394	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	199129	38308394	12996172	1182	22918										
SOX10	6663	broad.mit.edu	37	chr22	38374042	38374042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggccttcccgttcttccgccGcctgggctggtacttgtagt	12	14	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:38374042G>A	ENST00000396884.2	-	3	811	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000470555.1_5'Flank|SOX10_ENST00000360880.2_Missense_Mutation_p.R177W|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	177					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)	p.R177W(1)		NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					TTCTTCCGCCGCCTGGGCTGG	0.667																																					Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)											1	Substitution - Missense(1)	large_intestine(1)	22											29	27	28					22																	38374042		2202	4300	6502	36703988	SO:0001583	missense	6663				CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"SRY (sex determining region Y)-boxes"	11190	protein-coding gene	gene with protein product	"dominant megacolon, mouse, human homolog of"	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.529C>T	22.37:g.38374042G>A	ENSP00000380093:p.Arg177Trp		36703988	B4DV62|Q6FHW7	Missense_Mutation	SNP	ENST00000396884.2	37	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.348366	0.61183	.	.	ENSG00000100146	ENST00000396884;ENST00000360880;ENST00000416937;ENST00000427770	D;D;D	0.99176	-5.52;-5.52;-5.42	4.24	2.05	0.26809	High mobility group, HMG1/HMG2 (1);	0.000000	0.85682	D	0.000000	D	0.99236	0.9734	M	0.88377	2.95	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.99780	1.1027	10	0.87932	D	0	.	12.7189	0.57131	0.0:0.0:0.3476:0.6524	.	177	P56693	SOX10_HUMAN	W	177	ENSP00000380093:R177W;ENSP00000354130:R177W;ENSP00000414853:R177W	ENSP00000354130:R177W	R	-	1	2	SOX10	36703988	0.996000	0.38824	0.991000	0.47740	0.782000	0.44232	0.254000	0.18314	0.169000	0.19679	0.455000	0.32223	CGG		0.667	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		A	38374042	G	A	38374042	3	1	77	1	0	0	0	0	1	0	0	0	14978	1086	38	1	879	1	SOX10	22	38374042	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	65648	38374042	12930524	1183	22919										
SUN2	25777	broad.mit.edu	37	chr22	39147013	39147015	+	In_Frame_Del	DEL	CTC	CTC	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tctctgagccacccgtgcctCtcctcctccgcacccgcagg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	CTC	CTC	CTC	-	CTC	CTC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:39147013_39147015delCTC	ENST00000405510.1	-	5	670_672	c.312_314delGAG	c.(310-315)aggaga>aga	p.104_105RR>R	SUN2_ENST00000406622.1_In_Frame_Del_p.104_105RR>R|SUN2_ENST00000411587.2_Intron|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000405018.1_In_Frame_Del_p.104_105RR>R|SUN2_ENST00000216064.4_In_Frame_Del_p.104_105RR>R	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	104	LMNA-binding. {ECO:0000250}.|Poly-Arg.|Ser-rich.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)	p.R105delR(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						ACCCGTGCCTCTCCTCCTCCGCA	0.655																																																1	Deletion - In frame(1)	large_intestine(1)	22																																								37476961	SO:0001651	inframe_deletion	25777			AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.312_314delGAG	22.37:g.39147019_39147021delCTC	ENSP00000385740:p.Arg105del		37476959	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	In_Frame_Del	DEL	ENST00000405510.1	37	CCDS13978.1																																																																																				0.655	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		-	39147015	CTC	-	39147013	7	5	77	1	0	1	0	1	0	0	0	0	15431	913	32	0	1899	0	SUN2	22	39147013	In_Frame_Del	DEL	CTC	TCGA-AG-A02N-01A-11W-A096-10	772971	39147013	12157553	1184	22920										
CBX7	23492	broad.mit.edu	37	chr22	39530443	39530443	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcgcagcaggctcccactcGccagccgcctgcaggacgtc	12	18	0	0	rs376032300		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:39530443G>A	ENST00000216133.5	-	5	766	c.561C>T	c.(559-561)ggC>ggT	p.G187G	CBX7_ENST00000475962.1_Intron|CBX7_ENST00000401405.3_Silent_p.G94G	NM_175709.3	NP_783640.1	O95931	CBX7_HUMAN	chromobox homolog 7	187					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sebaceous gland development (GO:0048733)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|single-stranded RNA binding (GO:0003727)	p.G187G(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7	Melanoma(58;0.04)					GCTCCCACTCGCCAGCCGCCT	0.682																																					GBM(46;845 904 3560 9866 23971)											1	Substitution - coding silent(1)	large_intestine(1)	22						G		0,4280		0,0,2140	12	16	15		561	3.5	1	22		15	1,8475		0,1,4237	no	coding-synonymous	CBX7	NM_175709.3		0,1,6377	AA,AG,GG		0.0118,0.0,0.0078		187/252	39530443	1,12755	2140	4238	6378	37860389	SO:0001819	synonymous_variant	23492				CCDS13986.1	22q13.1	2010-07-06			ENSG00000100307	ENSG00000100307			1557	protein-coding gene	gene with protein product		608457					Standard	NM_175709		Approved		uc003axb.3	O95931	OTTHUMG00000150418	ENST00000216133.5:c.561C>T	22.37:g.39530443G>A			37860389	Q86T17	Silent	SNP	ENST00000216133.5	37	CCDS13986.1																																																																																				0.682	CBX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318020.1	NM_175709		A	39530443	G	A	39530443	2	1	77	1	0	0	0	0	0	0	0	1	2729	1074	38	1		1	CBX7	22	39530443	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	383430	39530443	11774123	1185	22921										
TNRC6B	23112	broad.mit.edu	37	chr22	40669466	40669466	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacggctggggggagagtgaCgggccagtcacaggagctcg	20	9	1	2	rs370055398		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:40669466C>T	ENST00000454349.2	+	7	3214	c.3003C>T	c.(3001-3003)gaC>gaT	p.D1001D	TNRC6B_ENST00000402203.1_Silent_p.D254D|TNRC6B_ENST00000335727.9_Silent_p.D948D|TNRC6B_ENST00000301923.9_Silent_p.D254D	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1001					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D1015D(1)		breast(1)	1						GGGAGAGTGACGGGCCAGTCA	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	22						C	,,	0,3832		0,0,1916	23	27	25		762,3003,2844	-1.5	1	22		25	1,8253		0,1,4126	no	coding-synonymous,coding-synonymous,coding-synonymous	TNRC6B	NM_001024843.1,NM_001162501.1,NM_015088.2	,,	0,1,6042	TT,TC,CC		0.0121,0.0,0.0083	,,	254/1030,1001/1834,948/1724	40669466	1,12085	1916	4127	6043	38999412	SO:0001819	synonymous_variant	23112			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3003C>T	22.37:g.40669466C>T			38999412	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	37	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352675	0.24512	0.0	1.21E-4	ENSG00000100354	ENST00000446273	.	.	.	6.04	-1.54	0.08584	.	.	.	.	.	T	0.55146	0.1902	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51965	-0.8638	4	.	.	.	-13.852	9.9474	0.41618	0.0:0.285:0.0:0.715	.	.	.	.	M	744	.	.	T	+	2	0	TNRC6B	38999412	0.869000	0.29996	0.997000	0.53966	0.998000	0.95712	-0.071000	0.11505	-0.053000	0.13289	0.563000	0.77884	ACG		0.488	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40669466	C	T	40669466	2	4	77	1	0	0	0	0	0	0	0	1	16380	535	19	1		1	TNRC6B	22	40669466	Silent	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1139023	40669466	10635100	1186	22922										
PMM1	5372	broad.mit.edu	37	chr22	41980043	41980043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gatgttcagcatgccattccGgaactcgatgaaggttccac	10	11	1	1	rs190292776		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:41980043G>A	ENST00000216259.7	-	5	478	c.394C>T	c.(394-396)Cgg>Tgg	p.R132W	PMM1_ENST00000466645.1_5'UTR	NM_002676.2	NP_002667.2	Q92871	PMM1_HUMAN	phosphomannomutase 1	132					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	metal ion binding (GO:0046872)|phosphomannomutase activity (GO:0004615)	p.R132W(1)		NS(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(2)	11						ATGCCATTCCGGAACTCGATG	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		17387	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											97	87	90					22																	41980043		2203	4300	6503	40309989	SO:0001583	missense	5372				CCDS14020.1	22q13	2008-12-01			ENSG00000100417	ENSG00000100417	5.4.2.8		9114	protein-coding gene	gene with protein product	"brain glucose-1,6-bisphosphatase"	601786				9070917, 9271215	Standard	NM_002676		Approved	Sec53	uc003bal.2	Q92871	OTTHUMG00000150972	ENST00000216259.7:c.394C>T	22.37:g.41980043G>A	ENSP00000216259:p.Arg132Trp		40309989	A8K003|Q92586	Missense_Mutation	SNP	ENST00000216259.7	37	CCDS14020.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	25.8	4.674186	0.88445	.	.	ENSG00000100417	ENST00000216259	D	0.99239	-5.61	5.41	5.41	0.78517	HAD-like domain (1);	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97896	1.0300	10	0.87932	D	0	-17.0047	19.1954	0.93686	0.0:0.0:1.0:0.0	.	132	Q92871	PMM1_HUMAN	W	132	ENSP00000216259:R132W	ENSP00000216259:R132W	R	-	1	2	PMM1	40309989	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.266000	0.72540	2.537000	0.85549	0.563000	0.77884	CGG		0.592	PMM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320711.3	NM_002676		A	41980043	G	A	41980043	3	1	77	1	0	0	0	0	1	0	0	0	12167	1115	39	1	410	1	PMM1	22	41980043	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1310577	41980043	9324523	1187	22923										
ARHGAP8	23779	broad.mit.edu	37	chr22	45241179	45241179	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	aaaaatcaaggcgaactcatCccccctgtgctgaggttcac					rs147582478	byFrequency	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:45241179delC	ENST00000389774.2	+	9	861	c.720delC	c.(718-720)atcfs	p.I240fs	ARHGAP8_ENST00000389773.5_Frame_Shift_Del_p.I331fs|PRR5-ARHGAP8_ENST00000361473.5_Frame_Shift_Del_p.I340fs|ARHGAP8_ENST00000336963.4_Frame_Shift_Del_p.I209fs|PRR5-ARHGAP8_ENST00000352766.7_Frame_Shift_Del_p.I419fs|ARHGAP8_ENST00000356099.6_Frame_Shift_Del_p.I209fs|ARHGAP8_ENST00000517296.3_Frame_Shift_Del_p.I419fs	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	240	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.P242fs*3(1)|p.P247fs*3(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GCGAACTCATCCCCCCTGTGC	0.532																																																2	Deletion - Frameshift(2)	large_intestine(2)	22											77	75	76					22																	45241179		2203	4300	6503	43619843	SO:0001589	frameshift_variant	553158			AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.720delC	22.37:g.45241179delC	ENSP00000374424:p.Ile240fs		43619843	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Frame_Shift_Del	DEL	ENST00000389774.2	37	CCDS33664.1																																																																																				0.532	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		-	45241179	C	-	45241179	7	5	77	1	0	1	0	1	0	0	0	0	888	845	30	0	750	0	ARHGAP8	22	45241179	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	3261136	45241179	6063387	1188	22924										
RIBC2	26150	broad.mit.edu	37	chr22	45813815	45813815	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaagaacgcccgtgctgaacAaaaatgcgcaggtaatgaaa							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:45813815delA	ENST00000342894.3	+	3	740	c.326delA	c.(325-327)caafs	p.Q109fs	RIBC2_ENST00000538017.1_Frame_Shift_Del_p.Q177fs			Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2	109						nucleus (GO:0005634)		p.K110fs*36(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|skin(2)|urinary_tract(1)	10		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CGTGCTGAACAAAAATGCGCA	0.423																																																1	Deletion - Frameshift(1)	large_intestine(1)	22											28	29	29					22																	45813815		2202	4294	6496	44192479	SO:0001589	frameshift_variant	26150			AK098586		22q13.3	2004-08-18	2004-08-18	2004-08-18	ENSG00000128408	ENSG00000128408			13241	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 11"	C22orf11		12477932	Standard	NM_015653		Approved	DKFZp566F0546, FLJ25720	uc011aqs.3	Q9H4K1	OTTHUMG00000151332	ENST00000342894.3:c.326delA	22.37:g.45813815delA	ENSP00000342529:p.Gln109fs		44192479	Q6ICD0|Q9Y413	Frame_Shift_Del	DEL	ENST00000342894.3	37																																																																																					0.423	RIBC2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000322250.1	NM_015653		-	45813815	A	-	45813815	7	5	77	1	0	1	0	1	0	0	0	0	13390	130	5	0	539	0	RIBC2	22	45813815	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	572636	45813815	5490751	1189	22925										
TBC1D22A	25771	broad.mit.edu	37	chr22	47189586	47189586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gacggccaaccgtgtgctgcGtaaccacagccagcggcagg	14	14	0	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:47189586G>A	ENST00000337137.4	+	3	474	c.308G>A	c.(307-309)cGt>cAt	p.R103H	TBC1D22A_ENST00000407381.3_Missense_Mutation_p.R103H|TBC1D22A_ENST00000406733.1_Missense_Mutation_p.R56H|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.R84H|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.R56H|TBC1D22A_ENST00000472791.1_3'UTR	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	103							protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)	p.R103H(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		CGTGTGCTGCGTAACCACAGC	0.711																																																1	Substitution - Missense(1)	large_intestine(1)	22											34	30	31					22																	47189586		2203	4300	6503	45568250	SO:0001583	missense	25771			AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.308G>A	22.37:g.47189586G>A	ENSP00000336724:p.Arg103His		45568250	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	37	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145264	0.37825	.	.	ENSG00000054611	ENST00000337137;ENST00000380995;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T;T	0.45668	1.9;0.89;1.92;1.9;1.9	4.66	1.27	0.21489	.	0.265374	0.38897	N	0.001538	T	0.28896	0.0717	L	0.44542	1.39	0.34454	D	0.700978	P;D;P;P	0.54397	0.887;0.966;0.944;0.887	B;B;B;B	0.41988	0.255;0.372;0.255;0.255	T	0.37572	-0.9700	10	0.36615	T	0.2	-4.3567	5.4237	0.16413	0.4995:0.0:0.5005:0.0	.	103;84;103;103	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	H	103;56;103;84;56	ENSP00000336724:R103H;ENSP00000370383:R56H;ENSP00000384036:R103H;ENSP00000347932:R84H;ENSP00000385634:R56H	ENSP00000336724:R103H	R	+	2	0	TBC1D22A	45568250	1.000000	0.71417	0.654000	0.29608	0.267000	0.26476	3.311000	0.51919	0.582000	0.29556	0.511000	0.50034	CGT		0.711	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		A	47189586	G	A	47189586	3	1	77	1	0	0	0	0	1	0	0	0	15650	1145	40	1	318	1	TBC1D22A	22	47189586	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1375771	47189586	4114980	1190	22926										
ZBED4	9889	broad.mit.edu	37	chr22	50278437	50278437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cagctctgtgtcctcgtctcCagtaaagccggtcagagagt	11	12	3	1	rs533958242		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:50278437C>T	ENST00000216268.5	+	2	1604	c.1127C>T	c.(1126-1128)cCa>cTa	p.P376L		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	376						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P376L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		TCCTCGTCTCCAGTAAAGCCG	0.632													C|||	1	0.000199681	0	0	5008	,	,		17467	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	22											51	54	53					22																	50278437		2203	4300	6503	48664441	SO:0001583	missense	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1127C>T	22.37:g.50278437C>T	ENSP00000216268:p.Pro376Leu		48664441	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595999	0.46318	.	.	ENSG00000100426	ENST00000216268	T	0.54675	0.56	5.18	4.17	0.49024	.	0.127623	0.53938	D	0.000054	T	0.50188	0.1601	L	0.56769	1.78	0.54753	D	0.999983	B	0.18461	0.028	B	0.17433	0.018	T	0.53760	-0.8393	10	0.87932	D	0	-2.3307	13.6742	0.62443	0.0:0.9262:0.0:0.0738	.	376	O75132	ZBED4_HUMAN	L	376	ENSP00000216268:P376L	ENSP00000216268:P376L	P	+	2	0	ZBED4	48664441	0.397000	0.25270	0.023000	0.16930	0.002000	0.02628	4.061000	0.57485	1.427000	0.47276	0.655000	0.94253	CCA		0.632	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50278437	C	T	50278437	3	4	77	1	0	0	0	0	1	0	0	0	17559	594	21	3	1129	3	ZBED4	22	50278437	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	3088851	50278437	1026129	1191	22927										
ZBED4	9889	broad.mit.edu	37	chr22	50280645	50280645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctgaagaaggcgtcctggcCggggctgtccgcgctggccg	17	14	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chr22:50280645C>T	ENST00000216268.5	+	2	3812	c.3335C>T	c.(3334-3336)cCg>cTg	p.P1112L		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	1112						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P1112L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		GCGTCCTGGCCGGGGCTGTCC	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	22											55	50	51					22																	50280645		2203	4300	6503	48666649	SO:0001583	missense	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.3335C>T	22.37:g.50280645C>T	ENSP00000216268:p.Pro1112Leu		48666649	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.512889	0.64522	.	.	ENSG00000100426	ENST00000216268	T	0.57907	0.37	5.17	5.17	0.71159	HAT dimerisation (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84628	0.0688	10	0.72032	D	0.01	-34.8119	18.861	0.92271	0.0:1.0:0.0:0.0	.	1112	O75132	ZBED4_HUMAN	L	1112	ENSP00000216268:P1112L	ENSP00000216268:P1112L	P	+	2	0	ZBED4	48666649	1.000000	0.71417	0.963000	0.40424	0.245000	0.25701	7.309000	0.78937	2.703000	0.92315	0.650000	0.86243	CCG		0.592	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50280645	C	T	50280645	3	4	77	1	0	0	0	0	1	0	0	0	17559	652	23	1	3337	1	ZBED4	22	50280645	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	2208	50280645	1023921	1192	22928										
MXRA5	25878	broad.mit.edu	37	chrX	3235154	3235154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agctgcctacctgaagagcgCgtcgatcatcctcttggacg	11	13	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:3235154C>T	ENST00000217939.6	-	6	6722	c.6568G>A	c.(6568-6570)Gcg>Acg	p.A2190T		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2190	Ig-like C2-type 6.					extracellular vesicular exosome (GO:0070062)		p.A2190T(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTGAAGAGCGCGTCGATCATC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	X											15	15	15					X																	3235154		2183	4279	6462	3245154	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6568G>A	X.37:g.3235154C>T	ENSP00000217939:p.Ala2190Thr		3245154	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.414630	0.25465	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.78246	-1.16	3.34	-2.35	0.06684	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.606082	0.12367	U	0.475123	T	0.60856	0.2301	N	0.16266	0.395	0.36331	D	0.858861	D	0.54964	0.969	P	0.47827	0.558	T	0.60722	-0.7207	10	0.29301	T	0.29	.	4.9572	0.14048	0.5633:0.1982:0.0:0.2385	.	2190	Q9NR99	MXRA5_HUMAN	T	2190	ENSP00000217939:A2190T	ENSP00000217939:A2190T	A	-	1	0	MXRA5	3245154	1.000000	0.71417	0.020000	0.16555	0.001000	0.01503	0.759000	0.26461	-0.441000	0.07201	-0.865000	0.03005	GCG		0.602	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3235154	C	T	3235154	3	4	77	1	0	0	0	0	1	0	0	0	10033	768	27	1	1926	1	MXRA5	23	3235154	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10		3235154	152035406	1193	22929										
MXRA5	25878	broad.mit.edu	37	chrX	3235540	3235540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaatgtgaatgctgagccccGggggcagcgagatgttctcc	15	10	1	3	rs200199741		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:3235540G>A	ENST00000217939.6	-	6	6336	c.6182C>T	c.(6181-6183)cCg>cTg	p.P2061L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2061	Ig-like C2-type 5.					extracellular vesicular exosome (GO:0070062)		p.P2061L(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GCTGAGCCCCGGGGGCAGCGA	0.682													G|||	0	0	0	0	3775	,	,		12631	0		0	False		,,,				2504	0															2	Substitution - Missense(2)	large_intestine(2)	X											26	22	23					X																	3235540		2188	4276	6464	3245540	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6182C>T	X.37:g.3235540G>A	ENSP00000217939:p.Pro2061Leu		3245540	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1	6.027727546714888E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	1.979	-0.434624	0.04669	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.65916	-0.18	3.63	3.63	0.41609	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.36703	U	0.002442	T	0.36082	0.0954	N	0.12569	0.235	0.09310	N	1	P	0.50369	0.934	B	0.42522	0.39	T	0.13176	-1.0519	10	0.19590	T	0.45	.	3.0866	0.06279	0.1964:0.0:0.5547:0.2489	.	2061	Q9NR99	MXRA5_HUMAN	L	2061	ENSP00000217939:P2061L	ENSP00000217939:P2061L	P	-	2	0	MXRA5	3245540	0.462000	0.25791	0.189000	0.23252	0.031000	0.12232	2.420000	0.44679	1.440000	0.47531	0.597000	0.82753	CCG		0.682	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3235540	G	A	3235540	3	1	77	1	0	0	0	0	1	0	0	0	10033	1116	39	1	2312	1	MXRA5	23	3235540	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	386	3235540	152035020	1194	22930										
MXRA5	25878	broad.mit.edu	37	chrX	3241421	3241421	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtttgccatgtttatccttcGtctagattcaaacactctgc	6	11	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:3241421G>A	ENST00000217939.6	-	5	2459	c.2305C>T	c.(2305-2307)Cga>Tga	p.R769*		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	769						extracellular vesicular exosome (GO:0070062)		p.R769*(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TTTATCCTTCGTCTAGATTCA	0.453																																																2	Substitution - Nonsense(2)	large_intestine(2)	X											122	108	112					X																	3241421		2203	4300	6503	3251421	SO:0001587	stop_gained	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2305C>T	X.37:g.3241421G>A	ENSP00000217939:p.Arg769*		3251421	Q6P1M7|Q9Y3Y8	Nonsense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	g	36	5.678698	0.96764	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	.	.	.	3.63	1.38	0.22167	.	0.000000	0.34828	U	0.003645	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6057	0.45392	0.0:0.0:0.4626:0.5373	.	.	.	.	X	769	.	ENSP00000217939:R769X	R	-	1	2	MXRA5	3251421	0.948000	0.32251	0.004000	0.12327	0.255000	0.26057	1.538000	0.36094	0.397000	0.25310	0.529000	0.55759	CGA		0.453	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3241421	G	A	3241421	4	1	77	1	0	0	0	0	0	1	0	0	10033	1153	40	1	6193	1	MXRA5	23	3241421	Nonsense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	5881	3241421	152029139	1195	22931										
CLCN4	1183	broad.mit.edu	37	chrX	10188908	10188908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttcggcagtgcctggtgaCgcggagcgggtgagtagccg	19	10	0	2	rs483352716		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:10188908C>T	ENST00000380833.4	+	12	2574	c.2183C>T	c.(2182-2184)aCg>aTg	p.T728M	CLCN4_ENST00000380829.1_Missense_Mutation_p.T697M|CLCN4_ENST00000421085.2_Missense_Mutation_p.T634M	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	728	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.T728M(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TGCCTGGTGACGCGGAGCGGG	0.572																																					Melanoma(74;1050 1296 1576 30544 38374)											1	Substitution - Missense(1)	large_intestine(1)	X											82	69	74					X																	10188908		2203	4300	6503	10148908	SO:0001583	missense	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.2183C>T	X.37:g.10188908C>T	ENSP00000370213:p.Thr728Met		10148908	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	c	26.3	4.722808	0.89298	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.94457	-3.43;-3.43;-3.43	5.36	5.36	0.76844	Cystathionine beta-synthase, core (3);	0.000000	0.85682	D	0.000000	D	0.95996	0.8696	L	0.52823	1.66	0.80722	D	1	D	0.59357	0.985	P	0.60886	0.88	D	0.96231	0.9168	10	0.59425	D	0.04	-26.3598	18.267	0.90055	0.0:1.0:0.0:0.0	.	728	P51793	CLCN4_HUMAN	M	728;697;634	ENSP00000370213:T728M;ENSP00000370209:T697M;ENSP00000405754:T634M	ENSP00000370209:T697M	T	+	2	0	CLCN4	10148908	1.000000	0.71417	0.884000	0.34674	0.973000	0.67179	7.649000	0.83500	2.253000	0.74438	0.591000	0.81541	ACG		0.572	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			T	10188908	C	T	10188908	3	4	77	1	0	0	0	0	1	0	0	0	3471	536	19	1	2221	1	CLCN4	23	10188908	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	6947487	10188908	145081652	1196	22932										
FRMPD4	9758	broad.mit.edu	37	chrX	12734435	12734435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cccggggaggccccctgtgaGgcagactacagaagtctagc	14	13	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:12734435G>T	ENST00000380682.1	+	15	2363	c.1857G>T	c.(1855-1857)gaG>gaT	p.E619D		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	619					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.E619D(1)|p.E609D(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CCCCCTGTGAGGCAGACTACA	0.532																																																2	Substitution - Missense(2)	large_intestine(2)	X											79	79	79					X																	12734435		2203	4300	6503	12644356	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1857G>T	X.37:g.12734435G>T	ENSP00000370057:p.Glu619Asp		12644356	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.688396	0.29962	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.22743	1.94	5.86	2.14	0.27477	.	0.401550	0.28470	N	0.015224	T	0.15825	0.0381	L	0.54323	1.7	0.09310	N	1	B;B	0.31026	0.004;0.304	B;B	0.23574	0.004;0.047	T	0.14839	-1.0458	10	0.27785	T	0.31	.	7.0236	0.24928	0.5507:0.0:0.4493:0.0	.	611;619	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	D	619;610;608	ENSP00000370057:E619D	ENSP00000304583:E608D	E	+	3	2	FRMPD4	12644356	1.000000	0.71417	0.880000	0.34516	0.868000	0.49771	1.625000	0.37029	0.634000	0.30469	0.600000	0.82982	GAG		0.532	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12734435	G	T	12734435	3	4	77	1	0	0	0	0	1	0	0	0	6078	991	35	2	1915	2	FRMPD4	23	12734435	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2545527	12734435	142536125	1197	22933										
GLRA2	2742	broad.mit.edu	37	chrX	14625262	14625262	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ctttacctcagttgggtacaCgatgaatgacctgatatttg	9	8	1	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:14625262C>T	ENST00000218075.4	+	6	1117	c.587C>T	c.(586-588)aCg>aTg	p.T196M	GLRA2_ENST00000443437.2_Missense_Mutation_p.T107M|GLRA2_ENST00000355020.4_Missense_Mutation_p.T196M	NM_002063.3	NP_002054.1	P23416	GLRA2_HUMAN	glycine receptor, alpha 2	196					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)|synapse assembly (GO:0007416)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.T196M(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(22)|ovary(1)|prostate(1)|skin(2)	37	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)|Lindane(DB00431)	GTTGGGTACACGATGAATGAC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											144	131	136					X																	14625262		2203	4300	6503	14535183	SO:0001583	missense	2742				CCDS14160.1, CCDS48085.1, CCDS55371.1	Xp22.2	2012-02-07			ENSG00000101958	ENSG00000101958		"Ligand-gated ion channels / Glycine receptors"	4327	protein-coding gene	gene with protein product		305990		GLR			Standard	NM_002063		Approved		uc010nep.3	P23416	OTTHUMG00000021166	ENST00000218075.4:c.587C>T	X.37:g.14625262C>T	ENSP00000218075:p.Thr196Met		14535183	A8K0J6|B2R6I8|B7Z4F5|J3KQ59|Q53YX7|Q6ICQ0|Q99862	Missense_Mutation	SNP	ENST00000218075.4	37	CCDS14160.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918089	0.92249	.	.	ENSG00000101958	ENST00000443437;ENST00000218075;ENST00000355020;ENST00000415367	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	5.58	5.58	0.84498	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.91529	0.7325	M	0.93854	3.465	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.994	D	0.93462	0.6811	10	0.87932	D	0	.	18.7972	0.91999	0.0:1.0:0.0:0.0	.	180;196;196	B7Z4E9;P23416;P23416-2	.;GLRA2_HUMAN;.	M	107;196;196;180	ENSP00000387756:T107M;ENSP00000218075:T196M;ENSP00000347123:T196M;ENSP00000391606:T180M	ENSP00000218075:T196M	T	+	2	0	GLRA2	14535183	1.000000	0.71417	0.921000	0.36526	0.994000	0.84299	7.701000	0.84566	2.471000	0.83476	0.600000	0.82982	ACG		0.383	GLRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055829.1			T	14625262	C	T	14625262	3	4	77	1	0	0	0	0	1	0	0	0	6475	536	19	1	681	1	GLRA2	23	14625262	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	1890827	14625262	140645298	1198	22934										
FANCB	2187	broad.mit.edu	37	chrX	14882750	14882750	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tacaacgaaaaagaggtttcCtccacctgaatccataagtt	6	10	0	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:14882750C>A	ENST00000324138.3	-	2	1036	c.883G>T	c.(883-885)Gga>Tga	p.G295*	FANCB_ENST00000398334.1_Nonsense_Mutation_p.G295*	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	295					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)		p.G295*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					AAGAGGTTTCCTCCACCTGAA	0.368								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Nonsense(1)	large_intestine(1)	X											100	88	92					X																	14882750		2203	4300	6503	14792671	SO:0001587	stop_gained	2187	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.883G>T	X.37:g.14882750C>A	ENSP00000326819:p.Gly295*		14792671	B2RMZ4|Q7Z2U2|Q86XG1	Nonsense_Mutation	SNP	ENST00000324138.3	37	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	C	35	5.544977	0.96488	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.43	4.33	0.51752	.	0.850064	0.10678	N	0.646674	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-0.4179	9.1198	0.36780	0.0:0.7696:0.0:0.2304	.	.	.	.	X	295	.	ENSP00000326819:G295X	G	-	1	0	FANCB	14792671	0.005000	0.15991	0.001000	0.08648	0.962000	0.63368	1.025000	0.30090	0.903000	0.36546	0.513000	0.50165	GGA		0.368	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		A	14882750	C	A	14882750	4	1	77	1	0	0	0	0	0	1	0	0	5682	690	24	2	1728	2	FANCB	23	14882750	Nonsense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	257488	14882750	140387810	1199	22935										
NHS	4810	broad.mit.edu	37	chrX	17745016	17745016	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gaacctcagttagatgcttcGgatattccaccattcaaaga	7	10	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:17745016G>A	ENST00000380060.3	+	6	3065	c.2727G>A	c.(2725-2727)tcG>tcA	p.S909S	NHS_ENST00000398097.3_Silent_p.S753S	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	930					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.S909S(1)		breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TAGATGCTTCGGATATTCCAC	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	X											166	156	159					X																	17745016		2203	4300	6503	17654937	SO:0001819	synonymous_variant	4810				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.2727G>A	X.37:g.17745016G>A			17654937	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Silent	SNP	ENST00000380060.3	37	CCDS14181.1																																																																																				0.433	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		A	17745016	G	A	17745016	2	1	77	1	0	0	0	0	0	0	0	1	10442	1103	39	1		1	NHS	23	17745016	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	2862266	17745016	137525544	1200	22936										
ZNF645	158506	broad.mit.edu	37	chrX	22291957	22291957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cctcagaaacagcattatgcGccacctccatctccatcatc	4	17	3	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:22291957G>A	ENST00000323684.1	+	1	893	c.849G>A	c.(847-849)gcG>gcA	p.A283A		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	283	Pro-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A283A(3)		cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						AGCATTATGCGCCACCTCCAT	0.473																																																3	Substitution - coding silent(3)	large_intestine(2)|urinary_tract(1)	X											150	116	127					X																	22291957		2203	4300	6503	22201878	SO:0001819	synonymous_variant	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.849G>A	X.37:g.22291957G>A			22201878	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																				0.473	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		A	22291957	G	A	22291957	2	1	77	1	0	0	0	0	0	0	0	1	18100	1074	38	1		1	ZNF645	23	22291957	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4546941	22291957	132978603	1201	22937										
CASK	8573	broad.mit.edu	37	chrX	41428984	41428984	+	Frame_Shift_Del	DEL	T	T	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	acaatgatttagttcattcaTttttaaagtgattccctgtt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:41428984delT	ENST00000378163.1	-	16	1993	c.1519delA	c.(1519-1521)atgfs	p.M507fs	CASK_ENST00000472704.1_5'UTR|RNU6-1321P_ENST00000390905.1_RNA|CASK_ENST00000378154.1_Frame_Shift_Del_p.M507fs|CASK_ENST00000361962.4_Frame_Shift_Del_p.M507fs|CASK_ENST00000442742.2_Frame_Shift_Del_p.M507fs|CASK_ENST00000318588.9_Frame_Shift_Del_p.M507fs|CASK_ENST00000378166.4_Frame_Shift_Del_p.M507fs|CASK_ENST00000378158.1_Frame_Shift_Del_p.M507fs|CASK_ENST00000421587.2_Frame_Shift_Del_p.M501fs			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	507	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)	p.M507fs*1(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						AGTTCATTCATTTTTAAAGTG	0.303																																					NSCLC(42;104 1086 3090 27189 35040)											1	Deletion - Frameshift(1)	large_intestine(1)	X											92	89	90					X																	41428984		2202	4300	6502	41313928	SO:0001589	frameshift_variant	8573			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1519delA	X.37:g.41428984delT	ENSP00000367405:p.Met507fs		41313928	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Frame_Shift_Del	DEL	ENST00000378163.1	37																																																																																					0.303	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		-	41428984	T	-	41428984	7	5	77	1	0	1	0	1	0	0	0	0	2671	1493	52	0	1309	0	CASK	23	41428984	Frame_Shift_Del	DEL	T	TCGA-AG-A02N-01A-11W-A096-10	19137027	41428984	113841576	1202	22938										
KCND1	3750	broad.mit.edu	37	chrX	48826473	48826473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtagaagaattccttctccGagctgcccagcaaggtgtct	10	12	2	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:48826473G>A	ENST00000218176.3	-	1	1503	c.206C>T	c.(205-207)tCg>tTg	p.S69L	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	69					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)	p.S69L(1)		endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	TTCCTTCTCCGAGCTGCCCAG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	X											46	31	36					X																	48826473		2203	4300	6503	48711417	SO:0001583	missense	3750			AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.206C>T	X.37:g.48826473G>A	ENSP00000218176:p.Ser69Leu		48711417	A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	37	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	G	7.149	0.583285	0.13749	.	.	ENSG00000102057	ENST00000218176	T	0.34472	1.36	4.5	3.64	0.41730	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.084250	0.49916	D	0.000129	T	0.20820	0.0501	N	0.16166	0.38	0.44508	D	0.99745	B	0.27594	0.182	B	0.26693	0.072	T	0.05115	-1.0905	10	0.27785	T	0.31	.	10.8444	0.46735	0.097:0.0:0.903:0.0	.	69	Q9NSA2	KCND1_HUMAN	L	69	ENSP00000218176:S69L	ENSP00000218176:S69L	S	-	2	0	KCND1	48711417	1.000000	0.71417	0.143000	0.22291	0.103000	0.19146	9.601000	0.98297	1.029000	0.39812	0.513000	0.50165	TCG		0.567	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		A	48826473	G	A	48826473	3	1	77	1	0	0	0	0	1	0	0	0	8039	1059	37	1	1761	1	KCND1	23	48826473	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	7397489	48826473	106444087	1203	22939										
PRICKLE3	4007	broad.mit.edu	37	chrX	49032336	49032336	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gtgattatgatgatggtggcGgcgacggctgggggccctgg	20	7	0	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:49032336G>A	ENST00000376317.3	-	9	1628	c.1534C>T	c.(1534-1536)Cgc>Tgc	p.R512C	PRICKLE3_ENST00000540849.1_Missense_Mutation_p.R444C|PRICKLE3_ENST00000538114.1_Missense_Mutation_p.R336C|PRICKLE3_ENST00000536904.1_Missense_Mutation_p.R431C	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)	512							zinc ion binding (GO:0008270)	p.R512C(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						tgatggtggCGGCGACGGCTG	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	X											46	37	40					X																	49032336		2203	4300	6503	48919280	SO:0001583	missense	4007			BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"LIM domain only 6"	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.1534C>T	X.37:g.49032336G>A	ENSP00000365494:p.Arg512Cys		48919280	B7Z8F2|O76007|Q53XR5	Missense_Mutation	SNP	ENST00000376317.3	37	CCDS14320.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	4.775|4.775	0.144177|0.144177	0.09134|0.09134	.|.	.|.	ENSG00000012211|ENSG00000012211	ENST00000453382|ENST00000376317;ENST00000536904;ENST00000540849;ENST00000538114	.|T;T;T;T	.|0.70399	.|-0.44;-0.44;-0.44;-0.48	3.79|3.79	1.87|1.87	0.25490|0.25490	.|.	.|0.647725	.|0.12850	.|N	.|0.433981	T|T	0.50905|0.50905	0.1643|0.1643	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.06786	.|0.0;0.001;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.45220|0.45220	-0.9276|-0.9276	5|10	.|0.87932	.|D	.|0	-4.721|-4.721	4.0521|4.0521	0.09800|0.09800	0.1331:0.0:0.6389:0.228|0.1331:0.0:0.6389:0.228	.|.	.|474;431;512	.|B7Z6S4;B7Z8F2;O43900	.|.;.;PRIC3_HUMAN	L|C	524|512;431;444;336	.|ENSP00000365494:R512C;ENSP00000441385:R431C;ENSP00000446051:R444C;ENSP00000441743:R336C	.|ENSP00000365494:R512C	P|R	-|-	2|1	0|0	PRICKLE3|PRICKLE3	48919280|48919280	0.051000|0.051000	0.20477|0.20477	0.001000|0.001000	0.08648|0.08648	0.025000|0.025000	0.11179|0.11179	2.693000|2.693000	0.47027|0.47027	0.647000|0.647000	0.30713|0.30713	0.455000|0.455000	0.32223|0.32223	CCG|CGC		0.662	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060811.1	NM_006150		A	49032336	G	A	49032336	3	1	77	1	0	0	0	0	1	0	0	0	12522	1116	39	1	317	1	PRICKLE3	23	49032336	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	205863	49032336	106238224	1204	22940										
DGKK	139189	broad.mit.edu	37	chrX	50144116	50144116	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcaacattccttggaaaaccGtctcctacagtcatcatgca	6	13	3	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:50144116G>A	ENST00000376025.2	-	0	1389							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R240W(1)		central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					TTGGAAAACCGTCTCCTACAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	X											70	58	62					X																	50144116		1927	4130	6057	50160856			139189			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50144116G>A			50160856	B2RP91	Missense_Mutation	SNP	ENST00000376025.2	37																																																																																					0.448	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742		A	50144116	G	A	50144116	1	1	77	0	1	0	0	0	0	0	0	0	4483	1144	40	1		1	DGKK	23	50144116	RNA	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1111780	50144116	105126444	1205	22941										
IQSEC2	23096	broad.mit.edu	37	chrX	53283905	53283905	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gcttgccctcgaagtacgcgGggttctgtgccttctcatac	11	13	2	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:53283905G>T	ENST00000375368.5	-	3	1378	c.1178C>A	c.(1177-1179)cCc>cAc	p.P393H	IQSEC2_ENST00000396435.3_Missense_Mutation_p.P403H|IQSEC2_ENST00000375365.2_Missense_Mutation_p.P198H			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	393					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P400H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						GAAGTACGCGGGGTTCTGTGC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	X											45	29	34					X																	53283905		2202	4300	6502	53300630	SO:0001583	missense	23096			AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.1178C>A	X.37:g.53283905G>T	ENSP00000364517:p.Pro393His		53300630	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	37		.	.	.	.	.	.	.	.	.	.	G	24.5	4.540031	0.85917	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	D;D;D	0.81499	-1.5;-1.5;-1.5	5.09	5.09	0.68999	.	0.301216	0.29059	N	0.013275	T	0.78084	0.4228	L	0.27053	0.805	0.40365	D	0.979282	D;P	0.54207	0.965;0.867	P;P	0.53313	0.723;0.466	T	0.75096	-0.3438	10	0.17369	T	0.5	.	16.3278	0.82994	0.0:0.0:1.0:0.0	.	403;198	Q5JU85-2;Q5JU85-3	.;.	H	403;393;198	ENSP00000379712:P403H;ENSP00000364517:P393H;ENSP00000364514:P198H	ENSP00000364514:P198H	P	-	2	0	IQSEC2	53300630	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	9.424000	0.97464	2.108000	0.64289	0.513000	0.50165	CCC		0.622	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53283905	G	T	53283905	3	4	77	1	0	0	0	0	1	0	0	0	7839	1232	43	2	3306	2	IQSEC2	23	53283905	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3139789	53283905	101986655	1206	22942										
ZXDB	158586	broad.mit.edu	37	chrX	57619606	57619606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tgcgaggagagcttccccacGcaggccaaactcagcgccca	11	16	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:57619606G>A	ENST00000374888.1	+	1	1338	c.1125G>A	c.(1123-1125)acG>acA	p.T375T		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	375	Required for interaction with ZXDC. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.T375T(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						GCTTCCCCACGCAGGCCAAAC	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	X											105	88	94					X																	57619606		2203	4300	6503	57636331	SO:0001819	synonymous_variant	158586			L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.1125G>A	X.37:g.57619606G>A			57636331	A8K151|Q9UBB3	Silent	SNP	ENST00000374888.1	37	CCDS35313.1																																																																																				0.562	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		A	57619606	G	A	57619606	2	1	77	1	0	0	0	0	0	0	0	1	18290	1074	38	1		1	ZXDB	23	57619606	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	4335701	57619606	97650954	1207	22943										
FAM123B	139285	broad.mit.edu	37	chrX	63412648	63412648	+	Frame_Shift_Del	DEL	A	A	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cggtgacggcggatactgctAaaaaagccttttaggccttt							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:63412648delA	ENST00000330258.3	-	2	791	c.519delT	c.(517-519)tttfs	p.F173fs	AMER1_ENST00000403336.1_Frame_Shift_Del_p.F173fs|AMER1_ENST00000374869.3_Frame_Shift_Del_p.F173fs	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	173					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.F173fs*36(6)									GGATACTGCTAAAAAAGCCTT	0.562																																																73	Whole gene deletion(67)|Deletion - Frameshift(6)	kidney(65)|large_intestine(7)|ovary(1)	X											52	50	51					X																	63412648		2203	4300	6503	63329373	SO:0001589	frameshift_variant	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.519delT	X.37:g.63412648delA	ENSP00000329117:p.Phe173fs		63329373	A2IB86|Q8N885	Frame_Shift_Del	DEL	ENST00000330258.3	37	CCDS14377.2																																																																																				0.562	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		-	63412648	A	-	63412648	7	5	77	1	0	1	0	1	0	0	0	0	5439	359	13	0	2892	0	FAM123B	23	63412648	Frame_Shift_Del	DEL	A	TCGA-AG-A02N-01A-11W-A096-10	5793042	63412648	91857912	1208	22944										
MSN	4478	broad.mit.edu	37	chrX	64949552	64949552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ataagtctggctacctggccGgagacaagttgctcccgcag	12	12	1	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:64949552G>A	ENST00000360270.5	+	4	617	c.445G>A	c.(445-447)Gga>Aga	p.G149R		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	149	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.G149R(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						CTACCTGGCCGGAGACAAGTT	0.587			T	ALK	ALCL																																		Dom	yes		X	Xq11.2-q12	4478	moesin		L	1	Substitution - Missense(1)	large_intestine(1)	X											53	36	42					X																	64949552		2203	4300	6503	64866277	SO:0001583	missense	4478			M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.445G>A	X.37:g.64949552G>A	ENSP00000353408:p.Gly149Arg		64866277		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484133	0.44147	.	.	ENSG00000147065	ENST00000360270	T	0.76968	-1.06	5.85	5.85	0.93711	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.152115	0.64402	D	0.000012	T	0.64549	0.2608	N	0.21282	0.65	0.40583	D	0.981417	B	0.06786	0.001	B	0.09377	0.004	T	0.60347	-0.7281	10	0.29301	T	0.29	.	11.9562	0.52983	0.0848:0.0:0.9152:0.0	.	149	P26038	MOES_HUMAN	R	149	ENSP00000353408:G149R	ENSP00000353408:G149R	G	+	1	0	MSN	64866277	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	1.686000	0.37669	2.484000	0.83849	0.529000	0.55759	GGA		0.587	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		A	64949552	G	A	64949552	3	1	77	1	0	0	0	0	1	0	0	0	9915	1117	39	1	459	1	MSN	23	64949552	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	1536904	64949552	90321008	1209	22945										
KIAA2022	340533	broad.mit.edu	37	chrX	73960071	73960071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	caactttttgtgtgtcggtcCgttattgcctaaagtgctca	9	9	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:73960071C>T	ENST00000055682.6	-	3	4932	c.4321G>A	c.(4321-4323)Gga>Aga	p.G1441R		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1441					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.G1441R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TGTGTCGGTCCGTTATTGCCT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	X											212	175	187					X																	73960071		2203	4300	6503	73876796	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4321G>A	X.37:g.73960071C>T	ENSP00000055682:p.Gly1441Arg		73876796	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.05|15.05	2.719519|2.719519	0.48728|0.48728	.|.	.|.	ENSG00000050030|ENSG00000050030	ENST00000373468;ENST00000055682|ENST00000424929	T;T|.	0.33216|.	1.42;1.42|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.277109|.	0.41938|.	D|.	0.000789|.	T|T	0.52008|0.52008	0.1708|0.1708	N|N	0.17082|0.17082	0.46|0.46	0.53688|0.53688	D|D	0.999972|0.999972	P|.	0.39022|.	0.655|.	B|.	0.36885|.	0.235|.	T|T	0.48714|0.48714	-0.9011|-0.9011	10|5	0.62326|.	D|.	0.03|.	-0.9325|-0.9325	18.1933|18.1933	0.89813|0.89813	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1441|.	Q5QGS0|.	K2022_HUMAN|.	R|Q	1441|42	ENSP00000362567:G1441R;ENSP00000055682:G1441R|.	ENSP00000055682:G1441R|.	G|R	-|-	1|2	0|0	KIAA2022|KIAA2022	73876796|73876796	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.995000|0.995000	0.86356|0.86356	7.487000|7.487000	0.81328|0.81328	2.234000|2.234000	0.73211|0.73211	0.544000|0.544000	0.68410|0.68410	GGA|CGG		0.453	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		T	73960071	C	T	73960071	3	4	77	1	0	0	0	0	1	0	0	0	8290	661	23	1	237	1	KIAA2022	23	73960071	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	9010519	73960071	81310489	1210	22946										
CPXCR1	53336	broad.mit.edu	37	chrX	88008695	88008696	+	Frame_Shift_Ins	INS	-	-	C													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agagcttcttctacttcagaINScccccattcccagaaaattg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:88008695_88008696insC	ENST00000276127.4	+	3	539_540	c.280_281insC	c.(280-282)accfs	p.T94fs	CPXCR1_ENST00000373111.1_Frame_Shift_Ins_p.T94fs	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	94							metal ion binding (GO:0046872)	p.I96fs*13(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						TCTACTTCAGACCCCCATTCCC	0.411																																																1	Insertion - Frameshift(1)	large_intestine(1)	X																																								87895352	SO:0001589	frameshift_variant	53336			AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.285dupC	X.37:g.88008700_88008700dupC	ENSP00000276127:p.Thr94fs		87895351	B2R9F9|D3DTE7|Q96RS3	Frame_Shift_Ins	INS	ENST00000276127.4	37	CCDS14458.1																																																																																				0.411	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		C	88008696	-	C	88008695	7	5	77	1	0	1	1	0	0	0	0	0	3842	275	10	0	282	0	CPXCR1	23	88008695	Frame_Shift_Ins	INS	-	TCGA-AG-A02N-01A-11W-A096-10	14048624	88008695	67261865	1211	22947										
NXF5	55998	broad.mit.edu	37	chrX	101096514	101096514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	agtagggcgcagtaaaatgaCtgacaaatatacatatctgc	9	7	1	2	rs192990689		TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:101096514C>T	ENST00000361708.2	-	6	616	c.257G>A	c.(256-258)aGt>aAt	p.S86N	NXF5_ENST00000473265.2_Missense_Mutation_p.S86N|NXF5_ENST00000537026.1_Missense_Mutation_p.S86N			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	86	RRM.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.S86N(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						AGTAAAATGACTGACAAATAT	0.473													T|||	1	0.000264901	8e-04	0	3775	,	,		14878	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X											171	136	148					X																	101096514		2203	4300	6503	100983170	SO:0001583	missense	55998			AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.257G>A	X.37:g.101096514C>T	ENSP00000355286:p.Ser86Asn		100983170	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Missense_Mutation	SNP	ENST00000361708.2	37		4	0.0024110910186859553	2	0.0040650406504065045	0	0.0	1	0.0017482517482517483	2	0.002638522427440633	.	0.005	-2.126138	0.00342	.	.	ENSG00000126952	ENST00000537026;ENST00000473265;ENST00000361708	T;T;T	0.41400	1.0;1.0;1.0	2.18	-2.76	0.05896	.	0.467752	0.22608	N	0.057870	T	0.09335	0.0230	N	0.00599	-1.345	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.24728	-1.0152	10	0.02654	T	1	.	9.9481	0.41623	0.0:0.7303:0.0:0.2697	.	86	A2RRM0	.	N	86	ENSP00000442401:S86N;ENSP00000426978:S86N;ENSP00000355286:S86N	ENSP00000263032:S86N	S	-	2	0	NXF5	100983170	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-1.307000	0.02733	-1.505000	0.01807	-0.948000	0.02665	AGT		0.473	NXF5-201	KNOWN	basic	protein_coding	protein_coding				T	101096514	C	T	101096514	3	4	77	1	0	0	0	0	1	0	0	0	10817	565	20	3	884	3	NXF5	23	101096514	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	13087819	101096514	54174046	1212	22948										
TEX13A	56157	broad.mit.edu	37	chrX	104464718	104464718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccgggaggccgcctccttgcGttccgtctcctgctgctccc	11	19	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:104464718G>A	ENST00000413579.1	-	2	475	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372575.1_Missense_Mutation_p.R122C|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Missense_Mutation_p.R122C			Q9BXU3	TX13A_HUMAN	testis expressed 13A	122							zinc ion binding (GO:0008270)	p.R122C(1)		large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCCTCCTTGCGTTCCGTCTCC	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	X											35	36	36					X																	104464718		2157	4228	6385	104351374	SO:0001583	missense	56157			AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"testis expressed sequence 13A"			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.364C>T	X.37:g.104464718G>A	ENSP00000399753:p.Arg122Cys		104351374	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	G	5.108	0.205570	0.09704	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	2.84	-1.11	0.09840	.	0.676215	0.11195	N	0.589443	T	0.24774	0.0601	.	.	.	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.002;0.002	T	0.18147	-1.0346	8	0.49607	T	0.09	.	2.6694	0.05063	0.4195:0.0:0.3649:0.2156	.	122;122	C9JWK0;Q9BXU3	.;TX13A_HUMAN	C	122	.	ENSP00000361656:R122C	R	-	1	0	TEX13A	104351374	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.439000	0.06897	-0.445000	0.07159	-1.421000	0.01109	CGC		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		A	104464718	G	A	104464718	3	1	77	1	0	0	0	0	1	0	0	0	15815	1145	40	1	875	1	TEX13A	23	104464718	Missense_Mutation	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	3368204	104464718	50805842	1213	22949										
CHRDL1	91851	broad.mit.edu	37	chrX	109964647	109964647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	gggtgcattgattgggttgcCgattctgaaagagcccttca	13	8	2	3			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:109964647C>T	ENST00000372045.1	-	5	523	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	CHRDL1_ENST00000372042.1_Missense_Mutation_p.R138Q|CHRDL1_ENST00000444321.2_Missense_Mutation_p.R137Q|CHRDL1_ENST00000482160.1_Intron|CHRDL1_ENST00000434224.1_Intron|CHRDL1_ENST00000394797.4_Missense_Mutation_p.R137Q|CHRDL1_ENST00000218054.4_Missense_Mutation_p.R137Q			Q9BU40	CRDL1_HUMAN	chordin-like 1	131	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.R137Q(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						ATTGGGTTGCCGATTCTGAAA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	X											379	305	330					X																	109964647		2203	4300	6503	109851303	SO:0001583	missense	91851			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"megalocornea 1 (X-linked)"	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.392G>A	X.37:g.109964647C>T	ENSP00000361115:p.Arg131Gln		109851303	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Missense_Mutation	SNP	ENST00000372045.1	37		.	.	.	.	.	.	.	.	.	.	C	26.3	4.727441	0.89390	.	.	ENSG00000101938	ENST00000372045;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000444321	T;T;T;T;T	0.19105	2.19;2.17;2.17;2.4;2.17	4.93	4.93	0.64822	von Willebrand factor, type C (3);	0.118609	0.56097	D	0.000036	T	0.41743	0.1172	L	0.57536	1.79	0.52099	D	0.999943	D;D;D;D;D	0.71674	0.997;0.998;0.997;0.997;0.998	D;D;D;D;D	0.76575	0.968;0.979;0.968;0.968;0.988	T	0.11616	-1.0580	9	.	.	.	-9.7761	14.7269	0.69351	0.0:1.0:0.0:0.0	.	137;132;117;131;138	E9PGS5;Q9BU40-2;Q59FB2;Q9BU40;D3DUY6	.;.;.;CRDL1_HUMAN;.	Q	131;137;137;138;137	ENSP00000361115:R131Q;ENSP00000218054:R137Q;ENSP00000378276:R137Q;ENSP00000361112:R138Q;ENSP00000399739:R137Q	.	R	-	2	0	CHRDL1	109851303	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.932000	0.63476	2.384000	0.81235	0.529000	0.55759	CGG		0.488	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234		T	109964647	C	T	109964647	3	4	77	1	0	0	0	0	1	0	0	0	3379	652	23	1	995	1	CHRDL1	23	109964647	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	5499929	109964647	45305913	1214	22950										
AMOT	154796	broad.mit.edu	37	chrX	112065639	112065639	+	Frame_Shift_Del	DEL	G	G	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccttgaagggatattctggtGgggggcctcggtgttccatg							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:112065639delG	ENST00000524145.1	-	2	790	c.716delC	c.(715-717)ccafs	p.P240fs	AMOT_ENST00000462114.1_5'Flank|AMOT_ENST00000371962.1_Frame_Shift_Del_p.P8fs|AMOT_ENST00000371959.3_Frame_Shift_Del_p.P240fs|AMOT_ENST00000304758.1_Intron|AMOT_ENST00000371958.1_Frame_Shift_Del_p.P8fs			Q4VCS5	AMOT_HUMAN	angiomotin	240					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)	p.P239fs*14(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						ATATTCTGGTGGGGGGCCTCG	0.557																																																1	Deletion - Frameshift(1)	large_intestine(1)	X											130	110	116					X																	112065639		692	1591	2283	111952295	SO:0001589	frameshift_variant	154796			AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.716delC	X.37:g.112065639delG	ENSP00000429013:p.Pro240fs		111952295	Q504X5|Q9HD27|Q9UPT1	Frame_Shift_Del	DEL	ENST00000524145.1	37	CCDS48154.1																																																																																				0.557	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		-	112065639	G	-	112065639	7	5	77	1	0	1	0	1	0	0	0	0	582	1348	47	0	2582	0	AMOT	23	112065639	Frame_Shift_Del	DEL	G	TCGA-AG-A02N-01A-11W-A096-10	2100992	112065639	43204921	1215	22951										
SAGE1	55511	broad.mit.edu	37	chrX	134989980	134989980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ggcaacagctgatatgccagCcatgagtaccagggatcagc	12	11	1	2			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:134989980C>T	ENST00000370709.3	+	9	1139	c.1139C>T	c.(1138-1140)gCc>gTc	p.A380V	SAGE1_ENST00000535938.1_Missense_Mutation_p.A380V|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000324447.3_Missense_Mutation_p.A380V			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	380						nucleus (GO:0005634)		p.A380V(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GATATGCCAGCCATGAGTACC	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	X											185	153	164					X																	134989980		2203	4299	6502	134817646	SO:0001583	missense	55511			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1139C>T	X.37:g.134989980C>T	ENSP00000359743:p.Ala380Val		134817646	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	C	7.464	0.645351	0.14451	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.36878	1.23;1.23;1.23	0.67	-1.34	0.09143	.	0.137375	0.49305	U	0.000158	T	0.30916	0.0780	N	0.24115	0.695	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.41963	-0.9479	9	0.14656	T	0.56	.	.	.	.	.	380	Q9NXZ1	SAGE1_HUMAN	V	380	ENSP00000323191:A380V;ENSP00000445959:A380V;ENSP00000359743:A380V	ENSP00000323191:A380V	A	+	2	0	SAGE1	134817646	0.002000	0.14202	0.002000	0.10522	0.007000	0.05969	-0.677000	0.05215	-2.098000	0.00850	-1.468000	0.01013	GCC		0.443	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		T	134989980	C	T	134989980	3	4	77	1	0	0	0	0	1	0	0	0	13846	739	26	3	1173	3	SAGE1	23	134989980	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	22924341	134989980	20280580	1216	22952										
MAP7D3	79649	broad.mit.edu	37	chrX	135314331	135314331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	attcgtcgctagtacatttaCgcaagggtacagtgacatac	9	9	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:135314331C>T	ENST00000316077.9	-	8	1005	c.785G>A	c.(784-786)cGt>cAt	p.R262H	MAP7D3_ENST00000370661.1_Missense_Mutation_p.R227H|MAP7D3_ENST00000370663.5_Missense_Mutation_p.R244H	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	262					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.R559H(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					AGTACATTTACGCAAGGGTAC	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	X											143	129	134					X																	135314331		1933	4130	6063	135141997	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.785G>A	X.37:g.135314331C>T	ENSP00000318086:p.Arg262His		135141997	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	C	9.793	1.178484	0.21787	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663	T;T;T	0.64991	2.25;-0.13;-0.13	5.42	-4.02	0.04034	.	1.846280	0.03330	N	0.193170	T	0.38081	0.1027	L	0.27053	0.805	0.09310	N	1	B;B;P	0.38078	0.179;0.179;0.617	B;B;B	0.26614	0.021;0.032;0.071	T	0.19877	-1.0292	10	0.46703	T	0.11	0.0912	1.2926	0.02063	0.3852:0.2695:0.0917:0.2536	.	244;262;227	B4DWD2;Q8IWC1;Q8IWC1-3	.;MA7D3_HUMAN;.	H	227;262;244	ENSP00000359695:R227H;ENSP00000318086:R262H;ENSP00000359697:R244H	ENSP00000318086:R262H	R	-	2	0	MAP7D3	135141997	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.339000	0.07832	-1.409000	0.02038	-0.302000	0.09304	CGT		0.403	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			T	135314331	C	T	135314331	3	4	77	1	0	0	0	0	1	0	0	0	9299	536	19	1	1889	1	MAP7D3	23	135314331	Missense_Mutation	SNP	C	TCGA-AG-A02N-01A-11W-A096-10	324351	135314331	19956229	1217	22953										
MAMLD1	10046	broad.mit.edu	37	chrX	149638772	149638772	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cacgcccaccagctgaaggcGttggcagccagcaagcaggg	14	14	0	1			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:149638772G>A	ENST00000370401.2	+	4	1237	c.927G>A	c.(925-927)gcG>gcA	p.A309A	MAMLD1_ENST00000262858.5_Silent_p.A309A|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000432680.2_Silent_p.A284A|MAMLD1_ENST00000426613.2_Silent_p.A284A			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	309					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.A236A(1)|p.A309A(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTGAAGGCGTTGGCAGCCA	0.632																																																2	Substitution - coding silent(2)	large_intestine(2)	X											80	57	65					X																	149638772		2203	4300	6503	149389430	SO:0001819	synonymous_variant	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.927G>A	X.37:g.149638772G>A			149389430	B2RCQ4|B4DG93|B9EGA5	Silent	SNP	ENST00000370401.2	37	CCDS14693.2																																																																																				0.632	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		A	149638772	G	A	149638772	2	1	77	1	0	0	0	0	0	0	0	1	9238	1132	40	1		1	MAMLD1	23	149638772	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	14324441	149638772	5631788	1218	22954										
GABRQ	55879	broad.mit.edu	37	chrX	151821062	151821062	+	Frame_Shift_Del	DEL	C	C	-													0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	ccccatcaccccagcgcaggCccccctggcaagcccggaaa							TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:151821062delC	ENST00000370306.2	+	9	1237	c.1217delC	c.(1216-1218)gccfs	p.A406fs		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	406					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.L408fs*10(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCAGCGCAGGCCCCCCTGGCA	0.587																																																1	Deletion - Frameshift(1)	large_intestine(1)	X											65	62	63					X																	151821062		2203	4300	6503	151571718	SO:0001589	frameshift_variant	55879			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1217delC	X.37:g.151821062delC	ENSP00000359329:p.Ala406fs		151571718	A6NFN1|Q32MB4|Q9NZK8	Frame_Shift_Del	DEL	ENST00000370306.2	37	CCDS14707.1																																																																																				0.587	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		-	151821062	C	-	151821062	7	5	77	1	0	1	0	1	0	0	0	0	6194	739	26	0	1251	0	GABRQ	23	151821062	Frame_Shift_Del	DEL	C	TCGA-AG-A02N-01A-11W-A096-10	2182290	151821062	3449498	1219	22955										
MAGEA12	4111	broad.mit.edu	37	chrX	151900015	151900015	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	tagcatgcaggatcactgccGgggacctgccggtactccag	13	13	1	0			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:151900015G>A	ENST00000357916.4	-	2	941	c.786C>T	c.(784-786)ccC>ccT	p.P262P	MAGEA12_ENST00000393869.3_Silent_p.P262P|CSAG4_ENST00000361201.4_RNA|MAGEA12_ENST00000393900.3_Silent_p.P262P	NM_005367.5	NP_005358.2	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	262	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.P262P(1)		breast(5)|large_intestine(5)|liver(1)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					GATCACTGCCGGGGACCTGCC	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	X											134	132	133					X																	151900015		2203	4300	6503	151650671	SO:0001819	synonymous_variant	4111				CCDS76048.1	Xq28	2009-03-13			ENSG00000213401	ENSG00000213401			6799	protein-coding gene	gene with protein product	"cancer/testis antigen family 1, member 12"	300177		MAGE12		8575766	Standard	NM_001166386		Approved	CT1.12	uc004fgc.3	P43365	OTTHUMG00000022650	ENST00000357916.4:c.786C>T	X.37:g.151900015G>A			151650671	Q9NSD3	Silent	SNP	ENST00000357916.4	37	CCDS14710.1																																																																																				0.552	MAGEA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058764.1	NM_005367		A	151900015	G	A	151900015	2	1	77	1	0	0	0	0	0	0	0	1	9196	1103	39	1		1	MAGEA12	23	151900015	Silent	SNP	G	TCGA-AG-A02N-01A-11W-A096-10	78953	151900015	3370545	1220	22956										
BGN	633	broad.mit.edu	37	chrX	152771346	152771346	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00163800163800164	2	1	0.0195557361090884	0	0.0196195742030245	0.444444444444444	1	0	cgtcctggtgaacaacaagaTctccaagatccatgagaagg	10	10	1	4			TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AG-A02N-01A-11W-A096-10	TCGA-AG-A02N-11A-11W-A096-10	g.chrX:152771346T>A	ENST00000331595.4	+	4	563	c.377T>A	c.(376-378)aTc>aAc	p.I126N	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	126					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)	p.I126N(1)		breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AACAACAAGATCTCCAAGATC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	X											46	37	40					X																	152771346		2203	4297	6500	152424540	SO:0001583	missense	633			AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1044	protein-coding gene	gene with protein product	"biglycan proteoglycan"	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.377T>A	X.37:g.152771346T>A	ENSP00000327336:p.Ile126Asn		152424540	D3DWU3|P13247	Missense_Mutation	SNP	ENST00000331595.4	37	CCDS14721.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407732	0.83340	.	.	ENSG00000182492	ENST00000331595;ENST00000431891;ENST00000370204;ENST00000430380	T;T;T	0.63580	-0.05;0.08;-0.05	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.85557	0.5724	H	0.98027	4.13	0.80722	D	1	D	0.60575	0.988	D	0.69307	0.963	D	0.90248	0.4291	10	0.87932	D	0	-31.1783	12.7655	0.57388	0.0:0.0:0.0:1.0	.	126	P21810	PGS1_HUMAN	N	126;143;65;65	ENSP00000327336:I126N;ENSP00000402525:I143N;ENSP00000359223:I65N	ENSP00000327336:I126N	I	+	2	0	BGN	152424540	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.733000	0.84916	1.721000	0.51461	0.388000	0.25769	ATC		0.612	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711		A	152771346	T	A	152771346	3	1	77	1	0	0	0	0	1	0	0	0	1419	1435	50	5	387	5	BGN	23	152771346	Missense_Mutation	SNP	T	TCGA-AG-A02N-01A-11W-A096-10	871331	152771346	2499214	1221	22957										
ACOT7	11332	broad.mit.edu	37	chr1	6393599	6393599	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgacaggggcacataccacaGggtggccttattggtcagct	13	11	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:6393599G>A	ENST00000377855.2	-	4	624	c.478C>T	c.(478-480)Ctg>Ttg	p.L160L	ACOT7_ENST00000377842.3_Silent_p.L109L|ACOT7_ENST00000361521.4_Silent_p.L150L|ACOT7_ENST00000377845.3_Silent_p.L130L|ACOT7_ENST00000541130.1_Silent_p.L130L|ACOT7_ENST00000545482.1_Silent_p.L45L|ACOT7_ENST00000608083.1_Silent_p.L118L	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	160					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.L150L(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		ACATACCACAGGGTGGCCTTA	0.547																																					GBM(74;673 1226 4974 11850 13190)											1	Substitution - coding silent(1)	large_intestine(1)	1											178	153	161					1																	6393599		2203	4300	6503	6316186	SO:0001819	synonymous_variant	11332			AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"Acyl CoA thioesterases"	24157	protein-coding gene	gene with protein product	"brain acyl CoA hydrolase"	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.478C>T	1.37:g.6393599G>A			6316186	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Silent	SNP	ENST00000377855.2	37	CCDS65.1																																																																																				0.547	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274		A	6393599	G	A	6393599	2	1	78	1	0	0	0	0	0	0	0	1	155	991	35	3		3	ACOT7	1	6393599	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		6393599	242857022	1	22958										
CLCN6	1185	broad.mit.edu	37	chr1	11889346	11889346	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgccgacagatgtcctcttcGagtcaaatcggtaatgactc	9	11	2	2	rs374880026		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:11889346G>A	ENST00000346436.6	+	13	1267	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	CLCN6_ENST00000376496.3_Silent_p.S405S|CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376487.3_Silent_p.S383S|CLCN6_ENST00000312413.6_Missense_Mutation_p.E350K	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	405					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.S405S(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCCTCTTCGAGTCAAATCG	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G	,LYS/GLU	0,4406		0,0,2203	219	198	205		1215,1048	-1.2	0	1		205	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,missense	CLCN6	NM_001286.2,NM_021736.2	,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	405/870,350/354	11889346	1,13005	2203	4300	6503	11811933	SO:0001819	synonymous_variant	1185			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1215G>A	1.37:g.11889346G>A			11811933	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.425728	0.25639	0.0	1.16E-4	ENSG00000011021	ENST00000312413;ENST00000376492	D	0.92446	-3.04	5.83	-1.2	0.09554	.	.	.	.	.	D	0.85647	0.5745	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74711	-0.3573	8	0.66056	D	0.02	-2.4379	7.0666	0.25156	0.3642:0.3015:0.3343:0.0	.	350	P51797-3	.	K	350	ENSP00000308367:E350K	ENSP00000308367:E350K	E	+	1	0	CLCN6	11811933	.	.	0.004000	0.12327	0.008000	0.06430	.	.	-0.097000	0.12307	-0.140000	0.14226	GAG		0.502	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11889346	G	A	11889346	2	1	78	1	0	0	0	0	0	0	0	1	3473	1059	37	1		1	CLCN6	1	11889346	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	5495747	11889346	237361275	2	22959										
VPS13D	55187	broad.mit.edu	37	chr1	12331175	12331175	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gatcgtttgctagtgggtgaTttcattgtaagtgggcatcc	13	6	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:12331175T>C	ENST00000358136.3	+	17	2227	c.2097T>C	c.(2095-2097)gaT>gaC	p.D699D	VPS13D_ENST00000356315.4_Silent_p.D699D	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.D699D(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TAGTGGGTGATTTCATTGTAA	0.458																																																1	Substitution - coding silent(1)	large_intestine(1)	1											88	82	84					1																	12331175		2203	4300	6503	12253762	SO:0001819	synonymous_variant	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.2097T>C	1.37:g.12331175T>C			12253762		Silent	SNP	ENST00000358136.3	37	CCDS30588.1																																																																																				0.458	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12331175	T	C	12331175	2	2	78	1	0	0	0	0	0	0	0	1	17232	1490	52	4		4	VPS13D	1	12331175	Silent	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	441829	12331175	236919446	3	22960										
AGMAT	79814	broad.mit.edu	37	chr1	15901300	15901300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gacaagatcacagcccatcaCgttcaggccttgacaacccc	7	16	3	2	rs199886325		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:15901300C>T	ENST00000375826.3	-	6	1079	c.937G>A	c.(937-939)Gtg>Atg	p.V313M	DNAJC16_ENST00000375849.1_3'UTR|DNAJC16_ENST00000483270.1_3'UTR	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	313					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)	p.V313M(2)		endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCCCATCACGTTCAGGCCT	0.463													C|||	1	0.000199681	0	0	5008	,	,		21008	0.001		0	False		,,,				2504	0				NSCLC(126;1678 1780 25805 43508 49531)											2	Substitution - Missense(2)	large_intestine(2)	1											126	106	113					1																	15901300		2203	4300	6503	15773887	SO:0001583	missense	79814			AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.937G>A	1.37:g.15901300C>T	ENSP00000364986:p.Val313Met		15773887	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	15.23	2.771109	0.49680	.	.	ENSG00000116771	ENST00000375826	D	0.86366	-2.11	5.93	3.02	0.34903	Ureohydrolase domain (1);	0.245141	0.41605	D	0.000852	D	0.86814	0.6023	M	0.81179	2.53	0.39136	D	0.961941	B	0.25521	0.128	B	0.35770	0.21	D	0.83799	0.0235	10	0.54805	T	0.06	-21.7355	5.5346	0.17003	0.1508:0.6384:0.0:0.2109	.	313	Q9BSE5	SPEB_HUMAN	M	313	ENSP00000364986:V313M	ENSP00000364986:V313M	V	-	1	0	AGMAT	15773887	0.866000	0.29940	0.974000	0.42286	0.954000	0.61252	0.971000	0.29396	0.822000	0.34565	0.603000	0.83216	GTG		0.463	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		T	15901300	C	T	15901300	3	4	78	1	0	0	0	0	1	0	0	0	385	536	19	1	129	1	AGMAT	1	15901300	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	3570125	15901300	233349321	4	22961										
SPEN	23013	broad.mit.edu	37	chr1	16264407	16264408	+	Missense_Mutation	DNP	CC	CC	AT													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	caacgtcctggcccatcggtCcctgcccctttctgaaggag							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:16264407_16264408CC>AT	ENST00000375759.3	+	13	10814_10815	c.10610_10611CC>AT	c.(10609-10611)tCC>tAT	p.S3537Y		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3537	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.S3537>?(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		GCCCATCGGTCCCTGCCCCTTT	0.619																																																1	Complex(1)	large_intestine(1)	1																																								16136995	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	Exception_encountered	1.37:g.16264407_16264408delinsAT	ENSP00000364912:p.Ser3537Tyr		16136994	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	DNP	ENST00000375759.3	37	CCDS164.1																																																																																				0.619	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		AT	16264408	CC	AT	16264407	3	1	78	1	0	0	0	0	1	0	0	0	15077	855	30	2	10660	2	SPEN	1	16264407	Missense_Mutation	DNP	CC	TCGA-AG-A02X-01A-01W-A00E-09	363107	16264407	232986214	5	22962										
PUM1	9698	broad.mit.edu	37	chr1	31426732	31426732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aagagaaaagagtgctgctcGggctgaagaggctggaggcg	18	6	0	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:31426732G>A	ENST00000257075.5	-	15	2513	c.2420C>T	c.(2419-2421)cCg>cTg	p.P807L	PUM1_ENST00000373747.3_Missense_Mutation_p.P808L|PUM1_ENST00000423018.2_Missense_Mutation_p.P663L|PUM1_ENST00000440538.2_Missense_Mutation_p.P781L|PUM1_ENST00000424085.2_Missense_Mutation_p.P565L|PUM1_ENST00000373741.4_Missense_Mutation_p.P843L|PUM1_ENST00000373742.2_Missense_Mutation_p.P748L|PUM1_ENST00000426105.2_Missense_Mutation_p.P807L	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	807	Ser-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)	p.P807L(1)		breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		AGTGCTGCTCGGGCTGAAGAG	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	1											122	128	126					1																	31426732		2203	4300	6503	31199319	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2420C>T	1.37:g.31426732G>A	ENSP00000257075:p.Pro807Leu		31199319	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173761	0.78452	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.19394	2.19;2.15;2.43;2.43;2.47;2.42;2.47;2.17	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.26846	0.0657	L	0.51422	1.61	0.80722	D	1	P;D;P;P;P;P;P;P	0.55800	0.898;0.973;0.898;0.947;0.755;0.607;0.755;0.755	B;B;B;P;B;B;B;B	0.46510	0.29;0.394;0.201;0.519;0.189;0.069;0.126;0.189	T	0.02026	-1.1227	10	0.12103	T	0.63	-8.0362	19.8132	0.96556	0.0:0.0:1.0:0.0	.	748;663;843;781;807;807;808;807	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	L	565;807;808;545;807;781;843;663;748	ENSP00000400141:P565L;ENSP00000257075:P807L;ENSP00000362852:P808L;ENSP00000391723:P807L;ENSP00000401777:P781L;ENSP00000362846:P843L;ENSP00000399440:P663L;ENSP00000362847:P748L	ENSP00000257075:P807L	P	-	2	0	PUM1	31199319	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.753000	0.98904	2.785000	0.95823	0.655000	0.94253	CCG		0.537	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			A	31426732	G	A	31426732	3	1	78	1	0	0	0	0	1	0	0	0	12862	1116	39	1	1178	1	PUM1	1	31426732	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	15162325	31426732	217823889	6	22963										
MACF1	23499	broad.mit.edu	37	chr1	39853736	39853736	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tatctgaggaactttactcaGggtctggtagaagatgcccc	11	9	3	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:39853736G>A	ENST00000372915.3	+	57	15324	c.15237G>A	c.(15235-15237)caG>caA	p.Q5079Q	MACF1_ENST00000539005.1_Silent_p.Q2991Q|MACF1_ENST00000567887.1_Silent_p.Q5111Q|MACF1_ENST00000361689.2_Silent_p.Q3012Q|MACF1_ENST00000289893.4_Silent_p.Q3514Q|MACF1_ENST00000317713.7_Silent_p.Q3012Q|MACF1_ENST00000545844.1_Silent_p.Q3012Q|MACF1_ENST00000564288.1_Silent_p.Q5074Q			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5079					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.Q3012Q(1)|p.Q3514Q(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACTTTACTCAGGGTCTGGTAG	0.507																																																2	Substitution - coding silent(2)	large_intestine(2)	1											50	52	51					1																	39853736		2203	4300	6503	39626323	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.15237G>A	1.37:g.39853736G>A			39626323	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	G	2.402	-0.337330	0.05278	.	.	ENSG00000127603	ENST00000372925	.	.	.	6.03	4.17	0.49024	.	.	.	.	.	T	0.59238	0.2179	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55192	-0.8179	4	.	.	.	.	9.019	0.36188	0.2929:0.0:0.7071:0.0	.	.	.	.	R	2125	.	.	G	+	1	0	MACF1	39626323	0.870000	0.30015	0.994000	0.49952	0.944000	0.59088	1.159000	0.31749	0.887000	0.36136	-0.137000	0.14449	GGG		0.507	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39853736	G	A	39853736	2	1	78	1	0	0	0	0	0	0	0	1	9174	991	35	3		3	MACF1	1	39853736	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	8427004	39853736	209396885	7	22964										
LRP8	7804	broad.mit.edu	37	chr1	53746321	53746321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tctccccgtcgcagcgccacGaggcaggtacacacttgtgg	12	15	1	0	rs147119774		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:53746321G>A	ENST00000306052.6	-	4	535	c.434C>T	c.(433-435)tCg>tTg	p.S145L	LRP8_ENST00000347547.2_Missense_Mutation_p.S145L|LRP8_ENST00000354412.3_Missense_Mutation_p.S145L|LRP8_ENST00000465675.1_5'UTR|LRP8_ENST00000371454.2_Missense_Mutation_p.S145L	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	145	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.S145L(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						GCAGCGCCACGAGGCAGGTAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1						G	LEU/SER,LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	103	81	89		434,434,434,434	4.3	0.6	1	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	LRP8	NM_001018054.2,NM_004631.4,NM_017522.4,NM_033300.3	145,145,145,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	145/905,145/964,145/701,145/794	53746321	1,13005	2203	4300	6503	53518909	SO:0001583	missense	7804			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.434C>T	1.37:g.53746321G>A	ENSP00000303634:p.Ser145Leu		53518909	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841991	0.71488	0.0	1.16E-4	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000354412;ENST00000347547	D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76	4.26	4.26	0.50523	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	.	.	.	.	D	0.96084	0.8724	L	0.50993	1.605	0.20563	N	0.999886	P;P;D;D	0.63880	0.913;0.886;0.993;0.981	B;B;D;P	0.63488	0.257;0.22;0.915;0.657	D	0.90373	0.4382	9	0.17832	T	0.49	.	15.982	0.80116	0.0:0.0:1.0:0.0	.	145;145;145;145	Q14114-2;Q14114-4;Q14114-3;Q14114	.;.;.;LRP8_HUMAN	L	145	ENSP00000303634:S145L;ENSP00000360509:S145L;ENSP00000346391:S145L;ENSP00000334522:S145L	ENSP00000303634:S145L	S	-	2	0	LRP8	53518909	0.169000	0.23002	0.576000	0.28549	0.894000	0.52154	2.517000	0.45529	2.400000	0.81607	0.561000	0.74099	TCG		0.612	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		A	53746321	G	A	53746321	3	1	78	1	0	0	0	0	1	0	0	0	8992	1059	37	1	2521	1	LRP8	1	53746321	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	13892585	53746321	195504300	8	22965										
ST6GALNAC5	81849	broad.mit.edu	37	chr1	77510258	77510258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttactcgccacaagatgctgCagtttgatgagctcttcaag	9	10	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:77510258C>A	ENST00000477717.1	+	3	866	c.631C>A	c.(631-633)Cag>Aag	p.Q211K		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	211					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)	p.Q211K(2)		endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						CAAGATGCTGCAGTTTGATGA	0.567																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											117	118	118					1																	77510258		2203	4300	6503	77282846	SO:0001583	missense	81849				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.631C>A	1.37:g.77510258C>A	ENSP00000417583:p.Gln211Lys		77282846	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	37	CCDS673.1	.	.	.	.	.	.	.	.	.	.	C	5.766	0.325713	0.10900	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.28666	1.6	5.46	5.46	0.80206	.	0.208574	0.51477	D	0.000096	T	0.12347	0.0300	N	0.16307	0.4	0.58432	D	0.999998	B	0.06786	0.001	B	0.17722	0.019	T	0.05500	-1.0881	10	0.29301	T	0.29	-36.9101	19.307	0.94167	0.0:1.0:0.0:0.0	.	211	Q9BVH7	SIA7E_HUMAN	K	211;121	ENSP00000417583:Q211K	ENSP00000436263:Q211K	Q	+	1	0	ST6GALNAC5	77282846	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	5.947000	0.70242	2.543000	0.85770	0.655000	0.94253	CAG		0.567	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77510258	C	A	77510258	3	1	78	1	0	0	0	0	1	0	0	0	15266	711	25	2	641	2	ST6GALNAC5	1	77510258	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	23763937	77510258	171740363	9	22966										
VAV3	10451	broad.mit.edu	37	chr1	108507465	108507465	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	accttgcaatggatgagccaCtgcgcgcactgcttccacgg	11	14	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:108507465C>T	ENST00000370056.4	-	1	301	c.27G>A	c.(25-27)caG>caA	p.Q9Q	VAV3-AS1_ENST00000438318.1_RNA|VAV3_ENST00000527011.1_Silent_p.Q9Q|VAV3_ENST00000371846.4_De_novo_Start_OutOfFrame	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	9	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.Q9Q(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		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)		GGATGAGCCACTGCGCGCACT	0.726																																																1	Substitution - coding silent(1)	large_intestine(1)	1											49	40	43					1																	108507465		2203	4300	6503	108308988	SO:0001819	synonymous_variant	10451			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.27G>A	1.37:g.108507465C>T			108308988	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Silent	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583715	0.28268	.	.	ENSG00000134215	ENST00000490388	.	.	.	4.77	1.67	0.24075	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	.	6.7393	0.23426	0.0:0.6878:0.1455:0.1667	.	.	.	.	N	4	.	.	S	-	2	0	VAV3	108308988	0.948000	0.32251	1.000000	0.80357	0.992000	0.81027	0.051000	0.14141	0.464000	0.27142	0.456000	0.33151	AGT		0.726	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108507465	C	T	108507465	2	4	78	1	0	0	0	0	0	0	0	1	17173	564	20	3		3	VAV3	1	108507465	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	30997207	108507465	140743156	10	22967										
BCAS2	10286	broad.mit.edu	37	chr1	115113321	115113321	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aataggaaaaaacaatttacCttaacttctgaagttccttc	4	8	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:115113321C>T	ENST00000369541.3	-	5	517	c.470G>A	c.(469-471)aGa>aAa	p.R157K	BCAS2_ENST00000485021.1_5'UTR	NM_005872.2	NP_005863.1	O75934	SPF27_HUMAN	breast carcinoma amplified sequence 2	157					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cell junction (GO:0030054)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)		p.R157K(1)		biliary_tract(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)	13	all_epithelial(7;9.54e-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)		AACAATTTACCTTAACTTCTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	1											35	29	31					1																	115113321		2184	4292	6476	114914844	SO:0001630	splice_region_variant	10286			AB020623	CCDS874.1	1p13.2	2010-01-25			ENSG00000116752	ENSG00000116752			975	protein-coding gene	gene with protein product		605783				9731529, 10403562	Standard	NM_005872		Approved	DAM1, SPF27, Snt309	uc001efa.3	O75934	OTTHUMG00000011898	ENST00000369541.3:c.470+1G>A	1.37:g.115113321C>T			114914844	Q6FGS0	Missense_Mutation	SNP	ENST00000369541.3	37	CCDS874.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595112	0.66219	.	.	ENSG00000116752	ENST00000369541	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.37945	0.1022	L	0.28115	0.83	0.80722	D	1	B	0.17268	0.021	B	0.17098	0.017	T	0.22173	-1.0224	8	.	.	.	-22.1505	20.1467	0.98079	0.0:1.0:0.0:0.0	.	157	O75934	SPF27_HUMAN	K	157	.	.	R	-	2	0	BCAS2	114914844	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.129000	0.77225	2.838000	0.97847	0.655000	0.94253	AGA		0.303	BCAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032871.1	NM_005872	Missense_Mutation	T	115113321	C	T	115113321	5	4	78	1	0	0	0	0	0	0	1	0	1352	695	24	3	219	3	BCAS2	1	115113321	Splice_Site	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	6605856	115113321	134137300	11	22968										
KCNN3	3782	broad.mit.edu	37	chr1	154841979	154841979	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agggggctggcctgtcggtgCcggctgcctccgccaggccc	17	16	0	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:154841979C>A	ENST00000271915.4	-	1	777	c.462G>T	c.(460-462)cgG>cgT	p.R154R	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	159					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.R154R(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	CCTGTCGGTGCCGGCTGCCTC	0.632																																																1	Substitution - coding silent(1)	large_intestine(1)	1											29	32	31					1																	154841979		2202	4299	6501	153108603	SO:0001819	synonymous_variant	3782			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.462G>T	1.37:g.154841979C>A			153108603	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																				0.632	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154841979	C	A	154841979	2	1	78	1	0	0	0	0	0	0	0	1	8101	726	26	2		2	KCNN3	1	154841979	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	39728658	154841979	94408642	12	22969										
FCRL2	79368	broad.mit.edu	37	chr1	157737124	157737124	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gcagtcaaagagaggttgaaGgaggcccctcctccagaggg	15	10	1	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:157737124G>T	ENST00000361516.3	-	6	1107	c.1059C>A	c.(1057-1059)tcC>tcA	p.S353S	FCRL2_ENST00000469986.1_Silent_p.S100S|FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000392274.3_Silent_p.S353S	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	353	Ig-like C2-type 4.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.S353S(1)|p.S100S(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGAGGTTGAAGGAGGCCCCTC	0.567																																																2	Substitution - coding silent(2)	large_intestine(2)	1											76	83	81					1																	157737124		2203	4300	6503	156003748	SO:0001819	synonymous_variant	79368			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1059C>A	1.37:g.157737124G>T			156003748	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Silent	SNP	ENST00000361516.3	37	CCDS1168.1																																																																																				0.567	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		T	157737124	G	T	157737124	2	4	78	1	0	0	0	0	0	0	0	1	5814	987	35	2		2	FCRL2	1	157737124	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	2895145	157737124	91513497	13	22970										
NIT1	4817	broad.mit.edu	37	chr1	161089332	161089332	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tggctgtccttgggtggtttCcatgagcgtggccaagactg	15	9	0	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:161089332C>G	ENST00000368009.2	+	4	463	c.387C>G	c.(385-387)ttC>ttG	p.F129L	PFDN2_ENST00000368010.3_5'Flank|NIT1_ENST00000496861.1_3'UTR|PFDN2_ENST00000468311.1_5'Flank|NIT1_ENST00000368008.1_Missense_Mutation_p.F129L|NIT1_ENST00000392190.5_Missense_Mutation_p.F93L|NIT1_ENST00000368007.4_Missense_Mutation_p.F114L|DEDD_ENST00000489249.1_5'Flank	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	129	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)	p.F129L(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGGGTGGTTTCCATGAGCGTG	0.517											OREG0013937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	1											75	69	71					1																	161089332		2203	4300	6503	159355956	SO:0001583	missense	4817			AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.387C>G	1.37:g.161089332C>G	ENSP00000356988:p.Phe129Leu	1814	159355956	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	37	CCDS1218.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354884	0.41700	.	.	ENSG00000158793	ENST00000368009;ENST00000368007;ENST00000368008;ENST00000392190	D;D;D;D	0.87103	-1.94;-1.94;-2.21;-1.94	4.67	3.68	0.42216	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.72011	0.3408	L	0.37750	1.13	0.53005	D	0.999969	B;B;B	0.31640	0.285;0.211;0.333	B;B;B	0.39660	0.132;0.208;0.306	T	0.66995	-0.5782	10	0.10902	T	0.67	-13.7426	9.5928	0.39557	0.0:0.8881:0.0:0.1119	.	114;129;129	Q86X76-4;B1AQP4;Q86X76	.;.;NIT1_HUMAN	L	129;114;129;93	ENSP00000356988:F129L;ENSP00000356986:F114L;ENSP00000356987:F129L;ENSP00000376028:F93L	ENSP00000356986:F114L	F	+	3	2	NIT1	159355956	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.000000	0.49481	2.421000	0.82119	0.467000	0.42956	TTC		0.517	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			G	161089332	C	G	161089332	3	3	78	1	0	0	0	0	1	0	0	0	10464	854	30	5	458	5	NIT1	1	161089332	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	3352208	161089332	88161289	14	22971										
TSEN15	116461	broad.mit.edu	37	chr1	184041328	184041328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aggcatctcgaaagttgcaaGgtgatccagatttgccgatg	12	8	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:184041328G>A	ENST00000361641.1	+	4	470	c.391G>A	c.(391-393)Ggt>Agt	p.G131S	TSEN15_ENST00000533373.1_Splice_Site_p.E131K|TSEN15_ENST00000423085.2_Intron	NM_052965.2	NP_443197.1	Q8WW01	SEN15_HUMAN	TSEN15 tRNA splicing endonuclease subunit	131					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)	tRNA-intron endonuclease activity (GO:0000213)	p.G131S(1)		breast(1)|kidney(3)|large_intestine(2)|lung(2)	8						AAAGTTGCAAGGTGATCCAGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	1											147	136	140					1																	184041328		2203	4300	6503	182307951	SO:0001583	missense	116461			AF288394	CCDS1361.1, CCDS44286.1, CCDS72993.1	1q25	2013-08-06	2013-08-06	2008-06-12	ENSG00000198860	ENSG00000198860		"tRNA splicing endonuclease subunits"	16791	protein-coding gene	gene with protein product		608756	"chromosome 1 open reading frame 19", "tRNA splicing endonuclease 15 homolog (S. cerevisiae)"	C1orf19		11318611, 17166513	Standard	XM_006711148		Approved		uc001gqt.4	Q8WW01	OTTHUMG00000035461	ENST00000361641.1:c.391G>A	1.37:g.184041328G>A	ENSP00000355299:p.Gly131Ser		182307951	B4DKP0|Q9BZQ5	Missense_Mutation	SNP	ENST00000361641.1	37	CCDS1361.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.61|12.61	1.988651|1.988651	0.35131|0.35131	.|.	.|.	ENSG00000198860|ENSG00000198860	ENST00000533373|ENST00000361641	T|T	0.31769|0.43688	1.48|0.94	5.95|5.95	2.76|2.76	0.32466|0.32466	.|.	.|0.718988	.|0.13135	.|N	.|0.411138	T|T	0.15089|0.15089	0.0364|0.0364	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.29971|0.29971	-0.9994|-0.9994	7|10	0.87932|0.07813	D|T	0|0.8	-5.4584|-5.4584	4.4128|4.4128	0.11441|0.11441	0.0843:0.1527:0.6054:0.1576|0.0843:0.1527:0.6054:0.1576	.|.	.|131	.|Q8WW01	.|SEN15_HUMAN	K|S	131|131	ENSP00000436996:E131K|ENSP00000355299:G131S	ENSP00000436996:E131K|ENSP00000355299:G131S	E|G	+|+	1|1	0|0	TSEN15|TSEN15	182307951|182307951	0.831000|0.831000	0.29352|0.29352	0.605000|0.605000	0.28930|0.28930	0.989000|0.989000	0.77384|0.77384	1.563000|1.563000	0.36364|0.36364	1.530000|1.530000	0.49136|0.49136	0.655000|0.655000	0.94253|0.94253	GAA|GGT		0.398	TSEN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086132.1			A	184041328	G	A	184041328	3	1	78	1	0	0	0	0	1	0	0	0	16651	1000	35	3	405	3	TSEN15	1	184041328	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	22951996	184041328	65209293	15	22972										
HMCN1	83872	broad.mit.edu	37	chr1	186092143	186092143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgctgtggacaagcccatcaCgttatcctgtgaagcagatg	11	10	1	2	rs370916387		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:186092143C>T	ENST00000271588.4	+	81	12519	c.12290C>T	c.(12289-12291)aCg>aTg	p.T4097M	HMCN1_ENST00000367492.2_Missense_Mutation_p.T4097M	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4097	Ig-like C2-type 40.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.T4097M(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGCCCATCACGTTATCCTGT	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	1						C	MET/THR	0,4406		0,0,2203	116	97	103		12290	-1.2	0	1		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	HMCN1	NM_031935.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	4097/5636	186092143	1,13005	2203	4300	6503	184358766	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12290C>T	1.37:g.186092143C>T	ENSP00000271588:p.Thr4097Met		184358766	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	3.752	-0.051329	0.07407	0.0	1.16E-4	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68181	-0.31;-0.31	5.85	-1.22	0.09494	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.637600	0.17373	N	0.176594	T	0.59404	0.2191	M	0.66378	2.025	0.09310	N	1	B	0.20261	0.043	B	0.15484	0.013	T	0.50259	-0.8849	10	0.38643	T	0.18	.	10.6051	0.45390	0.0:0.4481:0.0:0.5519	.	4097	Q96RW7	HMCN1_HUMAN	M	4097	ENSP00000271588:T4097M;ENSP00000356462:T4097M	ENSP00000271588:T4097M	T	+	2	0	HMCN1	184358766	0.036000	0.19791	0.000000	0.03702	0.027000	0.11550	0.404000	0.20999	-0.525000	0.06391	-0.302000	0.09304	ACG		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186092143	C	T	186092143	3	4	78	1	0	0	0	0	1	0	0	0	7241	536	19	1	12612	1	HMCN1	1	186092143	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2050815	186092143	63158478	16	22973										
PTPN14	5784	broad.mit.edu	37	chr1	214549706	214549706	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gctgtgctgaaaatgccattCgcctttttctttggaatttg	9	8	1	1	rs146527644	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:214549706C>T	ENST00000366956.5	-	15	2957	c.2763G>A	c.(2761-2763)gcG>gcA	p.A921A	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	921	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.A921A(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AAATGCCATTCGCCTTTTTCT	0.463																																					Colon(92;557 1424 24372 34121 40073)											1	Substitution - coding silent(1)	large_intestine(1)	1											171	165	167					1																	214549706		2203	4300	6503	212616329	SO:0001819	synonymous_variant	5784			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2763G>A	1.37:g.214549706C>T			212616329	Q5VSI0	Silent	SNP	ENST00000366956.5	37	CCDS1514.1																																																																																				0.463	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214549706	C	T	214549706	2	4	78	1	0	0	0	0	0	0	0	1	12818	871	31	1		1	PTPN14	1	214549706	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	28457563	214549706	34700915	17	22974										
ESRRG	2104	broad.mit.edu	37	chr1	216896586	216896586	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gaaagaaaaaaggtacctacTcttcctcgtagtgcagggaa	10	8	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr1:216896586T>C	ENST00000408911.3	-	1	209	c.56A>G	c.(55-57)gAg>gGg	p.E19G	ESRRG_ENST00000366938.2_Intron|ESRRG_ENST00000391890.3_5'UTR|ESRRG_ENST00000359162.2_Intron|ESRRG_ENST00000360012.3_Intron|ESRRG_ENST00000463665.1_Intron|ESRRG_ENST00000361395.2_Intron|ESRRG_ENST00000366940.2_Intron|ESRRG_ENST00000487276.1_Intron|ESRRG_ENST00000366937.1_5'UTR|ESRRG_ENST00000493603.1_Intron|ESRRG_ENST00000361525.3_Intron|ESRRG_ENST00000493748.1_Intron	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	19				E -> K (in Ref. 4; AAQ93376). {ECO:0000305}.	gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E19G(1)		endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	AGGTACCTACTCTTCCTCGTA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	1											87	85	85					1																	216896586		1888	4101	5989	214963209	SO:0001630	splice_region_variant	2104			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.56+1A>G	1.37:g.216896586T>C			214963209	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020378	0.54576	.	.	ENSG00000196482	ENST00000408911	D	0.93604	-3.25	5.45	5.45	0.79879	.	0.427969	0.21090	N	0.080338	D	0.85405	0.5689	N	0.08118	0	0.80722	D	1	B	0.18461	0.028	B	0.15870	0.014	T	0.80975	-0.1142	10	0.23302	T	0.38	.	15.1643	0.72811	0.0:0.0:0.0:1.0	.	19	P62508	ERR3_HUMAN	G	19	ENSP00000386171:E19G	ENSP00000386171:E19G	E	-	2	0	ESRRG	214963209	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.276000	0.78559	2.056000	0.61249	0.482000	0.46254	GAG		0.478	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	Missense_Mutation	C	216896586	T	C	216896586	5	2	78	1	0	0	0	0	0	0	1	0	5275	1565	54	4	1348	4	ESRRG	1	216896586	Splice_Site	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	2346880	216896586	32354035	18	22975										
FSHR	2492	broad.mit.edu	37	chr2	49190040	49190040	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tagcagccacacttgctcagCagaatgaagaaatctctgcg	9	11	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:49190040C>A	ENST00000406846.2	-	10	2039	c.1920G>T	c.(1918-1920)ctG>ctT	p.L640L	FSHR_ENST00000304421.4_Silent_p.L614L|FSHR_ENST00000541117.1_Silent_p.L376L|FSHR_ENST00000346173.3_Silent_p.L578L	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	640					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)	p.L640L(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		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)|Suramin(DB04786)|Urofollitropin(DB00094)	ACTTGCTCAGCAGAATGAAGA	0.458									Gonadal Dysgenesis, 46 XX																																							1	Substitution - coding silent(1)	large_intestine(1)	2											81	82	81					2																	49190040		2203	4300	6503	49043544	SO:0001819	synonymous_variant	2492	Familial Cancer Database			CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1920G>T	2.37:g.49190040C>A			49043544	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Silent	SNP	ENST00000406846.2	37	CCDS1843.1																																																																																				0.458	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190040	C	A	49190040	2	1	78	1	0	0	0	0	0	0	0	1	6092	697	25	2		2	FSHR	2	49190040	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09		49190040	194009333	19	22976										
FSHR	2492	broad.mit.edu	37	chr2	49190545	49190545	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agtccagctgcatggcatgcGtgatggtatgccatctttcc	11	11	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:49190545G>T	ENST00000406846.2	-	10	1534	c.1415C>A	c.(1414-1416)aCg>aAg	p.T472K	FSHR_ENST00000304421.4_Missense_Mutation_p.T446K|FSHR_ENST00000541117.1_Missense_Mutation_p.T208K|FSHR_ENST00000346173.3_Missense_Mutation_p.T410K	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	472					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)	p.T472K(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		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)|Suramin(DB04786)|Urofollitropin(DB00094)	CATGGCATGCGTGATGGTATG	0.542									Gonadal Dysgenesis, 46 XX																																							1	Substitution - Missense(1)	large_intestine(1)	2											56	50	52					2																	49190545		2203	4300	6503	49044049	SO:0001583	missense	2492	Familial Cancer Database			CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1415C>A	2.37:g.49190545G>T	ENSP00000384708:p.Thr472Lys		49044049	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281612	0.80692	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.996	T	0.63514	-0.6620	9	.	.	.	.	18.891	0.92403	0.0:0.0:1.0:0.0	.	446;410;472	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	K	472;410;446;208	ENSP00000384708:T472K;ENSP00000333908:T410K;ENSP00000306780:T446K;ENSP00000444172:T208K	.	T	-	2	0	FSHR	49044049	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.657000	0.98554	2.941000	0.99782	0.655000	0.94253	ACG		0.542	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			T	49190545	G	T	49190545	3	4	78	1	0	0	0	0	1	0	0	0	6092	1145	40	2	676	2	FSHR	2	49190545	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	505	49190545	194008828	20	22977										
DARS	1615	broad.mit.edu	37	chr2	136668998	136668998	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gttagcagttgaggatcatgTattctttgagctcctgacaa	10	7	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:136668998T>C	ENST00000264161.4	-	14	1511	c.1296A>G	c.(1294-1296)atA>atG	p.I432M	DARS_ENST00000537273.1_Missense_Mutation_p.I332M	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	432					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.I432M(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	GAGGATCATGTATTCTTTGAG	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	2											216	209	211					2																	136668998		2203	4300	6503	136385468	SO:0001583	missense	1615			J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.1296A>G	2.37:g.136668998T>C	ENSP00000264161:p.Ile432Met		136385468	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	ENST00000264161.4	37	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.454814	0.63290	.	.	ENSG00000115866	ENST00000264161;ENST00000422708;ENST00000537273	T;D;T	0.82255	0.81;-1.59;0.81	5.52	0.0525	0.14302	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.148983	0.64402	D	0.000012	D	0.91462	0.7305	H	0.96430	3.82	0.58432	D	0.999994	D	0.55605	0.972	D	0.74674	0.984	D	0.88313	0.2957	10	0.87932	D	0	-7.0996	5.227	0.15399	0.4051:0.0:0.3042:0.2907	.	432	P14868	SYDC_HUMAN	M	432;119;332	ENSP00000264161:I432M;ENSP00000387508:I119M;ENSP00000444192:I332M	ENSP00000264161:I432M	I	-	3	3	DARS	136385468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.026000	0.30103	0.336000	0.23639	0.383000	0.25322	ATA		0.353	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349		C	136668998	T	C	136668998	3	2	78	1	0	0	0	0	1	0	0	0	4247	1628	57	4	221	4	DARS	2	136668998	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	87478453	136668998	106530375	21	22978										
KCNH7	90134	broad.mit.edu	37	chr2	163250944	163250944	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	caatttccttcttcttagttTacagttgtctccttctgaat	4	10	4	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:163250944T>A	ENST00000332142.5	-	12	2764	c.2665A>T	c.(2665-2667)Aaa>Taa	p.K889*		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	889					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.K889*(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CTTCTTAGTTTACAGTTGTCT	0.338																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Nonsense(1)	large_intestine(1)	2											164	152	156					2																	163250944		2203	4298	6501	162959190	SO:0001587	stop_gained	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2665A>T	2.37:g.163250944T>A	ENSP00000331727:p.Lys889*		162959190	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Nonsense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	T	40	8.248740	0.98724	.	.	ENSG00000184611	ENST00000332142	.	.	.	5.84	5.84	0.93424	.	0.211412	0.48286	D	0.000188	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	16.2159	0.82217	0.0:0.0:0.0:1.0	.	.	.	.	X	889	.	ENSP00000331727:K889X	K	-	1	0	KCNH7	162959190	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	4.645000	0.61404	2.243000	0.73865	0.533000	0.62120	AAA		0.338	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163250944	T	A	163250944	4	1	78	1	0	0	0	0	0	1	0	0	8058	1763	61	5	945	5	KCNH7	2	163250944	Nonsense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	26581946	163250944	79948429	22	22979										
SCN3A	6328	broad.mit.edu	37	chr2	165997367	165997367	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cagtgagtctctcctgctttCgctgtcttcaaatgtgctgt	9	11	3	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:165997367C>T	ENST00000360093.3	-	13	2304	c.1813G>A	c.(1813-1815)Gaa>Aaa	p.E605K	SCN3A_ENST00000283254.7_Missense_Mutation_p.E605K|SCN3A_ENST00000409101.3_Missense_Mutation_p.E605K	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	605					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E605K(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCTGCTTTCGCTGTCTTCA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	2											198	145	163					2																	165997367		2203	4300	6503	165705613	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1813G>A	2.37:g.165997367C>T	ENSP00000353206:p.Glu605Lys		165705613	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	23.1	4.370473	0.82573	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06	6.07	5.2	0.72013	Domain of unknown function DUF3451 (1);	0.000000	0.64402	D	0.000006	D	0.96466	0.8847	M	0.88704	2.975	0.80722	D	1	D;D;B;B;D	0.76494	0.992;0.999;0.007;0.007;0.99	P;D;B;B;B	0.73380	0.716;0.98;0.004;0.004;0.216	D	0.97017	0.9740	10	0.66056	D	0.02	.	15.3736	0.74587	0.0:0.9336:0.0:0.0664	.	605;605;605;605;605	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	K	605	ENSP00000353206:E605K;ENSP00000283254:E605K;ENSP00000386726:E605K;ENSP00000403348:E605K	ENSP00000283254:E605K	E	-	1	0	SCN3A	165705613	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.935000	0.70145	1.587000	0.49959	-0.136000	0.14681	GAA		0.478	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		T	165997367	C	T	165997367	3	4	78	1	0	0	0	0	1	0	0	0	13955	893	31	1	4253	1	SCN3A	2	165997367	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2746423	165997367	77202006	23	22980										
TTN	7273	broad.mit.edu	37	chr2	179648886	179648886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tacttcctttttcacctcaaCgccagcttcactcttgtaag	4	14	4	0	rs376768790	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:179648886C>T	ENST00000591111.1	-	16	2910	c.2686G>A	c.(2686-2688)Gtt>Att	p.V896I	TTN_ENST00000342175.6_Missense_Mutation_p.V850I|TTN_ENST00000342992.6_Missense_Mutation_p.V896I|TTN_ENST00000359218.5_Missense_Mutation_p.V850I|TTN_ENST00000460472.2_Missense_Mutation_p.V850I|TTN_ENST00000360870.5_Missense_Mutation_p.V896I|TTN_ENST00000589042.1_Missense_Mutation_p.V896I			Q8WZ42	TITIN_HUMAN	titin	33718					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V850I(3)|p.V896I(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCACCTCAACGCCAGCTTCA	0.547													C|||	3	0.000599042	8e-04	0	5008	,	,		16490	0.001		0.001	False		,,,				2504	0															5	Substitution - Missense(5)	large_intestine(5)	2						C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	157	124	135		2548,2548,2686,2686,2548	1.8	1	2		135	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	850/27119,850/27052,896/5605,896/33424,850/26927	179648886	1,13005	2203	4300	6503	179357131	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2686G>A	2.37:g.179648886C>T	ENSP00000465570:p.Val896Ile		179357131	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	9.914	1.210309	0.22289	0.0	1.16E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.61627	0.09;0.27;0.25;0.26;0.5	5.52	1.84	0.25277	Ribonuclease H-like (1);	.	.	.	.	T	0.31918	0.0812	N	0.02247	-0.625	0.19575	N	0.999969	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.28459	-1.0043	9	0.87932	D	0	.	10.5203	0.44914	0.0:0.2293:0.0:0.7707	.	850;850;850;896;896	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	I	896;850;850;850;850;896	ENSP00000343764:V896I;ENSP00000434586:V850I;ENSP00000340554:V850I;ENSP00000352154:V850I;ENSP00000354117:V896I	ENSP00000340554:V850I	V	-	1	0	TTN	179357131	0.550000	0.26489	0.995000	0.50966	0.392000	0.30506	0.262000	0.18460	0.138000	0.18790	-1.084000	0.02203	GTT		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179648886	C	T	179648886	3	4	78	1	0	0	0	0	1	0	0	0	16775	536	19	1	108690	1	TTN	2	179648886	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	13651519	179648886	63550487	24	22981										
COL5A2	1290	broad.mit.edu	37	chr2	189898826	189898826	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	caaactggcccaatttcaacGccgaattcctggtctgtgcc	8	14	2	0	rs142895373	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:189898826G>A	ENST00000374866.3	-	54	4744	c.4470C>T	c.(4468-4470)ggC>ggT	p.G1490G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1490	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.G1490G(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CAATTTCAACGCCGAATTCCT	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	2						G		1,4405	2.1+/-5.4	0,1,2202	154	125	135		4470	2.4	0.4	2	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	COL5A2	NM_000393.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1490/1500	189898826	1,13005	2203	4300	6503	189607071	SO:0001819	synonymous_variant	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4470C>T	2.37:g.189898826G>A			189607071	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	37	CCDS33350.1																																																																																				0.473	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		A	189898826	G	A	189898826	2	1	78	1	0	0	0	0	0	0	0	1	3703	1074	38	1		1	COL5A2	2	189898826	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	10249940	189898826	53300547	25	22982										
TNS1	7145	broad.mit.edu	37	chr2	218751339	218751339	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttgttcattttgatggagccGgagagcaggccactgaagta	13	7	1	3	rs13419876	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:218751339G>A	ENST00000171887.4	-	11	974	c.522C>T	c.(520-522)tcC>tcT	p.S174S	TNS1_ENST00000430930.1_Silent_p.S174S|TNS1_ENST00000419504.1_Silent_p.S174S|TNS1_ENST00000310858.6_Silent_p.S205S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	174	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.S174S(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		TGATGGAGCCGGAGAGCAGGC	0.522											OREG0015188	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	133	0.0265575	0.0953	0.0086	5008	,	,		20049	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	2						G		340,4066	169.4+/-200.1	17,306,1880	137	118	124		522	-3.4	1	2	dbSNP_121	124	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	TNS1	NM_022648.4		17,312,6174	AA,AG,GG		0.0698,7.7167,2.6603		174/1736	218751339	346,12660	2203	4300	6503	218459584	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.522C>T	2.37:g.218751339G>A		2253	218459584	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.522	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218751339	G	A	218751339	2	1	78	1	0	0	0	0	0	0	0	1	16382	1103	39	1		1	TNS1	2	218751339	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	28852513	218751339	24448034	26	22983										
WDR69	164781	broad.mit.edu	37	chr2	228769723	228769723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cggggtcttttgatcataccGttgtagtgtgggacgctgat	14	7	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:228769723G>A	ENST00000309931.2	+	8	810	c.727G>A	c.(727-729)Gtt>Att	p.V243I	DAW1_ENST00000545118.1_Missense_Mutation_p.V228I|DAW1_ENST00000373666.2_Missense_Mutation_p.V243I	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	243						cilium (GO:0005929)		p.V243I(1)									TGATCATACCGTTGTAGTGTG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											162	166	165					2																	228769723		2203	4300	6503	228477967	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.727G>A	2.37:g.228769723G>A	ENSP00000311899:p.Val243Ile		228477967	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.438736	0.43326	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000545118	T;T;T	0.57107	0.42;0.42;0.42	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.423751	0.24564	N	0.037453	T	0.41073	0.1143	L	0.33245	0.995	0.24203	N	0.995502	B	0.21821	0.061	B	0.22152	0.038	T	0.16188	-1.0411	10	0.08381	T	0.77	.	16.2822	0.82697	0.0:0.0:1.0:0.0	.	243	Q8N136	WDR69_HUMAN	I	243;243;228	ENSP00000362770:V243I;ENSP00000311899:V243I;ENSP00000437887:V228I	ENSP00000311899:V243I	V	+	1	0	WDR69	228477967	1.000000	0.71417	0.283000	0.24790	0.780000	0.44128	6.399000	0.73248	2.449000	0.82847	0.491000	0.48974	GTT		0.408	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		A	228769723	G	A	228769723	3	1	78	1	0	0	0	0	1	0	0	0	17359	1145	40	1	757	1	WDR69	2	228769723	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	10018384	228769723	14429650	27	22984										
CHRNG	1146	broad.mit.edu	37	chr2	233409534	233409534	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgtggcagcctgaagcaggcTgccccagccatccaggcctg	13	15	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr2:233409534T>A	ENST00000389494.3	+	11	1323	c.1302T>A	c.(1300-1302)gcT>gcA	p.A434A	CHRNG_ENST00000389492.3_Silent_p.A382A	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	434					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)	p.A434A(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		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;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	TGAAGCAGGCTGCCCCAGCCA	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	2											26	30	29					2																	233409534		2203	4299	6502	233117778	SO:0001819	synonymous_variant	1146			X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1967	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, gamma (muscle)"	100730	"cholinergic receptor, nicotinic, gamma"	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.1302T>A	2.37:g.233409534T>A			233117778	B3KWM8|Q14DU4|Q53RG2	Silent	SNP	ENST00000389494.3	37	CCDS33400.1																																																																																				0.557	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199		A	233409534	T	A	233409534	2	1	78	1	0	0	0	0	0	0	0	1	3402	1567	55	5		5	CHRNG	2	233409534	Silent	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	4639811	233409534	9789839	28	22985										
CNTN6	27255	broad.mit.edu	37	chr3	1444040	1444040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agacagagtaaaactcatatTttggaaacaaacaatacatc	5	7	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:1444040T>C	ENST00000446702.2	+	22	3483	c.2856T>C	c.(2854-2856)atT>atC	p.I952I	CNTN6_ENST00000350110.2_Silent_p.I952I|CNTN6_ENST00000539053.1_Silent_p.I880I			Q9UQ52	CNTN6_HUMAN	contactin 6	952	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.I952I(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AAACTCATATTTTGGAAACAA	0.373																																																1	Substitution - coding silent(1)	large_intestine(1)	3											93	96	95					3																	1444040		2203	4299	6502	1419040	SO:0001819	synonymous_variant	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2856T>C	3.37:g.1444040T>C			1419040	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																				0.373	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		C	1444040	T	C	1444040	2	2	78	1	0	0	0	0	0	0	0	1	3651	1829	64	4		4	CNTN6	3	1444040	Silent	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09		1444040	196578390	29	22986										
SUSD5	26032	broad.mit.edu	37	chr3	33216511	33216511	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcatcccccatttccaagccGgtgcggccctgcaggatggt	11	15	1	0	rs376717049		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:33216511G>A	ENST00000309558.3	-	4	882	c.465C>T	c.(463-465)acC>acT	p.T155T		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	155	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)	p.T155T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TTTCCAAGCCGGTGCGGCCCT	0.587																																																1	Substitution - coding silent(1)	large_intestine(1)	3						G		1,4089		0,1,2044	65	72	70		465	-11.4	0.2	3		70	0,8354		0,0,4177	no	coding-synonymous	SUSD5	NM_015551.1		0,1,6221	AA,AG,GG		0.0,0.0244,0.0080		155/630	33216511	1,12443	2045	4177	6222	33191515	SO:0001819	synonymous_variant	26032			AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.465C>T	3.37:g.33216511G>A			33191515		Silent	SNP	ENST00000309558.3	37	CCDS46787.1																																																																																				0.587	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054		A	33216511	G	A	33216511	2	1	78	1	0	0	0	0	0	0	0	1	15450	1103	39	1		1	SUSD5	3	33216511	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	31772471	33216511	164805919	30	22987										
C3orf39	84892	broad.mit.edu	37	chr3	43121536	43121536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ctggccggcccttcaccacgCgccgtatggtttgaatgagg	13	13	1	2	rs143394182	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:43121536C>T	ENST00000344697.2	-	2	1733	c.1388G>A	c.(1387-1389)cGc>cAc	p.R463H	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R463H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	463					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)	p.R463H(1)									CTTCACCACGCGCCGTATGGT	0.627													C|||	4	0.000798722	0.003	0	5008	,	,		21085	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						C	HIS/ARG	13,4393	20.2+/-43.8	0,13,2190	43	42	42		1388	4.7	0.9	3	dbSNP_134	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	C3orf39	NM_032806.4	29	0,14,6489	TT,TC,CC		0.0116,0.2951,0.1076	benign	463/581	43121536	14,12992	2203	4300	6503	43096540	SO:0001583	missense	84892			AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1388G>A	3.37:g.43121536C>T	ENSP00000344125:p.Arg463His		43096540	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	11.78	1.741508	0.30865	0.002951	1.16E-4	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.77098	-1.07;-1.07	5.53	4.66	0.58398	.	0.462954	0.24312	N	0.039637	T	0.52041	0.1710	L	0.29908	0.895	0.27707	N	0.945591	P	0.39940	0.696	B	0.26969	0.075	T	0.56329	-0.7997	10	0.51188	T	0.08	-26.1697	9.5495	0.39301	0.0:0.8244:0.0:0.1756	.	463	Q8NAT1	AGO61_HUMAN	H	463	ENSP00000408992:R463H;ENSP00000344125:R463H	ENSP00000344125:R463H	R	-	2	0	C3orf39	43096540	0.991000	0.36638	0.872000	0.34217	0.944000	0.59088	2.476000	0.45171	1.347000	0.45714	0.650000	0.86243	CGC		0.627	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		T	43121536	C	T	43121536	3	4	78	1	0	0	0	0	1	0	0	0	2235	768	27	1	358	1	C3orf39	3	43121536	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	9905025	43121536	154900894	31	22988										
CCDC36	339834	broad.mit.edu	37	chr3	49294557	49294557	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcagcaggtgctcttcccaaGacaactggctactttccagc	8	14	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:49294557G>A	ENST00000438782.1	+	8	1863	c.1627G>A	c.(1627-1629)Gac>Aac	p.D543N	CCDC36_ENST00000452691.2_Missense_Mutation_p.D543N|RP11-3B7.1_ENST00000440528.3_5'Flank|CCDC36_ENST00000296449.5_Missense_Mutation_p.D543N			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	543								p.D533N(1)		endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		CTCTTCCCAAGACAACTGGCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	3											72	75	74					3																	49294557		2203	4300	6503	49269561	SO:0001583	missense	339834			AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"cancer/testis antigen 74"						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.1627G>A	3.37:g.49294557G>A	ENSP00000391788:p.Asp543Asn		49269561	C9JJL0|Q05DG9|Q96LP7	Missense_Mutation	SNP	ENST00000438782.1	37	CCDS33755.2	.	.	.	.	.	.	.	.	.	.	G	18.14	3.556650	0.65425	.	.	ENSG00000173421	ENST00000296449;ENST00000438782;ENST00000452691;ENST00000309062	T;T;T	0.50277	0.75;0.75;0.75	4.31	-0.136	0.13473	.	0.802027	0.11380	N	0.569861	T	0.33644	0.0870	L	0.32530	0.975	0.09310	N	1	B	0.15930	0.015	B	0.16722	0.016	T	0.32188	-0.9916	10	0.72032	D	0.01	-3.7855	6.575	0.22560	0.5285:0.0:0.4715:0.0	.	543	Q8IYA8	CCD36_HUMAN	N	543;543;543;523	ENSP00000296449:D543N;ENSP00000391788:D543N;ENSP00000407837:D543N	ENSP00000296449:D543N	D	+	1	0	CCDC36	49269561	0.006000	0.16342	0.024000	0.17045	0.857000	0.48899	0.062000	0.14389	0.063000	0.16370	0.561000	0.74099	GAC		0.537	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173		A	49294557	G	A	49294557	3	1	78	1	0	0	0	0	1	0	0	0	2814	942	33	3	1653	3	CCDC36	3	49294557	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	6173021	49294557	148727873	32	22989										
CACNA2D3	55799	broad.mit.edu	37	chr3	54537563	54537563	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ataaatgaaagggacaaagaCgggaattttttggagctggg	14	3	0	2	rs532127932		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:54537563C>T	ENST00000474759.1	+	5	474	c.426C>T	c.(424-426)gaC>gaT	p.D142D	CACNA2D3_ENST00000415676.2_Silent_p.D142D|CACNA2D3_ENST00000490478.1_Silent_p.D48D|CACNA2D3_ENST00000288197.5_Silent_p.D142D	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	142						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.D142D(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	GGGACAAAGACGGGAATTTTT	0.393													C|||	1	0.000199681	8e-04	0	5008	,	,		20358	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	3											138	128	131					3																	54537563		1840	4090	5930	54512603	SO:0001819	synonymous_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.426C>T	3.37:g.54537563C>T			54512603	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																				0.393	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54537563	C	T	54537563	2	4	78	1	0	0	0	0	0	0	0	1	2556	535	19	1		1	CACNA2D3	3	54537563	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	5243006	54537563	143484867	33	22990										
FRMD4B	23150	broad.mit.edu	37	chr3	69244463	69244463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agtttctccttcttctttagTtcaaggattttttctctctt	4	9	6	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:69244463T>C	ENST00000398540.3	-	15	1370	c.1287A>G	c.(1285-1287)gaA>gaG	p.E429E	FRMD4B_ENST00000542259.1_Silent_p.E375E|FRMD4B_ENST00000478263.1_Silent_p.E81E	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	429					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)		p.E375E(1)		NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TCTTCTTTAGTTCAAGGATTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	3											83	81	81					3																	69244463		1824	4074	5898	69327153	SO:0001819	synonymous_variant	23150			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1287A>G	3.37:g.69244463T>C			69327153	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																				0.423	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69244463	T	C	69244463	2	2	78	1	0	0	0	0	0	0	0	1	6071	1722	60	4		4	FRMD4B	3	69244463	Silent	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	14706900	69244463	128777967	34	22991										
PDZRN3	23024	broad.mit.edu	37	chr3	73432900	73432900	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgctcccgcagcaggcggtcCcgcacgggcctcttggtgat	14	16	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:73432900C>T	ENST00000263666.4	-	10	2931	c.2817G>A	c.(2815-2817)cgG>cgA	p.R939R	PDZRN3_ENST00000479530.1_Silent_p.R656R|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Silent_p.R661R|PDZRN3_ENST00000462146.2_Silent_p.R596R|PDZRN3_ENST00000466780.1_Silent_p.R596R	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	939					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R939R(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GCAGGCGGTCCCGCACGGGCC	0.677																																																1	Substitution - coding silent(1)	large_intestine(1)	3											34	35	35					3																	73432900		2203	4300	6503	73515590	SO:0001819	synonymous_variant	23024			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2817G>A	3.37:g.73432900C>T			73515590	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.564|7.564	0.665309|0.665309	0.14710|0.14710	.|.	.|.	ENSG00000121440|ENSG00000121440	ENST00000494559|ENST00000416926	.|.	.|.	.|.	5.4|5.4	-3.69|-3.69	0.04450|0.04450	.|.	.|.	.|.	.|.	.|.	T|T	0.51669|0.51669	0.1688|0.1688	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50092|0.50092	-0.8868|-0.8868	4|4	.|.	.|.	.|.	.|.	8.8133|8.8133	0.34981|0.34981	0.0811:0.5072:0.3234:0.0883|0.0811:0.5072:0.3234:0.0883	.|.	.|.	.|.	.|.	E|R	255|659	.|.	.|.	G|G	-|-	2|1	0|0	PDZRN3|PDZRN3	73515590|73515590	0.091000|0.091000	0.21658|0.21658	0.975000|0.975000	0.42487|0.42487	0.941000|0.941000	0.58515|0.58515	-0.543000|-0.543000	0.06084|0.06084	-0.589000|-0.589000	0.05874|0.05874	-0.951000|-0.951000	0.02657|0.02657	GGG|GGA		0.677	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73432900	C	T	73432900	2	4	78	1	0	0	0	0	0	0	0	1	11740	610	22	3		3	PDZRN3	3	73432900	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	4188437	73432900	124589530	35	22992										
KIAA1407	57577	broad.mit.edu	37	chr3	113697080	113697080	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgcttgccctgagaatcgatCttcacctccctgaccatgtt	7	14	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:113697080C>T	ENST00000295878.3	-	16	2705	c.2559G>A	c.(2557-2559)aaG>aaA	p.K853K		NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	853								p.K853K(1)		endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GAGAATCGATCTTCACCTCCC	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	3											129	123	125					3																	113697080		2203	4300	6503	115179770	SO:0001819	synonymous_variant	57577			AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2559G>A	3.37:g.113697080C>T			115179770	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	37	CCDS2977.1																																																																																				0.428	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113697080	C	T	113697080	2	4	78	1	0	0	0	0	0	0	0	1	8250	912	32	3		3	KIAA1407	3	113697080	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	40264180	113697080	84325350	36	22993										
MRAS	22808	broad.mit.edu	37	chr3	138117398	138117398	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gagcaaggaaaagaaatggcGaccaaacacaatgtaggtgt	12	6	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr3:138117398G>A	ENST00000289104.4	+	4	1082	c.435G>A	c.(433-435)gcG>gcA	p.A145A	MRAS_ENST00000423968.2_Silent_p.A145A|MRAS_ENST00000464896.1_Silent_p.A69A|MRAS_ENST00000474559.1_Silent_p.A145A	NM_001085049.2|NM_001252090.1|NM_001252091.1|NM_012219.4	NP_001078518.1|NP_001239019.1|NP_001239020.1|NP_036351.3	O14807	RASM_HUMAN	muscle RAS oncogene homolog	145					actin cytoskeleton organization (GO:0030036)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|Ras protein signal transduction (GO:0007265)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)	p.A145A(1)		kidney(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	14						AAGAAATGGCGACCAAACACA	0.502																																																1	Substitution - coding silent(1)	large_intestine(1)	3											126	114	118					3																	138117398		2203	4300	6503	139600088	SO:0001819	synonymous_variant	22808			AF022080	CCDS3100.1, CCDS58855.1	3q22.3	2014-05-09			ENSG00000158186	ENSG00000158186			7227	protein-coding gene	gene with protein product		608435				9400994, 10446149	Standard	NM_012219		Approved	M-RAs, R-RAS3, RRAS3	uc003esi.4	O14807	OTTHUMG00000159888	ENST00000289104.4:c.435G>A	3.37:g.138117398G>A			139600088	B4DIK0|Q86WX8	Silent	SNP	ENST00000289104.4	37	CCDS3100.1																																																																																				0.502	MRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357990.1			A	138117398	G	A	138117398	2	1	78	1	0	0	0	0	0	0	0	1	9785	1045	37	1		1	MRAS	3	138117398	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	24420318	138117398	59905032	37	22994										
EPHA5	2044	broad.mit.edu	37	chr4	66189890	66189890	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tttcttgaaggctgttcatgAtcttcttctggtgaccgaca	9	9	5	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:66189890A>T	ENST00000273854.3	-	18	3656	c.3056T>A	c.(3055-3057)aTc>aAc	p.I1019N	EPHA5_ENST00000432638.2_Missense_Mutation_p.I856N|EPHA5_ENST00000354839.4_Missense_Mutation_p.I997N	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	1019	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.I1019N(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GCTGTTCATGATCTTCTTCTG	0.433										TSP Lung(17;0.13)																																						1	Substitution - Missense(1)	large_intestine(1)	4											122	110	114					4																	66189890		2203	4300	6503	65872485	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.3056T>A	4.37:g.66189890A>T	ENSP00000273854:p.Ile1019Asn		65872485	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.012359	0.75046	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839	T;T;T	0.68765	-0.35;-0.35;-0.35	5.25	5.25	0.73442	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.56097	D	0.000025	D	0.86527	0.5954	M	0.94142	3.5	0.80722	D	1	D;D;D;D	0.89917	0.972;1.0;0.981;1.0	D;D;P;D	0.97110	0.933;1.0;0.89;0.99	D	0.90453	0.4440	10	0.87932	D	0	.	15.1623	0.72793	1.0:0.0:0.0:0.0	.	998;1020;997;1019	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	N	1019;856;997	ENSP00000273854:I1019N;ENSP00000389208:I856N;ENSP00000346899:I997N	ENSP00000273854:I1019N	I	-	2	0	EPHA5	65872485	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	1.980000	0.57719	0.455000	0.32223	ATC		0.433	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66189890	A	T	66189890	3	4	78	1	0	0	0	0	1	0	0	0	5183	333	12	5	61	5	EPHA5	4	66189890	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09		66189890	124964386	38	22995										
SLC4A4	8671	broad.mit.edu	37	chr4	72429564	72429564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttaaaattccaatggacatcAtggaacagcaacctttccta	5	10	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:72429564A>G	ENST00000264485.5	+	24	3271	c.3154A>G	c.(3154-3156)Atg>Gtg	p.M1052V	SLC4A4_ENST00000340595.3_Missense_Mutation_p.M1008V|SLC4A4_ENST00000425175.1_Intron|SLC4A4_ENST00000351898.6_Missense_Mutation_p.M968V	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	1052					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.M1008V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	AATGGACATCATGGAACAGCA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											152	158	156					4																	72429564		2203	4300	6503	72648428	SO:0001583	missense	8671			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.3154A>G	4.37:g.72429564A>G	ENSP00000264485:p.Met1052Val		72648428	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	7.750	0.703080	0.15172	.	.	ENSG00000080493	ENST00000264485;ENST00000351898;ENST00000340595	T;T;T	0.75154	-0.91;-0.58;-0.91	5.46	4.25	0.50352	.	0.037886	0.85682	D	0.000000	T	0.56572	0.1994	N	0.24115	0.695	0.80722	D	1	B;B;B	0.20164	0.012;0.042;0.025	B;B;B	0.21546	0.017;0.035;0.01	T	0.49643	-0.8918	10	0.02654	T	1	.	12.5178	0.56042	0.8603:0.1397:0.0:0.0	.	968;1008;1052	Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	V	1052;968;1008	ENSP00000264485:M1052V;ENSP00000307349:M968V;ENSP00000344272:M1008V	ENSP00000264485:M1052V	M	+	1	0	SLC4A4	72648428	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.988000	0.76212	0.885000	0.36088	-0.619000	0.04042	ATG		0.358	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		G	72429564	A	G	72429564	3	3	78	1	0	0	0	0	1	0	0	0	14693	217	8	4	3365	4	SLC4A4	4	72429564	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09	6239674	72429564	118724712	39	22996										
IBSP	3381	broad.mit.edu	37	chr4	88732921	88732921	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tacacgggcgccaatgaataCgacaatggatatgaaatcta	9	8	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:88732921C>T	ENST00000226284.5	+	7	880	c.813C>T	c.(811-813)taC>taT	p.Y271Y		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	271					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)		p.Y271Y(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		CCAATGAATACGACAATGGAT	0.478																																																2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	4											67	63	64					4																	88732921		2203	4300	6503	88951945	SO:0001819	synonymous_variant	3381				CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"bone sialoprotein", "bone sialoprotein II"	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.813C>T	4.37:g.88732921C>T			88951945		Silent	SNP	ENST00000226284.5	37	CCDS3624.1																																																																																				0.478	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2			T	88732921	C	T	88732921	2	4	78	1	0	0	0	0	0	0	0	1	7496	547	19	1		1	IBSP	4	88732921	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	16303357	88732921	102421355	40	22997										
TACR3	6870	broad.mit.edu	37	chr4	104640427	104640427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	attgaccaacgtgttgaaggCggccatggaggcgtcggaga	16	8	0	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:104640427C>T	ENST00000304883.2	-	1	546	c.406G>A	c.(406-408)Gcc>Acc	p.A136T		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	136					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.A136T(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		GTGTTGAAGGCGGCCATGGAG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	4											110	100	103					4																	104640427		2203	4300	6503	104859876	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.406G>A	4.37:g.104640427C>T	ENSP00000303325:p.Ala136Thr		104859876	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.609154	0.87258	.	.	ENSG00000169836	ENST00000304883	T	0.35973	1.28	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.120606	0.56097	D	0.000031	T	0.38374	0.1038	L	0.33093	0.98	0.80722	D	1	D	0.67145	0.996	P	0.48704	0.587	T	0.16276	-1.0408	10	0.48119	T	0.1	.	17.8687	0.88804	0.0:1.0:0.0:0.0	.	136	P29371	NK3R_HUMAN	T	136	ENSP00000303325:A136T	ENSP00000303325:A136T	A	-	1	0	TACR3	104859876	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	7.455000	0.80726	2.446000	0.82766	0.591000	0.81541	GCC		0.517	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		T	104640427	C	T	104640427	3	4	78	1	0	0	0	0	1	0	0	0	15546	768	27	1	1011	1	TACR3	4	104640427	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	15907506	104640427	86513849	41	22998										
PDE5A	8654	broad.mit.edu	37	chr4	120528116	120528116	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgacataaggctgtgacatcCaaatgactagaaatatcctt	7	8	0	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:120528116C>T	ENST00000354960.3	-	2	808	c.489G>A	c.(487-489)ttG>ttA	p.L163L	PDE5A_ENST00000394439.1_Silent_p.L111L|PDE5A_ENST00000264805.5_Silent_p.L121L	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	163					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.L163L(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	CTGTGACATCCAAATGACTAG	0.438																																																1	Substitution - coding silent(1)	large_intestine(1)	4											126	121	123					4																	120528116		2203	4300	6503	120747564	SO:0001819	synonymous_variant	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.489G>A	4.37:g.120528116C>T			120747564	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	37	CCDS3713.1																																																																																				0.438	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		T	120528116	C	T	120528116	2	4	78	1	0	0	0	0	0	0	0	1	11675	593	21	3		3	PDE5A	4	120528116	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	15887689	120528116	70626160	42	22999										
QRFPR	84109	broad.mit.edu	37	chr4	122250509	122250509	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gagaattctcagccagttcaGacctaaagagagcaagatgt	10	8	2	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr4:122250509G>C	ENST00000394427.2	-	6	1667	c.1256C>G	c.(1255-1257)tCt>tGt	p.S419C	QRFPR_ENST00000334383.5_3'UTR|Y_RNA_ENST00000384419.1_RNA	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	419					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.S419C(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						AGCCAGTTCAGACCTAAAGAG	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	130	132					4																	122250509		2203	4300	6503	122469959	SO:0001583	missense	84109			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.1256C>G	4.37:g.122250509G>C	ENSP00000377948:p.Ser419Cys		122469959		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780705	0.49891	.	.	ENSG00000186867	ENST00000394427	T	0.74209	-0.82	4.63	3.78	0.43462	.	0.325600	0.25938	N	0.027332	T	0.64692	0.2621	L	0.29908	0.895	0.80722	D	1	B	0.21821	0.061	B	0.22152	0.038	T	0.63269	-0.6675	10	0.59425	D	0.04	.	14.5419	0.68002	0.0:0.164:0.836:0.0	.	419	Q96P65	QRFPR_HUMAN	C	419	ENSP00000377948:S419C	ENSP00000377948:S419C	S	-	2	0	QRFPR	122469959	0.998000	0.40836	0.696000	0.30242	0.644000	0.38419	3.633000	0.54295	1.139000	0.42245	0.313000	0.20887	TCT		0.368	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		C	122250509	G	C	122250509	3	2	78	1	0	0	0	0	1	0	0	0	12915	942	33	5	43	5	QRFPR	4	122250509	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	1722393	122250509	68903767	43	23000										
SLC1A3	6507	broad.mit.edu	37	chr5	36671175	36671175	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	catcagggaagatgggaatgCgagctgtagtctattatatg	13	5	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr5:36671175C>T	ENST00000265113.4	+	4	840	c.364C>T	c.(364-366)Cga>Tga	p.R122*	SLC1A3_ENST00000381918.3_Nonsense_Mutation_p.R122*|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	122					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.R122*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GATGGGAATGCGAGCTGTAGT	0.468																																																1	Substitution - Nonsense(1)	large_intestine(1)	5											119	107	111					5																	36671175		2203	4300	6503	36706932	SO:0001587	stop_gained	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.364C>T	5.37:g.36671175C>T	ENSP00000265113:p.Arg122*		36706932	B2R5T3|Q4JCQ8	Nonsense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	C	40	8.070883	0.98638	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	.	.	.	4.7	3.76	0.43208	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.1434	13.5571	0.61765	0.2394:0.7606:0.0:0.0	.	.	.	.	X	122;70;122	.	ENSP00000265113:R122X	R	+	1	2	SLC1A3	36706932	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.520000	0.45554	2.421000	0.82119	0.655000	0.94253	CGA		0.468	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		T	36671175	C	T	36671175	4	4	78	1	0	0	0	0	0	1	0	0	14470	760	27	1	391	1	SLC1A3	5	36671175	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09		36671175	144244085	44	23001										
PJA2	9867	broad.mit.edu	37	chr5	108679941	108679941	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gtgaaagaaatggtgacaggGcaactctgttgctatatcat	11	6	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr5:108679941G>C	ENST00000361189.2	-	9	2190	c.1951C>G	c.(1951-1953)Ccc>Gcc	p.P651A	PJA2_ENST00000361557.3_Missense_Mutation_p.P651A	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	651	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.				long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P651A(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		TGGTGACAGGGCAACTCTGTT	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	5											83	77	79					5																	108679941		2202	4300	6502	108707840	SO:0001583	missense	9867			AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1951C>G	5.37:g.108679941G>C	ENSP00000354775:p.Pro651Ala		108707840	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723733	0.89298	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.72282	-0.64;-0.64	6.17	6.17	0.99709	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.64402	D	0.000001	D	0.87095	0.6092	M	0.85197	2.74	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.87287	0.2296	10	0.87932	D	0	-9.1349	20.8794	0.99867	0.0:0.0:1.0:0.0	.	651	O43164	PJA2_HUMAN	A	651	ENSP00000354775:P651A;ENSP00000355284:P651A	ENSP00000354775:P651A	P	-	1	0	PJA2	108707840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.635000	0.83286	2.941000	0.99782	0.655000	0.94253	CCC		0.338	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		C	108679941	G	C	108679941	3	2	78	1	0	0	0	0	1	0	0	0	11993	1203	42	5	183	5	PJA2	5	108679941	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	72008766	108679941	72235319	45	23002										
APC	324	broad.mit.edu	37	chr5	112175216	112175216	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgcaaatagcagaaataaaaGaaaagattggaactaggtca	9	4	1	3	rs121913224		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr5:112175216G>T	ENST00000457016.1	+	16	4305	c.3925G>T	c.(3925-3927)Gaa>Taa	p.E1309*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1309*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1309*			P25054	APC_HUMAN	adenomatous polyposis coli	1309	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			E -> G (in Ref. 1; AAA60353/AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*4(42)|p.E1309*(25)|p.I1311fs*4(2)|p.?(1)|p.E1309fs*6(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.E1309K(1)|p.K1308fs*4(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAATAAAAGAAAAGATTGG	0.423		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	75	Deletion - Frameshift(45)|Substitution - Nonsense(25)|Insertion - Frameshift(3)|Unknown(1)|Substitution - Missense(1)	large_intestine(71)|upper_aerodigestive_tract(1)|stomach(1)|soft_tissue(1)|skin(1)	5	GRCh37	CD084022|CD941590|CM920052	APC	D|M							54	55	55					5																	112175216		2202	4300	6502	112203115	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3925G>T	5.37:g.112175216G>T	ENSP00000413133:p.Glu1309*		112203115	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	37	6.023820	0.97211	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	5.73	5.73	0.89815	.	0.365794	0.32503	N	0.006002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.1954	19.8705	0.96849	0.0:0.0:1.0:0.0	.	.	.	.	X	1309	.	.	E	+	1	0	APC	112203115	1.000000	0.71417	0.971000	0.41717	0.520000	0.34377	7.454000	0.80714	2.861000	0.98227	0.655000	0.94253	GAA		0.423	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175216	G	T	112175216	4	4	78	1	0	0	0	0	0	1	0	0	763	943	33	2	3983	2	APC	5	112175216	Nonsense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	3495275	112175216	68740044	46	23003										
PCDHGA9	56107	broad.mit.edu	37	chr5	140782967	140782967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	acgaaatcgcggttcctggaGcacgttatccacttccagaa	9	12	0	1	rs370218984		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr5:140782967G>A	ENST00000573521.1	+	1	448	c.448G>A	c.(448-450)Gca>Aca	p.A150T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	150	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTTCCTGGAGCACGTTATCC	0.488																																																0			5											74	77	76					5																	140782967		1946	4150	6096	140763151	SO:0001583	missense	56107			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.448G>A	5.37:g.140782967G>A	ENSP00000460274:p.Ala150Thr		140763151	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.488	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		A	140782967	G	A	140782967	3	1	78	1	0	0	0	0	1	0	0	0	11592	971	34	3	450	3	PCDHGA9	5	140782967	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	28607751	140782967	40132293	47	23004										
CDHR2	54825	broad.mit.edu	37	chr5	175995737	175995737	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aatgaccctctgacctatggGatgagcggccccaatgccta	10	13	1	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr5:175995737G>T	ENST00000510636.1	+	4	457	c.183G>T	c.(181-183)ggG>ggT	p.G61G	CDHR2_ENST00000261944.5_Silent_p.G61G|CDHR2_ENST00000506348.1_Silent_p.G61G	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G61G(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						TGACCTATGGGATGAGCGGCC	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	5											108	101	104					5																	175995737		2203	4300	6503	175928343	SO:0001819	synonymous_variant	54825			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.183G>T	5.37:g.175995737G>T			175928343	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																				0.607	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	175995737	G	T	175995737	2	4	78	1	0	0	0	0	0	0	0	1	3125	1161	41	2		2	CDHR2	5	175995737	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	35212770	175995737	4919523	48	23005										
FOXF2	2295	broad.mit.edu	37	chr6	1394987	1394987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgtgtgacagaaaagatttcGtcctcaacttcaatgggatt	9	7	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:1394987G>A	ENST00000259806.1	+	2	1342	c.1228G>A	c.(1228-1230)Gtc>Atc	p.V410I		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	410					embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.V410I(1)		large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		AAAAGATTTCGTCCTCAACTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	6											217	189	198					6																	1394987		2203	4300	6503	1339986	SO:0001583	missense	2295			U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"Forkhead boxes"	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.1228G>A	6.37:g.1394987G>A	ENSP00000259806:p.Val410Ile		1339986	Q5TGJ1|Q9UQ85	Missense_Mutation	SNP	ENST00000259806.1	37	CCDS4472.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.869074	0.91587	.	.	ENSG00000137273	ENST00000259806	D	0.94576	-3.46	5.76	5.76	0.90799	.	0.086095	0.45361	D	0.000361	D	0.96473	0.8849	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.95932	0.8939	10	0.52906	T	0.07	.	18.9641	0.92689	0.0:0.0:1.0:0.0	.	410	Q12947	FOXF2_HUMAN	I	410	ENSP00000259806:V410I	ENSP00000259806:V410I	V	+	1	0	FOXF2	1339986	1.000000	0.71417	0.992000	0.48379	0.721000	0.41392	7.305000	0.78891	2.713000	0.92767	0.655000	0.94253	GTC		0.453	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1			A	1394987	G	A	1394987	3	1	78	1	0	0	0	0	1	0	0	0	6025	1145	40	1	1234	1	FOXF2	6	1394987	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		1394987	169720080	49	23006										
LTB	4050	broad.mit.edu	37	chr6	31548597	31548597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ctccggagctgcaccaggccGccgaaccccacgctcgtgta	11	18	0	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:31548597G>A	ENST00000429299.2	-	4	631	c.624C>T	c.(622-624)ggC>ggT	p.G208G	LTB_ENST00000483972.1_5'UTR|LTB_ENST00000446745.2_3'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	208					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.G208G(2)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GCACCAGGCCGCCGAACCCCA	0.657																																																2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	6											48	31	37					6																	31548597		1510	2709	4219	31656576	SO:0001819	synonymous_variant	4050			L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.624C>T	6.37:g.31548597G>A			31656576	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																				0.657	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31548597	G	A	31548597	2	1	78	1	0	0	0	0	0	0	0	1	9099	1074	38	1		1	LTB	6	31548597	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	30153610	31548597	139566470	50	23007										
KIAA0240	23506	broad.mit.edu	37	chr6	42819912	42819912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gaggcaagcacagatccctgGgctcttgagcaccacactgc	11	14	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:42819912G>A	ENST00000314073.5	+	7	2098	c.1922G>A	c.(1921-1923)gGg>gAg	p.G641E	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.G641E			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	641								p.G641E(1)									CAGATCCCTGGGCTCTTGAGC	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											97	80	86					6																	42819912		2203	4300	6503	42927890	SO:0001583	missense	23506			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.1922G>A	6.37:g.42819912G>A	ENSP00000313933:p.Gly641Glu		42927890	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.380584	0.61845	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.47177	0.85;0.85	5.14	5.14	0.70334	.	0.184794	0.38663	N	0.001612	T	0.31857	0.0810	L	0.36672	1.1	0.37443	D	0.914492	P;P	0.47762	0.835;0.9	P;P	0.44990	0.466;0.466	T	0.07558	-1.0766	10	0.33141	T	0.24	-2.1386	16.7878	0.85578	0.0:0.0:1.0:0.0	.	641;641	Q6AI39;B7Z2G7	K0240_HUMAN;.	E	641	ENSP00000313933:G641E;ENSP00000377723:G641E	ENSP00000313933:G641E	G	+	2	0	KIAA0240	42927890	1.000000	0.71417	0.975000	0.42487	0.928000	0.56348	4.180000	0.58296	2.377000	0.81083	0.462000	0.41574	GGG		0.527	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		A	42819912	G	A	42819912	3	1	78	1	0	0	0	0	1	0	0	0	8185	1232	43	3	1940	3	KIAA0240	6	42819912	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	11271315	42819912	128295155	51	23008										
TMEM63B	55362	broad.mit.edu	37	chr6	44114658	44114658	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcgcctaatgttcctcgatgCagagaggtaagggactgggg	15	8	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:44114658C>A	ENST00000259746.9	+	11	1040	c.857C>A	c.(856-858)gCa>gAa	p.A286E	TMEM63B_ENST00000323267.6_Missense_Mutation_p.A286E			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	286					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.A286E(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TTCCTCGATGCAGAGAGGTAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	6											85	72	76					6																	44114658		2203	4300	6503	44222636	SO:0001583	missense	55362			BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.857C>A	6.37:g.44114658C>A	ENSP00000259746:p.Ala286Glu		44222636	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	37	CCDS34461.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.10|14.10	2.434962|2.434962	0.43224|0.43224	.|.	.|.	ENSG00000137216|ENSG00000137216	ENST00000259746;ENST00000323267|ENST00000371893	T;T|.	0.36520|.	1.25;1.25|.	4.54|4.54	3.59|3.59	0.41128|0.41128	.|.	0.117031|.	0.64402|.	D|.	0.000019|.	T|T	0.43010|0.43010	0.1228|0.1228	L|L	0.31926|0.31926	0.97|0.97	0.48901|0.48901	D|D	0.999729|0.999729	B;P|.	0.34724|.	0.015;0.465|.	B;B|.	0.34242|.	0.011;0.178|.	T|T	0.28744|0.28744	-1.0034|-1.0034	10|5	0.07813|.	T|.	0.8|.	.|.	13.6798|13.6798	0.62476|0.62476	0.1544:0.8455:0.0:0.0|0.1544:0.8455:0.0:0.0	.|.	286;286|.	Q5T3F8;Q5T3F8-2|.	TM63B_HUMAN;.|.	E|K	286|215	ENSP00000259746:A286E;ENSP00000327154:A286E|.	ENSP00000259746:A286E|.	A|Q	+|+	2|1	0|0	TMEM63B|TMEM63B	44222636|44222636	0.981000|0.981000	0.34729|0.34729	0.989000|0.989000	0.46669|0.46669	0.981000|0.981000	0.71138|0.71138	2.554000|2.554000	0.45845|0.45845	2.501000|2.501000	0.84356|0.84356	0.650000|0.650000	0.86243|0.86243	GCA|CAG		0.552	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		A	44114658	C	A	44114658	3	1	78	1	0	0	0	0	1	0	0	0	16230	710	25	2	895	2	TMEM63B	6	44114658	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	1294746	44114658	127000409	52	23009										
MED23	9439	broad.mit.edu	37	chr6	131929191	131929191	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ataagatgatctctgcctttAatcagtcctcgccctgctaa	6	12	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:131929191A>G	ENST00000368068.3	-	12	1277	c.1098T>C	c.(1096-1098)atT>atC	p.I366I	MED23_ENST00000368060.3_Silent_p.I366I|MED23_ENST00000540546.1_Silent_p.I372I|MED23_ENST00000368058.1_Silent_p.I372I|MED23_ENST00000403834.3_Silent_p.I372I|MED23_ENST00000354577.4_Silent_p.I372I|MED23_ENST00000545957.1_Intron|MED23_ENST00000368053.4_Silent_p.I372I|MED23_ENST00000539158.1_Silent_p.I366I	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	366					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.I366I(1)|p.I372I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		CTCTGCCTTTAATCAGTCCTC	0.363																																																2	Substitution - coding silent(2)	large_intestine(2)	6											89	90	90					6																	131929191		2203	4300	6503	131970884	SO:0001819	synonymous_variant	9439			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.1098T>C	6.37:g.131929191A>G			131970884	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Silent	SNP	ENST00000368068.3	37	CCDS5147.1																																																																																				0.363	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			G	131929191	A	G	131929191	2	3	78	1	0	0	0	0	0	0	0	1	9471	358	13	4		4	MED23	6	131929191	Silent	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09	87814533	131929191	39185876	53	23010										
LTV1	84946	broad.mit.edu	37	chr6	144179116	144179116	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	catgaggagaaatgaacagcTgaccctacatgatgagaggt	12	7	0	6			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:144179116T>A	ENST00000367576.5	+	6	901	c.767T>A	c.(766-768)cTg>cAg	p.L256Q		NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	256						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L256Q(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		AATGAACAGCTGACCCTACAT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	6											70	71	71					6																	144179116		2203	4300	6503	144220809	SO:0001583	missense	84946			BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 93", "LTV1 homolog (S. cerevisiae)"	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.767T>A	6.37:g.144179116T>A	ENSP00000356548:p.Leu256Gln		144220809	Q96JX8	Missense_Mutation	SNP	ENST00000367576.5	37	CCDS5201.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.866561	0.91511	.	.	ENSG00000135521	ENST00000367576	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.75591	0.3870	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.77705	-0.2488	9	0.48119	T	0.1	-7.1932	16.1445	0.81555	0.0:0.0:0.0:1.0	.	256	Q96GA3	LTV1_HUMAN	Q	256	.	ENSP00000356548:L256Q	L	+	2	0	LTV1	144220809	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.650000	0.83521	2.223000	0.72356	0.477000	0.44152	CTG		0.408	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860		A	144179116	T	A	144179116	3	1	78	1	0	0	0	0	1	0	0	0	9110	1580	55	5	789	5	LTV1	6	144179116	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	12249925	144179116	26935951	54	23011										
C6orf97	80129	broad.mit.edu	37	chr6	151857487	151857487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tctttcggaagtcccggtcaCgcgggagcagttaaaccact	11	12	2	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr6:151857487C>T	ENST00000239374.7	+	2	191	c.92C>T	c.(91-93)aCg>aTg	p.T31M	CCDC170_ENST00000544131.1_3'UTR|CCDC170_ENST00000367290.5_Missense_Mutation_p.T31M	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	31								p.T31M(1)									GTCCCGGTCACGCGGGAGCAG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	6											104	97	99					6																	151857487		1854	4094	5948	151899180	SO:0001583	missense	80129			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.92C>T	6.37:g.151857487C>T	ENSP00000239374:p.Thr31Met		151899180	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.086199	0.36855	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.11821	2.75;2.74	5.95	3.17	0.36434	.	0.491298	0.22181	N	0.063519	T	0.16257	0.0391	M	0.73962	2.25	0.26952	N	0.966002	D	0.71674	0.998	P	0.59288	0.855	T	0.05451	-1.0884	10	0.87932	D	0	-1.2721	9.129	0.36833	0.0:0.7463:0.1219:0.1318	.	31	Q8IYT3	CF097_HUMAN	M	31	ENSP00000239374:T31M;ENSP00000356259:T31M	ENSP00000239374:T31M	T	+	2	0	C6orf97	151899180	0.675000	0.27558	0.047000	0.18901	0.001000	0.01503	1.302000	0.33459	0.389000	0.25086	-0.157000	0.13467	ACG		0.433	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		T	151857487	C	T	151857487	3	4	78	1	0	0	0	0	1	0	0	0	2380	536	19	1	98	1	C6orf97	6	151857487	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	7678371	151857487	19257580	55	23012										
SNX13	23161	broad.mit.edu	37	chr7	17861245	17861245	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agtgatggcatataatgcatAtgtcttgccatgatcattac	8	7	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:17861245A>G	ENST00000409389.1	-	18	1937	c.1765T>C	c.(1765-1767)Tat>Cat	p.Y589H	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000428135.3_Missense_Mutation_p.Y578H			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	589	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.Y578H(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TATAATGCATATGTCTTGCCA	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	7											127	122	124					7																	17861245		1939	4137	6076	17827770	SO:0001583	missense	23161			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1765T>C	7.37:g.17861245A>G	ENSP00000386705:p.Tyr589His		17827770	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	A	18.04	3.535385	0.64972	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.38722	1.12;1.12	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.52322	0.1727	L	0.55743	1.74	0.80722	D	1	P;P;D	0.53151	0.941;0.599;0.958	P;B;P	0.53313	0.723;0.345;0.601	T	0.50398	-0.8833	10	0.42905	T	0.14	-5.253	16.056	0.80805	1.0:0.0:0.0:0.0	.	375;589;578	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	H	589;578;626	ENSP00000386705:Y589H;ENSP00000398789:Y578H	ENSP00000242044:Y626H	Y	-	1	0	SNX13	17827770	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.887000	0.92456	2.178000	0.69098	0.533000	0.62120	TAT		0.413	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		G	17861245	A	G	17861245	3	3	78	1	0	0	0	0	1	0	0	0	14921	449	16	4	1177	4	SNX13	7	17861245	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09		17861245	141277418	56	23013										
ZNF498	221785	broad.mit.edu	37	chr7	99227098	99227098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcagtcggagctccaatctcGtcaggcaccagcgaacccac	9	16	3	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:99227098G>A	ENST00000394152.2	+	8	1417	c.1090G>A	c.(1090-1092)Gtc>Atc	p.V364I	ZSCAN25_ENST00000262941.6_Missense_Mutation_p.V292I|ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.V364I	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	364					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V364I(1)									CTCCAATCTCGTCAGGCACCA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	7											76	70	72					7																	99227098		2203	4300	6503	99065034	SO:0001583	missense	221785			AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1090G>A	7.37:g.99227098G>A	ENSP00000377708:p.Val364Ile		99065034	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	G	8.305	0.820861	0.16678	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.52295	0.67;0.67;0.67	3.77	3.77	0.43336	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41194	D	0.000933	T	0.30230	0.0758	N	0.10837	0.055	0.09310	N	1	P;P	0.52061	0.882;0.95	P;P	0.49597	0.482;0.616	T	0.14227	-1.0480	10	0.07813	T	0.8	-19.2235	9.5985	0.39589	0.0:0.2138:0.7862:0.0	.	292;364	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	I	364;364;292	ENSP00000377708:V364I;ENSP00000334800:V364I;ENSP00000262941:V292I	ENSP00000262941:V292I	V	+	1	0	ZNF498	99065034	0.000000	0.05858	0.333000	0.25482	0.823000	0.46562	0.508000	0.22692	2.394000	0.81467	0.561000	0.74099	GTC		0.547	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		A	99227098	G	A	99227098	3	1	78	1	0	0	0	0	1	0	0	0	17986	1145	40	1	1108	1	ZNF498	7	99227098	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	81365853	99227098	59911565	57	23014										
SRRT	51593	broad.mit.edu	37	chr7	100485102	100485102	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aggaactgggcaaggataagTggctgtgtcctctcagtggc	15	8	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:100485102T>G	ENST00000347433.4	+	16	2295	c.2137T>G	c.(2137-2139)Tgg>Ggg	p.W713G	SRRT_ENST00000432932.1_Missense_Mutation_p.W712G|SRRT_ENST00000457580.2_Missense_Mutation_p.W713G|SRRT_ENST00000388793.4_Missense_Mutation_p.W712G			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	713					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.W713G(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CAAGGATAAGTGGCTGTGTCC	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	7											139	114	122					7																	100485102		2203	4300	6503	100323038	SO:0001583	missense	51593				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2137T>G	7.37:g.100485102T>G	ENSP00000314491:p.Trp713Gly		100323038	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.993414	0.74703	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000342198;ENST00000432932;ENST00000347433;ENST00000448764	.	.	.	4.83	4.83	0.62350	Arsenite-resistance protein 2 (1);	0.000000	0.85682	D	0.000000	T	0.79793	0.4507	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.69078	0.996;0.996;0.996;0.997	D;D;D;D	0.81914	0.986;0.991;0.991;0.995	T	0.83196	-0.0081	9	0.87932	D	0	.	12.3543	0.55165	0.0:0.0:0.0:1.0	.	712;712;713;713	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	G	713;712;78;712;713;343	.	ENSP00000344670:W78G	W	+	1	0	SRRT	100323038	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.440000	0.80464	2.020000	0.59435	0.247000	0.18012	TGG		0.572	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		G	100485102	T	G	100485102	3	3	78	1	0	0	0	0	1	0	0	0	15211	1696	59	4	2195	4	SRRT	7	100485102	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	1258004	100485102	58653561	58	23015										
AKR1B10	57016	broad.mit.edu	37	chr7	134221874	134221874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tccaagggcatcaccgttacGgcctacagccccctgggctc	10	17	1	0	rs568011657		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:134221874G>A	ENST00000359579.4	+	6	944	c.624G>A	c.(622-624)acG>acA	p.T208T		NM_020299.4	NP_064695.3	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10 (aldose reductase)	208					cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aldo-keto reductase (NADP) activity (GO:0004033)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|retinal dehydrogenase activity (GO:0001758)	p.T208T(2)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(9)|skin(5)	20						TCACCGTTACGGCCTACAGCC	0.483													g|||	1	0.000199681	0	0	5008	,	,		16791	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	large_intestine(2)	7											15	24	21					7																	134221874		2145	4279	6424	133872414	SO:0001819	synonymous_variant	57016			AF052577	CCDS5832.1	7q33	2010-04-08			ENSG00000198074	ENSG00000198074		"Aldo-keto reductases"	382	protein-coding gene	gene with protein product	"aldose reductase-like 1", "aldo-keto reductase family 1, member B11 (aldose reductase-like)", "aldose reductase-like peptide", "aldose reductase-related protein", "small intestine reductase"	604707		AKR1B11		9765596, 9565553	Standard	NM_020299		Approved	AKR1B12, ARL-1, HIS, ARL1, HSI, ALDRLn	uc003vrr.3	O60218	OTTHUMG00000155356	ENST00000359579.4:c.624G>A	7.37:g.134221874G>A			133872414	A4D1P1|O75890|Q6FHF3|Q8IWZ1	Silent	SNP	ENST00000359579.4	37	CCDS5832.1																																																																																				0.483	AKR1B10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339615.1	NM_020299		A	134221874	G	A	134221874	2	1	78	1	0	0	0	0	0	0	0	1	467	1103	39	1		1	AKR1B10	7	134221874	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	33736772	134221874	24916789	59	23016										
NUP205	23165	broad.mit.edu	37	chr7	135286244	135286244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	taagcagcttgacacctatgCcccctttcctggtatatgct	7	13	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:135286244C>T	ENST00000285968.6	+	17	2527	c.2501C>T	c.(2500-2502)gCc>gTc	p.A834V		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	834					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.A834V(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GACACCTATGCCCCCTTTCCT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	7											176	169	171					7																	135286244		2203	4300	6503	134936784	SO:0001583	missense	23165			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.2501C>T	7.37:g.135286244C>T	ENSP00000285968:p.Ala834Val		134936784	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144823	0.77888	.	.	ENSG00000155561	ENST00000285968	T	0.32272	1.46	5.76	5.76	0.90799	.	0.046469	0.85682	D	0.000000	T	0.33118	0.0852	L	0.40543	1.245	0.80722	D	1	B	0.33777	0.425	B	0.37508	0.252	T	0.02844	-1.1103	10	0.35671	T	0.21	-32.9722	19.9616	0.97254	0.0:1.0:0.0:0.0	.	834	Q92621	NU205_HUMAN	V	834	ENSP00000285968:A834V	ENSP00000285968:A834V	A	+	2	0	NUP205	134936784	1.000000	0.71417	0.995000	0.50966	0.922000	0.55478	5.956000	0.70315	2.724000	0.93272	0.561000	0.74099	GCC		0.398	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			T	135286244	C	T	135286244	3	4	78	1	0	0	0	0	1	0	0	0	10790	739	26	3	2567	3	NUP205	7	135286244	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	1064370	135286244	23852419	60	23017										
DGKI	9162	broad.mit.edu	37	chr7	137148244	137148244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agaactcttactgtagcacgCgggagtggctgagatctttc	12	9	2	2	rs568336252		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:137148244C>T	ENST00000288490.5	-	28	2750	c.2750G>A	c.(2749-2751)cGc>cAc	p.R917H	DGKI_ENST00000453654.2_Intron|DGKI_ENST00000446122.1_Missense_Mutation_p.R899H|DGKI_ENST00000424189.2_Missense_Mutation_p.R930H	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	917					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R917H(1)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CTGTAGCACGCGGGAGTGGCT	0.532													C|||	1	0.000199681	0	0	5008	,	,		20781	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	7											116	105	109					7																	137148244		2203	4300	6503	136798784	SO:0001583	missense	9162			AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2750G>A	7.37:g.137148244C>T	ENSP00000288490:p.Arg917His		136798784	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457715	0.26161	.	.	ENSG00000157680	ENST00000424189;ENST00000288490;ENST00000446122	T;T	0.35048	1.33;1.53	5.91	0.421	0.16451	.	3.008490	0.00744	N	0.001024	T	0.19967	0.0480	N	0.08118	0	0.19300	N	0.999976	B	0.02656	0.0	B	0.01281	0.0	T	0.16100	-1.0414	10	0.15066	T	0.55	.	7.5503	0.27793	0.0:0.3563:0.0:0.6437	.	917	O75912	DGKI_HUMAN	H	920;917;899	ENSP00000288490:R917H;ENSP00000399131:R899H	ENSP00000288490:R917H	R	-	2	0	DGKI	136798784	0.674000	0.27549	0.295000	0.24960	0.937000	0.57800	0.853000	0.27777	0.134000	0.18681	-0.136000	0.14681	CGC		0.532	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137148244	C	T	137148244	3	4	78	1	0	0	0	0	1	0	0	0	4482	768	27	1	475	1	DGKI	7	137148244	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	1862000	137148244	21990419	61	23018										
HIPK2	28996	broad.mit.edu	37	chr7	139416487	139416487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggaggctcacagtgcttcgaCgcattaggttgtgtggtccg	15	9	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr7:139416487C>T	ENST00000406875.3	-	2	441	c.347G>A	c.(346-348)cGt>cAt	p.R116H	HIPK2_ENST00000428878.2_Missense_Mutation_p.R116H|HIPK2_ENST00000342645.6_Missense_Mutation_p.R116H	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	116	Transcriptional corepression. {ECO:0000250}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)	p.R116H(1)		breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					AGTGCTTCGACGCATTAGGTT	0.557																																																1	Substitution - Missense(1)	large_intestine(1)	7											102	86	91					7																	139416487		1568	3582	5150	139062973	SO:0001583	missense	28996			AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.347G>A	7.37:g.139416487C>T	ENSP00000385571:p.Arg116His		139062973	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	37		.	.	.	.	.	.	.	.	.	.	C	14.93	2.682968	0.47991	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.52983	0.64;0.66;0.69	5.28	5.28	0.74379	.	.	.	.	.	T	0.68109	0.2965	.	.	.	0.80722	D	1	P;D	0.76494	0.703;0.999	B;D	0.80764	0.103;0.994	T	0.64888	-0.6301	8	0.30078	T	0.28	.	18.9194	0.92519	0.0:1.0:0.0:0.0	.	116;116	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	H	116	ENSP00000385571:R116H;ENSP00000413724:R116H;ENSP00000343108:R116H	ENSP00000343108:R116H	R	-	2	0	HIPK2	139062973	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.070000	0.71220	2.454000	0.82982	0.563000	0.77884	CGT		0.557	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		T	139416487	C	T	139416487	3	4	78	1	0	0	0	0	1	0	0	0	7138	536	19	1	3305	1	HIPK2	7	139416487	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2268243	139416487	19722176	62	23019										
ANK1	286	broad.mit.edu	37	chr8	41545720	41545720	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gagataacagccatcttcatCtctgcctgctctgtcccact	6	15	4	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr8:41545720C>T	ENST00000347528.4	-	35	4295	c.4212G>A	c.(4210-4212)gaG>gaA	p.E1404E	ANK1_ENST00000352337.4_Silent_p.E1404E|ANK1_ENST00000289734.7_Silent_p.E1404E|ANK1_ENST00000396945.1_Silent_p.E1404E|ANK1_ENST00000265709.8_Silent_p.E1445E|ANK1_ENST00000379758.2_Silent_p.E1404E|ANK1_ENST00000396942.1_Silent_p.E1404E	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1404	55 kDa regulatory domain.|Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E1404E(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	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)			CCATCTTCATCTCTGCCTGCT	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	8											271	226	241					8																	41545720		2203	4300	6503	41664877	SO:0001819	synonymous_variant	286			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4212G>A	8.37:g.41545720C>T			41664877	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	0.619	-0.822042	0.02755	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.33381	0.0861	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40683	-0.9550	4	.	.	.	.	2.9288	0.05793	0.4892:0.0906:0.2541:0.1662	.	.	.	.	N	726	.	.	D	-	1	0	ANK1	41664877	0.977000	0.34250	0.029000	0.17559	0.174000	0.22865	0.281000	0.18810	-2.044000	0.00911	-0.309000	0.09137	GAT		0.542	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41545720	C	T	41545720	2	4	78	1	0	0	0	0	0	0	0	1	620	912	32	3		3	ANK1	8	41545720	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09		41545720	104818302	63	23020										
ZNF34	80778	broad.mit.edu	37	chr8	146003460	146003460	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ccgtaggtctccagcatcacGtccctgtagaggcccctctg	10	16	3	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr8:146003460G>A	ENST00000343459.4	-	4	251	c.186C>T	c.(184-186)gaC>gaT	p.D62D	ZNF34_ENST00000429371.2_Silent_p.D41D			Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	62	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D62D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)		CCAGCATCACGTCCCTGTAGA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	8											39	43	41					8																	146003460		2185	4297	6482	145974264	SO:0001819	synonymous_variant	80778			BC028136	CCDS47945.1, CCDS69562.1	8q24	2013-01-08	2006-05-11					"Zinc fingers, C2H2-type", "-"	13098	protein-coding gene	gene with protein product		194526	"zinc finger protein 34 (KOX 32)"			8104631, 2014798	Standard	XM_005272349		Approved	KOX32	uc003zdy.4	Q8IZ26		ENST00000343459.4:c.186C>T	8.37:g.146003460G>A			145974264	D3DWN1|Q9BSZ0	De_novo_Start_OutOfFrame	SNP	ENST00000343459.4	37	CCDS47945.1																																																																																				0.637	ZNF34-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382936.1	NM_030580		A	146003460	G	A	146003460	2	1	78	1	0	0	0	0	0	0	0	1	17895	1136	40	1		1	ZNF34	8	146003460	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	104457740	146003460	360562	64	23021										
TAF1L	138474	broad.mit.edu	37	chr9	32631660	32631660	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gcaacaggtttcgaaggtggCacatttgtttgataatagag	12	5	0	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr9:32631660C>A	ENST00000242310.4	-	1	4007	c.3918G>T	c.(3916-3918)gtG>gtT	p.V1306V	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1306					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.V1306V(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCGAAGGTGGCACATTTGTTT	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	9											189	188	188					9																	32631660		2203	4300	6503	32621660	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3918G>T	9.37:g.32631660C>A			32621660	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.433	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32631660	C	A	32631660	2	1	78	1	0	0	0	0	0	0	0	1	15562	697	25	2		2	TAF1L	9	32631660	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09		32631660	108581771	65	23022										
UBAP2	55833	broad.mit.edu	37	chr9	33988990	33988990	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cattctctgccacgattgccGcctcttcctttccggttgtt	7	15	2	0	rs140158168	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr9:33988990G>A	ENST00000379238.1	-	5	540	c.423C>T	c.(421-423)ggC>ggT	p.G141G	UBAP2_ENST00000418786.2_Silent_p.G141G|UBAP2_ENST00000449054.1_Silent_p.G141G|UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000360802.1_Silent_p.G141G|UBAP2_ENST00000379239.4_5'UTR					ubiquitin associated protein 2									p.G141G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CACGATTGCCGCCTCTTCCTT	0.438													G|||	2	0.000399361	0.0015	0	5008	,	,		16625	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	9											247	232	237					9																	33988990		2203	4300	6503	33978990	SO:0001819	synonymous_variant	55833			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.423C>T	9.37:g.33988990G>A			33978990		Silent	SNP	ENST00000379238.1	37	CCDS6547.1																																																																																				0.438	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		A	33988990	G	A	33988990	2	1	78	1	0	0	0	0	0	0	0	1	16877	1074	38	1		1	UBAP2	9	33988990	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	1357330	33988990	107224441	66	23023										
SEC24C	9632	broad.mit.edu	37	chr10	75528843	75528843	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gctggctgggctagatggggAcaaaacagtgactgtggagt	17	6	0	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr10:75528843A>G	ENST00000339365.2	+	18	2519	c.2357A>G	c.(2356-2358)gAc>gGc	p.D786G	SEC24C_ENST00000540668.1_Missense_Mutation_p.D34G|SEC24C_ENST00000535742.1_Missense_Mutation_p.D34G|SEC24C_ENST00000411652.2_Missense_Mutation_p.D667G|SEC24C_ENST00000345254.4_Missense_Mutation_p.D786G|SEC24C_ENST00000496827.1_3'UTR	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	786					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.D786G(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					CTAGATGGGGACAAAACAGTG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	10											89	77	81					10																	75528843		2203	4300	6503	75198849	SO:0001583	missense	9632			D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2357A>G	10.37:g.75528843A>G	ENSP00000343405:p.Asp786Gly		75198849	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.672701	0.88445	.	.	ENSG00000176986	ENST00000535742;ENST00000345254;ENST00000540668;ENST00000339365;ENST00000411652	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.72	5.72	0.89469	Sec23/Sec24 beta-sandwich (1);	0.128990	0.64402	D	0.000001	T	0.64249	0.2581	M	0.94142	3.5	0.80722	D	1	B;P;P	0.46512	0.182;0.493;0.879	B;B;P	0.57911	0.122;0.349;0.829	T	0.74819	-0.3535	10	0.87932	D	0	-5.2312	15.9993	0.80280	1.0:0.0:0.0:0.0	.	667;786;786	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	G	34;786;34;786;667	ENSP00000446174:D34G;ENSP00000321845:D786G;ENSP00000445023:D34G;ENSP00000343405:D786G;ENSP00000402913:D667G	ENSP00000343405:D786G	D	+	2	0	SEC24C	75198849	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.339000	0.96797	2.184000	0.69523	0.383000	0.25322	GAC		0.567	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			G	75528843	A	G	75528843	3	3	78	1	0	0	0	0	1	0	0	0	14033	275	10	4	2419	4	SEC24C	10	75528843	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09		75528843	60005904	67	23024										
MYST4	23522	broad.mit.edu	37	chr10	76741653	76741653	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tttcatcctccagcaaatgaAatttaccgaaggaaagacct	6	10	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr10:76741653A>C	ENST00000287239.4	+	11	2829	c.2340A>C	c.(2338-2340)gaA>gaC	p.E780D	KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372714.1_Missense_Mutation_p.E488D|KAT6B_ENST00000372711.1_Missense_Mutation_p.E597D|KAT6B_ENST00000372724.1_Missense_Mutation_p.E488D|KAT6B_ENST00000372725.1_Missense_Mutation_p.E488D	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	780	Catalytic.|Interaction with BRPF1.|MYST-type HAT.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E780D(1)									CAGCAAATGAAATTTACCGAA	0.338																																																1	Substitution - Missense(1)	large_intestine(1)	10											47	51	49					10																	76741653		2203	4299	6502	76411659	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2340A>C	10.37:g.76741653A>C	ENSP00000287239:p.Glu780Asp		76411659	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	12.53	1.966940	0.34659	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.81996	-1.52;-1.52;-1.56;-1.52;-1.54	5.98	-0.369	0.12534	.	0.000000	0.49916	D	0.000130	D	0.87589	0.6215	M	0.78456	2.415	0.50813	D	0.999896	D;B;P	0.63046	0.992;0.049;0.953	D;B;D	0.70227	0.968;0.013;0.938	D	0.84060	0.0374	10	0.87932	D	0	-14.5127	6.4018	0.21642	0.56:0.1233:0.3167:0.0	.	597;488;780	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	D	488;488;780;488;597	ENSP00000361810:E488D;ENSP00000361809:E488D;ENSP00000287239:E780D;ENSP00000361799:E488D;ENSP00000361796:E597D	ENSP00000287239:E780D	E	+	3	2	KAT6B	76411659	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	3.083000	0.50136	-0.298000	0.08921	-0.290000	0.09829	GAA		0.338	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76741653	A	C	76741653	3	2	78	1	0	0	0	0	1	0	0	0	10135	11	1	4	2374	4	MYST4	10	76741653	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09	1212810	76741653	58793094	68	23025										
SLC18A2	6571	broad.mit.edu	37	chr10	119014840	119014840	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tttgtggggaagacggctccGttcctggtgctggccgccct	15	12	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr10:119014840G>A	ENST00000298472.5	+	7	896	c.753G>A	c.(751-753)ccG>ccA	p.P251P	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	251					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.P251P(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AGACGGCTCCGTTCCTGGTGC	0.642																																																1	Substitution - coding silent(1)	large_intestine(1)	10											68	64	66					10																	119014840		2203	4300	6503	119004830	SO:0001819	synonymous_variant	6571			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.753G>A	10.37:g.119014840G>A			119004830	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																				0.642	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		A	119014840	G	A	119014840	2	1	78	1	0	0	0	0	0	0	0	1	14463	1132	40	1		1	SLC18A2	10	119014840	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	42273187	119014840	16519907	69	23026										
LDLRAD3	143458	broad.mit.edu	37	chr11	36248930	36248930	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agccaggcggagcagaatgcGtcggaagtaggctccccacc	14	13	0	1	rs140347483	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:36248930G>A	ENST00000315571.5	+	5	771	c.750G>A	c.(748-750)gcG>gcA	p.A250A	LDLRAD3_ENST00000529759.1_3'UTR|LDLRAD3_ENST00000524419.1_Silent_p.A240A|LDLRAD3_ENST00000528989.1_Silent_p.A201A	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	250					receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.A250A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				AGCAGAATGCGTCGGAAGTAG	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	11						G		0,4404		0,0,2202	79	70	73		750	-9.1	0.1	11	dbSNP_134	73	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	LDLRAD3	NM_174902.2		0,2,6498	AA,AG,GG		0.0233,0.0,0.0154		250/346	36248930	2,12998	2202	4298	6500	36205506	SO:0001819	synonymous_variant	143458			AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.750G>A	11.37:g.36248930G>A			36205506	B7Z1U3|B9EG81|Q8NBJ0	Silent	SNP	ENST00000315571.5	37	CCDS31462.1																																																																																				0.607	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		A	36248930	G	A	36248930	2	1	78	1	0	0	0	0	0	0	0	1	8729	1132	40	1		1	LDLRAD3	11	36248930	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		36248930	98757586	70	23027										
OR8K3	219473	broad.mit.edu	37	chr11	56085940	56085940	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgtcctcaccaagttggactCcaggttgcaaacccctatgt	8	13	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:56085940C>A	ENST00000312711.1	+	1	158	c.158C>A	c.(157-159)tCc>tAc	p.S53Y		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S53Y(1)		central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					AAGTTGGACTCCAGGTTGCAA	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	11											210	200	204					11																	56085940		2201	4296	6497	55842516	SO:0001583	missense	219473			AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.158C>A	11.37:g.56085940C>A	ENSP00000323555:p.Ser53Tyr		55842516	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	37	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	C	3.268	-0.149739	0.06585	.	.	ENSG00000181689	ENST00000312711	T	0.00441	7.41	4.56	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.790420	0.11658	N	0.542115	T	0.00552	0.0018	M	0.85462	2.755	0.09310	N	1	B	0.22541	0.071	B	0.28232	0.087	T	0.33929	-0.9849	10	0.66056	D	0.02	.	7.3709	0.26800	0.3103:0.3858:0.3039:0.0	.	53	Q8NH51	OR8K3_HUMAN	Y	53	ENSP00000323555:S53Y	ENSP00000323555:S53Y	S	+	2	0	OR8K3	55842516	0.000000	0.05858	0.013000	0.15412	0.033000	0.12548	-1.447000	0.02396	0.228000	0.21019	0.637000	0.83480	TCC		0.423	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		A	56085940	C	A	56085940	3	1	78	1	0	0	0	0	1	0	0	0	11275	855	30	2	160	2	OR8K3	11	56085940	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	19837010	56085940	78920576	71	23028										
VWCE	220001	broad.mit.edu	37	chr11	61040716	61040716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggtgaagcaacactgcccagGgcccagccgccactcttctc	10	17	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:61040716G>A	ENST00000335613.5	-	13	2040	c.1654C>T	c.(1654-1656)Cct>Tct	p.P552S	VWCE_ENST00000535710.1_Missense_Mutation_p.P17S	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	552	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P552S(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CACTGCCCAGGGCCCAGCCGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	11											28	28	28					11																	61040716		2203	4299	6502	60797292	SO:0001583	missense	220001			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1654C>T	11.37:g.61040716G>A	ENSP00000334186:p.Pro552Ser		60797292	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162232	0.78226	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	T;T	0.79141	-1.24;-1.24	4.53	4.53	0.55603	von Willebrand factor, type C (4);	0.000000	0.41823	D	0.000807	D	0.85440	0.5697	L	0.58810	1.83	0.36852	D	0.887941	D	0.89917	1.0	D	0.91635	0.999	D	0.88812	0.3292	10	0.59425	D	0.04	.	15.0772	0.72084	0.0:0.0:1.0:0.0	.	552	Q96DN2	VWCE_HUMAN	S	552;17	ENSP00000334186:P552S;ENSP00000442570:P17S	ENSP00000334186:P552S	P	-	1	0	VWCE	60797292	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.296000	0.72751	2.092000	0.63282	0.471000	0.43371	CCT		0.647	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61040716	G	A	61040716	3	1	78	1	0	0	0	0	1	0	0	0	17285	1232	43	3	1245	3	VWCE	11	61040716	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	4954776	61040716	73965800	72	23029										
AHNAK	79026	broad.mit.edu	37	chr11	62298426	62298426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cttgggtcctgagacaacaaCgtcagccttaggcaagttca	10	11	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:62298426C>T	ENST00000378024.4	-	5	3737	c.3463G>A	c.(3463-3465)Gtt>Att	p.V1155I	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1155					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V1155I(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GAGACAACAACGTCAGCCTTA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	11											164	159	161					11																	62298426		2202	4299	6501	62055002	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3463G>A	11.37:g.62298426C>T	ENSP00000367263:p.Val1155Ile		62055002	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	0.004	-2.334960	0.00227	.	.	ENSG00000124942	ENST00000378024	T	0.00565	6.56	4.88	-0.269	0.12930	.	0.894418	0.09220	N	0.832096	T	0.00271	0.0008	N	0.03084	-0.415	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.30179	-0.9987	10	0.18276	T	0.48	-1.5912	5.5602	0.17140	0.0:0.302:0.2513:0.4466	.	1155	Q09666	AHNK_HUMAN	I	1155	ENSP00000367263:V1155I	ENSP00000367263:V1155I	V	-	1	0	AHNAK	62055002	0.000000	0.05858	0.085000	0.20634	0.083000	0.17756	-3.470000	0.00460	-0.322000	0.08615	-0.288000	0.09946	GTT		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62298426	C	T	62298426	3	4	78	1	0	0	0	0	1	0	0	0	414	536	19	1	14329	1	AHNAK	11	62298426	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	1257710	62298426	72708090	73	23030										
ANO1	55107	broad.mit.edu	37	chr11	69972281	69972282	+	Missense_Mutation	DNP	CA	CA	TG													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttcctgtacggatgcgccacCatggatgaaaacatccccag							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:69972281_69972282CA>TG	ENST00000355303.5	+	10	1382_1383	c.1077_1078CA>TG	c.(1075-1080)acCAtg>acTGtg	p.M360V	ANO1_ENST00000538023.1_Missense_Mutation_p.M360V|ANO1_ENST00000530676.1_Missense_Mutation_p.M244V|ANO1_ENST00000398543.2_Missense_Mutation_p.M244V|ANO1_ENST00000316296.5_Missense_Mutation_p.M332V|ANO1_ENST00000531349.1_Missense_Mutation_p.M95V	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	360					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.T359>?(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	GATGCGCCACCATGGATGAAAA	0.594																																																2	Complex(2)	large_intestine(2)	11																																								69649930	SO:0001583	missense	55107			BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	Exception_encountered	11.37:g.69972281_69972282delinsTG	ENSP00000347454:p.Met360Val		69649929	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	DNP	ENST00000355303.5	37	CCDS44663.1																																																																																				0.594	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		TG	69972282	CA	TG	69972281	3	4	78	1	0	0	0	0	1	0	0	0	695	581	21	3	1115	3	ANO1	11	69972281	Missense_Mutation	DNP	CA	TCGA-AG-A02X-01A-01W-A00E-09	7673855	69972281	65034235	74	23031										
RPS3	6188	broad.mit.edu	37	chr11	75111750	75111750	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tggattagtttgtcgctgatGgcatcttcaaagctgaactg	11	7	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:75111750G>C	ENST00000531188.1	+	2	105	c.43G>C	c.(43-45)Ggc>Cgc	p.G15R	RPS3_ENST00000534440.1_Missense_Mutation_p.G15R|RPS3_ENST00000526608.1_Missense_Mutation_p.G15R|RPS3_ENST00000529285.1_3'UTR|SNORD15A_ENST00000384214.1_RNA|RPS3_ENST00000530164.1_Missense_Mutation_p.G15R|RPS3_ENST00000527446.1_Missense_Mutation_p.G15R|RPS3_ENST00000278572.6_Missense_Mutation_p.G15R|RPS3_ENST00000524851.1_Missense_Mutation_p.G15R	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	15					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)	p.G15R(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						TGTCGCTGATGGCATCTTCAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											141	128	132					11																	75111750		2200	4293	6493	74789398	SO:0001583	missense	6188				CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.43G>C	11.37:g.75111750G>C	ENSP00000434643:p.Gly15Arg		74789398	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	37	CCDS8236.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.298560|5.298560	0.95574|0.95574	.|.	.|.	ENSG00000149273|ENSG00000149273	ENST00000531188;ENST00000530164;ENST00000530689;ENST00000278572;ENST00000534440;ENST00000527446;ENST00000526608;ENST00000527273;ENST00000524851|ENST00000525933	.|.	.|.	.|.	5.73|5.73	5.73|5.73	0.89815|0.89815	K homology domain-like, alpha/beta (1);K Homology, prokaryotic type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87545|0.87545	0.6204|0.6204	H|H	0.95260|0.95260	3.645|3.645	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.90740|0.90740	0.4649|0.4649	9|5	0.87932|.	D|.	0|.	-10.7319|-10.7319	17.4078|17.4078	0.87477|0.87477	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	15|.	P23396|.	RS3_HUMAN|.	R|I	15|5	.|.	ENSP00000278572:G15R|.	G|M	+|+	1|3	0|0	RPS3|RPS3	74789398|74789398	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.713000|9.713000	0.98740|0.98740	2.712000|2.712000	0.92718|0.92718	0.557000|0.557000	0.71058|0.71058	GGC|ATG		0.448	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		C	75111750	G	C	75111750	3	2	78	1	0	0	0	0	1	0	0	0	13680	1348	47	5	49	5	RPS3	11	75111750	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	5139469	75111750	59894766	75	23032										
MMP20	9313	broad.mit.edu	37	chr11	102487622	102487622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cacatcaggaactccacagcGaggcttcttgatcacgttca	8	13	4	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:102487622G>T	ENST00000260228.2	-	2	307	c.295C>A	c.(295-297)Cgc>Agc	p.R99S	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	89					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R99S(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ACTCCACAGCGAGGCTTCTTG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											159	136	143					11																	102487622		2203	4299	6502	101992832	SO:0001583	missense	9313			Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.295C>A	11.37:g.102487622G>T	ENSP00000260228:p.Arg99Ser		101992832	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.616000	0.66672	.	.	ENSG00000137674	ENST00000260228	T	0.58652	0.32	5.09	5.09	0.68999	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85366	0.5680	H	0.99042	4.41	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.90430	0.4423	10	0.87932	D	0	.	14.6757	0.68978	0.0:0.0:0.8543:0.1456	.	99	O60882	MMP20_HUMAN	S	99	ENSP00000260228:R99S	ENSP00000260228:R99S	R	-	1	0	MMP20	101992832	0.981000	0.34729	0.999000	0.59377	0.502000	0.33828	1.776000	0.38594	2.804000	0.96469	0.655000	0.94253	CGC		0.448	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			T	102487622	G	T	102487622	3	4	78	1	0	0	0	0	1	0	0	0	9689	1058	37	2	1192	2	MMP20	11	102487622	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	27375872	102487622	32518894	76	23033										
PATE1	160065	broad.mit.edu	37	chr11	125616235	125616235	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttgctggaactccccatcctGctctgctgctttaggggtga	11	12	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:125616235G>T	ENST00000305738.5	+	1	48	c.36G>T	c.(34-36)ctG>ctT	p.L12L	PATE1_ENST00000437148.2_Silent_p.L12L	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	12						extracellular region (GO:0005576)		p.L12L(1)		large_intestine(1)|lung(5)	6						tccccatcctgctctgctgct	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	11											160	142	148					11																	125616235		2201	4299	6500	125121445	SO:0001819	synonymous_variant	160065			AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"PATE family"	24664	protein-coding gene	gene with protein product	"expressed in prostate and testis"	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.36G>T	11.37:g.125616235G>T			125121445	Q3KNX2	Silent	SNP	ENST00000305738.5	37	CCDS8464.1																																																																																				0.527	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294		T	125616235	G	T	125616235	2	4	78	1	0	0	0	0	0	0	0	1	11504	1306	46	2		2	PATE1	11	125616235	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	23128613	125616235	9390281	77	23034										
OPCML	4978	broad.mit.edu	37	chr11	132306017	132306017	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gcattggtgttcccaagcttGttcgtggccacacaagtata	10	10	0	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr11:132306017G>T	ENST00000331898.7	-	6	1478	c.900C>A	c.(898-900)aaC>aaA	p.N300K	OPCML_ENST00000541867.1_Missense_Mutation_p.N300K|OPCML_ENST00000374778.4_Missense_Mutation_p.N259K|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000524381.1_Missense_Mutation_p.N293K	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	300	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.N300K(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TCCCAAGCTTGTTCGTGGCCA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	11											135	117	123					11																	132306017		2201	4297	6498	131811227	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.900C>A	11.37:g.132306017G>T	ENSP00000330862:p.Asn300Lys		131811227	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026229	0.75390	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46	5.91	4.97	0.65823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94128	0.8117	H	0.99820	4.81	0.54753	D	0.999986	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	D	0.94788	0.7959	10	0.87932	D	0	-32.5005	10.2529	0.43379	0.1571:0.0:0.8429:0.0	.	300;293;299;300	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	K	300;293;259;267;300	ENSP00000330862:N300K;ENSP00000434750:N293K;ENSP00000363910:N259K;ENSP00000445496:N300K	ENSP00000330862:N300K	N	-	3	2	OPCML	131811227	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.729000	0.47327	1.442000	0.47568	0.650000	0.86243	AAC		0.488	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132306017	G	T	132306017	3	4	78	1	0	0	0	0	1	0	0	0	10905	1368	48	2	145	2	OPCML	11	132306017	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	6689782	132306017	2700499	78	23035										
EFCAB4B	84766	broad.mit.edu	37	chr12	3782661	3782661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ctcctcatgggcttcttggaGctgggagatgattctggtca	13	9	4	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:3782661G>A	ENST00000252322.1	-	7	1090	c.622C>T	c.(622-624)Ctc>Ttc	p.L208F	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.L208F|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.L208F	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		208					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L208F(1)		breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			GCTTCTTGGAGCTGGGAGATG	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											150	140	144					12																	3782661		2203	4300	6503	3652922	SO:0001583	missense	84766																														ENST00000252322.1:c.622C>T	12.37:g.3782661G>A	ENSP00000252322:p.Leu208Phe		3652922	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758449	0.69763	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.24538	1.85;2.11;2.05	4.55	4.55	0.56014	.	0.063724	0.64402	D	0.000008	T	0.55097	0.1899	M	0.85299	2.745	0.37943	D	0.932402	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.974;0.989;0.997	T	0.67515	-0.5651	10	0.72032	D	0.01	-18.7922	14.8173	0.70045	0.0:0.0:1.0:0.0	.	208;208;208	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	F	208	ENSP00000409382:L208F;ENSP00000412496:L208F;ENSP00000252322:L208F	ENSP00000252322:L208F	L	-	1	0	EFCAB4B	3652922	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.280000	0.65603	2.064000	0.61679	0.650000	0.86243	CTC		0.478	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			A	3782661	G	A	3782661	3	1	78	1	0	0	0	0	1	0	0	0	4948	971	34	3	1821	3	EFCAB4B	12	3782661	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		3782661	130069234	79	23036										
ACSM4	341392	broad.mit.edu	37	chr12	7463188	7463188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cagcaaaagacatcctctacCggctgcgagcatccaaggcc	9	15	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:7463188C>T	ENST00000399422.4	+	3	514	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	156					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						CATCCTCTACCGGCTGCGAGC	0.547																																																0			12											33	35	34					12																	7463188		2029	4182	6211	7354455	SO:0001583	missense	341392				CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"Acyl-CoA synthetase family"	32016	protein-coding gene	gene with protein product	"similar to olfactory specific medium-chain acyl CoA synthetase"	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.466C>T	12.37:g.7463188C>T	ENSP00000382349:p.Arg156Trp		7354455	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	37	CCDS44825.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.319989	0.60634	.	.	ENSG00000215009	ENST00000399422	T	0.42900	0.96	3.48	2.48	0.30137	AMP-dependent synthetase/ligase (1);	0.000000	0.35970	U	0.002867	T	0.72045	0.3412	H	0.96833	3.89	0.40449	D	0.980121	D	0.89917	1.0	D	0.97110	1.0	T	0.79759	-0.1668	10	0.87932	D	0	-16.6489	9.8458	0.41026	0.2043:0.7957:0.0:0.0	.	156	P0C7M7	ACSM4_HUMAN	W	156	ENSP00000382349:R156W	ENSP00000382349:R156W	R	+	1	2	ACSM4	7354455	0.025000	0.19082	1.000000	0.80357	0.932000	0.56968	0.039000	0.13884	1.964000	0.57103	0.655000	0.94253	CGG		0.547	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		T	7463188	C	T	7463188	3	4	78	1	0	0	0	0	1	0	0	0	186	643	23	1	476	1	ACSM4	12	7463188	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	3680527	7463188	126388707	80	23037										
SLC2A14	144195	broad.mit.edu	37	chr12	7980192	7980192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gagctccagcacggtgacttGcttttcttgtgacatccttg	10	11	1	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:7980192G>T	ENST00000543909.1	-	12	1591	c.832C>A	c.(832-834)Caa>Aaa	p.Q278K	SLC2A14_ENST00000396589.2_Missense_Mutation_p.Q278K|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000535295.1_Missense_Mutation_p.Q169K|SLC2A14_ENST00000431042.2_Missense_Mutation_p.Q255K|SLC2A14_ENST00000340749.5_Missense_Mutation_p.Q255K|SLC2A14_ENST00000539924.1_Missense_Mutation_p.Q293K|SLC2A14_ENST00000542546.1_Missense_Mutation_p.Q169K			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	278					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)	p.Q278K(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		ACGGTGACTTGCTTTTCTTGT	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	12											92	106	101					12																	7980192		2203	4300	6503	7871459	SO:0001583	missense	144195			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.832C>A	12.37:g.7980192G>T	ENSP00000440480:p.Gln278Lys		7871459	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.703952	0.00719	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	T;T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	3.58	1.22	0.21188	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.242170	0.01830	N	0.034625	T	0.48409	0.1498	N	0.02120	-0.675	0.35557	D	0.804333	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.61879	-0.6972	10	0.02654	T	1	.	3.9559	0.09390	0.1379:0.0:0.3465:0.5156	.	293;169;255;278	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	K	255;278;255;278;169;169;293	ENSP00000340450:Q255K;ENSP00000440480:Q278K;ENSP00000407287:Q255K;ENSP00000379834:Q278K;ENSP00000440492:Q169K;ENSP00000443903:Q169K;ENSP00000445929:Q293K	ENSP00000340450:Q255K	Q	-	1	0	SLC2A14	7871459	0.998000	0.40836	0.775000	0.31657	0.343000	0.28985	0.764000	0.26532	0.423000	0.26033	0.585000	0.79938	CAA		0.517	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		T	7980192	G	T	7980192	3	4	78	1	0	0	0	0	1	0	0	0	14580	1328	46	2	750	2	SLC2A14	12	7980192	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	517004	7980192	125871703	81	23038										
KRAS	3845	broad.mit.edu	37	chr12	25380276	25380276	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcattgcactgtactcctctTgacctgctgtgtcgagaata	8	11	2	2	rs121913240		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:25380276T>A	ENST00000256078.4	-	3	245	c.182A>T	c.(181-183)cAa>cTa	p.Q61L	KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61L	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61L(73)|p.Q61R(56)|p.Q61P(12)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GTACTCCTCTTGACCTGCTGT	0.418	Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	141	Substitution - Missense(141)	large_intestine(63)|lung(27)|thyroid(14)|haematopoietic_and_lymphoid_tissue(9)|pancreas(6)|skin(5)|stomach(3)|cervix(3)|upper_aerodigestive_tract(2)|soft_tissue(1)|central_nervous_system(1)|biliary_tract(1)|endometrium(1)|urinary_tract(1)|gastrointestinal_tract_(site_indeterminate)(1)|breast(1)|prostate(1)|kidney(1)	12											109	97	101					12																	25380276		2203	4300	6503	25271543	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.182A>T	12.37:g.25380276T>A	ENSP00000256078:p.Gln61Leu		25271543	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.889058	0.91814	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.83992	-1.79;-1.79	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.92097	0.7495	H	0.96333	3.805	0.80722	D	1	D;P	0.58970	0.984;0.812	P;P	0.53689	0.732;0.69	D	0.94295	0.7532	10	0.72032	D	0.01	.	15.5753	0.76373	0.0:0.0:0.0:1.0	.	61;61	P01116-2;P01116	.;RASK_HUMAN	L	61	ENSP00000308495:Q61L;ENSP00000256078:Q61L	ENSP00000256078:Q61L	Q	-	2	0	KRAS	25271543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.983000	0.88140	2.326000	0.78906	0.533000	0.62120	CAA		0.418	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25380276	T	A	25380276	3	1	78	1	0	0	0	0	1	0	0	0	8459	1812	63	5	520	5	KRAS	12	25380276	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	17400084	25380276	108471619	82	23039										
BICD1	636	broad.mit.edu	37	chr12	32447003	32447003	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ataagttccgggaggcacggCtccttcaggactatactgaa	11	10	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:32447003C>T	ENST00000281474.5	+	3	605	c.502C>T	c.(502-504)Ctc>Ttc	p.L168F	BICD1_ENST00000548411.1_Missense_Mutation_p.L168F	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	168					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.L168F(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GGAGGCACGGCTCCTTCAGGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											65	65	65					12																	32447003		2203	4300	6503	32338270	SO:0001583	missense	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.502C>T	12.37:g.32447003C>T	ENSP00000281474:p.Leu168Phe		32338270	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	37	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817849	0.90790	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.57907	0.37;0.37	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000002	T	0.77308	0.4111	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77963	-0.2390	10	0.36615	T	0.2	.	18.7935	0.91983	0.0:1.0:0.0:0.0	.	168;168	F8W113;Q96G01	.;BICD1_HUMAN	F	168	ENSP00000446793:L168F;ENSP00000281474:L168F	ENSP00000281474:L168F	L	+	1	0	BICD1	32338270	1.000000	0.71417	0.962000	0.40283	0.849000	0.48306	5.624000	0.67764	2.663000	0.90544	0.555000	0.69702	CTC		0.403	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32447003	C	T	32447003	3	4	78	1	0	0	0	0	1	0	0	0	1429	797	28	3	512	3	BICD1	12	32447003	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	7066727	32447003	101404892	83	23040										
PCBP2	5094	broad.mit.edu	37	chr12	53854854	53854854	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gctacccaactcaactgagcGggccatcactattgctggca	9	14	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:53854854G>A	ENST00000439930.3	+	6	453	c.431G>A	c.(430-432)cGg>cAg	p.R144Q	PCBP2_ENST00000541275.1_Missense_Mutation_p.R144Q|RP11-793H13.8_ENST00000547717.1_RNA|PCBP2_ENST00000546463.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000359462.5_Missense_Mutation_p.R144Q|PCBP2_ENST00000552296.2_Missense_Mutation_p.R144Q|PCBP2_ENST00000552819.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000455667.3_Missense_Mutation_p.R144Q|PCBP2_ENST00000437231.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000359282.5_Missense_Mutation_p.R144Q|PCBP2_ENST00000549863.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000548933.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000447282.1_Missense_Mutation_p.R144Q|PCBP2_ENST00000603815.1_Missense_Mutation_p.R144Q			Q15366	PCBP2_HUMAN	poly(rC) binding protein 2	144	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of defense response to virus (GO:0050687)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|ubiquitin protein ligase binding (GO:0031625)	p.R144Q(1)		central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15						TCAACTGAGCGGGCCATCACT	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	12											138	113	121					12																	53854854		2203	4300	6503	52141121	SO:0001583	missense	5094			BC035420	CCDS8859.1, CCDS44900.1, CCDS44901.1, CCDS44902.1, CCDS44903.1, CCDS44904.1, CCDS55830.1	12q13.13	2013-10-30	2001-11-28		ENSG00000197111	ENSG00000197111			8648	protein-coding gene	gene with protein product	"heterogenous nuclear ribonucleoprotein E2"	601210	"poly(rC)-binding protein 2"			8833161	Standard	NM_001098620		Approved	HNRPE2, hnRNP-E2, HNRNPE2	uc001sdc.4	Q15366	OTTHUMG00000169439	ENST00000439930.3:c.431G>A	12.37:g.53854854G>A	ENSP00000408949:p.Arg144Gln		52141121	A8K7X6|F8VYL7|G3V0E8|I6L8F9|Q32Q82|Q59HD4|Q68Y55|Q6IPF4|Q6PKG5	Missense_Mutation	SNP	ENST00000439930.3	37	CCDS44901.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.7|28.7	4.943213|4.943213	0.92526|0.92526	.|.	.|.	ENSG00000197111|ENSG00000197111	ENST00000546652|ENST00000541275;ENST00000359282;ENST00000447282;ENST00000437231;ENST00000439930;ENST00000549863;ENST00000359462;ENST00000550927;ENST00000546463;ENST00000551104;ENST00000550520;ENST00000552296;ENST00000552083;ENST00000552819;ENST00000455667;ENST00000548933;ENST00000379777;ENST00000553064	T|T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.50001|0.35236	0.76|1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32	5.38|5.38	5.38|5.38	0.77491|0.77491	.|K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.59514|0.59514	0.2199|0.2199	M|M	0.90198|0.90198	3.095|3.095	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P;P;P;P;B	.|0.52577	.|0.954;0.884;0.894;0.769;0.933;0.871;0.546;0.558;0.346	.|P;P;P;P;P;P;B;B;P	.|0.50825	.|0.63;0.627;0.651;0.48;0.473;0.519;0.215;0.431;0.536	T|T	0.69379|0.69379	-0.5161|-0.5161	7|10	0.22706|0.87932	T|D	0.39|0	.|.	18.1345|18.1345	0.89614|0.89614	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|144;105;144;144;144;144;144;144;144	.|B4DLC0;F8VRG9;Q15366;Q32Q82;G3V0E8;F8VYL7;Q68Y55;Q6IPF4;A8K7X6	.|.;.;PCBP2_HUMAN;.;.;.;.;.;.	R|Q	157|144;144;144;144;144;144;144;86;144;144;136;144;105;144;144;144;106;8	ENSP00000447068:G157R|ENSP00000446130:R144Q;ENSP00000352228:R144Q;ENSP00000394116:R144Q;ENSP00000390304:R144Q;ENSP00000408949:R144Q;ENSP00000447670:R144Q;ENSP00000352438:R144Q;ENSP00000448762:R144Q;ENSP00000446601:R144Q;ENSP00000448847:R136Q;ENSP00000448927:R144Q;ENSP00000449070:R144Q;ENSP00000388008:R144Q;ENSP00000449062:R144Q	ENSP00000447068:G157R|ENSP00000352228:R144Q	G|R	+|+	1|2	0|0	PCBP2|PCBP2	52141121|52141121	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.597000|9.597000	0.98273|0.98273	2.822000|2.822000	0.97130|0.97130	0.558000|0.558000	0.71614|0.71614	GGG|CGG		0.468	PCBP2-027	NOVEL	NAGNAG_splice_site|non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407545.2	NM_005016		A	53854854	G	A	53854854	3	1	78	1	0	0	0	0	1	0	0	0	11532	1116	39	1	453	1	PCBP2	12	53854854	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	21407851	53854854	79997041	84	23041										
LRRC43	254050	broad.mit.edu	37	chr12	122677340	122677340	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tattagttgaggaatctcctGaagaggtcgtggaagacgtc	13	6	1	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr12:122677340G>T	ENST00000339777.4	+	7	1166	c.1138G>T	c.(1138-1140)Gaa>Taa	p.E380*	LRRC43_ENST00000425921.1_Nonsense_Mutation_p.E195*	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	380	Glu-rich.							p.E195*(1)|p.E380*(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	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)		GGAATCTCCTGAAGAGGTCGT	0.512																																																2	Substitution - Nonsense(2)	large_intestine(2)	12											108	105	106					12																	122677340		1979	4182	6161	121243293	SO:0001587	stop_gained	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1138G>T	12.37:g.122677340G>T	ENSP00000344233:p.Glu380*		121243293	Q6ZVT9	Nonsense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180015	0.57800	.	.	ENSG00000158113	ENST00000339777;ENST00000289014;ENST00000425921	.	.	.	3.39	1.48	0.22813	.	0.719989	0.12543	N	0.459692	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-3.1366	9.4746	0.38864	0.0:0.4252:0.5748:0.0	.	.	.	.	X	380;251;195	.	ENSP00000289014:E251X	E	+	1	0	LRRC43	121243293	0.804000	0.28969	0.009000	0.14445	0.052000	0.14988	1.007000	0.29860	0.403000	0.25479	0.655000	0.94253	GAA		0.512	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122677340	G	T	122677340	4	4	78	1	0	0	0	0	0	1	0	0	9030	1291	45	2	1164	2	LRRC43	12	122677340	Nonsense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	68822486	122677340	11174555	85	23042										
BRCA2	675	broad.mit.edu	37	chr13	32911879	32911879	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agtcagtttgaatttactcaGtttagaaaaccaagctacat	6	7	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr13:32911879G>A	ENST00000380152.3	+	11	3620	c.3387G>A	c.(3385-3387)caG>caA	p.Q1129Q	BRCA2_ENST00000544455.1_Silent_p.Q1129Q			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1129					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.Q1129Q(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AATTTACTCAGTTTAGAAAAC	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	2	Substitution - coding silent(2)	large_intestine(2)	13											55	57	56					13																	32911879		2202	4298	6500	31809879	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3387G>A	13.37:g.32911879G>A			31809879	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32911879	G	A	32911879	2	1	78	1	0	0	0	0	0	0	0	1	1502	1020	36	3		3	BRCA2	13	32911879	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		32911879	82257999	86	23043										
WDFY2	115825	broad.mit.edu	37	chr13	52313196	52313196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcctctcaggtggggtgaccGctctctgttgggacccagtc	13	13	2	1	rs138993465		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr13:52313196G>A	ENST00000298125.5	+	7	790	c.610G>A	c.(610-612)Gct>Act	p.A204T		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	204							metal ion binding (GO:0046872)	p.A204T(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		TGGGGTGACCGCTCTCTGTTG	0.517																																																1	Substitution - Missense(1)	large_intestine(1)	13						G	THR/ALA	1,4405		0,1,2202	161	150	154		610	5.3	1	13	dbSNP_134	154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	WDFY2	NM_052950.3	58	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign	204/401	52313196	4,13002	2203	4300	6503	51211197	SO:0001583	missense	115825			AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20482	protein-coding gene	gene with protein product		610418	"WD40 and FYVE domain containing 2"				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.610G>A	13.37:g.52313196G>A	ENSP00000298125:p.Ala204Thr		51211197	B1AL86|Q96CS1	Missense_Mutation	SNP	ENST00000298125.5	37	CCDS9429.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836725	0.50951	2.27E-4	3.49E-4	ENSG00000139668	ENST00000298125	T	0.61510	0.1	6.16	5.27	0.74061	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.094496	0.64402	D	0.000001	T	0.44787	0.1310	L	0.47190	1.495	0.58432	D	0.999999	P;B	0.42123	0.771;0.12	B;B	0.28305	0.088;0.034	T	0.50882	-0.8775	10	0.49607	T	0.09	-7.9892	13.1204	0.59323	0.0:0.0:0.7303:0.2697	.	101;204	Q96LK4;Q96P53	.;WDFY2_HUMAN	T	204	ENSP00000298125:A204T	ENSP00000298125:A204T	A	+	1	0	WDFY2	51211197	1.000000	0.71417	0.960000	0.40013	0.971000	0.66376	4.974000	0.63771	2.937000	0.99478	0.650000	0.86243	GCT		0.517	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950		A	52313196	G	A	52313196	3	1	78	1	0	0	0	0	1	0	0	0	17309	1087	38	1	636	1	WDFY2	13	52313196	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	19401317	52313196	62856682	87	23044										
PCDH20	64881	broad.mit.edu	37	chr13	61986782	61986782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ctctagtaaatattcattatTgtatggtttgtaaggtgata	8	3	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr13:61986782T>C	ENST00000409186.1	-	5	3555	c.1450A>G	c.(1450-1452)Aat>Gat	p.N484D	PCDH20_ENST00000409204.4_Missense_Mutation_p.N484D			Q8N6Y1	PCD20_HUMAN	protocadherin 20	484	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.N457D(1)|p.N484D(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TATTCATTATTGTATGGTTTG	0.408																																																2	Substitution - Missense(2)	large_intestine(2)	13											112	111	111					13																	61986782		2203	4300	6503	60884783	SO:0001583	missense	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1450A>G	13.37:g.61986782T>C	ENSP00000386653:p.Asn484Asp		60884783	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	T	1.390	-0.580979	0.03854	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.60672	0.17;0.17	5.95	5.95	0.96441	.	0.523932	0.19710	N	0.107839	T	0.41351	0.1155	N	0.25825	0.765	0.44227	D	0.997064	B	0.12630	0.006	B	0.14023	0.01	T	0.28299	-1.0048	10	0.06625	T	0.88	.	12.8711	0.57965	0.0:0.0:0.1357:0.8643	.	484	A8K1K9	.	D	484;484;230	ENSP00000387250:N484D;ENSP00000386653:N484D	ENSP00000351500:N230D	N	-	1	0	PCDH20	60884783	0.995000	0.38212	0.926000	0.36857	0.944000	0.59088	3.826000	0.55738	2.276000	0.75962	0.528000	0.53228	AAT		0.408	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		C	61986782	T	C	61986782	3	2	78	1	0	0	0	0	1	0	0	0	11546	1812	63	4	1409	4	PCDH20	13	61986782	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	9673586	61986782	53183096	88	23045										
LRFN5	145581	broad.mit.edu	37	chr14	42355896	42355896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agctcagatctgtccaaagcGttgtgtctgtcagattttgt	10	8	4	2	rs553209511		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:42355896G>A	ENST00000298119.4	+	3	1257	c.68G>A	c.(67-69)cGt>cAt	p.R23H	LRFN5_ENST00000554171.1_Missense_Mutation_p.R23H|LRFN5_ENST00000554120.1_Missense_Mutation_p.R23H	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	23	LRRNT.					integral component of membrane (GO:0016021)		p.R23H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGTCCAAAGCGTTGTGTCTGT	0.398										HNSCC(30;0.082)			G|||	1	0.000199681	0	0	5008	,	,		17221	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	14											94	85	88					14																	42355896		2203	4300	6503	41425646	SO:0001583	missense	145581			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.68G>A	14.37:g.42355896G>A	ENSP00000298119:p.Arg23His		41425646	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369914	0.42003	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.52057	0.81;0.68;0.68	5.56	5.56	0.83823	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.56097	D	0.000022	T	0.42359	0.1199	L	0.52905	1.665	0.58432	D	0.999999	B;P	0.37352	0.223;0.591	B;B	0.32724	0.112;0.151	T	0.28933	-1.0028	10	0.19590	T	0.45	.	17.0193	0.86429	0.0:0.0:1.0:0.0	.	23;23	G3V364;Q96NI6	.;LRFN5_HUMAN	H	23	ENSP00000298119:R23H;ENSP00000451897:R23H;ENSP00000451067:R23H	ENSP00000298119:R23H	R	+	2	0	LRFN5	41425646	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.062000	0.89475	2.595000	0.87683	0.650000	0.86243	CGT		0.398	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		A	42355896	G	A	42355896	3	1	78	1	0	0	0	0	1	0	0	0	8970	1145	40	1	70	1	LRFN5	14	42355896	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		42355896	64993644	89	23046										
PRKCH	5583	broad.mit.edu	37	chr14	61997205	61997205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tatgagatgctctgtggtcaCgcgccttttgaggcagagaa	13	8	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:61997205C>T	ENST00000332981.5	+	12	2038	c.1653C>T	c.(1651-1653)caC>caT	p.H551H	RP11-47I22.4_ENST00000556347.1_Missense_Mutation_p.T56M|PRKCH_ENST00000555082.1_Silent_p.H390H	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	551	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)	p.H551H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		TCTGTGGTCACGCGCCTTTTG	0.552																																					Melanoma(135;863 1779 8064 14443 26348)											1	Substitution - coding silent(1)	large_intestine(1)	14											227	182	197					14																	61997205		2203	4300	6503	61066958	SO:0001819	synonymous_variant	5583			M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1653C>T	14.37:g.61997205C>T			61066958	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	37	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	C	0.904	-0.721293	0.03182	.	.	ENSG00000258989	ENST00000556347	.	.	.	5.63	-8.41	0.00961	.	.	.	.	.	T	0.65375	0.2685	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71826	-0.4475	4	.	.	.	.	18.6888	0.91576	0.0:0.2196:0.0:0.7804	.	.	.	.	M	56	.	.	T	+	2	0	RP11-47I22.4	61066958	0.000000	0.05858	0.147000	0.22382	0.201000	0.24016	-4.501000	0.00224	-1.614000	0.01575	-0.808000	0.03180	ACG		0.552	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61997205	C	T	61997205	2	4	78	1	0	0	0	0	0	0	0	1	12547	535	19	1		1	PRKCH	14	61997205	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	19641309	61997205	45352335	90	23047										
TMED10	10972	broad.mit.edu	37	chr14	75601626	75601626	+	Frame_Shift_Del	DEL	G	G	-													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggccttgaagaagcgtcgcaGgtagaagacctgccaggtag							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:75601626delG	ENST00000303575.4	-	5	673	c.622delC	c.(622-624)ctgfs	p.L208fs	TMED10_ENST00000557670.1_5'UTR|RP11-950C14.7_ENST00000556236.1_RNA	NM_006827.5	NP_006818.3	P49755	TMEDA_HUMAN	transmembrane emp24-like trafficking protein 10 (yeast)	208	Interaction with ARF1.|Interaction with COPG1.				beta-amyloid formation (GO:0034205)|cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPI-coated vesicle budding (GO:0035964)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|kidney development (GO:0001822)|protein oligomerization (GO:0051259)|regulated secretory pathway (GO:0045055)|response to acid chemical (GO:0001101)|response to alkaloid (GO:0043279)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle targeting, to, from or within Golgi (GO:0048199)	cis-Golgi network (GO:0005801)|COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	syntaxin binding (GO:0019905)	p.L208fs*10(1)		endometrium(1)|large_intestine(5)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(234;0.0126)		AAGCGTCGCAGGTAGAAGACC	0.453																																																1	Deletion - Frameshift(1)	large_intestine(1)	14											101	97	98					14																	75601626		2203	4300	6503	74671379	SO:0001589	frameshift_variant	10972			AL832012, X97442	CCDS9840.1	14q24.3	2008-08-11			ENSG00000170348	ENSG00000170348			16998	protein-coding gene	gene with protein product		605406				7596406, 8663407	Standard	NM_006827		Approved	TMP21, P24(DELTA)	uc001xrm.1	P49755		ENST00000303575.4:c.622delC	14.37:g.75601626delG	ENSP00000303145:p.Leu208fs		74671379	B2R605|Q15602|Q16536|Q86TC2|Q86TS5	Frame_Shift_Del	DEL	ENST00000303575.4	37	CCDS9840.1																																																																																				0.453	TMED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415034.1	NM_006827		-	75601626	G	-	75601626	7	5	78	1	0	1	0	1	0	0	0	0	16042	991	35	0	41	0	TMED10	14	75601626	Frame_Shift_Del	DEL	G	TCGA-AG-A02X-01A-01W-A00E-09	13604421	75601626	31747914	91	23048	28	2								
TMED10	10972	broad.mit.edu	37	chr14	75601629	75601630	+	Frame_Shift_Del	DEL	AG	AG	-													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cttgaagaagcgtcgcaggtAgaagacctgccaggtagcta							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:75601629_75601630delAG	ENST00000303575.4	-	5	669_670	c.618_619delCT	c.(616-621)ttctacfs	p.FY206fs	TMED10_ENST00000557670.1_5'UTR|RP11-950C14.7_ENST00000556236.1_RNA	NM_006827.5	NP_006818.3	P49755	TMEDA_HUMAN	transmembrane emp24-like trafficking protein 10 (yeast)	206	Interaction with COPG1.				beta-amyloid formation (GO:0034205)|cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPI-coated vesicle budding (GO:0035964)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|kidney development (GO:0001822)|protein oligomerization (GO:0051259)|regulated secretory pathway (GO:0045055)|response to acid chemical (GO:0001101)|response to alkaloid (GO:0043279)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle targeting, to, from or within Golgi (GO:0048199)	cis-Golgi network (GO:0005801)|COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	syntaxin binding (GO:0019905)	p.F206fs*13(1)		endometrium(1)|large_intestine(5)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(234;0.0126)		CGTCGCAGGTAGAAGACCTGCC	0.446																																																1	Deletion - Frameshift(1)	large_intestine(1)	14																																								74671383	SO:0001589	frameshift_variant	10972			AL832012, X97442	CCDS9840.1	14q24.3	2008-08-11			ENSG00000170348	ENSG00000170348			16998	protein-coding gene	gene with protein product		605406				7596406, 8663407	Standard	NM_006827		Approved	TMP21, P24(DELTA)	uc001xrm.1	P49755		ENST00000303575.4:c.618_619delCT	14.37:g.75601629_75601630delAG	ENSP00000303145:p.Phe206fs		74671382	B2R605|Q15602|Q16536|Q86TC2|Q86TS5	Frame_Shift_Del	DEL	ENST00000303575.4	37	CCDS9840.1																																																																																				0.446	TMED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415034.1	NM_006827		-	75601630	AG	-	75601629	7	5	78	1	0	1	0	1	0	0	0	0	16042	420	15	0	44	0	TMED10	14	75601629	Frame_Shift_Del	DEL	AG	TCGA-AG-A02X-01A-01W-A00E-09	3	75601629	31747911	92	23049	28	2								
ATG2B	55102	broad.mit.edu	37	chr14	96769547	96769547	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gtgttctgagaggctggaatCacaatcaggtttgcatggcg	14	7	3	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:96769547C>T	ENST00000359933.4	-	33	5781	c.4888G>A	c.(4888-4890)Gat>Aat	p.D1630N	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1630					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.D1630N(1)		breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGGCTGGAATCACAATCAGGT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	14											89	90	89					14																	96769547		2203	4300	6503	95839300	SO:0001583	missense	55102			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4888G>A	14.37:g.96769547C>T	ENSP00000353010:p.Asp1630Asn		95839300	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	12.48	1.950197	0.34377	.	.	ENSG00000066739	ENST00000359933	T	0.10668	2.85	5.74	2.98	0.34508	.	1.180830	0.05551	N	0.567478	T	0.09555	0.0235	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.14023	0.01	T	0.41466	-0.9507	10	0.34782	T	0.22	.	11.2991	0.49295	0.0:0.8045:0.0:0.1955	.	1630	Q96BY7	ATG2B_HUMAN	N	1630	ENSP00000353010:D1630N	ENSP00000261834:D274N	D	-	1	0	ATG2B	95839300	0.011000	0.17503	0.000000	0.03702	0.656000	0.38851	1.246000	0.32803	0.463000	0.27118	0.563000	0.77884	GAT		0.428	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96769547	C	T	96769547	3	4	78	1	0	0	0	0	1	0	0	0	1095	826	29	3	1388	3	ATG2B	14	96769547	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	21167918	96769547	10579993	93	23050										
EML1	2009	broad.mit.edu	37	chr14	100405582	100405582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgacatcaatgccgtctgtcGggcccatgagaagaaactcc	10	13	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:100405582G>A	ENST00000262233.6	+	21	2379	c.2240G>A	c.(2239-2241)cGg>cAg	p.R747Q	EML1_ENST00000334192.4_Missense_Mutation_p.R766Q|EML1_ENST00000327921.9_Missense_Mutation_p.R735Q	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	747	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R766Q(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GCCGTCTGTCGGGCCCATGAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	14											125	112	116					14																	100405582		2203	4300	6503	99475335	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.2240G>A	14.37:g.100405582G>A	ENSP00000262233:p.Arg747Gln		99475335	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117755	0.77323	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.17854	2.25;2.25;2.25	4.56	4.56	0.56223	.	0.051684	0.64402	D	0.000001	T	0.47710	0.1460	M	0.90082	3.085	0.80722	D	1	P;D;D	0.71674	0.926;0.998;0.959	B;P;B	0.61397	0.388;0.888;0.293	T	0.62205	-0.6903	10	0.87932	D	0	-22.3911	17.6609	0.88193	0.0:0.0:1.0:0.0	.	735;747;766	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	Q	735;747;766;766	ENSP00000327384:R735Q;ENSP00000262233:R747Q;ENSP00000334314:R766Q	ENSP00000262233:R747Q	R	+	2	0	EML1	99475335	1.000000	0.71417	0.997000	0.53966	0.556000	0.35491	7.627000	0.83176	2.240000	0.73641	0.561000	0.74099	CGG		0.552	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		A	100405582	G	A	100405582	3	1	78	1	0	0	0	0	1	0	0	0	5109	1116	39	1	2383	1	EML1	14	100405582	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	3636035	100405582	6943958	94	23051										
ZNF839	55778	broad.mit.edu	37	chr14	102792654	102792654	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gaacagggctccatgttgacCcctttgtctgcctctgaccc	9	15	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:102792654C>T	ENST00000558850.1	+	2	623	c.273C>T	c.(271-273)acC>acT	p.T91T	ZNF839_ENST00000262236.5_Silent_p.T91T|ZNF839_ENST00000559185.1_Silent_p.T91T|ZNF839_ENST00000442396.2_Silent_p.T207T	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	91							metal ion binding (GO:0046872)	p.T207T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CCATGTTGACCCCTTTGTCTG	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	14											29	29	29					14																	102792654		1907	4114	6021	101862407	SO:0001819	synonymous_variant	55778			AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 131"	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.273C>T	14.37:g.102792654C>T			101862407	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																				0.517	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		T	102792654	C	T	102792654	2	4	78	1	0	0	0	0	0	0	0	1	18227	610	22	3		3	ZNF839	14	102792654	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2387072	102792654	4556886	95	23052										
TRAF3	7187	broad.mit.edu	37	chr14	103342695	103342695	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttgaatggtctgtcttacagGtgcatttaaaaaatgattgc	9	5	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr14:103342695G>A	ENST00000560371.1	+	5	620	c.403G>A	c.(403-405)Gtg>Atg	p.V135M	TRAF3_ENST00000351691.5_Splice_Site_p.V135M|TRAF3_ENST00000539721.1_Splice_Site_p.V135M|TRAF3_ENST00000347662.4_Splice_Site_p.V135M|TRAF3_ENST00000392745.2_Splice_Site_p.V135M	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	135					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V135M(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		TGTCTTACAGGTGCATTTAAA	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	14											80	79	79					14																	103342695		2203	4300	6503	102412448	SO:0001630	splice_region_variant	7187			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.403-1G>A	14.37:g.103342695G>A			102412448	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465396	0.43839	.	.	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.68	5.68	0.88126	Zinc finger, TRAF-type (1);TRAF-like (1);Seven In Absentia Homolog-type (1);	0.233421	0.45867	D	0.000337	T	0.13286	0.0322	N	0.14661	0.345	0.33505	D	0.590431	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.09377	0.004;0.004;0.004	T	0.20240	-1.0281	9	.	.	.	-38.7074	7.7535	0.28911	0.1916:0.0:0.8084:0.0	.	135;135;135	Q13114-2;A6NHG8;Q13114	.;.;TRAF3_HUMAN	M	135	ENSP00000376500:V135M;ENSP00000328003:V135M;ENSP00000332468:V135M;ENSP00000445998:V135M	.	V	+	1	0	TRAF3	102412448	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	2.387000	0.44389	2.835000	0.97688	0.650000	0.86243	GTG		0.378	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	Missense_Mutation	A	103342695	G	A	103342695	5	1	78	1	0	0	0	0	0	0	1	0	16479	1275	44	3	417	3	TRAF3	14	103342695	Splice_Site	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	550041	103342695	4006845	96	23053										
IQCH	64799	broad.mit.edu	37	chr15	67687771	67687771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agctgtggccgatatgttagAcatacccatcctgggctctg	11	11	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr15:67687771A>G	ENST00000335894.4	+	13	1841	c.1775A>G	c.(1774-1776)gAc>gGc	p.D592G	IQCH_ENST00000358767.3_Intron|IQCH_ENST00000360277.4_Intron|IQCH_ENST00000546225.1_Intron	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	592								p.D592G(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		GATATGTTAGACATACCCATC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	15											134	124	127					15																	67687771		2201	4299	6500	65474825	SO:0001583	missense	64799			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1775A>G	15.37:g.67687771A>G	ENSP00000336861:p.Asp592Gly		65474825	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	.	.	.	.	.	.	.	.	.	.	A	5.048	0.194498	0.09599	.	.	ENSG00000103599	ENST00000335894	T	0.43688	0.94	6.17	5.05	0.67936	.	0.764469	0.13052	N	0.417595	T	0.33789	0.0875	L	0.32530	0.975	0.28283	N	0.923887	B	0.09022	0.002	B	0.15052	0.012	T	0.20840	-1.0263	10	0.26408	T	0.33	-3.91	12.4477	0.55659	0.935:0.0:0.065:0.0	.	592	Q86VS3	IQCH_HUMAN	G	592	ENSP00000336861:D592G	ENSP00000336861:D592G	D	+	2	0	IQCH	65474825	0.095000	0.21747	0.001000	0.08648	0.138000	0.21146	3.516000	0.53436	1.146000	0.42352	0.533000	0.62120	GAC		0.473	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		G	67687771	A	G	67687771	3	3	78	1	0	0	0	0	1	0	0	0	7832	275	10	4	1953	4	IQCH	15	67687771	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09		67687771	34843621	97	23054										
AKAP13	11214	broad.mit.edu	37	chr15	86124044	86124044	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	actgaagaaggaaaacttctGgtggtttcagaaagctctgc	11	7	3	3	rs143505118	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr15:86124044G>C	ENST00000394518.2	+	7	2840	c.2745G>C	c.(2743-2745)ctG>ctC	p.L915L	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.L915L	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	915					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.L915L(1)		NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GAAAACTTCTGGTGGTTTCAG	0.443													G|||	7	0.00139776	0	0.0101	5008	,	,		21629	0		0	False		,,,				2504	0				Melanoma(94;603 1453 3280 32295 32951)											1	Substitution - coding silent(1)	large_intestine(1)	15						G	,	4,4400	6.2+/-15.9	0,4,2198	65	69	67		2745,2745	-0.3	0	15	dbSNP_134	67	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	0,6,6495	CC,CG,GG		0.0233,0.0908,0.0461	,	915/2818,915/2814	86124044	6,12996	2202	4299	6501	83925048	SO:0001819	synonymous_variant	11214			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2745G>C	15.37:g.86124044G>C			83925048	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																				0.443	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86124044	G	C	86124044	2	2	78	1	0	0	0	0	0	0	0	1	449	1335	47	5		5	AKAP13	15	86124044	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	18436273	86124044	16407348	98	23055										
MAN2A2	4122	broad.mit.edu	37	chr15	91448538	91448539	+	Missense_Mutation	DNP	AA	AA	CC													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tggagcagcttttggaggagAaccatgagattatcagccat							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr15:91448538_91448539AA>CC	ENST00000559717.1	+	3	649_650	c.190_191AA>CC	c.(190-192)AAc>CCc	p.N64P	MAN2A2_ENST00000360468.3_Missense_Mutation_p.N64P|MAN2A2_ENST00000431652.2_5'Flank			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	64					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.N64>?(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TTTGGAGGAGAACCATGAGATT	0.545																																																1	Complex(1)	large_intestine(1)	15																																								89249543	SO:0001583	missense	4122			L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		Exception_encountered	15.37:g.91448538_91448539delinsCC	ENSP00000452948:p.Asn64Pro		89249542	A6NH12|A8K1E8|Q13754	Missense_Mutation	DNP	ENST00000559717.1	37	CCDS32332.1																																																																																				0.545	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		CC	91448539	AA	CC	91448538	3	2	78	1	0	0	0	0	1	0	0	0	9245	246	9	4	196	4	MAN2A2	15	91448538	Missense_Mutation	DNP	AA	TCGA-AG-A02X-01A-01W-A00E-09	5324494	91448538	11082854	99	23056										
SRRM2	23524	broad.mit.edu	37	chr16	2815262	2815262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cccacttcggcagaggagtcGgtctggatcatctccagagg	13	12	3	2	rs184005236	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:2815262G>A	ENST00000301740.8	+	11	5282	c.4733G>A	c.(4732-4734)cGg>cAg	p.R1578Q		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1578	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.L1573_G1580delLRQRSRSG(1)|p.R1578Q(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CAGAGGAGTCGGTCTGGATCA	0.517													G|||	3	0.000599042	8e-04	0	5008	,	,		18495	0.002		0	False		,,,				2504	0															2	Substitution - Missense(1)|Deletion - In frame(1)	large_intestine(1)|lung(1)	16						G	GLN/ARG	0,4396		0,0,2198	78	68	72		4733	-0.9	0.5	16		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	SRRM2	NM_016333.3	43	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	benign	1578/2753	2815262	1,12995	2198	4300	6498	2755263	SO:0001583	missense	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.4733G>A	16.37:g.2815262G>A	ENSP00000301740:p.Arg1578Gln		2755263	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	9.598	1.127849	0.20959	0.0	1.16E-4	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.25250	1.81	5.38	-0.849	0.10723	.	0.428231	0.22176	N	0.063562	T	0.17365	0.0417	L	0.46157	1.445	0.22066	N	0.999385	B	0.31519	0.327	B	0.20767	0.031	T	0.08513	-1.0718	10	0.44086	T	0.13	1.1459	9.2851	0.37753	0.4535:0.0:0.5465:0.0	.	1578	Q9UQ35	SRRM2_HUMAN	Q	1578;1578;830	ENSP00000301740:R1578Q	ENSP00000301740:R1578Q	R	+	2	0	SRRM2	2755263	0.570000	0.26651	0.513000	0.27749	0.995000	0.86356	1.109000	0.31135	-0.421000	0.07416	0.655000	0.94253	CGG		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2815262	G	A	2815262	3	1	78	1	0	0	0	0	1	0	0	0	15208	1116	39	1	4771	1	SRRM2	16	2815262	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		2815262	87539491	100	23057										
ALG1	56052	broad.mit.edu	37	chr16	5125440	5125440	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gctggttcgtgggctgccttTgtggaagcaagctcgtcatt	14	9	1	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:5125440T>G	ENST00000262374.5	+	4	473	c.442T>G	c.(442-444)Tgt>Ggt	p.C148G	ALG1_ENST00000544428.1_Missense_Mutation_p.C37G|ALG1_ENST00000588623.1_Missense_Mutation_p.C37G	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	148					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)	p.C148G(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				GGGCTGCCTTTGTGGAAGCAA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	16											195	165	175					16																	5125440		2197	4300	6497	5065441	SO:0001583	missense	56052			AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"Glycosyltransferase group 1 domain containing"	18294	protein-coding gene	gene with protein product		605907	"asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)", "asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.442T>G	16.37:g.5125440T>G	ENSP00000262374:p.Cys148Gly		5065441	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695928	0.30052	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	D;D	0.81996	-1.56;-1.56	5.74	3.43	0.39272	.	0.308479	0.36101	N	0.002795	T	0.71962	0.3402	L	0.47716	1.5	0.35567	D	0.805187	B;B	0.26195	0.144;0.121	B;B	0.25987	0.065;0.059	T	0.66337	-0.5949	10	0.26408	T	0.33	-3.0578	2.506	0.04645	0.1998:0.238:0.0:0.5622	.	37;148	B4DP08;Q9BT22	.;ALG1_HUMAN	G	148;37	ENSP00000262374:C148G;ENSP00000440019:C37G	ENSP00000262374:C148G	C	+	1	0	ALG1	5065441	0.734000	0.28142	0.996000	0.52242	0.996000	0.88848	0.950000	0.29122	1.005000	0.39183	0.528000	0.53228	TGT		0.562	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		G	5125440	T	G	5125440	3	3	78	1	0	0	0	0	1	0	0	0	510	1812	63	4	456	4	ALG1	16	5125440	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	2310178	5125440	85229313	101	23058										
MYH11	4629	broad.mit.edu	37	chr16	15917267	15917267	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgcagaagaggccagagtacGtctgcagacagagaacccag	13	11	1	5			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:15917267G>A	ENST00000300036.5	-	3	456	c.347C>T	c.(346-348)aCg>aTg	p.T116M	MYH11_ENST00000576790.2_Splice_Site_p.T116M|MYH11_ENST00000452625.2_Splice_Site_p.T116M|MYH11_ENST00000396324.3_Splice_Site_p.T116M	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	116	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.T116M(2)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCAGAGTACGTCTGCAGACA	0.512			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	2	Substitution - Missense(2)	large_intestine(2)	16											138	112	121					16																	15917267		2197	4300	6497	15824768	SO:0001630	splice_region_variant	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.346-1C>T	16.37:g.15917267G>A			15824768	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	De_novo_Start_OutOfFrame	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294417	0.81025	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.58	5.58	0.84498	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.96084	0.8724	H	0.99931	4.975	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.992;0.992;0.992;0.992	D	0.98281	1.0508	10	0.87932	D	0	.	18.557	0.91089	0.0:0.0:1.0:0.0	.	116;116;116;116;116	Q4G140;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	M	116	ENSP00000300036:T116M;ENSP00000345136:T116M;ENSP00000379616:T116M;ENSP00000407821:T116M	ENSP00000300036:T116M	T	-	2	0	MYH11	15824768	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	9.813000	0.99286	2.626000	0.88956	0.655000	0.94253	ACG		0.512	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	Missense_Mutation	A	15917267	G	A	15917267	5	1	78	1	0	0	0	0	0	0	1	0	10061	1159	40	1	5787	1	MYH11	16	15917267	Splice_Site	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	10791827	15917267	74437486	102	23059										
IQCK	124152	broad.mit.edu	37	chr16	19838379	19838379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcctgagattcaagaactgcGtcagtggcagaagaaacttc	10	9	2	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:19838379G>A	ENST00000320394.6	+	9	1421	c.722G>A	c.(721-723)cGt>cAt	p.R241H	IQCK_ENST00000562762.1_3'UTR|IQCK_ENST00000541926.1_Missense_Mutation_p.V213I|IQCK_ENST00000564186.1_Missense_Mutation_p.R241H|IQCK_ENST00000433597.2_Missense_Mutation_p.R153H	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	241								p.R241H(1)		kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						CAAGAACTGCGTCAGTGGCAG	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	16											125	120	122					16																	19838379		2197	4300	6497	19745880	SO:0001583	missense	124152			AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.722G>A	16.37:g.19838379G>A	ENSP00000324901:p.Arg241His		19745880	B2RDU0|O43327|Q8NFF4	Missense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.00|16.00	2.998595|2.998595	0.54147|0.54147	.|.	.|.	ENSG00000174628|ENSG00000174628	ENST00000320394;ENST00000433597|ENST00000541926	T;T|.	0.23950|.	1.88;1.88|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.56097|.	D|.	0.000039|.	T|T	0.71358|0.71358	0.3330|0.3330	M|M	0.75777|0.75777	2.31|2.31	0.46564|0.46564	D|D	0.999104|0.999104	D|D	0.89917|0.59767	1.0|0.986	D|P	0.91635|0.50082	0.999|0.63	T|T	0.72494|0.72494	-0.4276|-0.4276	9|7	.|.	.|.	.|.	-15.2706|-15.2706	17.7591|17.7591	0.88459|0.88459	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	241|213	Q8N0W5|B4DXE1	IQCK_HUMAN|.	H|I	241;153|213	ENSP00000324901:R241H;ENSP00000406013:R153H|.	.|.	R|V	+|+	2|1	0|0	IQCK|IQCK	19745880|19745880	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	6.311000|6.311000	0.72835|0.72835	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.448	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208		A	19838379	G	A	19838379	3	1	78	1	0	0	0	0	1	0	0	0	7834	1145	40	1	752	1	IQCK	16	19838379	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	3921112	19838379	70516374	103	23060										
LONP2	83752	broad.mit.edu	37	chr16	48311297	48311297	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgcatcatcaacggcttgaaGactgtgggagtgaacaaccc	11	11	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:48311297G>T	ENST00000285737.4	+	8	1383	c.1290G>T	c.(1288-1290)aaG>aaT	p.K430N	LONP2_ENST00000535754.1_Missense_Mutation_p.K386N	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal									p.K430N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ACGGCTTGAAGACTGTGGGAG	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	16											120	108	112					16																	48311297		2200	4300	6500	46868798	SO:0001583	missense	83752			AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.1290G>T	16.37:g.48311297G>T	ENSP00000285737:p.Lys430Asn		46868798		Missense_Mutation	SNP	ENST00000285737.4	37	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701644	0.88924	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754;ENST00000416006	D;D;D	0.93488	-3.23;-3.23;-3.23	5.81	5.81	0.92471	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97247	0.9100	M	0.88512	2.96	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69142	0.947;0.962	D	0.96987	0.9719	10	0.54805	T	0.06	-25.1234	20.0762	0.97745	0.0:0.0:1.0:0.0	.	386;430	B7ZKL7;Q86WA8	.;LONP2_HUMAN	N	430;159;386;386	ENSP00000285737:K430N;ENSP00000445426:K386N;ENSP00000415983:K386N	ENSP00000285737:K430N	K	+	3	2	LONP2	46868798	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	5.749000	0.68704	2.756000	0.94617	0.655000	0.94253	AAG		0.502	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		T	48311297	G	T	48311297	3	4	78	1	0	0	0	0	1	0	0	0	8922	933	33	2	1320	2	LONP2	16	48311297	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	28472918	48311297	42043456	104	23061										
ARL2BP	23568	broad.mit.edu	37	chr16	57286134	57286134	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ttagtggtgacttcattgtgCaaatcatcttctctgccagc	8	10	4	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:57286134C>A	ENST00000219204.3	+	6	717	c.447C>A	c.(445-447)tgC>tgA	p.C149*	ARL2BP_ENST00000562023.1_Nonsense_Mutation_p.C109*|RP11-407G23.3_ENST00000564376.1_RNA	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	149					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)	p.C149*(1)|p.C149W(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						CTTCATTGTGCAAATCATCTT	0.488																																																2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	16											145	116	126					16																	57286134		2198	4300	6498	55843635	SO:0001587	stop_gained	23568			AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"binder of Arl2"	615407	"retinitis pigmentosa 66 (autosomal recessive)"	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.447C>A	16.37:g.57286134C>A	ENSP00000219204:p.Cys149*		55843635	B3KQJ5|Q504R0	Nonsense_Mutation	SNP	ENST00000219204.3	37	CCDS10776.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.329318	0.81690	.	.	ENSG00000102931	ENST00000219204	.	.	.	6.02	2.99	0.34606	.	0.673781	0.13107	U	0.413307	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-9.4214	8.8503	0.35194	0.0:0.7383:0.1241:0.1377	.	.	.	.	X	149	.	ENSP00000219204:C149X	C	+	3	2	ARL2BP	55843635	1.000000	0.71417	0.993000	0.49108	0.978000	0.69477	2.486000	0.45259	0.414000	0.25790	0.650000	0.86243	TGC		0.488	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106		A	57286134	C	A	57286134	4	1	78	1	0	0	0	0	0	1	0	0	935	718	25	2	469	2	ARL2BP	16	57286134	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	8974837	57286134	33068619	105	23062										
CDH16	1014	broad.mit.edu	37	chr16	66946430	66946430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggaagtgatgaactcaggggCgtgatcattgatatctgtga	14	5	3	5			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:66946430C>T	ENST00000299752.4	-	11	1529	c.1336G>A	c.(1336-1338)Gcc>Acc	p.A446T	CDH16_ENST00000565796.1_Missense_Mutation_p.A446T|CDH16_ENST00000394055.3_Missense_Mutation_p.A446T|CDH16_ENST00000568632.1_Missense_Mutation_p.A349T|CDH16_ENST00000570262.1_Missense_Mutation_p.A366T	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	446	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.A446T(1)		endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		AACTCAGGGGCGTGATCATTG	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	16											137	123	128					16																	66946430		2200	4300	6500	65503931	SO:0001583	missense	1014			AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"Cadherins / Major cadherins"	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.1336G>A	16.37:g.66946430C>T	ENSP00000299752:p.Ala446Thr		65503931	B4DPA8|H3BPD3|Q6UW93	Missense_Mutation	SNP	ENST00000299752.4	37	CCDS10823.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192769	0.38707	.	.	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	T;T	0.61742	0.08;0.08	4.82	4.82	0.62117	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.131519	0.50627	D	0.000107	T	0.68879	0.3049	M	0.71036	2.16	0.32330	N	0.561231	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.941;0.996;0.914	T	0.66677	-0.5863	10	0.02654	T	1	-17.9328	13.2824	0.60224	0.0:1.0:0.0:0.0	.	446;446;446	O75309-2;B2R7S8;O75309	.;.;CAD16_HUMAN	T	446;446;410	ENSP00000377619:A446T;ENSP00000299752:A446T	ENSP00000299752:A446T	A	-	1	0	CDH16	65503931	0.796000	0.28864	0.999000	0.59377	0.652000	0.38707	1.154000	0.31688	2.526000	0.85167	0.561000	0.74099	GCC		0.577	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062		T	66946430	C	T	66946430	3	4	78	1	0	0	0	0	1	0	0	0	3107	768	27	1	1185	1	CDH16	16	66946430	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	9660296	66946430	23408323	106	23063										
PLA2G15	23659	broad.mit.edu	37	chr16	68293226	68293227	+	Missense_Mutation	DNP	TC	TC	CA													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ccgcaagttcttccaggacaTcggctttgaagatggctggc							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	TC	TC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr16:68293226_68293227TC>CA	ENST00000219345.5	+	6	988_989	c.905_906TC>CA	c.(904-906)aTC>aCA	p.I302T	RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000444212.2_Missense_Mutation_p.I102T|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000413021.2_Missense_Mutation_p.I208T|PLA2G15_ENST00000566188.1_3'UTR	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	302					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)	p.I302>?(1)		kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						TTCCAGGACATCGGCTTTGAAG	0.574																																																1	Complex(1)	large_intestine(1)	16																																								66850728	SO:0001583	missense	23659			AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"lysophospholipase 3 (lysosomal phospholipase A2)"	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	Exception_encountered	16.37:g.68293226_68293227delinsCA	ENSP00000219345:p.Ile302Thr		66850727	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Missense_Mutation	DNP	ENST00000219345.5	37	CCDS10864.1																																																																																				0.574	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320		CA	68293227	TC	CA	68293226	3	2	78	1	0	0	0	0	1	0	0	0	12023	1435	50	4	927	4	PLA2G15	16	68293226	Missense_Mutation	DNP	TC	TCGA-AG-A02X-01A-01W-A00E-09	1346796	68293226	22061527	107	23064										
METT10D	79066	broad.mit.edu	37	chr17	2323345	2323345	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agatccctgttctggccctcAacccagtgcatctccactaa	6	16	3	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:2323345A>G	ENST00000263092.6	-	10	1735	c.1608T>C	c.(1606-1608)gtT>gtC	p.V536V	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Silent_p.V318V	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	536							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.V536V(1)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						TCTGGCCCTCAACCCAGTGCA	0.493																																																1	Substitution - coding silent(1)	large_intestine(1)	17											83	88	87					17																	2323345		2063	4204	6267	2270095	SO:0001819	synonymous_variant	79066			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1608T>C	17.37:g.2323345A>G			2270095	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Silent	SNP	ENST00000263092.6	37	CCDS42232.1																																																																																				0.493	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		G	2323345	A	G	2323345	2	3	78	1	0	0	0	0	0	0	0	1	9520	117	5	4		4	METT10D	17	2323345	Silent	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09		2323345	78871865	108	23065										
SPATA22	84690	broad.mit.edu	37	chr17	3370833	3370833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tctttttctgattgaacaacGgaacaggcaaacagcctaaa	7	9	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:3370833G>A	ENST00000573128.1	-	3	542	c.59C>T	c.(58-60)cCg>cTg	p.P20L	SPATA22_ENST00000397168.3_Missense_Mutation_p.P20L|SPATA22_ENST00000575375.1_Missense_Mutation_p.P20L|SPATA22_ENST00000268981.5_Missense_Mutation_p.P20L|SPATA22_ENST00000541913.1_Missense_Mutation_p.P20L|SPATA22_ENST00000355380.4_Intron|SPATA22_ENST00000572969.1_Missense_Mutation_p.P20L			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	20					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)		p.P20L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						ATTGAACAACGGAACAGGCAA	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	17											92	92	92					17																	3370833		2203	4300	6503	3317583	SO:0001583	missense	84690			AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.59C>T	17.37:g.3370833G>A	ENSP00000459580:p.Pro20Leu		3317583	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	37	CCDS11027.1	.	.	.	.	.	.	.	.	.	.	g	20.8	4.052630	0.75960	.	.	ENSG00000141255	ENST00000397168;ENST00000268981;ENST00000541913	T;T;T	0.60171	0.21;0.62;0.43	5.38	5.38	0.77491	.	0.000000	0.46758	D	0.000277	T	0.67702	0.2921	L	0.32530	0.975	0.53005	D	0.999967	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.70281	-0.4915	10	0.87932	D	0	-3.0994	16.677	0.85281	0.0:0.0:1.0:0.0	.	20;20;20	F5GWB9;B4DXB1;Q8NHS9	.;.;SPT22_HUMAN	L	20	ENSP00000380354:P20L;ENSP00000268981:P20L;ENSP00000441920:P20L	ENSP00000268981:P20L	P	-	2	0	SPATA22	3317583	1.000000	0.71417	0.996000	0.52242	0.892000	0.51952	6.568000	0.73987	2.695000	0.91970	0.563000	0.77884	CCG		0.323	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598		A	3370833	G	A	3370833	3	1	78	1	0	0	0	0	1	0	0	0	15047	1116	39	1	1060	1	SPATA22	17	3370833	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	1047488	3370833	77824377	109	23066										
TP53	7157	broad.mit.edu	37	chr17	7577085	7577085	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cttgcggagattctcttcctCtgtgcgccggtctctcccag	10	15	3	1	rs112431538		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:7577085C>A	ENST00000269305.4	-	8	1042	c.853G>T	c.(853-855)Gag>Tag	p.E285*	TP53_ENST00000455263.2_Nonsense_Mutation_p.E285*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E285*|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Nonsense_Mutation_p.E285*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E285*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	285	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in a sporadic cancer; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726, ECO:0000269|PubMed:1694291}.|E -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E285K(111)|p.E285*(24)|p.0?(8)|p.E285Q(4)|p.?(2)|p.R283fs*16(2)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.E285fs*60(1)|p.G279fs*59(1)|p.R283fs*56(1)|p.E285fs*20(1)|p.E285fs*13(1)|p.R283fs*59(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCTCTTCCTCTGTGCGCCGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	165	Substitution - Missense(115)|Substitution - Nonsense(24)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(2)	urinary_tract(53)|breast(18)|large_intestine(15)|lung(11)|upper_aerodigestive_tract(10)|stomach(8)|haematopoietic_and_lymphoid_tissue(8)|central_nervous_system(6)|oesophagus(6)|liver(6)|skin(5)|prostate(4)|bone(4)|biliary_tract(3)|ovary(3)|adrenal_gland(1)|soft_tissue(1)|eye(1)|pancreas(1)|thyroid(1)	17	GRCh37	CM995136	TP53	M	rs112431538						91	78	82					17																	7577085		2203	4300	6503	7517810	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.853G>T	17.37:g.7577085C>A	ENSP00000269305:p.Glu285*		7517810	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	36	5.741087	0.96873	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-38.0538	15.807	0.78520	0.0:1.0:0.0:0.0	.	.	.	.	X	285;285;285;285;285;274;153	.	ENSP00000269305:E285X	E	-	1	0	TP53	7517810	1.000000	0.71417	0.900000	0.35374	0.716000	0.41182	7.587000	0.82613	2.579000	0.87056	0.462000	0.41574	GAG		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577085	C	A	7577085	4	1	78	1	0	0	0	0	0	1	0	0	16421	922	32	2	433	2	TP53	17	7577085	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	4206252	7577085	73618125	110	23067										
DNAH2	146754	broad.mit.edu	37	chr17	7679354	7679354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ccccccagtcctggcttggcGatgtggaacagaccatgagg	13	13	0	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:7679354G>A	ENST00000572933.1	+	31	6294	c.4834G>A	c.(4834-4836)Gat>Aat	p.D1612N	DNAH2_ENST00000389173.2_Missense_Mutation_p.D1612N			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1612	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.D1612N(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGGCTTGGCGATGTGGAACA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	17											82	73	76					17																	7679354		2203	4300	6503	7620079	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4834G>A	17.37:g.7679354G>A	ENSP00000458355:p.Asp1612Asn		7620079	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509518	0.85282	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.60920	0.15	5.66	5.66	0.87406	Dynein heavy chain, domain-2 (1);	0.182827	0.45126	D	0.000395	T	0.55768	0.1941	L	0.43701	1.375	0.80722	D	1	P	0.35507	0.506	B	0.39339	0.297	T	0.51521	-0.8695	10	0.31617	T	0.26	.	18.5315	0.90993	0.0:0.0:1.0:0.0	.	1612	Q9P225	DYH2_HUMAN	N	1612	ENSP00000373825:D1612N	ENSP00000353818:D1612N	D	+	1	0	DNAH2	7620079	1.000000	0.71417	0.387000	0.26183	0.383000	0.30230	6.648000	0.74359	2.666000	0.90696	0.655000	0.94253	GAT		0.607	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7679354	G	A	7679354	3	1	78	1	0	0	0	0	1	0	0	0	4613	1058	37	1	4952	1	DNAH2	17	7679354	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	102269	7679354	73515856	111	23068										
RICH2	9912	broad.mit.edu	37	chr17	12888092	12888092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	actttgagcaaatcgcggccCactcctaagccgcgacagag	10	14	0	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:12888092C>T	ENST00000379672.5	+	20	2484	c.2184C>T	c.(2182-2184)ccC>ccT	p.P728P	ARHGAP44_ENST00000340825.3_Silent_p.P722P|ARHGAP44_ENST00000262444.9_Silent_p.P728P	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	728					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)	p.P728P(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						AATCGCGGCCCACTCCTAAGC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	17											37	40	39					17																	12888092		1959	4150	6109	12828817	SO:0001819	synonymous_variant	9912				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.2184C>T	17.37:g.12888092C>T			12828817	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																				0.622	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		T	12888092	C	T	12888092	2	4	78	1	0	0	0	0	0	0	0	1	13394	581	21	3		3	RICH2	17	12888092	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	5208738	12888092	68307118	112	23069										
FBXW10	10517	broad.mit.edu	37	chr17	18653069	18653069	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aattcactccggtgtatatcCgaaatgaataggctgttttc	8	8	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:18653069C>T	ENST00000395665.4	+	3	926	c.705C>T	c.(703-705)tcC>tcT	p.S235S	FBXW10_ENST00000308799.4_Silent_p.S235S|FBXW10_ENST00000395667.1_Silent_p.S235S|FBXW10_ENST00000301938.4_Silent_p.S235S			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	235								p.S235S(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GGTGTATATCCGAAATGAATA	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	17											141	117	125					17																	18653069		2203	4300	6503	18593794	SO:0001819	synonymous_variant	10517			BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.705C>T	17.37:g.18653069C>T			18593794	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Silent	SNP	ENST00000395665.4	37	CCDS11199.3																																																																																				0.468	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		T	18653069	C	T	18653069	2	4	78	1	0	0	0	0	0	0	0	1	5782	639	23	1		1	FBXW10	17	18653069	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	5764977	18653069	62542141	113	23070										
GFAP	2670	broad.mit.edu	37	chr17	42985483	42985483	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	acgatgttcctcttgaggtgGccttctgacacagacttggt	11	10	2	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr17:42985483G>T	ENST00000253408.5	-	8	1271	c.1206C>A	c.(1204-1206)ggC>ggA	p.G402G	GFAP_ENST00000588735.1_Splice_Site_p.G28G	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	402	Tail.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)	p.G402G(1)		endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				TCTTGAGGTGGCCTTCTGACA	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	17											223	184	197					17																	42985483		2203	4300	6503	40341009	SO:0001819	synonymous_variant	2670			S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"Intermediate filaments type III"	4235	protein-coding gene	gene with protein product	"intermediate filament protein"	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1206C>A	17.37:g.42985483G>T			40341009	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																				0.592	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		T	42985483	G	T	42985483	2	4	78	1	0	0	0	0	0	0	0	1	6357	1190	42	2		2	GFAP	17	42985483	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	24332414	42985483	38209727	114	23071										
LAMA3	3909	broad.mit.edu	37	chr18	21481180	21481180	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gggattctttaaatgaatacGaagccaaactcagtgacctt	8	8	2	2	rs373464847		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr18:21481180G>A	ENST00000313654.9	+	48	6335	c.6094G>A	c.(6094-6096)Gaa>Aaa	p.E2032K	LAMA3_ENST00000399516.3_Missense_Mutation_p.E1976K|LAMA3_ENST00000587184.1_Missense_Mutation_p.E367K|LAMA3_ENST00000269217.6_Missense_Mutation_p.E423K|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2032	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.E2032K(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	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)					AAATGAATACGAAGCCAAACT	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	18						G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	70	67	68		1267,5926,1099,6094	5.7	1	18		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	423/1725,1976/3278,367/1669,2032/3334	21481180	1,13005	2203	4300	6503	19735178	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.6094G>A	18.37:g.21481180G>A	ENSP00000324532:p.Glu2032Lys		19735178	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.036732	0.93630	0.0	1.16E-4	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;D;T	0.82984	2.86;-1.67;2.86	5.65	5.65	0.86999	Laminin I (1);	.	.	.	.	D	0.91338	0.7268	M	0.77616	2.38	0.50467	D	0.99987	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;0.997;1.0;0.999	D	0.89168	0.3535	9	0.34782	T	0.22	.	20.0887	0.97806	0.0:0.0:1.0:0.0	.	367;423;1976;2032	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	K	2032;1976;423	ENSP00000324532:E2032K;ENSP00000382432:E1976K;ENSP00000269217:E423K	ENSP00000269217:E423K	E	+	1	0	LAMA3	19735178	1.000000	0.71417	0.995000	0.50966	0.806000	0.45545	3.936000	0.56568	2.825000	0.97269	0.655000	0.94253	GAA		0.512	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21481180	G	A	21481180	3	1	78	1	0	0	0	0	1	0	0	0	8629	1059	37	1	6459	1	LAMA3	18	21481180	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		21481180	56596068	115	23072										
SMAD4	4089	broad.mit.edu	37	chr18	48575116	48575116	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gtctctggaggtggcctgatCttcacaaaaatgaactaaaa	9	8	3	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr18:48575116C>T	ENST00000342988.3	+	3	848	c.310C>T	c.(310-312)Ctt>Ttt	p.L104F	SMAD4_ENST00000398417.2_Missense_Mutation_p.L104F|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.L104F|SMAD4_ENST00000452201.2_Missense_Mutation_p.L104F	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	104	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)|p.L104F(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GTGGCCTGATCTTCACAAAAA	0.383																																																41	Whole gene deletion(36)|Unknown(4)|Substitution - Missense(1)	pancreas(26)|large_intestine(4)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											161	147	152					18																	48575116		2203	4300	6503	46829114	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.310C>T	18.37:g.48575116C>T	ENSP00000341551:p.Leu104Phe		46829114	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750807	0.89753	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	D;D;D	0.82984	-1.67;-1.67;-1.67	5.48	4.61	0.57282	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.92103	0.7497	M	0.90145	3.09	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	D	0.93270	0.6651	10	0.87932	D	0	.	13.1749	0.59621	0.0:0.9212:0.0:0.0788	.	104	Q13485	SMAD4_HUMAN	F	104	ENSP00000409551:L104F;ENSP00000341551:L104F;ENSP00000381452:L104F	ENSP00000341551:L104F	L	+	1	0	SMAD4	46829114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.793000	0.85851	1.289000	0.44618	0.585000	0.79938	CTT		0.383	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48575116	C	T	48575116	3	4	78	1	0	0	0	0	1	0	0	0	14797	913	32	3	316	3	SMAD4	18	48575116	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	27093936	48575116	29502132	116	23073										
SERPINB12	89777	broad.mit.edu	37	chr18	61228355	61228355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gattcaattttaccacacgaCgattgaaagtgttgatttcc	7	8	1	2	rs367909045		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr18:61228355C>T	ENST00000269491.1	+	4	422	c.422C>T	c.(421-423)aCg>aTg	p.T141M	SERPINB12_ENST00000382768.1_Missense_Mutation_p.T161M	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	141					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T141M(1)		kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						TACCACACGACGATTGAAAGT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	18						C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	118	114	116		422	5.6	0.6	18		116	0,8600		0,0,4300	no	missense	SERPINB12	NM_080474.1	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	141/406	61228355	1,13005	2203	4300	6503	59379335	SO:0001583	missense	89777			AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"Serine (or cysteine) peptidase inhibitors"	14220	protein-coding gene	gene with protein product		615662	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.422C>T	18.37:g.61228355C>T	ENSP00000269491:p.Thr141Met		59379335	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	37	CCDS11984.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872010	0.33069	2.27E-4	0.0	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.84730	-1.89;-1.89	5.59	5.59	0.84812	Serpin domain (3);	0.086453	0.50627	D	0.000114	D	0.91831	0.7415	M	0.73598	2.24	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.79784	0.989;0.993	D	0.85719	0.1324	10	0.56958	D	0.05	.	16.439	0.83894	0.0:0.8601:0.1399:0.0	.	161;141	Q3SYB4;Q96P63	.;SPB12_HUMAN	M	141;161	ENSP00000269491:T141M;ENSP00000372218:T161M	ENSP00000269491:T141M	T	+	2	0	SERPINB12	59379335	0.000000	0.05858	0.559000	0.28332	0.134000	0.20937	-0.031000	0.12287	2.789000	0.95967	0.655000	0.94253	ACG		0.383	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		T	61228355	C	T	61228355	3	4	78	1	0	0	0	0	1	0	0	0	14136	536	19	1	436	1	SERPINB12	18	61228355	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	12653239	61228355	16848893	117	23074										
MOBKL2A	126308	broad.mit.edu	37	chr19	2078278	2078279	+	Frame_Shift_Ins	INS	-	-	C													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agcggtactcatacttggggINSccccccgacatgacggggca					rs200521330		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:2078278_2078279insC	ENST00000357066.3	-	3	660_661	c.281_282insG	c.(280-282)ggcfs	p.G94fs	MOB3A_ENST00000592280.1_Frame_Shift_Ins_p.G94fs|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	94						intracellular (GO:0005622)	metal ion binding (GO:0046872)	p.K96fs*3(1)									CATACTTGGGGCCCCCCGACAT	0.614																																																1	Insertion - Frameshift(1)	large_intestine(1)	19																																								2029279	SO:0001589	frameshift_variant	126308			AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.282dupG	19.37:g.2078284_2078284dupC	ENSP00000349575:p.Gly94fs		2029278	B3KTF1|O75249|Q8TF69	Frame_Shift_Ins	INS	ENST00000357066.3	37	CCDS12081.1																																																																																				0.614	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		C	2078279	-	C	2078278	7	5	78	1	0	1	1	0	0	0	0	0	9714	1190	42	0	383	0	MOBKL2A	19	2078278	Frame_Shift_Ins	INS	-	TCGA-AG-A02X-01A-01W-A00E-09		2078278	57050705	118	23075										
CACNA1A	773	broad.mit.edu	37	chr19	13414691	13414691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cctcgttccagtcttcgcccGtcaggatctgaaaggggagg	13	12	3	1	rs121908212		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:13414691G>A	ENST00000360228.5	-	16	1993	c.1994C>T	c.(1993-1995)aCg>aTg	p.T665M	CACNA1A_ENST00000573710.2_Missense_Mutation_p.T666M	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	666					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.T666M(3)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GTCTTCGCCCGTCAGGATCTG	0.597																																																3	Substitution - Missense(3)	large_intestine(3)	19	GRCh37	CM960238	CACNA1A	M	rs121908212						121	123	122					19																	13414691		2003	4160	6163	13275691	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1994C>T	19.37:g.13414691G>A	ENSP00000353362:p.Thr665Met		13275691	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064260	0.55432	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98889	-5.21	4.58	3.55	0.40652	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99357	0.9774	H	0.97023	3.925	0.48901	A	0.999722	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.99624	1.0984	9	0.87932	D	0	.	11.6149	0.51083	0.0887:0.0:0.9113:0.0	.	666;666;665	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	M	665;666;666;666	ENSP00000353362:T665M	ENSP00000317661:T666M	T	-	2	0	CACNA1A	13275691	1.000000	0.71417	0.966000	0.40874	0.989000	0.77384	9.507000	0.97996	1.151000	0.42436	-0.229000	0.12294	ACG		0.597	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13414691	G	A	13414691	3	1	78	1	0	0	0	0	1	0	0	0	2544	1145	40	1	5765	1	CACNA1A	19	13414691	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	11336413	13414691	45714292	119	23076										
CYP4F22	126410	broad.mit.edu	37	chr19	15661490	15661490	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gctgttcctccctaggtgtaCaacccctaccgctttgaccc	7	17	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:15661490C>A	ENST00000269703.3	+	13	1540	c.1341C>A	c.(1339-1341)taC>taA	p.Y447*	CYP4F22_ENST00000601005.2_Nonsense_Mutation_p.Y447*	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	447						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.Y447*(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						CCTAGGTGTACAACCCCTACC	0.607																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											107	92	97					19																	15661490		2203	4300	6503	15522490	SO:0001587	stop_gained	126410				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.1341C>A	19.37:g.15661490C>A	ENSP00000269703:p.Tyr447*		15522490	Q8N8H4	Nonsense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103349	0.94245	.	.	ENSG00000171954	ENST00000269703	.	.	.	4.76	1.4	0.22301	.	0.182059	0.47455	D	0.000221	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	6.4895	0.22107	0.0:0.6128:0.0:0.3872	.	.	.	.	X	447	.	ENSP00000269703:Y447X	Y	+	3	2	CYP4F22	15522490	0.998000	0.40836	0.387000	0.26183	0.980000	0.70556	0.736000	0.26130	0.530000	0.28619	0.557000	0.71058	TAC		0.607	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		A	15661490	C	A	15661490	4	1	78	1	0	0	0	0	0	1	0	0	4195	489	17	2	1383	2	CYP4F22	19	15661490	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2246799	15661490	43467493	120	23077										
CALR3	125972	broad.mit.edu	37	chr19	16594825	16594825	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agtgatgttaagttccagtcGtactctatgctgccggattc	10	9	1	1	rs145046810	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:16594825G>A	ENST00000269881.3	-	5	656	c.594C>T	c.(592-594)taC>taT	p.Y198Y	CALR3_ENST00000602234.1_5'UTR|CTD-3222D19.2_ENST00000409035.1_Intron	NM_145046.4	NP_659483.2	Q96L12	CALR3_HUMAN	calreticulin 3	198	4 X approximate repeats.|P-domain.				cell differentiation (GO:0030154)|protein folding (GO:0006457)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.Y198Y(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|prostate(1)|skin(1)	15						AGTTCCAGTCGTACTCTATGC	0.423													G|||	3	0.000599042	0	0	5008	,	,		12800	0.001		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	19						G		0,4406		0,0,2203	131	114	120		594	-2.3	0.8	19	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CALR3	NM_145046.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		198/385	16594825	1,13005	2203	4300	6503	16455825	SO:0001819	synonymous_variant	125972			AK058084	CCDS12344.1	19p13.11	2014-09-17				ENSG00000269058			20407	protein-coding gene	gene with protein product	"cancer/testis antigen 93", "calsperin"	611414				12384296	Standard	NM_145046		Approved	CRT2, FLJ25355, MGC26577, CT93	uc002ned.3	Q96L12		ENST00000269881.3:c.594C>T	19.37:g.16594825G>A			16455825	D9N574|Q96LN3	Silent	SNP	ENST00000269881.3	37	CCDS12344.1																																																																																				0.423	CALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461089.1	NM_145046		A	16594825	G	A	16594825	2	1	78	1	0	0	0	0	0	0	0	1	2599	1140	40	1		1	CALR3	19	16594825	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	933335	16594825	42534158	121	23078										
ZNF98	148198	broad.mit.edu	37	chr19	22574881	22574881	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggttgaggattgtttaaaagCtttgccacattcttcacact	8	8	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:22574881C>G	ENST00000357774.5	-	4	1277	c.1156G>C	c.(1156-1158)Gct>Cct	p.A386P		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	386					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A386P(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TGTTTAAAAGCTTTGCCACAT	0.403																																																2	Substitution - Missense(2)	large_intestine(2)	19											4	4	4					19																	22574881		1449	3407	4856	22366721	SO:0001583	missense	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1156G>C	19.37:g.22574881C>G	ENSP00000350418:p.Ala386Pro		22366721		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	10.36	1.328296	0.24080	.	.	ENSG00000197360	ENST00000357774	T	0.36699	1.24	1.28	0.0656	0.14357	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47838	0.1467	L	0.59967	1.855	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.32771	-0.9894	9	0.87932	D	0	.	2.6633	0.05033	0.4315:0.3818:0.0:0.1867	.	386	A6NK75	ZNF98_HUMAN	P	386	ENSP00000350418:A386P	ENSP00000350418:A386P	A	-	1	0	ZNF98	22366721	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-1.829000	0.01701	-0.117000	0.11872	-0.704000	0.03662	GCT		0.403	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		G	22574881	C	G	22574881	3	3	78	1	0	0	0	0	1	0	0	0	18242	797	28	5	566	5	ZNF98	19	22574881	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	5980056	22574881	36554102	122	23079										
ZNF492	57615	broad.mit.edu	37	chr19	22847640	22847640	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	taagagaattcatactggagAgaagccctacaaatgtgaag	10	6	1	3			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:22847640A>C	ENST00000456783.2	+	4	1413	c.1169A>C	c.(1168-1170)gAg>gCg	p.E390A	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	390					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E390A(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				CATACTGGAGAGAAGCCCTAC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	19											25	27	26					19																	22847640		2003	4145	6148	22639480	SO:0001583	missense	57615			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1169A>C	19.37:g.22847640A>C	ENSP00000413660:p.Glu390Ala		22639480	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	6.302	0.423905	0.11928	.	.	ENSG00000229676	ENST00000456783	T	0.27557	1.66	1.12	1.12	0.20585	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43010	0.1228	M	0.78801	2.425	0.30562	N	0.764371	P	0.45594	0.862	P	0.52481	0.7	T	0.46247	-0.9205	9	0.66056	D	0.02	.	5.8144	0.18484	1.0:0.0:0.0:0.0	.	390	Q9P255	ZN492_HUMAN	A	390	ENSP00000413660:E390A	ENSP00000413660:E390A	E	+	2	0	ZNF492	22639480	0.955000	0.32602	0.217000	0.23759	0.219000	0.24729	2.939000	0.48995	0.231000	0.21079	0.228000	0.17796	GAG		0.378	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		C	22847640	A	C	22847640	3	2	78	1	0	0	0	0	1	0	0	0	17982	304	11	4	1179	4	ZNF492	19	22847640	Missense_Mutation	SNP	A	TCGA-AG-A02X-01A-01W-A00E-09	272759	22847640	36281343	123	23080										
DMKN	93099	broad.mit.edu	37	chr19	36002330	36002330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cacccaggaggactcactgcCgctgtcacctctgctgccac	9	18	3	0	rs371442207		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:36002330C>T	ENST00000339686.3	-	5	1077	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	DMKN_ENST00000424570.2_Missense_Mutation_p.G301S|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000447113.2_Missense_Mutation_p.G301S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G301S|DMKN_ENST00000440396.1_Missense_Mutation_p.G301S|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G301S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000414866.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	301	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G301S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	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)			GACTCACTGCCGCTGTCACCT	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	19						C	,,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4404		0,0,2202	41	35	37		,,901,901,901,901,901	-2	0	19		37	1,8597	1.2+/-3.3	0,1,4298	no	intron,intron,missense,missense,missense,missense,missense	DMKN	NM_001126056.2,NM_001190347.1,NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001126058.2,NM_001126057.2	,,56,56,56,56,56	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,benign,benign,benign,benign,benign	,,301/477,301/370,301/437,301/387,301/399	36002330	1,13001	2202	4299	6501	40694170	SO:0001583	missense	93099			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.901G>A	19.37:g.36002330C>T	ENSP00000342012:p.Gly301Ser		40694170	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	5.559	0.288064	0.10513	0.0	1.16E-4	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.19394	2.84;2.15;2.29;2.26;2.2;2.35	2.42	-2.0	0.07433	.	1.748700	0.03862	N	0.274171	T	0.07143	0.0181	N	0.02011	-0.69	0.09310	N	1	B;B;B;B;B	0.31968	0.349;0.231;0.349;0.349;0.154	B;B;B;B;B	0.23852	0.049;0.049;0.049;0.049;0.022	T	0.18999	-1.0319	10	0.30854	T	0.27	.	6.2094	0.20621	0.0:0.585:0.0:0.415	.	301;301;301;301;301	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	301	ENSP00000342012:G301S;ENSP00000394908:G301S;ENSP00000415277:G301S;ENSP00000414743:G301S;ENSP00000388404:G301S;ENSP00000409513:G301S	ENSP00000342012:G301S	G	-	1	0	DMKN	40694170	0.002000	0.14202	0.000000	0.03702	0.189000	0.23516	-0.701000	0.05075	-0.362000	0.08113	-0.657000	0.03884	GGC		0.642	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	36002330	C	T	36002330	3	4	78	1	0	0	0	0	1	0	0	0	4593	652	23	1	894	1	DMKN	19	36002330	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	13154690	36002330	23126653	124	23081										
PPP1R15A	23645	broad.mit.edu	37	chr19	49377362	49377362	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tgccccagggccgcaatcctCagccccagcccagaggcccc	10	21	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:49377362C>A	ENST00000200453.5	+	2	1141	c.872C>A	c.(871-873)tCa>tAa	p.S291*		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	291	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)	p.S291*(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CCGCAATCCTCAGCCCCAGCC	0.597																																																1	Substitution - Nonsense(1)	large_intestine(1)	19											53	66	62					19																	49377362		2203	4300	6503	54069174	SO:0001587	stop_gained	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.872C>A	19.37:g.49377362C>A	ENSP00000200453:p.Ser291*		54069174	B4DKQ3|Q6IA96|Q9NVU6	Nonsense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	C	35	5.417171	0.96092	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	.	.	.	4.64	-0.29	0.12847	.	1.819990	0.03232	N	0.179138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	2.0683	3.938	0.09314	0.165:0.5533:0.0:0.2816	.	.	.	.	X	291;131;249	.	ENSP00000200453:S291X	S	+	2	0	PPP1R15A	54069174	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.041000	0.13927	-0.114000	0.11936	-0.145000	0.13849	TCA		0.597	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49377362	C	A	49377362	4	1	78	1	0	0	0	0	0	1	0	0	12397	838	29	2	874	2	PPP1R15A	19	49377362	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	13375032	49377362	9751621	125	23082										
SIGLEC9	27180	broad.mit.edu	37	chr19	51629341	51629341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	atgtctttctgtcccagaccCgcctcagaacttgaccatga	7	14	3	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:51629341C>T	ENST00000250360.3	+	3	771	c.704C>T	c.(703-705)cCg>cTg	p.P235L	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.P235L	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	235					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.P235L(2)|p.P235Q(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GTCCCAGACCCGCCTCAGAAC	0.617																																																3	Substitution - Missense(3)	large_intestine(1)|lung(1)|endometrium(1)	19											96	86	89					19																	51629341		2203	4300	6503	56321153	SO:0001583	missense	27180			AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.704C>T	19.37:g.51629341C>T	ENSP00000250360:p.Pro235Leu		56321153	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	9.265	1.044286	0.19748	.	.	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.14144	2.53;2.72	3.02	1.95	0.26073	Immunoglobulin-like fold (1);	0.814645	0.10039	N	0.723659	T	0.13200	0.0320	M	0.71581	2.175	0.09310	N	1	P	0.44578	0.838	B	0.30401	0.115	T	0.20107	-1.0285	10	0.62326	D	0.03	.	7.6805	0.28511	0.0:0.7367:0.2633:0.0	.	235	Q9Y336	SIGL9_HUMAN	L	235	ENSP00000413861:P235L;ENSP00000250360:P235L	ENSP00000250360:P235L	P	+	2	0	SIGLEC9	56321153	0.005000	0.15991	0.004000	0.12327	0.011000	0.07611	1.712000	0.37940	0.443000	0.26582	-0.413000	0.06143	CCG		0.617	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		T	51629341	C	T	51629341	3	4	78	1	0	0	0	0	1	0	0	0	14352	652	23	1	714	1	SIGLEC9	19	51629341	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2251979	51629341	7499642	126	23083										
FCAR	2204	broad.mit.edu	37	chr19	55396781	55396781	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcataaaaaactccacgtacCgagagataggcagaagactg	9	9	1	3	rs587641627	byFrequency	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:55396781C>T	ENST00000355524.3	+	3	215	c.205C>T	c.(205-207)Cga>Tga	p.R69*	FCAR_ENST00000345937.4_Nonsense_Mutation_p.R69*|FCAR_ENST00000469767.1_Nonsense_Mutation_p.R69*|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391726.3_Nonsense_Mutation_p.R57*|FCAR_ENST00000353758.4_Intron|FCAR_ENST00000391725.3_Nonsense_Mutation_p.R69*|FCAR_ENST00000391723.3_Nonsense_Mutation_p.R57*|FCAR_ENST00000391724.3_Nonsense_Mutation_p.R57*|FCAR_ENST00000359272.4_Nonsense_Mutation_p.R57*	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	69	Ig-like C2-type 1.				immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R69*(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		CTCCACGTACCGAGAGATAGG	0.483																																																2	Substitution - Nonsense(2)	large_intestine(2)	19											122	110	114					19																	55396781		2203	4300	6503	60088593	SO:0001587	stop_gained	2204			X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.205C>T	19.37:g.55396781C>T	ENSP00000347714:p.Arg69*		60088593	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Nonsense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	.	.	.	.	.	.	.	.	.	.	C	9.814	1.183887	0.21870	.	.	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000359272;ENST00000391723;ENST00000391724	.	.	.	3.05	-6.1	0.02138	.	7.999500	0.01094	N	0.005251	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	1.053	0.01584	0.1762:0.2937:0.3063:0.2237	.	.	.	.	X	69;57;69;69;69;57;57;57	.	ENSP00000338257:R69X	R	+	1	2	FCAR	60088593	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.175000	0.00571	-2.165000	0.00781	-1.011000	0.02470	CGA		0.483	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		T	55396781	C	T	55396781	4	4	78	1	0	0	0	0	0	1	0	0	5792	644	23	1	215	1	FCAR	19	55396781	Nonsense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	3767440	55396781	3732202	127	23084										
NLRP8	126205	broad.mit.edu	37	chr19	56473459	56473459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agagagcaatgggctgcatcGttggtggcaagacttatgct	14	7	0	2	rs187510597		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:56473459G>A	ENST00000291971.3	+	4	2140	c.2069G>A	c.(2068-2070)cGt>cAt	p.R690H	NLRP8_ENST00000590542.1_Missense_Mutation_p.R690H	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	690					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.R690H(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GGGCTGCATCGTTGGTGGCAA	0.483													G|||	1	0.000199681	0	0	5008	,	,		19775	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	19											198	171	180					19																	56473459		2203	4300	6503	61165271	SO:0001583	missense	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2069G>A	19.37:g.56473459G>A	ENSP00000291971:p.Arg690His		61165271	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	11	0.005036630036630037	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	0.035	-1.309582	0.01342	.	.	ENSG00000179709	ENST00000291971	D	0.87491	-2.26	1.94	-3.89	0.04193	.	.	.	.	.	T	0.49457	0.1558	N	0.01188	-0.97	0.09310	N	1	B;B	0.12013	0.004;0.005	B;B	0.12156	0.0;0.007	T	0.49322	-0.8952	9	0.15066	T	0.55	.	1.1247	0.01732	0.2558:0.1391:0.4092:0.1959	.	690;690	Q86W28-2;Q86W28	.;NALP8_HUMAN	H	690	ENSP00000291971:R690H	ENSP00000291971:R690H	R	+	2	0	NLRP8	61165271	0.006000	0.16342	0.000000	0.03702	0.003000	0.03518	-0.180000	0.09754	-1.976000	0.00996	-1.196000	0.01674	CGT		0.483	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56473459	G	A	56473459	3	1	78	1	0	0	0	0	1	0	0	0	10514	1145	40	1	2083	1	NLRP8	19	56473459	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	1076678	56473459	2655524	128	23085										
CHMP2A	27243	broad.mit.edu	37	chr19	59063081	59063081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agcatcagctagggctgaggCtgcggcctctgcttttttcc	12	12	2	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr19:59063081C>A	ENST00000600118.1	-	5	1029	c.604G>T	c.(604-606)Gcc>Tcc	p.A202S	CHMP2A_ENST00000312547.2_Missense_Mutation_p.A202S|CHMP2A_ENST00000601220.1_Missense_Mutation_p.A202S			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	202	Interaction with VPS4B.				endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)	p.A202S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		AGGGCTGAGGCTGCGGCCTCT	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	19											53	61	58					19																	59063081		2203	4300	6503	63754893	SO:0001583	missense	27243			AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"Charged multivesicular body proteins"	30216	protein-coding gene	gene with protein product	"putative breast adenocarcinoma marker (32kD)", "VPS2 homolog A (S. cerevisiae)"	610893	"chromatin modifying protein 2A"			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.604G>T	19.37:g.59063081C>A	ENSP00000469240:p.Ala202Ser		63754893	B2R4W6|Q3ZTT0	Missense_Mutation	SNP	ENST00000600118.1	37	CCDS12986.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.209360	0.39003	.	.	ENSG00000130724	ENST00000312547	T	0.77750	-1.12	4.83	4.83	0.62350	.	0.054879	0.64402	D	0.000001	T	0.57125	0.2032	N	0.08118	0	0.58432	D	0.999999	B	0.25904	0.137	B	0.11329	0.006	T	0.55755	-0.8091	10	0.12766	T	0.61	.	15.8263	0.78709	0.0:1.0:0.0:0.0	.	202	O43633	CHM2A_HUMAN	S	202	ENSP00000310440:A202S	ENSP00000310440:A202S	A	-	1	0	CHMP2A	63754893	0.997000	0.39634	0.868000	0.34077	0.691000	0.40173	3.646000	0.54396	2.686000	0.91538	0.650000	0.86243	GCC		0.607	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453		A	59063081	C	A	59063081	3	1	78	1	0	0	0	0	1	0	0	0	3360	797	28	2	68	2	CHMP2A	19	59063081	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	2589622	59063081	65902	129	23086										
HNF4A	3172	broad.mit.edu	37	chr20	43043249	43043249	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aggagcagctgctggttctcGttgagtgggccaagtacatc	14	9	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr20:43043249G>A	ENST00000316099.4	+	5	684	c.595G>A	c.(595-597)Gtt>Att	p.V199I	HNF4A_ENST00000443598.2_Missense_Mutation_p.V199I|HNF4A_ENST00000415691.2_Missense_Mutation_p.V199I|HNF4A_ENST00000316673.4_Missense_Mutation_p.V177I|HNF4A_ENST00000609795.1_Missense_Mutation_p.V177I|HNF4A_ENST00000457232.1_Missense_Mutation_p.V177I	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	199					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V177I(1)|p.V199I(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GCTGGTTCTCGTTGAGTGGGC	0.622																																					Colon(79;2 1269 8820 14841 52347)											2	Substitution - Missense(2)	large_intestine(2)	20											109	82	91					20																	43043249		2203	4300	6503	42476663	SO:0001583	missense	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.595G>A	20.37:g.43043249G>A	ENSP00000312987:p.Val199Ile		42476663	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	37	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	G	34	5.391721	0.95988	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.95554	-3.74;-3.74;-3.74;-3.74;-3.74	5.75	5.75	0.90469	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.95717	0.8607	L	0.46157	1.445	0.80722	D	1	P;B;B;P;P;P;B	0.48503	0.911;0.426;0.426;0.497;0.911;0.891;0.369	P;B;B;B;P;P;B	0.51355	0.667;0.383;0.312;0.398;0.667;0.537;0.316	D	0.95739	0.8781	10	0.66056	D	0.02	.	19.9577	0.97228	0.0:0.0:1.0:0.0	.	192;199;199;199;177;177;177	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	I	177;177;199;199;229;199	ENSP00000315180:V177I;ENSP00000396216:V177I;ENSP00000312987:V199I;ENSP00000410911:V199I;ENSP00000412111:V199I	ENSP00000312987:V199I	V	+	1	0	HNF4A	42476663	1.000000	0.71417	0.317000	0.25265	0.908000	0.53690	9.869000	0.99810	2.714000	0.92807	0.563000	0.77884	GTT		0.622	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			A	43043249	G	A	43043249	3	1	78	1	0	0	0	0	1	0	0	0	7274	1145	40	1	666	1	HNF4A	20	43043249	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		43043249	19982271	130	23087										
MATN4	8785	broad.mit.edu	37	chr20	43932965	43932965	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	agcgggggcgatgccatggcGcgcagggagcccacgtccgc	18	14	0	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr20:43932965G>A	ENST00000372754.1	-	2	554	c.546C>T	c.(544-546)cgC>cgT	p.R182R	MATN4_ENST00000342716.4_Silent_p.R182R|MATN4_ENST00000353917.5_Silent_p.R182R|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000537548.1_Silent_p.R182R|MATN4_ENST00000372751.4_Intron|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000360607.6_Silent_p.R182R|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000372756.1_Silent_p.R182R			O95460	MATN4_HUMAN	matrilin 4	182	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)		p.R182R(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				ATGCCATGGCGCGCAGGGAGC	0.697																																																1	Substitution - coding silent(1)	large_intestine(1)	20											29	28	29					20																	43932965		2199	4293	6492	43366379	SO:0001819	synonymous_variant	8785			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.546C>T	20.37:g.43932965G>A			43366379	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																					0.697	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			A	43932965	G	A	43932965	2	1	78	1	0	0	0	0	0	0	0	1	9366	1074	38	1		1	MATN4	20	43932965	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	889716	43932965	19092555	131	23088										
ZNF335	63925	broad.mit.edu	37	chr20	44592468	44592468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cgggcaggagggggctgcgtTctctgcatctgactggctca	16	11	3	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr20:44592468T>C	ENST00000322927.2	-	8	1364	c.1264A>G	c.(1264-1266)Aac>Gac	p.N422D	ZNF335_ENST00000426788.1_Missense_Mutation_p.N267D	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	422					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.N422D(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GGGGCTGCGTTCTCTGCATCT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	20											80	77	78					20																	44592468		2203	4300	6503	44025875	SO:0001583	missense	63925			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1264A>G	20.37:g.44592468T>C	ENSP00000325326:p.Asn422Asp		44025875	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.683987	0.47991	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.10573	3.01;2.86	4.81	2.52	0.30459	.	0.278333	0.39407	N	0.001361	T	0.07593	0.0191	L	0.32530	0.975	0.46044	D	0.99883	B;B	0.29301	0.241;0.023	B;B	0.29942	0.109;0.023	T	0.36212	-0.9757	10	0.25751	T	0.34	-7.7559	6.7685	0.23581	0.0:0.0802:0.1535:0.7663	.	267;422	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	D	422;199;267	ENSP00000325326:N422D;ENSP00000397098:N267D	ENSP00000243961:N199D	N	-	1	0	ZNF335	44025875	1.000000	0.71417	0.001000	0.08648	0.831000	0.47069	4.007000	0.57093	0.338000	0.23692	0.454000	0.30748	AAC		0.637	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		C	44592468	T	C	44592468	3	2	78	1	0	0	0	0	1	0	0	0	17891	1783	62	4	2848	4	ZNF335	20	44592468	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	659503	44592468	18433052	132	23089										
CDH22	64405	broad.mit.edu	37	chr20	44806600	44806600	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ctcaccaaccaggatgagaaCgcagaccaagagggcgatga	12	11	1	4			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr20:44806600C>T	ENST00000372262.3	-	10	2300	c.1900G>A	c.(1900-1902)Gtt>Att	p.V634I	CDH22_ENST00000537909.1_Missense_Mutation_p.V634I	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	634					brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V634I(2)		endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				AGGATGAGAACGCAGACCAAG	0.652																																																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	20											59	53	55					20																	44806600		2203	4300	6503	44240007	SO:0001583	missense	64405			AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1900G>A	20.37:g.44806600C>T	ENSP00000361336:p.Val634Ile		44240007	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	2.424	-0.332413	0.05314	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.36157	1.27;1.27	4.43	2.33	0.28932	.	0.213481	0.40640	N	0.001041	T	0.15089	0.0364	N	0.11064	0.09	0.34914	D	0.747784	B	0.18968	0.032	B	0.10450	0.005	T	0.27434	-1.0074	10	0.02654	T	1	.	9.8426	0.41008	0.0:0.7982:0.0:0.2018	.	634	Q9UJ99	CAD22_HUMAN	I	634	ENSP00000361336:V634I;ENSP00000437790:V634I	ENSP00000361336:V634I	V	-	1	0	CDH22	44240007	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	0.691000	0.25467	1.092000	0.41356	-0.140000	0.14226	GTT		0.652	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		T	44806600	C	T	44806600	3	4	78	1	0	0	0	0	1	0	0	0	3113	536	19	1	594	1	CDH22	20	44806600	Missense_Mutation	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09	214132	44806600	18218920	133	23090										
SS18L1	26039	broad.mit.edu	37	chr20	60747793	60747793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cagcagggtgccgcgcagcaGcagacgtactcccagcagca	13	15	0	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr20:60747793G>A	ENST00000331758.3	+	9	998	c.972G>A	c.(970-972)caG>caA	p.Q324Q	SS18L1_ENST00000421564.1_Silent_p.Q324Q|SS18L1_ENST00000370848.4_Silent_p.Q327Q	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	324	Gln-rich.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)		p.Q324Q(1)	SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			CCGCGCAGCAGCAGACGTACT	0.667			T	SSX1	synovial sarcoma																																		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	1	Substitution - coding silent(1)	large_intestine(1)	20											54	57	56					20																	60747793		2203	4300	6503	60181188	SO:0001819	synonymous_variant	26039			AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.972G>A	20.37:g.60747793G>A			60181188	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Silent	SNP	ENST00000331758.3	37	CCDS13491.1																																																																																				0.667	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			A	60747793	G	A	60747793	2	1	78	1	0	0	0	0	0	0	0	1	15215	962	34	3		3	SS18L1	20	60747793	Silent	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	15941193	60747793	2277727	134	23091										
DSCAM	1826	broad.mit.edu	37	chr21	41684282	41684282	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	tcaaagggttgtatgaaaggCggaactgcaagaaaaaagaa	12	4	1	3	rs200014864		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr21:41684282C>T	ENST00000400454.1	-	9	2265	c.1788G>A	c.(1786-1788)ccG>ccA	p.P596P		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	596	Ig-like C2-type 7.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.P596P(2)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTATGAAAGGCGGAACTGCAA	0.448													C|||	1	0.000199681	8e-04	0	5008	,	,		17079	0		0	False		,,,				2504	0				Melanoma(134;970 1778 1785 21664 32388)											2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	21						C		1,3731		0,1,1865	32	30	31		1788	-3.8	0.9	21		31	0,8210		0,0,4105	no	coding-synonymous	DSCAM	NM_001389.3		0,1,5970	TT,TC,CC		0.0,0.0268,0.0084		596/2013	41684282	1,11941	1866	4105	5971	40606152	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.1788G>A	21.37:g.41684282C>T			40606152	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.448	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41684282	C	T	41684282	2	4	78	1	0	0	0	0	0	0	0	1	4779	755	27	1		1	DSCAM	21	41684282	Silent	SNP	C	TCGA-AG-A02X-01A-01W-A00E-09		41684282	6445613	135	23092										
MICAL3	57553	broad.mit.edu	37	chr22	18293510	18293511	+	Missense_Mutation	DNP	GT	GT	CC													0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	aagctcctcctgcttggcctGtctccgagctgccttttgca							TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	GT	GT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chr22:18293510_18293511GT>CC	ENST00000441493.2	-	28	5866_5867	c.5514_5515AC>GG	c.(5512-5517)agACag>agGGag	p.Q1839E	MICAL3_ENST00000580469.1_5'UTR|XXbac-B461K10.4_ENST00000476405.1_RNA	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1839					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.R1838>?(1)|p.R216>?(1)		large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TGCTTGGCCTGTCTCCGAGCTG	0.579																																																2	Complex(2)	large_intestine(2)	22																																								16673511	SO:0001583	missense	57553			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.5514_5515delinsCC	22.37:g.18293510_18293511delinsCC	ENSP00000416015:p.Gln1839Glu		16673510	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	DNP	ENST00000441493.2	37	CCDS46659.1																																																																																				0.579	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			CC	18293511	GT	CC	18293510	3	2	78	1	0	0	0	0	1	0	0	0	9601	1386	48	5	513	5	MICAL3	22	18293510	Missense_Mutation	DNP	GT	TCGA-AG-A02X-01A-01W-A00E-09		18293510	33011056	136	23093										
MAGEH1	28986	broad.mit.edu	37	chrX	55479265	55479265	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gatttataaaccggtgccccGtagcagtccggtggagtatg	13	9	0	0			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chrX:55479265G>A	ENST00000342972.1	+	1	728	c.458G>A	c.(457-459)cGt>cAt	p.R153H	hsa-mir-4536-2_ENST00000583537.1_RNA	NM_014061.3	NP_054780.2	Q9H213	MAGH1_HUMAN	melanoma antigen family H, 1	153	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)		p.R153H(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|skin(2)	15						CCGGTGCCCCGTAGCAGTCCG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	X											87	84	85					X																	55479265		2203	4300	6503	55495990	SO:0001583	missense	28986			AF320912	CCDS14369.1	Xp11.22	2008-02-05			ENSG00000187601	ENSG00000187601			24092	protein-coding gene	gene with protein product		300548				12414813, 9485030	Standard	NM_014061		Approved	APR1	uc004dum.3	Q9H213	OTTHUMG00000021655	ENST00000342972.1:c.458G>A	X.37:g.55479265G>A	ENSP00000343706:p.Arg153His		55495990	B2R8V9|Q5JRJ3|Q9Y5M2	Missense_Mutation	SNP	ENST00000342972.1	37	CCDS14369.1	.	.	.	.	.	.	.	.	.	.	.	0.257	-1.002332	0.02128	.	.	ENSG00000187601	ENST00000342972	T	0.04706	3.57	3.17	-0.924	0.10462	.	0.243358	0.21702	N	0.070413	T	0.01287	0.0042	N	0.00991	-1.07	0.09310	N	1	B	0.25206	0.12	B	0.19148	0.024	T	0.43766	-0.9371	10	0.33141	T	0.24	-4.3863	3.4565	0.07518	0.3952:0.1997:0.4051:0.0	.	153	Q9H213	MAGH1_HUMAN	H	153	ENSP00000343706:R153H	ENSP00000343706:R153H	R	+	2	0	MAGEH1	55495990	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.110000	0.15437	-0.365000	0.08076	-0.195000	0.12781	CGT		0.527	MAGEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056868.1	NM_014061		A	55479265	G	A	55479265	3	1	78	1	0	0	0	0	1	0	0	0	9218	1145	40	1	460	1	MAGEH1	23	55479265	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09		55479265	99791295	137	23094										
RAB40AL	282808	broad.mit.edu	37	chrX	102192956	102192956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	cctgaatgccaggatgatgcGaggcctctcctactccctca	9	15	2	2			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chrX:102192956G>A	ENST00000218249.5	+	1	757	c.710G>A	c.(709-711)cGa>cAa	p.R237Q	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	237					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.R237Q(2)		endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						AGGATGATGCGAGGCCTCTCC	0.572																																																2	Substitution - Missense(2)	large_intestine(2)	X											137	121	126					X																	102192956		2203	4300	6503	102079612	SO:0001583	missense	282808			BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"Ras like GTPase"	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.710G>A	X.37:g.102192956G>A	ENSP00000218249:p.Arg237Gln		102079612	Q495H3	Missense_Mutation	SNP	ENST00000218249.5	37	CCDS35353.1	.	.	.	.	.	.	.	.	.	.	.	12.10	1.838037	0.32513	.	.	ENSG00000102128	ENST00000218249	T	0.70631	-0.5	0.819	-1.01	0.10169	.	0.150621	0.24377	U	0.039052	T	0.35595	0.0937	N	0.02011	-0.69	0.23138	N	0.998234	B	0.02656	0.0	B	0.01281	0.0	T	0.19516	-1.0303	10	0.38643	T	0.18	.	4.3847	0.11311	0.7076:0.0:0.2924:0.0	.	237	P0C0E4	RB40L_HUMAN	Q	237	ENSP00000218249:R237Q	ENSP00000218249:R237Q	R	+	2	0	RAB40AL	102079612	1.000000	0.71417	0.817000	0.32601	0.433000	0.31745	4.587000	0.60991	-0.422000	0.07405	-0.386000	0.06593	CGA		0.572	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834		A	102192956	G	A	102192956	3	1	78	1	0	0	0	0	1	0	0	0	12977	1058	37	1	712	1	RAB40AL	23	102192956	Missense_Mutation	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	46713691	102192956	53077604	138	23095										
ELF4	2000	broad.mit.edu	37	chrX	129205130	129205130	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	gatgcctttctctcgctgggTccacttgatgtacttgggac	11	11	1	1			TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chrX:129205130T>A	ENST00000308167.5	-	7	1073	c.694A>T	c.(694-696)Acc>Tcc	p.T232S	ELF4_ENST00000335997.7_Missense_Mutation_p.T232S	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)									p.T232S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TCTCGCTGGGTCCACTTGATG	0.527			T	ERG	AML																																		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	1	Substitution - Missense(1)	large_intestine(1)	X											153	126	135					X																	129205130		2203	4300	6503	129032811	SO:0001583	missense	2000			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.694A>T	X.37:g.129205130T>A	ENSP00000311280:p.Thr232Ser		129032811		Missense_Mutation	SNP	ENST00000308167.5	37	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.893576	0.91889	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	T;T	0.57752	0.38;0.38	5.45	5.45	0.79879	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (3);	0.053268	0.85682	D	0.000000	T	0.70736	0.3258	M	0.73598	2.24	0.58432	D	0.999998	D	0.62365	0.991	D	0.74348	0.983	T	0.74648	-0.3595	10	0.87932	D	0	.	12.3614	0.55205	0.0:0.0:0.0:1.0	.	232	Q99607	ELF4_HUMAN	S	232	ENSP00000338608:T232S;ENSP00000311280:T232S	ENSP00000311280:T232S	T	-	1	0	ELF4	129032811	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.013000	0.88655	1.823000	0.53134	0.417000	0.27973	ACC		0.527	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		A	129205130	T	A	129205130	3	1	78	1	0	0	0	0	1	0	0	0	5069	1667	58	5	1309	5	ELF4	23	129205130	Missense_Mutation	SNP	T	TCGA-AG-A02X-01A-01W-A00E-09	27012174	129205130	26065430	139	23096										
HAUS7	11219	broad.mit.edu	37	chrX	152728110	152728110	+	De_novo_Start_OutOfFrame	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0431654676258993	6	1	0.453318152244632	1.09551886792453	0.405747728860936	0.148606811145511	0.584839708379108	0	ggcgcacacagcatcagctcGtggcccagcttcgtcatttc	10	15	2	0	rs368562448		TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A02X-01A-01W-A00E-09	TCGA-AG-A02X-10A-01W-A00E-09	g.chrX:152728110G>A	ENST00000334497.2	-	0	341				TREX2_ENST00000330912.2_De_novo_Start_OutOfFrame|HAUS7_ENST00000421080.2_De_novo_Start_OutOfFrame|HAUS7_ENST00000370210.1_Silent_p.H104H|TREX2_ENST00000338525.2_De_novo_Start_InFrame|TREX2_ENST00000370232.1_De_novo_Start_InFrame|HAUS7_ENST00000370211.4_Silent_p.H114H|HAUS7_ENST00000370212.3_Silent_p.H114H			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2						DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)	p.H114H(1)		endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCATCAGCTCGTGGCCCAGCT	0.612								Editing and processing nucleases																																								1	Substitution - coding silent(1)	large_intestine(1)	X						A		0,3835		0,0,1632,571	94	69	77		342	-1.1	0.8	X		77	1,6727		0,1,2427,1872	no	coding-synonymous	HAUS7	NM_017518.6		0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095		114/369	152728110	1,10562	2203	4300	6503	152381304			55559			AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.-801C>T	X.37:g.152728110G>A			152381304	Q45F08|Q9UN77	Silent	SNP	ENST00000334497.2	37																																																																																					0.612	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		A	152728110	G	A	152728110	1	1	78	1	0	1	0	0	0	0	0	0	6992	1136	40	1		1	HAUS7	23	152728110	De_novo_Start_OutOfFrame	SNP	G	TCGA-AG-A02X-01A-01W-A00E-09	23522980	152728110	2542450	140	23097										
PRAMEF4	400735	broad.mit.edu	37	chr1	12941807	12941807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tctgctctggggaaacgtagCgagagacatccatgtgggag	15	8	2	1	rs562920609		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr1:12941807C>T	ENST00000235349.5	-	3	813	c.743G>A	c.(742-744)cGc>cAc	p.R248H		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	248					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.R248H(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGAAACGTAGCGAGAGACATC	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	1											252	302	284					1																	12941807		1442	2515	3957	12864394	SO:0001583	missense	400735				CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.743G>A	1.37:g.12941807C>T	ENSP00000235349:p.Arg248His		12864394	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.056274	0.00390	.	.	ENSG00000243073	ENST00000235349	T	0.50548	0.74	1.02	-2.03	0.07365	.	1.275850	0.05537	N	0.565066	T	0.18257	0.0438	N	0.03050	-0.425	0.09310	N	1	B	0.17268	0.021	B	0.16722	0.016	T	0.04242	-1.0966	10	0.15066	T	0.55	.	0.456	0.00509	0.196:0.2286:0.3292:0.2461	.	248	O60810	PRAM4_HUMAN	H	248	ENSP00000235349:R248H	ENSP00000235349:R248H	R	-	2	0	PRAMEF4	12864394	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.376000	0.02561	-2.157000	0.00789	-1.441000	0.01070	CGC		0.483	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		T	12941807	C	T	12941807	3	4	79	1	0	0	0	0	1	0	0	0	12471	768	27	1	701	1	PRAMEF4	1	12941807	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		12941807	236308814	1	23098										
GRIK3	2899	broad.mit.edu	37	chr1	37346245	37346245	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ggccacccacctgtactgtcGtcatagaccacggtggctga	11	14	1	2	rs377438243		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr1:37346245G>A	ENST00000373091.3	-	3	556	c.540C>T	c.(538-540)gaC>gaT	p.D180D	GRIK3_ENST00000373093.4_Silent_p.D180D	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	180					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.D180D(2)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CTGTACTGTCGTCATAGACCA	0.612																																																2	Substitution - coding silent(2)	large_intestine(2)	1											259	247	251					1																	37346245		2203	4300	6503	37118832	SO:0001819	synonymous_variant	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.540C>T	1.37:g.37346245G>A			37118832	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																				0.612	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37346245	G	A	37346245	2	1	79	1	0	0	0	0	0	0	0	1	6796	1136	40	1		1	GRIK3	1	37346245	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	24404438	37346245	211904376	2	23099										
MRPL37	51253	broad.mit.edu	37	chr1	54678234	54678234	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gtacttactggacaaagccaAtttacgaccacaccgccttc	6	14	0	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr1:54678234A>T	ENST00000360840.5	+	5	970	c.893A>T	c.(892-894)aAt>aTt	p.N298I	MRPL37_ENST00000605337.1_Missense_Mutation_p.N298I|MRPL37_ENST00000336230.6_Missense_Mutation_p.N167I	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	298					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.N298I(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						GACAAAGCCAATTTACGACCA	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	1											183	181	181					1																	54678234		2203	4300	6503	54450822	SO:0001583	missense	51253			AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"Mitochondrial ribosomal proteins / large subunits"	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.893A>T	1.37:g.54678234A>T	ENSP00000354086:p.Asn298Ile		54450822	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	37	CCDS589.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.30|12.30	1.897956|1.897956	0.33535|0.33535	.|.	.|.	ENSG00000116221|ENSG00000116221	ENST00000398219|ENST00000360840;ENST00000329505;ENST00000336230	.|T;T	.|0.16457	.|2.34;2.34	5.25|5.25	2.62|2.62	0.31277|0.31277	.|.	.|0.343513	.|0.36778	.|N	.|0.002405	T|T	0.31857|0.31857	0.0810|0.0810	M|M	0.71581|0.71581	2.175|2.175	0.27914|0.27914	N|N	0.938501|0.938501	.|D;P;P	.|0.67145	.|0.996;0.942;0.772	.|P;P;B	.|0.59546	.|0.859;0.691;0.346	T|T	0.11179|0.11179	-1.0598|-1.0598	5|10	.|0.62326	.|D	.|0.03	-6.158|-6.158	8.2949|8.2949	0.31980|0.31980	0.7591:0.0:0.2409:0.0|0.7591:0.0:0.2409:0.0	.|.	.|167;235;298	.|A6NHR2;E9PB99;Q9BZE1	.|.;.;RM37_HUMAN	F|I	83|298;235;167	.|ENSP00000354086:N298I;ENSP00000338526:N167I	.|ENSP00000328799:N235I	I|N	+|+	1|2	0|0	MRPL37|MRPL37	54450822|54450822	0.006000|0.006000	0.16342|0.16342	0.014000|0.014000	0.15608|0.15608	0.033000|0.033000	0.12548|0.12548	0.653000|0.653000	0.24902|0.24902	0.210000|0.210000	0.20664|0.20664	0.533000|0.533000	0.62120|0.62120	ATT|AAT		0.532	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491		T	54678234	A	T	54678234	3	4	79	1	0	0	0	0	1	0	0	0	9830	101	4	5	911	5	MRPL37	1	54678234	Missense_Mutation	SNP	A	TCGA-AG-A032-01A-01W-A00E-09	17331989	54678234	194572387	3	23100										
KCNJ9	3765	broad.mit.edu	37	chr1	160057420	160057420	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttttgaggtgcccacaccttCgtgcagtgctcgagagctgg	13	11	0	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr1:160057420C>A	ENST00000368088.3	+	3	1237	c.995C>A	c.(994-996)tCg>tAg	p.S332*		NM_004983.2	NP_004974.2	Q92806	KCNJ9_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 9	332					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein activated inward rectifier potassium channel activity (GO:0015467)	p.S332*(1)		biliary_tract(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(2)	16	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCCACACCTTCGTGCAGTGCT	0.617																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											65	60	62					1																	160057420		2203	4300	6503	158324044	SO:0001587	stop_gained	3765			U52152	CCDS1194.1	1q23.2	2011-07-05			ENSG00000162728	ENSG00000162728		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6270	protein-coding gene	gene with protein product		600932				8575783, 16382105	Standard	NM_004983		Approved	Kir3.3, GIRK3	uc001fuy.1	Q92806	OTTHUMG00000024072	ENST00000368088.3:c.995C>A	1.37:g.160057420C>A	ENSP00000357067:p.Ser332*		158324044	Q5JW75	Nonsense_Mutation	SNP	ENST00000368088.3	37	CCDS1194.1	.	.	.	.	.	.	.	.	.	.	c	37	6.172365	0.97348	.	.	ENSG00000162728	ENST00000368088	.	.	.	4.21	4.21	0.49690	.	0.076672	0.53938	D	0.000054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	10.9489	0.47317	0.0:0.6688:0.3312:0.0	.	.	.	.	X	332	.	ENSP00000357067:S332X	S	+	2	0	KCNJ9	158324044	0.000000	0.05858	0.871000	0.34182	0.907000	0.53573	0.407000	0.21049	1.909000	0.55274	0.550000	0.68814	TCG		0.617	KCNJ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060628.1	NM_004983		A	160057420	C	A	160057420	4	1	79	1	0	0	0	0	0	1	0	0	8078	893	31	2	1001	2	KCNJ9	1	160057420	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	105379186	160057420	89193201	4	23101										
PLEKHA3	65977	broad.mit.edu	37	chr2	179355479	179355479	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgcagctgaaagacagaggtGgctggtcgctctggggagct	17	8	1	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr2:179355479G>A	ENST00000234453.5	+	3	653	c.251G>A	c.(250-252)tGg>tAg	p.W84*	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	84	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)	p.W84*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AGACAGAGGTGGCTGGTCGCT	0.418																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											58	58	58					2																	179355479		2203	4300	6503	179063725	SO:0001587	stop_gained	65977			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.251G>A	2.37:g.179355479G>A	ENSP00000234453:p.Trp84*		179063725	Q4ZG69|Q86TQ1|Q9NXT3	Nonsense_Mutation	SNP	ENST00000234453.5	37	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	39	7.430874	0.98279	.	.	ENSG00000116095	ENST00000234453	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0387	19.8265	0.96619	0.0:0.0:1.0:0.0	.	.	.	.	X	84	.	ENSP00000234453:W84X	W	+	2	0	PLEKHA3	179063725	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.672000	0.90937	0.563000	0.77884	TGG		0.418	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		A	179355479	G	A	179355479	4	1	79	1	0	0	0	0	0	1	0	0	12088	1357	47	3	261	3	PLEKHA3	2	179355479	Nonsense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		179355479	63843894	5	23102										
TTN	7273	broad.mit.edu	37	chr2	179509334	179509334	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gtttttcaggaactttcttcTttggaatagctttaaagaat	7	5	3	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr2:179509334T>G	ENST00000591111.1	-	168	35719	c.35495A>C	c.(35494-35496)aAg>aCg	p.K11832T	RP11-171I2.3_ENST00000605021.1_lincRNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.K10905T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.K13473T			Q8WZ42	TITIN_HUMAN	titin	11832	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K10905T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTTTCTTCTTTGGAATAGC	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	2											94	83	86					2																	179509334		1796	4061	5857	179217579	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.35495A>C	2.37:g.179509334T>G	ENSP00000465570:p.Lys11832Thr		179217579	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.27|12.27	1.888189|1.888189	0.33348|0.33348	.|.	.|.	ENSG00000155657|ENSG00000155657	ENST00000426232|ENST00000342992;ENST00000429997;ENST00000446966;ENST00000434777	.|T	.|0.67523	.|-0.27	5.68|5.68	1.96|1.96	0.26148|0.26148	.|Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.|.	.|.	.|.	.|.	T|T	0.58250|0.58250	0.2109|0.2109	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|B;P	.|0.46706	.|0.18;0.883	.|B;P	.|0.46629	.|0.193;0.522	T|T	0.56529|0.56529	-0.7964|-0.7964	5|9	.|0.87932	.|D	.|0	.|.	8.877|8.877	0.35352|0.35352	0.0:0.3123:0.0:0.6877|0.0:0.3123:0.0:0.6877	.|.	.|11832;312	.|Q8WZ42;A2TKE4	.|TITIN_HUMAN;.	N|T	179|10905;312;312;132	.|ENSP00000343764:K10905T	.|ENSP00000343764:K10905T	K|K	-|-	3|2	2|0	TTN|TTN	179217579|179217579	0.997000|0.997000	0.39634|0.39634	0.980000|0.980000	0.43619|0.43619	0.913000|0.913000	0.54294|0.54294	0.416000|0.416000	0.21198|0.21198	0.156000|0.156000	0.19299|0.19299	-0.353000|-0.353000	0.07706|0.07706	AAA|AAG		0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179509334	T	G	179509334	3	3	79	1	0	0	0	0	1	0	0	0	16775	1609	56	4	67855	4	TTN	2	179509334	Missense_Mutation	SNP	T	TCGA-AG-A032-01A-01W-A00E-09	153855	179509334	63690039	6	23103										
TTN	7273	broad.mit.edu	37	chr2	179604087	179604087	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	atttgttatggatgttgtgaGgtgtacaatatcaccttcct	9	6	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr2:179604087G>T	ENST00000591111.1	-	46	13146	c.12922C>A	c.(12922-12924)Ctc>Atc	p.L4308I	TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L4454I|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L4262I|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Missense_Mutation_p.L4387I|TTN_ENST00000589042.1_Missense_Mutation_p.L4625I|TTN-AS1_ENST00000590773.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12071	Ig-like 23.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.L4262I(1)|p.L4454I(1)|p.L4387I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATGTTGTGAGGTGTACAATA	0.388																																																3	Substitution - Missense(3)	large_intestine(3)	2											149	133	138					2																	179604087		1917	4138	6055	179312332	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12922C>A	2.37:g.179604087G>T	ENSP00000465570:p.Leu4308Ile		179312332	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	9.998	1.232593	0.22626	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.74421	-0.84;-0.84;-0.84	5.93	1.62	0.23740	.	.	.	.	.	T	0.75997	0.3926	M	0.82132	2.575	0.09310	N	1	B;B;B	0.25351	0.124;0.124;0.124	B;B;B	0.31614	0.074;0.074;0.133	T	0.69840	-0.5036	9	0.87932	D	0	.	10.859	0.46815	0.3436:0.0:0.6564:0.0	.	4262;4387;4454	D3DPF9;E7EQE6;E7ET18	.;.;.	I	4262;4454;4387;4262	ENSP00000434586:L4262I;ENSP00000340554:L4454I;ENSP00000352154:L4387I	ENSP00000340554:L4454I	L	-	1	0	TTN	179312332	0.843000	0.29541	0.037000	0.18230	0.943000	0.58893	1.423000	0.34837	0.417000	0.25871	0.655000	0.94253	CTC		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179604087	G	T	179604087	3	4	79	1	0	0	0	0	1	0	0	0	16775	1000	35	2	90916	2	TTN	2	179604087	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	94753	179604087	63595286	7	23104										
CXCR2	3579	broad.mit.edu	37	chr2	218999857	218999857	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gccgcctccaaggtgaatggCtggatttttggcacattcct	11	11	0	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr2:218999857C>A	ENST00000318507.2	+	3	760	c.333C>A	c.(331-333)ggC>ggA	p.G111G		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	111					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)	p.G111G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						AGGTGAATGGCTGGATTTTTG	0.557																																																1	Substitution - coding silent(1)	large_intestine(1)	2											107	101	103					2																	218999857		2203	4297	6500	218708102	SO:0001819	synonymous_variant	3579			U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6027	protein-coding gene	gene with protein product		146928	"interleukin 8 receptor, beta"	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.333C>A	2.37:g.218999857C>A			218708102	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																				0.557	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557		A	218999857	C	A	218999857	2	1	79	1	0	0	0	0	0	0	0	1	4097	784	28	2		2	CXCR2	2	218999857	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	39395770	218999857	24199516	8	23105										
ITIH1	3697	broad.mit.edu	37	chr3	52825622	52825622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	atgccacgatggtggtgaggAaccgccggctcacggtcacc	14	13	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr3:52825622A>G	ENST00000273283.2	+	21	2608	c.2584A>G	c.(2584-2586)Aac>Gac	p.N862D	ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Missense_Mutation_p.N720D|ITIH1_ENST00000405128.3_Missense_Mutation_p.N228D|ITIH1_ENST00000537050.1_Missense_Mutation_p.N574D	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	862	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.N862D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GGTGGTGAGGAACCGCCGGCT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	3											69	70	70					3																	52825622		2203	4300	6503	52800662	SO:0001583	missense	3697				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2584A>G	3.37:g.52825622A>G	ENSP00000273283:p.Asn862Asp		52800662	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.269560	0.40095	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11169	2.8;2.8;2.8;2.8;2.8	5.61	3.23	0.37069	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.345097	0.34555	N	0.003866	T	0.14700	0.0355	M	0.66939	2.045	0.26289	N	0.978152	B;B;B	0.24920	0.002;0.01;0.114	B;B;B	0.33196	0.013;0.07;0.159	T	0.15607	-1.0431	10	0.56958	D	0.05	-18.573	8.1346	0.31048	0.7773:0.0:0.2227:0.0	.	720;228;862	F5H165;B5MCP1;P19827	.;.;ITIH1_HUMAN	D	862;720;574;415;228	ENSP00000273283:N862D;ENSP00000443973:N720D;ENSP00000443847:N574D;ENSP00000395836:N415D;ENSP00000384589:N228D	ENSP00000273283:N862D	N	+	1	0	ITIH1	52800662	1.000000	0.71417	0.939000	0.37840	0.868000	0.49771	3.111000	0.50360	0.420000	0.25954	0.482000	0.46254	AAC		0.582	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		G	52825622	A	G	52825622	3	3	79	1	0	0	0	0	1	0	0	0	7924	246	9	4	2666	4	ITIH1	3	52825622	Missense_Mutation	SNP	A	TCGA-AG-A032-01A-01W-A00E-09		52825622	145196808	9	23106										
CPNE4	131034	broad.mit.edu	37	chr3	131415403	131415403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	taccttgtcatccaatttccGtgcattgaatgcaagctcaa	6	11	2	1	rs373479979		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr3:131415403G>A	ENST00000512055.1	-	9	2616	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	CPNE4_ENST00000429747.1_Missense_Mutation_p.R164W|CPNE4_ENST00000512332.1_Missense_Mutation_p.R182W|CPNE4_ENST00000502818.1_Missense_Mutation_p.R182W|CPNE4_ENST00000511604.1_Missense_Mutation_p.R164W			Q96A23	CPNE4_HUMAN	copine IV	164	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)		p.R164W(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						TCCAATTTCCGTGCATTGAAT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	3						G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	182	164	170		490	4.7	1	3		170	0,8600		0,0,4300	no	missense	CPNE4	NM_130808.1	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	164/558	131415403	1,13005	2203	4300	6503	132898093	SO:0001583	missense	131034			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.490C>T	3.37:g.131415403G>A	ENSP00000421705:p.Arg164Trp		132898093	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.066590	0.76301	2.27E-4	0.0	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881	T;T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58;1.45	5.61	4.68	0.58851	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.213702	0.45126	D	0.000382	D	0.83672	0.5305	M	0.90198	3.095	0.58432	D	0.999998	D;D	0.67145	0.996;0.992	P;P	0.56612	0.802;0.788	D	0.87329	0.2323	10	0.72032	D	0.01	-18.7718	15.3146	0.74065	0.0:0.0:0.8596:0.1404	.	182;164	Q96A23-2;Q96A23	.;CPNE4_HUMAN	W	164;164;182;164;182;164	ENSP00000421705:R164W;ENSP00000411904:R164W;ENSP00000424853:R182W;ENSP00000423811:R164W;ENSP00000421646:R182W;ENSP00000425506:R164W	ENSP00000411904:R164W	R	-	1	2	CPNE4	132898093	1.000000	0.71417	0.983000	0.44433	0.877000	0.50540	2.679000	0.46909	2.646000	0.89796	0.655000	0.94253	CGG		0.403	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		A	131415403	G	A	131415403	3	1	79	1	0	0	0	0	1	0	0	0	3820	1144	40	1	1231	1	CPNE4	3	131415403	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	78589781	131415403	66607027	10	23107										
LPHN3	23284	broad.mit.edu	37	chr4	62778452	62778452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttcagcttcagaaaagagagCgctcttgcagagcctatgtc	10	10	3	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:62778452C>T	ENST00000514591.1	+	12	2214	c.1885C>T	c.(1885-1887)Cgc>Tgc	p.R629C	LPHN3_ENST00000511324.1_Missense_Mutation_p.R697C|LPHN3_ENST00000508946.1_Missense_Mutation_p.R629C|LPHN3_ENST00000514157.1_Missense_Mutation_p.R629C|LPHN3_ENST00000545650.1_Missense_Mutation_p.R629C|LPHN3_ENST00000507625.1_Missense_Mutation_p.R697C|LPHN3_ENST00000508693.1_Missense_Mutation_p.R697C|LPHN3_ENST00000506700.1_Missense_Mutation_p.R629C|LPHN3_ENST00000512091.2_Missense_Mutation_p.R629C|LPHN3_ENST00000504896.1_Missense_Mutation_p.R629C|LPHN3_ENST00000506720.1_Missense_Mutation_p.R697C|LPHN3_ENST00000514996.1_Missense_Mutation_p.R629C|LPHN3_ENST00000507164.1_Missense_Mutation_p.R697C|LPHN3_ENST00000509896.1_Missense_Mutation_p.R697C|LPHN3_ENST00000506746.1_Missense_Mutation_p.R697C			Q9HAR2	LPHN3_HUMAN	latrophilin 3	623					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.R629C(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GAAAAGAGAGCGCTCTTGCAG	0.363																																																3	Substitution - Missense(3)	large_intestine(3)	4											173	155	161					4																	62778452		1835	4095	5930	62461047	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1885C>T	4.37:g.62778452C>T	ENSP00000422533:p.Arg629Cys		62461047	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944410	0.73672	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.71341	-0.53;-0.52;-0.54;-0.54;-0.53;-0.52;-0.54;-0.54;-0.53;-0.53;-0.53;-0.55;-0.56;-0.55;-0.54	5.63	5.63	0.86233	.	.	.	.	.	T	0.82235	0.4993	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70935	0.971;0.933	D	0.83369	0.0006	9	0.87932	D	0	.	18.655	0.91450	0.0:1.0:0.0:0.0	.	629;629	E9PE04;Q9HAR2-2	.;.	C	629;629;697;697;629;629;629;697;697;697;629;629;629;697;697;629	ENSP00000423388:R629C;ENSP00000422533:R629C;ENSP00000423787:R697C;ENSP00000425033:R697C;ENSP00000424120:R629C;ENSP00000439831:R629C;ENSP00000421476:R697C;ENSP00000424030:R697C;ENSP00000421372:R697C;ENSP00000425201:R629C;ENSP00000423434:R629C;ENSP00000421627:R629C;ENSP00000420931:R697C;ENSP00000425884:R697C;ENSP00000424258:R629C	ENSP00000280009:R629C	R	+	1	0	LPHN3	62461047	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.047000	0.76599	2.645000	0.89757	0.561000	0.74099	CGC		0.363	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62778452	C	T	62778452	3	4	79	1	0	0	0	0	1	0	0	0	8946	768	27	1	1923	1	LPHN3	4	62778452	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		62778452	128375824	11	23108										
THAP9	79725	broad.mit.edu	37	chr4	83838792	83838792	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	aaatcatgtactgaaagtgaAtagtgccacccaactcttta	6	9	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:83838792A>C	ENST00000302236.5	+	5	1478	c.1427A>C	c.(1426-1428)aAt>aCt	p.N476T	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	476					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.N476T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				CTGAAAGTGAATAGTGCCACC	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	4											123	129	127					4																	83838792		2203	4300	6503	84057816	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.1427A>C	4.37:g.83838792A>C	ENSP00000305533:p.Asn476Thr		84057816	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.239745	0.22711	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.90261	-2.64	3.87	3.87	0.44632	.	0.000000	0.51477	D	0.000084	D	0.92685	0.7675	L	0.54323	1.7	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.91482	0.5205	10	0.38643	T	0.18	-29.6152	11.3618	0.49648	1.0:0.0:0.0:0.0	.	476	Q9H5L6	THAP9_HUMAN	T	476	ENSP00000305533:N476T	ENSP00000305533:N476T	N	+	2	0	THAP9	84057816	0.999000	0.42202	0.623000	0.29173	0.009000	0.06853	5.498000	0.66931	1.983000	0.57843	0.533000	0.62120	AAT		0.388	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		C	83838792	A	C	83838792	3	2	79	1	0	0	0	0	1	0	0	0	15890	101	4	4	1445	4	THAP9	4	83838792	Missense_Mutation	SNP	A	TCGA-AG-A032-01A-01W-A00E-09	21060340	83838792	107315484	12	23109										
MTTP	4547	broad.mit.edu	37	chr4	100532311	100532311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	atgttgcagcaaaattgtccGtcgagttctgaaggaaatgg	12	6	1	1	rs201863511		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:100532311G>A	ENST00000265517.5	+	13	1984	c.1781G>A	c.(1780-1782)cGt>cAt	p.R594H	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.R594H|MTTP_ENST00000511045.1_Missense_Mutation_p.R621H			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	594	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.R594H(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	AAAATTGTCCGTCGAGTTCTG	0.398													G|||	1	0.000199681	8e-04	0	5008	,	,		17440	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4											143	133	136					4																	100532311		2203	4300	6503	100751334	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1781G>A	4.37:g.100532311G>A	ENSP00000265517:p.Arg594His		100751334	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.27	2.484374	0.44147	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.70986	-0.53;-0.53;-0.53	5.84	5.0	0.66597	Lipid transport protein, N-terminal (1);Vitellinogen, superhelical (2);	0.154327	0.64402	N	0.000012	T	0.65565	0.2703	L	0.46157	1.445	0.49299	D	0.999773	B;B	0.22003	0.063;0.019	B;B	0.17098	0.017;0.006	T	0.63906	-0.6531	10	0.62326	D	0.03	-0.3192	14.9731	0.71249	0.0681:0.0:0.9319:0.0	.	621;594	E9PBP6;P55157	.;MTP_HUMAN	H	621;594;594	ENSP00000427679:R621H;ENSP00000400821:R594H;ENSP00000265517:R594H	ENSP00000265517:R594H	R	+	2	0	MTTP	100751334	1.000000	0.71417	0.961000	0.40146	0.600000	0.36913	4.296000	0.59055	1.485000	0.48380	0.655000	0.94253	CGT		0.398	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100532311	G	A	100532311	3	1	79	1	0	0	0	0	1	0	0	0	9994	1145	40	1	1831	1	MTTP	4	100532311	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	16693519	100532311	90621965	13	23110										
ANK2	287	broad.mit.edu	37	chr4	114288823	114288823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cctgcgatcaccctcctatcGtctcagaggaagacatttct	7	14	3	2	rs146476345		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:114288823G>A	ENST00000357077.4	+	42	11187	c.11134G>A	c.(11134-11136)Gtc>Atc	p.V3712I	ANK2_ENST00000509550.1_Missense_Mutation_p.V803I|ANK2_ENST00000510275.2_Missense_Mutation_p.V279I|ANK2_ENST00000264366.6_Missense_Mutation_p.V3679I|ANK2_ENST00000394537.3_Missense_Mutation_p.V1627I|ANK2_ENST00000506722.1_Missense_Mutation_p.V1618I	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3712					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.V3712I(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CCCTCCTATCGTCTCAGAGGA	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	91	87	88		4852,11134,4879	5.6	0.9	4	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	1618/1864,3712/3958,1627/1873	114288823	1,13005	2203	4300	6503	114508272	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.11134G>A	4.37:g.114288823G>A	ENSP00000349588:p.Val3712Ile		114508272	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.607706|4.607706	0.87157|0.87157	0.0|0.0	1.16E-4|1.16E-4	ENSG00000145362|ENSG00000145362	ENST00000514960|ENST00000506722;ENST00000431447;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550;ENST00000510275;ENST00000505342	.|T;T;T;T;T;D;D	.|0.97089	.|-0.62;-0.6;-0.68;-0.68;-1.32;-2.27;-4.24	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.49305	.|D	.|0.000151	D|D	0.98213|0.98213	0.9409|0.9409	M|M	0.71036|0.71036	2.16|2.16	0.48901|0.48901	D|D	0.999726|0.999726	.|D;D;D;B;D;D	.|0.89917	.|0.994;0.998;0.987;0.037;1.0;0.965	.|P;P;B;B;D;P	.|0.83275	.|0.539;0.803;0.403;0.014;0.996;0.746	D|D	0.97760|0.97760	1.0220|1.0220	5|10	.|0.34782	.|T	.|0.22	.|.	19.6501|19.6501	0.95796|0.95796	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|803;662;628;1627;3712;1618	.|E9PCH6;F8W694;Q7Z344;Q01484-2;Q01484-4;Q01484-5	.|.;.;.;.;.;.	H|I	628|1618;662;1627;3712;3679;1618;803;279;722	.|ENSP00000421067:V1618I;ENSP00000378044:V1627I;ENSP00000349588:V3712I;ENSP00000264366:V3679I;ENSP00000426944:V803I;ENSP00000421023:V279I;ENSP00000422498:V722I	.|ENSP00000264366:V3679I	R|V	+|+	2|1	0|0	ANK2|ANK2	114508272|114508272	1.000000|1.000000	0.71417|0.71417	0.901000|0.901000	0.35422|0.35422	0.739000|0.739000	0.42172|0.42172	7.562000|7.562000	0.82300|0.82300	2.651000|2.651000	0.90000|0.90000	0.491000|0.491000	0.48974|0.48974	CGT|GTC		0.488	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114288823	G	A	114288823	3	1	79	1	0	0	0	0	1	0	0	0	621	1145	40	1	11365	1	ANK2	4	114288823	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	13756512	114288823	76865453	14	23111										
DCHS2	54798	broad.mit.edu	37	chr4	155241580	155241580	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttttcatttcctgagaggatGctgtatgttacttttccatt	7	7	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:155241580G>A	ENST00000357232.4	-	14	3605	c.3606C>T	c.(3604-3606)agC>agT	p.S1202S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1202	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S1202S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGAGAGGATGCTGTATGTTA	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	4											197	179	185					4																	155241580		2203	4300	6503	155461030	SO:0001819	synonymous_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3606C>T	4.37:g.155241580G>A			155461030	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.408	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155241580	G	A	155241580	2	1	79	1	0	0	0	0	0	0	0	1	4294	1310	46	3		3	DCHS2	4	155241580	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	40952757	155241580	35912696	15	23112										
GUCY1A3	2982	broad.mit.edu	37	chr4	156631752	156631752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gaggtttttaaaatatgttaCgaggaagatgaaaacatcct	9	4	0	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr4:156631752C>T	ENST00000296518.7	+	6	644	c.435C>T	c.(433-435)taC>taT	p.Y145Y	GUCY1A3_ENST00000515602.1_3'UTR|GUCY1A3_ENST00000506455.1_Silent_p.Y145Y|GUCY1A3_ENST00000511507.1_Silent_p.Y145Y|GUCY1A3_ENST00000455639.2_Silent_p.Y145Y|GUCY1A3_ENST00000511108.1_Silent_p.Y145Y|GUCY1A3_ENST00000513574.1_Silent_p.Y145Y|GUCY1A3_ENST00000393832.3_5'UTR			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	145					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.Y145Y(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		AAATATGTTACGAGGAAGATG	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	4											71	78	76					4																	156631752		2203	4300	6503	156851202	SO:0001819	synonymous_variant	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.435C>T	4.37:g.156631752C>T			156851202	D3DP19|D6RDW3|O43843|Q8TAH3	De_novo_Start_OutOfFrame	SNP	ENST00000296518.7	37	CCDS34085.1																																																																																				0.398	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156631752	C	T	156631752	2	4	79	1	0	0	0	0	0	0	0	1	6915	547	19	1		1	GUCY1A3	4	156631752	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	1390172	156631752	34522524	16	23113										
CDH18	1016	broad.mit.edu	37	chr5	19483526	19483526	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gcccatctctctcgcatgcaCaaaccctgatggtgagggtg	11	13	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr5:19483526C>A	ENST00000507958.1	-	14	2756	c.1766G>T	c.(1765-1767)tGt>tTt	p.C589F	CDH18_ENST00000274170.4_Missense_Mutation_p.C589F|CDH18_ENST00000382275.1_Missense_Mutation_p.C589F|CDH18_ENST00000502796.1_Missense_Mutation_p.V553L|CDH18_ENST00000506372.1_Missense_Mutation_p.V554L			Q13634	CAD18_HUMAN	cadherin 18, type 2	589	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C589F(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTCGCATGCACAAACCCTGAT	0.517																																																2	Substitution - Missense(2)	large_intestine(2)	5											83	70	75					5																	19483526		2203	4300	6503	19519283	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1766G>T	5.37:g.19483526C>A	ENSP00000425093:p.Cys589Phe		19519283	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.0|24.0	4.484315|4.484315	0.84854|0.84854	.|.	.|.	ENSG00000145526|ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170|ENST00000506372;ENST00000502796;ENST00000515257	T;T;T|T;T;T	0.53423|0.57752	0.62;0.62;0.62|0.38;0.41;0.48	5.54|5.54	5.54|5.54	0.83059|0.83059	Cadherin (4);Cadherin-like (1);|.	0.102468|.	0.64402|.	D|.	0.000002|.	T|T	0.66117|0.66117	0.2757|0.2757	M|M	0.93978|0.93978	3.48|3.48	0.80722|0.80722	D|D	1|1	D|B	0.89917|0.14438	1.0|0.01	D|B	0.85130|0.18263	0.997|0.021	T|T	0.66913|0.66913	-0.5803|-0.5803	9|8	.|.	.|.	.|.	.|.	18.0513|18.0513	0.89349|0.89349	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	589|553	Q13634|B4DHG6	CAD18_HUMAN|.	F|L	589|554;553;420	ENSP00000371710:C589F;ENSP00000425093:C589F;ENSP00000274170:C589F|ENSP00000424931:V554L;ENSP00000422138:V553L;ENSP00000427383:V420L	.|.	C|V	-|-	2|1	0|0	CDH18|CDH18	19519283|19519283	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.487000|7.487000	0.81328|0.81328	2.615000|2.615000	0.88500|0.88500	0.655000|0.655000	0.94253|0.94253	TGT|GTG		0.517	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19483526	C	A	19483526	3	1	79	1	0	0	0	0	1	0	0	0	3109	478	17	2	614	2	CDH18	5	19483526	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		19483526	161431734	17	23114										
APC	324	broad.mit.edu	37	chr5	112151261	112151261	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gtagcacacactctgcacctCgaaggctgacaagtcatctg	9	13	3	1	rs137854568		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr5:112151261C>T	ENST00000457016.1	+	9	1284	c.904C>T	c.(904-906)Cga>Tga	p.R302*	APC_ENST00000257430.4_Nonsense_Mutation_p.R302*|APC_ENST00000508376.2_Nonsense_Mutation_p.R302*			P25054	APC_HUMAN	adenomatous polyposis coli	302	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R302*(13)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCTGCACCTCGAAGGCTGAC	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	13	Substitution - Nonsense(13)	large_intestine(13)	5	GRCh37	CM910029	APC	M	rs137854568						113	100	104					5																	112151261		2202	4300	6502	112179160	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.904C>T	5.37:g.112151261C>T	ENSP00000413133:p.Arg302*		112179160	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.654520	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5148	18.9031	0.92451	0.0:1.0:0.0:0.0	.	.	.	.	X	302;284;302;302;302	.	ENSP00000257430:R302X	R	+	1	2	APC	112179160	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.567000	0.60850	2.520000	0.84964	0.650000	0.86243	CGA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112151261	C	T	112151261	4	4	79	1	0	0	0	0	0	1	0	0	763	876	31	1	934	1	APC	5	112151261	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	92667735	112151261	68763999	18	23115										
APC	324	broad.mit.edu	37	chr5	112175255	112175255	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cagctgaagatcctgtgagcGaagttccagcagtgtcacag	12	10	1	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr5:112175255G>T	ENST00000457016.1	+	16	4344	c.3964G>T	c.(3964-3966)Gaa>Taa	p.E1322*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1322*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1322*			P25054	APC_HUMAN	adenomatous polyposis coli	1322	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1322*(16)|p.E1322fs*8(2)|p.?(1)|p.K1192fs*3(1)|p.V1320fs*8(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCCTGTGAGCGAAGTTCCAGC	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	22	Substitution - Nonsense(16)|Deletion - Frameshift(5)|Unknown(1)	large_intestine(20)|soft_tissue(1)|skin(1)	5											60	62	61					5																	112175255		2202	4300	6502	112203154	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3964G>T	5.37:g.112175255G>T	ENSP00000413133:p.Glu1322*		112203154	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	38	6.792240	0.97841	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	5.16	0.70880	.	0.282778	0.39475	N	0.001354	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.9003	15.0118	0.71555	0.0685:0.0:0.9315:0.0	.	.	.	.	X	1322	.	.	E	+	1	0	APC	112203154	1.000000	0.71417	0.996000	0.52242	0.469000	0.32828	4.886000	0.63149	1.566000	0.49654	0.655000	0.94253	GAA		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175255	G	T	112175255	4	4	79	1	0	0	0	0	0	1	0	0	763	1059	37	2	4022	2	APC	5	112175255	Nonsense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	23994	112175255	68740005	19	23116										
ODZ2	57451	broad.mit.edu	37	chr5	167420159	167420159	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gccattgccgcggccctcctCttggctattttgctggcgta	11	14	1	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr5:167420159C>A	ENST00000518659.1	+	5	1197	c.1158C>A	c.(1156-1158)ctC>ctA	p.L386L	TENM2_ENST00000520394.1_Silent_p.L195L|TENM2_ENST00000545108.1_Silent_p.L386L|TENM2_ENST00000519204.1_Silent_p.L265L|TENM2_ENST00000403607.2_Silent_p.L219L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	386					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.L219L(1)|p.L386L(1)									CGGCCCTCCTCTTGGCTATTT	0.527																																																2	Substitution - coding silent(2)	large_intestine(2)	5											41	42	42					5																	167420159		1921	4121	6042	167352737	SO:0001819	synonymous_variant	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1158C>A	5.37:g.167420159C>A			167352737	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																					0.527	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167420159	C	A	167420159	2	1	79	1	0	0	0	0	0	0	0	1	10866	900	32	2		2	ODZ2	5	167420159	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	55244904	167420159	13495101	20	23117										
UIMC1	51720	broad.mit.edu	37	chr5	176396700	176396700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tagcggaagcatcagaaggcCggcaactctgaaacaagtga	12	9	2	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr5:176396700C>T	ENST00000377227.4	-	5	497	c.365G>A	c.(364-366)cGg>cAg	p.R122Q	UIMC1_ENST00000511320.1_Missense_Mutation_p.R122Q|UIMC1_ENST00000377219.2_Missense_Mutation_p.R122Q|UIMC1_ENST00000503273.1_5'Flank|UIMC1_ENST00000506128.1_Missense_Mutation_p.R122Q			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	122	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)	p.R122Q(2)		NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCAGAAGGCCGGCAACTCTG	0.498																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	5											103	99	100					5																	176396700		2203	4300	6503	176329306	SO:0001583	missense	51720			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.365G>A	5.37:g.176396700C>T	ENSP00000366434:p.Arg122Gln		176329306	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	C	9.257	1.042222	0.19748	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000509236	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.64	2.47	0.30058	Ubiquitin interacting motif (1);	0.486110	0.19314	N	0.117319	T	0.16471	0.0396	N	0.19112	0.55	0.46542	D	0.999096	B	0.21147	0.052	B	0.08055	0.003	T	0.06625	-1.0816	10	0.26408	T	0.33	0.0817	7.2125	0.25941	0.0:0.6133:0.0:0.3867	.	122	Q96RL1	UIMC1_HUMAN	Q	122;122;122;122;44;122	ENSP00000366434:R122Q;ENSP00000366425:R122Q;ENSP00000421926:R122Q;ENSP00000427480:R122Q;ENSP00000423885:R122Q	ENSP00000366425:R122Q	R	-	2	0	UIMC1	176329306	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.491000	0.22419	0.747000	0.32809	-0.258000	0.10820	CGG		0.498	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		T	176396700	C	T	176396700	3	4	79	1	0	0	0	0	1	0	0	0	17011	652	23	1	1838	1	UIMC1	5	176396700	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	8976541	176396700	4518560	21	23118										
OR12D3	81797	broad.mit.edu	37	chr6	29342571	29342571	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gtttctgagagccacaaaaaCtcaggtgtgcagtcatgaca	10	9	3	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:29342571C>A	ENST00000396806.3	-	1	497	c.494G>T	c.(493-495)aGt>aTt	p.S165I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S165I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						GCCACAAAAACTCAGGTGTGC	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											77	77	77					6																	29342571		1510	2709	4219	29450550	SO:0001583	missense	81797				CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.494G>T	6.37:g.29342571C>A	ENSP00000380023:p.Ser165Ile		29450550	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.236886	0.22711	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.00084	8.75	4.18	-7.04	0.01578	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	M	0.75884	2.315	0.09310	N	1	P	0.41498	0.752	P	0.45474	0.482	T	0.13124	-1.0521	9	0.59425	D	0.04	-0.494	9.0382	0.36300	0.0:0.1499:0.4681:0.382	.	165	Q9UGF7	O12D3_HUMAN	I	165	ENSP00000380023:S165I	ENSP00000366348:S165I	S	-	2	0	OR12D3	29450550	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.564000	0.05936	-0.942000	0.03695	0.195000	0.17529	AGT		0.473	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			A	29342571	C	A	29342571	3	1	79	1	0	0	0	0	1	0	0	0	10963	565	20	2	460	2	OR12D3	6	29342571	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		29342571	141772496	22	23119										
VARS2	57176	broad.mit.edu	37	chr6	30889937	30889937	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cccctgtcacttttggaaacGggcagcgaccttctgctgtt	10	13	2	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:30889937G>A	ENST00000321897.5	+	19	2483	c.1851G>A	c.(1849-1851)acG>acA	p.T617T	VARS2_ENST00000416670.2_Silent_p.T617T|VARS2_ENST00000541562.1_Silent_p.T647T|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.T477T			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	617					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)	p.T617T(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TTTTGGAAACGGGCAGCGACC	0.622																																																1	Substitution - coding silent(1)	large_intestine(1)	6											98	111	106					6																	30889937		1509	2709	4218	30997916	SO:0001819	synonymous_variant	57176			AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1851G>A	6.37:g.30889937G>A			30997916	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																				0.622	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		A	30889937	G	A	30889937	2	1	79	1	0	0	0	0	0	0	0	1	17164	1103	39	1		1	VARS2	6	30889937	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	1547366	30889937	140225130	23	23120										
ZNF292	23036	broad.mit.edu	37	chr6	87970070	87970070	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gttcatctagaggcagaccaCgggattggactaagggcaag	14	8	2	2	rs367626971	byFrequency	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:87970070C>T	ENST00000369577.3	+	8	6766	c.6723C>T	c.(6721-6723)caC>caT	p.H2241H	ZNF292_ENST00000339907.4_Silent_p.H2236H	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2241						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.H2241H(1)|p.H2096H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AGGCAGACCACGGGATTGGAC	0.423													C|||	60	0.0119808	0	0	5008	,	,		20938	0		0	False		,,,				2504	0.0613															2	Substitution - coding silent(2)	large_intestine(2)	6											93	91	92					6																	87970070		1893	4120	6013	88026789	SO:0001819	synonymous_variant	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6723C>T	6.37:g.87970070C>T			88026789	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	37	CCDS47457.1																																																																																				0.423	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		T	87970070	C	T	87970070	2	4	79	1	0	0	0	0	0	0	0	1	17865	535	19	1		1	ZNF292	6	87970070	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	57080133	87970070	83144997	24	23121										
TAAR6	319100	broad.mit.edu	37	chr6	132891469	132891469	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	aataacagcgttatgagcagCaattcatccctgctggtggc	10	10	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:132891469C>A	ENST00000275198.1	+	1	9	c.9C>A	c.(7-9)agC>agA	p.S3R		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	3					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.S3R(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		TTATGAGCAGCAATTCATCCC	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	6											80	77	78					6																	132891469		2203	4300	6503	132933162	SO:0001583	missense	319100			AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"GPCR / Class A : Trace amine associated receptors"	20978	protein-coding gene	gene with protein product		608923	"trace amine receptor 4"	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.9C>A	6.37:g.132891469C>A	ENSP00000275198:p.Ser3Arg		132933162	Q5VUQ4	Missense_Mutation	SNP	ENST00000275198.1	37	CCDS5155.1	.	.	.	.	.	.	.	.	.	.	C	10.51	1.370995	0.24771	.	.	ENSG00000146383	ENST00000275198	T	0.62364	0.03	5.01	-1.13	0.09775	.	0.663319	0.13676	U	0.370542	T	0.21307	0.0513	L	0.38531	1.155	0.09310	N	1	B	0.15930	0.015	B	0.15484	0.013	T	0.17806	-1.0357	10	0.30854	T	0.27	0.2753	2.7874	0.05377	0.1268:0.2432:0.1243:0.5058	.	3	Q96RI8	TAAR6_HUMAN	R	3	ENSP00000275198:S3R	ENSP00000275198:S3R	S	+	3	2	TAAR6	132933162	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.060000	0.11712	-0.480000	0.06803	-0.222000	0.12452	AGC		0.468	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067		A	132891469	C	A	132891469	3	1	79	1	0	0	0	0	1	0	0	0	15531	709	25	2	11	2	TAAR6	6	132891469	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	44921399	132891469	38223598	25	23122										
GRM1	2911	broad.mit.edu	37	chr6	146720509	146720509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttcaagacccgcaacgtgccCgccaacttcaacgaggccaa	8	16	2	1	rs138085475		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:146720509C>T	ENST00000282753.1	+	7	2569	c.2334C>T	c.(2332-2334)ccC>ccT	p.P778P	GRM1_ENST00000355289.4_Silent_p.P778P|GRM1_ENST00000392299.2_Silent_p.P778P|GRM1_ENST00000492807.2_Silent_p.P778P|GRM1_ENST00000361719.2_Silent_p.P778P|GRM1_ENST00000507907.1_Silent_p.P778P			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	778					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.P778P(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCAACGTGCCCGCCAACTTCA	0.507													C|||	1	0.000199681	8e-04	0	5008	,	,		22282	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	6						C	,	0,4406		0,0,2203	160	140	147		2334,2334	3.8	1	6	dbSNP_134	147	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	GRM1	NM_000838.3,NM_001114329.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	778/1195,778/907	146720509	1,13005	2203	4300	6503	146762202	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2334C>T	6.37:g.146720509C>T			146762202	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																				0.507	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146720509	C	T	146720509	2	4	79	1	0	0	0	0	0	0	0	1	6817	639	23	1		1	GRM1	6	146720509	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	13829040	146720509	24394558	26	23123										
FNDC1	84624	broad.mit.edu	37	chr6	159670205	159670205	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttgatctggctggaaggaaaCgatttgttggtaaatataat	11	3	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr6:159670205C>T	ENST00000297267.9	+	16	5025	c.4825C>T	c.(4825-4827)Cga>Tga	p.R1609*	FNDC1_ENST00000340366.6_Nonsense_Mutation_p.R1546*	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1609					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1609*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGGAAGGAAACGATTTGTTGG	0.443																																																1	Substitution - Nonsense(1)	large_intestine(1)	6											38	39	39					6																	159670205		1893	4112	6005	159590195	SO:0001587	stop_gained	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4825C>T	6.37:g.159670205C>T	ENSP00000297267:p.Arg1609*		159590195	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Nonsense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	46|46	12.160670|12.160670	0.99642|0.99642	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	.|.	.|.	.|.	5.57|5.57	2.54|2.54	0.30619|0.30619	.|.	0.152154|.	0.46145|.	D|.	0.000320|.	.|T	.|0.47544	.|0.1451	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.46005	.|-0.9222	.|3	.|.	.|.	.|.	-1.4313|-1.4313	13.1779|13.1779	0.59637|0.59637	0.5316:0.4684:0.0:0.0|0.5316:0.4684:0.0:0.0	.|.	.|.	.|.	.|.	X|M	1609;1546|1504	.|.	.|.	R|T	+|+	1|2	2|0	FNDC1|FNDC1	159590195|159590195	0.994000|0.994000	0.37717|0.37717	0.998000|0.998000	0.56505|0.56505	0.977000|0.977000	0.68977|0.68977	0.980000|0.980000	0.29513|0.29513	0.644000|0.644000	0.30656|0.30656	0.650000|0.650000	0.86243|0.86243	CGA|ACG		0.443	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159670205	C	T	159670205	4	4	79	1	0	0	0	0	0	1	0	0	5987	528	19	1	4887	1	FNDC1	6	159670205	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	12949696	159670205	11444862	27	23124										
GPR141	353345	broad.mit.edu	37	chr7	37780301	37780301	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cacatccacatgtacctcacGttcctattctatgtggtgat	6	12	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:37780301G>A	ENST00000447769.1	+	4	595	c.306G>A	c.(304-306)acG>acA	p.T102T	GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Silent_p.T102T|EPDR1_ENST00000476620.1_Intron			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T102T(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGTACCTCACGTTCCTATTCT	0.468																																																1	Substitution - coding silent(1)	large_intestine(1)	7											118	102	108					7																	37780301		2203	4300	6503	37746826	SO:0001819	synonymous_variant	353345			AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"GPCR / Class A : Orphans"	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.306G>A	7.37:g.37780301G>A			37746826	A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	37	CCDS5451.1																																																																																				0.468	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		A	37780301	G	A	37780301	2	1	79	1	0	0	0	0	0	0	0	1	6669	1132	40	1		1	GPR141	7	37780301	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		37780301	121358362	28	23125										
PON1	5444	broad.mit.edu	37	chr7	94937330	94937330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	agagttcacatacttgccatCgggtgaaatgttgattccat	9	8	1	3	rs564064745		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:94937330C>T	ENST00000222381.3	-	6	922	c.691G>A	c.(691-693)Gat>Aat	p.D231N	PON1_ENST00000542556.1_Missense_Mutation_p.D231N	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	231					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.D231N(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	TACTTGCCATCGGGTGAAATG	0.358													C|||	1	0.000199681	0	0	5008	,	,		17334	0.001		0	False		,,,				2504	0				GBM(119;715 1622 17358 22490 33240)											1	Substitution - Missense(1)	large_intestine(1)	7											102	88	93					7																	94937330		2203	4300	6503	94775266	SO:0001583	missense	5444			AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"Paraoxonases"	9204	protein-coding gene	gene with protein product	"esterase A", "arylesterase 1"	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.691G>A	7.37:g.94937330C>T	ENSP00000222381:p.Asp231Asn		94775266	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.634421	0.47049	.	.	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.57907	0.37;0.37	4.95	4.95	0.65309	Six-bladed beta-propeller, TolB-like (1);	0.045394	0.85682	D	0.000000	T	0.61160	0.2325	M	0.79011	2.435	0.54753	D	0.999989	P;P	0.49447	0.907;0.924	B;P	0.45276	0.343;0.475	T	0.66468	-0.5916	10	0.46703	T	0.11	-28.2714	18.7584	0.91840	0.0:1.0:0.0:0.0	.	231;231	F5H4W9;P27169	.;PON1_HUMAN	N	231	ENSP00000222381:D231N;ENSP00000444854:D231N	ENSP00000222381:D231N	D	-	1	0	PON1	94775266	0.999000	0.42202	1.000000	0.80357	0.801000	0.45260	4.313000	0.59160	2.739000	0.93911	0.491000	0.48974	GAT		0.358	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		T	94937330	C	T	94937330	3	4	79	1	0	0	0	0	1	0	0	0	12279	884	31	1	392	1	PON1	7	94937330	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	57157029	94937330	64201333	29	23126										
AZGP1	563	broad.mit.edu	37	chr7	99569542	99569542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgtatctaaagaactggaggTcattgagtgagccaagggcc	13	7	2	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:99569542T>C	ENST00000292401.4	-	2	300	c.164A>G	c.(163-165)gAc>gGc	p.D55G	AZGP1_ENST00000411734.1_Missense_Mutation_p.D52G	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	55					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)	p.D55G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GAACTGGAGGTCATTGAGTGA	0.498																																																1	Substitution - Missense(1)	large_intestine(1)	7											110	105	107					7																	99569542		2203	4300	6503	99407478	SO:0001583	missense	563			BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"Immunoglobulin superfamily / C1-set domain containing"	910	protein-coding gene	gene with protein product		194460	"alpha-2-glycoprotein 1, zinc"			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.164A>G	7.37:g.99569542T>C	ENSP00000292401:p.Asp55Gly		99407478	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	37	CCDS5680.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.838|6.838	0.523854|0.523854	0.13066|0.13066	.|.	.|.	ENSG00000160862|ENSG00000160862	ENST00000292401;ENST00000411734|ENST00000419575	D;D|.	0.90504|.	-2.68;-2.68|.	1.51|1.51	0.291|0.291	0.15732|0.15732	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	0.244102|.	0.20964|.	U|.	0.082518|.	T|T	0.34193|0.34193	0.0889|0.0889	L|L	0.48174|0.48174	1.505|1.505	0.24090|0.24090	N|N	0.995914|0.995914	P|.	0.35411|.	0.5|.	B|.	0.35655|.	0.207|.	T|T	0.28106|0.28106	-1.0054|-1.0054	10|5	0.72032|.	D|.	0.01|.	.|.	3.4563|3.4563	0.07516|0.07516	0.0:0.2299:0.0:0.7701|0.0:0.2299:0.0:0.7701	.|.	55|.	P25311|.	ZA2G_HUMAN|.	G|A	55;52|26	ENSP00000292401:D55G;ENSP00000396093:D52G|.	ENSP00000292401:D55G|.	D|T	-|-	2|1	0|0	AZGP1|AZGP1	99407478|99407478	1.000000|1.000000	0.71417|0.71417	0.228000|0.228000	0.23943|0.23943	0.004000|0.004000	0.04260|0.04260	1.319000|1.319000	0.33655|0.33655	0.065000|0.065000	0.16485|0.16485	-0.818000|-0.818000	0.03119|0.03119	GAC|ACC		0.498	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185		C	99569542	T	C	99569542	3	2	79	1	0	0	0	0	1	0	0	0	1240	1667	58	4	744	4	AZGP1	7	99569542	Missense_Mutation	SNP	T	TCGA-AG-A032-01A-01W-A00E-09	4632212	99569542	59569121	30	23127										
CCDC136	64753	broad.mit.edu	37	chr7	128457890	128457890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tctcggctttgctctggtgcTggtgggctgagacgtcgtcc	15	11	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:128457890T>C	ENST00000297788.4	+	17	3809	c.3442T>C	c.(3442-3444)Tgg>Cgg	p.W1148R	CCDC136_ENST00000378685.4_Missense_Mutation_p.W428R|CCDC136_ENST00000471729.1_Intron|CCDC136_ENST00000464832.1_Missense_Mutation_p.W440R|CCDC136_ENST00000487361.1_Missense_Mutation_p.W509R	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1148						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.W1148R(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						GCTCTGGTGCTGGTGGGCTGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	7											255	255	255					7																	128457890		2128	4235	6363	128245126	SO:0001583	missense	64753				CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.3442T>C	7.37:g.128457890T>C	ENSP00000297788:p.Trp1148Arg		128245126	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	37	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694945	0.68386	.	.	ENSG00000128596	ENST00000378685;ENST00000464832;ENST00000487361;ENST00000297788	T;T;T;T	0.53857	0.71;0.67;0.6;0.71	4.9	4.9	0.64082	.	0.252110	0.36374	N	0.002627	T	0.67702	0.2921	M	0.64997	1.995	0.33031	D	0.530123	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.997	T	0.77335	-0.2626	10	0.87932	D	0	.	11.201	0.48741	0.0:0.0:0.0:1.0	.	509;1148;428	C9JE17;Q96JN2;Q96JN2-3	.;CC136_HUMAN;.	R	428;440;509;1148	ENSP00000367956:W428R;ENSP00000419515:W440R;ENSP00000420509:W509R;ENSP00000297788:W1148R	ENSP00000297788:W1148R	W	+	1	0	CCDC136	128245126	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.141000	0.64814	1.958000	0.56883	0.459000	0.35465	TGG		0.562	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		C	128457890	T	C	128457890	3	2	79	1	0	0	0	0	1	0	0	0	2776	1580	55	4	3508	4	CCDC136	7	128457890	Missense_Mutation	SNP	T	TCGA-AG-A032-01A-01W-A00E-09	28888348	128457890	30680773	31	23128										
WEE2	494551	broad.mit.edu	37	chr7	141408825	141408825	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	actccagtgtcacaccctctCaaatgtcctgagacaccagc	6	16	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:141408825C>T	ENST00000397541.2	+	1	673	c.267C>T	c.(265-267)ctC>ctT	p.L89L	WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000462383.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	89					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.L89L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					CACACCCTCTCAAATGTCCTG	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)	7											127	124	125					7																	141408825		1954	4169	6123	141055294	SO:0001819	synonymous_variant	494551			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.267C>T	7.37:g.141408825C>T			141055294		Silent	SNP	ENST00000397541.2	37	CCDS43660.1																																																																																				0.522	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		T	141408825	C	T	141408825	2	4	79	1	0	0	0	0	0	0	0	1	17385	813	29	3		3	WEE2	7	141408825	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	12950935	141408825	17729838	32	23129										
ESYT2	57488	broad.mit.edu	37	chr7	158534259	158534259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gcagctcctgggtggcgatgGgcagcgagatgtccgaggcg	19	10	0	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr7:158534259G>A	ENST00000251527.5	-	17	2269	c.2204C>T	c.(2203-2205)cCc>cTc	p.P735L	ESYT2_ENST00000435514.2_Missense_Mutation_p.P170L	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	763					endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.P735L(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GGTGGCGATGGGCAGCGAGAT	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	7											54	51	52					7																	158534259		2203	4300	6503	158227020	SO:0001583	missense	57488			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2204C>T	7.37:g.158534259G>A	ENSP00000251527:p.Pro735Leu		158227020	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.22|18.22	3.576772|3.576772	0.65878|0.65878	.|.	.|.	ENSG00000117868|ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514;ENST00000377650|ENST00000429474	T;T;T|.	0.22945|.	1.93;1.93;2.36|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.70640|0.70640	0.3247|0.3247	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	P;B|.	0.37233|.	0.588;0.368|.	B;B|.	0.43274|.	0.224;0.414|.	T|T	0.68458|0.68458	-0.5403|-0.5403	10|7	0.17369|0.37606	T|T	0.5|0.19	-18.3444|-18.3444	17.885|17.885	0.88851|0.88851	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	735;763|.	A0FGR8-2;A0FGR8|.	.;ESYT2_HUMAN|.	L|S	735;784;726;170;170|518	ENSP00000251527:P735L;ENSP00000275418:P726L;ENSP00000411488:P170L|.	ENSP00000251527:P735L|ENSP00000395865:P518S	P|P	-|-	2|1	0|0	ESYT2|ESYT2	158227020|158227020	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.684000|0.684000	0.39900|0.39900	9.357000|9.357000	0.97099|0.97099	2.541000|2.541000	0.85698|0.85698	0.655000|0.655000	0.94253|0.94253	CCC|CCA		0.637	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		A	158534259	G	A	158534259	3	1	79	1	0	0	0	0	1	0	0	0	5278	1232	43	3	501	3	ESYT2	7	158534259	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	17125434	158534259	604404	33	23130										
SORBS3	10174	broad.mit.edu	37	chr8	22414313	22414313	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gcctcccagcacacccagaaCtggtcagccacgtggaccaa	9	17	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr8:22414313C>G	ENST00000240123.7	+	4	689	c.306C>G	c.(304-306)aaC>aaG	p.N102K	SORBS3_ENST00000523402.1_Missense_Mutation_p.N102K	NM_005775.4	NP_005766.3	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3	102					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.N102K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)	18		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		ACACCCAGAACTGGTCAGCCA	0.642																																																1	Substitution - Missense(1)	large_intestine(1)	8											88	73	78					8																	22414313		2203	4300	6503	22470258	SO:0001583	missense	10174				CCDS6031.1	8p21.3	2008-02-05			ENSG00000120896	ENSG00000120896			30907	protein-coding gene	gene with protein product		610795				9885244, 12510380	Standard	NM_001018003		Approved	SCAM-1, SH3D4, vinexin	uc003xbv.3	O60504	OTTHUMG00000131728	ENST00000240123.7:c.306C>G	8.37:g.22414313C>G	ENSP00000240123:p.Asn102Lys		22470258	Q5BJE4|Q6NX54|Q96FY4|Q9UQE4	Missense_Mutation	SNP	ENST00000240123.7	37	CCDS6031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.16|14.16	2.453242|2.453242	0.43531|0.43531	.|.	.|.	ENSG00000120896|ENSG00000120896	ENST00000520563;ENST00000524057|ENST00000240123;ENST00000523402	.|T	.|0.07114	.|3.22	4.88|4.88	3.99|3.99	0.46301|0.46301	.|.	.|0.456399	.|0.18239	.|N	.|0.147318	T|T	0.06005|0.06005	0.0156|0.0156	N|N	0.17082|0.17082	0.46|0.46	0.80722|0.80722	D|D	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.09377	.|0.004	T|T	0.31696|0.31696	-0.9934|-0.9934	5|10	.|0.38643	.|T	.|0.18	-12.8834|-12.8834	11.2415|11.2415	0.48972|0.48972	0.0:0.8147:0.1853:0.0|0.0:0.8147:0.1853:0.0	.|.	.|102	.|O60504	.|VINEX_HUMAN	V|K	57;39|102	.|ENSP00000240123:N102K	.|ENSP00000240123:N102K	L|N	+|+	1|3	2|2	SORBS3|SORBS3	22470258|22470258	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	0.863000|0.863000	0.27913|0.27913	1.020000|1.020000	0.39573|0.39573	0.650000|0.650000	0.86243|0.86243	CTG|AAC		0.642	SORBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254647.3	NM_005775		G	22414313	C	G	22414313	3	3	79	1	0	0	0	0	1	0	0	0	14966	564	20	5	316	5	SORBS3	8	22414313	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		22414313	123949709	34	23131										
KIAA1967	57805	broad.mit.edu	37	chr8	22473349	22473349	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cctagaacctgctgtcatcgCacgccctggctgtgtaaacc	9	15	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr8:22473349C>A	ENST00000308511.4	+	13	1781	c.1532C>A	c.(1531-1533)gCa>gAa	p.A511E	CCAR2_ENST00000520861.1_Missense_Mutation_p.A186E|CCAR2_ENST00000389279.3_Missense_Mutation_p.A511E|RP11-582J16.5_ENST00000521025.1_RNA			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	511					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)	p.A511E(1)									GCTGTCATCGCACGCCCTGGC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8											86	94	91					8																	22473349		2203	4300	6503	22529294	SO:0001583	missense	57805			AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1532C>A	8.37:g.22473349C>A	ENSP00000310670:p.Ala511Glu		22529294	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.3|23.3	4.400672|4.400672	0.83120|0.83120	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.39406|.	1.18;1.18;1.08|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.211578|.	0.38959|.	N|.	0.001514|.	T|T	0.74405|0.74405	0.3712|0.3712	M|M	0.67397|0.67397	2.05|2.05	0.35553|0.35553	D|D	0.804059|0.804059	D;D|.	0.71674|.	0.998;0.996|.	D;P|.	0.67382|.	0.951;0.895|.	T|T	0.77330|0.77330	-0.2628|-0.2628	10|5	0.27082|.	T|.	0.32|.	-14.8773|-14.8773	18.1378|18.1378	0.89627|0.89627	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	186;511|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	E|N	511;511;186|203	ENSP00000310670:A511E;ENSP00000373930:A511E;ENSP00000429773:A186E|.	ENSP00000310670:A511E|.	A|H	+|+	2|1	0|0	KIAA1967|KIAA1967	22529294|22529294	0.997000|0.997000	0.39634|0.39634	0.424000|0.424000	0.26647|0.26647	0.967000|0.967000	0.64934|0.64934	3.865000|3.865000	0.56033|0.56033	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GCA|CAC		0.577	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22473349	C	A	22473349	3	1	79	1	0	0	0	0	1	0	0	0	8286	710	25	2	1578	2	KIAA1967	8	22473349	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	59036	22473349	123890673	35	23132										
CNBD1	168975	broad.mit.edu	37	chr8	88364008	88364008	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttataggatttgtgaaactaCgatcaaataaagtggtaagt	9	3	1	1	rs75840995	byFrequency	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr8:88364008C>T	ENST00000518476.1	+	9	1189	c.1138C>T	c.(1138-1140)Cga>Tga	p.R380*		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	380								p.R380*(2)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TGTGAAACTACGATCAAATAA	0.284													C|||	2	0.000399361	0	0	5008	,	,		14048	0.001		0.001	False		,,,				2504	0															2	Substitution - Nonsense(2)	large_intestine(2)	8											66	62	63					8																	88364008		1795	4034	5829	88433124	SO:0001587	stop_gained	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1138C>T	8.37:g.88364008C>T	ENSP00000430073:p.Arg380*		88433124		Nonsense_Mutation	SNP	ENST00000518476.1	37	CCDS55259.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.98	3.927408	0.73327	.	.	ENSG00000176571	ENST00000518476	.	.	.	5.22	1.26	0.21427	.	1.332330	0.05197	N	0.504149	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-0.1799	2.3862	0.04366	0.1534:0.5309:0.1489:0.1668	.	.	.	.	X	380	.	ENSP00000430073:R380X	R	+	1	2	CNBD1	88433124	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.073000	0.14640	-0.062000	0.13088	-0.324000	0.08512	CGA		0.284	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		T	88364008	C	T	88364008	4	4	79	1	0	0	0	0	0	1	0	0	3597	528	19	1	1172	1	CNBD1	8	88364008	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	65890659	88364008	58000014	36	23133										
NFX1	4799	broad.mit.edu	37	chr9	33311154	33311154	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ccctgcctttatgacaaaaaCatgtgaatgtggacgaacca	8	10	0	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr9:33311154C>A	ENST00000379540.3	+	6	1489	c.1427C>A	c.(1426-1428)aCa>aAa	p.T476K	NFX1_ENST00000318524.6_Missense_Mutation_p.T476K|NFX1_ENST00000379521.4_Missense_Mutation_p.T476K	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	476					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T476K(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATGACAAAAACATGTGAATGT	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	9											149	145	146					9																	33311154		2203	4300	6503	33301154	SO:0001583	missense	4799			U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1427C>A	9.37:g.33311154C>A	ENSP00000368856:p.Thr476Lys		33301154	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	37	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067052	0.36470	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.31769	1.48;1.48;1.48	5.56	5.56	0.83823	.	0.237466	0.43416	D	0.000568	T	0.22781	0.0550	N	0.20685	0.6	0.41867	D	0.990256	B;B;B;B;B	0.19331	0.035;0.021;0.0;0.004;0.001	B;B;B;B;B	0.20184	0.028;0.007;0.001;0.009;0.007	T	0.04885	-1.0920	10	0.23891	T	0.37	.	17.094	0.86630	0.0:1.0:0.0:0.0	.	476;360;476;476;476	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	K	476	ENSP00000368856:T476K;ENSP00000368836:T476K;ENSP00000317695:T476K	ENSP00000317695:T476K	T	+	2	0	NFX1	33301154	0.970000	0.33590	0.913000	0.36048	0.907000	0.53573	2.992000	0.49417	2.629000	0.89072	0.644000	0.83932	ACA		0.418	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			A	33311154	C	A	33311154	3	1	79	1	0	0	0	0	1	0	0	0	10418	478	17	2	1449	2	NFX1	9	33311154	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		33311154	107902277	37	23134										
KIAA1529	100499483	broad.mit.edu	37	chr9	100122345	100122346	+	Missense_Mutation	DNP	AG	AG	CT													0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ggattcagtaccttaactgcAgcctggacagggtgtccatg							TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr9:100122345_100122346AG>CT	ENST00000357054.1	+	37	4425_4426	c.3490_3491AG>CT	c.(3490-3492)AGc>CTc	p.S1164L	RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.S1193L|CCDC180_ENST00000375202.2_Missense_Mutation_p.S1193L|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1164						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.S1164>?(1)									CCTTAACTGCAGCCTGGACAGG	0.525																																																1	Complex(1)	large_intestine(1)	9																																								99162167	SO:0001583	missense	57653			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	Exception_encountered	9.37:g.100122345_100122346delinsCT	ENSP00000349562:p.Ser1164Leu		99162166	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	DNP	ENST00000357054.1	37																																																																																					0.525	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		CT	100122346	AG	CT	100122345	3	2	79	1	0	0	0	0	1	0	0	0	8261	188	7	4	3592	4	KIAA1529	9	100122345	Missense_Mutation	DNP	AG	TCGA-AG-A032-01A-01W-A00E-09	66811191	100122345	41091086	38	23135										
SVEP1	79987	broad.mit.edu	37	chr9	113191540	113191540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tcactggttcacacacaggaGgggaatgactccaagaactg	11	10	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr9:113191540G>A	ENST00000401783.2	-	35	6026	c.5690C>T	c.(5689-5691)cCt>cTt	p.P1897L	SVEP1_ENST00000297826.5_5'Flank|SVEP1_ENST00000374469.1_Missense_Mutation_p.P1874L	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1897	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.P1900L(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACACACAGGAGGGGAATGACT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	9											44	42	43					9																	113191540		1846	4095	5941	112231361	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5690C>T	9.37:g.113191540G>A	ENSP00000384917:p.Pro1897Leu		112231361	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	3.303	-0.142446	0.06669	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.62639	0.01;0.01	5.17	4.24	0.50183	Complement control module (2);Sushi/SCR/CCP (3);	0.216381	0.49305	N	0.000153	T	0.45518	0.1346	N	0.26130	0.795	0.80722	D	1	B	0.13594	0.008	B	0.13407	0.009	T	0.29912	-0.9996	10	0.23302	T	0.38	.	9.6195	0.39712	0.1655:0.0:0.8344:0.0	.	1897	Q4LDE5	SVEP1_HUMAN	L	1897;1874	ENSP00000384917:P1897L;ENSP00000363593:P1874L	ENSP00000363593:P1874L	P	-	2	0	SVEP1	112231361	0.994000	0.37717	0.988000	0.46212	0.714000	0.41099	2.102000	0.41796	1.243000	0.43853	0.650000	0.86243	CCT		0.378	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113191540	G	A	113191540	3	1	79	1	0	0	0	0	1	0	0	0	15459	1000	35	3	5081	3	SVEP1	9	113191540	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	13069195	113191540	28021891	39	23136										
FRMPD2	143162	broad.mit.edu	37	chr10	49450376	49450376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tcagcaggatggagtgcaggGgctcgcagagctgcaggggc	19	9	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr10:49450376G>A	ENST00000374201.3	-	5	697	c.395C>T	c.(394-396)cCc>cTc	p.P132L	FRMPD2_ENST00000305531.3_Missense_Mutation_p.P108L|FRMPD2_ENST00000407470.4_Missense_Mutation_p.P101L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	132	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)	p.P132L(1)		NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		GGAGTGCAGGGGCTCGCAGAG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	10											55	56	56					10																	49450376		2203	4300	6503	49120382	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.395C>T	10.37:g.49450376G>A	ENSP00000363317:p.Pro132Leu		49120382	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149699	0.57151	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.28666	1.66;1.6;1.6	5.36	5.36	0.76844	KIND (2);	.	.	.	.	T	0.52629	0.1746	M	0.67953	2.075	0.39700	D	0.971165	D;D;D	0.76494	0.999;0.984;0.999	D;P;D	0.69479	0.964;0.554;0.951	T	0.57010	-0.7884	9	0.72032	D	0.01	.	14.582	0.68298	0.0:0.0:1.0:0.0	.	108;132;101	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	L	132;108;101	ENSP00000363317:P132L;ENSP00000307079:P108L;ENSP00000384339:P101L	ENSP00000307079:P108L	P	-	2	0	FRMPD2	49120382	0.988000	0.35896	0.423000	0.26634	0.559000	0.35586	2.150000	0.42254	2.513000	0.84729	0.655000	0.94253	CCC		0.617	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		A	49450376	G	A	49450376	3	1	79	1	0	0	0	0	1	0	0	0	6077	1232	43	3	3634	3	FRMPD2	10	49450376	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		49450376	86084371	40	23137										
FAM178A	55719	broad.mit.edu	37	chr10	102707604	102707604	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cctaatgccagtaatctgcaGgtataaataaatacattttt	5	7	1	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr10:102707604G>T	ENST00000238961.4	+	15	3662	c.3120G>T	c.(3118-3120)caG>caT	p.Q1040H	FAM178A_ENST00000370269.3_Splice_Site_p.Q1040H	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1040						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.Q1040H(1)									GTAATCTGCAGGtataaataa	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											54	59	58					10																	102707604		2202	4299	6501	102697594	SO:0001630	splice_region_variant	55719			AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.3120+1G>T	10.37:g.102707604G>T			102697594	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854388	0.71719	.	.	ENSG00000119906	ENST00000238961;ENST00000370269	T;T	0.39406	1.09;1.08	5.6	5.6	0.85130	.	0.145372	0.47852	D	0.000216	T	0.64283	0.2584	M	0.69823	2.125	0.51233	D	0.99991	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.66110	-0.6005	10	0.87932	D	0	-5.4997	15.4641	0.75384	0.0:0.0:1.0:0.0	.	1040;1040	Q8IX21;B1AL17	F178A_HUMAN;.	H	1040	ENSP00000238961:Q1040H;ENSP00000359292:Q1040H	ENSP00000238961:Q1040H	Q	+	3	2	FAM178A	102697594	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	5.896000	0.69822	2.793000	0.96121	0.591000	0.81541	CAG		0.373	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3		Missense_Mutation	T	102707604	G	T	102707604	5	4	79	1	0	0	0	0	0	0	1	0	5519	1014	35	2	3178	2	FAM178A	10	102707604	Splice_Site	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	53257228	102707604	32827143	41	23138										
NOLC1	9221	broad.mit.edu	37	chr10	103921966	103921966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	aaaaccaagaagaagcggggCagctaccggggaggctcaat	14	9	1	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr10:103921966C>T	ENST00000605788.1	+	13	2275	c.2040C>T	c.(2038-2040)ggC>ggT	p.G680G	NOLC1_ENST00000477977.1_Intron|NOLC1_ENST00000405356.1_Silent_p.G690G|NOLC1_ENST00000488254.2_Silent_p.G681G|NOLC1_ENST00000603742.1_Silent_p.G399G	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	680					cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)	p.G680G(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AGAAGCGGGGCAGCTACCGGG	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	10											154	173	167					10																	103921966		2203	4300	6503	103911956	SO:0001819	synonymous_variant	9221			Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.2040C>T	10.37:g.103921966C>T			103911956	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																				0.537	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		T	103921966	C	T	103921966	2	4	79	1	0	0	0	0	0	0	0	1	10560	697	25	3		3	NOLC1	10	103921966	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	1214362	103921966	31612781	42	23139										
TCF7L2	6934	broad.mit.edu	37	chr10	114912149	114912149	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	acgagctggcccggaaggagCgacagcttcatatgcaactg	13	11	1	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr10:114912149C>T	ENST00000355995.4	+	11	1726	c.1219C>T	c.(1219-1221)Cga>Tga	p.R407*	TCF7L2_ENST00000369397.4_Nonsense_Mutation_p.R384*|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000536810.1_Nonsense_Mutation_p.R407*|TCF7L2_ENST00000369389.1_Nonsense_Mutation_p.R118*|TCF7L2_ENST00000534894.1_Nonsense_Mutation_p.R407*|TCF7L2_ENST00000542695.1_Nonsense_Mutation_p.R123*|TCF7L2_ENST00000538897.1_Nonsense_Mutation_p.R407*|TCF7L2_ENST00000369386.1_Nonsense_Mutation_p.R50*|TCF7L2_ENST00000545257.1_Nonsense_Mutation_p.R407*|TCF7L2_ENST00000355717.4_Nonsense_Mutation_p.R431*|TCF7L2_ENST00000352065.5_Nonsense_Mutation_p.R384*|TCF7L2_ENST00000543371.1_Nonsense_Mutation_p.R407*			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	407					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R384*(2)|p.R407*(2)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCGGAAGGAGCGACAGCTTCA	0.527			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	4	Substitution - Nonsense(4)	large_intestine(4)	10											168	173	172					10																	114912149		2203	4300	6503	114902139	SO:0001587	stop_gained	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1219C>T	10.37:g.114912149C>T	ENSP00000348274:p.Arg407*		114902139	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Nonsense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	c	45	11.714383	0.99594	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945;ENST00000369386	.	.	.	5.66	5.66	0.87406	.	0.065778	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.2749	14.5692	0.68200	0.1461:0.8539:0.0:0.0	.	.	.	.	X	407;407;407;407;431;407;407;384;384;123;118;124;50	.	ENSP00000277945:R124X	R	+	1	2	TCF7L2	114902139	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.055000	0.49916	2.669000	0.90835	0.655000	0.94253	CGA		0.527	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114912149	C	T	114912149	4	4	79	1	0	0	0	0	0	1	0	0	15737	760	27	1	1406	1	TCF7L2	10	114912149	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	10990183	114912149	20622598	43	23140										
C10orf137	26098	broad.mit.edu	37	chr10	127408419	127408419	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gagccgagggtccgccggccGgggccgccgctcgaggaggg	21	14	0	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr10:127408419G>C	ENST00000356792.4	+	1	275	c.43G>C	c.(43-45)Ggg>Cgg	p.G15R	C10orf137_ENST00000337623.3_Missense_Mutation_p.G15R|RP11-383C5.5_ENST00000430970.1_RNA|RP11-383C5.4_ENST00000423178.2_lincRNA	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		15					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.G15R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TCCGCCGGCCGGGGCCGCCGC	0.697																																																1	Substitution - Missense(1)	large_intestine(1)	10											15	19	18					10																	127408419		2181	4271	6452	127398409	SO:0001583	missense	26098																														ENST00000356792.4:c.43G>C	10.37:g.127408419G>C	ENSP00000349244:p.Gly15Arg		127398409	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148880	0.37923	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	T;T	0.38560	1.13;1.13	4.42	4.42	0.53409	.	0.425841	0.20099	N	0.099279	T	0.23846	0.0577	N	0.08118	0	0.33666	D	0.610305	P;P;P	0.46457	0.878;0.878;0.49	B;B;B	0.37833	0.259;0.259;0.259	T	0.43750	-0.9372	10	0.66056	D	0.02	.	14.4215	0.67187	0.0:0.0:1.0:0.0	.	15;15;15	Q3B7T1;Q3B7T1-5;Q3B7T1-3	EDRF1_HUMAN;.;.	R	15	ENSP00000349244:G15R;ENSP00000336727:G15R	ENSP00000336727:G15R	G	+	1	0	C10orf137	127398409	0.407000	0.25352	0.270000	0.24601	0.085000	0.17905	3.824000	0.55723	2.447000	0.82792	0.655000	0.94253	GGG		0.697	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			C	127408419	G	C	127408419	3	2	79	1	0	0	0	0	1	0	0	0	1598	1116	39	5	45	5	C10orf137	10	127408419	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	12496270	127408419	8126328	44	23141										
C11orf41	25758	broad.mit.edu	37	chr11	33581342	33581342	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gcagtcaccttggtgtacgtCgtgggcaatcagagcacatt	12	10	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:33581342C>T	ENST00000321505.4	+	6	3192	c.3012C>T	c.(3010-3012)gtC>gtT	p.V1004V	KIAA1549L_ENST00000389726.3_Silent_p.V1010V|KIAA1549L_ENST00000265654.5_Silent_p.V1010V			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1004						integral component of membrane (GO:0016021)		p.V1010V(1)|p.V1004V(1)									TGGTGTACGTCGTGGGCAATC	0.582																																																2	Substitution - coding silent(2)	large_intestine(2)	11											101	100	100					11																	33581342		2147	4243	6390	33537918	SO:0001819	synonymous_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3012C>T	11.37:g.33581342C>T			33537918	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373908	0.24857	.	.	ENSG00000110427	ENST00000526400	.	.	.	5.42	1.19	0.21007	.	.	.	.	.	T	0.42245	0.1194	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26643	-1.0097	4	.	.	.	-5.1646	1.2122	0.01907	0.1818:0.1529:0.3623:0.303	.	.	.	.	L	402	.	.	S	+	2	0	C11orf41	33537918	0.910000	0.30920	1.000000	0.80357	0.984000	0.73092	-0.019000	0.12546	0.358000	0.24211	0.573000	0.79308	TCG		0.582	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33581342	C	T	33581342	2	4	79	1	0	0	0	0	0	0	0	1	1644	871	31	1		1	C11orf41	11	33581342	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		33581342	101425174	45	23142										
C11orf85	283129	broad.mit.edu	37	chr11	64707210	64707210	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ctgcaggggtgggacaattcGccctggcaggctgtgtcccc	15	13	0	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:64707210G>A	ENST00000301896.5	-	10	649	c.576C>T	c.(574-576)ggC>ggT	p.G192G	C11orf85_ENST00000530444.1_Nonsense_Mutation_p.R136*|C11orf85_ENST00000432175.1_Silent_p.G192G|C11orf85_ENST00000536065.1_Nonsense_Mutation_p.R108*	NM_001037225.1	NP_001032302.1	Q3KP22	CK085_HUMAN	chromosome 11 open reading frame 85	192								p.G192G(1)		breast(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	7						GGGACAATTCGCCCTGGCAGG	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)	11											81	78	79					11																	64707210		2201	4297	6498	64463786	SO:0001819	synonymous_variant	283129			AK093130, BC033501	CCDS31603.1, CCDS73316.1	11q13.1	2012-08-10			ENSG00000168070	ENSG00000168070			27441	protein-coding gene	gene with protein product						14702039	Standard	XM_005273918		Approved		uc001ocb.1	Q3KP22		ENST00000301896.5:c.576C>T	11.37:g.64707210G>A			64463786	B3KS99	Nonsense_Mutation	SNP	ENST00000301896.5	37	CCDS31603.1	.	.	.	.	.	.	.	.	.	.	G	44	11.131308	0.99520	.	.	ENSG00000168070	ENST00000532617;ENST00000530444;ENST00000536065	.	.	.	3.43	-1.21	0.09524	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-4.2001	1.7501	0.02970	0.1132:0.1633:0.3419:0.3816	.	.	.	.	X	35;136;108	.	ENSP00000434568:R136X	R	-	1	2	C11orf85	64463786	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.295000	0.19065	-0.216000	0.10048	0.563000	0.77884	CGA		0.532	C11orf85-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385477.1	NM_001037225		A	64707210	G	A	64707210	2	1	79	1	0	0	0	0	0	0	0	1	1672	1074	38	1		1	C11orf85	11	64707210	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	31125868	64707210	70299306	46	23143										
P4HA3	283208	broad.mit.edu	37	chr11	74009335	74009335	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gtcttccactctccgtaagaTcctcggaagagactgacagc	9	13	2	3			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:74009335T>C	ENST00000331597.4	-	4	684	c.639A>G	c.(637-639)ggA>ggG	p.G213G	P4HA3_ENST00000427714.2_Silent_p.G213G	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	213						endoplasmic reticulum (GO:0005783)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.G213G(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(1)	15	Breast(11;2.31e-05)					CTCCGTAAGATCCTCGGAAGA	0.498																																																1	Substitution - coding silent(1)	large_intestine(1)	11											123	111	115					11																	74009335		2200	4293	6493	73686983	SO:0001819	synonymous_variant	283208			AY327887	CCDS8230.1, CCDS73347.1	11q13	2008-12-09	2008-12-09			ENSG00000149380			30135	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(III)"	608987	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III"			14500733	Standard	XM_005273924		Approved	C-P4Halpha(III)	uc001ouz.3	Q7Z4N8		ENST00000331597.4:c.639A>G	11.37:g.74009335T>C			73686983	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Silent	SNP	ENST00000331597.4	37	CCDS8230.1																																																																																				0.498	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		C	74009335	T	C	74009335	2	2	79	1	0	0	0	0	0	0	0	1	11389	1422	50	4		4	P4HA3	11	74009335	Silent	SNP	T	TCGA-AG-A032-01A-01W-A00E-09	9302125	74009335	60997181	47	23144										
GRM5	2915	broad.mit.edu	37	chr11	88300544	88300544	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	aaggcgatatacttggcctcGttgaagttagctggaacatt	11	7	0	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:88300544G>A	ENST00000305447.4	-	7	2456	c.2307C>T	c.(2305-2307)aaC>aaT	p.N769N	GRM5_ENST00000455756.2_Silent_p.N769N|GRM5_ENST00000393297.1_Silent_p.N769N|GRM5_ENST00000305432.5_Silent_p.N769N|GRM5_ENST00000418177.2_Silent_p.N769N	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	769					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.N769N(2)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	ACTTGGCCTCGTTGAAGTTAG	0.433																																																2	Substitution - coding silent(2)	large_intestine(2)	11											190	167	175					11																	88300544		2201	4299	6500	87940192	SO:0001819	synonymous_variant	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.2307C>T	11.37:g.88300544G>A			87940192	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																				0.433	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88300544	G	A	88300544	2	1	79	1	0	0	0	0	0	0	0	1	6821	1136	40	1		1	GRM5	11	88300544	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	14291209	88300544	46705972	48	23145										
KCNJ1	3758	broad.mit.edu	37	chr11	128710019	128710019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	acaaagaatataaaccttgaCtgtgcctccacattgccaaa	5	11	0	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:128710019C>A	ENST00000392664.2	-	2	293	c.177G>T	c.(175-177)caG>caT	p.Q59H	KCNJ1_ENST00000392665.2_Missense_Mutation_p.Q40H|KCNJ1_ENST00000392666.1_Missense_Mutation_p.Q40H|KCNJ1_ENST00000440599.2_Missense_Mutation_p.Q40H|KCNJ1_ENST00000324036.3_Missense_Mutation_p.Q40H	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	59					cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.Q59H(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	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)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	TAAACCTTGACTGTGCCTCCA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	11											198	184	189					11																	128710019		2201	4297	6498	128215229	SO:0001583	missense	3758			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.177G>T	11.37:g.128710019C>A	ENSP00000376432:p.Gln59His		128215229	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.923832	0.52653	.	.	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664;ENST00000324003	D;D;D;D;D;D	0.94046	-3.34;-3.34;-3.34;-3.34;-3.34;-3.34	5.66	0.076	0.14401	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.257343	0.41294	D	0.000902	D	0.93795	0.8016	M	0.61703	1.905	0.45946	D	0.998777	P	0.43477	0.808	P	0.54312	0.748	D	0.92062	0.5657	10	0.66056	D	0.02	.	11.3338	0.49492	0.0:0.6384:0.0:0.3616	.	59	P48048	IRK1_HUMAN	H	40;40;40;40;59;40	ENSP00000376433:Q40H;ENSP00000376434:Q40H;ENSP00000406320:Q40H;ENSP00000316233:Q40H;ENSP00000376432:Q59H;ENSP00000316136:Q40H	ENSP00000316136:Q40H	Q	-	3	2	KCNJ1	128215229	0.995000	0.38212	0.410000	0.26471	0.901000	0.52897	0.471000	0.22100	0.054000	0.16065	0.455000	0.32223	CAG		0.453	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		A	128710019	C	A	128710019	3	1	79	1	0	0	0	0	1	0	0	0	8064	564	20	2	1002	2	KCNJ1	11	128710019	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	40409475	128710019	6296497	49	23146										
OPCML	4978	broad.mit.edu	37	chr11	132307179	132307179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	atcgttcaacgcgctgcattCgtactccccggactggtctc	9	15	2	0	rs148167692		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr11:132307179C>T	ENST00000331898.7	-	4	1179	c.601G>A	c.(601-603)Gaa>Aaa	p.E201K	OPCML_ENST00000374778.4_Missense_Mutation_p.E160K|OPCML_ENST00000524381.1_Missense_Mutation_p.E194K|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Missense_Mutation_p.E201K	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	201	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.E201K(2)|p.E201Q(1)|p.E194Q(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GCGCTGCATTCGTACTCCCCG	0.532																																																4	Substitution - Missense(4)	lung(2)|large_intestine(1)|skin(1)	11											107	92	97					11																	132307179		2201	4297	6498	131812389	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.601G>A	11.37:g.132307179C>T	ENSP00000330862:p.Glu201Lys		131812389	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	35	5.482640	0.96307	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.39056	1.32;1.32;1.1;1.1	5.6	5.6	0.85130	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049848	0.85682	D	0.000000	T	0.66376	0.2783	M	0.71206	2.165	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.997;0.992;0.995	T	0.68488	-0.5395	10	0.87932	D	0	-21.1241	19.225	0.93815	0.0:1.0:0.0:0.0	.	201;194;200;201	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	K	201;194;160;168;201	ENSP00000330862:E201K;ENSP00000434750:E194K;ENSP00000363910:E160K;ENSP00000445496:E201K	ENSP00000330862:E201K	E	-	1	0	OPCML	131812389	1.000000	0.71417	0.955000	0.39395	0.841000	0.47740	7.487000	0.81328	2.639000	0.89480	0.563000	0.77884	GAA		0.532	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132307179	C	T	132307179	3	4	79	1	0	0	0	0	1	0	0	0	10905	893	31	1	452	1	OPCML	11	132307179	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	3597160	132307179	2699337	50	23147										
SLC2A3	6515	broad.mit.edu	37	chr12	8083194	8083194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	atggtaaaacccagtagcagCggccatagctcttcagaccc	9	13	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:8083194C>T	ENST00000075120.7	-	5	795	c.555G>A	c.(553-555)ccG>ccA	p.P185P		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	185					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)	p.P185P(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		CCAGTAGCAGCGGCCATAGCT	0.443																																					Colon(96;424 1461 14416 20933 23688)											1	Substitution - coding silent(1)	large_intestine(1)	12											104	101	102					12																	8083194		2203	4300	6503	7974461	SO:0001819	synonymous_variant	6515			M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.555G>A	12.37:g.8083194C>T			7974461	B2R606|D3DUU6|Q6I9U2|Q9UG15	Silent	SNP	ENST00000075120.7	37	CCDS8586.1																																																																																				0.443	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		T	8083194	C	T	8083194	2	4	79	1	0	0	0	0	0	0	0	1	14582	755	27	1		1	SLC2A3	12	8083194	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		8083194	125768701	51	23148										
KRAS	3845	broad.mit.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000311936.3_Missense_Mutation_p.G12C|KRAS_ENST00000557334.1_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	12.37:g.25398285C>A	ENSP00000256078:p.Gly12Cys		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398285	C	A	25398285	3	1	79	1	0	0	0	0	1	0	0	0	8459	594	21	2	672	2	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	17315091	25398285	108453610	52	23149										
SYT10	341359	broad.mit.edu	37	chr12	33579274	33579274	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tctcaaaaacttcagtaggaGcacttgaaatgctctgtgga	9	8	3	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:33579274G>C	ENST00000228567.3	-	2	604	c.308C>G	c.(307-309)gCt>gGt	p.A103G	SYT10_ENST00000567656.1_5'Flank|SYT10_ENST00000535526.1_5'UTR	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	103					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.A103G(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TTCAGTAGGAGCACTTGAAAT	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	12											94	95	95					12																	33579274		2203	4300	6503	33470541	SO:0001583	missense	341359			AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.308C>G	12.37:g.33579274G>C	ENSP00000228567:p.Ala103Gly		33470541	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	G	7.367	0.625951	0.14257	.	.	ENSG00000110975	ENST00000228567	T	0.48836	0.8	4.1	4.1	0.47936	.	0.000000	0.41194	U	0.000940	T	0.33440	0.0863	N	0.25647	0.755	0.80722	D	1	B	0.11235	0.004	B	0.10450	0.005	T	0.11941	-1.0567	10	0.08599	T	0.76	.	16.6077	0.84835	0.0:0.0:1.0:0.0	.	103	Q6XYQ8	SYT10_HUMAN	G	103	ENSP00000228567:A103G	ENSP00000228567:A103G	A	-	2	0	SYT10	33470541	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	6.568000	0.73987	2.572000	0.86782	0.655000	0.94253	GCT		0.413	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		C	33579274	G	C	33579274	3	2	79	1	0	0	0	0	1	0	0	0	15505	971	34	5	1287	5	SYT10	12	33579274	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	8180989	33579274	100272621	53	23150										
ARID2	196528	broad.mit.edu	37	chr12	46211554	46211554	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ctggactcccaaatgaagtgGactttgctattaacgtatgc	9	9	0	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:46211554G>T	ENST00000334344.6	+	5	692	c.520G>T	c.(520-522)Gac>Tac	p.D174Y	ARID2_ENST00000422737.1_Missense_Mutation_p.D25Y	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	174					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D174Y(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAATGAAGTGGACTTTGCTAT	0.373			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)	12											101	91	94					12																	46211554		2203	4300	6503	44497821	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.520G>T	12.37:g.46211554G>T	ENSP00000335044:p.Asp174Tyr		44497821	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.6|26.6	4.757739|4.757739	0.89843|0.89843	.|.	.|.	ENSG00000189079|ENSG00000189079	ENST00000334344;ENST00000422737|ENST00000549153;ENST00000338636	T;T|.	0.51817|.	0.69;0.69|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78130|0.78130	0.4235|0.4235	M|M	0.74467|0.74467	2.265|2.265	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.80647|0.80647	-0.1289|-0.1289	10|6	0.87932|0.87932	D|D	0|0	-8.148|-8.148	19.1056|19.1056	0.93293|0.93293	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	174|.	Q68CP9|.	ARID2_HUMAN|.	Y|C	174;25|65	ENSP00000335044:D174Y;ENSP00000415650:D25Y|.	ENSP00000335044:D174Y|ENSP00000339739:W65C	D|W	+|+	1|3	0|0	ARID2|ARID2	44497821|44497821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.864000|9.864000	0.99589|0.99589	2.499000|2.499000	0.84300|0.84300	0.555000|0.555000	0.69702|0.69702	GAC|TGG		0.373	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46211554	G	T	46211554	3	4	79	1	0	0	0	0	1	0	0	0	915	1174	41	2	538	2	ARID2	12	46211554	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	12632280	46211554	87640341	54	23151										
KRT73	319101	broad.mit.edu	37	chr12	53012206	53012206	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tccactgagccctttgccccCtgctcggtaggaggatgagc	12	14	0	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:53012206C>A	ENST00000305748.3	-	1	137	c.103G>T	c.(103-105)Ggg>Tgg	p.G35W		NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	35	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.G35W(2)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTTTGCCCCCTGCTCGGTAG	0.647																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	12											50	58	55					12																	53012206		2203	4300	6503	51298473	SO:0001583	missense	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.103G>T	12.37:g.53012206C>A	ENSP00000307014:p.Gly35Trp		51298473	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.258502	0.23051	.	.	ENSG00000186049	ENST00000305748	D	0.85629	-2.01	4.43	3.54	0.40534	.	0.240552	0.28778	N	0.014170	D	0.86163	0.5867	M	0.89840	3.065	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.78607	-0.2138	10	0.48119	T	0.1	.	9.5219	0.39140	0.0:0.8177:0.0:0.1823	.	35	Q86Y46	K2C73_HUMAN	W	35	ENSP00000307014:G35W	ENSP00000307014:G35W	G	-	1	0	KRT73	51298473	0.007000	0.16637	0.060000	0.19600	0.046000	0.14306	2.187000	0.42602	1.169000	0.42739	0.655000	0.94253	GGG		0.647	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		A	53012206	C	A	53012206	3	1	79	1	0	0	0	0	1	0	0	0	8507	681	24	2	1555	2	KRT73	12	53012206	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	6800652	53012206	80839689	55	23152										
DCTN2	10540	broad.mit.edu	37	chr12	57927776	57927776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgtcctgctcaggccgagaaTgtagttcataagtgacaagg	12	8	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:57927776T>C	ENST00000548249.1	-	7	896	c.629A>G	c.(628-630)cAt>cGt	p.H210R	DCTN2_ENST00000551400.1_5'Flank|DCTN2_ENST00000543672.1_Missense_Mutation_p.H215R|DCTN2_ENST00000537439.1_Missense_Mutation_p.H187R|DCTN2_ENST00000434715.3_Missense_Mutation_p.H215R	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	210					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)	p.H215R(2)		endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						AGGCCGAGAATGTAGTTCATA	0.507																																																2	Substitution - Missense(2)	large_intestine(2)	12											117	120	119					12																	57927776		1928	4123	6051	56214043	SO:0001583	missense	10540			U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.629A>G	12.37:g.57927776T>C	ENSP00000447824:p.His210Arg		56214043	B2RBK5|Q86YN2|Q9BW17	Missense_Mutation	SNP	ENST00000548249.1	37	CCDS58245.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568378	0.86439	.	.	ENSG00000175203	ENST00000548249;ENST00000434715;ENST00000543672;ENST00000537439;ENST00000354743;ENST00000543105;ENST00000546758;ENST00000550954	.	.	.	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.64472	0.2601	L	0.60455	1.87	0.80722	D	1	D;D;D	0.55172	0.962;0.97;0.969	P;P;P	0.53954	0.67;0.738;0.666	T	0.61481	-0.7054	9	0.27082	T	0.32	-16.9276	14.5159	0.67818	0.0:0.0:0.0:1.0	.	210;215;210	F8WAG8;F5H2S7;Q13561	.;.;DCTN2_HUMAN	R	210;215;215;187;210;123;94;224	.	ENSP00000346785:H210R	H	-	2	0	DCTN2	56214043	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	5.547000	0.67249	2.326000	0.78906	0.533000	0.62120	CAT		0.507	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400		C	57927776	T	C	57927776	3	2	79	1	0	0	0	0	1	0	0	0	4313	1464	51	4	608	4	DCTN2	12	57927776	Missense_Mutation	SNP	T	TCGA-AG-A032-01A-01W-A00E-09	4915570	57927776	75924119	56	23153										
EEA1	8411	broad.mit.edu	37	chr12	93213269	93213269	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cttatcgccaatttgacgtaGaacttgttccaaatcattct	5	10	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:93213269G>C	ENST00000322349.8	-	14	1807	c.1543C>G	c.(1543-1545)Cta>Gta	p.L515V		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	515	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.L515V(1)		endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						ATTTGACGTAGAACTTGTTCC	0.279																																																1	Substitution - Missense(1)	large_intestine(1)	12											40	40	40					12																	93213269		2201	4300	6501	91737400	SO:0001583	missense	8411			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.1543C>G	12.37:g.93213269G>C	ENSP00000317955:p.Leu515Val		91737400	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.687787	0.48097	.	.	ENSG00000102189	ENST00000322349	T	0.77750	-1.12	5.55	2.67	0.31697	.	0.000000	0.41194	D	0.000940	T	0.78691	0.4323	L	0.36672	1.1	0.46927	D	0.999252	D	0.69078	0.997	D	0.72625	0.978	T	0.74572	-0.3621	10	0.30078	T	0.28	.	8.7735	0.34747	0.2916:0.0:0.7084:0.0	.	515	Q15075	EEA1_HUMAN	V	515	ENSP00000317955:L515V	ENSP00000317955:L515V	L	-	1	2	EEA1	91737400	0.982000	0.34865	0.997000	0.53966	0.960000	0.62799	1.717000	0.37991	1.327000	0.45338	0.460000	0.39030	CTA		0.279	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		C	93213269	G	C	93213269	3	2	79	1	0	0	0	0	1	0	0	0	4932	933	33	5	2756	5	EEA1	12	93213269	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	35285493	93213269	40638626	57	23154										
ANAPC5	51433	broad.mit.edu	37	chr12	121789949	121789949	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cctctcacctgcagcaggggCaggagcagctggttgagcct	14	13	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr12:121789949C>T	ENST00000261819.3	-	1	316	c.195G>A	c.(193-195)ctG>ctA	p.L65L	ANAPC5_ENST00000541887.1_Silent_p.L65L	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	65					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.L65L(1)		breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GCAGCAGGGGCAGGAGCAGCT	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	12											29	29	29					12																	121789949		2201	4295	6496	120274332	SO:0001819	synonymous_variant	51433			AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.195G>A	12.37:g.121789949C>T			120274332	E9PFB2|Q8N4H7|Q9BQD4	Silent	SNP	ENST00000261819.3	37	CCDS9220.1																																																																																				0.647	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			T	121789949	C	T	121789949	2	4	79	1	0	0	0	0	0	0	0	1	605	697	25	3		3	ANAPC5	12	121789949	Silent	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	28576680	121789949	12061946	58	23155										
NDRG2	57447	broad.mit.edu	37	chr14	21489993	21489993	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cactttaggtactgcaggacGcaagggatcatgtctgcaag	12	9	2	0	rs370648416		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr14:21489993G>A	ENST00000556147.1	-	6	1330	c.390C>T	c.(388-390)tgC>tgT	p.C130C	NDRG2_ENST00000360463.3_Silent_p.C116C|NDRG2_ENST00000298687.5_Silent_p.C130C|NDRG2_ENST00000350792.3_Silent_p.C116C|NDRG2_ENST00000554143.1_Silent_p.C116C|NDRG2_ENST00000554277.1_5'Flank|NDRG2_ENST00000397858.1_Silent_p.C130C|NDRG2_ENST00000397853.3_Silent_p.C130C|NDRG2_ENST00000397847.2_Silent_p.C130C|NDRG2_ENST00000555158.1_Silent_p.C116C|NDRG2_ENST00000298684.5_Silent_p.C116C|NDRG2_ENST00000397855.3_Silent_p.C116C|NDRG2_ENST00000553503.1_Silent_p.C116C|NDRG2_ENST00000403829.3_Silent_p.C126C|NDRG2_ENST00000397856.3_Silent_p.C116C|NDRG2_ENST00000554104.1_Silent_p.C43C|AL161668.5_ENST00000533984.1_lincRNA|NDRG2_ENST00000397851.2_Silent_p.C130C|NDRG2_ENST00000397844.2_Silent_p.C116C			Q9UN36	NDRG2_HUMAN	NDRG family member 2	130					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)		p.C130C(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		ACTGCAGGACGCAAGGGATCA	0.527																																																1	Substitution - coding silent(1)	large_intestine(1)	14						G	,,,,,,,	0,4406		0,0,2203	102	94	96		348,390,348,390,348,390,390,348	2.7	1	14		96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG2	NM_016250.2,NM_201535.1,NM_201536.1,NM_201537.1,NM_201538.1,NM_201539.1,NM_201540.1,NM_201541.1	,,,,,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,,,,,	116/358,130/372,116/358,130/372,116/358,130/372,130/372,116/358	21489993	2,13004	2203	4300	6503	20559833	SO:0001819	synonymous_variant	57447			AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.390C>T	14.37:g.21489993G>A			20559833	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	Silent	SNP	ENST00000556147.1	37	CCDS9565.1																																																																																				0.527	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1			A	21489993	G	A	21489993	2	1	79	1	0	0	0	0	0	0	0	1	10283	1079	38	1		1	NDRG2	14	21489993	Silent	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		21489993	85859547	59	23156										
MESDC2	23184	broad.mit.edu	37	chr15	81274364	81274364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttcctctgtctccttctcagTagggcttcctgatacagtga	8	12	3	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr15:81274364T>C	ENST00000261758.4	-	2	459	c.373A>G	c.(373-375)Act>Gct	p.T125A		NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	125	Chaperone domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)		p.T125A(1)		cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						TCCTTCTCAGTAGGGCTTCCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	15											139	118	125					15																	81274364		2203	4300	6503	79061419	SO:0001583	missense	23184			D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.373A>G	15.37:g.81274364T>C	ENSP00000261758:p.Thr125Ala		79061419	B4DW84|D3DW96|Q969U1	Missense_Mutation	SNP	ENST00000261758.4	37	CCDS32308.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861125	0.71949	.	.	ENSG00000117899	ENST00000261758	.	.	.	5.13	5.13	0.70059	.	0.104629	0.64402	D	0.000004	T	0.66665	0.2812	M	0.61703	1.905	0.80722	D	1	P	0.47409	0.895	P	0.51974	0.686	T	0.71045	-0.4706	9	0.72032	D	0.01	-1.7563	14.9677	0.71208	0.0:0.0:0.0:1.0	.	125	Q14696	MESD_HUMAN	A	125	.	ENSP00000261758:T125A	T	-	1	0	MESDC2	79061419	1.000000	0.71417	0.932000	0.37286	0.541000	0.35023	5.935000	0.70145	1.932000	0.55993	0.533000	0.62120	ACT		0.463	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		C	81274364	T	C	81274364	3	2	79	1	0	0	0	0	1	0	0	0	9511	1638	57	4	339	4	MESDC2	15	81274364	Missense_Mutation	SNP	T	TCGA-AG-A032-01A-01W-A00E-09		81274364	21257028	60	23157										
CHD2	1106	broad.mit.edu	37	chr15	93567803	93567804	+	Missense_Mutation	DNP	AG	AG	TT													0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ccattgcaccctgcagtctcAgatcctcgctcacccccttc							TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr15:93567803_93567804AG>TT	ENST00000394196.4	+	39	6423_6424	c.5355_5356AG>TT	c.(5353-5358)tcAGat>tcTTat	p.D1786Y		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1786					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CTGCAGTCTCAGATCCTCGCTC	0.515																																																0			15																																								91368808	SO:0001583	missense	1106			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	Exception_encountered	15.37:g.93567803_93567804delinsTT	ENSP00000377747:p.Asp1786Tyr		91368807	C6G482|Q96IP5	Missense_Mutation	DNP	ENST00000394196.4	37	CCDS10374.2																																																																																				0.515	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		TT	93567804	AG	TT	93567803	3	4	79	1	0	0	0	0	1	0	0	0	3331	175	7	5	5509	5	CHD2	15	93567803	Missense_Mutation	DNP	AG	TCGA-AG-A032-01A-01W-A00E-09	12293439	93567803	8963589	61	23158										
SCNN1G	6340	broad.mit.edu	37	chr16	23197740	23197740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gcatcgtggtgtcccgcggcCgtctgcgccgcctcctctgg	14	17	2	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr16:23197740C>T	ENST00000300061.2	+	2	291	c.148C>T	c.(148-150)Cgt>Tgt	p.R50C		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	50					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)	p.R50C(1)		NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GTCCCGCGGCCGTCTGCGCCG	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	16											59	55	57					16																	23197740		2197	4300	6497	23105241	SO:0001583	missense	6340			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.148C>T	16.37:g.23197740C>T	ENSP00000300061:p.Arg50Cys		23105241	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	37	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525727	0.64860	.	.	ENSG00000166828	ENST00000300061	T	0.63417	-0.04	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.81108	0.4754	M	0.84082	2.675	0.58432	D	0.999999	D	0.89917	1.0	D	0.73380	0.98	D	0.83870	0.0273	10	0.87932	D	0	-34.9274	17.8144	0.88627	0.0:1.0:0.0:0.0	.	50	P51170	SCNNG_HUMAN	C	50	ENSP00000300061:R50C	ENSP00000300061:R50C	R	+	1	0	SCNN1G	23105241	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	5.696000	0.68287	2.538000	0.85594	0.561000	0.74099	CGT		0.632	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		T	23197740	C	T	23197740	3	4	79	1	0	0	0	0	1	0	0	0	13967	652	23	1	150	1	SCNN1G	16	23197740	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		23197740	67157013	62	23159										
MAPK3	5595	broad.mit.edu	37	chr16	30128045	30128045	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgtctcctggaagatgagctCcttcagccgctccttaggta	10	12	2	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr16:30128045C>A	ENST00000263025.4	-	8	1168	c.1084G>T	c.(1084-1086)Gag>Tag	p.E362*	GDPD3_ENST00000406256.3_5'Flank|MAPK3_ENST00000484663.1_Nonsense_Mutation_p.E248*|MAPK3_ENST00000395200.1_Nonsense_Mutation_p.E294*|MAPK3_ENST00000403394.1_3'UTR|MAPK3_ENST00000395202.1_Nonsense_Mutation_p.E318*|MAPK3_ENST00000322266.5_Nonsense_Mutation_p.E318*|MAPK3_ENST00000494643.1_5'Flank	NM_002746.2	NP_002737.2	P27361	MK03_HUMAN	mitogen-activated protein kinase 3	362					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage induced protein phosphorylation (GO:0006975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-1-mediated signaling pathway (GO:0070498)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apolipoprotein binding (GO:2000657)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to exogenous dsRNA (GO:0043330)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)	p.E362*(1)								Arsenic trioxide(DB01169)|Sulindac(DB00605)	AAGATGAGCTCCTTCAGCCGC	0.637																																																1	Substitution - Nonsense(1)	large_intestine(1)	16											55	59	58					16																	30128045		2197	4300	6497	30035546	SO:0001587	stop_gained	5595			M84490	CCDS10672.1, CCDS42148.1, CCDS42149.1	16p11.2	2011-06-10			ENSG00000102882	ENSG00000102882	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6877	protein-coding gene	gene with protein product		601795		PRKM3		9628824	Standard	NM_001109891		Approved	ERK1, p44mapk, p44erk1	uc002dws.3	P27361	OTTHUMG00000132149	ENST00000263025.4:c.1084G>T	16.37:g.30128045C>A	ENSP00000263025:p.Glu362*		30035546	A8CZ58|B0LPG3|Q8NHX1	Nonsense_Mutation	SNP	ENST00000263025.4	37	CCDS10672.1	.	.	.	.	.	.	.	.	.	.	C	34	5.305747	0.95601	.	.	ENSG00000102882	ENST00000263025;ENST00000484663;ENST00000322266;ENST00000395200;ENST00000395202;ENST00000478356	.	.	.	5.79	5.79	0.91817	.	0.182248	0.47093	D	0.000241	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-8.544	18.7978	0.92003	0.0:1.0:0.0:0.0	.	.	.	.	X	362;248;318;294;318;125	.	ENSP00000263025:E362X	E	-	1	0	MAPK3	30035546	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.639000	0.83342	2.735000	0.93741	0.655000	0.94253	GAG		0.637	MAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255196.2			A	30128045	C	A	30128045	4	1	79	1	0	0	0	0	0	1	0	0	9309	864	30	2	59	2	MAPK3	16	30128045	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	6930305	30128045	60226708	63	23160										
SPNS3	201305	broad.mit.edu	37	chr17	4337389	4337389	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cctggagcctgcccccgtggAgggcctacgtggctgccgcc	15	17	0	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr17:4337389A>C	ENST00000355530.2	+	1	407	c.127A>C	c.(127-129)Agg>Cgg	p.R43R	SPNS3_ENST00000576069.1_3'UTR|SPNS3_ENST00000333476.2_5'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	43					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.R43R(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GCCCCCGTGGAGGGCCTACGT	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	17											73	72	72					17																	4337389		2203	4300	6503	4284138	SO:0001819	synonymous_variant	201305				CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.127A>C	17.37:g.4337389A>C			4284138	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																				0.657	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538		C	4337389	A	C	4337389	2	2	79	1	0	0	0	0	0	0	0	1	15115	295	11	4		4	SPNS3	17	4337389	Silent	SNP	A	TCGA-AG-A032-01A-01W-A00E-09		4337389	76857821	64	23161										
TP53	7157	broad.mit.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	79	1	0	0	0	0	1	0	0	0	16421	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	3240150	7577539	73617671	65	23162										
RAB11FIP4	84440	broad.mit.edu	37	chr17	29858687	29858688	+	Nonsense_Mutation	DNP	CA	CA	GG													0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	aacttccggctgaggcagtaCatggacaagattatcctcgc							TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr17:29858687_29858688CA>GG	ENST00000325874.8	+	15	2080_2081	c.1851_1852CA>GG	c.(1849-1854)taCAtg>taGGtg	p.617_618YM>*V	RAB11FIP4_ENST00000394744.2_Nonsense_Mutation_p.515_516YM>*V	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	617	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.Y617>?(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				TGAGGCAGTACATGGACAAGAT	0.569																																																1	Complex(1)	large_intestine(1)	17																																								26882808	SO:0001587	stop_gained	84440			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"EF-hand domain containing"	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	Exception_encountered	17.37:g.29858687_29858688delinsGG	ENSP00000312837:p.Y617_M618delins*V		26882807	Q52LI1|Q8N829|Q8NDT7|Q969D8	Nonsense_Mutation	DNP	ENST00000325874.8	37	CCDS11267.1																																																																																				0.569	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932		GG	29858688	CA	GG	29858687	4	3	79	1	0	0	0	0	0	1	0	0	12933	489	17	5	1909	5	RAB11FIP4	17	29858687	Nonsense_Mutation	DNP	CA	TCGA-AG-A032-01A-01W-A00E-09	22281148	29858687	51336523	66	23163										
CCL18	6362	broad.mit.edu	37	chr17	34397894	34397894	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgactattctgaaaccagccCccagtgccccaagccaggtg	9	15	1	2			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr17:34397894C>A	ENST00000004921.3	+	2	218	c.155C>A	c.(154-156)cCc>cAc	p.P52H	AC069363.1_ENST00000590992.1_RNA|AC069363.1_ENST00000588864.1_RNA	NM_002988.2	NP_002979.1	P55774	CCL18_HUMAN	chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)	52					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to biotic stimulus (GO:0009607)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)	p.P52H(1)		endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GAAACCAGCCCCCAGTGCCCC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	17											59	56	57					17																	34397894		2203	4300	6503	31422007	SO:0001583	missense	6362			Y13710	CCDS11306.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000006074	ENSG00000275385		"Chemokine ligands"	10616	protein-coding gene	gene with protein product		603757	"small inducible cytokine subfamily A (Cys-Cys), member 18, pulmonary and activation-regulated"	SCYA18		9233607, 10049593	Standard	NM_002988		Approved	DC-CK1, PARC, AMAC-1, DCCK1, MIP-4, CKb7	uc002hku.3	P55774	OTTHUMG00000188410	ENST00000004921.3:c.155C>A	17.37:g.34397894C>A	ENSP00000004921:p.Pro52His		31422007	B5BUM2|Q53X71	Missense_Mutation	SNP	ENST00000004921.3	37	CCDS11306.1	.	.	.	.	.	.	.	.	.	.	.	14.40	2.524958	0.44969	.	.	ENSG00000006074	ENST00000004921	T	0.14640	2.49	3.56	1.5	0.22942	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.272209	0.36303	N	0.002677	T	0.20536	0.0494	.	.	.	0.21802	N	0.999536	D	0.55385	0.971	P	0.55391	0.775	T	0.04635	-1.0937	9	0.59425	D	0.04	.	5.0734	0.14618	0.1231:0.2202:0.6568:0.0	.	52	P55774	CCL18_HUMAN	H	52	ENSP00000004921:P52H	ENSP00000004921:P52H	P	+	2	0	CCL18	31422007	0.992000	0.36948	0.462000	0.27118	0.001000	0.01503	1.673000	0.37534	0.312000	0.23038	-0.839000	0.03059	CCC		0.552	CCL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256583.1	NM_002988		A	34397894	C	A	34397894	3	1	79	1	0	0	0	0	1	0	0	0	2895	623	22	2	161	2	CCL18	17	34397894	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	4539207	34397894	46797316	67	23164										
LRRC30	339291	broad.mit.edu	37	chr18	7231726	7231726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cttgcacgtgggctcgaatcGcctggaaaacatcgctgaga	12	11	0	1	rs180848748		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr18:7231726G>A	ENST00000383467.2	+	1	604	c.590G>A	c.(589-591)cGc>cAc	p.R197H		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	197								p.R197H(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						GGCTCGAATCGCCTGGAAAAC	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	18											82	86	85					18																	7231726		2109	4250	6359	7221726	SO:0001583	missense	339291				CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422			30219	protein-coding gene	gene with protein product							Standard	NM_001105581		Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.590G>A	18.37:g.7231726G>A	ENSP00000372959:p.Arg197His		7221726		Missense_Mutation	SNP	ENST00000383467.2	37	CCDS42409.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879296	0.72294	.	.	ENSG00000206422	ENST00000383467	T	0.25912	1.77	5.65	4.77	0.60923	.	0.332635	0.35495	N	0.003171	T	0.20495	0.0493	L	0.61036	1.89	0.36203	D	0.850872	P	0.39737	0.685	B	0.28385	0.089	T	0.19386	-1.0307	10	0.46703	T	0.11	.	8.3312	0.32187	0.2422:0.0:0.7578:0.0	.	197	A6NM36	LRC30_HUMAN	H	197	ENSP00000372959:R197H	ENSP00000372959:R197H	R	+	2	0	LRRC30	7221726	0.985000	0.35326	1.000000	0.80357	0.980000	0.70556	3.065000	0.49994	2.827000	0.97445	0.650000	0.86243	CGC		0.542	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442140.1	XM_292678		A	7231726	G	A	7231726	3	1	79	1	0	0	0	0	1	0	0	0	9014	1087	38	1	592	1	LRRC30	18	7231726	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		7231726	70845522	68	23165										
TSHZ3	57616	broad.mit.edu	37	chr19	31770274	31770274	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tgccgttgttcttctccgagGagggctggtgcaggttgagg	17	8	2	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr19:31770274G>A	ENST00000240587.4	-	2	752	c.425C>T	c.(424-426)tCc>tTc	p.S142F		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	142	Ser-rich.				in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S142F(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTTCTCCGAGGAGGGCTGGTG	0.592																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	92	90					19																	31770274		2199	4289	6488	36462114	SO:0001583	missense	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.425C>T	19.37:g.31770274G>A	ENSP00000240587:p.Ser142Phe		36462114	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	G	9.000	0.979906	0.18812	.	.	ENSG00000121297	ENST00000240587	T	0.12672	2.66	5.77	5.77	0.91146	.	0.203527	0.31673	U	0.007251	T	0.10766	0.0263	L	0.27053	0.805	0.37297	D	0.908547	B	0.19445	0.036	B	0.18871	0.023	T	0.21415	-1.0246	10	0.23302	T	0.38	-22.5611	13.6465	0.62286	0.0796:0.0:0.9204:0.0	.	142	Q63HK5	TSH3_HUMAN	F	142	ENSP00000240587:S142F	ENSP00000240587:S142F	S	-	2	0	TSHZ3	36462114	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.546000	0.82137	2.701000	0.92244	0.650000	0.86243	TCC		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31770274	G	A	31770274	3	1	79	1	0	0	0	0	1	0	0	0	16665	1174	41	3	2824	3	TSHZ3	19	31770274	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		31770274	27358709	69	23166										
SIPA1L3	23094	broad.mit.edu	37	chr19	38610443	38610443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ctccacactcaaaatcttctAtggacgaggagaccacatct	6	13	4	1	rs150292475		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr19:38610443A>G	ENST00000222345.6	+	9	3298	c.2789A>G	c.(2788-2790)tAt>tGt	p.Y930C		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	930					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)	p.Y930C(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AAAATCTTCTATGGACGAGGA	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	19						A	CYS/TYR	0,4406		0,0,2203	58	64	62		2789	5.6	1	19	dbSNP_134	62	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SIPA1L3	NM_015073.1	194	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	probably-damaging	930/1782	38610443	2,13004	2203	4300	6503	43302283	SO:0001583	missense	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2789A>G	19.37:g.38610443A>G	ENSP00000222345:p.Tyr930Cys		43302283	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.788943	0.70337	0.0	2.33E-4	ENSG00000105738	ENST00000222345	D	0.88431	-2.38	5.63	5.63	0.86233	.	0.064498	0.64402	D	0.000005	D	0.94118	0.8114	M	0.79011	2.435	0.52501	D	0.999951	D	0.89917	1.0	D	0.81914	0.995	D	0.94754	0.7930	10	0.87932	D	0	-11.3605	14.836	0.70183	1.0:0.0:0.0:0.0	.	930	O60292	SI1L3_HUMAN	C	930	ENSP00000222345:Y930C	ENSP00000222345:Y930C	Y	+	2	0	SIPA1L3	43302283	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.412000	0.80091	2.154000	0.67381	0.533000	0.62120	TAT		0.547	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		G	38610443	A	G	38610443	3	3	79	1	0	0	0	0	1	0	0	0	14368	449	16	4	2815	4	SIPA1L3	19	38610443	Missense_Mutation	SNP	A	TCGA-AG-A032-01A-01W-A00E-09	6840169	38610443	20518540	70	23167										
CGB2	114336	broad.mit.edu	37	chr19	49536406	49536406	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	caggcctcctcttcctcaaaGgcccctccccccagccttcc	5	23	2	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr19:49536406G>C	ENST00000359342.6	+	3	538	c.420G>C	c.(418-420)aaG>aaC	p.K140N	CTB-60B18.6_ENST00000591656.1_Intron	NM_033378.1	NP_203696.2	Q6NT52	CGB2_HUMAN	chorionic gonadotropin, beta polypeptide 2	172						extracellular region (GO:0005576)		p.K140N(1)		large_intestine(1)|lung(1)|stomach(1)	3		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CTTCCTCAAAGGCCCCTCCCC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											26	39	35					19																	49536406		2188	4287	6475	54228218	SO:0001583	missense	114336			K03184	CCDS12750.2	19q13.32	2008-02-05			ENSG00000104818	ENSG00000104818			16722	protein-coding gene	gene with protein product		608824				6194155	Standard	NM_033378		Approved		uc002plw.3	Q6NT52	OTTHUMG00000150185	ENST00000359342.6:c.420G>C	19.37:g.49536406G>C	ENSP00000352295:p.Lys140Asn		54228218	B9ZVM5	Missense_Mutation	SNP	ENST00000359342.6	37	CCDS12750.2	.	.	.	.	.	.	.	.	.	.	g	7.101	0.574114	0.13623	.	.	ENSG00000104818	ENST00000359342	T	0.48836	0.8	1.79	0.649	0.17806	.	.	.	.	.	T	0.51176	0.1659	L	0.38838	1.175	0.21740	N	0.999564	P;P;D	0.54772	0.947;0.947;0.968	D;D;P	0.67231	0.95;0.95;0.895	T	0.34477	-0.9827	9	0.54805	T	0.06	.	5.492	0.16781	0.0:0.0:0.6754:0.3246	.	172;142;158	Q6NT52;P01233;P01233-2	CGB2_HUMAN;CGHB_HUMAN;.	N	140	ENSP00000352295:K140N	ENSP00000352295:K140N	K	+	3	2	CGB2	54228218	0.449000	0.25689	0.060000	0.19600	0.064000	0.16182	-0.016000	0.12613	0.283000	0.22279	0.184000	0.17185	AAG		0.647	CGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316745.1	NM_033378		C	49536406	G	C	49536406	3	2	79	1	0	0	0	0	1	0	0	0	3304	991	35	5	430	5	CGB2	19	49536406	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	10925963	49536406	9592577	71	23168										
PRKCG	5582	broad.mit.edu	37	chr19	54395831	54395831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ggactgggaccggacctcccGcaacgacttcatgggggcca	14	14	1	0			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr19:54395831G>A	ENST00000263431.3	+	7	1037	c.755G>A	c.(754-756)cGc>cAc	p.R252H	PRKCG_ENST00000536044.1_Missense_Mutation_p.R252H|PRKCG_ENST00000542049.1_Missense_Mutation_p.R139H|PRKCG_ENST00000540413.1_Missense_Mutation_p.R252H	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	252	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.R252H(2)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CGGACCTCCCGCAACGACTTC	0.677																																																2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	19											56	44	48					19																	54395831		2203	4300	6503	59087643	SO:0001583	missense	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.755G>A	19.37:g.54395831G>A	ENSP00000263431:p.Arg252His		59087643	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668309	0.88348	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	4.11	4.11	0.48088	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.60222	0.2252	M	0.62209	1.925	0.54753	D	0.99998	D;P;D;D;D	0.89917	0.994;0.951;1.0;0.96;0.961	D;P;D;P;P	0.73708	0.981;0.455;0.962;0.59;0.792	T	0.64984	-0.6278	9	0.72032	D	0.01	.	14.2039	0.65721	0.0:0.0:1.0:0.0	.	139;252;252;252;252	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	H	252;252;252;139	ENSP00000440541:R252H;ENSP00000443493:R252H;ENSP00000263431:R252H;ENSP00000438090:R139H	ENSP00000263431:R252H	R	+	2	0	PRKCG	59087643	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	9.062000	0.93920	1.990000	0.58119	0.455000	0.32223	CGC		0.677	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54395831	G	A	54395831	3	1	79	1	0	0	0	0	1	0	0	0	12546	1087	38	1	781	1	PRKCG	19	54395831	Missense_Mutation	SNP	G	TCGA-AG-A032-01A-01W-A00E-09	4859425	54395831	4733152	72	23169										
MACROD2	140733	broad.mit.edu	37	chr20	15866456	15866456	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ttgaaatgaaagaagattcaGgtattaaattcatactttta	6	3	2	4			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr20:15866456G>T	ENST00000310348.4	+	10	775	c.775G>T	c.(775-777)Gat>Tat	p.D259Y	MACROD2_ENST00000217246.4_Splice_Site_p.D259Y|MACROD2_ENST00000378058.3_Splice_Site_p.D24Y|MACROD2_ENST00000402914.1_Splice_Site_p.D24Y			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	259	Glu-rich.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.D24Y(1)|p.D259Y(1)		breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AGAAGATTCAGGTATTAAATT	0.279																																																2	Substitution - Missense(2)	large_intestine(2)	20											78	93	88					20																	15866456		2198	4292	6490	15814456	SO:0001630	splice_region_variant	140733			BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.775+1G>T	20.37:g.15866456G>T			15814456	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560876	0.65538	.	.	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058	T;T;T;T	0.56776	2.27;2.26;0.44;0.44	5.35	5.35	0.76521	.	0.000000	0.52532	D	0.000070	T	0.68879	0.3049	L	0.56769	1.78	0.39076	D	0.960801	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.71324	-0.4627	10	0.66056	D	0.02	-26.8684	15.2906	0.73862	0.0:0.0:1.0:0.0	.	259;259	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	Y	259;259;24;24	ENSP00000217246:D259Y;ENSP00000309809:D259Y;ENSP00000385290:D24Y;ENSP00000367297:D24Y	ENSP00000217246:D259Y	D	+	1	0	MACROD2	15814456	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	4.450000	0.60041	2.885000	0.99019	0.655000	0.94253	GAT		0.279	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	Missense_Mutation	T	15866456	G	T	15866456	5	4	79	1	0	0	0	0	0	0	1	0	9176	1014	35	2	813	2	MACROD2	20	15866456	Splice_Site	SNP	G	TCGA-AG-A032-01A-01W-A00E-09		15866456	47159064	73	23170										
MYLK2	85366	broad.mit.edu	37	chr20	30411368	30411369	+	Nonsense_Mutation	DNP	CA	CA	TT													0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	agtgaattcagtatgaactcCaaggaggcgctcggagggtg							TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr20:30411368_30411369CA>TT	ENST00000375994.2	+	4	1134_1135	c.861_862CA>TT	c.(859-864)tcCAag>tcTTag	p.K288*	MYLK2_ENST00000375985.4_Nonsense_Mutation_p.K288*			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	288	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.S287>?(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GTATGAACTCCAAGGAGGCGCT	0.614											OREG0025856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Complex(1)	large_intestine(1)	20																																								29875030	SO:0001587	stop_gained	85366			AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"skeletal muscle myosin light chain kinase"	606566	"myosin light chain kinase 2, skeletal muscle"				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	Exception_encountered	20.37:g.30411368_30411369delinsTT	ENSP00000365162:p.Lys288*	817	29875029	Q569L1|Q96I84	Nonsense_Mutation	DNP	ENST00000375994.2	37	CCDS13191.1																																																																																				0.614	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118		TT	30411369	CA	TT	30411368	4	4	79	1	0	0	0	0	0	1	0	0	10087	581	21	3	875	3	MYLK2	20	30411368	Nonsense_Mutation	DNP	CA	TCGA-AG-A032-01A-01W-A00E-09	14544912	30411368	32614152	74	23171										
UPB1	51733	broad.mit.edu	37	chr22	24896172	24896172	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	cagcggaggagcagctgagaCgaccccgcattgtgcacgtg	15	12	0	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chr22:24896172C>T	ENST00000326010.5	+	2	546	c.202C>T	c.(202-204)Cga>Tga	p.R68*	UPB1_ENST00000413389.2_Intron|UPB1_ENST00000382760.2_Nonsense_Mutation_p.R68*	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	68					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)	p.R68*(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					GCAGCTGAGACGACCCCGCAT	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	22											82	85	84					22																	24896172		2203	4300	6503	23226172	SO:0001587	stop_gained	51733			AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.202C>T	22.37:g.24896172C>T	ENSP00000324343:p.Arg68*		23226172	A3KMF8|Q9UIR3	Nonsense_Mutation	SNP	ENST00000326010.5	37	CCDS13827.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.531090	0.85706	.	.	ENSG00000100024	ENST00000326010;ENST00000382760;ENST00000426507	.	.	.	4.73	-1.97	0.07503	.	1.084730	0.06991	N	0.821697	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-4.6678	3.3069	0.07003	0.2849:0.3735:0.2589:0.0827	.	.	.	.	X	68	.	ENSP00000324343:R68X	R	+	1	2	UPB1	23226172	0.001000	0.12720	0.009000	0.14445	0.814000	0.46013	0.112000	0.15479	-0.466000	0.06943	0.561000	0.74099	CGA		0.542	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1			T	24896172	C	T	24896172	4	4	79	1	0	0	0	0	0	1	0	0	17042	528	19	1	208	1	UPB1	22	24896172	Nonsense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		24896172	26408394	75	23172										
DMD	1756	broad.mit.edu	37	chrX	32360315	32360315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	agttggctccactgccattgCggccccatcctcagacaagc	9	16	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chrX:32360315C>T	ENST00000357033.4	-	41	6030	c.5824G>A	c.(5824-5826)Gca>Aca	p.A1942T	DMD_ENST00000378677.2_Missense_Mutation_p.A1938T	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1942					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.A601T(1)|p.A1938T(1)|p.A1937T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				ACTGCCATTGCGGCCCCATCC	0.493																																																3	Substitution - Missense(3)	large_intestine(3)	X											102	71	81					X																	32360315		2202	4300	6502	32270236	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5824G>A	X.37:g.32360315C>T	ENSP00000354923:p.Ala1942Thr		32270236	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418223	0.25552	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.53206	0.63;0.63	5.76	3.91	0.45181	.	0.000000	0.36778	U	0.002420	T	0.28962	0.0719	N	0.19112	0.55	0.80722	D	1	B;B;B;B;B	0.28419	0.176;0.211;0.211;0.094;0.094	B;B;B;B;B	0.21708	0.021;0.036;0.036;0.025;0.015	T	0.05886	-1.0858	10	0.14656	T	0.56	.	12.1216	0.53895	0.1349:0.7384:0.1267:0.0	.	1934;1942;1938;601;598	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	T	1934;601;598;1938;1942;1942;1819	ENSP00000367948:A1938T;ENSP00000354923:A1942T	ENSP00000354923:A1942T	A	-	1	0	DMD	32270236	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	3.142000	0.50601	1.163000	0.42636	-0.237000	0.12165	GCA		0.493	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32360315	C	T	32360315	3	4	79	1	0	0	0	0	1	0	0	0	4591	768	27	1	5537	1	DMD	23	32360315	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09		32360315	122910245	76	23173										
DACH2	117154	broad.mit.edu	37	chrX	86069705	86069705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	tttcagctactatgcaaaagCgcctgaagaaggagaaaaaa	9	7	1	3	rs146920220		TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chrX:86069705C>T	ENST00000373125.4	+	10	1552	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	DACH2_ENST00000508860.1_Missense_Mutation_p.R351C|DACH2_ENST00000510272.1_Missense_Mutation_p.R299C|DACH2_ENST00000373131.1_Missense_Mutation_p.R505C	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	518	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R518C(1)|p.R505C(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						TATGCAAAAGCGCCTGAAGAA	0.413																																																2	Substitution - Missense(2)	large_intestine(2)	X						C	CYS/ARG,CYS/ARG,CYS/ARG	1,3834		0,1,1631,571	51	49	50		1513,1051,1552	4.8	1	X	dbSNP_134	50	0,6728		0,0,2428,1872	no	missense,missense,missense	DACH2	NM_001139514.1,NM_001139515.1,NM_053281.3	180,180,180	0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095	probably-damaging,probably-damaging,probably-damaging	505/572,351/433,518/600	86069705	1,10562	2203	4300	6503	85956361	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1552C>T	X.37:g.86069705C>T	ENSP00000362217:p.Arg518Cys		85956361	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230699	0.79688	2.61E-4	0.0	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.89746	-2.52;-2.56	4.76	4.76	0.60689	.	0.000000	0.64402	D	0.000003	D	0.94128	0.8117	M	0.76727	2.345	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.997;0.997	D	0.95005	0.8146	10	0.87932	D	0	.	17.002	0.86383	0.0:1.0:0.0:0.0	.	384;518;505;518	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	C	518;505;518;351;299;351;183	ENSP00000362223:R505C;ENSP00000362217:R518C	ENSP00000345134:R518C	R	+	1	0	DACH2	85956361	1.000000	0.71417	0.995000	0.50966	0.869000	0.49853	7.370000	0.79589	1.932000	0.55993	0.415000	0.27848	CGC		0.413	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	86069705	C	T	86069705	3	4	79	1	0	0	0	0	1	0	0	0	4227	768	27	1	1590	1	DACH2	23	86069705	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	53709390	86069705	69200855	77	23174										
UBE2NL	389898	broad.mit.edu	37	chrX	142967509	142967509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.357788944723618	1.61005025125628	0.201256281407035	1	1	0	ggtccccagccctgcagatcCgcacagttctgctatcgatc	9	16	1	1			TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A032-01A-01W-A00E-09	TCGA-AG-A032-10A-01W-A00E-09	g.chrX:142967509C>T	ENST00000370494.1	+	1	337	c.307C>T	c.(307-309)Cgc>Tgc	p.R103C		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	103						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)	p.R103C(1)		breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					CCTGCAGATCCGCACAGTTCT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	X											108	94	99					X																	142967509		2203	4300	6503	142795175	SO:0001583	missense	389898					Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"Ubiquitin-conjugating enzymes E2"	31710	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2N-like"			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.307C>T	X.37:g.142967509C>T	ENSP00000359525:p.Arg103Cys		142795175	E9KL27	Missense_Mutation	SNP	ENST00000370494.1	37	CCDS35420.1	.	.	.	.	.	.	.	.	.	.	C	3.542	-0.093443	0.07053	.	.	ENSG00000102069	ENST00000370494	T	0.39056	1.1	1.16	-0.908	0.10517	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.265427	0.19850	U	0.104652	T	0.49762	0.1576	M	0.92412	3.305	0.80722	D	1	P	0.35612	0.512	B	0.41466	0.358	T	0.44726	-0.9309	10	0.66056	D	0.02	11.1641	3.4429	0.07470	0.2395:0.5766:0.0:0.1839	.	103	Q5JXB2	UE2NL_HUMAN	C	103	ENSP00000359525:R103C	ENSP00000359525:R103C	R	+	1	0	UBE2NL	142795175	1.000000	0.71417	0.995000	0.50966	0.036000	0.12997	3.460000	0.53028	-0.490000	0.06707	-1.274000	0.01402	CGC		0.423	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989		T	142967509	C	T	142967509	3	4	79	1	0	0	0	0	1	0	0	0	16907	652	23	1	309	1	UBE2NL	23	142967509	Missense_Mutation	SNP	C	TCGA-AG-A032-01A-01W-A00E-09	56897804	142967509	12303051	78	23175										
LRRC47	57470	broad.mit.edu	37	chr1	3703695	3703695	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gcacggcccttgcccttcccGccaccacggcctccgacgcg	10	22	0	0	rs376974812		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:3703695G>A	ENST00000378251.1	-	2	822	c.795C>T	c.(793-795)ggC>ggT	p.G265G	RP1-286D6.5_ENST00000607459.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	265							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)	p.G265G(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	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)		TGCCCTTCCCGCCACCACGGC	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)	1						G		0,4406		0,0,2203	81	62	68		795	-2.4	0	1		68	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRRC47	NM_020710.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		265/584	3703695	2,13004	2203	4300	6503	3693555	SO:0001819	synonymous_variant	57470			AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.795C>T	1.37:g.3703695G>A			3693555	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																				0.657	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710		A	3703695	G	A	3703695	2	1	80	1	0	0	0	0	0	0	0	1	9033	1074	38	1		1	LRRC47	1	3703695	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10		3703695	245546926	1	23176										
H6PD	9563	broad.mit.edu	37	chr1	9305568	9305568	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gctggccacagaactcgggaCctttttccaggaggaggaga	14	10	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:9305568C>G	ENST00000377403.2	+	2	877	c.575C>G	c.(574-576)aCc>aGc	p.T192S	H6PD_ENST00000602477.1_Missense_Mutation_p.T203S	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	192	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)	p.T192S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	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)		GAACTCGGGACCTTTTTCCAG	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											40	42	41					1																	9305568		2203	4300	6503	9228155	SO:0001583	missense	9563			AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.575C>G	1.37:g.9305568C>G	ENSP00000366620:p.Thr192Ser		9228155	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	.	.	.	.	.	.	.	.	.	.	C	0.783	-0.761505	0.02996	.	.	ENSG00000049239	ENST00000377403	D	0.98044	-4.68	5.31	2.11	0.27256	NAD(P)-binding domain (1);Glucose-6-phosphate dehydrogenase, NAD-binding (1);	0.341251	0.37669	N	0.001981	D	0.85230	0.5649	N	0.00633	-1.31	0.09310	N	0.999999	B	0.10296	0.003	B	0.10450	0.005	T	0.79699	-0.1694	10	0.02654	T	1	-25.0442	5.7694	0.18245	0.0776:0.3055:0.4983:0.1185	.	192	O95479	G6PE_HUMAN	S	192	ENSP00000366620:T192S	ENSP00000366620:T192S	T	+	2	0	H6PD	9228155	0.562000	0.26586	0.999000	0.59377	0.951000	0.60555	1.241000	0.32743	0.741000	0.32674	-0.203000	0.12734	ACC		0.627	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		G	9305568	C	G	9305568	3	3	80	1	0	0	0	0	1	0	0	0	6957	507	18	5	577	5	H6PD	1	9305568	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	5601873	9305568	239945053	2	23177										
UBE4B	10277	broad.mit.edu	37	chr1	10132264	10132264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cccagctacctccccaatagGtgcatcaggtaagcccaagc	8	16	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:10132264G>A	ENST00000253251.8	+	2	1042	c.203G>A	c.(202-204)gGt>gAt	p.G68D	UBE4B_ENST00000343090.6_Missense_Mutation_p.G68D|UBE4B_ENST00000377153.1_Missense_Mutation_p.G68D|UBE4B_ENST00000377157.3_5'UTR					ubiquitination factor E4B									p.G68D(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TCCCCAATAGGTGCATCAGGT	0.493																																																1	Substitution - Missense(1)	large_intestine(1)	1											61	59	59					1																	10132264		2203	4300	6503	10054851	SO:0001583	missense	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.203G>A	1.37:g.10132264G>A	ENSP00000253251:p.Gly68Asp		10054851		Missense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.961112	0.92791	.	.	ENSG00000130939	ENST00000253251;ENST00000377153;ENST00000343090	T;T	0.55234	0.74;0.53	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.49830	0.1580	L	0.27053	0.805	0.80722	D	1	D;D	0.57257	0.964;0.979	P;P	0.51193	0.638;0.662	T	0.34675	-0.9819	10	0.11794	T	0.64	-17.4749	19.2392	0.93875	0.0:0.0:1.0:0.0	.	68;68	O95155;O95155-2	UBE4B_HUMAN;.	D	68	ENSP00000253251:G68D;ENSP00000343001:G68D	ENSP00000253251:G68D	G	+	2	0	UBE4B	10054851	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.153000	0.94687	2.544000	0.85801	0.563000	0.77884	GGT		0.493	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		A	10132264	G	A	10132264	3	1	80	1	0	0	0	0	1	0	0	0	16923	1261	44	3	209	3	UBE4B	1	10132264	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	826696	10132264	239118357	3	23178										
EPHA8	2046	broad.mit.edu	37	chr1	22915454	22915454	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcccctggacccaggtggccGcagtgacatcacctacaatg	10	15	1	1	rs373378884		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:22915454G>T	ENST00000166244.3	+	5	1142	c.1070G>T	c.(1069-1071)cGc>cTc	p.R357L	EPHA8_ENST00000374644.4_Missense_Mutation_p.R357L|EPHA8_ENST00000538803.1_Missense_Mutation_p.R357L	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	357	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.R357L(2)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		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;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCAGGTGGCCGCAGTGACATC	0.662																																																2	Substitution - Missense(2)	large_intestine(2)	1											39	34	36					1																	22915454		2203	4300	6503	22788041	SO:0001583	missense	2046			BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1070G>T	1.37:g.22915454G>T	ENSP00000166244:p.Arg357Leu		22788041	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699404	0.88830	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.58210	0.35;0.35;0.35	4.17	4.17	0.49024	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.76133	0.3945	M	0.89840	3.065	0.80722	D	1	P;D	0.71674	0.698;0.998	P;D	0.68353	0.477;0.957	T	0.82663	-0.0346	10	0.87932	D	0	.	15.5494	0.76137	0.0:0.0:1.0:0.0	.	357;357	P29322;P29322-2	EPHA8_HUMAN;.	L	357	ENSP00000166244:R357L;ENSP00000363775:R357L;ENSP00000440274:R357L	ENSP00000166244:R357L	R	+	2	0	EPHA8	22788041	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.511000	0.98006	2.307000	0.77673	0.491000	0.48974	CGC		0.662	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22915454	G	T	22915454	3	4	80	1	0	0	0	0	1	0	0	0	5186	1087	38	2	1088	2	EPHA8	1	22915454	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	12783190	22915454	226335167	4	23179										
CCDC28B	79140	broad.mit.edu	37	chr1	32669954	32669954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agaagaagacaatggctgacCgtaacctggaccagctgctt	11	10	0	4	rs200265063		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:32669954C>T	ENST00000373602.5	+	4	846	c.499C>T	c.(499-501)Cgt>Tgt	p.R167C	IQCC_ENST00000291358.6_5'Flank|CCDC28B_ENST00000483009.1_Intron|RP4-622L5.7_ENST00000421616.1_RNA|RP4-622L5.7_ENST00000373604.4_RNA|IQCC_ENST00000537469.1_5'Flank|CCDC28B_ENST00000421922.2_Missense_Mutation_p.R167C	NM_024296.3	NP_077272.2	Q9BUN5	CC28B_HUMAN	coiled-coil domain containing 28B	167					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R167C(1)		large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AATGGCTGACCGTAACCTGGA	0.562																																																1	Substitution - Missense(1)	large_intestine(1)	1											127	120	123					1																	32669954		2203	4300	6503	32442541	SO:0001583	missense	79140			BC022848	CCDS354.2, CCDS72749.1	1p36.11-p34.2	2008-02-05			ENSG00000160050	ENSG00000160050			28163	protein-coding gene	gene with protein product		610162				16327777	Standard	XM_006710892		Approved	MGC1203, RP4-622L5.5	uc001bul.1	Q9BUN5	OTTHUMG00000005738	ENST00000373602.5:c.499C>T	1.37:g.32669954C>T	ENSP00000362704:p.Arg167Cys		32442541	A8K789|Q8TBV8	Missense_Mutation	SNP	ENST00000373602.5	37	CCDS354.2	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021045	0.54576	.	.	ENSG00000160050	ENST00000373602;ENST00000421922	T;T	0.47869	0.86;0.83	4.74	2.82	0.32997	.	0.117065	0.64402	D	0.000015	T	0.47691	0.1459	L	0.47716	1.5	0.50467	D	0.999878	D	0.64830	0.994	P	0.51918	0.684	T	0.45026	-0.9289	10	0.62326	D	0.03	-15.6326	8.6313	0.33922	0.2818:0.6432:0.0:0.075	.	167	Q9BUN5	CC28B_HUMAN	C	167	ENSP00000362704:R167C;ENSP00000413017:R167C	ENSP00000362704:R167C	R	+	1	0	CCDC28B	32442541	0.999000	0.42202	0.797000	0.32132	0.544000	0.35116	1.437000	0.34991	0.707000	0.31934	0.556000	0.70494	CGT		0.562	CCDC28B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015723.4	NM_024296		T	32669954	C	T	32669954	3	4	80	1	0	0	0	0	1	0	0	0	2809	652	23	1	509	1	CCDC28B	1	32669954	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	9754500	32669954	216580667	5	23180										
CYP4B1	1580	broad.mit.edu	37	chr1	47282756	47282756	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atgacttatctgaccatgtgCatcaaggagagcttccgcct	9	11	2	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:47282756C>T	ENST00000271153.4	+	9	1143	c.1107C>T	c.(1105-1107)tgC>tgT	p.C369C	CYP4B1_ENST00000371923.4_Silent_p.C370C|CYP4B1_ENST00000452782.2_Silent_p.C207C|CYP4B1_ENST00000371919.4_Silent_p.C355C			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	369					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.C369C(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TGACCATGTGCATCAAGGAGA	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	1											174	160	165					1																	47282756		2203	4300	6503	47055343	SO:0001819	synonymous_variant	1580			BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1107C>T	1.37:g.47282756C>T			47055343	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	37	CCDS542.1																																																																																				0.542	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		T	47282756	C	T	47282756	2	4	80	1	0	0	0	0	0	0	0	1	4191	718	25	3		3	CYP4B1	1	47282756	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	14612802	47282756	201967865	6	23181										
C1orf103	55791	broad.mit.edu	37	chr1	111494793	111494793	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcttggtaactacatttttcActgtatttacaggagataca	6	7	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:111494793A>T	ENST00000369763.4	-	2	1103	c.713T>A	c.(712-714)gTg>gAg	p.V238E	LRIF1_ENST00000494675.1_Intron|RP11-96K19.2_ENST00000440689.1_RNA|LRIF1_ENST00000485275.2_Intron	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.V238E(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						TACATTTTTCACTGTATTTAC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	1											114	111	112					1																	111494793		2203	4300	6503	111296316	SO:0001583	missense	55791			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.713T>A	1.37:g.111494793A>T	ENSP00000358778:p.Val238Glu		111296316	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	37	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.157760	0.57368	.	.	ENSG00000121931	ENST00000369763	T	0.53857	0.6	5.81	4.65	0.58169	.	0.000000	0.64402	D	0.000002	T	0.49626	0.1568	L	0.34521	1.04	0.80722	D	1	D	0.67145	0.996	D	0.69479	0.964	T	0.56505	-0.7968	10	0.87932	D	0	-5.3293	10.6498	0.45642	0.8573:0.0:0.0:0.1427	.	238	Q5T3J3	LRIF1_HUMAN	E	238	ENSP00000358778:V238E	ENSP00000358778:V238E	V	-	2	0	LRIF1	111296316	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.231000	0.78106	2.226000	0.72624	0.482000	0.46254	GTG		0.383	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		T	111494793	A	T	111494793	3	4	80	1	0	0	0	0	1	0	0	0	1983	159	6	5	1608	5	C1orf103	1	111494793	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	64212037	111494793	137755828	7	23182										
NGF	4803	broad.mit.edu	37	chr1	115828849	115828849	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgctttgagtcaatgccccGgcacccgctgtcaacgggat	12	13	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:115828849G>C	ENST00000369512.2	-	3	736	c.568C>G	c.(568-570)Cgg>Ggg	p.R190G	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)	190					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|adult locomotory behavior (GO:0008344)|apoptotic signaling pathway (GO:0097190)|circadian rhythm (GO:0007623)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|nerve growth factor processing (GO:0032455)|neuron apoptotic process (GO:0051402)|neuron projection morphogenesis (GO:0048812)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axon extension (GO:0045773)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotrophin TRK receptor signaling pathway (GO:0051388)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|Ras protein signal transduction (GO:0007265)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of neurotransmitter secretion (GO:0046928)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)	nerve growth factor receptor binding (GO:0005163)|receptor signaling protein activity (GO:0005057)	p.R190G(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Clenbuterol(DB01407)	TCAATGCCCCGGCACCCGCTG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	87	88					1																	115828849		2203	4300	6503	115630372	SO:0001583	missense	4803				CCDS882.1	1p13.1	2014-09-17	2008-02-07	2008-02-07	ENSG00000134259	ENSG00000134259		"Endogenous ligands"	7808	protein-coding gene	gene with protein product		162030		NGFB			Standard	XM_006710663		Approved		uc001efu.1	P01138	OTTHUMG00000011880	ENST00000369512.2:c.568C>G	1.37:g.115828849G>C	ENSP00000358525:p.Arg190Gly		115630372	A1A4E5|Q6FHA0|Q96P60|Q9P2Q8|Q9UKL8	Missense_Mutation	SNP	ENST00000369512.2	37	CCDS882.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.959893	0.53400	.	.	ENSG00000134259	ENST00000369512	T	0.71222	-0.55	4.9	0.0956	0.14486	Nerve growth factor-related (5);Nerve growth factor conserved site (1);	0.070282	0.56097	D	0.000032	T	0.77651	0.4162	M	0.82132	2.575	0.53005	D	0.999962	D	0.89917	1.0	D	0.74674	0.984	T	0.81362	-0.0967	10	0.62326	D	0.03	-17.5583	14.1173	0.65161	0.0:0.0:0.3503:0.6496	.	190	P01138	NGF_HUMAN	G	190	ENSP00000358525:R190G	ENSP00000358525:R190G	R	-	1	2	NGF	115630372	0.999000	0.42202	0.998000	0.56505	0.942000	0.58702	0.920000	0.28705	0.118000	0.18165	0.455000	0.32223	CGG		0.512	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	NM_002506		C	115828849	G	C	115828849	3	2	80	1	0	0	0	0	1	0	0	0	10426	1115	39	5	161	5	NGF	1	115828849	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	4334056	115828849	133421772	8	23183										
FMO3	2328	broad.mit.edu	37	chr1	171083342	171083342	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	taccccttccttgatgagtcTatcatcaaaagcagaaacaa	5	11	3	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:171083342T>A	ENST00000367755.4	+	7	1134	c.1023T>A	c.(1021-1023)tcT>tcA	p.S341S	FMO3_ENST00000392085.2_Silent_p.S341S|FMO3_ENST00000538429.1_Silent_p.S278S|FMO3_ENST00000542847.1_Silent_p.S321S	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	341					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.S341S(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	TTGATGAGTCTATCATCAAAA	0.418																																																1	Substitution - coding silent(1)	large_intestine(1)	1											126	120	122					1																	171083342		2203	4300	6503	169349966	SO:0001819	synonymous_variant	2328			BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.1023T>A	1.37:g.171083342T>A			169349966	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	37	CCDS1292.1																																																																																				0.418	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		A	171083342	T	A	171083342	2	1	80	1	0	0	0	0	0	0	0	1	5975	1509	53	5		5	FMO3	1	171083342	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10	55254493	171083342	78167279	9	23184										
TNN	63923	broad.mit.edu	37	chr1	175067474	175067474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cattttccttccagatattgAcagccccaaaaacctggtga	6	12	0	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:175067474A>G	ENST00000239462.4	+	9	1975	c.1862A>G	c.(1861-1863)gAc>gGc	p.D621G		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	621	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.D621G(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CCAGATATTGACAGCCCCAAA	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	1											108	119	116					1																	175067474		2203	4300	6503	173334097	SO:0001583	missense	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1862A>G	1.37:g.175067474A>G	ENSP00000239462:p.Asp621Gly		173334097	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263952	0.80358	.	.	ENSG00000120332	ENST00000239462	T	0.04406	3.63	5.23	5.23	0.72850	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	H	0.95850	3.73	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.45131	-0.9282	10	0.49607	T	0.09	.	13.659	0.62354	1.0:0.0:0.0:0.0	.	621;621	B3KXB6;Q9UQP3	.;TENN_HUMAN	G	621	ENSP00000239462:D621G	ENSP00000239462:D621G	D	+	2	0	TNN	173334097	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	4.396000	0.59684	2.101000	0.63845	0.377000	0.23210	GAC		0.502	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		G	175067474	A	G	175067474	3	3	80	1	0	0	0	0	1	0	0	0	16362	275	10	4	1892	4	TNN	1	175067474	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	3984132	175067474	74183147	10	23185										
TNR	7143	broad.mit.edu	37	chr1	175365794	175365794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gatggtgacaccactccaatCtccaggcacccgctgctgga	10	15	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:175365794C>A	ENST00000367674.2	-	5	1834	c.1126G>T	c.(1126-1128)Gat>Tat	p.D376Y	TNR_ENST00000263525.2_Missense_Mutation_p.D376Y			Q92752	TENR_HUMAN	tenascin R	376	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.D376Y(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCACTCCAATCTCCAGGCACC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	1											89	78	81					1																	175365794		2203	4300	6503	173632417	SO:0001583	missense	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1126G>T	1.37:g.175365794C>A	ENSP00000356646:p.Asp376Tyr		173632417	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.186351|4.186351	0.78789|0.78789	.|.	.|.	ENSG00000116147|ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673|ENST00000422274	T;T|.	0.58506|.	0.33;0.33|.	5.96|5.96	5.96|5.96	0.96718|0.96718	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.053543|.	0.64402|.	D|.	0.000001|.	T|T	0.67795|0.67795	0.2931|0.2931	M|M	0.72894|0.72894	2.215|2.215	0.58432|0.58432	D|D	0.999998|0.999998	D|P	0.76494|0.52842	0.999|0.956	D|P	0.77557|0.44732	0.99|0.459	T|T	0.68693|0.68693	-0.5341|-0.5341	10|7	0.72032|.	D|.	0.01|.	.|.	19.9958|19.9958	0.97383|0.97383	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	376|341	Q92752|B4DIX8	TENR_HUMAN|.	Y|I	376|100	ENSP00000356646:D376Y;ENSP00000263525:D376Y|.	ENSP00000263525:D376Y|.	D|R	-|-	1|2	0|0	TNR|TNR	173632417|173632417	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.559000|4.559000	0.60796|0.60796	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAT|AGA		0.597	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175365794	C	A	175365794	3	1	80	1	0	0	0	0	1	0	0	0	16377	913	32	2	3026	2	TNR	1	175365794	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	298320	175365794	73884827	11	23186										
RD3	343035	broad.mit.edu	37	chr1	211652487	211652487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgatgtcgctggcgaagggcGagatgcgcgcgcgggtcttg	19	9	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:211652487G>A	ENST00000367002.4	-	3	1642	c.479C>T	c.(478-480)tCg>tTg	p.S160L	RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	160					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)			p.S160L(1)		central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		GGCGAAGGGCGAGATGCGCGC	0.687																																																1	Substitution - Missense(1)	large_intestine(1)	1											28	26	27					1																	211652487		2202	4297	6499	209719110	SO:0001583	missense	343035			AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"chromosome 1 open reading frame 36"	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.479C>T	1.37:g.211652487G>A	ENSP00000355969:p.Ser160Leu		209719110	A8K595	Missense_Mutation	SNP	ENST00000367002.4	37	CCDS1498.1	.	.	.	.	.	.	.	.	.	.	G	9.292	1.050855	0.19827	.	.	ENSG00000198570	ENST00000367002	T	0.10099	2.91	4.33	1.91	0.25777	.	0.671285	0.15281	N	0.270697	T	0.05273	0.0140	N	0.22421	0.69	0.09310	N	0.999999	B	0.31680	0.335	B	0.24974	0.057	T	0.39187	-0.9626	10	0.13470	T	0.59	-4.7972	5.7171	0.17966	0.1238:0.0:0.5648:0.3113	.	160	Q7Z3Z2	RD3_HUMAN	L	160	ENSP00000355969:S160L	ENSP00000355969:S160L	S	-	2	0	RD3	209719110	0.998000	0.40836	0.191000	0.23289	0.630000	0.37929	3.193000	0.50997	0.927000	0.37143	0.555000	0.69702	TCG		0.687	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059		A	211652487	G	A	211652487	3	1	80	1	0	0	0	0	1	0	0	0	13224	1059	37	1	112	1	RD3	1	211652487	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	36286693	211652487	37598134	12	23187										
TAF5L	27097	broad.mit.edu	37	chr1	229730579	229730579	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gcgggtacgtccgatcaaatGaccacagcctggcggtgcgg	15	12	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:229730579G>C	ENST00000366676.1	-	4	1234	c.1235C>G	c.(1234-1236)tCa>tGa	p.S412*	TAF5L_ENST00000258281.2_Nonsense_Mutation_p.S412*			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	412					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.S412*(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CCGATCAAATGACCACAGCCT	0.542																																																1	Substitution - Nonsense(1)	large_intestine(1)	1											99	97	98					1																	229730579		2203	4300	6503	227797202	SO:0001587	stop_gained	27097			AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"WD repeat domain containing"	17304	protein-coding gene	gene with protein product	"PCAF associated factor 65 beta"		"TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.1235C>G	1.37:g.229730579G>C	ENSP00000355636:p.Ser412*		227797202	Q5TDI5|Q5TDI6|Q8IW31	Nonsense_Mutation	SNP	ENST00000366676.1	37	CCDS1581.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014828	0.93404	.	.	ENSG00000135801	ENST00000366676;ENST00000258281	.	.	.	5.79	4.88	0.63580	.	0.314599	0.34484	N	0.003930	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-5.0454	10.3713	0.44055	0.0703:0.1343:0.7954:0.0	.	.	.	.	X	412	.	ENSP00000258281:S412X	S	-	2	0	TAF5L	227797202	1.000000	0.71417	0.982000	0.44146	0.569000	0.35902	5.584000	0.67490	1.451000	0.47736	-0.136000	0.14681	TCA		0.542	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409		C	229730579	G	C	229730579	4	2	80	1	0	0	0	0	0	1	0	0	15568	1294	45	5	538	5	TAF5L	1	229730579	Nonsense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	18078092	229730579	19520042	13	23188										
RYR2	6262	broad.mit.edu	37	chr1	237802317	237802317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttccccattctactttagggGagagtgtggaggaaaatgca	12	7	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:237802317G>A	ENST00000366574.2	+	46	7248	c.6931G>A	c.(6931-6933)Gag>Aag	p.E2311K	RYR2_ENST00000360064.6_Missense_Mutation_p.E2309K|RYR2_ENST00000542537.1_Missense_Mutation_p.E2295K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2311	4 X approximate repeats.		E -> D (in CPVT1). {ECO:0000269|PubMed:12093772}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.E2309K(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TACTTTAGGGGAGAGTGTGGA	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	1											120	117	118					1																	237802317		1877	4114	5991	235868940	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.6931G>A	1.37:g.237802317G>A	ENSP00000355533:p.Glu2311Lys		235868940	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.010279	0.93346	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.95885	-3.84;-3.84;-3.84	5.05	5.05	0.67936	Intracellular calcium-release channel (1);	0.000000	0.64402	D	0.000005	D	0.97666	0.9235	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98408	1.0571	10	0.87932	D	0	-17.0922	18.7649	0.91868	0.0:0.0:1.0:0.0	.	2311	Q92736	RYR2_HUMAN	K	2311;2309;2295	ENSP00000355533:E2311K;ENSP00000353174:E2309K;ENSP00000443798:E2295K	ENSP00000353174:E2309K	E	+	1	0	RYR2	235868940	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.675000	0.98638	2.498000	0.84270	0.561000	0.74099	GAG		0.388	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237802317	G	A	237802317	3	1	80	1	0	0	0	0	1	0	0	0	13806	1175	41	3	7113	3	RYR2	1	237802317	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	8071738	237802317	11448304	14	23189										
FH	2271	broad.mit.edu	37	chr1	241665824	241665824	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	acatggttccccatgacttgGgctgcaaccatggtcattgc	10	12	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr1:241665824G>A	ENST00000366560.3	-	8	1193	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	385					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)	p.A385A(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		CCATGACTTGGGCTGCAACCA	0.418			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	1	Substitution - coding silent(1)	large_intestine(1)	1											104	87	93					1																	241665824		2203	4300	6503	239732447	SO:0001819	synonymous_variant	2271	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1155C>T	1.37:g.241665824G>A			239732447	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																				0.418	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241665824	G	A	241665824	2	1	80	1	0	0	0	0	0	0	0	1	5894	1219	43	3		3	FH	1	241665824	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	3863507	241665824	7584797	15	23190										
TSSC1	7260	broad.mit.edu	37	chr2	3358400	3358400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagtttgaggtgttaaggcaCgtgcctgcaggagggaagaa	16	6	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:3358400C>T	ENST00000382125.4	-	2	239	c.47G>A	c.(46-48)cGt>cAt	p.R16H	TSSC1_ENST00000443925.2_Missense_Mutation_p.R16H|TSSC1_ENST00000398659.4_Missense_Mutation_p.R16H	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	16								p.R16H(1)		breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		TGTTAAGGCACGTGCCTGCAG	0.363																																					Colon(140;1261 1762 4183 34270 49743)											1	Substitution - Missense(1)	large_intestine(1)	2											84	81	82					2																	3358400		2203	4300	6503	3337407	SO:0001583	missense	7260			AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"WD repeat domain containing"	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.47G>A	2.37:g.3358400C>T	ENSP00000371559:p.Arg16His		3337407	D6W4Y1|O43179|Q53S19|Q53SG2	Missense_Mutation	SNP	ENST00000382125.4	37	CCDS1651.1	.	.	.	.	.	.	.	.	.	.	c	22.6	4.306831	0.81247	.	.	ENSG00000032389	ENST00000382125;ENST00000398659;ENST00000443925;ENST00000444776	D;D	0.97378	-3.52;-4.36	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	D	0.98397	0.9467	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99075	1.0835	10	0.87932	D	0	-0.4511	15.0171	0.71594	0.0:1.0:0.0:0.0	.	16	Q53HC9	TSSC1_HUMAN	H	16	ENSP00000371559:R16H;ENSP00000381652:R16H	ENSP00000371559:R16H	R	-	2	0	TSSC1	3337407	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	6.132000	0.71676	2.478000	0.83669	0.558000	0.71614	CGT		0.363	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		T	3358400	C	T	3358400	3	4	80	1	0	0	0	0	1	0	0	0	16706	536	19	1	1148	1	TSSC1	2	3358400	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10		3358400	239840973	16	23191										
C2orf15	80705	broad.mit.edu	37	chr2	99767052	99767052	+	Intron	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cacttagtaaatctgctactCaggtatctgctatacatatg	6	9	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:99767052C>G	ENST00000393483.3	-	1	225				C2ORF15_ENST00000409684.1_Missense_Mutation_p.Q45E|C2ORF15_ENST00000302513.2_Missense_Mutation_p.Q45E	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.Q45E(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						ATCTGCTACTCAGGTATCTGC	0.368																																																1	Substitution - Missense(1)	large_intestine(1)	2											61	62	62					2																	99767052		2203	4300	6503	99133484	SO:0001627	intron_variant	150590			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.619+4103G>C	2.37:g.99767052C>G			99133484	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.718688	0.30503	.	.	ENSG00000241962	ENST00000302513;ENST00000409684	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	T	0.33147	0.0853	N	0.08118	0	0.80722	D	1	P	0.35872	0.525	B	0.33454	0.164	T	0.40175	-0.9577	8	0.87932	D	0	-0.0011	13.7268	0.62763	0.0:1.0:0.0:0.0	.	45	Q8WU43	CB015_HUMAN	E	45	.	ENSP00000302202:Q45E	Q	+	1	0	C2orf15	99133484	0.987000	0.35691	0.958000	0.39756	0.756000	0.42949	3.369000	0.52365	2.605000	0.88082	0.462000	0.41574	CAG		0.368	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		G	99767052	C	G	99767052	1	3	80	0	1	0	0	0	0	0	0	0	2162	827	29	5		5	C2orf15	2	99767052	Intron	SNP	C	TCGA-AG-A036-01A-12W-A096-10	96408652	99767052	143432321	17	23192										
AFF3	3899	broad.mit.edu	37	chr2	100168047	100168047	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cccatgagcagatccaggtcGttgaagaattctagggggac	13	9	1	4	rs201311680		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:100168047G>A	ENST00000409236.2	-	23	3682	c.3570C>T	c.(3568-3570)aaC>aaT	p.N1190N	AFF3_ENST00000317233.4_Silent_p.N1190N|AFF3_ENST00000356421.2_Silent_p.N1215N|AFF3_ENST00000409579.1_Silent_p.N1215N			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	1190					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.N1215N(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GATCCAGGTCGTTGAAGAATT	0.537																																																1	Substitution - coding silent(1)	large_intestine(1)	2											64	61	62					2																	100168047		2203	4300	6503	99534479	SO:0001819	synonymous_variant	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.3570C>T	2.37:g.100168047G>A			99534479	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																				0.537	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		A	100168047	G	A	100168047	2	1	80	1	0	0	0	0	0	0	0	1	358	1136	40	1		1	AFF3	2	100168047	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	400995	100168047	143031326	18	23193										
AFF3	3899	broad.mit.edu	37	chr2	100199293	100199293	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccgtgaggctgcagctggctGtcggccttaggctttttgct	14	11	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:100199293G>T	ENST00000409236.2	-	15	2872	c.2760C>A	c.(2758-2760)gaC>gaA	p.D920E	AFF3_ENST00000317233.4_Missense_Mutation_p.D920E|AFF3_ENST00000356421.2_Missense_Mutation_p.D945E|AFF3_ENST00000409579.1_Missense_Mutation_p.D945E			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	920					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.D945E(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GCAGCTGGCTGTCGGCCTTAG	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	2											132	120	124					2																	100199293		2203	4300	6503	99565725	SO:0001583	missense	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2760C>A	2.37:g.100199293G>T	ENSP00000387207:p.Asp920Glu		99565725	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	5.340	0.247972	0.10130	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.93	4.12	0.48240	.	0.201183	0.40908	N	0.000999	T	0.18551	0.0445	N	0.00114	-2.085	0.25476	N	0.987786	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.34700	-0.9818	10	0.02654	T	1	.	10.1629	0.42862	0.0:0.6929:0.2086:0.0984	.	920;945	P51826;P51826-2	AFF3_HUMAN;.	E	920;945;945;920	ENSP00000317421:D920E;ENSP00000348793:D945E;ENSP00000386834:D945E;ENSP00000387207:D920E	ENSP00000317421:D920E	D	-	3	2	AFF3	99565725	1.000000	0.71417	0.916000	0.36221	0.940000	0.58332	2.013000	0.40942	0.837000	0.34925	0.655000	0.94253	GAC		0.488	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		T	100199293	G	T	100199293	3	4	80	1	0	0	0	0	1	0	0	0	358	1368	48	2	956	2	AFF3	2	100199293	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	31246	100199293	143000080	19	23194										
DPP10	57628	broad.mit.edu	37	chr2	116572435	116572435	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gactgggattccgtactcatTgacatggataatgtcattgt	10	7	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:116572435T>A	ENST00000410059.1	+	20	2247	c.1767T>A	c.(1765-1767)atT>atA	p.I589I	DPP10_ENST00000393147.2_Silent_p.I593I|DPP10_ENST00000409163.1_Silent_p.I539I|DPP10_ENST00000310323.8_Silent_p.I582I	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	589						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.I589I(1)|p.I582I(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CCGTACTCATTGACATGGATA	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	2											141	136	138					2																	116572435		2203	4300	6503	116288905	SO:0001819	synonymous_variant	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1767T>A	2.37:g.116572435T>A			116288905	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																				0.423	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116572435	T	A	116572435	2	1	80	1	0	0	0	0	0	0	0	1	4738	1800	63	5		5	DPP10	2	116572435	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10	16373142	116572435	126626938	20	23195										
TFCP2L1	29842	broad.mit.edu	37	chr2	121989409	121989409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagcagccctcacctcgttgCtcaccaccacatggatgccc	7	19	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:121989409C>T	ENST00000263707.5	-	13	1431	c.1334G>A	c.(1333-1335)aGc>aAc	p.S445N		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	445					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S445N(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CACCTCGTTGCTCACCACCAC	0.632																																																1	Substitution - Missense(1)	large_intestine(1)	2											77	66	70					2																	121989409		2203	4300	6503	121705879	SO:0001583	missense	29842			AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1334G>A	2.37:g.121989409C>T	ENSP00000263707:p.Ser445Asn		121705879	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	37	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.232428	0.58777	.	.	ENSG00000115112	ENST00000263707	T	0.22743	1.94	5.43	4.52	0.55395	.	0.143803	0.64402	N	0.000003	T	0.27663	0.0680	M	0.73962	2.25	0.53005	D	0.999965	B	0.24882	0.113	B	0.27380	0.079	T	0.05886	-1.0858	10	0.56958	D	0.05	.	12.1288	0.53932	0.0:0.9122:0.0:0.0878	.	445	Q9NZI6	TF2L1_HUMAN	N	445	ENSP00000263707:S445N	ENSP00000263707:S445N	S	-	2	0	TFCP2L1	121705879	0.995000	0.38212	0.989000	0.46669	0.872000	0.50106	1.341000	0.33907	1.207000	0.43291	0.491000	0.48974	AGC		0.632	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	121989409	C	T	121989409	3	4	80	1	0	0	0	0	1	0	0	0	15835	797	28	3	117	3	TFCP2L1	2	121989409	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	5416974	121989409	121209964	21	23196										
THSD7B	80731	broad.mit.edu	37	chr2	137814076	137814076	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttcatgttgacgggtggacaAgtcacctgtctaactgtggt	12	8	3	1	rs546067581		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:137814076A>C	ENST00000409968.1	+	3	404	c.226A>C	c.(226-228)Agt>Cgt	p.S76R	THSD7B_ENST00000272643.3_Missense_Mutation_p.S76R|THSD7B_ENST00000413152.2_Missense_Mutation_p.S45R|THSD7B_ENST00000543459.1_5'Flank			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	76	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.S76R(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CGGGTGGACAAGTCACCTGTC	0.532													A|||	1	0.000199681	0	0	5008	,	,		19145	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	2											82	89	87					2																	137814076		2026	4199	6225	137530546	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.226A>C	2.37:g.137814076A>C	ENSP00000387145:p.Ser76Arg		137530546		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	A	15.94	2.980694	0.53827	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.60548	0.18;0.18;0.18	5.89	3.5	0.40072	.	0.170423	0.64402	D	0.000008	T	0.48995	0.1531	L	0.31476	0.935	0.80722	D	1	P	0.44734	0.842	P	0.51945	0.685	T	0.40079	-0.9582	10	0.11485	T	0.65	.	6.205	0.20598	0.7452:0.0:0.1352:0.1196	.	45	C9JKN6	.	R	76;76;45	ENSP00000387145:S76R;ENSP00000272643:S76R;ENSP00000413841:S45R	ENSP00000272643:S76R	S	+	1	0	THSD7B	137530546	0.999000	0.42202	0.693000	0.30195	0.985000	0.73830	4.439000	0.59968	0.475000	0.27415	0.477000	0.44152	AGT		0.532	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		C	137814076	A	C	137814076	3	2	80	1	0	0	0	0	1	0	0	0	15919	72	3	4	139	4	THSD7B	2	137814076	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	15824667	137814076	105385297	22	23197										
LRP1B	53353	broad.mit.edu	37	chr2	141458027	141458027	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcagaaagatgtatacttttTaatattgttcttcctgaata	5	5	2	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:141458027T>G	ENST00000389484.3	-	41	7562	c.6591A>C	c.(6589-6591)ttA>ttC	p.L2197F		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2197					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.L2197F(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		GTATACTTTTTAATATTGTTC	0.388										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	large_intestine(1)	2											93	98	96					2																	141458027		2203	4300	6503	141174497	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6591A>C	2.37:g.141458027T>G	ENSP00000374135:p.Leu2197Phe		141174497	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513899	0.64522	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.92911	-3.13	4.47	3.21	0.36854	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.56097	U	0.000038	D	0.92799	0.7710	L	0.52364	1.645	0.42393	D	0.99253	D	0.71674	0.998	D	0.83275	0.996	D	0.91120	0.4929	10	0.45353	T	0.12	.	5.8495	0.18685	0.0:0.0867:0.1691:0.7442	.	2197	Q9NZR2	LRP1B_HUMAN	F	2197;2135	ENSP00000374135:L2197F	ENSP00000374135:L2197F	L	-	3	2	LRP1B	141174497	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.470000	0.22084	1.766000	0.52107	0.477000	0.44152	TTA		0.388	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141458027	T	G	141458027	3	3	80	1	0	0	0	0	1	0	0	0	8984	1751	61	4	7412	4	LRP1B	2	141458027	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	3643951	141458027	101741346	23	23198										
RIF1	55183	broad.mit.edu	37	chr2	152322629	152322629	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atgaaatctcatcacctgttAataaggtaaggggaatgagg	11	5	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:152322629A>C	ENST00000243326.5	+	29	7078	c.6595A>C	c.(6595-6597)Aat>Cat	p.N2199H	RIF1_ENST00000428287.2_Missense_Mutation_p.N2199H|RIF1_ENST00000453091.2_Missense_Mutation_p.N2199H|RIF1_ENST00000430328.2_Missense_Mutation_p.N2199H|RIF1_ENST00000444746.2_Missense_Mutation_p.N2199H			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.N2199H(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATCACCTGTTAATAAGGTAAG	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	2											50	53	52					2																	152322629		2201	4298	6499	152030875	SO:0001583	missense	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.6595A>C	2.37:g.152322629A>C	ENSP00000243326:p.Asn2199His		152030875	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	6.304	0.424223	0.11928	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.11712	2.78;2.75;2.75;2.78;2.75	6.16	3.91	0.45181	.	0.572763	0.20487	N	0.091364	T	0.10551	0.0258	L	0.51422	1.61	0.18873	N	0.999987	B;B	0.11235	0.004;0.004	B;B	0.09377	0.003;0.004	T	0.26916	-1.0089	10	0.28530	T	0.3	-1.4171	8.8834	0.35389	0.7368:0.1521:0.0:0.1111	.	2199;2199	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	H	2199	ENSP00000390181:N2199H;ENSP00000414615:N2199H;ENSP00000415691:N2199H;ENSP00000243326:N2199H;ENSP00000416123:N2199H	ENSP00000243326:N2199H	N	+	1	0	RIF1	152030875	0.975000	0.34042	0.931000	0.37212	0.127000	0.20565	2.513000	0.45494	0.628000	0.30357	0.528000	0.53228	AAT		0.408	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			C	152322629	A	C	152322629	3	2	80	1	0	0	0	0	1	0	0	0	13396	362	13	4	6709	4	RIF1	2	152322629	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	10864602	152322629	90876744	24	23199										
PRPF40A	55660	broad.mit.edu	37	chr2	153514525	153514525	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctctcgctcagcatcggattCtggagagtcctgtatgaata	10	10	3	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:153514525C>A	ENST00000410080.1	-	25	3119	c.2578G>T	c.(2578-2580)Gaa>Taa	p.E860*		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	887					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E756*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						GCATCGGATTCTGGAGAGTCC	0.338																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											103	85	91					2																	153514525		1811	4067	5878	153222771	SO:0001587	stop_gained	55660			AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.2578G>T	2.37:g.153514525C>A	ENSP00000386458:p.Glu860*		153222771	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Nonsense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	C	44	11.258635	0.99538	.	.	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961	.	.	.	5.41	5.41	0.78517	.	0.093853	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-18.8005	16.3008	0.82811	0.0:1.0:0.0:0.0	.	.	.	.	X	860;869;756;811	.	ENSP00000348770:E869X	E	-	1	0	PRPF40A	153222771	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.440000	0.66563	2.702000	0.92279	0.563000	0.77884	GAA		0.338	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		A	153514525	C	A	153514525	4	1	80	1	0	0	0	0	0	1	0	0	12605	922	32	2	222	2	PRPF40A	2	153514525	Nonsense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	1191896	153514525	89684848	25	23200										
XIRP2	129446	broad.mit.edu	37	chr2	168100237	168100237	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggatgtttgaaacacagccgTtggacacaattaacaaagat	9	7	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:168100237T>C	ENST00000409195.1	+	9	2424	c.2335T>C	c.(2335-2337)Ttg>Ctg	p.L779L	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Silent_p.L779L|XIRP2_ENST00000409273.1_Silent_p.L557L|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	604					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.L779L(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACACAGCCGTTGGACACAAT	0.408																																																1	Substitution - coding silent(1)	large_intestine(1)	2											70	65	67					2																	168100237		1860	4097	5957	167808483	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2335T>C	2.37:g.168100237T>C			167808483	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																				0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168100237	T	C	168100237	2	2	80	1	0	0	0	0	0	0	0	1	17470	1722	60	4		4	XIRP2	2	168100237	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10	14585712	168100237	75099136	26	23201										
CHN1	1123	broad.mit.edu	37	chr2	175711665	175711665	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcgttttctttcagagttgcTcttctaacaagtgatgtcaa	7	8	5	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:175711665T>A	ENST00000409900.3	-	7	883	c.570A>T	c.(568-570)agA>agT	p.R190S	CHN1_ENST00000488080.1_5'UTR|CHN1_ENST00000409597.1_5'Flank|CHN1_ENST00000409156.3_Intron|CHN1_ENST00000295497.7_Missense_Mutation_p.R65S	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	190					ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)	p.R190S(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			TCAGAGTTGCTCTTCTAACAA	0.363			T	TAF15	extraskeletal myxoid chondrosarcoma																																		Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	1	Substitution - Missense(1)	large_intestine(1)	2											50	43	45					2																	175711665		1793	4013	5806	175419911	SO:0001583	missense	1123				CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656		"Rho GTPase activating proteins", "SH2 domain containing"	1943	protein-coding gene	gene with protein product	"Chimerin 1 (GTPase-activating protein, rho, 2)", "chimaerin 1"	118423	"Duane retraction syndrome 2", "chimerin (chimaerin) 1"	CHN, DURS2		2299665, 15013773, 18653847	Standard	NM_001822		Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.570A>T	2.37:g.175711665T>A	ENSP00000386741:p.Arg190Ser		175419911	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	Missense_Mutation	SNP	ENST00000409900.3	37	CCDS46455.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.107066	0.77096	.	.	ENSG00000128656	ENST00000409900;ENST00000295497;ENST00000443238;ENST00000444573	T;T;T;D	0.93426	-0.54;-0.48;-1.46;-3.22	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.94565	0.8249	L	0.38175	1.15	0.80722	D	1	P;D	0.76494	0.895;0.999	P;D	0.70016	0.573;0.967	D	0.94705	0.7887	10	0.49607	T	0.09	.	16.1199	0.81342	0.0:0.0:0.0:1.0	.	190;65	P15882;P15882-2	CHIN_HUMAN;.	S	190;65;16;65	ENSP00000386741:R190S;ENSP00000295497:R65S;ENSP00000409798:R16S;ENSP00000392603:R65S	ENSP00000295497:R65S	R	-	3	2	CHN1	175419911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.372000	0.52387	2.194000	0.70268	0.533000	0.62120	AGA		0.363	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334453.1	NM_001822		A	175711665	T	A	175711665	3	1	80	1	0	0	0	0	1	0	0	0	3368	1548	54	5	837	5	CHN1	2	175711665	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	7611428	175711665	67487708	27	23202										
TTN	7273	broad.mit.edu	37	chr2	179424792	179424792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgtcatcagattttttgtaTtctacagtatatccagttat	6	6	3	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:179424792T>C	ENST00000591111.1	-	276	81368	c.81144A>G	c.(81142-81144)gaA>gaG	p.E27048E	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.E28689E|TTN_ENST00000342992.6_Silent_p.E26121E|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.E19816E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.E19749E|TTN_ENST00000460472.2_Silent_p.E19624E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27048	Fibronectin type-III 97. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E19624E(1)|p.E19816E(1)|p.E19749E(1)|p.E26119E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTTTTGTATTCTACAGTAT	0.423																																																4	Substitution - coding silent(4)	large_intestine(4)	2											70	67	68					2																	179424792		1848	4085	5933	179133038	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81144A>G	2.37:g.179424792T>C			179133038	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179424792	T	C	179424792	2	2	80	1	0	0	0	0	0	0	0	1	16775	1490	52	4		4	TTN	2	179424792	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10	3713127	179424792	63774581	28	23203										
DNAH7	56171	broad.mit.edu	37	chr2	196877517	196877517	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tttcaaacctttacattttaAgtagagtctctttggcagag	7	7	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:196877517A>T	ENST00000312428.6	-	10	1083	c.983T>A	c.(982-984)cTt>cAt	p.L328H	DNAH7_ENST00000410072.1_Missense_Mutation_p.L328H	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	328	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.L328H(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTACATTTTAAGTAGAGTCTC	0.323																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	77	78					2																	196877517		1813	4075	5888	196585762	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.983T>A	2.37:g.196877517A>T	ENSP00000311273:p.Leu328His		196585762	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.352042	0.41700	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.77	5.28	5.28	0.74379	.	0.090347	0.45606	D	0.000354	T	0.34774	0.0909	M	0.74881	2.28	0.39441	D	0.967247	P	0.35821	0.523	B	0.40534	0.332	T	0.25293	-1.0136	10	0.44086	T	0.13	.	12.7278	0.57180	1.0:0.0:0.0:0.0	.	328	Q8WXX0	DYH7_HUMAN	H	328	ENSP00000311273:L328H;ENSP00000386260:L328H	ENSP00000311273:L328H	L	-	2	0	DNAH7	196585762	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.576000	0.60915	1.999000	0.58509	0.482000	0.46254	CTT		0.323	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196877517	A	T	196877517	3	4	80	1	0	0	0	0	1	0	0	0	4617	72	3	5	11315	5	DNAH7	2	196877517	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	17452725	196877517	46321856	29	23204										
SGOL2	151246	broad.mit.edu	37	chr2	201438405	201438405	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aagtctactgtatctgaacaAgctgataaggaaaacaattt	7	6	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:201438405A>T	ENST00000357799.4	+	7	3434	c.3336A>T	c.(3334-3336)caA>caT	p.Q1112H		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	1112					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.Q1112H(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TATCTGAACAAGCTGATAAGG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	2											109	103	105					2																	201438405		1839	4079	5918	201146650	SO:0001583	missense	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.3336A>T	2.37:g.201438405A>T	ENSP00000350447:p.Gln1112His		201146650	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020974	0.35606	.	.	ENSG00000163535	ENST00000357799	T	0.16597	2.33	5.52	-3.67	0.04476	.	0.347785	0.24415	N	0.038736	T	0.11024	0.0269	L	0.55481	1.735	0.09310	N	0.999999	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12837	0.008;0.008;0.008	T	0.17137	-1.0379	10	0.41790	T	0.15	0.6691	1.5823	0.02637	0.2762:0.3089:0.2868:0.1281	.	1112;1112;1112	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	H	1112	ENSP00000350447:Q1112H	ENSP00000350447:Q1112H	Q	+	3	2	SGOL2	201146650	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.036000	0.13819	-0.791000	0.04486	0.528000	0.53228	CAA		0.378	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		T	201438405	A	T	201438405	3	4	80	1	0	0	0	0	1	0	0	0	14254	69	3	5	3358	5	SGOL2	2	201438405	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	4560888	201438405	41760968	30	23205										
MARCH4	57574	broad.mit.edu	37	chr2	217234552	217234552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cccagtgagtagcgatcctcGgtcttctccttacagaagtc	9	13	2	2	rs374936017		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:217234552G>A	ENST00000273067.4	-	1	2198	c.432C>T	c.(430-432)acC>acT	p.T144T		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	144						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T144T(2)		breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		AGCGATCCTCGGTCTTCTCCT	0.587																																																2	Substitution - coding silent(2)	large_intestine(2)	2											72	63	66					2																	217234552		2203	4300	6503	216942797	SO:0001819	synonymous_variant	57574			AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.432C>T	2.37:g.217234552G>A			216942797	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																				0.587	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		A	217234552	G	A	217234552	2	1	80	1	0	0	0	0	0	0	0	1	9333	1103	39	1		1	MARCH4	2	217234552	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	15796147	217234552	25964821	31	23206										
FEV	54738	broad.mit.edu	37	chr2	219848966	219848966	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atctcacctttctgaaccgcGgggctcagcggcccccagct	10	17	3	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:219848966G>A	ENST00000295727.1	-	2	695	c.114C>T	c.(112-114)ccC>ccT	p.P38P		NM_017521.2	NP_059991.1	Q99581	FEV_HUMAN	FEV (ETS oncogene family)	38					cell differentiation (GO:0030154)|neuron fate specification (GO:0048665)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P38P(1)	EWSR1/FEV(11)|FUS/FEV(2)	large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTGAACCGCGGGGCTCAGCG	0.657			T	"EWSR1,  FUS"	Ewing sarcoma																																NSCLC(198;941 2228 4658 24163 34665)		Dom	yes		2	2q36	54738	FEV protein - (HSRNAFEV)		M	1	Substitution - coding silent(1)	large_intestine(1)	2											9	10	10					2																	219848966		2191	4288	6479	219557210	SO:0001819	synonymous_variant	54738				CCDS2428.1	2q36	2008-02-05			ENSG00000163497	ENSG00000163497			18562	protein-coding gene	gene with protein product		607150	"FEV (fifth Ewing variant)"			9121764	Standard	NM_017521		Approved	Pet-1	uc002vji.1	Q99581	OTTHUMG00000133080	ENST00000295727.1:c.114C>T	2.37:g.219848966G>A			219557210		Silent	SNP	ENST00000295727.1	37	CCDS2428.1																																																																																				0.657	FEV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256725.1			A	219848966	G	A	219848966	2	1	80	1	0	0	0	0	0	0	0	1	5841	1103	39	1		1	FEV	2	219848966	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	2614414	219848966	23350407	32	23207										
SLC4A3	6508	broad.mit.edu	37	chr2	220494319	220494319	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagttctccattggaagtgaCgaggatgacagtccaggcct	12	10	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr2:220494319C>T	ENST00000358055.3	+	5	1025	c.513C>T	c.(511-513)gaC>gaT	p.D171D	SLC4A3_ENST00000373762.3_Silent_p.D171D|SLC4A3_ENST00000373760.2_Silent_p.D171D|SLC4A3_ENST00000273063.6_Silent_p.D171D|AC009955.8_ENST00000455896.1_RNA|SLC4A3_ENST00000497589.1_Intron|SLC4A3_ENST00000317151.3_Silent_p.D171D			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	171					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.D171D(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTGGAAGTGACGAGGATGACA	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	2											43	43	43					2																	220494319		2203	4300	6503	220202563	SO:0001819	synonymous_variant	6508				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.513C>T	2.37:g.220494319C>T			220202563	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	De_novo_Start_InFrame	SNP	ENST00000358055.3	37	CCDS2445.1																																																																																				0.637	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220494319	C	T	220494319	2	4	80	1	0	0	0	0	0	0	0	1	14692	535	19	1		1	SLC4A3	2	220494319	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	645353	220494319	22705054	33	23208										
SCN10A	6336	broad.mit.edu	37	chr3	38833624	38833624	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gcccgagtggcactaaaccgGgaaatggtcctccctttgtt	11	12	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:38833624G>T	ENST00000449082.2	-	2	305	c.306C>A	c.(304-306)tcC>tcA	p.S102S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	102					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.S102S(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CACTAAACCGGGAAATGGTCC	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	3											187	183	184					3																	38833624		2203	4300	6503	38808628	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.306C>A	3.37:g.38833624G>T			38808628	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.443	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38833624	G	T	38833624	2	4	80	1	0	0	0	0	0	0	0	1	13949	1219	43	2		2	SCN10A	3	38833624	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10		38833624	159188806	34	23209										
NBEAL2	23218	broad.mit.edu	37	chr3	47039977	47039977	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	catccagtacatgtccagcaTagttcgggagcacagacaga	10	11	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:47039977T>A	ENST00000450053.3	+	22	3322	c.3143T>A	c.(3142-3144)aTa>aAa	p.I1048K	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.I1048K	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1048					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.I609K(1)|p.I1048K(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		ATGTCCAGCATAGTTCGGGAG	0.592											OREG0015546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				2	Substitution - Missense(2)	large_intestine(2)	3											51	53	52					3																	47039977		2066	4219	6285	47014981	SO:0001583	missense	23218			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.3143T>A	3.37:g.47039977T>A	ENSP00000415034:p.Ile1048Lys	943	47014981	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.01|14.01	2.406652|2.406652	0.42715|0.42715	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000292309;ENST00000450053|ENST00000416683	T;T|.	0.59083|.	0.52;0.29|.	5.31|5.31	4.12|4.12	0.48240|0.48240	Armadillo-like helical (1);|.	0.352161|.	0.29876|.	N|.	0.010979|.	T|.	0.59169|.	0.2174|.	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	B|.	0.32245|.	0.361|.	B|.	0.26416|.	0.069|.	T|.	0.56697|.	-0.7936|.	10|.	0.66056|.	D|.	0.02|.	.|.	8.6987|8.6987	0.34312|0.34312	0.0:0.14:0.0:0.86|0.0:0.14:0.0:0.86	.|.	1048|.	Q6ZNJ1|.	NBEL2_HUMAN|.	K|K	1048|520	ENSP00000292309:I1048K;ENSP00000415034:I1048K|.	ENSP00000292309:I1048K|.	I|X	+|+	2|1	0|0	NBEAL2|NBEAL2	47014981|47014981	1.000000|1.000000	0.71417|0.71417	0.780000|0.780000	0.31762|0.31762	0.487000|0.487000	0.33371|0.33371	4.567000|4.567000	0.60850|0.60850	2.234000|2.234000	0.73211|0.73211	0.459000|0.459000	0.35465|0.35465	ATA|TAG		0.592	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		A	47039977	T	A	47039977	3	1	80	1	0	0	0	0	1	0	0	0	10219	1406	49	5	3229	5	NBEAL2	3	47039977	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	8206353	47039977	150982453	35	23210										
RAD54L2	23132	broad.mit.edu	37	chr3	51697105	51697105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccccgtcagttcctcttccaCggctacctcagtcactgcca	6	19	4	0	rs139648304		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:51697105C>T	ENST00000409535.2	+	22	4198	c.4073C>T	c.(4072-4074)aCg>aTg	p.T1358M	RAD54L2_ENST00000296477.3_Missense_Mutation_p.T1052M	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1358						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)	p.T1358M(1)		NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TCCTCTTCCACGGCTACCTCA	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	114	109	110		4073	5.6	1	3	dbSNP_134	110	0,8600		0,0,4300	no	missense	RAD54L2	NM_015106.2	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	1358/1468	51697105	1,13005	2203	4300	6503	51672145	SO:0001583	missense	23132			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.4073C>T	3.37:g.51697105C>T	ENSP00000386520:p.Thr1358Met		51672145	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	15.63	2.891351	0.52014	2.27E-4	0.0	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.94046	-3.23;-3.34	5.56	5.56	0.83823	.	0.128261	0.50627	D	0.000112	D	0.86347	0.5911	N	0.08118	0	0.80722	D	1	P;D	0.57257	0.955;0.979	B;B	0.41299	0.289;0.353	D	0.87628	0.2514	10	0.37606	T	0.19	-8.4982	18.5281	0.90980	0.0:1.0:0.0:0.0	.	1358;947	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	M	1358;1052	ENSP00000386520:T1358M;ENSP00000296477:T1052M	ENSP00000296477:T1052M	T	+	2	0	RAD54L2	51672145	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.593000	0.46180	2.609000	0.88269	0.655000	0.94253	ACG		0.572	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		T	51697105	C	T	51697105	3	4	80	1	0	0	0	0	1	0	0	0	13031	536	19	1	4155	1	RAD54L2	3	51697105	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	4657128	51697105	146325325	36	23211										
NFKBIZ	64332	broad.mit.edu	37	chr3	101578204	101578204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agtccattcagcagagagctCcaccgtattagctccattag	8	12	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:101578204C>T	ENST00000326172.5	+	12	2261	c.2146C>T	c.(2146-2148)Cca>Tca	p.P716S	NFKBIZ_ENST00000326151.5_Missense_Mutation_p.P594S|NFKBIZ_ENST00000394054.2_Missense_Mutation_p.P616S	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	716	Interaction with NFKB1/p50. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P716S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						GCAGAGAGCTCCACCGTATTA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	3											95	91	93					3																	101578204		2203	4300	6503	103060894	SO:0001583	missense	64332			AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"Ankyrin repeat domain containing"	29805	protein-coding gene	gene with protein product	"IL-1 inducible nuclear ankyrin-repeat protein"	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.2146C>T	3.37:g.101578204C>T	ENSP00000325663:p.Pro716Ser		103060894	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723621	0.30593	.	.	ENSG00000144802	ENST00000394054;ENST00000326151;ENST00000326172	T;T;T	0.53423	0.62;0.66;0.66	5.53	3.66	0.41972	.	0.194828	0.45126	D	0.000385	T	0.17619	0.0423	N	0.02539	-0.55	0.30429	N	0.777334	B;B	0.25667	0.131;0.045	B;B	0.27715	0.082;0.012	T	0.28554	-1.0040	10	0.06625	T	0.88	-3.5266	6.6104	0.22749	0.0:0.5467:0.3433:0.11	.	594;716	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	S	616;594;716	ENSP00000377618:P616S;ENSP00000325593:P594S;ENSP00000325663:P716S	ENSP00000325593:P594S	P	+	1	0	NFKBIZ	103060894	0.998000	0.40836	0.992000	0.48379	0.979000	0.70002	2.318000	0.43779	0.747000	0.32809	0.655000	0.94253	CCA		0.433	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		T	101578204	C	T	101578204	3	4	80	1	0	0	0	0	1	0	0	0	10414	855	30	3	2192	3	NFKBIZ	3	101578204	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	49881099	101578204	96444226	37	23212										
PIK3R4	30849	broad.mit.edu	37	chr3	130409453	130409453	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgggagccttggcagaatgtGagcgtcttgactcgtcctcc	13	11	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:130409453G>C	ENST00000356763.3	-	14	3701	c.3144C>G	c.(3142-3144)ctC>ctG	p.L1048L	PIK3R4_ENST00000512677.1_5'UTR	NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	1048					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1048L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GGCAGAATGTGAGCGTCTTGA	0.403																																																1	Substitution - coding silent(1)	large_intestine(1)	3											113	108	110					3																	130409453		2203	4300	6503	131892143	SO:0001819	synonymous_variant	30849			Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.3144C>G	3.37:g.130409453G>C			131892143	Q2TBF4	Silent	SNP	ENST00000356763.3	37	CCDS3067.1																																																																																				0.403	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		C	130409453	G	C	130409453	2	2	80	1	0	0	0	0	0	0	0	1	11952	1277	45	5		5	PIK3R4	3	130409453	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	28831249	130409453	67612977	38	23213										
FGF12	2257	broad.mit.edu	37	chr3	191888261	191888261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcataccttcaataggtttcGgtacaaaatgtgatgagggc	10	7	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr3:191888261G>A	ENST00000454309.2	-	4	1424	c.599C>T	c.(598-600)cCg>cTg	p.P200L	FGF12_ENST00000430714.1_Missense_Mutation_p.P101L|FGF12_ENST00000264730.3_Missense_Mutation_p.P138L|FGF12_ENST00000445105.2_Missense_Mutation_p.P138L|FGF12_ENST00000450716.1_Missense_Mutation_p.P138L	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	200					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)	p.P72L(1)|p.P200L(1)		endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		AATAGGTTTCGGTACAAAATG	0.428																																																2	Substitution - Missense(2)	large_intestine(2)	3											154	155	155					3																	191888261		2203	4300	6503	193370955	SO:0001583	missense	2257			U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"fibroblast growth factor 12B", "fibroblast growth factor homologous factor 1", "myocyte-activating factor", "fibroblast growth factor FGF-12b"	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.599C>T	3.37:g.191888261G>A	ENSP00000413496:p.Pro200Leu		193370955	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868522	0.91587	.	.	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000440901;ENST00000450716;ENST00000430714;ENST00000448795	T;T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.82870	0.5131	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83287	-0.0035	10	0.87932	D	0	.	19.6475	0.95784	0.0:0.0:1.0:0.0	.	138;200	P61328-2;P61328	.;FGF12_HUMAN	L	138;138;138;200;95;138;101;114	ENSP00000264730:P138L;ENSP00000393686:P138L;ENSP00000413496:P200L;ENSP00000400948:P95L;ENSP00000397635:P138L;ENSP00000410125:P101L;ENSP00000412904:P114L	ENSP00000264730:P138L	P	-	2	0	FGF12	193370955	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.476000	0.97823	2.885000	0.99019	0.655000	0.94253	CCG		0.428	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		A	191888261	G	A	191888261	3	1	80	1	0	0	0	0	1	0	0	0	5860	1116	39	1	140	1	FGF12	3	191888261	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	61478808	191888261	6134169	39	23214										
NCAPG	64151	broad.mit.edu	37	chr4	17829924	17829924	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gatgctgaaacattgcagaaAtgtcttattttatgctatga	8	5	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr4:17829924A>T	ENST00000251496.2	+	12	1853	c.1677A>T	c.(1675-1677)aaA>aaT	p.K559N		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	559					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.K559N(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		CATTGCAGAAATGTCTTATTT	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	4											137	135	136					4																	17829924		2203	4300	6503	17439022	SO:0001583	missense	64151			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.1677A>T	4.37:g.17829924A>T	ENSP00000251496:p.Lys559Asn		17439022	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	37	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.631598	0.67015	.	.	ENSG00000109805	ENST00000251496;ENST00000510063	T;T	0.52983	0.64;0.64	5.01	1.78	0.24846	Armadillo-type fold (1);	0.094038	0.64402	D	0.000001	T	0.62502	0.2433	M	0.76328	2.33	0.53005	D	0.999968	D	0.89917	1.0	D	0.79784	0.993	T	0.61797	-0.6989	10	0.72032	D	0.01	-17.5901	7.5322	0.27689	0.5015:0.0:0.4985:0.0	.	559	Q9BPX3	CND3_HUMAN	N	559;124	ENSP00000251496:K559N;ENSP00000425625:K124N	ENSP00000251496:K559N	K	+	3	2	NCAPG	17439022	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	0.702000	0.25631	0.488000	0.27723	-0.472000	0.04984	AAA		0.358	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		T	17829924	A	T	17829924	3	4	80	1	0	0	0	0	1	0	0	0	10238	98	4	5	1723	5	NCAPG	4	17829924	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10		17829924	173324352	40	23215										
SLC34A2	10568	broad.mit.edu	37	chr4	25664165	25664165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gagatgcccagcccaaccccGataagtacctcgaaggggcc	11	15	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr4:25664165G>A	ENST00000382051.3	+	2	93	c.43G>A	c.(43-45)Gat>Aat	p.D15N	SLC34A2_ENST00000504570.1_Missense_Mutation_p.D15N|SLC34A2_ENST00000503434.1_Missense_Mutation_p.D15N	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	15					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)	p.D15N(1)	SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GCCCAACCCCGATAAGTACCT	0.547			T	ROS1	NSCLC																																		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	1	Substitution - Missense(1)	large_intestine(1)	4											55	55	55					4																	25664165		2203	4300	6503	25273263	SO:0001583	missense	10568			AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.43G>A	4.37:g.25664165G>A	ENSP00000371483:p.Asp15Asn		25273263	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	37	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	G	2.796	-0.250195	0.05867	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	T;T;T;T;T	0.54279	0.58;1.97;1.97;1.97;0.58	5.52	-4.5	0.03493	.	1.911480	0.02175	N	0.060064	T	0.23611	0.0571	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41179	-0.9523	10	0.02654	T	1	1.7155	7.8636	0.29524	0.5117:0.0:0.3863:0.102	.	15;15	O95436-2;O95436	.;NPT2B_HUMAN	N	15	ENSP00000423038:D15N;ENSP00000425501:D15N;ENSP00000371483:D15N;ENSP00000423021:D15N;ENSP00000424266:D15N	ENSP00000371483:D15N	D	+	1	0	SLC34A2	25273263	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.088000	0.14979	-1.138000	0.02884	-0.238000	0.12139	GAT		0.547	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		A	25664165	G	A	25664165	3	1	80	1	0	0	0	0	1	0	0	0	14605	1058	37	1	45	1	SLC34A2	4	25664165	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	7834241	25664165	165490111	41	23216										
LRRC14B	389257	broad.mit.edu	37	chr5	195313	195313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agctgcgtgccgtgctgctgCgggctgaccgagaggacatc	16	12	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:195313C>T	ENST00000328278.3	+	2	1418	c.1390C>T	c.(1390-1392)Cgg>Tgg	p.R464W	CTD-2083E4.7_ENST00000563761.1_RNA	NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	464								p.R476W(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CGTGCTGCTGCGGGCTGACCG	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	5											110	122	118					5																	195313		2179	4278	6457	248313	SO:0001583	missense	389257				CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.1390C>T	5.37:g.195313C>T	ENSP00000327675:p.Arg464Trp		248313		Missense_Mutation	SNP	ENST00000328278.3	37	CCDS47184.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747772	0.30955	.	.	ENSG00000185028	ENST00000328278	T	0.01422	4.91	5.41	4.54	0.55810	.	0.419967	0.28317	N	0.015789	T	0.03871	0.0109	L	0.50333	1.59	0.09310	N	1	D	0.76494	0.999	P	0.56916	0.809	T	0.28235	-1.0050	10	0.72032	D	0.01	.	9.2007	0.37256	0.1652:0.6753:0.1594:0.0	.	464	A6NHZ5	LR14B_HUMAN	W	464	ENSP00000327675:R464W	ENSP00000327675:R464W	R	+	1	2	LRRC14B	248313	0.292000	0.24362	0.067000	0.19924	0.056000	0.15407	0.586000	0.23894	1.291000	0.44653	0.561000	0.74099	CGG		0.567	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478		T	195313	C	T	195313	3	4	80	1	0	0	0	0	1	0	0	0	8998	759	27	1	1396	1	LRRC14B	5	195313	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10		195313	180719947	42	23217										
ADAMTS16	170690	broad.mit.edu	37	chr5	5318311	5318311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgcctggctgggggccggcCggcctcaggctgcctcctgc	17	16	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:5318311C>T	ENST00000274181.7	+	22	3614	c.3476C>T	c.(3475-3477)cCg>cTg	p.P1159L		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	1159	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P1159L(1)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GGGGGCCGGCCGGCCTCAGGC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	5											32	38	36					5																	5318311		2059	4170	6229	5371311	SO:0001583	missense	170690			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.3476C>T	5.37:g.5318311C>T	ENSP00000274181:p.Pro1159Leu		5371311	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.977854	0.34942	.	.	ENSG00000145536	ENST00000274181	T	0.51071	0.72	4.69	3.77	0.43336	.	0.066204	0.64402	D	0.000011	T	0.42337	0.1198	M	0.79258	2.445	0.80722	D	1	P	0.38504	0.634	B	0.32864	0.154	T	0.30179	-0.9987	10	0.20046	T	0.44	.	9.2438	0.37513	0.0:0.8812:0.0:0.1188	.	1159	Q8TE57	ATS16_HUMAN	L	1159	ENSP00000274181:P1159L	ENSP00000274181:P1159L	P	+	2	0	ADAMTS16	5371311	0.786000	0.28738	0.588000	0.28705	0.031000	0.12232	2.704000	0.47118	1.022000	0.39626	0.563000	0.77884	CCG		0.647	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		T	5318311	C	T	5318311	3	4	80	1	0	0	0	0	1	0	0	0	261	652	23	1	3562	1	ADAMTS16	5	5318311	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	5122998	5318311	175596949	43	23218										
MARVELD2	153562	broad.mit.edu	37	chr5	68728916	68728916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gccacatcattcggaaagccGacaggttagtatgtgcagct	11	10	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:68728916G>A	ENST00000325631.5	+	5	1573	c.1499G>A	c.(1498-1500)cGa>cAa	p.R500Q	MARVELD2_ENST00000413223.2_Missense_Mutation_p.R384Q	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	500					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)		p.R500Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		TCGGAAAGCCGACAGGTTAGT	0.423																																																1	Substitution - Missense(1)	large_intestine(1)	5											105	101	102					5																	68728916		2203	4300	6503	68764672	SO:0001583	missense	153562			AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"tricellulin"	610572	"MARVEL (membrane-associating) domain containing 2", "deafness, autosomal recessive 49"	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.1499G>A	5.37:g.68728916G>A	ENSP00000323264:p.Arg500Gln		68764672	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	37	CCDS34175.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.789694	0.00623	.	.	ENSG00000152939	ENST00000325631;ENST00000454295;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T	0.39229	1.69;1.09;1.71;1.66;1.66	5.74	1.57	0.23409	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.436751	0.26130	N	0.026180	T	0.12220	0.0297	N	0.01705	-0.755	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.08055	0.002;0.003	T	0.28106	-1.0054	10	0.07482	T	0.82	-16.6217	4.3767	0.11274	0.4114:0.3218:0.2668:0.0	.	488;500	Q8N4S9-3;Q8N4S9	.;MALD2_HUMAN	Q	500;488;500;384;384	ENSP00000323264:R500Q;ENSP00000396244:R488Q;ENSP00000423490:R500Q;ENSP00000414776:R384Q;ENSP00000398922:R384Q	ENSP00000323264:R500Q	R	+	2	0	MARVELD2	68764672	0.001000	0.12720	0.011000	0.14972	0.053000	0.15095	-0.390000	0.07332	-0.008000	0.14320	-0.119000	0.15052	CGA		0.423	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		A	68728916	G	A	68728916	3	1	80	1	0	0	0	0	1	0	0	0	9348	1058	37	1	1513	1	MARVELD2	5	68728916	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	63410605	68728916	112186344	44	23219										
APC	324	broad.mit.edu	37	chr5	112151261	112151261	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtagcacacactctgcacctCgaaggctgacaagtcatctg	9	13	3	1	rs137854568		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:112151261C>T	ENST00000457016.1	+	9	1284	c.904C>T	c.(904-906)Cga>Tga	p.R302*	APC_ENST00000508376.2_Nonsense_Mutation_p.R302*|APC_ENST00000257430.4_Nonsense_Mutation_p.R302*			P25054	APC_HUMAN	adenomatous polyposis coli	302	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R302*(13)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTCTGCACCTCGAAGGCTGAC	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	13	Substitution - Nonsense(13)	large_intestine(13)	5	GRCh37	CM910029	APC	M	rs137854568						113	100	104					5																	112151261		2202	4300	6502	112179160	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.904C>T	5.37:g.112151261C>T	ENSP00000413133:p.Arg302*		112179160	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.654520	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5148	18.9031	0.92451	0.0:1.0:0.0:0.0	.	.	.	.	X	302;284;302;302;302	.	ENSP00000257430:R302X	R	+	1	2	APC	112179160	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.567000	0.60850	2.520000	0.84964	0.650000	0.86243	CGA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112151261	C	T	112151261	4	4	80	1	0	0	0	0	0	1	0	0	763	876	31	1	934	1	APC	5	112151261	Nonsense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	43422345	112151261	68763999	45	23220										
APC	324	broad.mit.edu	37	chr5	112175507	112175507	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gttcgattgccagctccgttCagagtgaaccatgcagtgga	12	10	1	2	rs587782518		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:112175507C>T	ENST00000457016.1	+	16	4596	c.4216C>T	c.(4216-4218)Cag>Tag	p.Q1406*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1406*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1406*			P25054	APC_HUMAN	adenomatous polyposis coli	1406	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1406*(15)|p.Q1406fs*11(1)|p.?(1)|p.K1192fs*3(1)|p.I1401fs*2(1)|p.Y1376fs*41(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCTCCGTTCAGAGTGAACC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(15)|Deletion - Frameshift(3)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(18)|soft_tissue(1)|skin(1)	5	GRCh37	CI084250|CM023011	APC	I|M							113	105	108					5																	112175507		2202	4300	6502	112203406	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4216C>T	5.37:g.112175507C>T	ENSP00000413133:p.Gln1406*		112203406	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.658788	0.98903	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.187376	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.0613	15.6825	0.77381	0.0:0.8637:0.1363:0.0	.	.	.	.	X	1406	.	.	Q	+	1	0	APC	112203406	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.175000	0.77632	1.615000	0.50252	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175507	C	T	112175507	4	4	80	1	0	0	0	0	0	1	0	0	763	827	29	3	4274	3	APC	5	112175507	Nonsense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	24246	112175507	68739753	46	23221										
PCDHB8	56128	broad.mit.edu	37	chr5	140558959	140558959	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgtcggacgtcaatgacaaCgcccccgccttcacccaaac	8	17	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:140558959C>T	ENST00000239444.2	+	1	1589	c.1344C>T	c.(1342-1344)aaC>aaT	p.N448N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	448	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N448N(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCAATGACAACGCCCCCGCCT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	5											163	209	193					5																	140558959		2203	4300	6503	140539143	SO:0001819	synonymous_variant	56128			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1344C>T	5.37:g.140558959C>T			140539143	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																				0.592	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140558959	C	T	140558959	2	4	80	1	0	0	0	0	0	0	0	1	11579	535	19	1		1	PCDHB8	5	140558959	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	28383452	140558959	40356301	47	23222										
PCDHGB2	56103	broad.mit.edu	37	chr5	140741735	140741735	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	attgccagacctcagcgaccGccgggagccctctgaccccc	10	19	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:140741735G>A	ENST00000522605.1	+	1	2033	c.2033G>A	c.(2032-2034)cGc>cAc	p.R678H	PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	678					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R678H(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCAGCGACCGCCGGGAGCCC	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	5											57	62	60					5																	140741735		2018	4191	6209	140721919	SO:0001583	missense	56103			AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2033G>A	5.37:g.140741735G>A	ENSP00000429018:p.Arg678His		140721919	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	4.776	0.144372	0.09134	.	.	ENSG00000253910	ENST00000522605	T	0.51071	0.72	4.95	-4.49	0.03504	.	.	.	.	.	T	0.29355	0.0731	L	0.43757	1.38	0.09310	N	1	B;B	0.15141	0.005;0.012	B;B	0.09377	0.003;0.004	T	0.26849	-1.0091	9	0.15499	T	0.54	.	3.8358	0.08893	0.4849:0.0999:0.3148:0.1004	.	678;678	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	H	678	ENSP00000429018:R678H	ENSP00000429018:R678H	R	+	2	0	PCDHGB2	140721919	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.816000	0.00752	-1.278000	0.02408	-1.439000	0.01073	CGC		0.597	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140741735	G	A	140741735	3	1	80	1	0	0	0	0	1	0	0	0	11594	1087	38	1	2035	1	PCDHGB2	5	140741735	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	182776	140741735	40173525	48	23223										
FBXO38	81545	broad.mit.edu	37	chr5	147796631	147796631	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cttgttagcaaccagaactcCaacaatgacgataataatgc	6	10	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:147796631C>A	ENST00000340253.5	+	12	1650	c.1482C>A	c.(1480-1482)tcC>tcA	p.S494S	FBXO38_ENST00000296701.6_Silent_p.S494S|FBXO38_ENST00000394370.3_Silent_p.S494S|FBXO38_ENST00000513826.1_Silent_p.S494S			Q6PIJ6	FBX38_HUMAN	F-box protein 38	494					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S494S(1)	ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAGAACTCCAACAATGACG	0.453																																																1	Substitution - coding silent(1)	large_intestine(1)	5											175	146	156					5																	147796631		2203	4300	6503	147776824	SO:0001819	synonymous_variant	81545			BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.1482C>A	5.37:g.147796631C>A			147776824	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Silent	SNP	ENST00000340253.5	37																																																																																					0.453	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		A	147796631	C	A	147796631	2	1	80	1	0	0	0	0	0	0	0	1	5765	581	21	2		2	FBXO38	5	147796631	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	7054896	147796631	33118629	49	23224										
HNRNPH1	3187	broad.mit.edu	37	chr5	179045226	179045226	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	accctctaccagccccaggtCtgtcataaggacctggccgc	9	17	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr5:179045226C>T	ENST00000356731.5	-	5	2170	c.635G>A	c.(634-636)aGa>aAa	p.R212K	HNRNPH1_ENST00000329433.6_Missense_Mutation_p.R212K|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.R212K|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000442819.2_Missense_Mutation_p.R212K|HNRNPH1_ENST00000510411.1_Missense_Mutation_p.R212K|HNRNPH1_ENST00000511300.2_5'Flank			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	212					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)	p.R212K(2)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						AGCCCCAGGTCTGTCATAAGG	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	5											138	131	133					5																	179045226		2203	4300	6503	178977832	SO:0001583	missense	3187			BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"RNA binding motif (RRM) containing"	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.635G>A	5.37:g.179045226C>T	ENSP00000349168:p.Arg212Lys		178977832	B3KW86|D3DWQ2|Q6IBM4	Missense_Mutation	SNP	ENST00000356731.5	37	CCDS4446.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	24.6|24.6	4.551327|4.551327	0.86127|0.86127	.|.	.|.	ENSG00000169045|ENSG00000169045	ENST00000521173;ENST00000508103;ENST00000506721|ENST00000393432;ENST00000442819;ENST00000356731;ENST00000329433;ENST00000510411;ENST00000523921;ENST00000523137;ENST00000505811	T;T|T;T;T;T;T;T;T;T	0.36340|0.30714	1.26;1.26|2.67;2.67;2.67;2.65;2.69;2.48;1.52;2.0	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58949|0.58949	0.2158|0.2158	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	.|D	.|0.57571	.|0.98	.|P	.|0.58970	.|0.849	T|T	0.64795|0.64795	-0.6323|-0.6323	7|10	0.87932|0.87932	D|D	0|0	-11.3825|-11.3825	19.809|19.809	0.96540|0.96540	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|212	.|P31943	.|HNRH1_HUMAN	N|K	87;166;166|212;212;212;212;212;26;164;212	ENSP00000425732:D166N;ENSP00000420850:D166N|ENSP00000377082:R212K;ENSP00000397797:R212K;ENSP00000349168:R212K;ENSP00000327539:R212K;ENSP00000426275:R212K;ENSP00000429270:R26K;ENSP00000427986:R164K;ENSP00000424087:R212K	ENSP00000420850:D166N|ENSP00000327539:R212K	D|R	-|-	1|2	0|0	HNRNPH1|HNRNPH1	178977832|178977832	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.445000|7.445000	0.80570|0.80570	2.753000|2.753000	0.94483|0.94483	0.585000|0.585000	0.79938|0.79938	GAC|AGA		0.493	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520		T	179045226	C	T	179045226	3	4	80	1	0	0	0	0	1	0	0	0	7287	913	32	3	746	3	HNRNPH1	5	179045226	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	31248595	179045226	1870034	50	23225										
E2F3	1871	broad.mit.edu	37	chr6	20481593	20481593	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aaagagaaggatttatgataTcaccaacgttctggaaggca	10	6	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:20481593T>C	ENST00000346618.3	+	3	728	c.662T>C	c.(661-663)aTc>aCc	p.I221T	E2F3_ENST00000535432.1_Missense_Mutation_p.I90T	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	221	Leucine-zipper.				mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I221T(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	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)			ATTTATGATATCACCAACGTT	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	6											172	173	173					6																	20481593		2203	4300	6503	20589572	SO:0001583	missense	1871			Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.662T>C	6.37:g.20481593T>C	ENSP00000262904:p.Ile221Thr		20589572	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.610678	0.87258	.	.	ENSG00000112242	ENST00000378646;ENST00000346618;ENST00000535432	T;T	0.37584	1.19;1.57	5.68	5.68	0.88126	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.71693	0.3370	H	0.98559	4.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.84020	0.0353	10	0.87932	D	0	.	16.2164	0.82224	0.0:0.0:0.0:1.0	.	221;90	O00716;Q68DT0	E2F3_HUMAN;.	T	100;221;90	ENSP00000262904:I221T;ENSP00000443418:I90T	ENSP00000262904:I221T	I	+	2	0	E2F3	20589572	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.289000	0.77006	0.533000	0.62120	ATC		0.473	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			C	20481593	T	C	20481593	3	2	80	1	0	0	0	0	1	0	0	0	4879	1435	50	4	672	4	E2F3	6	20481593	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		20481593	150633474	51	23226										
COL21A1	81578	broad.mit.edu	37	chr6	56029248	56029248	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccttgaagtcctggttttccCggaggacaaatacagggagc	12	10	0	1	rs140409980		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:56029248C>T	ENST00000244728.5	-	9	1741	c.1344G>A	c.(1342-1344)ccG>ccA	p.P448P	COL21A1_ENST00000535941.1_Silent_p.P448P|COL21A1_ENST00000370819.1_Silent_p.P445P	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	448	Collagen-like 1.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.P448P(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CTGGTTTTCCCGGAGGACAAA	0.423																																																2	Substitution - coding silent(2)	large_intestine(2)	6																																								56137207	SO:0001819	synonymous_variant	81578			AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.1344G>A	6.37:g.56029248C>T			56137207	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	C	8.441	0.850895	0.17034	.	.	ENSG00000124749	ENST00000456983	.	.	.	5.26	-10.5	0.00291	.	.	.	.	.	T	0.15869	0.0382	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40251	-0.9573	4	.	.	.	.	2.0542	0.03578	0.2862:0.3548:0.098:0.261	.	.	.	.	Q	33	.	.	R	-	2	0	COL21A1	56137207	0.078000	0.21339	0.469000	0.27204	0.869000	0.49853	-0.941000	0.03925	-2.325000	0.00638	-2.240000	0.00288	CGG		0.423	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	56029248	C	T	56029248	2	4	80	1	0	0	0	0	0	0	0	1	3686	639	23	1		1	COL21A1	6	56029248	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	35547655	56029248	115085819	52	23227										
FHL5	9457	broad.mit.edu	37	chr6	97052725	97052725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cttttgctgccaaggatgagCgcctgctgtgcacggagtgc	14	11	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:97052725C>T	ENST00000326771.2	+	4	639	c.259C>T	c.(259-261)Cgc>Tgc	p.R87C	FHL5_ENST00000541107.1_Missense_Mutation_p.R87C	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	87	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R87C(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		CAAGGATGAGCGCCTGCTGTG	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	6											123	113	116					6																	97052725		2203	4300	6503	97159446	SO:0001583	missense	9457			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.259C>T	6.37:g.97052725C>T	ENSP00000326022:p.Arg87Cys		97159446	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.609870	0.66558	.	.	ENSG00000112214	ENST00000541107;ENST00000326771;ENST00000450218	D;D;D	0.88354	-2.37;-2.37;-2.37	5.36	3.47	0.39725	Zinc finger, LIM-type (4);	0.000000	0.46145	D	0.000316	D	0.90872	0.7132	M	0.82323	2.585	0.39064	D	0.960578	D	0.89917	1.0	P	0.61658	0.892	D	0.91419	0.5157	10	0.87932	D	0	.	8.0258	0.30436	0.1189:0.6983:0.1154:0.0674	.	87	Q5TD97	FHL5_HUMAN	C	87	ENSP00000442357:R87C;ENSP00000326022:R87C;ENSP00000396390:R87C	ENSP00000326022:R87C	R	+	1	0	FHL5	97159446	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.371000	0.20450	1.392000	0.46585	0.655000	0.94253	CGC		0.527	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		T	97052725	C	T	97052725	3	4	80	1	0	0	0	0	1	0	0	0	5900	768	27	1	265	1	FHL5	6	97052725	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	41023477	97052725	74062342	53	23228										
KIAA0408	9729	broad.mit.edu	37	chr6	127768831	127768831	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttgttgatcatggggtccccAtgaggtatattagttacatt	10	6	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:127768831A>G	ENST00000483725.3	-	5	969	c.633T>C	c.(631-633)caT>caC	p.H211H	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	211								p.H211H(1)		endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		TGGGGTCCCCATGAGGTATAT	0.358																																																1	Substitution - coding silent(1)	large_intestine(1)	6											42	44	43					6																	127768831		2192	4285	6477	127810524	SO:0001819	synonymous_variant	9729			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.633T>C	6.37:g.127768831A>G			127810524	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Silent	SNP	ENST00000483725.3	37	CCDS34531.1																																																																																				0.358	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		G	127768831	A	G	127768831	2	3	80	1	0	0	0	0	0	0	0	1	8195	214	8	4		4	KIAA0408	6	127768831	Silent	SNP	A	TCGA-AG-A036-01A-12W-A096-10	30716106	127768831	43346236	54	23229										
SHPRH	257218	broad.mit.edu	37	chr6	146262922	146262922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cgacataatttaattctgaaCgcagtacatcataggtaatg	7	7	2	1	rs574465156		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:146262922C>T	ENST00000367505.2	-	10	2591	c.2327G>A	c.(2326-2328)cGt>cAt	p.R776H	SHPRH_ENST00000275233.7_Missense_Mutation_p.R776H|SHPRH_ENST00000438092.2_Missense_Mutation_p.R776H|SHPRH_ENST00000367503.3_Missense_Mutation_p.R776H			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	776	Helicase ATP-binding; second part. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R776H(2)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TAATTCTGAACGCAGTACATC	0.418																																																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	6											67	69	68					6																	146262922		1954	4149	6103	146304615	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.2327G>A	6.37:g.146262922C>T	ENSP00000356475:p.Arg776His		146304615	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	35	5.541068	0.96474	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.91	5.91	0.95273	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.64402	D	0.000001	D	0.96809	0.8958	M	0.80616	2.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96408	0.9302	10	0.66056	D	0.02	-17.2053	20.298	0.98569	0.0:1.0:0.0:0.0	.	665;776;776	Q149N8-2;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	H	776	ENSP00000356475:R776H;ENSP00000356473:R776H;ENSP00000412797:R776H;ENSP00000275233:R776H	ENSP00000275233:R776H	R	-	2	0	SHPRH	146304615	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	7.430000	0.80321	2.801000	0.96364	0.650000	0.86243	CGT		0.418	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146262922	C	T	146262922	3	4	80	1	0	0	0	0	1	0	0	0	14328	536	19	1	2852	1	SHPRH	6	146262922	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	18494091	146262922	24852145	55	23230										
SASH1	23328	broad.mit.edu	37	chr6	148865916	148865916	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctgaaaacaagctgcacgctGaaggcatcgatctcacggag	11	11	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:148865916G>A	ENST00000367467.3	+	18	3785	c.3310G>A	c.(3310-3312)Gaa>Aaa	p.E1104K		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	1104					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.E1104K(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCTGCACGCTGAAGGCATCGA	0.567																																																1	Substitution - Missense(1)	large_intestine(1)	6											33	33	33					6																	148865916		2203	4300	6503	148907609	SO:0001583	missense	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.3310G>A	6.37:g.148865916G>A	ENSP00000356437:p.Glu1104Lys		148907609	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.713735	0.68730	.	.	ENSG00000111961	ENST00000367467;ENST00000537769	T	0.52754	0.65	5.11	4.23	0.50019	.	0.046857	0.85682	D	0.000000	T	0.38772	0.1053	L	0.32530	0.975	0.51482	D	0.999924	D;D	0.58620	0.983;0.983	P;P	0.53313	0.723;0.723	T	0.43572	-0.9383	10	0.87932	D	0	-20.056	15.509	0.75766	0.0:0.1389:0.8611:0.0	.	1085;1104	Q6P4R9;O94885	.;SASH1_HUMAN	K	1104;514	ENSP00000356437:E1104K	ENSP00000356437:E1104K	E	+	1	0	SASH1	148907609	1.000000	0.71417	0.523000	0.27875	0.233000	0.25261	6.094000	0.71431	1.132000	0.42129	0.655000	0.94253	GAA		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148865916	G	A	148865916	3	1	80	1	0	0	0	0	1	0	0	0	13885	1291	45	3	3380	3	SASH1	6	148865916	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	2602994	148865916	22249151	56	23231										
SYNE1	23345	broad.mit.edu	37	chr6	152642927	152642927	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttctttcgtttcctgaacccAacatttcacagaattgatct	4	11	3	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:152642927A>T	ENST00000367255.5	-	83	16613	c.16012T>A	c.(16012-16014)Tgg>Agg	p.W5338R	SYNE1_ENST00000448038.1_Missense_Mutation_p.W5267R|SYNE1_ENST00000341594.5_Missense_Mutation_p.W5011R|SYNE1_ENST00000423061.1_Missense_Mutation_p.W5267R|SYNE1_ENST00000265368.4_Missense_Mutation_p.W5338R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5338					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.W5338R(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCCTGAACCCAACATTTCACA	0.398										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	large_intestine(2)	6											170	160	163					6																	152642927		2203	4300	6503	152684620	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16012T>A	6.37:g.152642927A>T	ENSP00000356224:p.Trp5338Arg		152684620	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	17.61	3.431572	0.62844	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.56941	0.56;0.57;0.47;0.57;0.43	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000030	T	0.65729	0.2719	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.999	T	0.69851	-0.5033	10	0.59425	D	0.04	.	15.6915	0.77457	1.0:0.0:0.0:0.0	.	5338;5338;5338;5267	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	R	5338;5267;5338;5267;5011	ENSP00000356224:W5338R;ENSP00000396024:W5267R;ENSP00000265368:W5338R;ENSP00000390975:W5267R;ENSP00000341887:W5011R	ENSP00000265368:W5338R	W	-	1	0	SYNE1	152684620	1.000000	0.71417	0.928000	0.36995	0.939000	0.58152	8.491000	0.90468	2.107000	0.64212	0.533000	0.62120	TGG		0.398	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152642927	A	T	152642927	3	4	80	1	0	0	0	0	1	0	0	0	15484	130	5	5	10710	5	SYNE1	6	152642927	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	3777011	152642927	18472140	57	23232										
CNKSR3	154043	broad.mit.edu	37	chr6	154749310	154749310	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aacccatcataggttgatttGatgtacatgccctggagtga	10	8	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:154749310G>C	ENST00000607772.1	-	7	1225	c.681C>G	c.(679-681)atC>atG	p.I227M	CNKSR3_ENST00000433165.2_Missense_Mutation_p.I52M|CNKSR3_ENST00000479339.1_Missense_Mutation_p.I147M	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	227	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.I227M(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		AGGTTGATTTGATGTACATGC	0.343																																																1	Substitution - Missense(1)	large_intestine(1)	6											136	120	126					6																	154749310		2203	4300	6503	154791002	SO:0001583	missense	154043			AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.681C>G	6.37:g.154749310G>C	ENSP00000475915:p.Ile227Met		154791002	Q5SGD5|Q96N65	Missense_Mutation	SNP	ENST00000607772.1	37	CCDS5246.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.423308	0.62733	.	.	ENSG00000153721	ENST00000367209;ENST00000367213;ENST00000433165;ENST00000479339;ENST00000424998;ENST00000454664	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.75	4.86	0.63082	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	M	0.70903	2.155	0.44395	D	0.9973	D	0.89917	1.0	D	0.91635	0.999	T	0.66709	-0.5855	10	0.87932	D	0	.	14.1848	0.65598	0.0:0.0:0.7088:0.2912	.	227	Q6P9H4	CNKR3_HUMAN	M	25;227;52;147;12;52	ENSP00000356182:I227M;ENSP00000414185:I52M;ENSP00000418975:I147M;ENSP00000406740:I52M	ENSP00000356178:I25M	I	-	3	3	CNKSR3	154791002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.643000	0.54374	1.364000	0.46038	0.655000	0.94253	ATC		0.343	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		C	154749310	G	C	154749310	3	2	80	1	0	0	0	0	1	0	0	0	3614	1280	45	5	1014	5	CNKSR3	6	154749310	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	2106383	154749310	16365757	58	23233										
FNDC1	84624	broad.mit.edu	37	chr6	159688885	159688885	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggaagaggtgaagaccattgCcaatttgtggattcacacct	11	8	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:159688885C>G	ENST00000297267.9	+	22	5696	c.5496C>G	c.(5494-5496)tgC>tgG	p.C1832W	FNDC1_ENST00000340366.6_Missense_Mutation_p.C1769W	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1832					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.C1832W(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AAGACCATTGCCAATTTGTGG	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	6											111	108	109					6																	159688885		1951	4154	6105	159608875	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.5496C>G	6.37:g.159688885C>G	ENSP00000297267:p.Cys1832Trp		159608875	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.46|18.46	3.629461|3.629461	0.67015|0.67015	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.57752|.	0.38;0.38|.	5.58|5.58	3.75|3.75	0.43078|0.43078	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.50154|0.50154	0.1599|0.1599	M|M	0.69358|0.69358	2.11|2.11	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.50482|0.50482	-0.8823|-0.8823	9|5	.|.	.|.	.|.	-29.7065|-29.7065	8.9188|8.9188	0.35599|0.35599	0.0:0.7511:0.0:0.2489|0.0:0.7511:0.0:0.2489	.|.	1832|.	Q4ZHG4|.	FNDC1_HUMAN|.	W|A	1832;1769|1728	ENSP00000297267:C1832W;ENSP00000342460:C1769W|.	.|.	C|P	+|+	3|1	2|0	FNDC1|FNDC1	159608875|159608875	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.293000|1.293000	0.33353|0.33353	0.660000|0.660000	0.30964|0.30964	0.491000|0.491000	0.48974|0.48974	TGC|CCA		0.428	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		G	159688885	C	G	159688885	3	3	80	1	0	0	0	0	1	0	0	0	5987	747	26	5	5582	5	FNDC1	6	159688885	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	4939575	159688885	11426182	59	23234										
THBS2	7058	broad.mit.edu	37	chr6	169626379	169626379	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gacgtagggacaattgtctcGttcattgaagacatctgtaa	10	7	3	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr6:169626379G>A	ENST00000366787.3	-	17	2683	c.2434C>T	c.(2434-2436)Cga>Tga	p.R812*	THBS2_ENST00000488355.1_5'Flank|XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	812					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R812*(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		CAATTGTCTCGTTCATTGAAG	0.463																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Substitution - Nonsense(1)	large_intestine(1)	6											94	88	90					6																	169626379		2203	4300	6503	169368304	SO:0001587	stop_gained	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2434C>T	6.37:g.169626379G>A	ENSP00000355751:p.Arg812*		169368304	A6H8N1|A7E232|Q5RI52	Nonsense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	39	7.389846	0.98255	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	.	.	.	4.75	-1.93	0.07594	.	0.000000	0.34291	U	0.004094	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.1537	16.1098	0.81255	0.0:0.0:0.3623:0.6377	.	.	.	.	X	812;70	.	ENSP00000355751:R812X	R	-	1	2	THBS2	169368304	0.002000	0.14202	0.854000	0.33618	0.191000	0.23601	0.069000	0.14552	-0.267000	0.09325	-0.313000	0.08912	CGA		0.463	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		A	169626379	G	A	169626379	4	1	80	1	0	0	0	0	0	1	0	0	15893	1153	40	1	1112	1	THBS2	6	169626379	Nonsense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	9937494	169626379	1488688	60	23235										
GLI3	2737	broad.mit.edu	37	chr7	42004360	42004360	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tagaactgaccagagtaattCtgcagattagagcacagcgg	11	8	1	5			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr7:42004360C>A	ENST00000395925.3	-	15	4395	c.4311G>T	c.(4309-4311)caG>caT	p.Q1437H	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1437					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q1437H(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CAGAGTAATTCTGCAGATTAG	0.512									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							1	Substitution - Missense(1)	large_intestine(1)	7											65	67	67					7																	42004360		2203	4300	6503	41970885	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4311G>T	7.37:g.42004360C>A	ENSP00000379258:p.Gln1437His		41970885	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.519604	0.44866	.	.	ENSG00000106571	ENST00000395925	T	0.15372	2.43	5.62	2.71	0.32032	.	0.130576	0.52532	D	0.000079	T	0.20333	0.0489	L	0.49778	1.585	0.80722	D	1	P	0.44478	0.836	P	0.49192	0.602	T	0.01262	-1.1402	10	0.44086	T	0.13	.	6.9724	0.24656	0.0:0.6622:0.1291:0.2086	.	1437	P10071	GLI3_HUMAN	H	1437	ENSP00000379258:Q1437H	ENSP00000379258:Q1437H	Q	-	3	2	GLI3	41970885	1.000000	0.71417	0.994000	0.49952	0.863000	0.49368	1.809000	0.38922	1.360000	0.45960	0.655000	0.94253	CAG		0.512	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42004360	C	A	42004360	3	1	80	1	0	0	0	0	1	0	0	0	6459	912	32	2	435	2	GLI3	7	42004360	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10		42004360	117134303	61	23236										
ABCB4	5244	broad.mit.edu	37	chr7	87056200	87056200	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggcagccttttcatcatttaGttcaaattcttctgactgga	7	9	5	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr7:87056200G>C	ENST00000265723.4	-	16	2041	c.1930C>G	c.(1930-1932)Cta>Gta	p.L644V	ABCB4_ENST00000358400.3_Missense_Mutation_p.L644V|ABCB4_ENST00000359206.3_Missense_Mutation_p.L644V|ABCB4_ENST00000545634.1_Missense_Mutation_p.L644V|ABCB4_ENST00000453593.1_Missense_Mutation_p.L644V	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	644	Interaction with HAX1. {ECO:0000250}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.L644V(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TCATCATTTAGTTCAAATTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	7											97	94	95					7																	87056200		2203	4300	6503	86894136	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1930C>G	7.37:g.87056200G>C	ENSP00000265723:p.Leu644Val		86894136	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.478700	0.01035	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.86956	-2.13;-2.19;-2.18;-2.19;-2.13	4.92	1.93	0.25924	.	418.330000	0.00550	U	0.000260	T	0.75693	0.3884	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.14438	0.002;0.007;0.01	B;B;B	0.15484	0.005;0.013;0.004	T	0.63703	-0.6577	10	0.30078	T	0.28	-0.5506	9.585	0.39510	0.2559:0.0:0.7441:0.0	.	644;644;644	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	V	644	ENSP00000352135:L644V;ENSP00000351172:L644V;ENSP00000265723:L644V;ENSP00000392983:L644V;ENSP00000437465:L644V	ENSP00000265723:L644V	L	-	1	2	ABCB4	86894136	0.340000	0.24792	0.024000	0.17045	0.110000	0.19582	0.217000	0.17603	0.674000	0.31244	0.655000	0.94253	CTA		0.408	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		C	87056200	G	C	87056200	3	2	80	1	0	0	0	0	1	0	0	0	43	1020	36	5	1982	5	ABCB4	7	87056200	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	45051840	87056200	72082463	62	23237										
ZC3HC1	51530	broad.mit.edu	37	chr7	129663442	129663442	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gggtgtctcctgttcccatgCttcgggtcactgggcgagtt	14	11	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr7:129663442C>G	ENST00000358303.4	-	8	1226	c.1142G>C	c.(1141-1143)aGc>aCc	p.S381T	ZC3HC1_ENST00000360708.5_Intron|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.S360T|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.S338T|RP11-306G20.1_ENST00000480018.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	381					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.S381T(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TGTTCCCATGCTTCGGGTCAC	0.612																																					Melanoma(115;540 1606 16325 28853 48167)											1	Substitution - Missense(1)	large_intestine(1)	7											128	107	114					7																	129663442		2203	4300	6503	129450678	SO:0001583	missense	51530			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1142G>C	7.37:g.129663442C>G	ENSP00000351052:p.Ser381Thr		129450678	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246124	0.80024	.	.	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	T;T;T	0.52295	1.13;1.17;0.67	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.64249	0.2581	M	0.64997	1.995	0.54753	D	0.999985	D;D	0.69078	0.997;0.997	D;D	0.65684	0.937;0.931	T	0.57021	-0.7882	10	0.21540	T	0.41	-14.2958	18.2248	0.89914	0.0:1.0:0.0:0.0	.	381;338	Q86WB0;C9J0I9	NIPA_HUMAN;.	T	381;360;338	ENSP00000351052:S381T;ENSP00000309301:S360T;ENSP00000418533:S338T	ENSP00000309301:S360T	S	-	2	0	ZC3HC1	129450678	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	5.412000	0.66392	2.659000	0.90383	0.655000	0.94253	AGC		0.612	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		G	129663442	C	G	129663442	3	3	80	1	0	0	0	0	1	0	0	0	17616	797	28	5	378	5	ZC3HC1	7	129663442	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	42607242	129663442	29475221	63	23238										
GALNTL5	168391	broad.mit.edu	37	chr7	151699964	151699964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctctcctcttgtaaggggaaCttttgattggaacctacaat	8	9	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr7:151699964C>A	ENST00000392800.2	+	6	1078	c.824C>A	c.(823-825)aCt>aAt	p.T275N	GALNTL5_ENST00000483959.1_3'UTR|GALNTL5_ENST00000431418.2_Missense_Mutation_p.T275N	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	275					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.T275N(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GTAAGGGGAACTTTTGATTGG	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	7											126	131	129					7																	151699964		2203	4300	6503	151330897	SO:0001583	missense	168391			AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.824C>A	7.37:g.151699964C>A	ENSP00000376548:p.Thr275Asn		151330897	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.705446	0.30232	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.59083	0.29;0.29	4.83	-1.58	0.08479	Glycosyl transferase, family 2 (1);	0.470425	0.18166	N	0.149631	T	0.27900	0.0687	N	0.03930	-0.32	0.09310	N	1	B;B	0.24576	0.021;0.106	B;B	0.26094	0.032;0.066	T	0.20306	-1.0279	10	0.87932	D	0	.	5.3972	0.16276	0.0:0.3087:0.3462:0.3451	.	26;275	A8MZD3;Q7Z4T8	.;GLTL5_HUMAN	N	275	ENSP00000392582:T275N;ENSP00000376548:T275N	ENSP00000376548:T275N	T	+	2	0	GALNTL5	151330897	1.000000	0.71417	0.000000	0.03702	0.034000	0.12701	3.184000	0.50926	-0.116000	0.11893	-0.142000	0.14014	ACT		0.433	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		A	151699964	C	A	151699964	3	1	80	1	0	0	0	0	1	0	0	0	6244	565	20	2	842	2	GALNTL5	7	151699964	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	22036522	151699964	7438699	64	23239										
MLL3	58508	broad.mit.edu	37	chr7	151859627	151859627	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gggcagtttgttctctaattCtgtacatagctggcctgctg	11	9	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr7:151859627C>T	ENST00000262189.6	-	43	11253	c.11035G>A	c.(11035-11037)Gaa>Aaa	p.E3679K	KMT2C_ENST00000355193.2_Missense_Mutation_p.E3679K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3679					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E3679K(2)									TTCTCTAATTCTGTACATAGC	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	7											156	159	158					7																	151859627		2203	4300	6503	151490560	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11035G>A	7.37:g.151859627C>T	ENSP00000262189:p.Glu3679Lys		151490560	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.34|18.34	3.602253|3.602253	0.66445|0.66445	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.89746|.	-2.16;-1.86;-2.56|.	5.51|5.51	4.62|4.62	0.57501|0.57501	.|.	0.322393|.	0.21103|.	U|.	0.080126|.	T|T	0.72326|0.72326	0.3446|0.3446	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	P;P;P|.	0.39665|.	0.682;0.649;0.649|.	B;B;B|.	0.41510|.	0.197;0.254;0.359|.	T|T	0.72144|0.72144	-0.4379|-0.4379	10|5	0.66056|.	D|.	0.02|.	.|.	16.2171|16.2171	0.82237|0.82237	0.0:0.8669:0.1331:0.0|0.0:0.8669:0.1331:0.0	.|.	3679;2740;3679|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	K|K	3679;3679;265|1184	ENSP00000262189:E3679K;ENSP00000347325:E3679K;ENSP00000410411:E265K|.	ENSP00000262189:E3679K|.	E|R	-|-	1|2	0|0	MLL3|MLL3	151490560|151490560	1.000000|1.000000	0.71417|0.71417	0.004000|0.004000	0.12327|0.12327	0.007000|0.007000	0.05969|0.05969	5.597000|5.597000	0.67577|0.67577	1.289000|1.289000	0.44618|0.44618	0.650000|0.650000	0.86243|0.86243	GAA|AGA		0.493	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151859627	C	T	151859627	3	4	80	1	0	0	0	0	1	0	0	0	9652	922	32	3	3768	3	MLL3	7	151859627	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	159663	151859627	7279036	65	23240										
TNFRSF10B	8795	broad.mit.edu	37	chr8	22887136	22887136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtctcaccctgtgcggcactTccggcacatctcaggagaat	10	14	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:22887136T>C	ENST00000276431.4	-	4	747	c.463A>G	c.(463-465)Aag>Gag	p.K155E	TNFRSF10B_ENST00000542226.1_Missense_Mutation_p.K4E|TNFRSF10B_ENST00000519910.1_5'UTR|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.K155E	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	155					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)	p.K155E(1)		NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		GTGCGGCACTTCCGGCACATC	0.582																																					GBM(94;1064 1342 1839 21060 42553)											1	Substitution - Missense(1)	large_intestine(1)	8											50	42	44					8																	22887136		2203	4300	6503	22943081	SO:0001583	missense	8795			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.463A>G	8.37:g.22887136T>C	ENSP00000276431:p.Lys155Glu		22943081	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	t	13.86	2.363787	0.41902	.	.	ENSG00000120889	ENST00000276431;ENST00000347739;ENST00000542226	T;T;T	0.30182	1.54;1.54;1.54	3.93	-4.63	0.03359	TNFR/CD27/30/40/95 cysteine-rich region (3);	0.566743	0.16675	U	0.204186	T	0.34716	0.0907	M	0.69248	2.105	0.09310	N	1	P;P;D;P	0.61697	0.787;0.597;0.99;0.589	B;B;P;B	0.58970	0.219;0.363;0.849;0.41	T	0.15435	-1.0437	10	0.30854	T	0.27	.	2.8066	0.05429	0.1524:0.0992:0.4675:0.281	.	4;155;155;155	B7Z588;B5BU36;O14763;O14763-2	.;.;TR10B_HUMAN;.	E	155;155;4	ENSP00000276431:K155E;ENSP00000317859:K155E;ENSP00000443386:K4E	ENSP00000276431:K155E	K	-	1	0	TNFRSF10B	22943081	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.186000	0.09670	-0.957000	0.03627	-1.117000	0.02048	AAG		0.582	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187		C	22887136	T	C	22887136	3	2	80	1	0	0	0	0	1	0	0	0	16320	1792	62	4	883	4	TNFRSF10B	8	22887136	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		22887136	123476886	66	23241										
SULF1	23213	broad.mit.edu	37	chr8	70541873	70541873	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gcctggcctcacttgcttcaCgcatgacaacaaccactggc	8	16	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:70541873C>T	ENST00000260128.4	+	19	2960	c.2243C>T	c.(2242-2244)aCg>aTg	p.T748M	SULF1_ENST00000402687.4_Missense_Mutation_p.T748M|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000419716.3_Missense_Mutation_p.T748M|SULF1_ENST00000458141.2_Missense_Mutation_p.T748M	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	748					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.T748M(1)		breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			ACTTGCTTCACGCATGACAAC	0.547																																																1	Substitution - Missense(1)	large_intestine(1)	8											140	125	130					8																	70541873		2203	4300	6503	70704427	SO:0001583	missense	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2243C>T	8.37:g.70541873C>T	ENSP00000260128:p.Thr748Met		70704427	Q86YV8|Q8NCA2|Q9UPS5	De_novo_Start_OutOfFrame	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742611	0.89573	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	T;T;T;T	0.15139	2.45;2.45;2.45;2.45	4.75	4.75	0.60458	Alkaline-phosphatase-like, core domain (1);	0.106709	0.64402	D	0.000005	T	0.41419	0.1158	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	P	0.59288	0.855	T	0.42565	-0.9444	10	0.54805	T	0.06	.	17.9404	0.89025	0.0:1.0:0.0:0.0	.	748	Q8IWU6	SULF1_HUMAN	M	748	ENSP00000403040:T748M;ENSP00000260128:T748M;ENSP00000385704:T748M;ENSP00000390315:T748M	ENSP00000260128:T748M	T	+	2	0	SULF1	70704427	1.000000	0.71417	0.959000	0.39883	0.906000	0.53458	7.622000	0.83099	2.440000	0.82611	0.655000	0.94253	ACG		0.547	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70541873	C	T	70541873	3	4	80	1	0	0	0	0	1	0	0	0	15409	536	19	1	2301	1	SULF1	8	70541873	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	47654737	70541873	75822149	67	23242										
RDH10	157506	broad.mit.edu	37	chr8	74233228	74233228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atccctgagccatgaactaaAggctgctgaaaaggatggaa	11	8	0	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:74233228A>G	ENST00000240285.5	+	4	1364	c.686A>G	c.(685-687)aAg>aGg	p.K229R	RP11-434I12.2_ENST00000514599.1_RNA|RP11-434I12.2_ENST00000517475.1_RNA|RDH10_ENST00000519380.1_Missense_Mutation_p.K64R	NM_172037.4	NP_742034.1	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10 (all-trans)	229					bud elongation involved in lung branching (GO:0060449)|ear development (GO:0043583)|embryonic camera-type eye development (GO:0031076)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|gonad development (GO:0008406)|in utero embryonic development (GO:0001701)|metanephros development (GO:0001656)|neural crest cell development (GO:0014032)|nose development (GO:0043584)|phototransduction, visible light (GO:0007603)|primary lung bud formation (GO:0060431)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.K229R(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	11	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			CATGAACTAAAGGCTGCTGAA	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	8											141	133	136					8																	74233228		2203	4300	6503	74395782	SO:0001583	missense	157506			AF456765	CCDS6213.1	8q21.11	2011-09-20			ENSG00000121039	ENSG00000121039	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	19975	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 16C, member 4"	607599				12407145, 19027726	Standard	NM_172037		Approved	SDR16C4	uc003xzi.3	Q8IZV5	OTTHUMG00000164492	ENST00000240285.5:c.686A>G	8.37:g.74233228A>G	ENSP00000240285:p.Lys229Arg		74395782		Missense_Mutation	SNP	ENST00000240285.5	37	CCDS6213.1	.	.	.	.	.	.	.	.	.	.	A	13.64	2.296936	0.40594	.	.	ENSG00000121039	ENST00000240285;ENST00000519380	D;T	0.89415	-2.51;0.74	5.43	5.43	0.79202	NAD(P)-binding domain (1);	0.090755	0.85682	D	0.000000	T	0.75576	0.3868	N	0.04724	-0.175	0.53005	D	0.99996	B	0.17667	0.023	B	0.19391	0.025	T	0.71391	-0.4607	10	0.02654	T	1	.	15.6454	0.77046	1.0:0.0:0.0:0.0	.	229	Q8IZV5	RDH10_HUMAN	R	229;64	ENSP00000240285:K229R;ENSP00000428132:K64R	ENSP00000240285:K229R	K	+	2	0	RDH10	74395782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.319000	0.59197	2.279000	0.76181	0.533000	0.62120	AAG		0.428	RDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378982.1			G	74233228	A	G	74233228	3	3	80	1	0	0	0	0	1	0	0	0	13226	72	3	4	700	4	RDH10	8	74233228	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	3691355	74233228	72130794	68	23243										
HEY1	23462	broad.mit.edu	37	chr8	80677423	80677423	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cctcattctacatcagttctTtaaaaagctccgatctccgt	4	13	5	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:80677423T>G	ENST00000354724.3	-	5	1114	c.915A>C	c.(913-915)taA>taC	p.*305Y	HEY1_ENST00000337919.5_Nonstop_Mutation_p.*309Y|HEY1_ENST00000523976.1_Nonstop_Mutation_p.*215Y|RP11-27N21.3_ENST00000607172.1_lincRNA|HEY1_ENST00000435063.2_5'UTR	NM_012258.3	NP_036390.3	Q9Y5J3	HEY1_HUMAN	hes-related family bHLH transcription factor with YRPW motif 1	0					angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.*305Y(1)	HEY1/NCOA2(10)	cervix(1)|kidney(2)|large_intestine(5)|lung(14)	22	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			CATCAGTTCTTTAAAAAGCTC	0.483			T	NCOA2	mesenchymal chondrosarcoma						OREG0018837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											Dom	yes		8	8q21	23462	hairy/enhancer-of-split related with YRPW motif 1		M	1	Nonstop extension(1)	large_intestine(1)	8											31	28	29					8																	80677423		2066	4072	6138	80839978	SO:0001578	stop_lost	23462			AF151522	CCDS6225.1, CCDS43749.1, CCDS64915.1	8q21	2013-10-17	2013-10-17					"Basic helix-loop-helix proteins"	4880	protein-coding gene	gene with protein product		602953	"hairy/enhancer-of-split related with YRPW motif 1"			10415358, 10403790	Standard	NM_001040708		Approved	HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31	uc003ybl.3	Q9Y5J3		ENST00000354724.3:c.915A>C	8.37:g.80677423T>G		1200	80839978	B2R883|Q5TZS3|Q8NAM2|Q9NYP4	Nonstop_Mutation	SNP	ENST00000354724.3	37	CCDS6225.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462140	0.43736	.	.	ENSG00000164683	ENST00000354724;ENST00000542205;ENST00000337919;ENST00000523976	.	.	.	5.79	4.65	0.58169	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3569	0.38173	0.0:0.1359:0.0:0.8641	.	.	.	.	Y	305;309;309;215	.	.	X	-	3	2	HEY1	80839978	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.647000	0.61418	2.209000	0.71365	0.533000	0.62120	TAA		0.483	HEY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379516.1	NM_012258		G	80677423	T	G	80677423	4	3	80	1	0	0	0	0	0	0	0	0	7099	1848	64	4	3	4	HEY1	8	80677423	Nonstop_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	6444195	80677423	65686599	69	23244										
RUNX1T1	862	broad.mit.edu	37	chr8	92998514	92998514	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccttagtacggtgagagatcGccttgttttttctaccatgt	9	9	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:92998514G>A	ENST00000523629.1	-	9	1571	c.1117C>T	c.(1117-1119)Cga>Tga	p.R373*	RUNX1T1_ENST00000422361.2_Nonsense_Mutation_p.R336*|RUNX1T1_ENST00000396218.1_Nonsense_Mutation_p.R346*|RUNX1T1_ENST00000360348.2_Nonsense_Mutation_p.R336*|RUNX1T1_ENST00000265814.3_Nonsense_Mutation_p.R373*|RUNX1T1_ENST00000436581.2_Nonsense_Mutation_p.R384*|RUNX1T1_ENST00000518844.1_Nonsense_Mutation_p.R346*|RUNX1T1_ENST00000520724.1_Nonsense_Mutation_p.R336*	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	373	Important for oligomerization.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R336*(1)|p.R373*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GTGAGAGATCGCCTTGTTTTT	0.433																																																2	Substitution - Nonsense(2)	large_intestine(2)	8											129	127	128					8																	92998514		2203	4300	6503	93067690	SO:0001587	stop_gained	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1117C>T	8.37:g.92998514G>A	ENSP00000428543:p.Arg373*		93067690	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Nonsense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	35	5.475773	0.96291	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.258	14.5933	0.68386	0.0:0.0:0.8542:0.1458	.	.	.	.	X	373;346;373;336;336;336;384;346	.	ENSP00000265814:R373X	R	-	1	2	RUNX1T1	93067690	1.000000	0.71417	0.763000	0.31416	0.997000	0.91878	7.500000	0.81588	2.677000	0.91161	0.655000	0.94253	CGA		0.433	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	92998514	G	A	92998514	4	1	80	1	0	0	0	0	0	1	0	0	13784	1095	38	1	713	1	RUNX1T1	8	92998514	Nonsense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	12321091	92998514	53365508	70	23245										
TRPS1	7227	broad.mit.edu	37	chr8	116632238	116632238	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggctccaggatctggccctcGccttcacttgcaacgtttct	9	15	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:116632238G>A	ENST00000220888.5	-	2	207	c.48C>T	c.(46-48)ggC>ggT	p.G16G	TRPS1_ENST00000519076.1_Silent_p.G16G|TRPS1_ENST00000395715.3_Silent_p.G29G|TRPS1_ENST00000519674.1_Silent_p.G16G|TRPS1_ENST00000520276.1_Silent_p.G20G			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	16					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G16G(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			TCTGGCCCTCGCCTTCACTTG	0.438									Langer-Giedion syndrome																																							1	Substitution - coding silent(1)	large_intestine(1)	8											80	74	76					8																	116632238		1840	4095	5935	116701413	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.48C>T	8.37:g.116632238G>A			116701413	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.438	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116632238	G	A	116632238	2	1	80	1	0	0	0	0	0	0	0	1	16633	1074	38	1		1	TRPS1	8	116632238	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	23633724	116632238	29731784	71	23246										
ZNF7	7553	broad.mit.edu	37	chr8	146067308	146067308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aatcagcatcagagaatccaCacgggagagaaaccctttaa	8	10	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr8:146067308C>T	ENST00000528372.1	+	5	1056	c.816C>T	c.(814-816)caC>caT	p.H272H	ZNF7_ENST00000529819.1_3'UTR|ZNF7_ENST00000325241.6_Silent_p.H272H|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Silent_p.H176H|ZNF7_ENST00000446747.2_Silent_p.H283H			P17097	ZNF7_HUMAN	zinc finger protein 7	272					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H272H(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		AGAGAATCCACACGGGAGAGA	0.478																																																1	Substitution - coding silent(1)	large_intestine(1)	8											78	81	80					8																	146067308		2203	4300	6503	146038112	SO:0001819	synonymous_variant	7553			AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.816C>T	8.37:g.146067308C>T			146038112	B4DT08|D3DWN6|P17015|Q8N8Y4	Silent	SNP	ENST00000528372.1	37	CCDS6435.1																																																																																				0.478	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		T	146067308	C	T	146067308	2	4	80	1	0	0	0	0	0	0	0	1	18141	477	17	3		3	ZNF7	8	146067308	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	29435070	146067308	296714	72	23247										
TEK	7010	broad.mit.edu	37	chr9	27183556	27183556	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	caaagcttctggctggccgcTacctactaatgaagaaatga	9	10	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:27183556T>C	ENST00000380036.4	+	8	1572	c.1130T>C	c.(1129-1131)cTa>cCa	p.L377P	TEK_ENST00000519097.1_Missense_Mutation_p.L230P|TEK_ENST00000406359.4_Missense_Mutation_p.L334P	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	377	Ig-like C2-type 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L377P(1)		breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	GGCTGGCCGCTACCTACTAAT	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	9											142	157	152					9																	27183556		2203	4300	6503	27173556	SO:0001583	missense	7010			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.1130T>C	9.37:g.27183556T>C	ENSP00000369375:p.Leu377Pro		27173556	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.904573	0.52333	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.52	4.37	0.52481	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.179623	0.26727	N	0.022820	T	0.36303	0.0962	L	0.34521	1.04	0.58432	D	0.999997	P;B;D;D	0.76494	0.917;0.098;0.999;0.996	B;B;D;P	0.91635	0.445;0.084;0.999;0.893	T	0.03773	-1.1005	10	0.31617	T	0.26	.	10.6709	0.45757	0.0:0.0:0.1606:0.8394	.	230;410;334;377	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	P	230;377;334;334;187	ENSP00000430686:L230P;ENSP00000369375:L377P;ENSP00000383977:L334P;ENSP00000428337:L187P	ENSP00000343716:L334P	L	+	2	0	TEK	27173556	0.834000	0.29399	0.784000	0.31847	0.969000	0.65631	1.880000	0.39628	1.015000	0.39444	0.533000	0.62120	CTA		0.443	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			C	27183556	T	C	27183556	3	2	80	1	0	0	0	0	1	0	0	0	15790	1522	53	4	1160	4	TEK	9	27183556	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		27183556	114029875	73	23248										
PALM2	114299	broad.mit.edu	37	chr9	112705199	112705199	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttcagaaggctggacaatcaAgcttaggaggagggcacgtg	15	7	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:112705199A>G	ENST00000374531.2	+	7	708	c.634A>G	c.(634-636)Agc>Ggc	p.S212G	PALM2_ENST00000483909.1_Missense_Mutation_p.S210G|PALM2_ENST00000448454.2_Missense_Mutation_p.S246G|PALM2_ENST00000314527.4_Missense_Mutation_p.S244G|PALM2-AKAP2_ENST00000302798.7_Intron|AKAP2_ENST00000510514.5_Intron|AKAP2_ENST00000555236.1_Intron|PALM2-AKAP2_ENST00000374530.3_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	212					regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)		p.S212G(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						TGGACAATCAAGCTTAGGAGG	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	9											87	76	80					9																	112705199		2203	4300	6503	111745020	SO:0001583	missense	445815			AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.634A>G	9.37:g.112705199A>G	ENSP00000363656:p.Ser212Gly		111745020	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	37	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.557756	0.27827	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000413420	T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19	6.17	5.02	0.67125	.	.	.	.	.	T	0.16342	0.0393	N	0.22421	0.69	0.80722	D	1	B;B	0.15141	0.007;0.012	B;B	0.19666	0.026;0.02	T	0.02821	-1.1106	9	0.87932	D	0	.	11.8857	0.52600	0.8608:0.0:0.0:0.1392	.	212;246	Q8IXS6;D3YTA4	PALM2_HUMAN;.	G	212;246;210;244;244	ENSP00000363656:S212G;ENSP00000400206:S246G;ENSP00000417525:S210G;ENSP00000323805:S244G;ENSP00000397839:S244G	ENSP00000397839:S244G	S	+	1	0	PALM2-AKAP2;PALM2	111745020	1.000000	0.71417	0.986000	0.45419	0.866000	0.49608	6.004000	0.70709	1.117000	0.41842	-0.438000	0.05819	AGC		0.473	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293		G	112705199	A	G	112705199	3	3	80	1	0	0	0	0	1	0	0	0	11440	72	3	4	766	4	PALM2	9	112705199	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	85521643	112705199	28508232	74	23249										
RAB14	51552	broad.mit.edu	37	chr9	123943812	123943812	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgaatgttctgatagattttCttggcagcctcaaggaaggc	11	7	3	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:123943812C>G	ENST00000373840.4	-	8	747	c.510G>C	c.(508-510)aaG>aaC	p.K170N		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family	170					embryo development (GO:0009790)|endocytic recycling (GO:0032456)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi to endosome transport (GO:0006895)|GTP catabolic process (GO:0006184)|intracellular transport (GO:0046907)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.K170N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GATAGATTTTCTTGGCAGCCT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	9											84	79	81					9																	123943812		2203	4300	6503	122983633	SO:0001583	missense	51552			AF152463	CCDS6827.1	9q32-q34.11	2008-07-21			ENSG00000119396	ENSG00000119396		"RAB, member RAS oncogene"	16524	protein-coding gene	gene with protein product	"F protein-binding protein 1", "bA165P4.3 (member RAS oncogene family)", "small GTP binding protein RAB14"	612673				9792283, 15004230	Standard	NM_016322		Approved	FBP, RAB-14	uc004blc.3	P61106	OTTHUMG00000020582	ENST00000373840.4:c.510G>C	9.37:g.123943812C>G	ENSP00000362946:p.Lys170Asn		122983633	B3KR31|P35287|Q5JVD4|Q6Q7K5|Q969L0|Q9UI11	Missense_Mutation	SNP	ENST00000373840.4	37	CCDS6827.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193961	0.38707	.	.	ENSG00000119396	ENST00000373840;ENST00000451303	T;T	0.78126	-1.15;-1.15	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.69015	0.3064	L	0.39085	1.19	0.80722	D	1	B	0.09022	0.002	B	0.19666	0.026	T	0.62101	-0.6925	10	0.30078	T	0.28	.	12.6402	0.56705	0.0:0.9253:0.0:0.0747	.	170	P61106	RAB14_HUMAN	N	170	ENSP00000362946:K170N;ENSP00000400107:K170N	ENSP00000362946:K170N	K	-	3	2	RAB14	122983633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.009000	0.70745	2.820000	0.97059	0.650000	0.86243	AAG		0.463	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	NM_016322		G	123943812	C	G	123943812	3	3	80	1	0	0	0	0	1	0	0	0	12937	912	32	5	141	5	RAB14	9	123943812	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	11238613	123943812	17269619	75	23250										
OR1L6	392390	broad.mit.edu	37	chr9	125512580	125512580	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgctattgggttcttgcagcAtctcccacctacattccctg	7	14	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:125512580A>T	ENST00000373684.1	+	1	562	c.562A>T	c.(562-564)Atc>Ttc	p.I188F	OR1L6_ENST00000304720.2_Missense_Mutation_p.I152F			Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L, member 6	188						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I188F(1)		breast(1)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	12						TTCTTGCAGCATCTCCCACCT	0.507																																																1	Substitution - Missense(1)	large_intestine(1)	9											187	144	158					9																	125512580		2203	4300	6503	124552401	SO:0001583	missense	392390				CCDS35130.1, CCDS35130.2	9q33.2	2013-09-20			ENSG00000171459	ENSG00000171459		"GPCR / Class A : Olfactory receptors"	8218	protein-coding gene	gene with protein product				OR1L7			Standard	NM_001004453		Approved		uc022bna.1	Q8NGR2	OTTHUMG00000020621	ENST00000373684.1:c.562A>T	9.37:g.125512580A>T	ENSP00000362788:p.Ile188Phe		124552401	Q6IFM8|Q96R80	Missense_Mutation	SNP	ENST00000373684.1	37		.	.	.	.	.	.	.	.	.	.	.	12.40	1.926878	0.34002	.	.	ENSG00000171459	ENST00000373684;ENST00000304720	T;T	0.37058	1.22;7.54	4.62	2.11	0.27256	GPCR, rhodopsin-like superfamily (1);	0.106321	0.41823	D	0.000804	T	0.35998	0.0951	N	0.25332	0.735	0.21064	N	0.999797	D	0.60575	0.988	P	0.62435	0.902	T	0.05115	-1.0905	10	0.51188	T	0.08	-29.2836	5.0299	0.14404	0.6951:0.0:0.0932:0.2118	.	188	Q8NGR2	OR1L6_HUMAN	F	188;152	ENSP00000362788:I188F;ENSP00000304235:I152F	ENSP00000304235:I152F	I	+	1	0	OR1L6	124552401	0.000000	0.05858	1.000000	0.80357	0.882000	0.50991	-1.670000	0.01956	0.914000	0.36822	0.533000	0.62120	ATC		0.507	OR1L6-201	KNOWN	basic	protein_coding	protein_coding				T	125512580	A	T	125512580	3	4	80	1	0	0	0	0	1	0	0	0	10997	217	8	5	456	5	OR1L6	9	125512580	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	1568768	125512580	15700851	76	23251										
SCAI	286205	broad.mit.edu	37	chr9	127764298	127764298	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agtggccgacaggtaaatcaGaagcacgctattggcaggca	13	9	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:127764298G>A	ENST00000336505.6	-	12	1148	c.1090C>T	c.(1090-1092)Ctg>Ttg	p.L364L	SCAI_ENST00000487795.1_5'UTR|SCAI_ENST00000373549.4_Silent_p.L387L	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	364					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.L387L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						AGGTAAATCAGAAGCACGCTA	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	9											114	109	111					9																	127764298		1899	4126	6025	126804119	SO:0001819	synonymous_variant	286205			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1090C>T	9.37:g.127764298G>A			126804119	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	37	CCDS48017.1																																																																																				0.423	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		A	127764298	G	A	127764298	2	1	80	1	0	0	0	0	0	0	0	1	13906	933	33	3		3	SCAI	9	127764298	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	2251718	127764298	13449133	77	23252										
SARDH	1757	broad.mit.edu	37	chr9	136529131	136529131	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccgctcttcacaaagtccagCgagacctaggagcagaggtg	12	12	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:136529131C>T	ENST00000371872.4	-	21	2894	c.2637G>A	c.(2635-2637)tcG>tcA	p.S879S	SARDH_ENST00000469828.1_5'UTR|SARDH_ENST00000439388.1_Silent_p.S879S|SARDH_ENST00000371868.1_Silent_p.S329S|SARDH_ENST00000422262.2_Silent_p.S711S	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	879					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.S879S(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CAAAGTCCAGCGAGACCTAGG	0.582																																																1	Substitution - coding silent(1)	large_intestine(1)	9											85	70	75					9																	136529131		2203	4300	6503	135518952	SO:0001819	synonymous_variant	1757				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2637G>A	9.37:g.136529131C>T			135518952	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																				0.582	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			T	136529131	C	T	136529131	2	4	80	1	0	0	0	0	0	0	0	1	13878	755	27	1		1	SARDH	9	136529131	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	8764833	136529131	4684300	78	23253										
CAMSAP1	157922	broad.mit.edu	37	chr9	138706953	138706953	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgatacttgcctccaatatgGaattcttgtggggttcgttc	10	8	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr9:138706953G>T	ENST00000389532.4	-	16	4560	c.4496C>A	c.(4495-4497)tCc>tAc	p.S1499Y	CAMSAP1_ENST00000483991.1_5'UTR|CAMSAP1_ENST00000409386.3_Missense_Mutation_p.S1510Y|CAMSAP1_ENST00000312405.6_Missense_Mutation_p.S1221Y	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	1499	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)	p.S1499Y(1)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CTCCAATATGGAATTCTTGTG	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	9											121	102	109					9																	138706953		2203	4300	6503	137846774	SO:0001583	missense	157922			AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.4496C>A	9.37:g.138706953G>T	ENSP00000374183:p.Ser1499Tyr		137846774	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	37	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	G	13.21	2.168676	0.38315	.	.	ENSG00000130559	ENST00000389532;ENST00000312405;ENST00000409386	T;T;T	0.15017	2.47;2.46;2.47	5.49	4.56	0.56223	PRC-barrel-like (1);Microtubule-binding calmodulin-regulated spectrin-associated, C-terminal (2);	0.137765	0.51477	D	0.000095	T	0.28863	0.0716	N	0.22421	0.69	0.41443	D	0.987935	D;D	0.76494	0.999;0.993	D;D	0.74023	0.982;0.964	T	0.12915	-1.0529	10	0.87932	D	0	-3.0362	16.0468	0.80725	0.0:0.1345:0.8655:0.0	.	1499;1510	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	Y	1499;1221;1510	ENSP00000374183:S1499Y;ENSP00000312463:S1221Y;ENSP00000386420:S1510Y	ENSP00000312463:S1221Y	S	-	2	0	CAMSAP1	137846774	1.000000	0.71417	0.162000	0.22713	0.243000	0.25628	4.977000	0.63792	1.257000	0.44085	0.655000	0.94253	TCC		0.373	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		T	138706953	G	T	138706953	3	4	80	1	0	0	0	0	1	0	0	0	2617	1174	41	2	320	2	CAMSAP1	9	138706953	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	2177822	138706953	2506478	79	23254										
WAC	51322	broad.mit.edu	37	chr10	28900738	28900738	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agtctccgatgtctttaacaTctgatgcgtcatccccaaga	7	12	4	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr10:28900738T>C	ENST00000354911.4	+	10	1485	c.1324T>C	c.(1324-1326)Tct>Cct	p.S442P	WAC_ENST00000347934.4_Missense_Mutation_p.S339P|WAC_ENST00000375646.1_Missense_Mutation_p.S290P|WAC_ENST00000375664.4_Missense_Mutation_p.S397P	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	442					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)	p.S442P(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						GTCTTTAACATCTGATGCGTC	0.373																																																1	Substitution - Missense(1)	large_intestine(1)	10											156	138	144					10																	28900738		2203	4300	6503	28940744	SO:0001583	missense	51322			AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1324T>C	10.37:g.28900738T>C	ENSP00000346986:p.Ser442Pro		28940744	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	37	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.635617	0.67130	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911;ENST00000338396	T;T;T;T	0.28895	1.59;1.75;1.62;1.59	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.32530	0.975	0.80722	D	1	D;D;P	0.76494	0.969;0.999;0.948	P;D;B	0.80764	0.649;0.994;0.446	T	0.45308	-0.9270	10	0.87932	D	0	-12.1921	16.1617	0.81721	0.0:0.0:0.0:1.0	.	397;339;442	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	P	397;290;339;442;5	ENSP00000364816:S397P;ENSP00000364797:S290P;ENSP00000311106:S339P;ENSP00000346986:S442P	ENSP00000341462:S5P	S	+	1	0	WAC	28940744	1.000000	0.71417	0.898000	0.35279	0.088000	0.18126	7.997000	0.88414	2.275000	0.75901	0.528000	0.53228	TCT		0.373	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		C	28900738	T	C	28900738	3	2	80	1	0	0	0	0	1	0	0	0	17287	1435	50	4	1362	4	WAC	10	28900738	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		28900738	106634009	80	23255										
TBC1D12	23232	broad.mit.edu	37	chr10	96260074	96260074	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gctgtaggaaatgaactaaaTatcactcctggtttgtattc	8	7	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr10:96260074T>C	ENST00000225235.4	+	6	1619	c.1509T>C	c.(1507-1509)aaT>aaC	p.N503N		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	503	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.N503N(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				ATGAACTAAATATCACTCCTG	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	10											147	135	139					10																	96260074		1877	4110	5987	96250064	SO:0001819	synonymous_variant	23232			AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1509T>C	10.37:g.96260074T>C			96250064	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Silent	SNP	ENST00000225235.4	37	CCDS41553.1																																																																																				0.413	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			C	96260074	T	C	96260074	2	2	80	1	0	0	0	0	0	0	0	1	15640	1403	49	4		4	TBC1D12	10	96260074	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10	67359336	96260074	39274673	81	23256										
GPR123	84435	broad.mit.edu	37	chr10	134940770	134940770	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agcggaggggtcccctttatCatctgtggggtcacggctgc	15	11	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr10:134940770C>A	ENST00000392607.3	+	6	871	c.435C>A	c.(433-435)atC>atA	p.I145I	GPR123_ENST00000392606.2_Silent_p.I48I|GPR123_ENST00000607359.1_Silent_p.I865I	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	145					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.I865I(1)|p.I145I(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TCCCCTTTATCATCTGTGGGG	0.642																																																2	Substitution - coding silent(2)	large_intestine(2)	10											55	47	50					10																	134940770		2203	4299	6502	134790760	SO:0001819	synonymous_variant	84435			AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.435C>A	10.37:g.134940770C>A			134790760	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																				0.642	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			A	134940770	C	A	134940770	2	1	80	1	0	0	0	0	0	0	0	1	6657	816	29	2		2	GPR123	10	134940770	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	38680696	134940770	593977	82	23257										
MUC5B	727897	broad.mit.edu	37	chr11	1272288	1272288	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agctccaaagccacttcctcCtccagtccaaggactgcaac	6	17	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:1272288C>A	ENST00000529681.1	+	31	14236	c.14178C>A	c.(14176-14178)tcC>tcA	p.S4726S	MUC5B_ENST00000447027.1_Silent_p.S4729S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4726	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.S4681S(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		ccacttcctcctccaGTCCAA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	11											146	171	163					11																	1272288		2155	4244	6399	1228864	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14178C>A	11.37:g.1272288C>A			1228864	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.602	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1272288	C	A	1272288	2	1	80	1	0	0	0	0	0	0	0	1	10009	668	24	2		2	MUC5B	11	1272288	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10		1272288	133734228	83	23258										
OR51G2	81282	broad.mit.edu	37	chr11	4935953	4935953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctaacactagacacagttagTaacaaaaggcatgcgtcact	7	10	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:4935953T>C	ENST00000322013.3	-	1	969	c.941A>G	c.(940-942)tAc>tGc	p.Y314C	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	314						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y314C(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACACAGTTAGTAACAAAAGGC	0.413																																																1	Substitution - Missense(1)	large_intestine(1)	11											89	71	77					11																	4935953		2201	4298	6499	4892529	SO:0001583	missense	81282			AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.941A>G	11.37:g.4935953T>C	ENSP00000322593:p.Tyr314Cys		4892529	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.155740	0.38021	.	.	ENSG00000176893	ENST00000322013	T	0.00614	6.21	4.46	-8.93	0.00771	.	0.780759	0.10873	N	0.624718	T	0.00328	0.0010	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49661	-0.8916	10	0.87932	D	0	.	1.7036	0.02877	0.288:0.3902:0.1927:0.1291	.	314	Q8NGK0	O51G2_HUMAN	C	314	ENSP00000322593:Y314C	ENSP00000322593:Y314C	Y	-	2	0	OR51G2	4892529	0.002000	0.14202	0.000000	0.03702	0.668000	0.39293	0.052000	0.14163	-2.539000	0.00486	0.491000	0.48974	TAC		0.413	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		C	4935953	T	C	4935953	3	2	80	1	0	0	0	0	1	0	0	0	11130	1638	57	4	7	4	OR51G2	11	4935953	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	3663665	4935953	130070563	84	23259										
RRP8	23378	broad.mit.edu	37	chr11	6622578	6622578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagccgctgtgccatgcgggCtcgcaaagcccctgcccgag	13	17	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:6622578C>T	ENST00000254605.6	-	3	835	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	RRP8_ENST00000534343.1_Intron|ILK_ENST00000420936.2_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000528995.1_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	240					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.A240T(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						GCCATGCGGGCTCGCAAAGCC	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	11											30	30	30					11																	6622578		2201	4296	6497	6579154	SO:0001583	missense	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.718G>A	11.37:g.6622578C>T	ENSP00000254605:p.Ala240Thr		6579154	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288768	0.59976	.	.	ENSG00000132275	ENST00000254605;ENST00000533907	T;T	0.46819	0.86;0.86	5.85	4.9	0.64082	.	0.182212	0.48767	N	0.000166	T	0.38453	0.1041	L	0.43152	1.355	0.80722	D	1	P	0.36577	0.558	B	0.39217	0.294	T	0.15492	-1.0435	10	0.22706	T	0.39	-27.2435	7.8881	0.29661	0.1557:0.7582:0.0:0.0861	.	240	O43159	RRP8_HUMAN	T	240	ENSP00000254605:A240T;ENSP00000436246:A240T	ENSP00000254605:A240T	A	-	1	0	RRP8	6579154	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	2.724000	0.47285	1.390000	0.46547	-0.355000	0.07637	GCC		0.627	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6622578	C	T	6622578	3	4	80	1	0	0	0	0	1	0	0	0	13727	797	28	3	672	3	RRP8	11	6622578	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	1686625	6622578	128383938	85	23260										
SPTY2D1	144108	broad.mit.edu	37	chr11	18636366	18636366	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gggccactgacagaccgcccCggggggcccaagccactcac	13	18	1	2	rs558612480		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:18636366C>T	ENST00000336349.5	-	3	1690	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	485	Ser-rich.							p.P485P(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						CAGACCGCCCCGGGGGGCCCA	0.602													C|||	1	0.000199681	0	0	5008	,	,		17391	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	large_intestine(1)	11											27	30	29					11																	18636366		2199	4293	6492	18592942	SO:0001819	synonymous_variant	144108			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1455G>A	11.37:g.18636366C>T			18592942	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Silent	SNP	ENST00000336349.5	37	CCDS31441.1																																																																																				0.602	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		T	18636366	C	T	18636366	2	4	80	1	0	0	0	0	0	0	0	1	15165	639	23	1		1	SPTY2D1	11	18636366	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	12013788	18636366	116370150	86	23261										
PRRG4	79056	broad.mit.edu	37	chr11	32874973	32874973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttcttatgaacaggcagtggCgctgaccagaaaacacagtg	11	9	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:32874973C>T	ENST00000257836.3	+	6	834	c.581C>T	c.(580-582)gCg>gTg	p.A194V		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	194						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.A194V(1)		large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					CAGGCAGTGGCGCTGACCAGA	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	11											128	121	123					11																	32874973		2202	4299	6501	32831549	SO:0001583	missense	79056			AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.581C>T	11.37:g.32874973C>T	ENSP00000257836:p.Ala194Val		32831549		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504563	0.44558	.	.	ENSG00000135378	ENST00000257836	D	0.98044	-4.68	5.55	4.62	0.57501	.	0.208186	0.50627	D	0.000109	D	0.97586	0.9209	M	0.69358	2.11	0.46521	D	0.999083	D	0.69078	0.997	P	0.55615	0.78	D	0.96765	0.9564	10	0.39692	T	0.17	-13.7402	12.8143	0.57657	0.1641:0.8358:0.0:0.0	.	194	Q9BZD6	TMG4_HUMAN	V	194	ENSP00000257836:A194V	ENSP00000257836:A194V	A	+	2	0	PRRG4	32831549	0.999000	0.42202	1.000000	0.80357	0.201000	0.24016	3.116000	0.50399	1.308000	0.44962	0.544000	0.68410	GCG		0.478	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081		T	32874973	C	T	32874973	3	4	80	1	0	0	0	0	1	0	0	0	12642	768	27	1	599	1	PRRG4	11	32874973	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	14238607	32874973	102131543	87	23262										
OR4X2	119764	broad.mit.edu	37	chr11	48267470	48267470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gttctacacagtgataaccgCgatcctgaaccctgtcatct	7	13	3	2	rs180995599	byFrequency	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:48267470C>T	ENST00000302329.3	+	1	863	c.815C>T	c.(814-816)gCg>gTg	p.A272V		NM_001004727.1	NP_001004727.1	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X, member 2	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A272V(1)		breast(1)|large_intestine(4)|lung(12)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	20						GTGATAACCGCGATCCTGAAC	0.473													C|||	3	0.000599042	0.0015	0	5008	,	,		21327	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						C	VAL/ALA	0,4402		0,0,2201	96	88	91		815	4.6	0	11		91	1,8595	1.2+/-3.3	0,1,4297	yes	missense	OR4X2	NM_001004727.1	64	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	272/304	48267470	1,12997	2201	4298	6499	48224046	SO:0001583	missense	119764			AB065847	CCDS31486.1	11p11.2	2012-08-09			ENSG00000172208	ENSG00000172208		"GPCR / Class A : Olfactory receptors"	15184	protein-coding gene	gene with protein product							Standard	NM_001004727		Approved		uc001ngs.1	Q8NGF9	OTTHUMG00000165302	ENST00000302329.3:c.815C>T	11.37:g.48267470C>T	ENSP00000307751:p.Ala272Val		48224046	B2RNK3|Q6IF73|Q96R63	Missense_Mutation	SNP	ENST00000302329.3	37	CCDS31486.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.66	1.704494	0.30232	0.0	1.16E-4	ENSG00000172208	ENST00000302329	T	0.38560	1.13	5.47	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000054	T	0.25382	0.0617	N	0.08118	0	0.20975	N	0.999814	P	0.35745	0.518	B	0.36378	0.223	T	0.19679	-1.0298	10	0.87932	D	0	.	12.08	0.53665	0.0:0.9164:0.0:0.0836	.	272	Q8NGF9	OR4X2_HUMAN	V	272	ENSP00000307751:A272V	ENSP00000307751:A272V	A	+	2	0	OR4X2	48224046	0.767000	0.28508	0.024000	0.17045	0.003000	0.03518	4.550000	0.60733	1.301000	0.44836	-0.145000	0.13849	GCG		0.473	OR4X2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383376.2	NM_001004727		T	48267470	C	T	48267470	3	4	80	1	0	0	0	0	1	0	0	0	11116	768	27	1	817	1	OR4X2	11	48267470	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	15392497	48267470	86739046	88	23263										
TYR	7299	broad.mit.edu	37	chr11	88961018	88961018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tagtccacttactgggatagCggatgcctctcaaagcagca	10	11	1	0	rs151206295	byFrequency	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:88961018C>T	ENST00000263321.5	+	3	1566	c.1064C>T	c.(1063-1065)gCg>gTg	p.A355V		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	355			A -> E (in OCA1A).|A -> P (in OCA1A). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:11295837, ECO:0000269|PubMed:15146472}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A355V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	ACTGGGATAGCGGATGCCTCT	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	11	GRCh37	CM942071	TYR	M	rs151206295	C	VAL/ALA	0,4402		0,0,2201	124	104	111		1064	5.1	1	11	dbSNP_134	111	2,8594	2.2+/-6.3	0,2,4296	yes	missense	TYR	NM_000372.4	64	0,2,6497	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	355/530	88961018	2,12996	2201	4298	6499	88600666	SO:0001583	missense	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1064C>T	11.37:g.88961018C>T	ENSP00000263321:p.Ala355Val		88600666	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493946	0.84962	0.0	2.33E-4	ENSG00000077498	ENST00000263321	D	0.98889	-5.21	5.12	5.12	0.69794	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.175294	0.48767	D	0.000163	D	0.98741	0.9577	M	0.75447	2.3	0.58432	D	0.999994	D	0.61080	0.989	P	0.56751	0.805	D	0.99157	1.0860	9	.	.	.	.	18.5246	0.90967	0.0:1.0:0.0:0.0	.	355	P14679	TYRO_HUMAN	V	355	ENSP00000263321:A355V	.	A	+	2	0	TYR	88600666	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.425000	0.66470	2.546000	0.85860	0.650000	0.86243	GCG		0.383	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		T	88961018	C	T	88961018	3	4	80	1	0	0	0	0	1	0	0	0	16853	768	27	1	1074	1	TYR	11	88961018	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	40693548	88961018	46045498	89	23264										
FAT3	120114	broad.mit.edu	37	chr11	92534751	92534751	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	actccctccactcggattccCagcccgaaaaggtaatggaa	8	14	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:92534751C>T	ENST00000298047.6	+	9	8589	c.8572C>T	c.(8572-8574)Cag>Tag	p.Q2858*	FAT3_ENST00000525166.1_Nonsense_Mutation_p.Q2708*|FAT3_ENST00000409404.2_Nonsense_Mutation_p.Q2858*			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2858	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q2858*(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CTCGGATTCCCAGCCCGAAAA	0.502										TCGA Ovarian(4;0.039)																																						2	Substitution - Nonsense(2)	large_intestine(2)	11											60	61	60					11																	92534751		1972	4153	6125	92174399	SO:0001587	stop_gained	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.8572C>T	11.37:g.92534751C>T	ENSP00000298047:p.Gln2858*		92174399	B5MDB0|Q96AU6	Nonsense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	49	15.424441	0.99833	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	.	.	.	6.04	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	9.1728	0.37093	0.1289:0.5316:0.3395:0.0	.	.	.	.	X	2858;2858;2708	.	ENSP00000298047:Q2858X	Q	+	1	0	FAT3	92174399	0.826000	0.29277	1.000000	0.80357	0.907000	0.53573	2.124000	0.42006	2.873000	0.98535	0.563000	0.77884	CAG		0.502	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92534751	C	T	92534751	4	4	80	1	0	0	0	0	0	1	0	0	5710	595	21	3	8606	3	FAT3	11	92534751	Nonsense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	3573733	92534751	42471765	90	23265										
GRIA4	2893	broad.mit.edu	37	chr11	105845161	105845161	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	caagtccagggcagaagcgaAgagaatgaaggtggcaaaga	15	6	0	4			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:105845161A>C	ENST00000530497.1	+	15	2534	c.2534A>C	c.(2533-2535)aAg>aCg	p.K845T	GRIA4_ENST00000393127.2_Missense_Mutation_p.K845T|RNU6-277P_ENST00000516272.1_RNA|GRIA4_ENST00000533094.1_3'UTR|GRIA4_ENST00000282499.5_Missense_Mutation_p.K845T|GRIA4_ENST00000525187.1_Missense_Mutation_p.K845T			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	845					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.K845T(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GCAGAAGCGAAGAGAATGAAG	0.468																																																2	Substitution - Missense(2)	large_intestine(2)	11											154	140	145					11																	105845161		2201	4299	6500	105350371	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2534A>C	11.37:g.105845161A>C	ENSP00000435775:p.Lys845Thr		105350371	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134177	0.77662	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.14391	2.65;2.51;2.65;2.51	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000001	T	0.37404	0.1002	M	0.67569	2.06	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.91635	0.933;0.999	T	0.08371	-1.0725	10	0.66056	D	0.02	.	16.1968	0.82036	1.0:0.0:0.0:0.0	.	845;845	P48058;G3V164	GRIA4_HUMAN;.	T	845	ENSP00000282499:K845T;ENSP00000376835:K845T;ENSP00000435775:K845T;ENSP00000432180:K845T	ENSP00000282499:K845T	K	+	2	0	GRIA4	105350371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.307000	0.96226	2.225000	0.72522	0.533000	0.62120	AAG		0.468	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			C	105845161	A	C	105845161	3	2	80	1	0	0	0	0	1	0	0	0	6791	72	3	4	2748	4	GRIA4	11	105845161	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	13310410	105845161	29161355	91	23266										
KIAA1826	84437	broad.mit.edu	37	chr11	105880291	105880291	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgtccttctttctgaattcGaagtctgtctttctctacct	6	11	5	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:105880291G>A	ENST00000301919.4	-	3	2424	c.1009C>T	c.(1009-1011)Cga>Tga	p.R337*	MSANTD4_ENST00000529805.1_Intron	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	337						nucleus (GO:0005634)		p.R337*(1)									TTCTGAATTCGAAGTCTGTCT	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	11											105	99	101					11																	105880291		2201	4298	6499	105385501	SO:0001587	stop_gained	84437			AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.1009C>T	11.37:g.105880291G>A	ENSP00000304713:p.Arg337*		105385501	Q96JK1|Q96JZ3|Q9H2N4	Nonsense_Mutation	SNP	ENST00000301919.4	37	CCDS31663.1	.	.	.	.	.	.	.	.	.	.	G	49	15.045949	0.99820	.	.	ENSG00000170903	ENST00000301919	.	.	.	5.66	2.67	0.31697	.	0.140928	0.47852	D	0.000209	.	.	.	.	.	.	0.54753	D	0.999985	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.4888	14.802	0.69924	0.0:0.0:0.6075:0.3925	.	.	.	.	X	337	.	ENSP00000304713:R337X	R	-	1	2	KIAA1826	105385501	1.000000	0.71417	0.141000	0.22245	0.948000	0.59901	2.642000	0.46596	0.279000	0.22186	0.491000	0.48974	CGA		0.383	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		A	105880291	G	A	105880291	4	1	80	1	0	0	0	0	0	1	0	0	8281	1066	37	1	32	1	KIAA1826	11	105880291	Nonsense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	35130	105880291	29126225	92	23267										
C11orf87	399947	broad.mit.edu	37	chr11	109294862	109294862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctgtgctcctccgcctccacCgccagcctccagtccccaag	7	22	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:109294862C>T	ENST00000327419.6	+	2	906	c.503C>T	c.(502-504)cCg>cTg	p.P168L	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	168						integral component of membrane (GO:0016021)		p.P168L(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						CCGCCTCCACCGCCAGCCTCC	0.652																																																1	Substitution - Missense(1)	large_intestine(1)	11											40	42	41					11																	109294862		2201	4298	6499	108800072	SO:0001583	missense	399947			AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"neuronal integral membrane protein 1"					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.503C>T	11.37:g.109294862C>T	ENSP00000331581:p.Pro168Leu		108800072	B4E169	Missense_Mutation	SNP	ENST00000327419.6	37	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	C	8.125	0.781771	0.16120	.	.	ENSG00000185742	ENST00000327419	.	.	.	3.42	0.388	0.16264	.	.	.	.	.	T	0.18130	0.0435	N	0.08118	0	0.32620	N	0.523484	B	0.15719	0.014	B	0.08055	0.003	T	0.16424	-1.0403	8	0.33141	T	0.24	-5.3732	3.1802	0.06582	0.186:0.4978:0.0:0.3162	.	168	Q6NUJ2	CK087_HUMAN	L	168	.	ENSP00000331581:P168L	P	+	2	0	C11orf87	108800072	0.000000	0.05858	0.934000	0.37439	0.983000	0.72400	0.007000	0.13174	0.095000	0.17434	-0.123000	0.14984	CCG		0.652	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645		T	109294862	C	T	109294862	3	4	80	1	0	0	0	0	1	0	0	0	1673	652	23	1	505	1	C11orf87	11	109294862	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	3414571	109294862	25711654	93	23268										
SCN2B	6327	broad.mit.edu	37	chr11	118037755	118037755	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	acagccaggaagcccccgacGgaggcacccacaatcacggc	11	17	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:118037755G>A	ENST00000278947.5	-	4	736	c.495C>T	c.(493-495)tcC>tcT	p.S165S		NM_004588.4	NP_004579.1	O60939	SCN2B_HUMAN	sodium channel, voltage-gated, type II, beta subunit	165					cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|nervous system development (GO:0007399)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	voltage-gated sodium channel complex (GO:0001518)	sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.S165S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	7	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;3.19e-05)|Epithelial(105;0.00117)	Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCCCCCGACGGAGGCACCCA	0.607																																																1	Substitution - coding silent(1)	large_intestine(1)	11											92	88	90					11																	118037755		2200	4296	6496	117542965	SO:0001819	synonymous_variant	6327			AY358945	CCDS8390.1	11q23.3	2013-09-19	2012-02-28		ENSG00000149575	ENSG00000149575		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	10589	protein-coding gene	gene with protein product		601327	"sodium channel, voltage-gated, type II, beta polypeptide", "sodium channel, voltage-gated, type II, beta"			10198179	Standard	NM_004588		Approved		uc001psf.2	O60939	OTTHUMG00000048248	ENST00000278947.5:c.495C>T	11.37:g.118037755G>A			117542965	O75302|Q9UNN3	Silent	SNP	ENST00000278947.5	37	CCDS8390.1																																																																																				0.607	SCN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109748.2	NM_004588		A	118037755	G	A	118037755	2	1	80	1	0	0	0	0	0	0	0	1	13954	1103	39	1		1	SCN2B	11	118037755	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	8742893	118037755	16968761	94	23269										
CDON	50937	broad.mit.edu	37	chr11	125889553	125889553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttttccccggattttatagcGcacctcagctttggggttac	9	11	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr11:125889553G>A	ENST00000392693.3	-	4	584	c.457C>T	c.(457-459)Cgc>Tgc	p.R153C	CDON_ENST00000263577.7_Missense_Mutation_p.R153C	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	153	Ig-like C2-type 2.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R153C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		ATTTTATAGCGCACCTCAGCT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	11											132	136	135					11																	125889553		2201	4299	6500	125394763	SO:0001583	missense	50937			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.457C>T	11.37:g.125889553G>A	ENSP00000376458:p.Arg153Cys		125394763	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.284979|4.284979	0.80803|0.80803	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000534661|ENST00000392693;ENST00000263577;ENST00000531586	.|T;T;T	.|0.61510	.|2.65;2.65;0.1	5.33|5.33	4.42|4.42	0.53409|0.53409	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.000000	.|0.53938	.|D	.|0.000041	T|T	0.79046|0.79046	0.4380|0.4380	M|M	0.89287|0.89287	3.02|3.02	0.53688|0.53688	D|D	0.999971|0.999971	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.998;1.0;0.999	T|T	0.82831|0.82831	-0.0263|-0.0263	5|10	.|0.54805	.|T	.|0.06	-18.783|-18.783	14.5518|14.5518	0.68073|0.68073	0.0706:0.0:0.9294:0.0|0.0706:0.0:0.9294:0.0	.|.	.|153;153;153	.|E9PRD8;Q4KMG0;Q4KMG0-2	.|.;CDON_HUMAN;.	V|C	128|153	.|ENSP00000376458:R153C;ENSP00000263577:R153C;ENSP00000434212:R153C	.|ENSP00000263577:R153C	A|R	-|-	2|1	0|0	CDON|CDON	125394763|125394763	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.884000|0.884000	0.51177|0.51177	6.387000|6.387000	0.73191|0.73191	1.384000|1.384000	0.46424|0.46424	-0.215000|-0.215000	0.12644|0.12644	GCG|CGC		0.448	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		A	125889553	G	A	125889553	3	1	80	1	0	0	0	0	1	0	0	0	3176	1087	38	1	3405	1	CDON	11	125889553	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	7851798	125889553	9116963	95	23270										
KDM5A	5927	broad.mit.edu	37	chr12	419112	419112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	actcccatatacaccaatgtCggtccgggggctcagcacct	9	15	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:419112C>T	ENST00000399788.2	-	22	3597	c.3235G>A	c.(3235-3237)Gac>Aac	p.D1079N	KDM5A_ENST00000382815.4_Missense_Mutation_p.D1079N	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1079					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.D1079N(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						ACACCAATGTCGGTCCGGGGG	0.353			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	2	Substitution - Missense(2)	large_intestine(2)	12											60	57	58					12																	419112		1794	4067	5861	289373	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.3235G>A	12.37:g.419112C>T	ENSP00000382688:p.Asp1079Asn		289373	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	C	33	5.285384	0.95517	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	D;D;D	0.86562	-2.14;-1.96;-1.75	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.88047	0.6332	L	0.56280	1.765	0.80722	D	1	P;P;D	0.55172	0.939;0.791;0.97	P;B;P	0.46253	0.509;0.115;0.509	D	0.88160	0.2857	10	0.54805	T	0.06	-20.4149	20.3081	0.98638	0.0:1.0:0.0:0.0	.	1079;1079;1079	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	N	698;1038;1079;1079;698	ENSP00000382688:D1079N;ENSP00000372265:D1079N;ENSP00000440622:D698N	ENSP00000261253:D698N	D	-	1	0	KDM5A	289373	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.447000	0.80620	2.795000	0.96236	0.655000	0.94253	GAC		0.353	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		T	419112	C	T	419112	3	4	80	1	0	0	0	0	1	0	0	0	8154	884	31	1	1865	1	KDM5A	12	419112	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10		419112	133432783	96	23271										
CDCA3	83461	broad.mit.edu	37	chr12	6958266	6958266	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atggtcctggccttgctcccAtgctcgtcctccagttttca	8	15	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:6958266A>G	ENST00000538862.2	-	6	1649	c.748T>C	c.(748-750)Tgg>Cgg	p.W250R	CDCA3_ENST00000540683.1_3'UTR|CDCA3_ENST00000604599.1_5'Flank|CDCA3_ENST00000229265.6_Missense_Mutation_p.W225R|CDCA3_ENST00000422785.3_Intron|CDCA3_ENST00000535406.1_Missense_Mutation_p.W250R			Q99618	CDCA3_HUMAN	cell division cycle associated 3	250					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.W250R(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(1)|stomach(1)	8						CCTTGCTCCCATGCTCGTCCT	0.537																																																1	Substitution - Missense(1)	large_intestine(1)	12											119	98	105					12																	6958266		2203	4300	6503	6828527	SO:0001583	missense	83461			BG354576	CCDS8565.1, CCDS73428.1	12p13.31	2010-07-20				ENSG00000111665			14624	protein-coding gene	gene with protein product	"trigger of mitotic entry 1"	607749				9074930, 12188893	Standard	XR_242988		Approved	TOME-1, GRCC8	uc001qrg.2	Q99618		ENST00000538862.2:c.748T>C	12.37:g.6958266A>G	ENSP00000442068:p.Trp250Arg		6828527	A8K5V6|D3DUS6	Missense_Mutation	SNP	ENST00000538862.2	37	CCDS8565.1	.	.	.	.	.	.	.	.	.	.	A	5.975	0.363798	0.11296	.	.	ENSG00000111665	ENST00000229265;ENST00000538862;ENST00000535406	.	.	.	5.53	1.87	0.25490	.	0.501816	0.20111	N	0.099007	T	0.45216	0.1331	L	0.40543	1.245	0.58432	D	0.999997	B	0.18166	0.026	B	0.22601	0.04	T	0.23368	-1.0190	9	0.39692	T	0.17	-9.2387	8.4256	0.32727	0.7842:0.0:0.2158:0.0	.	250	Q99618	CDCA3_HUMAN	R	225;250;250	.	ENSP00000229265:W225R	W	-	1	0	CDCA3	6828527	0.831000	0.29352	0.257000	0.24404	0.038000	0.13279	1.461000	0.35255	0.167000	0.19631	0.533000	0.62120	TGG		0.537	CDCA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401940.2	NM_031299		G	6958266	A	G	6958266	3	3	80	1	0	0	0	0	1	0	0	0	3093	217	8	4	62	4	CDCA3	12	6958266	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	6539154	6958266	126893629	97	23272										
PYROXD1	79912	broad.mit.edu	37	chr12	21590727	21590727	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtggtcggcggcggcatcgcGggcgtcacttgtgcggagca	19	11	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:21590727G>C	ENST00000240651.9	+	1	117	c.63G>C	c.(61-63)gcG>gcC	p.A21A	PYROXD1_ENST00000545178.1_Silent_p.A21A|PYROXD1_ENST00000538582.1_5'Flank	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	21							oxidoreductase activity (GO:0016491)	p.A21A(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						GCGGCATCGCGGGCGTCACTT	0.682																																																1	Substitution - coding silent(1)	large_intestine(1)	12											18	22	21					12																	21590727		2201	4298	6499	21481994	SO:0001819	synonymous_variant	79912			AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.63G>C	12.37:g.21590727G>C			21481994	A6NKI6|B3KWN8|Q9H6P1	Silent	SNP	ENST00000240651.9	37	CCDS31755.1																																																																																				0.682	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854		C	21590727	G	C	21590727	2	2	80	1	0	0	0	0	0	0	0	1	12903	1103	39	5		5	PYROXD1	12	21590727	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	14632461	21590727	112261168	98	23273										
IFLTD1	160492	broad.mit.edu	37	chr12	25699468	25699468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgattcatcctgtttcttcgGaactgagaaggggctggcat	12	8	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:25699468G>A	ENST00000282881.6	-	3	417	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	IFLTD1_ENST00000445693.1_Missense_Mutation_p.P27S|IFLTD1_ENST00000539744.1_5'UTR|IFLTD1_ENST00000458174.2_Missense_Mutation_p.P111S|IFLTD1_ENST00000413632.2_Missense_Mutation_p.P111S	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		90					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)	p.P90S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TGTTTCTTCGGAACTGAGAAG	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	12											44	42	43					12																	25699468		2203	4298	6501	25590735	SO:0001583	missense	160492																														ENST00000282881.6:c.268C>T	12.37:g.25699468G>A	ENSP00000282881:p.Pro90Ser		25590735	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052796	0.19907	.	.	ENSG00000152936	ENST00000282881;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000538178;ENST00000540106;ENST00000542224	T;T;T;T	0.18960	2.72;2.7;2.18;2.49	4.94	-0.369	0.12534	.	.	.	.	.	T	0.11281	0.0275	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.27932	0.047;0.194;0.094;0.123	B;B;B;B	0.23275	0.02;0.045;0.027;0.02	T	0.26815	-1.0092	9	0.72032	D	0.01	.	3.066	0.06214	0.2825:0.0:0.3985:0.3189	.	27;111;111;90	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9	.;.;.;ILFT1_HUMAN	S	90;111;27;111;65;65;65	ENSP00000282881:P90S;ENSP00000407353:P111S;ENSP00000407043:P27S;ENSP00000393150:P111S	ENSP00000282881:P90S	P	-	1	0	IFLTD1	25590735	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.262000	0.08682	-0.163000	0.10946	-0.897000	0.02905	CCG		0.378	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			A	25699468	G	A	25699468	3	1	80	1	0	0	0	0	1	0	0	0	7551	1174	41	3	922	3	IFLTD1	12	25699468	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	4108741	25699468	108152427	99	23274										
KRT82	3888	broad.mit.edu	37	chr12	52797552	52797552	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctctagcctcacgcggtcccCggacacacagtccagctgcc	9	19	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:52797552C>T	ENST00000257974.2	-	2	630	c.553G>A	c.(553-555)Ggg>Agg	p.G185R	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	185	Coil 1B.|Rod.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.G185R(1)|p.S184fs*1(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		ACGCGGTCCCCGGACACACAG	0.592																																																2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|large_intestine(1)	12											66	71	69					12																	52797552		2203	4300	6503	51083819	SO:0001583	missense	3888			Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"-", "Intermediate filaments type II, keratins (basic)"	6459	protein-coding gene	gene with protein product	"hard keratin type II 2"	601078	"keratin, hair, basic, 2"	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.553G>A	12.37:g.52797552C>T	ENSP00000257974:p.Gly185Arg		51083819		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	.	.	.	.	.	.	.	.	.	.	C	9.070	0.996662	0.19043	.	.	ENSG00000161850	ENST00000257974	T	0.75589	-0.95	5.21	4.32	0.51571	Filament (1);	0.126723	0.35179	N	0.003381	T	0.64011	0.2560	L	0.39633	1.23	0.27431	N	0.953991	B	0.25169	0.119	B	0.26094	0.066	T	0.61187	-0.7113	10	0.87932	D	0	.	7.4794	0.27395	0.0:0.7143:0.1373:0.1484	.	185	Q9NSB4	KRT82_HUMAN	R	185	ENSP00000257974:G185R	ENSP00000257974:G185R	G	-	1	0	KRT82	51083819	0.000000	0.05858	0.856000	0.33681	0.177000	0.22998	-0.268000	0.08607	1.336000	0.45506	0.462000	0.41574	GGG		0.592	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52797552	C	T	52797552	3	4	80	1	0	0	0	0	1	0	0	0	8517	652	23	1	1020	1	KRT82	12	52797552	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	27098084	52797552	81054343	100	23275										
ZNF385A	25946	broad.mit.edu	37	chr12	54765484	54765484	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atcctggggctggccccagtCcattctccatggaaactgtt	10	13	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:54765484C>G	ENST00000338010.5	-	5	490	c.437G>C	c.(436-438)gGa>gCa	p.G146A	ZNF385A_ENST00000551109.1_Missense_Mutation_p.G126A|RP11-753H16.3_ENST00000550474.1_RNA|ZNF385A_ENST00000546970.1_Missense_Mutation_p.G126A|ZNF385A_ENST00000394313.2_Missense_Mutation_p.G126A|RP11-753H16.5_ENST00000552785.1_RNA|ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000352268.6_Intron|ZNF385A_ENST00000551771.1_Intron	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	146	Necessary for binding to ITPR1, CEBPA and p53/TP53 mRNAs. {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G126A(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						TGGCCCCAGTCCATTCTCCAT	0.582																																																2	Substitution - Missense(2)	large_intestine(2)	12											45	50	48					12																	54765484		2203	4300	6503	53051751	SO:0001583	missense	25946			AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"zinc finger protein 385"	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.437G>C	12.37:g.54765484C>G	ENSP00000338927:p.Gly146Ala		53051751	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Missense_Mutation	SNP	ENST00000338010.5	37	CCDS44911.1	.	.	.	.	.	.	.	.	.	.	C	1.319	-0.599919	0.03744	.	.	ENSG00000161642	ENST00000551109;ENST00000394313;ENST00000338010;ENST00000546970;ENST00000546919;ENST00000549937;ENST00000549962;ENST00000547210;ENST00000550774;ENST00000550120	T;T;T;T;T;T;T;T;T	0.45668	1.52;1.52;1.51;1.52;1.52;1.59;0.89;0.89;0.96	3.43	3.43	0.39272	.	0.355152	0.21932	N	0.067020	T	0.14356	0.0347	N	0.03608	-0.345	0.80722	D	1	P;B;B	0.37500	0.597;0.143;0.056	B;B;B	0.29077	0.098;0.028;0.01	T	0.15150	-1.0447	10	0.07175	T	0.84	-0.308	10.5707	0.45198	0.0:1.0:0.0:0.0	.	126;126;126	F8VRY0;Q96PM9;F1T0F1	.;Z385A_HUMAN;.	A	126;126;146;126;126;154;109;126;126;89	ENSP00000449161:G126A;ENSP00000377849:G126A;ENSP00000338927:G146A;ENSP00000446913:G126A;ENSP00000448466:G126A;ENSP00000448567:G154A;ENSP00000450149:G109A;ENSP00000448264:G126A;ENSP00000449462:G126A	ENSP00000338927:G146A	G	-	2	0	ZNF385A	53051751	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.855000	0.48333	1.942000	0.56320	0.561000	0.74099	GGA		0.582	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481		G	54765484	C	G	54765484	3	3	80	1	0	0	0	0	1	0	0	0	17915	855	30	5	739	5	ZNF385A	12	54765484	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	1967932	54765484	79086411	101	23276										
NCKAP1L	3071	broad.mit.edu	37	chr12	54901673	54901673	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttctcaacaccattgatgccTgccagtgccattttgatatc	6	12	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:54901673T>A	ENST00000293373.6	+	4	422	c.343T>A	c.(343-345)Tgc>Agc	p.C115S	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.C65S	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	115					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)	p.C115S(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CATTGATGCCTGCCAGTGCCA	0.418																																																1	Substitution - Missense(1)	large_intestine(1)	12											241	228	233					12																	54901673		2203	4300	6503	53187940	SO:0001583	missense	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.343T>A	12.37:g.54901673T>A	ENSP00000293373:p.Cys115Ser		53187940	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527560	0.44969	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.28895	1.59;1.59	5.53	5.53	0.82687	.	0.049689	0.85682	D	0.000000	T	0.34542	0.0901	L	0.46741	1.465	0.58432	D	0.999997	P	0.48089	0.905	P	0.49597	0.616	T	0.05435	-1.0885	10	0.13853	T	0.58	-12.873	13.603	0.62031	0.0:0.0:0.0:1.0	.	115	P55160	NCKPL_HUMAN	S	115;65	ENSP00000293373:C115S;ENSP00000445596:C65S	ENSP00000293373:C115S	C	+	1	0	NCKAP1L	53187940	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	3.178000	0.50879	2.100000	0.63781	0.374000	0.22700	TGC		0.418	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		A	54901673	T	A	54901673	3	1	80	1	0	0	0	0	1	0	0	0	10253	1580	55	5	357	5	NCKAP1L	12	54901673	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	136189	54901673	78950222	102	23277										
GLIPR1	11010	broad.mit.edu	37	chr12	75874745	75874745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	caaatattttgccagatatcGaaaatgaagatttcatcaaa	5	6	2	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:75874745G>A	ENST00000266659.3	+	1	286	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K		NM_006851.2	NP_006842.2	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1	29					cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E29K(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	14						GCCAGATATCGAAAATGAAGA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	12											92	87	89					12																	75874745		2203	4300	6503	74161012	SO:0001583	missense	11010			U16307	CCDS9011.1	12q14.1	2008-08-15	2008-08-15			ENSG00000139278			17001	protein-coding gene	gene with protein product		602692	"GLI pathogenesis-related 1 (glioma)"			7607567, 8973356	Standard	NM_006851		Approved	RTVP1, GliPR	uc001sxs.3	P48060	OTTHUMG00000169757	ENST00000266659.3:c.85G>A	12.37:g.75874745G>A	ENSP00000266659:p.Glu29Lys		74161012	A7YET6|F8VUC2|Q15409|Q969K2	Missense_Mutation	SNP	ENST00000266659.3	37	CCDS9011.1	.	.	.	.	.	.	.	.	.	.	G	5.239	0.229495	0.09916	.	.	ENSG00000139278	ENST00000266659;ENST00000456650	T;T	0.41400	1.0;1.0	6.03	-2.8	0.05823	CAP domain (2);	0.834705	0.11253	N	0.583421	T	0.18425	0.0442	N	0.14661	0.345	0.09310	N	1	B;B	0.12630	0.006;0.001	B;B	0.08055	0.003;0.001	T	0.31779	-0.9931	10	0.08837	T	0.75	.	6.7535	0.23499	0.4329:0.2017:0.3653:0.0	.	29;29	F6VVE8;P48060	.;GLIP1_HUMAN	K	29	ENSP00000266659:E29K;ENSP00000391144:E29K	ENSP00000266659:E29K	E	+	1	0	GLIPR1	74161012	0.000000	0.05858	0.000000	0.03702	0.559000	0.35586	-0.048000	0.11944	-0.588000	0.05882	-0.137000	0.14449	GAA		0.403	GLIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405722.1	NM_006851		A	75874745	G	A	75874745	3	1	80	1	0	0	0	0	1	0	0	0	6461	1059	37	1	87	1	GLIPR1	12	75874745	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	20973072	75874745	57977150	103	23278										
EPYC	1833	broad.mit.edu	37	chr12	91363838	91363838	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tacctggaggtgaagggctcGtagattttctgggagtggca	16	6	1	2	rs374036301		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:91363838G>C	ENST00000261172.3	-	6	873	c.781C>G	c.(781-783)Cga>Gga	p.R261G		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	261					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)	p.R261G(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						TGAAGGGCTCGTAGATTTTCT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	12											210	212	211					12																	91363838		2203	4300	6503	89887969	SO:0001583	missense	1833			AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.781C>G	12.37:g.91363838G>C	ENSP00000261172:p.Arg261Gly		89887969	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955270	0.34471	.	.	ENSG00000083782	ENST00000261172	T	0.02682	4.2	5.33	3.44	0.39384	.	0.279542	0.37053	N	0.002274	T	0.09024	0.0223	M	0.75615	2.305	0.09310	N	1	P	0.51449	0.945	P	0.50136	0.632	T	0.03443	-1.1036	10	0.87932	D	0	.	14.3393	0.66614	0.0:0.0:0.7301:0.2699	.	261	Q99645	EPYC_HUMAN	G	261	ENSP00000261172:R261G	ENSP00000261172:R261G	R	-	1	2	EPYC	89887969	0.690000	0.27699	0.007000	0.13788	0.271000	0.26615	3.984000	0.56923	0.582000	0.29556	0.467000	0.42956	CGA		0.478	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950		C	91363838	G	C	91363838	3	2	80	1	0	0	0	0	1	0	0	0	5214	1153	40	5	195	5	EPYC	12	91363838	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	15489093	91363838	42488057	104	23279										
CRADD	8738	broad.mit.edu	37	chr12	94243920	94243920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccacccccacaacgtgcagtCgcaggtggtggaggccttca	12	15	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:94243920C>T	ENST00000542893.2	+	3	791	c.473C>T	c.(472-474)tCg>tTg	p.S158L	CRADD_ENST00000332896.3_Missense_Mutation_p.S158L|CRADD_ENST00000548483.1_Intron|CRADD_ENST00000541813.1_Intron|CRADD_ENST00000548330.1_3'UTR			P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with death domain	158	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death domain binding (GO:0070513)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)	p.S158L(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)	8						AACGTGCAGTCGCAGGTGGTG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	12											54	49	50					12																	94243920		2203	4300	6503	92768051	SO:0001583	missense	8738			U84388	CCDS9048.1	12q21.33-q23.1	2008-08-04				ENSG00000169372			2340	protein-coding gene	gene with protein product	"RIP-associated ICH1/CED3-homologous protein with death domain"	603454				8985253, 9044836	Standard	NM_003805		Approved	RAIDD	uc001tda.3	P78560		ENST00000542893.2:c.473C>T	12.37:g.94243920C>T	ENSP00000439068:p.Ser158Leu		92768051	B7Z2Q5	Missense_Mutation	SNP	ENST00000542893.2	37	CCDS9048.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766118	0.90020	.	.	ENSG00000169372	ENST00000332896;ENST00000542893	D;D	0.93604	-3.25;-3.25	5.76	5.76	0.90799	Death (3);DEATH-like (2);	0.353759	0.30374	N	0.009775	D	0.95268	0.8465	M	0.68952	2.095	0.80722	D	1	D	0.67145	0.996	P	0.55112	0.769	D	0.94244	0.7487	10	0.41790	T	0.15	-4.6403	19.9772	0.97314	0.0:1.0:0.0:0.0	.	158	P78560	CRADD_HUMAN	L	158	ENSP00000327647:S158L;ENSP00000439068:S158L	ENSP00000327647:S158L	S	+	2	0	CRADD	92768051	0.999000	0.42202	0.948000	0.38648	0.971000	0.66376	3.926000	0.56491	2.724000	0.93272	0.563000	0.77884	TCG		0.657	CRADD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408515.1	NM_003805		T	94243920	C	T	94243920	3	4	80	1	0	0	0	0	1	0	0	0	3851	893	31	1	479	1	CRADD	12	94243920	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	2880082	94243920	39607975	105	23280										
PTPN11	5781	broad.mit.edu	37	chr12	112926270	112926270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tggaattggccggacagggaCgttcattgtgattgatattc	13	6	1	2	rs121918457		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:112926270C>T	ENST00000351677.2	+	12	1601	c.1403C>T	c.(1402-1404)aCg>aTg	p.T468M		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	472	Substrate binding. {ECO:0000250}.|Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		G -> A (in LEOPARD1). {ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:15389709}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.T468M(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CGGACAGGGACGTTCATTGTG	0.443			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	1	Substitution - Missense(1)	large_intestine(1)	12	GRCh37	CM021672	PTPN11	M	rs121918457						126	116	120					12																	112926270		2203	4300	6503	111410653	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1403C>T	12.37:g.112926270C>T	ENSP00000340944:p.Thr468Met		111410653	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764120	0.89932	.	.	ENSG00000179295	ENST00000351677	D	0.99537	-6.11	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.99718	0.9891	M	0.92738	3.34	0.80722	A	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97478	1.0045	9	0.72032	D	0.01	.	18.7696	0.91885	0.0:1.0:0.0:0.0	.	468	Q06124-2	.	M	468	ENSP00000340944:T468M	ENSP00000340944:T468M	T	+	2	0	PTPN11	111410653	1.000000	0.71417	0.951000	0.38953	0.819000	0.46315	7.397000	0.79903	2.508000	0.84585	0.650000	0.86243	ACG		0.443	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112926270	C	T	112926270	3	4	80	1	0	0	0	0	1	0	0	0	12815	536	19	1	1449	1	PTPN11	12	112926270	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	18682350	112926270	20925625	106	23281										
SBNO1	55206	broad.mit.edu	37	chr12	123815038	123815038	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctttcagcatcatactttaaGtcatttgaaacactaaacct	3	10	3	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:123815038G>A	ENST00000602398.1	-	9	1189	c.1062C>T	c.(1060-1062)gaC>gaT	p.D354D	SBNO1_ENST00000267176.4_Silent_p.D353D|SBNO1_ENST00000420886.2_Silent_p.D354D|SBNO1_ENST00000602750.1_Silent_p.D353D			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	354					regulation of transcription, DNA-templated (GO:0006355)			p.D353D(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CATACTTTAAGTCATTTGAAA	0.274																																																1	Substitution - coding silent(1)	large_intestine(1)	12											72	72	72					12																	123815038		2202	4297	6499	122380991	SO:0001819	synonymous_variant	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1062C>T	12.37:g.123815038G>A			122380991	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																				0.274	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123815038	G	A	123815038	2	1	80	1	0	0	0	0	0	0	0	1	13899	1020	36	3		3	SBNO1	12	123815038	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	10888768	123815038	10036857	107	23282										
RIMBP2	23504	broad.mit.edu	37	chr12	130919422	130919422	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	taggaagacgctccttttctCtaacttggaaagaaaaagga	9	7	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:130919422C>A	ENST00000261655.4	-	11	2222	c.2059G>T	c.(2059-2061)Gag>Tag	p.E687*	RIMBP2_ENST00000535703.1_Nonsense_Mutation_p.E595*|RIMBP2_ENST00000536002.1_Nonsense_Mutation_p.E595*	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	687					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.E687*(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTCCTTTTCTCTAACTTGGAA	0.592																																																1	Substitution - Nonsense(1)	large_intestine(1)	12											42	48	46					12																	130919422		2203	4300	6503	129485375	SO:0001587	stop_gained	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2059G>T	12.37:g.130919422C>A	ENSP00000261655:p.Glu687*		129485375	Q96ID2	Nonsense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	C	50	16.814226	0.99872	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	.	.	.	5.0	5.0	0.66597	.	0.127979	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-18.018	18.3226	0.90243	0.0:1.0:0.0:0.0	.	.	.	.	X	687;595;595;595	.	ENSP00000261655:E687X	E	-	1	0	RIMBP2	129485375	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.548000	0.82154	2.309000	0.77851	0.561000	0.74099	GAG		0.592	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130919422	C	A	130919422	4	1	80	1	0	0	0	0	0	1	0	0	13400	922	32	2	1135	2	RIMBP2	12	130919422	Nonsense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	7104384	130919422	2932473	108	23283										
RAN	5901	broad.mit.edu	37	chr12	131357439	131357439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cttcgtgaaacgtcatttgaCtggtgaatttgagaagaagt	11	5	1	5			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr12:131357439C>T	ENST00000543796.1	+	3	353	c.95C>T	c.(94-96)aCt>aTt	p.T32I	RAN_ENST00000392367.3_Missense_Mutation_p.T32I|RAN_ENST00000254675.3_5'UTR|RAN_ENST00000392369.2_Missense_Mutation_p.T32I|RAN_ENST00000541630.1_5'UTR			P62826	RAN_HUMAN	RAN, member RAS oncogene family	32					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.T32I(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		CGTCATTTGACTGGTGAATTT	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	12											337	321	327					12																	131357439		2203	4300	6503	129923392	SO:0001583	missense	5901			M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341			9846	protein-coding gene	gene with protein product		601179				8421051	Standard	XM_005253592		Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.95C>T	12.37:g.131357439C>T	ENSP00000446215:p.Thr32Ile		129923392	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	37	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.360201	0.61403	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000392369;ENST00000535090;ENST00000392367	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	3.72	2.81	0.32909	Small GTP-binding protein domain (1);	0.057033	0.64402	D	0.000001	T	0.78000	0.4215	M	0.79011	2.435	0.80722	D	1	B;B	0.25390	0.125;0.125	B;B	0.32980	0.156;0.156	T	0.75952	-0.3136	10	0.66056	D	0.02	-7.5365	9.9664	0.41727	0.0:0.8979:0.0:0.1021	.	32;32	A8K3Z8;P62826	.;RAN_HUMAN	I	32;50;32;28;32	ENSP00000446215:T32I;ENSP00000396127:T50I;ENSP00000376176:T32I;ENSP00000444042:T28I;ENSP00000376174:T32I	ENSP00000376174:T32I	T	+	2	0	RAN	129923392	1.000000	0.71417	0.724000	0.30704	0.495000	0.33615	6.785000	0.75089	0.675000	0.31264	0.511000	0.50034	ACT		0.398	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		T	131357439	C	T	131357439	3	4	80	1	0	0	0	0	1	0	0	0	13061	565	20	3	101	3	RAN	12	131357439	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	438017	131357439	2494456	109	23284										
TMTC4	84899	broad.mit.edu	37	chr13	101321036	101321036	+	5'UTR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gctcccggctccagcattatGctggttaggaatctgcagga	12	11	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr13:101321036G>C	ENST00000376234.3	-	0	148				TMTC4_ENST00000342624.5_Missense_Mutation_p.H6D|TMTC4_ENST00000328767.5_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4							integral component of membrane (GO:0016021)		p.H6D(1)		breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCAGCATTATGCTGGTTAGGA	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	13											59	58	58					13																	101321036		1890	4102	5992	100119037	SO:0001623	5_prime_UTR_variant	84899				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.-42C>G	13.37:g.101321036G>C			100119037	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	g	16.21	3.059670	0.55325	.	.	ENSG00000125247	ENST00000342624;ENST00000475272	T	0.59638	0.25	5.54	5.54	0.83059	.	0.347798	0.24666	N	0.036587	T	0.54565	0.1866	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.50874	-0.8776	9	0.62326	D	0.03	.	19.5038	0.95106	0.0:0.0:1.0:0.0	.	6	Q5T4D3-3	.	D	6	ENSP00000343871:H6D	ENSP00000343871:H6D	H	-	1	0	TMTC4	100119037	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	6.775000	0.75018	2.624000	0.88883	0.550000	0.68814	CAT		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		C	101321036	G	C	101321036	1	2	80	0	1	0	0	0	0	0	0	0	16302	1319	46	5		5	TMTC4	13	101321036	5'UTR	SNP	G	TCGA-AG-A036-01A-12W-A096-10		101321036	13848842	110	23285										
NALCN	259232	broad.mit.edu	37	chr13	102047655	102047655	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	agtgctcgaaggtcattggcGtattcatacaaacagaaatg	10	7	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr13:102047655G>C	ENST00000251127.6	-	3	251	c.170C>G	c.(169-171)aCg>aGg	p.T57R	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Missense_Mutation_p.T57R|NALCN_ENST00000376200.5_Missense_Mutation_p.T57R	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	57					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.T57R(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGTCATTGGCGTATTCATACA	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	13											154	118	130					13																	102047655		2203	4300	6503	100845656	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.170C>G	13.37:g.102047655G>C	ENSP00000251127:p.Thr57Arg		100845656	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411513	0.83340	.	.	ENSG00000102452	ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582	D;D;D	0.97772	-4.53;-4.53;-4.53	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.98713	0.9568	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99701	1.1004	10	0.72032	D	0.01	.	19.7619	0.96323	0.0:0.0:1.0:0.0	.	57;57	F2Z323;Q8IZF0	.;NALCN_HUMAN	R	57	ENSP00000251127:T57R;ENSP00000365367:T57R;ENSP00000365373:T57R	ENSP00000251127:T57R	T	-	2	0	NALCN	100845656	1.000000	0.71417	0.999000	0.59377	0.693000	0.40251	9.476000	0.97823	2.681000	0.91329	0.561000	0.74099	ACG		0.443	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		C	102047655	G	C	102047655	3	2	80	1	0	0	0	0	1	0	0	0	10178	1145	40	5	5214	5	NALCN	13	102047655	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	726619	102047655	13122223	111	23286										
OR4K1	79544	broad.mit.edu	37	chr14	20404494	20404494	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tcctacaccatcattttgatCggtgtccgatgcaggtcctc	8	13	1	1	rs141997601		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr14:20404494C>T	ENST00000285600.4	+	1	728	c.669C>T	c.(667-669)atC>atT	p.I223I		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I223I(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		TCATTTTGATCGGTGTCCGAT	0.423													C|||	1	0.000199681	0	0	5008	,	,		29108	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	14											124	119	121					14																	20404494		2203	4300	6503	19474334	SO:0001819	synonymous_variant	79544				CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"GPCR / Class A : Olfactory receptors"	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.669C>T	14.37:g.20404494C>T			19474334	B9EKV9|Q8NGD6|Q96R73	Silent	SNP	ENST00000285600.4	37	CCDS32025.1																																																																																				0.423	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1			T	20404494	C	T	20404494	2	4	80	1	0	0	0	0	0	0	0	1	11098	874	31	1		1	OR4K1	14	20404494	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10		20404494	86945046	112	23287										
DHRS4	10901	broad.mit.edu	37	chr14	24423018	24423018	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atgcacaaggcggggctgctAggcctctgtgcccgggcttg	16	12	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr14:24423018A>T	ENST00000313250.5	+	1	224	c.21A>T	c.(19-21)ctA>ctT	p.L7L	DHRS4_ENST00000397075.3_Silent_p.L7L|DHRS4_ENST00000397073.2_De_novo_Start_OutOfFrame|DHRS4_ENST00000558581.1_Silent_p.L7L|DHRS4_ENST00000308178.8_De_novo_Start_OutOfFrame|DHRS4_ENST00000558263.1_Silent_p.L7L|DHRS4_ENST00000421831.1_De_novo_Start_OutOfFrame|DHRS4_ENST00000382761.3_De_novo_Start_OutOfFrame|DHRS4_ENST00000397074.3_Silent_p.L7L|DHRS4_ENST00000559632.1_Silent_p.L7L|DHRS4_ENST00000543741.2_Silent_p.L7L|DHRS4-AS1_ENST00000556379.1_RNA	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	7					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)	p.L7L(1)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CGGGGCTGCTAGGCCTCTGTG	0.662																																																1	Substitution - coding silent(1)	large_intestine(1)	14											49	53	52					14																	24423018		2203	4300	6503	23492858	SO:0001819	synonymous_variant	10901			AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	16985	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 2"	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.21A>T	14.37:g.24423018A>T			23492858	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																				0.662	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			T	24423018	A	T	24423018	2	4	80	1	0	0	0	0	0	0	0	1	4503	407	15	5		5	DHRS4	14	24423018	Silent	SNP	A	TCGA-AG-A036-01A-12W-A096-10	4018524	24423018	82926522	113	23288										
PRKD1	5587	broad.mit.edu	37	chr14	30396523	30396525	+	In_Frame_Del	DEL	GCA	GCA	-													0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtagtccccggacgagtcctGcagcagcagcaccggctcac							TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	GCA	GCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr14:30396523_30396525delGCA	ENST00000331968.5	-	1	423_425	c.194_196delTGC	c.(193-198)ctgcag>cag	p.L65del	PRKD1_ENST00000415220.2_In_Frame_Del_p.L65del	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	65					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.L65delL(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GACGAGTCCTGCAGCAGCAGCAC	0.709																																																2	Deletion - In frame(2)	large_intestine(2)	14																																								29466276	SO:0001651	inframe_deletion	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.194_196delTGC	14.37:g.30396532_30396534delGCA	ENSP00000333568:p.Leu65del		29466274	A6NL64|B2RAF6	In_Frame_Del	DEL	ENST00000331968.5	37	CCDS9637.1																																																																																				0.709	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		-	30396525	GCA	-	30396523	7	5	80	1	0	1	0	1	0	0	0	0	12552	1328	46	0	2614	0	PRKD1	14	30396523	In_Frame_Del	DEL	GCA	TCGA-AG-A036-01A-12W-A096-10	5973505	30396523	76953017	114	23289										
EIF2B2	8892	broad.mit.edu	37	chr14	75470009	75470010	+	Missense_Mutation	DNP	CA	CA	GT													0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gagctgatccgcagagagggCaggaggatgacggccgctca							TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr14:75470009_75470010CA>GT	ENST00000266126.5	+	2	275_276	c.195_196CA>GT	c.(193-198)ggCAgg>ggGTgg	p.R66W	RP11-950C14.3_ENST00000554430.1_RNA	NM_014239.3	NP_055054.1	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa	66					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|central nervous system development (GO:0007417)|gene expression (GO:0010467)|myelination (GO:0042552)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)	p.G65>?(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.00661)		GCAGAGAGGGCAGGAGGATGAC	0.594																																																1	Complex(1)	large_intestine(1)	14																																								74539763	SO:0001583	missense	8892				CCDS9836.1	14q24.3	2008-08-11	2002-08-29			ENSG00000119718			3258	protein-coding gene	gene with protein product		606454	"eukaryotic translation initiation factor 2B, subunit 2 (beta, 39kD)"			8887689	Standard	NM_014239		Approved	EIF2B, EIF-2Bbeta	uc001xrc.2	P49770		Exception_encountered	14.37:g.75470009_75470010delinsGT	ENSP00000266126:p.Arg66Trp		74539762	O43201	Missense_Mutation	DNP	ENST00000266126.5	37	CCDS9836.1																																																																																				0.594	EIF2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414993.1	NM_014239		GT	75470010	CA	GT	75470009	3	3	80	1	0	0	0	0	1	0	0	0	5012	697	25	5	201	5	EIF2B2	14	75470009	Missense_Mutation	DNP	CA	TCGA-AG-A036-01A-12W-A096-10	45073486	75470009	31879531	115	23290										
UNC13C	440279	broad.mit.edu	37	chr15	54786896	54786896	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	taatgaatatgtgcgtgaacTtcctgccttcaaggatgctg	10	8	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr15:54786896T>G	ENST00000260323.11	+	19	5024	c.5024T>G	c.(5023-5025)cTt>cGt	p.L1675R	UNC13C_ENST00000545554.1_Missense_Mutation_p.L1675R|UNC13C_ENST00000537900.1_Missense_Mutation_p.L1673R	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1675	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.L1675R(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GTGCGTGAACTTCCTGCCTTC	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	15											167	162	164					15																	54786896		1856	4096	5952	52574188	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5024T>G	15.37:g.54786896T>G	ENSP00000260323:p.Leu1675Arg		52574188	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382471	0.82792	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;D;T	0.81499	-1.49;-1.5;-1.49	5.87	5.87	0.94306	Munc13 homology 1 (1);	0.000000	0.85682	D	0.000000	D	0.90497	0.7023	M	0.85373	2.75	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.91240	0.5021	10	0.54805	T	0.06	.	15.7569	0.78037	0.0:0.0:0.0:1.0	.	1675	Q8NB66	UN13C_HUMAN	R	1675;1675;1673	ENSP00000260323:L1675R;ENSP00000438156:L1675R;ENSP00000442569:L1673R	ENSP00000260323:L1675R	L	+	2	0	UNC13C	52574188	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	CTT		0.353	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54786896	T	G	54786896	3	3	80	1	0	0	0	0	1	0	0	0	17026	1609	56	4	5094	4	UNC13C	15	54786896	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		54786896	47744496	116	23291										
ALDH1A2	8854	broad.mit.edu	37	chr15	58257942	58257942	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagtcagcatcagcaaaaatAatattaggacttttgcctcc	6	10	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr15:58257942A>G	ENST00000249750.4	-	8	1649	c.882T>C	c.(880-882)atT>atC	p.I294I	ALDH1A2_ENST00000537372.1_Silent_p.I273I|ALDH1A2_ENST00000347587.3_Silent_p.I256I|ALDH1A2_ENST00000559517.1_Silent_p.I198I|ALDH1A2_ENST00000558231.1_Silent_p.I265I	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	294					9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)	p.I294I(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	CAGCAAAAATAATATTAGGAC	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	15											117	118	118					15																	58257942		2192	4292	6484	56045234	SO:0001819	synonymous_variant	8854			AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"Aldehyde dehydrogenases"	15472	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 2"	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.882T>C	15.37:g.58257942A>G			56045234	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Silent	SNP	ENST00000249750.4	37	CCDS10163.1																																																																																				0.413	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1			G	58257942	A	G	58257942	2	3	80	1	0	0	0	0	0	0	0	1	491	358	13	4		4	ALDH1A2	15	58257942	Silent	SNP	A	TCGA-AG-A036-01A-12W-A096-10	3471046	58257942	44273450	117	23292										
SMAD3	4088	broad.mit.edu	37	chr15	67479829	67479829	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccgcatgagcttcgtcaaagGctggggagcggagtacaggt	16	9	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr15:67479829G>C	ENST00000327367.4	+	8	1446	c.1136G>C	c.(1135-1137)gGc>gCc	p.G379A	SMAD3_ENST00000537194.2_Missense_Mutation_p.G184A|SMAD3_ENST00000439724.3_Missense_Mutation_p.G335A|SMAD3_ENST00000540846.2_Missense_Mutation_p.G274A	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	379	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G379A(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		TTCGTCAAAGGCTGGGGAGCG	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	15											112	107	109					15																	67479829		2201	4299	6500	65266883	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.1136G>C	15.37:g.67479829G>C	ENSP00000332973:p.Gly379Ala		65266883	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.046774	0.93740	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.99483	-5.99;-5.99;-5.99;-5.99	5.71	5.71	0.89125	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.103998	0.64402	D	0.000003	D	0.99684	0.9881	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.97802	1.0245	10	0.87932	D	0	.	19.8575	0.96767	0.0:0.0:1.0:0.0	.	335;379	B7Z4Z5;P84022	.;SMAD3_HUMAN	A	379;379;274;335;184	ENSP00000332973:G379A;ENSP00000437757:G274A;ENSP00000401133:G335A;ENSP00000445348:G184A	ENSP00000332973:G379A	G	+	2	0	SMAD3	65266883	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.633000	0.98432	2.698000	0.92095	0.561000	0.74099	GGC		0.597	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		C	67479829	G	C	67479829	3	2	80	1	0	0	0	0	1	0	0	0	14796	1203	42	5	1244	5	SMAD3	15	67479829	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	9221887	67479829	35051563	118	23293										
RASGRF1	5923	broad.mit.edu	37	chr15	79339164	79339164	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggcggccatccgcagcgggcGcaggaaattgttgacaagga	16	10	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr15:79339164G>A	ENST00000419573.3	-	5	1076	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C	RASGRF1_ENST00000558480.2_Missense_Mutation_p.R268C|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	268	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R268C(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGCAGCGGGCGCAGGAAATTG	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	15											133	107	116					15																	79339164		2196	4293	6489	77126219	SO:0001583	missense	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.802C>T	15.37:g.79339164G>A	ENSP00000405963:p.Arg268Cys		77126219	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639842	0.67244	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.65178	-0.14	4.03	4.03	0.46877	Dbl homology (DH) domain (5);	0.072935	0.53938	D	0.000041	T	0.72374	0.3452	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.997	T	0.75758	-0.3205	10	0.87932	D	0	.	13.7003	0.62604	0.0:0.0:1.0:0.0	.	268;268;268;268	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	C	268	ENSP00000405963:R268C	ENSP00000378224:R268C	R	-	1	0	RASGRF1	77126219	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.169000	0.42434	2.072000	0.62099	0.655000	0.94253	CGC		0.587	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79339164	G	A	79339164	3	1	80	1	0	0	0	0	1	0	0	0	13109	1087	38	1	3115	1	RASGRF1	15	79339164	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	11859335	79339164	23192228	119	23294										
STX4	6810	broad.mit.edu	37	chr16	31051088	31051088	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgtccatcaccgtcgtcctCctagcagtcatcattggcgt	9	14	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr16:31051088C>T	ENST00000313843.3	+	10	1173	c.858C>T	c.(856-858)ctC>ctT	p.L286L	STX4_ENST00000493902.1_3'UTR|STX4_ENST00000394998.1_Silent_p.L284L	NM_004604.3	NP_004595.2	Q12846	STX4_HUMAN	syntaxin 4	286	Interaction with CENPF. {ECO:0000250}.				blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|neurotransmitter transport (GO:0006836)|platelet activation (GO:0030168)|post-Golgi vesicle-mediated transport (GO:0006892)|SNARE complex assembly (GO:0035493)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|membrane (GO:0016020)|myelin sheath adaxonal region (GO:0035749)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)		p.L286L(1)		NS(2)|breast(1)|large_intestine(3)|lung(3)	9						CCGTCGTCCTCCTAGCAGTCA	0.602																																																1	Substitution - coding silent(1)	large_intestine(1)	16											329	247	275					16																	31051088		2197	4300	6497	30958589	SO:0001819	synonymous_variant	6810			AF026007	CCDS10700.1, CCDS61916.1	16p11.2	2008-02-05	2006-04-25	2006-04-25	ENSG00000103496	ENSG00000103496			11439	protein-coding gene	gene with protein product		186591	"syntaxin 4A (placental)"	STX4A		8206394, 16339081	Standard	NM_001272095		Approved	p35-2	uc002eak.4	Q12846	OTTHUMG00000132404	ENST00000313843.3:c.858C>T	16.37:g.31051088C>T			30958589	A8MXY0|Q15525|Q6FHE8	Silent	SNP	ENST00000313843.3	37	CCDS10700.1																																																																																				0.602	STX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255538.3	NM_004604		T	31051088	C	T	31051088	2	4	80	1	0	0	0	0	0	0	0	1	15386	842	30	3		3	STX4	16	31051088	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10		31051088	59303665	120	23295										
MYLK3	91807	broad.mit.edu	37	chr16	46766140	46766140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ccagaaccacgctgccagccTcggcgcctgggggcatcctc	12	18	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr16:46766140T>C	ENST00000394809.4	-	4	1557	c.1442A>G	c.(1441-1443)gAg>gGg	p.E481G	MYLK3_ENST00000536476.1_Missense_Mutation_p.E140G	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	481					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.E481G(1)|p.E560G(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GCTGCCAGCCTCGGCGCCTGG	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	16											22	24	23					16																	46766140		2203	4299	6502	45323641	SO:0001583	missense	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1442A>G	16.37:g.46766140T>C	ENSP00000378288:p.Glu481Gly		45323641	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	t	11.71	1.720987	0.30503	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.69306	-0.39;-0.37	5.27	4.11	0.48088	.	0.709521	0.11565	N	0.551335	T	0.56906	0.2017	L	0.60455	1.87	0.34466	D	0.702259	B;P	0.44627	0.255;0.839	B;B	0.36134	0.078;0.218	T	0.64373	-0.6423	10	0.30854	T	0.27	.	7.7395	0.28833	0.1865:0.0:0.0:0.8135	.	481;481	B5BUL9;Q32MK0	.;MYLK3_HUMAN	G	481;140	ENSP00000378288:E481G;ENSP00000439297:E140G	ENSP00000378288:E481G	E	-	2	0	MYLK3	45323641	0.284000	0.24287	0.846000	0.33378	0.023000	0.10783	1.294000	0.33365	1.981000	0.57761	0.454000	0.30748	GAG		0.652	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		C	46766140	T	C	46766140	3	2	80	1	0	0	0	0	1	0	0	0	10088	1551	54	4	1057	4	MYLK3	16	46766140	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	15715052	46766140	43588613	121	23296										
SLC12A3	6559	broad.mit.edu	37	chr16	56906353	56906353	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	catctgaggacaaggcctccAaaggcttcttcagctaccgg	10	13	3	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr16:56906353A>G	ENST00000563236.1	+	7	968	c.943A>G	c.(943-945)Aaa>Gaa	p.K315E	SLC12A3_ENST00000566786.1_Missense_Mutation_p.K314E|SLC12A3_ENST00000438926.2_Missense_Mutation_p.K315E|SLC12A3_ENST00000262502.5_Missense_Mutation_p.K314E			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	315					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)	p.K315E(1)		breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CAAGGCCTCCAAAGGCTTCTT	0.572																																																1	Substitution - Missense(1)	large_intestine(1)	16											82	74	77					16																	56906353		2198	4300	6498	55463854	SO:0001583	missense	6559				CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.943A>G	16.37:g.56906353A>G	ENSP00000456149:p.Lys315Glu		55463854	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354659	0.61293	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.72	5.72	0.89469	Amino acid permease domain (1);	0.087786	0.85682	D	0.000000	T	0.67211	0.2869	M	0.66378	2.025	0.52501	D	0.999954	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.15052	0.007;0.012;0.007	T	0.65569	-0.6136	9	0.72032	D	0.01	.	15.9825	0.80121	1.0:0.0:0.0:0.0	.	314;315;315	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	E	314;315	.	ENSP00000262502:K315E	K	+	1	0	SLC12A3	55463854	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.995000	0.63908	2.182000	0.69389	0.459000	0.35465	AAA		0.572	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			G	56906353	A	G	56906353	3	3	80	1	0	0	0	0	1	0	0	0	14421	131	5	4	969	4	SLC12A3	16	56906353	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10	10140213	56906353	33448400	122	23297										
KIAA0182	23199	broad.mit.edu	37	chr16	85690941	85690941	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtccaacaccccttgcatccGgtgcccaccccacaccacac	5	22	0	0	rs371123194		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr16:85690941G>A	ENST00000253458.7	+	8	1547	c.1371G>A	c.(1369-1371)ccG>ccA	p.P457P	GSE1_ENST00000393243.1_Silent_p.P384P|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000405402.2_Silent_p.P353P	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	457								p.P457P(1)									CCTTGCATCCGGTGCCCACCC	0.637																																																1	Substitution - coding silent(1)	large_intestine(1)	16						G	,	2,4392	4.2+/-10.8	0,2,2195	68	60	62		1059,1371	-5.1	0.2	16		62	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	KIAA0182	NM_001134473.1,NM_014615.2	,	0,2,6493	AA,AG,GG		0.0,0.0455,0.0154	,	353/1114,457/1218	85690941	2,12988	2197	4298	6495	84248442	SO:0001819	synonymous_variant	23199			D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1371G>A	16.37:g.85690941G>A			84248442	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	G	4.505	0.093638	0.08632	4.55E-4	0.0	ENSG00000131149	ENST00000412692	.	.	.	5.07	-5.06	0.02946	.	.	.	.	.	T	0.17492	0.0420	.	.	.	0.29076	N	0.883013	.	.	.	.	.	.	T	0.33497	-0.9866	4	.	.	.	-32.0284	1.3781	0.02225	0.2518:0.1771:0.3756:0.1955	.	.	.	.	Q	264	.	.	R	+	2	0	KIAA0182	84248442	0.000000	0.05858	0.213000	0.23690	0.571000	0.35966	-0.565000	0.05929	-0.387000	0.07809	-0.314000	0.08810	CGG		0.637	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85690941	G	A	85690941	2	1	80	1	0	0	0	0	0	0	0	1	8180	1103	39	1		1	KIAA0182	16	85690941	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	28784588	85690941	4663812	123	23298										
TP53	7157	broad.mit.edu	37	chr17	7578509	7578509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aacccacagctgcacagggcAggtcttggccagttggcaaa	12	12	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:7578509A>G	ENST00000269305.4	-	5	610	c.421T>C	c.(421-423)Tgc>Cgc	p.C141R	TP53_ENST00000359597.4_Missense_Mutation_p.C141R|TP53_ENST00000420246.2_Missense_Mutation_p.C141R|TP53_ENST00000455263.2_Missense_Mutation_p.C141R|TP53_ENST00000445888.2_Missense_Mutation_p.C141R|TP53_ENST00000413465.2_Missense_Mutation_p.C141R|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	141	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		C -> A (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C141R(13)|p.0?(8)|p.A138_P142delAKTCP(4)|p.N131fs*27(2)|p.C141S(2)|p.C141fs*8(2)|p.L137_W146del10(1)|p.K139fs*4(1)|p.A45_P49delAKTCP(1)|p.C141fs*34(1)|p.C141fs*30(1)|p.C9R(1)|p.A6_P10delAKTCP(1)|p.A138_V143delAKTCPV(1)|p.C48R(1)|p.C141fs*29(1)|p.C141A(1)|p.C141G(1)|p.K139_C141>N(1)|p.K139fs*29(1)|p.T140fs*28(1)|p.C141fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCACAGGGCAGGTCTTGGCC	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	47	Substitution - Missense(19)|Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Insertion - Frameshift(4)|Complex - frameshift(1)|Complex - deletion inframe(1)	ovary(11)|large_intestine(7)|breast(7)|central_nervous_system(5)|bone(4)|upper_aerodigestive_tract(2)|stomach(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|prostate(2)|biliary_tract(1)|lung(1)|oesophagus(1)	17											56	55	56					17																	7578509		2203	4300	6503	7519234	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.421T>C	17.37:g.7578509A>G	ENSP00000269305:p.Cys141Arg		7519234	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	13.32	2.203306	0.38905	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99820	-6.93;-6.93;-6.93;-6.93;-6.93;-6.93;-6.93;-6.93;-6.93	5.48	4.41	0.53225	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.046412	0.85682	D	0.000000	D	0.99806	0.9916	M	0.90309	3.105	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.994;1.0;0.999;1.0;1.0	D	0.97577	1.0108	10	0.87932	D	0	-26.1094	9.8103	0.40820	0.918:0.0:0.082:0.0	.	102;141;141;48;141;141;141	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	141;141;141;141;141;141;130;48;9;48;9;141	ENSP00000410739:C141R;ENSP00000352610:C141R;ENSP00000269305:C141R;ENSP00000398846:C141R;ENSP00000391127:C141R;ENSP00000391478:C141R;ENSP00000425104:C9R;ENSP00000423862:C48R;ENSP00000424104:C141R	ENSP00000269305:C141R	C	-	1	0	TP53	7519234	1.000000	0.71417	0.996000	0.52242	0.026000	0.11368	5.164000	0.64954	1.020000	0.39573	-0.256000	0.11100	TGC		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578509	A	G	7578509	3	3	80	1	0	0	0	0	1	0	0	0	16421	188	7	4	877	4	TP53	17	7578509	Missense_Mutation	SNP	A	TCGA-AG-A036-01A-12W-A096-10		7578509	73616701	124	23299										
DNAH9	1770	broad.mit.edu	37	chr17	11645560	11645560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gctggtggcagaaggattcaTtgaagcccagtcattagcca	12	9	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:11645560T>C	ENST00000262442.4	+	30	6109	c.6041T>C	c.(6040-6042)aTt>aCt	p.I2014T	AC005701.1_ENST00000584990.1_RNA|DNAH9_ENST00000454412.2_Missense_Mutation_p.I2014T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2014	AAA 1. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.I2014T(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		GAAGGATTCATTGAAGCCCAG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	17											196	172	180					17																	11645560		2203	4300	6503	11586285	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6041T>C	17.37:g.11645560T>C	ENSP00000262442:p.Ile2014Thr		11586285	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940399	0.52972	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.11604	2.76;2.76	5.61	5.61	0.85477	.	0.070705	0.64402	D	0.000015	T	0.08268	0.0206	N	0.11201	0.11	0.80722	D	1	B	0.16603	0.018	B	0.29077	0.098	T	0.39210	-0.9625	10	0.26408	T	0.33	.	16.1462	0.81575	0.0:0.0:0.0:1.0	.	2014	Q9NYC9	DYH9_HUMAN	T	2014;2014;596	ENSP00000262442:I2014T;ENSP00000414874:I2014T	ENSP00000262442:I2014T	I	+	2	0	DNAH9	11586285	1.000000	0.71417	0.949000	0.38748	0.988000	0.76386	6.260000	0.72502	2.276000	0.75962	0.524000	0.50904	ATT		0.458	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11645560	T	C	11645560	3	2	80	1	0	0	0	0	1	0	0	0	4619	1493	52	4	6159	4	DNAH9	17	11645560	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	4067051	11645560	69549650	125	23300										
UNC45B	146862	broad.mit.edu	37	chr17	33491148	33491148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	acctgcgctgtgacccggagCgcgatcacttccgcaagatc	11	15	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:33491148C>T	ENST00000268876.5	+	9	1211	c.1114C>T	c.(1114-1116)Cgc>Tgc	p.R372C	UNC45B_ENST00000394570.2_Missense_Mutation_p.R372C|UNC45B_ENST00000591048.1_Missense_Mutation_p.R372C|RP11-799D4.3_ENST00000585646.1_RNA|UNC45B_ENST00000433649.1_Missense_Mutation_p.R372C|UNC45B_ENST00000378449.1_Missense_Mutation_p.R372C	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	372					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.R372C(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGACCCGGAGCGCGATCACTT	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	17											181	171	175					17																	33491148		2203	4300	6503	30515261	SO:0001583	missense	146862			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1114C>T	17.37:g.33491148C>T	ENSP00000268876:p.Arg372Cys		30515261	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711746	0.68730	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	4.41	3.36	0.38483	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.69823	2.125	0.51767	D	0.999931	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.991;0.999;0.998	T	0.68254	-0.5457	10	0.87932	D	0	-18.5649	11.6617	0.51349	0.2764:0.7236:0.0:0.0	.	372;372;372	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	C	372	ENSP00000378071:R372C;ENSP00000268876:R372C;ENSP00000412840:R372C;ENSP00000367710:R372C	ENSP00000268876:R372C	R	+	1	0	UNC45B	30515261	1.000000	0.71417	0.933000	0.37362	0.958000	0.62258	3.989000	0.56958	2.461000	0.83175	0.462000	0.41574	CGC		0.532	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		T	33491148	C	T	33491148	3	4	80	1	0	0	0	0	1	0	0	0	17029	768	27	1	1144	1	UNC45B	17	33491148	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	21845588	33491148	47704062	126	23301										
KRT32	3882	broad.mit.edu	37	chr17	39623441	39623441	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gcaggcagaccgaaggcaggCatgccatgggctggcagaca	16	11	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:39623441C>A	ENST00000225899.3	-	1	240	c.137G>T	c.(136-138)tGc>tTc	p.C46F	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	46	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.C46F(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				CGAAGGCAGGCATGCCATGGG	0.657																																																1	Substitution - Missense(1)	large_intestine(1)	17											36	39	38					17																	39623441		2203	4300	6503	36876967	SO:0001583	missense	3882			X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.137G>T	17.37:g.39623441C>A	ENSP00000225899:p.Cys46Phe		36876967		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	C	5.969	0.362767	0.11296	.	.	ENSG00000108759	ENST00000225899	D	0.97232	-4.3	3.92	0.77	0.18497	.	0.545228	0.15505	N	0.258843	D	0.90745	0.7095	L	0.35593	1.075	0.09310	N	1	B	0.23058	0.079	B	0.20577	0.03	T	0.79130	-0.1930	10	0.06236	T	0.91	.	4.2717	0.10789	0.0:0.5979:0.1888:0.2132	.	46	Q14532	K1H2_HUMAN	F	46	ENSP00000225899:C46F	ENSP00000225899:C46F	C	-	2	0	KRT32	36876967	0.000000	0.05858	0.003000	0.11579	0.747000	0.42532	-0.094000	0.11094	0.228000	0.21019	0.563000	0.77884	TGC		0.657	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		A	39623441	C	A	39623441	3	1	80	1	0	0	0	0	1	0	0	0	8489	710	25	2	1237	2	KRT32	17	39623441	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	6132293	39623441	41571769	127	23302										
OR4D1	26689	broad.mit.edu	37	chr17	56232547	56232547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aacaccacacaggtatcaatGtttgtcctcttagggttttc	7	10	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:56232547G>A	ENST00000268912.5	+	1	54	c.33G>A	c.(31-33)atG>atA	p.M11I		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	11					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M11I(1)		kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						AGGTATCAATGTTTGTCCTCT	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	17											119	116	117					17																	56232547		1916	4123	6039	53587546	SO:0001583	missense	26689			X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"GPCR / Class A : Olfactory receptors"	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.33G>A	17.37:g.56232547G>A	ENSP00000365451:p.Met11Ile		53587546	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	g	8.083	0.772709	0.16051	.	.	ENSG00000141194	ENST00000268912	T	0.01068	5.38	5.63	-3.01	0.05463	.	0.816727	0.10097	U	0.716396	T	0.00695	0.0023	N	0.11131	0.1	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47459	-0.9116	10	0.87932	D	0	-1.6373	2.2751	0.04100	0.431:0.1198:0.3265:0.1227	.	11	Q15615	OR4D1_HUMAN	I	11	ENSP00000365451:M11I	ENSP00000365451:M11I	M	+	3	0	OR4D1	53587546	0.000000	0.05858	0.032000	0.17829	0.042000	0.13812	-0.821000	0.04452	-0.396000	0.07703	-0.266000	0.10368	ATG		0.408	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			A	56232547	G	A	56232547	3	1	80	1	0	0	0	0	1	0	0	0	11084	1377	48	3	35	3	OR4D1	17	56232547	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	16609106	56232547	24962663	128	23303										
MTMR4	9110	broad.mit.edu	37	chr17	56569102	56569102	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cgagagacttgaatgtgttcGtaacatgagttacagacgag	12	6	0	4	rs143878413		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:56569102G>A	ENST00000323456.5	-	19	3634	c.3510C>T	c.(3508-3510)taC>taT	p.Y1170Y	MTMR4_ENST00000579925.1_Silent_p.Y1113Y	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	1170					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)	p.Y1170Y(1)		breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GAATGTGTTCGTAACATGAGT	0.488																																																1	Substitution - coding silent(1)	large_intestine(1)	17						G		1,4405	2.1+/-5.4	0,1,2202	115	99	105		3510	1.9	1	17	dbSNP_134	105	0,8600		0,0,4300	no	coding-synonymous	MTMR4	NM_004687.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1170/1196	56569102	1,13005	2203	4300	6503	53924101	SO:0001819	synonymous_variant	9110			AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.3510C>T	17.37:g.56569102G>A			53924101	D3DTZ6|Q8IV27|Q9Y4D5	Silent	SNP	ENST00000323456.5	37	CCDS11608.1																																																																																				0.488	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		A	56569102	G	A	56569102	2	1	80	1	0	0	0	0	0	0	0	1	9976	1140	40	1		1	MTMR4	17	56569102	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	336555	56569102	24626108	129	23304										
KCNH6	81033	broad.mit.edu	37	chr17	61607569	61607569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cctggccaagtgcagcagccGcagcttgtcccagcgcctgt	12	16	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr17:61607569G>A	ENST00000583023.1	+	3	436	c.425G>A	c.(424-426)cGc>cAc	p.R142H	KCNH6_ENST00000314672.5_Missense_Mutation_p.R142H|KCNH6_ENST00000580652.1_Missense_Mutation_p.R142H|KCNH6_ENST00000456941.2_Missense_Mutation_p.R142H|KCNH6_ENST00000581784.1_Missense_Mutation_p.R142H	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	142	PAC.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.R142H(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGCAGCAGCCGCAGCTTGTCC	0.637																																																1	Substitution - Missense(1)	large_intestine(1)	17											59	56	57					17																	61607569		2203	4300	6503	58961301	SO:0001583	missense	81033			AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.425G>A	17.37:g.61607569G>A	ENSP00000463533:p.Arg142His		58961301	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.873785	0.33069	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.99264	-5.12;-5.65	4.58	2.48	0.30137	.	0.464165	0.17953	N	0.156446	D	0.95623	0.8577	N	0.08118	0	0.29661	N	0.843257	B;B;B;B;B	0.14438	0.01;0.006;0.007;0.006;0.001	B;B;B;B;B	0.10450	0.002;0.002;0.005;0.003;0.001	D	0.93724	0.7035	10	0.35671	T	0.21	.	9.2217	0.37382	0.2479:0.0:0.7521:0.0	.	19;142;142;142;142	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	H	142	ENSP00000318212:R142H;ENSP00000396900:R142H	ENSP00000318212:R142H	R	+	2	0	KCNH6	58961301	0.299000	0.24426	1.000000	0.80357	0.957000	0.61999	2.051000	0.41307	1.107000	0.41642	0.561000	0.74099	CGC		0.637	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		A	61607569	G	A	61607569	3	1	80	1	0	0	0	0	1	0	0	0	8057	1087	38	1	435	1	KCNH6	17	61607569	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	5038467	61607569	19587641	130	23305										
PTPRM	5797	broad.mit.edu	37	chr18	8394505	8394505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gccgcagtgggacgttctgcGccatcagcatcgtatgtgag	14	11	2	1	rs142178302	byFrequency	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr18:8394505G>A	ENST00000332175.8	+	30	5238	c.4201G>A	c.(4201-4203)Gcc>Acc	p.A1401T	PTPRM_ENST00000400060.4_Missense_Mutation_p.A1415T|PTPRM_ENST00000400053.4_Missense_Mutation_p.A1339T|PTPRM_ENST00000444013.1_Missense_Mutation_p.A1188T|PTPRM_ENST00000580170.1_Missense_Mutation_p.A1414T	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1401	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A1401T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GACGTTCTGCGCCATCAGCAT	0.537													G|||	2	0.000399361	0	0	5008	,	,		19482	0.001		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	18						G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	78	58	65		4240,4201	5.8	1	18	dbSNP_134	65	0,8600		0,0,4300	yes	missense,missense	PTPRM	NM_001105244.1,NM_002845.3	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1414/1466,1401/1453	8394505	1,13005	2203	4300	6503	8384505	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.4201G>A	18.37:g.8394505G>A	ENSP00000331418:p.Ala1401Thr		8384505	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	32	5.151972	0.94645	2.27E-4	0.0	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.75	5.75	0.90469	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.121135	0.56097	D	0.000035	T	0.31575	0.0801	L	0.37697	1.125	0.80722	D	1	D;D;D	0.76494	0.999;0.979;0.998	D;P;P	0.69824	0.966;0.624;0.766	T	0.01661	-1.1301	10	0.13108	T	0.6	.	19.9923	0.97371	0.0:0.0:1.0:0.0	.	1188;1414;1401	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	T	1401;1415;1339;1188	ENSP00000331418:A1401T;ENSP00000382933:A1415T;ENSP00000382927:A1339T;ENSP00000387608:A1188T	ENSP00000331418:A1401T	A	+	1	0	PTPRM	8384505	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	8.010000	0.88615	2.727000	0.93392	0.650000	0.86243	GCC		0.537	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	8394505	G	A	8394505	3	1	80	1	0	0	0	0	1	0	0	0	12843	1087	38	1	4366	1	PTPRM	18	8394505	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10		8394505	69682743	131	23306										
KIAA1632	57724	broad.mit.edu	37	chr18	43495483	43495483	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtgagtttcctacctgagtgGgcgtggccaagccctccaca	12	13	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr18:43495483G>T	ENST00000282041.5	-	20	3720	c.3686C>A	c.(3685-3687)cCc>cAc	p.P1229H	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1229					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.P1229H(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TACCTGAGTGGGCGTGGCCAA	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	18											88	92	90					18																	43495483		2099	4220	6319	41749481	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3686C>A	18.37:g.43495483G>T	ENSP00000282041:p.Pro1229His		41749481	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210180	0.39003	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.11063	2.81	5.51	5.51	0.81932	.	0.202176	0.31989	N	0.006748	T	0.19248	0.0462	L	0.34521	1.04	0.09310	N	0.999999	D;D	0.53885	0.963;0.963	P;P	0.53593	0.73;0.73	T	0.01889	-1.1253	10	0.62326	D	0.03	-4.0504	19.4214	0.94723	0.0:0.0:1.0:0.0	.	1229;1229	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	H	1229;104	ENSP00000282041:P1229H	ENSP00000282041:P1229H	P	-	2	0	EPG5	41749481	1.000000	0.71417	0.404000	0.26397	0.057000	0.15508	5.787000	0.69013	2.598000	0.87819	0.650000	0.86243	CCC		0.448	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		T	43495483	G	T	43495483	3	4	80	1	0	0	0	0	1	0	0	0	8270	1232	43	2	4153	2	KIAA1632	18	43495483	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	35100978	43495483	34581765	132	23307										
PHLPP1	23239	broad.mit.edu	37	chr18	60562287	60562287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	acctttccaataatcatttaGgggacttcccactggcagtc	7	12	1	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr18:60562287G>C	ENST00000262719.5	+	5	2344	c.2110G>C	c.(2110-2112)Ggg>Cgg	p.G704R	PHLPP1_ENST00000400316.4_Missense_Mutation_p.G192R			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	704					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.G191R(1)		endometrium(2)|kidney(2)|lung(13)	17						TAATCATTTAGGGGACTTCCC	0.448																																																1	Substitution - Missense(1)	large_intestine(1)	18											58	56	56					18																	60562287		1876	4110	5986	58713267	SO:0001583	missense	23239			AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.2110G>C	18.37:g.60562287G>C	ENSP00000262719:p.Gly704Arg		58713267	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	37	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	G	20.2	3.943508	0.73672	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.24151	1.87;1.87	5.81	5.81	0.92471	.	.	.	.	.	T	0.42245	0.1194	L	0.37697	1.125	0.51012	D	0.9999	D	0.64830	0.994	D	0.66497	0.944	T	0.03025	-1.1081	9	0.34782	T	0.22	-19.5691	20.0831	0.97789	0.0:0.0:1.0:0.0	.	704	O60346	PHLP1_HUMAN	R	192;704	ENSP00000383170:G192R;ENSP00000262719:G704R	ENSP00000262719:G704R	G	+	1	0	PHLPP1	58713267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.064000	0.64338	2.765000	0.95021	0.655000	0.94253	GGG		0.448	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		C	60562287	G	C	60562287	3	2	80	1	0	0	0	0	1	0	0	0	11885	1000	35	5	2128	5	PHLPP1	18	60562287	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	17066804	60562287	17514961	133	23308										
CDH19	28513	broad.mit.edu	37	chr18	64235761	64235761	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aaactcagactcaggttccaCagcccttccagtagcgatgt	8	13	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr18:64235761C>A	ENST00000540086.1	-	3	628	c.382G>T	c.(382-384)Gtg>Ttg	p.V128L	CDH19_ENST00000262150.2_Missense_Mutation_p.V128L	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	233	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V128L(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TCAGGTTCCACAGCCCTTCCA	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	18											141	136	137					18																	64235761		2203	4299	6502	62386741	SO:0001583	missense	28513			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.382G>T	18.37:g.64235761C>A	ENSP00000439593:p.Val128Leu		62386741	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132796	0.37630	.	.	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.45276	0.9;0.9	5.87	5.0	0.66597	Cadherin (4);Cadherin-like (1);	0.135540	0.49916	D	0.000134	T	0.15349	0.0370	N	0.05592	-0.015	0.37848	D	0.929295	B;P	0.36874	0.379;0.572	B;B	0.28305	0.041;0.088	T	0.24657	-1.0154	10	0.02654	T	1	.	8.0061	0.30325	0.0:0.7249:0.1318:0.1433	.	128;128	F5H1K0;Q9H159	.;CAD19_HUMAN	L	128;128;73	ENSP00000262150:V128L;ENSP00000439593:V128L	ENSP00000262150:V128L	V	-	1	0	CDH19	62386741	0.740000	0.28207	1.000000	0.80357	0.998000	0.95712	1.108000	0.31123	1.497000	0.48584	0.591000	0.81541	GTG		0.433	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		A	64235761	C	A	64235761	3	1	80	1	0	0	0	0	1	0	0	0	3110	478	17	2	1976	2	CDH19	18	64235761	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	3673474	64235761	13841487	134	23309										
MUC16	94025	broad.mit.edu	37	chr19	9086657	9086657	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ctgtgtgttcagccttgggcTgcttcccttactagaatctg	10	11	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:9086657T>G	ENST00000397910.4	-	1	5361	c.5158A>C	c.(5158-5160)Agc>Cgc	p.S1720R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1720	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S1720R(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCCTTGGGCTGCTTCCCTTA	0.493																																																2	Substitution - Missense(2)	large_intestine(2)	19											156	146	149					19																	9086657		1977	4179	6156	8947657	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5158A>C	19.37:g.9086657T>G	ENSP00000381008:p.Ser1720Arg		8947657	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.819	-0.038222	0.07497	.	.	ENSG00000181143	ENST00000397910	T	0.02656	4.21	1.33	1.33	0.21861	.	.	.	.	.	T	0.01695	0.0054	N	0.08118	0	.	.	.	B	0.13594	0.008	B	0.06405	0.002	T	0.32877	-0.9890	8	0.87932	D	0	.	4.7934	0.13259	0.0:0.0:0.0:1.0	.	1720	B5ME49	.	R	1720	ENSP00000381008:S1720R	ENSP00000381008:S1720R	S	-	1	0	MUC16	8947657	0.017000	0.18338	0.003000	0.11579	0.119000	0.20118	0.669000	0.25142	0.838000	0.34948	0.260000	0.18958	AGC		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9086657	T	G	9086657	3	3	80	1	0	0	0	0	1	0	0	0	10003	1580	55	4	38701	4	MUC16	19	9086657	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10		9086657	50042326	135	23310										
C19orf2	8725	broad.mit.edu	37	chr19	30502021	30502021	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gtccgaataaatactggaaaGaataccactttaaaattcag	6	7	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:30502021G>A	ENST00000542441.2	+	9	1353	c.1056G>A	c.(1054-1056)aaG>aaA	p.K352K	URI1_ENST00000392271.1_Silent_p.K276K|URI1_ENST00000312051.6_Silent_p.K312K|URI1_ENST00000360605.4_Silent_p.K334K			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	352					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.K352K(1)									ATACTGGAAAGAATACCACTT	0.363																																																1	Substitution - coding silent(1)	large_intestine(1)	19											55	60	59					19																	30502021		2203	4300	6503	35193861	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1056G>A	19.37:g.30502021G>A			35193861	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.363	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30502021	G	A	30502021	2	1	80	1	0	0	0	0	0	0	0	1	1917	933	33	3		3	C19orf2	19	30502021	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	21415364	30502021	28626962	136	23311										
UPK1A	11045	broad.mit.edu	37	chr19	36164423	36164423	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cagggccaggagctgacccgCctctgggaccgcgtcatgat	14	14	2	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:36164423C>T	ENST00000222275.2	+	4	444	c.444C>T	c.(442-444)cgC>cgT	p.R148R	UPK1A-AS1_ENST00000443196.1_RNA|UPK1A_ENST00000379013.2_Silent_p.R148R	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	148					epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)	p.R148R(1)		breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGCTGACCCGCCTCTGGGACC	0.647																																																1	Substitution - coding silent(1)	large_intestine(1)	19											26	27	27					19																	36164423		2195	4293	6488	40856263	SO:0001819	synonymous_variant	11045			AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"Tetraspanins"	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.444C>T	19.37:g.36164423C>T			40856263	Q3KNU5|Q3KNU6	Silent	SNP	ENST00000222275.2	37	CCDS12470.1																																																																																				0.647	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3			T	36164423	C	T	36164423	2	4	80	1	0	0	0	0	0	0	0	1	17047	726	26	3		3	UPK1A	19	36164423	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	5662402	36164423	22964560	137	23312										
ACTN4	81	broad.mit.edu	37	chr19	39212269	39212269	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aagcacgaggccttcgagagCgacctggctgcgcaccagga	14	13	0	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:39212269C>T	ENST00000252699.2	+	12	1459	c.1383C>T	c.(1381-1383)agC>agT	p.S461S	ACTN4_ENST00000390009.3_Silent_p.S242S|ACTN4_ENST00000424234.2_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	461					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S461S(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCTTCGAGAGCGACCTGGCTG	0.612																																					Colon(168;199 1940 10254 46213 46384)											1	Substitution - coding silent(1)	large_intestine(1)	19											115	88	98					19																	39212269		2203	4300	6503	43904109	SO:0001819	synonymous_variant	81			D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1383C>T	19.37:g.39212269C>T			43904109	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																				0.612	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			T	39212269	C	T	39212269	2	4	80	1	0	0	0	0	0	0	0	1	207	767	27	1		1	ACTN4	19	39212269	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	3047846	39212269	19916714	138	23313										
ZNF285	26974	broad.mit.edu	37	chr19	44891946	44891946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tctggggctcggtcattatgTtggctttcctccacgattct	10	11	3	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:44891946T>C	ENST00000330997.4	-	4	525	c.461A>G	c.(460-462)aAc>aGc	p.N154S	ZNF285_ENST00000544719.2_Missense_Mutation_p.N154S|ZNF285_ENST00000591679.1_Missense_Mutation_p.N161S|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N154S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GGTCATTATGTTGGCTTTCCT	0.428																																																1	Substitution - Missense(1)	large_intestine(1)	19											88	88	88					19																	44891946		2201	4297	6498	49583786	SO:0001583	missense	26974			AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.461A>G	19.37:g.44891946T>C	ENSP00000333595:p.Asn154Ser		49583786	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	1.358	-0.589579	0.03799	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.05382	3.45	2.52	-5.04	0.02964	.	.	.	.	.	T	0.02610	0.0079	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.43228	-0.9404	9	0.15066	T	0.55	.	2.4255	0.04458	0.1317:0.4068:0.2656:0.1958	.	178;154	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	S	177;154	ENSP00000333595:N154S	ENSP00000333595:N154S	N	-	2	0	ZNF285	49583786	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	-4.122000	0.00290	-2.502000	0.00509	0.248000	0.18094	AAC		0.428	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44891946	T	C	44891946	3	2	80	1	0	0	0	0	1	0	0	0	17861	1725	60	4	1315	4	ZNF285	19	44891946	Missense_Mutation	SNP	T	TCGA-AG-A036-01A-12W-A096-10	5679677	44891946	14237037	139	23314										
ZNF583	147949	broad.mit.edu	37	chr19	56935268	56935268	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttatgaatgtaaagtatgtaGgaaagccttcagccaaattg	9	5	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr19:56935268G>A	ENST00000333201.9	+	5	1451	c.1241G>A	c.(1240-1242)aGg>aAg	p.R414K	ZNF583_ENST00000291598.7_Missense_Mutation_p.R414K|ZNF583_ENST00000585612.1_Intron	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R414K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		AAAGTATGTAGGAAAGCCTTC	0.408																																																1	Substitution - Missense(1)	large_intestine(1)	19											62	65	64					19																	56935268		2203	4300	6503	61627080	SO:0001583	missense	147949			AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1241G>A	19.37:g.56935268G>A	ENSP00000388502:p.Arg414Lys		61627080	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.803319	0.90623	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.13307	2.6;2.6	4.57	4.57	0.56435	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.160951	0.30392	N	0.009732	T	0.09862	0.0242	N	0.16098	0.37	0.36646	D	0.877133	B	0.25048	0.117	B	0.28916	0.096	T	0.27971	-1.0058	9	.	.	.	.	16.6374	0.85062	0.0:0.0:1.0:0.0	.	414	Q96ND8	ZN583_HUMAN	K	414	ENSP00000291598:R414K;ENSP00000388502:R414K	.	R	+	2	0	ZNF583	61627080	0.999000	0.42202	0.006000	0.13384	0.998000	0.95712	6.239000	0.72356	2.542000	0.85734	0.563000	0.77884	AGG		0.408	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		A	56935268	G	A	56935268	3	1	80	1	0	0	0	0	1	0	0	0	18054	1000	35	3	1255	3	ZNF583	19	56935268	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	12043322	56935268	2193715	140	23315										
PIGU	128869	broad.mit.edu	37	chr20	33173278	33173278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ggggatggtgtagaagaagaCgttgatctgaaacacacata	13	5	1	5	rs577900938		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr20:33173278C>T	ENST00000374820.2	-	8	849	c.829G>A	c.(829-831)Gtc>Atc	p.V277I	PIGU_ENST00000452740.2_Missense_Mutation_p.V297I|PIGU_ENST00000480175.1_Intron			Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class U	297	May be involved in recognition of long- chain fatty acids in GPI.				attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|regulation of JAK-STAT cascade (GO:0046425)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V297I(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	9						TAGAAGAAGACGTTGATCTGA	0.468													C|||	1	0.000199681	0	0.0014	5008	,	,		20586	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	20											161	150	154					20																	33173278		2203	4300	6503	32636939	SO:0001583	missense	128869			AL118520	CCDS13239.1	20q11.22	2013-02-26	2006-11-07	2006-11-07	ENSG00000101464	ENSG00000101464		"Phosphatidylinositol glycan anchor biosynthesis"	15791	protein-coding gene	gene with protein product	"GPI transamidase subunit"	608528	"CDC91 (cell division cycle 91, S. cerevisiae, homolog)-like 1", "CDC91 cell division cycle 91-like 1 (S. cerevisiae)"	CDC91L1		12802054, 15034568	Standard	NM_080476		Approved	bA346K17.2, GAB1	uc002xas.3	Q9H490	OTTHUMG00000032304	ENST00000374820.2:c.829G>A	20.37:g.33173278C>T	ENSP00000363953:p.Val277Ile		32636939	Q7Z489|Q8N2F2	Missense_Mutation	SNP	ENST00000374820.2	37		.	.	.	.	.	.	.	.	.	.	C	18.99	3.740470	0.69304	.	.	ENSG00000101464	ENST00000217446;ENST00000374820;ENST00000452740;ENST00000438215	.	.	.	5.37	1.3	0.21679	.	0.059218	0.64402	N	0.000003	T	0.48095	0.1481	N	0.21545	0.675	0.53688	D	0.999972	B;B;D	0.71674	0.009;0.043;0.998	B;B;P	0.62014	0.011;0.008;0.897	T	0.30679	-0.9970	9	0.13108	T	0.6	.	9.8215	0.40885	0.0:0.7224:0.0:0.2776	.	297;277;297	E7EVL4;Q9H490-2;Q9H490	.;.;PIGU_HUMAN	I	297;277;297;43	.	ENSP00000217446:V297I	V	-	1	0	PIGU	32636939	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.562000	0.60816	0.021000	0.15133	-0.136000	0.14681	GTC		0.468	PIGU-201	KNOWN	basic	protein_coding	protein_coding		NM_080476		T	33173278	C	T	33173278	3	4	80	1	0	0	0	0	1	0	0	0	11931	536	19	1	434	1	PIGU	20	33173278	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10		33173278	29852242	141	23316										
SRMS	6725	broad.mit.edu	37	chr20	62173557	62173557	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tccccttgcgcatgagttccGtgacgatgtacacaggctcc	10	14	0	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr20:62173557G>A	ENST00000217188.1	-	5	945	c.905C>T	c.(904-906)aCg>aTg	p.T302M		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	302	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.T302M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CATGAGTTCCGTGACGATGTA	0.682																																																1	Substitution - Missense(1)	large_intestine(1)	20											97	76	83					20																	62173557		2199	4300	6499	61644001	SO:0001583	missense	6725				CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.905C>T	20.37:g.62173557G>A	ENSP00000217188:p.Thr302Met		61644001		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332161	0.60853	.	.	ENSG00000125508	ENST00000217188	T	0.09723	2.95	4.62	3.66	0.41972	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000019	T	0.17789	0.0427	N	0.16708	0.43	0.49687	D	0.999814	D	0.89917	1.0	D	0.97110	1.0	T	0.03524	-1.1028	10	0.87932	D	0	.	12.6783	0.56908	0.0829:0.0:0.9171:0.0	.	302	Q9H3Y6	SRMS_HUMAN	M	302	ENSP00000217188:T302M	ENSP00000217188:T302M	T	-	2	0	SRMS	61644001	1.000000	0.71417	0.945000	0.38365	0.232000	0.25224	7.570000	0.82390	0.928000	0.37168	0.561000	0.74099	ACG		0.682	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		A	62173557	G	A	62173557	3	1	80	1	0	0	0	0	1	0	0	0	15191	1145	40	1	577	1	SRMS	20	62173557	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	29000279	62173557	851963	142	23317										
USP25	29761	broad.mit.edu	37	chr21	17138320	17138320	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttcttgatatttgaaggataGtaatggaaacttggaattag	10	2	1	2			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr21:17138320G>T	ENST00000285679.6	+	3	497	c.128G>T	c.(127-129)aGt>aTt	p.S43I	USP25_ENST00000400183.2_Missense_Mutation_p.S43I|USP25_ENST00000351097.5_Missense_Mutation_p.S43I|USP25_ENST00000285681.2_Missense_Mutation_p.S43I	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	43	UBA-like.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.S43I(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		TTGAAGGATAGTAATGGAAAC	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	21											86	81	83					21																	17138320		2203	4300	6503	16060191	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.128G>T	21.37:g.17138320G>T	ENSP00000285679:p.Ser43Ile		16060191	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.706912	0.89018	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.44083	1.32;1.36;0.93;1.36	5.42	5.42	0.78866	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.61451	0.2348	L	0.50333	1.59	0.80722	D	1	D;D;D;D	0.89917	0.998;0.995;1.0;0.998	D;D;D;D	0.78314	0.979;0.986;0.986;0.991	T	0.63305	-0.6667	10	0.87932	D	0	.	19.2158	0.93778	0.0:0.0:1.0:0.0	.	43;43;43;43	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	I	43	ENSP00000285681:S43I;ENSP00000285679:S43I;ENSP00000299574:S43I;ENSP00000383044:S43I	ENSP00000285679:S43I	S	+	2	0	USP25	16060191	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.552000	0.86080	0.561000	0.74099	AGT		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17138320	G	T	17138320	3	4	80	1	0	0	0	0	1	0	0	0	17096	1029	36	2	138	2	USP25	21	17138320	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10		17138320	30991575	143	23318										
CHAF1B	8208	broad.mit.edu	37	chr21	37766863	37766863	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	aggggccacttagaagatgtGtatgatatttgctgggcaac	13	6	0	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr21:37766863G>A	ENST00000314103.5	+	5	547	c.396G>A	c.(394-396)gtG>gtA	p.V132V	CHAF1B_ENST00000480486.1_3'UTR	NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	132					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)	p.V132V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						TAGAAGATGTGTATGATATTT	0.423																																																1	Substitution - coding silent(1)	large_intestine(1)	21											185	180	182					21																	37766863		2203	4300	6503	36688733	SO:0001819	synonymous_variant	8208			U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259		"WD repeat domain containing"	1911	protein-coding gene	gene with protein product	"M-phase phosphoprotein 7", "Chromatin assembly factor I, p60 subunit", "human chromatin assembly factor-I p60 subunit"	601245				7600578, 8792829	Standard	NM_005441		Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.396G>A	21.37:g.37766863G>A			36688733	Q99548	Silent	SNP	ENST00000314103.5	37	CCDS13644.1																																																																																				0.423	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441		A	37766863	G	A	37766863	2	1	80	1	0	0	0	0	0	0	0	1	3318	1364	48	3		3	CHAF1B	21	37766863	Silent	SNP	G	TCGA-AG-A036-01A-12W-A096-10	20628543	37766863	10363032	144	23319										
KCNJ6	3763	broad.mit.edu	37	chr21	39086698	39086698	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	ttgatatccgtctggttcaaCgggatgaactccccctccga	9	13	2	2	rs373930118		TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr21:39086698C>T	ENST00000609713.1	-	3	1351	c.762G>A	c.(760-762)ccG>ccA	p.P254P	KCNJ6-IT1_ENST00000435001.1_RNA|KCNJ6_ENST00000288309.6_Silent_p.P254P	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	254					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)	p.P254P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	TCTGGTTCAACGGGATGAACT	0.502																																					Pancreas(48;379 1118 2936 19024 28214)											1	Substitution - coding silent(1)	large_intestine(1)	21						C		1,3817		0,1,1908	110	111	111		762	-4.6	0.4	21		111	0,8286		0,0,4143	no	coding-synonymous	KCNJ6	NM_002240.2		0,1,6051	TT,TC,CC		0.0,0.0262,0.0083		254/424	39086698	1,12103	1909	4143	6052	38008568	SO:0001819	synonymous_variant	3763			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.762G>A	21.37:g.39086698C>T			38008568	Q3MJ74|Q53WW6	Silent	SNP	ENST00000609713.1	37	CCDS42927.1																																																																																				0.502	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		T	39086698	C	T	39086698	2	4	80	1	0	0	0	0	0	0	0	1	8076	523	19	1		1	KCNJ6	21	39086698	Silent	SNP	C	TCGA-AG-A036-01A-12W-A096-10	1319835	39086698	9043197	145	23320										
PRDM15	63977	broad.mit.edu	37	chr21	43230561	43230561	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	atggaggccctggtggacacCttggtcccgcacagctggca	14	13	0	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr21:43230561C>G	ENST00000269844.3	-	28	3809	c.3699G>C	c.(3697-3699)aaG>aaC	p.K1233N	PRDM15_ENST00000447207.2_Missense_Mutation_p.K867N|PRDM15_ENST00000538201.1_Missense_Mutation_p.K887N|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000422911.1_Missense_Mutation_p.K924N|PRDM15_ENST00000398548.1_Missense_Mutation_p.K904N	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.K1233N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGGTGGACACCTTGGTCCCGC	0.662																																																1	Substitution - Missense(1)	large_intestine(1)	21											81	56	65					21																	43230561		2203	4299	6502	42103630	SO:0001583	missense	63977			AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3699G>C	21.37:g.43230561C>G	ENSP00000269844:p.Lys1233Asn		42103630	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	c	15.26	2.780975	0.49891	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.09538	4.72;4.72;4.72;4.72;2.97	4.11	0.455	0.16649	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	.	.	.	.	T	0.14442	0.0349	N	0.24115	0.695	0.42674	D	0.993523	B;D;D	0.89917	0.014;1.0;1.0	B;D;D	0.91635	0.012;0.998;0.999	T	0.18555	-1.0333	9	0.40728	T	0.16	-26.2487	5.3073	0.15811	0.1554:0.55:0.0:0.2945	.	1233;924;904	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	N	924;904;887;867;1233	ENSP00000408592:K924N;ENSP00000381556:K904N;ENSP00000444044:K887N;ENSP00000390245:K867N;ENSP00000269844:K1233N	ENSP00000269844:K1233N	K	-	3	2	PRDM15	42103630	0.989000	0.36119	1.000000	0.80357	0.789000	0.44602	0.307000	0.19296	0.192000	0.20272	-0.851000	0.03033	AAG		0.662	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		G	43230561	C	G	43230561	3	3	80	1	0	0	0	0	1	0	0	0	12490	680	24	5	840	5	PRDM15	21	43230561	Missense_Mutation	SNP	C	TCGA-AG-A036-01A-12W-A096-10	4143863	43230561	4899334	146	23321										
GCAT	23464	broad.mit.edu	37	chr22	38212307	38212307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	cccggctggcctctcgcatgGcggatgacatgctgaagaga	14	12	1	3			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chr22:38212307G>A	ENST00000248924.6	+	8	1143	c.1087G>A	c.(1087-1089)Gcg>Acg	p.A363T	GCAT_ENST00000323205.6_Missense_Mutation_p.A389T	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	363					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)	p.A363T(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	CTCTCGCATGGCGGATGACAT	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	22											53	47	49					22																	38212307		2203	4300	6503	36542253	SO:0001583	missense	23464			AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"2-amino-3-ketobutyrate coenzyme A ligase"	607422	"glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.1087G>A	22.37:g.38212307G>A	ENSP00000248924:p.Ala363Thr		36542253	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	.	.	.	.	.	.	.	.	.	.	G	35	5.413965	0.96072	.	.	ENSG00000100116	ENST00000323205;ENST00000248924	D;D	0.91124	-2.79;-2.79	4.92	4.92	0.64577	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.996;0.997	D	0.96127	0.9089	10	0.87932	D	0	-13.888	18.2955	0.90145	0.0:0.0:1.0:0.0	.	389;363	E2QC23;O75600	.;KBL_HUMAN	T	389;363	ENSP00000371110:A389T;ENSP00000248924:A363T	ENSP00000248924:A363T	A	+	1	0	GCAT	36542253	1.000000	0.71417	0.985000	0.45067	0.970000	0.65996	8.955000	0.93058	2.576000	0.86940	0.561000	0.74099	GCG		0.582	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		A	38212307	G	A	38212307	3	1	80	1	0	0	0	0	1	0	0	0	6304	1203	42	3	1195	3	GCAT	22	38212307	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10		38212307	13092259	147	23322										
GLUD2	2747	broad.mit.edu	37	chrX	120182603	120182603	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	gaagacttcaaattgcaacaTgggtccattctgggcttccc	9	11	2	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chrX:120182603T>C	ENST00000328078.1	+	1	1142	c.1065T>C	c.(1063-1065)caT>caC	p.H355H		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	355					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)	p.H355H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AATTGCAACATGGGTCCATTC	0.473																																																1	Substitution - coding silent(1)	large_intestine(1)	X											209	190	196					X																	120182603		2203	4300	6503	120010284	SO:0001819	synonymous_variant	2747			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1065T>C	X.37:g.120182603T>C			120010284	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																				0.473	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		C	120182603	T	C	120182603	2	2	80	1	0	0	0	0	0	0	0	1	6497	1461	51	4		4	GLUD2	23	120182603	Silent	SNP	T	TCGA-AG-A036-01A-12W-A096-10		120182603	35087957	148	23323										
ZNF280C	55609	broad.mit.edu	37	chrX	129364660	129364660	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	catggacgttctgatttaacAattactcccaaaaatttagt	5	8	1	1			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chrX:129364660A>T	ENST00000370978.4	-	9	966	c.813T>A	c.(811-813)atT>atA	p.I271I		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I271I(1)		endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						CTGATTTAACAATTACTCCCA	0.348																																																1	Substitution - coding silent(1)	large_intestine(1)	X											120	112	115					X																	129364660		2202	4300	6502	129192341	SO:0001819	synonymous_variant	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.813T>A	X.37:g.129364660A>T			129192341	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																				0.348	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129364660	A	T	129364660	2	4	80	1	0	0	0	0	0	0	0	1	17855	126	5	5		5	ZNF280C	23	129364660	Silent	SNP	A	TCGA-AG-A036-01A-12W-A096-10	9182057	129364660	25905900	149	23324										
CLIC2	1193	broad.mit.edu	37	chrX	154528113	154528113	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0733333333333333	11	1	0.896453089244851	1.97305464618484	0.616241725109786	1	1	0	tgtaccttggaggagccaggGtttgttctaaaaactcctca	10	9	2	0			TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AG-A036-01A-12W-A096-10	TCGA-AG-A036-11A-11W-A096-10	g.chrX:154528113G>C	ENST00000369449.2	-	3	496	c.278C>G	c.(277-279)aCc>aGc	p.T93S	CLIC2_ENST00000465553.1_5'UTR	NM_001289.4	NP_001280.3	O15247	CLIC2_HUMAN	chloride intracellular channel 2	93	N-terminal.|Required for insertion into the membrane. {ECO:0000250}.				chloride transmembrane transport (GO:1902476)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|oxidation-reduction process (GO:0055114)|positive regulation of binding (GO:0051099)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|signal transduction (GO:0007165)|transport (GO:0006810)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|glutathione peroxidase activity (GO:0004602)|voltage-gated chloride channel activity (GO:0005247)	p.T93S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	18	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AGGAGCCAGGGTTTGTTCTAA	0.368																																					Melanoma(108;581 1592 2289 21669 28822)											1	Substitution - Missense(1)	large_intestine(1)	X											92	90	91					X																	154528113		2203	4300	6503	154181307	SO:0001583	missense	1193			AJ000217	CCDS14767.1	Xq28	2012-09-26			ENSG00000155962	ENSG00000155962		"Ion channels / Chloride channels : Intracellular"	2063	protein-coding gene	gene with protein product		300138				9339381	Standard	NM_001289		Approved	XAP121	uc004fnf.3	O15247	OTTHUMG00000022660	ENST00000369449.2:c.278C>G	X.37:g.154528113G>C	ENSP00000358460:p.Thr93Ser		154181307	A8K9S0|O15174|Q5JT80|Q8TCE3	Missense_Mutation	SNP	ENST00000369449.2	37	CCDS14767.1	.	.	.	.	.	.	.	.	.	.	.	11.43	1.635109	0.29068	.	.	ENSG00000155962	ENST00000369449	T	0.25579	1.79	5.06	4.18	0.49190	Glutathione S-transferase/chloride channel, C-terminal (1);Thioredoxin-like fold (2);	0.155750	0.56097	D	0.000031	T	0.27663	0.0680	M	0.71871	2.18	0.32532	N	0.534766	B;B	0.18166	0.026;0.011	B;B	0.28305	0.088;0.045	T	0.25363	-1.0134	10	0.13108	T	0.6	-10.2638	11.0982	0.48157	0.0998:0.0:0.9002:0.0	.	111;93	Q86YM0;O15247	.;CLIC2_HUMAN	S	93	ENSP00000358460:T93S	ENSP00000358460:T93S	T	-	2	0	CLIC2	154181307	0.931000	0.31567	0.998000	0.56505	0.908000	0.53690	1.265000	0.33027	2.262000	0.75019	0.415000	0.27848	ACC		0.368	CLIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058793.1	NM_001289		C	154528113	G	C	154528113	3	2	80	1	0	0	0	0	1	0	0	0	3532	1261	44	5	481	5	CLIC2	23	154528113	Missense_Mutation	SNP	G	TCGA-AG-A036-01A-12W-A096-10	25163453	154528113	742447	150	23325										
PANK4	55229	hgsc.bcm.edu	37	chr1	2451298	2451298	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atgaggttcccgctcagcccGagagtctggtgggcgccgcc	15	14	2	2	rs34724650	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:2451298G>A	ENST00000378466.3	-	6	807	c.795C>T	c.(793-795)ctC>ctT	p.L265L	PANK4_ENST00000491212.1_5'Flank|PANK4_ENST00000435556.3_Silent_p.L226L	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	265					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CGCTCAGCCCGAGAGTCTGGT	0.672													G|||	6	0.00119808	0	0.0043	5008	,	,		12255	0		0.003	False		,,,				2504	0															0			1						G		3,4321		0,3,2159	16	19	18		795	3.1	1	1	dbSNP_126	18	21,8501		0,21,4240	no	coding-synonymous	PANK4	NM_018216.1		0,24,6399	AA,AG,GG		0.2464,0.0694,0.1868		265/774	2451298	24,12822	2162	4261	6423	2441158	SO:0001819	synonymous_variant	55229			AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.795C>T	1.37:g.2451298G>A			2441158	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Silent	SNP	ENST00000378466.3	37	CCDS42.1																																																																																				0.672	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			A	2451298	G	A	2451298	2	1	81	1	0	0	0	0	0	0	0	1	11450	1045	37	1		1	PANK4	1	2451298	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		2451298	246799323	1	23326										
UBR4	23352	hgsc.bcm.edu	37	chr1	19499567	19499567	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgcaagatggtggtacagtcGatactacagaaggatgagat	13	5	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:19499567G>A	ENST00000375254.3	-	25	3339	c.3312C>T	c.(3310-3312)atC>atT	p.I1104I	UBR4_ENST00000375267.2_Silent_p.I1104I|UBR4_ENST00000375217.2_Silent_p.I1104I|UBR4_ENST00000375226.2_Silent_p.I1104I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1104					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGGTACAGTCGATACTACAGA	0.423																																																0			1											87	83	84					1																	19499567		2203	4300	6503	19372154	SO:0001819	synonymous_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3312C>T	1.37:g.19499567G>A			19372154	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.423	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19499567	G	A	19499567	2	1	81	1	0	0	0	0	0	0	0	1	16944	1048	37	1		1	UBR4	1	19499567	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	17048269	19499567	229751054	2	23327										
C1orf151	440574	hgsc.bcm.edu	37	chr1	19949996	19949996	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tggccattagccttcggttcTggcatgggattaggaatggc	14	8	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:19949996T>A	ENST00000322753.6	+	3	197	c.141T>A	c.(139-141)tcT>tcA	p.S47S	MINOS1_ENST00000486890.1_3'UTR|MINOS1-NBL1_ENST00000602662.1_Intron	NM_001032363.3|NM_001204082.1|NM_001204083.1	NP_001027535.1|NP_001191011.1|NP_001191012.1	Q5TGZ0	MIC10_HUMAN	mitochondrial inner membrane organizing system 1	47						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)											CCTTCGGTTCTGGCATGGGAT	0.383																																																0			1											171	169	170					1																	19949996		2203	4300	6503	19822583	SO:0001819	synonymous_variant	440574			AK094318	CCDS30620.1, CCDS72719.1	1p36.13	2013-10-11	2011-10-04	2011-10-04	ENSG00000173436	ENSG00000173436			32068	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 151"	C1orf151		21944719	Standard	NM_001032363		Approved	RP5-1056L3.2, FLJ36999, MIO10	uc021ohu.1	Q5TGZ0	OTTHUMG00000002712	ENST00000322753.6:c.141T>A	1.37:g.19949996T>A			19822583	Q96G68	Silent	SNP	ENST00000322753.6	37	CCDS30620.1																																																																																				0.383	MINOS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007697.2	NM_001032363		A	19949996	T	A	19949996	2	1	81	1	0	0	0	0	0	0	0	1	2011	1567	55	5		5	C1orf151	1	19949996	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	450429	19949996	229300625	3	23328										
AMY2B	280	hgsc.bcm.edu	37	chr1	104115837	104115837	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gattttaatgatggtaaatgTaaaactggaagtggagatat	11	1	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:104115837T>G	ENST00000361355.4	+	5	1084	c.468T>G	c.(466-468)tgT>tgG	p.C156W	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	156					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		ATGGTAAATGTAAAACTGGAA	0.398																																																0			1											206	221	216					1																	104115837		2203	4294	6497	103917360	SO:0001583	missense	280			M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"amylase, alpha 2B; pancreatic"	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.468T>G	1.37:g.104115837T>G	ENSP00000354610:p.Cys156Trp		103917360	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.953003	0.53293	.	.	ENSG00000240038	ENST00000361355	D	0.97959	-4.63	4.58	2.27	0.28462	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98947	0.9642	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98038	1.0380	10	0.87932	D	0	.	7.079	0.25221	0.0:0.2546:0.0:0.7454	.	156	P19961	AMY2B_HUMAN	W	156	ENSP00000354610:C156W	ENSP00000354610:C156W	C	+	3	2	AMY2B	103917360	0.988000	0.35896	0.834000	0.33040	0.801000	0.45260	0.947000	0.29082	0.624000	0.30286	0.524000	0.50904	TGT		0.398	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		G	104115837	T	G	104115837	3	3	81	1	0	0	0	0	1	0	0	0	595	1644	57	4	478	4	AMY2B	1	104115837	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	84165841	104115837	145134784	4	23329										
AMY2B	280	hgsc.bcm.edu	37	chr1	104118134	104118134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acgagtaatgtcaagctaccGttggccaagacagtttcaaa	9	9	2	1	rs150608402	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:104118134G>A	ENST00000361355.4	+	9	1689	c.1073G>A	c.(1072-1074)cGt>cAt	p.R358H	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	358					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TCAAGCTACCGTTGGCCAAGA	0.338																																																0			1						G	HIS/ARG	0,4406		0,0,2203	218	222	221		1073	1.2	0.5	1	dbSNP_134	221	3,8597	3.0+/-9.4	0,3,4297	no	missense	AMY2B	NM_020978.3	29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	358/512	104118134	3,13003	2203	4300	6503	103919657	SO:0001583	missense	280			M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"amylase, alpha 2B; pancreatic"	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.1073G>A	1.37:g.104118134G>A	ENSP00000354610:p.Arg358His		103919657	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.208692	0.39003	0.0	3.49E-4	ENSG00000240038	ENST00000361355	.	.	.	5.14	1.21	0.21127	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.055506	0.64402	D	0.000002	T	0.12902	0.0313	N	0.25647	0.755	0.32141	N	0.585544	B	0.15473	0.013	B	0.04013	0.001	T	0.18116	-1.0347	9	0.23302	T	0.38	.	9.3535	0.38153	0.2963:0.0:0.7037:0.0	.	358	P19961	AMY2B_HUMAN	H	358	.	ENSP00000354610:R358H	R	+	2	0	AMY2B	103919657	0.049000	0.20398	0.537000	0.28052	0.896000	0.52359	2.165000	0.42396	-0.050000	0.13356	0.563000	0.77884	CGT		0.338	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		A	104118134	G	A	104118134	3	1	81	1	0	0	0	0	1	0	0	0	595	1145	40	1	1099	1	AMY2B	1	104118134	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	2297	104118134	145132487	5	23330										
MOV10	4343	hgsc.bcm.edu	37	chr1	113239068	113239068	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acacctcccaggttggtctcGgcccagtttcccattgatca	8	15	2	1	rs61742214	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:113239068G>T	ENST00000413052.2	+	13	2283	c.1893G>T	c.(1891-1893)tcG>tcT	p.S631S	MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369645.1_Silent_p.S631S|MOV10_ENST00000369644.1_Silent_p.S575S|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000357443.2_Silent_p.S631S	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	631					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GGTTGGTCTCGGCCCAGTTTC	0.562																																																0			1											116	107	110					1																	113239068		2203	4300	6503	113040591	SO:0001819	synonymous_variant	4343			AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1893G>T	1.37:g.113239068G>T			113040591	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																				0.562	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		T	113239068	G	T	113239068	2	4	81	1	0	0	0	0	0	0	0	1	9748	1103	39	2		2	MOV10	1	113239068	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	9120934	113239068	136011553	6	23331										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117142715	117142715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgatgcttaggcggacgttgTtgctggactcagccttctcg	13	10	2	1	rs142843832		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:117142715T>C	ENST00000369486.3	-	7	2642	c.1877A>G	c.(1876-1878)aAc>aGc	p.N626S	IGSF3_ENST00000318837.6_Missense_Mutation_p.N646S|IGSF3_ENST00000369483.1_Missense_Mutation_p.N646S	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	626	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		GCGGACGTTGTTGCTGGACTC	0.602													T|||	1	0.000199681	8e-04	0	5008	,	,		16224	0		0	False		,,,				2504	0															0			1						T	SER/ASN,SER/ASN	6,4400	11.4+/-27.6	0,6,2197	83	61	69		1877,1937	4.8	1	1	dbSNP_134	69	0,8600		0,0,4300	no	missense,missense	IGSF3	NM_001007237.1,NM_001542.2	46,46	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	possibly-damaging,possibly-damaging	626/1195,646/1215	117142715	6,13000	2203	4300	6503	116944238	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1877A>G	1.37:g.117142715T>C	ENSP00000358498:p.Asn626Ser		116944238	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	11.96	1.795447	0.31777	0.001362	0.0	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.11712	2.75;2.75;2.75	4.8	4.8	0.61643	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.184033	0.47852	D	0.000212	T	0.05686	0.0149	N	0.03608	-0.345	0.38402	D	0.945686	D;D;D	0.71674	0.961;0.998;0.968	P;D;P	0.64595	0.652;0.927;0.764	T	0.51687	-0.8674	10	0.28530	T	0.3	-60.2109	12.3358	0.55067	0.0:0.0:0.0:1.0	.	646;626;646	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	S	626;646;646	ENSP00000358498:N626S;ENSP00000358495:N646S;ENSP00000321184:N646S	ENSP00000321184:N646S	N	-	2	0	IGSF3	116944238	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.299000	0.59073	2.001000	0.58596	0.374000	0.22700	AAC		0.602	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117142715	T	C	117142715	3	2	81	1	0	0	0	0	1	0	0	0	7622	1725	60	4	1727	4	IGSF3	1	117142715	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	3903647	117142715	132107906	7	23332										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118537087	118537087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gattaggagggacaattgtaTcttccttttttacttgccat	8	7	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:118537087T>C	ENST00000336338.5	-	35	5185	c.5120A>G	c.(5119-5121)gAt>gGt	p.D1707G		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1707			D -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GACAATTGTATCTTCCTTTTT	0.408																																																0			1											183	161	168					1																	118537087		2203	4300	6503	118338610	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5120A>G	1.37:g.118537087T>C	ENSP00000337804:p.Asp1707Gly		118338610	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.258963	0.23051	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.19806	2.12	5.64	4.52	0.55395	.	0.551968	0.22144	N	0.064012	T	0.10551	0.0258	M	0.66939	2.045	0.09310	N	1	P	0.46142	0.873	B	0.41412	0.356	T	0.16748	-1.0392	10	0.66056	D	0.02	.	5.8512	0.18694	0.0:0.0832:0.1675:0.7493	.	1707	Q6Q759	SPG17_HUMAN	G	1707;187	ENSP00000337804:D1707G	ENSP00000337804:D1707G	D	-	2	0	SPAG17	118338610	0.013000	0.17824	0.011000	0.14972	0.009000	0.06853	1.432000	0.34936	1.160000	0.42584	0.528000	0.53228	GAT		0.408	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		C	118537087	T	C	118537087	3	2	81	1	0	0	0	0	1	0	0	0	15018	1435	50	4	1607	4	SPAG17	1	118537087	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	1394372	118537087	130713534	8	23333										
FLG	2312	hgsc.bcm.edu	37	chr1	152279805	152279805	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccgtctcctgattgttcatcGttacgagtttgtctgcttgc	9	11	3	1	rs113878714	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:152279805G>A	ENST00000368799.1	-	3	7592	c.7557C>T	c.(7555-7557)aaC>aaT	p.N2519N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2519	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATTGTTCATCGTTACGAGTTT	0.592									Ichthyosis				g|||	12	0.00239617	0.0076	0.0029	5008	,	,		20136	0		0	False		,,,				2504	0															0			1						G		28,4378	34.3+/-65.2	0,28,2175	361	336	344		7557	-3.9	0	1	dbSNP_132	344	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		0,28,6475	AA,AG,GG		0.0,0.6355,0.2153		2519/4062	152279805	28,12978	2203	4300	6503	150546429	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7557C>T	1.37:g.152279805G>A			150546429	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152279805	G	A	152279805	2	1	81	1	0	0	0	0	0	0	0	1	5941	1136	40	1		1	FLG	1	152279805	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	33742718	152279805	96970816	9	23334										
LCE1E	353135	hgsc.bcm.edu	37	chr1	152759796	152759796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atgtcctgccagcagagccaGcagcagtgccagccccctcc	10	18	0	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:152759796G>A	ENST00000368770.3	+	2	74	c.21G>A	c.(19-21)caG>caA	p.Q7Q	LCE1E_ENST00000368771.1_Silent_p.Q7Q	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	7	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCAGAGCCAGCAGCAGTGCC	0.602																																																0			1											120	128	125					1																	152759796		2203	4300	6503	151026420	SO:0001819	synonymous_variant	353135			BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"Late cornified envelopes"	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.21G>A	1.37:g.152759796G>A			151026420	D3DV30	Silent	SNP	ENST00000368770.3	37	CCDS1024.1																																																																																				0.602	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353		A	152759796	G	A	152759796	2	1	81	1	0	0	0	0	0	0	0	1	8685	962	34	3		3	LCE1E	1	152759796	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	479991	152759796	96490825	10	23335										
INSRR	3645	hgsc.bcm.edu	37	chr1	156821809	156821809	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cagctgtgacacagcgccagGactcatactggtaggtgcct	12	12	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:156821809G>T	ENST00000368195.3	-	3	1208	c.812C>A	c.(811-813)tCc>tAc	p.S271Y	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	271					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACAGCGCCAGGACTCATACTG	0.662																																																0			1											24	24	24					1																	156821809		2202	4297	6499	155088433	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.812C>A	1.37:g.156821809G>T	ENSP00000357178:p.Ser271Tyr		155088433	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.681167	0.68042	.	.	ENSG00000027644	ENST00000368195	T	0.32023	1.47	4.62	4.62	0.57501	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.983616	0.08276	N	0.970654	T	0.17662	0.0424	.	.	.	0.31067	N	0.713448	P	0.43938	0.822	B	0.41299	0.353	T	0.05194	-1.0900	9	0.72032	D	0.01	.	11.3961	0.49843	0.0:0.2952:0.7048:0.0	.	271	P14616	INSRR_HUMAN	Y	271	ENSP00000357178:S271Y	ENSP00000357178:S271Y	S	-	2	0	INSRR	155088433	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	4.524000	0.60552	2.419000	0.82065	0.456000	0.33151	TCC		0.662	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156821809	G	T	156821809	3	4	81	1	0	0	0	0	1	0	0	0	7795	1174	41	2	3160	2	INSRR	1	156821809	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	4062013	156821809	92428812	11	23336										
CD1C	911	hgsc.bcm.edu	37	chr1	158262530	158262530	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcaactgggcactaaacatgGtgatattcttcctaatgctg	9	9	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:158262530G>T	ENST00000368170.3	+	4	1034	c.755G>T	c.(754-756)gGt>gTt	p.G252V		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	252	Ig-like.				antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)	p.G252V(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					ACTAAACATGGTGATATTCTT	0.532																																																1	Substitution - Missense(1)	lung(1)	1											148	145	146					1																	158262530		2203	4300	6503	156529154	SO:0001583	missense	911			M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.755G>T	1.37:g.158262530G>T	ENSP00000357152:p.Gly252Val		156529154	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	37	CCDS1175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	12.15|12.15	1.853116|1.853116	0.32699|0.32699	.|.	.|.	ENSG00000158481|ENSG00000158481	ENST00000368169;ENST00000368170;ENST00000454192|ENST00000443761	T|.	0.02863|.	4.13|.	3.62|3.62	-0.814|-0.814	0.10846|0.10846	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);|.	0.601763|.	0.13907|.	N|.	0.354518|.	T|T	0.34745|0.34745	0.0908|0.0908	M|M	0.77820|0.77820	2.39|2.39	0.09310|0.09310	N|N	0.999997|0.999997	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.994;0.997|.	T|T	0.40869|0.40869	-0.9540|-0.9540	10|5	0.87932|.	D|.	0|.	.|.	6.4748|6.4748	0.22028|0.22028	0.5149:0.0:0.4851:0.0|0.5149:0.0:0.4851:0.0	.|.	252;252|.	E9PGC9;P29017|.	.;CD1C_HUMAN|.	V|C	252;252;55|186	ENSP00000357152:G252V|.	ENSP00000357151:G252V|.	G|W	+|+	2|3	0|0	CD1C|CD1C	156529154|156529154	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.018000|0.018000	0.13422|0.13422	-0.268000|-0.268000	0.09312|0.09312	-0.355000|-0.355000	0.07637|0.07637	GGT|TGG		0.532	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		T	158262530	G	T	158262530	3	4	81	1	0	0	0	0	1	0	0	0	2982	1261	44	2	769	2	CD1C	1	158262530	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	1440721	158262530	90988091	12	23337										
CD1E	913	hgsc.bcm.edu	37	chr1	158325848	158325848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggcagctggcctgtcctgtcGggtgaaacacagcagtctag	14	11	1	1	rs371931193		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:158325848G>A	ENST00000368167.3	+	4	1096	c.857G>A	c.(856-858)cGg>cAg	p.R286Q	CD1E_ENST00000368166.3_Missense_Mutation_p.R97Q|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368160.3_Missense_Mutation_p.R286Q|CD1E_ENST00000452291.2_Missense_Mutation_p.R97Q|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368165.3_Missense_Mutation_p.R196Q|CD1E_ENST00000368156.1_Missense_Mutation_p.R196Q|CD1E_ENST00000444681.2_Missense_Mutation_p.R187Q|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000434258.1_Missense_Mutation_p.R284Q|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368164.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	286	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CTGTCCTGTCGGGTGAAACAC	0.572																																																0			1											69	73	71					1																	158325848		2203	4300	6503	156592472	SO:0001583	missense	913			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.857G>A	1.37:g.158325848G>A	ENSP00000357149:p.Arg286Gln		156592472	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860006	0.32884	.	.	ENSG00000158488	ENST00000434258;ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368160;ENST00000368156	T;T;T;T;T;T;T;T	0.02812	4.15;4.15;4.15;4.15;4.15;4.15;4.15;4.15	4.28	2.4	0.29515	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.439735	0.16938	N	0.193383	T	0.01905	0.0060	L	0.48174	1.505	0.09310	N	1	D;D;D;D;D;P;P;D;D;P;P	0.71674	0.989;0.998;0.997;0.977;0.993;0.936;0.954;0.991;0.982;0.661;0.718	P;P;P;P;P;B;B;P;P;B;B	0.52066	0.687;0.687;0.689;0.558;0.673;0.31;0.2;0.544;0.579;0.156;0.227	T	0.47315	-0.9127	10	0.49607	T	0.09	-10.4128	6.2352	0.20758	0.2296:0.0:0.7704:0.0	.	97;187;284;286;187;196;97;286;286;97;196	B4E057;B4E042;E7ET31;A2RRL5;E7EP01;P15812-5;P15812-9;P15812-2;P15812;P15812-8;P15812-6	.;.;.;.;.;.;.;.;CD1E_HUMAN;.;.	Q	284;187;286;97;196;97;286;196	ENSP00000401957:R284Q;ENSP00000402906:R187Q;ENSP00000357149:R286Q;ENSP00000416228:R97Q;ENSP00000357147:R196Q;ENSP00000357148:R97Q;ENSP00000357142:R286Q;ENSP00000357138:R196Q	ENSP00000357138:R196Q	R	+	2	0	CD1E	156592472	0.000000	0.05858	0.030000	0.17652	0.847000	0.48162	0.016000	0.13377	0.456000	0.26937	0.563000	0.77884	CGG		0.572	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158325848	G	A	158325848	3	1	81	1	0	0	0	0	1	0	0	0	2984	1116	39	1	871	1	CD1E	1	158325848	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	63318	158325848	90924773	13	23338										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158606540	158606540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agtcctgggagctcactcgtAtcaacttctccctaaaatca	6	13	4	0	rs377763465		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:158606540A>G	ENST00000368147.4	-	37	5381	c.5201T>C	c.(5200-5202)aTa>aCa	p.I1734T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1734					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GCTCACTCGTATCAACTTCTC	0.473																																																0			1						A	THR/ILE	0,3762		0,0,1881	110	107	108		5201	2.9	0	1		108	1,8221		0,1,4110	no	missense	SPTA1	NM_003126.2	89	0,1,5991	GG,GA,AA		0.0122,0.0,0.0083	benign	1734/2420	158606540	1,11983	1881	4111	5992	156873164	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5201T>C	1.37:g.158606540A>G	ENSP00000357129:p.Ile1734Thr		156873164	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	5.789	0.329980	0.10956	0.0	1.22E-4	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46451	0.87;0.87	5.26	2.94	0.34122	.	.	.	.	.	T	0.08403	0.0209	N	0.17474	0.49	0.09310	N	1	B	0.14012	0.009	B	0.23150	0.044	T	0.40813	-0.9543	9	0.13853	T	0.58	.	6.1365	0.20237	0.754:0.1629:0.0831:0.0	.	1734	P02549	SPTA1_HUMAN	T	1734	ENSP00000357130:I1734T;ENSP00000357129:I1734T	ENSP00000357129:I1734T	I	-	2	0	SPTA1	156873164	0.431000	0.25546	0.002000	0.10522	0.008000	0.06430	5.254000	0.65457	0.460000	0.27045	0.528000	0.53228	ATA		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158606540	A	G	158606540	3	3	81	1	0	0	0	0	1	0	0	0	15155	449	16	4	2122	4	SPTA1	1	158606540	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	280692	158606540	90644081	14	23339										
TNFSF4	7292	hgsc.bcm.edu	37	chr1	173157660	173157660	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aaacttttgacaatacttacCggtaaattgtactttgatac	5	7	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:173157660C>T	ENST00000281834.3	-	2	338	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	TNFSF4_ENST00000488053.1_5'UTR|TNFSF4_ENST00000367718.1_Splice_Site_p.E18K	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	68					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						CAATACTTACCGGTAAATTGT	0.318																																																0			1											73	82	79					1																	173157660		2203	4299	6502	171424283	SO:0001630	splice_region_variant	7292			D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11934	protein-coding gene	gene with protein product		603594	"tax-transcriptionally activated glycoprotein 1, 34kD"	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.202+1G>A	1.37:g.173157660C>T			171424283	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.712978	0.00706	.	.	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	.	.	.	4.87	-4.42	0.03579	Tumour necrosis factor (1);Tumour necrosis factor-like (1);	1.761270	0.02461	N	0.086582	T	0.02767	0.0083	N	0.01352	-0.895	0.19300	N	0.999976	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15263	-1.0443	9	0.08381	T	0.77	1.7144	7.0802	0.25227	0.0:0.4722:0.138:0.3898	.	68;18	P23510;Q8IV74	TNFL4_HUMAN;.	K	18;68;18	.	ENSP00000281834:E68K	E	-	1	0	TNFSF4	171424283	0.001000	0.12720	0.006000	0.13384	0.019000	0.09904	-0.955000	0.03869	-0.924000	0.03780	-0.793000	0.03317	GAA		0.318	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1		Missense_Mutation	T	173157660	C	T	173157660	5	4	81	1	0	0	0	0	0	0	1	0	16349	666	23	1	357	1	TNFSF4	1	173157660	Splice_Site	SNP	C	TCGA-AH-6544-01A-11D-1826-10	14551120	173157660	76092961	15	23340										
RNASEL	6041	hgsc.bcm.edu	37	chr1	182544693	182544693	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tctgaaaatacagggaagggTctccaatttttaatttcatc	7	7	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:182544693T>C	ENST00000367559.3	-	7	2313	c.2060A>G	c.(2059-2061)gAc>gGc	p.D687G	RNASEL_ENST00000444138.1_Missense_Mutation_p.D687G	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	687	KEN. {ECO:0000255|PROSITE- ProRule:PRU00725}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CAGGGAAGGGTCTCCAATTTT	0.398																																																0			1											83	80	81					1																	182544693		2203	4300	6503	180811316	SO:0001583	missense	6041			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"Ankyrin repeat domain containing"	10050	protein-coding gene	gene with protein product		180435	"prostate cancer 1"	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.2060A>G	1.37:g.182544693T>C	ENSP00000356530:p.Asp687Gly		180811316	Q5W0L2|Q6AI46	Missense_Mutation	SNP	ENST00000367559.3	37	CCDS1347.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.477107	0.63849	.	.	ENSG00000135828	ENST00000367559;ENST00000444138	T;T	0.30981	1.51;1.51	5.11	3.96	0.45880	PUG domain (1);KEN domain, ribonuclease activator (2);	0.654660	0.14485	N	0.316728	T	0.41558	0.1164	L	0.56769	1.78	0.80722	D	1	P	0.51537	0.946	P	0.53224	0.721	T	0.20571	-1.0271	10	0.72032	D	0.01	-7.2216	9.2431	0.37509	0.1613:0.0:0.0:0.8387	.	687	Q05823	RN5A_HUMAN	G	687	ENSP00000356530:D687G;ENSP00000411147:D687G	ENSP00000356530:D687G	D	-	2	0	RNASEL	180811316	0.781000	0.28676	0.458000	0.27068	0.041000	0.13682	2.589000	0.46145	0.870000	0.35726	0.533000	0.62120	GAC		0.398	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133		C	182544693	T	C	182544693	3	2	81	1	0	0	0	0	1	0	0	0	13453	1667	58	4	169	4	RNASEL	1	182544693	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	9387033	182544693	66705928	16	23341										
CFHR5	81494	hgsc.bcm.edu	37	chr1	196963367	196963367	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	taccaatttgggtggtcaccTaactttccaacatgcaaagg	8	10	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:196963367T>G	ENST00000256785.4	+	4	697	c.588T>G	c.(586-588)ccT>ccG	p.P196P	CFHR5_ENST00000367414.5_Silent_p.P220P			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	196	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						GGTGGTCACCTAACTTTCCAA	0.318																																																0			1											88	97	94					1																	196963367		2203	4300	6503	195229990	SO:0001819	synonymous_variant	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.588T>G	1.37:g.196963367T>G			195229990	Q2NKK2	Silent	SNP	ENST00000256785.4	37	CCDS1387.1																																																																																				0.318	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		G	196963367	T	G	196963367	2	3	81	1	0	0	0	0	0	0	0	1	3294	1509	53	4		4	CFHR5	1	196963367	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	14418674	196963367	52287254	17	23342										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202699084	202699084	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cgctcactggagaggccctcTctttccaggcgtctcttcag	10	15	4	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:202699084T>C	ENST00000367265.3	-	26	5412	c.4248A>G	c.(4246-4248)agA>agG	p.R1416R	KDM5B_ENST00000367264.2_Silent_p.R1452R	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1416					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AGAGGCCCTCTCTTTCCAGGC	0.463																																																0			1											105	99	101					1																	202699084		2203	4300	6503	200965707	SO:0001819	synonymous_variant	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.4248A>G	1.37:g.202699084T>C			200965707	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																				0.463	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		C	202699084	T	C	202699084	2	2	81	1	0	0	0	0	0	0	0	1	8155	1548	54	4		4	KDM5B	1	202699084	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	5735717	202699084	46551537	18	23343										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228432236	228432236	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gggagtacagctgtgaggctGggggccagagagtctccttc	17	9	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:228432236G>A	ENST00000422127.1	+	11	3489	c.3445G>A	c.(3445-3447)Ggg>Agg	p.G1149R	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.G1149R|OBSCN_ENST00000570156.2_Missense_Mutation_p.G1241R|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1149	Ig-like 11.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGTGAGGCTGGGGGCCAGAG	0.542																																																0			1											93	101	98					1																	228432236		2026	4177	6203	226498859	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3445G>A	1.37:g.228432236G>A	ENSP00000409493:p.Gly1149Arg		226498859	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	12.44	1.938851	0.34189	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.11930	2.73;2.73	3.59	2.67	0.31697	Immunoglobulin subtype (1);	0.154071	0.41396	N	0.000898	T	0.26231	0.0640	L	0.50847	1.595	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.978	T	0.01795	-1.1272	10	0.20046	T	0.44	.	11.0641	0.47966	0.0924:0.0:0.9076:0.0	.	1149;1149	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	1149	ENSP00000284548:G1149R;ENSP00000409493:G1149R	ENSP00000284548:G1149R	G	+	1	0	OBSCN	226498859	1.000000	0.71417	0.987000	0.45799	0.385000	0.30292	5.659000	0.68010	0.711000	0.32018	0.449000	0.29647	GGG		0.542	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228432236	G	A	228432236	3	1	81	1	0	0	0	0	1	0	0	0	10843	1348	47	3	3483	3	OBSCN	1	228432236	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	25733152	228432236	20818385	19	23344										
RYR2	6262	hgsc.bcm.edu	37	chr1	237796984	237796984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtttgatcatctcagttattTactggaaaacagcagtgttg	9	6	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:237796984T>C	ENST00000366574.2	+	43	6979	c.6662T>C	c.(6661-6663)tTa>tCa	p.L2221S	RYR2_ENST00000542537.1_Missense_Mutation_p.L2205S|RYR2_ENST00000360064.6_Missense_Mutation_p.L2219S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2221	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTCAGTTATTTACTGGAAAAC	0.333																																																0			1											134	126	129					1																	237796984		1832	4089	5921	235863607	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.6662T>C	1.37:g.237796984T>C	ENSP00000355533:p.Leu2221Ser		235863607	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.315799	0.81469	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.90732	-2.72;-2.72;-2.72	4.9	4.9	0.64082	Intracellular calcium-release channel (1);	0.000000	0.45126	D	0.000394	D	0.94971	0.8373	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95601	0.8663	10	0.87932	D	0	-8.6294	14.8247	0.70101	0.0:0.0:0.0:1.0	.	2221	Q92736	RYR2_HUMAN	S	2221;2219;2205	ENSP00000355533:L2221S;ENSP00000353174:L2219S;ENSP00000443798:L2205S	ENSP00000353174:L2219S	L	+	2	0	RYR2	235863607	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.950000	0.87804	1.957000	0.56846	0.460000	0.39030	TTA		0.333	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237796984	T	C	237796984	3	2	81	1	0	0	0	0	1	0	0	0	13806	1764	61	4	6832	4	RYR2	1	237796984	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	9364748	237796984	11453637	20	23345										
PLD5	200150	hgsc.bcm.edu	37	chr1	242264040	242264040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggaaaggtgtgattcttttgTtcttttgtagcacaagcatt	10	5	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr1:242264040T>C	ENST00000536534.2	-	9	1525	c.1284A>G	c.(1282-1284)gaA>gaG	p.E428E	PLD5_ENST00000442594.2_Silent_p.E336E|PLD5_ENST00000427495.1_Silent_p.E366E			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	428						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GATTCTTTTGTTCTTTTGTAG	0.408																																																0			1											214	187	196					1																	242264040		2203	4300	6503	240330663	SO:0001819	synonymous_variant	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1284A>G	1.37:g.242264040T>C			240330663	A1KXV0|B7Z324|Q494U9|Q8NB22	Silent	SNP	ENST00000536534.2	37	CCDS1621.2																																																																																				0.408	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		C	242264040	T	C	242264040	2	2	81	1	0	0	0	0	0	0	0	1	12080	1722	60	4		4	PLD5	1	242264040	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	4467056	242264040	6986581	21	23346										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11334408	11334408	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tctaaaaccatgtaaggattGgattgttctttatcttgttc	7	6	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:11334408G>A	ENST00000315872.6	-	29	4030	c.3582C>T	c.(3580-3582)tcC>tcT	p.S1194S	ROCK2_ENST00000401753.1_Silent_p.S951S	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	1194	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		S -> P (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TGTAAGGATTGGATTGTTCTT	0.274																																																0			2											92	88	89					2																	11334408		1798	4040	5838	11251859	SO:0001819	synonymous_variant	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.3582C>T	2.37:g.11334408G>A			11251859	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	37	CCDS42654.1																																																																																				0.274	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11334408	G	A	11334408	2	1	81	1	0	0	0	0	0	0	0	1	13555	1335	47	3		3	ROCK2	2	11334408	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		11334408	231864965	22	23347										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48873886	48873886	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tggaaatgagcataaaatcgTgcctgaagctttgttgtgtc	11	6	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:48873886T>C	ENST00000403751.3	+	6	720	c.683T>C	c.(682-684)gTg>gCg	p.V228A	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.V932A|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.V885A|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.V932A|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.V194A|LHCGR_ENST00000420913.3_Intron|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.V932A|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.V932A	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	228					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CATAAAATCGTGCCTGAAGCT	0.418																																																0			2											123	110	115					2																	48873886		2203	4300	6503	48727390	SO:0001583	missense	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.683T>C	2.37:g.48873886T>C	ENSP00000384597:p.Val228Ala		48727390	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	T	0.355	-0.942426	0.02322	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T	0.44881	2.91;2.89;2.91;2.91;3.15;0.91	4.52	-4.37	0.03633	.	1.770990	0.03153	N	0.168183	T	0.14614	0.0353	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.001;0.0	T	0.09122	-1.0689	10	0.15066	T	0.55	.	2.603	0.04871	0.1539:0.4421:0.1569:0.247	.	194;885;932;228;932	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	A	932;932;932;932;885;227;237;194;228	ENSP00000385499:V932A;ENSP00000385701:V932A;ENSP00000378236:V932A;ENSP00000311493:V932A;ENSP00000378234:V885A;ENSP00000396702:V237A	ENSP00000384597:V228A	V	+	2	0	STON1-GTF2A1L;GTF2A1L	48727390	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	0.302000	0.19192	-0.700000	0.05070	0.402000	0.26972	GTG		0.418	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		C	48873886	T	C	48873886	3	2	81	1	0	0	0	0	1	0	0	0	6874	1696	59	4	705	4	GTF2A1L	2	48873886	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	37539478	48873886	194325487	23	23348										
XPO1	7514	hgsc.bcm.edu	37	chr2	61713084	61713084	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	catccaacagagggggaacaAaattttcagcgacctgttgg	11	9	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:61713084A>C	ENST00000401558.2	-	20	3054	c.2327T>G	c.(2326-2328)tTt>tGt	p.F776C	XPO1_ENST00000406957.1_Missense_Mutation_p.F776C|RP11-355B11.2_ENST00000578974.2_RNA|XPO1_ENST00000404992.2_Missense_Mutation_p.F776C|RP11-355B11.2_ENST00000605437.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	776					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AGGGGGAACAAAATTTTCAGC	0.388			Mis		CLL																																	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	0			2											50	48	49					2																	61713084		2203	4300	6503	61566588	SO:0001583	missense	7514			Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2327T>G	2.37:g.61713084A>C	ENSP00000384863:p.Phe776Cys		61566588	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.581048	0.86748	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.69561	-0.41;-0.41;-0.41	6.16	6.16	0.99307	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83220	0.5207	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.83667	0.0164	10	0.44086	T	0.13	-22.6201	16.8061	0.85666	1.0:0.0:0.0:0.0	.	423;776	B3KWD0;O14980	.;XPO1_HUMAN	C	776	ENSP00000384863:F776C;ENSP00000385942:F776C;ENSP00000385559:F776C	ENSP00000384863:F776C	F	-	2	0	XPO1	61566588	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.236000	0.95360	2.367000	0.80283	0.528000	0.53228	TTT		0.388	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61713084	A	C	61713084	3	2	81	1	0	0	0	0	1	0	0	0	17485	14	1	4	912	4	XPO1	2	61713084	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	12839198	61713084	181486289	24	23349										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315374	70315374	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agcagatttgcctggtcatgCtggagacgctctcccagtct	11	12	3	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:70315374C>A	ENST00000303577.5	+	1	790	c.499C>A	c.(499-501)Ctg>Atg	p.L167M	PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	167					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						CCTGGTCATGCTGGAGACGCT	0.642																																					Colon(85;1146 1307 3484 18706 25380)											0			2											51	47	48					2																	70315374		2203	4300	6503	70168878	SO:0001583	missense	5093				CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.499C>A	2.37:g.70315374C>A	ENSP00000305556:p.Leu167Met		70168878	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	37	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941483	0.53079	.	.	ENSG00000169564	ENST00000303577	T	0.44083	0.93	4.03	3.16	0.36331	K Homology (1);	0.000000	0.64402	D	0.000004	T	0.47710	0.1460	L	0.46157	1.445	0.58432	D	0.999997	P	0.41214	0.742	P	0.53006	0.715	T	0.45789	-0.9237	10	0.52906	T	0.07	.	10.0866	0.42421	0.0:0.8997:0.0:0.1003	.	167	Q15365	PCBP1_HUMAN	M	167	ENSP00000305556:L167M	ENSP00000305556:L167M	L	+	1	2	PCBP1	70168878	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.639000	0.61361	1.303000	0.44873	0.650000	0.86243	CTG		0.642	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70315374	C	A	70315374	3	1	81	1	0	0	0	0	1	0	0	0	11531	796	28	2	501	2	PCBP1	2	70315374	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	8602290	70315374	172883999	25	23350										
CD207	50489	hgsc.bcm.edu	37	chr2	71060828	71060828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	caagctgccctggagtgcccGgatctttgtatttaaagcac	10	11	1	0	rs370455494		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:71060828G>A	ENST00000410009.3	-	3	559	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	172					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TGGAGTGCCCGGATCTTTGTA	0.428																																																0			2						G	TRP/ARG	0,3698		0,0,1849	82	73	75		514	4.1	0	2		75	1,8199		0,1,4099	no	missense	CD207	NM_015717.3	101	0,1,5948	AA,AG,GG		0.0122,0.0,0.0084	probably-damaging	172/329	71060828	1,11897	1849	4100	5949	70914336	SO:0001583	missense	50489			AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.514C>T	2.37:g.71060828G>A	ENSP00000386378:p.Arg172Trp		70914336		Missense_Mutation	SNP	ENST00000410009.3	37		.	.	.	.	.	.	.	.	.	.	G	6.526	0.465360	0.12402	0.0	1.22E-4	ENSG00000116031	ENST00000410009	T	0.29917	1.55	4.12	4.12	0.48240	.	1.382280	0.04510	N	0.382668	T	0.25568	0.0622	L	0.27053	0.805	0.09310	N	1	D	0.67145	0.996	B	0.39590	0.304	T	0.32719	-0.9896	10	0.59425	D	0.04	.	12.1703	0.54155	0.0:0.0:1.0:0.0	.	172	Q9UJ71	CLC4K_HUMAN	W	172	ENSP00000386378:R172W	ENSP00000386378:R172W	R	-	1	2	CD207	70914336	0.043000	0.20138	0.029000	0.17559	0.004000	0.04260	1.111000	0.31159	2.568000	0.86640	0.655000	0.94253	CGG		0.428	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		A	71060828	G	A	71060828	3	1	81	1	0	0	0	0	1	0	0	0	2989	1115	39	1	488	1	CD207	2	71060828	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	745454	71060828	172138545	26	23351										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80101311	80101311	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agcatttctccgccacccagAtgtcgccgctacgagagcca	9	16	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:80101311A>G	ENST00000402739.4	+	5	700	c.695A>G	c.(694-696)gAt>gGt	p.D232G	CTNNA2_ENST00000496558.1_Missense_Mutation_p.D232G|CTNNA2_ENST00000466387.1_Missense_Mutation_p.D232G|CTNNA2_ENST00000540488.1_Missense_Mutation_p.D232G|CTNNA2_ENST00000361291.4_Missense_Mutation_p.D266G|CTNNA2_ENST00000541047.1_Missense_Mutation_p.D232G	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	232					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CGCCACCCAGATGTCGCCGCT	0.577																																																0			2											52	56	55					2																	80101311		2074	4223	6297	79954819	SO:0001583	missense	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.695A>G	2.37:g.80101311A>G	ENSP00000384638:p.Asp232Gly		79954819	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	A	22.4	4.289435	0.80914	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.50752	0.1634	M	0.81802	2.56	0.80722	D	1	P;P;P	0.43885	0.575;0.82;0.82	P;P;P	0.48425	0.503;0.577;0.577	T	0.49881	-0.8892	10	0.23891	T	0.37	.	15.9724	0.80031	1.0:0.0:0.0:0.0	.	232;232;232	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	G	232;232;266;232;232;232	ENSP00000418191:D232G;ENSP00000419295:D232G;ENSP00000355398:D266G;ENSP00000384638:D232G;ENSP00000444675:D232G;ENSP00000441705:D232G	ENSP00000355398:D266G	D	+	2	0	CTNNA2	79954819	1.000000	0.71417	0.976000	0.42696	0.811000	0.45836	9.339000	0.96797	2.169000	0.68431	0.528000	0.53228	GAT		0.577	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		G	80101311	A	G	80101311	3	3	81	1	0	0	0	0	1	0	0	0	4019	333	12	4	713	4	CTNNA2	2	80101311	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	9040483	80101311	163098062	27	23352										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131519855	131519855	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agatgccccaacaaaggggcGcagctggaccccaaaggggg	15	12	0	1	rs376219909		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:131519855G>A	ENST00000423981.1	+	2	320	c.210G>A	c.(208-210)gcG>gcA	p.A70A	AMER3_ENST00000321420.4_Silent_p.A70A	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	70					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										ACAAAGGGGCGCAGCTGGACC	0.637																																																0			2						G	,,,	0,4390		0,0,2195	18	28	25		210,210,210,210	-10.8	0	2		25	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	,,,	0,1,6489	AA,AG,GG		0.0116,0.0,0.0077	,,,	70/862,70/862,70/862,70/862	131519855	1,12979	2195	4295	6490	131236325	SO:0001819	synonymous_variant	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.210G>A	2.37:g.131519855G>A			131236325	B7ZLH6	Silent	SNP	ENST00000423981.1	37	CCDS2164.1																																																																																				0.637	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131519855	G	A	131519855	2	1	81	1	0	0	0	0	0	0	0	1	5440	1074	38	1		1	FAM123C	2	131519855	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	51418544	131519855	111679518	28	23353										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520306	131520306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gccaggacctgttggacagcGagctcctggccgatgcatcc	13	14	0	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:131520306G>A	ENST00000423981.1	+	2	771	c.661G>A	c.(661-663)Gag>Aag	p.E221K	AMER3_ENST00000321420.4_Missense_Mutation_p.E221K	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	221					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										GTTGGACAGCGAGCTCCTGGC	0.677																																																0			2											40	47	44					2																	131520306		2199	4293	6492	131236776	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.661G>A	2.37:g.131520306G>A	ENSP00000392700:p.Glu221Lys		131236776	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.941296	0.73557	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.19938	2.11;2.11	5.21	5.21	0.72293	.	0.066701	0.56097	D	0.000024	T	0.42177	0.1191	M	0.65975	2.015	0.38725	D	0.953527	D	0.69078	0.997	D	0.63033	0.91	T	0.40739	-0.9547	10	0.66056	D	0.02	.	14.6296	0.68647	0.0:0.0:1.0:0.0	.	221	Q8N944	F123C_HUMAN	K	221	ENSP00000314914:E221K;ENSP00000392700:E221K	ENSP00000314914:E221K	E	+	1	0	FAM123C	131236776	1.000000	0.71417	0.203000	0.23512	0.472000	0.32918	7.661000	0.83786	2.597000	0.87782	0.561000	0.74099	GAG		0.677	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131520306	G	A	131520306	3	1	81	1	0	0	0	0	1	0	0	0	5440	1059	37	1	663	1	FAM123C	2	131520306	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	451	131520306	111679067	29	23354										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160901619	160901619	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtcagaaccgatttacctgcTtgaatgcatttcttgagact	8	9	2	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:160901619T>A	ENST00000283243.7	-	2	365	c.159A>T	c.(157-159)caA>caT	p.Q53H	PLA2R1_ENST00000392771.1_Missense_Mutation_p.Q53H	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	53	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ATTTACCTGCTTGAATGCATT	0.373																																																0			2											57	55	56					2																	160901619		2203	4300	6503	160609865	SO:0001583	missense	22925			U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.159A>T	2.37:g.160901619T>A	ENSP00000283243:p.Gln53His		160609865	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.109913	0.56398	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.38560	1.13;1.13	6.17	0.346	0.16017	Ricin B-related lectin (1);Ricin B lectin (2);	0.362916	0.29314	N	0.012507	T	0.50514	0.1620	M	0.77103	2.36	0.35553	D	0.804004	D;D;D	0.62365	0.975;0.989;0.991	P;P;P	0.55391	0.775;0.742;0.687	T	0.58451	-0.7634	10	0.72032	D	0.01	.	5.2015	0.15267	0.0:0.2486:0.2519:0.4994	.	53;53;53	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	H	53	ENSP00000283243:Q53H;ENSP00000376524:Q53H	ENSP00000283243:Q53H	Q	-	3	2	PLA2R1	160609865	1.000000	0.71417	0.997000	0.53966	0.478000	0.33099	0.801000	0.27055	0.105000	0.17753	-0.290000	0.09829	CAA		0.373	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			A	160901619	T	A	160901619	3	1	81	1	0	0	0	0	1	0	0	0	12041	1606	56	5	4356	5	PLA2R1	2	160901619	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	29381313	160901619	82297754	30	23355										
KLHL23	151230	hgsc.bcm.edu	37	chr2	170592587	170592587	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aatggacagaaggtttgccaAtgctcaatgccaggtattac	10	8	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:170592587A>G	ENST00000392647.2	+	2	1307	c.1063A>G	c.(1063-1065)Atg>Gtg	p.M355V	KLHL23_ENST00000272797.4_Missense_Mutation_p.M355V|KLHL23_ENST00000602521.1_Intron	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	355										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						AGGTTTGCCAATGCTCAATGC	0.468																																																0			2											220	208	212					2																	170592587		2203	4300	6503	170300833	SO:0001583	missense	151230			BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1063A>G	2.37:g.170592587A>G	ENSP00000376419:p.Met355Val		170300833	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	37	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858812	0.71834	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	T;T;T	0.71103	-0.54;-0.54;-0.54	5.8	5.8	0.92144	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.87398	0.6167	M	0.91140	3.18	0.29478	N	0.85653	D	0.69078	0.997	D	0.76071	0.987	D	0.90196	0.4253	9	0.87932	D	0	.	16.1508	0.81622	1.0:0.0:0.0:0.0	.	355	Q8NBE8	KLH23_HUMAN	V	355;355;176	ENSP00000272797:M355V;ENSP00000376419:M355V;ENSP00000394732:M176V	ENSP00000272797:M355V	M	+	1	0	KLHL23	170300833	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.491000	0.81471	2.207000	0.71202	0.528000	0.53228	ATG		0.468	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		G	170592587	A	G	170592587	3	3	81	1	0	0	0	0	1	0	0	0	8399	101	4	4	1065	4	KLHL23	2	170592587	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	9690968	170592587	72606786	31	23356										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179247881	179247881	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aacattggtaaagacctgtcTaaagtctctatgcctgtgga	9	8	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:179247881T>C	ENST00000190611.4	+	17	2128	c.1752T>C	c.(1750-1752)tcT>tcC	p.S584S	OSBPL6_ENST00000315022.2_Silent_p.S588S|OSBPL6_ENST00000359685.3_Silent_p.S548S|OSBPL6_ENST00000392505.2_Silent_p.S609S|OSBPL6_ENST00000409045.3_Silent_p.S553S|OSBPL6_ENST00000409631.1_Silent_p.S548S	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	584					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			AAGACCTGTCTAAAGTCTCTA	0.507																																																0			2											81	83	82					2																	179247881		2203	4300	6503	178956127	SO:0001819	synonymous_variant	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1752T>C	2.37:g.179247881T>C			178956127	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																				0.507	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		C	179247881	T	C	179247881	2	2	81	1	0	0	0	0	0	0	0	1	11312	1509	53	4		4	OSBPL6	2	179247881	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	8655294	179247881	63951492	32	23357										
TTN	7273	hgsc.bcm.edu	37	chr2	179457221	179457221	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atttcaagcttgctaccaacTggagtcacatcaattcttgc	6	11	4	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:179457221T>C	ENST00000591111.1	-	251	54812	c.54588A>G	c.(54586-54588)ccA>ccG	p.P18196P	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000359218.5_Silent_p.P10897P|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342175.6_Silent_p.P10964P|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Silent_p.P10772P|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Silent_p.P19837P|TTN_ENST00000342992.6_Silent_p.P17269P|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18196	Ig-like 105.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCTACCAACTGGAGTCACAT	0.398																																																0			2											283	263	269					2																	179457221		1900	4115	6015	179165467	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.54588A>G	2.37:g.179457221T>C			179165467	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179457221	T	C	179457221	2	2	81	1	0	0	0	0	0	0	0	1	16775	1567	55	4		4	TTN	2	179457221	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	209340	179457221	63742152	33	23358										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187618691	187618691	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aatcatggtcggggaatggtCaaggaacataacaatcattt	10	6	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:187618691C>T	ENST00000304698.5	+	6	1130	c.927C>T	c.(925-927)gtC>gtT	p.V309V		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	309						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GGGGAATGGTCAAGGAACATA	0.378																																																0			2											129	123	125					2																	187618691		2203	4300	6503	187326936	SO:0001819	synonymous_variant	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.927C>T	2.37:g.187618691C>T			187326936	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																				0.378	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		T	187618691	C	T	187618691	2	4	81	1	0	0	0	0	0	0	0	1	5507	813	29	3		3	FAM171B	2	187618691	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	8161470	187618691	55580682	34	23359										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197878358	197878358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agccagatccagagcagtgcGgcctttctcatccctgatgt	10	13	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:197878358G>A	ENST00000328737.2	-	18	1802	c.1726C>T	c.(1726-1728)Cgc>Tgc	p.R576C	ANKRD44_ENST00000282272.8_Missense_Mutation_p.R593C|ANKRD44_ENST00000337207.5_Missense_Mutation_p.R576C|ANKRD44_ENST00000450567.1_Missense_Mutation_p.R576C			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	601										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGAGCAGTGCGGCCTTTCTCA	0.502																																																0			2											226	215	218					2																	197878358		2203	4300	6503	197586603	SO:0001583	missense	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1726C>T	2.37:g.197878358G>A	ENSP00000331516:p.Arg576Cys		197586603	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		.	.	.	.	.	.	.	.	.	.	G	15.72	2.915765	0.52546	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886	T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.79534	0.4462	M	0.62154	1.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79704	-0.1692	10	0.42905	T	0.14	.	17.2648	0.87083	0.0:0.0:1.0:0.0	.	619	Q8N8A2-2	.	C	416;593;576;576;576;276	ENSP00000403415:R416C;ENSP00000282272:R593C;ENSP00000331516:R576C;ENSP00000402420:R576C;ENSP00000338794:R576C;ENSP00000416319:R276C	ENSP00000282272:R593C	R	-	1	0	ANKRD44	197586603	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.310000	0.59141	2.294000	0.77228	0.655000	0.94253	CGC		0.502	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	197878358	G	A	197878358	3	1	81	1	0	0	0	0	1	0	0	0	672	1116	39	1	1069	1	ANKRD44	2	197878358	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	10259667	197878358	45321015	35	23360										
MAP2	4133	hgsc.bcm.edu	37	chr2	210560823	210560823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtcagggtcccacagcgtgcGttttgcagccctagagcagc	13	13	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:210560823G>A	ENST00000360351.4	+	7	4435	c.3929G>A	c.(3928-3930)cGt>cAt	p.R1310H	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.R1306H	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1310					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CACAGCGTGCGTTTTGCAGCC	0.512																																					Pancreas(27;423 979 28787 29963)											0			2											110	111	111					2																	210560823		2203	4300	6503	210269068	SO:0001583	missense	10988				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3929G>A	2.37:g.210560823G>A	ENSP00000353508:p.Arg1310His		210269068	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497729	0.44455	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.26810	1.71;1.71	5.73	5.73	0.89815	MAP2/Tau projection (1);	0.103218	0.43579	D	0.000545	T	0.36358	0.0964	L	0.47716	1.5	0.54753	D	0.999988	D;D	0.56968	0.973;0.978	P;P	0.54312	0.632;0.748	T	0.05370	-1.0889	10	0.87932	D	0	-8.663	13.141	0.59434	0.0729:0.0:0.9271:0.0	.	1306;1310	P11137-3;P11137	.;MAP2_HUMAN	H	1310;1306	ENSP00000353508:R1310H;ENSP00000392164:R1306H	ENSP00000353508:R1310H	R	+	2	0	MAP2	210269068	1.000000	0.71417	1.000000	0.80357	0.472000	0.32918	7.279000	0.78599	2.718000	0.92993	0.650000	0.86243	CGT		0.512	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210560823	G	A	210560823	3	1	81	1	0	0	0	0	1	0	0	0	9265	1145	40	1	3943	1	MAP2	2	210560823	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	12682465	210560823	32638550	36	23361										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212288942	212288942	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gctgaggcaaacgttctcctTtctctaataaatcagggatt	8	9	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:212288942T>C	ENST00000342788.4	-	23	3114	c.2804A>G	c.(2803-2805)aAa>aGa	p.K935R	ERBB4_ENST00000402597.1_Missense_Mutation_p.K925R|ERBB4_ENST00000436443.1_Missense_Mutation_p.K935R	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	935	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K935I(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACGTTCTCCTTTCTCTAATAA	0.393										TSP Lung(8;0.080)																																						1	Substitution - Missense(1)	lung(1)	2											113	110	111					2																	212288942		2203	4300	6503	211997187	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2804A>G	2.37:g.212288942T>C	ENSP00000342235:p.Lys935Arg		211997187	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.142859	0.77888	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	D;D;D	0.82711	-1.64;-1.64;-1.64	6.16	6.16	0.99307	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81678	0.4873	L	0.31294	0.92	0.80722	D	1	P;B;P;P	0.40211	0.659;0.018;0.659;0.707	B;B;B;P	0.46389	0.381;0.324;0.381;0.515	D	0.83458	0.0052	10	0.72032	D	0.01	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	925;925;935;935	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	R	935;935;925	ENSP00000342235:K935R;ENSP00000403204:K935R;ENSP00000385565:K925R	ENSP00000342235:K935R	K	-	2	0	ERBB4	211997187	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.980000	0.88113	2.367000	0.80283	0.528000	0.53228	AAA		0.393	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212288942	T	C	212288942	3	2	81	1	0	0	0	0	1	0	0	0	5222	1841	64	4	1146	4	ERBB4	2	212288942	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	1728119	212288942	30910431	37	23362										
VWC2L	402117	hgsc.bcm.edu	37	chr2	215440510	215440510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtggaagcctgctcagtgttCgaaacgtgaatgccaaggca	13	9	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:215440510C>T	ENST00000312504.5	+	4	1437	c.635C>T	c.(634-636)tCg>tTg	p.S212L	AC107218.3_ENST00000412896.1_RNA|AC107218.3_ENST00000437883.1_RNA|VWC2L_ENST00000427124.1_3'UTR	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	212					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						GCTCAGTGTTCGAAACGTGAA	0.473																																																0			2											226	222	223					2																	215440510		2036	4193	6229	215148755	SO:0001583	missense	402117			AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.635C>T	2.37:g.215440510C>T	ENSP00000308976:p.Ser212Leu		215148755	A6NC69|B2RUW7|B7X8X1	Missense_Mutation	SNP	ENST00000312504.5	37	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.986362	0.35036	.	.	ENSG00000174453	ENST00000312504	T	0.44083	0.93	5.58	4.71	0.59529	.	.	.	.	.	T	0.27169	0.0666	N	0.14661	0.345	0.80722	D	1	B	0.12630	0.006	B	0.08055	0.003	T	0.03840	-1.0999	9	0.27082	T	0.32	-1.1663	14.1936	0.65654	0.0:0.9285:0.0:0.0714	.	212	B2RUY7	VWC2L_HUMAN	L	212	ENSP00000308976:S212L	ENSP00000308976:S212L	S	+	2	0	VWC2L	215148755	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.745000	0.68672	1.360000	0.45960	0.655000	0.94253	TCG		0.473	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		T	215440510	C	T	215440510	3	4	81	1	0	0	0	0	1	0	0	0	17284	893	31	1	645	1	VWC2L	2	215440510	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	3151568	215440510	27758863	38	23363										
ATIC	471	hgsc.bcm.edu	37	chr2	216177301	216177301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttggtttgaatctggtcgctTccggagggactgcaaaagct	13	8	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:216177301T>C	ENST00000236959.9	+	2	426	c.100T>C	c.(100-102)Tcc>Ccc	p.S34P	ATIC_ENST00000435675.1_Missense_Mutation_p.S33P|ATIC_ENST00000540518.1_5'UTR	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	34					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	TCTGGTCGCTTCCGGAGGGAC	0.468			T	ALK	ALCL																																		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	0			2											92	90	91					2																	216177301		2203	4300	6503	215885546	SO:0001583	missense	471				CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.100T>C	2.37:g.216177301T>C	ENSP00000236959:p.Ser34Pro		215885546	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	37	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.037540	0.93630	.	.	ENSG00000138363	ENST00000236959;ENST00000435675	D;D	0.83335	-1.71;-1.71	5.41	5.41	0.78517	Methylglyoxal synthase-like domain (4);	0.000000	0.85682	D	0.000000	D	0.93446	0.7909	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95153	0.8274	10	0.87932	D	0	-14.0384	15.1233	0.72463	0.0:0.0:0.0:1.0	.	33;34	E9PBU3;P31939	.;PUR9_HUMAN	P	34;33	ENSP00000236959:S34P;ENSP00000415935:S33P	ENSP00000236959:S34P	S	+	1	0	ATIC	215885546	1.000000	0.71417	0.995000	0.50966	0.910000	0.53928	6.610000	0.74178	2.058000	0.61347	0.533000	0.62120	TCC		0.468	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044		C	216177301	T	C	216177301	3	2	81	1	0	0	0	0	1	0	0	0	1106	1783	62	4	106	4	ATIC	2	216177301	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	736791	216177301	27022072	39	23364										
C2orf24	27013	hgsc.bcm.edu	37	chr2	220037364	220037364	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctccatgacactgaaaagggAacattgctgaggctgaggaa	12	8	0	4			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:220037364A>C	ENST00000409789.1	-	9	1604	c.1177T>G	c.(1177-1179)Tcc>Gcc	p.S393A	SLC23A3_ENST00000295738.7_5'Flank|SLC23A3_ENST00000455516.2_5'Flank|SLC23A3_ENST00000409878.3_5'Flank|SLC23A3_ENST00000396775.3_5'Flank|CNPPD1_ENST00000360507.5_Missense_Mutation_p.S393A			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	393					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						CTGAAAAGGGAACATTGCTGA	0.572																																																0			2											94	93	94					2																	220037364		2203	4300	6503	219745608	SO:0001583	missense	27013			AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 24"	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.1177T>G	2.37:g.220037364A>C	ENSP00000386277:p.Ser393Ala		219745608	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	37	CCDS2433.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.706656	0.48412	.	.	ENSG00000115649	ENST00000360507;ENST00000409789	T;T	0.16073	2.37;2.37	5.04	3.9	0.45041	.	0.665977	0.15884	N	0.239911	T	0.11793	0.0287	N	0.24115	0.695	0.22803	N	0.998719	P	0.46656	0.882	B	0.41236	0.351	T	0.10314	-1.0635	10	0.40728	T	0.16	-10.9626	8.8662	0.35286	0.9149:0.0:0.0851:0.0	.	393	Q9BV87	CNPD1_HUMAN	A	393	ENSP00000353698:S393A;ENSP00000386277:S393A	ENSP00000353698:S393A	S	-	1	0	CNPPD1	219745608	1.000000	0.71417	0.999000	0.59377	0.522000	0.34438	2.876000	0.48498	0.955000	0.37878	0.533000	0.62120	TCC		0.572	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680		C	220037364	A	C	220037364	3	2	81	1	0	0	0	0	1	0	0	0	2165	246	9	4	59	4	C2orf24	2	220037364	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	3860063	220037364	23162009	40	23365										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224856595	224856595	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggctgccacgaaagtgcgttTctttgtgttctcgggttgga	14	8	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:224856595T>C	ENST00000258405.4	-	4	852	c.610A>G	c.(610-612)Aaa>Gaa	p.K204E	SERPINE2_ENST00000409304.1_Missense_Mutation_p.K204E|SERPINE2_ENST00000447280.2_Missense_Mutation_p.K216E|SERPINE2_ENST00000409840.3_Missense_Mutation_p.K204E	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	204			K -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		AAAGTGCGTTTCTTTGTGTTC	0.537																																																0			2											162	122	136					2																	224856595		2203	4300	6503	224564839	SO:0001583	missense	5270			M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.610A>G	2.37:g.224856595T>C	ENSP00000258405:p.Lys204Glu		224564839	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	37	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.252796	0.39797	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	5.8	5.8	0.92144	Serpin domain (3);	0.093302	0.64402	D	0.000001	T	0.81394	0.4813	N	0.26042	0.785	0.46499	D	0.999074	P;P	0.48407	0.91;0.91	P;P	0.51657	0.676;0.676	T	0.77975	-0.2385	10	0.02654	T	1	.	16.1506	0.81618	0.0:0.0:0.0:1.0	.	216;204	B4DIF2;P07093	.;GDN_HUMAN	E	204;204;204;216;204	ENSP00000386412:K204E;ENSP00000258405:K204E;ENSP00000386969:K204E;ENSP00000415786:K216E;ENSP00000408452:K204E	ENSP00000258405:K204E	K	-	1	0	SERPINE2	224564839	1.000000	0.71417	0.850000	0.33497	0.635000	0.38103	4.678000	0.61641	2.206000	0.71126	0.528000	0.53228	AAA		0.537	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		C	224856595	T	C	224856595	3	2	81	1	0	0	0	0	1	0	0	0	14149	1792	62	4	610	4	SERPINE2	2	224856595	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	4819231	224856595	18342778	41	23366										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226273776	226273776	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aacctagcctatttgaaagaGaagaatgaaaaacgccgaag	9	7	0	4			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr2:226273776G>T	ENST00000272907.6	+	2	593	c.180G>T	c.(178-180)gaG>gaT	p.E60D	NYAP2_ENST00000409269.2_Missense_Mutation_p.E60D	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	60					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												ATTTGAAAGAGAAGAATGAAA	0.383																																																0			2											62	54	56					2																	226273776		1842	4088	5930	225982020	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.180G>T	2.37:g.226273776G>T	ENSP00000272907:p.Glu60Asp		225982020	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521944	0.64747	.	.	ENSG00000144460	ENST00000272907;ENST00000409269	T	0.48522	0.81	5.82	1.53	0.23141	.	0.062767	0.64402	D	0.000009	T	0.61565	0.2357	M	0.72894	2.215	0.34609	D	0.717413	D;D	0.71674	0.998;0.998	D;D	0.77557	0.99;0.99	T	0.68481	-0.5397	10	0.56958	D	0.05	-31.3877	8.2198	0.31534	0.4978:0.0:0.5022:0.0	.	60;60	Q9P242-2;Q9P242	.;K1486_HUMAN	D	60	ENSP00000272907:E60D	ENSP00000272907:E60D	E	+	3	2	KIAA1486	225982020	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.666000	0.25097	0.391000	0.25143	0.557000	0.71058	GAG		0.383	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226273776	G	T	226273776	3	4	81	1	0	0	0	0	1	0	0	0	8258	933	33	2	182	2	KIAA1486	2	226273776	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	1417181	226273776	16925597	42	23367										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10084272	10084272	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttggtgatggataagttgtcGtctattagattggaggattt	13	2	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:10084272G>T	ENST00000419585.1	+	11	974	c.813G>T	c.(811-813)tcG>tcT	p.S271S	FANCD2_ENST00000383807.1_Silent_p.S271S|FANCD2_ENST00000287647.3_Silent_p.S271S|FANCD2_ENST00000383806.1_Silent_p.S271S			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	271	Interaction with BRCA2.|Interaction with FANCE.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.S271S(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		ATAAGTTGTCGTCTATTAGAT	0.373			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	2	Substitution - coding silent(2)	endometrium(2)	3	GRCh37	CD072417	FANCD2	D							247	245	246					3																	10084272		2203	4300	6503	10059272	SO:0001819	synonymous_variant	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.813G>T	3.37:g.10084272G>T			10059272	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																				0.373	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			T	10084272	G	T	10084272	2	4	81	1	0	0	0	0	0	0	0	1	5684	1132	40	2		2	FANCD2	3	10084272	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		10084272	187938158	43	23368										
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113804666	113804666	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcacaactttgaacactactTtgggtttttccattacatcc	5	11	0	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:113804666T>G	ENST00000493014.1	+	6	913	c.845T>G	c.(844-846)tTt>tGt	p.F282C	QTRTD1_ENST00000485050.1_Missense_Mutation_p.F400C|QTRTD1_ENST00000479882.1_Missense_Mutation_p.F265C|QTRTD1_ENST00000281273.4_Missense_Mutation_p.F388C	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GAACACTACTTTGGGTTTTTC	0.463																																																0			3											179	151	161					3																	113804666		2203	4300	6503	115287356	SO:0001583	missense	79691			AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.845T>G	3.37:g.113804666T>G	ENSP00000419169:p.Phe282Cys		115287356		Missense_Mutation	SNP	ENST00000493014.1	37	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180617	0.57800	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	6.08	6.08	0.98989	.	0.175549	0.51477	D	0.000081	T	0.75679	0.3882	L	0.57536	1.79	0.43149	D	0.994915	D;P	0.89917	1.0;0.629	D;B	0.71870	0.975;0.222	T	0.77792	-0.2455	9	0.66056	D	0.02	-15.637	15.2149	0.73258	0.0:0.0:0.0:1.0	.	282;388	B7Z472;Q9H974	.;QTRD1_HUMAN	C	400;388;265;282	.	ENSP00000281273:F388C	F	+	2	0	QTRTD1	115287356	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.344000	0.52174	2.333000	0.79357	0.533000	0.62120	TTT		0.463	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		G	113804666	T	G	113804666	3	3	81	1	0	0	0	0	1	0	0	0	12923	1841	64	4	1193	4	QTRTD1	3	113804666	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	103720394	113804666	84217764	44	23369										
C3orf37	56941	hgsc.bcm.edu	37	chr3	129023621	129023621	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tcctagagcaatggctgaagCgggagaaggaggaggaacct	16	7	0	3	rs36104687		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:129023621C>A	ENST00000383463.4	+	7	1107	c.1018C>A	c.(1018-1020)Cgg>Agg	p.R340R	HMCES_ENST00000502878.2_Silent_p.R340R|HMCES_ENST00000417226.2_Silent_p.R298R|HMCES_ENST00000389735.3_Silent_p.R340R	NM_020187.2	NP_064572.2	Q96FZ2	HMCES_HUMAN	5-hydroxymethylcytosine (hmC) binding, ES cell-specific	340							DNA binding (GO:0003677)|peptidase activity (GO:0008233)										ATGGCTGAAGCGGGAGAAGGA	0.562																																																0			3											61	54	57					3																	129023621		2203	4300	6503	130506311	SO:0001819	synonymous_variant	56941			AF201934	CCDS33852.1	3q21.3	2013-08-30	2013-08-30	2013-08-30	ENSG00000183624	ENSG00000183624			24446	protein-coding gene	gene with protein product	"SOS response associated peptidase domain containing 1"		"chromosome 3 open reading frame 37"	C3orf37		23434322, 23945014	Standard	XM_005247636		Approved	DC12, SRAPD1	uc003elt.3	Q96FZ2	OTTHUMG00000159452	ENST00000383463.4:c.1018C>A	3.37:g.129023621C>A			130506311	A6NJR9|Q96G34|Q9NRP3	Silent	SNP	ENST00000383463.4	37	CCDS33852.1																																																																																				0.562	HMCES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355470.2	NM_020187		A	129023621	C	A	129023621	2	1	81	1	0	0	0	0	0	0	0	1	2233	759	27	2		2	C3orf37	3	129023621	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	15218955	129023621	68998809	45	23370										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134920412	134920412	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgagatgaattatgtgcatCgggacctggctgctaggaac	13	8	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:134920412C>A	ENST00000398015.3	+	12	2597	c.2227C>A	c.(2227-2229)Cgg>Agg	p.R743R	EPHB1_ENST00000493838.1_Silent_p.R304R	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	743	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.R743W(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						TTATGTGCATCGGGACCTGGC	0.547																																																2	Substitution - Missense(2)	large_intestine(2)	3											209	211	210					3																	134920412		2200	4300	6500	136403102	SO:0001819	synonymous_variant	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2227C>A	3.37:g.134920412C>A			136403102	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																				0.547	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134920412	C	A	134920412	2	1	81	1	0	0	0	0	0	0	0	1	5187	875	31	2		2	EPHB1	3	134920412	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	5896791	134920412	63102018	46	23371										
CP	1356	hgsc.bcm.edu	37	chr3	148928087	148928087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgttcttcagtggcaagcaaCatgtatgtatactgctctcc	8	10	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:148928087C>T	ENST00000264613.6	-	3	736	c.474G>A	c.(472-474)atG>atA	p.M158I		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	158	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TGGCAAGCAACATGTATGTAT	0.438																																																0			3											201	177	185					3																	148928087		2203	4300	6503	150410777	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.474G>A	3.37:g.148928087C>T	ENSP00000264613:p.Met158Ile		150410777	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.245301	0.22796	.	.	ENSG00000047457	ENST00000264613	D	0.98531	-4.98	5.8	0.895	0.19247	Cupredoxin (2);Multicopper oxidase, type 3 (1);	1.016750	0.07794	N	0.955430	D	0.91168	0.7218	N	0.01473	-0.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	D	0.85220	0.1026	10	0.36615	T	0.2	-0.6037	5.852	0.18697	0.0:0.1854:0.2537:0.561	.	158;158	A8K5A4;P00450	.;CERU_HUMAN	I	158	ENSP00000264613:M158I	ENSP00000264613:M158I	M	-	3	0	CP	150410777	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.477000	0.06583	-0.067000	0.12976	0.557000	0.71058	ATG		0.438	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		T	148928087	C	T	148928087	3	4	81	1	0	0	0	0	1	0	0	0	3793	478	17	3	2791	3	CP	3	148928087	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	14007675	148928087	49094343	47	23372										
LEKR1	389170	hgsc.bcm.edu	37	chr3	156763176	156763176	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agagaatgtgaagaacgcttTgaactgacagaggctttgag	13	5	0	7			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:156763176T>C	ENST00000470811.1	+	14	2139	c.804T>C	c.(802-804)ttT>ttC	p.F268F	LEKR1_ENST00000356539.4_Silent_p.F572F			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	268										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AAGAACGCTTTGAACTGACAG	0.448																																																0			3											92	94	93					3																	156763176		2203	4300	6503	158245870	SO:0001819	synonymous_variant	389170			AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.804T>C	3.37:g.156763176T>C			158245870		Silent	SNP	ENST00000470811.1	37																																																																																					0.448	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		C	156763176	T	C	156763176	2	2	81	1	0	0	0	0	0	0	0	1	8739	1809	63	4		4	LEKR1	3	156763176	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	7835089	156763176	41259254	48	23373										
ZBBX	79740	hgsc.bcm.edu	37	chr3	167023480	167023480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	caaagcttggcctcttatacAgattgctcaattccaaggat	7	10	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:167023480A>T	ENST00000392766.2	-	17	2016	c.1676T>A	c.(1675-1677)cTg>cAg	p.L559Q	ZBBX_ENST00000392764.1_Missense_Mutation_p.L530Q|ZBBX_ENST00000307529.5_Missense_Mutation_p.L559Q|ZBBX_ENST00000455345.2_Missense_Mutation_p.L559Q|ZBBX_ENST00000392767.2_Missense_Mutation_p.L559Q	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	559						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CCTCTTATACAGATTGCTCAA	0.318																																																0			3											74	65	68					3																	167023480		1801	4065	5866	168506174	SO:0001583	missense	79740			AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1676T>A	3.37:g.167023480A>T	ENSP00000376519:p.Leu559Gln		168506174	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	A	8.092	0.774661	0.16051	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.11169	2.97;2.97;2.98;2.98;2.8	5.3	4.11	0.48088	.	0.635593	0.14755	N	0.300368	T	0.07143	0.0181	N	0.24115	0.695	0.09310	N	1	P;P	0.46912	0.886;0.819	B;B	0.38562	0.276;0.142	T	0.25813	-1.0121	10	0.37606	T	0.19	0.7106	8.3737	0.32430	0.8184:0.0:0.0:0.1816	.	559;559	A8MT70-2;A8MT70	.;ZBBX_HUMAN	Q	559;559;559;559;530	ENSP00000376519:L559Q;ENSP00000376520:L559Q;ENSP00000390232:L559Q;ENSP00000305065:L559Q;ENSP00000376517:L530Q	ENSP00000305065:L559Q	L	-	2	0	ZBBX	168506174	0.210000	0.23517	0.002000	0.10522	0.009000	0.06853	1.831000	0.39141	0.922000	0.37019	0.528000	0.53228	CTG		0.318	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		T	167023480	A	T	167023480	3	4	81	1	0	0	0	0	1	0	0	0	17556	188	7	5	746	5	ZBBX	3	167023480	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	10260304	167023480	30998950	49	23374										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atcctctctctgaaatcactGagcaggagaaagattttcta	7	9	4	4	rs104886003		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)	3											61	60	60					3																	178936091		1813	4072	5885	180418785	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys		180418785	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936091	G	A	178936091	3	1	81	1	0	0	0	0	1	0	0	0	11944	1291	45	3	1667	3	PIK3CA	3	178936091	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	11912611	178936091	19086339	50	23375										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229578	8229578	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctggctgacatctacagccgCaagtgcctgccccacctggt	10	16	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:8229578C>T	ENST00000245105.3	+	12	2224	c.2157C>T	c.(2155-2157)cgC>cgT	p.R719R	SH3TC1_ENST00000539824.1_Silent_p.R643R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	719			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.							NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TCTACAGCCGCAAGTGCCTGC	0.647																																					NSCLC(145;2298 2623 35616 37297)											0			4											55	55	55					4																	8229578		2203	4300	6503	8280478	SO:0001819	synonymous_variant	54436			AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2157C>T	4.37:g.8229578C>T			8280478	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																				0.647	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8229578	C	T	8229578	2	4	81	1	0	0	0	0	0	0	0	1	14298	697	25	3		3	SH3TC1	4	8229578	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10		8229578	182924698	51	23376										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13604875	13604875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gggttctttctccccagggtTcattttggacacagcacttt	9	11	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:13604875T>G	ENST00000040738.5	-	10	3784	c.3649A>C	c.(3649-3651)Aac>Cac	p.N1217H		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1217						nucleus (GO:0005634)	DNA binding (GO:0003677)										TCCCCAGGGTTCATTTTGGAC	0.403																																																0			4											159	164	162					4																	13604875		2203	4300	6503	13213973	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.3649A>C	4.37:g.13604875T>G	ENSP00000040738:p.Asn1217His		13213973	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	7.296	0.612115	0.14066	.	.	ENSG00000038219	ENST00000040738	T	0.07216	3.21	5.02	-1.6	0.08426	.	1.204370	0.05921	N	0.633493	T	0.08403	0.0209	L	0.27053	0.805	0.09310	N	1	P	0.50943	0.94	P	0.46975	0.533	T	0.36286	-0.9754	10	0.48119	T	0.1	-2.46	7.1259	0.25471	0.1252:0.4533:0.0:0.4215	.	1217	Q8NFC6	BOD1L_HUMAN	H	1217	ENSP00000040738:N1217H	ENSP00000040738:N1217H	N	-	1	0	BOD1L	13213973	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.274000	0.08537	-0.400000	0.07656	0.533000	0.62120	AAC		0.403	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13604875	T	G	13604875	3	3	81	1	0	0	0	0	1	0	0	0	1484	1783	62	4	5574	4	BOD1L	4	13604875	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	5375297	13604875	177549401	52	23377										
TXK	7294	hgsc.bcm.edu	37	chr4	48096116	48096116	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gctgcattgtgctggtgataCcagattaactcagggattga	12	7	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:48096116C>A	ENST00000264316.4	-	8	772	c.687G>T	c.(685-687)tgG>tgT	p.W229C	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	229	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						GCTGGTGATACCAGATTAACT	0.488																																																0			4											149	144	146					4																	48096116		2203	4300	6503	47790873	SO:0001583	missense	7294			L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"SH2 domain containing"	12434	protein-coding gene	gene with protein product		600058	"PTK4 protein tyrosine kinase 4"	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.687G>T	4.37:g.48096116C>A	ENSP00000264316:p.Trp229Cys		47790873	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193297	0.38707	.	.	ENSG00000074966	ENST00000264316	D	0.92397	-3.03	5.24	3.53	0.40419	SH2 motif (5);	0.801655	0.11137	N	0.595713	D	0.83613	0.5292	N	0.14661	0.345	0.80722	D	1	P	0.44521	0.837	B	0.38562	0.276	T	0.79027	-0.1971	10	0.72032	D	0.01	.	8.0366	0.30496	0.0:0.7516:0.0:0.2484	.	229	P42681	TXK_HUMAN	C	229	ENSP00000264316:W229C	ENSP00000264316:W229C	W	-	3	0	TXK	47790873	0.192000	0.23301	0.988000	0.46212	0.963000	0.63663	0.358000	0.20216	0.787000	0.33731	0.655000	0.94253	TGG		0.488	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		A	48096116	C	A	48096116	3	1	81	1	0	0	0	0	1	0	0	0	16826	508	18	2	928	2	TXK	4	48096116	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	34491241	48096116	143058160	53	23378										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69184445	69184445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctcggcgaactcctgaaaatCgtctgttgggaataagattt	10	8	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:69184445C>T	ENST00000344157.4	-	14	2059	c.1724G>A	c.(1723-1725)cGa>cAa	p.R575Q	YTHDC1_ENST00000579690.1_Missense_Mutation_p.R583Q|YTHDC1_ENST00000355665.3_Missense_Mutation_p.R557Q	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	575	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TCCTGAAAATCGTCTGTTGGG	0.343																																																0			4											60	62	61					4																	69184445		2203	4300	6503	68867040	SO:0001583	missense	91746			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1724G>A	4.37:g.69184445C>T	ENSP00000339245:p.Arg575Gln		68867040	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991219	0.74703	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.25579	1.81;1.79	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.40839	0.1133	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	0.988;1.0	P;D	0.67548	0.467;0.952	T	0.16778	-1.0391	10	0.52906	T	0.07	.	19.5102	0.95139	0.0:1.0:0.0:0.0	.	557;575	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	Q	575;557	ENSP00000339245:R575Q;ENSP00000347888:R557Q	ENSP00000339245:R575Q	R	-	2	0	YTHDC1	68867040	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.725000	0.74752	2.615000	0.88500	0.591000	0.81541	CGA		0.343	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		T	69184445	C	T	69184445	3	4	81	1	0	0	0	0	1	0	0	0	17536	884	31	1	475	1	YTHDC1	4	69184445	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	21088329	69184445	121969831	54	23379										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73179472	73179472	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aggagccaaatttagtccatGacccccaattgccatcttgt	7	12	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:73179472G>T	ENST00000286657.4	-	12	1703	c.1667C>A	c.(1666-1668)tCa>tAa	p.S556*		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	556	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTAGTCCATGACCCCCAATT	0.398																																					NSCLC(168;1941 2048 2918 13048 43078)											0			4											144	112	123					4																	73179472		2203	4300	6503	73398336	SO:0001587	stop_gained	9508			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1667C>A	4.37:g.73179472G>T	ENSP00000286657:p.Ser556*		73398336	A1L3U9|Q9BXZ8	Nonsense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	G	39	7.570756	0.98365	.	.	ENSG00000156140	ENST00000286657	.	.	.	6.02	5.17	0.71159	.	0.328330	0.28718	N	0.014367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2102	0.73219	0.0672:0.0:0.9328:0.0	.	.	.	.	X	556	.	ENSP00000286657:S556X	S	-	2	0	ADAMTS3	73398336	1.000000	0.71417	0.987000	0.45799	0.946000	0.59487	7.903000	0.87398	1.548000	0.49413	0.650000	0.86243	TCA		0.398	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73179472	G	T	73179472	4	4	81	1	0	0	0	0	0	1	0	0	267	1294	45	2	1994	2	ADAMTS3	4	73179472	Nonsense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	3995027	73179472	117974804	55	23380										
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80929682	80929682	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccttcttactcaccactttgCagcaaaggggccaaaaccac	6	15	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:80929682C>A	ENST00000307333.7	-	12	1036	c.1034G>T	c.(1033-1035)tGc>tTc	p.C345F	ANTXR2_ENST00000346652.6_Missense_Mutation_p.C242F|ANTXR2_ENST00000404191.1_Missense_Mutation_p.C268F|ANTXR2_ENST00000403729.2_Missense_Mutation_p.C345F	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	345					reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						CACCACTTTGCAGCAAAGGGG	0.388									Juvenile Hyaline Fibromatosis																																							0			4											101	94	96					4																	80929682		1894	4134	6028	81148706	SO:0001583	missense	118429	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.1034G>T	4.37:g.80929682C>A	ENSP00000306185:p.Cys345Phe		81148706	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Missense_Mutation	SNP	ENST00000307333.7	37	CCDS47086.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.819242	0.71028	.	.	ENSG00000163297	ENST00000403729;ENST00000404191;ENST00000346652;ENST00000307333	T;T;T;T	0.52526	2.18;0.66;2.02;2.18	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.70351	0.3214	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.97110	0.994;0.999;1.0	T	0.74765	-0.3554	10	0.87932	D	0	-12.0682	15.6282	0.76878	0.0:1.0:0.0:0.0	.	242;345;345	P58335-2;P58335;P58335-4	.;ANTR2_HUMAN;.	F	345;268;242;345	ENSP00000385575:C345F;ENSP00000384028:C268F;ENSP00000314883:C242F;ENSP00000306185:C345F	ENSP00000306185:C345F	C	-	2	0	ANTXR2	81148706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.521000	0.67086	2.552000	0.86080	0.591000	0.81541	TGC		0.388	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		A	80929682	C	A	80929682	3	1	81	1	0	0	0	0	1	0	0	0	712	710	25	2	498	2	ANTXR2	4	80929682	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	7750210	80929682	110224594	56	23381										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85678299	85678299	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tcgatctcccaccagcacttCtgcccacgttgaatcctaag	6	16	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:85678299C>T	ENST00000295888.4	-	33	5611	c.5204G>A	c.(5203-5205)aGa>aAa	p.R1735K	WDFY3_ENST00000322366.6_Missense_Mutation_p.R1735K	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1735					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		ACCAGCACTTCTGCCCACGTT	0.413																																																0			4											103	97	99					4																	85678299		2203	4300	6503	85897323	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.5204G>A	4.37:g.85678299C>T	ENSP00000295888:p.Arg1735Lys		85897323	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.517708	0.64634	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.63744	-0.06;-0.06	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.57110	0.2031	L	0.50333	1.59	0.80722	D	1	P	0.35527	0.507	B	0.28232	0.087	T	0.53906	-0.8372	10	0.28530	T	0.3	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	1735	Q8IZQ1	WDFY3_HUMAN	K	1735	ENSP00000318466:R1735K;ENSP00000295888:R1735K	ENSP00000295888:R1735K	R	-	2	0	WDFY3	85897323	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	AGA		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85678299	C	T	85678299	3	4	81	1	0	0	0	0	1	0	0	0	17310	913	32	3	5520	3	WDFY3	4	85678299	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	4748617	85678299	105475977	57	23382										
TACR3	6870	hgsc.bcm.edu	37	chr4	104511030	104511030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	catggactccattctggtcaCggtgtacatactgctttgcc	9	12	2	0	rs553885967		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:104511030C>T	ENST00000304883.2	-	5	1347	c.1207G>A	c.(1207-1209)Gtg>Atg	p.V403M	RP11-297P16.3_ENST00000512401.1_RNA|RP11-297P16.3_ENST00000502936.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	403					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.V403M(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		ATTCTGGTCACGGTGTACATA	0.498																																																1	Substitution - Missense(1)	prostate(1)	4											235	217	223					4																	104511030		2203	4300	6503	104730479	SO:0001583	missense	6870			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1207G>A	4.37:g.104511030C>T	ENSP00000303325:p.Val403Met		104730479	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491957	0.64074	.	.	ENSG00000169836	ENST00000304883	T	0.65732	-0.17	5.81	5.81	0.92471	.	0.070759	0.64402	D	0.000020	T	0.64427	0.2597	M	0.75447	2.3	0.46061	D	0.998848	D	0.53462	0.96	B	0.39465	0.3	T	0.71052	-0.4704	10	0.54805	T	0.06	.	19.0794	0.93175	0.0:1.0:0.0:0.0	.	403	P29371	NK3R_HUMAN	M	403	ENSP00000303325:V403M	ENSP00000303325:V403M	V	-	1	0	TACR3	104730479	0.958000	0.32768	0.981000	0.43875	0.972000	0.66771	1.867000	0.39499	2.746000	0.94184	0.591000	0.81541	GTG		0.498	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		T	104511030	C	T	104511030	3	4	81	1	0	0	0	0	1	0	0	0	15546	536	19	1	194	1	TACR3	4	104511030	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	18832731	104511030	86643246	58	23383										
RNF150	57484	hgsc.bcm.edu	37	chr4	142053630	142053630	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atccagttcttgccgcgggtCggggcggcgaacttggtgtt	16	10	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:142053630C>T	ENST00000515673.2	-	1	366	c.333G>A	c.(331-333)ccG>ccA	p.P111P	RNF150_ENST00000507500.1_Silent_p.P111P|RNF150_ENST00000306799.3_Silent_p.P111P|RNF150_ENST00000420921.2_Intron			Q9ULK6	RN150_HUMAN	ring finger protein 150	111	PA.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					TGCCGCGGGTCGGGGCGGCGA	0.667																																																0			4											35	31	32					4																	142053630		2202	4300	6502	142273080	SO:0001819	synonymous_variant	57484			AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.333G>A	4.37:g.142053630C>T			142273080	Q3T1D0|Q6ZNW6	Silent	SNP	ENST00000515673.2	37	CCDS34065.1																																																																																				0.667	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		T	142053630	C	T	142053630	2	4	81	1	0	0	0	0	0	0	0	1	13488	871	31	1		1	RNF150	4	142053630	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	37542600	142053630	49100646	59	23384										
OTUD4	54726	hgsc.bcm.edu	37	chr4	146072024	146072024	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gacactgtgttccagctttcTgggggaggtgccttgaggtt	15	8	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr4:146072024T>G	ENST00000447906.2	-	12	1189	c.1002A>C	c.(1000-1002)ccA>ccC	p.P334P	Y_RNA_ENST00000459374.1_RNA|OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Silent_p.P269P			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	334					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					TCCAGCTTTCTGGGGGAGGTG	0.408																																																0			4											65	62	63					4																	146072024		2203	4300	6503	146291474	SO:0001819	synonymous_variant	54726				CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"OTU domain containing"	24949	protein-coding gene	gene with protein product		611744	"OTU domain containing 4"			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.1002A>C	4.37:g.146072024T>G			146291474	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Silent	SNP	ENST00000447906.2	37																																																																																					0.408	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		G	146072024	T	G	146072024	2	3	81	1	0	0	0	0	0	0	0	1	11345	1567	55	4		4	OTUD4	4	146072024	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	4018394	146072024	45082252	60	23385										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	156287	156287	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gaggggggcaccgtcctggcGcggctgaggagagaagagct	20	9	0	3	rs6554830	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:156287G>A	ENST00000283426.6	+	8	1292	c.1242G>A	c.(1240-1242)gcG>gcA	p.A414A		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	414							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CCGTCCTGGCGCGGCTGAGGA	0.612													G|||	737	0.147165	0.3767	0.0951	5008	,	,		17550	0.0129		0.1233	False		,,,				2504	0.0368															0			5						G		1579,2827	492.9+/-362.5	290,999,914	61	57	59		1242	-7.3	0.1	5	dbSNP_116	59	1065,7535	224.5+/-260.9	61,943,3296	no	coding-synonymous	PLEKHG4B	NM_052909.3		351,1942,4210	AA,AG,GG		12.3837,35.8375,20.3291		414/1272	156287	2644,10362	2203	4300	6503	209287	SO:0001819	synonymous_variant	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1242G>A	5.37:g.156287G>A			209287		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																				0.612	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	156287	G	A	156287	2	1	81	1	0	0	0	0	0	0	0	1	12103	1074	38	1		1	PLEKHG4B	5	156287	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		156287	180758973	61	23386										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37226749	37226749	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atcttgtttgtatcttatatCccaataatggattgataaac	5	6	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:37226749C>G	ENST00000508244.1	-	11	2041	c.1948G>C	c.(1948-1950)Gat>Cat	p.D650H	C5orf42_ENST00000425232.2_Missense_Mutation_p.D650H|C5orf42_ENST00000274258.7_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	650						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TATCTTATATCCCAATAATGG	0.338																																																0			5											36	29	31					5																	37226749		692	1589	2281	37262506	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.1948G>C	5.37:g.37226749C>G	ENSP00000421690:p.Asp650His		37262506	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	16.96	3.264899	0.59431	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	D;D	0.98901	-5.22;-5.22	5.22	5.22	0.72569	.	0.077006	0.49916	U	0.000129	D	0.98466	0.9489	M	0.62723	1.935	0.80722	D	1	D	0.64830	0.994	P	0.56474	0.799	D	0.98956	1.0796	10	0.59425	D	0.04	-9.7011	15.3994	0.74827	0.0:0.8507:0.1493:0.0	.	650	E9PH94	.	H	650	ENSP00000421690:D650H;ENSP00000389014:D650H	ENSP00000389014:D650H	D	-	1	0	C5orf42	37262506	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	4.486000	0.60286	2.440000	0.82611	0.591000	0.81541	GAT		0.338	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37226749	C	G	37226749	3	3	81	1	0	0	0	0	1	0	0	0	2307	855	30	5	7809	5	C5orf42	5	37226749	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	37070462	37226749	143688511	62	23387										
RGS7BP	401190	hgsc.bcm.edu	37	chr5	63871662	63871662	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acatccagctgcagtgctgcTtagaaatgtataccacagag	9	10	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:63871662T>A	ENST00000334025.2	+	3	720	c.394T>A	c.(394-396)Tta>Ata	p.L132I	RNU6-294P_ENST00000364999.1_RNA|RGS7BP_ENST00000508162.1_3'UTR	NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	132					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		GCAGTGCTGCTTAGAAATGTA	0.428																																																0			5											107	104	105					5																	63871662		2203	4300	6503	63907418	SO:0001583	missense	401190			BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"regulator of G-protein signalling 7 binding protein"			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.394T>A	5.37:g.63871662T>A	ENSP00000334851:p.Leu132Ile		63907418	B7Z3X1	Missense_Mutation	SNP	ENST00000334025.2	37	CCDS34170.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.813298	0.90707	.	.	ENSG00000186479	ENST00000334025	T	0.56275	0.47	5.91	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	L	0.34521	1.04	0.52099	D	0.999941	D	0.67145	0.996	D	0.75484	0.986	T	0.60556	-0.7240	10	0.72032	D	0.01	-6.4395	8.4949	0.33121	0.0:0.1493:0.0:0.8507	.	132	Q6MZT1	R7BP_HUMAN	I	132	ENSP00000334851:L132I	ENSP00000334851:L132I	L	+	1	2	RGS7BP	63907418	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.290000	0.51755	1.072000	0.40860	0.533000	0.62120	TTA		0.428	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875		A	63871662	T	A	63871662	3	1	81	1	0	0	0	0	1	0	0	0	13348	1606	56	5	404	5	RGS7BP	5	63871662	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	26644913	63871662	117043598	63	23388										
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	81	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	48302969	112174631	68740629	64	23389			1	11		3	3	1050	N	C_A	1.976061e-05
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	81	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	1008	112175639	68739621	65	23390			1	11		3	3	1050	N	C_A	1.976061e-05
APC	324	hgsc.bcm.edu	37	chr5	112175680	112175680	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcacctactgctgaaaagagAgagagtggacctaagcaagc	12	9	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:112175680A>G	ENST00000457016.1	+	16	4769	c.4389A>G	c.(4387-4389)agA>agG	p.R1463R	APC_ENST00000257430.4_Silent_p.R1463R|APC_ENST00000508376.2_Silent_p.R1463R|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1463	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1464fs*8(17)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.K1462fs*5(1)|p.?(1)|p.R1463S(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGAAAAGAGAGAGAGTGGAC	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	22	Deletion - Frameshift(19)|Substitution - Missense(1)|Unknown(1)|Complex - frameshift(1)	large_intestine(18)|thyroid(1)|stomach(1)|soft_tissue(1)|skin(1)	5											85	80	82					5																	112175680		2202	4300	6502	112203579	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4389A>G	5.37:g.112175680A>G			112203579	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175680	A	G	112175680	2	3	81	1	0	0	0	0	0	0	0	1	763	301	11	4		4	APC	5	112175680	Silent	SNP	A	TCGA-AH-6544-01A-11D-1826-10	41	112175680	68739580	66	23391			1	11		3	3	1050	N	C_A	1.976061e-05
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140175635	140175635	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tcacttcccatctcagagaaCgcttccctgggcactgtcat	7	15	3	1	rs139541416		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:140175635C>T	ENST00000526136.1	+	1	1086	c.1086C>T	c.(1084-1086)aaC>aaT	p.N362N	PCDHA2_ENST00000378132.1_Silent_p.N362N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Silent_p.N362N|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	362	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCAGAGAACGCTTCCCTGG	0.483																																																0			5						C	,,,	1,4405	2.1+/-5.4	0,1,2202	95	80	85		,1086,,1086	0.8	0.2	5	dbSNP_134	85	0,8600		0,0,4300	no	intron,coding-synonymous,intron,coding-synonymous	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	,362/949,,362/825	140175635	1,13005	2203	4300	6503	140155819	SO:0001819	synonymous_variant	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1086C>T	5.37:g.140175635C>T			140155819	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																				0.483	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140175635	C	T	140175635	2	4	81	1	0	0	0	0	0	0	0	1	11555	535	19	1		1	PCDHA2	5	140175635	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	27999955	140175635	40739625	67	23392										
CSF1R	1436	hgsc.bcm.edu	37	chr5	149450119	149450119	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggcttcaggcggggcagagaGagggtgaaggtgtgcctgca	20	7	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:149450119G>A	ENST00000286301.3	-	8	1389	c.1098C>T	c.(1096-1098)ctC>ctT	p.L366L	CSF1R_ENST00000543093.1_Missense_Mutation_p.S302F	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	366	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.L366L(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GGGGCAGAGAGAGGGTGAAGG	0.592																																																1	Substitution - coding silent(1)	central_nervous_system(1)	5											24	24	24					5																	149450119		2157	4204	6361	149430312	SO:0001819	synonymous_variant	1436			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.1098C>T	5.37:g.149450119G>A			149430312	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996637	0.35226	.	.	ENSG00000182578	ENST00000543093	T	0.37235	1.21	5.58	3.65	0.41850	.	.	.	.	.	T	0.51329	0.1668	.	.	.	0.21220	N	0.999759	D	0.69078	0.997	D	0.64237	0.923	T	0.35351	-0.9792	8	0.37606	T	0.19	.	11.7524	0.51855	0.0:0.3437:0.6563:0.0	.	302	B5A955	.	F	302	ENSP00000445282:S302F	ENSP00000445282:S302F	S	-	2	0	CSF1R	149430312	0.833000	0.29383	0.429000	0.26710	0.865000	0.49528	0.977000	0.29475	1.325000	0.45301	0.561000	0.74099	TCT		0.592	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		A	149450119	G	A	149450119	2	1	81	1	0	0	0	0	0	0	0	1	3938	929	33	3		3	CSF1R	5	149450119	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	9274484	149450119	31465141	68	23393										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170343583	170343583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	taaaaaggatacttgaaaacCctcaggtatttatgaagtaa	7	5	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:170343583C>T	ENST00000523189.1	+	9	1113	c.949C>T	c.(949-951)Cct>Tct	p.P317S		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	317					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACTTGAAAACCCTCAGGTATT	0.328			T	TRD@	ALL																																		Dom	yes		5	5q34	64901	RAN binding protein 17		L	0			5											64	69	67					5																	170343583		2203	4298	6501	170276188	SO:0001583	missense	64901			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.949C>T	5.37:g.170343583C>T	ENSP00000427975:p.Pro317Ser		170276188	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	15.85|15.85	2.953869|2.953869	0.53293|0.53293	.|.	.|.	ENSG00000204764|ENSG00000204764	ENST00000522734|ENST00000523189;ENST00000545246	.|T	.|0.27890	.|1.64	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Armadillo-type fold (1);	0.000000|0.000000	0.64402|0.64402	D|D	0.000016|0.000016	T|T	0.27098|0.27098	0.0664|0.0664	L|L	0.45581|0.45581	1.43|1.43	0.58432|0.58432	D|D	0.999998|0.999998	.|P	.|0.42785	.|0.79	.|B	.|0.38327	.|0.271	T|T	0.05920|0.05920	-1.0856|-1.0856	6|10	.|0.07325	.|T	.|0.83	-16.3|-16.3	18.4493|18.4493	0.90697|0.90697	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|317	.|Q9H2T7	.|RBP17_HUMAN	L|S	99|317;213	.|ENSP00000427975:P317S	.|ENSP00000373770:P317S	P|P	+|+	2|1	0|0	RANBP17|RANBP17	170276188|170276188	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.509000|7.509000	0.81698|0.81698	2.663000|2.663000	0.90544|0.90544	0.655000|0.655000	0.94253|0.94253	CCC|CCT		0.328	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		T	170343583	C	T	170343583	3	4	81	1	0	0	0	0	1	0	0	0	13064	623	22	3	983	3	RANBP17	5	170343583	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	20893464	170343583	10571677	69	23394										
NOP16	51491	hgsc.bcm.edu	37	chr5	175811236	175811236	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgtgatgtaaaccagtcacTccacctccatcttcctcttc	4	16	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:175811236T>C	ENST00000389158.5	-	5	968	c.533A>G	c.(532-534)gAg>gGg	p.E178G	NOP16_ENST00000510123.1_Missense_Mutation_p.S148G|NOP16_ENST00000507413.1_Silent_p.G53G			Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein	178				E -> D (in Ref. 5; CAG33450). {ECO:0000305}.		intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	8						AACCAGTCACTCCACCTCCAT	0.537																																																0			5											124	125	125					5																	175811236		2007	4170	6177	175743842	SO:0001583	missense	51491				CCDS43403.1, CCDS58991.1	5q35.2	2012-12-10	2012-12-10		ENSG00000048162	ENSG00000048162			26934	protein-coding gene	gene with protein product	"hypothetical protein HSPC111", "HBV pre-S2 trans-regulated protein 3"	612861	"nucleolar protein 16 homolog (yeast)", "NOP16 nucleolar protein homolog (yeast)"			10810093, 11042152	Standard	NM_001291308		Approved	HSPC111, HSPC185, LOC51491	uc003mee.4	Q9Y3C1	OTTHUMG00000163186	ENST00000389158.5:c.533A>G	5.37:g.175811236T>C	ENSP00000373810:p.Glu178Gly		175743842	B4DV13|D6RGD3|Q05D05|Q6IAI6|Q8IXL5	Missense_Mutation	SNP	ENST00000389158.5	37	CCDS43403.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.956|9.956	1.221417|1.221417	0.22457|0.22457	.|.	.|.	ENSG00000048162|ENSG00000048162	ENST00000389158|ENST00000510123;ENST00000341213;ENST00000451293	.|.	.|.	.|.	5.35|5.35	1.6|1.6	0.23607|0.23607	.|.	.|0.727618	.|0.14101	.|N	.|0.341388	T|T	0.37839|0.37839	0.1018|0.1018	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999999|0.999999	B|P;P	0.02656|0.35745	0.0|0.518;0.518	B|B;B	0.04013|0.30401	0.001|0.115;0.115	T|T	0.15636|0.15636	-1.0430|-1.0430	7|9	.|0.66056	.|D	.|0.02	-1.017|-1.017	8.2334|8.2334	0.31612|0.31612	0.0:0.065:0.2522:0.6827|0.0:0.065:0.2522:0.6827	.|.	178|149;148	Q9Y3C1|Q6PIM0;D6RGD3	NOP16_HUMAN|.;.	G|G	178|148;153;149	.|.	.|ENSP00000340662:S153G	E|S	-|-	2|1	0|0	NOP16|NOP16	175743842|175743842	0.973000|0.973000	0.33851|0.33851	0.532000|0.532000	0.27989|0.27989	0.021000|0.021000	0.10359|0.10359	1.868000|1.868000	0.39509|0.39509	0.191000|0.191000	0.20236|0.20236	-0.996000|-0.996000	0.02517|0.02517	GAG|AGT		0.537	NOP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371963.1	NM_016391		C	175811236	T	C	175811236	3	2	81	1	0	0	0	0	1	0	0	0	10568	1551	54	4	6	4	NOP16	5	175811236	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	5467653	175811236	5104024	70	23395										
UNC5A	90249	hgsc.bcm.edu	37	chr5	176289776	176289776	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtgcccgccacgcagatcttCttcaagtgcaacggggagtg	13	12	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:176289776C>G	ENST00000329542.4	+	2	496	c.222C>G	c.(220-222)ttC>ttG	p.F74L	UNC5A_ENST00000261961.3_5'Flank	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	74	Ig-like.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	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)			CGCAGATCTTCTTCAAGTGCA	0.637																																																0			5											146	140	142					5																	176289776		2203	4300	6503	176222382	SO:0001583	missense	90249			AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.222C>G	5.37:g.176289776C>G	ENSP00000332737:p.Phe74Leu		176222382	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	37	CCDS34299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.9|20.9	4.063686|4.063686	0.76187|0.76187	.|.	.|.	ENSG00000113763|ENSG00000113763	ENST00000329542|ENST00000509580	T|.	0.21734|.	1.99|.	3.92|3.92	3.92|3.92	0.45320|0.45320	Immunoglobulin-like fold (1);|.	0.081796|.	0.51477|.	D|.	0.000087|.	T|T	0.58409|0.58409	0.2120|0.2120	L|L	0.38531|0.38531	1.155|1.155	0.80722|0.80722	D|D	1|1	B;P|.	0.35401|.	0.157;0.499|.	B;B|.	0.33620|.	0.129;0.167|.	T|T	0.56360|0.56360	-0.7992|-0.7992	10|5	0.87932|.	D|.	0|.	-34.2782|-34.2782	16.4942|16.4942	0.84223|0.84223	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	74;74|.	Q6ZN44;Q6ZN44-2|.	UNC5A_HUMAN;.|.	L|V	74|40	ENSP00000332737:F74L|.	ENSP00000332737:F74L|.	F|L	+|+	3|1	2|0	UNC5A|UNC5A	176222382|176222382	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.821000|5.821000	0.69257|0.69257	2.206000|2.206000	0.71126|0.71126	0.561000|0.561000	0.74099|0.74099	TTC|CTT		0.637	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		G	176289776	C	G	176289776	3	3	81	1	0	0	0	0	1	0	0	0	17031	912	32	5	228	5	UNC5A	5	176289776	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	478540	176289776	4625484	71	23396										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178505825	178505825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgaagaagctgtggaatttgAgagcgagatagaagaagagc	15	3	0	7			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr5:178505825A>G	ENST00000315475.6	+	5	698	c.392A>G	c.(391-393)gAg>gGg	p.E131G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GTGGAATTTGAGAGCGAGATA	0.378																																																0			5											88	94	92					5																	178505825		2203	4300	6503	178438431	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.392A>G	5.37:g.178505825A>G	ENSP00000324064:p.Glu131Gly		178438431	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	11.86	1.765119	0.31228	.	.	ENSG00000177932	ENST00000315475	T	0.05925	3.37	3.87	2.66	0.31614	.	.	.	.	.	T	0.04998	0.0134	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.38499	-0.9658	9	0.39692	T	0.17	-4.6231	7.2189	0.25975	0.7724:0.2276:0.0:0.0	.	131	Q86Y25	Z354C_HUMAN	G	131	ENSP00000324064:E131G	ENSP00000324064:E131G	E	+	2	0	ZNF354C	178438431	0.057000	0.20700	0.003000	0.11579	0.019000	0.09904	1.850000	0.39328	0.610000	0.30035	0.482000	0.46254	GAG		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178505825	A	G	178505825	3	3	81	1	0	0	0	0	1	0	0	0	17905	304	11	4	406	4	ZNF354C	5	178505825	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	2216049	178505825	2409435	72	23397										
HFE	3077	hgsc.bcm.edu	37	chr6	26091083	26091083	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctccaggttcacactctctgCactacctcttcatgggtgcc	7	16	4	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:26091083C>G	ENST00000357618.5	+	2	213	c.91C>G	c.(91-93)Cac>Gac	p.H31D	HFE_ENST00000461397.1_Missense_Mutation_p.H31D|HFE_ENST00000488199.1_Intron|HFE_ENST00000353147.5_Intron|HFE_ENST00000317896.7_Missense_Mutation_p.H31D|HFE_ENST00000336625.8_Missense_Mutation_p.H31D|HFE_ENST00000397022.3_Intron|HFE_ENST00000349999.4_Intron|HFE_ENST00000470149.1_Missense_Mutation_p.H31D|HFE_ENST00000309234.6_Missense_Mutation_p.H31D|HFE_ENST00000352392.4_Intron	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	31	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACACTCTCTGCACTACCTCTT	0.512									Hemochromatosis																																							0			6											180	164	169					6																	26091083		2203	4300	6503	26199062	SO:0001583	missense	3077	Familial Cancer Database			CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.91C>G	6.37:g.26091083C>G	ENSP00000417404:p.His31Asp		26199062	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026614	0.54683	.	.	ENSG00000010704	ENST00000317896;ENST00000535098;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000309234	T;T;T;T;T;T	0.00691	5.84;5.84;5.84;5.84;5.84;5.84	5.44	2.66	0.31614	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.744352	0.12311	N	0.480154	T	0.00496	0.0016	L	0.39245	1.2	0.09310	N	1	P;P;P;P;P	0.47962	0.903;0.531;0.531;0.801;0.834	P;B;B;B;P	0.48089	0.566;0.101;0.101;0.338;0.469	T	0.52540	-0.8562	10	0.87932	D	0	.	6.3854	0.21558	0.3227:0.5928:0.0:0.0844	.	31;31;31;31;31	Q6B0J5;Q30201-7;Q30201-10;Q30201-3;Q30201	.;.;.;.;HFE_HUMAN	D	31	ENSP00000313776:H31D;ENSP00000417404:H31D;ENSP00000419725:H31D;ENSP00000337819:H31D;ENSP00000420802:H31D;ENSP00000311698:H31D	ENSP00000311698:H31D	H	+	1	0	HFE	26199062	0.004000	0.15560	0.243000	0.24186	0.989000	0.77384	0.192000	0.17096	0.388000	0.25054	0.655000	0.94253	CAC		0.512	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1			G	26091083	C	G	26091083	3	3	81	1	0	0	0	0	1	0	0	0	7102	710	25	5	97	5	HFE	6	26091083	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10		26091083	145023984	73	23398										
OR2J2	26707	hgsc.bcm.edu	37	chr6	29141602	29141602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acacaccaatgtacttcttcCtttcaaacctctcatttctg	2	14	4	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:29141602C>A	ENST00000377167.2	+	1	292	c.190C>A	c.(190-192)Ctt>Att	p.L64I		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						GTACTTCTTCCTTTCAAACCT	0.488																																																0			6											159	150	153					6																	29141602		2031	4227	6258	29249581	SO:0001583	missense	26707				CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"GPCR / Class A : Olfactory receptors"	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.190C>A	6.37:g.29141602C>A	ENSP00000366372:p.Leu64Ile		29249581	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.759357	0.31137	.	.	ENSG00000204700	ENST00000377167	T	0.13778	2.56	2.3	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.25901	0.0631	M	0.87900	2.915	0.31825	N	0.625468	D	0.76494	0.999	D	0.83275	0.996	T	0.04509	-1.0946	9	0.87932	D	0	.	7.4684	0.27334	0.2581:0.7419:0.0:0.0	.	64	O76002	OR2J2_HUMAN	I	64	ENSP00000366372:L64I	ENSP00000366372:L64I	L	+	1	0	OR2J2	29249581	0.470000	0.25854	1.000000	0.80357	0.390000	0.30446	-0.050000	0.11904	1.265000	0.44215	0.205000	0.17691	CTT		0.488	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			A	29141602	C	A	29141602	3	1	81	1	0	0	0	0	1	0	0	0	11034	681	24	2	192	2	OR2J2	6	29141602	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	3050519	29141602	141973465	74	23399										
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429933	29429933	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gctgtctgccagcccctccaCtatgccaccatcatccaccc	5	21	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:29429933C>G	ENST00000377136.1	+	4	852	c.387C>G	c.(385-387)caC>caG	p.H129Q	OR2H1_ENST00000396792.2_Missense_Mutation_p.H129Q|OR2H1_ENST00000377132.1_Missense_Mutation_p.H129Q|OR2H1_ENST00000377133.1_Missense_Mutation_p.H129Q|OR2H1_ENST00000442615.1_Missense_Mutation_p.H129Q|OR2H1_ENST00000473369.1_3'UTR			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						AGCCCCTCCACTATGCCACCA	0.587																																																0			6											166	172	170					6																	29429933		1510	2708	4218	29537912	SO:0001583	missense	26716			AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.387C>G	6.37:g.29429933C>G	ENSP00000366340:p.His129Gln		29537912	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	C	6.689	0.495696	0.12762	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01152	5.26;5.26;5.26;5.26;5.26	2.92	1.02	0.19986	GPCR, rhodopsin-like superfamily (1);	0.201508	0.25601	N	0.029544	T	0.00552	0.0018	M	0.71581	2.175	0.24460	N	0.994442	B	0.24368	0.102	B	0.17433	0.018	T	0.46582	-0.9181	10	0.62326	D	0.03	.	3.9555	0.09388	0.17:0.5357:0.0:0.2943	.	129	Q9GZK4	OR2H1_HUMAN	Q	129	ENSP00000366340:H129Q;ENSP00000366337:H129Q;ENSP00000393254:H129Q;ENSP00000366336:H129Q;ENSP00000380010:H129Q	ENSP00000366336:H129Q	H	+	3	2	OR2H1	29537912	0.000000	0.05858	0.996000	0.52242	0.425000	0.31504	-1.958000	0.01519	0.200000	0.20447	-0.369000	0.07265	CAC		0.587	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			G	29429933	C	G	29429933	3	3	81	1	0	0	0	0	1	0	0	0	11032	564	20	5	389	5	OR2H1	6	29429933	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	288331	29429933	141685134	75	23400										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33171361	33171361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agcagtaggggcactggcagGcacagcctgtgcccttctca	13	13	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:33171361G>T	ENST00000374677.3	+	7	1554	c.1181G>T	c.(1180-1182)gGc>gTc	p.G394V	RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000463972.1_3'UTR|RXRB_ENST00000374685.4_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.G394V	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	394					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GCACTGGCAGGCACAGCCTGT	0.537																																																0			6											69	72	71					6																	33171361		2015	4169	6184	33279339	SO:0001583	missense	7922			AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1181G>T	6.37:g.33171361G>T	ENSP00000363809:p.Gly394Val		33279339	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	37	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128440	0.77549	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.75260	-0.92;-0.92	4.79	4.79	0.61399	.	0.117700	0.56097	D	0.000025	D	0.89969	0.6869	H	0.97390	3.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93052	0.6466	10	0.87932	D	0	-13.1473	15.3789	0.74637	0.0:0.0:1.0:0.0	.	375;394	B4DVK8;Q92504	.;S39A7_HUMAN	V	394;375;299;394	ENSP00000363807:G394V;ENSP00000363809:G394V	ENSP00000363807:G394V	G	+	2	0	SLC39A7	33279339	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.398000	0.79919	2.494000	0.84150	0.549000	0.68633	GGC		0.537	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		T	33171361	G	T	33171361	3	4	81	1	0	0	0	0	1	0	0	0	14660	1203	42	2	1207	2	SLC39A7	6	33171361	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	3741428	33171361	137943706	76	23401										
C6orf222	389384	hgsc.bcm.edu	37	chr6	36293094	36293094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgtccagcggaagctcctcTccaggttcctggctctctga	10	15	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:36293094T>C	ENST00000437635.2	-	6	1311	c.1134A>G	c.(1132-1134)ggA>ggG	p.G378G		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	378										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						GAAGCTCCTCTCCAGGTTCCT	0.567																																																0			6											62	66	65					6																	36293094		2203	4300	6503	36401072	SO:0001819	synonymous_variant	389384				CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.1134A>G	6.37:g.36293094T>C			36401072	B2RTY8	Silent	SNP	ENST00000437635.2	37	CCDS34439.1																																																																																				0.567	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		C	36293094	T	C	36293094	2	2	81	1	0	0	0	0	0	0	0	1	2362	1538	54	4		4	C6orf222	6	36293094	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	3121733	36293094	134821973	77	23402										
BAI3	577	hgsc.bcm.edu	37	chr6	70049302	70049302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgcggttctggccatgacagAtaaacgctccatattgtttc	9	10	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:70049302A>G	ENST00000370598.1	+	26	4186	c.3365A>G	c.(3364-3366)gAt>gGt	p.D1122G	BAI3_ENST00000546190.1_Missense_Mutation_p.D86G|BAI3_ENST00000238918.8_Missense_Mutation_p.D328G	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1122					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GCCATGACAGATAAACGCTCC	0.463																																																0			6											297	272	281					6																	70049302		2203	4300	6503	70106023	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3365A>G	6.37:g.70049302A>G	ENSP00000359630:p.Asp1122Gly		70106023	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	A	17.27	3.346845	0.61073	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.47177	0.85;0.85;0.85	5.74	5.74	0.90152	GPCR, family 2-like (1);	0.098091	0.64402	D	0.000003	T	0.52175	0.1718	L	0.39692	1.235	0.58432	D	0.999999	D;D;P	0.69078	0.997;0.997;0.846	D;D;P	0.83275	0.996;0.994;0.515	T	0.54159	-0.8335	10	0.48119	T	0.1	.	16.0356	0.80625	1.0:0.0:0.0:0.0	.	328;1122;1122	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	G	1122;328;86	ENSP00000359630:D1122G;ENSP00000238918:D328G;ENSP00000441821:D86G	ENSP00000238918:D328G	D	+	2	0	BAI3	70106023	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.187000	0.69744	0.528000	0.53228	GAT		0.463	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	70049302	A	G	70049302	3	3	81	1	0	0	0	0	1	0	0	0	1301	333	12	4	3459	4	BAI3	6	70049302	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	33756208	70049302	101065765	78	23403										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119324731	119324731	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tccactttgagcttctcttcTtctttcatggcagcaattgt	6	11	4	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:119324731T>C	ENST00000338891.7	-	8	2315	c.1872A>G	c.(1870-1872)gaA>gaG	p.E624E	FAM184A_ENST00000521531.1_Silent_p.E624E|FAM184A_ENST00000352896.5_Silent_p.E504E|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Silent_p.E504E	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	624						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GCTTCTCTTCTTCTTTCATGG	0.333																																																0			6											104	95	98					6																	119324731		1829	4089	5918	119366430	SO:0001819	synonymous_variant	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1872A>G	6.37:g.119324731T>C			119366430	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																				0.333	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119324731	T	C	119324731	2	2	81	1	0	0	0	0	0	0	0	1	5527	1606	56	4		4	FAM184A	6	119324731	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	49275429	119324731	51790336	79	23404										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136878914	136878914	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agtcaagtctgtttgtttcgAaagtcaatgatagccttcca	8	8	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:136878914A>C	ENST00000359015.4	-	30	4467	c.4107T>G	c.(4105-4107)ttT>ttG	p.F1369L	MAP3K5_ENST00000355845.4_Missense_Mutation_p.F616L	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1369					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTTTGTTTCGAAAGTCAATGA	0.408																																																0			6											141	123	129					6																	136878914		2203	4300	6503	136920607	SO:0001583	missense	4217			U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.4107T>G	6.37:g.136878914A>C	ENSP00000351908:p.Phe1369Leu		136920607	A6NIA0|B4DGB2|Q5THN3|Q99461	Missense_Mutation	SNP	ENST00000359015.4	37	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.803123	0.50315	.	.	ENSG00000197442	ENST00000359015;ENST00000355845	D;D	0.85773	-2.03;-2.03	5.46	1.7	0.24286	Sterile alpha motif/pointed domain (1);	0.246535	0.42548	D	0.000683	T	0.58666	0.2138	L	0.36672	1.1	0.33267	D	0.560454	B	0.20887	0.049	B	0.19148	0.024	T	0.30119	-0.9989	10	0.22109	T	0.4	.	8.1104	0.30911	0.6581:0.0:0.3419:0.0	.	1369	Q99683	M3K5_HUMAN	L	1369;616	ENSP00000351908:F1369L;ENSP00000348104:F616L	ENSP00000348104:F616L	F	-	3	2	MAP3K5	136920607	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	1.305000	0.33493	0.050000	0.15949	0.533000	0.62120	TTT		0.408	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			C	136878914	A	C	136878914	3	2	81	1	0	0	0	0	1	0	0	0	9283	243	9	4	21	4	MAP3K5	6	136878914	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	17554183	136878914	34236153	80	23405										
NUP43	348995	hgsc.bcm.edu	37	chr6	150063650	150063650	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggtgcactgctataggaaggActgccagggcctgtgtggta	16	8	0	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:150063650A>T	ENST00000340413.2	-	4	454	c.378T>A	c.(376-378)agT>agA	p.S126R	NUP43_ENST00000460354.2_Missense_Mutation_p.S126R|NUP43_ENST00000463048.3_5'Flank|NUP43_ENST00000367403.3_Missense_Mutation_p.S187R|NUP43_ENST00000367404.4_Missense_Mutation_p.S126R	NM_198887.1	NP_942590.1	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	126					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				breast(1)|large_intestine(2)|lung(8)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		TATAGGAAGGACTGCCAGGGC	0.468																																																0			6											178	159	165					6																	150063650		2203	4300	6503	150105343	SO:0001583	missense	348995			AF514997	CCDS5218.1	6q25.1	2013-01-10			ENSG00000120253	ENSG00000120253		"WD repeat domain containing"	21182	protein-coding gene	gene with protein product		608141				12196509	Standard	XM_005266961		Approved	bA350J20.1, FLJ13287	uc003qmz.3	Q8NFH3	OTTHUMG00000015795	ENST00000340413.2:c.378T>A	6.37:g.150063650A>T	ENSP00000342262:p.Ser126Arg		150105343	B4E2F0|Q9H8S0	Missense_Mutation	SNP	ENST00000340413.2	37	CCDS5218.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.677759	0.29783	.	.	ENSG00000120253	ENST00000340413;ENST00000460354;ENST00000367403;ENST00000367404;ENST00000543637	T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76	5.27	-3.17	0.05202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.329273	0.30118	N	0.010370	T	0.61974	0.2390	L	0.29908	0.895	0.32409	N	0.550904	D;B	0.65815	0.995;0.037	D;B	0.70487	0.969;0.064	T	0.64110	-0.6484	10	0.37606	T	0.19	-6.537	10.9275	0.47199	0.5013:0.0:0.4987:0.0	.	126;126	B4E2F0;Q8NFH3	.;NUP43_HUMAN	R	126;126;187;126;133	ENSP00000342262:S126R;ENSP00000432401:S126R;ENSP00000356373:S187R;ENSP00000356374:S126R;ENSP00000438031:S133R	ENSP00000342262:S126R	S	-	3	2	NUP43	150105343	0.479000	0.25925	0.973000	0.42090	0.993000	0.82548	-0.411000	0.07142	-0.502000	0.06596	0.533000	0.62120	AGT		0.468	NUP43-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396947.1	NM_198887		T	150063650	A	T	150063650	3	4	81	1	0	0	0	0	1	0	0	0	10796	272	10	5	784	5	NUP43	6	150063650	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	13184736	150063650	21051417	81	23406										
LPA	4018	hgsc.bcm.edu	37	chr6	161006215	161006215	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cctcggtagcagtcctggacCccagtgctgttttcagttgg	12	12	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr6:161006215C>A	ENST00000316300.5	-	26	4196	c.4152G>T	c.(4150-4152)ggG>ggT	p.G1384G	LPA_ENST00000447678.1_Silent_p.G1384G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3892	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	AGTCCTGGACCCCAGTGCTGT	0.443																																																0			6											159	162	161					6																	161006215		2178	4296	6474	160926205	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4152G>T	6.37:g.161006215C>A			160926205	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	161006215	C	A	161006215	2	1	81	1	0	0	0	0	0	0	0	1	8932	610	22	2		2	LPA	6	161006215	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	10942565	161006215	10108852	82	23407										
HECW1	23072	hgsc.bcm.edu	37	chr7	43485148	43485148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtctggaatcccccgtggcaGgtccaagcaatcggagagaa	13	11	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:43485148G>A	ENST00000395891.2	+	11	2982	c.2377G>A	c.(2377-2379)Ggt>Agt	p.G793S	HECW1_ENST00000453890.1_Missense_Mutation_p.G793S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	793					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CCCCGTGGCAGGTCCAAGCAA	0.577																																																0			7											9	10	10					7																	43485148		1790	3897	5687	43451673	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2377G>A	7.37:g.43485148G>A	ENSP00000379228:p.Gly793Ser		43451673	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811754	0.32053	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.33865	1.39;1.46	5.33	4.43	0.53597	.	0.265451	0.43110	D	0.000610	T	0.32615	0.0835	L	0.36672	1.1	0.52099	D	0.999945	P;P	0.48911	0.751;0.917	B;B	0.44108	0.245;0.441	T	0.03221	-1.1059	10	0.27785	T	0.31	.	15.2222	0.73320	0.0:0.0:0.8583:0.1417	.	793;793	B4DH42;Q76N89	.;HECW1_HUMAN	S	793	ENSP00000379228:G793S;ENSP00000407774:G793S	ENSP00000265522:G793S	G	+	1	0	HECW1	43451673	1.000000	0.71417	0.657000	0.29651	0.378000	0.30076	7.472000	0.80996	1.201000	0.43203	0.655000	0.94253	GGT		0.577	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43485148	G	A	43485148	3	1	81	1	0	0	0	0	1	0	0	0	7063	1000	35	3	2411	3	HECW1	7	43485148	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10		43485148	115653515	83	23408										
COBL	23242	hgsc.bcm.edu	37	chr7	51095859	51095859	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tccctctgggaagactgaacCagtgagaaacaggagcttct	11	10	2	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:51095859C>T	ENST00000265136.7	-	10	3099	c.2934G>A	c.(2932-2934)ctG>ctA	p.L978L	COBL_ENST00000395542.2_Silent_p.L1060L	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	978					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					AAGACTGAACCAGTGAGAAAC	0.557																																					NSCLC(189;2119 2138 12223 30818 34679)											0			7											73	68	70					7																	51095859		2203	4300	6503	51063353	SO:0001819	synonymous_variant	23242			AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.2934G>A	7.37:g.51095859C>T			51063353	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1																																																																																				0.557	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51095859	C	T	51095859	2	4	81	1	0	0	0	0	0	0	0	1	3659	581	21	3		3	COBL	7	51095859	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	7610711	51095859	108042804	84	23409										
SGCE	8910	hgsc.bcm.edu	37	chr7	94248263	94248263	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttctgcttgatatggcaacgGgaagtctaattttggtgaaa	11	5	2	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:94248263G>A	ENST00000265735.7	-	5	579	c.469C>T	c.(469-471)Ccg>Tcg	p.P157S	SGCE_ENST00000415788.2_Missense_Mutation_p.P193S|SGCE_ENST00000437425.2_Missense_Mutation_p.P116S|SGCE_ENST00000428696.2_Missense_Mutation_p.P157S|SGCE_ENST00000447873.1_Missense_Mutation_p.P157S|SGCE_ENST00000445866.2_Missense_Mutation_p.P157S	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	157					cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	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)			TATGGCAACGGGAAGTCTAAT	0.353																																																0			7											82	75	78					7																	94248263		2203	4300	6503	94086199	SO:0001583	missense	8910			AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.469C>T	7.37:g.94248263G>A	ENSP00000265735:p.Pro157Ser		94086199	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Missense_Mutation	SNP	ENST00000265735.7	37	CCDS5637.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392848	0.42410	.	.	ENSG00000127990	ENST00000265735;ENST00000445866;ENST00000437425;ENST00000447873;ENST00000428696;ENST00000415788	D;D;D;D;D;D	0.98280	-4.45;-4.46;-4.84;-4.46;-4.46;-4.46	5.54	5.54	0.83059	Dystroglycan-type cadherin-like (1);	0.047393	0.85682	D	0.000000	D	0.98169	0.9395	L	0.38531	1.155	0.80722	D	1	D;P;B;B;D	0.89917	1.0;0.904;0.256;0.34;0.999	D;P;B;B;D	0.97110	1.0;0.659;0.262;0.113;0.996	D	0.97615	1.0132	10	0.27785	T	0.31	-9.3439	19.8647	0.96799	0.0:0.0:1.0:0.0	.	193;116;157;157;157	B7Z2R4;E9PEH6;E9PF60;G5E9K6;O43556	.;.;.;.;SGCE_HUMAN	S	157;157;116;157;157;193	ENSP00000265735:P157S;ENSP00000398930:P157S;ENSP00000394061:P116S;ENSP00000388734:P157S;ENSP00000397536:P157S;ENSP00000405313:P193S	ENSP00000265735:P157S	P	-	1	0	SGCE	94086199	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.004000	0.88535	2.775000	0.95449	0.655000	0.94253	CCG		0.353	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			A	94248263	G	A	94248263	3	1	81	1	0	0	0	0	1	0	0	0	14239	1232	43	3	1024	3	SGCE	7	94248263	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	43152404	94248263	64890400	85	23410										
ARMC10	83787	hgsc.bcm.edu	37	chr7	102738780	102738780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cctttccctttatgacagccAcgtagcaaaggagattcttc	7	12	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:102738780A>G	ENST00000323716.3	+	7	1204	c.812A>G	c.(811-813)cAc>cGc	p.H271R	ARMC10_ENST00000441711.2_Missense_Mutation_p.H236R|ARMC10_ENST00000425331.1_Missense_Mutation_p.H212R|ARMC10_ENST00000454559.1_Missense_Mutation_p.H177R|ARMC10_ENST00000541300.1_Missense_Mutation_p.H153R|ARMC10_ENST00000428183.2_Missense_Mutation_p.H212R	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	271					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						TATGACAGCCACGTAGCAAAG	0.323																																																0			7											38	36	36					7																	102738780		2202	4299	6501	102526016	SO:0001583	missense	83787			AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.812A>G	7.37:g.102738780A>G	ENSP00000319412:p.His271Arg		102526016	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	37	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	A	3.914	-0.019585	0.07634	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153;ENST00000431642	T;T;T;T;T;T;T;T	0.48522	1.59;1.59;1.59;1.59;1.59;1.59;0.81;1.59	5.42	1.6	0.23607	Armadillo-like helical (1);Armadillo-type fold (1);	0.536654	0.21849	N	0.068201	T	0.32071	0.0817	L	0.46157	1.445	0.09310	N	1	B;B;B;B;B;B;B	0.21381	0.001;0.004;0.007;0.055;0.004;0.002;0.002	B;B;B;B;B;B;B	0.24974	0.006;0.006;0.009;0.057;0.017;0.006;0.009	T	0.17837	-1.0356	10	0.11182	T	0.66	-9.4756	3.9723	0.09458	0.5197:0.1762:0.3041:0.0	.	212;153;177;199;212;236;271	B4DWJ8;F5GX65;Q8N2F6-4;C9J5N7;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;.;ARM10_HUMAN	R	271;212;236;177;212;153;199;113	ENSP00000319412:H271R;ENSP00000396654:H212R;ENSP00000413619:H236R;ENSP00000405612:H177R;ENSP00000397969:H212R;ENSP00000440463:H153R;ENSP00000398201:H199R;ENSP00000406840:H113R	ENSP00000319412:H271R	H	+	2	0	ARMC10	102526016	0.056000	0.20664	0.113000	0.21522	0.871000	0.50021	0.669000	0.25142	0.399000	0.25367	0.482000	0.46254	CAC		0.323	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		G	102738780	A	G	102738780	3	3	81	1	0	0	0	0	1	0	0	0	951	159	6	4	838	4	ARMC10	7	102738780	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	8490517	102738780	56399883	86	23411										
FEZF1	389549	hgsc.bcm.edu	37	chr7	121942355	121942355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggaaagccttgttgcagataTtgcacttgaactgcttctcc	9	10	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:121942355T>C	ENST00000442488.2	-	4	1191	c.1124A>G	c.(1123-1125)aAt>aGt	p.N375S	FEZF1-AS1_ENST00000428449.1_RNA|FEZF1_ENST00000331178.4_Missense_Mutation_p.N371S|FEZF1-AS1_ENST00000437317.1_RNA|FEZF1_ENST00000427185.2_Missense_Mutation_p.N325S	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	375					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						GTTGCAGATATTGCACTTGAA	0.468																																																0			7											164	139	147					7																	121942355		2203	4300	6503	121729591	SO:0001583	missense	389549			AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"Zinc fingers, C2H2-type"	22788	protein-coding gene	gene with protein product		613301	"zinc finger protein 312B"	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.1124A>G	7.37:g.121942355T>C	ENSP00000411145:p.Asn375Ser		121729591	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	T	9.482	1.098428	0.20552	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.07216	3.21;3.21;3.21	5.4	4.24	0.50183	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.100263	0.64402	D	0.000003	T	0.05640	0.0148	N	0.17379	0.485	0.39856	D	0.973317	B;B	0.30326	0.276;0.234	B;B	0.32393	0.145;0.09	T	0.44802	-0.9304	10	0.15952	T	0.53	-17.5714	11.377	0.49735	0.0:0.0707:0.0:0.9293	.	375;325	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	S	375;371;325	ENSP00000411145:N375S;ENSP00000332777:N371S;ENSP00000392727:N325S	ENSP00000332777:N371S	N	-	2	0	FEZF1	121729591	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.470000	0.53100	1.062000	0.40625	0.459000	0.35465	AAT		0.468	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613		C	121942355	T	C	121942355	3	2	81	1	0	0	0	0	1	0	0	0	5844	1493	52	4	307	4	FEZF1	7	121942355	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	19203575	121942355	37196308	87	23412										
GPR37	2861	hgsc.bcm.edu	37	chr7	124387044	124387044	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcagtcactagagagcaggtGatggtgaaaagcgtgggcaa	16	6	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:124387044G>T	ENST00000303921.2	-	2	2027	c.1377C>A	c.(1375-1377)atC>atA	p.I459I		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	459					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GAGAGCAGGTGATGGTGAAAA	0.473																																																0			7											137	120	126					7																	124387044		2203	4300	6503	124174280	SO:0001819	synonymous_variant	2861				CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1377C>A	7.37:g.124387044G>T			124174280	A4D0Y6|O00348|O14768|Q8TD39	Silent	SNP	ENST00000303921.2	37	CCDS5792.1																																																																																				0.473	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		T	124387044	G	T	124387044	2	4	81	1	0	0	0	0	0	0	0	1	6711	1280	45	2		2	GPR37	7	124387044	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	2444689	124387044	34751619	88	23413										
FLNC	2318	hgsc.bcm.edu	37	chr7	128484813	128484813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acaggtggcctggggctgacCgtagagggcccctgcgaggc	18	12	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:128484813C>T	ENST00000325888.8	+	21	3555	c.3294C>T	c.(3292-3294)acC>acT	p.T1098T	FLNC_ENST00000346177.6_Silent_p.T1098T	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1098					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TGGGGCTGACCGTAGAGGGCC	0.637																																																0			7											54	64	61					7																	128484813		2059	4213	6272	128272049	SO:0001819	synonymous_variant	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3294C>T	7.37:g.128484813C>T			128272049	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																				0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128484813	C	T	128484813	2	4	81	1	0	0	0	0	0	0	0	1	5954	639	23	1		1	FLNC	7	128484813	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	4097769	128484813	30653850	89	23414										
KEL	3792	hgsc.bcm.edu	37	chr7	142641482	142641482	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cccatctccacctgcagttgAgcaacctggagagagacaca	9	14	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:142641482A>G	ENST00000355265.2	-	13	1893	c.1419T>C	c.(1417-1419)gcT>gcC	p.A473A	KEL_ENST00000479768.2_5'Flank	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	473					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CCTGCAGTTGAGCAACCTGGA	0.537																																																0			7											73	75	75					7																	142641482		2203	4300	6503	142351604	SO:0001819	synonymous_variant	3792			BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1419T>C	7.37:g.142641482A>G			142351604	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																				0.537	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		G	142641482	A	G	142641482	2	3	81	1	0	0	0	0	0	0	0	1	8163	291	11	4		4	KEL	7	142641482	Silent	SNP	A	TCGA-AH-6544-01A-11D-1826-10	14156669	142641482	16497181	90	23415										
EZH2	2146	hgsc.bcm.edu	37	chr7	148515175	148515175	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtggggtctttatccgctcaGcggtgagagcagcagcaaac	14	10	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr7:148515175G>T	ENST00000460911.1	-	10	1107	c.1019C>A	c.(1018-1020)gCt>gAt	p.A340D	RNU7-20P_ENST00000515903.1_RNA|EZH2_ENST00000483967.1_Missense_Mutation_p.A331D|EZH2_ENST00000476773.1_Missense_Mutation_p.A331D|EZH2_ENST00000541220.1_Missense_Mutation_p.A331D|EZH2_ENST00000320356.2_Missense_Mutation_p.A345D|EZH2_ENST00000536783.1_3'UTR|EZH2_ENST00000350995.2_Missense_Mutation_p.A301D|EZH2_ENST00000478654.1_Missense_Mutation_p.A331D			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	340	Interaction with CDYL.|Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TATCCGCTCAGCGGTGAGAGC	0.493			Mis		DLBCL																																		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	0			7											114	112	112					7																	148515175		2203	4300	6503	148146108	SO:0001583	missense	2146				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1019C>A	7.37:g.148515175G>T	ENSP00000419711:p.Ala340Asp		148146108	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	g	18.77	3.695261	0.68386	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	5.78	5.78	0.91487	.	0.057124	0.64402	D	0.000001	T	0.73179	0.3554	N	0.19112	0.55	0.80722	D	1	D;B;B;B;B;P	0.55800	0.973;0.216;0.216;0.418;0.002;0.73	P;B;B;B;B;P	0.47346	0.544;0.079;0.055;0.145;0.006;0.452	T	0.72940	-0.4139	10	0.33141	T	0.24	.	14.8087	0.69977	0.0:0.0:0.856:0.144	.	340;331;331;340;301;345	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	D	331;345;340;301;331;331;331	ENSP00000417062:A331D;ENSP00000320147:A345D;ENSP00000419711:A340D;ENSP00000223193:A301D;ENSP00000443219:A331D;ENSP00000419050:A331D;ENSP00000419856:A331D	ENSP00000320147:A345D	A	-	2	0	EZH2	148146108	1.000000	0.71417	0.962000	0.40283	0.974000	0.67602	6.892000	0.75644	2.724000	0.93272	0.563000	0.77884	GCT		0.493	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		T	148515175	G	T	148515175	3	4	81	1	0	0	0	0	1	0	0	0	5347	971	34	2	1265	2	EZH2	7	148515175	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	5873693	148515175	10623488	91	23416										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2092607	2092607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gaccttgaatctgacctgcaCggtgtttggaaaccctgacc	10	12	1	3	rs368659851		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:2092607C>T	ENST00000262113.4	+	37	4241	c.4100C>T	c.(4099-4101)aCg>aTg	p.T1367M	MYOM2_ENST00000523438.1_Missense_Mutation_p.T792M|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1367	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTGACCTGCACGGTGTTTGGA	0.542																																																0			8						C	MET/THR	0,4406		0,0,2203	91	92	92		4100	5.2	1	8		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYOM2	NM_003970.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1367/1466	2092607	1,13005	2203	4300	6503	2080014	SO:0001583	missense	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.4100C>T	8.37:g.2092607C>T	ENSP00000262113:p.Thr1367Met		2080014	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.238146	0.58886	0.0	1.16E-4	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.69561	-0.41;-0.41	5.24	5.24	0.73138	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81297	0.4793	M	0.70842	2.15	0.46437	D	0.999043	D	0.89917	1.0	D	0.69654	0.965	T	0.82610	-0.0372	10	0.62326	D	0.03	.	19.1927	0.93674	0.0:1.0:0.0:0.0	.	1367	P54296	MYOM2_HUMAN	M	1367;792	ENSP00000262113:T1367M;ENSP00000428396:T792M	ENSP00000262113:T1367M	T	+	2	0	MYOM2	2080014	0.986000	0.35501	0.984000	0.44739	0.794000	0.44872	2.712000	0.47186	2.584000	0.87258	0.655000	0.94253	ACG		0.542	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2092607	C	T	2092607	3	4	81	1	0	0	0	0	1	0	0	0	10122	536	19	1	4242	1	MYOM2	8	2092607	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10		2092607	144271415	92	23417										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3205602	3205602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tttctattttatagatacacTcatggttattatcataattg	4	5	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:3205602T>C	ENST00000520002.1	-	23	3944	c.3389A>G	c.(3388-3390)gAg>gGg	p.E1130G	CSMD1_ENST00000602723.1_Missense_Mutation_p.E1130G|CSMD1_ENST00000542608.1_Missense_Mutation_p.E1129G|CSMD1_ENST00000602557.1_Missense_Mutation_p.E1130G|CSMD1_ENST00000400186.3_Missense_Mutation_p.E1130G|CSMD1_ENST00000539096.1_Missense_Mutation_p.E1129G|CSMD1_ENST00000537824.1_Missense_Mutation_p.E1129G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1130	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				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)		ATAGATACACTCATGGTTATT	0.383																																																0			8											78	71	73					8																	3205602		1814	4066	5880	3193009	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3389A>G	8.37:g.3205602T>C	ENSP00000430733:p.Glu1130Gly		3193009	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.40|18.40	3.615781|3.615781	0.66672|0.66672	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.19669|.	2.13;2.13;2.13;2.13;2.13|.	5.64|5.64	5.64|5.64	0.86602|0.86602	CUB (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86264|.	0.5891|.	M|M	0.94101|0.94101	3.495|3.495	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;1.0|.	D;D;D|.	0.97110|.	0.996;1.0;0.999|.	D|.	0.89961|.	0.4086|.	10|.	0.49607|.	T|.	0.09|.	.|.	15.8625|15.8625	0.79035|0.79035	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1130;1130;1130|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	G|W	1130;1130;992;1129;1129;1129|609	ENSP00000383047:E1130G;ENSP00000430733:E1130G;ENSP00000441462:E1129G;ENSP00000446243:E1129G;ENSP00000441675:E1129G|.	ENSP00000320445:E992G|.	E|X	-|-	2|3	0|0	CSMD1|CSMD1	3193009|3193009	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.184000|0.184000	0.23303|0.23303	7.852000|7.852000	0.86927|0.86927	2.135000|2.135000	0.66039|0.66039	0.528000|0.528000	0.53228|0.53228	GAG|TGA		0.383	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	3205602	T	C	3205602	3	2	81	1	0	0	0	0	1	0	0	0	3950	1551	54	4	7504	4	CSMD1	8	3205602	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	1112995	3205602	143158420	93	23418										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470559	10470559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggtcttccccactggctgccGtgagggcgctggccctgccc	14	17	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:10470559G>A	ENST00000382483.3	-	4	1272	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	350					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.T350K(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ACTGGCTGCCGTGAGGGCGCT	0.672																																																1	Substitution - Missense(1)	lung(1)	8											52	57	55					8																	10470559		2069	4204	6273	10507969	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1049C>T	8.37:g.10470559G>A	ENSP00000371923:p.Thr350Met		10507969	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.343992	0.41498	.	.	ENSG00000183638	ENST00000382483	T	0.04706	3.57	4.01	1.97	0.26223	.	.	.	.	.	T	0.13243	0.0321	L	0.50333	1.59	0.09310	N	1	D	0.76494	0.999	D	0.67231	0.95	T	0.08146	-1.0736	9	0.72032	D	0.01	-0.6656	8.949	0.35776	0.0975:0.2572:0.6453:0.0	.	350	A6NKC6	.	M	350	ENSP00000371923:T350M	ENSP00000371923:T350M	T	-	2	0	RP1L1	10507969	0.022000	0.18835	0.010000	0.14722	0.010000	0.07245	2.457000	0.45005	0.655000	0.30866	0.313000	0.20887	ACG		0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10470559	G	A	10470559	3	1	81	1	0	0	0	0	1	0	0	0	13570	1145	40	1	6157	1	RP1L1	8	10470559	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	7264957	10470559	135893463	94	23419										
DLC1	10395	hgsc.bcm.edu	37	chr8	12957209	12957209	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atggagcccggcacgttgtcGtagatgctcaggcggctgct	15	11	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:12957209G>A	ENST00000276297.4	-	9	3046	c.2637C>T	c.(2635-2637)taC>taT	p.Y879Y	DLC1_ENST00000520226.1_Silent_p.Y368Y|DLC1_ENST00000512044.2_Silent_p.Y476Y|DLC1_ENST00000358919.2_Silent_p.Y442Y	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	879	Focal adhesion-targeting (FAT).				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCACGTTGTCGTAGATGCTCA	0.587																																																0			8											60	52	55					8																	12957209		2203	4300	6503	13001580	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2637C>T	8.37:g.12957209G>A			13001580	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.587	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	12957209	G	A	12957209	2	1	81	1	0	0	0	0	0	0	0	1	4561	1140	40	1		1	DLC1	8	12957209	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	2486650	12957209	133406813	95	23420										
DLC1	10395	hgsc.bcm.edu	37	chr8	13259111	13259111	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gagtccagccgcgccctatcTcgatcttctcttatttcctg	7	15	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:13259111T>C	ENST00000276297.4	-	3	1450	c.1041A>G	c.(1039-1041)cgA>cgG	p.R347R	DLC1_ENST00000316609.5_Silent_p.R347R|DLC1_ENST00000511869.1_Silent_p.R347R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	347					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCGCCCTATCTCGATCTTCTC	0.438																																																0			8											132	118	123					8																	13259111		2203	4300	6503	13303482	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1041A>G	8.37:g.13259111T>C			13303482	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.438	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13259111	T	C	13259111	2	2	81	1	0	0	0	0	0	0	0	1	4561	1538	54	4		4	DLC1	8	13259111	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	301902	13259111	133104911	96	23421										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20110479	20110479	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgcgcgcgctggctcttctgCgaggcctgcttgagcttgtt	14	12	2	1	rs368337680		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:20110479C>T	ENST00000381569.1	-	3	1320	c.963G>A	c.(961-963)tcG>tcA	p.S321S	LZTS1_ENST00000265801.6_Silent_p.S321S|LZTS1_ENST00000522290.1_Silent_p.S321S			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	321					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GGCTCTTCTGCGAGGCCTGCT	0.682																																																0			8											26	27	27					8																	20110479		2202	4299	6501	20154759	SO:0001819	synonymous_variant	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.963G>A	8.37:g.20110479C>T			20154759	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																				0.682	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		T	20110479	C	T	20110479	2	4	81	1	0	0	0	0	0	0	0	1	9168	755	27	1		1	LZTS1	8	20110479	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	6851368	20110479	126253543	97	23422										
MCM4	4173	hgsc.bcm.edu	37	chr8	48882514	48882514	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acagaaacttttttcagagaAacgtgtggaattgcttaagg	10	5	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:48882514A>C	ENST00000262105.2	+	10	1540	c.1331A>C	c.(1330-1332)aAa>aCa	p.K444T	MCM4_ENST00000523944.1_Missense_Mutation_p.K444T|MCM4_ENST00000518680.1_3'UTR	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	444					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				TTTTCAGAGAAACGTGTGGAA	0.403																																																0			8											137	136	136					8																	48882514		2203	4300	6503	49045067	SO:0001583	missense	4173				CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1331A>C	8.37:g.48882514A>C	ENSP00000262105:p.Lys444Thr		49045067	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	A	18.49	3.634486	0.67130	.	.	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229;ENST00000520637	T;T;T	0.08634	4.08;4.08;3.07	6.17	6.17	0.99709	.	0.177959	0.64402	D	0.000014	T	0.06781	0.0173	N	0.08118	0	0.80722	D	1	B;B	0.20887	0.049;0.049	B;B	0.25759	0.063;0.063	T	0.37888	-0.9686	10	0.87932	D	0	-41.208	16.8222	0.85835	1.0:0.0:0.0:0.0	.	444;444	B3KMX0;P33991	.;MCM4_HUMAN	T	444;444;431;404;162	ENSP00000430194:K444T;ENSP00000262105:K444T;ENSP00000427875:K162T	ENSP00000262105:K444T	K	+	2	0	MCM4	49045067	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.930000	0.75858	2.371000	0.80710	0.533000	0.62120	AAA		0.403	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		C	48882514	A	C	48882514	3	2	81	1	0	0	0	0	1	0	0	0	9419	14	1	4	1369	4	MCM4	8	48882514	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	28772035	48882514	97481508	98	23423										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617275	77617275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agctcctcagtaataaatgcGtctccgccataatacagggg	9	11	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:77617275G>A	ENST00000521891.2	+	2	1400	c.952G>A	c.(952-954)Gtc>Atc	p.V318I	ZFHX4_ENST00000518282.1_Missense_Mutation_p.V318I|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Missense_Mutation_p.V318I|ZFHX4_ENST00000455469.2_Missense_Mutation_p.V318I	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TAATAAATGCGTCTCCGCCAT	0.418										HNSCC(33;0.089)																																						0			8											136	127	130					8																	77617275		1869	4112	5981	77779830	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.952G>A	8.37:g.77617275G>A	ENSP00000430497:p.Val318Ile		77779830	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	9.614	1.132100	0.21041	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.47528	0.84;0.88;0.85;0.85	5.53	3.75	0.43078	.	0.000000	0.40064	U	0.001193	T	0.22704	0.0548	N	0.04880	-0.145	0.58432	D	0.99999	B;B;B;B	0.28880	0.036;0.061;0.061;0.226	B;B;B;B	0.20577	0.005;0.017;0.011;0.03	T	0.05209	-1.0899	10	0.14252	T	0.57	.	11.6957	0.51542	0.1409:0.0:0.8591:0.0	.	318;318;318;318	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	I	318	ENSP00000430497:V318I;ENSP00000399605:V318I;ENSP00000050961:V318I;ENSP00000430848:V318I	ENSP00000050961:V318I	V	+	1	0	ZFHX4	77779830	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.755000	0.55197	0.899000	0.36444	0.655000	0.94253	GTC		0.418	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77617275	G	A	77617275	3	1	81	1	0	0	0	0	1	0	0	0	17674	1145	40	1	954	1	ZFHX4	8	77617275	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	28734761	77617275	68746747	99	23424										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88365961	88365961	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agttcctttcacgtgcacaaTcattaccaaaaaagaagttg	6	9	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:88365961T>G	ENST00000518476.1	+	10	1301	c.1250T>G	c.(1249-1251)aTc>aGc	p.I417S		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	417										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						ACGTGCACAATCATTACCAAA	0.343																																																0			8											88	87	88					8																	88365961		1846	4086	5932	88435077	SO:0001583	missense	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1250T>G	8.37:g.88365961T>G	ENSP00000430073:p.Ile417Ser		88435077		Missense_Mutation	SNP	ENST00000518476.1	37	CCDS55259.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.89|12.89	2.072484|2.072484	0.36566|0.36566	.|.	.|.	ENSG00000176571|ENSG00000176571	ENST00000518476|ENST00000523299;ENST00000521593	D|.	0.93859|.	-3.3|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);|.	0.627042|.	0.13631|.	N|.	0.373715|.	T|T	0.48021|0.48021	0.1477|0.1477	L|L	0.56769|0.56769	1.78|1.78	0.09310|0.09310	N|N	1|1	P|.	0.51537|.	0.946|.	P|.	0.60541|.	0.876|.	T|T	0.40059|0.40059	-0.9583|-0.9583	10|5	0.87932|.	D|.	0|.	-2.7604|-2.7604	11.1056|11.1056	0.48201|0.48201	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	417|.	Q8NA66|.	CNBD1_HUMAN|.	S|A	417|109;54	ENSP00000430073:I417S|.	ENSP00000430073:I417S|.	I|S	+|+	2|1	0|0	CNBD1|CNBD1	88435077|88435077	0.105000|0.105000	0.21958|0.21958	0.002000|0.002000	0.10522|0.10522	0.169000|0.169000	0.22640|0.22640	3.947000|3.947000	0.56652|0.56652	1.880000|1.880000	0.54463|0.54463	0.454000|0.454000	0.30748|0.30748	ATC|TCA		0.343	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		G	88365961	T	G	88365961	3	3	81	1	0	0	0	0	1	0	0	0	3597	1435	50	4	1288	4	CNBD1	8	88365961	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	10748686	88365961	57998061	100	23425										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106814831	106814831	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aaaagtgtttatctcagtctGagcggacgaccacgtctccc	9	12	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr8:106814831G>A	ENST00000407775.2	+	8	2771	c.2521G>A	c.(2521-2523)Gag>Aag	p.E841K	RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.E709K|ZFPM2_ENST00000378472.4_Missense_Mutation_p.E572K|ZFPM2_ENST00000520492.1_Missense_Mutation_p.E709K|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	841					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATCTCAGTCTGAGCGGACGAC	0.468																																																0			8											48	43	45					8																	106814831		1949	4169	6118	106884007	SO:0001583	missense	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2521G>A	8.37:g.106814831G>A	ENSP00000384179:p.Glu841Lys		106884007	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.965352	0.53507	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.20598	2.06;2.49;2.49;3.7	5.86	5.86	0.93980	.	0.047622	0.85682	D	0.000000	T	0.16385	0.0394	N	0.22421	0.69	0.80722	D	1	B	0.32245	0.361	B	0.22386	0.039	T	0.03184	-1.1063	10	0.35671	T	0.21	.	20.1802	0.98196	0.0:0.0:1.0:0.0	.	841	Q8WW38	FOG2_HUMAN	K	841;709;709;572	ENSP00000384179:E841K;ENSP00000430757:E709K;ENSP00000428720:E709K;ENSP00000367733:E572K	ENSP00000367733:E572K	E	+	1	0	ZFPM2	106884007	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.869000	0.99810	2.777000	0.95525	0.655000	0.94253	GAG		0.468	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106814831	G	A	106814831	3	1	81	1	0	0	0	0	1	0	0	0	17697	1291	45	3	2551	3	ZFPM2	8	106814831	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	18448870	106814831	39549191	101	23426										
WASH1	0	hgsc.bcm.edu	37	chr9	18075	18075	+	IGR	DEL	G	G	-													0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtgcttgctctggatcctgtGgcgggggcgtctctgcaggc							TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:18075delG								None (None upstream) : MIR1302-2 (9581 downstream)																							TGGATCCTGTGGCGGGGGCGT	0.662																																																0			9																																								8075	SO:0001628	intergenic_variant	375690																															9.37:g.18075delG			8075		Frame_Shift_Del	DEL		37																																																																																				0	0.662									-	18075	G	-	18075	6	5	81	0	1	1	0	1	0	0	0	0	17295	1348	47	0		0	WASH1	9	18075	IGR	DEL	G	TCGA-AH-6544-01A-11D-1826-10		18075	141195356	102	23427										
GLIPR2	152007	hgsc.bcm.edu	37	chr9	36148567	36148567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttctgaggccctggccagcaCgaggatcctcaagcacagcc	11	15	2	1	rs201812895		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:36148567C>T	ENST00000377960.4	+	3	180	c.146C>T	c.(145-147)aCg>aTg	p.T49M	GLIPR2_ENST00000396613.3_3'UTR|GLIPR2_ENST00000377959.1_Missense_Mutation_p.T49M|GLIPR2_ENST00000474050.1_3'UTR	NM_022343.2	NP_071738.1	Q9H4G4	GAPR1_HUMAN	GLI pathogenesis-related 2	49	SCP.				positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(3)	10						CTGGCCAGCACGAGGATCCTC	0.592													C|||	1	0.000199681	0	0	5008	,	,		17326	0		0.001	False		,,,				2504	0															0			9						C	MET/THR	0,4406		0,0,2203	99	83	88		146	5.6	1	9		88	1,8599	1.2+/-3.3	0,1,4299	no	missense	GLIPR2	NM_022343.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	49/155	36148567	1,13005	2203	4300	6503	36138567	SO:0001583	missense	152007			AY039756	CCDS6598.1, CCDS69595.1, CCDS75832.1, CCDS75833.1	9p13.3	2008-08-15	2008-08-15	2008-08-15	ENSG00000122694	ENSG00000122694			18007	protein-coding gene	gene with protein product		607141	"chromosome 9 open reading frame 19"	C9orf19		12137952, 11865038	Standard	NM_022343		Approved	GAPR-1	uc003zyz.3	Q9H4G4	OTTHUMG00000019900	ENST00000377960.4:c.146C>T	9.37:g.36148567C>T	ENSP00000367196:p.Thr49Met		36138567	Q5VZR1|Q8N2S6|Q8WWC9|Q8WX36	Missense_Mutation	SNP	ENST00000377960.4	37	CCDS6598.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.3	4.124752	0.77436	0.0	1.16E-4	ENSG00000122694	ENST00000377959;ENST00000377960	T;T	0.45276	0.9;2.44	5.61	5.61	0.85477	CAP domain (3);	0.196919	0.52532	N	0.000064	T	0.57344	0.2047	L	0.47716	1.5	0.80722	D	1	D;D;D;P	0.89917	1.0;0.998;0.995;0.502	D;P;P;B	0.72338	0.977;0.866;0.71;0.166	T	0.53662	-0.8407	10	0.48119	T	0.1	-10.0846	15.4923	0.75619	0.0:1.0:0.0:0.0	.	49;246;49;49	B4DQC5;D3DRP5;Q9H4G4;Q5VZR0	.;.;GAPR1_HUMAN;.	M	49	ENSP00000367195:T49M;ENSP00000367196:T49M	ENSP00000367195:T49M	T	+	2	0	GLIPR2	36138567	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.260000	0.65490	2.793000	0.96121	0.655000	0.94253	ACG		0.592	GLIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052414.1	NM_022343		T	36148567	C	T	36148567	3	4	81	1	0	0	0	0	1	0	0	0	6464	536	19	1	156	1	GLIPR2	9	36148567	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	36130492	36148567	105064864	103	23428										
ZNF782	158431	hgsc.bcm.edu	37	chr9	99581837	99581837	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgagccttttcttttgaataCtgacagtgtggggccatcag	11	8	2	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:99581837C>T	ENST00000481138.1	-	6	1129	c.468G>A	c.(466-468)caG>caA	p.Q156Q	ZNF782_ENST00000535338.1_Silent_p.Q24Q|ZNF782_ENST00000466833.1_5'UTR	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	156					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				CTTTTGAATACTGACAGTGTG	0.433																																																0			9											86	88	88					9																	99581837		2203	4300	6503	98621658	SO:0001819	synonymous_variant	158431			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.468G>A	9.37:g.99581837C>T			98621658	B2RNR0	Silent	SNP	ENST00000481138.1	37	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	C	8.776	0.927094	0.18056	.	.	ENSG00000196597	ENST00000289032	.	.	.	3.28	-4.64	0.03349	.	.	.	.	.	T	0.26810	0.0656	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29274	-1.0017	4	.	.	.	.	6.4881	0.22099	0.0:0.2462:0.1481:0.6057	.	.	.	.	I	145	.	.	V	-	1	0	ZNF782	98621658	0.000000	0.05858	0.000000	0.03702	0.723000	0.41478	-1.921000	0.01569	-1.265000	0.02449	-0.143000	0.13931	GTA		0.433	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		T	99581837	C	T	99581837	2	4	81	1	0	0	0	0	0	0	0	1	18194	564	20	3		3	ZNF782	9	99581837	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	63433270	99581837	41631594	104	23429										
AKNA	80709	hgsc.bcm.edu	37	chr9	117119200	117119200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggggtgaaactctgcttgttTctgagcccacaaagccactg	11	11	2	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:117119200T>C	ENST00000307564.4	-	13	2950	c.2789A>G	c.(2788-2790)gAa>gGa	p.E930G	AKNA_ENST00000374075.5_Missense_Mutation_p.E849G|AKNA_ENST00000223791.3_Missense_Mutation_p.E390G|AKNA_ENST00000374088.3_Missense_Mutation_p.E930G	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	930	PEST.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TCTGCTTGTTTCTGAGCCCAC	0.562																																																0			9											188	159	168					9																	117119200		2203	4300	6503	116159021	SO:0001583	missense	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2789A>G	9.37:g.117119200T>C	ENSP00000303769:p.Glu930Gly		116159021	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.902696	0.72754	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T	0.37235	1.49;1.49;1.21;1.46	5.3	5.3	0.74995	.	0.000000	0.53938	D	0.000059	T	0.52549	0.1741	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	T	0.49380	-0.8946	10	0.37606	T	0.19	-19.9975	11.6392	0.51222	0.0:0.0:0.0:1.0	.	930;849	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	G	930;930;390;849	ENSP00000303769:E930G;ENSP00000363201:E930G;ENSP00000223791:E390G;ENSP00000363188:E849G	ENSP00000223791:E390G	E	-	2	0	AKNA	116159021	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	4.015000	0.57152	2.009000	0.58944	0.379000	0.24179	GAA		0.562	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117119200	T	C	117119200	3	2	81	1	0	0	0	0	1	0	0	0	463	1783	62	4	1570	4	AKNA	9	117119200	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	17537363	117119200	24094231	105	23430										
OR1J4	26219	hgsc.bcm.edu	37	chr9	125282097	125282097	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cacattggggtcaccatcctCaaggctccatctactaaggg	9	13	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:125282097C>A	ENST00000340750.1	+	1	678	c.678C>A	c.(676-678)ctC>ctA	p.L226L		NM_001004452.1	NP_001004452.1	Q8NGS1	OR1J4_HUMAN	olfactory receptor, family 1, subfamily J, member 4	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	20						TCACCATCCTCAAGGCTCCAT	0.463																																																0			9											157	142	147					9																	125282097		2203	4300	6503	124321918	SO:0001819	synonymous_variant	26219			X64979	CCDS35122.1	9q33.2	2013-09-20			ENSG00000239590	ENSG00000239590		"GPCR / Class A : Olfactory receptors"	8211	protein-coding gene	gene with protein product						1370859	Standard	NM_001004452		Approved	HTPCRX01, HSHTPCRX01	uc011lyw.2	Q8NGS1	OTTHUMG00000020606	ENST00000340750.1:c.678C>A	9.37:g.125282097C>A			124321918	A3KFM0|Q6IEZ3|Q96R89	Silent	SNP	ENST00000340750.1	37	CCDS35122.1																																																																																				0.463	OR1J4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053936.1			A	125282097	C	A	125282097	2	1	81	1	0	0	0	0	0	0	0	1	10992	813	29	2		2	OR1J4	9	125282097	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	8162897	125282097	15931334	106	23431										
OR1L8	138881	hgsc.bcm.edu	37	chr9	125330507	125330507	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cttttctgacaggaagttcaTcagcatcttggggacaacgc	10	10	4	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:125330507T>C	ENST00000304865.2	-	1	331	c.250A>G	c.(250-252)Atg>Gtg	p.M84V		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	84						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						AGGAAGTTCATCAGCATCTTG	0.458																																																0			9											79	82	81					9																	125330507		2203	4300	6503	124370328	SO:0001583	missense	138881				CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"GPCR / Class A : Olfactory receptors"	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.250A>G	9.37:g.125330507T>C	ENSP00000306607:p.Met84Val		124370328	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.177281	0.00312	.	.	ENSG00000171496	ENST00000304865	T	0.01963	4.53	4.39	0.287	0.15714	GPCR, rhodopsin-like superfamily (1);	0.573976	0.14122	N	0.339964	T	0.00496	0.0016	N	0.00119	-2.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45818	-0.9235	10	0.02654	T	1	-0.3644	6.5298	0.22320	0.0:0.642:0.1318:0.2262	.	84	Q8NGR8	OR1L8_HUMAN	V	84	ENSP00000306607:M84V	ENSP00000306607:M84V	M	-	1	0	OR1L8	124370328	0.000000	0.05858	0.004000	0.12327	0.806000	0.45545	-1.854000	0.01664	-0.006000	0.14370	-0.731000	0.03576	ATG		0.458	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1			C	125330507	T	C	125330507	3	2	81	1	0	0	0	0	1	0	0	0	10998	1435	50	4	683	4	OR1L8	9	125330507	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	48410	125330507	15882924	107	23432										
SH2D3C	10044	hgsc.bcm.edu	37	chr9	130506979	130506979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtagtgactggaaggtggccGggttgaaggaagaagtgact	18	4	0	4	rs370528837		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:130506979G>A	ENST00000314830.8	-	7	1777	c.1664C>T	c.(1663-1665)cCg>cTg	p.P555L	SH2D3C_ENST00000429553.1_Missense_Mutation_p.P201L|SH2D3C_ENST00000373276.3_Missense_Mutation_p.P487L|SH2D3C_ENST00000420366.1_Missense_Mutation_p.P397L|SH2D3C_ENST00000471939.1_5'UTR|SH2D3C_ENST00000373277.4_Missense_Mutation_p.P398L|SH2D3C_ENST00000373274.3_Missense_Mutation_p.P395L	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	555					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GAAGGTGGCCGGGTTGAAGGA	0.597																																																0			9						G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	112	112	112		602,602,1190,1184,1193,1664	3.6	0.8	9		112	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	SH2D3C	NM_001142531.1,NM_001142532.1,NM_001142533.1,NM_001142534.1,NM_005489.2,NM_170600.2	98,98,98,98,98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	201/507,201/507,397/703,395/701,398/704,555/861	130506979	1,13005	2203	4300	6503	129546800	SO:0001583	missense	10044			AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.1664C>T	9.37:g.130506979G>A	ENSP00000317817:p.Pro555Leu		129546800	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	37	CCDS6877.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740313	0.30865	0.0	1.16E-4	ENSG00000095370	ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	5.42	3.58	0.41010	.	0.046120	0.85682	N	0.000000	T	0.43033	0.1229	L	0.42581	1.335	0.80722	D	1	P;D;B;B;P	0.53619	0.906;0.961;0.274;0.072;0.929	B;B;B;B;B	0.39876	0.201;0.312;0.028;0.039;0.293	T	0.27839	-1.0062	10	0.12430	T	0.62	-35.3138	10.5231	0.44931	0.1584:0.0:0.8416:0.0	.	395;555;487;398;397	E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.;SH2D3_HUMAN;.;.;.	L	398;397;487;395;201;555	ENSP00000362374:P398L;ENSP00000388536:P397L;ENSP00000362373:P487L;ENSP00000362371:P395L;ENSP00000394632:P201L;ENSP00000317817:P555L	ENSP00000317817:P555L	P	-	2	0	SH2D3C	129546800	1.000000	0.71417	0.755000	0.31263	0.412000	0.31113	3.499000	0.53310	0.653000	0.30826	-0.221000	0.12465	CCG		0.597	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		A	130506979	G	A	130506979	3	1	81	1	0	0	0	0	1	0	0	0	14271	1116	39	1	942	1	SH2D3C	9	130506979	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	5176472	130506979	10706452	108	23433										
GTF3C5	9328	hgsc.bcm.edu	37	chr9	135933284	135933284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aagacgaggaggatgaggagGaggaggaagaggaggaggag	23	1	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr9:135933284G>A	ENST00000372097.5	+	11	1800	c.1477G>A	c.(1477-1479)Gag>Aag	p.E493K	GTF3C5_ENST00000372108.5_Missense_Mutation_p.E500K|GTF3C5_ENST00000372099.6_Missense_Mutation_p.E484K|GTF3C5_ENST00000342018.8_Missense_Mutation_p.E431K	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	493	Glu-rich.|Poly-Glu.				5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		ggatgaggaggaggaggaaga	0.582																																																0			9											94	76	82					9																	135933284		2203	4300	6503	134923105	SO:0001583	missense	9328			AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.1477G>A	9.37:g.135933284G>A	ENSP00000361169:p.Glu493Lys		134923105	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	SNP	ENST00000372097.5	37	CCDS6958.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.060065	0.76074	.	.	ENSG00000148308	ENST00000372097;ENST00000372099;ENST00000372108;ENST00000342018	T;T;T;T	0.46451	0.88;0.88;0.9;0.87	5.1	5.1	0.69264	.	0.469100	0.24438	N	0.038536	T	0.41926	0.1180	M	0.65975	2.015	0.80722	D	1	P;P	0.36282	0.493;0.546	B;B	0.30495	0.116;0.09	T	0.39643	-0.9604	10	0.33940	T	0.23	10.8254	17.4822	0.87675	0.0:0.0:1.0:0.0	.	500;493	Q9Y5Q8-3;Q9Y5Q8	.;TF3C5_HUMAN	K	493;484;500;431	ENSP00000361169:E493K;ENSP00000361171:E484K;ENSP00000361180:E500K;ENSP00000339530:E431K	ENSP00000339530:E431K	E	+	1	0	GTF3C5	134923105	1.000000	0.71417	0.612000	0.29024	0.645000	0.38454	8.730000	0.91510	2.354000	0.79902	0.491000	0.48974	GAG		0.582	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		A	135933284	G	A	135933284	3	1	81	1	0	0	0	0	1	0	0	0	6897	1175	41	3	1544	3	GTF3C5	9	135933284	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	5426305	135933284	5280147	109	23434										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27306508	27306508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttcaatctcctgtttatactGtttgacttgaccaagttcta	5	9	3	2	rs569348833		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:27306508G>T	ENST00000376087.4	-	30	4594	c.4429C>A	c.(4429-4431)Cag>Aag	p.Q1477K	ANKRD26_ENST00000436985.2_Missense_Mutation_p.Q1493K|ANKRD26_ENST00000376070.3_Missense_Mutation_p.Q1034K	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1476					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TGTTTATACTGTTTGACTTGA	0.333																																																0			10											146	133	138					10																	27306508		1838	4084	5922	27346514	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4429C>A	10.37:g.27306508G>T	ENSP00000365255:p.Gln1477Lys		27346514	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	G	9.828	1.187695	0.21870	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.35421	3.81;1.31;1.32	5.08	2.12	0.27331	.	0.122950	0.35291	N	0.003305	T	0.20780	0.0500	L	0.28192	0.835	0.09310	N	1	B;B;P	0.38677	0.172;0.107;0.642	B;B;B	0.38327	0.163;0.078;0.271	T	0.08330	-1.0727	10	0.37606	T	0.19	.	3.4809	0.07602	0.0838:0.1482:0.4628:0.3052	.	1477;1476;1493	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	K	1034;1477;1493	ENSP00000365238:Q1034K;ENSP00000365255:Q1477K;ENSP00000405112:Q1493K	ENSP00000365238:Q1034K	Q	-	1	0	ANKRD26	27346514	1.000000	0.71417	0.005000	0.12908	0.083000	0.17756	4.529000	0.60588	0.234000	0.21139	0.455000	0.32223	CAG		0.333	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			T	27306508	G	T	27306508	3	4	81	1	0	0	0	0	1	0	0	0	654	1386	48	2	723	2	ANKRD26	10	27306508	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10		27306508	108228239	110	23435										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27324249	27324249	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aaaattcattttgtcctgtaAacgagaacattcatctcttg	5	8	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:27324249A>C	ENST00000376087.4	-	24	3295	c.3130T>G	c.(3130-3132)Tta>Gta	p.L1044V	ANKRD26_ENST00000436985.2_Missense_Mutation_p.L1060V|ANKRD26_ENST00000376070.3_Missense_Mutation_p.L601V	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1043					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTGTCCTGTAAACGAGAACAT	0.343																																																0			10											114	105	108					10																	27324249		1872	4097	5969	27364255	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3130T>G	10.37:g.27324249A>C	ENSP00000365255:p.Leu1044Val		27364255	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	A	4.709	0.131864	0.08981	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.19250	2.16;2.16;2.16	5.84	-2.71	0.05986	.	0.340666	0.20657	N	0.088093	T	0.23926	0.0579	L	0.37507	1.11	0.09310	N	1	D;D;B	0.71674	0.998;0.997;0.036	D;D;B	0.83275	0.996;0.991;0.014	T	0.12091	-1.0561	10	0.45353	T	0.12	.	1.6613	0.02792	0.4589:0.2291:0.2012:0.1109	.	1044;1043;1060	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	V	601;1044;1060	ENSP00000365238:L601V;ENSP00000365255:L1044V;ENSP00000405112:L1060V	ENSP00000365238:L601V	L	-	1	2	ANKRD26	27364255	0.007000	0.16637	0.000000	0.03702	0.017000	0.09413	-0.089000	0.11180	-0.409000	0.07553	0.482000	0.46254	TTA		0.343	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			C	27324249	A	C	27324249	3	2	81	1	0	0	0	0	1	0	0	0	654	11	1	4	2046	4	ANKRD26	10	27324249	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	17741	27324249	108210498	111	23436										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55913044	55913044	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgacccttcgtctgcgtcgaCtgcagtgagctggaattgaa	12	10	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:55913044C>A	ENST00000320301.6	-	14	1994	c.1600G>T	c.(1600-1602)Gtc>Ttc	p.V534F	PCDH15_ENST00000395445.1_Missense_Mutation_p.V541F|PCDH15_ENST00000437009.1_Missense_Mutation_p.V534F|PCDH15_ENST00000409834.1_Missense_Mutation_p.V145F|PCDH15_ENST00000395430.1_Missense_Mutation_p.V534F|PCDH15_ENST00000395446.1_Missense_Mutation_p.V534F|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.V497F|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.V539F|PCDH15_ENST00000395438.1_Missense_Mutation_p.V534F|PCDH15_ENST00000361849.3_Missense_Mutation_p.V534F|PCDH15_ENST00000373965.2_Missense_Mutation_p.V541F|PCDH15_ENST00000373955.1_Missense_Mutation_p.V534F|PCDH15_ENST00000395433.1_Missense_Mutation_p.V512F|PCDH15_ENST00000373957.3_Missense_Mutation_p.V512F	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	534	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCTGCGTCGACTGCAGTGAGC	0.438										HNSCC(58;0.16)																																						0			10											101	95	97					10																	55913044		2203	4300	6503	55583050	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1600G>T	10.37:g.55913044C>A	ENSP00000322604:p.Val534Phe		55583050	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797779	0.31777	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.31	4.4	0.53042	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.40815	0.1132	L	0.45581	1.43	0.30405	N	0.779689	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.17852	0.02;0.009;0.009;0.009;0.024;0.009;0.02;0.003;0.009;0.009;0.009;0.009;0.001;0.009;0.009	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.26693	0.072;0.02;0.02;0.02;0.029;0.02;0.072;0.013;0.02;0.02;0.02;0.02;0.005;0.02;0.02	T	0.46582	-0.9181	9	0.72032	D	0.01	.	5.6745	0.17741	0.1455:0.639:0.1404:0.0752	.	512;534;534;539;534;497;534;534;541;541;534;539;534;512;534	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	F	541;539;534;534;145;541;534;497;534;512;512;534;534;539;534;534	ENSP00000363076:V541F;ENSP00000410304:V539F;ENSP00000378826:V534F;ENSP00000386693:V145F;ENSP00000378832:V541F;ENSP00000378833:V534F;ENSP00000378820:V497F;ENSP00000354950:V534F;ENSP00000378821:V512F;ENSP00000363068:V512F;ENSP00000322604:V534F;ENSP00000378818:V534F;ENSP00000412628:V534F;ENSP00000363066:V534F	ENSP00000322604:V534F	V	-	1	0	PCDH15	55583050	0.007000	0.16637	0.811000	0.32455	0.993000	0.82548	0.051000	0.14141	1.372000	0.46190	0.557000	0.71058	GTC		0.438	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55913044	C	A	55913044	3	1	81	1	0	0	0	0	1	0	0	0	11542	565	20	2	5966	2	PCDH15	10	55913044	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	28588795	55913044	79621703	112	23437										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114910883	114910883	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtcggctcactccatagttcGtaagtgttgctgtttttctc	9	10	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:114910883G>A	ENST00000355995.4	+	9	1508		c.e9+1		TCF7L2_ENST00000538897.1_Splice_Site|TCF7L2_ENST00000352065.5_Splice_Site|TCF7L2_ENST00000355717.4_Splice_Site|TCF7L2_ENST00000369389.1_Splice_Site|TCF7L2_ENST00000545257.1_Splice_Site|TCF7L2_ENST00000542695.1_Splice_Site|TCF7L2_ENST00000369386.1_Splice_Site|TCF7L2_ENST00000534894.1_Splice_Site|TCF7L2_ENST00000543371.1_Splice_Site|TCF7L2_ENST00000369397.4_Splice_Site|TCF7L2_ENST00000536810.1_Splice_Site			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)						blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TCCATAGTTCGTAAGTGTTGC	0.527			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											251	196	214					10																	114910883		2203	4300	6503	114900873	SO:0001630	splice_region_variant	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1001+1G>A	10.37:g.114910883G>A			114900873	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Splice_Site	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	g	19.91	3.915037	0.72983	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6683	0.91501	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCF7L2	114900873	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.384000	0.97219	2.413000	0.81919	0.655000	0.94253	.		0.527	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	Intron	A	114910883	G	A	114910883	5	1	81	1	0	0	0	0	0	0	1	0	15737	1159	40	1	1181	1	TCF7L2	10	114910883	Splice_Site	SNP	G	TCGA-AH-6544-01A-11D-1826-10	58997839	114910883	20623864	113	23438										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128830403	128830403	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcatgactaaatccacaggcCgaagcaaagaagctggaaga	11	9	0	3	rs371528496		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:128830403C>T	ENST00000280333.6	+	18	1777	c.1668C>T	c.(1666-1668)gcC>gcT	p.A556A		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	556	DHR-1.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		ATCCACAGGCCGAAGCAAAGA	0.502																																																0			10						C		0,4110		0,0,2055	21	22	22		1623	-7.7	0.4	10		22	4,8402		0,4,4199	no	coding-synonymous	DOCK1	NM_001380.3		0,4,6254	TT,TC,CC		0.0476,0.0,0.032		541/1851	128830403	4,12512	2055	4203	6258	128720393	SO:0001819	synonymous_variant	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1668C>T	10.37:g.128830403C>T			128720393	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																					0.502	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	128830403	C	T	128830403	2	4	81	1	0	0	0	0	0	0	0	1	4695	639	23	1		1	DOCK1	10	128830403	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	13919520	128830403	6704344	114	23439										
ADAM8	101	hgsc.bcm.edu	37	chr10	135086833	135086833	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgtcgtcgctgaccccgcaGgtcccggccgtctgcagcag	13	17	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr10:135086833G>T	ENST00000445355.3	-	6	548	c.498C>A	c.(496-498)acC>acA	p.T166T	ADAM8_ENST00000485491.2_Silent_p.T127T|ADAM8_ENST00000415217.3_Silent_p.T166T|ADAM8_ENST00000559180.1_5'UTR	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	166					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		TGACCCCGCAGGTCCCGGCCG	0.697																																																0			10											9	11	11					10																	135086833		2122	4210	6332	134936823	SO:0001819	synonymous_variant	101			D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"ADAM metallopeptidase domain containing", "CD molecules"	215	protein-coding gene	gene with protein product		602267	"a disintegrin and metalloproteinase domain 8"			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.498C>A	10.37:g.135086833G>T			134936823	B4DVM6|H0YL36|H0YLR0|H0YN39	Silent	SNP	ENST00000445355.3	37	CCDS31319.2																																																																																				0.697	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109		T	135086833	G	T	135086833	2	4	81	1	0	0	0	0	0	0	0	1	252	987	35	2		2	ADAM8	10	135086833	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	6256430	135086833	447914	115	23440										
OR51B4	79339	hgsc.bcm.edu	37	chr11	5322807	5322807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gttgtacctcagtggtgtgcGgatggcaatgaaacagtcat	13	7	2	1	rs142325891	byFrequency	TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:5322807G>A	ENST00000380224.1	-	1	419	c.370C>T	c.(370-372)Cgc>Tgc	p.R124C	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	124					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGTGGTGTGCGGATGGCAATG	0.453																																																0			11						G	CYS/ARG	1,4401	2.1+/-5.4	0,1,2200	186	174	178		370	-3.1	0	11	dbSNP_134	178	0,8594		0,0,4297	no	missense	OR51B4	NM_033179.2	180	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign	124/311	5322807	1,12995	2201	4297	6498	5279383	SO:0001583	missense	79339			BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.370C>T	11.37:g.5322807G>A	ENSP00000369573:p.Arg124Cys		5279383	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.502499	0.00157	2.27E-4	0.0	ENSG00000183251	ENST00000380224	T	0.10005	2.92	4.71	-3.13	0.05266	GPCR, rhodopsin-like superfamily (1);	0.466636	0.20302	N	0.095010	T	0.02494	0.0076	N	0.00966	-1.09	0.09310	N	0.999999	B	0.17465	0.022	B	0.12837	0.008	T	0.37526	-0.9702	10	0.02654	T	1	.	12.9978	0.58657	0.7448:0.0:0.2552:0.0	.	124	Q9Y5P0	O51B4_HUMAN	C	124	ENSP00000369573:R124C	ENSP00000369573:R124C	R	-	1	0	OR51B4	5279383	0.000000	0.05858	0.005000	0.12908	0.053000	0.15095	-1.912000	0.01582	-0.884000	0.03976	-0.126000	0.14955	CGC		0.453	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		A	5322807	G	A	5322807	3	1	81	1	0	0	0	0	1	0	0	0	11121	1116	39	1	565	1	OR51B4	11	5322807	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10		5322807	129683709	116	23441										
OR2D3	120775	hgsc.bcm.edu	37	chr11	6942322	6942322	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tttgtgtccaagtttatcttCctgggtctttcacaggactt	8	9	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:6942322C>G	ENST00000317834.3	+	1	118	c.90C>G	c.(88-90)ttC>ttG	p.F30L		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGTTTATCTTCCTGGGTCTTT	0.408																																																0			11											93	96	95					11																	6942322		2201	4296	6497	6898898	SO:0001583	missense	120775			BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"GPCR / Class A : Olfactory receptors"	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.90C>G	11.37:g.6942322C>G	ENSP00000320560:p.Phe30Leu		6898898	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	C	7.663	0.685261	0.14973	.	.	ENSG00000178358	ENST00000317834	T	0.00606	6.26	5.16	1.01	0.19927	.	1.060660	0.07410	N	0.892250	T	0.00178	0.0005	N	0.00113	-2.09	0.24373	N	0.994825	B	0.02656	0.0	B	0.04013	0.001	T	0.45071	-0.9286	10	0.02654	T	1	-15.7798	2.4247	0.04456	0.1377:0.4163:0.2847:0.1613	.	30	Q8NGH3	OR2D3_HUMAN	L	30	ENSP00000320560:F30L	ENSP00000320560:F30L	F	+	3	2	OR2D3	6898898	0.000000	0.05858	0.936000	0.37596	0.680000	0.39746	-0.903000	0.04084	0.101000	0.17610	0.655000	0.94253	TTC		0.408	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684		G	6942322	C	G	6942322	3	3	81	1	0	0	0	0	1	0	0	0	11026	854	30	5	92	5	OR2D3	11	6942322	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	1619515	6942322	128064194	117	23442										
CTR9	9646	hgsc.bcm.edu	37	chr11	10778348	10778348	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tacagaggagctcttgcttaCtataagaaagcattgcgtac	9	8	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:10778348C>T	ENST00000361367.2	+	5	981	c.555C>T	c.(553-555)taC>taT	p.Y185Y		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	185					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CTCTTGCTTACTATAAGAAAG	0.343																																																0			11											111	121	118					11																	10778348		2201	4294	6495	10734924	SO:0001819	synonymous_variant	9646			D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"Tetratricopeptide (TTC) repeat domain containing"	16850	protein-coding gene	gene with protein product		609366	"SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.555C>T	11.37:g.10778348C>T			10734924	D3DQV8|Q15015	Silent	SNP	ENST00000361367.2	37	CCDS7805.1																																																																																				0.343	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		T	10778348	C	T	10778348	2	4	81	1	0	0	0	0	0	0	0	1	4030	576	20	3		3	CTR9	11	10778348	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	3836026	10778348	124228168	118	23443										
OR4B1	119765	hgsc.bcm.edu	37	chr11	48239031	48239031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttgtcattctggtcaacttgAggaaccattctgcagagggg	12	8	4	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:48239031A>G	ENST00000309562.2	+	1	688	c.670A>G	c.(670-672)Agg>Ggg	p.R224G		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GGTCAACTTGAGGAACCATTC	0.468																																																0			11											143	112	122					11																	48239031		2201	4298	6499	48195607	SO:0001583	missense	119765			AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"GPCR / Class A : Olfactory receptors"	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.670A>G	11.37:g.48239031A>G	ENSP00000311605:p.Arg224Gly		48195607	Q6IF75|Q96R64	Missense_Mutation	SNP	ENST00000309562.2	37	CCDS31485.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082871	0.36758	.	.	ENSG00000175619	ENST00000309562	T	0.00253	8.43	5.5	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.00552	0.0018	M	0.80616	2.505	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.34601	-0.9822	10	0.87932	D	0	.	10.7372	0.46133	0.84:0.16:0.0:0.0	.	224	Q8NGF8	OR4B1_HUMAN	G	224	ENSP00000311605:R224G	ENSP00000311605:R224G	R	+	1	2	OR4B1	48195607	0.103000	0.21917	0.971000	0.41717	0.326000	0.28443	2.003000	0.40844	0.879000	0.35944	0.411000	0.27672	AGG		0.468	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470		G	48239031	A	G	48239031	3	3	81	1	0	0	0	0	1	0	0	0	11075	295	11	4	672	4	OR4B1	11	48239031	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	37460683	48239031	86767485	119	23444										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418984	55418984	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgttgtgacagccaacagtgGtaccattgctctggggagtt	13	8	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:55418984G>T	ENST00000312422.2	+	1	605	c.605G>T	c.(604-606)gGt>gTt	p.G202V		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GCCAACAGTGGTACCATTGCT	0.463																																																0			11											237	180	200					11																	55418984		2177	4044	6221	55175560	SO:0001583	missense	219431			BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.605G>T	11.37:g.55418984G>T	ENSP00000310337:p.Gly202Val		55175560	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638247	0.47153	.	.	ENSG00000174982	ENST00000312422	T	0.33865	1.39	5.35	4.38	0.52667	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000049	T	0.52677	0.1749	L	0.58810	1.83	0.22648	N	0.998894	D	0.89917	1.0	D	0.78314	0.991	T	0.41179	-0.9523	10	0.87932	D	0	.	10.4935	0.44764	0.0:0.0:0.8064:0.1936	.	202	Q8NH73	OR4S2_HUMAN	V	202	ENSP00000310337:G202V	ENSP00000310337:G202V	G	+	2	0	OR4S2	55175560	0.060000	0.20803	0.185000	0.23176	0.741000	0.42261	-0.232000	0.09055	2.508000	0.84585	0.542000	0.68232	GGT		0.463	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55418984	G	T	55418984	3	4	81	1	0	0	0	0	1	0	0	0	11114	1261	44	2	607	2	OR4S2	11	55418984	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	7179953	55418984	79587532	120	23445										
TIGD3	220359	hgsc.bcm.edu	37	chr11	65123728	65123728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttcattcccccctgagccacCtcccccggggctcacatccc	6	22	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:65123728C>T	ENST00000309880.5	+	2	656	c.449C>T	c.(448-450)cCt>cTt	p.P150L		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	150						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						CCTGAGCCACCTCCCCCGGGG	0.607																																																0			11											78	84	82					11																	65123728		2200	4295	6495	64880304	SO:0001583	missense	220359				CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.449C>T	11.37:g.65123728C>T	ENSP00000308354:p.Pro150Leu		64880304		Missense_Mutation	SNP	ENST00000309880.5	37	CCDS8101.1	.	.	.	.	.	.	.	.	.	.	C	11.92	1.782454	0.31502	.	.	ENSG00000173825	ENST00000309880	T	0.13657	2.57	3.81	3.81	0.43845	.	0.000000	0.34025	N	0.004323	T	0.11793	0.0287	L	0.27053	0.805	0.21740	N	0.99957	D	0.54207	0.965	P	0.45449	0.481	T	0.11397	-1.0589	10	0.46703	T	0.11	-7.0416	11.4586	0.50197	0.0:1.0:0.0:0.0	.	150	Q6B0B8	TIGD3_HUMAN	L	150	ENSP00000308354:P150L	ENSP00000308354:P150L	P	+	2	0	TIGD3	64880304	0.009000	0.17119	0.168000	0.22838	0.388000	0.30384	1.087000	0.30865	2.159000	0.67721	0.456000	0.33151	CCT		0.607	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719		T	65123728	C	T	65123728	3	4	81	1	0	0	0	0	1	0	0	0	15936	681	24	3	451	3	TIGD3	11	65123728	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	9704744	65123728	69882788	121	23446										
FAM168A	23201	hgsc.bcm.edu	37	chr11	73122548	73122548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gagcagtgttactctgggtcGgtgggaccttgtatggtgtc	16	7	1	0	rs200934649		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:73122548G>A	ENST00000064778.4	-	6	622	c.338C>T	c.(337-339)cCg>cTg	p.P113L	RP11-809N8.4_ENST00000536855.1_RNA|FAM168A_ENST00000450446.2_Intron|RP11-809N8.4_ENST00000542598.1_RNA|FAM168A_ENST00000356467.4_Missense_Mutation_p.P104L			Q92567	F168A_HUMAN	family with sequence similarity 168, member A	113										endometrium(3)|kidney(1)|lung(1)	5						ACTCTGGGTCGGTGGGACCTT	0.532													G|||	1	0.000199681	0	0	5008	,	,		15258	0		0.001	False		,,,				2504	0															0			11											79	79	79					11																	73122548		1928	4110	6038	72800196	SO:0001583	missense	23201			BC014932	CCDS41689.1, CCDS66165.1, CCDS73346.1	11q13.4	2008-06-11	2008-06-11	2008-06-11		ENSG00000054965			28999	protein-coding gene	gene with protein product	"tongue cancer chemotherapy resistance-associated protein 1"		"KIAA0280"	KIAA0280			Standard	XM_005273852		Approved	TCRP1	uc001oty.1	Q92567		ENST00000064778.4:c.338C>T	11.37:g.73122548G>A	ENSP00000064778:p.Pro113Leu		72800196	A2ICY2|A2ID81|Q86UG2	Missense_Mutation	SNP	ENST00000064778.4	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.41	3.381601	0.61845	.	.	ENSG00000054965	ENST00000064778;ENST00000356467	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	L	0.47716	1.5	0.80722	D	1	D;D	0.61080	0.989;0.989	P;P	0.48270	0.572;0.572	T	0.51156	-0.8741	9	0.11182	T	0.66	.	18.9043	0.92454	0.0:0.0:1.0:0.0	.	113;104	Q92567;Q92567-2	F168A_HUMAN;.	L	113;104	.	ENSP00000064778:P113L	P	-	2	0	FAM168A	72800196	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	4.504000	0.60414	2.710000	0.92621	0.650000	0.86243	CCG		0.532	FAM168A-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000397424.1	NM_015159		A	73122548	G	A	73122548	3	1	81	1	0	0	0	0	1	0	0	0	5501	1116	39	1	408	1	FAM168A	11	73122548	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	7998820	73122548	61883968	122	23447										
ATM	472	hgsc.bcm.edu	37	chr11	108126967	108126967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aaattcagaaactcttgtccGgtgttcacgtcttttggtgg	10	8	4	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:108126967G>T	ENST00000452508.2	+	15	2339	c.2150G>T	c.(2149-2151)cGg>cTg	p.R717L	ATM_ENST00000278616.4_Missense_Mutation_p.R717L			Q13315	ATM_HUMAN	ATM serine/threonine kinase	717					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ACTCTTGTCCGGTGTTCACGT	0.328			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											104	97	99					11																	108126967		2201	4298	6499	107632177	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2150G>T	11.37:g.108126967G>T	ENSP00000388058:p.Arg717Leu		107632177	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126006	0.56721	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.75367	-0.93;-0.93;-0.93	5.45	3.39	0.38822	Armadillo-type fold (1);	0.198965	0.44902	D	0.000406	T	0.70011	0.3175	M	0.67953	2.075	0.35212	D	0.775232	P	0.36282	0.546	B	0.33846	0.171	T	0.76310	-0.3006	10	0.62326	D	0.03	.	11.7433	0.51804	0.1528:0.0:0.8472:0.0	.	717	Q13315	ATM_HUMAN	L	717	ENSP00000435747:R717L;ENSP00000278616:R717L;ENSP00000388058:R717L	ENSP00000278616:R717L	R	+	2	0	ATM	107632177	1.000000	0.71417	0.998000	0.56505	0.874000	0.50279	1.921000	0.40035	0.657000	0.30906	0.557000	0.71058	CGG		0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108126967	G	T	108126967	3	4	81	1	0	0	0	0	1	0	0	0	1110	1116	39	2	2200	2	ATM	11	108126967	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	35004419	108126967	26879549	123	23448										
CD3D	915	hgsc.bcm.edu	37	chr11	118211203	118211203	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccaggtccagtcttgtaatgTctgagagcagtgttcccacc	10	12	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:118211203T>C	ENST00000300692.4	-	2	297	c.161A>G	c.(160-162)gAc>gGc	p.D54G	CD3D_ENST00000392884.2_Missense_Mutation_p.D54G|CD3D_ENST00000529594.1_Intron	NM_000732.4	NP_000723.1	P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	54					cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	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;3.04e-05)	Muromonab(DB00075)	TCTTGTAATGTCTGAGAGCAG	0.458																																																0			11											223	165	184					11																	118211203		2200	4296	6496	117716413	SO:0001583	missense	915			X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286		"CD molecules"	1673	protein-coding gene	gene with protein product		186790	"CD3d antigen, delta polypeptide (TiT3 complex)"	T3D			Standard	NM_000732		Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000300692.4:c.161A>G	11.37:g.118211203T>C	ENSP00000300692:p.Asp54Gly		117716413	A8MVP6	Missense_Mutation	SNP	ENST00000300692.4	37	CCDS8394.1	.	.	.	.	.	.	.	.	.	.	T	9.914	1.210438	0.22289	.	.	ENSG00000167286	ENST00000300692;ENST00000392884	T;T	0.65364	-0.15;0.87	5.36	-0.942	0.10398	Immunoglobulin-like fold (1);	2.500750	0.00906	N	0.002419	T	0.45637	0.1352	N	0.14661	0.345	0.09310	N	1	B;B	0.18741	0.03;0.0	B;B	0.15870	0.014;0.0	T	0.29882	-0.9997	10	0.30078	T	0.28	1.3961	8.9861	0.35994	0.0:0.4263:0.0:0.5737	.	54;54	A8MVP6;P04234	.;CD3D_HUMAN	G	54	ENSP00000300692:D54G;ENSP00000376622:D54G	ENSP00000300692:D54G	D	-	2	0	CD3D	117716413	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.646000	0.05403	-0.066000	0.12998	-0.379000	0.06801	GAC		0.458	CD3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392128.1	NM_000732		C	118211203	T	C	118211203	3	2	81	1	0	0	0	0	1	0	0	0	3016	1667	58	4	370	4	CD3D	11	118211203	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	10084236	118211203	16795313	124	23449										
OPCML	4978	hgsc.bcm.edu	37	chr11	132527056	132527056	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agcaggtgtacggaccttcgTcatacacatccacattttgg	9	11	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr11:132527056T>G	ENST00000331898.7	-	2	904	c.326A>C	c.(325-327)gAc>gCc	p.D109A	OPCML_ENST00000524381.1_Missense_Mutation_p.D102A|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Missense_Mutation_p.D109A|OPCML_ENST00000374778.4_Missense_Mutation_p.D68A	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	109	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CGGACCTTCGTCATACACATC	0.502																																																0			11											250	194	213					11																	132527056		2201	4297	6498	132032266	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.326A>C	11.37:g.132527056T>G	ENSP00000330862:p.Asp109Ala		132032266	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.893519	0.91889	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.83	5.83	0.93111	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83681	0.5307	H	0.96301	3.8	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.81914	0.995;0.995;0.995;0.995	D	0.89002	0.3422	10	0.87932	D	0	-23.7099	16.1846	0.81942	0.0:0.0:0.0:1.0	.	109;102;109;109	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	A	109;102;68;76;109	ENSP00000330862:D109A;ENSP00000434750:D102A;ENSP00000363910:D68A;ENSP00000445496:D109A	ENSP00000330862:D109A	D	-	2	0	OPCML	132032266	1.000000	0.71417	0.939000	0.37840	0.932000	0.56968	7.985000	0.88162	2.229000	0.72834	0.533000	0.62120	GAC		0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		G	132527056	T	G	132527056	3	3	81	1	0	0	0	0	1	0	0	0	10905	1667	58	4	735	4	OPCML	11	132527056	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	14315853	132527056	2479460	125	23450										
CSDA	8531	hgsc.bcm.edu	37	chr12	10862555	10862555	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cgtgagcgacggtcaaaggtCtgtcccacgtggtaaggcgg	16	10	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr12:10862555C>T	ENST00000228251.4	-	6	932	c.732G>A	c.(730-732)caG>caA	p.Q244Q	YBX3_ENST00000546164.1_5'UTR|YBX3_ENST00000279550.7_Intron	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	244					3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)										GGTCAAAGGTCTGTCCCACGT	0.587																																																0			12											68	69	68					12																	10862555		2203	4300	6503	10753822	SO:0001819	synonymous_variant	8531			L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138			2428	protein-coding gene	gene with protein product	"cold-shock domain containing A1"	603437	"cold shock domain protein A"	CSDA		2977358, 8710501	Standard	NM_003651		Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.732G>A	12.37:g.10862555C>T			10753822	B2RBW6|Q14121|Q969N6|Q96B76	Silent	SNP	ENST00000228251.4	37	CCDS8630.1																																																																																				0.587	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399628.1	NM_003651		T	10862555	C	T	10862555	2	4	81	1	0	0	0	0	0	0	0	1	3933	912	32	3		3	CSDA	12	10862555	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10		10862555	122989340	126	23451										
SOX5	6660	hgsc.bcm.edu	37	chr12	23687261	23687261	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atttctccattgatgtcctcGgcctgtatctcttctttgat	6	11	3	2	rs138618584		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr12:23687261G>A	ENST00000451604.2	-	15	2285	c.2184C>T	c.(2182-2184)gcC>gcT	p.A728A	SOX5_ENST00000309359.1_Silent_p.A715A|SOX5_ENST00000541536.1_Silent_p.A607A|SOX5_ENST00000537393.1_Silent_p.A693A|SOX5_ENST00000545921.1_Silent_p.A718A|SOX5_ENST00000546136.1_Silent_p.A715A|SOX5_ENST00000381381.2_Silent_p.A607A|SOX5_ENST00000396007.2_Silent_p.A342A			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	728					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.A728A(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TGATGTCCTCGGCCTGTATCT	0.473																																																1	Substitution - coding silent(1)	lung(1)	12						G	,,	1,4405	2.1+/-5.4	0,1,2202	233	194	207		2184,2145,1026	0.5	1	12	dbSNP_134	207	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SOX5	NM_006940.4,NM_152989.2,NM_178010.1	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	728/764,715/751,342/378	23687261	1,13005	2203	4300	6503	23578528	SO:0001819	synonymous_variant	6660			AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.2184C>T	12.37:g.23687261G>A			23578528	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Silent	SNP	ENST00000451604.2	37	CCDS8699.1																																																																																				0.473	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		A	23687261	G	A	23687261	2	1	81	1	0	0	0	0	0	0	0	1	14991	1103	39	1		1	SOX5	12	23687261	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	12824706	23687261	110164634	127	23452										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	81	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	1711023	25398284	108453611	128	23453										
GALNT6	11226	hgsc.bcm.edu	37	chr12	51754530	51754530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aggacatttccacgttctccCctccccagatctccatctga	5	17	3	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr12:51754530C>T	ENST00000543196.2	-	6	1347	c.1142G>A	c.(1141-1143)gGg>gAg	p.G381E	GALNT6_ENST00000356317.3_Missense_Mutation_p.G381E			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	381	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CACGTTCTCCCCTCCCCAGAT	0.542																																																0			12											130	111	117					12																	51754530		2203	4300	6503	50040797	SO:0001583	missense	11226			Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.1142G>A	12.37:g.51754530C>T	ENSP00000444171:p.Gly381Glu		50040797	Q8IYH4|Q9H6G2|Q9UIV5	Missense_Mutation	SNP	ENST00000543196.2	37	CCDS8813.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917701	0.92249	.	.	ENSG00000139629	ENST00000543196;ENST00000356317;ENST00000546163	T;T	0.67865	-0.29;-0.29	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	D	0.87533	0.6201	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91152	0.4954	10	0.87932	D	0	.	17.2924	0.87160	0.0:1.0:0.0:0.0	.	381	Q8NCL4	GALT6_HUMAN	E	381;381;362	ENSP00000444171:G381E;ENSP00000348668:G381E	ENSP00000348668:G381E	G	-	2	0	GALNT6	50040797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.609000	0.82925	2.816000	0.96949	0.563000	0.77884	GGG		0.542	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		T	51754530	C	T	51754530	3	4	81	1	0	0	0	0	1	0	0	0	6237	623	22	3	750	3	GALNT6	12	51754530	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	26356246	51754530	82097365	129	23454										
XPOT	11260	hgsc.bcm.edu	37	chr12	64823982	64823982	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	taatggagaagtttaaaattCtgttagaaaagttgatgctg	10	2	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr12:64823982C>G	ENST00000332707.5	+	17	2420	c.1891C>G	c.(1891-1893)Ctg>Gtg	p.L631V		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	631	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GTTTAAAATTCTGTTAGAAAA	0.413																																																0			12											61	61	61					12																	64823982		2203	4300	6503	63110249	SO:0001583	missense	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.1891C>G	12.37:g.64823982C>G	ENSP00000327821:p.Leu631Val		63110249	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.745629	0.30955	.	.	ENSG00000184575	ENST00000332707;ENST00000538086	T;T	0.67171	0.94;-0.25	5.28	4.37	0.52481	Armadillo-like helical (1);Armadillo-type fold (1);	0.155711	0.44097	D	0.000492	T	0.49167	0.1541	L	0.31578	0.945	0.50632	D	0.999886	B	0.02656	0.0	B	0.04013	0.001	T	0.40346	-0.9568	9	.	.	.	.	8.1901	0.31363	0.0:0.7195:0.154:0.1265	.	631	O43592	XPOT_HUMAN	V	631;153	ENSP00000327821:L631V;ENSP00000444345:L153V	.	L	+	1	2	XPOT	63110249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.358000	0.44134	2.646000	0.89796	0.650000	0.86243	CTG		0.413	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		G	64823982	C	G	64823982	3	3	81	1	0	0	0	0	1	0	0	0	17490	912	32	5	1953	5	XPOT	12	64823982	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	13069452	64823982	69027913	130	23455										
FREM2	341640	hgsc.bcm.edu	37	chr13	39425975	39425975	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccaaggatggctcggccaccTctggagaagactaccaccct	10	15	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:39425975T>G	ENST00000280481.7	+	11	7111	c.6895T>G	c.(6895-6897)Tct>Gct	p.S2299A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2299	Calx-beta 5.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTCGGCCACCTCTGGAGAAGA	0.527																																																0			13											58	59	59					13																	39425975		2203	4300	6503	38323975	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6895T>G	13.37:g.39425975T>G	ENSP00000280481:p.Ser2299Ala		38323975	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.902760	0.92035	.	.	ENSG00000150893	ENST00000280481	T	0.26067	1.76	5.63	5.63	0.86233	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.37999	0.1024	N	0.21583	0.68	0.80722	D	1	D;P	0.71674	0.998;0.937	D;P	0.81914	0.995;0.841	T	0.25572	-1.0128	10	0.56958	D	0.05	.	15.8341	0.78787	0.0:0.0:0.0:1.0	.	2299;2299	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	A	2299	ENSP00000280481:S2299A	ENSP00000280481:S2299A	S	+	1	0	FREM2	38323975	1.000000	0.71417	0.912000	0.35992	0.839000	0.47603	6.174000	0.71943	2.144000	0.66660	0.533000	0.62120	TCT		0.527	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39425975	T	G	39425975	3	3	81	1	0	0	0	0	1	0	0	0	6064	1551	54	4	6937	4	FREM2	13	39425975	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10		39425975	75743903	131	23456										
RB1	5925	hgsc.bcm.edu	37	chr13	48947598	48947598	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttaaattcagcaagtgatcaAccttcagaaaatctgatttc	5	8	4	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:48947598A>G	ENST00000267163.4	+	12	1323	c.1185A>G	c.(1183-1185)caA>caG	p.Q395Q		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	395	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAAGTGATCAACCTTCAGAAA	0.289		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											103	111	108					13																	48947598		2203	4289	6492	47845599	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1185A>G	13.37:g.48947598A>G			47845599	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.289	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48947598	A	G	48947598	2	3	81	1	0	0	0	0	0	0	0	1	13135	40	2	4		4	RB1	13	48947598	Silent	SNP	A	TCGA-AH-6544-01A-11D-1826-10	9521623	48947598	66222280	132	23457										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49772150	49772150	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtgggtgcaggccctttcagTgaagtagtagcctgtgtgac	15	8	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:49772150T>C	ENST00000492622.2	+	22	2828	c.2523T>C	c.(2521-2523)agT>agC	p.S841S	FNDC3A_ENST00000541916.1_Silent_p.S841S|FNDC3A_ENST00000398316.3_Silent_p.S785S	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	841	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GCCCTTTCAGTGAAGTAGTAG	0.423																																																0			13											72	71	71					13																	49772150		2203	4300	6503	48670151	SO:0001819	synonymous_variant	22862			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.2523T>C	13.37:g.49772150T>C			48670151	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	37	CCDS41886.1																																																																																				0.423	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		C	49772150	T	C	49772150	2	2	81	1	0	0	0	0	0	0	0	1	5988	1693	59	4		4	FNDC3A	13	49772150	Silent	SNP	T	TCGA-AH-6544-01A-11D-1826-10	824552	49772150	65397728	133	23458										
UTP14C	9724	hgsc.bcm.edu	37	chr13	52603442	52603442	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggaaggagcagccagccattGctcccattgaacatgcgctc	11	13	0	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:52603442G>T	ENST00000521776.2	+	2	1235	c.502G>T	c.(502-504)Gct>Tct	p.A168S	ALG11_ENST00000521508.1_3'UTR|ALG11_ENST00000523764.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	168					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.A168T(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		GCCAGCCATTGCTCCCATTGA	0.527																																																1	Substitution - Missense(1)	ovary(1)	13											60	61	61					13																	52603442		2203	4300	6503	51501443	SO:0001583	missense	440138			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.502G>T	13.37:g.52603442G>T	ENSP00000428619:p.Ala168Ser		51501443	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	.	.	.	.	.	.	.	.	.	.	G	9.069	0.996363	0.19043	.	.	ENSG00000253797	ENST00000521776	T	0.17054	2.3	2.46	0.419	0.16438	.	0.321302	0.36444	N	0.002593	T	0.12433	0.0302	L	0.52905	1.665	0.09310	N	1	P	0.41475	0.751	B	0.37731	0.257	T	0.16424	-1.0403	10	0.30078	T	0.28	-0.2829	4.656	0.12618	0.1432:0.4548:0.402:0.0	.	168	Q5TAP6	UT14C_HUMAN	S	168	ENSP00000428619:A168S	ENSP00000428619:A168S	A	+	1	0	UTP14C	51501443	0.001000	0.12720	0.006000	0.13384	0.975000	0.68041	0.435000	0.21510	-0.056000	0.13221	0.448000	0.29417	GCT		0.527	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		T	52603442	G	T	52603442	3	4	81	1	0	0	0	0	1	0	0	0	17136	1319	46	2	504	2	UTP14C	13	52603442	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	2831292	52603442	62566436	134	23459										
THSD1	55901	hgsc.bcm.edu	37	chr13	52952782	52952782	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ggtgtgctgcacttggctggCcggccgaacctcctccacag	13	15	0	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:52952782C>G	ENST00000258613.4	-	5	1501	c.1323G>C	c.(1321-1323)cgG>cgC	p.R441R	THSD1_ENST00000349258.4_Silent_p.R388R|THSD1_ENST00000544466.1_Silent_p.R62R	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	441					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		ACTTGGCTGGCCGGCCGAACC	0.557																																																0			13											80	81	81					13																	52952782		2203	4300	6503	51850783	SO:0001819	synonymous_variant	55901			AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1323G>C	13.37:g.52952782C>G			51850783	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Silent	SNP	ENST00000258613.4	37	CCDS9432.1																																																																																				0.557	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			G	52952782	C	G	52952782	2	3	81	1	0	0	0	0	0	0	0	1	15916	726	26	5		5	THSD1	13	52952782	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	349340	52952782	62217096	135	23460										
NALCN	259232	hgsc.bcm.edu	37	chr13	101728279	101728279	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tcacacaagcgcccatcatgTaagtatatgcattctgaaat	6	10	3	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr13:101728279T>G	ENST00000251127.6	-	35	3980	c.3899A>C	c.(3898-3900)tAc>tCc	p.Y1300S		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1300					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCCCATCATGTAAGTATATGC	0.323																																																0			13											100	97	98					13																	101728279		2203	4294	6497	100526280	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3899A>C	13.37:g.101728279T>G	ENSP00000251127:p.Tyr1300Ser		100526280	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182808	0.78677	.	.	ENSG00000102452	ENST00000251127	D	0.98474	-4.95	5.84	5.84	0.93424	Ion transport (1);	0.055265	0.85682	D	0.000000	D	0.97688	0.9242	L	0.49350	1.555	0.80722	D	1	B	0.33318	0.408	P	0.44732	0.459	D	0.97979	1.0348	10	0.62326	D	0.03	.	16.1973	0.82040	0.0:0.0:0.0:1.0	.	1300	Q8IZF0	NALCN_HUMAN	S	1300	ENSP00000251127:Y1300S	ENSP00000251127:Y1300S	Y	-	2	0	NALCN	100526280	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.694000	0.84235	2.222000	0.72286	0.533000	0.62120	TAC		0.323	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		G	101728279	T	G	101728279	3	3	81	1	0	0	0	0	1	0	0	0	10178	1638	57	4	1357	4	NALCN	13	101728279	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	48775497	101728279	13441599	136	23461										
FBXO34	55030	hgsc.bcm.edu	37	chr14	55818417	55818417	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atgctgttgattgtatgagcAgagagcttgtgtcccttact	11	7	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr14:55818417A>G	ENST00000313833.4	+	2	1554	c.1309A>G	c.(1309-1311)Aga>Gga	p.R437G	FBXO34_ENST00000440021.1_Missense_Mutation_p.R437G	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	437										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						TTGTATGAGCAGAGAGCTTGT	0.433																																																0			14											137	128	131					14																	55818417		2203	4300	6503	54888170	SO:0001583	missense	55030			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1309A>G	14.37:g.55818417A>G	ENSP00000313159:p.Arg437Gly		54888170	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	A	1.064	-0.672112	0.03403	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.18338	2.22;2.22	5.34	-2.78	0.05859	.	0.737426	0.12571	N	0.457314	T	0.13543	0.0328	L	0.51422	1.61	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.22068	-1.0227	10	0.52906	T	0.07	-2.1816	7.0394	0.25010	0.2925:0.3605:0.347:0.0	.	437	Q9NWN3	FBX34_HUMAN	G	437	ENSP00000313159:R437G;ENSP00000394117:R437G	ENSP00000313159:R437G	R	+	1	2	FBXO34	54888170	0.007000	0.16637	0.005000	0.12908	0.004000	0.04260	0.127000	0.15790	-0.669000	0.05289	-0.256000	0.11100	AGA		0.433	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			G	55818417	A	G	55818417	3	3	81	1	0	0	0	0	1	0	0	0	5763	180	7	4	1311	4	FBXO34	14	55818417	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10		55818417	51531123	137	23462										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96784098	96784098	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gaaagtattaatgagctgacTggctactgaaagcccaatgc	10	8	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr14:96784098T>G	ENST00000359933.4	-	19	3867	c.2974A>C	c.(2974-2976)Agt>Cgt	p.S992R		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	992					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ATGAGCTGACTGGCTACTGAA	0.348																																																0			14											100	96	97					14																	96784098		1832	4100	5932	95853851	SO:0001583	missense	55102			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.2974A>C	14.37:g.96784098T>G	ENSP00000353010:p.Ser992Arg		95853851	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	34	5.379615	0.95945	.	.	ENSG00000066739	ENST00000359933	T	0.42131	0.98	5.54	5.54	0.83059	.	0.141530	0.46145	U	0.000305	T	0.62588	0.2440	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65804	-0.6079	10	0.87932	D	0	.	15.9843	0.80138	0.0:0.0:0.0:1.0	.	992	Q96BY7	ATG2B_HUMAN	R	992	ENSP00000353010:S992R	ENSP00000353010:S992R	S	-	1	0	ATG2B	95853851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.709000	0.84645	2.228000	0.72767	0.533000	0.62120	AGT		0.348	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96784098	T	G	96784098	3	3	81	1	0	0	0	0	1	0	0	0	1095	1580	55	4	3358	4	ATG2B	14	96784098	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	40965681	96784098	10565442	138	23463										
AQR	9716	hgsc.bcm.edu	37	chr15	35149069	35149069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gtgcagatacagctcctaccAcagtaggggtggtctcagat	12	10	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:35149069A>G	ENST00000156471.5	-	35	4607	c.4382T>C	c.(4381-4383)gTg>gCg	p.V1461A		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1461					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGCTCCTACCACAGTAGGGGT	0.532																																																0			15											129	133	132					15																	35149069		2007	4191	6198	32936361	SO:0001583	missense	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.4382T>C	15.37:g.35149069A>G	ENSP00000156471:p.Val1461Ala		32936361	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	37	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	A	4.048	0.006607	0.07866	.	.	ENSG00000021776	ENST00000543879	.	.	.	4.83	-1.64	0.08318	.	1.432370	0.04597	N	0.397864	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	9	0.10636	T	0.68	-0.8352	0.8242	0.01117	0.3524:0.175:0.3033:0.1693	.	1461	O60306	AQR_HUMAN	A	1461	.	ENSP00000445700:V1461A	V	-	2	0	AQR	32936361	0.000000	0.05858	0.001000	0.08648	0.028000	0.11728	-1.175000	0.03102	0.050000	0.15949	0.455000	0.32223	GTG		0.532	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35149069	A	G	35149069	3	3	81	1	0	0	0	0	1	0	0	0	835	159	6	4	79	4	AQR	15	35149069	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10		35149069	67382323	139	23464										
MEIS2	4212	hgsc.bcm.edu	37	chr15	37184403	37184403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atgaatgtccataacctgtcCgccaacattgggatctacag	8	11	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:37184403C>T	ENST00000561208.1	-	12	1823	c.1405G>A	c.(1405-1407)Gga>Aga	p.G469R	MEIS2_ENST00000340545.5_3'UTR|MEIS2_ENST00000444725.1_3'UTR|MEIS2_ENST00000397620.2_3'UTR|MEIS2_ENST00000424352.2_3'UTR|MEIS2_ENST00000219869.9_3'UTR|MEIS2_ENST00000557796.2_3'UTR|MEIS2_ENST00000382766.2_Missense_Mutation_p.G462R|MEIS2_ENST00000397624.3_3'UTR|MEIS2_ENST00000559085.1_3'UTR|MEIS2_ENST00000559408.1_5'Flank|MEIS2_ENST00000338564.5_Missense_Mutation_p.G462R			O14770	MEIS2_HUMAN	Meis homeobox 2	469	Transcriptional activation domain.				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		ATAACCTGTCCGCCAACATTG	0.458																																																0			15											181	198	192					15																	37184403		2201	4297	6498	34971695	SO:0001583	missense	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.1405G>A	15.37:g.37184403C>T	ENSP00000453793:p.Gly469Arg		34971695	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.134738	0.56828	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766	D;D	0.86769	-2.17;-2.17	5.97	5.97	0.96955	.	0.403516	0.27946	N	0.017203	D	0.91583	0.7341	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	0.999;0.991;0.996;1.0	D;P;P;D	0.80764	0.931;0.542;0.572;0.994	D	0.91108	0.4920	10	0.54805	T	0.06	-7.6365	13.5989	0.62007	0.0:0.9294:0.0:0.0706	.	462;469;449;165	O14770-4;O14770;B7Z6F6;Q6V703	.;MEIS2_HUMAN;.;.	R	469;462;462	ENSP00000341400:G462R;ENSP00000372216:G462R	ENSP00000326296:G469R	G	-	1	0	MEIS2	34971695	1.000000	0.71417	0.973000	0.42090	0.921000	0.55340	6.044000	0.71012	2.820000	0.97059	0.655000	0.94253	GGA		0.458	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		T	37184403	C	T	37184403	3	4	81	1	0	0	0	0	1	0	0	0	9498	661	23	1	32	1	MEIS2	15	37184403	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	2035334	37184403	65346989	140	23465										
LRRC57	255252	hgsc.bcm.edu	37	chr15	42837318	42837318	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gaagtttctttatttcaaaaAgattgccttccacagcaagc	6	9	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:42837318A>T	ENST00000323443.2	-	4	1002	c.635T>A	c.(634-636)cTt>cAt	p.L212H	LRRC57_ENST00000563454.1_Missense_Mutation_p.L212H|LRRC57_ENST00000397130.3_Missense_Mutation_p.L212H			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	212						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		TATTTCAAAAAGATTGCCTTC	0.423																																																0			15											96	96	96					15																	42837318		2203	4299	6502	40624610	SO:0001583	missense	255252			AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.635T>A	15.37:g.42837318A>T	ENSP00000326817:p.Leu212His		40624610	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	37	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.767581	0.90020	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.52526	0.66;0.66	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.71307	0.3324	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74714	-0.3572	10	0.45353	T	0.12	.	15.3514	0.74389	1.0:0.0:0.0:0.0	.	212	Q8N9N7	LRC57_HUMAN	H	212	ENSP00000326817:L212H;ENSP00000380319:L212H	ENSP00000326817:L212H	L	-	2	0	LRRC57	40624610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.688000	0.91260	2.038000	0.60285	0.455000	0.32223	CTT		0.423	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		T	42837318	A	T	42837318	3	4	81	1	0	0	0	0	1	0	0	0	9042	72	3	5	92	5	LRRC57	15	42837318	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	5652915	42837318	59694074	141	23466										
TTBK2	146057	hgsc.bcm.edu	37	chr15	43044268	43044268	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgacctgatctgtgttgaccCatgaaactggccttggaatt	10	9	1	4			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:43044268C>T	ENST00000267890.6	-	14	3284	c.3176G>A	c.(3175-3177)tGg>tAg	p.W1059*		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	1059					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.W1059*(1)		NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		TGTGTTGACCCATGAAACTGG	0.498																																																1	Substitution - Nonsense(1)	ovary(1)	15											148	156	153					15																	43044268		1987	4167	6154	40831560	SO:0001587	stop_gained	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.3176G>A	15.37:g.43044268C>T	ENSP00000267890:p.Trp1059*		40831560	O94932|Q6ZN52|Q8IVV1	Nonsense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	C	40	8.003259	0.98605	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	.	.	.	5.91	5.91	0.95273	.	0.067767	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2983	0.98569	0.0:1.0:0.0:0.0	.	.	.	.	X	1059;989;1464	.	ENSP00000263802:W1464X	W	-	2	0	TTBK2	40831560	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.648000	0.54410	2.802000	0.96397	0.655000	0.94253	TGG		0.498	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		T	43044268	C	T	43044268	4	4	81	1	0	0	0	0	0	1	0	0	16717	595	21	3	566	3	TTBK2	15	43044268	Nonsense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	206950	43044268	59487124	142	23467										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43708533	43708533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aggacaggatgacagccattCgcttataccactttctttgg	9	10	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:43708533C>A	ENST00000263801.3	-	22	5000	c.4748G>T	c.(4747-4749)cGa>cTa	p.R1583L	TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1588L|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1538L|TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1588L	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1583	Tudor-like.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		GACAGCCATTCGCTTATACCA	0.488								Other conserved DNA damage response genes																																								0			15											182	155	164					15																	43708533		2201	4298	6499	41495825	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.4748G>T	15.37:g.43708533C>A	ENSP00000263801:p.Arg1583Leu		41495825	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864001	0.91511	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	5.87	4.96	0.65561	Translation protein SH3-like, subgroup (1);Tumour suppressor p53-binding protein-1 Tudor (1);	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;0.999;0.999	D;D;D;D	0.85130	0.997;0.989;0.981;0.981	T	0.61178	-0.7115	10	0.39692	T	0.17	-3.4691	15.5374	0.76013	0.0:0.9336:0.0:0.0664	.	1588;1583;1588;1588	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	L	1583;1588;1538;1588	ENSP00000263801:R1583L;ENSP00000371475:R1588L;ENSP00000371470:R1538L;ENSP00000393497:R1588L	ENSP00000263801:R1583L	R	-	2	0	TP53BP1	41495825	1.000000	0.71417	0.938000	0.37757	0.993000	0.82548	5.692000	0.68256	1.626000	0.50381	0.655000	0.94253	CGA		0.488	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43708533	C	A	43708533	3	1	81	1	0	0	0	0	1	0	0	0	16423	884	31	2	1198	2	TP53BP1	15	43708533	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	664265	43708533	58822859	143	23468										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57730535	57730535	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cccatacgcccagcctagccCaataagaaacctgaaacagc	6	16	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr15:57730535C>A	ENST00000281282.5	+	2	416	c.338C>A	c.(337-339)cCa>cAa	p.P113Q		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	113	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.P113Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		CAGCCTAGCCCAATAAGAAAC	0.488																																																1	Substitution - Missense(1)	lung(1)	15											42	45	44					15																	57730535		2192	4292	6484	55517827	SO:0001583	missense	84952			AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.338C>A	15.37:g.57730535C>A	ENSP00000281282:p.Pro113Gln		55517827	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	2.490	-0.317539	0.05386	.	.	ENSG00000128849	ENST00000281282	T	0.80909	-1.43	4.64	3.72	0.42706	.	1.516220	0.04069	N	0.307641	T	0.77678	0.4166	L	0.56769	1.78	0.09310	N	1	P	0.34780	0.468	B	0.32864	0.154	T	0.64424	-0.6411	10	0.59425	D	0.04	-5.7758	5.9681	0.19336	0.1702:0.691:0.0:0.1388	.	113	Q0VF96	CGNL1_HUMAN	Q	113	ENSP00000281282:P113Q	ENSP00000281282:P113Q	P	+	2	0	CGNL1	55517827	0.001000	0.12720	0.003000	0.11579	0.001000	0.01503	1.049000	0.30392	1.160000	0.42584	-0.175000	0.13238	CCA		0.488	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		A	57730535	C	A	57730535	3	1	81	1	0	0	0	0	1	0	0	0	3310	594	21	2	340	2	CGNL1	15	57730535	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	14022002	57730535	44800857	144	23469										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3817735	3817735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcctactttttttgcgcggcTgcgaaggagatgttgactga	13	8	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:3817735T>C	ENST00000262367.5	-	16	4045	c.3236A>G	c.(3235-3237)cAg>cGg	p.Q1079R	CREBBP_ENST00000382070.3_Missense_Mutation_p.Q1041R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1079					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTTGCGCGGCTGCGAAGGAGA	0.418			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											185	170	175					16																	3817735		2197	4300	6497	3757736	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3236A>G	16.37:g.3817735T>C	ENSP00000262367:p.Gln1079Arg		3757736	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375527	0.24857	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.16597	2.33;2.33	5.61	5.61	0.85477	Bromodomain (1);	0.000000	0.64402	D	0.000001	T	0.37404	0.1002	M	0.62723	1.935	0.80722	D	1	D;D	0.54601	0.967;0.967	D;D	0.65140	0.932;0.932	T	0.02774	-1.1112	10	0.31617	T	0.26	-12.9594	16.1054	0.81216	0.0:0.0:0.0:1.0	.	1109;1079	Q4LE28;Q92793	.;CBP_HUMAN	R	1079;1109;1041	ENSP00000262367:Q1079R;ENSP00000371502:Q1041R	ENSP00000262367:Q1079R	Q	-	2	0	CREBBP	3757736	1.000000	0.71417	0.997000	0.53966	0.031000	0.12232	7.158000	0.77470	2.266000	0.75297	0.533000	0.62120	CAG		0.418	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3817735	T	C	3817735	3	2	81	1	0	0	0	0	1	0	0	0	3867	1580	55	4	4156	4	CREBBP	16	3817735	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10		3817735	86537018	145	23470										
SNX29	92017	hgsc.bcm.edu	37	chr16	12571616	12571616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cgatgaatggaatatttatcGccggtatacagagttcagga	11	6	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:12571616G>A	ENST00000566228.1	+	19	2147	c.2078G>A	c.(2077-2079)cGc>cAc	p.R693H	SNX29_ENST00000306030.3_Missense_Mutation_p.R308H|SNX29_ENST00000323433.4_Missense_Mutation_p.R308H	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	693	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.R308L(2)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						AATATTTATCGCCGGTATACA	0.403																																																2	Substitution - Missense(2)	lung(2)	16											70	67	68					16																	12571616		1872	4102	5974	12479117	SO:0001583	missense	92017			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.2078G>A	16.37:g.12571616G>A	ENSP00000456480:p.Arg693His		12479117	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469584	0.84533	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	T;T	0.65732	-0.17;-0.17	5.73	5.73	0.89815	.	0.066079	0.64402	D	0.000014	T	0.77877	0.4196	M	0.79011	2.435	0.35923	D	0.831953	.	.	.	.	.	.	D	0.84068	0.0378	8	0.87932	D	0	-21.6809	17.3886	0.87424	0.0:0.0:1.0:0.0	.	.	.	.	H	308	ENSP00000306940:R308H;ENSP00000322226:R308H	ENSP00000306940:R308H	R	+	2	0	SNX29	12479117	1.000000	0.71417	0.636000	0.29352	0.710000	0.40934	9.236000	0.95360	2.699000	0.92147	0.655000	0.94253	CGC		0.403	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			A	12571616	G	A	12571616	3	1	81	1	0	0	0	0	1	0	0	0	14935	1087	38	1	965	1	SNX29	16	12571616	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	8753881	12571616	77783137	146	23471										
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20486735	20486735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tgggtgcccccattgtttacCggatgttgctacagcaggat	12	10	0	0	rs367739019		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:20486735C>T	ENST00000573854.1	+	7	1060	c.946C>T	c.(946-948)Cgg>Tgg	p.R316W	ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000536134.1_Missense_Mutation_p.R88W|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R316W|ACSM2A_ENST00000575690.1_Missense_Mutation_p.R316W|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R316W|ACSM2A_ENST00000417235.2_Missense_Mutation_p.R237W	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	316					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.R316R(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						CATTGTTTACCGGATGTTGCT	0.507													c|||	1	0.000199681	0	0	5008	,	,		19395	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	lung(1)	16						C	TRP/ARG	1,4405		0,1,2202	174	144	154		946	2.4	1	16		154	0,8596		0,0,4298	no	missense	ACSM2A	NM_001010845.2	101	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	316/578	20486735	1,13001	2203	4298	6501	20394236	SO:0001583	missense	123876			AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.946C>T	16.37:g.20486735C>T	ENSP00000459451:p.Arg316Trp		20394236	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485171	0.44147	2.27E-4	0.0	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	3.36	2.36	0.29203	AMP-dependent synthetase/ligase (1);	0.165686	0.28504	N	0.015107	T	0.73118	0.3546	M	0.93375	3.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.77024	-0.2741	10	0.87932	D	0	-6.8521	10.5011	0.44806	0.1961:0.8039:0.0:0.0	.	237;316	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	W	237;316;88;316	ENSP00000392169:R237W;ENSP00000219054:R316W;ENSP00000445082:R88W;ENSP00000379411:R316W	ENSP00000219054:R316W	R	+	1	2	ACSM2A	20394236	1.000000	0.71417	0.962000	0.40283	0.427000	0.31564	2.351000	0.44071	0.574000	0.29417	0.298000	0.19748	CGG		0.507	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		T	20486735	C	T	20486735	3	4	81	1	0	0	0	0	1	0	0	0	183	643	23	1	968	1	ACSM2A	16	20486735	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	7915119	20486735	69868018	147	23472										
USP31	57478	hgsc.bcm.edu	37	chr16	23116834	23116834	+	Frame_Shift_Del	DEL	G	G	-													0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acagtcccagacagaggtacGgccacaccaatcctcatgca							TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:23116834delG	ENST00000219689.7	-	5	1016	c.1017delC	c.(1015-1017)gccfs	p.A339fs		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		ACAGAGGTACGGCCACACCAA	0.468																																																0			16											123	100	108					16																	23116834		2197	4300	6497	23024335	SO:0001589	frameshift_variant	84196			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1017delC	16.37:g.23116834delG	ENSP00000219689:p.Ala339fs		23024335	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000219689.7	37	CCDS10607.1																																																																																				0.468	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		-	23116834	G	-	23116834	7	5	81	1	0	1	0	1	0	0	0	0	17102	1103	39	0	3089	0	USP31	16	23116834	Frame_Shift_Del	DEL	G	TCGA-AH-6544-01A-11D-1826-10	2630099	23116834	67237919	148	23473										
XPO6	23214	hgsc.bcm.edu	37	chr16	28112887	28112887	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcaaagaagccatcaaagtcGactgaggccatgttgtagat	11	8	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:28112887G>A	ENST00000304658.5	-	23	3668	c.3168C>T	c.(3166-3168)gtC>gtT	p.V1056V	XPO6_ENST00000565698.1_Silent_p.V1042V	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	1056					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						CATCAAAGTCGACTGAGGCCA	0.532																																																0			16											77	82	80					16																	28112887		2063	4207	6270	28020388	SO:0001819	synonymous_variant	23214			AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.3168C>T	16.37:g.28112887G>A			28020388	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Silent	SNP	ENST00000304658.5	37	CCDS42135.1																																																																																				0.532	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28112887	G	A	28112887	2	1	81	1	0	0	0	0	0	0	0	1	17488	1045	37	1		1	XPO6	16	28112887	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	4996053	28112887	62241866	149	23474										
CDH1	999	hgsc.bcm.edu	37	chr16	68849520	68849520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cctccacagccaccgtcaccGtggatgtgctggatgtgaat	11	13	1	1	rs587782113		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr16:68849520G>A	ENST00000261769.5	+	10	1614	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.V414M	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	475	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACCGTCACCGTGGATGTGCT	0.522			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	1	Unknown(1)	breast(1)	16											176	152	160					16																	68849520		2198	4300	6498	67407021	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1423G>A	16.37:g.68849520G>A	ENSP00000261769:p.Val475Met		67407021	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.680394	0.68042	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.72725	-0.68;-0.68	5.7	5.7	0.88788	Cadherin (4);Cadherin-like (2);	0.000000	0.45867	D	0.000325	D	0.90191	0.6934	H	0.96633	3.855	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	D	0.92959	0.6387	10	0.87932	D	0	.	19.433	0.94779	0.0:0.0:1.0:0.0	.	414;475	Q9UII8;P12830	.;CADH1_HUMAN	M	475;493;475;414	ENSP00000261769:V475M;ENSP00000414946:V414M	ENSP00000261769:V475M	V	+	1	0	CDH1	67407021	1.000000	0.71417	0.903000	0.35520	0.561000	0.35649	6.289000	0.72696	2.694000	0.91930	0.555000	0.69702	GTG		0.522	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68849520	G	A	68849520	3	1	81	1	0	0	0	0	1	0	0	0	3101	1145	40	1	1461	1	CDH1	16	68849520	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	40736633	68849520	21505233	150	23475										
TP53	7157	hgsc.bcm.edu	37	chr17	7577529	7577529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccagtgtgatgatggtgaggAtgggcctccggttcatgccg	16	9	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:7577529A>G	ENST00000269305.4	-	7	941	c.752T>C	c.(751-753)aTc>aCc	p.I251T	TP53_ENST00000413465.2_Missense_Mutation_p.I251T|TP53_ENST00000455263.2_Missense_Mutation_p.I251T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.I251T|TP53_ENST00000445888.2_Missense_Mutation_p.I251T|TP53_ENST00000420246.2_Missense_Mutation_p.I251T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	251	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in sporadic cancers; somatic mutation).|I -> M (in LFS; germline mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|I -> T (in sporadic cancers; somatic mutation).|I -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I251S(11)|p.I251N(10)|p.0?(8)|p.I251T(4)|p.I251_T253delILT(4)|p.L252delL(3)|p.I251del(2)|p.P250_L252delPIL(2)|p.I251fs*12(1)|p.P250_T253delPILT(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1)|p.I251fs*13(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGTGAGGATGGGCCTCCG	0.582		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	50	Substitution - Missense(25)|Deletion - In frame(14)|Whole gene deletion(8)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(6)|stomach(6)|haematopoietic_and_lymphoid_tissue(6)|upper_aerodigestive_tract(5)|oesophagus(4)|liver(4)|bone(4)|breast(4)|central_nervous_system(3)|prostate(3)|ovary(2)|thyroid(1)|soft_tissue(1)|skin(1)	17											153	111	125					17																	7577529		2203	4300	6503	7518254	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.752T>C	17.37:g.7577529A>G	ENSP00000269305:p.Ile251Thr		7518254	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.545728	0.65198	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99854	-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	L	0.49699	1.58	0.80722	D	1	D;P;D;D;D	0.89917	0.997;0.728;1.0;0.998;1.0	D;D;D;D;D	0.97110	1.0;0.964;1.0;0.999;1.0	D	0.96787	0.9579	10	0.87932	D	0	-1.7057	12.3101	0.54924	1.0:0.0:0.0:0.0	.	251;251;251;251;251	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	T	251;251;251;251;251;251;240;119	ENSP00000410739:I251T;ENSP00000352610:I251T;ENSP00000269305:I251T;ENSP00000398846:I251T;ENSP00000391127:I251T;ENSP00000391478:I251T;ENSP00000425104:I119T	ENSP00000269305:I251T	I	-	2	0	TP53	7518254	1.000000	0.71417	0.998000	0.56505	0.536000	0.34869	9.087000	0.94110	2.074000	0.62210	0.379000	0.24179	ATC		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577529	A	G	7577529	3	3	81	1	0	0	0	0	1	0	0	0	16421	333	12	4	538	4	TP53	17	7577529	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10		7577529	73617681	151	23476										
TP53	7157	hgsc.bcm.edu	37	chr17	7578268	7578268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aatttccttccactcggataAgatgctgaggaggggccaga	12	9	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:7578268A>C	ENST00000269305.4	-	6	770	c.581T>G	c.(580-582)cTt>cGt	p.L194R	TP53_ENST00000413465.2_Missense_Mutation_p.L194R|TP53_ENST00000455263.2_Missense_Mutation_p.L194R|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.L194R|TP53_ENST00000445888.2_Missense_Mutation_p.L194R|TP53_ENST00000420246.2_Missense_Mutation_p.L194R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	194	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		L -> F (in sporadic cancers; somatic mutation).|L -> H (in sporadic cancers; somatic mutation).|L -> I (in sporadic cancers; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763}.|L -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.L194R(47)|p.L194P(8)|p.L194H(8)|p.0?(8)|p.?(6)|p.L101R(5)|p.L62R(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.L194fs*15(1)|p.L194fs*14(1)|p.L101H(1)|p.L194fs*52(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.L62H(1)|p.I195fs*52(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACTCGGATAAGATGCTGAGG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	108	Substitution - Missense(75)|Whole gene deletion(8)|Deletion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Insertion - Frameshift(1)|Complex - frameshift(1)	breast(19)|lung(14)|ovary(14)|large_intestine(11)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(6)|oesophagus(6)|biliary_tract(5)|skin(5)|bone(4)|upper_aerodigestive_tract(3)|stomach(3)|central_nervous_system(2)|pancreas(2)|liver(2)|soft_tissue(1)|prostate(1)	17											97	87	90					17																	7578268		2203	4300	6503	7518993	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.581T>G	17.37:g.7578268A>C	ENSP00000269305:p.Leu194Arg		7518993	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.029856	0.54790	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.984;1.0;1.0;1.0;1.0	D	0.96375	0.9277	10	0.87932	D	0	-29.6709	13.709	0.62656	1.0:0.0:0.0:0.0	.	155;194;194;101;194;194;194	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	194;194;194;194;194;194;183;101;62;101;62	ENSP00000410739:L194R;ENSP00000352610:L194R;ENSP00000269305:L194R;ENSP00000398846:L194R;ENSP00000391127:L194R;ENSP00000391478:L194R;ENSP00000425104:L62R;ENSP00000423862:L101R	ENSP00000269305:L194R	L	-	2	0	TP53	7518993	1.000000	0.71417	0.300000	0.25030	0.031000	0.12232	9.287000	0.95975	2.183000	0.69458	0.533000	0.62120	CTT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578268	A	C	7578268	3	2	81	1	0	0	0	0	1	0	0	0	16421	72	3	4	713	4	TP53	17	7578268	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	739	7578268	73616942	152	23477										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18205275	18205275	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ttttccagttgaattctacgAtaccatctttgtggtcatga	7	8	3	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:18205275A>G	ENST00000321105.5	-	8	1053	c.839T>C	c.(838-840)aTc>aCc	p.I280T	TOP3A_ENST00000540524.1_5'Flank|TOP3A_ENST00000542570.1_Missense_Mutation_p.I185T	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	280					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GAATTCTACGATACCATCTTT	0.403																																																0			17											174	151	159					17																	18205275		2203	4300	6503	18146000	SO:0001583	missense	7156			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.839T>C	17.37:g.18205275A>G	ENSP00000321636:p.Ile280Thr		18146000	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	A	9.562	1.118635	0.20877	.	.	ENSG00000177302	ENST00000321105;ENST00000542570	T;T	0.21191	2.02;2.02	6.07	-0.231	0.13086	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);	1.440510	0.03495	N	0.217243	T	0.05181	0.0138	N	0.00630	-1.315	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34502	-0.9826	10	0.02654	T	1	-0.2725	4.1664	0.10308	0.3991:0.1047:0.3942:0.102	.	185;280	B4DK80;Q13472	.;TOP3A_HUMAN	T	280;185	ENSP00000321636:I280T;ENSP00000442336:I185T	ENSP00000321636:I280T	I	-	2	0	TOP3A	18146000	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-0.069000	0.11542	-0.296000	0.08947	0.533000	0.62120	ATC		0.403	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			G	18205275	A	G	18205275	3	3	81	1	0	0	0	0	1	0	0	0	16407	333	12	4	2214	4	TOP3A	17	18205275	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	10627007	18205275	62989935	153	23478										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37881616	37881616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tggcgctggagtccattctcCgccggcggttcacccaccag	12	16	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:37881616C>T	ENST00000269571.5	+	22	2845	c.2686C>T	c.(2686-2688)Cgc>Tgc	p.R896C	MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000406381.2_Missense_Mutation_p.R866C|ERBB2_ENST00000541774.1_Missense_Mutation_p.R881C|ERBB2_ENST00000445658.2_Missense_Mutation_p.R620C|ERBB2_ENST00000584601.1_Missense_Mutation_p.R866C|ERBB2_ENST00000540147.1_Missense_Mutation_p.R866C|ERBB2_ENST00000584450.1_Missense_Mutation_p.R896C			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	896	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.R896C(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GTCCATTCTCCGCCGGCGGTT	0.602		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	1	Substitution - Missense(1)	breast(1)	17											66	66	66					17																	37881616		2203	4300	6503	35135142	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2686C>T	17.37:g.37881616C>T	ENSP00000269571:p.Arg896Cys		35135142	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508512	0.44660	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02	5.62	3.22	0.36961	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.47637	0.1456	L	0.27053	0.805	0.80722	D	1	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.09377	0.004;0.001;0.004	T	0.46119	-0.9214	9	0.51188	T	0.08	.	10.9662	0.47414	0.1356:0.785:0.0:0.0794	.	620;881;896	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	C	866;881;620;896;866	ENSP00000385185:R866C;ENSP00000446466:R881C;ENSP00000404047:R620C;ENSP00000269571:R896C;ENSP00000443562:R866C	ENSP00000269571:R896C	R	+	1	0	ERBB2	35135142	0.860000	0.29831	1.000000	0.80357	0.977000	0.68977	2.210000	0.42816	1.316000	0.45131	0.563000	0.77884	CGC		0.602	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37881616	C	T	37881616	3	4	81	1	0	0	0	0	1	0	0	0	5219	652	23	1	2772	1	ERBB2	17	37881616	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	19676341	37881616	43313594	154	23479										
CDC6	990	hgsc.bcm.edu	37	chr17	38447789	38447789	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atcggctgcctgccagggaaAgggagatggatgtcatcagg	16	8	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:38447789A>T	ENST00000209728.4	+	4	1000	c.529A>T	c.(529-531)Agg>Tgg	p.R177W		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	177					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						TGCCAGGGAAAGGGAGATGGA	0.498																																																0			17											92	98	96					17																	38447789		2203	4300	6503	35701315	SO:0001583	missense	990			U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.529A>T	17.37:g.38447789A>T	ENSP00000209728:p.Arg177Trp		35701315	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.402030	0.83120	.	.	ENSG00000094804	ENST00000209728	T	0.57107	0.42	5.86	3.62	0.41486	.	0.417878	0.30320	N	0.009886	T	0.28599	0.0708	N	0.08118	0	0.26352	N	0.977181	B	0.31640	0.333	B	0.26310	0.068	T	0.17868	-1.0355	10	0.72032	D	0.01	-5.5457	7.9383	0.29944	0.7842:0.1429:0.0729:0.0	.	177	Q99741	CDC6_HUMAN	W	177	ENSP00000209728:R177W	ENSP00000209728:R177W	R	+	1	2	CDC6	35701315	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.962000	0.40442	0.555000	0.29079	0.528000	0.53228	AGG		0.498	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			T	38447789	A	T	38447789	3	4	81	1	0	0	0	0	1	0	0	0	3089	63	3	5	539	5	CDC6	17	38447789	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	566173	38447789	42747421	155	23480										
TUBD1	51174	hgsc.bcm.edu	37	chr17	57944002	57944002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tttgcacatctttcccacgaAgaatgaccaagttagcaatg	7	10	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:57944002A>T	ENST00000592426.1	-	6	1043	c.1043T>A	c.(1042-1044)cTt>cAt	p.L348H	TUBD1_ENST00000346141.6_Missense_Mutation_p.L94H|TUBD1_ENST00000394239.3_Missense_Mutation_p.L348H|TUBD1_ENST00000325752.3_Missense_Mutation_p.L348H|TUBD1_ENST00000340993.6_Missense_Mutation_p.L293H|TUBD1_ENST00000376094.4_Intron|TUBD1_ENST00000539018.1_Missense_Mutation_p.L132H			Q9UJT1	TBD_HUMAN	tubulin, delta 1	348					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	TTTCCCACGAAGAATGACCAA	0.388																																																0			17											128	116	120					17																	57944002		2203	4300	6503	55298784	SO:0001583	missense	51174			AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"Tubulins"	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.1043T>A	17.37:g.57944002A>T	ENSP00000468518:p.Leu348His		55298784	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	37	CCDS11620.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632132	0.87660	.	.	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000346141;ENST00000394239;ENST00000539018	T;T;D;T	0.82344	-1.28;-0.96;-1.6;-0.92	5.4	5.4	0.78164	Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91717	0.7381	M	0.85299	2.745	0.58432	D	0.999991	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.78314	0.99;0.991;0.971;0.987;0.984	D	0.93063	0.6476	10	0.87932	D	0	-18.848	15.716	0.77670	1.0:0.0:0.0:0.0	.	348;94;293;293;348	E9PCA7;Q9UJT1-3;Q5KU37;Q9UJT1-2;Q9UJT1	.;.;.;.;TBD_HUMAN	H	348;293;94;348;132	ENSP00000320797:L348H;ENSP00000342399:L293H;ENSP00000342561:L94H;ENSP00000377785:L348H	ENSP00000320797:L348H	L	-	2	0	TUBD1	55298784	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.403000	0.90208	2.167000	0.68274	0.528000	0.53228	CTT		0.388	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261		T	57944002	A	T	57944002	3	4	81	1	0	0	0	0	1	0	0	0	16802	72	3	5	330	5	TUBD1	17	57944002	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	19496213	57944002	23251208	156	23481										
SSTR2	6752	hgsc.bcm.edu	37	chr17	71165931	71165931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	caagtggaggagaccccggaCggccaagatgatcaccatgg	14	11	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:71165931C>T	ENST00000357585.2	+	2	842	c.473C>T	c.(472-474)aCg>aTg	p.T158M	RP11-143K11.5_ENST00000580671.1_RNA|SSTR2_ENST00000315332.2_Missense_Mutation_p.T158M	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	158					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)			endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	AGACCCCGGACGGCCAAGATG	0.572																																																0			17											74	68	70					17																	71165931		2203	4300	6503	68677526	SO:0001583	missense	6752				CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"GPCR / Class A : Somatostatin receptors"	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.473C>T	17.37:g.71165931C>T	ENSP00000350198:p.Thr158Met		68677526	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	37	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.943812	0.34283	.	.	ENSG00000180616	ENST00000357585;ENST00000315332	T;T	0.38077	1.16;1.16	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.170682	0.53938	D	0.000057	T	0.22085	0.0532	N	0.03930	-0.32	0.49687	D	0.99981	B	0.22414	0.069	B	0.17722	0.019	T	0.08391	-1.0724	10	0.48119	T	0.1	.	19.635	0.95728	0.0:1.0:0.0:0.0	.	158	P30874	SSR2_HUMAN	M	158	ENSP00000350198:T158M;ENSP00000326616:T158M	ENSP00000326616:T158M	T	+	2	0	SSTR2	68677526	0.997000	0.39634	0.997000	0.53966	0.991000	0.79684	2.678000	0.46900	2.733000	0.93635	0.655000	0.94253	ACG		0.572	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1			T	71165931	C	T	71165931	3	4	81	1	0	0	0	0	1	0	0	0	15237	536	19	1	475	1	SSTR2	17	71165931	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	13221929	71165931	10029279	157	23482										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74287366	74287366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aagagtgacatcttggcctgGggccttctgggcaggaattc	14	9	2	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:74287366G>A	ENST00000262765.5	-	4	3123	c.2944C>T	c.(2944-2946)Cca>Tca	p.P982S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	982										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						TCTTGGCCTGGGGCCTTCTGG	0.547																																																0			17											71	72	72					17																	74287366		2203	4300	6503	71798961	SO:0001583	missense	84074			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.2944C>T	17.37:g.74287366G>A	ENSP00000262765:p.Pro982Ser		71798961	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	G	7.463	0.645142	0.14451	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08984	3.03	4.99	-0.7	0.11273	.	.	.	.	.	T	0.04861	0.0131	L	0.29908	0.895	0.09310	N	1	B;B	0.30281	0.275;0.275	B;B	0.28916	0.096;0.046	T	0.41016	-0.9532	9	0.31617	T	0.26	-0.1817	1.2588	0.01997	0.2588:0.1492:0.4384:0.1536	.	982;982	B5MD94;Q9H0J4	.;QRIC2_HUMAN	S	982	ENSP00000262765:P982S	ENSP00000262765:P982S	P	-	1	0	QRICH2	71798961	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-1.560000	0.02160	-0.022000	0.13986	-0.215000	0.12644	CCA		0.547	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74287366	G	A	74287366	3	1	81	1	0	0	0	0	1	0	0	0	12917	1232	43	3	2111	3	QRICH2	17	74287366	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	3121435	74287366	6907844	158	23483										
PRPSAP1	5635	hgsc.bcm.edu	37	chr17	74324917	74324917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gaatgacggccaaacccagaCgcagtctctccgcataggac	10	14	1	2	rs375906385		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr17:74324917C>T	ENST00000446526.3	-	7	1107	c.662G>A	c.(661-663)cGt>cAt	p.R221H	PRPSAP1_ENST00000324684.4_Missense_Mutation_p.R118H	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	192					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						CAAACCCAGACGCAGTCTCTC	0.527													C|||	1	0.000199681	0	0	5008	,	,		17126	0.001		0	False		,,,				2504	0															0			17						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	99	71	80		662	5.7	1	17		80	0,8600		0,0,4300	no	missense	PRPSAP1	NM_002766.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	221/386	74324917	1,13005	2203	4300	6503	71836512	SO:0001583	missense	5635			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.662G>A	17.37:g.74324917C>T	ENSP00000414624:p.Arg221His		71836512	B2R6M4|Q96H06	Missense_Mutation	SNP	ENST00000446526.3	37	CCDS11743.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976482	0.92982	2.27E-4	0.0	ENSG00000161542	ENST00000446526;ENST00000324684;ENST00000435555;ENST00000436498	T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95	5.73	5.73	0.89815	.	0.053679	0.85682	D	0.000000	T	0.81987	0.4939	L	0.39467	1.215	0.80722	D	1	D;P	0.89917	1.0;0.839	D;B	0.69479	0.964;0.233	T	0.80542	-0.1336	10	0.46703	T	0.11	.	20.2602	0.98440	0.0:1.0:0.0:0.0	.	192;221	Q14558;Q14558-2	KPRA_HUMAN;.	H	221;118;118;118	ENSP00000414624:R221H;ENSP00000314973:R118H;ENSP00000392838:R118H;ENSP00000387494:R118H	ENSP00000314973:R118H	R	-	2	0	PRPSAP1	71836512	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.776000	0.85560	2.861000	0.98227	0.655000	0.94253	CGT		0.527	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766		T	74324917	C	T	74324917	3	4	81	1	0	0	0	0	1	0	0	0	12615	536	19	1	511	1	PRPSAP1	17	74324917	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	37551	74324917	6870293	159	23484										
TYMS	7298	hgsc.bcm.edu	37	chr18	669144	669144	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	aaccaaccctgacgacagaaGaatcatcatgtgcgcttgga	9	11	2	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr18:669144G>A	ENST00000323274.10	+	4	666	c.527G>A	c.(526-528)aGa>aAa	p.R176K	TYMS_ENST00000323250.5_Missense_Mutation_p.R93K|TYMS_ENST00000581920.1_3'UTR|TYMS_ENST00000323224.7_Intron	NM_001071.2	NP_001062.1	P04818	TYSY_HUMAN	thymidylate synthetase	176					aging (GO:0007568)|cartilage development (GO:0051216)|circadian rhythm (GO:0007623)|deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|developmental growth (GO:0048589)|dTMP biosynthetic process (GO:0006231)|dTTP biosynthetic process (GO:0006235)|dUMP metabolic process (GO:0046078)|G1/S transition of mitotic cell cycle (GO:0000082)|immortalization of host cell by virus (GO:0019088)|intestinal epithelial cell maturation (GO:0060574)|mitotic cell cycle (GO:0000278)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|organ regeneration (GO:0031100)|polysaccharide metabolic process (GO:0005976)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to organophosphorus (GO:0046683)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|response to vitamin A (GO:0033189)|small molecule metabolic process (GO:0044281)|tetrahydrofolate metabolic process (GO:0046653)|uracil metabolic process (GO:0019860)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cofactor binding (GO:0048037)|drug binding (GO:0008144)|folic acid binding (GO:0005542)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|thymidylate synthase activity (GO:0004799)			endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(2)	8					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Raltitrexed(DB00293)|Trifluridine(DB00432)|Trimethoprim(DB00440)	GACGACAGAAGAATCATCATG	0.433																																																0			18											134	108	117					18																	669144		2203	4300	6503	659144	SO:0001583	missense	7298			X02308	CCDS11821.1	18p11.31-p11.21	2014-09-17			ENSG00000176890	ENSG00000176890	2.1.1.45		12441	protein-coding gene	gene with protein product		188350		TS			Standard	NM_001071		Approved	Tsase, TMS, HsT422	uc010dka.1	P04818	OTTHUMG00000131473	ENST00000323274.10:c.527G>A	18.37:g.669144G>A	ENSP00000315644:p.Arg176Lys		659144	Q8WYK3|Q8WYK4	Missense_Mutation	SNP	ENST00000323274.10	37	CCDS11821.1	.	.	.	.	.	.	.	.	.	.	G	36	5.641104	0.96693	.	.	ENSG00000176890	ENST00000323274;ENST00000323250	.	.	.	5.33	5.33	0.75918	Thymidylate synthase/dCMP hydroxymethylase domain (2);	0.000000	0.85682	D	0.000000	D	0.91095	0.7197	H	0.99777	4.77	0.80722	D	1	D;P	0.56035	0.974;0.943	P;P	0.58660	0.617;0.843	D	0.95302	0.8404	9	0.87932	D	0	-15.4925	18.9965	0.92815	0.0:0.0:1.0:0.0	.	93;176	Q8WYK4;P04818	.;TYSY_HUMAN	K	176;93	.	ENSP00000314902:R93K	R	+	2	0	TYMS	659144	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.307000	0.96226	2.496000	0.84212	0.467000	0.42956	AGA		0.433	TYMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254316.1	NM_001071		A	669144	G	A	669144	3	1	81	1	0	0	0	0	1	0	0	0	16852	942	33	3	541	3	TYMS	18	669144	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10		669144	77408104	160	23485										
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43205790	43205790	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctccaaagcagtgggctaccTcacgggcgacatgaaggagt	13	11	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr18:43205790T>C	ENST00000255226.6	+	3	1109	c.293T>C	c.(292-294)cTc>cCc	p.L98P	SLC14A2_ENST00000586448.1_Missense_Mutation_p.L98P	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	98					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTGGGCTACCTCACGGGCGAC	0.562																																																0			18											64	59	61					18																	43205790		2203	4300	6503	41459788	SO:0001583	missense	8170			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.293T>C	18.37:g.43205790T>C	ENSP00000255226:p.Leu98Pro		41459788	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520008	0.64634	.	.	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.59364	0.76;0.27	5.46	5.46	0.80206	.	0.327366	0.33382	N	0.004979	T	0.73257	0.3564	M	0.71581	2.175	0.58432	D	0.999992	P;D	0.71674	0.924;0.998	B;D	0.63488	0.44;0.915	T	0.76844	-0.2809	10	0.87932	D	0	-17.3514	15.3612	0.74475	0.0:0.0:0.0:1.0	.	98;98	Q15849;E7EPU1	UT2_HUMAN;.	P	98	ENSP00000255226:L98P;ENSP00000320689:L98P	ENSP00000255226:L98P	L	+	2	0	SLC14A2	41459788	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	5.579000	0.67457	2.293000	0.77203	0.528000	0.53228	CTC		0.562	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			C	43205790	T	C	43205790	3	2	81	1	0	0	0	0	1	0	0	0	14434	1551	54	4	299	4	SLC14A2	18	43205790	Missense_Mutation	SNP	T	TCGA-AH-6544-01A-11D-1826-10	42536646	43205790	34871458	161	23486										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72592993	72592993	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgtttgttgttgcaacaggCgagaagtcgtttctgtgtga	13	6	1	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr18:72592993C>T	ENST00000299687.5	+	5	5046	c.5046C>T	c.(5044-5046)ggC>ggT	p.G1682G	ZNF407_ENST00000584235.1_3'UTR|ZNF407_ENST00000577538.1_Splice_Site_p.G1682G	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1682					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TTGCAACAGGCGAGAAGTCGT	0.517																																																0			18											57	60	59					18																	72592993		1971	4153	6124	70721981	SO:0001630	splice_region_variant	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.5045-1C>T	18.37:g.72592993C>T			70721981	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.517	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	Silent	T	72592993	C	T	72592993	5	4	81	1	0	0	0	0	0	0	1	0	17926	782	27	1	5174	1	ZNF407	18	72592993	Splice_Site	SNP	C	TCGA-AH-6544-01A-11D-1826-10	29387203	72592993	5484255	162	23487										
STK11	6794	hgsc.bcm.edu	37	chr19	1207080	1207080	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctgatgggggacctgctgggGgaaggctcttacggcaaggt	18	8	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:1207080G>T	ENST00000326873.7	+	1	1341	c.168G>T	c.(166-168)ggG>ggT	p.G56G	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	56	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)|p.E57fs*107(1)|p.G56fs*4(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTGCTGGGGGAAGGCTCTT	0.607		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																												yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	25	Whole gene deletion(20)|Deletion - Frameshift(2)|Unknown(2)|Insertion - Frameshift(1)	cervix(15)|lung(4)|breast(1)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19											42	46	45					19																	1207080		2087	4200	6287	1158080	SO:0001819	synonymous_variant	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.168G>T	19.37:g.1207080G>T			1158080	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																				0.607	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1207080	G	T	1207080	2	4	81	1	0	0	0	0	0	0	0	1	15326	1219	43	2		2	STK11	19	1207080	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		1207080	57921903	163	23488										
KHSRP	8570	hgsc.bcm.edu	37	chr19	6416316	6416316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agaggatactcactgtggggGagccccgggtggcccctggt	17	11	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:6416316G>A	ENST00000398148.3	-	15	1683	c.1591C>T	c.(1591-1593)Ccc>Tcc	p.P531S	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	531	Ala/Gly/Pro-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CACTGTGGGGGAGCCCCGGGT	0.632																																					Colon(55;593 1006 2067 9135 22980)											0			19											11	13	12					19																	6416316		1831	4081	5912	6367316	SO:0001583	missense	8570			U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1591C>T	19.37:g.6416316G>A	ENSP00000381216:p.Pro531Ser		6367316	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Missense_Mutation	SNP	ENST00000398148.3	37	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629212	0.46944	.	.	ENSG00000088247	ENST00000398148;ENST00000201886	T	0.51325	0.71	5.21	5.21	0.72293	.	0.127256	0.52532	N	0.000066	T	0.36138	0.0956	N	0.19112	0.55	0.41399	D	0.987661	B	0.30914	0.3	B	0.29077	0.098	T	0.25222	-1.0138	10	0.46703	T	0.11	.	17.5431	0.87853	0.0:0.0:1.0:0.0	.	531	Q92945	FUBP2_HUMAN	S	531	ENSP00000381216:P531S	ENSP00000201886:P531S	P	-	1	0	KHSRP	6367316	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	4.330000	0.59266	2.425000	0.82216	0.655000	0.94253	CCC		0.632	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			A	6416316	G	A	6416316	3	1	81	1	0	0	0	0	1	0	0	0	8172	1174	41	3	568	3	KHSRP	19	6416316	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	5209236	6416316	52712667	164	23489										
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790576	19790576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	acaaatgtaaacaatgtggtAaagccttcatttccgcaggt	8	8	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:19790576A>G	ENST00000592502.1	+	4	888	c.778A>G	c.(778-780)Aaa>Gaa	p.K260E	ZNF101_ENST00000415784.2_Missense_Mutation_p.K140E|ZNF101_ENST00000444249.2_3'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						ACAATGTGGTAAAGCCTTCAT	0.393																																																0			19											42	40	41					19																	19790576		2203	4300	6503	19651576	SO:0001583	missense	94039			AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.778A>G	19.37:g.19790576A>G	ENSP00000468049:p.Lys260Glu		19651576	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582837	0.46006	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.27104	1.69;1.69	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41465	0.1160	M	0.80422	2.495	0.29330	N	0.866779	D	0.59767	0.986	P	0.59012	0.85	T	0.32613	-0.9900	8	.	.	.	.	4.8392	0.13481	0.9998:0.0:2.0E-4:0.0	.	260	Q8IZC7	ZN101_HUMAN	E	260;260;140	ENSP00000319716:K260E;ENSP00000400952:K140E	.	K	+	1	0	ZNF101	19651576	0.293000	0.24371	0.136000	0.22124	0.136000	0.21042	0.958000	0.29227	0.263000	0.21812	0.260000	0.18958	AAA		0.393	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		G	19790576	A	G	19790576	3	3	81	1	0	0	0	0	1	0	0	0	17753	363	13	4	792	4	ZNF101	19	19790576	Missense_Mutation	SNP	A	TCGA-AH-6544-01A-11D-1826-10	13374260	19790576	39338407	165	23490										
PHLDB3	653583	hgsc.bcm.edu	37	chr19	44006279	44006279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cctcagctccttcctctggcGctgtagctccttcactcgct	7	18	3	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:44006279G>A	ENST00000292140.5	-	3	730	c.370C>T	c.(370-372)Cgc>Tgc	p.R124C	PHLDB3_ENST00000599242.1_Missense_Mutation_p.R124C	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	124							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				TTCCTCTGGCGCTGTAGCTCC	0.657																																																0			19											26	28	27					19																	44006279		2202	4295	6497	48698119	SO:0001583	missense	653583				CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.370C>T	19.37:g.44006279G>A	ENSP00000292140:p.Arg124Cys		48698119	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483661	0.84854	.	.	ENSG00000176531	ENST00000292140	T	0.47528	0.84	4.11	4.11	0.48088	.	0.938103	0.08873	N	0.881237	T	0.62732	0.2452	L	0.47716	1.5	0.39113	D	0.961502	D;D	0.89917	1.0;1.0	D;P	0.72338	0.977;0.848	T	0.59558	-0.7432	10	0.72032	D	0.01	.	12.2619	0.54655	0.0:0.0:1.0:0.0	.	124;124	Q6NSJ2-2;Q6NSJ2	.;PHLB3_HUMAN	C	124	ENSP00000292140:R124C	ENSP00000292140:R124C	R	-	1	0	PHLDB3	48698119	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.602000	0.61098	2.040000	0.60383	0.306000	0.20318	CGC		0.657	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	44006279	G	A	44006279	3	1	81	1	0	0	0	0	1	0	0	0	11884	1087	38	1	1608	1	PHLDB3	19	44006279	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	24215703	44006279	15122704	166	23491										
FCGRT	2217	hgsc.bcm.edu	37	chr19	50017733	50017733	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gagaggggccgcggaaacctGgagtggaagggtgagccgga	21	7	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:50017733G>A	ENST00000221466.5	+	4	1077	c.591G>A	c.(589-591)ctG>ctA	p.L197L	FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000426395.3_Silent_p.L197L|FCGRT_ENST00000596975.1_Intron	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	197	Alpha-2.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		GCGGAAACCTGGAGTGGAAGG	0.662																																																0			19											18	21	20					19																	50017733		2203	4297	6500	54709545	SO:0001819	synonymous_variant	2217			U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"Immunoglobulin superfamily / C1-set domain containing"	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.591G>A	19.37:g.50017733G>A			54709545	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	G	9.210	1.030653	0.19512	.	.	ENSG00000104870	ENST00000415900	.	.	.	4.2	-1.24	0.09435	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9412	0.29959	0.0:0.5101:0.3124:0.1775	.	.	.	.	X	143	.	ENSP00000391574:W143X	W	+	2	0	FCGRT	54709545	1.000000	0.71417	0.999000	0.59377	0.755000	0.42902	0.522000	0.22909	0.041000	0.15688	0.511000	0.50034	TGG		0.662	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			A	50017733	G	A	50017733	2	1	81	1	0	0	0	0	0	0	0	1	5805	1335	47	3		3	FCGRT	19	50017733	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	6011454	50017733	9111250	167	23492										
AKT1S1	11284	hgsc.bcm.edu	37	chr19	50373291	50373291	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agcgcgcgcatgctcgccgcGatgcggtccaggtcgggcga	17	14	0	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:50373291G>A	ENST00000322344.3	-	0	0				PNKP_ENST00000595792.1_5'Flank|PNKP_ENST00000600910.1_5'Flank|AKT1S1_ENST00000391831.1_Silent_p.I218I|AKT1S1_ENST00000391832.3_Silent_p.I218I|AKT1S1_ENST00000391834.2_Silent_p.I218I|PNKP_ENST00000600573.1_5'Flank|AKT1S1_ENST00000344175.5_Silent_p.I218I|AKT1S1_ENST00000391833.1_Silent_p.I218I|AKT1S1_ENST00000391835.1_Silent_p.I238I|PNKP_ENST00000596014.1_5'Flank	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase						dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		TGCTCGCCGCGATGCGGTCCA	0.726								Other BER factors																																								0			19											9	9	9					19																	50373291		2161	4220	6381	55065103	SO:0001631	upstream_gene_variant	84335			AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60			19.37:g.50373291G>A	Exception_encountered		55065103	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Silent	SNP	ENST00000322344.3	37	CCDS12783.1																																																																																				0.726	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		A	50373291	G	A	50373291	1	1	81	0	1	0	0	0	0	0	0	0	479	1048	37	1		1	AKT1S1	19	50373291	5'Flank	SNP	G	TCGA-AH-6544-01A-11D-1826-10	355558	50373291	8755692	168	23493										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51022391	51022391	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tccgagatgtattccagccgCttgagctcgcccaggtccag	11	14	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:51022391C>T	ENST00000599957.1	-	3	776	c.579G>A	c.(577-579)aaG>aaA	p.K193K	LRRC4B_ENST00000389201.3_Silent_p.K193K			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	193					positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		ATTCCAGCCGCTTGAGCTCGC	0.652																																																0			19											37	44	41					19																	51022391		2182	4288	6470	55714203	SO:0001819	synonymous_variant	94030			BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.579G>A	19.37:g.51022391C>T			55714203	Q3ZCQ4|Q58F20	Silent	SNP	ENST00000599957.1	37	CCDS42595.1																																																																																				0.652	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		T	51022391	C	T	51022391	2	4	81	1	0	0	0	0	0	0	0	1	9036	796	28	3		3	LRRC4B	19	51022391	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	649100	51022391	8106592	169	23494										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56443516	56443516	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ctcaagtttgcccaggggatAcgcgggaagtgcccctgggg	16	11	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:56443516A>G	ENST00000342929.3	-	1	161	c.162T>C	c.(160-162)cgT>cgC	p.R54R	NLRP13_ENST00000588751.1_Silent_p.R54R	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	54	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CCCAGGGGATACGCGGGAAGT	0.552																																																0			19											58	61	60					19																	56443516		2203	4300	6503	61135328	SO:0001819	synonymous_variant	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.162T>C	19.37:g.56443516A>G			61135328	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																				0.552	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		G	56443516	A	G	56443516	2	3	81	1	0	0	0	0	0	0	0	1	10506	378	14	4		4	NLRP13	19	56443516	Silent	SNP	A	TCGA-AH-6544-01A-11D-1826-10	5421125	56443516	2685467	170	23495										
USP29	57663	hgsc.bcm.edu	37	chr19	57640913	57640913	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cagcaggggttccccaatttGggaaacacctgttacatgaa	10	10	0	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr19:57640913G>T	ENST00000254181.4	+	4	1324	c.870G>T	c.(868-870)ttG>ttT	p.L290F	USP29_ENST00000598197.1_Missense_Mutation_p.L290F	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	290	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCCCCAATTTGGGAAACACCT	0.468																																																0			19											75	72	73					19																	57640913		2203	4300	6503	62332725	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.870G>T	19.37:g.57640913G>T	ENSP00000254181:p.Leu290Phe		62332725		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.743190	0.49151	.	.	ENSG00000131864	ENST00000254181	T	0.78126	-1.15	2.68	2.68	0.31781	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.27176	U	0.020566	D	0.82379	0.5024	L	0.48877	1.53	0.31200	N	0.69994	D	0.89917	1.0	D	0.87578	0.998	T	0.81344	-0.0975	10	0.62326	D	0.03	-4.5761	11.5415	0.50669	0.0:0.0:1.0:0.0	.	290	Q9HBJ7	UBP29_HUMAN	F	290	ENSP00000254181:L290F	ENSP00000254181:L290F	L	+	3	2	USP29	62332725	1.000000	0.71417	0.974000	0.42286	0.718000	0.41266	1.551000	0.36233	1.774000	0.52232	0.585000	0.79938	TTG		0.468	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			T	57640913	G	T	57640913	3	4	81	1	0	0	0	0	1	0	0	0	17099	1339	47	2	872	2	USP29	19	57640913	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	1197397	57640913	1488070	171	23496										
MAVS	57506	hgsc.bcm.edu	37	chr20	3838404	3838404	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcggcactgaggggctgtgaGctagttgatctcgcggacga	17	9	1	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr20:3838404G>A	ENST00000428216.2	+	3	368	c.240G>A	c.(238-240)gaG>gaA	p.E80E	MAVS_ENST00000358134.6_Silent_p.E80E|MAVS_ENST00000416600.2_Intron	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	80					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GGGGCTGTGAGCTAGTTGATC	0.637																																																0			20											142	113	123					20																	3838404		2203	4300	6503	3786404	SO:0001819	synonymous_variant	57506			DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"virus-induced signaling adaptor", "IFN-B promoter stimulator 1", "CARD adaptor inducing IFN-beta"	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.240G>A	20.37:g.3838404G>A			3786404	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Silent	SNP	ENST00000428216.2	37	CCDS33437.1																																																																																				0.637	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746		A	3838404	G	A	3838404	2	1	81	1	0	0	0	0	0	0	0	1	9368	962	34	3		3	MAVS	20	3838404	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10		3838404	59187116	172	23497										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57768026	57768026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	agccagggaggtgggaatggGcagtggggcagaactgggct	21	6	0	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr20:57768026G>T	ENST00000371030.2	+	1	1952	c.1952G>T	c.(1951-1953)gGc>gTc	p.G651V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	651							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GTGGGAATGGGCAGTGGGGCA	0.567																																																0			20											58	68	65					20																	57768026		2036	4178	6214	57201421	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1952G>T	20.37:g.57768026G>T	ENSP00000360069:p.Gly651Val		57201421	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.083009	0.36758	.	.	ENSG00000124203	ENST00000371030	T	0.04502	3.61	5.09	-5.47	0.02600	.	0.520830	0.17398	N	0.175665	T	0.02304	0.0071	L	0.34521	1.04	0.19300	N	0.999979	B	0.30281	0.275	B	0.17979	0.02	T	0.34004	-0.9846	10	0.49607	T	0.09	-2.477	1.2164	0.01915	0.2272:0.3129:0.265:0.1949	.	651	Q5JPB2	ZN831_HUMAN	V	651	ENSP00000360069:G651V	ENSP00000360069:G651V	G	+	2	0	ZNF831	57201421	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.233000	0.17911	-0.876000	0.04017	-0.136000	0.14681	GGC		0.567	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57768026	G	T	57768026	3	4	81	1	0	0	0	0	1	0	0	0	18224	1203	42	2	1954	2	ZNF831	20	57768026	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	53929622	57768026	5257494	173	23498										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60921205	60921205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gctccccagagaagttgggcCggcagtagcatcgacccgtc	13	14	0	1	rs571258684		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr20:60921205C>T	ENST00000252999.3	-	10	1415	c.1349G>A	c.(1348-1350)cGg>cAg	p.R450Q	LAMA5_ENST00000370677.3_Missense_Mutation_p.R450Q|LAMA5_ENST00000370692.3_Missense_Mutation_p.R450Q	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	450	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GAAGTTGGGCCGGCAGTAGCA	0.652													C|||	1	0.000199681	0	0	5008	,	,		18025	0.001		0	False		,,,				2504	0															0			20											52	46	48					20																	60921205		2200	4297	6497	60354600	SO:0001583	missense	3911			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.1349G>A	20.37:g.60921205C>T	ENSP00000252999:p.Arg450Gln		60354600	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.655772	0.29425	.	.	ENSG00000130702	ENST00000252999;ENST00000370692;ENST00000370677	T;T;T	0.61742	0.08;0.08;0.08	4.78	1.31	0.21738	EGF-like, laminin (4);EGF-like region, conserved site (1);	0.106822	0.64402	N	0.000009	T	0.39410	0.1077	L	0.38649	1.16	0.32022	N	0.600716	B	0.30511	0.282	B	0.21546	0.035	T	0.44221	-0.9342	10	0.66056	D	0.02	.	5.6324	0.17518	0.0:0.3578:0.0:0.6422	.	450	O15230	LAMA5_HUMAN	Q	450	ENSP00000252999:R450Q;ENSP00000359726:R450Q;ENSP00000359711:R450Q	ENSP00000252999:R450Q	R	-	2	0	LAMA5	60354600	0.998000	0.40836	1.000000	0.80357	0.172000	0.22775	3.090000	0.50191	0.440000	0.26502	-0.258000	0.10820	CGG		0.652	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60921205	C	T	60921205	3	4	81	1	0	0	0	0	1	0	0	0	8631	652	23	1	10022	1	LAMA5	20	60921205	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	3153179	60921205	2104315	174	23499										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34011221	34011221	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	taacaaatgagacttacttgCggttgtgaggaagcttctga	11	6	1	3	rs372695378		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr21:34011221C>T	ENST00000322229.7	-	30	3911	c.3912G>A	c.(3910-3912)ccG>ccA	p.P1304P	SYNJ1_ENST00000382499.2_Silent_p.P1343P|SYNJ1_ENST00000382491.3_Silent_p.P1257P|SYNJ1_ENST00000357345.3_Silent_p.P1288P|SYNJ1_ENST00000433931.2_Silent_p.P1343P			O43426	SYNJ1_HUMAN	synaptojanin 1	1304	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.P1304P(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GACTTACTTGCGGTTGTGAGG	0.408																																																1	Substitution - coding silent(1)	ovary(1)	21											185	192	189					21																	34011221		2203	4300	6503	32933092	SO:0001819	synonymous_variant	8867			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.3912G>A	21.37:g.34011221C>T			32933092	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	37	CCDS54484.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.298|0.298	-0.975504|-0.975504	0.02215|0.02215	.|.	.|.	ENSG00000159082|ENSG00000159082	ENST00000438952|ENST00000418301	.|.	.|.	.|.	5.45|5.45	-1.31|-1.31	0.09230|0.09230	.|.	.|.	.|.	.|.	.|.	T|T	0.57636|0.57636	0.2067|0.2067	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52472|0.52472	-0.8571|-0.8571	4|4	.|.	.|.	.|.	.|.	11.0891|11.0891	0.48104|0.48104	0.0:0.4996:0.0:0.5004|0.0:0.4996:0.0:0.5004	.|.	.|.	.|.	.|.	T|H	180|125	.|.	.|.	A|R	-|-	1|2	0|0	SYNJ1|SYNJ1	32933092|32933092	0.261000|0.261000	0.24063|0.24063	0.016000|0.016000	0.15963|0.15963	0.073000|0.073000	0.16967|0.16967	-0.425000|-0.425000	0.07017|0.07017	-0.507000|-0.507000	0.06549|0.06549	-0.137000|-0.137000	0.14449|0.14449	GCA|CGC		0.408	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34011221	C	T	34011221	2	4	81	1	0	0	0	0	0	0	0	1	15491	755	27	1		1	SYNJ1	21	34011221	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10		34011221	14118674	175	23500										
C2CD2	25966	hgsc.bcm.edu	37	chr21	43327181	43327181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cagtagtgaccacagtcccaCagggcatcaccgtgcggtcc	11	15	1	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr21:43327181C>T	ENST00000380486.3	-	10	1479	c.1238G>A	c.(1237-1239)tGt>tAt	p.C413Y	C2CD2_ENST00000329623.7_Missense_Mutation_p.C258Y	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	413						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						CACAGTCCCACAGGGCATCAC	0.572																																																0			21											86	77	80					21																	43327181		2203	4300	6503	42200250	SO:0001583	missense	25966			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1238G>A	21.37:g.43327181C>T	ENSP00000369853:p.Cys413Tyr		42200250	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319812	0.81469	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.25250	1.83;1.81	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.48857	0.1523	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.37686	-0.9695	10	0.17832	T	0.49	-12.0695	18.0791	0.89437	0.0:1.0:0.0:0.0	.	258;413	Q6P6D1;Q9Y426	.;CU025_HUMAN	Y	258;413	ENSP00000329302:C258Y;ENSP00000369853:C413Y	ENSP00000329302:C258Y	C	-	2	0	C2CD2	42200250	1.000000	0.71417	0.991000	0.47740	0.919000	0.55068	5.467000	0.66737	2.413000	0.81919	0.655000	0.94253	TGT		0.572	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		T	43327181	C	T	43327181	3	4	81	1	0	0	0	0	1	0	0	0	2158	478	17	3	872	3	C2CD2	21	43327181	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	9315960	43327181	4802714	176	23501										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46658574	46658574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gatcctcacgcgctggatgaCgcaggcgtttatctgacagg	13	11	2	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chr22:46658574C>T	ENST00000253255.5	-	1	645	c.646G>A	c.(646-648)Gtc>Atc	p.V216I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	216	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CGCTGGATGACGCAGGCGTTT	0.667																																																0			22											29	27	28					22																	46658574		2202	4299	6501	45037238	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.646G>A	22.37:g.46658574C>T	ENSP00000253255:p.Val216Ile		45037238	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	C	7.060	0.566285	0.13560	.	.	ENSG00000130943	ENST00000253255	T	0.36157	1.27	4.31	-8.62	0.00881	Egg jelly receptor, REJ-like (1);	13.678900	0.00166	N	0.000005	T	0.18635	0.0447	N	0.24115	0.695	0.09310	N	1	B	0.22146	0.065	B	0.08055	0.003	T	0.08911	-1.0699	10	0.20519	T	0.43	0.0245	4.7493	0.13052	0.0822:0.1846:0.1884:0.5449	.	216	Q9NTG1	PKDRE_HUMAN	I	216	ENSP00000253255:V216I	ENSP00000253255:V216I	V	-	1	0	PKDREJ	45037238	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.937000	0.01547	-2.617000	0.00442	-0.467000	0.05162	GTC		0.667	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46658574	C	T	46658574	3	4	81	1	0	0	0	0	1	0	0	0	12001	536	19	1	6119	1	PKDREJ	22	46658574	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10		46658574	4645992	177	23502										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29935625	29935625	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gagctttctttgggtacagcGgagatgtcagtcctttaatt	11	7	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:29935625G>T	ENST00000378993.1	+	7	1496	c.823G>T	c.(823-825)Gga>Tga	p.G275*	IL1RAPL1_ENST00000302196.4_Nonsense_Mutation_p.G275*	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	275	Ig-like C2-type 3.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.G275*(1)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						TGGGTACAGCGGAGATGTCAG	0.348																																																1	Substitution - Nonsense(1)	ovary(1)	X											59	55	57					X																	29935625		2202	4300	6502	29845546	SO:0001587	stop_gained	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.823G>T	X.37:g.29935625G>T	ENSP00000368278:p.Gly275*		29845546	A0AVG4|Q9UJ53	Nonsense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	G	44	10.819807	0.99472	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1532	0.93499	0.0:0.0:1.0:0.0	.	.	.	.	X	275	.	.	G	+	1	0	IL1RAPL1	29845546	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	9.431000	0.97494	2.474000	0.83562	0.600000	0.82982	GGA		0.348	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29935625	G	T	29935625	4	4	81	1	0	0	0	0	0	1	0	0	7682	1117	39	2	845	2	IL1RAPL1	23	29935625	Nonsense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10		29935625	125334935	178	23503										
DDX3X	1654	hgsc.bcm.edu	37	chrX	41203509	41203509	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	tagttttcataccgatctagAgttcgtccttgcgtggttta	9	8	2	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:41203509A>G	ENST00000399959.2	+	10	1737	c.882A>G	c.(880-882)agA>agG	p.R294R	DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000457138.2_Silent_p.R278R|DDX3X_ENST00000478993.1_3'UTR|RN7SL15P_ENST00000582825.1_RNA	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	294	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with GSK3B.|Necessary for interaction with XPO1.		R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						ACCGATCTAGAGTTCGTCCTT	0.373										HNSCC(61;0.18)																																						0			X											217	199	205					X																	41203509		2203	4300	6503	41088453	SO:0001819	synonymous_variant	1654			U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"DEAD-boxes"	2745	protein-coding gene	gene with protein product		300160	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.882A>G	X.37:g.41203509A>G			41088453	A8K538|B4E3E8|O15536	Silent	SNP	ENST00000399959.2	37	CCDS43931.1																																																																																				0.373	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		G	41203509	A	G	41203509	2	3	81	1	0	0	0	0	0	0	0	1	4364	301	11	4		4	DDX3X	23	41203509	Silent	SNP	A	TCGA-AH-6544-01A-11D-1826-10	11267884	41203509	114067051	179	23504										
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56591890	56591890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gcagccccccctggctccacCggctctggtggccccacggg	13	20	1	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:56591890C>T	ENST00000338222.5	+	1	1865	c.1584C>T	c.(1582-1584)acC>acT	p.T528T		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	528					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						CTGGCTCCACCGGCTCTGGTG	0.622																																					Esophageal Squamous(104;218 1492 6022 10838 28884)											0			X											8	9	9					X																	56591890		2169	4243	6412	56608615	SO:0001819	synonymous_variant	29978			AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"Ubiquilin family"	12509	protein-coding gene	gene with protein product	"NEDD4 binding protein 4"	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1584C>T	X.37:g.56591890C>T			56608615	O94798|Q5D027|Q9H3W6|Q9HAZ4	Silent	SNP	ENST00000338222.5	37	CCDS14374.1																																																																																				0.622	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		T	56591890	C	T	56591890	2	4	81	1	0	0	0	0	0	0	0	1	16937	639	23	1		1	UBQLN2	23	56591890	Silent	SNP	C	TCGA-AH-6544-01A-11D-1826-10	15388381	56591890	98678670	180	23505										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63411783	63411783	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	atcactattgggggcggattCttgctggtcactctgaggag	14	8	4	1			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:63411783C>A	ENST00000330258.3	-	2	1656	c.1384G>T	c.(1384-1386)Gaa>Taa	p.E462*	AMER1_ENST00000403336.1_Nonsense_Mutation_p.E462*|AMER1_ENST00000374869.3_Nonsense_Mutation_p.E462*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	462					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.E462*(2)									GGGGCGGATTCTTGCTGGTCA	0.547																																																69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	X											95	71	79					X																	63411783		2203	4300	6503	63328508	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1384G>T	X.37:g.63411783C>A	ENSP00000329117:p.Glu462*		63328508	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	40	8.150724	0.98678	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.32	5.32	0.75619	.	0.191892	0.43416	D	0.000580	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.9457	16.762	0.85514	0.0:1.0:0.0:0.0	.	.	.	.	X	462	.	ENSP00000329117:E462X	E	-	1	0	FAM123B	63328508	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	7.320000	0.79064	2.618000	0.88619	0.600000	0.82982	GAA		0.547	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411783	C	A	63411783	4	1	81	1	0	0	0	0	0	1	0	0	5439	922	32	2	2027	2	FAM123B	23	63411783	Nonsense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	6819893	63411783	91858777	181	23506										
NLGN3	54413	hgsc.bcm.edu	37	chrX	70387356	70387356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	ccgtgacaaccctgagacccGccgtaaaacactggtggcac	10	15	0	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:70387356G>A	ENST00000358741.3	+	7	1712	c.1409G>A	c.(1408-1410)cGc>cAc	p.R470H	NLGN3_ENST00000374051.3_Missense_Mutation_p.R450H|NLGN3_ENST00000536169.1_Missense_Mutation_p.R430H|NLGN3_ENST00000476589.1_3'UTR	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	470					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.R450H(1)		biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					CCTGAGACCCGCCGTAAAACA	0.567																																					Esophageal Squamous(103;760 1488 16849 22250 40351)											1	Substitution - Missense(1)	large_intestine(1)	X											53	43	46					X																	70387356		2203	4300	6503	70304081	SO:0001583	missense	54413			AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.1409G>A	X.37:g.70387356G>A	ENSP00000351591:p.Arg470His		70304081	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	37	CCDS55441.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.501428|4.501428	0.85176|0.85176	.|.	.|.	ENSG00000196338|ENSG00000196338	ENST00000542063|ENST00000536169;ENST00000374051;ENST00000395855;ENST00000358741	.|T;T;T;T	.|0.58940	.|0.3;0.3;0.3;0.3	4.9|4.9	4.9|4.9	0.64082|0.64082	.|Carboxylesterase, type B (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.74053|0.74053	0.3666|0.3666	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;0.999;0.999	T|T	0.76724|0.76724	-0.2854|-0.2854	5|10	.|0.62326	.|D	.|0.03	.|.	17.3394|17.3394	0.87291|0.87291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|430;470;450	.|D3DVV1;Q9NZ94;Q9NZ94-2	.|.;NLGN3_HUMAN;.	T|H	333|430;450;430;470	.|ENSP00000445298:R430H;ENSP00000363163:R450H;ENSP00000379196:R430H;ENSP00000351591:R470H	.|ENSP00000351591:R470H	A|R	+|+	1|2	0|0	NLGN3|NLGN3	70304081|70304081	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.657000|9.657000	0.98554|0.98554	2.277000|2.277000	0.76020|0.76020	0.508000|0.508000	0.49915|0.49915	GCC|CGC		0.567	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		A	70387356	G	A	70387356	3	1	81	1	0	0	0	0	1	0	0	0	10494	1087	38	1	1431	1	NLGN3	23	70387356	Missense_Mutation	SNP	G	TCGA-AH-6544-01A-11D-1826-10	6975573	70387356	84883204	182	23507										
POU3F4	5456	hgsc.bcm.edu	37	chrX	82764379	82764379	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cagccgcatgaggtttattcGcacaccgtgaaaacagacac	9	12	0	3			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:82764379G>A	ENST00000373200.2	+	1	1111	c.1047G>A	c.(1045-1047)tcG>tcA	p.S349S	RP3-326L13.2_ENST00000607095.1_RNA|RP3-326L13.3_ENST00000607789.1_lincRNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	349					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						AGGTTTATTCGCACACCGTGA	0.532																																																0			X											21	18	19					X																	82764379		2200	4296	6496	82651035	SO:0001819	synonymous_variant	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.1047G>A	X.37:g.82764379G>A			82651035	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	37	CCDS14450.1																																																																																				0.532	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		A	82764379	G	A	82764379	2	1	81	1	0	0	0	0	0	0	0	1	12308	1074	38	1		1	POU3F4	23	82764379	Silent	SNP	G	TCGA-AH-6544-01A-11D-1826-10	12377023	82764379	72506181	183	23508										
CAPN6	827	hgsc.bcm.edu	37	chrX	110489890	110489890	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cagttggaccacccttcttaCgcaggtacagagacttcaga	9	12	2	2	rs201824799		TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:110489890C>G	ENST00000324068.1	-	13	2008	c.1841G>C	c.(1840-1842)cGt>cCt	p.R614P	CAPN6_ENST00000541758.1_Missense_Mutation_p.R359P	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	614	C2.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						ACCCTTCTTACGCAGGTACAG	0.507																																																0			X											189	136	154					X																	110489890		2203	4300	6503	110376546	SO:0001583	missense	827			AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1841G>C	X.37:g.110489890C>G	ENSP00000317214:p.Arg614Pro		110376546	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	37	CCDS14555.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162050	0.57368	.	.	ENSG00000077274	ENST00000324068;ENST00000541758	T;T	0.68903	-0.36;-0.36	5.37	4.51	0.55191	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	1.074500	0.07000	N	0.823094	T	0.76285	0.3966	L	0.46157	1.445	0.48341	D	0.999632	D	0.71674	0.998	D	0.68192	0.956	T	0.64918	-0.6294	10	0.72032	D	0.01	.	8.5428	0.33404	0.0:0.8192:0.0:0.1808	.	614	Q9Y6Q1	CAN6_HUMAN	P	614;359	ENSP00000317214:R614P;ENSP00000441736:R359P	ENSP00000317214:R614P	R	-	2	0	CAPN6	110376546	0.750000	0.28316	1.000000	0.80357	0.998000	0.95712	1.591000	0.36665	1.250000	0.43966	0.589000	0.80489	CGT		0.507	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			G	110489890	C	G	110489890	3	3	81	1	0	0	0	0	1	0	0	0	2636	536	19	5	88	5	CAPN6	23	110489890	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	27725511	110489890	44780670	184	23509										
PRRG3	79057	hgsc.bcm.edu	37	chrX	150869330	150869330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	cacagtccggctagagagcaCcctctacctccctgagctct	8	17	2	2			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrX:150869330C>A	ENST00000370353.3	+	4	911	c.521C>A	c.(520-522)aCc>aAc	p.T174N	PRRG3_ENST00000538575.1_Missense_Mutation_p.T174N			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	174						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					CTAGAGAGCACCCTCTACCTC	0.672																																																0			X											48	38	41					X																	150869330		2202	4300	6502	150619986	SO:0001583	missense	79057			AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.521C>A	X.37:g.150869330C>A	ENSP00000359378:p.Thr174Asn		150619986	A1A523|A1A575|Q8N2N6	Missense_Mutation	SNP	ENST00000370353.3	37	CCDS14699.1	.	.	.	.	.	.	.	.	.	.	C	9.761	1.170085	0.21621	.	.	ENSG00000130032	ENST00000538575;ENST00000370353	D;D	0.98280	-4.84;-4.84	4.31	2.32	0.28847	.	0.457400	0.19232	N	0.119391	D	0.92532	0.7628	N	0.14661	0.345	0.31120	N	0.709007	B	0.33694	0.421	B	0.35550	0.205	D	0.89086	0.3479	9	.	.	.	-25.4068	1.971	0.03406	0.2085:0.4755:0.1992:0.1168	.	174	Q9BZD7	TMG3_HUMAN	N	174	ENSP00000440217:T174N;ENSP00000359378:T174N	.	T	+	2	0	PRRG3	150619986	0.959000	0.32827	0.995000	0.50966	0.320000	0.28249	1.384000	0.34396	0.926000	0.37118	0.523000	0.50628	ACC		0.672	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		A	150869330	C	A	150869330	3	1	81	1	0	0	0	0	1	0	0	0	12641	507	18	2	531	2	PRRG3	23	150869330	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10	40379440	150869330	4401230	185	23510										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	5605726	5605726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	0.751084727468969	1.77339449541284	0.644870725604671	0.103188405797102	0.466258722490609	0	gccacagctcttctctgccaCaggttattgccctccatcgt	7	16	2	0			TCGA-AH-6544-01A-11D-1826-10	TCGA-AH-6544-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	12456af5-23f0-4e3f-a623-ce1866ab375e	739c1712-069d-4442-8eb1-d91149388521	g.chrY:5605726C>A	ENST00000215473.6	+	6	3766	c.3766C>A	c.(3766-3768)Cag>Aag	p.Q1256K				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1256					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTCTCTGCCACAGGTTATTGC	0.547																																																0			Y																																								5665726	SO:0001583	missense	83259			AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3766C>A	Y.37:g.5605726C>A	ENSP00000215473:p.Gln1256Lys		5665726	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000215473.6	37																																																																																					0.547	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973		A	5605726	C	A	5605726	3	1	81	1	0	0	0	0	1	0	0	0	11540	479	17	2	3842	2	PCDH11Y	24	5605726	Missense_Mutation	SNP	C	TCGA-AH-6544-01A-11D-1826-10		5605726	53767840	186	23511										
VAV3	10451	hgsc.bcm.edu	37	chr1	108313293	108313293	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	caaagtttctgtatatttttCttctgtctgcttaatttctg	5	7	5	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:108313293C>T	ENST00000370056.4	-	6	887	c.613G>A	c.(613-615)Gaa>Aaa	p.E205K	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000527011.1_Missense_Mutation_p.E205K|VAV3_ENST00000371846.4_Missense_Mutation_p.E140K	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	205	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.E205*(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		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)		GTATATTTTTCTTCTGTCTGC	0.279																																																1	Substitution - Nonsense(1)	ovary(1)	1											119	122	121					1																	108313293		2201	4298	6499	108114816	SO:0001583	missense	10451			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.613G>A	1.37:g.108313293C>T	ENSP00000359073:p.Glu205Lys		108114816	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380261	0.82682	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.62105	0.05;0.05;0.05	5.8	5.8	0.92144	Dbl homology (DH) domain (5);Calponin homology domain (1);	0.052398	0.85682	D	0.000000	T	0.65386	0.2686	L	0.43152	1.355	0.58432	D	0.999999	B;D;B;D	0.64830	0.051;0.994;0.397;0.972	B;P;B;P	0.60682	0.041;0.842;0.304;0.878	T	0.59768	-0.7392	10	0.33940	T	0.23	.	20.0706	0.97721	0.0:1.0:0.0:0.0	.	205;205;140;205	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4	.;.;.;VAV3_HUMAN	K	205;205;140	ENSP00000359073:E205K;ENSP00000432540:E205K;ENSP00000360912:E140K	ENSP00000359073:E205K	E	-	1	0	VAV3	108114816	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.229000	0.78088	2.744000	0.94065	0.655000	0.94253	GAA		0.279	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108313293	C	T	108313293	3	4	82	1	0	0	0	0	1	0	0	0	17173	922	32	3	2043	3	VAV3	1	108313293	Missense_Mutation	SNP	C	TCGA-AH-6547-01A-11D-1826-10		108313293	140937328	1	23512										
INTS3	65123	hgsc.bcm.edu	37	chr1	153724879	153724879	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tcaggccttgagtcctcagtTcacaggtaagtagggtctta	11	9	4	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:153724879T>C	ENST00000318967.2	+	8	1422	c.854T>C	c.(853-855)tTc>tCc	p.F285S	RP11-216N14.9_ENST00000434575.1_RNA|INTS3_ENST00000435409.2_Missense_Mutation_p.F285S|INTS3_ENST00000512605.1_Missense_Mutation_p.F79S|snoU13_ENST00000458994.1_RNA|RP11-216N14.8_ENST00000453778.1_RNA|INTS3_ENST00000456435.1_Missense_Mutation_p.F79S|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	286					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGTCCTCAGTTCACAGGTAAG	0.448																																																0			1											243	222	229					1																	153724879		2203	4300	6503	151991503	SO:0001583	missense	65123			BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.854T>C	1.37:g.153724879T>C	ENSP00000318641:p.Phe285Ser		151991503	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.255995	0.80246	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	3.99	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.74966	0.3786	M	0.86573	2.825	0.58432	D	0.999998	D;D;D	0.69078	0.981;0.997;0.997	D;D;D	0.79108	0.959;0.992;0.986	T	0.79964	-0.1581	9	0.87932	D	0	.	11.1537	0.48476	0.0:0.0:0.0:1.0	.	79;286;285	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	S	285;79;285;79	.	ENSP00000318641:F285S	F	+	2	0	INTS3	151991503	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.249000	0.78278	1.803000	0.52742	0.397000	0.26171	TTC		0.448	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		C	153724879	T	C	153724879	3	2	82	1	0	0	0	0	1	0	0	0	7800	1783	62	4	884	4	INTS3	1	153724879	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10	45411586	153724879	95525742	2	23513										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156926339	156926339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ggctcatgtaggtattgaggGcgaagtccatgggggcgctg	18	7	1	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:156926339G>A	ENST00000361409.2	-	18	2166	c.1424C>T	c.(1423-1425)gCc>gTc	p.A475V	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.A515V	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	475	RGSL. {ECO:0000255|PROSITE- ProRule:PRU00171}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGTATTGAGGGCGAAGTCCAT	0.532																																																0			1											153	130	137					1																	156926339		2203	4300	6503	155192963	SO:0001583	missense	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.1424C>T	1.37:g.156926339G>A	ENSP00000354644:p.Ala475Val		155192963	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477778	0.63849	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	D;D	0.83075	-1.68;-1.68	5.08	5.08	0.68730	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.53938	D	0.000060	T	0.81178	0.4768	L	0.35288	1.05	0.80722	D	1	D;D	0.89917	1.0;0.967	D;P	0.91635	0.999;0.742	T	0.76044	-0.3103	10	0.08837	T	0.75	-19.752	18.2585	0.90025	0.0:0.0:1.0:0.0	.	475;515	O15085;O15085-2	ARHGB_HUMAN;.	V	515;475	ENSP00000357177:A515V;ENSP00000354644:A475V	ENSP00000354644:A475V	A	-	2	0	ARHGEF11	155192963	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.446000	0.66600	2.635000	0.89317	0.585000	0.79938	GCC		0.532	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156926339	G	A	156926339	3	1	82	1	0	0	0	0	1	0	0	0	896	1203	42	3	3236	3	ARHGEF11	1	156926339	Missense_Mutation	SNP	G	TCGA-AH-6547-01A-11D-1826-10	3201460	156926339	92324282	3	23514										
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158914825	158914825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aaccccatccagcagttcctTcaccaaggtacaatatcctg	5	15	1	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:158914825T>C	ENST00000368140.1	+	7	1597	c.1352T>C	c.(1351-1353)tTc>tCc	p.F451S	PYHIN1_ENST00000392252.3_Missense_Mutation_p.F442S|PYHIN1_ENST00000392254.2_Missense_Mutation_p.F451S|PYHIN1_ENST00000368138.3_Missense_Mutation_p.F442S|PYHIN1_ENST00000485134.1_3'UTR	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	451					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AGCAGTTCCTTCACCAAGGTA	0.448																																																0			1											136	137	136					1																	158914825		2203	4300	6503	157181449	SO:0001583	missense	149628			AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1352T>C	1.37:g.158914825T>C	ENSP00000357122:p.Phe451Ser		157181449	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.527427	0.27299	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.04758	3.56;3.56;3.59;3.58	1.88	-2.46	0.06461	.	.	.	.	.	T	0.00875	0.0029	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.12630	0.006;0.006;0.006;0.003	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47649	-0.9101	9	0.87932	D	0	.	2.3064	0.04175	0.2301:0.4043:0.0:0.3655	.	442;451;442;451	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	S	451;442;451;442	ENSP00000357122:F451S;ENSP00000357120:F442S;ENSP00000376083:F451S;ENSP00000376082:F442S	ENSP00000357120:F442S	F	+	2	0	PYHIN1	157181449	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-1.181000	0.03085	-0.658000	0.05366	0.377000	0.23210	TTC		0.448	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		C	158914825	T	C	158914825	3	2	82	1	0	0	0	0	1	0	0	0	12902	1783	62	4	1374	4	PYHIN1	1	158914825	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10	1988486	158914825	90335796	4	23515										
USH2A	7399	hgsc.bcm.edu	37	chr1	216497642	216497642	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tattttccttcttcctttgaAtccttatttccgttggttgt	5	9	1	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:216497642A>G	ENST00000307340.3	-	7	1582	c.1196T>C	c.(1195-1197)aTt>aCt	p.I399T	USH2A_ENST00000366943.2_Missense_Mutation_p.I399T|USH2A_ENST00000366942.3_Missense_Mutation_p.I399T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	399	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTCCTTTGAATCCTTATTTC	0.313										HNSCC(13;0.011)																																						0			1											85	91	89					1																	216497642		2200	4295	6495	214564265	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1196T>C	1.37:g.216497642A>G	ENSP00000305941:p.Ile399Thr		214564265	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943170	0.73672	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;D;D	0.82619	-1.63;-1.63;-1.63	5.52	4.39	0.52855	Laminin, N-terminal (3);	0.305510	0.22328	N	0.061507	D	0.91102	0.7199	M	0.87269	2.87	0.58432	D	0.999999	D;P	0.89917	1.0;0.889	D;P	0.74348	0.983;0.526	D	0.91238	0.5019	10	0.87932	D	0	.	11.1893	0.48675	0.9279:0.0:0.0721:0.0	.	399;399	O75445-2;O75445	.;USH2A_HUMAN	T	399	ENSP00000305941:I399T;ENSP00000355910:I399T;ENSP00000355909:I399T	ENSP00000305941:I399T	I	-	2	0	USH2A	214564265	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	5.008000	0.63991	0.918000	0.36919	0.533000	0.62120	ATT		0.313	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216497642	A	G	216497642	3	3	82	1	0	0	0	0	1	0	0	0	17076	101	4	4	14690	4	USH2A	1	216497642	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10	57582817	216497642	32752979	5	23516										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	82	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-AH-6547-01A-11D-1826-10	23873272	240370914	8879707	6	23517										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63101560	63101560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ttcaagaactagaaactgaaAggcgagtgaaaagaaaggcc	11	6	1	5			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:63101560A>G	ENST00000263991.5	+	11	1665	c.1183A>G	c.(1183-1185)Agg>Ggg	p.R395G	EHBP1_ENST00000405015.3_Missense_Mutation_p.R360G|EHBP1_ENST00000354487.3_Missense_Mutation_p.R360G|EHBP1_ENST00000405289.1_Missense_Mutation_p.R360G|EHBP1_ENST00000431489.1_Missense_Mutation_p.R360G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	395			R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGAAACTGAAAGGCGAGTGAA	0.378																																																0			2											98	108	104					2																	63101560		2203	4300	6503	62955064	SO:0001583	missense	23301			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.1183A>G	2.37:g.63101560A>G	ENSP00000263991:p.Arg395Gly		62955064	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242526	0.39598	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T	0.74002	-0.8;-0.8;-0.79;-0.79;-0.79	5.13	3.95	0.45737	.	0.467690	0.24752	N	0.035895	T	0.62073	0.2398	L	0.43152	1.355	0.37765	D	0.926455	P;B;B	0.35684	0.515;0.13;0.009	B;B;B	0.29862	0.108;0.022;0.031	T	0.59984	-0.7351	10	0.20046	T	0.44	.	12.0596	0.53555	0.8503:0.1497:0.0:0.0	.	360;360;395	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	G	360;360;395;360;360	ENSP00000384143:R360G;ENSP00000403783:R360G;ENSP00000263991:R395G;ENSP00000346482:R360G;ENSP00000385524:R360G	ENSP00000263991:R395G	R	+	1	2	EHBP1	62955064	1.000000	0.71417	0.992000	0.48379	0.964000	0.63967	3.296000	0.51802	0.884000	0.36064	0.528000	0.53228	AGG		0.378	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		G	63101560	A	G	63101560	3	3	82	1	0	0	0	0	1	0	0	0	4986	63	3	4	1221	4	EHBP1	2	63101560	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10		63101560	180097813	7	23518										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98392471	98392471	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ttcaccttgcgctgaagaggTtttcctttccctgaggataa	9	10	1	3			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:98392471T>C	ENST00000186436.5	-	32	4383	c.4155A>G	c.(4153-4155)aaA>aaG	p.K1385K		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1385	Lys-rich.					integral component of membrane (GO:0016021)		p.K1272K(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						GCTGAAGAGGTTTTCCTTTCC	0.433																																																1	Substitution - coding silent(1)	ovary(1)	2											155	150	151					2																	98392471		1879	4104	5983	97758903	SO:0001819	synonymous_variant	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.4155A>G	2.37:g.98392471T>C			97758903		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																				0.433	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		C	98392471	T	C	98392471	2	2	82	1	0	0	0	0	0	0	0	1	16083	1722	60	4		4	TMEM131	2	98392471	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10	35290911	98392471	144806902	8	23519										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113067586	113067586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	cttcggtaactacagtgatgAcaactttggtaactacggtc	9	9	0	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:113067586A>G	ENST00000409871.1	+	4	862	c.461A>G	c.(460-462)gAc>gGc	p.D154G	ZC3H6_ENST00000343936.4_Missense_Mutation_p.D154G	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	154							metal ion binding (GO:0046872)	p.D154G(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TACAGTGATGACAACTTTGGT	0.363																																																1	Substitution - Missense(1)	ovary(1)	2											77	72	74					2																	113067586		1881	4113	5994	112784057	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.461A>G	2.37:g.113067586A>G	ENSP00000386764:p.Asp154Gly		112784057	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618229	0.46736	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15718	2.4;2.4	3.09	3.09	0.35607	.	1.025170	0.07767	N	0.951061	T	0.12817	0.0311	N	0.22421	0.69	0.33846	D	0.632094	P	0.34522	0.455	B	0.34093	0.175	T	0.20806	-1.0264	10	0.66056	D	0.02	-16.8445	7.9401	0.29952	1.0:0.0:0.0:0.0	.	154	P61129	ZC3H6_HUMAN	G	154;154;131	ENSP00000386764:D154G;ENSP00000340298:D154G	ENSP00000340298:D154G	D	+	2	0	ZC3H6	112784057	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.476000	0.60216	1.671000	0.50874	0.459000	0.35465	GAC		0.363	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		G	113067586	A	G	113067586	3	3	82	1	0	0	0	0	1	0	0	0	17610	275	10	4	475	4	ZC3H6	2	113067586	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10	14675115	113067586	130131787	9	23520										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15727739	15727739	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	cgaaacttactgtccatttcCatcttgaatatccactgcat	4	12	1	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:15727739C>A	ENST00000399451.2	-	19	2318	c.1951G>T	c.(1951-1953)Gga>Tga	p.G651*	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Nonsense_Mutation_p.G684*	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	651						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGTCCATTTCCATCTTGAATA	0.368																																																0			3											131	111	118					3																	15727739		1900	4117	6017	15702743	SO:0001587	stop_gained	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1951G>T	3.37:g.15727739C>A	ENSP00000382379:p.Gly651*		15702743	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Nonsense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	C	40	8.459582	0.98820	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	.	.	.	X	651;684;651	.	ENSP00000373287:G684X	G	-	1	0	ANKRD28	15702743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.718000	0.92993	0.655000	0.94253	GGA		0.368	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		A	15727739	C	A	15727739	4	1	82	1	0	0	0	0	0	1	0	0	656	603	21	2	1250	2	ANKRD28	3	15727739	Nonsense_Mutation	SNP	C	TCGA-AH-6547-01A-11D-1826-10		15727739	182294691	10	23521										
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38307445	38307445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tgtgtgttctcaacttcctgTctcccttctacttttttgcc	5	13	3	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:38307445T>C	ENST00000311856.4	+	1	143	c.94T>C	c.(94-96)Tct>Cct	p.S32P	SLC22A13_ENST00000450935.2_5'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	32					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		CAACTTCCTGTCTCCCTTCTA	0.502																																																0			3											219	182	194					3																	38307445		2203	4300	6503	38282449	SO:0001583	missense	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.94T>C	3.37:g.38307445T>C	ENSP00000310241:p.Ser32Pro		38282449	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	37	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	.	4.528	0.097917	0.08681	.	.	ENSG00000172940	ENST00000311856	T	0.65549	-0.16	4.55	-9.11	0.00711	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.848720	0.02502	N	0.090608	T	0.69788	0.3150	M	0.78637	2.42	0.09310	N	0.999998	P;P	0.51147	0.942;0.836	P;P	0.52881	0.712;0.519	T	0.74090	-0.3777	10	0.34782	T	0.22	.	11.8312	0.52297	0.6963:0.0:0.2063:0.0974	.	32;32	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	P	32	ENSP00000310241:S32P	ENSP00000310241:S32P	S	+	1	0	SLC22A13	38282449	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.530000	0.00944	-3.802000	0.00105	-0.433000	0.05886	TCT		0.502	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38307445	T	C	38307445	3	2	82	1	0	0	0	0	1	0	0	0	14481	1667	58	4	96	4	SLC22A13	3	38307445	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10	22579706	38307445	159714985	11	23522										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41267276	41267276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gaaaatggttgccttgctcaAcaaaacaaatgttaaattct	6	7	2	0	rs35288908	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:41267276A>G	ENST00000349496.5	+	6	1140	c.860A>G	c.(859-861)aAc>aGc	p.N287S	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N287S|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N287S|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N280S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N287S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	287					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N287S(2)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GCCTTGCTCAACAAAACAAAT	0.388		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	2	Substitution - Missense(2)	large_intestine(2)	3	GRCh37	CM043757	CTNNB1	M	rs35288908	A	SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	122	119	120		860,860,860	5.7	1	3	dbSNP_126	120	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense,missense	CTNNB1	NM_001098209.1,NM_001098210.1,NM_001904.3	46,46,46	0,13,6490	GG,GA,AA		0.1395,0.0227,0.1	benign,benign,benign	287/782,287/782,287/782	41267276	13,12993	2203	4300	6503	41242280	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.860A>G	3.37:g.41267276A>G	ENSP00000344456:p.Asn287Ser		41242280	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370081	0.24771	2.27E-4	0.001395	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.184600	0.56097	D	0.000034	T	0.37598	0.1009	N	0.02315	-0.6	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28933	-1.0028	10	0.20519	T	0.43	-1.1628	16.0129	0.80417	1.0:0.0:0.0:0.0	rs35288908	215;287	B4DSW9;P35222	.;CTNB1_HUMAN	S	287;287;287;280;287	ENSP00000385604:N287S;ENSP00000379486:N287S;ENSP00000344456:N287S;ENSP00000411226:N280S;ENSP00000379488:N287S	ENSP00000344456:N287S	N	+	2	0	CTNNB1	41242280	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.328000	0.65887	2.184000	0.69523	0.482000	0.46254	AAC		0.388	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41267276	A	G	41267276	3	3	82	1	0	0	0	0	1	0	0	0	4022	43	2	4	878	4	CTNNB1	3	41267276	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10	2959831	41267276	156755154	12	23523										
BBX	56987	hgsc.bcm.edu	37	chr3	107497277	107497277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	cagcctccctcaatatagtcCtgttacatttgaccggaaat	6	12	1	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:107497277C>A	ENST00000325805.8	+	13	2401	c.2114C>A	c.(2113-2115)cCt>cAt	p.P705H	BBX_ENST00000473542.1_3'UTR|BBX_ENST00000415149.2_Missense_Mutation_p.P705H|BBX_ENST00000406780.1_Missense_Mutation_p.P705H|BBX_ENST00000416476.2_Missense_Mutation_p.L369M|BBX_ENST00000402543.1_Missense_Mutation_p.P705H			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	705	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P705L(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CAATATAGTCCTGTTACATTT	0.418																																																1	Substitution - Missense(1)	ovary(1)	3											96	96	96					3																	107497277		2203	4300	6503	108979967	SO:0001583	missense	56987			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2114C>A	3.37:g.107497277C>A	ENSP00000319974:p.Pro705His		108979967	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.36|19.36	3.812354|3.812354	0.70912|0.70912	.|.	.|.	ENSG00000114439|ENSG00000114439	ENST00000416476|ENST00000415149;ENST00000402543;ENST00000325805;ENST00000406780	D|T;T;T;T	0.99136|0.61627	-5.47|0.09;0.09;0.09;0.09	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69860|0.69860	0.3158|0.3158	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D;D|D;D	0.89917|0.89917	1.0;0.996|1.0;1.0	D;P|D;D	0.78314|0.97110	0.991;0.823|1.0;0.998	T|T	0.71241|0.71241	-0.4651|-0.4651	9|10	0.87932|0.87932	D|D	0|0	-9.5728|-9.5728	20.327|20.327	0.98704|0.98704	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	16;369|705;705	Q9NRU5;A2RRM7|Q8WY36;Q8WY36-2	.;.|BBX_HUMAN;.	M|H	369|705	ENSP00000403860:L369M|ENSP00000408358:P705H;ENSP00000385317:P705H;ENSP00000319974:P705H;ENSP00000385530:P705H	ENSP00000403860:L369M|ENSP00000319974:P705H	L|P	+|+	1|2	2|0	BBX|BBX	108979967|108979967	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	7.487000|7.487000	0.81328|0.81328	2.794000|2.794000	0.96219|0.96219	0.650000|0.650000	0.86243|0.86243	CTG|CCT		0.418	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		A	107497277	C	A	107497277	3	1	82	1	0	0	0	0	1	0	0	0	1344	681	24	2	2152	2	BBX	3	107497277	Missense_Mutation	SNP	C	TCGA-AH-6547-01A-11D-1826-10	66230001	107497277	90525153	13	23524										
GPR149	344758	hgsc.bcm.edu	37	chr3	154055524	154055524	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tcttcctctctttttctgtaAgctttatttaacaactggat	4	9	3	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:154055524A>G	ENST00000389740.2	-	4	2259	c.2160T>C	c.(2158-2160)gcT>gcC	p.A720A		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	720					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTTTCTGTAAGCTTTATTTA	0.433																																																0			3											315	291	299					3																	154055524		1910	4118	6028	155538218	SO:0001819	synonymous_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2160T>C	3.37:g.154055524A>G			155538218		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																				0.433	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		G	154055524	A	G	154055524	2	3	82	1	0	0	0	0	0	0	0	1	6674	59	3	4		4	GPR149	3	154055524	Silent	SNP	A	TCGA-AH-6547-01A-11D-1826-10	46558247	154055524	43966906	14	23525										
ABCF3	55324	hgsc.bcm.edu	37	chr3	183909026	183909026	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tctctgtgtctgctgatctcGagtctcgcatctgtgtggta	11	10	5	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:183909026G>T	ENST00000429586.2	+	16	1737	c.1552G>T	c.(1552-1554)Gag>Tag	p.E518*	ABCF3_ENST00000292808.5_Nonsense_Mutation_p.E512*|EIF2B5_ENST00000444495.1_Intron	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	518	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCTGATCTCGAGTCTCGCAT	0.537																																																0			3											189	163	171					3																	183909026		2203	4300	6503	185391720	SO:0001587	stop_gained	55324			U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"ATP binding cassette transporters / subfamily F"	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1552G>T	3.37:g.183909026G>T	ENSP00000411471:p.Glu518*		185391720	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Nonsense_Mutation	SNP	ENST00000429586.2	37	CCDS3254.1	.	.	.	.	.	.	.	.	.	.	G	39	7.839535	0.98519	.	.	ENSG00000161204	ENST00000429586;ENST00000292808	.	.	.	5.93	5.93	0.95920	.	0.100946	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-25.7026	19.3249	0.94258	0.0:0.0:1.0:0.0	.	.	.	.	X	518;512	.	ENSP00000292808:E512X	E	+	1	0	ABCF3	185391720	1.000000	0.71417	0.977000	0.42913	0.993000	0.82548	9.476000	0.97823	2.805000	0.96524	0.655000	0.94253	GAG		0.537	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358		T	183909026	G	T	183909026	4	4	82	1	0	0	0	0	0	1	0	0	67	1059	37	2	1614	2	ABCF3	3	183909026	Nonsense_Mutation	SNP	G	TCGA-AH-6547-01A-11D-1826-10	29853502	183909026	14113404	15	23526										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153251905	153251905	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ttaggagatttgagttctccTcgcctccagttagtatcaat	8	9	2	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr4:153251905T>C	ENST00000281708.4	-	7	2330	c.1101A>G	c.(1099-1101)cgA>cgG	p.R367R	FBXW7_ENST00000393956.3_Silent_p.R191R|FBXW7_ENST00000296555.5_Silent_p.R249R|FBXW7_ENST00000603548.1_Silent_p.R367R|FBXW7_ENST00000603841.1_Silent_p.R367R|FBXW7_ENST00000263981.5_Silent_p.R287R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	367					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAGTTCTCCTCGCCTCCAGT	0.393			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											331	284	300					4																	153251905		2203	4300	6503	153471355	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1101A>G	4.37:g.153251905T>C			153471355	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.393	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153251905	T	C	153251905	2	2	82	1	0	0	0	0	0	0	0	1	5788	1538	54	4		4	FBXW7	4	153251905	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10		153251905	37902371	16	23527										
NEIL3	55247	hgsc.bcm.edu	37	chr4	178283452	178283452	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ttttcctgcagtgggcagatTtgtccttcccattctgcaac	8	12	1	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr4:178283452T>C	ENST00000264596.3	+	10	1763	c.1645T>C	c.(1645-1647)Ttg>Ctg	p.L549L		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	549					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		GTGGGCAGATTTGTCCTTCCC	0.393								Base excision repair (BER), DNA glycosylases																																								0			4											85	86	86					4																	178283452		2203	4300	6503	178520446	SO:0001819	synonymous_variant	55247			AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1645T>C	4.37:g.178283452T>C			178520446	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																				0.393	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		C	178283452	T	C	178283452	2	2	82	1	0	0	0	0	0	0	0	1	10351	1838	64	4		4	NEIL3	4	178283452	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10	25031547	178283452	12870824	17	23528										
CDH18	1016	hgsc.bcm.edu	37	chr5	19571820	19571820	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gtggttcatctacatccccaAcaatgatcttcagcatagta	6	11	4	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:19571820A>G	ENST00000507958.1	-	10	2111	c.1121T>C	c.(1120-1122)gTt>gCt	p.V374A	CDH18_ENST00000511273.1_Missense_Mutation_p.V374A|CDH18_ENST00000506372.1_Missense_Mutation_p.V374A|CDH18_ENST00000382275.1_Missense_Mutation_p.V374A|CDH18_ENST00000274170.4_Missense_Mutation_p.V374A|CDH18_ENST00000502796.1_Missense_Mutation_p.V374A			Q13634	CAD18_HUMAN	cadherin 18, type 2	374	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TACATCCCCAACAATGATCTT	0.418																																																0			5											154	128	137					5																	19571820		2203	4300	6503	19607577	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1121T>C	5.37:g.19571820A>G	ENSP00000425093:p.Val374Ala		19607577	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.693288	0.88735	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;0.1;-0.62	5.17	5.17	0.71159	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.88980	0.6585	H	0.97023	3.925	0.51012	D	0.999908	D;P	0.67145	0.996;0.844	D;P	0.76071	0.987;0.801	D	0.92441	0.5962	9	.	.	.	.	14.131	0.65253	1.0:0.0:0.0:0.0	.	374;374	B4DHG6;Q13634	.;CAD18_HUMAN	A	374;374;374;374;374;374;320;374	ENSP00000371710:V374A;ENSP00000425093:V374A;ENSP00000274170:V374A;ENSP00000424931:V374A;ENSP00000422138:V374A;ENSP00000427383:V320A;ENSP00000425854:V374A	.	V	-	2	0	CDH18	19607577	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.808000	0.91939	2.095000	0.63458	0.533000	0.62120	GTT		0.418	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		G	19571820	A	G	19571820	3	3	82	1	0	0	0	0	1	0	0	0	3109	43	2	4	1275	4	CDH18	5	19571820	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10		19571820	161343440	18	23529										
APC	324	hgsc.bcm.edu	37	chr5	112174316	112174316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ccgacctagcccataaaataCatagtgcaaatcatatggat	6	10	1	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112174316C>T	ENST00000457016.1	+	16	3405	c.3025C>T	c.(3025-3027)Cat>Tat	p.H1009Y	APC_ENST00000508376.2_Missense_Mutation_p.H1009Y|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.H1009Y			P25054	APC_HUMAN	adenomatous polyposis coli	1009	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.H1009Y(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCATAAAATACATAGTGCAAA	0.363		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Missense(1)|Unknown(1)	urinary_tract(1)|skin(1)	5											87	87	87					5																	112174316		2202	4300	6502	112202215	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3025C>T	5.37:g.112174316C>T	ENSP00000413133:p.His1009Tyr		112202215	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.057203	0.55325	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94457	-2.67;-3.43;-2.67;-2.67;-2.85	5.76	5.76	0.90799	.	0.047871	0.85682	D	0.000000	D	0.92525	0.7626	L	0.44542	1.39	0.54753	D	0.999989	P;P	0.49185	0.92;0.92	B;B	0.40636	0.335;0.335	D	0.93212	0.6601	10	0.72032	D	0.01	-15.4009	19.9596	0.97236	0.0:1.0:0.0:0.0	.	1011;1009	Q4LE70;P25054	.;APC_HUMAN	Y	1009;991;1009;1009;1009	ENSP00000413133:H1009Y;ENSP00000423224:H991Y;ENSP00000257430:H1009Y;ENSP00000427089:H1009Y;ENSP00000423828:H1009Y	ENSP00000257430:H1009Y	H	+	1	0	APC	112202215	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.294000	0.78760	2.726000	0.93360	0.655000	0.94253	CAT		0.363	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174316	C	T	112174316	3	4	82	1	0	0	0	0	1	0	0	0	763	478	17	3	3083	3	APC	5	112174316	Missense_Mutation	SNP	C	TCGA-AH-6547-01A-11D-1826-10	92602496	112174316	68740944	19	23530			1	12		3	3	1307	N	C_A	1.642195e-06
APC	324	hgsc.bcm.edu	37	chr5	112175155	112175155	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tcagctgaagatgaaataggAtgtaatcagacgacacagga	11	6	2	4			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112175155A>G	ENST00000457016.1	+	16	4244	c.3864A>G	c.(3862-3864)ggA>ggG	p.G1288G	APC_ENST00000508376.2_Silent_p.G1288G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.G1288G			P25054	APC_HUMAN	adenomatous polyposis coli	1288	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)|p.C1289fs*16(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATGAAATAGGATGTAATCAGA	0.368		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											57	59	58					5																	112175155		2202	4300	6502	112203054	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3864A>G	5.37:g.112175155A>G			112203054	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.368	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175155	A	G	112175155	2	3	82	1	0	0	0	0	0	0	0	1	763	320	12	4		4	APC	5	112175155	Silent	SNP	A	TCGA-AH-6547-01A-11D-1826-10	839	112175155	68740105	20	23531			1	12		3	3	1307	N	C_A	1.642195e-06
APC	324	hgsc.bcm.edu	37	chr5	112175622	112175622	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aacacctccaccacctcctcAaacagctcaaaccaagcgag	4	18	2	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112175622A>C	ENST00000457016.1	+	16	4711	c.4331A>C	c.(4330-4332)cAa>cCa	p.Q1444P	APC_ENST00000508376.2_Missense_Mutation_p.Q1444P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1444P			P25054	APC_HUMAN	adenomatous polyposis coli	1444	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.P1441fs*28(1)|p.S1436fs*22(1)|p.P1441fs*27(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCACCTCCTCAAACAGCTCAA	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											111	97	102					5																	112175622		2202	4300	6502	112203521	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4331A>C	5.37:g.112175622A>C	ENSP00000413133:p.Gln1444Pro		112203521	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	9.291	1.050634	0.19827	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90004	-2.6;-2.6;-2.6	6.17	5.0	0.66597	.	0.103035	0.64402	D	0.000002	T	0.80824	0.4697	N	0.24115	0.695	0.49582	D	0.999807	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.73142	-0.4076	9	.	.	.	-11.4032	12.9375	0.58322	0.745:0.255:0.0:0.0	.	1446;1444	Q4LE70;P25054	.;APC_HUMAN	P	1444	ENSP00000413133:Q1444P;ENSP00000257430:Q1444P;ENSP00000427089:Q1444P	.	Q	+	2	0	APC	112203521	0.989000	0.36119	0.789000	0.31954	0.930000	0.56654	2.810000	0.47979	1.137000	0.42214	0.533000	0.62120	CAA		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175622	A	C	112175622	3	2	82	1	0	0	0	0	1	0	0	0	763	130	5	4	4389	4	APC	5	112175622	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10	467	112175622	68739638	21	23532			1	12		3	3	1307	N	C_A	1.642195e-06
CCDC126	90693	hgsc.bcm.edu	37	chr7	23682719	23682719	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aataaaagaacgaatgtctcGggcagtatcagatagcagtt	10	6	2	2	rs368070236		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr7:23682719G>A	ENST00000307471.3	+	4	865	c.408G>A	c.(406-408)tcG>tcA	p.S136S	CCDC126_ENST00000409765.1_Silent_p.S136S|CCDC126_ENST00000410069.1_Silent_p.S136S	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	136					protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)	p.S136S(1)		endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						CGAATGTCTCGGGCAGTATCA	0.428																																																1	Substitution - coding silent(1)	ovary(1)	7						G		2,4404	4.2+/-10.8	0,2,2201	89	75	80		408	-9.3	0.6	7		80	0,8600		0,0,4300	no	coding-synonymous	CCDC126	NM_138771.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		136/141	23682719	2,13004	2203	4300	6503	23649244	SO:0001819	synonymous_variant	90693			BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193			22398	protein-coding gene	gene with protein product						12477932	Standard	NM_138771		Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.408G>A	7.37:g.23682719G>A			23649244	A8K1J6|Q6UWP1|Q75MQ6	Silent	SNP	ENST00000307471.3	37	CCDS5384.1																																																																																				0.428	CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250259.1	NM_138771		A	23682719	G	A	23682719	2	1	82	1	0	0	0	0	0	0	0	1	2768	1103	39	1		1	CCDC126	7	23682719	Silent	SNP	G	TCGA-AH-6547-01A-11D-1826-10		23682719	135455944	22	23533										
ST18	9705	hgsc.bcm.edu	37	chr8	53025885	53025885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	catatgcttcaaaattctgcTcactgataggtccctaaatg	6	10	3	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:53025885T>C	ENST00000276480.7	-	26	3700	c.3017A>G	c.(3016-3018)gAg>gGg	p.E1006G		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	1006					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E1006V(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				AAAATTCTGCTCACTGATAGG	0.433																																																1	Substitution - Missense(1)	ovary(1)	8											125	109	115					8																	53025885		2203	4300	6503	53188438	SO:0001583	missense	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.3017A>G	8.37:g.53025885T>C	ENSP00000276480:p.Glu1006Gly		53188438	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.029609	0.93518	.	.	ENSG00000147488	ENST00000276480	T	0.54675	0.56	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.71736	0.3375	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74500	-0.3645	10	0.87932	D	0	-25.6995	16.4416	0.83903	0.0:0.0:0.0:1.0	.	1006	O60284	ST18_HUMAN	G	1006	ENSP00000276480:E1006G	ENSP00000276480:E1006G	E	-	2	0	ST18	53188438	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.285000	0.76669	0.477000	0.44152	GAG		0.433	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			C	53025885	T	C	53025885	3	2	82	1	0	0	0	0	1	0	0	0	15251	1551	54	4	130	4	ST18	8	53025885	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10		53025885	93338137	23	23534										
PLEKHF2	79666	hgsc.bcm.edu	37	chr8	96166990	96166990	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ctcctttaaatgatatgtctGatgatgatgacgatgatgat	9	5	1	7			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:96166990G>T	ENST00000315367.3	+	2	959	c.718G>T	c.(718-720)Gat>Tat	p.D240Y	PLEKHF2_ENST00000519516.1_Missense_Mutation_p.D240Y	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	240					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)	p.D240N(1)		breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					TGATATGTCTGATGATGATGA	0.438																																																1	Substitution - Missense(1)	ovary(1)	8											77	74	75					8																	96166990		2203	4300	6503	96236166	SO:0001583	missense	79666			AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"Zinc fingers, FYVE domain containing", "Pleckstrin homology (PH) domain containing"	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.718G>T	8.37:g.96166990G>T	ENSP00000322373:p.Asp240Tyr		96236166		Missense_Mutation	SNP	ENST00000315367.3	37	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619251	0.46736	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	D;D	0.81499	-1.5;-1.5	5.81	5.81	0.92471	.	0.090894	0.64402	D	0.000001	T	0.81098	0.4752	N	0.08118	0	0.80722	D	1	D	0.71674	0.998	D	0.67725	0.953	D	0.85140	0.0980	10	0.72032	D	0.01	-19.809	20.0925	0.97824	0.0:0.0:1.0:0.0	.	240	Q9H8W4	PKHF2_HUMAN	Y	240	ENSP00000322373:D240Y;ENSP00000427792:D240Y	ENSP00000322373:D240Y	D	+	1	0	PLEKHF2	96236166	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	9.080000	0.94040	2.756000	0.94617	0.557000	0.71058	GAT		0.438	PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613		T	96166990	G	T	96166990	3	4	82	1	0	0	0	0	1	0	0	0	12098	1290	45	2	720	2	PLEKHF2	8	96166990	Missense_Mutation	SNP	G	TCGA-AH-6547-01A-11D-1826-10	43141105	96166990	50197032	24	23535										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116631434	116631434	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	agcacaccagaaaacacagaAcggttgaccttctggaagtc	9	11	1	3			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:116631434A>G	ENST00000220888.5	-	2	1011	c.852T>C	c.(850-852)cgT>cgC	p.R284R	TRPS1_ENST00000395715.3_Silent_p.R297R|TRPS1_ENST00000519674.1_Silent_p.R284R|TRPS1_ENST00000520276.1_Silent_p.R288R|TRPS1_ENST00000519076.1_Silent_p.R238R			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	284					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			AAAACACAGAACGGTTGACCT	0.453									Langer-Giedion syndrome																																							0			8											96	90	92					8																	116631434		1919	4147	6066	116700609	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.852T>C	8.37:g.116631434A>G			116700609	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.453	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116631434	A	G	116631434	2	3	82	1	0	0	0	0	0	0	0	1	16633	30	2	4		4	TRPS1	8	116631434	Silent	SNP	A	TCGA-AH-6547-01A-11D-1826-10	20464444	116631434	29732588	25	23536										
CTSL1	1514	hgsc.bcm.edu	37	chr9	90343678	90343678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tgctttccagtatgttcaggAtaatggaggcctggactctg	12	8	2	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr9:90343678A>G	ENST00000343150.5	+	5	1465	c.575A>G	c.(574-576)gAt>gGt	p.D192G	CTSL_ENST00000340342.6_Missense_Mutation_p.D192G|CTSL_ENST00000495822.1_3'UTR|CTSL_ENST00000342020.5_Missense_Mutation_p.D192G			P07711	CATL1_HUMAN	cathepsin L	192					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										TATGTTCAGGATAATGGAGGC	0.483																																																0			9											103	93	96					9																	90343678		2203	4300	6503	89533498	SO:0001583	missense	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.575A>G	9.37:g.90343678A>G	ENSP00000345344:p.Asp192Gly		89533498	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	37	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951815	0.53186	.	.	ENSG00000135047	ENST00000343150;ENST00000340342;ENST00000342020	T;T;T	0.23147	1.92;1.92;1.92	4.51	3.37	0.38596	Peptidase C1A, papain C-terminal (2);	0.141383	0.64402	D	0.000008	T	0.34424	0.0897	M	0.78344	2.41	0.80722	D	1	B	0.18310	0.027	B	0.33690	0.168	T	0.21143	-1.0254	10	0.66056	D	0.02	.	9.8521	0.41064	0.9186:0.0:0.0814:0.0	.	192	P07711	CATL1_HUMAN	G	192	ENSP00000345344:D192G;ENSP00000365061:D192G;ENSP00000340470:D192G	ENSP00000365061:D192G	D	+	2	0	CTSL1	89533498	1.000000	0.71417	0.001000	0.08648	0.019000	0.09904	5.154000	0.64894	0.757000	0.33036	0.533000	0.62120	GAT		0.483	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		G	90343678	A	G	90343678	3	3	82	1	0	0	0	0	1	0	0	0	4044	333	12	4	589	4	CTSL1	9	90343678	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10		90343678	50869753	26	23537										
OMD	4958	hgsc.bcm.edu	37	chr9	95179145	95179145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gacagatacataagtgaagaAggcaaaccaggaggcattga	12	6	0	4			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr9:95179145A>G	ENST00000375550.4	-	2	971	c.696T>C	c.(694-696)ccT>ccC	p.P232P	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	232					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TAAGTGAAGAAGGCAAACCAG	0.343			T	USP6	aneurysmal bone cysts																																		Dom	yes		9	9q22.31	4958	osteomodulin		M	0			9											102	103	103					9																	95179145		2203	4300	6503	94218966	SO:0001819	synonymous_variant	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.696T>C	9.37:g.95179145A>G			94218966	Q5TBF4	Silent	SNP	ENST00000375550.4	37	CCDS6696.1																																																																																				0.343	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		G	95179145	A	G	95179145	2	3	82	1	0	0	0	0	0	0	0	1	10896	59	3	4		4	OMD	9	95179145	Silent	SNP	A	TCGA-AH-6547-01A-11D-1826-10	4835467	95179145	46034286	27	23538										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720864	89720864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aagccaaccgatacttttctCcaaattttaaggtcagttaa	5	9	2	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr10:89720864C>T	ENST00000371953.3	+	8	2372	c.1015C>T	c.(1015-1017)Cca>Tca	p.P339S	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	339	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.P339S(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.S338fs*1(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATACTTTTCTCCAAATTTTAA	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	54	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(3)|Substitution - Missense(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|thyroid(1)|large_intestine(1)|soft_tissue(1)|endometrium(1)	10											50	53	52					10																	89720864		2203	4299	6502	89710844	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1015C>T	10.37:g.89720864C>T	ENSP00000361021:p.Pro339Ser		89710844	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520567	0.85495	.	.	ENSG00000171862	ENST00000371953	D	0.86030	-2.06	5.37	5.37	0.77165	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.90587	0.7049	M	0.64170	1.965	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	D	0.89724	0.3921	9	.	.	.	-4.5206	19.0916	0.93228	0.0:1.0:0.0:0.0	.	339	P60484	PTEN_HUMAN	S	339	ENSP00000361021:P339S	.	P	+	1	0	PTEN	89710844	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.405000	0.80007	2.516000	0.84829	0.591000	0.81541	CCA		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720864	C	T	89720864	3	4	82	1	0	0	0	0	1	0	0	0	12772	855	30	3	1045	3	PTEN	10	89720864	Missense_Mutation	SNP	C	TCGA-AH-6547-01A-11D-1826-10		89720864	45813883	28	23539										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872965	55872965	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gctctcatcactgggccttaTgtgattggctttatagactc	9	10	2	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr11:55872965T>C	ENST00000313503.1	+	1	447	c.447T>C	c.(445-447)taT>taC	p.Y149Y		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTGGGCCTTATGTGATTGGCT	0.458										HNSCC(53;0.14)																																						0			11											217	195	202					11																	55872965		2201	4296	6497	55629541	SO:0001819	synonymous_variant	390151			AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.447T>C	11.37:g.55872965T>C			55629541	Q6IFC1	Silent	SNP	ENST00000313503.1	37	CCDS31518.1																																																																																				0.458	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		C	55872965	T	C	55872965	2	2	82	1	0	0	0	0	0	0	0	1	11269	1471	51	4		4	OR8H2	11	55872965	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10		55872965	79133551	29	23540										
GPR44	11251	hgsc.bcm.edu	37	chr11	60620803	60620803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	cacaccggccgcaccacctgCaggcagcggtccaggctgat	12	17	0	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr11:60620803C>T	ENST00000332539.4	-	2	504	c.393G>A	c.(391-393)ctG>ctA	p.L131L	RP11-804A23.4_ENST00000538705.1_RNA	NM_004778.2	NP_004769.2	Q9Y5Y4	PD2R2_HUMAN	prostaglandin D2 receptor 2	131					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|calcium-mediated signaling (GO:0019722)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|prostaglandin D receptor activity (GO:0004956)|prostaglandin F receptor activity (GO:0004958)|prostaglandin J receptor activity (GO:0001785)	p.L131L(1)								Indomethacin(DB00328)|Sulindac(DB00605)	GCACCACCTGCAGGCAGCGGT	0.642																																																1	Substitution - coding silent(1)	ovary(1)	11											18	19	19					11																	60620803		2198	4296	6494	60377379	SO:0001819	synonymous_variant	11251			AF118265	CCDS7994.1	11q12-q13.3	2012-08-08	2011-11-11	2011-11-11		ENSG00000183134		"CD molecules", "GPCR / Class A : Prostanoid receptors"	4502	protein-coding gene	gene with protein product	"chemoattractant receptor homologous molecule expressed on T helper type 2 cells"	604837	"G protein-coupled receptor 44"	GPR44		10036181	Standard	NM_004778		Approved	CRTH2, CD294, DP2	uc001nqc.2	Q9Y5Y4		ENST00000332539.4:c.393G>A	11.37:g.60620803C>T			60377379	O94765|Q4QRI6	Silent	SNP	ENST00000332539.4	37	CCDS7994.1																																																																																				0.642	PTGDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396328.1	NM_004778		T	60620803	C	T	60620803	2	4	82	1	0	0	0	0	0	0	0	1	6715	697	25	3		3	GPR44	11	60620803	Silent	SNP	C	TCGA-AH-6547-01A-11D-1826-10	4747838	60620803	74385713	30	23541										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671196	25671196	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tgaacagatgaagcaagataGgatcaccagataccaggttg	11	7	1	5	rs552336745		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr13:25671196G>T	ENST00000281589.3	+	1	897	c.860G>T	c.(859-861)aGg>aTg	p.R287M		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	287					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAGCAAGATAGGATCACCAGA	0.403																																																0			13											185	178	181					13																	25671196		2203	4300	6503	24569196	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.860G>T	13.37:g.25671196G>T	ENSP00000281589:p.Arg287Met		24569196	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.132654	0.37630	.	.	ENSG00000151846	ENST00000281589	T	0.32272	1.46	0.875	-0.0746	0.13730	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.45126	U	0.000389	T	0.42494	0.1205	M	0.87038	2.855	0.46298	D	0.998971	P	0.51240	0.943	P	0.51135	0.66	T	0.35500	-0.9786	10	0.72032	D	0.01	.	5.4221	0.16405	0.2335:0.0:0.7665:0.0	.	287	Q9H361	PABP3_HUMAN	M	287	ENSP00000281589:R287M	ENSP00000281589:R287M	R	+	2	0	PABPC3	24569196	1.000000	0.71417	0.985000	0.45067	0.699000	0.40488	4.902000	0.63266	-0.085000	0.12573	-0.657000	0.03884	AGG		0.403	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		T	25671196	G	T	25671196	3	4	82	1	0	0	0	0	1	0	0	0	11396	1000	35	2	862	2	PABPC3	13	25671196	Missense_Mutation	SNP	G	TCGA-AH-6547-01A-11D-1826-10		25671196	89498682	31	23542										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58831429	58831429	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aaaataagaattgagaatggAatggaaatgacaaatactgt	9	2	0	3			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr14:58831429A>G	ENST00000355431.3	+	20	2995	c.2622A>G	c.(2620-2622)ggA>ggG	p.G874G	ARID4A_ENST00000395168.3_Silent_p.G874G|ARID4A_ENST00000431317.2_Silent_p.G874G|ARID4A_ENST00000348476.3_Silent_p.G874G	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	874					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G874G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TTGAGAATGGAATGGAAATGA	0.333																																																1	Substitution - coding silent(1)	ovary(1)	14											69	64	66					14																	58831429		2203	4298	6501	57901182	SO:0001819	synonymous_variant	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2622A>G	14.37:g.58831429A>G			57901182	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																				0.333	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		G	58831429	A	G	58831429	2	3	82	1	0	0	0	0	0	0	0	1	919	233	9	4		4	ARID4A	14	58831429	Silent	SNP	A	TCGA-AH-6547-01A-11D-1826-10		58831429	48518111	32	23543										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34529012	34529012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tatatgctgatatatcactgTcatgctgccatagacatcac	6	10	3	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr15:34529012T>C	ENST00000354181.3	-	23	3431	c.2939A>G	c.(2938-2940)gAc>gGc	p.D980G	SLC12A6_ENST00000560164.1_Missense_Mutation_p.D792G|SLC12A6_ENST00000458406.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000560611.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000397702.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000451844.2_Missense_Mutation_p.D792G|SLC12A6_ENST00000558589.1_Missense_Mutation_p.D971G|SLC12A6_ENST00000397707.2_Missense_Mutation_p.D965G|SLC12A6_ENST00000558667.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000290209.5_Missense_Mutation_p.D929G			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	980					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TATATCACTGTCATGCTGCCA	0.428																																																0			15											126	110	115					15																	34529012		2201	4298	6499	32316304	SO:0001583	missense	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.2939A>G	15.37:g.34529012T>C	ENSP00000346112:p.Asp980Gly		32316304	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654574	0.67472	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.16	5.16	0.70880	.	0.051702	0.64402	D	0.000001	T	0.58018	0.2093	M	0.84585	2.705	0.80722	D	1	P;P;P;B	0.41748	0.717;0.761;0.594;0.278	P;B;B;B	0.47864	0.559;0.354;0.356;0.15	T	0.66089	-0.6010	10	0.87932	D	0	.	14.1126	0.65132	0.0:0.0:0.0:1.0	.	965;980;929;792	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	G	929;965;971;921;921;792	ENSP00000290209:D929G;ENSP00000380819:D965G;ENSP00000380814:D921G;ENSP00000387725:D921G;ENSP00000390199:D792G	ENSP00000290209:D929G	D	-	2	0	SLC12A6	32316304	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.868000	0.87116	2.174000	0.68829	0.528000	0.53228	GAC		0.428	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		C	34529012	T	C	34529012	3	2	82	1	0	0	0	0	1	0	0	0	14424	1667	58	4	529	4	SLC12A6	15	34529012	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10		34529012	68002380	33	23544										
MKL2	57496	hgsc.bcm.edu	37	chr16	14339512	14339512	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tgccttctagcctggatgacTtaaaggtgacaattgcaact	9	9	1	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr16:14339512T>C	ENST00000341243.5	+	9	1174	c.1174T>C	c.(1174-1176)Tta>Cta	p.L392L	MKL2_ENST00000574045.1_Silent_p.L403L|MKL2_ENST00000318282.5_Silent_p.L403L|MKL2_ENST00000571589.1_Silent_p.L403L			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	392	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.L403V(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCTGGATGACTTAAAGGTGAC	0.433																																																1	Substitution - Missense(1)	ovary(1)	16											156	139	144					16																	14339512		2197	4300	6497	14247013	SO:0001819	synonymous_variant	57496			AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1174T>C	16.37:g.14339512T>C			14247013	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	37																																																																																					0.433	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		C	14339512	T	C	14339512	2	2	82	1	0	0	0	0	0	0	0	1	9632	1606	56	4		4	MKL2	16	14339512	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10		14339512	76015241	34	23545										
PROCA1	6830	hgsc.bcm.edu	37	chr17	27030881	27030881	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	cgggcttttcttcttagtcaActggcctttcttggcttttt	8	10	4	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr17:27030881A>G	ENST00000314616.6	+	0	6518				PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Silent_p.L238L|PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Silent_p.L236L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TTCTTAGTCAACTGGCCTTTC	0.483																																																0			17											100	105	103					17																	27030881		2203	4300	6503	24055008	SO:0001628	intergenic_variant	147011			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27030881A>G			24055008	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				0.483	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27030881	A	G	27030881	1	3	82	0	1	0	0	0	0	0	0	0	12580	40	2	4		4	PROCA1	17	27030881	IGR	SNP	A	TCGA-AH-6547-01A-11D-1826-10		27030881	54164329	35	23546										
LRRC37B	114659	hgsc.bcm.edu	37	chr17	30376234	30376234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tgaaaatggaatgttcagaaAcacatgtgcaagggagctgt	12	5	1	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr17:30376234A>G	ENST00000341671.7	+	10	2502	c.2497A>G	c.(2497-2499)Aca>Gca	p.T833A	LRRC37B_ENST00000327564.7_Missense_Mutation_p.T860A|LRRC37B_ENST00000584368.1_Missense_Mutation_p.T794A|LRRC37B_ENST00000394713.3_Missense_Mutation_p.T782A|LRRC37B_ENST00000543378.2_Missense_Mutation_p.T751A	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	833						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				ATGTTCAGAAACACATGTGCA	0.488																																																0			17											89	80	83					17																	30376234		2203	4300	6503	27400347	SO:0001583	missense	114659			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.2497A>G	17.37:g.30376234A>G	ENSP00000340519:p.Thr833Ala		27400347	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	1.155	-0.645590	0.03531	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	1.78	-3.57	0.04612	.	.	.	.	.	T	0.30665	0.0772	M	0.76574	2.34	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49051	-0.8979	9	0.02654	T	1	.	4.0288	0.09700	0.2639:0.4144:0.3217:0.0	.	782;833	Q17RC9;Q96QE4	.;LR37B_HUMAN	A	751;860;782;833	ENSP00000443345:T751A;ENSP00000332536:T860A;ENSP00000378202:T782A;ENSP00000340519:T833A	ENSP00000332536:T860A	T	+	1	0	LRRC37B	27400347	0.000000	0.05858	0.008000	0.14137	0.000000	0.00434	-0.854000	0.04299	-1.484000	0.01856	-0.956000	0.02647	ACA		0.488	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		G	30376234	A	G	30376234	3	3	82	1	0	0	0	0	1	0	0	0	9023	43	2	4	2535	4	LRRC37B	17	30376234	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10	3345353	30376234	50818976	36	23547										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48604721	48604721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gctggggaccggattacccaAgacagagcatcaaagaaaca	11	10	1	3	rs377767372|rs121912579		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr18:48604721A>G	ENST00000342988.3	+	12	2081	c.1543A>G	c.(1543-1545)Aga>Gga	p.R515G	SMAD4_ENST00000398417.2_Missense_Mutation_p.R515G|SMAD4_ENST00000588745.1_Missense_Mutation_p.R419G|SMAD4_ENST00000586253.1_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	515	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.	Necessary for heterotrimerization.			atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R515*(3)|p.?(2)|p.R515fs*22(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGATTACCCAAGACAGAGCAT	0.498																																																42	Whole gene deletion(36)|Substitution - Nonsense(3)|Unknown(2)|Deletion - Frameshift(1)	pancreas(30)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											104	98	100					18																	48604721		2203	4300	6503	46858719	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1543A>G	18.37:g.48604721A>G	ENSP00000341551:p.Arg515Gly		46858719	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.271137	0.59649	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.99688	-6.41;-6.41	6.08	4.93	0.64822	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.100580	0.64402	D	0.000002	D	0.99486	0.9817	H	0.95611	3.695	0.80722	D	1	P	0.34615	0.459	B	0.37346	0.247	D	0.97837	1.0266	10	0.87932	D	0	.	11.9417	0.52905	0.5591:0.4409:0.0:0.0	.	515	Q13485	SMAD4_HUMAN	G	515	ENSP00000341551:R515G;ENSP00000381452:R515G	ENSP00000341551:R515G	R	+	1	2	SMAD4	46858719	0.985000	0.35326	0.998000	0.56505	0.998000	0.95712	2.856000	0.48341	1.113000	0.41760	0.533000	0.62120	AGA		0.498	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48604721	A	G	48604721	3	3	82	1	0	0	0	0	1	0	0	0	14797	64	3	4	1585	4	SMAD4	18	48604721	Missense_Mutation	SNP	A	TCGA-AH-6547-01A-11D-1826-10		48604721	29472527	37	23548										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33424370	33424370	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	tccccaccttcctgtgacgaCgccttctcagcctctttgag	7	17	2	2	rs138753622		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr19:33424370C>T	ENST00000305768.5	-	8	961	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CEP89_ENST00000590597.2_Silent_p.A291A	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	291					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.A291A(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CCTGTGACGACGCCTTCTCAG	0.383																																																1	Substitution - coding silent(1)	ovary(1)	19						C		1,4405	2.1+/-5.4	0,1,2202	209	189	196		873	-10.2	0	19	dbSNP_134	196	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CEP89	NM_032816.3		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		291/784	33424370	6,13000	2203	4300	6503	38116210	SO:0001819	synonymous_variant	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.873G>A	19.37:g.33424370C>T			38116210	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																				0.383	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		T	33424370	C	T	33424370	2	4	82	1	0	0	0	0	0	0	0	1	2765	523	19	1		1	CCDC123	19	33424370	Silent	SNP	C	TCGA-AH-6547-01A-11D-1826-10		33424370	25704613	38	23549										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8755294	8755294	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gacttgaaggacaaacaacaGcagcagctgcttaatcttcg	9	10	1	1	rs139859188	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr20:8755294G>T	ENST00000338037.6	+	27	3066	c.3039G>T	c.(3037-3039)caG>caT	p.Q1013H	PLCB1_ENST00000378637.2_Missense_Mutation_p.Q1013H|PLCB1_ENST00000378641.3_Missense_Mutation_p.Q1013H|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1013					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.Q1013H(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						ACAAACAACAGCAGCAGCTGC	0.418																																																1	Substitution - Missense(1)	lung(1)	20											108	108	108					20																	8755294		2203	4300	6503	8703294	SO:0001583	missense	23236			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3039G>T	20.37:g.8755294G>T	ENSP00000338185:p.Gln1013His		8703294	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.992039	0.54041	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.47528	0.84;0.84;0.84	5.63	3.29	0.37713	PLC-beta, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40546	0.1121	L	0.56769	1.78	0.58432	D	0.99999	P;B	0.36789	0.57;0.335	B;B	0.33960	0.173;0.134	T	0.15896	-1.0421	10	0.36615	T	0.2	.	10.27	0.43477	0.1883:0.0:0.8117:0.0	.	1013;1013	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	H	1013;1013;1013;933;933	ENSP00000367908:Q1013H;ENSP00000338185:Q1013H;ENSP00000367904:Q1013H	ENSP00000338185:Q1013H	Q	+	3	2	PLCB1	8703294	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.659000	0.37387	0.491000	0.27793	0.650000	0.86243	CAG		0.418	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8755294	G	T	8755294	3	4	82	1	0	0	0	0	1	0	0	0	12058	962	34	2	3145	2	PLCB1	20	8755294	Missense_Mutation	SNP	G	TCGA-AH-6547-01A-11D-1826-10		8755294	54270226	39	23550										
ZBP1	81030	hgsc.bcm.edu	37	chr20	56190003	56190003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	gtccagaaggtgcctgctctTcatcctgtacaagtctcggt	10	12	3	1			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr20:56190003T>C	ENST00000371173.3	-	4	619	c.442A>G	c.(442-444)Aag>Gag	p.K148E	ZBP1_ENST00000343535.4_Missense_Mutation_p.K148E|ZBP1_ENST00000340462.4_Missense_Mutation_p.K125E|ZBP1_ENST00000541799.1_Missense_Mutation_p.K148E|ZBP1_ENST00000395822.3_Missense_Mutation_p.K73E|ZBP1_ENST00000538947.1_5'Flank	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	148					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TGCCTGCTCTTCATCCTGTAC	0.562																																																0			20											246	196	213					20																	56190003		2203	4300	6503	55623409	SO:0001583	missense	81030			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.442A>G	20.37:g.56190003T>C	ENSP00000360215:p.Lys148Glu		55623409	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.846520	0.32606	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	3.39	1.07	0.20283	Winged helix-turn-helix transcription repressor DNA-binding (1);Double-stranded RNA-specific adenosine deaminase (DRADA) (1);	1.361350	0.04816	N	0.436027	T	0.22666	0.0547	N	0.08118	0	0.09310	N	1	B;B;B;B	0.24651	0.046;0.108;0.108;0.108	B;B;B;B	0.22386	0.008;0.026;0.039;0.026	T	0.20706	-1.0267	10	0.44086	T	0.13	-6.4876	3.591	0.07989	0.0:0.1227:0.2294:0.6479	.	148;148;73;148	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	E	148;73;125;148;148;148	ENSP00000360215:K148E;ENSP00000379167:K73E;ENSP00000344954:K125E;ENSP00000340584:K148E;ENSP00000440552:K148E	ENSP00000344954:K125E	K	-	1	0	ZBP1	55623409	0.010000	0.17322	0.023000	0.16930	0.296000	0.27459	-0.232000	0.09055	0.200000	0.20447	0.533000	0.62120	AAG		0.562	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		C	56190003	T	C	56190003	3	2	82	1	0	0	0	0	1	0	0	0	17560	1792	62	4	944	4	ZBP1	20	56190003	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10	47434709	56190003	6835517	40	23551										
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671269	39671269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	caaggccaacagaccccgcgTcatgtccaagagtgggcaca	11	14	1	2			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr21:39671269T>C	ENST00000328656.4	+	4	389	c.86T>C	c.(85-87)gTc>gCc	p.V29A	KCNJ15_ENST00000398938.2_Missense_Mutation_p.V29A|KCNJ15_ENST00000398934.1_Missense_Mutation_p.V29A|KCNJ15_ENST00000398930.1_Missense_Mutation_p.V29A|KCNJ15_ENST00000398932.1_Missense_Mutation_p.V29A	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	29					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	AGACCCCGCGTCATGTCCAAG	0.552																																																0			21											98	79	86					21																	39671269		2203	4300	6503	38593139	SO:0001583	missense	3772			Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.86T>C	21.37:g.39671269T>C	ENSP00000331698:p.Val29Ala		38593139	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.356052	0.82243	.	.	ENSG00000157551	ENST00000549805;ENST00000547341;ENST00000549932;ENST00000547595;ENST00000548700;ENST00000551422;ENST00000328656;ENST00000398928;ENST00000398925;ENST00000443341;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	T;T;T;T;T;T;D;D;T;T;D;D;D;D;D;D;D	0.94576	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-2.56;-3.09;-0.88;-0.42;-2.56;-2.56;-2.91;-2.56;-2.56;-3.09;-3.46	5.08	5.08	0.68730	.	0.138110	0.48767	U	0.000175	D	0.92335	0.7568	L	0.38175	1.15	0.58432	D	0.999998	P	0.51653	0.947	P	0.47075	0.536	D	0.91725	0.5392	10	0.35671	T	0.21	.	15.1426	0.72623	0.0:0.0:0.0:1.0	.	29	Q99712	IRK15_HUMAN	A	29	ENSP00000448770:V29A;ENSP00000447111:V29A;ENSP00000448676:V29A;ENSP00000450254:V29A;ENSP00000448886:V29A;ENSP00000449419:V29A;ENSP00000331698:V29A;ENSP00000381902:V29A;ENSP00000381899:V29A;ENSP00000413013:V29A;ENSP00000381911:V29A;ENSP00000381905:V29A;ENSP00000414487:V29A;ENSP00000381904:V29A;ENSP00000381907:V29A;ENSP00000381901:V29A;ENSP00000400849:V29A	ENSP00000331698:V29A	V	+	2	0	KCNJ15	38593139	1.000000	0.71417	0.995000	0.50966	0.924000	0.55760	7.803000	0.85983	2.047000	0.60756	0.383000	0.25322	GTC		0.552	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		C	39671269	T	C	39671269	3	2	82	1	0	0	0	0	1	0	0	0	8070	1667	58	4	88	4	KCNJ15	21	39671269	Missense_Mutation	SNP	T	TCGA-AH-6547-01A-11D-1826-10		39671269	8458626	41	23552										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-													0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	ctgactcagtggttcttccaCctcgctctcctgactcaggg					rs1058237|rs144469326	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs		8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				0.642	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138168	CCTC	-	8138165	7	5	82	1	0	1	0	1	0	0	0	0	17183	507	18	0	95	0	VCX2	23	8138165	Frame_Shift_Del	DEL	CCTC	TCGA-AH-6547-01A-11D-1826-10		8138165	147132395	42	23553										
TSPAN7	7102	hgsc.bcm.edu	37	chrX	38530641	38530641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.756838905775076	NA	0.756838905775076	1	1	0	aattttcagtatgccatgttTctgtccctggtgttcctggc	9	10	2	0			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chrX:38530641T>C	ENST00000378482.2	+	3	459	c.282T>C	c.(280-282)ttT>ttC	p.F94F	TSPAN7_ENST00000545599.1_Silent_p.F68F|TSPAN7_ENST00000488893.1_3'UTR|TSPAN7_ENST00000422612.2_Silent_p.F120F|TSPAN7_ENST00000286824.6_Silent_p.F111F|TM4SF2_ENST00000465127.1_Silent_p.F124F	NM_004615.3	NP_004606.2	P41732	TSN7_HUMAN	tetraspanin 7	94					viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	11						ATGCCATGTTTCTGTCCCTGG	0.443																																																0			X											371	314	333					X																	38530641		2202	4300	6502	38415585	SO:0001819	synonymous_variant	7102			D29808	CCDS14248.1	Xp11.4	2013-02-14	2005-03-21	2005-03-21	ENSG00000156298	ENSG00000156298		"CD molecules", "Tetraspanins"	11854	protein-coding gene	gene with protein product		300096	"transmembrane 4 superfamily member 2", "mental retardation, X-linked 58"	MXS1, TM4SF2, MRX58		12070254	Standard	NM_004615		Approved	DXS1692E, TALLA-1, A15, CD231	uc004deg.4	P41732	OTTHUMG00000024090	ENST00000378482.2:c.282T>C	X.37:g.38530641T>C			38415585	B2R5W7|D3DWB1|Q8WVG5|Q9UEY9	Silent	SNP	ENST00000378482.2	37	CCDS14248.1																																																																																				0.443	TSPAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356412.1			C	38530641	T	C	38530641	2	2	82	1	0	0	0	0	0	0	0	1	16692	1780	62	4		4	TSPAN7	23	38530641	Silent	SNP	T	TCGA-AH-6547-01A-11D-1826-10	30392476	38530641	116739919	43	23554										
CHD5	26038	hgsc.bcm.edu	37	chr1	6181181	6181181	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	caacctctcggcagctgctcCggggagggcggggccttctc	15	15	2	0	rs35026547		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:6181181C>T	ENST00000262450.3	-	33	4995	c.4896G>A	c.(4894-4896)ccG>ccA	p.P1632P	CHD5_ENST00000378021.1_Silent_p.P489P	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGCTGCTCCGGGGAGGGCG	0.657																																																0			1											21	25	24					1																	6181181		2203	4300	6503	6103768	SO:0001819	synonymous_variant	450091			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.4896G>A	1.37:g.6181181C>T			6103768	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																				0.657	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6181181	C	T	6181181	2	4	83	1	0	0	0	0	0	0	0	1	3334	639	23	1		1	CHD5	1	6181181	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10		6181181	243069440	1	23555										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7792593	7792593	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acggggtcccagcagcacaaAcaggcgagcggaggcggcag	17	12	0	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:7792593A>G	ENST00000303635.7	+	12	3207	c.3000A>G	c.(2998-3000)aaA>aaG	p.K1000K	CAMTA1_ENST00000439411.2_Silent_p.K1000K	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1000					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGCAGCACAAACAGGCGAGCG	0.632			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0			1											55	61	59					1																	7792593		2203	4299	6502	7715180	SO:0001819	synonymous_variant	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3000A>G	1.37:g.7792593A>G			7715180	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																				0.632	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	7792593	A	G	7792593	2	3	83	1	0	0	0	0	0	0	0	1	2619	40	2	4		4	CAMTA1	1	7792593	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	1611412	7792593	241458028	2	23556										
DFFA	1676	hgsc.bcm.edu	37	chr1	10527267	10527267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctggaggtcctcctctgataGgaggatgatgctggacagat	14	8	1	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:10527267G>T	ENST00000377038.3	-	3	488	c.421C>A	c.(421-423)Cta>Ata	p.L141I	DFFA_ENST00000377036.2_Missense_Mutation_p.L141I	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	141					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		TCCTCTGATAGGAGGATGATG	0.532																																																0			1											156	148	151					1																	10527267		2203	4300	6503	10449854	SO:0001583	missense	1676			AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"DNA fragmentation factor, 45 kD, alpha subunit"	601882	"DNA fragmentation factor, 45 kD, alpha polypeptide"			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.421C>A	1.37:g.10527267G>T	ENSP00000366237:p.Leu141Ile		10449854	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520700	0.44866	.	.	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.68	3.7	0.42460	DNA fragmentation factor 45kDa, C-terminal (2);	0.044831	0.85682	D	0.000000	T	0.51210	0.1661	L	0.60455	1.87	0.33457	D	0.584437	P;P	0.52692	0.814;0.955	B;P	0.52424	0.38;0.698	T	0.65191	-0.6228	9	0.62326	D	0.03	-3.7304	7.3501	0.26686	0.084:0.0:0.6002:0.3158	.	141;141	O00273-2;O00273	.;DFFA_HUMAN	I	141	.	ENSP00000366235:L141I	L	-	1	2	DFFA	10449854	1.000000	0.71417	0.986000	0.45419	0.118000	0.20060	4.178000	0.58284	1.407000	0.46875	0.650000	0.86243	CTA		0.532	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401		T	10527267	G	T	10527267	3	4	83	1	0	0	0	0	1	0	0	0	4463	991	35	2	614	2	DFFA	1	10527267	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	2734674	10527267	238723354	3	23557										
MPL	4352	hgsc.bcm.edu	37	chr1	43805160	43805160	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tgcagaggcctcactcagccTctgctctggaccagtctcca	9	16	5	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:43805160T>C	ENST00000372470.3	+	4	652	c.610T>C	c.(610-612)Tct>Cct	p.S204P	MPL_ENST00000413998.2_Missense_Mutation_p.S204P	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	204	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)	p.S204P(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TCACTCAGCCTCTGCTCTGGA	0.567			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											87	84	85					1																	43805160		2203	4300	6503	43577747	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.610T>C	1.37:g.43805160T>C	ENSP00000361548:p.Ser204Pro		43577747	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	T	1.415	-0.574377	0.03882	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	T;T	0.80824	-1.42;-1.16	4.5	-5.13	0.02884	Fibronectin, type III (3);	0.842808	0.10744	N	0.639085	T	0.48370	0.1496	N	0.02916	-0.46	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.33979	-0.9847	10	0.28530	T	0.3	1.2049	2.0421	0.03553	0.1264:0.32:0.1245:0.4292	.	197;204;204	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	P	204	ENSP00000361548:S204P;ENSP00000414004:S204P	ENSP00000361546:S204P	S	+	1	0	MPL	43577747	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-1.137000	0.03219	-1.090000	0.03069	-0.345000	0.07892	TCT		0.567	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		C	43805160	T	C	43805160	3	2	83	1	0	0	0	0	1	0	0	0	9760	1551	54	4	624	4	MPL	1	43805160	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	33277893	43805160	205445461	4	23558										
BSND	7809	hgsc.bcm.edu	37	chr1	55472904	55472904	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gtcatccacaagggctcagaCgagagtgaaggggaaagacg	15	8	2	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:55472904C>T	ENST00000371265.4	+	3	761	c.507C>T	c.(505-507)gaC>gaT	p.D169D		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	169					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						AGGGCTCAGACGAGAGTGAAG	0.607																																					Ovarian(191;1657 2078 22894 42033 48899)											0			1											85	76	79					1																	55472904		2203	4300	6503	55245492	SO:0001819	synonymous_variant	7809			AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"deafness, autosomal recessive 73", "Bartter syndrome, infantile, with sensorineural deafness (Barttin)"	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.507C>T	1.37:g.55472904C>T			55245492	Q6NT28	Silent	SNP	ENST00000371265.4	37	CCDS602.1																																																																																				0.607	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176		T	55472904	C	T	55472904	2	4	83	1	0	0	0	0	0	0	0	1	1534	535	19	1		1	BSND	1	55472904	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	11667744	55472904	193777717	5	23559										
MIER1	57708	hgsc.bcm.edu	37	chr1	67411869	67411869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agatgaccatgaatttgatcCatcagctgacatgctggttc	9	9	1	5			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:67411869C>A	ENST00000355356.3	+	3	220	c.71C>A	c.(70-72)cCa>cAa	p.P24Q	MIER1_ENST00000371018.3_Missense_Mutation_p.P41Q|MIER1_ENST00000371014.1_Missense_Mutation_p.P77Q|MIER1_ENST00000371016.1_Missense_Mutation_p.P41Q|MIER1_ENST00000401041.1_Missense_Mutation_p.P77Q|MIER1_ENST00000479067.1_3'UTR|MIER1_ENST00000371012.2_Missense_Mutation_p.P41Q|MIER1_ENST00000357692.2_Missense_Mutation_p.P41Q|MIER1_ENST00000401042.3_Missense_Mutation_p.P24Q|MIER1_ENST00000355977.6_Intron	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	24					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GAATTTGATCCATCAGCTGAC	0.343																																																0			1											118	107	111					1																	67411869		1853	4092	5945	67184457	SO:0001583	missense	57708				CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.71C>A	1.37:g.67411869C>A	ENSP00000347514:p.Pro24Gln		67184457	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	37	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891634	0.91889	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000371012;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94	5.24	5.24	0.73138	.	0.110094	0.64402	D	0.000006	T	0.41604	0.1166	M	0.72353	2.195	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.979;0.998;0.999;0.998;0.999;0.996;0.991	T	0.35871	-0.9771	10	0.87932	D	0	-27.2707	19.2207	0.93795	0.0:1.0:0.0:0.0	.	41;41;24;24;41;77;77	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;.;.	Q	45;41;41;77;41;77;41;24;24	ENSP00000360057:P41Q;ENSP00000350321:P41Q;ENSP00000383820:P77Q;ENSP00000360055:P41Q;ENSP00000360053:P77Q;ENSP00000360051:P41Q;ENSP00000383821:P24Q;ENSP00000347514:P24Q	ENSP00000347514:P24Q	P	+	2	0	MIER1	67184457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.466000	0.80914	2.621000	0.88768	0.655000	0.94253	CCA		0.343	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		A	67411869	C	A	67411869	3	1	83	1	0	0	0	0	1	0	0	0	9610	594	21	2	321	2	MIER1	1	67411869	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	11938965	67411869	181838752	6	23560										
USP33	23032	hgsc.bcm.edu	37	chr1	78180333	78180333	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agaaagtcattatttgaaatAgggccaggttcggcaaaggt	12	5	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:78180333A>G	ENST00000370793.1	-	20	2620	c.2274T>C	c.(2272-2274)ccT>ccC	p.P758P	USP33_ENST00000370792.3_Silent_p.P750P|USP33_ENST00000357428.1_Silent_p.P758P|USP33_ENST00000370794.3_Silent_p.P727P	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	758	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						TATTTGAAATAGGGCCAGGTT	0.348																																					Melanoma(152;72 1870 11110 26780 42647)											0			1											93	94	93					1																	78180333		2203	4300	6503	77952921	SO:0001819	synonymous_variant	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.2274T>C	1.37:g.78180333A>G			77952921	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	A	9.584	1.124357	0.20959	.	.	ENSG00000077254	ENST00000481579	.	.	.	5.21	0.0388	0.14202	.	.	.	.	.	T	0.28764	0.0713	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17167	-1.0378	4	.	.	.	.	4.4599	0.11661	0.463:0.0:0.3293:0.2077	.	.	.	.	P	363	.	.	L	-	2	0	USP33	77952921	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.711000	0.25764	0.375000	0.24679	-0.250000	0.11733	CTA		0.348	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		G	78180333	A	G	78180333	2	3	83	1	0	0	0	0	0	0	0	1	17104	407	15	4		4	USP33	1	78180333	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	10768464	78180333	171070288	7	23561										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111146775	111146775	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gaagtggactgctggtacccGatggtgctgttggaataggt	16	6	0	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:111146775G>A	ENST00000485317.1	-	3	1303	c.630C>T	c.(628-630)atC>atT	p.I210I	KCNA2_ENST00000316361.4_Silent_p.I210I|KCNA2_ENST00000369770.3_Silent_p.I210I|KCNA2_ENST00000525120.1_Intron|KCNA2_ENST00000440270.1_Silent_p.I210I			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	210					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	GCTGGTACCCGATGGTGCTGT	0.483																																					Pancreas(18;568 735 10587 23710 36357)											0			1											155	152	153					1																	111146775		2203	4300	6503	110948298	SO:0001819	synonymous_variant	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.630C>T	1.37:g.111146775G>A			110948298	Q86XG6	Silent	SNP	ENST00000485317.1	37	CCDS827.1																																																																																				0.483	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146775	G	A	111146775	2	1	83	1	0	0	0	0	0	0	0	1	8024	1048	37	1		1	KCNA2	1	111146775	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	32966442	111146775	138103846	8	23562										
RPTN	126638	hgsc.bcm.edu	37	chr1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-													0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cttgtctctcaggctgactgTggtgggaatctctgtcttgt					rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152129101	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	152129066	7	5	83	1	0	1	0	1	0	0	0	0	13701	1696	59	0	1849	0	RPTN	1	152129066	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TCGA-AH-6549-01A-11D-1826-10	40982291	152129066	97121555	9	23563										
FLG	2312	hgsc.bcm.edu	37	chr1	152285797	152285797	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cctgccttcctcctctgcttGaccccgggtgtccacgaatg	9	17	1	1	rs146559843		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152285797G>A	ENST00000368799.1	-	3	1600	c.1565C>T	c.(1564-1566)tCa>tTa	p.S522L	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	522	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCTCTGCTTGACCCCGGGTG	0.587									Ichthyosis																																							0			1											358	357	357					1																	152285797		2203	4300	6503	150552421	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1565C>T	1.37:g.152285797G>A	ENSP00000357789:p.Ser522Leu		150552421	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	12.06	1.823358	0.32237	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.03745	3.82	3.19	-0.57	0.11753	.	.	.	.	.	T	0.05227	0.0139	M	0.77616	2.38	0.09310	N	1	D	0.62365	0.991	D	0.65573	0.936	T	0.24584	-1.0156	9	0.40728	T	0.16	.	5.0672	0.14587	0.0:0.2058:0.3751:0.4191	.	522	P20930	FILA_HUMAN	L	522;54	ENSP00000357789:S522L	ENSP00000357789:S522L	S	-	2	0	FLG	150552421	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.196000	0.17176	0.130000	0.18549	0.603000	0.83216	TCA		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152285797	G	A	152285797	3	1	83	1	0	0	0	0	1	0	0	0	5941	1294	45	3	10624	3	FLG	1	152285797	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	156731	152285797	96964824	10	23564										
FLG2	388698	hgsc.bcm.edu	37	chr1	152324057	152324057	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctgtccatgagtagttccgtGtctctcatgaactgaggatc	10	10	2	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152324057G>T	ENST00000388718.5	-	3	6277	c.6205C>A	c.(6205-6207)Cac>Aac	p.H2069N	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2069					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGTTCCGTGTCTCTCATGA	0.537																																																0			1											544	480	502					1																	152324057		2203	4300	6503	150590681	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6205C>A	1.37:g.152324057G>T	ENSP00000373370:p.His2069Asn		150590681	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	7.239	0.600831	0.13939	.	.	ENSG00000143520	ENST00000388718	T	0.03689	3.84	4.32	2.24	0.28232	.	.	.	.	.	T	0.01061	0.0035	L	0.50333	1.59	0.09310	N	1	B	0.34061	0.436	B	0.27796	0.083	T	0.44802	-0.9304	9	0.13470	T	0.59	.	6.8391	0.23953	0.0:0.1962:0.601:0.2028	.	2069	Q5D862	FILA2_HUMAN	N	2069	ENSP00000373370:H2069N	ENSP00000373370:H2069N	H	-	1	0	FLG2	150590681	0.019000	0.18553	0.184000	0.23157	0.006000	0.05464	0.895000	0.28363	1.167000	0.42706	-0.190000	0.12839	CAC		0.537	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152324057	G	T	152324057	3	4	83	1	0	0	0	0	1	0	0	0	5942	1377	48	2	974	2	FLG2	1	152324057	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	38260	152324057	96926564	11	23565										
FLG2	388698	hgsc.bcm.edu	37	chr1	152328900	152328900	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cttgatgtagactcatgctgGccacaagtttgacctgagcc	10	11	1	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152328900G>T	ENST00000388718.5	-	3	1434	c.1362C>A	c.(1360-1362)ggC>ggA	p.G454G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	454	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.G454G(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTCATGCTGGCCACAAGTTT	0.493																																																1	Substitution - coding silent(1)	lung(1)	1											185	178	180					1																	152328900		2203	4300	6503	150595524	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1362C>A	1.37:g.152328900G>T			150595524	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.493	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152328900	G	T	152328900	2	4	83	1	0	0	0	0	0	0	0	1	5942	1190	42	2		2	FLG2	1	152328900	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	4843	152328900	96921721	12	23566										
SHC1	6464	hgsc.bcm.edu	37	chr1	154942742	154942742	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atcccctccccatcatcagcTgcccttcctggctccccctt	4	22	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:154942742T>C	ENST00000368445.5	-	1	475	c.261A>G	c.(259-261)gcA>gcG	p.A87A	SHC1_ENST00000606391.1_Intron|SHC1_ENST00000368453.4_Intron|SHC1_ENST00000368450.1_Intron|SHC1_ENST00000448116.2_Silent_p.A87A|SHC1_ENST00000368449.4_Intron	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	87					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CATCATCAGCTGCCCTTCCTG	0.672																																					NSCLC(4;32 234 1864 2492 3259 13747 17376)											0			1											26	31	30					1																	154942742		2203	4297	6500	153209366	SO:0001819	synonymous_variant	6464			U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.261A>G	1.37:g.154942742T>C			153209366	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1																																																																																				0.672	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		C	154942742	T	C	154942742	2	2	83	1	0	0	0	0	0	0	0	1	14307	1567	55	4		4	SHC1	1	154942742	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	2613842	154942742	94307879	13	23567										
IFI16	3428	hgsc.bcm.edu	37	chr1	159023463	159023463	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acctgctttgaattggcaccGaaaagtgggaataccgggga	13	8	0	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:159023463G>A	ENST00000295809.7	+	11	2481	c.2226G>A	c.(2224-2226)ccG>ccA	p.P742P	IFI16_ENST00000340979.6_Silent_p.P630P|IFI16_ENST00000448393.2_Silent_p.P630P|IFI16_ENST00000359709.3_Silent_p.P686P|IFI16_ENST00000368132.3_Silent_p.P686P|IFI16_ENST00000430894.2_Silent_p.P690P|IFI16_ENST00000368131.4_Silent_p.P686P			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	742	HIN-200 2. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 core domain.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					AATTGGCACCGAAAAGTGGGA	0.423																																																0			1											136	132	133					1																	159023463		2203	4300	6503	157290087	SO:0001819	synonymous_variant	3428			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.2226G>A	1.37:g.159023463G>A			157290087	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Silent	SNP	ENST00000295809.7	37		.	.	.	.	.	.	.	.	.	.	G	0.689	-0.795272	0.02862	.	.	ENSG00000163565	ENST00000448393	.	.	.	0.628	-1.26	0.09376	.	.	.	.	.	T	0.06554	0.0168	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37103	-0.9720	3	.	.	.	.	.	.	.	.	.	.	.	Q	451	.	.	R	+	2	0	IFI16	157290087	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.043000	0.12043	-1.359000	0.02174	-1.362000	0.01212	CGA		0.423	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531		A	159023463	G	A	159023463	2	1	83	1	0	0	0	0	0	0	0	1	7532	1045	37	1		1	IFI16	1	159023463	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	4080721	159023463	90227158	14	23568										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200818159	200818159	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tctgaaatggtgcatcttagGatgaaactagaagaaaagag	11	4	2	5			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:200818159G>T	ENST00000236925.4	+	12	2344	c.2295G>T	c.(2293-2295)agG>agT	p.R765S	CAMSAP2_ENST00000358823.2_Missense_Mutation_p.R754S|CAMSAP2_ENST00000413307.2_Missense_Mutation_p.R738S			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	765					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										TGCATCTTAGGATGAAACTAG	0.468																																																0			1											74	80	78					1																	200818159		2203	4300	6503	199084782	SO:0001583	missense	23271			AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2295G>T	1.37:g.200818159G>T	ENSP00000236925:p.Arg765Ser		199084782	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	37		.	.	.	.	.	.	.	.	.	.	G	13.66	2.303709	0.40795	.	.	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.69175	-0.38;-0.38;-0.38	5.41	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.59197	0.2176	L	0.48877	1.53	0.58432	D	0.999997	P;P;P	0.48764	0.915;0.745;0.9	P;B;P	0.45610	0.474;0.293;0.487	T	0.52230	-0.8603	10	0.32370	T	0.25	-17.2843	8.7163	0.34414	0.1378:0.1246:0.7376:0.0	.	738;765;754	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	S	754;738;765	ENSP00000351684:R754S;ENSP00000416800:R738S;ENSP00000236925:R765S	ENSP00000236925:R765S	R	+	3	2	CAMSAP1L1	199084782	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	2.224000	0.42945	0.249000	0.21456	0.484000	0.47621	AGG		0.468	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200818159	G	T	200818159	3	4	83	1	0	0	0	0	1	0	0	0	2618	1165	41	2	2304	2	CAMSAP1L1	1	200818159	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	41794696	200818159	48432462	15	23569										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214549631	214549631	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atcagctctactcgattctcCtcataggggacaacttcacg	7	13	5	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:214549631C>A	ENST00000366956.5	-	15	3032	c.2838G>T	c.(2836-2838)gaG>gaT	p.E946D	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	946	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.E946E(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CTCGATTCTCCTCATAGGGGA	0.463																																					Colon(92;557 1424 24372 34121 40073)											1	Substitution - coding silent(1)	kidney(1)	1											186	179	181					1																	214549631		2203	4300	6503	212616254	SO:0001583	missense	5784			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2838G>T	1.37:g.214549631C>A	ENSP00000355923:p.Glu946Asp		212616254	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	4.693	0.128794	0.08981	.	.	ENSG00000152104	ENST00000366956	T	0.78707	-1.2	5.29	5.29	0.74685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.66733	0.2819	N	0.02334	-0.595	0.80722	D	1	D	0.61080	0.989	D	0.71414	0.973	T	0.65998	-0.6032	10	0.02654	T	1	.	12.3131	0.54940	0.0:0.9227:0.0:0.0773	.	946	Q15678	PTN14_HUMAN	D	946	ENSP00000355923:E946D	ENSP00000355923:E946D	E	-	3	2	PTPN14	212616254	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.040000	0.41203	2.468000	0.83385	0.655000	0.94253	GAG		0.463	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214549631	C	A	214549631	3	1	83	1	0	0	0	0	1	0	0	0	12818	680	24	2	745	2	PTPN14	1	214549631	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	13731472	214549631	34700990	16	23570										
RAB4A	5867	hgsc.bcm.edu	37	chr1	229433367	229433367	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	accttcttagaagcctccagAtttgctcaagaaaatggcaa	7	10	2	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:229433367A>G	ENST00000366690.4	+	5	637	c.429A>G	c.(427-429)agA>agG	p.R143R	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	143					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				AAGCCTCCAGATTTGCTCAAG	0.378																																					Esophageal Squamous(11;250 603 9619 16563)											0			1											93	91	92					1																	229433367		2203	4300	6503	227499990	SO:0001819	synonymous_variant	5867			BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"RAB, member RAS oncogene"	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.429A>G	1.37:g.229433367A>G			227499990	Q5T7P7|Q9BQ44	Silent	SNP	ENST00000366690.4	37	CCDS31050.1																																																																																				0.378	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578		G	229433367	A	G	229433367	2	3	83	1	0	0	0	0	0	0	0	1	12983	330	12	4		4	RAB4A	1	229433367	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	14883736	229433367	19817254	17	23571										
C1orf101	257044	hgsc.bcm.edu	37	chr1	244780890	244780890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggagacttaaatcaaccataCgagattatcaacagttctaa	6	8	3	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:244780890C>T	ENST00000366534.4	+	20	2604	c.2550C>T	c.(2548-2550)taC>taT	p.Y850Y	C1orf101_ENST00000366531.3_Silent_p.Y699Y|C1orf101_ENST00000366533.4_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	850						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			ATCAACCATACGAGATTATCA	0.338																																																0			1											232	184	199					1																	244780890		692	1589	2281	242847513	SO:0001819	synonymous_variant	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.2550C>T	1.37:g.244780890C>T			242847513	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																				0.338	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		T	244780890	C	T	244780890	2	4	83	1	0	0	0	0	0	0	0	1	1982	547	19	1		1	C1orf101	1	244780890	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	15347523	244780890	4469731	18	23572										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29259556	29259556	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atcactgttgcagacaacctCaactccaagaactcagggat	7	12	3	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:29259556C>G	ENST00000379558.4	+	18	2919	c.2568C>G	c.(2566-2568)ctC>ctG	p.L856L	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Silent_p.L801L	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	856										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CAGACAACCTCAACTCCAAGA	0.582																																																0			2											118	87	98					2																	29259556		2203	4300	6503	29113060	SO:0001819	synonymous_variant	165186			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2568C>G	2.37:g.29259556C>G			29113060	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																				0.582	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		G	29259556	C	G	29259556	2	3	83	1	0	0	0	0	0	0	0	1	5521	813	29	5		5	FAM179A	2	29259556	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10		29259556	213939817	19	23573										
DQX1	165545	hgsc.bcm.edu	37	chr2	74751165	74751165	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggatggtgtcccagtagatgGgggaaggtctctcaccaggc	16	9	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:74751165G>T	ENST00000404568.3	-	4	920	c.701C>A	c.(700-702)cCc>cAc	p.P234H	DQX1_ENST00000495597.1_5'UTR|DQX1_ENST00000393951.2_Missense_Mutation_p.P234H	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	234						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.P116L(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CCAGTAGATGGGGGAAGGTCT	0.547																																																1	Substitution - Missense(1)	ovary(1)	2											72	71	71					2																	74751165		2203	4300	6503	74604673	SO:0001583	missense	165545			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.701C>A	2.37:g.74751165G>T	ENSP00000384621:p.Pro234His		74604673	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	4.240	0.043452	0.08196	.	.	ENSG00000144045	ENST00000393951;ENST00000404568;ENST00000451518	T;T;T	0.22743	3.31;3.31;1.94	5.38	1.22	0.21188	DEAD-like helicase (1);	0.695877	0.13971	N	0.350163	T	0.16811	0.0404	L	0.50333	1.59	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.27191	-1.0081	10	0.87932	D	0	-20.0491	3.6203	0.08093	0.4228:0.0:0.4066:0.1706	.	234	Q8TE96	DQX1_HUMAN	H	234;234;116	ENSP00000377523:P234H;ENSP00000384621:P234H;ENSP00000392969:P116H	ENSP00000377523:P234H	P	-	2	0	DQX1	74604673	0.004000	0.15560	0.003000	0.11579	0.020000	0.10135	1.354000	0.34056	0.160000	0.19432	0.609000	0.83330	CCC		0.547	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74751165	G	T	74751165	3	4	83	1	0	0	0	0	1	0	0	0	4762	1232	43	2	1488	2	DQX1	2	74751165	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	45491609	74751165	168448208	20	23574										
CNNM4	26504	hgsc.bcm.edu	37	chr2	97427829	97427829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agctcaatatgatccagggtGccctggaactacggaccaaa	10	11	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:97427829G>T	ENST00000377075.2	+	1	1191	c.1093G>T	c.(1093-1095)Gcc>Tcc	p.A365S		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	365					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GATCCAGGGTGCCCTGGAACT	0.512																																																0			2											85	75	79					2																	97427829		2203	4300	6503	96791556	SO:0001583	missense	26504			AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1093G>T	2.37:g.97427829G>T	ENSP00000366275:p.Ala365Ser		96791556	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114536	0.77210	.	.	ENSG00000158158	ENST00000377075	T	0.77229	-1.08	5.19	4.28	0.50868	.	0.063550	0.64402	N	0.000009	D	0.91338	0.7268	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93422	0.6778	10	0.87932	D	0	-4.6656	13.6727	0.62436	0.0:0.0:0.8438:0.1561	.	365	Q6P4Q7	CNNM4_HUMAN	S	365	ENSP00000366275:A365S	ENSP00000366275:A365S	A	+	1	0	CNNM4	96791556	1.000000	0.71417	0.983000	0.44433	0.962000	0.63368	9.807000	0.99171	1.119000	0.41883	0.655000	0.94253	GCC		0.512	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		T	97427829	G	T	97427829	3	4	83	1	0	0	0	0	1	0	0	0	3621	1319	46	2	1095	2	CNNM4	2	97427829	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	22676664	97427829	145771544	21	23575										
PDE1A	5136	hgsc.bcm.edu	37	chr2	183053745	183053745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	catggttgacttccgatcacAaagtggggaaaatggaagcc	12	8	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:183053745A>G	ENST00000410103.1	-	12	1299	c.1216T>C	c.(1216-1218)Tgt>Cgt	p.C406R	PDE1A_ENST00000456212.1_Missense_Mutation_p.C406R|PDE1A_ENST00000331935.6_Missense_Mutation_p.C406R|PDE1A_ENST00000536095.1_Missense_Mutation_p.C302R|PDE1A_ENST00000435564.1_Missense_Mutation_p.C406R|PDE1A_ENST00000358139.2_Missense_Mutation_p.C406R|PDE1A_ENST00000351439.5_Missense_Mutation_p.C390R|PDE1A_ENST00000346717.4_Missense_Mutation_p.C372R|PDE1A_ENST00000409365.1_Missense_Mutation_p.C390R	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	406	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	TTCCGATCACAAAGTGGGGAA	0.418																																																0			2											182	189	187					2																	183053745		2203	4300	6503	182761990	SO:0001583	missense	5136				CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"Phosphodiesterases"	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.1216T>C	2.37:g.183053745A>G	ENSP00000387037:p.Cys406Arg		182761990	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	37	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271533	0.80469	.	.	ENSG00000115252	ENST00000435564;ENST00000346717;ENST00000536095;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	D;D;D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.6	5.6	0.85130	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.045414	0.85682	D	0.000000	D	0.94142	0.8121	H	0.96996	3.92	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;1.0;0.999	D	0.95903	0.8917	10	0.87932	D	0	.	15.2579	0.73599	1.0:0.0:0.0:0.0	.	302;372;406;390;406	B7Z3A7;P54750-3;P54750;P54750-2;P54750-4	.;.;PDE1A_HUMAN;.;.	R	406;372;302;390;406;390;406;406;406	ENSP00000410309:C406R;ENSP00000329112:C372R;ENSP00000439938:C302R;ENSP00000386767:C390R;ENSP00000331574:C406R;ENSP00000309269:C390R;ENSP00000387037:C406R;ENSP00000350858:C406R;ENSP00000408874:C406R	ENSP00000331574:C406R	C	-	1	0	PDE1A	182761990	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.542000	0.90647	2.254000	0.74563	0.482000	0.46254	TGT		0.418	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			G	183053745	A	G	183053745	3	3	83	1	0	0	0	0	1	0	0	0	11664	130	5	4	485	4	PDE1A	2	183053745	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	85625916	183053745	60145628	22	23576										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201437640	201437640	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acaatttctgaaaatctacaAgtcacaaatgaatttcaaac	3	8	4	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:201437640A>G	ENST00000357799.4	+	7	2669	c.2571A>G	c.(2569-2571)caA>caG	p.Q857Q		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	857					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AAAATCTACAAGTCACAAATG	0.294																																																0			2											85	84	84					2																	201437640		1805	4067	5872	201145885	SO:0001819	synonymous_variant	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2571A>G	2.37:g.201437640A>G			201145885	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																				0.294	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201437640	A	G	201437640	2	3	83	1	0	0	0	0	0	0	0	1	14254	69	3	4		4	SGOL2	2	201437640	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	18383895	201437640	41761733	23	23577										
CNTN4	152330	hgsc.bcm.edu	37	chr3	2942482	2942482	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctacatacaagtggctaaaaAatggcgaacctctgctaact	7	10	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:2942482A>C	ENST00000397461.1	+	10	1438	c.1054A>C	c.(1054-1056)Aat>Cat	p.N352H	CNTN4_ENST00000427331.1_Missense_Mutation_p.N352H|CNTN4_ENST00000418658.1_Missense_Mutation_p.N352H|CNTN4_ENST00000475817.1_3'UTR|CNTN4_ENST00000448906.2_Missense_Mutation_p.N24H|CNTN4_ENST00000358480.3_Missense_Mutation_p.N133H|CNTN4_ENST00000397459.2_Missense_Mutation_p.N24H	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	352	Ig-like C2-type 4.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GTGGCTAAAAAATGGCGAACC	0.398																																																0			3											138	110	119					3																	2942482		2203	4300	6503	2917482	SO:0001583	missense	152330			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.1054A>C	3.37:g.2942482A>C	ENSP00000380602:p.Asn352His		2917482	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.881618	0.72294	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906;ENST00000473845	T;T;T;T;T;T;T	0.76186	0.78;0.78;0.78;0.78;-1.0;-1.0;-1.0	5.41	5.41	0.78517	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061265	0.64402	D	0.000005	D	0.85965	0.5820	M	0.86343	2.81	0.53005	D	0.999965	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.982;0.994;0.962	D	0.87584	0.2486	10	0.87932	D	0	.	8.7563	0.34648	0.8822:0.0:0.1178:0.0	.	352;352;352	Q8IWV2-3;B3KTK4;Q8IWV2	.;.;CNTN4_HUMAN	H	352;352;352;133;24;24;30	ENSP00000396010:N352H;ENSP00000380602:N352H;ENSP00000413642:N352H;ENSP00000351267:N133H;ENSP00000380600:N24H;ENSP00000392077:N24H;ENSP00000422120:N30H	ENSP00000351267:N133H	N	+	1	0	CNTN4	2917482	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.410000	0.66381	2.171000	0.68590	0.533000	0.62120	AAT		0.398	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			C	2942482	A	C	2942482	3	2	83	1	0	0	0	0	1	0	0	0	3649	14	1	4	1084	4	CNTN4	3	2942482	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10		2942482	195079948	24	23578										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4821291	4821291	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcaggcacgacagtgaaaacGcagagaggatactttataac	11	8	0	2	rs373973399		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:4821291G>A	ENST00000443694.2	+	46	6304	c.6304G>A	c.(6304-6306)Gca>Aca	p.A2102T	ITPR1_ENST00000423119.2_Missense_Mutation_p.A2069T|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.A2102T|ITPR1_ENST00000354582.6_Missense_Mutation_p.A2102T|ITPR1_ENST00000357086.4_Missense_Mutation_p.A2069T|ITPR1_ENST00000456211.2_Missense_Mutation_p.A2054T			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2117					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.A2054T(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CAGTGAAAACGCAGAGAGGAT	0.502																																																1	Substitution - Missense(1)	large_intestine(1)	3											119	120	120					3																	4821291		1989	4154	6143	4796291	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.6304G>A	3.37:g.4821291G>A	ENSP00000401671:p.Ala2102Thr		4796291	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	33	5.222462	0.95139	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92965	-3.12;-3.13;-3.14;-3.14;-3.12;-3.12	5.28	4.39	0.52855	.	0.051084	0.85682	D	0.000000	D	0.95962	0.8685	M	0.90977	3.165	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.58520	0.74;0.84	D	0.95493	0.8571	10	0.33940	T	0.23	.	15.8769	0.79170	0.0:0.1358:0.8642:0.0	.	2117;2069	Q14643;G5E9P1	ITPR1_HUMAN;.	T	2117;2102;2102;2069;563;2069;2054;2102	ENSP00000306253:A2102T;ENSP00000346595:A2102T;ENSP00000405934:A2069T;ENSP00000349597:A2069T;ENSP00000397885:A2054T;ENSP00000401671:A2102T	ENSP00000306253:A2102T	A	+	1	0	ITPR1	4796291	1.000000	0.71417	0.217000	0.23759	0.985000	0.73830	9.772000	0.98984	1.191000	0.43056	0.585000	0.79938	GCA		0.502	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4821291	G	A	4821291	3	1	83	1	0	0	0	0	1	0	0	0	7941	1087	38	1	6535	1	ITPR1	3	4821291	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	1878809	4821291	193201139	25	23579										
VHL	7428	hgsc.bcm.edu	37	chr3	10188302	10188302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttgacggacagcctatttttGccaatatcacactgccaggt	8	11	1	1	rs587780077		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:10188302G>A	ENST00000256474.2	+	2	1285	c.445G>A	c.(445-447)Gcc>Acc	p.A149T	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	149	Involved in binding to CCT complex.		A -> T (in VHLD; type II). {ECO:0000269|PubMed:9452106}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.A149fs*26(4)|p.A149fs*24(3)|p.F148fs*9(1)|p.F148fs*11(1)|p.I147fs*10(1)|p.A149fs*11(1)|p.A149P(1)|p.P146fs*23(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCCTATTTTTGCCAATATCAC	0.413		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	14	Deletion - Frameshift(7)|Insertion - Frameshift(5)|Substitution - Missense(1)|Complex - frameshift(1)	kidney(14)	3	GRCh37	CM951288|CM982010|HD971374	VHL	D|M							199	186	191					3																	10188302		2203	4300	6503	10163302	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.445G>A	3.37:g.10188302G>A	ENSP00000256474:p.Ala149Thr		10163302	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771662	0.90108	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99789	-6.75	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.111909	0.64402	D	0.000011	D	0.99542	0.9836	L	0.53249	1.67	0.80722	D	1	D	0.69078	0.997	D	0.63597	0.916	D	0.98054	1.0389	10	0.44086	T	0.13	-0.1953	15.9164	0.79521	0.0:0.0:1.0:0.0	.	149	P40337	VHL_HUMAN	T	149;67	ENSP00000256474:A149T	ENSP00000256474:A149T	A	+	1	0	VHL	10163302	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.278000	0.78587	2.428000	0.82296	0.563000	0.77884	GCC		0.413	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10188302	G	A	10188302	3	1	83	1	0	0	0	0	1	0	0	0	17202	1319	46	3	451	3	VHL	3	10188302	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	5367011	10188302	187834128	26	23580										
LTF	4057	hgsc.bcm.edu	37	chr3	46479450	46479450	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cgggaggttgagcactttttCagattagtaatgcctgcgac	12	8	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:46479450C>T	ENST00000231751.4	-	16	2374	c.2079G>A	c.(2077-2079)ctG>ctA	p.L693L	LTF_ENST00000426532.2_Silent_p.L649L|LTF_ENST00000417439.1_Silent_p.L691L|LTF_ENST00000493056.1_5'Flank	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	693	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGCACTTTTTCAGATTAGTAA	0.458																																																0			3											215	204	208					3																	46479450		2203	4299	6502	46454454	SO:0001819	synonymous_variant	4057				CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.2079G>A	3.37:g.46479450C>T			46454454	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																				0.458	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		T	46479450	C	T	46479450	2	4	83	1	0	0	0	0	0	0	0	1	9108	813	29	3		3	LTF	3	46479450	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	36291148	46479450	151542980	27	23581										
SETD2	29072	hgsc.bcm.edu	37	chr3	47129647	47129647	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tttctgctccaaagtttcaaTtctaaccattagccgggata	6	10	3	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:47129647T>C	ENST00000409792.3	-	10	5275	c.5233A>G	c.(5233-5235)Att>Gtt	p.I1745V	snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1745					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AAAGTTTCAATTCTAACCATT	0.418			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0			3											127	133	131					3																	47129647		2203	4300	6503	47104651	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5233A>G	3.37:g.47129647T>C	ENSP00000386759:p.Ile1745Val		47104651	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545589	0.65198	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.88046	-2.33	4.46	4.46	0.54185	.	0.000000	0.52532	D	0.000066	T	0.68915	0.3053	N	0.01505	-0.83	0.42176	D	0.99166	B;B	0.30236	0.274;0.274	B;B	0.25614	0.062;0.062	T	0.72571	-0.4253	10	0.48119	T	0.1	.	14.2024	0.65712	0.0:0.0:0.0:1.0	.	1745;1745	F2Z317;Q9BYW2	.;SETD2_HUMAN	V	1745	ENSP00000386759:I1745V	ENSP00000386759:I1745V	I	-	1	0	SETD2	47104651	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.618000	0.67722	1.995000	0.58328	0.528000	0.53228	ATT		0.418	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47129647	T	C	47129647	3	2	83	1	0	0	0	0	1	0	0	0	14168	1493	52	4	2509	4	SETD2	3	47129647	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	650197	47129647	150892783	28	23582										
WDR6	11180	hgsc.bcm.edu	37	chr3	49051072	49051072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccgggagggtctgcatggccGtgagatcacttgtgtaaagc	15	9	2	1	rs546787787		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:49051072G>A	ENST00000608424.1	+	2	2144	c.2105G>A	c.(2104-2106)cGt>cAt	p.R702H	WDR6_ENST00000415265.2_Missense_Mutation_p.R150H|WDR6_ENST00000395474.3_Missense_Mutation_p.R732H|WDR6_ENST00000448293.1_Missense_Mutation_p.R651H			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	702					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CTGCATGGCCGTGAGATCACT	0.587											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			3											82	71	75					3																	49051072		2203	4300	6503	49026076	SO:0001583	missense	11180			AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"WD repeat domain containing"	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2105G>A	3.37:g.49051072G>A	ENSP00000477389:p.Arg702His	959	49026076	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		.	.	.	.	.	.	.	.	.	.	G	17.86	3.491680	0.64074	.	.	ENSG00000178252	ENST00000395474;ENST00000415265;ENST00000448293	T;T;T	0.70631	2.79;-0.5;-0.5	5.49	5.49	0.81192	WD40 repeat-like-containing domain (1);	0.049393	0.85682	D	0.000000	D	0.84777	0.5547	M	0.75264	2.295	0.42134	D	0.991488	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.987;0.948;0.997	D	0.86322	0.1693	10	0.87932	D	0	-23.0479	19.3757	0.94508	0.0:0.0:1.0:0.0	.	150;702;651	E9PBK6;Q9NNW5;E9PDU5	.;WDR6_HUMAN;.	H	732;150;651	ENSP00000378857:R732H;ENSP00000412195:R150H;ENSP00000413432:R651H	ENSP00000378857:R732H	R	+	2	0	WDR6	49026076	1.000000	0.71417	0.971000	0.41717	0.984000	0.73092	6.089000	0.71384	2.583000	0.87209	0.561000	0.74099	CGT		0.587	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			A	49051072	G	A	49051072	3	1	83	1	0	0	0	0	1	0	0	0	17350	1145	40	1	2201	1	WDR6	3	49051072	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	1921425	49051072	148971358	29	23583										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113187725	113187725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tggtttggagtctcttgacaGcattggtagcattcagagca	12	7	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:113187725G>A	ENST00000295872.4	-	9	1032	c.773C>T	c.(772-774)gCt>gTt	p.A258V		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	258					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TCTCTTGACAGCATTGGTAGC	0.413																																																0			3											88	79	82					3																	113187725		2203	4300	6503	114670415	SO:0001583	missense	0			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.773C>T	3.37:g.113187725G>A	ENSP00000295872:p.Ala258Val		114670415	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433986	0.25813	.	.	ENSG00000163611	ENST00000295872	T	0.32515	1.45	5.05	3.24	0.37175	.	0.289600	0.37906	N	0.001898	T	0.17323	0.0416	L	0.33245	0.995	0.41048	D	0.985286	P;P	0.41393	0.748;0.506	B;B	0.36134	0.218;0.218	T	0.04268	-1.0964	10	0.23891	T	0.37	-8.2206	5.4437	0.16523	0.3329:0.0:0.6671:0.0	.	154;258	B3KX77;Q8N0Z3	.;SPICE_HUMAN	V	258	ENSP00000295872:A258V	ENSP00000295872:A258V	A	-	2	0	SPICE1	114670415	0.995000	0.38212	0.996000	0.52242	0.045000	0.14185	2.968000	0.49224	1.263000	0.44181	-0.218000	0.12543	GCT		0.413	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113187725	G	A	113187725	3	1	83	1	0	0	0	0	1	0	0	0	2828	971	34	3	1834	3	CCDC52	3	113187725	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	64136653	113187725	84834705	30	23584										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158284035	158284035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttggtttggcaatgctggtgGctttgattgagttctgttac	13	5	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:158284035G>A	ENST00000264426.9	+	15	2770	c.2491G>A	c.(2491-2493)Gct>Act	p.A831T	GRIA2_ENST00000296526.7_Missense_Mutation_p.A831T|GRIA2_ENST00000449365.1_Missense_Mutation_p.A784T|GRIA2_ENST00000507898.1_Missense_Mutation_p.A784T|GRIA2_ENST00000393815.2_Missense_Mutation_p.A784T|AC079233.1_ENST00000578227.1_RNA	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	831					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.A831T(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	AATGCTGGTGGCTTTGATTGA	0.468																																																2	Substitution - Missense(2)	lung(2)	4											150	135	140					4																	158284035		2203	4300	6503	158503485	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2491G>A	4.37:g.158284035G>A	ENSP00000264426:p.Ala831Thr		158503485	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.4|24.4	4.532538|4.532538	0.85812|0.85812	.|.	.|.	ENSG00000120251|ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365|ENST00000510854	T;T;T;T;T|.	0.15718|.	2.4;2.4;2.44;2.44;2.4|.	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83857|0.83857	0.5345|0.5345	M|M	0.84948|0.84948	2.725|2.725	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;0.997|.	D;D;D|.	0.87578|.	0.998;0.998;0.98|.	D|D	0.83604|0.83604	0.0130|0.0130	10|5	0.87932|.	D|.	0|.	.|.	20.6721|20.6721	0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	831;831;784|.	P42262;P42262-2;A8MT92|.	GRIA2_HUMAN;.;.|.	T|D	784;784;831;831;784|161	ENSP00000426845:A784T;ENSP00000377403:A784T;ENSP00000296526:A831T;ENSP00000264426:A831T;ENSP00000389837:A784T|.	ENSP00000264426:A831T|.	A|G	+|+	1|2	0|0	GRIA2|GRIA2	158503485|158503485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.869000|9.869000	0.99810|0.99810	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GCT|GGC		0.468	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158284035	G	A	158284035	3	1	83	1	0	0	0	0	1	0	0	0	6789	1203	42	3	2668	3	GRIA2	4	158284035	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10		158284035	32870241	31	23585										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160264556	160264556	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tgccctcatgttcaggactcGgtgagtatgtcatcttcagt	10	10	5	1	rs201720107		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:160264556G>A	ENST00000264431.4	+	16	3190	c.2771G>A	c.(2770-2772)cGg>cAg	p.R924Q		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	924	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TTCAGGACTCGGTGAGTATGT	0.398																																																0			4						G	GLN/ARG	1,3877		0,1,1938	101	98	99		2771	4.9	1	4		99	1,8275		0,1,4137	yes	missense-near-splice	RAPGEF2	NM_014247.2	43	0,2,6075	AA,AG,GG		0.0121,0.0258,0.0165	possibly-damaging	924/1500	160264556	2,12152	1939	4138	6077	160484006	SO:0001630	splice_region_variant	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2771+1G>A	4.37:g.160264556G>A			160484006	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359615	0.82353	2.58E-4	1.21E-4	ENSG00000109756	ENST00000264431	T	0.38560	1.13	5.73	4.89	0.63831	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.043792	0.85682	D	0.000000	T	0.42086	0.1187	L	0.55481	1.735	0.80722	D	1	P	0.42078	0.77	B	0.40659	0.336	T	0.36625	-0.9740	10	0.46703	T	0.11	.	14.6849	0.69042	0.0697:0.0:0.9303:0.0	.	924	Q9Y4G8	RPGF2_HUMAN	Q	924	ENSP00000264431:R924Q	ENSP00000264431:R924Q	R	+	2	0	RAPGEF2	160484006	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.864000	0.99589	1.425000	0.47237	0.491000	0.48974	CGG		0.398	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	Missense_Mutation	A	160264556	G	A	160264556	5	1	83	1	0	0	0	0	0	0	1	0	13081	1130	39	1	2833	1	RAPGEF2	4	160264556	Splice_Site	SNP	G	TCGA-AH-6549-01A-11D-1826-10	1980521	160264556	30889720	32	23586										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183713469	183713469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gccagcggcagtacatcttcGaatacgatatgtgggaccgc	12	11	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:183713469G>A	ENST00000511685.1	+	26	5767	c.5644G>A	c.(5644-5646)Gaa>Aaa	p.E1882K	TENM3_ENST00000406950.2_Missense_Mutation_p.E1882K			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1882					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTACATCTTCGAATACGATAT	0.498																																																0			4											95	97	96					4																	183713469		2044	4180	6224	183950463	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5644G>A	4.37:g.183713469G>A	ENSP00000424226:p.Glu1882Lys		183950463	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725012	0.89298	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86694	-2.16;-2.16	5.18	5.18	0.71444	.	.	.	.	.	D	0.83852	0.5344	M	0.71581	2.175	0.80722	D	1	P	0.44006	0.824	B	0.22386	0.039	D	0.87245	0.2269	9	0.62326	D	0.03	.	18.8905	0.92399	0.0:0.0:1.0:0.0	.	1882	Q9P273	TEN3_HUMAN	K	1882	ENSP00000424226:E1882K;ENSP00000385276:E1882K	ENSP00000385276:E1882K	E	+	1	0	ODZ3	183950463	1.000000	0.71417	0.964000	0.40570	0.983000	0.72400	9.623000	0.98386	2.688000	0.91661	0.591000	0.81541	GAA		0.498	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183713469	G	A	183713469	3	1	83	1	0	0	0	0	1	0	0	0	10867	1059	37	1	5742	1	ODZ3	4	183713469	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	23448913	183713469	7440807	33	23587										
FAT1	2195	hgsc.bcm.edu	37	chr4	187629652	187629652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	caagaccttggtggacgcttTtctgtcacttgttgttactt	9	9	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:187629652T>C	ENST00000441802.2	-	2	1539	c.1330A>G	c.(1330-1332)Aaa>Gaa	p.K444E		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	444	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTGGACGCTTTTCTGTCACTT	0.413										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											216	211	212					4																	187629652		1890	4126	6016	187866646	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1330A>G	4.37:g.187629652T>C	ENSP00000406229:p.Lys444Glu		187866646		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	2.482	-0.319416	0.05386	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	D;T	0.81996	-1.56;0.14	5.35	4.15	0.48705	Cadherin (3);Cadherin-like (1);	0.280194	0.44285	D	0.000478	T	0.73892	0.3645	L	0.37561	1.115	0.37357	D	0.911062	B	0.33120	0.398	B	0.37144	0.242	T	0.68887	-0.5290	10	0.06099	T	0.92	.	12.7126	0.57098	0.0:0.0:0.1372:0.8628	.	444	Q14517	FAT1_HUMAN	E	444	ENSP00000406229:K444E;ENSP00000423736:K444E	ENSP00000260147:K444E	K	-	1	0	FAT1	187866646	1.000000	0.71417	0.391000	0.26233	0.795000	0.44927	4.030000	0.57260	1.013000	0.39391	0.459000	0.35465	AAA		0.413	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		C	187629652	T	C	187629652	3	2	83	1	0	0	0	0	1	0	0	0	5708	1850	64	4	12540	4	FAT1	4	187629652	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	3916183	187629652	3524624	34	23588										
TRIML2	205860	hgsc.bcm.edu	37	chr4	189018291	189018291	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gtgatatgagcgggctccagAtgctcaagcagcagtgactt	13	9	1	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:189018291A>T	ENST00000512729.1	-	6	893	c.519T>A	c.(517-519)caT>caA	p.H173Q	TRIML2_ENST00000326754.3_Missense_Mutation_p.H198Q	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	173					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		CGGGCTCCAGATGCTCAAGCA	0.493																																																0			4											126	122	123					4																	189018291		2203	4300	6503	189255285	SO:0001583	missense	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.519T>A	4.37:g.189018291A>T	ENSP00000422581:p.His173Gln		189255285	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	37	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	A	6.722	0.502008	0.12822	.	.	ENSG00000179046	ENST00000512729;ENST00000326754	T;T	0.57595	3.63;0.39	4.51	-0.315	0.12746	.	0.766357	0.11596	N	0.548211	T	0.27489	0.0675	N	0.08118	0	0.09310	N	1	B;B	0.18461	0.028;0.004	B;B	0.16722	0.016;0.004	T	0.20338	-1.0278	10	0.22706	T	0.39	.	7.6956	0.28592	0.4367:0.0:0.5633:0.0	.	198;173	B7ZLC3;Q8N7C3	.;TRIMM_HUMAN	Q	173;198	ENSP00000422581:H173Q;ENSP00000317498:H198Q	ENSP00000317498:H198Q	H	-	3	2	TRIML2	189255285	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.489000	0.22387	-0.038000	0.13624	-0.937000	0.02696	CAT		0.493	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		T	189018291	A	T	189018291	3	4	83	1	0	0	0	0	1	0	0	0	16591	330	12	5	652	5	TRIML2	4	189018291	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	1388639	189018291	2135985	35	23589										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5460921	5460921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aaatggaggttagggagatgGataagtcagtacaaactgag	14	3	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:5460921G>A	ENST00000296564.7	+	13	1696	c.1474G>A	c.(1474-1476)Gat>Aat	p.D492N		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		492					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TAGGGAGATGGATAAGTCAGT	0.438																																																0			5											94	98	96					5																	5460921		1972	4152	6124	5513921	SO:0001583	missense	23379																														ENST00000296564.7:c.1474G>A	5.37:g.5460921G>A	ENSP00000296564:p.Asp492Asn		5513921	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117346	0.56505	.	.	ENSG00000164151	ENST00000296564	T	0.13420	2.59	4.64	2.82	0.32997	.	0.623486	0.16171	N	0.226267	T	0.12944	0.0314	L	0.32530	0.975	0.09310	N	1	P	0.48016	0.904	P	0.46718	0.525	T	0.10245	-1.0638	10	0.52906	T	0.07	-6.7037	6.5835	0.22609	0.1:0.1821:0.7179:0.0	.	492	Q9Y2F5	K0947_HUMAN	N	492	ENSP00000296564:D492N	ENSP00000296564:D492N	D	+	1	0	KIAA0947	5513921	0.135000	0.22499	0.000000	0.03702	0.037000	0.13140	3.133000	0.50531	0.478000	0.27488	0.305000	0.20034	GAT		0.438	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			A	5460921	G	A	5460921	3	1	83	1	0	0	0	0	1	0	0	0	8223	1174	41	3	1524	3	KIAA0947	5	5460921	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10		5460921	175454339	36	23590										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67589618	67589618	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctcagtttcaagaaaaaagtCgagaatatgatagattatat	7	4	2	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:67589618C>T	ENST00000521381.1	+	11	1997	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.R191*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.R461*|PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.R98*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.R461*|PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.R161*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.R461*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	461					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)|p.F456_R461>S(1)|p.F456_R461del(1)|p.Q457_R461del(1)|p.R461*(1)|p.T454_D464del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AGAAAAAAGTCGAGAATATGA	0.279			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	7	Deletion - In frame(3)|Substitution - Nonsense(1)|Whole gene deletion(1)|Complex - deletion inframe(1)|Unknown(1)	endometrium(4)|large_intestine(2)|lung(1)	5											45	49	47					5																	67589618		2184	4265	6449	67625374	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1381C>T	5.37:g.67589618C>T	ENSP00000428056:p.Arg461*		67625374	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079198	0.94050	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.1	2.12	0.27331	.	0.185230	0.43110	D	0.000617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9788	17.5497	0.87872	0.3803:0.6197:0.0:0.0	.	.	.	.	X	461;461;461;461;161;98;191;134;98	.	ENSP00000274335:R461X	R	+	1	2	PIK3R1	67625374	0.959000	0.32827	0.987000	0.45799	0.824000	0.46624	0.433000	0.21477	0.405000	0.25532	-0.824000	0.03097	CGA		0.279	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67589618	C	T	67589618	4	4	83	1	0	0	0	0	0	1	0	0	11949	876	31	1	1549	1	PIK3R1	5	67589618	Nonsense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	62128697	67589618	113325642	37	23591										
FAM81B	153643	hgsc.bcm.edu	37	chr5	94785910	94785910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acaaatacagaaaacaaagaTggatttagagaaatataaag	7	3	0	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:94785910T>C	ENST00000283357.5	+	10	1329	c.1283T>C	c.(1282-1284)aTg>aCg	p.M428T		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	428						nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		AAAACAAAGATGGATTTAGAG	0.338																																																0			5											119	113	114					5																	94785910		1811	4074	5885	94811666	SO:0001583	missense	153643				CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.1283T>C	5.37:g.94785910T>C	ENSP00000283357:p.Met428Thr		94811666		Missense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566118	0.65651	.	.	ENSG00000153347	ENST00000283357;ENST00000512365	T	0.19250	2.16	5.62	5.62	0.85841	.	0.238711	0.45126	D	0.000384	T	0.36799	0.0980	M	0.66939	2.045	0.27631	N	0.948026	D	0.56035	0.974	P	0.53861	0.736	T	0.26258	-1.0108	10	0.39692	T	0.17	-17.7928	14.7984	0.69894	0.0:0.0:0.0:1.0	.	428	Q96LP2	FA81B_HUMAN	T	428;103	ENSP00000283357:M428T	ENSP00000283357:M428T	M	+	2	0	FAM81B	94811666	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.291000	0.51764	2.133000	0.65898	0.482000	0.46254	ATG		0.338	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		C	94785910	T	C	94785910	3	2	83	1	0	0	0	0	1	0	0	0	5648	1464	51	4	1321	4	FAM81B	5	94785910	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	27196292	94785910	86129350	38	23592										
APC	324	hgsc.bcm.edu	37	chr5	112175772	112175772	+	Frame_Shift_Del	DEL	A	A	-													0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tttattacattttgccacggAaagtactccagatggatttt							TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:112175772delA	ENST00000457016.1	+	16	4861	c.4481delA	c.(4480-4482)gaafs	p.E1494fs	APC_ENST00000257430.4_Frame_Shift_Del_p.E1494fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1494fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1494	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.K1454fs*3(1)|p.T1493fs*17(1)|p.S1495fs*19(1)|p.K1192fs*3(1)|p.E1494fs*12(1)|p.E1494fs*11(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTGCCACGGAAAGTACTCCA	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Deletion - Frameshift(3)|Complex - frameshift(2)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(4)|thyroid(1)|soft_tissue(1)|skin(1)	5											70	72	71					5																	112175772		2201	4300	6501	112203671	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4481delA	5.37:g.112175772delA	ENSP00000413133:p.Glu1494fs		112203671	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175772	A	-	112175772	7	5	83	1	0	1	0	1	0	0	0	0	763	246	9	0	4539	0	APC	5	112175772	Frame_Shift_Del	DEL	A	TCGA-AH-6549-01A-11D-1826-10	17389862	112175772	68739488	39	23593										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256833	140256833	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggtgcgggccacgtggtggcGaaagtgcgcgcggtggacgc	21	10	0	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:140256833G>A	ENST00000398631.2	+	1	1776	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	592	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGTGGTGGCGAAAGTGCGCG	0.697																																					Pancreas(113;759 1672 13322 24104 50104)											0			5											324	295	305					5																	140256833		2203	4299	6502	140237017	SO:0001819	synonymous_variant	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1776G>A	5.37:g.140256833G>A			140237017	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																				0.697	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256833	G	A	140256833	2	1	83	1	0	0	0	0	0	0	0	1	11553	1045	37	1		1	PCDHA12	5	140256833	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	28081061	140256833	40658427	40	23594										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794236	140794236	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atttactccctggctgaagaCaccatccagggggtacctct	9	13	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:140794236C>T	ENST00000398610.2	+	1	1494	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	498	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCTGAAGACACCATCCAGG	0.527																																																0			5											130	138	135					5																	140794236		2122	4277	6399	140774420	SO:0001819	synonymous_variant	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1494C>T	5.37:g.140794236C>T			140774420	Q9Y5E0	Silent	SNP	ENST00000398610.2	37	CCDS47292.1																																																																																				0.527	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140794236	C	T	140794236	2	4	83	1	0	0	0	0	0	0	0	1	11582	477	17	3		3	PCDHGA10	5	140794236	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	537403	140794236	40121024	41	23595										
FLT4	2324	hgsc.bcm.edu	37	chr5	180045831	180045831	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttcgagaaccgcgcgaagagGaccctgtcgctgctccccgg	13	15	0	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:180045831G>A	ENST00000261937.6	-	21	3018	c.2940C>T	c.(2938-2940)gtC>gtT	p.V980V	FLT4_ENST00000424276.2_5'Flank|FLT4_ENST00000502649.1_Silent_p.V980V|FLT4_ENST00000393347.3_Silent_p.V980V	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	980	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCGCGAAGAGGACCCTGTCGC	0.672																																					Colon(97;1075 1466 27033 27547 35871)											0			5											14	18	17					5																	180045831		2173	4278	6451	179978437	SO:0001819	synonymous_variant	2324			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2940C>T	5.37:g.180045831G>A			179978437	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																				0.672	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180045831	G	A	180045831	2	1	83	1	0	0	0	0	0	0	0	1	5963	1161	41	3		3	FLT4	5	180045831	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	39251595	180045831	869429	42	23596										
NQO2	4835	hgsc.bcm.edu	37	chr6	3010339	3010339	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agaatgtggctgtagatgaaCtgagcaggcagggctgcacc	15	8	0	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:3010339C>T	ENST00000338130.2	+	6	800	c.88C>T	c.(88-90)Ctg>Ttg	p.L30L	NQO2_ENST00000380430.1_Silent_p.L30L|NQO2_ENST00000380441.1_Silent_p.L30L|NQO2_ENST00000380454.4_Silent_p.L30L|NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380455.4_Silent_p.L30L			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	30					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	TGTAGATGAACTGAGCAGGCA	0.463																																																0			6											113	98	103					6																	3010339		2203	4300	6503	2955338	SO:0001819	synonymous_variant	4835			U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"NAD(P)H menadione oxidoreductase 2, dioxin-inducible"	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.88C>T	6.37:g.3010339C>T			2955338	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																				0.463	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1			T	3010339	C	T	3010339	2	4	83	1	0	0	0	0	0	0	0	1	10643	564	20	3		3	NQO2	6	3010339	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10		3010339	168104728	43	23597										
AIF1	199	hgsc.bcm.edu	37	chr6	31584094	31584094	+	Intron	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agagagggtctccccaccttCtccccatccccatcctctgc	6	20	3	1	rs13195276		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:31584094C>G	ENST00000376059.3	+	5	342				AIF1_ENST00000376049.4_Intron	NM_001623.3	NP_001614.3	P55008	AIF1_HUMAN	allograft inflammatory factor 1						actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cellular response to interferon-gamma (GO:0071346)|inflammatory response (GO:0006954)|microglial cell activation (GO:0001774)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell proliferation (GO:0048662)|phagocytosis, engulfment (GO:0006911)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|Rac protein signal transduction (GO:0016601)|ruffle assembly (GO:0097178)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|ruffle membrane (GO:0032587)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)|ovary(1)	3						TCCCCACCTTCTCCCCATCCC	0.537																																					Ovarian(23;358 734 36938 38933 52312)											0			6											72	56	62					6																	31584094		1511	2709	4220	31692073	SO:0001627	intron_variant	199			U19713	CCDS4706.1, CCDS34398.1	6p21.3	2013-01-10			ENSG00000204472	ENSG00000204472		"EF-hand domain containing"	352	protein-coding gene	gene with protein product	"interferon gamma responsive transcript", "ionized calcium-binding adapter molecule 1"	601833				8912632	Standard	NM_032955		Approved	IRT-1, AIF-1, Em:AF129756.17, IBA1	uc003nuy.3	P55008	OTTHUMG00000031246	ENST00000376059.3:c.197-27C>G	6.37:g.31584094C>G			31692073	A8K406|O43904|Q9UIV4|Q9UKS9	Missense_Mutation	SNP	ENST00000376059.3	37	CCDS4706.1																																																																																				0.537	AIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076512.3			G	31584094	C	G	31584094	1	3	83	0	1	0	0	0	0	0	0	0	424	913	32	5		5	AIF1	6	31584094	Intron	SNP	C	TCGA-AH-6549-01A-11D-1826-10	28573755	31584094	139530973	44	23598										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41533605	41533605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cagcagcggcggggccacagGgacaactgcaagtggcacgg	17	12	0	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:41533605G>T	ENST00000307972.4	+	1	119	c.107G>T	c.(106-108)gGg>gTg	p.G36V	FOXP4_ENST00000373060.1_Missense_Mutation_p.G36V|FOXP4_ENST00000373057.3_Missense_Mutation_p.G36V|FOXP4_ENST00000409208.1_Missense_Mutation_p.G36V|FOXP4_ENST00000373063.3_Missense_Mutation_p.G36V			Q8IVH2	FOXP4_HUMAN	forkhead box P4	36					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGGGCCACAGGGACAACTGCA	0.622																																																0			6											78	79	78					6																	41533605		2203	4300	6503	41641583	SO:0001583	missense	116113			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.107G>T	6.37:g.41533605G>T	ENSP00000309823:p.Gly36Val		41641583	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.786378	0.31593	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.90133	-2.62;-2.61;-2.62;-2.62;-2.62	5.21	4.34	0.51931	.	0.360853	0.28847	N	0.013945	T	0.74876	0.3774	N	0.22421	0.69	0.41096	D	0.98563	B;B;B	0.34372	0.451;0.451;0.451	B;B;B	0.28709	0.093;0.093;0.093	T	0.76016	-0.3113	10	0.42905	T	0.14	.	13.9996	0.64424	0.0:0.1512:0.8488:0.0	.	36;36;36	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	V	36	ENSP00000362151:G36V;ENSP00000362154:G36V;ENSP00000386958:G36V;ENSP00000362148:G36V;ENSP00000309823:G36V	ENSP00000309823:G36V	G	+	2	0	FOXP4	41641583	0.560000	0.26570	0.170000	0.22879	0.321000	0.28281	0.000000	0.12993	1.194000	0.43101	0.655000	0.94253	GGG		0.622	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		T	41533605	G	T	41533605	3	4	83	1	0	0	0	0	1	0	0	0	6048	1232	43	2	109	2	FOXP4	6	41533605	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	9949511	41533605	129581462	45	23599										
TCTE1	202500	hgsc.bcm.edu	37	chr6	44254085	44254085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tccaggtgccgctcgaagaaCatgcgtttccagctgccgcc	11	15	0	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:44254085C>T	ENST00000371505.4	-	3	584	c.462G>A	c.(460-462)atG>atA	p.M154I	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_Start_Codon_SNP_p.M1I|TCTE1_ENST00000371503.3_Start_Codon_SNP_p.M1I	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	154										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCTCGAAGAACATGCGTTTCC	0.612																																																0			6											66	57	60					6																	44254085		2203	4300	6503	44362063	SO:0001583	missense	202500			BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.462G>A	6.37:g.44254085C>T	ENSP00000360560:p.Met154Ile		44362063	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.504763	0.64410	.	.	ENSG00000146221	ENST00000371505;ENST00000371503;ENST00000371504	T;T;T	0.53423	0.62;0.65;0.65	4.95	4.02	0.46733	.	0.276808	0.45126	D	0.000384	T	0.34600	0.0903	M	0.73962	2.25	0.80722	D	1	B	0.32573	0.376	B	0.28305	0.088	T	0.43540	-0.9385	10	0.45353	T	0.12	-17.2649	14.6954	0.69118	0.0:0.8542:0.1458:0.0	.	154	Q5JU00	TCTE1_HUMAN	I	154;1;1	ENSP00000360560:M154I;ENSP00000360558:M1I;ENSP00000360559:M1I	ENSP00000360558:M1I	M	-	3	0	TCTE1	44362063	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.729000	0.68538	2.284000	0.76573	0.563000	0.77884	ATG		0.612	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		T	44254085	C	T	44254085	3	4	83	1	0	0	0	0	1	0	0	0	15756	478	17	3	1055	3	TCTE1	6	44254085	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	2720480	44254085	126860982	46	23600										
PHF3	23469	hgsc.bcm.edu	37	chr6	64416110	64416110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agtcaacgttctctcctgctCcacggtaattttctctgttg	7	12	3	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:64416110C>T	ENST00000262043.3	+	12	3899	c.3559C>T	c.(3559-3561)Cca>Tca	p.P1187S	PHF3_ENST00000393387.1_Missense_Mutation_p.P1187S			Q92576	PHF3_HUMAN	PHD finger protein 3	1187					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			CTCTCCTGCTCCACGGTAATT	0.363																																					GBM(135;136 1820 29512 34071 46235)											0			6											58	55	56					6																	64416110		2203	4300	6503	64474069	SO:0001583	missense	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.3559C>T	6.37:g.64416110C>T	ENSP00000262043:p.Pro1187Ser		64474069	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	C	6.972	0.549254	0.13374	.	.	ENSG00000118482	ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387	T;T;T;T	0.45276	2.17;0.9;2.27;2.27	5.65	5.65	0.86999	.	0.000000	0.35870	N	0.002921	T	0.20659	0.0497	L	0.41236	1.265	0.43141	D	0.994891	P	0.49090	0.919	B	0.42882	0.401	T	0.02581	-1.1138	10	0.24483	T	0.36	-3.9059	9.7272	0.40339	0.0:0.6689:0.2589:0.0722	.	1187	Q92576	PHF3_HUMAN	S	1001;456;1187;1187	ENSP00000424694:P1001S;ENSP00000425338:P456S;ENSP00000262043:P1187S;ENSP00000377048:P1187S	ENSP00000262043:P1187S	P	+	1	0	PHF3	64474069	1.000000	0.71417	1.000000	0.80357	0.290000	0.27261	1.809000	0.38922	2.648000	0.89879	0.655000	0.94253	CCA		0.363	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			T	64416110	C	T	64416110	3	4	83	1	0	0	0	0	1	0	0	0	11867	855	30	3	3601	3	PHF3	6	64416110	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	20162025	64416110	106698957	47	23601										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102483299	102483299	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctggtcaaaagtaatgaagaAggaatccagcgagtcctcac	10	9	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:102483299A>G	ENST00000421544.1	+	14	2659	c.2169A>G	c.(2167-2169)gaA>gaG	p.E723E	GRIK2_ENST00000369138.1_Silent_p.E723E|GRIK2_ENST00000369137.3_Silent_p.E647E|GRIK2_ENST00000413795.1_Silent_p.E723E|GRIK2_ENST00000318991.6_Silent_p.E723E|GRIK2_ENST00000369134.4_Silent_p.E674E	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	723					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GTAATGAAGAAGGAATCCAGC	0.423																																																0			6											147	146	147					6																	102483299		2203	4299	6502	102589992	SO:0001819	synonymous_variant	2901				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2169A>G	6.37:g.102483299A>G			102589992	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																				0.423	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102483299	A	G	102483299	2	3	83	1	0	0	0	0	0	0	0	1	6795	69	3	4		4	GRIK2	6	102483299	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	38067189	102483299	68631768	48	23602										
RSPH4A	345895	hgsc.bcm.edu	37	chr6	116951622	116951622	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tcagaatatacccccctggaCaacacggttatcctcaaatc	5	14	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:116951622C>G	ENST00000229554.5	+	5	1960	c.1823C>G	c.(1822-1824)aCa>aGa	p.T608R	RSPH4A_ENST00000368580.4_Missense_Mutation_p.T361R|RSPH4A_ENST00000368581.4_Missense_Mutation_p.Q563E	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	608					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CCCCCCTGGACAACACGGTTA	0.393									Kartagener syndrome																																							0			6											185	162	170					6																	116951622		2203	4300	6503	117058315	SO:0001583	missense	345895	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"radial spokehead-like 3"	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1823C>G	6.37:g.116951622C>G	ENSP00000229554:p.Thr608Arg		117058315	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.90|10.90	1.482414|1.482414	0.26598|0.26598	.|.	.|.	ENSG00000111834|ENSG00000111834	ENST00000368581|ENST00000229554;ENST00000447842;ENST00000368580	T|T;T	0.62364|0.19669	0.03|2.13;2.13	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.098018	.|0.64402	.|D	.|0.000002	T|T	0.32556|0.32556	0.0833|0.0833	.|.	.|.	.|.	0.20926|0.20926	N|N	0.999828|0.999828	P|D	0.36837|0.60575	0.571|0.988	B|D	0.30855|0.63283	0.121|0.913	T|T	0.09335|0.09335	-1.0679|-1.0679	8|9	0.42905|0.72032	T|D	0.14|0.01	-12.7041|-12.7041	16.8765|16.8765	0.86053|0.86053	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	563|608	Q5TD94-3|Q5TD94	.|RSH4A_HUMAN	E|R	563|608;403;361	ENSP00000357570:Q563E|ENSP00000229554:T608R;ENSP00000357569:T361R	ENSP00000357570:Q563E|ENSP00000229554:T608R	Q|T	+|+	1|2	0|0	RSPH4A|RSPH4A	117058315|117058315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.195000|0.195000	0.23768|0.23768	3.668000|3.668000	0.54554|0.54554	2.592000|2.592000	0.87571|0.87571	0.591000|0.591000	0.81541|0.81541	CAA|ACA		0.393	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892		G	116951622	C	G	116951622	3	3	83	1	0	0	0	0	1	0	0	0	13743	479	17	5	1841	5	RSPH4A	6	116951622	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	14468323	116951622	54163445	49	23603										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128326363	128326363	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cctgccgggtattccccatgGcatctttgcgttttttagca	9	12	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:128326363G>T	ENST00000368215.3	-	15	2356	c.2357C>A	c.(2356-2358)gCc>gAc	p.A786D	PTPRK_ENST00000368207.3_Missense_Mutation_p.A797D|PTPRK_ENST00000532331.1_Missense_Mutation_p.A787D|PTPRK_ENST00000368226.4_Missense_Mutation_p.A787D|PTPRK_ENST00000368213.5_Missense_Mutation_p.A787D|PTPRK_ENST00000368227.3_Missense_Mutation_p.A787D|PTPRK_ENST00000368210.3_Missense_Mutation_p.A787D|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	786					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A787V(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATTCCCCATGGCATCTTTGCG	0.453																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											87	73	78					6																	128326363		2203	4299	6502	128368056	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2357C>A	6.37:g.128326363G>T	ENSP00000357198:p.Ala786Asp		128368056	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.42|17.42	3.384015|3.384015	0.61845|0.61845	.|.	.|.	ENSG00000152894|ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000415055;ENST00000427676|ENST00000415046	T;T;T;T;T;T;T;T|.	0.12039|.	3.11;3.11;3.12;3.11;3.11;3.11;3.05;2.72|.	5.87|5.87	5.01|5.01	0.66863|0.66863	.|.	0.108147|.	0.64402|.	D|.	0.000006|.	T|T	0.45236|0.45236	0.1332|0.1332	L|L	0.38175|0.38175	1.15|1.15	0.46458|0.46458	D|D	0.999057|0.999057	B;B;B;P;B;P|.	0.39940|.	0.421;0.417;0.382;0.696;0.421;0.557|.	B;B;B;P;B;B|.	0.47206|.	0.203;0.15;0.287;0.541;0.116;0.232|.	T|T	0.43393|0.43393	-0.9394|-0.9394	10|5	0.52906|.	T|.	0.07|.	.|.	15.1687|15.1687	0.72850|0.72850	0.0679:0.0:0.9321:0.0|0.0679:0.0:0.9321:0.0	.|.	797;787;787;668;786;787|.	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2|.	.;.;.;.;PTPRK_HUMAN;.|.	D|T	787;787;787;787;787;786;797;30;668|68	ENSP00000357209:A787D;ENSP00000357210:A787D;ENSP00000432973:A787D;ENSP00000357196:A787D;ENSP00000357193:A787D;ENSP00000357198:A786D;ENSP00000357190:A797D;ENSP00000408180:A30D|.	ENSP00000357190:A797D|.	A|P	-|-	2|1	0|0	PTPRK|PTPRK	128368056|128368056	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.996000|0.996000	0.88848|0.88848	4.762000|4.762000	0.62250|0.62250	1.487000|1.487000	0.48415|0.48415	0.650000|0.650000	0.86243|0.86243	GCC|CCA		0.453	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			T	128326363	G	T	128326363	3	4	83	1	0	0	0	0	1	0	0	0	12842	1203	42	2	2048	2	PTPRK	6	128326363	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	11374741	128326363	42788704	50	23604										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654160	159654160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gattcccaccctaagcttagCtcaggtatccatggagacga	9	12	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:159654160C>A	ENST00000297267.9	+	11	2816	c.2616C>A	c.(2614-2616)agC>agA	p.S872R	FNDC1_ENST00000340366.6_Missense_Mutation_p.S809R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	872					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTAAGCTTAGCTCAGGTATCC	0.637																																																0			6											27	33	31					6																	159654160		1979	4155	6134	159574150	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2616C>A	6.37:g.159654160C>A	ENSP00000297267:p.Ser872Arg		159574150	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.45|12.45	1.940671|1.940671	0.34283|0.34283	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.07444	.|3.19;4.01	4.71|4.71	2.49|2.49	0.30216|0.30216	.|.	.|0.797369	.|0.11657	.|N	.|0.542181	T|T	0.01092|0.01092	0.0036|0.0036	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.48592|0.48592	-0.9022|-0.9022	5|10	.|0.19590	.|T	.|0.45	-4.6351|-4.6351	4.7504|4.7504	0.13057|0.13057	0.0:0.6333:0.0:0.3667|0.0:0.6333:0.0:0.3667	.|.	.|809;872	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	I|R	768|872;809	.|ENSP00000297267:S872R;ENSP00000342460:S809R	.|ENSP00000297267:S872R	L|S	+|+	1|3	0|2	FNDC1|FNDC1	159574150|159574150	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.063000|0.063000	0.16089|0.16089	0.589000|0.589000	0.23939|0.23939	1.122000|1.122000	0.41944|0.41944	-0.136000|-0.136000	0.14681|0.14681	CTC|AGC		0.637	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159654160	C	A	159654160	3	1	83	1	0	0	0	0	1	0	0	0	5987	796	28	2	2658	2	FNDC1	6	159654160	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	31327797	159654160	11460907	51	23605										
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224622	26224622	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	taatacctctgtcatcaagtCtaattcctctcactctgtgt	4	12	6	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:26224622C>G	ENST00000056233.3	+	4	1563	c.1304C>G	c.(1303-1305)tCt>tGt	p.S435C		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	435					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GTCATCAAGTCTAATTCCTCT	0.403																																																0			7											126	134	131					7																	26224622		2203	4300	6503	26191147	SO:0001583	missense	9603			AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1304C>G	7.37:g.26224622C>G	ENSP00000056233:p.Ser435Cys		26191147	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	C	6.439	0.449123	0.12223	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.40756	1.02	5.23	2.33	0.28932	.	0.228514	0.46758	D	0.000274	T	0.42787	0.1218	M	0.85630	2.765	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	T	0.48843	-0.8999	10	0.87932	D	0	-0.6589	4.5559	0.12136	0.1269:0.6134:0.1227:0.137	.	435	Q9Y4A8	NF2L3_HUMAN	C	435;141	ENSP00000056233:S435C	ENSP00000056233:S435C	S	+	2	0	NFE2L3	26191147	0.000000	0.05858	0.003000	0.11579	0.058000	0.15608	0.488000	0.22371	0.262000	0.21774	-0.216000	0.12614	TCT		0.403	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			G	26224622	C	G	26224622	3	3	83	1	0	0	0	0	1	0	0	0	10400	913	32	5	1318	5	NFE2L3	7	26224622	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		26224622	132914041	52	23606										
HECW1	23072	hgsc.bcm.edu	37	chr7	43591930	43591930	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcggaataacactgagtaccGgggaggtgagtgggcaggag	19	6	0	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:43591930G>C	ENST00000395891.2	+	28	5110	c.4505G>C	c.(4504-4506)cGg>cCg	p.R1502P	HECW1_ENST00000453890.1_Missense_Mutation_p.R1468P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1502	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACTGAGTACCGGGGAGGTGAG	0.478																																																0			7											86	91	89					7																	43591930		2028	4174	6202	43558455	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4505G>C	7.37:g.43591930G>C	ENSP00000379228:p.Arg1502Pro		43558455	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	32	5.181288	0.94846	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.57752	0.38;0.38	5.81	5.81	0.92471	HECT (4);	0.058126	0.64402	D	0.000001	T	0.79399	0.4439	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.99	T	0.82733	-0.0311	10	0.87932	D	0	.	20.0628	0.97684	0.0:0.0:1.0:0.0	.	1468;1502	B4DH42;Q76N89	.;HECW1_HUMAN	P	1502;1468;1502	ENSP00000379228:R1502P;ENSP00000407774:R1468P	ENSP00000265522:R1502P	R	+	2	0	HECW1	43558455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.414000	0.97362	2.745000	0.94114	0.655000	0.94253	CGG		0.478	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		C	43591930	G	C	43591930	3	2	83	1	0	0	0	0	1	0	0	0	7063	1116	39	5	4607	5	HECW1	7	43591930	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	17367308	43591930	115546733	53	23607										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91711952	91711952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gccagttataaagaaaaggcTgaaaaacttcaagaagagct	9	6	1	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:91711952T>C	ENST00000359028.2	+	33	8397	c.8172T>C	c.(8170-8172)gcT>gcC	p.A2724A	AKAP9_ENST00000358100.2_Silent_p.A2724A|AKAP9_ENST00000356239.3_Silent_p.A2712A			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2724	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGAAAAGGCTGAAAAACTTC	0.338			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											51	53	52					7																	91711952		2203	4300	6503	91549888	SO:0001819	synonymous_variant	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8172T>C	7.37:g.91711952T>C			91549888	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																					0.338	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		C	91711952	T	C	91711952	2	2	83	1	0	0	0	0	0	0	0	1	459	1567	55	4		4	AKAP9	7	91711952	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	48120022	91711952	67426711	54	23608										
SMO	6608	hgsc.bcm.edu	37	chr7	128846154	128846154	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcaagacctcctacttccacCtgctcacctggtcactcccc	5	20	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:128846154C>T	ENST00000249373.3	+	5	1364	c.1084C>T	c.(1084-1086)Ctg>Ttg	p.L362L		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	362					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTACTTCCACCTGCTCACCTG	0.567			Mis		skin basal cell																																		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	0			7											209	166	181					7																	128846154		2203	4300	6503	128633390	SO:0001819	synonymous_variant	54498			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1084C>T	7.37:g.128846154C>T			128633390	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																				0.567	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		T	128846154	C	T	128846154	2	4	83	1	0	0	0	0	0	0	0	1	14837	680	24	3		3	SMO	7	128846154	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	37134202	128846154	30292509	55	23609										
MLL3	58508	hgsc.bcm.edu	37	chr7	151879124	151879124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggatggcctatttgctgttgTctcattcatttgaaggggcc	12	8	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:151879124T>C	ENST00000262189.6	-	36	6039	c.5821A>G	c.(5821-5823)Aca>Gca	p.T1941A	KMT2C_ENST00000355193.2_Missense_Mutation_p.T1941A	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1941	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTTGCTGTTGTCTCATTCATT	0.453																																																0			7											112	117	115					7																	151879124		2203	4300	6503	151510057	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5821A>G	7.37:g.151879124T>C	ENSP00000262189:p.Thr1941Ala		151510057	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	2.114	-0.402965	0.04865	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.40476	1.03;1.03	5.09	-0.457	0.12186	.	0.513490	0.15780	N	0.244982	T	0.18173	0.0436	N	0.17082	0.46	0.19300	N	0.999975	B;B	0.17667	0.001;0.023	B;B	0.08055	0.002;0.003	T	0.15925	-1.0420	10	0.15952	T	0.53	.	2.0138	0.03493	0.1121:0.2247:0.1287:0.5346	.	1941;1002	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	A	1941	ENSP00000262189:T1941A;ENSP00000347325:T1941A	ENSP00000262189:T1941A	T	-	1	0	MLL3	151510057	0.429000	0.25530	0.001000	0.08648	0.497000	0.33675	-0.061000	0.11693	-0.327000	0.08551	-0.490000	0.04691	ACA		0.453	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151879124	T	C	151879124	3	2	83	1	0	0	0	0	1	0	0	0	9652	1667	58	4	9010	4	MLL3	7	151879124	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	23032970	151879124	7259539	56	23610										
DLC1	10395	hgsc.bcm.edu	37	chr8	12960306	12960306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tttgtatactcactcgtttcCgatgaggactaatttctagc	7	9	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:12960306C>A	ENST00000276297.4	-	8	1968	c.1559G>T	c.(1558-1560)cGg>cTg	p.R520L	DLC1_ENST00000520226.1_Missense_Mutation_p.R9L|DLC1_ENST00000358919.2_Missense_Mutation_p.R83L|DLC1_ENST00000512044.2_Missense_Mutation_p.R117L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	520					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CACTCGTTTCCGATGAGGACT	0.368																																																0			8											186	180	182					8																	12960306		2203	4300	6503	13004677	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1559G>T	8.37:g.12960306C>A	ENSP00000276297:p.Arg520Leu		13004677	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688264	0.88639	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.50277	0.75;0.75;0.75;3.11	5.85	5.85	0.93711	.	0.052329	0.85682	D	0.000000	T	0.68265	0.2982	L	0.58810	1.83	0.80722	D	1	D;P;D	0.89917	1.0;0.95;0.98	D;P;D	0.87578	0.998;0.737;0.961	T	0.67309	-0.5703	10	0.72032	D	0.01	.	20.5471	0.99284	0.0:1.0:0.0:0.0	.	520;117;83	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	L	520;83;117;9	ENSP00000276297:R520L;ENSP00000351797:R83L;ENSP00000422595:R117L;ENSP00000428028:R9L	ENSP00000276297:R520L	R	-	2	0	DLC1	13004677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.113000	0.50376	2.941000	0.99782	0.655000	0.94253	CGG		0.368	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	12960306	C	A	12960306	3	1	83	1	0	0	0	0	1	0	0	0	4561	652	23	2	3071	2	DLC1	8	12960306	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		12960306	133403716	57	23611										
OPRK1	4986	hgsc.bcm.edu	37	chr8	54141940	54141940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gactctgctagtgctctgccGctccatcctcatcttcagtg	8	15	5	0	rs202165724		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:54141940G>A	ENST00000265572.3	-	4	1357	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.R354W|OPRK1_ENST00000524278.1_Missense_Mutation_p.R265W	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	354					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GTGCTCTGCCGCTCCATCCTC	0.483													G|||	1	0.000199681	0	0	5008	,	,		21096	0.001		0	False		,,,				2504	0															0			8											100	90	93					8																	54141940		2203	4300	6503	54304493	SO:0001583	missense	4986				CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.1060C>T	8.37:g.54141940G>A	ENSP00000265572:p.Arg354Trp		54304493	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	37	CCDS6152.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.54	1.378101	0.24944	.	.	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.61040	0.14;0.14;0.14	5.8	2.88	0.33553	.	0.456643	0.24896	N	0.034723	T	0.55970	0.1954	M	0.73962	2.25	0.39824	D	0.972871	P	0.35242	0.492	B	0.35727	0.209	T	0.60642	-0.7223	10	0.66056	D	0.02	.	9.7171	0.40281	0.0681:0.0:0.551:0.3808	.	354	P41145	OPRK_HUMAN	W	354;265;354;340	ENSP00000265572:R354W;ENSP00000430923:R265W;ENSP00000429706:R354W	ENSP00000265572:R354W	R	-	1	2	OPRK1	54304493	0.994000	0.37717	0.933000	0.37362	0.288000	0.27193	1.542000	0.36137	0.765000	0.33221	0.650000	0.86243	CGG		0.483	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			A	54141940	G	A	54141940	3	1	83	1	0	0	0	0	1	0	0	0	10916	1086	38	1	86	1	OPRK1	8	54141940	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	41181634	54141940	92222082	58	23612										
PREX2	80243	hgsc.bcm.edu	37	chr8	69028025	69028025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	catattctcctaaattagaaCgtaagacatcagagggcata	7	8	2	3	rs200550325		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:69028025C>T	ENST00000288368.4	+	26	3461	c.3184C>T	c.(3184-3186)Cgt>Tgt	p.R1062C		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1062					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TAAATTAGAACGTAAGACATC	0.348													C|||	1	0.000199681	0	0.0014	5008	,	,		19240	0		0	False		,,,				2504	0															0			8						C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	122	115	117		3184	5.9	1	8		117	0,8600		0,0,4300	no	missense	PREX2	NM_024870.2	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging	1062/1607	69028025	2,13004	2203	4300	6503	69190579	SO:0001583	missense	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3184C>T	8.37:g.69028025C>T	ENSP00000288368:p.Arg1062Cys		69190579	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	18.27	3.587503	0.66105	4.54E-4	0.0	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.60040	0.22	5.86	5.86	0.93980	.	0.323970	0.35040	N	0.003495	T	0.46444	0.1393	N	0.22421	0.69	0.58432	D	0.99999	P	0.40000	0.698	B	0.33799	0.17	T	0.51529	-0.8694	10	0.62326	D	0.03	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	1062	Q70Z35	PREX2_HUMAN	C	1062;1065	ENSP00000288368:R1062C	ENSP00000288368:R1062C	R	+	1	0	PREX2	69190579	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.680000	0.61656	2.937000	0.99478	0.650000	0.86243	CGT		0.348	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69028025	C	T	69028025	3	4	83	1	0	0	0	0	1	0	0	0	12511	536	19	1	3515	1	PREX2	8	69028025	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	14886085	69028025	77335997	59	23613										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113988189	113988189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gtccttggacgtgttggggtCcagacctgaatttctgagac	13	9	1	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:113988189C>T	ENST00000297405.5	-	7	1463	c.1219G>A	c.(1219-1221)Gac>Aac	p.D407N	CSMD3_ENST00000343508.3_Missense_Mutation_p.D367N|CSMD3_ENST00000352409.3_Missense_Mutation_p.D407N|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	407						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D407Y(1)|p.D367Y(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTGTTGGGGTCCAGACCTGAA	0.478										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						2	Substitution - Missense(2)	lung(2)	8											217	189	199					8																	113988189		2203	4300	6503	114057365	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1219G>A	8.37:g.113988189C>T	ENSP00000297405:p.Asp407Asn		114057365	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724099	0.68959	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000352409	T;T;T	0.19532	2.14;2.14;2.16	6.17	6.17	0.99709	.	0.629156	0.14680	N	0.304829	T	0.21761	0.0524	N	0.22421	0.69	0.35922	D	0.831885	B;B	0.32245	0.247;0.361	B;B	0.37304	0.078;0.246	T	0.20405	-1.0276	10	0.22706	T	0.39	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	407;367	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	N	367;407;407	ENSP00000345799:D367N;ENSP00000297405:D407N;ENSP00000343124:D407N	ENSP00000297405:D407N	D	-	1	0	CSMD3	114057365	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.742000	0.55097	2.941000	0.99782	0.655000	0.94253	GAC		0.478	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113988189	C	T	113988189	3	4	83	1	0	0	0	0	1	0	0	0	3952	855	30	3	10164	3	CSMD3	8	113988189	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	44960164	113988189	32375833	60	23614										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37737192	37737192	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acccagttacctccattttcCtctggcctggaaacaaacaa	5	14	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr9:37737192C>G	ENST00000539465.1	+	14	2094	c.1501C>G	c.(1501-1503)Ctc>Gtc	p.L501V	FRMPD1_ENST00000541302.1_Missense_Mutation_p.L370V|FRMPD1_ENST00000536622.1_Missense_Mutation_p.L323V|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.L501V			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	501						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTCCATTTTCCTCTGGCCTGG	0.527																																																0			9											108	96	100					9																	37737192		2203	4300	6503	37727192	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1501C>G	9.37:g.37737192C>G	ENSP00000444411:p.Leu501Val		37727192	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.231053	0.22626	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	5.45	3.48	0.39840	.	0.403653	0.26542	N	0.023797	T	0.07324	0.0185	N	0.22421	0.69	0.23743	N	0.996967	B;B	0.14438	0.004;0.01	B;B	0.12837	0.002;0.008	T	0.34502	-0.9826	10	0.16420	T	0.52	-3.577	12.1514	0.54051	0.3089:0.6911:0.0:0.0	.	370;501	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	V	501;501;323;370	ENSP00000366995:L501V;ENSP00000444411:L501V;ENSP00000437762:L323V;ENSP00000444804:L370V	ENSP00000366995:L501V	L	+	1	0	FRMPD1	37727192	0.962000	0.33011	1.000000	0.80357	0.973000	0.67179	1.955000	0.40372	1.290000	0.44636	0.591000	0.81541	CTC		0.527	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		G	37737192	C	G	37737192	3	3	83	1	0	0	0	0	1	0	0	0	6076	681	24	5	1551	5	FRMPD1	9	37737192	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		37737192	103476239	61	23615										
PTPLA	9200	hgsc.bcm.edu	37	chr10	17636294	17636294	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aagtcttattgaaaacattcCtgttttcttcacatgcggca	6	9	3	1	rs536952738	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:17636294C>A	ENST00000361271.3	-	6	731	c.694G>T	c.(694-696)Gga>Tga	p.G232*		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	232					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)	p.G232*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						GAAAACATTCCTGTTTTCTTC	0.318																																																1	Substitution - Nonsense(1)	lung(1)	10											71	72	72					10																	17636294		2203	4294	6497	17676300	SO:0001587	stop_gained	9200			AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.694G>T	10.37:g.17636294C>A	ENSP00000355308:p.Gly232*		17676300	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Nonsense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148376	0.78001	.	.	ENSG00000165996	ENST00000361271	.	.	.	5.72	5.72	0.89469	.	0.105361	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.8521	20.2406	0.98372	0.0:1.0:0.0:0.0	.	.	.	.	X	232	.	ENSP00000355308:G232X	G	-	1	0	PTPLA	17676300	1.000000	0.71417	0.969000	0.41365	0.574000	0.36063	6.074000	0.71253	2.857000	0.98124	0.650000	0.86243	GGA		0.318	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		A	17636294	C	A	17636294	4	1	83	1	0	0	0	0	0	1	0	0	12809	690	24	2	180	2	PTPLA	10	17636294	Nonsense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		17636294	117898453	62	23616										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18937509	18937509	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gttgtaaatgatggaggatgTgacaggtgctttaacaaagt	13	3	0	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:18937509T>C	ENST00000377304.4	-	2	559	c.141A>G	c.(139-141)tcA>tcG	p.S47S	RP11-139J15.7_ENST00000606425.1_Silent_p.S35S	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	47							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						ATGGAGGATGTGACAGGTGCT	0.348																																																0			10											214	202	206					10																	18937509		2203	4300	6503	18977515	SO:0001819	synonymous_variant	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.141A>G	10.37:g.18937509T>C			18977515	B0YJ54	Silent	SNP	ENST00000377304.4	37	CCDS7130.1																																																																																				0.348	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		C	18937509	T	C	18937509	2	2	83	1	0	0	0	0	0	0	0	1	10713	1683	59	4		4	NSUN6	10	18937509	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	1301215	18937509	116597238	63	23617										
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82269162	82269162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggttccgggagttcttcgagAgcaacatcaagtcctaccgg	12	11	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:82269162A>G	ENST00000429989.3	+	5	608	c.385A>G	c.(385-387)Agc>Ggc	p.S129G	TSPAN14_ENST00000372164.3_Missense_Mutation_p.S112G|TSPAN14_ENST00000341863.6_Intron|TSPAN14_ENST00000481124.1_Intron|TSPAN14_ENST00000372158.1_Missense_Mutation_p.S129G|TSPAN14_ENST00000372156.1_Missense_Mutation_p.S129G	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	129					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GTTCTTCGAGAGCAACATCAA	0.582																																																0			10											111	95	100					10																	82269162		2203	4300	6503	82259142	SO:0001583	missense	81619			AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"Tetraspanins"	23303	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 14"	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.385A>G	10.37:g.82269162A>G	ENSP00000396270:p.Ser129Gly		82259142	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	37	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.819668	0.50633	.	.	ENSG00000108219	ENST00000429989;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000372156	D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23	5.45	5.45	0.79879	Tetraspanin, EC2 domain (1);	0.683157	0.15992	N	0.234765	T	0.76407	0.3983	N	0.10874	0.06	0.29256	N	0.871647	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.68228	-0.5464	10	0.34782	T	0.22	-32.0593	13.4682	0.61268	1.0:0.0:0.0:0.0	.	129;112	Q8NG11;Q8NG11-2	TSN14_HUMAN;.	G	129;99;112;129;129	ENSP00000396270:S129G;ENSP00000361230:S99G;ENSP00000361237:S112G;ENSP00000361231:S129G;ENSP00000361229:S129G	ENSP00000361229:S129G	S	+	1	0	TSPAN14	82259142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.794000	0.62482	2.064000	0.61679	0.533000	0.62120	AGC		0.582	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		G	82269162	A	G	82269162	3	3	83	1	0	0	0	0	1	0	0	0	16678	304	11	4	399	4	TSPAN14	10	82269162	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	63331653	82269162	53265585	64	23618										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717628	89717628	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agatcctcagtttgtggtctGccagctaaaggtgaagatat	11	7	2	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:89717628G>T	ENST00000371953.3	+	7	2010	c.653G>T	c.(652-654)tGc>tTc	p.C218F	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	218	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.Q214fs*1(1)|p.?(1)|p.Q214fs*22(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTTGTGGTCTGCCAGCTAAAG	0.408		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - frameshift(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	10											127	110	116					10																	89717628		2203	4300	6503	89707608	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.653G>T	10.37:g.89717628G>T	ENSP00000361021:p.Cys218Phe		89707608	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.291817	0.23564	.	.	ENSG00000171862	ENST00000371953	D	0.84223	-1.82	5.67	4.77	0.60923	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.147938	0.64402	D	0.000005	T	0.65770	0.2723	N	0.08118	0	0.50467	D	0.99987	B	0.12013	0.005	B	0.15870	0.014	T	0.60068	-0.7335	9	.	.	.	-4.5893	5.4251	0.16421	0.2701:0.0:0.7299:0.0	.	218	P60484	PTEN_HUMAN	F	218	ENSP00000361021:C218F	.	C	+	2	0	PTEN	89707608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.024000	0.76443	2.677000	0.91161	0.585000	0.79938	TGC		0.408	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89717628	G	T	89717628	3	4	83	1	0	0	0	0	1	0	0	0	12772	1319	46	2	679	2	PTEN	10	89717628	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	7448466	89717628	45817119	65	23619										
CUTC	51076	hgsc.bcm.edu	37	chr10	101502947	101502947	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aagcagagtgttcagatcccAgtttttgtgatgattcggcc	11	8	1	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:101502947A>G	ENST00000370476.5	+	4	360	c.231A>G	c.(229-231)ccA>ccG	p.P77P	CUTC_ENST00000493385.1_3'UTR	NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	77			P -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		TTCAGATCCCAGTTTTTGTGA	0.398																																																0			10											204	187	193					10																	101502947		2203	4300	6503	101492937	SO:0001819	synonymous_variant	51076			AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"cutC copper transporter homolog (E. coli)"			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.231A>G	10.37:g.101502947A>G			101492937	Q5TCZ8|Q9Y321	Silent	SNP	ENST00000370476.5	37	CCDS7483.1																																																																																				0.398	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960		G	101502947	A	G	101502947	2	3	83	1	0	0	0	0	0	0	0	1	4069	175	7	4		4	CUTC	10	101502947	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	11785319	101502947	34031800	66	23620										
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118441351	118441351	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atgacattctccaccaaaaaGgtccgactctgccgattacg	7	13	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:118441351G>T	ENST00000369209.3	-	8	977	c.873C>A	c.(871-873)acC>acA	p.T291T		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	291						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		CCACCAAAAAGGTCCGACTCT	0.478											OREG0020558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			10											111	108	109					10																	118441351		1954	4138	6092	118431341	SO:0001819	synonymous_variant	259217			AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"Heat shock proteins / HSP70"	19022	protein-coding gene	gene with protein product		610701	"heat shock 70kD protein 12A"			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.873C>A	10.37:g.118441351G>T		1488	118431341		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																				0.478	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		T	118441351	G	T	118441351	2	4	83	1	0	0	0	0	0	0	0	1	7425	987	35	2		2	HSPA12A	10	118441351	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	16938404	118441351	17093396	67	23621										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128925984	128925984	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tggagaaacttctccggaccGtgaaccgaaccgtcatttcc	9	13	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:128925984G>T	ENST00000280333.6	+	27	2849	c.2740G>T	c.(2740-2742)Gtg>Ttg	p.V914L		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	914					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TCTCCGGACCGTGAACCGAAC	0.478																																																0			10											129	116	120					10																	128925984		1928	4110	6038	128815974	SO:0001583	missense	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2740G>T	10.37:g.128925984G>T	ENSP00000280333:p.Val914Leu		128815974	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	16.62	3.174629	0.57692	.	.	ENSG00000150760	ENST00000280333	T	0.55413	0.52	4.88	4.88	0.63580	.	0.077055	0.50627	D	0.000106	T	0.47637	0.1456	L	0.37697	1.125	0.54753	D	0.999989	B;B	0.21753	0.028;0.06	B;B	0.29663	0.063;0.105	T	0.37103	-0.9720	10	0.27785	T	0.31	.	18.4202	0.90587	0.0:0.0:1.0:0.0	.	914;914	B2RUU3;Q14185	.;DOCK1_HUMAN	L	914	ENSP00000280333:V914L	ENSP00000280333:V914L	V	+	1	0	DOCK1	128815974	1.000000	0.71417	0.962000	0.40283	0.963000	0.63663	5.118000	0.64673	2.416000	0.81992	0.557000	0.71058	GTG		0.478	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	128925984	G	T	128925984	3	4	83	1	0	0	0	0	1	0	0	0	4695	1145	40	2	2846	2	DOCK1	10	128925984	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	10484633	128925984	6608763	68	23622										
OR51T1	401665	hgsc.bcm.edu	37	chr11	4903553	4903553	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctactatcctcacagacaggAtggtcctggtgatagggctg	12	10	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:4903553A>G	ENST00000322049.1	+	1	424	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Missense_Mutation_p.M169V			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CACAGACAGGATGGTCCTGGT	0.502																																																0			11											157	137	144					11																	4903553		2201	4298	6499	4860129	SO:0001583	missense	401665			BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.424A>G	11.37:g.4903553A>G	ENSP00000322679:p.Met142Val		4860129	Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	37		.	.	.	.	.	.	.	.	.	.	A	0	-2.755926	0.00085	.	.	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.34667	1.35;1.35	4.68	0.947	0.19555	GPCR, rhodopsin-like superfamily (1);	0.745901	0.11988	N	0.510130	T	0.13072	0.0317	N	0.03304	-0.355	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.31530	-0.9940	10	0.05721	T	0.95	.	8.3607	0.32357	0.7502:0.0:0.2498:0.0	.	142	Q8NGJ9	O51T1_HUMAN	V	169;142	ENSP00000369738:M169V;ENSP00000322679:M142V	ENSP00000322679:M142V	M	+	1	0	OR51T1	4860129	0.001000	0.12720	0.140000	0.22221	0.009000	0.06853	1.282000	0.33226	0.303000	0.22785	0.397000	0.26171	ATG		0.502	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		G	4903553	A	G	4903553	3	3	83	1	0	0	0	0	1	0	0	0	11137	333	12	4	507	4	OR51T1	11	4903553	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10		4903553	130102963	69	23623										
STK33	65975	hgsc.bcm.edu	37	chr11	8435184	8435184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cactttctgggttatttttcCattccttcatcatctctaat	3	11	4	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:8435184C>A	ENST00000447869.1	-	11	2120	c.1202G>T	c.(1201-1203)tGg>tTg	p.W401L	STK33_ENST00000534493.1_Missense_Mutation_p.W360L|STK33_ENST00000396672.1_Missense_Mutation_p.W401L|STK33_ENST00000315204.1_Missense_Mutation_p.W401L|STK33_ENST00000473980.1_5'UTR|STK33_ENST00000358872.3_Missense_Mutation_p.W214L|STK33_ENST00000396673.1_Intron			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	401					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GTTATTTTTCCATTCCTTCAT	0.358																																																0			11											218	193	201					11																	8435184		2201	4296	6497	8391760	SO:0001583	missense	65975			AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.1202G>T	11.37:g.8435184C>A	ENSP00000416750:p.Trp401Leu		8391760	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225391	0.58668	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000534493	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	5.9	5.9	0.94986	Protein kinase-like domain (1);	0.630533	0.16861	N	0.196522	T	0.20536	0.0494	L	0.47190	1.495	0.80722	D	1	P	0.34864	0.473	B	0.24848	0.056	T	0.02404	-1.1164	10	0.72032	D	0.01	.	15.7822	0.78269	0.0:1.0:0.0:0.0	.	401	Q9BYT3	STK33_HUMAN	L	401;401;401;214;360	ENSP00000416750:W401L;ENSP00000320754:W401L;ENSP00000379905:W401L;ENSP00000351743:W214L;ENSP00000436418:W360L	ENSP00000320754:W401L	W	-	2	0	STK33	8391760	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.600000	0.54052	2.786000	0.95864	0.563000	0.77884	TGG		0.358	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		A	8435184	C	A	8435184	3	1	83	1	0	0	0	0	1	0	0	0	15339	595	21	2	350	2	STK33	11	8435184	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	3531631	8435184	126571332	70	23624										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735520	18735520	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agcagtgcctggtcttccccGcgctccatggacacgcgttc	11	16	1	0	rs369745010		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:18735520G>A	ENST00000513874.1	-	14	2113	c.1974C>T	c.(1972-1974)cgC>cgT	p.R658R	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	658	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						GGTCTTCCCCGCGCTCCATGG	0.592													g|||	1	0.000199681	0	0	5008	,	,		24225	0.001		0	False		,,,				2504	0															0			11								0,4390		0,0,2195	113	118	116		1974	-0.6	0	11		116	1,8565	1.2+/-3.3	0,1,4282	no	coding-synonymous	IGSF22	NM_173588.3		0,1,6477	AA,AG,GG		0.0117,0.0,0.0077		658/1327	18735520	1,12955	2195	4283	6478	18692096	SO:0001819	synonymous_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1974C>T	11.37:g.18735520G>A			18692096	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																				0.592	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18735520	G	A	18735520	2	1	83	1	0	0	0	0	0	0	0	1	7621	1074	38	1		1	IGSF22	11	18735520	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	10300336	18735520	116270996	71	23625										
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606580	55606580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gactgaattaattctatttgCggtgatggcctatgaccact	9	8	1	3	rs562661348		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:55606580C>T	ENST00000378396.1	+	1	353	c.353C>T	c.(352-354)gCg>gTg	p.A118V		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A118V(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ATTCTATTTGCGGTGATGGCC	0.423													-|||	1	0.000199681	0	0.0014	5008	,	,		18662	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	11											122	118	119					11																	55606580		2201	4296	6497	55363156	SO:0001583	missense	390144			AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"GPCR / Class A : Olfactory receptors"	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.353C>T	11.37:g.55606580C>T	ENSP00000367649:p.Ala118Val		55363156	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	14.25	2.478779	0.44044	.	.	ENSG00000205029	ENST00000378396	T	0.02015	4.5	4.47	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.07954	0.0199	M	0.76433	2.335	0.09310	N	1	D	0.55605	0.972	P	0.53593	0.73	T	0.08994	-1.0695	9	0.72032	D	0.01	-5.0358	11.1707	0.48569	0.0:0.9083:0.0:0.0917	.	118	Q8NGK9	OR5DG_HUMAN	V	118	ENSP00000367649:A118V	ENSP00000367649:A118V	A	+	2	0	OR5D16	55363156	0.001000	0.12720	0.009000	0.14445	0.743000	0.42351	1.590000	0.36654	1.048000	0.40298	0.530000	0.56133	GCG		0.423	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		T	55606580	C	T	55606580	3	4	83	1	0	0	0	0	1	0	0	0	11187	768	27	1	355	1	OR5D16	11	55606580	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	36871060	55606580	79399936	72	23626										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62300430	62300430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	catttcaggagtcttcacttTagtacctttcatctttcctt	4	11	5	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:62300430T>C	ENST00000378024.4	-	5	1733	c.1459A>G	c.(1459-1461)Aaa>Gaa	p.K487E	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	487					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTCTTCACTTTAGTACCTTTC	0.468																																																0			11											121	130	127					11																	62300430		2202	4299	6501	62057006	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1459A>G	11.37:g.62300430T>C	ENSP00000367263:p.Lys487Glu		62057006	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.302606	0.40795	.	.	ENSG00000124942	ENST00000378024	T	0.01665	4.7	5.52	5.52	0.82312	.	0.405543	0.19048	N	0.124117	T	0.11024	0.0269	M	0.88105	2.93	0.24841	N	0.992462	D	0.60575	0.988	D	0.79108	0.992	T	0.37934	-0.9684	10	0.08837	T	0.75	-7.8668	14.6263	0.68624	0.0:0.0:0.0:1.0	.	487	Q09666	AHNK_HUMAN	E	487	ENSP00000367263:K487E	ENSP00000367263:K487E	K	-	1	0	AHNAK	62057006	0.596000	0.26866	0.984000	0.44739	0.683000	0.39861	1.807000	0.38902	2.096000	0.63516	0.454000	0.30748	AAA		0.468	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62300430	T	C	62300430	3	2	83	1	0	0	0	0	1	0	0	0	414	1763	61	4	16333	4	AHNAK	11	62300430	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	6693850	62300430	72706086	73	23627										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65793355	65793355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agcctcaccgtggtggggcaCgccagaggaatagtgggata	16	9	1	1	rs543744984		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:65793355C>T	ENST00000312106.5	-	1	633	c.496G>A	c.(496-498)Gtg>Atg	p.V166M		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	166	His-rich.				calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.V166M(2)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGGTGGGGCACGCCAGAGGAA	0.582																																																2	Substitution - Missense(2)	ovary(1)|endometrium(1)	11											57	53	54					11																	65793355		2201	4296	6497	65549931	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.496G>A	11.37:g.65793355C>T	ENSP00000309052:p.Val166Met		65549931	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	4.959	0.178073	0.09443	.	.	ENSG00000175294	ENST00000312106	D	0.96940	-4.18	3.43	1.5	0.22942	.	.	.	.	.	D	0.84556	0.5498	N	0.03115	-0.41	0.09310	N	1	D	0.56287	0.975	B	0.32090	0.14	T	0.79339	-0.1844	9	0.22706	T	0.39	2.3962	8.0048	0.30319	0.0:0.7774:0.0:0.2226	.	166	Q8NEC5	CTSR1_HUMAN	M	166	ENSP00000309052:V166M	ENSP00000309052:V166M	V	-	1	0	CATSPER1	65549931	0.996000	0.38824	0.000000	0.03702	0.049000	0.14656	0.009000	0.13219	0.228000	0.21019	-0.657000	0.03884	GTG		0.582	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		T	65793355	C	T	65793355	3	4	83	1	0	0	0	0	1	0	0	0	2693	536	19	1	1894	1	CATSPER1	11	65793355	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	3492925	65793355	69213161	74	23628										
TSKU	25987	hgsc.bcm.edu	37	chr11	76507126	76507126	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctgccttcacgacgcacagtCagggccgggcactacacgtg	12	15	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:76507126C>T	ENST00000527881.1	+	2	1492	c.466C>T	c.(466-468)Cag>Tag	p.Q156*	TSKU_ENST00000333090.4_Nonsense_Mutation_p.Q156*			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	156					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					GACGCACAGTCAGGGCCGGGC	0.657																																																0			11											79	77	78					11																	76507126		2200	4292	6492	76184774	SO:0001587	stop_gained	25987			AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.466C>T	11.37:g.76507126C>T	ENSP00000434847:p.Gln156*		76184774	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Nonsense_Mutation	SNP	ENST00000527881.1	37	CCDS8246.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.261694	0.39995	.	.	ENSG00000182704	ENST00000333090;ENST00000439807;ENST00000527881	.	.	.	5.0	4.08	0.47627	.	0.364149	0.31554	N	0.007460	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-15.6443	13.3926	0.60832	0.1589:0.8411:0.0:0.0	.	.	.	.	X	156;124;156	.	ENSP00000332668:Q156X	Q	+	1	0	TSKU	76184774	1.000000	0.71417	0.847000	0.33407	0.008000	0.06430	4.043000	0.57354	1.081000	0.41110	-0.188000	0.12872	CAG		0.657	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		T	76507126	C	T	76507126	4	4	83	1	0	0	0	0	0	1	0	0	16667	827	29	3	468	3	TSKU	11	76507126	Nonsense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	10713771	76507126	58499390	75	23629										
INTS4	92105	hgsc.bcm.edu	37	chr11	77639588	77639588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggcctccacagcagcaatacGaacctctagaaaaaagaaca	7	12	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:77639588G>A	ENST00000534064.1	-	11	1205	c.1171C>T	c.(1171-1173)Cgt>Tgt	p.R391C	INTS4_ENST00000529807.1_Missense_Mutation_p.R391C|INTS4_ENST00000525931.1_5'UTR	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	391					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GCAGCAATACGAACCTCTAGA	0.493																																																0			11											7	6	6					11																	77639588		2159	4178	6337	77317236	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1171C>T	11.37:g.77639588G>A	ENSP00000434466:p.Arg391Cys		77317236	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741648	0.69304	.	.	ENSG00000149262	ENST00000534064;ENST00000354849;ENST00000529807	T;T	0.74315	-0.83;0.26	3.84	3.84	0.44239	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84999	0.5597	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86773	0.1974	10	0.87932	D	0	-10.8824	11.5458	0.50693	0.0:0.0:0.821:0.179	.	391	Q96HW7	INT4_HUMAN	C	391;242;391	ENSP00000434466:R391C;ENSP00000433644:R391C	ENSP00000346913:R242C	R	-	1	0	INTS4	77317236	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.779000	0.68948	2.132000	0.65825	0.471000	0.43371	CGT		0.493	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77639588	G	A	77639588	3	1	83	1	0	0	0	0	1	0	0	0	7801	1058	37	1	1772	1	INTS4	11	77639588	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	1132462	77639588	57366928	76	23630										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85436931	85436931	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttggttcaagcacttgttttCcatgaacttttccaccagag	7	10	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:85436931C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.G714E|SYTL2_ENST00000525423.1_Missense_Mutation_p.G190E|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Missense_Mutation_p.G190E|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000524452.1_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.G190V(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTGTTTTCCATGAACTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											118	111	114					11																	85436931		2203	4299	6502	85114579	SO:0001627	intron_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2007G>A	11.37:g.85436931C>T			85114579	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	8.776	0.926992	0.18056	.	.	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.25579	1.79;1.81;1.81	6.17	-3.84	0.04256	.	1.580750	0.03505	N	0.218707	T	0.11623	0.0283	N	0.12746	0.255	0.09310	N	0.999997	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.08055	0.003;0.003;0.003	T	0.18493	-1.0335	9	.	.	.	1.7323	2.926	0.05784	0.12:0.3509:0.0956:0.4335	.	190;190;190	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	E	714;190;190	ENSP00000352065:G714E;ENSP00000346576:G190E;ENSP00000432694:G190E	.	G	-	2	0	SYTL2	85114579	0.000000	0.05858	0.001000	0.08648	0.686000	0.39977	-2.817000	0.00751	-0.200000	0.10300	0.655000	0.94253	GGA		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85436931	C	T	85436931	1	4	83	0	1	0	0	0	0	0	0	0	15522	855	30	3		3	SYTL2	11	85436931	Intron	SNP	C	TCGA-AH-6549-01A-11D-1826-10	7797343	85436931	49569585	77	23631										
MMP27	64066	hgsc.bcm.edu	37	chr11	102573488	102573488	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agaaaattagactcacctgcTccatccttggtccagttttc	6	12	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:102573488T>C	ENST00000260229.4	-	4	706	c.615A>G	c.(613-615)ggA>ggG	p.G205G		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	205					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	ACTCACCTGCTCCATCCTTGG	0.418																																																0			11											93	101	98					11																	102573488		2203	4299	6502	102078698	SO:0001819	synonymous_variant	64066			AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.615A>G	11.37:g.102573488T>C			102078698	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																				0.418	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		C	102573488	T	C	102573488	2	2	83	1	0	0	0	0	0	0	0	1	9694	1538	54	4		4	MMP27	11	102573488	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	17136557	102573488	32433028	78	23632										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103173911	103173911	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccatcttgataattatttctCcgggtgctgatccttctcag	7	11	3	2	rs199766341		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:103173911C>A	ENST00000375735.2	+	76	11329	c.11185C>A	c.(11185-11187)Ccg>Acg	p.P3729T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.P3736T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3729	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AATTATTTCTCCGGGTGCTGA	0.403																																																0			11											86	82	83					11																	103173911		1812	4082	5894	102679121	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11185C>A	11.37:g.103173911C>A	ENSP00000364887:p.Pro3729Thr		102679121	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632884	0.67015	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.14893	2.47;2.47	5.35	5.35	0.76521	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.35098	0.0920	M	0.70108	2.13	0.54753	D	0.999985	P;P	0.42123	0.771;0.729	P;B	0.49953	0.627;0.32	T	0.03384	-1.1042	10	0.49607	T	0.09	.	19.0562	0.93066	0.0:1.0:0.0:0.0	.	3729;3736	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	T	3729;3736	ENSP00000364887:P3729T;ENSP00000381167:P3736T	ENSP00000364887:P3729T	P	+	1	0	DYNC2H1	102679121	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.269000	0.65542	2.520000	0.84964	0.655000	0.94253	CCG		0.403	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	103173911	C	A	103173911	3	1	83	1	0	0	0	0	1	0	0	0	4857	855	30	2	11512	2	DYNC2H1	11	103173911	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	600423	103173911	31832605	79	23633										
CASP1	834	hgsc.bcm.edu	37	chr11	104899870	104899870	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cctggtgtggaagagcagaaAgcgataaaatccttctctat	10	8	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:104899870A>G	ENST00000533400.1	-	7	1022	c.987T>C	c.(985-987)gcT>gcC	p.A329A	CASP1_ENST00000528974.1_Silent_p.A290A|CASP1_ENST00000436863.3_Silent_p.A329A|CASP1_ENST00000527979.1_Silent_p.A292A|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000526568.1_Silent_p.A236A|CASP1_ENST00000393136.4_Silent_p.A308A|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000593315.1_Silent_p.A308A|CASP1_ENST00000598974.1_Silent_p.A329A|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000525825.1_Silent_p.A308A|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000446369.1_Intron	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	329					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	AAGAGCAGAAAGCGATAAAAT	0.398																																					NSCLC(41;1246 1743 4934)											0			11											122	113	116					11																	104899870		2202	4299	6501	104405080	SO:0001819	synonymous_variant	834			U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"Caspases"	1499	protein-coding gene	gene with protein product	"caspase-1", "interleukin 1, beta, convertase"	147678	"caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)", "caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.987T>C	11.37:g.104899870A>G			104405080	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																				0.398	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292		G	104899870	A	G	104899870	2	3	83	1	0	0	0	0	0	0	0	1	2674	59	3	4		4	CASP1	11	104899870	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	1725959	104899870	30106646	80	23634										
ATM	472	hgsc.bcm.edu	37	chr11	108216547	108216547	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aattttcaaccagttttccgTtacttctgcatggaaaaatt	5	8	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:108216547T>C	ENST00000452508.2	+	59	8685	c.8496T>C	c.(8494-8496)cgT>cgC	p.R2832R	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.R2832R			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2832	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> C (in AT and B-cell non-Hodgkin lymphoma). {ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:9288106, ECO:0000269|PubMed:9443866}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CAGTTTTCCGTTACTTCTGCA	0.348			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											150	156	154					11																	108216547		2200	4298	6498	107721757	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8496T>C	11.37:g.108216547T>C			107721757	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108216547	T	C	108216547	2	2	83	1	0	0	0	0	0	0	0	1	1110	1712	60	4		4	ATM	11	108216547	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	3316677	108216547	26789969	81	23635										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129735843	129735844	+	Frame_Shift_Del	DEL	AG	AG	-													0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttcattggctggctgatcacAgagaggggaactgtgatccg							TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:129735843_129735844delAG	ENST00000446488.3	-	24	3669_3670	c.3566_3567delCT	c.(3565-3567)tctfs	p.S1189fs	NFRKB_ENST00000524746.1_Frame_Shift_Del_p.S1189fs|NFRKB_ENST00000304521.5_Frame_Shift_Del_p.S1189fs|NFRKB_ENST00000524794.1_Frame_Shift_Del_p.S1214fs	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1189					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		GGCTGATCACAGAGAGGGGAAC	0.49																																																0			11																																								129241054	SO:0001589	frameshift_variant	4798				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3566_3567delCT	11.37:g.129735847_129735848delAG	ENSP00000400476:p.Ser1189fs		129241053	Q12869|Q15312|Q9H048	Frame_Shift_Del	DEL	ENST00000446488.3	37	CCDS44770.1																																																																																				0.49	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		-	129735844	AG	-	129735843	7	5	83	1	0	1	0	1	0	0	0	0	10415	175	7	0	344	0	NFRKB	11	129735843	Frame_Shift_Del	DEL	AG	TCGA-AH-6549-01A-11D-1826-10	21519296	129735843	5270673	82	23636										
LRP6	4040	hgsc.bcm.edu	37	chr12	12340026	12340026	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aacgtcaaggcaaaaggatgTggaagggaacctttaaccac	11	8	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:12340026T>C	ENST00000261349.4	-	4	751	c.675A>G	c.(673-675)ccA>ccG	p.P225P	LRP6_ENST00000543091.1_Silent_p.P225P	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	225	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CAAAAGGATGTGGAAGGGAAC	0.398																																																0			12											110	93	99					12																	12340026		2203	4300	6503	12231293	SO:0001819	synonymous_variant	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.675A>G	12.37:g.12340026T>C			12231293	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																				0.398	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12340026	T	C	12340026	2	2	83	1	0	0	0	0	0	0	0	1	8991	1683	59	4		4	LRP6	12	12340026	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10		12340026	121511869	83	23637										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22666294	22666294	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aagggccccccttcttttccAgcactaccacttcccattcc	4	19	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:22666294A>G	ENST00000333957.4	-	9	1227	c.972T>C	c.(970-972)gcT>gcC	p.A324A	C2CD5_ENST00000536386.1_Silent_p.A315A|C2CD5_ENST00000396028.2_Silent_p.A315A|C2CD5_ENST00000544930.1_Silent_p.A117A|C2CD5_ENST00000542676.1_Silent_p.A324A|C2CD5_ENST00000446597.1_Silent_p.A324A|C2CD5_ENST00000545552.1_Silent_p.A315A	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	324					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTCTTTTCCAGCACTACCAC	0.363																																																0			12											130	121	124					12																	22666294		2203	4300	6503	22557561	SO:0001819	synonymous_variant	9847			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.972T>C	12.37:g.22666294A>G			22557561	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																				0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		G	22666294	A	G	22666294	2	3	83	1	0	0	0	0	0	0	0	1	8203	175	7	4		4	KIAA0528	12	22666294	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	10326268	22666294	111185601	84	23638										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	83	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	2731990	25398284	108453611	85	23639										
STK38L	23012	hgsc.bcm.edu	37	chr12	27462048	27462048	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tatgttttttatcttttaggTgcggttggtccagaagaaag	11	4	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:27462048T>C	ENST00000389032.3	+	5	480	c.311T>C	c.(310-312)gTg>gCg	p.V104A	STK38L_ENST00000539577.1_Splice_Site_p.V11A	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					ATCTTTTAGGTGCGGTTGGTC	0.348																																																0			12											78	78	78					12																	27462048		2203	4300	6503	27353315	SO:0001630	splice_region_variant	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.310-1T>C	12.37:g.27462048T>C			27353315		Missense_Mutation	SNP	ENST00000389032.3	37	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.361762	0.82353	.	.	ENSG00000211455	ENST00000541191;ENST00000389032;ENST00000545470;ENST00000539577;ENST00000543246;ENST00000544969	T;T;T;T;T;T	0.60672	1.51;1.51;0.17;0.17;1.51;1.51	4.63	4.63	0.57726	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77343	0.4116	M	0.87328	2.875	0.80722	D	1	P;D	0.55385	0.868;0.971	P;D	0.64506	0.734;0.926	T	0.82390	-0.0481	10	0.87932	D	0	.	14.3604	0.66768	0.0:0.0:0.0:1.0	.	11;104	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	A	104;104;63;11;104;104	ENSP00000437856:V104A;ENSP00000373684:V104A;ENSP00000439457:V63A;ENSP00000446386:V11A;ENSP00000442253:V104A;ENSP00000440279:V104A	ENSP00000373684:V104A	V	+	2	0	STK38L	27353315	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.980000	0.88113	1.860000	0.53959	0.383000	0.25322	GTG		0.348	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	Missense_Mutation	C	27462048	T	C	27462048	5	2	83	1	0	0	0	0	0	0	1	0	15343	1710	59	4	325	4	STK38L	12	27462048	Splice_Site	SNP	T	TCGA-AH-6549-01A-11D-1826-10	2063764	27462048	106389847	86	23640										
HOXC11	3227	hgsc.bcm.edu	37	chr12	54367195	54367195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cctgccccaggccccctctcGtcagatctcctatccctact	5	21	3	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:54367195G>A	ENST00000546378.1	+	1	286	c.170G>A	c.(169-171)cGt>cAt	p.R57H	HOTAIR_ENST00000455246.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.R57H|HOTAIR_ENST00000424518.1_RNA			O43248	HXC11_HUMAN	homeobox C11	57					anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(1)|ovary(1)	2						GCCCCCTCTCGTCAGATCTCC	0.637			T	NUP98	AML																																		Dom	yes		12	12q13.3	3227	homeo box C11		L	0			12											110	118	115					12																	54367195		2203	4300	6503	52653462	SO:0001583	missense	3227				CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"Homeoboxes / ANTP class : HOXL subclass"	5123	protein-coding gene	gene with protein product		605559	"homeo box C11"	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.170G>A	12.37:g.54367195G>A	ENSP00000446680:p.Arg57His		52653462	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	37	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594102	0.66219	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	T;T	0.47177	0.85;0.85	4.32	4.32	0.51571	Domain of unknown function DUF3528, homeobox protein, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	M	0.63428	1.95	0.54753	D	0.999989	P	0.50710	0.938	P	0.49528	0.614	T	0.60831	-0.7185	10	0.54805	T	0.06	.	16.1042	0.81209	0.0:0.0:1.0:0.0	.	57	O43248	HXC11_HUMAN	H	57	ENSP00000446680:R57H;ENSP00000243082:R57H	ENSP00000243082:R57H	R	+	2	0	HOXC11	52653462	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	6.221000	0.72243	2.390000	0.81377	0.561000	0.74099	CGT		0.637	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2			A	54367195	G	A	54367195	3	1	83	1	0	0	0	0	1	0	0	0	7331	1145	40	1	172	1	HOXC11	12	54367195	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	26905147	54367195	79484700	87	23641										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70983905	70983905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcaccacagaatcattgaagAgtaggatccgatactgctcc	9	11	1	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:70983905A>G	ENST00000261266.5	-	6	1264	c.1235T>C	c.(1234-1236)cTc>cCc	p.L412P	PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000551525.1_Missense_Mutation_p.L629P|PTPRB_ENST00000550358.1_Missense_Mutation_p.L630P|PTPRB_ENST00000538708.1_Missense_Mutation_p.L412P|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.L630P	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	412	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L412P(1)		breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATCATTGAAGAGTAGGATCCG	0.507											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	lung(1)	12											131	131	131					12																	70983905		2010	4196	6206	69270172	SO:0001583	missense	5787			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1235T>C	12.37:g.70983905A>G	ENSP00000261266:p.Leu412Pro	1126	69270172	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	18.35	3.604596	0.66445	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.63	5.63	0.86233	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.132141	0.51477	D	0.000086	T	0.80138	0.4568	M	0.88640	2.97	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.84338	0.0525	10	0.87932	D	0	.	15.839	0.78831	1.0:0.0:0.0:0.0	.	412;509;629;630;412;630	F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;PTPRB_HUMAN;.	P	630;630;630;412;412;629;509	ENSP00000334928:L630P;ENSP00000448058:L630P;ENSP00000438927:L412P;ENSP00000261266:L412P;ENSP00000448349:L629P;ENSP00000446982:L509P	ENSP00000261266:L412P	L	-	2	0	PTPRB	69270172	1.000000	0.71417	0.998000	0.56505	0.632000	0.37999	7.969000	0.87988	2.130000	0.65690	0.533000	0.62120	CTC		0.507	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70983905	A	G	70983905	3	3	83	1	0	0	0	0	1	0	0	0	12833	304	11	4	4866	4	PTPRB	12	70983905	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	16616710	70983905	62867990	88	23642										
CEP290	80184	hgsc.bcm.edu	37	chr12	88474162	88474162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tttcacttcatcttcatggtTttcttgaagcctgatgtaaa	6	8	5	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:88474162T>C	ENST00000552810.1	-	38	5366	c.5023A>G	c.(5023-5025)Aac>Gac	p.N1675D	CEP290_ENST00000309041.7_Missense_Mutation_p.N1677D|CEP290_ENST00000547691.2_Missense_Mutation_p.N735D|CEP290_ENST00000397838.3_Missense_Mutation_p.N735D	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TCTTCATGGTTTTCTTGAAGC	0.363																																																0			12											108	97	100					12																	88474162		1818	4077	5895	86998293	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5023A>G	12.37:g.88474162T>C	ENSP00000448012:p.Asn1675Asp		86998293	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	6.754	0.507937	0.12883	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92	4.35	4.35	0.52113	.	0.424145	0.27420	N	0.019448	D	0.84669	0.5523	N	0.24115	0.695	0.26288	N	0.978165	B	0.21309	0.054	B	0.20384	0.029	T	0.67879	-0.5556	10	0.11485	T	0.65	.	13.8052	0.63225	0.0:0.0:0.0:1.0	.	1675	O15078	CE290_HUMAN	D	735;1675;1677;735	ENSP00000446905:N735D;ENSP00000448012:N1675D;ENSP00000308021:N1677D;ENSP00000380938:N735D	ENSP00000308021:N1677D	N	-	1	0	CEP290	86998293	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	2.451000	0.44952	1.731000	0.51592	0.377000	0.23210	AAC		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88474162	T	C	88474162	3	2	83	1	0	0	0	0	1	0	0	0	3259	1841	64	4	2484	4	CEP290	12	88474162	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	17490257	88474162	45377733	89	23643										
CDK17	5128	hgsc.bcm.edu	37	chr12	96688840	96688840	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gttctgtggtttcaagtctcGatgcaatacctttcttctat	7	9	5	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:96688840G>T	ENST00000261211.3	-	10	1537	c.934C>A	c.(934-936)Cga>Aga	p.R312R	CDK17_ENST00000553042.1_5'UTR|CDK17_ENST00000542666.1_Silent_p.R259R|CDK17_ENST00000543119.2_Silent_p.R312R	NM_001170464.2|NM_002595.4	NP_001163935.1|NP_002586.2	Q00537	CDK17_HUMAN	cyclin-dependent kinase 17	312	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)	p.R312G(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(11)|ovary(4)|prostate(2)|skin(1)	37						TTCAAGTCTCGATGCAATACC	0.343																																																2	Substitution - Missense(2)	ovary(1)|lung(1)	12											137	129	132					12																	96688840		2203	4300	6503	95212971	SO:0001819	synonymous_variant	0				CCDS9061.1, CCDS53819.1	12q23.1	2011-11-08	2009-12-16	2009-12-16		ENSG00000059758		"Cyclin-dependent kinases"	8750	protein-coding gene	gene with protein product		603440	"PCTAIRE protein kinase 2"	PCTK2		9370357, 19884882	Standard	NM_001170464		Approved	PCTAIRE2	uc009ztk.3	Q00537		ENST00000261211.3:c.934C>A	12.37:g.96688840G>T			95212971	A8K1U6|B2RCQ2|Q8NEB8	Silent	SNP	ENST00000261211.3	37	CCDS9061.1																																																																																				0.343	CDK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408751.1	NM_002595		T	96688840	G	T	96688840	2	4	83	1	0	0	0	0	0	0	0	1	3139	1066	37	2		2	CDK17	12	96688840	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	8214678	96688840	37163055	90	23644										
RAD9B	144715	hgsc.bcm.edu	37	chr12	110960201	110960201	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acagaggaagtgccagggtcTctgtgtctcagaaaggtaaa	13	7	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:110960201T>C	ENST00000409778.3	+	8	927	c.903T>C	c.(901-903)tcT>tcC	p.S301S	RAD9B_ENST00000409246.1_Silent_p.S298S|RAD9B_ENST00000409300.1_Silent_p.S370S|RAD9B_ENST00000392672.4_Silent_p.S370S|RAD9B_ENST00000409425.1_Silent_p.S298S			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	367					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						TGCCAGGGTCTCTGTGTCTCA	0.478																																																0			12											65	50	55					12																	110960201		2203	4300	6503	109444584	SO:0001819	synonymous_variant	144715				CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.903T>C	12.37:g.110960201T>C			109444584	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Silent	SNP	ENST00000409778.3	37																																																																																					0.478	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442		C	110960201	T	C	110960201	2	2	83	1	0	0	0	0	0	0	0	1	13033	1538	54	4		4	RAD9B	12	110960201	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	14271361	110960201	22891694	91	23645										
TCTN2	79867	hgsc.bcm.edu	37	chr12	124189172	124189172	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tcacctgagcatccgcatccTcatctcggatgctggcgcgg	11	15	3	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:124189172T>C	ENST00000303372.5	+	15	1834	c.1706T>C	c.(1705-1707)cTc>cCc	p.L569P	TCTN2_ENST00000426174.2_Missense_Mutation_p.L568P|RP11-338K17.8_ENST00000538837.1_lincRNA	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	569					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATCCGCATCCTCATCTCGGAT	0.532																																																0			12											84	67	73					12																	124189172		2203	4300	6503	122755125	SO:0001583	missense	79867			AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1706T>C	12.37:g.124189172T>C	ENSP00000304941:p.Leu569Pro		122755125	A8K7Y8|B3KPW5|Q9H966	Missense_Mutation	SNP	ENST00000303372.5	37	CCDS9253.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.695957	0.68386	.	.	ENSG00000168778	ENST00000426174;ENST00000303372	D;D	0.86694	-2.16;-2.16	5.7	5.7	0.88788	.	0.229124	0.35615	N	0.003097	D	0.92770	0.7701	M	0.76574	2.34	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	D	0.93250	0.6634	10	0.62326	D	0.03	-34.4659	14.8739	0.70481	0.0:0.0:0.0:1.0	.	568;569	A8K7Y8;Q96GX1	.;TECT2_HUMAN	P	568;569	ENSP00000395171:L568P;ENSP00000304941:L569P	ENSP00000304941:L569P	L	+	2	0	TCTN2	122755125	0.994000	0.37717	0.945000	0.38365	0.579000	0.36224	3.287000	0.51732	2.299000	0.77371	0.529000	0.55759	CTC		0.532	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		C	124189172	T	C	124189172	3	2	83	1	0	0	0	0	1	0	0	0	15762	1551	54	4	1764	4	TCTN2	12	124189172	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	13228971	124189172	9662723	92	23646										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20025364	20025364	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tatctagaaaccgcacaactTcctaaaaaagacaaacacat	3	11	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:20025364T>A	ENST00000400230.2	-	11	787	c.743A>T	c.(742-744)gAa>gTa	p.E248V	TPTE2_ENST00000382978.1_Splice_Site_p.E208V|TPTE2_ENST00000390680.2_Splice_Site_p.E171V|TPTE2_ENST00000400103.2_Splice_Site_p.E137V|TPTE2_ENST00000255310.6_Splice_Site_p.E171V|TPTE2_ENST00000457266.2_Splice_Site_p.E137V|TPTE2_ENST00000382975.4_Splice_Site_p.E208V|TPTE2_ENST00000382977.4_Splice_Site_p.E248V			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	248	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		CCGCACAACTTCCTAAAAAAG	0.333																																																0			13											98	87	91					13																	20025364		2203	4300	6503	18923364	SO:0001630	splice_region_variant	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.742-1A>T	13.37:g.20025364T>A			18923364	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	t	12.17	1.857568	0.32791	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	2.63	2.63	0.31362	Phosphatase tensin type (1);	0.118680	0.56097	D	0.000029	T	0.48169	0.1485	M	0.86178	2.8	0.58432	D	0.999994	P;D;D	0.57257	0.929;0.979;0.965	P;P;P	0.57620	0.824;0.788;0.542	T	0.51426	-0.8707	9	.	.	.	-28.2763	7.1515	0.25614	0.0:0.0:0.0:1.0	.	137;171;248	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	V	208;137;248;171;171;248;208;137;248;117	ENSP00000372438:E208V;ENSP00000382974:E137V;ENSP00000383089:E248V;ENSP00000255310:E171V;ENSP00000375098:E171V;ENSP00000372437:E248V;ENSP00000372435:E208V;ENSP00000442218:E137V	.	E	-	2	0	TPTE2	18923364	1.000000	0.71417	0.987000	0.45799	0.146000	0.21551	5.681000	0.68175	1.460000	0.47911	0.163000	0.16589	GAA		0.333	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	Missense_Mutation	A	20025364	T	A	20025364	5	1	83	1	0	0	0	0	0	0	1	0	16471	1797	62	5	865	5	TPTE2	13	20025364	Splice_Site	SNP	T	TCGA-AH-6549-01A-11D-1826-10		20025364	95144514	93	23647										
NBEA	26960	hgsc.bcm.edu	37	chr13	36229754	36229754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tatttggccattgggatgtgGtcacttgcttggccaggtcc	13	9	1	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:36229754G>A	ENST00000400445.3	+	54	8701	c.8167G>A	c.(8167-8169)Gtc>Atc	p.V2723I	NBEA_ENST00000379922.3_Missense_Mutation_p.V301I|NBEA_ENST00000537702.1_Missense_Mutation_p.V516I|NBEA_ENST00000540320.1_Missense_Mutation_p.V2723I|NBEA_ENST00000379939.2_Missense_Mutation_p.V2720I|NBEA_ENST00000310336.4_Missense_Mutation_p.V2723I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2723					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTGGGATGTGGTCACTTGCTT	0.483																																																0			13											216	222	220					13																	36229754		2087	4225	6312	35127754	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8167G>A	13.37:g.36229754G>A	ENSP00000383295:p.Val2723Ile		35127754	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	35	5.544882	0.96488	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80003	0.4544	L	0.60904	1.88	0.80722	D	1	B;D;D	0.71674	0.149;0.998;0.957	B;D;P	0.67231	0.386;0.95;0.859	T	0.77294	-0.2641	10	0.46703	T	0.11	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	2723;301;2720	Q8NFP9;Q8NFP9-2;Q5T321	NBEA_HUMAN;.;.	I	2723;2723;2720;2723;1350;301;516;301	ENSP00000440951:V2723I;ENSP00000383295:V2723I;ENSP00000369271:V2720I;ENSP00000308534:V2723I;ENSP00000440233:V516I;ENSP00000369254:V301I	ENSP00000308534:V2723I	V	+	1	0	NBEA	35127754	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.694000	0.98686	2.882000	0.98803	0.655000	0.94253	GTC		0.483	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	36229754	G	A	36229754	3	1	83	1	0	0	0	0	1	0	0	0	10217	1261	44	3	8381	3	NBEA	13	36229754	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	16204390	36229754	78940124	94	23648										
FREM2	341640	hgsc.bcm.edu	37	chr13	39454504	39454504	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aatcgaggtattggcaaaagAagtgtggagtaccattctct	11	6	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:39454504A>T	ENST00000280481.7	+	24	9306	c.9090A>T	c.(9088-9090)agA>agT	p.R3030S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3030					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTGGCAAAAGAAGTGTGGAGT	0.488																																																0			13											107	100	103					13																	39454504		2203	4300	6503	38352504	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9090A>T	13.37:g.39454504A>T	ENSP00000280481:p.Arg3030Ser		38352504	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.421842	0.62622	.	.	ENSG00000150893	ENST00000280481	T	0.27402	1.67	5.89	-1.66	0.08265	.	0.000000	0.85682	D	0.000000	T	0.50343	0.1610	M	0.87682	2.9	0.58432	D	0.999995	D	0.71674	0.998	D	0.65987	0.94	T	0.52830	-0.8523	10	0.87932	D	0	.	7.5545	0.27817	0.521:0.1135:0.3655:0.0	.	3030	Q5SZK8	FREM2_HUMAN	S	3030	ENSP00000280481:R3030S	ENSP00000280481:R3030S	R	+	3	2	FREM2	38352504	0.998000	0.40836	0.938000	0.37757	0.356000	0.29392	0.784000	0.26816	-0.188000	0.10499	0.460000	0.39030	AGA		0.488	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39454504	A	T	39454504	3	4	83	1	0	0	0	0	1	0	0	0	6064	243	9	5	9184	5	FREM2	13	39454504	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	3224750	39454504	75715374	95	23649										
RB1	5925	hgsc.bcm.edu	37	chr13	49037913	49037913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	atgcaaagtgaagaatatagAccttaaattcaaaatcattg	6	5	2	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:49037913A>G	ENST00000267163.4	+	21	2291	c.2153A>G	c.(2152-2154)gAc>gGc	p.D718G		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	718	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAGAATATAGACCTTAAATTC	0.299		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											113	118	116					13																	49037913		2203	4292	6495	47935914	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2153A>G	13.37:g.49037913A>G	ENSP00000267163:p.Asp718Gly		47935914	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796854	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92348	-3.02	6.07	6.07	0.98685	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.95723	0.8609	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96024	0.9011	10	0.87932	D	0	-15.7516	16.6406	0.85098	1.0:0.0:0.0:0.0	.	718	P06400	RB_HUMAN	G	697;718	ENSP00000267163:D718G	ENSP00000267163:D718G	D	+	2	0	RB1	47935914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.326000	0.78906	0.533000	0.62120	GAC		0.299	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	49037913	A	G	49037913	3	3	83	1	0	0	0	0	1	0	0	0	13135	275	10	4	2235	4	RB1	13	49037913	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	9583409	49037913	66131965	96	23650										
MLNR	2862	hgsc.bcm.edu	37	chr13	49794957	49794957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tccgcgcgctcatcgctgtgCtctgggccgtggcgctgctc	14	16	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:49794957C>A	ENST00000218721.1	+	1	484	c.484C>A	c.(484-486)Ctc>Atc	p.L162I	MLNR_ENST00000398307.1_Missense_Mutation_p.L162I	NM_001507.1	NP_001498.1	O43193	MTLR_HUMAN	motilin receptor	162					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone-releasing hormone receptor activity (GO:0016520)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)	14		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;6.1e-09)		CATCGCTGTGCTCTGGGCCGT	0.721																																																0			13											7	8	7					13																	49794957		2170	4257	6427	48692958	SO:0001583	missense	2862			AF034632	CCDS9414.1	13q14-q21	2012-08-08	2004-05-27	2004-05-28	ENSG00000102539	ENSG00000102539		"GPCR / Class A : Motilin receptors"	4495	protein-coding gene	gene with protein product		602885	"G protein-coupled receptor 38"	GPR38		9441746	Standard	NM_001507		Approved		uc010tgj.2	O43193	OTTHUMG00000016909	ENST00000218721.1:c.484C>A	13.37:g.49794957C>A	ENSP00000218721:p.Leu162Ile		48692958		Missense_Mutation	SNP	ENST00000218721.1	37	CCDS9414.1	.	.	.	.	.	.	.	.	.	.	c	19.25	3.791343	0.70452	.	.	ENSG00000102539	ENST00000218721;ENST00000398307	T;T	0.70516	-0.49;-0.49	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67211	0.2869	N	0.11698	0.16	0.35328	D	0.785388	D	0.89917	1.0	D	0.87578	0.998	T	0.64275	-0.6446	10	0.02654	T	1	-18.536	15.7998	0.78443	0.0:1.0:0.0:0.0	.	162	O43193	MTLR_HUMAN	I	162	ENSP00000218721:L162I;ENSP00000381352:L162I	ENSP00000218721:L162I	L	+	1	0	MLNR	48692958	1.000000	0.71417	0.994000	0.49952	0.348000	0.29142	4.788000	0.62439	2.062000	0.61559	0.558000	0.71614	CTC		0.721	MLNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044897.1	NM_001507		A	49794957	C	A	49794957	3	1	83	1	0	0	0	0	1	0	0	0	9662	797	28	2	486	2	MLNR	13	49794957	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	757044	49794957	65374921	97	23651										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328216	88328216	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aatgacaatcttttgtccagTttacccaacaatcttttccg	4	11	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:88328216T>C	ENST00000325089.6	+	2	792	c.573T>C	c.(571-573)agT>agC	p.S191S	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	191					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTTTGTCCAGTTTACCCAACA	0.483																																																0			13											85	86	86					13																	88328216		2203	4300	6503	87126217	SO:0001819	synonymous_variant	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.573T>C	13.37:g.88328216T>C			87126217	B3KNB8|B4DSH5|Q5VT81	Silent	SNP	ENST00000325089.6	37	CCDS9465.1																																																																																				0.483	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			C	88328216	T	C	88328216	2	2	83	1	0	0	0	0	0	0	0	1	14783	1722	60	4		4	SLITRK5	13	88328216	Silent	SNP	T	TCGA-AH-6549-01A-11D-1826-10	38533259	88328216	26841662	98	23652										
NALCN	259232	hgsc.bcm.edu	37	chr13	101844369	101844369	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gtccattacgtccacccatcCttcctgggtgaggatctgga	10	13	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:101844369C>T	ENST00000251127.6	-	14	1744	c.1663G>A	c.(1663-1665)Gga>Aga	p.G555R	NALCN_ENST00000376196.3_Missense_Mutation_p.G555R|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	555					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCCACCCATCCTTCCTGGGTG	0.433																																																0			13											136	98	111					13																	101844369		2203	4300	6503	100642370	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1663G>A	13.37:g.101844369C>T	ENSP00000251127:p.Gly555Arg		100642370	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	31	5.099966	0.94197	.	.	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.99888	-7.54;-7.54	5.48	5.48	0.80851	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99891	0.9948	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.99;0.991	D	0.96510	0.9378	10	0.87932	D	0	.	19.7249	0.96160	0.0:1.0:0.0:0.0	.	555;555;555	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	R	555	ENSP00000251127:G555R;ENSP00000365367:G555R	ENSP00000251127:G555R	G	-	1	0	NALCN	100642370	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.356000	0.79445	2.735000	0.93741	0.650000	0.86243	GGA		0.433	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101844369	C	T	101844369	3	4	83	1	0	0	0	0	1	0	0	0	10178	690	24	3	3677	3	NALCN	13	101844369	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	13516153	101844369	13325509	99	23653										
C14orf37	145407	hgsc.bcm.edu	37	chr14	58604742	58604742	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cccaacagttggtctgcctcAgactcatatacagagacaga	8	12	3	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:58604742A>C	ENST00000267485.7	-	2	1529	c.1335T>G	c.(1333-1335)tcT>tcG	p.S445S	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	445						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GGTCTGCCTCAGACTCATATA	0.358																																																0			14											77	79	79					14																	58604742		2203	4300	6503	57674495	SO:0001819	synonymous_variant	145407				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1335T>G	14.37:g.58604742A>C			57674495	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																				0.358	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		C	58604742	A	C	58604742	2	2	83	1	0	0	0	0	0	0	0	1	1775	175	7	4		4	C14orf37	14	58604742	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10		58604742	48744798	100	23654										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60903654	60903654	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aattttgaccctgtccaaatGaaaatggaaaactaaaatca	5	7	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:60903654G>T	ENST00000321731.3	-	18	1832	c.1673C>A	c.(1672-1674)tCa>tAa	p.S558*		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	558					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		CTGTCCAAATGAAAATGGAAA	0.338																																																0			14											148	168	161					14																	60903654		2203	4296	6499	59973407	SO:0001587	stop_gained	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1673C>A	14.37:g.60903654G>T	ENSP00000324920:p.Ser558*		59973407	Q08AQ4	Nonsense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	37	6.205991	0.97376	.	.	ENSG00000179008	ENST00000321731	.	.	.	5.17	5.17	0.71159	.	0.287405	0.25159	N	0.032686	.	.	.	.	.	.	0.53688	D	0.999976	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5617	17.6578	0.88182	0.0:0.0:1.0:0.0	.	.	.	.	X	558	.	ENSP00000324920:S558X	S	-	2	0	C14orf39	59973407	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.202000	0.72131	2.408000	0.81797	0.557000	0.71058	TCA		0.338	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		T	60903654	G	T	60903654	4	4	83	1	0	0	0	0	0	1	0	0	1776	1294	45	2	94	2	C14orf39	14	60903654	Nonsense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	2298912	60903654	46445886	101	23655										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73729497	73729497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cctggactgggtggagatgcCggatcaccagcgccaccctt	13	14	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:73729497C>T	ENST00000554301.1	+	18	2848	c.2685C>T	c.(2683-2685)gcC>gcT	p.A895A	PAPLN_ENST00000381166.3_Silent_p.A895A|PAPLN_ENST00000555445.1_Silent_p.A879A|PAPLN_ENST00000427855.1_Silent_p.A895A|PAPLN_ENST00000340738.5_Silent_p.A868A|PAPLN_ENST00000554314.1_3'UTR			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	895						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GTGGAGATGCCGGATCACCAG	0.667																																																0			14											14	16	15					14																	73729497		2198	4293	6491	72799250	SO:0001819	synonymous_variant	89932			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2685C>T	14.37:g.73729497C>T			72799250	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																					0.667	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		T	73729497	C	T	73729497	2	4	83	1	0	0	0	0	0	0	0	1	11459	639	23	1		1	PAPLN	14	73729497	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	12825843	73729497	33620043	102	23656										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959334	25959334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcagctgggtgtgaacctccGcaggaagtcttctatcgtct	12	11	3	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr15:25959334G>A	ENST00000356865.6	-	10	1942	c.1831C>T	c.(1831-1833)Cgg>Tgg	p.R611W		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	611					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GTGAACCTCCGCAGGAAGTCT	0.592																																																0			15											44	49	48					15																	25959334		2203	4300	6503	23510427	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1831C>T	15.37:g.25959334G>A	ENSP00000349325:p.Arg611Trp		23510427	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.146206	0.37923	.	.	ENSG00000206190	ENST00000356865	T	0.11495	2.77	4.41	3.47	0.39725	HAD-like domain (1);	0.269079	0.37437	N	0.002095	T	0.27349	0.0671	L	0.57536	1.79	0.44345	D	0.99723	D	0.89917	1.0	D	0.70716	0.97	T	0.01819	-1.1267	10	0.72032	D	0.01	-30.2031	13.514	0.61530	0.0:0.0:0.8427:0.1573	.	611	O60312	AT10A_HUMAN	W	611	ENSP00000349325:R611W	ENSP00000349325:R611W	R	-	1	2	ATP10A	23510427	0.994000	0.37717	0.045000	0.18777	0.098000	0.18820	2.859000	0.48364	1.043000	0.40175	0.655000	0.94253	CGG		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25959334	G	A	25959334	3	1	83	1	0	0	0	0	1	0	0	0	1117	1086	38	1	2716	1	ATP10A	15	25959334	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10		25959334	76572058	103	23657										
UACA	55075	hgsc.bcm.edu	37	chr15	70991976	70991977	+	Frame_Shift_Del	DEL	AT	AT	-													0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gctttcatcaatcggtcatcAtatttattccaatctgctgc							TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr15:70991976_70991977delAT	ENST00000322954.6	-	2	286_287	c.101_102delAT	c.(100-102)tatfs	p.Y34fs	UACA_ENST00000379983.2_Frame_Shift_Del_p.Y21fs|UACA_ENST00000539319.1_Frame_Shift_Del_p.Y34fs|UACA_ENST00000560441.1_Frame_Shift_Del_p.Y21fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	34					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						ATCGGTCATCATATTTATTCCA	0.356																																																0			15																																								68779031	SO:0001589	frameshift_variant	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.101_102delAT	15.37:g.70991978_70991979delAT	ENSP00000314556:p.Tyr34fs		68779030	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Del	DEL	ENST00000322954.6	37	CCDS10235.1																																																																																				0.356	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			-	70991977	AT	-	70991976	7	5	83	1	0	1	0	1	0	0	0	0	16864	224	8	0	4220	0	UACA	15	70991976	Frame_Shift_Del	DEL	AT	TCGA-AH-6549-01A-11D-1826-10	45032642	70991976	31539416	104	23658										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3614280	3614280	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cgtcctgcactcatccaagcCgtccaggatcaggagggccc	11	16	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:3614280C>T	ENST00000301749.7	-	0	1063				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCATCCAAGCCGTCCAGGATC	0.637																																																0			16											37	42	41					16																	3614280		1987	4180	6167	3554281			197358			BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3614280C>T			3554281	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	18.27	3.587266	0.66105	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.89763	0.6809	.	.	.	0.41104	D	0.985696	D	0.89917	1.0	D	0.85130	0.997	D	0.91494	0.5214	9	0.87932	D	0	.	15.6704	0.77270	0.0:1.0:0.0:0.0	.	267	C9JLH9	.	S	220;220;220;267;202	ENSP00000301749:G220S;ENSP00000352039:G220S;ENSP00000414415:G267S;ENSP00000323897:G202S	ENSP00000301749:G220S	G	-	1	0	NLRC3	3554281	1.000000	0.71417	0.772000	0.31596	0.795000	0.44927	7.818000	0.86416	2.273000	0.75805	0.655000	0.94253	GGC		0.637	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3614280	C	T	3614280	1	4	83	0	1	0	0	0	0	0	0	0	10499	652	23	1		1	NLRC3	16	3614280	RNA	SNP	C	TCGA-AH-6549-01A-11D-1826-10		3614280	86740473	105	23659										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786078	3786078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agtgctctcttcctttttccTctcctcttcttcttgttcta	3	14	6	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:3786078T>C	ENST00000262367.5	-	28	5496	c.4687A>G	c.(4687-4689)Agg>Ggg	p.R1563G	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1525G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1563	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TCCTTTTTCCTCTCCTCTTCT	0.517			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											308	220	250					16																	3786078		2197	4300	6497	3726079	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4687A>G	16.37:g.3786078T>C	ENSP00000262367:p.Arg1563Gly		3726079	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	15.42	2.827625	0.50845	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93547	-3.24;-3.24	5.2	4.09	0.47781	.	0.000000	0.85682	D	0.000000	D	0.96725	0.8931	M	0.88640	2.97	0.58432	D	0.999999	D;D	0.62365	0.991;0.991	D;D	0.78314	0.991;0.991	D	0.96435	0.9322	10	0.62326	D	0.03	-24.6377	11.8222	0.52245	0.0:0.0:0.1466:0.8534	.	1593;1563	Q4LE28;Q92793	.;CBP_HUMAN	G	1563;1593;1525;152	ENSP00000262367:R1563G;ENSP00000371502:R1525G	ENSP00000262367:R1563G	R	-	1	2	CREBBP	3726079	0.722000	0.28017	0.998000	0.56505	0.989000	0.77384	0.982000	0.29539	0.898000	0.36418	0.454000	0.30748	AGG		0.517	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3786078	T	C	3786078	3	2	83	1	0	0	0	0	1	0	0	0	3867	1550	54	4	2657	4	CREBBP	16	3786078	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	171798	3786078	86568675	106	23660										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24104235	24104235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gaccaaaaccatcaaatgctCcctcaaccctgagtggaatg	7	13	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:24104235C>T	ENST00000321728.7	+	6	828	c.653C>T	c.(652-654)tCc>tTc	p.S218F	PRKCB_ENST00000303531.7_Missense_Mutation_p.S218F|PRKCB_ENST00000482000.1_3'UTR	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	218	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	ATCAAATGCTCCCTCAACCCT	0.478																																																0			16											158	130	140					16																	24104235		2197	4300	6497	24011736	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.653C>T	16.37:g.24104235C>T	ENSP00000318315:p.Ser218Phe		24011736	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340552	0.60963	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.50001	0.76;0.76	5.38	5.38	0.77491	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.061993	0.64402	D	0.000003	T	0.52306	0.1726	M	0.72576	2.205	0.46279	D	0.99896	B;B	0.13145	0.005;0.007	B;B	0.18263	0.019;0.021	T	0.52917	-0.8511	10	0.72032	D	0.01	.	18.4836	0.90820	0.0:1.0:0.0:0.0	.	218;218	P05771-2;P05771	.;KPCB_HUMAN	F	218	ENSP00000318315:S218F;ENSP00000305355:S218F	ENSP00000305355:S218F	S	+	2	0	PRKCB	24011736	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	4.725000	0.61979	2.681000	0.91329	0.650000	0.86243	TCC		0.478	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		T	24104235	C	T	24104235	3	4	83	1	0	0	0	0	1	0	0	0	12542	855	30	3	675	3	PRKCB	16	24104235	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	20318157	24104235	66250518	107	23661										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29884659	29884659	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	caaagccctcatagcagaagAagcgcagagactcgcccgcc	10	15	1	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:29884659A>C	ENST00000308713.5	-	14	2917	c.2390T>G	c.(2389-2391)tTc>tGc	p.F797C	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.F753C|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.F683C|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.F727C	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	797	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ATAGCAGAAGAAGCGCAGAGA	0.627																																																0			16											111	110	110					16																	29884659		2197	4300	6497	29792160	SO:0001583	missense	26470			AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.2390T>G	16.37:g.29884659A>C	ENSP00000312550:p.Phe797Cys		29792160	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.674506	0.67928	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42	4.39	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.254772	0.28161	N	0.016372	D	0.85234	0.5650	H	0.94808	3.585	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.996;0.999;0.995;0.996;0.995	D;P;D;P;P;P	0.70016	0.967;0.905;0.934;0.847;0.905;0.847	D	0.89043	0.3450	10	0.87932	D	0	.	12.7207	0.57140	1.0:0.0:0.0:0.0	.	753;797;683;727;797;727	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	C	727;797;683;753	ENSP00000310206:F727C;ENSP00000312550:F797C;ENSP00000319215:F683C;ENSP00000439412:F753C	ENSP00000312550:F797C	F	-	2	0	SEZ6L2	29792160	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.761000	0.91691	1.831000	0.53308	0.533000	0.62120	TTC		0.627	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		C	29884659	A	C	29884659	3	2	83	1	0	0	0	0	1	0	0	0	14181	246	9	4	401	4	SEZ6L2	16	29884659	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	5780424	29884659	60470094	108	23662										
SLC9A5	6553	hgsc.bcm.edu	37	chr16	67300007	67300007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccagctgctgtgatattaacCgtggagtctgaggaggagga	15	7	1	2	rs372783358		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:67300007C>T	ENST00000299798.11	+	15	2162	c.2097C>T	c.(2095-2097)acC>acT	p.T699T	CTC-277H1.7_ENST00000573063.1_RNA	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	699					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		TGATATTAACCGTGGAGTCTG	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		20991	0		0	False		,,,				2504	0															0			16											72	72	72					16																	67300007		2073	4217	6290	65857508	SO:0001819	synonymous_variant	6553				CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"Solute carriers"	11078	protein-coding gene	gene with protein product		600477	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 5", "solute carrier family 9 (sodium/hydrogen exchanger), member 5"			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.2097C>T	16.37:g.67300007C>T			65857508	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																				0.577	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1			T	67300007	C	T	67300007	2	4	83	1	0	0	0	0	0	0	0	1	14754	639	23	1		1	SLC9A5	16	67300007	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	37415348	67300007	23054746	109	23663										
C16orf3	2622	hgsc.bcm.edu	37	chr16	90095573	90095573	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gcagcctacggggcaggctaCggggcagcttacggggcagg	19	11	0	0	rs77382359		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:90095573C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V60I|GAS8_ENST00000536122.1_Intron	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		gggcaggctacggggcagctt	0.672																																																0			16											22	20	21					16																	90095573		2194	4299	6493	88623074	SO:0001627	intron_variant	750			AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"growth arrest-specific 11"	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1443C>T	16.37:g.90095573C>T			88623074	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	c	0.708	-0.788068	0.02884	.	.	ENSG00000221819	ENST00000408886	T	0.47177	0.85	.	.	.	.	.	.	.	.	T	0.22244	0.0536	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	.	.	.	.	.	68	O95177	CP003_HUMAN	I	60	ENSP00000386218:V60I	.	V	-	1	0	C16orf3	88623074	0.031000	0.19500	0.015000	0.15790	0.017000	0.09413	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTA		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2			T	90095573	C	T	90095573	1	4	83	0	1	0	0	0	0	0	0	0	1816	536	19	1		1	C16orf3	16	90095573	Intron	SNP	C	TCGA-AH-6549-01A-11D-1826-10	22795566	90095573	259180	110	23664										
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	83	1	0	0	0	0	1	0	0	0	16421	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		7577538	73617672	111	23665										
TP53	7157	hgsc.bcm.edu	37	chr17	7578282	7578282	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cggataagatgctgaggaggGgccagacctaagagcaatca	14	8	1	4	rs55764374		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:7578282G>T	ENST00000269305.4	-	6	756	c.567C>A	c.(565-567)gcC>gcA	p.A189A	TP53_ENST00000445888.2_Silent_p.A189A|TP53_ENST00000455263.2_Silent_p.A189A|TP53_ENST00000413465.2_Silent_p.A189A|TP53_ENST00000359597.4_Silent_p.A189A|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Silent_p.A189A	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	189	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in a sporadic cancer; somatic mutation).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in a sporadic cancer; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.A189_V197delAPPQHLIRV(4)|p.G187fs*16(2)|p.A189A(2)|p.D186_P191delDGLAPP(1)|p.?(1)|p.P190fs*19(1)|p.G187fs*64(1)|p.A189_Q192>E(1)|p.L188_P191del(1)|p.A189_P190>X(1)|p.A189fs*53(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTGAGGAGGGGCCAGACCTA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	24	Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(3)|Complex - deletion inframe(2)|Substitution - coding silent(2)|Insertion - Frameshift(1)|Complex - frameshift(1)|Unknown(1)	skin(5)|bone(4)|liver(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|ovary(2)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)	17											88	79	82					17																	7578282		2203	4300	6503	7519007	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.567C>A	17.37:g.7578282G>T			7519007	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578282	G	T	7578282	2	4	83	1	0	0	0	0	0	0	0	1	16421	1219	43	2		2	TP53	17	7578282	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	744	7578282	73616928	112	23666										
KRT222	125113	hgsc.bcm.edu	37	chr17	38818271	38818272	+	Frame_Shift_Ins	INS	-	-	T													0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agcctcttcatctttgtccaINStttttttgcttatgtcttct							TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:38818271_38818272insT	ENST00000476049.1	-	2	162_163	c.121_122insA	c.(121-123)atgfs	p.M41fs	KRT222_ENST00000394052.3_Frame_Shift_Ins_p.M41fs			Q8N1A0	KT222_HUMAN	keratin 222	41						intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1)	15						ATCTTTGTCCATTTTTTTGCTT	0.426																																																0			17																																								36071798	SO:0001589	frameshift_variant	0			AK092967	CCDS11371.1	17q21.2	2013-06-25	2009-08-25	2009-08-25	ENSG00000213424	ENSG00000213424		"-"	28695	protein-coding gene	gene with protein product			"keratin 222 pseudogene"	KRT222P		16831889	Standard	NM_152349		Approved	KA21, MGC45562	uc002hvc.2	Q8N1A0	OTTHUMG00000133374	ENST00000476049.1:c.122dupA	17.37:g.38818278_38818278dupT	ENSP00000463483:p.Met41fs		36071797	Q7Z368	Frame_Shift_Ins	INS	ENST00000476049.1	37	CCDS11371.1																																																																																				0.426	KRT222-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000447539.1	NM_152349		T	38818272	-	T	38818271	7	5	83	1	0	1	1	0	0	0	0	0	8480	217	8	0	785	0	KRT222	17	38818271	Frame_Shift_Ins	INS	-	TCGA-AH-6549-01A-11D-1826-10	31239989	38818271	42376939	113	23667										
EVPL	2125	hgsc.bcm.edu	37	chr17	74005245	74005245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agctcgtacaccgcgtcctcCgcggcccgcctcttctgggc	11	19	2	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:74005245C>T	ENST00000301607.3	-	22	4294	c.4041G>A	c.(4039-4041)gcG>gcA	p.A1347A	EVPL_ENST00000586740.1_Silent_p.A1369A	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1347	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCGCGTCCTCCGCGGCCCGCC	0.682																																																0			17											48	53	51					17																	74005245		2201	4297	6498	71516840	SO:0001819	synonymous_variant	2125			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4041G>A	17.37:g.74005245C>T			71516840	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																				0.682	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74005245	C	T	74005245	2	4	83	1	0	0	0	0	0	0	0	1	5305	639	23	1		1	EVPL	17	74005245	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	35186974	74005245	7189965	114	23668										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21897130	21897130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	taccgtgcatactgcttgagTcaggtgtttgcatccctggc	11	11	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr18:21897130T>C	ENST00000319481.3	-	11	1059	c.853A>G	c.(853-855)Act>Gct	p.T285A		NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	285	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)	p.T285P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ACTGCTTGAGTCAGGTGTTTG	0.368																																																1	Substitution - Missense(1)	ovary(1)	18											109	106	107					18																	21897130		2203	4300	6503	20151128	SO:0001583	missense	114876			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.853A>G	18.37:g.21897130T>C	ENSP00000320291:p.Thr285Ala		20151128	B7Z7D3|Q9BZF5|Q9NW87	Missense_Mutation	SNP	ENST00000319481.3	37	CCDS11884.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211954	0.79240	.	.	ENSG00000141447	ENST00000319481	T	0.40225	1.04	5.73	5.73	0.89815	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.048710	0.85682	D	0.000000	T	0.55737	0.1939	L	0.50333	1.59	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.75020	0.985;0.97	T	0.49041	-0.8980	10	0.11794	T	0.64	-23.2478	16.0013	0.80294	0.0:0.0:0.0:1.0	.	285;285	B0YJ56;Q9BXW6	.;OSBL1_HUMAN	A	285	ENSP00000320291:T285A	ENSP00000320291:T285A	T	-	1	0	OSBPL1A	20151128	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.896000	0.75665	2.180000	0.69256	0.528000	0.53228	ACT		0.368	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		C	21897130	T	C	21897130	3	2	83	1	0	0	0	0	1	0	0	0	11308	1667	58	4	2071	4	OSBPL1A	18	21897130	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10		21897130	56180118	115	23669										
TLE6	79816	hgsc.bcm.edu	37	chr19	2978266	2978266	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccagcccagacccaagggccCcccgaaaagcacttcggtga	10	17	0	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:2978266C>A	ENST00000246112.4	+	2	236	c.35C>A	c.(34-36)cCc>cAc	p.P12H	TLE6_ENST00000482627.1_Missense_Mutation_p.P12H|TLE6_ENST00000452088.1_Intron	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	12					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		CCCAAGGGCCCCCCGAAAAGC	0.577																																																0			19											24	25	25					19																	2978266		692	1591	2283	2929266	SO:0001583	missense	79816			AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"WD repeat domain containing"	30788	protein-coding gene	gene with protein product		612399	"transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.35C>A	19.37:g.2978266C>A	ENSP00000246112:p.Pro12His		2929266	J3KMZ1	Missense_Mutation	SNP	ENST00000246112.4	37	CCDS45910.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613579	0.28712	.	.	ENSG00000104953	ENST00000447920;ENST00000453329;ENST00000246112	T	0.25250	1.81	1.59	1.59	0.23543	.	.	.	.	.	T	0.16685	0.0401	N	0.08118	0	0.21064	N	0.999794	P	0.43352	0.804	P	0.47015	0.534	T	0.11179	-1.0598	9	0.87932	D	0	.	6.6424	0.22917	0.0:1.0:0.0:0.0	.	12	C9JGZ7	.	H	12	ENSP00000246112:P12H	ENSP00000246112:P12H	P	+	2	0	TLE6	2929266	0.008000	0.16893	0.006000	0.13384	0.002000	0.02628	0.453000	0.21811	1.227000	0.43598	0.462000	0.41574	CCC		0.577	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760		A	2978266	C	A	2978266	3	1	83	1	0	0	0	0	1	0	0	0	15981	623	22	2	37	2	TLE6	19	2978266	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		2978266	56150717	116	23670										
RFX1	5989	hgsc.bcm.edu	37	chr19	14076266	14076266	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccctcacactctcaccttcaCccgcagcatctcctcgggga	6	20	4	0	rs377533889		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:14076266C>A	ENST00000254325.4	-	16	2440	c.2206G>T	c.(2206-2208)Gtg>Ttg	p.V736L		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	736					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			CTCACCTTCACCCGCAGCATC	0.617																																																0			19											171	181	178					19																	14076266		2203	4300	6503	13937266	SO:0001583	missense	5989				CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"trans-acting regulatory factor 1", "enhancer factor C", "MHC class II regulatory factor RFX"	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.2206G>T	19.37:g.14076266C>A	ENSP00000254325:p.Val736Leu		13937266		Missense_Mutation	SNP	ENST00000254325.4	37	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	c	14.07	2.424629	0.43020	.	.	ENSG00000132005	ENST00000254325	T	0.07908	3.15	4.02	4.02	0.46733	.	0.130838	0.52532	D	0.000076	T	0.08758	0.0217	L	0.39245	1.2	0.41086	D	0.985564	B	0.21688	0.059	B	0.20184	0.028	T	0.19614	-1.0300	10	0.27785	T	0.31	-22.0861	15.0907	0.72192	0.0:1.0:0.0:0.0	.	736	P22670	RFX1_HUMAN	L	736	ENSP00000254325:V736L	ENSP00000254325:V736L	V	-	1	0	RFX1	13937266	0.998000	0.40836	1.000000	0.80357	0.919000	0.55068	2.463000	0.45058	2.074000	0.62210	0.462000	0.41574	GTG		0.617	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		A	14076266	C	A	14076266	3	1	83	1	0	0	0	0	1	0	0	0	13299	507	18	2	757	2	RFX1	19	14076266	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	11098000	14076266	45052717	117	23671										
HAPLN4	404037	hgsc.bcm.edu	37	chr19	19372262	19372262	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggccctgactcacccagcacGtgcacgaccttcttccggcc	9	19	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:19372262G>A	ENST00000291481.7	-	2	177	c.114C>T	c.(112-114)caC>caT	p.H38H	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	38					cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	CACCCAGCACGTGCACGACCT	0.706																																																0			19											31	25	27					19																	19372262		2197	4292	6489	19233262	SO:0001819	synonymous_variant	404037			AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.114C>T	19.37:g.19372262G>A			19233262	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	37	CCDS12398.1																																																																																				0.706	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		A	19372262	G	A	19372262	2	1	83	1	0	0	0	0	0	0	0	1	6978	1136	40	1		1	HAPLN4	19	19372262	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	5295996	19372262	39756721	118	23672										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30477315	30477315	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ctgtaggtttagttgagcacCggaaagaacgtaggtaccca	12	8	0	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:30477315C>A	ENST00000542441.2	+	4	655	c.358C>A	c.(358-360)Cgg>Agg	p.R120R	URI1_ENST00000312051.6_Silent_p.R80R|URI1_ENST00000392271.1_Silent_p.R44R|URI1_ENST00000360605.4_Silent_p.R102R			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	120					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.R120W(1)									AGTTGAGCACCGGAAAGAACG	0.423																																																1	Substitution - Missense(1)	kidney(1)	19											147	140	143					19																	30477315		2203	4300	6503	35169155	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.358C>A	19.37:g.30477315C>A			35169155	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.423	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30477315	C	A	30477315	2	1	83	1	0	0	0	0	0	0	0	1	1917	643	23	2		2	C19orf2	19	30477315	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	11105053	30477315	28651668	119	23673										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768401	31768401	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttcttggactgcaggggcggCggggtggccacagcagcctt	17	11	1	0	rs368908849		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:31768401C>T	ENST00000240587.4	-	2	2625	c.2298G>A	c.(2296-2298)ccG>ccA	p.P766P		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	766					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P766P(1)|p.P583P(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GCAGGGGCGGCGGGGTGGCCA	0.597													C|||	1	0.000199681	8e-04	0	5008	,	,		16006	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	large_intestine(2)	19						C		0,4406		0,0,2203	65	64	64		2298	-8	0.2	19		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TSHZ3	NM_020856.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		766/1082	31768401	1,13005	2203	4300	6503	36460241	SO:0001819	synonymous_variant	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2298G>A	19.37:g.31768401C>T			36460241	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																				0.597	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31768401	C	T	31768401	2	4	83	1	0	0	0	0	0	0	0	1	16665	755	27	1		1	TSHZ3	19	31768401	Silent	SNP	C	TCGA-AH-6549-01A-11D-1826-10	1291086	31768401	27360582	120	23674										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37441552	37441552	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	cagagaattcatacgggtgaGaaaccctatgcatgtacagt	10	8	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:37441552G>A	ENST00000333987.7	+	7	2003	c.1497G>A	c.(1495-1497)gaG>gaA	p.E499E	ZNF568_ENST00000415168.1_Silent_p.E435E|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	499					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATACGGGTGAGAAACCCTATG	0.383																																																0			19											67	73	71					19																	37441552		2183	4294	6477	42133392	SO:0001819	synonymous_variant	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1497G>A	19.37:g.37441552G>A			42133392	B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	ENST00000333987.7	37	CCDS42558.1																																																																																				0.383	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		A	37441552	G	A	37441552	2	1	83	1	0	0	0	0	0	0	0	1	18038	933	33	3		3	ZNF568	19	37441552	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	5673151	37441552	21687431	121	23675										
RYR1	6261	hgsc.bcm.edu	37	chr19	38976617	38976617	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	accacttcgctgaggcccccGcatcatttctcgcccccctg	7	20	2	1	rs572516017	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:38976617G>A	ENST00000359596.3	+	34	5322	c.5322G>A	c.(5320-5322)ccG>ccA	p.P1774P	RYR1_ENST00000360985.3_Silent_p.P1774P|RYR1_ENST00000355481.4_Silent_p.P1774P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1774	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGAGGCCCCCGCATCATTTCT	0.692													G|||	2	0.000399361	0	0	5008	,	,		15752	0.002		0	False		,,,				2504	0															0			19											37	36	36					19																	38976617		2203	4300	6503	43668457	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5322G>A	19.37:g.38976617G>A			43668457	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.692	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38976617	G	A	38976617	2	1	83	1	0	0	0	0	0	0	0	1	13805	1074	38	1		1	RYR1	19	38976617	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	1535065	38976617	20152366	122	23676										
ZNF160	90338	hgsc.bcm.edu	37	chr19	53571463	53571463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttgccatatgggtagttagaCttgatcttaccctaaaggct	9	8	1	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:53571463C>A	ENST00000429604.1	-	7	2739	c.2324G>T	c.(2323-2325)aGt>aTt	p.S775I	ZNF160_ENST00000418871.1_Missense_Mutation_p.S775I|ZNF160_ENST00000601421.1_Missense_Mutation_p.S739I|ZNF160_ENST00000599056.1_Missense_Mutation_p.S775I	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	775					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		GGTAGTTAGACTTGATCTTAC	0.433																																																0			19											134	123	127					19																	53571463		2203	4300	6503	58263275	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.2324G>T	19.37:g.53571463C>A	ENSP00000406201:p.Ser775Ile		58263275	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	C	4.458	0.084920	0.08583	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.15952	2.38;2.38	2.24	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18759	0.0450	L	0.35341	1.055	0.09310	N	1	D	0.61697	0.99	P	0.61658	0.892	T	0.13335	-1.0513	9	0.30854	T	0.27	.	3.1973	0.06637	0.3482:0.4148:0.0:0.237	.	775	Q9HCG1	ZN160_HUMAN	I	775	ENSP00000406201:S775I;ENSP00000409597:S775I	ENSP00000409597:S775I	S	-	2	0	ZNF160	58263275	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-4.557000	0.00216	-0.622000	0.05626	0.467000	0.42956	AGT		0.433	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		A	53571463	C	A	53571463	3	1	83	1	0	0	0	0	1	0	0	0	17778	565	20	2	136	2	ZNF160	19	53571463	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	14594846	53571463	5557520	123	23677										
SNX5	27131	hgsc.bcm.edu	37	chr20	17929566	17929566	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	aatgttgagcatgtagtatcGgaggagctctgttagcttca	12	6	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:17929566G>A	ENST00000377768.3	-	11	1198	c.886C>T	c.(886-888)Cga>Tga	p.R296*	SNX5_ENST00000377759.4_Nonsense_Mutation_p.R296*|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	296	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)	p.R296*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						ATGTAGTATCGGAGGAGCTCT	0.413																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											94	90	91					20																	17929566		2203	4300	6503	17877566	SO:0001587	stop_gained	27131			AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.886C>T	20.37:g.17929566G>A	ENSP00000366998:p.Arg296*		17877566	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Nonsense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318136	0.95682	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277	.	.	.	4.97	1.37	0.22104	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1945	0.25845	0.0896:0.0:0.362:0.5484	.	.	.	.	X	296;296;259	.	ENSP00000366988:R296X	R	-	1	2	SNX5	17877566	1.000000	0.71417	0.738000	0.30950	0.879000	0.50718	3.189000	0.50965	0.612000	0.30071	-0.878000	0.02970	CGA		0.413	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			A	17929566	G	A	17929566	4	1	83	1	0	0	0	0	0	1	0	0	14942	1124	39	1	344	1	SNX5	20	17929566	Nonsense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10		17929566	45095954	124	23678										
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39991144	39991144	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agggccagctcccggccatcAaggctctggtgcagcctccg	13	16	2	0	rs41307177	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:39991144A>G	ENST00000332312.3	-	4	1257	c.1065T>C	c.(1063-1065)ctT>ctC	p.L355L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	355						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCGGCCATCAAGGCTCTGGT	0.682													A|||	406	0.0810703	0.0598	0.1225	5008	,	,		15115	0.003		0.1799	False		,,,				2504	0.0593															0			20						A		377,4021		11,355,1833	13	16	15		1065	-1.5	1	20	dbSNP_127	15	1411,7175		132,1147,3014	no	coding-synonymous	EMILIN3	NM_052846.1		143,1502,4847	GG,GA,AA		16.4337,8.5721,13.7708		355/767	39991144	1788,11196	2199	4293	6492	39424558	SO:0001819	synonymous_variant	90187			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1065T>C	20.37:g.39991144A>G			39424558	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.682	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		G	39991144	A	G	39991144	2	3	83	1	0	0	0	0	0	0	0	1	5108	117	5	4		4	EMILIN3	20	39991144	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	22061578	39991144	23034376	125	23679										
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39991171	39991171	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tggtgcagcctccggctggcGgcctgaccctcctcacattg	12	16	1	1	rs61739307	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:39991171G>A	ENST00000332312.3	-	4	1230	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	346						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCGGCTGGCGGCCTGACCCT	0.672													G|||	405	0.0808706	0.059	0.1225	5008	,	,		14633	0.003		0.1799	False		,,,				2504	0.0593															0			20						G		390,4012		16,358,1827	15	17	16		1038	-10.3	0.2	20	dbSNP_129	16	1433,7165		130,1173,2996	no	coding-synonymous	EMILIN3	NM_052846.1		146,1531,4823	AA,AG,GG		16.6667,8.8596,14.0231		346/767	39991171	1823,11177	2201	4299	6500	39424585	SO:0001819	synonymous_variant	90187			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1038C>T	20.37:g.39991171G>A			39424585	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.672	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		A	39991171	G	A	39991171	2	1	83	1	0	0	0	0	0	0	0	1	5108	1103	39	1		1	EMILIN3	20	39991171	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	27	39991171	23034349	126	23680										
SALL4	57167	hgsc.bcm.edu	37	chr20	50406985	50406985	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tcatcatggcagatagcgccGgtgctgccgttctcacccac	10	15	3	1	rs13043248	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:50406985G>A	ENST00000217086.4	-	2	2148	c.2037C>T	c.(2035-2037)acC>acT	p.T679T	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	679					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGATAGCGCCGGTGCTGCCGT	0.587													G|||	221	0.0441294	0.0038	0.0562	5008	,	,		18487	0.0268		0.1153	False		,,,				2504	0.0348															0			20						G		103,4303	80.4+/-118.8	0,103,2100	63	53	56		2037	-10.3	0	20	dbSNP_121	56	960,7640	211.0+/-251.7	62,836,3402	no	coding-synonymous	SALL4	NM_020436.3		62,939,5502	AA,AG,GG		11.1628,2.3377,8.1732		679/1054	50406985	1063,11943	2203	4300	6503	49840392	SO:0001819	synonymous_variant	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2037C>T	20.37:g.50406985G>A			49840392	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50406985	G	A	50406985	2	1	83	1	0	0	0	0	0	0	0	1	13850	1103	39	1		1	SALL4	20	50406985	Silent	SNP	G	TCGA-AH-6549-01A-11D-1826-10	10415814	50406985	12618535	127	23681										
RUNX1	861	hgsc.bcm.edu	37	chr21	36231785	36231785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	acttacttcgaggttctcggGgcccatccactgtgattttg	10	11	1	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr21:36231785G>T	ENST00000344691.4	-	3	2095	c.518C>A	c.(517-519)cCc>cAc	p.P173H	RUNX1_ENST00000325074.5_Missense_Mutation_p.P188H|RUNX1_ENST00000399240.1_Missense_Mutation_p.P173H|RUNX1_ENST00000300305.3_Missense_Mutation_p.P200H|RUNX1_ENST00000437180.1_Missense_Mutation_p.P200H|RUNX1_ENST00000358356.5_Missense_Mutation_p.P173H|RUNX1_ENST00000486278.2_Missense_Mutation_p.P176H	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	173	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						AGGTTCTCGGGGCCCATCCAC	0.557			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	0			21											286	250	262					21																	36231785		2203	4300	6503	35153655	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.518C>A	21.37:g.36231785G>T	ENSP00000340690:p.Pro173His		35153655	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477319	0.84640	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	D;D;D;D;D;D;D;D	0.99766	-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69	5.12	5.12	0.69794	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	M	0.91196	3.185	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.994;0.999;0.995;0.986;0.99;0.936;0.999	D	0.96865	0.9635	10	0.87932	D	0	-28.2152	16.0721	0.80941	0.0:0.0:1.0:0.0	.	200;173;173;176;200;188;173	Q2TAM6;Q01196-5;Q01196-3;C9JK12;Q01196-8;Q01196-10;Q01196	.;.;.;.;.;.;RUNX1_HUMAN	H	173;200;200;188;173;176;173;188;176	ENSP00000340690:P173H;ENSP00000300305:P200H;ENSP00000409227:P200H;ENSP00000319459:P188H;ENSP00000382184:P173H;ENSP00000351123:P173H;ENSP00000382182:P188H;ENSP00000438019:P176H	ENSP00000300305:P200H	P	-	2	0	RUNX1	35153655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.430000	0.97488	2.377000	0.81083	0.655000	0.94253	CCC		0.557	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			T	36231785	G	T	36231785	3	4	83	1	0	0	0	0	1	0	0	0	13783	1232	43	2	892	2	RUNX1	21	36231785	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10		36231785	11898110	128	23682										
TTC3	7267	hgsc.bcm.edu	37	chr21	38525373	38525373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ccatgcttctcaaagaattgCtttcttggaaagttttgagc	8	8	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr21:38525373C>T	ENST00000399017.2	+	27	5283	c.2536C>T	c.(2536-2538)Ctt>Ttt	p.L846F	TTC3_ENST00000354749.2_Missense_Mutation_p.L846F|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.L846F|TTC3_ENST00000540756.1_Missense_Mutation_p.L536F	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	846					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CAAAGAATTGCTTTCTTGGAA	0.368																																					Ovarian(38;194 1649 35661)											0			21											67	72	70					21																	38525373		2203	4300	6503	37447243	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2536C>T	21.37:g.38525373C>T	ENSP00000381981:p.Leu846Phe		37447243	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.662102	0.67700	.	.	ENSG00000182670	ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T	0.50548	2.55;2.55;2.86;0.74;2.86;2.86	5.31	4.41	0.53225	.	0.112528	0.39909	N	0.001227	T	0.55940	0.1952	M	0.62723	1.935	0.39186	D	0.962869	P;D	0.59767	0.839;0.986	B;P	0.53954	0.351;0.738	T	0.63107	-0.6711	10	0.87932	D	0	-13.7571	10.7736	0.46338	0.1481:0.7093:0.1426:0.0	.	536;846	B4DSZ9;P53804	.;TTC3_HUMAN	F	846;828;846;536;846;846	ENSP00000403943:L846F;ENSP00000391891:L828F;ENSP00000347889:L846F;ENSP00000442875:L536F;ENSP00000381981:L846F;ENSP00000346791:L846F	ENSP00000346791:L846F	L	+	1	0	TTC3	37447243	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.118000	0.31246	1.341000	0.45600	0.650000	0.86243	CTT		0.368	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38525373	C	T	38525373	3	4	83	1	0	0	0	0	1	0	0	0	16737	797	28	3	2638	3	TTC3	21	38525373	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	2293588	38525373	9604522	129	23683										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19208966	19208966	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gccagatgggggtctcgcttCtcacagtagcggcccaccac	12	15	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:19208966C>A	ENST00000263200.10	-	17	2802	c.2730G>T	c.(2728-2730)gaG>gaT	p.E910D	CLTCL1_ENST00000427926.1_Missense_Mutation_p.E910D|CLTCL1_ENST00000353891.5_Missense_Mutation_p.E910D	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	910	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GGTCTCGCTTCTCACAGTAGC	0.557			T	?	ALCL																																		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	0			22											31	33	32					22																	19208966		2090	4235	6325	17588966	SO:0001583	missense	8218				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2730G>T	22.37:g.19208966C>A	ENSP00000445677:p.Glu910Asp		17588966	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454318	0.43634	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.27402	1.67;1.67;1.67	3.63	1.31	0.21738	Tetratricopeptide-like helical (1);Armadillo-type fold (2);	0.000000	0.64402	D	0.000001	T	0.58104	0.2099	H	0.94886	3.595	0.52099	D	0.999946	D;D	0.76494	0.999;0.998	D;D	0.91635	0.999;0.998	T	0.58295	-0.7661	10	0.87932	D	0	-15.0034	4.2723	0.10792	0.0:0.4141:0.0:0.5859	.	910;910	P53675-2;P53675	.;CLH2_HUMAN	D	910	ENSP00000439662:E910D;ENSP00000445677:E910D;ENSP00000441158:E910D	ENSP00000445677:E910D	E	-	3	2	CLTCL1	17588966	1.000000	0.71417	0.998000	0.56505	0.110000	0.19582	1.386000	0.34419	0.733000	0.32492	0.462000	0.41574	GAG		0.557	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19208966	C	A	19208966	3	1	83	1	0	0	0	0	1	0	0	0	3573	912	32	2	2256	2	CLTCL1	22	19208966	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10		19208966	32095600	130	23684										
NF2	4771	hgsc.bcm.edu	37	chr22	30035156	30035156	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttttatcctgagaatgctgaAgaggagctggttcaggagat	13	5	1	4	rs535626069		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:30035156A>G	ENST00000338641.4	+	3	759	c.318A>G	c.(316-318)gaA>gaG	p.E106E	NF2_ENST00000413209.2_Silent_p.E106E|NF2_ENST00000403435.1_Silent_p.E106E|NF2_ENST00000397789.3_Silent_p.E106E|NF2_ENST00000403999.3_Silent_p.E106E|NF2_ENST00000361676.4_Silent_p.E64E|NF2_ENST00000334961.7_Intron|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Intron|NF2_ENST00000353887.4_Intron|NF2_ENST00000361166.4_Silent_p.E106E	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	106	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		E -> G (in NF2). {ECO:0000269|PubMed:8081368, ECO:0000269|PubMed:9643284}.		actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.H95fs*3(1)|p.V86_Q111>E(1)|p.A105fs*20(1)|p.L97fs*17(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AGAATGCTGAAGAGGAGCTGG	0.448			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2				A|||	1	0.000199681	8e-04	0	5008	,	,		20266	0		0	False		,,,				2504	0					yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	7	Unknown(3)|Deletion - Frameshift(3)|Complex - deletion inframe(1)	soft_tissue(3)|stomach(1)|large_intestine(1)|lung(1)|kidney(1)	22											137	120	126					22																	30035156		2203	4300	6503	28365156	SO:0001819	synonymous_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.318A>G	22.37:g.30035156A>G			28365156	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Silent	SNP	ENST00000338641.4	37	CCDS13861.1																																																																																				0.448	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		G	30035156	A	G	30035156	2	3	83	1	0	0	0	0	0	0	0	1	10388	69	3	4		4	NF2	22	30035156	Silent	SNP	A	TCGA-AH-6549-01A-11D-1826-10	10826190	30035156	21269410	131	23685										
CYTH4	27128	hgsc.bcm.edu	37	chr22	37690749	37690749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ttgcccaaatcgactgcttcGagagtgcggaggagaggtga	15	8	0	3			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:37690749G>A	ENST00000248901.6	+	3	338	c.151G>A	c.(151-153)Gag>Aag	p.E51K	CYTH4_ENST00000405206.3_Missense_Mutation_p.E51K|CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000402997.1_Missense_Mutation_p.E51K	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	51					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						CGACTGCTTCGAGAGTGCGGA	0.587																																																0			22											131	120	124					22																	37690749		2203	4300	6503	36020695	SO:0001583	missense	27128			AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"Pleckstrin homology (PH) domain containing"	9505	protein-coding gene	gene with protein product		606514	"pleckstrin homology, Sec7 and coiled/coil domains 4", "pleckstrin homology, Sec7 and coiled-coil domains 4"	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.151G>A	22.37:g.37690749G>A	ENSP00000248901:p.Glu51Lys		36020695	Q5R3F9|Q9UGT6	Missense_Mutation	SNP	ENST00000248901.6	37	CCDS13946.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917968	0.33815	.	.	ENSG00000100055	ENST00000457992;ENST00000248901;ENST00000422721;ENST00000402997;ENST00000405206	T;T;T;T	0.47869	0.83;3.23;0.84;0.84	4.78	4.78	0.61160	.	0.459587	0.24258	N	0.040111	T	0.40694	0.1127	L	0.58810	1.83	0.44380	D	0.997286	B;B	0.27679	0.031;0.185	B;B	0.25614	0.014;0.062	T	0.39272	-0.9622	10	0.44086	T	0.13	.	6.917	0.24365	0.0948:0.1787:0.7265:0.0	.	51;64	Q9UIA0;Q9H7Q0	CYH4_HUMAN;.	K	51;51;64;51;51	ENSP00000405442:E51K;ENSP00000248901:E51K;ENSP00000385997:E51K;ENSP00000384280:E51K	ENSP00000248901:E51K	E	+	1	0	CYTH4	36020695	0.001000	0.12720	0.938000	0.37757	0.723000	0.41478	0.985000	0.29578	2.195000	0.70347	0.561000	0.74099	GAG		0.587	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			A	37690749	G	A	37690749	3	1	83	1	0	0	0	0	1	0	0	0	4212	1059	37	1	161	1	CYTH4	22	37690749	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	7655593	37690749	13613817	132	23686										
PAGE2	203569	hgsc.bcm.edu	37	chrX	55117792	55117792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	catggaagcttttcaacaggAactggctctgcttaagatag	10	8	2	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:55117792A>G	ENST00000374968.4	+	4	325	c.221A>G	c.(220-222)gAa>gGa	p.E74G	PAGE2_ENST00000374965.1_Missense_Mutation_p.E57G	NM_207339.2	NP_997222.1	Q7Z2X7	PAGE2_HUMAN	P antigen family, member 2 (prostate associated)	74										endometrium(1)|large_intestine(2)|lung(1)|ovary(2)	6						TTTCAACAGGAACTGGCTCTG	0.398																																																0			X											76	80	79					X																	55117792		2171	4290	6461	55134517	SO:0001583	missense	203569			BC054022	CCDS14367.1	Xp11.22	2009-06-17			ENSG00000234068	ENSG00000234068			31804	protein-coding gene	gene with protein product		300738	"G antigen, family C, 2"	GAGEC2		9724777	Standard	NM_207339		Approved	MGC62094, PAGE-2, CT16.4		Q7Z2X7	OTTHUMG00000021648	ENST00000374968.4:c.221A>G	X.37:g.55117792A>G	ENSP00000364107:p.Glu74Gly		55134517	Q5JRK7|Q5JRK8	Missense_Mutation	SNP	ENST00000374968.4	37	CCDS14367.1	.	.	.	.	.	.	.	.	.	.	a	4.669	0.124320	0.08931	.	.	ENSG00000234068	ENST00000374968;ENST00000374965	T;T	0.26373	1.74;1.74	1.13	-0.159	0.13379	.	.	.	.	.	T	0.32585	0.0834	M	0.84433	2.695	0.09310	N	1	P	0.36683	0.565	B	0.40825	0.341	T	0.34030	-0.9845	9	0.87932	D	0	.	3.9312	0.09286	0.6225:0.3775:0.0:0.0	.	74	Q7Z2X7	GGEE2_HUMAN	G	74;57	ENSP00000364107:E74G;ENSP00000364104:E57G	ENSP00000364104:E57G	E	+	2	0	PAGE2	55134517	0.016000	0.18221	0.001000	0.08648	0.013000	0.08279	0.408000	0.21065	-0.109000	0.12044	-1.716000	0.00709	GAA		0.398	PAGE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056857.1	NM_207339		G	55117792	A	G	55117792	3	3	83	1	0	0	0	0	1	0	0	0	11421	246	9	4	231	4	PAGE2	23	55117792	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10		55117792	100152768	133	23687										
ATRX	546	hgsc.bcm.edu	37	chrX	76937492	76937492	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	tttcttctctctaccatatgCtccattcttactctttttat	1	12	5	0			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:76937492C>T	ENST00000373344.5	-	9	3470	c.3256G>A	c.(3256-3258)Gca>Aca	p.A1086T	ATRX_ENST00000395603.3_Missense_Mutation_p.A1048T|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1086					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTACCATATGCTCCATTCTTA	0.363			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)	X											145	160	155					X																	76937492		2202	4290	6492	76824148	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3256G>A	X.37:g.76937492C>T	ENSP00000362441:p.Ala1086Thr		76824148	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	7.002	0.555044	0.13436	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.91740	-2.89;-2.9	5.56	-0.0726	0.13739	.	1.224500	0.05574	N	0.571506	T	0.78071	0.4226	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.0;0.001	T	0.66304	-0.5957	10	0.14252	T	0.57	-0.6494	2.337	0.04250	0.1131:0.3352:0.32:0.2317	.	1086;1018;1048;1086	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	T	1086;1048;1013	ENSP00000362441:A1086T;ENSP00000378967:A1048T	ENSP00000362441:A1086T	A	-	1	0	ATRX	76824148	0.000000	0.05858	0.078000	0.20375	0.923000	0.55619	-2.055000	0.01397	0.132000	0.18615	-0.305000	0.09177	GCA		0.363	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		T	76937492	C	T	76937492	3	4	83	1	0	0	0	0	1	0	0	0	1209	797	28	3	4330	3	ATRX	23	76937492	Missense_Mutation	SNP	C	TCGA-AH-6549-01A-11D-1826-10	21819700	76937492	78333068	134	23688										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718503	142718503	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gttcaatatacttgattaaaTtgtagtcagcctggagatac	8	6	2	2			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:142718503T>C	ENST00000381779.4	-	2	647	c.422A>G	c.(421-423)aAt>aGt	p.N141S	SLITRK4_ENST00000356928.1_Missense_Mutation_p.N141S|SLITRK4_ENST00000338017.4_Missense_Mutation_p.N141S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	141						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CTTGATTAAATTGTAGTCAGC	0.368																																																0			X											82	82	82					X																	142718503		2203	4300	6503	142546169	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.422A>G	X.37:g.142718503T>C	ENSP00000371198:p.Asn141Ser		142546169	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.986423	0.53934	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.72615	-0.67;-0.67;-0.67	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.84933	0.5582	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87364	0.2346	10	0.87932	D	0	-12.0771	13.1529	0.59500	0.0:0.0:0.0:1.0	.	141	Q8IW52	SLIK4_HUMAN	S	141	ENSP00000371198:N141S;ENSP00000349400:N141S;ENSP00000336627:N141S	ENSP00000336627:N141S	N	-	2	0	SLITRK4	142546169	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.788000	0.52465	0.486000	0.48141	AAT		0.368	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142718503	T	C	142718503	3	2	83	1	0	0	0	0	1	0	0	0	14782	1493	52	4	2095	4	SLITRK4	23	142718503	Missense_Mutation	SNP	T	TCGA-AH-6549-01A-11D-1826-10	65781011	142718503	12552057	135	23689										
PASD1	139135	hgsc.bcm.edu	37	chrX	150840856	150840856	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	agaagaagctacaggagcggAagaagtggcaggggcagatg	18	5	0	4			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:150840856A>T	ENST00000370357.4	+	14	1884	c.1639A>T	c.(1639-1641)Aag>Tag	p.K547*		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	547	Lys-rich.					nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					Acaggagcggaagaagtggca	0.532																																																0			X											52	52	52					X																	150840856		2203	4300	6503	150591512	SO:0001587	stop_gained	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1639A>T	X.37:g.150840856A>T	ENSP00000359382:p.Lys547*		150591512	Q3MNE0|Q69HD7|Q8N7X9	Nonsense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610478	0.66558	.	.	ENSG00000166049	ENST00000370357	.	.	.	0.681	-1.36	0.09085	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	547	.	ENSP00000359382:K547X	K	+	1	0	PASD1	150591512	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	0.095000	0.15127	-1.213000	0.02617	-0.749000	0.03505	AAG		0.532	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		T	150840856	A	T	150840856	4	4	83	1	0	0	0	0	0	1	0	0	11502	247	9	5	1689	5	PASD1	23	150840856	Nonsense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	8122353	150840856	4429704	136	23690										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153135086	153135086	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	gctcaggatcagggcgccacGctgaatccggtacttctggt	13	12	3	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:153135086G>A	ENST00000370060.1	-	11	1345	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C	L1CAM_ENST00000361981.3_Missense_Mutation_p.R381C|L1CAM_ENST00000538883.1_Missense_Mutation_p.R388C|L1CAM_ENST00000370057.3_Missense_Mutation_p.R386C|L1CAM_ENST00000370055.1_Missense_Mutation_p.R381C|L1CAM_ENST00000543994.1_Missense_Mutation_p.R388C|L1CAM_ENST00000361699.4_Missense_Mutation_p.R386C	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	386	Ig-like C2-type 4.		R -> C (in HSAS). {ECO:0000269|PubMed:9744477}.		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.R386C(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGGCGCCACGCTGAATCCGG	0.622																																																1	Substitution - Missense(1)	endometrium(1)	X	GRCh37	CM981152	L1CAM	M							86	71	76					X																	153135086		2202	4299	6501	152788280	SO:0001583	missense	3897			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1156C>T	X.37:g.153135086G>A	ENSP00000359077:p.Arg386Cys		152788280	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972345	0.53614	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.6	1.45	0.22620	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.420400	0.04316	N	0.349796	T	0.71307	0.3324	L	0.43152	1.355	0.09310	N	1	D;D;D	0.57571	0.98;0.961;0.969	B;B;P	0.58172	0.237;0.319;0.834	T	0.53947	-0.8366	10	0.72032	D	0.01	.	5.7768	0.18283	0.088:0.4315:0.3758:0.1048	.	381;386;386	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	C	386;388;386;388;381;381;386	ENSP00000359077:R386C;ENSP00000438430:R388C;ENSP00000359074:R386C;ENSP00000439645:R388C;ENSP00000354712:R381C;ENSP00000359072:R381C;ENSP00000355380:R386C	ENSP00000355380:R386C	R	-	1	0	L1CAM	152788280	0.001000	0.12720	0.000000	0.03702	0.886000	0.51366	0.156000	0.16382	0.101000	0.17610	0.483000	0.47432	CGT		0.622	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153135086	G	A	153135086	3	1	83	1	0	0	0	0	1	0	0	0	8610	1087	38	1	2693	1	L1CAM	23	153135086	Missense_Mutation	SNP	G	TCGA-AH-6549-01A-11D-1826-10	2294230	153135086	2135474	137	23691										
TMLHE	55217	hgsc.bcm.edu	37	chrX	154754254	154754254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0507246376811594	7	1	0.750736434108527	3.21744186046512	0.476658053402239	1	1	0	ggcagtggtctcgaagccagAcgtaatcaaagcgcatcacg	12	11	3	1			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:154754254A>G	ENST00000334398.3	-	3	366	c.221T>C	c.(220-222)gTc>gCc	p.V74A	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.V74A	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	74					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)			breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	TCGAAGCCAGACGTAATCAAA	0.428																																																0			X											156	135	143					X																	154754254		2202	4300	6502	154407448	SO:0001583	missense	55217			AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.221T>C	X.37:g.154754254A>G	ENSP00000335261:p.Val74Ala		154407448	A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Missense_Mutation	SNP	ENST00000334398.3	37	CCDS14768.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054643	0.75960	.	.	ENSG00000185973	ENST00000334398;ENST00000369439	D;T	0.83914	-1.78;-1.25	3.81	3.81	0.43845	Domain of unknown function, DUF971 (1);	0.000000	0.85682	D	0.000000	D	0.88945	0.6575	M	0.76574	2.34	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	D	0.87759	0.2597	10	0.39692	T	0.17	-10.9097	10.2175	0.43177	1.0:0.0:0.0:0.0	.	74;74;74	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	A	74	ENSP00000335261:V74A;ENSP00000358447:V74A	ENSP00000335261:V74A	V	-	2	0	TMLHE	154407448	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.698000	0.84413	1.476000	0.48215	0.417000	0.27973	GTC		0.428	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196		G	154754254	A	G	154754254	3	3	83	1	0	0	0	0	1	0	0	0	16271	275	10	4	1208	4	TMLHE	23	154754254	Missense_Mutation	SNP	A	TCGA-AH-6549-01A-11D-1826-10	1619168	154754254	516306	138	23692										
USP24	23358	hgsc.bcm.edu	37	chr1	55612633	55612633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attcacaaacatcctggccaGttacaagacactcccagatc	5	14	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:55612633G>A	ENST00000294383.6	-	19	2218	c.2219C>T	c.(2218-2220)aCt>aTt	p.T740I	USP24_ENST00000407756.1_Missense_Mutation_p.T580I	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	740					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						ATCCTGGCCAGTTACAAGACA	0.388																																																0			1											116	111	113					1																	55612633		1862	4105	5967	55385221	SO:0001583	missense	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2219C>T	1.37:g.55612633G>A	ENSP00000294383:p.Thr740Ile		55385221	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854533	0.71719	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02258	4.37;4.37	5.71	5.71	0.89125	.	0.061993	0.64402	D	0.000004	T	0.02970	0.0088	L	0.29908	0.895	0.49299	D	0.999774	B	0.30482	0.281	B	0.26969	0.075	T	0.60161	-0.7317	10	0.39692	T	0.17	.	19.8535	0.96748	0.0:0.0:1.0:0.0	.	580	B7WPF4	.	I	740;580	ENSP00000294383:T740I;ENSP00000385700:T580I	ENSP00000294383:T740I	T	-	2	0	USP24	55385221	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.686000	0.91538	0.585000	0.79938	ACT		0.388	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55612633	G	A	55612633	3	1	84	1	0	0	0	0	1	0	0	0	17095	1029	36	3	5843	3	USP24	1	55612633	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		55612633	193637988	1	23693										
FGGY	55277	hgsc.bcm.edu	37	chr1	59812054	59812054	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggaaatgcaggccccgaaacTtctgtggctgaaagaggtga	14	8	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:59812054T>G	ENST00000303721.7	+	4	623	c.449T>G	c.(448-450)cTt>cGt	p.L150R	FGGY_ENST00000371212.1_Intron|FGGY_ENST00000371218.4_Missense_Mutation_p.L150R|FGGY_ENST00000474476.1_3'UTR	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	150					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					GCCCCGAAACTTCTGTGGCTG	0.512																																																0			1											116	89	98					1																	59812054		2203	4300	6503	59584642	SO:0001583	missense	55277				CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.449T>G	1.37:g.59812054T>G	ENSP00000305922:p.Leu150Arg		59584642	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	T	22.7	4.321772	0.81580	.	.	ENSG00000172456	ENST00000413489;ENST00000371218;ENST00000303721	T;T;T	0.61742	0.08;0.08;0.08	5.5	5.5	0.81552	Carbohydrate kinase, FGGY, N-terminal (1);	0.000000	0.64402	D	0.000001	D	0.82504	0.5051	H	0.94734	3.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	D	0.87522	0.2447	9	.	.	.	-14.8172	15.4464	0.75235	0.0:0.0:0.0:1.0	.	150;150;150	Q96C11-3;F2Z2V1;Q96C11	.;.;FGGY_HUMAN	R	150	ENSP00000406607:L150R;ENSP00000360262:L150R;ENSP00000305922:L150R	.	L	+	2	0	FGGY	59584642	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.979000	0.76154	2.308000	0.77769	0.533000	0.62120	CTT		0.512	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		G	59812054	T	G	59812054	3	3	84	1	0	0	0	0	1	0	0	0	5890	1609	56	4	459	4	FGGY	1	59812054	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	4199421	59812054	189438567	2	23694										
NEXN	91624	hgsc.bcm.edu	37	chr1	78383900	78383900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggaacgaaaacgcagaattgAgcaggatatgttagaaaaga	12	4	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:78383900A>G	ENST00000334785.7	+	5	573	c.389A>G	c.(388-390)gAg>gGg	p.E130G	NEXN_ENST00000294624.8_Missense_Mutation_p.E130G|NEXN_ENST00000457030.1_Missense_Mutation_p.E130G|NEXN_ENST00000330010.8_Missense_Mutation_p.E66G	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		CGCAGAATTGAGCAGGATATG	0.378																																																0			1											130	127	128					1																	78383900		1908	4116	6024	78156488	SO:0001583	missense	91624			AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.389A>G	1.37:g.78383900A>G	ENSP00000333938:p.Glu130Gly		78156488		Missense_Mutation	SNP	ENST00000334785.7	37	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.26|19.26	3.792549|3.792549	0.70452|0.70452	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000401035;ENST00000457030;ENST00000330010;ENST00000294624;ENST00000334785;ENST00000440324|ENST00000342754	T;T;T;T;T;T|.	0.70631|.	-0.46;0.04;-0.28;-0.5;-0.0;-0.3|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.000000|.	0.53938|.	D|.	0.000060|.	T|T	0.68467|0.68467	0.3004|0.3004	M|M	0.73962|0.73962	2.25|2.25	0.43255|0.43255	D|D	0.995187|0.995187	P;P;P;P|.	0.50819|.	0.807;0.939;0.899;0.594|.	B;P;B;B|.	0.45610|.	0.231;0.487;0.421;0.231|.	T|T	0.69580|0.69580	-0.5107|-0.5107	10|5	0.62326|.	D|.	0.03|.	-16.3273|-16.3273	15.5278|15.5278	0.75925|0.75925	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	66;130;130;66|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	G|G	66;130;66;130;130;130|30	ENSP00000383814:E66G;ENSP00000388048:E130G;ENSP00000327363:E66G;ENSP00000294624:E130G;ENSP00000333938:E130G;ENSP00000411902:E130G|.	ENSP00000294624:E130G|.	E|S	+|+	2|1	0|0	NEXN|NEXN	78156488|78156488	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	5.907000|5.907000	0.69908|0.69908	2.320000|2.320000	0.78422|0.78422	0.528000|0.528000	0.53228|0.53228	GAG|AGC		0.378	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		G	78383900	A	G	78383900	3	3	84	1	0	0	0	0	1	0	0	0	10386	304	11	4	403	4	NEXN	1	78383900	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	18571846	78383900	170866721	3	23695										
PTGFR	5737	hgsc.bcm.edu	37	chr1	78958857	78958857	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtcacaaaaccaatatttcaTtctacgaaaattacatccaa	2	10	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:78958857T>C	ENST00000370757.3	+	2	666	c.429T>C	c.(427-429)caT>caC	p.H143H	PTGFR_ENST00000370756.3_Silent_p.H143H|PTGFR_ENST00000370758.1_Silent_p.H143H	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	143					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	CAATATTTCATTCTACGAAAA	0.418																																																0			1											163	157	159					1																	78958857		2203	4300	6503	78731445	SO:0001819	synonymous_variant	5737			AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.429T>C	1.37:g.78958857T>C			78731445	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	37	CCDS686.1																																																																																				0.418	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78958857	T	C	78958857	2	2	84	1	0	0	0	0	0	0	0	1	12784	1490	52	4		4	PTGFR	1	78958857	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	574957	78958857	170291764	4	23696										
RORC	6097	hgsc.bcm.edu	37	chr1	151789209	151789209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gcatcggtttcggctggtgcGgtcgatggggcagttctgct	17	9	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:151789209G>A	ENST00000318247.6	-	4	336	c.229C>T	c.(229-231)Cgc>Tgc	p.R77C	RORC_ENST00000392697.3_Missense_Mutation_p.R131C|RORC_ENST00000480719.1_5'Flank|RORC_ENST00000356728.6_Missense_Mutation_p.R56C	NM_005060.3	NP_005051.2	P51449	RORG_HUMAN	RAR-related orphan receptor C	77					adipose tissue development (GO:0060612)|cellular response to sterol (GO:0036315)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lymph node development (GO:0048535)|negative regulation of thymocyte apoptotic process (GO:0070244)|Peyer's patch development (GO:0048541)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of fat cell differentiation (GO:0045598)|regulation of gamma-delta T cell differentiation (GO:0045586)|regulation of glucose metabolic process (GO:0010906)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|T cell differentiation in thymus (GO:0033077)|T-helper 17 cell differentiation (GO:0072539)|T-helper cell differentiation (GO:0042093)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CGGCTGGTGCGGTCGATGGGG	0.652																																																0			1											34	28	30					1																	151789209		2201	4300	6501	150055833	SO:0001583	missense	6097			U16997	CCDS1004.1, CCDS30856.1	1q21	2013-01-16			ENSG00000143365	ENSG00000143365		"Nuclear hormone receptors"	10260	protein-coding gene	gene with protein product		602943				7811290	Standard	NM_005060		Approved	RZRG, RORG, NR1F3, TOR	uc001ezh.3	P51449	OTTHUMG00000013053	ENST00000318247.6:c.229C>T	1.37:g.151789209G>A	ENSP00000327025:p.Arg77Cys		150055833	Q5SZR9|Q8N5V7|Q8NCY8	Missense_Mutation	SNP	ENST00000318247.6	37	CCDS1004.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429552	0.83776	.	.	ENSG00000143365	ENST00000356728;ENST00000392697;ENST00000318247	D;D;D	0.97665	-4.48;-4.48;-4.48	5.24	5.24	0.73138	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.64402	U	0.000008	D	0.98308	0.9439	M	0.89353	3.025	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.983;0.999;1.0;1.0	D	0.99153	1.0859	10	0.87932	D	0	.	11.4353	0.50064	0.0:0.0:0.8198:0.1802	.	77;131;77;56	B6ZGS6;B4DPR1;P51449;F1D8P6	.;.;RORG_HUMAN;.	C	56;131;77	ENSP00000349164:R56C;ENSP00000376461:R131C;ENSP00000327025:R77C	ENSP00000327025:R77C	R	-	1	0	RORC	150055833	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.480000	0.66820	2.436000	0.82500	0.563000	0.77884	CGC		0.652	RORC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036626.1			A	151789209	G	A	151789209	3	1	84	1	0	0	0	0	1	0	0	0	13567	1116	39	1	1359	1	RORC	1	151789209	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	72830352	151789209	97461412	5	23697										
FLG	2312	hgsc.bcm.edu	37	chr1	152277299	152277299	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agcctgtccatggcctgacaCtgactgtgtgtctgactctt	10	12	2	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:152277299C>G	ENST00000368799.1	-	3	10098	c.10063G>C	c.(10063-10065)Gtg>Ctg	p.V3355L	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3355	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGCCTGACACTGACTGTGTG	0.567									Ichthyosis																																							0			1											355	358	357					1																	152277299		2203	4300	6503	150543923	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10063G>C	1.37:g.152277299C>G	ENSP00000357789:p.Val3355Leu		150543923	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.835906	0.32421	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00801	5.68	3.92	0.711	0.18162	.	.	.	.	.	T	0.00637	0.0021	M	0.79805	2.47	0.09310	N	1	B	0.30146	0.27	B	0.32533	0.147	T	0.37526	-0.9702	9	0.41790	T	0.15	0.1891	7.0783	0.25217	0.1818:0.4831:0.3351:0.0	.	3355	P20930	FILA_HUMAN	L	3355;293	ENSP00000357789:V3355L	ENSP00000357786:V293L	V	-	1	0	FLG	150543923	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.105000	0.10907	0.048000	0.15891	0.454000	0.30748	GTG		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152277299	C	G	152277299	3	3	84	1	0	0	0	0	1	0	0	0	5941	565	20	5	2126	5	FLG	1	152277299	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	488090	152277299	96973322	6	23698										
INSRR	3645	hgsc.bcm.edu	37	chr1	156823762	156823762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gctcctggttcttctccacaCgcacagccccacgcagcacg	8	19	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:156823762C>T	ENST00000368195.3	-	2	815	c.419G>A	c.(418-420)cGt>cAt	p.R140H	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	140					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTTCTCCACACGCACAGCCCC	0.627																																																0			1											60	54	56					1																	156823762		2203	4300	6503	155090386	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.419G>A	1.37:g.156823762C>T	ENSP00000357178:p.Arg140His		155090386	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919867	0.92249	.	.	ENSG00000027644	ENST00000368195	T	0.80123	-1.34	5.06	5.06	0.68205	EGF receptor, L domain (1);	0.000000	0.48767	D	0.000164	D	0.88362	0.6416	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.89995	0.4110	9	0.87932	D	0	.	15.916	0.79517	0.0:1.0:0.0:0.0	.	140	P14616	INSRR_HUMAN	H	140	ENSP00000357178:R140H	ENSP00000357178:R140H	R	-	2	0	INSRR	155090386	1.000000	0.71417	0.949000	0.38748	0.989000	0.77384	7.811000	0.86092	2.367000	0.80283	0.557000	0.71058	CGT		0.627	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156823762	C	T	156823762	3	4	84	1	0	0	0	0	1	0	0	0	7795	536	19	1	3557	1	INSRR	1	156823762	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	4546463	156823762	92426859	7	23699										
CD1A	909	hgsc.bcm.edu	37	chr1	158226761	158226761	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atgggacatggtatctccgcGcaaccctggaggtggccgct	14	12	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:158226761G>A	ENST00000289429.5	+	4	1323	c.790G>A	c.(790-792)Gca>Aca	p.A264T		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	264	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.A264T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	GTATCTCCGCGCAACCCTGGA	0.627																																																1	Substitution - Missense(1)	large_intestine(1)	1											91	84	87					1																	158226761		2203	4300	6503	156493385	SO:0001583	missense	913			M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.790G>A	1.37:g.158226761G>A	ENSP00000289429:p.Ala264Thr		156493385	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	37	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.349793	0.41599	.	.	ENSG00000158477	ENST00000289429	T	0.02863	4.13	3.84	0.883	0.19177	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	1.471120	0.04702	N	0.416033	T	0.03348	0.0097	M	0.65498	2.005	0.09310	N	1	D	0.54964	0.969	P	0.54238	0.746	T	0.35847	-0.9772	10	0.59425	D	0.04	-0.5712	6.7352	0.23405	0.2614:0.0:0.7386:0.0	.	264	P06126	CD1A_HUMAN	T	264	ENSP00000289429:A264T	ENSP00000289429:A264T	A	+	1	0	CD1A	156493385	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.065000	0.11617	0.080000	0.16959	0.491000	0.48974	GCA		0.627	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		A	158226761	G	A	158226761	3	1	84	1	0	0	0	0	1	0	0	0	2980	1087	38	1	804	1	CD1A	1	158226761	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	1402999	158226761	91023860	8	23700										
DPT	1805	hgsc.bcm.edu	37	chr1	168683528	168683529	+	Missense_Mutation	DNP	TC	TC	AA													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actcccgatccagcactgacTcgaagtagcggctctggaat					rs143369045	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T|C	T|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:168683528_168683529TC>AA	ENST00000367817.3	-	2	450_451	c.361_362GA>TT	c.(361-363)GAg>TTg	p.E121L		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	121	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.E121Q(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					CAGCACTGACTCGAAGTAGCGG	0.54																																																1	Substitution - Missense(1)	ovary(1)	1																																								166950152|166950153	SO:0001583	missense	1805			BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.361_362delinsAA	1.37:g.168683528_168683529delinsAA	ENSP00000356791:p.Glu121Leu		166950152|166950153	A8K981|Q8N4R2|Q9UIX8	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000367817.3	37	CCDS1275.1																																																																																				0.54	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937		AA	168683529	TC	AA	168683528	3	1	84	1	0	0	0	0	1	0	0	0	4750	1551	54	5	255	5	DPT	1	168683528	Missense_Mutation	DNP	TC	TCGA-AH-6643-01A-11D-1826-10	10456767	168683528	80567093	9	23701										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173545824	173545824	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	taattacaagttcgatcttcGgtttaaaagttaaagaatct	6	5	2	1	rs540891244		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:173545824G>T	ENST00000367714.3	-	8	1300	c.878C>A	c.(877-879)cCg>cAg	p.P293Q	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Missense_Mutation_p.P191Q|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	293					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TTCGATCTTCGGTTTAAAAGT	0.398																																																0			1											75	74	74					1																	173545824		2203	4300	6503	171812447	SO:0001583	missense	284525			AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.878C>A	1.37:g.173545824G>T	ENSP00000356687:p.Pro293Gln		171812447	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.986817	0.53934	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.19669	2.13;2.13	5.48	5.48	0.80851	Cation/H+ exchanger (1);	0.112631	0.39985	N	0.001220	T	0.32466	0.0830	M	0.63843	1.955	0.29726	N	0.838259	D	0.76494	0.999	D	0.76071	0.987	T	0.07121	-1.0789	10	0.54805	T	0.06	-7.2997	14.8871	0.70579	0.0:0.0:1.0:0.0	.	293	Q5TAH2	S9A11_HUMAN	Q	293;191	ENSP00000356687:P293Q;ENSP00000445437:P191Q	ENSP00000356687:P293Q	P	-	2	0	SLC9A11	171812447	0.998000	0.40836	0.932000	0.37286	0.323000	0.28346	4.334000	0.59291	2.572000	0.86782	0.655000	0.94253	CCG		0.398	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173545824	G	T	173545824	3	4	84	1	0	0	0	0	1	0	0	0	14748	1116	39	2	2580	2	SLC9A11	1	173545824	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	4862296	173545824	75704797	10	23702										
ELF3	1999	hgsc.bcm.edu	37	chr1	201983018	201983019	+	Frame_Shift_Ins	INS	-	-	G													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcatccacccggagctcaacINSgagggcctcatgaagtggga					rs149307595		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:201983018_201983019insG	ENST00000359651.3	+	7	4059_4060	c.867_868insG	c.(868-870)gagfs	p.E290fs	ELF3_ENST00000367283.3_Frame_Shift_Ins_p.E290fs|ELF3_ENST00000367284.5_Frame_Shift_Ins_p.E290fs|RP11-510N19.5_ENST00000504773.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CGGAGCTCAACGAGGGCCTCAT	0.584																																																0			1																																								200249642	SO:0001589	frameshift_variant	1999			AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.868dupG	1.37:g.201983019_201983019dupG	ENSP00000352673:p.Glu290fs		200249641		Frame_Shift_Ins	INS	ENST00000359651.3	37	CCDS1419.1																																																																																				0.584	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		G	201983019	-	G	201983018	7	5	84	1	0	1	1	0	0	0	0	0	5068	535	19	0	893	0	ELF3	1	201983018	Frame_Shift_Ins	INS	-	TCGA-AH-6643-01A-11D-1826-10	28437194	201983018	47267603	11	23703										
CENPF	1063	hgsc.bcm.edu	37	chr1	214795474	214795474	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cgcctgcaaggacatgaaaaAgaaatgaaaggccaagtgaa	11	7	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:214795474A>G	ENST00000366955.3	+	7	1086	c.918A>G	c.(916-918)aaA>aaG	p.K306K		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.K306K(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GACATGAAAAAGAAATGAAAG	0.343																																					Colon(80;575 1284 11000 14801 43496)											1	Substitution - coding silent(1)	ovary(1)	1											102	106	105					1																	214795474		2203	4300	6503	212862097	SO:0001819	synonymous_variant	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.918A>G	1.37:g.214795474A>G			212862097	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.343	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214795474	A	G	214795474	2	3	84	1	0	0	0	0	0	0	0	1	3237	69	3	4		4	CENPF	1	214795474	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	12812456	214795474	34455147	12	23704										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228526606	228526606	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aggccttcgtggaggagctgCagttcctgcagagccaccac	13	13	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:228526606C>T	ENST00000422127.1	+	69	17181	c.17137C>T	c.(17137-17139)Cag>Tag	p.Q5713*	OBSCN_ENST00000570156.2_Nonsense_Mutation_p.Q6670*|OBSCN_ENST00000366707.4_Nonsense_Mutation_p.Q3347*|OBSCN_ENST00000284548.11_Nonsense_Mutation_p.Q5713*|OBSCN_ENST00000366709.4_Nonsense_Mutation_p.Q2832*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5713	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.Q6295*(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGAGGAGCTGCAGTTCCTGCA	0.652																																																1	Substitution - Nonsense(1)	breast(1)	1											14	17	16					1																	228526606		1973	4029	6002	226593229	SO:0001587	stop_gained	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17137C>T	1.37:g.228526606C>T	ENSP00000409493:p.Gln5713*		226593229	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	64|64	81.266435|81.266435	0.99994|0.99994	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|.	.|.	.|.	4.97|4.97	3.99|3.99	0.46301|0.46301	.|.	.|0.469539	.|0.21692	.|N	.|0.070550	T|.	0.74291|.	0.3697|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.81152|.	-0.1063|.	3|.	.|0.66056	.|D	.|0.02	.|.	15.9294|15.9294	0.79648|0.79648	0.144:0.856:0.0:0.0|0.144:0.856:0.0:0.0	.|.	.|.	.|.	.|.	V|X	328|5713;5713;3347;2832	.|.	.|ENSP00000284548:Q5713X	A|Q	+|+	2|1	0|0	OBSCN|OBSCN	226593229|226593229	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	0.640000|0.640000	0.24705|0.24705	2.597000|2.597000	0.87782|0.87782	0.491000|0.491000	0.48974|0.48974	GCA|CAG		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228526606	C	T	228526606	4	4	84	1	0	0	0	0	0	1	0	0	10843	711	25	3	17407	3	OBSCN	1	228526606	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	13731132	228526606	20724015	13	23705										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231342439	231342439	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actttgtgtaccatcgacggTcttcacttcaacagcaccta	6	13	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:231342439T>C	ENST00000366653.5	+	7	1722	c.1722T>C	c.(1720-1722)ggT>ggC	p.G574G	TRIM67_ENST00000366652.2_Silent_p.G574G|TRIM67_ENST00000449018.3_Silent_p.G512G|TRIM67_ENST00000444294.3_Silent_p.G572G			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	574	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				CCATCGACGGTCTTCACTTCA	0.507																																																0			1											79	86	84					1																	231342439		2069	4223	6292	229409062	SO:0001819	synonymous_variant	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1722T>C	1.37:g.231342439T>C			229409062	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																				0.507	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		C	231342439	T	C	231342439	2	2	84	1	0	0	0	0	0	0	0	1	16580	1654	58	4		4	TRIM67	1	231342439	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	2815833	231342439	17908182	14	23706										
ACTN2	88	hgsc.bcm.edu	37	chr1	236850015	236850015	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtgcagtacaactacgtgtaCgacgaggatgagtacatgat	12	7	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:236850015C>G	ENST00000366578.4	+	1	208	c.42C>G	c.(40-42)taC>taG	p.Y14*	ACTN2_ENST00000542672.1_Nonsense_Mutation_p.Y14*|ACTN2_ENST00000492634.1_3'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	14	Actin-binding.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	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)			ACTACGTGTACGACGAGGATG	0.672																																																0			1											57	51	53					1																	236850015		2203	4300	6503	234916638	SO:0001587	stop_gained	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.42C>G	1.37:g.236850015C>G	ENSP00000355537:p.Tyr14*		234916638	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Nonsense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	C	39	7.600613	0.98384	.	.	ENSG00000077522	ENST00000542672;ENST00000366578	.	.	.	3.74	2.77	0.32553	.	0.615537	0.16663	N	0.204709	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.7388	0.28829	0.0:0.7504:0.0:0.2496	.	.	.	.	X	14	.	ENSP00000355537:Y14X	Y	+	3	2	ACTN2	234916638	0.662000	0.27439	0.991000	0.47740	0.984000	0.73092	-0.254000	0.08781	0.687000	0.31509	0.407000	0.27541	TAC		0.672	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		G	236850015	C	G	236850015	4	3	84	1	0	0	0	0	0	1	0	0	205	547	19	5	44	5	ACTN2	1	236850015	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	5507576	236850015	12400606	15	23707										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524965	248524966	+	Frame_Shift_Del	DEL	CA	CA	-													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cttcagacaatccaaacatcCaatggccaatatcacctgga					rs561405021	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr1:248524965_248524966delCA	ENST00000366475.1	+	1	83_84	c.83_84delCA	c.(82-84)ccafs	p.P28fs		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCAAACATCCAATGGCCAATA	0.5														146	0.0291534	0	0.0187	5008	,	,		16475	0.0645		0.0099	False		,,,				2504	0.0593															0			1																																								246591589	SO:0001589	frameshift_variant	127074			BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.83_84delCA	1.37:g.248524965_248524966delCA	ENSP00000355431:p.Pro28fs		246591588	Q6IEZ8	Frame_Shift_Del	DEL	ENST00000366475.1	37	CCDS31113.1																																																																																				0.5	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		-	248524966	CA	-	248524965	7	5	84	1	0	1	0	1	0	0	0	0	11058	594	21	0	85	0	OR2T4	1	248524965	Frame_Shift_Del	DEL	CA	TCGA-AH-6643-01A-11D-1826-10	11674950	248524965	725656	16	23708										
APOB	338	hgsc.bcm.edu	37	chr2	21229068	21229068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctcccagagggaatatatgcGttggagtgtggcttctccag	13	9	1	1	rs12713559		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:21229068G>A	ENST00000233242.1	-	26	10799	c.10672C>T	c.(10672-10674)Cgc>Tgc	p.R3558C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3558			R -> C (in FDB; dbSNP:rs12713559). {ECO:0000269|PubMed:7883971, ECO:0000269|PubMed:9259199}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATATATGCGTTGGAGTGTG	0.463													G|||	1	0.000199681	0	0.0014	5008	,	,		20702	0		0	False		,,,				2504	0															0			2	GRCh37	CM950076	APOB	M	rs12713559	G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	67	69	68	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	10672	5.8	0.9	2	dbSNP_126	68	8,8592	7.1+/-27.0	0,8,4292	yes	missense	APOB	NM_000384.2	180	0,11,6492	AA,AG,GG		0.093,0.0681,0.0846	probably-damaging	3558/4564	21229068	11,12995	2203	4300	6503	21082573	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10672C>T	2.37:g.21229068G>A	ENSP00000233242:p.Arg3558Cys		21082573	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	22.5	4.304485	0.81136	6.81E-4	9.3E-4	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.79845	-1.31	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000016	D	0.90480	0.7018	M	0.77616	2.38	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90681	0.4605	9	0.87932	D	0	.	20.1731	0.98165	0.0:0.0:1.0:0.0	rs12713559;rs17241062;rs52821409;rs58474560;rs12713559	3558	P04114	APOB_HUMAN	C	3558	ENSP00000233242:R3558C	ENSP00000233242:R3558C	R	-	1	0	APOB	21082573	1.000000	0.71417	0.933000	0.37362	0.533000	0.34776	7.933000	0.87642	2.768000	0.95171	0.655000	0.94253	CGC		0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21229068	G	A	21229068	3	1	84	1	0	0	0	0	1	0	0	0	785	1145	40	1	3035	1	APOB	2	21229068	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		21229068	221970305	17	23709										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25982386	25982386	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgggagtagtaaaagcagtcGttgctggcaatctccaggaa	13	7	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:25982386G>A	ENST00000435504.4	-	9	1197	c.904C>T	c.(904-906)Cga>Tga	p.R302*	ASXL2_ENST00000336112.4_Nonsense_Mutation_p.R274*|ASXL2_ENST00000404843.1_Nonsense_Mutation_p.R42*|ASXL2_ENST00000272341.4_Nonsense_Mutation_p.R42*			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	302					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAAGCAGTCGTTGCTGGCAA	0.413																																																0			2											196	185	188					2																	25982386		1916	4142	6058	25835890	SO:0001587	stop_gained	55252					2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.904C>T	2.37:g.25982386G>A	ENSP00000391447:p.Arg302*		25835890	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Nonsense_Mutation	SNP	ENST00000435504.4	37		.	.	.	.	.	.	.	.	.	.	G	45	11.879899	0.99613	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	.	.	.	5.73	3.81	0.43845	.	0.068975	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.4682	13.4983	0.61438	0.0:0.0:0.7167:0.2833	.	.	.	.	X	302;274;42;42	.	ENSP00000272341:R42X	R	-	1	2	ASXL2	25835890	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	1.831000	0.39141	1.407000	0.46875	0.650000	0.86243	CGA		0.413	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		A	25982386	G	A	25982386	4	1	84	1	0	0	0	0	0	1	0	0	1068	1153	40	1	3423	1	ASXL2	2	25982386	Nonsense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	4753318	25982386	217216987	18	23710										
ALK	238	hgsc.bcm.edu	37	chr2	29940447	29940447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attaaacatatacttaccatAtcggctgcgatgagacagga	8	8	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:29940447A>G	ENST00000389048.3	-	2	1690	c.784T>C	c.(784-786)Tat>Cat	p.Y262H	ALK_ENST00000431873.1_Missense_Mutation_p.Y262H	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	262					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TACTTACCATATCGGCTGCGA	0.398			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	0			2											103	96	99					2																	29940447		2203	4300	6503	29793951	SO:0001583	missense	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.784T>C	2.37:g.29940447A>G	ENSP00000373700:p.Tyr262His		29793951	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414367	0.42817	.	.	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.10960	4.47;2.82	5.4	5.4	0.78164	Concanavalin A-like lectin/glucanase (1);	.	.	.	.	T	0.07503	0.0189	N	0.24115	0.695	0.30757	N	0.744502	B	0.17852	0.024	B	0.18263	0.021	T	0.14839	-1.0458	8	.	.	.	.	7.8259	0.29315	0.9024:0.0:0.0976:0.0	.	262	Q9UM73	ALK_HUMAN	H	262	ENSP00000373700:Y262H;ENSP00000414027:Y262H	.	Y	-	1	0	ALK	29793951	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	3.832000	0.55783	2.163000	0.67991	0.533000	0.62120	TAT		0.398	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29940447	A	G	29940447	3	3	84	1	0	0	0	0	1	0	0	0	525	449	16	4	4190	4	ALK	2	29940447	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	3958061	29940447	213258926	19	23711										
PUS10	150962	hgsc.bcm.edu	37	chr2	61180216	61180216	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctgtaggtctttgtcttttcTtcttcaccttctttcatatg	5	10	7	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:61180216T>C	ENST00000316752.6	-	15	1485	c.1224A>G	c.(1222-1224)gaA>gaG	p.E408E	PUS10_ENST00000407787.1_Silent_p.E408E	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	408					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TTGTCTTTTCTTCTTCACCTT	0.318																																																0			2											286	268	274					2																	61180216		2203	4300	6503	61033720	SO:0001819	synonymous_variant	150962			AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.1224A>G	2.37:g.61180216T>C			61033720	Q5JPJ5|Q96MI8	Silent	SNP	ENST00000316752.6	37	CCDS1865.1																																																																																				0.318	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		C	61180216	T	C	61180216	2	2	84	1	0	0	0	0	0	0	0	1	12868	1606	56	4		4	PUS10	2	61180216	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	31239769	61180216	182019157	20	23712										
BMP10	27302	hgsc.bcm.edu	37	chr2	69093516	69093517	+	Missense_Mutation	DNP	TT	TT	CC													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctttctccctcattatccccTttgctctccagcacttcaaa							TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:69093516_69093517TT>CC	ENST00000295379.1	-	2	679_680	c.521_522AA>GG	c.(520-522)aAA>aGG	p.K174R		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	174					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)	p.K174N(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						CATTATCCCCTTTGCTCTCCAG	0.446																																																1	Substitution - Missense(1)	ovary(1)	2																																								68947020|68947021	SO:0001583	missense	27302			AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"Bone morphogenetic proteins", "Endogenous ligands"	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.521_522delinsCC	2.37:g.69093516_69093517delinsCC	ENSP00000295379:p.Lys174Arg		68947020|68947021	Q53R17|Q6NTE0	Silent|Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1																																																																																				0.446	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482		CC	69093517	TT	CC	69093516	3	2	84	1	0	0	0	0	1	0	0	0	1458	1606	56	4	756	4	BMP10	2	69093516	Missense_Mutation	DNP	TT	TCGA-AH-6643-01A-11D-1826-10	7913300	69093516	174105857	21	23713										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70081985	70081985	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tatggcctttcttgaaactgAacaaggaaaaccatttgtgt	8	7	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:70081985A>G	ENST00000282570.3	+	9	1216	c.965A>G	c.(964-966)gAa>gGa	p.E322G		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	322					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						CTTGAAACTGAACAAGGAAAA	0.318																																																0			2											76	78	77					2																	70081985		2203	4293	6496	69935489	SO:0001583	missense	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.965A>G	2.37:g.70081985A>G	ENSP00000282570:p.Glu322Gly		69935489	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	37	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.212980	0.58452	.	.	ENSG00000087338	ENST00000282570	T	0.56941	0.43	4.87	4.87	0.63330	.	0.166067	0.52532	D	0.000070	T	0.50137	0.1598	L	0.59436	1.845	0.52501	D	0.999959	B	0.27932	0.194	B	0.29524	0.103	T	0.54227	-0.8325	10	0.62326	D	0.03	-7.5524	12.459	0.55721	1.0:0.0:0.0:0.0	.	322	Q96IK5	GMCL1_HUMAN	G	322	ENSP00000282570:E322G	ENSP00000282570:E322G	E	+	2	0	GMCL1	69935489	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.641000	0.61375	2.042000	0.60477	0.528000	0.53228	GAA		0.318	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70081985	A	G	70081985	3	3	84	1	0	0	0	0	1	0	0	0	6505	246	9	4	999	4	GMCL1	2	70081985	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	988469	70081985	173117388	22	23714										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043820	71043820	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtatttgccgtttccaaactGgcattcaacatctgaatttc	6	10	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:71043820G>A	ENST00000272367.2	-	4	769	c.693C>T	c.(691-693)gcC>gcT	p.A231A	CLEC4F_ENST00000426626.1_Silent_p.A231A	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	231					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TTTCCAAACTGGCATTCAACA	0.403																																					Colon(107;10 2157 6841 26035)											0			2											79	76	77					2																	71043820		2203	4300	6503	70897328	SO:0001819	synonymous_variant	165530			AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.693C>T	2.37:g.71043820G>A			70897328	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																				0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71043820	G	A	71043820	2	1	84	1	0	0	0	0	0	0	0	1	3522	1335	47	3		3	CLEC4F	2	71043820	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	961835	71043820	172155553	23	23715										
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74531799	74531799	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tggaagcccaatgtggatagGagggcattctgtggacacgg	16	7	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:74531799G>T	ENST00000377634.4	-	7	487	c.88C>A	c.(88-90)Cct>Act	p.P30T	SLC4A5_ENST00000359484.4_Intron|SLC4A5_ENST00000423644.1_Missense_Mutation_p.P30T|SLC4A5_ENST00000357822.5_Missense_Mutation_p.P30T|SLC4A5_ENST00000483195.1_Intron|SLC4A5_ENST00000394019.2_Missense_Mutation_p.P30T|SLC4A5_ENST00000346834.4_Missense_Mutation_p.P30T|SLC4A5_ENST00000377632.1_Missense_Mutation_p.P30T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000358683.4_Intron					solute carrier family 4 (sodium bicarbonate cotransporter), member 5									p.P30T(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ATGTGGATAGGAGGGCATTCT	0.488																																																1	Substitution - Missense(1)	ovary(1)	2											62	62	62					2																	74531799		2203	4300	6503	74385307	SO:0001583	missense	57835			AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"Solute carriers"	18168	protein-coding gene	gene with protein product		606757	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.88C>A	2.37:g.74531799G>T	ENSP00000366861:p.Pro30Thr		74385307		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	G	2.559	-0.302379	0.05495	.	.	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000423644;ENST00000357822;ENST00000377632;ENST00000377634;ENST00000425249;ENST00000444570;ENST00000436454	T;T;T;T;T;T;T	0.75589	-0.95;-0.76;-0.4;-0.95;-0.76;-0.95;-0.12	4.93	1.21	0.21127	.	0.187555	0.47455	D	0.000237	T	0.29491	0.0735	N	0.00462	-1.47	0.09310	N	0.999999	B;B;B;B	0.14012	0.002;0.002;0.009;0.002	B;B;B;B	0.13407	0.006;0.004;0.009;0.006	T	0.43180	-0.9407	10	0.02654	T	1	.	3.818	0.08824	0.6112:0.1869:0.2018:0.0	.	30;30;30;30	Q9BY07-4;E7EQT3;Q9BY07;Q9BY07-3	.;.;S4A5_HUMAN;.	T	30	ENSP00000377587:P30T;ENSP00000251768:P30T;ENSP00000395804:P30T;ENSP00000350475:P30T;ENSP00000366859:P30T;ENSP00000366861:P30T;ENSP00000405678:P30T	ENSP00000251768:P30T	P	-	1	0	SLC4A5	74385307	0.957000	0.32711	0.523000	0.27875	0.052000	0.14988	1.080000	0.30779	0.115000	0.18071	-0.484000	0.04775	CCT		0.488	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3			T	74531799	G	T	74531799	3	4	84	1	0	0	0	0	1	0	0	0	14694	1174	41	2	3425	2	SLC4A5	2	74531799	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	3487979	74531799	168667574	24	23716										
DDX18	8886	hgsc.bcm.edu	37	chr2	118579562	118579562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atgggtggcagtaacagatcTgctgaagcacagaaacttgg	13	7	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:118579562T>C	ENST00000263239.2	+	6	1004	c.876T>C	c.(874-876)tcT>tcC	p.S292S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	292	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GTAACAGATCTGCTGAAGCAC	0.473																																																0			2											133	125	128					2																	118579562		2203	4300	6503	118296032	SO:0001819	synonymous_variant	8886			X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.876T>C	2.37:g.118579562T>C			118296032	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Silent	SNP	ENST00000263239.2	37	CCDS2120.1																																																																																				0.473	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		C	118579562	T	C	118579562	2	2	84	1	0	0	0	0	0	0	0	1	4351	1567	55	4		4	DDX18	2	118579562	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	44047763	118579562	124619811	25	23717										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179170934	179170934	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gagttcagatgagaagggcaTttcccctgctcataaaacat	9	9	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:179170934T>C	ENST00000190611.4	+	3	399	c.23T>C	c.(22-24)aTt>aCt	p.I8T	OSBPL6_ENST00000409045.3_Missense_Mutation_p.I8T|OSBPL6_ENST00000409631.1_Missense_Mutation_p.I8T|OSBPL6_ENST00000392505.2_Missense_Mutation_p.I8T|OSBPL6_ENST00000357080.4_Missense_Mutation_p.I8T|OSBPL6_ENST00000359685.3_Missense_Mutation_p.I8T	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	8					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			GAGAAGGGCATTTCCCCTGCT	0.448																																																0			2											163	138	147					2																	179170934		2203	4300	6503	178879180	SO:0001583	missense	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.23T>C	2.37:g.179170934T>C	ENSP00000190611:p.Ile8Thr		178879180	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963456	0.53507	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.87	5.87	0.94306	.	0.505476	0.16012	U	0.233763	T	0.27313	0.0670	N	0.03608	-0.345	0.41354	D	0.987381	B;B;B;B;B	0.22683	0.03;0.02;0.073;0.018;0.073	B;B;B;B;B	0.21917	0.037;0.034;0.033;0.01;0.025	T	0.17745	-1.0359	10	0.18276	T	0.48	-6.8914	15.5573	0.76208	0.0:0.0:0.0:1.0	.	8;8;8;8;8	Q9BZF3-4;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;OSBL6_HUMAN;.	T	8	ENSP00000376293:I8T;ENSP00000352713:I8T;ENSP00000349591:I8T;ENSP00000387248:I8T;ENSP00000190611:I8T;ENSP00000386885:I8T	ENSP00000190611:I8T	I	+	2	0	OSBPL6	178879180	1.000000	0.71417	0.935000	0.37517	0.979000	0.70002	3.877000	0.56123	2.371000	0.80710	0.533000	0.62120	ATT		0.448	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		C	179170934	T	C	179170934	3	2	84	1	0	0	0	0	1	0	0	0	11312	1493	52	4	25	4	OSBPL6	2	179170934	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	60591372	179170934	64028439	26	23718										
TTN	7273	hgsc.bcm.edu	37	chr2	179438325	179438325	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtgacctttagctttgttacTtggacttctgaggctacatt	9	8	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:179438325T>C	ENST00000591111.1	-	276	67835	c.67611A>G	c.(67609-67611)caA>caG	p.Q22537Q	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.Q15238Q|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Silent_p.Q24178Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Q15305Q|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342992.6_Silent_p.Q21610Q|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Silent_p.Q15113Q|TTN-AS1_ENST00000591332.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22537	Fibronectin type-III 63. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> H (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Q15113H(2)|p.Q15305H(1)|p.Q21608H(1)|p.Q15238H(1)|p.Q21610H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTTGTTACTTGGACTTCTG	0.423																																																6	Substitution - Missense(6)	lung(5)|stomach(1)	2											281	277	278					2																	179438325		1937	4134	6071	179146571	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67611A>G	2.37:g.179438325T>C			179146571	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179438325	T	C	179438325	2	2	84	1	0	0	0	0	0	0	0	1	16775	1606	56	4		4	TTN	2	179438325	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	267391	179438325	63761048	27	23719										
TTN	7273	hgsc.bcm.edu	37	chr2	179474937	179474937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tatgagatccttcacagtccAtgacagtttgttctcaccag	7	11	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:179474937A>G	ENST00000591111.1	-	221	46617	c.46393T>C	c.(46393-46395)Tgg>Cgg	p.W15465R	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.W8166R|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.W17106R|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.W8233R|TTN_ENST00000342992.6_Missense_Mutation_p.W14538R|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.W8041R			Q8WZ42	TITIN_HUMAN	titin	15465	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCACAGTCCATGACAGTTTG	0.423																																																0			2											183	180	181					2																	179474937		1943	4140	6083	179183182	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46393T>C	2.37:g.179474937A>G	ENSP00000465570:p.Trp15465Arg		179183182	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.26	2.182687	0.38511	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.48	5.48	0.80851	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70272	0.3205	M	0.63843	1.955	0.54753	D	0.999988	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.73672	-0.3909	9	0.87932	D	0	.	15.5783	0.76410	1.0:0.0:0.0:0.0	.	8041;8166;8233;15465	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	14538;8041;8233;8166;8041	ENSP00000343764:W14538R;ENSP00000434586:W8041R;ENSP00000340554:W8233R;ENSP00000352154:W8166R	ENSP00000340554:W8233R	W	-	1	0	TTN	179183182	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	7.384000	0.79751	2.081000	0.62600	0.533000	0.62120	TGG		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179474937	A	G	179474937	3	3	84	1	0	0	0	0	1	0	0	0	16775	217	8	4	56745	4	TTN	2	179474937	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	36612	179474937	63724436	28	23720										
TTN	7273	hgsc.bcm.edu	37	chr2	179623847	179623847	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcaaattgagtcattctaaaGaaccgagatggcttgatttt	8	6	3	4	rs267599082		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:179623847G>T	ENST00000591111.1	-	44	10391	c.10167C>A	c.(10165-10167)ttC>ttA	p.F3389L	TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.F3343L|TTN_ENST00000589042.1_Missense_Mutation_p.F3389L|TTN_ENST00000360870.5_Missense_Mutation_p.F3389L|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.F3343L|TTN_ENST00000342992.6_Missense_Mutation_p.F3389L|TTN_ENST00000460472.2_Missense_Mutation_p.F3343L			Q8WZ42	TITIN_HUMAN	titin	13707	Ig-like 20.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCATTCTAAAGAACCGAGATG	0.383																																																0			2											136	119	124					2																	179623847		2203	4300	6503	179332092	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10167C>A	2.37:g.179623847G>T	ENSP00000465570:p.Phe3389Leu		179332092	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	16.10	3.028214	0.54790	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.92	5.92	0.95590	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76933	0.4057	L	0.58510	1.815	0.31244	N	0.694855	P;P;P;P;D	0.61697	0.9;0.9;0.9;0.9;0.99	P;P;P;P;P	0.59424	0.493;0.493;0.493;0.493;0.857	T	0.78671	-0.2113	9	0.87932	D	0	.	15.4039	0.74863	0.068:0.0:0.932:0.0	.	3343;3343;3343;3389;3389	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	3389;3343;3343;3343;3343;3389	ENSP00000343764:F3389L;ENSP00000434586:F3343L;ENSP00000340554:F3343L;ENSP00000352154:F3343L;ENSP00000354117:F3389L	ENSP00000340554:F3343L	F	-	3	2	TTN	179332092	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.675000	0.61619	2.804000	0.96469	0.655000	0.94253	TTC		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179623847	G	T	179623847	3	4	84	1	0	0	0	0	1	0	0	0	16775	933	33	2	101097	2	TTN	2	179623847	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	148910	179623847	63575526	29	23721										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207172850	207172850	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aatgttgtggttctgaagtaAgttttgattctgatgaccct	10	5	2	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:207172850A>C	ENST00000374423.3	+	5	3984	c.3598A>C	c.(3598-3600)Agt>Cgt	p.S1200R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1200							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TTCTGAAGTAAGTTTTGATTC	0.423																																																0			2											96	92	93					2																	207172850		1910	4138	6048	206881095	SO:0001583	missense	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3598A>C	2.37:g.207172850A>C	ENSP00000363545:p.Ser1200Arg		206881095	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.881078	0.72294	.	.	ENSG00000204186	ENST00000374423	T	0.55588	0.51	4.1	4.1	0.47936	.	.	.	.	.	T	0.58921	0.2156	L	0.55990	1.75	0.28743	N	0.901869	D	0.59357	0.985	P	0.53360	0.724	T	0.56420	-0.7982	9	0.72032	D	0.01	.	11.4432	0.50109	1.0:0.0:0.0:0.0	.	1200	Q9HCK1	ZDBF2_HUMAN	R	1200	ENSP00000363545:S1200R	ENSP00000363545:S1200R	S	+	1	0	ZDBF2	206881095	1.000000	0.71417	0.965000	0.40720	0.728000	0.41692	3.916000	0.56416	2.074000	0.62210	0.528000	0.53228	AGT		0.423	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207172850	A	C	207172850	3	2	84	1	0	0	0	0	1	0	0	0	17638	72	3	4	3608	4	ZDBF2	2	207172850	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	27549003	207172850	36026523	30	23722										
MAP2	4133	hgsc.bcm.edu	37	chr2	210574917	210574917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccaaccactgccagacctgaAgaatgtcaaatccaaaatcg	6	13	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:210574917A>G	ENST00000360351.4	+	12	5518	c.5012A>G	c.(5011-5013)aAg>aGg	p.K1671R	MAP2_ENST00000199940.6_Missense_Mutation_p.K372R|MAP2_ENST00000447185.1_Missense_Mutation_p.K1667R|MAP2_ENST00000361559.4_Missense_Mutation_p.K315R|MAP2_ENST00000475600.1_3'UTR|MAP2_ENST00000392194.1_Missense_Mutation_p.K315R	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1671					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CCAGACCTGAAGAATGTCAAA	0.463																																					Pancreas(27;423 979 28787 29963)											0			2											71	59	63					2																	210574917		2203	4300	6503	210283162	SO:0001583	missense	10988				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.5012A>G	2.37:g.210574917A>G	ENSP00000353508:p.Lys1671Arg		210283162	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.862074	0.91511	.	.	ENSG00000078018	ENST00000199940;ENST00000360351;ENST00000361559;ENST00000392194;ENST00000447185	D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000013	D	0.97611	0.9217	M	0.80183	2.485	0.80722	D	1	D;D;D;D;B	0.76494	0.999;0.998;0.992;0.999;0.236	D;D;D;D;B	0.87578	0.995;0.994;0.987;0.998;0.444	D	0.98076	1.0401	10	0.56958	D	0.05	-9.5702	15.7792	0.78246	1.0:0.0:0.0:0.0	.	1667;315;316;1671;372	P11137-3;P11137-2;Q59FX9;P11137;Q8IUX2	.;.;.;MAP2_HUMAN;.	R	372;1671;315;315;1667	ENSP00000199940:K372R;ENSP00000353508:K1671R;ENSP00000355290:K315R;ENSP00000376032:K315R;ENSP00000392164:K1667R	ENSP00000199940:K372R	K	+	2	0	MAP2	210283162	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.287000	0.95975	2.129000	0.65627	0.383000	0.25322	AAG		0.463	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210574917	A	G	210574917	3	3	84	1	0	0	0	0	1	0	0	0	9265	72	3	4	5221	4	MAP2	2	210574917	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	3402067	210574917	32624456	31	23723										
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238672329	238672329	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gttggatggaaaacttgaccAagaaggtgatgatgtacaaa	12	4	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr2:238672329A>G	ENST00000392000.4	+	11	2090	c.1973A>G	c.(1972-1974)cAa>cGa	p.Q658R	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.Q602R|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.Q634R	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	658					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		AAACTTGACCAAGAAGGTGAT	0.428																																																0			2											62	61	61					2																	238672329		2203	4300	6503	238337068	SO:0001583	missense	9208			AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.1973A>G	2.37:g.238672329A>G	ENSP00000375857:p.Gln658Arg		238337068	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.691494	0.30052	.	.	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.10099	2.91;2.92;2.92	4.76	-7.13	0.01532	.	2.305150	0.01807	N	0.033222	T	0.08223	0.0205	L	0.47716	1.5	0.09310	N	1	B;B;B	0.16396	0.017;0.01;0.017	B;B;B	0.15052	0.012;0.005;0.012	T	0.36163	-0.9759	10	0.46703	T	0.11	0.004	0.8364	0.01140	0.3659:0.192:0.2707:0.1714	.	602;658;634	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	R	602;634;658	ENSP00000289175:Q602R;ENSP00000244815:Q634R;ENSP00000375857:Q658R	ENSP00000244815:Q634R	Q	+	2	0	LRRFIP1	238337068	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-1.218000	0.02976	-0.717000	0.04955	0.533000	0.62120	CAA		0.428	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		G	238672329	A	G	238672329	3	3	84	1	0	0	0	0	1	0	0	0	9056	130	5	4	2691	4	LRRFIP1	2	238672329	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	28097412	238672329	4527044	32	23724										
LHFPL4	375323	hgsc.bcm.edu	37	chr3	9547828	9547828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cttggccccacacatgtcccGgatggtctcggcatcccagc	10	17	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:9547828G>A	ENST00000287585.6	-	3	751	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W		NM_198560.2	NP_940962.1	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 4	169						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(3)|skin(1)	10	Medulloblastoma(99;0.227)					CACATGTCCCGGATGGTCTCG	0.627																																																0			3											125	105	112					3																	9547828		2203	4300	6503	9522828	SO:0001583	missense	375612			AY278320	CCDS33691.1	3p25.3	2006-06-13			ENSG00000156959	ENSG00000156959			29568	protein-coding gene	gene with protein product		610240				15905332	Standard	NM_198560		Approved		uc003bry.3	Q7Z7J7	OTTHUMG00000155066	ENST00000287585.6:c.466C>T	3.37:g.9547828G>A	ENSP00000287585:p.Arg156Trp		9522828	A1L383|A4D0Q5	Missense_Mutation	SNP	ENST00000287585.6	37	CCDS33691.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880163	0.72294	.	.	ENSG00000156959	ENST00000287585	T	0.74526	-0.85	5.27	4.34	0.51931	.	0.000000	0.64402	U	0.000012	D	0.83899	0.5354	M	0.76838	2.35	0.54753	D	0.999988	D	0.76494	0.999	D	0.65140	0.932	D	0.85834	0.1393	10	0.87932	D	0	-4.0494	12.4244	0.55538	0.0:0.0:0.6634:0.3366	.	156	Q7Z7J7	LHPL4_HUMAN	W	156	ENSP00000287585:R156W	ENSP00000287585:R156W	R	-	1	2	LHFPL4	9522828	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.083000	0.41615	2.488000	0.83962	0.591000	0.81541	CGG		0.627	LHFPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338298.1	NM_198560		A	9547828	G	A	9547828	3	1	84	1	0	0	0	0	1	0	0	0	8790	1115	39	1	285	1	LHFPL4	3	9547828	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		9547828	188474602	33	23725										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14768414	14768414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttgcccctctccagctgaacCgcagaatcagcaacatggac	8	15	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:14768414C>T	ENST00000253697.3	+	11	2025	c.1573C>T	c.(1573-1575)Cgc>Tgc	p.R525C	C3orf20_ENST00000435614.1_Missense_Mutation_p.R403C|C3orf20_ENST00000412910.1_Missense_Mutation_p.R403C	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	525						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCAGCTGAACCGCAGAATCAG	0.532																																																0			3											88	80	83					3																	14768414		2203	4300	6503	14743418	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1573C>T	3.37:g.14768414C>T	ENSP00000253697:p.Arg525Cys		14743418	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801753	0.50315	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.12774	2.65;2.65;2.65	3.94	3.94	0.45596	.	1.301920	0.05136	N	0.493495	T	0.23133	0.0559	L	0.57536	1.79	0.09310	N	0.999999	D;D	0.59767	0.986;0.986	P;P	0.47015	0.534;0.534	T	0.23762	-1.0179	10	0.54805	T	0.06	-10.1533	11.7571	0.51882	0.0:1.0:0.0:0.0	.	403;525	Q8ND61-2;Q8ND61	.;CC020_HUMAN	C	525;403;403	ENSP00000253697:R525C;ENSP00000402933:R403C;ENSP00000396081:R403C	ENSP00000253697:R525C	R	+	1	0	C3orf20	14743418	0.001000	0.12720	0.009000	0.14445	0.004000	0.04260	0.878000	0.28126	2.490000	0.84030	0.491000	0.48974	CGC		0.532	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14768414	C	T	14768414	3	4	84	1	0	0	0	0	1	0	0	0	2219	652	23	1	1607	1	C3orf20	3	14768414	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	5220586	14768414	183254016	34	23726										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15727737	15727737	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atcgaaacttactgtccattTccatcttgaatatccactgc	4	12	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:15727737T>C	ENST00000399451.2	-	19	2320	c.1953A>G	c.(1951-1953)ggA>ggG	p.G651G	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Silent_p.G684G	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	651						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						ACTGTCCATTTCCATCTTGAA	0.373																																																0			3											131	111	117					3																	15727737		1901	4116	6017	15702741	SO:0001819	synonymous_variant	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1953A>G	3.37:g.15727737T>C			15702741	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	37	CCDS46769.1																																																																																				0.373	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15727737	T	C	15727737	2	2	84	1	0	0	0	0	0	0	0	1	656	1770	62	4		4	ANKRD28	3	15727737	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	959323	15727737	182294693	35	23727										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64133061	64133061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctgcagtgacagggggtctaCgtcggctgacagccggttag	16	10	1	2	rs568569832		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:64133061C>T	ENST00000295902.6	-	7	1690	c.1105G>A	c.(1105-1107)Gta>Ata	p.V369I	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.V425I	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	369					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		AGGGGGTCTACGTCGGCTGAC	0.607													C|||	1	0.000199681	0	0.0014	5008	,	,		17392	0		0	False		,,,				2504	0															0			3											89	100	96					3																	64133061		2203	4300	6503	64108101	SO:0001583	missense	166336			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1105G>A	3.37:g.64133061C>T	ENSP00000295902:p.Val369Ile		64108101	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.890172	0.33348	.	.	ENSG00000163637	ENST00000295902	T	0.59364	0.27	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000005	T	0.53530	0.1802	L	0.50333	1.59	0.80722	D	1	B	0.34329	0.449	B	0.26614	0.071	T	0.50939	-0.8768	10	0.39692	T	0.17	-39.3612	20.6634	0.99662	0.0:1.0:0.0:0.0	.	369	Q7Z3G6	PRIC2_HUMAN	I	369	ENSP00000295902:V369I	ENSP00000295902:V369I	V	-	1	0	PRICKLE2	64108101	1.000000	0.71417	0.987000	0.45799	0.002000	0.02628	6.066000	0.71185	2.894000	0.99253	0.655000	0.94253	GTA		0.607	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64133061	C	T	64133061	3	4	84	1	0	0	0	0	1	0	0	0	12521	536	19	1	1437	1	PRICKLE2	3	64133061	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	48405324	64133061	133889369	36	23728										
WDR5B	54554	hgsc.bcm.edu	37	chr3	122133513	122133513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cttgtaatttctgcacaatcTctttagtctgaaggttccaa	6	9	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:122133513T>C	ENST00000330689.4	-	1	1369	c.863A>G	c.(862-864)gAg>gGg	p.E288G	RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	288										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		CTGCACAATCTCTTTAGTCTG	0.393																																																0			3											154	143	147					3																	122133513		2203	4300	6503	123616203	SO:0001583	missense	54554			AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.863A>G	3.37:g.122133513T>C	ENSP00000330381:p.Glu288Gly		123616203	B2RCM9|Q9NUL4	Missense_Mutation	SNP	ENST00000330689.4	37	CCDS3012.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308303	0.81247	.	.	ENSG00000196981	ENST00000330689	T	0.62639	0.01	4.77	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.045885	0.85682	D	0.000000	T	0.60702	0.2289	L	0.61387	1.9	0.80722	D	1	B	0.27932	0.194	B	0.31191	0.125	T	0.64249	-0.6452	10	0.66056	D	0.02	.	12.5914	0.56445	0.0:0.0:0.0:1.0	.	288	Q86VZ2	WDR5B_HUMAN	G	288	ENSP00000330381:E288G	ENSP00000330381:E288G	E	-	2	0	WDR5B	123616203	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.030000	0.76484	2.137000	0.66172	0.459000	0.35465	GAG		0.393	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		C	122133513	T	C	122133513	3	2	84	1	0	0	0	0	1	0	0	0	17349	1551	54	4	133	4	WDR5B	3	122133513	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	58000452	122133513	75888917	37	23729										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670617	134670617	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cggaatggtttttacctcgcTtttcaggattatggagcctg	11	8	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:134670617T>C	ENST00000398015.3	+	3	898	c.528T>C	c.(526-528)gcT>gcC	p.A176A	EPHB1_ENST00000488154.1_Intron	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	176	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						TTTACCTCGCTTTTCAGGATT	0.458																																																0			3											259	248	251					3																	134670617		1915	4136	6051	136153307	SO:0001819	synonymous_variant	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.528T>C	3.37:g.134670617T>C			136153307	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																				0.458	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		C	134670617	T	C	134670617	2	2	84	1	0	0	0	0	0	0	0	1	5187	1596	56	4		4	EPHB1	3	134670617	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	12537104	134670617	63351813	38	23730										
HPS3	84343	hgsc.bcm.edu	37	chr3	148885692	148885692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	taagatagactctgtggtggAaaaaactgttgcctgaactt	10	6	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:148885692A>G	ENST00000296051.2	+	16	2949	c.2809A>G	c.(2809-2811)Aaa>Gaa	p.K937E	HPS3_ENST00000460120.1_Missense_Mutation_p.K772E	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	937					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TCTGTGGTGGAAAAAACTGTT	0.318									Hermansky-Pudlak syndrome																																							0			3											90	96	94					3																	148885692		2203	4299	6502	150368382	SO:0001583	missense	84343	Familial Cancer Database	HPS, HPS1-8	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2809A>G	3.37:g.148885692A>G	ENSP00000296051:p.Lys937Glu		150368382	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.798654	0.50208	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.65916	-0.18;-0.18	5.68	4.54	0.55810	.	0.235751	0.50627	N	0.000103	T	0.57932	0.2087	L	0.47716	1.5	0.80722	D	1	P;P	0.52692	0.955;0.841	P;B	0.45712	0.491;0.341	T	0.57142	-0.7862	10	0.42905	T	0.14	-16.7649	11.2763	0.49168	0.9291:0.0:0.0709:0.0	.	772;937	G5E9V4;Q969F9	.;HPS3_HUMAN	E	937;772	ENSP00000296051:K937E;ENSP00000418230:K772E	ENSP00000296051:K937E	K	+	1	0	HPS3	150368382	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.009000	0.57110	0.996000	0.38943	0.528000	0.53228	AAA		0.318	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		G	148885692	A	G	148885692	3	3	84	1	0	0	0	0	1	0	0	0	7361	247	9	4	2871	4	HPS3	3	148885692	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	14215075	148885692	49136738	39	23731										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155267601	155267601	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctagaattttgcctttcaaaCtttgagggcttggaagctgc	10	8	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:155267601C>T	ENST00000340059.7	-	9	1300	c.1301G>A	c.(1300-1302)aGt>aAt	p.S434N	PLCH1_ENST00000460012.1_Missense_Mutation_p.S416N|PLCH1_ENST00000447496.2_Missense_Mutation_p.S434N|PLCH1_ENST00000334686.6_Missense_Mutation_p.S416N|PLCH1_ENST00000414191.1_Missense_Mutation_p.S416N|PLCH1_ENST00000494598.1_Missense_Mutation_p.S434N	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	434	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GCCTTTCAAACTTTGAGGGCT	0.403																																																0			3											102	97	99					3																	155267601		2203	4300	6503	156750295	SO:0001583	missense	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.1301G>A	3.37:g.155267601C>T	ENSP00000345988:p.Ser434Asn		156750295	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.910276	0.33721	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.37	5.37	0.77165	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.262540	0.48767	D	0.000167	T	0.44519	0.1297	N	0.21448	0.665	0.28124	N	0.930499	B;B;B	0.14012	0.007;0.009;0.002	B;B;B	0.17979	0.011;0.02;0.003	T	0.23190	-1.0195	10	0.17832	T	0.49	.	9.7895	0.40697	0.0:0.8408:0.0:0.1592	.	416;434;434	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	N	434;416;434;434;416;416	ENSP00000419100:S434N;ENSP00000417502:S416N;ENSP00000402759:S434N;ENSP00000345988:S434N;ENSP00000335469:S416N;ENSP00000412977:S416N	ENSP00000335469:S416N	S	-	2	0	PLCH1	156750295	0.976000	0.34144	0.933000	0.37362	0.999000	0.98932	1.581000	0.36558	2.658000	0.90341	0.650000	0.86243	AGT		0.403	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155267601	C	T	155267601	3	4	84	1	0	0	0	0	1	0	0	0	12068	565	20	3	3855	3	PLCH1	3	155267601	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	6381909	155267601	42754829	40	23732										
WDR49	151790	hgsc.bcm.edu	37	chr3	167245795	167245795	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttttgttcttactggagttaAgacagtactcctgaatgaaa	8	6	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:167245795A>C	ENST00000308378.3	-	11	1666	c.1361T>G	c.(1360-1362)cTt>cGt	p.L454R	WDR49_ENST00000453925.2_Intron|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.L279R	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	454										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						ACTGGAGTTAAGACAGTACTC	0.358																																																0			3											112	107	108					3																	167245795		2203	4300	6503	168728489	SO:0001583	missense	151790			AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1361T>G	3.37:g.167245795A>C	ENSP00000311343:p.Leu454Arg		168728489	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506894	0.44558	.	.	ENSG00000174776	ENST00000308378;ENST00000476376	T;T	0.58060	0.36;1.63	5.7	4.55	0.56014	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.461172	0.21899	N	0.067469	T	0.53206	0.1782	M	0.71920	2.185	0.80722	D	1	P	0.50272	0.933	P	0.45037	0.467	T	0.53272	-0.8462	10	0.42905	T	0.14	.	8.745	0.34580	0.9115:0.0:0.0885:0.0	.	454	Q8IV35	WDR49_HUMAN	R	454;279	ENSP00000311343:L454R;ENSP00000420508:L279R	ENSP00000311343:L454R	L	-	2	0	WDR49	168728489	0.999000	0.42202	1.000000	0.80357	0.373000	0.29922	3.597000	0.54031	1.005000	0.39183	0.455000	0.32223	CTT		0.358	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		C	167245795	A	C	167245795	3	2	84	1	0	0	0	0	1	0	0	0	17342	72	3	4	752	4	WDR49	3	167245795	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	11978194	167245795	30776635	41	23733										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936050	178936050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggaaaatgacaaagaacagcTcaaagcaatttctacacgag	8	8	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:178936050T>C	ENST00000263967.3	+	10	1749	c.1592T>C	c.(1591-1593)cTc>cCc	p.L531P		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	531	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.L531P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAAGAACAGCTCAAAGCAATT	0.338		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	breast(1)	3											42	43	42					3																	178936050		1797	4059	5856	180418744	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1592T>C	3.37:g.178936050T>C	ENSP00000263967:p.Leu531Pro		180418744	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.376442	0.82682	.	.	ENSG00000121879	ENST00000263967	T	0.76709	-1.04	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.070144	0.64402	D	0.000016	D	0.90800	0.7111	M	0.93241	3.395	0.80722	D	1	D	0.63880	0.993	D	0.69479	0.964	D	0.93093	0.6501	10	0.87932	D	0	-30.4996	16.1026	0.81194	0.0:0.0:0.0:1.0	.	531	P42336	PK3CA_HUMAN	P	531	ENSP00000263967:L531P	ENSP00000263967:L531P	L	+	2	0	PIK3CA	180418744	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.698000	0.84413	2.198000	0.70561	0.383000	0.25322	CTC		0.338	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178936050	T	C	178936050	3	2	84	1	0	0	0	0	1	0	0	0	11944	1551	54	4	1626	4	PIK3CA	3	178936050	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	11690255	178936050	19086380	42	23734										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178938935	178938935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	caaacaggagaagaaggatgAaacacaaaaggtgtgtgact	12	5	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:178938935A>G	ENST00000263967.3	+	14	2334	c.2177A>G	c.(2176-2178)gAa>gGa	p.E726G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	726			E -> K (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAGAAGGATGAAACACAAAAG	0.428		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											88	77	81					3																	178938935		1914	4118	6032	180421629	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2177A>G	3.37:g.178938935A>G	ENSP00000263967:p.Glu726Gly		180421629	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504732	0.64410	.	.	ENSG00000121879	ENST00000263967	T	0.80994	-1.44	5.6	5.6	0.85130	Protein kinase-like domain (1);	0.166180	0.38778	U	0.001568	T	0.76976	0.4063	L	0.46157	1.445	0.80722	D	1	P	0.46064	0.872	B	0.42738	0.396	T	0.75482	-0.3302	10	0.27082	T	0.32	-19.3819	15.7853	0.78297	1.0:0.0:0.0:0.0	.	726	P42336	PK3CA_HUMAN	G	726	ENSP00000263967:E726G	ENSP00000263967:E726G	E	+	2	0	PIK3CA	180421629	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.962000	0.93254	2.129000	0.65627	0.533000	0.62120	GAA		0.428	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178938935	A	G	178938935	3	3	84	1	0	0	0	0	1	0	0	0	11944	246	9	4	2227	4	PIK3CA	3	178938935	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	2885	178938935	19083495	43	23735										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951967	178951967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttttctcaatgatgcttggcTctggaatgccagaactacaa	8	9	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:178951967T>C	ENST00000263967.3	+	21	3179	c.3022T>C	c.(3022-3024)Tct>Cct	p.S1008P	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1008	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.S1008P(3)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GATGCTTGGCTCTGGAATGCC	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	3											113	101	105					3																	178951967		1885	4106	5991	180434661	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3022T>C	3.37:g.178951967T>C	ENSP00000263967:p.Ser1008Pro		180434661	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848321	0.71603	.	.	ENSG00000121879	ENST00000263967	D	0.82255	-1.59	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.89681	0.6785	M	0.86740	2.835	0.80722	D	1	P	0.52316	0.952	P	0.51701	0.677	D	0.91272	0.5045	10	0.72032	D	0.01	-16.2835	16.635	0.85050	0.0:0.0:0.0:1.0	.	1008	P42336	PK3CA_HUMAN	P	1008	ENSP00000263967:S1008P	ENSP00000263967:S1008P	S	+	1	0	PIK3CA	180434661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.510000	0.81708	2.330000	0.79161	0.477000	0.44152	TCT		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178951967	T	C	178951967	3	2	84	1	0	0	0	0	1	0	0	0	11944	1551	54	4	3100	4	PIK3CA	3	178951967	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	13032	178951967	19070463	44	23736										
FXR1	8087	hgsc.bcm.edu	37	chr3	180669154	180669154	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gaagatttaatgggcctggcAataggaacacatggtagtaa	12	5	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:180669154A>G	ENST00000357559.4	+	8	1083	c.699A>G	c.(697-699)gcA>gcG	p.A233A	FXR1_ENST00000468861.1_Silent_p.A148A|FXR1_ENST00000445140.2_Silent_p.A233A|FXR1_ENST00000305586.7_Silent_p.A148A|FXR1_ENST00000491062.1_Silent_p.A184A|FXR1_ENST00000480918.1_Silent_p.A220A	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	233	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.		A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			TGGGCCTGGCAATAGGAACAC	0.393																																																0			3											103	99	100					3																	180669154		2203	4300	6503	182151848	SO:0001819	synonymous_variant	8087			M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.699A>G	3.37:g.180669154A>G			182151848	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	37	CCDS3238.1																																																																																				0.393	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			G	180669154	A	G	180669154	2	3	84	1	0	0	0	0	0	0	0	1	6134	117	5	4		4	FXR1	3	180669154	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	1717187	180669154	17353276	45	23737										
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186503977	186503977	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aaaatggatcaaaatgtttgTtttggatgaagcagatgaaa	10	2	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr3:186503977T>C	ENST00000323963.5	+	6	606	c.542T>C	c.(541-543)gTt>gCt	p.V181A	EIF4A2_ENST00000440191.2_Missense_Mutation_p.V182A|SNORD2_ENST00000459163.1_RNA|SNORA63_ENST00000363548.1_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.V86A|RP11-573D15.9_ENST00000577781.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	181	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		V -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		AAAATGTTTGTTTTGGATGAA	0.328			T	BCL6	NHL																																		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	0			3											79	78	78					3																	186503977		2203	4300	6503	187986671	SO:0001583	missense	1974			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.542T>C	3.37:g.186503977T>C	ENSP00000326381:p.Val181Ala		187986671	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.016483	0.75161	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.34072	1.38;1.38;1.38	5.13	5.13	0.70059	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64394	0.2594	M	0.92555	3.32	0.80722	D	1	P;B;B;B	0.39391	0.671;0.025;0.303;0.352	P;B;P;P	0.54431	0.752;0.202;0.463;0.598	T	0.71467	-0.4584	10	0.72032	D	0.01	-12.8887	13.2127	0.59834	0.0:0.0:0.0:1.0	.	37;86;182;181	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	A	181;182;86	ENSP00000326381:V181A;ENSP00000398370:V182A;ENSP00000348925:V86A	ENSP00000326381:V181A	V	+	2	0	EIF4A2	187986671	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.271000	0.78506	2.281000	0.76405	0.528000	0.53228	GTT		0.328	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		C	186503977	T	C	186503977	3	2	84	1	0	0	0	0	1	0	0	0	5038	1725	60	4	564	4	EIF4A2	3	186503977	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	5834823	186503977	11518453	46	23738										
MFSD7	84179	hgsc.bcm.edu	37	chr4	678565	678565	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctggcagccccggcagagggCggggtggggggcacactctc	19	13	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:678565C>T	ENST00000404286.2	-	5	681	c.666G>A	c.(664-666)ccG>ccA	p.P222P	MFSD7_ENST00000515118.1_Silent_p.P125P|MFSD7_ENST00000503156.1_Silent_p.P158P|MFSD7_ENST00000322224.4_Silent_p.P222P|MFSD7_ENST00000347950.5_Silent_p.P103P|MFSD7_ENST00000513740.1_5'Flank	NM_032219.2	NP_115595.2	Q6UXD7	MFSD7_HUMAN	major facilitator superfamily domain containing 7	222					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				cervix(1)|kidney(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	11						CGGCAGAGGGCGGGGTGGGGG	0.662																																																0			4											21	27	25					4																	678565		2196	4287	6483	668565	SO:0001819	synonymous_variant	84179			AK025922	CCDS3338.1, CCDS75086.1	4p16.3	2013-05-22			ENSG00000169026	ENSG00000169026		"Solute carriers"	26177	protein-coding gene	gene with protein product						12975309	Standard	XM_005272295		Approved	FLJ22269, LP2561	uc003gax.3	Q6UXD7	OTTHUMG00000119001	ENST00000404286.2:c.666G>A	4.37:g.678565C>T			668565	A8K7J5|Q6XYD4|Q8N6H1|Q9H6H6	Silent	SNP	ENST00000404286.2	37																																																																																					0.662	MFSD7-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358585.1	NM_032219		T	678565	C	T	678565	2	4	84	1	0	0	0	0	0	0	0	1	9567	755	27	1		1	MFSD7	4	678565	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10		678565	190475711	47	23739										
FAM193A	8603	hgsc.bcm.edu	37	chr4	2698260	2698260	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttgcagtttataaatagctcCgaaaccaaaccagtgagcag	8	9	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:2698260C>T	ENST00000324666.5	+	16	2925	c.2574C>T	c.(2572-2574)tcC>tcT	p.S858S	FAM193A_ENST00000545951.1_Silent_p.S858S|FAM193A_ENST00000505311.1_Silent_p.S858S|FAM193A_ENST00000382839.3_Silent_p.S858S|FAM193A_ENST00000502458.1_Silent_p.S880S	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	858								p.S858S(1)		NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						TAAATAGCTCCGAAACCAAAC	0.512																																																1	Substitution - coding silent(1)	ovary(1)	4											101	95	97					4																	2698260		2203	4300	6503	2668058	SO:0001819	synonymous_variant	0			AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.2574C>T	4.37:g.2698260C>T			2668058	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Silent	SNP	ENST00000324666.5	37	CCDS58875.1																																																																																				0.512	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		T	2698260	C	T	2698260	2	4	84	1	0	0	0	0	0	0	0	1	5540	639	23	1		1	FAM193A	4	2698260	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	2019695	2698260	188456016	48	23740										
GPR125	166647	hgsc.bcm.edu	37	chr4	22463424	22463424	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actactaataagattgtttcGgaggtccctgttaaaaataa	7	6	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:22463424G>A	ENST00000334304.5	-	3	606	c.337C>T	c.(337-339)Cga>Tga	p.R113*	GPR125_ENST00000502482.1_Nonsense_Mutation_p.R113*	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	113					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				AGATTGTTTCGGAGGTCCCTG	0.338																																																0			4											59	62	61					4																	22463424		2203	4300	6503	22072522	SO:0001587	stop_gained	166647			AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.337C>T	4.37:g.22463424G>A	ENSP00000334952:p.Arg113*		22072522	Q6UXK9|Q86SQ5|Q8TC55	Nonsense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	39	7.533284	0.98342	.	.	ENSG00000152990	ENST00000334304;ENST00000502482	.	.	.	5.71	4.79	0.61399	.	0.054599	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.2018	10.5153	0.44885	0.0:0.0:0.7165:0.2835	.	.	.	.	X	113	.	ENSP00000334952:R113X	R	-	1	2	GPR125	22072522	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.414000	0.52693	2.709000	0.92574	0.655000	0.94253	CGA		0.338	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			A	22463424	G	A	22463424	4	1	84	1	0	0	0	0	0	1	0	0	6659	1124	39	1	3696	1	GPR125	4	22463424	Nonsense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	19765164	22463424	168690852	49	23741										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54256783	54256783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attcttttgaagataaaccaTggcgtaaacctggtaagatt	8	6	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:54256783T>C	ENST00000337488.6	+	7	687	c.493T>C	c.(493-495)Tgg>Cgg	p.W165R	FIP1L1_ENST00000507166.1_Missense_Mutation_p.W165R|FIP1L1_ENST00000358575.5_Missense_Mutation_p.W150R|FIP1L1_ENST00000507922.1_Missense_Mutation_p.W150R|FIP1L1_ENST00000306932.6_Missense_Mutation_p.W150R	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	165	Necessary for stimulating PAPOLA activity.|Sufficient for interaction with CPSF4.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.W165R(1)		large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AGATAAACCATGGCGTAAACC	0.323			T	PDGFRA	idiopathic hypereosinophilic syndrome																																		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	1	Substitution - Missense(1)	ovary(1)	4											96	95	95					4																	54256783		2203	4300	6503	53951540	SO:0001583	missense	81608			AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.493T>C	4.37:g.54256783T>C	ENSP00000336752:p.Trp165Arg		53951540	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.750677	0.69533	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	D	0.99748	-6.62	5.43	5.43	0.79202	Pre-mRNA polyadenylation factor Fip1 (1);	0.000000	0.64402	D	0.000004	D	0.99816	0.9919	H	0.96430	3.82	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;D;D;D	0.97110	0.999;0.991;1.0;1.0	D	0.96749	0.9552	9	.	.	.	-5.8529	15.4589	0.75339	0.0:0.0:0.0:1.0	.	150;150;165;150	G3XAD6;Q6UN15-3;Q6UN15;Q6UN15-4	.;.;FIP1_HUMAN;.	R	165;150;150;150;165	ENSP00000423325:W165R	.	W	+	1	0	FIP1L1	53951540	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.662000	0.83803	2.048000	0.60808	0.482000	0.46254	TGG		0.323	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		C	54256783	T	C	54256783	3	2	84	1	0	0	0	0	1	0	0	0	5915	1464	51	4	519	4	FIP1L1	4	54256783	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	31793359	54256783	136897493	50	23742										
AASDH	132949	hgsc.bcm.edu	37	chr4	57220881	57220881	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ataaaacaacctaaaaatacTtggccactgccttcctgaat	4	11	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:57220881T>G	ENST00000205214.6	-	7	1380	c.1200A>C	c.(1198-1200)caA>caC	p.Q400H	AASDH_ENST00000513376.1_Missense_Mutation_p.Q300H|AASDH_ENST00000434343.2_Intron|AASDH_ENST00000451613.1_Missense_Mutation_p.Q400H|AASDH_ENST00000502617.1_Missense_Mutation_p.Q400H|AASDH_ENST00000510762.1_5'Flank|AASDH_ENST00000602986.1_Missense_Mutation_p.Q247H	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	400					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CTAAAAATACTTGGCCACTGC	0.333																																																0			4											98	105	102					4																	57220881		2203	4300	6503	56915638	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1200A>C	4.37:g.57220881T>G	ENSP00000205214:p.Gln400His		56915638	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891235	0.72524	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.27	5.27	0.74061	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.64170	0.2574	M	0.72894	2.215	0.50039	D	0.999844	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.85130	0.976;0.991;0.981;0.997	T	0.68550	-0.5379	10	0.87932	D	0	-13.7308	15.1804	0.72952	0.0:0.0:0.0:1.0	.	247;400;400;400	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	H	400;300;400;247;400	ENSP00000205214:Q400H;ENSP00000423760:Q300H;ENSP00000409656:Q400H;ENSP00000421171:Q400H	ENSP00000205214:Q400H	Q	-	3	2	AASDH	56915638	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.762000	0.47597	1.988000	0.58038	0.477000	0.44152	CAA		0.333	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		G	57220881	T	G	57220881	3	3	84	1	0	0	0	0	1	0	0	0	22	1606	56	4	2132	4	AASDH	4	57220881	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	2964098	57220881	133933395	51	23743										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537383	88537383	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cagcgacagcagtgatagcaGtgacagcagcgacagcagcg	14	11	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:88537383G>T	ENST00000282478.7	+	4	3602	c.3569G>T	c.(3568-3570)aGt>aTt	p.S1190I	DSPP_ENST00000399271.1_Missense_Mutation_p.S1190I|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1190	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		agtgatagcagtgacagcagc	0.567																																																0			4											49	68	61					4																	88537383		1632	2904	4536	88756407	SO:0001583	missense	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3569G>T	4.37:g.88537383G>T	ENSP00000282478:p.Ser1190Ile		88756407	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	0.852	-0.738394	0.03111	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88664	-2.41;-2.41	2.5	1.64	0.23874	.	.	.	.	.	D	0.85133	0.5627	L	0.34521	1.04	0.19300	N	0.999979	P	0.42518	0.782	P	0.49332	0.607	T	0.74222	-0.3735	9	0.40728	T	0.16	7.0E-4	5.294	0.15743	0.1691:0.0:0.8309:0.0	.	1190	Q9NZW4	DSPP_HUMAN	I	1190	ENSP00000382213:S1190I;ENSP00000282478:S1190I	ENSP00000282478:S1190I	S	+	2	0	DSPP	88756407	0.019000	0.18553	0.573000	0.28510	0.016000	0.09150	0.779000	0.26746	0.621000	0.30232	0.298000	0.19748	AGT		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88537383	G	T	88537383	3	4	84	1	0	0	0	0	1	0	0	0	4793	1029	36	2	3583	2	DSPP	4	88537383	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	31316502	88537383	102616893	52	23744										
BMPR1B	658	hgsc.bcm.edu	37	chr4	96051102	96051102	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tggatgggaaagtggcgtggCgaaaaggtagctgtgaaagt	18	3	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:96051102C>T	ENST00000515059.1	+	9	958	c.675C>T	c.(673-675)ggC>ggT	p.G225G	BMPR1B_ENST00000264568.4_Silent_p.G225G|BMPR1B_ENST00000440890.2_Silent_p.G255G|BMPR1B_ENST00000394931.1_Silent_p.G225G	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		AGTGGCGTGGCGAAAAGGTAG	0.448																																																0			4											153	159	157					4																	96051102		2203	4300	6503	96270125	SO:0001819	synonymous_variant	658			D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.675C>T	4.37:g.96051102C>T			96270125	B2R953|B4DSV1|P78366	Silent	SNP	ENST00000515059.1	37	CCDS3642.1																																																																																				0.448	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		T	96051102	C	T	96051102	2	4	84	1	0	0	0	0	0	0	0	1	1471	755	27	1		1	BMPR1B	4	96051102	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	7513719	96051102	95103174	53	23745										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123132181	123132181	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cctgataaacttcatgtagaAatggaactttctccagattc	6	9	2	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:123132181A>G	ENST00000264501.4	+	20	2551	c.2178A>G	c.(2176-2178)gaA>gaG	p.E726E	KIAA1109_ENST00000455637.1_Silent_p.E726E|KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Silent_p.E726E			Q2LD37	K1109_HUMAN	KIAA1109	726					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTCATGTAGAAATGGAACTTT	0.383																																																0			4											100	91	94					4																	123132181		1830	4087	5917	123351631	SO:0001819	synonymous_variant	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2178A>G	4.37:g.123132181A>G			123351631	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	8.965	0.971449	0.18736	.	.	ENSG00000138688	ENST00000424425	.	.	.	4.97	0.989	0.19802	.	.	.	.	.	T	0.58308	0.2113	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52764	-0.8532	4	.	.	.	.	10.0526	0.42225	0.6477:0.0:0.3523:0.0	.	.	.	.	D	559	.	.	N	+	1	0	KIAA1109	123351631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.352000	0.34033	0.294000	0.22547	0.477000	0.44152	AAT		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123132181	A	G	123132181	2	3	84	1	0	0	0	0	0	0	0	1	8229	11	1	4		4	KIAA1109	4	123132181	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	27081079	123132181	68022095	54	23746										
MMAA	166785	hgsc.bcm.edu	37	chr4	146575149	146575149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtttctgatctctttagggtAtcaaaaggggtataatcgag	11	5	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr4:146575149A>G	ENST00000281317.5	+	6	2033	c.823A>G	c.(823-825)Atc>Gtc	p.I275V	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	275					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCTTTAGGGTATCAAAAGGGG	0.368																																																0			4											181	179	180					4																	146575149		2203	4300	6503	146794599	SO:0001583	missense	387254			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.823A>G	4.37:g.146575149A>G	ENSP00000281317:p.Ile275Val		146794599	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775749	0.70107	.	.	ENSG00000151611	ENST00000281317;ENST00000537246	D	0.90788	-2.73	5.78	5.78	0.91487	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.89248	0.6661	L	0.53671	1.685	0.80722	D	1	B	0.33448	0.412	B	0.35931	0.214	D	0.88194	0.2879	10	0.45353	T	0.12	-13.1358	16.1215	0.81361	1.0:0.0:0.0:0.0	.	275	Q8IVH4	MMAA_HUMAN	V	275	ENSP00000281317:I275V	ENSP00000281317:I275V	I	+	1	0	MMAA	146794599	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	8.923000	0.92808	2.208000	0.71279	0.528000	0.53228	ATC		0.368	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			G	146575149	A	G	146575149	3	3	84	1	0	0	0	0	1	0	0	0	9669	449	16	4	841	4	MMAA	4	146575149	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	23442968	146575149	44579127	55	23747										
ADCY2	108	hgsc.bcm.edu	37	chr5	7626421	7626421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcaagttggaatttgaaaaaCgtcaacaggtaatggatgtt	10	4	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:7626421C>T	ENST00000338316.4	+	4	801	c.712C>T	c.(712-714)Cgt>Tgt	p.R238C		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	238					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						ATTTGAAAAACGTCAACAGGT	0.378																																																0			5											108	101	103					5																	7626421		2203	4300	6503	7679421	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.712C>T	5.37:g.7626421C>T	ENSP00000342952:p.Arg238Cys		7679421	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	17.77	3.472281	0.63737	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000515681	T	0.77489	-1.1	5.09	5.09	0.68999	Adenylyl cyclase class-3/4/guanylyl cyclase (1);	0.129142	0.50627	D	0.000117	D	0.82903	0.5138	L	0.51914	1.62	0.80722	D	1	D	0.89917	1.0	D	0.63488	0.915	D	0.84343	0.0528	10	0.87932	D	0	.	12.7744	0.57439	0.1631:0.8369:0.0:0.0	.	238	Q08462	ADCY2_HUMAN	C	238;89;27	ENSP00000342952:R238C	ENSP00000342952:R238C	R	+	1	0	ADCY2	7679421	1.000000	0.71417	0.973000	0.42090	0.928000	0.56348	2.734000	0.47368	2.520000	0.84964	0.655000	0.94253	CGT		0.378	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7626421	C	T	7626421	3	4	84	1	0	0	0	0	1	0	0	0	294	536	19	1	726	1	ADCY2	5	7626421	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10		7626421	173288839	56	23748										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94244963	94244963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aaattgcacaaacctgccaaTgaaatcatcccttttcccag	4	13	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:94244963T>C	ENST00000515393.1	-	10	1644	c.1645A>G	c.(1645-1647)Att>Gtt	p.I549V	MCTP1_ENST00000429576.2_Missense_Mutation_p.I282V|MCTP1_ENST00000312216.8_Missense_Mutation_p.I328V|MCTP1_ENST00000505078.1_Missense_Mutation_p.I65V|MCTP1_ENST00000505208.1_Missense_Mutation_p.I328V	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	549	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.I549L(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AACCTGCCAATGAAATCATCC	0.358																																																1	Substitution - Missense(1)	ovary(1)	5											82	77	79					5																	94244963		2203	4300	6503	94270719	SO:0001583	missense	79772				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1645A>G	5.37:g.94244963T>C	ENSP00000424126:p.Ile549Val		94270719	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	37	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.525886	0.44969	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568	T;T;T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	5.68	5.68	0.88126	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093490	0.64402	D	0.000001	T	0.72112	0.3420	L	0.58354	1.805	0.58432	D	0.999998	B;B;B	0.33379	0.41;0.199;0.199	B;B;B	0.41174	0.349;0.216;0.138	T	0.68861	-0.5297	10	0.26408	T	0.33	-14.5208	15.9332	0.79683	0.0:0.0:0.0:1.0	.	549;282;328	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	V	549;282;65;328;269;210;328;150	ENSP00000424126:I549V;ENSP00000391639:I282V;ENSP00000426417:I65V;ENSP00000308957:I328V;ENSP00000423410:I269V;ENSP00000431075:I210V;ENSP00000426438:I328V;ENSP00000426294:I150V	ENSP00000308957:I328V	I	-	1	0	MCTP1	94270719	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	7.698000	0.84413	2.164000	0.68074	0.477000	0.44152	ATT		0.358	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		C	94244963	T	C	94244963	3	2	84	1	0	0	0	0	1	0	0	0	9430	1464	51	4	1410	4	MCTP1	5	94244963	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	86618542	94244963	86670297	57	23749										
APC	324	hgsc.bcm.edu	37	chr5	112151204	112151204	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atttttagggttcaactacaCgaatggaccatgaaacagcc	8	9	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:112151204C>T	ENST00000457016.1	+	9	1227	c.847C>T	c.(847-849)Cga>Tga	p.R283*	APC_ENST00000508376.2_Nonsense_Mutation_p.R283*|APC_ENST00000257430.4_Nonsense_Mutation_p.R283*			P25054	APC_HUMAN	adenomatous polyposis coli	283	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R283*(11)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCAACTACACGAATGGACCA	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	11	Substitution - Nonsense(11)	large_intestine(11)	5	GRCh37	CM920030	APC	M							108	98	102					5																	112151204		2202	4300	6502	112179103	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.847C>T	5.37:g.112151204C>T	ENSP00000413133:p.Arg283*		112179103	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381748	0.98786	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	4.22	0.49857	.	0.134048	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.044	12.9775	0.58546	0.2942:0.7058:0.0:0.0	.	.	.	.	X	283;265;283;283;283	.	ENSP00000257430:R283X	R	+	1	2	APC	112179103	1.000000	0.71417	0.953000	0.39169	0.976000	0.68499	5.216000	0.65246	1.244000	0.43870	0.650000	0.86243	CGA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112151204	C	T	112151204	4	4	84	1	0	0	0	0	0	1	0	0	763	528	19	1	877	1	APC	5	112151204	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	17906241	112151204	68764056	58	23750										
APC	324	hgsc.bcm.edu	37	chr5	112175507	112175507	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gttcgattgccagctccgttCagagtgaaccatgcagtgga	12	10	1	2	rs587782518		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:112175507C>T	ENST00000457016.1	+	16	4596	c.4216C>T	c.(4216-4218)Cag>Tag	p.Q1406*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1406*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1406*			P25054	APC_HUMAN	adenomatous polyposis coli	1406	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1406*(15)|p.Q1406fs*11(1)|p.?(1)|p.K1192fs*3(1)|p.I1401fs*2(1)|p.Y1376fs*41(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCTCCGTTCAGAGTGAACC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(15)|Deletion - Frameshift(3)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(18)|soft_tissue(1)|skin(1)	5	GRCh37	CI084250|CM023011	APC	I|M							113	105	108					5																	112175507		2202	4300	6502	112203406	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4216C>T	5.37:g.112175507C>T	ENSP00000413133:p.Gln1406*		112203406	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.658788	0.98903	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	5.3	0.74995	.	0.187376	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.0613	15.6825	0.77381	0.0:0.8637:0.1363:0.0	.	.	.	.	X	1406	.	.	Q	+	1	0	APC	112203406	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.175000	0.77632	1.615000	0.50252	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175507	C	T	112175507	4	4	84	1	0	0	0	0	0	1	0	0	763	827	29	3	4274	3	APC	5	112175507	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	24303	112175507	68739753	59	23751										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229622	140229622	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtgtcagtgcacgcggagagCggcaaggtgtacgcgctgca	17	10	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:140229622C>T	ENST00000532602.1	+	1	2575	c.1542C>T	c.(1540-1542)agC>agT	p.S514S	PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.S514S|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	514	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCGGAGAGCGGCAAGGTGT	0.692																																					Melanoma(55;1800 1972 14909)											0			5																																								140209806	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1542C>T	5.37:g.140229622C>T			140209806	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.692	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140229622	C	T	140229622	2	4	84	1	0	0	0	0	0	0	0	1	11562	767	27	1		1	PCDHA9	5	140229622	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	28054115	140229622	40685638	60	23752										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169446021	169446021	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	acctatattagagatgacacTtatccctgaggctgagctcc	8	11	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:169446021T>G	ENST00000256935.8	+	33	3370	c.3290T>G	c.(3289-3291)cTt>cGt	p.L1097R	DOCK2_ENST00000540750.1_Missense_Mutation_p.L158R|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.L589R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1097	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGATGACACTTATCCCTGAG	0.423																																																0			5											205	198	201					5																	169446021		2203	4300	6503	169378599	SO:0001583	missense	1794			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3290T>G	5.37:g.169446021T>G	ENSP00000256935:p.Leu1097Arg		169378599	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.529505	0.85706	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.52295	0.67;0.67;0.67	4.8	4.8	0.61643	.	0.000000	0.64402	D	0.000001	T	0.75184	0.3815	M	0.92122	3.275	0.53688	D	0.99997	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.82358	-0.0497	10	0.87932	D	0	.	14.3619	0.66779	0.0:0.0:0.0:1.0	.	589;1097	E7ERW7;Q92608	.;DOCK2_HUMAN	R	1097;589;158	ENSP00000256935:L1097R;ENSP00000429283:L589R;ENSP00000438827:L158R	ENSP00000256935:L1097R	L	+	2	0	DOCK2	169378599	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.938000	0.87678	1.795000	0.52594	0.528000	0.53228	CTT		0.423	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169446021	T	G	169446021	3	3	84	1	0	0	0	0	1	0	0	0	4698	1609	56	4	3420	4	DOCK2	5	169446021	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	29216399	169446021	11469239	61	23753										
MGAT1	4245	hgsc.bcm.edu	37	chr5	180218983	180218983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gctggttcagcttgataaacTtgaggtgctggtcaaagaac	12	7	2	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr5:180218983T>C	ENST00000446023.2	-	3	1739	c.989A>G	c.(988-990)aAg>aGg	p.K330R	MGAT1_ENST00000333055.3_Missense_Mutation_p.K330R|MGAT1_ENST00000427865.2_Missense_Mutation_p.K330R|MGAT1_ENST00000307826.4_Missense_Mutation_p.K330R|MGAT1_ENST00000393340.3_Missense_Mutation_p.K330R	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	330					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTGATAAACTTGAGGTGCTG	0.587																																																0			5											78	86	83					5																	180218983		2203	4300	6503	180151589	SO:0001583	missense	116255			M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.989A>G	5.37:g.180218983T>C	ENSP00000404718:p.Lys330Arg		180151589	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.520466	0.27211	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82	4.52	4.52	0.55395	.	0.060876	0.64402	D	0.000007	T	0.70996	0.3288	N	0.13003	0.285	0.42305	D	0.992197	B	0.20368	0.044	B	0.22753	0.041	T	0.66752	-0.5844	10	0.38643	T	0.18	-27.9198	6.8757	0.24145	0.0:0.1028:0.0:0.8972	.	330	P26572	MGAT1_HUMAN	R	330;330;330;330;187;330	ENSP00000332073:K330R;ENSP00000311888:K330R;ENSP00000404718:K330R;ENSP00000377010:K330R;ENSP00000402838:K330R	ENSP00000311888:K330R	K	-	2	0	MGAT1	180151589	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	3.347000	0.52200	2.030000	0.59900	0.533000	0.62120	AAG		0.587	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		C	180218983	T	C	180218983	3	2	84	1	0	0	0	0	1	0	0	0	9572	1609	56	4	352	4	MGAT1	5	180218983	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	10772962	180218983	696277	62	23754										
HUS1B	135458	hgsc.bcm.edu	37	chr6	656918	656918	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aacagctctagacagcctttGccggtgatcttggcgcgaaa	11	11	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:656918G>A	ENST00000380907.2	-	1	45	c.27C>T	c.(25-27)ggC>ggT	p.G9G	EXOC2_ENST00000448181.3_Intron|EXOC2_ENST00000230449.4_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	9					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		GACAGCCTTTGCCGGTGATCT	0.652																																																0			6											65	62	63					6																	656918		2198	4287	6485	601918	SO:0001819	synonymous_variant	135458			AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"HUS1 (S. pombe) checkpoint homolog b"			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.27C>T	6.37:g.656918G>A			601918	Q5T4Z2	Silent	SNP	ENST00000380907.2	37	CCDS4470.1																																																																																				0.652	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959		A	656918	G	A	656918	2	1	84	1	0	0	0	0	0	0	0	1	7481	1306	46	3		3	HUS1B	6	656918	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10		656918	170458149	63	23755										
RREB1	6239	hgsc.bcm.edu	37	chr6	7248754	7248754	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attgttccaggggaaaggccAtacaaatgtcagacctgcga	11	9	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:7248754A>G	ENST00000349384.6	+	12	4931	c.4617A>G	c.(4615-4617)ccA>ccG	p.P1539P	RREB1_ENST00000379933.3_Silent_p.P1539P|RREB1_ENST00000379938.2_Silent_p.P1594P|RREB1_ENST00000334984.6_Silent_p.P1328P	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1539					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGGAAAGGCCATACAAATGTC	0.542																																																0			6											69	66	67					6																	7248754		2203	4300	6503	7193753	SO:0001819	synonymous_variant	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4617A>G	6.37:g.7248754A>G			7193753	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																				0.542	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			G	7248754	A	G	7248754	2	3	84	1	0	0	0	0	0	0	0	1	13716	204	8	4		4	RREB1	6	7248754	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	6591836	7248754	163866313	64	23756										
HIST1H4I	8294	hgsc.bcm.edu	37	chr6	27107355	27107355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccgccatggacgtggtctacGcgctcaagcgccagggccgc	14	16	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:27107355G>A	ENST00000354348.2	+	1	280	c.268G>A	c.(268-270)Gcg>Acg	p.A90T	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	90					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(1)	1						CGTGGTCTACGCGCTCAAGCG	0.592			T	BCL6	NHL																																		Dom	yes		6	6p21.3	8294	"histone 1, H4i (H4FM)"		L	0			6											65	62	63					6																	27107355		2203	4300	6503	27215334	SO:0001583	missense	8294			AB000905	CCDS4620.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198339	ENSG00000276180		"Histones / Replication-dependent"	4793	protein-coding gene	gene with protein product		602833	"H4 histone family, member M", "histone 1, H4i"	H4FM		8988030, 9439656, 12408966	Standard	NM_003495		Approved	H4/m	uc003niy.1	P62805	OTTHUMG00000014471	ENST00000354348.2:c.268G>A	6.37:g.27107355G>A	ENSP00000346316:p.Ala90Thr		27215334	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000354348.2	37	CCDS4620.1	.	.	.	.	.	.	.	.	.	.	.	15.38	2.815543	0.50527	.	.	ENSG00000198339	ENST00000354348	T	0.80033	-1.33	3.8	3.8	0.43715	.	0.000000	0.40302	U	0.001138	D	0.88206	0.6374	M	0.90425	3.115	0.47476	D	0.999432	.	.	.	.	.	.	D	0.90226	0.4275	8	0.62326	D	0.03	.	13.9996	0.64424	0.0:0.0:1.0:0.0	.	.	.	.	T	90	ENSP00000346316:A90T	ENSP00000346316:A90T	A	+	1	0	HIST1H4I	27215334	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	5.891000	0.69782	2.068000	0.61886	0.655000	0.94253	GCG		0.592	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495		A	27107355	G	A	27107355	3	1	84	1	0	0	0	0	1	0	0	0	7194	1087	38	1	270	1	HIST1H4I	6	27107355	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	19858601	27107355	144007712	65	23757										
BAI3	577	hgsc.bcm.edu	37	chr6	70048837	70048837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgagcctcatagcggtttgaCgctcaaatgtgccaagtgtg	12	9	2	2	rs376079687		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:70048837C>T	ENST00000370598.1	+	25	4039	c.3218C>T	c.(3217-3219)aCg>aTg	p.T1073M	BAI3_ENST00000238918.8_Missense_Mutation_p.T279M|BAI3_ENST00000546190.1_Missense_Mutation_p.T37M	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1073					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AGCGGTTTGACGCTCAAATGT	0.413																																																0			6						C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	224	220	221		3218	6.2	1	6		221	0,8600		0,0,4300	no	missense	BAI3	NM_001704.2	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1073/1523	70048837	1,13005	2203	4300	6503	70105558	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3218C>T	6.37:g.70048837C>T	ENSP00000359630:p.Thr1073Met		70105558	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146269	0.77888	2.27E-4	0.0	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.46063	2.0;2.63;0.88	6.16	6.16	0.99307	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	L	0.49778	1.585	0.53688	D	0.999976	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.78314	0.98;0.91;0.991	T	0.29731	-1.0002	10	0.33940	T	0.23	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	279;1073;1073	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	M	1073;279;37	ENSP00000359630:T1073M;ENSP00000238918:T279M;ENSP00000441821:T37M	ENSP00000238918:T279M	T	+	2	0	BAI3	70105558	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.920000	0.70017	2.937000	0.99478	0.650000	0.86243	ACG		0.413	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	70048837	C	T	70048837	3	4	84	1	0	0	0	0	1	0	0	0	1301	536	19	1	3308	1	BAI3	6	70048837	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	42941482	70048837	101066230	66	23758										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76072581	76072581	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	acccgtaatgagcctccagaAcctcaggcttggttttctct	8	13	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:76072581A>C	ENST00000237172.7	-	3	659	c.329T>G	c.(328-330)gTt>gGt	p.V110G	FILIP1_ENST00000370020.1_Missense_Mutation_p.V11G|RP11-415D17.3_ENST00000591821.2_RNA|RP11-415D17.3_ENST00000609544.1_RNA|RP11-415D17.3_ENST00000588761.1_RNA|RP11-415D17.3_ENST00000419709.1_RNA|RP11-415D17.3_ENST00000415457.2_RNA|RP11-415D17.3_ENST00000440220.1_RNA|FILIP1_ENST00000393004.2_Missense_Mutation_p.V110G	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	110										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						AGCCTCCAGAACCTCAGGCTT	0.507																																																0			6											132	131	131					6																	76072581		2203	4300	6503	76129301	SO:0001583	missense	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.329T>G	6.37:g.76072581A>C	ENSP00000237172:p.Val110Gly		76129301	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	A	11.77	1.737673	0.30774	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.50548	0.74;0.74;0.74	5.99	2.39	0.29439	Cortactin-binding protein-2, N-terminal (1);	0.311269	0.35870	N	0.002923	T	0.19208	0.0461	L	0.38175	1.15	0.80722	D	1	B;B;B	0.32653	0.379;0.091;0.074	B;B;B	0.31101	0.089;0.124;0.076	T	0.05053	-1.0909	10	0.49607	T	0.09	-7.0988	9.2961	0.37815	0.7983:0.0:0.2017:0.0	.	110;110;110	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	G	110;110;11	ENSP00000376728:V110G;ENSP00000237172:V110G;ENSP00000359037:V11G	ENSP00000237172:V110G	V	-	2	0	FILIP1	76129301	0.999000	0.42202	1.000000	0.80357	0.389000	0.30415	1.513000	0.35823	0.517000	0.28361	0.533000	0.62120	GTT		0.507	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		C	76072581	A	C	76072581	3	2	84	1	0	0	0	0	1	0	0	0	5913	43	2	4	3328	4	FILIP1	6	76072581	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	6023744	76072581	95042486	67	23759										
MCHR2	84539	hgsc.bcm.edu	37	chr6	100403984	100403984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccaggatttgtttaaaagttCggcagaggtgttccaacaag	11	7	0	1	rs142259467		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:100403984C>T	ENST00000281806.2	-	2	354	c.40G>A	c.(40-42)Gaa>Aaa	p.E14K	MCHR2_ENST00000369212.2_Missense_Mutation_p.E14K	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E14K(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TTTAAAAGTTCGGCAGAGGTG	0.388																																																2	Substitution - Missense(2)	large_intestine(1)|skin(1)	6											144	145	145					6																	100403984		2203	4300	6503	100510705	SO:0001583	missense	84539			AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"GPCR / Class A : MCH receptors"	20867	protein-coding gene	gene with protein product		606111	"G protein-coupled receptor 145"	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.40G>A	6.37:g.100403984C>T	ENSP00000281806:p.Glu14Lys		100510705	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Missense_Mutation	SNP	ENST00000281806.2	37	CCDS5044.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320291	0.41096	.	.	ENSG00000152034	ENST00000445970;ENST00000281806;ENST00000369212	T;T;T	0.69306	-0.39;-0.39;-0.39	4.86	3.98	0.46160	.	0.459428	0.18287	N	0.145830	T	0.25306	0.0615	L	0.27053	0.805	0.23325	N	0.9979	B	0.27853	0.191	B	0.15052	0.012	T	0.10245	-1.0638	10	0.06099	T	0.92	.	11.704	0.51587	0.0:0.9058:0.0:0.0942	.	14	Q969V1	MCHR2_HUMAN	K	14	ENSP00000403490:E14K;ENSP00000281806:E14K;ENSP00000358214:E14K	ENSP00000281806:E14K	E	-	1	0	MCHR2	100510705	0.715000	0.27946	0.967000	0.41034	0.528000	0.34623	1.606000	0.36826	2.386000	0.81285	0.561000	0.74099	GAA		0.388	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503		T	100403984	C	T	100403984	3	4	84	1	0	0	0	0	1	0	0	0	9413	893	31	1	1002	1	MCHR2	6	100403984	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	24331403	100403984	70711083	68	23760										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119301435	119301435	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtaagccgctgtcgttcttgCgtaaactgggcttgcagttg	13	9	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:119301435C>T	ENST00000338891.7	-	10	2612	c.2169G>A	c.(2167-2169)acG>acA	p.T723T	FAM184A_ENST00000352896.5_Silent_p.T603T|FAM184A_ENST00000368475.4_Silent_p.T603T|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000521531.1_Silent_p.T723T	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	723						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GTCGTTCTTGCGTAAACTGGG	0.433																																																0			6											104	100	101					6																	119301435		1904	4121	6025	119343134	SO:0001819	synonymous_variant	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2169G>A	6.37:g.119301435C>T			119343134	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																				0.433	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119301435	C	T	119301435	2	4	84	1	0	0	0	0	0	0	0	1	5527	755	27	1		1	FAM184A	6	119301435	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	18897451	119301435	51813632	69	23761										
TRMT11	60487	hgsc.bcm.edu	37	chr6	126317171	126317171	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgcaagaaatttgatgaaacGgacagtgtgtgccaagtaag	12	5	0	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:126317171G>T	ENST00000334379.5	+	3	318	c.197G>T	c.(196-198)cGg>cTg	p.R66L	TRMT11_ENST00000450358.1_Missense_Mutation_p.R66L|TRMT11_ENST00000368332.3_Missense_Mutation_p.R66L|TRMT11_ENST00000489934.1_3'UTR	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	66					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)	p.R66L(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		TTGATGAAACGGACAGTGTGT	0.363											OREG0017650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	ovary(1)	6											150	132	138					6																	126317171		2203	4300	6503	126358864	SO:0001583	missense	60487			AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 75"	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.197G>T	6.37:g.126317171G>T	ENSP00000333934:p.Arg66Leu	1548	126358864	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Missense_Mutation	SNP	ENST00000334379.5	37	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977274	0.92982	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	T;T;T	0.70045	-0.45;-0.38;-0.43	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.85699	0.5757	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.88965	0.3396	10	0.87932	D	0	-3.7565	19.4836	0.95020	0.0:0.0:1.0:0.0	.	66;66	Q7Z4G4-2;Q7Z4G4	.;TRM11_HUMAN	L	66;66;66;3;3	ENSP00000333934:R66L;ENSP00000405140:R66L;ENSP00000357316:R66L	ENSP00000333934:R66L	R	+	2	0	TRMT11	126358864	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.548000	0.90669	2.595000	0.87683	0.555000	0.69702	CGG		0.363	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820		T	126317171	G	T	126317171	3	4	84	1	0	0	0	0	1	0	0	0	16602	1116	39	2	207	2	TRMT11	6	126317171	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	7015736	126317171	44797896	70	23762										
MYB	4602	hgsc.bcm.edu	37	chr6	135521267	135521267	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtcaatcttagaaagctctcCaagaactcctacaccattca	4	13	4	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:135521267C>G	ENST00000367814.4	+	11	1577	c.1391C>G	c.(1390-1392)cCa>cGa	p.P464R	MYB_ENST00000534121.1_Missense_Mutation_p.P569R|MYB_ENST00000341911.5_Missense_Mutation_p.P585R|MYB_ENST00000528774.1_Missense_Mutation_p.P582R|MYB_ENST00000534044.1_Missense_Mutation_p.P464R|MYB_ENST00000316528.8_Missense_Mutation_p.P464R|MYB_ENST00000525369.1_Missense_Mutation_p.P379R|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000533624.1_Missense_Mutation_p.P429R|MYB_ENST00000442647.2_Missense_Mutation_p.P461R|MYB_ENST00000527615.1_Missense_Mutation_p.P464R	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	464	Negative regulatory domain. {ECO:0000250}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GAAAGCTCTCCAAGAACTCCT	0.368			T	NFIB	adenoid cystic carcinoma																																		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	0			6											94	99	97					6																	135521267		2203	4300	6503	135562960	SO:0001583	missense	4602				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1391C>G	6.37:g.135521267C>G	ENSP00000356788:p.Pro464Arg		135562960	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749078	0.69533	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.8	5.8	0.92144	C-myb, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.74921	0.3780	M	0.86651	2.83	0.80722	D	1	B;B;B;D;D;D;D;P;B	0.89917	0.04;0.148;0.082;1.0;1.0;1.0;1.0;0.473;0.148	B;B;B;D;D;D;D;B;B	0.97110	0.057;0.133;0.039;1.0;0.999;1.0;0.999;0.347;0.133	T	0.78342	-0.2241	10	0.87932	D	0	-9.958	20.0545	0.97645	0.0:1.0:0.0:0.0	.	429;464;461;582;379;569;585;464;464	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	R	585;461;464;464;464;464;379;582;569;464;429	ENSP00000339992:P585R;ENSP00000410825:P461R;ENSP00000326328:P464R;ENSP00000356788:P464R;ENSP00000433227:P464R;ENSP00000435938:P379R;ENSP00000434723:P582R;ENSP00000432851:P569R;ENSP00000435055:P464R;ENSP00000436605:P429R	ENSP00000237302:P464R	P	+	2	0	MYB	135562960	1.000000	0.71417	0.968000	0.41197	0.998000	0.95712	7.757000	0.85209	2.748000	0.94277	0.655000	0.94253	CCA		0.368	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			G	135521267	C	G	135521267	3	3	84	1	0	0	0	0	1	0	0	0	10037	594	21	5	1800	5	MYB	6	135521267	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	9204096	135521267	35593800	71	23763										
TAB2	23118	hgsc.bcm.edu	37	chr6	149691206	149691206	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aaaaattccctgaagtacctGaagttgttgtatccaggtgc	9	8	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:149691206G>A	ENST00000367456.1	+	3	650	c.73G>A	c.(73-75)Gaa>Aaa	p.E25K	TAB2_ENST00000286332.5_Missense_Mutation_p.E25K|TAB2_ENST00000536230.1_Intron|TAB2_ENST00000392282.1_Missense_Mutation_p.E25K|TAB2_ENST00000538427.1_Missense_Mutation_p.E25K			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	25	CUE. {ECO:0000255|PROSITE- ProRule:PRU00468}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						TGAAGTACCTGAAGTTGTTGT	0.373																																																0			6											141	130	133					6																	149691206		2203	4300	6503	149732899	SO:0001583	missense	23118			AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"mitogen-activated protein kinase kinase kinase 7 interacting protein 2"	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.73G>A	6.37:g.149691206G>A	ENSP00000356426:p.Glu25Lys		149732899	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Missense_Mutation	SNP	ENST00000367456.1	37	CCDS5214.1	.	.	.	.	.	.	.	.	.	.	G	35	5.539501	0.96474	.	.	ENSG00000055208	ENST00000392282;ENST00000538427;ENST00000367456;ENST00000286332	T;T;T;T	0.76709	-1.04;-0.93;-0.93;-0.93	5.68	5.68	0.88126	Ubiquitin system component Cue (3);	0.000000	0.85682	D	0.000000	T	0.71617	0.3361	L	0.29908	0.895	0.80722	D	1	P	0.45348	0.856	P	0.48454	0.578	T	0.75513	-0.3291	10	0.72032	D	0.01	-13.2666	20.1467	0.98079	0.0:0.0:1.0:0.0	.	25	Q9NYJ8	TAB2_HUMAN	K	25	ENSP00000376106:E25K;ENSP00000445752:E25K;ENSP00000356426:E25K;ENSP00000286332:E25K	ENSP00000286332:E25K	E	+	1	0	TAB2	149732899	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.384000	0.97219	2.838000	0.97847	0.655000	0.94253	GAA		0.373	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3			A	149691206	G	A	149691206	3	1	84	1	0	0	0	0	1	0	0	0	15535	1291	45	3	75	3	TAB2	6	149691206	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	14169939	149691206	21423861	72	23764										
RSPH3	83861	hgsc.bcm.edu	37	chr6	159401923	159401923	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggcgattttttgtgatgtctCgttgtgcttgtgcattattt	11	5	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:159401923C>T	ENST00000252655.1	-	6	1357	c.1168G>A	c.(1168-1170)Gag>Aag	p.E390K	RSPH3_ENST00000297262.3_Missense_Mutation_p.E294K|RSPH3_ENST00000367069.2_Missense_Mutation_p.E248K|RSPH3_ENST00000449822.1_Missense_Mutation_p.E152K	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	390								p.E390K(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TGTGATGTCTCGTTGTGCTTG	0.502																																																1	Substitution - Missense(1)	ovary(1)	6											250	199	216					6																	159401923		2203	4300	6503	159321911	SO:0001583	missense	83861			AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1168G>A	6.37:g.159401923C>T	ENSP00000252655:p.Glu390Lys		159321911	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103879	0.76983	.	.	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.41949	0.1181	M	0.81614	2.55	0.51767	D	0.99993	D;D	0.89917	0.999;1.0	D;D	0.72982	0.972;0.979	T	0.17592	-1.0364	10	0.39692	T	0.17	-34.8515	18.2981	0.90154	0.0:1.0:0.0:0.0	.	294;390	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	K	248;152;390;294	ENSP00000356036:E248K;ENSP00000393195:E152K;ENSP00000252655:E390K;ENSP00000297262:E294K	ENSP00000252655:E390K	E	-	1	0	RSPH3	159321911	1.000000	0.71417	0.001000	0.08648	0.063000	0.16089	7.148000	0.77389	2.660000	0.90430	0.467000	0.42956	GAG		0.502	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		T	159401923	C	T	159401923	3	4	84	1	0	0	0	0	1	0	0	0	13742	893	31	1	526	1	RSPH3	6	159401923	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	9710717	159401923	11713144	73	23765										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159652961	159652961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cggaggacaatgggaaacccGaaaaacctgagccttcctca	10	12	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:159652961G>A	ENST00000297267.9	+	11	1617	c.1417G>A	c.(1417-1419)Gaa>Aaa	p.E473K	FNDC1_ENST00000340366.6_Missense_Mutation_p.E410K	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	473					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGGGAAACCCGAAAAACCTGA	0.507																																																0			6											45	48	47					6																	159652961		1942	4151	6093	159572951	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1417G>A	6.37:g.159652961G>A	ENSP00000297267:p.Glu473Lys		159572951	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.477|5.477	0.273055|0.273055	0.10349|0.10349	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.06687|.	3.27;4.09|.	5.69|5.69	-1.57|-1.57	0.08506|0.08506	.|.	3.116370|.	0.01366|.	N|.	0.012416|.	T|T	0.04272|0.04272	0.0118|0.0118	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14805|.	0.011;0.006|.	B;B|.	0.14578|.	0.011;0.003|.	T|T	0.38607|0.38607	-0.9653|-0.9653	10|5	0.07813|.	T|.	0.8|.	-0.8896|-0.8896	2.8561|2.8561	0.05572|0.05572	0.1938:0.3902:0.2961:0.1198|0.1938:0.3902:0.2961:0.1198	.|.	410;473|.	Q4ZHG4-2;Q4ZHG4|.	.;FNDC1_HUMAN|.	K|Q	473;410|368	ENSP00000297267:E473K;ENSP00000342460:E410K|.	ENSP00000297267:E473K|.	E|R	+|+	1|2	0|0	FNDC1|FNDC1	159572951|159572951	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.032000|0.032000	0.12392|0.12392	0.243000|0.243000	0.18106|0.18106	-0.197000|-0.197000	0.10350|0.10350	-0.211000|-0.211000	0.12701|0.12701	GAA|CGA		0.507	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159652961	G	A	159652961	3	1	84	1	0	0	0	0	1	0	0	0	5987	1059	37	1	1459	1	FNDC1	6	159652961	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	251038	159652961	11462106	74	23766										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159660580	159660580	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	acccccgtggtgagtcctgaCggcctcccactctttgggca	11	16	1	2	rs368545994		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr6:159660580C>T	ENST00000297267.9	+	14	4412	c.4212C>T	c.(4210-4212)gaC>gaT	p.D1404D	FNDC1_ENST00000340366.6_Silent_p.D1341D|FNDC1-IT1_ENST00000419703.1_RNA	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1404					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGAGTCCTGACGGCCTCCCAC	0.512																																																0			6						C		0,3730		0,0,1865	21	25	24		4212	-9.6	1	6		24	1,8205		0,1,4102	no	coding-synonymous	FNDC1	NM_032532.2		0,1,5967	TT,TC,CC		0.0122,0.0,0.0084		1404/1895	159660580	1,11935	1865	4103	5968	159580570	SO:0001819	synonymous_variant	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4212C>T	6.37:g.159660580C>T			159580570	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	9.217	1.032473	0.19590	0.0	1.22E-4	ENSG00000164694	ENST00000329629	.	.	.	5.11	-9.55	0.00569	.	.	.	.	.	T	0.17959	0.0431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40175	-0.9577	4	.	.	.	-16.8429	3.206	0.06666	0.0951:0.3525:0.1944:0.3579	.	.	.	.	W	1300	.	.	R	+	1	2	FNDC1	159580570	0.006000	0.16342	0.956000	0.39512	0.993000	0.82548	-1.636000	0.02016	-1.966000	0.01009	-0.136000	0.14681	CGG		0.512	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159660580	C	T	159660580	2	4	84	1	0	0	0	0	0	0	0	1	5987	535	19	1		1	FNDC1	6	159660580	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	7619	159660580	11454487	75	23767										
CARD11	84433	hgsc.bcm.edu	37	chr7	2962953	2962953	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cgtgccccacagaggtgaccGaaggccggaagggtctgcag	16	12	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:2962953G>A	ENST00000396946.4	-	16	2358	c.1955C>T	c.(1954-1956)tCg>tTg	p.S652L		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	652					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.S645L(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		AGAGGTGACCGAAGGCCGGAA	0.652			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	1	Substitution - Missense(1)	lung(1)	7											31	36	34					7																	2962953		2190	4285	6475	2929479	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1955C>T	7.37:g.2962953G>A	ENSP00000380150:p.Ser652Leu		2929479	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	14.57	2.574010	0.45902	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.49432	0.78;0.78	4.89	4.89	0.63831	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	L	0.27053	0.805	0.80722	D	1	D	0.56746	0.977	B	0.43052	0.406	T	0.31696	-0.9934	10	0.44086	T	0.13	-8.5532	16.2253	0.82286	0.0:0.0:1.0:0.0	.	652	Q9BXL7	CAR11_HUMAN	L	652;123	ENSP00000380150:S652L;ENSP00000347695:S123L	ENSP00000347695:S123L	S	-	2	0	CARD11	2929479	1.000000	0.71417	0.928000	0.36995	0.294000	0.27393	9.051000	0.93849	2.273000	0.75805	0.555000	0.69702	TCG		0.652	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2962953	G	A	2962953	3	1	84	1	0	0	0	0	1	0	0	0	2651	1059	37	1	1549	1	CARD11	7	2962953	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		2962953	156175710	76	23768										
PMS2	5395	hgsc.bcm.edu	37	chr7	6026616	6026616	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	catgtcctgagtatttactaActtttgacaaatgtcagaac	6	8	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:6026616A>G	ENST00000265849.7	-	11	1885	c.1780T>C	c.(1780-1782)Tta>Cta	p.L594L	PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Silent_p.L488L|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	594					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		GTATTTACTAACTTTTGACAA	0.368			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	0			7											99	105	103					7																	6026616		2203	4300	6503	5993142	SO:0001819	synonymous_variant	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1780T>C	7.37:g.6026616A>G			5993142	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.368	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		G	6026616	A	G	6026616	2	3	84	1	0	0	0	0	0	0	0	1	12174	40	2	4		4	PMS2	7	6026616	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	3063663	6026616	153112047	77	23769										
ANKMY2	57037	hgsc.bcm.edu	37	chr7	16649337	16649337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attttctgatactttctctaAtgatcttttcttgatacact	3	8	4	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:16649337A>G	ENST00000306999.2	-	7	1043	c.800T>C	c.(799-801)aTt>aCt	p.I267T		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	267						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		ACTTTCTCTAATGATCTTTTC	0.393																																																0			7											106	107	107					7																	16649337		2203	4300	6503	16615862	SO:0001583	missense	57037			AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.800T>C	7.37:g.16649337A>G	ENSP00000303570:p.Ile267Thr		16615862	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	37	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.891196	0.72524	.	.	ENSG00000106524	ENST00000306999	D	0.82526	-1.62	6.03	6.03	0.97812	.	0.198948	0.53938	D	0.000057	D	0.84297	0.5441	M	0.76328	2.33	0.54753	D	0.999988	P	0.49253	0.921	B	0.42625	0.393	D	0.86719	0.1941	10	0.72032	D	0.01	-19.4836	16.5582	0.84512	1.0:0.0:0.0:0.0	.	267	Q8IV38	ANKY2_HUMAN	T	267	ENSP00000303570:I267T	ENSP00000303570:I267T	I	-	2	0	ANKMY2	16615862	1.000000	0.71417	0.990000	0.47175	0.958000	0.62258	8.962000	0.93254	2.308000	0.77769	0.533000	0.62120	ATT		0.393	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		G	16649337	A	G	16649337	3	3	84	1	0	0	0	0	1	0	0	0	635	101	4	4	541	4	ANKMY2	7	16649337	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	10622721	16649337	142489326	78	23770										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21765557	21765557	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aagaaattattgccctgggcTgacaaaattgcccagtttac	8	9	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:21765557T>C	ENST00000409508.3	+	45	7426	c.7395T>C	c.(7393-7395)gcT>gcC	p.A2465A	DNAH11_ENST00000328843.6_Silent_p.A2472A	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2472					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TGCCCTGGGCTGACAAAATTG	0.403									Kartagener syndrome																																							0			7											64	68	66					7																	21765557		1836	4076	5912	21732082	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.7395T>C	7.37:g.21765557T>C			21732082	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37																																																																																					0.403	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		C	21765557	T	C	21765557	2	2	84	1	0	0	0	0	0	0	0	1	4610	1567	55	4		4	DNAH11	7	21765557	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	5116220	21765557	137373106	79	23771										
FAM126A	84668	hgsc.bcm.edu	37	chr7	22999942	22999942	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tttcttgatattcgagaggaAgttggtgtgatttcaacttg	11	4	2	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:22999942A>C	ENST00000432176.2	-	10	1156	c.924T>G	c.(922-924)acT>acG	p.T308T	FAM126A_ENST00000498833.1_5'UTR|FAM126A_ENST00000409923.1_Silent_p.T308T	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	308					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TTCGAGAGGAAGTTGGTGTGA	0.393																																																0			7											273	242	253					7																	22999942		2203	4300	6503	22966467	SO:0001819	synonymous_variant	84668			BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"down regulated by Ctnnb1, a"	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.924T>G	7.37:g.22999942A>C			22966467	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1	.	.	.	.	.	.	.	.	.	.	a	10.34	1.322796	0.23994	.	.	ENSG00000122591	ENST00000440481	.	.	.	5.36	1.54	0.23209	.	.	.	.	.	T	0.45135	0.1327	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23404	-1.0189	4	.	.	.	-12.2436	2.8599	0.05583	0.5586:0.1279:0.0682:0.2453	.	.	.	.	R	360	.	.	L	-	2	0	FAM126A	22966467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.097000	0.50251	0.083000	0.17047	0.524000	0.50904	CTT		0.393	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581		C	22999942	A	C	22999942	2	2	84	1	0	0	0	0	0	0	0	1	5445	59	3	4		4	FAM126A	7	22999942	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	1234385	22999942	136138721	80	23772										
STX1A	6804	hgsc.bcm.edu	37	chr7	73117265	73117265	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atgatctcactgtgccgcgtCtcaatctcgctcagagcctg	9	14	4	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:73117265C>A	ENST00000222812.3	-	8	614	c.588G>T	c.(586-588)gaG>gaT	p.E196D	WBSCR22_ENST00000423166.2_Intron|STX1A_ENST00000395156.3_Missense_Mutation_p.E196D|STX1A_ENST00000484736.1_5'Flank|STX1A_ENST00000395154.3_Missense_Mutation_p.E196D|STX1A_ENST00000395155.3_Missense_Mutation_p.E196D	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	196	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				TGTGCCGCGTCTCAATCTCGC	0.602																																																0			7											127	88	101					7																	73117265		2203	4300	6503	72755201	SO:0001583	missense	6804				CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.588G>T	7.37:g.73117265C>A	ENSP00000222812:p.Glu196Asp		72755201	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Missense_Mutation	SNP	ENST00000222812.3	37	CCDS34655.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.845056	0.91197	.	.	ENSG00000106089	ENST00000428377;ENST00000222812;ENST00000395156;ENST00000395154;ENST00000395155	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.41	3.59	0.41128	t-SNARE (1);Target SNARE coiled-coil domain (2);	0.000000	0.85682	D	0.000000	T	0.44498	0.1296	M	0.86268	2.805	0.80722	D	1	P;D;P	0.57257	0.694;0.979;0.814	P;P;B	0.53988	0.739;0.703;0.356	T	0.52343	-0.8588	10	0.87932	D	0	-41.2047	10.4212	0.44352	0.0:0.835:0.0:0.165	.	196;196;196	Q7Z5K3;Q16623-3;Q16623	.;.;STX1A_HUMAN	D	105;196;196;196;196	ENSP00000222812:E196D;ENSP00000378585:E196D;ENSP00000378583:E196D;ENSP00000378584:E196D	ENSP00000222812:E196D	E	-	3	2	STX1A	72755201	1.000000	0.71417	0.995000	0.50966	0.813000	0.45954	3.832000	0.55783	1.295000	0.44724	0.561000	0.74099	GAG		0.602	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603		A	73117265	C	A	73117265	3	1	84	1	0	0	0	0	1	0	0	0	15382	912	32	2	290	2	STX1A	7	73117265	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	50117323	73117265	86021398	81	23773										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81601176	81601176	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actctattaatcaaatccgcGttacctaacacagaaaaaga	4	10	2	2	rs147499376	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:81601176G>A	ENST00000356253.5	-	26	2349	c.2094C>T	c.(2092-2094)aaC>aaT	p.N698N	CACNA2D1_ENST00000356860.3_Silent_p.N686N|CACNA2D1_ENST00000535308.1_5'Flank			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	698					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TCAAATCCGCGTTACCTAACA	0.294													G|||	6	0.00119808	8e-04	0	5008	,	,		14947	0		0.003	False		,,,				2504	0.002															0			7						G		0,4404		0,0,2202	68	70	69		2058	-4.7	0.8	7	dbSNP_134	69	2,8588	2.2+/-6.3	0,2,4293	no	coding-synonymous	CACNA2D1	NM_000722.2		0,2,6495	AA,AG,GG		0.0233,0.0,0.0154		686/1092	81601176	2,12992	2202	4295	6497	81439112	SO:0001819	synonymous_variant	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2094C>T	7.37:g.81601176G>A			81439112	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	2.527	-0.309369	0.05458	0.0	2.33E-4	ENSG00000153956	ENST00000443883	.	.	.	5.22	-4.69	0.03299	.	.	.	.	.	T	0.63768	0.2539	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64647	-0.6358	4	.	.	.	-21.5342	15.1701	0.72865	0.8629:0.0:0.1371:0.0	.	.	.	.	M	197	.	.	T	-	2	0	CACNA2D1	81439112	0.275000	0.24201	0.803000	0.32268	0.463000	0.32649	0.269000	0.18589	-0.773000	0.04596	-0.203000	0.12734	ACG		0.294	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				A	81601176	G	A	81601176	2	1	84	1	0	0	0	0	0	0	0	1	2554	1136	40	1		1	CACNA2D1	7	81601176	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	8483911	81601176	77537487	82	23774										
BRI3	55971	hgsc.bcm.edu	37	chr7	97920546	97920546	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgccccaactgtggagccacCttcgcttaaagggaacacca	9	14	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:97920546C>T	ENST00000005260.8	-	0	3622				BRI3_ENST00000297290.3_Silent_p.T123T|BRI3_ENST00000473967.1_3'UTR|BRI3_ENST00000539286.1_Intron	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.T123T(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			GTGGAGCCACCTTCGCTTAAA	0.473																																																1	Substitution - coding silent(1)	lung(1)	7											118	90	100					7																	97920546		2203	4300	6503	97758482	SO:0001628	intergenic_variant	81618			AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117		7.37:g.97920546C>T			97758482	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																				0.473	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		T	97920546	C	T	97920546	1	4	84	0	1	0	0	0	0	0	0	0	1515	668	24	3		3	BRI3	7	97920546	IGR	SNP	C	TCGA-AH-6643-01A-11D-1826-10	16319370	97920546	61218117	83	23775										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107342416	107342416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agcttccagtcaaagtgaacGttcccaaagtgccaatccat	7	12	1	1	rs199789119		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:107342416G>A	ENST00000265715.3	+	17	2172	c.1948G>A	c.(1948-1950)Gtt>Att	p.V650I	SLC26A4_ENST00000544569.1_Missense_Mutation_p.V237I|SLC26A4_ENST00000541474.1_Missense_Mutation_p.V211I|SLC26A4_ENST00000543100.1_Missense_Mutation_p.V219I	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	650	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						CAAAGTGAACGTTCCCAAAGT	0.463									Pendred syndrome				G|||	1	0.000199681	0	0	5008	,	,		18989	0		0	False		,,,				2504	0.001															0			7											131	110	117					7																	107342416		2203	4300	6503	107129652	SO:0001583	missense	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1948G>A	7.37:g.107342416G>A	ENSP00000265715:p.Val650Ile		107129652	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.443248	0.63067	.	.	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94897	-3.21;-3.49;-3.55;-3.55	5.89	5.89	0.94794	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.067894	0.56097	D	0.000026	D	0.91727	0.7384	L	0.50919	1.6	0.37831	D	0.928733	P;P;P	0.46706	0.883;0.688;0.734	B;B;B	0.40825	0.189;0.307;0.341	D	0.91242	0.5022	10	0.27785	T	0.31	.	13.8722	0.63626	0.0781:0.0:0.9219:0.0	.	211;237;650	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	I	650;211;237;219	ENSP00000265715:V650I;ENSP00000439743:V211I;ENSP00000437427:V237I;ENSP00000441209:V219I	ENSP00000265715:V650I	V	+	1	0	SLC26A4	107129652	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.799000	0.75160	2.783000	0.95769	0.655000	0.94253	GTT		0.463	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		A	107342416	G	A	107342416	3	1	84	1	0	0	0	0	1	0	0	0	14556	1145	40	1	2010	1	SLC26A4	7	107342416	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	9421870	107342416	51796247	84	23776										
KCND2	3751	hgsc.bcm.edu	37	chr7	119915600	119915600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	caggatctttaagttttcccGccactctcaaggcctgcgca	8	14	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:119915600G>A	ENST00000331113.4	+	1	1879	c.914G>A	c.(913-915)cGc>cAc	p.R305H		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	305					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AAGTTTTCCCGCCACTCTCAA	0.512																																																0			7											77	69	72					7																	119915600		2203	4300	6503	119702836	SO:0001583	missense	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.914G>A	7.37:g.119915600G>A	ENSP00000333496:p.Arg305His		119702836	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.696516	0.88830	.	.	ENSG00000184408	ENST00000331113	D	0.98762	-5.12	5.4	5.4	0.78164	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99281	0.9749	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99239	1.0884	9	.	.	.	.	19.5371	0.95257	0.0:0.0:1.0:0.0	.	305	Q9NZV8	KCND2_HUMAN	H	305	ENSP00000333496:R305H	.	R	+	2	0	KCND2	119702836	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.706000	0.92434	0.557000	0.71058	CGC		0.512	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		A	119915600	G	A	119915600	3	1	84	1	0	0	0	0	1	0	0	0	8040	1087	38	1	916	1	KCND2	7	119915600	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	12573184	119915600	39223063	85	23777										
FEZF1	389549	hgsc.bcm.edu	37	chr7	121943863	121943863	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctactccagaagggtatttcTccaccgccgggaccaccagt	9	15	1	1	rs77195921		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:121943863T>C	ENST00000442488.2	-	1	696	c.629A>G	c.(628-630)gAg>gGg	p.E210G	FEZF1-AS1_ENST00000437317.1_RNA|FEZF1_ENST00000331178.4_Missense_Mutation_p.E210G|FEZF1_ENST00000427185.2_Missense_Mutation_p.E160G|FEZF1-AS1_ENST00000428449.1_RNA	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	210					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						AGGGTATTTCTCCACCGCCGG	0.522																																																0			7											55	61	59					7																	121943863		2203	4300	6503	121731099	SO:0001583	missense	389549			AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"Zinc fingers, C2H2-type"	22788	protein-coding gene	gene with protein product		613301	"zinc finger protein 312B"	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.629A>G	7.37:g.121943863T>C	ENSP00000411145:p.Glu210Gly		121731099	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	T	12.46	1.945747	0.34377	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.08546	3.08;3.23;3.2	4.72	4.72	0.59763	.	0.150338	0.64402	D	0.000015	T	0.07413	0.0187	L	0.27053	0.805	0.38234	D	0.941116	B;P	0.36535	0.281;0.557	B;B	0.33890	0.057;0.172	T	0.28170	-1.0052	10	0.66056	D	0.02	-27.419	14.6406	0.68723	0.0:0.0:0.0:1.0	.	210;160	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	G	210;210;160	ENSP00000411145:E210G;ENSP00000332777:E210G;ENSP00000392727:E160G	ENSP00000332777:E210G	E	-	2	0	FEZF1	121731099	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	2.958000	0.49145	2.097000	0.63578	0.454000	0.30748	GAG		0.522	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613		C	121943863	T	C	121943863	3	2	84	1	0	0	0	0	1	0	0	0	5844	1551	54	4	814	4	FEZF1	7	121943863	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	2028263	121943863	37194800	86	23778										
IQUB	154865	hgsc.bcm.edu	37	chr7	123152365	123152365	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gttgaattgactatattctgAgcttcatacttctcctgttg	7	8	3	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:123152365A>G	ENST00000466202.1	-	2	606	c.30T>C	c.(28-30)gcT>gcC	p.A10A	IQUB_ENST00000324698.6_Silent_p.A10A|IQUB_ENST00000434450.1_Silent_p.A10A|IQUB_ENST00000488987.1_Intron	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	10					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CTATATTCTGAGCTTCATACT	0.333																																																0			7											79	78	79					7																	123152365		2203	4300	6503	122939601	SO:0001819	synonymous_variant	154865			AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.30T>C	7.37:g.123152365A>G			122939601	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																				0.333	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		G	123152365	A	G	123152365	2	3	84	1	0	0	0	0	0	0	0	1	7841	291	11	4		4	IQUB	7	123152365	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	1208502	123152365	35986298	87	23779										
AKR1B1	231	hgsc.bcm.edu	37	chr7	134134495	134134495	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccacgtgtccagaatgttggTgtcactgggaaccacattgc	11	11	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:134134495T>A	ENST00000285930.4	-	4	485	c.406A>T	c.(406-408)Acc>Tcc	p.T136S	AKR1B1_ENST00000489022.1_5'UTR	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	136					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	AGAATGTTGGTGTCACTGGGA	0.453																																																0			7											188	170	176					7																	134134495		2203	4300	6503	133785035	SO:0001583	missense	231			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.406A>T	7.37:g.134134495T>A	ENSP00000285930:p.Thr136Ser		133785035	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Missense_Mutation	SNP	ENST00000285930.4	37	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.554091	0.45487	.	.	ENSG00000085662	ENST00000285930	T	0.12672	2.66	5.74	2.05	0.26809	NADP-dependent oxidoreductase domain (3);	0.186853	0.56097	D	0.000021	T	0.08044	0.0201	N	0.25094	0.71	0.23440	N	0.997677	B	0.06786	0.001	B	0.06405	0.002	T	0.29882	-0.9997	10	0.36615	T	0.2	.	6.4597	0.21950	0.0:0.1382:0.1324:0.7293	.	136	P15121	ALDR_HUMAN	S	136	ENSP00000285930:T136S	ENSP00000285930:T136S	T	-	1	0	AKR1B1	133785035	0.997000	0.39634	0.002000	0.10522	0.148000	0.21650	3.808000	0.55598	0.172000	0.19760	0.459000	0.35465	ACC		0.453	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		A	134134495	T	A	134134495	3	1	84	1	0	0	0	0	1	0	0	0	466	1696	59	5	572	5	AKR1B1	7	134134495	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	10982130	134134495	25004168	88	23780										
TAS2R5	54429	hgsc.bcm.edu	37	chr7	141490252	141490252	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atggaagcctggtggtctggAgttttagagaatggatcaga	15	4	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:141490252A>C	ENST00000247883.4	+	1	236	c.91A>C	c.(91-93)Agt>Cgt	p.S31R		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	31					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GGTGGTCTGGAGTTTTAGAGA	0.498																																																0			7											103	102	103					7																	141490252		2203	4300	6503	141136721	SO:0001583	missense	54429			AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.91A>C	7.37:g.141490252A>C	ENSP00000247883:p.Ser31Arg		141136721	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.347123	0.24426	.	.	ENSG00000127366	ENST00000247883	T	0.37058	1.22	4.13	1.59	0.23543	.	.	.	.	.	T	0.42562	0.1208	L	0.36672	1.1	0.23559	N	0.997415	D	0.61697	0.99	D	0.67900	0.954	T	0.19289	-1.0310	9	0.87932	D	0	.	4.6723	0.12694	0.6061:0.201:0.0:0.1929	.	31	Q9NYW4	TA2R5_HUMAN	R	31	ENSP00000247883:S31R	ENSP00000247883:S31R	S	+	1	0	TAS2R5	141136721	0.983000	0.35010	0.155000	0.22561	0.004000	0.04260	1.665000	0.37449	0.215000	0.20761	0.459000	0.35465	AGT		0.498	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1			C	141490252	A	C	141490252	3	2	84	1	0	0	0	0	1	0	0	0	15622	304	11	4	93	4	TAS2R5	7	141490252	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	7355757	141490252	17648411	89	23781										
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150174281	150174281	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcacctctcggctccgggccCagccagtcaccaagaccagc	9	19	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr7:150174281C>A	ENST00000307271.3	+	5	1985	c.1411C>A	c.(1411-1413)Cag>Aag	p.Q471K		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	471	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GCTCCGGGCCCAGCCAGTCAC	0.602																																																0			7											69	68	68					7																	150174281		2203	4300	6503	149805214	SO:0001583	missense	155038			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1411C>A	7.37:g.150174281C>A	ENSP00000305107:p.Gln471Lys		149805214		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.336141	0.24253	.	.	ENSG00000171115	ENST00000307271	T	0.33865	1.39	4.44	1.48	0.22813	AIG1 (1);	0.167176	0.28549	N	0.014959	T	0.16642	0.0400	N	0.25380	0.74	0.09310	N	1	B	0.15719	0.014	B	0.16289	0.015	T	0.27571	-1.0070	10	0.02654	T	1	.	4.6076	0.12385	0.393:0.5014:0.0:0.1056	.	471	Q8ND71	GIMA8_HUMAN	K	471	ENSP00000305107:Q471K	ENSP00000305107:Q471K	Q	+	1	0	GIMAP8	149805214	0.000000	0.05858	0.156000	0.22583	0.016000	0.09150	-0.515000	0.06290	1.099000	0.41499	-0.152000	0.13540	CAG		0.602	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		A	150174281	C	A	150174281	3	1	84	1	0	0	0	0	1	0	0	0	6405	595	21	2	1425	2	GIMAP8	7	150174281	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	8684029	150174281	8964382	90	23782										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2964063	2964063	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgcataccttcacatgttggGagagaaccctcaaactgcaa	8	11	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:2964063G>C	ENST00000520002.1	-	47	7494	c.6939C>G	c.(6937-6939)ctC>ctG	p.L2313L	CSMD1_ENST00000602723.1_Silent_p.L2313L|CSMD1_ENST00000542608.1_Silent_p.L2312L|CSMD1_ENST00000602557.1_Silent_p.L2313L|CSMD1_ENST00000400186.3_Silent_p.L2313L|CSMD1_ENST00000537824.1_Silent_p.L2312L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2313	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				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)		CACATGTTGGGAGAGAACCCT	0.428																																																0			8											58	56	57					8																	2964063		1904	4135	6039	2951470	SO:0001819	synonymous_variant	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6939C>G	8.37:g.2964063G>C			2951470	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	0.011	-1.721894	0.00700	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.31	0.182	0.15077	.	.	.	.	.	T	0.41396	0.1157	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	.	1.0933	0.01668	0.3438:0.2449:0.2792:0.1321	.	.	.	.	A	1793	.	.	P	-	1	0	CSMD1	2951470	0.643000	0.27269	0.003000	0.11579	0.002000	0.02628	-0.224000	0.09164	-0.280000	0.09154	-0.259000	0.10710	CCC		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2964063	G	C	2964063	2	2	84	1	0	0	0	0	0	0	0	1	3950	1161	41	5		5	CSMD1	8	2964063	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10		2964063	143399959	91	23783										
PRSS55	203074	hgsc.bcm.edu	37	chr8	10396009	10396009	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gacagtggggggcctctggtCtgcaccccagagcctggtga	16	12	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:10396009C>A	ENST00000328655.3	+	5	805	c.765C>A	c.(763-765)gtC>gtA	p.V255V	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Intron	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	255	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GGCCTCTGGTCTGCACCCCAG	0.587																																																0			8											58	64	62					8																	10396009		2203	4300	6503	10433419	SO:0001819	synonymous_variant	0			AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.765C>A	8.37:g.10396009C>A			10433419	E5RJX5	Silent	SNP	ENST00000328655.3	37	CCDS5976.1																																																																																				0.587	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10396009	C	A	10396009	2	1	84	1	0	0	0	0	0	0	0	1	12668	900	32	2		2	PRSS55	8	10396009	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	7431946	10396009	135968013	92	23784										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24192996	24192996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggtgtgcagaccagcaaaagAtgagtgcgacctgcctgaaa	13	9	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:24192996A>G	ENST00000265769.4	+	14	1519	c.1409A>G	c.(1408-1410)gAt>gGt	p.D470G	ADAM28_ENST00000437154.2_Missense_Mutation_p.D470G|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.D217G|ADAM28_ENST00000540823.1_Missense_Mutation_p.D237G|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	470	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CCAGCAAAAGATGAGTGCGAC	0.433																																					NSCLC(193;488 2149 22258 34798 40734)											0			8											134	125	128					8																	24192996		2203	4300	6503	24248941	SO:0001583	missense	10863			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1409A>G	8.37:g.24192996A>G	ENSP00000265769:p.Asp470Gly		24248941	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.884561	0.51908	.	.	ENSG00000042980	ENST00000265769;ENST00000397649;ENST00000540823;ENST00000437154	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	5.8	5.8	0.92144	Blood coagulation inhibitor, Disintegrin (5);	.	.	.	.	T	0.14527	0.0351	N	0.13299	0.325	0.50467	D	0.999872	P;P;P;P	0.52170	0.868;0.951;0.951;0.913	P;P;P;P	0.59012	0.85;0.665;0.665;0.767	T	0.24835	-1.0149	9	0.27082	T	0.32	.	14.0996	0.65046	1.0:0.0:0.0:0.0	.	237;470;470;470	B4DDY3;B2RMV5;Q9UKQ2;Q9UKQ2-2	.;.;ADA28_HUMAN;.	G	470;217;237;470	ENSP00000265769:D470G;ENSP00000380770:D217G;ENSP00000443743:D237G;ENSP00000393699:D470G	ENSP00000265769:D470G	D	+	2	0	ADAM28	24248941	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.162000	0.71874	2.213000	0.71641	0.528000	0.53228	GAT		0.433	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		G	24192996	A	G	24192996	3	3	84	1	0	0	0	0	1	0	0	0	246	333	12	4	1463	4	ADAM28	8	24192996	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	13796987	24192996	122171026	93	23785										
ADRB3	155	hgsc.bcm.edu	37	chr8	37823677	37823677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cgcagccagtggcgcccaacGgccagtggccagtcagcgcc	14	17	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:37823677G>A	ENST00000345060.3	-	1	806	c.311C>T	c.(310-312)cCg>cTg	p.P104L	ADRB3_ENST00000520341.1_5'Flank	NM_000025.2	NP_000016.1	P13945	ADRB3_HUMAN	adrenoceptor beta 3	104					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|aging (GO:0007568)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|diet induced thermogenesis (GO:0002024)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|generation of precursor metabolites and energy (GO:0006091)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of MAPK cascade (GO:0043410)|response to antibiotic (GO:0046677)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta-adrenergic receptor activity (GO:0004939)|beta3-adrenergic receptor activity (GO:0015052)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)	9	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Bethanidine(DB00217)|Bopindolol(DB08807)|Bupranolol(DB08808)|Clenbuterol(DB01407)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Isoprenaline(DB01064)|Mephentermine(DB01365)|Mirabegron(DB08893)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Propranolol(DB00571)|Trimipramine(DB00726)	GGCGCCCAACGGCCAGTGGCC	0.682																																																0			8											15	17	16					8																	37823677		2150	4234	6384	37942834	SO:0001583	missense	155			AY487247	CCDS6099.1	8p12	2012-08-08	2012-05-09			ENSG00000188778		"GPCR / Class A : Adrenoceptors : beta"	288	protein-coding gene	gene with protein product		109691	"adrenergic, beta-3-, receptor"			7898940, 15123695	Standard	NM_000025		Approved		uc003xkr.2	P13945		ENST00000345060.3:c.311C>T	8.37:g.37823677G>A	ENSP00000343782:p.Pro104Leu		37942834	Q4JFT4	Missense_Mutation	SNP	ENST00000345060.3	37	CCDS6099.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.087481	0.36855	.	.	ENSG00000188778	ENST00000345060	T	0.26067	1.76	4.51	3.63	0.41609	GPCR, rhodopsin-like superfamily (1);	0.294943	0.33290	N	0.005072	T	0.11239	0.0274	N	0.11673	0.155	0.46927	D	0.999252	B	0.31879	0.344	B	0.24155	0.051	T	0.16748	-1.0392	10	0.24483	T	0.36	.	9.0423	0.36325	0.1716:0.0:0.8284:0.0	.	104	P13945	ADRB3_HUMAN	L	104	ENSP00000343782:P104L	ENSP00000343782:P104L	P	-	2	0	ADRB3	37942834	0.933000	0.31639	1.000000	0.80357	0.969000	0.65631	1.004000	0.29822	1.263000	0.44181	0.313000	0.20887	CCG		0.682	ADRB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376826.1	NM_000025		A	37823677	G	A	37823677	3	1	84	1	0	0	0	0	1	0	0	0	342	1116	39	1	923	1	ADRB3	8	37823677	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	13630681	37823677	108540345	94	23786										
DPYS	1807	hgsc.bcm.edu	37	chr8	105459697	105459697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcttgaaagagttaacacctTtatcttgcacaaggattttc	6	8	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:105459697T>C	ENST00000351513.2	-	3	590	c.458A>G	c.(457-459)aAa>aGa	p.K153R		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	153					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GTTAACACCTTTATCTTGCAC	0.363																																																0			8											123	112	115					8																	105459697		2203	4300	6503	105528873	SO:0001583	missense	1807			D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.458A>G	8.37:g.105459697T>C	ENSP00000276651:p.Lys153Arg		105528873		Missense_Mutation	SNP	ENST00000351513.2	37	CCDS6302.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466352	0.43839	.	.	ENSG00000147647	ENST00000351513;ENST00000521573	D;D	0.90197	-2.49;-2.63	6.02	6.02	0.97574	Amidohydrolase 1 (1);	0.046077	0.85682	D	0.000000	D	0.87075	0.6087	L	0.42581	1.335	0.44073	D	0.996824	B	0.06786	0.001	B	0.12837	0.008	T	0.82313	-0.0519	10	0.19590	T	0.45	-24.7732	16.5494	0.84464	0.0:0.0:0.0:1.0	.	153	Q14117	DPYS_HUMAN	R	153;100	ENSP00000276651:K153R;ENSP00000430246:K100R	ENSP00000276651:K153R	K	-	2	0	DPYS	105528873	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	5.942000	0.70203	2.299000	0.77371	0.528000	0.53228	AAA		0.363	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		C	105459697	T	C	105459697	3	2	84	1	0	0	0	0	1	0	0	0	4757	1841	64	4	1129	4	DPYS	8	105459697	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	67636020	105459697	40904325	95	23787										
GLI4	2738	hgsc.bcm.edu	37	chr8	144351679	144351679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gcctcagcttcacctccatgGgcatcaacatggtactcacc	7	16	4	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:144351679G>A	ENST00000523522.1	+	1	152	c.113G>A	c.(112-114)gGg>gAg	p.G38E	GLI4_ENST00000517468.1_Missense_Mutation_p.G38E|GLI4_ENST00000340042.1_Missense_Mutation_p.G38E|GLI4_ENST00000344692.3_Missense_Mutation_p.G38E|GLI4_ENST00000521682.1_Missense_Mutation_p.G38E|ZFP41_ENST00000522452.1_Intron			P10075	GLI4_HUMAN	GLI family zinc finger 4	38					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G38V(1)		endometrium(3)|large_intestine(1)|lung(5)	9	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CACCTCCATGGGCATCAACAT	0.647																																																1	Substitution - Missense(1)	endometrium(1)	8											184	172	176					8																	144351679		2203	4300	6503	144423054	SO:0001583	missense	2738				CCDS6398.1	8q24.3	2013-01-08	2009-03-05		ENSG00000250571	ENSG00000250571		"Zinc fingers, C2H2-type"	4320	protein-coding gene	gene with protein product		165280	"GLI-Kruppel family member GLI4", "glioma-associated oncogene family zinc finger 4"			2850480	Standard	NM_138465		Approved	HKR4, ZNF928	uc003yxx.3	P10075	OTTHUMG00000164952	ENST00000523522.1:c.113G>A	8.37:g.144351679G>A	ENSP00000430987:p.Gly38Glu		144423054	Q96CK9	Missense_Mutation	SNP	ENST00000523522.1	37	CCDS6398.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.686410	0.47991	.	.	ENSG00000250571	ENST00000521682;ENST00000340042;ENST00000344692;ENST00000517468;ENST00000523522;ENST00000520021;ENST00000517530	T;T	0.05513	3.43;3.43	4.39	0.636	0.17729	.	.	.	.	.	T	0.04182	0.0116	L	0.27053	0.805	0.09310	N	1	B	0.18461	0.028	B	0.09377	0.004	T	0.41161	-0.9524	9	0.45353	T	0.12	.	3.0576	0.06189	0.358:0.2214:0.4205:0.0	.	38	P10075	GLI4_HUMAN	E	38;38;38;38;38;38;15	ENSP00000345024:G38E;ENSP00000430987:G38E	ENSP00000345024:G38E	G	+	2	0	GLI4	144423054	0.001000	0.12720	0.001000	0.08648	0.877000	0.50540	0.982000	0.29539	0.272000	0.22027	0.563000	0.77884	GGG		0.647	GLI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381128.2			A	144351679	G	A	144351679	3	1	84	1	0	0	0	0	1	0	0	0	6460	1232	43	3	115	3	GLI4	8	144351679	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	38891982	144351679	2012343	96	23788										
ADCK5	203054	hgsc.bcm.edu	37	chr8	145618211	145618211	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	accttggccatgcggctgacCgccctcctggctcgtgctct	11	17	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr8:145618211C>T	ENST00000308860.6	+	15	1709	c.1665C>T	c.(1663-1665)acC>acT	p.T555T	MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'Flank	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	555						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-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;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGCGGCTGACCGCCCTCCTGG	0.716																																																0			8											27	24	25					8																	145618211		2181	4291	6472	145589019	SO:0001819	synonymous_variant	203054			BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.1665C>T	8.37:g.145618211C>T			145589019	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Silent	SNP	ENST00000308860.6	37	CCDS34965.1																																																																																				0.716	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922		T	145618211	C	T	145618211	2	4	84	1	0	0	0	0	0	0	0	1	291	639	23	1		1	ADCK5	8	145618211	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	1266532	145618211	745811	97	23789										
VLDLR	7436	hgsc.bcm.edu	37	chr9	2641486	2641486	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gattgtgacagtggagaagaTgaagaaaactgtggtaagaa	14	2	0	6			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr9:2641486T>C	ENST00000382100.3	+	4	791	c.435T>C	c.(433-435)gaT>gaC	p.D145D	VLDLR_ENST00000382099.2_Silent_p.D145D|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	145	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		GTGGAGAAGATGAAGAAAACT	0.463																																																0			9											268	241	250					9																	2641486		2203	4300	6503	2631486	SO:0001819	synonymous_variant	7436				CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.435T>C	9.37:g.2641486T>C			2631486	B2RMZ7|D3DRH6|Q5VVF6	Silent	SNP	ENST00000382100.3	37	CCDS6446.1																																																																																				0.463	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		C	2641486	T	C	2641486	2	2	84	1	0	0	0	0	0	0	0	1	17214	1461	51	4		4	VLDLR	9	2641486	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10		2641486	138571945	98	23790										
ERMP1	79956	hgsc.bcm.edu	37	chr9	5801200	5801200	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agaaacactctctttggcttCggattagcaggattggagct	11	8	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr9:5801200C>T	ENST00000339450.5	-	11	2132	c.2043G>A	c.(2041-2043)ccG>ccA	p.P681P	ERMP1_ENST00000381506.3_3'UTR|ERMP1_ENST00000543230.1_Silent_p.P259P|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	681						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.P681P(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TCTTTGGCTTCGGATTAGCAG	0.398																																																1	Substitution - coding silent(1)	ovary(1)	9											116	113	114					9																	5801200		2203	4300	6503	5791200	SO:0001819	synonymous_variant	79956			AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.2043G>A	9.37:g.5801200C>T			5791200	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																				0.398	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		T	5801200	C	T	5801200	2	4	84	1	0	0	0	0	0	0	0	1	5249	871	31	1		1	ERMP1	9	5801200	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	3159714	5801200	135412231	99	23791										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98244290	98244290	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cagaagcagtccaaaggtgtAataatcaaacaagggtaaag	10	6	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr9:98244290A>G	ENST00000331920.6	-	5	986	c.687T>C	c.(685-687)atT>atC	p.I229I	PTCH1_ENST00000418258.1_Silent_p.I78I|PTCH1_ENST00000421141.1_Silent_p.I78I|PTCH1_ENST00000375274.2_Silent_p.I228I|PTCH1_ENST00000429896.2_Silent_p.I78I|PTCH1_ENST00000468211.2_Silent_p.I163I|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000430669.2_Silent_p.I163I|PTCH1_ENST00000437951.1_Silent_p.I163I	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	229					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CCAAAGGTGTAATAATCAAAC	0.423																																																0			9											83	76	78					9																	98244290		2203	4300	6503	97284111	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.687T>C	9.37:g.98244290A>G			97284111	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.423	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		G	98244290	A	G	98244290	2	3	84	1	0	0	0	0	0	0	0	1	12764	358	13	4		4	PTCH1	9	98244290	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	92443090	98244290	42969141	100	23792										
NEK6	10783	hgsc.bcm.edu	37	chr9	127083759	127083759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aactgaaccacccaaatatcAtcaagtatttggactcgttt	5	10	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr9:127083759A>G	ENST00000320246.5	+	5	461	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	NEK6_ENST00000373603.1_Missense_Mutation_p.I106V|NEK6_ENST00000540326.1_Missense_Mutation_p.I124V|NEK6_ENST00000546191.1_Missense_Mutation_p.I106V|NEK6_ENST00000394199.2_Missense_Mutation_p.I140V|NEK6_ENST00000539416.1_Missense_Mutation_p.I131V|NEK6_ENST00000545174.1_Missense_Mutation_p.I106V|NEK6_ENST00000373600.3_Missense_Mutation_p.I140V	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						CCCAAATATCATCAAGTATTT	0.557																																					NSCLC(122;934 1785 18647 44295 45571)											0			9											98	79	85					9																	127083759		2203	4300	6503	126123580	SO:0001583	missense	10783			AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"putative serine-threonine protein kinase"	604884	"NIMA (never in mitosis gene a)-related kinase 6"			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.316A>G	9.37:g.127083759A>G	ENSP00000319734:p.Ile106Val		126123580	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Missense_Mutation	SNP	ENST00000320246.5	37	CCDS6854.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504861	0.64410	.	.	ENSG00000119408	ENST00000373603;ENST00000540326;ENST00000373600;ENST00000320246;ENST00000373601;ENST00000545174;ENST00000444973;ENST00000454453;ENST00000373596;ENST00000425237;ENST00000423785;ENST00000394199;ENST00000546191;ENST00000422297;ENST00000539416;ENST00000447379	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.28069	3.67;3.67;3.67;3.67;3.67;2.43;1.63;3.67;2.43;3.67;3.67;3.67;2.43;3.67;3.67	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.23370	0.0565	N	0.12471	0.22	0.58432	D	0.999999	P;P;P;P	0.43477	0.692;0.808;0.722;0.638	P;P;P;P	0.49597	0.54;0.616;0.447;0.616	T	0.03784	-1.1004	10	0.02654	T	1	.	14.5176	0.67830	1.0:0.0:0.0:0.0	.	131;140;106;124	Q9HC98-4;Q9HC98-2;Q9HC98;Q9HC98-3	.;.;NEK6_HUMAN;.	V	106;124;140;106;38;106;106;38;106;106;140;140;106;106;131;106	ENSP00000362705:I106V;ENSP00000441469:I124V;ENSP00000362702:I140V;ENSP00000319734:I106V;ENSP00000442636:I106V;ENSP00000389517:I106V;ENSP00000405215:I38V;ENSP00000362698:I106V;ENSP00000403087:I106V;ENSP00000399847:I140V;ENSP00000377749:I140V;ENSP00000441426:I106V;ENSP00000411401:I106V;ENSP00000439651:I131V;ENSP00000403414:I106V	ENSP00000319734:I106V	I	+	1	0	NEK6	126123580	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.802000	0.91910	2.021000	0.59480	0.533000	0.62120	ATC		0.557	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397		G	127083759	A	G	127083759	3	3	84	1	0	0	0	0	1	0	0	0	10359	217	8	4	515	4	NEK6	9	127083759	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	28839469	127083759	14129672	101	23793										
ASS1	445	hgsc.bcm.edu	37	chr9	133346259	133346259	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccggtcactcccaagaacccGtggagcatggatgagaacct	11	13	1	2	rs113818350		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr9:133346259G>A	ENST00000372394.1	+	8	1015	c.534G>A	c.(532-534)ccG>ccA	p.P178P	ASS1_ENST00000352480.5_Silent_p.P178P|ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000372393.3_Silent_p.P178P			P00966	ASSY_HUMAN	argininosuccinate synthase 1	178					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	CCAAGAACCCGTGGAGCATGG	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		18561	0		0	False		,,,				2504	0															0			9						G	,	1,4405	2.1+/-5.4	0,1,2202	175	177	176		534,534	-8.5	0.3	9	dbSNP_132	176	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ASS1	NM_000050.4,NM_054012.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	178/413,178/413	133346259	1,13005	2203	4300	6503	132336080	SO:0001819	synonymous_variant	445			X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.534G>A	9.37:g.133346259G>A			132336080	Q6LDL2|Q86UZ0|Q96GT4	Silent	SNP	ENST00000372394.1	37	CCDS6933.1																																																																																				0.612	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050		A	133346259	G	A	133346259	2	1	84	1	0	0	0	0	0	0	0	1	1062	1132	40	1		1	ASS1	9	133346259	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	6262500	133346259	7867172	102	23794										
VIM	7431	hgsc.bcm.edu	37	chr10	17271980	17271980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aggacatcatgcgcctccggGagaagtaaggctgcgcccat	13	12	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:17271980G>A	ENST00000224237.5	+	1	704	c.559G>A	c.(559-561)Gag>Aag	p.E187K	VIM_ENST00000485947.1_3'UTR|VIM_ENST00000544301.1_Missense_Mutation_p.E187K|VIM-AS1_ENST00000605833.1_RNA			P08670	VIME_HUMAN	vimentin	187	Coil 1B.|Rod.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.E187*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCGCCTCCGGGAGAAGTAAGG	0.701																																																1	Substitution - Nonsense(1)	large_intestine(1)	10											13	14	14					10																	17271980		2176	4244	6420	17311986	SO:0001583	missense	7431			M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.559G>A	10.37:g.17271980G>A	ENSP00000224237:p.Glu187Lys		17311986	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	37	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.044653	0.93685	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533	D;D	0.88741	-2.42;-2.42	5.15	5.15	0.70609	Filament (1);	0.000000	0.45606	U	0.000348	D	0.85168	0.5635	N	0.17922	0.545	0.80722	D	1	B;B;D;D;B	0.52996	0.27;0.228;0.957;0.957;0.27	B;B;P;P;B	0.48901	0.087;0.052;0.594;0.594;0.087	T	0.83168	-0.0095	10	0.19147	T	0.46	.	18.6077	0.91272	0.0:0.0:1.0:0.0	.	187;174;174;187;187	Q53HU8;F5H288;B3KRK8;B0YJC4;P08670	.;.;.;.;VIME_HUMAN	K	187;187;174	ENSP00000446007:E187K;ENSP00000224237:E187K	ENSP00000224237:E187K	E	+	1	0	VIM	17311986	1.000000	0.71417	0.994000	0.49952	0.961000	0.63080	3.759000	0.55227	2.376000	0.81061	0.551000	0.68910	GAG		0.701	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		A	17271980	G	A	17271980	3	1	84	1	0	0	0	0	1	0	0	0	17206	1175	41	3	561	3	VIM	10	17271980	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		17271980	118262767	103	23795										
ABI1	10006	hgsc.bcm.edu	37	chr10	27066141	27066141	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aaaataccaatctctcttcgTgccactttctccttatgaat	3	12	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:27066141T>C	ENST00000376142.2	-	3	386	c.315A>G	c.(313-315)gcA>gcG	p.A105A	ABI1_ENST00000536334.1_Silent_p.A105A|ABI1_ENST00000376137.4_Silent_p.A105A|ABI1_ENST00000376166.1_Silent_p.A105A|ABI1_ENST00000473481.1_5'UTR|ABI1_ENST00000355394.4_Silent_p.A105A|ABI1_ENST00000346832.5_Silent_p.A122A|ABI1_ENST00000376160.1_Silent_p.A105A|ABI1_ENST00000376170.4_Silent_p.A105A|ABI1_ENST00000376140.3_Silent_p.A105A|ABI1_ENST00000376138.3_Silent_p.A105A|ABI1_ENST00000376139.2_Silent_p.A105A|ABI1_ENST00000490841.2_Intron|ABI1_ENST00000376134.3_Silent_p.A105A|ABI1_ENST00000359188.4_Silent_p.A105A	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	105	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTCTCTTCGTGCCACTTTCT	0.328																																																0			10											91	80	83					10																	27066141		2203	4300	6503	27106147	SO:0001819	synonymous_variant	10006			U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"spectrin SH3 domain binding protein 1"	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.315A>G	10.37:g.27066141T>C			27106147	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Silent	SNP	ENST00000376142.2	37	CCDS7150.1																																																																																				0.328	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1	NM_005470		C	27066141	T	C	27066141	2	2	84	1	0	0	0	0	0	0	0	1	88	1683	59	4		4	ABI1	10	27066141	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	9794161	27066141	108468606	104	23796										
ITGB1	3688	hgsc.bcm.edu	37	chr10	33209233	33209233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcccctgttccattcaccccGttcttgcagtaagatttgta	6	13	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:33209233G>A	ENST00000396033.2	-	10	1344	c.1209C>T	c.(1207-1209)aaC>aaT	p.N403N	ITGB1_ENST00000302278.3_Silent_p.N403N|ITGB1_ENST00000423113.1_Silent_p.N403N|ITGB1_ENST00000374956.4_Silent_p.N403N	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	403					axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)	p.N403N(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CATTCACCCCGTTCTTGCAGT	0.358																																																1	Substitution - coding silent(1)	ovary(1)	10											152	129	137					10																	33209233		2203	4300	6503	33249239	SO:0001819	synonymous_variant	3688			BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1209C>T	10.37:g.33209233G>A			33249239	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																				0.358	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		A	33209233	G	A	33209233	2	1	84	1	0	0	0	0	0	0	0	1	7911	1136	40	1		1	ITGB1	10	33209233	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	6143092	33209233	102325514	105	23797										
NRP1	8829	hgsc.bcm.edu	37	chr10	33502450	33502450	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgatgatgcccctcacgatcTtctcctcccccaggtctatt	6	16	4	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:33502450T>G	ENST00000265371.4	-	10	2003	c.1478A>C	c.(1477-1479)aAg>aCg	p.K493T	NRP1_ENST00000395995.1_Missense_Mutation_p.K493T|NRP1_ENST00000374875.1_Missense_Mutation_p.K312T|NRP1_ENST00000374867.2_Missense_Mutation_p.K493T|NRP1_ENST00000374822.4_Missense_Mutation_p.K493T|NRP1_ENST00000374821.5_Missense_Mutation_p.K493T|NRP1_ENST00000374823.5_Missense_Mutation_p.K493T|NRP1_ENST00000374816.3_Missense_Mutation_p.K493T|RP11-342D11.2_ENST00000451530.1_RNA|NRP1_ENST00000432372.2_Missense_Mutation_p.K493T			O14786	NRP1_HUMAN	neuropilin 1	493	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	CCTCACGATCTTCTCCTCCCC	0.547																																					Melanoma(104;886 1489 44640 45944 51153)											0			10											171	151	158					10																	33502450		2203	4300	6503	33542456	SO:0001583	missense	8829			AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1478A>C	10.37:g.33502450T>G	ENSP00000265371:p.Lys493Thr		33542456	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	37	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.789527	0.50102	.	.	ENSG00000099250	ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000432372	D;D;D;D;D;D;D;D;D	0.98164	-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76	5.95	3.56	0.40772	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.081437	0.85682	N	0.000000	D	0.96571	0.8881	L	0.44542	1.39	0.58432	D	0.999999	B;B;B;B;B;B;B;B;B	0.32350	0.016;0.198;0.366;0.039;0.004;0.008;0.016;0.016;0.007	B;B;B;B;B;B;B;B;B	0.41946	0.173;0.285;0.371;0.233;0.012;0.037;0.123;0.111;0.05	D	0.93850	0.7144	10	0.52906	T	0.07	-20.9239	8.8565	0.35231	0.0:0.0657:0.1277:0.8066	.	493;493;493;493;493;493;493;312;493	A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;Q5JWQ6;E9PEP6	.;.;.;.;.;.;NRP1_HUMAN;.;.	T	493;312;493;493;493;493;493;493;166	ENSP00000265371:K493T;ENSP00000364009:K312T;ENSP00000364001:K493T;ENSP00000379317:K493T;ENSP00000363955:K493T;ENSP00000363954:K493T;ENSP00000363956:K493T;ENSP00000363949:K493T;ENSP00000408911:K166T	ENSP00000265371:K493T	K	-	2	0	NRP1	33542456	1.000000	0.71417	0.995000	0.50966	0.909000	0.53808	5.182000	0.65059	0.467000	0.27218	-0.290000	0.09829	AAG		0.547	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			G	33502450	T	G	33502450	3	3	84	1	0	0	0	0	1	0	0	0	10691	1609	56	4	1340	4	NRP1	10	33502450	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	293217	33502450	102032297	106	23798										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49409390	49409390	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctgtgacaaatgtgtgcttcTtcccagtgacactgcttgtg	10	10	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:49409390T>G	ENST00000374201.3	-	15	2137	c.1835A>C	c.(1834-1836)aAg>aCg	p.K612T	FRMPD2_ENST00000407470.4_Missense_Mutation_p.K580T|FRMPD2_ENST00000305531.3_Missense_Mutation_p.K587T	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	612	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TGTGTGCTTCTTCCCAGTGAC	0.473																																																0			10											207	169	182					10																	49409390		2203	4300	6503	49079396	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.1835A>C	10.37:g.49409390T>G	ENSP00000363317:p.Lys612Thr		49079396	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	17.65	3.441203	0.63067	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	D;D;D	0.86956	-2.19;-2.19;-2.19	5.02	3.84	0.44239	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	.	.	.	.	D	0.90559	0.7041	L	0.59436	1.845	0.38682	D	0.952562	D;D;D	0.89917	1.0;0.996;1.0	D;D;D	0.91635	0.999;0.977;0.999	D	0.89201	0.3557	9	0.36615	T	0.2	.	10.3396	0.43870	0.1474:0.0:0.0:0.8526	.	587;612;580	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	T	612;587;580	ENSP00000363317:K612T;ENSP00000307079:K587T;ENSP00000384339:K580T	ENSP00000307079:K587T	K	-	2	0	FRMPD2	49079396	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	3.242000	0.51384	0.809000	0.34255	0.533000	0.62120	AAG		0.473	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		G	49409390	T	G	49409390	3	3	84	1	0	0	0	0	1	0	0	0	6077	1609	56	4	2154	4	FRMPD2	10	49409390	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	15906940	49409390	86125357	107	23799										
ASAH2	56624	hgsc.bcm.edu	37	chr10	52005168	52005169	+	Missense_Mutation	DNP	GG	GG	TT													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgggcagctgtggagccctgGgtggctggagggctttgggt					rs374685598		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:52005168_52005169GG>TT	ENST00000395526.4	-	2	172_173	c.173_174CC>AA	c.(172-174)aCC>aAA	p.T58K	ASAH2_ENST00000329428.6_Missense_Mutation_p.T39K|ASAH2_ENST00000447815.1_Missense_Mutation_p.T58K	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	58					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						TGGAGCCCTGGGTGGCTGGAGG	0.505																																																0			10																																								51675174|51675175	SO:0001583	missense	56624			AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.173_174delinsTT	10.37:g.52005168_52005169delinsTT	ENSP00000378897:p.Thr58Lys		51675174|51675175	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent|Missense_Mutation	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																				0.505	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		TT	52005169	GG	TT	52005168	3	4	84	1	0	0	0	0	1	0	0	0	1008	1219	43	2	2244	2	ASAH2	10	52005168	Missense_Mutation	DNP	GG	TCGA-AH-6643-01A-11D-1826-10	2595778	52005168	83529579	108	23800										
COX15	1355	hgsc.bcm.edu	37	chr10	101487249	101487249	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggaattctgcttcccattccTcttggcttgtaggtggcttc	10	11	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:101487249T>C	ENST00000016171.5	-	3	394	c.344A>G	c.(343-345)gAg>gGg	p.E115G	COX15_ENST00000370483.5_Missense_Mutation_p.E115G|CUTC_ENST00000493385.1_Intron			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	115					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		TTCCCATTCCTCTTGGCTTGT	0.398																																																0			10											193	191	192					10																	101487249		2203	4300	6503	101477239	SO:0001583	missense	1355			AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.344A>G	10.37:g.101487249T>C	ENSP00000016171:p.Glu115Gly		101477239	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	37	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.973827	0.53720	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	D;D	0.83914	-1.78;-1.78	4.49	4.49	0.54785	Peptidase cysteine/serine, trypsin-like (1);	0.227915	0.42964	D	0.000629	D	0.88983	0.6586	M	0.91354	3.2	0.45554	D	0.998506	B;B	0.26672	0.156;0.083	B;B	0.39339	0.287;0.297	D	0.89662	0.3877	10	0.62326	D	0.03	-9.5272	14.2519	0.66026	0.0:0.0:0.0:1.0	.	115;115	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	G	115	ENSP00000359514:E115G;ENSP00000016171:E115G	ENSP00000016171:E115G	E	-	2	0	COX15	101477239	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.022000	0.41030	2.030000	0.59900	0.460000	0.39030	GAG		0.398	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		C	101487249	T	C	101487249	3	2	84	1	0	0	0	0	1	0	0	0	3770	1551	54	4	986	4	COX15	10	101487249	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	49482081	101487249	34047498	109	23801										
PKD2L1	9033	hgsc.bcm.edu	37	chr10	102089792	102089792	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gaagggggaccactgtaggcGgggttgtcccaggctccact	16	11	0	0	rs201861031		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:102089792G>A	ENST00000318222.3	-	1	451	c.69C>T	c.(67-69)ccC>ccT	p.P23P	PKD2L1_ENST00000353274.3_Silent_p.P23P|PKD2L1_ENST00000338519.3_Silent_p.P23P	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	23					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		CACTGTAGGCGGGGTTGTCCC	0.642																																																0			10						G		0,4406		0,0,2203	60	65	63		69	-10.6	0.9	10		63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PKD2L1	NM_016112.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		23/806	102089792	1,13005	2203	4300	6503	102079782	SO:0001819	synonymous_variant	9033			AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.69C>T	10.37:g.102089792G>A			102079782	O75972|Q5W039|Q9UP35|Q9UPA2	Silent	SNP	ENST00000318222.3	37	CCDS7492.1																																																																																				0.642	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		A	102089792	G	A	102089792	2	1	84	1	0	0	0	0	0	0	0	1	11998	1103	39	1		1	PKD2L1	10	102089792	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	602543	102089792	33444955	110	23802										
CALHM2	51063	hgsc.bcm.edu	37	chr10	105209516	105209516	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agcaccagggcgggcacgccGatggccgccagcccgtacag	15	16	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr10:105209516G>A	ENST00000260743.5	-	3	706	c.183C>T	c.(181-183)atC>atT	p.I61I	CALHM2_ENST00000369788.3_Silent_p.I61I|CALHM2_ENST00000393235.1_Silent_p.I61I|RP11-225H22.7_ENST00000608063.1_RNA|CALHM2_ENST00000494180.1_5'UTR	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	61					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						CGGGCACGCCGATGGCCGCCA	0.652																																																0			10											41	49	46					10																	105209516		2203	4299	6502	105199506	SO:0001819	synonymous_variant	51063			BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"family with sequence similarity 26, member B"	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.183C>T	10.37:g.105209516G>A			105199506	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	37	CCDS7549.1																																																																																				0.652	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		A	105209516	G	A	105209516	2	1	84	1	0	0	0	0	0	0	0	1	2589	1048	37	1		1	CALHM2	10	105209516	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	3119724	105209516	30325231	111	23803										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1261118	1261118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtggctgctacgacaaggacGgaaactactatgacgtcggt	13	9	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:1261118G>A	ENST00000529681.1	+	28	3731	c.3673G>A	c.(3673-3675)Gga>Aga	p.G1225R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.G1228R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1225	Cys-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.G1228R(1)|p.G1225R(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CGACAAGGACGGAAACTACTA	0.652																																																2	Substitution - Missense(2)	endometrium(2)	11											32	33	33					11																	1261118		2044	4187	6231	1217694	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3673G>A	11.37:g.1261118G>A	ENSP00000436812:p.Gly1225Arg		1217694	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639688	0.29157	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20332	2.08;2.25	4.36	2.41	0.29592	.	.	.	.	.	T	0.34308	0.0893	M	0.84082	2.675	0.09310	N	1	D;D	0.57899	0.981;0.981	P;P	0.48270	0.474;0.572	T	0.21861	-1.0233	9	0.87932	D	0	.	10.5492	0.45079	0.1615:0.0:0.8385:0.0	.	1918;1228	A7Y9J9;E9PBJ0	.;.	R	1225;1228;1226;1295	ENSP00000436812:G1225R;ENSP00000415793:G1228R	ENSP00000343037:G1226R	G	+	1	0	MUC5B	1217694	1.000000	0.71417	0.005000	0.12908	0.016000	0.09150	6.351000	0.73022	0.835000	0.34877	0.442000	0.29010	GGA		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1261118	G	A	1261118	3	1	84	1	0	0	0	0	1	0	0	0	10009	1117	39	1	3792	1	MUC5B	11	1261118	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		1261118	133745398	112	23804										
OR52I2	143502	hgsc.bcm.edu	37	chr11	4608250	4608250	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccatgtacatcatagccctgTtaggaaacaccatcatcgtg	7	12	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:4608250T>G	ENST00000312614.4	+	1	230	c.208T>G	c.(208-210)Tta>Gta	p.L70V		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATAGCCCTGTTAGGAAACAC	0.498																																																0			11											263	247	252					11																	4608250		2201	4298	6499	4564826	SO:0001583	missense	143502			BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"GPCR / Class A : Olfactory receptors"	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.208T>G	11.37:g.4608250T>G	ENSP00000308764:p.Leu70Val		4564826	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	.	.	.	.	.	.	.	.	.	.	T	0.027	-1.363268	0.01235	.	.	ENSG00000226288	ENST00000312614	T	0.02656	4.21	4.1	-7.17	0.01511	.	0.735006	0.11170	N	0.592079	T	0.01222	0.0040	N	0.22421	0.69	0.09310	N	1	B	0.24651	0.108	B	0.23275	0.045	T	0.48352	-0.9043	10	0.05436	T	0.98	-0.2694	2.299	0.04157	0.1103:0.234:0.3686:0.2871	.	70	Q8NH67	O52I2_HUMAN	V	70	ENSP00000308764:L70V	ENSP00000308764:L70V	L	+	1	2	OR52I2	4564826	0.000000	0.05858	0.015000	0.15790	0.286000	0.27126	-5.642000	0.00107	-0.935000	0.03728	-0.516000	0.04426	TTA		0.498	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170		G	4608250	T	G	4608250	3	3	84	1	0	0	0	0	1	0	0	0	11152	1722	60	4	210	4	OR52I2	11	4608250	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	3347132	4608250	130398266	113	23805										
OR51F2	119694	hgsc.bcm.edu	37	chr11	4843563	4843563	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attaagcagattcaaaaggcCattatcaaggtcttaattca	6	7	4	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:4843563C>T	ENST00000322110.5	+	1	1013	c.948C>T	c.(946-948)gcC>gcT	p.A316A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCAAAAGGCCATTATCAAGG	0.373																																																0			11											120	120	120					11																	4843563		2201	4298	6499	4800139	SO:0001819	synonymous_variant	119694			BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"GPCR / Class A : Olfactory receptors"	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.948C>T	11.37:g.4843563C>T			4800139	Q6IFI1	Silent	SNP	ENST00000322110.5	37	CCDS31361.1																																																																																				0.373	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753		T	4843563	C	T	4843563	2	4	84	1	0	0	0	0	0	0	0	1	11128	581	21	3		3	OR51F2	11	4843563	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	235313	4843563	130162953	114	23806										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33689562	33689562	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gcgccctccacagcggcctcGcagcagagcctggcagaaaa	12	16	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:33689562G>A	ENST00000321505.4	+	20	5592	c.5412G>A	c.(5410-5412)tcG>tcA	p.S1804S	KIAA1549L_ENST00000389726.3_Silent_p.S1810S|RP4-541C22.5_ENST00000534431.1_RNA			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1804						integral component of membrane (GO:0016021)											CAGCGGCCTCGCAGCAGAGCC	0.677																																																0			11											40	47	45					11																	33689562		2030	4186	6216	33646138	SO:0001819	synonymous_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.5412G>A	11.37:g.33689562G>A			33646138	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																				0.677	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33689562	G	A	33689562	2	1	84	1	0	0	0	0	0	0	0	1	1644	1074	38	1		1	C11orf41	11	33689562	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	28845999	33689562	101316954	115	23807										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587289	55587289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aactgcatacccccatgtacTttttcctcagccaactctcc	3	17	2	0	rs199935417		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:55587289T>C	ENST00000333976.4	+	1	204	c.184T>C	c.(184-186)Ttt>Ctt	p.F62L		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				CCCCATGTACTTTTTCCTCAG	0.428																																																0			11											258	237	244					11																	55587289		2200	4296	6496	55343865	SO:0001583	missense	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.184T>C	11.37:g.55587289T>C	ENSP00000335025:p.Phe62Leu		55343865	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	14.69	2.611751	0.46631	.	.	ENSG00000186119	ENST00000333976	T	0.00551	6.65	4.94	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	N	0.001140	T	0.00754	0.0025	M	0.74467	2.265	0.32381	N	0.554556	P	0.35872	0.525	B	0.36418	0.224	T	0.25710	-1.0124	10	0.62326	D	0.03	-37.1952	6.5929	0.22656	0.1543:0.0:0.1609:0.6847	.	62	Q8NGL1	OR5DI_HUMAN	L	62	ENSP00000335025:F62L	ENSP00000335025:F62L	F	+	1	0	OR5D18	55343865	0.330000	0.24705	1.000000	0.80357	0.997000	0.91878	0.677000	0.25262	0.834000	0.34852	0.514000	0.50259	TTT		0.428	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		C	55587289	T	C	55587289	3	2	84	1	0	0	0	0	1	0	0	0	11188	1609	56	4	186	4	OR5D18	11	55587289	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	21897727	55587289	79419227	116	23808										
STX5	6811	hgsc.bcm.edu	37	chr11	62595063	62595063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gggtgaattcactgcgttgtCggacagcacgcaaagctggc	14	10	1	1	rs542193132		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:62595063C>T	ENST00000294179.3	-	3	419	c.266G>A	c.(265-267)cGa>cAa	p.R89Q	STX5_ENST00000541317.1_5'UTR|STX5_ENST00000394690.1_Missense_Mutation_p.R35Q|STX5_ENST00000377897.4_Missense_Mutation_p.R89Q	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	89					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)	p.R89Q(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						ACTGCGTTGTCGGACAGCACG	0.483																																																1	Substitution - Missense(1)	endometrium(1)	11											133	120	125					11																	62595063		2201	4299	6500	62351639	SO:0001583	missense	6811			U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236			11440	protein-coding gene	gene with protein product		603189	"syntaxin 5A"	STX5A		9188044, 11959998	Standard	NM_003164		Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.266G>A	11.37:g.62595063C>T	ENSP00000294179:p.Arg89Gln		62351639	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	Missense_Mutation	SNP	ENST00000294179.3	37	CCDS8038.2	.	.	.	.	.	.	.	.	.	.	C	13.47	2.245997	0.39697	.	.	ENSG00000162236	ENST00000377897;ENST00000294179;ENST00000394690	T;T;T	0.41065	1.57;1.57;1.01	5.37	5.37	0.77165	t-SNARE (1);	0.168259	0.44902	D	0.000401	T	0.18509	0.0444	N	0.08118	0	0.80722	D	1	B;B	0.24618	0.039;0.107	B;B	0.12837	0.008;0.004	T	0.12734	-1.0536	10	0.05959	T	0.93	-4.9805	10.1035	0.42519	0.0:0.9093:0.0:0.0907	.	89;89	F8W8Q9;Q13190	.;STX5_HUMAN	Q	89;89;35	ENSP00000367129:R89Q;ENSP00000294179:R89Q;ENSP00000378182:R35Q	ENSP00000294179:R89Q	R	-	2	0	STX5	62351639	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.704000	0.37857	2.524000	0.85096	0.655000	0.94253	CGA		0.483	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290113.1	NM_003164		T	62595063	C	T	62595063	3	4	84	1	0	0	0	0	1	0	0	0	15387	884	31	1	837	1	STX5	11	62595063	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	7007774	62595063	72411453	117	23809										
RELA	5970	hgsc.bcm.edu	37	chr11	65427176	65427176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agaaaggacaggcggcaggcGgaggggcctgcctgatgggt	20	8	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:65427176G>A	ENST00000406246.3	-	6	781	c.520C>T	c.(520-522)Cgc>Tgc	p.R174C	RELA_ENST00000308639.9_Missense_Mutation_p.R171C|RELA_ENST00000525693.1_Missense_Mutation_p.R174C	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	174	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GGCGGCAGGCGGAGGGGCCTG	0.602																																																0			11											56	60	58					11																	65427176		2201	4296	6497	65183752	SO:0001583	missense	5970			Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.520C>T	11.37:g.65427176G>A	ENSP00000384273:p.Arg174Cys		65183752	Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	37	CCDS31609.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.07|15.07	2.724104|2.724104	0.48728|0.48728	.|.	.|.	ENSG00000173039|ENSG00000173039	ENST00000532879|ENST00000406246;ENST00000525693;ENST00000308639;ENST00000426617;ENST00000545816;ENST00000532999;ENST00000534558;ENST00000527749	.|T;T;T;T;T;T	.|0.45668	.|0.89;0.89;0.89;0.89;0.89;0.89	4.71|4.71	3.77|3.77	0.43336|0.43336	.|Rel homology (3);p53-like transcription factor, DNA-binding (1);	.|0.455930	.|0.21823	.|N	.|0.068595	T|T	0.25827|0.25827	0.0629|0.0629	N|N	0.20986|0.20986	0.625|0.625	0.40244|0.40244	D|D	0.977997|0.977997	.|P;P;D;P;D;P	.|0.56521	.|0.818;0.742;0.976;0.75;0.963;0.633	.|B;B;B;B;B;B	.|0.37692	.|0.063;0.228;0.192;0.256;0.203;0.068	T|T	0.11446|0.11446	-1.0587|-1.0587	6|10	0.72032|0.44086	D|T	0.01|0.13	-9.0333|-9.0333	12.0832|12.0832	0.53682|0.53682	0.0:0.2216:0.7784:0.0|0.0:0.2216:0.7784:0.0	.|.	.|174;161;171;174;185;174	.|Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082;Q2TAM5	.|.;.;.;TF65_HUMAN;.;.	L|C	154|174;174;171;174;185;185;165;143	.|ENSP00000384273:R174C;ENSP00000432537:R174C;ENSP00000311508:R171C;ENSP00000433526:R185C;ENSP00000434372:R165C;ENSP00000436545:R143C	ENSP00000432922:P124L|ENSP00000311508:R171C	P|R	-|-	2|1	0|0	RELA|RELA	65183752|65183752	0.966000|0.966000	0.33281|0.33281	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	1.863000|1.863000	0.39459|0.39459	2.163000|2.163000	0.67991|0.67991	0.455000|0.455000	0.32223|0.32223	CCG|CGC		0.602	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		A	65427176	G	A	65427176	3	1	84	1	0	0	0	0	1	0	0	0	13253	1116	39	1	1159	1	RELA	11	65427176	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	2832113	65427176	69579340	118	23810										
OPCML	4978	hgsc.bcm.edu	37	chr11	132527052	132527052	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	acagagcaggtgtacggaccTtcgtcatacacatccacatt	8	12	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr11:132527052T>G	ENST00000331898.7	-	2	908	c.330A>C	c.(328-330)gaA>gaC	p.E110D	OPCML_ENST00000524381.1_Missense_Mutation_p.E103D|OPCML_ENST00000374778.4_Missense_Mutation_p.E69D|OPCML_ENST00000541867.1_Missense_Mutation_p.E110D|OPCML_ENST00000529038.1_5'UTR	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	110	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TGTACGGACCTTCGTCATACA	0.502																																																0			11											255	198	218					11																	132527052		2201	4297	6498	132032262	SO:0001583	missense	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.330A>C	11.37:g.132527052T>G	ENSP00000330862:p.Glu110Asp		132032262	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145134	0.77888	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.83	-2.65	0.06095	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.44117	0.1278	M	0.72576	2.205	0.49213	D	0.999763	D;D;D;D	0.58620	0.983;0.983;0.983;0.983	P;P;P;P	0.59948	0.866;0.866;0.866;0.866	T	0.45963	-0.9225	10	0.34782	T	0.22	-18.1468	13.2901	0.60267	0.0:0.5498:0.0:0.4502	.	110;103;110;110	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	D	110;103;69;77;110	ENSP00000330862:E110D;ENSP00000434750:E103D;ENSP00000363910:E69D;ENSP00000445496:E110D	ENSP00000330862:E110D	E	-	3	2	OPCML	132032262	0.996000	0.38824	0.965000	0.40720	0.941000	0.58515	0.439000	0.21575	-0.236000	0.09753	0.533000	0.62120	GAA		0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		G	132527052	T	G	132527052	3	3	84	1	0	0	0	0	1	0	0	0	10905	1606	56	4	731	4	OPCML	11	132527052	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	67099876	132527052	2479464	119	23811										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4725013	4725013	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agcaccgactgcagaacctcGcccacactgcatcctttgtc	7	17	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:4725013G>T	ENST00000545990.2	-	6	2978	c.2454C>A	c.(2452-2454)ggC>ggA	p.G818G	AKAP3_ENST00000228850.1_Silent_p.G818G|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	818					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GCAGAACCTCGCCCACACTGC	0.577																																																0			12											130	107	115					12																	4725013		2203	4300	6503	4595274	SO:0001819	synonymous_variant	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2454C>A	12.37:g.4725013G>T			4595274	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																				0.577	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		T	4725013	G	T	4725013	2	4	84	1	0	0	0	0	0	0	0	1	452	1074	38	2		2	AKAP3	12	4725013	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10		4725013	129126882	120	23812										
CHD4	1108	hgsc.bcm.edu	37	chr12	6690894	6690894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggagtttttggggagggtgaCcctggctgggacatcttctt	16	7	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:6690894C>T	ENST00000357008.2	-	31	4765	c.4602G>A	c.(4600-4602)ggG>ggA	p.G1534G	CHD4_ENST00000544040.1_Silent_p.G1527G|CHD4_ENST00000544484.1_Silent_p.G1559G|SCARNA11_ENST00000516089.1_RNA|CHD4_ENST00000309577.6_Silent_p.G1562G|RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000540960.1_5'Flank	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1534					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						GGGAGGGTGACCCTGGCTGGG	0.557																																					Colon(32;586 792 4568 16848 45314)											0			12											202	192	195					12																	6690894		2203	4300	6503	6561155	SO:0001819	synonymous_variant	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.4602G>A	12.37:g.6690894C>T			6561155	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																				0.557	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		T	6690894	C	T	6690894	2	4	84	1	0	0	0	0	0	0	0	1	3333	494	18	3		3	CHD4	12	6690894	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	1965881	6690894	127161001	121	23813										
C1RL	51279	hgsc.bcm.edu	37	chr12	7248993	7248993	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcaagcccccagggtcaattCttgccattcatcactccctt	5	16	5	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:7248993C>A	ENST00000266542.4	-	6	1550	c.1458G>T	c.(1456-1458)aaG>aaT	p.K486N	C1RL_ENST00000544702.1_3'UTR|C1RL_ENST00000504702.2_Intron|C1RL_ENST00000545280.1_Intron	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	486					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AGGGTCAATTCTTGCCATTCA	0.582																																																0			12											99	96	97					12																	7248993		2203	4300	6503	7140135	SO:0001583	missense	51279			AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.1458G>T	12.37:g.7248993C>A	ENSP00000266542:p.Lys486Asn		7140135	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	37	CCDS8573.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.028889	0.35797	.	.	ENSG00000139178	ENST00000266542	D	0.87966	-2.32	4.68	0.185	0.15096	.	0.915744	0.09394	N	0.808196	T	0.61887	0.2383	N	0.02120	-0.675	0.09310	N	0.999999	P	0.44627	0.839	B	0.41813	0.367	T	0.60530	-0.7245	10	0.09084	T	0.74	.	0.6743	0.00864	0.1915:0.3828:0.1873:0.2384	.	486	Q9NZP8	C1RL_HUMAN	N	486	ENSP00000266542:K486N	ENSP00000266542:K486N	K	-	3	2	C1RL	7140135	0.000000	0.05858	0.003000	0.11579	0.042000	0.13812	-0.284000	0.08422	0.224000	0.20940	0.511000	0.50034	AAG		0.582	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546		A	7248993	C	A	7248993	3	1	84	1	0	0	0	0	1	0	0	0	1979	912	32	2	9	2	C1RL	12	7248993	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	558099	7248993	126602902	122	23814										
PRB1	5542	hgsc.bcm.edu	37	chr12	11506650	11506650	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cctggaggtgggggaccttgAggtctgttgcctccttgtgg	17	9	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:11506650A>C	ENST00000500254.2	-	3	351				PRB1_ENST00000545626.1_Intron|PRB1_ENST00000546254.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGGGACCTTGAGGTCTGTTGC	0.612																																																0			12											16	13	14					12																	11506650		1285	2277	3562	11397917	SO:0001627	intron_variant	5933				CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.313+73T>G	12.37:g.11506650A>C			11397917	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Silent	SNP	ENST00000500254.2	37	CCDS8642.1																																																																																				0.612	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		C	11506650	A	C	11506650	1	2	84	0	1	0	0	0	0	0	0	0	12476	291	11	4		4	PRB1	12	11506650	Intron	SNP	A	TCGA-AH-6643-01A-11D-1826-10	4257657	11506650	122345245	123	23815										
KRT3	3850	hgsc.bcm.edu	37	chr12	53189685	53189685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actgccaaagccacctgctcCgctccggaagccataggccc	9	18	0	0	rs370673258		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:53189685C>T	ENST00000417996.2	-	1	216	c.142G>A	c.(142-144)Gga>Aga	p.G48R	KRT3_ENST00000309505.3_Missense_Mutation_p.G48R	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	48	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						CCACCTGCTCCGCTCCGGAAG	0.672																																																0			12						C	ARG/GLY	1,4405		0,1,2202	48	64	58		142	4.1	0	12		58	0,8600		0,0,4300	no	missense	KRT3	NM_057088.2	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	48/629	53189685	1,13005	2203	4300	6503	51475952	SO:0001583	missense	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.142G>A	12.37:g.53189685C>T	ENSP00000413479:p.Gly48Arg		51475952	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	c	5.539	0.284282	0.10513	2.27E-4	0.0	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.94000	-3.33;-3.33	5.01	4.13	0.48395	.	0.150870	0.30930	N	0.008598	D	0.93497	0.7925	L	0.59912	1.85	0.29403	N	0.861766	D	0.62365	0.991	P	0.52710	0.707	D	0.90216	0.4268	10	0.62326	D	0.03	.	12.0201	0.53337	0.0:0.9193:0.0:0.0807	.	48	P12035	K2C3_HUMAN	R	48	ENSP00000413479:G48R;ENSP00000312206:G48R	ENSP00000312206:G48R	G	-	1	0	KRT3	51475952	0.007000	0.16637	0.014000	0.15608	0.074000	0.17049	1.146000	0.31589	1.259000	0.44117	0.555000	0.69702	GGA		0.672	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		T	53189685	C	T	53189685	3	4	84	1	0	0	0	0	1	0	0	0	8487	661	23	1	1780	1	KRT3	12	53189685	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	41683035	53189685	80662210	124	23816										
ESYT1	23344	hgsc.bcm.edu	37	chr12	56531355	56531355	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtttcttggggggactggtgAagggcaagtcagacccctat	15	8	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:56531355A>G	ENST00000394048.5	+	18	2275	c.2011A>G	c.(2011-2013)Aag>Gag	p.K671E	ESYT1_ENST00000541590.1_Missense_Mutation_p.K681E|ESYT1_ENST00000267113.4_Missense_Mutation_p.K681E	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	671	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						GGGACTGGTGAAGGGCAAGTC	0.537																																																0			12											148	152	150					12																	56531355		2203	4300	6503	54817622	SO:0001583	missense	23344			AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.2011A>G	12.37:g.56531355A>G	ENSP00000377612:p.Lys671Glu		54817622	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	37	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.866003	0.91511	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.70282	-0.47;-0.47;-0.47	5.22	3.99	0.46301	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.100333	0.64402	D	0.000003	T	0.70937	0.3281	N	0.25647	0.755	0.54753	D	0.999988	D;D	0.76494	0.999;0.996	D;D	0.76575	0.988;0.936	T	0.65421	-0.6172	10	0.18710	T	0.47	-22.7381	11.1822	0.48636	0.8463:0.1537:0.0:0.0	.	681;671	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	E	671;625;681;681	ENSP00000377612:K671E;ENSP00000267113:K681E;ENSP00000445952:K681E	ENSP00000267113:K681E	K	+	1	0	ESYT1	54817622	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.011000	0.49567	2.108000	0.64289	0.533000	0.62120	AAG		0.537	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		G	56531355	A	G	56531355	3	3	84	1	0	0	0	0	1	0	0	0	5277	247	9	4	2111	4	ESYT1	12	56531355	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	3341670	56531355	77320540	125	23817										
NAP1L1	4673	hgsc.bcm.edu	37	chr12	76447074	76447074	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cacgtcccttgtgtttctgcTtcttcttaatagttttcaaa	5	10	4	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:76447074T>C	ENST00000261182.8	-	10	1313	c.827A>G	c.(826-828)aAg>aGg	p.K276R	NAP1L1_ENST00000548044.1_Missense_Mutation_p.K235R|NAP1L1_ENST00000542344.1_Missense_Mutation_p.K234R|NAP1L1_ENST00000393263.3_Missense_Mutation_p.K276R|NAP1L1_ENST00000549596.1_Missense_Mutation_p.K276R|NAP1L1_ENST00000547773.1_Missense_Mutation_p.K213R|NAP1L1_ENST00000544816.1_Missense_Mutation_p.K93R|NAP1L1_ENST00000431879.3_Missense_Mutation_p.K208R|NAP1L1_ENST00000552342.1_Missense_Mutation_p.K287R|NAP1L1_ENST00000535020.2_Missense_Mutation_p.K276R|NAP1L1_ENST00000547993.1_Missense_Mutation_p.K93R	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	276					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				GTGTTTCTGCTTCTTCTTAAT	0.348																																																0			12											135	137	136					12																	76447074		2203	4300	6503	74733341	SO:0001583	missense	4673				CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.827A>G	12.37:g.76447074T>C	ENSP00000261182:p.Lys276Arg		74733341	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	37	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.285740	0.80803	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000544816;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000547993;ENST00000552342;ENST00000548044	T;T;T;T;T;T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.61022	0.2314	L	0.61036	1.89	0.80722	D	1	P;P;P;P;B;B;P	0.51351	0.847;0.455;0.847;0.944;0.04;0.027;0.934	P;P;P;P;B;B;P	0.49561	0.615;0.612;0.615;0.612;0.199;0.119;0.612	T	0.64097	-0.6487	10	0.56958	D	0.05	.	16.4323	0.83853	0.0:0.0:0.0:1.0	.	276;234;287;276;208;213;276	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	R	276;270;276;208;213;93;234;276;276;93;287;235	ENSP00000261182:K276R;ENSP00000450236:K270R;ENSP00000376947:K276R;ENSP00000409795:K208R;ENSP00000448167:K213R;ENSP00000437507:K93R;ENSP00000444759:K234R;ENSP00000445008:K276R;ENSP00000447793:K276R;ENSP00000448007:K93R;ENSP00000447196:K287R;ENSP00000449649:K235R	ENSP00000261182:K276R	K	-	2	0	NAP1L1	74733341	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.037000	0.88933	2.282000	0.76494	0.529000	0.55759	AAG		0.348	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		C	76447074	T	C	76447074	3	2	84	1	0	0	0	0	1	0	0	0	10186	1609	56	4	372	4	NAP1L1	12	76447074	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	19915719	76447074	57404821	126	23818										
CCDC38	120935	hgsc.bcm.edu	37	chr12	96300225	96300225	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tggacagtcctttttgtgtcGgaacctgtgaagaaagttga	12	6	0	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:96300225G>A	ENST00000344280.3	-	5	866	c.309C>T	c.(307-309)tcC>tcT	p.S103S		NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	103										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTTTGTGTCGGAACCTGTGA	0.338																																																0			12											81	77	78					12																	96300225		2203	4300	6503	94824356	SO:0001819	synonymous_variant	120935			AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.309C>T	12.37:g.96300225G>A			94824356	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																				0.338	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496		A	96300225	G	A	96300225	2	1	84	1	0	0	0	0	0	0	0	1	2816	1103	39	1		1	CCDC38	12	96300225	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	19853151	96300225	37551670	127	23819										
ACTR6	64431	hgsc.bcm.edu	37	chr12	100617606	100617606	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggtggaaaattgatatcagaGaatgatgattttgaagatat	11	1	1	6			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:100617606G>A	ENST00000188312.2	+	11	1869	c.1104G>A	c.(1102-1104)gaG>gaA	p.E368E	ACTR6_ENST00000546902.1_Silent_p.E286E|ACTR6_ENST00000552376.1_Silent_p.E348E|ACTR6_ENST00000551617.1_Silent_p.E266E	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	368						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						TGATATCAGAGAATGATGATT	0.338																																																0			12											118	123	121					12																	100617606		2203	4300	6503	99141737	SO:0001819	synonymous_variant	64431			AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.1104G>A	12.37:g.100617606G>A			99141737	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Silent	SNP	ENST00000188312.2	37	CCDS9074.1																																																																																				0.338	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408159.1	NM_022496		A	100617606	G	A	100617606	2	1	84	1	0	0	0	0	0	0	0	1	216	933	33	3		3	ACTR6	12	100617606	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	4317381	100617606	33234289	128	23820										
IFT81	28981	hgsc.bcm.edu	37	chr12	110581326	110581326	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gagccagctatgggccattcTgatcttcttgaacttgaatc	9	10	3	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:110581326T>C	ENST00000242591.5	+	9	1427	c.921T>C	c.(919-921)tcT>tcC	p.S307S	IFT81_ENST00000552912.1_Silent_p.S307S|IFT81_ENST00000549009.1_3'UTR|IFT81_ENST00000361948.4_Silent_p.S307S	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	307					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						TGGGCCATTCTGATCTTCTTG	0.299																																																0			12											71	83	79					12																	110581326		2189	4281	6470	109065709	SO:0001819	synonymous_variant	28981			AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"Intraflagellar transport homologs"	14313	protein-coding gene	gene with protein product		605489	"carnitine deficiency-associated, expressed in ventricle 1", "intraflagellar transport 81 homolog (Chlamydomonas)"	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.921T>C	12.37:g.110581326T>C			109065709	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Silent	SNP	ENST00000242591.5	37	CCDS41831.1																																																																																				0.299	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		C	110581326	T	C	110581326	2	2	84	1	0	0	0	0	0	0	0	1	7586	1567	55	4		4	IFT81	12	110581326	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	9963720	110581326	23270569	129	23821										
TRAFD1	10906	hgsc.bcm.edu	37	chr12	112578641	112578641	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aggagactgagtgccctttgCggcttgctgtctgccagcac	13	12	1	2	rs201271111		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:112578641C>T	ENST00000257604.5	+	5	873	c.256C>T	c.(256-258)Cgg>Tgg	p.R86W	TRAFD1_ENST00000412615.2_Missense_Mutation_p.R86W	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	86					negative regulation of innate immune response (GO:0045824)|response to cytokine (GO:0034097)		metal ion binding (GO:0046872)			kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						GTGCCCTTTGCGGCTTGCTGT	0.453													C|||	1	0.000199681	0	0	5008	,	,		20570	0		0.001	False		,,,				2504	0															0			12											69	66	67					12																	112578641		2203	4300	6503	111063024	SO:0001583	missense	10906			AB007447	CCDS9160.1	12q24.13	2013-01-25			ENSG00000135148	ENSG00000135148			24808	protein-coding gene	gene with protein product		613197				12477932	Standard	NM_006700		Approved	FLN29	uc001ttp.3	O14545	OTTHUMG00000169640	ENST00000257604.5:c.256C>T	12.37:g.112578641C>T	ENSP00000257604:p.Arg86Trp		111063024	A8K5L6|B4DI89	Missense_Mutation	SNP	ENST00000257604.5	37	CCDS9160.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	19.33	3.807314	0.70797	.	.	ENSG00000135148	ENST00000412615;ENST00000549358;ENST00000257604;ENST00000552896	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.7	2.44	0.29823	.	0.263092	0.38164	N	0.001783	T	0.63141	0.2486	M	0.85542	2.76	0.53688	D	0.999978	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.983	T	0.72447	-0.4291	10	0.87932	D	0	-7.4732	15.7607	0.78076	0.3851:0.6149:0.0:0.0	.	86;86	F8VNX8;O14545	.;TRAD1_HUMAN	W	86	ENSP00000396526:R86W;ENSP00000449319:R86W;ENSP00000257604:R86W;ENSP00000450357:R86W	ENSP00000257604:R86W	R	+	1	2	TRAFD1	111063024	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.004000	0.49513	0.702000	0.31825	0.563000	0.77884	CGG		0.453	TRAFD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405214.1	NM_006700		T	112578641	C	T	112578641	3	4	84	1	0	0	0	0	1	0	0	0	16487	759	27	1	270	1	TRAFD1	12	112578641	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	1997315	112578641	21273254	130	23822										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112915523	112915523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tttcagattacatcaatgcaAatatcatcatggtaagcttt	5	7	4	1	rs28933386		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:112915523A>G	ENST00000351677.2	+	8	1120	c.922A>G	c.(922-924)Aat>Gat	p.N308D	PTPN11_ENST00000392597.1_Missense_Mutation_p.N308D	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	308	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		N -> D (in NS1; common mutation). {ECO:0000269|PubMed:11704759, ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12161469, ECO:0000269|PubMed:12634870, ECO:0000269|PubMed:12960218}.|N -> S (in NS1; some patients also manifest giant cell lesions of bone and soft tissue). {ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12960218}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.N308D(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CATCAATGCAAATATCATCAT	0.378			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12	GRCh37	CM013422	PTPN11	M	rs28933386	A	ASP/ASN	0,4406		0,0,2203	206	178	188	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	922	4.5	1	12	dbSNP_125	188	1,8599	1.2+/-3.3	0,1,4299	no	missense	PTPN11	NM_002834.3	23	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	308/594	112915523	1,13005	2203	4300	6503	111399906	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.922A>G	12.37:g.112915523A>G	ENSP00000340944:p.Asn308Asp		111399906	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.834908	0.71373	0.0	1.16E-4	ENSG00000179295	ENST00000392597;ENST00000351677	D;D	0.99479	-5.98;-5.98	5.64	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.99342	0.9769	H	0.96430	3.82	0.80722	A	1	B;B	0.31910	0.229;0.346	B;B	0.39840	0.167;0.311	D	0.99958	1.1671	9	0.72032	D	0.01	.	11.3384	0.49518	0.9292:0.0:0.0708:0.0	rs28933386	308;308	Q06124-2;Q06124-3	.;.	D	308	ENSP00000376376:N308D;ENSP00000340944:N308D	ENSP00000340944:N308D	N	+	1	0	PTPN11	111399906	1.000000	0.71417	0.965000	0.40720	0.991000	0.79684	8.869000	0.92326	0.998000	0.38996	0.524000	0.50904	AAT		0.378	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112915523	A	G	112915523	3	3	84	1	0	0	0	0	1	0	0	0	12815	14	1	4	952	4	PTPN11	12	112915523	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	336882	112915523	20936372	131	23823										
IQCD	115811	hgsc.bcm.edu	37	chr12	113645406	113645406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	caaacaggaaaccacggagcTctatcaggctgtcaataaaa	8	10	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:113645406T>C	ENST00000416617.2	-	2	756	c.566A>G	c.(565-567)gAg>gGg	p.E189G	IQCD_ENST00000546692.1_Missense_Mutation_p.E189G|IQCD_ENST00000299732.2_Missense_Mutation_p.E189G			Q96DY2	IQCD_HUMAN	IQ motif containing D	189										endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						ACCACGGAGCTCTATCAGGCT	0.478																																																0			12											100	95	97					12																	113645406		2203	4300	6503	112129789	SO:0001583	missense	115811			BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 10"					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.566A>G	12.37:g.113645406T>C	ENSP00000400669:p.Glu189Gly		112129789	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	37		.	.	.	.	.	.	.	.	.	.	T	20.3	3.963493	0.74016	.	.	ENSG00000166578	ENST00000299732;ENST00000416617;ENST00000546692;ENST00000392574	T;T;T	0.12361	2.69;2.69;2.69	5.25	5.25	0.73442	.	0.137587	0.47852	D	0.000205	T	0.37265	0.0997	M	0.74258	2.255	0.54753	D	0.999985	D;D	0.89917	0.999;1.0	D;D	0.72982	0.974;0.979	T	0.20773	-1.0265	10	0.87932	D	0	-29.2873	14.1294	0.65242	0.0:0.0:0.0:1.0	.	189;189	F8VZV9;Q96DY2-2	.;.	G	189	ENSP00000299732:E189G;ENSP00000400669:E189G;ENSP00000446623:E189G	ENSP00000299732:E189G	E	-	2	0	IQCD	112129789	0.993000	0.37304	0.044000	0.18714	0.004000	0.04260	4.086000	0.57664	1.977000	0.57605	0.460000	0.39030	GAG		0.478	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451		C	113645406	T	C	113645406	3	2	84	1	0	0	0	0	1	0	0	0	7826	1551	54	4	485	4	IQCD	12	113645406	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	729883	113645406	20206489	132	23824										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126137028	126137028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tccatcctggctgagaagacGgtgattgtcctggatgaccg	13	10	0	4			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:126137028G>A	ENST00000299308.3	+	8	1949	c.1941G>A	c.(1939-1941)acG>acA	p.T647T	TMEM132B_ENST00000535886.1_Silent_p.T159T	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	647						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		CTGAGAAGACGGTGATTGTCC	0.572																																																0			12											33	35	35					12																	126137028		2076	4228	6304	124702981	SO:0001819	synonymous_variant	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1941G>A	12.37:g.126137028G>A			124702981	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																				0.572	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		A	126137028	G	A	126137028	2	1	84	1	0	0	0	0	0	0	0	1	16085	1103	39	1		1	TMEM132B	12	126137028	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	12491622	126137028	7714867	133	23825										
MMP17	4326	hgsc.bcm.edu	37	chr12	132335618	132335618	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tctgtggctgcgggcgtggaCgcggcagaggggccccgcgc	20	13	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr12:132335618C>T	ENST00000360564.1	+	10	1713	c.1611C>T	c.(1609-1611)gaC>gaT	p.D537D	MMP17_ENST00000535004.1_Silent_p.D77D|MMP17_ENST00000535291.1_Silent_p.D453D	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	537					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	CGGGCGTGGACGCGGCAGAGG	0.692																																																0			12											25	25	25					12																	132335618		2195	4294	6489	130901571	SO:0001819	synonymous_variant	4326			X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"matrix metalloproteinase 17 (membrane-inserted)"			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1611C>T	12.37:g.132335618C>T			130901571	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																				0.692	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		T	132335618	C	T	132335618	2	4	84	1	0	0	0	0	0	0	0	1	9686	535	19	1		1	MMP17	12	132335618	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	6198590	132335618	1516277	134	23826										
RNF6	6049	hgsc.bcm.edu	37	chr13	26788761	26788761	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccctactctggatcgagttcTatttgcaatactatcccgat	6	12	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr13:26788761T>A	ENST00000381588.4	-	5	2010	c.1258A>T	c.(1258-1260)Aga>Tga	p.R420*	RNF6_ENST00000381570.3_Nonsense_Mutation_p.R420*|RNF6_ENST00000346166.3_Nonsense_Mutation_p.R420*|RNF6_ENST00000399762.2_Nonsense_Mutation_p.R64*|RNF6_ENST00000468480.1_Intron	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	420	Arg-rich.				negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		GATCGAGTTCTATTTGCAATA	0.458																																																0			13											116	114	115					13																	26788761		2203	4300	6503	25686761	SO:0001587	stop_gained	6049			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1258A>T	13.37:g.26788761T>A	ENSP00000371000:p.Arg420*		25686761	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Nonsense_Mutation	SNP	ENST00000381588.4	37	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.678495	0.88542	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	.	.	.	4.41	0.254	0.15557	.	0.124010	0.52532	D	0.000068	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2058	13.5195	0.61559	0.0:0.0:0.5704:0.4296	.	.	.	.	X	420;420;420;64	.	ENSP00000342121:R420X	R	-	1	2	RNF6	25686761	1.000000	0.71417	0.328000	0.25416	0.747000	0.42532	1.358000	0.34102	-0.095000	0.12351	0.455000	0.32223	AGA		0.458	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		A	26788761	T	A	26788761	4	1	84	1	0	0	0	0	0	1	0	0	13535	1530	53	5	803	5	RNF6	13	26788761	Nonsense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10		26788761	88381117	135	23827										
FLT3	2322	hgsc.bcm.edu	37	chr13	28608472	28608472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gacaaattagcagggttaaaAcgacaatgaagaggagacaa	11	5	0	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr13:28608472A>G	ENST00000241453.7	-	13	1751	c.1670T>C	c.(1669-1671)gTt>gCt	p.V557A	FLT3_ENST00000537084.1_Missense_Mutation_p.V557A|FLT3_ENST00000380982.4_Missense_Mutation_p.V557A	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	557			V -> I (in dbSNP:rs35958982). {ECO:0000269|PubMed:17344846}.		B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGGGTTAAAACGACAATGAA	0.393			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13											96	89	92					13																	28608472		2203	4300	6503	27506472	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1670T>C	13.37:g.28608472A>G	ENSP00000241453:p.Val557Ala		27506472	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.466433	0.26335	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.78595	-1.12;-1.19;-0.93	5.83	5.83	0.93111	.	0.552763	0.17442	N	0.174076	T	0.72748	0.3499	L	0.50333	1.59	0.09310	N	1	B;B	0.16802	0.019;0.004	B;B	0.12156	0.007;0.005	T	0.65919	-0.6051	10	0.72032	D	0.01	.	11.2703	0.49136	0.9292:0.0:0.0708:0.0	.	557;557	P36888-2;P36888	.;FLT3_HUMAN	A	557	ENSP00000241453:V557A;ENSP00000370369:V557A;ENSP00000438139:V557A	ENSP00000241453:V557A	V	-	2	0	FLT3	27506472	0.567000	0.26626	0.005000	0.12908	0.516000	0.34256	5.917000	0.69989	2.226000	0.72624	0.533000	0.62120	GTT		0.393	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			G	28608472	A	G	28608472	3	3	84	1	0	0	0	0	1	0	0	0	5961	43	2	4	1359	4	FLT3	13	28608472	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	1819711	28608472	86561406	136	23828										
BRCA2	675	hgsc.bcm.edu	37	chr13	32913536	32913536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtagtagaaaaacttctgtgAgtcagacttcattacttgaa	8	6	3	4	rs397507756		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr13:32913536A>G	ENST00000380152.3	+	11	5277	c.5044A>G	c.(5044-5046)Agt>Ggt	p.S1682G	BRCA2_ENST00000544455.1_Missense_Mutation_p.S1682G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1682	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AACTTCTGTGAGTCAGACTTC	0.328			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											33	36	35					13																	32913536		2187	4287	6474	31811536	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5044A>G	13.37:g.32913536A>G	ENSP00000369497:p.Ser1682Gly		31811536	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	9.258	1.042569	0.19748	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.87650	-2.28;-2.28	5.76	3.22	0.36961	.	0.501323	0.22848	N	0.054886	T	0.79862	0.4519	L	0.35854	1.095	0.19300	N	0.999979	B	0.22909	0.077	B	0.23419	0.046	T	0.68435	-0.5409	10	0.49607	T	0.09	.	8.0637	0.30648	0.8122:0.0:0.0664:0.1214	.	1682	P51587	BRCA2_HUMAN	G	1682	ENSP00000369497:S1682G;ENSP00000439902:S1682G	ENSP00000369497:S1682G	S	+	1	0	BRCA2	31811536	0.216000	0.23585	0.037000	0.18230	0.241000	0.25554	2.109000	0.41863	0.400000	0.25396	0.533000	0.62120	AGT		0.328	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32913536	A	G	32913536	3	3	84	1	0	0	0	0	1	0	0	0	1502	304	11	4	5082	4	BRCA2	13	32913536	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10	4305064	32913536	82256342	137	23829										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60407364	60407364	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tccatgttttcgtgtaacttCgaaagtgtctcatattgttc	7	8	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr13:60407364C>A	ENST00000400324.4	-	24	3124	c.2904G>T	c.(2902-2904)tcG>tcT	p.S968S	DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.S922S|DIAPH3_ENST00000377908.2_Silent_p.S957S|DIAPH3_ENST00000400319.1_Silent_p.S898S|DIAPH3_ENST00000267215.4_Silent_p.S968S|DIAPH3_ENST00000400330.1_Silent_p.S968S	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	968	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CGTGTAACTTCGAAAGTGTCT	0.363																																																0			13											129	116	120					13																	60407364		1837	4085	5922	59305365	SO:0001819	synonymous_variant	81624			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2904G>T	13.37:g.60407364C>A			59305365	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																				0.363	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60407364	C	A	60407364	2	1	84	1	0	0	0	0	0	0	0	1	4531	871	31	2		2	DIAPH3	13	60407364	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	27493828	60407364	54762514	138	23830										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103518117	103518117	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gaacaaggcgaagaggaactGgtaggaactagggagggaga	18	4	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr13:103518117G>C	ENST00000355739.4	+	9	3478	c.2055G>C	c.(2053-2055)ctG>ctC	p.L685L	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.G1111R|ERCC5_ENST00000375954.1_5'UTR	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	685					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					AAGAGGAACTGGTAGGAACTA	0.517			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	0			13											49	45	46					13																	103518117		2203	4300	6503	102316118	SO:0001819	synonymous_variant	2073	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2055G>C	13.37:g.103518117G>C			102316118	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																				0.517	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			C	103518117	G	C	103518117	2	2	84	1	0	0	0	0	0	0	0	1	5229	1335	47	5		5	ERCC5	13	103518117	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	43110753	103518117	11651761	139	23831										
LTB4R2	56413	hgsc.bcm.edu	37	chr14	24780890	24780890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aaagtggtggggcagggccgCggcaatggagacccgggggg	22	8	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr14:24780890C>T	ENST00000528054.1	+	1	2730	c.1113C>T	c.(1111-1113)cgC>cgT	p.R371R	LTB4R2_ENST00000543919.1_Silent_p.R340R|CIDEB_ENST00000258807.5_5'Flank|LTB4R_ENST00000345363.3_5'UTR|CIDEB_ENST00000555817.1_5'Flank|CIDEB_ENST00000336557.5_5'Flank|LTB4R2_ENST00000533293.1_Silent_p.R340R|LTB4R_ENST00000396789.4_5'Flank			Q9NPC1	LT4R2_HUMAN	leukotriene B4 receptor 2	371					chemotaxis (GO:0006935)|keratinocyte migration (GO:0051546)|negative regulation of adenylate cyclase activity (GO:0007194)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene B4 receptor activity (GO:0001632)|leukotriene receptor activity (GO:0004974)			endometrium(1)|lung(1)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.018)		GGCAGGGCCGCGGCAATGGAG	0.652																																																0			14											32	40	37					14																	24780890		2192	4267	6459	23850730	SO:0001819	synonymous_variant	56413			AB008193	CCDS9625.1, CCDS9625.2	14q12	2014-04-11			ENSG00000213906	ENSG00000213906		"GPCR / Class A : Leukotriene receptors"	19260	protein-coding gene	gene with protein product		605773				11006272, 10934229	Standard	NM_001164692		Approved	BLTR2, BLT2, JULF2, NOP9	uc001wor.3	Q9NPC1	OTTHUMG00000186500	ENST00000528054.1:c.1113C>T	14.37:g.24780890C>T			23850730	Q5KU28|Q9NPE5	Silent	SNP	ENST00000528054.1	37																																																																																					0.652	LTB4R2-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000073194.4			T	24780890	C	T	24780890	2	4	84	1	0	0	0	0	0	0	0	1	9101	755	27	1		1	LTB4R2	14	24780890	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10		24780890	82568650	140	23832										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95921951	95921951	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttcctcatctcttccagttcTccggtgatcttctctgcacc	5	16	5	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr14:95921951T>C	ENST00000334258.5	-	5	914	c.900A>G	c.(898-900)ggA>ggG	p.G300G	SYNE3_ENST00000553340.1_Silent_p.G300G|SYNE3_ENST00000554873.1_Silent_p.G57G|SYNE3_ENST00000557275.1_Silent_p.G300G	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	300					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CTTCCAGTTCTCCGGTGATCT	0.622																																																0			14											106	112	110					14																	95921951		2203	4300	6503	94991704	SO:0001819	synonymous_variant	161176			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.900A>G	14.37:g.95921951T>C			94991704	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																				0.622	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		C	95921951	T	C	95921951	2	2	84	1	0	0	0	0	0	0	0	1	1780	1538	54	4		4	C14orf49	14	95921951	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	71141061	95921951	11427589	141	23833										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99642456	99642456	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aagccgtgcgtgttctgcgcGtgctgcagcaggaaccacgc	14	13	1	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr14:99642456G>A	ENST00000357195.3	-	4	726	c.717C>T	c.(715-717)caC>caT	p.H239H	BCL11B_ENST00000443726.2_Silent_p.H45H|BCL11B_ENST00000345514.2_Silent_p.H168H	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	239					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		TGTTCTGCGCGTGCTGCAGCA	0.647			T	TLX3	T-ALL																																		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	0			14											32	30	31					14																	99642456		2201	4299	6500	98712209	SO:0001819	synonymous_variant	64919			AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.717C>T	14.37:g.99642456G>A			98712209	Q9H162	Silent	SNP	ENST00000357195.3	37	CCDS9950.1																																																																																				0.647	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		A	99642456	G	A	99642456	2	1	84	1	0	0	0	0	0	0	0	1	1365	1136	40	1		1	BCL11B	14	99642456	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	3720505	99642456	7707084	142	23834										
RTL1	388015	hgsc.bcm.edu	37	chr14	101349854	101349854	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gaatccaccagggcctggacCgcgacgctgtggtaggggtt	16	11	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr14:101349854C>T	ENST00000534062.1	-	1	1330	c.1272G>A	c.(1270-1272)gcG>gcA	p.A424A	MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	424					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GGGCCTGGACCGCGACGCTGT	0.602																																																0			14											22	23	23					14																	101349854		692	1591	2283	100419607	SO:0001819	synonymous_variant	388015				CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.1272G>A	14.37:g.101349854C>T			100419607	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																				0.602	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		T	101349854	C	T	101349854	2	4	84	1	0	0	0	0	0	0	0	1	13761	639	23	1		1	RTL1	14	101349854	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	1707398	101349854	5999686	143	23835										
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382522	22382522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agaatttatcctccttggtcTgactcagtctcaagatattc	6	10	3	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr15:22382522T>C	ENST00000328795.4	+	1	141	c.50T>C	c.(49-51)cTg>cCg	p.L17P	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTCCTTGGTCTGACTCAGTCT	0.353																																																0			15											139	135	137					15																	22382522		2187	4260	6447	19883886	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.50T>C	15.37:g.22382522T>C	ENSP00000332500:p.Leu17Pro		19883886	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	8.244	0.807557	0.16467	.	.	ENSG00000183706	ENST00000328795	T	0.00344	8.02	3.24	3.24	0.37175	.	0.000000	0.37857	N	0.001901	T	0.01061	0.0035	H	0.94658	3.565	0.22412	N	0.999123	D	0.89917	1.0	D	0.83275	0.996	T	0.14420	-1.0473	10	0.87932	D	0	-8.0908	9.793	0.40717	0.0:0.0:0.0:1.0	.	17	Q8N0Y3	OR4N4_HUMAN	P	17	ENSP00000332500:L17P	ENSP00000332500:L17P	L	+	2	0	OR4N4	19883886	0.081000	0.21417	0.160000	0.22671	0.108000	0.19459	2.867000	0.48428	1.465000	0.48006	0.164000	0.16699	CTG		0.353	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382522	T	C	22382522	3	2	84	1	0	0	0	0	1	0	0	0	11109	1580	55	4	52	4	OR4N4	15	22382522	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10		22382522	80148870	144	23836										
MGA	23269	hgsc.bcm.edu	37	chr15	42042703	42042703	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtgctgacttcactgttttgGatttggaagaagatgatgaa	12	4	1	5			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr15:42042703G>C	ENST00000570161.1	+	16	6898	c.6898G>C	c.(6898-6900)Gat>Cat	p.D2300H	MGA_ENST00000566586.1_Missense_Mutation_p.D2091H|MGA_ENST00000545763.1_Missense_Mutation_p.D2091H|MGA_ENST00000219905.7_Missense_Mutation_p.D2300H|MGA_ENST00000389936.4_Missense_Mutation_p.D2261H			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CACTGTTTTGGATTTGGAAGA	0.408																																																0			15											115	106	109					15																	42042703		1926	4126	6052	39829995	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.6898G>C	15.37:g.42042703G>C	ENSP00000457035:p.Asp2300His		39829995	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082545	0.36758	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.87412	-2.23;-2.23;-2.25	5.11	2.12	0.27331	.	0.970504	0.08436	N	0.946207	T	0.79857	0.4518	N	0.19112	0.55	0.24012	N	0.996179	B;B;B;B	0.34103	0.003;0.005;0.437;0.437	B;B;B;B	0.38655	0.006;0.015;0.278;0.201	T	0.68322	-0.5439	10	0.51188	T	0.08	.	7.2643	0.26222	0.1484:0.1377:0.7138:0.0	.	916;2091;2300;2261	B4DVS1;F5H7K2;E7ENI0;Q8IWI9	.;.;.;MGAP_HUMAN	H	2300;2261;2091	ENSP00000219905:D2300H;ENSP00000374586:D2261H;ENSP00000442467:D2091H	ENSP00000219905:D2300H	D	+	1	0	MGA	39829995	1.000000	0.71417	0.934000	0.37439	0.981000	0.71138	1.054000	0.30455	0.286000	0.22352	0.591000	0.81541	GAT		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	42042703	G	C	42042703	3	2	84	1	0	0	0	0	1	0	0	0	9570	1174	41	5	6960	5	MGA	15	42042703	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	19660181	42042703	60488689	145	23837										
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43940168	43940168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cttggctcaagccttgcaaaTgctcaatgagagagaaagta	10	8	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr15:43940168T>C	ENST00000321596.5	-	2	291	c.92A>G	c.(91-93)cAt>cGt	p.H31R	CATSPER2_ENST00000464721.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.H37R|CATSPER2_ENST00000396879.1_Missense_Mutation_p.H31R|CATSPER2_ENST00000355438.2_Missense_Mutation_p.H31R|CATSPER2_ENST00000354127.4_Missense_Mutation_p.H31R|STRC_ENST00000541030.1_Intron			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	31					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.H31L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GCCTTGCAAATGCTCAATGAG	0.473																																																1	Substitution - Missense(1)	ovary(1)	15											183	181	182					15																	43940168		2199	4296	6495	41727460	SO:0001583	missense	117155			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.92A>G	15.37:g.43940168T>C	ENSP00000321463:p.His31Arg		41727460	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694243	0.48202	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438;ENST00000432420;ENST00000409481;ENST00000419473	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	2.64	2.64	0.31445	.	2.597920	0.01853	N	0.036089	T	0.60157	0.2247	M	0.73598	2.24	0.29336	N	0.866362	D;D;D	0.76494	0.999;0.998;0.997	D;D;P	0.71184	0.972;0.935;0.863	T	0.18053	-1.0349	10	0.48119	T	0.1	.	7.0877	0.25267	0.0:0.0:0.0:1.0	.	31;37;31	Q96P56-4;F8W9H2;Q96P56	.;.;CTSR2_HUMAN	R	31;31;37;31;31;31;31;31;31	ENSP00000380088:H31R;ENSP00000371180:H37R;ENSP00000321463:H31R;ENSP00000339137:H31R;ENSP00000347613:H31R;ENSP00000407694:H31R;ENSP00000386595:H31R	ENSP00000299989:H31R	H	-	2	0	CATSPER2	41727460	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	3.580000	0.53907	1.219000	0.43474	0.155000	0.16302	CAT		0.473	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		C	43940168	T	C	43940168	3	2	84	1	0	0	0	0	1	0	0	0	2694	1464	51	4	1587	4	CATSPER2	15	43940168	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	1897465	43940168	58591224	146	23838										
TMOD3	29766	hgsc.bcm.edu	37	chr15	52181329	52181329	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agtagtaatggtgttgaccaAgaacatttttcaagtgagta	10	4	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr15:52181329A>G	ENST00000308580.7	+	5	764	c.483A>G	c.(481-483)caA>caG	p.Q161Q	RP11-56B16.5_ENST00000558142.1_RNA|TMOD3_ENST00000544199.1_Silent_p.Q161Q	NM_014547.4	NP_055362.1	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	161						striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14				all cancers(107;0.00194)		GTGTTGACCAAGAACATTTTT	0.299																																					Colon(122;1837 2251 18387 22826)											0			15											74	75	75					15																	52181329		2194	4278	6472	49968621	SO:0001819	synonymous_variant	29766			AF177171	CCDS10145.1	15q21.1-q21.2	2008-05-14			ENSG00000138594	ENSG00000138594			11873	protein-coding gene	gene with protein product		605112				10662549	Standard	NM_014547		Approved	UTMOD	uc002abn.3	Q9NYL9	OTTHUMG00000131803	ENST00000308580.7:c.483A>G	15.37:g.52181329A>G			49968621	B2R6G7|Q9NT43|Q9NZR0	Silent	SNP	ENST00000308580.7	37	CCDS10145.1																																																																																				0.299	TMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254740.3			G	52181329	A	G	52181329	2	3	84	1	0	0	0	0	0	0	0	1	16274	69	3	4		4	TMOD3	15	52181329	Silent	SNP	A	TCGA-AH-6643-01A-11D-1826-10	8241161	52181329	50350063	147	23839										
TMC3	342125	hgsc.bcm.edu	37	chr15	81625315	81625315	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctggggtacagctccacaatGtcacctgaagcatctatctt	8	12	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr15:81625315G>A	ENST00000359440.5	-	22	2883	c.2748C>T	c.(2746-2748)gaC>gaT	p.D916D	RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Silent_p.D917D|RP11-761I4.3_ENST00000560973.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						GCTCCACAATGTCACCTGAAG	0.498																																																0			15											71	70	70					15																	81625315		1951	4146	6097	79412370	SO:0001819	synonymous_variant	342125			AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2748C>T	15.37:g.81625315G>A			79412370		Silent	SNP	ENST00000359440.5	37	CCDS45324.1																																																																																				0.498	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		A	81625315	G	A	81625315	2	1	84	1	0	0	0	0	0	0	0	1	16025	1368	48	3		3	TMC3	15	81625315	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	29443986	81625315	20906077	148	23840										
E4F1	1877	hgsc.bcm.edu	37	chr16	2282783	2282783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gcccctacaagtgctccaagTgtggaaagagcttccgggag	13	11	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:2282783T>C	ENST00000301727.4	+	6	805	c.757T>C	c.(757-759)Tgt>Cgt	p.C253R	E4F1_ENST00000564139.1_Missense_Mutation_p.C253R|E4F1_ENST00000565090.1_Missense_Mutation_p.C253R|RP11-304L19.12_ENST00000564055.1_lincRNA	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	253	Mediates dimerization, DNA-binding, transcription repression of CCNA2 and interaction with HMGA2.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.C253G(1)		ovary(1)	1						GTGCTCCAAGTGTGGAAAGAG	0.612																																																1	Substitution - Missense(1)	ovary(1)	16											60	68	65					16																	2282783		2197	4300	6497	2222784	SO:0001583	missense	1877			U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"Zinc fingers, C2H2-type"	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.757T>C	16.37:g.2282783T>C	ENSP00000301727:p.Cys253Arg		2222784	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	37	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.448737	0.63178	.	.	ENSG00000167967	ENST00000301727	D	0.85955	-2.05	5.84	5.84	0.93424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94036	0.8089	M	0.92691	3.335	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95240	0.8350	10	0.87932	D	0	-8.6789	15.0285	0.71687	0.0:0.0:0.0:1.0	.	249;253;253	E9PFZ8;E7EMF7;Q66K89	.;.;E4F1_HUMAN	R	253	ENSP00000301727:C253R	ENSP00000301727:C253R	C	+	1	0	E4F1	2222784	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.846000	0.86887	2.234000	0.73211	0.459000	0.35465	TGT		0.612	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424		C	2282783	T	C	2282783	3	2	84	1	0	0	0	0	1	0	0	0	4885	1696	59	4	779	4	E4F1	16	2282783	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10		2282783	88071970	149	23841										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786078	3786078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agtgctctcttcctttttccTctcctcttcttcttgttcta	3	14	6	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:3786078T>C	ENST00000262367.5	-	28	5496	c.4687A>G	c.(4687-4689)Agg>Ggg	p.R1563G	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1525G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1563	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TCCTTTTTCCTCTCCTCTTCT	0.517			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											308	220	250					16																	3786078		2197	4300	6497	3726079	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4687A>G	16.37:g.3786078T>C	ENSP00000262367:p.Arg1563Gly		3726079	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	15.42	2.827625	0.50845	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93547	-3.24;-3.24	5.2	4.09	0.47781	.	0.000000	0.85682	D	0.000000	D	0.96725	0.8931	M	0.88640	2.97	0.58432	D	0.999999	D;D	0.62365	0.991;0.991	D;D	0.78314	0.991;0.991	D	0.96435	0.9322	10	0.62326	D	0.03	-24.6377	11.8222	0.52245	0.0:0.0:0.1466:0.8534	.	1593;1563	Q4LE28;Q92793	.;CBP_HUMAN	G	1563;1593;1525;152	ENSP00000262367:R1563G;ENSP00000371502:R1525G	ENSP00000262367:R1563G	R	-	1	2	CREBBP	3726079	0.722000	0.28017	0.998000	0.56505	0.989000	0.77384	0.982000	0.29539	0.898000	0.36418	0.454000	0.30748	AGG		0.517	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3786078	T	C	3786078	3	2	84	1	0	0	0	0	1	0	0	0	3867	1550	54	4	2657	4	CREBBP	16	3786078	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	1503295	3786078	86568675	150	23842										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10031897	10031897	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cctcggggatgtaggagaacTtctccagcatagaagatgca	12	9	1	3			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:10031897T>G	ENST00000396573.2	-	4	1235	c.926A>C	c.(925-927)aAg>aCg	p.K309T	GRIN2A_ENST00000566670.1_5'Flank|GRIN2A_ENST00000404927.2_Missense_Mutation_p.K309T|GRIN2A_ENST00000330684.3_Missense_Mutation_p.K309T|GRIN2A_ENST00000562109.1_Missense_Mutation_p.K309T|GRIN2A_ENST00000535259.1_Missense_Mutation_p.K152T|GRIN2A_ENST00000396575.2_Missense_Mutation_p.K309T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	309					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.K309T(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTAGGAGAACTTCTCCAGCAT	0.572																																																1	Substitution - Missense(1)	lung(1)	16											79	64	69					16																	10031897		2197	4300	6497	9939398	SO:0001583	missense	2903				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.926A>C	16.37:g.10031897T>G	ENSP00000379818:p.Lys309Thr		9939398	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	t	14.78	2.637115	0.47049	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18	5.2	-2.02	0.07388	.	0.317437	0.37577	N	0.002032	T	0.10294	0.0252	L	0.51422	1.61	0.35392	D	0.790814	B;B;B	0.30146	0.082;0.27;0.005	B;B;B	0.41135	0.113;0.348;0.013	T	0.18999	-1.0319	9	.	.	.	.	10.4219	0.44354	0.0:0.376:0.0:0.624	.	152;309;309	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	T	309;309;152;309;309	ENSP00000379818:K309T;ENSP00000385872:K309T;ENSP00000441572:K152T;ENSP00000332549:K309T;ENSP00000379820:K309T	.	K	-	2	0	GRIN2A	9939398	0.997000	0.39634	0.224000	0.23877	0.936000	0.57629	2.671000	0.46842	-0.579000	0.05952	-0.441000	0.05720	AAG		0.572	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			G	10031897	T	G	10031897	3	3	84	1	0	0	0	0	1	0	0	0	6800	1609	56	4	3512	4	GRIN2A	16	10031897	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	6245819	10031897	80322856	151	23843										
GPR139	124274	hgsc.bcm.edu	37	chr16	20043451	20043451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agatggcggtggtcttccccGtggagtagccacggagacga	16	10	1	2	rs144787739	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:20043451G>A	ENST00000570682.1	-	2	968	c.668C>T	c.(667-669)aCg>aTg	p.T223M		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	223					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						GGTCTTCCCCGTGGAGTAGCC	0.527																																																0			16											79	82	81					16																	20043451		2203	4300	6503	19950952	SO:0001583	missense	124274			AY255545	CCDS32398.1	16p13.11	2012-08-21						"GPCR / Class A : Orphans"	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.668C>T	16.37:g.20043451G>A	ENSP00000458791:p.Thr223Met		19950952	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	37	CCDS32398.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996335	0.54147	.	.	ENSG00000180269	ENST00000326571	.	.	.	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.049812	0.85682	D	0.000000	T	0.36635	0.0974	N	0.19112	0.55	0.80722	D	1	P	0.43314	0.803	B	0.30782	0.12	T	0.35847	-0.9772	9	0.48119	T	0.1	-18.7989	18.8873	0.92383	0.0:0.0:1.0:0.0	.	223	Q6DWJ6	GP139_HUMAN	M	223	.	ENSP00000370779:T223M	T	-	2	0	GPR139	19950952	1.000000	0.71417	0.956000	0.39512	0.988000	0.76386	9.230000	0.95299	2.708000	0.92522	0.655000	0.94253	ACG		0.527	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911		A	20043451	G	A	20043451	3	1	84	1	0	0	0	0	1	0	0	0	6668	1145	40	1	397	1	GPR139	16	20043451	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	10011554	20043451	70311302	152	23844										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24046770	24046770	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gaatgtgcacaagcgctgcgTgatgaatgttcccagcctgt	12	10	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:24046770T>C	ENST00000321728.7	+	5	606	c.431T>C	c.(430-432)gTg>gCg	p.V144A	PRKCB_ENST00000303531.7_Missense_Mutation_p.V144A	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	144			V -> M (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	AAGCGCTGCGTGATGAATGTT	0.632																																																0			16											116	95	102					16																	24046770		2197	4300	6497	23954271	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.431T>C	16.37:g.24046770T>C	ENSP00000318315:p.Val144Ala		23954271	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.862083	0.32884	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	D;D	0.92699	-3.09;-3.09	5.07	5.07	0.68467	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.070149	0.56097	D	0.000028	D	0.85474	0.5705	N	0.20328	0.56	0.80722	D	1	B;B	0.23540	0.033;0.087	B;B	0.32090	0.086;0.14	T	0.80027	-0.1554	10	0.08599	T	0.76	.	13.9459	0.64084	0.0:0.0:0.0:1.0	.	144;144	P05771-2;P05771	.;KPCB_HUMAN	A	144	ENSP00000318315:V144A;ENSP00000305355:V144A	ENSP00000305355:V144A	V	+	2	0	PRKCB	23954271	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.621000	0.83083	2.030000	0.59900	0.460000	0.39030	GTG		0.632	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		C	24046770	T	C	24046770	3	2	84	1	0	0	0	0	1	0	0	0	12542	1696	59	4	449	4	PRKCB	16	24046770	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	4003319	24046770	66307983	153	23845										
SPN	6693	hgsc.bcm.edu	37	chr16	29675098	29675098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgctggtggtaagcccagacGctctggggagcacaacagca	14	11	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:29675098G>A	ENST00000360121.3	+	2	141	c.49G>A	c.(49-51)Gct>Act	p.A17T	SPN_ENST00000395389.2_Missense_Mutation_p.A17T	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A17T(1)		central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						AAGCCCAGACGCTCTGGGGAG	0.592																																																1	Substitution - Missense(1)	skin(1)	16											117	127	124					16																	29675098		2197	4300	6497	29582599	SO:0001583	missense	10522			J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.49G>A	16.37:g.29675098G>A	ENSP00000353238:p.Ala17Thr		29582599	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000360121.3	37	CCDS10650.1	.	.	.	.	.	.	.	.	.	.	.	16.32	3.090097	0.55968	.	.	ENSG00000197471	ENST00000395389;ENST00000436527;ENST00000360121	T;T;T	0.31247	1.5;1.5;1.5	3.17	-6.35	0.01975	.	2.233910	0.02623	N	0.103463	T	0.13200	0.0320	N	0.22421	0.69	0.09310	N	1	B	0.18610	0.029	B	0.09377	0.004	T	0.25537	-1.0129	10	0.07175	T	0.84	6.5025	0.342	0.00335	0.3716:0.2307:0.1396:0.2581	.	17	P16150	LEUK_HUMAN	T	17	ENSP00000378787:A17T;ENSP00000412907:A17T;ENSP00000353238:A17T	ENSP00000353238:A17T	A	+	1	0	SPN	29582599	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.774000	0.00777	-1.645000	0.01515	0.561000	0.74099	GCT		0.592	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			A	29675098	G	A	29675098	3	1	84	1	0	0	0	0	1	0	0	0	15112	1087	38	1	51	1	SPN	16	29675098	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	5628328	29675098	60679655	154	23846										
CMTM1	113540	hgsc.bcm.edu	37	chr16	66611099	66611099	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	agaaggcatttactctatgtCgggggggtaagtagaggcct	15	6	1	2	rs140837467	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:66611099C>T	ENST00000457188.2	+	3	454	c.333C>T	c.(331-333)gtC>gtT	p.V111V	CMTM1_ENST00000529506.1_Silent_p.V12V|CMTM2_ENST00000268595.2_5'Flank|CKLF-CMTM1_ENST00000527729.1_Silent_p.V57V|CMTM1_ENST00000533666.1_Intron|CMTM1_ENST00000379500.2_Silent_p.V228V|CMTM1_ENST00000533953.1_Silent_p.V180V|CMTM1_ENST00000332695.7_Silent_p.V64V|CMTM1_ENST00000328020.6_Silent_p.V228V|CMTM1_ENST00000336328.6_Silent_p.V58V|RP11-403P17.2_ENST00000568430.1_RNA|CMTM1_ENST00000531885.1_Silent_p.V58V|CMTM1_ENST00000528324.1_Silent_p.V111V|CMTM2_ENST00000379486.2_5'Flank	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	111	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		TACTCTATGTCGGGGGGGTAA	0.403													C|||	5	0.000998403	0	0	5008	,	,		17638	0.005		0	False		,,,				2504	0															0			16											56	55	55					16																	66611099		2201	4300	6501	65168600	SO:0001819	synonymous_variant	113540			AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"chemokine-like factor super family 1", "chemokine-like factor superfamily 1"	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.333C>T	16.37:g.66611099C>T			65168600	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Silent	SNP	ENST00000457188.2	37	CCDS45503.1																																																																																				0.403	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999		T	66611099	C	T	66611099	2	4	84	1	0	0	0	0	0	0	0	1	3588	871	31	1		1	CMTM1	16	66611099	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	36936001	66611099	23743654	155	23847										
CMTM2	146225	hgsc.bcm.edu	37	chr16	66620926	66620926	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttcaacgacctgattgcttgTgcgttccttgtgggagccgt	12	10	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:66620926T>C	ENST00000268595.2	+	3	622	c.471T>C	c.(469-471)tgT>tgC	p.C157C	CMTM2_ENST00000379486.2_Silent_p.C104C	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	157	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		TGATTGCTTGTGCGTTCCTTG	0.542																																																0			16											234	178	197					16																	66620926		2201	4300	6501	65178427	SO:0001819	synonymous_variant	146225			BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"chemokine-like factor super family 2", "chemokine-like factor superfamily 2"	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.471T>C	16.37:g.66620926T>C			65178427	Q5I2A4|Q8N7E5	Silent	SNP	ENST00000268595.2	37	CCDS10814.1																																																																																				0.542	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			C	66620926	T	C	66620926	2	2	84	1	0	0	0	0	0	0	0	1	3589	1702	59	4		4	CMTM2	16	66620926	Silent	SNP	T	TCGA-AH-6643-01A-11D-1826-10	9827	66620926	23733827	156	23848										
CDH1	999	hgsc.bcm.edu	37	chr16	68846036	68846036	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ggttgtgtcgatctctctgcAgagtttccctacgtataccc	9	12	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr16:68846036A>G	ENST00000261769.5	+	8	1199		c.e8-1		CDH1_ENST00000562836.1_Splice_Site|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Splice_Site	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)						adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		ATCTCTCTGCAGAGTTTCCCT	0.507			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	4	Unknown(4)	stomach(2)|breast(2)	16											240	174	196					16																	68846036		2198	4300	6498	67403537	SO:0001630	splice_region_variant	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1009-1A>G	16.37:g.68846036A>G			67403537	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Splice_Site	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457624	0.26161	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1473	0.48438	0.9279:0.0:0.0721:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDH1	67403537	1.000000	0.71417	0.958000	0.39756	0.088000	0.18126	6.766000	0.74970	2.276000	0.75962	0.454000	0.30748	.		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Intron	G	68846036	A	G	68846036	5	3	84	1	0	0	0	0	0	0	1	0	3101	202	7	4	1037	4	CDH1	16	68846036	Splice_Site	SNP	A	TCGA-AH-6643-01A-11D-1826-10	2225110	68846036	21508717	157	23849										
TP53	7157	hgsc.bcm.edu	37	chr17	7579361	7579361	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aatgcaagaagcccagacggAaaccgtagctgccctggtag	12	11	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:7579361A>C	ENST00000269305.4	-	4	515	c.326T>G	c.(325-327)tTc>tGc	p.F109C	TP53_ENST00000420246.2_Missense_Mutation_p.F109C|TP53_ENST00000413465.2_Missense_Mutation_p.F109C|TP53_ENST00000445888.2_Missense_Mutation_p.F109C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.F109C|TP53_ENST00000455263.2_Missense_Mutation_p.F109C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	109	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.		F -> C (in sporadic cancers; somatic mutation).|F -> L (in a sporadic cancer; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.F109C(4)|p.F109S(4)|p.G59fs*23(3)|p.G108_F109delGF(2)|p.F109_R110delFR(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y107fs*38(1)|p.Y103_L111>L(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCCAGACGGAAACCGTAGCT	0.612		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	31	Substitution - Missense(8)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Complex - deletion inframe(2)	upper_aerodigestive_tract(5)|large_intestine(5)|stomach(4)|bone(4)|breast(4)|central_nervous_system(2)|lung(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|ovary(1)	17											62	59	60					17																	7579361		2203	4300	6503	7520086	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.326T>G	17.37:g.7579361A>C	ENSP00000269305:p.Phe109Cys		7520086	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104070	0.76983	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99853	-7.18;-7.18;-7.18;-7.18;-7.18;-7.18;-7.18;-7.18	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.104685	0.64402	D	0.000004	D	0.99866	0.9937	M	0.90977	3.165	0.47862	D	0.999536	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.997;0.999;0.999;1.0;0.999;0.998	D	0.96432	0.9320	10	0.87932	D	0	-31.6488	12.5363	0.56144	1.0:0.0:0.0:0.0	.	70;109;109;109;109;109;109	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	109	ENSP00000410739:F109C;ENSP00000352610:F109C;ENSP00000269305:F109C;ENSP00000398846:F109C;ENSP00000391127:F109C;ENSP00000391478:F109C;ENSP00000424104:F109C;ENSP00000426252:F109C	ENSP00000269305:F109C	F	-	2	0	TP53	7520086	1.000000	0.71417	0.868000	0.34077	0.936000	0.57629	7.389000	0.79806	2.125000	0.65367	0.533000	0.62120	TTC		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7579361	A	C	7579361	3	2	84	1	0	0	0	0	1	0	0	0	16421	246	9	4	976	4	TP53	17	7579361	Missense_Mutation	SNP	A	TCGA-AH-6643-01A-11D-1826-10		7579361	73615849	158	23850										
MYH1	4619	hgsc.bcm.edu	37	chr17	10408265	10408265	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tccttcatgttggccatctcCttctctgtctctgcactttt	5	14	4	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:10408265C>T	ENST00000226207.5	-	22	2647	c.2553G>A	c.(2551-2553)aaG>aaA	p.K851K	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	851					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TGGCCATCTCCTTCTCTGTCT	0.448																																																0			17											148	137	141					17																	10408265		2203	4300	6503	10348990	SO:0001819	synonymous_variant	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2553G>A	17.37:g.10408265C>T			10348990	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																				0.448	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10408265	C	T	10408265	2	4	84	1	0	0	0	0	0	0	0	1	10059	680	24	3		3	MYH1	17	10408265	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	2828904	10408265	70786945	159	23851										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11583192	11583192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	accttatggctgttaaagaaCggcagagtaacactgatgag	11	7	0	4	rs8070501	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:11583192C>T	ENST00000262442.4	+	18	3540	c.3472C>T	c.(3472-3474)Cgg>Tgg	p.R1158W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R1158W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1158	Stem. {ECO:0000250}.		R -> W (in dbSNP:rs8070501).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		TGTTAAAGAACGGCAGAGTAA	0.408													C|||	57	0.0113818	0.0408	0.0029	5008	,	,		18781	0.001		0	False		,,,				2504	0															0			17						C	TRP/ARG	164,4242	111.6+/-149.8	6,152,2045	136	129	132		3472	2.5	0.9	17	dbSNP_116	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DNAH9	NM_001372.3	101	6,154,6343	TT,TC,CC		0.0233,3.7222,1.2763	probably-damaging	1158/4487	11583192	166,12840	2203	4300	6503	11523917	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.3472C>T	17.37:g.11583192C>T	ENSP00000262442:p.Arg1158Trp		11523917	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	14.02	2.409862	0.42715	0.037222	2.33E-4	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25414	1.8;1.8	5.69	2.5	0.30297	.	0.257159	0.32343	N	0.006221	T	0.25717	0.0626	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.60865	-0.7178	10	0.87932	D	0	.	16.2874	0.82727	0.6259:0.3741:0.0:0.0	rs8070501;rs52812603;rs56633662;rs8070501	1158	Q9NYC9	DYH9_HUMAN	W	1158	ENSP00000262442:R1158W;ENSP00000414874:R1158W	ENSP00000262442:R1158W	R	+	1	2	DNAH9	11523917	0.585000	0.26774	0.926000	0.36857	0.245000	0.25701	0.963000	0.29293	0.294000	0.22547	0.650000	0.86243	CGG		0.408	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11583192	C	T	11583192	3	4	84	1	0	0	0	0	1	0	0	0	4619	527	19	1	3542	1	DNAH9	17	11583192	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	1174927	11583192	69612018	160	23852										
PIGS	94005	hgsc.bcm.edu	37	chr17	26887161	26887161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cctcaatgtcccagtagacaTcatgggacttggggtctggg	13	10	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:26887161T>C	ENST00000308360.7	-	7	1100	c.725A>G	c.(724-726)gAt>gGt	p.D242G	PIGS_ENST00000395346.2_Missense_Mutation_p.D234G|PIGS_ENST00000543734.1_Missense_Mutation_p.D181G|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	242					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)	p.D242G(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					CCAGTAGACATCATGGGACTT	0.532																																																1	Substitution - Missense(1)	kidney(1)	17											86	76	80					17																	26887161		2203	4300	6503	23911288	SO:0001583	missense	94005				CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.725A>G	17.37:g.26887161T>C	ENSP00000309430:p.Asp242Gly		23911288	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.391179	0.42410	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.44482	0.92;0.92;0.92	5.95	4.88	0.63580	.	0.228534	0.51477	D	0.000091	T	0.41696	0.1170	M	0.68952	2.095	0.41399	D	0.987667	P;P	0.44344	0.833;0.799	B;B	0.43445	0.42;0.295	T	0.27739	-1.0065	10	0.22706	T	0.39	-10.7882	8.9431	0.35742	0.0:0.0658:0.1266:0.8076	.	242;234	Q96S52;Q96S52-2	PIGS_HUMAN;.	G	234;242;181	ENSP00000378755:D234G;ENSP00000309430:D242G;ENSP00000438447:D181G	ENSP00000309430:D242G	D	-	2	0	PIGS	23911288	0.982000	0.34865	0.998000	0.56505	0.363000	0.29612	2.418000	0.44662	1.088000	0.41272	-0.256000	0.11100	GAT		0.532	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		C	26887161	T	C	26887161	3	2	84	1	0	0	0	0	1	0	0	0	11929	1435	50	4	966	4	PIGS	17	26887161	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	15303969	26887161	54308049	161	23853										
NF1	4763	hgsc.bcm.edu	37	chr17	29562982	29562982	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	actcctggatcctttattacGaattgtgatcacatcctctg	6	11	2	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:29562982G>T	ENST00000358273.4	+	29	4300	c.3917G>T	c.(3916-3918)cGa>cTa	p.R1306L	NF1_ENST00000356175.3_Missense_Mutation_p.R1306L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1306	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCTTTATTACGAATTGTGATC	0.363			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17											140	130	133					17																	29562982		2203	4300	6503	26587108	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3917G>T	17.37:g.29562982G>T	ENSP00000351015:p.Arg1306Leu		26587108	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774539	0.90108	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.79352	-0.2;-1.26;-1.26	5.94	5.94	0.96194	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	D	0.85809	0.5783	L	0.48986	1.54	0.80722	D	1	P;B;D;B	0.63046	0.808;0.023;0.992;0.339	P;B;D;B	0.72982	0.496;0.024;0.979;0.195	T	0.83326	-0.0015	10	0.39692	T	0.17	.	20.3552	0.98837	0.0:0.0:1.0:0.0	.	1306;356;1306;1306	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	L	1306;1306;972	ENSP00000351015:R1306L;ENSP00000348498:R1306L;ENSP00000389907:R972L	ENSP00000348498:R1306L	R	+	2	0	NF1	26587108	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.592000	0.82676	2.812000	0.96745	0.557000	0.71058	CGA		0.363	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29562982	G	T	29562982	3	4	84	1	0	0	0	0	1	0	0	0	10387	1058	37	2	4092	2	NF1	17	29562982	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	2675821	29562982	51632228	162	23854										
CD79B	974	hgsc.bcm.edu	37	chr17	62009607	62009607	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tggctgggcacaggagacaaCgccagcctggccatggtcac	14	13	1	1	rs199930415		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:62009607C>T	ENST00000006750.3	-	1	107	c.15G>A	c.(13-15)gcG>gcA	p.A5A	CD79B_ENST00000392795.3_Silent_p.A5A|CD79B_ENST00000349817.2_Silent_p.A5A	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	5					B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.A5A(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CAGGAGACAACGCCAGCCTGG	0.622			"Mis, O"		DLBCL																																		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	1	Substitution - coding silent(1)	kidney(1)	17											88	68	75					17																	62009607		2203	4300	6503	59363339	SO:0001819	synonymous_variant	974			L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1699	protein-coding gene	gene with protein product		147245	"CD79B antigen (immunoglobulin-associated beta)"	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.15G>A	17.37:g.62009607C>T			59363339	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	37	CCDS11655.1																																																																																				0.622	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			T	62009607	C	T	62009607	2	4	84	1	0	0	0	0	0	0	0	1	3043	523	19	1		1	CD79B	17	62009607	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	32446625	62009607	19185603	163	23855										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288735	74288735	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	atctgatctgcaccaggttgGaccaagccaggctgatatgc	11	11	2	2	rs368383298		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr17:74288735G>A	ENST00000262765.5	-	4	1754	c.1575C>T	c.(1573-1575)gtC>gtT	p.V525V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	525	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CACCAGGTTGGACCAAGCCAG	0.532																																																0			17											164	133	143					17																	74288735		2203	4300	6503	71800330	SO:0001819	synonymous_variant	84074			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1575C>T	17.37:g.74288735G>A			71800330	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																				0.532	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288735	G	A	74288735	2	1	84	1	0	0	0	0	0	0	0	1	12917	1161	41	3		3	QRICH2	17	74288735	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	12279128	74288735	6906475	164	23856										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55317593	55317602	+	Splice_Site	DEL	TTATACCTTA	TTATACCTTA	-													0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttgggaaaggactatattctTtataccttatcactttctga					rs188965072	byFrequency	TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	TTATACCTTA	TTATACCTTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr18:55317593_55317602delTTATACCTTA	ENST00000283684.4	-	26	3527_3531	c.3528_3532delTAAGGTATAA	c.(3526-3534)gataaggta>gata	p.KV1177fs	RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA|ATP8B1_ENST00000536015.1_Splice_Site_p.KV1177fs			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	1177					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				ACTATATTCTTTATACCTTATCACTTTCTG	0.438																																																0			18																																								53468600	SO:0001630	splice_region_variant	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.3531+1TAAGGTATAA>-	18.37:g.55317593_55317602delTTATACCTTA			53468591	Q9BTP8	In_Frame_Del	DEL	ENST00000283684.4	37	CCDS11965.1																																																																																				0.438	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	Frame_Shift_Del	-	55317602	TTATACCTTA	-	55317593	8	5	84	1	0	1	0	1	0	0	1	0	1195	1856	64	0		0	ATP8B1	18	55317593	Splice_Site	DEL	TTATACCTTA	TCGA-AH-6643-01A-11D-1826-10		55317593	22759655	165	23857										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2413777	2413777	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	catcgtgagctggggaatcgGgtgtgcggaagcccggcgtc	18	10	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:2413777G>C	ENST00000332578.3	+	9	1232	c.1232G>C	c.(1231-1233)gGg>gCg	p.G411A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	411	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		TGGGGAATCGGGTGTGCGGAA	0.647																																																0			19											62	68	66					19																	2413777		2203	4300	6503	2364777	SO:0001583	missense	360200			AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1232G>C	19.37:g.2413777G>C	ENSP00000330264:p.Gly411Ala		2364777	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598482	0.46318	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.89746	-2.56	3.93	3.93	0.45458	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.274143	0.25517	N	0.030132	D	0.94486	0.8225	M	0.85197	2.74	0.54753	D	0.999988	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.953	D	0.95294	0.8397	10	0.72032	D	0.01	.	14.5809	0.68288	0.0:0.0:1.0:0.0	.	411;445	Q7Z410;E7EMP4	TMPS9_HUMAN;.	A	445;411	ENSP00000330264:G411A	ENSP00000330264:G411A	G	+	2	0	TMPRSS9	2364777	1.000000	0.71417	0.100000	0.21137	0.024000	0.10985	9.769000	0.98969	1.755000	0.51935	0.555000	0.69702	GGG		0.647	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		C	2413777	G	C	2413777	3	2	84	1	0	0	0	0	1	0	0	0	16292	1232	43	5	1266	5	TMPRSS9	19	2413777	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		2413777	56715206	166	23858										
XAB2	56949	hgsc.bcm.edu	37	chr19	7685874	7685874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cgtacacggccatggcatgcCgggccaggccccactcctcc	11	19	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:7685874C>T	ENST00000358368.4	-	14	1866	c.1829G>A	c.(1828-1830)cGg>cAg	p.R610Q	XAB2_ENST00000534844.1_Missense_Mutation_p.R607Q	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	610					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CATGGCATGCCGGGCCAGGCC	0.662								Direct reversal of damage;Nucleotide excision repair (NER)																																								0			19											14	13	13					19																	7685874		2177	4273	6450	7591874	SO:0001583	missense	56949			AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.1829G>A	19.37:g.7685874C>T	ENSP00000351137:p.Arg610Gln		7591874	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	37	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277297	0.95459	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.04049	3.72;3.72	4.4	4.4	0.53042	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	T	0.16300	0.0392	M	0.89214	3.015	0.80722	D	1	D	0.65815	0.995	P	0.48552	0.581	T	0.11470	-1.0586	10	0.62326	D	0.03	-29.631	15.7467	0.77949	0.0:1.0:0.0:0.0	.	610	Q9HCS7	SYF1_HUMAN	Q	610;607	ENSP00000351137:R610Q;ENSP00000438225:R607Q	ENSP00000351137:R610Q	R	-	2	0	XAB2	7591874	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.663000	0.68038	1.984000	0.57885	0.467000	0.42956	CGG		0.662	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		T	7685874	C	T	7685874	3	4	84	1	0	0	0	0	1	0	0	0	17458	652	23	1	762	1	XAB2	19	7685874	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	5272097	7685874	51443109	167	23859										
MUC16	94025	hgsc.bcm.edu	37	chr19	9074564	9074564	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtctcaatctctgtggtctcGgaggagccaaatactgatgt	11	9	3	1	rs370292934		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:9074564G>A	ENST00000397910.4	-	3	13085	c.12882C>T	c.(12880-12882)tcC>tcT	p.S4294S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4296	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGTGGTCTCGGAGGAGCCAA	0.522													G|||	1	0.000199681	0	0	5008	,	,		22938	0.001		0	False		,,,				2504	0															0			19											109	106	107					19																	9074564		2034	4182	6216	8935564	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12882C>T	19.37:g.9074564G>A			8935564	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9074564	G	A	9074564	2	1	84	1	0	0	0	0	0	0	0	1	10003	1103	39	1		1	MUC16	19	9074564	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	1388690	9074564	50054419	168	23860										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087432	9087432	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tcctctgtcaaactggtactCagccatgttgccatggggag	11	11	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:9087432C>A	ENST00000397910.4	-	1	4586	c.4383G>T	c.(4381-4383)ctG>ctT	p.L1461L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1461	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACTGGTACTCAGCCATGTTG	0.483																																																0			19											113	112	113					19																	9087432		1966	4147	6113	8948432	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4383G>T	19.37:g.9087432C>A			8948432	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9087432	C	A	9087432	2	1	84	1	0	0	0	0	0	0	0	1	10003	813	29	2		2	MUC16	19	9087432	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	12868	9087432	50041551	169	23861										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934886	30934886	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccactctgcggcaagcgcttCcgcttcaacagcatcctctc	7	18	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:30934886C>T	ENST00000355537.3	+	2	564	c.417C>T	c.(415-417)ttC>ttT	p.F139F		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	139					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.F139F(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCAAGCGCTTCCGCTTCAACA	0.637																																																1	Substitution - coding silent(1)	ovary(1)	19											66	54	58					19																	30934886		2203	4300	6503	35626726	SO:0001819	synonymous_variant	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.417C>T	19.37:g.30934886C>T			35626726	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																				0.637	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30934886	C	T	30934886	2	4	84	1	0	0	0	0	0	0	0	1	18013	854	30	3		3	ZNF536	19	30934886	Silent	SNP	C	TCGA-AH-6643-01A-11D-1826-10	21847454	30934886	28194097	170	23862										
UBA2	10054	hgsc.bcm.edu	37	chr19	34934804	34934804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tatctcctgacagagctgacCctgaagctgcctgtgagtaa	10	11	1	5			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:34934804C>T	ENST00000246548.4	+	7	707	c.637C>T	c.(637-639)Cct>Tct	p.P213S	UBA2_ENST00000439527.2_Missense_Mutation_p.P117S	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	213					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CAGAGCTGACCCTGAAGCTGC	0.323																																																0			19											95	97	96					19																	34934804		2203	4300	6503	39626644	SO:0001583	missense	10054			BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.637C>T	19.37:g.34934804C>T	ENSP00000246548:p.Pro213Ser		39626644	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Missense_Mutation	SNP	ENST00000246548.4	37	CCDS12439.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.895650	0.91962	.	.	ENSG00000126261	ENST00000542624;ENST00000246548;ENST00000439527	T;T	0.58060	0.36;1.51	5.02	5.02	0.67125	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.000000	0.85682	D	0.000000	T	0.63988	0.2558	M	0.81802	2.56	0.80722	D	1	P	0.52170	0.951	P	0.48304	0.573	T	0.68849	-0.5300	10	0.45353	T	0.12	-11.4467	17.4857	0.87687	0.0:1.0:0.0:0.0	.	213	Q9UBT2	SAE2_HUMAN	S	86;213;117	ENSP00000246548:P213S;ENSP00000437484:P117S	ENSP00000246548:P213S	P	+	1	0	UBA2	39626644	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.313000	0.78978	2.477000	0.83638	0.591000	0.81541	CCT		0.323	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		T	34934804	C	T	34934804	3	4	84	1	0	0	0	0	1	0	0	0	16868	623	22	3	663	3	UBA2	19	34934804	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	3999918	34934804	24194179	171	23863										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42863347	42863347	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cgagttcagcagcgacgttcTgctctaccaggtcaactgca	10	13	4	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:42863347T>G	ENST00000251268.6	+	31	5441	c.5441T>G	c.(5440-5442)cTg>cGg	p.L1814R	MEGF8_ENST00000334370.4_Missense_Mutation_p.L1747R	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1814					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				AGCGACGTTCTGCTCTACCAG	0.647																																																0			19											44	35	38					19																	42863347		2202	4300	6502	47555187	SO:0001583	missense	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.5441T>G	19.37:g.42863347T>G	ENSP00000251268:p.Leu1814Arg		47555187	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	T	19.88	3.909055	0.72868	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.62941	-0.01;-0.01	4.69	4.69	0.59074	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.143577	0.36591	N	0.002513	T	0.68091	0.2963	L	0.28556	0.865	0.80722	D	1	D;D	0.71674	0.998;0.996	D;P	0.72625	0.978;0.899	T	0.72124	-0.4385	10	0.87932	D	0	-9.448	13.1429	0.59444	0.0:0.0:0.0:1.0	.	1814;1747	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	R	1747;1814	ENSP00000334219:L1747R;ENSP00000251268:L1814R	ENSP00000251268:L1814R	L	+	2	0	MEGF8	47555187	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	3.708000	0.54845	1.756000	0.51951	0.374000	0.22700	CTG		0.647	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42863347	T	G	42863347	3	3	84	1	0	0	0	0	1	0	0	0	9493	1580	55	4	5358	4	MEGF8	19	42863347	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	7928543	42863347	16265636	172	23864										
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52130922	52130922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccagcacagggagggggccgGccgggctcgaaaggagcatc	18	12	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:52130922G>A	ENST00000534261.2	-	7	1474	c.1075C>T	c.(1075-1077)Ccg>Tcg	p.P359S	SIGLEC5_ENST00000429354.3_Missense_Mutation_p.P359S|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.P359S|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.P359S|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.P359S			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	359					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		GAGGGGGCCGGCCGGGCTCGA	0.672																																																0			19											10	13	12					19																	52130922		2190	4284	6474	56822734	SO:0001583	missense	8778			U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1075C>T	19.37:g.52130922G>A	ENSP00000473238:p.Pro359Ser		56822734		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.697842	0.30142	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	D;D	0.95377	-3.69;-3.69	4.15	4.15	0.48705	.	3.326270	0.01401	N	0.013593	D	0.98283	0.9431	M	0.88181	2.935	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	D	0.87290	0.2298	10	0.87932	D	0	.	12.1214	0.53893	0.0:0.0:1.0:0.0	.	359	O15389	SIGL5_HUMAN	S	359	ENSP00000222107:P359S;ENSP00000415200:P359S	ENSP00000222107:P359S	P	-	1	0	SIGLEC5	56822734	0.780000	0.28664	0.024000	0.17045	0.005000	0.04900	4.107000	0.57811	2.311000	0.77944	0.551000	0.68910	CCG		0.672	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		A	52130922	G	A	52130922	3	1	84	1	0	0	0	0	1	0	0	0	14348	1203	42	3	596	3	SIGLEC5	19	52130922	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	9267575	52130922	6998061	173	23865										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313398	54313398	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aagctgtagtacctctcacaGttgatgtccttctggaagat	9	9	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:54313398G>T	ENST00000324134.6	-	3	1683	c.1515C>A	c.(1513-1515)aaC>aaA	p.N505K	NLRP12_ENST00000391772.1_Missense_Mutation_p.N505K|NLRP12_ENST00000354278.3_Missense_Mutation_p.N505K|NLRP12_ENST00000345770.5_Missense_Mutation_p.N505K|NLRP12_ENST00000351894.4_Missense_Mutation_p.N505K|NLRP12_ENST00000391773.1_Missense_Mutation_p.N505K|NLRP12_ENST00000535162.1_Missense_Mutation_p.N505K|NLRP12_ENST00000391775.3_Missense_Mutation_p.N505K	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	505	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.N505N(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		ACCTCTCACAGTTGATGTCCT	0.527																																																1	Substitution - coding silent(1)	ovary(1)	19											119	120	119					19																	54313398		2203	4300	6503	59005210	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.1515C>A	19.37:g.54313398G>T	ENSP00000319377:p.Asn505Lys		59005210	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	9.879	1.200950	0.22121	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	4.43	0.696	0.18075	NACHT nucleoside triphosphatase (1);	0.832776	0.10064	N	0.720507	T	0.68751	0.3035	N	0.02802	-0.49	0.58432	D	0.999996	B;B;B;B	0.12013	0.005;0.001;0.001;0.001	B;B;B;B	0.08055	0.003;0.002;0.002;0.002	T	0.54423	-0.8296	10	0.22109	T	0.4	.	9.2723	0.37679	0.0:0.2867:0.5665:0.1468	.	505;505;505;505	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	K	505	ENSP00000319377:N505K;ENSP00000438030:N505K;ENSP00000340473:N505K;ENSP00000346231:N505K;ENSP00000375655:N505K;ENSP00000375653:N505K;ENSP00000375652:N505K	ENSP00000319377:N505K	N	-	3	2	NLRP12	59005210	0.001000	0.12720	0.421000	0.26609	0.833000	0.47200	1.098000	0.31000	0.407000	0.25591	0.485000	0.47835	AAC		0.527	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54313398	G	T	54313398	3	4	84	1	0	0	0	0	1	0	0	0	10505	1020	36	2	1798	2	NLRP12	19	54313398	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	2182476	54313398	4815585	174	23866										
PEG3	5178	hgsc.bcm.edu	37	chr19	57325595	57325595	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tctggctcagcagcctccacTtctggctcggcagcctccac	9	18	3	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr19:57325595T>G	ENST00000326441.9	-	10	4578	c.4215A>C	c.(4213-4215)gaA>gaC	p.E1405D	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.E1405D|PEG3_ENST00000593695.1_Missense_Mutation_p.E1279D|PEG3_ENST00000598410.1_Missense_Mutation_p.E1281D|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1405	3 X 7 AA repeat of P-E-V-E-A-A-E.|Glu-rich.				apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CAGCCTCCACTTCTGGCTCGG	0.572																																																0			19											44	47	46					19																	57325595		2180	4254	6434	62017407	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4215A>C	19.37:g.57325595T>G	ENSP00000326581:p.Glu1405Asp		62017407	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.454787	0.43634	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02737	4.18;4.18	3.93	-7.13	0.01532	.	0.000000	0.41823	D	0.000806	T	0.01800	0.0057	L	0.29908	0.895	.	.	.	P;P;P	0.47762	0.9;0.9;0.9	B;B;B	0.42112	0.376;0.376;0.376	T	0.19160	-1.0314	9	0.56958	D	0.05	-16.9672	4.9568	0.14046	0.129:0.5741:0.1304:0.1665	.	1281;1405;1340	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	D	1405	ENSP00000326581:E1405D;ENSP00000403051:E1405D	ENSP00000326581:E1405D	E	-	3	2	ZIM2	62017407	0.000000	0.05858	0.018000	0.16275	0.428000	0.31595	-2.927000	0.00690	-1.613000	0.01577	-0.326000	0.08463	GAA		0.572	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			G	57325595	T	G	57325595	3	3	84	1	0	0	0	0	1	0	0	0	11751	1606	56	4	555	4	PEG3	19	57325595	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	3012197	57325595	1803388	175	23867										
PDYN	5173	hgsc.bcm.edu	37	chr20	1961100	1961100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gagcttgggacgaatgcgccGcaagaagcccccatagcgtt	13	12	0	1	rs201486601		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:1961100G>A	ENST00000217305.2	-	4	859	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	PDYN_ENST00000540134.1_Missense_Mutation_p.R212W|RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000539905.1_Missense_Mutation_p.R212W	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	212			R -> W (in SCA23; the mutant PDYN protein is produced, but processing to opioid peptides is dramatically affected, with increased levels of dynorphin A compared to dynorphin B; mutant dynorphin A is neurotoxic to cultured striatal neurons, suggesting a dominant-negative effect; dbSNP:rs201486601). {ECO:0000269|PubMed:21035104}.		cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CGAATGCGCCGCAAGAAGCCC	0.587													G|||	1	0.000199681	0	0.0014	5008	,	,		16226	0		0	False		,,,				2504	0															0			20											102	113	109					20																	1961100		2203	4300	6503	1909100	SO:0001583	missense	5173				CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.634C>T	20.37:g.1961100G>A	ENSP00000217305:p.Arg212Trp		1909100	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	20.2	3.944983	0.73672	.	.	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	D;D;D	0.85556	-2.0;-2.0;-2.0	5.0	-3.04	0.05412	.	0.000000	0.85682	D	0.000000	D	0.92378	0.7581	M	0.89601	3.045	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	D	0.91682	0.5359	10	0.59425	D	0.04	-24.1261	16.3704	0.83355	0.0:0.0:0.2532:0.7468	.	212	P01213	PDYN_HUMAN	W	212	ENSP00000440185:R212W;ENSP00000442259:R212W;ENSP00000217305:R212W	ENSP00000217305:R212W	R	-	1	2	PDYN	1909100	1.000000	0.71417	0.822000	0.32727	0.984000	0.73092	0.612000	0.24283	-0.750000	0.04740	0.313000	0.20887	CGG		0.587	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			A	1961100	G	A	1961100	3	1	84	1	0	0	0	0	1	0	0	0	11730	1086	38	1	134	1	PDYN	20	1961100	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10		1961100	61064420	176	23868										
TGM6	343641	hgsc.bcm.edu	37	chr20	2397925	2397925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gcaaggcggtgaacaggctgTtcggcgtggaagcctctgga	17	9	1	1	rs199968743		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:2397925T>C	ENST00000202625.2	+	10	1445	c.1384T>C	c.(1384-1386)Ttc>Ctc	p.F462L	TGM6_ENST00000381423.1_Missense_Mutation_p.F462L	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	462					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	GAACAGGCTGTTCGGCGTGGA	0.617																																																0			20											34	29	31					20																	2397925		2203	4299	6502	2345925	SO:0001583	missense	343641			AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1384T>C	20.37:g.2397925T>C	ENSP00000202625:p.Phe462Leu		2345925	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	T	0.312	-0.966965	0.02232	.	.	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.79352	-1.1;-1.26	4.54	2.83	0.33086	.	0.831098	0.09649	U	0.773870	T	0.59998	0.2235	N	0.16478	0.41	0.24015	N	0.996168	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.45338	-0.9268	10	0.28530	T	0.3	-11.0013	5.3108	0.15829	0.0:0.2038:0.0:0.7962	.	462;462	O95932-2;O95932	.;TGM3L_HUMAN	L	462	ENSP00000202625:F462L;ENSP00000370831:F462L	ENSP00000202625:F462L	F	+	1	0	TGM6	2345925	0.947000	0.32204	0.675000	0.29917	0.065000	0.16274	0.151000	0.16283	0.463000	0.27118	0.460000	0.39030	TTC		0.617	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		C	2397925	T	C	2397925	3	2	84	1	0	0	0	0	1	0	0	0	15873	1725	60	4	1422	4	TGM6	20	2397925	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	436825	2397925	60627595	177	23869										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16474981	16474981	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cacttatttgtccattccttGgtcaattcttgaacctgaaa	5	10	2	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:16474981G>A	ENST00000354981.2	-	12	1414	c.1257C>T	c.(1255-1257)acC>acT	p.T419T	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000408042.1_Silent_p.T419T|KIF16B_ENST00000355755.3_Silent_p.T419T	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	419					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TCCATTCCTTGGTCAATTCTT	0.308																																																0			20											99	88	92					20																	16474981		2199	4297	6496	16422981	SO:0001819	synonymous_variant	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.1257C>T	20.37:g.16474981G>A			16422981	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																				0.308	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16474981	G	A	16474981	2	1	84	1	0	0	0	0	0	0	0	1	8299	1335	47	3		3	KIF16B	20	16474981	Silent	SNP	G	TCGA-AH-6643-01A-11D-1826-10	14077056	16474981	46550539	178	23870										
MYL9	10398	hgsc.bcm.edu	37	chr20	35177484	35177484	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ctgcccctgcccgcaggtttCatccatgaggaccacctccg	9	18	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:35177484C>A	ENST00000279022.2	+	4	455	c.351C>A	c.(349-351)ttC>ttA	p.F117L	RP5-977B1.7_ENST00000425233.1_RNA|MYL9_ENST00000346786.2_Missense_Mutation_p.F63L|RP5-977B1.11_ENST00000561134.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	117	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				CCGCAGGTTTCATCCATGAGG	0.602																																																0			20											64	59	61					20																	35177484		2203	4300	6503	34610898	SO:0001583	missense	10398			J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"Myosins / Light chain", "EF-hand domain containing"	15754	protein-coding gene	gene with protein product	"myosin regulatory light chain 2, smooth muscle isoform", "myosin regulatory light chain 1"	609905	"myosin, light polypeptide 9, regulatory"			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.351C>A	20.37:g.35177484C>A	ENSP00000279022:p.Phe117Leu		34610898	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Missense_Mutation	SNP	ENST00000279022.2	37	CCDS13276.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.277111	0.23307	.	.	ENSG00000101335	ENST00000279022;ENST00000346786	T;T	0.78816	-1.21;2.98	4.7	-3.05	0.05396	EF-hand-like domain (1);	0.221758	0.46145	D	0.000303	T	0.62889	0.2465	L	0.42744	1.35	0.19300	N	0.99998	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.48222	-0.9054	10	0.16896	T	0.51	.	10.7229	0.46050	0.0:0.4035:0.0:0.5965	.	63;117	Q9BUF9;P24844	.;MYL9_HUMAN	L	117;63	ENSP00000279022:F117L;ENSP00000217313:F63L	ENSP00000279022:F117L	F	+	3	2	MYL9	34610898	0.995000	0.38212	0.610000	0.28997	0.365000	0.29674	0.485000	0.22324	-0.865000	0.04073	-0.302000	0.09304	TTC		0.602	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		A	35177484	C	A	35177484	3	1	84	1	0	0	0	0	1	0	0	0	10084	825	29	2	361	2	MYL9	20	35177484	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	18702503	35177484	27848036	179	23871										
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45850063	45850063	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgtgctcgaggagctcccctGggaggacttatttagtgttt	13	8	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:45850063G>A	ENST00000311275.7	-	20	3512	c.3259C>T	c.(3259-3261)Cag>Tag	p.Q1087*	ZMYND8_ENST00000262975.4_Nonsense_Mutation_p.Q1041*|ZMYND8_ENST00000352431.2_Nonsense_Mutation_p.Q1061*|ZMYND8_ENST00000446994.2_Nonsense_Mutation_p.Q978*|ZMYND8_ENST00000372023.3_Nonsense_Mutation_p.Q1009*|ZMYND8_ENST00000536340.1_Nonsense_Mutation_p.Q1114*|ZMYND8_ENST00000471951.2_Nonsense_Mutation_p.Q1107*|ZMYND8_ENST00000461685.1_Nonsense_Mutation_p.Q1061*|ZMYND8_ENST00000355972.4_Nonsense_Mutation_p.Q1087*|ZMYND8_ENST00000396281.4_Nonsense_Mutation_p.Q1087*|ZMYND8_ENST00000458360.2_Nonsense_Mutation_p.Q955*|ZMYND8_ENST00000540497.1_Nonsense_Mutation_p.Q1035*|ZMYND8_ENST00000360911.3_Nonsense_Mutation_p.Q1036*	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	1087					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GAGCTCCCCTGGGAGGACTTA	0.542																																																0			20											115	97	103					20																	45850063		2203	4300	6503	45283470	SO:0001587	stop_gained	23613			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.3259C>T	20.37:g.45850063G>A	ENSP00000312237:p.Gln1087*		45283470	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Nonsense_Mutation	SNP	ENST00000311275.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.677406|6.677406	0.97755|0.97755	.|.	.|.	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.335390	.|0.34314	.|N	.|0.004062	T|.	0.66519|.	0.2797|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.61242|.	-0.7102|.	3|.	.|0.20046	.|T	.|0.44	-0.9225|-0.9225	17.6984|17.6984	0.88288|0.88288	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	968|1036;1087;955;1042;1108;1061;1087;1114;1087;978;1061;1009;1035	.|.	.|ENSP00000262975:Q1042X	P|Q	-|-	2|1	0|0	ZMYND8|ZMYND8	45283470|45283470	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.062000|0.062000	0.15995|0.15995	6.611000|6.611000	0.74183|0.74183	2.599000|2.599000	0.87857|0.87857	0.650000|0.650000	0.86243|0.86243	CCA|CAG		0.542	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		A	45850063	G	A	45850063	4	1	84	1	0	0	0	0	0	1	0	0	17750	1357	47	3	401	3	ZMYND8	20	45850063	Nonsense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	10672579	45850063	17175457	180	23872										
CBLN4	140689	hgsc.bcm.edu	37	chr20	54579076	54579076	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	aggaagaggagcccttggagTccgtggccgggttcgagtcg	18	9	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr20:54579076T>C	ENST00000064571.2	-	1	1452	c.152A>G	c.(151-153)gAc>gGc	p.D51G		NM_080617.5	NP_542184.1	Q9NTU7	CBLN4_HUMAN	cerebellin 4 precursor	51					protein secretion (GO:0009306)	cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(1)|lung(10)|ovary(3)|pancreas(1)	17			Colorectal(105;0.202)			GCCCTTGGAGTCCGTGGCCGG	0.682																																																0			20											63	63	63					20																	54579076		2203	4300	6503	54012483	SO:0001583	missense	140689			AY358527	CCDS13448.1	20q13	2004-08-19	2004-08-19	2004-08-19	ENSG00000054803	ENSG00000054803			16231	protein-coding gene	gene with protein product		615029	"cerebellin precursor-like 1"	CBLNL1			Standard	NM_080617		Approved	dJ885A10.1	uc002xxa.4	Q9NTU7	OTTHUMG00000032782	ENST00000064571.2:c.152A>G	20.37:g.54579076T>C	ENSP00000064571:p.Asp51Gly		54012483	A8K0S5	Missense_Mutation	SNP	ENST00000064571.2	37	CCDS13448.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462394	0.63513	.	.	ENSG00000054803	ENST00000064571	D	0.85258	-1.96	5.16	5.16	0.70880	.	0.144833	0.64402	D	0.000005	D	0.82342	0.5016	M	0.66939	2.045	0.80722	D	1	P	0.37864	0.61	B	0.33521	0.165	T	0.81113	-0.1080	10	0.25106	T	0.35	-29.2465	15.2996	0.73936	0.0:0.0:0.0:1.0	.	51	Q9NTU7	CBLN4_HUMAN	G	51	ENSP00000064571:D51G	ENSP00000064571:D51G	D	-	2	0	CBLN4	54012483	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.620000	0.61226	2.073000	0.62155	0.533000	0.62120	GAC		0.682	CBLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079783.2	NM_080617		C	54579076	T	C	54579076	3	2	84	1	0	0	0	0	1	0	0	0	2713	1667	58	4	465	4	CBLN4	20	54579076	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	8729013	54579076	8446444	181	23873										
TPTE	7179	hgsc.bcm.edu	37	chr21	10934966	10934966	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tgtagactcgatagtggtttCggtgtttcttatctagaaac	10	6	2	2	rs200020621		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr21:10934966C>G	ENST00000361285.4	-	15	1156	c.827G>C	c.(826-828)cGa>cCa	p.R276P	TPTE_ENST00000342420.5_Missense_Mutation_p.R238P|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.R258P	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	276	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R258Q(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATAGTGGTTTCGGTGTTTCTT	0.363																																																1	Substitution - Missense(1)	large_intestine(1)	21											255	227	236					21																	10934966		2203	4300	6503	9956837	SO:0001583	missense	7179			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.827G>C	21.37:g.10934966C>G	ENSP00000355208:p.Arg276Pro		9956837	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.359451	0.00016	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	T;T;T	0.25579	1.79;1.79;1.79	2.25	-4.5	0.03493	Phosphatase tensin type (1);	0.874116	0.10137	N	0.711356	T	0.05547	0.0146	N	0.00966	-1.09	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.002;0.003	T	0.30327	-0.9982	10	0.06625	T	0.88	-0.2719	5.8332	0.18593	0.0:0.3712:0.3367:0.2922	.	238;258;276	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	P	258;276;238	ENSP00000298232:R258P;ENSP00000355208:R276P;ENSP00000344441:R238P	ENSP00000298232:R258P	R	-	2	0	TPTE	9956837	0.000000	0.05858	0.003000	0.11579	0.047000	0.14425	-2.618000	0.00880	-1.604000	0.01595	-1.247000	0.01520	CGA		0.363	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			G	10934966	C	G	10934966	3	3	84	1	0	0	0	0	1	0	0	0	16470	884	31	5	868	5	TPTE	21	10934966	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10		10934966	37194929	182	23874										
KRTAP24-1	643803	hgsc.bcm.edu	37	chr21	31655095	31655095	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tccaggagccagagatttccTtggtagctactgggtaagca	12	9	0	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr21:31655095T>G	ENST00000340345.4	-	1	181	c.156A>C	c.(154-156)caA>caC	p.Q52H		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	52						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						AGAGATTTCCTTGGTAGCTAC	0.488																																																0			21											91	90	91					21																	31655095		1933	4155	6088	30576966	SO:0001583	missense	643803			AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"Keratin associated proteins"	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.156A>C	21.37:g.31655095T>G	ENSP00000339238:p.Gln52His		30576966	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	37	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.183720	0.38609	.	.	ENSG00000188694	ENST00000340345	T	0.05139	3.49	5.06	2.69	0.31865	.	0.243752	0.32533	N	0.005977	T	0.05960	0.0155	L	0.41824	1.3	0.31815	N	0.626742	B	0.28760	0.221	B	0.33846	0.171	T	0.07252	-1.0782	10	0.46703	T	0.11	-6.5804	4.5767	0.12238	0.0:0.0989:0.1992:0.7019	.	52	Q3LI83	KR241_HUMAN	H	52	ENSP00000339238:Q52H	ENSP00000339238:Q52H	Q	-	3	2	KRTAP24-1	30576966	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.799000	0.27028	0.983000	0.38602	0.482000	0.46254	CAA		0.488	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455		G	31655095	T	G	31655095	3	3	84	1	0	0	0	0	1	0	0	0	8564	1606	56	4	612	4	KRTAP24-1	21	31655095	Missense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	20720129	31655095	16474800	183	23875										
ADRBK2	157	hgsc.bcm.edu	37	chr22	26114292	26114292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ttctgactcagtggcagcgtCgctatttttacctctttcca	7	12	3	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr22:26114292C>T	ENST00000324198.6	+	19	1927	c.1735C>T	c.(1735-1737)Cgc>Tgc	p.R579C		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	579	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	GTGGCAGCGTCGCTATTTTTA	0.483																																																0			22											124	124	124					22																	26114292		2203	4300	6503	24444292	SO:0001583	missense	157			X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1735C>T	22.37:g.26114292C>T	ENSP00000317578:p.Arg579Cys		24444292	Q9UGW9	Missense_Mutation	SNP	ENST00000324198.6	37	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265548	0.80358	.	.	ENSG00000100077	ENST00000324198	T	0.80393	-1.37	5.3	4.25	0.50352	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.87188	0.6115	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.88482	0.3069	10	0.87932	D	0	-11.7234	14.4571	0.67423	0.1483:0.8517:0.0:0.0	.	579	P35626	ARBK2_HUMAN	C	579	ENSP00000317578:R579C	ENSP00000317578:R579C	R	+	1	0	ADRBK2	24444292	1.000000	0.71417	0.323000	0.25347	0.990000	0.78478	5.259000	0.65485	1.321000	0.45227	0.655000	0.94253	CGC		0.483	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		T	26114292	C	T	26114292	3	4	84	1	0	0	0	0	1	0	0	0	344	884	31	1	1809	1	ADRBK2	22	26114292	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10		26114292	25190274	184	23876										
NF2	4771	hgsc.bcm.edu	37	chr22	30038259	30038259	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	tctgtgctcctggcttcttaCgccgtccaggccaaggtagg	12	13	2	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr22:30038259C>A	ENST00000338641.4	+	4	873	c.432C>A	c.(430-432)taC>taA	p.Y144*	NF2_ENST00000361452.4_Nonsense_Mutation_p.Y103*|NF2_ENST00000361166.4_Nonsense_Mutation_p.Y144*|NF2_ENST00000413209.2_Nonsense_Mutation_p.Y144*|NF2_ENST00000403435.1_Nonsense_Mutation_p.Y144*|NF2_ENST00000403999.3_Nonsense_Mutation_p.Y144*|NF2_ENST00000353887.4_Nonsense_Mutation_p.Y61*|NF2_ENST00000347330.5_Nonsense_Mutation_p.Y61*|NF2_ENST00000397789.3_Nonsense_Mutation_p.Y144*|NF2_ENST00000361676.4_Nonsense_Mutation_p.Y102*|NF2_ENST00000334961.7_Nonsense_Mutation_p.Y61*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	144	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.V122_K149del(5)|p.Y144*(4)|p.?(2)|p.Y144fs*1(1)|p.Y144fs*5(1)|p.Y144fs*29(1)|p.K123fs*2(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TGGCTTCTTACGCCGTCCAGG	0.448			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	15	Deletion - In frame(5)|Substitution - Nonsense(4)|Deletion - Frameshift(3)|Unknown(2)|Insertion - Frameshift(1)	soft_tissue(8)|meninges(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)	22	GRCh37	CM045424|CM077954	NF2	M							78	75	76					22																	30038259		2203	4300	6503	28368259	SO:0001587	stop_gained	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.432C>A	22.37:g.30038259C>A	ENSP00000344666:p.Tyr144*		28368259	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	33	5.290713	0.95546	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.24	-10.5	0.00291	.	0.059373	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.7817	0.99721	0.0:0.2486:0.0:0.7514	.	.	.	.	X	144;61;144;144;103;144;144;61;61;144;102;144	.	.	Y	+	3	2	NF2	28368259	0.003000	0.15002	0.088000	0.20740	0.887000	0.51463	-1.378000	0.02556	-2.437000	0.00552	-1.553000	0.00894	TAC		0.448	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		A	30038259	C	A	30038259	4	1	84	1	0	0	0	0	0	1	0	0	10388	547	19	2	446	2	NF2	22	30038259	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	3923967	30038259	21266307	185	23877										
APOBEC3C	27350	hgsc.bcm.edu	37	chr22	39411748	39411748	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	cctggaagacgggcgtcttcCgaaaccaggtagcaccaaag	12	12	1	1			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr22:39411748C>T	ENST00000361441.4	+	2	446	c.166C>T	c.(166-168)Cga>Tga	p.R56*	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	56					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					GGGCGTCTTCCGAAACCAGGT	0.522																																																0			22											74	71	72					22																	39411748		2203	4300	6503	37741694	SO:0001587	stop_gained	27350			AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"Apolipoprotein B mRNA editing enzymes"	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.166C>T	22.37:g.39411748C>T	ENSP00000355340:p.Arg56*		37741694	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Nonsense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	20.1	3.939747	0.73557	.	.	ENSG00000244509	ENST00000361441	.	.	.	2.08	-2.02	0.07388	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.9283	0.05792	0.48:0.3521:0.0:0.1679	.	.	.	.	X	56	.	ENSP00000355340:R56X	R	+	1	2	APOBEC3C	37741694	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.063000	0.11655	-0.421000	0.07416	-0.451000	0.05528	CGA		0.522	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508		T	39411748	C	T	39411748	4	4	84	1	0	0	0	0	0	1	0	0	791	644	23	1	172	1	APOBEC3C	22	39411748	Nonsense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10	9373489	39411748	11892818	186	23878										
PDGFB	5155	hgsc.bcm.edu	37	chr22	39621756	39621756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	caagggtctccttcagtgccGtcttgtcatgcgtgtgcttg	12	11	4	0	rs531185137		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chr22:39621756G>A	ENST00000331163.6	-	6	1485	c.698C>T	c.(697-699)aCg>aTg	p.T233M	PDGFB_ENST00000381551.4_Missense_Mutation_p.T218M	NM_002608.2	NP_002599.1	P01127	PDGFB_HUMAN	platelet-derived growth factor beta polypeptide	233					actin cytoskeleton organization (GO:0030036)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|branching involved in salivary gland morphogenesis (GO:0060445)|cell chemotaxis (GO:0060326)|cell growth (GO:0016049)|cell projection assembly (GO:0030031)|cellular response to growth factor stimulus (GO:0071363)|cellular response to mycophenolic acid (GO:0071506)|DNA replication (GO:0006260)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|metanephric glomerular endothelium development (GO:0072264)|metanephric glomerular mesangial cell development (GO:0072255)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|monocyte chemotaxis (GO:0002548)|negative regulation of cell migration (GO:0030336)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|paracrine signaling (GO:0038001)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of metanephric mesenchymal cell migration (GO:2000591)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to wounding (GO:0009611)|substrate-dependent cell migration (GO:0006929)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|collagen binding (GO:0005518)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|superoxide-generating NADPH oxidase activator activity (GO:0016176)		COL1A1/PDGFB(429)	central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Melanoma(58;0.04)					CTTCAGTGCCGTCTTGTCATG	0.627			T	COL1A1	DFSP																																		Dom	yes		22	22q12.3-q13.1	5155	platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)		M	0			22											184	133	150					22																	39621756		2203	4300	6503	37951702	SO:0001583	missense	5155				CCDS13987.1, CCDS33650.1	22q13.1	2012-10-02	2011-05-19		ENSG00000100311	ENSG00000100311			8800	protein-coding gene	gene with protein product	"oncogene SIS", "becaplermin"	190040	"platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)"	SIS		2991848, 1661670	Standard	NM_002608		Approved	SSV	uc003axf.3	P01127	OTTHUMG00000151029	ENST00000331163.6:c.698C>T	22.37:g.39621756G>A	ENSP00000330382:p.Thr233Met		37951702	G3XAG8|P78431|Q15354|Q6FHE7|Q9UF23	Missense_Mutation	SNP	ENST00000331163.6	37	CCDS13987.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.261435	0.39995	.	.	ENSG00000100311	ENST00000331163;ENST00000381551	T;T	0.44881	0.91;0.91	5.3	-7.99	0.01131	.	1.136760	0.06381	N	0.715224	T	0.23492	0.0568	N	0.14661	0.345	0.09310	N	1	P;P	0.38992	0.521;0.653	B;B	0.37480	0.128;0.251	T	0.42310	-0.9459	10	0.62326	D	0.03	-3.1384	11.2086	0.48784	0.1684:0.0:0.5628:0.2688	.	233;218	P01127;G3XAG8	PDGFB_HUMAN;.	M	233;218	ENSP00000330382:T233M;ENSP00000370963:T218M	ENSP00000330382:T233M	T	-	2	0	PDGFB	37951702	0.566000	0.26618	0.099000	0.21106	0.928000	0.56348	-0.056000	0.11787	-1.289000	0.02375	-1.608000	0.00805	ACG		0.627	PDGFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321043.1	NM_002608		A	39621756	G	A	39621756	3	1	84	1	0	0	0	0	1	0	0	0	11689	1145	40	1	31	1	PDGFB	22	39621756	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	210008	39621756	11682810	187	23879										
WWC3	55841	hgsc.bcm.edu	37	chrX	10106966	10106966	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	ccgtggcctgctgcgggaggCcgagcggcaggtgggggtcc	21	12	0	0			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chrX:10106966C>A	ENST00000380861.4	+	21	3465	c.3074C>A	c.(3073-3075)gCc>gAc	p.A1025D	WWC3_ENST00000454666.1_Missense_Mutation_p.A1025D	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	1025					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CTGCGGGAGGCCGAGCGGCAG	0.716																																																0			X											10	10	10					X																	10106966		2147	4169	6316	10066966	SO:0001583	missense	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.3074C>A	X.37:g.10106966C>A	ENSP00000370242:p.Ala1025Asp		10066966	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379977	0.82682	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.49432	0.78;0.78	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.71492	0.3346	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75207	-0.3399	9	.	.	.	-20.0608	17.361	0.87350	0.0:1.0:0.0:0.0	.	1025	Q9ULE0	WWC3_HUMAN	D	1025;1025;520	ENSP00000370242:A1025D;ENSP00000399584:A1025D	.	A	+	2	0	WWC3	10066966	1.000000	0.71417	0.918000	0.36340	0.541000	0.35023	5.562000	0.67346	2.370000	0.80446	0.529000	0.55759	GCC		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10106966	C	A	10106966	3	1	84	1	0	0	0	0	1	0	0	0	17453	739	26	2	3152	2	WWC3	23	10106966	Missense_Mutation	SNP	C	TCGA-AH-6643-01A-11D-1826-10		10106966	145163594	188	23880										
PHEX	5251	hgsc.bcm.edu	37	chrX	22108571	22108571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	accaagcaacactctccctgGccgtgagggaagactacctt	9	14	1	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chrX:22108571G>A	ENST00000379374.4	+	6	1253	c.688G>A	c.(688-690)Gcc>Acc	p.A230T	PHEX_ENST00000535894.1_Missense_Mutation_p.A133T|PHEX_ENST00000537599.1_Missense_Mutation_p.A230T	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	230					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						ACTCTCCCTGGCCGTGAGGGA	0.423																																																0			X											133	100	111					X																	22108571		2203	4300	6503	22018492	SO:0001583	missense	5251			U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.688G>A	X.37:g.22108571G>A	ENSP00000368682:p.Ala230Thr		22018492	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	37	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.298610	0.60195	.	.	ENSG00000102174	ENST00000379374;ENST00000537599;ENST00000535894	D;D;D	0.82167	-1.58;-1.58;-1.58	5.78	5.78	0.91487	Peptidase M13 (1);	0.165679	0.56097	D	0.000036	T	0.66046	0.2750	N	0.02011	-0.69	0.80722	D	1	B;B	0.27013	0.137;0.166	B;B	0.31946	0.058;0.138	T	0.69450	-0.5142	10	0.87932	D	0	.	13.2379	0.59979	0.0:0.0:0.6834:0.3166	.	230;230	F5GXU4;P78562	.;PHEX_HUMAN	T	230;230;133	ENSP00000368682:A230T;ENSP00000440362:A230T;ENSP00000439418:A133T	ENSP00000368682:A230T	A	+	1	0	PHEX	22018492	0.875000	0.30112	0.959000	0.39883	0.964000	0.63967	1.631000	0.37092	2.429000	0.82318	0.513000	0.50165	GCC		0.423	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		A	22108571	G	A	22108571	3	1	84	1	0	0	0	0	1	0	0	0	11850	1203	42	3	710	3	PHEX	23	22108571	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	12001605	22108571	133161989	189	23881										
OTC	5009	hgsc.bcm.edu	37	chrX	38211975	38211975	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	gtttaatctgaggatcctgtTaaacaatgcagcttttagaa	8	6	1	2	rs72552297		TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chrX:38211975T>A	ENST00000039007.4	+	1	178	c.26T>A	c.(25-27)tTa>tAa	p.L9*	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	9					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	AGGATCCTGTTAAACAATGCA	0.418																																																0			X	GRCh37	CM065362	OTC	M							154	126	136					X																	38211975		2202	4300	6502	38096919	SO:0001587	stop_gained	5009			K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.26T>A	X.37:g.38211975T>A	ENSP00000039007:p.Leu9*		38096919	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Nonsense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	T	37	6.390867	0.97529	.	.	ENSG00000036473	ENST00000039007	.	.	.	5.77	5.77	0.91146	.	0.570391	0.17778	N	0.162330	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.6709	11.3138	0.49379	0.0:0.0:0.0:1.0	.	.	.	.	X	9	.	ENSP00000039007:L9X	L	+	2	0	OTC	38096919	0.998000	0.40836	0.940000	0.37924	0.644000	0.38419	4.046000	0.57376	1.944000	0.56390	0.486000	0.48141	TTA		0.418	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			A	38211975	T	A	38211975	4	1	84	1	0	0	0	0	0	1	0	0	11332	1764	61	5	28	5	OTC	23	38211975	Nonsense_Mutation	SNP	T	TCGA-AH-6643-01A-11D-1826-10	16103404	38211975	117058585	190	23882										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128614769	128614769	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157068062827225	3	1	0.237686964140434	0	0.265112383079715	0.205882352941176	0.66867542651632	0	attgaaaatcctgaacatttGgctgttttggaggccgtgga	12	6	0	2			TCGA-AH-6643-01A-11D-1826-10	TCGA-AH-6643-11A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0dda2877-007f-4ced-b4a8-d1cf5ecbb4f3	2627ba9d-31da-4d64-a36f-1e2afa0645b5	g.chrX:128614769G>C	ENST00000371122.4	-	19	2480	c.2351C>G	c.(2350-2352)cCa>cGa	p.P784R	SMARCA1_ENST00000371123.1_Missense_Mutation_p.P772R|SMARCA1_ENST00000371121.3_Missense_Mutation_p.P772R	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	784					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						CTGAACATTTGGCTGTTTTGG	0.343																																																0			X											62	62	62					X																	128614769		2203	4300	6503	128442450	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.2351C>G	X.37:g.128614769G>C	ENSP00000360163:p.Pro784Arg		128442450	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.392400	0.62066	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.84	5.15	5.15	0.70609	ATPase, nucleosome remodelling ISWI, HAND domain (2);	0.000000	0.64402	D	0.000010	D	0.96253	0.8778	M	0.92122	3.275	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.992;0.996	D	0.95707	0.8754	10	0.25751	T	0.34	-7.3753	17.7545	0.88445	0.0:0.0:1.0:0.0	.	763;784;772;784	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	R	772;772;784;763	ENSP00000360162:P772R;ENSP00000360164:P772R;ENSP00000360163:P784R;ENSP00000404275:P763R	ENSP00000360162:P772R	P	-	2	0	SMARCA1	128442450	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.804000	0.99143	2.123000	0.65237	0.468000	0.43344	CCA		0.343	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		C	128614769	G	C	128614769	3	2	84	1	0	0	0	0	1	0	0	0	14805	1348	47	5	837	5	SMARCA1	23	128614769	Missense_Mutation	SNP	G	TCGA-AH-6643-01A-11D-1826-10	90402794	128614769	26655791	191	23883										
CHD5	26038	hgsc.bcm.edu	37	chr1	6228223	6228223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccctcacctctttcttcttcCgcttccctttacacttgttt	2	17	4	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:6228223C>T	ENST00000262450.3	-	2	293	c.194G>A	c.(193-195)cGg>cAg	p.R65Q	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0	Interaction with ASNA1/TRC40.				tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TTTCTTCTTCCGCTTCCCTTT	0.592																																																0			1											150	147	148					1																	6228223		2203	4300	6503	6150810	SO:0001583	missense	450091			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.194G>A	1.37:g.6228223C>T	ENSP00000262450:p.Arg65Gln		6150810	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.643548	0.67244	.	.	ENSG00000116254	ENST00000262450	D	0.91577	-2.87	4.9	4.9	0.64082	.	0.167775	0.23393	U	0.048675	D	0.88727	0.6515	L	0.50333	1.59	0.80722	D	1	D	0.57571	0.98	B	0.44108	0.441	D	0.89741	0.3933	10	0.56958	D	0.05	-23.9777	14.7953	0.69873	0.0:1.0:0.0:0.0	.	65	Q8TDI0	CHD5_HUMAN	Q	65	ENSP00000262450:R65Q	ENSP00000262450:R65Q	R	-	2	0	CHD5	6150810	0.999000	0.42202	0.985000	0.45067	0.910000	0.53928	4.172000	0.58243	2.245000	0.73994	0.313000	0.20887	CGG		0.592	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6228223	C	T	6228223	3	4	85	1	0	0	0	0	1	0	0	0	3334	652	23	1	5830	1	CHD5	1	6228223	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		6228223	243022398	1	23884										
SLC2A7	155184	hgsc.bcm.edu	37	chr1	9078345	9078345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	taggaagactccaacgatgaCgaaaacctcggtcattgttc	9	10	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:9078345C>T	ENST00000400906.1	-	5	525	c.526G>A	c.(526-528)Gtc>Atc	p.V176I		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	176					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CCAACGATGACGAAAACCTCG	0.592																																																0			1											110	94	100					1																	9078345		2203	4300	6503	9000932	SO:0001583	missense	155184			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.526G>A	1.37:g.9078345C>T	ENSP00000383698:p.Val176Ile		9000932	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	.	.	.	.	.	.	.	.	.	.	C	0.855	-0.737190	0.03111	.	.	ENSG00000197241	ENST00000400906	T	0.71698	-0.59	4.51	1.64	0.23874	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.065540	0.56097	D	0.000021	T	0.33614	0.0869	N	0.01529	-0.815	0.27879	N	0.93975	B	0.23937	0.094	B	0.25759	0.063	T	0.41395	-0.9511	10	0.02654	T	1	.	6.7754	0.23617	0.0:0.5088:0.0:0.4912	.	176	Q6PXP3	GTR7_HUMAN	I	176	ENSP00000383698:V176I	ENSP00000383698:V176I	V	-	1	0	SLC2A7	9000932	0.991000	0.36638	0.022000	0.16811	0.573000	0.36030	1.766000	0.38491	0.173000	0.19788	0.561000	0.74099	GTC		0.592	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		T	9078345	C	T	9078345	3	4	85	1	0	0	0	0	1	0	0	0	14587	536	19	1	1044	1	SLC2A7	1	9078345	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	2850122	9078345	240172276	2	23885										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45475346	45475346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gtctgtcaggcaggacacgtTgaactcctcctggggagggg	16	10	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:45475346T>C	ENST00000372172.4	-	5	840	c.769A>G	c.(769-771)Aac>Gac	p.N257D	UROD_ENST00000246337.4_5'Flank|HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	257	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CAGGACACGTTGAACTCCTCC	0.582																																																0			1											59	58	59					1																	45475346		2119	4215	6334	45247933	SO:0001583	missense	79654			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.769A>G	1.37:g.45475346T>C	ENSP00000361245:p.Asn257Asp		45247933	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	37	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.970021	0.34754	.	.	ENSG00000126107	ENST00000372172	T	0.71579	-0.58	4.9	4.9	0.64082	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	1.365760	0.04597	N	0.397844	T	0.58004	0.2092	N	0.08118	0	0.80722	D	1	B	0.28820	0.224	B	0.28553	0.091	T	0.10245	-1.0638	10	0.35671	T	0.21	.	14.8076	0.69968	0.0:0.0:0.0:1.0	.	257	Q5T447	HECD3_HUMAN	D	257	ENSP00000361245:N257D	ENSP00000361245:N257D	N	-	1	0	HECTD3	45247933	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	4.781000	0.62389	1.965000	0.57142	0.460000	0.39030	AAC		0.582	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		C	45475346	T	C	45475346	3	2	85	1	0	0	0	0	1	0	0	0	7062	1812	63	4	1884	4	HECTD3	1	45475346	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	36397001	45475346	203775275	3	23886										
ZRANB2	9406	hgsc.bcm.edu	37	chr1	71536630	71536630	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tattactatcttcttcttcaCtggcatcaagattatatttt	3	8	5	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:71536630C>G	ENST00000370920.3	-	7	864	c.563G>C	c.(562-564)aGt>aCt	p.S188T	ZRANB2_ENST00000254821.6_Missense_Mutation_p.S188T	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	188	Required for nuclear targeting.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						TTCTTCTTCACTGGCATCAAG	0.358																																																0			1											141	141	141					1																	71536630		2203	4300	6503	71309218	SO:0001583	missense	9406			AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"Zinc fingers, RAN-binding domain containing"	13058	protein-coding gene	gene with protein product		604347	"zinc finger protein 265"	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.563G>C	1.37:g.71536630C>G	ENSP00000359958:p.Ser188Thr		71309218	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Missense_Mutation	SNP	ENST00000370920.3	37	CCDS659.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.642269	0.47153	.	.	ENSG00000132485	ENST00000370920;ENST00000254821	T;T	0.65549	-0.14;-0.16	6.06	6.06	0.98353	.	0.126820	0.85682	D	0.000000	T	0.40546	0.1121	N	0.24115	0.695	0.53005	D	0.99996	B;P	0.35612	0.378;0.512	B;B	0.35353	0.099;0.201	T	0.33650	-0.9860	10	0.31617	T	0.26	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	188;188	O95218;O95218-2	ZRAB2_HUMAN;.	T	188	ENSP00000359958:S188T;ENSP00000254821:S188T	ENSP00000254821:S188T	S	-	2	0	ZRANB2	71309218	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.880000	0.98712	0.650000	0.86243	AGT		0.358	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350		G	71536630	C	G	71536630	3	3	85	1	0	0	0	0	1	0	0	0	18262	565	20	5	483	5	ZRANB2	1	71536630	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	26061284	71536630	177713991	4	23887										
MSH4	4438	hgsc.bcm.edu	37	chr1	76355053	76355053	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atttatgaaagaaatgaaagAggtacccaaacaaaactttt	6	5	0	4			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:76355053A>G	ENST00000263187.3	+	16	2329	c.2225A>G	c.(2224-2226)gAg>gGg	p.E742G		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	742					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GAAATGAAAGAGGTACCCAAA	0.259								Mismatch excision repair (MMR)																																								0			1											49	57	54					1																	76355053		2188	4252	6440	76127641	SO:0001630	splice_region_variant	4438			U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.2226+1A>G	1.37:g.76355053A>G			76127641	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.481979	0.84747	.	.	ENSG00000057468	ENST00000263187	D	0.90788	-2.73	5.31	5.31	0.75309	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96839	0.8968	H	0.98314	4.2	0.58432	D	0.999999	D	0.56746	0.977	D	0.64687	0.928	D	0.98358	1.0547	10	0.87932	D	0	-23.0364	15.2688	0.73683	1.0:0.0:0.0:0.0	.	742	O15457	MSH4_HUMAN	G	742	ENSP00000263187:E742G	ENSP00000263187:E742G	E	+	2	0	MSH4	76127641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.958000	0.93099	2.019000	0.59389	0.528000	0.53228	GAG		0.259	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	Missense_Mutation	G	76355053	A	G	76355053	5	3	85	1	0	0	0	0	0	0	1	0	9902	318	11	4	2287	4	MSH4	1	76355053	Splice_Site	SNP	A	TCGA-AH-6644-01A-21D-1826-10	4818423	76355053	172895568	5	23888										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79383653	79383653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cacccacaacaatgagatagAgatgtatgccttcaatgcac	7	11	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:79383653A>G	ENST00000370742.3	-	11	1607	c.1544T>C	c.(1543-1545)cTc>cCc	p.L515P		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	515					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.L515P(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AATGAGATAGAGATGTATGCC	0.393																																																1	Substitution - Missense(1)	ovary(1)	1											144	135	138					1																	79383653		1878	4110	5988	79156241	SO:0001583	missense	64123			AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1544T>C	1.37:g.79383653A>G	ENSP00000359778:p.Leu515Pro		79156241	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.329922	0.81690	.	.	ENSG00000162618	ENST00000370742	T	0.60171	0.21	6.08	6.08	0.98989	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.79173	0.4401	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84435	0.0579	9	.	.	.	.	16.6512	0.85203	1.0:0.0:0.0:0.0	.	515	Q9HBW9	ELTD1_HUMAN	P	515	ENSP00000359778:L515P	.	L	-	2	0	ELTD1	79156241	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.339000	0.96797	2.333000	0.79357	0.482000	0.46254	CTC		0.393	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		G	79383653	A	G	79383653	3	3	85	1	0	0	0	0	1	0	0	0	5097	304	11	4	548	4	ELTD1	1	79383653	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	3028600	79383653	169866968	6	23889										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155450113	155450113	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agaaaacactttagaagcagGgatttttaaagtccttttag	8	5	0	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:155450113G>C	ENST00000368346.3	-	3	3187	c.2548C>G	c.(2548-2550)Cct>Gct	p.P850A	ASH1L_ENST00000392403.3_Missense_Mutation_p.P850A			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	850					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTAGAAGCAGGGATTTTTAAA	0.398																																																0			1											99	108	105					1																	155450113		2202	4300	6502	153716737	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2548C>G	1.37:g.155450113G>C	ENSP00000357330:p.Pro850Ala		153716737	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	G	12.28	1.889539	0.33348	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88975	-2.45;-2.45	5.31	5.31	0.75309	.	0.217765	0.41001	D	0.000963	T	0.66147	0.2760	N	0.03608	-0.345	0.80722	D	1	B;B	0.24576	0.064;0.106	B;B	0.22880	0.019;0.042	T	0.69053	-0.5247	10	0.54805	T	0.06	.	12.1502	0.54046	0.0784:0.0:0.9216:0.0	.	850;850	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	A	850	ENSP00000357330:P850A;ENSP00000376204:P850A	ENSP00000357330:P850A	P	-	1	0	ASH1L	153716737	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.767000	0.55288	2.768000	0.95171	0.650000	0.86243	CCT		0.398	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155450113	G	C	155450113	3	2	85	1	0	0	0	0	1	0	0	0	1042	1232	43	5	6450	5	ASH1L	1	155450113	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	76066460	155450113	93800508	7	23890										
MSTO1	55154	hgsc.bcm.edu	37	chr1	155582325	155582325	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gggagcctgggcctgcgaccCgagccacctgtcagcttccc	13	17	1	0	rs140753725		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:155582325C>T	ENST00000245564.2	+	9	954	c.930C>T	c.(928-930)ccC>ccT	p.P310P	MSTO1_ENST00000368341.4_Silent_p.P275P|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|RP11-29H23.4_ENST00000456382.2_RNA|MSTO1_ENST00000483734.1_3'UTR	NM_001256532.1|NM_001256533.1|NM_018116.3	NP_001243461.1|NP_001243462.1|NP_060586.2	Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	310					mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					GCCTGCGACCCGAGCCACCTG	0.562																																																0			1						C		0,4406		0,0,2203	76	71	73		930	-6.5	0	1	dbSNP_134	73	1,8599		0,1,4299	no	coding-synonymous	MSTO1	NM_018116.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		310/571	155582325	1,13005	2203	4300	6503	153848949	SO:0001819	synonymous_variant	55154			BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459			29678	protein-coding gene	gene with protein product			"misato homolog 1 (Drosophila)"			16545939, 17349998	Standard	NM_018116		Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000245564.2:c.930C>T	1.37:g.155582325C>T			153848949	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	Silent	SNP	ENST00000245564.2	37	CCDS1114.1																																																																																				0.562	MSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039408.1	NM_018116		T	155582325	C	T	155582325	2	4	85	1	0	0	0	0	0	0	0	1	9924	639	23	1		1	MSTO1	1	155582325	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	132212	155582325	93668296	8	23891			1	13		2	2	15	N	G_C	6.376445e-05
MSTO1	55154	hgsc.bcm.edu	37	chr1	155582339	155582339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcgacccgagccacctgtcaGcttcccttacctgcattatg	8	16	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:155582339G>A	ENST00000245564.2	+	9	968	c.944G>A	c.(943-945)aGc>aAc	p.S315N	MSTO1_ENST00000368341.4_Missense_Mutation_p.S280N|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|RP11-29H23.4_ENST00000456382.2_RNA|MSTO1_ENST00000483734.1_3'UTR	NM_001256532.1|NM_001256533.1|NM_018116.3	NP_001243461.1|NP_001243462.1|NP_060586.2	Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	315					mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					CCACCTGTCAGCTTCCCTTAC	0.582																																																0			1											75	70	72					1																	155582339		2203	4300	6503	153848963	SO:0001583	missense	55154			BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459			29678	protein-coding gene	gene with protein product			"misato homolog 1 (Drosophila)"			16545939, 17349998	Standard	NM_018116		Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000245564.2:c.944G>A	1.37:g.155582339G>A	ENSP00000245564:p.Ser315Asn		153848963	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	Missense_Mutation	SNP	ENST00000245564.2	37	CCDS1114.1	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.807686	0.00606	.	.	ENSG00000125459	ENST00000245564;ENST00000368341	T;T	0.44881	0.91;0.91	3.44	-6.87	0.01671	Tubulin/FtsZ, GTPase domain (2);	1.094980	0.07025	N	0.827382	T	0.06005	0.0156	N	0.12182	0.205	0.09310	N	0.999999	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0;0.001;0.001	B;B;B;B;B;B;B	0.06405	0.001;0.0;0.002;0.0;0.0;0.002;0.001	T	0.27020	-1.0086	10	0.13470	T	0.59	.	11.1676	0.48552	0.2022:0.5097:0.288:0.0	.	260;315;280;137;315;315;315	B4DLS9;A8K3J5;Q9BUK6-7;Q9BUK6-5;Q9BUK6;Q9BUK6-2;Q9BUK6-3	.;.;.;.;MSTO1_HUMAN;.;.	N	315;280	ENSP00000245564:S315N;ENSP00000357325:S280N	ENSP00000245564:S315N	S	+	2	0	MSTO1	153848963	0.000000	0.05858	0.001000	0.08648	0.168000	0.22595	-0.492000	0.06467	-3.214000	0.00213	-0.684000	0.03749	AGC		0.582	MSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039408.1	NM_018116		A	155582339	G	A	155582339	3	1	85	1	0	0	0	0	1	0	0	0	9924	971	34	3	978	3	MSTO1	1	155582339	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	14	155582339	93668282	9	23892			1	13		2	2	15	N	G_C	6.376445e-05
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179886702	179886702	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttctttagtactcctgaggtAgaaaccactgctgttcaaga	8	9	2	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:179886702A>G	ENST00000606911.2	+	10	1271	c.1080A>G	c.(1078-1080)gtA>gtG	p.V360V	TOR1AIP1_ENST00000528443.2_Silent_p.V361V|TOR1AIP1_ENST00000271583.3_Silent_p.V376V|TOR1AIP1_ENST00000474875.1_3'UTR|TOR1AIP1_ENST00000435319.4_Silent_p.V239V			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	360	Interaction with TOR1A.				positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						CTCCTGAGGTAGAAACCACTG	0.448																																																0			1											106	112	110					1																	179886702		2203	4300	6503	178153325	SO:0001819	synonymous_variant	26092				CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"lamina associated polypeptide 1B"	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1080A>G	1.37:g.179886702A>G			178153325	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Silent	SNP	ENST00000606911.2	37	CCDS1335.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.703622	0.30232	.	.	ENSG00000143337	ENST00000447964	.	.	.	5.87	-3.88	0.04205	.	.	.	.	.	.	.	.	.	.	.	0.21147	N	0.999772	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.9205	4.0535	0.09806	0.3966:0.1083:0.3899:0.1052	.	.	.	.	W	95	.	.	X	+	2	0	TOR1AIP1	178153325	0.000000	0.05858	0.000000	0.03702	0.743000	0.42351	-0.300000	0.08243	-1.045000	0.03250	-0.256000	0.11100	TAG		0.448	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		G	179886702	A	G	179886702	2	3	85	1	0	0	0	0	0	0	0	1	16412	407	15	4		4	TOR1AIP1	1	179886702	Silent	SNP	A	TCGA-AH-6644-01A-21D-1826-10	24304363	179886702	69363919	10	23893										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183099546	183099546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctgtccagccaaattagccgTttacagaatatccggaatac	7	11	0	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:183099546T>C	ENST00000258341.4	+	19	3605	c.3348T>C	c.(3346-3348)cgT>cgC	p.R1116R		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1116	Domain II and I.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AAATTAGCCGTTTACAGAATA	0.428																																																0			1											91	86	87					1																	183099546		2203	4300	6503	181366169	SO:0001819	synonymous_variant	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.3348T>C	1.37:g.183099546T>C			181366169	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																				0.428	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		C	183099546	T	C	183099546	2	2	85	1	0	0	0	0	0	0	0	1	8636	1712	60	4		4	LAMC1	1	183099546	Silent	SNP	T	TCGA-AH-6644-01A-21D-1826-10	3212844	183099546	66151075	11	23894										
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185269215	185269215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cagtcctttttgaccatatgGatcagagccaccaacgatgt	8	11	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:185269215G>A	ENST00000367498.3	-	13	2039	c.1417C>T	c.(1417-1419)Cca>Tca	p.P473S	IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.P255S|IVNS1ABP_ENST00000459929.1_5'UTR	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	473					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						TGACCATATGGATCAGAGCCA	0.318																																																0			1											112	105	107					1																	185269215		2203	4300	6503	183535838	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1417C>T	1.37:g.185269215G>A	ENSP00000356468:p.Pro473Ser		183535838	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173592	0.57584	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.76186	-0.11;-1.0	5.61	5.61	0.85477	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.63046	0.2478	N	0.05078	-0.115	0.80722	D	1	B;P;P	0.34955	0.005;0.477;0.477	B;B;B	0.40444	0.008;0.329;0.329	T	0.64495	-0.6394	10	0.38643	T	0.18	.	20.0018	0.97417	0.0:0.0:1.0:0.0	.	255;174;473	A8MVR0;Q6MZF3;Q9Y6Y0	.;.;NS1BP_HUMAN	S	473;255	ENSP00000356468:P473S;ENSP00000375864:P255S	ENSP00000356468:P473S	P	-	1	0	IVNS1ABP	183535838	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	9.388000	0.97237	2.793000	0.96121	0.655000	0.94253	CCA		0.318	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		A	185269215	G	A	185269215	3	1	85	1	0	0	0	0	1	0	0	0	7951	1174	41	3	523	3	IVNS1ABP	1	185269215	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	2169669	185269215	63981406	12	23895										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226822488	226822488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggggacgtcatgctgcagggTctggccctcaggcaggggcg	19	11	3	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr1:226822488T>C	ENST00000272117.3	-	7	2724	c.2725A>G	c.(2725-2727)Acc>Gcc	p.T909A	ITPKB_ENST00000429204.1_Missense_Mutation_p.T909A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	909					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TGCTGCAGGGTCTGGCCCTCA	0.597																																					Colon(84;110 1851 5306 33547)											0			1											89	72	78					1																	226822488		2203	4300	6503	224889111	SO:0001583	missense	3707			AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.2725A>G	1.37:g.226822488T>C	ENSP00000272117:p.Thr909Ala		224889111	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.340448	0.60963	.	.	ENSG00000143772	ENST00000272117;ENST00000429204	T;T	0.13778	2.56;2.56	5.05	5.05	0.67936	.	0.185344	0.48767	D	0.000173	T	0.19967	0.0480	M	0.87547	2.89	0.28034	N	0.934017	B	0.34255	0.445	B	0.35727	0.209	T	0.26430	-1.0103	10	0.38643	T	0.18	-30.7112	5.485	0.16745	0.0:0.226:0.0:0.774	.	909	P27987	IP3KB_HUMAN	A	909	ENSP00000272117:T909A;ENSP00000411152:T909A	ENSP00000272117:T909A	T	-	1	0	ITPKB	224889111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.026000	0.41069	1.911000	0.55334	0.454000	0.30748	ACC		0.597	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		C	226822488	T	C	226822488	3	2	85	1	0	0	0	0	1	0	0	0	7939	1667	58	4	119	4	ITPKB	1	226822488	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	41553273	226822488	22428133	13	23896										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70081986	70081986	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atggcctttcttgaaactgaAcaaggaaaaccatttgtgtc	8	8	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:70081986A>G	ENST00000282570.3	+	9	1217	c.966A>G	c.(964-966)gaA>gaG	p.E322E		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	322					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						TTGAAACTGAACAAGGAAAAC	0.318																																																0			2											76	79	78					2																	70081986		2203	4293	6496	69935490	SO:0001819	synonymous_variant	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.966A>G	2.37:g.70081986A>G			69935490	Q9H826|Q9H8V7|Q9H927	Silent	SNP	ENST00000282570.3	37	CCDS1895.1																																																																																				0.318	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70081986	A	G	70081986	2	3	85	1	0	0	0	0	0	0	0	1	6505	40	2	4		4	GMCL1	2	70081986	Silent	SNP	A	TCGA-AH-6644-01A-21D-1826-10		70081986	173117387	14	23897										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71627287	71627287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgaagtcaaagccactgaaaActgtgctaaagaagctattt	8	7	1	3	rs571966370		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:71627287A>G	ENST00000409544.1	+	14	3263	c.2633A>G	c.(2632-2634)aAc>aGc	p.N878S	ZNF638_ENST00000264447.4_Missense_Mutation_p.N878S|ZNF638_ENST00000355812.3_Missense_Mutation_p.N878S	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	878					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GCCACTGAAAACTGTGCTAAA	0.284																																																0			2											103	112	109					2																	71627287		2203	4299	6502	71480795	SO:0001583	missense	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2633A>G	2.37:g.71627287A>G	ENSP00000386433:p.Asn878Ser		71480795	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	A	4.124	0.021314	0.08006	.	.	ENSG00000075292	ENST00000394137;ENST00000355812;ENST00000264447;ENST00000409544	T;T;T	0.56103	0.48;1.53;1.53	4.65	2.21	0.28008	.	0.548591	0.17945	N	0.156710	T	0.29288	0.0729	N	0.24115	0.695	0.09310	N	0.999999	P;P;P;P	0.41313	0.622;0.739;0.739;0.745	B;B;B;B	0.36464	0.112;0.164;0.225;0.192	T	0.10917	-1.0609	10	0.11794	T	0.64	-3.9397	6.3078	0.21149	0.7939:0.0:0.2061:0.0	.	878;878;878;878	A8K583;Q14966-4;Q14966-3;Q14966	.;.;.;ZN638_HUMAN	S	457;878;878;878	ENSP00000348066:N878S;ENSP00000264447:N878S;ENSP00000386433:N878S	ENSP00000264447:N878S	N	+	2	0	ZNF638	71480795	0.942000	0.31987	0.166000	0.22797	0.079000	0.17450	1.830000	0.39131	0.822000	0.34565	0.460000	0.39030	AAC		0.284	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71627287	A	G	71627287	3	3	85	1	0	0	0	0	1	0	0	0	18094	43	2	4	2683	4	ZNF638	2	71627287	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	1545301	71627287	171572086	15	23898										
DPP10	57628	hgsc.bcm.edu	37	chr2	116447456	116447456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctccagaagtagaggactccGtcttgcagtacgcggcctgg	13	12	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:116447456G>A	ENST00000410059.1	+	7	1015	c.535G>A	c.(535-537)Gtc>Atc	p.V179I	DPP10_ENST00000393147.2_Missense_Mutation_p.V183I|DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000310323.8_Missense_Mutation_p.V172I|DPP10_ENST00000409163.1_Missense_Mutation_p.V129I	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	179						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGAGGACTCCGTCTTGCAGTA	0.438																																																0			2											84	91	89					2																	116447456		2203	4300	6503	116163926	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.535G>A	2.37:g.116447456G>A	ENSP00000386565:p.Val179Ile		116163926	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.164856	0.38217	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.44	-2.02	0.07388	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.225321	0.36778	N	0.002414	T	0.22859	0.0552	L	0.55481	1.735	0.24648	N	0.993537	B;B;B;B	0.22800	0.027;0.075;0.034;0.034	B;B;B;B	0.20955	0.013;0.018;0.032;0.022	T	0.33650	-0.9860	10	0.15499	T	0.54	-12.1613	11.1686	0.48558	0.491:0.0:0.509:0.0	.	172;183;175;179	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	I	179;129;175;183;172;129	ENSP00000386565:V179I;ENSP00000387038:V129I;ENSP00000376854:V175I;ENSP00000376855:V183I;ENSP00000309066:V172I	ENSP00000309066:V172I	V	+	1	0	DPP10	116163926	0.323000	0.24643	0.908000	0.35775	0.965000	0.64279	0.668000	0.25127	-0.308000	0.08792	-0.237000	0.12165	GTC		0.438	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116447456	G	A	116447456	3	1	85	1	0	0	0	0	1	0	0	0	4738	1145	40	1	732	1	DPP10	2	116447456	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	44820169	116447456	126751917	16	23899										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540046	133540046	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tctggatgccttccagaagtTtctagcttggatgtactgct	10	9	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:133540046T>C	ENST00000409261.1	-	14	4711	c.4338A>G	c.(4336-4338)gaA>gaG	p.E1446E	NCKAP5_ENST00000317721.6_Silent_p.E1446E|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1446										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TTCCAGAAGTTTCTAGCTTGG	0.542																																																0			2											49	48	48					2																	133540046		1929	4126	6055	133256516	SO:0001819	synonymous_variant	0			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4338A>G	2.37:g.133540046T>C			133256516	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				0.542	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133540046	T	C	133540046	2	2	85	1	0	0	0	0	0	0	0	1	10254	1838	64	4		4	NCKAP5	2	133540046	Silent	SNP	T	TCGA-AH-6644-01A-21D-1826-10	17092590	133540046	109659327	17	23900										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141460038	141460038	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttcggccatgctattcccatGcttacaaggacaaccttctc	6	14	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:141460038G>A	ENST00000389484.3	-	38	7079	c.6108C>T	c.(6106-6108)agC>agT	p.S2036S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2036					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S2036R(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CTATTCCCATGCTTACAAGGA	0.423										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											1	Substitution - Missense(1)	ovary(1)	2											116	107	110					2																	141460038		2203	4300	6503	141176508	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6108C>T	2.37:g.141460038G>A			141176508	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.423	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141460038	G	A	141460038	2	1	85	1	0	0	0	0	0	0	0	1	8984	1310	46	3		3	LRP1B	2	141460038	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	7919992	141460038	101739335	18	23901										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141607702	141607702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	acagtttctaacccagttccGttaataaaagctcgtttaat	5	9	1	0	rs368565366		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:141607702G>A	ENST00000389484.3	-	29	5879	c.4908C>T	c.(4906-4908)aaC>aaT	p.N1636N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1636					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ACCCAGTTCCGTTAATAAAAG	0.318										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2						A		1,4405	4.2+/-10.8	0,1,2202	162	169	167		4908	0.2	1	2		167	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1636/4600	141607702	1,13005	2203	4300	6503	141324172	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4908C>T	2.37:g.141607702G>A			141324172	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.318	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141607702	G	A	141607702	2	1	85	1	0	0	0	0	0	0	0	1	8984	1136	40	1		1	LRP1B	2	141607702	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	147664	141607702	101591671	19	23902										
RIF1	55183	hgsc.bcm.edu	37	chr2	152293375	152293375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tacggagccccgggaactccCcgaatgaacctgagttcgaa	11	13	0	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:152293375C>T	ENST00000433166.2	+	10	1069	c.1019C>T	c.(1018-1020)cCc>cTc	p.P340L	RIF1_ENST00000243326.5_Silent_p.P410P|RIF1_ENST00000428287.2_Silent_p.P410P|RIF1_ENST00000453091.2_Silent_p.P410P|RIF1_ENST00000430328.2_Silent_p.P410P|RIF1_ENST00000444746.2_Silent_p.P410P			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		CGGGAACTCCCCGAATGAACC	0.423																																																0			2											54	52	53					2																	152293375		2203	4300	6503	152001621	SO:0001583	missense	55791			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000433166.2:c.1019C>T	2.37:g.152293375C>T	ENSP00000396865:p.Pro340Leu		152001621	A0AVS0|Q9NS16	Silent	SNP	ENST00000433166.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.06|18.06	3.538669|3.538669	0.65085|0.65085	.|.	.|.	ENSG00000080345|ENSG00000080345	ENST00000433166|ENST00000414861	.|T	.|0.52526	.|0.66	5.4|5.4	-3.64|-3.64	0.04515|0.04515	.|.	0.214262|0.214262	0.49916|0.49916	D|D	0.000134|0.000134	T|T	0.36386|0.36386	0.0965|0.0965	.|.	.|.	.|.	0.24701|0.24701	N|N	0.993251|0.993251	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.32508|0.32508	-0.9904|-0.9904	6|7	0.87932|0.44086	D|T	0|0.13	-1.6492|-1.6492	5.7012|5.7012	0.17883|0.17883	0.3554:0.2584:0.0:0.3862|0.3554:0.2584:0.0:0.3862	.|.	.|.	.|.	.|.	L|S	340|402	.|ENSP00000390486:P402S	ENSP00000396865:P340L|ENSP00000390486:P402S	P|P	+|+	2|1	0|0	RIF1|RIF1	152001621|152001621	0.002000|0.002000	0.14202|0.14202	0.040000|0.040000	0.18447|0.18447	0.678000|0.678000	0.39670|0.39670	-1.480000|-1.480000	0.02325|0.02325	-0.356000|-0.356000	0.08187|0.08187	0.557000|0.557000	0.71058|0.71058	CCC|CCG		0.423	RIF1-201	KNOWN	basic	protein_coding	protein_coding				T	152293375	C	T	152293375	3	4	85	1	0	0	0	0	1	0	0	0	13396	610	22	3	1272	3	RIF1	2	152293375	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	10685673	152293375	90905998	20	23903										
ITGB6	3694	hgsc.bcm.edu	37	chr2	160968619	160968619	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttgatgctgtgaatgatggtTttcccctcattatctgtagt	9	7	2	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:160968619T>A	ENST00000283249.2	-	13	2310	c.2073A>T	c.(2071-2073)aaA>aaT	p.K691N	ITGB6_ENST00000428609.2_Missense_Mutation_p.K649N|ITGB6_ENST00000409872.1_Missense_Mutation_p.K691N|ITGB6_ENST00000409967.2_Missense_Mutation_p.K584N	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	691					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						GAATGATGGTTTTCCCCTCAT	0.398																																																0			2											235	210	218					2																	160968619		2203	4300	6503	160676865	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.2073A>T	2.37:g.160968619T>A	ENSP00000283249:p.Lys691Asn		160676865	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520630	0.44866	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.90504	-2.68;-2.68;-1.72;-2.68	6.04	6.04	0.98038	Integrin beta subunit, tail (2);	0.308735	0.34628	N	0.003808	D	0.87775	0.6262	M	0.65975	2.015	0.31206	N	0.699196	B;B	0.22746	0.074;0.074	B;B	0.23018	0.043;0.043	T	0.82741	-0.0307	10	0.26408	T	0.33	.	8.504	0.33175	0.0:0.1463:0.0:0.8537	.	649;691	E9PEE8;P18564	.;ITB6_HUMAN	N	691;649;584;691	ENSP00000283249:K691N;ENSP00000408024:K649N;ENSP00000386828:K584N;ENSP00000386367:K691N	ENSP00000283249:K691N	K	-	3	2	ITGB6	160676865	0.996000	0.38824	1.000000	0.80357	0.898000	0.52572	1.476000	0.35420	2.317000	0.78254	0.460000	0.39030	AAA		0.398	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		A	160968619	T	A	160968619	3	1	85	1	0	0	0	0	1	0	0	0	7920	1838	64	5	305	5	ITGB6	2	160968619	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	8675244	160968619	82230754	21	23904										
IFIH1	64135	hgsc.bcm.edu	37	chr2	163137949	163137950	+	Frame_Shift_Del	DEL	GA	GA	-													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	actggtttgttttctttcttGagtctattgtttttcaactt							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:163137949_163137950delGA	ENST00000263642.2	-	7	1807_1808	c.1412_1413delTC	c.(1411-1413)ctcfs	p.L471fs		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	471	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TTTCTTTCTTGAGTCTATTGTT	0.416																																																0			2																																								162846196	SO:0001589	frameshift_variant	64135			AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1412_1413delTC	2.37:g.163137949_163137950delGA	ENSP00000263642:p.Leu471fs		162846195	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Frame_Shift_Del	DEL	ENST00000263642.2	37	CCDS2217.1																																																																																				0.416	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		-	163137950	GA	-	163137949	7	5	85	1	0	1	0	1	0	0	0	0	7541	1277	45	0	1704	0	IFIH1	2	163137949	Frame_Shift_Del	DEL	GA	TCGA-AH-6644-01A-21D-1826-10	2169330	163137949	80061424	22	23905										
TTN	7273	hgsc.bcm.edu	37	chr2	179637980	179637980	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tttagaactgggcttgatttCcttgtccttaaaattccaca	6	9	0	2	rs149660690	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr2:179637980C>A	ENST00000591111.1	-	33	7935	c.7711G>T	c.(7711-7713)Gaa>Taa	p.E2571*	TTN_ENST00000589042.1_Nonsense_Mutation_p.E2571*|TTN_ENST00000359218.5_Nonsense_Mutation_p.E2525*|TTN_ENST00000460472.2_Nonsense_Mutation_p.E2525*|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.E2525*|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.E2571*|TTN_ENST00000360870.5_Nonsense_Mutation_p.E2571*			Q8WZ42	TITIN_HUMAN	titin	12894					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGCTTGATTTCCTTGTCCTTA	0.353																																																0			2											43	45	44					2																	179637980		2203	4300	6503	179346225	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7711G>T	2.37:g.179637980C>A	ENSP00000465570:p.Glu2571*		179346225	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	48	14.884999	0.99814	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.7558	0.85498	0.0:0.8713:0.1287:0.0	.	.	.	.	X	2571;2525;2525;2525;2525;2571	.	ENSP00000340554:E2525X	E	-	1	0	TTN	179346225	0.999000	0.42202	0.999000	0.59377	0.487000	0.33371	4.291000	0.59025	2.685000	0.91497	0.650000	0.86243	GAA		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179637980	C	A	179637980	4	1	85	1	0	0	0	0	0	1	0	0	16775	864	30	2	103597	2	TTN	2	179637980	Nonsense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	16500031	179637980	63561393	23	23906										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15126516	15126516	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tttaaagttacctcgaatctTtgcagactcagtatttgttc	6	8	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:15126516T>A	ENST00000253699.3	-	7	1040	c.427A>T	c.(427-429)Aag>Tag	p.K143*	ZFYVE20_ENST00000476527.2_Nonsense_Mutation_p.K143*|ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000435849.3_Nonsense_Mutation_p.K143*	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	143	Necessary for the correct targeting to endosomes.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						CCTCGAATCTTTGCAGACTCA	0.378																																																0			3											93	88	90					3																	15126516		2203	4300	6503	15101520	SO:0001587	stop_gained	64145			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.427A>T	3.37:g.15126516T>A	ENSP00000253699:p.Lys143*		15101520	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Nonsense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	T	39	7.392050	0.98255	.	.	ENSG00000131381	ENST00000253699;ENST00000476527;ENST00000435849	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.6863	15.7182	0.77685	0.0:0.0:0.0:1.0	.	.	.	.	X	143	.	ENSP00000253699:K143X	K	-	1	0	ZFYVE20	15101520	1.000000	0.71417	0.920000	0.36463	0.079000	0.17450	5.994000	0.70623	2.112000	0.64535	0.528000	0.53228	AAG		0.378	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15126516	T	A	15126516	4	1	85	1	0	0	0	0	0	1	0	0	17705	1850	64	5	1959	5	ZFYVE20	3	15126516	Nonsense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10		15126516	182895914	24	23907										
SACM1L	22908	hgsc.bcm.edu	37	chr3	45751048	45751048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgtcttgaatgtggatggatTttacttttcaacaacatatg	8	5	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:45751048T>C	ENST00000389061.5	+	5	596	c.392T>C	c.(391-393)tTt>tCt	p.F131S	SACM1L_ENST00000464524.1_3'UTR|SACM1L_ENST00000541314.1_Missense_Mutation_p.F70S|SACM1L_ENST00000418611.1_Missense_Mutation_p.F28S	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	131	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GTGGATGGATTTTACTTTTCA	0.358																																																0			3											125	119	121					3																	45751048		2203	4300	6503	45726052	SO:0001583	missense	22908			AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.392T>C	3.37:g.45751048T>C	ENSP00000373713:p.Phe131Ser		45726052	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.027102	0.93518	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000438671;ENST00000541314	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	6.17	6.17	0.99709	Synaptojanin, N-terminal (2);	0.051139	0.85682	D	0.000000	D	0.84629	0.5514	H	0.94503	3.545	0.80722	D	1	P;D	0.65815	0.955;0.995	P;D	0.67103	0.854;0.949	D	0.88768	0.3262	10	0.87932	D	0	-12.3056	16.8222	0.85835	0.0:0.0:0.0:1.0	.	70;131	B4DK71;Q9NTJ5	.;SAC1_HUMAN	S	28;131;70;70	ENSP00000396387:F28S;ENSP00000373713:F131S;ENSP00000411966:F70S;ENSP00000443373:F70S	ENSP00000373713:F131S	F	+	2	0	SACM1L	45726052	1.000000	0.71417	0.990000	0.47175	0.999000	0.98932	7.685000	0.84117	2.371000	0.80710	0.533000	0.62120	TTT		0.358	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		C	45751048	T	C	45751048	3	2	85	1	0	0	0	0	1	0	0	0	13840	1841	64	4	410	4	SACM1L	3	45751048	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	30624532	45751048	152271382	25	23908										
LNP1	348801	hgsc.bcm.edu	37	chr3	100170693	100170693	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agaggatgggtcattcaaggAgccactggaatcaaaaggaa	13	6	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:100170693A>G	ENST00000383693.3	+	3	1567	c.287A>G	c.(286-288)gAg>gGg	p.E96G	LNP1_ENST00000489752.1_Missense_Mutation_p.E109G	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	96										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						TCATTCAAGGAGCCACTGGAA	0.453																																																0			3											106	99	101					3																	100170693		1847	4089	5936	101653383	SO:0001583	missense	348801				CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.287A>G	3.37:g.100170693A>G	ENSP00000373191:p.Glu96Gly		101653383	B7ZLT3	Missense_Mutation	SNP	ENST00000383693.3	37	CCDS43120.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826167	0.50739	.	.	ENSG00000206535	ENST00000383693;ENST00000489752	.	.	.	5.32	3.95	0.45737	.	0.297478	0.31010	N	0.008432	T	0.27798	0.0684	L	0.32530	0.975	0.09310	N	1	B	0.23735	0.09	B	0.26310	0.068	T	0.08126	-1.0737	9	0.33141	T	0.24	-12.2161	4.733	0.12974	0.7283:0.0:0.1008:0.1709	.	96	A1A4G5	LNP1_HUMAN	G	96;109	.	ENSP00000373191:E96G	E	+	2	0	LNP1	101653383	0.988000	0.35896	0.244000	0.24202	0.832000	0.47134	1.311000	0.33562	2.033000	0.60031	0.378000	0.23410	GAG		0.453	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1			G	100170693	A	G	100170693	3	3	85	1	0	0	0	0	1	0	0	0	8887	304	11	4	293	4	LNP1	3	100170693	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	54419645	100170693	97851737	26	23909										
HSPBAP1	79663	hgsc.bcm.edu	37	chr3	122459920	122459920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tcagggcacacacaagcataCgggtgattgcctcttctacc	9	13	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:122459920C>T	ENST00000306103.2	-	7	1009	c.866G>A	c.(865-867)cGt>cAt	p.R289H	HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	289						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		CACAAGCATACGGGTGATTGC	0.453																																																0			3											127	128	127					3																	122459920		2203	4300	6503	123942610	SO:0001583	missense	79663			AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"HSPB (heat shock 27kD) associated protein 1"			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.866G>A	3.37:g.122459920C>T	ENSP00000302562:p.Arg289His		123942610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.884285	0.72410	.	.	ENSG00000169087	ENST00000306103	T	0.11712	2.75	5.35	4.48	0.54585	Cupin, JmjC-type (1);	0.709852	0.13791	N	0.362502	T	0.30916	0.0780	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.01065	-1.1463	10	0.54805	T	0.06	.	11.6393	0.51222	0.0:0.9187:0.0:0.0813	.	289	Q96EW2	HBAP1_HUMAN	H	289	ENSP00000302562:R289H	ENSP00000302562:R289H	R	-	2	0	HSPBAP1	123942610	0.997000	0.39634	0.502000	0.27614	0.783000	0.44284	4.599000	0.61076	1.496000	0.48567	0.655000	0.94253	CGT		0.453	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610		T	122459920	C	T	122459920	3	4	85	1	0	0	0	0	1	0	0	0	7446	536	19	1	608	1	HSPBAP1	3	122459920	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	22289227	122459920	75562510	27	23910										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126723977	126723977	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cctgacctctcagctggcgtCaactgctccttcgaggactt	9	15	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:126723977C>T	ENST00000393409.2	+	6	1788	c.1788C>T	c.(1786-1788)gtC>gtT	p.V596V	PLXNA1_ENST00000251772.4_Silent_p.V573V	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	596					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CAGCTGGCGTCAACTGCTCCT	0.672																																																0			3											63	49	54					3																	126723977		2201	4299	6500	128206667	SO:0001819	synonymous_variant	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1788C>T	3.37:g.126723977C>T			128206667		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																				0.672	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126723977	C	T	126723977	2	4	85	1	0	0	0	0	0	0	0	1	12150	813	29	3		3	PLXNA1	3	126723977	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	4264057	126723977	71298453	28	23911										
FOXL2	668	hgsc.bcm.edu	37	chr3	138665165	138665165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cttctcgaacatgtcttcgcAggccgggtccagcgtccagt	11	14	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:138665165A>G	ENST00000330315.3	-	1	817	c.400T>C	c.(400-402)Tgc>Cgc	p.C134R	RP11-548O1.3_ENST00000495287.1_lincRNA|C3orf72_ENST00000383165.3_5'Flank	NM_023067.3	NP_075555.1	P58012	FOXL2_HUMAN	forkhead box L2	134			C -> W (in granulosa-cell tumors of the ovary; not commonly found in other tumor types). {ECO:0000269|PubMed:19516027, ECO:0000269|PubMed:19956657}.		apoptotic DNA fragmentation (GO:0006309)|cell differentiation (GO:0030154)|embryonic eye morphogenesis (GO:0048048)|extraocular skeletal muscle development (GO:0002074)|female somatic sex determination (GO:0019101)|granulosa cell differentiation (GO:0060014)|menstruation (GO:0042703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	cysteine-type endopeptidase regulator activity involved in apoptotic process (GO:0043028)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin conjugating enzyme binding (GO:0031624)			large_intestine(1)|lung(1)|ovary(333)|skin(1)	336						ATGTCTTCGCAGGCCGGGTCC	0.682			Mis		granulosa-cell tumour of the ovary		"Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"																																Dom	yes		3	3q23	668	forkhead box L2	yes	O	0			3											33	31	32					3																	138665165		2202	4298	6500	140147855	SO:0001583	missense	668			AF301906	CCDS3105.1	3q23	2008-04-10			ENSG00000183770	ENSG00000183770		"Forkhead boxes"	1092	protein-coding gene	gene with protein product		605597		BPES		1941972	Standard	NM_023067		Approved	BPES1	uc003esw.3	P58012	OTTHUMG00000159889	ENST00000330315.3:c.400T>C	3.37:g.138665165A>G	ENSP00000333188:p.Cys134Arg		140147855	Q4ZGJ3	Missense_Mutation	SNP	ENST00000330315.3	37	CCDS3105.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049655	0.75846	.	.	ENSG00000183770	ENST00000330315;ENST00000542203	D	0.95205	-3.64	3.76	3.76	0.43208	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	U	0.000000	D	0.95436	0.8518	L	0.55834	1.745	0.80722	D	1	D	0.58620	0.983	P	0.61874	0.895	D	0.95595	0.8658	10	0.87932	D	0	.	12.7528	0.57318	1.0:0.0:0.0:0.0	.	134	P58012	FOXL2_HUMAN	R	134	ENSP00000333188:C134R	ENSP00000333188:C134R	C	-	1	0	FOXL2	140147855	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.589000	0.67523	1.468000	0.48064	0.352000	0.21897	TGC		0.682	FOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357999.1			G	138665165	A	G	138665165	3	3	85	1	0	0	0	0	1	0	0	0	6036	188	7	4	734	4	FOXL2	3	138665165	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	11941188	138665165	59357265	29	23912										
CPB1	1360	hgsc.bcm.edu	37	chr3	148563303	148563303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aggccctggctgatttcatcCgcaacaaactctcttccatc	6	15	2	1	rs142211299		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:148563303C>T	ENST00000491148.1	+	10	1205	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	CPB1_ENST00000282957.4_Missense_Mutation_p.R291C			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	291						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R291C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGATTTCATCCGCAACAAACT	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	3						C	CYS/ARG	0,4406		0,0,2203	135	132	133		871	5.7	1	3	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	missense	CPB1	NM_001871.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	291/418	148563303	1,13005	2203	4300	6503	150045993	SO:0001583	missense	1360			AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.871C>T	3.37:g.148563303C>T	ENSP00000417222:p.Arg291Cys		150045993	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	37	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883883	0.91814	0.0	1.16E-4	ENSG00000153002	ENST00000491148;ENST00000282957	T;T	0.12039	2.72;2.72	5.69	5.69	0.88448	Peptidase M14, carboxypeptidase A (2);	0.048732	0.85682	D	0.000000	T	0.47619	0.1455	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54437	-0.8294	10	0.87932	D	0	.	19.8033	0.96518	0.0:1.0:0.0:0.0	.	291	P15086	CBPB1_HUMAN	C	291	ENSP00000417222:R291C;ENSP00000282957:R291C	ENSP00000282957:R291C	R	+	1	0	CPB1	150045993	1.000000	0.71417	0.988000	0.46212	0.778000	0.44026	7.468000	0.80943	2.677000	0.91161	0.655000	0.94253	CGC		0.463	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		T	148563303	C	T	148563303	3	4	85	1	0	0	0	0	1	0	0	0	3802	652	23	1	905	1	CPB1	3	148563303	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	9898138	148563303	49459127	30	23913										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936094	178936094	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctctctctgaaatcactgagCaggagaaagattttctatgg	9	8	4	4	rs121913286		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:178936094C>A	ENST00000263967.3	+	10	1793	c.1636C>A	c.(1636-1638)Cag>Aag	p.Q546K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	546	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		Q -> E (in BC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> K (in OC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> P (found in an anaplastic astrocytoma sample; unknown pathological significance). {ECO:0000269|PubMed:15289301}.|Q -> R (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q546K(89)|p.Q546E(12)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATCACTGAGCAGGAGAAAGA	0.358		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	101	Substitution - Missense(101)	large_intestine(55)|breast(17)|endometrium(15)|central_nervous_system(3)|lung(3)|ovary(3)|skin(2)|cervix(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)	3											61	61	61					3																	178936094		1814	4072	5886	180418788	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1636C>A	3.37:g.178936094C>A	ENSP00000263967:p.Gln546Lys		180418788	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838482	0.91117	.	.	ENSG00000121879	ENST00000263967	T	0.62232	0.04	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75191	0.3816	M	0.64404	1.975	0.80722	D	1	D	0.58970	0.984	P	0.58660	0.843	T	0.73833	-0.3858	10	0.46703	T	0.11	-14.2064	20.0024	0.97423	0.0:1.0:0.0:0.0	.	546	P42336	PK3CA_HUMAN	K	546	ENSP00000263967:Q546K	ENSP00000263967:Q546K	Q	+	1	0	PIK3CA	180418788	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.487000	0.81328	2.722000	0.93159	0.467000	0.42956	CAG		0.358	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936094	C	A	178936094	3	1	85	1	0	0	0	0	1	0	0	0	11944	711	25	2	1670	2	PIK3CA	3	178936094	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	30372791	178936094	19086336	31	23914										
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186793465	186793465	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttcttcgatagtgcctgcacGatgggtgcctaccacccgct	10	14	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr3:186793465G>A	ENST00000169298.3	+	8	1769	c.1095G>A	c.(1093-1095)acG>acA	p.T365T	ST6GAL1_ENST00000457772.2_Silent_p.T134T|ST6GAL1_ENST00000448044.1_Silent_p.T365T	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	365					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GTGCCTGCACGATGGGTGCCT	0.512																																																0			3											119	102	108					3																	186793465		2203	4300	6503	188276159	SO:0001819	synonymous_variant	6480			X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"ST6Gal I"	109675	"sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.1095G>A	3.37:g.186793465G>A			188276159	A8KA14|B2R513|D3DNV3	Silent	SNP	ENST00000169298.3	37	CCDS3285.1																																																																																				0.512	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		A	186793465	G	A	186793465	2	1	85	1	0	0	0	0	0	0	0	1	15260	1045	37	1		1	ST6GAL1	3	186793465	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	7857371	186793465	11228965	32	23915										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388974	1388974	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cgcctgctcacacgtgccgaTgcggagtgcccgcctgctca	12	17	2	0	rs71614969	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr4:1388974T>C	ENST00000324803.4	+	1	3635	c.675T>C	c.(673-675)gaT>gaC	p.D225D		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	225					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACGTGCCGATGCGGAGTGCC	0.667													N|||	706	0.140974	0.087	0.1888	5008	,	,		14021	0.0268		0.2326	False		,,,				2504	0.2035															0			4											177	128	145					4																	1388974		2168	4272	6440	1378974	SO:0001819	synonymous_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.675T>C	4.37:g.1388974T>C			1378974	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																				0.667	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1388974	T	C	1388974	2	2	85	1	0	0	0	0	0	0	0	1	3883	1461	51	4		4	CRIPAK	4	1388974	Silent	SNP	T	TCGA-AH-6644-01A-21D-1826-10		1388974	189765302	33	23916										
WFS1	7466	hgsc.bcm.edu	37	chr4	6288867	6288867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cctttgaagaagtcctggagAgggccaaggccggggacccc	15	12	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr4:6288867A>G	ENST00000226760.1	+	3	450	c.280A>G	c.(280-282)Agg>Ggg	p.R94G	WFS1_ENST00000503569.1_Missense_Mutation_p.R94G	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	94					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		AGTCCTGGAGAGGGCCAAGGC	0.582																																																0			4											52	50	51					4																	6288867		2176	4249	6425	6339768	SO:0001583	missense	7466			AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.280A>G	4.37:g.6288867A>G	ENSP00000226760:p.Arg94Gly		6339768	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	37	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.302313	0.40694	.	.	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.93811	-3.29;-3.29	3.84	3.84	0.44239	.	0.284353	0.38778	N	0.001564	D	0.90280	0.6960	L	0.52573	1.65	0.28657	N	0.90633	B	0.27679	0.185	B	0.33620	0.167	T	0.82659	-0.0348	10	0.25751	T	0.34	-22.206	10.6348	0.45558	1.0:0.0:0.0:0.0	.	94	O76024	WFS1_HUMAN	G	94	ENSP00000423337:R94G;ENSP00000226760:R94G	ENSP00000226760:R94G	R	+	1	2	WFS1	6339768	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	6.802000	0.75175	1.623000	0.50342	0.459000	0.35465	AGG		0.582	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			G	6288867	A	G	6288867	3	3	85	1	0	0	0	0	1	0	0	0	17400	295	11	4	286	4	WFS1	4	6288867	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	4899893	6288867	184865409	34	23917										
KIT	3815	hgsc.bcm.edu	37	chr4	55592132	55592132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	attctagtgcattcaagcacAatggcacggttgaatgtaag	10	7	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr4:55592132A>G	ENST00000288135.5	+	9	1553	c.1456A>G	c.(1456-1458)Aat>Gat	p.N486D		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	486	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N486D(1)|p.D479fs*2(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTCAAGCACAATGGCACGGT	0.403		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	2	Substitution - Missense(1)|Deletion - Frameshift(1)	soft_tissue(1)|bone(1)	4											138	123	128					4																	55592132		2203	4300	6503	55286889	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1456A>G	4.37:g.55592132A>G	ENSP00000288135:p.Asn486Asp		55286889	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727065	0.69074	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.03242	4.0;4.0	6.02	6.02	0.97574	Immunoglobulin-like fold (1);	0.084638	0.49916	D	0.000122	T	0.10465	0.0256	M	0.72894	2.215	0.44214	D	0.99704	B;P	0.37636	0.21;0.603	B;P	0.44359	0.069;0.447	T	0.00768	-1.1574	10	0.52906	T	0.07	.	15.1157	0.72401	1.0:0.0:0.0:0.0	.	486;486	P10721-2;P10721	.;KIT_HUMAN	D	486	ENSP00000288135:N486D;ENSP00000390987:N486D	ENSP00000288135:N486D	N	+	1	0	KIT	55286889	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	6.446000	0.73460	2.311000	0.77944	0.533000	0.62120	AAT		0.403	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55592132	A	G	55592132	3	3	85	1	0	0	0	0	1	0	0	0	8350	130	5	4	1490	4	KIT	4	55592132	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	49303265	55592132	135562144	35	23918										
PLA2G12A	81579	hgsc.bcm.edu	37	chr4	110635576	110635576	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aatgacacctgcatgcggctCgttggctgtccagatatggt	12	10	0	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr4:110635576C>A	ENST00000243501.5	-	4	794	c.527G>T	c.(526-528)cGa>cTa	p.R176L	PLA2G12A_ENST00000502283.1_Missense_Mutation_p.R174L	NM_030821.4	NP_110448.2	Q9BZM1	PG12A_HUMAN	phospholipase A2, group XIIA	176					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			kidney(1)|lung(1)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000268)		GCATGCGGCTCGTTGGCTGTC	0.398																																																0			4											169	170	170					4																	110635576		2203	4300	6503	110855025	SO:0001583	missense	81579				CCDS3686.1	4q25	2010-11-24	2004-01-13	2004-01-14	ENSG00000123739	ENSG00000123739	3.1.1.4		18554	protein-coding gene	gene with protein product		611652	"phospholipase A2, group XII"	PLA2G12		11031251	Standard	NM_030821		Approved		uc003hzp.3	Q9BZM1	OTTHUMG00000131915	ENST00000243501.5:c.527G>T	4.37:g.110635576C>A	ENSP00000243501:p.Arg176Leu		110855025	Q9BZ89	Missense_Mutation	SNP	ENST00000243501.5	37	CCDS3686.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495711	0.85069	.	.	ENSG00000123739	ENST00000243501;ENST00000502283	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.83571	0.5283	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84288	0.0498	9	0.72032	D	0.01	-12.7909	18.844	0.92196	0.0:1.0:0.0:0.0	.	176;176	Q542Y6;Q9BZM1	.;PG12A_HUMAN	L	176;174	.	ENSP00000243501:R176L	R	-	2	0	PLA2G12A	110855025	1.000000	0.71417	0.918000	0.36340	0.255000	0.26057	7.208000	0.77907	2.894000	0.99253	0.655000	0.94253	CGA		0.398	PLA2G12A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254868.3			A	110635576	C	A	110635576	3	1	85	1	0	0	0	0	1	0	0	0	12021	884	31	2	46	2	PLA2G12A	4	110635576	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	55043444	110635576	80518700	36	23919										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15616099	15616099	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctgtttcttccaggcaaaggCagctcgagcatctcatctga	9	12	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:15616099C>A	ENST00000504595.1	+	2	526	c.45C>A	c.(43-45)ggC>ggA	p.G15G	FBXL7_ENST00000510662.1_5'UTR|FBXL7_ENST00000329673.7_Silent_p.G3G	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	15					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CAGGCAAAGGCAGCTCGAGCA	0.507																																																0			5											80	80	80					5																	15616099		1997	4174	6171	15669099	SO:0001819	synonymous_variant	23194			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.45C>A	5.37:g.15616099C>A			15669099	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	37	CCDS54833.1																																																																																				0.507	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15616099	C	A	15616099	2	1	85	1	0	0	0	0	0	0	0	1	5743	697	25	2		2	FBXL7	5	15616099	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10		15616099	165299161	37	23920										
CDH9	1007	hgsc.bcm.edu	37	chr5	26988292	26988292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	acatccagccacgcttggtgCgacgtagcattttaccgtca	9	13	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:26988292C>T	ENST00000231021.4	-	2	321	c.149G>A	c.(148-150)cGc>cAc	p.R50H		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	50					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ACGCTTGGTGCGACGTAGCAT	0.393																																					Melanoma(8;187 585 15745 40864 52829)											0			5											121	115	117					5																	26988292		2203	4300	6503	27024049	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.149G>A	5.37:g.26988292C>T	ENSP00000231021:p.Arg50His		27024049	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	32	5.138442	0.94560	.	.	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	T;T;T	0.00585	6.39;6.39;6.39	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.02156	0.0067	L	0.49126	1.545	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.72849	-0.4168	9	.	.	.	.	18.2526	0.90009	0.0:1.0:0.0:0.0	.	50;50	E7EPN0;Q9ULB4	.;CADH9_HUMAN	H	50	ENSP00000231021:R50H;ENSP00000426239:R50H;ENSP00000422538:R50H	.	R	-	2	0	CDH9	27024049	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.157000	0.77461	2.652000	0.90054	0.591000	0.81541	CGC		0.393	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26988292	C	T	26988292	3	4	85	1	0	0	0	0	1	0	0	0	3123	768	27	1	2264	1	CDH9	5	26988292	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	11372193	26988292	153926968	38	23921										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55195898	55195898	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cttttgggtgtctatgatttCttataattctcttgggaagt	9	5	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:55195898C>A	ENST00000447346.2	+	8	1072	c.1007C>A	c.(1006-1008)tCt>tAt	p.S336Y	IL31RA_ENST00000396834.1_Missense_Mutation_p.S317Y|IL31RA_ENST00000354961.4_Missense_Mutation_p.S317Y|IL31RA_ENST00000490985.1_Missense_Mutation_p.S194Y|IL31RA_ENST00000297015.3_Missense_Mutation_p.S194Y|IL31RA_ENST00000396836.2_Missense_Mutation_p.S336Y|IL31RA_ENST00000359040.5_Missense_Mutation_p.S336Y	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	304	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				TCTATGATTTCTTATAATTCT	0.443																																																0			5											139	151	147					5																	55195898		2203	4300	6503	55231655	SO:0001583	missense	133396			AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1007C>A	5.37:g.55195898C>A	ENSP00000415900:p.Ser336Tyr		55231655	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	C	10.59	1.394236	0.25205	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22	4.41	3.46	0.39613	Fibronectin, type III (1);	0.328024	0.31936	N	0.006840	T	0.16428	0.0395	L	0.45581	1.43	0.31987	N	0.60511	B;B;B;B;B	0.33637	0.236;0.2;0.2;0.2;0.42	B;B;B;B;B	0.34652	0.091;0.09;0.061;0.142;0.187	T	0.12837	-1.0532	10	0.56958	D	0.05	-14.719	11.2958	0.49277	0.182:0.818:0.0:0.0	.	304;336;317;336;336	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	Y	336;317;336;336;194;194;317	ENSP00000380048:S336Y;ENSP00000380046:S317Y;ENSP00000415900:S336Y;ENSP00000351935:S336Y;ENSP00000297015:S194Y;ENSP00000427533:S194Y;ENSP00000347047:S317Y	ENSP00000297015:S194Y	S	+	2	0	IL31RA	55231655	0.949000	0.32298	0.939000	0.37840	0.666000	0.39218	2.588000	0.46137	2.445000	0.82738	0.655000	0.94253	TCT		0.443	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		A	55195898	C	A	55195898	3	1	85	1	0	0	0	0	1	0	0	0	7712	913	32	2	1037	2	IL31RA	5	55195898	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	28207606	55195898	125719362	39	23922										
RNF180	285671	hgsc.bcm.edu	37	chr5	63621206	63621206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cactccatgcccattgtgtcGgacaattatttctagagtct	7	11	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:63621206G>A	ENST00000389100.4	+	6	1493	c.1421G>A	c.(1420-1422)cGg>cAg	p.R474Q		NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	474	Interaction with ZIC2. {ECO:0000250}.				adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		CCATTGTGTCGGACAATTATT	0.393																																																0			5											149	117	127					5																	63621206		692	1591	2283	63656962	SO:0001583	missense	285671			AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"RING-type (C3HC4) zinc fingers"	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.1421G>A	5.37:g.63621206G>A	ENSP00000373752:p.Arg474Gln		63656962	Q0JSU3|Q495A8|Q8NBD1	Missense_Mutation	SNP	ENST00000389100.4	37	CCDS47219.1	.	.	.	.	.	.	.	.	.	.	G	33	5.199531	0.94997	.	.	ENSG00000164197	ENST00000389100	D	0.82711	-1.64	5.02	5.02	0.67125	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.277119	0.30658	N	0.009144	D	0.88224	0.6379	M	0.75447	2.3	0.80722	D	1	D	0.58970	0.984	P	0.53102	0.718	D	0.90007	0.4118	10	0.87932	D	0	-1.5118	17.6992	0.88290	0.0:0.0:1.0:0.0	.	474	Q86T96	RN180_HUMAN	Q	474	ENSP00000373752:R474Q	ENSP00000373752:R474Q	R	+	2	0	RNF180	63656962	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.302000	0.96175	2.485000	0.83878	0.643000	0.83706	CGG		0.393	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		A	63621206	G	A	63621206	3	1	85	1	0	0	0	0	1	0	0	0	13501	1116	39	1	1463	1	RNF180	5	63621206	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	8425308	63621206	117294054	40	23923										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65342359	65342359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tattgttaaccatgatgatgTttttgaggtatgattttatg	9	2	0	4			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:65342359T>C	ENST00000284037.5	+	18	2170	c.1781T>C	c.(1780-1782)gTt>gCt	p.V594A	ERBB2IP_ENST00000506030.1_Missense_Mutation_p.V594A|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.V590A|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.V594A|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.V594A|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.V594A|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.V594A|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.V594A|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.V594A	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	594					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CATGATGATGTTTTTGAGGTA	0.328																																																0			5											118	125	123					5																	65342359		2203	4300	6503	65378115	SO:0001583	missense	55914				CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.1781T>C	5.37:g.65342359T>C	ENSP00000284037:p.Val594Ala		65378115	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258229	0.39896	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5;3.5;3.5;3.5;3.5	5.68	3.34	0.38264	.	0.347112	0.29551	N	0.011840	T	0.03564	0.0102	N	0.08118	0	0.24318	N	0.995057	B;B;B;B;B;B;B	0.24132	0.052;0.075;0.075;0.024;0.0;0.098;0.091	B;B;B;B;B;B;B	0.26969	0.069;0.051;0.051;0.031;0.001;0.075;0.05	T	0.37776	-0.9691	10	0.56958	D	0.05	.	7.1522	0.25616	0.0:0.2452:0.0:0.7548	.	594;594;594;590;594;594;594	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	A	594;594;594;594;594;594;590;594;594	ENSP00000284037:V594A;ENSP00000370330:V594A;ENSP00000370326:V594A;ENSP00000370323:V594A;ENSP00000370322:V594A;ENSP00000370325:V594A;ENSP00000422766:V590A;ENSP00000426632:V594A;ENSP00000422015:V594A	ENSP00000284037:V594A	V	+	2	0	ERBB2IP	65378115	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	0.253000	0.18296	0.992000	0.38840	0.533000	0.62120	GTT		0.328	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		C	65342359	T	C	65342359	3	2	85	1	0	0	0	0	1	0	0	0	5220	1725	60	4	1843	4	ERBB2IP	5	65342359	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	1721153	65342359	115572901	41	23924										
APC	324	hgsc.bcm.edu	37	chr5	112173849	112173849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgaaaaagatagaagtttggAgagagaacgcggaattggtc	14	3	0	5			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:112173849A>G	ENST00000457016.1	+	16	2938	c.2558A>G	c.(2557-2559)gAg>gGg	p.E853G	APC_ENST00000257430.4_Missense_Mutation_p.E853G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.E853G			P25054	APC_HUMAN	adenomatous polyposis coli	853	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAGTTTGGAGAGAGAACGC	0.448		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											66	67	66					5																	112173849		2202	4300	6502	112201748	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2558A>G	5.37:g.112173849A>G	ENSP00000413133:p.Glu853Gly		112201748	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778440	0.31502	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94330	-2.67;-3.4;-2.67;-2.67;-2.85	6.16	6.16	0.99307	.	0.073236	0.56097	D	0.000021	D	0.89234	0.6657	L	0.34521	1.04	0.36291	D	0.856434	B;B	0.23937	0.0;0.094	B;B	0.16722	0.001;0.016	D	0.87781	0.2612	10	0.33940	T	0.23	-17.3326	15.3771	0.74615	1.0:0.0:0.0:0.0	.	855;853	Q4LE70;P25054	.;APC_HUMAN	G	853;835;853;853;853	ENSP00000413133:E853G;ENSP00000423224:E835G;ENSP00000257430:E853G;ENSP00000427089:E853G;ENSP00000423828:E853G	ENSP00000257430:E853G	E	+	2	0	APC	112201748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.742000	0.74843	2.367000	0.80283	0.528000	0.53228	GAG		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173849	A	G	112173849	3	3	85	1	0	0	0	0	1	0	0	0	763	304	11	4	2616	4	APC	5	112173849	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	46831490	112173849	68741411	42	23925										
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	85	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	1790	112175639	68739621	43	23926										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692763	135692763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cagcagcgcgtcccccacccGtgccaggttctccttcttca	8	19	3	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:135692763G>A	ENST00000513104.1	-	2	595	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	TRPC7_ENST00000355180.3_Missense_Mutation_p.R105W|TRPC7_ENST00000426057.2_Missense_Mutation_p.R105W	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	105					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R105W(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCCCCCACCCGTGCCAGGTTC	0.652																																																2	Substitution - Missense(2)	large_intestine(2)	5											56	65	62					5																	135692763		2203	4300	6503	135720662	SO:0001583	missense	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.313C>T	5.37:g.135692763G>A	ENSP00000426070:p.Arg105Trp		135720662	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	37	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.06|18.06	3.540262|3.540262	0.65085|0.65085	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193|ENST00000352189;ENST00000378459;ENST00000502753	T;T;T|.	0.71103|.	-0.54;-0.54;-0.54|.	5.0|5.0	4.06|4.06	0.47325|0.47325	Ankyrin repeat-containing domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71854|0.71854	0.3389|0.3389	M|M	0.78637|0.78637	2.42|2.42	0.33398|0.33398	D|D	0.576973|0.576973	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.993;0.982;0.999;0.998|.	T|T	0.79364|0.79364	-0.1834|-0.1834	10|5	0.87932|.	D|.	0|.	-15.3684|-15.3684	16.0147|16.0147	0.80427|0.80427	0.0:0.0:0.8568:0.1432|0.0:0.0:0.8568:0.1432	.|.	105;105;105;105|.	Q8IWP7;F5H5U9;Q70T25;Q9HCX4|.	.;.;.;TRPC7_HUMAN|.	W|M	105|104	ENSP00000347312:R105W;ENSP00000441628:R105W;ENSP00000426070:R105W|.	ENSP00000265193:R105W|.	R|T	-|-	1|2	2|0	TRPC7|TRPC7	135720662|135720662	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.980000|0.980000	0.70556|0.70556	3.406000|3.406000	0.52637|0.52637	2.608000|2.608000	0.88229|0.88229	0.561000|0.561000	0.74099|0.74099	CGG|ACG		0.652	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692763	G	A	135692763	3	1	85	1	0	0	0	0	1	0	0	0	16624	1144	40	1	2319	1	TRPC7	5	135692763	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	23517124	135692763	45222497	44	23927										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202772	140202772	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggagaacaacccgccaggctGccacatcttcacggtgtctg	11	14	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:140202772G>T	ENST00000529859.1	+	1	1412	c.1412G>T	c.(1411-1413)tGc>tTc	p.C471F	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.C471F|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.C471F	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	471	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCCAGGCTGCCACATCTTC	0.672																																																0			5											72	76	75					5																	140202772		2203	4300	6503	140182956	SO:0001583	missense	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1412G>T	5.37:g.140202772G>T	ENSP00000436557:p.Cys471Phe		140182956	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	9.838	1.190382	0.21954	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.51071	0.72;0.72;0.72	3.86	2.0	0.26442	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.35422	0.0931	N	0.01874	-0.695	0.09310	N	1	P;P;B	0.45283	0.806;0.855;0.307	P;B;B	0.55112	0.769;0.266;0.06	T	0.38908	-0.9639	9	0.87932	D	0	.	10.6099	0.45415	0.0884:0.5581:0.3534:0.0	.	471;471;471	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	F	471	ENSP00000433416:C471F;ENSP00000436557:C471F;ENSP00000367366:C471F	ENSP00000367366:C471F	C	+	2	0	PCDHA5	140182956	0.000000	0.05858	0.950000	0.38849	0.714000	0.41099	-0.063000	0.11655	0.207000	0.20607	0.461000	0.40582	TGC		0.672	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140202772	G	T	140202772	3	4	85	1	0	0	0	0	1	0	0	0	11558	1319	46	2	1414	2	PCDHA5	5	140202772	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	4510009	140202772	40712488	45	23928										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250913	140250913	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcccacgctggtgtgctcccGcgcggtggggagctggtcat	17	13	1	0	rs374687707		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:140250913G>A	ENST00000398640.2	+	1	2225	c.2225G>A	c.(2224-2226)cGc>cAc	p.R742H	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	742	6 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTGCTCCCGCGCGGTGGGG	0.677																																																0			5											29	31	31					5																	140250913		2203	4300	6503	140231097	SO:0001583	missense	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2225G>A	5.37:g.140250913G>A	ENSP00000381636:p.Arg742His		140231097	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	7.643	0.681315	0.14907	.	.	ENSG00000249158	ENST00000398640	T	0.11604	2.76	4.6	2.37	0.29283	.	.	.	.	.	T	0.05640	0.0148	N	0.11064	0.09	0.22571	N	0.998978	B;B	0.27732	0.187;0.002	B;B	0.30029	0.11;0.004	T	0.44574	-0.9319	9	0.19590	T	0.45	.	7.384	0.26872	0.1685:0.1512:0.6803:0.0	.	742;742	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	H	742	ENSP00000381636:R742H	ENSP00000381636:R742H	R	+	2	0	PCDHA11	140231097	1.000000	0.71417	0.990000	0.47175	0.145000	0.21501	2.796000	0.47869	0.894000	0.36317	0.655000	0.94253	CGC		0.677	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140250913	G	A	140250913	3	1	85	1	0	0	0	0	1	0	0	0	11552	1087	38	1	2227	1	PCDHA11	5	140250913	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	48141	140250913	40664347	46	23929										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573591	140573591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	caacgcccaggtcacctactCgctgctgccgccccaagacc	8	20	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:140573591C>T	ENST00000239446.4	+	1	1650	c.1466C>T	c.(1465-1467)tCg>tTg	p.S489L		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	489	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTCACCTACTCGCTGCTGCCG	0.667																																																0			5											84	98	93					5																	140573591		2203	4298	6501	140553775	SO:0001583	missense	56126			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1466C>T	5.37:g.140573591C>T	ENSP00000239446:p.Ser489Leu		140553775	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	16.95	3.262969	0.59431	.	.	ENSG00000120324	ENST00000239446	T	0.03094	4.05	3.32	3.32	0.38043	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.20047	0.0482	M	0.86097	2.795	0.33743	D	0.619694	D	0.89917	1.0	D	0.81914	0.995	T	0.38286	-0.9668	9	0.72032	D	0.01	.	14.8575	0.70351	0.0:1.0:0.0:0.0	.	489	Q9UN67	PCDBA_HUMAN	L	489	ENSP00000239446:S489L	ENSP00000239446:S489L	S	+	2	0	PCDHB10	140553775	0.102000	0.21896	1.000000	0.80357	0.734000	0.41952	0.489000	0.22387	1.880000	0.54463	0.549000	0.68633	TCG		0.667	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140573591	C	T	140573591	3	4	85	1	0	0	0	0	1	0	0	0	11566	893	31	1	1468	1	PCDHB10	5	140573591	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	322678	140573591	40341669	47	23930										
FAT2	2196	hgsc.bcm.edu	37	chr5	150922759	150922759	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	accaggctgtctttcaccttGaccacaccagtgactgggtt	9	13	2	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:150922759G>T	ENST00000261800.5	-	9	7941	c.7929C>A	c.(7927-7929)gtC>gtA	p.V2643V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2643	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTTCACCTTGACCACACCAG	0.488																																																0			5											133	126	128					5																	150922759		2203	4300	6503	150902952	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7929C>A	5.37:g.150922759G>T			150902952	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.488	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150922759	G	T	150922759	2	4	85	1	0	0	0	0	0	0	0	1	5709	1277	45	2		2	FAT2	5	150922759	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	10349168	150922759	29992501	48	23931										
NSD1	64324	hgsc.bcm.edu	37	chr5	176696731	176696731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tttgtggactcaccaggcccGagtcttcccttacatggagg	11	12	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr5:176696731G>A	ENST00000439151.2	+	16	5477	c.5432G>A	c.(5431-5433)cGa>cAa	p.R1811Q	NSD1_ENST00000361032.4_Missense_Mutation_p.R1708Q|NSD1_ENST00000347982.4_Missense_Mutation_p.R1542Q|NSD1_ENST00000354179.4_Missense_Mutation_p.R1542Q	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1811	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	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)		CACCAGGCCCGAGTCTTCCCT	0.443			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	0			5											116	110	112					5																	176696731		2203	4300	6503	176629337	SO:0001583	missense	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.5432G>A	5.37:g.176696731G>A	ENSP00000395929:p.Arg1811Gln		176629337	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	36	5.755959	0.96898	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032;ENST00000508029;ENST00000503056;ENST00000515735	T;T;T;T;D;T;T	0.92595	-0.52;-0.52;-0.52;-0.52;-3.07;-0.52;1.58	5.38	5.38	0.77491	PWWP (3);	0.000000	0.49305	D	0.000143	D	0.95730	0.8611	M	0.65677	2.01	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.95754	0.8794	10	0.72032	D	0.01	.	19.4967	0.95075	0.0:0.0:1.0:0.0	.	1542;1708;1811	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	Q	1542;1811;1542;1708;25;25;25	ENSP00000346111:R1542Q;ENSP00000395929:R1811Q;ENSP00000343209:R1542Q;ENSP00000354310:R1708Q;ENSP00000425120:R25Q;ENSP00000424024:R25Q;ENSP00000423048:R25Q	ENSP00000343209:R1542Q	R	+	2	0	NSD1	176629337	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	9.813000	0.99286	2.678000	0.91216	0.585000	0.79938	CGA		0.443	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176696731	G	A	176696731	3	1	85	1	0	0	0	0	1	0	0	0	10700	1058	37	1	5490	1	NSD1	5	176696731	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	25773972	176696731	4218529	49	23932										
BTN3A3	10384	hgsc.bcm.edu	37	chr6	26452620	26452620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gaaccataagctacaggcacGcactgaagcactttactgat	8	11	0	2	rs144256388		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:26452620G>A	ENST00000244519.2	+	11	1979	c.1736G>A	c.(1735-1737)cGc>cAc	p.R579H	BTN3A3_ENST00000339789.4_Missense_Mutation_p.R537H|BTN3A3_ENST00000361232.3_Missense_Mutation_p.R530H	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	579					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.R579H(1)		cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						CTACAGGcacgcactgaagca	0.463																																																1	Substitution - Missense(1)	lung(1)	6						G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	36	32	33		1106,1736,1589	-3	0	6	dbSNP_134	33	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	BTN3A3	NM_001242803.1,NM_006994.4,NM_197974.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	369/375,579/585,530/536	26452620	1,13005	2203	4300	6503	26560599	SO:0001583	missense	10384			U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.1736G>A	6.37:g.26452620G>A	ENSP00000244519:p.Arg579His		26560599	B4DWI7|E9PCP5	Missense_Mutation	SNP	ENST00000244519.2	37	CCDS4611.1	.	.	.	.	.	.	.	.	.	.	G	0.596	-0.831123	0.02713	0.0	1.16E-4	ENSG00000111801	ENST00000244519;ENST00000339789;ENST00000361232	T;T;T	0.39229	1.15;1.09;1.09	1.48	-2.96	0.05547	.	.	.	.	.	T	0.05777	0.0151	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31364	-0.9946	9	0.40728	T	0.16	.	1.5152	0.02504	0.4283:0.0:0.2652:0.3064	.	530;579	E9PCP5;O00478	.;BT3A3_HUMAN	H	579;537;530	ENSP00000244519:R579H;ENSP00000344968:R537H;ENSP00000355238:R530H	ENSP00000244519:R579H	R	+	2	0	BTN3A3	26560599	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-1.866000	0.01647	-0.330000	0.08514	-1.006000	0.02489	CGC		0.463	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994		A	26452620	G	A	26452620	3	1	85	1	0	0	0	0	1	0	0	0	1567	1087	38	1	1770	1	BTN3A3	6	26452620	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10		26452620	144662447	50	23933										
MAS1L	116511	hgsc.bcm.edu	37	chr6	29455289	29455289	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agttagcagagtcacctgtaAgaaccccactgccgagcagc	10	13	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:29455289A>G	ENST00000377127.3	-	1	449	c.391T>C	c.(391-393)Tta>Cta	p.L131L		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	131					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L131L(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						GTCACCTGTAAGAACCCCACT	0.507																																					NSCLC(153;755 1987 3859 11251 32945)											1	Substitution - coding silent(1)	ovary(1)	6											65	61	62					6																	29455289		2203	4300	6503	29563268	SO:0001819	synonymous_variant	116511			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.391T>C	6.37:g.29455289A>G			29563268	Q5SUN5	Silent	SNP	ENST00000377127.3	37	CCDS4661.1																																																																																				0.507	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		G	29455289	A	G	29455289	2	3	85	1	0	0	0	0	0	0	0	1	9351	69	3	4		4	MAS1L	6	29455289	Silent	SNP	A	TCGA-AH-6644-01A-21D-1826-10	3002669	29455289	141659778	51	23934										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33657928	33657928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	accacgtgggctacatcctgAccagtgtcctgggcctcttt	10	14	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:33657928A>G	ENST00000374316.5	+	52	8045	c.6985A>G	c.(6985-6987)Acc>Gcc	p.T2329A	ITPR3_ENST00000605930.1_Missense_Mutation_p.T2329A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2329					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTACATCCTGACCAGTGTCCT	0.597																																																0			6											120	96	104					6																	33657928		2203	4300	6503	33765906	SO:0001583	missense	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6985A>G	6.37:g.33657928A>G	ENSP00000363435:p.Thr2329Ala		33765906	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728936	0.89390	.	.	ENSG00000096433	ENST00000374316	D	0.98362	-4.89	5.18	5.18	0.71444	Ion transport (1);	0.051258	0.85682	D	0.000000	D	0.98040	0.9354	L	0.52266	1.64	0.54753	D	0.999984	P;D	0.63046	0.67;0.992	B;D	0.67231	0.403;0.95	D	0.99833	1.1055	10	0.87932	D	0	-20.3344	15.0372	0.71757	1.0:0.0:0.0:0.0	.	2329;1999	Q14573;Q59ES2	ITPR3_HUMAN;.	A	2329	ENSP00000363435:T2329A	ENSP00000363435:T2329A	T	+	1	0	ITPR3	33765906	1.000000	0.71417	0.964000	0.40570	0.980000	0.70556	9.339000	0.96797	1.976000	0.57569	0.379000	0.24179	ACC		0.597	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		G	33657928	A	G	33657928	3	3	85	1	0	0	0	0	1	0	0	0	7943	275	10	4	7187	4	ITPR3	6	33657928	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	4202639	33657928	137457139	52	23935										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42211092	42211092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cgcactgagccaccgtcttgGacttcacctgccgggaaagc	11	15	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:42211092G>T	ENST00000372922.4	-	15	3315	c.2753C>A	c.(2752-2754)tCc>tAc	p.S918Y	TRERF1_ENST00000372917.4_Missense_Mutation_p.S835Y|TRERF1_ENST00000541110.1_Missense_Mutation_p.S938Y|TRERF1_ENST00000340840.2_Missense_Mutation_p.S835Y|TRERF1_ENST00000354325.2_Missense_Mutation_p.S835Y	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	918	Interacts with CREBBP.|SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CACCGTCTTGGACTTCACCTG	0.493																																																0			6											102	90	94					6																	42211092		2203	4300	6503	42319070	SO:0001583	missense	55809			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2753C>A	6.37:g.42211092G>T	ENSP00000362013:p.Ser918Tyr		42319070	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	g	26.4	4.735041	0.89482	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	6.16	6.16	0.99307	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.64402	D	0.000018	T	0.42720	0.1215	L	0.38531	1.155	0.52501	D	0.999956	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.993	D;D;D;D;D	0.87578	0.998;0.996;0.996;0.998;0.983	T	0.26121	-1.0112	10	0.87932	D	0	-21.77	20.4596	0.99160	0.0:0.0:1.0:0.0	.	835;938;918;674;674	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	Y	938;835;918;835;835	ENSP00000439689:S938Y;ENSP00000362008:S835Y;ENSP00000362013:S918Y;ENSP00000339438:S835Y;ENSP00000346285:S835Y	ENSP00000339438:S835Y	S	-	2	0	TRERF1	42319070	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.989000	0.76219	2.937000	0.99478	0.651000	0.88453	TCC		0.493	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		T	42211092	G	T	42211092	3	4	85	1	0	0	0	0	1	0	0	0	16515	1174	41	2	865	2	TRERF1	6	42211092	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	8553164	42211092	128903975	53	23936										
GSTA5	221357	hgsc.bcm.edu	37	chr6	52696671	52696671	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	acctgaaaatcttccttgctTcttctaaagatttctcatcc	3	12	4	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:52696671T>C	ENST00000370989.2	-	6	673	c.644A>G	c.(643-645)gAa>gGa	p.E215G	GSTA5_ENST00000284562.2_Missense_Mutation_p.E215G|GSTA5_ENST00000475052.1_5'UTR			Q7RTV2	GSTA5_HUMAN	glutathione S-transferase alpha 5	215					glutathione metabolic process (GO:0006749)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Lung NSC(77;0.0912)				Glutathione(DB00143)	CTTCCTTGCTTCTTCTAAAGA	0.453																																																0			6											142	137	139					6																	52696671		2203	4300	6503	52804630	SO:0001583	missense	221357			BK000212	CCDS4946.1	6p12.2	2012-06-21	2008-11-26		ENSG00000182793	ENSG00000182793	2.5.1.18	"Glutathione S-transferases / Soluble"	19662	protein-coding gene	gene with protein product		607605	"glutathione S-transferase A5"			12042665	Standard	NM_153699		Approved		uc003pba.1	Q7RTV2	OTTHUMG00000014857	ENST00000370989.2:c.644A>G	6.37:g.52696671T>C	ENSP00000360028:p.Glu215Gly		52804630	Q5SZC2	Missense_Mutation	SNP	ENST00000370989.2	37	CCDS4946.1	.	.	.	.	.	.	.	.	.	.	T	4.194	0.034694	0.08101	.	.	ENSG00000182793	ENST00000370989;ENST00000284562	T;T	0.01613	4.73;4.73	2.37	2.37	0.29283	Glutathione S-transferase, C-terminal-like (1);	0.889303	0.09686	N	0.769158	T	0.00967	0.0032	M	0.75264	2.295	0.09310	N	1	B	0.22211	0.066	B	0.15484	0.013	T	0.43015	-0.9417	10	0.30078	T	0.28	.	6.5957	0.22672	0.0:0.0:0.2436:0.7564	.	215	Q7RTV2	GSTA5_HUMAN	G	215	ENSP00000360028:E215G;ENSP00000284562:E215G	ENSP00000284562:E215G	E	-	2	0	GSTA5	52804630	0.000000	0.05858	0.015000	0.15790	0.039000	0.13416	-0.325000	0.07976	1.091000	0.41335	0.254000	0.18369	GAA		0.453	GSTA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040917.1	NM_153699		C	52696671	T	C	52696671	3	2	85	1	0	0	0	0	1	0	0	0	6855	1783	62	4	28	4	GSTA5	6	52696671	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	10485579	52696671	118418396	54	23937										
DST	667	hgsc.bcm.edu	37	chr6	56496754	56496754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gagttcgaatctgtctaatcAgccgatcttcacagttctct	7	11	6	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:56496754A>G	ENST00000361203.3	-	25	3264	c.3257T>C	c.(3256-3258)cTg>cCg	p.L1086P	DST_ENST00000518935.1_Missense_Mutation_p.L760P|DST_ENST00000370788.2_Missense_Mutation_p.L1086P|DST_ENST00000244364.6_Missense_Mutation_p.L760P|DST_ENST00000370769.4_Missense_Mutation_p.L1086P|DST_ENST00000446842.2_Missense_Mutation_p.L760P|DST_ENST00000312431.6_Missense_Mutation_p.L1086P|DST_ENST00000421834.2_Missense_Mutation_p.L1086P|DST_ENST00000370754.5_Missense_Mutation_p.L1264P|DST_ENST00000370765.6_Missense_Mutation_p.L760P			Q03001	DYST_HUMAN	dystonin	1086					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGTCTAATCAGCCGATCTTC	0.383																																																0			6											111	109	110					6																	56496754		2203	4300	6503	56604713	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3257T>C	6.37:g.56496754A>G	ENSP00000354508:p.Leu1086Pro		56604713	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	25.1	4.602445	0.87157	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.70631	0.74;0.74;0.74;0.74;0.74;0.74;0.74;-0.5;0.74;0.74;0.74;-0.07	5.84	5.84	0.93424	.	0.000000	0.39146	N	0.001457	T	0.80523	0.4639	M	0.71581	2.175	0.35126	D	0.767546	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D	0.91635	0.972;0.997;0.972;0.99;0.999;0.999;0.972;0.983	T	0.83177	-0.0091	9	0.72032	D	0.01	.	16.2233	0.82274	1.0:0.0:0.0:0.0	.	1086;1086;1264;760;760;760;1086;760	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	P	760;1264;1086;1086;760;1086;1086;1086;760;1126;760;760	ENSP00000244364:L760P;ENSP00000359790:L1264P;ENSP00000359805:L1086P;ENSP00000400883:L1086P;ENSP00000393645:L760P;ENSP00000307959:L1086P;ENSP00000359824:L1086P;ENSP00000354508:L1086P;ENSP00000404924:L760P;ENSP00000431030:L1126P;ENSP00000359801:L760P;ENSP00000431003:L760P	ENSP00000244364:L760P	L	-	2	0	DST	56604713	0.997000	0.39634	0.225000	0.23894	0.974000	0.67602	7.518000	0.81795	2.243000	0.73865	0.482000	0.46254	CTG		0.383	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56496754	A	G	56496754	3	3	85	1	0	0	0	0	1	0	0	0	4794	188	7	4	18156	4	DST	6	56496754	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	3800083	56496754	114618313	55	23938										
BAI3	577	hgsc.bcm.edu	37	chr6	69949023	69949023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tctctctggctaggtacataCgctctgagagatccataata	8	10	3	2	rs145280281	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:69949023C>T	ENST00000370598.1	+	20	3540	c.2719C>T	c.(2719-2721)Cgc>Tgc	p.R907C	BAI3_ENST00000238918.8_Missense_Mutation_p.R113C	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	907					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TAGGTACATACGCTCTGAGAG	0.368																																																0			6						C	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	179	174	175		2719	5.3	1	6	dbSNP_134	175	11,8585	8.4+/-32.0	0,11,4287	yes	missense	BAI3	NM_001704.2	180	0,15,6486	TT,TC,CC		0.128,0.0908,0.1154	probably-damaging	907/1523	69949023	15,12987	2203	4298	6501	70005744	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2719C>T	6.37:g.69949023C>T	ENSP00000359630:p.Arg907Cys		70005744	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.792583	0.70452	9.08E-4	0.00128	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.52754	0.65;0.65	5.26	5.26	0.73747	GPCR, family 2-like (1);	0.056171	0.64402	D	0.000002	T	0.65123	0.2661	M	0.89353	3.025	0.80722	D	1	D;D;D	0.89917	0.995;0.999;1.0	P;P;D	0.67103	0.832;0.83;0.949	T	0.72544	-0.4261	10	0.87932	D	0	.	12.1006	0.53780	0.2923:0.7077:0.0:0.0	.	113;907;907	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	C	907;113	ENSP00000359630:R907C;ENSP00000238918:R113C	ENSP00000238918:R113C	R	+	1	0	BAI3	70005744	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.113000	0.57851	2.450000	0.82876	0.655000	0.94253	CGC		0.368	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69949023	C	T	69949023	3	4	85	1	0	0	0	0	1	0	0	0	1301	536	19	1	2789	1	BAI3	6	69949023	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	13452269	69949023	101166044	56	23939										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152674812	152674812	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tcacgtggctctcgtccagtAtctcctgagctctagctccc	8	16	4	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:152674812A>G	ENST00000367255.5	-	68	11595	c.10994T>C	c.(10993-10995)aTa>aCa	p.I3665T	SYNE1_ENST00000265368.4_Missense_Mutation_p.I3665T|SYNE1_ENST00000423061.1_Missense_Mutation_p.I3650T|SYNE1_ENST00000448038.1_Missense_Mutation_p.I3650T|SYNE1_ENST00000341594.5_Missense_Mutation_p.I3636T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3665					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCGTCCAGTATCTCCTGAGC	0.517										HNSCC(10;0.0054)																																						0			6											161	134	143					6																	152674812		2203	4300	6503	152716505	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10994T>C	6.37:g.152674812A>G	ENSP00000356224:p.Ile3665Thr		152716505	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428924	0.43122	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.75	5.75	0.90469	.	0.188980	0.36444	N	0.002595	T	0.24699	0.0599	L	0.51422	1.61	0.80722	D	1	B;B;B;B	0.28552	0.215;0.215;0.215;0.178	B;B;B;B	0.29942	0.043;0.043;0.043;0.109	T	0.10636	-1.0621	10	0.72032	D	0.01	.	16.0707	0.80928	1.0:0.0:0.0:0.0	.	3665;3665;3665;3650	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	T	3665;3650;3665;3650;3636	ENSP00000356224:I3665T;ENSP00000396024:I3650T;ENSP00000265368:I3665T;ENSP00000390975:I3650T;ENSP00000341887:I3636T	ENSP00000265368:I3665T	I	-	2	0	SYNE1	152716505	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.162000	0.77515	2.194000	0.70268	0.533000	0.62120	ATA		0.517	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152674812	A	G	152674812	3	3	85	1	0	0	0	0	1	0	0	0	15484	449	16	4	15788	4	SYNE1	6	152674812	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	82725789	152674812	18440255	57	23940										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152712653	152712653	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cctcctgcccagcaccgtggCcttcttcactcagaagctgc	8	18	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr6:152712653C>A	ENST00000367255.5	-	52	8364	c.7763G>T	c.(7762-7764)gGc>gTc	p.G2588V	SYNE1_ENST00000265368.4_Missense_Mutation_p.G2588V|SYNE1_ENST00000423061.1_Missense_Mutation_p.G2595V|SYNE1_ENST00000448038.1_Missense_Mutation_p.G2595V|SYNE1_ENST00000341594.5_Missense_Mutation_p.G2627V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2588					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCACCGTGGCCTTCTTCACT	0.473										HNSCC(10;0.0054)																																						0			6											44	47	46					6																	152712653		2203	4300	6503	152754346	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.7763G>T	6.37:g.152712653C>A	ENSP00000356224:p.Gly2588Val		152754346	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	15.67	2.900795	0.52227	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	5.79	5.79	0.91817	.	0.100043	0.44285	D	0.000477	T	0.46132	0.1377	M	0.64997	1.995	0.80722	D	1	D;D;D;P	0.61697	0.99;0.97;0.97;0.481	P;P;P;B	0.59056	0.82;0.851;0.851;0.161	T	0.10497	-1.0627	10	0.29301	T	0.29	.	20.04	0.97581	0.0:1.0:0.0:0.0	.	2571;2588;2588;2595	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	V	2588;2595;2588;2595;2627	ENSP00000356224:G2588V;ENSP00000396024:G2595V;ENSP00000265368:G2588V;ENSP00000390975:G2595V;ENSP00000341887:G2627V	ENSP00000265368:G2588V	G	-	2	0	SYNE1	152754346	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.440000	0.80464	2.733000	0.93635	0.655000	0.94253	GGC		0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152712653	C	A	152712653	3	1	85	1	0	0	0	0	1	0	0	0	15484	739	26	2	19083	2	SYNE1	6	152712653	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	37841	152712653	18402414	58	23941										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11632944	11632944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctttttcttcaaattctggaCactccttttcactgccaatg	4	12	4	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:11632944C>T	ENST00000423059.4	-	3	1459	c.1208G>A	c.(1207-1209)tGt>tAt	p.C403Y		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	403	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		AAATTCTGGACACTCCTTTTC	0.493										HNSCC(18;0.044)																																						0			7											91	87	88					7																	11632944		1912	4138	6050	11599469	SO:0001583	missense	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1208G>A	7.37:g.11632944C>T	ENSP00000406482:p.Cys403Tyr		11599469		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490382	0.64074	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.69306	-0.39	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94193	0.7443	10	0.66056	D	0.02	.	18.8505	0.92227	0.0:1.0:0.0:0.0	.	403	Q9UPZ6	THS7A_HUMAN	Y	403	ENSP00000406482:C403Y	ENSP00000262042:C403Y	C	-	2	0	THSD7A	11599469	1.000000	0.71417	0.898000	0.35279	0.387000	0.30353	7.484000	0.81180	2.460000	0.83146	0.561000	0.74099	TGT		0.493	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11632944	C	T	11632944	3	4	85	1	0	0	0	0	1	0	0	0	15918	478	17	3	3865	3	THSD7A	7	11632944	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		11632944	147505719	59	23942										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21659670	21659670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tactaaagtctgatgaacaaCtttttgaaactctagagcac	6	8	2	4			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:21659670C>A	ENST00000409508.3	+	25	4505	c.4474C>A	c.(4474-4476)Ctt>Att	p.L1492I	DNAH11_ENST00000465593.1_3'UTR|DNAH11_ENST00000328843.6_Missense_Mutation_p.L1497I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1497	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TGATGAACAACTTTTTGAAAC	0.313									Kartagener syndrome																																							0			7											73	65	67					7																	21659670		1808	4068	5876	21626195	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4474C>A	7.37:g.21659670C>A	ENSP00000475939:p.Leu1492Ile		21626195	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	13.90	2.374400	0.42105	.	.	ENSG00000105877	ENST00000328843	T	0.60424	0.19	4.9	4.0	0.46444	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000001	T	0.61261	0.2333	.	.	.	0.50171	D	0.999855	D	0.89917	1.0	D	0.87578	0.998	T	0.59467	-0.7449	9	0.02654	T	1	.	12.2648	0.54672	0.0:0.9146:0.0:0.0854	.	1497	Q96DT5	DYH11_HUMAN	I	1497	ENSP00000330671:L1497I	ENSP00000330671:L1497I	L	+	1	0	DNAH11	21626195	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	5.472000	0.66768	1.127000	0.42034	0.563000	0.77884	CTT		0.313	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21659670	C	A	21659670	3	1	85	1	0	0	0	0	1	0	0	0	4610	565	20	2	4587	2	DNAH11	7	21659670	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	10026726	21659670	137478993	60	23943										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48559814	48559814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	actttctgggctggatcttcGtgcaactggcctcgcagggc	13	12	2	0	rs369296047		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:48559814G>A	ENST00000435803.1	+	53	13999	c.13975G>A	c.(13975-13977)Gtg>Atg	p.V4659M	ABCA13_ENST00000544596.1_Missense_Mutation_p.V389M	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4659					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTGGATCTTCGTGCAACTGGC	0.502																																																0			7						G	MET/VAL	1,3889		0,1,1944	92	85	87		13975	1.7	0	7		87	0,8294		0,0,4147	no	missense	ABCA13	NM_152701.3	21	0,1,6091	AA,AG,GG		0.0,0.0257,0.0082	probably-damaging	4659/5059	48559814	1,12183	1945	4147	6092	48530360	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13975G>A	7.37:g.48559814G>A	ENSP00000411096:p.Val4659Met		48530360	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434944	0.25813	2.57E-4	0.0	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.86956	-2.19;-2.19;-2.19	5.14	1.69	0.24217	.	0.326853	0.22054	N	0.065280	D	0.87079	0.6088	L	0.55481	1.735	0.24740	N	0.993046	P;D;D	0.69078	0.873;0.967;0.997	B;B;P	0.55011	0.26;0.308;0.766	T	0.78595	-0.2143	10	0.62326	D	0.03	.	7.507	0.27551	0.3172:0.0:0.6828:0.0	.	389;2361;4659	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	M	4659;432;389	ENSP00000411096:V4659M;ENSP00000391042:V432M;ENSP00000442634:V389M	ENSP00000391042:V432M	V	+	1	0	ABCA13	48530360	0.574000	0.26684	0.023000	0.16930	0.129000	0.20672	0.706000	0.25690	0.413000	0.25759	0.655000	0.94253	GTG		0.502	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48559814	G	A	48559814	3	1	85	1	0	0	0	0	1	0	0	0	31	1145	40	1	14014	1	ABCA13	7	48559814	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	26900144	48559814	110578849	61	23944										
C7orf66	154907	hgsc.bcm.edu	37	chr7	108524300	108524300	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttgtggtgcagaaagaatgaGtacagcctatgtgcaatgga	13	5	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:108524300G>T	ENST00000379007.2	-	2	166	c.112C>A	c.(112-114)Ctc>Atc	p.L38I		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	38						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						GAAAGAATGAGTACAGCCTAT	0.453																																																0			7											113	100	105					7																	108524300		2203	4300	6503	108311536	SO:0001583	missense	154907			AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.112C>A	7.37:g.108524300G>T	ENSP00000368292:p.Leu38Ile		108311536		Missense_Mutation	SNP	ENST00000379007.2	37	CCDS34735.1	.	.	.	.	.	.	.	.	.	.	G	9.578	1.122770	0.20877	.	.	ENSG00000205174	ENST00000379007	.	.	.	3.47	-0.68	0.11346	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	P	0.36633	0.562	B	0.35353	0.201	T	0.21245	-1.0251	7	.	.	.	.	4.288	0.10863	0.2242:0.3681:0.4077:0.0	.	38	A4D0T2	CG066_HUMAN	I	38	.	.	L	-	1	0	C7orf66	108311536	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.244000	0.18124	-0.149000	0.11215	0.563000	0.77884	CTC		0.453	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607		T	108524300	G	T	108524300	3	4	85	1	0	0	0	0	1	0	0	0	2418	1029	36	2	239	2	C7orf66	7	108524300	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	59964486	108524300	50614363	62	23945										
PDIA4	9601	hgsc.bcm.edu	37	chr7	148701158	148701158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctctagctgcttgcagtgccCgcaccatggcgcgtagaact	11	14	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:148701158C>T	ENST00000286091.4	-	10	1898	c.1666G>A	c.(1666-1668)Ggg>Agg	p.G556R		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	556	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			TTGCAGTGCCCGCACCATGGC	0.577																																																0			7											146	136	139					7																	148701158		2203	4300	6503	148332091	SO:0001583	missense	9601			BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1666G>A	7.37:g.148701158C>T	ENSP00000286091:p.Gly556Arg		148332091	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800099	0.90538	.	.	ENSG00000155660	ENST00000286091	T	0.10099	2.91	5.81	5.81	0.92471	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56649	-0.7944	10	0.87932	D	0	.	20.0734	0.97734	0.0:1.0:0.0:0.0	.	556	P13667	PDIA4_HUMAN	R	556	ENSP00000286091:G556R	ENSP00000286091:G556R	G	-	1	0	PDIA4	148332091	1.000000	0.71417	0.998000	0.56505	0.620000	0.37586	7.574000	0.82434	2.751000	0.94390	0.555000	0.69702	GGG		0.577	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		T	148701158	C	T	148701158	3	4	85	1	0	0	0	0	1	0	0	0	11701	652	23	1	275	1	PDIA4	7	148701158	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	40176858	148701158	10437505	63	23946										
MLL3	58508	hgsc.bcm.edu	37	chr7	151962211	151962211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atccaggcacattccatgatAgtgctgaccacaagtagtac	8	11	0	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr7:151962211A>G	ENST00000262189.6	-	8	1314	c.1096T>C	c.(1096-1098)Tat>Cat	p.Y366H	KMT2C_ENST00000355193.2_Missense_Mutation_p.Y366H	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	366					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										ATTCCATGATAGTGCTGACCA	0.448																																																0			7											389	349	362					7																	151962211		2203	4300	6503	151593144	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1096T>C	7.37:g.151962211A>G	ENSP00000262189:p.Tyr366His		151593144	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.024678	0.35701	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.99089	-5.41;-5.41	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38111	U	0.001814	D	0.99180	0.9716	M	0.81682	2.555	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.99406	1.0929	10	0.87932	D	0	.	14.395	0.67005	1.0:0.0:0.0:0.0	.	366	Q8NEZ4	MLL3_HUMAN	H	366	ENSP00000262189:Y366H;ENSP00000347325:Y366H	ENSP00000262189:Y366H	Y	-	1	0	MLL3	151593144	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	9.287000	0.95975	1.843000	0.53566	0.455000	0.32223	TAT		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151962211	A	G	151962211	3	3	85	1	0	0	0	0	1	0	0	0	9652	420	15	4	13847	4	MLL3	7	151962211	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	3261053	151962211	7176452	64	23947										
MCPH1	79648	hgsc.bcm.edu	37	chr8	6312726	6312726	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	catgtgacggctttaaggacCtcatcaaacctcatgaggaa	9	10	3	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr8:6312726C>G	ENST00000344683.5	+	9	1964	c.1888C>G	c.(1888-1890)Ctc>Gtc	p.L630V		NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	630					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CTTTAAGGACCTCATCAAACC	0.338																																					Colon(95;1448 1467 8277 34473 35819)											0			8											141	134	136					8																	6312726		1845	4106	5951	6300134	SO:0001583	missense	79648			AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1888C>G	8.37:g.6312726C>G	ENSP00000342924:p.Leu630Val		6300134	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	C	5.816	0.334857	0.11013	.	.	ENSG00000147316	ENST00000344683	T	0.04119	3.7	5.75	4.88	0.63580	.	0.707440	0.12787	N	0.439213	T	0.11410	0.0278	M	0.65975	2.015	0.30937	N	0.726263	P	0.52316	0.952	P	0.49477	0.612	T	0.04593	-1.0940	10	0.38643	T	0.18	-8.3686	10.712	0.45988	0.0:0.913:0.0:0.087	.	630	Q8NEM0	MCPH1_HUMAN	V	630	ENSP00000342924:L630V	ENSP00000342924:L630V	L	+	1	0	MCPH1	6300134	0.002000	0.14202	0.026000	0.17262	0.394000	0.30568	1.142000	0.31540	1.430000	0.47334	0.650000	0.86243	CTC		0.338	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		G	6312726	C	G	6312726	3	3	85	1	0	0	0	0	1	0	0	0	9428	681	24	5	1930	5	MCPH1	8	6312726	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		6312726	140051296	65	23948										
NRG1	3084	hgsc.bcm.edu	37	chr8	32505823	32505823	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atccttcccttcacccacccGgaaccctgaggtgagaacgc	8	17	1	2	rs550578958		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr8:32505823G>A	ENST00000405005.3	+	5	502				NRG1_ENST00000287842.3_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.R196Q|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000520407.1_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TCACCCACCCGGAACCCTGAG	0.498																																																0			8											114	96	102					8																	32505823		2203	4300	6503	32625365	SO:0001627	intron_variant	3084			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31420G>A	8.37:g.32505823G>A			32625365	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759403	0.49468	.	.	ENSG00000157168	ENST00000520502;ENST00000523041	.	.	.	5.77	3.87	0.44632	.	.	.	.	.	T	0.30479	0.0766	N	0.12182	0.205	0.80722	D	1	B;B	0.12013	0.005;0.005	B;B	0.14023	0.01;0.005	T	0.14504	-1.0470	8	0.35671	T	0.21	.	6.6639	0.23029	0.0877:0.0:0.6382:0.274	.	196;196	Q53F54;Q02297-10	.;.	Q	196;156	.	ENSP00000433289:R196Q	R	+	2	0	NRG1	32625365	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	2.660000	0.46749	2.885000	0.99019	0.655000	0.94253	CGG		0.498	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			A	32505823	G	A	32505823	1	1	85	0	1	0	0	0	0	0	0	0	10678	1116	39	1		1	NRG1	8	32505823	Intron	SNP	G	TCGA-AH-6644-01A-21D-1826-10	26193097	32505823	113858199	66	23949										
CYP7B1	9420	hgsc.bcm.edu	37	chr8	65527711	65527711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctgccatagcttctgggtgcCgcagaagataatacattgcc	10	11	1	2	rs201867790		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr8:65527711C>T	ENST00000310193.3	-	4	1102	c.929G>A	c.(928-930)cGg>cAg	p.R310Q	CYP7B1_ENST00000523954.1_5'UTR	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	310					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)	p.R310Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TTCTGGGTGCCGCAGAAGATA	0.473													C|||	1	0.000199681	0	0	5008	,	,		18550	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	8						C	GLN/ARG	0,4406		0,0,2203	92	85	87		929	-1.7	1	8		87	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CYP7B1	NM_004820.3	43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	310/507	65527711	3,13003	2203	4300	6503	65690265	SO:0001583	missense	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.929G>A	8.37:g.65527711C>T	ENSP00000310721:p.Arg310Gln		65690265	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.38	2.219232	0.39201	0.0	3.49E-4	ENSG00000172817	ENST00000310193	T	0.69685	-0.42	5.93	-1.71	0.08133	.	0.597985	0.19021	N	0.124813	T	0.52273	0.1724	L	0.37507	1.11	0.24162	N	0.995656	B	0.31519	0.327	B	0.31812	0.136	T	0.45425	-0.9262	10	0.39692	T	0.17	-29.0678	12.2283	0.54474	0.0:0.5489:0.0:0.4511	.	310	O75881	CP7B1_HUMAN	Q	310	ENSP00000310721:R310Q	ENSP00000310721:R310Q	R	-	2	0	CYP7B1	65690265	0.996000	0.38824	0.991000	0.47740	0.995000	0.86356	0.437000	0.21543	-0.221000	0.09973	-0.150000	0.13652	CGG		0.473	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			T	65527711	C	T	65527711	3	4	85	1	0	0	0	0	1	0	0	0	4203	652	23	1	603	1	CYP7B1	8	65527711	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	33021888	65527711	80836311	67	23950										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68007881	68007881	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tatcatagaccagaccaagaTcctgaagtaagtgaagaaat	8	7	1	6			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr8:68007881T>C	ENST00000262210.5	+	6	895	c.864T>C	c.(862-864)gaT>gaC	p.D288D	CSPP1_ENST00000412460.1_5'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	323					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CAGACCAAGATCCTGAAGTAA	0.368																																																0			8											65	60	61					8																	68007881		1841	4085	5926	68170435	SO:0001819	synonymous_variant	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.864T>C	8.37:g.68007881T>C			68170435	A6ND63|Q70F00|Q8TBC1	Silent	SNP	ENST00000262210.5	37	CCDS43744.1																																																																																				0.368	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		C	68007881	T	C	68007881	2	2	85	1	0	0	0	0	0	0	0	1	3968	1432	50	4		4	CSPP1	8	68007881	Silent	SNP	T	TCGA-AH-6644-01A-21D-1826-10	2480170	68007881	78356141	68	23951										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92982963	92982963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tttggcctcggcgaccgtgcGctccatcttggccctctctg	11	16	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr8:92982963G>A	ENST00000523629.1	-	11	1916	c.1462C>T	c.(1462-1464)Cgc>Tgc	p.R488C	RUNX1T1_ENST00000518844.1_Missense_Mutation_p.R461C|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.R451C|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.R451C|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.R461C|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.R488C|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.R499C|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.R451C	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	488					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GCGACCGTGCGCTCCATCTTG	0.617																																																0			8											82	68	73					8																	92982963		2203	4300	6503	93052139	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1462C>T	8.37:g.92982963G>A	ENSP00000428543:p.Arg488Cys		93052139	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.022722	0.93462	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.65554	0.2702	M	0.77820	2.39	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;P;D	0.80764	0.95;0.993;0.899;0.994	T	0.68484	-0.5396	10	0.87932	D	0	-17.0871	14.7957	0.69876	0.0:0.0:0.8558:0.1442	.	499;451;488;461	E7EPN4;Q7Z4J5;Q06455;Q06455-2	.;.;MTG8_HUMAN;.	C	488;461;488;451;451;451;499;461	ENSP00000428543:R488C;ENSP00000379520:R461C;ENSP00000265814:R488C;ENSP00000353504:R451C;ENSP00000390137:R451C;ENSP00000428742:R451C;ENSP00000402257:R499C;ENSP00000430728:R461C	ENSP00000265814:R488C	R	-	1	0	RUNX1T1	93052139	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.871000	0.87180	2.729000	0.93468	0.655000	0.94253	CGC		0.617	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	92982963	G	A	92982963	3	1	85	1	0	0	0	0	1	0	0	0	13784	1087	38	1	360	1	RUNX1T1	8	92982963	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	24975082	92982963	53381059	69	23952										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100136921	100136921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgagaaacccctgattgaacGtggaagcaggtgagaaccaa	12	8	0	4	rs186799713		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:100136921G>A	ENST00000357054.1	+	47	5599	c.4664G>A	c.(4663-4665)cGt>cAt	p.R1555H	CCDC180_ENST00000529487.1_Missense_Mutation_p.R1610H|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.R1610H|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1555						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTGATTGAACGTGGAAGCAGG	0.512													G|||	1	0.000199681	0	0	5008	,	,		21246	0.001		0	False		,,,				2504	0															0			9											66	58	61					9																	100136921		2203	4300	6503	99176742	SO:0001583	missense	0			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.4664G>A	9.37:g.100136921G>A	ENSP00000349562:p.Arg1555His		99176742	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	21.3	4.134413	0.77662	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.18174	2.29;2.23;2.23	3.99	3.99	0.46301	.	0.000000	0.64402	D	0.000010	T	0.39860	0.1094	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.23547	-1.0185	10	0.72032	D	0.01	-14.5754	11.9238	0.52808	0.0:0.0:1.0:0.0	.	1749;1555	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	H	1555;1610;1610	ENSP00000349562:R1555H;ENSP00000364348:R1610H;ENSP00000434727:R1610H	ENSP00000349562:R1555H	R	+	2	0	C9orf174	99176742	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	4.760000	0.62235	2.529000	0.85273	0.655000	0.94253	CGT		0.512	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		A	100136921	G	A	100136921	3	1	85	1	0	0	0	0	1	0	0	0	8261	1145	40	1	4806	1	KIAA1529	9	100136921	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10		100136921	41076510	70	23953										
DBC1	1620	hgsc.bcm.edu	37	chr9	121930133	121930133	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aggcggatctcgttgctgatGaaggtggtgtggacgtagag	18	5	1	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:121930133G>A	ENST00000265922.3	-	8	1976	c.1515C>T	c.(1513-1515)ttC>ttT	p.F505F	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	505					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CGTTGCTGATGAAGGTGGTGT	0.552																																																0			9											275	193	221					9																	121930133		2203	4300	6503	120969954	SO:0001819	synonymous_variant	57805			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1515C>T	9.37:g.121930133G>A			120969954	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																				0.552	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	121930133	G	A	121930133	2	1	85	1	0	0	0	0	0	0	0	1	4253	1281	45	3		3	DBC1	9	121930133	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	21793212	121930133	19283298	71	23954										
OR1B1	347169	hgsc.bcm.edu	37	chr9	125391391	125391391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggctagtaagcaggcacaccGttggtgattcattaccaaag	11	9	1	1	rs139868007	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:125391391G>A	ENST00000304833.3	-	1	461	c.424C>T	c.(424-426)Cgg>Tgg	p.R142W	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						CAGGCACACCGTTGGTGATTC	0.532													G|||	3	0.000599042	0.0015	0	5008	,	,		20825	0.001		0	False		,,,				2504	0															0			9						G	TRP/ARG	10,4396	16.8+/-37.8	0,10,2193	100	79	86		424	-0.1	0	9	dbSNP_134	86	0,8600		0,0,4300	yes	missense	OR1B1	NM_001004450.1	101	0,10,6493	AA,AG,GG		0.0,0.227,0.0769	benign	142/319	125391391	10,12996	2203	4300	6503	124431212	SO:0001583	missense	347169			AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.424C>T	9.37:g.125391391G>A	ENSP00000303151:p.Arg142Trp		124431212	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	5.152	0.213563	0.09757	0.00227	0.0	ENSG00000171484	ENST00000304833	T	0.41065	1.01	4.26	-0.134	0.13481	GPCR, rhodopsin-like superfamily (1);	0.619816	0.13379	N	0.392300	T	0.27027	0.0662	L	0.39020	1.185	0.09310	N	1	B	0.14438	0.01	B	0.18561	0.022	T	0.28681	-1.0036	10	0.87932	D	0	-2.2736	1.8041	0.03077	0.2642:0.1347:0.4549:0.1463	.	142	Q8NGR6	OR1B1_HUMAN	W	142	ENSP00000303151:R142W	ENSP00000303151:R142W	R	-	1	2	OR1B1	124431212	0.000000	0.05858	0.016000	0.15963	0.183000	0.23260	-0.974000	0.03794	0.151000	0.19162	-0.149000	0.13747	CGG		0.532	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		A	125391391	G	A	125391391	3	1	85	1	0	0	0	0	1	0	0	0	10982	1144	40	1	535	1	OR1B1	9	125391391	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	3461258	125391391	15822040	72	23955										
ABL1	25	hgsc.bcm.edu	37	chr9	133729537	133729537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	actccaaggaaaaccttctcGctggacccagtgaaaatgac	8	12	1	2	rs369393102		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:133729537G>A	ENST00000318560.5	+	2	547	c.166G>A	c.(166-168)Gct>Act	p.A56T		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	56	CAP.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)	p.A56T(1)		breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	AAACCTTCTCGCTGGACCCAG	0.488			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	1	Substitution - Missense(1)	endometrium(1)	9						G	THR/ALA,THR/ALA	0,4406		0,0,2203	139	138	138		166,223	5.8	1	9		138	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ABL1	NM_005157.4,NM_007313.2	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	56/1131,75/1150	133729537	1,13005	2203	4300	6503	132719358	SO:0001583	missense	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.166G>A	9.37:g.133729537G>A	ENSP00000323315:p.Ala56Thr		132719358	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.817290	0.70912	0.0	1.16E-4	ENSG00000097007	ENST00000372348;ENST00000438426;ENST00000318560	T;T	0.36340	1.26;1.26	5.85	5.85	0.93711	Src homology-3 domain (1);	0.105641	0.64402	D	0.000004	T	0.25791	0.0628	N	0.24115	0.695	0.47778	D	0.999516	B;B	0.20164	0.011;0.042	B;B	0.09377	0.003;0.004	T	0.03287	-1.1052	10	0.41790	T	0.15	.	12.7664	0.57394	0.0:0.0:0.7434:0.2566	.	56;93	P00519;Q59FK4	ABL1_HUMAN;.	T	75;102;56	ENSP00000361423:A75T;ENSP00000323315:A56T	ENSP00000323315:A56T	A	+	1	0	ABL1	132719358	0.996000	0.38824	0.980000	0.43619	0.987000	0.75469	2.229000	0.42990	2.779000	0.95612	0.638000	0.83543	GCT		0.488	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133729537	G	A	133729537	3	1	85	1	0	0	0	0	1	0	0	0	92	1087	38	1	312	1	ABL1	9	133729537	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	8338146	133729537	7483894	73	23956										
FAM78A	286336	hgsc.bcm.edu	37	chr9	134136564	134136564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgacgggcacggcccatgtgAcgctggggtaaaagttgtca	15	9	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:134136564A>G	ENST00000372271.3	-	2	864	c.497T>C	c.(496-498)gTc>gCc	p.V166A	FAM78A_ENST00000247295.4_5'UTR|FAM78A_ENST00000372269.3_Missense_Mutation_p.V163A	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	166										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		GGCCCATGTGACGCTGGGGTA	0.592																																																0			9											131	119	123					9																	134136564		2203	4300	6503	133126385	SO:0001583	missense	286336			AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 59"	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.497T>C	9.37:g.134136564A>G	ENSP00000361345:p.Val166Ala		133126385	Q86VQ9|Q9H7P4	Missense_Mutation	SNP	ENST00000372271.3	37	CCDS6941.2	.	.	.	.	.	.	.	.	.	.	A	23.7	4.452583	0.84209	.	.	ENSG00000126882	ENST00000372269;ENST00000372271;ENST00000464831	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.77572	0.4150	M	0.75777	2.31	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.72625	0.978;0.978	T	0.80915	-0.1169	9	0.87932	D	0	-57.7356	13.7403	0.62845	1.0:0.0:0.0:0.0	.	166;163	Q5JUQ0;Q5JUQ2	FA78A_HUMAN;.	A	163;166;135	.	ENSP00000361343:V163A	V	-	2	0	FAM78A	133126385	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.287000	0.95975	1.894000	0.54839	0.379000	0.24179	GTC		0.592	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387		G	134136564	A	G	134136564	3	3	85	1	0	0	0	0	1	0	0	0	5645	275	10	4	358	4	FAM78A	9	134136564	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	407027	134136564	7076867	74	23957										
SARDH	1757	hgsc.bcm.edu	37	chr9	136577775	136577775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atgcatgtccttctccgggcGcccatggatgatccagtggg	13	12	1	1	rs79196288	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:136577775G>A	ENST00000371872.4	-	10	1551	c.1294C>T	c.(1294-1296)Cgc>Tgc	p.R432C	SARDH_ENST00000422262.2_Missense_Mutation_p.R264C|SARDH_ENST00000439388.1_Missense_Mutation_p.R432C	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	432					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.R432C(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TTCTCCGGGCGCCCATGGATG	0.637													G|||	5	0.000998403	8e-04	0	5008	,	,		16296	0.004		0	False		,,,				2504	0															1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	9											66	66	66					9																	136577775		2203	4300	6503	135567596	SO:0001583	missense	1757				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1294C>T	9.37:g.136577775G>A	ENSP00000360938:p.Arg432Cys		135567596	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	17.49	3.401866	0.62288	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227	D;D;D	0.85484	-1.99;-1.99;-1.99	4.68	3.77	0.43336	.	0.105347	0.64402	D	0.000003	D	0.88100	0.6346	M	0.82517	2.595	0.80722	D	1	D	0.71674	0.998	P	0.60886	0.88	D	0.90179	0.4241	10	0.87932	D	0	-28.7148	12.1658	0.54129	0.0834:0.0:0.9166:0.0	.	432	Q9UL12	SARDH_HUMAN	C	432;432;264;432;432	ENSP00000360938:R432C;ENSP00000403084:R432C;ENSP00000415537:R264C	ENSP00000360938:R432C	R	-	1	0	SARDH	135567596	1.000000	0.71417	0.997000	0.53966	0.336000	0.28762	6.415000	0.73328	2.140000	0.66376	0.563000	0.77884	CGC		0.637	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			A	136577775	G	A	136577775	3	1	85	1	0	0	0	0	1	0	0	0	13878	1087	38	1	1510	1	SARDH	9	136577775	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	2441211	136577775	4635656	75	23958										
CARD9	64170	hgsc.bcm.edu	37	chr9	139262114	139262114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cgagcgtctccagctgctgcCgcctgagcctgccctccacg	11	19	1	1	rs147340708		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:139262114C>T	ENST00000371732.5	-	8	1409	c.1244G>A	c.(1243-1245)cGg>cAg	p.R415Q	CARD9_ENST00000460290.1_5'Flank|CARD9_ENST00000371734.3_Missense_Mutation_p.R415Q	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	415					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CAGCTGCTGCCGCCTGAGCCT	0.721																																																0			9						C	GLN/ARG,GLN/ARG	1,4365		0,1,2182	23	22	23		1244,1244	2.8	1	9	dbSNP_134	23	0,8576		0,0,4288	no	missense,missense	CARD9	NM_052813.4,NM_052814.3	43,43	0,1,6470	TT,TC,CC		0.0,0.0229,0.0077	benign,benign	415/537,415/493	139262114	1,12941	2183	4288	6471	138381935	SO:0001583	missense	64170			AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.1244G>A	9.37:g.139262114C>T	ENSP00000360797:p.Arg415Gln		138381935	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	37	CCDS6997.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526213	0.44969	2.29E-4	0.0	ENSG00000187796	ENST00000371734;ENST00000371732	T;T	0.33865	1.39;1.39	3.76	2.8	0.32819	.	0.206543	0.30742	N	0.008964	T	0.23410	0.0566	L	0.37850	1.14	0.80722	D	1	B;B;B	0.23490	0.086;0.068;0.041	B;B;B	0.15052	0.012;0.012;0.003	T	0.06041	-1.0849	10	0.38643	T	0.18	-25.1955	5.4639	0.16632	0.0:0.813:0.0:0.187	.	311;415;415	B4DIK5;Q9H257-2;Q9H257	.;.;CARD9_HUMAN	Q	415	ENSP00000360799:R415Q;ENSP00000360797:R415Q	ENSP00000360797:R415Q	R	-	2	0	CARD9	138381935	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	2.016000	0.40971	0.810000	0.34279	0.591000	0.81541	CGG		0.721	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813		T	139262114	C	T	139262114	3	4	85	1	0	0	0	0	1	0	0	0	2658	652	23	1	443	1	CARD9	9	139262114	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	2684339	139262114	1951317	76	23959										
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139693652	139693667	+	Frame_Shift_Del	DEL	CAGGACTGGGCTTTGG	CAGGACTGGGCTTTGG	-													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcaacatccgccgcggggccCaggactgggctttggccaag							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	CAGGACTGGGCTTTGG	CAGGACTGGGCTTTGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr9:139693652_139693667delCAGGACTGGGCTTTGG	ENST00000338005.6	+	2	204_219	c.169_184delCAGGACTGGGCTTTGG	c.(169-186)caggactgggctttggccfs	p.QDWALA57fs	RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.17_ENST00000456614.2_Frame_Shift_Del_p.QDWALA113fs|RP11-216L13.18_ENST00000471502.1_RNA|KIAA1984_ENST00000371682.3_3'UTR	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		57										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CCGCGGGGCCCAGGACTGGGCTTTGGCCAAGAAGGT	0.648																																																0			9																																								138813488	SO:0001589	frameshift_variant	84960																														ENST00000338005.6:c.169_184delCAGGACTGGGCTTTGG	9.37:g.139693652_139693667delCAGGACTGGGCTTTGG	ENSP00000338013:p.Gln57fs		138813473	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Frame_Shift_Del	DEL	ENST00000338005.6	37	CCDS43906.1																																																																																				0.648	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			-	139693667	CAGGACTGGGCTTTGG	-	139693652	7	5	85	1	0	1	0	1	0	0	0	0	8287	595	21	0	175	0	KIAA1984	9	139693652	Frame_Shift_Del	DEL	CAGGACTGGGCTTTGG	TCGA-AH-6644-01A-21D-1826-10	431538	139693652	1519779	77	23960										
IL2RA	3559	hgsc.bcm.edu	37	chr10	6063567	6063567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tagagccctgtatccctggaCgcactgataataaaccatct	7	12	1	2	rs201188114	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr10:6063567C>T	ENST00000379959.3	-	4	630	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	IL2RA_ENST00000379954.1_Intron|IL2RA_ENST00000256876.6_Missense_Mutation_p.V153I	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	153	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	TATCCCTGGACGCACTGATAA	0.532													C|||	76	0.0151757	0	0	5008	,	,		20179	0		0	False		,,,				2504	0.0777															0			10											181	159	166					10																	6063567		2203	4300	6503	6103573	SO:0001583	missense	3559			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.457G>A	10.37:g.6063567C>T	ENSP00000369293:p.Val153Ile		6103573	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	37	CCDS7076.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.665796	0.00765	.	.	ENSG00000134460	ENST00000379959;ENST00000256876	T;T	0.64618	-0.11;-0.11	4.32	-8.63	0.00878	Complement control module (2);Sushi/SCR/CCP (3);	3.538250	0.00575	N	0.000303	T	0.25306	0.0615	N	0.00483	-1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39333	-0.9619	10	0.13470	T	0.59	-21.2916	10.7762	0.46350	0.0:0.1025:0.2484:0.6491	.	153	P01589	IL2RA_HUMAN	I	153	ENSP00000369293:V153I;ENSP00000256876:V153I	ENSP00000256876:V153I	V	-	1	0	IL2RA	6103573	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.365000	0.00245	-2.798000	0.00353	-0.827000	0.03088	GTC		0.532	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		T	6063567	C	T	6063567	3	4	85	1	0	0	0	0	1	0	0	0	7707	536	19	1	381	1	IL2RA	10	6063567	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		6063567	129471180	78	23961										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7682790	7682790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cttttctctctctgtaatttCgccctgatacaccttgtctc	4	14	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr10:7682790C>T	ENST00000256861.6	-	4	406	c.328G>A	c.(328-330)Gaa>Aaa	p.E110K	ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000434980.1_5'Flank|ITIH5_ENST00000397146.2_Missense_Mutation_p.E110K|ITIH5_ENST00000397145.2_Missense_Mutation_p.E110K	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	110	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TCTGTAATTTCGCCCTGATAC	0.373																																																0			10											226	219	221					10																	7682790		2203	4300	6503	7722796	SO:0001583	missense	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.328G>A	10.37:g.7682790C>T	ENSP00000256861:p.Glu110Lys		7722796	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	17.14	3.313441	0.60414	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.24350	1.86;1.86;1.86	5.71	4.81	0.61882	Vault protein inter-alpha-trypsin (2);	0.416738	0.28853	N	0.013929	T	0.17916	0.0430	.	.	.	0.42695	D	0.993593	P;P	0.46656	0.574;0.882	B;B	0.36289	0.036;0.221	T	0.02167	-1.1202	9	0.34782	T	0.22	-30.6759	12.0934	0.53739	0.0:0.9198:0.0:0.0802	.	110;110	G5E9D8;Q86UX2	.;ITIH5_HUMAN	K	110	ENSP00000256861:E110K;ENSP00000380333:E110K;ENSP00000380332:E110K	ENSP00000256861:E110K	E	-	1	0	ITIH5	7722796	0.998000	0.40836	0.999000	0.59377	0.777000	0.43975	3.418000	0.52721	2.678000	0.91216	0.563000	0.77884	GAA		0.373	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7682790	C	T	7682790	3	4	85	1	0	0	0	0	1	0	0	0	7928	893	31	1	2681	1	ITIH5	10	7682790	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	1619223	7682790	127851957	79	23962										
MSMB	4477	hgsc.bcm.edu	37	chr10	51562381	51562381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cccaaaaaagacctgttctgTcagtgaatggataatctaat	7	8	3	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr10:51562381T>C	ENST00000358559.2	+	4	413	c.326T>C	c.(325-327)gTc>gCc	p.V109A	NCOA4_ENST00000374087.4_5'Flank|MSMB_ENST00000298239.6_Missense_Mutation_p.S74P|NCOA4_ENST00000414907.2_5'Flank|NCOA4_ENST00000438493.1_5'Flank|NCOA4_ENST00000430396.2_5'Flank|NCOA4_ENST00000452682.1_5'Flank	NM_002443.3	NP_002434.1	P08118	MSMB_HUMAN	microseminoprotein, beta-	109						extracellular space (GO:0005615)|nucleus (GO:0005634)		p.V109D(1)		lung(4)|ovary(2)|prostate(1)	7						ACCTGTTCTGTCAGTGAATGG	0.468																																																1	Substitution - Missense(1)	ovary(1)	10											172	146	155					10																	51562381		2203	4300	6503	51232387	SO:0001583	missense	4477			BC005257	CCDS73095.1, CCDS73096.1	10q11.2	2014-05-06			ENSG00000138294	ENSG00000263639			7372	protein-coding gene	gene with protein product		157145				1783399	Standard	NM_002443		Approved	PSP-94, PSP57, PSP94, IGBF, MSP, MSPB, PN44, PRPS, PSP	uc001jiq.3	P08118	OTTHUMG00000188315	ENST00000358559.2:c.326T>C	10.37:g.51562381T>C	ENSP00000351363:p.Val109Ala		51232387	B1API6|P11999|Q13125|Q6IAY9|Q9UC59	Missense_Mutation	SNP	ENST00000358559.2	37	CCDS7235.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.19|13.19	2.163035|2.163035	0.38217|0.38217	.|.	.|.	ENSG00000138294|ENSG00000138294	ENST00000298239|ENST00000358559	T|T	0.28255|0.12984	1.62|2.63	4.18|4.18	4.18|4.18	0.49190|0.49190	.|.	.|0.451809	.|0.20798	.|N	.|0.085481	T|T	0.24509|0.24509	0.0594|0.0594	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D|D	0.76494|0.54964	0.999|0.969	D|P	0.72075|0.55112	0.976|0.769	T|T	0.03483|0.03483	-1.1032|-1.1032	8|9	0.87932|0.87932	D|D	0|0	-14.1726|-14.1726	9.9184|9.9184	0.41448|0.41448	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	74|109	P08118-2|P08118	.|MSMB_HUMAN	P|A	74|109	ENSP00000298239:S74P|ENSP00000351363:V109A	ENSP00000298239:S74P|ENSP00000351363:V109A	S|V	+|+	1|2	0|0	MSMB|MSMB	51232387|51232387	0.266000|0.266000	0.24112|0.24112	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	3.032000|3.032000	0.49736|0.49736	2.126000|2.126000	0.65437|0.65437	0.528000|0.528000	0.53228|0.53228	TCA|GTC		0.468	MSMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048034.1	NM_002443, NM_138634		C	51562381	T	C	51562381	3	2	85	1	0	0	0	0	1	0	0	0	9913	1667	58	4	340	4	MSMB	10	51562381	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	43879591	51562381	83972366	80	23963										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62648827	62648828	+	Frame_Shift_Ins	INS	-	-	AC													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgctcggattgcattgtcaaINSacacatccttgataccaaac							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr10:62648827_62648828insAC	ENST00000337910.5	-	6	935_936	c.598_599insGT	c.(598-600)tttfs	p.F200fs	RHOBTB1_ENST00000357917.4_Frame_Shift_Ins_p.F200fs	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	200	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					TGCATTGTCAAACACATCCTTG	0.47																																																0			10																																								62318834	SO:0001589	frameshift_variant	9886			AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.597_598dupGT	10.37:g.62648830_62648831dupAC	ENSP00000338671:p.Phe200fs		62318833		Frame_Shift_Ins	INS	ENST00000337910.5	37	CCDS7261.1																																																																																				0.47	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			AC	62648828	-	AC	62648827	7	5	85	1	0	1	1	0	0	0	0	0	13370	14	1	0	1515	0	RHOBTB1	10	62648827	Frame_Shift_Ins	INS	-	TCGA-AH-6644-01A-21D-1826-10	11086446	62648827	72885920	81	23964										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108357185	108357185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tgtactgagttttggttgagCgtgtggatcagcaattctga	13	5	2	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr10:108357185C>T	ENST00000263054.6	-	24	3196	c.3189G>A	c.(3187-3189)acG>acA	p.T1063T	SORCS1_ENST00000369698.1_Silent_p.T598T|SORCS1_ENST00000344440.6_Silent_p.T1063T|SORCS1_ENST00000478809.2_5'Flank	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1063					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.T1063T(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TTTGGTTGAGCGTGTGGATCA	0.433																																																1	Substitution - coding silent(1)	large_intestine(1)	10											150	139	143					10																	108357185		2203	4300	6503	108347175	SO:0001819	synonymous_variant	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3189G>A	10.37:g.108357185C>T			108347175	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	9.235	1.036802	0.19669	.	.	ENSG00000108018	ENST00000452214	.	.	.	5.71	-0.0738	0.13733	.	.	.	.	.	T	0.40196	0.1107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27468	-1.0073	4	.	.	.	-12.778	0.9283	0.01329	0.2442:0.3528:0.1199:0.283	.	.	.	.	H	78	.	.	R	-	2	0	SORCS1	108347175	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	0.675000	0.25232	0.323000	0.23307	-0.181000	0.13052	CGC		0.433	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108357185	C	T	108357185	2	4	85	1	0	0	0	0	0	0	0	1	14967	755	27	1		1	SORCS1	10	108357185	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	45708358	108357185	27177562	82	23965										
IFITM5	387733	hgsc.bcm.edu	37	chr11	299396	299396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agatcaagtggtctcgaggcGgggggtgcggggcccccagt	19	10	2	1	rs142041432		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:299396G>A	ENST00000382614.2	-	1	130	c.95C>T	c.(94-96)cCg>cTg	p.P32L		NM_001025295.2	NP_001020466.1	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	32					bone mineralization (GO:0030282)|regulation of bone mineralization (GO:0030500)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		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;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTCTCGAGGCGGGGGGTGCGG	0.677													g|||	1	0.000199681	8e-04	0	5008	,	,		8764	0		0	False		,,,				2504	0															0			11						G	LEU/PRO	9,4363		0,9,2177	27	24	25		95	2.8	0	11	dbSNP_134	25	0,8568		0,0,4284	yes	missense	IFITM5	NM_001025295.1	98	0,9,6461	AA,AG,GG		0.0,0.2059,0.0696	benign	32/133	299396	9,12931	2186	4284	6470	289396	SO:0001583	missense	387733			AA463818, CR747200, DY654432	CCDS31323.1	11p15.5	2010-05-12			ENSG00000206013	ENSG00000206013			16644	protein-coding gene	gene with protein product		614757				11106657, 12659663, 18442316	Standard	NM_001025295		Approved	fragilis4, Hrmp1, BRIL	uc001low.2	A6NNB3	OTTHUMG00000165355	ENST00000382614.2:c.95C>T	11.37:g.299396G>A	ENSP00000372059:p.Pro32Leu		289396		Missense_Mutation	SNP	ENST00000382614.2	37	CCDS31323.1	.	.	.	.	.	.	.	.	.	.	G	6.223	0.409312	0.11812	0.002059	0.0	ENSG00000206013	ENST00000382614	D	0.86164	-2.08	3.77	2.84	0.33178	.	0.155904	0.42682	D	0.000665	T	0.74839	0.3769	N	0.25144	0.715	0.35078	D	0.763142	B	0.25007	0.116	B	0.18561	0.022	T	0.69296	-0.5182	10	0.22706	T	0.39	-9.9755	8.6	0.33738	0.1189:0.0:0.8811:0.0	.	32	A6NNB3	IFM5_HUMAN	L	32	ENSP00000372059:P32L	ENSP00000372059:P32L	P	-	2	0	IFITM5	289396	0.306000	0.24490	0.002000	0.10522	0.017000	0.09413	0.844000	0.27654	0.547000	0.28938	0.561000	0.74099	CCG		0.677	IFITM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383588.1	NM_001025295		A	299396	G	A	299396	3	1	85	1	0	0	0	0	1	0	0	0	7550	1116	39	1	311	1	IFITM5	11	299396	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10		299396	134707120	83	23966										
SYT8	90019	hgsc.bcm.edu	37	chr11	1857174	1857174	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggatgctcagcaatgggggtGcctgcagctctccctggagt	15	11	2	0	rs190754396		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:1857174G>T	ENST00000381968.3	+	4	487	c.359G>T	c.(358-360)tGc>tTc	p.C120F	SYT8_ENST00000535046.1_Missense_Mutation_p.C258F|SYT8_ENST00000341958.3_Missense_Mutation_p.C106F|SYT8_ENST00000483280.1_3'UTR|SYT8_ENST00000436964.2_Missense_Mutation_p.C106F	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	120	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		C -> R (in dbSNP:rs564271). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CAATGGGGGTGCCTGCAGCTC	0.632																																																0			11											47	50	49					11																	1857174		2202	4299	6501	1813750	SO:0001583	missense	90019			AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"Synaptotagmins"	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.359G>T	11.37:g.1857174G>T	ENSP00000371394:p.Cys120Phe		1813750	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	.	.	.	.	.	.	.	.	.	.	g	6.469	0.454703	0.12283	.	.	ENSG00000149043	ENST00000436964;ENST00000535046;ENST00000381968;ENST00000341958	T;T;T;T	0.18174	2.27;2.23;3.19;3.19	3.54	1.32	0.21799	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.09158	0.0226	N	0.14661	0.345	0.09310	N	1	B;B;B	0.28584	0.216;0.001;0.005	B;B;B	0.24701	0.055;0.0;0.0	T	0.28839	-1.0031	9	0.87932	D	0	.	5.5656	0.17168	0.1981:0.1618:0.64:0.0	.	106;120;106	C9JSK3;Q8NBV8;A6NCR4	.;SYT8_HUMAN;.	F	106;258;120;106	ENSP00000414626:C106F;ENSP00000443325:C258F;ENSP00000371394:C120F;ENSP00000343691:C106F	ENSP00000343691:C106F	C	+	2	0	SYT8	1813750	0.002000	0.14202	0.585000	0.28666	0.233000	0.25261	1.297000	0.33400	0.579000	0.29504	0.305000	0.20034	TGC		0.632	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4			T	1857174	G	T	1857174	3	4	85	1	0	0	0	0	1	0	0	0	15519	1319	46	2	373	2	SYT8	11	1857174	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	1557778	1857174	133149342	84	23967										
USH1C	10083	hgsc.bcm.edu	37	chr11	17552956	17552957	+	Frame_Shift_Del	DEL	GG	GG	-													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tcctctgcacctggagcgccGgggggtcagctgatcatatt							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:17552956_17552957delGG	ENST00000318024.4	-	3	345_346	c.237_238delCC	c.(235-240)ccccggfs	p.R81fs	USH1C_ENST00000005226.7_Frame_Shift_Del_p.R81fs|USH1C_ENST00000527720.1_Frame_Shift_Del_p.R50fs|USH1C_ENST00000527020.1_Frame_Shift_Del_p.R81fs	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	81	N-terminal domain.				auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CTGGAGCGCCGGGGGGTCAGCT	0.624																																																0			11																																								17509533	SO:0001589	frameshift_variant	10083			AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.237_238delCC	11.37:g.17552960_17552961delGG	ENSP00000317018:p.Arg81fs		17509532	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Frame_Shift_Del	DEL	ENST00000318024.4	37	CCDS31438.1																																																																																				0.624	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		-	17552957	GG	-	17552956	7	5	85	1	0	1	0	1	0	0	0	0	17074	1115	39	0	2639	0	USH1C	11	17552956	Frame_Shift_Del	DEL	GG	TCGA-AH-6644-01A-21D-1826-10	15695782	17552956	117453560	85	23968										
FAM111A	63901	hgsc.bcm.edu	37	chr11	58920237	58920237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	acttattctgggacagtgcaActacgggttacgccacctgc	10	12	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:58920237A>G	ENST00000528737.1	+	5	3914	c.1096A>G	c.(1096-1098)Act>Gct	p.T366A	FAM111A_ENST00000533703.1_Missense_Mutation_p.T366A|FAM111A_ENST00000531147.1_Missense_Mutation_p.T366A|FAM111A_ENST00000420244.1_Missense_Mutation_p.T366A|FAM111A_ENST00000361723.3_Missense_Mutation_p.T366A			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	366	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				GGACAGTGCAACTACGGGTTA	0.393																																																0			11											108	107	107					11																	58920237		2201	4295	6496	58676813	SO:0001583	missense	63901			AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1096A>G	11.37:g.58920237A>G	ENSP00000434435:p.Thr366Ala		58676813	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	CCDS7973.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971006	0.34754	.	.	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.73	3.32	0.38043	Peptidase cysteine/serine, trypsin-like (1);	1.020260	0.07794	N	0.955349	T	0.35828	0.0945	L	0.44542	1.39	0.09310	N	1	B	0.20164	0.042	B	0.16289	0.015	T	0.29366	-1.0014	10	0.46703	T	0.11	-18.0317	7.362	0.26752	0.7064:0.1503:0.0:0.1433	.	366	Q96PZ2	F111A_HUMAN	A	366	ENSP00000434435:T366A;ENSP00000406683:T366A;ENSP00000355264:T366A;ENSP00000433154:T366A;ENSP00000431631:T366A	ENSP00000355264:T366A	T	+	1	0	FAM111A	58676813	0.003000	0.15002	0.000000	0.03702	0.006000	0.05464	1.361000	0.34136	0.476000	0.27440	0.533000	0.62120	ACT		0.393	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		G	58920237	A	G	58920237	3	3	85	1	0	0	0	0	1	0	0	0	5415	43	2	4	1102	4	FAM111A	11	58920237	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	41367281	58920237	76086279	86	23969										
C11orf9	745	hgsc.bcm.edu	37	chr11	61548455	61548455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cagccagagctttgggaccaCgcagctccgacagtccccct	10	17	0	1	rs200193085		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:61548455C>T	ENST00000278836.5	+	20	2606	c.2510C>T	c.(2509-2511)aCg>aTg	p.T837M	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Missense_Mutation_p.T802M|MYRF_ENST00000389602.4_Missense_Mutation_p.T228M	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	837					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTTGGGACCACGCAGCTCCGA	0.647																																																0			11											71	67	69					11																	61548455		2202	4299	6501	61305031	SO:0001583	missense	745				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2510C>T	11.37:g.61548455C>T	ENSP00000278836:p.Thr837Met		61305031	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	37	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647910	0.87958	.	.	ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000389602	T;T;T	0.33865	1.39;1.4;1.41	5.19	5.19	0.71726	.	0.156344	0.42548	D	0.000686	T	0.54287	0.1849	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;P	0.66602	0.945;0.897;0.84	T	0.53500	-0.8430	10	0.54805	T	0.06	-7.6456	16.6024	0.84819	0.0:1.0:0.0:0.0	.	228;802;837	B4DHB2;Q9Y2G1-2;Q9Y2G1	.;.;MRF_HUMAN	M	837;802;228	ENSP00000278836:T837M;ENSP00000265460:T802M;ENSP00000374253:T228M	ENSP00000265460:T802M	T	+	2	0	C11orf9	61305031	0.977000	0.34250	1.000000	0.80357	0.990000	0.78478	1.813000	0.38962	2.586000	0.87340	0.655000	0.94253	ACG		0.647	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		T	61548455	C	T	61548455	3	4	85	1	0	0	0	0	1	0	0	0	1675	536	19	1	2614	1	C11orf9	11	61548455	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	2628218	61548455	73458061	87	23970										
SIPA1	6494	hgsc.bcm.edu	37	chr11	65417427	65417427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccttgtgcccacagtcatgtCggaggcgggcagtgggaccc	15	13	1	0	rs371556373	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:65417427C>T	ENST00000394224.3	+	13	3049	c.2753C>T	c.(2752-2754)tCg>tTg	p.S918L	SIPA1_ENST00000534313.1_Missense_Mutation_p.S918L|SIPA1_ENST00000527525.1_Missense_Mutation_p.S816L|MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000394227.3_Missense_Mutation_p.S816L	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	918					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						ACAGTCATGTCGGAGGCGGGC	0.632													C|||	2	0.000399361	8e-04	0	5008	,	,		18156	0.001		0	False		,,,				2504	0															0			11						C	LEU/SER,LEU/SER	2,4400	4.2+/-10.8	0,2,2199	67	70	69		2753,2753	4.3	0.9	11		69	0,8594		0,0,4297	no	missense,missense	SIPA1	NM_006747.3,NM_153253.29	145,145	0,2,6496	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	918/1043,918/1043	65417427	2,12994	2201	4297	6498	65174003	SO:0001583	missense	6494			AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2753C>T	11.37:g.65417427C>T	ENSP00000377771:p.Ser918Leu		65174003	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.335414	0.60853	4.54E-4	0.0	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.87029	-2.12;-2.2;-2.12;-2.2	4.26	4.26	0.50523	.	0.000000	0.47455	U	0.000224	D	0.88702	0.6508	L	0.32530	0.975	0.34926	D	0.748864	D;D	0.89917	1.0;0.98	D;B	0.79108	0.992;0.366	D	0.91070	0.4892	10	0.45353	T	0.12	-10.5652	12.1843	0.54229	0.0:1.0:0.0:0.0	.	816;918	F6RY50;Q96FS4	.;SIPA1_HUMAN	L	918;816;918;816	ENSP00000436269:S918L;ENSP00000433686:S816L;ENSP00000377771:S918L;ENSP00000377774:S816L	ENSP00000377771:S918L	S	+	2	0	SIPA1	65174003	1.000000	0.71417	0.856000	0.33681	0.361000	0.29550	5.953000	0.70290	1.929000	0.55896	0.297000	0.19635	TCG		0.632	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		T	65417427	C	T	65417427	3	4	85	1	0	0	0	0	1	0	0	0	14365	893	31	1	2799	1	SIPA1	11	65417427	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	3868972	65417427	69589089	88	23971										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65788339	65788339	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	atccagcgtgagcaaggtgaAgagggtgaagatggtggtga	18	4	0	6			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:65788339A>G	ENST00000312106.5	-	6	2007	c.1870T>C	c.(1870-1872)Ttc>Ctc	p.F624L		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	624					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						AGCAAGGTGAAGAGGGTGAAG	0.627																																																0			11											126	81	96					11																	65788339		2201	4296	6497	65544915	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1870T>C	11.37:g.65788339A>G	ENSP00000309052:p.Phe624Leu		65544915	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.583444	0.86748	.	.	ENSG00000175294	ENST00000312106	D	0.99136	-5.47	4.43	4.43	0.53597	Ion transport (1);	0.000000	0.35903	N	0.002910	D	0.98887	0.9623	M	0.68317	2.08	0.41036	D	0.985199	D	0.76494	0.999	D	0.80764	0.994	D	0.99577	1.0972	10	0.72032	D	0.01	-36.8504	10.0079	0.41968	1.0:0.0:0.0:0.0	.	624	Q8NEC5	CTSR1_HUMAN	L	624	ENSP00000309052:F624L	ENSP00000309052:F624L	F	-	1	0	CATSPER1	65544915	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.360000	0.66086	1.863000	0.54032	0.459000	0.35465	TTC		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		G	65788339	A	G	65788339	3	3	85	1	0	0	0	0	1	0	0	0	2693	72	3	4	500	4	CATSPER1	11	65788339	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	370912	65788339	69218177	89	23972										
CAPN5	726	hgsc.bcm.edu	37	chr11	76795984	76795984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agaactactcagccctgaggCgggactgccggcgcaggaag	15	12	1	2	rs149132399	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:76795984C>T	ENST00000278559.3	+	2	241	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	CAPN5_ENST00000531028.1_Missense_Mutation_p.R18W|CAPN5_ENST00000529629.1_Missense_Mutation_p.R18W|CAPN5_ENST00000456580.2_Missense_Mutation_p.R18W	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	18				R -> Q (in Ref. 1; AAC51869). {ECO:0000305}.	proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						AGCCCTGAGGCGGGACTGCCG	0.652																																																0			11						C	TRP/ARG	8,4392	14.3+/-33.2	0,8,2192	50	52	51		52	3.1	1	11	dbSNP_134	51	0,8584	1.2+/-3.3	0,0,4292	yes	missense	CAPN5	NM_004055.4	101	0,8,6484	TT,TC,CC		0.0,0.1818,0.0616	probably-damaging	18/641	76795984	8,12976	2200	4292	6492	76473632	SO:0001583	missense	726				CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.52C>T	11.37:g.76795984C>T	ENSP00000278559:p.Arg18Trp		76473632	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.32	2.500376	0.44455	0.001818	0.0	ENSG00000149260	ENST00000278559;ENST00000527066;ENST00000530987;ENST00000360841;ENST00000529629;ENST00000456580;ENST00000544318	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.18	3.1	0.35709	Peptidase C2, calpain, catalytic domain (1);	0.120863	0.53938	D	0.000049	T	0.61185	0.2327	M	0.76170	2.325	0.48452	D	0.999657	D;D;D;D	0.76494	0.999;0.997;0.997;0.998	P;P;P;P	0.59424	0.857;0.821;0.821;0.803	T	0.65537	-0.6144	10	0.87932	D	0	.	10.3217	0.43769	0.539:0.4609:0.0:0.0	.	56;18;58;18	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	W	18;18;18;58;18;18;18	ENSP00000278559:R18W;ENSP00000435894:R18W;ENSP00000432332:R18W;ENSP00000409996:R18W	ENSP00000278559:R18W	R	+	1	2	CAPN5	76473632	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	4.768000	0.62293	1.156000	0.42514	0.655000	0.94253	CGG		0.652	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		T	76795984	C	T	76795984	3	4	85	1	0	0	0	0	1	0	0	0	2635	759	27	1	54	1	CAPN5	11	76795984	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	11007645	76795984	58210532	90	23973										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106579265	106579265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tggttgggctgacattgatgCgccgagggtgacttcccgac	15	10	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:106579265C>T	ENST00000526355.2	-	7	2432	c.1964G>A	c.(1963-1965)cGc>cAc	p.R655H	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.R676H|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.R686H	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	655					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	GACATTGATGCGCCGAGGGTG	0.522																																																0			11											158	150	153					11																	106579265		2201	4298	6499	106084475	SO:0001583	missense	2977			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.1964G>A	11.37:g.106579265C>T	ENSP00000431245:p.Arg655His		106084475	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.617047	0.87359	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.81579	-1.51;-1.51;-1.51	6.02	5.11	0.69529	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.146255	0.31495	N	0.007559	D	0.89361	0.6693	M	0.80183	2.485	0.45946	D	0.998774	D;D;B	0.89917	0.999;1.0;0.066	D;D;B	0.70487	0.95;0.969;0.019	D	0.90721	0.4635	10	0.72032	D	0.01	.	14.5493	0.68054	0.0:0.9302:0.0:0.0698	.	676;686;655	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	H	655;686;676	ENSP00000431245:R655H;ENSP00000282249:R686H;ENSP00000344874:R676H	ENSP00000282249:R686H	R	-	2	0	GUCY1A2	106084475	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.910000	0.63321	1.561000	0.49584	0.655000	0.94253	CGC		0.522	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			T	106579265	C	T	106579265	3	4	85	1	0	0	0	0	1	0	0	0	6914	768	27	1	242	1	GUCY1A2	11	106579265	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	29783281	106579265	28427251	91	23974										
C11orf57	55216	hgsc.bcm.edu	37	chr11	111953315	111953316	+	Frame_Shift_Ins	INS	-	-	A													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agcagaaaaaaaggtcacacINSaaaaaacagaagaaaagcaa							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr11:111953315_111953316insA	ENST00000280352.9	+	6	1134_1135	c.498_499insA	c.(499-501)aaafs	p.K167fs	C11orf57_ENST00000420986.2_Frame_Shift_Ins_p.K167fs|C11orf57_ENST00000532163.1_Frame_Shift_Ins_p.K139fs|C11orf57_ENST00000393047.3_Frame_Shift_Ins_p.K168fs|TIMM8B_ENST00000507614.1_5'Flank	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	167	Lys-rich.									autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGGTCACACAAAAAACAGAA	0.411																																																0			11																																								111458526	SO:0001589	frameshift_variant	55216			BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.504dupA	11.37:g.111953321_111953321dupA	ENSP00000339076:p.Lys167fs		111458525	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Ins	INS	ENST00000280352.9	37	CCDS41715.1																																																																																				0.411	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		A	111953316	-	A	111953315	7	5	85	1	0	1	1	0	0	0	0	0	1654	477	17	0	519	0	C11orf57	11	111953315	Frame_Shift_Ins	INS	-	TCGA-AH-6644-01A-21D-1826-10	5374050	111953315	23053201	92	23975										
CLEC4D	338339	hgsc.bcm.edu	37	chr12	8667891	8667891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttgctgtagttttcatcttaCttctcagtgtctgttttatt	6	7	4	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr12:8667891C>T	ENST00000299665.2	+	2	281	c.88C>T	c.(88-90)Ctt>Ttt	p.L30F		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	30					innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					TTTCATCTTACTTCTCAGTGT	0.378																																																0			12											242	204	217					12																	8667891		2203	4300	6503	8559158	SO:0001583	missense	338339			AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"C-type lectin domain containing"	14554	protein-coding gene	gene with protein product		609964	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.88C>T	12.37:g.8667891C>T	ENSP00000299665:p.Leu30Phe		8559158	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	37	CCDS8593.1	.	.	.	.	.	.	.	.	.	.	C	0.631	-0.817207	0.02776	.	.	ENSG00000166527	ENST00000382064;ENST00000299665	T;T	0.12039	2.72;3.24	3.36	-1.06	0.10002	.	.	.	.	.	T	0.07773	0.0195	L	0.31371	0.925	0.09310	N	1	B	0.20368	0.044	B	0.17722	0.019	T	0.37549	-0.9701	9	0.37606	T	0.19	.	1.3817	0.02231	0.3793:0.3121:0.1864:0.1222	.	30	Q8WXI8	CLC4D_HUMAN	F	30	ENSP00000371496:L30F;ENSP00000299665:L30F	ENSP00000299665:L30F	L	+	1	0	CLEC4D	8559158	0.000000	0.05858	0.031000	0.17742	0.011000	0.07611	-0.997000	0.03705	-0.231000	0.09825	0.549000	0.68633	CTT		0.378	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387		T	8667891	C	T	8667891	3	4	85	1	0	0	0	0	1	0	0	0	3520	565	20	3	94	3	CLEC4D	12	8667891	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		8667891	125184004	93	23976										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	85	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	16730393	25398284	108453611	94	23977										
PAN2	9924	hgsc.bcm.edu	37	chr12	56718842	56718842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gaatgtggggctctaatccaGcaaacaaggtcttattgtag	11	7	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr12:56718842G>A	ENST00000425394.2	-	10	1926	c.1550C>T	c.(1549-1551)gCt>gTt	p.A517V	PAN2_ENST00000440411.3_Missense_Mutation_p.A517V|PAN2_ENST00000548043.1_Missense_Mutation_p.A517V|PAN2_ENST00000257931.5_Missense_Mutation_p.A517V	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CTCTAATCCAGCAAACAAGGT	0.448																																																0			12											224	214	218					12																	56718842		2203	4300	6503	55005109	SO:0001583	missense	147945			AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1550C>T	12.37:g.56718842G>A	ENSP00000401721:p.Ala517Val		55005109		Missense_Mutation	SNP	ENST00000425394.2	37	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884227	0.91814	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	4.85	4.85	0.62838	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (1);	0.000000	0.85682	D	0.000000	T	0.11707	0.0285	L	0.46670	1.46	0.80722	D	1	P;P;P	0.51057	0.909;0.909;0.941	P;P;P	0.53313	0.58;0.58;0.723	T	0.02683	-1.1124	10	0.42905	T	0.14	-11.9064	17.1133	0.86682	0.0:0.0:1.0:0.0	.	517;517;517	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	V	517	ENSP00000401721:A517V;ENSP00000388231:A517V;ENSP00000257931:A517V;ENSP00000449861:A517V	ENSP00000257931:A517V	A	-	2	0	PAN2	55005109	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.735000	0.98825	2.404000	0.81709	0.557000	0.71058	GCT		0.448	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		A	56718842	G	A	56718842	3	1	85	1	0	0	0	0	1	0	0	0	11445	971	34	3	2126	3	PAN2	12	56718842	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	31320558	56718842	77133053	95	23978										
CCDC59	29080	hgsc.bcm.edu	37	chr12	82747086	82747086	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctctcctgttttctcctctcGaattcctaaaattattaaca	2	12	3	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr12:82747086G>A	ENST00000256151.7	-	4	981	c.570C>T	c.(568-570)ttC>ttT	p.F190F	CCDC59_ENST00000548126.1_5'UTR	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	190					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						TTCTCCTCTCGAATTCCTAAA	0.328																																																0			12											91	86	87					12																	82747086		2203	4299	6502	81271217	SO:0001819	synonymous_variant	29080			AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.570C>T	12.37:g.82747086G>A			81271217	Q9H2V5|Q9NW62	Silent	SNP	ENST00000256151.7	37	CCDS9023.1																																																																																				0.328	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		A	82747086	G	A	82747086	2	1	85	1	0	0	0	0	0	0	0	1	2835	1049	37	1		1	CCDC59	12	82747086	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	26028244	82747086	51104809	96	23979										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25828083	25828083	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tggtgagacttcctttgggtCaccatccaactggccacacc	9	14	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr13:25828083C>T	ENST00000381801.5	-	11	1926	c.1165G>A	c.(1165-1167)Gac>Aac	p.D389N	MTMR6_ENST00000540661.1_Missense_Mutation_p.D389N	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	389	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TCCTTTGGGTCACCATCCAAC	0.408																																																0			13											95	83	88					13																	25828083		2203	4300	6503	24726083	SO:0001583	missense	9107			AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1165G>A	13.37:g.25828083C>T	ENSP00000371221:p.Asp389Asn		24726083	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	37	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	C	34	5.347414	0.95807	.	.	ENSG00000139505	ENST00000540661;ENST00000541021;ENST00000381801	D;D	0.90133	-2.62;-2.62	5.66	5.66	0.87406	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.92394	0.7586	L	0.49571	1.57	0.80722	D	1	D;P	0.55605	0.972;0.817	P;P	0.54026	0.74;0.456	D	0.91985	0.5598	10	0.49607	T	0.09	.	19.7417	0.96234	0.0:1.0:0.0:0.0	.	389;389	Q9Y217;Q9Y217-2	MTMR6_HUMAN;.	N	389	ENSP00000443161:D389N;ENSP00000371221:D389N	ENSP00000371221:D389N	D	-	1	0	MTMR6	24726083	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.767000	0.85331	2.665000	0.90641	0.650000	0.86243	GAC		0.408	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		T	25828083	C	T	25828083	3	4	85	1	0	0	0	0	1	0	0	0	9977	826	29	3	716	3	MTMR6	13	25828083	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		25828083	89341795	97	23980										
C13orf30	144809	hgsc.bcm.edu	37	chr13	43362741	43362741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccctaggctatattactcaaCgggaagccttgtcttatgct	8	11	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr13:43362741C>T	ENST00000537894.1	+	4	358	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	FAM216B_ENST00000313851.1_Missense_Mutation_p.R79W	NM_182508.2	NP_872314.1	Q8N7L0	F216B_HUMAN	family with sequence similarity 216, member B	79																	TATTACTCAACGGGAAGCCTT	0.388																																																0			13											107	106	106					13																	43362741		2203	4300	6503	42260741	SO:0001583	missense	144809			AK098238	CCDS9386.1	13q14.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000179813	ENSG00000179813			26883	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 30"	C13orf30			Standard	NM_182508		Approved	FLJ40919	uc010tfk.2	Q8N7L0	OTTHUMG00000016809	ENST00000537894.1:c.235C>T	13.37:g.43362741C>T	ENSP00000445786:p.Arg79Trp		42260741	B1ALI3	Missense_Mutation	SNP	ENST00000537894.1	37	CCDS9386.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549158	0.45383	.	.	ENSG00000179813	ENST00000537894;ENST00000313851	T;T	0.50548	0.74;0.74	4.21	2.43	0.29744	.	0.978989	0.08323	N	0.963563	T	0.43765	0.1262	N	0.22421	0.69	0.09310	N	1	D	0.63880	0.993	P	0.50896	0.653	T	0.34229	-0.9837	10	0.72032	D	0.01	0.0844	9.4108	0.38491	0.3849:0.6151:0.0:0.0	.	79	Q8N7L0	CM030_HUMAN	W	79	ENSP00000445786:R79W;ENSP00000319336:R79W	ENSP00000319336:R79W	R	+	1	2	C13orf30	42260741	0.001000	0.12720	0.178000	0.23040	0.905000	0.53344	0.159000	0.16442	0.685000	0.31468	0.655000	0.94253	CGG		0.388	FAM216B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044705.2	NM_182508		T	43362741	C	T	43362741	3	4	85	1	0	0	0	0	1	0	0	0	1729	527	19	1	245	1	C13orf30	13	43362741	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	17534658	43362741	71807137	98	23981										
CCNB1IP1	57820	hgsc.bcm.edu	37	chr14	20784386	20784386	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aaactagactaagcactaacCtgatatgtccagaaggccag	8	10	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr14:20784386C>A	ENST00000398169.3	-	5	913	c.297G>T	c.(295-297)caG>caT	p.Q99H	CCNB1IP1_ENST00000437553.2_Splice_Site_p.Q99H|CCNB1IP1_ENST00000353689.4_Splice_Site_p.Q99H|CCNB1IP1_ENST00000358932.4_Splice_Site_p.Q99H|CCNB1IP1_ENST00000398160.2_Splice_Site_p.Q99H|CCNB1IP1_ENST00000398163.2_Splice_Site_p.Q99H			Q9NPC3	CIP1_HUMAN	cyclin B1 interacting protein 1, E3 ubiquitin protein ligase	99					blastocyst formation (GO:0001825)|chiasma assembly (GO:0051026)|protein ubiquitination (GO:0016567)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		HMGA2/CCNB1IP1(2)	breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	9	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;8.86e-07)|all cancers(55;4.98e-06)	GBM - Glioblastoma multiforme(265;0.0164)		AAGCACTAACCTGATATGTCC	0.413			T	HMGA2	leiomyoma																																		Dom	yes		14	14q11.2	57820	"cyclin B1 interacting protein 1, E3 ubiquitin protein ligase"		M	0			14											63	65	64					14																	20784386		2203	4300	6503	19854226	SO:0001630	splice_region_variant	57820			AF216381	CCDS9547.1	14q11.2	2014-02-04	2011-01-31	2004-01-14	ENSG00000100814	ENSG00000100814			19437	protein-coding gene	gene with protein product	"human enhancer of invasion 10"	608249	"chromosome 14 open reading frame 18", "cyclin B1 interacting protein 1"	C14orf18		12612082, 21779533	Standard	NM_021178		Approved	HEI10	uc001vwy.4	Q9NPC3	OTTHUMG00000029509	ENST00000398169.3:c.297+1G>T	14.37:g.20784386C>A			19854226		Missense_Mutation	SNP	ENST00000398169.3	37	CCDS9547.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.722659	0.89298	.	.	ENSG00000100814	ENST00000398160;ENST00000398169;ENST00000358932;ENST00000353689;ENST00000437553;ENST00000398163;ENST00000557665	.	.	.	6.07	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.80665	0.4666	M	0.84433	2.695	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.83214	-0.0072	8	.	.	.	-11.7759	14.171	0.65510	0.0:0.9276:0.0:0.0724	.	99	Q9NPC3	CIP1_HUMAN	H	99	.	.	Q	-	3	2	CCNB1IP1	19854226	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.287000	0.65645	1.578000	0.49821	0.655000	0.94253	CAG		0.413	CCNB1IP1-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073538.3	NM_021178, NM_182849, NM_182851, NM_182852	Missense_Mutation	A	20784386	C	A	20784386	5	1	85	1	0	0	0	0	0	0	1	0	2918	695	24	2	548	2	CCNB1IP1	14	20784386	Splice_Site	SNP	C	TCGA-AH-6644-01A-21D-1826-10		20784386	86565154	99	23982										
KLHDC2	23588	hgsc.bcm.edu	37	chr14	50241377	50241377	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cttgtttggaggacaccattCaagaggcaataccaataagg	10	8	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr14:50241377C>G	ENST00000298307.5	+	3	1193	c.332C>G	c.(331-333)tCa>tGa	p.S111*	KLHDC2_ENST00000557247.1_Nonsense_Mutation_p.S111*|KLHDC2_ENST00000554589.1_Nonsense_Mutation_p.S111*|KLHDC2_ENST00000553538.1_3'UTR	NM_014315.2	NP_055130.1	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	111						nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	all_epithelial(31;0.000959)|Breast(41;0.0117)					GGACACCATTCAAGAGGCAAT	0.393																																																0			14											240	226	231					14																	50241377		2203	4300	6503	49311127	SO:0001587	stop_gained	23588			AK001771	CCDS9693.1	14q21.3	2003-01-15			ENSG00000165516	ENSG00000165516			20231	protein-coding gene	gene with protein product		611280				11384994	Standard	NM_014315		Approved	HCLP-1, LCP	uc001wwx.3	Q9Y2U9	OTTHUMG00000140288	ENST00000298307.5:c.332C>G	14.37:g.50241377C>G	ENSP00000298307:p.Ser111*		49311127	B3KPF9|Q6IAF0|Q86TY9	Nonsense_Mutation	SNP	ENST00000298307.5	37	CCDS9693.1	.	.	.	.	.	.	.	.	.	.	C	44	10.884797	0.99483	.	.	ENSG00000165516	ENST00000298307;ENST00000554589;ENST00000557247	.	.	.	5.86	5.86	0.93980	.	0.060409	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-14.0293	20.1781	0.98191	0.0:1.0:0.0:0.0	.	.	.	.	X	111	.	ENSP00000298307:S111X	S	+	2	0	KLHDC2	49311127	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	4.370000	0.59517	2.778000	0.95560	0.591000	0.81541	TCA		0.393	KLHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276869.1			G	50241377	C	G	50241377	4	3	85	1	0	0	0	0	0	1	0	0	8377	838	29	5	342	5	KLHDC2	14	50241377	Nonsense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	29456991	50241377	57108163	100	23983										
PRTG	283659	hgsc.bcm.edu	37	chr15	55919279	55919279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggctatgccaacacctacagCaatgccagtcattgattttt	7	11	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr15:55919279C>T	ENST00000389286.4	-	17	2901	c.2854G>A	c.(2854-2856)Gct>Act	p.A952T		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ACACCTACAGCAATGCCAGTC	0.373																																																0			15											117	113	115					15																	55919279		1929	4134	6063	53706571	SO:0001583	missense	283659			AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2854G>A	15.37:g.55919279C>T	ENSP00000373937:p.Ala952Thr		53706571		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.585947	0.46110	.	.	ENSG00000166450	ENST00000389286	T	0.50001	0.76	5.17	3.28	0.37604	.	0.391879	0.28635	N	0.014655	T	0.34077	0.0885	L	0.29908	0.895	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.18241	-1.0343	10	0.54805	T	0.06	-12.3768	9.8547	0.41079	0.0:0.8355:0.0:0.1645	.	952	Q2VWP7	PRTG_HUMAN	T	952	ENSP00000373937:A952T	ENSP00000373937:A952T	A	-	1	0	PRTG	53706571	0.998000	0.40836	0.770000	0.31555	0.997000	0.91878	2.325000	0.43840	1.188000	0.43014	0.557000	0.71058	GCT		0.373	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		T	55919279	C	T	55919279	3	4	85	1	0	0	0	0	1	0	0	0	12672	710	25	3	614	3	PRTG	15	55919279	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		55919279	46612113	101	23984										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65703614	65703614	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcagcccccaggctacagttTagcactgcagcctgctctgg	11	15	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr15:65703614T>A	ENST00000352385.2	-	2	374	c.165A>T	c.(163-165)ctA>ctT	p.L55L		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	55	Ig-like C2-type 1.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GGCTACAGTTTAGCACTGCAG	0.647																																																0			15											39	36	37					15																	65703614		2201	4299	6500	63490667	SO:0001819	synonymous_variant	57722				CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.165A>T	15.37:g.65703614T>A			63490667	Q9HCE4	Silent	SNP	ENST00000352385.2	37	CCDS10206.1																																																																																				0.647	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65703614	T	A	65703614	2	1	85	1	0	0	0	0	0	0	0	1	7590	1741	61	5		5	IGDCC4	15	65703614	Silent	SNP	T	TCGA-AH-6644-01A-21D-1826-10	9784335	65703614	36827778	102	23985										
WHAMM	123720	hgsc.bcm.edu	37	chr15	83495232	83495232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cataagatactctcgtcagcAtcacagtattcagatggtga	8	9	4	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr15:83495232A>C	ENST00000286760.4	+	7	1628	c.1529A>C	c.(1528-1530)cAt>cCt	p.H510P		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	510	Mediates interaction with microtubules. {ECO:0000269|PubMed:23027905}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						TCTCGTCAGCATCACAGTATT	0.448																																																0			15											131	125	127					15																	83495232		1962	4157	6119	81292286	SO:0001583	missense	123720			AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"WAS protein homology region 2 domain containing 1"	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.1529A>C	15.37:g.83495232A>C	ENSP00000286760:p.His510Pro		81292286	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263092	0.80358	.	.	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.08008	3.14	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.30792	0.0776	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02774	-1.1112	10	0.72032	D	0.01	.	15.0909	0.72192	1.0:0.0:0.0:0.0	.	510	Q8TF30	WHAMM_HUMAN	P	510	ENSP00000286760:H510P	ENSP00000234505:H510P	H	+	2	0	WHAMM	81292286	1.000000	0.71417	0.905000	0.35620	0.928000	0.56348	7.820000	0.86633	2.158000	0.67659	0.455000	0.32223	CAT		0.448	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1			C	83495232	A	C	83495232	3	2	85	1	0	0	0	0	1	0	0	0	17401	217	8	4	1555	4	WHAMM	15	83495232	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	17791618	83495232	19036160	103	23986										
SOLH	6650	hgsc.bcm.edu	37	chr16	597984	597984	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gagccccccacccactgcccCgactgtggggccgacaagcc	11	20	0	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:597984C>T	ENST00000219611.2	+	4	1509	c.1146C>T	c.(1144-1146)ccC>ccT	p.P382P	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	382					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCCACTGCCCCGACTGTGGGG	0.731																																																0			16											4	5	5					16																	597984		1790	3710	5500	537985	SO:0001819	synonymous_variant	6650			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1146C>T	16.37:g.597984C>T			537985	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																				0.731	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		T	597984	C	T	597984	2	4	85	1	0	0	0	0	0	0	0	1	14962	639	23	1		1	SOLH	16	597984	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10		597984	89756769	104	23987										
TPSAB1	7177	hgsc.bcm.edu	37	chr16	1291615	1291615	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aacgtctccagccacgtccaCacggtcaccctgccccctgc	7	21	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:1291615C>G	ENST00000338844.3	+	4	447	c.414C>G	c.(412-414)caC>caG	p.H138Q	TPSAB1_ENST00000461509.2_Missense_Mutation_p.H145Q	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	138	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				GCCACGTCCACACGGTCACCC	0.657																																																0			16											25	21	22					16																	1291615		2198	4295	6493	1231616	SO:0001583	missense	7177			M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"tryptase alpha II", "tryptase beta I", "tryptase-I", "tryptase-II", "tryptase-III"	191080	"tryptase beta 1"	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.414C>G	16.37:g.1291615C>G	ENSP00000343577:p.His138Gln		1231616	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.334345	0.00227	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.87650	-2.28;-2.28	3.51	-0.0492	0.13836	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.483819	0.17526	N	0.171072	T	0.62270	0.2414	N	0.01771	-0.73	0.25255	N	0.989642	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.53394	-0.8445	10	0.07990	T	0.79	.	8.1558	0.31167	0.0:0.2912:0.5797:0.1291	.	129;138	Q15661-2;Q15661	.;TRYB1_HUMAN	Q	138;145	ENSP00000343577:H138Q;ENSP00000418247:H145Q	ENSP00000343577:H138Q	H	+	3	2	TPSAB1	1231616	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	-1.833000	0.01695	-0.171000	0.10797	0.479000	0.44913	CAC		0.657	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294		G	1291615	C	G	1291615	3	3	85	1	0	0	0	0	1	0	0	0	16463	477	17	5	424	5	TPSAB1	16	1291615	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	693631	1291615	89063138	105	23988										
SYT17	51760	hgsc.bcm.edu	37	chr16	19191848	19191848	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aagtctacatacagcctgacGcggaggatttcgagtaagta	11	8	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:19191848G>A	ENST00000355377.2	+	4	716	c.318G>A	c.(316-318)acG>acA	p.T106T	SYT17_ENST00000562711.2_Silent_p.T102T|SYT17_ENST00000562034.1_Silent_p.T45T|SYT17_ENST00000568115.1_Silent_p.T45T	NM_016524.2	NP_057608.2	Q9BSW7	SYT17_HUMAN	synaptotagmin XVII	106					exocytosis (GO:0006887)	membrane (GO:0016020)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	17						ACAGCCTGACGCGGAGGATTT	0.567											OREG0023658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			16											73	63	67					16																	19191848		2197	4300	6497	19099349	SO:0001819	synonymous_variant	51760				CCDS10575.1	16p12.3	2013-01-21			ENSG00000103528	ENSG00000103528		"Synaptotagmins"	24119	protein-coding gene	gene with protein product	"B/K protein"					10493829	Standard	NM_016524		Approved		uc002dfw.3	Q9BSW7	OTTHUMG00000131461	ENST00000355377.2:c.318G>A	16.37:g.19191848G>A		731	19099349	O43330|Q9NZ18	Silent	SNP	ENST00000355377.2	37	CCDS10575.1																																																																																				0.567	SYT17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254286.2	NM_016524		A	19191848	G	A	19191848	2	1	85	1	0	0	0	0	0	0	0	1	15512	1074	38	1		1	SYT17	16	19191848	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	17900233	19191848	71162905	106	23989										
PLK1	5347	hgsc.bcm.edu	37	chr16	23690582	23690582	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cattcaccgcagcctcgcccAccagcacgtcgtaggattcc	8	18	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:23690582A>G	ENST00000300093.4	+	1	440	c.329A>G	c.(328-330)cAc>cGc	p.H110R	PLK1_ENST00000564202.1_3'UTR	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		AGCCTCGCCCACCAGCACGTC	0.582																																					Colon(12;240 564 27038 33155)											0			16											61	58	59					16																	23690582		2197	4300	6497	23598083	SO:0001583	missense	5347				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.329A>G	16.37:g.23690582A>G	ENSP00000300093:p.His110Arg		23598083	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.777668	0.90195	.	.	ENSG00000166851	ENST00000300093;ENST00000425844;ENST00000330792	T	0.78481	-1.18	4.55	4.55	0.56014	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.155441	0.64402	D	0.000020	D	0.89220	0.6653	H	0.94542	3.55	0.80722	D	1	D	0.59357	0.985	P	0.60415	0.874	D	0.91670	0.5349	10	0.87932	D	0	-12.5677	11.8876	0.52610	1.0:0.0:0.0:0.0	.	110	P53350	PLK1_HUMAN	R	110;13;110	ENSP00000300093:H110R	ENSP00000300093:H110R	H	+	2	0	PLK1	23598083	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.169000	0.89672	1.917000	0.55516	0.459000	0.35465	CAC		0.582	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		G	23690582	A	G	23690582	3	3	85	1	0	0	0	0	1	0	0	0	12125	159	6	4	331	4	PLK1	16	23690582	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	4498734	23690582	66664171	107	23990										
ZNF668	79759	hgsc.bcm.edu	37	chr16	31072703	31072703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cttgcactctcggcacacaaActgggggggcttctcgtcag	12	13	3	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:31072703A>G	ENST00000538906.1	-	3	2330	c.1546T>C	c.(1546-1548)Ttt>Ctt	p.F516L	ZNF668_ENST00000394983.2_Missense_Mutation_p.F516L|ZNF668_ENST00000417110.2_5'Flank|ZNF668_ENST00000426488.2_Missense_Mutation_p.F539L|ZNF668_ENST00000300849.4_Missense_Mutation_p.F516L|ZNF668_ENST00000535577.1_Missense_Mutation_p.F516L|ZNF668_ENST00000539836.3_Missense_Mutation_p.F539L	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGGCACACAAACTGGGGGGGC	0.662																																					Colon(181;1111 1980 5060 10512 25785)											0			16											48	52	51					16																	31072703		2197	4300	6497	30980204	SO:0001583	missense	79759				CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1546T>C	16.37:g.31072703A>G	ENSP00000440149:p.Phe516Leu		30980204	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429032	0.43122	.	.	ENSG00000167394	ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.04	3.89	0.44902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.242073	0.33419	N	0.004931	T	0.23572	0.0570	N	0.08118	0	0.30265	N	0.79284	B	0.29531	0.247	B	0.21360	0.034	T	0.16958	-1.0385	10	0.87932	D	0	-10.633	7.2712	0.26258	0.7895:0.0:0.0:0.2105	.	516	Q96K58	ZN668_HUMAN	L	539;516;516;516;516	ENSP00000442573:F539L;ENSP00000441349:F516L;ENSP00000440149:F516L;ENSP00000378434:F516L;ENSP00000300849:F516L	ENSP00000300849:F516L	F	-	1	0	ZNF668	30980204	0.000000	0.05858	0.864000	0.33941	0.721000	0.41392	1.097000	0.30988	2.129000	0.65627	0.459000	0.35465	TTT		0.662	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		G	31072703	A	G	31072703	3	3	85	1	0	0	0	0	1	0	0	0	18114	43	2	4	317	4	ZNF668	16	31072703	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	7382121	31072703	59282050	108	23991										
MYST1	84148	hgsc.bcm.edu	37	chr16	31131665	31131665	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggcccatacttacagttaacCggcggctggacgagtgggta	14	10	0	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:31131665C>T	ENST00000543774.2	+	4	627	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	KAT8_ENST00000219797.4_Missense_Mutation_p.R98W|RP11-196G11.4_ENST00000576336.1_RNA|KAT8_ENST00000448516.2_Missense_Mutation_p.R98W			Q9H7Z6	KAT8_HUMAN	K(lysine) acetyltransferase 8	98	Chromo.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|myeloid cell differentiation (GO:0030099)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	histone acetyltransferase complex (GO:0000123)|kinetochore (GO:0000776)|MLL1 complex (GO:0071339)|MSL complex (GO:0072487)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|transcription factor binding (GO:0008134)	p.R98W(2)									TACAGTTAACCGGCGGCTGGA	0.577																																																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	16											79	76	77					16																	31131665		2197	4300	6497	31039166	SO:0001583	missense	84148			AF217501	CCDS10706.1, CCDS45468.1	16p11.1	2013-01-10	2011-07-21	2011-07-21	ENSG00000103510	ENSG00000103510	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17933	protein-coding gene	gene with protein product		609912	"MYST histone acetyltransferase 1"	MYST1		10786633	Standard	NM_032188		Approved	MOF, FLJ14040, hMOF, ZC2HC8	uc002eax.3	Q9H7Z6	OTTHUMG00000132410	ENST00000543774.2:c.292C>T	16.37:g.31131665C>T	ENSP00000456933:p.Arg98Trp		31039166	A8K4Z1|G5E9P2|Q659G0|Q7LC17|Q8IY59|Q8WYB4|Q8WZ14|Q9HAC5|Q9NR35	Missense_Mutation	SNP	ENST00000543774.2	37	CCDS10706.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266161	0.80358	.	.	ENSG00000103510	ENST00000219797;ENST00000448516	T;T	0.50548	0.74;0.74	5.83	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.73606	0.3608	M	0.89968	3.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79916	-0.1601	10	0.87932	D	0	-33.3908	13.8716	0.63622	0.1825:0.8174:0.0:0.0	.	98;98	Q9H7Z6;G5E9P2	KAT8_HUMAN;.	W	98	ENSP00000219797:R98W;ENSP00000406037:R98W	ENSP00000219797:R98W	R	+	1	2	KAT8	31039166	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.752000	0.38349	1.377000	0.46286	0.655000	0.94253	CGG		0.577	KAT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000255546.3	NM_032188		T	31131665	C	T	31131665	3	4	85	1	0	0	0	0	1	0	0	0	10132	643	23	1	302	1	MYST1	16	31131665	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	58962	31131665	59223088	109	23992										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67576922	67576922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	caagccctgccccagatcccTcagagtctacggttcagagt	9	15	3	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr16:67576922T>C	ENST00000379312.3	+	13	2366	c.2245T>C	c.(2245-2247)Tca>Cca	p.S749P	CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.S765P|CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.S759P|FAM65A_ENST00000540839.3_Missense_Mutation_p.S765P|FAM65A_ENST00000042381.4_Missense_Mutation_p.S745P|CTD-2012K14.4_ENST00000564717.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	749	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CCCAGATCCCTCAGAGTCTAC	0.602																																																0			16											98	107	104					16																	67576922		2198	4300	6498	66134423	SO:0001583	missense	79567			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2245T>C	16.37:g.67576922T>C	ENSP00000368614:p.Ser749Pro		66134423	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.018|2.018	-0.425367|-0.425367	0.04701|0.04701	.|.	.|.	ENSG00000039523|ENSG00000039523	ENST00000428437|ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	.|T;T;T	.|0.13901	.|2.55;2.55;2.55	5.2|5.2	2.21|2.21	0.28008|0.28008	.|.	.|0.913413	.|0.09448	.|N	.|0.800797	T|T	0.07413|0.07413	0.0187|0.0187	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0	T|T	0.45220|0.45220	-0.9276|-0.9276	5|10	.|0.15499	.|T	.|0.54	0.3111|0.3111	6.7282|6.7282	0.23369|0.23369	0.0:0.6212:0.0:0.3788|0.0:0.6212:0.0:0.3788	.|.	.|759;765;749;765	.|B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.|.;.;FA65A_HUMAN;.	P|P	739|749;745;765;759	.|ENSP00000368614:S749P;ENSP00000042381:S745P;ENSP00000400099:S765P	.|ENSP00000042381:S745P	L|S	+|+	2|1	0|0	FAM65A|FAM65A	66134423|66134423	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.020000|0.020000	0.10135|0.10135	0.571000|0.571000	0.23669|0.23669	0.245000|0.245000	0.21373|0.21373	-0.227000|-0.227000	0.12334|0.12334	CTC|TCA		0.602	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		C	67576922	T	C	67576922	3	2	85	1	0	0	0	0	1	0	0	0	5618	1551	54	4	2279	4	FAM65A	16	67576922	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	36445257	67576922	22777831	110	23993										
SMG6	23293	hgsc.bcm.edu	37	chr17	2186960	2186960	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	caagctcatgagactctcctTggcagtcaggatagggttgc	12	10	3	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr17:2186960T>C	ENST00000263073.6	-	7	2457	c.2407A>G	c.(2407-2409)Aag>Gag	p.K803E	SMG6_ENST00000544865.1_Missense_Mutation_p.K772E	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	803					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGACTCTCCTTGGCAGTCAGG	0.502																																					Melanoma(59;28 1088 11621 25887 46638 50814)											0			17											171	137	148					17																	2186960		2203	4300	6503	2133710	SO:0001583	missense	23293			AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.2407A>G	17.37:g.2186960T>C	ENSP00000263073:p.Lys803Glu		2133710	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.918683	0.92249	.	.	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.18174	2.23;2.23	4.97	4.97	0.65823	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.36276	0.0961	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.05920	-1.0856	10	0.48119	T	0.1	-10.3572	14.6587	0.68852	0.0:0.0:0.0:1.0	.	803	Q86US8	EST1A_HUMAN	E	803;772	ENSP00000263073:K803E;ENSP00000443920:K772E	ENSP00000263073:K803E	K	-	1	0	SMG6	2133710	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.656000	0.83736	1.854000	0.53819	0.397000	0.26171	AAG		0.502	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			C	2186960	T	C	2186960	3	2	85	1	0	0	0	0	1	0	0	0	14834	1821	63	4	1904	4	SMG6	17	2186960	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10		2186960	79008250	111	23994										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11865409	11865409	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tcaacccccagtcgttcctgActgccatcatgcagtccacg	7	17	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr17:11865409A>G	ENST00000262442.4	+	68	13137	c.13069A>G	c.(13069-13071)Act>Gct	p.T4357A	DNAH9_ENST00000608377.1_Missense_Mutation_p.T669A|RP11-1096G20.5_ENST00000580270.1_RNA|DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Missense_Mutation_p.T4281A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4357					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		GTCGTTCCTGACTGCCATCAT	0.537																																																0			17											71	65	67					17																	11865409		2203	4300	6503	11806134	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.13069A>G	17.37:g.11865409A>G	ENSP00000262442:p.Thr4357Ala		11806134	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.895392	0.72639	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.17213	2.29;2.29;2.29	5.04	5.04	0.67666	Dynein heavy chain (1);	0.051026	0.85682	D	0.000000	T	0.51227	0.1662	H	0.95079	3.62	0.53688	D	0.999973	D	0.89917	1.0	D	0.97110	1.0	T	0.62751	-0.6788	10	0.87932	D	0	.	9.4478	0.38708	0.9211:0.0:0.0789:0.0	.	4357	Q9NYC9	DYH9_HUMAN	A	4357;4281;2863;669	ENSP00000262442:T4357A;ENSP00000414874:T4281A;ENSP00000379323:T669A	ENSP00000262442:T4357A	T	+	1	0	DNAH9	11806134	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	4.987000	0.63857	2.116000	0.64780	0.533000	0.62120	ACT		0.537	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11865409	A	G	11865409	3	3	85	1	0	0	0	0	1	0	0	0	4619	275	10	4	13339	4	DNAH9	17	11865409	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	9678449	11865409	69329801	112	23995										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27016477	27016477	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctggaatacgatgaatcagcCgaggatgccaatcctgcagg	12	10	1	1	rs200547240		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr17:27016477C>T	ENST00000314616.6	+	25	3523	c.3240C>T	c.(3238-3240)gcC>gcT	p.A1080A	SUPT6H_ENST00000347486.4_Silent_p.A1080A	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1080	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					ATGAATCAGCCGAGGATGCCA	0.512													C|||	1	0.000199681	0	0.0014	5008	,	,		19822	0		0	False		,,,				2504	0															0			17											97	87	91					17																	27016477		2203	4300	6503	24040604	SO:0001819	synonymous_variant	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3240C>T	17.37:g.27016477C>T			24040604	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27016477	C	T	27016477	2	4	85	1	0	0	0	0	0	0	0	1	15439	639	23	1		1	SUPT6H	17	27016477	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	15151068	27016477	54178733	113	23996										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37880998	37880998	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggaagcatacgtgatggctgGtgtgggctccccatatgtct	14	9	1	1	rs144434331		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr17:37880998G>T	ENST00000269571.5	+	20	2486	c.2327G>T	c.(2326-2328)gGt>gTt	p.G776V	ERBB2_ENST00000584450.1_Missense_Mutation_p.G776V|ERBB2_ENST00000445658.2_Missense_Mutation_p.G500V|ERBB2_ENST00000540147.1_Missense_Mutation_p.G746V|ERBB2_ENST00000584601.1_Missense_Mutation_p.G746V|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000406381.2_Missense_Mutation_p.G746V|ERBB2_ENST00000541774.1_Missense_Mutation_p.G761V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	776	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> S (in a gastric adenocarcinoma sample; somatic mutation; dbSNP:rs28933369). {ECO:0000269|PubMed:15457249, ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.G776>VC(9)|p.G776V(2)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GTGATGGCTGGTGTGGGCTCC	0.577		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	11	Complex - insertion inframe(9)|Substitution - Missense(2)	lung(9)|ovary(2)	17											92	91	91					17																	37880998		2203	4300	6503	35134524	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2327G>T	17.37:g.37880998G>T	ENSP00000269571:p.Gly776Val		35134524	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.050211	0.55218	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	5.3	5.3	0.74995	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.85635	0.5742	N	0.20445	0.575	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.998	D;D;D	0.79784	0.959;0.993;0.959	D	0.87980	0.2742	9	0.72032	D	0.01	.	18.5686	0.91126	0.0:0.0:1.0:0.0	.	500;761;776	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	746;761;500;776;746	ENSP00000385185:G746V;ENSP00000446466:G761V;ENSP00000404047:G500V;ENSP00000269571:G776V;ENSP00000443562:G746V	ENSP00000269571:G776V	G	+	2	0	ERBB2	35134524	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.917000	0.87498	2.478000	0.83669	0.563000	0.77884	GGT		0.577	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37880998	G	T	37880998	3	4	85	1	0	0	0	0	1	0	0	0	5219	1261	44	2	2405	2	ERBB2	17	37880998	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	10864521	37880998	43314212	114	23997										
WNK4	65266	hgsc.bcm.edu	37	chr17	40948558	40948558	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gctcccaggagcagcgggcaAgcaagggggtgacattcgcc	16	12	0	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr17:40948558A>G	ENST00000246914.5	+	18	3712	c.3691A>G	c.(3691-3693)Agc>Ggc	p.S1231G	CNTD1_ENST00000588408.1_5'Flank|CNTD1_ENST00000588527.1_5'Flank	NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	1231					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		GCAGCGGGCAAGCAAGGGGGT	0.632																																					Esophageal Squamous(6;201 374 4964 23855 42828)											0			17											58	57	57					17																	40948558		2203	4300	6503	38202084	SO:0001583	missense	65266			AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"protein kinase, lysine deficient 4"	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.3691A>G	17.37:g.40948558A>G	ENSP00000246914:p.Ser1231Gly		38202084	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.086047	0.55861	.	.	ENSG00000126562	ENST00000246914	T	0.74947	-0.89	5.51	5.51	0.81932	.	0.272298	0.26248	N	0.025470	T	0.75042	0.3796	L	0.45137	1.4	0.80722	D	1	D	0.56521	0.976	P	0.49922	0.626	T	0.78331	-0.2245	10	0.72032	D	0.01	-13.0924	15.2775	0.73753	1.0:0.0:0.0:0.0	.	1231	Q96J92	WNK4_HUMAN	G	1231	ENSP00000246914:S1231G	ENSP00000246914:S1231G	S	+	1	0	WNK4	38202084	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.247000	0.65416	2.096000	0.63516	0.533000	0.62120	AGC		0.632	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1			G	40948558	A	G	40948558	3	3	85	1	0	0	0	0	1	0	0	0	17420	72	3	4	3761	4	WNK4	17	40948558	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	3067560	40948558	40246652	115	23998										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178346	65178347	+	Frame_Shift_Ins	INS	-	-	A													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttccccttcatagggaaggtINSaaaaaaggtttgtagaggtg					rs372593790		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr18:65178346_65178347insA	ENST00000310045.7	-	2	5002_5003	c.3529_3530insT	c.(3529-3531)tacfs	p.Y1177fs	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1167					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				ATAGGGAAGGTAAAAAAGGTTT	0.356																																																0			18																																								63329327	SO:0001589	frameshift_variant	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3530dupT	18.37:g.65178352_65178352dupA	ENSP00000310565:p.Tyr1177fs		63329326	Q17RH1|Q6P5Z3	Frame_Shift_Ins	INS	ENST00000310045.7	37	CCDS11995.1																																																																																				0.356	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65178347	-	A	65178346	7	5	85	1	0	1	1	0	0	0	0	0	4786	1638	57	0	142	0	DSEL	18	65178346	Frame_Shift_Ins	INS	-	TCGA-AH-6644-01A-21D-1826-10		65178346	12898902	116	23999										
ATP5D	513	hgsc.bcm.edu	37	chr19	1242530	1242530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccttcggcatcctggcggccCacgtgcccacgctgcaggtc	12	18	0	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:1242530C>T	ENST00000215375.2	+	2	318	c.217C>T	c.(217-219)Cac>Tac	p.H73Y	ATP5D_ENST00000591660.1_Missense_Mutation_p.H73Y|ATP5D_ENST00000395633.1_Missense_Mutation_p.H73Y	NM_001687.4	NP_001678.1	P30049	ATPD_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	73					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|response to copper ion (GO:0046688)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			large_intestine(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)	Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCTGGCGGCCCACGTGCCCAC	0.657																																																0			19											18	14	16					19																	1242530		2153	4218	6371	1193530	SO:0001583	missense	513			X63423	CCDS12058.1	19p13.3	2012-10-12			ENSG00000099624	ENSG00000099624		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	837	protein-coding gene	gene with protein product		603150				1531933	Standard	NM_001687		Approved		uc002lro.3	P30049		ENST00000215375.2:c.217C>T	19.37:g.1242530C>T	ENSP00000215375:p.His73Tyr		1193530	D6W5Y3|Q6FG90	Missense_Mutation	SNP	ENST00000215375.2	37	CCDS12058.1	.	.	.	.	.	.	.	.	.	.	C	34	5.409910	0.96072	.	.	ENSG00000099624	ENST00000215375;ENST00000395633	.	.	.	5.12	5.12	0.69794	ATPase, F1 complex, delta/epsilon subunit, N-terminal (4);	0.000000	0.85682	D	0.000000	D	0.91257	0.7244	H	0.99391	4.545	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.94977	0.8122	9	0.87932	D	0	-12.6787	16.0299	0.80570	0.0:1.0:0.0:0.0	.	73	P30049	ATPD_HUMAN	Y	73	.	ENSP00000215375:H73Y	H	+	1	0	ATP5D	1193530	1.000000	0.71417	0.749000	0.31150	0.584000	0.36387	7.389000	0.79806	2.371000	0.80710	0.462000	0.41574	CAC		0.657	ATP5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449958.1	NM_001687		T	1242530	C	T	1242530	3	4	85	1	0	0	0	0	1	0	0	0	1151	594	21	3	223	3	ATP5D	19	1242530	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		1242530	57886453	117	24000										
SAFB	6294	hgsc.bcm.edu	37	chr19	5641841	5641841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cagaaattgataatggaagcGttgcagattgtgtcgaagac	12	5	0	4			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:5641841G>A	ENST00000292123.5	+	4	537	c.430G>A	c.(430-432)Gtt>Att	p.V144I	SAFB_ENST00000538656.1_Intron|SAFB_ENST00000454510.1_Intron|SAFB_ENST00000433404.1_De_novo_Start_OutOfFrame|SAFB_ENST00000592224.1_Missense_Mutation_p.V144I|SAFB_ENST00000588852.1_Missense_Mutation_p.V144I|SAFB_ENST00000586934.1_3'UTR	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	144					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V144I(1)		breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		TAATGGAAGCGTTGCAGATTG	0.483																																					Colon(88;338 1345 6184 8214 20897)											1	Substitution - Missense(1)	ovary(1)	19											158	155	156					19																	5641841		2203	4300	6503	5592841	SO:0001583	missense	6294			L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.430G>A	19.37:g.5641841G>A	ENSP00000292123:p.Val144Ile		5592841	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	37	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103163	0.20632	.	.	ENSG00000160633	ENST00000292123	T	0.10288	2.89	5.7	4.67	0.58626	.	0.122641	0.36303	N	0.002678	T	0.08447	0.0210	L	0.34521	1.04	0.80722	D	1	B;B;B;B;B	0.32365	0.367;0.013;0.367;0.236;0.367	B;B;B;B;B	0.20577	0.03;0.002;0.03;0.03;0.03	T	0.19289	-1.0310	10	0.40728	T	0.16	-17.463	13.0308	0.58840	0.0745:0.0:0.9255:0.0	.	144;144;144;144;144	B7ZLP5;B7Z2H3;A0AV56;Q15424;B7ZLP6	.;.;.;SAFB1_HUMAN;.	I	144	ENSP00000292123:V144I	ENSP00000292123:V144I	V	+	1	0	SAFB	5592841	0.826000	0.29277	0.076000	0.20297	0.234000	0.25298	2.253000	0.43205	1.411000	0.46957	0.557000	0.71058	GTT		0.483	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			A	5641841	G	A	5641841	3	1	85	1	0	0	0	0	1	0	0	0	13843	1145	40	1	444	1	SAFB	19	5641841	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	4399311	5641841	53487142	118	24001										
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975914	7975914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gaagcacggtgtcatccaccGcgacgtcaagccctccaaca	9	16	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:7975914G>A	ENST00000397979.3	+	7	779	c.725G>A	c.(724-726)cGc>cAc	p.R242H	MAP2K7_ENST00000545011.1_Missense_Mutation_p.R284H|MAP2K7_ENST00000397981.3_Missense_Mutation_p.R242H|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397983.3_Missense_Mutation_p.R258H	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						GTCATCCACCGCGACGTCAAG	0.632																																																0			19											39	44	42					19																	7975914		2131	4248	6379	7881914	SO:0001583	missense	5609			AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.725G>A	19.37:g.7975914G>A	ENSP00000381066:p.Arg242His		7881914	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Missense_Mutation	SNP	ENST00000397979.3	37	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	G	34	5.397612	0.96009	.	.	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70107	0.3186	H	0.96861	3.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.80725	-0.1254	10	0.87932	D	0	-5.6414	17.0918	0.86624	0.0:0.0:1.0:0.0	.	242;242	O14733-4;O14733	.;MP2K7_HUMAN	H	242;258;284;258;242	ENSP00000381068:R242H;ENSP00000381070:R258H;ENSP00000443946:R284H;ENSP00000381066:R242H	ENSP00000381066:R242H	R	+	2	0	MAP2K7	7881914	1.000000	0.71417	0.973000	0.42090	0.794000	0.44872	7.581000	0.82535	2.711000	0.92665	0.561000	0.74099	CGC		0.632	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			A	7975914	G	A	7975914	3	1	85	1	0	0	0	0	1	0	0	0	9272	1087	38	1	751	1	MAP2K7	19	7975914	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	2334073	7975914	51153069	119	24002										
OR7C2	26658	hgsc.bcm.edu	37	chr19	15052431	15052431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	taccatcatcggaaacctgcTcatcatcctgaccatcagtt	5	14	4	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:15052431T>C	ENST00000248072.3	+	1	131	c.131T>C	c.(130-132)cTc>cCc	p.L44P		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					GGAAACCTGCTCATCATCCTG	0.517																																																0			19											109	90	97					19																	15052431		2203	4300	6503	14913431	SO:0001583	missense	26658			U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.131T>C	19.37:g.15052431T>C	ENSP00000248072:p.Leu44Pro		14913431	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	37	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	t	12.32	1.902536	0.33628	.	.	ENSG00000127529	ENST00000248072	T	0.02890	4.12	4.11	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.407528	0.17826	U	0.160681	T	0.24275	0.0588	H	0.99026	4.405	0.52099	D	0.999944	D	0.76494	0.999	D	0.69824	0.966	T	0.03706	-1.1011	10	0.87932	D	0	.	7.8022	0.29180	0.0:0.1033:0.0:0.8967	.	44	O60412	OR7C2_HUMAN	P	44	ENSP00000248072:L44P	ENSP00000248072:L44P	L	+	2	0	OR7C2	14913431	0.000000	0.05858	0.990000	0.47175	0.266000	0.26442	-0.193000	0.09573	0.738000	0.32606	0.421000	0.28195	CTC		0.517	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			C	15052431	T	C	15052431	3	2	85	1	0	0	0	0	1	0	0	0	11249	1551	54	4	133	4	OR7C2	19	15052431	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	7076517	15052431	44076552	120	24003										
RYR1	6261	hgsc.bcm.edu	37	chr19	39070731	39070731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	catgggggtcaagacgctgcGcaccatcctgtcctctgtca	11	14	3	1	rs193922875		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:39070731G>A	ENST00000359596.3	+	100	14474	c.14474G>A	c.(14473-14475)cGc>cAc	p.R4825H	RYR1_ENST00000355481.4_Missense_Mutation_p.R4820H|RYR1_ENST00000360985.3_Missense_Mutation_p.R4820H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4825			R -> C (in CCD). {ECO:0000269|PubMed:11709545}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AAGACGCTGCGCACCATCCTG	0.597																																																0			19	GRCh37	CM064214	RYR1	M		G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	104	73	83		14474,14459	4.6	1	19		83	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	4825/5039,4820/5034	39070731	1,13005	2203	4300	6503	43762571	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14474G>A	19.37:g.39070731G>A	ENSP00000352608:p.Arg4825His		43762571	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222307	0.58560	0.0	1.16E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98889	-5.21;-5.21;-5.21	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000001	D	0.99227	0.9731	M	0.88031	2.925	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.99177	1.0866	10	0.87932	D	0	.	17.129	0.86722	0.0:0.0:1.0:0.0	.	4820;4825	P21817-2;P21817	.;RYR1_HUMAN	H	4825;4820;4820	ENSP00000352608:R4825H;ENSP00000347667:R4820H;ENSP00000354254:R4820H	ENSP00000347667:R4820H	R	+	2	0	RYR1	43762571	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.646000	0.98474	2.357000	0.79964	0.462000	0.41574	CGC		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39070731	G	A	39070731	3	1	85	1	0	0	0	0	1	0	0	0	13805	1087	38	1	14872	1	RYR1	19	39070731	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	24018300	39070731	20058252	121	24004										
LYPD4	147719	hgsc.bcm.edu	37	chr19	42342224	42342224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	agagataagaccggcagacgCgactgtaggaggcaatggac	15	8	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:42342224C>T	ENST00000330743.3	-	4	1534	c.323G>A	c.(322-324)cGc>cAc	p.R108H	AC020956.3_ENST00000593354.1_lincRNA|LYPD4_ENST00000601246.1_Missense_Mutation_p.R73H|LYPD4_ENST00000343055.4_Missense_Mutation_p.R73H	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	108						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						CCGGCAGACGCGACTGTAGGA	0.527																																																0			19											140	121	127					19																	42342224		2203	4300	6503	47034064	SO:0001583	missense	147719			AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.323G>A	19.37:g.42342224C>T	ENSP00000328737:p.Arg108His		47034064	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	c	9.958	1.222069	0.22457	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.11930	3.36;2.73	4.03	0.164	0.14990	.	0.403702	0.21602	N	0.071926	T	0.08935	0.0221	L	0.37697	1.125	0.20074	N	0.999937	B;B	0.14012	0.009;0.005	B;B	0.12156	0.007;0.003	T	0.32107	-0.9919	10	0.25106	T	0.35	-6.0779	6.7586	0.23528	0.0:0.6741:0.0:0.3259	.	73;108	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	H	108;73	ENSP00000328737:R108H;ENSP00000339568:R73H	ENSP00000328737:R108H	R	-	2	0	LYPD4	47034064	0.065000	0.20965	0.198000	0.23420	0.707000	0.40811	0.003000	0.13083	0.107000	0.17824	0.457000	0.33378	CGC		0.527	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506		T	42342224	C	T	42342224	3	4	85	1	0	0	0	0	1	0	0	0	9142	768	27	1	425	1	LYPD4	19	42342224	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	3271493	42342224	16786759	122	24005										
PRR12	57479	hgsc.bcm.edu	37	chr19	50102730	50102730	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	acttcctcaagtcaggcaagCgccacccaccactctaccag	6	18	3	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:50102730C>T	ENST00000418929.2	+	5	3892	c.3880C>T	c.(3880-3882)Cgc>Tgc	p.R1294C		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		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)		GTCAGGCAAGCGCCACCCACC	0.637																																																0			19											11	14	13					19																	50102730		2076	4198	6274	54794542	SO:0001583	missense	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.3880C>T	19.37:g.50102730C>T	ENSP00000394510:p.Arg1294Cys		54794542	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864748	0.32977	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	5.2	5.2	0.72013	.	0.155289	0.30401	N	0.009701	T	0.69663	0.3136	L	0.50333	1.59	0.54753	D	0.999984	D	0.89917	1.0	D	0.83275	0.996	T	0.72087	-0.4396	9	0.87932	D	0	-25.7136	12.58	0.56386	0.1665:0.8334:0.0:0.0	.	1294	Q9ULL5-3	.	C	1294;474;474	.	ENSP00000246798:R474C	R	+	1	0	PRR12	54794542	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.755000	0.47540	2.424000	0.82194	0.563000	0.77884	CGC		0.637	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50102730	C	T	50102730	3	4	85	1	0	0	0	0	1	0	0	0	12618	768	27	1	3898	1	PRR12	19	50102730	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	7760506	50102730	9026253	123	24006										
ZNF473	25888	hgsc.bcm.edu	37	chr19	50542449	50542449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	cctcaaggatgtcggcatggActtcaccttgggagactggg	14	10	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:50542449A>G	ENST00000595661.1	+	4	536	c.41A>G	c.(40-42)gAc>gGc	p.D14G	ZNF473_ENST00000601364.1_Missense_Mutation_p.D14G|ZNF473_ENST00000445728.3_Missense_Mutation_p.D2G|ZNF473_ENST00000391821.2_Missense_Mutation_p.D14G|ZNF473_ENST00000270617.3_Missense_Mutation_p.D14G			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		GTCGGCATGGACTTCACCTTG	0.577																																																0			19											203	167	179					19																	50542449		2203	4300	6503	55234261	SO:0001583	missense	25888			AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.41A>G	19.37:g.50542449A>G	ENSP00000472808:p.Asp14Gly		55234261	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	37	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.396859	0.42512	.	.	ENSG00000142528	ENST00000270617;ENST00000391821;ENST00000445728	T;T;T	0.02140	4.43;4.43;4.43	5.11	2.98	0.34508	Krueppel-associated box (4);	0.164261	0.28940	N	0.013652	T	0.04318	0.0119	M	0.79693	2.465	0.28664	N	0.906004	B	0.31989	0.35	B	0.34652	0.187	T	0.12091	-1.0561	10	0.42905	T	0.14	-24.4293	6.3722	0.21487	0.7561:0.1595:0.0844:0.0	.	14	Q8WTR7	ZN473_HUMAN	G	14;14;2	ENSP00000270617:D14G;ENSP00000375697:D14G;ENSP00000388961:D2G	ENSP00000270617:D14G	D	+	2	0	ZNF473	55234261	1.000000	0.71417	0.998000	0.56505	0.019000	0.09904	6.197000	0.72100	0.485000	0.27652	0.528000	0.53228	GAC		0.577	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		G	50542449	A	G	50542449	3	3	85	1	0	0	0	0	1	0	0	0	17970	275	10	4	47	4	ZNF473	19	50542449	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	439719	50542449	8586534	124	24007										
TFPT	29844	hgsc.bcm.edu	37	chr19	54618051	54618051	+	Frame_Shift_Del	DEL	A	A	-													0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctgagcctggcggcgctgagAactcctcaaagcccacggct							TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:54618051delA	ENST00000391759.1	-	2	458	c.53delT	c.(52-54)ttcfs	p.F18fs	TFPT_ENST00000391757.1_Frame_Shift_Del_p.F18fs|PRPF31_ENST00000419967.1_5'Flank|PRPF31_ENST00000321030.4_5'Flank|TFPT_ENST00000391758.1_Frame_Shift_Del_p.F9fs	NM_013342.3	NP_037474.1	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner (in childhood Leukemia)	18					apoptotic signaling pathway (GO:0097190)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(2)	4	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					CGGCGCTGAGAACTCCTCAAA	0.627			T	TCF3	pre-B ALL																																		Dom	yes		19	19q13	29844	TCF3 (E2A) fusion partner (in childhood Leukemia)		L	0			19											90	94	92					19																	54618051		2203	4300	6503	59309863	SO:0001589	frameshift_variant	29844			AF052052	CCDS12878.1	19q13	2011-07-06			ENSG00000105619	ENSG00000105619		"INO80 complex subunits"	13630	protein-coding gene	gene with protein product	"amida, partner of the E2A", "INO80 complex subunit F"	609519				10644725, 16230350	Standard	NM_013342		Approved	FB1, amida, INO80F	uc010yej.1	P0C1Z6	OTTHUMG00000065906	ENST00000391759.1:c.53delT	19.37:g.54618051delA	ENSP00000375639:p.Phe18fs		59309863		Frame_Shift_Del	DEL	ENST00000391759.1	37	CCDS12878.1																																																																																				0.627	TFPT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141215.4	NM_013342		-	54618051	A	-	54618051	7	5	85	1	0	1	0	1	0	0	0	0	15849	246	9	0	728	0	TFPT	19	54618051	Frame_Shift_Del	DEL	A	TCGA-AH-6644-01A-21D-1826-10	4075602	54618051	4510932	125	24008										
LILRB4	11006	hgsc.bcm.edu	37	chr19	55179204	55179204	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tggggaattcctggacacaaAggacagacaggcagaagagg	15	7	0	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr19:55179204A>G	ENST00000391736.1	+	13	1475	c.1160A>G	c.(1159-1161)aAg>aGg	p.K387R	LILRB4_ENST00000430952.2_Missense_Mutation_p.K386R|LILRB4_ENST00000391733.3_Missense_Mutation_p.K388R|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000270452.2_Missense_Mutation_p.K387R	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	387					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CTGGACACAAAGGACAGACAG	0.597																																																0			19											75	72	73					19																	55179204		2198	4299	6497	59871016	SO:0001583	missense	11006			U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1160A>G	19.37:g.55179204A>G	ENSP00000375616:p.Lys387Arg		59871016	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	A	4.613	0.113922	0.08831	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391733;ENST00000434286	T;T;T;T;T	0.00500	7.13;7.13;7.13;7.15;6.96	2.36	-1.48	0.08745	.	.	.	.	.	T	0.00412	0.0013	L	0.52011	1.625	0.09310	N	1	B;B;B;B	0.34372	0.002;0.004;0.451;0.068	B;B;B;B	0.32289	0.001;0.001;0.143;0.014	T	0.40794	-0.9544	9	0.72032	D	0.01	.	3.0821	0.06266	0.4975:0.2272:0.2752:0.0	.	386;388;386;387	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	R	387;387;386;388;386	ENSP00000375616:K387R;ENSP00000270452:K387R;ENSP00000408995:K386R;ENSP00000375613:K388R;ENSP00000401962:K386R	ENSP00000270452:K387R	K	+	2	0	LILRB4	59871016	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.613000	0.24299	-0.688000	0.05155	-1.527000	0.00925	AAG		0.597	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			G	55179204	A	G	55179204	3	3	85	1	0	0	0	0	1	0	0	0	8816	72	3	4	1202	4	LILRB4	19	55179204	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	561153	55179204	3949779	126	24009										
FASTKD5	60493	hgsc.bcm.edu	37	chr20	3127926	3127926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttaaatggtaatggcttcagGttaacatcaagctggacctc	9	8	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:3127926G>A	ENST00000380266.3	-	2	2112	c.1791C>T	c.(1789-1791)aaC>aaT	p.N597N	UBOX5_ENST00000348031.2_Intron|UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000217173.2_Intron	NM_021826.4	NP_068598.1	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	597					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(2)	19						ATGGCTTCAGGTTAACATCAA	0.468																																																0			20											61	69	67					20																	3127926		2201	4300	6501	3075926	SO:0001819	synonymous_variant	60493			BC007413	CCDS13048.1	20p13	2006-07-07			ENSG00000215251	ENSG00000215251			25790	protein-coding gene	gene with protein product		614272				11347906	Standard	NM_021826		Approved	FLJ13149	uc002whz.4	Q7L8L6	OTTHUMG00000031727	ENST00000380266.3:c.1791C>T	20.37:g.3127926G>A			3075926	Q96JN3|Q9H5D1|Q9H8Y3	Silent	SNP	ENST00000380266.3	37	CCDS13048.1																																																																																				0.468	FASTKD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077701.2	NM_021826		A	3127926	G	A	3127926	2	1	85	1	0	0	0	0	0	0	0	1	5707	1252	44	3		3	FASTKD5	20	3127926	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10		3127926	59897594	127	24010										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9459613	9459613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	aattggaagccgagatggacCgcagaccagcaacagtagta	12	9	0	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:9459613C>T	ENST00000378493.1	+	35	3520	c.3505C>T	c.(3505-3507)Cgc>Tgc	p.R1169C	PLCB4_ENST00000334005.3_Missense_Mutation_p.P1181L|PLCB4_ENST00000278655.4_Missense_Mutation_p.R1169C|PLCB4_ENST00000414679.2_Missense_Mutation_p.R1181C|PLCB4_ENST00000378473.3_Missense_Mutation_p.R1181C|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.P1181L			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1169					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.P1181Q(1)		NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CGAGATGGACCGCAGACCAGC	0.443																																																1	Substitution - Missense(1)	lung(1)	20											168	137	147					20																	9459613		2203	4300	6503	9407613	SO:0001583	missense	5332				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3505C>T	20.37:g.9459613C>T	ENSP00000367754:p.Arg1169Cys		9407613	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.37|15.37	2.813360|2.813360	0.50527|0.50527	.|.	.|.	ENSG00000101333|ENSG00000101333	ENST00000334005;ENST00000378501|ENST00000378473;ENST00000278655;ENST00000378493;ENST00000414679	T;T|T;T;T;T	0.19250|0.23147	2.16;2.16|2.11;2.11;2.11;1.92	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.129409|.	0.35646|.	N|.	0.003076|.	T|T	0.36386|0.36386	0.0965|0.0965	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	P|P;D;D	0.38642|0.64830	0.641|0.923;0.994;0.99	B|B;P;B	0.31547|0.47102	0.132|0.132;0.537;0.336	T|T	0.11131|0.11131	-1.0600|-1.0600	9|8	0.87932|0.52906	D|T	0|0.07	.|.	19.5796|19.5796	0.95461|0.95461	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1181|1181;1016;1169	Q15147-4|E2QRH8;Q15147-2;Q15147	.|.;.;PLCB4_HUMAN	L|C	1181|1181;1169;1169;1017	ENSP00000334105:P1181L;ENSP00000367762:P1181L|ENSP00000367734:R1181C;ENSP00000278655:R1169C;ENSP00000367754:R1169C;ENSP00000390616:R1017C	ENSP00000334105:P1181L|ENSP00000278655:R1169C	P|R	+|+	2|1	0|0	PLCB4|PLCB4	9407613|9407613	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	1.000000|1.000000	0.99986|0.99986	6.557000|6.557000	0.73937|0.73937	2.624000|2.624000	0.88883|0.88883	0.655000|0.655000	0.94253|0.94253	CCG|CGC		0.443	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			T	9459613	C	T	9459613	3	4	85	1	0	0	0	0	1	0	0	0	12061	652	23	1	3724	1	PLCB4	20	9459613	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	6331687	9459613	53565907	128	24011										
DEFB118	117285	hgsc.bcm.edu	37	chr20	29960872	29960872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ttttaacagtaaggttcacgAcagactactttgaagtaagc	8	7	1	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:29960872A>G	ENST00000253381.2	+	2	304	c.271A>G	c.(271-273)Aca>Gca	p.T91A		NM_054112.2	NP_473453.1	Q96PH6	DB118_HUMAN	defensin, beta 118	91					cell-matrix adhesion (GO:0007160)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(7)|ovary(3)|pancreas(1)|prostate(1)	14	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			AAGGTTCACGACAGACTACTT	0.453																																																0			20											120	112	115					20																	29960872		2203	4300	6503	29424533	SO:0001583	missense	117285			AF347073	CCDS13177.1	20q11.21	2008-02-01	2002-05-09	2002-05-10	ENSG00000131068	ENSG00000131068		"Defensins, beta"	16196	protein-coding gene	gene with protein product		607650	"chromosome 20 open reading frame 63"	C20orf63		11564719, 15033915	Standard	NM_054112		Approved	dJ1018D12.3, DEFB-18, ESC42	uc002wvr.3	Q96PH6	OTTHUMG00000032161	ENST00000253381.2:c.271A>G	20.37:g.29960872A>G	ENSP00000253381:p.Thr91Ala		29424533	Q17RC4|Q8N691|Q9NUH0	Missense_Mutation	SNP	ENST00000253381.2	37	CCDS13177.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.948005	0.34377	.	.	ENSG00000131068	ENST00000253381	T	0.08634	3.07	2.3	-0.253	0.12996	.	.	.	.	.	T	0.04770	0.0129	N	0.24115	0.695	0.09310	N	1	P	0.51057	0.941	B	0.41036	0.346	T	0.34428	-0.9829	9	0.37606	T	0.19	.	2.8955	0.05689	0.4837:0.2616:0.0:0.2547	.	91	Q96PH6	DB118_HUMAN	A	91	ENSP00000253381:T91A	ENSP00000253381:T91A	T	+	1	0	DEFB118	29424533	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.311000	0.02723	-0.076000	0.12775	0.528000	0.53228	ACA		0.453	DEFB118-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078501.2	NM_054112		G	29960872	A	G	29960872	3	3	85	1	0	0	0	0	1	0	0	0	4416	275	10	4	277	4	DEFB118	20	29960872	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	20501259	29960872	33064648	129	24012										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40827935	40827935	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccttcatcattgcggctggcGctgagcttggtggtgggttt	15	9	2	1	rs145661499		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:40827935G>A	ENST00000373187.1	-	16	2435	c.2436C>T	c.(2434-2436)agC>agT	p.S812S	PTPRT_ENST00000356100.2_Silent_p.S821S|PTPRT_ENST00000373201.1_Silent_p.S802S|PTPRT_ENST00000373190.1_Silent_p.S812S|PTPRT_ENST00000373193.3_Silent_p.S815S|PTPRT_ENST00000373198.4_Silent_p.S831S|PTPRT_ENST00000373184.1_Silent_p.S802S			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	812					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.S834R(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGCGGCTGGCGCTGAGCTTGG	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		17978	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	20											220	229	226					20																	40827935		2052	4202	6254	40261349	SO:0001819	synonymous_variant	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2436C>T	20.37:g.40827935G>A			40261349	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																				0.577	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40827935	G	A	40827935	2	1	85	1	0	0	0	0	0	0	0	1	12849	1078	38	1		1	PTPRT	20	40827935	Silent	SNP	G	TCGA-AH-6644-01A-21D-1826-10	10867063	40827935	22197585	130	24013										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130463	45130463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gtgttcattctcttacactgActgcagtttgacttcacaat	6	10	3	2			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:45130463A>G	ENST00000347606.4	-	5	1697	c.1515T>C	c.(1513-1515)agT>agC	p.S505S	ZNF334_ENST00000457685.2_Silent_p.S467S|ZNF334_ENST00000593880.1_Silent_p.S528S	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S505S(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TCTTACACTGACTGCAGTTTG	0.393																																																1	Substitution - coding silent(1)	ovary(1)	20											166	154	158					20																	45130463		2203	4299	6502	44563870	SO:0001819	synonymous_variant	55713			AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1515T>C	20.37:g.45130463A>G			44563870	Q5T6U2|Q9NVW4	Silent	SNP	ENST00000347606.4	37	CCDS33480.1																																																																																				0.393	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			G	45130463	A	G	45130463	2	3	85	1	0	0	0	0	0	0	0	1	17890	272	10	4		4	ZNF334	20	45130463	Silent	SNP	A	TCGA-AH-6644-01A-21D-1826-10	4302528	45130463	17895057	131	24014										
PREX1	57580	hgsc.bcm.edu	37	chr20	47260971	47260971	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccccatctcgtcgctgcccaAgtaggagctgttacttctca	8	15	2	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:47260971A>T	ENST00000371941.3	-	27	3599	c.3577T>A	c.(3577-3579)Ttg>Atg	p.L1193M	PREX1_ENST00000396220.1_Missense_Mutation_p.L1193M|PREX1_ENST00000496915.1_5'Flank	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1193					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TCGCTGCCCAAGTAGGAGCTG	0.547																																																0			20											96	74	82					20																	47260971		2203	4300	6503	46694378	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3577T>A	20.37:g.47260971A>T	ENSP00000361009:p.Leu1193Met		46694378	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	A	18.78	3.696023	0.68386	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.38560	1.13;1.13	5.14	2.06	0.26882	.	0.000000	0.42548	U	0.000682	T	0.56232	0.1971	L	0.60455	1.87	0.47009	D	0.999287	D;D	0.89917	0.996;1.0	D;D	0.97110	0.944;1.0	T	0.53851	-0.8380	10	0.46703	T	0.11	.	11.0336	0.47787	0.2666:0.0:0.7334:0.0	.	1193;490	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	M	1193	ENSP00000361009:L1193M;ENSP00000379522:L1193M	ENSP00000361009:L1193M	L	-	1	2	PREX1	46694378	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.470000	0.35354	0.559000	0.29153	-0.146000	0.13790	TTG		0.547	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47260971	A	T	47260971	3	4	85	1	0	0	0	0	1	0	0	0	12510	69	3	5	1458	5	PREX1	20	47260971	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	2130508	47260971	15764549	132	24015										
GNAS	2778	hgsc.bcm.edu	37	chr20	57415470	57415470	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ctccccgagtgcctagagtaCgaggaagagttcgactacga	12	11	0	2	rs373276011		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:57415470C>T	ENST00000313949.7	+	1	698	c.309C>T	c.(307-309)taC>taT	p.Y103Y	GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000371098.2_Silent_p.Y103Y|GNAS-AS1_ENST00000424094.2_RNA|GNAS_ENST00000371075.3_Silent_p.Y103Y|GNAS-AS1_ENST00000443966.1_RNA			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.Y103Y(1)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCCTAGAGTACGAGGAAGAGT	0.627			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	1	Substitution - coding silent(1)	prostate(1)	20						C		2,4404	4.2+/-10.8	0,2,2201	79	81	80		309	4.2	1	20		80	0,8600		0,0,4300	no	coding-synonymous	GNAS	NM_016592.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		103/246	57415470	2,13004	2203	4300	6503	56848865	SO:0001819	synonymous_variant	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000313949.7:c.309C>T	20.37:g.57415470C>T			56848865	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000313949.7	37	CCDS13471.1																																																																																				0.627	GNAS-002	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080418.7	NM_000516		T	57415470	C	T	57415470	2	4	85	1	0	0	0	0	0	0	0	1	6530	547	19	1		1	GNAS	20	57415470	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	10154499	57415470	5610050	133	24016										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62200924	62200924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcacacggaagcgctcacccCgtgcgtagagccggcctggc	14	16	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr20:62200924C>T	ENST00000467148.1	-	4	734	c.665G>A	c.(664-666)cGg>cAg	p.R222Q	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	222					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCGCTCACCCCGTGCGTAGAG	0.672																																																0			20											14	15	14					20																	62200924		2171	4273	6444	61671368	SO:0001583	missense	85441			AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.665G>A	20.37:g.62200924C>T	ENSP00000417401:p.Arg222Gln		61671368	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.687124	0.00738	.	.	ENSG00000130589	ENST00000467148	T	0.02280	4.36	4.5	-2.48	0.06423	.	2.574830	0.01368	N	0.012460	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.43782	-0.9370	10	0.11182	T	0.66	-1.2993	3.1595	0.06515	0.1296:0.4269:0.1324:0.311	.	222	Q9BYK8	PR285_HUMAN	Q	222	ENSP00000417401:R222Q	ENSP00000417401:R222Q	R	-	2	0	RP4-697K14.7	61671368	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.036000	0.13819	-0.903000	0.03881	-0.471000	0.05019	CGG		0.672	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62200924	C	T	62200924	3	4	85	1	0	0	0	0	1	0	0	0	12519	652	23	1	7371	1	PRIC285	20	62200924	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10	4785454	62200924	824596	134	24017										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221699	43221699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gctgacggtatcaaaggtcaCggtcaggattgagttgtcca	13	8	3	2	rs149361413	byFrequency	TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr21:43221699C>T	ENST00000269844.3	-	31	4335	c.4225G>A	c.(4225-4227)Gtg>Atg	p.V1409M	PRDM15_ENST00000447207.2_Missense_Mutation_p.V1043M|PRDM15_ENST00000398548.1_Missense_Mutation_p.V1080M|PRDM15_ENST00000538201.1_Missense_Mutation_p.V1063M|PRDM15_ENST00000422911.1_Missense_Mutation_p.V1100M|PRDM15_ENST00000470586.1_5'UTR	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TCAAAGGTCACGGTCAGGATT	0.602																																																0			21							MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	62	56	58		3238,4225	4.3	1	21	dbSNP_134	58	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	PRDM15	NM_001040424.1,NM_022115.3	21,21	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	probably-damaging,probably-damaging	1080/1179,1409/1508	43221699	4,13002	2203	4300	6503	42094768	SO:0001583	missense	63977			AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4225G>A	21.37:g.43221699C>T	ENSP00000269844:p.Val1409Met		42094768	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	c	20.2	3.950009	0.73787	2.27E-4	3.49E-4	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	4.29	4.29	0.51040	.	.	.	.	.	T	0.43211	0.1237	L	0.27053	0.805	0.52501	D	0.999953	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.992;0.997	T	0.48364	-0.9042	9	0.87932	D	0	-30.6355	15.7568	0.78037	0.0:1.0:0.0:0.0	.	1409;1100;1080	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	M	1100;1080;1063;1043;1409	ENSP00000408592:V1100M;ENSP00000381556:V1080M;ENSP00000444044:V1063M;ENSP00000390245:V1043M;ENSP00000269844:V1409M	ENSP00000269844:V1409M	V	-	1	0	PRDM15	42094768	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	7.206000	0.77891	1.934000	0.56057	0.558000	0.71614	GTG		0.602	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43221699	C	T	43221699	3	4	85	1	0	0	0	0	1	0	0	0	12490	536	19	1	302	1	PRDM15	21	43221699	Missense_Mutation	SNP	C	TCGA-AH-6644-01A-21D-1826-10		43221699	4908196	135	24018										
CBX6	23466	hgsc.bcm.edu	37	chr22	39262247	39262247	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccaatgctgccaccgcccccAgcggcgcctgctaccccagc	9	22	0	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr22:39262247A>C	ENST00000407418.3	-	5	1329	c.1206T>G	c.(1204-1206)gcT>gcG	p.A402A	CBX6_ENST00000216083.6_Silent_p.A384A			O95503	CBX6_HUMAN	chromobox homolog 6	402					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(58;0.04)					CACCGCCCCCAGCGGCGCCTG	0.637																																																0			22											24	25	25					22																	39262247		2201	4299	6500	37592193	SO:0001819	synonymous_variant	23466				CCDS13980.1	22q13.1	2013-04-23			ENSG00000183741	ENSG00000183741			1556	protein-coding gene	gene with protein product							Standard	NM_014292		Approved		uc003awl.3	O95503	OTTHUMG00000150456	ENST00000407418.3:c.1206T>G	22.37:g.39262247A>C			37592193	A8KAH0|Q96EM5	Silent	SNP	ENST00000407418.3	37	CCDS13980.1																																																																																				0.637	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292		C	39262247	A	C	39262247	2	2	85	1	0	0	0	0	0	0	0	1	2728	175	7	4		4	CBX6	22	39262247	Silent	SNP	A	TCGA-AH-6644-01A-21D-1826-10		39262247	12042319	136	24019										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51117290	51117290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ccacctggacttccgcactcGcgatgggctcactgccgtgc	11	17	1	0			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chr22:51117290G>A	ENST00000414786.2	+	5	769	c.542G>A	c.(541-543)cGc>cAc	p.R181H	SHANK3_ENST00000262795.3_Missense_Mutation_p.R181H|SHANK3_ENST00000445220.2_Missense_Mutation_p.R181H			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	181					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R181H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		TTCCGCACTCGCGATGGGCTC	0.667																																																1	Substitution - Missense(1)	endometrium(1)	22											34	37	36					22																	51117290		2119	4220	6339	49464156	SO:0001583	missense	85358			AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.542G>A	22.37:g.51117290G>A	ENSP00000464552:p.Arg181His		49464156	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	G	13.61	2.287970	0.40494	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.18016	2.24;2.24	5.07	4.05	0.47172	.	.	.	.	.	T	0.27967	0.0689	L	0.41124	1.26	0.09310	N	1	D	0.76494	0.999	P	0.62491	0.903	T	0.03662	-1.1015	9	0.48119	T	0.1	.	10.5407	0.45031	0.0941:0.0:0.9059:0.0	.	181	F2Z3L0	.	H	181	ENSP00000442518:R181H;ENSP00000446078:R181H	ENSP00000442518:R181H	R	+	2	0	SHANK3	49464156	0.995000	0.38212	0.033000	0.17914	0.008000	0.06430	6.038000	0.70964	2.349000	0.79799	0.557000	0.71058	CGC		0.667	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		A	51117290	G	A	51117290	3	1	85	1	0	0	0	0	1	0	0	0	14303	1087	38	1	560	1	SHANK3	22	51117290	Missense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10	11855043	51117290	187276	137	24020										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412095	63412095	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggtcaccaggcaggaacttcGcttggtcccatctcggtttg	12	12	2	0	rs137852217		TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chrX:63412095G>A	ENST00000330258.3	-	2	1344	c.1072C>T	c.(1072-1074)Cga>Tga	p.R358*	AMER1_ENST00000374869.3_Nonsense_Mutation_p.R358*|AMER1_ENST00000403336.1_Nonsense_Mutation_p.R358*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	358					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R358*(9)									CAGGAACTTCGCTTGGTCCCA	0.527																																																76	Whole gene deletion(67)|Substitution - Nonsense(9)	kidney(70)|large_intestine(5)|ovary(1)	X	GRCh37	CM090019	FAM123B	M	rs137852217						153	136	142					X																	63412095		2203	4300	6503	63328820	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1072C>T	X.37:g.63412095G>A	ENSP00000329117:p.Arg358*		63328820	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	38	7.185009	0.98121	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.18	1.24	0.21308	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3576	13.9688	0.64225	0.0:0.0:0.3525:0.6475	.	.	.	.	X	358	.	ENSP00000329117:R358X	R	-	1	2	FAM123B	63328820	0.081000	0.21417	0.853000	0.33588	0.996000	0.88848	0.184000	0.16939	-0.004000	0.14419	0.529000	0.55759	CGA		0.527	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63412095	G	A	63412095	4	1	85	1	0	0	0	0	0	1	0	0	5439	1095	38	1	2339	1	FAM123B	23	63412095	Nonsense_Mutation	SNP	G	TCGA-AH-6644-01A-21D-1826-10		63412095	91858465	138	24021										
IRS4	8471	hgsc.bcm.edu	37	chrX	107976412	107976412	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	ggagagagaaatatccatacAgcactcagaaaatgggtcga	11	7	1	3			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chrX:107976412A>T	ENST00000372129.2	-	1	3239	c.3163T>A	c.(3163-3165)Tgt>Agt	p.C1055S	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	1055					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						ATATCCATACAGCACTCAGAA	0.522																																																0			X											81	79	80					X																	107976412		2203	4300	6503	107863068	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.3163T>A	X.37:g.107976412A>T	ENSP00000361202:p.Cys1055Ser		107863068		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.175170	0.57692	.	.	ENSG00000133124	ENST00000372129	T	0.52057	0.68	5.38	2.95	0.34219	.	0.311162	0.29653	N	0.011550	T	0.27524	0.0676	L	0.27053	0.805	0.33740	D	0.619359	B	0.26483	0.15	B	0.28991	0.097	T	0.20338	-1.0278	10	0.15499	T	0.54	-11.0692	3.8058	0.08776	0.5538:0.0:0.1021:0.3441	.	1055	O14654	IRS4_HUMAN	S	1055	ENSP00000361202:C1055S	ENSP00000361202:C1055S	C	-	1	0	IRS4	107863068	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.078000	0.30754	1.982000	0.57802	0.486000	0.48141	TGT		0.522	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107976412	A	T	107976412	3	4	85	1	0	0	0	0	1	0	0	0	7863	188	7	5	614	5	IRS4	23	107976412	Missense_Mutation	SNP	A	TCGA-AH-6644-01A-21D-1826-10	44564317	107976412	47294148	139	24022										
IRS4	8471	hgsc.bcm.edu	37	chrX	107978810	107978810	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	tcctcgtcggttagacacagCcggaacacgccgctcagctc	10	16	1	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chrX:107978810C>A	ENST00000372129.2	-	1	841	c.765G>T	c.(763-765)cgG>cgT	p.R255R	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	255	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TTAGACACAGCCGGAACACGC	0.612																																																0			X											56	47	50					X																	107978810		2203	4300	6503	107865466	SO:0001819	synonymous_variant	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.765G>T	X.37:g.107978810C>A			107865466		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																				0.612	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107978810	C	A	107978810	2	1	85	1	0	0	0	0	0	0	0	1	7863	726	26	2		2	IRS4	23	107978810	Silent	SNP	C	TCGA-AH-6644-01A-21D-1826-10	2398	107978810	47291750	140	24023										
FLNA	2316	hgsc.bcm.edu	37	chrX	153577744	153577744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0283687943262411	4	1	0.403058361391695	1.4510101010101	0.324853007688829	0.545454545454546	1	0	gcccacctgctttgctgcagTctactgtgaagctgctcttc	9	14	2	1			TCGA-AH-6644-01A-21D-1826-10	TCGA-AH-6644-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5aeb740f-44f1-4a21-9d60-53f5eea32995	c40489ed-f82a-486a-b4bf-e8dd9264e37a	g.chrX:153577744T>C	ENST00000369850.3	-	47	7978	c.7742A>G	c.(7741-7743)gAc>gGc	p.D2581G	FLNA_ENST00000422373.1_Missense_Mutation_p.D2573G|FLNA_ENST00000498491.1_5'UTR|FLNA_ENST00000369856.3_Missense_Mutation_p.D714G|FLNA_ENST00000360319.4_Missense_Mutation_p.D2573G|FLNA_ENST00000344736.4_Missense_Mutation_p.D2541G	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2581	Self-association site, tail.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTTGCTGCAGTCTACTGTGAA	0.657																																																0			X											51	54	53					X																	153577744		1961	4115	6076	153230938	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.7742A>G	X.37:g.153577744T>C	ENSP00000358866:p.Asp2581Gly		153230938	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373166	0.61624	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	6.04	6.04	0.98038	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94245	0.8152	M	0.93283	3.4	0.80722	D	1	B;B;D;D	0.76494	0.001;0.016;0.999;0.999	B;B;D;D	0.75484	0.0;0.043;0.986;0.986	D	0.95232	0.8343	10	0.59425	D	0.04	.	15.5122	0.75793	0.0:0.0:0.0:1.0	.	714;2573;2581;2581	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	G	2573;2249;2573;2581;714;2541	ENSP00000353467:D2573G;ENSP00000416926:D2573G;ENSP00000358866:D2581G;ENSP00000358872:D714G;ENSP00000358863:D2541G	ENSP00000358863:D2541G	D	-	2	0	FLNA	153230938	1.000000	0.71417	0.999000	0.59377	0.881000	0.50899	6.205000	0.72148	2.047000	0.60756	0.430000	0.28490	GAC		0.657	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			C	153577744	T	C	153577744	3	2	85	1	0	0	0	0	1	0	0	0	5952	1667	58	4	209	4	FLNA	23	153577744	Missense_Mutation	SNP	T	TCGA-AH-6644-01A-21D-1826-10	45598934	153577744	1692816	141	24024										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561557	11561557	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	accgctcgcggcaagcctccCgagccccccgcgtcatcccc	9	23	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:11561557C>T	ENST00000294484.6	+	2	646	c.508C>T	c.(508-510)Cga>Tga	p.R170*	PTCHD2_ENST00000389575.3_Nonsense_Mutation_p.R170*	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	170					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCAAGCCTCCCGAGCCCCCCG	0.682																																																0			1											12	15	14					1																	11561557		1893	4089	5982	11484144	SO:0001587	stop_gained	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.508C>T	1.37:g.11561557C>T	ENSP00000294484:p.Arg170*		11484144	Q5VTU9|Q9UJD6	Nonsense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981249	0.53827	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	.	.	.	5.53	-3.03	0.05429	.	0.429524	0.22945	N	0.053731	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.4	13.1682	0.59583	0.2811:0.6473:0.0716:0.0	.	.	.	.	X	170	.	ENSP00000294484:R170X	R	+	1	2	PTCHD2	11484144	0.063000	0.20901	0.010000	0.14722	0.072000	0.16883	-0.093000	0.11111	-0.258000	0.09446	-0.410000	0.06199	CGA		0.682	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11561557	C	T	11561557	4	4	86	1	0	0	0	0	0	1	0	0	12767	644	23	1	510	1	PTCHD2	1	11561557	Nonsense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		11561557	237689064	1	24025										
CATSPER4	378807	hgsc.bcm.edu	37	chr1	26527920	26527920	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttgaacaggcgctcgtcgacGagcgggtcgttggagactac	15	10	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:26527920G>T	ENST00000456354.2	+	9	1342	c.1275G>T	c.(1273-1275)acG>acT	p.T425T		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	425					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.T425T(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCGTCGACGAGCGGGTCGT	0.577																																																1	Substitution - coding silent(1)	ovary(1)	1											102	92	95					1																	26527920		2203	4300	6503	26400507	SO:0001819	synonymous_variant	378807			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1275G>T	1.37:g.26527920G>T			26400507	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																				0.577	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		T	26527920	G	T	26527920	2	4	86	1	0	0	0	0	0	0	0	1	2696	1045	37	2		2	CATSPER4	1	26527920	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10	14966363	26527920	222722701	2	24026										
PUM1	9698	hgsc.bcm.edu	37	chr1	31426559	31426559	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agtgccaaagccaagtactcAcctggacccatgctggtctt	9	13	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:31426559A>C	ENST00000257075.5	-	15	2685		c.e15+1		PUM1_ENST00000423018.2_Splice_Site|PUM1_ENST00000424085.2_Splice_Site|PUM1_ENST00000440538.2_Splice_Site|PUM1_ENST00000373741.4_Splice_Site|PUM1_ENST00000373742.2_Splice_Site|PUM1_ENST00000373747.3_Splice_Site|PUM1_ENST00000426105.2_Splice_Site	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1						membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CCAAGTACTCACCTGGACCCA	0.413																																																0			1											106	116	112					1																	31426559		2203	4300	6503	31199146	SO:0001630	splice_region_variant	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2591+1T>G	1.37:g.31426559A>C			31199146	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Splice_Site	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.028601	0.75390	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000525843;ENST00000426105;ENST00000498419;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742;ENST00000529846;ENST00000525997	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7636	0.78106	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PUM1	31199146	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.339000	0.96797	2.210000	0.71456	0.533000	0.62120	.		0.413	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		Intron	C	31426559	A	C	31426559	5	2	86	1	0	0	0	0	0	0	1	0	12862	173	6	4	1005	4	PUM1	1	31426559	Splice_Site	SNP	A	TCGA-CI-6619-01B-11D-1826-10	4898639	31426559	217824062	3	24027										
FAM167B	84734	hgsc.bcm.edu	37	chr1	32713034	32713034	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aaacctgccatgtccctgggGctactgaaattccaggcagt	10	12	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:32713034G>C	ENST00000373582.3	+	1	201	c.12G>C	c.(10-12)ggG>ggC	p.G4G		NM_032648.2	NP_116037.2	Q9BTA0	F167B_HUMAN	family with sequence similarity 167, member B	4										endometrium(1)|large_intestine(1)|lung(1)|ovary(2)	5						TGTCCCTGGGGCTACTGAAAT	0.587																																																0			1											60	67	65					1																	32713034		2048	4202	6250	32485621	SO:0001819	synonymous_variant	84734			BC004269	CCDS358.2	1p35.1	2010-08-27	2008-06-11	2008-06-11	ENSG00000183615	ENSG00000183615			28133	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 90"	C1orf90		12477932	Standard	NM_032648		Approved	MGC10820	uc001buw.3	Q9BTA0	OTTHUMG00000007462	ENST00000373582.3:c.12G>C	1.37:g.32713034G>C			32485621	Q5TDH6	Silent	SNP	ENST00000373582.3	37	CCDS358.2																																																																																				0.587	FAM167B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019615.2	NM_032648		C	32713034	G	C	32713034	2	2	86	1	0	0	0	0	0	0	0	1	5500	1190	42	5		5	FAM167B	1	32713034	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10	1286475	32713034	216537587	4	24028										
CLSPN	63967	hgsc.bcm.edu	37	chr1	36209097	36209097	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atcatttgaaacaagccgaaAgtctccaaattcctcctcct	4	13	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:36209097A>T	ENST00000318121.3	-	17	3058	c.3001T>A	c.(3001-3003)Ttt>Att	p.F1001I	CLSPN_ENST00000520551.1_Missense_Mutation_p.F948I|CLSPN_ENST00000373220.3_Missense_Mutation_p.F937I|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000251195.5_Missense_Mutation_p.F1001I	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1001					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACAAGCCGAAAGTCTCCAAAT	0.378																																																0			1											165	157	160					1																	36209097		2203	4300	6503	35981684	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3001T>A	1.37:g.36209097A>T	ENSP00000312995:p.Phe1001Ile		35981684	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110652	0.56398	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.25912	1.77;1.78;1.82;1.82	5.29	5.29	0.74685	.	0.060670	0.64402	D	0.000004	T	0.48132	0.1483	M	0.66939	2.045	0.40289	D	0.978487	D;P	0.67145	0.996;0.797	D;P	0.77557	0.99;0.615	T	0.44772	-0.9306	10	0.38643	T	0.18	-12.6596	14.3462	0.66665	1.0:0.0:0.0:0.0	.	937;1001	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	I	1001;1001;937;948	ENSP00000251195:F1001I;ENSP00000312995:F1001I;ENSP00000362317:F937I;ENSP00000428848:F948I	ENSP00000251195:F1001I	F	-	1	0	CLSPN	35981684	1.000000	0.71417	0.997000	0.53966	0.188000	0.23474	5.232000	0.65332	2.125000	0.65367	0.459000	0.35465	TTT		0.378	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		T	36209097	A	T	36209097	3	4	86	1	0	0	0	0	1	0	0	0	3566	72	3	5	1054	5	CLSPN	1	36209097	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	3496063	36209097	213041524	5	24029										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55144987	55144987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	taaaggacctgctgctggccGccctggaagggctgaaaggc	15	11	0	1	rs554316180		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:55144987G>A	ENST00000421030.2	+	12	2386	c.2101G>A	c.(2101-2103)Gcc>Acc	p.A701T	MROH7_ENST00000339553.5_Missense_Mutation_p.A701T|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.A701T|MROH7_ENST00000545244.1_Missense_Mutation_p.A269T|MROH7_ENST00000395690.2_Missense_Mutation_p.A701T|MROH7_ENST00000454855.2_Missense_Mutation_p.A219T|MROH7_ENST00000409996.1_Missense_Mutation_p.A269T	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	701						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GCTGCTGGCCGCCCTGGAAGG	0.592													G|||	1	0.000199681	0	0	5008	,	,		18498	0.001		0	False		,,,				2504	0															0			1											71	78	76					1																	55144987		1921	4127	6048	54917575	SO:0001583	missense	374977			AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.2101G>A	1.37:g.55144987G>A	ENSP00000396622:p.Ala701Thr		54917575	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902147	0.33628	.	.	ENSG00000184313	ENST00000421030;ENST00000545244;ENST00000414867;ENST00000339553;ENST00000409996;ENST00000454855;ENST00000395690	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	4.88	3.95	0.45737	.	0.000000	0.47093	D	0.000243	T	0.41236	0.1150	L	0.33485	1.01	0.32843	D	0.505581	D;D;D	0.89917	0.999;1.0;0.997	D;D;P	0.71414	0.95;0.973;0.67	T	0.42882	-0.9425	10	0.22706	T	0.39	-6.3043	8.1381	0.31067	0.1075:0.0:0.8925:0.0	.	701;701;269	F8W8P2;Q68CQ1;F5H7R4	.;HEAT8_HUMAN;.	T	701;269;730;701;269;219;701	ENSP00000396622:A701T;ENSP00000442333:A269T;ENSP00000343211:A701T;ENSP00000387048:A269T;ENSP00000401130:A219T;ENSP00000379044:A701T	ENSP00000343211:A701T	A	+	1	0	HEATR8	54917575	0.974000	0.33945	0.992000	0.48379	0.751000	0.42716	2.215000	0.42862	2.250000	0.74265	0.557000	0.71058	GCC		0.592	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		A	55144987	G	A	55144987	3	1	86	1	0	0	0	0	1	0	0	0	2022	1087	38	1	2139	1	C1orf175	1	55144987	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	18935890	55144987	194105634	6	24030										
AGL	178	hgsc.bcm.edu	37	chr1	100349686	100349686	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtattcctaggcaaaattgaAgaagtagttcttgaagctag	10	5	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:100349686A>G	ENST00000294724.4	+	18	2797	c.2319A>G	c.(2317-2319)gaA>gaG	p.E773E	AGL_ENST00000361522.4_Silent_p.E756E|AGL_ENST00000370165.3_Silent_p.E773E|AGL_ENST00000361302.3_Silent_p.E757E|AGL_ENST00000370163.3_Silent_p.E773E|AGL_ENST00000370161.2_Silent_p.E757E|AGL_ENST00000361915.3_Silent_p.E773E	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	773					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GCAAAATTGAAGAAGTAGTTC	0.303																																																0			1											78	83	81					1																	100349686		2203	4297	6500	100122274	SO:0001819	synonymous_variant	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2319A>G	1.37:g.100349686A>G			100122274	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																				0.303	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100349686	A	G	100349686	2	3	86	1	0	0	0	0	0	0	0	1	384	69	3	4		4	AGL	1	100349686	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	45204699	100349686	148900935	7	24031										
FAM102B	284611	hgsc.bcm.edu	37	chr1	109154825	109154825	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctttgcagatctaaacctggCagagtttgctggatcaggaa	11	8	2	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:109154825C>A	ENST00000370035.3	+	4	654	c.314C>A	c.(313-315)gCa>gAa	p.A105E	FAM102B_ENST00000405454.1_Missense_Mutation_p.A105E	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	105										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		CTAAACCTGGCAGAGTTTGCT	0.368																																																0			1											104	104	104					1																	109154825		2203	4300	6503	108956348	SO:0001583	missense	284611			CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"sym-3 homolog B (C. elegans)"						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.314C>A	1.37:g.109154825C>A	ENSP00000359052:p.Ala105Glu		108956348	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Missense_Mutation	SNP	ENST00000370035.3	37	CCDS30786.2	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572444	0.86542	.	.	ENSG00000162636	ENST00000370035;ENST00000405454;ENST00000437902	T;T	0.56275	0.47;0.47	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52289	0.1725	M	0.87827	2.91	0.80722	D	1	P	0.43231	0.801	B	0.38378	0.272	T	0.67181	-0.5735	10	0.72032	D	0.01	-18.1451	19.0387	0.92989	0.0:1.0:0.0:0.0	.	105	Q5T8I3	F102B_HUMAN	E	105	ENSP00000359052:A105E;ENSP00000386084:A105E	ENSP00000359052:A105E	A	+	2	0	FAM102B	108956348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.805000	0.86005	2.500000	0.84329	0.655000	0.94253	GCA		0.368	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883		A	109154825	C	A	109154825	3	1	86	1	0	0	0	0	1	0	0	0	5399	710	25	2	328	2	FAM102B	1	109154825	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	8805139	109154825	140095796	8	24032										
MPZ	4359	hgsc.bcm.edu	37	chr1	161276238	161276238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atcacagctcccagaacgacCccgtacctagttggcactag	8	15	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:161276238C>T	ENST00000533357.1	-	4	531	c.465G>A	c.(463-465)ggG>ggA	p.G155G	MPZ_ENST00000526189.1_5'UTR|MPZ_ENST00000336559.4_Silent_p.G155G|MPZ_ENST00000360451.6_Silent_p.G165G|MPZ_ENST00000491222.2_5'UTR	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	155					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			CCAGAACGACCCCGTACCTAG	0.592																																																0			1											116	104	108					1																	161276238		2203	4300	6503	159542862	SO:0001819	synonymous_variant	4359			BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"Immunoglobulin superfamily / V-set domain containing"	7225	protein-coding gene	gene with protein product		159440	"Charcot-Marie-Tooth neuropathy 1B"	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.465G>A	1.37:g.161276238C>T			159542862	Q16072|Q5VTH4|Q92677|Q9BR67	Silent	SNP	ENST00000533357.1	37	CCDS1229.2																																																																																				0.592	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530		T	161276238	C	T	161276238	2	4	86	1	0	0	0	0	0	0	0	1	9778	610	22	3		3	MPZ	1	161276238	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	52121413	161276238	87974383	9	24033										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200972808	200972808	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgtcctggttcactaccaccTtgttcttgatgttgcgggcc	10	12	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:200972808T>C	ENST00000422435.2	-	8	1434	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	KIF21B_ENST00000360529.5_Missense_Mutation_p.K373R|KIF21B_ENST00000461742.2_Missense_Mutation_p.K373R|KIF21B_ENST00000332129.2_Missense_Mutation_p.K373R	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	373					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CACTACCACCTTGTTCTTGAT	0.542																																																0			1											193	148	163					1																	200972808		2203	4300	6503	199239431	SO:0001583	missense	23046			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1118A>G	1.37:g.200972808T>C	ENSP00000411831:p.Lys373Arg		199239431	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	t	16.77	3.215667	0.58452	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.19	5.19	0.71726	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.52573	1.65	0.52501	D	0.999952	D;D;B;D	0.56746	0.961;0.961;0.006;0.977	P;P;B;P	0.51974	0.489;0.489;0.005;0.686	T	0.73132	-0.4079	10	0.52906	T	0.07	.	9.5798	0.39481	0.0:0.0786:0.0:0.9214	.	373;373;373;373	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	R	373	ENSP00000328494:K373R;ENSP00000353724:K373R;ENSP00000433808:K373R;ENSP00000411831:K373R	ENSP00000328494:K373R	K	-	2	0	KIF21B	199239431	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.128000	0.64733	1.959000	0.56917	0.524000	0.50904	AAG		0.542	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200972808	T	C	200972808	3	2	86	1	0	0	0	0	1	0	0	0	8310	1609	56	4	3864	4	KIF21B	1	200972808	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	39696570	200972808	48277813	10	24034										
KCNH1	3756	hgsc.bcm.edu	37	chr1	210977424	210977424	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggaagtcccgaacactgttgAgcatctcatggtatctgttg	11	9	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:210977424A>G	ENST00000271751.4	-	8	1574	c.1547T>C	c.(1546-1548)cTc>cCc	p.L516P	KCNH1_ENST00000367007.4_Missense_Mutation_p.L489P			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	516					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.L516P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		AACACTGTTGAGCATCTCATG	0.478																																																1	Substitution - Missense(1)	ovary(1)	1											161	147	152					1																	210977424		2203	4300	6503	209044047	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1547T>C	1.37:g.210977424A>G	ENSP00000271751:p.Leu516Pro		209044047	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414958	0.83449	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.97256	-4.31;-4.31	5.6	5.6	0.85130	Cyclic nucleotide-binding-like (1);	0.060386	0.64402	D	0.000003	D	0.98226	0.9413	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69824	0.966;0.954	D	0.99323	1.0907	10	0.87932	D	0	.	15.7772	0.78232	1.0:0.0:0.0:0.0	.	489;516	Q14CL3;O95259	.;KCNH1_HUMAN	P	516;489	ENSP00000271751:L516P;ENSP00000355974:L489P	ENSP00000271751:L516P	L	-	2	0	KCNH1	209044047	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.982000	0.93471	2.137000	0.66172	0.418000	0.28097	CTC		0.478	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		G	210977424	A	G	210977424	3	3	86	1	0	0	0	0	1	0	0	0	8052	304	11	4	1438	4	KCNH1	1	210977424	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	10004616	210977424	38273197	11	24035										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371056	240371121	+	In_Frame_Del	DEL	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	-													0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tacctcctccaccccctctaCccggagcgggcataccccct					rs139764401|rs71646825|rs557827551|rs537036439|rs71646826|rs141912031|rs202207586|rs71646890|rs11586155|rs71646889|rs71646891|rs71646887|rs375298881|rs71646827|rs373490785	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENST00000319653.9	+	5	3174_3239	c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	c.(2944-3009)cccggagcgggcataccccctcctcccccacttcccggagcgggcataccccctccgcccccacttdel	p.PGAGIPPPPPLPGAGIPPPPPL1070del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1070	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1131T(2)|p.P1143P(1)|p.G1128A(1)|p.G1128G(1)|p.P1134L(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTTCCCGGAGCGG	0.714																																																6	Substitution - Missense(4)|Substitution - coding silent(2)	lung(3)|prostate(1)|ovary(1)|large_intestine(1)	1																																								238437744	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	1.37:g.240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENSP00000318884:p.Pro1070_Leu1091del		238437679	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.714	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240371121	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	-	240371056	7	5	86	1	0	1	0	1	0	0	0	0	5969	507	18	0	2962	0	FMN2	1	240371056	In_Frame_Del	DEL	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	TCGA-CI-6619-01B-11D-1826-10	29393632	240371056	8879565	12	24036										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655202	247655202	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tctacggaaccatcatctacGtgtacctgaagccggccaac	8	14	3	1	rs118113848	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:247655202G>A	ENST00000522351.1	+	0	833							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R258L(1)|p.R258H(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-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)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CATCATCTACGTGTACCTGAA	0.532													G|||	4	0.000798722	0	0	5008	,	,		17476	0.004		0	False		,,,				2504	0															2	Substitution - Missense(2)	lung(1)|endometrium(1)	1						G	HIS/ARG	0,4406		0,0,2203	132	115	121		773	-1	1	1	dbSNP_132	121	2,8598	2.2+/-6.3	0,2,4298	no	missense	OR2W5	NM_001004698.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	258/321	247655202	2,13004	2203	4300	6503	245721825			441932					1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247655202G>A			245721825	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																					0.532	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		A	247655202	G	A	247655202	1	1	86	0	1	0	0	0	0	0	0	0	11065	1145	40	1		1	OR2W5	1	247655202	RNA	SNP	G	TCGA-CI-6619-01B-11D-1826-10	7284146	247655202	1595419	13	24037										
APOB	338	hgsc.bcm.edu	37	chr2	21230730	21230730	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aaacagtgccatgcctttagCagttagaacactgtggccca	9	11	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:21230730C>A	ENST00000233242.1	-	26	9137	c.9010G>T	c.(9010-9012)Gct>Tct	p.A3004S		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3004					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGCCTTTAGCAGTTAGAACA	0.408																																																0			2											71	75	74					2																	21230730		2203	4300	6503	21084235	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9010G>T	2.37:g.21230730C>A	ENSP00000233242:p.Ala3004Ser		21084235	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.349945	0.41599	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00848	5.62	5.87	5.87	0.94306	.	0.207969	0.33670	N	0.004662	T	0.04003	0.0112	M	0.68317	2.08	0.53688	D	0.999977	D	0.69078	0.997	P	0.60789	0.879	T	0.33471	-0.9867	10	0.62326	D	0.03	.	14.3787	0.66897	0.0:0.9298:0.0:0.0702	.	3004	P04114	APOB_HUMAN	S	3004	ENSP00000233242:A3004S	ENSP00000233242:A3004S	A	-	1	0	APOB	21084235	0.049000	0.20398	0.083000	0.20561	0.647000	0.38526	1.505000	0.35736	2.780000	0.95670	0.655000	0.94253	GCT		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21230730	C	A	21230730	3	1	86	1	0	0	0	0	1	0	0	0	785	710	25	2	4697	2	APOB	2	21230730	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		21230730	221968643	14	24038										
MSH2	4436	hgsc.bcm.edu	37	chr2	47639567	47639567	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aaatagataattcaaagaggAggaattctgatcacagaaag	9	4	3	4			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:47639567A>G	ENST00000233146.2	+	4	883	c.660A>G	c.(658-660)ggA>ggG	p.G220G	MSH2_ENST00000543555.1_Silent_p.G154G|MSH2_ENST00000406134.1_Silent_p.G220G	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	220					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCAAAGAGGAGGAATTCTGA	0.313			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	2											47	48	48					2																	47639567		2203	4300	6503	47493071	SO:0001819	synonymous_variant	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.660A>G	2.37:g.47639567A>G			47493071	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																				0.313	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			G	47639567	A	G	47639567	2	3	86	1	0	0	0	0	0	0	0	1	9900	291	11	4		4	MSH2	2	47639567	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	26408837	47639567	195559806	15	24039										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48848421	48848421	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cttgcaccaaacattgcaatCgtcaacaggttggataccat	7	11	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:48848421C>A	ENST00000403751.3	+	3	276	c.239C>A	c.(238-240)tCg>tAg	p.S80*	GTF2A1L_ENST00000430487.2_Nonsense_Mutation_p.S46*|GTF2A1L_ENST00000468326.1_3'UTR|STON1-GTF2A1L_ENST00000394754.1_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000309827.2_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000402114.2_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000394751.3_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000405008.1_Nonsense_Mutation_p.S784*	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	80					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACATTGCAATCGTCAACAGGT	0.383																																																0			2											75	75	75					2																	48848421		2203	4300	6503	48701925	SO:0001587	stop_gained	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.239C>A	2.37:g.48848421C>A	ENSP00000384597:p.Ser80*		48701925	B4DY14|Q53FD9|Q5D050	Nonsense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	36	5.771749	0.96922	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000448460;ENST00000437125;ENST00000430487;ENST00000403751	.	.	.	3.59	3.59	0.41128	.	0.480024	0.20172	N	0.097715	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.8977	0.47031	0.0:0.8087:0.1913:0.0	.	.	.	.	X	784;784;784;784;784;79;46;80;46;80	.	ENSP00000384597:S80X	S	+	2	0	STON1-GTF2A1L;GTF2A1L	48701925	0.974000	0.33945	0.679000	0.29978	0.362000	0.29581	2.179000	0.42528	1.997000	0.58415	0.563000	0.77884	TCG		0.383	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		A	48848421	C	A	48848421	4	1	86	1	0	0	0	0	0	1	0	0	6874	893	31	2	249	2	GTF2A1L	2	48848421	Nonsense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	1208854	48848421	194350952	16	24040										
THSD7B	80731	hgsc.bcm.edu	37	chr2	138208522	138208522	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtggaattggagtgagaattCgatccaaatggctaaaagaa	12	4	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:138208522C>T	ENST00000409968.1	+	15	3245	c.3067C>T	c.(3067-3069)Cga>Tga	p.R1023*	THSD7B_ENST00000413152.2_Nonsense_Mutation_p.R992*|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Nonsense_Mutation_p.R1023*			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1023	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.R1023*(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AGTGAGAATTCGATCCAAATG	0.408																																																1	Substitution - Nonsense(1)	skin(1)	2											93	88	90					2																	138208522		1866	4110	5976	137924992	SO:0001587	stop_gained	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3067C>T	2.37:g.138208522C>T	ENSP00000387145:p.Arg1023*		137924992		Nonsense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	43	10.496149	0.99416	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.87	4.05	0.47172	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7785	0.69749	0.4926:0.5074:0.0:0.0	.	.	.	.	X	1023;1023;992	.	ENSP00000272643:R1023X	R	+	1	2	THSD7B	137924992	0.980000	0.34600	1.000000	0.80357	0.998000	0.95712	0.841000	0.27613	0.795000	0.33922	0.655000	0.94253	CGA		0.408	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	138208522	C	T	138208522	4	4	86	1	0	0	0	0	0	1	0	0	15919	876	31	1	3028	1	THSD7B	2	138208522	Nonsense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	89360101	138208522	104990851	17	24041										
ORC4L	5000	hgsc.bcm.edu	37	chr2	148730337	148730337	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcctgatcctcggggtccgaTaataaggacagagttactct	10	10	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:148730337T>C	ENST00000392857.5	-	4	303	c.196A>G	c.(196-198)Atc>Gtc	p.I66V	ORC4_ENST00000536575.1_Intron|ORC4_ENST00000392858.1_Missense_Mutation_p.I66V|ORC4_ENST00000540442.1_5'UTR|ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000264169.2_Missense_Mutation_p.I66V|ORC4_ENST00000535373.1_Missense_Mutation_p.I66V	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	66					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)	p.I66F(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						CGGGGTCCGATAATAAGGACA	0.333																																																1	Substitution - Missense(1)	ovary(1)	2											69	72	71					2																	148730337		2203	4300	6503	148446807	SO:0001583	missense	5000			AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"ATPases / AAA-type"	8490	protein-coding gene	gene with protein product		603056	"origin recognition complex, subunit 4 (yeast homolog)-like", "origin recognition complex, subunit 4-like (yeast)", "origin recognition complex, subunit 4-like (S. cerevisiae)", "origin recognition complex, subunit 4 homolog (S. cerevisiae)"	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.196A>G	2.37:g.148730337T>C	ENSP00000376597:p.Ile66Val		148446807	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.865607	0.32977	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.88	1.01	0.19927	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.112463	0.64402	N	0.000006	T	0.18173	0.0436	N	0.14661	0.345	0.80722	D	1	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.16722	0.006;0.016;0.004	T	0.09707	-1.0662	10	0.16896	T	0.51	-8.4926	8.9634	0.35860	0.0:0.2852:0.0:0.7148	.	66;66;66	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	V	66	ENSP00000264169:I66V;ENSP00000441953:I66V;ENSP00000376598:I66V;ENSP00000376597:I66V;ENSP00000413939:I66V;ENSP00000391484:I66V;ENSP00000403105:I66V	ENSP00000264169:I66V	I	-	1	0	ORC4	148446807	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.753000	0.38359	-0.049000	0.13379	0.533000	0.62120	ATC		0.333	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742		C	148730337	T	C	148730337	3	2	86	1	0	0	0	0	1	0	0	0	11295	1406	49	4	1158	4	ORC4L	2	148730337	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	10521815	148730337	94469036	18	24042										
HAT1	8520	hgsc.bcm.edu	37	chr2	172844219	172844219	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtaactgacatgagtgatgcCgaacaatacagaagctacag	10	8	0	4			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:172844219C>T	ENST00000264108.4	+	10	1071	c.1035C>T	c.(1033-1035)gcC>gcT	p.A345A	SLC25A12_ENST00000472748.1_Intron|HAT1_ENST00000392584.1_Silent_p.A260A	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	345					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)	p.A345A(1)		breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TGAGTGATGCCGAACAATACA	0.348																																																1	Substitution - coding silent(1)	lung(1)	2											131	132	132					2																	172844219		2203	4300	6503	172552465	SO:0001819	synonymous_variant	8520			AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1035C>T	2.37:g.172844219C>T			172552465	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Silent	SNP	ENST00000264108.4	37	CCDS2245.1																																																																																				0.348	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		T	172844219	C	T	172844219	2	4	86	1	0	0	0	0	0	0	0	1	6985	639	23	1		1	HAT1	2	172844219	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	24113882	172844219	70355154	19	24043										
TTN	7273	hgsc.bcm.edu	37	chr2	179635038	179635038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	catcctttggctttttaatgAtcttgacagctaagaggaaa	8	7	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:179635038A>G	ENST00000591111.1	-	36	8614	c.8390T>C	c.(8389-8391)aTc>aCc	p.I2797T	TTN_ENST00000342175.6_Missense_Mutation_p.I2751T|TTN_ENST00000359218.5_Missense_Mutation_p.I2751T|TTN_ENST00000342992.6_Missense_Mutation_p.I2797T|TTN_ENST00000460472.2_Missense_Mutation_p.I2751T|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.I2797T|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I2797T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13125					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTTTAATGATCTTGACAGC	0.393																																																0			2											98	96	97					2																	179635038		2203	4300	6503	179343283	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8390T>C	2.37:g.179635038A>G	ENSP00000465570:p.Ile2797Thr		179343283	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.82	2.349759	0.41599	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54	6.06	6.06	0.98353	Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87208	0.6120	M	0.91459	3.21	0.36185	D	0.849692	D;D;D;D;D	0.76494	0.978;0.978;0.978;0.989;0.999	P;P;P;D;D	0.69479	0.871;0.871;0.871;0.927;0.964	D	0.92372	0.5906	9	0.87932	D	0	.	16.6154	0.84909	1.0:0.0:0.0:0.0	.	2751;2751;2751;2797;2797	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	2797;2751;2751;2751;2751;2797	ENSP00000343764:I2797T;ENSP00000434586:I2751T;ENSP00000340554:I2751T;ENSP00000352154:I2751T;ENSP00000354117:I2797T	ENSP00000340554:I2751T	I	-	2	0	TTN	179343283	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.927000	0.92846	2.315000	0.78130	0.533000	0.62120	ATC		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179635038	A	G	179635038	3	3	86	1	0	0	0	0	1	0	0	0	16775	333	12	4	102906	4	TTN	2	179635038	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	6790819	179635038	63564335	20	24044										
ACSL3	2181	hgsc.bcm.edu	37	chr2	223786008	223786008	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttcaatgcagaaaaccaaccTcatagcaaaccattgccctc	4	14	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:223786008T>A	ENST00000357430.3	+	8	1347	c.816T>A	c.(814-816)ccT>ccA	p.P272P	AC097461.4_ENST00000446709.1_RNA|ACSL3_ENST00000392066.3_Silent_p.P272P	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	272					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	AAAACCAACCTCATAGCAAAC	0.358			T	ETV1	prostate																																		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	0			2											141	137	138					2																	223786008		2203	4300	6503	223494252	SO:0001819	synonymous_variant	2181			D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"Acyl-CoA synthetase family"	3570	protein-coding gene	gene with protein product		602371	"fatty-acid-Coenzyme A ligase, long-chain 3"	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.816T>A	2.37:g.223786008T>A			223494252	Q60I92|Q8IUM9	Silent	SNP	ENST00000357430.3	37	CCDS2455.1																																																																																				0.358	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		A	223786008	T	A	223786008	2	1	86	1	0	0	0	0	0	0	0	1	178	1538	54	5		5	ACSL3	2	223786008	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	44150970	223786008	19413365	21	24045										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19436739	19436739	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctccttgcacactggatggcGtgtatctggtacgtcattgg	12	10	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:19436739G>A	ENST00000328405.2	+	7	1379	c.1113G>A	c.(1111-1113)gcG>gcA	p.A371A	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_Silent_p.A12A	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	371					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						ACTGGATGGCGTGTATCTGGT	0.453																																					NSCLC(124;1625 1765 8018 24930 42026)											0			3											170	146	154					3																	19436739		2203	4300	6503	19411743	SO:0001819	synonymous_variant	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1113G>A	3.37:g.19436739G>A			19411743	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																				0.453	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		A	19436739	G	A	19436739	2	1	86	1	0	0	0	0	0	0	0	1	8059	1132	40	1		1	KCNH8	3	19436739	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10		19436739	178585691	22	24046										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436805	52436805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aatcacccaccttgaacttcTtcctcttctctacctcctcc	1	19	4	1	rs372282516		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:52436805T>C	ENST00000460680.1	-	15	2444	c.1973A>G	c.(1972-1974)aAg>aGg	p.K658R	BAP1_ENST00000296288.5_Missense_Mutation_p.K640R	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				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)		CTTGAACTTCTTCCTCTTCTC	0.547			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															GBM(101;493 1458 7992 21037 25532)		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0			3						T	ARG/LYS	0,4406		0,0,2203	234	218	224		1973	4.8	1	3		224	1,8599	1.2+/-3.3	0,1,4299	no	missense	BAP1	NM_004656.2	26	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	658/730	52436805	1,13005	2203	4300	6503	52411845	SO:0001583	missense	9223			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1973A>G	3.37:g.52436805T>C	ENSP00000417132:p.Lys658Arg		52411845	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.15|16.15	3.042685|3.042685	0.55003|0.55003	0.0|0.0	1.16E-4|1.16E-4	ENSG00000163930|ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368|ENST00000469613	T;T;T|.	0.48522|.	0.81;0.81;0.81|.	5.94|5.94	4.78|4.78	0.61160|0.61160	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54481|0.54481	0.1861|0.1861	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	B|.	0.29531|.	0.247|.	B|.	0.31191|.	0.125|.	T|T	0.49113|0.49113	-0.8973|-0.8973	10|5	0.54805|.	T|.	0.06|.	.|.	11.7594|11.7594	0.51894|0.51894	0.0:0.0693:0.0:0.9307|0.0:0.0693:0.0:0.9307	.|.	658|.	Q92560|.	BAP1_HUMAN|.	R|G	658;640;182|58	ENSP00000417132:K658R;ENSP00000296288:K640R;ENSP00000420647:K182R|.	ENSP00000296288:K640R|.	K|R	-|-	2|1	0|2	BAP1|BAP1	52411845|52411845	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.182000|6.182000	0.71995|0.71995	1.065000|1.065000	0.40693|0.40693	0.533000|0.533000	0.62120|0.62120	AAG|AGA		0.547	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			C	52436805	T	C	52436805	3	2	86	1	0	0	0	0	1	0	0	0	1312	1609	56	4	228	4	BAP1	3	52436805	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	33000066	52436805	145585625	23	24047										
CHDH	55349	hgsc.bcm.edu	37	chr3	53857360	53857360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gatggtcatgtccatccagcCgaagccctcctgctggaagc	11	14	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:53857360C>T	ENST00000315251.6	-	3	1113	c.676G>A	c.(676-678)Ggc>Agc	p.G226S		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	226					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	TCCATCCAGCCGAAGCCCTCC	0.602																																																0			3											42	43	42					3																	53857360		2203	4300	6503	53832400	SO:0001583	missense	55349			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.676G>A	3.37:g.53857360C>T	ENSP00000319851:p.Gly226Ser		53832400	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	C	36	5.605073	0.96626	.	.	ENSG00000016391	ENST00000315251	T	0.42900	0.96	5.72	5.72	0.89469	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56470	0.1987	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.56625	-0.7948	10	0.66056	D	0.02	-37.0968	19.8824	0.96903	0.0:1.0:0.0:0.0	.	226	Q8NE62	CHDH_HUMAN	S	226	ENSP00000319851:G226S	ENSP00000319851:G226S	G	-	1	0	CHDH	53832400	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.414000	0.80117	2.702000	0.92279	0.557000	0.71058	GGC		0.602	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		T	53857360	C	T	53857360	3	4	86	1	0	0	0	0	1	0	0	0	3339	652	23	1	1136	1	CHDH	3	53857360	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	1420555	53857360	144165070	24	24048										
MYH15	22989	hgsc.bcm.edu	37	chr3	108224571	108224571	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gaaataaaaatttctttaccTctccatctgctgtctcaaca	3	11	4	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:108224571T>C	ENST00000273353.3	-	3	310	c.254A>G	c.(253-255)gAg>gGg	p.E85G		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	85						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTTCTTTACCTCTCCATCTGC	0.333																																																0			3											189	174	179					3																	108224571		1861	4108	5969	109707261	SO:0001630	splice_region_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.255+1A>G	3.37:g.108224571T>C			109707261		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	8.102	0.776942	0.16120	.	.	ENSG00000144821	ENST00000273353	D	0.81739	-1.53	3.54	2.4	0.29515	Myosin, N-terminal, SH3-like (1);	.	.	.	.	T	0.77785	0.4182	M	0.64997	1.995	0.24112	N	0.995834	B	0.20671	0.047	B	0.30316	0.114	T	0.70299	-0.4910	9	0.72032	D	0.01	.	7.6036	0.28089	0.0:0.1913:0.0:0.8087	.	85	Q9Y2K3	MYH15_HUMAN	G	85	ENSP00000273353:E85G	ENSP00000273353:E85G	E	-	2	0	MYH15	109707261	0.995000	0.38212	0.987000	0.45799	0.116000	0.19942	0.330000	0.19715	0.739000	0.32628	0.533000	0.62120	GAG		0.333	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation	C	108224571	T	C	108224571	5	2	86	1	0	0	0	0	0	0	1	0	10064	1565	54	4	5746	4	MYH15	3	108224571	Splice_Site	SNP	T	TCGA-CI-6619-01B-11D-1826-10	54367211	108224571	89797859	25	24049										
WDR52	55779	hgsc.bcm.edu	37	chr3	113085054	113085054	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttgtcatgcatattgaagtgCcagtagtccaccaaactggt	9	9	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:113085054C>A	ENST00000295868.2	-	19	2709	c.2547G>T	c.(2545-2547)tgG>tgT	p.W849C	WDR52_ENST00000393845.2_Missense_Mutation_p.W849C	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TATTGAAGTGCCAGTAGTCCA	0.353																																																0			3											99	91	94					3																	113085054		2203	4300	6503	114567744	SO:0001583	missense	55779																														ENST00000295868.2:c.2547G>T	3.37:g.113085054C>A	ENSP00000295868:p.Trp849Cys		114567744		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575070	0.65878	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.17054	2.3;2.3	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.45135	0.1327	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.24225	-1.0166	8	.	.	.	.	17.733	0.88384	0.0:1.0:0.0:0.0	.	849;849	Q96MT7;Q96MT7-2	WDR52_HUMAN;.	C	849	ENSP00000377428:W849C;ENSP00000295868:W849C	.	W	-	3	0	WDR52	114567744	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.523000	0.67099	2.793000	0.96121	0.650000	0.86243	TGG		0.353	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113085054	C	A	113085054	3	1	86	1	0	0	0	0	1	0	0	0	17344	740	26	2	3100	2	WDR52	3	113085054	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	4860483	113085054	84937376	26	24050										
RNF13	11342	hgsc.bcm.edu	37	chr3	149613280	149613280	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gttttaaatgcacagagagcAggatacaaggcagccatagt	11	7	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:149613280A>G	ENST00000344229.3	+	6	1044	c.342A>G	c.(340-342)gcA>gcG	p.A114A	RNF13_ENST00000392894.3_Silent_p.A114A|RNF13_ENST00000361785.6_5'UTR	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	114	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CACAGAGAGCAGGATACAAGG	0.343																																																0			3											134	113	120					3																	149613280		2203	4300	6503	151095970	SO:0001819	synonymous_variant	11342			AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"RING-type (C3HC4) zinc fingers"	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.342A>G	3.37:g.149613280A>G			151095970	A6NC87|B3KR12|Q05D66|Q6IBJ9	Silent	SNP	ENST00000344229.3	37	CCDS3146.1																																																																																				0.343	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384		G	149613280	A	G	149613280	2	3	86	1	0	0	0	0	0	0	0	1	13474	175	7	4		4	RNF13	3	149613280	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	36528226	149613280	48409150	27	24051										
LRRC31	79782	hgsc.bcm.edu	37	chr3	169566000	169566000	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttagtgtttccagaagcagcTtcaagttgccaccaacacac	7	12	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:169566000T>C	ENST00000316428.5	-	8	1292	c.1235A>G	c.(1234-1236)aAg>aGg	p.K412R	LRRC31_ENST00000264676.5_Missense_Mutation_p.K356R|LRRC31_ENST00000523069.1_Missense_Mutation_p.K412R	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	412				K -> E (in Ref. 3; BAB15589). {ECO:0000305}.						cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CAGAAGCAGCTTCAAGTTGCC	0.473																																																0			3											78	79	79					3																	169566000		2001	4181	6182	171048694	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1235A>G	3.37:g.169566000T>C	ENSP00000325978:p.Lys412Arg		171048694	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	T	5.250	0.231496	0.09969	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.53857	0.6;0.6;0.6	4.61	2.16	0.27623	.	0.504809	0.22750	N	0.056084	T	0.49253	0.1546	M	0.75264	2.295	0.21147	N	0.999774	P;B	0.42692	0.787;0.083	B;B	0.41988	0.372;0.022	T	0.36986	-0.9725	10	0.27785	T	0.31	-5.4006	7.1729	0.25728	0.0:0.0775:0.1471:0.7754	.	356;412	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	R	412;356;412	ENSP00000325978:K412R;ENSP00000264676:K356R;ENSP00000429145:K412R	ENSP00000264676:K356R	K	-	2	0	LRRC31	171048694	1.000000	0.71417	0.825000	0.32803	0.015000	0.08874	1.899000	0.39818	0.155000	0.19261	-0.313000	0.08912	AAG		0.473	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		C	169566000	T	C	169566000	3	2	86	1	0	0	0	0	1	0	0	0	9015	1609	56	4	431	4	LRRC31	3	169566000	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	19952720	169566000	28456430	28	24052										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178942591	178942591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgtttcagaacaatgagatcAtctttaaaaatggggatggt	10	4	3	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178942591A>G	ENST00000263967.3	+	16	2555	c.2398A>G	c.(2398-2400)Atc>Gtc	p.I800V		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	800	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAATGAGATCATCTTTAAAAA	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											144	134	137					3																	178942591		1857	4094	5951	180425285	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2398A>G	3.37:g.178942591A>G	ENSP00000263967:p.Ile800Val		180425285	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.471237	0.84533	.	.	ENSG00000121879	ENST00000263967	T	0.77750	-1.12	5.39	5.39	0.77823	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88500	0.6453	M	0.87827	2.91	0.80722	D	1	D	0.67145	0.996	D	0.63381	0.914	D	0.90685	0.4608	10	0.87932	D	0	-10.5967	15.7036	0.77560	1.0:0.0:0.0:0.0	.	800	P42336	PK3CA_HUMAN	V	800	ENSP00000263967:I800V	ENSP00000263967:I800V	I	+	1	0	PIK3CA	180425285	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.807000	0.91935	2.173000	0.68751	0.460000	0.39030	ATC		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178942591	A	G	178942591	3	3	86	1	0	0	0	0	1	0	0	0	11944	217	8	4	2456	4	PIK3CA	3	178942591	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	9376591	178942591	19079839	29	24053			1	14		4	4	9446	A		1.395611e-05
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951978	178951978	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgcttggctctggaatgccAgaactacaatcttttgatga	9	8	2	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178951978A>G	ENST00000263967.3	+	21	3190	c.3033A>G	c.(3031-3033)ccA>ccG	p.P1011P	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1011	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.P1011P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTGGAATGCCAGAACTACAAT	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - coding silent(1)	large_intestine(1)	3											111	99	102					3																	178951978		1882	4110	5992	180434672	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3033A>G	3.37:g.178951978A>G			180434672	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951978	A	G	178951978	2	3	86	1	0	0	0	0	0	0	0	1	11944	175	7	4		4	PIK3CA	3	178951978	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	9387	178951978	19070452	30	24054			1	14		4	4	9446	A		1.395611e-05
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951998	178951998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agaactacaatcttttgatgAcattgcatacattcgaaaga	6	7	1	4			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178951998A>G	ENST00000263967.3	+	21	3210	c.3053A>G	c.(3052-3054)gAc>gGc	p.D1018G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1018	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCTTTTGATGACATTGCATAC	0.398		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											107	95	99					3																	178951998		1877	4118	5995	180434692	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3053A>G	3.37:g.178951998A>G	ENSP00000263967:p.Asp1018Gly		180434692	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.718873	0.68844	.	.	ENSG00000121879	ENST00000263967	D	0.82167	-1.58	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.91998	0.7465	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.93021	0.6440	10	0.87932	D	0	-20.7568	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1018	P42336	PK3CA_HUMAN	G	1018	ENSP00000263967:D1018G	ENSP00000263967:D1018G	D	+	2	0	PIK3CA	180434692	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.798000	0.91888	2.333000	0.79357	0.482000	0.46254	GAC		0.398	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951998	A	G	178951998	3	3	86	1	0	0	0	0	1	0	0	0	11944	275	10	4	3131	4	PIK3CA	3	178951998	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	20	178951998	19070432	31	24055			1	14		4	4	9446	A		1.395611e-05
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952036	178952036	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agaccctagccttagataaaActgagcaagaggctttggag	11	8	0	4			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178952036A>G	ENST00000263967.3	+	21	3248	c.3091A>G	c.(3091-3093)Act>Gct	p.T1031A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1031	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTTAGATAAAACTGAGCAAGA	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											93	82	86					3																	178952036		1872	4117	5989	180434730	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3091A>G	3.37:g.178952036A>G	ENSP00000263967:p.Thr1031Ala		180434730	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.855179	0.32791	.	.	ENSG00000121879	ENST00000263967	D	0.81739	-1.53	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.258350	0.36972	N	0.002317	D	0.84611	0.5510	M	0.88181	2.935	0.58432	D	0.999999	B	0.18013	0.025	B	0.18561	0.022	T	0.82585	-0.0384	10	0.72032	D	0.01	-20.0073	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1031	P42336	PK3CA_HUMAN	A	1031	ENSP00000263967:T1031A	ENSP00000263967:T1031A	T	+	1	0	PIK3CA	180434730	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.555000	0.45854	2.333000	0.79357	0.482000	0.46254	ACT		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952036	A	G	178952036	3	3	86	1	0	0	0	0	1	0	0	0	11944	43	2	4	3169	4	PIK3CA	3	178952036	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	38	178952036	19070394	32	24056			1	14		4	4	9446	A		1.395611e-05
FGF12	2257	hgsc.bcm.edu	37	chr3	192078255	192078255	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ccttggtcccatcaatggtaCcatctgggtgcatctgcagg	11	12	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:192078255C>A	ENST00000454309.2	-	2	1097	c.272G>T	c.(271-273)gGt>gTt	p.G91V	FGF12_ENST00000445105.2_Missense_Mutation_p.G29V|FGF12_ENST00000450716.1_Missense_Mutation_p.G29V|FGF12_ENST00000264730.3_Missense_Mutation_p.G29V|FGF12_ENST00000430714.1_Intron	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	91					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ATCAATGGTACCATCTGGGTG	0.408																																																0			3											175	150	158					3																	192078255		2203	4300	6503	193560949	SO:0001583	missense	2257			U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"fibroblast growth factor 12B", "fibroblast growth factor homologous factor 1", "myocyte-activating factor", "fibroblast growth factor FGF-12b"	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.272G>T	3.37:g.192078255C>A	ENSP00000413496:p.Gly91Val		193560949	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558103	0.86231	.	.	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	D;D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64;-2.64;-2.64	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	H	0.96301	3.8	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.967;0.996	D	0.98117	1.0423	10	0.87932	D	0	.	18.4573	0.90725	0.0:1.0:0.0:0.0	.	29;91	P61328-2;P61328	.;FGF12_HUMAN	V	29;29;29;91;29;5;29	ENSP00000264730:G29V;ENSP00000393686:G29V;ENSP00000413496:G91V;ENSP00000397635:G29V;ENSP00000412904:G5V;ENSP00000395517:G29V	ENSP00000264730:G29V	G	-	2	0	FGF12	193560949	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.398000	0.79919	2.613000	0.88420	0.591000	0.81541	GGT		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		A	192078255	C	A	192078255	3	1	86	1	0	0	0	0	1	0	0	0	5860	507	18	2	475	2	FGF12	3	192078255	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	13126219	192078255	5944175	33	24057										
CCKAR	886	hgsc.bcm.edu	37	chr4	26483526	26483526	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gaggcggcgctctgcggaggCggtgtcgtaggcccgccagg	20	12	1	0	rs115488558		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:26483526C>T	ENST00000295589.3	-	5	1215	c.1021G>A	c.(1021-1023)Gcc>Acc	p.A341T		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	341					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	TCTGCGGAGGCGGTGTCGTAG	0.587																																																0			4						C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	103	93	97		1021	3.5	0.6	4	dbSNP_132	97	0,8600		0,0,4300	yes	missense	CCKAR	NM_000730.2	58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	341/429	26483526	2,13004	2203	4300	6503	26092624	SO:0001583	missense	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1021G>A	4.37:g.26483526C>T	ENSP00000295589:p.Ala341Thr		26092624	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	6.814	0.519356	0.13005	4.54E-4	0.0	ENSG00000163394	ENST00000295589	T	0.71579	-0.58	5.29	3.46	0.39613	GPCR, rhodopsin-like superfamily (1);	0.399005	0.27691	N	0.018255	T	0.51534	0.1680	N	0.21545	0.675	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.26121	-1.0112	10	0.12766	T	0.61	.	10.3464	0.43909	0.0:0.791:0.1351:0.0739	.	341	P32238	CCKAR_HUMAN	T	341	ENSP00000295589:A341T	ENSP00000295589:A341T	A	-	1	0	CCKAR	26092624	0.000000	0.05858	0.556000	0.28293	0.564000	0.35744	0.084000	0.14891	1.234000	0.43709	0.563000	0.77884	GCC		0.587	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			T	26483526	C	T	26483526	3	4	86	1	0	0	0	0	1	0	0	0	2886	768	27	1	269	1	CCKAR	4	26483526	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		26483526	164670750	34	24058										
KIT	3815	hgsc.bcm.edu	37	chr4	55599348	55599348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gaatgattctaattatgtggTtaaaggaaacgtgagtaccc	10	5	1	2	rs121913524		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:55599348T>C	ENST00000288135.5	+	17	2571	c.2474T>C	c.(2473-2475)gTt>gCt	p.V825A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	825	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V825A(27)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATTATGTGGTTAAAGGAAAC	0.373		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	27	Substitution - Missense(27)	haematopoietic_and_lymphoid_tissue(27)	4											150	153	152					4																	55599348		2203	4300	6503	55294105	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2474T>C	4.37:g.55599348T>C	ENSP00000288135:p.Val825Ala		55294105	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.521679	0.85600	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.82255	-1.59;-1.59	5.47	5.47	0.80525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000093	D	0.84529	0.5492	N	0.16478	0.41	0.80722	D	1	P;D	0.76494	0.945;0.999	P;D	0.87578	0.815;0.998	D	0.87077	0.2163	10	0.62326	D	0.03	.	15.5485	0.76129	0.0:0.0:0.0:1.0	.	821;825	P10721-2;P10721	.;KIT_HUMAN	A	825;821	ENSP00000288135:V825A;ENSP00000390987:V821A	ENSP00000288135:V825A	V	+	2	0	KIT	55294105	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.130000	0.71663	2.084000	0.62774	0.477000	0.44152	GTT		0.373	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55599348	T	C	55599348	3	2	86	1	0	0	0	0	1	0	0	0	8350	1725	60	4	2540	4	KIT	4	55599348	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	29115822	55599348	135554928	35	24059										
RASGEF1B	153020	hgsc.bcm.edu	37	chr4	82355042	82355042	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cagatactgcaagatcttccGgtccctctcaaatggacact	7	13	2	2	rs201599232		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:82355042G>C	ENST00000264400.2	-	12	1427	c.1276C>G	c.(1276-1278)Cgg>Ggg	p.R426G	RASGEF1B_ENST00000509081.1_Missense_Mutation_p.R425G|RASGEF1B_ENST00000335927.7_Missense_Mutation_p.R384G	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	426	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						AAGATCTTCCGGTCCCTCTCA	0.413																																																0			4						G	GLY/ARG	0,4406		0,0,2203	211	187	196		1276	5.1	1	4		196	1,8599	1.2+/-3.3	0,1,4299	no	missense	RASGEF1B	NM_152545.1	125	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	426/474	82355042	1,13005	2203	4300	6503	82574066	SO:0001583	missense	153020			AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1276C>G	4.37:g.82355042G>C	ENSP00000264400:p.Arg426Gly		82574066	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403906	0.62288	0.0	1.16E-4	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.31510	1.49;1.49;1.49	5.05	5.05	0.67936	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.43077	0.1231	M	0.75615	2.305	0.80722	D	1	B;B;B	0.29627	0.252;0.252;0.25	B;B;B	0.36608	0.229;0.229;0.115	T	0.44590	-0.9318	10	0.59425	D	0.04	.	18.1775	0.89766	0.0:0.0:1.0:0.0	.	384;425;426	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	G	425;426;384	ENSP00000425393:R425G;ENSP00000264400:R426G;ENSP00000338437:R384G	ENSP00000264400:R426G	R	-	1	2	RASGEF1B	82574066	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.230000	0.58632	2.640000	0.89533	0.585000	0.79938	CGG		0.413	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545		C	82355042	G	C	82355042	3	2	86	1	0	0	0	0	1	0	0	0	13107	1115	39	5	157	5	RASGEF1B	4	82355042	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	26755694	82355042	108799234	36	24060										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103459065	103459065	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggcccatcccatggtggactAcctggtgcctctagtgaaaa	11	12	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:103459065A>G	ENST00000505458.1	+	5	484	c.207A>G	c.(205-207)ctA>ctG	p.L69L	NFKB1_ENST00000394820.4_Silent_p.L69L|NFKB1_ENST00000226574.4_Silent_p.L70L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	69	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L70L(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	ATGGTGGACTACCTGGTGCCT	0.393																																																1	Substitution - coding silent(1)	ovary(1)	4											162	153	156					4																	103459065		2203	4300	6503	103678093	SO:0001819	synonymous_variant	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.207A>G	4.37:g.103459065A>G			103678093	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																				0.393	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103459065	A	G	103459065	2	3	86	1	0	0	0	0	0	0	0	1	10406	378	14	4		4	NFKB1	4	103459065	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	21104023	103459065	87695211	37	24061										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153258991	153258995	+	Frame_Shift_Del	DEL	TGGGG	TGGGG	-													0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aaatgaagtctcgttgaaacTggggttctatcacttgcatc							TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	TGGGG	TGGGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:153258991_153258995delTGGGG	ENST00000281708.4	-	5	2049_2053	c.820_824delCCCCA	c.(820-825)ccccagfs	p.PQ274fs	FBXW7_ENST00000296555.5_Frame_Shift_Del_p.PQ156fs|FBXW7_ENST00000393956.3_Frame_Shift_Del_p.PQ98fs|RP11-461L13.2_ENST00000605147.1_RNA|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.PQ274fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.PQ194fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.PQ274fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	274					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TCGTTGAAACTGGGGTTCTATCACT	0.361			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4																																								153478445	SO:0001589	frameshift_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.820_824delCCCCA	4.37:g.153258991_153258995delTGGGG	ENSP00000281708:p.Pro274fs		153478441	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				0.361	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			-	153258995	TGGGG	-	153258991	7	5	86	1	0	1	0	1	0	0	0	0	5788	1580	55	0	1331	0	FBXW7	4	153258991	Frame_Shift_Del	DEL	TGGGG	TCGA-CI-6619-01B-11D-1826-10	49799926	153258991	37895285	38	24062										
PDGFC	56034	hgsc.bcm.edu	37	chr4	157732157	157732157	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcactgggttcctcaacttcTacaaaatcatacctgcaaaa	4	12	4	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:157732157T>A	ENST00000502773.1	-	3	817	c.327A>T	c.(325-327)gtA>gtT	p.V109V	PDGFC_ENST00000542208.1_5'UTR|PDGFC_ENST00000541126.1_5'UTR|PDGFC_ENST00000422544.2_Silent_p.V109V	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	109	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		CCTCAACTTCTACAAAATCAT	0.383																																																0			4											63	60	61					4																	157732157		2203	4299	6502	157951607	SO:0001819	synonymous_variant	56034			AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.327A>T	4.37:g.157732157T>A			157951607	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																				0.383	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			A	157732157	T	A	157732157	2	1	86	1	0	0	0	0	0	0	0	1	11690	1509	53	5		5	PDGFC	4	157732157	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	4473166	157732157	33422119	39	24063										
CDH18	1016	hgsc.bcm.edu	37	chr5	19721514	19721514	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agaatgctgtaaaccacccgAgcgctgtttccataggtagg	11	10	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:19721514A>G	ENST00000507958.1	-	7	1575	c.585T>C	c.(583-585)gcT>gcC	p.A195A	CDH18_ENST00000382275.1_Silent_p.A195A|CDH18_ENST00000506372.1_Silent_p.A195A|CDH18_ENST00000511273.1_Silent_p.A195A|CDH18_ENST00000274170.4_Silent_p.A195A|CDH18_ENST00000502796.1_Silent_p.A195A			Q13634	CAD18_HUMAN	cadherin 18, type 2	195	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AAACCACCCGAGCGCTGTTTC	0.468																																																0			5											153	136	142					5																	19721514		2203	4300	6503	19757271	SO:0001819	synonymous_variant	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.585T>C	5.37:g.19721514A>G			19757271	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																				0.468	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		G	19721514	A	G	19721514	2	3	86	1	0	0	0	0	0	0	0	1	3109	291	11	4		4	CDH18	5	19721514	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10		19721514	161193746	40	24064										
RAB3C	115827	hgsc.bcm.edu	37	chr5	58147071	58147071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gccttgtggatatcatctgcGacaaaatgtcagagagtttg	11	7	3	1	rs199850819		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:58147071G>A	ENST00000282878.4	+	5	746	c.577G>A	c.(577-579)Gac>Aac	p.D193N	CTD-2176I21.2_ENST00000510198.1_RNA	NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	193					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		TATCATCTGCGACAAAATGTC	0.468																																																0			5											138	123	128					5																	58147071		2203	4300	6503	58182828	SO:0001583	missense	115827			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"RAB, member RAS oncogene"	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.577G>A	5.37:g.58147071G>A	ENSP00000282878:p.Asp193Asn		58182828		Missense_Mutation	SNP	ENST00000282878.4	37	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.739560	0.69304	.	.	ENSG00000152932	ENST00000282878	T	0.79352	-1.26	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000005	T	0.67429	0.2892	N	0.17838	0.53	0.80722	D	1	B	0.12630	0.006	B	0.12837	0.008	T	0.60026	-0.7343	10	0.19590	T	0.45	-21.3131	20.3539	0.98825	0.0:0.0:1.0:0.0	.	193	Q96E17	RAB3C_HUMAN	N	193	ENSP00000282878:D193N	ENSP00000282878:D193N	D	+	1	0	RAB3C	58182828	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.860000	0.99555	2.826000	0.97356	0.655000	0.94253	GAC		0.468	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453		A	58147071	G	A	58147071	3	1	86	1	0	0	0	0	1	0	0	0	12970	1058	37	1	595	1	RAB3C	5	58147071	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	38425557	58147071	122768189	41	24065										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75996931	75996931	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agatcaattaaactagatggAaaaggagaacccaaaggggc	11	6	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:75996931A>G	ENST00000274364.6	+	34	4695	c.4398A>G	c.(4396-4398)ggA>ggG	p.G1466G	CTD-2384B11.2_ENST00000507514.1_RNA|IQGAP2_ENST00000396234.3_Silent_p.G962G|IQGAP2_ENST00000379730.3_Silent_p.G968G|IQGAP2_ENST00000502745.1_Silent_p.G962G	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1466					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AACTAGATGGAAAAGGAGAAC	0.423																																																0			5											96	94	95					5																	75996931		2203	4300	6503	76032687	SO:0001819	synonymous_variant	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4398A>G	5.37:g.75996931A>G			76032687	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1																																																																																				0.423	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		G	75996931	A	G	75996931	2	3	86	1	0	0	0	0	0	0	0	1	7836	233	9	4		4	IQGAP2	5	75996931	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	17849860	75996931	104918329	42	24066										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93732091	93732091	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctttcttcaattcaacaaatTtttttgacatttttctctca	1	9	5	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:93732091T>G	ENST00000513200.3	-	16	3083	c.3011A>C	c.(3010-3012)aAa>aCa	p.K1004T	KIAA0825_ENST00000427991.2_Missense_Mutation_p.K1004T	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1004										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTCAACAAATTTTTTTGACAT	0.373																																																0			5											34	29	31					5																	93732091		692	1590	2282	93757847	SO:0001583	missense	285600			BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3011A>C	5.37:g.93732091T>G	ENSP00000424618:p.Lys1004Thr		93757847	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	37		.	.	.	.	.	.	.	.	.	.	T	9.646	1.140237	0.21205	.	.	ENSG00000185261	ENST00000513200;ENST00000427991	T;T	0.46819	0.86;0.86	5.34	4.18	0.49190	.	.	.	.	.	T	0.28499	0.0705	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05517	-1.0880	9	0.41790	T	0.15	.	7.6659	0.28430	0.0:0.0735:0.1405:0.786	.	1004;1004	Q8IV33;C9J0Q2	K0825_HUMAN;.	T	1004	ENSP00000424618:K1004T;ENSP00000400288:K1004T	ENSP00000400288:K1004T	K	-	2	0	KIAA0825	93757847	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.024000	0.41049	0.886000	0.36113	-0.371000	0.07208	AAA		0.373	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		G	93732091	T	G	93732091	3	3	86	1	0	0	0	0	1	0	0	0	2301	1841	64	4	836	4	C5orf36	5	93732091	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	17735160	93732091	87183169	43	24067										
APC	324	hgsc.bcm.edu	37	chr5	112174880	112174880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cacagaaacagtcattttcaTtctcaaagagttcatctgga	6	9	5	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:112174880T>C	ENST00000457016.1	+	16	3969	c.3589T>C	c.(3589-3591)Ttc>Ctc	p.F1197L	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.F1197L|APC_ENST00000508376.2_Missense_Mutation_p.F1197L			P25054	APC_HUMAN	adenomatous polyposis coli	1197	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		F -> S (in gastric cancer).		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTCATTTTCATTCTCAAAGAG	0.363		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											84	88	87					5																	112174880		2202	4300	6502	112202779	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3589T>C	5.37:g.112174880T>C	ENSP00000413133:p.Phe1197Leu		112202779	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461227	0.26248	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.89552	-2.31;-2.31;-2.31;-2.53	5.91	5.91	0.95273	.	0.231571	0.45867	D	0.000324	D	0.82568	0.5065	L	0.27053	0.805	0.34995	D	0.755371	B;B	0.26318	0.146;0.146	B;B	0.24974	0.057;0.057	T	0.82452	-0.0450	9	.	.	.	-12.8334	16.0187	0.80464	0.0:0.0:0.0:1.0	.	1199;1197	Q4LE70;P25054	.;APC_HUMAN	L	1197	ENSP00000413133:F1197L;ENSP00000257430:F1197L;ENSP00000427089:F1197L;ENSP00000423828:F1197L	.	F	+	1	0	APC	112202779	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.476000	0.66793	2.261000	0.74972	0.533000	0.62120	TTC		0.363	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112174880	T	C	112174880	3	2	86	1	0	0	0	0	1	0	0	0	763	1493	52	4	3647	4	APC	5	112174880	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	18442789	112174880	68740380	44	24068										
APC	324	hgsc.bcm.edu	37	chr5	112175358	112175358	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	caaagctgttgaattttcttCaggagcgaaatctccctcca	7	11	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:112175358C>G	ENST00000457016.1	+	16	4447	c.4067C>G	c.(4066-4068)tCa>tGa	p.S1356*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1356*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1356*			P25054	APC_HUMAN	adenomatous polyposis coli	1356	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1356*(11)|p.G1357fs*13(2)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATTTTCTTCAGGAGCGAAA	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(11)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5											62	64	63					5																	112175358		2202	4300	6502	112203257	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4067C>G	5.37:g.112175358C>G	ENSP00000413133:p.Ser1356*		112203257	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	9.058983	0.99051	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.141330	0.49916	D	0.000133	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.6466	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1356	.	.	S	+	2	0	APC	112203257	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCA		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175358	C	G	112175358	4	3	86	1	0	0	0	0	0	1	0	0	763	838	29	5	4125	5	APC	5	112175358	Nonsense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	478	112175358	68739902	45	24069										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115346463	115346463	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	attatattgagattgaaacaGcacttgagttaaccaagtac	7	6	0	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:115346463G>T	ENST00000357872.4	+	14	2243	c.2119G>T	c.(2119-2121)Gca>Tca	p.A707S		NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		707						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A707T(1)									GATTGAAACAGCACTTGAGTT	0.343																																																1	Substitution - Missense(1)	central_nervous_system(1)	5											123	122	122					5																	115346463		2201	4300	6501	115374362	SO:0001583	missense	0																														ENST00000357872.4:c.2119G>T	5.37:g.115346463G>T	ENSP00000350541:p.Ala707Ser		115374362	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764795	0.90020	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.05925	3.37	6.03	6.03	0.97812	.	0.158255	0.44285	D	0.000469	T	0.33323	0.0859	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.04593	-1.0940	10	0.56958	D	0.05	.	19.3283	0.94273	0.0:0.0:1.0:0.0	.	707	Q6Q4G3	AMPQ_HUMAN	S	707;696	ENSP00000350541:A707S	ENSP00000350541:A707S	A	+	1	0	AC010282.1	115374362	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	6.003000	0.70701	2.861000	0.98227	0.655000	0.94253	GCA		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115346463	G	T	115346463	3	4	86	1	0	0	0	0	1	0	0	0	834	971	34	2	2173	2	AQPEP	5	115346463	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	3171105	115346463	65568797	46	24070										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118469391	118469391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atctaatagtttaaaattaaGtatttttacgcctaatgtta	4	4	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:118469391G>A	ENST00000311085.8	+	12	1852	c.1772G>A	c.(1771-1773)aGt>aAt	p.S591N	DMXL1_ENST00000539542.1_Missense_Mutation_p.S591N	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	591										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TTAAAATTAAGTATTTTTACG	0.378																																																0			5											80	80	80					5																	118469391		2202	4300	6502	118497290	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1772G>A	5.37:g.118469391G>A	ENSP00000309690:p.Ser591Asn		118497290		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.157150	0.38119	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.16324	2.97;2.35	5.43	5.43	0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.10852	0.0265	N	0.12182	0.205	0.58432	D	0.999999	B;B	0.34226	0.443;0.139	B;B	0.29077	0.098;0.045	T	0.23940	-1.0174	9	.	.	.	-16.2905	19.2239	0.93810	0.0:0.0:1.0:0.0	.	591;591	F5H269;Q9Y485	.;DMXL1_HUMAN	N	591	ENSP00000309690:S591N;ENSP00000439479:S591N	.	S	+	2	0	DMXL1	118497290	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.431000	0.73395	2.562000	0.86427	0.591000	0.81541	AGT		0.378	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118469391	G	A	118469391	3	1	86	1	0	0	0	0	1	0	0	0	4605	1029	36	3	1818	3	DMXL1	5	118469391	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	3122928	118469391	62445869	47	24071										
PPIC	5480	hgsc.bcm.edu	37	chr5	122361521	122361521	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aacaccacatgtttgccgtcCaaccaggtgggcttggtcaa	10	12	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:122361521C>T	ENST00000306442.4	-	4	583	c.468G>A	c.(466-468)ttG>ttA	p.L156L		NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	156	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	GTTTGCCGTCCAACCAGGTGG	0.438																																					Ovarian(99;690 1502 20765 45543 49568)											0			5											84	72	76					5																	122361521		2203	4300	6503	122389420	SO:0001819	synonymous_variant	5480			S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.468G>A	5.37:g.122361521C>T			122389420	A4LBB5	Silent	SNP	ENST00000306442.4	37	CCDS4133.1																																																																																				0.438	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943		T	122361521	C	T	122361521	2	4	86	1	0	0	0	0	0	0	0	1	12354	593	21	3		3	PPIC	5	122361521	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	3892130	122361521	58553739	48	24072										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129243804	129243804	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gagtttcttagatcgctaaaCagcagtaagcctctctacct	7	11	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:129243804C>T	ENST00000305031.4	+	2	1195	c.837C>T	c.(835-837)aaC>aaT	p.N279N	CTC-575N7.1_ENST00000503616.1_RNA|CTC-575N7.1_ENST00000515569.1_RNA|CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	279					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GATCGCTAAACAGCAGTAAGC	0.423																																																0			5											75	77	77					5																	129243804		2203	4300	6503	129271703	SO:0001819	synonymous_variant	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.837C>T	5.37:g.129243804C>T			129271703	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																				0.423	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		T	129243804	C	T	129243804	2	4	86	1	0	0	0	0	0	0	0	1	3419	477	17	3		3	CHSY3	5	129243804	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	6882283	129243804	51671456	49	24073										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140588820	140588820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agtgttaatgaaaaaccccaCgcagtttttacaaattgagc	7	8	0	2	rs143200514		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:140588820C>T	ENST00000239450.2	+	1	530	c.341C>T	c.(340-342)aCg>aTg	p.T114M	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	114	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAAAACCCCACGCAGTTTTTA	0.448																																																0			5											90	100	97					5																	140588820		2203	4300	6503	140569004	SO:0001583	missense	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.341C>T	5.37:g.140588820C>T	ENSP00000239450:p.Thr114Met		140569004	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	1.592	-0.528831	0.04112	.	.	ENSG00000120328	ENST00000239450	T	0.51574	0.7	4.25	3.09	0.35607	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.20941	0.0504	N	0.05078	-0.115	0.27767	N	0.94361	P	0.43973	0.823	B	0.32677	0.15	T	0.03306	-1.1050	9	0.31617	T	0.26	.	8.7747	0.34753	0.0:0.0954:0.0:0.9046	.	114	Q9Y5F1	PCDBC_HUMAN	M	114	ENSP00000239450:T114M	ENSP00000239450:T114M	T	+	2	0	PCDHB12	140569004	0.247000	0.23920	0.001000	0.08648	0.084000	0.17831	3.399000	0.52586	0.619000	0.30197	-0.367000	0.07326	ACG		0.448	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		T	140588820	C	T	140588820	3	4	86	1	0	0	0	0	1	0	0	0	11568	536	19	1	343	1	PCDHB12	5	140588820	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	11345016	140588820	40326440	50	24074										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141051195	141051195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcttccggaagagacccagaCggtactttcgggagatgaac	13	10	0	4	rs149532200	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:141051195C>T	ENST00000239440.4	-	12	1861	c.1796G>A	c.(1795-1797)cGt>cAt	p.R599H	ARAP3_ENST00000513878.1_Missense_Mutation_p.R261H|ARAP3_ENST00000508305.1_Missense_Mutation_p.R521H	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	599	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GAGACCCAGACGGTACTTTCG	0.637																																																0			5						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	37	37	37		1796	2.5	0.9	5	dbSNP_134	37	2,8598	2.2+/-6.3	0,2,4298	no	missense	ARAP3	NM_022481.5	29	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	possibly-damaging	599/1545	141051195	3,13003	2203	4300	6503	141031379	SO:0001583	missense	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1796G>A	5.37:g.141051195C>T	ENSP00000239440:p.Arg599His		141031379	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985377	0.74474	2.27E-4	2.33E-4	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.44083	0.93;0.93;0.93	3.44	2.55	0.30701	.	0.211226	0.31335	U	0.007827	T	0.47857	0.1468	L	0.33485	1.01	0.24492	N	0.9943	P;D;D	0.89917	0.694;1.0;0.99	B;D;P	0.69824	0.14;0.966;0.751	T	0.29150	-1.0021	10	0.51188	T	0.08	.	9.4582	0.38767	0.0:0.8891:0.0:0.1109	.	261;521;599	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	H	521;599;261	ENSP00000421826:R521H;ENSP00000239440:R599H;ENSP00000421468:R261H	ENSP00000239440:R599H	R	-	2	0	ARAP3	141031379	0.994000	0.37717	0.886000	0.34754	0.955000	0.61496	3.085000	0.50151	0.618000	0.30179	0.563000	0.77884	CGT		0.637	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		T	141051195	C	T	141051195	3	4	86	1	0	0	0	0	1	0	0	0	840	536	19	1	2926	1	ARAP3	5	141051195	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	462375	141051195	39864065	51	24075										
KCTD16	57528	hgsc.bcm.edu	37	chr5	143586926	143586926	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgaaagcagagaccctgatCgagccccagaaagatacacc	9	12	0	5			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:143586926C>T	ENST00000507359.3	+	2	1740	c.649C>T	c.(649-651)Cga>Tga	p.R217*	KCTD16_ENST00000512467.1_Nonsense_Mutation_p.R217*	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	217					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)		p.R217G(1)		large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGACCCTGATCGAGCCCCAGA	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	5											60	65	63					5																	143586926		2203	4300	6503	143567119	SO:0001587	stop_gained	57528			AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.649C>T	5.37:g.143586926C>T	ENSP00000426548:p.Arg217*		143567119	Q9P2M9	Nonsense_Mutation	SNP	ENST00000507359.3	37	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	47	13.333572	0.99735	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	.	.	.	5.69	2.85	0.33270	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.719	0.77694	0.6228:0.3772:0.0:0.0	.	.	.	.	X	217	.	ENSP00000426548:R217X	R	+	1	2	KCTD16	143567119	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.417000	0.34770	0.298000	0.22638	0.561000	0.74099	CGA		0.453	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		T	143586926	C	T	143586926	4	4	86	1	0	0	0	0	0	1	0	0	8124	876	31	1	651	1	KCTD16	5	143586926	Nonsense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	2535731	143586926	37328334	52	24076										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172324048	172324048	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atcctcttcctcttcctctcGgagctcaccggatttataac	5	15	4	0	rs543897451		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:172324048G>T	ENST00000393784.3	+	3	265	c.126G>T	c.(124-126)tcG>tcT	p.S42S	ERGIC1_ENST00000523291.1_Silent_p.S42S|ERGIC1_ENST00000519860.1_3'UTR	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	42					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S42S(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCTTCCTCTCGGAGCTCACCG	0.512																																																1	Substitution - coding silent(1)	ovary(1)	5											255	195	215					5																	172324048		2203	4300	6503	172256654	SO:0001819	synonymous_variant	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.126G>T	5.37:g.172324048G>T			172256654	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	37	CCDS34292.1																																																																																				0.512	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		T	172324048	G	T	172324048	2	4	86	1	0	0	0	0	0	0	0	1	5236	1103	39	2		2	ERGIC1	5	172324048	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10	28737122	172324048	8591212	53	24077										
ERVFRDE1	405754	hgsc.bcm.edu	37	chr6	11105463	11105463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctttggagcagttgctgagcTttttccaataacgggaaatc	10	8	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:11105463T>C	ENST00000472091.1	-	2	456	c.81A>G	c.(79-81)aaA>aaG	p.K27K	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Silent_p.K27K	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	27					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						GTTGCTGAGCTTTTTCCAATA	0.507																																																0			6											61	61	61					6																	11105463		2203	4300	6503	11213449	SO:0001819	synonymous_variant	0			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.81A>G	6.37:g.11105463T>C			11213449		Silent	SNP	ENST00000472091.1	37	CCDS4519.1																																																																																				0.507	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		C	11105463	T	C	11105463	2	2	86	1	0	0	0	0	0	0	0	1	5259	1606	56	4		4	ERVFRDE1	6	11105463	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10		11105463	160009604	54	24078										
HIST1H4J	8363	hgsc.bcm.edu	37	chr6	27792188	27792188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	acgcgctcaagcgccagggcCgcaccctctacggtttcggt	12	16	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:27792188C>T	ENST00000355057.1	+	1	305	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C		NM_021968.3	NP_068803.1	P62805	H4_HUMAN	histone cluster 1, H4j	96					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(1)|pancreas(1)	4						GCGCCAGGGCCGCACCCTCTA	0.577																																																0			6											26	28	27					6																	27792188		2200	4289	6489	27900167	SO:0001583	missense	8363			J00188	CCDS4630.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197238	ENSG00000197238		"Histones / Replication-dependent"	4785	protein-coding gene	gene with protein product		602826	"H4 histone family, member E", "histone 1, H4j"	H4FE		6265100, 9439656, 12408966	Standard	NM_021968		Approved	H4/e, H4F2iv	uc003njp.3	P62805	OTTHUMG00000014487	ENST00000355057.1:c.286C>T	6.37:g.27792188C>T	ENSP00000347168:p.Arg96Cys		27900167	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000355057.1	37	CCDS4630.1	.	.	.	.	.	.	.	.	.	.	.	19.42	3.823247	0.71143	.	.	ENSG00000197238	ENST00000355057	.	.	.	3.93	3.93	0.45458	.	0.000000	0.64402	U	0.000001	T	0.66982	0.2845	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.72427	-0.4297	6	0.72032	D	0.01	.	13.9744	0.64262	0.0:1.0:0.0:0.0	.	.	.	.	C	96	.	ENSP00000347168:R96C	R	+	1	0	HIST1H4J	27900167	1.000000	0.71417	0.970000	0.41538	0.346000	0.29079	7.340000	0.79292	2.134000	0.65973	0.585000	0.79938	CGC		0.577	HIST1H4J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040155.1	NM_021968		T	27792188	C	T	27792188	3	4	86	1	0	0	0	0	1	0	0	0	7195	652	23	1	288	1	HIST1H4J	6	27792188	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	16686725	27792188	143322879	55	24079										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33657928	33657928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	accacgtgggctacatcctgAccagtgtcctgggcctcttt	10	14	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:33657928A>G	ENST00000374316.5	+	52	8045	c.6985A>G	c.(6985-6987)Acc>Gcc	p.T2329A	ITPR3_ENST00000605930.1_Missense_Mutation_p.T2329A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2329					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTACATCCTGACCAGTGTCCT	0.597																																																0			6											120	96	104					6																	33657928		2203	4300	6503	33765906	SO:0001583	missense	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6985A>G	6.37:g.33657928A>G	ENSP00000363435:p.Thr2329Ala		33765906	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728936	0.89390	.	.	ENSG00000096433	ENST00000374316	D	0.98362	-4.89	5.18	5.18	0.71444	Ion transport (1);	0.051258	0.85682	D	0.000000	D	0.98040	0.9354	L	0.52266	1.64	0.54753	D	0.999984	P;D	0.63046	0.67;0.992	B;D	0.67231	0.403;0.95	D	0.99833	1.1055	10	0.87932	D	0	-20.3344	15.0372	0.71757	1.0:0.0:0.0:0.0	.	2329;1999	Q14573;Q59ES2	ITPR3_HUMAN;.	A	2329	ENSP00000363435:T2329A	ENSP00000363435:T2329A	T	+	1	0	ITPR3	33765906	1.000000	0.71417	0.964000	0.40570	0.980000	0.70556	9.339000	0.96797	1.976000	0.57569	0.379000	0.24179	ACC		0.597	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		G	33657928	A	G	33657928	3	3	86	1	0	0	0	0	1	0	0	0	7943	275	10	4	7187	4	ITPR3	6	33657928	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	5865740	33657928	137457139	56	24080										
TTK	7272	hgsc.bcm.edu	37	chr6	80745121	80745121	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgttagaggcagttcacacAatccatcaacatggtattta	7	8	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:80745121A>G	ENST00000369798.2	+	16	2022	c.1911A>G	c.(1909-1911)acA>acG	p.T637T	TTK_ENST00000509894.1_Silent_p.T636T|TTK_ENST00000230510.3_Silent_p.T636T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CAGTTCACACAATCCATCAAC	0.299																																																0			6											86	83	84					6																	80745121		2203	4300	6503	80801840	SO:0001819	synonymous_variant	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1911A>G	6.37:g.80745121A>G			80801840	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Silent	SNP	ENST00000369798.2	37	CCDS4993.1																																																																																				0.299	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			G	80745121	A	G	80745121	2	3	86	1	0	0	0	0	0	0	0	1	16760	117	5	4		4	TTK	6	80745121	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	47087193	80745121	90369946	57	24081										
RARS2	57038	hgsc.bcm.edu	37	chr6	88255345	88255345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgtacttaccaaactgcatgCcccaatcgccaaggtaattt	6	12	0	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:88255345C>T	ENST00000369536.5	-	7	569	c.524G>A	c.(523-525)gGc>gAc	p.G175D		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	175					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		AAACTGCATGCCCCAATCGCC	0.299																																																0			6											124	131	129					6																	88255345		2203	4298	6501	88312064	SO:0001583	missense	57038			AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.524G>A	6.37:g.88255345C>T	ENSP00000358549:p.Gly175Asp		88312064	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.6|26.6	4.752906|4.752906	0.89753|0.89753	.|.	.|.	ENSG00000146282|ENSG00000146282	ENST00000451155|ENST00000369536;ENST00000369523	.|D	.|0.83992	.|-1.79	6.17|6.17	6.17|6.17	0.99709|0.99709	.|Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94689|0.94689	0.8287|0.8287	H|H	0.97707|0.97707	4.06|4.06	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.95512|0.95512	0.8587|0.8587	5|10	.|0.87932	.|D	.|0	.|.	19.6509|19.6509	0.95805|0.95805	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|175	.|Q5T160	.|SYRM_HUMAN	T|D	203|175;202	.|ENSP00000358549:G175D	.|ENSP00000358536:G202D	A|G	-|-	1|2	0|0	RARS2|RARS2	88312064|88312064	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.389000|6.389000	0.73199|0.73199	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCA|GGC		0.299	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88255345	C	T	88255345	3	4	86	1	0	0	0	0	1	0	0	0	13096	739	26	3	1268	3	RARS2	6	88255345	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	7510224	88255345	82859722	58	24082										
ACAT2	39	hgsc.bcm.edu	37	chr6	160197202	160197202	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtcttattgaagttaaaacaGatgagtttcctcgccatggg	10	7	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:160197202G>C	ENST00000367048.4	+	6	2415	c.655G>C	c.(655-657)Gat>Cat	p.D219H	ACAT2_ENST00000472052.1_3'UTR|ACAT2_ENST00000541436.1_Missense_Mutation_p.D248H	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	219					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGTTAAAACAGATGAGTTTCC	0.448																																																0			6											121	115	117					6																	160197202		2203	4300	6503	160117192	SO:0001583	missense	8435			AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.655G>C	6.37:g.160197202G>C	ENSP00000356015:p.Asp219His		160117192	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	37	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557648	0.86231	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	D;D	0.95342	-3.68;-3.68	5.94	5.08	0.68730	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	H	0.99156	4.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99552	1.0966	10	0.87932	D	0	-0.0876	15.0966	0.72238	0.0676:0.0:0.9324:0.0	.	248;219	B7Z233;Q9BWD1	.;THIC_HUMAN	H	219;248	ENSP00000356015:D219H;ENSP00000437850:D248H	ENSP00000356015:D219H	D	+	1	0	ACAT2	160117192	1.000000	0.71417	0.981000	0.43875	0.993000	0.82548	9.397000	0.97276	1.527000	0.49086	0.561000	0.74099	GAT		0.448	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		C	160197202	G	C	160197202	3	2	86	1	0	0	0	0	1	0	0	0	122	942	33	5	677	5	ACAT2	6	160197202	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	71941857	160197202	10917865	59	24083										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20444382	20444382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgtgcagtggaagaggcacgTgtgtgtgtggaaggtgtgag	20	3	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:20444382T>C	ENST00000222573.4	+	11	2503	c.1819T>C	c.(1819-1821)Tgt>Cgt	p.C607R	ITGB8_ENST00000537992.1_Missense_Mutation_p.C472R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	607	Cysteine-rich tandem repeats.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AAGAGGCACGTGTGTGTGTGG	0.557																																																0			7											195	154	167					7																	20444382		2203	4300	6503	20410907	SO:0001583	missense	3696				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1819T>C	7.37:g.20444382T>C	ENSP00000222573:p.Cys607Arg		20410907	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	37	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.662441	0.88251	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.97831	-4.56;-4.56	5.65	5.65	0.86999	EGF, extracellular (1);	0.000000	0.85682	D	0.000000	D	0.98868	0.9617	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99811	1.1041	10	0.87932	D	0	.	16.175	0.81844	0.0:0.0:0.0:1.0	.	607	P26012	ITB8_HUMAN	R	472;607	ENSP00000441561:C472R;ENSP00000222573:C607R	ENSP00000222573:C607R	C	+	1	0	ITGB8	20410907	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.336000	0.79245	2.274000	0.75844	0.528000	0.53228	TGT		0.557	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		C	20444382	T	C	20444382	3	2	86	1	0	0	0	0	1	0	0	0	7922	1696	59	4	1861	4	ITGB8	7	20444382	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10		20444382	138694281	60	24084										
STK31	56164	hgsc.bcm.edu	37	chr7	23810668	23810668	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ataatttcaaatacatatagTcaagtactgcaaaagattca	4	6	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:23810668T>C	ENST00000355870.3	+	14	1877	c.1758T>C	c.(1756-1758)agT>agC	p.S586S	STK31_ENST00000354639.3_Silent_p.S563S|STK31_ENST00000433467.2_Silent_p.S586S|STK31_ENST00000428484.1_Silent_p.S563S|STK31_ENST00000405627.3_3'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	586						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATACATATAGTCAAGTACTGC	0.353																																																0			7											176	177	176					7																	23810668		2203	4300	6503	23777193	SO:0001819	synonymous_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1758T>C	7.37:g.23810668T>C			23777193	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				0.353	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		C	23810668	T	C	23810668	2	2	86	1	0	0	0	0	0	0	0	1	15335	1664	58	4		4	STK31	7	23810668	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	3366286	23810668	135327995	61	24085										
FKBP9	11328	hgsc.bcm.edu	37	chr7	33016063	33016063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggatgtgtgtgggtgagaagCgcatcatcaccattcctcct	12	10	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:33016063C>T	ENST00000242209.4	+	4	824	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C	FKBP9_ENST00000489038.1_3'UTR|FKBP9_ENST00000538443.1_Missense_Mutation_p.R81C|FKBP9_ENST00000538336.1_Missense_Mutation_p.R272C|AVL9_ENST00000404479.1_Intron	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	219	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			GGGTGAGAAGCGCATCATCAC	0.483																																																0			7											165	143	151					7																	33016063		2202	4286	6488	32982588	SO:0001583	missense	11328			AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.655C>T	7.37:g.33016063C>T	ENSP00000242209:p.Arg219Cys		32982588	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459301	0.84317	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443	D;D;D	0.87887	-2.31;-2.31;-2.31	4.73	4.73	0.59995	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.000000	0.85682	D	0.000000	D	0.94735	0.8301	M	0.89715	3.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95748	0.8789	10	0.72032	D	0.01	-14.008	18.074	0.89422	0.0:1.0:0.0:0.0	.	272;219;219	B7Z6H3;O95302;B3KQQ0	.;FKBP9_HUMAN;.	C	219;272;81	ENSP00000242209:R219C;ENSP00000439250:R272C;ENSP00000437504:R81C	ENSP00000242209:R219C	R	+	1	0	FKBP9	32982588	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.960000	0.70348	2.341000	0.79615	0.455000	0.32223	CGC		0.483	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		T	33016063	C	T	33016063	3	4	86	1	0	0	0	0	1	0	0	0	5934	768	27	1	669	1	FKBP9	7	33016063	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	9205395	33016063	126122600	62	24086										
BBS9	27241	hgsc.bcm.edu	37	chr7	33217166	33217166	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cataatcttcagagaacagcCtgcaatatgacctatggatc	7	10	2	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:33217166C>T	ENST00000242067.6	+	5	926	c.405C>T	c.(403-405)gcC>gcT	p.A135A	RNA5SP229_ENST00000410809.1_RNA|BBS9_ENST00000355070.2_Silent_p.A135A|BBS9_ENST00000396127.2_Silent_p.A135A|BBS9_ENST00000350941.3_Silent_p.A135A|BBS9_ENST00000425508.2_Silent_p.A90A|BBS9_ENST00000354265.4_Silent_p.A135A	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	135					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			AGAGAACAGCCTGCAATATGA	0.333									Bardet-Biedl syndrome																																							0			7											166	156	159					7																	33217166		2203	4300	6503	33183691	SO:0001819	synonymous_variant	27241	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.405C>T	7.37:g.33217166C>T			33183691	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Silent	SNP	ENST00000242067.6	37	CCDS43566.1																																																																																				0.333	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			T	33217166	C	T	33217166	2	4	86	1	0	0	0	0	0	0	0	1	1343	668	24	3		3	BBS9	7	33217166	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	201103	33217166	125921497	63	24087										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45011719	45011719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcccctcacactcacactgtGcacagtcatgttgagtcctg	8	15	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:45011719G>A	ENST00000258787.7	-	6	860	c.724C>T	c.(724-726)Cac>Tac	p.H242Y		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	242	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CTCACACTGTGCACAGTCATG	0.562																																																0			7											267	207	227					7																	45011719		2203	4300	6503	44978244	SO:0001583	missense	64005			AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.724C>T	7.37:g.45011719G>A	ENSP00000258787:p.His242Tyr		44978244	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	8.187	0.795222	0.16327	.	.	ENSG00000136286	ENST00000258787	D	0.87179	-2.22	2.8	2.8	0.32819	Myosin head, motor domain (2);	0.818686	0.10273	N	0.694573	T	0.76877	0.4049	L	0.29908	0.895	0.09310	N	1	B;B	0.24533	0.105;0.002	B;B	0.23150	0.044;0.003	T	0.61098	-0.7131	10	0.13108	T	0.6	.	7.1836	0.25786	0.0:0.0:0.7341:0.2658	.	242;242	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	Y	242	ENSP00000258787:H242Y	ENSP00000258787:H242Y	H	-	1	0	MYO1G	44978244	0.011000	0.17503	0.003000	0.11579	0.056000	0.15407	0.628000	0.24522	1.857000	0.53885	0.561000	0.74099	CAC		0.562	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			A	45011719	G	A	45011719	3	1	86	1	0	0	0	0	1	0	0	0	10104	1319	46	3	2400	3	MYO1G	7	45011719	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	11794553	45011719	114126944	64	24088										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50097724	50097724	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cctgtggatgttatttgtgcAgtgcggttttctactaaagg	12	6	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:50097724A>C	ENST00000046087.2	-	4	417	c.348T>G	c.(346-348)acT>acG	p.T116T	ZPBP_ENST00000419417.1_Silent_p.T115T|ZPBP_ENST00000491129.1_5'Flank	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	116					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TTATTTGTGCAGTGCGGTTTT	0.353																																																0			7											102	103	103					7																	50097724		2203	4300	6503	50068270	SO:0001819	synonymous_variant	11055			D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.348T>G	7.37:g.50097724A>C			50068270	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	37	CCDS5509.1																																																																																				0.353	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		C	50097724	A	C	50097724	2	2	86	1	0	0	0	0	0	0	0	1	18258	175	7	4		4	ZPBP	7	50097724	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	5086005	50097724	109040939	65	24089										
ACHE	43	hgsc.bcm.edu	37	chr7	100490108	100490108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tccacaggggccaggagagcGtggaagcacggtgttcaaag	16	9	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:100490108G>A	ENST00000412389.1	-	2	1555	c.1400C>T	c.(1399-1401)aCg>aTg	p.T467M	ACHE_ENST00000241069.5_Missense_Mutation_p.T467M|ACHE_ENST00000428317.1_Missense_Mutation_p.T467M|ACHE_ENST00000419336.2_Missense_Mutation_p.T379M|ACHE_ENST00000302913.4_Missense_Mutation_p.T467M|ACHE_ENST00000411582.1_Missense_Mutation_p.T467M|UFSP1_ENST00000388761.2_5'Flank			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	467					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CCAGGAGAGCGTGGAAGCACG	0.652																																																0			7											47	48	47					7																	100490108		2203	4300	6503	100328044	SO:0001583	missense	43				CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1400C>T	7.37:g.100490108G>A	ENSP00000394976:p.Thr467Met		100328044	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	G	8.651	0.898262	0.17686	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000411582;ENST00000422451	T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	3.92	3.92	0.45320	Carboxylesterase, type B (1);	0.189628	0.42964	D	0.000636	T	0.67748	0.2926	L	0.31578	0.945	0.09310	N	1	D;D;D	0.89917	0.981;1.0;0.999	P;D;P	0.65773	0.665;0.938;0.873	T	0.57728	-0.7761	10	0.56958	D	0.05	.	9.095	0.36634	0.0:0.0:0.7812:0.2188	.	379;467;467	P22303-3;P22303-2;P22303	.;.;ACES_HUMAN	M	379;467;467;467;467;467;467	ENSP00000403474:T379M;ENSP00000241069:T467M;ENSP00000414858:T467M;ENSP00000303211:T467M;ENSP00000394976:T467M;ENSP00000404865:T467M	ENSP00000241069:T467M	T	-	2	0	ACHE	100328044	0.987000	0.35691	0.826000	0.32828	0.404000	0.30871	2.636000	0.46545	2.202000	0.70862	0.491000	0.48974	ACG		0.652	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		A	100490108	G	A	100490108	3	1	86	1	0	0	0	0	1	0	0	0	141	1145	40	1	591	1	ACHE	7	100490108	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	50392384	100490108	58648555	66	24090										
C7orf58	79974	hgsc.bcm.edu	37	chr7	120768470	120768470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aaaggaactaaatcagtgtcTgtccttagaagaaattaact	7	6	2	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:120768470T>C	ENST00000310396.5	+	11	1804	c.1337T>C	c.(1336-1338)cTg>cCg	p.L446P	CPED1_ENST00000450913.2_Missense_Mutation_p.L446P|CPED1_ENST00000423795.1_Missense_Mutation_p.L226P	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	446						endoplasmic reticulum (GO:0005783)											AATCAGTGTCTGTCCTTAGAA	0.348																																																0			7											90	91	91					7																	120768470		2203	4300	6503	120555706	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.1337T>C	7.37:g.120768470T>C	ENSP00000309772:p.Leu446Pro		120555706	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.565339	0.65651	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.66099	1.11;-0.19;0.78;0.9;0.41	5.74	5.74	0.90152	.	0.268462	0.30850	N	0.008741	T	0.77605	0.4155	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.994;0.953	T	0.80165	-0.1496	10	0.87932	D	0	.	13.4072	0.60919	0.0:0.0:0.0:1.0	.	226;446;446	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	P	446;446;446;226;226	ENSP00000309772:L446P;ENSP00000398082:L446P;ENSP00000406122:L446P;ENSP00000415573:L226P;ENSP00000391952:L226P	ENSP00000309772:L446P	L	+	2	0	C7orf58	120555706	0.994000	0.37717	0.883000	0.34634	0.681000	0.39784	4.637000	0.61346	2.191000	0.70037	0.477000	0.44152	CTG		0.348	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		C	120768470	T	C	120768470	3	2	86	1	0	0	0	0	1	0	0	0	2411	1580	55	4	1375	4	C7orf58	7	120768470	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	20278362	120768470	38370193	67	24091										
FAM40B	57464	hgsc.bcm.edu	37	chr7	129091565	129091565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	acggcggctgaaggtggcccGggctgttctctacctggccc	15	14	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:129091565G>A	ENST00000249344.2	+	4	426	c.386G>A	c.(385-387)cGg>cAg	p.R129Q	STRIP2_ENST00000435494.2_Missense_Mutation_p.R129Q	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	129					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											AAGGTGGCCCGGGCTGTTCTC	0.562																																																0			7											56	58	57					7																	129091565		2203	4300	6503	128878801	SO:0001583	missense	57464			AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog B (yeast)"		"family with sequence similarity 40, member B"	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.386G>A	7.37:g.129091565G>A	ENSP00000249344:p.Arg129Gln		128878801	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106905	0.94292	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.55760	0.51;0.5	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.75744	0.3891	M	0.89287	3.02	0.80722	D	1	D;P	0.71674	0.998;0.938	D;P	0.76575	0.988;0.511	T	0.79734	-0.1679	10	0.48119	T	0.1	-15.4226	15.256	0.73585	0.0:0.0:1.0:0.0	.	129;129	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	Q	129	ENSP00000249344:R129Q;ENSP00000392393:R129Q	ENSP00000249344:R129Q	R	+	2	0	FAM40B	128878801	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.885000	0.92439	2.262000	0.75019	0.650000	0.86243	CGG		0.562	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		A	129091565	G	A	129091565	3	1	86	1	0	0	0	0	1	0	0	0	5580	1116	39	1	400	1	FAM40B	7	129091565	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	8323095	129091565	30047098	68	24092										
SMARCD3	6604	hgsc.bcm.edu	37	chr7	150938678	150938678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gggcctggacaatggctgagCggctctgtgtgtgcagcccc	16	12	1	1	rs139896646		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:150938678C>T	ENST00000262188.8	-	8	1249	c.839G>A	c.(838-840)cGc>cAc	p.R280H	SMARCD3_ENST00000356800.2_Missense_Mutation_p.R267H|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000477169.1_5'Flank|SMARCD3_ENST00000392811.2_Missense_Mutation_p.R267H	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	280	SWIB.				cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AATGGCTGAGCGGCTCTGTGT	0.562																																																0			7						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	37	33	35		839,800,800	5.5	1	7	dbSNP_134	35	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SMARCD3	NM_001003801.1,NM_001003802.1,NM_003078.3	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	280/484,267/471,267/471	150938678	1,13005	2203	4300	6503	150569611	SO:0001583	missense	6604			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60C", "Swp73-like protein", "SWI/SNF complex 60 kDa subunit C", "60kDa BRG-1/Brm associated factor subunit c"	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.839G>A	7.37:g.150938678C>T	ENSP00000262188:p.Arg280His		150569611	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	37	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055819	0.93793	0.0	1.16E-4	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.55588	0.51;0.52;0.52	5.48	5.48	0.80851	SWIB domain (1);SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.80082	0.4558	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.989;0.993	D	0.85275	0.1058	10	0.87932	D	0	-12.7736	16.8808	0.86062	0.0:1.0:0.0:0.0	.	280;267;280	B7Z4U8;Q6STE5-2;Q6STE5	.;.;SMRD3_HUMAN	H	280;267;267;232	ENSP00000262188:R280H;ENSP00000376558:R267H;ENSP00000349254:R267H	ENSP00000262188:R280H	R	-	2	0	SMARCD3	150569611	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.572000	0.86782	0.655000	0.94253	CGC		0.562	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		T	150938678	C	T	150938678	3	4	86	1	0	0	0	0	1	0	0	0	14816	768	27	1	636	1	SMARCD3	7	150938678	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	21847113	150938678	8199985	69	24093										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71053502	71053502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggatgctggctgctgggttcCgaatcatacctccttggact	12	11	1	0	rs560768671		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:71053502C>T	ENST00000452400.2	-	14	3126	c.2945G>A	c.(2944-2946)cGg>cAg	p.R982Q	NCOA2_ENST00000267974.4_Missense_Mutation_p.R70Q	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	982					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TGCTGGGTTCCGAATCATACC	0.572			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"								C|||	1	0.000199681	0	0	5008	,	,		16562	0.001		0	False		,,,				2504	0						Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0			8											61	66	65					8																	71053502		2064	4215	6279	71216056	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2945G>A	8.37:g.71053502C>T	ENSP00000399968:p.Arg982Gln		71216056	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.01|17.01	3.278609|3.278609	0.59758|0.59758	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000518363|ENST00000452400;ENST00000267974	.|T;T	.|0.07021	.|4.81;3.23	6.05|6.05	6.05|6.05	0.98169|0.98169	.|.	.|0.187477	.|0.46442	.|D	.|0.000290	T|T	0.26882|0.26882	0.0658|0.0658	L|L	0.60455|0.60455	1.87|1.87	0.48288|0.48288	D|D	0.999622|0.999622	.|D;D	.|0.89917	.|1.0;0.991	.|D;B	.|0.70227	.|0.968;0.405	T|T	0.00059|0.00059	-1.2166|-1.2166	5|10	.|0.28530	.|T	.|0.3	.|.	20.6013|20.6013	0.99457|0.99457	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|70;982	.|F8WAJ2;Q15596	.|.;NCOA2_HUMAN	R|Q	83|982;70	.|ENSP00000399968:R982Q;ENSP00000267974:R70Q	.|ENSP00000267974:R70Q	G|R	-|-	1|2	0|0	NCOA2|NCOA2	71216056|71216056	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.927000|0.927000	0.56198|0.56198	2.930000|2.930000	0.48924|0.48924	2.878000|2.878000	0.98634|0.98634	0.650000|0.650000	0.86243|0.86243	GGA|CGG		0.572	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			T	71053502	C	T	71053502	3	4	86	1	0	0	0	0	1	0	0	0	10260	652	23	1	1489	1	NCOA2	8	71053502	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		71053502	75310520	70	24094										
CNBD1	168975	hgsc.bcm.edu	37	chr8	87878745	87878745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgccgatgtcttctcttccaGcagctattttgtctcacatg	7	12	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:87878745G>A	ENST00000518476.1	+	1	73	c.22G>A	c.(22-24)Gca>Aca	p.A8T		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	8										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TTCTCTTCCAGCAGCTATTTT	0.453																																																0			8											103	95	98					8																	87878745		1960	4162	6122	87947861	SO:0001583	missense	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.22G>A	8.37:g.87878745G>A	ENSP00000430073:p.Ala8Thr		87947861		Missense_Mutation	SNP	ENST00000518476.1	37	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	G	2.246	-0.372694	0.05034	.	.	ENSG00000176571	ENST00000518476	T	0.18174	2.23	4.78	-1.86	0.07760	.	1.752230	0.03492	N	0.216755	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.25916	-1.0118	10	0.23302	T	0.38	.	3.4266	0.07413	0.2651:0.0:0.2918:0.4431	.	8	Q8NA66	CNBD1_HUMAN	T	8	ENSP00000430073:A8T	ENSP00000430073:A8T	A	+	1	0	CNBD1	87947861	0.000000	0.05858	0.000000	0.03702	0.931000	0.56810	-0.464000	0.06688	-0.517000	0.06461	0.563000	0.77884	GCA		0.453	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		A	87878745	G	A	87878745	3	1	86	1	0	0	0	0	1	0	0	0	3597	971	34	3	24	3	CNBD1	8	87878745	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	16825243	87878745	58485277	71	24095										
MMP16	4325	hgsc.bcm.edu	37	chr8	89128918	89128918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gggcactgtcggtagaggtcTtgtaggtggaggaatcttgt	17	5	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:89128918T>C	ENST00000286614.6	-	6	1182	c.901A>G	c.(901-903)Aga>Gga	p.R301G	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	301					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R301*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGTAGAGGTCTTGTAGGTGGA	0.512																																																1	Substitution - Nonsense(1)	ovary(1)	8											198	205	202					8																	89128918		2203	4300	6503	89198034	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.901A>G	8.37:g.89128918T>C	ENSP00000286614:p.Arg301Gly		89198034	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294493	0.40594	.	.	ENSG00000156103	ENST00000286614	T	0.16897	2.31	5.79	3.32	0.38043	.	0.154467	0.52532	D	0.000077	T	0.17365	0.0417	M	0.62723	1.935	0.44380	D	0.997288	B;B	0.12013	0.005;0.0	B;B	0.15052	0.012;0.001	T	0.06144	-1.0843	10	0.11794	T	0.64	.	12.6824	0.56928	0.0:0.0:0.2603:0.7397	.	301;301	P51512-2;P51512	.;MMP16_HUMAN	G	301	ENSP00000286614:R301G	ENSP00000286614:R301G	R	-	1	2	MMP16	89198034	1.000000	0.71417	0.974000	0.42286	0.998000	0.95712	2.488000	0.45276	0.412000	0.25729	0.455000	0.32223	AGA		0.512	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		C	89128918	T	C	89128918	3	2	86	1	0	0	0	0	1	0	0	0	9685	1617	56	4	1098	4	MMP16	8	89128918	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	1250173	89128918	57235104	72	24096										
SCAI	286205	hgsc.bcm.edu	37	chr9	127733651	127733651	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ataatgttctttgcctacccGaaaaatcttgtgcatcctca	5	11	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr9:127733651G>T	ENST00000336505.6	-	17	1730	c.1672C>A	c.(1672-1674)Cgg>Agg	p.R558R	SCAI_ENST00000373549.4_Silent_p.R581R	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	558					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTGCCTACCCGAAAAATCTTG	0.313																																																0			9											93	85	87					9																	127733651		1822	4081	5903	126773472	SO:0001819	synonymous_variant	0			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1672C>A	9.37:g.127733651G>T			126773472	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	37	CCDS48017.1																																																																																				0.313	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		T	127733651	G	T	127733651	2	4	86	1	0	0	0	0	0	0	0	1	13906	1057	37	2		2	SCAI	9	127733651	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10		127733651	13479780	73	24097										
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6264905	6264905	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tggtcatctgccaccaggccGtcctgcgctgcctgcttgcc	11	17	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:6264905G>C	ENST00000379775.4	+	11	1501	c.1171G>C	c.(1171-1173)Gtc>Ctc	p.V391L	PFKFB3_ENST00000540253.1_Missense_Mutation_p.V405L|PFKFB3_ENST00000379782.3_Missense_Mutation_p.V391L|PFKFB3_ENST00000317350.4_Missense_Mutation_p.V391L|PFKFB3_ENST00000360521.2_Missense_Mutation_p.V391L|PFKFB3_ENST00000379785.1_Missense_Mutation_p.V391L|PFKFB3_ENST00000379789.4_Missense_Mutation_p.V371L|PFKFB3_ENST00000536985.1_Intron	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	391	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CCACCAGGCCGTCCTGCGCTG	0.647																																																0			10											67	50	56					10																	6264905		2203	4300	6503	6304911	SO:0001583	missense	5209				CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.1171G>C	10.37:g.6264905G>C	ENSP00000369100:p.Val391Leu		6304911	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	37	CCDS7078.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.846500|4.846500	0.91277|0.91277	.|.	.|.	ENSG00000170525|ENSG00000170525	ENST00000450232|ENST00000379789;ENST00000379784;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.|T;T;T;T;T;T;T	.|0.73258	.|-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.21|5.21	5.21|5.21	0.72293|0.72293	.|Histidine phosphatase superfamily, clade-1 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87935|0.87935	0.6303|0.6303	M|M	0.91612|0.91612	3.225|3.225	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.996;1.0;0.997	.|D;D;D;D	.|0.87578	.|0.998;0.985;0.98;0.988	D|D	0.90643|0.90643	0.4576|0.4576	5|10	.|0.87932	.|D	.|0	0.0715|0.0715	18.7523|18.7523	0.91820|0.91820	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|405;391;391;371	.|B7Z955;Q16875-2;Q16875;Q5VX15	.|.;.;F263_HUMAN;.	P|L	71|371;117;405;391;391;391;391;391;391	.|ENSP00000369115:V371L;ENSP00000446384:V405L;ENSP00000369105:V391L;ENSP00000369111:V391L;ENSP00000369108:V391L;ENSP00000353712:V391L;ENSP00000369100:V391L	.|ENSP00000369105:V391L	R|V	+|+	2|1	0|0	PFKFB3|PFKFB3	6304911|6304911	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.734000|0.734000	0.41952|0.41952	9.469000|9.469000	0.97679|0.97679	2.431000|2.431000	0.82371|0.82371	0.462000|0.462000	0.41574|0.41574	CGT|GTC		0.647	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			C	6264905	G	C	6264905	3	2	86	1	0	0	0	0	1	0	0	0	11793	1145	40	5	1233	5	PFKFB3	10	6264905	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10		6264905	129269842	74	24098										
NMT2	9397	hgsc.bcm.edu	37	chr10	15175312	15175312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	caaagaatacggttcttggcGtacgttgtctttatctggtt	10	7	3	1	rs540952796		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:15175312G>A	ENST00000378165.4	-	4	522	c.442C>T	c.(442-444)Cgc>Tgc	p.R148C	NMT2_ENST00000540259.1_De_novo_Start_OutOfFrame|NMT2_ENST00000535341.1_Missense_Mutation_p.R135C|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Missense_Mutation_p.R135C	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	148					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						GGTTCTTGGCGTACGTTGTCT	0.398													G|||	1	0.000199681	0	0	5008	,	,		19974	0		0	False		,,,				2504	0.001				Melanoma(117;1345 1645 4130 12688 30625)											0			10											168	165	166					10																	15175312		2203	4300	6503	15215318	SO:0001583	missense	9397			AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.442C>T	10.37:g.15175312G>A	ENSP00000367407:p.Arg148Cys		15215318	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324475	0.81580	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000535341	T	0.50277	0.75	5.81	5.81	0.92471	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, N-terminal (1);	0.050733	0.85682	D	0.000000	T	0.69744	0.3145	H	0.95365	3.66	0.80722	D	1	P;P;P	0.51537	0.909;0.946;0.909	B;P;B	0.46510	0.381;0.519;0.381	T	0.80600	-0.1310	10	0.87932	D	0	-15.6528	20.0726	0.97729	0.0:0.0:1.0:0.0	.	148;135;148	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	C	148;135;179;135	ENSP00000367407:R148C	ENSP00000367385:R179C	R	-	1	0	NMT2	15215318	1.000000	0.71417	0.254000	0.24359	0.941000	0.58515	5.165000	0.64959	2.738000	0.93877	0.655000	0.94253	CGC		0.398	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808		A	15175312	G	A	15175312	3	1	86	1	0	0	0	0	1	0	0	0	10535	1145	40	1	1090	1	NMT2	10	15175312	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	8910407	15175312	120359435	75	24099										
MRC1	4360	hgsc.bcm.edu	37	chr10	17865239	17865239	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcatttaaattatgcctgggAgtgccatcaaaaacggactg	10	8	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:17865239A>G	ENST00000331429.2	+	2	331	c.228A>G	c.(226-228)ggA>ggG	p.G76G	MRC1L1_ENST00000457317.1_Silent_p.G76G																breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TATGCCTGGGAGTGCCATCAA	0.453																																																0			10											165	166	166					10																	17865239		2033	3971	6004	17905245	SO:0001819	synonymous_variant	414308																														ENST00000331429.2:c.228A>G	10.37:g.17865239A>G			17905245		Silent	SNP	ENST00000331429.2	37																																																																																					0.453	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1			G	17865239	A	G	17865239	2	3	86	1	0	0	0	0	0	0	0	1	9786	291	11	4		4	MRC1	10	17865239	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	2689927	17865239	117669508	76	24100										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624305	89624305	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gattcgacttagacttgaccTgtatccatttctgcggctgc	9	11	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:89624305T>C	ENST00000371953.3	+	1	1436	c.79T>C	c.(79-81)Tat>Cat	p.Y27H	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	27	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> S (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Y27D(2)|p.Y27N(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGACTTGACCTGTATCCATTT	0.463		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Unknown(13)|Substitution - Missense(3)	prostate(14)|central_nervous_system(10)|skin(7)|lung(6)|ovary(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|kidney(1)	10											155	148	150					10																	89624305		2203	4300	6503	89614285	SO:0001630	splice_region_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.79+1T>C	10.37:g.89624305T>C			89614285	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.821122	0.90873	.	.	ENSG00000171862	ENST00000371953	D	0.98762	-5.12	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.071107	0.64402	D	0.000018	D	0.99064	0.9679	H	0.96691	3.865	0.80722	D	1	P	0.45396	0.857	P	0.48524	0.58	D	0.99246	1.0886	9	.	.	.	-0.7134	14.1807	0.65572	0.0:0.0:0.0:1.0	.	27	P60484	PTEN_HUMAN	H	27	ENSP00000361021:Y27H	.	Y	+	1	0	PTEN	89614285	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.216000	0.77974	1.996000	0.58369	0.459000	0.35465	TAT		0.463	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Missense_Mutation	C	89624305	T	C	89624305	5	2	86	1	0	0	0	0	0	0	1	0	12772	1594	55	4	81	4	PTEN	10	89624305	Splice_Site	SNP	T	TCGA-CI-6619-01B-11D-1826-10	71759066	89624305	45910442	77	24101										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720776	89720776	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atttgcagtatagagcgtgcAgataatgacaaggaatatct	10	5	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:89720776A>C	ENST00000371953.3	+	8	2284	c.927A>C	c.(925-927)gcA>gcC	p.A309A	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	309	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.R308fs*7(1)|p.A309A(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TAGAGCGTGCAGATAATGACA	0.343		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(2)|Unknown(2)|Substitution - coding silent(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)|liver(1)	10											106	103	104					10																	89720776		2203	4299	6502	89710756	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.927A>C	10.37:g.89720776A>C			89710756	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.343	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89720776	A	C	89720776	2	2	86	1	0	0	0	0	0	0	0	1	12772	175	7	4		4	PTEN	10	89720776	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	96471	89720776	45813971	78	24102										
PSD	5662	hgsc.bcm.edu	37	chr10	104173750	104173750	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcagggggttggggaggcagCtcaaaggtgaagaaggggct	21	5	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:104173750C>T	ENST00000020673.5	-	5	1855	c.1329G>A	c.(1327-1329)gaG>gaA	p.E443E	PSD_ENST00000406432.1_Silent_p.E443E|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	443	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		GGGGAGGCAGCTCAAAGGTGA	0.657																																																0			10											51	64	59					10																	104173750		2203	4300	6503	104163740	SO:0001819	synonymous_variant	79176			X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1329G>A	10.37:g.104173750C>T			104163740	B1AKX7|D3DR87|Q15673|Q8IVG0	Silent	SNP	ENST00000020673.5	37	CCDS31272.1																																																																																				0.657	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			T	104173750	C	T	104173750	2	4	86	1	0	0	0	0	0	0	0	1	12680	796	28	3		3	PSD	10	104173750	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	14452974	104173750	31360997	79	24103										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114925643	114925643	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cccctcctcatcaattgcacAgccgtcgacttcttccttac	4	18	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:114925643A>G	ENST00000355995.4	+	15	2279	c.1772A>G	c.(1771-1773)cAg>cGg	p.Q591R	TCF7L2_ENST00000542695.1_Missense_Mutation_p.Q307R|TCF7L2_ENST00000543371.1_Missense_Mutation_p.Q574R|TCF7L2_ENST00000536810.1_Missense_Mutation_p.Q574R|TCF7L2_ENST00000369386.1_3'UTR|TCF7L2_ENST00000538897.1_3'UTR|TCF7L2_ENST00000369397.4_Missense_Mutation_p.Q568R|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000545257.1_Missense_Mutation_p.Q591R|TCF7L2_ENST00000355717.4_3'UTR			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	591					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TCAATTGCACAGCCGTCGACT	0.642			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											40	47	45					10																	114925643		2203	4300	6503	114915633	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1772A>G	10.37:g.114925643A>G	ENSP00000348274:p.Gln591Arg		114915633	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	A	11.40	1.627388	0.28978	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000369397;ENST00000542695	D;D;D;D;D;D	0.98437	-4.91;-4.91;-4.89;-4.93;-4.92;-4.91	5.08	5.08	0.68730	.	0.677027	0.14027	N	0.346395	D	0.97238	0.9097	N	0.16478	0.41	0.41169	D	0.986151	P;B;D;B;B;B;B	0.56521	0.936;0.323;0.976;0.003;0.003;0.002;0.001	P;B;D;B;B;B;B	0.66351	0.885;0.363;0.943;0.002;0.002;0.004;0.002	D	0.95385	0.8476	10	0.19590	T	0.45	-14.2705	14.8505	0.70292	1.0:0.0:0.0:0.0	.	591;462;506;551;551;574;568	Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ8;C6ZRK5;Q9NQB0-7;Q6FHW4	TF7L2_HUMAN;.;.;.;.;.;.	R	591;591;574;574;568;307	ENSP00000348274:Q591R;ENSP00000440547:Q591R;ENSP00000444972:Q574R;ENSP00000446238:Q574R;ENSP00000358404:Q568R;ENSP00000443883:Q307R	ENSP00000348274:Q591R	Q	+	2	0	TCF7L2	114915633	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	4.516000	0.60496	1.902000	0.55061	0.460000	0.39030	CAG		0.642	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		G	114925643	A	G	114925643	3	3	86	1	0	0	0	0	1	0	0	0	15737	188	7	4	2052	4	TCF7L2	10	114925643	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	10751893	114925643	20609104	80	24104										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121685736	121685736	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcttttgaagttggcgccggAcaggtgagtttacatattga	12	6	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:121685736A>G	ENST00000369075.3	+	13	2382	c.2310A>G	c.(2308-2310)ggA>ggG	p.G770G	SEC23IP_ENST00000543134.1_Silent_p.G559G	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	770					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTGGCGCCGGACAGGTGAGTT	0.398																																																0			10											135	138	137					10																	121685736		2203	4300	6503	121675726	SO:0001819	synonymous_variant	11196			AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2310A>G	10.37:g.121685736A>G			121675726	D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	CCDS7618.1																																																																																				0.398	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			G	121685736	A	G	121685736	2	3	86	1	0	0	0	0	0	0	0	1	14030	262	10	4		4	SEC23IP	10	121685736	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	6760093	121685736	13849011	81	24105										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5536733	5536733	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgttgttcctgtgatggtggTggaggtgggggtgaagactg	20	3	0	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:5536733T>C	ENST00000380184.1	-	1	1202	c.939A>G	c.(937-939)ccA>ccG	p.P313P	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	313	Poly-Pro.									endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		GTGATGGTGGTGGAGGTGGGG	0.498																																																0			11											180	159	166					11																	5536733		2201	4297	6498	5493309	SO:0001819	synonymous_variant	143630			AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.939A>G	11.37:g.5536733T>C			5493309	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																				0.498	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		C	5536733	T	C	5536733	2	2	86	1	0	0	0	0	0	0	0	1	16940	1683	59	4		4	UBQLNL	11	5536733	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10		5536733	129469783	82	24106										
PTPMT1	114971	hgsc.bcm.edu	37	chr11	47593119	47593119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agctggatgttcttaaagagTtccacaagcagattactgca	9	8	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:47593119T>C	ENST00000326674.9	+	4	566	c.544T>C	c.(544-546)Ttc>Ctc	p.F182L	NDUFS3_ENST00000533507.1_3'UTR|PTPMT1_ENST00000534775.1_3'UTR|PTPMT1_ENST00000326656.8_Missense_Mutation_p.F118L|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000426530.2_3'UTR	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	182	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						TCTTAAAGAGTTCCACAAGCA	0.478																																																0			11											122	113	116					11																	47593119		1901	4129	6030	47549695	SO:0001583	missense	114971			BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.544T>C	11.37:g.47593119T>C	ENSP00000325958:p.Phe182Leu		47549695	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.940835	0.92526	.	.	ENSG00000110536	ENST00000326656;ENST00000326674	T;T	0.61274	1.82;0.12	5.93	5.93	0.95920	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.075144	0.53938	U	0.000046	T	0.70482	0.3229	M	0.63428	1.95	0.49130	D	0.999757	D;D	0.69078	0.995;0.997	P;P	0.61800	0.894;0.865	T	0.71603	-0.4543	10	0.49607	T	0.09	-8.3213	14.6096	0.68507	0.0:0.0:0.0:1.0	.	118;182	Q8WUK0-2;Q8WUK0	.;PTPM1_HUMAN	L	118;182	ENSP00000325882:F118L;ENSP00000325958:F182L	ENSP00000325882:F118L	F	+	1	0	PTPMT1	47549695	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	6.376000	0.73141	2.271000	0.75665	0.533000	0.62120	TTC		0.478	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879		C	47593119	T	C	47593119	3	2	86	1	0	0	0	0	1	0	0	0	12813	1725	60	4	663	4	PTPMT1	11	47593119	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	42056386	47593119	87413397	83	24107										
OR5AN1	390195	hgsc.bcm.edu	37	chr11	59132242	59132242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttgtattattcagtactttaTcttttcaacgatgggactga	7	6	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:59132242T>C	ENST00000313940.2	+	1	358	c.311T>C	c.(310-312)aTc>aCc	p.I104T		NM_001004729.1	NP_001004729.1	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN, member 1	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	21						CAGTACTTTATCTTTTCAACG	0.433																																																0			11											204	187	193					11																	59132242		2201	4295	6496	58888818	SO:0001583	missense	390195			AB065806	CCDS31559.1	11q12.1	2012-08-09			ENSG00000176495	ENSG00000176495		"GPCR / Class A : Olfactory receptors"	15255	protein-coding gene	gene with protein product		615702					Standard	NM_001004729		Approved		uc010rks.2	Q8NGI8	OTTHUMG00000167337	ENST00000313940.2:c.311T>C	11.37:g.59132242T>C	ENSP00000320302:p.Ile104Thr		58888818	B9EIS2|Q6IEV4	Missense_Mutation	SNP	ENST00000313940.2	37	CCDS31559.1	.	.	.	.	.	.	.	.	.	.	T	5.152	0.213567	0.09757	.	.	ENSG00000176495	ENST00000313940	T	0.00397	7.57	4.42	4.42	0.53409	GPCR, rhodopsin-like superfamily (1);	0.722427	0.12385	N	0.473539	T	0.00300	0.0009	L	0.37750	1.13	0.09310	N	1	P	0.37914	0.611	B	0.33750	0.169	T	0.56432	-0.7980	10	0.87932	D	0	-4.2895	12.7707	0.57419	0.0:0.0:0.0:1.0	.	104	Q8NGI8	O5AN1_HUMAN	T	104	ENSP00000320302:I104T	ENSP00000320302:I104T	I	+	2	0	OR5AN1	58888818	0.277000	0.24220	0.035000	0.18076	0.033000	0.12548	3.149000	0.50655	1.745000	0.51790	0.533000	0.62120	ATC		0.433	OR5AN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394231.1	NM_001004729		C	59132242	T	C	59132242	3	2	86	1	0	0	0	0	1	0	0	0	11174	1435	50	4	313	4	OR5AN1	11	59132242	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	11539123	59132242	75874274	84	24108										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64677563	64677563	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtggccaggcgcagtagggcGgccagccggtccagggcccc	18	15	0	0	rs200504454		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:64677563G>C	ENST00000377264.3	-	13	1924	c.1812C>G	c.(1810-1812)gcC>gcG	p.A604A	ATG2A_ENST00000421419.2_Silent_p.A604A	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	604					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GCAGTAGGGCGGCCAGCCGGT	0.731																																																0			11											14	19	18					11																	64677563		2188	4277	6465	64434139	SO:0001819	synonymous_variant	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1812C>G	11.37:g.64677563G>C			64434139	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	G	0.251	-1.006815	0.02112	.	.	ENSG00000110046	ENST00000418259	.	.	.	4.64	-2.16	0.07080	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.30794	-0.9966	4	.	.	.	.	4.9991	0.14255	0.5313:0.2878:0.1808:0.0	.	.	.	.	G	406	.	.	R	-	1	0	ATG2A	64434139	0.001000	0.12720	0.289000	0.24876	0.084000	0.17831	-0.350000	0.07721	-0.149000	0.11215	-1.195000	0.01675	CGC		0.731	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		C	64677563	G	C	64677563	2	2	86	1	0	0	0	0	0	0	0	1	1094	1103	39	5		5	ATG2A	11	64677563	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10	5545321	64677563	70328953	85	24109										
ZW10	9183	hgsc.bcm.edu	37	chr11	113608342	113608342	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcagaaattgctgtattgagTaaagtccccatagccttgca	8	9	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:113608342T>C	ENST00000200135.3	-	14	2112	c.1968A>G	c.(1966-1968)ttA>ttG	p.L656L		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	656					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		CTGTATTGAGTAAAGTCCCCA	0.438																																																0			11											156	144	148					11																	113608342		2201	4296	6497	113113552	SO:0001819	synonymous_variant	9183			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1968A>G	11.37:g.113608342T>C			113113552	A1A528	Silent	SNP	ENST00000200135.3	37	CCDS8363.1																																																																																				0.438	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		C	113608342	T	C	113608342	2	2	86	1	0	0	0	0	0	0	0	1	18286	1635	57	4		4	ZW10	11	113608342	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	48930779	113608342	21398174	86	24110										
ROBO3	64221	hgsc.bcm.edu	37	chr11	124740592	124740592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggcggagaacagtgtgggccGcgctgaagcatctggctccc	16	12	1	2	rs373820994		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:124740592G>A	ENST00000397801.1	+	6	1193	c.1001G>A	c.(1000-1002)cGc>cAc	p.R334H	ROBO3_ENST00000538940.1_Missense_Mutation_p.R312H	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	334	Ig-like C2-type 3.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		AGTGTGGGCCGCGCTGAAGCA	0.582																																																0			11						G	HIS/ARG	0,4288		0,0,2144	47	52	50		1001	3.3	0.8	11		50	2,8514		0,2,4256	no	missense	ROBO3	NM_022370.3	29	0,2,6400	AA,AG,GG		0.0235,0.0,0.0156	probably-damaging	334/1387	124740592	2,12802	2144	4258	6402	124245802	SO:0001583	missense	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1001G>A	11.37:g.124740592G>A	ENSP00000380903:p.Arg334His		124245802		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403699	0.62288	0.0	2.35E-4	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.67523	-0.27;-0.27	4.21	3.29	0.37713	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.35646	N	0.003061	T	0.68979	0.3060	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.68926	-0.5280	10	0.62326	D	0.03	.	7.2509	0.26148	0.2777:0.0:0.7223:0.0	.	334	Q96MS0	ROBO3_HUMAN	H	334;312	ENSP00000380903:R334H;ENSP00000441797:R312H	ENSP00000380903:R334H	R	+	2	0	ROBO3	124245802	1.000000	0.71417	0.810000	0.32431	0.801000	0.45260	3.958000	0.56737	1.110000	0.41699	0.462000	0.41574	CGC		0.582	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		A	124740592	G	A	124740592	3	1	86	1	0	0	0	0	1	0	0	0	13552	1087	38	1	1023	1	ROBO3	11	124740592	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	11132250	124740592	10265924	87	24111										
ETS1	2113	hgsc.bcm.edu	37	chr11	128332291	128332291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tggcttgacgtccagcatggCgtgcagctcctcaggggtgt	15	11	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:128332291C>T	ENST00000319397.6	-	8	1600	c.1291G>A	c.(1291-1293)Gcc>Acc	p.A431T	ETS1_ENST00000535549.1_Missense_Mutation_p.A215T|ETS1_ENST00000392668.4_Missense_Mutation_p.A475T|ETS1_ENST00000526145.2_Missense_Mutation_p.A344T|ETS1_ENST00000531611.1_3'UTR|ETS1_ENST00000345075.4_Missense_Mutation_p.A344T	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	431					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		TCCAGCATGGCGTGCAGCTCC	0.587																																																0			11											105	90	95					11																	128332291		2201	4297	6498	127837501	SO:0001583	missense	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.1291G>A	11.37:g.128332291C>T	ENSP00000324578:p.Ala431Thr		127837501	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190611	0.78789	.	.	ENSG00000134954	ENST00000345075;ENST00000535549;ENST00000392668;ENST00000319397;ENST00000526145	T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55	5.96	5.96	0.96718	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.10809	0.0264	L	0.28344	0.845	0.80722	D	1	P;B;P	0.46395	0.877;0.165;0.569	B;B;B	0.32864	0.154;0.015;0.041	T	0.05273	-1.0895	10	0.45353	T	0.12	.	20.4082	0.99013	0.0:1.0:0.0:0.0	.	431;215;475	P14921;F5GYX9;Q6N087	ETS1_HUMAN;.;.	T	344;215;475;431;344	ENSP00000340485:A344T;ENSP00000441430:A215T;ENSP00000376436:A475T;ENSP00000324578:A431T;ENSP00000433500:A344T	ENSP00000324578:A431T	A	-	1	0	ETS1	127837501	1.000000	0.71417	0.994000	0.49952	0.888000	0.51559	5.782000	0.68973	2.814000	0.96858	0.655000	0.94253	GCC		0.587	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		T	128332291	C	T	128332291	3	4	86	1	0	0	0	0	1	0	0	0	5288	768	27	1	38	1	ETS1	11	128332291	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	3591699	128332291	6674225	88	24112										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7585297	7585297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tctccctgaacaggagttgtTtccatccactagcctcaaac	6	14	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:7585297T>C	ENST00000313599.3	-	4	538	c.481A>G	c.(481-483)Aac>Gac	p.N161D	CD163L1_ENST00000416109.2_Missense_Mutation_p.N171D|CD163L1_ENST00000396630.1_Missense_Mutation_p.N161D			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	161	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CAGGAGTTGTTTCCATCCACT	0.438																																																0			12											87	82	84					12																	7585297		2203	4300	6503	7476564	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.481A>G	12.37:g.7585297T>C	ENSP00000315945:p.Asn161Asp		7476564	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	1.449	-0.565630	0.03910	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.35048	1.33;1.33;1.33	2.22	-2.95	0.05564	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.14399	0.0348	N	0.03903	-0.33	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.30765	-0.9967	9	0.20519	T	0.43	.	9.9234	0.41478	0.0:0.7101:0.0:0.2899	.	171;161	E7EVK4;Q9NR16	.;C163B_HUMAN	D	161;171;161	ENSP00000315945:N161D;ENSP00000393474:N171D;ENSP00000379871:N161D	ENSP00000315945:N161D	N	-	1	0	CD163L1	7476564	0.000000	0.05858	0.002000	0.10522	0.228000	0.25075	-1.924000	0.01565	-0.836000	0.04229	0.460000	0.39030	AAC		0.438	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7585297	T	C	7585297	3	2	86	1	0	0	0	0	1	0	0	0	2974	1841	64	4	3944	4	CD163L1	12	7585297	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10		7585297	126266598	89	24113										
PRB4	5545	hgsc.bcm.edu	37	chr12	11461534	11461596	+	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-													0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggggacggtgggactggttgCctccttgtgggggtggtctt					rs11054244|rs59021567|rs11054243|rs551775057|rs12303607|rs199532199|rs148027029|rs71057722|rs59189129|rs536297617	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENST00000535904.1	-	3	354_416	c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	c.(319-384)ggaaaccagtcccaaggtaccccacctcctccaggaaagccagaaagaccacccccacaaggaggc>ggc	p.107_128GNQSQGTPPPPGKPERPPPQGG>G	PRB4_ENST00000445719.2_Splice_Site_p.107_112GNQSQG>G|PRB4_ENST00000279575.1_In_Frame_Del_p.107_128GNQSQGTPPPPGKPERPPPQGG>G			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)		p.P115L(1)|p.G118E(1)|p.P117T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTGCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTTCCTCCTTGTG	0.605										HNSCC(22;0.051)																																						3	Substitution - Missense(3)	lung(1)|kidney(1)|skin(1)	12																																								11352863	SO:0001651	inframe_deletion	5545				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	12.37:g.11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENSP00000442834:p.Gly107_Gly127del		11352801	A1L439|O00600|P02813|P10161|P10162|P81489	In_Frame_Del	DEL	ENST00000535904.1	37	CCDS8641.1																																																																																				0.605	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461596	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-	11461534	7	5	86	1	0	1	0	1	0	0	0	0	12479	739	26	0	364	0	PRB4	12	11461534	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	TCGA-CI-6619-01B-11D-1826-10	3876237	11461534	122390361	90	24114										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18836250	18836250	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tctggaaaacagaggaatacGacgataacctgcaaaaggaa	10	7	1	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:18836250G>T	ENST00000538330.1	-	11	1477	c.1096C>A	c.(1096-1098)Cgt>Agt	p.R366S	PLCZ1_ENST00000266505.7_Missense_Mutation_p.R584S|PLCZ1_ENST00000447925.2_Missense_Mutation_p.R582S|PLCZ1_ENST00000539875.1_Missense_Mutation_p.R391S|PLCZ1_ENST00000541695.1_3'UTR|PLCZ1_ENST00000435379.1_Missense_Mutation_p.R389S|PLCZ1_ENST00000534932.1_Missense_Mutation_p.R65S					phospholipase C, zeta 1									p.R584C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					AGAGGAATACGACGATAACCT	0.383																																																1	Substitution - Missense(1)	lung(1)	12											107	98	101					12																	18836250		2203	4300	6503	18727517	SO:0001583	missense	89869			AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.1096C>A	12.37:g.18836250G>T	ENSP00000445880:p.Arg366Ser		18727517		Missense_Mutation	SNP	ENST00000538330.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.26|12.26	1.885022|1.885022	0.33255|0.33255	.|.	.|.	ENSG00000139151|ENSG00000139151	ENST00000534932;ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000539875|ENST00000536023	T;T;T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63;2.63;2.63|.	5.34|5.34	4.39|4.39	0.52855|0.52855	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);|.	0.308722|.	0.33515|.	N|.	0.004826|.	T|.	0.31765|.	0.0807|.	N|N	0.04090|0.04090	-0.28|-0.28	0.54753|0.54753	D|D	0.999981|0.999981	B;B|.	0.32128|.	0.304;0.357|.	B;B|.	0.28709|.	0.069;0.093|.	T|.	0.10894|.	-1.0610|.	10|.	0.87932|.	D|.	0|.	.|.	10.3184|10.3184	0.43751|0.43751	0.0:0.0:0.7906:0.2094|0.0:0.0:0.7906:0.2094	.|.	584;366|.	Q86YW0;Q8N7S5|.	PLCZ1_HUMAN;.|.	S|X	65;366;584;582;389;391|76	ENSP00000438826:R65S;ENSP00000445880:R366S;ENSP00000266505:R584S;ENSP00000402358:R582S;ENSP00000400504:R389S;ENSP00000445026:R391S|.	ENSP00000266505:R584S|.	R|S	-|-	1|2	0|0	PLCZ1|PLCZ1	18727517|18727517	0.531000|0.531000	0.26338|0.26338	0.997000|0.997000	0.53966|0.53966	0.382000|0.382000	0.30200|0.30200	3.279000|3.279000	0.51670|0.51670	2.776000|2.776000	0.95493|0.95493	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.383	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		T	18836250	G	T	18836250	3	4	86	1	0	0	0	0	1	0	0	0	12075	1058	37	2	80	2	PLCZ1	12	18836250	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	7374716	18836250	115015645	91	24115										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43846451	43846451	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgaatcagtattacatgatCgaaatttcatcctgcggccc	7	10	2	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:43846451C>T	ENST00000389420.3	-	13	1807	c.1808G>A	c.(1807-1809)cGa>cAa	p.R603Q	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.R603Q	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	603	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		ATTACATGATCGAAATTTCAT	0.398																																																0			12											78	67	70					12																	43846451		2203	4300	6503	42132718	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1808G>A	12.37:g.43846451C>T	ENSP00000374071:p.Arg603Gln		42132718	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	35	5.437596	0.96168	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.49720	0.77;0.77	4.85	4.85	0.62838	.	0.000000	0.43416	D	0.000561	T	0.55481	0.1923	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.57900	-0.7731	10	0.44086	T	0.13	.	18.851	0.92230	0.0:1.0:0.0:0.0	.	603	P59510	ATS20_HUMAN	Q	603	ENSP00000374071:R603Q;ENSP00000448341:R603Q	ENSP00000374068:R603Q	R	-	2	0	ADAMTS20	42132718	0.998000	0.40836	0.995000	0.50966	0.998000	0.95712	3.766000	0.55280	2.624000	0.88883	0.563000	0.77884	CGA		0.398	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43846451	C	T	43846451	3	4	86	1	0	0	0	0	1	0	0	0	266	884	31	1	4031	1	ADAMTS20	12	43846451	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	25010201	43846451	90005444	92	24116										
ARID2	196528	hgsc.bcm.edu	37	chr12	46245966	46245966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aagatatcaaaagtgatttgAgaaaaccgctagttaatgga	9	4	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:46245966A>G	ENST00000334344.6	+	15	4232	c.4060A>G	c.(4060-4062)Aga>Gga	p.R1354G	ARID2_ENST00000422737.1_Missense_Mutation_p.R1205G|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Missense_Mutation_p.R964G|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1354					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAGTGATTTGAGAAAACCGCT	0.348			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0			12											65	64	64					12																	46245966		2203	4300	6503	44532233	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4060A>G	12.37:g.46245966A>G	ENSP00000335044:p.Arg1354Gly		44532233	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971335	0.34754	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.33654	1.4	6.07	6.07	0.98685	.	0.040149	0.85682	D	0.000000	T	0.24392	0.0591	N	0.08118	0	0.80722	D	1	B;B;B	0.16802	0.019;0.019;0.011	B;B;B	0.18561	0.022;0.022;0.005	T	0.06499	-1.0823	10	0.87932	D	0	-5.9255	16.6288	0.85011	1.0:0.0:0.0:0.0	.	1354;964;1354	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	G	1354;471;471;1205;964	ENSP00000335044:R1354G	ENSP00000335044:R1354G	R	+	1	2	ARID2	44532233	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.690000	0.91272	2.326000	0.78906	0.533000	0.62120	AGA		0.348	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46245966	A	G	46245966	3	3	86	1	0	0	0	0	1	0	0	0	915	296	11	4	4118	4	ARID2	12	46245966	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	2399515	46245966	87605929	93	24117										
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571248	50571248	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cctttctgcaactcttccacCcacagactcttcactctgct	3	18	5	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:50571248C>G	ENST00000341247.4	-	11	2028	c.1879G>C	c.(1879-1881)Ggt>Cgt	p.G627R	LIMA1_ENST00000394943.3_Missense_Mutation_p.G628R|LIMA1_ENST00000552783.1_Missense_Mutation_p.G468R|LIMA1_ENST00000547825.1_Missense_Mutation_p.G325R|LIMA1_ENST00000552823.1_Missense_Mutation_p.G467R|LIMA1_ENST00000552909.1_Missense_Mutation_p.G466R|LIMA1_ENST00000552491.1_Missense_Mutation_p.G324R	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	627					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						ACTCTTCCACCCACAGACTCT	0.458																																																0			12											268	276	274					12																	50571248		2203	4300	6503	48857515	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1879G>C	12.37:g.50571248C>G	ENSP00000340184:p.Gly627Arg		48857515	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	1.775	-0.483428	0.04383	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.83837	-1.03;-1.03;-1.35;-1.77;-1.03;-1.36;-1.35	5.7	5.7	0.88788	.	0.810925	0.11593	N	0.548543	T	0.79941	0.4533	L	0.57536	1.79	0.09310	N	1	B;B;B	0.18610	0.013;0.013;0.029	B;B;B	0.18871	0.008;0.008;0.023	T	0.65146	-0.6239	10	0.26408	T	0.33	.	11.2795	0.49186	0.0:0.89:0.0:0.11	.	637;627;466	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	R	324;325;467;628;627;468;466;546	ENSP00000448463:G324R;ENSP00000448706:G325R;ENSP00000450266:G467R;ENSP00000378400:G628R;ENSP00000340184:G627R;ENSP00000448779:G468R;ENSP00000450087:G466R	ENSP00000340184:G627R	G	-	1	0	LIMA1	48857515	0.006000	0.16342	0.021000	0.16686	0.118000	0.20060	2.081000	0.41596	2.850000	0.98022	0.650000	0.86243	GGT		0.458	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		G	50571248	C	G	50571248	3	3	86	1	0	0	0	0	1	0	0	0	8819	623	22	5	404	5	LIMA1	12	50571248	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	4325282	50571248	83280647	94	24118										
LIMA1	51474	hgsc.bcm.edu	37	chr12	50642509	50642509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgatagtgaggtccattgcCgtctattaaatggagatgat	11	5	1	4			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:50642509C>T	ENST00000341247.4	-	2	175	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	LIMA1_ENST00000394943.3_Missense_Mutation_p.R9Q	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	9					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GGTCCATTGCCGTCTATTAAA	0.388																																																0			12											170	151	158					12																	50642509		2203	4300	6503	48928776	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.26G>A	12.37:g.50642509C>T	ENSP00000340184:p.Arg9Gln		48928776	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.361317	0.41801	.	.	ENSG00000050405	ENST00000394943;ENST00000341247;ENST00000551691;ENST00000550592	D;T	0.85411	-1.98;-1.24	4.7	2.86	0.33363	.	0.276630	0.33670	N	0.004665	T	0.70422	0.3222	N	0.21583	0.68	0.80722	D	1	B;B	0.30193	0.07;0.272	B;B	0.16289	0.003;0.015	T	0.62779	-0.6782	10	0.29301	T	0.29	-6.9825	8.9102	0.35548	0.0:0.8158:0.0:0.1842	.	18;9	Q59FE8;Q9UHB6	.;LIMA1_HUMAN	Q	9	ENSP00000378400:R9Q;ENSP00000340184:R9Q	ENSP00000340184:R9Q	R	-	2	0	LIMA1	48928776	0.987000	0.35691	0.999000	0.59377	0.979000	0.70002	0.530000	0.23036	0.659000	0.30945	0.655000	0.94253	CGG		0.388	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		T	50642509	C	T	50642509	3	4	86	1	0	0	0	0	1	0	0	0	8819	652	23	1	2296	1	LIMA1	12	50642509	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	71261	50642509	83209386	95	24119										
MUCL1	118430	hgsc.bcm.edu	37	chr12	55250571	55250571	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cagctggtcctgctgatgatGaagcccctgatgctgaaacc	11	12	0	5			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:55250571G>A	ENST00000308796.6	+	3	164	c.118G>A	c.(118-120)Gaa>Aaa	p.E40K	MUCL1_ENST00000547990.1_3'UTR|MUCL1_ENST00000546809.1_Missense_Mutation_p.E35K	NM_058173.2	NP_477521.1	Q96DR8	MUCL1_HUMAN	mucin-like 1	40	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|membrane (GO:0016020)				breast(1)|kidney(1)|lung(1)	3						tgctgatgatgaagcccctga	0.502																																																0			12											103	81	88					12																	55250571		2203	4300	6503	53536838	SO:0001583	missense	118430			AF414087	CCDS8885.1	12q13.2	2007-07-02							30588	protein-coding gene	gene with protein product	"small breast epithelial mucin"	610857				12019145	Standard	NM_058173		Approved	SBEM	uc001sgk.3	Q96DR8		ENST00000308796.6:c.118G>A	12.37:g.55250571G>A	ENSP00000311364:p.Glu40Lys		53536838	Q0VG95|Q32ZB5	Missense_Mutation	SNP	ENST00000308796.6	37	CCDS8885.1	.	.	.	.	.	.	.	.	.	.	G	5.182	0.219210	0.09863	.	.	ENSG00000172551	ENST00000546809;ENST00000308796	.	.	.	2.09	-1.68	0.08212	.	9.544620	0.01122	U	0.005800	T	0.30947	0.0781	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.41036	0.346	T	0.33007	-0.9885	8	0.87932	D	0	.	5.6198	0.17451	0.5843:0.0:0.4157:0.0	.	40	Q96DR8	MUCL1_HUMAN	K	35;40	.	ENSP00000311364:E40K	E	+	1	0	MUCL1	53536838	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.066000	0.01385	-0.446000	0.07149	0.561000	0.74099	GAA		0.502	MUCL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406062.1	NM_058173		A	55250571	G	A	55250571	3	1	86	1	0	0	0	0	1	0	0	0	10012	1291	45	3	128	3	MUCL1	12	55250571	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	4608062	55250571	78601324	96	24120										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81799572	81799572	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggggtgtgtcataccttctcAtggactttctgtccaggttc	11	10	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:81799572A>G	ENST00000549396.1	-	8	916	c.756T>C	c.(754-756)caT>caC	p.H252H	PPFIA2_ENST00000550584.2_Silent_p.H252H|PPFIA2_ENST00000549325.1_Silent_p.H234H|PPFIA2_ENST00000407050.4_Silent_p.H178H|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550359.2_Silent_p.H99H|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000552948.1_Silent_p.H252H|PPFIA2_ENST00000333447.7_Silent_p.H234H|PPFIA2_ENST00000548586.1_Silent_p.H252H|PPFIA2_ENST00000443686.3_Silent_p.H153H	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	252	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						ATACCTTCTCATGGACTTTCT	0.373																																																0			12											101	93	96					12																	81799572		1914	4120	6034	80323703	SO:0001819	synonymous_variant	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.756T>C	12.37:g.81799572A>G			80323703	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	A	8.862	0.947074	0.18356	.	.	ENSG00000139220	ENST00000548790	.	.	.	5.15	3.99	0.46301	.	.	.	.	.	T	0.59142	0.2172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55121	-0.8190	4	.	.	.	-16.3209	9.0926	0.36621	0.905:0.0:0.095:0.0	.	.	.	.	T	70	.	.	M	-	2	0	PPFIA2	80323703	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.882000	0.48546	0.899000	0.36444	0.455000	0.32223	ATG		0.373	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			G	81799572	A	G	81799572	2	3	86	1	0	0	0	0	0	0	0	1	12341	214	8	4		4	PPFIA2	12	81799572	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	26549001	81799572	52052323	97	24121										
CEP290	80184	hgsc.bcm.edu	37	chr12	88465168	88465168	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcgtattcccaaaacctgatCaacagtcatgccagttgttt	6	11	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:88465168C>A	ENST00000552810.1	-	43	6257	c.5914G>T	c.(5914-5916)Gat>Tat	p.D1972Y	CEP290_ENST00000397838.3_Missense_Mutation_p.D1032Y|CEP290_ENST00000309041.7_Missense_Mutation_p.D1974Y|CEP290_ENST00000547691.2_Missense_Mutation_p.D1032Y	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1972					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAAACCTGATCAACAGTCATG	0.323																																																0			12											142	127	132					12																	88465168		1811	4077	5888	86989299	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5914G>T	12.37:g.88465168C>A	ENSP00000448012:p.Asp1972Tyr		86989299	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.836618	0.71373	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.70399	0.16;-0.48;-0.48;0.16	5.23	4.28	0.50868	.	0.042775	0.85682	D	0.000000	T	0.80783	0.4689	M	0.70595	2.14	0.54753	D	0.999989	D	0.63880	0.993	P	0.62740	0.906	T	0.82518	-0.0417	10	0.66056	D	0.02	.	12.9114	0.58182	0.0:0.914:0.0:0.086	.	1972	O15078	CE290_HUMAN	Y	1032;1972;1974;1032	ENSP00000446905:D1032Y;ENSP00000448012:D1972Y;ENSP00000308021:D1974Y;ENSP00000380938:D1032Y	ENSP00000308021:D1974Y	D	-	1	0	CEP290	86989299	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.174000	0.65015	1.208000	0.43306	0.484000	0.47621	GAT		0.323	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88465168	C	A	88465168	3	1	86	1	0	0	0	0	1	0	0	0	3259	826	29	2	1573	2	CEP290	12	88465168	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	6665596	88465168	45386727	98	24122										
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102043144	102043144	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agggagcaacaaaggctgatGctgcagaatattcagtaatg	12	6	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:102043144G>A	ENST00000550270.1	+	13	1228	c.1228G>A	c.(1228-1230)Gct>Act	p.A410T	MYBPC1_ENST00000392934.3_Missense_Mutation_p.A397T|MYBPC1_ENST00000361466.2_Missense_Mutation_p.A435T|MYBPC1_ENST00000549145.1_Missense_Mutation_p.A423T|MYBPC1_ENST00000360610.2_Missense_Mutation_p.A410T|MYBPC1_ENST00000547509.1_Missense_Mutation_p.A396T|MYBPC1_ENST00000361685.2_Missense_Mutation_p.A435T|MYBPC1_ENST00000547405.1_Missense_Mutation_p.A384T|MYBPC1_ENST00000545503.2_Missense_Mutation_p.A410T|MYBPC1_ENST00000541119.1_Missense_Mutation_p.A398T|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000553190.1_Missense_Mutation_p.A410T|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000441232.1_Missense_Mutation_p.A410T|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000551300.1_Missense_Mutation_p.A311T|MYBPC1_ENST00000536007.1_Missense_Mutation_p.A391T|MYBPC1_ENST00000452455.2_Missense_Mutation_p.A410T			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	410	Ig-like C2-type 3.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AAAGGCTGATGCTGCAGAATA	0.398																																																0			12											191	174	179					12																	102043144		2203	4300	6503	100567275	SO:0001583	missense	4604				CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1228G>A	12.37:g.102043144G>A	ENSP00000449702:p.Ala410Thr		100567275	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	3.297	-0.143683	0.06627	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.98	0.805	0.18703	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.660490	0.03710	N	0.250087	T	0.49304	0.1549	N	0.20807	0.61	0.09310	N	0.999995	B;B;B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B	0.09377	0.004;0.0;0.001;0.0;0.001;0.002;0.0;0.001;0.001;0.0;0.0	T	0.21280	-1.0250	10	0.14252	T	0.57	.	6.831	0.23911	0.493:0.0:0.0626:0.4444	.	391;398;410;410;397;384;410;410;435;435;423	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	T	384;410;410;410;397;396;435;423;410;435;410;391;398;435;311;410	ENSP00000448175:A384T;ENSP00000400908:A410T;ENSP00000388989:A410T;ENSP00000353822:A410T;ENSP00000376665:A397T;ENSP00000447362:A396T;ENSP00000354845:A435T;ENSP00000447660:A423T;ENSP00000447900:A410T;ENSP00000440034:A410T;ENSP00000446128:A391T;ENSP00000442847:A398T;ENSP00000354849:A435T;ENSP00000447116:A311T;ENSP00000449702:A410T	ENSP00000353822:A410T	A	+	1	0	MYBPC1	100567275	0.604000	0.26932	0.015000	0.15790	0.010000	0.07245	2.207000	0.42788	-0.095000	0.12351	-1.619000	0.00793	GCT		0.398	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			A	102043144	G	A	102043144	3	1	86	1	0	0	0	0	1	0	0	0	10041	1319	46	3	1361	3	MYBPC1	12	102043144	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	13577976	102043144	31808751	99	24123										
PSPC1	55269	hgsc.bcm.edu	37	chr13	20325440	20325440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttagcattaattggtgttcaTgcctagctgcttccatttct	7	9	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:20325440T>C	ENST00000338910.4	-	4	1097	c.938A>G	c.(937-939)cAt>cGt	p.H313R		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	313	Sufficient for paraspeckles localization.|Sufficient for perinucleolar caps localization and interaction with NONO.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TTGGTGTTCATGCCTAGCTGC	0.398																																																0			13											287	264	272					13																	20325440		1928	4127	6055	19223440	SO:0001583	missense	55269			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.938A>G	13.37:g.20325440T>C	ENSP00000343966:p.His313Arg		19223440	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313494	0.60414	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.16073	2.37	4.83	4.83	0.62350	.	0.112999	0.64402	D	0.000011	T	0.21347	0.0514	M	0.66297	2.02	0.53688	D	0.999977	P	0.45672	0.864	B	0.39299	0.296	T	0.04307	-1.0961	10	0.51188	T	0.08	-18.8568	14.705	0.69183	0.0:0.0:0.0:1.0	.	313	Q8WXF1	PSPC1_HUMAN	R	313;253	ENSP00000343966:H313R	ENSP00000343966:H313R	H	-	2	0	PSPC1	19223440	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	7.988000	0.88194	1.943000	0.56356	0.454000	0.30748	CAT		0.398	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			C	20325440	T	C	20325440	3	2	86	1	0	0	0	0	1	0	0	0	12750	1464	51	4	657	4	PSPC1	13	20325440	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10		20325440	94844438	100	24124										
COG6	57511	hgsc.bcm.edu	37	chr13	40297568	40297568	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aacactgtacagcaacataaAcctgaacaggtaagtgcata	7	9	0	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:40297568A>G	ENST00000455146.3	+	16	1733	c.1683A>G	c.(1681-1683)aaA>aaG	p.K561K	COG6_ENST00000416691.1_Silent_p.K561K	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	561					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		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)		AGCAACATAAACCTGAACAGG	0.398																																																0			13											99	90	93					13																	40297568		2203	4299	6502	39195568	SO:0001819	synonymous_variant	57511			AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1683A>G	13.37:g.40297568A>G			39195568	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Silent	SNP	ENST00000455146.3	37	CCDS9370.1																																																																																				0.398	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40297568	A	G	40297568	2	3	86	1	0	0	0	0	0	0	0	1	3668	40	2	4		4	COG6	13	40297568	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	19972128	40297568	74872310	101	24125										
RB1	5925	hgsc.bcm.edu	37	chr13	48881429	48881429	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttggtaggcttgagtttgaaGaaacagaagaacctgatttt	11	4	0	6			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:48881429G>T	ENST00000267163.4	+	2	289	c.151G>T	c.(151-153)Gaa>Taa	p.E51*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	51					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)|p.E51*(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TGAGTTTGAAGAAACAGAAGA	0.313		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	19	Whole gene deletion(15)|Unknown(3)|Substitution - Nonsense(1)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|central_nervous_system(1)|endometrium(1)|stomach(1)	13											115	114	114					13																	48881429		2203	4298	6501	47779430	SO:0001587	stop_gained	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.151G>T	13.37:g.48881429G>T	ENSP00000267163:p.Glu51*		47779430	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	36	5.888494	0.97068	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	4.74	3.88	0.44766	.	0.591344	0.18246	N	0.147093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	9.591	0.39545	0.101:0.0:0.899:0.0	.	.	.	.	X	30;51	.	ENSP00000267163:E51X	E	+	1	0	RB1	47779430	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	3.074000	0.50065	1.077000	0.40990	0.650000	0.86243	GAA		0.313	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48881429	G	T	48881429	4	4	86	1	0	0	0	0	0	1	0	0	13135	943	33	2	157	2	RB1	13	48881429	Nonsense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	8583861	48881429	66288449	102	24126										
RB1	5925	hgsc.bcm.edu	37	chr13	49033838	49033838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ccacagtgtatcggctagccTatctccggctaaatacactt	7	13	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:49033838T>C	ENST00000267163.4	+	20	2113	c.1975T>C	c.(1975-1977)Tat>Cat	p.Y659H		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	659	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.Y659H(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCGGCTAGCCTATCTCCGGCT	0.378		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	27	Whole gene deletion(15)|Unknown(11)|Substitution - Missense(1)	bone(10)|haematopoietic_and_lymphoid_tissue(5)|breast(5)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13											73	78	77					13																	49033838		2203	4300	6503	47931839	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1975T>C	13.37:g.49033838T>C	ENSP00000267163:p.Tyr659His		47931839	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.019440	0.75275	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.90900	-2.75	5.79	5.79	0.91817	Retinoblastoma-associated protein, B-box (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95880	0.8898	10	0.87932	D	0	.	16.1338	0.81465	0.0:0.0:0.0:1.0	.	659	P06400	RB_HUMAN	H	638;659	ENSP00000267163:Y659H	ENSP00000267163:Y659H	Y	+	1	0	RB1	47931839	1.000000	0.71417	0.926000	0.36857	0.782000	0.44232	7.698000	0.84413	2.216000	0.71823	0.528000	0.53228	TAT		0.378	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	49033838	T	C	49033838	3	2	86	1	0	0	0	0	1	0	0	0	13135	1522	53	4	2053	4	RB1	13	49033838	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	152409	49033838	66136040	103	24127										
CYSLTR2	57105	hgsc.bcm.edu	37	chr13	49281933	49281933	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cagaaaaggccatccacagaAggcaaagacaaagtgtgttt	10	8	0	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:49281933A>T	ENST00000282018.3	+	1	983	c.980A>T	c.(979-981)aAg>aTg	p.K327M		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	327					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	CATCCACAGAAGGCAAAGACA	0.443																																																0			13											77	71	73					13																	49281933		2203	4300	6503	48179934	SO:0001583	missense	57105			AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.980A>T	13.37:g.49281933A>T	ENSP00000282018:p.Lys327Met		48179934	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.021314	0.54576	.	.	ENSG00000152207	ENST00000282018	T	0.38560	1.13	5.51	3.03	0.35002	.	3.293900	0.01734	U	0.029019	T	0.22936	0.0554	N	0.08118	0	0.09310	N	1	P	0.35077	0.483	B	0.21546	0.035	T	0.20538	-1.0272	10	0.39692	T	0.17	.	6.4304	0.21794	0.776:0.0:0.0771:0.1468	.	327	Q9NS75	CLTR2_HUMAN	M	327	ENSP00000282018:K327M	ENSP00000282018:K327M	K	+	2	0	CYSLTR2	48179934	0.001000	0.12720	0.001000	0.08648	0.055000	0.15305	0.423000	0.21313	0.368000	0.24481	0.533000	0.62120	AAG		0.443	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			T	49281933	A	T	49281933	3	4	86	1	0	0	0	0	1	0	0	0	4208	72	3	5	982	5	CYSLTR2	13	49281933	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	248095	49281933	65887945	104	24128										
SLC39A2	29986	hgsc.bcm.edu	37	chr14	21469413	21469413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctgccttgctgtcctggctcAtaaggggcttgtggtgtttg	14	9	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:21469413A>G	ENST00000298681.4	+	4	762	c.605A>G	c.(604-606)cAt>cGt	p.H202R	SLC39A2_ENST00000554422.1_3'UTR|RP11-84C10.4_ENST00000557335.1_RNA	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	202					transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		GTCCTGGCTCATAAGGGGCTT	0.527																																																0			14											140	117	125					14																	21469413		2203	4300	6503	20539253	SO:0001583	missense	29986			AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"Solute carriers"	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.605A>G	14.37:g.21469413A>G	ENSP00000298681:p.His202Arg		20539253	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121291	0.77436	.	.	ENSG00000165794	ENST00000298681	T	0.74421	-0.84	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91420	0.5158	10	0.87932	D	0	-9.9851	13.9183	0.63914	1.0:0.0:0.0:0.0	.	202	Q9NP94	S39A2_HUMAN	R	202	ENSP00000298681:H202R	ENSP00000298681:H202R	H	+	2	0	SLC39A2	20539253	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	8.483000	0.90442	2.170000	0.68504	0.533000	0.62120	CAT		0.527	SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579		G	21469413	A	G	21469413	3	3	86	1	0	0	0	0	1	0	0	0	14655	217	8	4	619	4	SLC39A2	14	21469413	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10		21469413	85880127	105	24129										
CHD8	57680	hgsc.bcm.edu	37	chr14	21875078	21875078	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tttttcagtcgatgggcttcAtcaatgataacacaacgcca	7	10	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:21875078A>T	ENST00000557364.1	-	14	3107	c.2844T>A	c.(2842-2844)gaT>gaA	p.D948E	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Missense_Mutation_p.D669E|CHD8_ENST00000399982.2_Missense_Mutation_p.D948E			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	948	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GATGGGCTTCATCAATGATAA	0.453																																																0			14											96	87	90					14																	21875078		1968	4155	6123	20944918	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2844T>A	14.37:g.21875078A>T	ENSP00000451601:p.Asp948Glu		20944918	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.279095|4.279095	0.80692|0.80692	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	D;D;D|.	0.99857|.	-7.22;-7.22;-7.22|.	5.41|5.41	5.41|5.41	0.78517|0.78517	DEAD-like helicase (2);SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.89005|.	0.6592|.	H|H	0.99659|0.99659	4.685|4.685	0.58432|0.58432	D|D	0.999992|0.999992	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|.	0.91663|.	0.5344|.	10|.	0.87932|.	D|.	0|.	-23.4087|-23.4087	9.5|9.5	0.39011|0.39011	0.9185:0.0:0.0815:0.0|0.9185:0.0:0.0815:0.0	.|.	948;669|.	Q9HCK8;Q9HCK8-2|.	CHD8_HUMAN;.|.	E|R	669;948;668;948|174	ENSP00000406288:D669E;ENSP00000382863:D948E;ENSP00000451601:D948E|.	ENSP00000262707:D668E|.	D|X	-|-	3|1	2|0	CHD8|CHD8	20944918|20944918	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	0.807000|0.807000	0.27140|0.27140	2.272000|2.272000	0.75746|0.75746	0.459000|0.459000	0.35465|0.35465	GAT|TGA		0.453	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21875078	A	T	21875078	3	4	86	1	0	0	0	0	1	0	0	0	3337	214	8	5	5001	5	CHD8	14	21875078	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	405665	21875078	85474462	106	24130										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31578715	31578715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcttgagacgaccaactcgaAactctccagggtcatctcgc	9	14	3	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:31578715A>G	ENST00000399332.1	-	36	6856	c.6368T>C	c.(6367-6369)tTt>tCt	p.F2123S	HECTD1_ENST00000553700.1_Missense_Mutation_p.F2123S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2123					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.F2123Y(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		ACCAACTCGAAACTCTCCAGG	0.473																																																1	Substitution - Missense(1)	ovary(1)	14											107	109	108					14																	31578715		2051	4207	6258	30648466	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6368T>C	14.37:g.31578715A>G	ENSP00000382269:p.Phe2123Ser		30648466	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	29.3|29.3	4.996740|4.996740	0.93167|0.93167	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332	T|T;T	0.11930|0.14516	2.73|2.5;2.5	5.73|5.73	5.73|5.73	0.89815|0.89815	.|HECT (1);	0.000000|0.000000	0.85682|0.85682	U|U	0.000000|0.000000	T|T	0.31420|0.31420	0.0796|0.0796	L|L	0.58925|0.58925	1.835|1.835	0.80722|0.80722	D|D	1|1	.|D	.|0.54601	.|0.967	.|D	.|0.63033	.|0.91	T|T	0.01001|0.01001	-1.1485|-1.1485	7|10	.|0.31617	.|T	.|0.26	-13.3026|-13.3026	16.0096|16.0096	0.80391|0.80391	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2123	.|Q9ULT8	.|HECD1_HUMAN	L|S	489|2123;2125;2123	ENSP00000451260:F489L|ENSP00000450697:F2123S;ENSP00000382269:F2123S	.|ENSP00000261312:F2125S	F|F	-|-	1|2	0|0	HECTD1|HECTD1	30648466|30648466	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	8.678000|8.678000	0.91211|0.91211	2.184000|2.184000	0.69523|0.69523	0.477000|0.477000	0.44152|0.44152	TTC|TTT		0.473	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			G	31578715	A	G	31578715	3	3	86	1	0	0	0	0	1	0	0	0	7060	14	1	4	1496	4	HECTD1	14	31578715	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	9703637	31578715	75770825	107	24131										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36039877	36039877	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cacggcttgcatttatagctGttgctctaaccataatgggt	9	9	1	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:36039877G>T	ENST00000389698.3	-	38	6314	c.5924C>A	c.(5923-5925)aCa>aAa	p.T1975K	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.T2022K|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.T1975K|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.T1988K	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1975	Minimal domain that binds to TCF3/E12. {ECO:0000250}.|Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.T1975R(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTTATAGCTGTTGCTCTAAC	0.363																																																1	Substitution - Missense(1)	breast(1)	14											55	51	52					14																	36039877		2203	4297	6500	35109628	SO:0001583	missense	0			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.5924C>A	14.37:g.36039877G>T	ENSP00000374348:p.Thr1975Lys		35109628	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.308097|5.308097	0.95629|0.95629	.|.	.|.	ENSG00000174373|ENSG00000174373	ENST00000554573|ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	.|D;D;D;D;D;D	.|0.92699	.|-3.09;-3.09;-3.09;-3.09;-3.09;-3.09	5.96|5.96	5.96|5.96	0.96718|0.96718	.|Rap/ran-GAP (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96037|0.96037	0.8709|0.8709	M|M	0.70903|0.70903	2.155|2.155	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.997;1.0;0.994;0.999	D|D	0.95744|0.95744	0.8786|0.8786	5|10	.|0.87932	.|D	.|0	-16.1049|-16.1049	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2022;1988;1975;1975	.|Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.|.;.;.;RGPA1_HUMAN	K|K	258|1975;1975;1975;2022;613;1988;2022	.|ENSP00000374348:T1975K;ENSP00000302647:T1975K;ENSP00000258840:T2022K;ENSP00000451133:T613K;ENSP00000371803:T1988K;ENSP00000451877:T2022K	.|ENSP00000258840:T2022K	Q|T	-|-	1|2	0|0	RALGAPA1|RALGAPA1	35109628|35109628	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	CAG|ACA		0.363	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		T	36039877	G	T	36039877	3	4	86	1	0	0	0	0	1	0	0	0	13050	1377	48	2	351	2	RALGAPA1	14	36039877	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	4461162	36039877	71309663	108	24132										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91931635	91931635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctctattatggcagagttcaTcagattgtagcgggatccat	10	8	3	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:91931635T>C	ENST00000554943.1	-	11	1904	c.1789A>G	c.(1789-1791)Atg>Gtg	p.M597V	SMEK1_ENST00000555718.1_5'UTR|SMEK1_ENST00000555462.1_Missense_Mutation_p.M358V|SMEK1_ENST00000337238.4_Missense_Mutation_p.M584V|SMEK1_ENST00000554684.1_Missense_Mutation_p.M584V|SMEK1_ENST00000428424.2_Missense_Mutation_p.M358V			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	597					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GCAGAGTTCATCAGATTGTAG	0.299																																																0			14											94	97	96					14																	91931635		2203	4300	6503	91001388	SO:0001583	missense	55671			AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1789A>G	14.37:g.91931635T>C	ENSP00000450883:p.Met597Val		91001388	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	37		.	.	.	.	.	.	.	.	.	.	T	11.41	1.629466	0.28978	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	6.17	5.02	0.67125	Armadillo-type fold (1);	0.033652	0.85682	D	0.000000	T	0.25791	0.0628	N	0.19112	0.55	0.54753	D	0.999988	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.11329	0.006;0.0;0.001	T	0.02758	-1.1114	10	0.45353	T	0.12	-18.5462	12.8957	0.58098	0.1219:0.0:0.0:0.8781	.	358;597;584	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	V	584;584;358;597;358;584	ENSP00000450864:M584V;ENSP00000337125:M584V;ENSP00000392704:M358V;ENSP00000450883:M597V;ENSP00000450891:M358V;ENSP00000452596:M584V	ENSP00000337125:M584V	M	-	1	0	SMEK1	91001388	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.307000	0.51888	1.129000	0.42072	-0.336000	0.08194	ATG		0.299	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		C	91931635	T	C	91931635	3	2	86	1	0	0	0	0	1	0	0	0	14830	1435	50	4	732	4	SMEK1	14	91931635	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	55891758	91931635	15417905	109	24133										
SERPINA6	866	hgsc.bcm.edu	37	chr14	94780730	94780730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gccctggagaagctgggcccGtgtgtggccacaggtgccca	16	13	0	1	rs199699199		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:94780730G>A	ENST00000341584.3	-	2	402	c.256C>T	c.(256-258)Cgg>Tgg	p.R86W		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	86					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	AGCTGGGCCCGTGTGTGGCCA	0.557													G|||	1	0.000199681	0	0	5008	,	,		20254	0		0	False		,,,				2504	0.001															0			14						G	TRP/ARG	0,4406		0,0,2203	57	59	59		256	1.7	0	14		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	SERPINA6	NM_001756.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	86/406	94780730	1,13005	2203	4300	6503	93850483	SO:0001583	missense	866			J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"Serine (or cysteine) peptidase inhibitors"	1540	protein-coding gene	gene with protein product	"corticosteroid binding globulin", "transcortin"	122500	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.256C>T	14.37:g.94780730G>A	ENSP00000342850:p.Arg86Trp		93850483	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947664	0.34377	0.0	1.16E-4	ENSG00000170099	ENST00000341584;ENST00000557225	D;D	0.85258	-1.96;-1.96	4.7	1.68	0.24146	Serpin domain (3);	1.892330	0.02844	N	0.128250	D	0.85978	0.5823	M	0.84219	2.685	0.09310	N	1	B	0.32829	0.386	B	0.33799	0.17	T	0.65886	-0.6059	10	0.59425	D	0.04	.	4.2057	0.10488	0.0757:0.1416:0.4896:0.2931	.	86	P08185	CBG_HUMAN	W	86	ENSP00000342850:R86W;ENSP00000452018:R86W	ENSP00000342850:R86W	R	-	1	2	SERPINA6	93850483	0.235000	0.23794	0.000000	0.03702	0.166000	0.22503	2.993000	0.49425	0.153000	0.19213	-0.309000	0.09137	CGG		0.557	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756		A	94780730	G	A	94780730	3	1	86	1	0	0	0	0	1	0	0	0	14130	1144	40	1	977	1	SERPINA6	14	94780730	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	2849095	94780730	12568810	110	24134										
SLC24A5	283652	hgsc.bcm.edu	37	chr15	48431257	48431257	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	attacattactttttctaacCacaccagattgtagaaaaaa	3	8	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr15:48431257C>G	ENST00000341459.3	+	7	1036	c.963C>G	c.(961-963)acC>acG	p.T321T	SLC24A5_ENST00000449382.2_Silent_p.T261T	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	321					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TTTTTCTAACCACACCAGATT	0.338																																																0			15											70	70	70					15																	48431257		2197	4292	6489	46218549	SO:0001819	synonymous_variant	283652			AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.963C>G	15.37:g.48431257C>G			46218549	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Silent	SNP	ENST00000341459.3	37	CCDS10128.1																																																																																				0.338	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		G	48431257	C	G	48431257	2	3	86	1	0	0	0	0	0	0	0	1	14506	581	21	5		5	SLC24A5	15	48431257	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10		48431257	54100135	111	24135										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58622786	58622786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcgtaataaatgcctgtctgCctcaggaccgtgccgattca	10	12	3	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr16:58622786C>T	ENST00000317147.5	-	3	459	c.127G>A	c.(127-129)Gca>Aca	p.A43T	CNOT1_ENST00000441024.2_Missense_Mutation_p.A43T|CNOT1_ENST00000569240.1_Missense_Mutation_p.A43T	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	43					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGCCTGTCTGCCTCAGGACCG	0.373																																																0			16											73	62	66					16																	58622786		2198	4299	6497	57180287	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.127G>A	16.37:g.58622786C>T	ENSP00000320949:p.Ala43Thr		57180287	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	37	6.045014	0.97231	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.23147	1.92;1.92	5.95	5.95	0.96441	.	0.108239	0.64402	D	0.000007	T	0.51244	0.1663	M	0.64404	1.975	0.80722	D	1	D;P;D	0.71674	0.998;0.956;0.997	D;P;D	0.78314	0.991;0.651;0.935	T	0.29243	-1.0018	9	.	.	.	.	20.458	0.99154	0.0:1.0:0.0:0.0	.	43;43;43	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	T	43	ENSP00000320949:A43T;ENSP00000413113:A43T	.	A	-	1	0	CNOT1	57180287	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.835000	0.97688	0.650000	0.86243	GCA		0.373	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		T	58622786	C	T	58622786	3	4	86	1	0	0	0	0	1	0	0	0	3623	739	26	3	7413	3	CNOT1	16	58622786	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		58622786	31731967	112	24136										
TP53	7157	hgsc.bcm.edu	37	chr17	7577532	7577532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtgtgatgatggtgaggatgGgcctccggttcatgccgccc	16	10	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:7577532G>A	ENST00000269305.4	-	7	938	c.749C>T	c.(748-750)cCc>cTc	p.P250L	TP53_ENST00000413465.2_Missense_Mutation_p.P250L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P250L|TP53_ENST00000445888.2_Missense_Mutation_p.P250L|TP53_ENST00000420246.2_Missense_Mutation_p.P250L|TP53_ENST00000455263.2_Missense_Mutation_p.P250L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	250	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P250L(45)|p.0?(8)|p.?(5)|p.P250H(4)|p.P250F(3)|p.P250N(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.R248_P250delRRP(1)|p.P250_T253delPILT(1)|p.N247_P250delNRRP(1)|p.R249_P250delRP(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGTGAGGATGGGCCTCCGGTT	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	80	Substitution - Missense(56)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(1)	large_intestine(14)|lung(10)|breast(10)|upper_aerodigestive_tract(5)|biliary_tract(5)|skin(5)|ovary(5)|stomach(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|oesophagus(3)|liver(2)|urinary_tract(1)|eye(1)|peritoneum(1)|pancreas(1)|thyroid(1)	17	GRCh37	CM973401	TP53	M							154	112	126					17																	7577532		2203	4300	6503	7518257	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.749C>T	17.37:g.7577532G>A	ENSP00000269305:p.Pro250Leu		7518257	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504438	0.85176	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99885	-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.996;0.998;0.998;1.0	D	0.96045	0.9027	10	0.87932	D	0	-1.5308	15.3618	0.74483	0.0:0.0:1.0:0.0	.	250;250;250;250;250	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	L	250;250;250;250;250;250;239;118	ENSP00000410739:P250L;ENSP00000352610:P250L;ENSP00000269305:P250L;ENSP00000398846:P250L;ENSP00000391127:P250L;ENSP00000391478:P250L;ENSP00000425104:P118L	ENSP00000269305:P250L	P	-	2	0	TP53	7518257	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	9.601000	0.98297	2.564000	0.86499	0.462000	0.41574	CCC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577532	G	A	7577532	3	1	86	1	0	0	0	0	1	0	0	0	16421	1232	43	3	541	3	TP53	17	7577532	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10		7577532	73617678	113	24137										
TP53	7157	hgsc.bcm.edu	37	chr17	7579393	7579393	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ccctggtaggttttctgggaAgggacagaagatgacagggg	17	6	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:7579393A>G	ENST00000269305.4	-	4	483	c.294T>C	c.(292-294)ccT>ccC	p.P98P	TP53_ENST00000413465.2_Silent_p.P98P|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Silent_p.P98P|TP53_ENST00000445888.2_Silent_p.P98P|TP53_ENST00000420246.2_Silent_p.P98P|TP53_ENST00000455263.2_Silent_p.P98P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	98	Interaction with WWOX.		P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S99fs*48(3)|p.S99fs*23(3)|p.Q100fs*37(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTTTCTGGGAAGGGACAGAAG	0.642		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	24	Deletion - Frameshift(16)|Whole gene deletion(8)	bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|central_nervous_system(3)|ovary(3)|lung(2)|pancreas(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|liver(1)	17											50	52	51					17																	7579393		2203	4300	6503	7520118	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.294T>C	17.37:g.7579393A>G			7520118	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.642	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7579393	A	G	7579393	2	3	86	1	0	0	0	0	0	0	0	1	16421	59	3	4		4	TP53	17	7579393	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	1861	7579393	73615817	114	24138										
NF1	4763	hgsc.bcm.edu	37	chr17	29496930	29496930	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ttacaggaattaactgtttgTtcagaagacaatgttgatgt	9	4	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:29496930T>C	ENST00000358273.4	+	5	884	c.501T>C	c.(499-501)tgT>tgC	p.C167C	NF1_ENST00000431387.4_Silent_p.C167C|NF1_ENST00000356175.3_Silent_p.C167C	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	167					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.C167*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TAACTGTTTGTTCAGAAGACA	0.323			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(4)|Substitution - Nonsense(1)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)|thyroid(1)	17											92	91	91					17																	29496930		2203	4300	6503	26521056	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.501T>C	17.37:g.29496930T>C			26521056	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.323	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29496930	T	C	29496930	2	2	86	1	0	0	0	0	0	0	0	1	10387	1731	60	4		4	NF1	17	29496930	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	21917537	29496930	51698280	115	24139										
PGAP3	93210	hgsc.bcm.edu	37	chr17	37844108	37844108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgctagactcatgtagattgGctggcgggagcggaagtgat	16	6	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:37844108G>A	ENST00000300658.4	-	1	252	c.160C>T	c.(160-162)Cca>Tca	p.P54S	PGAP3_ENST00000429199.2_Missense_Mutation_p.P54S|ERBB2_ENST00000578199.1_5'Flank|PGAP3_ENST00000579146.1_Missense_Mutation_p.P54S|ERBB2_ENST00000584601.1_5'Flank|PGAP3_ENST00000378011.4_Missense_Mutation_p.P54S|ERBB2_ENST00000406381.2_5'Flank	NM_033419.3	NP_219487.3	Q96FM1	PGAP3_HUMAN	post-GPI attachment to proteins 3	54					GPI anchor biosynthetic process (GO:0006506)|GPI anchor metabolic process (GO:0006505)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12						ATGTAGATTGGCTGGCGGGAG	0.642																																																0			17											21	20	20					17																	37844108		2202	4297	6499	35097634	SO:0001583	missense	93210			AB088396	CCDS32641.1	17q21.2	2009-06-02	2009-06-02	2009-06-02		ENSG00000161395			23719	protein-coding gene	gene with protein product	"post-GPI attachment to proteins 3"	611801	"per1-like domain containing 1"	PERLD1		15010812, 17021251, 17314402	Standard	NM_001291728		Approved	MGC9753, CAB2, PP1498, PER1	uc002hsj.3	Q96FM1		ENST00000300658.4:c.160C>T	17.37:g.37844108G>A	ENSP00000300658:p.Pro54Ser		35097634	B4DGK7|Q86Z03|Q8NBJ8	Missense_Mutation	SNP	ENST00000300658.4	37	CCDS32641.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415179	0.96092	.	.	ENSG00000161395	ENST00000300658;ENST00000378011;ENST00000429199	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.77565	0.4149	M	0.72576	2.205	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.993;0.996	T	0.76005	-0.3117	9	0.34782	T	0.22	-9.3794	16.7954	0.85600	0.0:0.0:1.0:0.0	.	54;54;54	B4DGK7;Q96FM1-2;Q96FM1	.;.;PGAP3_HUMAN	S	54	.	ENSP00000300658:P54S	P	-	1	0	PGAP3	35097634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.622000	0.74233	2.519000	0.84933	0.561000	0.74099	CCA		0.642	PGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444825.2	NM_033419		A	37844108	G	A	37844108	3	1	86	1	0	0	0	0	1	0	0	0	11810	1203	42	3	834	3	PGAP3	17	37844108	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	8347178	37844108	43351102	116	24140										
BRCA1	672	hgsc.bcm.edu	37	chr17	41244523	41244523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcccatttctctttcaggtgAcattgaatgttcctcaaagt	6	10	3	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:41244523A>G	ENST00000357654.3	-	10	3143	c.3025T>C	c.(3025-3027)Tca>Cca	p.S1009P	BRCA1_ENST00000346315.3_Missense_Mutation_p.S1009P|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S1009P|BRCA1_ENST00000493795.1_Missense_Mutation_p.S962P|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S1009P|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.S713P	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1009					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTTTCAGGTGACATTGAATGT	0.348			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0			17											109	108	108					17																	41244523		2203	4300	6503	38498049	SO:0001583	missense	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3025T>C	17.37:g.41244523A>G	ENSP00000350283:p.Ser1009Pro		38498049	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	A	9.406	1.079152	0.20227	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	4.61	3.51	0.40186	.	0.000000	0.41938	D	0.000792	D	0.87144	0.6104	M	0.85373	2.75	0.09310	N	1	D;D;D;D;P;D	0.89917	0.997;0.999;0.995;0.999;0.927;1.0	D;D;D;D;P;D	0.78314	0.916;0.946;0.929;0.979;0.677;0.991	T	0.78565	-0.2155	10	0.66056	D	0.02	.	9.5687	0.39414	0.8434:0.0:0.0:0.1566	.	1009;968;1009;1009;1009;1009	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	P	1009;1009;1009;1009;713;1009;962	ENSP00000350283:S1009P;ENSP00000326002:S1009P;ENSP00000246907:S1009P;ENSP00000310938:S713P;ENSP00000418960:S1009P;ENSP00000418775:S962P	ENSP00000310938:S713P	S	-	1	0	BRCA1	38498049	0.858000	0.29795	0.039000	0.18376	0.013000	0.08279	5.359000	0.66074	0.874000	0.35823	-0.341000	0.08007	TCA		0.348	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41244523	A	G	41244523	3	3	86	1	0	0	0	0	1	0	0	0	1501	275	10	4	2692	4	BRCA1	17	41244523	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	3400415	41244523	39950687	117	24141										
TEX14	56155	hgsc.bcm.edu	37	chr17	56676693	56676693	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tcctcactgccaaaacaacaCgcctctctctccatcttatc	2	18	4	0	rs142675831		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:56676693C>T	ENST00000240361.8	-	14	2116	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	TEX14_ENST00000349033.5_Silent_p.A671A|TEX14_ENST00000389934.3_Silent_p.A671A			Q8IWB6	TEX14_HUMAN	testis expressed 14	677					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.A671A(1)|p.A677A(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAAAACAACACGCCTCTCTCT	0.493																																																2	Substitution - coding silent(2)	endometrium(2)	17						C	,,	1,4405	2.1+/-5.4	0,1,2202	146	140	142		2031,2013,2013	-10.5	0	17	dbSNP_134	142	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	677/1498,671/1452,671/1492	56676693	1,13005	2203	4300	6503	54031692	SO:0001819	synonymous_variant	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2031G>A	17.37:g.56676693C>T			54031692	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																				0.493	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56676693	C	T	56676693	2	4	86	1	0	0	0	0	0	0	0	1	15817	523	19	1		1	TEX14	17	56676693	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	15432170	56676693	24518517	118	24142										
CSH1	1442	hgsc.bcm.edu	37	chr17	61972614	61972614	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aagagaaggagaggccaagcGcttgggcactgttccctccc	13	12	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:61972614G>A	ENST00000316193.8	-	5	598				CSH1_ENST00000329882.8_Silent_p.S225S|CSH1_ENST00000453363.3_Intron	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GAGGCCAAGCGCTTGGGCACT	0.542									Russell-Silver syndrome																																							0			17											68	69	69					17																	61972614		2192	4297	6489	59326346	SO:0001627	intron_variant	1442	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.457-35C>T	17.37:g.61972614G>A			59326346	P01243|Q0VDB1|Q14407	Silent	SNP	ENST00000316193.8	37	CCDS11649.1																																																																																				0.542	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		A	61972614	G	A	61972614	1	1	86	0	1	0	0	0	0	0	0	0	3946	1078	38	1		1	CSH1	17	61972614	Intron	SNP	G	TCGA-CI-6619-01B-11D-1826-10	5295921	61972614	19222596	119	24143										
DNAH17	9489	hgsc.bcm.edu	37	chr17	76423179	76423179	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tctccaggatgtcgtccagcAcggccttcacctggaagcca	10	15	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:76423179A>G	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Missense_Mutation_p.V4223A|DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000585328.1_Missense_Mutation_p.V4195A	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			GTCGTCCAGCACGGCCTTCAC	0.587																																					Esophageal Squamous(45;182 1126 10685 43198)											0			17											31	25	27					17																	76423179		2199	4288	6487	73934774	SO:0001628	intergenic_variant	8632				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76423179A>G			73934774	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150332	0.57151	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.09630	2.96	4.99	4.99	0.66335	.	0.130940	0.34200	N	0.004162	T	0.17023	0.0409	M	0.73372	2.23	0.46609	D	0.999127	B	0.14438	0.01	B	0.22152	0.038	T	0.01869	-1.1257	10	0.59425	D	0.04	.	14.6892	0.69072	1.0:0.0:0.0:0.0	.	4195	E7EUM8	.	A	4195;4223	ENSP00000374490:V4223A	ENSP00000300671:V4195A	V	-	2	0	DNAH17	73934774	0.870000	0.30015	0.997000	0.53966	0.504000	0.33889	5.278000	0.65592	1.880000	0.54463	0.533000	0.62120	GTG		0.587	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		G	76423179	A	G	76423179	1	3	86	0	1	0	0	0	0	0	0	0	4612	159	6	4		4	DNAH17	17	76423179	IGR	SNP	A	TCGA-CI-6619-01B-11D-1826-10	14450565	76423179	4772031	120	24144										
CHST9	83539	hgsc.bcm.edu	37	chr18	24496363	24496363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tctttcatcggaagagtgccTatccttaaagttgggaaatt	9	7	2	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr18:24496363T>C	ENST00000284224.8	-	6	1469	c.1192A>G	c.(1192-1194)Agg>Ggg	p.R398G	AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000580774.1_3'UTR|CHST9_ENST00000581714.1_Missense_Mutation_p.R398G|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000579964.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	398					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					GAAGAGTGCCTATCCTTAAAG	0.368																																																0			18											155	142	146					18																	24496363		1839	4091	5930	22750361	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.1192A>G	18.37:g.24496363T>C	ENSP00000284224:p.Arg398Gly		22750361	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610254	0.46527	.	.	ENSG00000154080	ENST00000284224	T	0.73681	-0.77	6.07	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.74191	0.3684	L	0.35542	1.07	0.80722	D	1	B	0.29162	0.235	P	0.45343	0.477	T	0.71111	-0.4687	10	0.38643	T	0.18	-25.1503	13.5852	0.61926	0.0:0.0:0.1297:0.8703	.	398	Q7L1S5	CHST9_HUMAN	G	398	ENSP00000284224:R398G	ENSP00000284224:R398G	R	-	1	2	CHST9	22750361	1.000000	0.71417	0.960000	0.40013	0.976000	0.68499	3.206000	0.51098	1.100000	0.41517	0.533000	0.62120	AGG		0.368	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		C	24496363	T	C	24496363	3	2	86	1	0	0	0	0	1	0	0	0	3417	1521	53	4	143	4	CHST9	18	24496363	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10		24496363	53580885	121	24145										
BRD4	23476	hgsc.bcm.edu	37	chr19	15379766	15379766	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	agtgttgaagtcctggatacAttcctgagcattccagtaat	9	8	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:15379766A>G	ENST00000263377.2	-	3	594	c.373T>C	c.(373-375)Tgt>Cgt	p.C125R	BRD4_ENST00000371835.4_Missense_Mutation_p.C125R|BRD4_ENST00000360016.5_Missense_Mutation_p.C125R	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	125	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TCCTGGATACATTCCTGAGCA	0.443			T	C15orf55	lethal midline carcinoma of young people																																		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	0			19											170	153	159					19																	15379766		2203	4300	6503	15240766	SO:0001583	missense	23476			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.373T>C	19.37:g.15379766A>G	ENSP00000263377:p.Cys125Arg		15240766	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314965	0.81358	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.28895	1.59;1.59;1.59	5.25	5.25	0.73442	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000003	T	0.61739	0.2371	M	0.89095	3.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.70142	-0.4953	10	0.87932	D	0	-6.8729	14.1422	0.65327	1.0:0.0:0.0:0.0	.	125;125;125	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	R	125	ENSP00000263377:C125R;ENSP00000360901:C125R;ENSP00000353112:C125R	ENSP00000263377:C125R	C	-	1	0	BRD4	15240766	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	1.987000	0.57996	0.533000	0.62120	TGT		0.443	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		G	15379766	A	G	15379766	3	3	86	1	0	0	0	0	1	0	0	0	1507	217	8	4	3802	4	BRD4	19	15379766	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10		15379766	43749217	122	24146										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545420	23545420	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tttacaaccttttcttaactGtaaattctcatgtccacatt	2	10	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:23545420G>A	ENST00000300619.7	-	4	566	c.361C>T	c.(361-363)Cag>Tag	p.Q121*	ZNF91_ENST00000397082.2_Nonsense_Mutation_p.Q89*|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	121					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q121K(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTTCTTAACTGTAAATTCTCA	0.358																																																1	Substitution - Missense(1)	ovary(1)	19											66	69	68					19																	23545420		2122	4266	6388	23337260	SO:0001587	stop_gained	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.361C>T	19.37:g.23545420G>A	ENSP00000300619:p.Gln121*		23337260	A8K5E1|B7Z6G6	Nonsense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496023	0.26774	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	.	.	.	0.987	-1.05	0.10036	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	3.3973	0.07311	0.0:0.0:0.5482:0.4518	.	.	.	.	X	121;89	.	ENSP00000300619:Q121X	Q	-	1	0	ZNF91	23337260	0.001000	0.12720	0.007000	0.13788	0.597000	0.36814	-0.381000	0.07417	0.436000	0.26393	0.174000	0.16983	CAG		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23545420	G	A	23545420	4	1	86	1	0	0	0	0	0	1	0	0	18239	1386	48	3	3218	3	ZNF91	19	23545420	Nonsense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10	8165654	23545420	35583563	123	24147										
HPN	3249	hgsc.bcm.edu	37	chr19	35556185	35556185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cctgtgtgcctcccagctgcCggccaggccctggtggatgg	15	15	0	0	rs199890888	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:35556185C>T	ENST00000262626.2	+	10	1668	c.843C>T	c.(841-843)gcC>gcT	p.A281A	HPN_ENST00000597419.1_Silent_p.A123A|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000392226.1_Silent_p.A281A	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	281	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	TCCCAGCTGCCGGCCAGGCCC	0.612													C|||	3	0.000599042	0	0	5008	,	,		19083	0.003		0	False		,,,				2504	0															0			19											79	65	70					19																	35556185		2203	4300	6503	40248025	SO:0001819	synonymous_variant	3249				CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.843C>T	19.37:g.35556185C>T			40248025	B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																				0.612	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35556185	C	T	35556185	2	4	86	1	0	0	0	0	0	0	0	1	7357	639	23	1		1	HPN	19	35556185	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	12010765	35556185	23572798	124	24148										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40368416	40368416	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggtccccaccacccatgcagAcgtccagaacacagcccttg	8	18	0	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:40368416A>G	ENST00000221347.6	-	28	12939	c.12932T>C	c.(12931-12933)gTc>gCc	p.V4311A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4311						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			ACCCATGCAGACGTCCAGAAC	0.622																																																0			19											136	139	138					19																	40368416		2203	4297	6500	45060256	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12932T>C	19.37:g.40368416A>G	ENSP00000221347:p.Val4311Ala		45060256	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.916642	0.33815	.	.	ENSG00000090920	ENST00000221347	T	0.77098	-1.07	4.08	4.08	0.47627	Uncharacterised domain, cysteine-rich (2);	0.260617	0.31167	U	0.008139	T	0.64182	0.2575	L	0.39692	1.235	0.23802	N	0.996805	B	0.29085	0.232	B	0.27076	0.076	T	0.50389	-0.8834	10	0.02654	T	1	.	12.4404	0.55621	1.0:0.0:0.0:0.0	.	4311	Q9Y6R7	FCGBP_HUMAN	A	4311	ENSP00000221347:V4311A	ENSP00000221347:V4311A	V	-	2	0	FCGBP	45060256	0.005000	0.15991	0.997000	0.53966	0.708000	0.40852	2.418000	0.44662	1.848000	0.53677	0.254000	0.18369	GTC		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40368416	A	G	40368416	3	3	86	1	0	0	0	0	1	0	0	0	5797	275	10	4	3321	4	FCGBP	19	40368416	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	4812231	40368416	18760567	125	24149										
ZNF224	7767	hgsc.bcm.edu	37	chr19	44612142	44612142	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gggcttcagctggtcctcaaCtcgtctgacccatcagagac	10	14	4	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:44612142C>G	ENST00000336976.6	+	6	2083	c.1829C>G	c.(1828-1830)aCt>aGt	p.T610S	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	610					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				TGGTCCTCAACTCGTCTGACC	0.448																																																0			19											82	83	83					19																	44612142		2203	4300	6503	49303982	SO:0001583	missense	7767			AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1829C>G	19.37:g.44612142C>G	ENSP00000337368:p.Thr610Ser		49303982	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	.	.	.	.	.	.	.	.	.	.	c	0.010	-1.756597	0.00657	.	.	ENSG00000186019	ENST00000336976	T	0.59502	0.26	2.37	-1.82	0.07857	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19127	0.0459	N	0.01134	-0.995	0.09310	N	1	B	0.16802	0.019	B	0.17433	0.018	T	0.29640	-1.0005	9	0.02654	T	1	.	5.8389	0.18623	0.5975:0.2882:0.1143:0.0	.	610	Q9NZL3	ZN224_HUMAN	S	610	ENSP00000337368:T610S	ENSP00000337368:T610S	T	+	2	0	ZNF224	49303982	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.251000	0.08818	-0.485000	0.06754	0.591000	0.81541	ACT		0.448	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		G	44612142	C	G	44612142	3	3	86	1	0	0	0	0	1	0	0	0	17817	565	20	5	1843	5	ZNF224	19	44612142	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	4243726	44612142	14516841	126	24150										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44831652	44831652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gggtagtccttaccatagtcTtcgcttttatagaatttatc	7	8	1	1	rs192670888		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:44831652T>C	ENST00000337401.4	-	5	2764	c.2676A>G	c.(2674-2676)gaA>gaG	p.E892E	ZNF112_ENST00000536500.1_Silent_p.E909E|ZNF112_ENST00000354340.4_Silent_p.E886E	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	892					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TACCATAGTCTTCGCTTTTAT	0.388													T|||	1	0.000199681	0	0	5008	,	,		17680	0.001		0	False		,,,				2504	0															0			19											72	68	69					19																	44831652		2203	4299	6502	49523492	SO:0001819	synonymous_variant	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2676A>G	19.37:g.44831652T>C			49523492	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																				0.388	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		C	44831652	T	C	44831652	2	2	86	1	0	0	0	0	0	0	0	1	17677	1606	56	4		4	ZFP112	19	44831652	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	219510	44831652	14297331	127	24151										
TRPM4	54795	hgsc.bcm.edu	37	chr19	49703897	49703897	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gtgttcttcttcctcttcttCctcggcgtgtggctggtagc	11	12	4	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:49703897C>T	ENST00000252826.5	+	19	2934	c.2808C>T	c.(2806-2808)ttC>ttT	p.F936F	TRPM4_ENST00000427978.2_Silent_p.F791F|TRPM4_ENST00000355712.5_Silent_p.F582F	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	936					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		TCCTCTTCTTCCTCGGCGTGT	0.602																																																0			19											54	51	52					19																	49703897		2203	4300	6503	54395709	SO:0001819	synonymous_variant	54795			AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.2808C>T	19.37:g.49703897C>T			54395709	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	37	CCDS33073.1																																																																																				0.602	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49703897	C	T	49703897	2	4	86	1	0	0	0	0	0	0	0	1	16628	854	30	3		3	TRPM4	19	49703897	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	4872245	49703897	9425086	128	24152										
C19orf51	352909	hgsc.bcm.edu	37	chr19	55673654	55673654	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	acttccaggaaggtctcgctTcgctctacggagagagggag	14	10	2	1	rs3848618	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:55673654T>C	ENST00000524407.2	-	5	360	c.327A>G	c.(325-327)cgA>cgG	p.R109R	DNAAF3_ENST00000455045.1_Silent_p.R55R|DNAAF3_ENST00000587789.2_5'Flank|DNAAF3_ENST00000391720.4_Silent_p.R156R|CTD-2587H24.5_ENST00000591665.1_RNA|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000527223.2_Silent_p.R177R			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	109					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGGTCTCGCTTCGCTCTACGG	0.577													c|||	643	0.128395	0.0688	0.2651	5008	,	,		12792	0.2024		0.0169	False		,,,				2504	0.1503															0			19						C		111,3373		2,107,1633	11	13	13		468	-4.6	0.1	19	dbSNP_108	13	158,7134		0,158,3488	yes	coding-synonymous	C19orf51	NM_178837.3		2,265,5121	CC,CT,TT		2.1668,3.186,2.4963		156/589	55673654	269,10507	1742	3646	5388	60365466	SO:0001819	synonymous_variant	352909			AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"chromosome 19 open reading frame 51", "ciliary dyskinesia, primary 2"	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.327A>G	19.37:g.55673654T>C			60365466	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1																																																																																				0.577	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837		C	55673654	T	C	55673654	2	2	86	1	0	0	0	0	0	0	0	1	1939	1770	62	4		4	C19orf51	19	55673654	Silent	SNP	T	TCGA-CI-6619-01B-11D-1826-10	5969757	55673654	3455329	129	24153										
PEG3	5178	hgsc.bcm.edu	37	chr19	57328029	57328029	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cacgttcacgttcatgttcaCgctcattatctttgtcatcc	5	13	6	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:57328029C>A	ENST00000326441.9	-	10	2144	c.1781G>T	c.(1780-1782)cGt>cTt	p.R594L	ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R468L|PEG3_ENST00000598410.1_Missense_Mutation_p.R470L|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R594L|ZIM2_ENST00000601070.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	594			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R594H(1)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ttcatgttcacgctcatTATC	0.453																																																1	Substitution - Missense(1)	large_intestine(1)	19											107	83	91					19																	57328029		2203	4300	6503	62019841	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.1781G>T	19.37:g.57328029C>A	ENSP00000326581:p.Arg594Leu		62019841	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	9.368	1.069879	0.20147	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.03358	3.96;3.96	1.94	1.94	0.25998	.	0.173402	0.28171	N	0.016329	T	0.03608	0.0103	L	0.46157	1.445	.	.	.	B;B;P	0.38827	0.247;0.247;0.649	B;B;B	0.34489	0.065;0.065;0.184	T	0.15292	-1.0442	9	0.66056	D	0.02	.	7.4011	0.26965	0.0:1.0:0.0:0.0	.	470;594;529	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	L	594	ENSP00000326581:R594L;ENSP00000403051:R594L	ENSP00000326581:R594L	R	-	2	0	ZIM2	62019841	0.002000	0.14202	0.004000	0.12327	0.404000	0.30871	0.388000	0.20735	1.397000	0.46682	0.650000	0.86243	CGT		0.453	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57328029	C	A	57328029	3	1	86	1	0	0	0	0	1	0	0	0	11751	536	19	2	2989	2	PEG3	19	57328029	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10	1654375	57328029	1800954	130	24154										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3002012	3002012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ggacctatgggaatattcggGtgtctgtagaggatgtgact	15	5	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:3002012G>A	ENST00000216877.6	+	13	1472	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	PTPRA_ENST00000380393.3_Missense_Mutation_p.V367M|PTPRA_ENST00000318266.5_Missense_Mutation_p.V358M|PTPRA_ENST00000358719.4_Missense_Mutation_p.V223M|PTPRA_ENST00000425918.2_Missense_Mutation_p.V378M|PTPRA_ENST00000356147.3_Missense_Mutation_p.V358M|PTPRA_ENST00000399903.2_Missense_Mutation_p.V367M	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	367	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GAATATTCGGGTGTCTGTAGA	0.507																																																0			20											204	164	177					20																	3002012		2203	4300	6503	2950012	SO:0001583	missense	5786				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1072G>A	20.37:g.3002012G>A	ENSP00000216877:p.Val358Met		2950012	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014943	0.93404	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000425918;ENST00000318266;ENST00000356147	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	4.68	4.68	0.58851	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.146530	0.45126	U	0.000384	T	0.64450	0.2599	H	0.97983	4.12	0.80722	D	1	D;D;D	0.89917	1.0;0.995;1.0	D;D;D	0.83275	0.996;0.917;0.987	T	0.79801	-0.1650	10	0.87932	D	0	.	18.1483	0.89665	0.0:0.0:1.0:0.0	.	378;367;358	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	M	367;358;367;223;378;358;358	ENSP00000369756:V367M;ENSP00000216877:V358M;ENSP00000382787:V367M;ENSP00000351559:V223M;ENSP00000393553:V378M;ENSP00000314568:V358M;ENSP00000348468:V358M	ENSP00000216877:V358M	V	+	1	0	PTPRA	2950012	1.000000	0.71417	0.998000	0.56505	0.860000	0.49131	9.625000	0.98406	2.584000	0.87258	0.563000	0.77884	GTG		0.507	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			A	3002012	G	A	3002012	3	1	86	1	0	0	0	0	1	0	0	0	12832	1261	44	3	1141	3	PTPRA	20	3002012	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10		3002012	60023508	131	24155										
HCK	3055	hgsc.bcm.edu	37	chr20	30681683	30681683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cagattgcagaaggcatggcCttcatcgagcagaggaacta	12	9	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:30681683C>T	ENST00000520553.1	+	11	1293	c.1047C>T	c.(1045-1047)gcC>gcT	p.A349A	HCK_ENST00000518730.1_Silent_p.A348A|HCK_ENST00000375862.2_Silent_p.A369A|HCK_ENST00000538448.1_Silent_p.A349A|HCK_ENST00000375852.2_Silent_p.A370A|HCK_ENST00000534862.1_Silent_p.A350A	NM_001172129.1|NM_001172130.1|NM_001172131.1|NM_002110.3	NP_001165600.1|NP_001165601.1|NP_001165602.1|NP_002101.2	P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	370	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	AAGGCATGGCCTTCATCGAGC	0.562																																																0			20											153	104	120					20																	30681683		2203	4300	6503	30145344	SO:0001819	synonymous_variant	3055			AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"SH2 domain containing"	4840	protein-coding gene	gene with protein product		142370	"hemopoietic cell kinase"			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000520553.1:c.1047C>T	20.37:g.30681683C>T			30145344	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Silent	SNP	ENST00000520553.1	37	CCDS54455.1																																																																																				0.562	HCK-006	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000375751.1			T	30681683	C	T	30681683	2	4	86	1	0	0	0	0	0	0	0	1	7015	668	24	3		3	HCK	20	30681683	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	27679671	30681683	32343837	132	24156										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31022871	31022871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctcagttgcatccggatgttAgaactgaatgtgagtctggc	12	8	2	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:31022871A>G	ENST00000375687.4	+	13	2780	c.2356A>G	c.(2356-2358)Aga>Gga	p.R786G	ASXL1_ENST00000306058.5_Missense_Mutation_p.R781G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	786					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.H782fs*8(1)|p.R786G(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TCCGGATGTTAGAACTGAATG	0.552			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	20											78	70	73					20																	31022871		2203	4300	6503	30486532	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2356A>G	20.37:g.31022871A>G	ENSP00000364839:p.Arg786Gly		30486532	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.232443	0.58777	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.26373	1.74;1.74	5.17	4.05	0.47172	.	0.328852	0.37219	N	0.002188	T	0.44498	0.1296	M	0.72118	2.19	0.37189	D	0.903857	D;D	0.69078	0.997;0.991	P;P	0.61874	0.895;0.761	T	0.52503	-0.8567	10	0.49607	T	0.09	-14.8326	11.2115	0.48802	0.8466:0.1534:0.0:0.0	.	781;786	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	G	786;786;786;707;781	ENSP00000364839:R786G;ENSP00000305119:R781G	ENSP00000305119:R781G	R	+	1	2	ASXL1	30486532	0.991000	0.36638	0.845000	0.33349	0.881000	0.50899	2.875000	0.48491	1.064000	0.40671	0.533000	0.62120	AGA		0.552	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31022871	A	G	31022871	3	3	86	1	0	0	0	0	1	0	0	0	1067	412	15	4	2412	4	ASXL1	20	31022871	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	341188	31022871	32002649	133	24157										
GSS	2937	hgsc.bcm.edu	37	chr20	33524779	33524779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cattctctatggcacgctggTcaaatatgtttctttccttc	6	11	3	0	rs28938472		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:33524779T>C	ENST00000216951.2	-	7	754	c.656A>G	c.(655-657)gAc>gGc	p.D219G	GSS_ENST00000451957.2_Missense_Mutation_p.D108G|GSS_ENST00000541098.1_Missense_Mutation_p.D91G	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	219			D -> A (in GSS deficiency).|D -> G (in GSS deficiency; dbSNP:rs28938472). {ECO:0000269|PubMed:8896573}.		aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	GGCACGCTGGTCAAATATGTT	0.498																																																0			20	GRCh37	CM960787|CM970698	GSS	M	rs28938472						158	140	146					20																	33524779		2203	4300	6503	32988440	SO:0001583	missense	5621				CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.656A>G	20.37:g.33524779T>C	ENSP00000216951:p.Asp219Gly		32988440	B2R697|B6F210|E1P5P9|Q4TTD9	Missense_Mutation	SNP	ENST00000216951.2	37	CCDS13245.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.994984	0.93167	.	.	ENSG00000100983	ENST00000216951;ENST00000541098;ENST00000451957	D;D;D	0.94723	-3.5;-3.5;-3.5	5.9	5.9	0.94986	PreATP-grasp-like fold (1);Glutathione synthase, substrate-binding, eukaryotic (2);	0.168662	0.64402	D	0.000006	D	0.97923	0.9317	M	0.93375	3.41	0.80722	A	1	D;D	0.76494	0.999;0.998	D;D	0.73380	0.98;0.975	D	0.98894	1.0774	9	0.72032	D	0.01	-25.3403	15.993	0.80220	0.0:0.0:0.0:1.0	rs28938472	108;219	B6F210;P48637	.;GSHB_HUMAN	G	219;91;108	ENSP00000216951:D219G;ENSP00000439744:D91G;ENSP00000407517:D108G	ENSP00000216951:D219G	D	-	2	0	GSS	32988440	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.309000	0.78937	2.248000	0.74166	0.459000	0.35465	GAC		0.498	GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2			C	33524779	T	C	33524779	3	2	86	1	0	0	0	0	1	0	0	0	6850	1667	58	4	796	4	GSS	20	33524779	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	2501908	33524779	29500741	134	24158										
ELMO2	63916	hgsc.bcm.edu	37	chr20	44999993	44999993	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	acagagaaatgaacctacttTtctcctgcagggattcaaat	7	9	2	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:44999993T>A	ENST00000290246.6	-	19	1993	c.1799A>T	c.(1798-1800)aAa>aTa	p.K600I	ELMO2_ENST00000439931.2_Missense_Mutation_p.K612I|ELMO2_ENST00000372176.1_Missense_Mutation_p.K512I|ELMO2_ENST00000445496.2_Missense_Mutation_p.K417I|ELMO2_ENST00000454865.2_Missense_Mutation_p.K332I|ELMO2_ENST00000396391.1_Missense_Mutation_p.K600I|ELMO2_ENST00000352077.2_Missense_Mutation_p.K598I	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	600	PH.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				GAACCTACTTTTCTCCTGCAG	0.488																																																0			20											101	99	100					20																	44999993		2203	4300	6503	44433400	SO:0001583	missense	63916			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1799A>T	20.37:g.44999993T>A	ENSP00000290246:p.Lys600Ile		44433400	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	37	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.673718	0.67928	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000452857;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077	T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	4.45	4.45	0.53987	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	M	0.85041	2.73	0.80722	D	1	P;D;D;B	0.62365	0.85;0.991;0.991;0.447	P;D;P;B	0.64595	0.666;0.927;0.903;0.365	T	0.75505	-0.3294	10	0.87932	D	0	-16.302	13.3564	0.60631	0.0:0.0:0.0:1.0	.	612;332;417;600	B4DRL5;B4DZ20;B7Z1S8;Q96JJ3	.;.;.;ELMO2_HUMAN	I	600;512;167;600;612;417;332;598	ENSP00000290246:K600I;ENSP00000361249:K512I;ENSP00000414329:K167I;ENSP00000379673:K600I;ENSP00000396519:K612I;ENSP00000409920:K417I;ENSP00000415641:K332I;ENSP00000326172:K598I	ENSP00000290246:K600I	K	-	2	0	ELMO2	44433400	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.825000	0.86693	2.000000	0.58554	0.533000	0.62120	AAA		0.488	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		A	44999993	T	A	44999993	3	1	86	1	0	0	0	0	1	0	0	0	5079	1841	64	5	379	5	ELMO2	20	44999993	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	11475214	44999993	18025527	135	24159										
ELMO2	63916	hgsc.bcm.edu	37	chr20	45004386	45004386	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	cttgaaggacatatagctgaTgggccatctcagttttgatg	11	7	1	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:45004386T>G	ENST00000290246.6	-	12	1045	c.851A>C	c.(850-852)cAt>cCt	p.H284P	ELMO2_ENST00000439931.2_Missense_Mutation_p.H296P|ELMO2_ENST00000372176.1_Missense_Mutation_p.H196P|ELMO2_ENST00000445496.2_Missense_Mutation_p.H101P|ELMO2_ENST00000454865.2_Missense_Mutation_p.H16P|ELMO2_ENST00000396391.1_Missense_Mutation_p.H284P|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000352077.2_Missense_Mutation_p.H282P	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	284					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)	p.H284L(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				ATATAGCTGATGGGCCATCTC	0.502																																																1	Substitution - Missense(1)	ovary(1)	20											128	113	118					20																	45004386		2203	4300	6503	44437793	SO:0001583	missense	63916			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.851A>C	20.37:g.45004386T>G	ENSP00000290246:p.His284Pro		44437793	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	37	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575878	0.86645	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546;ENST00000450812	T;T;T;T;T;T;T;T;T	0.38560	2.19;1.93;2.19;1.65;1.56;1.27;2.19;1.13;1.16	4.99	4.99	0.66335	Terpene synthase-like (1);	0.000000	0.85682	D	0.000000	T	0.66790	0.2825	M	0.82193	2.58	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.986;0.999;0.993;0.987;0.986	T	0.72730	-0.4205	10	0.87932	D	0	-17.0858	14.0317	0.64619	0.0:0.0:0.0:1.0	.	296;16;284;101;284	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	P	284;196;284;296;101;16;282;72;284	ENSP00000290246:H284P;ENSP00000361249:H196P;ENSP00000379673:H284P;ENSP00000396519:H296P;ENSP00000409920:H101P;ENSP00000415641:H16P;ENSP00000326172:H282P;ENSP00000388962:H72P;ENSP00000416181:H284P	ENSP00000290246:H284P	H	-	2	0	ELMO2	44437793	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.868000	0.87116	2.096000	0.63516	0.454000	0.30748	CAT		0.502	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		G	45004386	T	G	45004386	3	3	86	1	0	0	0	0	1	0	0	0	5079	1464	51	4	1355	4	ELMO2	20	45004386	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	4393	45004386	18021134	136	24160										
RUNX1	861	hgsc.bcm.edu	37	chr21	36171606	36171606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	caagtggcttacttgagagtCgactggaaagttctgcagag	13	7	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr21:36171606C>T	ENST00000344691.4	-	5	2455	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	RUNX1_ENST00000437180.1_Missense_Mutation_p.R320Q|RUNX1_ENST00000399240.1_Missense_Mutation_p.R229Q|RUNX1_ENST00000325074.5_Missense_Mutation_p.R308Q|RUNX1_ENST00000300305.3_Missense_Mutation_p.R320Q	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	293	Interaction with KAT6A.|Pro/Ser/Thr-rich.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R320fs*165(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						ACTTGAGAGTCGACTGGAAAG	0.522			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	1	Complex - frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	21											140	130	133					21																	36171606		2203	4300	6503	35093476	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.878G>A	21.37:g.36171606C>T	ENSP00000340690:p.Arg293Gln		35093476	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536667	0.65085	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000431176;ENST00000399245	D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78	5.78	5.78	0.91487	.	0.143790	0.47455	D	0.000221	D	0.93953	0.8064	L	0.51422	1.61	0.80722	D	1	B;B;P;B;D	0.69078	0.026;0.218;0.535;0.048;0.997	B;B;B;B;D	0.70227	0.003;0.016;0.049;0.008;0.968	D	0.93421	0.6777	10	0.51188	T	0.08	-9.4081	19.6065	0.95583	0.0:1.0:0.0:0.0	.	296;188;320;308;293	C9JK12;Q01196-11;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	Q	293;320;320;308;229;54;296	ENSP00000340690:R293Q;ENSP00000300305:R320Q;ENSP00000409227:R320Q;ENSP00000319459:R308Q;ENSP00000382184:R229Q	ENSP00000300305:R320Q	R	-	2	0	RUNX1	35093476	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.581000	0.74045	2.731000	0.93534	0.650000	0.86243	CGA		0.522	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			T	36171606	C	T	36171606	3	4	86	1	0	0	0	0	1	0	0	0	13783	884	31	1	491	1	RUNX1	21	36171606	Missense_Mutation	SNP	C	TCGA-CI-6619-01B-11D-1826-10		36171606	11958289	137	24161										
PPM1F	9647	hgsc.bcm.edu	37	chr22	22277784	22277784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gcaggtagtcctcggagcccGtcagcgcccgggaagctgca	15	14	1	0	rs144940091		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:22277784G>A	ENST00000263212.5	-	8	1151	c.1046C>T	c.(1045-1047)aCg>aTg	p.T349M	PPM1F_ENST00000407142.1_Missense_Mutation_p.T181M|PPM1F_ENST00000538191.1_Missense_Mutation_p.T245M	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	349					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		CTCGGAGCCCGTCAGCGCCCG	0.637													G|||	1	0.000199681	0	0	5008	,	,		16544	0.001		0	False		,,,				2504	0															0			22											45	49	48					22																	22277784		2203	4300	6503	20607784	SO:0001583	missense	9647			D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.1046C>T	22.37:g.22277784G>A	ENSP00000263212:p.Thr349Met		20607784	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	37	CCDS13796.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.49	2.550561	0.45383	.	.	ENSG00000100034	ENST00000263212;ENST00000407142;ENST00000406981;ENST00000538191	T;T;T	0.11277	2.79;2.79;2.79	5.23	4.17	0.49024	Protein phosphatase 2C-like (5);	0.847094	0.10581	N	0.657927	T	0.32645	0.0836	M	0.71036	2.16	0.09310	N	1	D;D	0.89917	1.0;0.998	D;D	0.70716	0.97;0.967	T	0.06075	-1.0847	10	0.52906	T	0.07	-13.385	14.5396	0.67984	0.0:0.2704:0.7296:0.0	.	245;349	B7Z2C3;P49593	.;PPM1F_HUMAN	M	349;181;181;245	ENSP00000263212:T349M;ENSP00000384930:T181M;ENSP00000439915:T245M	ENSP00000263212:T349M	T	-	2	0	PPM1F	20607784	0.002000	0.14202	0.741000	0.31004	0.264000	0.26372	0.610000	0.24253	2.721000	0.93114	0.655000	0.94253	ACG		0.637	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		A	22277784	G	A	22277784	3	1	86	1	0	0	0	0	1	0	0	0	12373	1145	40	1	322	1	PPM1F	22	22277784	Missense_Mutation	SNP	G	TCGA-CI-6619-01B-11D-1826-10		22277784	29026782	138	24162										
EP300	2033	hgsc.bcm.edu	37	chr22	41569717	41569717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	tgagtaggggcaacaagaagAaacccgggatgcccaatgta	13	8	0	3			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:41569717A>G	ENST00000263253.7	+	29	5927	c.4708A>G	c.(4708-4710)Aaa>Gaa	p.K1570E	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1570	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAACAAGAAGAAACCCGGGAT	0.448			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											152	160	157					22																	41569717		2203	4300	6503	39899663	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4708A>G	22.37:g.41569717A>G	ENSP00000263253:p.Lys1570Glu		39899663	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.356564	0.82243	.	.	ENSG00000100393	ENST00000263253	D	0.92911	-3.13	5.52	5.52	0.82312	.	0.000000	0.48767	D	0.000171	D	0.95868	0.8655	M	0.79475	2.455	0.47862	D	0.999533	D	0.76494	0.999	D	0.83275	0.996	D	0.96248	0.9181	10	0.66056	D	0.02	-13.6072	15.643	0.77020	1.0:0.0:0.0:0.0	.	1570	Q09472	EP300_HUMAN	E	1570	ENSP00000263253:K1570E	ENSP00000263253:K1570E	K	+	1	0	EP300	39899663	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.237000	0.95368	2.094000	0.63399	0.533000	0.62120	AAA		0.448	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41569717	A	G	41569717	3	3	86	1	0	0	0	0	1	0	0	0	5161	247	9	4	4822	4	EP300	22	41569717	Missense_Mutation	SNP	A	TCGA-CI-6619-01B-11D-1826-10	19291933	41569717	9734849	139	24163										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45789613	45789613	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atcccagcattctgcaattcActtctaataagattcaattc	3	11	4	1			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:45789613A>G	ENST00000357450.4	-	9	1445	c.1446T>C	c.(1444-1446)agT>agC	p.S482S	SMC1B_ENST00000404354.3_Silent_p.S482S	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	482					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTGCAATTCACTTCTAATAA	0.373																																																0			22											121	108	112					22																	45789613		1838	4085	5923	44168277	SO:0001819	synonymous_variant	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1446T>C	22.37:g.45789613A>G			44168277	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																				0.373	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		G	45789613	A	G	45789613	2	3	86	1	0	0	0	0	0	0	0	1	14819	156	6	4		4	SMC1B	22	45789613	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	4219896	45789613	5514953	140	24164										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50664611	50664611	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	acgtagccatgtgtccagtaCaacttatctaaggtagggtg	11	8	1	0	rs142499686	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:50664611C>T	ENST00000248846.5	-	9	1805	c.1701G>A	c.(1699-1701)ttG>ttA	p.L567L	TUBGCP6_ENST00000439308.2_Silent_p.L567L|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	567			L -> S (in dbSNP:rs4838865). {ECO:0000269|PubMed:11694571}.		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		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)		GTGTCCAGTACAACTTATCTA	0.577													C|||	3	0.000599042	8e-04	0.0014	5008	,	,		15444	0		0.001	False		,,,				2504	0															0			22						C		3,4403	2.1+/-5.4	0,3,2200	213	198	203		1701	-8.5	0	22	dbSNP_134	203	13,8587	6.4+/-24.3	0,13,4287	no	coding-synonymous	TUBGCP6	NM_020461.3		0,16,6487	TT,TC,CC		0.1512,0.0681,0.123		567/1820	50664611	16,12990	2203	4300	6503	49006738	SO:0001819	synonymous_variant	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1701G>A	22.37:g.50664611C>T			49006738	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																				0.577	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		T	50664611	C	T	50664611	2	4	86	1	0	0	0	0	0	0	0	1	16810	477	17	3		3	TUBGCP6	22	50664611	Silent	SNP	C	TCGA-CI-6619-01B-11D-1826-10	4874998	50664611	639955	141	24165										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-													0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	ctgactcagtggttcttccaCctcgctctcctgactcaggg					rs1058237|rs144469326	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs		8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				0.642	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138168	CCTC	-	8138165	7	5	86	1	0	1	0	1	0	0	0	0	17183	507	18	0	95	0	VCX2	23	8138165	Frame_Shift_Del	DEL	CCTC	TCGA-CI-6619-01B-11D-1826-10		8138165	147132395	142	24166										
DMD	1756	hgsc.bcm.edu	37	chrX	32827653	32827653	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	atgcctaattgatatctggcGatgttgaatgcatgttccag	10	7	1	2	rs138335295		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:32827653G>A	ENST00000357033.4	-	7	812	c.606C>T	c.(604-606)atC>atT	p.I202I	DMD_ENST00000378677.2_Silent_p.I198I|DMD_ENST00000288447.4_Silent_p.I194I	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	202	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				GATATCTGGCGATGTTGAATG	0.408																																																0			X						G	,,,,	1,3832		0,1,1630,571	189	140	157		582,606,237,594,237	-10.2	0.4	X	dbSNP_134	157	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	0,1,4058,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,,,,	194/3678,202/3686,79/3563,198/3682,79/3563	32827653	1,10560	2202	4300	6502	32737574	SO:0001819	synonymous_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.606C>T	X.37:g.32827653G>A			32737574	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																				0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32827653	G	A	32827653	2	1	86	1	0	0	0	0	0	0	0	1	4591	1048	37	1		1	DMD	23	32827653	Silent	SNP	G	TCGA-CI-6619-01B-11D-1826-10	24689488	32827653	122442907	143	24167										
PAK3	5063	hgsc.bcm.edu	37	chrX	110366490	110366490	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	aggcttcgctctatcttcccAggaggaggggataaaagtaa	12	8	2	0			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:110366490A>G	ENST00000372010.1	+	5	601	c.159A>G	c.(157-159)ccA>ccG	p.P53P	PAK3_ENST00000425146.1_Silent_p.P53P|PAK3_ENST00000417227.1_Silent_p.P53P|PAK3_ENST00000519681.1_Silent_p.P53P|PAK3_ENST00000360648.4_Silent_p.P53P|PAK3_ENST00000518291.1_Silent_p.P53P|PAK3_ENST00000446737.1_Silent_p.P53P|PAK3_ENST00000372007.5_Silent_p.P53P|PAK3_ENST00000262836.4_Silent_p.P53P			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	53					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTATCTTCCCAGGAGGAGGGG	0.448										TSP Lung(19;0.15)																																						0			X											74	73	73					X																	110366490		2203	4300	6503	110253146	SO:0001819	synonymous_variant	8874			AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.159A>G	X.37:g.110366490A>G			110253146	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Silent	SNP	ENST00000372010.1	37	CCDS48153.1																																																																																				0.448	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		G	110366490	A	G	110366490	2	3	86	1	0	0	0	0	0	0	0	1	11433	175	7	4		4	PAK3	23	110366490	Silent	SNP	A	TCGA-CI-6619-01B-11D-1826-10	77538837	110366490	44904070	144	24168										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138832229	138832229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0206896551724138	3	1	0.337606490872211	1.45045751633987	0.133205282112845	1	1	0	gagtgtcaatgttgatgtgcTgttccagtagactataggcc	12	7	1	2			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:138832229T>C	ENST00000327569.3	-	24	2890	c.2792A>G	c.(2791-2793)cAg>cGg	p.Q931R	ATP11C_ENST00000359686.2_Missense_Mutation_p.Q931R|ATP11C_ENST00000370543.1_Missense_Mutation_p.Q931R|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000370557.1_Missense_Mutation_p.Q925R|ATP11C_ENST00000361648.2_Missense_Mutation_p.Q931R	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	931			Q -> P (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Q931P(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGTGCTGTTCCAGTAG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	X											215	182	193					X																	138832229		2203	4300	6503	138659895	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.2792A>G	X.37:g.138832229T>C	ENSP00000332756:p.Gln931Arg		138659895	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.479344	0.84747	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.93213	0.7838	M	0.67397	2.05	0.58432	D	0.999996	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.87578	0.998;0.995;0.998	D	0.92283	0.5835	10	0.33940	T	0.23	.	14.3858	0.66942	0.0:0.0:0.0:1.0	.	931;931;931	Q8NB49-3;Q8NB49;Q8NB49-2	.;AT11C_HUMAN;.	R	925;931;931;931;931	ENSP00000359588:Q925R;ENSP00000355165:Q931R;ENSP00000332756:Q931R;ENSP00000359574:Q931R;ENSP00000352715:Q931R	ENSP00000332756:Q931R	Q	-	2	0	ATP11C	138659895	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.698000	0.84413	1.996000	0.58369	0.481000	0.45027	CAG		0.383	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		C	138832229	T	C	138832229	3	2	86	1	0	0	0	0	1	0	0	0	1122	1580	55	4	697	4	ATP11C	23	138832229	Missense_Mutation	SNP	T	TCGA-CI-6619-01B-11D-1826-10	28465739	138832229	16438331	145	24169										
MIB2	142678	hgsc.bcm.edu	37	chr1	1558755	1558796	+	Splice_Site	DEL	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	-													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cccatggtggcctgagaataCcctctgcccacaggtcccga					rs368037861|rs374321114|rs12755088|rs201820622	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:1558755_1558796delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	ENST00000357210.4	+	3	326_354	c.110_138delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	c.(109-138)accctctgcccacaggtcccgagcagcccg>a	p.TLCPQVPSSP37del	MIB2_ENST00000378712.1_Intron|MIB2_ENST00000360522.4_Splice_Site_p.TLCPQVPSSP37del|MIB2_ENST00000378710.3_Splice_Site_p.TLCPQVPSSP37del|MIB2_ENST00000505820.2_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000378708.1_Intron|MIB2_ENST00000520777.1_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000355826.5_Intron|MIB2_ENST00000518681.1_Splice_Site_p.TLCPQVPSSP94del|MIB2_ENST00000504599.1_Start_Codon_Del|MIB2_ENST00000512004.1_3'UTR	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	37					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCTGAGAATACCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGACCCCTCTGCCC	0.711																																																0			1																																								1548659	SO:0001630	splice_region_variant	142678			AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	30577	protein-coding gene	gene with protein product		611141	"zinc finger, ZZ type with ankyrin repeat domain 1", "mindbomb homolog 2 (Drosophila)"	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.111-1CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC>-	1.37:g.1558755_1558796delCCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC			1548618	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	In_Frame_Del	DEL	ENST00000357210.4	37																																																																																					0.711	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	In_Frame_Del	-	1558796	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	-	1558755	8	5	87	1	0	1	0	1	0	0	1	0	9597	522	18	0		0	MIB2	1	1558755	Splice_Site	DEL	CCCTCTGCCCACAGGTCCCGAGCAGCCCGGCCCACCATGGAC	TCGA-CI-6620-01A-11D-1826-10		1558755	247691866	1	24170										
CASP9	842	hgsc.bcm.edu	37	chr1	15844623	15844623	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	accgacatcaccaaatcctcCagaaccaatgtccactggtc	5	16	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:15844623C>T	ENST00000333868.5	-	2	494	c.400G>A	c.(400-402)Gga>Aga	p.G134R	CASP9_ENST00000375890.4_Missense_Mutation_p.G51R|CASP9_ENST00000469637.1_5'Flank|CASP9_ENST00000546424.1_Missense_Mutation_p.G134R|CASP9_ENST00000348549.5_Missense_Mutation_p.G134R	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	134					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CCAAATCCTCCAGAACCAATG	0.522																																																0			1											112	100	104					1																	15844623		2203	4300	6503	15717210	SO:0001583	missense	842			U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 56"	602234	"caspase 9, apoptosis-related cysteine protease"			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.400G>A	1.37:g.15844623C>T	ENSP00000330237:p.Gly134Arg		15717210	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	.	.	.	.	.	.	.	.	.	.	C	8.144	0.785883	0.16189	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000375890;ENST00000447522;ENST00000440484	T;T;T;T;T;T	0.10099	4.64;4.67;2.91;4.6;3.93;3.58	4.77	2.88	0.33553	.	1.735820	0.02593	N	0.100170	T	0.11922	0.0290	L	0.50333	1.59	0.09310	N	1	B;P;B	0.44521	0.033;0.837;0.037	B;B;B	0.39876	0.027;0.312;0.067	T	0.25187	-1.0139	10	0.16896	T	0.51	.	6.4847	0.22083	0.0:0.787:0.0:0.213	.	134;134;134	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	R	134;134;134;51;51;134	ENSP00000449584:G134R;ENSP00000330237:G134R;ENSP00000255256:G134R;ENSP00000365051:G51R;ENSP00000396540:G51R;ENSP00000411304:G134R	ENSP00000330237:G134R	G	-	1	0	CASP9	15717210	0.001000	0.12720	0.136000	0.22124	0.093000	0.18481	-0.019000	0.12546	1.365000	0.46057	0.563000	0.77884	GGA		0.522	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996		T	15844623	C	T	15844623	3	4	87	1	0	0	0	0	1	0	0	0	2685	603	21	3	882	3	CASP9	1	15844623	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	14285868	15844623	233405998	2	24171										
PADI1	29943	hgsc.bcm.edu	37	chr1	17556621	17556621	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caatgagaaattcctggaggAcatgtcttatctgacattga	9	7	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:17556621A>G	ENST00000375471.4	+	9	1063	c.971A>G	c.(970-972)gAc>gGc	p.D324G		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	324					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.D324G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		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)	TTCCTGGAGGACATGTCTTAT	0.517																																					Esophageal Squamous(80;414 1257 4580 27746 50832)											1	Substitution - Missense(1)	lung(1)	1											107	98	101					1																	17556621		2203	4300	6503	17429208	SO:0001583	missense	29943			AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.971A>G	1.37:g.17556621A>G	ENSP00000364620:p.Asp324Gly		17429208	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	A	8.880	0.951330	0.18431	.	.	ENSG00000142623	ENST00000375471	T	0.23950	1.88	4.99	3.8	0.43715	Protein-arginine deiminase, C-terminal (1);	0.545977	0.19466	N	0.113591	T	0.23886	0.0578	L	0.43923	1.385	0.37424	D	0.913756	P	0.36712	0.566	B	0.40702	0.338	T	0.10428	-1.0630	10	0.25106	T	0.35	-30.0529	10.614	0.45439	0.7244:0.2756:0.0:0.0	.	324	Q9ULC6	PADI1_HUMAN	G	324	ENSP00000364620:D324G	ENSP00000364620:D324G	D	+	2	0	PADI1	17429208	0.034000	0.19679	0.995000	0.50966	0.204000	0.24138	0.356000	0.20181	2.009000	0.58944	0.383000	0.25322	GAC		0.517	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		G	17556621	A	G	17556621	3	3	87	1	0	0	0	0	1	0	0	0	11408	275	10	4	1005	4	PADI1	1	17556621	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	1711998	17556621	231694000	3	24172										
USP48	84196	hgsc.bcm.edu	37	chr1	22021622	22021622	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agtgctttctcaccacgaacTtttctatgtcgcatacttcg	6	12	2	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:22021622T>C	ENST00000308271.9	-	23	3468	c.2820A>G	c.(2818-2820)aaA>aaG	p.K940K	USP48_ENST00000529637.1_Silent_p.K952K|USP48_ENST00000400301.1_Intron|USP48_ENST00000374732.3_Intron	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	940	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.K940N(1)		NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CACCACGAACTTTTCTATGTC	0.378																																																1	Substitution - Missense(1)	ovary(1)	1											162	154	157					1																	22021622		2203	4299	6502	21894209	SO:0001819	synonymous_variant	84196			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2820A>G	1.37:g.22021622T>C			21894209	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																				0.378	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		C	22021622	T	C	22021622	2	2	87	1	0	0	0	0	0	0	0	1	17119	1606	56	4		4	USP48	1	22021622	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	4465001	22021622	227228999	4	24173										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27057980	27057980	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcagtctccttaccagcagcAgcaacctcagcagccagcac	7	17	3	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:27057980A>G	ENST00000324856.7	+	3	2059	c.1688A>G	c.(1687-1689)cAg>cGg	p.Q563R	ARID1A_ENST00000457599.2_Missense_Mutation_p.Q563R|ARID1A_ENST00000374152.2_Missense_Mutation_p.Q180R	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	563	Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		TACCAGCAGCAGCAACCTCAG	0.647			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											162	165	164					1																	27057980		2203	4300	6503	26930567	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1688A>G	1.37:g.27057980A>G	ENSP00000320485:p.Gln563Arg		26930567	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.367684	0.42003	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02656	4.37;4.21;4.27	5.44	4.31	0.51392	.	0.185795	0.47455	D	0.000221	T	0.02342	0.0072	N	0.24115	0.695	0.80722	D	1	P;P;P	0.42409	0.534;0.779;0.671	B;B;B	0.38500	0.142;0.275;0.142	T	0.64635	-0.6361	10	0.15066	T	0.55	-2.009	11.5642	0.50796	0.8508:0.1492:0.0:0.0	.	563;563;217	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	R	563;563;180	ENSP00000320485:Q563R;ENSP00000387636:Q563R;ENSP00000363267:Q180R	ENSP00000320485:Q563R	Q	+	2	0	ARID1A	26930567	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.450000	0.73477	1.063000	0.40649	0.533000	0.62120	CAG		0.647	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27057980	A	G	27057980	3	3	87	1	0	0	0	0	1	0	0	0	913	188	7	4	1698	4	ARID1A	1	27057980	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	5036358	27057980	222192641	5	24174										
MACF1	23499	hgsc.bcm.edu	37	chr1	39905073	39905073	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttctggtatgacatggcagcTctcctgaccaccatcaaaga	8	12	3	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:39905073T>C	ENST00000372915.3	+	71	18132	c.18045T>C	c.(18043-18045)gcT>gcC	p.A6015A	MACF1_ENST00000289893.4_Silent_p.A4559A|MACF1_ENST00000567887.1_Silent_p.A6153A|MACF1_ENST00000564288.1_Silent_p.A6116A|MACF1_ENST00000361689.2_Silent_p.A4057A|MACF1_ENST00000539005.1_Silent_p.A3927A|MACF1_ENST00000317713.7_Silent_p.A4057A|MACF1_ENST00000545844.1_Silent_p.A4057A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6015					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			ACATGGCAGCTCTCCTGACCA	0.458																																																0			1											86	80	82					1																	39905073		2203	4300	6503	39677660	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18045T>C	1.37:g.39905073T>C			39677660	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	T	10.95	1.494532	0.26774	.	.	ENSG00000127603	ENST00000372925	.	.	.	5.77	-0.902	0.10537	.	.	.	.	.	T	0.54398	0.1856	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48210	-0.9055	4	.	.	.	.	8.6957	0.34293	0.0:0.6008:0.154:0.2453	.	.	.	.	P	3061	.	.	S	+	1	0	MACF1	39677660	0.460000	0.25776	0.998000	0.56505	0.997000	0.91878	-0.254000	0.08781	-0.108000	0.12066	0.528000	0.53228	TCT		0.458	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39905073	T	C	39905073	2	2	87	1	0	0	0	0	0	0	0	1	9174	1538	54	4		4	MACF1	1	39905073	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	12847093	39905073	209345548	6	24175										
C1orf183	55924	hgsc.bcm.edu	37	chr1	112269921	112269921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctttctctcctttgggttcaCgtgcccccccagtctcaccc	6	19	3	0	rs371956554		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:112269921C>T	ENST00000357260.5	-	2	744	c.563G>A	c.(562-564)cGt>cAt	p.R188H	FAM212B_ENST00000534365.1_Intron|FAM212B_ENST00000444059.2_Missense_Mutation_p.R173H	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	188										cervix(1)|endometrium(1)	2						TTTGGGTTCACGTGCCCCCCC	0.577																																																0			1						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	67	66	66		563,518	1.2	0	1		66	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C1orf183	NM_019099.4,NM_198926.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	188/298,173/283	112269921	1,13005	2203	4300	6503	112071444	SO:0001583	missense	55924			AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 183"	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.563G>A	1.37:g.112269921C>T	ENSP00000349805:p.Arg188His		112071444	B3KP38|B4DF94|Q9NTI6	Missense_Mutation	SNP	ENST00000357260.5	37	CCDS841.1	.	.	.	.	.	.	.	.	.	.	C	7.342	0.621032	0.14193	0.0	1.16E-4	ENSG00000197852	ENST00000357260;ENST00000444059	.	.	.	5.3	1.19	0.21007	.	0.898267	0.09763	N	0.759003	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	P;P	0.43024	0.798;0.798	B;B	0.35550	0.205;0.205	T	0.26292	-1.0107	9	0.38643	T	0.18	-37.0073	1.7452	0.02961	0.1681:0.4877:0.163:0.1812	.	173;188	Q9NTI7-2;Q9NTI7	.;CA183_HUMAN	H	188;173	.	ENSP00000349805:R188H	R	-	2	0	C1orf183	112071444	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.255000	0.08769	0.198000	0.20407	0.484000	0.47621	CGT		0.577	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033060.2	NM_019099		T	112269921	C	T	112269921	3	4	87	1	0	0	0	0	1	0	0	0	2025	536	19	1	334	1	C1orf183	1	112269921	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	72364848	112269921	136980700	7	24176										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120506311	120506311	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctggtcactgcagatggcgcCcatgtacccgggattgcaga	13	12	1	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:120506311C>A	ENST00000256646.2	-	11	2020	c.1801G>T	c.(1801-1803)Ggc>Tgc	p.G601C		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	601	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.G601C(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGATGGCGCCCATGTACCCG	0.527			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Missense(1)	central_nervous_system(1)	1											231	204	213					1																	120506311		2203	4300	6503	120307834	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.1801G>T	1.37:g.120506311C>A	ENSP00000256646:p.Gly601Cys		120307834	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830727	0.91036	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	T	0.34072	1.38	5.73	5.73	0.89815	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38164	U	0.001799	T	0.77370	0.4120	H	0.99764	4.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.997;1.0	D	0.87234	0.2262	10	0.87932	D	0	.	19.248	0.93909	0.0:1.0:0.0:0.0	.	562;601;601	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	C	601;562	ENSP00000256646:G601C	ENSP00000256646:G601C	G	-	1	0	NOTCH2	120307834	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	7.729000	0.84864	2.861000	0.98227	0.655000	0.94253	GGC		0.527	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120506311	C	A	120506311	3	1	87	1	0	0	0	0	1	0	0	0	10579	623	22	2	5710	2	NOTCH2	1	120506311	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	8236390	120506311	128744310	8	24177										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815492	156815492	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gcgcctccagcgggggcagaAcctgaccaggaggtgggtgc	18	12	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:156815492A>G	ENST00000368195.3	-	10	2489	c.2093T>C	c.(2092-2094)gTt>gCt	p.V698A	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	698	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CGGGGGCAGAACCTGACCAGG	0.617																																																0			1											46	45	45					1																	156815492		2203	4300	6503	155082116	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2093T>C	1.37:g.156815492A>G	ENSP00000357178:p.Val698Ala		155082116	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	A	0.034	-1.316804	0.01331	.	.	ENSG00000027644	ENST00000368195	T	0.73152	-0.72	4.58	-3.43	0.04810	Fibronectin, type III (2);	1.122080	0.06836	N	0.794908	T	0.14313	0.0346	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05767	-1.0865	9	0.06757	T	0.87	.	1.473	0.02420	0.2116:0.1416:0.37:0.2769	.	698	P14616	INSRR_HUMAN	A	698	ENSP00000357178:V698A	ENSP00000357178:V698A	V	-	2	0	INSRR	155082116	0.241000	0.23857	0.119000	0.21687	0.606000	0.37113	-0.463000	0.06696	-0.502000	0.06596	0.459000	0.35465	GTT		0.617	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		G	156815492	A	G	156815492	3	3	87	1	0	0	0	0	1	0	0	0	7795	43	2	4	1851	4	INSRR	1	156815492	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	36309181	156815492	92435129	9	24178										
ASPM	259266	hgsc.bcm.edu	37	chr1	197070657	197070657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tttttgtagcccactgaagcTtttggtagaaacaatactgc	8	8	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:197070657T>C	ENST00000367409.4	-	18	7980	c.7724A>G	c.(7723-7725)aAg>aGg	p.K2575R	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2575					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CCACTGAAGCTTTTGGTAGAA	0.318																																																0			1											55	50	52					1																	197070657		2202	4297	6499	195337280	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7724A>G	1.37:g.197070657T>C	ENSP00000356379:p.Lys2575Arg		195337280	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.523694	0.27299	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.71817	-0.6	5.15	4.03	0.46877	.	0.766419	0.12705	N	0.446024	T	0.72439	0.3460	M	0.70903	2.155	0.09310	N	1	P;B	0.40875	0.731;0.017	P;B	0.49752	0.621;0.013	T	0.58999	-0.7536	10	0.15952	T	0.53	.	5.1767	0.15139	0.1325:0.148:0.0:0.7194	.	561;2575	E7EQ84;Q8IZT6	.;ASPM_HUMAN	R	2575;561	ENSP00000356379:K2575R	ENSP00000356376:K561R	K	-	2	0	ASPM	195337280	0.000000	0.05858	0.047000	0.18901	0.969000	0.65631	0.510000	0.22723	0.900000	0.36469	-0.385000	0.06624	AAG		0.318	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		C	197070657	T	C	197070657	3	2	87	1	0	0	0	0	1	0	0	0	1057	1609	56	4	2753	4	ASPM	1	197070657	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	40255165	197070657	52179964	10	24179										
ABCB10	23456	hgsc.bcm.edu	37	chr1	229667428	229667428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctccaggagctcccagaggcGcccccctgcacccagtcctt	9	20	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:229667428G>A	ENST00000344517.4	-	7	1432	c.1390C>T	c.(1390-1392)Cgc>Tgc	p.R464C		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	464					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TCCCAGAGGCGCCCCCCTGCA	0.512																																																0			1											75	83	80					1																	229667428		2203	4300	6503	227734051	SO:0001583	missense	23456			U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1390C>T	1.37:g.229667428G>A	ENSP00000355637:p.Arg464Cys		227734051	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	37	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183300	0.78677	.	.	ENSG00000135776	ENST00000344517	D	0.87179	-2.22	5.96	5.03	0.67393	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93759	0.8005	H	0.96460	3.825	0.80722	D	1	D	0.61697	0.99	P	0.51079	0.658	D	0.95430	0.8515	10	0.72032	D	0.01	-19.3968	16.4122	0.83722	0.0:0.0:0.8674:0.1326	.	464	Q9NRK6	ABCBA_HUMAN	C	464	ENSP00000355637:R464C	ENSP00000355637:R464C	R	-	1	0	ABCB10	227734051	1.000000	0.71417	0.961000	0.40146	0.977000	0.68977	5.920000	0.70017	1.482000	0.48325	0.650000	0.86243	CGC		0.512	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		A	229667428	G	A	229667428	3	1	87	1	0	0	0	0	1	0	0	0	41	1087	38	1	854	1	ABCB10	1	229667428	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	32596771	229667428	19583193	11	24180										
GALNT2	2590	hgsc.bcm.edu	37	chr1	230338901	230338901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agggaaagtacggtggccagActttaaccaggaagcttatg	13	7	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:230338901A>G	ENST00000366672.4	+	3	311	c.239A>G	c.(238-240)gAc>gGc	p.D80G	GALNT2_ENST00000541865.1_5'UTR|GALNT2_ENST00000543760.1_Missense_Mutation_p.D42G	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	80					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CGGTGGCCAGACTTTAACCAG	0.517																																																0			1											147	147	147					1																	230338901		2203	4300	6503	228405524	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.239A>G	1.37:g.230338901A>G	ENSP00000355632:p.Asp80Gly		228405524	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389350	0.61956	.	.	ENSG00000143641	ENST00000543760;ENST00000366672	T;T	0.55234	0.54;0.53	5.77	5.77	0.91146	.	1.713610	0.05220	U	0.508464	T	0.46560	0.1399	L	0.34521	1.04	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.15350	-1.0440	10	0.07644	T	0.81	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	80;42	Q10471;G3V1S6	GALT2_HUMAN;.	G	42;80	ENSP00000445017:D42G;ENSP00000355632:D80G	ENSP00000355632:D80G	D	+	2	0	GALNT2	228405524	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.125000	0.77193	2.326000	0.78906	0.533000	0.62120	GAC		0.517	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		G	230338901	A	G	230338901	3	3	87	1	0	0	0	0	1	0	0	0	6233	275	10	4	249	4	GALNT2	1	230338901	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	671473	230338901	18911720	12	24181										
GNG4	2786	hgsc.bcm.edu	37	chr1	235715439	235715439	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gtacaaaagaacttcttctcGcgaaaggggttttctgatgc	10	8	3	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr1:235715439G>A	ENST00000366598.4	-	3	413	c.198C>T	c.(196-198)cgC>cgT	p.R66R	GNG4_ENST00000366597.1_Silent_p.R66R|GNG4_ENST00000484517.1_5'UTR|GNG4_ENST00000391854.2_Silent_p.R66R|GNG4_ENST00000450593.1_Silent_p.R66R			P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein), gamma 4	66					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell growth (GO:0030308)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			ACTTCTTCTCGCGAAAGGGGT	0.512																																																0			1											170	168	169					1																	235715439		2203	4300	6503	233782062	SO:0001819	synonymous_variant	2786			BC022485	CCDS1607.1	1q42.3	2008-02-05			ENSG00000168243	ENSG00000168243			4407	protein-coding gene	gene with protein product		604388				7665596	Standard	NM_001098721		Approved		uc001hxh.4	P50150	OTTHUMG00000040740	ENST00000366598.4:c.198C>T	1.37:g.235715439G>A			233782062		Silent	SNP	ENST00000366598.4	37	CCDS1607.1																																																																																				0.512	GNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097906.1	NM_004485		A	235715439	G	A	235715439	2	1	87	1	0	0	0	0	0	0	0	1	6549	1074	38	1		1	GNG4	1	235715439	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	5376538	235715439	13535182	13	24182										
PQLC3	130814	hgsc.bcm.edu	37	chr2	11300652	11300652	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccgccgctgacctacctggaGtaccccatcctcatcgcgca	8	19	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:11300652G>A	ENST00000295083.3	+	2	379	c.204G>A	c.(202-204)gaG>gaA	p.E68E	PQLC3_ENST00000402361.1_Silent_p.E68E|PQLC3_ENST00000441908.2_Silent_p.E68E|PQLC3_ENST00000476787.1_3'UTR	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	68						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		CCTACCTGGAGTACCCCATCC	0.592																																																0			2											163	139	147					2																	11300652		2203	4300	6503	11218103	SO:0001819	synonymous_variant	130814			BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 22"	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.204G>A	2.37:g.11300652G>A			11218103	B2R8K1|B4DWA4	Silent	SNP	ENST00000295083.3	37	CCDS1679.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329526	0.24167	.	.	ENSG00000162976	ENST00000428481	.	.	.	5.01	3.17	0.36434	.	.	.	.	.	T	0.56262	0.1973	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51624	-0.8682	4	.	.	.	-23.0111	7.5261	0.27656	0.2049:0.0:0.7951:0.0	.	.	.	.	I	48	.	.	V	+	1	0	PQLC3	11218103	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.295000	0.33377	1.066000	0.40716	0.561000	0.74099	GTA		0.592	PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391		A	11300652	G	A	11300652	2	1	87	1	0	0	0	0	0	0	0	1	12454	1020	36	3		3	PQLC3	2	11300652	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10		11300652	231898721	14	24183										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24438975	24438975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttctgctgtaacagagctgcTccattaagctggcagctgca	10	11	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:24438975T>C	ENST00000355123.4	-	32	4376	c.3933A>G	c.(3931-3933)ggA>ggG	p.G1311G	AC009228.1_ENST00000413254.1_RNA|AC009228.1_ENST00000430105.1_RNA|AC009228.1_ENST00000413989.1_RNA|ITSN2_ENST00000361999.3_Silent_p.G1284G	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1311	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAGAGCTGCTCCATTAAGCT	0.522																																																0			2											79	79	79					2																	24438975		2203	4300	6503	24292479	SO:0001819	synonymous_variant	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3933A>G	2.37:g.24438975T>C			24292479	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																				0.522	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		C	24438975	T	C	24438975	2	2	87	1	0	0	0	0	0	0	0	1	7948	1538	54	4		4	ITSN2	2	24438975	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	13138323	24438975	218760398	15	24184										
MCFD2	90411	hgsc.bcm.edu	37	chr2	47136283	47136283	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gagcaggccacacaggaaggGggttctgagcagggatctca	16	9	2	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:47136283G>C	ENST00000409105.1	-	3	207	c.28C>G	c.(28-30)Ccc>Gcc	p.P10A	MCFD2_ENST00000493804.1_Intron|MCFD2_ENST00000409147.1_Intron|MCFD2_ENST00000319466.4_Missense_Mutation_p.P10A|MCFD2_ENST00000409218.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409207.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409973.1_Missense_Mutation_p.P10A|MCFD2_ENST00000409800.1_Intron|MCFD2_ENST00000444761.2_Intron|AC016722.4_ENST00000429761.1_RNA|MCFD2_ENST00000409913.1_Intron	NM_001171506.2	NP_001164977.1	Q8NI22	MCFD2_HUMAN	multiple coagulation factor deficiency 2	10					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			central_nervous_system(1)|large_intestine(1)|lung(2)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Antihemophilic Factor(DB00025)	CACAGGAAGGGGGTTCTGAGC	0.577																																																0			2											35	38	37					2																	47136283		2203	4300	6503	46989787	SO:0001583	missense	90411			AF475284	CCDS33192.1, CCDS54354.1, CCDS54355.1	2p21	2014-09-17			ENSG00000180398	ENSG00000180398		"EF-hand domain containing"	18451	protein-coding gene	gene with protein product		607788				12717434, 2463956	Standard	NM_139279		Approved	F5F8D, LMAN1IP, SDNSF	uc021vha.1	Q8NI22	OTTHUMG00000153100	ENST00000409105.1:c.28C>G	2.37:g.47136283G>C	ENSP00000386651:p.Pro10Ala		46989787	A8K7W2|D6W5A9|E9PD95|Q53SS3|Q68D61|Q8N3M5	Missense_Mutation	SNP	ENST00000409105.1	37	CCDS33192.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702211	0.30232	.	.	ENSG00000180398	ENST00000409105;ENST00000319466;ENST00000409207;ENST00000409973;ENST00000409218;ENST00000412438;ENST00000417180	D;D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78;-1.78	5.36	2.4	0.29515	.	0.490245	0.24488	N	0.038084	T	0.66733	0.2819	L	0.27053	0.805	0.36606	D	0.874934	B	0.20368	0.044	B	0.15870	0.014	T	0.57585	-0.7786	10	0.16896	T	0.51	-9.5311	5.5064	0.16856	0.2455:0.0:0.6031:0.1514	.	10	Q8NI22	MCFD2_HUMAN	A	10	ENSP00000386651:P10A;ENSP00000317271:P10A;ENSP00000386386:P10A;ENSP00000386279:P10A;ENSP00000386261:P10A;ENSP00000402717:P10A	ENSP00000317271:P10A	P	-	1	0	MCFD2	46989787	0.011000	0.17503	0.180000	0.23079	0.897000	0.52465	0.511000	0.22739	0.848000	0.35191	0.561000	0.74099	CCC		0.577	MCFD2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329518.1	NM_139279		C	47136283	G	C	47136283	3	2	87	1	0	0	0	0	1	0	0	0	9411	1232	43	5	424	5	MCFD2	2	47136283	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	22697308	47136283	196063090	16	24185										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520567	131520567	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atgaagcctctgacttcaccAggttctgggacagtgtgaat	11	9	3	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:131520567A>G	ENST00000423981.1	+	2	1032	c.922A>G	c.(922-924)Agg>Ggg	p.R308G	AMER3_ENST00000321420.4_Missense_Mutation_p.R308G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	308					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R308W(1)									TGACTTCACCAGGTTCTGGGA	0.657																																																1	Substitution - Missense(1)	ovary(1)	2											32	38	36					2																	131520567		2202	4299	6501	131237037	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.922A>G	2.37:g.131520567A>G	ENSP00000392700:p.Arg308Gly		131237037	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	A	7.947	0.744053	0.15710	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.16196	2.36;2.36	5.21	4.04	0.47022	.	0.525997	0.20253	N	0.096032	T	0.10895	0.0266	N	0.14661	0.345	0.19575	N	0.999962	B	0.14805	0.011	B	0.19391	0.025	T	0.23547	-1.0185	10	0.40728	T	0.16	.	10.7781	0.46361	0.8406:0.1594:0.0:0.0	.	308	Q8N944	F123C_HUMAN	G	308	ENSP00000314914:R308G;ENSP00000392700:R308G	ENSP00000314914:R308G	R	+	1	2	FAM123C	131237037	0.988000	0.35896	0.338000	0.25549	0.133000	0.20885	6.134000	0.71689	0.913000	0.36797	-0.488000	0.04728	AGG		0.657	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		G	131520567	A	G	131520567	3	3	87	1	0	0	0	0	1	0	0	0	5440	179	7	4	924	4	FAM123C	2	131520567	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	84384284	131520567	111678806	17	24186										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165952157	165952157	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	catatacaggctgaagtttaAcctaaatgatattgaaaata	6	5	0	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:165952157A>G	ENST00000360093.3	-	25	4786	c.4295T>C	c.(4294-4296)gTt>gCt	p.V1432A	SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000409101.3_Splice_Site_p.V1383A|SCN3A_ENST00000540861.1_5'Flank|SCN3A_ENST00000283254.7_Splice_Site_p.V1432A	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1432					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAGTTTAACCTAAATGAT	0.264																																																0			2											37	36	37					2																	165952157		2197	4294	6491	165660403	SO:0001630	splice_region_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4294-1T>C	2.37:g.165952157A>G			165660403	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	10.23	1.293585	0.23564	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101	D;D;D	0.96522	-4.04;-4.04;-3.99	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000003	D	0.95739	0.8614	M	0.85542	2.76	0.80722	D	1	B;B;B	0.25272	0.122;0.122;0.01	B;B;B	0.25291	0.059;0.059;0.042	D	0.94256	0.7498	10	0.66056	D	0.02	.	10.8051	0.46514	0.8589:0.0:0.0:0.1411	.	1383;1383;1432	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	A	1432;1432;1383	ENSP00000353206:V1432A;ENSP00000283254:V1432A;ENSP00000386726:V1383A	ENSP00000283254:V1432A	V	-	2	0	SCN3A	165660403	1.000000	0.71417	1.000000	0.80357	0.074000	0.17049	3.968000	0.56809	2.333000	0.79357	0.482000	0.46254	GTT		0.264	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	Missense_Mutation	G	165952157	A	G	165952157	5	3	87	1	0	0	0	0	0	0	1	0	13955	57	2	4	1723	4	SCN3A	2	165952157	Splice_Site	SNP	A	TCGA-CI-6620-01A-11D-1826-10	34431590	165952157	77247216	18	24187										
TTN	7273	hgsc.bcm.edu	37	chr2	179641543	179641543	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cccattgctcttggccatatCgcaaatggaggggctccagt	11	12	1	0	rs368122582		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:179641543C>A	ENST00000591111.1	-	28	5272	c.5048G>T	c.(5047-5049)cGa>cTa	p.R1683L	RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R1683L|TTN_ENST00000360870.5_Missense_Mutation_p.R1683L|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R1683L|TTN_ENST00000342175.6_Missense_Mutation_p.R1637L|TTN_ENST00000460472.2_Missense_Mutation_p.R1637L|TTN_ENST00000359218.5_Missense_Mutation_p.R1637L|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12526					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGCCATATCGCAAATGGAG	0.458																																																0			2											78	74	75					2																	179641543		2203	4300	6503	179349788	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.5048G>T	2.37:g.179641543C>A	ENSP00000465570:p.Arg1683Leu		179349788	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.46	2.245101	0.39697	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.69561	-0.41;-0.23;-0.24;-0.2;-0.07	5.33	5.33	0.75918	Ribonuclease H-like (1);	.	.	.	.	T	0.73598	0.3607	N	0.24115	0.695	0.40384	D	0.979479	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.995;0.995;0.995;0.995;0.999	T	0.78196	-0.2298	9	0.87932	D	0	.	19.0298	0.92952	0.0:1.0:0.0:0.0	.	1637;1637;1637;1683;1683	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	1683;1637;1637;1637;1637;1683	ENSP00000343764:R1683L;ENSP00000434586:R1637L;ENSP00000340554:R1637L;ENSP00000352154:R1637L;ENSP00000354117:R1683L	ENSP00000340554:R1637L	R	-	2	0	TTN	179349788	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.757000	0.85209	2.518000	0.84900	0.650000	0.86243	CGA		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179641543	C	A	179641543	3	1	87	1	0	0	0	0	1	0	0	0	16775	884	31	2	106280	2	TTN	2	179641543	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	13689386	179641543	63557830	19	24188										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196737143	196737143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctttatacagagtcattgtgCcatttacgatttgtgtggtc	9	7	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:196737143C>T	ENST00000312428.6	-	40	6564	c.6464G>A	c.(6463-6465)gGc>gAc	p.G2155D		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2155	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGTCATTGTGCCATTTACGAT	0.318																																																0			2											168	150	155					2																	196737143		1827	4085	5912	196445388	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.6464G>A	2.37:g.196737143C>T	ENSP00000311273:p.Gly2155Asp		196445388	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248389	0.59103	.	.	ENSG00000118997	ENST00000312428	T	0.35421	1.31	4.53	3.62	0.41486	.	0.310442	0.34245	N	0.004121	T	0.53658	0.1810	M	0.76727	2.345	0.80722	D	1	P	0.46912	0.886	P	0.55260	0.772	T	0.61441	-0.7062	10	0.87932	D	0	.	14.3448	0.66654	0.0:0.8503:0.1497:0.0	.	2155	Q8WXX0	DYH7_HUMAN	D	2155	ENSP00000311273:G2155D	ENSP00000311273:G2155D	G	-	2	0	DNAH7	196445388	0.092000	0.21681	0.974000	0.42286	0.972000	0.66771	1.582000	0.36568	1.215000	0.43411	0.650000	0.86243	GGC		0.318	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196737143	C	T	196737143	3	4	87	1	0	0	0	0	1	0	0	0	4617	739	26	3	5714	3	DNAH7	2	196737143	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	17095600	196737143	46462230	20	24189										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215866332	215866332	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttttagcctctctctccattTcatctatggtttttgctgcc	5	12	4	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:215866332T>C	ENST00000272895.7	-	21	3032	c.2813A>G	c.(2812-2814)gAa>gGa	p.E938G	ABCA12_ENST00000389661.4_Missense_Mutation_p.E620G	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	938					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TCTCTCCATTTCATCTATGGT	0.388																																					Ovarian(66;664 1488 5121 34295)											0			2											188	179	182					2																	215866332		2203	4300	6503	215574577	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2813A>G	2.37:g.215866332T>C	ENSP00000272895:p.Glu938Gly		215574577	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.005699	0.54254	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87334	-2.24;-2.24	5.77	5.77	0.91146	.	0.083518	0.51477	D	0.000092	D	0.89801	0.6820	M	0.73962	2.25	0.80722	D	1	P;B	0.51653	0.947;0.246	P;B	0.50378	0.639;0.197	D	0.88456	0.3052	10	0.27785	T	0.31	.	16.0948	0.81112	0.0:0.0:0.0:1.0	.	938;620	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	G	938;620	ENSP00000272895:E938G;ENSP00000374312:E620G	ENSP00000272895:E938G	E	-	2	0	ABCA12	215574577	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	6.513000	0.73742	2.206000	0.71126	0.459000	0.35465	GAA		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215866332	T	C	215866332	3	2	87	1	0	0	0	0	1	0	0	0	30	1783	62	4	5106	4	ABCA12	2	215866332	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	19129189	215866332	27333041	21	24190										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238259820	238259820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcgttctccaggagcaccagCggcacctccgcttccctgga	10	17	1	0	rs372154635		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:238259820C>T	ENST00000295550.4	-	27	7221	c.6769G>A	c.(6769-6771)Gct>Act	p.A2257T	COL6A3_ENST00000472056.1_Missense_Mutation_p.A1650T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A2056T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2051T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2051T|COL6A3_ENST00000346358.4_Missense_Mutation_p.A2057T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2257	Collagen-like 4.|Triple-helical region.			A -> R (in Ref. 1; CAA36267 and 7; M20778). {ECO:0000305}.	axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		GGAGCACCAGCGGCACCTCCG	0.572																																																0			2						C	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	95	79	85		6151,4948,6769	2.5	0	2		85	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	58,58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	2051/2972,1650/2571,2257/3178	238259820	2,13004	2203	4300	6503	237924559	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6769G>A	2.37:g.238259820C>T	ENSP00000295550:p.Ala2257Thr		237924559	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	6.249	0.414096	0.11870	0.0	2.33E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.93659	-3.21;-3.21;-3.26;-3.21;-3.26;-3.21	5.42	2.55	0.30701	.	0.360730	0.23440	N	0.048145	D	0.85004	0.5598	L	0.31294	0.92	0.09310	N	1	B;B;B;B	0.16396	0.01;0.01;0.017;0.004	B;B;B;B	0.08055	0.001;0.001;0.003;0.001	T	0.70417	-0.4877	10	0.26408	T	0.33	.	3.8456	0.08933	0.123:0.4958:0.2847:0.0964	.	1650;1650;2051;2257	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	2257;2056;2051;1650;2051;2057	ENSP00000295550:A2257T;ENSP00000315609:A2056T;ENSP00000315873:A2051T;ENSP00000418285:A1650T;ENSP00000386844:A2051T;ENSP00000295546:A2057T	ENSP00000295550:A2257T	A	-	1	0	COL6A3	237924559	0.007000	0.16637	0.001000	0.08648	0.042000	0.13812	0.351000	0.20096	0.658000	0.30925	0.650000	0.86243	GCT		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238259820	C	T	238259820	3	4	87	1	0	0	0	0	1	0	0	0	3707	768	27	1	2836	1	COL6A3	2	238259820	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	22393488	238259820	4939553	22	24191										
KIF1A	547	hgsc.bcm.edu	37	chr2	241657477	241657477	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gcggccctaccgtatggtccCggccaggagggggttgaagg	18	11	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr2:241657477C>T	ENST00000320389.7	-	46	5178	c.5020G>A	c.(5020-5022)Ggg>Agg	p.G1674R	KIF1A_ENST00000498729.2_Missense_Mutation_p.G1775R	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1674					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		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)		CGTATGGTCCCGGCCAGGAGG	0.662																																																0			2											23	29	27					2																	241657477		2086	4213	6299	241306150	SO:0001583	missense	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.5020G>A	2.37:g.241657477C>T	ENSP00000322791:p.Gly1674Arg		241306150	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324389	0.81580	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308	T;T	0.81247	-1.36;-1.47	4.3	4.3	0.51218	Pleckstrin homology domain (1);	0.000000	0.85682	U	0.000000	D	0.89361	0.6693	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;0.993	D;P	0.76575	0.988;0.866	D	0.91248	0.5027	10	0.87932	D	0	.	16.3405	0.83080	0.0:1.0:0.0:0.0	.	1775;1674	F5H045;Q12756	.;KIF1A_HUMAN	R	1674;1775;1783	ENSP00000322791:G1674R;ENSP00000438388:G1775R	ENSP00000322791:G1674R	G	-	1	0	KIF1A	241306150	1.000000	0.71417	0.879000	0.34478	0.585000	0.36419	7.560000	0.82277	1.949000	0.56562	0.563000	0.77884	GGG		0.662	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		T	241657477	C	T	241657477	3	4	87	1	0	0	0	0	1	0	0	0	8304	652	23	1	60	1	KIF1A	2	241657477	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	3397657	241657477	1541896	23	24192										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15727739	15727739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cgaaacttactgtccatttcCatcttgaatatccactgcat	4	12	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:15727739C>T	ENST00000399451.2	-	19	2318	c.1951G>A	c.(1951-1953)Gga>Aga	p.G651R	ANKRD28_ENST00000383777.1_Missense_Mutation_p.G684R|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	651						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGTCCATTTCCATCTTGAATA	0.368																																																0			3											131	111	118					3																	15727739		1900	4117	6017	15702743	SO:0001583	missense	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1951G>A	3.37:g.15727739C>T	ENSP00000382379:p.Gly651Arg		15702743	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.281168	0.59758	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.15487	2.42;2.42;2.42	5.79	5.79	0.91817	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	N	0.12611	0.24	0.80722	D	1	B;B;B	0.25390	0.08;0.125;0.105	B;B;B	0.19391	0.022;0.022;0.025	T	0.16541	-1.0399	10	0.27785	T	0.31	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	684;681;651	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	R	651;684;651	ENSP00000382379:G651R;ENSP00000373287:G684R;ENSP00000397341:G651R	ENSP00000373287:G684R	G	-	1	0	ANKRD28	15702743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.718000	0.92993	0.655000	0.94253	GGA		0.368	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		T	15727739	C	T	15727739	3	4	87	1	0	0	0	0	1	0	0	0	656	603	21	3	1250	3	ANKRD28	3	15727739	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		15727739	182294691	24	24193										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38104250	38104250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgtttttcctccaaagaagcCagcaccgataggagaattcc	8	11	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:38104250C>T	ENST00000308059.6	+	5	1073	c.1052C>T	c.(1051-1053)cCa>cTa	p.P351L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P351L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P351L					deleted in lung and esophageal cancer 1									p.P351R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCAAAGAAGCCAGCACCGATA	0.463																																																1	Substitution - Missense(1)	breast(1)	3											77	74	75					3																	38104250		1846	4093	5939	38079254	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1052C>T	3.37:g.38104250C>T	ENSP00000308597:p.Pro351Leu		38079254		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	6.499	0.460334	0.12342	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05649	3.42;3.41;3.65	4.67	3.8	0.43715	.	0.850025	0.10774	N	0.635668	T	0.07863	0.0197	L	0.56769	1.78	0.27107	N	0.962483	B;P;B;P	0.34864	0.344;0.473;0.335;0.473	B;B;B;B	0.31751	0.054;0.088;0.135;0.088	T	0.23190	-1.0195	10	0.26408	T	0.33	-3.0099	8.914	0.35570	0.0:0.8974:0.0:0.1026	.	351;351;351;351	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	351	ENSP00000308597:P351L;ENSP00000315914:P351L;ENSP00000410427:P351L	ENSP00000308597:P351L	P	+	2	0	DLEC1	38079254	0.071000	0.21146	0.175000	0.22980	0.200000	0.23975	0.735000	0.26115	1.324000	0.45282	-0.140000	0.14226	CCA		0.463	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38104250	C	T	38104250	3	4	87	1	0	0	0	0	1	0	0	0	4563	594	21	3	1070	3	DLEC1	3	38104250	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	22376511	38104250	159918180	25	24194										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57454539	57454539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cttttggttcttcttcaattTtctcttcttccaaagaccgt	4	11	5	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:57454539T>C	ENST00000351747.2	-	17	2453	c.2273A>G	c.(2272-2274)aAa>aGa	p.K758R	DNAH12_ENST00000389536.4_Missense_Mutation_p.K758R|snoU13_ENST00000459308.1_RNA	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	758	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTCTTCAATTTTCTCTTCTTC	0.294																																																0			3											130	105	113					3																	57454539		692	1591	2283	57429579	SO:0001583	missense	201625			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.2273A>G	3.37:g.57454539T>C	ENSP00000295937:p.Lys758Arg		57429579	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		.	.	.	.	.	.	.	.	.	.	T	7.149	0.583418	0.13749	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536	T;T;T	0.62105	0.05;1.92;3.59	4.39	0.673	0.17941	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.49304	0.1549	L	0.41415	1.275	0.51482	D	0.999925	B	0.06786	0.001	B	0.11329	0.006	T	0.38156	-0.9674	9	0.54805	T	0.06	.	8.5034	0.33173	0.0:0.3238:0.0:0.6762	.	758	Q6ZR08	DYH12_HUMAN	R	758	ENSP00000295937:K758R;ENSP00000418137:K758R;ENSP00000374187:K758R	ENSP00000295937:K758R	K	-	2	0	DNAH12	57429579	0.860000	0.29831	0.553000	0.28255	0.287000	0.27160	1.061000	0.30542	0.027000	0.15297	-0.911000	0.02809	AAA		0.294	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		C	57454539	T	C	57454539	3	2	87	1	0	0	0	0	1	0	0	0	4611	1841	64	4	7177	4	DNAH12	3	57454539	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	19350289	57454539	140567891	26	24195										
GPR128	84873	hgsc.bcm.edu	37	chr3	100362136	100362136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgagcaaatggagacttattCcttgtctttgggtaatcaat	9	6	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:100362136C>T	ENST00000273352.3	+	7	993	c.725C>T	c.(724-726)tCc>tTc	p.S242F	GPR128_ENST00000475887.1_Intron|SNORA31_ENST00000517180.1_RNA	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	242					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GAGACTTATTCCTTGTCTTTG	0.363																																					Pancreas(87;185 1975 7223 18722)											0			3											145	155	152					3																	100362136		2203	4300	6503	101844826	SO:0001583	missense	84873			AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.725C>T	3.37:g.100362136C>T	ENSP00000273352:p.Ser242Phe		101844826	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473135	0.63737	.	.	ENSG00000144820	ENST00000273352	T	0.40476	1.03	4.91	4.91	0.64330	.	0.000000	0.52532	D	0.000070	T	0.51041	0.1651	M	0.73598	2.24	0.80722	D	1	P	0.47350	0.894	P	0.47044	0.535	T	0.57997	-0.7714	10	0.72032	D	0.01	.	13.4682	0.61268	0.0:1.0:0.0:0.0	.	242	Q96K78	GP128_HUMAN	F	242	ENSP00000273352:S242F	ENSP00000273352:S242F	S	+	2	0	GPR128	101844826	0.981000	0.34729	0.870000	0.34147	0.824000	0.46624	3.202000	0.51067	2.553000	0.86117	0.650000	0.86243	TCC		0.363	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			T	100362136	C	T	100362136	3	4	87	1	0	0	0	0	1	0	0	0	6661	855	30	3	751	3	GPR128	3	100362136	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	42907597	100362136	97660294	27	24196										
ALCAM	214	hgsc.bcm.edu	37	chr3	105268975	105268975	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tttcttctttttccagacagAggaatctccttatattaatg	5	8	3	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:105268975A>G	ENST00000306107.5	+	12	1879	c.1379A>G	c.(1378-1380)gAg>gGg	p.E460G	ALCAM_ENST00000486979.2_Missense_Mutation_p.E409G|ALCAM_ENST00000472644.2_Missense_Mutation_p.E460G|ALCAM_ENST00000389927.4_Missense_Mutation_p.E182G	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	460	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTCCAGACAGAGGAATCTCCT	0.353																																																0			3											95	118	110					3																	105268975		2196	4294	6490	106751665	SO:0001583	missense	214			AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	400	protein-coding gene	gene with protein product		601662	"activated leucocyte cell adhesion molecule"			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1379A>G	3.37:g.105268975A>G	ENSP00000305988:p.Glu460Gly		106751665	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554794	0.65425	.	.	ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927	T;T;T;T	0.74209	4.05;4.05;4.05;-0.82	5.92	5.92	0.95590	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.619093	0.18841	N	0.129698	T	0.71392	0.3334	L	0.29908	0.895	0.38384	D	0.945206	P;P;P	0.47484	0.896;0.505;0.722	P;B;P	0.47941	0.519;0.355;0.562	T	0.73534	-0.3952	10	0.40728	T	0.16	-1.0867	16.3782	0.83418	1.0:0.0:0.0:0.0	.	182;460;460	Q6ZS95;B4DTU0;Q13740	.;.;CD166_HUMAN	G	460;460;409;182	ENSP00000305988:E460G;ENSP00000419236:E460G;ENSP00000418213:E409G;ENSP00000374577:E182G	ENSP00000305988:E460G	E	+	2	0	ALCAM	106751665	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.055000	0.71103	2.277000	0.76020	0.528000	0.53228	GAG		0.353	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627		G	105268975	A	G	105268975	3	3	87	1	0	0	0	0	1	0	0	0	487	304	11	4	1425	4	ALCAM	3	105268975	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	4906839	105268975	92753455	28	24197										
MYH15	22989	hgsc.bcm.edu	37	chr3	108124275	108124275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caagctggaaatgaagaatcTtgctttcattacgttccagg	9	8	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:108124275T>C	ENST00000273353.3	-	34	4762	c.4706A>G	c.(4705-4707)aAg>aGg	p.K1569R		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1569						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K1569M(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						ATGAAGAATCTTGCTTTCATT	0.318																																																1	Substitution - Missense(1)	ovary(1)	3											62	59	60					3																	108124275		1813	4069	5882	109606965	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.4706A>G	3.37:g.108124275T>C	ENSP00000273353:p.Lys1569Arg		109606965		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.406675	0.62399	.	.	ENSG00000144821	ENST00000273353	T	0.80824	-1.42	5.13	5.13	0.70059	Myosin tail (1);	.	.	.	.	D	0.87958	0.6309	M	0.63169	1.94	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.89008	0.3426	9	0.66056	D	0.02	.	15.1071	0.72329	0.0:0.0:0.0:1.0	.	1569	Q9Y2K3	MYH15_HUMAN	R	1569	ENSP00000273353:K1569R	ENSP00000273353:K1569R	K	-	2	0	MYH15	109606965	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.058000	0.57463	2.150000	0.67090	0.533000	0.62120	AAG		0.318	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		C	108124275	T	C	108124275	3	2	87	1	0	0	0	0	1	0	0	0	10064	1609	56	4	1170	4	MYH15	3	108124275	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	2855300	108124275	89898155	29	24198										
FAM162A	26355	hgsc.bcm.edu	37	chr3	122123189	122123189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	aggtcgcttcaaaaaggaagAtgaaatcccagagactgtct	10	8	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:122123189A>G	ENST00000477892.1	+	3	326	c.242A>G	c.(241-243)gAt>gGt	p.D81G	FAM162A_ENST00000232125.5_Missense_Mutation_p.D71G|FAM162A_ENST00000469967.1_Missense_Mutation_p.D81G	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	81	Required for proapoptotic activity.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						AAAAAGGAAGATGAAATCCCA	0.423																																																0			3											86	84	84					3																	122123189		1902	4120	6022	123605879	SO:0001583	missense	26355			AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"chromosome 3 open reading frame 28"	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.242A>G	3.37:g.122123189A>G	ENSP00000419088:p.Asp81Gly		123605879	Q9NRN6|Q9UJX8	Missense_Mutation	SNP	ENST00000477892.1	37	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208224	0.79240	.	.	ENSG00000114023	ENST00000232125;ENST00000477892;ENST00000469967;ENST00000440333	T;T;T	0.35421	1.31;1.31;1.31	5.65	5.65	0.86999	.	0.296854	0.39544	N	0.001323	T	0.48537	0.1505	M	0.76328	2.33	0.30516	N	0.76889	P;P	0.48834	0.916;0.722	P;B	0.49799	0.622;0.423	T	0.60265	-0.7297	10	0.72032	D	0.01	.	12.1892	0.54261	1.0:0.0:0.0:0.0	.	81;81	E9PH05;Q96A26	.;F162A_HUMAN	G	71;81;81;80	ENSP00000232125:D71G;ENSP00000419088:D81G;ENSP00000419491:D81G	ENSP00000232125:D71G	D	+	2	0	FAM162A	123605879	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	5.653000	0.67967	2.371000	0.80710	0.533000	0.62120	GAT		0.423	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367		G	122123189	A	G	122123189	3	3	87	1	0	0	0	0	1	0	0	0	5490	333	12	4	252	4	FAM162A	3	122123189	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	13998914	122123189	75899241	30	24199										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840199	142840199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gctctggctcgtcgttcttcGgcgagctattcaaccagaat	10	12	3	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:142840199G>A	ENST00000309575.3	+	2	1925	c.541G>A	c.(541-543)Ggc>Agc	p.G181S		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	181					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						GTCGTTCTTCGGCGAGCTATT	0.622																																																0			3											39	48	45					3																	142840199		2203	4300	6503	144322889	SO:0001583	missense	9435			BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.541G>A	3.37:g.142840199G>A	ENSP00000307911:p.Gly181Ser		144322889	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183040	0.94885	.	.	ENSG00000175040	ENST00000309575	D	0.82526	-1.62	4.45	4.45	0.53987	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000001	D	0.92211	0.7530	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92983	0.6408	10	0.48119	T	0.1	-6.4267	17.2545	0.87051	0.0:0.0:1.0:0.0	.	181	Q9Y4C5	CHST2_HUMAN	S	181	ENSP00000307911:G181S	ENSP00000307911:G181S	G	+	1	0	CHST2	144322889	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.651000	0.98493	2.295000	0.77249	0.407000	0.27541	GGC		0.622	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		A	142840199	G	A	142840199	3	1	87	1	0	0	0	0	1	0	0	0	3410	1116	39	1	543	1	CHST2	3	142840199	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	20717010	142840199	55182231	31	24200										
SI	6476	hgsc.bcm.edu	37	chr3	164785145	164785145	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tacaaagttttaccgttgctTttcctaataacttggatgct	6	8	0	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:164785145T>C	ENST00000264382.3	-	6	680	c.618A>G	c.(616-618)aaA>aaG	p.K206K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	206	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.K206N(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TACCGTTGCTTTTCCTAATAA	0.308										HNSCC(35;0.089)																																						1	Substitution - Missense(1)	ovary(1)	3											86	85	85					3																	164785145		2203	4298	6501	166267839	SO:0001819	synonymous_variant	6490			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.618A>G	3.37:g.164785145T>C			166267839	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																				0.308	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164785145	T	C	164785145	2	2	87	1	0	0	0	0	0	0	0	1	14334	1838	64	4		4	SI	3	164785145	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	21944946	164785145	33237285	32	24201										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952140	178952140	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttccacacaattaaacagcaTgcattgaactgaaaagataa	5	8	0	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr3:178952140T>C	ENST00000263967.3	+	21	3352	c.3195T>C	c.(3193-3195)caT>caC	p.H1065H	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1065	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|H -> Y (found in brain tumors; unknown pathological significance). {ECO:0000269|PubMed:15289301}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTAAACAGCATGCATTGAACT	0.398		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											89	79	82					3																	178952140		1907	4141	6048	180434834	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3195T>C	3.37:g.178952140T>C			180434834	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.398	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178952140	T	C	178952140	2	2	87	1	0	0	0	0	0	0	0	1	11944	1461	51	4		4	PIK3CA	3	178952140	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	14166995	178952140	19070290	33	24202										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389220	1389248	+	Frame_Shift_Del	DEL	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA	-													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cctgctcacacgtgccgacgTggagtgcccgcctgctcacg					rs1140009|rs200438890|rs141376932|rs550271289|rs150174653|rs145563943|rs547759244	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENST00000324803.4	+	1	3881_3909	c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	c.(919-951)cgtggagtgcccgcctgctcacgtgcccatatgfs	p.GVPACSRAHM308fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	308					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P310fs*95(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCGACGTGGAGTGCCCGCCTGCTCACGTGCCCATATGGAGTGCCC	0.668																																																1	Deletion - Frameshift(1)	prostate(1)	4								1378,2876		542,294,1291						0.8	0			153	3662,4580		1557,548,2016	no	frameshift	CRIPAK	NM_175918.3		2099,842,3307	A1A1,A1R,RR		44.431,32.393,40.3329				5040,7456				1379248	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	4.37:g.1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENSP00000323978:p.Gly308fs		1379220	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.668	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1389248	TGGAGTGCCCGCCTGCTCACGTGCCCATA	-	1389220	7	5	87	1	0	1	0	1	0	0	0	0	3883	1683	59	0	923	0	CRIPAK	4	1389220	Frame_Shift_Del	DEL	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TCGA-CI-6620-01A-11D-1826-10		1389220	189765056	34	24203										
KIT	3815	hgsc.bcm.edu	37	chr4	55592211	55592211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctttgcatttaaaggtaacaAcaaaggtatatttcttttta	5	5	1	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:55592211A>G	ENST00000288135.5	+	9	1632	c.1535A>G	c.(1534-1536)aAc>aGc	p.N512S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	512					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAAGGTAACAACAAAGGTATA	0.363		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4											79	72	74					4																	55592211		2203	4300	6503	55286968	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1535A>G	4.37:g.55592211A>G	ENSP00000288135:p.Asn512Ser		55286968	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	8.065	0.768914	0.15983	.	.	ENSG00000157404	ENST00000288135	T	0.75704	-0.96	6.02	-4.81	0.03180	.	0.525534	0.18335	N	0.144364	T	0.34395	0.0896	N	0.00926	-1.1	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18999	-1.0319	10	0.10377	T	0.69	.	9.1068	0.36703	0.3889:0.0:0.5056:0.1055	.	512	P10721	KIT_HUMAN	S	512	ENSP00000288135:N512S	ENSP00000288135:N512S	N	+	2	0	KIT	55286968	0.166000	0.22962	0.968000	0.41197	0.997000	0.91878	-0.582000	0.05814	-0.328000	0.08539	0.533000	0.62120	AAC		0.363	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55592211	A	G	55592211	3	3	87	1	0	0	0	0	1	0	0	0	8350	43	2	4	1569	4	KIT	4	55592211	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	54202991	55592211	135562065	35	24204										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78641724	78641725	+	Frame_Shift_Del	DEL	TG	TG	-													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgttgttctcaaccagccatTgaggatctaaaggccccagg							TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	TG	TG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:78641724_78641725delTG	ENST00000504123.1	-	12	1658_1659	c.1528_1529delCA	c.(1528-1530)caafs	p.Q510fs	CNOT6L_ENST00000264903.4_Frame_Shift_Del_p.Q510fs			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	510	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						AACCAGCCATTGAGGATCTAAA	0.47																																																0			4																																								78860749	SO:0001589	frameshift_variant	246175			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.1528_1529delCA	4.37:g.78641724_78641725delTG	ENSP00000424896:p.Gln510fs		78860748	Q9UF92	Frame_Shift_Del	DEL	ENST00000504123.1	37																																																																																					0.47	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			-	78641725	TG	-	78641724	7	5	87	1	0	1	0	1	0	0	0	0	3629	1812	63	0	142	0	CNOT6L	4	78641724	Frame_Shift_Del	DEL	TG	TCGA-CI-6620-01A-11D-1826-10	23049513	78641724	112512552	36	24205										
MAB21L2	10586	hgsc.bcm.edu	37	chr4	151504985	151504985	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctggagctacccggccagccGctcaacaactaccacatgaa	8	16	1	1	rs374360655		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:151504985G>A	ENST00000317605.4	+	1	1909	c.804G>A	c.(802-804)ccG>ccA	p.P268P	RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000357115.3_Intron|LRBA_ENST00000503716.1_5'Flank|LRBA_ENST00000535741.1_Intron	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	268					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		CCGGCCAGCCGCTCAACAACT	0.637																																																0			4											60	58	59					4																	151504985		2203	4300	6503	151724435	SO:0001819	synonymous_variant	10586			AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"mab-21 (C. elegans)-like 2"				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.804G>A	4.37:g.151504985G>A			151724435	B3KP37|Q9HBA7	Silent	SNP	ENST00000317605.4	37	CCDS3774.1																																																																																				0.637	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439		A	151504985	G	A	151504985	2	1	87	1	0	0	0	0	0	0	0	1	9172	1074	38	1		1	MAB21L2	4	151504985	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	72863261	151504985	39649291	37	24206										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247327	153247327	+	Frame_Shift_Del	DEL	T	T	-													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccatcaaaacatgtaaacacTggcctgtctcaatatcccaa							TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:153247327delT	ENST00000281708.4	-	10	2704	c.1475delA	c.(1474-1476)cagfs	p.Q492fs	FBXW7_ENST00000603841.1_Frame_Shift_Del_p.Q492fs|FBXW7_ENST00000296555.5_Frame_Shift_Del_p.Q374fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.Q492fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.Q412fs|FBXW7_ENST00000393956.3_Frame_Shift_Del_p.Q316fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	492					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGTAAACACTGGCCTGTCTC	0.433			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											135	126	129					4																	153247327		2203	4300	6503	153466777	SO:0001589	frameshift_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1475delA	4.37:g.153247327delT	ENSP00000281708:p.Gln492fs		153466777	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				0.433	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			-	153247327	T	-	153247327	7	5	87	1	0	1	0	1	0	0	0	0	5788	1580	55	0	660	0	FBXW7	4	153247327	Frame_Shift_Del	DEL	T	TCGA-CI-6620-01A-11D-1826-10	1742342	153247327	37906949	38	24207										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167656168	167656168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcatcattcataatatcgtcTtcatcatcctcatcatcagt	2	12	9	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:167656168T>C	ENST00000357154.3	-	12	1352	c.1215A>G	c.(1213-1215)gaA>gaG	p.E405E	SPOCK3_ENST00000421836.2_Silent_p.E354E|SPOCK3_ENST00000357545.4_Silent_p.E402E|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000534949.1_Silent_p.E309E|SPOCK3_ENST00000541637.1_Silent_p.E307E|SPOCK3_ENST00000535728.1_Silent_p.E273E|SPOCK3_ENST00000511531.1_Silent_p.E405E|SPOCK3_ENST00000504953.1_Silent_p.E402E|SPOCK3_ENST00000506886.1_Silent_p.E405E|SPOCK3_ENST00000510741.1_Silent_p.E362E|SPOCK3_ENST00000511269.1_Silent_p.E402E|SPOCK3_ENST00000502330.1_Silent_p.E405E|SPOCK3_ENST00000512681.1_Silent_p.E307E|SPOCK3_ENST00000541354.1_Silent_p.E285E	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	405	Asp-rich.			E -> G (in Ref. 4; BAG58265). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		taatatcgtcttcatcatcct	0.353																																																0			4											193	179	184					4																	167656168		2203	4299	6502	167892743	SO:0001819	synonymous_variant	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1215A>G	4.37:g.167656168T>C			167892743	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																				0.353	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			C	167656168	T	C	167656168	2	2	87	1	0	0	0	0	0	0	0	1	15120	1606	56	4		4	SPOCK3	4	167656168	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	14408841	167656168	23498108	39	24208										
AADAT	51166	hgsc.bcm.edu	37	chr4	170988506	170988506	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atgagccatgaaaccttcttCtccccattcgtgtagaagct	7	12	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr4:170988506C>T	ENST00000337664.4	-	9	1210	c.934G>A	c.(934-936)Gaa>Aaa	p.E312K	AADAT_ENST00000515480.1_Missense_Mutation_p.E312K|AADAT_ENST00000353187.2_Missense_Mutation_p.E312K|AADAT_ENST00000509167.1_Missense_Mutation_p.E316K	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	312					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		AAACCTTCTTCTCCCCATTCG	0.348																																																0			4											90	88	89					4																	170988506		2203	4300	6503	171225081	SO:0001583	missense	51166			AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"kynurenine aminotransferase II", "L kynurenine/alpha aminoadipate aminotransferase"	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.934G>A	4.37:g.170988506C>T	ENSP00000336808:p.Glu312Lys		171225081	B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	37	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	C	8.801	0.933006	0.18131	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	5.93	2.02	0.26589	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.325067	0.37053	N	0.002276	D	0.85570	0.5727	L	0.39085	1.19	0.40851	D	0.983756	B;B	0.24258	0.1;0.057	B;B	0.28465	0.079;0.09	T	0.75861	-0.3168	10	0.29301	T	0.29	-17.084	21.2527	0.99949	0.0:0.3899:0.6101:0.0	.	316;312	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	K	312;312;316;312	ENSP00000336808:E312K;ENSP00000423341:E312K;ENSP00000423190:E316K;ENSP00000226840:E312K	ENSP00000336808:E312K	E	-	1	0	AADAT	171225081	0.978000	0.34361	0.998000	0.56505	0.161000	0.22273	0.063000	0.14410	0.048000	0.15891	-0.176000	0.13171	GAA		0.348	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228		T	170988506	C	T	170988506	3	4	87	1	0	0	0	0	1	0	0	0	14	922	32	3	363	3	AADAT	4	170988506	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	3332338	170988506	20165770	40	24209										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599404	3599404	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	accttcgcagcccacacggcGccggcttattacccctacgg	9	18	0	0	rs200766970		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:3599404G>A	ENST00000302006.3	+	2	394	c.342G>A	c.(340-342)gcG>gcA	p.A114A	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	114					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCACACGGCGCCGGCTTATT	0.652																																																0			5											39	44	43					5																	3599404		2203	4300	6503	3652404	SO:0001819	synonymous_variant	79192			U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.342G>A	5.37:g.3599404G>A			3652404	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	37	CCDS34132.1																																																																																				0.652	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3599404	G	A	3599404	2	1	87	1	0	0	0	0	0	0	0	1	7864	1074	38	1		1	IRX1	5	3599404	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10		3599404	177315856	41	24210										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37120431	37120431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttattagaaaactgtgaccaTgttgattctctctatagtag	7	6	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:37120431T>C	ENST00000508244.1	-	48	9128	c.9035A>G	c.(9034-9036)cAt>cGt	p.H3012R	C5orf42_ENST00000425232.2_Missense_Mutation_p.H3012R|C5orf42_ENST00000274258.7_Missense_Mutation_p.H1910R|C5orf42_ENST00000512288.1_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3012						integral component of membrane (GO:0016021)		p.H1910R(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ACTGTGACCATGTTGATTCTC	0.353																																																1	Substitution - Missense(1)	ovary(1)	5											81	79	80					5																	37120431		2203	4300	6503	37156188	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9035A>G	5.37:g.37120431T>C	ENSP00000421690:p.His3012Arg		37156188	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	11.83	1.755291	0.31046	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.21	4.05	0.47172	.	0.623087	0.16618	N	0.206614	T	0.33323	0.0859	L	0.48362	1.52	0.09310	N	1	B;P	0.41848	0.007;0.763	B;B	0.33960	0.007;0.173	T	0.10847	-1.0612	10	0.20519	T	0.43	.	7.7843	0.29083	0.0:0.0948:0.0:0.9052	.	3012;1910	E9PH94;Q9H799	.;CE042_HUMAN	R	3012;3012;1910;2078	ENSP00000421690:H3012R;ENSP00000389014:H3012R;ENSP00000274258:H1910R;ENSP00000424223:H2078R	ENSP00000274258:H1910R	H	-	2	0	C5orf42	37156188	0.005000	0.15991	0.002000	0.10522	0.049000	0.14656	1.052000	0.30429	0.838000	0.34948	0.529000	0.55759	CAT		0.353	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37120431	T	C	37120431	3	2	87	1	0	0	0	0	1	0	0	0	2307	1464	51	4	574	4	C5orf42	5	37120431	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	33521027	37120431	143794829	42	24211										
SPZ1	84654	hgsc.bcm.edu	37	chr5	79617086	79617086	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gaaacagggaactctgcaagAgaagccaattcagataaact	9	8	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:79617086A>G	ENST00000296739.4	+	1	1297	c.1052A>G	c.(1051-1053)gAg>gGg	p.E351G		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	351					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		ACTCTGCAAGAGAAGCCAATT	0.393																																																0			5											84	80	81					5																	79617086		1842	4092	5934	79652842	SO:0001583	missense	84654				CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1052A>G	5.37:g.79617086A>G	ENSP00000369611:p.Glu351Gly		79652842	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.313297	0.23908	.	.	ENSG00000164299	ENST00000296739	T	0.34275	1.37	4.04	0.123	0.14709	.	1.013970	0.07924	N	0.976388	T	0.26919	0.0659	L	0.34521	1.04	0.09310	N	1	B	0.17667	0.023	B	0.16289	0.015	T	0.30880	-0.9963	10	0.54805	T	0.06	-13.0592	7.4159	0.27044	0.5626:0.0:0.4374:0.0	.	351	Q9BXG8	SPZ1_HUMAN	G	351	ENSP00000369611:E351G	ENSP00000369611:E351G	E	+	2	0	SPZ1	79652842	0.024000	0.19004	0.000000	0.03702	0.211000	0.24417	0.824000	0.27379	0.025000	0.15241	-0.385000	0.06624	GAG		0.393	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		G	79617086	A	G	79617086	3	3	87	1	0	0	0	0	1	0	0	0	15166	304	11	4	1054	4	SPZ1	5	79617086	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	42496655	79617086	101298174	43	24212										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94022411	94022411	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gtttcttctgagccactctcTcttcagaaaatggtaagtac	7	10	5	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:94022411T>C	ENST00000265140.5	+	16	2528	c.2109T>C	c.(2107-2109)tcT>tcC	p.S703S		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	703						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		AGCCACTCTCTCTTCAGAAAA	0.363																																																0			5											99	100	99					5																	94022411		2203	4300	6503	94048167	SO:0001819	synonymous_variant	84250			AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2109T>C	5.37:g.94022411T>C			94048167	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Silent	SNP	ENST00000265140.5	37	CCDS4071.2																																																																																				0.363	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		C	94022411	T	C	94022411	2	2	87	1	0	0	0	0	0	0	0	1	660	1538	54	4		4	ANKRD32	5	94022411	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	14405325	94022411	86892849	44	24213										
APC	324	hgsc.bcm.edu	37	chr5	112154869	112154869	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cggggcagtaaagaggctcgGgccagggccagtgcagcact	17	11	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:112154869G>A	ENST00000457016.1	+	10	1520	c.1140G>A	c.(1138-1140)cgG>cgA	p.R380R	APC_ENST00000257430.4_Silent_p.R380R|APC_ENST00000508376.2_Silent_p.R380R			P25054	APC_HUMAN	adenomatous polyposis coli	380	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGAGGCTCGGGCCAGGGCCA	0.507		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	0			5											57	54	55					5																	112154869		2202	4300	6502	112182768	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1140G>A	5.37:g.112154869G>A			112182768	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.507	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112154869	G	A	112154869	2	1	87	1	0	0	0	0	0	0	0	1	763	1219	43	3		3	APC	5	112154869	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	18132458	112154869	68760391	45	24214										
APC	324	hgsc.bcm.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	87	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	19048	112173917	68741343	46	24215										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140724410	140724410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gtgaatgccactgaccctgaCgagggattcaatgctcaagt	11	10	2	3	rs547334260		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:140724410C>T	ENST00000253812.6	+	1	810	c.810C>T	c.(808-810)gaC>gaT	p.D270D	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	270	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D270D(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGACCCTGACGAGGGATTCA	0.468													N|||	1	0.000199681	0	0.0014	5008	,	,		20544	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	endometrium(1)	5											52	54	54					5																	140724410		2051	4214	6265	140704594	SO:0001819	synonymous_variant	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.810C>T	5.37:g.140724410C>T			140704594	Q9Y5D4	Silent	SNP	ENST00000253812.6	37	CCDS47290.1																																																																																				0.468	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140724410	C	T	140724410	2	4	87	1	0	0	0	0	0	0	0	1	11586	535	19	1		1	PCDHGA3	5	140724410	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	28550493	140724410	40190850	47	24216										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149602710	149602710	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atgtaggcgatgcaggctgaCtcgtcgcccatcaggtggat	14	10	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:149602710C>T	ENST00000348628.6	-	17	1940	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	CAMK2A_ENST00000398376.3_Silent_p.E436E|CAMK2A_ENST00000351010.6_5'UTR	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	425					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCAGGCTGACTCGTCGCCCA	0.667																																																0			5											75	85	82					5																	149602710		2202	4300	6502	149582903	SO:0001819	synonymous_variant	815			AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.1275G>A	5.37:g.149602710C>T			149582903	Q9UL21|Q9Y2H4|Q9Y352	Silent	SNP	ENST00000348628.6	37	CCDS43386.1																																																																																				0.667	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		T	149602710	C	T	149602710	2	4	87	1	0	0	0	0	0	0	0	1	2605	564	20	3		3	CAMK2A	5	149602710	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	8878300	149602710	31312550	48	24217										
CCDC69	26112	hgsc.bcm.edu	37	chr5	150585025	150585025	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggtggctgttctggttctggTtcttggcgcttctggaagaa	15	7	4	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr5:150585025T>C	ENST00000355417.2	-	2	234	c.60A>G	c.(58-60)gaA>gaG	p.E20E	CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	20								p.E20D(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGTTCTGGTTCTTGGCGCT	0.572																																																1	Substitution - Missense(1)	ovary(1)	5											171	154	160					5																	150585025		2203	4300	6503	150565218	SO:0001819	synonymous_variant	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.60A>G	5.37:g.150585025T>C			150565218	A8K9X6	Silent	SNP	ENST00000355417.2	37	CCDS4312.1																																																																																				0.572	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		C	150585025	T	C	150585025	2	2	87	1	0	0	0	0	0	0	0	1	2847	1722	60	4		4	CCDC69	5	150585025	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	982315	150585025	30330235	49	24218										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24832525	24832525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttcctatgttctcatcactgAcagctgcgagtttctccatc	6	13	3	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:24832525A>G	ENST00000259698.4	-	17	2541	c.2366T>C	c.(2365-2367)gTc>gCc	p.V789A	FAM65B_ENST00000538035.1_Missense_Mutation_p.V768A	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	789					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						CTCATCACTGACAGCTGCGAG	0.438																																																0			6											198	147	162					6																	24832525		692	1591	2283	24940504	SO:0001583	missense	9750			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.2366T>C	6.37:g.24832525A>G	ENSP00000259698:p.Val789Ala		24940504	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957291	0.53400	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.38240	1.15;1.15	5.04	5.04	0.67666	.	0.644640	0.16377	N	0.217090	T	0.09512	0.0234	N	0.03608	-0.345	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.11329	0.004;0.006	T	0.07888	-1.0749	10	0.42905	T	0.14	-17.4841	14.4485	0.67370	1.0:0.0:0.0:0.0	.	768;789	F5GX51;Q9Y4F9	.;FA65B_HUMAN	A	789;768	ENSP00000259698:V789A;ENSP00000441138:V768A	ENSP00000259698:V789A	V	-	2	0	FAM65B	24940504	1.000000	0.71417	0.869000	0.34112	0.929000	0.56500	6.848000	0.75409	1.878000	0.54408	0.477000	0.44152	GTC		0.438	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			G	24832525	A	G	24832525	3	3	87	1	0	0	0	0	1	0	0	0	5619	275	10	4	868	4	FAM65B	6	24832525	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10		24832525	146282542	50	24219										
MDC1	9656	hgsc.bcm.edu	37	chr6	30671047	30671047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gctctccccgagcatccaccActcctgtgaagagcacctgt	8	17	1	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:30671047A>G	ENST00000376406.3	-	12	6346	c.5699T>C	c.(5698-5700)gTg>gCg	p.V1900A	MDC1_ENST00000376405.2_Missense_Mutation_p.V1636A|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1900	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGCATCCACCACTCCTGTGAA	0.612								Other conserved DNA damage response genes																																								0			6											60	66	64					6																	30671047		1509	2709	4218	30779026	SO:0001583	missense	9656			D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.5699T>C	6.37:g.30671047A>G	ENSP00000365588:p.Val1900Ala		30779026	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357129	0.82243	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	D;D	0.86432	-2.12;-2.12	5.19	5.19	0.71726	BRCT (3);	0.000000	0.33610	N	0.004740	D	0.91185	0.7223	M	0.76574	2.34	0.39624	D	0.970079	D;D	0.89917	0.993;1.0	D;D	0.81914	0.965;0.995	D	0.92315	0.5861	10	0.62326	D	0.03	-13.2275	13.3393	0.60535	1.0:0.0:0.0:0.0	.	1900;877	Q14676;Q14676-4	MDC1_HUMAN;.	A	1900;1636;1613;1466	ENSP00000365588:V1900A;ENSP00000365587:V1636A	ENSP00000365587:V1636A	V	-	2	0	MDC1	30779026	0.998000	0.40836	0.970000	0.41538	0.859000	0.49053	7.451000	0.80668	2.100000	0.63781	0.254000	0.18369	GTG		0.612	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		G	30671047	A	G	30671047	3	3	87	1	0	0	0	0	1	0	0	0	9433	159	6	4	586	4	MDC1	6	30671047	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	5838522	30671047	140444020	51	24220										
TCP11	6954	hgsc.bcm.edu	37	chr6	35088056	35088056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccagcaagactgaggccatgAcggttaactggtgcaactgg	13	10	0	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:35088056A>G	ENST00000512012.1	-	7	1151	c.995T>C	c.(994-996)gTc>gCc	p.V332A	TCP11_ENST00000311875.5_Missense_Mutation_p.V345A|TCP11_ENST00000373979.2_Missense_Mutation_p.V270A|TCP11_ENST00000444780.2_Missense_Mutation_p.V340A|TCP11_ENST00000418521.2_Missense_Mutation_p.V269A|TCP11_ENST00000412155.2_Missense_Mutation_p.V294A|TCP11_ENST00000373974.4_Missense_Mutation_p.V299A|TCP11_ENST00000244645.3_Missense_Mutation_p.V270A			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	332					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						TGAGGCCATGACGGTTAACTG	0.532																																																0			6											70	71	71					6																	35088056		2203	4300	6503	35196034	SO:0001583	missense	6954				CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"fertilization-promoting peptide receptor"	186982	"t-complex 11 (a murine tcp homolog)", "t-complex 11 homolog (mouse)"	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.995T>C	6.37:g.35088056A>G	ENSP00000425995:p.Val332Ala		35196034	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Missense_Mutation	SNP	ENST00000512012.1	37		.	.	.	.	.	.	.	.	.	.	A	12.30	1.895322	0.33442	.	.	ENSG00000124678	ENST00000373979;ENST00000412155;ENST00000244645;ENST00000311875;ENST00000444780;ENST00000373974;ENST00000418521;ENST00000512012;ENST00000486638	T;T;T;T;T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68;2.68;2.68;2.68;2.68	5.03	5.03	0.67393	.	0.711091	0.13681	N	0.370211	T	0.07279	0.0184	L	0.60455	1.87	0.09310	N	1	B;B;B;B;B;B	0.29188	0.236;0.236;0.236;0.236;0.236;0.083	B;B;B;B;B;B	0.34038	0.174;0.174;0.174;0.174;0.111;0.087	T	0.28870	-1.0030	10	0.19147	T	0.46	.	13.2819	0.60219	1.0:0.0:0.0:0.0	.	299;294;340;405;332;270	B7Z7G1;E7EP29;B7Z7B5;Q5TB88;Q8WWU5;Q8WWU5-2	.;.;.;.;TCP11_HUMAN;.	A	270;294;270;345;340;299;269;332;191	ENSP00000363091:V270A;ENSP00000402816:V294A;ENSP00000244645:V270A;ENSP00000308708:V345A;ENSP00000404479:V340A;ENSP00000363085:V299A;ENSP00000415320:V269A;ENSP00000425995:V332A;ENSP00000421103:V191A	ENSP00000244645:V270A	V	-	2	0	TCP11	35196034	0.997000	0.39634	0.967000	0.41034	0.130000	0.20726	5.258000	0.65479	2.022000	0.59522	0.455000	0.32223	GTC		0.532	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728		G	35088056	A	G	35088056	3	3	87	1	0	0	0	0	1	0	0	0	15752	275	10	4	528	4	TCP11	6	35088056	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	4417009	35088056	136027011	52	24221										
TULP1	7287	hgsc.bcm.edu	37	chr6	35477518	35477518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctgaggggtccttgtcggccTccccagaccctgcatgtgtg	13	14	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:35477518T>C	ENST00000229771.6	-	7	690	c.611A>G	c.(610-612)gAg>gGg	p.E204G	TULP1_ENST00000322263.4_Missense_Mutation_p.E151G	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	204					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						CTTGTCGGCCTCCCCAGACCC	0.602																																					GBM(55;1027 1091 11115 23439)											0			6											117	116	116					6																	35477518		2203	4300	6503	35585496	SO:0001583	missense	7287			U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.611A>G	6.37:g.35477518T>C	ENSP00000229771:p.Glu204Gly		35585496	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	CCDS4807.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.095286	0.76870	.	.	ENSG00000112041	ENST00000229771;ENST00000322263;ENST00000545327;ENST00000428978	D;D;T	0.83335	-1.71;-1.62;-0.18	4.16	4.16	0.48862	.	0.389460	0.23760	N	0.044821	D	0.83376	0.5241	L	0.59436	1.845	0.44330	D	0.997215	D;D	0.63880	0.993;0.988	D;P	0.63033	0.91;0.815	D	0.85118	0.0967	10	0.66056	D	0.02	-29.3315	9.5049	0.39040	0.0:0.0:0.0:1.0	.	151;204	O00294-2;O00294	.;TULP1_HUMAN	G	204;151;151;156	ENSP00000229771:E204G;ENSP00000319414:E151G;ENSP00000406765:E156G	ENSP00000229771:E204G	E	-	2	0	TULP1	35585496	0.746000	0.28272	0.877000	0.34402	0.042000	0.13812	2.839000	0.48207	1.747000	0.51819	0.379000	0.24179	GAG		0.602	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			C	35477518	T	C	35477518	3	2	87	1	0	0	0	0	1	0	0	0	16813	1551	54	4	1053	4	TULP1	6	35477518	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	389462	35477518	135637549	53	24222										
MCM3	4172	hgsc.bcm.edu	37	chr6	52138562	52138562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcgccatcctgctccccaggTgctctgtaacggtgcatccg	10	16	1	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:52138562T>C	ENST00000229854.7	-	10	1603	c.1527A>G	c.(1525-1527)gcA>gcG	p.A509A	MCM3_ENST00000419835.2_Silent_p.A463A|MCM3_ENST00000476448.1_5'Flank|MCM3_ENST00000596288.1_Silent_p.A554A			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	509					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					GCTCCCCAGGTGCTCTGTAAC	0.507																																																0			6											124	97	106					6																	52138562		2203	4300	6503	52246521	SO:0001819	synonymous_variant	4172			X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1527A>G	6.37:g.52138562T>C			52246521	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Silent	SNP	ENST00000229854.7	37																																																																																					0.507	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			C	52138562	T	C	52138562	2	2	87	1	0	0	0	0	0	0	0	1	9417	1683	59	4		4	MCM3	6	52138562	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	16661044	52138562	118976505	54	24223										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165756927	165756927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atttgccgtcaattttgtaaCgggccacagttttgtcacag	9	9	2	0	rs117826255	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:165756927C>T	ENST00000366882.1	-	20	2174	c.2020G>A	c.(2020-2022)Gtt>Att	p.V674I	PDE10A_ENST00000539869.2_Missense_Mutation_p.V684I|PDE10A_ENST00000354448.4_Missense_Mutation_p.V674I			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	674					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AATTTTGTAACGGGCCACAGT	0.388													C|||	2	0.000399361	0	0	5008	,	,		17547	0.002		0	False		,,,				2504	0				Esophageal Squamous(22;308 615 5753 12038 40624)											0			6						C	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	124	119	120		2050,2020	5.7	1	6	dbSNP_132	120	0,8600		0,0,4300	yes	missense,missense	PDE10A	NM_001130690.1,NM_006661.2	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	684/790,674/780	165756927	1,13005	2203	4300	6503	165676917	SO:0001583	missense	10846			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.2020G>A	6.37:g.165756927C>T	ENSP00000355847:p.Val674Ile		165676917	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	10.09	1.254205	0.22965	2.27E-4	0.0	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.76709	-1.04;-1.04	5.67	5.67	0.87782	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.054660	0.85682	D	0.000000	T	0.53802	0.1819	L	0.31207	0.915	0.58432	D	0.999991	B;B	0.22003	0.063;0.005	B;B	0.15870	0.014;0.007	T	0.56481	-0.7972	10	0.10636	T	0.68	.	19.3597	0.94432	0.0:1.0:0.0:0.0	.	684;674	Q9ULW9;Q9Y233	.;PDE10_HUMAN	I	674;702;684;674;673	ENSP00000355847:V674I;ENSP00000346435:V674I	ENSP00000341187:V684I	V	-	1	0	PDE10A	165676917	1.000000	0.71417	0.951000	0.38953	0.977000	0.68977	4.175000	0.58263	2.671000	0.90904	0.585000	0.79938	GTT		0.388	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165756927	C	T	165756927	3	4	87	1	0	0	0	0	1	0	0	0	11661	536	19	1	335	1	PDE10A	6	165756927	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	113618365	165756927	5358140	55	24224										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170168265	170168265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttttccttggagagcctgctAtggtaagtattaggtatttt	10	5	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr6:170168265A>G	ENST00000366773.3	+	11	1090	c.1057A>G	c.(1057-1059)Atg>Gtg	p.M353V	ERMARD_ENST00000588451.1_Missense_Mutation_p.M217V|ERMARD_ENST00000418781.3_Missense_Mutation_p.M353V|RP1-266L20.9_ENST00000586101.1_RNA|ERMARD_ENST00000366772.2_Missense_Mutation_p.M353V|ERMARD_ENST00000392095.4_Missense_Mutation_p.M227V	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	353					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AGAGCCTGCTATGGTAAGTAT	0.328																																																0			6											111	109	109					6																	170168265		2203	4300	6503	169910190	SO:0001583	missense	55780			AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1057A>G	6.37:g.170168265A>G	ENSP00000355735:p.Met353Val		169910190	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678369	0.47886	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.47177	0.86;0.85	5.1	5.1	0.69264	.	0.150630	0.46758	D	0.000263	T	0.60209	0.2251	M	0.71581	2.175	0.37030	D	0.896614	D;D;P	0.71674	0.998;0.996;0.61	D;D;B	0.76071	0.987;0.98;0.15	T	0.67452	-0.5667	10	0.72032	D	0.01	.	14.8493	0.70284	1.0:0.0:0.0:0.0	.	353;353;353	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	V	353;353;353;227;1	ENSP00000355735:M353V;ENSP00000375945:M227V	ENSP00000355733:M1V	M	+	1	0	C6orf70	169910190	0.986000	0.35501	0.932000	0.37286	0.873000	0.50193	2.842000	0.48230	2.059000	0.61396	0.533000	0.62120	ATG		0.328	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		G	170168265	A	G	170168265	3	3	87	1	0	0	0	0	1	0	0	0	2376	449	16	4	1099	4	C6orf70	6	170168265	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	4411338	170168265	946802	56	24225										
SCRN1	9805	hgsc.bcm.edu	37	chr7	29980316	29980316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	accttcttgtttttctaagcTgtctttgccagcaccgcagt	7	12	3	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:29980316T>C	ENST00000426154.1	-	5	897	c.721A>G	c.(721-723)Agc>Ggc	p.S241G	SCRN1_ENST00000409497.1_Missense_Mutation_p.S241G|SCRN1_ENST00000242059.5_Missense_Mutation_p.S241G|SCRN1_ENST00000434476.2_Missense_Mutation_p.S261G|SCRN1_ENST00000416113.2_Intron|SCRN1_ENST00000425819.2_Missense_Mutation_p.S173G	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	241					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)	p.S241C(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						TTTTCTAAGCTGTCTTTGCCA	0.473																																																1	Substitution - Missense(1)	ovary(1)	7											131	122	125					7																	29980316		2203	4300	6503	29946841	SO:0001583	missense	9805			D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.721A>G	7.37:g.29980316T>C	ENSP00000409068:p.Ser241Gly		29946841	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440997	0.43326	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000425819;ENST00000544388;ENST00000409497;ENST00000434476;ENST00000421434	T;T;T;T;T;T	0.18960	3.26;3.26;3.12;3.26;3.25;2.18	5.67	5.67	0.87782	.	0.272996	0.37261	N	0.002163	T	0.22820	0.0551	L	0.51422	1.61	0.80722	D	1	B;B;B	0.17268	0.021;0.021;0.008	B;B;B	0.25759	0.039;0.063;0.028	T	0.03524	-1.1028	9	.	.	.	-10.5716	14.7167	0.69275	0.0:0.0:0.0:1.0	.	261;261;241	C9JPG0;B4DHM0;Q12765	.;.;SCRN1_HUMAN	G	241;241;173;45;241;261;241	ENSP00000242059:S241G;ENSP00000409068:S241G;ENSP00000414245:S173G;ENSP00000386872:S241G;ENSP00000388942:S261G;ENSP00000413184:S241G	.	S	-	1	0	SCRN1	29946841	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	3.001000	0.49488	2.159000	0.67721	0.482000	0.46254	AGC		0.473	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766		C	29980316	T	C	29980316	3	2	87	1	0	0	0	0	1	0	0	0	13975	1580	55	4	539	4	SCRN1	7	29980316	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10		29980316	129158347	57	24226										
GUSB	2990	hgsc.bcm.edu	37	chr7	65444800	65444800	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atggcgatagtgattcggagCcgggagggcaggggccccac	18	10	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:65444800C>A	ENST00000304895.4	-	3	625	c.495G>T	c.(493-495)cgG>cgT	p.R165R	GUSB_ENST00000476486.1_Intron|GUSB_ENST00000421103.1_Intron|GUSB_ENST00000345660.6_Silent_p.R165R	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	165					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TGATTCGGAGCCGGGAGGGCA	0.617																																																0			7											137	138	138					7																	65444800		2203	4300	6503	65082235	SO:0001819	synonymous_variant	2990			M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.495G>T	7.37:g.65444800C>A			65082235	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	37	CCDS5530.1																																																																																				0.617	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		A	65444800	C	A	65444800	2	1	87	1	0	0	0	0	0	0	0	1	6923	726	26	2		2	GUSB	7	65444800	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	35464484	65444800	93693863	58	24227										
PON3	5446	hgsc.bcm.edu	37	chr7	94993256	94993256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cctcccttgggctgtagaaaAgaacataagtccagcgaaga	10	10	0	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:94993256A>G	ENST00000265627.5	-	6	624	c.614T>C	c.(613-615)cTt>cCt	p.L205P	PON3_ENST00000451904.1_Missense_Mutation_p.L205P|PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Missense_Mutation_p.L205P	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	205					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GCTGTAGAAAAGAACATAAGT	0.443																																																0			7											182	187	185					7																	94993256		2203	4300	6503	94831192	SO:0001583	missense	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.614T>C	7.37:g.94993256A>G	ENSP00000265627:p.Leu205Pro		94831192	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935290	0.73442	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.47177	0.85;0.85	5.27	4.12	0.48240	Six-bladed beta-propeller, TolB-like (1);	0.387835	0.28442	N	0.015332	T	0.58032	0.2094	M	0.66939	2.045	0.28015	N	0.934745	D;P	0.54397	0.966;0.953	P;P	0.55161	0.77;0.74	T	0.56842	-0.7912	10	0.87932	D	0	-2.1494	10.806	0.46518	0.9247:0.0:0.0753:0.0	.	253;205	B4E2I0;Q15166	.;PON3_HUMAN	P	205	ENSP00000265627:L205P;ENSP00000413276:L205P	ENSP00000265627:L205P	L	-	2	0	PON3	94831192	0.999000	0.42202	0.022000	0.16811	0.325000	0.28411	6.606000	0.74159	0.958000	0.37956	0.533000	0.62120	CTT		0.443	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		G	94993256	A	G	94993256	3	3	87	1	0	0	0	0	1	0	0	0	12281	72	3	4	466	4	PON3	7	94993256	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	29548456	94993256	64145407	59	24228										
MET	4233	hgsc.bcm.edu	37	chr7	116423473	116423473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caaagctgccagtgaagtggAtggctttggaaagtctgcaa	13	7	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:116423473A>G	ENST00000318493.6	+	19	3989	c.3802A>G	c.(3802-3804)Atg>Gtg	p.M1268V	MET_ENST00000397752.3_Missense_Mutation_p.M1250V|MET_ENST00000539704.1_Missense_Mutation_p.M120V			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AGTGAAGTGGATGGCTTTGGA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											94	92	93					7																	116423473		1873	4103	5976	116210709	SO:0001583	missense	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3802A>G	7.37:g.116423473A>G	ENSP00000317272:p.Met1268Val		116210709	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893463	0.72639	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37058	1.22;1.22;1.22	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65133	0.2662	M	0.85373	2.75	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.79108	0.988;0.992	T	0.71300	-0.4634	10	0.87932	D	0	.	16.2225	0.82267	1.0:0.0:0.0:0.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	V	1250;1268;120	ENSP00000380860:M1250V;ENSP00000317272:M1268V;ENSP00000445020:M120V	ENSP00000317272:M1268V	M	+	1	0	MET	116210709	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.289000	0.77006	0.460000	0.39030	ATG		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116423473	A	G	116423473	3	3	87	1	0	0	0	0	1	0	0	0	9515	333	12	4	3872	4	MET	7	116423473	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	21430217	116423473	42715190	60	24229										
DPP6	1804	hgsc.bcm.edu	37	chr7	154684138	154684138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cttcgtggaatgcttcaggaTccaggacaaactgctgacag	11	10	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr7:154684138T>C	ENST00000377770.3	+	26	2687	c.2546T>C	c.(2545-2547)aTc>aCc	p.I849T	DPP6_ENST00000332007.3_Missense_Mutation_p.I787T|DPP6_ENST00000404039.1_Missense_Mutation_p.I785T|DPP6_ENST00000427557.1_Missense_Mutation_p.I742T			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	849					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGCTTCAGGATCCAGGACAAA	0.502																																					NSCLC(125;1384 1783 2490 7422 34254)											0			7											135	145	142					7																	154684138		2132	4232	6364	154315071	SO:0001583	missense	1804			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2546T>C	7.37:g.154684138T>C	ENSP00000367001:p.Ile849Thr		154315071		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	T	6.207	0.406277	0.11754	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.66	4.66	0.58398	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.559774	0.19698	N	0.108106	T	0.22003	0.0530	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.16603	0.011;0.004;0.018;0.005	B;B;B;B	0.25759	0.063;0.027;0.045;0.045	T	0.15263	-1.0443	10	0.27785	T	0.31	-3.9013	10.0964	0.42478	0.1499:0.0:0.0:0.8501	.	742;787;849;785	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	T	785;849;787;742	ENSP00000385578:I785T;ENSP00000367001:I849T;ENSP00000328226:I787T;ENSP00000397303:I742T	ENSP00000328226:I787T	I	+	2	0	DPP6	154315071	0.960000	0.32886	0.548000	0.28192	0.853000	0.48598	3.391000	0.52530	1.745000	0.51790	0.533000	0.62120	ATC		0.502	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		C	154684138	T	C	154684138	3	2	87	1	0	0	0	0	1	0	0	0	4741	1435	50	4	2764	4	DPP6	7	154684138	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	38260665	154684138	4454525	61	24230										
DLC1	10395	hgsc.bcm.edu	37	chr8	12957877	12957877	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cttggacttggcagttttttCgtggcctttcatgctgaagc	11	9	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:12957877C>T	ENST00000276297.4	-	9	2378	c.1969G>A	c.(1969-1971)Gaa>Aaa	p.E657K	DLC1_ENST00000520226.1_Missense_Mutation_p.E146K|DLC1_ENST00000512044.2_Missense_Mutation_p.E254K|DLC1_ENST00000358919.2_Missense_Mutation_p.E220K	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	657					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCAGTTTTTTCGTGGCCTTTC	0.552																																																0			8											118	109	112					8																	12957877		2203	4300	6503	13002248	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1969G>A	8.37:g.12957877C>T	ENSP00000276297:p.Glu657Lys		13002248	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412427	0.25465	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.07216	3.43;3.25;3.24;3.21	4.74	4.74	0.60224	.	0.326661	0.35179	N	0.003389	T	0.10035	0.0246	M	0.69358	2.11	0.80722	D	1	P;B;P	0.51933	0.949;0.188;0.68	B;B;B	0.35039	0.194;0.042;0.119	T	0.05209	-1.0899	10	0.72032	D	0.01	.	13.988	0.64348	0.0:0.8485:0.1515:0.0	.	657;254;220	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	K	657;220;254;146	ENSP00000276297:E657K;ENSP00000351797:E220K;ENSP00000422595:E254K;ENSP00000428028:E146K	ENSP00000276297:E657K	E	-	1	0	DLC1	13002248	0.989000	0.36119	0.985000	0.45067	0.128000	0.20619	2.135000	0.42112	2.624000	0.88883	0.655000	0.94253	GAA		0.552	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	12957877	C	T	12957877	3	4	87	1	0	0	0	0	1	0	0	0	4561	893	31	1	2657	1	DLC1	8	12957877	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		12957877	133406145	62	24231										
DLC1	10395	hgsc.bcm.edu	37	chr8	13259111	13259111	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gagtccagccgcgccctatcTcgatcttctcttatttcctg	7	15	3	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:13259111T>C	ENST00000276297.4	-	3	1450	c.1041A>G	c.(1039-1041)cgA>cgG	p.R347R	DLC1_ENST00000316609.5_Silent_p.R347R|DLC1_ENST00000511869.1_Silent_p.R347R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	347					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCGCCCTATCTCGATCTTCTC	0.438																																																0			8											132	118	123					8																	13259111		2203	4300	6503	13303482	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1041A>G	8.37:g.13259111T>C			13303482	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.438	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13259111	T	C	13259111	2	2	87	1	0	0	0	0	0	0	0	1	4561	1538	54	4		4	DLC1	8	13259111	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	301234	13259111	133104911	63	24232										
CYP7B1	9420	hgsc.bcm.edu	37	chr8	65527669	65527669	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gacctgttgactgcagcaaaCggtcaatttcgtcacgcact	9	12	2	1	rs59035258	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:65527669C>T	ENST00000310193.3	-	4	1144	c.971G>A	c.(970-972)cGt>cAt	p.R324H	CYP7B1_ENST00000523954.1_5'UTR	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	324				R -> H (in Ref. 1; AAC95426). {ECO:0000305}.	bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				CTGCAGCAAACGGTCAATTTC	0.463													C|||	89	0.0177716	0.0015	0.0115	5008	,	,		18048	0.001		0.0427	False		,,,				2504	0.0358															0			8						C	HIS/ARG	40,4366	43.8+/-77.6	0,40,2163	115	107	110		971	-4.4	0.8	8	dbSNP_129	110	344,8256	118.3+/-177.8	8,328,3964	yes	missense	CYP7B1	NM_004820.3	29	8,368,6127	TT,TC,CC		4.0,0.9079,2.9525	benign	324/507	65527669	384,12622	2203	4300	6503	65690223	SO:0001583	missense	9420			AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.971G>A	8.37:g.65527669C>T	ENSP00000310721:p.Arg324His		65690223	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	42	0.019230769230769232	0	0.0	6	0.016574585635359115	0	0.0	36	0.047493403693931395	C	2.435	-0.329922	0.05314	0.009079	0.04	ENSG00000172817	ENST00000310193	T	0.69926	-0.44	5.93	-4.44	0.03557	.	0.617158	0.19131	N	0.121927	T	0.07593	0.0191	N	0.04018	-0.295	0.22112	N	0.999356	B	0.13145	0.007	B	0.11329	0.006	T	0.09100	-1.0690	10	0.11182	T	0.66	-19.8849	14.5279	0.67902	0.0:0.2062:0.0:0.7938	rs59035258;rs61729537	324	O75881	CP7B1_HUMAN	H	324	ENSP00000310721:R324H	ENSP00000310721:R324H	R	-	2	0	CYP7B1	65690223	1.000000	0.71417	0.763000	0.31416	0.995000	0.86356	0.783000	0.26802	-1.137000	0.02888	-0.140000	0.14226	CGT		0.463	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			T	65527669	C	T	65527669	3	4	87	1	0	0	0	0	1	0	0	0	4203	536	19	1	561	1	CYP7B1	8	65527669	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	52268558	65527669	80836353	64	24233										
TRIM55	84675	hgsc.bcm.edu	37	chr8	67062025	67062025	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgtccgtgctctgatcaaaaAgtattctgatcatttggaga	9	7	4	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:67062025A>G	ENST00000315962.4	+	5	1122	c.749A>G	c.(748-750)aAg>aGg	p.K250R	TRIM55_ENST00000276573.7_Missense_Mutation_p.K250R|TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000353317.5_Missense_Mutation_p.K250R	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	250					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CTGATCAAAAAGTATTCTGAT	0.428																																																0			8											133	131	131					8																	67062025		2203	4300	6503	67224579	SO:0001583	missense	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.749A>G	8.37:g.67062025A>G	ENSP00000323913:p.Lys250Arg		67224579	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.496600	0.44352	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	T;T;T	0.31247	1.5;1.55;1.5	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.27832	0.0685	L	0.38649	1.16	0.80722	D	1	B;B;B	0.21520	0.012;0.057;0.02	B;B;B	0.24006	0.018;0.05;0.032	T	0.03403	-1.1040	10	0.31617	T	0.26	.	15.898	0.79350	1.0:0.0:0.0:0.0	.	250;250;250	Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;TRI55_HUMAN;.	R	250	ENSP00000323913:K250R;ENSP00000297348:K250R;ENSP00000276573:K250R	ENSP00000276573:K250R	K	+	2	0	TRIM55	67224579	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	6.248000	0.72418	2.150000	0.67090	0.528000	0.53228	AAG		0.428	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		G	67062025	A	G	67062025	3	3	87	1	0	0	0	0	1	0	0	0	16569	72	3	4	767	4	TRIM55	8	67062025	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	1534356	67062025	79301997	65	24234										
PEX2	5828	hgsc.bcm.edu	37	chr8	77896008	77896008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcacaaaattcacacactgcTtgactttcccaaatgatgct	4	12	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:77896008T>C	ENST00000419564.2	-	4	871	c.407A>G	c.(406-408)aAg>aGg	p.K136R	PEX2_ENST00000357039.4_Missense_Mutation_p.K136R|PEX2_ENST00000522527.1_Missense_Mutation_p.K136R|PEX2_ENST00000520103.1_Missense_Mutation_p.K136R	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	136					bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	14						CACACACTGCTTGACTTTCCC	0.373																																																0			8											98	95	96					8																	77896008		2203	4300	6503	78058563	SO:0001583	missense	5828			M86852	CCDS6221.1	8q21.11	2010-02-09	2010-01-25	2010-01-25		ENSG00000164751		"RING-type (C3HC4) zinc fingers"	9717	protein-coding gene	gene with protein product	"Zellweger syndrome", "peroxin 2"	170993	"peroxisomal membrane protein 3 (35kD, Zellweger syndrome)", "peroxisomal membrane protein 3, 35kDa"	PXMP3		1546315, 8858157	Standard	NM_000318		Approved	PMP35, PAF-1, RNF72, ZWS3	uc022awf.1	P28328		ENST00000419564.2:c.407A>G	8.37:g.77896008T>C	ENSP00000400984:p.Lys136Arg		78058563	Q567S6|Q9BW41	Missense_Mutation	SNP	ENST00000419564.2	37	CCDS6221.1	.	.	.	.	.	.	.	.	.	.	T	8.396	0.840839	0.16891	.	.	ENSG00000164751	ENST00000357039;ENST00000419564;ENST00000520103;ENST00000522527;ENST00000518986	D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58	5.18	4.02	0.46733	Pex, N-terminal (1);	0.115856	0.56097	N	0.000027	T	0.68778	0.3038	N	0.22421	0.69	0.38453	D	0.947001	B	0.02656	0.0	B	0.04013	0.001	T	0.60510	-0.7249	10	0.12103	T	0.63	-16.6691	10.3466	0.43909	0.0:0.08:0.0:0.92	.	136	P28328	PEX2_HUMAN	R	136	ENSP00000349543:K136R;ENSP00000400984:K136R;ENSP00000428590:K136R;ENSP00000428638:K136R;ENSP00000429304:K136R	ENSP00000349543:K136R	K	-	2	0	PEX2	78058563	0.990000	0.36364	0.996000	0.52242	0.953000	0.61014	2.282000	0.43461	0.981000	0.38548	0.456000	0.33151	AAG		0.373	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		C	77896008	T	C	77896008	3	2	87	1	0	0	0	0	1	0	0	0	11776	1609	56	4	514	4	PEX2	8	77896008	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	10833983	77896008	68468014	66	24235										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110457743	110457743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caaccccaatgaagtctactGccgcactcccgctgggacca	8	17	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr8:110457743G>A	ENST00000378402.5	+	38	5749	c.5645G>A	c.(5644-5646)tGc>tAc	p.C1882Y		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1882	IPT/TIG 11.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.C1884Y(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAAGTCTACTGCCGCACTCCC	0.438										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	ovary(1)	8											48	48	48					8																	110457743		1918	4142	6060	110526919	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5645G>A	8.37:g.110457743G>A	ENSP00000367655:p.Cys1882Tyr		110526919	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967065	0.53507	.	.	ENSG00000205038	ENST00000378402	D	0.83163	-1.69	5.91	5.91	0.95273	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94476	0.8222	H	0.96633	3.855	0.50632	D	0.999887	D	0.89917	1.0	D	0.97110	1.0	D	0.95736	0.8779	10	0.87932	D	0	.	17.7921	0.88555	0.0:0.0:1.0:0.0	.	1882	Q86WI1	PKHL1_HUMAN	Y	1882	ENSP00000367655:C1882Y	ENSP00000367655:C1882Y	C	+	2	0	PKHD1L1	110526919	1.000000	0.71417	0.523000	0.27875	0.129000	0.20672	7.560000	0.82277	2.802000	0.96397	0.655000	0.94253	TGC		0.438	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110457743	G	A	110457743	3	1	87	1	0	0	0	0	1	0	0	0	12003	1319	46	3	5795	3	PKHD1L1	8	110457743	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	32561735	110457743	35906279	67	24236										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32631117	32631117	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tccagcatggattgagagatCtgagtcaatgaatgttttgg	12	5	2	4			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:32631117C>A	ENST00000242310.4	-	1	4550	c.4461G>T	c.(4459-4461)caG>caT	p.Q1487H	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1487					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ATTGAGAGATCTGAGTCAATG	0.428																																																0			9											191	175	181					9																	32631117		2203	4300	6503	32621117	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4461G>T	9.37:g.32631117C>A	ENSP00000418379:p.Gln1487His		32621117	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.629394	0.28978	.	.	ENSG00000122728	ENST00000242310	T	0.31769	1.48	0.489	0.489	0.16854	Bromodomain (4);	0.124572	0.56097	D	0.000028	T	0.23806	0.0576	L	0.59436	1.845	0.32448	N	0.5458	B	0.28419	0.211	B	0.29524	0.103	T	0.17592	-1.0364	10	0.62326	D	0.03	.	2.8749	0.05628	0.0:0.6151:0.0:0.3849	.	1487	Q8IZX4	TAF1L_HUMAN	H	1487	ENSP00000418379:Q1487H	ENSP00000418379:Q1487H	Q	-	3	2	TAF1L	32621117	0.284000	0.24287	0.984000	0.44739	0.380000	0.30137	0.203000	0.17315	0.514000	0.28300	0.205000	0.17691	CAG		0.428	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32631117	C	A	32631117	3	1	87	1	0	0	0	0	1	0	0	0	15562	912	32	2	1023	2	TAF1L	9	32631117	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		32631117	108582314	68	24237										
MCART1	92014	hgsc.bcm.edu	37	chr9	37887989	37887989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	aaggccgaaaaacaagacatTgctgagtccattccggaaaa	9	9	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:37887989T>C	ENST00000377716.2	-	3	1302	c.559A>G	c.(559-561)Aat>Gat	p.N187D	SLC25A51_ENST00000242275.6_Missense_Mutation_p.N187D|SLC25A51_ENST00000496760.1_Intron|SLC25A51_ENST00000380590.3_Missense_Mutation_p.N187D|RP11-613M10.9_ENST00000540557.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	187					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											AACAAGACATTGCTGAGTCCA	0.463																																																0			9											76	73	74					9																	37887989		2203	4296	6499	37877989	SO:0001583	missense	92014			BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"Solute carriers"	23323	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 1"	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.559A>G	9.37:g.37887989T>C	ENSP00000366945:p.Asn187Asp		37877989		Missense_Mutation	SNP	ENST00000377716.2	37	CCDS6614.1	.	.	.	.	.	.	.	.	.	.	.	23.1	4.380790	0.82792	.	.	ENSG00000122696	ENST00000380590;ENST00000377716;ENST00000242275	T;T;T	0.78816	-1.21;-1.21;-1.21	4.64	4.64	0.57946	Mitochondrial carrier domain (2);	0.058414	0.64402	N	0.000004	D	0.87406	0.6169	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88858	0.3324	10	0.72032	D	0.01	.	12.3163	0.54958	0.0:0.0:0.0:1.0	.	187	Q9H1U9	MCAR1_HUMAN	D	187	ENSP00000369964:N187D;ENSP00000366945:N187D;ENSP00000242275:N187D	ENSP00000242275:N187D	N	-	1	0	MCART1	37877989	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.568000	0.82369	1.868000	0.54150	0.477000	0.44152	AAT		0.463	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412		C	37887989	T	C	37887989	3	2	87	1	0	0	0	0	1	0	0	0	9399	1812	63	4	338	4	MCART1	9	37887989	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	5256872	37887989	103325442	69	24238										
APBA1	320	hgsc.bcm.edu	37	chr9	72071249	72071249	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cgcttccacgttctcctgggAgttggagcgaggcatccgcc	13	14	1	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:72071249A>G	ENST00000265381.4	-	8	1924	c.1702T>C	c.(1702-1704)Tcc>Ccc	p.S568P	APBA1_ENST00000470082.1_5'UTR	NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	568	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						TTCTCCTGGGAGTTGGAGCGA	0.562																																																0			9											241	231	234					9																	72071249		2203	4300	6503	71261069	SO:0001583	missense	320			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1702T>C	9.37:g.72071249A>G	ENSP00000265381:p.Ser568Pro		71261069	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268499	0.59540	.	.	ENSG00000107282	ENST00000265381	T	0.54675	0.56	6.06	6.06	0.98353	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.110411	0.64402	D	0.000008	T	0.59542	0.2201	L	0.41906	1.305	0.58432	D	0.999999	D	0.54397	0.966	P	0.55303	0.773	T	0.59490	-0.7445	10	0.49607	T	0.09	-18.3886	16.6003	0.84812	1.0:0.0:0.0:0.0	.	568	Q02410	APBA1_HUMAN	P	568	ENSP00000265381:S568P	ENSP00000265381:S568P	S	-	1	0	APBA1	71261069	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.224000	0.51238	2.319000	0.78375	0.533000	0.62120	TCC		0.562	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		G	72071249	A	G	72071249	3	3	87	1	0	0	0	0	1	0	0	0	756	304	11	4	835	4	APBA1	9	72071249	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	34183260	72071249	69142182	70	24239										
C9orf41	138199	hgsc.bcm.edu	37	chr9	77631258	77631258	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gcatccctttctgctttcccAgtttcactccagtctctcac	4	17	4	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:77631258A>T	ENST00000376834.3	-	3	668	c.516T>A	c.(514-516)acT>acA	p.T172T	RP11-197P3.5_ENST00000455336.2_RNA|C9orf41_ENST00000376837.3_Silent_p.T172T	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	172										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						CTGCTTTCCCAGTTTCACTCC	0.353																																																0			9											176	178	177					9																	77631258		2203	4300	6503	76821078	SO:0001819	synonymous_variant	138199			AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.516T>A	9.37:g.77631258A>T			76821078	Q7Z383|Q8N7C5	Silent	SNP	ENST00000376834.3	37	CCDS6649.1																																																																																				0.353	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		T	77631258	A	T	77631258	2	4	87	1	0	0	0	0	0	0	0	1	2488	175	7	5		5	C9orf41	9	77631258	Silent	SNP	A	TCGA-CI-6620-01A-11D-1826-10	5560009	77631258	63582173	71	24240										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112168802	112168802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctcccggctggctttgatgaAcatcaccacttggtcatgcg	10	13	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:112168802A>G	ENST00000374541.2	-	18	1836	c.1732T>C	c.(1732-1734)Ttc>Ctc	p.F578L	PTPN3_ENST00000412145.1_Missense_Mutation_p.F447L|PTPN3_ENST00000446349.1_Missense_Mutation_p.F402L|PTPN3_ENST00000262539.3_Missense_Mutation_p.F424L|PTPN3_ENST00000394827.3_Missense_Mutation_p.F46L	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	578	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GCTTTGATGAACATCACCACT	0.572																																																0			9											176	159	165					9																	112168802		2203	4300	6503	111208623	SO:0001583	missense	5774				CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1732T>C	9.37:g.112168802A>G	ENSP00000363667:p.Phe578Leu		111208623	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.205511	0.79127	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000394827;ENST00000262539	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.74	5.74	0.90152	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.24736	0.0600	N	0.02266	-0.62	0.80722	D	1	D;B;B	0.89917	1.0;0.333;0.047	D;B;B	0.87578	0.998;0.326;0.267	T	0.41466	-0.9507	10	0.13470	T	0.59	.	16.0229	0.80512	1.0:0.0:0.0:0.0	.	424;533;578	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	L	578;447;402;578;46;424	ENSP00000416654:F447L;ENSP00000395384:F402L;ENSP00000363667:F578L;ENSP00000378304:F46L;ENSP00000262539:F424L	ENSP00000262539:F424L	F	-	1	0	PTPN3	111208623	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.189000	0.69895	0.459000	0.35465	TTC		0.572	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			G	112168802	A	G	112168802	3	3	87	1	0	0	0	0	1	0	0	0	12826	43	2	4	1045	4	PTPN3	9	112168802	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	34537544	112168802	29044629	72	24241										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119976742	119976742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gcgggagacatggttggcccGcctaggtggctcctcatcct	14	13	1	1	rs554132287		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr9:119976742G>A	ENST00000313400.4	-	3	1010	c.910C>T	c.(910-912)Cgg>Tgg	p.R304W	ASTN2_ENST00000361209.2_Missense_Mutation_p.R304W|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.R304W			O75129	ASTN2_HUMAN	astrotactin 2	304					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TGGTTGGCCCGCCTAGGTGGC	0.587													G|||	1	0.000199681	8e-04	0	5008	,	,		16810	0		0	False		,,,				2504	0															0			9											77	76	76					9																	119976742		2203	4300	6503	119016563	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.910C>T	9.37:g.119976742G>A	ENSP00000314038:p.Arg304Trp		119016563	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	16.93	3.256896	0.59321	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.12569	2.85;2.85;2.67;2.78	5.16	3.08	0.35506	.	0.297842	0.26967	N	0.021589	T	0.15739	0.0379	N	0.14661	0.345	0.39201	D	0.963149	P;D;D	0.89917	0.932;0.993;1.0	B;P;D	0.67382	0.079;0.727;0.951	T	0.11348	-1.0591	9	.	.	.	-22.0226	8.2197	0.31534	0.0822:0.0:0.5902:0.3276	.	304;304;304	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	W	304;304;31;304	ENSP00000314038:R304W;ENSP00000363108:R304W;ENSP00000363098:R31W;ENSP00000354504:R304W	.	R	-	1	2	ASTN2	119016563	0.251000	0.23961	0.996000	0.52242	0.769000	0.43574	0.547000	0.23299	1.115000	0.41800	0.655000	0.94253	CGG		0.587	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119976742	G	A	119976742	3	1	87	1	0	0	0	0	1	0	0	0	1066	1086	38	1	3268	1	ASTN2	9	119976742	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	7807940	119976742	21236689	73	24242										
AKR1C4	1109	hgsc.bcm.edu	37	chr10	5247796	5247796	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggatctctctgccacatgggAggtgagtgcttggaggacag	16	8	2	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:5247796A>G	ENST00000380448.1	+	6	699	c.446A>G	c.(445-447)gAg>gGg	p.E149G	AKR1C4_ENST00000263126.1_Splice_Site_p.E149G			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	149					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.E149A(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						GCCACATGGGAGGTGAGTGCT	0.448																																																1	Substitution - Missense(1)	ovary(1)	10											119	105	109					10																	5247796		2203	4300	6503	5237796	SO:0001630	splice_region_variant	1109			M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"Aldo-keto reductases"	387	protein-coding gene	gene with protein product	"chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"	600451	"aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.447+1A>G	10.37:g.5247796A>G			5237796	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600639	0.28534	.	.	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.52526	0.66;0.66	3.16	3.16	0.36331	NADP-dependent oxidoreductase domain (3);	0.270365	0.31031	N	0.008395	T	0.42017	0.1184	L	0.37561	1.115	0.45390	D	0.998371	B	0.31459	0.324	B	0.39904	0.313	T	0.44605	-0.9317	10	0.72032	D	0.01	.	9.6032	0.39617	1.0:0.0:0.0:0.0	.	149	P17516	AK1C4_HUMAN	G	149	ENSP00000369814:E149G;ENSP00000263126:E149G	ENSP00000263126:E149G	E	+	2	0	AKR1C4	5237796	1.000000	0.71417	0.995000	0.50966	0.028000	0.11728	7.251000	0.78297	1.195000	0.43115	0.260000	0.18958	GAG		0.448	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	Missense_Mutation	G	5247796	A	G	5247796	5	3	87	1	0	0	0	0	0	0	1	0	472	318	11	4	460	4	AKR1C4	10	5247796	Splice_Site	SNP	A	TCGA-CI-6620-01A-11D-1826-10		5247796	130286951	74	24243										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18937509	18937509	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gttgtaaatgatggaggatgTgacaggtgctttaacaaagt	13	3	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:18937509T>C	ENST00000377304.4	-	2	559	c.141A>G	c.(139-141)tcA>tcG	p.S47S	RP11-139J15.7_ENST00000606425.1_Silent_p.S35S	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	47							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						ATGGAGGATGTGACAGGTGCT	0.348																																																0			10											214	202	206					10																	18937509		2203	4300	6503	18977515	SO:0001819	synonymous_variant	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.141A>G	10.37:g.18937509T>C			18977515	B0YJ54	Silent	SNP	ENST00000377304.4	37	CCDS7130.1																																																																																				0.348	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		C	18937509	T	C	18937509	2	2	87	1	0	0	0	0	0	0	0	1	10713	1683	59	4		4	NSUN6	10	18937509	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	13689713	18937509	116597238	75	24244										
CDH23	64072	hgsc.bcm.edu	37	chr10	73326628	73326628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttgacagcgcccgcggtatcGtcacagtgatccgggagctg	14	12	1	2	rs369624952		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:73326628G>A	ENST00000224721.6	+	6	579	c.574G>A	c.(574-576)Gtc>Atc	p.V192I	CDH23_ENST00000299366.7_Missense_Mutation_p.V232I|CDH23_ENST00000398842.3_Missense_Mutation_p.V187I|CDH23_ENST00000461841.3_Missense_Mutation_p.V232I|CDH23_ENST00000398809.4_Missense_Mutation_p.V187I	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCGCGGTATCGTCACAGTGAT	0.652																																																0			10						G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4104		0,0,2052	43	47	46		559,559,559,559,559	4.8	0.9	10		46	1,8375		0,1,4187	no	missense,missense,missense,missense,missense	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	29,29,29,29,29	0,1,6239	AA,AG,GG		0.0119,0.0,0.0080	benign,benign,benign,benign,benign	187/1382,187/1062,187/407,187/3355,187/531	73326628	1,12479	2052	4188	6240	72996634	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.574G>A	10.37:g.73326628G>A	ENSP00000224721:p.Val192Ile		72996634	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	9.582	1.123744	0.20959	0.0	1.19E-4	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.57107	0.42;0.42	5.7	4.8	0.61643	Cadherin (4);Cadherin-like (1);	0.093767	0.41097	N	0.000956	T	0.28566	0.0707	N	0.03029	-0.43	0.80722	D	1	B;B;B;B	0.20052	0.014;0.018;0.041;0.019	B;B;B;B	0.17722	0.004;0.019;0.006;0.015	T	0.08597	-1.0714	10	0.17832	T	0.49	.	14.9766	0.71277	0.0683:0.0:0.9317:0.0	.	187;187;187;187	A5D6V9;Q9H251;Q9H251-5;E7ESV7	.;CAD23_HUMAN;.;.	I	192;187;187;187;187;192;192;128	ENSP00000381789:V187I;ENSP00000381822:V187I	ENSP00000224721:V192I	V	+	1	0	CDH23	72996634	1.000000	0.71417	0.915000	0.36163	0.291000	0.27294	7.514000	0.81750	1.445000	0.47624	-0.219000	0.12488	GTC		0.652	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73326628	G	A	73326628	3	1	87	1	0	0	0	0	1	0	0	0	3114	1145	40	1	581	1	CDH23	10	73326628	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	54389119	73326628	62208119	76	24245										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717616	89717616	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atttaaccatgcagatcctcAgtttgtggtctgccagctaa	8	10	2	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr10:89717616A>G	ENST00000371953.3	+	7	1998	c.641A>G	c.(640-642)cAg>cGg	p.Q214R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	214	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.Q214fs*1(1)|p.?(1)|p.Q214fs*22(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GCAGATCCTCAGTTTGTGGTC	0.388		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - frameshift(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	10											113	100	104					10																	89717616		2203	4300	6503	89707596	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.641A>G	10.37:g.89717616A>G	ENSP00000361021:p.Gln214Arg		89707596	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960540	0.53400	.	.	ENSG00000171862	ENST00000371953	D	0.85339	-1.97	5.67	5.67	0.87782	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.164422	0.56097	D	0.000025	D	0.82692	0.5092	L	0.45228	1.405	0.80722	D	1	P	0.42584	0.784	B	0.43225	0.412	T	0.81786	-0.0773	9	.	.	.	-2.2072	15.9118	0.79477	1.0:0.0:0.0:0.0	.	214	P60484	PTEN_HUMAN	R	214	ENSP00000361021:Q214R	.	Q	+	2	0	PTEN	89707596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.973000	0.76116	2.162000	0.67917	0.477000	0.44152	CAG		0.388	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717616	A	G	89717616	3	3	87	1	0	0	0	0	1	0	0	0	12772	188	7	4	667	4	PTEN	10	89717616	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	16390988	89717616	45817131	77	24246										
OR2AG2	338755	hgsc.bcm.edu	37	chr11	6789380	6789380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	aaacagagatgatgttgtctTgtttggggctgtggaaggaa	15	3	1	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:6789380T>C	ENST00000338569.2	-	1	906	c.809A>G	c.(808-810)cAa>cGa	p.Q270R		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GATGTTGTCTTGTTTGGGGCT	0.512																																																0			11											152	138	143					11																	6789380		2201	4296	6497	6745956	SO:0001583	missense	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"GPCR / Class A : Olfactory receptors"	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.809A>G	11.37:g.6789380T>C	ENSP00000342697:p.Gln270Arg		6745956		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961065	0.53400	.	.	ENSG00000188124	ENST00000338569	T	0.00152	8.66	4.47	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000198	T	0.00300	0.0009	L	0.50919	1.6	0.26717	N	0.970863	D	0.89917	1.0	D	0.77557	0.99	T	0.54098	-0.8344	10	0.54805	T	0.06	.	7.6239	0.28202	0.1888:0.0:0.0:0.8112	.	270	A6NM03	O2AG2_HUMAN	R	270	ENSP00000342697:Q270R	ENSP00000342697:Q270R	Q	-	2	0	OR2AG2	6745956	0.000000	0.05858	0.580000	0.28601	0.992000	0.81027	-0.259000	0.08721	2.241000	0.73720	0.533000	0.62120	CAA		0.512	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		C	6789380	T	C	6789380	3	2	87	1	0	0	0	0	1	0	0	0	11016	1812	63	4	145	4	OR2AG2	11	6789380	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10		6789380	128217136	78	24247										
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18955439	18955439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caccttcatccacctcagacGcgtcctgcagagccctctgg	8	18	3	2	rs183845903		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:18955439G>A	ENST00000302797.3	-	1	1117	c.893C>T	c.(892-894)gCg>gTg	p.A298V	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	298				AS -> TP (in Ref. 2; AAL86880). {ECO:0000305}.	acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CACCTCAGACGCGTCCTGCAG	0.562													G|||	1	0.000199681	8e-04	0	5008	,	,		24102	0		0	False		,,,				2504	0															0			11											71	67	69					11																	18955439		2194	4286	6480	18912015	SO:0001583	missense	259249				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.893C>T	11.37:g.18955439G>A	ENSP00000305766:p.Ala298Val		18912015	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	10.27	1.304888	0.23736	.	.	ENSG00000170255	ENST00000302797	T	0.20332	2.08	2.28	1.35	0.21983	.	0.891913	0.09559	N	0.785768	T	0.06188	0.0160	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35748	-0.9776	10	0.30078	T	0.28	.	4.4439	0.11588	0.331:0.0:0.669:0.0	.	298	Q96LB2	MRGX1_HUMAN	V	298	ENSP00000305766:A298V	ENSP00000305766:A298V	A	-	2	0	MRGPRX1	18912015	0.000000	0.05858	0.036000	0.18154	0.088000	0.18126	-0.652000	0.05366	0.512000	0.28257	0.491000	0.48974	GCG		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		A	18955439	G	A	18955439	3	1	87	1	0	0	0	0	1	0	0	0	9796	1087	38	1	79	1	MRGPRX1	11	18955439	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	12166059	18955439	116051077	79	24248										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681572	55681572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	acagaagcataggcggaaggCcagtgtcatatgtatcaaag	12	7	2	1	rs17148883	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:55681572C>A	ENST00000344514.1	-	1	486	c.487G>T	c.(487-489)Gcc>Tcc	p.A163S		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	163			A -> P (in dbSNP:rs17148883).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGGCGGAAGGCCAGTGTCATA	0.438																																					Melanoma(48;171 1190 15239 43886 49348)											0			11											87	77	80					11																	55681572		2201	4296	6497	55438148	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.487G>T	11.37:g.55681572C>A	ENSP00000342448:p.Ala163Ser		55438148		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306775	0.23821	.	.	ENSG00000187612	ENST00000344514	T	0.00099	8.73	5.01	-10.0	0.00425	GPCR, rhodopsin-like superfamily (1);	0.563390	0.14710	N	0.302993	T	0.00144	0.0004	L	0.46741	1.465	0.09310	N	1	B	0.31290	0.318	B	0.43155	0.41	T	0.31668	-0.9935	10	0.87932	D	0	.	8.2433	0.31673	0.1908:0.1019:0.0:0.7073	.	163	Q8NH69	OR5W2_HUMAN	S	163	ENSP00000342448:A163S	ENSP00000342448:A163S	A	-	1	0	OR5W2	55438148	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.231000	0.01206	-1.772000	0.01292	-1.179000	0.01719	GCC		0.438	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		A	55681572	C	A	55681572	3	1	87	1	0	0	0	0	1	0	0	0	11216	739	26	2	447	2	OR5W2	11	55681572	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	36726133	55681572	79324944	80	24249										
OR10G8	219869	hgsc.bcm.edu	37	chr11	123901210	123901210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caccctgaggaacaaggaggTgaagaaagctctgttgaagc	13	8	1	4			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:123901210T>C	ENST00000431524.1	+	1	914	c.881T>C	c.(880-882)gTg>gCg	p.V294A		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AACAAGGAGGTGAAGAAAGCT	0.473																																																0			11											104	98	100					11																	123901210		2201	4299	6500	123406420	SO:0001583	missense	219869			AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.881T>C	11.37:g.123901210T>C	ENSP00000389072:p.Val294Ala		123406420	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.365784	0.41902	.	.	ENSG00000234560	ENST00000431524	T	0.39592	1.07	2.91	2.91	0.33838	.	0.000000	0.37761	N	0.001959	T	0.59404	0.2191	M	0.71206	2.165	0.28092	N	0.931774	D	0.64830	0.994	D	0.70716	0.97	T	0.54583	-0.8272	10	0.87932	D	0	.	11.0743	0.48021	0.0:0.0:0.0:1.0	.	294	Q8NGN5	O10G8_HUMAN	A	294	ENSP00000389072:V294A	ENSP00000389072:V294A	V	+	2	0	OR10G8	123406420	0.995000	0.38212	0.997000	0.53966	0.389000	0.30415	4.406000	0.59748	1.319000	0.45190	0.455000	0.32223	GTG		0.473	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		C	123901210	T	C	123901210	3	2	87	1	0	0	0	0	1	0	0	0	10934	1696	59	4	883	4	OR10G8	11	123901210	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	68219638	123901210	11105306	81	24250										
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130275579	130275579	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cgcctctgccagccggccccGcaggtgctagagcactcaga	12	17	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr11:130275579G>A	ENST00000257359.6	-	9	3250	c.2544C>T	c.(2542-2544)tgC>tgT	p.C848C		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	848	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		AGCCGGCCCCGCAGGTGCTAG	0.637																																																0			11											65	77	73					11																	130275579		2037	4201	6238	129780789	SO:0001819	synonymous_variant	11095			AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"ADAM metallopeptidases with thrombospondin type 1 motif"	224	protein-coding gene	gene with protein product		605175	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.2544C>T	11.37:g.130275579G>A			129780789	Q9NZS0	Silent	SNP	ENST00000257359.6	37	CCDS41732.1																																																																																				0.637	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		A	130275579	G	A	130275579	2	1	87	1	0	0	0	0	0	0	0	1	272	1079	38	1		1	ADAMTS8	11	130275579	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	6374369	130275579	4730937	82	24251										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	87	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		25398284	108453611	83	24252										
XPOT	11260	hgsc.bcm.edu	37	chr12	64812700	64812700	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	acctttatacgaaataaagcCgcccaagtcttcgccttgct	6	13	1	0	rs372746587		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:64812700C>T	ENST00000332707.5	+	6	844	c.315C>T	c.(313-315)gcC>gcT	p.A105A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	105	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GAAATAAAGCCGCCCAAGTCT	0.398																																																0			12						C		2,4404	2.1+/-5.4	0,2,2201	83	81	82		315	-2.6	1	12		82	0,8600		0,0,4300	no	coding-synonymous	XPOT	NM_007235.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		105/963	64812700	2,13004	2203	4300	6503	63098967	SO:0001819	synonymous_variant	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.315C>T	12.37:g.64812700C>T			63098967	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																				0.398	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		T	64812700	C	T	64812700	2	4	87	1	0	0	0	0	0	0	0	1	17490	639	23	1		1	XPOT	12	64812700	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	39414416	64812700	69039195	84	24253										
KSR2	283455	hgsc.bcm.edu	37	chr12	118293321	118293321	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccgtatttctccacagtctcGcacacctgttcatccgtcat	5	16	4	0	rs371982174		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr12:118293321G>A	ENST00000339824.5	-	3	1111	c.384C>T	c.(382-384)tgC>tgT	p.C128C	KSR2_ENST00000425217.1_Silent_p.C99C			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	128					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.C160C(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCACAGTCTCGCACACCTGTT	0.612																																																1	Substitution - coding silent(1)	central_nervous_system(1)	12						G		1,4163		0,1,2081	91	99	96		297	-2	1	12		96	0,8436		0,0,4218	no	coding-synonymous	KSR2	NM_173598.4		0,1,6299	AA,AG,GG		0.0,0.024,0.0079		99/922	118293321	1,12599	2082	4218	6300	116777704	SO:0001819	synonymous_variant	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.384C>T	12.37:g.118293321G>A			116777704	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					0.612	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		A	118293321	G	A	118293321	2	1	87	1	0	0	0	0	0	0	0	1	8604	1079	38	1		1	KSR2	12	118293321	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	53480621	118293321	15558574	85	24254										
RB1	5925	hgsc.bcm.edu	37	chr13	49037913	49037913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	atgcaaagtgaagaatatagAccttaaattcaaaatcattg	6	5	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr13:49037913A>G	ENST00000267163.4	+	21	2291	c.2153A>G	c.(2152-2154)gAc>gGc	p.D718G		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	718	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAGAATATAGACCTTAAATTC	0.299		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											113	118	116					13																	49037913		2203	4292	6495	47935914	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2153A>G	13.37:g.49037913A>G	ENSP00000267163:p.Asp718Gly		47935914	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796854	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92348	-3.02	6.07	6.07	0.98685	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.95723	0.8609	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96024	0.9011	10	0.87932	D	0	-15.7516	16.6406	0.85098	1.0:0.0:0.0:0.0	.	718	P06400	RB_HUMAN	G	697;718	ENSP00000267163:D718G	ENSP00000267163:D718G	D	+	2	0	RB1	47935914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.326000	0.78906	0.533000	0.62120	GAC		0.299	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	49037913	A	G	49037913	3	3	87	1	0	0	0	0	1	0	0	0	13135	275	10	4	2235	4	RB1	13	49037913	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10		49037913	66131965	86	24255										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25925284	25925284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccacctgggcagcagtgcagCgacaggcgtcatcaggcaag	14	13	2	0	rs116641809	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:25925284C>T	ENST00000356865.6	-	20	3961	c.3850G>A	c.(3850-3852)Gct>Act	p.A1284T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1284					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGCAGTGCAGCGACAGGCGTC	0.572													C|||	13	0.00259585	0	0.0101	5008	,	,		16818	0		0.006	False		,,,				2504	0															0			15						C	THR/ALA	5,4401	9.9+/-24.2	0,5,2198	131	120	124		3850	-2.6	0	15	dbSNP_132	124	77,8523	45.4+/-104.0	0,77,4223	yes	missense	ATP10A	NM_024490.3	58	0,82,6421	TT,TC,CC		0.8953,0.1135,0.6305	benign	1284/1500	25925284	82,12924	2203	4300	6503	23476377	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3850G>A	15.37:g.25925284C>T	ENSP00000349325:p.Ala1284Thr		23476377	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	6.597	0.478427	0.12521	0.001135	0.008953	ENSG00000206190	ENST00000356865	T	0.41758	0.99	5.07	-2.59	0.06209	.	0.568870	0.19381	N	0.115668	T	0.19927	0.0479	L	0.28400	0.85	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.10177	-1.0641	10	0.45353	T	0.12	-1.3667	10.8772	0.46917	0.0:0.4562:0.0:0.5438	.	1284	O60312	AT10A_HUMAN	T	1284	ENSP00000349325:A1284T	ENSP00000349325:A1284T	A	-	1	0	ATP10A	23476377	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.216000	0.17585	-0.776000	0.04578	-0.345000	0.07892	GCT		0.572	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25925284	C	T	25925284	3	4	87	1	0	0	0	0	1	0	0	0	1117	768	27	1	657	1	ATP10A	15	25925284	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		25925284	76606108	87	24256										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25947099	25947099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agggtgatgacctcctcgtcGtggtccagcagtttgcaggc	14	11	0	2	rs114930132	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:25947099G>A	ENST00000356865.6	-	13	2835	c.2724C>T	c.(2722-2724)caC>caT	p.H908H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	908					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCTCCTCGTCGTGGTCCAGCA	0.542													G|||	10	0.00199681	0.0045	0.0014	5008	,	,		20704	0		0	False		,,,				2504	0.0031															0			15						G		16,4390	24.3+/-50.5	0,16,2187	179	155	163		2724	-11	0	15	dbSNP_132	163	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,16,6487	AA,AG,GG		0.0,0.3631,0.123		908/1500	25947099	16,12990	2203	4300	6503	23498192	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2724C>T	15.37:g.25947099G>A			23498192	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.542	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25947099	G	A	25947099	2	1	87	1	0	0	0	0	0	0	0	1	1117	1136	40	1		1	ATP10A	15	25947099	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	21815	25947099	76584293	88	24257										
RYR3	6263	hgsc.bcm.edu	37	chr15	33936562	33936562	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctcagatcggccgcatgaatCtcgggacagatgccagtacc	11	13	2	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:33936562C>T	ENST00000389232.4	+	28	3677	c.3607C>T	c.(3607-3609)Ctc>Ttc	p.L1203F	RYR3_ENST00000415757.3_Missense_Mutation_p.L1203F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1203	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.L1203I(2)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCGCATGAATCTCGGGACAGA	0.517																																																2	Substitution - Missense(2)	lung(2)	15											69	69	69					15																	33936562		1963	4153	6116	31723854	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3607C>T	15.37:g.33936562C>T	ENSP00000373884:p.Leu1203Phe		31723854	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486127	0.44147	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.70045	-0.45;-0.45	5.13	5.13	0.70059	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000001	T	0.63640	0.2528	N	0.11064	0.09	0.58432	D	0.999999	B;D	0.76494	0.011;0.999	B;D	0.68483	0.016;0.958	T	0.60974	-0.7156	10	0.24483	T	0.36	.	13.4439	0.61129	0.0:0.9247:0.0:0.0753	.	1203;1203	Q15413-2;Q15413	.;RYR3_HUMAN	F	1203	ENSP00000373884:L1203F;ENSP00000399610:L1203F	ENSP00000354735:L1203F	L	+	1	0	RYR3	31723854	1.000000	0.71417	0.987000	0.45799	0.940000	0.58332	3.923000	0.56469	2.826000	0.97356	0.655000	0.94253	CTC		0.517	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33936562	C	T	33936562	3	4	87	1	0	0	0	0	1	0	0	0	13807	913	32	3	3717	3	RYR3	15	33936562	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	7989463	33936562	68594830	89	24258										
SPG21	51324	hgsc.bcm.edu	37	chr15	65262514	65262514	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caccgggccagatgaaaaatTtccaagaactatttttttga	7	8	0	4			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr15:65262514T>G	ENST00000204566.2	-	6	794	c.499A>C	c.(499-501)Aat>Cat	p.N167H	SPG21_ENST00000416889.2_Missense_Mutation_p.N140H|SPG21_ENST00000559199.1_Missense_Mutation_p.N13H|SPG21_ENST00000433215.2_Missense_Mutation_p.N167H	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	167					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GATGAAAAATTTCCAAGAACT	0.398																																																0			15											175	193	187					15																	65262514		2202	4299	6501	63049567	SO:0001583	missense	51324			AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.499A>C	15.37:g.65262514T>G	ENSP00000204566:p.Asn167His		63049567	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	37	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.264905	0.80358	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T;T	0.67171	-0.25;-0.25;-0.25	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.79387	0.4437	M	0.71206	2.165	0.80722	D	1	D;P	0.89917	1.0;0.951	D;P	0.74348	0.983;0.63	T	0.76069	-0.3094	10	0.21014	T	0.42	-15.5812	15.3687	0.74545	0.0:0.0:0.0:1.0	.	140;167	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	H	167;140;167	ENSP00000204566:N167H;ENSP00000394846:N140H;ENSP00000404111:N167H	ENSP00000204566:N167H	N	-	1	0	SPG21	63049567	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.015000	0.88690	2.311000	0.77944	0.533000	0.62120	AAT		0.398	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		G	65262514	T	G	65262514	3	3	87	1	0	0	0	0	1	0	0	0	15082	1841	64	4	443	4	SPG21	15	65262514	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	31325952	65262514	37268878	90	24259										
PRSS27	83886	hgsc.bcm.edu	37	chr16	2763552	2763552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgcaggcatccttcttgcccTcctcgaagccggcgcacagc	10	17	1	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:2763552T>C	ENST00000302641.3	-	5	710	c.656A>G	c.(655-657)gAg>gGg	p.E219G	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						CTTCTTGCCCTCCTCGAAGCC	0.592																																																0			16											228	164	186					16																	2763552		2198	4300	6498	2703553	SO:0001583	missense	83886			AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"Serine peptidases / Serine peptidases"	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.656A>G	16.37:g.2763552T>C	ENSP00000306390:p.Glu219Gly		2703553		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.358492	0.24598	.	.	ENSG00000172382	ENST00000302641;ENST00000543965	T	0.81163	-1.46	5.26	5.26	0.73747	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.53938	D	0.000046	T	0.73713	0.3622	L	0.35723	1.085	0.38950	D	0.958337	B;B	0.25809	0.071;0.135	B;B	0.27887	0.047;0.084	T	0.74520	-0.3638	10	0.62326	D	0.03	.	13.1214	0.59329	0.0:0.0:0.0:1.0	.	219;183	Q9BQR3;B3KP25	PRS27_HUMAN;.	G	219;183	ENSP00000306390:E219G	ENSP00000306390:E219G	E	-	2	0	PRSS27	2703553	1.000000	0.71417	0.995000	0.50966	0.139000	0.21198	3.749000	0.55150	1.991000	0.58162	0.363000	0.22086	GAG		0.592	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948		C	2763552	T	C	2763552	3	2	87	1	0	0	0	0	1	0	0	0	12655	1551	54	4	224	4	PRSS27	16	2763552	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10		2763552	87591201	91	24260										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3789726	3789726	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tttccccagaatccacaaacCtgaaacaaaagccagagccg	6	14	0	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:3789726C>T	ENST00000262367.5	-	25	4943		c.e25-1		CREBBP_ENST00000382070.3_Splice_Site	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein						cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ATCCACAAACCTGAAACAAAA	0.483			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											57	56	56					16																	3789726		2197	4300	6497	3729727	SO:0001630	splice_region_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4134-1G>A	16.37:g.3789726C>T			3729727	D3DUC9|O00147|Q16376|Q4LE28	Splice_Site	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564514	0.86439	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8419	0.96692	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CREBBP	3729727	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.713000	0.84693	2.767000	0.95098	0.561000	0.74099	.		0.483	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	Intron	T	3789726	C	T	3789726	5	4	87	1	0	0	0	0	0	0	1	0	3867	695	24	3	3223	3	CREBBP	16	3789726	Splice_Site	SNP	C	TCGA-CI-6620-01A-11D-1826-10	1026174	3789726	86565027	92	24261										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30991490	30991490	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agcggggctgactggctcaaCgacactcactgggtccatca	12	13	3	1	rs368388561		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:30991490C>T	ENST00000262519.8	+	14	5069	c.4383C>T	c.(4381-4383)aaC>aaT	p.N1461N		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1461	Interaction with ASH2L, RBBP5 and WDR5.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ACTGGCTCAACGACACTCACT	0.617																																																0			16						C		1,4393	2.1+/-5.4	0,1,2196	39	43	42		4383	-6.5	0.1	16		42	0,8600		0,0,4300	no	coding-synonymous	SETD1A	NM_014712.1		0,1,6496	TT,TC,CC		0.0,0.0228,0.0077		1461/1708	30991490	1,12993	2197	4300	6497	30898991	SO:0001819	synonymous_variant	9739			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.4383C>T	16.37:g.30991490C>T			30898991	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																				0.617	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		T	30991490	C	T	30991490	2	4	87	1	0	0	0	0	0	0	0	1	14167	535	19	1		1	SETD1A	16	30991490	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	27201764	30991490	59363263	93	24262										
GPT2	84706	hgsc.bcm.edu	37	chr16	46958408	46958408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cccttgcagggggccatgtaCgccttccctcggatcttcat	10	15	2	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:46958408C>T	ENST00000340124.4	+	10	1432	c.1320C>T	c.(1318-1320)taC>taT	p.Y440Y	GPT2_ENST00000440783.2_Silent_p.Y340Y	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2	440					2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|Phenelzine(DB00780)	GGGCCATGTACGCCTTCCCTC	0.562																																																0			16											103	98	100					16																	46958408		2203	4300	6503	45515909	SO:0001819	synonymous_variant	84706				CCDS10725.1, CCDS45478.1	16q12.1	2008-02-05			ENSG00000166123	ENSG00000166123	2.6.1.2		18062	protein-coding gene	gene with protein product		138210					Standard	NM_133443		Approved	ALT2	uc002eel.3	Q8TD30	OTTHUMG00000132541	ENST00000340124.4:c.1320C>T	16.37:g.46958408C>T			45515909	Q8N9E2	Silent	SNP	ENST00000340124.4	37	CCDS10725.1																																																																																				0.562	GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2			T	46958408	C	T	46958408	2	4	87	1	0	0	0	0	0	0	0	1	6759	547	19	1		1	GPT2	16	46958408	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	15966918	46958408	43396345	94	24263										
CDH5	1003	hgsc.bcm.edu	37	chr16	66434779	66434779	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caatgggatgccaagtcgcaCgggcaccagcacgctgaccg	13	14	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:66434779C>T	ENST00000341529.3	+	11	1845	c.1697C>T	c.(1696-1698)aCg>aTg	p.T566M	CDH5_ENST00000539168.1_Missense_Mutation_p.T5M	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	566	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	CCAAGTCGCACGGGCACCAGC	0.602																																																0			16											108	88	95					16																	66434779		2201	4300	6501	64992280	SO:0001583	missense	1003			X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"CD molecules", "Cadherins / Major cadherins"	1764	protein-coding gene	gene with protein product	"VE-cadherin"	601120	"cadherin 5, type 2, VE-cadherin (vascular epithelium)"			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1697C>T	16.37:g.66434779C>T	ENSP00000344115:p.Thr566Met		64992280	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017710	0.35606	.	.	ENSG00000179776	ENST00000341529;ENST00000379531;ENST00000539262;ENST00000539168	T;T	0.75477	0.56;-0.94	5.06	5.06	0.68205	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.87124	0.6099	M	0.87097	2.86	0.34762	D	0.732888	D	0.89917	1.0	D	0.81914	0.995	D	0.92262	0.5818	9	0.87932	D	0	.	13.5108	0.61511	0.0:0.7205:0.2795:0.0	.	566	P33151	CADH5_HUMAN	M	566;451;307;5	ENSP00000344115:T566M;ENSP00000461880:T5M	ENSP00000344115:T566M	T	+	2	0	CDH5	64992280	0.870000	0.30015	0.872000	0.34217	0.002000	0.02628	1.387000	0.34430	2.348000	0.79779	0.555000	0.69702	ACG		0.602	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		T	66434779	C	T	66434779	3	4	87	1	0	0	0	0	1	0	0	0	3119	536	19	1	1735	1	CDH5	16	66434779	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	19476371	66434779	23919974	95	24264										
CRISPLD2	83716	hgsc.bcm.edu	37	chr16	84883102	84883103	+	Frame_Shift_Ins	INS	-	-	T													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cagagaggtgctcggggcccINSatgtgcacgcactacacaca					rs8061351	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr16:84883102_84883103insT	ENST00000262424.5	+	4	695_696	c.471_472insT	c.(472-474)atgfs	p.M158fs	CRISPLD2_ENST00000566431.1_3'UTR|CRISPLD2_ENST00000567845.1_Frame_Shift_Ins_p.M158fs|CRISPLD2_ENST00000564567.1_Frame_Shift_Ins_p.M158fs	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	158	SCP.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						GCTCGGGGCCCATGTGCACGCA	0.619																																																0			16																																								83440604	SO:0001589	frameshift_variant	83716			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"LCCL domain containing cysteine-rich secretory protein 2"	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	Exception_encountered	16.37:g.84883102_84883103insT	ENSP00000262424:p.Met158fs		83440603	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Frame_Shift_Ins	INS	ENST00000262424.5	37	CCDS10949.1																																																																																				0.619	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		T	84883103	-	T	84883102	7	5	87	1	0	1	1	0	0	0	0	0	3889	581	21	0	481	0	CRISPLD2	16	84883102	Frame_Shift_Ins	INS	-	TCGA-CI-6620-01A-11D-1826-10	18448323	84883102	5471651	96	24265										
TP53	7157	hgsc.bcm.edu	37	chr17	7577582	7577583	+	Frame_Shift_Ins	INS	-	-	TGGA													0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgttacacatgtagttgtagINStggatggtggtacagtcaga							TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:7577582_7577583insTGGA	ENST00000269305.4	-	7	887_888	c.698_699insTCCA	c.(697-699)cacfs	p.-233fs	TP53_ENST00000359597.4_Frame_Shift_Ins_p.-233fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.-233fs|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(5)|p.H233fs*6(3)|p.H233L(2)|p.H233Q(2)|p.T230fs*6(2)|p.C229_H233delCTTIH(2)|p.H233R(1)|p.I232_Y236delIHYNY(1)|p.Y234fs*2(1)|p.H233del(1)|p.T230_Y234delTTIHY(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.I232fs*5(1)|p.H233_C242del10(1)|p.H233P(1)|p.Y234fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGTAGTTGTAGTGGATGGTGGT	0.564		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	35	Deletion - Frameshift(9)|Whole gene deletion(8)|Deletion - In frame(6)|Substitution - Missense(6)|Unknown(5)|Insertion - Frameshift(1)	upper_aerodigestive_tract(5)|biliary_tract(5)|breast(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|stomach(2)|central_nervous_system(2)|lung(2)|oesophagus(2)|ovary(2)|pleura(1)|salivary_gland(1)|urinary_tract(1)|liver(1)	17																																								7518308	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.695_698dupTCCA	17.37:g.7577583_7577586dupTGGA	ENSP00000269305:p.His233fs		7518307	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.564	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		TGGA	7577583	-	TGGA	7577582	7	5	87	1	0	1	1	0	0	0	0	0	16421	1020	36	0	591	0	TP53	17	7577582	Frame_Shift_Ins	INS	-	TCGA-CI-6620-01A-11D-1826-10		7577582	73617628	97	24266										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67270117	67270117	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	caccagcagaattttgaagaAgcagacttgttttgtattta	8	6	0	4			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:67270117A>G	ENST00000392676.3	-	20	2811	c.2747T>C	c.(2746-2748)cTt>cCt	p.L916P	ABCA5_ENST00000392677.2_Missense_Mutation_p.L916P|ABCA5_ENST00000588877.1_Missense_Mutation_p.L916P			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	916					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	ATTTTGAAGAAGCAGACTTGT	0.403																																																0			17											111	111	111					17																	67270117		2203	4300	6503	64781712	SO:0001583	missense	23461			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2747T>C	17.37:g.67270117A>G	ENSP00000376443:p.Leu916Pro		64781712	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106958	0.77096	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.90261	-2.64;-2.25	5.53	5.53	0.82687	.	0.113240	0.39759	N	0.001264	D	0.95408	0.8509	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95504	0.8580	9	.	.	.	.	15.6048	0.76658	1.0:0.0:0.0:0.0	.	916;916	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	P	916	ENSP00000376444:L916P;ENSP00000376443:L916P	.	L	-	2	0	ABCA5	64781712	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.583000	0.74053	2.222000	0.72286	0.477000	0.44152	CTT		0.403	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		G	67270117	A	G	67270117	3	3	87	1	0	0	0	0	1	0	0	0	35	72	3	4	2261	4	ABCA5	17	67270117	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	59692535	67270117	13925093	98	24267										
DNAH17	9489	hgsc.bcm.edu	37	chr17	76420232	76420232	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agtctgggtgtcccagcgagCccctgcagggacagtatggc	15	12	1	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:76420232C>T	ENST00000262764.6	+	0	1798				DNAH17_ENST00000586052.1_5'UTR|PGS1_ENST00000588281.1_3'UTR|DNAH17_ENST00000585328.1_Missense_Mutation_p.A4377T|AC061992.1_ENST00000600087.1_5'Flank|DNAH17_ENST00000389840.5_Missense_Mutation_p.A4405T	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TCCCAGCGAGCCCCTGCAGGG	0.637																																					Esophageal Squamous(45;182 1126 10685 43198)											0			17											26	28	27					17																	76420232		2203	4299	6502	73931827	SO:0001624	3_prime_UTR_variant	8632				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.*101C>T	17.37:g.76420232C>T			73931827	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.624165	0.87560	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.16073	2.37	5.23	5.23	0.72850	.	0.215793	0.32343	N	0.006225	T	0.62060	0.2397	H	0.98559	4.265	0.51012	D	0.9999	D	0.89917	1.0	D	0.91635	0.999	T	0.78309	-0.2254	10	0.87932	D	0	.	19.0108	0.92872	0.0:1.0:0.0:0.0	.	4377	E7EUM8	.	T	4377;4405	ENSP00000374490:A4405T	ENSP00000300671:A4377T	A	-	1	0	DNAH17	73931827	0.999000	0.42202	0.996000	0.52242	0.671000	0.39405	4.153000	0.58118	2.713000	0.92767	0.655000	0.94253	GCT		0.637	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		T	76420232	C	T	76420232	1	4	87	0	1	0	0	0	0	0	0	0	4612	739	26	3		3	DNAH17	17	76420232	3'UTR	SNP	C	TCGA-CI-6620-01A-11D-1826-10	9150115	76420232	4774978	99	24268										
DUS1L	64118	hgsc.bcm.edu	37	chr17	80019497	80019497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcctgggccctgcccacctgCgctcatgacgccctgcacac	9	20	1	1	rs114350519		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr17:80019497C>T	ENST00000354321.7	-	6	1179	c.694G>A	c.(694-696)Gca>Aca	p.A232T	DUS1L_ENST00000306796.5_Missense_Mutation_p.A232T			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	232							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	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)			TGCCCACCTGCGCTCATGACG	0.677													.|||	1	0.000199681	0	0	5008	,	,		7250	0.001		0	False		,,,				2504	0															0			17											66	61	62					17																	80019497		2203	4300	6503	77612786	SO:0001583	missense	64118				CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.694G>A	17.37:g.80019497C>T	ENSP00000346280:p.Ala232Thr		77612786	A6NHV4|Q96AI3	Missense_Mutation	SNP	ENST00000354321.7	37	CCDS32775.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.103184	0.56183	.	.	ENSG00000169718	ENST00000354321;ENST00000306796;ENST00000542088;ENST00000538833	T;T;T	0.29655	1.56;1.56;1.56	4.26	4.26	0.50523	Aldolase-type TIM barrel (1);	0.108387	0.64402	D	0.000007	T	0.71937	0.3399	H	0.98333	4.205	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.997	D	0.85254	0.1046	10	0.87932	D	0	.	16.9981	0.86373	0.0:1.0:0.0:0.0	.	105;232;101	B4DPG7;Q6P1R4;Q9BTJ3	.;DUS1L_HUMAN;.	T	232;232;105;100	ENSP00000346280:A232T;ENSP00000303515:A232T;ENSP00000445110:A100T	ENSP00000303515:A232T	A	-	1	0	DUS1L	77612786	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	7.290000	0.78711	2.069000	0.61940	0.563000	0.77884	GCA		0.677	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156		T	80019497	C	T	80019497	3	4	87	1	0	0	0	0	1	0	0	0	4816	768	27	1	759	1	DUS1L	17	80019497	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	3599265	80019497	1175713	100	24269										
TWSG1	57045	hgsc.bcm.edu	37	chr18	9396379	9396379	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctctcttccgggcactcacaGaaggagatactcagttgaat	9	11	3	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr18:9396379G>C	ENST00000262120.5	+	4	516	c.325G>C	c.(325-327)Gaa>Caa	p.E109Q	TWSG1_ENST00000581641.1_Missense_Mutation_p.E109Q	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	109					BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						GGCACTCACAGAAGGAGATAC	0.428																																																0			18											116	110	112					18																	9396379		2203	4300	6503	9386379	SO:0001583	missense	57045			AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"twisted gastrulation homolog 1 (Drosophila)"			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.325G>C	18.37:g.9396379G>C	ENSP00000262120:p.Glu109Gln		9386379	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	37	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.557750	0.65425	.	.	ENSG00000128791	ENST00000262120	.	.	.	5.33	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	M	0.68952	2.095	0.58432	D	0.999999	B	0.26002	0.139	B	0.24541	0.054	T	0.62412	-0.6860	9	0.72032	D	0.01	-19.7869	13.3428	0.60555	0.0771:0.0:0.9229:0.0	.	109	Q9GZX9	TWSG1_HUMAN	Q	109	.	ENSP00000262120:E109Q	E	+	1	0	TWSG1	9386379	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	7.821000	0.86641	1.232000	0.43678	0.561000	0.74099	GAA		0.428	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2			C	9396379	G	C	9396379	3	2	87	1	0	0	0	0	1	0	0	0	16825	943	33	5	335	5	TWSG1	18	9396379	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10		9396379	68680869	101	24270										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11096909	11096909	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctgagcatgcctctagtccaGttccagccagtggcccgtct	10	15	2	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:11096909G>A	ENST00000429416.3	+	5	681	c.400G>A	c.(400-402)Gtt>Att	p.V134I	SMARCA4_ENST00000413806.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000344626.4_Missense_Mutation_p.V134I|SMARCA4_ENST00000590574.1_Missense_Mutation_p.V134I|SMARCA4_ENST00000358026.2_Missense_Mutation_p.V134I|SMARCA4_ENST00000589677.1_Missense_Mutation_p.V134I|SMARCA4_ENST00000444061.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000450717.3_Missense_Mutation_p.V134I|SMARCA4_ENST00000541122.2_Missense_Mutation_p.V134I	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	134	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTCTAGTCCAGTTCCAGCCAG	0.632			"F, N, Mis"		NSCLC																																		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	1	Unknown(1)	lung(1)	19											42	44	43					19																	11096909		2203	4300	6503	10957909	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.400G>A	19.37:g.11096909G>A	ENSP00000395654:p.Val134Ile		10957909	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	6.020	0.372017	0.11409	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86627	-2.14;-2.15;-2.14;-2.13;-2.13;-2.13;-2.13	4.44	3.4	0.38934	.	0.000000	0.64402	D	0.000001	D	0.84365	0.5456	N	0.24115	0.695	0.34269	D	0.680781	B;B;B;P;B;B;B	0.44690	0.02;0.02;0.02;0.841;0.02;0.02;0.02	B;B;B;P;B;B;B	0.55824	0.018;0.011;0.011;0.785;0.018;0.018;0.018	D	0.83565	0.0109	10	0.16896	T	0.51	-16.0935	11.369	0.49690	0.09:0.0:0.91:0.0	.	134;134;134;134;134;134;134	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	I	134	ENSP00000395654:V134I;ENSP00000350720:V134I;ENSP00000343896:V134I;ENSP00000445036:V134I;ENSP00000392837:V134I;ENSP00000397783:V134I;ENSP00000414727:V134I	ENSP00000343896:V134I	V	+	1	0	SMARCA4	10957909	0.995000	0.38212	0.963000	0.40424	0.002000	0.02628	2.282000	0.43461	1.100000	0.41517	-0.373000	0.07131	GTT		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11096909	G	A	11096909	3	1	87	1	0	0	0	0	1	0	0	0	14807	1029	36	3	410	3	SMARCA4	19	11096909	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10		11096909	48032074	102	24271										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155167	22155167	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ctttgccacattcttcacatTtgtagggtttctctccagta	6	11	3	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:22155167T>A	ENST00000397126.4	-	4	2817	c.2669A>T	c.(2668-2670)aAa>aTa	p.K890I	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	890					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTCTTCACATTTGTAGGGTTT	0.388																																																0			19											44	47	46					19																	22155167		2074	4229	6303	21947007	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2669A>T	19.37:g.22155167T>A	ENSP00000380315:p.Lys890Ile		21947007		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.744421	0.30865	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.20881	2.04	2.58	-1.91	0.07641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35451	0.0932	.	.	.	0.09310	N	1	D	0.64830	0.994	D	0.91635	0.999	T	0.25882	-1.0119	8	0.62326	D	0.03	.	2.7988	0.05409	0.1885:0.2494:0.0:0.5621	.	790	O43345	ZN208_HUMAN	I	890;790	ENSP00000380315:K890I	ENSP00000380315:K890I	K	-	2	0	ZNF208	21947007	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-1.260000	0.02858	-1.490000	0.01842	-0.804000	0.03201	AAA		0.388	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22155167	T	A	22155167	3	1	87	1	0	0	0	0	1	0	0	0	17805	1841	64	5	1177	5	ZNF208	19	22155167	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	11058258	22155167	36973816	103	24272										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22271739	22271739	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	acataagagaattcatactaGagagaaggcctacaaatgtg	9	6	1	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:22271739G>C	ENST00000594947.1	+	4	1331	c.1187G>C	c.(1186-1188)aGa>aCa	p.R396T		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATTCATACTAGAGAGAAGGCC	0.363																																																0			19											43	49	47					19																	22271739		2103	4244	6347	22063579	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.1187G>C	19.37:g.22271739G>C	ENSP00000470209:p.Arg396Thr		22063579	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	4.470	0.087172	0.08583	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	1.11	0.20524	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36386	0.0965	L	0.37750	1.13	0.24261	N	0.995283	B	0.13594	0.008	B	0.08055	0.003	T	0.36212	-0.9757	8	0.87932	D	0	.	9.0461	0.36347	0.0:0.0:1.0:0.0	.	396	Q9Y2Q1	ZN257_HUMAN	T	396;368	.	ENSP00000380312:R368T	R	+	2	0	ZNF257	22063579	0.023000	0.18921	0.288000	0.24862	0.339000	0.28857	2.047000	0.41269	0.518000	0.28383	0.313000	0.20887	AGA		0.363	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			C	22271739	G	C	22271739	3	2	87	1	0	0	0	0	1	0	0	0	17839	942	33	5	1201	5	ZNF257	19	22271739	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	116572	22271739	36857244	104	24273										
ZNF461	92283	hgsc.bcm.edu	37	chr19	37129789	37129789	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ccagtatgaattctttgatgTtgaataaggtgtgaatgaag	11	3	1	5			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:37129789T>C	ENST00000588268.1	-	6	1685	c.1458A>G	c.(1456-1458)caA>caG	p.Q486Q	ZNF461_ENST00000360357.4_Silent_p.Q463Q|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	486					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TTCTTTGATGTTGAATAAGGT	0.388																																																0			19											70	74	73					19																	37129789		2201	4299	6500	41821629	SO:0001819	synonymous_variant	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.1458A>G	19.37:g.37129789T>C			41821629	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	37	CCDS54257.1																																																																																				0.388	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		C	37129789	T	C	37129789	2	2	87	1	0	0	0	0	0	0	0	1	17964	1722	60	4		4	ZNF461	19	37129789	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	14858050	37129789	21999194	105	24274										
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39965265	39965265	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggcatcgagcagaactccagCgactgggtaaccactgacat	11	12	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:39965265C>T	ENST00000599117.1	+	29	3298	c.2931C>T	c.(2929-2931)agC>agT	p.S977S	SUPT5H_ENST00000598725.1_Silent_p.S977S|SUPT5H_ENST00000359191.6_Silent_p.S973S|SUPT5H_ENST00000432763.2_Silent_p.S977S|SUPT5H_ENST00000402194.2_Silent_p.S973S			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	977					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGAACTCCAGCGACTGGGTAA	0.607																																																0			19											74	61	65					19																	39965265		2203	4300	6503	44657105	SO:0001819	synonymous_variant	6829			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2931C>T	19.37:g.39965265C>T			44657105	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																				0.607	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		T	39965265	C	T	39965265	2	4	87	1	0	0	0	0	0	0	0	1	15438	767	27	1		1	SUPT5H	19	39965265	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	2835476	39965265	19163718	106	24275										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644067	53644067	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	acctccagtatgaactctccGatgtcttgcaaggtgtgaat	9	10	2	2	rs138912076	byFrequency	TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:53644067G>A	ENST00000334197.7	-	5	2082	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W	ZNF347_ENST00000601469.2_Missense_Mutation_p.R673W|ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000452676.2_Missense_Mutation_p.R673W	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	672					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGAACTCTCCGATGTCTTGCA	0.423																																					Melanoma(64;205 1597 17324 45721)											0			19											164	148	154					19																	53644067		2203	4300	6503	58335879	SO:0001583	missense	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2014C>T	19.37:g.53644067G>A	ENSP00000334146:p.Arg672Trp		58335879	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	9.937	1.216547	0.22373	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07688	3.17;3.17	2.94	0.565	0.17309	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19644	0.0472	M	0.63208	1.945	0.22811	N	0.998705	D;B	0.76494	0.999;0.009	P;B	0.59948	0.866;0.008	T	0.07868	-1.0750	9	0.87932	D	0	.	9.9088	0.41392	0.0:0.0:0.6326:0.3674	.	673;672	G5E9N4;Q96SE7	.;ZN347_HUMAN	W	672;673	ENSP00000334146:R672W;ENSP00000405218:R673W	ENSP00000334146:R672W	R	-	1	2	ZNF347	58335879	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-2.901000	0.00704	0.087000	0.17167	0.655000	0.94253	CGG		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53644067	G	A	53644067	3	1	87	1	0	0	0	0	1	0	0	0	17900	1057	37	1	509	1	ZNF347	19	53644067	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	13678802	53644067	5484916	107	24276										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54301646	54301646	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agaccctcacaggcggcagaGcccagccggcagatgcccaa	12	16	1	3			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:54301646G>A	ENST00000324134.6	-	8	2946	c.2778C>T	c.(2776-2778)ggC>ggT	p.G926G	NLRP12_ENST00000345770.5_Silent_p.G927G|NLRP12_ENST00000535162.1_Silent_p.G926G|NLRP12_ENST00000354278.3_Intron|NLRP12_ENST00000391772.1_Intron|NLRP12_ENST00000391773.1_Silent_p.G927G|NLRP12_ENST00000351894.4_Intron|NLRP12_ENST00000391775.3_Intron	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	926					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGGCGGCAGAGCCCAGCCGGC	0.622																																																0			19											36	35	35					19																	54301646		2203	4300	6503	58993458	SO:0001819	synonymous_variant	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2778C>T	19.37:g.54301646G>A			58993458	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																				0.622	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54301646	G	A	54301646	2	1	87	1	0	0	0	0	0	0	0	1	10505	958	34	3		3	NLRP12	19	54301646	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	657579	54301646	4827337	108	24277										
LENG8	114823	hgsc.bcm.edu	37	chr19	54967586	54967586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggaacccgccccctaagggcCggggcggtcgaggggcccat	17	15	0	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:54967586C>T	ENST00000326764.5	+	10	1866	c.1387C>T	c.(1387-1389)Cgg>Tgg	p.R463W	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	426										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCCTAAGGGCCGGGGCGGTCG	0.667																																																0			19											25	31	29					19																	54967586		2201	4295	6496	59659398	SO:0001583	missense	114823			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1387C>T	19.37:g.54967586C>T	ENSP00000318374:p.Arg463Trp		59659398	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592606	0.86953	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.34859	1.38;1.35;1.34	4.52	4.52	0.55395	.	0.247523	0.33382	N	0.004976	T	0.45975	0.1369	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67548	0.952;0.952	T	0.49082	-0.8976	10	0.72032	D	0.01	-8.8628	15.6069	0.76679	0.0:1.0:0.0:0.0	.	463;426	Q96PV6-2;F8W9Q9	.;.	W	463;426;426;463	ENSP00000318374:R463W;ENSP00000365709:R426W;ENSP00000388053:R463W	ENSP00000301196:R426W	R	+	1	2	LENG8	59659398	1.000000	0.71417	0.997000	0.53966	0.905000	0.53344	4.289000	0.59013	2.466000	0.83321	0.555000	0.69702	CGG		0.667	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		T	54967586	C	T	54967586	3	4	87	1	0	0	0	0	1	0	0	0	8746	643	23	1	1421	1	LENG8	19	54967586	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	665940	54967586	4161397	109	24278										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815067	55815067	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agcgtgtggattctcccatgCtgagccgtcacgggaagcgg	15	11	2	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:55815067C>T	ENST00000309383.1	+	12	1436	c.1159C>T	c.(1159-1161)Ctg>Ttg	p.L387L	BRSK1_ENST00000326848.7_Silent_p.L82L|BRSK1_ENST00000590333.1_Silent_p.L403L	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	387					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		TTCTCCCATGCTGAGCCGTCA	0.607																																																0			19											62	72	69					19																	55815067		2203	4300	6503	60506879	SO:0001819	synonymous_variant	84446			AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1159C>T	19.37:g.55815067C>T			60506879	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																				0.607	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		T	55815067	C	T	55815067	2	4	87	1	0	0	0	0	0	0	0	1	1526	796	28	3		3	BRSK1	19	55815067	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	847481	55815067	3313916	110	24279										
ZNF628	89887	hgsc.bcm.edu	37	chr19	55994762	55994762	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gtgcagccccctacacctccGccccctcccgcacctcccaa	5	25	0	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:55994762G>A	ENST00000598519.1	+	3	2755	c.2202G>A	c.(2200-2202)ccG>ccA	p.P734P	NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.P730P|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	734	Pro-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CTACACCTCCGCCCCCTCCCG	0.711																																																0			19											8	7	7					19																	55994762		2071	4125	6196	60686574	SO:0001819	synonymous_variant	89887			AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2202G>A	19.37:g.55994762G>A			60686574	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																				0.711	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		A	55994762	G	A	55994762	2	1	87	1	0	0	0	0	0	0	0	1	18091	1074	38	1		1	ZNF628	19	55994762	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	179695	55994762	3134221	111	24280										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56407363	56407363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ttttcaaagccttacatagcAtcttgacaccatcagtatcc	4	12	3	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr19:56407363A>G	ENST00000342929.3	-	11	3079	c.3080T>C	c.(3079-3081)aTg>aCg	p.M1027T	NLRP13_ENST00000588751.1_Missense_Mutation_p.M1027T	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	1027							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CTTACATAGCATCTTGACACC	0.473																																																0			19											196	183	188					19																	56407363		2203	4300	6503	61099175	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.3080T>C	19.37:g.56407363A>G	ENSP00000343891:p.Met1027Thr		61099175	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.990810	0.00439	.	.	ENSG00000173572	ENST00000342929	T	0.51817	0.69	2.85	-5.69	0.02428	.	.	.	.	.	T	0.25938	0.0632	N	0.16833	0.445	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.13415	-1.0510	9	0.26408	T	0.33	.	9.1146	0.36750	0.7081:0.1102:0.1817:0.0	.	1027	Q86W25	NAL13_HUMAN	T	1027	ENSP00000343891:M1027T	ENSP00000343891:M1027T	M	-	2	0	NLRP13	61099175	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.581000	0.05820	-3.136000	0.00234	-1.317000	0.01298	ATG		0.473	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		G	56407363	A	G	56407363	3	3	87	1	0	0	0	0	1	0	0	0	10506	217	8	4	53	4	NLRP13	19	56407363	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10	412601	56407363	2721620	112	24281										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33328653	33328653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gcttcgccggttgccagaggAccctggactattggtcaaaa	12	11	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:33328653A>G	ENST00000374796.2	-	12	7977	c.5407T>C	c.(5407-5409)Tcc>Ccc	p.S1803P	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1803P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1803	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TTGCCAGAGGACCCTGGACTA	0.488																																																0			20											79	78	78					20																	33328653		2203	4300	6503	32792314	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5407T>C	20.37:g.33328653A>G	ENSP00000363929:p.Ser1803Pro		32792314	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211721	0.58452	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25085	1.82;1.82	5.65	5.65	0.86999	.	0.280434	0.31531	N	0.007485	T	0.14657	0.0354	N	0.12182	0.205	0.31858	N	0.621315	P	0.44090	0.826	B	0.41860	0.368	T	0.08146	-1.0736	10	0.25751	T	0.34	-7.4797	9.077	0.36527	0.8369:0.0:0.0:0.1631	.	1803	Q14686	NCOA6_HUMAN	P	1803	ENSP00000363929:S1803P;ENSP00000351894:S1803P	ENSP00000351894:S1803P	S	-	1	0	NCOA6	32792314	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.196000	0.51020	2.371000	0.80710	0.533000	0.62120	TCC		0.488	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		G	33328653	A	G	33328653	3	3	87	1	0	0	0	0	1	0	0	0	10264	275	10	4	804	4	NCOA6	20	33328653	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10		33328653	29696867	113	24282										
RBM12	10137	hgsc.bcm.edu	37	chr20	34242050	34242050	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	aggagggggatgagtttgtcCagaaggtcccatattttgct	14	6	0	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:34242050C>A	ENST00000374114.3	-	3	1458	c.1195G>T	c.(1195-1197)Gga>Tga	p.G399*	RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397446.1_Intron|RBM12_ENST00000374104.3_Nonsense_Mutation_p.G399*|RBM12_ENST00000359646.1_Nonsense_Mutation_p.G399*	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	399						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGAGTTTGTCCAGAAGGTCCC	0.488											OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			20											137	134	135					20																	34242050		2203	4300	6503	33705464	SO:0001587	stop_gained	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1195G>T	20.37:g.34242050C>A	ENSP00000363228:p.Gly399*	846	33705464	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Nonsense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	C	35	5.495324	0.96355	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	.	.	.	4.77	3.83	0.44106	.	0.503823	0.18724	N	0.132929	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-5.8808	13.2267	0.59919	0.0:0.9236:0.0:0.0764	.	.	.	.	X	399;399;399;198	.	ENSP00000339879:G198X	G	-	1	0	RBM12	33705464	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.609000	0.54117	1.251000	0.43983	0.549000	0.68633	GGA		0.488	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		A	34242050	C	A	34242050	4	1	87	1	0	0	0	0	0	1	0	0	13150	603	21	2	1607	2	RBM12	20	34242050	Nonsense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10	913397	34242050	28783470	114	24283										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61461027	61461027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggcccctctggagagccaggCgtccctgtgagtatctgcgg	15	13	2	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:61461027C>T	ENST00000343916.3	+	21	1104	c.1101C>T	c.(1099-1101)ggC>ggT	p.G367G		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	367	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GAGAGCCAGGCGTCCCTGTGA	0.662																																																0			20											29	37	34					20																	61461027		2193	4292	6485	60931472	SO:0001819	synonymous_variant	1299			AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1101C>T	20.37:g.61461027C>T			60931472	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																				0.662	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61461027	C	T	61461027	2	4	87	1	0	0	0	0	0	0	0	1	3715	755	27	1		1	COL9A3	20	61461027	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10	27218977	61461027	1564493	115	24284										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62076010	62076010	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cagccttggggccgtgactcAccttgctgtgggcatagacc	13	13	1	2			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr20:62076010A>G	ENST00000359125.2	-	4	865		c.e4+1		KCNQ2_ENST00000344462.4_Splice_Site|KCNQ2_ENST00000354587.3_Splice_Site|KCNQ2_ENST00000344425.5_Splice_Site|KCNQ2_ENST00000360480.3_Splice_Site|KCNQ2_ENST00000357249.2_Splice_Site|KCNQ2_ENST00000370224.1_Splice_Site|KCNQ2_ENST00000359689.1_Splice_Site	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2						axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCCGTGACTCACCTTGCTGTG	0.687																																																0			20											14	15	15					20																	62076010		2194	4283	6477	61546454	SO:0001630	splice_region_variant	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.690+1T>C	20.37:g.62076010A>G			61546454	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Splice_Site	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284296	0.59867	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222;ENST00000370221;ENST00000344425	.	.	.	3.89	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0255	0.58812	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KCNQ2	61546454	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	6.093000	0.71422	1.544000	0.49359	0.477000	0.44152	.		0.687	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	Intron	G	62076010	A	G	62076010	5	3	87	1	0	0	0	0	0	0	1	0	8104	173	6	4	2046	4	KCNQ2	20	62076010	Splice_Site	SNP	A	TCGA-CI-6620-01A-11D-1826-10	614983	62076010	949510	116	24285										
GABPA	2551	hgsc.bcm.edu	37	chr21	27124543	27124543	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agaacgccttgggataccctAtggtaataaaatgcataatt	8	7	0	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr21:27124543A>G	ENST00000354828.3	+	5	1078	c.551A>G	c.(550-552)tAt>tGt	p.Y184C	GABPA_ENST00000487266.1_3'UTR|GABPA_ENST00000400075.3_Missense_Mutation_p.Y184C	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	184	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						GGGATACCCTATGGTAATAAA	0.368																																																0			21											44	44	44					21																	27124543		2203	4299	6502	26046414	SO:0001583	missense	2551				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"human nuclear respiratory factor-2 subunit alpha", "nuclear respiratory factor 2 alpha subunit"	600609	"GA-binding protein transcription factor, alpha subunit (60kD)"			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.551A>G	21.37:g.27124543A>G	ENSP00000346886:p.Tyr184Cys		26046414	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.187081	0.57909	.	.	ENSG00000154727	ENST00000354828;ENST00000400075	T;T	0.29917	1.55;1.55	4.84	3.66	0.41972	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.187799	0.47852	D	0.000208	T	0.42131	0.1189	L	0.44542	1.39	0.80722	D	1	D	0.64830	0.994	D	0.63033	0.91	T	0.23619	-1.0183	10	0.56958	D	0.05	.	10.8759	0.46911	0.8587:0.0:0.0:0.1413	.	184	Q06546	GABPA_HUMAN	C	184	ENSP00000346886:Y184C;ENSP00000382948:Y184C	ENSP00000346886:Y184C	Y	+	2	0	GABPA	26046414	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.585000	0.90802	0.946000	0.37632	-0.333000	0.08304	TAT		0.368	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040		G	27124543	A	G	27124543	3	3	87	1	0	0	0	0	1	0	0	0	6176	449	16	4	565	4	GABPA	21	27124543	Missense_Mutation	SNP	A	TCGA-CI-6620-01A-11D-1826-10		27124543	21005352	117	24286										
TTC38	55020	hgsc.bcm.edu	37	chr22	46677512	46677512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gtaggctttatctattaaccCgacagacgcatggtcggtgc	11	10	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chr22:46677512C>T	ENST00000381031.3	+	7	708	c.632C>T	c.(631-633)cCg>cTg	p.P211L	TTC38_ENST00000445282.2_Missense_Mutation_p.P153L	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	211						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						TCTATTAACCCGACAGACGCA	0.562																																																0			22											112	112	112					22																	46677512		2000	4182	6182	45056176	SO:0001583	missense	55020				CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.632C>T	22.37:g.46677512C>T	ENSP00000370419:p.Pro211Leu		45056176	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.121353	0.77436	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.78246	0.67;-1.16	5.79	4.72	0.59763	Tetratricopeptide-like helical (1);	0.158344	0.64402	D	0.000020	T	0.81039	0.4740	M	0.68593	2.085	0.53005	D	0.999961	D;D	0.65815	0.995;0.995	P;P	0.55087	0.768;0.768	T	0.80890	-0.1180	10	0.51188	T	0.08	-9.3532	8.7618	0.34678	0.3362:0.5357:0.1281:0.0	.	153;211	E7ES35;Q5R3I4	.;TTC38_HUMAN	L	211;153	ENSP00000370419:P211L;ENSP00000393960:P153L	ENSP00000370419:P211L	P	+	2	0	TTC38	45056176	0.237000	0.23815	0.221000	0.23827	0.301000	0.27625	0.717000	0.25851	2.733000	0.93635	0.655000	0.94253	CCG		0.562	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		T	46677512	C	T	46677512	3	4	87	1	0	0	0	0	1	0	0	0	16746	652	23	1	658	1	TTC38	22	46677512	Missense_Mutation	SNP	C	TCGA-CI-6620-01A-11D-1826-10		46677512	4627054	118	24287										
CLCN4	1183	hgsc.bcm.edu	37	chrX	10182007	10182007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	gacagcatgactgtcgaggaCgtggagacgctcatcaagga	14	9	2	2	rs36049237		TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:10182007C>T	ENST00000380833.4	+	11	2254	c.1863C>T	c.(1861-1863)gaC>gaT	p.D621D	CLCN4_ENST00000421085.2_Silent_p.D527D|CLCN4_ENST00000380829.1_Silent_p.D590D|AC003666.1_ENST00000410201.1_RNA	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	621	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGTCGAGGACGTGGAGACGC	0.627													C|||	1	0.000264901	8e-04	0	3775	,	,		12410	0		0	False		,,,				2504	0				Melanoma(74;1050 1296 1576 30544 38374)											0			X						C		1,3834		0,0,1,1632,570	37	30	32		1863	-5.5	0.7	X	dbSNP_126	32	2,6726		0,2,0,2426,1872	no	coding-synonymous	CLCN4	NM_001830.3		0,2,1,4058,2442	TT,TC,T,CC,C		0.0297,0.0261,0.0284		621/761	10182007	3,10560	2203	4300	6503	10142007	SO:0001819	synonymous_variant	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1863C>T	X.37:g.10182007C>T			10142007	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																				0.627	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			T	10182007	C	T	10182007	2	4	87	1	0	0	0	0	0	0	0	1	3471	535	19	1		1	CLCN4	23	10182007	Silent	SNP	C	TCGA-CI-6620-01A-11D-1826-10		10182007	145088553	119	24288										
SAT1	6303	hgsc.bcm.edu	37	chrX	23803819	23803819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ataggttgcaatgaggtgtcGctgcagcagcatgcacttct	12	9	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:23803819G>A	ENST00000379270.4	+	6	541	c.362G>A	c.(361-363)cGc>cAc	p.R121H	SAT1_ENST00000379254.1_Missense_Mutation_p.R93H|RP13-314C10.5_ENST00000366134.2_RNA|SAT1_ENST00000489394.1_3'UTR	NM_002970.2	NP_002961.1	Q9H2B4	S26A1_HUMAN	spermidine/spermine N1-acetyltransferase 1	0					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			breast(1)|endometrium(3)|kidney(3)|lung(3)	10						ATGAGGTGTCGCTGCAGCAGC	0.418																																																0			X											117	110	113					X																	23803819		2203	4300	6503	23713740	SO:0001583	missense	81539			M55580	CCDS14207.1	Xp22.1	2011-11-16	2006-08-24	2006-08-24	ENSG00000130066	ENSG00000130066	2.3.1.57		10540	protein-coding gene	gene with protein product	"diamine N-acetyltransferase 1"	313020	"spermidine/spermine N1-acetyltransferase"	SAT		1985966, 1417826	Standard	NM_002970		Approved	SSAT	uc004dau.3	P21673	OTTHUMG00000021256	ENST00000379270.4:c.362G>A	X.37:g.23803819G>A	ENSP00000368572:p.Arg121His		23713740	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000379270.4	37	CCDS14207.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.031733	0.35797	.	.	ENSG00000130066	ENST00000379270;ENST00000379254	T;T	0.42131	0.98;0.98	5.62	5.62	0.85841	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	.	.	.	.	T	0.35098	0.0920	N	0.25332	0.735	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.06570	-1.0819	9	0.46703	T	0.11	.	18.6745	0.91524	0.0:0.0:1.0:0.0	.	121	P21673	SAT1_HUMAN	H	121;93	ENSP00000368572:R121H;ENSP00000368556:R93H	ENSP00000368556:R93H	R	+	2	0	SAT1	23713740	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	9.476000	0.97823	2.354000	0.79902	0.594000	0.82650	CGC		0.418	SAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056056.1	NM_002970		A	23803819	G	A	23803819	3	1	87	1	0	0	0	0	1	0	0	0	13888	1087	38	1	384	1	SAT1	23	23803819	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	13621812	23803819	131466741	120	24289										
RPGR	6103	hgsc.bcm.edu	37	chrX	38147244	38147244	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tcatattcatcactatcatcGttttcagtaagagctgtatc	5	9	5	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:38147244G>A	ENST00000339363.3	-	14	1790	c.1623C>T	c.(1621-1623)aaC>aaT	p.N541N	RPGR_ENST00000342811.3_Silent_p.N541N|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Silent_p.N541N|RPGR_ENST00000338898.3_3'UTR|RPGR_ENST00000309513.3_Silent_p.N479N|RPGR_ENST00000378505.2_Silent_p.N541N			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	541	Glu-rich.				cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CACTATCATCGTTTTCAGTAA	0.358																																																0			X											226	180	196					X																	38147244		2202	4300	6502	38032188	SO:0001819	synonymous_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1623C>T	X.37:g.38147244G>A			38032188	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																					0.358	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		A	38147244	G	A	38147244	2	1	87	1	0	0	0	0	0	0	0	1	13585	1136	40	1		1	RPGR	23	38147244	Silent	SNP	G	TCGA-CI-6620-01A-11D-1826-10	14343425	38147244	117123316	121	24290										
ZNF41	7592	hgsc.bcm.edu	37	chrX	47308221	47308221	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	cctgtataaacacttggatgTacatcaacctggggtttctg	9	9	2	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:47308221T>C	ENST00000377065.4	-	5	1587	c.948A>G	c.(946-948)gtA>gtG	p.V316V	ZNF41_ENST00000313116.7_Silent_p.V316V|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000397050.2_Silent_p.V326V	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				CACTTGGATGTACATCAACCT	0.398																																																0			X											71	69	69					X																	47308221		2203	4298	6501	47193165	SO:0001819	synonymous_variant	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.948A>G	X.37:g.47308221T>C			47193165	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Silent	SNP	ENST00000377065.4	37	CCDS14279.1																																																																																				0.398	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		C	47308221	T	C	47308221	2	2	87	1	0	0	0	0	0	0	0	1	17928	1625	57	4		4	ZNF41	23	47308221	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	9160977	47308221	107962339	122	24291										
HEPH	9843	hgsc.bcm.edu	37	chrX	65418745	65418745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	ggtggataaagaattctttcTtctcttcactgtgttggatg	10	6	4	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:65418745T>C	ENST00000343002.2	+	10	2403	c.1739T>C	c.(1738-1740)cTt>cCt	p.L580P	HEPH_ENST00000374727.3_Missense_Mutation_p.L583P|HEPH_ENST00000519389.1_Missense_Mutation_p.L634P|HEPH_ENST00000419594.1_Intron|HEPH_ENST00000336279.5_Missense_Mutation_p.L313P|HEPH_ENST00000441993.2_Missense_Mutation_p.L583P			Q9BQS7	HEPH_HUMAN	hephaestin	580	Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						GAATTCTTTCTTCTCTTCACT	0.433																																																0			X											147	126	133					X																	65418745		2203	4300	6503	65335470	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.1739T>C	X.37:g.65418745T>C	ENSP00000343939:p.Leu580Pro		65335470	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	t	17.49	3.401585	0.62288	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000343002;ENST00000425114	D;D;D;D;D;D	0.99129	-5.46;-5.46;-5.46;-5.46;-5.46;-5.46	4.43	4.43	0.53597	Cupredoxin (2);	0.000000	0.64402	D	0.000001	D	0.99302	0.9756	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99194	1.0871	10	0.87932	D	0	.	11.7993	0.52118	0.0:0.0:0.0:1.0	.	634;580	E9PHN8;Q9BQS7	.;HEPH_HUMAN	P	634;583;313;583;580;537	ENSP00000430620:L634P;ENSP00000363859:L583P;ENSP00000337418:L313P;ENSP00000411687:L583P;ENSP00000343939:L580P;ENSP00000398078:L537P	ENSP00000337418:L313P	L	+	2	0	HEPH	65335470	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	6.695000	0.74593	1.455000	0.47813	0.225000	0.17782	CTT		0.433	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		C	65418745	T	C	65418745	3	2	87	1	0	0	0	0	1	0	0	0	7075	1609	56	4	1943	4	HEPH	23	65418745	Missense_Mutation	SNP	T	TCGA-CI-6620-01A-11D-1826-10	18110524	65418745	89851815	123	24292										
NOX1	27035	hgsc.bcm.edu	37	chrX	100117757	100117757	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	agggagccatctgtggcctgTcggcttctgctatagcagtc	13	11	2	0			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:100117757T>C	ENST00000372966.3	-	5	595	c.390A>G	c.(388-390)cgA>cgG	p.R130R	NOX1_ENST00000372960.4_Silent_p.R93R|NOX1_ENST00000372964.1_Silent_p.R130R|NOX1_ENST00000217885.5_Silent_p.R130R	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	130	Ferric oxidoreductase.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						CTGTGGCCTGTCGGCTTCTGC	0.463																																																0			X											143	143	143					X																	100117757		2203	4299	6502	100004413	SO:0001819	synonymous_variant	27035			AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.390A>G	X.37:g.100117757T>C			100004413	A8K836|O95691|Q2PP02	Silent	SNP	ENST00000372966.3	37	CCDS14474.1																																																																																				0.463	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		C	100117757	T	C	100117757	2	2	87	1	0	0	0	0	0	0	0	1	10587	1654	58	4		4	NOX1	23	100117757	Silent	SNP	T	TCGA-CI-6620-01A-11D-1826-10	34699012	100117757	55152803	124	24293										
THOC2	57187	hgsc.bcm.edu	37	chrX	122772837	122772837	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tatttcaatgaatctactacAggtgttattaagttatcata	5	5	3	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:122772837A>T	ENST00000245838.8	-	17	1819	c.1788T>A	c.(1786-1788)ccT>ccA	p.P596P	THOC2_ENST00000491737.1_Silent_p.P481P|THOC2_ENST00000355725.4_Silent_p.P596P	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	596					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AATCTACTACAGGTGTTATTA	0.328																																																0			X											203	192	195					X																	122772837		1851	4087	5938	122600518	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1788T>A	X.37:g.122772837A>T			122600518	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				0.328	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			T	122772837	A	T	122772837	2	4	87	1	0	0	0	0	0	0	0	1	15904	175	7	5		5	THOC2	23	122772837	Silent	SNP	A	TCGA-CI-6620-01A-11D-1826-10	22655080	122772837	32497723	125	24294										
RBMX	27316	hgsc.bcm.edu	37	chrX	135956396	135956396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.50052303860523	4.58812785388128	0.264699683877766	1	1	0	tgaactgctgtaggaatcacGtggaggagggtacccccttt	13	9	1	1			TCGA-CI-6620-01A-11D-1826-10	TCGA-CI-6620-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	66011422-7627-4ec0-8c3a-bb1c46ac07a3	26e3b09a-9026-4d15-b54a-cc15db6d632f	g.chrX:135956396G>A	ENST00000320676.7	-	9	1235	c.1081C>T	c.(1081-1083)Cgt>Tgt	p.R361C	RBMX_ENST00000565438.1_Missense_Mutation_p.R233C|RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000570135.1_Missense_Mutation_p.R226C|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	361	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TAGGAATCACGTGGAGGAGGG	0.557																																																0			X											69	67	67					X																	135956396		2203	4300	6503	135784062	SO:0001583	missense	27316				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"RNA binding motif (RRM) containing"	9910	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G"	300199	"RNA binding motif protein, X chromosome"			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1081C>T	X.37:g.135956396G>A	ENSP00000359645:p.Arg361Cys		135784062	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	13.29	2.193159	0.38707	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.80566	-1.39	5.66	5.66	0.87406	.	0.000000	0.64402	U	0.000001	D	0.86678	0.5990	L	0.42245	1.32	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.87823	0.2639	10	0.87932	D	0	.	18.7648	0.91868	0.0:0.0:1.0:0.0	.	361	P38159	HNRPG_HUMAN	C	361;348	ENSP00000359645:R361C	ENSP00000359645:R361C	R	-	1	0	RBMX	135784062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.953000	0.63624	2.377000	0.81083	0.596000	0.82720	CGT		0.557	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139		A	135956396	G	A	135956396	3	1	87	1	0	0	0	0	1	0	0	0	13188	1145	40	1	153	1	RBMX	23	135956396	Missense_Mutation	SNP	G	TCGA-CI-6620-01A-11D-1826-10	13183559	135956396	19314164	126	24295										
DHDDS	79947	hgsc.bcm.edu	37	chr1	26774084	26774084	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tctgttttgcatacacatccCgtcatgagatcagcaatgct	7	11	3	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:26774084C>A	ENST00000236342.7	+	6	568	c.475C>A	c.(475-477)Cgt>Agt	p.R159S	DHDDS_ENST00000526219.1_Missense_Mutation_p.R120S|DHDDS_ENST00000360009.2_Missense_Mutation_p.R159S|DHDDS_ENST00000427245.2_Missense_Mutation_p.R159S|DHDDS_ENST00000374185.3_Missense_Mutation_p.R159S|DHDDS_ENST00000525682.2_Intron			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	159					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-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;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		ATACACATCCCGTCATGAGAT	0.473																																																0			1											153	138	143					1																	26774084		2203	4300	6503	26646671	SO:0001583	missense	79947			AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682			20603	protein-coding gene	gene with protein product		608172				12591616	Standard	NM_024887		Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000236342.7:c.475C>A	1.37:g.26774084C>A	ENSP00000236342:p.Arg159Ser		26646671	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	Missense_Mutation	SNP	ENST00000236342.7	37	CCDS282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.506800|4.506800	0.85282|0.85282	.|.	.|.	ENSG00000117682|ENSG00000117682	ENST00000416052|ENST00000374190;ENST00000374192;ENST00000427245;ENST00000236342;ENST00000526219;ENST00000374185;ENST00000360009;ENST00000533087;ENST00000436153;ENST00000430232	.|T;T;T;T;T;T;T	.|0.80909	.|-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.93|5.93	4.99|4.99	0.66335|0.66335	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91385|0.91385	0.7282|0.7282	M|M	0.93106|0.93106	3.38|3.38	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.973;0.966	.|D;D;P	.|0.91635	.|0.999;0.942;0.904	D|D	0.92603|0.92603	0.6093|0.6093	5|10	.|0.87932	.|D	.|0	-16.3942|-16.3942	13.3793|13.3793	0.60759|0.60759	0.321:0.679:0.0:0.0|0.321:0.679:0.0:0.0	.|.	.|120;159;159	.|Q86SQ9-3;Q86SQ9;Q86SQ9-2	.|.;DHDDS_HUMAN;.	Q|S	35|127;55;159;159;120;159;159;159;159;120	.|ENSP00000399177:R159S;ENSP00000236342:R159S;ENSP00000434219:R120S;ENSP00000363300:R159S;ENSP00000353104:R159S;ENSP00000436119:R159S;ENSP00000397584:R120S	.|ENSP00000236342:R159S	P|R	+|+	2|1	0|0	DHDDS|DHDDS	26646671|26646671	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	4.375000|4.375000	0.59549|0.59549	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	CCG|CGT		0.473	DHDDS-011	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392504.1	NM_024887		A	26774084	C	A	26774084	3	1	88	1	0	0	0	0	1	0	0	0	4489	652	23	2	493	2	DHDDS	1	26774084	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		26774084	222476537	1	24296										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32119210	32119210	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tatttcctacctggggggccGggaagaccattttctcctgc	11	12	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:32119210G>A	ENST00000373672.3	-	70	5118	c.4602C>T	c.(4600-4602)ccC>ccT	p.P1534P	COL16A1_ENST00000461217.1_5'UTR|RP11-73M7.6_ENST00000609549.1_RNA|RP11-73M7.6_ENST00000609338.1_RNA|RP11-73M7.6_ENST00000585660.1_RNA|RP11-73M7.6_ENST00000593188.1_RNA|RP11-73M7.6_ENST00000610216.1_RNA|RP11-73M7.6_ENST00000609625.1_RNA|RP11-73M7.6_ENST00000610043.1_RNA|RP11-73M7.6_ENST00000609033.1_RNA|COL16A1_ENST00000271069.6_Silent_p.P1534P|RP11-73M7.6_ENST00000607926.1_RNA|RP11-73M7.6_ENST00000609373.1_RNA|RP11-73M7.6_ENST00000591592.1_RNA|RP11-73M7.6_ENST00000608332.1_RNA|RP11-73M7.6_ENST00000591929.1_RNA|RP11-73M7.6_ENST00000587445.1_RNA|RP11-73M7.6_ENST00000589462.1_RNA|RP11-73M7.6_ENST00000585413.1_RNA|RP11-73M7.6_ENST00000608888.1_RNA|RP11-73M7.6_ENST00000608246.1_RNA|RP11-73M7.6_ENST00000445166.1_RNA	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1534	Collagen-like 8.|Triple-helical region 1 (COL1) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CTGGGGGGCCGGGAAGACCAT	0.453																																					Colon(143;498 1786 21362 25193 36625)											0			1											60	61	61					1																	32119210		1886	4108	5994	31891797	SO:0001819	synonymous_variant	1307			M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.4602C>T	1.37:g.32119210G>A			31891797	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																				0.453	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32119210	G	A	32119210	2	1	88	1	0	0	0	0	0	0	0	1	3679	1103	39	1		1	COL16A1	1	32119210	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	5345126	32119210	217131411	2	24297										
LHX8	431707	hgsc.bcm.edu	37	chr1	75602913	75602913	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aagtgtgtgtgcaacagttgCggcctggagatcgtggacaa	15	7	0	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:75602913C>T	ENST00000294638.5	+	4	898	c.234C>T	c.(232-234)tgC>tgT	p.C78C	LHX8_ENST00000356261.3_Silent_p.C68C|LHX8_ENST00000559413.1_3'UTR	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	78	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						GCAACAGTTGCGGCCTGGAGA	0.657																																																0			1											34	35	35					1																	75602913		2203	4300	6503	75375501	SO:0001819	synonymous_variant	431707			AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.234C>T	1.37:g.75602913C>T			75375501	E9PGE3	Silent	SNP	ENST00000294638.5	37	CCDS30756.1																																																																																				0.657	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		T	75602913	C	T	75602913	2	4	88	1	0	0	0	0	0	0	0	1	8799	776	27	1		1	LHX8	1	75602913	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	43483703	75602913	173647708	3	24298										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77510110	77510110	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aaccgccatgacctgctcaaCgtgagccagggcaccgtgtt	11	14	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:77510110C>T	ENST00000477717.1	+	3	718	c.483C>T	c.(481-483)aaC>aaT	p.N161N		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	161					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						ACCTGCTCAACGTGAGCCAGG	0.637																																																0			1											70	61	64					1																	77510110		2203	4300	6503	77282698	SO:0001819	synonymous_variant	81849				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.483C>T	1.37:g.77510110C>T			77282698	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																				0.637	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		T	77510110	C	T	77510110	2	4	88	1	0	0	0	0	0	0	0	1	15266	535	19	1		1	ST6GALNAC5	1	77510110	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	1907197	77510110	171740511	4	24299										
SASS6	163786	hgsc.bcm.edu	37	chr1	100573009	100573009	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtaatttttcctccttctcaGccaagagtttttcttgctga	6	10	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:100573009G>C	ENST00000287482.5	-	11	1387	c.1247C>G	c.(1246-1248)gCt>gGt	p.A416G	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.A249G	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	416					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		CTCCTTCTCAGCCAAGAGTTT	0.313																																																0			1											75	73	74					1																	100573009		2201	4292	6493	100345597	SO:0001583	missense	163786			AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1247C>G	1.37:g.100573009G>C	ENSP00000287482:p.Ala416Gly		100345597	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	37	CCDS764.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274833	0.23307	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.29655	1.56;1.56	5.49	5.49	0.81192	.	0.241662	0.43919	D	0.000501	T	0.11836	0.0288	L	0.28740	0.885	0.35069	D	0.762337	B	0.26041	0.14	B	0.25614	0.062	T	0.08106	-1.0738	10	0.21540	T	0.41	-15.521	14.9117	0.70761	0.0:0.1429:0.8571:0.0	.	416	Q6UVJ0	SAS6_HUMAN	G	416;389;249	ENSP00000287482:A416G;ENSP00000440169:A249G	ENSP00000287482:A416G	A	-	2	0	SASS6	100345597	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.281000	0.72632	2.573000	0.86826	0.585000	0.79938	GCT		0.313	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		C	100573009	G	C	100573009	3	2	88	1	0	0	0	0	1	0	0	0	13887	971	34	5	754	5	SASS6	1	100573009	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	23062899	100573009	148677612	5	24300										
HRNR	388697	hgsc.bcm.edu	37	chr1	152191578	152191578	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccctgacgtagatccatgtcGtccctggctagagaagtgac	11	12	0	4	rs141263661	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:152191578G>A	ENST00000368801.2	-	3	2602	c.2527C>T	c.(2527-2529)Cga>Tga	p.R843*	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	843					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GATCCATGTCGTCCCTGGCTA	0.552													G|||	5	0.000998403	8e-04	0	5008	,	,		21457	0.004		0	False		,,,				2504	0															0			1						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	137	136	137		2527	-3.4	0	1	dbSNP_134	137	0,8600		0,0,4300	yes	stop-gained	HRNR	NM_001009931.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		843/2851	152191578	1,13005	2203	4300	6503	150458202	SO:0001587	stop_gained	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2527C>T	1.37:g.152191578G>A	ENSP00000357791:p.Arg843*		150458202	Q5DT20|Q5U1F4	Nonsense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	34	5.384617	0.95967	2.27E-4	0.0	ENSG00000197915	ENST00000368801	.	.	.	3.33	-3.39	0.04868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	1.9825	0.03429	0.1146:0.1579:0.2486:0.479	.	.	.	.	X	843	.	ENSP00000357791:R843X	R	-	1	2	HRNR	150458202	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.228000	0.09114	-0.210000	0.10140	0.456000	0.33151	CGA		0.552	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152191578	G	A	152191578	4	1	88	1	0	0	0	0	0	1	0	0	7380	1153	40	1	6029	1	HRNR	1	152191578	Nonsense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	51618569	152191578	97059043	6	24301										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158651358	158651358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gatgtcagcacactcctgtaCatactgctggaacttcaggg	10	11	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:158651358C>T	ENST00000368147.4	-	4	670	c.490G>A	c.(490-492)Gta>Ata	p.V164I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	164					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.V164L(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CACTCCTGTACATACTGCTGG	0.552																																																1	Substitution - Missense(1)	ovary(1)	1											228	230	230					1																	158651358		2035	4195	6230	156917982	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.490G>A	1.37:g.158651358C>T	ENSP00000357129:p.Val164Ile		156917982	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	4.094	0.015492	0.07959	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.50277	0.75;0.75	5.15	-1.04	0.10068	.	.	.	.	.	T	0.06690	0.0171	N	0.11131	0.1	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.31806	-0.9930	9	0.22109	T	0.4	.	0.3116	0.00288	0.3859:0.1378:0.2203:0.256	.	164	P02549	SPTA1_HUMAN	I	164	ENSP00000357130:V164I;ENSP00000357129:V164I	ENSP00000357129:V164I	V	-	1	0	SPTA1	156917982	1.000000	0.71417	0.005000	0.12908	0.017000	0.09413	2.307000	0.43682	-0.358000	0.08162	-2.746000	0.00125	GTA		0.552	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158651358	C	T	158651358	3	4	88	1	0	0	0	0	1	0	0	0	15155	478	17	3	6965	3	SPTA1	1	158651358	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	6459780	158651358	90599263	7	24302										
DNM3	26052	hgsc.bcm.edu	37	chr1	172013550	172013550	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gttcaatgagaaagaattgcGaagagaaataagctatgcaa	10	4	1	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:172013550G>T	ENST00000355305.5	+	9	1311	c.1154G>T	c.(1153-1155)cGa>cTa	p.R385L	DNM3_ENST00000520906.1_Missense_Mutation_p.R385L|DNM3_ENST00000367733.2_Missense_Mutation_p.R385L|DNM3_ENST00000367731.1_Missense_Mutation_p.R385L|DNM3_ENST00000358155.4_Missense_Mutation_p.R385L			Q9UQ16	DYN3_HUMAN	dynamin 3	385					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						AAAGAATTGCGAAGAGAAATA	0.323																																																0			1											57	54	55					1																	172013550		1846	4088	5934	170280173	SO:0001583	missense	26052			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1154G>T	1.37:g.172013550G>T	ENSP00000347457:p.Arg385Leu		170280173	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		.	.	.	.	.	.	.	.	.	.	G	27.0	4.790746	0.90367	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.24	5.24	0.73138	.	0.062171	0.64402	D	0.000004	D	0.83031	0.5166	M	0.72576	2.205	0.80722	D	1	D;P;P;D	0.89917	1.0;0.883;0.941;0.984	D;B;P;P	0.85130	0.997;0.3;0.815;0.846	T	0.82506	-0.0423	10	0.46703	T	0.11	.	17.7539	0.88444	0.0:0.0:1.0:0.0	.	385;385;385;385	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	L	385;385;385;385;385;385;275	ENSP00000350876:R385L;ENSP00000356707:R385L;ENSP00000347457:R385L;ENSP00000356705:R385L;ENSP00000429701:R385L;ENSP00000429416:R275L	ENSP00000347457:R385L	R	+	2	0	DNM3	170280173	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	9.809000	0.99208	2.609000	0.88269	0.655000	0.94253	CGA		0.323	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		T	172013550	G	T	172013550	3	4	88	1	0	0	0	0	1	0	0	0	4684	1058	37	2	1188	2	DNM3	1	172013550	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	13362192	172013550	77237071	8	24303										
ASTN1	460	hgsc.bcm.edu	37	chr1	176845742	176845742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtcgcttggcctggagcgccGtcctgtgttgtccactcccc	12	16	0	0	rs373152514		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:176845742G>A	ENST00000367654.3	-	21	3629	c.3418C>T	c.(3418-3420)Cgg>Tgg	p.R1140W	ASTN1_ENST00000367657.3_Missense_Mutation_p.R1132W|ASTN1_ENST00000361833.2_Missense_Mutation_p.R1132W|ASTN1_ENST00000424564.2_Missense_Mutation_p.R1132W	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1140	Fibronectin type-III 1.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.R1132W(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CTGGAGCGCCGTCCTGTGTTG	0.577													G|||	1	0.000199681	0	0	5008	,	,		18580	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	prostate(1)	1						G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	114	88	97		3394,3394	4.2	1	1		97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ASTN1	NM_004319.1,NM_207108.1	101,101	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	1132/1295,1132/1217	176845742	2,13004	2203	4300	6503	175112365	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3418C>T	1.37:g.176845742G>A	ENSP00000356626:p.Arg1140Trp		175112365	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	G	23.6	4.441505	0.83993	2.27E-4	1.16E-4	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.17213	2.29;2.71;2.71;2.29	5.19	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.34366	0.0895	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.04017	-1.0984	10	0.87932	D	0	-17.3769	11.0346	0.47793	0.0:0.0:0.6384:0.3616	.	1132;1132	O14525-2;B1AJS1	.;.	W	1132;1132;1140;1132;1132	ENSP00000356629:R1132W;ENSP00000354536:R1132W;ENSP00000356626:R1140W;ENSP00000395041:R1132W	ENSP00000354536:R1132W	R	-	1	2	ASTN1	175112365	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	5.493000	0.66899	2.400000	0.81607	0.655000	0.94253	CGG		0.577	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176845742	G	A	176845742	3	1	88	1	0	0	0	0	1	0	0	0	1065	1144	40	1	506	1	ASTN1	1	176845742	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	4832192	176845742	72404879	9	24304										
ABL2	27	hgsc.bcm.edu	37	chr1	179084019	179084019	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gcaaaaatactcacatgctcTcataagttcataaaccttag	4	10	3	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:179084019T>C	ENST00000502732.1	-	9	1758	c.1555A>G	c.(1555-1557)Aga>Gga	p.R519G	ABL2_ENST00000507173.1_Missense_Mutation_p.R498G|ABL2_ENST00000511413.1_Missense_Mutation_p.R519G|ABL2_ENST00000367623.4_Missense_Mutation_p.R498G|ABL2_ENST00000344730.3_Missense_Mutation_p.R504G|ABL2_ENST00000392043.3_Missense_Mutation_p.R498G|ABL2_ENST00000408940.3_Missense_Mutation_p.R483G|ABL2_ENST00000512653.1_Missense_Mutation_p.R504G|ABL2_ENST00000504405.1_Missense_Mutation_p.R483G	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	519	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> I (somatic mutation in a lung squamous cell carcinoma). {ECO:0000269|PubMed:17344846}.		actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TCACATGCTCTCATAAGTTCA	0.378			T	ETV6	AML																																		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	0			1											95	98	97					1																	179084019		2203	4300	6503	177350642	SO:0001583	missense	27			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1555A>G	1.37:g.179084019T>C	ENSP00000427562:p.Arg519Gly		177350642	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	37	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.879119	0.72294	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413;ENST00000392043	D;D;D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	5.99	5.99	0.97316	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000021	D	0.87869	0.6286	L	0.61218	1.895	0.80722	D	1	D;D;D;P;P;D;P;P;P	0.65815	0.995;0.968;0.968;0.946;0.599;0.978;0.887;0.94;0.896	P;P;P;P;B;P;B;P;P	0.57371	0.819;0.621;0.621;0.621;0.21;0.711;0.397;0.584;0.468	D	0.88192	0.2878	10	0.52906	T	0.07	.	15.6531	0.77112	0.0:0.0:0.0:1.0	.	498;498;519;483;498;519;504;483;504	P42684-6;P42684-7;P42684-5;P42684-4;P42684-8;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;.;ABL2_HUMAN;.;.;.	G	519;483;504;504;483;498;498;519;498	ENSP00000427562:R519G;ENSP00000386152:R483G;ENSP00000339209:R504G;ENSP00000423578:R504G;ENSP00000426831:R483G;ENSP00000356595:R498G;ENSP00000423413:R498G;ENSP00000424697:R519G;ENSP00000375897:R498G	ENSP00000339209:R504G	R	-	1	2	ABL2	177350642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.001000	0.63946	2.292000	0.77174	0.482000	0.46254	AGA		0.378	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		C	179084019	T	C	179084019	3	2	88	1	0	0	0	0	1	0	0	0	93	1559	54	4	2054	4	ABL2	1	179084019	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	2238277	179084019	70166602	10	24305										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181726197	181726197	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcaatatctttgtggctctcAtcatcatcaccttccaggag	6	12	6	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:181726197A>C	ENST00000367573.2	+	30	4264	c.4264A>C	c.(4264-4266)Atc>Ctc	p.I1422L	CACNA1E_ENST00000367567.4_Missense_Mutation_p.I1029L|CACNA1E_ENST00000367570.1_Missense_Mutation_p.I1422L|CACNA1E_ENST00000358338.5_Missense_Mutation_p.I1354L|CACNA1E_ENST00000526775.1_Missense_Mutation_p.I1403L|CACNA1E_ENST00000357570.5_Missense_Mutation_p.I1373L|CACNA1E_ENST00000360108.3_Missense_Mutation_p.I1403L	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1422					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGTGGCTCTCATCATCATCAC	0.483																																																0			1											150	147	148					1																	181726197		1943	4164	6107	179992820	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4264A>C	1.37:g.181726197A>C	ENSP00000356545:p.Ile1422Leu		179992820	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644393	0.87859	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.99089	-5.41;-5.41;-5.41;-5.41;-5.41;-5.41;-5.41	5.75	4.6	0.57074	Ion transport (1);	0.048732	0.85682	N	0.000000	D	0.98782	0.9590	M	0.68593	2.085	0.80722	D	1	B;P;B	0.40638	0.282;0.725;0.009	P;P;B	0.54706	0.679;0.759;0.013	D	0.98364	1.0550	10	0.52906	T	0.07	.	12.5852	0.56414	0.8611:0.1389:0.0:0.0	.	1403;1422;1422	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	L	1422;1403;1373;1354;1029;1403;1422	ENSP00000356542:I1422L;ENSP00000434814:I1403L;ENSP00000350183:I1373L;ENSP00000351101:I1354L;ENSP00000356539:I1029L;ENSP00000353222:I1403L;ENSP00000356545:I1422L	ENSP00000350183:I1373L	I	+	1	0	CACNA1E	179992820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.210000	0.95106	0.972000	0.38314	0.533000	0.62120	ATC		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181726197	A	C	181726197	3	2	88	1	0	0	0	0	1	0	0	0	2548	217	8	4	4382	4	CACNA1E	1	181726197	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	2642178	181726197	67524424	11	24306										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213403864	213403864	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tacttgtaatggacacaaggAcagaacagactttcatttta	7	7	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:213403864A>T	ENST00000366960.3	+	9	1219	c.1069A>T	c.(1069-1071)Aca>Tca	p.T357S	RPS6KC1_ENST00000543470.1_Missense_Mutation_p.T145S|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.T345S|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.T60S|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	357	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GGACACAAGGACAGAACAGAC	0.343																																																0			1											64	67	66					1																	213403864		2202	4300	6502	211470487	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1069A>T	1.37:g.213403864A>T	ENSP00000355927:p.Thr357Ser		211470487	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.304406	0.81136	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.45	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	M	0.73753	2.245	0.58432	D	0.999995	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.85130	0.997;0.971;0.971	T	0.46596	-0.9180	10	0.46703	T	0.11	-13.3486	11.9727	0.53071	0.8699:0.0:0.0:0.1301	.	145;357;345	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	S	145;357;345;60	ENSP00000442306:T145S;ENSP00000355927:T357S;ENSP00000355926:T345S;ENSP00000439282:T60S	ENSP00000355926:T345S	T	+	1	0	RPS6KC1	211470487	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.960000	0.87893	0.982000	0.38575	0.533000	0.62120	ACA		0.343	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		T	213403864	A	T	213403864	3	4	88	1	0	0	0	0	1	0	0	0	13695	275	10	5	1103	5	RPS6KC1	1	213403864	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	31677667	213403864	35846757	12	24307										
NVL	4931	hgsc.bcm.edu	37	chr1	224499554	224499554	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	catcatcagaatagctttcaGtatacctcagtaaaaggagg	8	8	4	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr1:224499554G>C	ENST00000281701.6	-	5	549	c.290C>G	c.(289-291)aCt>aGt	p.T97S	NVL_ENST00000469075.1_Missense_Mutation_p.T97S|NVL_ENST00000340871.4_Intron|NVL_ENST00000482491.1_Intron|NVL_ENST00000391875.2_5'UTR|NVL_ENST00000468673.1_5'Flank|NVL_ENST00000361463.3_5'UTR	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	97						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ATAGCTTTCAGTATACCTCAG	0.338																																																0			1											147	146	146					1																	224499554		2203	4300	6503	222566177	SO:0001583	missense	4931			U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.290C>G	1.37:g.224499554G>C	ENSP00000281701:p.Thr97Ser		222566177	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	37	CCDS1541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.819|1.819	-0.472673|-0.472673	0.04445|0.04445	.|.	.|.	ENSG00000143748|ENSG00000143748	ENST00000281701;ENST00000469075;ENST00000488718;ENST00000461546|ENST00000469968	D;D;T|.	0.94417|.	-3.42;-3.38;1.6|.	5.67|5.67	3.57|3.57	0.40892|0.40892	.|.	0.306651|.	0.33792|.	N|.	0.004559|.	T|.	0.30262|.	0.0759|.	N|N	0.24115|0.24115	0.695|0.695	0.41498|0.41498	D|D	0.988268|0.988268	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|.	0.18335|.	-1.0340|.	10|.	0.08599|0.02654	T|T	0.76|1	-10.6586|-10.6586	4.0892|4.0892	0.09962|0.09962	0.1317:0.0:0.6348:0.2335|0.1317:0.0:0.6348:0.2335	.|.	97;97|.	B4DP98;O15381|.	.;NVL_HUMAN|.	S|X	97;97;97;131|70	ENSP00000281701:T97S;ENSP00000417826:T97S;ENSP00000418085:T131S|.	ENSP00000281701:T97S|ENSP00000419420:Y70X	T|Y	-|-	2|3	0|2	NVL|NVL	222566177|222566177	0.922000|0.922000	0.31269|0.31269	0.905000|0.905000	0.35620|0.35620	0.342000|0.342000	0.28953|0.28953	0.500000|0.500000	0.22562|0.22562	1.398000|1.398000	0.46701|0.46701	0.655000|0.655000	0.94253|0.94253	ACT|TAC		0.338	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		C	224499554	G	C	224499554	3	2	88	1	0	0	0	0	1	0	0	0	10811	1029	36	5	2356	5	NVL	1	224499554	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	11095690	224499554	24751067	13	24308										
MSH6	2956	hgsc.bcm.edu	37	chr2	48030737	48030738	+	Frame_Shift_Ins	INS	-	-	GA													0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atgacattctaataggctgtINSgaggaagaggagcaggaaaa							TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:48030737_48030738insGA	ENST00000234420.5	+	5	3503_3504	c.3351_3352insGA	c.(3352-3354)gagfs	p.E1118fs	MSH6_ENST00000540021.1_Frame_Shift_Ins_p.E988fs|MSH6_ENST00000538136.1_Frame_Shift_Ins_p.E816fs|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	1118	Poly-Glu.				ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TAATAGGCTGTGAGGAAGAGGA	0.426			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	2																																								47884242	SO:0001589	frameshift_variant	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.3352_3353dupGA	2.37:g.48030738_48030739dupGA	ENSP00000234420:p.Glu1118fs		47884241	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Frame_Shift_Ins	INS	ENST00000234420.5	37	CCDS1836.1																																																																																				0.426	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		GA	48030738	-	GA	48030737	7	5	88	1	0	1	1	0	0	0	0	0	9904	1702	59	0	3369	0	MSH6	2	48030737	Frame_Shift_Ins	INS	-	TCGA-CI-6621-01A-11D-1826-10		48030737	195168636	14	24309										
PAPOLG	64895	hgsc.bcm.edu	37	chr2	61018964	61018964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttgaagcaactcatgtaaagAaaaaacaacttcaccactac	4	10	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:61018964A>G	ENST00000238714.3	+	16	1714	c.1465A>G	c.(1465-1467)Aaa>Gaa	p.K489E		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	489					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			TCATGTAAAGAAAAAACAACT	0.323																																					GBM(183;1497 2932 21839 46797)											0			2											99	98	98					2																	61018964		2203	4300	6503	60872468	SO:0001583	missense	64895			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.1465A>G	2.37:g.61018964A>G	ENSP00000238714:p.Lys489Glu		60872468	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.513805	0.85389	.	.	ENSG00000115421	ENST00000238714;ENST00000378104;ENST00000412217	.	.	.	6.02	6.02	0.97574	Poly(A) polymerase, RNA-binding domain (2);Nucleotidyltransferase, class I, C-terminal-like (1);	0.089217	0.85682	D	0.000000	T	0.60077	0.2241	L	0.48642	1.525	0.49915	D	0.999837	P;D;P	0.55385	0.939;0.971;0.755	P;P;P	0.50934	0.589;0.654;0.61	T	0.64305	-0.6439	9	0.87932	D	0	-5.3497	12.1182	0.53878	0.8569:0.1431:0.0:0.0	.	178;23;489	E9PEP5;Q53T81;Q9BWT3	.;.;PAPOG_HUMAN	E	489;178;157	.	ENSP00000238714:K489E	K	+	1	0	PAPOLG	60872468	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.062000	0.76706	2.311000	0.77944	0.533000	0.62120	AAA		0.323	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		G	61018964	A	G	61018964	3	3	88	1	0	0	0	0	1	0	0	0	11462	247	9	4	1527	4	PAPOLG	2	61018964	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	12988227	61018964	182180409	15	24310										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043808	71043808	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aactgagcctgggtatttgcCgtttccaaactggcattcaa	9	10	1	1	rs370818847		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:71043808C>T	ENST00000272367.2	-	4	781	c.705G>A	c.(703-705)acG>acA	p.T235T	CLEC4F_ENST00000426626.1_Silent_p.T235T	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	235					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GGGTATTTGCCGTTTCCAAAC	0.418																																					Colon(107;10 2157 6841 26035)											0			2						C		0,4406		0,0,2203	75	73	74		705	1.4	0	2		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLEC4F	NM_173535.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		235/590	71043808	1,13005	2203	4300	6503	70897316	SO:0001819	synonymous_variant	165530			AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.705G>A	2.37:g.71043808C>T			70897316	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																				0.418	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		T	71043808	C	T	71043808	2	4	88	1	0	0	0	0	0	0	0	1	3522	639	23	1		1	CLEC4F	2	71043808	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	10024844	71043808	172155565	16	24311										
FAM176A	84141	hgsc.bcm.edu	37	chr2	75720624	75720624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gcaggaacttcttcccgggaCgccgcctgcagtctgtgtgg	14	13	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:75720624C>T	ENST00000233712.1	-	4	634	c.197G>A	c.(196-198)cGt>cAt	p.R66H	EVA1A_ENST00000410010.1_Missense_Mutation_p.R54H|EVA1A_ENST00000410071.1_Missense_Mutation_p.R66H|EVA1A_ENST00000393913.3_Missense_Mutation_p.R66H|EVA1A_ENST00000410113.1_Missense_Mutation_p.R66H|EVA1A_ENST00000490746.1_Intron	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	66					apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											CTTCCCGGGACGCCGCCTGCA	0.607																																																0			2											53	48	50					2																	75720624		2203	4300	6503	75574132	SO:0001583	missense	84141			BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"transmembrane protein 166", "family with sequence similarity 176, member A"	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.197G>A	2.37:g.75720624C>T	ENSP00000233712:p.Arg66His		75574132	D6W5J3|Q9HC41	Missense_Mutation	SNP	ENST00000233712.1	37	CCDS1959.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270728	0.23221	.	.	ENSG00000115363	ENST00000393913;ENST00000233712;ENST00000410113;ENST00000410010;ENST00000410071;ENST00000432649;ENST00000452003	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	4.9	1.8	0.24995	.	0.703036	0.14788	N	0.298393	T	0.30070	0.0753	L	0.42245	1.32	0.26934	N	0.966398	B	0.11235	0.004	B	0.06405	0.002	T	0.18903	-1.0322	10	0.44086	T	0.13	-2.3466	4.5148	0.11930	0.0:0.4849:0.2972:0.218	.	66	Q9H8M9	F176A_HUMAN	H	66;66;66;54;66;66;66	ENSP00000377490:R66H;ENSP00000233712:R66H;ENSP00000386435:R66H;ENSP00000386835:R54H;ENSP00000386930:R66H;ENSP00000398249:R66H;ENSP00000388105:R66H	ENSP00000233712:R66H	R	-	2	0	FAM176A	75574132	0.000000	0.05858	0.026000	0.17262	0.339000	0.28857	0.314000	0.19432	0.686000	0.31488	0.650000	0.86243	CGT		0.607	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181		T	75720624	C	T	75720624	3	4	88	1	0	0	0	0	1	0	0	0	5515	536	19	1	265	1	FAM176A	2	75720624	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	4676816	75720624	167478749	17	24312										
RIF1	55183	hgsc.bcm.edu	37	chr2	152293857	152293857	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ctttgttgcagttggaaaagAtgcccccggtaagagaattt	11	7	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:152293857A>G	ENST00000243326.5	+	12	1958	c.1475A>G	c.(1474-1476)gAt>gGt	p.D492G	RIF1_ENST00000444746.2_Missense_Mutation_p.D492G|RIF1_ENST00000428287.2_Missense_Mutation_p.D492G|RIF1_ENST00000453091.2_Missense_Mutation_p.D492G|RIF1_ENST00000433166.2_3'UTR|RIF1_ENST00000430328.2_Missense_Mutation_p.D492G			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GTTGGAAAAGATGCCCCCGGT	0.393																																																0			2											90	87	88					2																	152293857		2203	4300	6503	152002103	SO:0001583	missense	55791			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.1475A>G	2.37:g.152293857A>G	ENSP00000243326:p.Asp492Gly		152002103	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	14.66	2.602908	0.46423	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.45	4.28	0.50868	.	0.095236	0.64402	D	0.000001	T	0.69468	0.3114	L	0.60455	1.87	0.80722	D	1	D;D	0.58620	0.983;0.979	P;P	0.57548	0.697;0.823	T	0.68800	-0.5313	10	0.44086	T	0.13	-14.2986	11.7057	0.51595	0.8672:0.0:0.0:0.1328	.	492;492	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	G	492	ENSP00000390181:D492G;ENSP00000414615:D492G;ENSP00000415691:D492G;ENSP00000243326:D492G;ENSP00000416123:D492G	ENSP00000243326:D492G	D	+	2	0	RIF1	152002103	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	8.663000	0.91134	0.991000	0.38814	-0.710000	0.03640	GAT		0.393	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			G	152293857	A	G	152293857	3	3	88	1	0	0	0	0	1	0	0	0	13396	333	12	4	1521	4	RIF1	2	152293857	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	76573233	152293857	90905516	18	24313										
GRB14	2888	hgsc.bcm.edu	37	chr2	165476321	165476321	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccggaacatcaagatctttcTtttttctcctacagtaagag	6	10	4	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:165476321T>C	ENST00000263915.3	-	2	738	c.200A>G	c.(199-201)aAg>aGg	p.K67R		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	67					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.K67M(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						AAGATCTTTCTTTTTTCTCCT	0.368																																																1	Substitution - Missense(1)	ovary(1)	2											134	138	137					2																	165476321		2203	4300	6503	165184567	SO:0001583	missense	2888				CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.200A>G	2.37:g.165476321T>C	ENSP00000263915:p.Lys67Arg		165184567	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.147364	0.37923	.	.	ENSG00000115290	ENST00000263915;ENST00000446413;ENST00000424693	T;T;T	0.44482	1.92;1.51;0.92	5.31	2.87	0.33458	.	0.301451	0.28515	N	0.015075	T	0.26919	0.0659	N	0.22421	0.69	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.05683	-1.0870	10	0.66056	D	0.02	-0.5728	7.1349	0.25523	0.1457:0.0:0.1527:0.7016	.	67	Q14449	GRB14_HUMAN	R	67;22;9	ENSP00000263915:K67R;ENSP00000416786:K22R;ENSP00000401702:K9R	ENSP00000263915:K67R	K	-	2	0	GRB14	165184567	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.359000	0.44142	0.305000	0.22832	0.533000	0.62120	AAG		0.368	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			C	165476321	T	C	165476321	3	2	88	1	0	0	0	0	1	0	0	0	6778	1609	56	4	1474	4	GRB14	2	165476321	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	13182464	165476321	77723052	19	24314										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165552243	165552243	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcaacttccatatcaatgttGttatttttggcaacaccttc	4	10	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:165552243G>A	ENST00000392717.2	-	13	1891	c.1887C>T	c.(1885-1887)aaC>aaT	p.N629N	COBLL1_ENST00000375458.2_Silent_p.N553N|COBLL1_ENST00000409184.3_Silent_p.N591N|COBLL1_ENST00000194871.6_Silent_p.N658N|COBLL1_ENST00000342193.4_Silent_p.N591N			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	629						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						TATCAATGTTGTTATTTTTGG	0.348																																																0			2											205	195	198					2																	165552243		2203	4300	6503	165260489	SO:0001819	synonymous_variant	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1887C>T	2.37:g.165552243G>A			165260489	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37																																																																																					0.348	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165552243	G	A	165552243	2	1	88	1	0	0	0	0	0	0	0	1	3660	1368	48	3		3	COBLL1	2	165552243	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	75922	165552243	77647130	20	24315										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168101375	168101375	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgtaaaacaggaggagatccAaggtggggatgttcgtacag	15	5	0	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:168101375A>G	ENST00000409195.1	+	9	3562	c.3473A>G	c.(3472-3474)cAa>cGa	p.Q1158R	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.Q936R|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q1158R|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	983					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.Q1158L(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAGGAGATCCAAGGTGGGGAT	0.393																																																1	Substitution - Missense(1)	ovary(1)	2											86	77	80					2																	168101375		1860	4104	5964	167809621	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3473A>G	2.37:g.168101375A>G	ENSP00000386840:p.Gln1158Arg		167809621	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.892388	0.33442	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03152	4.03;4.03;4.03	5.91	4.73	0.59995	.	0.055308	0.64402	D	0.000001	T	0.06917	0.0176	M	0.70275	2.135	0.46185	D	0.99891	B;B;B	0.25809	0.083;0.135;0.135	B;B;B	0.23852	0.022;0.049;0.049	T	0.05971	-1.0853	10	0.54805	T	0.06	-5.0963	12.2267	0.54463	0.8574:0.1426:0.0:0.0	.	983;983;936	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	R	1158;1158;936	ENSP00000386840:Q1158R;ENSP00000295237:Q1158R;ENSP00000387255:Q936R	ENSP00000295237:Q1158R	Q	+	2	0	XIRP2	167809621	0.956000	0.32656	0.997000	0.53966	0.987000	0.75469	4.083000	0.57643	1.034000	0.39945	0.533000	0.62120	CAA		0.393	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168101375	A	G	168101375	3	3	88	1	0	0	0	0	1	0	0	0	17470	130	5	4	3503	4	XIRP2	2	168101375	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	2549132	168101375	75097998	21	24316										
TTN	7273	hgsc.bcm.edu	37	chr2	179471822	179471822	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	acttgttcttggcaataacaCggaacttatattcttgtccc	6	10	2	0	rs373526624	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:179471822C>T	ENST00000591111.1	-	228	48808	c.48584G>A	c.(48583-48585)cGt>cAt	p.R16195H	TTN_ENST00000359218.5_Missense_Mutation_p.R8896H|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R15268H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R8771H|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R8963H|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R17836H|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16195	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R8771H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGCAATAACACGGAACTTATA	0.413													C|||	7	0.00139776	0.0015	0	5008	,	,		19631	0		0	False		,,,				2504	0.0051															1	Substitution - Missense(1)	stomach(1)	2						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,3797		0,1,1898	195	190	192		26312,45803,26687,26888	5.3	1	2		192	0,8240		0,0,4120	no	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	0,1,6018	TT,TC,CC		0.0,0.0263,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging	8771/26927,15268/33424,8896/27052,8963/27119	179471822	1,12037	1899	4120	6019	179180067	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48584G>A	2.37:g.179471822C>T	ENSP00000465570:p.Arg16195His		179180067	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.37	2.514206	0.44763	2.63E-4	0.0	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	5.35	5.35	0.76521	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84929	0.5581	H	0.97131	3.945	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.90071	0.4163	9	0.87932	D	0	.	19.0709	0.93136	0.0:1.0:0.0:0.0	.	8771;8896;8963;16195	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	15268;8771;8963;8896;8771	ENSP00000343764:R15268H;ENSP00000434586:R8771H;ENSP00000340554:R8963H;ENSP00000352154:R8896H	ENSP00000340554:R8963H	R	-	2	0	TTN	179180067	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.045000	0.71020	2.515000	0.84797	0.561000	0.74099	CGT		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179471822	C	T	179471822	3	4	88	1	0	0	0	0	1	0	0	0	16775	536	19	1	54526	1	TTN	2	179471822	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	11370447	179471822	63727551	22	24317										
TTN	7273	hgsc.bcm.edu	37	chr2	179582394	179582394	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	agatgtctgcaaattagcatCatctttcaaaagaaccccat	5	10	4	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:179582394C>A	ENST00000591111.1	-	85	24480	c.24256G>T	c.(24256-24258)Gat>Tat	p.D8086Y	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D7159Y|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D8403Y			Q8WZ42	TITIN_HUMAN	titin	12275	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D7159H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAATTAGCATCATCTTTCAAA	0.413																																																1	Substitution - Missense(1)	ovary(1)	2											62	61	61					2																	179582394		1879	4100	5979	179290639	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24256G>T	2.37:g.179582394C>A	ENSP00000465570:p.Asp8086Tyr		179290639	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.85	1.468303	0.26335	.	.	ENSG00000155657	ENST00000342992	T	0.33654	1.4	5.73	5.73	0.89815	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56848	0.2013	M	0.81179	2.53	0.80722	D	1	D	0.61697	0.99	P	0.57244	0.816	T	0.61202	-0.7110	9	0.87932	D	0	.	13.9294	0.63986	0.0:0.9215:0.0:0.0785	.	8086	Q8WZ42	TITIN_HUMAN	Y	7159	ENSP00000343764:D7159Y	ENSP00000343764:D7159Y	D	-	1	0	TTN	179290639	0.867000	0.29959	0.986000	0.45419	0.995000	0.86356	3.236000	0.51336	2.854000	0.98071	0.655000	0.94253	GAT		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179582394	C	A	179582394	3	1	88	1	0	0	0	0	1	0	0	0	16775	826	29	2	79426	2	TTN	2	179582394	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	110572	179582394	63616979	23	24318										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189872848	189872849	+	Frame_Shift_Del	DEL	AG	AG	-													0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caccagggcctcgaggtaacAgaggtgaaagaggatctgag					rs546664098		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:189872848_189872849delAG	ENST00000304636.3	+	47	3675_3676	c.3505_3506delAG	c.(3505-3507)agafs	p.R1169fs	COL3A1_ENST00000317840.5_Frame_Shift_Del_p.R866fs	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1169	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TCGAGGTAACAGAGGTGAAAGA	0.446																																																0			2																																								189581094	SO:0001589	frameshift_variant	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.3505_3506delAG	2.37:g.189872850_189872851delAG	ENSP00000304408:p.Arg1169fs		189581093	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Frame_Shift_Del	DEL	ENST00000304636.3	37	CCDS2297.1																																																																																				0.446	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		-	189872849	AG	-	189872848	7	5	88	1	0	1	0	1	0	0	0	0	3694	180	7	0	3691	0	COL3A1	2	189872848	Frame_Shift_Del	DEL	AG	TCGA-CI-6621-01A-11D-1826-10	10290454	189872848	53326525	24	24319										
PMS1	5378	hgsc.bcm.edu	37	chr2	190728639	190728639	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aacctcattatctaatcaacCaaaacttgatgaactccttc	2	12	3	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:190728639C>A	ENST00000441310.2	+	10	2260	c.2027C>A	c.(2026-2028)cCa>cAa	p.P676Q	PMS1_ENST00000409823.3_Missense_Mutation_p.P637Q|PMS1_ENST00000447232.2_Intron|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000432292.3_Missense_Mutation_p.P500Q|PMS1_ENST00000418224.3_Missense_Mutation_p.P500Q	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	676					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)	p.P676L(1)|p.P676R(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TCTAATCAACCAAAACTTGAT	0.333			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																														yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	2	Substitution - Missense(2)	ovary(1)|lung(1)	2											82	88	86					2																	190728639		2203	4300	6503	190436884	SO:0001583	missense	5378				CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.2027C>A	2.37:g.190728639C>A	ENSP00000406490:p.Pro676Gln		190436884	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	37	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	C	8.287	0.816966	0.16607	.	.	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000432292;ENST00000424307;ENST00000452382	T;T;T;T;D;T	0.86030	1.9;1.9;1.9;1.9;-2.06;2.06	5.45	5.45	0.79879	.	0.156057	0.64402	D	0.000020	T	0.74512	0.3726	L	0.39397	1.21	0.36480	D	0.867774	B;B;B;B	0.32245	0.341;0.07;0.361;0.341	B;B;B;B	0.25884	0.064;0.026;0.057;0.064	T	0.72151	-0.4377	10	0.02654	T	1	-14.5228	13.6008	0.62018	0.247:0.753:0.0:0.0	.	676;637;637;676	Q4VAL4;Q5FBZ9;Q5FBZ3;P54277	.;.;.;PMS1_HUMAN	Q	500;676;500;637;500;615;64	ENSP00000406490:P676Q;ENSP00000404492:P500Q;ENSP00000387125:P637Q;ENSP00000398378:P500Q;ENSP00000389938:P615Q;ENSP00000396232:P64Q	ENSP00000376149:P500Q	P	+	2	0	PMS1	190436884	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.343000	0.59348	2.852000	0.98041	0.644000	0.83932	CCA		0.333	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			A	190728639	C	A	190728639	3	1	88	1	0	0	0	0	1	0	0	0	12173	594	21	2	2061	2	PMS1	2	190728639	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	855791	190728639	52470734	25	24320										
CRYGC	1420	hgsc.bcm.edu	37	chr2	208994333	208994333	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gagttgcagcggctgaaataCggctgcaggttggggcagtc	17	8	0	1	rs142890808	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:208994333C>T	ENST00000282141.3	-	2	121	c.84G>A	c.(82-84)ccG>ccA	p.P28P		NM_020989.3	NP_066269.1	P07315	CRGC_HUMAN	crystallin, gamma C	28	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(1)|large_intestine(2)|lung(5)	9				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GGCTGAAATACGGCTGCAGGT	0.572													C|||	2	0.000399361	0	0	5008	,	,		6949	0.001		0.001	False		,,,				2504	0															0			2						C		0,4406		0,0,2203	94	103	100		84	3.1	1	2	dbSNP_134	100	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CRYGC	NM_020989.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		28/175	208994333	4,13002	2203	4300	6503	208702578	SO:0001819	synonymous_variant	1420				CCDS2379.1	2q33.3	2013-02-14			ENSG00000163254	ENSG00000163254			2410	protein-coding gene	gene with protein product		123680		CRYG3			Standard	NM_020989		Approved		uc002vco.4	P07315	OTTHUMG00000132942	ENST00000282141.3:c.84G>A	2.37:g.208994333C>T			208702578	Q53R50	Silent	SNP	ENST00000282141.3	37	CCDS2379.1																																																																																				0.572	CRYGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256474.1	NM_020989		T	208994333	C	T	208994333	2	4	88	1	0	0	0	0	0	0	0	1	3922	523	19	1		1	CRYGC	2	208994333	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	18265694	208994333	34205040	26	24321										
PLCD4	84812	hgsc.bcm.edu	37	chr2	219494262	219494262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ggccctgaagcgggggtgccGctgcgtggaggtggatgtat	20	8	0	1	rs561847468		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:219494262G>A	ENST00000450993.2	+	8	1334	c.995G>A	c.(994-996)cGc>cAc	p.R332H	PLCD4_ENST00000417849.1_Missense_Mutation_p.R332H|PLCD4_ENST00000432688.1_Missense_Mutation_p.R332H	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	332	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CGGGGGTGCCGCTGCGTGGAG	0.582													G|||	1	0.000199681	0	0	5008	,	,		17563	0		0	False		,,,				2504	0.001															0			2											60	66	64					2																	219494262		2039	4181	6220	219202506	SO:0001583	missense	84812			AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"EF-hand domain containing"	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.995G>A	2.37:g.219494262G>A	ENSP00000388631:p.Arg332His		219202506	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	36	5.631575	0.96682	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.81415	-1.49;-1.49;-1.49	5.19	5.19	0.71726	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.85682	D	0.000000	D	0.95316	0.8480	H	0.99890	4.9	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97682	1.0173	10	0.87932	D	0	.	18.5059	0.90897	0.0:0.0:1.0:0.0	.	332	Q9BRC7	PLCD4_HUMAN	H	332	ENSP00000388631:R332H;ENSP00000396942:R332H;ENSP00000396185:R332H	ENSP00000251959:R332H	R	+	2	0	PLCD4	219202506	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.405000	0.97313	2.704000	0.92352	0.561000	0.74099	CGC		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1			A	219494262	G	A	219494262	3	1	88	1	0	0	0	0	1	0	0	0	12064	1087	38	1	1021	1	PLCD4	2	219494262	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	10499929	219494262	23705111	27	24322										
RHBDD1	84236	hgsc.bcm.edu	37	chr2	227778996	227778996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	agaagcacccaggaactatgAcacgtacacagcaggactga	10	11	0	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:227778996A>G	ENST00000341329.3	+	6	1027	c.785A>G	c.(784-786)gAc>gGc	p.D262G	RHBDD1_ENST00000409053.1_Missense_Mutation_p.D96G|RHBDD1_ENST00000493526.1_3'UTR|RHBDD1_ENST00000392062.2_Missense_Mutation_p.D262G	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	262					apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.D262G(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		AGGAACTATGACACGTACACA	0.488																																																1	Substitution - Missense(1)	ovary(1)	2											123	119	121					2																	227778996		2203	4300	6503	227487240	SO:0001583	missense	84236			AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.785A>G	2.37:g.227778996A>G	ENSP00000344779:p.Asp262Gly		227487240	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Missense_Mutation	SNP	ENST00000341329.3	37	CCDS2464.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662232	0.29515	.	.	ENSG00000144468	ENST00000341329;ENST00000392062;ENST00000409053	T;T	0.45668	0.89;0.89	6.06	4.9	0.64082	.	0.326994	0.34676	N	0.003766	T	0.43366	0.1244	L	0.56769	1.78	0.23314	N	0.997922	P;B	0.51351	0.944;0.009	P;B	0.47075	0.536;0.005	T	0.31251	-0.9950	10	0.27082	T	0.32	-11.713	10.4493	0.44513	0.8366:0.1634:0.0:0.0	.	53;262	Q8TEB9-2;Q8TEB9	.;RHBD1_HUMAN	G	262;262;96	ENSP00000344779:D262G;ENSP00000375914:D262G	ENSP00000344779:D262G	D	+	2	0	RHBDD1	227487240	0.761000	0.28439	0.194000	0.23346	0.426000	0.31534	2.084000	0.41625	1.087000	0.41251	0.528000	0.53228	GAC		0.488	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			G	227778996	A	G	227778996	3	3	88	1	0	0	0	0	1	0	0	0	13353	275	10	4	803	4	RHBDD1	2	227778996	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	8284734	227778996	15420377	28	24323										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238249186	238249186	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	actaatttgaagaagacgtcGtttggctcactggcgaaggt	12	7	1	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr2:238249186G>A	ENST00000295550.4	-	38	8825	c.8373C>T	c.(8371-8373)aaC>aaT	p.N2791N	COL6A3_ENST00000353578.4_Silent_p.N2585N|COL6A3_ENST00000347401.3_Silent_p.N2590N|COL6A3_ENST00000409809.1_Silent_p.N2585N|COL6A3_ENST00000346358.4_Silent_p.N2591N|COL6A3_ENST00000472056.1_Silent_p.N2184N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2791	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		AGAAGACGTCGTTTGGCTCAC	0.532																																																0			2											114	100	105					2																	238249186		2203	4300	6503	237913925	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8373C>T	2.37:g.238249186G>A			237913925	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.532	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238249186	G	A	238249186	2	1	88	1	0	0	0	0	0	0	0	1	3707	1136	40	1		1	COL6A3	2	238249186	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	10470190	238249186	4950187	29	24324										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14745919	14745919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cgaaactacaaggcaaagatGccctctcatctaatgttggc	8	11	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr3:14745919G>T	ENST00000253697.3	+	7	1406	c.954G>T	c.(952-954)atG>atT	p.M318I	C3orf20_ENST00000435614.1_Missense_Mutation_p.M196I|C3orf20_ENST00000412910.1_Missense_Mutation_p.M196I|C3orf20_ENST00000495387.1_3'UTR	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	318						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						AGGCAAAGATGCCCTCTCATC	0.512																																																0			3											124	131	128					3																	14745919		2203	4300	6503	14720923	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.954G>T	3.37:g.14745919G>T	ENSP00000253697:p.Met318Ile		14720923	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	G	0.772	-0.765465	0.02996	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08193	3.42;3.12;3.12	4.64	-3.56	0.04626	.	1.408720	0.04393	N	0.362683	T	0.03305	0.0096	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40232	-0.9574	10	0.07644	T	0.81	-0.2902	5.3883	0.16229	0.528:0.0:0.3332:0.1388	.	318	Q8ND61	CC020_HUMAN	I	318;196;196	ENSP00000253697:M318I;ENSP00000402933:M196I;ENSP00000396081:M196I	ENSP00000253697:M318I	M	+	3	0	C3orf20	14720923	0.000000	0.05858	0.001000	0.08648	0.191000	0.23601	-1.450000	0.02390	-1.111000	0.02988	-0.237000	0.12165	ATG		0.512	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14745919	G	T	14745919	3	4	88	1	0	0	0	0	1	0	0	0	2219	1319	46	2	972	2	C3orf20	3	14745919	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		14745919	183276511	30	24325										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38520643	38520643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	agcagtcgtggcagagtgaaCgggagatcttcagcacacct	13	10	2	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr3:38520643C>T	ENST00000352511.4	+	6	1163	c.691C>T	c.(691-693)Cgg>Tgg	p.R231W		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		GCAGAGTGAACGGGAGATCTT	0.592																																																0			3											163	157	159					3																	38520643		2203	4300	6503	38495647	SO:0001583	missense	93			X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.691C>T	3.37:g.38520643C>T	ENSP00000340361:p.Arg231Trp		38495647	Q4VAV0	Missense_Mutation	SNP	ENST00000352511.4	37	CCDS2679.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043424	0.36085	.	.	ENSG00000114739	ENST00000352511	D	0.93547	-3.24	4.61	1.74	0.24563	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.192399	0.42682	N	0.000678	D	0.90518	0.7029	M	0.80422	2.495	0.38355	D	0.944453	B	0.31752	0.338	B	0.18871	0.023	D	0.86130	0.1574	10	0.52906	T	0.07	.	8.2593	0.31775	0.5486:0.3733:0.0:0.0781	.	231	Q13705	AVR2B_HUMAN	W	231	ENSP00000340361:R231W	ENSP00000340361:R231W	R	+	1	2	ACVR2B	38495647	0.586000	0.26782	0.361000	0.25849	0.983000	0.72400	0.485000	0.22324	0.150000	0.19136	0.563000	0.77884	CGG		0.592	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		T	38520643	C	T	38520643	3	4	88	1	0	0	0	0	1	0	0	0	224	527	19	1	713	1	ACVR2B	3	38520643	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	23774724	38520643	159501787	31	24326										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49837196	49837196	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccccacccaccacctcctcaCcagagaccaccggagcaaag	6	21	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr3:49837196C>A	ENST00000412678.2	-	1	58		c.e1+1		CDHR4_ENST00000343366.4_Splice_Site|CDHR4_ENST00000487256.1_Splice_Site	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CACCTCCTCACCAGAGACCAC	0.562																																																0			3											76	85	82					3																	49837196		2076	4229	6305	49812200	SO:0001630	splice_region_variant	0				CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.49+1G>T	3.37:g.49837196C>A			49812200	Q6UXT0	Splice_Site	SNP	ENST00000412678.2	37	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812016	0.70797	.	.	ENSG00000187492	ENST00000412678;ENST00000343366;ENST00000487256	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9804	0.64301	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDHR4	49812200	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.122000	0.41987	2.424000	0.82194	0.655000	0.94253	.		0.562	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	Intron	A	49837196	C	A	49837196	5	1	88	1	0	0	0	0	0	0	1	0	3127	521	18	2	2392	2	CDHR4	3	49837196	Splice_Site	SNP	C	TCGA-CI-6621-01A-11D-1826-10	11316553	49837196	148185234	32	24327										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140265423	140265423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cctggccagtctcaccatccGccctggcaaaatggaaagcc	9	16	1	0	rs202013971		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr3:140265423G>A	ENST00000458420.3	+	10	1764	c.1574G>A	c.(1573-1575)cGc>cAc	p.R525H		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	525					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CTCACCATCCGCCCTGGCAAA	0.498										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											0			3											58	56	56					3																	140265423		2203	4300	6503	141748113	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1574G>A	3.37:g.140265423G>A	ENSP00000402460:p.Arg525His		141748113	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643905	0.87859	.	.	ENSG00000158258	ENST00000458420	T	0.02158	4.42	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);	0.000000	0.85682	D	0.000000	T	0.09862	0.0242	L	0.56199	1.76	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.08249	-1.0731	9	.	.	.	-13.5529	16.2435	0.82429	0.0:0.0:1.0:0.0	.	525	Q9H4D0	CSTN2_HUMAN	H	525	ENSP00000402460:R525H	.	R	+	2	0	CLSTN2	141748113	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.476000	0.97823	2.420000	0.82092	0.455000	0.32223	CGC		0.498	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140265423	G	A	140265423	3	1	88	1	0	0	0	0	1	0	0	0	3568	1087	38	1	1612	1	CLSTN2	3	140265423	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	90428227	140265423	57757007	33	24328										
EVC	2121	hgsc.bcm.edu	37	chr4	5798894	5798894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgcaggagctgcgggaacagCgtgcactggagcaggggtcc	18	10	0	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr4:5798894C>T	ENST00000264956.6	+	14	2216	c.2032C>T	c.(2032-2034)Cgt>Tgt	p.R678C	EVC_ENST00000515113.1_3'UTR|EVC_ENST00000382674.2_Missense_Mutation_p.R678C	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	678					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GCGGGAACAGCGTGCACTGGA	0.672																																																0			4											37	36	36					4																	5798894		2203	4300	6503	5849795	SO:0001583	missense	2121			AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2032C>T	4.37:g.5798894C>T	ENSP00000264956:p.Arg678Cys		5849795		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287739	0.23478	.	.	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.54071	0.59;0.59	5.04	2.95	0.34219	.	0.838124	0.10519	N	0.665193	T	0.35098	0.0920	N	0.14661	0.345	0.09310	N	0.999998	B	0.10296	0.003	B	0.04013	0.001	T	0.20739	-1.0266	10	0.38643	T	0.18	.	10.0359	0.42129	0.0:0.7999:0.0:0.2001	.	678	P57679	EVC_HUMAN	C	678	ENSP00000264956:R678C;ENSP00000372120:R678C	ENSP00000264956:R678C	R	+	1	0	EVC	5849795	0.147000	0.22687	0.497000	0.27552	0.763000	0.43281	1.739000	0.38217	1.135000	0.42183	-0.229000	0.12294	CGT		0.672	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			T	5798894	C	T	5798894	3	4	88	1	0	0	0	0	1	0	0	0	5298	768	27	1	2086	1	EVC	4	5798894	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		5798894	185355382	34	24329										
HSD17B11	51170	hgsc.bcm.edu	37	chr4	88278432	88278432	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tctcaatttctcaacttaccTtgtacttggatttttgatga	5	8	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr4:88278432T>C	ENST00000358290.4	-	5	1009	c.694A>G	c.(694-696)Agt>Ggt	p.S232G	HSD17B11_ENST00000507286.1_Splice_Site_p.S188G|HSD17B11_ENST00000507518.1_5'UTR	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	232					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		TCAACTTACCTTGTACTTGGA	0.378																																																0			4											130	107	115					4																	88278432		2202	4300	6502	88497456	SO:0001630	splice_region_variant	51170			AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	22960	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 2", "short chain dehydrogenase/reductase family 16C, member 2"	612831	"dehydrogenase/reductase (SDR family) member 8"	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.695+1A>G	4.37:g.88278432T>C			88497456	Q96HF6|Q9UKU4	Missense_Mutation	SNP	ENST00000358290.4	37	CCDS3619.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.937985	0.34189	.	.	ENSG00000198189	ENST00000358290;ENST00000507286	D;T	0.89485	-2.52;0.74	5.66	4.47	0.54385	NAD(P)-binding domain (1);	0.405503	0.27362	N	0.019716	T	0.80171	0.4574	N	0.20483	0.58	0.30689	N	0.751498	B	0.24426	0.103	B	0.21360	0.034	T	0.75010	-0.3468	10	0.40728	T	0.16	.	10.7948	0.46453	0.0:0.0755:0.0:0.9245	.	232	Q8NBQ5	DHB11_HUMAN	G	232;188	ENSP00000351035:S232G;ENSP00000423775:S188G	ENSP00000351035:S232G	S	-	1	0	HSD17B11	88497456	1.000000	0.71417	0.725000	0.30721	0.653000	0.38743	3.252000	0.51461	0.961000	0.38030	0.459000	0.35465	AGT		0.378	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	Missense_Mutation	C	88278432	T	C	88278432	5	2	88	1	0	0	0	0	0	0	1	0	7401	1623	56	4	220	4	HSD17B11	4	88278432	Splice_Site	SNP	T	TCGA-CI-6621-01A-11D-1826-10	82479538	88278432	102875844	35	24330										
SGMS2	166929	hgsc.bcm.edu	37	chr4	108831580	108831580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atcttttatttttttgagaaAaatgtacaaggctcaattcc	5	6	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr4:108831580A>G	ENST00000394684.4	+	7	1526	c.969A>G	c.(967-969)aaA>aaG	p.K323K	RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000359079.4_Silent_p.K323K|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000394686.3_Silent_p.K323K	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	323					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.K323N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		TTTTTGAGAAAAATGTACAAG	0.398																																																1	Substitution - Missense(1)	lung(1)	4											73	77	76					4																	108831580		2203	4300	6503	109051029	SO:0001819	synonymous_variant	166929			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.969A>G	4.37:g.108831580A>G			109051029	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	37	CCDS3677.1																																																																																				0.398	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		G	108831580	A	G	108831580	2	3	88	1	0	0	0	0	0	0	0	1	14252	11	1	4		4	SGMS2	4	108831580	Silent	SNP	A	TCGA-CI-6621-01A-11D-1826-10	20553148	108831580	82322696	36	24331										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13792144	13792144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgaagtagtgttcagcattcCctgccagacccgagaaagat	10	10	1	4			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr5:13792144C>T	ENST00000265104.4	-	50	8511	c.8407G>A	c.(8407-8409)Gga>Aga	p.G2803R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2803	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTCAGCATTCCCTGCCAGACC	0.388									Kartagener syndrome																																							0			5											79	75	77					5																	13792144		2203	4300	6503	13845144	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8407G>A	5.37:g.13792144C>T	ENSP00000265104:p.Gly2803Arg		13845144	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	32	5.138101	0.94560	.	.	ENSG00000039139	ENST00000265104	T	0.56103	0.48	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.87026	0.6075	H	0.99906	4.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93183	0.6576	10	0.87932	D	0	.	19.5581	0.95361	0.0:1.0:0.0:0.0	.	2803	Q8TE73	DYH5_HUMAN	R	2803	ENSP00000265104:G2803R	ENSP00000265104:G2803R	G	-	1	0	DNAH5	13845144	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.687000	0.84139	2.702000	0.92279	0.591000	0.81541	GGA		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13792144	C	T	13792144	3	4	88	1	0	0	0	0	1	0	0	0	4615	632	22	3	5587	3	DNAH5	5	13792144	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		13792144	167123116	37	24332										
APC	324	hgsc.bcm.edu	37	chr5	112175348	112175348	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cagccaggcacaaagctgttGaattttcttcaggagcgaaa	10	9	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr5:112175348G>T	ENST00000457016.1	+	16	4437	c.4057G>T	c.(4057-4059)Gaa>Taa	p.E1353*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1353*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1353*			P25054	APC_HUMAN	adenomatous polyposis coli	1353	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1353*(12)|p.E1353fs*19(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAAAGCTGTTGAATTTTCTTC	0.483		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(12)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5	GRCh37	CD972008	APC	D							62	65	64					5																	112175348		2202	4300	6502	112203247	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4057G>T	5.37:g.112175348G>T	ENSP00000413133:p.Glu1353*		112203247	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.431314	0.98808	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.111916	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8759	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1353	.	.	E	+	1	0	APC	112203247	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	5.308000	0.65768	2.861000	0.98227	0.655000	0.94253	GAA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175348	G	T	112175348	4	4	88	1	0	0	0	0	0	1	0	0	763	1291	45	2	4115	2	APC	5	112175348	Nonsense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	98383204	112175348	68739912	38	24333										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250689	140250689	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	acggccaccgtgctggtgtcGttggtggagagcggacaggc	18	10	0	1	rs377444052		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr5:140250689G>A	ENST00000398640.2	+	1	2001	c.2001G>A	c.(1999-2001)tcG>tcA	p.S667S	PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	667	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGTGTCGTTGGTGGAGA	0.667													.|||	1	0.000199681	0	0	5008	,	,		15278	0		0.001	False		,,,				2504	0															0			5						G	,,,,,,,,,,,,,,	0,4398		0,0,2199	31	37	35		,,2001,,,,,,,,,,,,2001	-1.5	0.9	5		35	6,8582		0,6,4288	no	intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,,,,,,,,,,,,,	0,6,6487	AA,AG,GG		0.0699,0.0,0.0462	,,,,,,,,,,,,,,	,,667/950,,,,,,,,,,,,667/811	140250689	6,12980	2199	4294	6493	140230873	SO:0001819	synonymous_variant	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2001G>A	5.37:g.140250689G>A			140230873	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																				0.667	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140250689	G	A	140250689	2	1	88	1	0	0	0	0	0	0	0	1	11552	1132	40	1		1	PCDHA11	5	140250689	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	28075341	140250689	40664571	39	24334										
FAF2	23197	hgsc.bcm.edu	37	chr5	175921228	175921228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttatttcactaataaacactAggatgctcttctgggcatgc	7	9	3	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr5:175921228A>G	ENST00000261942.6	+	7	666	c.613A>G	c.(613-615)Agg>Ggg	p.R205G		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	205					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						AATAAACACTAGGATGCTCTT	0.403																																																0			5											152	142	146					5																	175921228		2203	4300	6503	175853834	SO:0001583	missense	23197			BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"UBX domain containing"	24666	protein-coding gene	gene with protein product	"expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B"		"UBX domain containing 8"	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.613A>G	5.37:g.175921228A>G	ENSP00000261942:p.Arg205Gly		175853834	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Missense_Mutation	SNP	ENST00000261942.6	37	CCDS34296.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.12|12.12	1.843860|1.843860	0.32606|0.32606	.|.	.|.	ENSG00000113194|ENSG00000113194	ENST00000261942|ENST00000540174	T|.	0.43294|.	0.95|.	5.36|5.36	1.34|1.34	0.21922|0.21922	UAS (1);|.	0.087322|.	0.85682|.	D|.	0.000000|.	T|T	0.59851|0.59851	0.2224|0.2224	M|M	0.62723|0.62723	1.935|1.935	0.44579|0.44579	D|D	0.997547|0.997547	B|.	0.26002|.	0.139|.	B|.	0.27076|.	0.076|.	T|T	0.52983|0.52983	-0.8502|-0.8502	10|5	0.41790|.	T|.	0.15|.	-7.9639|-7.9639	8.5753|8.5753	0.33595|0.33595	0.6278:0.2518:0.0:0.1204|0.6278:0.2518:0.0:0.1204	.|.	205|.	Q96CS3|.	FAF2_HUMAN|.	G|G	205|205	ENSP00000261942:R205G|.	ENSP00000261942:R205G|.	R|S	+|+	1|1	2|0	FAF2|FAF2	175853834|175853834	0.997000|0.997000	0.39634|0.39634	0.174000|0.174000	0.22961|0.22961	0.623000|0.623000	0.37688|0.37688	3.599000|3.599000	0.54045|0.54045	0.041000|0.041000	0.15688|0.15688	-0.321000|-0.321000	0.08615|0.08615	AGG|AGT		0.403	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613		G	175921228	A	G	175921228	3	3	88	1	0	0	0	0	1	0	0	0	5386	411	15	4	639	4	FAF2	5	175921228	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	35670539	175921228	4994032	40	24335										
GMNN	51053	hgsc.bcm.edu	37	chr6	24784336	24784336	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aaatccatcctctcagtattGgaaggaagtggcagaaaaac	9	8	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:24784336G>T	ENST00000230056.3	+	5	628	c.296G>T	c.(295-297)tGg>tTg	p.W99L	GMNN_ENST00000356509.3_Missense_Mutation_p.W99L	NM_015895.4	NP_056979.1	O75496	GEMI_HUMAN	geminin, DNA replication inhibitor	99	Necessary and sufficient for interaction with IDAS and CDT1.				mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	10						TCTCAGTATTGGAAGGAAGTG	0.284																																																0			6											44	45	45					6																	24784336		2203	4300	6503	24892315	SO:0001583	missense	51053			AF067855	CCDS4560.1	6p21.32	2008-10-31			ENSG00000112312	ENSG00000112312			17493	protein-coding gene	gene with protein product		602842				9635433	Standard	NM_001251989		Approved	Gem	uc003nem.3	O75496	OTTHUMG00000014363	ENST00000230056.3:c.296G>T	6.37:g.24784336G>T	ENSP00000230056:p.Trp99Leu		24892315	B3KMM8|Q9H1Z1	Missense_Mutation	SNP	ENST00000230056.3	37	CCDS4560.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943275	0.92593	.	.	ENSG00000112312	ENST00000356509;ENST00000230056;ENST00000378054;ENST00000378059	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.60222	0.2252	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65438	-0.6168	10	0.72032	D	0.01	-14.9459	20.3472	0.98799	0.0:0.0:1.0:0.0	.	99	O75496	GEMI_HUMAN	L	99	ENSP00000348902:W99L;ENSP00000230056:W99L;ENSP00000367293:W99L;ENSP00000367298:W99L	ENSP00000230056:W99L	W	+	2	0	GMNN	24892315	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	8.238000	0.89809	2.890000	0.99128	0.650000	0.86243	TGG		0.284	GMNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040021.2	NM_015895		T	24784336	G	T	24784336	3	4	88	1	0	0	0	0	1	0	0	0	6513	1357	47	2	310	2	GMNN	6	24784336	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		24784336	146330731	41	24336										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39847134	39847134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caggtgccccaccttgcctcGgcatgggcctgcccctccct	10	20	0	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:39847134G>A	ENST00000398904.2	+	14	1908	c.1726G>A	c.(1726-1728)Ggc>Agc	p.G576S	DAAM2_ENST00000274867.4_Missense_Mutation_p.G576S|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.G576S			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	576	FH1.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					ACCTTGCCTCGGCATGGGCCT	0.672																																																0			6											35	36	36					6																	39847134		1887	4102	5989	39955112	SO:0001583	missense	23500			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1726G>A	6.37:g.39847134G>A	ENSP00000381876:p.Gly576Ser		39955112	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.271339	0.01421	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.82433	-1.61;-1.61;-1.61	4.63	-2.76	0.05896	Actin-binding FH2 (1);	0.955053	0.08667	N	0.911567	T	0.40767	0.1130	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.25916	-1.0118	10	0.27785	T	0.31	.	7.0044	0.24828	0.4344:0.1261:0.4395:0.0	.	576;576	G5EA45;Q86T65	.;DAAM2_HUMAN	S	576	ENSP00000274867:G576S;ENSP00000381876:G576S;ENSP00000437808:G576S	ENSP00000274867:G576S	G	+	1	0	DAAM2	39955112	0.649000	0.27322	0.001000	0.08648	0.001000	0.01503	0.963000	0.29293	-0.458000	0.07023	-0.172000	0.13284	GGC		0.672	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39847134	G	A	39847134	3	1	88	1	0	0	0	0	1	0	0	0	4222	1116	39	1	1776	1	DAAM2	6	39847134	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	15062798	39847134	131267933	42	24337										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42231140	42231140	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caacggtgctgttggtgaacCcctgagagctgggcttgggc	16	10	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:42231140C>A	ENST00000372922.4	-	8	2364	c.1802G>T	c.(1801-1803)gGg>gTg	p.G601V	TRERF1_ENST00000354325.2_Intron|TRERF1_ENST00000541110.1_Missense_Mutation_p.G601V|TRERF1_ENST00000372917.4_Intron|TRERF1_ENST00000340840.2_Intron	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	601	Interacts with CREBBP.|Pro-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GTTGGTGAACCCCTGAGAGCT	0.642																																																0			6											73	75	74					6																	42231140		2203	4300	6503	42339118	SO:0001583	missense	55809			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1802G>T	6.37:g.42231140C>A	ENSP00000362013:p.Gly601Val		42339118	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284735	0.40394	.	.	ENSG00000124496	ENST00000541110;ENST00000372922	T;T	0.10192	2.95;2.9	4.45	3.5	0.40072	.	0.385573	0.22047	N	0.065370	T	0.01558	0.0050	N	0.04508	-0.205	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.43766	-0.9371	10	0.21014	T	0.42	-15.6445	6.8425	0.23971	0.1768:0.577:0.2462:0.0	.	601;601	Q05GC8;Q96PN7	.;TREF1_HUMAN	V	601	ENSP00000439689:G601V;ENSP00000362013:G601V	ENSP00000362013:G601V	G	-	2	0	TRERF1	42339118	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.972000	0.49256	2.307000	0.77673	0.561000	0.74099	GGG		0.642	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42231140	C	A	42231140	3	1	88	1	0	0	0	0	1	0	0	0	16515	623	22	2	1844	2	TRERF1	6	42231140	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	2384006	42231140	128883927	43	24338										
DST	667	hgsc.bcm.edu	37	chr6	56483631	56483631	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gaaacagaaccatctttctgTgggtcatctgctcctctatg	8	11	5	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:56483631T>C	ENST00000370765.6	-	23	5308	c.5201A>G	c.(5200-5202)cAc>cGc	p.H1734R	DST_ENST00000370754.5_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	3810					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CATCTTTCTGTGGGTCATCTG	0.383																																																0			6											143	151	148					6																	56483631		2203	4300	6503	56591590	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.5201A>G	6.37:g.56483631T>C	ENSP00000359801:p.His1734Arg		56591590	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	10.16	1.274069	0.23221	.	.	ENSG00000151914	ENST00000370765	T	0.77229	-1.08	5.34	4.15	0.48705	.	.	.	.	.	T	0.39572	0.1083	.	.	.	0.20307	N	0.999915	B	0.06786	0.001	B	0.08055	0.003	T	0.04635	-1.0937	7	0.10377	T	0.69	.	9.5443	0.39271	0.0:0.1958:0.0:0.8042	.	1734	Q03001-3	.	R	1734	ENSP00000359801:H1734R	ENSP00000359801:H1734R	H	-	2	0	DST	56591590	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.877000	0.28106	0.923000	0.37045	0.528000	0.53228	CAC		0.383	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		C	56483631	T	C	56483631	3	2	88	1	0	0	0	0	1	0	0	0	4794	1696	59	4	15202	4	DST	6	56483631	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	14252491	56483631	114631436	44	24339										
IBTK	25998	hgsc.bcm.edu	37	chr6	82922423	82922423	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aatcttcctttccttacttaCcattttttctgacttagctt	2	11	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:82922423C>A	ENST00000306270.7	-	13	2841		c.e13+1		IBTK_ENST00000510291.1_Splice_Site|IBTK_ENST00000503631.1_Splice_Site|RNU6-130P_ENST00000411112.1_RNA	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase						negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TCCTTACTTACCATTTTTTCT	0.333																																																0			6											178	158	165					6																	82922423		2203	4299	6502	82979142	SO:0001630	splice_region_variant	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2291+1G>T	6.37:g.82922423C>A			82979142	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Splice_Site	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.060397	0.76074	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6923	0.96007	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IBTK	82979142	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	6.385000	0.73182	2.830000	0.97506	0.585000	0.79938	.		0.333	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	Intron	A	82922423	C	A	82922423	5	1	88	1	0	0	0	0	0	0	1	0	7497	521	18	2	1837	2	IBTK	6	82922423	Splice_Site	SNP	C	TCGA-CI-6621-01A-11D-1826-10	26438792	82922423	88192644	45	24340										
BACH2	60468	hgsc.bcm.edu	37	chr6	90660040	90660040	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcactgtctgcttccgagaaCgatccggattcgtcactgga	10	12	3	1	rs558363430		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:90660040C>T	ENST00000257749.4	-	7	2492	c.1785G>A	c.(1783-1785)tcG>tcA	p.S595S	RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000343122.3_Silent_p.S595S|BACH2_ENST00000537989.1_Silent_p.S595S	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	595						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		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)		CTTCCGAGAACGATCCGGATT	0.527																																																0			6											126	120	122					6																	90660040		2203	4300	6503	90716761	SO:0001819	synonymous_variant	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1785G>A	6.37:g.90660040C>T			90716761	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																				0.527	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		T	90660040	C	T	90660040	2	4	88	1	0	0	0	0	0	0	0	1	1285	523	19	1		1	BACH2	6	90660040	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	7737617	90660040	80455027	46	24341										
RSPH4A	345895	hgsc.bcm.edu	37	chr6	116948931	116948931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccacccaatccaaagatgccGcttctggggaaagatcttgg	10	12	2	2	rs367712020		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:116948931G>A	ENST00000229554.5	+	3	1198	c.1061G>A	c.(1060-1062)cGc>cAc	p.R354H	RSPH4A_ENST00000368580.4_Intron|RSPH4A_ENST00000368581.4_Missense_Mutation_p.R354H	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	354					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CAAAGATGCCGCTTCTGGGGA	0.448									Kartagener syndrome																																							0			6						G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	96	97	96		1061,1061	4.6	1	6		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RSPH4A	NM_001010892.2,NM_001161664.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	354/717,354/601	116948931	1,13005	2203	4300	6503	117055624	SO:0001583	missense	345895	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"radial spokehead-like 3"	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1061G>A	6.37:g.116948931G>A	ENSP00000229554:p.Arg354His		117055624	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011374	0.75046	0.0	1.16E-4	ENSG00000111834	ENST00000368581;ENST00000229554;ENST00000447842	T;T	0.34859	1.34;1.34	5.48	4.61	0.57282	.	0.110202	0.64402	N	0.000009	T	0.37156	0.0993	M	0.75264	2.295	0.58432	D	0.999997	D;P	0.65815	0.995;0.798	P;B	0.54815	0.761;0.229	T	0.38067	-0.9678	10	0.54805	T	0.06	-3.2385	8.3999	0.32579	0.1766:0.0:0.8234:0.0	.	354;354	Q5TD94-3;Q5TD94	.;RSH4A_HUMAN	H	354;354;149	ENSP00000357570:R354H;ENSP00000229554:R354H	ENSP00000229554:R354H	R	+	2	0	RSPH4A	117055624	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	7.678000	0.84035	1.294000	0.44707	0.591000	0.81541	CGC		0.448	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892		A	116948931	G	A	116948931	3	1	88	1	0	0	0	0	1	0	0	0	13743	1087	38	1	1071	1	RSPH4A	6	116948931	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	26288891	116948931	54166136	47	24342										
TAAR5	9038	hgsc.bcm.edu	37	chr6	132910614	132910614	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gggccagggagagcagcaggAagttggtgggcgtgtgaagc	21	6	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:132910614A>G	ENST00000258034.2	-	1	263	c.212T>C	c.(211-213)tTc>tCc	p.F71S		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	71					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		GAGCAGCAGGAAGTTGGTGGG	0.567																																																0			6											177	180	179					6																	132910614		2203	4300	6503	132952307	SO:0001583	missense	9038			AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"GPCR / Class A : Trace amine associated receptors"	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.212T>C	6.37:g.132910614A>G	ENSP00000258034:p.Phe71Ser		132952307	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Missense_Mutation	SNP	ENST00000258034.2	37	CCDS5156.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.546986	0.45383	.	.	ENSG00000135569	ENST00000258034	T	0.72835	-0.69	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.193775	0.34268	N	0.004109	T	0.73179	0.3554	M	0.79011	2.435	0.39703	D	0.971213	P	0.45531	0.86	P	0.49502	0.613	T	0.79112	-0.1937	10	0.87932	D	0	-10.4169	15.6558	0.77133	1.0:0.0:0.0:0.0	.	71	O14804	TAAR5_HUMAN	S	71	ENSP00000258034:F71S	ENSP00000258034:F71S	F	-	2	0	TAAR5	132952307	0.066000	0.20996	0.927000	0.36925	0.545000	0.35147	2.655000	0.46707	2.280000	0.76307	0.533000	0.62120	TTC		0.567	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967		G	132910614	A	G	132910614	3	3	88	1	0	0	0	0	1	0	0	0	15530	246	9	4	805	4	TAAR5	6	132910614	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	15961683	132910614	38204453	48	24343										
GRM1	2911	hgsc.bcm.edu	37	chr6	146720262	146720262	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caagaagaagatctgcacccGgaagcccaggttcatgagtg	12	10	2	4			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr6:146720262G>T	ENST00000282753.1	+	7	2322	c.2087G>T	c.(2086-2088)cGg>cTg	p.R696L	GRM1_ENST00000507907.1_Missense_Mutation_p.R696L|GRM1_ENST00000361719.2_Missense_Mutation_p.R696L|GRM1_ENST00000392299.2_Missense_Mutation_p.R696L|GRM1_ENST00000492807.2_Missense_Mutation_p.R696L|GRM1_ENST00000355289.4_Missense_Mutation_p.R696L			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	696			R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		ATCTGCACCCGGAAGCCCAGG	0.512																																																0			6											134	132	133					6																	146720262		2203	4300	6503	146761955	SO:0001583	missense	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2087G>T	6.37:g.146720262G>T	ENSP00000282753:p.Arg696Leu		146761955	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076017	0.76415	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22;-2.22	5.51	5.51	0.81932	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.90844	0.7124	L	0.54965	1.715	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.994	D;D;D	0.66716	0.935;0.946;0.935	D	0.91406	0.5147	10	0.87932	D	0	.	19.4081	0.94656	0.0:0.0:1.0:0.0	.	696;696;696	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	L	696	ENSP00000354896:R696L;ENSP00000376119:R696L;ENSP00000424095:R696L;ENSP00000282753:R696L;ENSP00000347437:R696L;ENSP00000425599:R696L	ENSP00000282753:R696L	R	+	2	0	GRM1	146761955	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.876000	0.87215	2.604000	0.88044	0.585000	0.79938	CGG		0.512	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146720262	G	T	146720262	3	4	88	1	0	0	0	0	1	0	0	0	6817	1116	39	2	2113	2	GRM1	6	146720262	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	13809648	146720262	24394805	49	24344										
NXPH1	30010	hgsc.bcm.edu	37	chr7	8790960	8790960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tggatggggcgattttcattCcaacatcaaaacagtgaagc	10	8	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr7:8790960C>T	ENST00000405863.1	+	3	1288	c.377C>T	c.(376-378)tCc>tTc	p.S126F	NXPH1_ENST00000602349.1_Missense_Mutation_p.S9F|NXPH1_ENST00000497400.1_3'UTR	NM_152745.2	NP_689958.1	P58417	NXPH1_HUMAN	neurexophilin 1	126	III.					extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|ovary(1)	17		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GATTTTCATTCCAACATCAAA	0.428																																																0			7											83	82	82					7																	8790960		1860	4096	5956	8757485	SO:0001583	missense	30010			AB047362	CCDS47540.1	7p22	2003-03-20			ENSG00000122584	ENSG00000122584			20693	protein-coding gene	gene with protein product		604639				9570794	Standard	NM_152745		Approved		uc003srv.3	P58417	OTTHUMG00000151941	ENST00000405863.1:c.377C>T	7.37:g.8790960C>T	ENSP00000384551:p.Ser126Phe		8757485	Q8NB31	Missense_Mutation	SNP	ENST00000405863.1	37	CCDS47540.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370553	0.61624	.	.	ENSG00000122584	ENST00000405863;ENST00000417186;ENST00000438764;ENST00000429542	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66346	0.2780	L	0.55990	1.75	0.80722	D	1	P	0.39022	0.655	B	0.43018	0.405	T	0.61118	-0.7127	9	0.35671	T	0.21	-12.742	20.8794	0.99867	0.0:1.0:0.0:0.0	.	126	P58417	NXPH1_HUMAN	F	126;9;126;126	.	ENSP00000384551:S126F	S	+	2	0	NXPH1	8757485	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.792000	0.85828	2.941000	0.99782	0.655000	0.94253	TCC		0.428	NXPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324591.1	NM_152745		T	8790960	C	T	8790960	3	4	88	1	0	0	0	0	1	0	0	0	10821	855	30	3	383	3	NXPH1	7	8790960	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		8790960	150347703	50	24345										
EGFR	1956	hgsc.bcm.edu	37	chr7	55242429	55242429	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcatagggactctggatcccAgaaggtgagaaagttaaaat	11	6	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr7:55242429A>G	ENST00000275493.2	+	19	2376	c.2199A>G	c.(2197-2199)ccA>ccG	p.P733P	EGFR_ENST00000454757.2_Silent_p.P680P|EGFR_ENST00000455089.1_Silent_p.P688P|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	733	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCTGGATCCCAGAAGGTGAGA	0.468		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											91	92	92					7																	55242429		2203	4300	6503	55209923	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2199A>G	7.37:g.55242429A>G			55209923	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.468	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55242429	A	G	55242429	2	3	88	1	0	0	0	0	0	0	0	1	4978	175	7	4		4	EGFR	7	55242429	Silent	SNP	A	TCGA-CI-6621-01A-11D-1826-10	46451469	55242429	103896234	51	24346										
WEE2	494551	hgsc.bcm.edu	37	chr7	141424833	141424833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttctgttttgaaggattaccGgcaccttcccaaagcagaca	8	11	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr7:141424833G>A	ENST00000397541.2	+	9	1635	c.1229G>A	c.(1228-1230)cGg>cAg	p.R410Q	WEE2-AS1_ENST00000488785.1_RNA|RNU1-82P_ENST00000390851.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000486906.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000471512.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	410	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					AAGGATTACCGGCACCTTCCC	0.468																																																0			7											90	88	89					7																	141424833		1945	4149	6094	141071302	SO:0001583	missense	494551			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.1229G>A	7.37:g.141424833G>A	ENSP00000380675:p.Arg410Gln		141071302		Missense_Mutation	SNP	ENST00000397541.2	37	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.799387	0.31869	.	.	ENSG00000214102	ENST00000397541	T	0.64618	-0.11	5.63	-3.84	0.04256	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.728220	0.12125	N	0.497339	T	0.45637	0.1352	L	0.28649	0.875	0.09310	N	1	B	0.15719	0.014	B	0.16289	0.015	T	0.26710	-1.0095	10	0.15499	T	0.54	.	15.2585	0.73603	0.0842:0.0:0.8258:0.09	.	410	P0C1S8	WEE2_HUMAN	Q	410	ENSP00000380675:R410Q	ENSP00000380675:R410Q	R	+	2	0	WEE2	141071302	0.000000	0.05858	0.013000	0.15412	0.921000	0.55340	-0.114000	0.10757	-1.319000	0.02286	-0.345000	0.07892	CGG		0.468	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		A	141424833	G	A	141424833	3	1	88	1	0	0	0	0	1	0	0	0	17385	1116	39	1	1263	1	WEE2	7	141424833	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	86182404	141424833	17713830	52	24347										
WDR86	349136	hgsc.bcm.edu	37	chr7	151093102	151093102	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccggtcaccagaagccccccGgccgcggcctcctccgcgca	11	22	1	1	rs112396535	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr7:151093102G>A	ENST00000334493.6	-	3	916	c.486C>T	c.(484-486)gcC>gcT	p.A162A	WDR86_ENST00000463000.1_5'Flank|WDR86_ENST00000469830.2_Silent_p.A162A|WDR86_ENST00000477459.1_Silent_p.A34A	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	162										breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAAGCCCCCCGGCCGCGGCCT	0.721													G|||	10	0.00199681	0	0	5008	,	,		14750	0.0099		0	False		,,,				2504	0															0			7																																								150724035	SO:0001819	synonymous_variant	349136			AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"WD repeat domain containing"	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.486C>T	7.37:g.151093102G>A			150724035	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Silent	SNP	ENST00000334493.6	37	CCDS5925.2																																																																																				0.721	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285		A	151093102	G	A	151093102	2	1	88	1	0	0	0	0	0	0	0	1	17374	1103	39	1		1	WDR86	7	151093102	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	9668269	151093102	8045561	53	24348										
RP1	6101	hgsc.bcm.edu	37	chr8	55538658	55538658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gaaaagtgatactgtaattgAatcaaatactttttgttcca	6	5	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr8:55538658A>G	ENST00000220676.1	+	4	2364	c.2216A>G	c.(2215-2217)gAa>gGa	p.E739G		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	739					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			ACTGTAATTGAATCAAATACT	0.333																																					Colon(91;1014 1389 7634 14542 40420)											0			8											33	33	33					8																	55538658		2203	4297	6500	55701211	SO:0001583	missense	10982			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2216A>G	8.37:g.55538658A>G	ENSP00000220676:p.Glu739Gly		55701211		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	6.386	0.439245	0.12104	.	.	ENSG00000104237	ENST00000220676	T	0.23552	1.9	5.93	4.77	0.60923	.	0.865829	0.10058	N	0.721260	T	0.21718	0.0523	L	0.34521	1.04	0.09310	N	1	P	0.50272	0.933	B	0.40901	0.343	T	0.07328	-1.0778	10	0.34782	T	0.22	.	12.2009	0.54323	0.9326:0.0:0.0673:0.0	.	739	P56715	RP1_HUMAN	G	739	ENSP00000220676:E739G	ENSP00000220676:E739G	E	+	2	0	RP1	55701211	0.793000	0.28825	0.979000	0.43373	0.011000	0.07611	3.076000	0.50081	2.270000	0.75569	0.482000	0.46254	GAA		0.333	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55538658	A	G	55538658	3	3	88	1	0	0	0	0	1	0	0	0	13569	246	9	4	2226	4	RP1	8	55538658	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10		55538658	90825364	54	24349										
PREX2	80243	hgsc.bcm.edu	37	chr8	69046378	69046378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cttctctgagcagctcatggCggccttgaaccagatgtttg	11	11	2	3	rs375506738		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr8:69046378C>T	ENST00000288368.4	+	32	4128	c.3851C>T	c.(3850-3852)gCg>gTg	p.A1284V		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1284					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CAGCTCATGGCGGCCTTGAAC	0.502																																																0			8						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	86	81	83		3851	5.4	1	8		83	0,8600		0,0,4300	no	missense	PREX2	NM_024870.2	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1284/1607	69046378	1,13005	2203	4300	6503	69208932	SO:0001583	missense	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3851C>T	8.37:g.69046378C>T	ENSP00000288368:p.Ala1284Val		69208932	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.197211	0.58126	2.27E-4	0.0	ENSG00000046889	ENST00000288368	T	0.57907	0.37	5.42	5.42	0.78866	.	0.202234	0.41712	D	0.000831	T	0.47266	0.1436	L	0.45581	1.43	0.50632	D	0.999886	B	0.15473	0.013	B	0.18561	0.022	T	0.42949	-0.9421	10	0.54805	T	0.06	.	12.9783	0.58549	0.0:0.916:0.0:0.084	.	1284	Q70Z35	PREX2_HUMAN	V	1284	ENSP00000288368:A1284V	ENSP00000288368:A1284V	A	+	2	0	PREX2	69208932	1.000000	0.71417	0.957000	0.39632	0.950000	0.60333	4.686000	0.61700	2.559000	0.86315	0.655000	0.94253	GCG		0.502	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69046378	C	T	69046378	3	4	88	1	0	0	0	0	1	0	0	0	12511	768	27	1	4206	1	PREX2	8	69046378	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	13507720	69046378	77317644	55	24350										
ZNF704	619279	hgsc.bcm.edu	37	chr8	81571875	81571875	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aggaaatgctgaagctgctgCcattgggggtgaacttggcc	15	8	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr8:81571875C>G	ENST00000327835.3	-	7	1208	c.977G>C	c.(976-978)gGc>gCc	p.G326A		NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	326							metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			GAAGCTGCTGCCATTGGGGGT	0.468																																																0			8											168	180	176					8																	81571875		2203	4300	6503	81734430	SO:0001583	missense	619279			AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.977G>C	8.37:g.81571875C>G	ENSP00000331462:p.Gly326Ala		81734430	B2RNE6|B9EGW6	Missense_Mutation	SNP	ENST00000327835.3	37	CCDS34913.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.588200	0.46110	.	.	ENSG00000164684	ENST00000327835	D	0.82619	-1.63	5.62	5.62	0.85841	.	0.094153	0.64402	D	0.000001	T	0.80019	0.4547	L	0.38838	1.175	0.52501	D	0.999956	B	0.32101	0.356	B	0.35182	0.197	T	0.77070	-0.2724	10	0.41790	T	0.15	-28.6935	20.0114	0.97452	0.0:1.0:0.0:0.0	.	326	Q6ZNC4	ZN704_HUMAN	A	326	ENSP00000331462:G326A	ENSP00000331462:G326A	G	-	2	0	ZNF704	81734430	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.823000	0.48081	2.795000	0.96236	0.655000	0.94253	GGC		0.468	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2	NM_001033723		G	81571875	C	G	81571875	3	3	88	1	0	0	0	0	1	0	0	0	18146	739	26	5	273	5	ZNF704	8	81571875	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	12525497	81571875	64792147	56	24351										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141034145	141034145	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cagtgtggcccgggcctccaGagtatttgaaattcaggaca	12	10	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr8:141034145G>C	ENST00000438773.2	-	18	2721	c.2588C>G	c.(2587-2589)tCt>tGt	p.S863C	TRAPPC9_ENST00000389327.3_Missense_Mutation_p.S854C|TRAPPC9_ENST00000389328.4_Missense_Mutation_p.S961C	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	863					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CGGGCCTCCAGAGTATTTGAA	0.458																																																0			8											60	64	62					8																	141034145		2203	4300	6503	141103327	SO:0001583	missense	83696			BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2588C>G	8.37:g.141034145G>C	ENSP00000405060:p.Ser863Cys		141103327	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.915460	0.73098	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.77896	0.4199	M	0.69358	2.11	0.48288	D	0.999627	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;0.997	T	0.77310	-0.2635	9	0.44086	T	0.13	.	17.6378	0.88128	0.0:0.0:1.0:0.0	.	961;863;854;961	A6NIF0;Q96Q05;Q96Q05-3;Q96Q05-2	.;TPPC9_HUMAN;.;.	C	961;854;863	.	ENSP00000373978:S854C	S	-	2	0	TRAPPC9	141103327	1.000000	0.71417	0.982000	0.44146	0.982000	0.71751	6.856000	0.75450	2.498000	0.84270	0.467000	0.42956	TCT		0.458	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		C	141034145	G	C	141034145	3	2	88	1	0	0	0	0	1	0	0	0	16505	942	33	5	882	5	TRAPPC9	8	141034145	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	59462270	141034145	5329877	57	24352										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19063006	19063006	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcattacagtcttttctcacCtcttctaccagatgatcttg	4	12	6	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr9:19063006C>A	ENST00000380502.3	-	14	2096	c.1629G>T	c.(1627-1629)gaG>gaT	p.E543D	HAUS6_ENST00000380496.1_Splice_Site_p.E407D|SCARNA8_ENST00000515924.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	543					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTTTTCTCACCTCTTCTACCA	0.418																																																0			9											162	147	152					9																	19063006		2203	4300	6503	19053006	SO:0001630	splice_region_variant	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1629+1G>T	9.37:g.19063006C>A			19053006	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603336	0.66445	.	.	ENSG00000147874	ENST00000380502;ENST00000380496;ENST00000415524	T;T;T	0.53423	1.64;1.63;0.62	5.54	4.64	0.57946	.	0.101103	0.64402	D	0.000002	T	0.64560	0.2609	M	0.72479	2.2	0.33816	D	0.628422	D;D;D;D	0.76494	0.971;0.971;0.999;0.971	P;P;D;P	0.83275	0.654;0.475;0.996;0.654	T	0.73206	-0.4056	9	.	.	.	-7.6635	10.8035	0.46502	0.0:0.912:0.0:0.088	.	508;543;407;543	Q7Z4H7-3;Q7Z4H7-2;Q5VY60;Q7Z4H7	.;.;.;HAUS6_HUMAN	D	543;407;59	ENSP00000369871:E543D;ENSP00000369865:E407D;ENSP00000409615:E59D	.	E	-	3	2	HAUS6	19053006	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.012000	0.49575	2.606000	0.88127	0.563000	0.77884	GAG		0.418	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	Missense_Mutation	A	19063006	C	A	19063006	5	1	88	1	0	0	0	0	0	0	1	0	6991	695	24	2	1254	2	HAUS6	9	19063006	Splice_Site	SNP	C	TCGA-CI-6621-01A-11D-1826-10		19063006	122150425	58	24353										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745571	37745571	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	accacatccccctagagaccCtcaaggacagagcagagaac	8	15	1	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr9:37745571C>G	ENST00000539465.1	+	16	4135	c.3542C>G	c.(3541-3543)cCt>cGt	p.P1181R	FRMPD1_ENST00000377765.3_Missense_Mutation_p.P1181R|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1181						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CCTAGAGACCCTCAAGGACAG	0.488																																																0			9											56	59	58					9																	37745571		2203	4300	6503	37735571	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3542C>G	9.37:g.37745571C>G	ENSP00000444411:p.Pro1181Arg		37735571	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	8.638	0.895230	0.17613	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.06371	3.31;3.31	5.01	2.03	0.26663	.	0.777035	0.11651	N	0.542782	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43798	-0.9369	10	0.34782	T	0.22	-7.7492	7.6939	0.28583	0.0:0.5924:0.3168:0.0908	.	1181	Q5SYB0	FRPD1_HUMAN	R	1181	ENSP00000366995:P1181R;ENSP00000444411:P1181R	ENSP00000366995:P1181R	P	+	2	0	FRMPD1	37735571	0.001000	0.12720	0.002000	0.10522	0.091000	0.18340	0.310000	0.19356	0.602000	0.29896	0.561000	0.74099	CCT		0.488	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		G	37745571	C	G	37745571	3	3	88	1	0	0	0	0	1	0	0	0	6076	681	24	5	3600	5	FRMPD1	9	37745571	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	18682565	37745571	103467860	59	24354										
CRAT	1384	hgsc.bcm.edu	37	chr9	131860875	131860875	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ggggtgatgttgaaccgcagCttcttgggcatgggcagggg	19	7	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr9:131860875C>A	ENST00000318080.2	-	9	1434	c.1140G>T	c.(1138-1140)aaG>aaT	p.K380N	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	380					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	TGAACCGCAGCTTCTTGGGCA	0.607																																																0			9											167	145	152					9																	131860875		2203	4300	6503	130900696	SO:0001583	missense	1384			X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1140G>T	9.37:g.131860875C>A	ENSP00000315013:p.Lys380Asn		130900696	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	37	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795540	0.70452	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	T	0.50813	0.73	5.13	2.23	0.28157	.	0.000000	0.85682	D	0.000000	T	0.66458	0.2791	H	0.94306	3.52	0.80722	D	1	D	0.57899	0.981	P	0.54238	0.746	T	0.70702	-0.4799	10	0.59425	D	0.04	-40.1931	8.1409	0.31082	0.0:0.6817:0.0:0.3183	.	380	P43155	CACP_HUMAN	N	299;380	ENSP00000315013:K380N	ENSP00000315013:K380N	K	-	3	2	CRAT	130900696	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.086000	0.30853	0.745000	0.32763	0.561000	0.74099	AAG		0.607	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			A	131860875	C	A	131860875	3	1	88	1	0	0	0	0	1	0	0	0	3853	796	28	2	764	2	CRAT	9	131860875	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	94115304	131860875	9352556	60	24355										
C10orf18	54906	hgsc.bcm.edu	37	chr10	5791443	5791443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ctccattggtgctttcccttCgacaaaaatctctgaggccc	7	14	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr10:5791443C>T	ENST00000328090.5	+	15	6684	c.6059C>T	c.(6058-6060)tCg>tTg	p.S2020L		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2020																	GCTTTCCCTTCGACAAAAATC	0.512																																																0			10											112	116	115					10																	5791443		1917	4141	6058	5831449	SO:0001583	missense	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.6059C>T	10.37:g.5791443C>T	ENSP00000328426:p.Ser2020Leu		5831449	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.928810	0.00493	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.03553	3.89	5.92	0.307	0.15811	.	0.744018	0.12076	N	0.501774	T	0.01387	0.0045	N	0.02391	-0.57	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49153	-0.8969	10	0.11182	T	0.66	.	5.2963	0.15754	0.0:0.2808:0.1402:0.579	.	2020	Q5VWN6	F208B_HUMAN	L	2020;1215	ENSP00000328426:S2020L	ENSP00000328426:S2020L	S	+	2	0	C10orf18	5831449	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.038000	0.13862	-0.162000	0.10964	-0.351000	0.07748	TCG		0.512	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5791443	C	T	5791443	3	4	88	1	0	0	0	0	1	0	0	0	1600	893	31	1	6105	1	C10orf18	10	5791443	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		5791443	129743304	61	24356										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7262397	7262397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caggtgaagccacattagccGccccttcacactcacaacgg	8	16	2	1	rs201914057	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr10:7262397G>A	ENST00000361972.4	-	11	1396	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W	SFMBT2_ENST00000397167.1_Missense_Mutation_p.R436W	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	436					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CACATTAGCCGCCCCTTCACA	0.522													G|||	2	0.000399361	0	0.0014	5008	,	,		19606	0		0.001	False		,,,				2504	0															0			10											237	224	228					10																	7262397		2203	4300	6503	7302403	SO:0001583	missense	57713			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1306C>T	10.37:g.7262397G>A	ENSP00000355109:p.Arg436Trp		7302403	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.10	2.733773	0.48939	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.46451	0.87;0.87	5.4	-1.48	0.08745	.	0.090804	0.64402	D	0.000001	T	0.64227	0.2579	M	0.86028	2.79	0.49687	D	0.999815	D	0.76494	0.999	D	0.65140	0.932	T	0.70766	-0.4783	10	0.51188	T	0.08	.	18.2371	0.89952	0.0:0.0:0.6077:0.3923	.	436	Q5VUG0	SMBT2_HUMAN	W	436	ENSP00000355109:R436W;ENSP00000380353:R436W	ENSP00000355109:R436W	R	-	1	2	SFMBT2	7302403	0.004000	0.15560	0.071000	0.20095	0.544000	0.35116	0.351000	0.20096	-0.561000	0.06094	-0.309000	0.09137	CGG		0.522	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7262397	G	A	7262397	3	1	88	1	0	0	0	0	1	0	0	0	14195	1086	38	1	1422	1	SFMBT2	10	7262397	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	1470954	7262397	128272350	62	24357										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88206045	88206045	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcctcctccttcttatgtttCtcttctgtaccatcagtctt	3	14	5	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr10:88206045C>G	ENST00000298767.5	-	16	3748	c.3276G>C	c.(3274-3276)gaG>gaC	p.E1092D	WAPAL_ENST00000484070.1_5'Flank|WAPAL_ENST00000372075.1_Missense_Mutation_p.E304D|WAPAL_ENST00000263070.7_Missense_Mutation_p.E304D	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1092	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TCTTATGTTTCTCTTCTGTAC	0.383																																																0			10											185	184	184					10																	88206045		2203	4300	6503	88196025	SO:0001583	missense	23063			AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3276G>C	10.37:g.88206045C>G	ENSP00000298767:p.Glu1092Asp		88196025	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.541097	0.45280	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.37058	1.22;1.22;1.22	5.51	4.42	0.53409	Armadillo-type fold (1);	0.279454	0.39544	N	0.001324	T	0.31263	0.0791	N	0.17594	0.5	0.40890	D	0.984064	P;B;P;D	0.53151	0.826;0.015;0.826;0.958	B;B;B;P	0.54889	0.259;0.006;0.259;0.763	T	0.02053	-1.1222	10	0.19590	T	0.45	.	10.0257	0.42070	0.0:0.7919:0.0:0.2081	.	1086;1130;1092;1129	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	D	1177;1092;1177;304;304	ENSP00000298767:E1092D;ENSP00000361145:E304D;ENSP00000263070:E304D	ENSP00000263070:E304D	E	-	3	2	WAPAL	88196025	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.342000	0.19926	2.581000	0.87130	0.655000	0.94253	GAG		0.383	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88206045	C	G	88206045	3	3	88	1	0	0	0	0	1	0	0	0	17288	912	32	5	312	5	WAPAL	10	88206045	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	80943648	88206045	47328702	63	24358										
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116075427	116075427	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcacgcatcagctcgatgccGgcctccggcgagggccactg	13	16	2	0	rs185015833		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr10:116075427G>A	ENST00000304129.4	-	6	533	c.504C>T	c.(502-504)gcC>gcT	p.A168A	AFAP1L2_ENST00000369271.3_Silent_p.A168A|AFAP1L2_ENST00000545353.1_Silent_p.A221A			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	168					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		GCTCGATGCCGGCCTCCGGCG	0.632																																																0			10											49	38	42					10																	116075427		2203	4300	6503	116065417	SO:0001819	synonymous_variant	84632			BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"Pleckstrin homology (PH) domain containing"	25901	protein-coding gene	gene with protein product		612420	"KIAA1914"	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.504C>T	10.37:g.116075427G>A			116065417	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																				0.632	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116075427	G	A	116075427	2	1	88	1	0	0	0	0	0	0	0	1	355	1103	39	1		1	AFAP1L2	10	116075427	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	27869382	116075427	19459320	64	24359										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129055679	129055679	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttcgactgggtgatcatgaaCatggtgcaaaataagtaagt	11	5	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr10:129055679C>T	ENST00000280333.6	+	29	3076	c.2967C>T	c.(2965-2967)aaC>aaT	p.N989N	DOCK1_ENST00000484400.1_3'UTR	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	989					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TGATCATGAACATGGTGCAAA	0.423																																																0			10											84	80	81					10																	129055679		1933	4143	6076	128945669	SO:0001819	synonymous_variant	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2967C>T	10.37:g.129055679C>T			128945669	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																					0.423	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	129055679	C	T	129055679	2	4	88	1	0	0	0	0	0	0	0	1	4695	477	17	3		3	DOCK1	10	129055679	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	12980252	129055679	6479068	65	24360										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735960	18735960	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atctgcatgcctggcaagtcCgtgatctgggggtcaggggt	16	9	3	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:18735960C>T	ENST00000513874.1	-	13	1801	c.1662G>A	c.(1660-1662)acG>acA	p.T554T	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	554										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CTGGCAAGTCCGTGATCTGGG	0.597																																																0			11											103	110	108					11																	18735960		2081	4206	6287	18692536	SO:0001819	synonymous_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1662G>A	11.37:g.18735960C>T			18692536	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																				0.597	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		T	18735960	C	T	18735960	2	4	88	1	0	0	0	0	0	0	0	1	7621	639	23	1		1	IGSF22	11	18735960	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10		18735960	116270556	66	24361										
FSHB	2488	hgsc.bcm.edu	37	chr11	30255300	30255300	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	acagcactgattgtactgtgCgaggcctggggcccagctac	13	12	0	1	rs374623109		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:30255300C>T	ENST00000417547.1	+	3	382	c.343C>T	c.(343-345)Cga>Tga	p.R115*	FSHB_ENST00000533718.1_Nonsense_Mutation_p.R115*|FSHB_ENST00000254122.3_Nonsense_Mutation_p.R115*	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	115					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)	p.R115*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						TTGTACTGTGCGAGGCCTGGG	0.517																																																1	Substitution - Nonsense(1)	large_intestine(1)	11						C	stop/ARG,stop/ARG	0,4404		0,0,2202	80	68	72		343,343	2.7	0.2	11		72	1,8597	1.2+/-3.3	0,1,4298	no	stop-gained,stop-gained	FSHB	NM_000510.2,NM_001018080.1	,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,	115/130,115/130	30255300	1,13001	2202	4299	6501	30211876	SO:0001587	stop_gained	2488				CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"Endogenous ligands"	3964	protein-coding gene	gene with protein product	"follitropin, beta chain", "follicle-stimulating hormone beta subunit"	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.343C>T	11.37:g.30255300C>T	ENSP00000416606:p.Arg115*		30211876	A2TF08|A5JVV3|Q14D61	Nonsense_Mutation	SNP	ENST00000417547.1	37	CCDS7868.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.947427	0.53186	0.0	1.16E-4	ENSG00000131808	ENST00000254122;ENST00000417547;ENST00000533718	.	.	.	5.65	2.67	0.31697	.	0.426305	0.22879	N	0.054524	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	15.0102	0.71545	0.693:0.307:0.0:0.0	.	.	.	.	X	115	.	ENSP00000254122:R115X	R	+	1	2	FSHB	30211876	0.012000	0.17670	0.220000	0.23810	0.393000	0.30537	-0.524000	0.06222	0.425000	0.26087	-0.182000	0.12963	CGA		0.517	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510		T	30255300	C	T	30255300	4	4	88	1	0	0	0	0	0	1	0	0	6091	760	27	1	349	1	FSHB	11	30255300	Nonsense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	11519340	30255300	104751216	67	24362										
KCTD21	283219	hgsc.bcm.edu	37	chr11	77884837	77884837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tttacctgtaccgtattaatCgaataatcttattgttcata	4	7	2	0	rs372134817		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:77884837C>T	ENST00000340067.3	-	2	1042	c.764G>A	c.(763-765)cGa>cAa	p.R255Q	KCTD21-AS1_ENST00000523626.2_RNA|KCTD21-AS1_ENST00000530261.1_RNA|KCTD21-AS1_ENST00000528468.1_RNA|KCTD21-AS1_ENST00000600795.1_RNA	NM_001029859.1	NP_001025030.1	Q4G0X4	KCD21_HUMAN	potassium channel tetramerization domain containing 21	255					protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(2)	11	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)			CCGTATTAATCGAATAATCTT	0.488																																																0			11						C	GLN/ARG	0,4400		0,0,2200	107	111	110		764	5.5	1	11		110	1,8583		0,1,4291	no	missense	KCTD21	NM_001029859.1	43	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	255/261	77884837	1,12983	2200	4292	6492	77562485	SO:0001583	missense	283219			AK095233	CCDS31645.1	11q14.1	2013-06-20	2013-06-20			ENSG00000188997			27452	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 21"			21472142	Standard	XM_005273925		Approved	KCASH2	uc001ozb.3	Q4G0X4		ENST00000340067.3:c.764G>A	11.37:g.77884837C>T	ENSP00000339340:p.Arg255Gln		77562485	B4DTR0	Missense_Mutation	SNP	ENST00000340067.3	37	CCDS31645.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.905838	0.92107	0.0	1.16E-4	ENSG00000188997	ENST00000340067	T	0.69306	-0.39	5.5	5.5	0.81552	.	0.000000	0.47852	D	0.000203	T	0.72676	0.3490	N	0.24115	0.695	0.42002	D	0.990899	D	0.89917	1.0	D	0.80764	0.994	T	0.75531	-0.3285	10	0.66056	D	0.02	.	17.7606	0.88463	0.0:1.0:0.0:0.0	.	255	Q4G0X4	KCD21_HUMAN	Q	255	ENSP00000339340:R255Q	ENSP00000339340:R255Q	R	-	2	0	KCTD21	77562485	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.890000	0.56220	2.861000	0.98227	0.655000	0.94253	CGA		0.488	KCTD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390057.1	NM_001029859		T	77884837	C	T	77884837	3	4	88	1	0	0	0	0	1	0	0	0	8130	884	31	1	22	1	KCTD21	11	77884837	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	47629537	77884837	57121679	68	24363										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92715176	92715176	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgtttgtgatctttgccatcTgctgggctccacttaactgc	9	11	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:92715176T>A	ENST00000257068.2	+	2	793	c.787T>A	c.(787-789)Tgc>Agc	p.C263S		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	263					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CTTTGCCATCTGCTGGGCTCC	0.557																																																0			11											165	139	148					11																	92715176		2201	4298	6499	92354824	SO:0001583	missense	4544			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.787T>A	11.37:g.92715176T>A	ENSP00000257068:p.Cys263Ser		92354824		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701564	0.68501	.	.	ENSG00000134640	ENST00000257068	T	0.51817	0.69	4.0	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64000	0.2559	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.63479	-0.6628	10	0.34782	T	0.22	-28.7179	13.3859	0.60795	0.0:0.0:0.0:1.0	.	263	P49286	MTR1B_HUMAN	S	263	ENSP00000257068:C263S	ENSP00000257068:C263S	C	+	1	0	MTNR1B	92354824	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	7.220000	0.78008	1.807000	0.52817	0.402000	0.26972	TGC		0.557	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92715176	T	A	92715176	3	1	88	1	0	0	0	0	1	0	0	0	9982	1580	55	5	793	5	MTNR1B	11	92715176	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	14830339	92715176	42291340	69	24364										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113105851	113105851	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tggcaaagggctgggtgagaTcagcgcggcctccgagttca	16	10	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:113105851T>A	ENST00000533760.1	+	13	2005	c.1406T>A	c.(1405-1407)aTc>aAc	p.I469N	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.I596N|NCAM1_ENST00000316851.7_Missense_Mutation_p.I587N	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	597	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CTGGGTGAGATCAGCGCGGCC	0.627																																																0			11											29	33	32					11																	113105851		2026	4158	6184	112611061	SO:0001583	missense	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1406T>A	11.37:g.113105851T>A	ENSP00000473281:p.Ile469Asn		112611061	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	T	17.96	3.515188	0.64634	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851;ENST00000433634	T;T	0.54071	1.07;0.59	5.84	5.84	0.93424	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.055536	0.64402	U	0.000002	T	0.42698	0.1214	.	.	.	0.45490	D	0.998453	P;P;P;P	0.40360	0.666;0.666;0.714;0.521	B;B;B;B	0.33521	0.13;0.067;0.11;0.165	T	0.39522	-0.9610	9	0.39692	T	0.17	-47.4708	14.7798	0.69756	0.0:0.0:0.0:1.0	.	597;587;597;587	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	N	469;596;587;31	ENSP00000384055:I596N;ENSP00000318472:I587N	ENSP00000318472:I587N	I	+	2	0	NCAM1	112611061	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.694000	0.54742	2.233000	0.73108	0.482000	0.46254	ATC		0.627	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		A	113105851	T	A	113105851	3	1	88	1	0	0	0	0	1	0	0	0	10233	1435	50	5	1845	5	NCAM1	11	113105851	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	20390675	113105851	21900665	70	24365										
OPCML	4978	hgsc.bcm.edu	37	chr11	132527046	132527046	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtctgcacagagcaggtgtaCggaccttcgtcatacacatc	10	12	2	1	rs369569350		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:132527046C>T	ENST00000331898.7	-	2	914	c.336G>A	c.(334-336)ccG>ccA	p.P112P	OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000524381.1_Silent_p.P105P|OPCML_ENST00000374778.4_Silent_p.P71P|OPCML_ENST00000541867.1_Silent_p.P112P	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	112	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		AGCAGGTGTACGGACCTTCGT	0.502																																																0			11						C	,	0,4402		0,0,2201	252	197	216		315,336	-11.7	0	11		216	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	OPCML	NM_001012393.1,NM_002545.3	,	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	,	105/339,112/346	132527046	1,12995	2201	4297	6498	132032256	SO:0001819	synonymous_variant	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.336G>A	11.37:g.132527046C>T			132032256	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Silent	SNP	ENST00000331898.7	37	CCDS8492.1																																																																																				0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132527046	C	T	132527046	2	4	88	1	0	0	0	0	0	0	0	1	10905	523	19	1		1	OPCML	11	132527046	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	19421195	132527046	2479470	71	24366										
SPATA19	219938	hgsc.bcm.edu	37	chr11	133714516	133714516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	acagcttttcctttatgcccCgagaagcctcttcttctgtc	6	14	3	1	rs371989839		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr11:133714516C>T	ENST00000299140.3	-	3	209	c.155G>A	c.(154-156)cGg>cAg	p.R52Q	SPATA19_ENST00000532889.1_Missense_Mutation_p.R52Q	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	52					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		CTTTATGCCCCGAGAAGCCTC	0.507																																																0			11						C	GLN/ARG	0,4402		0,0,2201	104	105	105		155	0.2	0.9	11		105	1,8593	1.2+/-3.3	0,1,4296	no	missense	SPATA19	NM_174927.1	43	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	benign	52/168	133714516	1,12995	2201	4297	6498	133219726	SO:0001583	missense	219938			AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"spergen 1", "cancer/testis antigen 132"	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.155G>A	11.37:g.133714516C>T	ENSP00000299140:p.Arg52Gln		133219726	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	37	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	C	3.802	-0.041422	0.07452	0.0	1.16E-4	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.47869	0.83;0.83	5.35	0.216	0.15258	.	0.364091	0.23591	N	0.046546	T	0.16514	0.0397	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18493	-1.0335	10	0.10902	T	0.67	0.4011	3.9247	0.09259	0.1476:0.2588:0.0:0.5937	.	52	Q7Z5L4	SPT19_HUMAN	Q	52	ENSP00000299140:R52Q;ENSP00000435248:R52Q	ENSP00000299140:R52Q	R	-	2	0	SPATA19	133219726	0.006000	0.16342	0.906000	0.35671	0.578000	0.36192	0.162000	0.16501	0.024000	0.15214	-1.286000	0.01371	CGG		0.507	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927		T	133714516	C	T	133714516	3	4	88	1	0	0	0	0	1	0	0	0	15043	652	23	1	364	1	SPATA19	11	133714516	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	1187470	133714516	1292000	72	24367										
SLC2A3	6515	hgsc.bcm.edu	37	chr12	8075422	8075422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ggtgagtttacttacagcagCggaggggaagagcaatccga	15	7	0	2	rs201737691		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:8075422C>T	ENST00000075120.7	-	9	1507	c.1267G>A	c.(1267-1269)Gct>Act	p.A423T		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	423					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)	p.A423S(2)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		CTTACAGCAGCGGAGGGGAAG	0.547																																					Colon(96;424 1461 14416 20933 23688)											2	Substitution - Missense(2)	lung(2)	12											46	47	47					12																	8075422		2203	4300	6503	7966689	SO:0001583	missense	6515			M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.1267G>A	12.37:g.8075422C>T	ENSP00000075120:p.Ala423Thr		7966689	B2R606|D3DUU6|Q6I9U2|Q9UG15	Missense_Mutation	SNP	ENST00000075120.7	37	CCDS8586.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503157	0.44558	.	.	ENSG00000059804	ENST00000075120;ENST00000540978	T	0.81078	-1.45	4.34	4.34	0.51931	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.119065	0.56097	D	0.000022	D	0.85483	0.5707	L	0.55481	1.735	0.35028	D	0.758461	D	0.57571	0.98	P	0.61477	0.889	D	0.90292	0.4323	10	0.87932	D	0	.	14.7219	0.69314	0.0:1.0:0.0:0.0	.	423	P11169	GTR3_HUMAN	T	423;349	ENSP00000075120:A423T	ENSP00000075120:A423T	A	-	1	0	SLC2A3	7966689	0.944000	0.32072	0.938000	0.37757	0.037000	0.13140	2.007000	0.40883	2.398000	0.81561	0.655000	0.94253	GCT		0.547	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		T	8075422	C	T	8075422	3	4	88	1	0	0	0	0	1	0	0	0	14582	768	27	1	231	1	SLC2A3	12	8075422	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		8075422	125776473	73	24368										
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10233936	10233936	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgaagagattgcaactcttgGgacgtatttcctaatctttc	8	8	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:10233936G>T	ENST00000315330.4	-	3	353	c.291C>A	c.(289-291)tcC>tcA	p.S97S	CLEC1A_ENST00000457018.2_Silent_p.S64S|CLEC1A_ENST00000420265.2_Intron|RN7SKP161_ENST00000411110.1_RNA	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	97					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						GCAACTCTTGGGACGTATTTC	0.423																																																0			12											128	127	127					12																	10233936		2203	4300	6503	10125203	SO:0001819	synonymous_variant	51267			AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.291C>A	12.37:g.10233936G>T			10125203	Q8IUW7|Q9NZH3	Silent	SNP	ENST00000315330.4	37	CCDS8612.1																																																																																				0.423	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		T	10233936	G	T	10233936	2	4	88	1	0	0	0	0	0	0	0	1	3511	1219	43	2		2	CLEC1A	12	10233936	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	2158514	10233936	123617959	74	24369										
LOH12CR1	118426	hgsc.bcm.edu	37	chr12	12514215	12514215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcagggctcccaggcctcacGgaacgtcagcaacgatcccg	11	16	3	0	rs144877374	byFrequency	TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:12514215G>A	ENST00000314565.4	+	2	465	c.134G>A	c.(133-135)cGg>cAg	p.R45Q	LOH12CR1_ENST00000298571.6_Intron|LOH12CR1_ENST00000542728.1_Missense_Mutation_p.R26Q	NM_058169.3	NP_477517.1	Q969J3	L12R1_HUMAN	loss of heterozygosity, 12, chromosomal region 1	45								p.R45Q(1)		kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		CAGGCCTCACGGAACGTCAGC	0.458																																																1	Substitution - Missense(1)	ovary(1)	12						G	GLN/ARG	0,4406		0,0,2203	190	172	178		134	6	1	12	dbSNP_134	178	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOH12CR1	NM_058169.3	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	45/197	12514215	1,13005	2203	4300	6503	12405482	SO:0001583	missense	118426			AY037865	CCDS8649.1, CCDS73448.1	12p12	2008-07-03			ENSG00000165714	ENSG00000165714			17950	protein-coding gene	gene with protein product						11896457, 15284860	Standard	XR_242885		Approved	LOH1CR12	uc001ral.2	Q969J3	OTTHUMG00000168542	ENST00000314565.4:c.134G>A	12.37:g.12514215G>A	ENSP00000321546:p.Arg45Gln		12405482	Q96QS5	Missense_Mutation	SNP	ENST00000314565.4	37	CCDS8649.1	.	.	.	.	.	.	.	.	.	.	g	15.16	2.752380	0.49362	0.0	1.16E-4	ENSG00000165714	ENST00000542728;ENST00000314565	T;T	0.30448	1.53;1.53	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.46328	0.1387	L	0.41710	1.295	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.06770	-1.0808	10	0.12766	T	0.61	-22.113	20.1362	0.98031	0.0:0.0:1.0:0.0	.	45	Q969J3	L12R1_HUMAN	Q	26;45	ENSP00000443023:R26Q;ENSP00000321546:R45Q	ENSP00000321546:R45Q	R	+	2	0	LOH12CR1	12405482	1.000000	0.71417	0.981000	0.43875	0.997000	0.91878	9.353000	0.97080	2.861000	0.98227	0.651000	0.88453	CGG		0.458	LOH12CR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400150.1			A	12514215	G	A	12514215	3	1	88	1	0	0	0	0	1	0	0	0	8920	1116	39	1	140	1	LOH12CR1	12	12514215	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	2280279	12514215	121337680	75	24370										
PYROXD1	79912	hgsc.bcm.edu	37	chr12	21590675	21590675	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtccggcagcatggaggcagCgcgccctcccccgacggcag	15	17	0	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:21590675C>G	ENST00000240651.9	+	1	65	c.11C>G	c.(10-12)gCg>gGg	p.A4G	PYROXD1_ENST00000538582.1_5'Flank|PYROXD1_ENST00000545178.1_Missense_Mutation_p.A4G	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	4							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						ATGGAGGCAGCGCGCCCTCCC	0.687																																																0			12											17	21	19					12																	21590675		2201	4300	6501	21481942	SO:0001583	missense	79912			AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.11C>G	12.37:g.21590675C>G	ENSP00000240651:p.Ala4Gly		21481942	A6NKI6|B3KWN8|Q9H6P1	Missense_Mutation	SNP	ENST00000240651.9	37	CCDS31755.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883879	0.72410	.	.	ENSG00000121350	ENST00000545178;ENST00000240651	.	.	.	5.57	3.72	0.42706	.	0.781535	0.11925	N	0.516320	T	0.38799	0.1054	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.27706	-1.0066	9	0.44086	T	0.13	.	9.221	0.37377	0.0:0.7752:0.1456:0.0792	.	4	Q8WU10	PYRD1_HUMAN	G	4	.	ENSP00000240651:A4G	A	+	2	0	PYROXD1	21481942	0.000000	0.05858	0.001000	0.08648	0.910000	0.53928	0.777000	0.26718	0.683000	0.31428	0.643000	0.83706	GCG		0.687	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854		G	21590675	C	G	21590675	3	3	88	1	0	0	0	0	1	0	0	0	12903	768	27	5	13	5	PYROXD1	12	21590675	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	9076460	21590675	112261220	76	24371										
SYT10	341359	hgsc.bcm.edu	37	chr12	33559864	33559864	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atacacactgaaatgtagttTtcggttgcttagttgatcat	8	6	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:33559864T>G	ENST00000228567.3	-	3	1233	c.937A>C	c.(937-939)Aaa>Caa	p.K313Q	RP11-438D14.2_ENST00000561632.1_lincRNA|SYT10_ENST00000567656.1_5'Flank|SYT10_ENST00000535526.1_Missense_Mutation_p.K132Q	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	313	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					AAATGTAGTTTTCGGTTGCTT	0.353																																																0			12											110	110	110					12																	33559864		2203	4300	6503	33451131	SO:0001583	missense	341359			AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.937A>C	12.37:g.33559864T>G	ENSP00000228567:p.Lys313Gln		33451131	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826698	0.71143	.	.	ENSG00000110975	ENST00000228567;ENST00000535526	T;T	0.07688	3.17;3.17	4.73	4.73	0.59995	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.44097	U	0.000485	T	0.18425	0.0442	L	0.33189	0.99	0.49299	D	0.999779	D	0.67145	0.996	D	0.72625	0.978	T	0.01081	-1.1458	10	0.54805	T	0.06	.	14.1024	0.65065	0.0:0.0:0.0:1.0	.	313	Q6XYQ8	SYT10_HUMAN	Q	313;132	ENSP00000228567:K313Q;ENSP00000438691:K132Q	ENSP00000228567:K313Q	K	-	1	0	SYT10	33451131	1.000000	0.71417	0.990000	0.47175	0.967000	0.64934	5.870000	0.69620	2.056000	0.61249	0.460000	0.39030	AAA		0.353	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		G	33559864	T	G	33559864	3	3	88	1	0	0	0	0	1	0	0	0	15505	1850	64	4	654	4	SYT10	12	33559864	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	11969189	33559864	100292031	77	24372										
ALDH2	217	hgsc.bcm.edu	37	chr12	112229927	112229927	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aagagagtgaccttggagctGggggggaagagccccaacat	16	8	0	3	rs554937672		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:112229927G>T	ENST00000261733.2	+	8	919	c.858G>T	c.(856-858)ctG>ctT	p.L286L	ALDH2_ENST00000416293.3_Silent_p.L239L	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	286					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)	p.K289fs*45(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	CCTTGGAGCTGGGGGGGAAGA	0.572			T	HMGA2	leiomyoma																																		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	2	Insertion - Frameshift(2)	ovary(2)	12																																								110714310	SO:0001819	synonymous_variant	217			M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.858G>T	12.37:g.112229927G>T			110714310	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Silent	SNP	ENST00000261733.2	37	CCDS9155.1																																																																																				0.572	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		T	112229927	G	T	112229927	2	4	88	1	0	0	0	0	0	0	0	1	496	1335	47	2		2	ALDH2	12	112229927	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	78670063	112229927	21621968	78	24373										
RFC5	5985	hgsc.bcm.edu	37	chr12	118462802	118462802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttccccgcctggaacatgtcGtggaagaagagaagtgagta	13	8	0	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr12:118462802G>A	ENST00000454402.2	+	6	686	c.568G>A	c.(568-570)Gtg>Atg	p.V190M	RFC5_ENST00000392542.2_Missense_Mutation_p.V169M|RFC5_ENST00000229043.3_Missense_Mutation_p.V105M	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	190					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGAACATGTCGTGGAAGAAGA	0.532																																																0			12											86	85	86					12																	118462802		2203	4300	6503	116947185	SO:0001583	missense	5985				CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.568G>A	12.37:g.118462802G>A	ENSP00000408295:p.Val190Met		116947185	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	37	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.254159	0.39896	.	.	ENSG00000111445	ENST00000229043;ENST00000454402;ENST00000392542	T;T;T	0.45276	1.46;0.9;1.9	5.47	1.09	0.20402	.	0.407102	0.26784	N	0.022512	T	0.31199	0.0789	M	0.68952	2.095	0.19300	N	0.99997	P;P;P	0.40476	0.5;0.5;0.718	B;B;B	0.22880	0.042;0.042;0.042	T	0.25012	-1.0144	10	0.62326	D	0.03	-13.1107	9.5861	0.39517	0.4026:0.0:0.5974:0.0	.	169;204;190	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	M	105;190;169	ENSP00000229043:V105M;ENSP00000408295:V190M;ENSP00000376325:V169M	ENSP00000229043:V105M	V	+	1	0	RFC5	116947185	0.140000	0.22579	0.004000	0.12327	0.955000	0.61496	0.840000	0.27600	0.290000	0.22444	0.563000	0.77884	GTG		0.532	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		A	118462802	G	A	118462802	3	1	88	1	0	0	0	0	1	0	0	0	13285	1145	40	1	596	1	RFC5	12	118462802	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	6232875	118462802	15389093	79	24374										
SACS	26278	hgsc.bcm.edu	37	chr13	23913600	23913600	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	taaaaatatctgacactgaaGggtattcttccagaatattt	6	6	2	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr13:23913600G>T	ENST00000382292.3	-	9	4688	c.4415C>A	c.(4414-4416)cCt>cAt	p.P1472H	SACS_ENST00000402364.1_Missense_Mutation_p.P722H|SACS_ENST00000382298.3_Missense_Mutation_p.P1472H			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1472					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGACACTGAAGGGTATTCTTC	0.343																																																0			13											83	83	83					13																	23913600		2203	4299	6502	22811600	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.4415C>A	13.37:g.23913600G>T	ENSP00000371729:p.Pro1472His		22811600	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895385	0.72639	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.93859	-3.3;-3.3;-3.3	5.79	5.79	0.91817	ATPase-like, ATP-binding domain (2);	0.054015	0.85682	D	0.000000	D	0.95608	0.8572	L	0.47716	1.5	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.95676	0.8728	10	0.87932	D	0	.	20.0413	0.97592	0.0:0.0:1.0:0.0	.	1472	Q9NZJ4	SACS_HUMAN	H	1472;722;1472	ENSP00000371729:P1472H;ENSP00000385844:P722H;ENSP00000371735:P1472H	ENSP00000371729:P1472H	P	-	2	0	SACS	22811600	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.476000	0.97823	2.751000	0.94390	0.650000	0.86243	CCT		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23913600	G	T	23913600	3	4	88	1	0	0	0	0	1	0	0	0	13841	1000	35	2	9328	2	SACS	13	23913600	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		23913600	91256278	80	24375										
POSTN	10631	hgsc.bcm.edu	37	chr13	38153364	38153364	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aaattcattctagacaacttActtctttcagaaagattttg	4	7	4	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr13:38153364A>C	ENST00000379747.4	-	13	1909		c.e13+1		POSTN_ENST00000541481.1_Splice_Site|POSTN_ENST00000379742.4_Splice_Site|POSTN_ENST00000379743.4_Splice_Site|POSTN_ENST00000379749.4_Splice_Site|POSTN_ENST00000541179.1_Splice_Site	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor						cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		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)		TAGACAACTTACTTCTTTCAG	0.318																																																0			13											82	75	78					13																	38153364		2203	4299	6502	37051364	SO:0001630	splice_region_variant	10631			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1791+1T>G	13.37:g.38153364A>C			37051364	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Splice_Site	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.089904	0.76756	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2774	0.82651	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POSTN	37051364	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	6.201000	0.72124	2.247000	0.74100	0.482000	0.46254	.		0.318	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	Intron	C	38153364	A	C	38153364	5	2	88	1	0	0	0	0	0	0	1	0	12290	405	14	4	761	4	POSTN	13	38153364	Splice_Site	SNP	A	TCGA-CI-6621-01A-11D-1826-10	14239764	38153364	77016514	81	24376										
RB1	5925	hgsc.bcm.edu	37	chr13	48923113	48923113	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atatctactgaaataaattcTgcattggtgctaaaagtttc	6	6	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr13:48923113T>C	ENST00000267163.4	+	6	699	c.561T>C	c.(559-561)tcT>tcC	p.S187S		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	187					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAATAAATTCTGCATTGGTGC	0.249		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	21	Whole gene deletion(15)|Unknown(6)	bone(11)|breast(6)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											62	67	65					13																	48923113		2198	4278	6476	47821114	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.561T>C	13.37:g.48923113T>C			47821114	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.249	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	48923113	T	C	48923113	2	2	88	1	0	0	0	0	0	0	0	1	13135	1567	55	4		4	RB1	13	48923113	Silent	SNP	T	TCGA-CI-6621-01A-11D-1826-10	10769749	48923113	66246765	82	24377										
RB1	5925	hgsc.bcm.edu	37	chr13	49037878	49037878	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	atttactagattatgatgtgTtccatgtatggcatatgcaa	8	5	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr13:49037878T>C	ENST00000267163.4	+	21	2256	c.2118T>C	c.(2116-2118)tgT>tgC	p.C706C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	706	Domain B.|Pocket; binds T and E1A.		C -> Y (in RB).		androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.M705_S707delMCS(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTATGATGTGTTCCATGTATG	0.303		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											95	101	99					13																	49037878		2203	4296	6499	47935879	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2118T>C	13.37:g.49037878T>C			47935879	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.303	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	49037878	T	C	49037878	2	2	88	1	0	0	0	0	0	0	0	1	13135	1731	60	4		4	RB1	13	49037878	Silent	SNP	T	TCGA-CI-6621-01A-11D-1826-10	114765	49037878	66132000	83	24378										
UTP14C	9724	hgsc.bcm.edu	37	chr13	52604326	52604326	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tccgaattgagggcactatcTcagaaattgaaggaaaaaca	9	7	1	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr13:52604326T>C	ENST00000521776.2	+	2	2119	c.1386T>C	c.(1384-1386)tcT>tcC	p.S462S		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	462					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		GGGCACTATCTCAGAAATTGA	0.498																																																0			13											92	97	96					13																	52604326		2203	4300	6503	51502327	SO:0001819	synonymous_variant	440138			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.1386T>C	13.37:g.52604326T>C			51502327	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	37	CCDS31978.1																																																																																				0.498	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		C	52604326	T	C	52604326	2	2	88	1	0	0	0	0	0	0	0	1	17136	1538	54	4		4	UTP14C	13	52604326	Silent	SNP	T	TCGA-CI-6621-01A-11D-1826-10	3566448	52604326	62565552	84	24379										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47530616	47530616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cagtctgtgtaatgaccatcCgctcagaacttcttaatgga	8	10	3	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr14:47530616C>T	ENST00000399232.2	-	7	1518	c.1154G>A	c.(1153-1155)cGg>cAg	p.R385Q	MDGA2_ENST00000439988.3_Missense_Mutation_p.R454Q|MDGA2_ENST00000357362.3_Missense_Mutation_p.R156Q|MDGA2_ENST00000426342.1_Missense_Mutation_p.R156Q	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	385	Ig-like 4.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R156Q(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						AATGACCATCCGCTCAGAACT	0.418																																																1	Substitution - Missense(1)	ovary(1)	14											158	142	147					14																	47530616		1897	4112	6009	46600366	SO:0001583	missense	161357			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1154G>A	14.37:g.47530616C>T	ENSP00000382178:p.Arg385Gln		46600366	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	C	33	5.282825	0.95489	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.64	5.64	0.86602	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47455	U	0.000235	T	0.70928	0.3280	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.73930	-0.3827	10	0.87932	D	0	.	18.2795	0.90094	0.0:1.0:0.0:0.0	.	385	Q7Z553	MDGA2_HUMAN	Q	385;156;454;156	ENSP00000400011:R385Q;ENSP00000405456:R156Q;ENSP00000382178:R454Q;ENSP00000349925:R156Q	ENSP00000349925:R156Q	R	-	2	0	MDGA2	46600366	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.770000	0.85390	2.658000	0.90341	0.655000	0.94253	CGG		0.418	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47530616	C	T	47530616	3	4	88	1	0	0	0	0	1	0	0	0	9437	652	23	1	1760	1	MDGA2	14	47530616	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		47530616	59818924	85	24380										
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70633479	70633479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	taccccgggcacctgatgtcCgcagaaccttgacctccata	8	16	0	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr14:70633479C>T	ENST00000381269.2	-	2	2414	c.1661G>A	c.(1660-1662)cGg>cAg	p.R554Q	SLC8A3_ENST00000528359.1_Missense_Mutation_p.R554Q|SLC8A3_ENST00000356921.2_Missense_Mutation_p.R554Q|SLC8A3_ENST00000534137.1_Missense_Mutation_p.R554Q|SLC8A3_ENST00000357887.3_Missense_Mutation_p.R554Q	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	554	Calx-beta 2.				blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)	p.R554L(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		ACCTGATGTCCGCAGAACCTT	0.493																																																1	Substitution - Missense(1)	central_nervous_system(1)	14											94	92	93					14																	70633479		2203	4300	6503	69703232	SO:0001583	missense	6547			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1661G>A	14.37:g.70633479C>T	ENSP00000370669:p.Arg554Gln		69703232	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270682	0.80469	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.69	5.69	0.88448	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.78868	0.4351	H	0.97465	4.01	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.83275	0.994;0.996;0.974;0.991	D	0.86178	0.1604	10	0.87932	D	0	.	19.8067	0.96534	0.0:1.0:0.0:0.0	.	554;554;554;554	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	Q	554	ENSP00000349392:R554Q;ENSP00000370669:R554Q;ENSP00000350560:R554Q;ENSP00000436688:R554Q;ENSP00000433531:R554Q	ENSP00000349392:R554Q	R	-	2	0	SLC8A3	69703232	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.818000	0.86416	2.672000	0.90937	0.650000	0.86243	CGG		0.493	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70633479	C	T	70633479	3	4	88	1	0	0	0	0	1	0	0	0	14745	652	23	1	1261	1	SLC8A3	14	70633479	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	23102863	70633479	36716061	86	24381										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102551684	102551684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gagaatgtttcttcacaatcTcctttattcttcgttcctcc	4	12	4	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr14:102551684T>C	ENST00000216281.8	-	4	819	c.614A>G	c.(613-615)gAg>gGg	p.E205G	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E327G|HSP90AA1_ENST00000441629.2_Missense_Mutation_p.E26G	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	205					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	CTTCACAATCTCCTTTATTCT	0.383																																																0			14											88	72	77					14																	102551684		2203	4300	6503	101621437	SO:0001583	missense	3320			M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.614A>G	14.37:g.102551684T>C	ENSP00000216281:p.Glu205Gly		101621437	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	37	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	t	20.2	3.947245	0.73672	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629;ENST00000553585	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	4.29	4.29	0.51040	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (2);	0.000000	0.85682	U	0.000000	T	0.22437	0.0541	M	0.89214	3.015	0.80722	D	1	B;P;P	0.48503	0.379;0.911;0.729	B;B;B	0.38056	0.247;0.264;0.117	T	0.36359	-0.9751	10	0.87932	D	0	-30.5266	13.741	0.62847	0.0:0.0:0.0:1.0	.	26;327;205	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	G	205;327;26;136	ENSP00000216281:E205G;ENSP00000335153:E327G;ENSP00000396189:E26G;ENSP00000450712:E136G	ENSP00000216281:E205G	E	-	2	0	HSP90AA1	101621437	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	6.097000	0.71452	1.723000	0.51488	0.528000	0.53228	GAG		0.383	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		C	102551684	T	C	102551684	3	2	88	1	0	0	0	0	1	0	0	0	7422	1551	54	4	1616	4	HSP90AA1	14	102551684	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	31918205	102551684	4797856	87	24382										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104470578	104470578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	acatctctcctttgaaggccGtgctggacgagtgtctagag	12	10	2	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr14:104470578G>A	ENST00000409874.4	+	14	1535	c.1487G>A	c.(1486-1488)cGt>cAt	p.R496H	TDRD9_ENST00000339063.5_Missense_Mutation_p.R496H	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	496	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TTTGAAGGCCGTGCTGGACGA	0.403																																																0			14											114	88	97					14																	104470578		2203	4300	6503	103540331	SO:0001583	missense	122402			AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1487G>A	14.37:g.104470578G>A	ENSP00000387303:p.Arg496His		103540331	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	37	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	G	32	5.191206	0.94923	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	D;D	0.99143	-5.48;-5.48	5.87	5.87	0.94306	Helicase, C-terminal (3);	0.092772	0.46758	D	0.000275	D	0.99563	0.9843	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	0.99;1.0	P;D	0.97110	0.671;1.0	D	0.98256	1.0496	10	0.62326	D	0.03	.	20.2033	0.98269	0.0:0.0:1.0:0.0	.	496;496	Q8NDG6-2;Q8NDG6	.;TDRD9_HUMAN	H	496	ENSP00000387303:R496H;ENSP00000343545:R496H	ENSP00000343545:R496H	R	+	2	0	TDRD9	103540331	1.000000	0.71417	0.993000	0.49108	0.916000	0.54674	5.737000	0.68606	2.779000	0.95612	0.655000	0.94253	CGT		0.403	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		A	104470578	G	A	104470578	3	1	88	1	0	0	0	0	1	0	0	0	15775	1145	40	1	1541	1	TDRD9	14	104470578	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	1918894	104470578	2878962	88	24383										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396965	396965	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	accaggcactgggggtcgggGagcatcttcggtgaaacttg	16	9	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:396965G>A	ENST00000262320.3	-	2	432	c.61C>T	c.(61-63)Ccc>Tcc	p.P21S	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.P21S	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	21					activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGGGGTCGGGGAGCATCTTCG	0.572																																																0			16											55	61	59					16																	396965		2203	4300	6503	336966	SO:0001583	missense	8312			AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.61C>T	16.37:g.396965G>A	ENSP00000262320:p.Pro21Ser		336966	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	37	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743788	0.89663	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.67171	-0.25;-0.22	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.83440	0.5255	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85614	0.1260	10	0.87932	D	0	-15.419	19.0272	0.92937	0.0:0.0:1.0:0.0	.	21;21	O15169-2;O15169	.;AXIN1_HUMAN	S	21	ENSP00000262320:P21S;ENSP00000346935:P21S	ENSP00000262320:P21S	P	-	1	0	AXIN1	336966	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.647000	0.98478	2.517000	0.84864	0.650000	0.86243	CCC		0.572	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	396965	G	A	396965	3	1	88	1	0	0	0	0	1	0	0	0	1237	1174	41	3	2567	3	AXIN1	16	396965	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		396965	89957788	89	24384										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27720104	27720104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tcctgtccaactggggcaacTcgtggtgggtgggtctcaca	14	11	1	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:27720104T>C	ENST00000261588.4	+	13	1487	c.1468T>C	c.(1468-1470)Tcg>Ccg	p.S490P	CTD-2049O4.1_ENST00000568831.1_RNA|KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA|CTD-2049O4.1_ENST00000563052.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	490						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CTGGGGCAACTCGTGGTGGGT	0.488																																																0			16											110	97	102					16																	27720104		2197	4300	6497	27627605	SO:0001583	missense	23247			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1468T>C	16.37:g.27720104T>C	ENSP00000261588:p.Ser490Pro		27627605	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	8.296	0.818744	0.16607	.	.	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.13307	2.6	5.49	-8.74	0.00838	.	1.284590	0.05115	N	0.489669	T	0.04634	0.0126	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.37888	-0.9686	10	0.26408	T	0.33	-3.2659	6.7198	0.23325	0.1897:0.5346:0.1804:0.0953	.	398;490	Q8N803;O60303	.;K0556_HUMAN	P	490;397	ENSP00000261588:S490P	ENSP00000261588:S490P	S	+	1	0	KIAA0556	27627605	0.000000	0.05858	0.000000	0.03702	0.769000	0.43574	-1.331000	0.02672	-2.154000	0.00792	-0.464000	0.05259	TCG		0.488	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		C	27720104	T	C	27720104	3	2	88	1	0	0	0	0	1	0	0	0	8204	1551	54	4	1518	4	KIAA0556	16	27720104	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	27323139	27720104	62634649	90	24385										
GPT2	84706	hgsc.bcm.edu	37	chr16	46943598	46943598	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtgaattctctgttgcagacGatcctgaagatcctcgtctc	9	11	2	4			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:46943598G>T	ENST00000340124.4	+	6	691	c.579G>T	c.(577-579)acG>acT	p.T193T	GPT2_ENST00000440783.2_Silent_p.T93T	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2	193					2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|Phenelzine(DB00780)	TGTTGCAGACGATCCTGAAGA	0.552																																																0			16											46	46	46					16																	46943598		2203	4300	6503	45501099	SO:0001819	synonymous_variant	84706				CCDS10725.1, CCDS45478.1	16q12.1	2008-02-05			ENSG00000166123	ENSG00000166123	2.6.1.2		18062	protein-coding gene	gene with protein product		138210					Standard	NM_133443		Approved	ALT2	uc002eel.3	Q8TD30	OTTHUMG00000132541	ENST00000340124.4:c.579G>T	16.37:g.46943598G>T			45501099	Q8N9E2	Silent	SNP	ENST00000340124.4	37	CCDS10725.1																																																																																				0.552	GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2			T	46943598	G	T	46943598	2	4	88	1	0	0	0	0	0	0	0	1	6759	1045	37	2		2	GPT2	16	46943598	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	19223494	46943598	43411155	91	24386										
SALL1	6299	hgsc.bcm.edu	37	chr16	51172863	51172863	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ggagaaacatgcacgaagccGttgacctctgtcttgatgag	12	9	2	4	rs143637930		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:51172863G>A	ENST00000251020.4	-	2	3303	c.3270C>T	c.(3268-3270)aaC>aaT	p.N1090N	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.N993N	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1090					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GCACGAAGCCGTTGACCTCTG	0.567																																					GBM(103;1352 1446 1855 4775 8890)											0			16						G	,	0,4396		0,0,2198	114	105	108		2979,3270	2.1	1	16	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	,	993/1228,1090/1325	51172863	1,12995	2198	4300	6498	49730364	SO:0001819	synonymous_variant	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3270C>T	16.37:g.51172863G>A			49730364	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																				0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51172863	G	A	51172863	2	1	88	1	0	0	0	0	0	0	0	1	13847	1136	40	1		1	SALL1	16	51172863	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	4229265	51172863	39181890	92	24387										
SLC7A6	9057	hgsc.bcm.edu	37	chr16	68325537	68325537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cctgtcctgctttgggggccTcaatgcatccatctttgctt	9	13	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:68325537T>C	ENST00000566454.1	+	8	1264	c.995T>C	c.(994-996)cTc>cCc	p.L332P	SLC7A6_ENST00000219343.6_Missense_Mutation_p.L332P	NM_001076785.2	NP_001070253.1			solute carrier family 7 (amino acid transporter light chain, y+L system), member 6											breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.0948)		TTTGGGGGCCTCAATGCATCC	0.498																																																0			16											305	257	273					16																	68325537		2198	4300	6498	66883038	SO:0001583	missense	9057			D87432	CCDS32470.1	16q22.1	2013-07-15	2011-07-12		ENSG00000103064	ENSG00000103064		"Solute carriers"	11064	protein-coding gene	gene with protein product		605641				9878049	Standard	NM_001076785		Approved	y+LAT-2, KIAA0245, LAT3, LAT-2	uc002evu.2	Q92536	OTTHUMG00000176544	ENST00000566454.1:c.995T>C	16.37:g.68325537T>C	ENSP00000455064:p.Leu332Pro		66883038		Missense_Mutation	SNP	ENST00000566454.1	37	CCDS32470.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543821	0.86022	.	.	ENSG00000103064	ENST00000219343	D	0.91180	-2.8	5.09	5.09	0.68999	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.96623	0.8898	H	0.96333	3.805	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.97530	1.0079	10	0.72032	D	0.01	.	13.0972	0.59200	0.0:0.0:0.0:1.0	.	332	Q92536	YLAT2_HUMAN	P	332	ENSP00000219343:L332P	ENSP00000219343:L332P	L	+	2	0	SLC7A6	66883038	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.719000	0.84751	2.036000	0.60181	0.533000	0.62120	CTC		0.498	SLC7A6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432466.1	NM_003983		C	68325537	T	C	68325537	3	2	88	1	0	0	0	0	1	0	0	0	14738	1551	54	4	1013	4	SLC7A6	16	68325537	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	17152674	68325537	22029216	93	24388										
CHST6	4166	hgsc.bcm.edu	37	chr16	75513568	75513568	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aagagttggcccacgaaggaCgagcccgagcgccacgagga	15	12	0	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr16:75513568C>T	ENST00000332272.4	-	3	338	c.159G>A	c.(157-159)tcG>tcA	p.S53S	CHST6_ENST00000390664.2_Silent_p.S53S|RP11-77K12.4_ENST00000530512.3_RNA	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	53			S -> L (in MCDC1). {ECO:0000269|PubMed:14609920, ECO:0000269|PubMed:14735064}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CCACGAAGGACGAGCCCGAGC	0.677																																																0			16											37	31	33					16																	75513568		2198	4300	6498	74071069	SO:0001819	synonymous_variant	4166			AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"Sulfotransferases, membrane-bound"	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.159G>A	16.37:g.75513568C>T			74071069	D3DUK3	Silent	SNP	ENST00000332272.4	37	CCDS10918.1																																																																																				0.677	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615		T	75513568	C	T	75513568	2	4	88	1	0	0	0	0	0	0	0	1	3414	523	19	1		1	CHST6	16	75513568	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	7188031	75513568	14841185	94	24389										
TP53	7157	hgsc.bcm.edu	37	chr17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cccaggacaggcacaaacacGcacctcaaagctgttccgtc	8	16	1	0	rs121913343		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	17	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65	56	59					17																	7577121		2203	4300	6503	7517846	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		7517846	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577121	G	A	7577121	3	1	88	1	0	0	0	0	1	0	0	0	16421	1087	38	1	469	1	TP53	17	7577121	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		7577121	73618089	95	24390										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45438836	45438836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttttggatagcatgggtatcCctataaaccgtgaaatttta	8	6	0	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr17:45438836C>T	ENST00000331493.2	+	10	1165	c.754C>T	c.(754-756)Cct>Tct	p.P252S	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	252						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.P252S(1)									CATGGGTATCCCTATAAACCG	0.353																																																1	Substitution - Missense(1)	central_nervous_system(1)	17											187	182	184					17																	45438836		2203	4300	6503	42793835	SO:0001583	missense	124989			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.754C>T	17.37:g.45438836C>T	ENSP00000332111:p.Pro252Ser		42793835	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	C	0.243	-1.012309	0.02095	.	.	ENSG00000178852	ENST00000331493;ENST00000344176	T	0.32753	1.44	3.78	-4.4	0.03600	EF-hand-like domain (1);	2.388750	0.01940	N	0.041821	T	0.24122	0.0584	L	0.31664	0.95	0.09310	N	1	B;B	0.18013	0.025;0.009	B;B	0.11329	0.005;0.006	T	0.32798	-0.9893	10	0.51188	T	0.08	-14.2263	10.8007	0.46487	0.0:0.171:0.0:0.829	.	204;252	Q8N7U2;Q8IY85	.;CQ057_HUMAN	S	252;204	ENSP00000332111:P252S	ENSP00000332111:P252S	P	+	1	0	C17orf57	42793835	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.880000	0.04183	-1.036000	0.03287	-0.218000	0.12543	CCT		0.353	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		T	45438836	C	T	45438836	3	4	88	1	0	0	0	0	1	0	0	0	1870	623	22	3	780	3	C17orf57	17	45438836	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	37861715	45438836	35756374	96	24391										
IMPA2	3613	hgsc.bcm.edu	37	chr18	12030353	12030353	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tgtccccaggtggacccctcGacctcatggcttgcagagtg	12	14	1	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr18:12030353G>A	ENST00000269159.3	+	8	1005	c.763G>A	c.(763-765)Gac>Aac	p.D255N	RP11-703I16.1_ENST00000587619.1_RNA|IMPA2_ENST00000589238.1_Missense_Mutation_p.D66N|IMPA2_ENST00000588927.1_Missense_Mutation_p.D66N	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	255					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	TGGACCCCTCGACCTCATGGC	0.557																																																0			18											59	54	56					18																	12030353		2203	4300	6503	12020353	SO:0001583	missense	3613			AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.763G>A	18.37:g.12030353G>A	ENSP00000269159:p.Asp255Asn		12020353	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	37	CCDS11855.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012312	0.75046	.	.	ENSG00000141401	ENST00000269159	T	0.54071	0.59	4.55	4.55	0.56014	.	0.056003	0.64402	D	0.000002	T	0.44201	0.1282	N	0.25245	0.725	0.80722	D	1	B;P	0.40302	0.016;0.712	B;B	0.40677	0.022;0.337	T	0.47249	-0.9132	10	0.45353	T	0.12	-38.1128	18.1888	0.89800	0.0:0.0:1.0:0.0	.	228;255	O14732-2;O14732	.;IMPA2_HUMAN	N	255	ENSP00000269159:D255N	ENSP00000269159:D255N	D	+	1	0	IMPA2	12020353	1.000000	0.71417	0.998000	0.56505	0.917000	0.54804	6.214000	0.72200	2.471000	0.83476	0.561000	0.74099	GAC		0.557	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1			A	12030353	G	A	12030353	3	1	88	1	0	0	0	0	1	0	0	0	7744	1058	37	1	793	1	IMPA2	18	12030353	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		12030353	66046895	97	24392										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43490628	43490628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtcagccacctcggtcaaacGtctcttcatttctttcaaca	5	14	6	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr18:43490628G>A	ENST00000282041.5	-	23	4097	c.4063C>T	c.(4063-4065)Cgt>Tgt	p.R1355C	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1355					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TCGGTCAAACGTCTCTTCATT	0.488											OREG0024952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			18											86	84	84					18																	43490628		1884	4124	6008	41744626	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4063C>T	18.37:g.43490628G>A	ENSP00000282041:p.Arg1355Cys	916	41744626	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	19.86	3.906187	0.72868	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.13778	2.56	5.22	5.22	0.72569	.	0.000000	0.56097	D	0.000023	T	0.38639	0.1048	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.17167	-1.0378	10	0.87932	D	0	-13.5852	18.7803	0.91930	0.0:0.0:1.0:0.0	.	1355;1355	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	C	1355;230	ENSP00000282041:R1355C	ENSP00000282041:R1355C	R	-	1	0	EPG5	41744626	1.000000	0.71417	0.995000	0.50966	0.944000	0.59088	4.869000	0.63028	2.443000	0.82685	0.655000	0.94253	CGT		0.488	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43490628	G	A	43490628	3	1	88	1	0	0	0	0	1	0	0	0	8270	1145	40	1	3764	1	KIAA1632	18	43490628	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	31460275	43490628	34586620	98	24393										
DAPK3	1613	hgsc.bcm.edu	37	chr19	3964332	3964332	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtcgatgagcttgattcgtgGgttgggcacgttcttgtcca	14	8	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:3964332G>T	ENST00000545797.2	-	4	706	c.463C>A	c.(463-465)Cca>Aca	p.P155T	MIR637_ENST00000385000.1_RNA|DAPK3_ENST00000301264.3_Missense_Mutation_p.P155T			O43293	DAPK3_HUMAN	death-associated protein kinase 3	155	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGATTCGTGGGTTGGGCACG	0.617																																																0			19											223	129	161					19																	3964332		2203	4300	6503	3915332	SO:0001583	missense	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.463C>A	19.37:g.3964332G>T	ENSP00000442973:p.Pro155Thr		3915332	A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	37	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536271	0.65085	.	.	ENSG00000167657	ENST00000301264;ENST00000545797;ENST00000442766	T;T	0.38887	1.11;1.11	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.31009	0.0783	N	0.13235	0.315	0.80722	D	1	B	0.30741	0.293	B	0.33890	0.172	T	0.08472	-1.0720	10	0.23302	T	0.38	.	18.3495	0.90333	0.0:0.0:1.0:0.0	.	155	O43293	DAPK3_HUMAN	T	155;155;10	ENSP00000301264:P155T;ENSP00000442973:P155T	ENSP00000301264:P155T	P	-	1	0	DAPK3	3915332	1.000000	0.71417	0.404000	0.26397	0.201000	0.24016	9.562000	0.98145	2.581000	0.87130	0.561000	0.74099	CCA		0.617	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		T	3964332	G	T	3964332	3	4	88	1	0	0	0	0	1	0	0	0	4243	1232	43	2	925	2	DAPK3	19	3964332	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10		3964332	55164651	99	24394										
FUT3	2525	hgsc.bcm.edu	37	chr19	5844673	5844673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	caggatcaggagggtggggcGggtgggagtggtgtcctgtc	22	6	1	0	rs370374203		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:5844673G>A	ENST00000303225.6	-	3	812	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Missense_Mutation_p.R60C|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000458379.2_Missense_Mutation_p.R60C|FUT3_ENST00000589918.1_Missense_Mutation_p.R60C	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	60					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						AGGGTGGGGCGGGTGGGAGTG	0.632																																					Esophageal Squamous(82;745 1728 24593 44831)											0			19						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4404		0,0,2202	22	26	25		178,178,178,178	-0.2	0	19		25	1,8595		0,1,4297	no	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	180,180,180,180	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	60/362,60/362,60/362,60/362	5844673	1,12999	2202	4298	6500	5795673	SO:0001583	missense	2525				CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"CD molecules", "Blood group antigens", "Fucosyltransferases"	4014	protein-coding gene	gene with protein product		111100	"fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.178C>T	19.37:g.5844673G>A	ENSP00000305603:p.Arg60Cys		5795673	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640263	0.47153	0.0	1.16E-4	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.24723	1.84;1.84	2.33	-0.17	0.13335	.	29.287000	0.00496	U	0.000142	T	0.40171	0.1106	M	0.65498	2.005	0.09310	N	1	D;D;D;D	0.67145	0.996;0.996;0.992;0.996	P;P;P;P	0.54270	0.708;0.708;0.747;0.708	T	0.16719	-1.0393	10	0.62326	D	0.03	.	4.8714	0.13635	0.3845:0.0:0.6155:0.0	.	60;60;60;60	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	C	60	ENSP00000305603:R60C;ENSP00000416443:R60C	ENSP00000305603:R60C	R	-	1	0	FUT3	5795673	0.000000	0.05858	0.002000	0.10522	0.368000	0.29767	-0.327000	0.07955	-0.144000	0.11314	0.205000	0.17691	CGC		0.632	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		A	5844673	G	A	5844673	3	1	88	1	0	0	0	0	1	0	0	0	6124	1116	39	1	911	1	FUT3	19	5844673	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	1880341	5844673	53284310	100	24395										
DMRTC2	63946	hgsc.bcm.edu	37	chr19	42351632	42351632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ctccaacctgcgcccgctgcCgcaaccatggtgtcaccgcc	9	20	1	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:42351632C>T	ENST00000269945.3	+	2	187	c.136C>T	c.(136-138)Cgc>Tgc	p.R46C	LYPD4_ENST00000330743.3_5'Flank|LYPD4_ENST00000601246.1_5'Flank|DMRTC2_ENST00000602098.1_3'UTR|DMRTC2_ENST00000596827.1_Missense_Mutation_p.R46C	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	46					male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						CGCCCGCTGCCGCAACCATGG	0.617																																																0			19											73	69	70					19																	42351632		2203	4300	6503	47043472	SO:0001583	missense	63946			AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.136C>T	19.37:g.42351632C>T	ENSP00000269945:p.Arg46Cys		47043472	Q8N6Q2|Q96M39|Q96SD4	Missense_Mutation	SNP	ENST00000269945.3	37	CCDS33034.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.403539	0.83230	.	.	ENSG00000142025	ENST00000269945	.	.	.	4.54	4.54	0.55810	DM DNA-binding (6);	0.131100	0.36134	N	0.002777	T	0.81245	0.4782	M	0.88377	2.95	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.84774	0.0769	9	0.87932	D	0	-11.9148	13.5035	0.61471	0.0:1.0:0.0:0.0	.	46;46	B4DX56;Q8IXT2	.;DMRTD_HUMAN	C	46	.	ENSP00000269945:R46C	R	+	1	0	DMRTC2	47043472	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.628000	0.54259	2.472000	0.83506	0.561000	0.74099	CGC		0.617	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283		T	42351632	C	T	42351632	3	4	88	1	0	0	0	0	1	0	0	0	4602	652	23	1	138	1	DMRTC2	19	42351632	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	36506959	42351632	16777351	101	24396										
IRGC	56269	hgsc.bcm.edu	37	chr19	44223631	44223631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	taccaccgcagctttggtctGgacgacgactcgctggccaa	11	14	1	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:44223631G>A	ENST00000244314.5	+	2	1120	c.921G>A	c.(919-921)ctG>ctA	p.L307L		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	307						membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				GCTTTGGTCTGGACGACGACT	0.672																																					Colon(189;350 2037 11447 13433 38914)											0			19											60	59	59					19																	44223631		2203	4299	6502	48915471	SO:0001819	synonymous_variant	56269			BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.921G>A	19.37:g.44223631G>A			48915471	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																				0.672	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		A	44223631	G	A	44223631	2	1	88	1	0	0	0	0	0	0	0	1	7859	1335	47	3		3	IRGC	19	44223631	Silent	SNP	G	TCGA-CI-6621-01A-11D-1826-10	1871999	44223631	14905352	102	24397										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47969266	47969266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	aggagcccagggccatgagcGtgaggttggacaccgtctca	15	11	1	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:47969266G>A	ENST00000236877.6	-	2	790	c.395C>T	c.(394-396)aCg>aTg	p.T132M	SLC8A2_ENST00000539381.1_Intron|SLC8A2_ENST00000542837.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	132					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GGCCATGAGCGTGAGGTTGGA	0.602																																																0			19											91	58	69					19																	47969266		2203	4300	6503	52661078	SO:0001583	missense	6543			AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.395C>T	19.37:g.47969266G>A	ENSP00000236877:p.Thr132Met		52661078	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	37	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.229838	0.79688	.	.	ENSG00000118160	ENST00000236877	T	0.71698	-0.59	4.25	4.25	0.50352	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	D	0.90092	0.6905	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94005	0.7279	10	0.87932	D	0	.	15.6004	0.76620	0.0:0.0:1.0:0.0	.	132	Q9UPR5	NAC2_HUMAN	M	132	ENSP00000236877:T132M	ENSP00000236877:T132M	T	-	2	0	SLC8A2	52661078	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	9.587000	0.98229	2.210000	0.71456	0.462000	0.41574	ACG		0.602	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			A	47969266	G	A	47969266	3	1	88	1	0	0	0	0	1	0	0	0	14744	1145	40	1	2406	1	SLC8A2	19	47969266	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	3745635	47969266	11159717	103	24398										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49001497	49001497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cccagggccccattctccgcCgccttctcctcgatgcctgg	9	20	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:49001497C>T	ENST00000600059.1	-	11	3056	c.2829G>A	c.(2827-2829)gcG>gcA	p.A943A	LMTK3_ENST00000270238.3_Silent_p.A972A			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	943	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CATTCTCCGCCGCCTTCTCCT	0.632																																																0			19											49	53	52					19																	49001497		1899	4109	6008	53693309	SO:0001819	synonymous_variant	114783			AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.2829G>A	19.37:g.49001497C>T			53693309	Q4G0U1	Silent	SNP	ENST00000600059.1	37																																																																																					0.632	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		T	49001497	C	T	49001497	2	4	88	1	0	0	0	0	0	0	0	1	8884	639	23	1		1	LMTK3	19	49001497	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	1032231	49001497	10127486	104	24399										
ZNF701	55762	hgsc.bcm.edu	37	chr19	53085918	53085918	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ttcctccagtcttcattactCacacaaaaacgggaagtaca	5	12	3	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr19:53085918C>T	ENST00000540331.1	+	5	1029	c.804C>T	c.(802-804)ctC>ctT	p.L268L	ZNF701_ENST00000391785.3_Silent_p.L202L|CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Silent_p.L268L	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		CTTCATTACTCACACAAAAAC	0.368																																					NSCLC(89;451 1475 9611 20673 52284)											0			19											51	55	54					19																	53085918		2203	4300	6503	57777730	SO:0001819	synonymous_variant	55762			AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.804C>T	19.37:g.53085918C>T			57777730	A2RRM8|B9EGF2|F5GZM6|Q66K42	Silent	SNP	ENST00000540331.1	37	CCDS54311.1																																																																																				0.368	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		T	53085918	C	T	53085918	2	4	88	1	0	0	0	0	0	0	0	1	18144	813	29	3		3	ZNF701	19	53085918	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	4084421	53085918	6043065	105	24400										
PHF20	51230	hgsc.bcm.edu	37	chr20	34457449	34457449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gatgtgaagtcccattaaaaCgtcctcggcttgacaaaaat	8	9	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr20:34457449C>T	ENST00000374012.3	+	7	1027	c.898C>T	c.(898-900)Cgt>Tgt	p.R300C	PHF20_ENST00000439301.1_3'UTR|PHF20_ENST00000481202.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	300					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CCCATTAAAACGTCCTCGGCT	0.383																																																0			20											147	146	146					20																	34457449		2203	4300	6503	33920863	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.898C>T	20.37:g.34457449C>T	ENSP00000363124:p.Arg300Cys		33920863	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070619	0.76301	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.53206	1.26;0.63;0.63	5.5	5.5	0.81552	.	0.348813	0.30781	N	0.008894	T	0.64918	0.2642	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.953;0.996;0.926	T	0.66878	-0.5812	10	0.87932	D	0	.	14.2584	0.66067	0.149:0.851:0.0:0.0	.	300;300;300	Q566Q2;Q9BVI0;Q66K49	.;PHF20_HUMAN;.	C	300	ENSP00000363124:R300C;ENSP00000341900:R300C;ENSP00000363112:R300C	ENSP00000341900:R300C	R	+	1	0	PHF20	33920863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.790000	0.38734	2.587000	0.87381	0.591000	0.81541	CGT		0.383	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		T	34457449	C	T	34457449	3	4	88	1	0	0	0	0	1	0	0	0	11862	536	19	1	920	1	PHF20	20	34457449	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10		34457449	28568071	106	24401										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39795345	39795345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gggcaagatcaagcattgccGtgtccagcaagagggccaga	14	10	1	3			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr20:39795345G>A	ENST00000373271.1	+	19	2552	c.2147G>A	c.(2146-2148)cGt>cAt	p.R716H	PLCG1_ENST00000244007.3_Missense_Mutation_p.R716H|PLCG1_ENST00000373272.2_Missense_Mutation_p.R716H	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	716	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				AAGCATTGCCGTGTCCAGCAA	0.557																																																0			20											137	124	128					20																	39795345		2203	4300	6503	39228759	SO:0001583	missense	5335			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2147G>A	20.37:g.39795345G>A	ENSP00000362368:p.Arg716His		39228759	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	G	35	5.561025	0.96527	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.66280	-0.2;-0.2;-0.2	5.9	5.9	0.94986	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (5);	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	M	0.83483	2.645	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.994;0.999;0.998;0.997	T	0.82522	-0.0415	10	0.56958	D	0.05	.	20.2748	0.98484	0.0:0.0:1.0:0.0	.	716;292;716;716	P19174-2;B4DMA3;P19174;A2A284	.;.;PLCG1_HUMAN;.	H	716	ENSP00000244007:R716H;ENSP00000362368:R716H;ENSP00000362369:R716H	ENSP00000244007:R716H	R	+	2	0	PLCG1	39228759	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.869000	0.99810	2.792000	0.96026	0.655000	0.94253	CGT		0.557	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		A	39795345	G	A	39795345	3	1	88	1	0	0	0	0	1	0	0	0	12066	1145	40	1	2221	1	PLCG1	20	39795345	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	5337896	39795345	23230175	107	24402										
STAU1	6780	hgsc.bcm.edu	37	chr20	47752392	47752392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	cgaaattcacaggcaagttcCgtttaagtgcaatctcaaac	7	10	2	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr20:47752392C>T	ENST00000371856.2	-	6	997	c.587G>A	c.(586-588)cGg>cAg	p.R196Q	STAU1_ENST00000340954.7_Missense_Mutation_p.R115Q|STAU1_ENST00000371802.1_Missense_Mutation_p.R115Q|STAU1_ENST00000347458.5_Missense_Mutation_p.R115Q|STAU1_ENST00000371828.3_Missense_Mutation_p.R115Q|STAU1_ENST00000371792.1_Missense_Mutation_p.R115Q|STAU1_ENST00000360426.4_Missense_Mutation_p.R115Q	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	196	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.R196Q(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			AGGCAAGTTCCGTTTAAGTGC	0.323																																																1	Substitution - Missense(1)	ovary(1)	20											102	93	96					20																	47752392		2202	4300	6502	47185799	SO:0001583	missense	6780				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.587G>A	20.37:g.47752392C>T	ENSP00000360922:p.Arg196Gln		47185799	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	37	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	C	36	5.678151	0.96764	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	T;T;T;T;T;T;T;T	0.76316	-0.25;-1.01;-1.01;-1.01;-1.01;-0.25;-1.01;-0.25	5.77	5.77	0.91146	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.050019	0.85682	D	0.000000	D	0.87732	0.6251	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.984	D	0.88075	0.2803	10	0.87932	D	0	-12.9136	19.5894	0.95501	0.0:1.0:0.0:0.0	.	196;115	O95793;Q5JW29	STAU1_HUMAN;.	Q	115;115;196;115;115;115;115;115;115	ENSP00000360893:R115Q;ENSP00000345425:R115Q;ENSP00000360922:R196Q;ENSP00000353604:R115Q;ENSP00000323443:R115Q;ENSP00000360867:R115Q;ENSP00000360857:R115Q;ENSP00000416779:R115Q	ENSP00000345425:R115Q	R	-	2	0	STAU1	47185799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.603000	0.74145	2.720000	0.93068	0.557000	0.71058	CGG		0.323	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		T	47752392	C	T	47752392	3	4	88	1	0	0	0	0	1	0	0	0	15311	652	23	1	1200	1	STAU1	20	47752392	Missense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	7957047	47752392	15273128	108	24403										
RBM38	55544	hgsc.bcm.edu	37	chr20	55982632	55982632	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tacatctacccaccagccatCgtgcagcccagcgtggtgat	9	15	1	1	rs569633738		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chr20:55982632C>T	ENST00000356208.5	+	4	625	c.450C>T	c.(448-450)atC>atT	p.I150I	RBM38_ENST00000440234.2_3'UTR|RBM38_ENST00000371219.2_Silent_p.I69I	NM_017495.5	NP_059965.2	Q9H0Z9	RBM38_HUMAN	RNA binding motif protein 38	150					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell cycle (GO:0007049)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|regulation of myotube differentiation (GO:0010830)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			CACCAGCCATCGTGCAGCCCA	0.652																																																0			20											35	46	43					20																	55982632		2172	4270	6442	55416038	SO:0001819	synonymous_variant	55544			X75314	CCDS46617.1, CCDS46618.1	20q13.31	2013-02-12	2006-07-11	2006-07-11	ENSG00000132819	ENSG00000132819		"RNA binding motif (RRM) containing"	15818	protein-coding gene	gene with protein product		612428	"RNA-binding region (RNP1, RRM) containing 1"	RNPC1			Standard	NM_017495		Approved	HSRNASEB, SEB4D, seb4B, dJ800J21.2	uc010zzj.2	Q9H0Z9	OTTHUMG00000032820	ENST00000356208.5:c.450C>T	20.37:g.55982632C>T			55416038	A6NDK1|A6NMU6|Q15350|Q15351|Q9BYK3|Q9BYK4	Missense_Mutation	SNP	ENST00000356208.5	37	CCDS46617.1																																																																																				0.652	RBM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079843.4	NM_183425		T	55982632	C	T	55982632	2	4	88	1	0	0	0	0	0	0	0	1	13169	874	31	1		1	RBM38	20	55982632	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	8230240	55982632	7042888	109	24404										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382405	24382405	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ctgctgctgctgctgctgctGctgctgctgctgctgctgct	13	14	0	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:24382405G>C								AC004552.1 (15382 upstream) : PDK3 (100932 downstream)																							tgctgctgctgctgctgctgc	0.602																																																0			X											2	3	2					X																	24382405		930	2265	3195	24292326	SO:0001628	intergenic_variant	100130302																															X.37:g.24382405G>C			24292326		Missense_Mutation	SNP		37																																																																																				0	0.602									C	24382405	G	C	24382405	1	2	88	0	1	0	0	0	0	0	0	0	5592	1319	46	5		5	FAM48B1	23	24382405	IGR	SNP	G	TCGA-CI-6621-01A-11D-1826-10		24382405	130888155	110	24405										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216827	78216828	+	Nonsense_Mutation	DNP	GG	GG	TT													0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	attttttacaccatggtaaaGgaaaccatcattagcagttg							TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:78216827_78216828GG>TT	ENST00000171757.2	+	4	1090_1091	c.810_811GG>TT	c.(808-813)aaGGaa>aaTTaa	p.270_271KE>N*	P2RY10_ENST00000544091.1_Nonsense_Mutation_p.270_271KE>N*	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						CCATGGTAAAGGAAACCATCAT	0.446																																																0			X																																								78103483|78103484	SO:0001587	stop_gained	27334			AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	Exception_encountered	X.37:g.78216827_78216828delinsTT	ENSP00000171757:p.K270_E271delinsN*		78103483|78103484	D3DTE5|Q4VBN7|Q86V16	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000171757.2	37	CCDS14442.1																																																																																				0.446	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			TT	78216828	GG	TT	78216827	4	4	88	1	0	0	0	0	0	1	0	0	11378	991	35	2	812	2	P2RY10	23	78216827	Nonsense_Mutation	DNP	GG	TCGA-CI-6621-01A-11D-1826-10	53834422	78216827	77053733	111	24406										
POF1B	79983	hgsc.bcm.edu	37	chrX	84562263	84562263	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ataaatctttctcaagtctcAtcttgtcattttccagtgac	4	10	5	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:84562263A>C	ENST00000262753.4	-	11	1215	c.1070T>G	c.(1069-1071)aTg>aGg	p.M357R	POF1B_ENST00000373145.3_Missense_Mutation_p.M357R	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	357						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						CTCAAGTCTCATCTTGTCATT	0.338																																																0			X											105	81	90					X																	84562263		2201	4296	6497	84448919	SO:0001583	missense	79983			BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.1070T>G	X.37:g.84562263A>C	ENSP00000262753:p.Met357Arg		84448919	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	.	.	.	.	.	.	.	.	.	.	A	9.204	1.029148	0.19512	.	.	ENSG00000124429	ENST00000262753;ENST00000373145	T;T	0.81247	-1.47;-1.47	5.24	5.24	0.73138	.	0.430476	0.29165	N	0.012958	T	0.53997	0.1831	N	0.03608	-0.345	0.22779	N	0.998747	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38351	-0.9665	10	0.14656	T	0.56	.	4.8721	0.13639	0.7151:0.188:0.0968:0.0	.	357;357	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	R	357	ENSP00000262753:M357R;ENSP00000362238:M357R	ENSP00000262753:M357R	M	-	2	0	POF1B	84448919	0.971000	0.33674	1.000000	0.80357	0.988000	0.76386	2.633000	0.46519	1.728000	0.51552	0.486000	0.48141	ATG		0.338	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		C	84562263	A	C	84562263	3	2	88	1	0	0	0	0	1	0	0	0	12213	217	8	4	727	4	POF1B	23	84562263	Missense_Mutation	SNP	A	TCGA-CI-6621-01A-11D-1826-10	6345436	84562263	70708297	112	24407										
BEX1	55859	hgsc.bcm.edu	37	chrX	102318190	102318190	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	actgtttactgctcgtttctCtttggactccattactccta	5	12	1	0			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:102318190C>A	ENST00000372728.3	-	3	252	c.13G>T	c.(13-15)Gag>Tag	p.E5*		NM_018476.3	NP_060946.3	Q9HBH7	BEX1_HUMAN	brain expressed, X-linked 1	5					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II activating transcription factor binding (GO:0001102)			endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12						GCTCGTTTCTCTTTGGACTCC	0.478																																																0			X											155	159	157					X																	102318190		2201	4291	6492	102204846	SO:0001587	stop_gained	84707				CCDS35354.1	Xq22.1	2014-03-21			ENSG00000133169	ENSG00000133169			1036	protein-coding gene	gene with protein product		300690				16221301	Standard	NM_018476		Approved		uc004ejt.1	Q9HBH7	OTTHUMG00000022708	ENST00000372728.3:c.13G>T	X.37:g.102318190C>A	ENSP00000361813:p.Glu5*		102204846	A0AVN1|A8K4J3|Q9NZ33	Nonsense_Mutation	SNP	ENST00000372728.3	37	CCDS35354.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.066383	0.55539	.	.	ENSG00000133169	ENST00000372728	.	.	.	3.1	1.99	0.26369	.	0.593314	0.14179	N	0.336194	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	4.2062	0.10490	0.0:0.7239:0.0:0.2761	.	.	.	.	X	5	.	ENSP00000361813:E5X	E	-	1	0	BEX1	102204846	0.546000	0.26457	0.245000	0.24217	0.204000	0.24138	0.016000	0.13377	0.465000	0.27167	0.600000	0.82982	GAG		0.478	BEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058925.1	NM_018476		A	102318190	C	A	102318190	4	1	88	1	0	0	0	0	0	1	0	0	1411	922	32	2	368	2	BEX1	23	102318190	Nonsense_Mutation	SNP	C	TCGA-CI-6621-01A-11D-1826-10	17755927	102318190	52952370	113	24408										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128649686	128649686	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	tttcatcagccaaaatgccaTtgactccattttcatataaa	3	10	3	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:128649686T>C	ENST00000371122.4	-	5	737	c.608A>G	c.(607-609)aAt>aGt	p.N203S	SMARCA1_ENST00000371121.3_Missense_Mutation_p.N203S|SMARCA1_ENST00000371123.1_Missense_Mutation_p.N203S|SMARCA1_ENST00000478420.1_5'UTR	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	203	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						CAAAATGCCATTGACTCCATT	0.368																																																0			X											86	84	85					X																	128649686		2203	4300	6503	128477367	SO:0001583	missense	6594			M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.608A>G	X.37:g.128649686T>C	ENSP00000360163:p.Asn203Ser		128477367	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476628	0.44044	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08	5.78	5.78	0.91487	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000001	D	0.90410	0.6998	L	0.46670	1.46	0.80722	D	1	P;P;B;P	0.40578	0.476;0.722;0.421;0.476	P;P;B;P	0.46275	0.51;0.51;0.376;0.51	D	0.87801	0.2625	10	0.09084	T	0.74	-21.8427	15.0274	0.71680	0.0:0.0:0.0:1.0	.	182;203;203;203	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	S	203;203;203;182	ENSP00000360162:N203S;ENSP00000360164:N203S;ENSP00000360163:N203S;ENSP00000404275:N182S	ENSP00000360162:N203S	N	-	2	0	SMARCA1	128477367	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	1.931000	0.55961	0.486000	0.48141	AAT		0.368	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		C	128649686	T	C	128649686	3	2	88	1	0	0	0	0	1	0	0	0	14805	1493	52	4	2636	4	SMARCA1	23	128649686	Missense_Mutation	SNP	T	TCGA-CI-6621-01A-11D-1826-10	26331496	128649686	26620874	114	24409										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153218216	153218216	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	ccacagtggccaccaccgcaGagccggcagactcctggccc	11	19	0	2			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:153218216G>A	ENST00000310441.7	-	19	5657	c.4691C>T	c.(4690-4692)tCt>tTt	p.S1564F	HCFC1_ENST00000354233.3_Missense_Mutation_p.S1495F|HCFC1_ENST00000369984.4_Missense_Mutation_p.S1608F	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1564					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACCACCGCAGAGCCGGCAGA	0.657											OREG0003630	type=REGULATORY REGION|Gene=BC010606|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			X											22	27	26					X																	153218216		2060	4179	6239	152871410	SO:0001583	missense	3054				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.4691C>T	X.37:g.153218216G>A	ENSP00000309555:p.Ser1564Phe	1753	152871410	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	37	CCDS44020.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604003	0.46423	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.03413	4.03;3.94;4.03	5.79	5.79	0.91817	.	0.417595	0.26542	N	0.023787	T	0.03053	0.0090	N	0.08118	0	0.32016	N	0.601403	P	0.47350	0.894	B	0.41813	0.367	T	0.27331	-1.0077	10	0.66056	D	0.02	.	14.2609	0.66085	0.0:0.0:1.0:0.0	.	1564	P51610	HCFC1_HUMAN	F	1564;1608;1495	ENSP00000309555:S1564F;ENSP00000359001:S1608F;ENSP00000346174:S1495F	ENSP00000309555:S1564F	S	-	2	0	HCFC1	152871410	0.990000	0.36364	0.898000	0.35279	0.565000	0.35776	2.399000	0.44495	2.443000	0.82685	0.513000	0.50165	TCT		0.657	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		A	153218216	G	A	153218216	3	1	88	1	0	0	0	0	1	0	0	0	7012	942	33	3	1448	3	HCFC1	23	153218216	Missense_Mutation	SNP	G	TCGA-CI-6621-01A-11D-1826-10	24568530	153218216	2052344	115	24410										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153699912	153699912	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	gtggagcagtcccgcctccaCgccagcgacttcagcgtcct	11	17	1	0	rs374284684		TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrX:153699912C>T	ENST00000369682.3	+	32	5626	c.5451C>T	c.(5449-5451)caC>caT	p.H1817H		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1817					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CCCGCCTCCACGCCAGCGACT	0.552													C|||	2	0.000529801	0	0	3775	,	,		15818	0.002		0	False		,,,				2504	0															0			X											91	71	78					X																	153699912		2203	4300	6503	153353106	SO:0001819	synonymous_variant	55558			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.5451C>T	X.37:g.153699912C>T			153353106	Q5HY36	Silent	SNP	ENST00000369682.3	37	CCDS14752.1																																																																																				0.552	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153699912	C	T	153699912	2	4	88	1	0	0	0	0	0	0	0	1	12152	535	19	1		1	PLXNA3	23	153699912	Silent	SNP	C	TCGA-CI-6621-01A-11D-1826-10	481696	153699912	1570648	116	24411										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16734128	16734128	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0341880341880342	4	1	0.413358427802337	1.73093841642229	0.234703514091158	1	1	0	accctcattgacagccaagcAcagtatccagttgtcaacac	6	14	2	1			TCGA-CI-6621-01A-11D-1826-10	TCGA-CI-6621-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f4785efc-e4b4-4bd0-b465-e4bd6321f1a2	d37343fb-f505-4303-a2ea-d3f8767c86c9	g.chrY:16734128A>T	ENST00000297967.5	+	1	228	c.129A>T	c.(127-129)gcA>gcT	p.A43A	NLGN4Y_ENST00000476359.1_3'UTR	NM_001164238.1	NP_001157710.1	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked	43					learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						ACAGCCAAGCACAGTATCCAG	0.458																																																0			Y																																								15243522	SO:0001819	synonymous_variant	22829				CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000297967.5:c.129A>T	Y.37:g.16734128A>T			15243522	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000297967.5	37	CCDS55553.1	.	.	.	.	.	.	.	.	.	.	.	0.279	-0.987493	0.02180	.	.	ENSG00000165246	ENST00000413217	.	.	.	1.55	0.0438	0.14223	.	.	.	.	.	T	0.19685	0.0473	.	.	.	.	.	.	.	.	.	.	.	.	T	0.13818	-1.0495	2	.	.	.	.	.	.	.	.	.	.	.	L	23	.	.	H	+	2	0	NLGN4Y	15243522	0.992000	0.36948	0.991000	0.47740	0.546000	0.35178	0.090000	0.15025	-0.132000	0.11557	0.155000	0.16302	CAC		0.458	NLGN4Y-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014893		T	16734128	A	T	16734128	2	4	88	1	0	0	0	0	0	0	0	1	10496	146	6	5		5	NLGN4Y	24	16734128	Silent	SNP	A	TCGA-CI-6621-01A-11D-1826-10		16734128	42639438	117	24412										
GPR157	80045	hgsc.bcm.edu	37	chr1	9165567	9165567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcagaaccaccagcaccggcGtctgcacggccggggagcca	14	16	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:9165567G>A	ENST00000377411.4	-	3	912	c.770C>T	c.(769-771)aCg>aTg	p.T257M	GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|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;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		CAGCACCGGCGTCTGCACGGC	0.652																																																0			1											41	40	40					1																	9165567		2202	4296	6498	9088154	SO:0001583	missense	80045			AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"GPCR / Class B : Orphans"	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.770C>T	1.37:g.9165567G>A	ENSP00000366628:p.Thr257Met		9088154	A2A334|Q8WWB8|Q9HA73	Missense_Mutation	SNP	ENST00000377411.4	37	CCDS100.2	.	.	.	.	.	.	.	.	.	.	G	2.610	-0.291023	0.05568	.	.	ENSG00000180758	ENST00000377411	T	0.37752	1.18	4.67	2.7	0.31948	GPCR, family 2-like (1);	0.476448	0.24674	N	0.036538	T	0.18215	0.0437	N	0.14661	0.345	0.19300	N	0.999975	B	0.19445	0.036	B	0.21708	0.036	T	0.13953	-1.0490	10	0.34782	T	0.22	-1.1133	4.1347	0.10166	0.2027:0.0:0.5149:0.2824	.	257	Q5UAW9	GP157_HUMAN	M	257	ENSP00000366628:T257M	ENSP00000366628:T257M	T	-	2	0	GPR157	9088154	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.982000	0.29539	0.452000	0.26830	0.549000	0.68633	ACG		0.652	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980		A	9165567	G	A	9165567	3	1	89	1	0	0	0	0	1	0	0	0	6682	1145	40	1	245	1	GPR157	1	9165567	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		9165567	240085054	1	24413										
MFN2	9927	hgsc.bcm.edu	37	chr1	12065898	12065898	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gacttccaggaagacattgaGttccatttctctctcggatg	9	10	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:12065898G>A	ENST00000235329.5	+	15	1948	c.1626G>A	c.(1624-1626)gaG>gaA	p.E542E	MFN2_ENST00000444836.1_Silent_p.E542E	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	542					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AAGACATTGAGTTCCATTTCT	0.532																																																0			1											214	192	200					1																	12065898		2203	4300	6503	11988485	SO:0001819	synonymous_variant	9927			AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.1626G>A	1.37:g.12065898G>A			11988485	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	37	CCDS30587.1																																																																																				0.532	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		A	12065898	G	A	12065898	2	1	89	1	0	0	0	0	0	0	0	1	9554	1020	36	3		3	MFN2	1	12065898	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	2900331	12065898	237184723	2	24414										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34128624	34128624	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccttcagcagaaccccgctcTccacaggcccatcccagatg	7	19	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:34128624T>C	ENST00000373380.1	-	5	960	c.740A>G	c.(739-741)gAg>gGg	p.E247G	CSMD2_ENST00000373381.4_Missense_Mutation_p.E1374G|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1334	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACCCCGCTCTCCACAGGCCC	0.597																																																0			1											91	84	87					1																	34128624		2203	4300	6503	33901211	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.740A>G	1.37:g.34128624T>C	ENSP00000362478:p.Glu247Gly		33901211	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37		.	.	.	.	.	.	.	.	.	.	T	16.71	3.198434	0.58126	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.18502	2.21;2.21	5.39	4.25	0.50352	CUB (5);	0.174210	0.49916	D	0.000129	T	0.27489	0.0675	L	0.55213	1.73	0.80722	D	1	P;B;B	0.52170	0.951;0.019;0.004	P;B;B	0.55112	0.769;0.029;0.029	T	0.01484	-1.1343	10	0.25106	T	0.35	.	12.0952	0.53750	0.0:0.0:0.1438:0.8562	.	247;1334;1374	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	G	1374;247	ENSP00000362479:E1374G;ENSP00000362478:E247G	ENSP00000241312:E1334G	E	-	2	0	CSMD2	33901211	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	7.984000	0.88150	0.971000	0.38288	-0.488000	0.04728	GAG		0.597	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		C	34128624	T	C	34128624	3	2	89	1	0	0	0	0	1	0	0	0	3951	1551	54	4	6638	4	CSMD2	1	34128624	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	22062726	34128624	215121997	3	24415										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42046815	42046815	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gggaggaaggaagggggctgCctgaaggggatgttggctgg	23	4	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:42046815C>T	ENST00000372583.1	-	4	4539	c.3654G>A	c.(3652-3654)agG>agA	p.R1218R	HIVEP3_ENST00000429157.2_Silent_p.R1218R|HIVEP3_ENST00000247584.5_Silent_p.R1218R|HIVEP3_ENST00000372584.1_Silent_p.R1218R|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1218					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				AAGGGGGCTGCCTGAAGGGGA	0.587																																																0			1											68	68	68					1																	42046815		2203	4300	6503	41819402	SO:0001819	synonymous_variant	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3654G>A	1.37:g.42046815C>T			41819402	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																				0.587	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42046815	C	T	42046815	2	4	89	1	0	0	0	0	0	0	0	1	7209	738	26	3		3	HIVEP3	1	42046815	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	7918191	42046815	207203806	4	24416										
PRKACB	5567	hgsc.bcm.edu	37	chr1	84644908	84644908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agactttttgaaaaaatgggAgaatccaactcaggtaagga	10	5	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:84644908A>G	ENST00000370689.2	+	2	359	c.95A>G	c.(94-96)gAg>gGg	p.E32G	PRKACB_ENST00000394839.2_Missense_Mutation_p.E35G|PRKACB_ENST00000370688.3_Missense_Mutation_p.E32G|PRKACB_ENST00000370685.3_Missense_Mutation_p.E79G|PRKACB_ENST00000470673.1_3'UTR|PRKACB_ENST00000394838.2_Missense_Mutation_p.E39G|PRKACB_ENST00000370682.3_Missense_Mutation_p.E36G|PRKACB_ENST00000370680.1_Missense_Mutation_p.E38G	NM_001242862.1|NM_002731.2	NP_001229791.1|NP_002722.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta	32					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		AAAAAATGGGAGAATCCAACT	0.239																																																0			1											20	21	21					1																	84644908		2071	4181	6252	84417496	SO:0001583	missense	5567			BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	2.7.11.1		9381	protein-coding gene	gene with protein product		176892					Standard	XM_005271016		Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370689.2:c.95A>G	1.37:g.84644908A>G	ENSP00000359723:p.Glu32Gly		84417496	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	Missense_Mutation	SNP	ENST00000370689.2	37	CCDS691.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.043924	0.55110	.	.	ENSG00000142875	ENST00000370689;ENST00000370688;ENST00000370685;ENST00000446538;ENST00000370684;ENST00000436133;ENST00000394838;ENST00000370682;ENST00000370679;ENST00000432111;ENST00000450730;ENST00000370680;ENST00000413538;ENST00000417530;ENST00000394839	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.71817	-0.37;-0.52;-0.38;-0.03;-0.52;-0.15;-0.36;-0.36;-0.21;-0.26;-0.52;-0.24;-0.18;-0.6	4.88	4.88	0.63580	Protein kinase-like domain (1);	0.048204	0.85682	D	0.000000	T	0.75459	0.3852	L	0.58669	1.825	0.80722	D	1	B;B;B;B;B;B;B;B;P;B	0.52170	0.001;0.001;0.001;0.001;0.002;0.001;0.002;0.001;0.951;0.001	B;B;B;B;B;B;B;B;D;B	0.68765	0.004;0.001;0.004;0.003;0.004;0.009;0.007;0.003;0.96;0.006	T	0.76979	-0.2758	10	0.46703	T	0.11	-15.9751	14.4848	0.67609	1.0:0.0:0.0:0.0	.	20;39;38;35;38;36;79;79;32;32	P22694-3;B4DKB0;B1APG3;B1APG4;P22694-6;P22694-7;P22694-2;B4E2L0;P22694;P22694-8	.;.;.;.;.;.;.;.;KAPCB_HUMAN;.	G	32;32;79;39;20;36;39;36;38;28;35;38;27;19;35	ENSP00000359723:E32G;ENSP00000359722:E32G;ENSP00000359719:E79G;ENSP00000401252:E39G;ENSP00000359718:E20G;ENSP00000390906:E36G;ENSP00000378314:E39G;ENSP00000359716:E36G;ENSP00000392275:E28G;ENSP00000393654:E35G;ENSP00000359714:E38G;ENSP00000397175:E27G;ENSP00000399326:E19G;ENSP00000378315:E35G	ENSP00000359713:E38G	E	+	2	0	PRKACB	84417496	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.191000	0.94940	1.831000	0.53308	0.477000	0.44152	GAG		0.239	PRKACB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027641.1	NM_182948		G	84644908	A	G	84644908	3	3	89	1	0	0	0	0	1	0	0	0	12532	304	11	4	292	4	PRKACB	1	84644908	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	42598093	84644908	164605713	5	24417										
GBP7	388646	hgsc.bcm.edu	37	chr1	89616037	89616037	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tccagtgacaaggattccctCtctcagggtcttggtctttg	10	11	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:89616037C>G	ENST00000294671.2	-	6	985	c.847G>C	c.(847-849)Gag>Cag	p.E283Q		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	283	GTPase domain (Globular). {ECO:0000250}.					membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		AGGATTCCCTCTCTCAGGGTC	0.403																																																0			1											89	91	90					1																	89616037		2203	4300	6503	89388625	SO:0001583	missense	388646			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.847G>C	1.37:g.89616037C>G	ENSP00000294671:p.Glu283Gln		89388625		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	C	8.060	0.767919	0.15983	.	.	ENSG00000213512	ENST00000294671	T	0.02369	4.32	3.4	0.0418	0.14214	Guanylate-binding protein, C-terminal (3);	0.672189	0.14643	N	0.307105	T	0.02230	0.0069	M	0.85299	2.745	0.09310	N	1	B	0.27068	0.167	B	0.30716	0.119	T	0.26189	-1.0110	10	0.39692	T	0.17	.	11.8101	0.52177	0.0:0.4789:0.5211:0.0	.	283	Q8N8V2	GBP7_HUMAN	Q	283	ENSP00000294671:E283Q	ENSP00000294671:E283Q	E	-	1	0	GBP7	89388625	0.000000	0.05858	0.008000	0.14137	0.029000	0.11900	0.928000	0.28831	-0.181000	0.10619	0.411000	0.27672	GAG		0.403	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		G	89616037	C	G	89616037	3	3	89	1	0	0	0	0	1	0	0	0	6299	922	32	5	1093	5	GBP7	1	89616037	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	4971129	89616037	159634584	6	24418										
BCAR3	8412	hgsc.bcm.edu	37	chr1	94033332	94033332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggagtttgctgaagggcttcAgctgtttctcatagagaatg	13	6	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:94033332A>G	ENST00000370244.1	-	12	2339	c.2051T>C	c.(2050-2052)cTg>cCg	p.L684P	BCAR3_ENST00000260502.6_Missense_Mutation_p.L684P|BCAR3_ENST00000539242.1_Missense_Mutation_p.L360P|BCAR3_ENST00000370247.3_Missense_Mutation_p.L593P|BCAR3_ENST00000370243.1_Missense_Mutation_p.L684P	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	684	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GAAGGGCTTCAGCTGTTTCTC	0.537																																																0			1											113	109	110					1																	94033332		2203	4300	6503	93805920	SO:0001583	missense	8412			U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.2051T>C	1.37:g.94033332A>G	ENSP00000359264:p.Leu684Pro		93805920	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.540563	0.85917	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	5.39	5.39	0.77823	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.52917	0.1764	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62845	-0.6768	10	0.87932	D	0	-20.2839	15.4037	0.74861	1.0:0.0:0.0:0.0	.	684;593	O75815;Q5TEW3	BCAR3_HUMAN;.	P	593;684;684;684;360	ENSP00000359267:L593P;ENSP00000260502:L684P;ENSP00000359264:L684P;ENSP00000359263:L684P;ENSP00000441343:L360P	ENSP00000260502:L684P	L	-	2	0	BCAR3	93805920	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.918000	0.92759	2.036000	0.60181	0.459000	0.35465	CTG		0.537	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			G	94033332	A	G	94033332	3	3	89	1	0	0	0	0	1	0	0	0	1350	188	7	4	438	4	BCAR3	1	94033332	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	4417295	94033332	155217289	7	24419										
PRMT6	55170	hgsc.bcm.edu	37	chr1	107599535	107599535	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atgatcgcggaccgcgtccgCaccgatgcctaccgcctggg	13	16	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:107599535C>T	ENST00000370078.1	+	1	235	c.198C>T	c.(196-198)cgC>cgT	p.R66R	PRMT6_ENST00000361318.5_Silent_p.R7R			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	66	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		ACCGCGTCCGCACCGATGCCT	0.637																																																0			1											37	46	43					1																	107599535		2064	4176	6240	107401058	SO:0001819	synonymous_variant	55170			AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.198C>T	1.37:g.107599535C>T			107401058	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Silent	SNP	ENST00000370078.1	37	CCDS41360.2																																																																																				0.637	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		T	107599535	C	T	107599535	2	4	89	1	0	0	0	0	0	0	0	1	12574	697	25	3		3	PRMT6	1	107599535	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	13566203	107599535	141651086	8	24420										
DCAF6	55827	hgsc.bcm.edu	37	chr1	168032995	168032995	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gccatcgcaactccaggacaAtggtaccaaatgttcatggc	9	12	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:168032995A>G	ENST00000312263.6	+	15	2368	c.2164A>G	c.(2164-2166)Atg>Gtg	p.M722V	DCAF6_ENST00000367843.3_Missense_Mutation_p.M742V|DCAF6_ENST00000432587.2_Missense_Mutation_p.M782V|DCAF6_ENST00000367840.3_Missense_Mutation_p.M813V	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	722					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.M742V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						CTCCAGGACAATGGTACCAAA	0.363																																																1	Substitution - Missense(1)	ovary(1)	1											94	93	93					1																	168032995		2203	4300	6503	166299619	SO:0001583	missense	0			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2164A>G	1.37:g.168032995A>G	ENSP00000311949:p.Met722Val		166299619	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.238902	0.58995	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.084494	0.85682	D	0.000000	T	0.77718	0.4172	L	0.36672	1.1	0.46260	D	0.998956	B;B;B;P;P	0.51653	0.011;0.402;0.019;0.656;0.947	B;B;B;P;D	0.65684	0.015;0.171;0.107;0.558;0.937	T	0.75025	-0.3463	9	0.13108	T	0.6	.	15.8679	0.79080	1.0:0.0:0.0:0.0	.	782;395;813;722;742	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	V	742;782;722;813	ENSP00000356817:M742V;ENSP00000396238:M782V;ENSP00000311949:M722V;ENSP00000356814:M813V	ENSP00000311949:M722V	M	+	1	0	DCAF6	166299619	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.792000	0.91856	2.166000	0.68216	0.459000	0.35465	ATG		0.363	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		G	168032995	A	G	168032995	3	3	89	1	0	0	0	0	1	0	0	0	4280	101	4	4	2286	4	DCAF6	1	168032995	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	60433460	168032995	81217626	9	24421										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186901975	186901975	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggtgtgatgaaggcattataCgaatcaggaattctggattg	13	4	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:186901975C>T	ENST00000367466.3	+	8	791	c.639C>T	c.(637-639)taC>taT	p.Y213Y	PLA2G4A_ENST00000442353.2_Silent_p.Y153Y|PLA2G4A_ENST00000466600.1_Intron	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	213	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	AGGCATTATACGAATCAGGAA	0.423																																																0			1											220	217	218					1																	186901975		2203	4300	6503	185168598	SO:0001819	synonymous_variant	5321			M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.639C>T	1.37:g.186901975C>T			185168598	B1AKG4|Q29R80	Silent	SNP	ENST00000367466.3	37	CCDS1372.1																																																																																				0.423	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186901975	C	T	186901975	2	4	89	1	0	0	0	0	0	0	0	1	12032	547	19	1		1	PLA2G4A	1	186901975	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	18868980	186901975	62348646	10	24422										
ADORA1	134	hgsc.bcm.edu	37	chr1	203134556	203134556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggagcccgtgatcaagtgcgAgttcgagaaggtcatcagca	14	9	3	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:203134556A>G	ENST00000367236.4	+	3	1430	c.509A>G	c.(508-510)gAg>gGg	p.E170G	ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000337894.4_Missense_Mutation_p.E170G|ADORA1_ENST00000367235.1_3'UTR|ADORA1_ENST00000309502.3_Missense_Mutation_p.E170G	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	170			E -> K (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	ATCAAGTGCGAGTTCGAGAAG	0.582																																																0			1											170	169	169					1																	203134556		2203	4300	6503	201401179	SO:0001583	missense	134			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.509A>G	1.37:g.203134556A>G	ENSP00000356205:p.Glu170Gly		201401179	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180436	0.38511	.	.	ENSG00000163485	ENST00000309502;ENST00000367236;ENST00000337894	T;T;T	0.37752	1.18;1.18;1.18	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.210893	0.49916	D	0.000122	T	0.32010	0.0815	L	0.37561	1.115	0.38267	D	0.942042	P;P;B	0.48998	0.601;0.918;0.001	B;B;B	0.43990	0.186;0.438;0.004	T	0.12604	-1.0541	10	0.19147	T	0.46	-26.1553	15.3381	0.74273	1.0:0.0:0.0:0.0	.	203;102;170	B7Z379;B7Z1L9;P30542	.;.;AA1R_HUMAN	G	170	ENSP00000308549:E170G;ENSP00000356205:E170G;ENSP00000338435:E170G	ENSP00000308549:E170G	E	+	2	0	ADORA1	201401179	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.155000	0.71833	2.091000	0.63221	0.459000	0.35465	GAG		0.582	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		G	203134556	A	G	203134556	3	3	89	1	0	0	0	0	1	0	0	0	326	304	11	4	515	4	ADORA1	1	203134556	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	16232581	203134556	46116065	11	24423										
USH2A	7399	hgsc.bcm.edu	37	chr1	216108060	216108060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggtaaaaggaaccagcccatCgatgagcacccaaaggtttg	11	10	0	1	rs370204550		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:216108060C>T	ENST00000307340.3	-	38	7584	c.7198G>A	c.(7198-7200)Gat>Aat	p.D2400N	USH2A_ENST00000366943.2_Missense_Mutation_p.D2400N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2400	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCAGCCCATCGATGAGCACC	0.383										HNSCC(13;0.011)																																						0			1						C	ASN/ASP	0,4406		0,0,2203	114	106	109		7198	-0.2	0	1		109	1,8599	1.2+/-3.3	0,1,4299	no	missense	USH2A	NM_206933.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	2400/5203	216108060	1,13005	2203	4300	6503	214174683	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7198G>A	1.37:g.216108060C>T	ENSP00000305941:p.Asp2400Asn		214174683	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	7.561	0.664722	0.14710	0.0	1.16E-4	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53640	0.61;0.61	5.81	-0.184	0.13280	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.937593	0.08792	N	0.893118	T	0.27832	0.0685	N	0.25144	0.715	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.23332	-1.0191	10	0.17369	T	0.5	.	5.0014	0.14266	0.0:0.2351:0.177:0.5879	.	2400	O75445	USH2A_HUMAN	N	2400	ENSP00000305941:D2400N;ENSP00000355910:D2400N	ENSP00000305941:D2400N	D	-	1	0	USH2A	214174683	0.000000	0.05858	0.000000	0.03702	0.796000	0.44982	-0.034000	0.12225	0.054000	0.16065	-0.136000	0.14681	GAT		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216108060	C	T	216108060	3	4	89	1	0	0	0	0	1	0	0	0	17076	884	31	1	8550	1	USH2A	1	216108060	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	12973504	216108060	33142561	12	24424										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231344753	231344753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	catcattttatccaatgacaAccagacagccacctgcagca	5	14	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:231344753A>G	ENST00000366653.5	+	8	1880	c.1880A>G	c.(1879-1881)aAc>aGc	p.N627S	TRIM67_ENST00000444294.3_Missense_Mutation_p.N625S|TRIM67_ENST00000366652.2_Missense_Mutation_p.N627S|TRIM67_ENST00000449018.3_Missense_Mutation_p.N565S			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	627	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TCCAATGACAACCAGACAGCC	0.582																																																0			1											89	98	95					1																	231344753		2155	4272	6427	229411376	SO:0001583	missense	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1880A>G	1.37:g.231344753A>G	ENSP00000355613:p.Asn627Ser		229411376	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334320	0.81801	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	T	0.79575	0.4469	M	0.76002	2.32	0.80722	D	1	P	0.45283	0.855	P	0.48334	0.574	T	0.78043	-0.2358	10	0.28530	T	0.3	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	627	Q6ZTA4	TRI67_HUMAN	S	625;627;565;627	ENSP00000412124:N625S;ENSP00000355612:N627S;ENSP00000400163:N565S;ENSP00000355613:N627S	ENSP00000355612:N627S	N	+	2	0	TRIM67	229411376	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	9.185000	0.94900	2.302000	0.77476	0.533000	0.62120	AAC		0.582	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		G	231344753	A	G	231344753	3	3	89	1	0	0	0	0	1	0	0	0	16580	43	2	4	1910	4	TRIM67	1	231344753	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	15236693	231344753	17905868	13	24425										
RYR2	6262	hgsc.bcm.edu	37	chr1	237433800	237433800	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tttctccccctttgcaggatGatgaagtggttctgcagtgc	11	10	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:237433800G>A	ENST00000366574.2	+	2	369	c.52G>A	c.(52-54)Gat>Aat	p.D18N	RYR2_ENST00000360064.6_Missense_Mutation_p.M15I|RYR2_ENST00000542537.1_Missense_Mutation_p.D2N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	18					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTGCAGGATGATGAAGTGGT	0.428																																																0			1											82	75	77					1																	237433800		1928	4143	6071	235500423	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.52G>A	1.37:g.237433800G>A	ENSP00000355533:p.Asp18Asn		235500423	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.809555|4.809555	0.90707|0.90707	.|.	.|.	ENSG00000198626|ENSG00000198626	ENST00000366574;ENST00000542537|ENST00000360064	D;D|D	0.99105|0.96104	-5.43;-5.43|-3.91	3.92|3.92	3.92|3.92	0.45320|0.45320	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);|.	.|0.574888	.|0.13040	.|U	.|0.418617	D|D	0.97455|0.97455	0.9167|0.9167	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D|.	0.56287|.	0.975|.	P|.	0.57371|.	0.819|.	D|D	0.97718|0.97718	1.0195|1.0195	9|8	0.87932|0.87932	D|D	0|0	.|.	16.139|16.139	0.81512|0.81512	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	18|.	Q92736|.	RYR2_HUMAN|.	N|I	18;2|15	ENSP00000355533:D18N;ENSP00000443798:D2N|ENSP00000353174:M15I	ENSP00000355533:D18N|ENSP00000353174:M15I	D|M	+|+	1|3	0|0	RYR2|RYR2	235500423|235500423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	9.493000|9.493000	0.97960|0.97960	2.014000|2.014000	0.59158|0.59158	0.453000|0.453000	0.30009|0.30009	GAT|ATG		0.428	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237433800	G	A	237433800	3	1	89	1	0	0	0	0	1	0	0	0	13806	1290	45	3	58	3	RYR2	1	237433800	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	6089047	237433800	11816821	14	24426										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371056	240371121	+	In_Frame_Del	DEL	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	-													0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tacctcctccaccccctctaCccggagcgggcataccccct					rs139764401|rs71646825|rs557827551|rs537036439|rs71646826|rs141912031|rs202207586|rs71646890|rs11586155|rs71646889|rs71646891|rs71646887|rs375298881|rs71646827|rs373490785	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENST00000319653.9	+	5	3174_3239	c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	c.(2944-3009)cccggagcgggcataccccctcctcccccacttcccggagcgggcataccccctccgcccccacttdel	p.PGAGIPPPPPLPGAGIPPPPPL1070del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1070	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1131T(2)|p.P1143P(1)|p.G1128A(1)|p.G1128G(1)|p.P1134L(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTTCCCGGAGCGG	0.714																																																6	Substitution - Missense(4)|Substitution - coding silent(2)	lung(3)|prostate(1)|ovary(1)|large_intestine(1)	1																																								238437744	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	1.37:g.240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENSP00000318884:p.Pro1070_Leu1091del		238437679	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.714	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240371121	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	-	240371056	7	5	89	1	0	1	0	1	0	0	0	0	5969	507	18	0	2962	0	FMN2	1	240371056	In_Frame_Del	DEL	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	TCGA-CI-6622-01A-11D-1826-10	2937256	240371056	8879565	15	24427										
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059483	248059483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctgtggccatcgaaggcaccGtctttgtcctggcggtgggt	15	11	1	0	rs61756679	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr1:248059483G>A	ENST00000360358.3	+	1	595	c.595G>A	c.(595-597)Gtc>Atc	p.V199I	OR2W3_ENST00000537741.1_Missense_Mutation_p.V199I	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V199I(1)		breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	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)			CGAAGGCACCGTCTTTGTCCT	0.587													G|||	49	0.00978435	0.034	0.0043	5008	,	,		20640	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	1						G	ILE/VAL	110,4296	84.4+/-122.9	4,102,2097	165	144	151		595	3.4	0	1	dbSNP_129	151	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR2W3	NM_001001957.2	29	4,104,6395	AA,AG,GG		0.0233,2.4966,0.8611	benign	199/315	248059483	112,12894	2203	4300	6503	246126106	SO:0001583	missense	343171			N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"GPCR / Class A : Olfactory receptors"	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.595G>A	1.37:g.248059483G>A	ENSP00000353516:p.Val199Ile		246126106	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	16	0.007326007326007326	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	5.486	0.274665	0.10403	0.024966	2.33E-4	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.00123	8.7;8.7	5.29	3.43	0.39272	GPCR, rhodopsin-like superfamily (1);	0.233518	0.30028	N	0.010584	T	0.00039	0.0001	N	0.13043	0.29	0.09310	N	1	B	0.19073	0.033	B	0.18263	0.021	T	0.21177	-1.0253	10	0.48119	T	0.1	.	6.2746	0.20973	0.2268:0.136:0.6372:0.0	rs61756679	199	Q7Z3T1	OR2W3_HUMAN	I	199	ENSP00000445853:V199I;ENSP00000353516:V199I	ENSP00000353516:V199I	V	+	1	0	OR2W3	246126106	0.000000	0.05858	0.049000	0.19019	0.091000	0.18340	-0.014000	0.12656	0.812000	0.34326	0.609000	0.83330	GTC		0.587	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		A	248059483	G	A	248059483	3	1	89	1	0	0	0	0	1	0	0	0	11064	1145	40	1	597	1	OR2W3	1	248059483	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	7688427	248059483	1191138	16	24428										
SOS1	6654	hgsc.bcm.edu	37	chr2	39213357	39213357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gctttcaggagggtctgagaTagaggtccggtctgatattg	15	6	3	3	rs374497013		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:39213357T>C	ENST00000426016.1	-	24	3696	c.3610A>G	c.(3610-3612)Atc>Gtc	p.I1204V	SOS1_ENST00000402219.2_Missense_Mutation_p.I1204V|SOS1_ENST00000395038.2_Missense_Mutation_p.I1189V			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1204					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				GGGTCTGAGATAGAGGTCCGG	0.498									Noonan syndrome																																							0			2						T	VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	138	146	143		3610	-11.2	0	2		143	0,8600		0,0,4300	no	missense	SOS1	NM_005633.3	29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	1204/1334	39213357	1,13005	2203	4300	6503	39066861	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3610A>G	2.37:g.39213357T>C	ENSP00000387784:p.Ile1204Val		39066861	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.410819	0.00014	2.27E-4	0.0	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038	T;T;T	0.75704	-0.79;-0.79;-0.96	5.58	-11.2	0.00127	.	1.364520	0.04344	N	0.354617	T	0.43831	0.1265	N	0.02011	-0.69	0.26423	N	0.976078	B	0.02656	0.0	B	0.01281	0.0	T	0.50816	-0.8783	10	0.15952	T	0.53	.	14.1255	0.65217	0.0:0.389:0.478:0.1329	.	1204	Q07889	SOS1_HUMAN	V	1204;1204;921;1189	ENSP00000387784:I1204V;ENSP00000384675:I1204V;ENSP00000378479:I1189V	ENSP00000378479:I1189V	I	-	1	0	SOS1	39066861	0.004000	0.15560	0.001000	0.08648	0.207000	0.24258	-1.537000	0.02206	-3.713000	0.00117	-2.209000	0.00301	ATC		0.498	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		C	39213357	T	C	39213357	3	2	89	1	0	0	0	0	1	0	0	0	14973	1406	49	4	395	4	SOS1	2	39213357	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10		39213357	203986016	17	24429										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315174	70315174	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cagcaggcccccggtcacccTgaggctggtggtgccggcca	15	16	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:70315174T>A	ENST00000303577.5	+	1	590	c.299T>A	c.(298-300)cTg>cAg	p.L100Q	PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	100	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L100P(1)|p.L100Q(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						CCGGTCACCCTGAGGCTGGTG	0.602																																					Colon(85;1146 1307 3484 18706 25380)											2	Substitution - Missense(2)	large_intestine(2)	2											59	73	68					2																	70315174		2201	4300	6501	70168678	SO:0001583	missense	5093				CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.299T>A	2.37:g.70315174T>A	ENSP00000305556:p.Leu100Gln		70168678	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	37	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551119	0.65311	.	.	ENSG00000169564	ENST00000303577	T	0.30714	1.52	4.16	4.16	0.48862	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.168590	0.40469	U	0.001094	T	0.60573	0.2279	M	0.91459	3.21	0.54753	D	0.999986	D	0.71674	0.998	D	0.70487	0.969	T	0.69781	-0.5052	10	0.87932	D	0	.	11.8577	0.52449	0.0:0.0:0.0:1.0	.	100	Q15365	PCBP1_HUMAN	Q	100	ENSP00000305556:L100Q	ENSP00000305556:L100Q	L	+	2	0	PCBP1	70168678	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.884000	0.69729	2.120000	0.65058	0.477000	0.44152	CTG		0.602	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70315174	T	A	70315174	3	1	89	1	0	0	0	0	1	0	0	0	11531	1580	55	5	301	5	PCBP1	2	70315174	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	31101817	70315174	172884199	18	24430										
TMEM182	130827	hgsc.bcm.edu	37	chr2	103378756	103378756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctttttggtggcttttggatCggattattggcttcttgcaa	11	6	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:103378756C>T	ENST00000412401.2	+	1	285	c.80C>T	c.(79-81)tCg>tTg	p.S27L	TMEM182_ENST00000409173.1_Intron|TMEM182_ENST00000409528.1_Intron	NM_144632.3	NP_653233.3	Q6ZP80	TM182_HUMAN	transmembrane protein 182	27						integral component of membrane (GO:0016021)		p.S27L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11						GCTTTTGGATCGGATTATTGG	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											170	164	166					2																	103378756		2203	4300	6503	102745188	SO:0001583	missense	130827			AK054856	CCDS2064.1	2q12.1	2009-08-25			ENSG00000170417	ENSG00000170417			26391	protein-coding gene	gene with protein product						12477932	Standard	NM_144632		Approved	FLJ30294	uc010fjb.3	Q6ZP80	OTTHUMG00000130779	ENST00000412401.2:c.80C>T	2.37:g.103378756C>T	ENSP00000394178:p.Ser27Leu		102745188	C9JML7|Q3B7B8|Q53TT9|Q6GMU0|Q8WW45|Q96NR4	Missense_Mutation	SNP	ENST00000412401.2	37	CCDS2064.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.997101	0.74818	.	.	ENSG00000170417	ENST00000412401	T	0.70516	-0.49	6.02	6.02	0.97574	.	0.049435	0.85682	D	0.000000	T	0.64461	0.2600	L	0.43152	1.355	0.39266	D	0.964296	P	0.44429	0.835	B	0.38327	0.271	T	0.71606	-0.4542	10	0.87932	D	0	-19.2839	15.9588	0.79910	0.0:0.866:0.134:0.0	.	27	Q6ZP80	TM182_HUMAN	L	27	ENSP00000394178:S27L	ENSP00000394178:S27L	S	+	2	0	TMEM182	102745188	0.978000	0.34361	0.998000	0.56505	0.973000	0.67179	2.471000	0.45127	2.865000	0.98341	0.655000	0.94253	TCG		0.398	TMEM182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253293.1	NM_144632		T	103378756	C	T	103378756	3	4	89	1	0	0	0	0	1	0	0	0	16140	893	31	1	82	1	TMEM182	2	103378756	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	33063582	103378756	139820617	19	24431										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166170618	166170618	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aagcaacaagaagaagctcaGgtatagtgaacaagcatacg	10	7	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:166170618G>A	ENST00000375437.2	+	10	1673	c.1383G>A	c.(1381-1383)caG>caA	p.Q461Q	SCN2A_ENST00000283256.6_Splice_Site_p.Q461Q|SCN2A_ENST00000357398.3_Splice_Site_p.Q461Q|SCN2A_ENST00000375427.2_Splice_Site_p.Q461Q	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	461					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.Q461Q(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGAAGCTCAGGTATAGTGAA	0.398																																																1	Substitution - coding silent(1)	ovary(1)	2											50	48	49					2																	166170618		2202	4299	6501	165878864	SO:0001630	splice_region_variant	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1383+1G>A	2.37:g.166170618G>A			165878864	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																				0.398	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	Silent	A	166170618	G	A	166170618	5	1	89	1	0	0	0	0	0	0	1	0	13953	1014	35	3	1513	3	SCN2A	2	166170618	Splice_Site	SNP	G	TCGA-CI-6622-01A-11D-1826-10	62791862	166170618	77028755	20	24432										
TTN	7273	hgsc.bcm.edu	37	chr2	179470014	179470014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	actcagacgcaacttaatagTtggaggcactgcaaagagaa	10	8	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:179470014T>A	ENST00000591111.1	-	230	49191	c.48967A>T	c.(48967-48969)Act>Tct	p.T16323S	TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T9024S|TTN_ENST00000460472.2_Missense_Mutation_p.T8899S|TTN_ENST00000342175.6_Missense_Mutation_p.T9091S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T15396S|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T17964S|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16323	Ig-like 100.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTTAATAGTTGGAGGCACT	0.413																																																0			2											26	24	24					2																	179470014		1874	4093	5967	179178259	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48967A>T	2.37:g.179470014T>A	ENSP00000465570:p.Thr16323Ser		179178259	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.10	2.137051	0.37728	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63913	-0.07;0.19;0.17;0.16	5.74	5.74	0.90152	Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50514	0.1620	N	0.20610	0.595	0.39445	D	0.967319	B;B;B;B	0.14012	0.003;0.003;0.003;0.009	B;B;B;B	0.11329	0.006;0.006;0.006;0.006	T	0.50947	-0.8767	9	0.87932	D	0	.	16.0476	0.80731	0.0:0.0:0.0:1.0	.	8899;9024;9091;16323	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	15396;8899;9091;9024;8899	ENSP00000343764:T15396S;ENSP00000434586:T8899S;ENSP00000340554:T9091S;ENSP00000352154:T9024S	ENSP00000340554:T9091S	T	-	1	0	TTN	179178259	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.625000	0.61262	2.190000	0.69967	0.460000	0.39030	ACT		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179470014	T	A	179470014	3	1	89	1	0	0	0	0	1	0	0	0	16775	1725	60	5	54135	5	TTN	2	179470014	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	13299396	179470014	63729359	21	24433										
TTN	7273	hgsc.bcm.edu	37	chr2	179594277	179594277	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tccacaggcttcagctctctGataaaggtggggggttctaa	12	9	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:179594277G>T	ENST00000591111.1	-	62	17879	c.17655C>A	c.(17653-17655)atC>atA	p.I5885I	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.I4958I|TTN_ENST00000589042.1_Silent_p.I6202I			Q8WZ42	TITIN_HUMAN	titin	12683	Ig-like 40.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGCTCTCTGATAAAGGTGG	0.453																																																0			2											81	76	77					2																	179594277		1841	4095	5936	179302522	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.17655C>A	2.37:g.179594277G>T			179302522	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179594277	G	T	179594277	2	4	89	1	0	0	0	0	0	0	0	1	16775	1280	45	2		2	TTN	2	179594277	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	124263	179594277	63605096	22	24434										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189854858	189854858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccggacgacctggagagcgaGgattgcctggacctccagtg	15	12	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:189854858G>A	ENST00000304636.3	+	9	897	c.727G>A	c.(727-729)Gga>Aga	p.G243R	COL3A1_ENST00000317840.5_Missense_Mutation_p.G243R	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	243	Triple-helical region.		G -> V (in EDS4).		aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TGGAGAGCGAGGATTGCCTGG	0.373																																																0			2											66	69	68					2																	189854858		2203	4300	6503	189563103	SO:0001583	missense	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.727G>A	2.37:g.189854858G>A	ENSP00000304408:p.Gly243Arg		189563103	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.630489	0.67015	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99353	-5.77;-5.53	5.57	5.57	0.84162	.	0.000000	0.50627	D	0.000115	D	0.99638	0.9867	H	0.97564	4.03	0.53688	D	0.999973	D	0.89917	1.0	D	0.97110	1.0	D	0.97732	1.0203	10	0.87932	D	0	.	14.7151	0.69262	0.0:0.0:0.855:0.1449	.	243	P02461	CO3A1_HUMAN	R	243	ENSP00000304408:G243R;ENSP00000315243:G243R	ENSP00000304408:G243R	G	+	1	0	COL3A1	189563103	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.135000	0.77276	2.767000	0.95098	0.591000	0.81541	GGA		0.373	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189854858	G	A	189854858	3	1	89	1	0	0	0	0	1	0	0	0	3694	1001	35	3	761	3	COL3A1	2	189854858	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	10260581	189854858	53344515	23	24435										
BOLL	66037	hgsc.bcm.edu	37	chr2	198631309	198631309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctgagctaccatcacaggggAgctacatacagaacgtgact	10	11	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:198631309A>G	ENST00000392296.4	-	7	808	c.499T>C	c.(499-501)Tcc>Ccc	p.S167P	BOLL_ENST00000321801.7_Missense_Mutation_p.S179P|BOLL_ENST00000433157.1_Missense_Mutation_p.S167P|BOLL_ENST00000282278.8_Missense_Mutation_p.S58P|BOLL_ENST00000430004.1_Missense_Mutation_p.S167P|AC011997.1_ENST00000409845.1_Intron	NM_033030.5	NP_149019.1	Q8N9W6	BOLL_HUMAN	boule-like RNA-binding protein	167	DAZ-like.				cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.S167A(1)		central_nervous_system(1)|endometrium(2)|lung(6)|ovary(3)|prostate(1)	13						ATCACAGGGGAGCTACATACA	0.338																																																1	Substitution - Missense(1)	ovary(1)	2											69	73	71					2																	198631309		2203	4300	6503	198339554	SO:0001583	missense	66037				CCDS2324.1, CCDS2325.1, CCDS63081.1	2q33	2013-10-17	2013-10-17		ENSG00000152430	ENSG00000152430		"RNA binding motif (RRM) containing"	14273	protein-coding gene	gene with protein product		606165	"bol (Drosophila boule homolog)-like", "bol, boule-like (Drosophila)"			11390979, 16001084	Standard	NM_197970		Approved	BOULE	uc002uut.2	Q8N9W6	OTTHUMG00000132747	ENST00000392296.4:c.499T>C	2.37:g.198631309A>G	ENSP00000376116:p.Ser167Pro		198339554	B4DZA4|Q0JW32|Q53T62|Q969U3	Missense_Mutation	SNP	ENST00000392296.4	37	CCDS2325.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358615	0.41801	.	.	ENSG00000152430	ENST00000430004;ENST00000392296;ENST00000321801;ENST00000282278;ENST00000433157	T;T;T;T	0.30448	1.53;1.69;1.68;1.69	4.63	4.63	0.57726	.	0.091045	0.46145	D	0.000315	T	0.40015	0.1100	N	0.24115	0.695	0.37135	D	0.901448	D;B;P;B;B	0.76494	0.999;0.111;0.504;0.044;0.074	D;B;B;B;B	0.80764	0.994;0.078;0.304;0.017;0.017	T	0.50381	-0.8835	10	0.87932	D	0	-19.7686	12.4045	0.55432	1.0:0.0:0.0:0.0	.	58;173;179;167;173	B4DZA4;Q8N9W6-2;Q8N9W6-3;Q8N9W6;Q8N9W6-4	.;.;.;BOLL_HUMAN;.	P	167;167;179;58;167	ENSP00000397711:S167P;ENSP00000376116:S167P;ENSP00000314792:S179P;ENSP00000396099:S167P	ENSP00000282278:S58P	S	-	1	0	BOLL	198339554	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.848000	0.55903	1.948000	0.56530	0.482000	0.46254	TCC		0.338	BOLL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256107.3	NM_033030		G	198631309	A	G	198631309	3	3	89	1	0	0	0	0	1	0	0	0	1490	304	11	4	372	4	BOLL	2	198631309	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	8776451	198631309	44568064	24	24436										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174442	207174442	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gctgataaaaaaaaacgttcGaagctaaaacatagagatct	7	6	1	2	rs140337696	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:207174442G>A	ENST00000374423.3	+	5	5576	c.5190G>A	c.(5188-5190)tcG>tcA	p.S1730S		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1730							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAAAACGTTCGAAGCTAAAAC	0.458													G|||	5	0.000998403	0.0038	0	5008	,	,		19142	0		0	False		,,,				2504	0															0			2						G		2,3734		0,2,1866	75	73	74		5190	-1.2	0	2	dbSNP_134	74	0,8214		0,0,4107	no	coding-synonymous	ZDBF2	NM_020923.1		0,2,5973	AA,AG,GG		0.0,0.0535,0.0167		1730/2355	207174442	2,11948	1868	4107	5975	206882687	SO:0001819	synonymous_variant	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5190G>A	2.37:g.207174442G>A			206882687	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																				0.458	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207174442	G	A	207174442	2	1	89	1	0	0	0	0	0	0	0	1	17638	1045	37	1		1	ZDBF2	2	207174442	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	8543133	207174442	36024931	25	24437										
CPS1	1373	hgsc.bcm.edu	37	chr2	211441114	211441114	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgcctacaaaggacagattcTcacaatggccaaccctatta	6	12	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr2:211441114T>C	ENST00000233072.5	+	3	477	c.281T>C	c.(280-282)cTc>cCc	p.L94P	CPS1_ENST00000430249.2_Missense_Mutation_p.L100P	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	94	Anthranilate phosphoribosyltransferase homolog.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GGACAGATTCTCACAATGGCC	0.408																																																0			2											186	170	175					2																	211441114		2203	4300	6503	211149359	SO:0001583	missense	1589			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.281T>C	2.37:g.211441114T>C	ENSP00000233072:p.Leu94Pro		211149359	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586152	0.86851	.	.	ENSG00000021826	ENST00000417946;ENST00000518043;ENST00000523702;ENST00000430249;ENST00000539150;ENST00000233072;ENST00000536125	D;D;D;D;D	0.95307	-3.67;-3.67;-3.67;-3.67;-3.67	5.96	5.96	0.96718	Carbamoyl-phosphate synthase, small subunit, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.98444	0.9482	H	0.97962	4.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.99755	1.1019	10	0.87932	D	0	-7.5435	16.4447	0.83919	0.0:0.0:0.0:1.0	.	104;94	Q59HF8;P31327	.;CPSM_HUMAN	P	94;94;100;100;102;94;94	ENSP00000388496:L94P;ENSP00000430697:L94P;ENSP00000430644:L100P;ENSP00000402608:L100P;ENSP00000233072:L94P	ENSP00000233072:L94P	L	+	2	0	CPS1	211149359	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.466000	0.80914	2.284000	0.76573	0.528000	0.53228	CTC		0.408	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			C	211441114	T	C	211441114	3	2	89	1	0	0	0	0	1	0	0	0	3829	1551	54	4	313	4	CPS1	2	211441114	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	4266672	211441114	31758259	26	24438										
DCLK3	85443	hgsc.bcm.edu	37	chr3	36779797	36779797	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agatgcttctctccccttgcGtgcctctcttccagagtggc	9	15	2	2	rs552055548		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:36779797G>A	ENST00000416516.2	-	2	844	c.354C>T	c.(352-354)caC>caT	p.H118H		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	118						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						CTCCCCTTGCGTGCCTCTCTT	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		18541	0		0	False		,,,				2504	0															0			3											136	138	137					3																	36779797		1881	4100	5981	36754801	SO:0001819	synonymous_variant	85443			AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"doublecortin and CaM kinase-like 3"	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.354C>T	3.37:g.36779797G>A			36754801		Silent	SNP	ENST00000416516.2	37	CCDS43064.1																																																																																				0.567	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		A	36779797	G	A	36779797	2	1	89	1	0	0	0	0	0	0	0	1	4299	1136	40	1		1	DCLK3	3	36779797	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10		36779797	161242633	27	24439										
KBTBD5	131377	hgsc.bcm.edu	37	chr3	42728220	42728220	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gctggaggcctcttctacaaCgaagacaacaaagaggaccc	10	12	2	2	rs201966674		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:42728220C>T	ENST00000287777.4	+	1	1210	c.1110C>T	c.(1108-1110)aaC>aaT	p.N370N		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	370					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											TCTTCTACAACGAAGACAACA	0.577																																																0			3											38	35	36					3																	42728220		2203	4300	6503	42703224	SO:0001819	synonymous_variant	131377			AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1110C>T	3.37:g.42728220C>T			42703224	Q86SI1|Q96MR2	Silent	SNP	ENST00000287777.4	37	CCDS2703.1																																																																																				0.577	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		T	42728220	C	T	42728220	2	4	89	1	0	0	0	0	0	0	0	1	8017	535	19	1		1	KBTBD5	3	42728220	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	5948423	42728220	155294210	28	24440										
CCR3	1232	hgsc.bcm.edu	37	chr3	46306816	46306816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttgggcaatgtggtggtggTgatgatcctcataaaataca	12	6	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:46306816T>C	ENST00000357422.2	+	4	710	c.167T>C	c.(166-168)gTg>gCg	p.V56A	CCR3_ENST00000545097.1_Missense_Mutation_p.V77A|CCR3_ENST00000541018.1_Missense_Mutation_p.V56A|CCR3_ENST00000395942.2_Missense_Mutation_p.V56A|CCR3_ENST00000395940.2_Missense_Mutation_p.V56A			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	56					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GTGGTGGTGGTGATGATCCTC	0.527																																																0			3											156	126	136					3																	46306816		2203	4300	6503	46281820	SO:0001583	missense	1232			AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.167T>C	3.37:g.46306816T>C	ENSP00000350003:p.Val56Ala		46281820	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	37	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.217981	0.58560	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000452454;ENST00000395942	T;T;T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	6.07	4.92	0.64577	GPCR, rhodopsin-like superfamily (1);	0.377567	0.22261	N	0.062401	D	0.86686	0.5992	M	0.88031	2.925	0.39196	D	0.963056	P;D;P;P	0.65815	0.931;0.995;0.673;0.72	P;D;B;P	0.68621	0.888;0.959;0.444;0.58	D	0.89215	0.3567	10	0.66056	D	0.02	.	11.6734	0.51415	0.0:0.0683:0.0:0.9317	.	56;56;77;56	Q8TDP5;Q8TDP6;F5GWL6;P51677	.;.;.;CCR3_HUMAN	A	56;77;56;56;56;56	ENSP00000350003:V56A;ENSP00000441600:V77A;ENSP00000440097:V56A;ENSP00000379271:V56A;ENSP00000389336:V56A;ENSP00000379273:V56A	ENSP00000350003:V56A	V	+	2	0	CCR3	46281820	1.000000	0.71417	0.908000	0.35775	0.222000	0.24845	6.270000	0.72563	2.326000	0.78906	0.533000	0.62120	GTG		0.527	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			C	46306816	T	C	46306816	3	2	89	1	0	0	0	0	1	0	0	0	2948	1696	59	4	236	4	CCR3	3	46306816	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	3578596	46306816	151715614	29	24441										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140123548	140123548	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aggactgctccccacagtacAgccagatctgcaactatgaa	8	13	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:140123548A>G	ENST00000458420.3	+	4	767	c.577A>G	c.(577-579)Agc>Ggc	p.S193G	AC092988.1_ENST00000580582.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.S193C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CCCACAGTACAGCCAGATCTG	0.527										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	3											142	120	127					3																	140123548		2203	4300	6503	141606238	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.577A>G	3.37:g.140123548A>G	ENSP00000402460:p.Ser193Gly		141606238	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.331649	0.60853	.	.	ENSG00000158258	ENST00000458420	T	0.49139	0.79	5.66	5.66	0.87406	Cadherin (4);Cadherin-like (1);	0.090356	0.85682	D	0.000000	T	0.53818	0.1820	L	0.33189	0.99	0.58432	D	0.999991	D	0.76494	0.999	D	0.79108	0.992	T	0.46105	-0.9215	10	0.10636	T	0.68	-26.7325	13.8537	0.63513	1.0:0.0:0.0:0.0	.	193	Q9H4D0	CSTN2_HUMAN	G	193	ENSP00000402460:S193G	ENSP00000402460:S193G	S	+	1	0	CLSTN2	141606238	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.452000	0.80683	2.153000	0.67306	0.460000	0.39030	AGC		0.527	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		G	140123548	A	G	140123548	3	3	89	1	0	0	0	0	1	0	0	0	3568	188	7	4	591	4	CLSTN2	3	140123548	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	93816732	140123548	57898882	30	24442										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146598	154146598	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccgaacacggtgtcggagctCggagagcatcccccagagcg	14	14	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:154146598C>T	ENST00000389740.2	-	1	906	c.807G>A	c.(805-807)ccG>ccA	p.P269P		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	269					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TGTCGGAGCTCGGAGAGCATC	0.667																																																0			3											30	34	32					3																	154146598		1875	4114	5989	155629292	SO:0001819	synonymous_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.807G>A	3.37:g.154146598C>T			155629292		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																				0.667	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154146598	C	T	154146598	2	4	89	1	0	0	0	0	0	0	0	1	6674	871	31	1		1	GPR149	3	154146598	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	14023050	154146598	43875832	31	24443										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916930	178916930	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aaaagtaattgaaccagtagGcaaccgtgaagaaaagatcc	9	7	0	4			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:178916930G>T	ENST00000263967.3	+	2	474	c.317G>T	c.(316-318)gGc>gTc	p.G106V		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	106			G -> V (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.G106V(6)|p.G106_R108delGNR(2)|p.G106_R108del(2)|p.G106A(1)|p.E103_G106>D(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAACCAGTAGGCAACCGTGAA	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	12	Substitution - Missense(7)|Deletion - In frame(4)|Complex - deletion inframe(1)	lung(4)|large_intestine(3)|breast(3)|endometrium(2)	3											90	86	87					3																	178916930		1825	4072	5897	180399624	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.317G>T	3.37:g.178916930G>T	ENSP00000263967:p.Gly106Val		180399624	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.216426	0.79352	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.74421	0.67;-0.84	5.52	5.52	0.82312	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.86928	0.6051	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86624	0.1881	9	.	.	.	-7.432	19.4271	0.94746	0.0:0.0:1.0:0.0	.	106	P42336	PK3CA_HUMAN	V	106	ENSP00000263967:G106V;ENSP00000417479:G106V	.	G	+	2	0	PIK3CA	180399624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.563000	0.82314	2.584000	0.87258	0.555000	0.69702	GGC		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916930	G	T	178916930	3	4	89	1	0	0	0	0	1	0	0	0	11944	1203	42	2	319	2	PIK3CA	3	178916930	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	24770332	178916930	19105500	32	24444										
ETV5	2119	hgsc.bcm.edu	37	chr3	185797727	185797727	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctctggaagcgaatggggggCgggggcggggcccacacctt	19	11	1	0	rs185636057	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr3:185797727C>T	ENST00000306376.5	-	7	775	c.529G>A	c.(529-531)Gcc>Acc	p.A177T	ETV5_ENST00000537818.1_Missense_Mutation_p.A219T|ETV5_ENST00000434744.1_Missense_Mutation_p.A177T|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	177					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			GAATGGGGGGCGGGGGCGGGG	0.622			T	"TMPRSS2, SCL45A3"	Prostate								C|||	4	0.000798722	0.003	0	5008	,	,		12942	0		0	False		,,,				2504	0						Dom	yes		3	3q28	2119	ets variant gene 5		E	0			3						C	THR/ALA	5,4401	9.9+/-24.2	0,5,2198	44	52	49		529	-2.8	0.2	3		49	0,8600		0,0,4300	yes	missense	ETV5	NM_004454.2	58	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign	177/511	185797727	5,13001	2203	4300	6503	187280421	SO:0001583	missense	2119			BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.529G>A	3.37:g.185797727C>T	ENSP00000306894:p.Ala177Thr		187280421	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	37	CCDS33906.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	3.837	-0.034583	0.07543	0.001135	0.0	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.09630	2.97;2.97;2.96	5.32	-2.83	0.05769	PEA3-type ETS-domain transcription factor, N-terminal (1);	2.223100	0.01467	N	0.016113	T	0.07999	0.0200	L	0.44542	1.39	0.24298	N	0.995135	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.37244	-0.9714	10	0.19590	T	0.45	.	12.5188	0.56048	0.0:0.7845:0.0:0.2155	.	177;219	P41161;B7Z7D7	ETV5_HUMAN;.	T	177;177;219	ENSP00000306894:A177T;ENSP00000413755:A177T;ENSP00000441737:A219T	ENSP00000306894:A177T	A	-	1	0	ETV5	187280421	0.000000	0.05858	0.211000	0.23655	0.133000	0.20885	-0.108000	0.10857	-0.710000	0.05001	-0.244000	0.11960	GCC		0.622	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		T	185797727	C	T	185797727	3	4	89	1	0	0	0	0	1	0	0	0	5295	768	27	1	1031	1	ETV5	3	185797727	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6880797	185797727	12224703	33	24445										
STK32B	55351	hgsc.bcm.edu	37	chr4	5468461	5468461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gaactgcgatcccacatttgAgcttgaagagatgattctag	10	8	1	4			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:5468461A>G	ENST00000282908.5	+	10	1363	c.941A>G	c.(940-942)gAg>gGg	p.E314G	STK32B_ENST00000510398.1_Missense_Mutation_p.E267G|STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000512636.1_Missense_Mutation_p.E237G	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CCCACATTTGAGCTTGAAGAG	0.448																																																0			4											81	72	75					4																	5468461		2203	4300	6503	5519362	SO:0001583	missense	55351			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.941A>G	4.37:g.5468461A>G	ENSP00000282908:p.Glu314Gly		5519362		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740065	0.89573	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.24908	1.83;1.83;1.83	5.17	5.17	0.71159	Protein kinase-like domain (1);	0.000000	0.42420	U	0.000712	T	0.55033	0.1895	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62666	-0.6806	10	0.72032	D	0.01	.	13.8534	0.63510	1.0:0.0:0.0:0.0	.	314	Q9NY57	ST32B_HUMAN	G	314;237;267	ENSP00000282908:E314G;ENSP00000423209:E237G;ENSP00000420984:E267G	ENSP00000282908:E314G	E	+	2	0	STK32B	5519362	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.923000	0.87546	1.952000	0.56665	0.472000	0.43445	GAG		0.448	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		G	5468461	A	G	5468461	3	3	89	1	0	0	0	0	1	0	0	0	15337	304	11	4	979	4	STK32B	4	5468461	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10		5468461	185685815	34	24446										
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25262150	25262150	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttgtttgttttgaaagacagGggcaatgataattggttagt	12	2	0	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:25262150G>T	ENST00000264864.6	+	6	1104	c.915G>T	c.(913-915)agG>agT	p.R305S	PI4K2B_ENST00000512921.1_Missense_Mutation_p.R209S	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	305	PI3K/PI4K.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				TGAAAGACAGGGGCAATGATA	0.294																																																0			4											115	124	121					4																	25262150		2203	4299	6502	24871248	SO:0001583	missense	55300			AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.915G>T	4.37:g.25262150G>T	ENSP00000264864:p.Arg305Ser		24871248	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	37	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.484187	0.63962	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	D;D	0.98914	-5.23;-5.23	5.76	3.13	0.36017	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.046975	0.85682	D	0.000000	D	0.99152	0.9707	H	0.97806	4.08	0.80722	D	1	P	0.50156	0.932	P	0.59221	0.854	D	0.98245	1.0490	10	0.87932	D	0	-8.3356	4.4678	0.11698	0.3696:0.0:0.4877:0.1428	.	305	Q8TCG2	P4K2B_HUMAN	S	209;305;274	ENSP00000423373:R209S;ENSP00000264864:R305S	ENSP00000264864:R305S	R	+	3	2	PI4K2B	24871248	0.996000	0.38824	1.000000	0.80357	0.953000	0.61014	0.342000	0.19926	0.466000	0.27193	0.650000	0.86243	AGG		0.294	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		T	25262150	G	T	25262150	3	4	89	1	0	0	0	0	1	0	0	0	11903	1223	43	2	937	2	PI4K2B	4	25262150	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	19793689	25262150	165892126	35	24447										
PGM2	55276	hgsc.bcm.edu	37	chr4	37847343	37847343	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agacttgctgtggcagaaaaGcaagacaggtaaaattaatt	10	5	0	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:37847343G>A	ENST00000381967.4	+	8	1099	c.999G>A	c.(997-999)aaG>aaA	p.K333K	PGM2_ENST00000537241.1_Silent_p.K173K|PGM2_ENST00000544359.1_Silent_p.K194K	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	333					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TGGCAGAAAAGCAAGACAGGT	0.388																																																0			4											83	86	85					4																	37847343		2203	4300	6503	37523738	SO:0001819	synonymous_variant	55276			BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.999G>A	4.37:g.37847343G>A			37523738	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																				0.388	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		A	37847343	G	A	37847343	2	1	89	1	0	0	0	0	0	0	0	1	11829	962	34	3		3	PGM2	4	37847343	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	12585193	37847343	153306933	36	24448										
OCIAD2	132299	hgsc.bcm.edu	37	chr4	48901894	48901894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttctcgcataatctttgagaTctctgctctgtggatgtgca	9	9	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:48901894T>A	ENST00000508632.1	-	3	347	c.115A>T	c.(115-117)Atc>Ttc	p.I39F	OCIAD2_ENST00000273860.4_Missense_Mutation_p.I39F|OCIAD2_ENST00000508069.2_Intron	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	39	OCIA.					endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						ATCTTTGAGATCTCTGCTCTG	0.388																																																0			4											202	191	194					4																	48901894		2203	4300	6503	48596651	SO:0001583	missense	132299			BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.115A>T	4.37:g.48901894T>A	ENSP00000423014:p.Ile39Phe		48596651	B4DPE7|Q8N544	Missense_Mutation	SNP	ENST00000508632.1	37	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.745412	0.30955	.	.	ENSG00000145247	ENST00000508632;ENST00000273860;ENST00000381464	T;T;T	0.43294	0.95;0.95;0.95	4.74	2.3	0.28687	.	0.214788	0.38663	N	0.001617	T	0.35393	0.0930	L	0.40543	1.245	0.36983	D	0.89438	B;P	0.49307	0.011;0.922	B;P	0.48030	0.013;0.564	T	0.25813	-1.0121	9	.	.	.	-1.6188	6.3242	0.21234	0.0:0.199:0.0:0.801	.	39;39	Q56VL3-2;Q56VL3	.;OCAD2_HUMAN	F	39	ENSP00000423014:I39F;ENSP00000273860:I39F;ENSP00000370873:I39F	.	I	-	1	0	OCIAD2	48596651	1.000000	0.71417	0.965000	0.40720	0.174000	0.22865	1.574000	0.36482	0.406000	0.25560	-0.464000	0.05259	ATC		0.388	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398		A	48901894	T	A	48901894	3	1	89	1	0	0	0	0	1	0	0	0	10849	1435	50	5	369	5	OCIAD2	4	48901894	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	11054551	48901894	142252382	37	24449										
CEP135	9662	hgsc.bcm.edu	37	chr4	56865777	56865777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgtagatgagaagacagaaaAgattgcaaatttgcaagaaa	10	3	0	6			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:56865777A>G	ENST00000257287.4	+	17	2370	c.2246A>G	c.(2245-2247)aAg>aGg	p.K749R		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	749					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AAGACAGAAAAGATTGCAAAT	0.333																																																0			4											70	78	75					4																	56865777		2203	4300	6503	56560534	SO:0001583	missense	9662			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2246A>G	4.37:g.56865777A>G	ENSP00000257287:p.Lys749Arg		56560534	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.280056	0.23392	.	.	ENSG00000174799	ENST00000257287	T	0.56941	0.43	5.18	2.73	0.32206	.	0.248856	0.47093	D	0.000257	T	0.30230	0.0758	N	0.17723	0.515	0.28411	N	0.9182	B	0.06786	0.001	B	0.12837	0.008	T	0.17623	-1.0363	10	0.10377	T	0.69	.	7.3434	0.26650	0.6558:0.0:0.3442:0.0	.	749	Q66GS9	CP135_HUMAN	R	749	ENSP00000257287:K749R	ENSP00000257287:K749R	K	+	2	0	CEP135	56560534	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	2.491000	0.45303	0.786000	0.33708	0.524000	0.50904	AAG		0.333	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56865777	A	G	56865777	3	3	89	1	0	0	0	0	1	0	0	0	3253	72	3	4	2308	4	CEP135	4	56865777	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	7963883	56865777	134288499	38	24450										
FGF5	2250	hgsc.bcm.edu	37	chr4	81207710	81207711	+	Frame_Shift_Ins	INS	-	-	TT													0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gccagaactttctttcacggINSttactgttcctgaaaagaaa							TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:81207710_81207711insTT	ENST00000312465.7	+	3	917_918	c.691_692insTT	c.(691-693)gttfs	p.V231fs	FGF5_ENST00000456523.3_3'UTR|FGF5_ENST00000503413.1_3'UTR	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	231					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						TTCTTTCACGGTTACTGTTCCT	0.48																																																0			4																																								81426735	SO:0001589	frameshift_variant	2250			M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"Endogenous ligands"	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.692_693dupTT	4.37:g.81207711_81207712dupTT	ENSP00000311697:p.Val231fs		81426734	B2R554|O75846|Q3Y8M3|Q8NF90	Frame_Shift_Ins	INS	ENST00000312465.7	37	CCDS34021.1																																																																																				0.48	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			TT	81207711	-	TT	81207710	7	5	89	1	0	1	1	0	0	0	0	0	5874	1261	44	0	701	0	FGF5	4	81207710	Frame_Shift_Ins	INS	-	TCGA-CI-6622-01A-11D-1826-10	24341933	81207710	109946566	39	24451										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90169745	90169745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cagatagtttgcaatctgggTctgttttgtggccgtttgtc	12	7	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:90169745T>C	ENST00000609438.1	-	2	2035	c.1517A>G	c.(1516-1518)gAc>gGc	p.D506G	GPRIN3_ENST00000333209.4_Missense_Mutation_p.D506G	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	506										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		GCAATCTGGGTCTGTTTTGTG	0.443																																																0			4											89	96	94					4																	90169745		2203	4300	6503	90388768	SO:0001583	missense	285513			AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1517A>G	4.37:g.90169745T>C	ENSP00000476603:p.Asp506Gly		90388768	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.376515	0.24857	.	.	ENSG00000185477	ENST00000333209	T	0.11495	2.77	5.38	0.0691	0.14372	.	0.713798	0.11522	N	0.555623	T	0.06508	0.0167	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36648	-0.9739	10	0.41790	T	0.15	-3.9639	4.8668	0.13613	0.0:0.2383:0.2826:0.4791	.	506	Q6ZVF9	GRIN3_HUMAN	G	506	ENSP00000328672:D506G	ENSP00000328672:D506G	D	-	2	0	GPRIN3	90388768	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.567000	0.23608	-0.094000	0.12374	-0.313000	0.08912	GAC		0.443	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		C	90169745	T	C	90169745	3	2	89	1	0	0	0	0	1	0	0	0	6752	1667	58	4	817	4	GPRIN3	4	90169745	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	8962035	90169745	100984531	40	24452										
TNIP3	79931	hgsc.bcm.edu	37	chr4	122068296	122068296	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aagtctctctcgatccgatcGttcctttttgaagtcttctt	6	11	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:122068296G>A	ENST00000509841.1	-	10	952	c.874C>T	c.(874-876)Cga>Tga	p.R292*	TNIP3_ENST00000507879.1_Nonsense_Mutation_p.R285*|TNIP3_ENST00000454328.1_Nonsense_Mutation_p.R215*|TNIP3_ENST00000057513.3_Nonsense_Mutation_p.R215*|TNIP3_ENST00000511909.1_5'UTR	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3									p.R215*(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						CGATCCGATCGTTCCTTTTTG	0.373																																																1	Substitution - Nonsense(1)	ovary(1)	4											193	187	189					4																	122068296		2203	4300	6503	122287746	SO:0001587	stop_gained	79931			AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.874C>T	4.37:g.122068296G>A	ENSP00000426613:p.Arg292*		122287746		Nonsense_Mutation	SNP	ENST00000509841.1	37	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	G	37	6.256847	0.97417	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	.	.	.	5.4	2.33	0.28932	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.629	13.3008	0.60324	0.0:0.0:0.3006:0.6994	.	.	.	.	X	215;215;285;292	.	ENSP00000057513:R215X	R	-	1	2	TNIP3	122287746	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	2.618000	0.46393	0.626000	0.30322	0.563000	0.77884	CGA		0.373	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		A	122068296	G	A	122068296	4	1	89	1	0	0	0	0	0	1	0	0	16355	1153	40	1	354	1	TNIP3	4	122068296	Nonsense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	31898551	122068296	69085980	41	24453										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122824121	122824121	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acaaatgattttggactaggAactagactgaaaggtggagg	13	4	0	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:122824121A>G	ENST00000379645.3	-	9	2422	c.2349T>C	c.(2347-2349)gtT>gtC	p.V783V	TRPC3_ENST00000264811.5_Silent_p.V710V|TRPC3_ENST00000513531.1_Silent_p.V655V	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	698	Binds to IP3R3.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TTGGACTAGGAACTAGACTGA	0.373																																																0			4											114	111	112					4																	122824121		2203	4300	6503	123043571	SO:0001819	synonymous_variant	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2349T>C	4.37:g.122824121A>G			123043571	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																				0.373	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		G	122824121	A	G	122824121	2	3	89	1	0	0	0	0	0	0	0	1	16619	233	9	4		4	TRPC3	4	122824121	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	755825	122824121	68330155	42	24454										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129012668	129012668	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gagtatattaagcgtcaaatGtaagtggatgtttgatgtaa	11	2	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:129012668G>A	ENST00000326639.6	+	7	879		c.e7+1		LARP1B_ENST00000264584.5_Splice_Site|LARP1B_ENST00000354456.3_Splice_Site|LARP1B_ENST00000432347.2_Splice_Site|LARP1B_ENST00000427266.1_Splice_Site|LARP1B_ENST00000441387.1_Splice_Site|LARP1B_ENST00000512292.1_Splice_Site|LARP1B_ENST00000394288.3_Splice_Site	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B							nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						AGCGTCAAATGTAAGTGGATG	0.313																																																0			4											123	115	118					4																	129012668		2203	4300	6503	129232118	SO:0001630	splice_region_variant	55132				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.668+1G>A	4.37:g.129012668G>A			129232118	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Splice_Site	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.320056	0.81469	.	.	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266;ENST00000507377	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7147	0.85395	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LARP1B	129232118	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.179000	0.94861	2.245000	0.73994	0.555000	0.69702	.		0.313	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	Intron	A	129012668	G	A	129012668	5	1	89	1	0	0	0	0	0	0	1	0	8651	1391	48	3	687	3	LARP1B	4	129012668	Splice_Site	SNP	G	TCGA-CI-6622-01A-11D-1826-10	6188547	129012668	62141608	43	24455										
LRBA	987	hgsc.bcm.edu	37	chr4	151336641	151336641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gttttggcccaaggaggaagTtcgacatcagacactactgt	11	9	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr4:151336641T>C	ENST00000357115.3	-	48	7419	c.7176A>G	c.(7174-7176)gaA>gaG	p.E2392E	LRBA_ENST00000535741.1_Silent_p.E2381E|LRBA_ENST00000507224.1_Silent_p.E2381E|LRBA_ENST00000510413.1_Silent_p.E2381E|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2392	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAGGAGGAAGTTCGACATCAG	0.378																																																0			4											122	112	116					4																	151336641		2203	4300	6503	151556091	SO:0001819	synonymous_variant	987			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.7176A>G	4.37:g.151336641T>C			151556091	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	8.833	0.940295	0.18281	.	.	ENSG00000198589	ENST00000509835	.	.	.	5.82	4.64	0.57946	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54576	-0.8273	4	.	.	.	.	6.9988	0.24797	0.1318:0.0698:0.0:0.7985	.	.	.	.	S	1034	.	.	N	-	2	0	LRBA	151556091	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.991000	0.40727	1.035000	0.39972	0.455000	0.32223	AAC		0.378	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151336641	T	C	151336641	2	2	89	1	0	0	0	0	0	0	0	1	8960	1722	60	4		4	LRBA	4	151336641	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	22323973	151336641	39817635	44	24456										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1216984	1216984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctttgtggacatgcagcagcGgtgcaacgcctccgaccccg	12	15	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:1216984G>A	ENST00000304460.10	+	8	1153	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	366					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			ATGCAGCAGCGGTGCAACGCC	0.612																																																0			5											173	159	163					5																	1216984		2203	4300	6503	1269984	SO:0001583	missense	340024			AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1097G>A	5.37:g.1216984G>A	ENSP00000305302:p.Arg366Gln		1269984	A8K446	Missense_Mutation	SNP	ENST00000304460.10	37	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	A	5.316	0.243677	0.10077	.	.	ENSG00000174358	ENST00000304460	T	0.73897	-0.79	4.85	0.99	0.19807	.	1.119860	0.06339	N	0.707702	T	0.52451	0.1735	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.30937	-0.9961	10	0.30854	T	0.27	.	5.1522	0.15015	0.2385:0.0:0.4686:0.2929	.	366	Q695T7	S6A19_HUMAN	Q	366	ENSP00000305302:R366Q	ENSP00000305302:R366Q	R	+	2	0	SLC6A19	1269984	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.563000	0.23547	-0.365000	0.08076	-2.817000	0.00109	CGG		0.612	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		A	1216984	G	A	1216984	3	1	89	1	0	0	0	0	1	0	0	0	14719	1116	39	1	1127	1	SLC6A19	5	1216984	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		1216984	179698276	45	24457										
NNT	23530	hgsc.bcm.edu	37	chr5	43704485	43704485	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gacgcgctccaggcgaaagtTagagaatcctatcagaagta	11	9	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:43704485T>A	ENST00000264663.5	+	22	3461	c.3240T>A	c.(3238-3240)gtT>gtA	p.V1080V	NNT_ENST00000512996.2_Silent_p.V949V|NNT_ENST00000344920.4_Silent_p.V1080V	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	1080					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					AGGCGAAAGTTAGAGAATCCT	0.423																																																0			5											100	90	93					5																	43704485		2203	4299	6502	43740242	SO:0001819	synonymous_variant	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.3240T>A	5.37:g.43704485T>A			43740242	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																				0.423	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43704485	T	A	43704485	2	1	89	1	0	0	0	0	0	0	0	1	10541	1741	61	5		5	NNT	5	43704485	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	42487501	43704485	137210775	46	24458										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75996929	75996929	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggagatcaattaaactagatGgaaaaggagaacccaaaggg	12	5	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:75996929G>T	ENST00000274364.6	+	34	4693	c.4396G>T	c.(4396-4398)Gga>Tga	p.G1466*	IQGAP2_ENST00000379730.3_Nonsense_Mutation_p.G968*|IQGAP2_ENST00000396234.3_Nonsense_Mutation_p.G962*|IQGAP2_ENST00000502745.1_Nonsense_Mutation_p.G962*|CTD-2384B11.2_ENST00000507514.1_RNA	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1466					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TAAACTAGATGGAAAAGGAGA	0.423																																																0			5											95	93	93					5																	75996929		2203	4300	6503	76032685	SO:0001587	stop_gained	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4396G>T	5.37:g.75996929G>T	ENSP00000274364:p.Gly1466*		76032685	A8K4V1|B7Z8A4|J3KR91	Nonsense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	44	11.085150	0.99513	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000396234;ENST00000502745	.	.	.	5.46	3.64	0.41730	.	0.466924	0.25052	N	0.033504	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-9.414	12.75	0.57304	0.1414:0.0:0.8586:0.0	.	.	.	.	X	1466;968;962;962	.	ENSP00000274364:G1466X	G	+	1	0	IQGAP2	76032685	1.000000	0.71417	0.395000	0.26283	0.215000	0.24574	3.468000	0.53086	1.427000	0.47276	0.655000	0.94253	GGA		0.423	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75996929	G	T	75996929	4	4	89	1	0	0	0	0	0	1	0	0	7836	1349	47	2	4530	2	IQGAP2	5	75996929	Nonsense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	32292444	75996929	104918331	47	24459										
GPR98	84059	hgsc.bcm.edu	37	chr5	90072330	90072330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aggagaagttgggatagctcCgtcatctaggcacatcctca	11	10	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:90072330C>T	ENST00000405460.2	+	61	12560	c.12464C>T	c.(12463-12465)cCg>cTg	p.P4155L		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4155	Calx-beta 28. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGGATAGCTCCGTCATCTAGG	0.428																																																0			5											128	126	127					5																	90072330		1923	4144	6067	90108086	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12464C>T	5.37:g.90072330C>T	ENSP00000384582:p.Pro4155Leu		90108086	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	4.757	0.140818	0.09083	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.28069	1.63	5.13	3.35	0.38373	.	0.548719	0.21413	N	0.074949	T	0.25344	0.0616	M	0.61703	1.905	0.09310	N	0.999993	P	0.52692	0.955	B	0.37198	0.243	T	0.21177	-1.0253	10	0.51188	T	0.08	.	7.3854	0.26880	0.1357:0.7145:0.0:0.1498	.	4155	Q8WXG9	GPR98_HUMAN	L	4155	ENSP00000384582:P4155L	ENSP00000296619:P4155L	P	+	2	0	GPR98	90108086	0.040000	0.19996	0.038000	0.18304	0.046000	0.14306	2.045000	0.41250	0.669000	0.31146	0.637000	0.83480	CCG		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90072330	C	T	90072330	3	4	89	1	0	0	0	0	1	0	0	0	6742	652	23	1	12706	1	GPR98	5	90072330	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	14075401	90072330	90842930	48	24460										
GIN1	54826	hgsc.bcm.edu	37	chr5	102432330	102432330	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	accccagtgttgtctctcagGacagcacatccactttctgt	7	14	3	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:102432330G>T	ENST00000399004.2	-	7	1303	c.1209C>A	c.(1207-1209)gtC>gtA	p.V403V	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	403					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TGTCTCTCAGGACAGCACATC	0.408																																																0			5											232	218	223					5																	102432330		1880	4114	5994	102460229	SO:0001819	synonymous_variant	54826			BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1209C>A	5.37:g.102432330G>T			102460229	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Silent	SNP	ENST00000399004.2	37	CCDS43349.1																																																																																				0.408	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		T	102432330	G	T	102432330	2	4	89	1	0	0	0	0	0	0	0	1	6406	1161	41	2		2	GIN1	5	102432330	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	12360000	102432330	78482930	49	24461										
APC	324	hgsc.bcm.edu	37	chr5	112116592	112116592	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cctgccaggatatggaaaaaCgagcacaggtaagttacttg	11	8	0	0	rs587781392		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:112116592C>T	ENST00000457016.1	+	6	1017	c.637C>T	c.(637-639)Cga>Tga	p.R213*	RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000257430.4_Nonsense_Mutation_p.R213*|APC_ENST00000508376.2_Nonsense_Mutation_p.R213*			P25054	APC_HUMAN	adenomatous polyposis coli	213	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R213*(20)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATGGAAAAACGAGCACAGGT	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(20)	large_intestine(19)|lung(1)	5	GRCh37	CM920027	APC	M							58	57	58					5																	112116592		2202	4300	6502	112144491	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.637C>T	5.37:g.112116592C>T	ENSP00000413133:p.Arg213*		112144491	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.046788	0.97231	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0079	14.2561	0.66053	0.4075:0.5925:0.0:0.0	.	.	.	.	X	213;223;213;213;213	.	ENSP00000257430:R213X	R	+	1	2	APC	112144491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.672000	0.46850	0.659000	0.30945	0.655000	0.94253	CGA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112116592	C	T	112116592	4	4	89	1	0	0	0	0	0	1	0	0	763	528	19	1	655	1	APC	5	112116592	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	9684262	112116592	68798668	50	24462										
APC	324	hgsc.bcm.edu	37	chr5	112175423	112175423	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gtccacctgaacactatgttCaggagaccccactcatgttt	7	13	2	2	rs121913329		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:112175423C>T	ENST00000457016.1	+	16	4512	c.4132C>T	c.(4132-4134)Cag>Tag	p.Q1378*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1378*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1378*			P25054	APC_HUMAN	adenomatous polyposis coli	1378	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1378*(47)|p.Q1378fs*7(2)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.Q1378fs*8(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)|p.Y1376fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACACTATGTTCAGGAGACCCC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	56	Substitution - Nonsense(47)|Deletion - Frameshift(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(49)|stomach(5)|soft_tissue(1)|skin(1)	5											91	87	88					5																	112175423		2202	4300	6502	112203322	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4132C>T	5.37:g.112175423C>T	ENSP00000413133:p.Gln1378*		112203322	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.764727	0.98945	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1139	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1378	.	.	Q	+	1	0	APC	112203322	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	5.761000	0.68801	2.941000	0.99782	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175423	C	T	112175423	4	4	89	1	0	0	0	0	0	1	0	0	763	827	29	3	4190	3	APC	5	112175423	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	58831	112175423	68739837	51	24463										
APC	324	hgsc.bcm.edu	37	chr5	112175653	112175653	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	accaagcgagaagtacctaaAaataaagcacctactgctga	7	10	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:112175653A>C	ENST00000457016.1	+	16	4742	c.4362A>C	c.(4360-4362)aaA>aaC	p.K1454N	APC_ENST00000257430.4_Missense_Mutation_p.K1454N|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.K1454N			P25054	APC_HUMAN	adenomatous polyposis coli	1454	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1454fs*3(1)|p.N1455fs*17(1)|p.K1192fs*3(1)|p.?(1)|p.P1453fs*4(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGTACCTAAAAATAAAGCAC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Deletion - Frameshift(3)|Unknown(1)|Complex - frameshift(1)	large_intestine(2)|thyroid(1)|soft_tissue(1)|skin(1)	5											89	81	84					5																	112175653		2202	4300	6502	112203552	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4362A>C	5.37:g.112175653A>C	ENSP00000413133:p.Lys1454Asn		112203552	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.415832	0.42817	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90197	-2.63;-2.63;-2.63	6.16	6.16	0.99307	.	0.133303	0.64402	D	0.000003	D	0.85995	0.5827	L	0.40543	1.245	0.46149	D	0.99889	P;P	0.46706	0.883;0.745	B;B	0.41571	0.36;0.188	D	0.84823	0.0797	9	.	.	.	-21.701	11.0377	0.47811	0.9314:0.0:0.0686:0.0	.	1456;1454	Q4LE70;P25054	.;APC_HUMAN	N	1454	ENSP00000413133:K1454N;ENSP00000257430:K1454N;ENSP00000427089:K1454N	.	K	+	3	2	APC	112203552	1.000000	0.71417	0.997000	0.53966	0.824000	0.46624	5.126000	0.64721	2.367000	0.80283	0.528000	0.53228	AAA		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175653	A	C	112175653	3	2	89	1	0	0	0	0	1	0	0	0	763	11	1	4	4420	4	APC	5	112175653	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	230	112175653	68739607	52	24464										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130769267	130769267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tggagtcaacagaacaattgCtcacgatgctggaccgtgaa	11	9	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:130769267C>T	ENST00000509018.1	-	25	4035	c.3830G>A	c.(3829-3831)aGc>aAc	p.S1277N	RAPGEF6_ENST00000507093.1_Missense_Mutation_p.S1285N|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.S1285N|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.S1290N|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.S1327N	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1277	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AGAACAATTGCTCACGATGCT	0.478																																					Melanoma(168;435 1955 13113 13877 23213)											0			5											157	134	142					5																	130769267		2203	4300	6503	130797166	SO:0001583	missense	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3830G>A	5.37:g.130769267C>T	ENSP00000421684:p.Ser1277Asn		130797166	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.863854	0.91511	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.37411	1.29;1.2;1.2;1.29;1.41	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.63838	0.2545	M	0.74258	2.255	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.998;0.998;0.999;0.998	D;D;D;D;D	0.87578	0.995;0.995;0.995;0.998;0.995	T	0.64466	-0.6401	10	0.66056	D	0.02	.	20.1356	0.98028	0.0:1.0:0.0:0.0	.	1285;1285;1327;1290;1277	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	N	1277;1290;1285;1285;1290;1327	ENSP00000421684:S1277N;ENSP00000309298:S1290N;ENSP00000426081:S1285N;ENSP00000296859:S1285N;ENSP00000426948:S1327N	ENSP00000426948:S1327N	S	-	2	0	RAPGEF6;FNIP1	130797166	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	5.747000	0.68689	2.755000	0.94549	0.650000	0.86243	AGC		0.478	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		T	130769267	C	T	130769267	3	4	89	1	0	0	0	0	1	0	0	0	13085	797	28	3	991	3	RAPGEF6	5	130769267	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	18593614	130769267	50145993	53	24465										
GFRA3	2676	hgsc.bcm.edu	37	chr5	137599964	137599964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cctcaccaaggctgcgggcaCggtgaacggtccaatagatg	13	12	1	2	rs201874513	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:137599964C>T	ENST00000274721.3	-	2	611	c.365G>A	c.(364-366)cGt>cAt	p.R122H	GFRA3_ENST00000378362.3_Missense_Mutation_p.R122H	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3	122					nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GCTGCGGGCACGGTGAACGGT	0.547													C|||	9	0.00179712	0	0	5008	,	,		20608	0.0089		0	False		,,,				2504	0															0			5											79	72	74					5																	137599964		2203	4300	6503	137627863	SO:0001583	missense	2676			AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.365G>A	5.37:g.137599964C>T	ENSP00000274721:p.Arg122His		137627863	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Missense_Mutation	SNP	ENST00000274721.3	37	CCDS4201.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.48	1.950022	0.34377	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	T;T	0.64438	-0.1;-0.1	5.28	0.0964	0.14490	GDNF/GAS1 (2);	0.765819	0.12459	N	0.467035	T	0.29850	0.0746	N	0.02539	-0.55	0.21984	N	0.999434	B;B	0.11235	0.003;0.004	B;B	0.06405	0.001;0.002	T	0.14392	-1.0474	10	0.46703	T	0.11	-0.0074	3.0095	0.06039	0.0881:0.3216:0.3285:0.2617	.	122;122	O60609-2;O60609	.;GFRA3_HUMAN	H	122	ENSP00000274721:R122H;ENSP00000367613:R122H	ENSP00000274721:R122H	R	-	2	0	GFRA3	137627863	0.976000	0.34144	0.920000	0.36463	0.855000	0.48748	0.208000	0.17415	-0.326000	0.08564	-0.291000	0.09656	CGT		0.547	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496		T	137599964	C	T	137599964	3	4	89	1	0	0	0	0	1	0	0	0	6369	536	19	1	865	1	GFRA3	5	137599964	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6830697	137599964	43315296	54	24466										
EGR1	1958	hgsc.bcm.edu	37	chr5	137803097	137803097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccagctcatcaaacccagccGcatgcgcaagtaccccaacc	6	19	2	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:137803097G>A	ENST00000239938.4	+	2	1231	c.959G>A	c.(958-960)cGc>cAc	p.R320H		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	320					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R320H(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AAACCCAGCCGCATGCGCAAG	0.622																																																1	Substitution - Missense(1)	ovary(1)	5											98	108	105					5																	137803097		2203	4300	6503	137830996	SO:0001583	missense	1958			M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"Zinc fingers, C2H2-type"	3238	protein-coding gene	gene with protein product	"nerve growth factor-induced protein A", "transcription factor ETR103", "zinc finger protein 225", "early growth response protein 1"	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.959G>A	5.37:g.137803097G>A	ENSP00000239938:p.Arg320His		137830996		Missense_Mutation	SNP	ENST00000239938.4	37	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889874	0.72524	.	.	ENSG00000120738	ENST00000239938	T	0.10960	2.82	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.39860	0.1094	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.50676	-0.8800	10	0.87932	D	0	-17.9847	16.2894	0.82739	0.0:0.0:1.0:0.0	.	320	P18146	EGR1_HUMAN	H	320	ENSP00000239938:R320H	ENSP00000239938:R320H	R	+	2	0	EGR1	137830996	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.657000	0.98554	2.315000	0.78130	0.557000	0.71058	CGC		0.622	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		A	137803097	G	A	137803097	3	1	89	1	0	0	0	0	1	0	0	0	4982	1087	38	1	965	1	EGR1	5	137803097	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	203133	137803097	43112163	55	24467										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140228508	140228508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acaaaagaatctgttcatcgCggaatccaggccgcttgact	9	11	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:140228508C>T	ENST00000532602.1	+	1	1461	c.428C>T	c.(427-429)gCg>gTg	p.A143V	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.A143V|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	143	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTTCATCGCGGAATCCAGG	0.557																																					Melanoma(55;1800 1972 14909)											0			5											92	85	87					5																	140228508		2203	4298	6501	140208692	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.428C>T	5.37:g.140228508C>T	ENSP00000436042:p.Ala143Val		140208692	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.933660	0.52866	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.52983	0.64;0.64	4.13	4.13	0.48395	Cadherin (3);Cadherin-like (1);	0.708972	0.10662	U	0.648542	T	0.48519	0.1504	L	0.59967	1.855	0.09310	N	1	P;P	0.49185	0.869;0.92	B;B	0.40825	0.329;0.341	T	0.48790	-0.9004	10	0.44086	T	0.13	.	16.9231	0.86168	0.0:1.0:0.0:0.0	.	143;143	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	V	143	ENSP00000436042:A143V;ENSP00000367362:A143V	ENSP00000367362:A143V	A	+	2	0	PCDHA9	140208692	0.000000	0.05858	0.089000	0.20774	0.465000	0.32709	-0.704000	0.05058	2.263000	0.75096	0.591000	0.81541	GCG		0.557	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140228508	C	T	140228508	3	4	89	1	0	0	0	0	1	0	0	0	11562	768	27	1	430	1	PCDHA9	5	140228508	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	2425411	140228508	40686752	56	24468										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237091	140237091	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gacgcggacgcgcaggagaaCgccctggtgtcctactctct	13	14	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:140237091C>T	ENST00000307360.5	+	1	1458	c.1458C>T	c.(1456-1458)aaC>aaT	p.N486N	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Silent_p.N486N|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	486	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCAGGAGAACGCCCTGGTGT	0.662																																																0			5											79	80	80					5																	140237091		2196	4273	6469	140217275	SO:0001819	synonymous_variant	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1458C>T	5.37:g.140237091C>T			140217275	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																				0.662	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237091	C	T	140237091	2	4	89	1	0	0	0	0	0	0	0	1	11551	535	19	1		1	PCDHA10	5	140237091	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	8583	140237091	40678169	57	24469										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148679892	148679892	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctccactcggggcccagcttCgtggaatccctctttgaaga	10	14	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:148679892C>T	ENST00000296721.4	+	3	302	c.204C>T	c.(202-204)ttC>ttT	p.F68F	AFAP1L1_ENST00000522492.1_3'UTR|AFAP1L1_ENST00000515000.1_Silent_p.F68F	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	68						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCCAGCTTCGTGGAATCCC	0.562																																																0			5											98	84	88					5																	148679892		2203	4300	6503	148660085	SO:0001819	synonymous_variant	134265			AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.204C>T	5.37:g.148679892C>T			148660085	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	37	CCDS34274.1																																																																																				0.562	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		T	148679892	C	T	148679892	2	4	89	1	0	0	0	0	0	0	0	1	354	883	31	1		1	AFAP1L1	5	148679892	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	8442801	148679892	32235368	58	24470										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176002350	176002350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctgtcttcctgtccatctccGtggtggaccagcctgacctt	9	15	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:176002350G>A	ENST00000510636.1	+	9	965	c.691G>A	c.(691-693)Gtg>Atg	p.V231M	CDHR2_ENST00000506348.1_Missense_Mutation_p.V231M|CDHR2_ENST00000261944.5_Missense_Mutation_p.V231M	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GTCCATCTCCGTGGTGGACCA	0.627																																																0			5											93	84	87					5																	176002350		2203	4300	6503	175934956	SO:0001583	missense	0			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.691G>A	5.37:g.176002350G>A	ENSP00000424565:p.Val231Met		175934956	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932771	0.52866	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.72835	-0.69;-0.69;-0.69	4.22	3.33	0.38152	Cadherin (2);Cadherin-like (2);	.	.	.	.	D	0.87257	0.6132	H	0.96301	3.8	0.28565	N	0.910913	D	0.89917	1.0	D	0.66979	0.948	T	0.81154	-0.1062	9	0.87932	D	0	-12.3437	10.3182	0.43749	0.095:0.0:0.905:0.0	.	231	Q9BYE9	CDHR2_HUMAN	M	231	ENSP00000424565:V231M;ENSP00000261944:V231M;ENSP00000421078:V231M	ENSP00000261944:V231M	V	+	1	0	CDHR2	175934956	0.990000	0.36364	0.096000	0.21009	0.853000	0.48598	2.601000	0.46249	0.962000	0.38057	0.478000	0.44815	GTG		0.627	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176002350	G	A	176002350	3	1	89	1	0	0	0	0	1	0	0	0	3125	1145	40	1	721	1	CDHR2	5	176002350	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	27322458	176002350	4912910	59	24471										
UNC5A	90249	hgsc.bcm.edu	37	chr5	176295878	176295878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcctggtggtgcgacaggccCgccttgctgacacggccaac	14	15	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr5:176295878C>T	ENST00000329542.4	+	5	908	c.634C>T	c.(634-636)Cgc>Tgc	p.R212C	UNC5A_ENST00000261961.3_Missense_Mutation_p.R172C	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	212	Ig-like C2-type.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	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)			GCGACAGGCCCGCCTTGCTGA	0.667																																																0			5											91	70	77					5																	176295878		2203	4300	6503	176228484	SO:0001583	missense	90249			AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.634C>T	5.37:g.176295878C>T	ENSP00000332737:p.Arg212Cys		176228484	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	37	CCDS34299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.202849|5.202849	0.94997|0.94997	.|.	.|.	ENSG00000113763|ENSG00000113763	ENST00000509580|ENST00000329542;ENST00000261961	.|T;T	.|0.68025	.|-0.3;-0.3	4.52|4.52	4.52|4.52	0.55395|0.55395	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84147|0.84147	0.5408|0.5408	M|M	0.87682|0.87682	2.9|2.9	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;0.998;0.999	D|D	0.87890|0.87890	0.2683|0.2683	5|10	.|0.87932	.|D	.|0	-35.6333|-35.6333	17.2675|17.2675	0.87092|0.87092	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|172;212;212	.|Q6ZN44-3;Q6ZN44;Q6ZN44-2	.|.;UNC5A_HUMAN;.	L|C	177|212;172	.|ENSP00000332737:R212C;ENSP00000261961:R172C	.|ENSP00000261961:R172C	P|R	+|+	2|1	0|0	UNC5A|UNC5A	176228484|176228484	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	4.905000|4.905000	0.63286|0.63286	2.068000|2.068000	0.61886|0.61886	0.561000|0.561000	0.74099|0.74099	CCG|CGC		0.667	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		T	176295878	C	T	176295878	3	4	89	1	0	0	0	0	1	0	0	0	17031	652	23	1	652	1	UNC5A	5	176295878	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	293528	176295878	4619382	60	24472										
DHX16	8449	hgsc.bcm.edu	37	chr6	30632672	30632672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatttgcaatagcagccaggAgctcctctcgaaatgggaac	11	10	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:30632672A>G	ENST00000376442.3	-	7	1418	c.1223T>C	c.(1222-1224)cTc>cCc	p.L408P	DHX16_ENST00000376437.5_5'Flank	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	408					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						AGCAGCCAGGAGCTCCTCTCG	0.577																																																0			6											88	79	82					6																	30632672		1511	2709	4220	30740651	SO:0001583	missense	8449			AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.1223T>C	6.37:g.30632672A>G	ENSP00000365625:p.Leu408Pro		30740651	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	37	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.345916	0.82022	.	.	ENSG00000204560	ENST00000376442	T	0.10005	2.92	5.18	5.18	0.71444	DEAD-like helicase (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.151251	0.45867	D	0.000332	T	0.44008	0.1273	H	0.99238	4.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.67397	-0.5681	10	0.87932	D	0	.	12.5698	0.56331	1.0:0.0:0.0:0.0	.	348;408	B4DZ28;O60231	.;DHX16_HUMAN	P	408	ENSP00000365625:L408P	ENSP00000365625:L408P	L	-	2	0	DHX16	30740651	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.005000	0.76323	1.959000	0.56917	0.402000	0.26972	CTC		0.577	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		G	30632672	A	G	30632672	3	3	89	1	0	0	0	0	1	0	0	0	4513	304	11	4	1958	4	DHX16	6	30632672	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10		30632672	140482395	61	24473										
PIM1	5292	hgsc.bcm.edu	37	chr6	37140933	37140933	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggggccaggttttcttcaggCagagggtctcttcaggtaac	14	9	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:37140933C>T	ENST00000373509.5	+	5	1142	c.769C>T	c.(769-771)Cag>Tag	p.Q257*	PIM1_ENST00000468243.1_3'UTR	NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	348	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	TTTCTTCAGGCAGAGGGTCTC	0.498			T	BCL6	NHL																																		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	0			6											92	90	91					6																	37140933		2203	4300	6503	37248911	SO:0001587	stop_gained	9361				CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"pim-1 oncogene"	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.769C>T	6.37:g.37140933C>T	ENSP00000362608:p.Gln257*		37248911	Q38RT9|Q5T7H7|Q96RG3	Nonsense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	41	9.030916	0.99042	.	.	ENSG00000137193	ENST00000373509	.	.	.	5.35	5.35	0.76521	.	0.127607	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	13.195	0.59732	0.1597:0.8403:0.0:0.0	.	.	.	.	X	257	.	ENSP00000362608:Q257X	Q	+	1	0	PIM1	37248911	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.354000	0.34056	2.660000	0.90430	0.591000	0.81541	CAG		0.498	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37140933	C	T	37140933	4	4	89	1	0	0	0	0	0	1	0	0	11958	711	25	3	787	3	PIM1	6	37140933	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6508261	37140933	133974134	62	24474										
ROS1	6098	hgsc.bcm.edu	37	chr6	117665427	117665427	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agagacagaaacgctttatcTaaaataagaagaaaccaaaa	6	6	1	4			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:117665427T>C	ENST00000368508.3	-	27	4520		c.e27-2		GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Splice_Site	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase						cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.?(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ACGCTTTATCTAAAATAAGAA	0.323			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	1	Unknown(1)	central_nervous_system(1)	6											109	108	108					6																	117665427		2203	4300	6503	117772120	SO:0001630	splice_region_variant	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4322-2A>G	6.37:g.117665427T>C			117772120	Q15368|Q5TDB5	Splice_Site	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020239	0.35606	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	.	.	.	5.16	3.91	0.45181	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6017	0.33749	0.1712:0.0:0.0:0.8288	.	.	.	.	.	-1	.	.	.	-	.	.	ROS1	117772120	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	3.397000	0.52572	2.077000	0.62373	0.459000	0.35465	.		0.323	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		Intron	C	117665427	T	C	117665427	5	2	89	1	0	0	0	0	0	0	1	0	13568	1536	53	4	2791	4	ROS1	6	117665427	Splice_Site	SNP	T	TCGA-CI-6622-01A-11D-1826-10	80524494	117665427	53449640	63	24475										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138599710	138599710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tcaacctgaagctctcccacGgtgactactacaggaagcgg	10	13	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:138599710G>A	ENST00000251691.4	+	13	2417	c.2251G>A	c.(2251-2253)Ggt>Agt	p.G751S		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GCTCTCCCACGGTGACTACTA	0.602																																																0			6											125	104	111					6																	138599710		2203	4300	6503	138641403	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2251G>A	6.37:g.138599710G>A	ENSP00000251691:p.Gly751Ser		138641403		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	2.027	-0.423256	0.04734	.	.	ENSG00000112379	ENST00000251691	T	0.39997	1.05	5.55	3.78	0.43462	SEC7-like (1);	0.928117	0.09256	N	0.827255	T	0.06690	0.0171	N	0.04746	-0.17	0.09310	N	0.999999	B	0.16603	0.018	B	0.08055	0.003	T	0.40175	-0.9577	10	0.14252	T	0.57	-11.781	6.7074	0.23258	0.1532:0.0:0.6959:0.1509	.	751	Q5TH69	BIG3_HUMAN	S	751	ENSP00000251691:G751S	ENSP00000251691:G751S	G	+	1	0	KIAA1244	138641403	0.999000	0.42202	0.020000	0.16555	0.478000	0.33099	3.329000	0.52060	0.714000	0.32081	-0.448000	0.05591	GGT		0.602	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138599710	G	A	138599710	3	1	89	1	0	0	0	0	1	0	0	0	8238	1116	39	1	2301	1	KIAA1244	6	138599710	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	20934283	138599710	32515357	64	24476										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138640982	138640982	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	attggtctgtcctgtgagctGgtggtggagcacattcaaag	14	7	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:138640982G>A	ENST00000251691.4	+	28	4783	c.4617G>A	c.(4615-4617)ctG>ctA	p.L1539L		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CCTGTGAGCTGGTGGTGGAGC	0.493																																																0			6											127	119	121					6																	138640982		2203	4300	6503	138682675	SO:0001819	synonymous_variant	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.4617G>A	6.37:g.138640982G>A			138682675		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																				0.493	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138640982	G	A	138640982	2	1	89	1	0	0	0	0	0	0	0	1	8238	1335	47	3		3	KIAA1244	6	138640982	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	41272	138640982	32474085	65	24477										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166952224	166952224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aggatctgccttctcaaagcCctccttcacatgatggctga	8	13	3	2	rs571609144		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr6:166952224C>T	ENST00000265678.4	-	2	371	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	RPS6KA2_ENST00000481261.2_5'UTR|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.G75S|RPS6KA2_ENST00000405189.3_5'UTR|RPS6KA2_ENST00000366863.2_5'UTR|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.G58S	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	50					axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TTCTCAAAGCCCTCCTTCACA	0.532																																																0			6											162	139	147					6																	166952224		2203	4300	6503	166872214	SO:0001583	missense	6196			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.148G>A	6.37:g.166952224C>T	ENSP00000265678:p.Gly50Ser		166872214	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	37	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.760358	0.49468	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000507371;ENST00000506565	T;T;T;T;T	0.69806	-0.41;-0.42;-0.43;-0.27;-0.33	4.9	4.9	0.64082	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71525	0.3350	L	0.52126	1.63	0.80722	D	1	B;B;D	0.69078	0.094;0.291;0.997	B;B;D	0.68765	0.048;0.159;0.96	T	0.71133	-0.4681	10	0.42905	T	0.14	.	16.9986	0.86375	0.0:1.0:0.0:0.0	.	75;58;50	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	S	50;75;58;34;75	ENSP00000265678:G50S;ENSP00000422435:G75S;ENSP00000427015:G58S;ENSP00000423114:G34S;ENSP00000425148:G75S	ENSP00000265678:G50S	G	-	1	0	RPS6KA2	166872214	1.000000	0.71417	0.001000	0.08648	0.085000	0.17905	7.201000	0.77847	2.434000	0.82447	0.655000	0.94253	GGC		0.532	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		T	166952224	C	T	166952224	3	4	89	1	0	0	0	0	1	0	0	0	13688	623	22	3	2133	3	RPS6KA2	6	166952224	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	28311242	166952224	4162843	66	24478										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4801867	4801867	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	caagcgagttcatccgcgccGgtggtggtcacccgggtgtg	16	12	2	0	rs570756478		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:4801867G>A	ENST00000328914.4	+	9	1974	c.1974G>A	c.(1972-1974)ccG>ccA	p.P658P	FOXK1_ENST00000446823.1_Silent_p.P495P	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CATCCGCGCCGGTGGTGGTCA	0.677																																																0			7											31	22	25					7																	4801867		2114	4160	6274	4768393	SO:0001819	synonymous_variant	221937			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1974G>A	7.37:g.4801867G>A			4768393		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																				0.677	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			A	4801867	G	A	4801867	2	1	89	1	0	0	0	0	0	0	0	1	6033	1103	39	1		1	FOXK1	7	4801867	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10		4801867	154336796	67	24479										
TWIST1	7291	hgsc.bcm.edu	37	chr7	19156558	19156558	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gggatgatcttccgcagcgcGgcgaacgcctcgttcagcga	14	13	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:19156558G>A	ENST00000242261.5	-	1	737	c.387C>T	c.(385-387)gcC>gcT	p.A129A	AC003986.7_ENST00000417460.1_RNA|AC003986.6_ENST00000419944.1_RNA	NM_000474.3	NP_000465.1	Q15672	TWST1_HUMAN	twist family bHLH transcription factor 1	129	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				aortic valve morphogenesis (GO:0003180)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in heart valve development (GO:2000793)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cranial suture morphogenesis (GO:0060363)|embryonic camera-type eye formation (GO:0060900)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cushion morphogenesis (GO:0003203)|eyelid development in camera-type eye (GO:0061029)|in utero embryonic development (GO:0001701)|mitral valve morphogenesis (GO:0003183)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of oxidative phosphorylation uncoupler activity (GO:2000276)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell motility (GO:2000147)|positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation (GO:2000802)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of bone mineralization (GO:0030500)|rhythmic process (GO:0048511)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription factor binding (GO:0008134)			lung(2)|upper_aerodigestive_tract(1)	3						TCCGCAGCGCGGCGAACGCCT	0.657																																																0			7											88	68	75					7																	19156558		2203	4300	6503	19123083	SO:0001819	synonymous_variant	7291			U80998	CCDS5367.1	7p21	2014-02-07	2013-10-17	2003-03-28	ENSG00000122691	ENSG00000122691		"Basic helix-loop-helix proteins"	12428	protein-coding gene	gene with protein product	"Saethre-Chotzen syndrome"	601622	"blepharophimosis, epicanthus inversus and ptosis 3", "acrocephalosyndactyly 3", "twist homolog 1 (Drosophila)", "twist basic helix-loop-helix transcription factor 1", "craniosynostosis"	ACS3, BPES3, TWIST, CRS		8995765, 11474656, 17343269	Standard	XR_428085		Approved	SCS, H-twist, BPES2, bHLHa38, CRS1	uc003sum.3	Q15672	OTTHUMG00000090821	ENST00000242261.5:c.387C>T	7.37:g.19156558G>A			19123083	A4D128|Q92487|Q99804	Silent	SNP	ENST00000242261.5	37	CCDS5367.1																																																																																				0.657	TWIST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207625.1	NM_000474		A	19156558	G	A	19156558	2	1	89	1	0	0	0	0	0	0	0	1	16823	1103	39	1		1	TWIST1	7	19156558	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	14354691	19156558	139982105	68	24480										
GCK	2645	hgsc.bcm.edu	37	chr7	44185154	44185154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agtgatgcgcattacgtcctCgctgcggctctcgcgcatgc	12	14	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:44185154C>T	ENST00000403799.3	-	9	1664	c.1195G>A	c.(1195-1197)Gag>Aag	p.E399K	GCK_ENST00000395796.3_Missense_Mutation_p.E398K|GCK_ENST00000437084.1_Missense_Mutation_p.E382K|GCK_ENST00000345378.2_Missense_Mutation_p.E400K	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	399	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						ATTACGTCCTCGCTGCGGCTC	0.682																																																0			7	GRCh37	CM051930	GCK	M							29	28	29					7																	44185154		2202	4300	6502	44151679	SO:0001583	missense	5871			AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.1195G>A	7.37:g.44185154C>T	ENSP00000384247:p.Glu399Lys		44151679	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	37	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972374	0.34848	.	.	ENSG00000106633	ENST00000336642;ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D;D	0.96232	-3.95;-3.95;-3.95;-3.95;-3.95	5.43	3.56	0.40772	Hexokinase, C-terminal (1);	0.425728	0.27198	N	0.020467	D	0.86033	0.5836	N	0.08118	0	0.35861	D	0.827512	B;B;B;P;B	0.34684	0.185;0.015;0.153;0.463;0.185	B;B;B;B;B	0.19666	0.015;0.002;0.009;0.026;0.015	D	0.84578	0.0659	10	0.05721	T	0.95	-20.552	10.2853	0.43564	0.0:0.6743:0.2538:0.072	.	399;400;398;382;399	P35557;P35557-2;P35557-3;C9JQD1;A7LFL1	HXK4_HUMAN;.;.;.;.	K	83;399;398;400;382	ENSP00000338009:E83K;ENSP00000384247:E399K;ENSP00000379142:E398K;ENSP00000223366:E400K;ENSP00000402840:E382K	ENSP00000338009:E83K	E	-	1	0	GCK	44151679	0.994000	0.37717	0.997000	0.53966	0.996000	0.88848	0.436000	0.21526	0.611000	0.30052	0.561000	0.74099	GAG		0.682	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			T	44185154	C	T	44185154	3	4	89	1	0	0	0	0	1	0	0	0	6313	893	31	1	210	1	GCK	7	44185154	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	25028596	44185154	114953509	69	24481										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50513668	50513668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	accagtcccaggaggaccaaAgagcaaaattcctttagggg	11	10	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:50513668A>G	ENST00000419119.1	-	2	2871	c.1318T>C	c.(1318-1320)Ttt>Ctt	p.F440L	FIGNL1_ENST00000433017.1_Missense_Mutation_p.F440L|FIGNL1_ENST00000356889.4_Missense_Mutation_p.F440L|FIGNL1_ENST00000395556.2_Missense_Mutation_p.F440L			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	440					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				GGAGGACCAAAGAGCAAAATT	0.438																																																0			7											51	54	53					7																	50513668		2203	4300	6503	50481162	SO:0001583	missense	63979			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1318T>C	7.37:g.50513668A>G	ENSP00000410811:p.Phe440Leu		50481162	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.905450	0.92107	.	.	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08	5.99	5.99	0.97316	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.95778	0.8626	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96136	0.9096	10	0.87932	D	0	-19.5814	15.6754	0.77316	1.0:0.0:0.0:0.0	.	440	Q6PIW4	FIGL1_HUMAN	L	440	ENSP00000349356:F440L;ENSP00000378924:F440L;ENSP00000399997:F440L;ENSP00000410811:F440L	ENSP00000349356:F440L	F	-	1	0	FIGNL1	50481162	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTT		0.438	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		G	50513668	A	G	50513668	3	3	89	1	0	0	0	0	1	0	0	0	5911	72	3	4	710	4	FIGNL1	7	50513668	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	6328514	50513668	108624995	70	24482										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77230118	77230118	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatgttcctatttgtattcaTtgcaggtacaaaagaatttc	7	6	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:77230118T>C	ENST00000248594.6	+	8	962	c.690T>C	c.(688-690)caT>caC	p.H230H	PTPN12_ENST00000415482.2_Silent_p.H111H|PTPN12_ENST00000435495.2_Silent_p.H100H	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	230	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TTTGTATTCATTGCAGGTACA	0.299																																																0			7											71	66	68					7																	77230118		2202	4300	6502	77068054	SO:0001819	synonymous_variant	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.690T>C	7.37:g.77230118T>C			77068054	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Silent	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	T	8.691	0.907335	0.17833	.	.	ENSG00000127947	ENST00000522115	.	.	.	5.17	1.46	0.22682	.	.	.	.	.	T	0.54046	0.1834	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43556	-0.9384	4	.	.	.	.	6.7703	0.23591	0.0:0.4646:0.0:0.5354	.	.	.	.	T	169	.	.	I	+	2	0	PTPN12	77068054	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.415000	0.34748	0.313000	0.23062	0.455000	0.32223	ATT		0.299	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			C	77230118	T	C	77230118	2	2	89	1	0	0	0	0	0	0	0	1	12816	1490	52	4		4	PTPN12	7	77230118	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	26716450	77230118	81908545	71	24483										
ZAN	7455	hgsc.bcm.edu	37	chr7	100352869	100352869	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agcgctgccctccaaatgccCgctacgaatcctgtgcttgt	9	15	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:100352869C>T	ENST00000348028.3	+	0	3310				ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000542585.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TCCAAATGCCCGCTACGAATC	0.572																																																0			7											128	134	132					7																	100352869		1961	4140	6101	100190805			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100352869C>T			100190805	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	c	13.46	2.245287	0.39697	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	D;D;D	0.90955	-2.76;-2.76;-2.76	4.86	4.86	0.63082	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.179933	0.27245	N	0.020245	D	0.88829	0.6543	L	0.31476	0.935	0.80722	D	1	D;D	0.56287	0.969;0.975	P;P	0.51229	0.533;0.663	D	0.89708	0.3910	10	0.62326	D	0.03	.	14.2135	0.65779	0.0:1.0:0.0:0.0	.	1049;1049	F5H0T8;Q9Y493	.;ZAN_HUMAN	C	1049	ENSP00000445943:R1049C;ENSP00000445091:R1049C;ENSP00000444427:R1049C	ENSP00000423579:R1049C	R	+	1	0	ZAN	100190805	1.000000	0.71417	0.496000	0.27539	0.060000	0.15804	5.970000	0.70431	2.609000	0.88269	0.651000	0.88453	CGC		0.572	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100352869	C	T	100352869	1	4	89	0	1	0	0	0	0	0	0	0	17553	652	23	1		1	ZAN	7	100352869	RNA	SNP	C	TCGA-CI-6622-01A-11D-1826-10	23122751	100352869	58785794	72	24484										
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103018944	103018944	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcatttccgacttccttagcGtacttccgcatggcctttct	7	14	1	0	rs577037869		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:103018944G>A	ENST00000306312.3	-	17	1995	c.1734C>T	c.(1732-1734)taC>taT	p.Y578Y	SLC26A5_ENST00000393727.1_Silent_p.Y578Y|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393729.1_Silent_p.Y541Y|SLC26A5_ENST00000354356.4_Silent_p.Y11Y|SLC26A5_ENST00000432958.2_Silent_p.Y546Y|SLC26A5_ENST00000339444.6_Silent_p.Y578Y|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393730.1_Silent_p.Y546Y|SLC26A5_ENST00000393723.1_Silent_p.Y546Y	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	578	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)	p.Y578Y(1)		endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						CTTCCTTAGCGTACTTCCGCA	0.453													G|||	1	0.000199681	0	0	5008	,	,		19434	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	7											275	217	236					7																	103018944		2203	4300	6503	102806180	SO:0001819	synonymous_variant	375611			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1734C>T	7.37:g.103018944G>A			102806180	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																				0.453	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		A	103018944	G	A	103018944	2	1	89	1	0	0	0	0	0	0	0	1	14557	1140	40	1		1	SLC26A5	7	103018944	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	2666075	103018944	56119719	73	24485										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106524645	106524645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tttattcctgtgcaggctacTgtgtggcaacctttgttctt	9	9	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:106524645T>C	ENST00000359195.3	+	9	3116	c.2806T>C	c.(2806-2808)Tgt>Cgt	p.C936R	PIK3CG_ENST00000496166.1_Missense_Mutation_p.C936R|PIK3CG_ENST00000440650.2_Missense_Mutation_p.C936R	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	936	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						TGCAGGCTACTGTGTGGCAAC	0.363																																																0			7											188	184	186					7																	106524645		2203	4300	6503	106311881	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2806T>C	7.37:g.106524645T>C	ENSP00000352121:p.Cys936Arg		106311881	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365524	0.82463	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.77750	-1.12;-1.12;-1.12	5.05	5.05	0.67936	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.088781	0.85682	D	0.000000	D	0.90875	0.7133	H	0.94423	3.535	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.93413	0.6770	10	0.87932	D	0	-14.91	14.9476	0.71044	0.0:0.0:0.0:1.0	.	936	P48736	PK3CG_HUMAN	R	936	ENSP00000392258:C936R;ENSP00000419260:C936R;ENSP00000352121:C936R	ENSP00000352121:C936R	C	+	1	0	PIK3CG	106311881	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.818000	0.86416	2.100000	0.63781	0.533000	0.62120	TGT		0.363	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			C	106524645	T	C	106524645	3	2	89	1	0	0	0	0	1	0	0	0	11947	1580	55	4	2836	4	PIK3CG	7	106524645	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	3505701	106524645	52614018	74	24486										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122303293	122303293	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atatcagagaccacttacctGacatgcattataaaggagct	7	9	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:122303293G>C	ENST00000449022.2	-	3	803	c.784C>G	c.(784-786)Cag>Gag	p.Q262E	CADPS2_ENST00000412584.2_Missense_Mutation_p.Q262E|CADPS2_ENST00000313070.7_Missense_Mutation_p.Q262E|CADPS2_ENST00000334010.7_Missense_Mutation_p.Q262E	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	262					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						CCACTTACCTGACATGCATTA	0.388																																																0			7											74	70	71					7																	122303293		1858	4105	5963	122090529	SO:0001583	missense	93664				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.784C>G	7.37:g.122303293G>C	ENSP00000398481:p.Gln262Glu		122090529	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801055	0.70567	.	.	ENSG00000081803	ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	T;T;T;T	0.48836	0.8;0.81;0.8;0.81	5.32	5.32	0.75619	.	0.054210	0.85682	D	0.000000	T	0.56775	0.2008	M	0.79258	2.445	0.80722	D	1	P;B	0.35700	0.516;0.278	B;B	0.38755	0.281;0.112	T	0.63681	-0.6582	10	0.87932	D	0	-5.896	18.9943	0.92806	0.0:0.0:1.0:0.0	.	262;262	Q86UW7-2;Q86UW7	.;CAPS2_HUMAN	E	262;262;262;229;262;262	ENSP00000325581:Q262E;ENSP00000333940:Q262E;ENSP00000400401:Q262E;ENSP00000398481:Q262E	ENSP00000325581:Q262E	Q	-	1	0	CADPS2	122090529	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.835000	0.99442	2.504000	0.84457	0.650000	0.86243	CAG		0.388	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		C	122303293	G	C	122303293	3	2	89	1	0	0	0	0	1	0	0	0	2577	1299	45	5	3262	5	CADPS2	7	122303293	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	15778648	122303293	36835370	75	24487										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138732534	138732534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aacttgggctacaaacataaCgacgtttttggcatcatacg	8	9	1	0	rs371159477		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:138732534C>T	ENST00000242351.5	-	13	2831	c.2515G>A	c.(2515-2517)Gtt>Att	p.V839I	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.V961I	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	839	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						ACAAACATAACGACGTTTTTG	0.393																																																0			7						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	126	126	126		2515	3.2	0.3	7		126	0,8600		0,0,4300	no	missense	ZC3HAV1	NM_020119.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	839/903	138732534	1,13005	2203	4300	6503	138383074	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2515G>A	7.37:g.138732534C>T	ENSP00000242351:p.Val839Ile		138383074	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	8.447	0.852142	0.17034	2.27E-4	0.0	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.13657	2.57;2.57	5.23	3.18	0.36537	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.465986	0.18129	N	0.150791	T	0.07593	0.0191	L	0.38531	1.155	0.49687	D	0.999819	P	0.36330	0.548	B	0.23574	0.047	T	0.30650	-0.9971	10	0.25106	T	0.35	.	5.4552	0.16586	0.0:0.6654:0.0:0.3346	.	839	Q7Z2W4	ZCCHV_HUMAN	I	839;961	ENSP00000242351:V839I;ENSP00000418385:V961I	ENSP00000242351:V839I	V	-	1	0	ZC3HAV1	138383074	0.000000	0.05858	0.344000	0.25628	0.333000	0.28666	0.408000	0.21065	1.342000	0.45619	-0.378000	0.06908	GTT		0.393	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		T	138732534	C	T	138732534	3	4	89	1	0	0	0	0	1	0	0	0	17614	536	19	1	197	1	ZC3HAV1	7	138732534	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	16429241	138732534	20406129	76	24488										
OR2A5	393046	hgsc.bcm.edu	37	chr7	143748302	143748302	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agtcccgccaccctgaggagCagcagaaggtcctttccctg	11	15	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr7:143748302C>A	ENST00000408906.2	+	1	842	c.808C>A	c.(808-810)Cag>Aag	p.Q270K		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CCCTGAGGAGCAGCAGAAGGT	0.562																																																0			7											99	98	98					7																	143748302		1999	4184	6183	143379235	SO:0001583	missense	393046			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.808C>A	7.37:g.143748302C>A	ENSP00000386208:p.Gln270Lys		143379235	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.774687	0.31411	.	.	ENSG00000221836	ENST00000408906	T	0.00137	8.68	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.299100	0.18182	U	0.149084	T	0.00144	0.0004	N	0.20986	0.625	0.24712	N	0.993193	B	0.17852	0.024	B	0.21151	0.033	T	0.47674	-0.9099	10	0.41790	T	0.15	.	11.5247	0.50573	0.1784:0.8216:0.0:0.0	.	270	Q96R48	OR2A5_HUMAN	K	270	ENSP00000386208:Q270K	ENSP00000386208:Q270K	Q	+	1	0	OR2A5	143379235	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.985000	0.03751	2.797000	0.96272	0.650000	0.86243	CAG		0.562	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			A	143748302	C	A	143748302	3	1	89	1	0	0	0	0	1	0	0	0	11012	711	25	2	810	2	OR2A5	7	143748302	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	5015768	143748302	15390361	77	24489										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2823318	2823318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tttgcagacaggtttgctcgGattccacctgccgtctttgg	11	11	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:2823318G>A	ENST00000520002.1	-	60	9817	c.9262C>T	c.(9262-9264)Ccg>Tcg	p.P3088S	CSMD1_ENST00000602557.1_Missense_Mutation_p.P3088S|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000537824.1_Missense_Mutation_p.P3087S|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3088	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.P2816K(1)|p.P3087K(1)		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)		GGTTTGCTCGGATTCCACCTG	0.428																																																2	Substitution - Missense(2)	lung(2)	8											79	79	79					8																	2823318		2003	4192	6195	2810725	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9262C>T	8.37:g.2823318G>A	ENSP00000430733:p.Pro3088Ser		2810725	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.027|8.027	0.760842|0.760842	0.15914|0.15914	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000520002;ENST00000318252;ENST00000537824|ENST00000335551	T;T|.	0.23348|.	1.91;1.91|.	5.42|5.42	3.62|3.62	0.41486|0.41486	Complement control module (2);Sushi/SCR/CCP (3);|.	0.244403|.	0.33980|.	N|.	0.004370|.	T|T	0.39600|0.39600	0.1084|0.1084	N|N	0.13235|0.13235	0.315|0.315	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.10451|0.10451	-1.0629|-1.0629	10|5	0.27785|.	T|.	0.31|.	.|.	12.3138|12.3138	0.54944|0.54944	0.0:0.1246:0.7341:0.1414|0.0:0.1246:0.7341:0.1414	.|.	3088;3088|.	E5RIG2;Q96PZ7|.	.;CSMD1_HUMAN|.	S|F	3088;2949;3087|2504	ENSP00000430733:P3088S;ENSP00000441462:P3087S|.	ENSP00000320445:P2949S|.	P|S	-|-	1|2	0|0	CSMD1|CSMD1	2810725|2810725	1.000000|1.000000	0.71417|0.71417	0.857000|0.857000	0.33713|0.33713	0.012000|0.012000	0.07955|0.07955	3.034000|3.034000	0.49751|0.49751	0.641000|0.641000	0.30601|0.30601	-0.121000|-0.121000	0.15023|0.15023	CCG|TCC		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2823318	G	A	2823318	3	1	89	1	0	0	0	0	1	0	0	0	3950	1174	41	3	1483	3	CSMD1	8	2823318	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		2823318	143540704	78	24490										
SGK223	157285	hgsc.bcm.edu	37	chr8	8197043	8197043	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gccaggctgtccgtggagccGgtggtgaagctgacgtggac	18	10	0	2	rs56187292		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:8197043G>C	ENST00000520004.1	-	4	2529	c.2265C>G	c.(2263-2265)acC>acG	p.T755T	SGK223_ENST00000330777.4_Silent_p.T755T			Q86YV5	SG223_HUMAN		757							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.T757T(1)|p.T755T(1)									CCGTGGAGCCGGTGGTGAAGC	0.532																																					GBM(34;731 755 10259 33573 33867)											2	Substitution - coding silent(2)	ovary(2)	8											72	84	80					8																	8197043		2092	4206	6298	8234453	SO:0001819	synonymous_variant	0																														ENST00000520004.1:c.2265C>G	8.37:g.8197043G>C			8234453	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																				0.532	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			C	8197043	G	C	8197043	2	2	89	1	0	0	0	0	0	0	0	1	14247	1103	39	5		5	SGK223	8	8197043	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	5373725	8197043	138166979	79	24491										
GPR124	25960	hgsc.bcm.edu	37	chr8	37695392	37695392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cctcggagggctgccagctcCgctccagccagcccaatgtc	11	18	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:37695392C>T	ENST00000412232.2	+	14	2207	c.2194C>T	c.(2194-2196)Cgc>Tgc	p.R732C	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	732	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CTGCCAGCTCCGCTCCAGCCA	0.706																																																0			8											11	11	11					8																	37695392		2120	4190	6310	37814550	SO:0001583	missense	25960			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.2194C>T	8.37:g.37695392C>T	ENSP00000406367:p.Arg732Cys		37814550	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894676	0.52121	.	.	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.69306	-0.39	5.34	5.34	0.76211	GPS domain (3);	0.512495	0.20002	N	0.101311	T	0.62109	0.2401	L	0.46157	1.445	0.09310	N	1	D	0.56287	0.975	P	0.45138	0.471	T	0.60915	-0.7168	10	0.52906	T	0.07	-22.3837	11.1401	0.48398	0.1333:0.7212:0.1454:0.0	.	732	Q96PE1	GP124_HUMAN	C	725;732	ENSP00000406367:R732C	ENSP00000406367:R732C	R	+	1	0	GPR124	37814550	0.239000	0.23836	0.975000	0.42487	0.951000	0.60555	2.629000	0.46485	2.520000	0.84964	0.603000	0.83216	CGC		0.706	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			T	37695392	C	T	37695392	3	4	89	1	0	0	0	0	1	0	0	0	6658	652	23	1	2227	1	GPR124	8	37695392	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	29498349	37695392	108668630	80	24492										
PREX2	80243	hgsc.bcm.edu	37	chr8	69017380	69017380	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttccatattttaggttcaagCttcagaaaggttttacaatt	6	6	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:69017380C>T	ENST00000288368.4	+	24	2992				PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2						adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TAGGTTCAAGCTTCAGAAAGG	0.428																																																0			8											145	132	137					8																	69017380		2203	4300	6503	69179934	SO:0001627	intron_variant	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2716-2964C>T	8.37:g.69017380C>T			69179934	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	3.501	-0.101731	0.06967	.	.	ENSG00000046889	ENST00000354677	.	.	.	2.43	1.25	0.21368	.	.	.	.	.	T	0.18923	0.0454	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.24584	-1.0156	7	0.21014	T	0.42	.	4.2285	0.10592	0.0:0.17:0.0:0.83	.	908	Q70Z35-3	.	V	908	.	ENSP00000346707:A908V	A	+	2	0	PREX2	69179934	0.009000	0.17119	0.001000	0.08648	0.008000	0.06430	0.781000	0.26774	0.380000	0.24823	-0.350000	0.07774	GCT		0.428	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69017380	C	T	69017380	1	4	89	0	1	0	0	0	0	0	0	0	12511	797	28	3		3	PREX2	8	69017380	Intron	SNP	C	TCGA-CI-6622-01A-11D-1826-10	31321988	69017380	77346642	81	24493										
PKIA	5569	hgsc.bcm.edu	37	chr8	79510668	79510668	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	attttattgcttcaggaagaAcaggtagaagaaatgcaata	9	4	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:79510668A>C	ENST00000396418.2	+	3	535	c.49A>C	c.(49-51)Aca>Cca	p.T17P	PKIA_ENST00000352966.5_Missense_Mutation_p.T17P|PKIA_ENST00000518467.1_Missense_Mutation_p.T17P	NM_006823.3|NM_181839.2	NP_006814.1|NP_862822.1	P61925	IPKA_HUMAN	protein kinase (cAMP-dependent, catalytic) inhibitor alpha	17					negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP-dependent protein kinase inhibitor activity (GO:0004862)|protein kinase A catalytic subunit binding (GO:0034236)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6						TTCAGGAAGAACAGGTAGAAG	0.373																																																0			8											154	143	147					8																	79510668		2203	4300	6503	79673223	SO:0001583	missense	5569			S76965	CCDS6222.1	8q21.13	2014-08-12			ENSG00000171033	ENSG00000171033			9017	protein-coding gene	gene with protein product		606059		PRKACN1		1770951	Standard	NM_006823		Approved		uc003ybb.3	P61925	OTTHUMG00000164618	ENST00000396418.2:c.49A>C	8.37:g.79510668A>C	ENSP00000379696:p.Thr17Pro		79673223	P04541|Q6IAV2	Missense_Mutation	SNP	ENST00000396418.2	37	CCDS6222.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314134	0.60414	.	.	ENSG00000171033	ENST00000396418;ENST00000352966;ENST00000518467	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.79034	0.4378	.	.	.	0.58432	D	0.999998	D	0.76494	0.999	D	0.81914	0.995	T	0.80441	-0.1381	7	.	.	.	.	15.4408	0.75181	1.0:0.0:0.0:0.0	.	17	P61925	IPKA_HUMAN	P	17	.	.	T	+	1	0	PKIA	79673223	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.976000	0.63785	2.045000	0.60652	0.477000	0.44152	ACA		0.373	PKIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379420.1			C	79510668	A	C	79510668	3	2	89	1	0	0	0	0	1	0	0	0	12004	43	2	4	51	4	PKIA	8	79510668	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	10493288	79510668	66853354	82	24494										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885308	88885308	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acatttagtggccctcaagtCccacagcttgatagttccag	8	12	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:88885308C>A	ENST00000319675.3	-	1	988	c.892G>T	c.(892-894)Gac>Tac	p.D298Y		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	298										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						GCCCTCAAGTCCCACAGCTTG	0.498																																																0			8											107	96	100					8																	88885308		2203	4300	6503	88954424	SO:0001583	missense	0			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.892G>T	8.37:g.88885308C>A	ENSP00000316496:p.Asp298Tyr		88954424		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418558	0.62622	.	.	ENSG00000176566	ENST00000319675	T	0.79141	-1.24	1.92	0.928	0.19443	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.88213	0.6376	M	0.92880	3.355	0.43667	D	0.996094	D	0.89917	1.0	D	0.97110	1.0	D	0.85693	0.1308	10	0.87932	D	0	.	7.7415	0.28843	0.0:0.7355:0.2644:0.0	.	298	Q8NA75	DC4L2_HUMAN	Y	298	ENSP00000316496:D298Y	ENSP00000316496:D298Y	D	-	1	0	DCAF4L2	88954424	1.000000	0.71417	0.110000	0.21437	0.626000	0.37791	2.460000	0.45031	-0.111000	0.12001	0.467000	0.42956	GAC		0.498	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885308	C	A	88885308	3	1	89	1	0	0	0	0	1	0	0	0	4278	855	30	2	299	2	DCAF4L2	8	88885308	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	9374640	88885308	57478714	83	24495										
MMP16	4325	hgsc.bcm.edu	37	chr8	89128758	89128758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgaaaacaaacatctcacgaCgaagaatagctagagtgtta	8	7	1	3	rs138174209		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:89128758C>T	ENST00000286614.6	-	6	1342	c.1061G>A	c.(1060-1062)cGt>cAt	p.R354H	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	354					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	CATCTCACGACGAAGAATAGC	0.433																																																0			8						C	HIS/ARG	0,4406		0,0,2203	90	88	89		1061	5.7	1	8	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	missense	MMP16	NM_005941.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	354/608	89128758	1,13005	2203	4300	6503	89197874	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.1061G>A	8.37:g.89128758C>T	ENSP00000286614:p.Arg354His		89197874	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901394	0.92035	0.0	1.16E-4	ENSG00000156103	ENST00000286614	T	0.10382	2.88	5.73	5.73	0.89815	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.48095	0.1481	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	T	0.60652	-0.7221	10	0.87932	D	0	.	20.2786	0.98501	0.0:1.0:0.0:0.0	.	354;354	P51512-2;P51512	.;MMP16_HUMAN	H	354	ENSP00000286614:R354H	ENSP00000286614:R354H	R	-	2	0	MMP16	89197874	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.868000	0.98415	0.557000	0.71058	CGT		0.433	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		T	89128758	C	T	89128758	3	4	89	1	0	0	0	0	1	0	0	0	9685	536	19	1	938	1	MMP16	8	89128758	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	243450	89128758	57235264	84	24496										
RSPO2	340419	hgsc.bcm.edu	37	chr8	108970482	108970482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tccccattcgctccaatgacCaacttcacatccttctagta	3	16	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:108970482C>T	ENST00000276659.5	-	5	1062	c.442G>A	c.(442-444)Ggt>Agt	p.G148S	RSPO2_ENST00000378439.2_Missense_Mutation_p.G84S|RSPO2_ENST00000517781.1_Missense_Mutation_p.G84S|RSPO2_ENST00000517939.1_Missense_Mutation_p.G81S	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	148	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.G148S(1)	EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			CTCCAATGACCAACTTCACAT	0.368																																																1	Substitution - Missense(1)	ovary(1)	8											108	105	106					8																	108970482		2203	4300	6503	109039658	SO:0001583	missense	340419			AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.442G>A	8.37:g.108970482C>T	ENSP00000276659:p.Gly148Ser		109039658	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310107	0.60414	.	.	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502;ENST00000521757	D;D;D;D;D;D	0.90676	-2.71;-2.71;-2.71;-1.99;-1.99;-2.71	5.81	5.81	0.92471	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.89238	0.6658	N	0.05619	-0.005	0.80722	D	1	D;P	0.89917	1.0;0.873	D;P	0.91635	0.999;0.543	D	0.83418	0.0031	10	0.06494	T	0.89	-2.6947	20.4375	0.99097	0.0:1.0:0.0:0.0	.	148;84	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	S	81;84;84;148;81;81	ENSP00000428940:G81S;ENSP00000427937:G84S;ENSP00000367698:G84S;ENSP00000276659:G148S;ENSP00000428614:G81S;ENSP00000430485:G81S	ENSP00000276659:G148S	G	-	1	0	RSPO2	109039658	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.711000	0.68400	2.906000	0.99361	0.655000	0.94253	GGT		0.368	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		T	108970482	C	T	108970482	3	4	89	1	0	0	0	0	1	0	0	0	13747	594	21	3	297	3	RSPO2	8	108970482	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	19841724	108970482	37393540	85	24497										
KCNV1	27012	hgsc.bcm.edu	37	chr8	110980326	110980326	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgaaaattaattcaaaaccaGaaatcatctcccccgctgct	4	12	3	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:110980326G>T	ENST00000524391.1	-	4	2526	c.1494C>A	c.(1492-1494)ttC>ttA	p.F498L	KCNV1_ENST00000297404.1_Missense_Mutation_p.F498L			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	498					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			TTCAAAACCAGAAATCATCTC	0.383																																																0			8											53	53	53					8																	110980326		2203	4300	6503	111049502	SO:0001583	missense	27012			AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.1494C>A	8.37:g.110980326G>T	ENSP00000435954:p.Phe498Leu		111049502	Q9UHJ4	Missense_Mutation	SNP	ENST00000524391.1	37	CCDS6314.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.586789	0.46110	.	.	ENSG00000164794	ENST00000524391;ENST00000297404;ENST00000545728	D;D	0.97161	-4.27;-4.27	5.4	3.58	0.41010	.	0.157757	0.44285	D	0.000461	D	0.90621	0.7059	N	0.12182	0.205	0.44694	D	0.997689	B	0.10296	0.003	B	0.04013	0.001	D	0.86025	0.1509	10	0.54805	T	0.06	.	5.9963	0.19495	0.2944:0.0:0.7056:0.0	.	498	Q6PIU1	KCNV1_HUMAN	L	498;498;374	ENSP00000435954:F498L;ENSP00000297404:F498L	ENSP00000297404:F498L	F	-	3	2	KCNV1	111049502	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.407000	0.34657	2.513000	0.84729	0.563000	0.77884	TTC		0.383	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		T	110980326	G	T	110980326	3	4	89	1	0	0	0	0	1	0	0	0	8115	933	33	2	12	2	KCNV1	8	110980326	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	2009844	110980326	35383696	86	24498										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139144881	139144881	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	accaagaaaaacttctccagGaagagttctgaatccagcac	7	11	2	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:139144881G>T	ENST00000395297.1	-	20	4346	c.4176C>A	c.(4174-4176)ttC>ttA	p.F1392L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1392										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ACTTCTCCAGGAAGAGTTCTG	0.527										HNSCC(54;0.14)																																						0			8											178	186	183					8																	139144881		1954	4149	6103	139214063	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.4176C>A	8.37:g.139144881G>T	ENSP00000378710:p.Phe1392Leu		139214063	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283436	0.80803	.	.	ENSG00000147724	ENST00000395297	T	0.22539	1.95	5.74	5.74	0.90152	.	0.059495	0.64402	D	0.000002	T	0.40119	0.1104	L	0.41492	1.28	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	T	0.09552	-1.0669	10	0.87932	D	0	-24.7186	18.9188	0.92516	0.0:0.0:1.0:0.0	.	1392	Q49AJ0	F135B_HUMAN	L	1392	ENSP00000378710:F1392L	ENSP00000378710:F1392L	F	-	3	2	FAM135B	139214063	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	5.806000	0.69150	2.732000	0.93576	0.591000	0.81541	TTC		0.527	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139144881	G	T	139144881	3	4	89	1	0	0	0	0	1	0	0	0	5465	1165	41	2	48	2	FAM135B	8	139144881	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	28164555	139144881	7219141	87	24499										
GRINA	2907	hgsc.bcm.edu	37	chr8	145066195	145066195	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttcatctctctcatcgtcctCagctgttgtggggacttccg	9	13	4	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr8:145066195C>T	ENST00000313269.5	+	4	920	c.642C>T	c.(640-642)ctC>ctT	p.L214L	GRINA_ENST00000395068.4_Silent_p.L214L	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	214						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCATCGTCCTCAGCTGTTGTG	0.557																																																0			8											215	202	206					8																	145066195		2203	4300	6503	145138183	SO:0001819	synonymous_variant	2907			NM_001009184	CCDS34961.1	8q24.3	2010-03-18	2008-04-01						4589	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 3"	138251		NMDARA1		1719427, 8406459	Standard	XM_005250899		Approved	HNRGW, TMBIM3, LFG1	uc003zao.1	Q7Z429		ENST00000313269.5:c.642C>T	8.37:g.145066195C>T			145138183	B3KXM7|O43836|Q8IVW7	Silent	SNP	ENST00000313269.5	37	CCDS34961.1	.	.	.	.	.	.	.	.	.	.	C	8.531	0.871048	0.17322	.	.	ENSG00000178719	ENST00000534791	.	.	.	4.85	2.9	0.33743	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-39.9416	6.0982	0.20033	0.0:0.7674:0.0:0.2326	.	.	.	.	X	138	.	.	Q	+	1	0	GRINA	145138183	0.999000	0.42202	1.000000	0.80357	0.950000	0.60333	0.626000	0.24492	1.287000	0.44583	0.650000	0.86243	CAG		0.557	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	NM_001009184		T	145066195	C	T	145066195	2	4	89	1	0	0	0	0	0	0	0	1	6806	813	29	3		3	GRINA	8	145066195	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	5921314	145066195	1297827	88	24500										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6013871	6013871	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatgcatcttgcataaatttTtccttcccaacagcaagacc	5	12	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr9:6013871T>C	ENST00000259569.5	-	1	1747	c.1737A>G	c.(1735-1737)gaA>gaG	p.E579E	RANBP6_ENST00000485372.1_5'UTR	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	579					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		GCATAAATTTTTCCTTCCCAA	0.398																																																0			9											159	153	155					9																	6013871		2203	4300	6503	6003871	SO:0001819	synonymous_variant	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.1737A>G	9.37:g.6013871T>C			6003871	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																				0.398	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		C	6013871	T	C	6013871	2	2	89	1	0	0	0	0	0	0	0	1	13068	1838	64	4		4	RANBP6	9	6013871	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10		6013871	135199560	89	24501										
DDX58	23586	hgsc.bcm.edu	37	chr9	32493914	32493914	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttttttgaaatcccaactttCaatggcttcataaagtccag	5	9	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr9:32493914C>T	ENST00000379883.2	-	3	425	c.268G>A	c.(268-270)Gaa>Aaa	p.E90K	DDX58_ENST00000545044.1_5'UTR|DDX58_ENST00000379868.1_5'UTR|DDX58_ENST00000379882.1_Missense_Mutation_p.E45K|DDX58_ENST00000542096.1_Missense_Mutation_p.E19K	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	90					cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TCCCAACTTTCAATGGCTTCA	0.284																																																0			9											32	34	33					9																	32493914		2197	4292	6489	32483914	SO:0001583	missense	23586			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.268G>A	9.37:g.32493914C>T	ENSP00000369213:p.Glu90Lys		32483914	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.696958	0.30142	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542096;ENST00000542960	T;T;T	0.05447	3.56;3.46;3.44	4.06	3.13	0.36017	.	0.861825	0.09674	N	0.770750	T	0.06325	0.0163	L	0.42245	1.32	0.80722	D	1	B;B;B	0.25955	0.138;0.085;0.085	B;B;B	0.22601	0.04;0.018;0.02	T	0.24048	-1.0171	10	0.21540	T	0.41	-11.5803	7.1974	0.25860	0.0:0.7274:0.1767:0.096	.	45;19;90	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	K	45;90;19;90	ENSP00000369212:E45K;ENSP00000369213:E90K;ENSP00000442160:E19K	ENSP00000369212:E45K	E	-	1	0	DDX58	32483914	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.706000	0.37878	1.254000	0.44035	0.650000	0.86243	GAA		0.284	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		T	32493914	C	T	32493914	3	4	89	1	0	0	0	0	1	0	0	0	4381	835	29	3	2573	3	DDX58	9	32493914	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	26480043	32493914	108719517	90	24502										
CEP110	11064	hgsc.bcm.edu	37	chr9	123877469	123877469	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	caactggaagaagctatacaActaaaaaaggtatgtaaaag	8	5	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr9:123877469A>G	ENST00000373855.1	+	11	1706	c.1446A>G	c.(1444-1446)caA>caG	p.Q482Q	CNTRL_ENST00000238341.5_Silent_p.Q482Q|CNTRL_ENST00000373865.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	482					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AAGCTATACAACTAAAAAAGG	0.318																																																0			9											68	70	69					9																	123877469		2203	4297	6500	122917290	SO:0001819	synonymous_variant	11064			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.1446A>G	9.37:g.123877469A>G			122917290	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																				0.318	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123877469	A	G	123877469	2	3	89	1	0	0	0	0	0	0	0	1	3251	40	2	4		4	CEP110	9	123877469	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	91383555	123877469	17335962	91	24503										
PARG	8505	hgsc.bcm.edu	37	chr10	51050074	51050074	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgaagagcatcgatggcaacGatctcagtgcagcgccgctg	13	11	1	2	rs375437639	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr10:51050074G>C	ENST00000402038.3	-	11	1007	c.1008C>G	c.(1006-1008)atC>atG	p.I336M		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	821	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CGATGGCAACGATCTCAGTGC	0.502																																																0			10											85	71	75					10																	51050074		692	1591	2283	50720080	SO:0001583	missense	8505			AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1008C>G	10.37:g.51050074G>C	ENSP00000384408:p.Ile336Met		50720080	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.36|15.36	2.811196|2.811196	0.50527|0.50527	.|.	.|.	ENSG00000227345|ENSG00000227345	ENST00000402038|ENST00000432127	.|.	.|.	.|.	5.5|5.5	-6.1|-6.1	0.02138|0.02138	.|.	0.053478|.	0.64402|.	D|.	0.000001|.	T|T	0.38214|0.38214	0.1032|0.1032	M|M	0.66378|0.66378	2.025|2.025	.|.	.|.	.|.	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D|.	0.81914|.	0.992;0.995;0.991;0.989;0.988;0.989;0.995|.	T|T	0.46261|0.46261	-0.9204|-0.9204	8|4	0.87932|.	D|.	0|.	-9.0389|-9.0389	3.4568|3.4568	0.07518|0.07518	0.3814:0.1116:0.398:0.1091|0.3814:0.1116:0.398:0.1091	.|.	739;821;372;89;336;361;821|.	Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4|.	.;PARG_HUMAN;.;.;.;.;.|.	M|W	336|37	.|.	ENSP00000384408:I336M|.	I|S	-|-	3|2	3|0	PARG|PARG	50720080|50720080	0.164000|0.164000	0.22935|0.22935	0.700000|0.700000	0.30305|0.30305	0.251000|0.251000	0.25915|0.25915	-0.277000|-0.277000	0.08502|0.08502	-0.914000|-0.914000	0.03827|0.03827	-0.440000|-0.440000	0.05779|0.05779	ATC|TCG		0.502	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		C	51050074	G	C	51050074	3	2	89	1	0	0	0	0	1	0	0	0	11479	1048	37	5	483	5	PARG	10	51050074	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		51050074	84484673	92	24504										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692911	89692911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agctggaaagggacgaactgGtgtaatgatatgtgcatatt	13	4	0	1	rs121909241		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr10:89692911G>T	ENST00000371953.3	+	5	1752	c.395G>T	c.(394-396)gGt>gTt	p.G132V		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	132	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		G -> V (in one patient with clinical findings suggesting hamartoma tumor syndrome). {ECO:0000269|PubMed:16752378}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.G132D(4)|p.Y27fs*1(2)|p.G132V(1)|p.A121_F145del(1)|p.R130fs*2(1)|p.T131fs*42(1)|p.F56fs*2(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGACGAACTGGTGTAATGATA	0.398		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	59	Whole gene deletion(37)|Deletion - Frameshift(11)|Substitution - Missense(5)|Unknown(5)|Deletion - In frame(1)	prostate(16)|central_nervous_system(14)|skin(6)|endometrium(5)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(4)|breast(3)|soft_tissue(1)|urinary_tract(1)	10	GRCh37	CM045431|CM063078|CM074468	PTEN	M	rs121909241						137	127	130					10																	89692911		2203	4300	6503	89682891	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.395G>T	10.37:g.89692911G>T	ENSP00000361021:p.Gly132Val		89682891	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827556	0.90955	.	.	ENSG00000171862	ENST00000371953	D	0.99532	-6.1	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99743	0.9898	M	0.93594	3.435	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97294	0.9926	8	.	.	.	-10.5526	18.7776	0.91918	0.0:0.0:1.0:0.0	.	132	P60484	PTEN_HUMAN	V	132	ENSP00000361021:G132V	.	G	+	2	0	PTEN	89682891	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.429000	0.97481	2.411000	0.81874	0.655000	0.94253	GGT		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89692911	G	T	89692911	3	4	89	1	0	0	0	0	1	0	0	0	12772	1261	44	2	413	2	PTEN	10	89692911	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	38642837	89692911	45841836	93	24505										
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96796960	96796960	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gtaactgcagtagtattgagGttctttaaatcatcaacaga	8	6	3	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr10:96796960G>A	ENST00000371270.3	-	9	1492	c.1398C>T	c.(1396-1398)aaC>aaT	p.N466N	CYP2C8_ENST00000535898.1_Silent_p.N364N	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	466					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	TAGTATTGAGGTTCTTTAAAT	0.428																																																0			10											141	145	143					10																	96796960		2203	4300	6503	96786950	SO:0001819	synonymous_variant	1558			M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.1398C>T	10.37:g.96796960G>A			96786950	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Silent	SNP	ENST00000371270.3	37	CCDS7438.1																																																																																				0.428	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		A	96796960	G	A	96796960	2	1	89	1	0	0	0	0	0	0	0	1	4173	1252	44	3		3	CYP2C8	10	96796960	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	7104049	96796960	38737787	94	24506										
PCGF6	84108	hgsc.bcm.edu	37	chr10	105110740	105110741	+	In_Frame_Ins	INS	-	-	GGAGGC													0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgagggcgggcggggagacaINSggaggcggaggcggcaaggc					rs201702163|rs113359610|rs60968810	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr10:105110740_105110741insGGAGGC	ENST00000369847.3	-	1	150_151	c.83_84insGCCTCC	c.(82-84)cct>ccGCCTCCt	p.28_28P>PPP	PCGF6_ENST00000490296.1_5'UTR|PCGF6_ENST00000337211.4_In_Frame_Ins_p.28_28P>PPP	NM_001011663.1	NP_001011663.1	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6	28	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)	8		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		gcggggagacaggaggcggagg	0.748														2236	0.446486	0.2269	0.4337	5008	,	,		11043	0.4325		0.5149	False		,,,				2504	0.6963															0			10							,	550,2140		138,274,933					,	1.3	0		dbSNP_132	6	1951,3319		581,789,1265	no	coding,coding	PCGF6	NM_032154.3,NM_001011663.1	,	719,1063,2198	A1A1,A1R,RR		37.0209,20.4461,31.4196	,	,		2501,5459				105100731	SO:0001652	inframe_insertion	84108			AB047006	CCDS7546.1, CCDS31275.1	10q24.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000156374	ENSG00000156374		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	21156	protein-coding gene	gene with protein product		607816	"ring finger protein 134"	RNF134		12167161	Standard	NM_032154		Approved	MBLR	uc001kwt.3	Q9BYE7	OTTHUMG00000018982	ENST00000369847.3:c.78_83dupGCCTCC	10.37:g.105110741_105110746dupGGAGGC	ENSP00000358862:p.ProPro28dup		105100730	A8K3R4|Q5SYD1|Q5SYD6|Q96ID9|Q96SJ1	In_Frame_Ins	INS	ENST00000369847.3	37	CCDS31275.1																																																																																				0.748	PCGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050132.1	NM_032154		GGAGGC	105110741	-	GGAGGC	105110740	7	5	89	1	0	1	1	0	0	0	0	0	11609	175	7	0	1008	0	PCGF6	10	105110740	In_Frame_Ins	INS	-	TCGA-CI-6622-01A-11D-1826-10	8313780	105110740	30424007	95	24507										
SLK	9748	hgsc.bcm.edu	37	chr10	105768065	105768065	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acgcatcaaaggagaacaagAgaaagagttgtccaaatttc	9	7	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr10:105768065A>G	ENST00000369755.3	+	12	3280	c.2735A>G	c.(2734-2736)gAg>gGg	p.E912G	SLK_ENST00000335753.4_Missense_Mutation_p.E912G|SLK_ENST00000474260.1_3'UTR	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	912					apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GGAGAACAAGAGAAAGAGTTG	0.363																																					NSCLC(111;540 1651 1927 4474 17706)											0			10											79	78	78					10																	105768065		2203	4300	6503	105758055	SO:0001583	missense	9748				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.2735A>G	10.37:g.105768065A>G	ENSP00000358770:p.Glu912Gly		105758055	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.909803	0.92107	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.36699	1.24;1.24	5.94	5.94	0.96194	Protein kinase-like domain (1);	0.093460	0.64402	D	0.000001	T	0.56906	0.2017	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.67145	0.996;0.994	D;D	0.68192	0.956;0.935	T	0.59139	-0.7510	10	0.87932	D	0	.	16.4075	0.83691	1.0:0.0:0.0:0.0	.	912;912	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	G	912	ENSP00000336824:E912G;ENSP00000358770:E912G	ENSP00000336824:E912G	E	+	2	0	SLK	105758055	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	9.339000	0.96797	2.275000	0.75901	0.528000	0.53228	GAG		0.363	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105768065	A	G	105768065	3	3	89	1	0	0	0	0	1	0	0	0	14785	304	11	4	2781	4	SLK	10	105768065	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	657325	105768065	29766682	96	24508										
ACCSL	390110	hgsc.bcm.edu	37	chr11	44069885	44069885	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agtgcctcttccttctgaggActctaggggtgatgtcagat	12	9	4	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:44069885A>G	ENST00000378832.1	+	1	355	c.299A>G	c.(298-300)gAc>gGc	p.D100G		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	100					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CCTTCTGAGGACTCTAGGGGT	0.562																																																0			11											82	85	84					11																	44069885		1958	4153	6111	44026461	SO:0001583	missense	390110				CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.299A>G	11.37:g.44069885A>G	ENSP00000368109:p.Asp100Gly		44026461		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	A	9.850	1.193305	0.22037	.	.	ENSG00000205126	ENST00000378832	T	0.69435	-0.4	4.67	0.695	0.18070	.	1.293030	0.04967	N	0.463128	T	0.47893	0.1470	N	0.16743	0.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25676	-1.0125	10	0.25751	T	0.34	-4.0406	5.4707	0.16668	0.6805:0.1465:0.1731:0.0	.	100	Q4AC99	1A1L2_HUMAN	G	100	ENSP00000368109:D100G	ENSP00000368109:D100G	D	+	2	0	ACCSL	44026461	0.001000	0.12720	0.004000	0.12327	0.036000	0.12997	0.846000	0.27682	0.245000	0.21373	0.533000	0.62120	GAC		0.562	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		G	44069885	A	G	44069885	3	3	89	1	0	0	0	0	1	0	0	0	134	275	10	4	301	4	ACCSL	11	44069885	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10		44069885	90936631	97	24509										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563351	55563351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatgcagtacttcctgtcctGcactgctgtggtgacagagt	12	10	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:55563351G>T	ENST00000335605.1	+	1	320	c.320G>T	c.(319-321)tGc>tTc	p.C107F		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TTCCTGTCCTGCACTGCTGTG	0.478																																																0			11											131	107	115					11																	55563351		2200	4296	6496	55319927	SO:0001583	missense	219436			AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.320G>T	11.37:g.55563351G>T	ENSP00000334456:p.Cys107Phe		55319927	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	g	11.26	1.585004	0.28268	.	.	ENSG00000186113	ENST00000335605	T	0.00623	6.15	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000143	T	0.01454	0.0047	N	0.25825	0.765	0.32888	D	0.511519	P	0.48503	0.911	P	0.55667	0.781	T	0.60515	-0.7248	10	0.66056	D	0.02	-19.9727	17.0729	0.86579	0.0:0.0:1.0:0.0	.	107	Q8NGL3	OR5DE_HUMAN	F	107	ENSP00000334456:C107F	ENSP00000334456:C107F	C	+	2	0	OR5D14	55319927	0.000000	0.05858	0.143000	0.22291	0.016000	0.09150	0.157000	0.16402	2.363000	0.80096	0.643000	0.83706	TGC		0.478	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		T	55563351	G	T	55563351	3	4	89	1	0	0	0	0	1	0	0	0	11186	1319	46	2	322	2	OR5D14	11	55563351	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	11493466	55563351	79443165	98	24510										
VWCE	220001	hgsc.bcm.edu	37	chr11	61039219	61039219	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggaaactcaaccccgttgtcGtcaagagagcagcctggatg	12	11	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:61039219G>A	ENST00000335613.5	-	14	2099	c.1713C>T	c.(1711-1713)gaC>gaT	p.D571D	VWCE_ENST00000535710.1_Silent_p.D36D	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	571	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CCCCGTTGTCGTCAAGAGAGC	0.532																																																0			11											112	83	93					11																	61039219		2203	4299	6502	60795795	SO:0001819	synonymous_variant	220001			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1713C>T	11.37:g.61039219G>A			60795795	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																				0.532	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61039219	G	A	61039219	2	1	89	1	0	0	0	0	0	0	0	1	17285	1136	40	1		1	VWCE	11	61039219	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	5475868	61039219	73967297	99	24511										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62299723	62299723	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gggcctttgagttctccttcCagctttggtacagttacatc	9	11	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:62299723C>T	ENST00000378024.4	-	5	2440	c.2166G>A	c.(2164-2166)ctG>ctA	p.L722L	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	722					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTTCTCCTTCCAGCTTTGGTA	0.463																																																0			11											266	235	245					11																	62299723		2202	4299	6501	62056299	SO:0001819	synonymous_variant	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.2166G>A	11.37:g.62299723C>T			62056299	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62299723	C	T	62299723	2	4	89	1	0	0	0	0	0	0	0	1	414	581	21	3		3	AHNAK	11	62299723	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	1260504	62299723	72706793	100	24512										
CD248	57124	hgsc.bcm.edu	37	chr11	66083290	66083290	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	taggccagggcaaagtcaggCggctgcgtaggctccatcca	14	12	1	0	rs186642249	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:66083290C>T	ENST00000311330.3	-	1	1225	c.1209G>A	c.(1207-1209)ccG>ccA	p.P403P	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	403	Pro-rich.				anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						CAAAGTCAGGCGGCTGCGTAG	0.632													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		17975	0		0	False		,,,				2504	0															0			11											80	80	80					11																	66083290		2200	4295	6495	65839866	SO:0001819	synonymous_variant	57124			AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"CD molecules"	18219	protein-coding gene	gene with protein product	"endosialin", "tumor endothelial marker 1"	606064	"CD164 sialomucin-like 1", "CD248 antigen, endosialin"	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.1209G>A	11.37:g.66083290C>T			65839866	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																				0.632	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404		T	66083290	C	T	66083290	2	4	89	1	0	0	0	0	0	0	0	1	2995	755	27	1		1	CD248	11	66083290	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	3783567	66083290	68923226	101	24513										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71726901	71726901	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tagctgctccacctggtggcGgaggccctgggaggcctgtt	16	12	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:71726901G>A	ENST00000393695.3	-	15	1979	c.1648C>T	c.(1648-1650)Cgc>Tgc	p.R550C	NUMA1_ENST00000351960.6_Intron|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.R550C	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						ACCTGGTGGCGGAGGCCCTGG	0.597			T	RARA	APL						OREG0021187	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	0			11											161	157	159					11																	71726901		2200	4293	6493	71404549	SO:0001583	missense	4926			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.1648C>T	11.37:g.71726901G>A	ENSP00000377298:p.Arg550Cys	1132	71404549		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586251	0.66105	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000542977;ENST00000537217	T;T;T;T	0.47177	2.64;2.65;1.43;0.85	5.82	5.82	0.92795	.	0.728694	0.13556	N	0.379112	T	0.60379	0.2264	L	0.50333	1.59	0.37277	D	0.907685	D;D;D;D	0.89917	1.0;0.995;0.987;1.0	D;P;B;D	0.65773	0.938;0.528;0.431;0.938	T	0.63585	-0.6604	10	0.87932	D	0	.	9.9669	0.41730	0.0:0.1282:0.6823:0.1895	.	556;34;550;550	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	C	550;550;113;550;550	ENSP00000351851:R550C;ENSP00000377298:R550C;ENSP00000444880:R550C;ENSP00000442936:R550C	ENSP00000351851:R550C	R	-	1	0	NUMA1	71404549	0.001000	0.12720	0.999000	0.59377	0.970000	0.65996	0.411000	0.21115	2.756000	0.94617	0.561000	0.74099	CGC		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			A	71726901	G	A	71726901	3	1	89	1	0	0	0	0	1	0	0	0	10781	1116	39	1	4751	1	NUMA1	11	71726901	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	5643611	71726901	63279615	102	24514										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76062525	76062525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gttaccctggtgagctctgcGgaatttcccagggagtttca	12	10	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:76062525G>T	ENST00000260045.3	-	5	1774	c.1669C>A	c.(1669-1671)Cgc>Agc	p.R557S	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	557					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R557C(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TGAGCTCTGCGGAATTTCCCA	0.398																																																1	Substitution - Missense(1)	ovary(1)	11											29	25	27					11																	76062525		2065	4162	6227	75740173	SO:0001583	missense	5612			AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1669C>A	11.37:g.76062525G>T	ENSP00000260045:p.Arg557Ser		75740173	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	G	8.325	0.825135	0.16678	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	5.13	3.12	0.35913	Ribonuclease H-like (1);	0.324194	0.38492	N	0.001675	T	0.40670	0.1126	L	0.36672	1.1	0.37062	D	0.898103	B	0.06786	0.001	B	0.01281	0.0	T	0.30119	-0.9989	9	0.14252	T	0.57	.	7.8485	0.29440	0.1485:0.1346:0.717:0.0	.	557	O43422	P52K_HUMAN	S	382;557	.	ENSP00000260045:R557S	R	-	1	0	PRKRIR	75740173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.935000	0.40173	1.342000	0.45619	0.644000	0.83932	CGC		0.398	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		T	76062525	G	T	76062525	3	4	89	1	0	0	0	0	1	0	0	0	12560	1116	39	2	620	2	PRKRIR	11	76062525	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	4335624	76062525	58943991	103	24515										
RBM7	10179	hgsc.bcm.edu	37	chr11	114276496	114276496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tcagagatctttctcttctcCagaaaattttcagagacaag	6	9	5	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:114276496C>T	ENST00000540163.1	+	4	1055	c.413C>T	c.(412-414)cCa>cTa	p.P138L	RBM7_ENST00000544582.1_Missense_Mutation_p.P138L|RP11-212D19.4_ENST00000544347.1_Nonsense_Mutation_p.Q136*|RBM7_ENST00000541475.1_Missense_Mutation_p.P139L|RBM7_ENST00000375490.5_Missense_Mutation_p.P139L|RBM7_ENST00000545678.1_Missense_Mutation_p.P18L			Q9Y580	RBM7_HUMAN	RNA binding motif protein 7	138					meiotic nuclear division (GO:0007126)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.56e-06)|Epithelial(105;4.17e-05)|all cancers(92;0.000348)		TTCTCTTCTCCAGAAAATTTT	0.333																																																0			11											91	88	89					11																	114276496		2201	4296	6497	113781706	SO:0001583	missense	10179			AF156098	CCDS8370.1, CCDS66233.1, CCDS73395.1	11q23.1-q23.2	2013-02-12			ENSG00000076053	ENSG00000076053		"RNA binding motif (RRM) containing"	9904	protein-coding gene	gene with protein product		612413				12477932	Standard	NM_001286045		Approved		uc001pov.3	Q9Y580		ENST00000540163.1:c.413C>T	11.37:g.114276496C>T	ENSP00000439918:p.Pro138Leu		113781706	B2R6K8|Q9NUT4	Missense_Mutation	SNP	ENST00000540163.1	37	CCDS8370.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303621	0.60305	.	.	ENSG00000076053	ENST00000540163;ENST00000375490;ENST00000541475;ENST00000544582;ENST00000545678	T;T;T;T	0.35236	1.32;2.32;2.26;2.11	5.69	5.69	0.88448	.	0.102674	0.64402	D	0.000002	T	0.42988	0.1227	L	0.58101	1.795	0.80722	D	1	P;B	0.48589	0.912;0.174	P;B	0.49502	0.613;0.066	T	0.11567	-1.0582	10	0.19590	T	0.45	-6.9988	14.1696	0.65500	0.1503:0.8497:0.0:0.0	.	138;138	Q6IRX3;Q9Y580	.;RBM7_HUMAN	L	138;139;139;138;18	ENSP00000439918:P138L;ENSP00000364639:P139L;ENSP00000440949:P139L;ENSP00000440923:P138L	ENSP00000364639:P139L	P	+	2	0	RBM7	113781706	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.728000	0.62000	2.683000	0.91414	0.655000	0.94253	CCA		0.333	RBM7-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399010.1	NM_016090		T	114276496	C	T	114276496	3	4	89	1	0	0	0	0	1	0	0	0	13182	594	21	3	427	3	RBM7	11	114276496	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	38213971	114276496	20730020	104	24516										
RNF214	257160	hgsc.bcm.edu	37	chr11	117105072	117105072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttatgtgcttccaaatcagaCgaaggtctcccagatggtct	9	10	3	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:117105072C>T	ENST00000531452.1	+	2	130	c.84C>T	c.(82-84)gaC>gaT	p.D28D	RNF214_ENST00000530849.1_Silent_p.D28D|RNF214_ENST00000531287.1_Silent_p.D28D|RNF214_ENST00000300650.4_Silent_p.D28D|PCSK7_ENST00000320934.3_5'Flank	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	28							zinc ion binding (GO:0008270)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		CCAAATCAGACGAAGGTCTCC	0.478																																																0			11											122	121	122					11																	117105072		1950	4140	6090	116610282	SO:0001819	synonymous_variant	257160			AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.84C>T	11.37:g.117105072C>T			116610282	B2RUW0|B4DTD1	Silent	SNP	ENST00000531452.1	37	CCDS41720.1																																																																																				0.478	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		T	117105072	C	T	117105072	2	4	89	1	0	0	0	0	0	0	0	1	13515	535	19	1		1	RNF214	11	117105072	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	2828576	117105072	17901444	105	24517										
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117975479	117975479	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aactggttctctgcctgtttCgacaacttcacagaagctct	7	12	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:117975479C>T	ENST00000437212.3	+	5	598	c.384C>T	c.(382-384)ttC>ttT	p.F128F	TMPRSS4_ENST00000534111.1_Silent_p.F126F|TMPRSS4_ENST00000522307.1_5'UTR|TMPRSS4_ENST00000523251.1_Silent_p.F88F|TMPRSS4_ENST00000522824.1_Silent_p.F128F			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	128	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.F128F(1)		breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	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)		CTGCCTGTTTCGACAACTTCA	0.562																																																1	Substitution - coding silent(1)	large_intestine(1)	11											85	69	74					11																	117975479		2200	4296	6496	117480689	SO:0001819	synonymous_variant	56649			AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"Serine peptidases / Transmembrane"	11878	protein-coding gene	gene with protein product	"transmembrane serine protease 3", "membrane-type serine protease 2", "type II membrane serine protease"	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.384C>T	11.37:g.117975479C>T			117480689	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Silent	SNP	ENST00000437212.3	37	CCDS31684.1	.	.	.	.	.	.	.	.	.	.	C	7.851	0.723955	0.15439	.	.	ENSG00000137648	ENST00000517544	.	.	.	5.16	-10.3	0.00346	.	.	.	.	.	.	.	.	.	.	.	0.26574	N	0.973507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0919	0.86624	0.0:0.7006:0.0:0.2994	.	.	.	.	X	95	.	.	R	+	1	2	TMPRSS4	117480689	0.000000	0.05858	0.024000	0.17045	0.800000	0.45204	-2.832000	0.00743	-2.703000	0.00397	-0.259000	0.10710	CGA		0.562	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		T	117975479	C	T	117975479	2	4	89	1	0	0	0	0	0	0	0	1	16288	883	31	1		1	TMPRSS4	11	117975479	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	870407	117975479	17031037	106	24518										
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122671936	122671936	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttgaagatccgtgtagagccCggcttatttgagtggacaaa	12	7	0	4	rs192006566		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:122671936C>A	ENST00000284273.5	+	11	1866	c.1491C>A	c.(1489-1491)ccC>ccA	p.P497P		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	497	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.P497P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		GTGTAGAGCCCGGCTTATTTG	0.453																																																1	Substitution - coding silent(1)	central_nervous_system(1)	11											148	145	146					11																	122671936		2202	4299	6501	122177146	SO:0001819	synonymous_variant	84959			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1491C>A	11.37:g.122671936C>A			122177146	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	37	CCDS31694.1																																																																																				0.453	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		A	122671936	C	A	122671936	2	1	89	1	0	0	0	0	0	0	0	1	16880	639	23	2		2	UBASH3B	11	122671936	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	4696457	122671936	12334580	107	24519										
C11orf63	79864	hgsc.bcm.edu	37	chr11	122805387	122805387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tacttcaacaaagcctgaatCgattgtgattatgcatgcct	7	9	1	2	rs139995595		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr11:122805387C>T	ENST00000531316.1	+	4	1330	c.1238C>T	c.(1237-1239)tCg>tTg	p.S413L	C11orf63_ENST00000227349.2_Missense_Mutation_p.S413L			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	413					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		AAGCCTGAATCGATTGTGATT	0.443																																																0			11						C	LEU/SER	1,4403	2.1+/-5.4	0,1,2201	84	81	82		1238	3.3	0	11	dbSNP_134	82	0,8598		0,0,4299	no	missense	C11orf63	NM_024806.2	145	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	413/779	122805387	1,13001	2202	4299	6501	122310597	SO:0001583	missense	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.1238C>T	11.37:g.122805387C>T	ENSP00000431669:p.Ser413Leu		122310597	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.246926	0.22796	2.27E-4	0.0	ENSG00000109944	ENST00000227349;ENST00000531316	T;T	0.25250	1.81;1.81	5.46	3.35	0.38373	.	1.268610	0.05383	N	0.537583	T	0.15392	0.0371	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.15867	-1.0422	10	0.46703	T	0.11	0.0432	8.0292	0.30454	0.1671:0.7415:0.0:0.0915	.	413	Q6NUN7	CK063_HUMAN	L	413	ENSP00000227349:S413L;ENSP00000431669:S413L	ENSP00000227349:S413L	S	+	2	0	C11orf63	122310597	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.962000	0.29280	1.267000	0.44247	0.585000	0.79938	TCG		0.443	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		T	122805387	C	T	122805387	3	4	89	1	0	0	0	0	1	0	0	0	1658	893	31	1	1316	1	C11orf63	11	122805387	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	133451	122805387	12201129	108	24520										
PRB4	5545	hgsc.bcm.edu	37	chr12	11461534	11461596	+	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-													0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggggacggtgggactggttgCctccttgtgggggtggtctt					rs11054244|rs59021567|rs11054243|rs551775057|rs12303607|rs199532199|rs148027029|rs71057722|rs59189129|rs536297617	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENST00000535904.1	-	3	354_416	c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	c.(319-384)ggaaaccagtcccaaggtaccccacctcctccaggaaagccagaaagaccacccccacaaggaggc>ggc	p.107_128GNQSQGTPPPPGKPERPPPQGG>G	PRB4_ENST00000445719.2_Splice_Site_p.107_112GNQSQG>G|PRB4_ENST00000279575.1_In_Frame_Del_p.107_128GNQSQGTPPPPGKPERPPPQGG>G			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)		p.P115L(1)|p.G118E(1)|p.P117T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTGCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTTCCTCCTTGTG	0.605										HNSCC(22;0.051)																																						3	Substitution - Missense(3)	lung(1)|kidney(1)|skin(1)	12																																								11352863	SO:0001651	inframe_deletion	5545				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	12.37:g.11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENSP00000442834:p.Gly107_Gly127del		11352801	A1L439|O00600|P02813|P10161|P10162|P81489	In_Frame_Del	DEL	ENST00000535904.1	37	CCDS8641.1																																																																																				0.605	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461596	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-	11461534	7	5	89	1	0	1	0	1	0	0	0	0	12479	739	26	0	364	0	PRB4	12	11461534	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	TCGA-CI-6622-01A-11D-1826-10		11461534	122390361	109	24521										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398283	25398284	+	In_Frame_Ins	INS	-	-	CCAGCT													0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aggcactcttgcctacgccaINSccagctccaactaccacaag					rs121913529		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:25398283_25398284insCCAGCT	ENST00000256078.4	-	2	98_99	c.35_36insAGCTGG	c.(34-36)ggt>ggAGCTGGt	p.12_12G>GAG	KRAS_ENST00000556131.1_In_Frame_Ins_p.12_12G>GAG|KRAS_ENST00000311936.3_In_Frame_Ins_p.12_12G>GAG|KRAS_ENST00000557334.1_In_Frame_Ins_p.12_12G>GAG	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12G(9)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12_G13insG(3)|p.G12Y(2)|p.G12C(1)|p.G13C(1)|p.G12N(1)|p.G12fs*3(1)|p.G12_G13insA(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TGCCTACGCCACCAGCTCCAAC	0.347	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15827	Substitution - Missense(15813)|Substitution - coding silent(9)|Insertion - In frame(4)|Deletion - Frameshift(1)	large_intestine(9458)|pancreas(3005)|lung(1513)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(168)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12																																								25289551	SO:0001652	inframe_insertion	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.30_35dupAGCTGG	12.37:g.25398284_25398289dupCCAGCT	ENSP00000256078:p.AlaGly12dup		25289550	A8K8Z5|B0LPF9|P01118|Q96D10	In_Frame_Ins	INS	ENST00000256078.4	37	CCDS8703.1																																																																																				0.347	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		CCAGCT	25398284	-	CCAGCT	25398283	7	5	89	1	0	1	1	0	0	0	0	0	8459	146	6	0	670	0	KRAS	12	25398283	In_Frame_Ins	INS	-	TCGA-CI-6622-01A-11D-1826-10	13936749	25398283	108453612	110	24522										
PCBP2	5094	hgsc.bcm.edu	37	chr12	53873204	53873204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttacaggctttcctcggagaCgggtggcatggggagcagct	16	9	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:53873204C>T	ENST00000439930.3	+	14	1098	c.1076C>T	c.(1075-1077)aCg>aTg	p.T359M	PCBP2_ENST00000548933.1_Missense_Mutation_p.T329M|PCBP2_ENST00000549863.1_Missense_Mutation_p.T315M|PCBP2_ENST00000359282.5_Missense_Mutation_p.T325M|PCBP2_ENST00000552819.1_Missense_Mutation_p.T316M|PCBP2_ENST00000359462.5_Missense_Mutation_p.T360M|PCBP2_ENST00000437231.1_Missense_Mutation_p.T312M|PCBP2_ENST00000546463.1_Missense_Mutation_p.T356M|PCBP2_ENST00000552296.2_Missense_Mutation_p.T355M|PCBP2_ENST00000447282.1_Missense_Mutation_p.T329M|PCBP2_ENST00000603815.1_Missense_Mutation_p.T359M|PCBP2_ENST00000455667.3_Missense_Mutation_p.T312M			Q15366	PCBP2_HUMAN	poly(rC) binding protein 2	359					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of defense response to virus (GO:0050687)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15						TCCTCGGAGACGGGTGGCATG	0.478																																																0			12											161	138	145					12																	53873204		2203	4300	6503	52159471	SO:0001583	missense	5094			BC035420	CCDS8859.1, CCDS44900.1, CCDS44901.1, CCDS44902.1, CCDS44903.1, CCDS44904.1, CCDS55830.1	12q13.13	2013-10-30	2001-11-28		ENSG00000197111	ENSG00000197111			8648	protein-coding gene	gene with protein product	"heterogenous nuclear ribonucleoprotein E2"	601210	"poly(rC)-binding protein 2"			8833161	Standard	NM_001098620		Approved	HNRPE2, hnRNP-E2, HNRNPE2	uc001sdc.4	Q15366	OTTHUMG00000169439	ENST00000439930.3:c.1076C>T	12.37:g.53873204C>T	ENSP00000408949:p.Thr359Met		52159471	A8K7X6|F8VYL7|G3V0E8|I6L8F9|Q32Q82|Q59HD4|Q68Y55|Q6IPF4|Q6PKG5	Missense_Mutation	SNP	ENST00000439930.3	37	CCDS44901.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.949929	0.34377	.	.	ENSG00000197111	ENST00000359282;ENST00000447282;ENST00000437231;ENST00000439930;ENST00000549863;ENST00000359462;ENST00000550927;ENST00000546463;ENST00000552296;ENST00000552083;ENST00000552819;ENST00000455667;ENST00000548933;ENST00000379777	T;T;T;T;T;T;T;T;T;T;T	0.32515	1.49;1.49;1.48;1.47;1.48;1.46;1.45;1.87;1.49;1.48;1.49	5.18	5.18	0.71444	.	0.054625	0.64402	D	0.000001	T	0.26376	0.0644	L	0.34521	1.04	0.80722	D	1	B;B;B;P;B;B;B;B;B;B	0.45396	0.057;0.144;0.089;0.857;0.009;0.131;0.132;0.009;0.081;0.081	B;B;B;B;B;B;B;B;B;B	0.38428	0.008;0.039;0.018;0.273;0.003;0.063;0.016;0.003;0.012;0.012	T	0.06679	-1.0813	10	0.59425	D	0.04	.	17.8359	0.88697	0.0:1.0:0.0:0.0	.	316;317;359;302;329;312;355;325;360;356	B4DXP5;F8VRG9;Q15366;F8VWQ4;Q32Q82;G3V0E8;F8VYL7;Q68Y55;Q6IPF4;A8K7X6	.;.;PCBP2_HUMAN;.;.;.;.;.;.;.	M	325;329;312;359;315;360;302;356;355;317;316;312;329;276	ENSP00000352228:T325M;ENSP00000394116:T329M;ENSP00000390304:T312M;ENSP00000408949:T359M;ENSP00000447670:T315M;ENSP00000352438:T360M;ENSP00000448762:T356M;ENSP00000448927:T355M;ENSP00000449070:T316M;ENSP00000388008:T312M;ENSP00000449062:T329M	ENSP00000352228:T325M	T	+	2	0	PCBP2	52159471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.637000	0.67854	2.597000	0.87782	0.563000	0.77884	ACG		0.478	PCBP2-027	NOVEL	NAGNAG_splice_site|non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407545.2	NM_005016		T	53873204	C	T	53873204	3	4	89	1	0	0	0	0	1	0	0	0	11532	536	19	1	1133	1	PCBP2	12	53873204	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	28474921	53873204	79978691	111	24523										
DCD	117159	hgsc.bcm.edu	37	chr12	55038510	55038510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttacagctatagtactgagTcaaggacgtctttaacgtca	8	9	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:55038510T>C	ENST00000293371.6	-	5	509	c.320A>G	c.(319-321)gAc>gGc	p.D107G	DCD_ENST00000456047.2_3'UTR	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	107					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				TAGTACTGAGTCAAGGACGTC	0.423																																																0			12											38	33	35					12																	55038510		2203	4300	6503	53324777	SO:0001583	missense	117159			AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.320A>G	12.37:g.55038510T>C	ENSP00000293371:p.Asp107Gly		53324777	A5JHP2|A5JHP3|P58461|Q53YJ2	Missense_Mutation	SNP	ENST00000293371.6	37	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	T	4.021	0.001422	0.07819	.	.	ENSG00000161634	ENST00000293371	.	.	.	2.4	-2.04	0.07343	.	.	.	.	.	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	D	0.55172	0.97	B	0.40602	0.334	T	0.15867	-1.0422	8	0.49607	T	0.09	.	3.0498	0.06166	0.0:0.2947:0.2315:0.4738	.	107	P81605	DCD_HUMAN	G	107	.	ENSP00000293371:D107G	D	-	2	0	DCD	53324777	.	.	0.000000	0.03702	0.002000	0.02628	.	.	-0.432000	0.07297	0.460000	0.39030	GAC		0.423	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283		C	55038510	T	C	55038510	3	2	89	1	0	0	0	0	1	0	0	0	4289	1667	58	4	16	4	DCD	12	55038510	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	1165306	55038510	78813385	112	24524										
AGAP2	100130776	hgsc.bcm.edu	37	chr12	58121196	58121196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cgcgtgtcgctttcccacacGcggttggccgtgtcgttgcc	13	15	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:58121196G>A	ENST00000542466.2	+	2	557	c.421G>A	c.(421-423)Gcg>Acg	p.A141T	AGAP2_ENST00000257897.3_Silent_p.R653R|RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000547588.1_Silent_p.R1009R					AGAP2 antisense RNA 1																		TTTCCCACACGCGGTTGGCCG	0.672																																																0			12											57	47	50					12																	58121196		2203	4299	6502	56407463	SO:0001583	missense	116986			BC039697, BC069024		12q14.1	2013-05-30			ENSG00000255737	ENSG00000255737		"Long non-coding RNAs"	48633	non-coding RNA	RNA, long non-coding							Standard	NR_027032		Approved				OTTHUMG00000170286	ENST00000542466.2:c.421G>A	12.37:g.58121196G>A	ENSP00000437523:p.Ala141Thr		56407463		Silent	SNP	ENST00000542466.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.84|16.84	3.233844|3.233844	0.58886|0.58886	.|.	.|.	ENSG00000255737|ENSG00000135439	ENST00000542466|ENST00000328568	.|T	.|0.46451	.|0.87	5.0|5.0	2.18|2.18	0.27775|0.27775	.|.	.|0.269566	.|0.41823	.|D	.|0.000819	T|T	0.51143|0.51143	0.1657|0.1657	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.39624|.	0.681|.	B|.	0.26614|.	0.071|.	T|T	0.50346|0.50346	-0.8839|-0.8839	7|7	0.87932|0.72032	D|D	0|0.01	.|.	9.7483|9.7483	0.40459|0.40459	0.2232:0.0:0.7768:0.0|0.2232:0.0:0.7768:0.0	.|.	141|.	B7Z718|.	.|.	T|C	141|853	.|ENSP00000328160:R853C	ENSP00000437523:A141T|ENSP00000328160:R853C	A|R	+|-	1|1	0|0	RP11-571M6.6|AGAP2	56407463|56407463	0.913000|0.913000	0.31002|0.31002	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.232000|1.232000	0.32636|0.32636	0.245000|0.245000	0.21373|0.21373	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.672	AGAP2-AS1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000408368.1			A	58121196	G	A	58121196	3	1	89	1	0	0	0	0	1	0	0	0	368	1074	38	1	563	1	AGAP2	12	58121196	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	3082686	58121196	75730699	113	24525										
NAP1L1	4673	hgsc.bcm.edu	37	chr12	76454036	76454036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggtttttgagagcattcactCgtcttttaactaccctaggc	8	10	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:76454036C>T	ENST00000261182.8	-	5	716	c.230G>A	c.(229-231)cGa>cAa	p.R77Q	NAP1L1_ENST00000542344.1_Missense_Mutation_p.R36Q|NAP1L1_ENST00000548044.1_Missense_Mutation_p.R36Q|NAP1L1_ENST00000431879.3_Missense_Mutation_p.R36Q|NAP1L1_ENST00000393263.3_Missense_Mutation_p.R77Q|NAP1L1_ENST00000552342.1_Missense_Mutation_p.R77Q|NAP1L1_ENST00000547773.1_Missense_Mutation_p.R14Q|NAP1L1_ENST00000547993.1_5'Flank|NAP1L1_ENST00000544816.1_5'UTR|NAP1L1_ENST00000549596.1_Missense_Mutation_p.R77Q|NAP1L1_ENST00000535020.2_Missense_Mutation_p.R77Q	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	77					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				AGCATTCACTCGTCTTTTAAC	0.378																																																0			12											127	111	116					12																	76454036		2203	4300	6503	74740303	SO:0001583	missense	4673				CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.230G>A	12.37:g.76454036C>T	ENSP00000261182:p.Arg77Gln		74740303	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	37	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819845	0.90873	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000552342;ENST00000548044;ENST00000550934;ENST00000551992;ENST00000548273;ENST00000551600;ENST00000547704;ENST00000551524;ENST00000547479	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	5.39	5.39	0.77823	.	0.052270	0.85682	N	0.000000	T	0.48390	0.1497	M	0.64997	1.995	0.80722	D	1	P;D;P;P;P;P;D	0.59357	0.931;0.969;0.931;0.905;0.662;0.949;0.985	P;P;P;P;P;B;P	0.53912	0.618;0.737;0.618;0.737;0.532;0.353;0.737	T	0.49495	-0.8934	10	0.87932	D	0	.	19.5142	0.95155	0.0:1.0:0.0:0.0	.	77;36;77;77;36;14;77	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	Q	77;71;77;36;14;36;77;77;77;36;77;77;36;77;77;36;103	ENSP00000261182:R77Q;ENSP00000450236:R71Q;ENSP00000376947:R77Q;ENSP00000409795:R36Q;ENSP00000448167:R14Q;ENSP00000444759:R36Q;ENSP00000445008:R77Q;ENSP00000447793:R77Q;ENSP00000447196:R77Q;ENSP00000449649:R36Q;ENSP00000448133:R77Q;ENSP00000448764:R77Q;ENSP00000446787:R36Q;ENSP00000448836:R77Q;ENSP00000446756:R77Q;ENSP00000448661:R36Q;ENSP00000449333:R103Q	ENSP00000261182:R77Q	R	-	2	0	NAP1L1	74740303	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.076000	0.71267	2.678000	0.91216	0.555000	0.69702	CGA		0.378	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		T	76454036	C	T	76454036	3	4	89	1	0	0	0	0	1	0	0	0	10186	884	31	1	989	1	NAP1L1	12	76454036	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	18332840	76454036	57397859	114	24526										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85277598	85277598	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gagagggatgaatccagaaaTggtgattagcagaatgagga	15	3	0	6			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr12:85277598T>C	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.I266V	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AATCCAGAAATGGTGATTAGC	0.403																																																0			12											83	76	79					12																	85277598		2203	4300	6503	83801729	SO:0001627	intron_variant	55117			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+39A>G	12.37:g.85277598T>C			83801729	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.323466	0.24080	.	.	ENSG00000072041	ENST00000450363	T	0.73258	-0.73	5.38	2.96	0.34315	.	.	.	.	.	T	0.51295	0.1666	N	0.16098	0.37	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.45381	-0.9265	9	0.87932	D	0	.	5.9566	0.19277	0.1457:0.0786:0.0:0.7757	.	266	Q9H9F5	.	V	266	ENSP00000390706:I266V	ENSP00000390706:I266V	I	-	1	0	SLC6A15	83801729	0.008000	0.16893	0.003000	0.11579	0.037000	0.13140	0.389000	0.20751	0.404000	0.25506	0.533000	0.62120	ATT		0.403	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		C	85277598	T	C	85277598	1	2	89	0	1	0	0	0	0	0	0	0	14715	1464	51	4		4	SLC6A15	12	85277598	Intron	SNP	T	TCGA-CI-6622-01A-11D-1826-10	8823562	85277598	48574297	115	24527										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25831346	25831346	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atccttaccatgaatcctttGattgtcctgtagtaggaatc	7	9	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr13:25831346G>T	ENST00000381801.5	-	9	1844	c.1083C>A	c.(1081-1083)atC>atA	p.I361I	MTMR6_ENST00000540661.1_Silent_p.I361I|MTMR6_ENST00000482345.1_5'Flank	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	361	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TGAATCCTTTGATTGTCCTGT	0.408																																																0			13											74	70	72					13																	25831346		2203	4300	6503	24729346	SO:0001819	synonymous_variant	9107			AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1083C>A	13.37:g.25831346G>T			24729346	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	37	CCDS9313.1																																																																																				0.408	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		T	25831346	G	T	25831346	2	4	89	1	0	0	0	0	0	0	0	1	9977	1280	45	2		2	MTMR6	13	25831346	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10		25831346	89338532	116	24528										
BRCA2	675	hgsc.bcm.edu	37	chr13	32912552	32912552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tttgtattcataaagatgaaAcggacttgctatttactgat	7	5	1	3	rs397507322		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr13:32912552A>G	ENST00000380152.3	+	11	4293	c.4060A>G	c.(4060-4062)Acg>Gcg	p.T1354A	BRCA2_ENST00000544455.1_Missense_Mutation_p.T1354A			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1354	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.E1353fs*5(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAAAGATGAAACGGACTTGCT	0.323			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	1	Deletion - Frameshift(1)	ovary(1)	13											60	61	61					13																	32912552		2203	4298	6501	31810552	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.4060A>G	13.37:g.32912552A>G	ENSP00000369497:p.Thr1354Ala		31810552	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	8.033	0.762153	0.15914	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00675	5.88;5.88	5.75	4.57	0.56435	.	0.534882	0.19957	N	0.102297	T	0.00815	0.0027	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.48801	-0.9003	10	0.59425	D	0.04	.	10.416	0.44322	0.9261:0.0:0.0739:0.0	.	1354	P51587	BRCA2_HUMAN	A	1354	ENSP00000369497:T1354A;ENSP00000439902:T1354A	ENSP00000369497:T1354A	T	+	1	0	BRCA2	31810552	0.010000	0.17322	0.010000	0.14722	0.291000	0.27294	2.150000	0.42254	1.008000	0.39264	0.460000	0.39030	ACG		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32912552	A	G	32912552	3	3	89	1	0	0	0	0	1	0	0	0	1502	43	2	4	4098	4	BRCA2	13	32912552	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	7081206	32912552	82257326	117	24529										
RB1	5925	hgsc.bcm.edu	37	chr13	48947598	48947598	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttaaattcagcaagtgatcaAccttcagaaaatctgatttc	5	8	4	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr13:48947598A>G	ENST00000267163.4	+	12	1323	c.1185A>G	c.(1183-1185)caA>caG	p.Q395Q		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	395	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAAGTGATCAACCTTCAGAAA	0.289		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											103	111	108					13																	48947598		2203	4289	6492	47845599	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1185A>G	13.37:g.48947598A>G			47845599	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.289	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48947598	A	G	48947598	2	3	89	1	0	0	0	0	0	0	0	1	13135	40	2	4		4	RB1	13	48947598	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	16035046	48947598	66222280	118	24530										
CKAP2	26586	hgsc.bcm.edu	37	chr13	53036690	53036690	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acattttctgaatgcctgaaCttgattaatgaggtagagtc	9	6	1	5			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr13:53036690C>A	ENST00000378037.5	+	5	1386	c.1296C>A	c.(1294-1296)aaC>aaA	p.N432K	CKAP2_ENST00000490903.1_Missense_Mutation_p.N383K|CKAP2_ENST00000258607.5_Missense_Mutation_p.N431K|CKAP2_ENST00000378034.3_Missense_Mutation_p.N431K	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		AATGCCTGAACTTGATTAATG	0.294																																																0			13											50	49	49					13																	53036690		2203	4300	6503	51934691	SO:0001583	missense	26586			AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1296C>A	13.37:g.53036690C>A	ENSP00000367276:p.Asn432Lys		51934691		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	.	.	.	.	.	.	.	.	.	.	.	10.72	1.429848	0.25726	.	.	ENSG00000136108	ENST00000398044;ENST00000258607;ENST00000378034;ENST00000378037;ENST00000490903	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	5.76	-0.484	0.12071	.	0.447250	0.24187	N	0.040759	T	0.26846	0.0657	L	0.49455	1.56	0.27658	N	0.947159	D;D;P;P	0.89917	1.0;1.0;0.884;0.865	D;D;B;B	0.87578	0.998;0.998;0.301;0.391	T	0.23726	-1.0180	10	0.15499	T	0.54	-8.873	2.0434	0.03555	0.1257:0.2882:0.357:0.2291	.	383;432;431;432	E9PD90;Q8WWK9;B2RMQ4;A8MYU4	.;CKAP2_HUMAN;.;.	K	432;431;431;432;383	ENSP00000258607:N431K;ENSP00000367273:N431K;ENSP00000367276:N432K;ENSP00000417830:N383K	ENSP00000258607:N431K	N	+	3	2	CKAP2	51934691	0.653000	0.27358	0.896000	0.35187	0.274000	0.26718	-0.607000	0.05648	-0.137000	0.11455	-0.175000	0.13238	AAC		0.294	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2			A	53036690	C	A	53036690	3	1	89	1	0	0	0	0	1	0	0	0	3448	564	20	2	1314	2	CKAP2	13	53036690	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	4089092	53036690	62133188	119	24531										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96622400	96622400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gtcgaatatctaatacataaGtatattcccaaatgtgtgaa	6	6	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr13:96622400G>A	ENST00000376747.3	-	12	1371	c.1301C>T	c.(1300-1302)aCt>aTt	p.T434I		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	434					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TAATACATAAGTATATTCCCA	0.303																																																0			13											76	79	78					13																	96622400		2203	4296	6499	95420401	SO:0001583	missense	0			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.1301C>T	13.37:g.96622400G>A	ENSP00000365938:p.Thr434Ile		95420401	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.676494	0.29783	.	.	ENSG00000102595	ENST00000376747	T	0.29917	1.55	5.22	-10.2	0.00374	.	0.747748	0.13092	N	0.414441	T	0.19208	0.0461	M	0.62723	1.935	0.26080	N	0.981104	B	0.31435	0.323	B	0.30943	0.122	T	0.14952	-1.0454	10	0.72032	D	0.01	0.533	2.9071	0.05725	0.1484:0.2175:0.1173:0.5168	.	434	Q9NYU1	UGGG2_HUMAN	I	434	ENSP00000365938:T434I	ENSP00000365938:T434I	T	-	2	0	UGGT2	95420401	0.000000	0.05858	0.003000	0.11579	0.618000	0.37518	-2.123000	0.01319	-1.072000	0.03141	0.455000	0.32223	ACT		0.303	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96622400	G	A	96622400	3	1	89	1	0	0	0	0	1	0	0	0	16982	1029	36	3	3361	3	UGGT2	13	96622400	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	43585710	96622400	18547478	120	24532										
MPP5	64398	hgsc.bcm.edu	37	chr14	67790521	67790521	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tattggccaaagaaggcaagAatccaaaggtaaagttttca	9	6	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr14:67790521A>G	ENST00000261681.4	+	14	2504	c.1843A>G	c.(1843-1845)Aat>Gat	p.N615D	ATP6V1D_ENST00000553974.1_Intron|MPP5_ENST00000555925.1_Missense_Mutation_p.N581D	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	615	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)	p.N615Y(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		AGAAGGCAAGAATCCAAAGGT	0.383																																																1	Substitution - Missense(1)	ovary(1)	14											70	70	70					14																	67790521		2203	4300	6503	66860274	SO:0001583	missense	64398			AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"stardust"	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.1843A>G	14.37:g.67790521A>G	ENSP00000261681:p.Asn615Asp		66860274	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Missense_Mutation	SNP	ENST00000261681.4	37	CCDS9779.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414664	0.62511	.	.	ENSG00000072415	ENST00000261681;ENST00000555925	T;T	0.13901	2.55;2.55	5.64	5.64	0.86602	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.85682	D	0.000000	T	0.12050	0.0293	N	0.13003	0.285	0.80722	D	1	P	0.39665	0.682	P	0.45538	0.484	T	0.28650	-1.0037	10	0.12766	T	0.61	.	15.8662	0.79067	1.0:0.0:0.0:0.0	.	615	Q8N3R9	MPP5_HUMAN	D	615;581	ENSP00000261681:N615D;ENSP00000451488:N581D	ENSP00000261681:N615D	N	+	1	0	MPP5	66860274	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.122000	0.71608	2.153000	0.67306	0.377000	0.23210	AAT		0.383	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474		G	67790521	A	G	67790521	3	3	89	1	0	0	0	0	1	0	0	0	9767	246	9	4	1889	4	MPP5	14	67790521	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10		67790521	39559019	121	24533										
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81682800	81682800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gttcatccactccatcatccAgaaagatgtctctcacatca	4	14	5	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr14:81682800A>G	ENST00000553612.1	-	2	492	c.89T>C	c.(88-90)cTg>cCg	p.L30P	GTF2A1_ENST00000434192.2_5'UTR	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	30			L -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		TCCATCATCCAGAAAGATGTC	0.308																																																0			14											68	67	67					14																	81682800		2203	4300	6503	80752553	SO:0001583	missense	2957			X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"General transcription factors"	4646	protein-coding gene	gene with protein product		600520	"glucose regulated protein, 58kD pseudogene"			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.89T>C	14.37:g.81682800A>G	ENSP00000452454:p.Leu30Pro		80752553	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	37	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.309626	0.81247	.	.	ENSG00000165417	ENST00000553612	T	0.50548	0.74	5.66	5.66	0.87406	Transcription factor IIA, alpha subunit, N-terminal (1);Transcription factor IIA, helical (1);	0.000000	0.85682	D	0.000000	T	0.70176	0.3194	M	0.80982	2.52	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	T	0.71820	-0.4477	10	0.44086	T	0.13	-9.5887	16.1762	0.81855	1.0:0.0:0.0:0.0	.	30	P52655	TF2AA_HUMAN	P	30	ENSP00000452454:L30P	ENSP00000298173:L30P	L	-	2	0	GTF2A1	80752553	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	8.963000	0.93385	2.283000	0.76528	0.477000	0.44152	CTG		0.308	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859		G	81682800	A	G	81682800	3	3	89	1	0	0	0	0	1	0	0	0	6873	188	7	4	1073	4	GTF2A1	14	81682800	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	13892279	81682800	25666740	122	24534										
GABRB3	2562	hgsc.bcm.edu	37	chr15	26812851	26812851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tccaatgttcctcttcaaccGaaagctcagtgacagtcgag	8	12	3	1	rs144496462		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:26812851G>A	ENST00000311550.5	-	7	823	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	GABRB3_ENST00000545868.1_Missense_Mutation_p.R153W|GABRB3_ENST00000299267.4_Missense_Mutation_p.R238W|GABRB3_ENST00000400188.3_Missense_Mutation_p.R167W|GABRB3_ENST00000541819.2_Missense_Mutation_p.R294W	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	238					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTCTTCAACCGAAAGCTCAGT	0.428																																																0			15						G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	121	104	109		712,457,499,712	5.1	1	15	dbSNP_134	109	0,8600		0,0,4300	no	missense,missense,missense,missense	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	101,101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign	238/474,153/389,167/403,238/474	26812851	1,13005	2203	4300	6503	24363944	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.712C>T	15.37:g.26812851G>A	ENSP00000308725:p.Arg238Trp		24363944	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033368	0.54896	2.27E-4	0.0	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28	6.06	5.08	0.68730	Neurotransmitter-gated ion-channel ligand-binding (3);	0.096499	0.64402	D	0.000001	T	0.75155	0.3811	M	0.61703	1.905	0.49687	D	0.999817	B;B;B	0.31730	0.337;0.083;0.161	B;B;B	0.21151	0.03;0.013;0.033	T	0.76586	-0.2905	10	0.87932	D	0	.	11.5757	0.50860	0.0:0.0:0.6664:0.3336	.	294;238;238	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	W	238;294;238;167;153	ENSP00000308725:R238W;ENSP00000442408:R294W;ENSP00000299267:R238W;ENSP00000383049:R167W;ENSP00000439169:R153W	ENSP00000299267:R238W	R	-	1	2	GABRB3	24363944	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.605000	0.61119	2.879000	0.98667	0.650000	0.86243	CGG		0.428	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26812851	G	A	26812851	3	1	89	1	0	0	0	0	1	0	0	0	6187	1057	37	1	721	1	GABRB3	15	26812851	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		26812851	75718541	123	24535										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34529012	34529012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tatatgctgatatatcactgTcatgctgccatagacatcac	6	10	3	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:34529012T>C	ENST00000354181.3	-	23	3431	c.2939A>G	c.(2938-2940)gAc>gGc	p.D980G	SLC12A6_ENST00000560611.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000290209.5_Missense_Mutation_p.D929G|SLC12A6_ENST00000451844.2_Missense_Mutation_p.D792G|SLC12A6_ENST00000397707.2_Missense_Mutation_p.D965G|SLC12A6_ENST00000560164.1_Missense_Mutation_p.D792G|SLC12A6_ENST00000558667.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000397702.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000458406.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000558589.1_Missense_Mutation_p.D971G			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	980					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TATATCACTGTCATGCTGCCA	0.428																																																0			15											126	110	115					15																	34529012		2201	4298	6499	32316304	SO:0001583	missense	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.2939A>G	15.37:g.34529012T>C	ENSP00000346112:p.Asp980Gly		32316304	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654574	0.67472	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.16	5.16	0.70880	.	0.051702	0.64402	D	0.000001	T	0.58018	0.2093	M	0.84585	2.705	0.80722	D	1	P;P;P;B	0.41748	0.717;0.761;0.594;0.278	P;B;B;B	0.47864	0.559;0.354;0.356;0.15	T	0.66089	-0.6010	10	0.87932	D	0	.	14.1126	0.65132	0.0:0.0:0.0:1.0	.	965;980;929;792	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	G	929;965;971;921;921;792	ENSP00000290209:D929G;ENSP00000380819:D965G;ENSP00000380814:D921G;ENSP00000387725:D921G;ENSP00000390199:D792G	ENSP00000290209:D929G	D	-	2	0	SLC12A6	32316304	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.868000	0.87116	2.174000	0.68829	0.528000	0.53228	GAC		0.428	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		C	34529012	T	C	34529012	3	2	89	1	0	0	0	0	1	0	0	0	14424	1667	58	4	529	4	SLC12A6	15	34529012	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	7716161	34529012	68002380	124	24536										
EXD1	161829	hgsc.bcm.edu	37	chr15	41476618	41476618	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tttttaccaaataagaagccTttgactttctcctctttccc	3	12	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:41476618T>C	ENST00000314992.5	-	10	1246	c.1056A>G	c.(1054-1056)aaA>aaG	p.K352K	EXD1_ENST00000458580.2_Silent_p.K410K	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	352							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						ATAAGAAGCCTTTGACTTTCT	0.388																																																0			15											130	141	137					15																	41476618		2203	4300	6503	39263910	SO:0001819	synonymous_variant	161829			BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"exonuclease 3'-5' domain-like 1"	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.1056A>G	15.37:g.41476618T>C			39263910	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	CCDS10072.1																																																																																				0.388	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		C	41476618	T	C	41476618	2	2	89	1	0	0	0	0	0	0	0	1	5310	1606	56	4		4	EXD1	15	41476618	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	6947606	41476618	61054774	125	24537										
TTBK2	146057	hgsc.bcm.edu	37	chr15	43045188	43045188	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agttcttttggtcccaggtcTtgagatttgttactttctct	8	8	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:43045188T>G	ENST00000267890.6	-	14	2364	c.2256A>C	c.(2254-2256)caA>caC	p.Q752H		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	752					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GTCCCAGGTCTTGAGATTTGT	0.413																																																0			15											207	195	199					15																	43045188		1854	4096	5950	40832480	SO:0001583	missense	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.2256A>C	15.37:g.43045188T>G	ENSP00000267890:p.Gln752His		40832480	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787457	0.31593	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.39056	1.1	5.64	3.22	0.36961	.	1.308940	0.04923	N	0.455412	T	0.38108	0.1028	L	0.54323	1.7	0.80722	D	1	B;B	0.14438	0.01;0.006	B;B	0.11329	0.006;0.003	T	0.53401	-0.8444	10	0.87932	D	0	.	1.6716	0.02813	0.1378:0.1603:0.1432:0.5587	.	683;752	Q6IQ55-2;Q6IQ55	.;TTBK2_HUMAN	H	752;682;1157	ENSP00000267890:Q752H	ENSP00000263802:Q1157H	Q	-	3	2	TTBK2	40832480	0.956000	0.32656	1.000000	0.80357	0.985000	0.73830	0.479000	0.22228	0.975000	0.38392	0.482000	0.46254	CAA		0.413	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		G	43045188	T	G	43045188	3	3	89	1	0	0	0	0	1	0	0	0	16717	1606	56	4	1486	4	TTBK2	15	43045188	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	1568570	43045188	59486204	126	24538										
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50264940	50264940	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttcgagaataatacatcttcCggtcccagtttataaaataa	5	8	1	1	rs370938976		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:50264940C>T	ENST00000284509.6	-	13	1223	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	ATP8B4_ENST00000559829.1_Missense_Mutation_p.R361Q	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	361						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		ATACATCTTCCGGTCCCAGTT	0.393																																																0			15						C	GLN/ARG	0,4392		0,0,2196	68	66	67		1082	4.1	1	15		67	1,8589	1.2+/-3.3	0,1,4294	no	missense	ATP8B4	NM_024837.2	43	0,1,6490	TT,TC,CC		0.0116,0.0,0.0077	benign	361/1193	50264940	1,12981	2196	4295	6491	48052232	SO:0001583	missense	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1082G>A	15.37:g.50264940C>T	ENSP00000284509:p.Arg361Gln		48052232	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322647	0.23994	0.0	1.16E-4	ENSG00000104043	ENST00000284509	T	0.62788	-0.0	4.99	4.07	0.47477	.	0.305435	0.29892	N	0.010928	T	0.50326	0.1609	L	0.45285	1.41	0.33279	D	0.561996	B	0.18741	0.03	B	0.17979	0.02	T	0.54282	-0.8317	10	0.15066	T	0.55	.	11.1627	0.48524	0.0:0.909:0.0:0.0909	.	361	Q8TF62	AT8B4_HUMAN	Q	361	ENSP00000284509:R361Q	ENSP00000284509:R361Q	R	-	2	0	ATP8B4	48052232	0.004000	0.15560	1.000000	0.80357	0.993000	0.82548	0.265000	0.18515	1.093000	0.41377	0.650000	0.86243	CGG		0.393	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		T	50264940	C	T	50264940	3	4	89	1	0	0	0	0	1	0	0	0	1198	652	23	1	2560	1	ATP8B4	15	50264940	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	7219752	50264940	52266452	127	24539										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52681443	52681443	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aagcttccttactttgtcagCaaaatgttggatgatgaaag	9	6	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:52681443C>A	ENST00000399231.3	-	13	1903	c.1660G>T	c.(1660-1662)Gct>Tct	p.A554S	MYO5A_ENST00000356338.6_Missense_Mutation_p.A554S|MYO5A_ENST00000553916.1_Missense_Mutation_p.A554S|MYO5A_ENST00000399233.2_Missense_Mutation_p.A554S|MYO5A_ENST00000358212.6_Missense_Mutation_p.A554S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	554	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ACTTTGTCAGCAAAATGTTGG	0.343																																																0			15											102	92	95					15																	52681443		1824	4075	5899	50468735	SO:0001583	missense	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1660G>T	15.37:g.52681443C>A	ENSP00000382177:p.Ala554Ser		50468735	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	C	34	5.345692	0.95807	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08	5.78	5.78	0.91487	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.97185	0.9080	M	0.93328	3.405	0.80722	D	1	D;D	0.69078	0.997;0.992	D;P	0.70935	0.971;0.863	D	0.96766	0.9565	10	0.45353	T	0.12	.	20.0137	0.97470	0.0:1.0:0.0:0.0	.	554;554	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	S	554;88;554;554;554;184;554	ENSP00000382177:A554S;ENSP00000382179:A554S;ENSP00000348693:A554S;ENSP00000350945:A554S;ENSP00000451109:A554S	ENSP00000348693:A554S	A	-	1	0	MYO5A	50468735	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.734000	0.93682	0.563000	0.77884	GCT		0.343	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		A	52681443	C	A	52681443	3	1	89	1	0	0	0	0	1	0	0	0	10108	710	25	2	4023	2	MYO5A	15	52681443	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	2416503	52681443	49849949	128	24540										
GTF2A2	2958	hgsc.bcm.edu	37	chr15	59931352	59931352	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cattctgtagtattggagccAgtatctaggaaacaaaagag	10	6	2	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:59931352A>G	ENST00000396060.2	-	5	490	c.309T>C	c.(307-309)acT>acC	p.T103T	GTF2A2_ENST00000484743.1_Silent_p.T68T|GTF2A2_ENST00000267869.4_5'UTR|GTF2A2_ENST00000396064.3_Missense_Mutation_p.L61P|GTF2A2_ENST00000396063.1_Silent_p.T103T|GTF2A2_ENST00000396061.1_Silent_p.T103T	NM_004492.2	NP_004483.1	P52657	T2AG_HUMAN	general transcription factor IIA, 2, 12kDa	103					gene expression (GO:0010467)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(2)|kidney(2)|lung(1)	5						TATTGGAGCCAGTATCTAGGA	0.279																																																0			15											51	57	55					15																	59931352		2188	4289	6477	57718644	SO:0001819	synonymous_variant	2958			BC001919	CCDS10173.1	15q21.3	2010-03-23	2002-08-29		ENSG00000140307	ENSG00000140307		"General transcription factors"	4647	protein-coding gene	gene with protein product		600519	"general transcription factor IIA, 2 (12kD subunit)"			7958899	Standard	NM_004492		Approved	TFIIA, HsT18745	uc002agg.3	P52657	OTTHUMG00000132725	ENST00000396060.2:c.309T>C	15.37:g.59931352A>G			57718644	A8MYQ7|Q6FGB5	Silent	SNP	ENST00000396060.2	37	CCDS10173.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291338	0.40494	.	.	ENSG00000140307	ENST00000396064	.	.	.	5.97	3.58	0.41010	.	.	.	.	.	T	0.56717	0.2004	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50947	-0.8767	5	0.39692	T	0.17	-53.0632	6.0228	0.19638	0.7205:0.1384:0.1411:0.0	.	.	.	.	P	61	.	ENSP00000379376:L61P	L	-	2	0	GTF2A2	57718644	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.315000	0.33608	0.456000	0.26937	0.533000	0.62120	CTG		0.279	GTF2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256067.2	NM_004492		G	59931352	A	G	59931352	2	3	89	1	0	0	0	0	0	0	0	1	6875	175	7	4		4	GTF2A2	15	59931352	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	7249909	59931352	42600040	129	24541										
NARG2	79664	hgsc.bcm.edu	37	chr15	60734670	60734670	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tcagtccataagcgacaaagTtcactttcagtcagagcttc	7	11	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:60734670T>C	ENST00000261520.4	-	12	2604	c.2370A>G	c.(2368-2370)gaA>gaG	p.E790E	NARG2_ENST00000439632.1_Silent_p.E653E	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						AGCGACAAAGTTCACTTTCAG	0.318																																																0			15											91	81	84					15																	60734670		2203	4300	6503	58521962	SO:0001819	synonymous_variant	79664																														ENST00000261520.4:c.2370A>G	15.37:g.60734670T>C			58521962		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																				0.318	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			C	60734670	T	C	60734670	2	2	89	1	0	0	0	0	0	0	0	1	10199	1722	60	4		4	NARG2	15	60734670	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	803318	60734670	41796722	130	24542										
PARP6	56965	hgsc.bcm.edu	37	chr15	72559093	72559093	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatgtaacctcacctgaacgCcatagagaaattcctctgat	7	11	2	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:72559093C>G	ENST00000569795.1	-	4	761	c.74G>C	c.(73-75)gGc>gCc	p.G25A	PARP6_ENST00000413097.2_5'UTR|CELF6_ENST00000569547.1_3'UTR|PARP6_ENST00000287196.9_Missense_Mutation_p.G25A|PARP6_ENST00000260376.7_Missense_Mutation_p.G25A			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	25							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CACCTGAACGCCATAGAGAAA	0.458																																																0			15											157	160	159					15																	72559093		1903	4125	6028	70346147	SO:0001583	missense	56965			AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.74G>C	15.37:g.72559093C>G	ENSP00000456348:p.Gly25Ala		70346147	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	37	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	C	27.5	4.839272	0.91117	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000336471	.	.	.	5.78	4.87	0.63330	.	0.048178	0.85682	D	0.000000	T	0.65386	0.2686	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.969	T	0.68784	-0.5317	9	0.66056	D	0.02	-24.4592	13.8865	0.63712	0.0:0.9271:0.0:0.0729	.	25;25	Q0VDG0;Q2NL67	.;PARP6_HUMAN	A	25	.	ENSP00000260376:G25A	G	-	2	0	PARP6	70346147	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.106000	0.77039	1.454000	0.47793	0.655000	0.94253	GGC		0.458	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		G	72559093	C	G	72559093	3	3	89	1	0	0	0	0	1	0	0	0	11495	739	26	5	1902	5	PARP6	15	72559093	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	11824423	72559093	29972299	131	24543										
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78893715	78893715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcatcaacagattcagaactAgagcttctcgtgaggttagc	10	9	3	4			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:78893715A>G	ENST00000326828.5	-	5	1653	c.1269T>C	c.(1267-1269)tcT>tcC	p.S423S	CHRNA3_ENST00000348639.3_Silent_p.S423S	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	423					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	ATTCAGAACTAGAGCTTCTCG	0.473																																																0			15											159	145	150					15																	78893715		2196	4293	6489	76680770	SO:0001819	synonymous_variant	1136				CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1269T>C	15.37:g.78893715A>G			76680770	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																				0.473	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			G	78893715	A	G	78893715	2	3	89	1	0	0	0	0	0	0	0	1	3390	407	15	4		4	CHRNA3	15	78893715	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	6334622	78893715	23637677	132	24544										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85478562	85478562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gtgccctcagctcatctgctCctacatcctgcggcctgtag	9	16	3	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:85478562C>T	ENST00000286749.3	+	14	1484	c.1394C>T	c.(1393-1395)tCc>tTc	p.S465F	SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Missense_Mutation_p.S465F|SLC28A1_ENST00000394573.1_Missense_Mutation_p.S465F|SLC28A1_ENST00000537624.1_Missense_Mutation_p.S465F			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	465					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CTCATCTGCTCCTACATCCTG	0.617																																																0			15											104	83	90					15																	85478562		2203	4299	6502	83279566	SO:0001583	missense	9154			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1394C>T	15.37:g.85478562C>T	ENSP00000286749:p.Ser465Phe		83279566	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070346	0.55539	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.08193	3.12;3.12;3.12;3.12	5.12	5.12	0.69794	Na dependent nucleoside transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	M	0.85945	2.785	0.80722	D	1	B;B;B	0.34399	0.452;0.136;0.245	B;B;B	0.39771	0.309;0.292;0.309	T	0.01349	-1.1378	10	0.72032	D	0.01	-9.3519	16.1077	0.81236	0.0:1.0:0.0:0.0	.	465;465;465	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	F	465	ENSP00000440546:S465F;ENSP00000444700:S465F;ENSP00000286749:S465F;ENSP00000378074:S465F	ENSP00000286749:S465F	S	+	2	0	SLC28A1	83279566	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	7.350000	0.79385	2.663000	0.90544	0.400000	0.26472	TCC		0.617	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85478562	C	T	85478562	3	4	89	1	0	0	0	0	1	0	0	0	14568	855	30	3	1515	3	SLC28A1	15	85478562	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6584847	85478562	17052830	133	24545										
ABHD2	11057	hgsc.bcm.edu	37	chr15	89719204	89719204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tcctgtgctgcgtcagcgtgTgccaggggtacagtgcactg	15	11	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:89719204T>C	ENST00000352732.5	+	6	1220	c.700T>C	c.(700-702)Tgc>Cgc	p.C234R	ABHD2_ENST00000355100.3_Missense_Mutation_p.C234R|ABHD2_ENST00000565973.1_Missense_Mutation_p.C234R	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	234					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					CGTCAGCGTGTGCCAGGGGTA	0.552																																					Colon(11;252 417 24570 33239 41878)											0			15											119	101	107					15																	89719204		2200	4299	6499	87520208	SO:0001583	missense	11057			X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"Abhydrolase domain containing"	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.700T>C	15.37:g.89719204T>C	ENSP00000268129:p.Cys234Arg		87520208	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195114	0.78902	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.42900	0.96;0.96	5.55	5.55	0.83447	Alpha/beta hydrolase fold-1 (1);	0.000000	0.85682	D	0.000000	T	0.66046	0.2750	M	0.76838	2.35	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.70630	-0.4819	10	0.72032	D	0.01	-0.6583	15.6965	0.77502	0.0:0.0:0.0:1.0	.	234	P08910	ABHD2_HUMAN	R	234	ENSP00000268129:C234R;ENSP00000347217:C234R	ENSP00000268129:C234R	C	+	1	0	ABHD2	87520208	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.179000	0.71974	2.095000	0.63458	0.523000	0.50628	TGC		0.552	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			C	89719204	T	C	89719204	3	2	89	1	0	0	0	0	1	0	0	0	82	1696	59	4	714	4	ABHD2	15	89719204	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	4240642	89719204	12812188	134	24546										
TARSL2	123283	hgsc.bcm.edu	37	chr15	102226160	102226160	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttttcaatctcaaaggtaaAcatgttctcgctgtaatgct	6	9	3	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr15:102226160A>G	ENST00000335968.3	-	11	1642	c.1426T>C	c.(1426-1428)Ttt>Ctt	p.F476L	snoU13_ENST00000458877.1_RNA	NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	476					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCAAAGGTAAACATGTTCTCG	0.463																																																0			15											158	145	150					15																	102226160		2203	4300	6503	100043683	SO:0001583	missense	123283			AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.1426T>C	15.37:g.102226160A>G	ENSP00000338093:p.Phe476Leu		100043683	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	A	32	5.182043	0.94885	.	.	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	T;T	0.69175	-0.38;-0.38	5.82	5.82	0.92795	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.89079	0.6613	H	0.98701	4.305	0.80722	D	1	D;D	0.89917	1.0;0.966	D;D	0.97110	1.0;0.91	D	0.93050	0.6465	10	0.87932	D	0	-20.4604	14.1334	0.65270	1.0:0.0:0.0:0.0	.	476;381	A2RTX5;A2RTX5-2	SYTC2_HUMAN;.	L	476;381;476	ENSP00000338093:F476L;ENSP00000439899:F476L	ENSP00000329291:F381L	F	-	1	0	TARSL2	100043683	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.103000	0.94232	2.234000	0.73211	0.533000	0.62120	TTT		0.463	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334		G	102226160	A	G	102226160	3	3	89	1	0	0	0	0	1	0	0	0	15600	43	2	4	1018	4	TARSL2	15	102226160	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	12506956	102226160	305232	135	24547										
ACSM5	54988	hgsc.bcm.edu	37	chr16	20448652	20448652	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcatcctgctgtcctggagtCggctgtggtcagcagcccag	14	13	1	0	rs533116284	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr16:20448652C>T	ENST00000331849.4	+	12	1646	c.1499C>T	c.(1498-1500)tCg>tTg	p.S500L	CTD-2194A8.2_ENST00000574654.1_RNA	NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	500					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GTCCTGGAGTCGGCTGTGGTC	0.567													C|||	2	0.000399361	0	0	5008	,	,		17823	0		0	False		,,,				2504	0.002															0			16											57	58	58					16																	20448652		2203	4300	6503	20356153	SO:0001583	missense	54988				CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"Acyl-CoA synthetase family"	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1499C>T	16.37:g.20448652C>T	ENSP00000327916:p.Ser500Leu		20356153	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824155	0.71143	.	.	ENSG00000183549	ENST00000331849	T	0.57436	0.4	4.89	2.82	0.32997	AMP-dependent synthetase/ligase (1);	0.222920	0.31909	N	0.006877	T	0.65852	0.2731	M	0.87180	2.865	0.33374	D	0.573922	P	0.43909	0.821	P	0.48189	0.57	T	0.79463	-0.1793	10	0.87932	D	0	-4.9349	14.0894	0.64980	0.0:0.7265:0.2735:0.0	.	500	Q6NUN0	ACSM5_HUMAN	L	500	ENSP00000327916:S500L	ENSP00000327916:S500L	S	+	2	0	ACSM5	20356153	0.969000	0.33509	0.981000	0.43875	0.736000	0.42039	2.313000	0.43735	0.516000	0.28340	0.650000	0.86243	TCG		0.567	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888		T	20448652	C	T	20448652	3	4	89	1	0	0	0	0	1	0	0	0	187	893	31	1	1541	1	ACSM5	16	20448652	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10		20448652	69906101	136	24548										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23205522	23205522	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttttccaccacccgatgcaTgggaattgctatactttcaa	6	12	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr16:23205522T>C	ENST00000300061.2	+	5	983	c.840T>C	c.(838-840)caT>caC	p.H280H	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	280					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	ACCCGATGCATGGGAATTGCT	0.488																																																0			16											114	109	110					16																	23205522		2197	4300	6497	23113023	SO:0001819	synonymous_variant	6340			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.840T>C	16.37:g.23205522T>C			23113023	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	37	CCDS10608.1																																																																																				0.488	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		C	23205522	T	C	23205522	2	2	89	1	0	0	0	0	0	0	0	1	13967	1461	51	4		4	SCNN1G	16	23205522	Silent	SNP	T	TCGA-CI-6622-01A-11D-1826-10	2756870	23205522	67149231	137	24549										
CPNE2	221184	hgsc.bcm.edu	37	chr16	57144699	57144699	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gccccagcagcgggggcagcCcccatgggcccccagtattg	14	17	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr16:57144699C>T	ENST00000535318.2	+	3	406	c.45C>T	c.(43-45)gcC>gcT	p.A15A	CPNE2_ENST00000565874.1_Silent_p.A15A|CPNE2_ENST00000290776.8_Silent_p.A15A|CPNE2_ENST00000537605.1_5'UTR			Q96FN4	CPNE2_HUMAN	copine II	15	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				CGGGGGCAGCCCCCATGGGCC	0.647																																																0			16											39	35	36					16																	57144699		2198	4299	6497	55702200	SO:0001819	synonymous_variant	221184				CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.45C>T	16.37:g.57144699C>T			55702200	Q68D19|Q719H8|Q86XP9	Silent	SNP	ENST00000535318.2	37	CCDS10774.1																																																																																				0.647	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		T	57144699	C	T	57144699	2	4	89	1	0	0	0	0	0	0	0	1	3818	610	22	3		3	CPNE2	16	57144699	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	33939177	57144699	33210054	138	24550										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70891663	70891663	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttcagagagatgagaggttcGgtagttttgcctaccagcag	13	7	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr16:70891663G>A	ENST00000393567.2	-	72	12390	c.12240C>T	c.(12238-12240)acC>acT	p.T4080T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4080					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGAGAGGTTCGGTAGTTTTGC	0.478																																																0			16											144	165	158					16																	70891663		1983	4179	6162	69449164	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12240C>T	16.37:g.70891663G>A			69449164	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.478	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70891663	G	A	70891663	2	1	89	1	0	0	0	0	0	0	0	1	7488	1103	39	1		1	HYDIN	16	70891663	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	13746964	70891663	19463090	139	24551										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77465417	77465417	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	agggagcttctggcattctgCgccgatcgctttttcctgcc	11	13	2	0	rs142460481	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr16:77465417C>T	ENST00000282849.5	-	3	688	c.270G>A	c.(268-270)gcG>gcA	p.A90A	ADAMTS18_ENST00000567121.1_5'UTR|RP11-449J10.1_ENST00000564358.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	90					eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TGGCATTCTGCGCCGATCGCT	0.478													C|||	4	0.000798722	0.003	0	5008	,	,		18853	0		0	False		,,,				2504	0															0			16						C		17,4379	24.3+/-50.5	0,17,2181	188	193	191		270	-9.1	0	16	dbSNP_134	191	0,8600		0,0,4300	no	coding-synonymous	ADAMTS18	NM_199355.2		0,17,6481	TT,TC,CC		0.0,0.3867,0.1308		90/1222	77465417	17,12979	2198	4300	6498	76022918	SO:0001819	synonymous_variant	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.270G>A	16.37:g.77465417C>T			76022918	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																				0.478	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77465417	C	T	77465417	2	4	89	1	0	0	0	0	0	0	0	1	263	755	27	1		1	ADAMTS18	16	77465417	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6573754	77465417	12889336	140	24552										
TP53	7157	hgsc.bcm.edu	37	chr17	7574011	7574011	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cattcagctctcggaacatcTcgaagcgctcacgcccacgg	9	16	4	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr17:7574011T>C	ENST00000269305.4	-	10	1205	c.1016A>G	c.(1015-1017)gAg>gGg	p.E339G	TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.E339G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	339	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		E -> K (in a sporadic cancer; somatic mutation; dbSNP:rs17882252). {ECO:0000269|Ref.12}.|E -> Q (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.F338_E339>L(1)|p.I332fs*5(1)|p.?(1)|p.F338fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGAACATCTCGAAGCGCTC	0.537		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	12	Whole gene deletion(8)|Unknown(2)|Deletion - Frameshift(2)	bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|pancreas(2)|large_intestine(1)|stomach(1)	17											61	47	52					17																	7574011		2203	4300	6503	7514736	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1016A>G	17.37:g.7574011T>C	ENSP00000269305:p.Glu339Gly		7514736	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.886244	0.72410	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.96856	-4.15;-4.15	5.43	4.36	0.52297	p53, tetramerisation domain (3);	0.053822	0.64402	D	0.000001	D	0.97567	0.9203	M	0.87617	2.895	0.49687	D	0.999817	D	0.53312	0.959	P	0.59825	0.864	D	0.97202	0.9865	10	0.87932	D	0	-17.4901	9.4308	0.38608	0.0:0.0847:0.0:0.9153	.	339	P04637	P53_HUMAN	G	339;339;328	ENSP00000269305:E339G;ENSP00000391478:E339G	ENSP00000269305:E339G	E	-	2	0	TP53	7514736	1.000000	0.71417	0.943000	0.38184	0.483000	0.33249	4.976000	0.63785	0.903000	0.36546	0.459000	0.35465	GAG		0.537	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7574011	T	C	7574011	3	2	89	1	0	0	0	0	1	0	0	0	16421	1551	54	4	173	4	TP53	17	7574011	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10		7574011	73621199	141	24553										
NF1	4763	hgsc.bcm.edu	37	chr17	29654736	29654736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctatcattcatatccggaccCgctgggaactgtcacagccc	8	15	3	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr17:29654736C>T	ENST00000358273.4	+	38	5871	c.5488C>T	c.(5488-5490)Cgc>Tgc	p.R1830C	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Missense_Mutation_p.R1809C	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1830	Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.R1830C(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TATCCGGACCCGCTGGGAACT	0.512			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17	GRCh37	CM077948	NF1	M							122	117	119					17																	29654736		2203	4300	6503	26678862	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5488C>T	17.37:g.29654736C>T	ENSP00000351015:p.Arg1830Cys		26678862	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423947	0.83667	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.96885	-4.16;-4.16;-4.16	5.8	4.76	0.60689	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.98163	0.9393	M	0.85945	2.785	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.986;0.999	D	0.98771	1.0728	10	0.87932	D	0	.	16.746	0.85471	0.1376:0.8624:0.0:0.0	.	859;1809;1830	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	C	1830;1809;1475	ENSP00000351015:R1830C;ENSP00000348498:R1809C;ENSP00000389907:R1475C	ENSP00000348498:R1809C	R	+	1	0	NF1	26678862	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	3.737000	0.55060	2.733000	0.93635	0.650000	0.86243	CGC		0.512	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29654736	C	T	29654736	3	4	89	1	0	0	0	0	1	0	0	0	10387	652	23	1	5699	1	NF1	17	29654736	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	22080725	29654736	51540474	142	24554										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42340079	42340079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctccagattctcctccatcaTgtcttcataatcatcctgtg	4	14	5	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr17:42340079T>C	ENST00000262418.6	-	3	186	c.31A>G	c.(31-33)Atg>Gtg	p.M11V	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	11				M -> D (in Ref. 9; AA sequence). {ECO:0000305}.	anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TCCTCCATCATGTCTTCATAA	0.592																																																0			17											99	90	93					17																	42340079		2203	4300	6503	39695605	SO:0001583	missense	6521				CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.31A>G	17.37:g.42340079T>C	ENSP00000262418:p.Met11Val		39695605	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	t	6.128	0.391765	0.11581	.	.	ENSG00000004939	ENST00000262418	T	0.73047	-0.71	5.01	-1.99	0.07457	.	5.991140	0.00166	N	0.000003	T	0.40171	0.1106	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26360	-1.0105	10	0.28530	T	0.3	.	4.6905	0.12778	0.0:0.3893:0.2788:0.3319	.	11;11	E2RVJ0;P02730	.;B3AT_HUMAN	V	11	ENSP00000262418:M11V	ENSP00000262418:M11V	M	-	1	0	SLC4A1	39695605	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.188000	0.09642	-0.657000	0.05373	-0.252000	0.11476	ATG		0.592	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		C	42340079	T	C	42340079	3	2	89	1	0	0	0	0	1	0	0	0	14687	1464	51	4	2776	4	SLC4A1	17	42340079	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	12685343	42340079	38855131	143	24555										
MBTD1	54799	hgsc.bcm.edu	37	chr17	49272710	49272710	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gatcccaatcatcaggaatcCgtcagctagcaccttttcaa	6	13	4	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr17:49272710C>A	ENST00000586178.1	-	13	1580	c.1237G>T	c.(1237-1239)Gga>Tga	p.G413*	MBTD1_ENST00000415868.1_Nonsense_Mutation_p.G413*|MBTD1_ENST00000376381.2_Intron	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	413					chromatin modification (GO:0016568)|embryonic skeletal system development (GO:0048706)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			ATCAGGAATCCGTCAGCTAGC	0.388																																																0			17											99	85	90					17																	49272710		2203	4300	6503	46627709	SO:0001587	stop_gained	54799			AK000062	CCDS11581.2	17q24.1	2003-01-15			ENSG00000011258	ENSG00000011258			19866	protein-coding gene	gene with protein product							Standard	NM_017643		Approved	SA49P01, FLJ20055	uc002itr.4	Q05BQ5	OTTHUMG00000150442	ENST00000586178.1:c.1237G>T	17.37:g.49272710C>A	ENSP00000468304:p.Gly413*		46627709	Q6ZVU7|Q9NXU1	Nonsense_Mutation	SNP	ENST00000586178.1	37	CCDS11581.2	.	.	.	.	.	.	.	.	.	.	C	37	6.384318	0.97524	.	.	ENSG00000011258	ENST00000405860;ENST00000415868	.	.	.	5.51	5.51	0.81932	.	0.053226	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.756	0.96291	0.0:1.0:0.0:0.0	.	.	.	.	X	413	.	ENSP00000386072:G413X	G	-	1	0	MBTD1	46627709	1.000000	0.71417	0.967000	0.41034	0.792000	0.44763	7.769000	0.85360	2.735000	0.93741	0.643000	0.83706	GGA		0.388	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			A	49272710	C	A	49272710	4	1	89	1	0	0	0	0	0	1	0	0	9390	661	23	2	669	2	MBTD1	17	49272710	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6932631	49272710	31922500	144	24556										
SOX9	6662	hgsc.bcm.edu	37	chr17	70120229	70120229	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccagccactacagcgagcagCagcagcactcgccccaacag	9	18	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr17:70120229C>T	ENST00000245479.2	+	3	1603	c.1231C>T	c.(1231-1233)Cag>Tag	p.Q411*		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	411					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CAGCGAGCAGCAGCAGCACTC	0.647																																					Pancreas(42;83 1041 2320 35205 39456)											0			17											194	181	186					17																	70120229		2203	4300	6503	67631824	SO:0001587	stop_gained	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.1231C>T	17.37:g.70120229C>T	ENSP00000245479:p.Gln411*		67631824	Q53Y80	Nonsense_Mutation	SNP	ENST00000245479.2	37	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	41	9.080138	0.99059	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	.	.	.	4.17	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	15.2649	0.73654	0.0:1.0:0.0:0.0	.	.	.	.	X	411;347	.	ENSP00000245479:Q411X	Q	+	1	0	SOX9	67631824	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.776000	0.47709	1.865000	0.54081	0.455000	0.32223	CAG		0.647	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70120229	C	T	70120229	4	4	89	1	0	0	0	0	0	1	0	0	14995	711	25	3	1241	3	SOX9	17	70120229	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	20847519	70120229	11074981	145	24557										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3188881	3188881	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgcctggatgccgtggactgCctggatgccgtggactgctt	15	11	0	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr18:3188881C>T	ENST00000356443.4	-	4	969	c.636G>A	c.(634-636)agG>agA	p.R212R	MYOM1_ENST00000261606.7_Silent_p.R212R|RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000400569.3_Silent_p.R212R	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	212	6 X 6 AA tandem repeats.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R212R(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCGTGGACTGCCTGGATGCCG	0.522																																																1	Substitution - coding silent(1)	central_nervous_system(1)	18											258	241	246					18																	3188881		2045	4187	6232	3178881	SO:0001819	synonymous_variant	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.636G>A	18.37:g.3188881C>T			3178881	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																				0.522	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3188881	C	T	3188881	2	4	89	1	0	0	0	0	0	0	0	1	10121	738	26	3		3	MYOM1	18	3188881	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10		3188881	74888367	146	24558										
INO80C	125476	hgsc.bcm.edu	37	chr18	33048591	33048591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gggctcagggaacgatgctcGtggccttcctcagggccagg	16	12	2	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr18:33048591G>A	ENST00000334598.7	-	5	679	c.563C>T	c.(562-564)aCg>aTg	p.T188M	INO80C_ENST00000590757.1_Missense_Mutation_p.T91M|INO80C_ENST00000586489.1_Missense_Mutation_p.T133M|INO80C_ENST00000592173.1_Intron|RP11-322E11.6_ENST00000589258.1_Intron|RP11-322E11.5_ENST00000591141.1_lincRNA|INO80C_ENST00000441607.2_Missense_Mutation_p.T224M	NM_194281.3	NP_919257.2	Q6PI98	IN80C_HUMAN	INO80 complex subunit C	188					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)				central_nervous_system(1)|endometrium(1)|lung(3)|prostate(2)|skin(1)	8						AACGATGCTCGTGGCCTTCCT	0.522																																																0			18											121	125	124					18																	33048591		2203	4300	6503	31302589	SO:0001583	missense	125476				CCDS11914.1, CCDS45853.1	18q12.2	2011-07-06	2008-08-07	2008-08-07	ENSG00000153391	ENSG00000153391		"INO80 complex subunits"	26994	protein-coding gene	gene with protein product	"IES6 homolog (S. cerevisiae)"		"chromosome 18 open reading frame 37"	C18orf37		16230350	Standard	NM_001098817		Approved	FLJ38183, hIes6, IES6	uc010dmt.3	Q6PI98	OTTHUMG00000132564	ENST00000334598.7:c.563C>T	18.37:g.33048591G>A	ENSP00000334473:p.Thr188Met		31302589	B4DUI4|E9PCS7|Q86WR1|Q8N994	Missense_Mutation	SNP	ENST00000334598.7	37	CCDS11914.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615070	0.87359	.	.	ENSG00000153391	ENST00000441607;ENST00000334598	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	T	0.75436	0.3849	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.951	T	0.76143	-0.3067	8	0.54805	T	0.06	.	16.7354	0.85445	0.0:0.0:1.0:0.0	.	224;188	E9PCS7;Q6PI98	.;IN80C_HUMAN	M	224;188	.	ENSP00000334473:T188M	T	-	2	0	INO80C	31302589	1.000000	0.71417	0.972000	0.41901	0.915000	0.54546	9.407000	0.97325	2.615000	0.88500	0.557000	0.71058	ACG		0.522	INO80C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255768.1	NM_194281		A	33048591	G	A	33048591	3	1	89	1	0	0	0	0	1	0	0	0	7769	1145	40	1	19	1	INO80C	18	33048591	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	29859710	33048591	45028657	147	24559										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61067847	61067847	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgaaaaaaatgttgagttgtTggcttctgttgctacagctt	10	5	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr18:61067847T>C	ENST00000238497.5	-	6	777	c.574A>G	c.(574-576)Aac>Gac	p.N192D	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	192					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						GTTGAGTTGTTGGCTTCTGTT	0.373																																																0			18											129	127	128					18																	61067847		2203	4300	6503	59218827	SO:0001583	missense	9525			AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.574A>G	18.37:g.61067847T>C	ENSP00000238497:p.Asn192Asp		59218827	Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	37	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.681649	0.47991	.	.	ENSG00000119541	ENST00000238497	D	0.92965	-3.14	6.11	6.11	0.99139	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.85221	0.5647	N	0.14661	0.345	0.80722	D	1	B;B;B	0.15141	0.012;0.012;0.012	B;B;B	0.26202	0.067;0.067;0.067	T	0.80464	-0.1371	10	0.09590	T	0.72	-28.0479	16.7021	0.85357	0.0:0.0:0.0:1.0	.	192;192;192	A8K5D8;A8K4G7;O75351	.;.;VPS4B_HUMAN	D	192	ENSP00000238497:N192D	ENSP00000238497:N192D	N	-	1	0	VPS4B	59218827	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.953000	0.87836	2.343000	0.79666	0.533000	0.62120	AAC		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		C	61067847	T	C	61067847	3	2	89	1	0	0	0	0	1	0	0	0	17253	1812	63	4	784	4	VPS4B	18	61067847	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	28019256	61067847	17009401	148	24560										
NETO1	81832	hgsc.bcm.edu	37	chr18	70526174	70526174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgacaggtggattttgttgtCcacagaaacgtccaattatt	9	7	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr18:70526174C>T	ENST00000327305.6	-	4	1013	c.356G>A	c.(355-357)gGa>gAa	p.G119E	NETO1_ENST00000397929.1_Missense_Mutation_p.G118E|NETO1_ENST00000583169.1_Missense_Mutation_p.G119E|NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Missense_Mutation_p.G118E	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	119	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ATTTTGTTGTCCACAGAAACG	0.383																																																0			18											92	92	92					18																	70526174		2203	4300	6503	68677154	SO:0001583	missense	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.356G>A	18.37:g.70526174C>T	ENSP00000313088:p.Gly119Glu		68677154	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	C	32	5.111966	0.94339	.	.	ENSG00000166342	ENST00000327305;ENST00000299430;ENST00000397929	T;T;T	0.64991	-0.13;-0.13;-0.13	5.35	5.35	0.76521	CUB (5);	0.000000	0.64402	D	0.000017	D	0.85669	0.5750	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.89354	0.3663	10	0.87932	D	0	-16.2312	19.438	0.94806	0.0:1.0:0.0:0.0	.	118;118;119	Q8TDF5-1;Q8TDF5-2;Q8TDF5	.;.;NETO1_HUMAN	E	119;118;118	ENSP00000313088:G119E;ENSP00000299430:G118E;ENSP00000381024:G118E	ENSP00000299430:G118E	G	-	2	0	NETO1	68677154	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.724000	0.84798	2.672000	0.90937	0.655000	0.94253	GGA		0.383	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70526174	C	T	70526174	3	4	89	1	0	0	0	0	1	0	0	0	10370	855	30	3	1282	3	NETO1	18	70526174	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	9458327	70526174	7551074	149	24561										
ODF3L2	284451	hgsc.bcm.edu	37	chr19	464316	464316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gtgtccgatggcgcacagggGgcaccttctctgggctgtag	16	11	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:464316G>A	ENST00000315489.4	-	4	633	c.398C>T	c.(397-399)cCc>cTc	p.P133L	ODF3L2_ENST00000382696.3_Missense_Mutation_p.P97L	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	133	Pro-rich.					cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						GCGCACAGGGGGCACCTTCTC	0.667																																																0			19											7	8	8					19																	464316		1778	3456	5234	415316	SO:0001583	missense	284451			AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 19"	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.398C>T	19.37:g.464316G>A	ENSP00000318029:p.Pro133Leu		415316	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	37	CCDS12027.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.832385	0.32421	.	.	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.44482	1.46;0.92	4.06	4.06	0.47325	.	0.191340	0.45867	D	0.000321	T	0.48169	0.1485	M	0.81341	2.54	0.58432	D	0.999999	P;P	0.47253	0.892;0.573	P;B	0.47376	0.545;0.345	T	0.48269	-0.9050	10	0.33141	T	0.24	-13.9542	7.8069	0.29209	0.1181:0.0:0.8819:0.0	.	97;133	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	L	133;97	ENSP00000318029:P133L;ENSP00000372143:P97L	ENSP00000318029:P133L	P	-	2	0	ODF3L2	415316	1.000000	0.71417	0.998000	0.56505	0.374000	0.29953	6.699000	0.74613	1.836000	0.53414	0.536000	0.68110	CCC		0.667	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577		A	464316	G	A	464316	3	1	89	1	0	0	0	0	1	0	0	0	10863	1232	43	3	475	3	ODF3L2	19	464316	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10		464316	58664667	150	24562										
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6182935	6182935	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttcaaggtcaactcaaaaaaGatgttggggtaggtggagca	13	5	3	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:6182935G>T	ENST00000586696.1	+	9	1356	c.1080G>T	c.(1078-1080)aaG>aaT	p.K360N	ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588485.1_Missense_Mutation_p.K173N|ACSBG2_ENST00000591403.1_Missense_Mutation_p.K360N|ACSBG2_ENST00000252669.5_Missense_Mutation_p.K360N|ACSBG2_ENST00000588304.1_Missense_Mutation_p.K310N			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	360					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACTCAAAAAAGATGTTGGGGT	0.517																																																0			19											79	76	77					19																	6182935		2203	4300	6503	6133935	SO:0001583	missense	81616				CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1080G>T	19.37:g.6182935G>T	ENSP00000465589:p.Lys360Asn		6133935	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	G	6.359	0.434355	0.12045	.	.	ENSG00000130377	ENST00000252669	T	0.17528	2.27	4.8	4.8	0.61643	AMP-dependent synthetase/ligase (1);	0.702299	0.11937	N	0.515166	T	0.26122	0.0637	M	0.64404	1.975	0.28616	N	0.908428	B;P	0.38335	0.142;0.627	B;P	0.44422	0.14;0.449	T	0.08764	-1.0706	10	0.17369	T	0.5	-15.1977	14.5883	0.68344	0.0:0.0:1.0:0.0	.	360;360	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	N	360	ENSP00000252669:K360N	ENSP00000252669:K360N	K	+	3	2	ACSBG2	6133935	0.594000	0.26849	0.217000	0.23759	0.019000	0.09904	0.870000	0.28010	2.197000	0.70478	0.455000	0.32223	AAG		0.517	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		T	6182935	G	T	6182935	3	4	89	1	0	0	0	0	1	0	0	0	174	933	33	2	1110	2	ACSBG2	19	6182935	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	5718619	6182935	52946048	151	24563										
CCDC105	126402	hgsc.bcm.edu	37	chr19	15121876	15121876	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccgcgtggagatgatcaaagGcggcggcaccttggagaagc	16	10	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:15121876G>T	ENST00000292574.3	+	1	321	c.239G>T	c.(238-240)gGc>gTc	p.G80V	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	80						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						ATGATCAAAGGCGGCGGCACC	0.701																																																0			19											8	9	9					19																	15121876		2134	4231	6365	14982876	SO:0001583	missense	126402			AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.239G>T	19.37:g.15121876G>T	ENSP00000292574:p.Gly80Val		14982876	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.683692	0.47991	.	.	ENSG00000160994	ENST00000292574	T	0.17054	2.3	4.03	4.03	0.46877	.	0.000000	0.41396	D	0.000894	T	0.27098	0.0664	L	0.34521	1.04	0.51233	D	0.999918	D	0.76494	0.999	D	0.65010	0.931	T	0.02288	-1.1182	10	0.72032	D	0.01	-21.9406	11.6793	0.51448	0.0:0.0:1.0:0.0	.	80	Q8IYK2	CC105_HUMAN	V	80	ENSP00000292574:G80V	ENSP00000292574:G80V	G	+	2	0	CCDC105	14982876	0.100000	0.21855	0.254000	0.24359	0.303000	0.27691	1.773000	0.38563	1.775000	0.52247	0.462000	0.41574	GGC		0.701	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482		T	15121876	G	T	15121876	3	4	89	1	0	0	0	0	1	0	0	0	2746	1203	42	2	241	2	CCDC105	19	15121876	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	8938941	15121876	44007107	152	24564										
PSG4	5672	hgsc.bcm.edu	37	chr19	43702283	43702283	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tggttttggacagctgcaacCtgtgagtcatagggaggctc	14	8	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:43702283C>A	ENST00000405312.3	-	3	812	c.575G>T	c.(574-576)aGg>aTg	p.R192M	PSG4_ENST00000244295.9_Missense_Mutation_p.R192M|PSG4_ENST00000433626.2_Intron	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	192	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CAGCTGCAACCTGTGAGTCAT	0.507																																																0			19											145	166	159					19																	43702283		2131	4273	6404	48394123	SO:0001583	missense	5672				CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9521	protein-coding gene	gene with protein product	"pregnancy-specific beta-1-glycoprotein 4"	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.575G>T	19.37:g.43702283C>A	ENSP00000384770:p.Arg192Met		48394123	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	c	10.29	1.309344	0.23821	.	.	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000451895	T;T;T	0.12984	2.63;2.63;2.63	1.96	0.848	0.18966	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39809	0.1092	M	0.92077	3.27	0.09310	N	0.999998	D;D;D	0.65815	0.995;0.979;0.985	D;P;D	0.71656	0.974;0.855;0.949	T	0.13818	-1.0495	9	0.87932	D	0	.	5.667	0.17700	0.0:0.8135:0.0:0.1865	.	208;192;192	C9JWP2;Q00888-2;Q00888	.;.;PSG4_HUMAN	M	192;192;208	ENSP00000244295:R192M;ENSP00000384770:R192M;ENSP00000388134:R208M	ENSP00000244295:R192M	R	-	2	0	PSG4	48394123	0.001000	0.12720	0.004000	0.12327	0.000000	0.00434	0.501000	0.22578	0.083000	0.17047	-1.218000	0.01608	AGG		0.507	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		A	43702283	C	A	43702283	3	1	89	1	0	0	0	0	1	0	0	0	12691	681	24	2	700	2	PSG4	19	43702283	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	28580407	43702283	15426700	153	24565										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44980971	44980971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cacactgattacattcatacGgtttttccccagtgtgaatt	6	10	1	2	rs567468606		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:44980971G>A	ENST00000221327.4	-	5	2008	c.1727C>T	c.(1726-1728)cCg>cTg	p.P576L	ZNF180_ENST00000391956.4_Missense_Mutation_p.P551L|ZNF180_ENST00000592529.1_Missense_Mutation_p.P549L|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	576					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P576L(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ACATTCATACGGTTTTTCCCC	0.408													G|||	1	0.000199681	0	0	5008	,	,		21305	0		0	False		,,,				2504	0.001				Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - Missense(1)	ovary(1)	19											104	104	104					19																	44980971		2203	4300	6503	49672811	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1727C>T	19.37:g.44980971G>A	ENSP00000221327:p.Pro576Leu		49672811	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137100	0.77775	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.56444	0.46;0.46	5.66	5.66	0.87406	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41823	D	0.000812	T	0.70055	0.3180	L	0.56340	1.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.71461	-0.4586	10	0.87932	D	0	-14.9646	18.5038	0.90890	0.0:0.0:1.0:0.0	.	551;575;576	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	L	576;551	ENSP00000221327:P576L;ENSP00000375818:P551L	ENSP00000221327:P576L	P	-	2	0	ZNF180	49672811	1.000000	0.71417	0.980000	0.43619	0.876000	0.50452	4.315000	0.59172	2.673000	0.90976	0.591000	0.81541	CCG		0.408	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44980971	G	A	44980971	3	1	89	1	0	0	0	0	1	0	0	0	17787	1116	39	1	355	1	ZNF180	19	44980971	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	1278688	44980971	14148012	154	24566										
ZNF615	284370	hgsc.bcm.edu	37	chr19	52497554	52497554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	acattcagtgcattcataatGtttcagttctgtatgagttc	7	7	4	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:52497554G>A	ENST00000602063.1	-	6	1124	c.775C>T	c.(775-777)Cat>Tat	p.H259Y	ZNF615_ENST00000598071.1_Missense_Mutation_p.H270Y|ZNF615_ENST00000391795.3_Missense_Mutation_p.H264Y|ZNF615_ENST00000594083.1_Missense_Mutation_p.H270Y|ZNF615_ENST00000376716.5_Missense_Mutation_p.H259Y			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	259					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H259Y(1)|p.H270Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CATTCATAATGTTTCAGTTCT	0.398																																																2	Substitution - Missense(2)	ovary(2)	19											160	148	152					19																	52497554		2203	4300	6503	57189366	SO:0001583	missense	284370			AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.775C>T	19.37:g.52497554G>A	ENSP00000473089:p.His259Tyr		57189366	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	G	5.602	0.295863	0.10622	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.07444	3.19;3.19	3.32	1.14	0.20703	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05593	0.0147	N	0.16368	0.405	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.36768	-0.9734	9	0.62326	D	0.03	.	8.0487	0.30564	0.2119:0.0:0.7881:0.0	.	264;266;270;259	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	Y	259;269;264;269	ENSP00000365906:H259Y;ENSP00000375672:H264Y	ENSP00000347019:H269Y	H	-	1	0	ZNF615	57189366	0.000000	0.05858	0.001000	0.08648	0.559000	0.35586	0.654000	0.24918	0.241000	0.21283	0.555000	0.69702	CAT		0.398	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52497554	G	A	52497554	3	1	89	1	0	0	0	0	1	0	0	0	18079	1377	48	3	1424	3	ZNF615	19	52497554	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	7516583	52497554	6631429	155	24567										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55814754	55814754	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cccagctgtgaggaccaggaCctgcctccccggaatgatgt	12	14	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:55814754C>A	ENST00000309383.1	+	11	1381	c.1104C>A	c.(1102-1104)gaC>gaA	p.D368E	BRSK1_ENST00000326848.7_Missense_Mutation_p.D63E|BRSK1_ENST00000590333.1_Missense_Mutation_p.D384E	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	368					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		AGGACCAGGACCTGCCTCCCC	0.572																																																0			19											71	70	71					19																	55814754		2203	4300	6503	60506566	SO:0001583	missense	84446			AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1104C>A	19.37:g.55814754C>A	ENSP00000310649:p.Asp368Glu		60506566	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Missense_Mutation	SNP	ENST00000309383.1	37	CCDS12921.1	.	.	.	.	.	.	.	.	.	.	.	10.37	1.332411	0.24167	.	.	ENSG00000160469	ENST00000309383;ENST00000543410;ENST00000326848	T;T	0.71341	-0.56;1.94	3.96	2.91	0.33838	.	0.000000	0.85682	D	0.000000	T	0.56877	0.2015	L	0.52011	1.625	0.44330	D	0.997218	B;P	0.36110	0.376;0.537	B;B	0.32928	0.145;0.155	T	0.49579	-0.8925	10	0.19147	T	0.46	.	7.7564	0.28927	0.0:0.8001:0.0:0.1999	.	368;384	Q8TDC3;Q8TDC3-2	BRSK1_HUMAN;.	E	368;63;63	ENSP00000310649:D368E;ENSP00000320853:D63E	ENSP00000310649:D368E	D	+	3	2	BRSK1	60506566	0.994000	0.37717	1.000000	0.80357	0.987000	0.75469	0.468000	0.22051	1.021000	0.39600	-0.291000	0.09656	GAC		0.572	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		A	55814754	C	A	55814754	3	1	89	1	0	0	0	0	1	0	0	0	1526	506	18	2	1146	2	BRSK1	19	55814754	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	3317200	55814754	3314229	156	24568										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56490768	56490768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tctgtgtcacaggctggaaaActgcctgttcacctccatct	8	13	4	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:56490768A>G	ENST00000291971.3	+	9	2956	c.2885A>G	c.(2884-2886)aAc>aGc	p.N962S	NLRP8_ENST00000590542.1_Missense_Mutation_p.N943S	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	962					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.N962I(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AGGCTGGAAAACTGCCTGTTC	0.512																																																1	Substitution - Missense(1)	ovary(1)	19											107	102	104					19																	56490768		2203	4300	6503	61182580	SO:0001583	missense	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2885A>G	19.37:g.56490768A>G	ENSP00000291971:p.Asn962Ser		61182580	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	A	0.026	-1.374975	0.01214	.	.	ENSG00000179709	ENST00000291971	T	0.53640	0.61	2.36	-4.45	0.03546	.	.	.	.	.	T	0.22704	0.0548	N	0.16307	0.4	0.09310	N	1	B;B	0.18610	0.029;0.008	B;B	0.25884	0.064;0.013	T	0.30707	-0.9969	9	0.10111	T	0.7	.	3.9846	0.09509	0.5893:0.0:0.2241:0.1866	.	943;962	Q86W28-2;Q86W28	.;NALP8_HUMAN	S	962	ENSP00000291971:N962S	ENSP00000291971:N962S	N	+	2	0	NLRP8	61182580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.827000	0.01704	-1.064000	0.03172	-1.175000	0.01729	AAC		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		G	56490768	A	G	56490768	3	3	89	1	0	0	0	0	1	0	0	0	10514	43	2	4	2919	4	NLRP8	19	56490768	Missense_Mutation	SNP	A	TCGA-CI-6622-01A-11D-1826-10	676014	56490768	2638215	157	24569										
C19orf18	147685	hgsc.bcm.edu	37	chr19	58469998	58469998	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttccatttttccattatgtGacgcattctttgttttgttt	5	8	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:58469998G>T	ENST00000314391.3	-	6	721	c.620C>A	c.(619-621)tCa>tAa	p.S207*		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	207						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)		TCCATTATGTGACGCATTCTT	0.413																																																0			19											73	69	70					19																	58469998		2203	4300	6503	63161810	SO:0001587	stop_gained	147685			BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.620C>A	19.37:g.58469998G>T	ENSP00000321519:p.Ser207*		63161810		Nonsense_Mutation	SNP	ENST00000314391.3	37	CCDS12967.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.522076	0.27211	.	.	ENSG00000177025	ENST00000314391	.	.	.	2.96	-0.907	0.10521	.	.	.	.	.	.	.	.	.	.	.	0.24686	N	0.993335	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2528	3.3087	0.07009	0.3858:0.2511:0.3631:0.0	.	.	.	.	X	207	.	ENSP00000321519:S207X	S	-	2	0	C19orf18	63161810	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.105000	0.10907	-0.224000	0.09928	0.485000	0.47835	TCA		0.413	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	NM_152474		T	58469998	G	T	58469998	4	4	89	1	0	0	0	0	0	1	0	0	1916	1294	45	2	31	2	C19orf18	19	58469998	Nonsense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	1979230	58469998	658985	158	24570										
ZNF606	80095	hgsc.bcm.edu	37	chr19	58489967	58489967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ttctccggtgtgcaatgaggTgagaactacagttaaaggat	12	6	1	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr19:58489967T>C	ENST00000341164.4	-	7	2701	c.2081A>G	c.(2080-2082)cAc>cGc	p.H694R	ZNF606_ENST00000536132.1_Missense_Mutation_p.H604R	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	694					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		TGCAATGAGGTGAGAACTACA	0.413																																																0			19											98	96	97					19																	58489967		2203	4300	6503	63181779	SO:0001583	missense	80095			AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2081A>G	19.37:g.58489967T>C	ENSP00000343617:p.His694Arg		63181779	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	8.335	0.827384	0.16749	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.12984	2.63;2.63	4.43	4.43	0.53597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000220	T	0.07458	0.0188	N	0.03294	-0.36	0.28415	N	0.918022	P	0.51653	0.947	B	0.44133	0.442	T	0.15492	-1.0435	10	0.32370	T	0.25	.	13.0673	0.59041	0.0:0.0:0.0:1.0	.	694	Q8WXB4	ZN606_HUMAN	R	694;604	ENSP00000343617:H694R;ENSP00000445624:H604R	ENSP00000343617:H694R	H	-	2	0	ZNF606	63181779	0.000000	0.05858	1.000000	0.80357	0.993000	0.82548	-0.042000	0.12063	1.965000	0.57142	0.459000	0.35465	CAC		0.413	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		C	58489967	T	C	58489967	3	2	89	1	0	0	0	0	1	0	0	0	18071	1696	59	4	301	4	ZNF606	19	58489967	Missense_Mutation	SNP	T	TCGA-CI-6622-01A-11D-1826-10	19969	58489967	639016	159	24571										
C20orf132	140699	hgsc.bcm.edu	37	chr20	35748189	35748189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	cttgtagccagtctttaaagCgggcaacagagtatatgctg	11	8	1	1	rs556574052		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr20:35748189C>T	ENST00000400441.3	-	18	2281	c.2282G>A	c.(2281-2283)cGc>cAc	p.R761H	MROH8_ENST00000217333.8_Missense_Mutation_p.R590H|MROH8_ENST00000441008.2_Missense_Mutation_p.R747H			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	330																	GTCTTTAAAGCGGGCAACAGA	0.493													C|||	1	0.000199681	0	0	5008	,	,		14574	0.001		0	False		,,,				2504	0															0			20											88	90	89					20																	35748189		1948	4157	6105	35181603	SO:0001583	missense	140699			AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.2282G>A	20.37:g.35748189C>T	ENSP00000383291:p.Arg761His		35181603	Q5JYQ6	Silent	SNP	ENST00000400441.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.16|13.16	2.153206|2.153206	0.38021|0.38021	.|.	.|.	ENSG00000101353|ENSG00000101353	ENST00000343811|ENST00000441008;ENST00000400441;ENST00000217333	.|T;T;T	.|0.66815	.|-0.23;1.43;-0.15	5.05|5.05	4.11|4.11	0.48088|0.48088	.|.	.|0.092343	.|0.46145	.|D	.|0.000305	T|T	0.70159|0.70159	0.3192|0.3192	L|L	0.32530|0.32530	0.975|0.975	0.36078|0.36078	D|D	0.842616|0.842616	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.996	T|T	0.73895|0.73895	-0.3838|-0.3838	5|10	.|0.39692	.|T	.|0.17	-9.1967|-9.1967	9.5596|9.5596	0.39360|0.39360	0.0:0.9015:0.0:0.0985|0.0:0.9015:0.0:0.0985	.|.	.|761;595	.|E7ETR9;Q9H579-2	.|.;.	T|H	788|747;761;590	.|ENSP00000392144:R747H;ENSP00000383291:R761H;ENSP00000217333:R590H	.|ENSP00000217333:R590H	A|R	-|-	1|2	0|0	C20orf132|C20orf132	35181603|35181603	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.066000|0.066000	0.16364|0.16364	2.209000|2.209000	0.42806|0.42806	1.262000|1.262000	0.44165|0.44165	0.650000|0.650000	0.86243|0.86243	GCT|CGC		0.493	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		T	35748189	C	T	35748189	3	4	89	1	0	0	0	0	1	0	0	0	2092	768	27	1	874	1	C20orf132	20	35748189	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10		35748189	27277331	160	24572										
ACTR5	79913	hgsc.bcm.edu	37	chr20	37377454	37377454	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aacctggagcttcaggagttGctgctggactacagcttcca	11	11	1	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr20:37377454G>C	ENST00000243903.4	+	1	370	c.333G>C	c.(331-333)ttG>ttC	p.L111F		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	111					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				TTCAGGAGTTGCTGCTGGACT	0.662																																																0			20											16	17	16					20																	37377454		2187	4271	6458	36810868	SO:0001583	missense	79913			AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"INO80 complex subunits"	14671	protein-coding gene	gene with protein product	"INO80 complex subunit M"		"ARP5 (actin-related protein 5, yeast) homolog"			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.333G>C	20.37:g.37377454G>C	ENSP00000243903:p.Leu111Phe		36810868	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Missense_Mutation	SNP	ENST00000243903.4	37	CCDS13308.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.477889	0.44044	.	.	ENSG00000101442	ENST00000243903	D	0.94417	-3.42	4.2	4.2	0.49525	.	0.068887	0.64402	D	0.000013	D	0.95971	0.8688	M	0.63428	1.95	0.54753	D	0.999981	D	0.89917	1.0	D	0.91635	0.999	D	0.93961	0.7240	10	0.10377	T	0.69	-17.1057	17.091	0.86622	0.0:0.0:1.0:0.0	.	111	Q9H9F9	ARP5_HUMAN	F	111	ENSP00000243903:L111F	ENSP00000243903:L111F	L	+	3	2	ACTR5	36810868	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	4.041000	0.57339	2.313000	0.78055	0.655000	0.94253	TTG		0.662	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		C	37377454	G	C	37377454	3	2	89	1	0	0	0	0	1	0	0	0	215	1310	46	5	335	5	ACTR5	20	37377454	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	1629265	37377454	25648066	161	24573										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42157978	42157978	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ggcattgaccctcaacacccGtccatgtacttcatcctcac	5	17	3	1	rs371655802		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr20:42157978G>A	ENST00000427442.2	+	9	1119	c.960G>A	c.(958-960)ccG>ccA	p.P320P	L3MBTL1_ENST00000444063.1_Silent_p.P252P|L3MBTL1_ENST00000373134.1_Silent_p.P252P|L3MBTL1_ENST00000373135.3_Silent_p.P252P|L3MBTL1_ENST00000418998.1_Silent_p.P320P			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	252				LR -> MC (in Ref. 1; AAC69438). {ECO:0000305}.	chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CTCAACACCCGTCCATGTACT	0.532																																																0			20						G	,	0,4406		0,0,2203	208	130	157		756,960	-7.7	0.7	20		157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	L3MBTL1	NM_015478.6,NM_032107.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	252/773,320/841	42157978	1,13005	2203	4300	6503	41591392	SO:0001819	synonymous_variant	26013			U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.960G>A	20.37:g.42157978G>A			41591392	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Silent	SNP	ENST00000427442.2	37	CCDS46602.2																																																																																				0.532	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		A	42157978	G	A	42157978	2	1	89	1	0	0	0	0	0	0	0	1	8613	1132	40	1		1	L3MBTL	20	42157978	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10	4780524	42157978	20867542	162	24574										
TAF4	6874	hgsc.bcm.edu	37	chr20	60639550	60639550	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atgttggtcgggttctgaggCggctgcggcaagcggggggc	21	8	1	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr20:60639550C>A	ENST00000252996.4	-	1	1316	c.1317G>T	c.(1315-1317)ccG>ccT	p.P439P	hsa-mir-3195_ENST00000585001.1_RNA	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	439					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			GGTTCTGAGGCGGCTGCGGCA	0.731																																																0			20											5	8	7					20																	60639550		2100	4181	6281	60072945	SO:0001819	synonymous_variant	6874			Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1317G>T	20.37:g.60639550C>A			60072945	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Silent	SNP	ENST00000252996.4	37	CCDS33500.1																																																																																				0.731	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60639550	C	A	60639550	2	1	89	1	0	0	0	0	0	0	0	1	15565	755	27	2		2	TAF4	20	60639550	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	18481572	60639550	2385970	163	24575										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28338138	28338138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aagccctcgcgggtgtagacGtgcaggatccgtgcggaccc	15	13	0	1			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr21:28338138G>A	ENST00000284987.5	-	1	694	c.573C>T	c.(571-573)caC>caT	p.H191H		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	191					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GGGTGTAGACGTGCAGGATCC	0.701																																					Esophageal Squamous(53;683 1080 10100 14424 45938)											0			21											19	22	21					21																	28338138		2198	4292	6490	27260009	SO:0001819	synonymous_variant	11096			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.573C>T	21.37:g.28338138G>A			27260009	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																				0.701	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28338138	G	A	28338138	2	1	89	1	0	0	0	0	0	0	0	1	269	1136	40	1		1	ADAMTS5	21	28338138	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10		28338138	19791757	164	24576										
KRTAP6-2	337967	hgsc.bcm.edu	37	chr21	31971163	31971163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	gcacccatagccatggtcgcCgtagtagtttccgtagtagc	11	12	0	0	rs533416500	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr21:31971163C>T	ENST00000334897.3	-	1	56	c.31G>A	c.(31-33)Ggc>Agc	p.G11S	KRTAP22-1_ENST00000334680.2_5'Flank	NM_181604.1	NP_853635.1	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	11						intermediate filament (GO:0005882)				endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11						CCATGGTCGCCGTAGTAGTTT	0.532																																																0			21											203	166	178					21																	31971163		2203	4300	6503	30893034	SO:0001583	missense	337967			AP001708	CCDS13600.1	21q22.1	2011-02-10			ENSG00000186930	ENSG00000186930		"Keratin associated proteins"	18932	protein-coding gene	gene with protein product						12359730	Standard	NM_181604		Approved	KAP6.2	uc011adc.2	Q3LI66	OTTHUMG00000057794	ENST00000334897.3:c.31G>A	21.37:g.31971163C>T	ENSP00000334560:p.Gly11Ser		30893034		Missense_Mutation	SNP	ENST00000334897.3	37	CCDS13600.1	.	.	.	.	.	.	.	.	.	.	C	7.934	0.741225	0.15642	.	.	ENSG00000186930	ENST00000334897	T	0.13657	2.57	4.37	3.48	0.39840	.	0.000000	0.39083	U	0.001475	T	0.30854	0.0778	.	.	.	0.26135	N	0.980351	D	0.89917	1.0	D	0.76071	0.987	T	0.02713	-1.1120	9	0.87932	D	0	.	8.4889	0.33089	0.0:0.896:0.0:0.104	.	11	Q3LI66	KRA62_HUMAN	S	11	ENSP00000334560:G11S	ENSP00000334560:G11S	G	-	1	0	KRTAP6-2	30893034	0.998000	0.40836	0.988000	0.46212	0.029000	0.11900	2.980000	0.49321	1.450000	0.47717	0.650000	0.86243	GGC		0.532	KRTAP6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128246.3			T	31971163	C	T	31971163	3	4	89	1	0	0	0	0	1	0	0	0	8592	652	23	1	160	1	KRTAP6-2	21	31971163	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	3633025	31971163	16158732	165	24577										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34011222	34011222	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	aacaaatgagacttacttgcGgttgtgaggaagcttctgaa	11	6	1	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr21:34011222G>T	ENST00000322229.7	-	30	3910	c.3911C>A	c.(3910-3912)cCg>cAg	p.P1304Q	SYNJ1_ENST00000433931.2_Missense_Mutation_p.P1343Q|SYNJ1_ENST00000382491.3_Missense_Mutation_p.P1257Q|SYNJ1_ENST00000382499.2_Missense_Mutation_p.P1343Q|SYNJ1_ENST00000357345.3_Missense_Mutation_p.P1288Q			O43426	SYNJ1_HUMAN	synaptojanin 1	1304	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						ACTTACTTGCGGTTGTGAGGA	0.408																																																0			21											190	196	194					21																	34011222		2203	4300	6503	32933093	SO:0001583	missense	8867			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.3911C>A	21.37:g.34011222G>T	ENSP00000322234:p.Pro1304Gln		32933093	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.373|1.373	-0.585544|-0.585544	0.03827|0.03827	.|.	.|.	ENSG00000159082|ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229|ENST00000418301	D;D;D;D;D|.	0.92647|.	-2.29;-3.06;-3.08;-2.27;-2.27|.	5.45|5.45	-1.3|-1.3	0.09259|0.09259	.|.	0.600804|.	0.17448|.	N|.	0.173869|.	T|T	0.22399|0.22399	0.0540|0.0540	N|N	0.24115|0.24115	0.695|0.695	0.20196|0.20196	N|N	0.999928|0.999928	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.001;0.001|.	T|T	0.29941|0.29941	-0.9995|-0.9995	10|5	0.24483|.	T|.	0.36|.	.|.	6.8562|6.8562	0.24042|0.24042	0.133:0.0:0.3591:0.5079|0.133:0.0:0.3591:0.5079	.|.	1257;1343;1304;1304;1288|.	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4|.	.;.;.;SYNJ1_HUMAN;.|.	Q|S	1257;1288;1343;1343;1304|125	ENSP00000371931:P1257Q;ENSP00000349903:P1288Q;ENSP00000371939:P1343Q;ENSP00000409667:P1343Q;ENSP00000322234:P1304Q|.	ENSP00000322234:P1304Q|.	P|R	-|-	2|1	0|0	SYNJ1|SYNJ1	32933093|32933093	0.420000|0.420000	0.25457|0.25457	0.009000|0.009000	0.14445|0.14445	0.073000|0.073000	0.16967|0.16967	0.567000|0.567000	0.23608|0.23608	-0.385000|-0.385000	0.07833|0.07833	-0.768000|-0.768000	0.03414|0.03414	CCG|CGC		0.408	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34011222	G	T	34011222	3	4	89	1	0	0	0	0	1	0	0	0	15491	1116	39	2	843	2	SYNJ1	21	34011222	Missense_Mutation	SNP	G	TCGA-CI-6622-01A-11D-1826-10	2040059	34011222	14118673	166	24578										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38877658	38877658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	caggaggacctggtgggcgaCgtgctggggagtcaggtcat	19	8	2	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr21:38877658C>T	ENST00000398960.2	+	9	1387	c.1312C>T	c.(1312-1314)Cgt>Tgt	p.R438C	DYRK1A_ENST00000455387.2_Missense_Mutation_p.R210C|DYRK1A_ENST00000451934.1_Missense_Mutation_p.R438C|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R429C|DYRK1A_ENST00000398956.2_Missense_Mutation_p.R438C|DYRK1A_ENST00000338785.3_Missense_Mutation_p.R438C|DYRK1A_ENST00000321219.8_Missense_Mutation_p.R438C	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	438	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TGGTGGGCGACGTGCTGGGGA	0.458																																					Melanoma(114;464 1602 31203 43785 45765)											0			21											89	85	86					21																	38877658		2203	4300	6503	37799528	SO:0001583	missense	1859			U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1312C>T	21.37:g.38877658C>T	ENSP00000381932:p.Arg438Cys		37799528	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.704997	0.68615	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.83	4.95	0.65309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	M	0.76727	2.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.997;0.998;0.994;0.997	T	0.69903	-0.5019	10	0.87932	D	0	.	14.9888	0.71371	0.0:0.9318:0.0:0.0682	.	438;438;438;429;438	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	C	438;429;438;438;438;438;210	ENSP00000342690:R438C;ENSP00000340373:R429C;ENSP00000319032:R438C;ENSP00000416089:R438C;ENSP00000381932:R438C;ENSP00000381929:R438C;ENSP00000407854:R210C	ENSP00000319032:R438C	R	+	1	0	DYRK1A	37799528	1.000000	0.71417	0.898000	0.35279	0.991000	0.79684	4.640000	0.61368	1.481000	0.48307	0.650000	0.86243	CGT		0.458	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38877658	C	T	38877658	3	4	89	1	0	0	0	0	1	0	0	0	4865	536	19	1	1346	1	DYRK1A	21	38877658	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	4866436	38877658	9252237	167	24579										
ZNF295	49854	hgsc.bcm.edu	37	chr21	43411346	43411346	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atgtgcgattggaagtgactCcagagtcgaaaattagtgcg	13	6	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr21:43411346C>A	ENST00000310826.5	-	3	3042	c.2859G>T	c.(2857-2859)tgG>tgT	p.W953C	ZBTB21_ENST00000465968.1_5'Flank|ZBTB21_ENST00000398499.1_Missense_Mutation_p.W953C|ZBTB21_ENST00000398505.3_Missense_Mutation_p.W752C|ZBTB21_ENST00000398511.3_Missense_Mutation_p.W953C	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	953					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										GGAAGTGACTCCAGAGTCGAA	0.498																																																0			21											82	78	80					21																	43411346		2203	4300	6503	42284415	SO:0001583	missense	49854			AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13083	protein-coding gene	gene with protein product			"zinc finger protein 295"	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.2859G>T	21.37:g.43411346C>A	ENSP00000308759:p.Trp953Cys		42284415	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820548	0.71028	.	.	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	5.72	5.72	0.89469	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.33904	0.0879	N	0.02247	-0.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.56914	-0.7900	10	0.52906	T	0.07	-16.1764	19.8946	0.96949	0.0:1.0:0.0:0.0	.	752;953	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	C	752;953;953;953	ENSP00000381517:W752C;ENSP00000308759:W953C;ENSP00000381512:W953C;ENSP00000381523:W953C	ENSP00000308759:W953C	W	-	3	0	ZNF295	42284415	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.288000	0.78691	2.711000	0.92665	0.655000	0.94253	TGG		0.498	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		A	43411346	C	A	43411346	3	1	89	1	0	0	0	0	1	0	0	0	17866	856	30	2	345	2	ZNF295	21	43411346	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	4533688	43411346	4718549	168	24580										
CECR2	27443	hgsc.bcm.edu	37	chr22	17990860	17990860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tatagggaaaacgtccacagCgcacaaaggcagagttgcat	11	9	0	1	rs372166419		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr22:17990860C>T	ENST00000400585.2	+	8	835	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C	CECR2_ENST00000262608.8_Missense_Mutation_p.R255C|CECR2_ENST00000400573.5_Missense_Mutation_p.R274C|CECR2_ENST00000342247.5_Intron			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	296					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		ACGTCCACAGCGCACAAAGGC	0.507																																																0			22						C	CYS/ARG	0,4086		0,0,2043	127	125	126		760	2.8	1	22		126	2,8380		0,2,4189	no	missense	CECR2	NM_031413.3	180	0,2,6232	TT,TC,CC		0.0239,0.0,0.016	probably-damaging	254/1443	17990860	2,12466	2043	4191	6234	16370860	SO:0001583	missense	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.397C>T	22.37:g.17990860C>T	ENSP00000383428:p.Arg133Cys		16370860	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Silent	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	C	16.07	3.019036	0.54576	0.0	2.39E-4	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.50001	0.76;0.76;0.76	3.77	2.75	0.32379	.	0.329738	0.21751	N	0.069665	T	0.49338	0.1551	M	0.67397	2.05	0.46823	D	0.99921	D;D;D	0.71674	0.998;0.985;0.985	P;P;P	0.47528	0.549;0.451;0.451	T	0.53542	-0.8424	10	0.87932	D	0	-1.3379	9.3281	0.38005	0.0:0.899:0.0:0.101	.	296;133;274	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	C	133;274;255	ENSP00000383428:R133C;ENSP00000383417:R274C;ENSP00000262608:R255C	ENSP00000262608:R255C	R	+	1	0	CECR2	16370860	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.162000	0.31786	0.794000	0.33899	0.585000	0.79938	CGC		0.507	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		T	17990860	C	T	17990860	3	4	89	1	0	0	0	0	1	0	0	0	3212	768	27	1	788	1	CECR2	22	17990860	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10		17990860	33313706	169	24581										
ADORA2A	135	hgsc.bcm.edu	37	chr22	24829521	24829521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ctttgtggtgtcactggcggCggccgacatcgcagtgggtg	17	10	1	0	rs4530	byFrequency	TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr22:24829521C>T	ENST00000337539.7	+	2	608	c.149C>T	c.(148-150)gCg>gTg	p.A50V	ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A_ENST00000496497.1_Intron|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	50			A -> V (in dbSNP:rs4530). {ECO:0000269|PubMed:10391209}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	TCACTGGCGGCGGCCGACATC	0.622													C|||	41	0.0081869	0.031	0	5008	,	,		17105	0		0	False		,,,				2504	0															0			22						C	VAL/ALA	103,4303	80.4+/-118.8	3,97,2103	164	107	127		149	3.5	1	22	dbSNP_52	127	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ADORA2A	NM_000675.4	64	3,105,6395	TT,TC,CC		0.093,2.3377,0.8535	benign	50/413	24829521	111,12895	2203	4300	6503	23159521	SO:0001583	missense	135			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.149C>T	22.37:g.24829521C>T	ENSP00000336630:p.Ala50Val		23159521	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	4.193	0.034564	0.08101	0.023377	9.3E-4	ENSG00000128271	ENST00000424232;ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596;ENST00000436735;ENST00000439591	T;T;T;T;T	0.32753	1.44;2.18;2.18;1.44;1.44	4.53	3.46	0.39613	GPCR, rhodopsin-like superfamily (1);	0.110120	0.64402	N	0.000008	T	0.02156	0.0067	N	0.01015	-1.05	0.49213	D	0.99976	B	0.31351	0.32	B	0.15870	0.014	T	0.31138	-0.9954	10	0.02654	T	1	-20.2401	10.8342	0.46677	0.0:0.9017:0.0:0.0983	rs4530;rs4530	50	P29274	AA2AR_HUMAN	V	50	ENSP00000404497:A50V;ENSP00000414802:A50V;ENSP00000336630:A50V;ENSP00000397071:A50V;ENSP00000400190:A50V	ENSP00000336630:A50V	A	+	2	0	ADORA2A	23159521	0.991000	0.36638	0.983000	0.44433	0.586000	0.36452	2.262000	0.43285	1.032000	0.39892	-0.367000	0.07326	GCG		0.622	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24829521	C	T	24829521	3	4	89	1	0	0	0	0	1	0	0	0	327	768	27	1	151	1	ADORA2A	22	24829521	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	6838661	24829521	26475045	170	24582										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160203	51160203	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	ccaccccctgaagagtttgcCaacggggtcctgctggccac	11	16	0	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chr22:51160203C>T	ENST00000414786.2	+	21	4127	c.3900C>T	c.(3898-3900)gcC>gcT	p.A1300A	SHANK3_ENST00000445220.2_Silent_p.A1316A|SHANK3_ENST00000262795.3_Silent_p.A1330A			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1314	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		AAGAGTTTGCCAACGGGGTCC	0.692																																																0			22											9	11	11					22																	51160203		1974	4144	6118	49507069	SO:0001819	synonymous_variant	85358			AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3900C>T	22.37:g.51160203C>T			49507069	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	37																																																																																					0.692	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160203	C	T	51160203	2	4	89	1	0	0	0	0	0	0	0	1	14303	581	21	3		3	SHANK3	22	51160203	Silent	SNP	C	TCGA-CI-6622-01A-11D-1826-10	26330682	51160203	144363	171	24583										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5811131	5811131	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tgcagagacatgatctcttcGttctggatgtgagcgatatc	11	8	2	3	rs187221748		TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chrX:5811131G>A	ENST00000381095.3	-	6	2805	c.2178C>T	c.(2176-2178)aaC>aaT	p.N726N	NLGN4X_ENST00000381092.1_Silent_p.N726N|NLGN4X_ENST00000275857.6_Silent_p.N726N|NLGN4X_ENST00000381093.2_Silent_p.N746N|NLGN4X_ENST00000538097.1_Silent_p.N726N	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	726					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TGATCTCTTCGTTCTGGATGT	0.552																																																0			X						G	,	0,3835		0,0,0,1632,571	157	116	130		2178,2178	-1.3	0.9	X		130	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	NLGN4X	NM_020742.2,NM_181332.1	,	0,0,1,4060,2442	AA,AG,A,GG,G		0.0149,0.0,0.0095	,	726/817,726/817	5811131	1,10562	2203	4300	6503	5821131	SO:0001819	synonymous_variant	57502			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.2178C>T	X.37:g.5811131G>A			5821131	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.552	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5811131	G	A	5811131	2	1	89	1	0	0	0	0	0	0	0	1	10495	1136	40	1		1	NLGN4X	23	5811131	Silent	SNP	G	TCGA-CI-6622-01A-11D-1826-10		5811131	149459429	172	24584										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53230860	53230860	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	catcttgcagataagctcctCatgggagaagacgcagtatc	10	10	2	3			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chrX:53230860C>A	ENST00000375401.3	-	14	2465	c.1933G>T	c.(1933-1935)Gag>Tag	p.E645*	KDM5C_ENST00000375383.3_Nonsense_Mutation_p.E604*|KDM5C_ENST00000404049.3_Nonsense_Mutation_p.E644*|KDM5C_ENST00000375379.3_Nonsense_Mutation_p.E645*|KDM5C_ENST00000452825.3_Nonsense_Mutation_p.E578*|KDM5C_ENST00000465402.1_5'UTR	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	645					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.E645*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						ATAAGCTCCTCATGGGAGAAG	0.572			"N, F, S"		clear cell renal carcinoma																																		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	1	Substitution - Nonsense(1)	kidney(1)	X											63	55	57					X																	53230860		2203	4300	6503	53247585	SO:0001587	stop_gained	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.1933G>T	X.37:g.53230860C>A	ENSP00000364550:p.Glu645*		53247585	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Nonsense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	C	44	11.265054	0.99539	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.5031	15.8095	0.78547	0.0:1.0:0.0:0.0	.	.	.	.	X	578;645;644;645;604	.	ENSP00000364528:E645X	E	-	1	0	KDM5C	53247585	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.818000	0.86416	2.331000	0.79229	0.600000	0.82982	GAG		0.572	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		A	53230860	C	A	53230860	4	1	89	1	0	0	0	0	0	1	0	0	8156	835	29	2	2899	2	KDM5C	23	53230860	Nonsense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	47419729	53230860	102039700	173	24585										
PAGE2	203569	hgsc.bcm.edu	37	chrX	55117793	55117793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	atggaagcttttcaacaggaActggctctgcttaagataga	10	7	2	2			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chrX:55117793A>G	ENST00000374968.4	+	4	326	c.222A>G	c.(220-222)gaA>gaG	p.E74E	PAGE2_ENST00000374965.1_Silent_p.E57E	NM_207339.2	NP_997222.1	Q7Z2X7	PAGE2_HUMAN	P antigen family, member 2 (prostate associated)	74										endometrium(1)|large_intestine(2)|lung(1)|ovary(2)	6						TTCAACAGGAACTGGCTCTGC	0.398																																																0			X											76	81	79					X																	55117793		2171	4290	6461	55134518	SO:0001819	synonymous_variant	203569			BC054022	CCDS14367.1	Xp11.22	2009-06-17			ENSG00000234068	ENSG00000234068			31804	protein-coding gene	gene with protein product		300738	"G antigen, family C, 2"	GAGEC2		9724777	Standard	NM_207339		Approved	MGC62094, PAGE-2, CT16.4		Q7Z2X7	OTTHUMG00000021648	ENST00000374968.4:c.222A>G	X.37:g.55117793A>G			55134518	Q5JRK7|Q5JRK8	Silent	SNP	ENST00000374968.4	37	CCDS14367.1																																																																																				0.398	PAGE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056857.1	NM_207339		G	55117793	A	G	55117793	2	3	89	1	0	0	0	0	0	0	0	1	11421	40	2	4		4	PAGE2	23	55117793	Silent	SNP	A	TCGA-CI-6622-01A-11D-1826-10	1886933	55117793	100152767	174	24586										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63490911	63490911	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342857142857143	6	1	0.452921336089653	2.28976897689769	0.32326150262085	0.64040536122916	1	0	tctagcatactctgcttgggCtgcagccctttgtcaaagcg	10	12	3	0			TCGA-CI-6622-01A-11D-1826-10	TCGA-CI-6622-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	bf3a398b-e3ec-45fd-92d4-d952e0c475c7	b17a5e0f-b91f-4b07-a908-19c3d4e11a59	g.chrX:63490911C>A	ENST00000374852.3	-	13	1591	c.1524G>T	c.(1522-1524)caG>caT	p.Q508H	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	508						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)|p.Q508H(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TCTGCTTGGGCTGCAGCCCTT	0.448																																																3	Whole gene deletion(2)|Substitution - Missense(1)	ovary(1)|lung(1)|large_intestine(1)	X											67	56	60					X																	63490911		2203	4300	6503	63407636	SO:0001583	missense	66036			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1524G>T	X.37:g.63490911C>A	ENSP00000363985:p.Gln508His		63407636	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.035|0.035	-1.313103|-1.313103	0.01331|0.01331	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000442913|ENST00000374852;ENST00000247400	.|D	.|0.94184	.|-3.37	3.75|3.75	-4.23|-4.23	0.03789|0.03789	.|.	.|0.140687	.|0.28354	.|U	.|0.015647	T|T	0.73690|0.73690	0.3619|0.3619	N|N	0.02539|0.02539	-0.55|-0.55	0.54753|0.54753	D|D	0.999986|0.999986	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.64170|0.64170	-0.6470|-0.6470	5|10	.|0.02654	.|T	.|1	.|.	7.6459|7.6459	0.28321|0.28321	0.0:0.1718:0.5747:0.2536|0.0:0.1718:0.5747:0.2536	.|.	.|508	.|Q96EF0	.|MTMR8_HUMAN	S|H	312|508;394	.|ENSP00000363985:Q508H	.|ENSP00000247400:Q394H	A|Q	-|-	1|3	0|2	MTMR8|MTMR8	63407636|63407636	0.630000|0.630000	0.27155|0.27155	0.021000|0.021000	0.16686|0.16686	0.023000|0.023000	0.10783|0.10783	-1.036000|-1.036000	0.03560|0.03560	-0.702000|-0.702000	0.05056|0.05056	-0.390000|-0.390000	0.06520|0.06520	GCC|CAG		0.448	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		A	63490911	C	A	63490911	3	1	89	1	0	0	0	0	1	0	0	0	9979	796	28	2	598	2	MTMR8	23	63490911	Missense_Mutation	SNP	C	TCGA-CI-6622-01A-11D-1826-10	8373118	63490911	91779649	175	24587										
CCNL2	81669	hgsc.bcm.edu	37	chr1	1322689	1322689	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcatacgacctcgagcgctcTcgtcgctgatctctgtagta	9	13	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:1322689T>C	ENST00000400809.3	-	11	1490	c.1485A>G	c.(1483-1485)cgA>cgG	p.R495R	CCNL2_ENST00000505849.1_5'UTR|CCNL2_ENST00000408952.5_Silent_p.R273R	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	495					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		TCGAGCGCTCTCGTCGCTGAT	0.592																																																0			1											151	159	157					1																	1322689		2203	4296	6499	1312552	SO:0001819	synonymous_variant	81669			AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.1485A>G	1.37:g.1322689T>C			1312552	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	37	CCDS30557.1																																																																																				0.592	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		C	1322689	T	C	1322689	2	2	90	1	0	0	0	0	0	0	0	1	2938	1538	54	4		4	CCNL2	1	1322689	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10		1322689	247927932	1	24588										
CROCC	9696	hgsc.bcm.edu	37	chr1	17281854	17281854	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctgctggaggatgcccgtgaCgggctgcggcgggagctgct	19	11	0	1	rs150383004	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:17281854C>T	ENST00000375541.5	+	24	3582	c.3513C>T	c.(3511-3513)gaC>gaT	p.D1171D		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ATGCCCGTGACGGGCTGCGGC	0.716																																																0			1						C		2,4354		0,2,2176	16	20	19		3513	-8.6	0	1	dbSNP_134	19	2,8550		0,2,4274	no	coding-synonymous	CROCC	NM_014675.3		0,4,6450	TT,TC,CC		0.0234,0.0459,0.031		1171/2018	17281854	4,12904	2178	4276	6454	17154441	SO:0001819	synonymous_variant	9696			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.3513C>T	1.37:g.17281854C>T			17154441		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																				0.716	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17281854	C	T	17281854	2	4	90	1	0	0	0	0	0	0	0	1	3899	535	19	1		1	CROCC	1	17281854	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	15959165	17281854	231968767	2	24589										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056181	27056181	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agatgggcaagatgagacctCagccatatggcgggactaac	13	9	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:27056181C>T	ENST00000324856.7	+	2	1548	c.1177C>T	c.(1177-1179)Cag>Tag	p.Q393*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q10*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q393*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	393					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q393*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		GATGAGACCTCAGCCATATGG	0.527			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Nonsense(1)	ovary(1)	1											107	109	109					1																	27056181		2203	4300	6503	26928768	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1177C>T	1.37:g.27056181C>T	ENSP00000320485:p.Gln393*		26928768	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.437309	0.97568	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	.	.	.	6.16	6.16	0.99307	.	0.059713	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-7.5437	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	393;393;10;10	.	ENSP00000320485:Q393X	Q	+	1	0	ARID1A	26928768	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.452000	0.80683	2.937000	0.99478	0.650000	0.86243	CAG		0.527	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27056181	C	T	27056181	4	4	90	1	0	0	0	0	0	1	0	0	913	827	29	3	1183	3	ARID1A	1	27056181	Nonsense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	9774327	27056181	222194440	3	24590										
EIF3I	8668	hgsc.bcm.edu	37	chr1	32691860	32691860	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atcatcatgttctccacggaCaagcagatgggctaccagtg	10	11	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:32691860C>T	ENST00000373586.1	+	5	411	c.339C>T	c.(337-339)gaC>gaT	p.D113D	EIF3I_ENST00000471486.1_3'UTR	NM_003757.2	NP_003748.1			eukaryotic translation initiation factor 3, subunit I											breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)				TCTCCACGGACAAGCAGATGG	0.557																																					Colon(102;1138 2140 2180 17876)											0			1											106	100	102					1																	32691860		2203	4300	6503	32464447	SO:0001819	synonymous_variant	8668			U39067	CCDS357.1	1p34.1	2013-01-10	2007-07-27	2007-07-27	ENSG00000084623	ENSG00000084623		"WD repeat domain containing"	3272	protein-coding gene	gene with protein product		603911	"eukaryotic translation initiation factor 3, subunit 2 beta, 36kDa"	EIF3S2		7566156, 8995409	Standard	NM_003757		Approved	TRIP-1, eIF3-beta, eIF3-p36, eIF3i	uc009vuc.3	Q13347	OTTHUMG00000007364	ENST00000373586.1:c.339C>T	1.37:g.32691860C>T			32464447		Silent	SNP	ENST00000373586.1	37	CCDS357.1																																																																																				0.557	EIF3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019282.2	NM_003757		T	32691860	C	T	32691860	2	4	90	1	0	0	0	0	0	0	0	1	5032	477	17	3		3	EIF3I	1	32691860	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5635679	32691860	216558761	4	24591										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34209047	34209047	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tccttgatgaccaggaaatcAaactgaggctccacgtcaat	8	11	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:34209047A>G	ENST00000373381.4	-	14	2183	c.2007T>C	c.(2005-2007)ttT>ttC	p.F669F		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	629	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCAGGAAATCAAACTGAGGCT	0.607																																																0			1											82	82	82					1																	34209047		2203	4300	6503	33981634	SO:0001819	synonymous_variant	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2007T>C	1.37:g.34209047A>G			33981634	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																					0.607	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		G	34209047	A	G	34209047	2	3	90	1	0	0	0	0	0	0	0	1	3951	127	5	4		4	CSMD2	1	34209047	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1517187	34209047	215041574	5	24592										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37325531	37325531	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cttctccacaatggccgagaCgtgtgggttgtccacattga	11	11	1	2	rs373548070		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:37325531C>A	ENST00000373091.3	-	6	890	c.874G>T	c.(874-876)Gtc>Ttc	p.V292F	GRIK3_ENST00000373093.4_Missense_Mutation_p.V292F|GRIK3_ENST00000462621.1_5'Flank	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	292					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				ATGGCCGAGACGTGTGGGTTG	0.587																																																0			1											101	105	103					1																	37325531		2203	4300	6503	37098118	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.874G>T	1.37:g.37325531C>A	ENSP00000362183:p.Val292Phe		37098118	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983410	0.93044	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.80994	-1.44;-1.44	5.7	5.7	0.88788	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.82132	2.575	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	D	0.89543	0.3794	10	0.45353	T	0.12	.	19.8471	0.96713	0.0:1.0:0.0:0.0	.	292;292	A9Z1Z8;Q13003	.;GRIK3_HUMAN	F	292	ENSP00000362183:V292F;ENSP00000362185:V292F	ENSP00000362183:V292F	V	-	1	0	GRIK3	37098118	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.688000	0.91661	0.655000	0.94253	GTC		0.587	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37325531	C	A	37325531	3	1	90	1	0	0	0	0	1	0	0	0	6796	536	19	2	1929	2	GRIK3	1	37325531	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	3116484	37325531	211925090	6	24593										
TIE1	7075	hgsc.bcm.edu	37	chr1	43783728	43783728	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gcggccaatggcatgcagtaCctgagtgagaagcaggtgtg	16	8	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:43783728C>A	ENST00000372476.3	+	17	2986	c.2907C>A	c.(2905-2907)taC>taA	p.Y969*	TIE1_ENST00000433781.2_Nonsense_Mutation_p.Y614*|TIE1_ENST00000473014.1_3'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	969	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCATGCAGTACCTGAGTGAGA	0.612																																																0			1											49	50	50					1																	43783728		2203	4300	6503	43556315	SO:0001587	stop_gained	7075			BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2907C>A	1.37:g.43783728C>A	ENSP00000361554:p.Tyr969*		43556315	B5A949|B5A950	Nonsense_Mutation	SNP	ENST00000372476.3	37	CCDS482.1	.	.	.	.	.	.	.	.	.	.	C	41	8.840990	0.98974	.	.	ENSG00000066056	ENST00000372476;ENST00000372475;ENST00000536913;ENST00000433781	.	.	.	6.06	4.13	0.48395	.	0.000000	0.35495	N	0.003180	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.143	0.48413	0.0:0.8449:0.0:0.1551	.	.	.	.	X	969;372;252;614	.	ENSP00000361553:Y372X	Y	+	3	2	TIE1	43556315	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.084000	0.41625	0.811000	0.34303	0.655000	0.94253	TAC		0.612	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		A	43783728	C	A	43783728	4	1	90	1	0	0	0	0	0	1	0	0	15932	518	18	2	2973	2	TIE1	1	43783728	Nonsense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	6458197	43783728	205466893	7	24594										
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52937648	52937648	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acatcttttacatactaaatCaagtatttcccgaaatcggt	4	9	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:52937648C>G	ENST00000371544.3	-	14	3116	c.2854G>C	c.(2854-2856)Gat>Cat	p.D952H	ZCCHC11_ENST00000371541.1_5'UTR|ZCCHC11_ENST00000257177.4_Missense_Mutation_p.D952H	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	952					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CATACTAAATCAAGTATTTCC	0.303																																																0			1											79	78	78					1																	52937648		2203	4300	6503	52710236	SO:0001583	missense	23318			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.2854G>C	1.37:g.52937648C>G	ENSP00000360599:p.Asp952His		52710236	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.674740	0.88445	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.56	5.56	0.83823	.	0.101890	0.64402	D	0.000003	T	0.65312	0.2679	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.68621	0.947;0.959	T	0.66724	-0.5851	10	0.62326	D	0.03	.	19.5244	0.95197	0.0:1.0:0.0:0.0	.	711;952	E9PKX1;Q5TAX3	.;TUT4_HUMAN	H	952;952;881;711	ENSP00000257177:D952H;ENSP00000360599:D952H;ENSP00000433486:D881H;ENSP00000435256:D711H	ENSP00000257177:D952H	D	-	1	0	ZCCHC11	52710236	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.267000	0.78462	2.619000	0.88677	0.650000	0.86243	GAT		0.303	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		G	52937648	C	G	52937648	3	3	90	1	0	0	0	0	1	0	0	0	17619	826	29	5	2151	5	ZCCHC11	1	52937648	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	9153920	52937648	196312973	8	24595										
L1TD1	54596	hgsc.bcm.edu	37	chr1	62675768	62675768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggaagaggaacagacttcagAacaggactcaacctttcagg	11	9	3	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:62675768A>G	ENST00000498273.1	+	4	1617	c.1322A>G	c.(1321-1323)gAa>gGa	p.E441G	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	441	Glu-rich.							p.E441G(1)|p.E441V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						CAGACTTCAGAACAGGACTCA	0.493																																																2	Substitution - Missense(2)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	1											72	68	69					1																	62675768		2203	4300	6503	62448356	SO:0001583	missense	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1322A>G	1.37:g.62675768A>G	ENSP00000419901:p.Glu441Gly		62448356	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.569768	0.28003	.	.	ENSG00000240563	ENST00000498273	T	0.15952	2.38	1.53	-3.07	0.05363	.	.	.	.	.	T	0.08313	0.0207	N	0.24115	0.695	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.29971	-0.9994	9	0.48119	T	0.1	.	0.229	0.00177	0.2447:0.1972:0.1663:0.3918	.	441	Q5T7N2	LITD1_HUMAN	G	441	ENSP00000419901:E441G	ENSP00000419901:E441G	E	+	2	0	L1TD1	62448356	0.005000	0.15991	0.000000	0.03702	0.673000	0.39480	0.035000	0.13797	-1.938000	0.01046	0.172000	0.16884	GAA		0.493	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		G	62675768	A	G	62675768	3	3	90	1	0	0	0	0	1	0	0	0	8611	246	9	4	1328	4	L1TD1	1	62675768	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9738120	62675768	186574853	9	24596										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74649272	74649272	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atgaaggccattgaacttcaCaaaaacaaaatctttttgac	5	8	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:74649272C>G	ENST00000395089.1	-	1	96	c.97G>C	c.(97-99)Gtg>Ctg	p.V33L	LRRIQ3_ENST00000370911.3_Missense_Mutation_p.V33L|LRRIQ3_ENST00000370909.2_Missense_Mutation_p.V33L|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.V33L			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	33										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						ttgaacttcacaaaaacaAAA	0.333																																																0			1											57	60	59					1																	74649272		2200	4295	6495	74421860	SO:0001583	missense	127255			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.97G>C	1.37:g.74649272C>G	ENSP00000378524:p.Val33Leu		74421860	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.701272	0.30142	.	.	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972;ENST00000370911	T;T;T;T	0.31247	2.55;2.55;1.5;2.55	5.06	-1.99	0.07457	.	0.783752	0.10842	N	0.628097	T	0.04363	0.0120	N	0.17082	0.46	0.25114	N	0.990692	B	0.26708	0.157	B	0.20767	0.031	T	0.42682	-0.9437	10	0.14656	T	0.56	.	7.1773	0.25753	0.0:0.4068:0.1139:0.4793	.	33	A6PVS8	LRIQ3_HUMAN	L	33	ENSP00000378524:V33L;ENSP00000346414:V33L;ENSP00000359946:V33L;ENSP00000359948:V33L	ENSP00000346414:V33L	V	-	1	0	LRRIQ3	74421860	0.995000	0.38212	0.966000	0.40874	0.971000	0.66376	0.509000	0.22707	-0.310000	0.08766	-0.302000	0.09304	GTG		0.333	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		G	74649272	C	G	74649272	3	3	90	1	0	0	0	0	1	0	0	0	9059	478	17	5	1805	5	LRRIQ3	1	74649272	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	11973504	74649272	174601349	10	24597										
MSH4	4438	hgsc.bcm.edu	37	chr1	76262704	76262704	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agatctcatcaacctcgcctTctgccccggcggtttccccg	8	18	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:76262704T>A	ENST00000263187.3	+	1	138	c.34T>A	c.(34-36)Tct>Act	p.S12T		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	12					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						AACCTCGCCTTCTGCCCCGGC	0.607								Mismatch excision repair (MMR)																																								0			1											45	44	44					1																	76262704		2203	4300	6503	76035292	SO:0001583	missense	4438			U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.34T>A	1.37:g.76262704T>A	ENSP00000263187:p.Ser12Thr		76035292	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864414	0.32977	.	.	ENSG00000057468	ENST00000263187	D	0.89123	-2.47	2.97	2.97	0.34412	.	.	.	.	.	T	0.60932	0.2307	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.12837	0.008	T	0.55854	-0.8075	9	0.66056	D	0.02	-0.0887	4.8348	0.13458	0.0:0.1408:0.0:0.8592	.	12	O15457	MSH4_HUMAN	T	12	ENSP00000263187:S12T	ENSP00000263187:S12T	S	+	1	0	MSH4	76035292	0.004000	0.15560	0.003000	0.11579	0.205000	0.24178	0.347000	0.20014	1.596000	0.50062	0.260000	0.18958	TCT		0.607	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		A	76262704	T	A	76262704	3	1	90	1	0	0	0	0	1	0	0	0	9902	1783	62	5	36	5	MSH4	1	76262704	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1613432	76262704	172987917	11	24598										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91404921	91404921	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgtgaggttgatccaaatgTtcgcttcacatcttgtttta	8	7	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:91404921T>C	ENST00000370440.1	-	3	2207	c.1990A>G	c.(1990-1992)Aca>Gca	p.T664A	ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.T664A|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	664					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GATCCAAATGTTCGCTTCACA	0.373																																																0			1											141	140	140					1																	91404921		2203	4300	6503	91177509	SO:0001583	missense	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.1990A>G	1.37:g.91404921T>C	ENSP00000359469:p.Thr664Ala		91177509	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	9.117	1.007980	0.19199	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.00578	6.44;6.44	6.02	2.52	0.30459	.	0.493565	0.22492	N	0.059345	T	0.00144	0.0004	L	0.36672	1.1	0.28812	N	0.898193	B	0.22480	0.07	B	0.21546	0.035	T	0.41520	-0.9504	10	0.07813	T	0.8	-3.0935	1.2141	0.01910	0.1242:0.2128:0.2174:0.4457	.	664	Q9H582	ZN644_HUMAN	A	664;664;236	ENSP00000359469:T664A;ENSP00000337008:T664A	ENSP00000337008:T664A	T	-	1	0	ZNF644	91177509	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.816000	0.27267	0.186000	0.20125	-0.263000	0.10527	ACA		0.373	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		C	91404921	T	C	91404921	3	2	90	1	0	0	0	0	1	0	0	0	18099	1725	60	4	2009	4	ZNF644	1	91404921	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	15142217	91404921	157845700	12	24599										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109814051	109814051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccgtcctcctgctgctgagcGccacgtggctgctggcactg	13	16	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:109814051G>A	ENST00000271332.3	+	27	7781	c.7720G>A	c.(7720-7722)Gcc>Acc	p.A2574T	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2574					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GCTGCTGAGCGCCACGTGGCT	0.637																																					NSCLC(158;1285 2011 34800 34852 42084)											0			1											103	85	91					1																	109814051		2203	4300	6503	109615574	SO:0001583	missense	1952			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.7720G>A	1.37:g.109814051G>A	ENSP00000271332:p.Ala2574Thr		109615574	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.743967	0.49151	.	.	ENSG00000143126	ENST00000271332	T	0.44482	0.92	4.59	3.67	0.42095	GPCR, family 2-like (1);	.	.	.	.	T	0.26593	0.0650	L	0.28344	0.845	0.31364	N	0.681051	D	0.56521	0.976	P	0.52909	0.713	T	0.04579	-1.0941	9	0.36615	T	0.2	.	13.7527	0.62917	0.0:0.0:0.8449:0.1551	.	2574	Q9HCU4	CELR2_HUMAN	T	2574	ENSP00000271332:A2574T	ENSP00000271332:A2574T	A	+	1	0	CELSR2	109615574	0.048000	0.20356	0.457000	0.27056	0.833000	0.47200	1.581000	0.36558	1.124000	0.41980	0.561000	0.74099	GCC		0.637	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109814051	G	A	109814051	3	1	90	1	0	0	0	0	1	0	0	0	3228	1087	38	1	7826	1	CELSR2	1	109814051	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	18409130	109814051	139436570	13	24600										
REG4	83998	hgsc.bcm.edu	37	chr1	120341217	120341217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gccccatcaatccactgccaCtgctgcctctgcaacaacag	6	18	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:120341217C>T	ENST00000354219.1	-	6	751	c.312G>A	c.(310-312)caG>caA	p.Q104Q	REG4_ENST00000256585.5_Silent_p.Q104Q|REG4_ENST00000530654.1_Intron	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	104	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)			central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		TCCACTGCCACTGCTGCCTCT	0.517																																																0			1											137	127	130					1																	120341217		2203	4300	6503	120142740	SO:0001819	synonymous_variant	83998			AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"regenerating gene type IV", " gastrointestinal secretory protein"	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.312G>A	1.37:g.120341217C>T			120142740	Q8NER6|Q8NER7	Silent	SNP	ENST00000354219.1	37	CCDS906.1																																																																																				0.517	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044		T	120341217	C	T	120341217	2	4	90	1	0	0	0	0	0	0	0	1	13251	564	20	3		3	REG4	1	120341217	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10527166	120341217	128909404	14	24601										
FLG	2312	hgsc.bcm.edu	37	chr1	152278093	152278093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgtcttgtgcctgctcatggCgggatccttgtcttcctcta	10	12	4	0	rs553781249	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:152278093C>T	ENST00000368799.1	-	3	9304	c.9269G>A	c.(9268-9270)cGc>cAc	p.R3090H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3090	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTCATGGCGGGATCCTTG	0.582									Ichthyosis				c|||	13	0.00259585	0.0091	0	5008	,	,		16620	0		0	False		,,,				2504	0.001															0			1																																								150544717	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9269G>A	1.37:g.152278093C>T	ENSP00000357789:p.Arg3090His		150544717	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	5.948	0.358913	0.11239	.	.	ENSG00000143631	ENST00000368799	T	0.01705	4.68	3.1	-3.68	0.04463	.	.	.	.	.	T	0.00271	0.0008	N	0.04636	-0.2	0.09310	N	1	P	0.35155	0.487	B	0.24541	0.054	T	0.45614	-0.9249	9	0.44086	T	0.13	.	4.4892	0.11805	0.0:0.3239:0.3493:0.3268	.	3090	P20930	FILA_HUMAN	H	3090	ENSP00000357789:R3090H	ENSP00000357789:R3090H	R	-	2	0	FLG	150544717	0.960000	0.32886	0.000000	0.03702	0.097000	0.18754	-0.243000	0.08915	-0.962000	0.03604	-0.384000	0.06662	CGC		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152278093	C	T	152278093	3	4	90	1	0	0	0	0	1	0	0	0	5941	768	27	1	2920	1	FLG	1	152278093	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	31936876	152278093	96972528	15	24602										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842330	154842330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggtggtggctgctgctgctgTtgctgctgctgctgctgctg	17	10	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:154842330T>C	ENST00000271915.4	-	1	426	c.111A>G	c.(109-111)caA>caG	p.Q37Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	37	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgttgctgctgct	0.677																																																0			1											8	8	8					1																	154842330		1936	3838	5774	153108954	SO:0001819	synonymous_variant	3782			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.111A>G	1.37:g.154842330T>C			153108954	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																				0.677	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		C	154842330	T	C	154842330	2	2	90	1	0	0	0	0	0	0	0	1	8101	1722	60	4		4	KCNN3	1	154842330	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2564237	154842330	94408291	16	24603										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155313423	155313423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cttccaaagcttctcaatgcGaaagatgtcaagtttatctc	6	10	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:155313423G>A	ENST00000368346.3	-	23	8746	c.8107C>T	c.(8107-8109)Cgc>Tgc	p.R2703C	MIR555_ENST00000384987.1_RNA|ASH1L_ENST00000392403.3_Missense_Mutation_p.R2698C			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2703	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTCTCAATGCGAAAGATGTCA	0.488																																																0			1											111	105	107					1																	155313423		2203	4300	6503	153580047	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8107C>T	1.37:g.155313423G>A	ENSP00000357330:p.Arg2703Cys		153580047	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	G	22.8	4.342670	0.82022	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.87809	-2.3;-2.3	4.82	3.88	0.44766	Bromo adjacent homology (BAH) domain (3);	0.055371	0.64402	D	0.000001	D	0.89223	0.6654	L	0.56280	1.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.90640	0.4574	10	0.87932	D	0	.	13.7104	0.62665	0.0:0.0:0.8394:0.1606	.	2703;2698	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	C	2703;2698	ENSP00000357330:R2703C;ENSP00000376204:R2698C	ENSP00000357330:R2703C	R	-	1	0	ASH1L	153580047	1.000000	0.71417	0.969000	0.41365	0.982000	0.71751	6.019000	0.70818	1.178000	0.42870	0.561000	0.74099	CGC		0.488	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155313423	G	A	155313423	3	1	90	1	0	0	0	0	1	0	0	0	1042	1058	37	1	826	1	ASH1L	1	155313423	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	471093	155313423	93937198	17	24604										
FCRL3	115352	hgsc.bcm.edu	37	chr1	157668305	157668305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctcatcgtgataccaatatGtgtctccctgggctagggaa	10	10	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:157668305G>A	ENST00000368184.3	-	4	458	c.167C>T	c.(166-168)aCa>aTa	p.T56I	FCRL3_ENST00000368186.5_Missense_Mutation_p.T56I|FCRL3_ENST00000473231.1_5'Flank|RP11-367J7.3_ENST00000453692.1_RNA	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	56	Ig-like C2-type 1.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ATACCAATATGTGTCTCCCTG	0.448																																																0			1											192	169	177					1																	157668305		2203	4300	6503	155934929	SO:0001583	missense	115352			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.167C>T	1.37:g.157668305G>A	ENSP00000357167:p.Thr56Ile		155934929	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	G	2.629	-0.286780	0.05605	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.11063	2.81;2.81	5.46	-0.143	0.13444	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.054180	0.02832	N	0.126886	T	0.02156	0.0067	N	0.13327	0.33	0.09310	N	1	B;B	0.24186	0.099;0.081	B;B	0.28011	0.085;0.051	T	0.44772	-0.9306	10	0.21540	T	0.41	.	9.45	0.38721	0.661:0.0:0.339:0.0	.	56;56	Q96P31;Q96P31-6	FCRL3_HUMAN;.	I	56	ENSP00000357169:T56I;ENSP00000357167:T56I	ENSP00000292392:T56I	T	-	2	0	FCRL3	155934929	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.445000	0.06845	-0.053000	0.13289	0.591000	0.81541	ACA		0.448	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		A	157668305	G	A	157668305	3	1	90	1	0	0	0	0	1	0	0	0	5815	1377	48	3	2085	3	FCRL3	1	157668305	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2354882	157668305	91582316	18	24605										
CD1E	913	hgsc.bcm.edu	37	chr1	158324361	158324361	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agccctggtcccatggaaacTtcagcaagcaggagctgaaa	11	11	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:158324361T>G	ENST00000368167.3	+	2	492	c.253T>G	c.(253-255)Ttc>Gtc	p.F85V	CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368163.3_Missense_Mutation_p.F85V|CD1E_ENST00000444681.2_Intron|CD1E_ENST00000368161.3_Missense_Mutation_p.F85V|CD1E_ENST00000368160.3_Missense_Mutation_p.F85V|CD1E_ENST00000368166.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368155.3_Missense_Mutation_p.F85V|CD1E_ENST00000368156.1_Missense_Mutation_p.F85V|CD1E_ENST00000452291.2_Intron|CD1E_ENST00000434258.1_Missense_Mutation_p.F83V|CD1E_ENST00000368165.3_Missense_Mutation_p.F85V|CD1E_ENST00000464822.1_Intron|CD1E_ENST00000368164.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	85					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CCATGGAAACTTCAGCAAGCA	0.498																																																0			1											59	62	61					1																	158324361		2109	4272	6381	156590985	SO:0001583	missense	913			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.253T>G	1.37:g.158324361T>G	ENSP00000357149:p.Phe85Val		156590985	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.996658	0.54147	.	.	ENSG00000158488	ENST00000434258;ENST00000368167;ENST00000368165;ENST00000368163;ENST00000368160;ENST00000368161;ENST00000368156;ENST00000368155	T;T;T;T;T;T;T;T	0.06608	3.3;3.3;3.28;3.3;3.3;3.3;3.51;3.42	3.8	3.8	0.43715	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.000000	0.42294	D	0.000721	T	0.17238	0.0414	M	0.89095	3.005	0.80722	D	1	P;D;D;D;P;P;B;P	0.67145	0.863;0.979;0.979;0.996;0.863;0.952;0.1;0.714	P;P;P;D;P;P;B;P	0.71414	0.519;0.785;0.785;0.973;0.463;0.787;0.047;0.707	T	0.00641	-1.1631	10	0.62326	D	0.03	-26.5519	9.222	0.37382	0.0:0.0:0.0:1.0	.	83;85;85;85;85;85;85;85	E7ET31;P15812-5;P15812-7;P15812-2;P15812;P15812-3;P15812-6;P15812-4	.;.;.;.;CD1E_HUMAN;.;.;.	V	83;85;85;85;85;85;85;85	ENSP00000401957:F83V;ENSP00000357149:F85V;ENSP00000357147:F85V;ENSP00000357145:F85V;ENSP00000357142:F85V;ENSP00000357143:F85V;ENSP00000357138:F85V;ENSP00000357137:F85V	ENSP00000357137:F85V	F	+	1	0	CD1E	156590985	0.382000	0.25148	0.843000	0.33291	0.489000	0.33432	0.667000	0.25112	1.957000	0.56846	0.460000	0.39030	TTC		0.498	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		G	158324361	T	G	158324361	3	3	90	1	0	0	0	0	1	0	0	0	2984	1609	56	4	259	4	CD1E	1	158324361	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	656056	158324361	90926260	19	24606										
FMO3	2328	hgsc.bcm.edu	37	chr1	171086456	171086456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gccatactgacccagtgggaCcggtcgttgaaacccatgca	11	13	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:171086456C>A	ENST00000367755.4	+	9	1584	c.1473C>A	c.(1471-1473)gaC>gaA	p.D491E	FMO3_ENST00000538429.1_Missense_Mutation_p.D428E|FMO3_ENST00000392085.2_Missense_Mutation_p.D491E|FMO3_ENST00000542847.1_Missense_Mutation_p.D471E	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	491					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CCCAGTGGGACCGGTCGTTGA	0.517																																																0			1											119	109	112					1																	171086456		2203	4300	6503	169353080	SO:0001583	missense	2328			BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.1473C>A	1.37:g.171086456C>A	ENSP00000356729:p.Asp491Glu		169353080	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	C	9.269	1.045087	0.19748	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.36	1.11	0.20524	.	0.053541	0.85682	D	0.000000	T	0.13756	0.0333	L	0.35341	1.055	0.37004	D	0.895384	B;B;B	0.20052	0.003;0.041;0.003	B;B;B	0.26202	0.005;0.067;0.032	T	0.10337	-1.0634	10	0.13108	T	0.6	-25.9605	0.5426	0.00648	0.2413:0.3316:0.1984:0.2287	.	428;471;491	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	E	491;491;471;428	ENSP00000356729:D491E;ENSP00000375935:D491E;ENSP00000444073:D471E;ENSP00000439500:D428E	ENSP00000356729:D491E	D	+	3	2	FMO3	169353080	0.003000	0.15002	0.991000	0.47740	0.685000	0.39939	-0.489000	0.06490	0.232000	0.21100	-0.152000	0.13540	GAC		0.517	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		A	171086456	C	A	171086456	3	1	90	1	0	0	0	0	1	0	0	0	5975	506	18	2	1503	2	FMO3	1	171086456	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	12762095	171086456	78164165	20	24607										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172579290	172579290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aggaaaattgataaaaactcTaatacagactaagtcgggat	8	5	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:172579290T>C	ENST00000263688.3	+	24	3875	c.3656T>C	c.(3655-3657)cTa>cCa	p.L1219P	SUCO_ENST00000367723.4_Missense_Mutation_p.L1370P|SUCO_ENST00000608151.1_Missense_Mutation_p.L1371P|SUCO_ENST00000610051.1_Missense_Mutation_p.L848P	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1219					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ATAAAAACTCTAATACAGACT	0.418																																																0			1											57	59	58					1																	172579290		2202	4300	6502	170845913	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3656T>C	1.37:g.172579290T>C	ENSP00000263688:p.Leu1219Pro		170845913	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987737	0.53934	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.26	5.26	0.73747	.	0.156119	0.43579	D	0.000542	T	0.55641	0.1933	M	0.65975	2.015	0.80722	D	1	B;P;P	0.48503	0.296;0.911;0.911	B;P;P	0.49192	0.097;0.602;0.602	T	0.64166	-0.6471	9	0.87932	D	0	-9.4595	14.2866	0.66249	0.0:0.0:0.0:1.0	.	848;1371;1219	B4DYM4;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	P	1371;1219	.	ENSP00000263688:L1219P	L	+	2	0	C1orf9	170845913	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	5.789000	0.69029	2.115000	0.64714	0.528000	0.53228	CTA		0.418	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		C	172579290	T	C	172579290	3	2	90	1	0	0	0	0	1	0	0	0	2073	1522	53	4	3750	4	C1orf9	1	172579290	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1492834	172579290	76671331	21	24608										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176709259	176709259	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctgtggctctaaggacaTcctcccgcattggtctttcg	10	13	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:176709259T>A	ENST00000367662.3	+	14	5242	c.4078T>A	c.(4078-4080)Tcc>Acc	p.S1360T		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1360					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTAAGGACATCCTCCCGCAT	0.517																																																0			1											140	138	138					1																	176709259		2029	4176	6205	174975882	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4078T>A	1.37:g.176709259T>A	ENSP00000356634:p.Ser1360Thr		174975882	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	T	4.350	0.064468	0.08388	.	.	ENSG00000116183	ENST00000367662	T	0.01665	4.7	5.91	-4.66	0.03329	.	0.615939	0.19076	N	0.123375	T	0.01835	0.0058	M	0.69823	2.125	0.09310	N	0.999999	B	0.25850	0.136	B	0.25405	0.06	T	0.42498	-0.9448	10	0.25751	T	0.34	-0.2505	2.9409	0.05830	0.1114:0.3731:0.2289:0.2866	.	1360	Q9BXP8	PAPP2_HUMAN	T	1360	ENSP00000356634:S1360T	ENSP00000356634:S1360T	S	+	1	0	PAPPA2	174975882	0.008000	0.16893	0.009000	0.14445	0.049000	0.14656	1.112000	0.31172	-1.211000	0.02624	-0.290000	0.09829	TCC		0.517	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176709259	T	A	176709259	3	1	90	1	0	0	0	0	1	0	0	0	11464	1435	50	5	4181	5	PAPPA2	1	176709259	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	4129969	176709259	72541362	22	24609										
PRG4	10216	hgsc.bcm.edu	37	chr1	186280289	186280289	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtgcaactgtgaaggaaaaaCtttcttctttaaggtaacac	8	7	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:186280289C>G	ENST00000445192.2	+	9	3668	c.3623C>G	c.(3622-3624)aCt>aGt	p.T1208S	PRG4_ENST00000367485.4_Missense_Mutation_p.T1115S|PRG4_ENST00000367484.3_Missense_Mutation_p.T737S|PRG4_ENST00000367483.4_Missense_Mutation_p.T1167S|PRG4_ENST00000367486.3_Missense_Mutation_p.T1165S|RNU6-1240P_ENST00000365155.1_RNA	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1208					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GAAGGAAAAACTTTCTTCTTT	0.343																																																0			1											88	84	85					1																	186280289		2203	4300	6503	184546912	SO:0001583	missense	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3623C>G	1.37:g.186280289C>G	ENSP00000399679:p.Thr1208Ser		184546912	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.000144	0.35320	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.03212	4.01;4.01;4.01;4.01;4.01	4.86	4.86	0.63082	Hemopexin/matrixin (2);	0.000000	0.45126	U	0.000390	T	0.20129	0.0484	M	0.85859	2.78	0.39481	D	0.967888	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.00942	-1.1506	10	0.87932	D	0	-10.6096	13.7014	0.62611	0.0:0.9224:0.0:0.0776	.	1074;1115;1208;1167	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	S	1165;737;1167;1115;1208	ENSP00000356456:T1165S;ENSP00000356454:T737S;ENSP00000356453:T1167S;ENSP00000356455:T1115S;ENSP00000399679:T1208S	ENSP00000356453:T1167S	T	+	2	0	PRG4	184546912	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	4.275000	0.58927	2.386000	0.81285	0.585000	0.79938	ACT		0.343	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186280289	C	G	186280289	3	3	90	1	0	0	0	0	1	0	0	0	12515	565	20	5	3653	5	PRG4	1	186280289	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	9571030	186280289	62970332	23	24610										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190129886	190129886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aattttctgcgcctttaggaAaagttgtttcatgctgttct	8	7	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:190129886A>G	ENST00000367462.3	-	7	1327	c.1096T>C	c.(1096-1098)Ttc>Ctc	p.F366L	BRINP3_ENST00000534846.1_Missense_Mutation_p.F264L	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	366					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											GCCTTTAGGAAAAGTTGTTTC	0.393																																																0			1											145	149	147					1																	190129886		2203	4300	6503	188396509	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1096T>C	1.37:g.190129886A>G	ENSP00000356432:p.Phe366Leu		188396509	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	6.053	0.378116	0.11466	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.15256	2.71;2.44	5.75	4.6	0.57074	.	0.309345	0.36234	N	0.002705	T	0.06690	0.0171	N	0.04508	-0.205	0.35441	D	0.794884	B;B	0.12630	0.006;0.003	B;B	0.08055	0.003;0.001	T	0.22312	-1.0220	10	0.02654	T	1	.	11.0791	0.48049	0.8443:0.1557:0.0:0.0	.	264;366	B7Z260;Q76B58	.;FAM5C_HUMAN	L	366;264	ENSP00000356432:F366L;ENSP00000438022:F264L	ENSP00000356432:F366L	F	-	1	0	FAM5C	188396509	1.000000	0.71417	0.988000	0.46212	0.983000	0.72400	3.930000	0.56522	0.972000	0.38314	0.467000	0.42956	TTC		0.393	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		G	190129886	A	G	190129886	3	3	90	1	0	0	0	0	1	0	0	0	5613	14	1	4	1212	4	FAM5C	1	190129886	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	3849597	190129886	59120735	24	24611										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200817795	200817795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttcttcgttgagagattataCtgtaagcttggactctgaca	9	7	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:200817795C>T	ENST00000236925.4	+	12	1980	c.1931C>T	c.(1930-1932)aCt>aTt	p.T644I	CAMSAP2_ENST00000358823.2_Missense_Mutation_p.T633I|CAMSAP2_ENST00000413307.2_Missense_Mutation_p.T617I			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	644					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AGAGATTATACTGTAAGCTTG	0.403																																																0			1											136	134	135					1																	200817795		2203	4300	6503	199084418	SO:0001583	missense	23271			AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1931C>T	1.37:g.200817795C>T	ENSP00000236925:p.Thr644Ile		199084418	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	37		.	.	.	.	.	.	.	.	.	.	C	18.32	3.597335	0.66332	.	.	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.44482	0.92;0.92;0.92	5.62	5.62	0.85841	.	0.155786	0.56097	D	0.000028	T	0.55768	0.1941	L	0.47716	1.5	0.58432	D	0.999998	D;D;D	0.71674	0.998;0.964;0.979	P;P;P	0.59889	0.865;0.614;0.846	T	0.48514	-0.9029	10	0.36615	T	0.2	-26.7531	19.6614	0.95875	0.0:1.0:0.0:0.0	.	617;644;633	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	I	633;617;644	ENSP00000351684:T633I;ENSP00000416800:T617I;ENSP00000236925:T644I	ENSP00000236925:T644I	T	+	2	0	CAMSAP1L1	199084418	1.000000	0.71417	0.974000	0.42286	0.993000	0.82548	5.907000	0.69908	2.633000	0.89246	0.655000	0.94253	ACT		0.403	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200817795	C	T	200817795	3	4	90	1	0	0	0	0	1	0	0	0	2618	565	20	3	1940	3	CAMSAP1L1	1	200817795	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10687909	200817795	48432826	25	24612										
ATP2B4	493	hgsc.bcm.edu	37	chr1	203708819	203708819	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	accactcctggatgaggaagAggaggaaaatcctgacaagg	13	8	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:203708819A>G	ENST00000357681.5	+	21	4578	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	ATP2B4_ENST00000341360.2_3'UTR|ATP2B4_ENST00000367218.3_3'UTR|ATP2B4_ENST00000367219.3_3'UTR|ATP2B4_ENST00000391954.2_3'UTR	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	1188					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.E1152V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GATGAGGAAGAGGAGGAAAAT	0.498																																																1	Substitution - Missense(1)	ovary(1)	1											123	110	114					1																	203708819		2203	4300	6503	201975442	SO:0001583	missense	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.3455A>G	1.37:g.203708819A>G	ENSP00000350310:p.Glu1152Gly		201975442	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	37	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012101	0.54468	.	.	ENSG00000058668	ENST00000357681	T	0.79554	-1.28	5.46	5.46	0.80206	.	1.166840	0.06393	N	0.717426	T	0.77558	0.4148	L	0.38175	1.15	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.57717	-0.7763	10	0.51188	T	0.08	-11.0127	15.1947	0.73078	1.0:0.0:0.0:0.0	.	1152	P23634-6	.	G	1152	ENSP00000350310:E1152G	ENSP00000350310:E1152G	E	+	2	0	ATP2B4	201975442	1.000000	0.71417	0.966000	0.40874	0.400000	0.30750	2.550000	0.45811	2.077000	0.62373	0.533000	0.62120	GAG		0.498	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		G	203708819	A	G	203708819	3	3	90	1	0	0	0	0	1	0	0	0	1143	304	11	4	3715	4	ATP2B4	1	203708819	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	2891024	203708819	45541802	26	24613										
USH2A	7399	hgsc.bcm.edu	37	chr1	216500979	216500979	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcgaaaatcttgcattcttcCgacaaactgctctaaacctg	5	12	3	0	rs111033280		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:216500979C>G	ENST00000307340.3	-	5	1188	c.802G>C	c.(802-804)Gga>Cga	p.G268R	USH2A_ENST00000366942.3_Missense_Mutation_p.G268R|USH2A_ENST00000366943.2_Missense_Mutation_p.G268R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	268			G -> R (in USH2A; unknown pathological significance). {ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGCATTCTTCCGACAAACTGC	0.363										HNSCC(13;0.011)																																						0			1	GRCh37	CM080595	USH2A	M	rs111033280						144	137	139					1																	216500979		2203	4300	6503	214567602	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.802G>C	1.37:g.216500979C>G	ENSP00000305941:p.Gly268Arg		214567602	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.441589	0.83993	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;D;D	0.90444	-2.67;-2.67;-2.67	5.52	4.59	0.56863	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.40385	U	0.001117	D	0.95053	0.8398	M	0.78049	2.395	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95516	0.8590	10	0.87932	D	0	.	15.4614	0.75359	0.1397:0.8603:0.0:0.0	.	268;268	O75445-2;O75445	.;USH2A_HUMAN	R	268	ENSP00000305941:G268R;ENSP00000355910:G268R;ENSP00000355909:G268R	ENSP00000305941:G268R	G	-	1	0	USH2A	214567602	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.352000	0.66028	1.278000	0.44430	0.563000	0.77884	GGA		0.363	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216500979	C	G	216500979	3	3	90	1	0	0	0	0	1	0	0	0	17076	661	23	5	15092	5	USH2A	1	216500979	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	12792160	216500979	32749642	27	24614										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228468143	228468143	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctctgcccgcctggaggtcCgaggtgagtcatcccacgag	13	15	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:228468143C>T	ENST00000422127.1	+	29	7971	c.7927C>T	c.(7927-7929)Cga>Tga	p.R2643*	OBSCN_ENST00000359599.6_Nonsense_Mutation_p.R1490*|OBSCN_ENST00000284548.11_Nonsense_Mutation_p.R2643*|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Nonsense_Mutation_p.R3072*|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2643	Ig-like 25.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCTGGAGGTCCGAGGTGAGTC	0.652																																																0			1											28	32	31					1																	228468143		2091	4209	6300	226534766	SO:0001587	stop_gained	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7927C>T	1.37:g.228468143C>T	ENSP00000409493:p.Arg2643*		226534766	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	c	49	16.007496	0.99851	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	.	.	.	5.3	1.57	0.23409	.	0.598909	0.16224	N	0.223927	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	13.1531	0.59500	0.6032:0.3968:0.0:0.0	.	.	.	.	X	2643;2643;1490;342;49	.	ENSP00000284548:R2643X	R	+	1	2	OBSCN	226534766	1.000000	0.71417	0.189000	0.23252	0.753000	0.42808	4.401000	0.59716	0.012000	0.14892	0.550000	0.68814	CGA		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228468143	C	T	228468143	4	4	90	1	0	0	0	0	0	1	0	0	10843	644	23	1	8037	1	OBSCN	1	228468143	Nonsense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	11967164	228468143	20782478	28	24615										
RYR2	6262	hgsc.bcm.edu	37	chr1	237947292	237947292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tccacgaacctgcgaaggacAtcggcttcaacgtcgccgtc	10	15	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:237947292A>G	ENST00000366574.2	+	90	12597	c.12280A>G	c.(12280-12282)Atc>Gtc	p.I4094V	RYR2_ENST00000360064.6_Missense_Mutation_p.I4100V|RYR2_ENST00000542537.1_Missense_Mutation_p.I4078V|RYR2_ENST00000609119.1_3'UTR	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4094					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGCGAAGGACATCGGCTTCAA	0.502																																																0			1											43	44	44					1																	237947292		2023	4201	6224	236013915	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12280A>G	1.37:g.237947292A>G	ENSP00000355533:p.Ile4094Val		236013915	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.290484	0.80914	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	T;D;T	0.97505	-0.11;-4.41;-0.11	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000005	D	0.98191	0.9402	M	0.75615	2.305	0.80722	D	1	P;P	0.51240	0.943;0.912	D;P	0.66716	0.946;0.809	D	0.99226	1.0880	10	0.87932	D	0	.	16.2303	0.82332	1.0:0.0:0.0:0.0	.	1068;4094	B4DGV4;Q92736	.;RYR2_HUMAN	V	4094;4100;4078;1068	ENSP00000355533:I4094V;ENSP00000353174:I4100V;ENSP00000443798:I4078V	ENSP00000353174:I4100V	I	+	1	0	RYR2	236013915	1.000000	0.71417	0.999000	0.59377	0.760000	0.43138	9.287000	0.95975	2.233000	0.73108	0.533000	0.62120	ATC		0.502	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237947292	A	G	237947292	3	3	90	1	0	0	0	0	1	0	0	0	13806	217	8	4	12638	4	RYR2	1	237947292	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9479149	237947292	11303329	29	24616										
WDR64	128025	hgsc.bcm.edu	37	chr1	241929585	241929585	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caagtagaaggatataatttGatagcagctggaaccttaaa	9	5	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:241929585G>C	ENST00000366552.2	+	15	2190	c.1983G>C	c.(1981-1983)ttG>ttC	p.L661F	WDR64_ENST00000437684.2_Missense_Mutation_p.L661F	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	661										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GATATAATTTGATAGCAGCTG	0.333																																																0			1											140	139	139					1																	241929585		2203	4300	6503	239996208	SO:0001583	missense	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1983G>C	1.37:g.241929585G>C	ENSP00000355510:p.Leu661Phe		239996208	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.00|11.00	1.510691|1.510691	0.27036|0.27036	.|.	.|.	ENSG00000162843|ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635|ENST00000425826	T;T;T|.	0.60171|.	0.21;0.21;0.21|.	4.91|4.91	4.91|4.91	0.64330|0.64330	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.376505|.	0.19403|.	N|.	0.115136|.	T|.	0.72003|.	0.3407|.	M|M	0.68952|0.68952	2.095|2.095	0.38019|0.38019	D|D	0.93477|0.93477	D;P|.	0.69078|.	0.997;0.89|.	D;P|.	0.65684|.	0.937;0.481|.	T|.	0.75233|.	-0.3390|.	10|.	0.30854|.	T|.	0.27|.	-5.8978|-5.8978	15.0212|15.0212	0.71632|0.71632	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	661;381|.	B1ANS9;D1MPS4|.	WDR64_HUMAN;.|.	F|S	661;661;432|140	ENSP00000355510:L661F;ENSP00000402446:L661F;ENSP00000406656:L432F|.	ENSP00000355510:L661F|.	L|X	+|+	3|2	2|2	WDR64|WDR64	239996208|239996208	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.154000|0.154000	0.21943|0.21943	5.343000|5.343000	0.65976|0.65976	2.276000|2.276000	0.75962|0.75962	0.650000|0.650000	0.86243|0.86243	TTG|TGA		0.333	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		C	241929585	G	C	241929585	3	2	90	1	0	0	0	0	1	0	0	0	17355	1281	45	5	2041	5	WDR64	1	241929585	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	3982293	241929585	7321036	30	24617										
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343714	248343714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgaatcctaaaatttgtggaCttatggctaccttctcctgg	8	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:248343714C>T	ENST00000359682.2	+	1	427	c.427C>T	c.(427-429)Ctt>Ttt	p.L143F		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AATTTGTGGACTTATGGCTAC	0.428																																																0			1											205	213	210					1																	248343714		2203	4300	6503	246410337	SO:0001583	missense	391194			AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.427C>T	1.37:g.248343714C>T	ENSP00000352710:p.Leu143Phe		246410337	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	c	4.638	0.118564	0.08881	.	.	ENSG00000198601	ENST00000359682	T	0.00188	8.59	1.28	-0.154	0.13399	GPCR, rhodopsin-like superfamily (1);	0.000000	0.24050	U	0.042006	T	0.00178	0.0005	L	0.53249	1.67	0.09310	N	1	B	0.26512	0.151	B	0.36766	0.232	T	0.39333	-0.9619	10	0.39692	T	0.17	.	1.3921	0.02253	0.2007:0.4341:0.1997:0.1655	.	143	Q96R28	OR2M2_HUMAN	F	143	ENSP00000352710:L143F	ENSP00000352710:L143F	L	+	1	0	OR2M2	246410337	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-4.021000	0.00311	0.669000	0.31146	0.298000	0.19748	CTT		0.428	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		T	248343714	C	T	248343714	3	4	90	1	0	0	0	0	1	0	0	0	11041	565	20	3	429	3	OR2M2	1	248343714	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	6414129	248343714	906907	31	24618										
ZNF692	55657	hgsc.bcm.edu	37	chr1	249144901	249144901	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgcaggggtttttctccagtGtggatacgtctgtggatgac	14	7	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr1:249144901G>C	ENST00000306601.4	-	11	1399	c.1233C>G	c.(1231-1233)caC>caG	p.H411Q	ZNF692_ENST00000366471.3_Missense_Mutation_p.H366Q|ZNF692_ENST00000451251.1_Missense_Mutation_p.H416Q|ZNF692_ENST00000427146.1_Missense_Mutation_p.H366Q|ZNF692_ENST00000366469.5_Missense_Mutation_p.H410Q	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TTTCTCCAGTGTGGATACGTC	0.577																																																0			1											89	84	86					1																	249144901		2203	4300	6503	247111524	SO:0001583	missense	55657			BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163		"Zinc fingers, C2H2-type"	26049	protein-coding gene	gene with protein product						12477932	Standard	NM_001136036		Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.1233C>G	1.37:g.249144901G>C	ENSP00000305483:p.His411Gln		247111524	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	Missense_Mutation	SNP	ENST00000306601.4	37	CCDS31127.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.23|19.23	3.788105|3.788105	0.70337|0.70337	.|.	.|.	ENSG00000171163|ENSG00000171163	ENST00000476503|ENST00000306601;ENST00000427146;ENST00000366470;ENST00000366471;ENST00000366469;ENST00000451251	T|T;T;T;T;T	0.67698|0.66995	-0.28|-0.24;-0.24;-0.24;-0.24;-0.24	4.54|4.54	2.66|2.66	0.31614|0.31614	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000|0.000000	0.64402|0.64402	D|D	0.000020|0.000020	T|T	0.82222|0.82222	0.4990|0.4990	M|M	0.92507|0.92507	3.315|3.315	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.998;0.998;1.0;0.998	.|D;D;D;D;D	.|0.87578	.|0.998;0.98;0.98;0.998;0.966	T|T	0.82458|0.82458	-0.0447|-0.0447	8|10	0.87932|0.87932	D|D	0|0	-12.4799|-12.4799	6.2913|6.2913	0.21061|0.21061	0.2195:0.0:0.7805:0.0|0.2195:0.0:0.7805:0.0	.|.	.|416;366;239;411;144	.|B4DXZ0;Q9BU19-2;Q9BU19-3;Q9BU19;Q59EV5	.|.;.;.;ZN692_HUMAN;.	D|Q	165|411;366;239;366;410;416	ENSP00000431582:H165D|ENSP00000305483:H411Q;ENSP00000390044:H366Q;ENSP00000355427:H366Q;ENSP00000355425:H410Q;ENSP00000391200:H416Q	ENSP00000431582:H165D|ENSP00000305483:H411Q	H|H	-|-	1|3	0|2	ZNF692|ZNF692	247111524|247111524	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.948000|0.948000	0.59901|0.59901	4.154000|4.154000	0.58125|0.58125	1.277000|1.277000	0.44412|0.44412	0.462000|0.462000	0.41574|0.41574	CAC|CAC		0.577	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097298.1	NM_017865		C	249144901	G	C	249144901	3	2	90	1	0	0	0	0	1	0	0	0	18136	1368	48	5	334	5	ZNF692	1	249144901	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	801187	249144901	105720	32	24619										
SH3YL1	26751	hgsc.bcm.edu	37	chr2	231084	231084	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttcgttgtccttcattttcaTacttttcagtaaaggaatca	5	8	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:231084T>C	ENST00000405430.1	-	9	1017	c.641A>G	c.(640-642)tAt>tGt	p.Y214C	SH3YL1_ENST00000403712.2_Missense_Mutation_p.Y214C|SH3YL1_ENST00000415006.2_Missense_Mutation_p.Y118C|SH3YL1_ENST00000403657.1_Missense_Mutation_p.Y118C|SH3YL1_ENST00000403658.1_Missense_Mutation_p.Y118C|SH3YL1_ENST00000356150.5_Missense_Mutation_p.Y214C|SH3YL1_ENST00000468321.1_5'UTR			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	214					phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)	p.Y118C(1)		large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		TTCATTTTCATACTTTTCAGT	0.393																																																1	Substitution - Missense(1)	ovary(1)	2											143	136	138					2																	231084		1881	4100	5981	221084	SO:0001583	missense	26751				CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.641A>G	2.37:g.231084T>C	ENSP00000384269:p.Tyr214Cys		221084	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Missense_Mutation	SNP	ENST00000405430.1	37		.	.	.	.	.	.	.	.	.	.	T	15.48	2.846325	0.51164	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005;ENST00000431160	T;T;T;T;T;T;T	0.26067	2.04;2.0;2.02;1.88;1.88;2.02;1.76	5.11	3.93	0.45458	.	0.502845	0.20526	N	0.090610	T	0.36635	0.0974	L	0.32530	0.975	0.58432	D	0.999998	D;P;D;D	0.89917	1.0;0.806;1.0;1.0	D;B;D;D	0.97110	1.0;0.446;0.998;0.999	T	0.04103	-1.0977	10	0.48119	T	0.1	-6.6767	9.5344	0.39213	0.1576:0.0:0.0:0.8424	.	118;214;214;118	Q96HL8-4;Q96HL8-2;Q96HL8;Q96HL8-3	.;.;SH3Y1_HUMAN;.	C	118;214;118;214;214;118;146;170	ENSP00000404143:Y118C;ENSP00000384276:Y214C;ENSP00000385668:Y118C;ENSP00000384269:Y214C;ENSP00000348471:Y214C;ENSP00000383928:Y118C;ENSP00000416312:Y146C	ENSP00000348471:Y214C	Y	-	2	0	SH3YL1	221084	1.000000	0.71417	0.979000	0.43373	0.487000	0.33371	3.346000	0.52190	0.760000	0.33108	0.455000	0.32223	TAT		0.393	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677		C	231084	T	C	231084	3	2	90	1	0	0	0	0	1	0	0	0	14300	1406	49	4	403	4	SH3YL1	2	231084	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10		231084	242968289	33	24620										
TPO	7173	hgsc.bcm.edu	37	chr2	1491665	1491665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggtgcaggatcagctgatgaAcgaggagctgacggaaaggc	17	7	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:1491665A>G	ENST00000345913.4	+	10	1761	c.1670A>G	c.(1669-1671)aAc>aGc	p.N557S	TPO_ENST00000337415.3_Missense_Mutation_p.N557S|TPO_ENST00000346956.3_Missense_Mutation_p.N557S|TPO_ENST00000349624.3_Missense_Mutation_p.N384S|TPO_ENST00000329066.4_Missense_Mutation_p.N557S|TPO_ENST00000382201.3_Intron|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Missense_Mutation_p.N384S	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	557					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CAGCTGATGAACGAGGAGCTG	0.562																																																0			2											135	111	120					2																	1491665		2203	4300	6503	1470672	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1670A>G	2.37:g.1491665A>G	ENSP00000318820:p.Asn557Ser		1470672	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	A	1.771	-0.484393	0.04383	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.88	3.72	0.42706	.	0.276012	0.38326	N	0.001735	T	0.43322	0.1242	L	0.29908	0.895	0.20074	N	0.999936	B;P;B	0.39352	0.36;0.669;0.412	B;B;B	0.37451	0.161;0.19;0.25	T	0.20140	-1.0284	10	0.21540	T	0.41	-22.4378	5.7928	0.18369	0.7731:0.0:0.0793:0.1476	.	557;384;557	P07202-4;P07202-5;P07202	.;.;PERT_HUMAN	S	557;557;557;384;557;384;486	ENSP00000337263:N557S;ENSP00000318820:N557S;ENSP00000263886:N557S;ENSP00000332044:N384S;ENSP00000329869:N557S;ENSP00000371633:N384S;ENSP00000405788:N486S	ENSP00000329869:N557S	N	+	2	0	TPO	1470672	0.895000	0.30542	0.732000	0.30844	0.685000	0.39939	1.879000	0.39618	0.715000	0.32103	0.482000	0.46254	AAC		0.562	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		G	1491665	A	G	1491665	3	3	90	1	0	0	0	0	1	0	0	0	16450	43	2	4	1704	4	TPO	2	1491665	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1260581	1491665	241707708	34	24621										
E2F6	1876	hgsc.bcm.edu	37	chr2	11587813	11587813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggtcccgacaccttcagaccTtttgttactggtctgaccct	8	14	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:11587813T>C	ENST00000381525.3	-	6	1008	c.739A>G	c.(739-741)Agg>Ggg	p.R247G	E2F6_ENST00000546212.1_Missense_Mutation_p.R172G|E2F6_ENST00000362009.4_3'UTR|E2F6_ENST00000542100.1_Missense_Mutation_p.R172G|E2F6_ENST00000307236.4_Missense_Mutation_p.R215G	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6	247	Transcription repression.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		CCTTCAGACCTTTTGTTACTG	0.458																																																0			2											102	93	96					2																	11587813		1880	4105	5985	11505264	SO:0001583	missense	1876			AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.739A>G	2.37:g.11587813T>C	ENSP00000370936:p.Arg247Gly		11505264	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Missense_Mutation	SNP	ENST00000381525.3	37	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	T	9.749	1.167010	0.21621	.	.	ENSG00000169016	ENST00000381525;ENST00000307236;ENST00000542100;ENST00000546212	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	4.88	-7.31	0.01441	.	3.278190	0.00654	N	0.000577	T	0.04048	0.0113	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34925	-0.9809	10	0.48119	T	0.1	17.3777	3.0861	0.06278	0.1853:0.1219:0.0931:0.5996	.	247;215	O75461;G5E936	E2F6_HUMAN;.	G	247;215;172;172	ENSP00000370936:R247G;ENSP00000302159:R215G;ENSP00000446315:R172G;ENSP00000438864:R172G	ENSP00000302159:R215G	R	-	1	2	E2F6	11505264	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.524000	0.06222	-1.305000	0.02327	0.533000	0.62120	AGG		0.458	E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952		C	11587813	T	C	11587813	3	2	90	1	0	0	0	0	1	0	0	0	4882	1608	56	4	114	4	E2F6	2	11587813	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	10096148	11587813	231611560	35	24622										
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17699407	17699407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atctgcttcccactgactgaTttctccacacacgagtctgt	6	14	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:17699407T>G	ENST00000399080.2	-	1	299	c.276A>C	c.(274-276)aaA>aaC	p.K92N		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	92										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CACTGACTGATTTCTCCACAC	0.453																																																0			2											95	95	95					2																	17699407		1880	4113	5993	17562888	SO:0001583	missense	729475			AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.276A>C	2.37:g.17699407T>G	ENSP00000382030:p.Lys92Asn		17562888		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.346339	0.82022	.	.	ENSG00000214842	ENST00000399080	T	0.34472	1.36	3.45	-6.9	0.01655	.	.	.	.	.	T	0.21186	0.0510	L	0.27053	0.805	0.09310	N	1	P	0.49635	0.926	B	0.42995	0.404	T	0.20907	-1.0261	9	0.51188	T	0.08	-2.9426	6.9651	0.24619	0.0:0.3738:0.4408:0.1854	.	92	Q09MP3	R51A2_HUMAN	N	92	ENSP00000382030:K92N	ENSP00000382030:K92N	K	-	3	2	RAD51AP2	17562888	0.000000	0.05858	0.000000	0.03702	0.830000	0.47004	-1.714000	0.01881	-1.516000	0.01782	0.402000	0.26972	AAA		0.453	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		G	17699407	T	G	17699407	3	3	90	1	0	0	0	0	1	0	0	0	13024	1490	52	4	3215	4	RAD51AP2	2	17699407	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	6111594	17699407	225499966	36	24623										
C2orf79	391356	hgsc.bcm.edu	37	chr2	25013425	25013425	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gttgcagggtctcggccagcTcctttagggtggtctcatct	13	11	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:25013425T>G	ENST00000328379.5	-	2	282	c.278A>C	c.(277-279)gAg>gCg	p.E93A	CENPO_ENST00000380834.2_5'Flank|CENPO_ENST00000260662.1_5'Flank|PTRHD1_ENST00000487316.1_5'UTR|CENPO_ENST00000473706.1_5'Flank	NM_001013663.1	NP_001013685.1	Q6GMV3	PTRD1_HUMAN	peptidyl-tRNA hydrolase domain containing 1	93						extracellular vesicular exosome (GO:0070062)	aminoacyl-tRNA hydrolase activity (GO:0004045)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|skin(1)	6						CTCGGCCAGCTCCTTTAGGGT	0.507																																																0			2											92	79	84					2																	25013425		2203	4300	6503	24866929	SO:0001583	missense	391356				CCDS33156.1	2p23.3	2011-05-09	2011-05-09	2011-05-09	ENSG00000184924	ENSG00000184924			33782	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 79"	C2orf79		12477932	Standard	NM_001013663		Approved	LOC391356	uc002rfm.3	Q6GMV3	OTTHUMG00000151978	ENST00000328379.5:c.278A>C	2.37:g.25013425T>G	ENSP00000330389:p.Glu93Ala		24866929		Missense_Mutation	SNP	ENST00000328379.5	37	CCDS33156.1	.	.	.	.	.	.	.	.	.	.	T	9.362	1.068158	0.20067	.	.	ENSG00000184924	ENST00000328379	T	0.27720	1.65	5.08	-0.501	0.12008	Peptidyl-tRNA hydrolase II domain (2);	0.702237	0.14187	N	0.335631	T	0.11537	0.0281	N	0.05414	-0.055	0.26063	N	0.981324	B	0.02656	0.0	B	0.06405	0.002	T	0.31943	-0.9925	10	0.14656	T	0.56	-4.2503	5.0624	0.14564	0.3883:0.0:0.2863:0.3254	.	93	Q6GMV3	PTRD1_HUMAN	A	93	ENSP00000330389:E93A	ENSP00000330389:E93A	E	-	2	0	PTRHD1	24866929	0.000000	0.05858	0.993000	0.49108	0.991000	0.79684	0.015000	0.13355	0.111000	0.17947	0.533000	0.62120	GAG		0.507	PTRHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324626.3	NM_001013663		G	25013425	T	G	25013425	3	3	90	1	0	0	0	0	1	0	0	0	2202	1551	54	4	148	4	C2orf79	2	25013425	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	7314018	25013425	218185948	37	24624										
ADCY3	109	hgsc.bcm.edu	37	chr2	25141305	25141305	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acgatggggctgaggctgagGggcagcgtgatgaagaagga	20	5	0	5			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:25141305G>T	ENST00000260600.5	-	1	1403	c.552C>A	c.(550-552)ccC>ccA	p.P184P		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	184					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TGAGGCTGAGGGGCAGCGTGA	0.622																																																0			2											74	80	78					2																	25141305		2203	4300	6503	24994809	SO:0001819	synonymous_variant	114			AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.552C>A	2.37:g.25141305G>T			24994809	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																				0.622	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			T	25141305	G	T	25141305	2	4	90	1	0	0	0	0	0	0	0	1	295	1219	43	2		2	ADCY3	2	25141305	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	127880	25141305	218058068	38	24625										
MTA3	57504	hgsc.bcm.edu	37	chr2	42922931	42922932	+	Frame_Shift_Ins	INS	-	-	A													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggaaatcattgactagcatcINSattgaatattattacatgtg							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:42922931_42922932insA	ENST00000405094.1	+	10	918_919	c.918_919insA	c.(919-921)attfs	p.I307fs	MTA3_ENST00000472767.1_3'UTR|MTA3_ENST00000407270.3_Frame_Shift_Ins_p.I307fs|MTA3_ENST00000406911.1_Frame_Shift_Ins_p.I307fs|MTA3_ENST00000406652.1_Frame_Shift_Ins_p.I251fs|MTA3_ENST00000405592.1_Frame_Shift_Ins_p.I251fs			Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	307	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.					intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						TGACTAGCATCATTGAATATTA	0.282																																																0			2																																								42776436	SO:0001589	frameshift_variant	57504			AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935		"GATA zinc finger domain containing"	23784	protein-coding gene	gene with protein product		609050	"metastasis associated gene family, member 3"			12705869, 14613024	Standard	NM_001282755		Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000405094.1:c.919dupA	2.37:g.42922932_42922932dupA	ENSP00000385823:p.Ile307fs		42776435	Q9NSP2|Q9ULF4	Frame_Shift_Ins	INS	ENST00000405094.1	37																																																																																					0.282	MTA3-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318159.1	NM_020744		A	42922932	-	A	42922931	7	5	90	1	0	1	1	0	0	0	0	0	9940	816	29	0	956	0	MTA3	2	42922931	Frame_Shift_Ins	INS	-	TCGA-CI-6624-01C-11D-1826-10	17781626	42922931	200276442	39	24626										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55562020	55562020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttttaaattagttatttttTtctgtaataattcattttct	2	3	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:55562020T>C	ENST00000436346.1	-	15	2778	c.1937A>G	c.(1936-1938)aAa>aGa	p.K646R	CCDC88A_ENST00000336838.6_Missense_Mutation_p.K646R|AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000599352.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.K646R|CCDC88A_ENST00000413716.2_Missense_Mutation_p.K646R|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000594078.1_RNA|AC012358.8_ENST00000608103.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	646					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						AGTTATTTTTTTCTGTAATAA	0.239																																																0			2											13	12	12					2																	55562020		2127	4172	6299	55415524	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1937A>G	2.37:g.55562020T>C	ENSP00000410608:p.Lys646Arg		55415524	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	T	13.28	2.189154	0.38707	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.06	5.06	0.68205	.	0.000000	0.51477	U	0.000096	T	0.47116	0.1428	L	0.31752	0.955	0.80722	D	1	B;D;D	0.71674	0.188;0.998;0.998	B;D;D	0.78314	0.062;0.991;0.957	T	0.38779	-0.9645	10	0.35671	T	0.21	-24.677	14.8159	0.70034	0.0:0.0:0.0:1.0	.	646;646;646	B7ZM78;Q3V6T2-2;Q3V6T2-3	.;.;.	R	646	ENSP00000338728:K646R;ENSP00000263630:K646R;ENSP00000410608:K646R;ENSP00000404431:K646R	ENSP00000263630:K646R	K	-	2	0	CCDC88A	55415524	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.937000	0.70162	1.896000	0.54893	0.459000	0.35465	AAA		0.239	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55562020	T	C	55562020	3	2	90	1	0	0	0	0	1	0	0	0	2869	1841	64	4	3750	4	CCDC88A	2	55562020	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	12639089	55562020	187637353	40	24627										
VRK2	7444	hgsc.bcm.edu	37	chr2	58275998	58275998	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aagaaatgaaaaatacaaacTtcctattccatttccagaag	4	8	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:58275998T>C	ENST00000435505.2	+	5	777	c.32T>C	c.(31-33)cTt>cCt	p.L11P	VRK2_ENST00000417641.2_Missense_Mutation_p.L11P|VRK2_ENST00000440705.2_Intron|VRK2_ENST00000412104.2_Missense_Mutation_p.L11P|VRK2_ENST00000340157.4_Missense_Mutation_p.L11P			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	11					cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L11H(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						AAATACAAACTTCCTATTCCA	0.378																																																1	Substitution - Missense(1)	ovary(1)	2											81	85	84					2																	58275998		2203	4300	6503	58129502	SO:0001583	missense	7444			AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.32T>C	2.37:g.58275998T>C	ENSP00000408002:p.Leu11Pro		58129502	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065626	0.76187	.	.	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000423109;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000428021	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.72003	0.3407	M	0.86028	2.79	0.80722	D	1	D;D;P	0.89917	1.0;0.999;0.94	D;D;P	0.77557	0.99;0.987;0.824	T	0.76992	-0.2753	10	0.87932	D	0	-15.3956	14.9988	0.71455	0.0:0.0:0.0:1.0	.	11;11;11	Q86Y07-2;Q86Y07-5;Q86Y07	.;.;VRK2_HUMAN	P	11;11;11;11;11;11;16	ENSP00000408002:L11P;ENSP00000402375:L11P;ENSP00000404156:L11P;ENSP00000342381:L11P;ENSP00000404961:L16P	ENSP00000342381:L11P	L	+	2	0	VRK2	58129502	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.124000	0.64709	2.279000	0.76181	0.533000	0.62120	CTT		0.378	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		C	58275998	T	C	58275998	3	2	90	1	0	0	0	0	1	0	0	0	17260	1609	56	4	34	4	VRK2	2	58275998	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2713978	58275998	184923375	41	24628										
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102808570	102808570	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgtgttttgggtccaataaAgtggtataaggtaaaaaaga	11	2	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:102808570A>C	ENST00000264257.2	+	4	605	c.479A>C	c.(478-480)aAg>aCg	p.K160T	IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.K160T	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	160	Ig-like C2-type 2.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						GGTCCAATAAAGTGGTATAAG	0.308																																																0			2											77	75	76					2																	102808570		2203	4300	6503	102175002	SO:0001583	missense	8808			U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.479A>C	2.37:g.102808570A>C	ENSP00000264257:p.Lys160Thr		102175002	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	A	10.14	1.268974	0.23221	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.11930	2.73;2.73;2.73	5.4	-4.05	0.03998	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.685751	0.15046	N	0.283570	T	0.04092	0.0114	N	0.12637	0.245	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.39375	-0.9617	10	0.06757	T	0.87	.	2.5154	0.04667	0.2975:0.3817:0.0741:0.2467	.	160	Q9HB29	ILRL2_HUMAN	T	160	ENSP00000264257:K160T;ENSP00000387611:K160T;ENSP00000442184:K160T	ENSP00000264257:K160T	K	+	2	0	IL1RL2	102175002	0.024000	0.19004	0.016000	0.15963	0.011000	0.07611	-0.057000	0.11768	-0.877000	0.04012	-1.402000	0.01139	AAG		0.308	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		C	102808570	A	C	102808570	3	2	90	1	0	0	0	0	1	0	0	0	7685	72	3	4	489	4	IL1RL2	2	102808570	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	44532572	102808570	140390803	42	24629										
ACOXL	55289	hgsc.bcm.edu	37	chr2	111744754	111744754	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aaccactctttggcctgctcCaaaactgggctgaatctgtg	9	12	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:111744754C>A	ENST00000389811.4	+	14	1443	c.1219C>A	c.(1219-1221)Caa>Aaa	p.Q407K	ACOXL_ENST00000439055.1_Missense_Mutation_p.Q377K			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	407					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						TGGCCTGCTCCAAAACTGGGC	0.498																																																0			2											102	80	88					2																	111744754		2203	4300	6503	111461225	SO:0001583	missense	55289				CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"acyl-Coenzyme A oxidase-like"				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.1219C>A	2.37:g.111744754C>A	ENSP00000374461:p.Gln407Lys		111461225	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		.	.	.	.	.	.	.	.	.	.	C	5.276	0.236302	0.10023	.	.	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	T;T;T	0.69306	-0.39;-0.39;-0.39	5.35	3.56	0.40772	Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.753212	0.11413	N	0.566555	T	0.48822	0.1521	L	0.27053	0.805	0.21147	N	0.999772	B;B;B	0.20261	0.043;0.034;0.001	B;B;B	0.18561	0.016;0.022;0.002	T	0.27536	-1.0071	10	0.06494	T	0.89	-24.7234	10.1068	0.42539	0.0:0.8348:0.0:0.1652	.	377;377;407	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	K	407;377;228;215	ENSP00000374461:Q407K;ENSP00000407761:Q377K;ENSP00000387832:Q215K	ENSP00000374461:Q407K	Q	+	1	0	ACOXL	111461225	0.086000	0.21541	0.003000	0.11579	0.938000	0.57974	0.955000	0.29188	0.762000	0.33152	0.591000	0.81541	CAA		0.498	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		A	111744754	C	A	111744754	3	1	90	1	0	0	0	0	1	0	0	0	161	595	21	2	1175	2	ACOXL	2	111744754	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	8936184	111744754	131454619	43	24630										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112849344	112849344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tattttagcagttattgactCcatttttgtgtggttcatat	7	5	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:112849344C>T	ENST00000283206.4	+	11	1457	c.1088C>T	c.(1087-1089)tCc>tTc	p.S363F	TMEM87B_ENST00000463427.1_3'UTR	NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	363						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						GTTATTGACTCCATTTTTGTG	0.299																																																0			2											271	232	245					2																	112849344		2203	4298	6501	112565815	SO:0001583	missense	84910			AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.1088C>T	2.37:g.112849344C>T	ENSP00000283206:p.Ser363Phe		112565815	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	37	CCDS33275.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564350	0.86335	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.74	5.74	0.90152	.	0.162448	0.56097	D	0.000029	T	0.77611	0.4156	M	0.72118	2.19	0.80722	D	1	D	0.69078	0.997	D	0.68943	0.961	T	0.78971	-0.1993	9	0.87932	D	0	-15.3363	15.7886	0.78332	0.0:1.0:0.0:0.0	.	363	Q96K49	TM87B_HUMAN	F	363	.	ENSP00000283206:S363F	S	+	2	0	TMEM87B	112565815	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.669000	0.74462	2.873000	0.98535	0.563000	0.77884	TCC		0.299	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		T	112849344	C	T	112849344	3	4	90	1	0	0	0	0	1	0	0	0	16250	855	30	3	1130	3	TMEM87B	2	112849344	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1104590	112849344	130350029	44	24631										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125281916	125281916	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tggcctgtggcactcggttaGcatcaacgccaggaggaacc	13	12	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:125281916G>C	ENST00000431078.1	+	9	1725	c.1361G>C	c.(1360-1362)aGc>aCc	p.S454T		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	454	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CACTCGGTTAGCATCAACGCC	0.527																																																0			2											77	82	80					2																	125281916		2080	4221	6301	124998386	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1361G>C	2.37:g.125281916G>C	ENSP00000399013:p.Ser454Thr		124998386	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647910	0.47258	.	.	ENSG00000155052	ENST00000431078	T	0.77620	-1.11	5.95	4.16	0.48862	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.095877	0.45361	D	0.000365	T	0.59865	0.2225	N	0.20845	0.615	0.41006	D	0.984965	B	0.24092	0.097	B	0.27170	0.077	T	0.55667	-0.8105	10	0.32370	T	0.25	.	4.6813	0.12736	0.2261:0.169:0.6049:0.0	.	454	Q8WYK1	CNTP5_HUMAN	T	454	ENSP00000399013:S454T	ENSP00000399013:S454T	S	+	2	0	CNTNAP5	124998386	1.000000	0.71417	0.997000	0.53966	0.345000	0.29048	1.695000	0.37763	1.542000	0.49330	-0.123000	0.14984	AGC		0.527	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			C	125281916	G	C	125281916	3	2	90	1	0	0	0	0	1	0	0	0	3656	971	34	5	1395	5	CNTNAP5	2	125281916	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	12432572	125281916	117917457	45	24632										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141751586	141751586	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagtttactgaatcctcatcGcttccgtctaggcagtcatc	7	13	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:141751586G>A	ENST00000389484.3	-	16	3593	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	874	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S874S(2)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		AATCCTCATCGCTTCCGTCTA	0.428										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											2	Substitution - coding silent(2)	large_intestine(2)	2											127	121	123					2																	141751586		2203	4300	6503	141468056	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2622C>T	2.37:g.141751586G>A			141468056	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.428	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141751586	G	A	141751586	2	1	90	1	0	0	0	0	0	0	0	1	8984	1078	38	1		1	LRP1B	2	141751586	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	16469670	141751586	101447787	46	24633										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153484985	153484985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtaaaatcgagaggctcatgCagaagatgaccatcatggcc	11	9	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:153484985C>A	ENST00000475377.2	+	5	663	c.463C>A	c.(463-465)Cag>Aag	p.Q155K	FMNL2_ENST00000288670.9_Missense_Mutation_p.Q780K			Q96PY5	FMNL2_HUMAN	formin-like 2	780	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						GAGGCTCATGCAGAAGATGAC	0.498																																																0			2											130	134	133					2																	153484985		2114	4239	6353	153193231	SO:0001583	missense	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000475377.2:c.463C>A	2.37:g.153484985C>A	ENSP00000418959:p.Gln155Lys		153193231	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000475377.2	37		.	.	.	.	.	.	.	.	.	.	C	21.2	4.115529	0.77323	.	.	ENSG00000157827	ENST00000288670;ENST00000421344;ENST00000475377	T;T	0.16073	2.37;2.37	5.31	5.31	0.75309	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.099931	0.64402	D	0.000001	T	0.46444	0.1393	M	0.82630	2.6	0.80722	D	1	D;B;P	0.53885	0.963;0.407;0.723	D;B;P	0.71414	0.973;0.403;0.561	T	0.27971	-1.0058	10	0.32370	T	0.25	.	19.1722	0.93583	0.0:1.0:0.0:0.0	.	780;261;780	Q96PY5;Q6ZN96;Q96PY5-3	FMNL2_HUMAN;.;.	K	780;261;155	ENSP00000288670:Q780K;ENSP00000418959:Q155K	ENSP00000288670:Q780K	Q	+	1	0	FMNL2	153193231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.763000	0.94921	0.563000	0.77884	CAG		0.498	FMNL2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333583.3	NM_052905		A	153484985	C	A	153484985	3	1	90	1	0	0	0	0	1	0	0	0	5971	711	25	2	2408	2	FMNL2	2	153484985	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	11733399	153484985	89714388	47	24634										
GALNT13	114805	hgsc.bcm.edu	37	chr2	154801024	154801024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaaagacatgaggagatttgTctactgcaaggtggttctag	13	5	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:154801024T>C	ENST00000392825.3	+	3	581	c.14T>C	c.(13-15)gTc>gCc	p.V5A	GALNT13_ENST00000409237.1_Missense_Mutation_p.V5A	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	5					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						AGGAGATTTGTCTACTGCAAG	0.408																																																0			2											231	207	215					2																	154801024		2203	4300	6503	154509270	SO:0001583	missense	117248			AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.14T>C	2.37:g.154801024T>C	ENSP00000376570:p.Val5Ala		154509270	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	37	CCDS2199.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502793	0.26949	.	.	ENSG00000144278	ENST00000392825;ENST00000434213;ENST00000409237	T;T	0.52983	0.7;0.64	5.43	5.43	0.79202	.	0.145294	0.46145	N	0.000319	T	0.21962	0.0529	N	0.02391	-0.57	0.49299	D	0.999771	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.15435	-1.0437	10	0.08837	T	0.75	.	14.2927	0.66289	0.0:0.0:0.0:1.0	.	5;5	Q08ER7;Q8IUC8	.;GLT13_HUMAN	A	5	ENSP00000376570:V5A;ENSP00000387239:V5A	ENSP00000376570:V5A	V	+	2	0	GALNT13	154509270	0.959000	0.32827	1.000000	0.80357	0.993000	0.82548	1.441000	0.35035	2.056000	0.61249	0.477000	0.44152	GTC		0.408	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		C	154801024	T	C	154801024	3	2	90	1	0	0	0	0	1	0	0	0	6231	1667	58	4	16	4	GALNT13	2	154801024	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1316039	154801024	88398349	48	24635										
WDSUB1	151525	hgsc.bcm.edu	37	chr2	160112842	160112842	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgttgagacatcctcctctgAccaatcttcggtaaattgct	7	11	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:160112842A>T	ENST00000409990.3	-	9	1253	c.997T>A	c.(997-999)Tca>Aca	p.S333T	WDSUB1_ENST00000358147.4_Missense_Mutation_p.S241T|WDSUB1_ENST00000392796.3_Missense_Mutation_p.S333T|WDSUB1_ENST00000359774.4_Missense_Mutation_p.S333T|WDSUB1_ENST00000409124.1_Missense_Mutation_p.S333T	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	333	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.						ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						TCCTCCTCTGACCAATCTTCG	0.338																																																0			2											104	100	102					2																	160112842		2203	4300	6503	159821088	SO:0001583	missense	151525			AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"WD repeat domain containing", "Sterile alpha motif (SAM) domain containing", "U-box domain containing"	26697	protein-coding gene	gene with protein product			"WD repeat and SAM domain containing 1", "WD repeat, SAM and U-box domain containing 1"	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.997T>A	2.37:g.160112842A>T	ENSP00000387078:p.Ser333Thr		159821088	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.185002	0.78677	.	.	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	D;D;D;D;T	0.84800	-1.9;-1.9;-1.9;-1.9;2.25	5.76	5.76	0.90799	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.85682	D	0.000000	D	0.87354	0.6156	N	0.21142	0.635	0.58432	D	0.999999	D;D;B	0.76494	0.998;0.999;0.22	D;D;B	0.83275	0.994;0.996;0.249	D	0.88091	0.2813	10	0.46703	T	0.11	.	16.066	0.80870	1.0:0.0:0.0:0.0	.	241;333;333	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	T	333;241;333;333;333	ENSP00000352820:S333T;ENSP00000350866:S241T;ENSP00000376545:S333T;ENSP00000387078:S333T;ENSP00000386891:S333T	ENSP00000350866:S241T	S	-	1	0	WDSUB1	159821088	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.795000	0.91872	2.190000	0.69967	0.533000	0.62120	TCA		0.338	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		T	160112842	A	T	160112842	3	4	90	1	0	0	0	0	1	0	0	0	17381	275	10	5	445	5	WDSUB1	2	160112842	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	5311818	160112842	83086531	49	24636										
IFIH1	64135	hgsc.bcm.edu	37	chr2	163144688	163144688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttccaggctcagatgcttttTtcttcttgtctaagtgatcc	7	10	4	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:163144688T>C	ENST00000263642.2	-	5	1447	c.1052A>G	c.(1051-1053)aAa>aGa	p.K351R		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	351	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						AGATGCTTTTTTCTTCTTGTC	0.383																																																0			2											108	108	108					2																	163144688		2203	4300	6503	162852934	SO:0001583	missense	64135			AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1052A>G	2.37:g.163144688T>C	ENSP00000263642:p.Lys351Arg		162852934	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	T	9.158	1.017913	0.19355	.	.	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.05081	3.5	5.84	3.46	0.39613	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.286088	0.42964	D	0.000622	T	0.02610	0.0079	N	0.02854	-0.475	0.32066	N	0.595068	B	0.12630	0.006	B	0.14023	0.01	T	0.30090	-0.9990	10	0.17369	T	0.5	-9.9286	9.3498	0.38131	0.0:0.264:0.0:0.736	.	351	Q9BYX4	IFIH1_HUMAN	R	351	ENSP00000263642:K351R	ENSP00000263642:K351R	K	-	2	0	IFIH1	162852934	0.002000	0.14202	0.968000	0.41197	0.979000	0.70002	-0.068000	0.11561	1.054000	0.40438	0.528000	0.53228	AAA		0.383	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		C	163144688	T	C	163144688	3	2	90	1	0	0	0	0	1	0	0	0	7541	1841	64	4	2073	4	IFIH1	2	163144688	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	3031846	163144688	80054685	50	24637										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165552326	165552326	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttctgtgttctctggatagaCaattatttcattttgaacta	6	6	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:165552326C>A	ENST00000392717.2	-	13	1808	c.1804G>T	c.(1804-1806)Gtc>Ttc	p.V602F	COBLL1_ENST00000194871.6_Missense_Mutation_p.V631F|COBLL1_ENST00000342193.4_Missense_Mutation_p.V564F|COBLL1_ENST00000375458.2_Missense_Mutation_p.V526F|COBLL1_ENST00000409184.3_Missense_Mutation_p.V564F			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	602						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						TCTGGATAGACAATTATTTCA	0.303																																																0			2											57	52	54					2																	165552326		2202	4297	6499	165260572	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1804G>T	2.37:g.165552326C>A	ENSP00000376478:p.Val602Phe		165260572	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	C	1.328	-0.597522	0.03771	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.85	-0.43	0.12299	.	0.546302	0.17876	N	0.159015	T	0.17066	0.0410	N	0.19112	0.55	0.09310	N	1	B;B;B	0.12630	0.003;0.003;0.006	B;B;B	0.15870	0.006;0.007;0.014	T	0.10451	-1.0629	9	0.30854	T	0.27	-0.1016	2.8914	0.05677	0.1036:0.3873:0.2915:0.2176	.	602;631;564	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	F	526;564;564;602;631	.	ENSP00000194871:V631F	V	-	1	0	COBLL1	165260572	0.001000	0.12720	0.011000	0.14972	0.062000	0.15995	-0.355000	0.07671	0.378000	0.24764	-0.136000	0.14681	GTC		0.303	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165552326	C	A	165552326	3	1	90	1	0	0	0	0	1	0	0	0	3660	478	17	2	1822	2	COBLL1	2	165552326	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2407638	165552326	77647047	51	24638										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100409	168100409	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aaaggaaaaaataataggtaCagatgtctccagaaagtgtt	9	4	1	2	rs77595411		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:168100409C>A	ENST00000409195.1	+	9	2596	c.2507C>A	c.(2506-2508)aCa>aAa	p.T836K	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.T836K|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.T614K|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	661					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATAATAGGTACAGATGTCTCC	0.393																																																0			2											87	87	87					2																	168100409		1820	4076	5896	167808655	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2507C>A	2.37:g.168100409C>A	ENSP00000386840:p.Thr836Lys		167808655	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965673	0.53507	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02631	4.22;4.22;4.22	5.82	4.94	0.65067	.	0.481828	0.24422	N	0.038668	T	0.07593	0.0191	L	0.57536	1.79	0.33869	D	0.634673	P;P;P	0.43231	0.801;0.763;0.763	P;P;B	0.49192	0.602;0.466;0.387	T	0.06881	-1.0802	10	0.62326	D	0.03	-2.0698	12.3646	0.55222	0.0:0.8584:0.0:0.1416	.	661;661;614	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	K	836;836;614	ENSP00000386840:T836K;ENSP00000295237:T836K;ENSP00000387255:T614K	ENSP00000295237:T836K	T	+	2	0	XIRP2	167808655	0.890000	0.30428	0.998000	0.56505	0.989000	0.77384	3.763000	0.55257	1.437000	0.47472	0.650000	0.86243	ACA		0.393	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168100409	C	A	168100409	3	1	90	1	0	0	0	0	1	0	0	0	17470	478	17	2	2537	2	XIRP2	2	168100409	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2548083	168100409	75098964	52	24639										
LRP2	4036	hgsc.bcm.edu	37	chr2	170037974	170037974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtactctatgtaacccaggtGggcatctgcccagtagagta	11	10	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:170037974G>A	ENST00000263816.3	-	52	10438	c.10153C>T	c.(10153-10155)Cac>Tac	p.H3385Y	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3385					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TAACCCAGGTGGGCATCTGCC	0.413																																																0			2											176	152	160					2																	170037974		2203	4300	6503	169746220	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10153C>T	2.37:g.170037974G>A	ENSP00000263816:p.His3385Tyr		169746220	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790940	0.90367	.	.	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.95885	-3.84	5.7	5.7	0.88788	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.95294	0.8473	N	0.12182	0.205	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95951	0.8954	10	0.49607	T	0.09	.	19.8385	0.96670	0.0:0.0:1.0:0.0	.	3385	P98164	LRP2_HUMAN	Y	3385;80	ENSP00000263816:H3385Y	ENSP00000263816:H3385Y	H	-	1	0	LRP2	169746220	1.000000	0.71417	0.996000	0.52242	0.913000	0.54294	9.869000	0.99810	2.701000	0.92244	0.655000	0.94253	CAC		0.413	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170037974	G	A	170037974	3	1	90	1	0	0	0	0	1	0	0	0	8985	1348	47	3	3926	3	LRP2	2	170037974	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	1937565	170037974	73161399	53	24640										
TTN	7273	hgsc.bcm.edu	37	chr2	179397255	179397255	+	Frame_Shift_Del	DEL	G	G	-													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agtgtggagggcttcgacttGggggtgaagctgaaaaacct							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:179397255delG	ENST00000591111.1	-	308	99388	c.99164delC	c.(99163-99165)ccafs	p.P33055fs	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.P25756fs|TTN-AS1_ENST00000588257.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.P34696fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.P25631fs|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.P25823fs|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.P32128fs|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33055					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTCGACTTGGGGGTGAAGC	0.453																																																0			2											125	118	120					2																	179397255		1900	4132	6032	179105501	SO:0001589	frameshift_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.99164delC	2.37:g.179397255delG	ENSP00000465570:p.Pro33055fs		179105501	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	37																																																																																					0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179397255	G	-	179397255	7	5	90	1	0	1	0	1	0	0	0	0	16775	1348	47	0	3912	0	TTN	2	179397255	Frame_Shift_Del	DEL	G	TCGA-CI-6624-01C-11D-1826-10	9359281	179397255	63802118	54	24641										
TTN	7273	hgsc.bcm.edu	37	chr2	179472135	179472135	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caacattccttaccaaaaacTtctaccctggctgctgcaaa	4	14	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:179472135T>G	ENST00000591111.1	-	227	48581	c.48357A>C	c.(48355-48357)gaA>gaC	p.E16119D	TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E8820D|TTN_ENST00000589042.1_Missense_Mutation_p.E17760D|TTN_ENST00000460472.2_Missense_Mutation_p.E8695D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E8887D|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E15192D|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16119	Ig-like 99.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACCAAAAACTTCTACCCTGG	0.383																																																0			2											167	158	161					2																	179472135		1871	4091	5962	179180380	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48357A>C	2.37:g.179472135T>G	ENSP00000465570:p.Glu16119Asp		179180380	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	10.23	1.292435	0.23564	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.99	3.66	0.41972	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.43144	0.1234	N	0.03281	-0.365	0.32084	N	0.592799	B;B;B;B	0.28605	0.121;0.121;0.121;0.217	B;B;B;B	0.30855	0.069;0.069;0.069;0.121	T	0.53092	-0.8487	9	0.87932	D	0	.	8.2865	0.31932	0.0:0.2092:0.0:0.7908	.	8695;8820;8887;16119	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	15192;8695;8887;8820;8695	ENSP00000343764:E15192D;ENSP00000434586:E8695D;ENSP00000340554:E8887D;ENSP00000352154:E8820D	ENSP00000340554:E8887D	E	-	3	2	TTN	179180380	0.973000	0.33851	1.000000	0.80357	0.996000	0.88848	0.030000	0.13688	1.089000	0.41292	0.533000	0.62120	GAA		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179472135	T	G	179472135	3	3	90	1	0	0	0	0	1	0	0	0	16775	1606	56	4	54757	4	TTN	2	179472135	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	74880	179472135	63727238	55	24642										
TTN	7273	hgsc.bcm.edu	37	chr2	179650445	179650445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cacatggactaatctttccgTtgttagatctgtagttttct	7	8	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:179650445T>C	ENST00000591111.1	-	15	2619	c.2395A>G	c.(2395-2397)Acg>Gcg	p.T799A	TTN_ENST00000360870.5_Missense_Mutation_p.T799A|TTN_ENST00000359218.5_Missense_Mutation_p.T753A|TTN_ENST00000589042.1_Missense_Mutation_p.T799A|TTN_ENST00000460472.2_Missense_Mutation_p.T753A|TTN_ENST00000342175.6_Missense_Mutation_p.T753A|TTN_ENST00000342992.6_Missense_Mutation_p.T799A			Q8WZ42	TITIN_HUMAN	titin	33633			T -> M (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATCTTTCCGTTGTTAGATCT	0.418																																																0			2											237	225	229					2																	179650445		2203	4300	6503	179358690	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2395A>G	2.37:g.179650445T>C	ENSP00000465570:p.Thr799Ala		179358690	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	10.70	1.424570	0.25639	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.64085	-0.08;0.15;0.14;0.13;0.18	5.51	4.33	0.51752	Ribonuclease H-like (1);	.	.	.	.	T	0.45478	0.1344	L	0.27053	0.805	0.09310	N	1	B;B;B;B;B	0.27068	0.002;0.002;0.002;0.001;0.167	B;B;B;B;B	0.24269	0.002;0.002;0.004;0.002;0.052	T	0.42732	-0.9434	9	0.87932	D	0	.	4.2858	0.10855	0.1247:0.0689:0.1302:0.6762	.	753;753;753;799;799	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	799;753;753;753;753;799	ENSP00000343764:T799A;ENSP00000434586:T753A;ENSP00000340554:T753A;ENSP00000352154:T753A;ENSP00000354117:T799A	ENSP00000340554:T753A	T	-	1	0	TTN	179358690	0.999000	0.42202	0.956000	0.39512	0.991000	0.79684	1.750000	0.38329	0.980000	0.38523	0.533000	0.62120	ACG		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179650445	T	C	179650445	3	2	90	1	0	0	0	0	1	0	0	0	16775	1725	60	4	108985	4	TTN	2	179650445	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	178310	179650445	63548928	56	24643										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191301608	191301608	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttatgatcaacaagaagttGaagctatattcttggtgatc	8	5	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:191301608G>T	ENST00000392328.1	+	3	1177	c.853G>T	c.(853-855)Gaa>Taa	p.E285*	MFSD6_ENST00000281416.7_Nonsense_Mutation_p.E285*	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	285					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						ACAAGAAGTTGAAGCTATATT	0.423																																																0			2											231	220	224					2																	191301608		2203	4300	6503	191009853	SO:0001587	stop_gained	54842				CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.853G>T	2.37:g.191301608G>T	ENSP00000376141:p.Glu285*		191009853	D3KSZ4|Q86TH2|Q9NXM3	Nonsense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	G	36	5.870965	0.97049	.	.	ENSG00000151690	ENST00000392328;ENST00000281416	.	.	.	6.07	6.07	0.98685	.	0.045213	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-24.3956	19.632	0.95713	0.0:0.0:1.0:0.0	.	.	.	.	X	285	.	ENSP00000281416:E285X	E	+	1	0	MFSD6	191009853	1.000000	0.71417	0.974000	0.42286	0.837000	0.47467	6.639000	0.74314	2.890000	0.99128	0.650000	0.86243	GAA		0.423	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			T	191301608	G	T	191301608	4	4	90	1	0	0	0	0	0	1	0	0	9565	1291	45	2	855	2	MFSD6	2	191301608	Nonsense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	11651163	191301608	51897765	57	24644										
STAT1	6772	hgsc.bcm.edu	37	chr2	191862981	191862981	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cattaaatacatcttcttgaGtaacagctgttcttgtttct	5	8	4	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:191862981G>C	ENST00000361099.3	-	8	982	c.595C>G	c.(595-597)Ctc>Gtc	p.L199V	STAT1_ENST00000540176.1_Intron|STAT1_ENST00000392323.2_Missense_Mutation_p.L201V|STAT1_ENST00000392322.3_Missense_Mutation_p.L199V|STAT1_ENST00000409465.1_Missense_Mutation_p.L199V	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	199					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			ATCTTCTTGAGTAACAGCTGT	0.343																																																0			2											168	161	163					2																	191862981		2202	4298	6500	191571226	SO:0001583	missense	6772				CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.595C>G	2.37:g.191862981G>C	ENSP00000354394:p.Leu199Val		191571226	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	G	3.437	-0.114914	0.06881	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323;ENST00000544783	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	4.59	1.45	0.22620	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.491379	0.22687	N	0.056875	T	0.51907	0.1702	M	0.67700	2.07	0.35015	D	0.757296	B;B	0.12630	0.001;0.006	B;B	0.25884	0.006;0.064	T	0.55860	-0.8074	10	0.40728	T	0.16	-9.4431	7.8489	0.29442	0.0752:0.0:0.4869:0.4379	.	199;199	P42224-2;P42224	.;STAT1_HUMAN	V	199;199;199;201;107	ENSP00000354394:L199V;ENSP00000386244:L199V;ENSP00000376136:L199V;ENSP00000376137:L201V	ENSP00000354394:L199V	L	-	1	0	STAT1	191571226	0.923000	0.31300	0.103000	0.21229	0.204000	0.24138	1.417000	0.34770	0.599000	0.29845	-0.274000	0.10170	CTC		0.343	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		C	191862981	G	C	191862981	3	2	90	1	0	0	0	0	1	0	0	0	15303	1029	36	5	1733	5	STAT1	2	191862981	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	561373	191862981	51336392	58	24645										
HECW2	57520	hgsc.bcm.edu	37	chr2	197143338	197143338	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	actgctctgaagtgggagccGgggatcaatgaaagtggtgg	17	6	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:197143338G>A	ENST00000260983.3	-	15	3231	c.3049C>T	c.(3049-3051)Cgg>Tgg	p.R1017W	HECW2_ENST00000409111.1_Missense_Mutation_p.R661W	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1017	Interaction with TP73.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						AGTGGGAGCCGGGGATCAATG	0.532																																																0			2											160	128	139					2																	197143338		2203	4300	6503	196851583	SO:0001583	missense	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.3049C>T	2.37:g.197143338G>A	ENSP00000260983:p.Arg1017Trp		196851583	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.899316	0.72754	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	D;D	0.85411	-1.98;-1.98	5.02	4.12	0.48240	WW/Rsp5/WWP (4);	0.000000	0.85682	D	0.000000	D	0.93006	0.7774	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.93222	0.6609	10	0.87932	D	0	.	8.9623	0.35854	0.0765:0.0:0.778:0.1455	.	1017	Q9P2P5	HECW2_HUMAN	W	661;1017	ENSP00000386775:R661W;ENSP00000260983:R1017W	ENSP00000260983:R1017W	R	-	1	2	HECW2	196851583	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	4.515000	0.60489	2.596000	0.87737	0.655000	0.94253	CGG		0.532	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197143338	G	A	197143338	3	1	90	1	0	0	0	0	1	0	0	0	7064	1115	39	1	1729	1	HECW2	2	197143338	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	5280357	197143338	46056035	59	24646										
CDK15	65061	hgsc.bcm.edu	37	chr2	202698582	202698582	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tccttccagcttttcatgttTcaacttttgcggggcctggc	9	12	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:202698582T>A	ENST00000374598.4	+	7	618	c.618T>A	c.(616-618)ttT>ttA	p.F206L	CDK15_ENST00000450471.2_Missense_Mutation_p.F206L|CDK15_ENST00000434439.1_Missense_Mutation_p.F206L|CDK15_ENST00000488419.1_3'UTR|CDK15_ENST00000260967.2_Missense_Mutation_p.F155L|CDK15_ENST00000410091.3_Missense_Mutation_p.F155L			Q96Q40	CDK15_HUMAN	cyclin-dependent kinase 15	206	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|kidney(5)|large_intestine(1)|lung(14)|ovary(1)	26					Adenosine triphosphate(DB00171)	TTTTCATGTTTCAACTTTTGC	0.458																																																0			2											178	156	164					2																	202698582		2203	4300	6503	202406827	SO:0001583	missense	0			AB053308	CCDS2350.1, CCDS58746.1, CCDS58747.1	2q33.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000138395	ENSG00000138395		"Cyclin-dependent kinases"	14434	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7", "PFTAIRE protein kinase 2"	ALS2CR7, PFTK2		11586298, 16236519, 19884882	Standard	NM_139158		Approved	PFTAIRE2	uc002uyt.3	Q96Q40	OTTHUMG00000132838	ENST00000374598.4:c.618T>A	2.37:g.202698582T>A	ENSP00000363726:p.Phe206Leu		202406827	A8K8R9|B8ZZX0|C9J1N8|C9K003|F8W6H8|Q4ZG86|Q53TV1|Q6ZMR9|Q8IUP1	Missense_Mutation	SNP	ENST00000374598.4	37		.	.	.	.	.	.	.	.	.	.	T	22.4	4.282285	0.80692	.	.	ENSG00000138395	ENST00000410091;ENST00000260967;ENST00000450471;ENST00000434439;ENST00000374598	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.47	3.12	0.35913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.41096	0.1144	N	0.13235	0.315	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	T	0.38824	-0.9643	10	0.72032	D	0.01	-15.9685	5.3812	0.16192	0.0:0.3873:0.0:0.6127	.	185;206;206	Q96Q40-2;Q96Q40;F8W6H8	.;CDK15_HUMAN;.	L	155;155;206;206;206	ENSP00000386901:F155L;ENSP00000260967:F155L;ENSP00000406472:F206L;ENSP00000412775:F206L;ENSP00000363726:F206L	ENSP00000260967:F155L	F	+	3	2	CDK15	202406827	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.531000	0.45650	0.909000	0.36697	0.454000	0.30748	TTT		0.458	CDK15-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000336053.2			A	202698582	T	A	202698582	3	1	90	1	0	0	0	0	1	0	0	0	3137	1780	62	5	487	5	CDK15	2	202698582	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	5555244	202698582	40500791	60	24647										
SPEG	10290	hgsc.bcm.edu	37	chr2	220350102	220350102	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgaagccggctccgctggggCttctctcggccgcggaagga	16	14	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:220350102C>T	ENST00000312358.7	+	31	7776	c.7644C>T	c.(7642-7644)ggC>ggT	p.G2548G	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2548					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TCCGCTGGGGCTTCTCTCGGC	0.607																																																0			2											51	59	57					2																	220350102		1977	4144	6121	220058346	SO:0001819	synonymous_variant	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.7644C>T	2.37:g.220350102C>T			220058346	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																				0.607	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220350102	C	T	220350102	2	4	90	1	0	0	0	0	0	0	0	1	15075	784	28	3		3	SPEG	2	220350102	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	17651520	220350102	22849271	61	24648										
ACSL3	2181	hgsc.bcm.edu	37	chr2	223795495	223795495	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctctgtactggggatattgGagagtttgaacccgatggat	14	6	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:223795495G>T	ENST00000357430.3	+	14	2228	c.1697G>T	c.(1696-1698)gGa>gTa	p.G566V	AC013476.1_ENST00000582868.1_RNA|ACSL3_ENST00000392066.3_Missense_Mutation_p.G566V	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	566					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	GGGGATATTGGAGAGTTTGAA	0.338			T	ETV1	prostate																																		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	0			2											112	114	113					2																	223795495		2203	4300	6503	223503739	SO:0001583	missense	2181			D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"Acyl-CoA synthetase family"	3570	protein-coding gene	gene with protein product		602371	"fatty-acid-Coenzyme A ligase, long-chain 3"	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.1697G>T	2.37:g.223795495G>T	ENSP00000350012:p.Gly566Val		223503739	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	37	CCDS2455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.636319|4.636319	0.87760|0.87760	.|.	.|.	ENSG00000123983|ENSG00000123983	ENST00000407441|ENST00000357430;ENST00000392066	.|T;T	.|0.49139	.|0.79;0.79	5.74|5.74	5.74|5.74	0.90152|0.90152	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.72028	.|0.3410	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|T	.|0.74321	.|-0.3703	.|10	.|0.87932	.|D	.|0	-19.2626|-19.2626	19.9187|19.9187	0.97077|0.97077	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|566	.|O95573	.|ACSL3_HUMAN	X|V	67|566	.|ENSP00000350012:G566V;ENSP00000375918:G566V	.|ENSP00000350012:G566V	E|G	+|+	1|2	0|0	ACSL3|ACSL3	223503739|223503739	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	9.869000|9.869000	0.99810|0.99810	2.702000|2.702000	0.92279|0.92279	0.591000|0.591000	0.81541|0.81541	GAG|GGA		0.338	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		T	223795495	G	T	223795495	3	4	90	1	0	0	0	0	1	0	0	0	178	1174	41	2	1739	2	ACSL3	2	223795495	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	3445393	223795495	19403878	62	24649										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226378131	226378131	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccacgaaggaagttacgtggGcaaacatttccgcatgggat	12	9	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:226378131G>A	ENST00000272907.6	+	3	679	c.266G>A	c.(265-267)gGc>gAc	p.G89D	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	89					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGTTACGTGGGCAAACATTTC	0.498																																																0			2											78	82	80					2																	226378131		2049	4188	6237	226086375	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.266G>A	2.37:g.226378131G>A	ENSP00000272907:p.Gly89Asp		226086375	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.567097	0.86439	.	.	ENSG00000144460	ENST00000272907	T	0.31247	1.5	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	M	0.61703	1.905	0.80722	D	1	P	0.38827	0.649	B	0.38428	0.273	T	0.06180	-1.0841	10	0.34782	T	0.22	-29.9756	12.5326	0.56124	0.0762:0.0:0.9238:0.0	.	89	Q9P242	K1486_HUMAN	D	89	ENSP00000272907:G89D	ENSP00000272907:G89D	G	+	2	0	KIAA1486	226086375	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.409000	0.80053	2.532000	0.85374	0.563000	0.77884	GGC		0.498	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		A	226378131	G	A	226378131	3	1	90	1	0	0	0	0	1	0	0	0	8258	1203	42	3	272	3	KIAA1486	2	226378131	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2582636	226378131	16821242	63	24650										
DGKD	8527	hgsc.bcm.edu	37	chr2	234363415	234363415	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	actcacctttgcagagagtaTtacacggagaaatgtgtcat	9	8	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:234363415T>C	ENST00000264057.2	+	19	2283	c.2271T>C	c.(2269-2271)taT>taC	p.Y757Y	DGKD_ENST00000409813.3_Silent_p.Y713Y	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	757					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	GCAGAGAGTATTACACGGAGA	0.443																																																0			2											123	111	115					2																	234363415		2203	4300	6503	234028154	SO:0001819	synonymous_variant	8527			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2271T>C	2.37:g.234363415T>C			234028154	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	37	CCDS2504.1																																																																																				0.443	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		C	234363415	T	C	234363415	2	2	90	1	0	0	0	0	0	0	0	1	4478	1500	52	4		4	DGKD	2	234363415	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	7985284	234363415	8835958	64	24651										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238285464	238285465	+	Missense_Mutation	DNP	TG	TG	AT													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttaagagattcactatctgTggatgaagatctccaatctt					rs201085369		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T|G	T|G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr2:238285464_238285465TG>AT	ENST00000295550.4	-	7	3472_3473	c.3020_3021CA>AT	c.(3019-3021)cCA>cAT	p.P1007H	COL6A3_ENST00000392004.3_Missense_Mutation_p.P801H|COL6A3_ENST00000353578.4_Missense_Mutation_p.P801H|COL6A3_ENST00000392003.2_Missense_Mutation_p.P600H|COL6A3_ENST00000347401.3_Missense_Mutation_p.P806H|COL6A3_ENST00000472056.1_Missense_Mutation_p.P400H|COL6A3_ENST00000409809.1_Missense_Mutation_p.P801H|COL6A3_ENST00000346358.4_Missense_Mutation_p.P807H	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1007	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P1007P(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TCACTATCTGTGGATGAAGATC	0.49																																																1	Substitution - coding silent(1)	ovary(1)	2																																								237950203|237950204	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.3020_3021delinsAT	2.37:g.238285464_238285465delinsAT	ENSP00000295550:p.Pro1007His		237950203|237950204	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent|Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.49	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		AT	238285465	TG	AT	238285464	3	1	90	1	0	0	0	0	1	0	0	0	3707	1683	59	5	6711	5	COL6A3	2	238285464	Missense_Mutation	DNP	TG	TCGA-CI-6624-01C-11D-1826-10	3922049	238285464	4913909	65	24652										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1424682	1424682	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggatatatcatcatgttccgGccagtgggctcgacaacctg	11	11	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:1424682G>C	ENST00000446702.2	+	18	2850	c.2223G>C	c.(2221-2223)cgG>cgC	p.R741R	CNTN6_ENST00000539053.1_Silent_p.R669R|CNTN6_ENST00000350110.2_Silent_p.R741R			Q9UQ52	CNTN6_HUMAN	contactin 6	741	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TCATGTTCCGGCCAGTGGGCT	0.438																																																0			3											129	119	122					3																	1424682		2203	4300	6503	1399682	SO:0001819	synonymous_variant	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2223G>C	3.37:g.1424682G>C			1399682	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																				0.438	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		C	1424682	G	C	1424682	2	2	90	1	0	0	0	0	0	0	0	1	3651	1190	42	5		5	CNTN6	3	1424682	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10		1424682	196597748	66	24653										
VHL	7428	hgsc.bcm.edu	37	chr3	10188269	10188269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	accaaactgaattatttgtgCcatctctcaatgttgacgga	7	9	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:10188269C>T	ENST00000256474.2	+	2	1252	c.412C>T	c.(412-414)Cca>Tca	p.P138S	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	138	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.P138fs*1(2)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ATTATTTGTGCCATCTCTCAA	0.418		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	2	Deletion - Frameshift(2)	kidney(2)	3											218	202	207					3																	10188269		2203	4300	6503	10163269	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.412C>T	3.37:g.10188269C>T	ENSP00000256474:p.Pro138Ser		10163269	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.525453	0.85600	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99910	-7.91	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.055770	0.64402	D	0.000001	D	0.99885	0.9945	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95853	0.8876	10	0.72032	D	0.01	-3.5977	16.3181	0.82935	0.0:1.0:0.0:0.0	.	138	P40337	VHL_HUMAN	S	138;56	ENSP00000256474:P138S	ENSP00000256474:P138S	P	+	1	0	VHL	10163269	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	2.392000	0.44433	2.530000	0.85305	0.563000	0.77884	CCA		0.418	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		T	10188269	C	T	10188269	3	4	90	1	0	0	0	0	1	0	0	0	17202	739	26	3	418	3	VHL	3	10188269	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	8763587	10188269	187834161	67	24654										
VHL	7428	hgsc.bcm.edu	37	chr3	10188300	10188300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgttgacggacagcctatttTtgccaatatcacactgccag	8	11	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:10188300T>C	ENST00000256474.2	+	2	1283	c.443T>C	c.(442-444)tTt>tCt	p.F148S	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	148	Involved in binding to CCT complex.		Missing (in VHLD; type I).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.I147fs*11(2)|p.F148fs*25(2)|p.A149fs*25(1)|p.I147fs*25(1)|p.F148del(1)|p.F148S(1)|p.I147fs*10(1)|p.I147_F148del(1)|p.P146fs*23(1)|p.F148fs*26(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAGCCTATTTTTGCCAATATC	0.413		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	13	Deletion - Frameshift(8)|Deletion - In frame(2)|Insertion - Frameshift(2)|Substitution - Missense(1)	kidney(12)|adrenal_gland(1)	3											200	187	192					3																	10188300		2203	4300	6503	10163300	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.443T>C	3.37:g.10188300T>C	ENSP00000256474:p.Phe148Ser		10163300	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	17.65	3.441055	0.63067	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99826	-6.98	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.713701	0.13888	N	0.355806	D	0.98943	0.9641	L	0.34521	1.04	0.80722	D	1	P	0.39376	0.67	B	0.41088	0.347	D	0.99987	1.3423	10	0.09084	T	0.74	-2.6033	12.7607	0.57363	0.0:0.0:0.0:1.0	.	148	P40337	VHL_HUMAN	S	148;66	ENSP00000256474:F148S	ENSP00000256474:F148S	F	+	2	0	VHL	10163300	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.984000	0.49353	1.966000	0.57179	0.460000	0.39030	TTT		0.413	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188300	T	C	10188300	3	2	90	1	0	0	0	0	1	0	0	0	17202	1841	64	4	449	4	VHL	3	10188300	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	31	10188300	187834130	68	24655										
RBMS3	27303	hgsc.bcm.edu	37	chr3	30029654	30029654	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tatatgactgctgctgctccTatgcaagggacctacattcc	8	12	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:30029654T>C	ENST00000383767.2	+	13	1455	c.1119T>C	c.(1117-1119)ccT>ccC	p.P373P	RBMS3_ENST00000396583.3_Silent_p.P370P|RBMS3_ENST00000473799.1_3'UTR|RBMS3_ENST00000434693.2_Silent_p.P372P|RBMS3_ENST00000452462.1_Silent_p.P357P|RBMS3_ENST00000273139.9_Silent_p.P357P|RBMS3_ENST00000383766.2_Silent_p.P355P|RBMS3_ENST00000456853.1_Silent_p.P370P			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	373					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CTGCTGCTCCTATGCAAGGGA	0.418																																																0			3											108	96	100					3																	30029654		2203	4300	6503	30004658	SO:0001819	synonymous_variant	27303			AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.1119T>C	3.37:g.30029654T>C			30004658	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	37	CCDS33724.1																																																																																				0.418	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		C	30029654	T	C	30029654	2	2	90	1	0	0	0	0	0	0	0	1	13187	1509	53	4		4	RBMS3	3	30029654	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	19841354	30029654	167992776	69	24656										
CNOT10	25904	hgsc.bcm.edu	37	chr3	32761648	32761648	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aaagcaattttgagtacttaAgaggtaattatcgaaaagcc	8	5	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:32761648A>G	ENST00000328834.5	+	8	1103	c.787A>G	c.(787-789)Aga>Gga	p.R263G	CNOT10_ENST00000463697.1_3'UTR|CNOT10_ENST00000331889.6_Missense_Mutation_p.R263G|CNOT10_ENST00000538368.1_Missense_Mutation_p.R35G|CNOT10_ENST00000454516.2_Missense_Mutation_p.R323G	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	263					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						TGAGTACTTAAGAGGTAATTA	0.318																																																0			3											54	59	58					3																	32761648		2202	4299	6501	32736652	SO:0001583	missense	25904			BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.787A>G	3.37:g.32761648A>G	ENSP00000330060:p.Arg263Gly		32736652	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	37	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.012315	0.75046	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000540405;ENST00000538368;ENST00000454516	T;T;T;T	0.77098	-0.8;-0.8;-1.07;-0.8	5.78	-3.67	0.04476	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.85318	0.5669	M	0.72353	2.195	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.87578	0.983;0.998;0.996;0.994	D	0.84160	0.0428	10	0.52906	T	0.07	-19.8356	18.4722	0.90778	0.3758:0.6242:0.0:0.0	.	323;263;262;263	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	G	263;263;163;35;323	ENSP00000329376:R263G;ENSP00000330060:R263G;ENSP00000442552:R35G;ENSP00000399862:R323G	ENSP00000330060:R263G	R	+	1	2	CNOT10	32736652	1.000000	0.71417	0.929000	0.37066	0.918000	0.54935	2.447000	0.44917	-0.860000	0.04099	-0.545000	0.04230	AGA		0.318	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		G	32761648	A	G	32761648	3	3	90	1	0	0	0	0	1	0	0	0	3624	64	3	4	817	4	CNOT10	3	32761648	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	2731994	32761648	165260782	70	24657										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47042529	47042529	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgtgcaatctgctcaccaaCgtgctgttctcggtgacgtg	11	11	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:47042529C>T	ENST00000450053.3	+	28	4523	c.4344C>T	c.(4342-4344)aaC>aaT	p.N1448N	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Silent_p.N1264N	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1448					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGCTCACCAACGTGCTGTTCT	0.632																																																0			3											80	95	90					3																	47042529		2132	4233	6365	47017533	SO:0001819	synonymous_variant	23218			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4344C>T	3.37:g.47042529C>T			47017533	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006384	0.19199	.	.	ENSG00000160796	ENST00000416683	.	.	.	5.44	-3.06	0.05379	.	.	.	.	.	T	0.62527	0.2435	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60677	-0.7216	4	.	.	.	.	12.7995	0.57578	0.0:0.3396:0.0:0.6604	.	.	.	.	M	736	.	.	T	+	2	0	NBEAL2	47017533	0.680000	0.27605	0.955000	0.39395	0.959000	0.62525	-0.081000	0.11321	-0.571000	0.06014	-0.137000	0.14449	ACG		0.632	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47042529	C	T	47042529	2	4	90	1	0	0	0	0	0	0	0	1	10219	535	19	1		1	NBEAL2	3	47042529	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	14280881	47042529	150979901	71	24658										
PRKAR2A	5576	hgsc.bcm.edu	37	chr3	48820420	48820420	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcaaagctccatctcctaccGttctatgacataaaagttgt	5	11	3	1	rs201062271		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:48820420G>A	ENST00000265563.8	-	5	790	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	PRKAR2A_ENST00000454963.1_Splice_Site_p.R181W|PRKAR2A_ENST00000296446.8_Splice_Site_p.R181W	NM_004157.2	NP_004148.1	P13861	KAP2_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, alpha	181					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)		SLC26A6/PRKAR2A(2)	breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		ATCTCCTACCGTTCTATGACA	0.433																																																0			3											177	139	152					3																	48820420		2203	4300	6503	48795424	SO:0001630	splice_region_variant	5576				CCDS2778.1	3p21.3-p21.2	2009-07-10			ENSG00000114302	ENSG00000114302	2.7.11.1		9391	protein-coding gene	gene with protein product		176910		PRKAR2		9676433	Standard	NM_004157		Approved		uc003cux.1	P13861	OTTHUMG00000133540	ENST00000265563.8:c.542+1C>T	3.37:g.48820420G>A			48795424	Q16823|Q9BUB1	Missense_Mutation	SNP	ENST00000265563.8	37	CCDS2778.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719267	0.48728	.	.	ENSG00000114302	ENST00000265563;ENST00000454963;ENST00000296446	D;D;D	0.92911	-3.13;-3.13;-3.13	4.51	2.53	0.30540	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.329102	0.26967	N	0.021587	D	0.91868	0.7426	M	0.90082	3.085	0.53688	D	0.999973	B;B	0.32507	0.373;0.373	B;B	0.29598	0.104;0.079	D	0.89572	0.3814	10	0.72032	D	0.01	-2.8421	10.145	0.42758	0.0:0.1075:0.572:0.3205	.	181;181	Q9BUB1;P13861	.;KAP2_HUMAN	W	181	ENSP00000265563:R181W;ENSP00000394041:R181W;ENSP00000296446:R181W	ENSP00000265563:R181W	R	-	1	2	PRKAR2A	48795424	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.709000	0.25734	0.492000	0.27815	0.655000	0.94253	CGG		0.433	PRKAR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257518.1		Missense_Mutation	A	48820420	G	A	48820420	5	1	90	1	0	0	0	0	0	0	1	0	12539	1159	40	1	701	1	PRKAR2A	3	48820420	Splice_Site	SNP	G	TCGA-CI-6624-01C-11D-1826-10	1777891	48820420	149202010	72	24659										
MST1	63891	hgsc.bcm.edu	37	chr3	49724706	49724706	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcttccaggccattccggagAgtgggcgtgtacctgagggc	15	11	1	2	rs41291706		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:49724706A>G	ENST00000327697.6	+	0	0				MST1_ENST00000494828.2_5'UTR|MST1_ENST00000545762.1_Missense_Mutation_p.L109P|MST1_ENST00000383728.3_Silent_p.T86T|MST1_ENST00000449682.2_Silent_p.T161T|AC099668.5_ENST00000563780.1_RNA|RNF123_ENST00000432042.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CATTCCGGAGAGTGGGCGTGT	0.597																																																0			3											41	38	39					3																	49724706		2202	4300	6502	49699710	SO:0001631	upstream_gene_variant	6789			AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		3.37:g.49724706A>G	Exception_encountered		49699710	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.634004	0.67130	.	.	ENSG00000173531	ENST00000545762	T	0.52754	0.65	6.08	-12.2	0.00006	.	.	.	.	.	T	0.18551	0.0445	.	.	.	0.23677	N	0.997139	.	.	.	.	.	.	T	0.06588	-1.0818	5	.	.	.	.	0.8186	0.01107	0.2049:0.2584:0.248:0.2887	.	.	.	.	P	109	ENSP00000437535:L109P	.	L	-	2	0	MST1	49699710	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-1.140000	0.03210	-2.137000	0.00809	-1.869000	0.00555	CTC		0.597	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		G	49724706	A	G	49724706	1	3	90	0	1	0	0	0	0	0	0	0	9920	291	11	4		4	MST1	3	49724706	5'Flank	SNP	A	TCGA-CI-6624-01C-11D-1826-10	904286	49724706	148297724	73	24660										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57458291	57458291	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acctcatcattttcatcaaaGatgggattaattttcctagg	6	8	4	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:57458291G>T	ENST00000351747.2	-	14	1938	c.1758C>A	c.(1756-1758)atC>atA	p.I586I	DNAH12_ENST00000389536.4_Silent_p.I586I|snoU13_ENST00000459308.1_RNA	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	586	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTTCATCAAAGATGGGATTAA	0.323																																																0			3											111	92	98					3																	57458291		692	1587	2279	57433331	SO:0001819	synonymous_variant	201625			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1758C>A	3.37:g.57458291G>T			57433331	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	37																																																																																					0.323	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57458291	G	T	57458291	2	4	90	1	0	0	0	0	0	0	0	1	4611	932	33	2		2	DNAH12	3	57458291	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	7733585	57458291	140564139	74	24661										
MITF	4286	hgsc.bcm.edu	37	chr3	69987181	69987181	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	catggctatgcttacgcttaActccaactgtgaaaaagagg	9	9	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:69987181A>C	ENST00000448226.2	+	3	690	c.563A>C	c.(562-564)aAc>aCc	p.N188T	MITF_ENST00000352241.4_Missense_Mutation_p.N188T|MITF_ENST00000472437.1_Missense_Mutation_p.N136T|MITF_ENST00000394348.1_3'UTR|MITF_ENST00000394351.3_Missense_Mutation_p.N81T|MITF_ENST00000314557.6_Missense_Mutation_p.N81T|MITF_ENST00000328528.6_Missense_Mutation_p.N187T|MITF_ENST00000394355.2_Missense_Mutation_p.N163T|MITF_ENST00000314589.5_Missense_Mutation_p.N172T|MITF_ENST00000531774.1_Intron			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	188					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.N188T(1)|p.N81T(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		CTTACGCTTAACTCCAACTGT	0.493			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	2	Substitution - Missense(2)	lung(2)	3											79	69	72					3																	69987181		2203	4300	6503	70069871	SO:0001583	missense	4286				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.563A>C	3.37:g.69987181A>C	ENSP00000391803:p.Asn188Thr		70069871	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	A	13.32	2.201805	0.38905	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000472437;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351	T;T;T;T;T;T;T;T;T	0.22336	2.76;2.28;2.56;2.77;1.96;2.78;2.78;2.54;1.96	5.69	5.69	0.88448	.	0.259977	0.49916	D	0.000123	T	0.21550	0.0519	L	0.53249	1.67	0.45662	D	0.998585	B;P;B;B;P;B;P	0.40834	0.354;0.534;0.321;0.203;0.73;0.109;0.696	B;B;B;B;B;B;B	0.39876	0.101;0.205;0.205;0.099;0.312;0.099;0.205	T	0.02275	-1.1184	9	.	.	.	.	10.3096	0.43702	0.9267:0.0:0.0733:0.0	.	136;81;81;163;172;187;188	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	T	188;188;136;187;172;172;163;81;81	ENSP00000295600:N188T;ENSP00000391803:N188T;ENSP00000418845:N136T;ENSP00000327867:N187T;ENSP00000398639:N172T;ENSP00000324443:N172T;ENSP00000377884:N163T;ENSP00000324246:N81T;ENSP00000377880:N81T	.	N	+	2	0	MITF	70069871	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.046000	0.57376	2.147000	0.66899	0.533000	0.62120	AAC		0.493	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		C	69987181	A	C	69987181	3	2	90	1	0	0	0	0	1	0	0	0	9626	43	2	4	775	4	MITF	3	69987181	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	12528890	69987181	128035249	75	24662										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96533676	96533676	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agacgtggacaaggacccccAtcctacccagaacacctgcc	8	17	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:96533676A>T	ENST00000389672.5	+	1	247	c.209A>T	c.(208-210)cAt>cTt	p.H70L	EPHA6_ENST00000542517.1_5'UTR|EPHA6_ENST00000470610.2_Missense_Mutation_p.H70L	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						AAGGACCCCCATCCTACCCAG	0.647																																																0			3											19	25	23					3																	96533676		1939	4124	6063	98016366	SO:0001583	missense	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.209A>T	3.37:g.96533676A>T	ENSP00000374323:p.His70Leu		98016366	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	A	7.362	0.625086	0.14257	.	.	ENSG00000080224	ENST00000470610;ENST00000389672	T;T	0.74315	5.06;-0.83	5.45	-3.65	0.04502	.	.	.	.	.	T	0.45955	0.1368	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.25187	-1.0139	9	0.52906	T	0.07	.	1.0418	0.01560	0.3308:0.2853:0.2454:0.1386	.	70;70	B3KS12;E7EU71	.;.	L	70	ENSP00000420598:H70L;ENSP00000374323:H70L	ENSP00000374323:H70L	H	+	2	0	EPHA6	98016366	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.227000	0.09126	-0.519000	0.06444	-1.054000	0.02325	CAT		0.647	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		T	96533676	A	T	96533676	3	4	90	1	0	0	0	0	1	0	0	0	5184	217	8	5	211	5	EPHA6	3	96533676	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	26546495	96533676	101488754	76	24663										
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113497629	113497629	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttccaagctacccaaaatacTcgatgaagataaagaaagca	6	9	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:113497629T>C	ENST00000273398.3	+	2	137	c.29T>C	c.(28-30)cTc>cCc	p.L10P	ATP6V1A_ENST00000538620.1_5'UTR	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	10					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CCCAAAATACTCGATGAAGAT	0.299																																																0			3											68	69	68					3																	113497629		2203	4298	6501	114980319	SO:0001583	missense	523			L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.29T>C	3.37:g.113497629T>C	ENSP00000273398:p.Leu10Pro		114980319	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878776	0.33162	.	.	ENSG00000114573	ENST00000273398;ENST00000475322	D	0.86297	-2.1	5.6	-2.31	0.06765	.	0.812558	0.11185	N	0.590530	T	0.68888	0.3050	N	0.08118	0	0.35779	D	0.821539	B	0.06786	0.001	B	0.04013	0.001	T	0.56553	-0.7960	10	0.33141	T	0.24	-0.2848	5.7074	0.17915	0.0904:0.1547:0.5749:0.18	.	10	P38606	VATA_HUMAN	P	10	ENSP00000273398:L10P	ENSP00000273398:L10P	L	+	2	0	ATP6V1A	114980319	0.962000	0.33011	0.805000	0.32314	0.995000	0.86356	1.537000	0.36083	0.101000	0.17610	0.482000	0.46254	CTC		0.299	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		C	113497629	T	C	113497629	3	2	90	1	0	0	0	0	1	0	0	0	1178	1551	54	4	31	4	ATP6V1A	3	113497629	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	16963953	113497629	84524801	77	24664										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130463546	130463546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gttgtcttctggaagataagTgggcttaaaactggcaaaat	11	5	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:130463546T>C	ENST00000356763.3	-	2	1074	c.517A>G	c.(517-519)Act>Gct	p.T173A		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	173	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GGAAGATAAGTGGGCTTAAAA	0.428																																																0			3											83	82	82					3																	130463546		2203	4300	6503	131946236	SO:0001583	missense	30849			Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.517A>G	3.37:g.130463546T>C	ENSP00000349205:p.Thr173Ala		131946236	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	37	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671509	0.47781	.	.	ENSG00000196455	ENST00000356763	T	0.63913	-0.07	5.18	5.18	0.71444	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.57359	0.2048	N	0.19112	0.55	0.80722	D	1	P	0.44521	0.837	P	0.49561	0.615	T	0.59648	-0.7415	10	0.41790	T	0.15	-27.1119	15.317	0.74089	0.0:0.0:0.0:1.0	.	173	Q99570	PI3R4_HUMAN	A	173	ENSP00000349205:T173A	ENSP00000349205:T173A	T	-	1	0	PIK3R4	131946236	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.215000	0.72206	2.092000	0.63282	0.379000	0.24179	ACT		0.428	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		C	130463546	T	C	130463546	3	2	90	1	0	0	0	0	1	0	0	0	11952	1696	59	4	3635	4	PIK3R4	3	130463546	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	16965917	130463546	67558884	78	24665										
TF	7018	hgsc.bcm.edu	37	chr3	133485148	133485148	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgctatagcagtggtgaagAaatcagcttctgacctcacc	9	10	3	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:133485148A>T	ENST00000402696.3	+	12	1842	c.1357A>T	c.(1357-1359)Aaa>Taa	p.K453*	TF_ENST00000264998.3_Nonsense_Mutation_p.K326*	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	453	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	AGTGGTGAAGAAATCAGCTTC	0.493																																																0			3											218	212	214					3																	133485148		2203	4300	6503	134967838	SO:0001587	stop_gained	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1357A>T	3.37:g.133485148A>T	ENSP00000385834:p.Lys453*		134967838	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Nonsense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	.	.	.	.	.	.	.	.	.	.	A	40	8.506167	0.98841	.	.	ENSG00000091513	ENST00000402696;ENST00000264998	.	.	.	4.87	-4.34	0.03666	.	0.496690	0.25214	N	0.032295	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0228	6.8814	0.24174	0.4081:0.0:0.439:0.1529	.	.	.	.	X	453;326	.	ENSP00000264998:K326X	K	+	1	0	TF	134967838	0.397000	0.25270	0.000000	0.03702	0.075000	0.17131	1.110000	0.31147	-0.868000	0.04058	0.379000	0.24179	AAA		0.493	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133485148	A	T	133485148	4	4	90	1	0	0	0	0	0	1	0	0	15824	247	9	5	1403	5	TF	3	133485148	Nonsense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	3021602	133485148	64537282	79	24666										
STAG1	10274	hgsc.bcm.edu	37	chr3	136221520	136221520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctttcattggctctcttccCaatcattttatttctctcgg	4	13	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:136221520C>T	ENST00000383202.2	-	8	1034	c.778G>A	c.(778-780)Ggg>Agg	p.G260R	STAG1_ENST00000236698.5_Missense_Mutation_p.G260R|STAG1_ENST00000434713.2_Missense_Mutation_p.G34R	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	260					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GCTCTCTTCCCAATCATTTTA	0.388																																																0			3											170	161	164					3																	136221520		2203	4300	6503	137704210	SO:0001583	missense	56937			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.778G>A	3.37:g.136221520C>T	ENSP00000372689:p.Gly260Arg		137704210	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	C	34	5.369463	0.95900	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713	T;T;T	0.41400	1.0;1.0;1.0	5.67	5.67	0.87782	STAG (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63177	0.2489	M	0.72894	2.215	0.80722	D	1	B;D;B	0.54397	0.033;0.966;0.033	B;P;B	0.62491	0.141;0.903;0.141	T	0.58601	-0.7608	10	0.35671	T	0.21	.	19.7542	0.96283	0.0:1.0:0.0:0.0	.	277;260;260	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	R	260;260;34	ENSP00000372689:G260R;ENSP00000236698:G260R;ENSP00000404396:G34R	ENSP00000236698:G260R	G	-	1	0	STAG1	137704210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.786000	0.85741	2.677000	0.91161	0.491000	0.48974	GGG		0.388	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		T	136221520	C	T	136221520	3	4	90	1	0	0	0	0	1	0	0	0	15281	594	21	3	3106	3	STAG1	3	136221520	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2736372	136221520	61800910	80	24667										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158524841	158524841	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccaaacagatggggcacaatCatttttagctgctttgtttg	9	8	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:158524841C>G	ENST00000264266.8	+	4	404	c.342C>G	c.(340-342)atC>atG	p.I114M	MFSD1_ENST00000392813.4_Missense_Mutation_p.I124M|MFSD1_ENST00000415822.2_Missense_Mutation_p.I163M			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	114					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGGGCACAATCATTTTTAGCT	0.299																																					Pancreas(62;1186 1654 36636 37908)											0			3											111	103	106					3																	158524841		2203	4299	6502	160007535	SO:0001583	missense	64747			BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.342C>G	3.37:g.158524841C>G	ENSP00000264266:p.Ile114Met		160007535	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		.	.	.	.	.	.	.	.	.	.	C	15.54	2.862852	0.51482	.	.	ENSG00000118855	ENST00000486568;ENST00000415822;ENST00000392813;ENST00000264266;ENST00000474670;ENST00000482835	T;T;T;T;T;D	0.82081	0.2;0.41;0.38;0.41;0.41;-1.57	4.98	-0.254	0.12992	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.175219	0.49305	D	0.000154	D	0.85982	0.5824	M	0.74546	2.27	0.39370	D	0.966063	P;P	0.50528	0.932;0.936	P;D	0.64877	0.755;0.93	T	0.80839	-0.1203	10	0.45353	T	0.12	.	3.8171	0.08819	0.4025:0.2539:0.0:0.3436	.	124;114	C9JS94;Q9H3U5	.;MFSD1_HUMAN	M	98;163;124;114;87;103	ENSP00000417414:I98M;ENSP00000403117:I163M;ENSP00000376560:I124M;ENSP00000264266:I114M;ENSP00000419708:I87M;ENSP00000418503:I103M	ENSP00000264266:I114M	I	+	3	3	MFSD1	160007535	1.000000	0.71417	0.995000	0.50966	0.878000	0.50629	0.576000	0.23744	-0.301000	0.08882	-0.312000	0.09012	ATC		0.299	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		G	158524841	C	G	158524841	3	3	90	1	0	0	0	0	1	0	0	0	9557	816	29	5	503	5	MFSD1	3	158524841	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	22303321	158524841	39497589	81	24668										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906727	164906727	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tggttggtgccccaataaggTgagaatctccaggctgggct	14	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:164906727T>G	ENST00000475390.1	-	2	2335	c.1892A>C	c.(1891-1893)cAc>cCc	p.H631P	SLITRK3_ENST00000241274.3_Missense_Mutation_p.H631P			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	631					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						CCCAATAAGGTGAGAATCTCC	0.537										HNSCC(40;0.11)																																						0			3											34	37	36					3																	164906727		2203	4300	6503	166389421	SO:0001583	missense	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1892A>C	3.37:g.164906727T>G	ENSP00000420091:p.His631Pro		166389421	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.544054	0.00934	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.52526	0.66;0.66	5.02	2.51	0.30379	.	0.188409	0.26143	N	0.026099	T	0.27349	0.0671	N	0.19112	0.55	0.36127	D	0.84584	B	0.02656	0.0	B	0.01281	0.0	T	0.12243	-1.0555	10	0.24483	T	0.36	-3.9152	6.6196	0.22796	0.1534:0.0:0.1605:0.6861	.	631	O94933	SLIK3_HUMAN	P	631	ENSP00000420091:H631P;ENSP00000241274:H631P	ENSP00000241274:H631P	H	-	2	0	SLITRK3	166389421	0.530000	0.26330	0.017000	0.16124	0.028000	0.11728	0.799000	0.27028	0.420000	0.25954	0.533000	0.62120	CAC		0.537	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		G	164906727	T	G	164906727	3	3	90	1	0	0	0	0	1	0	0	0	14781	1696	59	4	1045	4	SLITRK3	3	164906727	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	6381886	164906727	33115703	82	24669										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936098	178936098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctctgaaatcactgagcaggAgaaagattttctatggagtc	10	7	3	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:178936098A>G	ENST00000263967.3	+	10	1797	c.1640A>G	c.(1639-1641)gAg>gGg	p.E547G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	547	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ACTGAGCAGGAGAAAGATTTT	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											62	62	62					3																	178936098		1812	4070	5882	180418792	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1640A>G	3.37:g.178936098A>G	ENSP00000263967:p.Glu547Gly		180418792	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543251	0.86022	.	.	ENSG00000121879	ENST00000263967	T	0.70399	-0.48	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85737	0.5766	M	0.87900	2.915	0.80722	D	1	D	0.67145	0.996	D	0.69479	0.964	D	0.88339	0.2973	10	0.87932	D	0	-14.9038	16.1026	0.81194	1.0:0.0:0.0:0.0	.	547	P42336	PK3CA_HUMAN	G	547	ENSP00000263967:E547G	ENSP00000263967:E547G	E	+	2	0	PIK3CA	180418792	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAG		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936098	A	G	178936098	3	3	90	1	0	0	0	0	1	0	0	0	11944	304	11	4	1674	4	PIK3CA	3	178936098	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	14029371	178936098	19086332	83	24670										
ATP11B	23200	hgsc.bcm.edu	37	chr3	182584055	182584055	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atattaattacatttttacaGattaaagaacatgatctctt	3	5	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:182584055G>C	ENST00000323116.5	+	14	1703		c.e14-1			NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			CATTTTTACAGATTAAAGAAC	0.348																																																0			3											47	46	46					3																	182584055		2203	4300	6503	184066749	SO:0001630	splice_region_variant	23200			AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.1444-1G>C	3.37:g.182584055G>C			184066749	Q96FN1|Q9UKK7	Splice_Site	SNP	ENST00000323116.5	37	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245565	0.59103	.	.	ENSG00000058063	ENST00000323116;ENST00000498086	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4801	0.95007	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP11B	184066749	1.000000	0.71417	0.999000	0.59377	0.637000	0.38172	8.924000	0.92827	2.759000	0.94783	0.650000	0.86243	.		0.348	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	Intron	C	182584055	G	C	182584055	5	2	90	1	0	0	0	0	0	0	1	0	1121	956	33	5	1497	5	ATP11B	3	182584055	Splice_Site	SNP	G	TCGA-CI-6624-01C-11D-1826-10	3647957	182584055	15438375	84	24671										
IL1RAP	3556	hgsc.bcm.edu	37	chr3	190347158	190347158	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtataagtcatagtagaacaGaagatgaaacaagaactcag	9	5	2	5			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:190347158G>C	ENST00000412504.2	+	8	1174	c.922G>C	c.(922-924)Gaa>Caa	p.E308Q	IL1RAP_ENST00000422485.1_Missense_Mutation_p.E308Q|IL1RAP_ENST00000447382.1_Missense_Mutation_p.E308Q|IL1RAP_ENST00000317757.3_Missense_Mutation_p.E308Q|IL1RAP_ENST00000434491.1_Missense_Mutation_p.E167Q|IL1RAP_ENST00000422940.1_Missense_Mutation_p.E308Q|IL1RAP_ENST00000072516.3_Missense_Mutation_p.E308Q|IL1RAP_ENST00000439062.1_Missense_Mutation_p.E308Q|IL1RAP_ENST00000443369.2_Missense_Mutation_p.E308Q			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	308	Ig-like C2-type 3.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		TAGTAGAACAGAAGATGAAAC	0.398																																																0			3											49	47	48					3																	190347158		2203	4300	6503	191829852	SO:0001583	missense	3556			AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.922G>C	3.37:g.190347158G>C	ENSP00000412053:p.Glu308Gln		191829852	B1NLD0|D3DNW0|O14915|Q86WJ7	Missense_Mutation	SNP	ENST00000412504.2	37	CCDS3298.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.69|16.69	3.194082|3.194082	0.58017|0.58017	.|.	.|.	ENSG00000196083|ENSG00000196083	ENST00000072516;ENST00000443369;ENST00000412504;ENST00000439062;ENST00000447382;ENST00000422485;ENST00000434491;ENST00000422940;ENST00000317757|ENST00000412080	T;T;T;T;T;T;T;T;T|.	0.14022|.	2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54|.	5.7|5.7	5.7|5.7	0.88788|0.88788	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.288241|.	0.38436|.	N|.	0.001690|.	T|T	0.70334|0.70334	0.3212|0.3212	L|L	0.56769|0.56769	1.78|1.78	0.39501|0.39501	D|D	0.968191|0.968191	D;D;P;D|.	0.64830|.	0.994;0.983;0.938;0.979|.	P;P;B;B|.	0.52386|.	0.697;0.469;0.218;0.37|.	T|T	0.69172|0.69172	-0.5215|-0.5215	10|5	0.23302|.	T|.	0.38|.	.|.	15.3482|15.3482	0.74359|0.74359	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	167;308;308;308|.	C9J9W1;Q9NPH3-5;Q9NPH3;Q9NPH3-2|.	.;.;IL1AP_HUMAN;.|.	Q|H	308;308;308;308;308;308;167;308;308|144	ENSP00000072516:E308Q;ENSP00000408893:E308Q;ENSP00000412053:E308Q;ENSP00000401132:E308Q;ENSP00000390541:E308Q;ENSP00000409352:E308Q;ENSP00000391899:E167Q;ENSP00000387371:E308Q;ENSP00000314807:E308Q|.	ENSP00000072516:E308Q|.	E|Q	+|+	1|3	0|2	IL1RAP|IL1RAP	191829852|191829852	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.849000|0.849000	0.48306|0.48306	4.814000|4.814000	0.62627|0.62627	2.705000|2.705000	0.92388|0.92388	0.650000|0.650000	0.86243|0.86243	GAA|CAG		0.398	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1			C	190347158	G	C	190347158	3	2	90	1	0	0	0	0	1	0	0	0	7681	943	33	5	948	5	IL1RAP	3	190347158	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	7763103	190347158	7675272	85	24672										
CCDC50	152137	hgsc.bcm.edu	37	chr3	191093014	191093014	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgttcatcgaagagatccctGtcatcctctagctcgggcaa	9	12	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:191093014G>T	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Silent_p.L204L	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		AGAGATCCCTGTCATCCTCTA	0.488																																																0			3											93	82	86					3																	191093014		2203	4300	6503	192575708	SO:0001627	intron_variant	152137			AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4934G>T	3.37:g.191093014G>T			192575708	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																				0.488	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		T	191093014	G	T	191093014	1	4	90	0	1	0	0	0	0	0	0	0	2826	1364	48	2		2	CCDC50	3	191093014	Intron	SNP	G	TCGA-CI-6624-01C-11D-1826-10	745856	191093014	6929416	86	24673										
TCTEX1D2	255758	hgsc.bcm.edu	37	chr3	196033843	196033843	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcacctctttgttctccaatCactacttgcaccaccatttt	2	15	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr3:196033843C>G	ENST00000325318.5	-	3	423	c.288G>C	c.(286-288)gtG>gtC	p.V96V	RP11-447L10.1_ENST00000431391.1_Silent_p.V96V	NM_152773.4	NP_689986.2	Q8WW35	TC1D2_HUMAN	Tctex1 domain containing 2	96										breast(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	7	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GTTCTCCAATCACTACTTGCA	0.323																																																0			3											221	203	209					3																	196033843		2203	4300	6503	197518240	SO:0001819	synonymous_variant	255758			BC021177	CCDS33929.1	3q29	2010-07-19			ENSG00000213123	ENSG00000213123			28482	protein-coding gene	gene with protein product						12477932	Standard	NM_152773		Approved	MGC33212	uc003fwi.3	Q8WW35	OTTHUMG00000155672	ENST00000325318.5:c.288G>C	3.37:g.196033843C>G			197518240	A6NCN5	Silent	SNP	ENST00000325318.5	37	CCDS33929.1																																																																																				0.323	TCTEX1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341166.1	NM_152773		G	196033843	C	G	196033843	2	3	90	1	0	0	0	0	0	0	0	1	15759	813	29	5		5	TCTEX1D2	3	196033843	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	4940829	196033843	1988587	87	24674										
UGT2A3	79799	hgsc.bcm.edu	37	chr4	69795685	69795685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	accaggtgaggtcatgggcaGctgatcgcaggtgcttggct	16	9	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:69795685G>A	ENST00000251566.4	-	6	1460	c.1430C>T	c.(1429-1431)gCt>gTt	p.A477V	UGT2A3_ENST00000420231.2_Missense_Mutation_p.A188V	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	477					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GTCATGGGCAGCTGATCGCAG	0.483																																																0			4											83	82	83					4																	69795685		2203	4300	6503	69830274	SO:0001583	missense	79799				CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.1430C>T	4.37:g.69795685G>A	ENSP00000251566:p.Ala477Val		69830274	Q9H6S4	Missense_Mutation	SNP	ENST00000251566.4	37	CCDS3525.1	.	.	.	.	.	.	.	.	.	.	G	10.13	1.265484	0.23136	.	.	ENSG00000135220	ENST00000251566;ENST00000420231	T;T	0.61627	0.09;0.09	2.22	1.34	0.21922	.	0.267128	0.36482	N	0.002564	T	0.74268	0.3694	M	0.89163	3.01	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.63283	-0.6672	10	0.87932	D	0	.	6.3908	0.21585	0.1678:0.0:0.8322:0.0	.	477	Q6UWM9	UD2A3_HUMAN	V	477;188	ENSP00000251566:A477V;ENSP00000440115:A188V	ENSP00000251566:A477V	A	-	2	0	UGT2A3	69830274	0.984000	0.35163	0.001000	0.08648	0.003000	0.03518	5.486000	0.66856	0.267000	0.21916	0.491000	0.48974	GCT		0.483	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		A	69795685	G	A	69795685	3	1	90	1	0	0	0	0	1	0	0	0	16995	971	34	3	157	3	UGT2A3	4	69795685	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10		69795685	121358591	88	24675										
HPSE	10855	hgsc.bcm.edu	37	chr4	84231914	84231914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctttcttcgaggctgaccaAcatcaggaccatagagtttt	8	10	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:84231914A>G	ENST00000405413.2	-	6	939	c.803T>C	c.(802-804)gTt>gCt	p.V268A	HPSE_ENST00000513463.1_Missense_Mutation_p.V210A|HPSE_ENST00000512196.1_Missense_Mutation_p.V268A|HPSE_ENST00000311412.5_Missense_Mutation_p.V268A	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	268					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	AGGCTGACCAACATCAGGACC	0.388																																																0			4											208	201	203					4																	84231914		2203	4300	6503	84450938	SO:0001583	missense	10855			AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.803T>C	4.37:g.84231914A>G	ENSP00000384262:p.Val268Ala		84450938	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848191	0.71603	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.11	5.11	0.69529	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.643383	0.16294	N	0.220767	T	0.49440	0.1557	L	0.56769	1.78	0.40041	D	0.975656	P;P;D	0.56746	0.892;0.95;0.977	B;P;P	0.54270	0.389;0.716;0.747	T	0.49890	-0.8891	10	0.49607	T	0.09	-2.178	14.7198	0.69297	1.0:0.0:0.0:0.0	.	268;210;268	E9PCA9;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	A	268;268;268;210	ENSP00000308107:V268A;ENSP00000384262:V268A;ENSP00000423265:V268A;ENSP00000421365:V210A	ENSP00000308107:V268A	V	-	2	0	HPSE	84450938	0.886000	0.30341	0.292000	0.24919	0.927000	0.56198	8.002000	0.88514	2.143000	0.66587	0.477000	0.44152	GTT		0.388	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84231914	A	G	84231914	3	3	90	1	0	0	0	0	1	0	0	0	7365	43	2	4	860	4	HPSE	4	84231914	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	14436229	84231914	106922362	89	24676										
ADH5	128	hgsc.bcm.edu	37	chr4	99997944	99997944	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aggtgctaaaggatctatttTagcaacagagatatcagcca	9	7	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:99997944T>A	ENST00000296412.8	-	5	525	c.475A>T	c.(475-477)Aaa>Taa	p.K159*	ADH5_ENST00000512991.1_5'UTR	NM_000671.3	NP_000662.3			alcohol dehydrogenase 5 (class III), chi polypeptide											endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)		GGATCTATTTTAGCAACAGAG	0.423																																																0			4											67	61	63					4																	99997944		1879	4116	5995	100216967	SO:0001587	stop_gained	128			M29872	CCDS47111.1	4q23	2012-07-13	2003-06-19		ENSG00000197894	ENSG00000197894	1.1.1.284	"Alcohol dehydrogenases"	253	protein-coding gene	gene with protein product		103710	"formaldehyde dehydrogenase"	FDH		1446828, 6424546	Standard	NM_000671		Approved	ADH-3, ADHX	uc003hui.3	P11766	OTTHUMG00000161230	ENST00000296412.8:c.475A>T	4.37:g.99997944T>A	ENSP00000296412:p.Lys159*		100216967		Nonsense_Mutation	SNP	ENST00000296412.8	37	CCDS47111.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.491381	0.84962	.	.	ENSG00000197894	ENST00000296412;ENST00000503130	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5959	0.76578	0.0:0.0:0.0:1.0	.	.	.	.	X	159;146	.	.	K	-	1	0	ADH5	100216967	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.096000	0.76960	2.277000	0.76020	0.528000	0.53228	AAA		0.423	ADH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364224.1	NM_000671		A	99997944	T	A	99997944	4	1	90	1	0	0	0	0	0	1	0	0	311	1763	61	5	669	5	ADH5	4	99997944	Nonsense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	15766030	99997944	91156332	90	24677										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103505914	103505914	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctctgtgtttgtccagcttCggaggaaatctgacttggaa	11	9	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:103505914C>A	ENST00000505458.1	+	11	1277	c.1000C>A	c.(1000-1002)Cgg>Agg	p.R334R	NFKB1_ENST00000394820.4_Silent_p.R334R|NFKB1_ENST00000226574.4_Silent_p.R335R|NFKB1_ENST00000600343.1_Silent_p.R154R			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	334	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	TGTCCAGCTTCGGAGGAAATC	0.358																																																0			4											63	67	65					4																	103505914		2203	4300	6503	103724952	SO:0001819	synonymous_variant	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1000C>A	4.37:g.103505914C>A			103724952	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																				0.358	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			A	103505914	C	A	103505914	2	1	90	1	0	0	0	0	0	0	0	1	10406	875	31	2		2	NFKB1	4	103505914	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	3507970	103505914	87648362	91	24678										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110384302	110384302	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtcctcctgcccctcatattGtgggatccactctaggatct	8	14	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:110384302G>C	ENST00000265175.5	+	2	434	c.379G>C	c.(379-381)Gtg>Ctg	p.V127L	SEC24B_ENST00000504968.2_Missense_Mutation_p.V158L|SEC24B_ENST00000399100.2_Missense_Mutation_p.V127L	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	127					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CCCTCATATTGTGGGATCCAC	0.488																																																0			4											130	129	129					4																	110384302		2015	4195	6210	110603751	SO:0001583	missense	10427			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.379G>C	4.37:g.110384302G>C	ENSP00000265175:p.Val127Leu		110603751	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	3.368	-0.129032	0.06753	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.79141	-1.04;-1.24;-1.2	4.74	-0.541	0.11858	.	1.903560	0.02261	N	0.067560	T	0.61640	0.2363	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.09022	0.0;0.002;0.0;0.002	B;B;B;B	0.06405	0.0;0.002;0.001;0.001	T	0.43845	-0.9366	10	0.39692	T	0.17	0.7928	1.8654	0.03197	0.2409:0.133:0.4896:0.1365	.	77;158;127;127	B4DTM6;B7ZKM8;O95487-2;O95487	.;.;.;SC24B_HUMAN	L	158;127;127	ENSP00000428564:V158L;ENSP00000382051:V127L;ENSP00000265175:V127L	ENSP00000265175:V127L	V	+	1	0	SEC24B	110603751	0.027000	0.19231	0.000000	0.03702	0.169000	0.22640	0.640000	0.24705	-0.068000	0.12953	0.467000	0.42956	GTG		0.488	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			C	110384302	G	C	110384302	3	2	90	1	0	0	0	0	1	0	0	0	14032	1377	48	5	385	5	SEC24B	4	110384302	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	6878388	110384302	80769974	92	24679										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119951306	119951306	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgttgacgacaacacacaagTtgtgaactttgactgggatt	10	8	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:119951306T>A	ENST00000429713.2	+	4	1558	c.1376T>A	c.(1375-1377)gTt>gAt	p.V459D	SYNPO2_ENST00000434046.2_Missense_Mutation_p.V459D|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.V459D	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	459						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AACACACAAGTTGTGAACTTT	0.468																																																0			4											148	147	148					4																	119951306		2203	4300	6503	120170754	SO:0001583	missense	171024			AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.1376T>A	4.37:g.119951306T>A	ENSP00000395143:p.Val459Asp		120170754	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.97|18.97	3.735980|3.735980	0.69189|0.69189	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.12039	.|2.72;2.73;2.72	5.55|5.55	2.93|2.93	0.34026|0.34026	.|.	.|0.405216	.|0.21674	.|N	.|0.070825	T|T	0.24122|0.24122	0.0584|0.0584	L|L	0.47716|0.47716	1.5|1.5	0.36445|0.36445	D|D	0.865715|0.865715	.|D;D;D;D	.|0.71674	.|0.998;0.995;0.996;0.998	.|P;P;P;P	.|0.62014	.|0.897;0.836;0.853;0.897	T|T	0.07195|0.07195	-1.0785|-1.0785	5|10	.|0.72032	.|D	.|0.01	-3.554|-3.554	8.6093|8.6093	0.33793|0.33793	0.0:0.1823:0.0:0.8177|0.0:0.1823:0.0:0.8177	.|.	.|459;459;459;459	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	R|D	410|459	.|ENSP00000306015:V459D;ENSP00000395143:V459D;ENSP00000390965:V459D	.|ENSP00000306015:V459D	S|V	+|+	3|2	2|0	SYNPO2|SYNPO2	120170754|120170754	1.000000|1.000000	0.71417|0.71417	0.003000|0.003000	0.11579|0.11579	0.254000|0.254000	0.26022|0.26022	3.246000|3.246000	0.51414|0.51414	0.303000|0.303000	0.22785|0.22785	0.460000|0.460000	0.39030|0.39030	AGT|GTT		0.468	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119951306	T	A	119951306	3	1	90	1	0	0	0	0	1	0	0	0	15496	1725	60	5	1390	5	SYNPO2	4	119951306	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	9567004	119951306	71202970	93	24680										
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144461614	144461614	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atagtagaacgtgctgagatGaaactcagactggattcaat	10	6	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:144461614G>T	ENST00000283131.3	+	14	2331	c.1869G>T	c.(1867-1869)atG>atT	p.M623I		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	623	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GTGCTGAGATGAAACTCAGAC	0.388																																																0			4											84	81	82					4																	144461614		2203	4300	6503	144681064	SO:0001583	missense	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.1869G>T	4.37:g.144461614G>T	ENSP00000283131:p.Met623Ile		144681064		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162767	0.57368	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.95412	-3.7	5.72	5.72	0.89469	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89203	0.6648	N	0.05078	-0.115	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	D	0.84245	0.0474	10	0.15952	T	0.53	-6.8529	19.892	0.96932	0.0:0.0:1.0:0.0	.	623	O60264	SMCA5_HUMAN	I	623;566;566	ENSP00000283131:M623I	ENSP00000283131:M623I	M	+	3	0	SMARCA5	144681064	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.917000	0.87498	2.704000	0.92352	0.563000	0.77884	ATG		0.388	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			T	144461614	G	T	144461614	3	4	90	1	0	0	0	0	1	0	0	0	14808	1290	45	2	1923	2	SMARCA5	4	144461614	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	24510308	144461614	46692662	94	24681										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155241687	155241687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gacatgggcattggggaaagAaataaaagtggggttgtggt	17	2	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:155241687A>G	ENST00000357232.4	-	14	3498	c.3499T>C	c.(3499-3501)Tct>Cct	p.S1167P		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1167	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TTGGGGAAAGAAATAAAAGTG	0.468																																																0			4											195	186	189					4																	155241687		2203	4300	6503	155461137	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3499T>C	4.37:g.155241687A>G	ENSP00000349768:p.Ser1167Pro		155461137	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060844	0.76074	.	.	ENSG00000197410	ENST00000357232	T	0.38240	1.15	5.56	5.56	0.83823	Cadherin (2);Cadherin-like (1);	0.000000	0.64402	D	0.000005	T	0.60314	0.2259	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63853	-0.6543	10	0.66056	D	0.02	.	15.721	0.77710	1.0:0.0:0.0:0.0	.	1167	Q6V1P9	PCD23_HUMAN	P	1167	ENSP00000349768:S1167P	ENSP00000349768:S1167P	S	-	1	0	DCHS2	155461137	1.000000	0.71417	0.076000	0.20297	0.878000	0.50629	5.901000	0.69861	2.117000	0.64856	0.383000	0.25322	TCT		0.468	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155241687	A	G	155241687	3	3	90	1	0	0	0	0	1	0	0	0	4294	246	9	4	5299	4	DCHS2	4	155241687	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	10780073	155241687	35912589	95	24682										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169321988	169321988	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aatacttacatccttttctgTgtcttcctcactttttcaag	3	11	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr4:169321988T>A	ENST00000511577.1	-	26	3727	c.3480A>T	c.(3478-3480)acA>acT	p.T1160T	DDX60L_ENST00000505890.1_Silent_p.T1160T|DDX60L_ENST00000260184.7_Silent_p.T1160T			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1160							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TCCTTTTCTGTGTCTTCCTCA	0.368																																																0			4											105	99	101					4																	169321988		1873	4096	5969	169558563	SO:0001819	synonymous_variant	91351			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3480A>T	4.37:g.169321988T>A			169558563	Q96ND6	Silent	SNP	ENST00000511577.1	37		.	.	.	.	.	.	.	.	.	.	T	2.374	-0.343582	0.05243	.	.	ENSG00000181381	ENST00000514580	T	0.40225	1.04	2.69	2.69	0.31865	.	9.491200	0.01873	U	0.037362	T	0.19167	0.0460	.	.	.	0.21652	N	0.999604	.	.	.	.	.	.	T	0.34477	-0.9827	7	0.02654	T	1	.	7.5201	0.27622	0.0:0.0:0.0:1.0	.	.	.	.	S	48	ENSP00000422920:T48S	ENSP00000422920:T48S	T	-	1	0	DDX60L	169558563	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.205000	0.09411	1.185000	0.42971	0.377000	0.23210	ACA		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169321988	T	A	169321988	2	1	90	1	0	0	0	0	0	0	0	1	4385	1683	59	5		5	DDX60L	4	169321988	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	14080301	169321988	21832288	96	24683										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527633	23527633	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgcagggagtgtgggcggggCtttagcaataagtcacacct	15	8	1	0	rs574001617		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:23527633C>G	ENST00000296682.3	+	11	2618	c.2436C>G	c.(2434-2436)ggC>ggG	p.G812G		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	812					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GTGGGCGGGGCTTTAGCAATA	0.572										HNSCC(3;0.000094)																																						0			5											36	48	44					5																	23527633		2141	4268	6409	23563390	SO:0001819	synonymous_variant	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2436C>G	5.37:g.23527633C>G			23563390	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																				0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		G	23527633	C	G	23527633	2	3	90	1	0	0	0	0	0	0	0	1	12497	784	28	5		5	PRDM9	5	23527633	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10		23527633	157387627	97	24684										
CDH9	1007	hgsc.bcm.edu	37	chr5	26906229	26906229	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgtctggtaatgcagtttttAttatgccttttggaaaaagc	9	5	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:26906229A>C	ENST00000231021.4	-	5	822	c.650T>G	c.(649-651)aTa>aGa	p.I217R		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	217	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TGCAGTTTTTATTATGCCTTT	0.373																																					Melanoma(8;187 585 15745 40864 52829)											0			5											165	150	155					5																	26906229		2203	4300	6503	26941986	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.650T>G	5.37:g.26906229A>C	ENSP00000231021:p.Ile217Arg		26941986	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.438345	0.83885	.	.	ENSG00000113100	ENST00000231021	T	0.70869	-0.52	5.5	5.5	0.81552	Cadherin (4);Cadherin-like (1);	0.046323	0.85682	D	0.000000	D	0.90219	0.6942	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93750	0.7058	9	.	.	.	.	14.7109	0.69232	1.0:0.0:0.0:0.0	.	217	Q9ULB4	CADH9_HUMAN	R	217	ENSP00000231021:I217R	.	I	-	2	0	CDH9	26941986	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.255000	0.95524	2.216000	0.71823	0.528000	0.53228	ATA		0.373	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		C	26906229	A	C	26906229	3	2	90	1	0	0	0	0	1	0	0	0	3123	449	16	4	1751	4	CDH9	5	26906229	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	3378596	26906229	154009031	98	24685										
SKP2	6502	hgsc.bcm.edu	37	chr5	36166732	36166732	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gccttccgctgcccacgatcAtttatggaccaaccattggc	8	15	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:36166732A>G	ENST00000274255.6	+	4	700	c.504A>G	c.(502-504)tcA>tcG	p.S168S	SKP2_ENST00000508514.1_Intron|SKP2_ENST00000274254.5_Silent_p.S168S|SKP2_ENST00000546211.1_5'UTR	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	168					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCCCACGATCATTTATGGACC	0.443																																																0			5											94	87	89					5																	36166732		2203	4300	6503	36202489	SO:0001819	synonymous_variant	6502			U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"F-boxes / Leucine-rich repeats"	10901	protein-coding gene	gene with protein product		601436	"S-phase kinase-associated protein 2 (p45)"			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.504A>G	5.37:g.36166732A>G			36202489	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Silent	SNP	ENST00000274255.6	37	CCDS3916.1																																																																																				0.443	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983		G	36166732	A	G	36166732	2	3	90	1	0	0	0	0	0	0	0	1	14399	204	8	4		4	SKP2	5	36166732	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9260503	36166732	144748528	99	24686										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38463081	38463081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caaatccccaggcatgatgcGgcagcttaacatcaatggag	10	11	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:38463081G>A	ENST00000354891.3	+	22	3213	c.2867G>A	c.(2866-2868)cGg>cAg	p.R956Q	CTD-2263F21.1_ENST00000510469.1_RNA|EGFLAM_ENST00000322350.5_Missense_Mutation_p.R948Q|EGFLAM_ENST00000506135.1_Missense_Mutation_p.R91Q|EGFLAM_ENST00000336740.6_Missense_Mutation_p.R714Q|EGFLAM_ENST00000514476.1_Missense_Mutation_p.R91Q|EGFLAM_ENST00000397202.2_Missense_Mutation_p.R314Q|EGFLAM_ENST00000397210.3_Missense_Mutation_p.R91Q	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	956	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GGCATGATGCGGCAGCTTAAC	0.468																																					Colon(62;485 1295 3347 17454)											0			5											135	115	122					5																	38463081		2203	4300	6503	38498838	SO:0001583	missense	133584			AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2867G>A	5.37:g.38463081G>A	ENSP00000346964:p.Arg956Gln		38498838	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	G	30	5.049758	0.93740	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580;ENST00000397210;ENST00000506135;ENST00000508131;ENST00000514476	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.32	5.32	0.75619	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.83741	0.5320	L	0.37466	1.105	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.968	D;D;D;P	0.77557	0.951;0.984;0.99;0.553	D	0.84268	0.0487	10	0.51188	T	0.08	-2.2619	19.0362	0.92980	0.0:0.0:1.0:0.0	.	314;714;956;948	Q63HQ2-3;Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;.;EGFLA_HUMAN;.	Q	956;948;714;314;714;91;91;91;91	ENSP00000346964:R956Q;ENSP00000313084:R948Q;ENSP00000337607:R714Q;ENSP00000380385:R314Q;ENSP00000380393:R91Q;ENSP00000425579:R91Q;ENSP00000427228:R91Q;ENSP00000423228:R91Q	ENSP00000313084:R948Q	R	+	2	0	EGFLAM	38498838	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	6.124000	0.71620	2.495000	0.84180	0.655000	0.94253	CGG		0.468	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38463081	G	A	38463081	3	1	90	1	0	0	0	0	1	0	0	0	4977	1116	39	1	2939	1	EGFLAM	5	38463081	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2296349	38463081	142452179	100	24687										
MRPS30	10884	hgsc.bcm.edu	37	chr5	44809433	44809434	+	In_Frame_Ins	INS	-	-	GAGCCC													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtctgccgccgcccccagcgINSgagcccgagcccgagcccga							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:44809433_44809434insGAGCCC	ENST00000507110.1	+	1	407_408	c.369_370insGAGCCC	c.(370-372)gag>GAGCCCgag	p.124_124E>EPE	RP11-53O19.1_ENST00000503452.1_RNA|RP11-53O19.1_ENST00000503179.1_RNA|RP11-53O19.1_ENST00000505302.1_RNA|RP11-53O19.1_ENST00000505401.1_RNA|RP11-53O19.1_ENST00000505637.1_RNA|RP11-53O19.1_ENST00000514597.1_RNA|RP11-53O19.1_ENST00000508123.1_RNA|RP11-53O19.1_ENST00000508945.1_RNA	NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	124					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					CGCCCCCAGCGgagcccgagcc	0.663																																																0			5																																								44845191	SO:0001652	inframe_insertion	10884			AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"Mitochondrial ribosomal proteins / small subunits"	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.382_387dupGAGCCC	5.37:g.44809434_44809439dupGAGCCC	Exception_encountered		44845190	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	In_Frame_Ins	INS	ENST00000507110.1	37	CCDS3951.1																																																																																				0.663	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640		GAGCCC	44809434	-	GAGCCC	44809433	7	5	90	1	0	1	1	0	0	0	0	0	9870	1103	39	0	371	0	MRPS30	5	44809433	In_Frame_Ins	INS	-	TCGA-CI-6624-01C-11D-1826-10	6346352	44809433	136105827	101	24688										
GPBP1	65056	hgsc.bcm.edu	37	chr5	56546943	56546943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcccacaaactgatgttcttTcaagttcacttgaggcagaa	7	10	3	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:56546943T>C	ENST00000506184.2	+	10	2240	c.1135T>C	c.(1135-1137)Tca>Cca	p.S379P	GPBP1_ENST00000538707.1_Missense_Mutation_p.S386P|GPBP1_ENST00000264779.6_Missense_Mutation_p.S386P|GPBP1_ENST00000511209.1_Missense_Mutation_p.S371P|GPBP1_ENST00000424459.3_Missense_Mutation_p.S399P|GPBP1_ENST00000454432.2_Missense_Mutation_p.S399P|GPBP1_ENST00000514387.2_Missense_Mutation_p.S208P			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	379					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		TGATGTTCTTTCAAGTTCACT	0.373																																																0			5											107	98	101					5																	56546943		2203	4300	6503	56582700	SO:0001583	missense	65056				CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.1135T>C	5.37:g.56546943T>C	ENSP00000421202:p.Ser379Pro		56582700	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Missense_Mutation	SNP	ENST00000506184.2	37	CCDS34162.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.906226	0.92107	.	.	ENSG00000062194	ENST00000424459;ENST00000514387;ENST00000506184;ENST00000454432;ENST00000511209;ENST00000264779;ENST00000538707	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.78407	0.4278	M	0.68317	2.08	0.51482	D	0.999921	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.994;0.997;0.996;0.997	T	0.80296	-0.1442	10	0.87932	D	0	-9.5324	16.607	0.84832	0.0:0.0:0.0:1.0	.	399;386;371;379	D4PHA4;Q86WP2-2;Q86WP2-3;Q86WP2	.;.;.;GPBP1_HUMAN	P	399;208;379;399;371;386;386	ENSP00000401596:S399P;ENSP00000421709:S208P;ENSP00000421202:S379P;ENSP00000403522:S399P;ENSP00000422337:S371P;ENSP00000264779:S386P;ENSP00000440090:S386P	ENSP00000264779:S386P	S	+	1	0	GPBP1	56582700	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.148000	0.71788	2.319000	0.78375	0.523000	0.50628	TCA		0.373	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913		C	56546943	T	C	56546943	3	2	90	1	0	0	0	0	1	0	0	0	6615	1783	62	4	1190	4	GPBP1	5	56546943	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	11737510	56546943	124368317	102	24689										
IPO11	51194	hgsc.bcm.edu	37	chr5	61747626	61747626	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtcccagacagtggcctgaaCtaattcccactcttatagag	8	12	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:61747626C>G	ENST00000325324.6	+	5	551	c.382C>G	c.(382-384)Cta>Gta	p.L128V	IPO11_ENST00000409296.3_Missense_Mutation_p.L168V|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	128					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GTGGCCTGAACTAATTCCCAC	0.398																																																0			5											105	95	99					5																	61747626		2203	4300	6503	61783383	SO:0001583	missense	51194			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.382C>G	5.37:g.61747626C>G	ENSP00000316651:p.Leu128Val		61783383	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.834592	0.71373	.	.	ENSG00000086200	ENST00000514647;ENST00000325324;ENST00000506200;ENST00000409296	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	5.43	3.65	0.41850	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.82848	0.5126	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.82575	-0.0389	10	0.51188	T	0.08	.	11.595	0.50968	0.0:0.8558:0.0:0.1442	.	168;128	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	V	128;128;128;168	ENSP00000427129:L128V;ENSP00000316651:L128V;ENSP00000427274:L128V;ENSP00000386992:L168V	ENSP00000316651:L128V	L	+	1	2	IPO11	61783383	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.680000	0.46918	0.666000	0.31087	-0.142000	0.14014	CTA		0.398	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		G	61747626	C	G	61747626	3	3	90	1	0	0	0	0	1	0	0	0	7814	564	20	5	520	5	IPO11	5	61747626	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5200683	61747626	119167634	103	24690										
FOXD1	2297	hgsc.bcm.edu	37	chr5	72744084	72744086	+	In_Frame_Del	DEL	TCC	TCC	-													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caccgccgccctcgtcgtcgTcctcctcttcctcgtcttct							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	TCC	TCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:72744084_72744086delTCC	ENST00000499003.3	-	1	266_268	c.102_104delGGA	c.(100-105)gaggac>gac	p.E34del	RP11-79P5.2_ENST00000514661.1_lincRNA|FOXD1_ENST00000513595.1_5'Flank	NM_004472.2	NP_004463.1	Q16676	FOXD1_HUMAN	forkhead box D1	34	Poly-Glu.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in ureteric bud branching (GO:0060678)|metanephric capsule development (GO:0072213)|metanephric capsule specification (GO:0072267)|metanephric nephron development (GO:0072210)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme development (GO:0072076)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of gene expression (GO:0010628)|positive regulation of kidney development (GO:0090184)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|lung(2)	4		Lung NSC(167;0.00327)|Ovarian(174;0.0175)|Prostate(461;0.151)		OV - Ovarian serous cystadenocarcinoma(47;1.07e-54)		ctcgtcgtcgtcctcctcttcct	0.709																																																0			5								10,3324		5,0,1662						-1.3	1			34	18,7122		8,2,3560	no	coding	FOXD1	NM_004472.2		13,2,5222	A1A1,A1R,RR		0.2521,0.2999,0.2673				28,10446				72779842	SO:0001651	inframe_deletion	2297			U59831	CCDS75259.1	5q13.2	2014-06-04			ENSG00000251493	ENSG00000251493		"Forkhead boxes"	3802	protein-coding gene	gene with protein product		601091		FKHL8		7957066, 8825632	Standard	NM_004472		Approved	FREAC4	uc003kcp.3	Q16676	OTTHUMG00000162495	ENST00000499003.3:c.102_104delGGA	5.37:g.72744087_72744089delTCC	ENSP00000462795:p.Glu34del		72779840	Q12949	In_Frame_Del	DEL	ENST00000499003.3	37																																																																																					0.709	FOXD1-001	KNOWN	sequence_error|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000369154.2	NM_004472		-	72744086	TCC	-	72744084	7	5	90	1	0	1	0	1	0	0	0	0	6015	1667	58	0	1295	0	FOXD1	5	72744084	In_Frame_Del	DEL	TCC	TCGA-CI-6624-01C-11D-1826-10	10996458	72744084	108171176	104	24691										
GFM2	84340	hgsc.bcm.edu	37	chr5	74037379	74037379	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctggtaacaaatcaaaaTtctcactaaattcttctaaa	3	9	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:74037379T>C	ENST00000296805.3	-	11	1362	c.905A>G	c.(904-906)aAt>aGt	p.N302S	GFM2_ENST00000345239.2_Missense_Mutation_p.N302S|GFM2_ENST00000427854.2_Missense_Mutation_p.N302S|GFM2_ENST00000509430.1_Missense_Mutation_p.N302S	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CAAATCAAAATTCTCACTAAA	0.299																																																0			5											43	45	45					5																	74037379		2198	4286	6484	74073135	SO:0001583	missense	84340			AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.905A>G	5.37:g.74037379T>C	ENSP00000296805:p.Asn302Ser		74073135		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636438	0.47049	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000509097	T;T;T;T;T	0.72835	0.12;0.25;0.12;-0.69;-0.01	5.74	4.53	0.55603	Protein synthesis factor, GTP-binding (1);	0.174215	0.64402	D	0.000010	T	0.62109	0.2401	N	0.20357	0.565	0.54753	D	0.999982	P;B;P;P;B	0.48764	0.915;0.013;0.853;0.911;0.017	P;B;B;P;B	0.47430	0.487;0.017;0.392;0.547;0.028	T	0.67106	-0.5754	10	0.56958	D	0.05	-16.358	13.0752	0.59083	0.0:0.0:0.1336:0.8664	.	302;302;302;302;302	F5H687;Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;.;RRF2M_HUMAN	S	302;302;302;302;302;260	ENSP00000296805:N302S;ENSP00000296804:N302S;ENSP00000427004:N302S;ENSP00000405808:N302S;ENSP00000421717:N260S	ENSP00000296805:N302S	N	-	2	0	GFM2	74073135	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.045000	0.71020	2.176000	0.68965	0.460000	0.39030	AAT		0.299	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		C	74037379	T	C	74037379	3	2	90	1	0	0	0	0	1	0	0	0	6362	1493	52	4	1510	4	GFM2	5	74037379	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1293295	74037379	106877881	105	24692										
AGGF1	55109	hgsc.bcm.edu	37	chr5	76335452	76335452	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	attctcgagtagatttgcaaCcttatccgacttctagcaca	6	11	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:76335452C>A	ENST00000312916.7	+	5	1160	c.778C>A	c.(778-780)Cct>Act	p.P260T		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	260					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		AGATTTGCAACCTTATCCGAC	0.333																																																0			5											80	78	78					5																	76335452		2203	4298	6501	76371208	SO:0001583	missense	55109			AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.778C>A	5.37:g.76335452C>A	ENSP00000316109:p.Pro260Thr		76371208	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.944594	0.34283	.	.	ENSG00000164252	ENST00000312916	D	0.89746	-2.56	5.11	0.96	0.19631	.	0.405345	0.27927	N	0.017290	T	0.77054	0.4074	L	0.31926	0.97	0.80722	D	1	B	0.12630	0.006	B	0.08055	0.003	T	0.62946	-0.6746	10	0.37606	T	0.19	-13.4083	0.4511	0.00501	0.1941:0.3264:0.1643:0.3151	.	260	Q8N302	AGGF1_HUMAN	T	260	ENSP00000316109:P260T	ENSP00000316109:P260T	P	+	1	0	AGGF1	76371208	1.000000	0.71417	0.993000	0.49108	0.921000	0.55340	1.686000	0.37669	0.177000	0.19895	0.585000	0.79938	CCT		0.333	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76335452	C	A	76335452	3	1	90	1	0	0	0	0	1	0	0	0	382	507	18	2	796	2	AGGF1	5	76335452	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2298073	76335452	104579808	106	24693										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101748715	101748715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttttttggttttgtgctttAgaatatgtacaccctgcaaa	7	6	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:101748715A>G	ENST00000506729.1	-	9	1776	c.1605T>C	c.(1603-1605)tcT>tcC	p.S535S	SLCO6A1_ENST00000513675.1_Silent_p.S282S|SLCO6A1_ENST00000379810.1_Silent_p.S282S|SLCO6A1_ENST00000389019.3_Silent_p.S473S|SLCO6A1_ENST00000379807.3_Silent_p.S535S			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	535	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TTTGTGCTTTAGAATATGTAC	0.234																																																0			5											20	20	20					5																	101748715		2185	4287	6472	101776614	SO:0001819	synonymous_variant	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1605T>C	5.37:g.101748715A>G			101776614	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																				0.234	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		G	101748715	A	G	101748715	2	3	90	1	0	0	0	0	0	0	0	1	14769	407	15	4		4	SLCO6A1	5	101748715	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	25413263	101748715	79166545	107	24694										
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	90	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10425916	112174631	68740629	108	24695			1	15		4	4	850	N	T_G_C_A	9.564976e-08
APC	324	hgsc.bcm.edu	37	chr5	112174684	112174684	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtaagccagtctttgtgtcaAgaagatgactatgaagatga	11	5	2	6	rs545574962		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:112174684A>C	ENST00000457016.1	+	16	3773	c.3393A>C	c.(3391-3393)caA>caC	p.Q1131H	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1131H|APC_ENST00000508376.2_Missense_Mutation_p.Q1131H			P25054	APC_HUMAN	adenomatous polyposis coli	1131	Asp/Glu-rich (acidic).|Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTTTGTGTCAAGAAGATGACT	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											73	67	69					5																	112174684		2202	4300	6502	112202583	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3393A>C	5.37:g.112174684A>C	ENSP00000413133:p.Gln1131His		112202583	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	8.557	0.876937	0.17395	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.93859	-2.57;-3.3;-2.57;-2.57;-2.75	5.74	0.223	0.15292	.	0.234286	0.44285	D	0.000463	T	0.81683	0.4874	N	0.12182	0.205	0.37341	D	0.910387	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.67217	-0.5726	10	0.17832	T	0.49	-8.3597	6.2467	0.20823	0.4147:0.0:0.419:0.1663	.	1133;1131	Q4LE70;P25054	.;APC_HUMAN	H	1131;1113;1131;1131;1131	ENSP00000413133:Q1131H;ENSP00000423224:Q1113H;ENSP00000257430:Q1131H;ENSP00000427089:Q1131H;ENSP00000423828:Q1131H	ENSP00000257430:Q1131H	Q	+	3	2	APC	112202583	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.724000	0.25954	0.085000	0.17107	-0.255000	0.11280	CAA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112174684	A	C	112174684	3	2	90	1	0	0	0	0	1	0	0	0	763	69	3	4	3451	4	APC	5	112174684	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	53	112174684	68740576	109	24696			1	15		4	4	850	N	T_G_C_A	9.564976e-08
APC	324	hgsc.bcm.edu	37	chr5	112175248	112175248	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	actaggtcagctgaagatccTgtgagcgaagttccagcagt	12	9	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:112175248T>C	ENST00000457016.1	+	16	4337	c.3957T>C	c.(3955-3957)ccT>ccC	p.P1319P	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.P1319P|APC_ENST00000508376.2_Silent_p.P1319P			P25054	APC_HUMAN	adenomatous polyposis coli	1319	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.V1320fs*12(1)|p.V1320fs*1(1)|p.K1192fs*3(1)|p.?(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGAAGATCCTGTGAGCGAAG	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Deletion - Frameshift(3)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5											61	62	62					5																	112175248		2202	4300	6502	112203147	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3957T>C	5.37:g.112175248T>C			112203147	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175248	T	C	112175248	2	2	90	1	0	0	0	0	0	0	0	1	763	1567	55	4		4	APC	5	112175248	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	564	112175248	68740012	110	24697			1	15		4	4	850	N	T_G_C_A	9.564976e-08
APC	324	hgsc.bcm.edu	37	chr5	112175480	112175480	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcagttcacttgatagttttGagagtcgttcgattgccagc	10	8	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:112175480G>T	ENST00000457016.1	+	16	4569	c.4189G>T	c.(4189-4191)Gag>Tag	p.E1397*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1397*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1397*			P25054	APC_HUMAN	adenomatous polyposis coli	1397	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1399fs*9(18)|p.E1397*(8)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.E1397fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATAGTTTTGAGAGTCGTTC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Deletion - Frameshift(20)|Substitution - Nonsense(8)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(28)|soft_tissue(1)|skin(1)	5	GRCh37	CM992136	APC	M							104	98	100					5																	112175480		2202	4300	6502	112203379	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4189G>T	5.37:g.112175480G>T	ENSP00000413133:p.Glu1397*		112203379	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	41	8.742411	0.98937	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.111909	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.9405	20.4898	0.99202	0.0:0.0:1.0:0.0	.	.	.	.	X	1397	.	.	E	+	1	0	APC	112203379	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.281000	0.78621	2.941000	0.99782	0.655000	0.94253	GAG		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175480	G	T	112175480	4	4	90	1	0	0	0	0	0	1	0	0	763	1291	45	2	4247	2	APC	5	112175480	Nonsense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	232	112175480	68739780	111	24698			1	15		4	4	850	N	T_G_C_A	9.564976e-08
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121758612	121758612	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcaactcttattacaaacacGcaaaagcccacaggaatcgc	5	13	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:121758612G>A	ENST00000261368.8	+	4	442	c.180G>A	c.(178-180)acG>acA	p.T60T	SNCAIP_ENST00000503116.2_Silent_p.T107T|SNCAIP_ENST00000379536.2_Silent_p.T60T|SNCAIP_ENST00000504884.2_Intron|SNCAIP_ENST00000261367.7_Silent_p.T107T|SNCAIP_ENST00000542191.1_Intron|SNCAIP_ENST00000379533.2_Silent_p.T107T|SNCAIP_ENST00000414317.2_Intron|SNCAIP_ENST00000379538.3_Intron	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	60					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TTACAAACACGCAAAAGCCCA	0.413																																																0			5											65	66	65					5																	121758612		2203	4300	6503	121786511	SO:0001819	synonymous_variant	9627			AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.180G>A	5.37:g.121758612G>A			121786511	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Silent	SNP	ENST00000261368.8	37	CCDS4131.1																																																																																				0.413	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121758612	G	A	121758612	2	1	90	1	0	0	0	0	0	0	0	1	14878	1074	38	1		1	SNCAIP	5	121758612	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	9583132	121758612	59156648	112	24699										
PCDHGA9	56107	hgsc.bcm.edu	37	chr5	140783404	140783404	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctctgctattccagcttaaTgaaaatactggggaaatatc	7	8	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:140783404T>G	ENST00000573521.1	+	1	885	c.885T>G	c.(883-885)aaT>aaG	p.N295K	PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	295	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGCTTAATGAAAATACTG	0.368																																																0			5											93	96	95					5																	140783404		1821	4090	5911	140763588	SO:0001583	missense	56107			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.885T>G	5.37:g.140783404T>G	ENSP00000460274:p.Asn295Lys		140763588	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.368	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		G	140783404	T	G	140783404	3	3	90	1	0	0	0	0	1	0	0	0	11592	1461	51	4	887	4	PCDHGA9	5	140783404	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	19024792	140783404	40131856	113	24700										
ARSI	340075	hgsc.bcm.edu	37	chr5	149678174	149678174	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gagtcctgtgtggatctggtAcctggtggggaggaggggaa	20	5	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:149678174A>G	ENST00000328668.7	-	2	892	c.313T>C	c.(313-315)Tac>Cac	p.Y105H		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	105					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGATCTGGTACCTGGTGGGG	0.612																																																0			5											49	55	53					5																	149678174		2181	4275	6456	149658367	SO:0001630	splice_region_variant	340075			AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.312-1T>C	5.37:g.149678174A>G			149658367	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.387005	0.61956	.	.	ENSG00000183876	ENST00000328668	D	0.97256	-4.31	4.41	4.41	0.53225	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96417	0.8831	M	0.61387	1.9	0.80722	D	1	P	0.37398	0.593	B	0.44163	0.443	D	0.96395	0.9292	10	0.51188	T	0.08	.	13.8417	0.63444	1.0:0.0:0.0:0.0	.	105	Q5FYB1	ARSI_HUMAN	H	105	ENSP00000333395:Y105H	ENSP00000333395:Y105H	Y	-	1	0	ARSI	149658367	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	9.139000	0.94554	1.860000	0.53959	0.459000	0.35465	TAC		0.612	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301	Missense_Mutation	G	149678174	A	G	149678174	5	3	90	1	0	0	0	0	0	0	1	0	995	405	14	4	1400	4	ARSI	5	149678174	Splice_Site	SNP	A	TCGA-CI-6624-01C-11D-1826-10	8894770	149678174	31237086	114	24701										
FAT2	2196	hgsc.bcm.edu	37	chr5	150946372	150946372	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aactgtggggtgtaatgattAatctgatatgtgcttaaaga	11	3	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:150946372A>G	ENST00000261800.5	-	1	2133	c.2121T>C	c.(2119-2121)atT>atC	p.I707I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	707					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTAATGATTAATCTGATATG	0.473																																																0			5											107	109	108					5																	150946372		2203	4300	6503	150926565	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2121T>C	5.37:g.150946372A>G			150926565	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.473	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150946372	A	G	150946372	2	3	90	1	0	0	0	0	0	0	0	1	5709	358	13	4		4	FAT2	5	150946372	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1268198	150946372	29968888	115	24702										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153026596	153026596	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctccacgtctgcttcattaCgccgagctttcccgttgata	7	15	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:153026596C>T	ENST00000285900.5	+	3	672	c.329C>T	c.(328-330)aCg>aTg	p.T110M	GRIA1_ENST00000518142.1_Intron|GRIA1_ENST00000448073.4_Missense_Mutation_p.T120M|GRIA1_ENST00000340592.5_Missense_Mutation_p.T110M|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000518783.1_Missense_Mutation_p.T120M|GRIA1_ENST00000521843.2_Missense_Mutation_p.T41M	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	110					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)	p.T110M(3)		NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	TGCTTCATTACGCCGAGCTTT	0.502																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	5											170	154	160					5																	153026596		2203	4300	6503	153006789	SO:0001583	missense	2890				CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.329C>T	5.37:g.153026596C>T	ENSP00000285900:p.Thr110Met		153006789	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669632	0.88348	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.55	5.55	0.83447	Extracellular ligand-binding receptor (1);	0.047603	0.85682	D	0.000000	D	0.92100	0.7496	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;0.981	D	0.92611	0.6099	10	0.87932	D	0	.	18.489	0.90839	0.0:1.0:0.0:0.0	.	120;120;120;110;110	E7ESV8;B7Z9G9;B7Z2W8;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	M	110;110;64;110;41;41;120;120	ENSP00000285900:T110M;ENSP00000339343:T110M;ENSP00000427864:T41M;ENSP00000442108:T41M;ENSP00000428994:T120M;ENSP00000415569:T120M	ENSP00000285900:T110M	T	+	2	0	GRIA1	153006789	1.000000	0.71417	0.359000	0.25824	0.866000	0.49608	7.581000	0.82535	2.612000	0.88384	0.655000	0.94253	ACG		0.502	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153026596	C	T	153026596	3	4	90	1	0	0	0	0	1	0	0	0	6788	536	19	1	339	1	GRIA1	5	153026596	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2080224	153026596	27888664	116	24703										
ITK	3702	hgsc.bcm.edu	37	chr5	156670686	156670686	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgtgcaagagattggcagtGggcaatttgggttggtgcat	16	4	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:156670686G>T	ENST00000422843.3	+	12	1266	c.1114G>T	c.(1114-1116)Ggg>Tgg	p.G372W	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	GATTGGCAGTGGGCAATTTGG	0.502			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	0			5											160	159	159					5																	156670686		2203	4300	6503	156603264	SO:0001583	missense	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1114G>T	5.37:g.156670686G>T	ENSP00000398655:p.Gly372Trp		156603264	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.981418	0.93044	.	.	ENSG00000113263	ENST00000422843	D	0.94897	-3.55	5.79	5.79	0.91817	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98937	0.9639	H	0.99897	4.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98874	1.0767	10	0.87932	D	0	.	20.0263	0.97523	0.0:0.0:1.0:0.0	.	372	Q08881	ITK_HUMAN	W	372	ENSP00000398655:G372W	ENSP00000398655:G372W	G	+	1	0	ITK	156603264	1.000000	0.71417	0.987000	0.45799	0.953000	0.61014	9.676000	0.98643	2.735000	0.93741	0.655000	0.94253	GGG		0.502	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156670686	G	T	156670686	3	4	90	1	0	0	0	0	1	0	0	0	7930	1348	47	2	1160	2	ITK	5	156670686	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	3644090	156670686	24244574	117	24704										
HRH2	3274	hgsc.bcm.edu	37	chr5	175111225	175111225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctgtccaggacccaaagccGagaacccaggcaacaggaag	12	13	0	1	rs141845922		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:175111225G>A	ENST00000231683.2	+	1	2762	c.989G>A	c.(988-990)cGa>cAa	p.R330Q	HRH2_ENST00000377291.2_Missense_Mutation_p.R330Q	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	330					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)	p.R330Q(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	ACCCAAAGCCGAGAACCCAGG	0.592																																																1	Substitution - Missense(1)	lung(1)	5						G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	81	85	84		989,989	-6.8	0	5	dbSNP_134	84	0,8600		0,0,4300	no	missense,missense	HRH2	NM_001131055.1,NM_022304.2	43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	330/398,330/360	175111225	1,13005	2203	4300	6503	175043831	SO:0001583	missense	3274				CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"GPCR / Class A : Histamine receptors"	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.989G>A	5.37:g.175111225G>A	ENSP00000231683:p.Arg330Gln		175043831	B5BUP7|Q14464|Q7Z5R9	Missense_Mutation	SNP	ENST00000231683.2	37	CCDS4395.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.289177	0.23478	2.27E-4	0.0	ENSG00000113749	ENST00000377291;ENST00000231683	T;T	0.64618	-0.11;-0.1	4.83	-6.8	0.01709	.	1.302740	0.05286	N	0.520242	T	0.39064	0.1064	N	0.19112	0.55	0.09310	N	1	B;B	0.17852	0.005;0.024	B;B	0.09377	0.0;0.004	T	0.24905	-1.0147	10	0.13470	T	0.59	.	8.3293	0.32175	0.5651:0.1868:0.248:0.0	.	330;330	P25021;Q7Z5R9	HRH2_HUMAN;.	Q	330	ENSP00000366506:R330Q;ENSP00000231683:R330Q	ENSP00000231683:R330Q	R	+	2	0	HRH2	175043831	0.000000	0.05858	0.000000	0.03702	0.782000	0.44232	-0.354000	0.07681	-1.505000	0.01807	0.650000	0.86243	CGA		0.592	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1			A	175111225	G	A	175111225	3	1	90	1	0	0	0	0	1	0	0	0	7377	1058	37	1	991	1	HRH2	5	175111225	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	18440539	175111225	5804035	118	24705										
FLT4	2324	hgsc.bcm.edu	37	chr5	180057235	180057235	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggggccgtaccgagcgcagcGtgacattgaggccggggatg	19	10	0	2	rs148392893		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr5:180057235G>C	ENST00000261937.6	-	4	581	c.503C>G	c.(502-504)aCg>aGg	p.T168R	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Missense_Mutation_p.T168R|FLT4_ENST00000393347.3_Missense_Mutation_p.T168R	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	168	Ig-like C2-type 2.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGAGCGCAGCGTGACATTGAG	0.642																																					Colon(97;1075 1466 27033 27547 35871)											0			5											88	78	81					5																	180057235		2200	4299	6499	179989841	SO:0001583	missense	2324			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.503C>G	5.37:g.180057235G>C	ENSP00000261937:p.Thr168Arg		179989841	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586977	0.66105	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	T;T;T	0.26223	1.75;1.75;1.75	5.42	5.42	0.78866	Tyrosine-protein kinase, vascular endothelial growth factor receptor 3 (VEGFR3), N-terminal (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57548	0.2061	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.994;0.994	D;D;D;D	0.97110	1.0;1.0;0.92;0.935	T	0.61946	-0.6958	9	0.72032	D	0.01	.	19.6098	0.95600	0.0:0.0:1.0:0.0	.	168;168;168;168	B5A927;P35916-3;E9PD35;P35916	.;.;.;VGFR3_HUMAN	R	168	ENSP00000261937:T168R;ENSP00000377016:T168R;ENSP00000426057:T168R	ENSP00000261937:T168R	T	-	2	0	FLT4	179989841	1.000000	0.71417	0.980000	0.43619	0.289000	0.27227	6.701000	0.74624	2.714000	0.92807	0.561000	0.74099	ACG		0.642	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			C	180057235	G	C	180057235	3	2	90	1	0	0	0	0	1	0	0	0	5963	1145	40	5	3704	5	FLT4	5	180057235	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	4946010	180057235	858025	119	24706										
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797678	29797678	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtagtcactggagctgcggtCgctgctgtgctgtggagaaa	16	8	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:29797678C>T	ENST00000360323.6	+	5	1005	c.981C>T	c.(979-981)gtC>gtT	p.V327V	HLA-G_ENST00000428701.1_Silent_p.V327V|HLA-G_ENST00000376815.3_Silent_p.V143V|HLA-G_ENST00000376818.3_Silent_p.V235V|HLA-G_ENST00000376828.2_Silent_p.V332V			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	327					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.V327V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						GAGCTGCGGTCGCTGCTGTGC	0.567																																																1	Substitution - coding silent(1)	central_nervous_system(1)	6											91	79	83					6																	29797678		2203	4300	6503	29905657	SO:0001819	synonymous_variant	3135				CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.981C>T	6.37:g.29797678C>T			29905657		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																				0.567	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797678	C	T	29797678	2	4	90	1	0	0	0	0	0	0	0	1	7233	871	31	1		1	HLA-G	6	29797678	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10		29797678	141317389	120	24707										
MICB	4277	hgsc.bcm.edu	37	chr6	31473513	31473513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgcgctatgacaggcagaaaCgcagggcaaagccccaggga	14	11	0	2	rs2240858	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:31473513C>T	ENST00000252229.6	+	2	269	c.190C>T	c.(190-192)Cgc>Tgc	p.R64C	MICB_ENST00000538442.1_Missense_Mutation_p.R32C|MICB_ENST00000399150.3_Missense_Mutation_p.R64C	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CAGGCAGAAACGCAGGGCAAA	0.572													c|||	4	0.000798722	0	0.0014	5008	,	,		19845	0		0	False		,,,				2504	0.0031															0			6											72	76	75					6																	31473513		1286	2551	3837	31581492	SO:0001583	missense	4277				CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"Immunoglobulin superfamily / C1-set domain containing"	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.190C>T	6.37:g.31473513C>T	ENSP00000252229:p.Arg64Cys		31581492		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	.	.	.	.	.	.	.	.	.	.	N	3.472	-0.107702	0.06924	.	.	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.01887	4.58;4.58;4.58	2.35	-4.71	0.03279	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.688810	0.03892	U	0.278939	T	0.00440	0.0014	N	0.12422	0.21	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.10450	0.002;0.004;0.005	T	0.47548	-0.9109	10	0.42905	T	0.14	.	2.3151	0.04197	0.1242:0.3189:0.378:0.1788	rs2240858	32;64;64	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	C	32;64;64	ENSP00000442345:R32C;ENSP00000382103:R64C;ENSP00000252229:R64C	ENSP00000252229:R64C	R	+	1	0	MICB	31581492	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.334000	0.02665	-1.193000	0.02688	-3.051000	0.00069	CGC		0.572	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931		T	31473513	C	T	31473513	3	4	90	1	0	0	0	0	1	0	0	0	9605	536	19	1	196	1	MICB	6	31473513	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1675835	31473513	139641554	121	24708										
BTNL2	56244	hgsc.bcm.edu	37	chr6	32364076	32364076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctccatgctctgtgcattcGccttgggggacaggtaacag	12	12	1	0	rs138515121	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:32364076G>A	ENST00000374993.1	-	5	817	c.818C>T	c.(817-819)gCg>gTg	p.A273V	BTNL2_ENST00000544175.1_5'UTR|BTNL2_ENST00000374995.3_Missense_Mutation_p.A179V|BTNL2_ENST00000540315.1_Missense_Mutation_p.A63V|BTNL2_ENST00000429232.2_Missense_Mutation_p.A180V|BTNL2_ENST00000454136.3_Missense_Mutation_p.A273V|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000414363.1_Missense_Mutation_p.A63V	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	273	Ig-like V-type 3.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CTGTGCATTCGCCTTGGGGGA	0.522													g|||	27	0.00539137	0.0174	0.0058	5008	,	,		21499	0		0	False		,,,				2504	0															0			6							VAL/ALA	54,2966		1,52,1457	96	82	87		818	0.1	0	6	dbSNP_134	87	0,5418		0,0,2709	yes	missense	BTNL2	NM_019602.1	64	1,52,4166	AA,AG,GG		0.0,1.7881,0.64	benign	273/456	32364076	54,8384	1510	2709	4219	32472054	SO:0001583	missense	56244			AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.818C>T	6.37:g.32364076G>A	ENSP00000364132:p.Ala273Val		32472054	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	g	5.390	0.257249	0.10239	0.017881	0.0	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000429232	T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94	5.16	0.135	0.14775	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.312890	0.05180	N	0.501248	T	0.02230	0.0069	N	0.03608	-0.345	0.09310	N	1	B;B	0.24963	0.115;0.048	B;B	0.20767	0.016;0.031	T	0.40478	-0.9561	10	0.21540	T	0.41	.	4.5611	0.12161	0.3979:0.0:0.4584:0.1437	.	63;273	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	V	273;179;63;273;63;180	ENSP00000364134:A179V;ENSP00000390512:A63V;ENSP00000364132:A273V;ENSP00000444714:A63V;ENSP00000411166:A180V	ENSP00000364132:A273V	A	-	2	0	BTNL2	32472054	0.000000	0.05858	0.000000	0.03702	0.736000	0.42039	0.472000	0.22116	0.080000	0.16959	-0.178000	0.13098	GCG		0.522	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		A	32364076	G	A	32364076	3	1	90	1	0	0	0	0	1	0	0	0	1568	1087	38	1	557	1	BTNL2	6	32364076	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	890563	32364076	138750991	122	24709										
DAXX	1616	hgsc.bcm.edu	37	chr6	33287859	33287859	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctgcatctgttccagatccTcctcctcttcagaatctgtg	6	15	4	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:33287859T>C	ENST00000374542.5	-	5	1598	c.1394A>G	c.(1393-1395)gAg>gGg	p.E465G	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000266000.6_Missense_Mutation_p.E465G|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000414083.2_Missense_Mutation_p.E390G|DAXX_ENST00000477162.1_5'UTR	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	465	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						ttccagatcctcctcctcttc	0.527			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	0			6											177	125	143					6																	33287859		2203	4300	6503	33395837	SO:0001583	missense	1616			AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1394A>G	6.37:g.33287859T>C	ENSP00000363668:p.Glu465Gly		33395837	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	37	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480554	0.26598	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083	T;T	0.03772	3.81;3.81	4.1	4.1	0.47936	.	0.352110	0.28504	N	0.015119	T	0.03263	0.0095	M	0.63428	1.95	0.33765	D	0.622304	P;P	0.41784	0.762;0.762	B;B	0.42163	0.378;0.378	T	0.39121	-0.9629	10	0.36615	T	0.2	-2.5961	9.6964	0.40161	0.0:0.0:0.0:1.0	.	477;465	B4E1C1;Q9UER7	.;DAXX_HUMAN	G	465;465;390	ENSP00000266000:E465G;ENSP00000363668:E465G	ENSP00000266000:E465G	E	-	2	0	DAXX	33395837	1.000000	0.71417	0.983000	0.44433	0.537000	0.34900	2.167000	0.42415	1.860000	0.53959	0.443000	0.29094	GAG		0.527	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			C	33287859	T	C	33287859	3	2	90	1	0	0	0	0	1	0	0	0	4249	1551	54	4	844	4	DAXX	6	33287859	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	923783	33287859	137827208	123	24710										
KCNK16	83795	hgsc.bcm.edu	37	chr6	39282826	39282826	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gggaagtcctggggtgtgacTtggactcctcttgctgctgt	15	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:39282826T>A	ENST00000373229.5	-	6	895	c.882A>T	c.(880-882)caA>caT	p.Q294H	KCNK17_ENST00000453413.2_5'Flank|KCNK16_ENST00000507712.1_Missense_Mutation_p.Q182H|KCNK16_ENST00000425054.2_3'UTR|KCNK16_ENST00000373227.4_Missense_Mutation_p.Q247H|KCNK17_ENST00000373231.4_5'Flank	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	294					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						GGGGTGTGACTTGGACTCCTC	0.597																																																0			6											157	143	148					6																	39282826		2203	4300	6503	39390804	SO:0001583	missense	83795			AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.882A>T	6.37:g.39282826T>A	ENSP00000362326:p.Gln294His		39390804	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	37	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.753884	0.31046	.	.	ENSG00000095981	ENST00000373229;ENST00000507712;ENST00000373227	T;T;T	0.16597	2.52;2.33;2.83	2.35	-1.81	0.07882	.	7739.210000	0.00166	N	0.000000	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B;B	0.30664	0.289;0.191	B;B	0.23150	0.044;0.02	T	0.35943	-0.9768	10	0.87932	D	0	.	6.4462	0.21877	0.0:0.3901:0.0:0.6099	.	247;294	Q96T55-5;Q96T55	.;KCNKG_HUMAN	H	294;182;247	ENSP00000362326:Q294H;ENSP00000423842:Q182H;ENSP00000362324:Q247H	ENSP00000362324:Q247H	Q	-	3	2	KCNK16	39390804	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	0.220000	0.17660	-0.543000	0.06240	-0.456000	0.05471	CAA		0.597	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		A	39282826	T	A	39282826	3	1	90	1	0	0	0	0	1	0	0	0	8084	1606	56	5	51	5	KCNK16	6	39282826	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	5994967	39282826	131832241	124	24711										
TFEB	7942	hgsc.bcm.edu	37	chr6	41652465	41652465	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgagtcgtccaggagcatgaGgtccagatccttcttggaca	12	10	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:41652465G>C	ENST00000230323.4	-	10	1604	c.1303C>G	c.(1303-1305)Ctc>Gtc	p.L435V	TFEB_ENST00000358871.2_Missense_Mutation_p.L449V|TFEB_ENST00000373033.1_Missense_Mutation_p.L435V|AL035588.1_ENST00000597468.1_5'Flank|TFEB_ENST00000403298.4_Missense_Mutation_p.L435V|TFEB_ENST00000420312.1_Missense_Mutation_p.L350V	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	435					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			AGGAGCATGAGGTCCAGATCC	0.672			T	ALPHA	renal (childhood epithelioid)																																		Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	0			6											68	63	65					6																	41652465		2202	4300	6502	41760443	SO:0001583	missense	7942			M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.1303C>G	6.37:g.41652465G>C	ENSP00000230323:p.Leu435Val		41760443	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Missense_Mutation	SNP	ENST00000230323.4	37	CCDS4858.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124590	0.56613	.	.	ENSG00000112561	ENST00000406563;ENST00000343317;ENST00000230323;ENST00000358871;ENST00000403298;ENST00000420312;ENST00000373033	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.05	2.11	0.27256	.	0.215065	0.37809	N	0.001929	T	0.53997	0.1831	L	0.60455	1.87	0.43714	D	0.996189	B;P;B	0.51449	0.201;0.945;0.073	B;P;B	0.55055	0.26;0.767;0.121	T	0.56007	-0.8050	10	0.54805	T	0.06	-16.6971	7.2089	0.25923	0.4534:0.0:0.5466:0.0	.	449;435;350	B0QYS6;P19484;P19484-2	.;TFEB_HUMAN;.	V	293;521;435;449;435;350;435	ENSP00000383998:L293V;ENSP00000343948:L521V;ENSP00000230323:L435V;ENSP00000351742:L449V;ENSP00000384203:L435V;ENSP00000412551:L350V;ENSP00000362124:L435V	ENSP00000230323:L435V	L	-	1	0	TFEB	41760443	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.600000	0.46240	0.444000	0.26612	0.655000	0.94253	CTC		0.672	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			C	41652465	G	C	41652465	3	2	90	1	0	0	0	0	1	0	0	0	15840	1000	35	5	131	5	TFEB	6	41652465	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2369639	41652465	129462602	125	24712										
PRPH2	5961	hgsc.bcm.edu	37	chr6	42689612	42689612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctgcagcatgtcgatggtcTtcttcatgaaacacctgcca	8	12	4	1	rs61755786		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:42689612T>C	ENST00000230381.5	-	1	700	c.461A>G	c.(460-462)aAg>aGg	p.K154R		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	154					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			GTCGATGGTCTTCTTCATGAA	0.542																																																0			6											119	105	110					6																	42689612		2203	4300	6503	42797590	SO:0001583	missense	5961				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.461A>G	6.37:g.42689612T>C	ENSP00000230381:p.Lys154Arg		42797590	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	T	8.112	0.779109	0.16120	.	.	ENSG00000112619	ENST00000230381	T	0.78816	-1.21	5.78	5.78	0.91487	Tetraspanin, EC2 domain (1);	0.042558	0.85682	D	0.000000	T	0.41166	0.1147	N	0.04686	-0.185	0.43874	D	0.996483	B	0.02656	0.0	B	0.11329	0.006	T	0.47195	-0.9136	10	0.09084	T	0.74	.	16.3979	0.83621	0.0:0.0:0.0:1.0	.	154	P23942	PRPH2_HUMAN	R	154	ENSP00000230381:K154R	ENSP00000230381:K154R	K	-	2	0	PRPH2	42797590	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.331000	0.52075	2.333000	0.79357	0.533000	0.62120	AAG		0.542	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		C	42689612	T	C	42689612	3	2	90	1	0	0	0	0	1	0	0	0	12611	1609	56	4	591	4	PRPH2	6	42689612	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1037147	42689612	128425455	126	24713										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43400851	43400851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gcccagccgccctcctactgGggaggccctgaacctactag	11	17	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:43400851G>A	ENST00000372530.4	+	3	1348	c.1133G>A	c.(1132-1134)gGg>gAg	p.G378E	ABCC10_ENST00000443426.2_Intron|ABCC10_ENST00000244533.3_Missense_Mutation_p.G335E	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	378	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CCTCCTACTGGGGAGGCCCTG	0.587																																																0			6											59	61	60					6																	43400851		2203	4300	6503	43508829	SO:0001583	missense	89845			U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.1133G>A	6.37:g.43400851G>A	ENSP00000361608:p.Gly378Glu		43508829	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617825	0.87359	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	D;D	0.97752	-4.52;-4.52	5.2	5.2	0.72013	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99233	0.9733	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99087	1.0839	10	0.87932	D	0	-10.6028	18.7462	0.91794	0.0:0.0:1.0:0.0	.	335;378	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	E	378;335	ENSP00000361608:G378E;ENSP00000244533:G335E	ENSP00000244533:G335E	G	+	2	0	ABCC10	43508829	1.000000	0.71417	0.945000	0.38365	0.985000	0.73830	9.869000	0.99810	2.445000	0.82738	0.561000	0.74099	GGG		0.587	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		A	43400851	G	A	43400851	3	1	90	1	0	0	0	0	1	0	0	0	50	1232	43	3	1006	3	ABCC10	6	43400851	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	711239	43400851	127714216	127	24714										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56918146	56918146	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggagaggtaaattgtttaaaTacacgttacagtgcaacaag	10	5	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:56918146T>C	ENST00000370733.4	+	4	1056	c.849T>C	c.(847-849)aaT>aaC	p.N283N	KIAA1586_ENST00000545356.1_Silent_p.N256N	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	283							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ATTGTTTAAATACACGTTACA	0.303																																																0			6											34	37	36					6																	56918146		2199	4292	6491	57026105	SO:0001819	synonymous_variant	57691			AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.849T>C	6.37:g.56918146T>C			57026105	A8K4M3|Q8IW25	Silent	SNP	ENST00000370733.4	37	CCDS34480.1																																																																																				0.303	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		C	56918146	T	C	56918146	2	2	90	1	0	0	0	0	0	0	0	1	8266	1403	49	4		4	KIAA1586	6	56918146	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	13517295	56918146	114196921	128	24715										
PHF3	23469	hgsc.bcm.edu	37	chr6	64401918	64401918	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gatacagtgaagcacaaggtCaaaattttaaaacgggtgag	11	5	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:64401918C>G	ENST00000262043.3	+	5	2821	c.2481C>G	c.(2479-2481)gtC>gtG	p.V827V	PHF3_ENST00000393387.1_Silent_p.V827V			Q92576	PHF3_HUMAN	PHD finger protein 3	827					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AGCACAAGGTCAAAATTTTAA	0.303																																					GBM(135;136 1820 29512 34071 46235)											0			6											46	48	47					6																	64401918		2203	4300	6503	64459877	SO:0001819	synonymous_variant	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2481C>G	6.37:g.64401918C>G			64459877	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1																																																																																				0.303	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			G	64401918	C	G	64401918	2	3	90	1	0	0	0	0	0	0	0	1	11867	813	29	5		5	PHF3	6	64401918	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	7483772	64401918	106713149	129	24716										
LCA5	167691	hgsc.bcm.edu	37	chr6	80197476	80197476	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttatccatattctgaattgGatacattcctagttggtacc	6	8	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:80197476G>C	ENST00000392959.1	-	9	1950	c.1339C>G	c.(1339-1341)Cca>Gca	p.P447A	LCA5_ENST00000369846.4_Missense_Mutation_p.P447A	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	447					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TTCTGAATTGGATACATTCCT	0.368																																																0			6											125	126	126					6																	80197476		2203	4300	6503	80254195	SO:0001583	missense	167691				CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1339C>G	6.37:g.80197476G>C	ENSP00000376686:p.Pro447Ala		80254195	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	G	0.618	-0.822325	0.02755	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.28666	1.6;1.6	5.62	2.74	0.32292	.	0.617506	0.14991	N	0.286697	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.13407	0.009	T	0.35151	-0.9800	10	0.37606	T	0.19	-0.5448	4.2777	0.10816	0.0791:0.1258:0.5296:0.2655	.	447	Q86VQ0	LCA5_HUMAN	A	447	ENSP00000358861:P447A;ENSP00000376686:P447A	ENSP00000358861:P447A	P	-	1	0	LCA5	80254195	0.045000	0.20229	0.002000	0.10522	0.002000	0.02628	0.826000	0.27407	0.705000	0.31890	0.491000	0.48974	CCA		0.368	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		C	80197476	G	C	80197476	3	2	90	1	0	0	0	0	1	0	0	0	8678	1174	41	5	758	5	LCA5	6	80197476	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	15795558	80197476	90917591	130	24717										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94120432	94120432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agctaagttctcaataatggAccagcacttcttgtagtaca	7	9	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:94120432A>G	ENST00000369303.4	-	3	803	c.619T>C	c.(619-621)Tcc>Ccc	p.S207P	EPHA7_ENST00000369297.1_Missense_Mutation_p.S207P	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	207	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TCAATAATGGACCAGCACTTC	0.438																																																0			6											79	83	81					6																	94120432		2203	4300	6503	94177153	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.619T>C	6.37:g.94120432A>G	ENSP00000358309:p.Ser207Pro		94177153	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181951	0.57800	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.72282	-0.64;4.38	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.65974	0.2743	L	0.38838	1.175	0.49213	D	0.999765	D;D;D;D	0.60575	0.965;0.967;0.988;0.98	P;P;P;P	0.55391	0.461;0.747;0.775;0.601	T	0.67193	-0.5732	10	0.40728	T	0.16	.	16.1819	0.81915	1.0:0.0:0.0:0.0	.	207;207;207;207	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	P	207	ENSP00000358309:S207P;ENSP00000358303:S207P	ENSP00000358303:S207P	S	-	1	0	EPHA7	94177153	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.961000	0.63681	2.279000	0.76181	0.533000	0.62120	TCC		0.438	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			G	94120432	A	G	94120432	3	3	90	1	0	0	0	0	1	0	0	0	5185	275	10	4	2437	4	EPHA7	6	94120432	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	13922956	94120432	76994635	131	24718										
BVES	11149	hgsc.bcm.edu	37	chr6	105564595	105564595	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctttatcatttaaggtgggaTcattcaatgagtagagctta	9	5	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:105564595T>A	ENST00000314641.5	-	6	1013	c.797A>T	c.(796-798)gAt>gTt	p.D266V	BVES_ENST00000446408.2_Missense_Mutation_p.D266V|BVES_ENST00000336775.5_Missense_Mutation_p.D266V	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	266					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TAAGGTGGGATCATTCAATGA	0.279																																																0			6											72	67	69					6																	105564595		2202	4296	6498	105671288	SO:0001583	missense	11149			AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.797A>T	6.37:g.105564595T>A	ENSP00000313172:p.Asp266Val		105671288	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	37	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.374234	0.82573	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.37411	1.2;1.2;1.2	5.55	5.55	0.83447	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.45736	0.1357	M	0.73217	2.22	0.80722	D	1	P	0.51791	0.948	P	0.56088	0.791	T	0.49934	-0.8886	10	0.66056	D	0.02	-33.8687	15.9824	0.80121	0.0:0.0:0.0:1.0	.	266	Q8NE79	POPD1_HUMAN	V	266	ENSP00000313172:D266V;ENSP00000337259:D266V;ENSP00000397310:D266V	ENSP00000313172:D266V	D	-	2	0	BVES	105671288	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.234000	0.73211	0.528000	0.53228	GAT		0.279	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		A	105564595	T	A	105564595	3	1	90	1	0	0	0	0	1	0	0	0	1578	1435	50	5	297	5	BVES	6	105564595	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	11444163	105564595	65550472	132	24719										
UTRN	7402	hgsc.bcm.edu	37	chr6	144768791	144768791	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acattggatcagctgagtgaGattggccaggatgtgggaca	15	6	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:144768791G>C	ENST00000367545.3	+	15	1776	c.1776G>C	c.(1774-1776)gaG>gaC	p.E592D		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	592	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AGCTGAGTGAGATTGGCCAGG	0.383																																																0			6											138	134	136					6																	144768791		2203	4300	6503	144810484	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1776G>C	6.37:g.144768791G>C	ENSP00000356515:p.Glu592Asp		144810484	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944182	0.53079	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.36340	1.26	5.87	1.17	0.20885	.	0.000000	0.53938	D	0.000041	T	0.14657	0.0354	L	0.48362	1.52	0.80722	D	1	P	0.45594	0.862	B	0.40982	0.345	T	0.04242	-1.0966	10	0.23302	T	0.38	.	11.1818	0.48633	0.3594:0.0:0.6406:0.0	.	592	P46939	UTRO_HUMAN	D	592	ENSP00000356515:E592D	ENSP00000356499:E592D	E	+	3	2	UTRN	144810484	0.990000	0.36364	0.996000	0.52242	0.970000	0.65996	0.210000	0.17455	-0.004000	0.14419	-0.119000	0.15052	GAG		0.383	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			C	144768791	G	C	144768791	3	2	90	1	0	0	0	0	1	0	0	0	17143	933	33	5	1834	5	UTRN	6	144768791	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	39204196	144768791	26346276	133	24720										
LATS1	9113	hgsc.bcm.edu	37	chr6	150005395	150005395	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgtattccatgtttccagaaTagcgctttgtttgagagttt	9	7	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:150005395T>C	ENST00000543571.1	-	4	1377	c.830A>G	c.(829-831)tAt>tGt	p.Y277C	LATS1_ENST00000392273.3_Missense_Mutation_p.Y277C|LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Missense_Mutation_p.Y277C	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		GTTTCCAGAATAGCGCTTTGT	0.542																																																0			6											179	170	173					6																	150005395		2203	4300	6503	150047088	SO:0001583	missense	9113			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.830A>G	6.37:g.150005395T>C	ENSP00000437550:p.Tyr277Cys		150047088		Missense_Mutation	SNP	ENST00000543571.1	37	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.755251	0.49362	.	.	ENSG00000131023	ENST00000543571;ENST00000253339;ENST00000392273	T;T;T	0.55052	0.54;0.54;3.08	4.83	4.83	0.62350	.	0.000000	0.47093	D	0.000245	T	0.57359	0.2048	L	0.50333	1.59	0.51482	D	0.999926	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.98;0.997	T	0.58261	-0.7667	9	.	.	.	.	14.3767	0.66884	0.0:0.0:0.0:1.0	.	129;277;277	Q59FN4;O95835-2;O95835	.;.;LATS1_HUMAN	C	277	ENSP00000437550:Y277C;ENSP00000253339:Y277C;ENSP00000444678:Y277C	.	Y	-	2	0	LATS1	150047088	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.508000	0.60441	1.802000	0.52723	0.533000	0.62120	TAT		0.542	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		C	150005395	T	C	150005395	3	2	90	1	0	0	0	0	1	0	0	0	8668	1406	49	4	2582	4	LATS1	6	150005395	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	5236604	150005395	21109672	134	24721										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152651268	152651268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctgatgcctggctttctcaTaagccaaggggtcaaggtgt	12	9	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:152651268T>G	ENST00000367255.5	-	78	15153	c.14552A>C	c.(14551-14553)tAt>tCt	p.Y4851S	SYNE1_ENST00000265368.4_Missense_Mutation_p.Y4851S|SYNE1_ENST00000448038.1_Missense_Mutation_p.Y4780S|SYNE1_ENST00000341594.5_Missense_Mutation_p.Y4598S|SYNE1_ENST00000423061.1_Missense_Mutation_p.Y4780S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4851					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCTTTCTCATAAGCCAAGGG	0.502										HNSCC(10;0.0054)																																						0			6											78	66	70					6																	152651268		2203	4300	6503	152692961	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.14552A>C	6.37:g.152651268T>G	ENSP00000356224:p.Tyr4851Ser		152692961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	0.503	-0.870093	0.02570	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52295	0.77;0.76;0.67;0.76;0.85	5.78	3.36	0.38483	.	0.359316	0.24085	N	0.041687	T	0.16214	0.0390	L	0.48642	1.525	0.31344	N	0.683261	B;B;B;B	0.33883	0.43;0.304;0.304;0.43	B;B;B;B	0.32762	0.142;0.072;0.072;0.152	T	0.10567	-1.0624	10	0.22706	T	0.39	.	5.0076	0.14295	0.1157:0.064:0.121:0.6993	.	4851;4851;4851;4780	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	S	4851;4780;4851;4780;4598	ENSP00000356224:Y4851S;ENSP00000396024:Y4780S;ENSP00000265368:Y4851S;ENSP00000390975:Y4780S;ENSP00000341887:Y4598S	ENSP00000265368:Y4851S	Y	-	2	0	SYNE1	152692961	0.998000	0.40836	0.110000	0.21437	0.095000	0.18619	2.776000	0.47709	0.448000	0.26722	-0.332000	0.08345	TAT		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152651268	T	G	152651268	3	3	90	1	0	0	0	0	1	0	0	0	15484	1406	49	4	12190	4	SYNE1	6	152651268	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2645873	152651268	18463799	135	24722										
LPA	4018	hgsc.bcm.edu	37	chr6	160977190	160977190	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	attaccatggtagcactgccGgaccacaggggtttgctcag	12	11	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr6:160977190G>T	ENST00000316300.5	-	30	4884	c.4840C>A	c.(4840-4842)Cgg>Agg	p.R1614R	LPA_ENST00000447678.1_Silent_p.R1614R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4122	Kringle 15. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TAGCACTGCCGGACCACAGGG	0.463																																																0			6											105	108	107					6																	160977190		2161	4296	6457	160897180	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4840C>A	6.37:g.160977190G>T			160897180	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.463	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	160977190	G	T	160977190	2	4	90	1	0	0	0	0	0	0	0	1	8932	1115	39	2		2	LPA	6	160977190	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	8325922	160977190	10137877	136	24723										
MAD1L1	8379	hgsc.bcm.edu	37	chr7	1976468	1976468	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tggtcctcgcgcaggcgctgCctggccacactggtggggtt	16	13	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:1976468C>A	ENST00000406869.1	-	17	2219	c.1662G>T	c.(1660-1662)agG>agT	p.R554S	MAD1L1_ENST00000402746.1_Missense_Mutation_p.R462S|MAD1L1_ENST00000399654.2_Missense_Mutation_p.R554S|MAD1L1_ENST00000265854.7_Missense_Mutation_p.R554S			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	554					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GCAGGCGCTGCCTGGCCACAC	0.667																																																0			7											26	32	30					7																	1976468		2170	4244	6414	1942994	SO:0001583	missense	8379			U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1662G>T	7.37:g.1976468C>A	ENSP00000385334:p.Arg554Ser		1942994	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.892801	0.52121	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000437877	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	4.77	3.88	0.44766	.	0.342816	0.32488	N	0.006022	T	0.24236	0.0587	L	0.59436	1.845	0.09310	N	1	P;P;B	0.45531	0.718;0.86;0.278	B;B;B	0.41332	0.354;0.279;0.148	T	0.13818	-1.0495	10	0.22109	T	0.4	-17.2986	11.0989	0.48161	0.0:0.9051:0.0:0.0949	.	553;462;554	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	S	462;554;554;105;554;105;10	ENSP00000384155:R462S;ENSP00000382562:R554S;ENSP00000385334:R554S;ENSP00000265854:R554S;ENSP00000394886:R105S;ENSP00000394069:R10S	ENSP00000265854:R554S	R	-	3	2	MAD1L1	1942994	0.892000	0.30473	0.360000	0.25837	0.989000	0.77384	1.605000	0.36815	2.199000	0.70637	0.555000	0.69702	AGG		0.667	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	1976468	C	A	1976468	3	1	90	1	0	0	0	0	1	0	0	0	9177	738	26	2	506	2	MAD1L1	7	1976468	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10		1976468	157162195	137	24724										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18975537	18975537	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	catctgtgatgcatcagaagCctgtgtaaatgcccttctag	9	10	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:18975537C>A	ENST00000432645.2	+	22	2900	c.2900C>A	c.(2899-2901)gCc>gAc	p.A967D	HDAC9_ENST00000441542.2_Missense_Mutation_p.A970D|HDAC9_ENST00000401921.1_Missense_Mutation_p.A926D|HDAC9_ENST00000406451.4_Missense_Mutation_p.A967D	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	967	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GCATCAGAAGCCTGTGTAAAT	0.423																																																0			7											173	165	168					7																	18975537		1890	4123	6013	18942062	SO:0001583	missense	9734			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2900C>A	7.37:g.18975537C>A	ENSP00000410337:p.Ala967Asp		18942062	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103885	0.94245	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.66	5.66	0.87406	Histone deacetylase domain (2);	0.096119	0.45867	D	0.000331	D	0.84678	0.5525	M	0.85197	2.74	0.80722	D	1	D;D;D;D;D	0.71674	0.992;0.998;0.998;0.998;0.998	P;P;P;P;P	0.59221	0.852;0.835;0.658;0.854;0.658	D	0.86812	0.1999	10	0.87932	D	0	-44.9098	19.7469	0.96255	0.0:1.0:0.0:0.0	.	215;926;970;967;967	Q8N926;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5	.;.;.;HDAC9_HUMAN;.	D	967;926;967;970;879	ENSP00000384657:A967D;ENSP00000383912:A926D;ENSP00000410337:A967D;ENSP00000408617:A970D	ENSP00000339165:A879D	A	+	2	0	HDAC9	18942062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.033000	0.70925	2.648000	0.89879	0.563000	0.77884	GCC		0.423	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18975537	C	A	18975537	3	1	90	1	0	0	0	0	1	0	0	0	7035	739	26	2	3108	2	HDAC9	7	18975537	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	16999069	18975537	140163126	138	24725										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21675658	21675658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgtctgttcagaagatattcGaatccagcttgtgaaagatg	10	6	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:21675658G>T	ENST00000409508.3	+	26	4701	c.4670G>T	c.(4669-4671)cGa>cTa	p.R1557L	DNAH11_ENST00000328843.6_Missense_Mutation_p.R1562L|DNAH11_ENST00000465593.1_3'UTR	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1562	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GAAGATATTCGAATCCAGCTT	0.388									Kartagener syndrome																																							0			7											85	79	81					7																	21675658		1861	4099	5960	21642183	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4670G>T	7.37:g.21675658G>T	ENSP00000475939:p.Arg1557Leu		21642183	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	25.5	4.642157	0.87859	.	.	ENSG00000105877	ENST00000328843	T	0.62232	0.04	5.56	3.75	0.43078	Dynein heavy chain, domain-2 (1);	0.154257	0.43919	D	0.000507	T	0.67543	0.2904	.	.	.	0.49389	D	0.999787	P	0.48503	0.911	P	0.51385	0.668	T	0.70710	-0.4797	9	0.66056	D	0.02	.	10.5061	0.44834	0.1594:0.0:0.8406:0.0	.	1562	Q96DT5	DYH11_HUMAN	L	1562	ENSP00000330671:R1562L	ENSP00000330671:R1562L	R	+	2	0	DNAH11	21642183	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.730000	0.47335	1.335000	0.45486	0.650000	0.86243	CGA		0.388	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21675658	G	T	21675658	3	4	90	1	0	0	0	0	1	0	0	0	4610	1058	37	2	4787	2	DNAH11	7	21675658	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2700121	21675658	137463005	139	24726										
HECW1	23072	hgsc.bcm.edu	37	chr7	43547684	43547684	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgatggcctattcgcggaaaGagctccagcgaaacaagctc	11	11	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:43547684G>A	ENST00000395891.2	+	23	4425	c.3820G>A	c.(3820-3822)Gag>Aag	p.E1274K	HECW1_ENST00000453890.1_Missense_Mutation_p.E1240K|AC011738.4_ENST00000436105.1_RNA	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1274	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TTCGCGGAAAGAGCTCCAGCG	0.552																																																0			7											78	81	80					7																	43547684		1972	4154	6126	43514209	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3820G>A	7.37:g.43547684G>A	ENSP00000379228:p.Glu1274Lys		43514209	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	36	5.933300	0.97116	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.43688	0.94;0.94	5.85	5.85	0.93711	HECT (3);	0.000000	0.85682	D	0.000000	T	0.63189	0.2490	L	0.53249	1.67	0.80722	D	1	D;D	0.71674	0.998;0.972	D;P	0.77004	0.989;0.694	T	0.62987	-0.6737	10	0.87932	D	0	.	20.1669	0.98153	0.0:0.0:1.0:0.0	.	1240;1274	B4DH42;Q76N89	.;HECW1_HUMAN	K	1274;1240;1274	ENSP00000379228:E1274K;ENSP00000407774:E1240K	ENSP00000265522:E1274K	E	+	1	0	HECW1	43514209	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.779000	0.99018	2.770000	0.95276	0.650000	0.86243	GAG		0.552	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43547684	G	A	43547684	3	1	90	1	0	0	0	0	1	0	0	0	7063	943	33	3	3902	3	HECW1	7	43547684	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	21872026	43547684	115590979	140	24727										
EGFR	1956	hgsc.bcm.edu	37	chr7	55242474	55242474	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtcgctatcaaggaattaagAgaagcaacatctccgaaagc	9	9	2	1	rs121913438|rs121913439|rs397517098|rs121913423|rs121913422|rs121913421|rs397517094|rs121913426|rs121913425|rs121913424|rs397509368|rs121913436|rs121913437|rs121913441|rs121913440|rs121913442|rs121913435		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:55242474A>G	ENST00000275493.2	+	19	2421	c.2244A>G	c.(2242-2244)agA>agG	p.R748R	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.R703R|EGFR_ENST00000454757.2_Silent_p.R695R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	748	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		ELREAT -> A (found in a lung cancer sample). {ECO:0000269|PubMed:15623594}.|ELREATS -> D (found in a lung cancer sample). {ECO:0000269|PubMed:15623594}.|Missing (found in a lung cancer sample). {ECO:0000269|PubMed:15623594}.|Missing (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.|R -> P (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.E746_A750del(1007)|p.L747_P753>S(123)|p.L747_A750>P(82)|p.L747_T751del(76)|p.E746_S752>V(57)|p.L747_S752del(34)|p.L747_T751>P(21)|p.E746_T751>A(21)|p.L747_E749del(16)|p.E746_E749del(9)|p.L747_T751>S(7)|p.L747_P753>Q(7)|p.K745_E749del(6)|p.E746_T751>V(6)|p.E746_S752>A(6)|p.E746_T751>VA(6)|p.L747_T751>Q(5)|p.E746_T751del(4)|p.E746_T751>I(4)|p.E746_S752>D(4)|p.E746_S752>I(4)|p.E746_A750>IP(3)|p.L747_S752>Q(3)|p.E746_T751>IP(3)|p.E746_T751>VP(3)|p.E746_A750>RP(2)|p.L747_S752>QH(2)|p.E746_S752del(2)|p.E746_P753>VS(2)|p.E746_A750>QP(2)|p.L747_K754del(2)|p.L747_K754>ST(1)|p.L747_P753del(1)|p.E746_A750>VP(1)|p.L747_K754>N(1)|p.E746_P753>IS(1)|p.E746_T751>L(1)|p.L747_R748>FP(1)|p.L747_T751>A(1)|p.I744_E749>LKR(1)|p.E746_P753>LS(1)|p.E746_T751>Q(1)|p.E746_T751>S(1)|p.E746_P753>VQ(1)|p.E746_A750>DP(1)|p.I744_A750>VK(1)|p.K745_A750del(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGGAATTAAGAGAAGCAACAT	0.478	E746_A750del(NCIH1650_LUNG)|E746_A750del(PC14_LUNG)|L747_P753>Q(HCC4006_LUNG)	8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	1545	Deletion - In frame(1158)|Complex - deletion inframe(386)|Complex - compound substitution(1)	lung(1520)|upper_aerodigestive_tract(7)|salivary_gland(6)|thyroid(3)|large_intestine(2)|breast(2)|ovary(2)|central_nervous_system(1)|prostate(1)|kidney(1)	7											112	107	109					7																	55242474		2203	4300	6503	55209968	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2244A>G	7.37:g.55242474A>G			55209968	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.478	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55242474	A	G	55242474	2	3	90	1	0	0	0	0	0	0	0	1	4978	301	11	4		4	EGFR	7	55242474	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	11694790	55242474	103896189	141	24728										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188621	57188621	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctattggaatttgaaaatttAccaaagactttgacatattt	5	5	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:57188621A>T	ENST00000331162.4	-	5	771	c.501T>A	c.(499-501)ggT>ggA	p.G167G		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			TTGAAAATTTACCAAAGACTT	0.299																																																0			7											32	31	31					7																	57188621		1820	4079	5899	57192563	SO:0001819	synonymous_variant	90827			AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.501T>A	7.37:g.57188621A>T			57192563		Silent	SNP	ENST00000331162.4	37	CCDS43590.1																																																																																				0.299	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		T	57188621	A	T	57188621	2	4	90	1	0	0	0	0	0	0	0	1	17972	378	14	5		5	ZNF479	7	57188621	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1946147	57188621	101950042	142	24729										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72891394	72891394	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttatttttggcttccatttcTttccgtttctgtttctctgc	5	10	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:72891394T>C	ENST00000339594.4	-	7	2735	c.2397A>G	c.(2395-2397)aaA>aaG	p.K799K	BAZ1B_ENST00000404251.1_Silent_p.K799K	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	799					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.K799K(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				cttccatttctttccgtttct	0.398																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											1	Substitution - coding silent(1)	ovary(1)	7											86	80	82					7																	72891394		2203	4300	6503	72529330	SO:0001819	synonymous_variant	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2397A>G	7.37:g.72891394T>C			72529330	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																				0.398	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72891394	T	C	72891394	2	2	90	1	0	0	0	0	0	0	0	1	1331	1606	56	4		4	BAZ1B	7	72891394	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	15702773	72891394	86247269	143	24730										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72891549	72891549	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtggcacagtgctgtcaagaTctgtagcttctcctctgacg	11	11	4	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:72891549T>A	ENST00000339594.4	-	7	2580	c.2242A>T	c.(2242-2244)Atc>Ttc	p.I748F	BAZ1B_ENST00000404251.1_Missense_Mutation_p.I748F	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	748					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTGTCAAGATCTGTAGCTTC	0.478																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											0			7											112	100	104					7																	72891549		2203	4300	6503	72529485	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2242A>T	7.37:g.72891549T>A	ENSP00000342434:p.Ile748Phe		72529485	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367044	0.61513	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.72167	-0.63;-0.63	5.79	5.79	0.91817	.	0.050134	0.85682	D	0.000000	T	0.70710	0.3255	L	0.52573	1.65	0.54753	D	0.999988	D	0.56521	0.976	P	0.46685	0.524	T	0.75252	-0.3383	10	0.87932	D	0	-18.6631	15.3014	0.73955	0.0:0.0:0.0:1.0	.	748	Q9UIG0	BAZ1B_HUMAN	F	748	ENSP00000342434:I748F;ENSP00000385442:I748F	ENSP00000342434:I748F	I	-	1	0	BAZ1B	72529485	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.219000	0.72231	2.219000	0.72066	0.459000	0.35465	ATC		0.478	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		A	72891549	T	A	72891549	3	1	90	1	0	0	0	0	1	0	0	0	1331	1435	50	5	2261	5	BAZ1B	7	72891549	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	155	72891549	86247114	144	24731										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77569463	77569463	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctacagacttggaacaactCacagcacattctgcttcaga	7	12	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:77569463C>G	ENST00000248550.7	+	13	1660	c.1584C>G	c.(1582-1584)ctC>ctG	p.L528L	PHTF2_ENST00000275575.7_Silent_p.L490L|PHTF2_ENST00000422959.2_Silent_p.L494L|PHTF2_ENST00000424760.1_Silent_p.L490L|PHTF2_ENST00000307305.8_Silent_p.L490L|PHTF2_ENST00000416283.2_Silent_p.L494L			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TGGAACAACTCACAGCACATT	0.378																																																0			7											116	107	110					7																	77569463		1869	4106	5975	77407399	SO:0001819	synonymous_variant	57157			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1584C>G	7.37:g.77569463C>G			77407399	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	37																																																																																					0.378	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77569463	C	G	77569463	2	3	90	1	0	0	0	0	0	0	0	1	11894	813	29	5		5	PHTF2	7	77569463	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	4677914	77569463	81569200	145	24732										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100088675	100088675	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agtccggcaggtcgtgctccAcacaccccggccctgcagcc	11	19	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:100088675A>T	ENST00000300179.2	+	6	2384	c.2225A>T	c.(2224-2226)cAc>cTc	p.H742L	NYAP1_ENST00000423930.1_Missense_Mutation_p.H743L|NYAP1_ENST00000496985.1_3'UTR|NYAP1_ENST00000454988.1_Missense_Mutation_p.H686L	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	742					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GTCGTGCTCCACACACCCCGG	0.617																																																0			7											21	22	22					7																	100088675		2173	4245	6418	99926611	SO:0001583	missense	222950			AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.2225A>T	7.37:g.100088675A>T	ENSP00000300179:p.His742Leu		99926611	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618508	0.46736	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.30182	1.54;1.54;1.54	5.08	3.89	0.44902	.	0.134283	0.33895	N	0.004449	T	0.16471	0.0396	N	0.12182	0.205	0.35635	D	0.810556	B;B	0.17038	0.02;0.02	B;B	0.13407	0.009;0.009	T	0.11397	-1.0589	10	0.33940	T	0.23	-10.3463	9.0419	0.36322	0.814:0.186:0.0:0.0	.	686;742	C9JS30;Q6ZVC0	.;CG051_HUMAN	L	742;743;686	ENSP00000300179:H742L;ENSP00000411861:H743L;ENSP00000394424:H686L	ENSP00000300179:H742L	H	+	2	0	C7orf51	99926611	0.860000	0.29831	0.998000	0.56505	0.359000	0.29487	1.854000	0.39368	0.842000	0.35045	0.260000	0.18958	CAC		0.617	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100088675	A	T	100088675	3	4	90	1	0	0	0	0	1	0	0	0	2406	159	6	5	2243	5	C7orf51	7	100088675	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	22519212	100088675	59049988	146	24733										
MUC17	140453	hgsc.bcm.edu	37	chr7	100675088	100675088	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acagcaccacacttttccccAgttctactgaagacacttca	4	15	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:100675088A>G	ENST00000306151.4	+	3	455	c.391A>G	c.(391-393)Agt>Ggt	p.S131G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	131	Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACTTTTCCCCAGTTCTACTGA	0.468																																																0			7											170	157	161					7																	100675088		2203	4300	6503	100461808	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.391A>G	7.37:g.100675088A>G	ENSP00000302716:p.Ser131Gly		100461808	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	0.095	-1.161341	0.01673	.	.	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.801	-1.6	0.08426	.	.	.	.	.	T	0.01730	0.0055	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44360	-0.9333	9	0.40728	T	0.16	.	3.2032	0.06657	0.543:0.2345:0.2225:0.0	.	131	Q685J3	MUC17_HUMAN	G	131	ENSP00000302716:S131G	ENSP00000302716:S131G	S	+	1	0	MUC17	100461808	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.664000	0.00201	-2.401000	0.00578	-1.360000	0.01215	AGT		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100675088	A	G	100675088	3	3	90	1	0	0	0	0	1	0	0	0	10004	188	7	4	401	4	MUC17	7	100675088	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	586413	100675088	58463575	147	24734										
MUC17	140453	hgsc.bcm.edu	37	chr7	100686648	100686648	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagtagtagtaccaccacatCtttttcaactactaaggaat	5	10	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:100686648C>A	ENST00000306151.4	+	3	12015	c.11951C>A	c.(11950-11952)tCt>tAt	p.S3984Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3984					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.S3984Y(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACCACCACATCTTTTTCAACT	0.473																																																1	Substitution - Missense(1)	ovary(1)	7											140	138	139					7																	100686648		2203	4300	6503	100473368	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.11951C>A	7.37:g.100686648C>A	ENSP00000302716:p.Ser3984Tyr		100473368	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	8.106	0.777676	0.16120	.	.	ENSG00000169876	ENST00000306151	T	0.01981	4.52	1.43	-1.99	0.07457	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	0.09310	N	1	P	0.42078	0.77	P	0.46253	0.509	T	0.46034	-0.9220	9	0.24483	T	0.36	.	2.8449	0.05540	0.3061:0.3887:0.3052:0.0	.	3984	Q685J3	MUC17_HUMAN	Y	3984	ENSP00000302716:S3984Y	ENSP00000302716:S3984Y	S	+	2	0	MUC17	100473368	0.000000	0.05858	0.007000	0.13788	0.536000	0.34869	-0.249000	0.08842	-0.108000	0.12066	0.424000	0.28305	TCT		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100686648	C	A	100686648	3	1	90	1	0	0	0	0	1	0	0	0	10004	913	32	2	11961	2	MUC17	7	100686648	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	11560	100686648	58452015	148	24735										
RELN	5649	hgsc.bcm.edu	37	chr7	103234213	103234213	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctgattttccaaatatcatTgctgatggtgtggcagcaca	9	8	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:103234213T>C	ENST00000428762.1	-	27	3987	c.3828A>G	c.(3826-3828)gcA>gcG	p.A1276A	RELN_ENST00000424685.2_Silent_p.A1276A|RELN_ENST00000343529.5_Silent_p.A1276A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1276					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CAAATATCATTGCTGATGGTG	0.403																																					NSCLC(146;835 1944 15585 22231 52158)											0			7											171	155	161					7																	103234213		2203	4300	6503	103021449	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.3828A>G	7.37:g.103234213T>C			103021449	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.403	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103234213	T	C	103234213	2	2	90	1	0	0	0	0	0	0	0	1	13257	1799	63	4		4	RELN	7	103234213	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2547565	103234213	55904450	149	24736										
MDFIC	29969	hgsc.bcm.edu	37	chr7	114619714	114619714	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgcagataatcgcaaactttCagcacctgtttctcaaaaaa	5	11	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:114619714C>T	ENST00000393486.1	+	4	961	c.371C>T	c.(370-372)tCa>tTa	p.S124L	MDFIC_ENST00000257724.3_Missense_Mutation_p.S233L	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						CGCAAACTTTCAGCACCTGTT	0.428																																																0			7											88	89	89					7																	114619714		2203	4300	6503	114406950	SO:0001583	missense	29969			AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.371C>T	7.37:g.114619714C>T	ENSP00000377126:p.Ser124Leu		114406950		Missense_Mutation	SNP	ENST00000393486.1	37	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277075	0.95459	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	5.98	0.97165	.	0.065965	0.64402	D	0.000009	D	0.82430	0.5035	M	0.77616	2.38	0.80722	D	1	D	0.69078	0.997	D	0.65874	0.939	T	0.81495	-0.0907	9	0.49607	T	0.09	-2.2248	20.452	0.99131	0.0:1.0:0.0:0.0	.	124	Q9P1T7	MDFIC_HUMAN	L	233;124;110;69	.	ENSP00000257724:S233L	S	+	2	0	MDFIC	114406950	0.999000	0.42202	0.997000	0.53966	0.989000	0.77384	6.317000	0.72862	2.838000	0.97847	0.591000	0.81541	TCA		0.428	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072		T	114619714	C	T	114619714	3	4	90	1	0	0	0	0	1	0	0	0	9435	838	29	3	754	3	MDFIC	7	114619714	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	11385501	114619714	44518949	150	24737										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653015	121653015	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gagattaaccaggcccatccCccaaaaggaaggcatgtatt	9	11	0	1	rs143582826		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:121653015C>A	ENST00000393386.2	+	12	4326	c.3915C>A	c.(3913-3915)ccC>ccA	p.P1305P	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_3'UTR	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1305					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AGGCCCATCCCCCAAAAGGAA	0.358																																																0			7											74	66	69					7																	121653015		2203	4300	6503	121440251	SO:0001819	synonymous_variant	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3915C>A	7.37:g.121653015C>A			121440251	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																				0.358	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121653015	C	A	121653015	2	1	90	1	0	0	0	0	0	0	0	1	12851	610	22	2		2	PTPRZ1	7	121653015	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	7033301	121653015	37485648	151	24738										
AASS	10157	hgsc.bcm.edu	37	chr7	121758477	121758477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agcttgcacagcctgactgcTattcctgtagttatgagcca	9	11	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:121758477T>C	ENST00000393376.1	-	5	666	c.571A>G	c.(571-573)Agc>Ggc	p.S191G	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.S191G			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	191	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.S191R(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						GCCTGACTGCTATTCCTGTAG	0.413																																																1	Substitution - Missense(1)	ovary(1)	7											118	109	112					7																	121758477		2203	4300	6503	121545713	SO:0001583	missense	10157			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.571A>G	7.37:g.121758477T>C	ENSP00000377040:p.Ser191Gly		121545713	O95462	Missense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	19.85	3.903752	0.72754	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	.	.	.	4.83	4.83	0.62350	.	0.177976	0.64402	D	0.000009	T	0.58779	0.2146	M	0.73962	2.25	0.50171	D	0.999853	P	0.40638	0.725	B	0.40982	0.345	T	0.58891	-0.7556	9	0.21014	T	0.42	-17.1179	14.6123	0.68524	0.0:0.0:0.0:1.0	.	191	Q9UDR5	AASS_HUMAN	G	191	.	ENSP00000351834:S191G	S	-	1	0	AASS	121545713	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.902000	0.69869	2.046000	0.60703	0.529000	0.55759	AGC		0.413	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		C	121758477	T	C	121758477	3	2	90	1	0	0	0	0	1	0	0	0	24	1522	53	4	2285	4	AASS	7	121758477	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	105462	121758477	37380186	152	24739										
AGK	55750	hgsc.bcm.edu	37	chr7	141315312	141315312	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	attggatttatcccactgggAgagaccagtagtttgagtca	11	7	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:141315312A>G	ENST00000355413.4	+	8	725	c.465A>G	c.(463-465)ggA>ggG	p.G155G	AGK_ENST00000473247.1_Silent_p.G127G|AGK_ENST00000535825.1_Silent_p.G152G	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	155	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					TCCCACTGGGAGAGACCAGTA	0.448																																																0			7											183	185	184					7																	141315312		2203	4300	6503	140961781	SO:0001819	synonymous_variant	55750			BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.465A>G	7.37:g.141315312A>G			140961781	Q75KN1|Q96GC3|Q9NP48	Silent	SNP	ENST00000355413.4	37	CCDS5865.1																																																																																				0.448	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		G	141315312	A	G	141315312	2	3	90	1	0	0	0	0	0	0	0	1	383	291	11	4		4	AGK	7	141315312	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	19556835	141315312	17823351	153	24740										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142574335	142574335	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aggatgtgtaacactgtgttTcctggggaggacacagggta	15	6	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:142574335T>A	ENST00000359396.3	-	6	833	c.588A>T	c.(586-588)ggA>ggT	p.G196G	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	196					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					ACACTGTGTTTCCTGGGGAGG	0.567																																																0			7											219	194	203					7																	142574335		2203	4300	6503	142284457	SO:0001630	splice_region_variant	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.587-1A>T	7.37:g.142574335T>A			142284457	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																				0.567	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	Silent	A	142574335	T	A	142574335	5	1	90	1	0	0	0	0	0	0	1	0	16640	1797	62	5	1629	5	TRPV6	7	142574335	Splice_Site	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1259023	142574335	16564328	154	24741										
TPK1	27010	hgsc.bcm.edu	37	chr7	144345964	144345964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agtctccattgatgaattcaGgcaaaaagctgaaagaaaca	8	7	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:144345964G>A	ENST00000360057.3	-	5	296	c.194C>T	c.(193-195)cCt>cTt	p.P65L	TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Missense_Mutation_p.P60L|TPK1_ENST00000549981.1_5'UTR|TPK1_ENST00000378099.3_Missense_Mutation_p.P65L	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	65					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	GATGAATTCAGGCAAAAAGCT	0.313																																					Ovarian(45;88 1034 2073 5829 28455)											0			7											96	108	104					7																	144345964		2203	4299	6502	143976897	SO:0001583	missense	27010			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.194C>T	7.37:g.144345964G>A	ENSP00000353165:p.Pro65Leu		143976897	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078404	0.76528	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099;ENST00000552881	D;D;D;D	0.88046	-2.33;-1.79;-2.33;-2.33	5.92	5.92	0.95590	Thiamin pyrophosphokinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.93966	0.8068	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94165	0.7418	10	0.66056	D	0.02	-23.8707	15.8207	0.78638	0.0:0.0:1.0:0.0	.	65;65;60	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	L	65;60;65;65	ENSP00000353165:P65L;ENSP00000438813:P60L;ENSP00000367339:P65L;ENSP00000448655:P65L	ENSP00000353165:P65L	P	-	2	0	TPK1	143976897	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.324000	0.59228	2.809000	0.96659	0.655000	0.94253	CCT		0.313	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		A	144345964	G	A	144345964	3	1	90	1	0	0	0	0	1	0	0	0	16444	1000	35	3	557	3	TPK1	7	144345964	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	1771629	144345964	14792699	155	24742										
ATG9B	285973	hgsc.bcm.edu	37	chr7	150720563	150720563	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gacatcctccagcaagatgcAggcaaagccattccgctggt	10	13	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr7:150720563A>T	ENST00000377974.2	-	3	703	c.628T>A	c.(628-630)Tgc>Agc	p.C210S	ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000444312.1_5'UTR|ATG9B_ENST00000605952.1_Missense_Mutation_p.C210S|ATG9B_ENST00000605938.1_Missense_Mutation_p.C210S			Q674R7	ATG9B_HUMAN	autophagy related 9B	210					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCAAGATGCAGGCAAAGCCA	0.617																																																0			7											32	36	35					7																	150720563		2057	4213	6270	150351496	SO:0001583	missense	285973			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"nitric oxide synthase 3 antisense", "ATG9 autophagy related 9 homolog B (S. cerevisiae)"	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.628T>A	7.37:g.150720563A>T	ENSP00000475005:p.Cys210Ser		150351496	A1A5D3|Q6JRW5|Q8N8I8	Missense_Mutation	SNP	ENST00000377974.2	37		.	.	.	.	.	.	.	.	.	.	A	13.48	2.250184	0.39797	.	.	ENSG00000248602	ENST00000377974;ENST00000397266;ENST00000545613	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.68979	0.3060	.	.	.	.	.	.	D	0.60160	0.987	D	0.62955	0.909	T	0.71692	-0.4516	7	0.25751	T	0.34	-31.5247	13.4119	0.60948	1.0:0.0:0.0:0.0	.	210	Q674R7	ATG9B_HUMAN	S	210	.	ENSP00000444232:C210S	C	-	1	0	AC010973.1	150351496	1.000000	0.71417	0.982000	0.44146	0.553000	0.35397	8.752000	0.91632	2.052000	0.61016	0.533000	0.62120	TGC		0.617	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173681		T	150720563	A	T	150720563	3	4	90	1	0	0	0	0	1	0	0	0	1104	188	7	5	2189	5	ATG9B	7	150720563	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	6374599	150720563	8418100	156	24743										
ADRB3	155	hgsc.bcm.edu	37	chr8	37823967	37823967	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	catggggcaagagagctgttCtcgtgaggccacggagccat	15	10	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:37823967C>A	ENST00000345060.3	-	1	516	c.21G>T	c.(19-21)gaG>gaT	p.E7D	ADRB3_ENST00000520341.1_5'Flank	NM_000025.2	NP_000016.1	P13945	ADRB3_HUMAN	adrenoceptor beta 3	7					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|aging (GO:0007568)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|diet induced thermogenesis (GO:0002024)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|generation of precursor metabolites and energy (GO:0006091)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of MAPK cascade (GO:0043410)|response to antibiotic (GO:0046677)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta-adrenergic receptor activity (GO:0004939)|beta3-adrenergic receptor activity (GO:0015052)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)	9	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Bethanidine(DB00217)|Bopindolol(DB08807)|Bupranolol(DB08808)|Clenbuterol(DB01407)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Isoprenaline(DB01064)|Mephentermine(DB01365)|Mirabegron(DB08893)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Propranolol(DB00571)|Trimipramine(DB00726)	GAGAGCTGTTCTCGTGAGGCC	0.692																																																0			8											12	15	14					8																	37823967		2195	4293	6488	37943124	SO:0001583	missense	155			AY487247	CCDS6099.1	8p12	2012-08-08	2012-05-09			ENSG00000188778		"GPCR / Class A : Adrenoceptors : beta"	288	protein-coding gene	gene with protein product		109691	"adrenergic, beta-3-, receptor"			7898940, 15123695	Standard	NM_000025		Approved		uc003xkr.2	P13945		ENST00000345060.3:c.21G>T	8.37:g.37823967C>A	ENSP00000343782:p.Glu7Asp		37943124	Q4JFT4	Missense_Mutation	SNP	ENST00000345060.3	37	CCDS6099.1	.	.	.	.	.	.	.	.	.	.	C	5.689	0.311756	0.10789	.	.	ENSG00000188778	ENST00000345060	T	0.55588	0.51	4.16	0.33	0.15929	.	1.000120	0.08080	N	1.000000	T	0.35970	0.0950	N	0.22421	0.69	0.09310	N	1	B	0.18741	0.03	B	0.20384	0.029	T	0.31724	-0.9933	10	0.56958	D	0.05	.	4.7949	0.13267	0.0:0.4405:0.3023:0.2572	.	7	P13945	ADRB3_HUMAN	D	7	ENSP00000343782:E7D	ENSP00000343782:E7D	E	-	3	2	ADRB3	37943124	0.001000	0.12720	0.114000	0.21550	0.073000	0.16967	-0.088000	0.11198	-0.048000	0.13401	0.462000	0.41574	GAG		0.692	ADRB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376826.1	NM_000025		A	37823967	C	A	37823967	3	1	90	1	0	0	0	0	1	0	0	0	342	912	32	2	1213	2	ADRB3	8	37823967	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10		37823967	108540055	157	24744										
TCEB1	6921	hgsc.bcm.edu	37	chr8	74868290	74868290	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ataggttttctcctctccatCtaaagtaaagtaagtagtga	7	7	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:74868290C>G	ENST00000522337.1	-	4	324		c.e4-1		TCEB1_ENST00000520242.1_Splice_Site|TCEB1_ENST00000602840.1_Splice_Site|TCEB1_ENST00000519487.1_Splice_Site|TCEB1_ENST00000284811.8_Splice_Site|TCEB1_ENST00000520210.1_Splice_Site|TCEB1_ENST00000518127.1_Splice_Site|TCEB1_ENST00000523815.1_Splice_Site			Q15369	ELOC_HUMAN	transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)						cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(2)|kidney(3)|lung(1)|prostate(1)	7	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)			TCCTCTCCATCTAAAGTAAAG	0.413																																																0			8											67	64	65					8																	74868290		2203	4300	6503	75030844	SO:0001630	splice_region_variant	6921			L34587	CCDS34910.1, CCDS56539.1	8q13.3	2010-04-21	2002-08-29		ENSG00000154582	ENSG00000154582			11617	protein-coding gene	gene with protein product		600788	"transcription elongation factor B (SIII), polypeptide 1 (15kD, elongin C)"			7821821, 7660122	Standard	NM_005648		Approved	SIII	uc003xzx.2	Q15369	OTTHUMG00000164501	ENST00000522337.1:c.5-1G>C	8.37:g.74868290C>G			75030844	E5RGD9|Q567Q6	Splice_Site	SNP	ENST00000522337.1	37	CCDS34910.1	.	.	.	.	.	.	.	.	.	.	c	19.71	3.877702	0.72294	.	.	ENSG00000154582	ENST00000518127;ENST00000520242;ENST00000519487;ENST00000284811;ENST00000522337;ENST00000523815;ENST00000519082;ENST00000519021	.	.	.	5.56	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3232	0.66502	0.0:0.9288:0.0:0.0712	.	.	.	.	.	-1	.	.	.	-	.	.	TCEB1	75030844	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	7.100000	0.76989	1.344000	0.45657	0.650000	0.86243	.		0.413	TCEB1-010	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000379020.1	NM_005648	Intron	G	74868290	C	G	74868290	5	3	90	1	0	0	0	0	0	0	1	0	15718	927	32	5	342	5	TCEB1	8	74868290	Splice_Site	SNP	C	TCGA-CI-6624-01C-11D-1826-10	37044323	74868290	71495732	158	24745										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617811	77617811	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaactcaccgatagtattggTaacaaagatttccctctctt	6	10	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:77617811T>A	ENST00000521891.2	+	2	1936	c.1488T>A	c.(1486-1488)ggT>ggA	p.G496G	ZFHX4_ENST00000455469.2_Silent_p.G496G|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000518282.1_Silent_p.G496G|ZFHX4_ENST00000050961.6_Silent_p.G496G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATAGTATTGGTAACAAAGATT	0.423										HNSCC(33;0.089)																																						0			8											48	48	48					8																	77617811		1958	4144	6102	77780366	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1488T>A	8.37:g.77617811T>A			77780366	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.423	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77617811	T	A	77617811	2	1	90	1	0	0	0	0	0	0	0	1	17674	1625	57	5		5	ZFHX4	8	77617811	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2749521	77617811	68746211	159	24746										
MMP16	4325	hgsc.bcm.edu	37	chr8	89128916	89128916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gggggcactgtcggtagaggTcttgtaggtggaggaatctt	18	5	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:89128916T>C	ENST00000286614.6	-	6	1184	c.903A>G	c.(901-903)agA>agG	p.R301R	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	301					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	TCGGTAGAGGTCTTGTAGGTG	0.512																																																0			8											198	205	202					8																	89128916		2203	4300	6503	89198032	SO:0001819	synonymous_variant	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.903A>G	8.37:g.89128916T>C			89198032	B2RAN7|Q14824|Q52H48	Silent	SNP	ENST00000286614.6	37	CCDS6246.1																																																																																				0.512	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		C	89128916	T	C	89128916	2	2	90	1	0	0	0	0	0	0	0	1	9685	1664	58	4		4	MMP16	8	89128916	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	11511105	89128916	57235106	160	24747										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109240604	109240604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttctctgctgaagagactgaAgtggagaactcacagactaa	10	8	2	5			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:109240604A>G	ENST00000220849.5	-	7	676	c.614T>C	c.(613-615)cTt>cCt	p.L205P	EIF3E_ENST00000519517.1_5'UTR|EIF3E_ENST00000519030.1_Missense_Mutation_p.L112P|RP11-35G22.1_ENST00000520037.1_RNA	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E									p.L205H(1)	EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			AAGAGACTGAAGTGGAGAACT	0.348																																					GBM(15;360 410 8460 34179 52246)											1	Substitution - Missense(1)	ovary(1)	8											74	74	74					8																	109240604		2203	4300	6503	109309780	SO:0001583	missense	3646			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.614T>C	8.37:g.109240604A>G	ENSP00000220849:p.Leu205Pro		109309780		Missense_Mutation	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403034	0.83230	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.50277	0.75;0.75;0.75	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.73946	0.3652	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.971	T	0.79902	-0.1607	10	0.87932	D	0	-11.5618	15.9153	0.79512	1.0:0.0:0.0:0.0	.	205;205	B2R806;P60228	.;EIF3E_HUMAN	P	205;112;78	ENSP00000220849:L205P;ENSP00000428796:L112P;ENSP00000430839:L78P	ENSP00000220849:L205P	L	-	2	0	EIF3E	109309780	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	9.287000	0.95975	2.213000	0.71641	0.477000	0.44152	CTT		0.348	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		G	109240604	A	G	109240604	3	3	90	1	0	0	0	0	1	0	0	0	5028	72	3	4	751	4	EIF3E	8	109240604	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	20111688	109240604	37123418	161	24748										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113293501	113293501	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctccatgcaggaataaatgActgaactagaaaatgttgtg	9	7	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:113293501A>T	ENST00000297405.5	-	59	9654	c.9410T>A	c.(9409-9411)gTc>gAc	p.V3137D	CSMD3_ENST00000343508.3_Missense_Mutation_p.V3097D|CSMD3_ENST00000352409.3_Missense_Mutation_p.V3067D|CSMD3_ENST00000455883.2_Missense_Mutation_p.V2968D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3137	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGAATAAATGACTGAACTAGA	0.428										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											127	112	117					8																	113293501		2203	4300	6503	113362677	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9410T>A	8.37:g.113293501A>T	ENSP00000297405:p.Val3137Asp		113362677	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267782	0.80469	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59	5.47	5.47	0.80525	Complement control module (2);Sushi/SCR/CCP (3);	0.338199	0.27327	N	0.019879	D	0.89518	0.6738	H	0.97315	3.98	0.80722	D	1	D;D;D	0.67145	0.996;0.98;0.971	D;D;P	0.70716	0.97;0.953;0.894	D	0.93185	0.6578	10	0.87932	D	0	.	15.6084	0.76692	1.0:0.0:0.0:0.0	.	2968;3137;3097	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	3097;3137;2407;2968;3067	ENSP00000345799:V3097D;ENSP00000297405:V3137D;ENSP00000341558:V2407D;ENSP00000412263:V2968D;ENSP00000343124:V3067D	ENSP00000297405:V3137D	V	-	2	0	CSMD3	113362677	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	9.284000	0.95882	2.086000	0.62901	0.524000	0.50904	GTC		0.428	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113293501	A	T	113293501	3	4	90	1	0	0	0	0	1	0	0	0	3952	275	10	5	1765	5	CSMD3	8	113293501	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	4052897	113293501	33070521	162	24749										
TRIB1	10221	hgsc.bcm.edu	37	chr8	126448706	126448706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagtgacattagttccttctTctgctaatccccaaaacctc	4	14	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:126448706T>C	ENST00000519576.1	+	2	682	c.419T>C	c.(418-420)tTc>tCc	p.F140S	TRIB1_ENST00000520847.1_Missense_Mutation_p.F205S|TRIB1_ENST00000311922.3_Missense_Mutation_p.F371S					tribbles pseudokinase 1											NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			AGTTCCTTCTTCTGCTAATCC	0.453																																																0			8											65	67	66					8																	126448706		2203	4300	6503	126517888	SO:0001583	missense	10221			AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"tribbles homolog 1 (Drosophila)"			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000519576.1:c.419T>C	8.37:g.126448706T>C	ENSP00000428879:p.Phe140Ser		126517888		Missense_Mutation	SNP	ENST00000519576.1	37		.	.	.	.	.	.	.	.	.	.	T	18.41	3.617795	0.66787	.	.	ENSG00000173334	ENST00000311922;ENST00000520847;ENST00000519576	T;T;T	0.48836	0.8;0.89;1.13	5.88	5.88	0.94601	.	0.000000	0.34531	U	0.003885	T	0.54647	0.1871	L	0.32530	0.975	0.80722	D	1	D	0.63046	0.992	P	0.58210	0.835	T	0.58154	-0.7686	10	0.87932	D	0	-27.9815	15.9721	0.80027	0.0:0.0:0.0:1.0	.	371	Q96RU8	TRIB1_HUMAN	S	371;205;140	ENSP00000312150:F371S;ENSP00000429063:F205S;ENSP00000428879:F140S	ENSP00000312150:F371S	F	+	2	0	TRIB1	126517888	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.764000	0.62264	2.257000	0.74773	0.459000	0.35465	TTC		0.453	TRIB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000381433.1	NM_025195		C	126448706	T	C	126448706	3	2	90	1	0	0	0	0	1	0	0	0	16522	1783	62	4	1122	4	TRIB1	8	126448706	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	13155205	126448706	19915316	163	24750										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133196504	133196504	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttacccaacatgcacaggggCttcctggcaaacttcagtcg	9	13	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:133196504C>A	ENST00000388996.4	-	3	1008	c.588G>T	c.(586-588)aaG>aaT	p.K196N	KCNQ3_ENST00000521134.1_Missense_Mutation_p.K76N|KCNQ3_ENST00000519445.1_Missense_Mutation_p.K196N	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	196					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGCACAGGGGCTTCCTGGCAA	0.522																																																0			8											94	94	94					8																	133196504		2203	4300	6503	133265686	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.588G>T	8.37:g.133196504C>A	ENSP00000373648:p.Lys196Asn		133265686	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793099	0.70452	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.98329	-4.87;-4.87;-4.87	5.87	4.06	0.47325	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97726	0.9254	L	0.36672	1.1	0.48341	D	0.99963	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.97692	1.0179	10	0.87932	D	0	-29.2397	9.3712	0.38254	0.0:0.7807:0.0:0.2193	.	196;196	E7ET42;O43525	.;KCNQ3_HUMAN	N	196;76;196;185;75	ENSP00000373648:K196N;ENSP00000429799:K76N;ENSP00000428790:K196N	ENSP00000373648:K196N	K	-	3	2	KCNQ3	133265686	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.286000	0.33273	1.480000	0.48289	0.655000	0.94253	AAG		0.522	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133196504	C	A	133196504	3	1	90	1	0	0	0	0	1	0	0	0	8105	796	28	2	2082	2	KCNQ3	8	133196504	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	6747798	133196504	13167518	164	24751										
TG	7038	hgsc.bcm.edu	37	chr8	133882057	133882057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctgggcagcaggcagccagGacggcctgtggcttgtaagt	17	10	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:133882057G>A	ENST00000220616.4	+	3	300	c.260G>A	c.(259-261)gGa>gAa	p.G87E	TG_ENST00000377869.1_Missense_Mutation_p.G87E	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	87	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		AGGCAGCCAGGACGGCCTGTG	0.627																																																0			8											51	48	49					8																	133882057		2203	4300	6503	133951239	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.260G>A	8.37:g.133882057G>A	ENSP00000220616:p.Gly87Glu		133951239	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.937079	0.34189	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.64085	-0.08;-0.08	5.16	4.28	0.50868	Thyroglobulin type-1 (5);	0.102227	0.43260	D	0.000600	T	0.65133	0.2662	M	0.83953	2.67	0.35251	D	0.778671	P	0.38420	0.63	B	0.36534	0.227	T	0.77512	-0.2560	10	0.87932	D	0	.	13.2177	0.59869	0.0:0.1593:0.8407:0.0	.	87	P01266	THYG_HUMAN	E	87	ENSP00000367100:G87E;ENSP00000220616:G87E	ENSP00000220616:G87E	G	+	2	0	TG	133951239	1.000000	0.71417	0.020000	0.16555	0.397000	0.30659	3.849000	0.55910	1.160000	0.42584	0.462000	0.41574	GGA		0.627	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133882057	G	A	133882057	3	1	90	1	0	0	0	0	1	0	0	0	15852	1174	41	3	270	3	TG	8	133882057	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	685553	133882057	12481965	165	24752										
BAI1	575	hgsc.bcm.edu	37	chr8	143603366	143603366	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgccttcctgcacttcttctTcctgtcctccttctgctggg	7	17	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr8:143603366T>A	ENST00000517894.1	+	21	3959	c.3065T>A	c.(3064-3066)tTc>tAc	p.F1022Y	BAI1_ENST00000323289.5_Missense_Mutation_p.F1022Y			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1022					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CACTTCTTCTTCCTGTCCTCC	0.692																																																0			8											40	47	45					8																	143603366		2198	4296	6494	143600368	SO:0001583	missense	575			AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3065T>A	8.37:g.143603366T>A	ENSP00000430945:p.Phe1022Tyr		143600368		Missense_Mutation	SNP	ENST00000517894.1	37		.	.	.	.	.	.	.	.	.	.	T	20.5	4.008632	0.75046	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.47177	0.85;0.85	3.5	3.5	0.40072	.	0.143965	0.47093	U	0.000251	T	0.49830	0.1580	L	0.36672	1.1	0.54753	D	0.999986	P	0.44006	0.824	P	0.54499	0.754	T	0.44787	-0.9305	10	0.40728	T	0.16	.	11.1951	0.48709	0.0:0.0:0.0:1.0	.	1022	E9PBK0	.	Y	1022	ENSP00000430945:F1022Y;ENSP00000313046:F1022Y	ENSP00000313046:F1022Y	F	+	2	0	BAI1	143600368	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.769000	0.85360	1.218000	0.43458	0.254000	0.18369	TTC		0.692	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143603366	T	A	143603366	3	1	90	1	0	0	0	0	1	0	0	0	1299	1783	62	5	3143	5	BAI1	8	143603366	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	9721309	143603366	2760656	166	24753										
PAX5	5079	hgsc.bcm.edu	37	chr9	37015164	37015164	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttggatcctccaattaccccAggcttgatgcttcctgtctc	7	14	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:37015164A>G	ENST00000358127.4	-	3	314	c.240T>C	c.(238-240)ccT>ccC	p.P80P	PAX5_ENST00000414447.1_Silent_p.P80P|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000377847.2_Silent_p.P80P|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000377852.2_Silent_p.P80P|PAX5_ENST00000520281.1_Silent_p.P80P|PAX5_ENST00000377853.2_Silent_p.P80P|PAX5_ENST00000523241.1_Silent_p.P80P|PAX5_ENST00000446742.1_Intron|PAX5_ENST00000520154.1_Silent_p.P80P	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	80	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.		P -> R. {ECO:0000269|PubMed:24013638}.		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(42)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		CAATTACCCCAGGCTTGATGC	0.458			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	42	Unknown(42)	haematopoietic_and_lymphoid_tissue(42)	9											197	203	201					9																	37015164		2203	4300	6503	37005164	SO:0001819	synonymous_variant	5079				CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"Paired boxes", "Homeoboxes / PRD class"	8619	protein-coding gene	gene with protein product	"B-cell lineage specific activator"	167414	"paired box gene 5 (B-cell lineage specific activator protein)", "paired box gene 5 (B-cell lineage specific activator)"			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.240T>C	9.37:g.37015164A>G			37005164	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Silent	SNP	ENST00000358127.4	37	CCDS6607.1																																																																																				0.458	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			G	37015164	A	G	37015164	2	3	90	1	0	0	0	0	0	0	0	1	11513	175	7	4		4	PAX5	9	37015164	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10		37015164	104198267	167	24754										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37740330	37740330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgagagccgcggctacaggaCcagtggctcgagtgagtcca	15	11	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:37740330C>A	ENST00000539465.1	+	15	2398	c.1805C>A	c.(1804-1806)aCc>aAc	p.T602N	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000536622.1_Missense_Mutation_p.T424N|FRMPD1_ENST00000377765.3_Missense_Mutation_p.T602N|FRMPD1_ENST00000541302.1_Missense_Mutation_p.T471N			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	602						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GGCTACAGGACCAGTGGCTCG	0.642																																																0			9											34	35	34					9																	37740330		2196	4282	6478	37730330	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1805C>A	9.37:g.37740330C>A	ENSP00000444411:p.Thr602Asn		37730330	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.339065	0.60963	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.22743	2.86;2.86;1.94;1.96	5.57	4.67	0.58626	.	0.164914	0.52532	D	0.000062	T	0.38374	0.1038	M	0.63843	1.955	0.49798	D	0.999829	D;D	0.89917	0.999;1.0	D;D	0.71414	0.933;0.973	T	0.11397	-1.0589	10	0.42905	T	0.14	-20.0983	8.5039	0.33175	0.0:0.8256:0.0:0.1744	.	471;602	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	N	602;602;424;471	ENSP00000366995:T602N;ENSP00000444411:T602N;ENSP00000437762:T424N;ENSP00000444804:T471N	ENSP00000366995:T602N	T	+	2	0	FRMPD1	37730330	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	3.228000	0.51270	1.362000	0.46000	0.561000	0.74099	ACC		0.642	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37740330	C	A	37740330	3	1	90	1	0	0	0	0	1	0	0	0	6076	507	18	2	1859	2	FRMPD1	9	37740330	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	725166	37740330	103473101	168	24755										
OMD	4958	hgsc.bcm.edu	37	chr9	95179145	95179145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gacagatacataagtgaagaAggcaaaccaggaggcattga	12	6	0	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:95179145A>G	ENST00000375550.4	-	2	971	c.696T>C	c.(694-696)ccT>ccC	p.P232P	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	232					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TAAGTGAAGAAGGCAAACCAG	0.343			T	USP6	aneurysmal bone cysts																																		Dom	yes		9	9q22.31	4958	osteomodulin		M	0			9											102	103	103					9																	95179145		2203	4300	6503	94218966	SO:0001819	synonymous_variant	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.696T>C	9.37:g.95179145A>G			94218966	Q5TBF4	Silent	SNP	ENST00000375550.4	37	CCDS6696.1																																																																																				0.343	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		G	95179145	A	G	95179145	2	3	90	1	0	0	0	0	0	0	0	1	10896	59	3	4		4	OMD	9	95179145	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	57438815	95179145	46034286	169	24756										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100431157	100431157	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gatgacgacagaagcagtgaCaggaaagacggggttcttga	15	6	1	5			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:100431157C>T	ENST00000375147.3	+	21	2302	c.2046C>T	c.(2044-2046)gaC>gaT	p.D682D		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	682					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				GAAGCAGTGACAGGAAAGACG	0.408																																					Ovarian(36;879 898 2893 44212 50307)											0			9											96	94	95					9																	100431157		2203	4300	6503	99470978	SO:0001819	synonymous_variant	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.2046C>T	9.37:g.100431157C>T			99470978	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	37	CCDS6728.1																																																																																				0.408	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		T	100431157	C	T	100431157	2	4	90	1	0	0	0	0	0	0	0	1	10242	477	17	3		3	NCBP1	9	100431157	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5252012	100431157	40782274	170	24757										
TEX10	54881	hgsc.bcm.edu	37	chr9	103090223	103090223	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggtaagccagccagccaacgGgataacactttactacgata	9	11	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:103090223G>C	ENST00000374902.4	-	8	1823	c.1647C>G	c.(1645-1647)tcC>tcG	p.S549S	TEX10_ENST00000535814.1_Silent_p.S552S	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	549						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		CCAGCCAACGGGATAACACTT	0.373																																																0			9											83	71	75					9																	103090223		2203	4300	6503	102130044	SO:0001819	synonymous_variant	54881			AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1647C>G	9.37:g.103090223G>C			102130044	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	37	CCDS6748.1																																																																																				0.373	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		C	103090223	G	C	103090223	2	2	90	1	0	0	0	0	0	0	0	1	15811	1219	43	5		5	TEX10	9	103090223	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2659066	103090223	38123208	171	24758										
SMC2	10592	hgsc.bcm.edu	37	chr9	106889739	106889739	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	catcagcaaacataaacgggAggctgaagatggtgctgcaa	12	8	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr9:106889739A>G	ENST00000286398.7	+	20	3056	c.2768A>G	c.(2767-2769)gAg>gGg	p.E923G	SMC2_ENST00000303219.8_Missense_Mutation_p.E923G|SMC2_ENST00000374787.3_Missense_Mutation_p.E923G|SMC2_ENST00000374793.3_Missense_Mutation_p.E923G	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	923					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						CATAAACGGGAGGCTGAAGAT	0.343																																																0			9											131	123	126					9																	106889739		2203	4300	6503	105929560	SO:0001583	missense	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2768A>G	9.37:g.106889739A>G	ENSP00000286398:p.Glu923Gly		105929560	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265727	0.59540	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.84	5.84	0.93424	RecF/RecN/SMC (1);	0.094159	0.64402	D	0.000001	T	0.80444	0.4624	M	0.82132	2.575	0.50813	D	0.999896	B	0.21309	0.054	B	0.30316	0.114	T	0.76650	-0.2881	10	0.33940	T	0.23	-9.511	15.0453	0.71822	1.0:0.0:0.0:0.0	.	923	O95347	SMC2_HUMAN	G	923	ENSP00000286398:E923G;ENSP00000363925:E923G;ENSP00000306152:E923G;ENSP00000363919:E923G	ENSP00000286398:E923G	E	+	2	0	SMC2	105929560	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.801000	0.75170	2.229000	0.72834	0.528000	0.53228	GAG		0.343	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			G	106889739	A	G	106889739	3	3	90	1	0	0	0	0	1	0	0	0	14820	304	11	4	2842	4	SMC2	9	106889739	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	3799516	106889739	34323692	172	24759										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7318857	7318857	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aagaatcaacatcttaccttAaacacttccattggaagagg	6	9	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:7318857A>C	ENST00000361972.4	-	7	957	c.867T>G	c.(865-867)ttT>ttG	p.F289L	SFMBT2_ENST00000397167.1_Missense_Mutation_p.F289L	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	289					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						ATCTTACCTTAAACACTTCCA	0.398																																																0			10											138	132	134					10																	7318857		2203	4300	6503	7358863	SO:0001583	missense	57713			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.867T>G	10.37:g.7318857A>C	ENSP00000355109:p.Phe289Leu		7358863	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.582875	0.65992	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.51325	0.71;0.71	5.69	2.4	0.29515	.	0.045483	0.85682	D	0.000000	T	0.60958	0.2309	M	0.72894	2.215	0.80722	D	1	P	0.50710	0.938	D	0.63283	0.913	T	0.58951	-0.7545	10	0.87932	D	0	.	8.2246	0.31562	0.6414:0.0:0.3586:0.0	.	289	Q5VUG0	SMBT2_HUMAN	L	289	ENSP00000355109:F289L;ENSP00000380353:F289L	ENSP00000355109:F289L	F	-	3	2	SFMBT2	7358863	1.000000	0.71417	0.994000	0.49952	0.920000	0.55202	3.165000	0.50778	0.109000	0.17891	0.533000	0.62120	TTT		0.398	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		C	7318857	A	C	7318857	3	2	90	1	0	0	0	0	1	0	0	0	14195	359	13	4	1877	4	SFMBT2	10	7318857	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10		7318857	128215890	173	24760										
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12856299	12856299	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccctactgggatgacatctcCgactctggtaggtctcccat	9	14	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:12856299C>T	ENST00000378847.3	+	7	1084	c.747C>T	c.(745-747)tcC>tcT	p.S249S	CAMK1D_ENST00000378845.1_Silent_p.S249S	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		ATGACATCTCCGACTCTGGTA	0.582																																																0			10											80	69	73					10																	12856299		2203	4300	6503	12896305	SO:0001819	synonymous_variant	57118			AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.747C>T	10.37:g.12856299C>T			12896305	B0YIY0|Q9HD31	Silent	SNP	ENST00000378847.3	37	CCDS7091.1																																																																																				0.582	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		T	12856299	C	T	12856299	2	4	90	1	0	0	0	0	0	0	0	1	2603	639	23	1		1	CAMK1D	10	12856299	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5537442	12856299	122678448	174	24761										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27317855	27317855	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttgactgtaacttttaactTggcattatctttttcaagcc	5	8	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:27317855T>C	ENST00000376087.4	-	27	4063	c.3898A>G	c.(3898-3900)Aag>Gag	p.K1300E	ANKRD26_ENST00000376070.3_Missense_Mutation_p.K857E|ANKRD26_ENST00000436985.2_Missense_Mutation_p.K1316E	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1299					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						ACTTTTAACTTGGCATTATCT	0.299																																																0			10											102	93	96					10																	27317855		1789	4055	5844	27357861	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3898A>G	10.37:g.27317855T>C	ENSP00000365255:p.Lys1300Glu		27357861	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	1.842	-0.467112	0.04476	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.77098	-1.07;-1.07;-1.07	4.69	-4.57	0.03421	.	0.512997	0.16736	N	0.201628	T	0.53965	0.1829	N	0.19112	0.55	0.26002	N	0.982102	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.11329	0.006;0.003;0.003	T	0.38802	-0.9644	10	0.19147	T	0.46	.	6.995	0.24777	0.0:0.4243:0.1305:0.4452	.	1300;1299;1316	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	E	857;1300;1316	ENSP00000365238:K857E;ENSP00000365255:K1300E;ENSP00000405112:K1316E	ENSP00000365238:K857E	K	-	1	0	ANKRD26	27357861	0.999000	0.42202	0.005000	0.12908	0.020000	0.10135	0.811000	0.27198	-1.118000	0.02961	-0.386000	0.06593	AAG		0.299	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			C	27317855	T	C	27317855	3	2	90	1	0	0	0	0	1	0	0	0	654	1821	63	4	1266	4	ANKRD26	10	27317855	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	14461556	27317855	108216892	175	24762										
MMRN2	79812	hgsc.bcm.edu	37	chr10	88703039	88703039	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggccctcccggatgacgtccAggtctaaatagagcttctgg	12	12	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:88703039A>T	ENST00000372027.5	-	6	1823	c.1502T>A	c.(1501-1503)cTg>cAg	p.L501Q	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	501					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						GATGACGTCCAGGTCTAAATA	0.642																																																0			10											62	57	59					10																	88703039		2203	4300	6503	88693019	SO:0001583	missense	79812			AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"EMI domain containing"	19888	protein-coding gene	gene with protein product		608925	"elastin microfibril interfacer 3"	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.1502T>A	10.37:g.88703039A>T	ENSP00000361097:p.Leu501Gln		88693019	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.691975	0.30052	.	.	ENSG00000173269	ENST00000372027;ENST00000443699	T	0.70749	-0.51	5.57	0.658	0.17855	.	1.098760	0.07110	N	0.842071	T	0.75072	0.3800	M	0.63843	1.955	0.09310	N	1	D;P;D	0.56035	0.974;0.93;0.966	P;P;P	0.54401	0.694;0.564;0.751	T	0.60949	-0.7161	10	0.26408	T	0.33	-1.0019	9.2644	0.37632	0.6171:0.0:0.3829:0.0	.	279;440;501	E7EN39;B4E3H8;Q9H8L6	.;.;MMRN2_HUMAN	Q	501;279	ENSP00000361097:L501Q	ENSP00000361097:L501Q	L	-	2	0	MMRN2	88693019	0.047000	0.20315	0.000000	0.03702	0.151000	0.21798	1.151000	0.31651	-0.119000	0.11830	0.379000	0.24179	CTG		0.642	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756		T	88703039	A	T	88703039	3	4	90	1	0	0	0	0	1	0	0	0	9701	188	7	5	1355	5	MMRN2	10	88703039	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	61385184	88703039	46831708	176	24763										
PTEN	5728	hgsc.bcm.edu	37	chr10	89725211	89725211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttgatgaagatcagcatacAcaaattacaaaagtctgaat	6	6	2	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:89725211A>G	ENST00000371953.3	+	9	2551	c.1194A>G	c.(1192-1194)acA>acG	p.T398T		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	398					activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATCAGCATACACAAATTACAA	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	47	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)	prostate(16)|central_nervous_system(10)|skin(5)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											16	17	16					10																	89725211		2161	4272	6433	89715191	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1194A>G	10.37:g.89725211A>G			89715191	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89725211	A	G	89725211	2	3	90	1	0	0	0	0	0	0	0	1	12772	146	6	4		4	PTEN	10	89725211	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1022172	89725211	45809536	177	24764										
CHUK	1147	hgsc.bcm.edu	37	chr10	101978562	101978562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caaatatacactttggatccTtcttcttaatcttctcatgc	3	11	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:101978562T>C	ENST00000370397.7	-	8	796	c.710A>G	c.(709-711)aAg>aGg	p.K237R		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CTTTGGATCCTTCTTCTTAAT	0.323																																					Ovarian(159;52 1904 10536 35305 37148)											0			10											118	111	113					10																	101978562		2203	4300	6503	101968552	SO:0001583	missense	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.710A>G	10.37:g.101978562T>C	ENSP00000359424:p.Lys237Arg		101968552	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	37	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582282	0.86748	.	.	ENSG00000213341	ENST00000370397	T	0.65549	-0.16	5.92	5.92	0.95590	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77350	0.4117	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.79470	-0.1790	10	0.72032	D	0.01	-16.8521	14.3262	0.66523	0.0:0.0:0.0:1.0	.	237	O15111	IKKA_HUMAN	R	237	ENSP00000359424:K237R	ENSP00000359424:K237R	K	-	2	0	CHUK	101968552	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.661000	0.83786	2.263000	0.75096	0.533000	0.62120	AAG		0.323	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101978562	T	C	101978562	3	2	90	1	0	0	0	0	1	0	0	0	3422	1609	56	4	1583	4	CHUK	10	101978562	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	12253351	101978562	33556185	178	24765										
NT5C2	22978	hgsc.bcm.edu	37	chr10	104865521	104865521	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtttccataggcatcgacttTcaaaagatttccatacagtg	7	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:104865521T>G	ENST00000404739.3	-	4	354	c.331A>C	c.(331-333)Aaa>Caa	p.K111Q	NT5C2_ENST00000423468.2_Missense_Mutation_p.K82Q|NT5C2_ENST00000343289.5_Missense_Mutation_p.K111Q|NT5C2_ENST00000369857.4_5'UTR			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	111					cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		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)	GCATCGACTTTCAAAAGATTT	0.358																																																0			10											140	129	133					10																	104865521		2203	4300	6503	104855511	SO:0001583	missense	22978			D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"purine 5' nucleotidase"	600417	"5'-nucleotidase (purine), cytosolic type B"	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.331A>C	10.37:g.104865521T>G	ENSP00000383960:p.Lys111Gln		104855511	B7Z382|D3DR91|Q5JUV5	Missense_Mutation	SNP	ENST00000404739.3	37	CCDS7544.1	.	.	.	.	.	.	.	.	.	.	T	32	5.120773	0.94385	.	.	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000423468;ENST00000452156;ENST00000458345;ENST00000369853	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	6.17	6.17	0.99709	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.75451	0.3851	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80765	-0.1236	10	0.87932	D	0	-23.6324	16.8222	0.85835	0.0:0.0:0.0:1.0	.	82;111	B7Z382;P49902	.;5NTC_HUMAN	Q	111;111;82;111;34;59	ENSP00000339479:K111Q;ENSP00000383960:K111Q;ENSP00000392236:K82Q;ENSP00000396468:K111Q;ENSP00000411330:K34Q	ENSP00000339479:K111Q	K	-	1	0	NT5C2	104855511	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAA		0.358	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229		G	104865521	T	G	104865521	3	3	90	1	0	0	0	0	1	0	0	0	10718	1792	62	4	1410	4	NT5C2	10	104865521	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2886959	104865521	30669226	179	24766										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118196356	118196356	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgtttcctgctctacactatAcacaatcccaatgcctatca	3	15	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:118196356A>C	ENST00000369230.3	+	2	329	c.183A>C	c.(181-183)atA>atC	p.I61I		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	61					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		TCTACACTATACACAATCCCA	0.398																																																0			10											169	155	160					10																	118196356		2203	4300	6503	118186346	SO:0001819	synonymous_variant	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.183A>C	10.37:g.118196356A>C			118186346		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.398	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		C	118196356	A	C	118196356	2	2	90	1	0	0	0	0	0	0	0	1	12183	381	14	4		4	PNLIPRP3	10	118196356	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	13330835	118196356	17338391	180	24767										
MKI67	4288	hgsc.bcm.edu	37	chr10	129905967	129905967	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cttgttggggtgtctgctgaTtctggtggagaagattcgca	15	6	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr10:129905967T>A	ENST00000368654.3	-	13	4512	c.4137A>T	c.(4135-4137)gaA>gaT	p.E1379D	MKI67_ENST00000368653.3_Missense_Mutation_p.E1019D	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1379	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGTCTGCTGATTCTGGTGGAG	0.507																																																0			10											178	167	171					10																	129905967		2203	4300	6503	129795957	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4137A>T	10.37:g.129905967T>A	ENSP00000357643:p.Glu1379Asp		129795957	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	11.91	1.780659	0.31502	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02916	4.11;4.11	4.25	-0.93	0.10441	.	.	.	.	.	T	0.05456	0.0144	L	0.51422	1.61	0.09310	N	1	B;B;D	0.57257	0.001;0.001;0.979	B;B;P	0.57846	0.006;0.006;0.828	T	0.35992	-0.9766	9	0.25751	T	0.34	.	2.9048	0.05718	0.312:0.1792:0.0:0.5088	.	1378;1019;1379	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	D	1379;1019;1378	ENSP00000357643:E1379D;ENSP00000357642:E1019D	ENSP00000357642:E1019D	E	-	3	2	MKI67	129795957	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.566000	0.00917	-0.244000	0.09639	-0.368000	0.07277	GAA		0.507	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129905967	T	A	129905967	3	1	90	1	0	0	0	0	1	0	0	0	9628	1490	52	5	5645	5	MKI67	10	129905967	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	11709611	129905967	5628780	181	24768										
NUP98	4928	hgsc.bcm.edu	37	chr11	3756485	3756485	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gagagtctccaaaaggtgagTatgttagactattgatgtgc	12	5	1	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:3756485T>A	ENST00000324932.7	-	13	1898	c.1478A>T	c.(1477-1479)tAc>tTc	p.Y493F	NUP98_ENST00000397007.4_Missense_Mutation_p.Y510F|NUP98_ENST00000397004.4_Missense_Mutation_p.Y493F|NUP98_ENST00000355260.3_Missense_Mutation_p.Y493F|NUP98_ENST00000359171.4_Missense_Mutation_p.Y493F	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	510					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.Y493F(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		AAAAGGTGAGTATGTTAGACT	0.378			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	1	Substitution - Missense(1)	kidney(1)	11											56	59	58					11																	3756485		2201	4298	6499	3713061	SO:0001583	missense	4928			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1478A>T	11.37:g.3756485T>A	ENSP00000316032:p.Tyr493Phe		3713061	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.1|29.1	4.973851|4.973851	0.92919|0.92919	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000529379|ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.|.	.|.	.|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.74794|0.74794	0.3763|0.3763	M|M	0.66939|0.66939	2.045|2.045	0.51767|0.51767	D|D	0.999935|0.999935	.|D;D;D;D	.|0.76494	.|0.998;0.99;0.999;0.999	.|D;P;D;D	.|0.85130	.|0.994;0.829;0.997;0.997	T|T	0.71130|0.71130	-0.4682|-0.4682	5|9	.|0.13108	.|T	.|0.6	-8.718|-8.718	14.7811|14.7811	0.69769|0.69769	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|510;493;493;493	.|P52948-3;P52948-4;P52948-2;P52948-5	.|.;.;.;.	S|F	95|493;493;493;493;510	.|.	.|ENSP00000316032:Y493F	T|Y	-|-	1|2	0|0	NUP98|NUP98	3713061|3713061	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.431000|7.431000	0.80335|0.80335	2.085000|2.085000	0.62840|0.62840	0.482000|0.482000	0.46254|0.46254	ACT|TAC		0.378	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3756485	T	A	3756485	3	1	90	1	0	0	0	0	1	0	0	0	10804	1638	57	5	4029	5	NUP98	11	3756485	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10		3756485	131250031	182	24769										
OR51B2	79345	hgsc.bcm.edu	37	chr11	5344652	5344652	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tattgtatttgcttggttttGatgctgtagatgacagggtt	12	3	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:5344652G>C	ENST00000328813.2	-	1	930	c.876C>G	c.(874-876)atC>atG	p.I292M	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	292						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTTGGTTTTGATGCTGTAGA	0.373																																																0			11											102	96	98					11																	5344652		2201	4297	6498	5301228	SO:0001583	missense	79345			AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"GPCR / Class A : Olfactory receptors"	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.876C>G	11.37:g.5344652G>C	ENSP00000327540:p.Ile292Met		5301228	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	.	.	.	.	.	.	.	.	.	.	G	9.521	1.108200	0.20714	.	.	ENSG00000184881	ENST00000328813	T	0.38722	1.12	4.38	0.026	0.14148	.	0.000000	0.39146	U	0.001456	T	0.33614	0.0869	M	0.71920	2.185	0.26246	N	0.978795	B	0.17667	0.023	B	0.17098	0.017	T	0.36456	-0.9747	10	0.72032	D	0.01	.	1.1063	0.01694	0.2771:0.2688:0.317:0.1372	.	292	Q9Y5P1	O51B2_HUMAN	M	292	ENSP00000327540:I292M	ENSP00000327540:I292M	I	-	3	3	OR51B2	5301228	0.000000	0.05858	0.998000	0.56505	0.928000	0.56348	-3.172000	0.00572	0.098000	0.17522	-0.175000	0.13238	ATC		0.373	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180		C	5344652	G	C	5344652	3	2	90	1	0	0	0	0	1	0	0	0	11120	1280	45	5	66	5	OR51B2	11	5344652	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	1588167	5344652	129661864	183	24770										
OR52W1	120787	hgsc.bcm.edu	37	chr11	6220833	6220833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttggccatggcctgtgatcGtgctgcggcaatagggcgtc	15	10	0	1	rs146972287		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:6220833G>A	ENST00000311352.2	+	1	458	c.380G>A	c.(379-381)cGt>cAt	p.R127H	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R127H(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCCTGTGATCGTGCTGCGGCA	0.557													G|||	1	0.000199681	8e-04	0	5008	,	,		24071	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	endometrium(1)	11						G	HIS/ARG	0,4402		0,0,2201	142	98	113		380	5.8	0.9	11	dbSNP_134	113	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR52W1	NM_001005178.1	29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	127/321	6220833	1,12993	2201	4296	6497	6177409	SO:0001583	missense	120787			AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"GPCR / Class A : Olfactory receptors"	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.380G>A	11.37:g.6220833G>A	ENSP00000309673:p.Arg127His		6177409	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.97	3.736425	0.69189	0.0	1.16E-4	ENSG00000175485	ENST00000311352	T	0.77489	-1.1	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.197016	0.25156	N	0.032710	D	0.90191	0.6934	M	0.92555	3.32	0.47308	D	0.999381	D	0.76494	0.999	P	0.60068	0.868	D	0.91810	0.5459	10	0.72032	D	0.01	.	19.1459	0.93467	0.0:0.0:1.0:0.0	.	127	Q6IF63	O52W1_HUMAN	H	127	ENSP00000309673:R127H	ENSP00000309673:R127H	R	+	2	0	OR52W1	6177409	1.000000	0.71417	0.936000	0.37596	0.471000	0.32888	7.373000	0.79623	2.767000	0.95098	0.655000	0.94253	CGT		0.557	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178		A	6220833	G	A	6220833	3	1	90	1	0	0	0	0	1	0	0	0	11163	1145	40	1	382	1	OR52W1	11	6220833	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	876181	6220833	128785683	184	24771										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6977230	6977230	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgataagtttaaaacttactTcaaatttaatttagactcag	4	5	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:6977230T>G	ENST00000278319.5	+	7	1610	c.1022T>G	c.(1021-1023)tTc>tGc	p.F341C	ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.F341C|ZNF215_ENST00000527171.1_3'UTR	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	341					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		AAAACTTACTTCAAATTTAAT	0.318																																																0			11											48	53	51					11																	6977230		2201	4294	6495	6933806	SO:0001583	missense	7762			AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.1022T>G	11.37:g.6977230T>G	ENSP00000278319:p.Phe341Cys		6933806	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.378863	0.42207	.	.	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.06687	3.27;3.27	3.99	2.82	0.32997	.	0.145178	0.32459	N	0.006062	T	0.08133	0.0203	N	0.08118	0	0.21719	N	0.999576	D	0.69078	0.997	P	0.55667	0.781	T	0.13764	-1.0497	10	0.87932	D	0	-0.2188	9.0113	0.36142	0.0:0.0:0.1866:0.8134	.	341	Q9UL58	ZN215_HUMAN	C	341	ENSP00000278319:F341C;ENSP00000393202:F341C	ENSP00000278319:F341C	F	+	2	0	ZNF215	6933806	0.005000	0.15991	0.002000	0.10522	0.022000	0.10575	1.548000	0.36201	0.832000	0.34804	0.533000	0.62120	TTC		0.318	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			G	6977230	T	G	6977230	3	3	90	1	0	0	0	0	1	0	0	0	17810	1783	62	4	1040	4	ZNF215	11	6977230	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	756397	6977230	128029286	185	24772										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9168658	9168658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atagaggaactgctccttctCgtcatcacagcgcaggaagg	11	11	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:9168658C>T	ENST00000328194.3	-	16	3096	c.2776G>A	c.(2776-2778)Gag>Aag	p.E926K	DENND5A_ENST00000527700.1_Missense_Mutation_p.E269K|DENND5A_ENST00000530044.1_Missense_Mutation_p.E926K	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	926	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGCTCCTTCTCGTCATCACAG	0.463																																																0			11											173	145	155					11																	9168658		2201	4296	6497	9125234	SO:0001583	missense	23258			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2776G>A	11.37:g.9168658C>T	ENSP00000328524:p.Glu926Lys		9125234	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.771634|5.771634	0.96922|0.96922	.|.	.|.	ENSG00000184014|ENSG00000184014	ENST00000328194;ENST00000530044;ENST00000527700|ENST00000524446	T;T;T|.	0.30182|.	1.54;1.54;1.54|.	5.64|5.64	5.64|5.64	0.86602|0.86602	RUN (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73179|0.73179	0.3554|0.3554	L|L	0.58669|0.58669	1.825|1.825	0.80722|0.80722	D|D	1|1	D;B|.	0.54047|.	0.964;0.348|.	P;B|.	0.51385|.	0.668;0.272|.	T|T	0.69694|0.69694	-0.5076|-0.5076	10|5	0.51188|.	T|.	0.08|.	.|.	19.7069|19.7069	0.96076|0.96076	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	926;926|.	E9PS91;Q6IQ26|.	.;DEN5A_HUMAN|.	K|Q	926;926;269|96	ENSP00000328524:E926K;ENSP00000435866:E926K;ENSP00000432549:E269K|.	ENSP00000328524:E926K|.	E|R	-|-	1|2	0|0	DENND5A|DENND5A	9125234|9125234	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.994000|0.994000	0.84299|0.84299	7.818000|7.818000	0.86416|0.86416	2.654000|2.654000	0.90174|0.90174	0.563000|0.563000	0.77884|0.77884	GAG|CGA		0.463	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		T	9168658	C	T	9168658	3	4	90	1	0	0	0	0	1	0	0	0	4447	893	31	1	1119	1	DENND5A	11	9168658	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2191428	9168658	125837858	186	24773										
PDE3B	5140	hgsc.bcm.edu	37	chr11	14853310	14853310	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gatgggagagaaatcaggaaGgattctcagtcaggtttgct	14	5	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:14853310G>C	ENST00000282096.4	+	9	2434	c.2081G>C	c.(2080-2082)aGg>aCg	p.R694T	PDE3B_ENST00000455098.2_Missense_Mutation_p.R643T	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	694					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	AAATCAGGAAGGATTCTCAGT	0.274																																																0			11											57	63	61					11																	14853310		2197	4291	6488	14809886	SO:0001583	missense	5140			U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2081G>C	11.37:g.14853310G>C	ENSP00000282096:p.Arg694Thr		14809886	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	37	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686806	0.68157	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.77358	-1.09;-1.09	5.95	5.04	0.67666	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.85609	0.5736	M	0.77103	2.36	0.53688	D	0.999974	D;D	0.67145	0.995;0.996	P;P	0.57502	0.82;0.822	D	0.87682	0.2548	10	0.72032	D	0.01	.	15.1414	0.72612	0.0675:0.0:0.9325:0.0	.	643;694	B7ZM37;Q13370	.;PDE3B_HUMAN	T	694;643	ENSP00000282096:R694T;ENSP00000388644:R643T	ENSP00000282096:R694T	R	+	2	0	PDE3B	14809886	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	7.113000	0.77095	1.529000	0.49120	-0.253000	0.11424	AGG		0.274	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		C	14853310	G	C	14853310	3	2	90	1	0	0	0	0	1	0	0	0	11669	1000	35	5	2115	5	PDE3B	11	14853310	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	5684652	14853310	120153206	187	24774										
QSER1	79832	hgsc.bcm.edu	37	chr11	32956633	32956633	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aacaaccagaagtcaaaacaGgatttattgcttctttctta	5	8	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:32956633G>C	ENST00000399302.2	+	4	3777	c.3442G>C	c.(3442-3444)Gga>Cga	p.G1148R	QSER1_ENST00000527788.1_Missense_Mutation_p.G909R	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1148										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AGTCAAAACAGGATTTATTGC	0.443																																																0			11											84	83	83					11																	32956633		1847	4090	5937	32913209	SO:0001583	missense	79832			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.3442G>C	11.37:g.32956633G>C	ENSP00000382241:p.Gly1148Arg		32913209	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.99|19.99	3.927918|3.927918	0.73327|0.73327	.|.	.|.	ENSG00000060749|ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788|ENST00000524678	T;T|.	0.75050|.	-0.52;-0.9|.	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.77618|0.77618	0.4157|0.4157	M|M	0.76002|0.76002	2.32|2.32	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	T|T	0.76623|0.76623	-0.2891|-0.2891	10|5	0.87932|.	D|.	0|.	.|.	19.573|19.573	0.95428|0.95428	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	909;909;1148|.	C9JJ88;Q2KHR3-2;Q2KHR3|.	.;.;QSER1_HUMAN|.	R|H	1148;909;909|168	ENSP00000382241:G1148R;ENSP00000432766:G909R|.	ENSP00000078652:G909R|.	G|Q	+|+	1|3	0|2	QSER1|QSER1	32913209|32913209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	9.476000|9.476000	0.97823|0.97823	2.628000|2.628000	0.89032|0.89032	0.563000|0.563000	0.77884|0.77884	GGA|CAG		0.443	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		C	32956633	G	C	32956633	3	2	90	1	0	0	0	0	1	0	0	0	12919	1001	35	5	3448	5	QSER1	11	32956633	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	18103323	32956633	102049883	188	24775										
ALX4	60529	hgsc.bcm.edu	37	chr11	44286517	44286517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctcgtagccattgaggcctgGgctgaggctggctgctccaa	14	12	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:44286517G>A	ENST00000329255.3	-	4	1226	c.1123C>T	c.(1123-1125)Cca>Tca	p.P375S		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	375					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						TTGAGGCCTGGGCTGAGGCTG	0.657																																																0			11											56	52	53					11																	44286517		2203	4299	6502	44243093	SO:0001583	missense	60529			AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"Homeoboxes / PRD class"	450	protein-coding gene	gene with protein product		605420	"parietal foramina 2", "aristaless-like homeobox 4"	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.1123C>T	11.37:g.44286517G>A	ENSP00000332744:p.Pro375Ser		44243093	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	37	CCDS31468.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770356	0.69992	.	.	ENSG00000052850	ENST00000329255	D	0.92495	-3.05	5.19	5.19	0.71726	.	0.296491	0.33772	N	0.004572	D	0.90584	0.7048	L	0.57536	1.79	0.39363	D	0.965952	B	0.22683	0.073	B	0.20184	0.028	D	0.87469	0.2413	10	0.30854	T	0.27	.	19.084	0.93194	0.0:0.0:1.0:0.0	.	375	Q9H161	ALX4_HUMAN	S	375	ENSP00000332744:P375S	ENSP00000332744:P375S	P	-	1	0	ALX4	44243093	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.802000	0.47916	2.575000	0.86900	0.561000	0.74099	CCA		0.657	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			A	44286517	G	A	44286517	3	1	90	1	0	0	0	0	1	0	0	0	558	1232	43	3	116	3	ALX4	11	44286517	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	11329884	44286517	90719999	189	24776										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135901	55135901	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggcggcctggattggaggctTtcttcactcattggttcaat	12	9	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:55135901T>G	ENST00000314706.3	+	1	542	c.542T>G	c.(541-543)tTt>tGt	p.F181C		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						ATTGGAGGCTTTCTTCACTCA	0.418																																																0			11											200	180	187					11																	55135901		2201	4296	6497	54892477	SO:0001583	missense	81328			AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.542T>G	11.37:g.55135901T>G	ENSP00000325065:p.Phe181Cys		54892477	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	37	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	-	10.50	1.367427	0.24771	.	.	ENSG00000181958	ENST00000314706	T	0.00188	8.59	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.258526	0.27460	N	0.019267	T	0.00300	0.0009	M	0.63843	1.955	0.09310	N	1	B	0.28378	0.209	B	0.43225	0.412	T	0.12734	-1.0536	10	0.46703	T	0.11	.	10.0108	0.41986	0.0:0.0:0.0:1.0	.	181	Q8NGL6	O4A15_HUMAN	C	181	ENSP00000325065:F181C	ENSP00000325065:F181C	F	+	2	0	OR4A15	54892477	0.000000	0.05858	0.034000	0.17996	0.512000	0.34134	0.766000	0.26560	1.456000	0.47831	0.403000	0.27427	TTT		0.418	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		G	55135901	T	G	55135901	3	3	90	1	0	0	0	0	1	0	0	0	11071	1841	64	4	544	4	OR4A15	11	55135901	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	10849384	55135901	79870615	190	24777										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541198	55541198	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtggaatacagaaccatctcTttctctggttgcatcatgca	8	10	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:55541198T>A	ENST00000361760.1	+	1	285	c.285T>A	c.(283-285)tcT>tcA	p.S95S		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GAACCATCTCTTTCTCTGGTT	0.403																																																0			11											185	179	181					11																	55541198		2200	4296	6496	55297774	SO:0001819	synonymous_variant	390142			BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.285T>A	11.37:g.55541198T>A			55297774	Q6IF68|Q6IFC9	Silent	SNP	ENST00000361760.1	37	CCDS31507.1																																																																																				0.403	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		A	55541198	T	A	55541198	2	1	90	1	0	0	0	0	0	0	0	1	11185	1596	56	5		5	OR5D13	11	55541198	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	405297	55541198	79465318	191	24778										
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927008	55927008	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcaaagaagtgagtggaattGggctgcatgtacatgaagag	14	4	1	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:55927008G>T	ENST00000313447.1	-	1	785	c.786C>A	c.(784-786)ccC>ccA	p.P262P		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	262						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P262P(1)		large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				GAGTGGAATTGGGCTGCATGT	0.418																																																1	Substitution - coding silent(1)	ovary(1)	11											109	94	99					11																	55927008		2201	4296	6497	55683584	SO:0001819	synonymous_variant	219453			BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"GPCR / Class A : Olfactory receptors"	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.786C>A	11.37:g.55927008G>T			55683584	Q6IFB5	Silent	SNP	ENST00000313447.1	37	CCDS31521.1																																																																																				0.418	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		T	55927008	G	T	55927008	2	4	90	1	0	0	0	0	0	0	0	1	11276	1335	47	2		2	OR8K5	11	55927008	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	385810	55927008	79079508	192	24779										
OR5AP2	338675	hgsc.bcm.edu	37	chr11	56409290	56409290	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agctgatgacaataaaacttGagaatgccatgatcacaatg	8	7	1	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:56409290G>A	ENST00000302981.1	-	1	625	c.626C>T	c.(625-627)tCa>tTa	p.S209L	OR5AP2_ENST00000544374.1_Missense_Mutation_p.S210L	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						AATAAAACTTGAGAATGCCAT	0.443																																																0			11											212	206	208					11																	56409290		2201	4296	6497	56165866	SO:0001583	missense	338675			AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"GPCR / Class A : Olfactory receptors"	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.626C>T	11.37:g.56409290G>A	ENSP00000303111:p.Ser209Leu		56165866	B2RNM8	Missense_Mutation	SNP	ENST00000302981.1	37	CCDS31534.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471436	0.43942	.	.	ENSG00000172464	ENST00000544374;ENST00000302981	T;T	0.36878	1.23;1.23	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000179	T	0.38639	0.1048	M	0.69185	2.1	0.09310	N	1	P	0.40000	0.698	B	0.40702	0.338	T	0.45011	-0.9290	10	0.62326	D	0.03	.	10.3966	0.44205	0.0:0.1431:0.7093:0.1476	.	209	Q8NGF4	O5AP2_HUMAN	L	210;209	ENSP00000442701:S210L;ENSP00000303111:S209L	ENSP00000303111:S209L	S	-	2	0	OR5AP2	56165866	0.051000	0.20477	1.000000	0.80357	0.910000	0.53928	2.063000	0.41423	2.588000	0.87417	0.637000	0.83480	TCA		0.443	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925		A	56409290	G	A	56409290	3	1	90	1	0	0	0	0	1	0	0	0	11175	1294	45	3	328	3	OR5AP2	11	56409290	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	482282	56409290	78597226	193	24780										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63681555	63681555	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttgggtgggcgacgccgggtTcgcaagggatggtggcggta	21	7	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:63681555T>C	ENST00000301459.4	-	8	1149	c.762A>G	c.(760-762)cgA>cgG	p.R254R	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	254					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GACGCCGGGTTCGCAAGGGAT	0.642																																																0			11											105	97	100					11																	63681555		2201	4297	6498	63438131	SO:0001819	synonymous_variant	283248			BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.762A>G	11.37:g.63681555T>C			63438131	Q96FP3	Silent	SNP	ENST00000301459.4	37	CCDS8052.1																																																																																				0.642	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		C	63681555	T	C	63681555	2	2	90	1	0	0	0	0	0	0	0	1	13220	1770	62	4		4	RCOR2	11	63681555	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	7272265	63681555	71324961	194	24781										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64681704	64681704	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgtgagtcggcagcccctggCgctgtagggagaaacagggt	17	9	0	2	rs373062101		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:64681704C>A	ENST00000377264.3	-	3	448	c.336G>T	c.(334-336)gcG>gcT	p.A112A	ATG2A_ENST00000421419.2_Splice_Site_p.A112A	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	112					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CAGCCCCTGGCGCTGTAGGGA	0.682																																																0			11											15	16	16					11																	64681704		2158	4229	6387	64438280	SO:0001630	splice_region_variant	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.335-1G>T	11.37:g.64681704C>A			64438280	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	c	3.771	-0.047637	0.07407	.	.	ENSG00000110046	ENST00000377262	.	.	.	4.07	-3.32	0.04973	.	0.209300	0.24172	N	0.040882	T	0.40222	0.1108	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25502	-1.0130	6	0.39692	T	0.17	.	0.268	0.00227	0.246:0.2333:0.2636:0.2571	.	.	.	.	S	110	.	ENSP00000366473:A110S	A	-	1	0	ATG2A	64438280	0.000000	0.05858	0.883000	0.34634	0.398000	0.30690	-1.598000	0.02087	-0.776000	0.04578	-0.482000	0.04802	GCC		0.682	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	Silent	A	64681704	C	A	64681704	5	1	90	1	0	0	0	0	0	0	1	0	1094	782	27	2	5636	2	ATG2A	11	64681704	Splice_Site	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1000149	64681704	70324812	195	24782										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66478110	66478110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	actgcagctggttctggaccCcgctaagggagttggccaac	13	12	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:66478110C>T	ENST00000533211.1	-	10	1347	c.1016G>A	c.(1015-1017)gGg>gAg	p.G339E	SPTBN2_ENST00000529997.1_Missense_Mutation_p.G339E|SPTBN2_ENST00000309996.2_Missense_Mutation_p.G339E|RN7SL12P_ENST00000473849.2_RNA			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	339					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTTCTGGACCCCGCTAAGGGA	0.622																																																0			11											73	58	63					11																	66478110		2200	4295	6495	66234686	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.1016G>A	11.37:g.66478110C>T	ENSP00000432568:p.Gly339Glu		66234686	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712653	0.68730	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262	T;T;T	0.64260	-0.09;-0.09;-0.09	5.0	5.0	0.66597	.	0.122296	0.56097	D	0.000038	T	0.80984	0.4729	M	0.82716	2.605	0.52099	D	0.999941	D	0.89917	1.0	D	0.85130	0.997	D	0.83567	0.0110	10	0.66056	D	0.02	.	17.2122	0.86934	0.0:1.0:0.0:0.0	.	339	O15020	SPTN2_HUMAN	E	339	ENSP00000432568:G339E;ENSP00000311489:G339E;ENSP00000433593:G339E	ENSP00000311489:G339E	G	-	2	0	SPTBN2	66234686	0.967000	0.33354	0.896000	0.35187	0.738000	0.42128	2.378000	0.44309	2.595000	0.87683	0.563000	0.77884	GGG		0.622	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66478110	C	T	66478110	3	4	90	1	0	0	0	0	1	0	0	0	15159	623	22	3	6272	3	SPTBN2	11	66478110	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1796406	66478110	68528406	196	24783										
SAPS3	55291	hgsc.bcm.edu	37	chr11	68331813	68331813	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgcccaccaggcatgagccaTtcagcttgttcagtaaacaa	8	12	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:68331813T>C	ENST00000393800.2	+	9	1142	c.888T>C	c.(886-888)caT>caC	p.H296H	PPP6R3_ENST00000524904.1_Silent_p.H296H|PPP6R3_ENST00000265636.5_Silent_p.H296H|PPP6R3_ENST00000534534.1_Intron|PPP6R3_ENST00000265637.4_Silent_p.H296H|PPP6R3_ENST00000393799.2_Silent_p.H296H|PPP6R3_ENST00000529710.1_Silent_p.H296H|PPP6R3_ENST00000527403.2_Silent_p.H296H|PPP6R3_ENST00000524845.1_Silent_p.H296H|PPP6R3_ENST00000393801.3_Silent_p.H296H	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	296					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GCATGAGCCATTCAGCTTGTT	0.413																																																0			11											107	108	107					11																	68331813		2200	4294	6494	68088389	SO:0001819	synonymous_variant	0			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.888T>C	11.37:g.68331813T>C			68088389	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																				0.413	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		C	68331813	T	C	68331813	2	2	90	1	0	0	0	0	0	0	0	1	13875	1490	52	4		4	SAPS3	11	68331813	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1853703	68331813	66674703	197	24784										
P2RY6	5031	hgsc.bcm.edu	37	chr11	73007692	73007692	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctggcggctggcctgccgctGaacatctgtgtcattaccca	11	14	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:73007692G>A	ENST00000393590.2	+	2	428	c.129G>A	c.(127-129)ctG>ctA	p.L43L	P2RY6_ENST00000542092.1_Silent_p.L43L|P2RY6_ENST00000540342.1_Silent_p.L43L|P2RY6_ENST00000393591.1_Silent_p.L43L|P2RY6_ENST00000349767.2_Silent_p.L43L|P2RY6_ENST00000393592.2_Silent_p.L43L|P2RY6_ENST00000538328.1_Silent_p.L43L|P2RY6_ENST00000540124.1_Silent_p.L43L	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	43					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						GCCTGCCGCTGAACATCTGTG	0.617																																																0			11											128	136	133					11																	73007692		2200	4293	6493	72685340	SO:0001819	synonymous_variant	5031				CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.129G>A	11.37:g.73007692G>A			72685340	Q15754	Silent	SNP	ENST00000393590.2	37	CCDS8220.1																																																																																				0.617	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			A	73007692	G	A	73007692	2	1	90	1	0	0	0	0	0	0	0	1	11385	1277	45	3		3	P2RY6	11	73007692	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	4675879	73007692	61998824	198	24785										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73834107	73834107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctcactgatgcaatacaCatcactcccaggagatgggg	10	12	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:73834107C>T	ENST00000334126.7	-	8	1517	c.1291G>A	c.(1291-1293)Gtg>Atg	p.V431M	C2CD3_ENST00000313663.7_Missense_Mutation_p.V431M			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	431					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATGCAATACACATCACTCCCA	0.448																																																0			11											80	79	79					11																	73834107		2200	4293	6493	73511755	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1291G>A	11.37:g.73834107C>T	ENSP00000334379:p.Val431Met		73511755	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	19.10	3.761572	0.69763	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.14640	2.49;2.51	5.52	4.55	0.56014	.	0.377637	0.26352	N	0.024861	T	0.27205	0.0667	L	0.56769	1.78	0.23449	N	0.997655	D;P	0.62365	0.991;0.919	P;P	0.60286	0.872;0.682	T	0.02991	-1.1085	10	0.62326	D	0.03	-0.6089	10.6088	0.45410	0.1477:0.7095:0.1427:0.0	.	431;431	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	M	431	ENSP00000334379:V431M;ENSP00000323339:V431M	ENSP00000323339:V431M	V	-	1	0	C2CD3	73511755	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.779000	0.38624	2.586000	0.87340	0.561000	0.74099	GTG		0.448	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		T	73834107	C	T	73834107	3	4	90	1	0	0	0	0	1	0	0	0	2160	478	17	3	4696	3	C2CD3	11	73834107	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	826415	73834107	61172409	199	24786										
EED	8726	hgsc.bcm.edu	37	chr11	85967512	85967512	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctgtagctggatctagaggCataattaggataataaatcc	10	6	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:85967512C>T	ENST00000263360.6	+	5	1196	c.510C>T	c.(508-510)ggC>ggT	p.G170G	EED_ENST00000351625.6_Silent_p.G170G|EED_ENST00000327320.4_Silent_p.G170G|EED_ENST00000528180.1_Silent_p.G170G	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	170	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				GATCTAGAGGCATAATTAGGA	0.378																																																0			11											99	99	99					11																	85967512		2202	4299	6501	85645160	SO:0001819	synonymous_variant	8726			AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"WD repeat domain containing"	3188	protein-coding gene	gene with protein product	"WD protein associating with integrin cytoplasmic tails 1"	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.510C>T	11.37:g.85967512C>T			85645160	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Silent	SNP	ENST00000263360.6	37	CCDS8273.1																																																																																				0.378	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797		T	85967512	C	T	85967512	2	4	90	1	0	0	0	0	0	0	0	1	4933	697	25	3		3	EED	11	85967512	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	12133405	85967512	49039004	200	24787										
FAT3	120114	hgsc.bcm.edu	37	chr11	92086824	92086824	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atagtatcgctagcctgaatTtgttaccatttgtcattaat	6	7	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:92086824T>A	ENST00000298047.6	+	1	1563	c.1546T>A	c.(1546-1548)Ttg>Atg	p.L516M	FAT3_ENST00000409404.2_Missense_Mutation_p.L516M|FAT3_ENST00000541502.1_Missense_Mutation_p.L516M|FAT3_ENST00000525166.1_Missense_Mutation_p.L366M			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	516	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAGCCTGAATTTGTTACCATT	0.388										TCGA Ovarian(4;0.039)																																						0			11											108	110	109					11																	92086824		1882	4112	5994	91726472	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1546T>A	11.37:g.92086824T>A	ENSP00000298047:p.Leu516Met		91726472	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	T	3.890	-0.024218	0.07634	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.84	-11.7	0.00046	.	.	.	.	.	T	0.24547	0.0595	L	0.28556	0.865	0.09310	N	1	P	0.35272	0.493	B	0.33690	0.168	T	0.23976	-1.0173	9	0.48119	T	0.1	.	3.7161	0.08438	0.124:0.3056:0.3251:0.2453	.	516	Q8TDW7-3	.	M	516;516;516;366	ENSP00000298047:L516M;ENSP00000387040:L516M;ENSP00000443786:L516M;ENSP00000432586:L366M	ENSP00000298047:L516M	L	+	1	2	FAT3	91726472	0.000000	0.05858	0.000000	0.03702	0.787000	0.44495	-2.003000	0.01463	-3.697000	0.00119	-1.963000	0.00474	TTG		0.388	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92086824	T	A	92086824	3	1	90	1	0	0	0	0	1	0	0	0	5710	1838	64	5	1548	5	FAT3	11	92086824	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	6119312	92086824	42919692	201	24788										
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107219711	107219711	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aacaaagtagctgctctatgGtgctgcaaagggactatcag	11	8	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:107219711G>T	ENST00000282251.5	-	14	2181	c.2154C>A	c.(2152-2154)caC>caA	p.H718Q	CWF19L2_ENST00000433523.1_Missense_Mutation_p.H718Q	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	718							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CTGCTCTATGGTGCTGCAAAG	0.388																																																0			11											75	74	75					11																	107219711		2201	4298	6499	106724921	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2154C>A	11.37:g.107219711G>T	ENSP00000282251:p.His718Gln		106724921	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846511	0.71603	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;D	0.89123	0.07;-2.47	5.86	2.78	0.32641	Histidine triad motif (1);Histidine triad-like motif (1);Cwf19-like, C-terminal domain-1 (1);	0.000000	0.85682	D	0.000000	D	0.95290	0.8472	H	0.95539	3.685	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.94393	0.7616	10	0.87932	D	0	-14.6588	8.9957	0.36050	0.2693:0.0:0.7307:0.0	.	718	Q2TBE0	C19L2_HUMAN	Q	718	ENSP00000282251:H718Q;ENSP00000387533:H718Q	ENSP00000282251:H718Q	H	-	3	2	CWF19L2	106724921	1.000000	0.71417	0.998000	0.56505	0.928000	0.56348	1.409000	0.34680	0.690000	0.31570	0.655000	0.94253	CAC		0.388	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		T	107219711	G	T	107219711	3	4	90	1	0	0	0	0	1	0	0	0	4078	1252	44	2	550	2	CWF19L2	11	107219711	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	15132887	107219711	27786805	202	24789										
FAM55D	54827	hgsc.bcm.edu	37	chr11	114453431	114453431	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agacatcctggccctcaggaAatccccgccatattgcttcc	7	16	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:114453431A>C	ENST00000375478.3	-	3	589	c.409T>G	c.(409-411)Ttc>Gtc	p.F137V	NXPE4_ENST00000424261.2_Intron	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	137						extracellular vesicular exosome (GO:0070062)											GCCCTCAGGAAATCCCCGCCA	0.572																																																0			11											76	81	80					11																	114453431		2198	4296	6494	113958641	SO:0001583	missense	54827			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.409T>G	11.37:g.114453431A>C	ENSP00000364627:p.Phe137Val		113958641	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.330667	0.60853	.	.	ENSG00000137634	ENST00000375478	T	0.20598	2.06	5.01	5.01	0.66863	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.085834	0.50627	D	0.000109	T	0.51092	0.1654	M	0.90082	3.085	0.34434	D	0.698832	D	0.89917	1.0	D	0.81914	0.995	T	0.70328	-0.4902	10	0.72032	D	0.01	.	10.6877	0.45852	0.8401:0.1599:0.0:0.0	.	137	Q6UWF7	FA55D_HUMAN	V	137	ENSP00000364627:F137V	ENSP00000364627:F137V	F	-	1	0	FAM55D	113958641	1.000000	0.71417	0.985000	0.45067	0.578000	0.36192	5.489000	0.66875	2.007000	0.58848	0.482000	0.46254	TTC		0.572	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		C	114453431	A	C	114453431	3	2	90	1	0	0	0	0	1	0	0	0	5606	14	1	4	1241	4	FAM55D	11	114453431	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	7233720	114453431	20553085	203	24790										
CEP164	22897	hgsc.bcm.edu	37	chr11	117278743	117278743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agttggagtcctctctttggGaagaggtgcagccccatgtc	13	10	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr11:117278743G>A	ENST00000278935.3	+	28	3751	c.3604G>A	c.(3604-3606)Gaa>Aaa	p.E1202K	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1202					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CTCTCTTTGGGAAGAGGTGCA	0.552																																																0			11											83	68	73					11																	117278743		2201	4293	6494	116783953	SO:0001583	missense	22897			AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.3604G>A	11.37:g.117278743G>A	ENSP00000278935:p.Glu1202Lys		116783953	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.355347	0.41700	.	.	ENSG00000110274	ENST00000278935;ENST00000529538	T	0.34472	1.36	5.17	4.24	0.50183	.	0.000000	0.49305	D	0.000151	T	0.55353	0.1915	M	0.74258	2.255	0.38895	D	0.957204	D;D;D	0.57257	0.979;0.979;0.979	P;P;P	0.60415	0.874;0.874;0.874	T	0.63278	-0.6673	10	0.62326	D	0.03	-7.843	13.321	0.60432	0.0:0.0:0.8414:0.1586	.	976;1202;1205	Q9NTH6;Q9UPV0;Q9UPV0-2	.;CE164_HUMAN;.	K	1202;1113	ENSP00000278935:E1202K	ENSP00000278935:E1202K	E	+	1	0	CEP164	116783953	1.000000	0.71417	0.738000	0.30950	0.495000	0.33615	6.548000	0.73896	1.270000	0.44297	0.591000	0.81541	GAA		0.552	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		A	117278743	G	A	117278743	3	1	90	1	0	0	0	0	1	0	0	0	3255	1175	41	3	3706	3	CEP164	11	117278743	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2825312	117278743	17727773	204	24791										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1987537	1987537	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	attgttggtgttcagaaaggCgtatccgtgcactccaagct	11	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:1987537C>T	ENST00000382722.5	-	16	2025	c.1663G>A	c.(1663-1665)Gcc>Acc	p.A555T	CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.A491T|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.A555T|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.A491T|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.A440T	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	555	Cache.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TTCAGAAAGGCGTATCCGTGC	0.577																																					Colon(2;101 179 21030 23310 28141)											0			12											65	71	69					12																	1987537		2078	4198	6276	1857798	SO:0001583	missense	93589			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1663G>A	12.37:g.1987537C>T	ENSP00000372169:p.Ala555Thr		1857798	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	35	5.458685	0.96240	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.09630	2.96	5.6	5.6	0.85130	Cache (1);	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.97110	0.889;1.0	T	0.16928	-1.0386	10	0.66056	D	0.02	.	19.6224	0.95663	0.0:1.0:0.0:0.0	.	555;555	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	T	491;555;555	ENSP00000372169:A555T	ENSP00000280663:A555T	A	-	1	0	CACNA2D4	1857798	1.000000	0.71417	0.991000	0.47740	0.883000	0.51084	7.818000	0.86416	2.630000	0.89119	0.655000	0.94253	GCC		0.577	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			T	1987537	C	T	1987537	3	4	90	1	0	0	0	0	1	0	0	0	2557	768	27	1	1842	1	CACNA2D4	12	1987537	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10		1987537	131864358	205	24792										
PARP11	57097	hgsc.bcm.edu	37	chr12	3939084	3939084	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgtgccacttcccacattctGccaagtaaaaccagccccac	5	17	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:3939084G>T	ENST00000228820.4	-	2	263	c.119C>A	c.(118-120)gCa>gAa	p.A40E	PARP11_ENST00000427057.2_5'UTR|PARP11_ENST00000447133.3_5'UTR|PARP11_ENST00000397096.2_Missense_Mutation_p.A33E	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	33	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			CCCACATTCTGCCAAGTAAAA	0.398																																																0			12											182	164	170					12																	3939084		2203	4300	6503	3809345	SO:0001583	missense	57097			AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.119C>A	12.37:g.3939084G>T	ENSP00000228820:p.Ala40Glu		3809345	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	37	CCDS8523.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.7|24.7	4.559194|4.559194	0.86335|0.86335	.|.	.|.	ENSG00000111224|ENSG00000111224	ENST00000397096;ENST00000228820|ENST00000450737	T;T|.	0.42131|.	0.98;0.98|.	5.52|5.52	4.62|4.62	0.57501|0.57501	WWE domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64080|0.64080	0.2566|0.2566	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	P;D|.	0.61697|.	0.539;0.99|.	B;D|.	0.63033|.	0.12;0.91|.	T|T	0.67825|0.67825	-0.5570|-0.5570	10|6	0.19590|0.87932	T|D	0.45|0	.|.	13.4619|13.4619	0.61231|0.61231	0.0:0.0:0.8423:0.1577|0.0:0.0:0.8423:0.1577	.|.	40;33|.	Q9NR21-4;Q9NR21|.	.;PAR11_HUMAN|.	E|K	33;40|19	ENSP00000380284:A33E;ENSP00000228820:A40E|.	ENSP00000228820:A40E|ENSP00000387481:Q19K	A|Q	-|-	2|1	0|0	PARP11|PARP11	3809345|3809345	1.000000|1.000000	0.71417|0.71417	0.944000|0.944000	0.38274|0.38274	0.998000|0.998000	0.95712|0.95712	8.705000|8.705000	0.91357|0.91357	1.542000|1.542000	0.49330|0.49330	0.563000|0.563000	0.77884|0.77884	GCA|CAG		0.398	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			T	3939084	G	T	3939084	3	4	90	1	0	0	0	0	1	0	0	0	11487	1319	46	2	925	2	PARP11	12	3939084	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	1951547	3939084	129912811	206	24793										
A2M	2	hgsc.bcm.edu	37	chr12	9243952	9243952	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aagtccagcatcttcagacaGgcagaaggcccctgccttcc	9	15	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:9243952G>T	ENST00000318602.7	-	19	2621	c.2314C>A	c.(2314-2316)Ctg>Atg	p.L772M		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	772					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TCTTCAGACAGGCAGAAGGCC	0.547																																																0			12											115	123	120					12																	9243952		2203	4300	6503	9135219	SO:0001583	missense	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2314C>A	12.37:g.9243952G>T	ENSP00000323929:p.Leu772Met		9135219	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	11.22	1.575017	0.28092	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.31510	1.49	5.28	3.46	0.39613	Alpha-2-macroglobulin (1);	0.243199	0.29133	N	0.013045	T	0.39410	0.1077	M	0.64404	1.975	0.29519	N	0.85362	D	0.61697	0.99	P	0.59546	0.859	T	0.32348	-0.9910	10	0.31617	T	0.26	.	3.0815	0.06264	0.1578:0.1708:0.5461:0.1253	.	772	P01023	A2MG_HUMAN	M	772;787	ENSP00000323929:L772M	ENSP00000323929:L772M	L	-	1	2	A2M	9135219	0.091000	0.21658	1.000000	0.80357	0.225000	0.24961	-0.144000	0.10280	0.627000	0.30340	-0.225000	0.12378	CTG		0.547	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9243952	G	T	9243952	3	4	90	1	0	0	0	0	1	0	0	0	4	991	35	2	2182	2	A2M	12	9243952	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	5304868	9243952	124607943	207	24794										
KLRC4	8302	hgsc.bcm.edu	37	chr12	10562102	10562102	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aatggagattttattgccctTaagtttcctttgctgcctct	7	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:10562102T>G	ENST00000309384.1	-	1	254	c.73A>C	c.(73-75)Aag>Cag	p.K25Q	KLRC4-KLRK1_ENST00000539300.1_Nonstop_Mutation_p.*16S	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	25					cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						TTATTGCCCTTAAGTTTCCTT	0.428																																																0			12											227	217	220					12																	10562102		2203	4300	6503	10453369	SO:0001583	missense	8302			U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"Killer cell lectin-like receptors"	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.73A>C	12.37:g.10562102T>G	ENSP00000310216:p.Lys25Gln		10453369	O60851	Missense_Mutation	SNP	ENST00000309384.1	37	CCDS8624.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175784	0.38413	.	.	ENSG00000183542	ENST00000309384	T	0.10668	2.85	4.0	2.83	0.33086	.	0.674231	0.13892	N	0.355553	T	0.29093	0.0723	M	0.79614	2.46	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05321	-1.0892	10	0.44086	T	0.13	.	6.6628	0.23024	0.0:0.1165:0.0:0.8835	.	25	O43908	NKG2F_HUMAN	Q	25	ENSP00000310216:K25Q	ENSP00000310216:K25Q	K	-	1	0	KLRC4	10453369	0.001000	0.12720	0.001000	0.08648	0.036000	0.12997	0.439000	0.21575	0.653000	0.30826	0.377000	0.23210	AAG		0.428	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431		G	10562102	T	G	10562102	3	3	90	1	0	0	0	0	1	0	0	0	8439	1763	61	4	419	4	KLRC4	12	10562102	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1318150	10562102	123289793	208	24795										
TAS2R30	259293	hgsc.bcm.edu	37	chr12	11286425	11286425	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcacaaaaagatgacaaaccAaaaatagcaaaggccccaac	5	11	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:11286425A>T	ENST00000539585.1	-	1	818	c.419T>A	c.(418-420)tTg>tAg	p.L140*	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	140					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						ATGACAAACCAAAAATAGCAA	0.383																																																0			12											118	127	124					12																	11286425		2149	4275	6424	11177692	SO:0001587	stop_gained	259293			AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19112	protein-coding gene	gene with protein product		613963	"taste receptor, type 2, member 47"	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.419T>A	12.37:g.11286425A>T	ENSP00000444736:p.Leu140*		11177692	Q645X7	Nonsense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	28.0	4.879691	0.91740	.	.	ENSG00000256188	ENST00000539585	.	.	.	2.3	1.01	0.19927	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.093	0.14718	0.6894:0.3106:0.0:0.0	.	.	.	.	X	140	.	ENSP00000444736:L140X	L	-	2	0	TAS2R30	11177692	0.008000	0.16893	0.005000	0.12908	0.031000	0.12232	2.378000	0.44309	0.126000	0.18424	0.254000	0.18369	TTG		0.383	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643		T	11286425	A	T	11286425	4	4	90	1	0	0	0	0	0	1	0	0	15612	131	5	5	544	5	TAS2R30	12	11286425	Nonsense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	724323	11286425	122565470	209	24796										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32134982	32134982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tggatggtgttcagactcttGctcaaactaatgaagagaaa	10	6	3	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:32134982G>C	ENST00000312561.4	+	4	1507	c.1093G>C	c.(1093-1095)Gct>Cct	p.A365P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	365																	TCAGACTCTTGCTCAAACTAA	0.358																																																0			12											72	74	74					12																	32134982		2203	4300	6503	32026249	SO:0001583	missense	55196			AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1093G>C	12.37:g.32134982G>C	ENSP00000310338:p.Ala365Pro		32026249	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	8.514	0.867234	0.17250	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.06142	3.98;3.34	4.93	-5.49	0.02584	.	1.161280	0.06333	N	0.706576	T	0.02970	0.0088	N	0.17082	0.46	0.09310	N	1	B	0.17038	0.02	B	0.21546	0.035	T	0.46034	-0.9220	9	.	.	.	.	0.5029	0.00582	0.2083:0.2148:0.246:0.3308	.	365	Q9HCM1	CL035_HUMAN	P	365	ENSP00000310338:A365P;ENSP00000370442:A365P	.	A	+	1	0	C12orf35	32026249	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-1.337000	0.02657	-0.934000	0.03733	-0.300000	0.09419	GCT		0.358	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		C	32134982	G	C	32134982	3	2	90	1	0	0	0	0	1	0	0	0	1686	1319	46	5	1095	5	C12orf35	12	32134982	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	20848557	32134982	101716913	210	24797										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39725513	39725513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttattgatgcccattgacagGaagtgatctagcaggtatcg	11	7	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:39725513G>T	ENST00000361418.5	-	22	3147	c.3132C>A	c.(3130-3132)ttC>ttA	p.F1044L	KIF21A_ENST00000395670.3_Missense_Mutation_p.F1044L|KIF21A_ENST00000361961.3_Missense_Mutation_p.F1031L|KIF21A_ENST00000541463.2_Missense_Mutation_p.F1008L|KIF21A_ENST00000544797.2_Missense_Mutation_p.F1031L			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1044					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				CCATTGACAGGAAGTGATCTA	0.368																																																0			12											185	165	172					12																	39725513		2203	4300	6503	38011780	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3132C>A	12.37:g.39725513G>T	ENSP00000354878:p.Phe1044Leu		38011780	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.83|15.83	2.949172|2.949172	0.53186|0.53186	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463;ENST00000551066|ENST00000552961	D;D;D;D;D;D;D|.	0.88741|.	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42|.	6.07|6.07	3.95|3.95	0.45737|0.45737	Prefoldin (1);|.	0.000000|.	0.56097|.	D|.	0.000028|.	T|T	0.52075|0.52075	0.1712|0.1712	L|L	0.31926|0.31926	0.97|0.97	0.49389|0.49389	D|D	0.999781|0.999781	B;B;B;B;B;B|.	0.30914|.	0.025;0.025;0.118;0.3;0.042;0.088|.	B;B;B;B;B;B|.	0.35182|.	0.022;0.022;0.1;0.197;0.057;0.047|.	T|T	0.46911|0.46911	-0.9157|-0.9157	10|5	0.13108|.	T|.	0.6|.	.|.	11.1785|11.1785	0.48614|0.48614	0.2143:0.0:0.7857:0.0|0.2143:0.0:0.7857:0.0	.|.	1031;1008;1044;1031;1044;98|.	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3;F5H0V8|.	.;.;KI21A_HUMAN;.;.;.|.	L|Y	1031;1044;1044;98;92;1031;1044;1008;65|392	ENSP00000354851:F1031L;ENSP00000379029:F1044L;ENSP00000448792:F92L;ENSP00000445606:F1031L;ENSP00000354878:F1044L;ENSP00000438075:F1008L;ENSP00000447070:F65L|.	ENSP00000344501:F1044L|.	F|S	-|-	3|2	2|0	KIF21A|KIF21A	38011780|38011780	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.323000|2.323000	0.43823|0.43823	1.583000|1.583000	0.49898|0.49898	0.655000|0.655000	0.94253|0.94253	TTC|TCC		0.368	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		T	39725513	G	T	39725513	3	4	90	1	0	0	0	0	1	0	0	0	8309	1165	41	2	1960	2	KIF21A	12	39725513	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	7590531	39725513	94126382	211	24798										
NELL2	4753	hgsc.bcm.edu	37	chr12	45001003	45001003	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgggcaggcacacacattagCggcaatacaggctcctccat	10	13	0	0	rs562088318		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:45001003C>T	ENST00000429094.2	-	15	2116	c.1612G>A	c.(1612-1614)Gct>Act	p.A538T	NELL2_ENST00000437801.2_Missense_Mutation_p.A588T|NELL2_ENST00000395487.2_Missense_Mutation_p.A537T|NELL2_ENST00000452445.2_Missense_Mutation_p.A538T|NELL2_ENST00000333837.4_Missense_Mutation_p.A561T|NELL2_ENST00000551601.1_Missense_Mutation_p.A537T|NELL2_ENST00000549027.1_Missense_Mutation_p.A537T	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	538	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CACACATTAGCGGCAATACAG	0.383													C|||	1	0.000199681	0	0	5008	,	,		17274	0.001		0	False		,,,				2504	0															0			12											88	83	85					12																	45001003		2203	4299	6502	43287270	SO:0001583	missense	4753			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1612G>A	12.37:g.45001003C>T	ENSP00000390680:p.Ala538Thr		43287270	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.276529	0.59758	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684	D;D;D;D;D;D;D	0.91631	-2.24;-2.24;-2.88;-2.24;-2.24;-2.42;-2.24	5.68	3.6	0.41247	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.110795	0.64402	D	0.000004	T	0.76926	0.4056	N	0.04355	-0.22	0.32615	N	0.524155	B;B;B;B;B	0.31680	0.004;0.327;0.335;0.226;0.318	B;B;B;B;B	0.25614	0.001;0.048;0.062;0.017;0.03	T	0.76769	-0.2837	10	0.46703	T	0.11	-11.6453	3.6592	0.08232	0.2587:0.5386:0.1151:0.0876	.	561;588;537;538;537	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	T	537;538;537;538;537;561;588;537	ENSP00000378866:A537T;ENSP00000390680:A538T;ENSP00000449332:A537T;ENSP00000394612:A538T;ENSP00000447927:A537T;ENSP00000327988:A561T;ENSP00000416341:A588T	ENSP00000327988:A561T	A	-	1	0	NELL2	43287270	1.000000	0.71417	0.937000	0.37676	0.985000	0.73830	4.799000	0.62517	1.543000	0.49345	0.655000	0.94253	GCT		0.383	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		T	45001003	C	T	45001003	3	4	90	1	0	0	0	0	1	0	0	0	10365	768	27	1	862	1	NELL2	12	45001003	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5275490	45001003	88850892	212	24799										
SLC16A7	9194	hgsc.bcm.edu	37	chr12	60168872	60168872	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	taggtttttttgcccccattAtattcttggctccatatgct	6	10	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:60168872A>T	ENST00000261187.4	+	4	960	c.796A>T	c.(796-798)Ata>Tta	p.I266L	SLC16A7_ENST00000552024.1_Missense_Mutation_p.I266L|SLC16A7_ENST00000543448.1_Missense_Mutation_p.I167L|SLC16A7_ENST00000547379.1_Missense_Mutation_p.I266L|SLC16A7_ENST00000552432.1_Missense_Mutation_p.I266L	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	266					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	TGCCCCCATTATATTCTTGGC	0.368																																																0			12											87	85	85					12																	60168872		2203	4300	6503	58455139	SO:0001583	missense	9194			AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"Solute carriers"	10928	protein-coding gene	gene with protein product		603654	"solute carrier family 16 (monocarboxylic acid transporters), member 7"			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.796A>T	12.37:g.60168872A>T	ENSP00000261187:p.Ile266Leu		58455139	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623707	0.66901	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448	T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43	5.76	3.06	0.35304	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.100345	0.64402	N	0.000002	T	0.32556	0.0833	L	0.31526	0.94	0.40197	D	0.977473	B	0.16166	0.016	B	0.24006	0.05	T	0.12811	-1.0533	9	.	.	.	.	1.5612	0.02595	0.4732:0.0:0.2456:0.2811	.	266	O60669	MOT2_HUMAN	L	266;266;266;266;266;167	ENSP00000449547:I266L;ENSP00000448071:I266L;ENSP00000448742:I266L;ENSP00000446722:I266L;ENSP00000261187:I266L;ENSP00000443731:I167L	.	I	+	1	0	SLC16A7	58455139	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	6.468000	0.73551	1.057000	0.40506	0.528000	0.53228	ATA		0.368	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		T	60168872	A	T	60168872	3	4	90	1	0	0	0	0	1	0	0	0	14450	449	16	5	806	5	SLC16A7	12	60168872	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	15167869	60168872	73683023	213	24800										
XPOT	11260	hgsc.bcm.edu	37	chr12	64814260	64814260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgaaactagtggaatctttgTgtcaagtattacagtctgct	9	6	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:64814260T>C	ENST00000332707.5	+	8	1331	c.802T>C	c.(802-804)Tgt>Cgt	p.C268R		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	268	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GGAATCTTTGTGTCAAGTATT	0.343																																																0			12											103	108	106					12																	64814260		2203	4299	6502	63100527	SO:0001583	missense	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.802T>C	12.37:g.64814260T>C	ENSP00000327821:p.Cys268Arg		63100527	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.407072	0.42715	.	.	ENSG00000184575	ENST00000332707	T	0.21361	2.01	4.89	4.89	0.63831	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.17365	0.0417	L	0.36672	1.1	0.80722	D	1	B	0.24186	0.099	B	0.14578	0.011	T	0.04509	-1.0946	9	.	.	.	.	15.2127	0.73238	0.0:0.0:0.0:1.0	.	268	O43592	XPOT_HUMAN	R	268	ENSP00000327821:C268R	.	C	+	1	0	XPOT	63100527	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.983000	0.70540	2.140000	0.66376	0.533000	0.62120	TGT		0.343	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		C	64814260	T	C	64814260	3	2	90	1	0	0	0	0	1	0	0	0	17490	1696	59	4	828	4	XPOT	12	64814260	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	4645388	64814260	69037635	214	24801										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86373589	86373589	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atgtgctgaaagagagatggTttaaaacggatcacattttt	10	4	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:86373589T>C	ENST00000604798.1	-	8	2119	c.915A>G	c.(913-915)aaA>aaG	p.K305K	MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000332156.1_Silent_p.K305K|MGAT4C_ENST00000393205.2_Silent_p.K334K|MGAT4C_ENST00000548651.1_Silent_p.K305K|MGAT4C_ENST00000549405.2_Silent_p.K305K|MGAT4C_ENST00000552808.2_Silent_p.K305K			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	305					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AGAGAGATGGTTTAAAACGGA	0.383																																																0			12											84	81	82					12																	86373589		2203	4300	6503	84897720	SO:0001819	synonymous_variant	25834				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.915A>G	12.37:g.86373589T>C			84897720	B4DRH2|Q4G199|Q9UIU5	Silent	SNP	ENST00000604798.1	37	CCDS9030.1																																																																																				0.383	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		C	86373589	T	C	86373589	2	2	90	1	0	0	0	0	0	0	0	1	9577	1722	60	4		4	MGAT4C	12	86373589	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	21559329	86373589	47478306	215	24802										
STAB2	55576	hgsc.bcm.edu	37	chr12	104086631	104086631	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tccattgtcgatggggacaaCgcagccacaaatggagtgat	12	9	0	1	rs703651	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:104086631C>T	ENST00000388887.2	+	31	3543	c.3339C>T	c.(3337-3339)aaC>aaT	p.N1113N		NM_017564.9	NP_060034.9			stabilin 2									p.N1113N(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ATGGGGACAACGCAGCCACAA	0.448													C|||	2343	0.467851	0.4463	0.4092	5008	,	,		18770	0.5585		0.4632	False		,,,				2504	0.4499															1	Substitution - coding silent(1)	stomach(1)	12						C		1941,2465	550.9+/-378.2	420,1101,682	164	139	147		3339	-9.7	0	12	dbSNP_86	147	3825,4775	536.4+/-383.0	839,2147,1314	no	coding-synonymous	STAB2	NM_017564.9		1259,3248,1996	TT,TC,CC		44.4767,44.0536,44.3334		1113/2552	104086631	5766,7240	2203	4300	6503	102610761	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3339C>T	12.37:g.104086631C>T			102610761		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.448	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104086631	C	T	104086631	2	4	90	1	0	0	0	0	0	0	0	1	15277	535	19	1		1	STAB2	12	104086631	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	17713042	104086631	29765264	216	24803										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108641832	108641832	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cacacactggactggctcaaGtttggcaagaaggtgctggt	13	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:108641832G>C	ENST00000332082.4	+	10	2228	c.1410G>C	c.(1408-1410)aaG>aaC	p.K470N	WSCD2_ENST00000549903.1_Missense_Mutation_p.K490N|WSCD2_ENST00000261400.3_Missense_Mutation_p.K490N|WSCD2_ENST00000547525.1_Missense_Mutation_p.K470N			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	470						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						ACTGGCTCAAGTTTGGCAAGA	0.597																																																0			12											71	76	74					12																	108641832		2080	4235	6315	107165962	SO:0001583	missense	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1410G>C	12.37:g.108641832G>C	ENSP00000331933:p.Lys470Asn		107165962	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	9.612	1.131551	0.21041	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.34275	1.37;4.62;1.37;4.62	4.46	2.61	0.31194	.	0.552872	0.17873	N	0.159110	T	0.31606	0.0802	M	0.66939	2.045	0.45172	D	0.998182	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.21965	-1.0230	10	0.51188	T	0.08	-20.9567	3.9791	0.09487	0.2929:0.1987:0.5085:0.0	.	490;470	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	N	470;490;470;490	ENSP00000448047:K470N;ENSP00000261400:K490N;ENSP00000331933:K470N;ENSP00000447272:K490N	ENSP00000261400:K490N	K	+	3	2	WSCD2	107165962	0.961000	0.32948	0.986000	0.45419	0.681000	0.39784	0.104000	0.15313	0.870000	0.35726	-0.137000	0.14449	AAG		0.597	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		C	108641832	G	C	108641832	3	2	90	1	0	0	0	0	1	0	0	0	17447	1020	36	5	1440	5	WSCD2	12	108641832	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	4555201	108641832	25210063	217	24804										
NAA25	80018	hgsc.bcm.edu	37	chr12	112516491	112516491	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cattttttcgaccattctctCagcaaggggcagaaacattg	8	10	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:112516491C>T	ENST00000261745.4	-	6	780	c.532G>A	c.(532-534)Gag>Aag	p.E178K		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	178						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						ACCATTCTCTCAGCAAGGGGC	0.378																																																0			12											168	153	158					12																	112516491		2203	4300	6503	111000874	SO:0001583	missense	0			AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.532G>A	12.37:g.112516491C>T	ENSP00000261745:p.Glu178Lys		111000874	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	36	5.958107	0.97145	.	.	ENSG00000111300	ENST00000261745	T	0.37752	1.18	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.63896	0.2550	M	0.81497	2.545	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.56318	-0.7999	10	0.24483	T	0.36	-16.5813	20.6013	0.99457	0.0:1.0:0.0:0.0	.	178;178	A8K8X0;Q14CX7	.;NAA25_HUMAN	K	178	ENSP00000261745:E178K	ENSP00000261745:E178K	E	-	1	0	NAA25	111000874	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.251000	0.78297	2.878000	0.98634	0.650000	0.86243	GAG		0.378	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112516491	C	T	112516491	3	4	90	1	0	0	0	0	1	0	0	0	10151	835	29	3	2462	3	NAA25	12	112516491	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	3874659	112516491	21335404	218	24805										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124398918	124398918	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctgatgcaccggcgcgtgaaGctgctgggggactgcctgct	16	12	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:124398918G>A	ENST00000409039.3	+	60	10066	c.10041G>A	c.(10039-10041)aaG>aaA	p.K3347K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3347					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GGCGCGTGAAGCTGCTGGGGG	0.602																																																0			12											53	59	57					12																	124398918		2065	4217	6282	122964871	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10041G>A	12.37:g.124398918G>A			122964871	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	6.575	0.474401	0.12521	.	.	ENSG00000197653	ENST00000540041	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	T	0.74726	0.3754	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73739	-0.3888	4	.	.	.	.	18.9088	0.92474	0.0:0.0:1.0:0.0	.	.	.	.	N	275	.	.	S	+	2	0	DNAH10	122964871	1.000000	0.71417	0.951000	0.38953	0.501000	0.33797	2.641000	0.46587	2.449000	0.82847	0.561000	0.74099	AGC		0.602	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124398918	G	A	124398918	2	1	90	1	0	0	0	0	0	0	0	1	4609	962	34	3		3	DNAH10	12	124398918	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	11882427	124398918	9452977	219	24806										
SLC15A4	121260	hgsc.bcm.edu	37	chr12	129299456	129299456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acagaggaagaccacaaaagCaaggccgacgcagacagtgg	13	10	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr12:129299456C>T	ENST00000266771.5	-	2	745	c.706G>A	c.(706-708)Gct>Act	p.A236T	SLC15A4_ENST00000539703.1_5'UTR	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	236					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		ACCACAAAAGCAAGGCCGACG	0.522																																																0			12											186	169	175					12																	129299456		2203	4300	6503	127865409	SO:0001583	missense	121260			AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"Solute carriers"	23090	protein-coding gene	gene with protein product		615806	"solute carrier family 15, member 4"			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.706G>A	12.37:g.129299456C>T	ENSP00000266771:p.Ala236Thr		127865409	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	37	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.351294	0.61183	.	.	ENSG00000139370	ENST00000266771	T	0.06528	3.29	5.79	2.76	0.32466	Major facilitator superfamily domain, general substrate transporter (1);	0.162084	0.56097	D	0.000030	T	0.15696	0.0378	L	0.53561	1.675	0.80722	D	1	P	0.50272	0.933	P	0.57057	0.812	T	0.00775	-1.1571	10	0.72032	D	0.01	.	13.5672	0.61826	0.6397:0.3603:0.0:0.0	.	236	Q8N697	S15A4_HUMAN	T	236	ENSP00000266771:A236T	ENSP00000266771:A236T	A	-	1	0	SLC15A4	127865409	0.992000	0.36948	0.014000	0.15608	0.083000	0.17756	3.077000	0.50089	0.748000	0.32831	0.655000	0.94253	GCT		0.522	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648		T	129299456	C	T	129299456	3	4	90	1	0	0	0	0	1	0	0	0	14438	710	25	3	1055	3	SLC15A4	12	129299456	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	4900538	129299456	4552439	220	24807										
CRYL1	51084	hgsc.bcm.edu	37	chr13	21006393	21006393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgtaggggccgtctccgggtGggggaccagctcaaccagcg	17	13	2	0	rs200561765		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:21006393G>A	ENST00000298248.7	-	5	543	c.481C>T	c.(481-483)Cac>Tac	p.H161Y	CRYL1_ENST00000480748.1_5'UTR|CRYL1_ENST00000382812.1_Missense_Mutation_p.H139Y|MIR4499_ENST00000584834.1_RNA	NM_015974.2	NP_057058.2	Q9Y2S2	CRYL1_HUMAN	crystallin, lambda 1	161					fatty acid metabolic process (GO:0006631)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|L-gulonate 3-dehydrogenase activity (GO:0050104)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)			NS(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		GTCTCCGGGTGGGGGACCAGC	0.592																																																0			13						G	TYR/HIS	0,3996		0,0,1998	50	52	51		481	5.4	1	13		51	2,8300		0,2,4149	yes	missense	CRYL1	NM_015974.2	83	0,2,6147	AA,AG,GG		0.0241,0.0,0.0163	probably-damaging	161/320	21006393	2,12296	1998	4151	6149	19904393	SO:0001583	missense	51084			AF077049	CCDS41871.1	13q11	2008-07-18			ENSG00000165475	ENSG00000165475			18246	protein-coding gene	gene with protein product	"crystallin, lamda 1", "L-gulonate 3-dehydrogenase", "lambda-crystallin homolog"	609877				12527201	Standard	NM_015974		Approved	GDH, lambda-CRY, MGC149525, MGC149526	uc001une.3	Q9Y2S2	OTTHUMG00000016516	ENST00000298248.7:c.481C>T	13.37:g.21006393G>A	ENSP00000298248:p.His161Tyr		19904393	A0PJ43|B3KN92|Q0VDI1|Q7Z4Z9|Q9P0G7	Missense_Mutation	SNP	ENST00000298248.7	37	CCDS41871.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577905	0.65878	0.0	2.41E-4	ENSG00000165475	ENST00000298248;ENST00000382812	T;T	0.76839	-1.05;-1.05	5.43	5.43	0.79202	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.096084	0.64402	D	0.000001	D	0.88749	0.6521	M	0.83012	2.62	0.80722	D	1	D;D	0.69078	0.985;0.997	P;D	0.66497	0.907;0.944	D	0.89483	0.3751	10	0.56958	D	0.05	-37.8474	19.239	0.93875	0.0:0.0:1.0:0.0	.	35;161	B4DWM9;Q9Y2S2	.;CRYL1_HUMAN	Y	161;139	ENSP00000298248:H161Y;ENSP00000372262:H139Y	ENSP00000298248:H161Y	H	-	1	0	CRYL1	19904393	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	8.495000	0.90481	2.533000	0.85409	0.491000	0.48974	CAC		0.592	CRYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044071.1	NM_015974		A	21006393	G	A	21006393	3	1	90	1	0	0	0	0	1	0	0	0	3926	1348	47	3	494	3	CRYL1	13	21006393	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10		21006393	94163485	221	24808										
FLT3	2322	hgsc.bcm.edu	37	chr13	28601271	28601271	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggggtaaaaactgaaattgtGttccttgaaaatctctgtcc	9	7	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:28601271G>T	ENST00000241453.7	-	17	2242	c.2161C>A	c.(2161-2163)Cac>Aac	p.H721N	FLT3_ENST00000537084.1_Missense_Mutation_p.H721N|FLT3_ENST00000380982.4_Missense_Mutation_p.H721N	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	721	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAAATTGTGTTCCTTGAAA	0.368			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13											176	180	179					13																	28601271		2203	4300	6503	27499271	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2161C>A	13.37:g.28601271G>T	ENSP00000241453:p.His721Asn		27499271	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622181	0.66787	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.77229	-1.01;-1.08;-0.82	6.03	5.17	0.71159	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67590	0.2909	N	0.05554	-0.025	0.37573	D	0.919502	D;B	0.57571	0.98;0.038	P;B	0.53912	0.737;0.18	T	0.67585	-0.5633	10	0.02654	T	1	.	16.5522	0.84475	0.0:0.0:0.8684:0.1316	.	721;721	P36888-2;P36888	.;FLT3_HUMAN	N	721	ENSP00000241453:H721N;ENSP00000370369:H721N;ENSP00000438139:H721N	ENSP00000241453:H721N	H	-	1	0	FLT3	27499271	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	3.033000	0.49743	1.515000	0.48885	0.655000	0.94253	CAC		0.368	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			T	28601271	G	T	28601271	3	4	90	1	0	0	0	0	1	0	0	0	5961	1377	48	2	852	2	FLT3	13	28601271	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	7594878	28601271	86568607	222	24809										
MTUS2	23281	hgsc.bcm.edu	37	chr13	29600215	29600215	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaggaggaaaggcggttgggCagtgggaataaggacagtgt	20	3	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:29600215C>A	ENST00000431530.3	+	1	1468	c.1410C>A	c.(1408-1410)ggC>ggA	p.G470G		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	460						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GGCGGTTGGGCAGTGGGAATA	0.507																																																0			13											79	84	82					13																	29600215		1951	4138	6089	28498215	SO:0001819	synonymous_variant	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1410C>A	13.37:g.29600215C>A			28498215	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	37	CCDS45022.1																																																																																				0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		A	29600215	C	A	29600215	2	1	90	1	0	0	0	0	0	0	0	1	9996	697	25	2		2	MTUS2	13	29600215	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	998944	29600215	85569663	223	24810										
BRCA2	675	hgsc.bcm.edu	37	chr13	32911778	32911778	+	Missense_Mutation	SNP	G	G	A													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agatgttattttccaagcagGattttaattcaaaccataat							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:32911778G>A	ENST00000380152.3	+	11	3519	c.3286G>A	c.(3286-3288)Gat>Aat	p.D1096N	BRCA2_ENST00000544455.1_Missense_Mutation_p.D1096N			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1096					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTCCAAGCAGGATTTTAATTC	0.313			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											48	51	50					13																	32911778		2196	4289	6485	31809778	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3286G>A	13.37:g.32911778G>A	ENSP00000369497:p.Asp1096Asn		31809778	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	8.600	0.886605	0.17540	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00958	5.5;5.5	5.75	3.98	0.46160	.	0.541770	0.17997	N	0.155022	T	0.01320	0.0043	M	0.77103	2.36	0.09310	N	1	P	0.43169	0.8	B	0.30646	0.118	T	0.50346	-0.8839	10	0.62326	D	0.03	.	5.845	0.18661	0.1406:0.0:0.585:0.2744	.	1096	P51587	BRCA2_HUMAN	N	1096	ENSP00000369497:D1096N;ENSP00000439902:D1096N	ENSP00000369497:D1096N	D	+	1	0	BRCA2	31809778	0.003000	0.15002	0.148000	0.22405	0.207000	0.24258	0.158000	0.16422	0.742000	0.32697	-0.140000	0.14226	GAT		0.313	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32911778	G	A	32911778	3	1	90	1	0	0	0	0	1	0	0	0	1502	1174	41	3	3324	3	BRCA2	13	32911778	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	3311563	32911778	82258100	224	24811	29	2								
BRCA2	675	hgsc.bcm.edu	37	chr13	32911780	32911780	+	Missense_Mutation	SNP	T	T	G													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atgttattttccaagcaggaTtttaattcaaaccataattt							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:32911780T>G	ENST00000380152.3	+	11	3521	c.3288T>G	c.(3286-3288)gaT>gaG	p.D1096E	BRCA2_ENST00000544455.1_Missense_Mutation_p.D1096E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1096					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CCAAGCAGGATTTTAATTCAA	0.313			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											47	50	49					13																	32911780		2196	4290	6486	31809780	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3288T>G	13.37:g.32911780T>G	ENSP00000369497:p.Asp1096Glu		31809780	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.819127	0.32145	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00856	5.61;5.61	5.75	3.25	0.37280	.	0.541770	0.17997	N	0.155022	T	0.02533	0.0077	M	0.77103	2.36	0.09310	N	1	D	0.58268	0.982	P	0.50109	0.631	T	0.35822	-0.9773	10	0.72032	D	0.01	.	7.9242	0.29865	0.0:0.1778:0.0:0.8222	.	1096	P51587	BRCA2_HUMAN	E	1096	ENSP00000369497:D1096E;ENSP00000439902:D1096E	ENSP00000369497:D1096E	D	+	3	2	BRCA2	31809780	0.024000	0.19004	0.208000	0.23602	0.520000	0.34377	0.338000	0.19858	0.938000	0.37419	0.533000	0.62120	GAT		0.313	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32911780	T	G	32911780	3	3	90	1	0	0	0	0	1	0	0	0	1502	1490	52	4	3326	4	BRCA2	13	32911780	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2	32911780	82258098	225	24812	29	2								
PDS5B	23047	hgsc.bcm.edu	37	chr13	33241960	33241960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctgaagaggacagctcaagcTattgagccatatattaccaa	8	9	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:33241960T>C	ENST00000315596.10	+	7	870	c.684T>C	c.(682-684)gcT>gcC	p.A228A		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	228					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		CAGCTCAAGCTATTGAGCCAT	0.303																																																0			13											53	50	51					13																	33241960		1821	4066	5887	32139960	SO:0001819	synonymous_variant	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.684T>C	13.37:g.33241960T>C			32139960	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	37	CCDS41878.1																																																																																				0.303	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		C	33241960	T	C	33241960	2	2	90	1	0	0	0	0	0	0	0	1	11723	1509	53	4		4	PDS5B	13	33241960	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	330180	33241960	81927918	226	24813										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42882668	42882668	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctcagtattggtgatgacagCactggtagctggtccaattt	11	8	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:42882668C>A	ENST00000025301.2	+	9	5371	c.5196C>A	c.(5194-5196)agC>agA	p.S1732R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1732	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GTGATGACAGCACTGGTAGCT	0.363																																																0			13											123	115	118					13																	42882668		2203	4300	6503	41780668	SO:0001583	missense	11215			AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.5196C>A	13.37:g.42882668C>A	ENSP00000025301:p.Ser1732Arg		41780668	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	C	18.40	3.616296	0.66672	.	.	ENSG00000023516	ENST00000025301	T	0.38240	1.15	5.3	1.58	0.23477	.	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	M	0.74258	2.255	0.43724	D	0.9962	D	0.89917	1.0	D	0.74348	0.983	T	0.55042	-0.8202	10	0.87932	D	0	.	9.4858	0.38928	0.0:0.6454:0.0:0.3546	.	1732	Q9UKA4	AKA11_HUMAN	R	1732	ENSP00000025301:S1732R	ENSP00000025301:S1732R	S	+	3	2	AKAP11	41780668	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	0.819000	0.27308	0.315000	0.23110	0.650000	0.86243	AGC		0.363	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42882668	C	A	42882668	3	1	90	1	0	0	0	0	1	0	0	0	447	709	25	2	5222	2	AKAP11	13	42882668	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	9640708	42882668	72287210	227	24814										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58298928	58298928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acgaaactgtgaatcccactGggaaaaagactttttgtaca	8	8	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:58298928G>A	ENST00000377918.3	+	4	3006	c.2980G>A	c.(2980-2982)Ggg>Agg	p.G994R		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	994					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GAATCCCACTGGGAAAAAGAC	0.418																																					Melanoma(72;952 1291 1619 12849 33676)											0			13											107	104	105					13																	58298928		2203	4300	6503	57196929	SO:0001583	missense	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.2980G>A	13.37:g.58298928G>A	ENSP00000367151:p.Gly994Arg		57196929	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.324683	0.60634	.	.	ENSG00000118946	ENST00000377918	T	0.49720	0.77	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	L	0.40543	1.245	0.58432	D	0.999999	D	0.54047	0.964	P	0.49301	0.606	T	0.33828	-0.9853	9	.	.	.	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	994	O14917	PCD17_HUMAN	R	994	ENSP00000367151:G994R	.	G	+	1	0	PCDH17	57196929	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.597000	0.82733	2.885000	0.99019	0.655000	0.94253	GGG		0.418	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58298928	G	A	58298928	3	1	90	1	0	0	0	0	1	0	0	0	11543	1348	47	3	2994	3	PCDH17	13	58298928	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	15416260	58298928	56870950	228	24815										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60584697	60584697	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cccctacaatgcataccgcaGagagaagtttaaccacatct	6	13	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:60584697G>A	ENST00000400324.4	-	8	1098	c.878C>T	c.(877-879)tCt>tTt	p.S293F	DIAPH3_ENST00000377908.2_Missense_Mutation_p.S282F|DIAPH3_ENST00000267215.4_Missense_Mutation_p.S293F|DIAPH3_ENST00000400330.1_Missense_Mutation_p.S293F|DIAPH3-AS1_ENST00000435636.1_RNA|DIAPH3_ENST00000400320.1_Missense_Mutation_p.S247F|DIAPH3_ENST00000400319.1_Missense_Mutation_p.S223F|DIAPH3-AS1_ENST00000432995.1_RNA|DIAPH3-AS1_ENST00000422052.1_RNA|DIAPH3_ENST00000465066.1_5'UTR	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	293	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GCATACCGCAGAGAGAAGTTT	0.373																																																0			13											47	47	47					13																	60584697		1855	4100	5955	59482698	SO:0001583	missense	81624			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.878C>T	13.37:g.60584697G>A	ENSP00000383178:p.Ser293Phe		59482698	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792342	0.90453	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.81	5.81	0.92471	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.116094	0.64402	D	0.000010	D	0.96030	0.8707	M	0.84433	2.695	0.54753	D	0.999985	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.95968	0.8967	10	0.72032	D	0.01	.	19.6863	0.95981	0.0:0.0:1.0:0.0	.	223;247;282;30;293	A8MYX0;C9JL55;C9JDG1;Q9NSV4-1;Q9NSV4	.;.;.;.;DIAP3_HUMAN	F	293;293;282;247;223;282;223;247;293;30;293	ENSP00000383178:S293F;ENSP00000383184:S293F;ENSP00000367141:S282F;ENSP00000383173:S223F;ENSP00000383174:S247F;ENSP00000267215:S293F	ENSP00000267214:S30F	S	-	2	0	DIAPH3	59482698	1.000000	0.71417	0.933000	0.37362	0.976000	0.68499	9.393000	0.97256	2.746000	0.94184	0.591000	0.81541	TCT		0.373	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60584697	G	A	60584697	3	1	90	1	0	0	0	0	1	0	0	0	4531	942	33	3	2807	3	DIAPH3	13	60584697	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2285769	60584697	54585181	229	24816										
RNF219	79596	hgsc.bcm.edu	37	chr13	79190700	79190700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tattttctggagtactgagcTgaaggcaactaagggacaaa	11	6	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:79190700T>C	ENST00000282003.6	-	6	1254	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R	RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560209.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	399							zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		AGTACTGAGCTGAAGGCAACT	0.423																																																0			13											126	116	119					13																	79190700		2203	4300	6503	78088701	SO:0001583	missense	79596			BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1196A>G	13.37:g.79190700T>C	ENSP00000282003:p.Gln399Arg		78088701	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.000691	0.54254	.	.	ENSG00000152193	ENST00000282003	T	0.14266	2.52	5.88	5.88	0.94601	.	0.000000	0.64402	D	0.000001	T	0.34279	0.0892	M	0.61703	1.905	0.41118	D	0.985797	D	0.76494	0.999	D	0.66084	0.941	T	0.02437	-1.1159	10	0.51188	T	0.08	-21.6407	16.3469	0.83138	0.0:0.0:0.0:1.0	.	399	Q5W0B1	RN219_HUMAN	R	399	ENSP00000282003:Q399R	ENSP00000282003:Q399R	Q	-	2	0	RNF219	78088701	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.078000	0.50096	2.263000	0.75096	0.529000	0.55759	CAG		0.423	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		C	79190700	T	C	79190700	3	2	90	1	0	0	0	0	1	0	0	0	13519	1580	55	4	988	4	RNF219	13	79190700	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	18606003	79190700	35979178	230	24817										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328396	88328396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctctaaaggattggttggaCagcatctcctattcagccct	8	11	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:88328396C>A	ENST00000325089.6	+	2	972	c.753C>A	c.(751-753)gaC>gaA	p.D251E	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	251	LRRCT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ATTGGTTGGACAGCATCTCCT	0.512																																																0			13											106	106	106					13																	88328396		2203	4300	6503	87126397	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.753C>A	13.37:g.88328396C>A	ENSP00000366283:p.Asp251Glu		87126397	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.365106	0.01235	.	.	ENSG00000165300	ENST00000325089	T	0.51071	0.72	5.61	4.77	0.60923	Cysteine-rich flanking region, C-terminal (1);	0.113102	0.64402	D	0.000016	T	0.16171	0.0389	N	0.00483	-1.445	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.10847	-1.0612	9	.	.	.	-22.3528	12.2237	0.54447	0.0:0.9175:0.0:0.0825	.	251	O94991	SLIK5_HUMAN	E	251	ENSP00000366283:D251E	.	D	+	3	2	SLITRK5	87126397	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.839000	0.48207	1.382000	0.46385	-0.339000	0.08088	GAC		0.512	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88328396	C	A	88328396	3	1	90	1	0	0	0	0	1	0	0	0	14783	477	17	2	755	2	SLITRK5	13	88328396	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	9137696	88328396	26841482	231	24818										
DCT	1638	hgsc.bcm.edu	37	chr13	95112465	95112465	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtcccatctgctttatcaaaCccttccaaagcattcctagg	5	14	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:95112465C>A	ENST00000377028.5	-	6	1472	c.1059G>T	c.(1057-1059)ggG>ggT	p.G353G	DCT_ENST00000490854.1_5'Flank|DCT_ENST00000446125.1_Silent_p.G353G	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	353					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CTTTATCAAACCCTTCCAAAG	0.408																																																0			13											75	71	72					13																	95112465		2203	4300	6503	93910466	SO:0001819	synonymous_variant	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1059G>T	13.37:g.95112465C>A			93910466	Q09GT4	Silent	SNP	ENST00000377028.5	37	CCDS9470.1																																																																																				0.408	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			A	95112465	C	A	95112465	2	1	90	1	0	0	0	0	0	0	0	1	4310	494	18	2		2	DCT	13	95112465	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	6784069	95112465	20057413	232	24819										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111077128	111077128	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gggtacaatgggccaccaggAttacaaggattcccgggact	13	10	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr13:111077128A>C	ENST00000360467.5	+	5	534	c.228A>C	c.(226-228)ggA>ggC	p.G76G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	76					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGCCACCAGGATTACAAGGAT	0.572																																																0			13											77	86	83					13																	111077128		1905	4107	6012	109875129	SO:0001819	synonymous_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.228A>C	13.37:g.111077128A>C			109875129	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																				0.572	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		C	111077128	A	C	111077128	2	2	90	1	0	0	0	0	0	0	0	1	3696	320	12	4		4	COL4A2	13	111077128	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	15964663	111077128	4092750	233	24820										
WDHD1	11169	hgsc.bcm.edu	37	chr14	55433308	55433308	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggtggttgtgaaatataactGaacgccaaaattgctcctat	9	7	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr14:55433308G>A	ENST00000360586.3	-	18	2260	c.2195C>T	c.(2194-2196)tCa>tTa	p.S732L	WDHD1_ENST00000421192.1_Missense_Mutation_p.S609L|WDHD1_ENST00000359167.4_Missense_Mutation_p.S250L|WDHD1_ENST00000420358.2_Missense_Mutation_p.S609L	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	732					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						AAATATAACTGAACGCCAAAA	0.313																																																0			14											84	75	78					14																	55433308		2201	4295	6496	54503058	SO:0001583	missense	11169			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2195C>T	14.37:g.55433308G>A	ENSP00000353793:p.Ser732Leu		54503058	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982611	0.74474	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.64991	0.24;0.78;-0.13	5.63	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.77758	0.4178	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.974	T	0.79266	-0.1874	10	0.49607	T	0.09	.	15.8595	0.79012	0.0:0.0:0.8632:0.1368	.	250;732	F8W7P7;O75717	.;WDHD1_HUMAN	L	732;250;609	ENSP00000353793:S732L;ENSP00000352085:S250L;ENSP00000391049:S609L	ENSP00000352085:S250L	S	-	2	0	WDHD1	54503058	1.000000	0.71417	0.806000	0.32338	0.642000	0.38348	9.229000	0.95273	1.368000	0.46115	0.591000	0.81541	TCA		0.313	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		A	55433308	G	A	55433308	3	1	90	1	0	0	0	0	1	0	0	0	17311	1294	45	3	1230	3	WDHD1	14	55433308	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10		55433308	51916232	234	24821										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890617	23890617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctgacactgccttgggaGcacagaaggtggcagcaaag	14	10	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:23890617G>A	ENST00000532292.1	-	1	558	c.464C>T	c.(463-465)gCt>gTt	p.A155V		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	38					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		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)		TGCCTTGGGAGCACAGAAGGT	0.597																																																0			15											38	42	40					15																	23890617		1990	4162	6152	21441710	SO:0001583	missense	54551			AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.464C>T	15.37:g.23890617G>A	ENSP00000433433:p.Ala155Val		21441710		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	G	14.93	2.682514	0.47991	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.08	3.14	0.36123	.	.	.	.	.	T	0.31451	0.0797	N	0.19112	0.55	0.18873	N	0.999988	.	.	.	.	.	.	T	0.19321	-1.0309	5	.	.	.	.	11.9757	0.53089	0.0:0.1771:0.8229:0.0	.	.	.	.	F	187	.	.	L	-	1	0	MAGEL2	21441710	0.016000	0.18221	0.067000	0.19924	0.991000	0.79684	1.589000	0.36644	1.253000	0.44018	0.655000	0.94253	CTC		0.597	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23890617	G	A	23890617	3	1	90	1	0	0	0	0	1	0	0	0	9219	971	34	3	1480	3	MAGEL2	15	23890617	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10		23890617	78640775	235	24822										
HERC2	8924	hgsc.bcm.edu	37	chr15	28422162	28422162	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccgtactcgccgaggccccaGgtgtacagttctccgctgga	12	15	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:28422162G>A	ENST00000261609.7	-	61	9474	c.9366C>T	c.(9364-9366)acC>acT	p.T3122T		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		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)		CGAGGCCCCAGGTGTACAGTT	0.557																																																0			15											56	53	54					15																	28422162		2203	4300	6503	26095757	SO:0001819	synonymous_variant	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9366C>T	15.37:g.28422162G>A			26095757		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.557	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28422162	G	A	28422162	2	1	90	1	0	0	0	0	0	0	0	1	7079	987	35	3		3	HERC2	15	28422162	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	4531545	28422162	74109230	236	24823										
RYR3	6263	hgsc.bcm.edu	37	chr15	34134166	34134166	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaagcggcggtgtggtcagaAggttgagaagccggaagctt	18	6	1	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:34134166A>T	ENST00000389232.4	+	91	13209	c.13139A>T	c.(13138-13140)aAg>aTg	p.K4380M	RYR3_ENST00000415757.3_Missense_Mutation_p.K4375M	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4380					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTGGTCAGAAGGTTGAGAAG	0.463																																																0			15											57	66	63					15																	34134166		1886	4103	5989	31921458	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13139A>T	15.37:g.34134166A>T	ENSP00000373884:p.Lys4380Met		31921458	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.623094	0.46840	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.94613	-3.47	5.28	2.94	0.34122	Ryanodine Receptor TM 4-6 (1);	0.453943	0.23791	N	0.044531	D	0.94735	0.8301	L	0.46157	1.445	0.28144	N	0.929683	P;D	0.67145	0.547;0.996	B;D	0.67382	0.323;0.951	D	0.88996	0.3418	10	0.62326	D	0.03	.	8.637	0.33955	0.8483:0.0:0.1517:0.0	.	4375;4380	Q15413-2;Q15413	.;RYR3_HUMAN	M	4380;4376	ENSP00000373884:K4380M	ENSP00000354735:K4376M	K	+	2	0	RYR3	31921458	0.848000	0.29623	0.928000	0.36995	0.542000	0.35054	1.378000	0.34328	1.035000	0.39972	0.533000	0.62120	AAG		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34134166	A	T	34134166	3	4	90	1	0	0	0	0	1	0	0	0	13807	72	3	5	13501	5	RYR3	15	34134166	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	5712004	34134166	68397226	237	24824										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54307060	54307060	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agctctctttacatgaggatCtttctccatggaaggaatgg	10	8	3	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:54307060C>G	ENST00000260323.11	+	1	1960	c.1960C>G	c.(1960-1962)Ctt>Gtt	p.L654V	UNC13C_ENST00000537900.1_Missense_Mutation_p.L654V|UNC13C_ENST00000545554.1_Missense_Mutation_p.L654V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	654					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACATGAGGATCTTTCTCCATG	0.423																																																0			15											126	124	125					15																	54307060		2001	4171	6172	52094352	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1960C>G	15.37:g.54307060C>G	ENSP00000260323:p.Leu654Val		52094352	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	8.125	0.781830	0.16120	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.83250	-1.7;-1.7;-1.7	5.26	4.34	0.51931	.	.	.	.	.	T	0.68632	0.3022	N	0.24115	0.695	0.26055	N	0.981434	B	0.34372	0.451	B	0.28139	0.086	T	0.59847	-0.7377	9	0.40728	T	0.16	.	7.0008	0.24809	0.0:0.7015:0.1504:0.1481	.	654	Q8NB66	UN13C_HUMAN	V	654	ENSP00000260323:L654V;ENSP00000438156:L654V;ENSP00000442569:L654V	ENSP00000260323:L654V	L	+	1	0	UNC13C	52094352	0.868000	0.29978	1.000000	0.80357	0.995000	0.86356	1.472000	0.35376	1.435000	0.47434	0.650000	0.86243	CTT		0.423	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54307060	C	G	54307060	3	3	90	1	0	0	0	0	1	0	0	0	17026	913	32	5	1962	5	UNC13C	15	54307060	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	20172894	54307060	48224332	238	24825										
HERC1	8925	hgsc.bcm.edu	37	chr15	64041865	64041865	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccatgagaaagagccaaacaAtgactgtctccaatagaaac	7	10	1	4			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:64041865A>G	ENST00000443617.2	-	9	2115	c.2028T>C	c.(2026-2028)caT>caC	p.H676H		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	676					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GAGCCAAACAATGACTGTCTC	0.348																																																0			15											50	45	47					15																	64041865		1850	4093	5943	61828918	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.2028T>C	15.37:g.64041865A>G			61828918	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.348	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	64041865	A	G	64041865	2	3	90	1	0	0	0	0	0	0	0	1	7078	98	4	4		4	HERC1	15	64041865	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9734805	64041865	38489527	239	24826										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77134175	77134175	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atgcccagtatcgagctcttAgatcaattttccgagggtgc	10	10	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:77134175A>C	ENST00000563290.1	-	5	388	c.293T>G	c.(292-294)cTa>cGa	p.L98R	SCAPER_ENST00000324767.7_Missense_Mutation_p.L98R|SCAPER_ENST00000538941.2_5'UTR			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	98						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TCGAGCTCTTAGATCAATTTT	0.408																																																0			15											150	139	142					15																	77134175		1821	4066	5887	74921230	SO:0001583	missense	49855			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.293T>G	15.37:g.77134175A>C	ENSP00000454973:p.Leu98Arg		74921230	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485088	0.84854	.	.	ENSG00000140386	ENST00000324767;ENST00000303521	T	0.30448	1.53	4.94	4.94	0.65067	.	0.000000	0.64402	D	0.000004	T	0.56906	0.2017	M	0.76838	2.35	0.50813	D	0.999893	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.996	T	0.63225	-0.6685	10	0.87932	D	0	.	14.6001	0.68435	1.0:0.0:0.0:0.0	.	98;113	Q6NSF1;Q9BY12-2	.;.	R	98;114	ENSP00000326924:L98R	ENSP00000303560:L114R	L	-	2	0	SCAPER	74921230	1.000000	0.71417	0.795000	0.32087	0.932000	0.56968	8.962000	0.93254	1.869000	0.54173	0.533000	0.62120	CTA		0.408	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		C	77134175	A	C	77134175	3	2	90	1	0	0	0	0	1	0	0	0	13915	420	15	4	4059	4	SCAPER	15	77134175	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	13092310	77134175	25397217	240	24827										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86814931	86814931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gacaggccatgaaatatgttAttacaagtaagttagagcgc	10	6	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:86814931A>G	ENST00000441037.2	+	14	2026	c.1931A>G	c.(1930-1932)tAt>tGt	p.Y644C	AGBL1_ENST00000421325.2_Missense_Mutation_p.Y644C|AGBL1_ENST00000389298.3_Missense_Mutation_p.Y375C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	644					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GAAATATGTTATTACAAGTAA	0.408																																																0			15											150	150	150					15																	86814931		1872	4096	5968	84615935	SO:0001583	missense	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1931A>G	15.37:g.86814931A>G	ENSP00000413001:p.Tyr644Cys		84615935	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.351523	0.41700	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.17213	2.29;2.3	5.21	5.21	0.72293	.	0.140827	0.48286	D	0.000183	T	0.56615	0.1997	H	0.96970	3.915	0.50632	D	0.999881	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	T	0.72623	-0.4237	10	0.87932	D	0	-22.5567	14.566	0.68176	1.0:0.0:0.0:0.0	.	343;375;644	Q96MI9-2;Q96MI9-3;Q96MI9	.;.;CBPC4_HUMAN	C	673;644;375	ENSP00000397173:Y644C;ENSP00000373949:Y375C	ENSP00000373949:Y375C	Y	+	2	0	AGBL1	84615935	1.000000	0.71417	0.396000	0.26296	0.027000	0.11550	8.640000	0.91028	2.100000	0.63781	0.528000	0.53228	TAT		0.408	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		G	86814931	A	G	86814931	3	3	90	1	0	0	0	0	1	0	0	0	375	449	16	4	1981	4	AGBL1	15	86814931	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9680756	86814931	15716461	241	24828										
NR2F2	7026	hgsc.bcm.edu	37	chr15	96877377	96877377	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctgaccaacggggatccccTcaactgccactcgtacctgt	9	16	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:96877377T>C	ENST00000394166.3	+	2	1904	c.515T>C	c.(514-516)cTc>cCc	p.L172P	NR2F2_ENST00000421109.2_Missense_Mutation_p.L39P|NR2F2_ENST00000453270.2_Missense_Mutation_p.L19P|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000394171.2_Missense_Mutation_p.L19P	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	172	Interaction with ZFPM2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GGGGATCCCCTCAACTGCCAC	0.647																																																0			15											123	118	120					15																	96877377		2197	4298	6495	94678381	SO:0001583	missense	7026			M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.515T>C	15.37:g.96877377T>C	ENSP00000377721:p.Leu172Pro		94678381	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	37	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643970	0.67244	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	D;D;D;D	0.94232	-3.38;-3.38;-3.33;-3.33	5.0	5.0	0.66597	Nuclear hormone receptor, ligand-binding (2);	0.068791	0.64402	D	0.000015	D	0.91855	0.7422	M	0.62723	1.935	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.15484	0.013;0.005	D	0.89500	0.3763	10	0.59425	D	0.04	.	14.6933	0.69101	0.0:0.0:0.0:1.0	.	172;39	P24468;Q3KQR7	COT2_HUMAN;.	P	39;172;19;19	ENSP00000401674:L39P;ENSP00000377721:L172P;ENSP00000377726:L19P;ENSP00000389853:L19P	ENSP00000377721:L172P	L	+	2	0	NR2F2	94678381	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.968000	0.87980	1.878000	0.54408	0.459000	0.35465	CTC		0.647	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			C	96877377	T	C	96877377	3	2	90	1	0	0	0	0	1	0	0	0	10659	1551	54	4	568	4	NR2F2	15	96877377	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	10062446	96877377	5654015	242	24829										
TARSL2	123283	hgsc.bcm.edu	37	chr15	102249040	102249040	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cttgctgacttctagtctttCaaaaggttgcttttctttta	6	8	4	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr15:102249040C>T	ENST00000335968.3	-	6	1102	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	296					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCTAGTCTTTCAAAAGGTTGC	0.378																																																0			15											131	127	128					15																	102249040		2203	4300	6503	100066563	SO:0001583	missense	123283			AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.886G>A	15.37:g.102249040C>T	ENSP00000338093:p.Glu296Lys		100066563	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.965373	0.92855	.	.	ENSG00000185418	ENST00000335968;ENST00000539112	T;T	0.12569	2.67;2.67	5.38	4.46	0.54185	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	M	0.85462	2.755	0.80722	D	1	D	0.56968	0.978	P	0.53006	0.715	T	0.17745	-1.0359	10	0.62326	D	0.03	-22.8991	11.622	0.51124	0.0:0.9136:0.0:0.0864	.	296	A2RTX5	SYTC2_HUMAN	K	296	ENSP00000338093:E296K;ENSP00000439899:E296K	ENSP00000338093:E296K	E	-	1	0	TARSL2	100066563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.532000	0.81985	1.246000	0.43901	0.655000	0.94253	GAA		0.378	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334		T	102249040	C	T	102249040	3	4	90	1	0	0	0	0	1	0	0	0	15600	835	29	3	1578	3	TARSL2	15	102249040	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	5371663	102249040	282352	243	24830										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1306347	1306347	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctgcccgtcctggcgagcccGgcctacgtggcccctggtga	14	17	0	1	rs2005937	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:1306347G>C	ENST00000211076.3	+	1	214	c.66G>C	c.(64-66)ccG>ccC	p.P22P	TPSD1_ENST00000397534.2_Silent_p.P15P|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	22			P -> R (in dbSNP:rs3865205). {ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TGGCGAGCCCGGCCTACGTGG	0.721													-|||	1100	0.219649	0.112	0.1571	5008	,	,		14369	0.3641		0.1938	False		,,,				2504	0.2873															0			16											31	38	36					16																	1306347		2197	4298	6495	1246348	SO:0001819	synonymous_variant	23430			AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.66G>C	16.37:g.1306347G>C			1246348	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																				0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			C	1306347	G	C	1306347	2	2	90	1	0	0	0	0	0	0	0	1	16465	1103	39	5		5	TPSD1	16	1306347	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10		1306347	89048406	244	24831										
SMG1	23049	hgsc.bcm.edu	37	chr16	18882777	18882777	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttcttcattaaaacagctgcTtccaaagcccaagtcattaa	4	11	3	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:18882777T>C	ENST00000446231.2	-	16	2623	c.2211A>G	c.(2209-2211)gaA>gaG	p.E737E	SMG1_ENST00000389467.3_Silent_p.E737E|snoU13_ENST00000459248.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	737	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AAACAGCTGCTTCCAAAGCCC	0.343																																																0			16											57	53	54					16																	18882777		1813	4081	5894	18790278	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2211A>G	16.37:g.18882777T>C			18790278	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.343	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18882777	T	C	18882777	2	2	90	1	0	0	0	0	0	0	0	1	14832	1606	56	4		4	SMG1	16	18882777	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	17576430	18882777	71471976	245	24832										
ACSM3	6296	hgsc.bcm.edu	37	chr16	20781479	20781479	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gcaacccctcagaatttctcCaactatgaatccatgaaaca	4	13	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:20781479C>T	ENST00000289416.5	+	2	598	c.123C>T	c.(121-123)tcC>tcT	p.S41S	ACSM3_ENST00000440284.2_Silent_p.S41S|ACSM3_ENST00000450120.2_5'Flank	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	41					cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)	p.S41S(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						AGAATTTCTCCAACTATGAAT	0.418																																																1	Substitution - coding silent(1)	ovary(1)	16											88	84	86					16																	20781479		2201	4300	6501	20688980	SO:0001819	synonymous_variant	6296			D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.123C>T	16.37:g.20781479C>T			20688980	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Silent	SNP	ENST00000289416.5	37	CCDS10589.1																																																																																				0.418	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		T	20781479	C	T	20781479	2	4	90	1	0	0	0	0	0	0	0	1	185	581	21	3		3	ACSM3	16	20781479	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1898702	20781479	69573274	246	24833										
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616166	30616166	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctcgcccgtgtggatgcgctGgtggatgacgagggccgtgc	18	11	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:30616166G>A	ENST00000287461.3	-	3	1259	c.922C>T	c.(922-924)Cag>Tag	p.Q308*	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'UTR	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	308					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			TGGATGCGCTGGTGGATGACG	0.672																																																0			16											57	41	47					16																	30616166		2197	4300	6497	30523667	SO:0001587	stop_gained	115509			BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.922C>T	16.37:g.30616166G>A	ENSP00000287461:p.Gln308*		30523667	Q658J5	Nonsense_Mutation	SNP	ENST00000287461.3	37	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	g	33	5.205899	0.95033	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	.	.	.	5.08	5.08	0.68730	.	0.000000	0.45126	D	0.000388	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-52.947	9.6912	0.40129	0.0923:0.0:0.9077:0.0	.	.	.	.	X	308	.	ENSP00000287461:Q308X	Q	-	1	0	ZNF689	30523667	0.996000	0.38824	1.000000	0.80357	0.673000	0.39480	1.998000	0.40796	2.821000	0.97095	0.555000	0.69702	CAG		0.672	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		A	30616166	G	A	30616166	4	1	90	1	0	0	0	0	0	1	0	0	18133	1357	47	3	584	3	ZNF689	16	30616166	Nonsense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	9834687	30616166	59738587	247	24834										
PRR14	78994	hgsc.bcm.edu	37	chr16	30664106	30664106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctaccatcaggatcctgTccacaggcagccgcctgcct	9	17	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:30664106T>C	ENST00000542965.2	+	3	713	c.257T>C	c.(256-258)gTc>gCc	p.V86A	PRR14_ENST00000300835.4_Missense_Mutation_p.V86A			Q9BWN1	PRR14_HUMAN	proline rich 14	86	Pro-rich.									breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CAGGATCCTGTCCACAGGCAG	0.642																																																0			16											45	45	45					16																	30664106		2197	4300	6497	30571607	SO:0001583	missense	78994			AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.257T>C	16.37:g.30664106T>C	ENSP00000441641:p.Val86Ala		30571607	Q8WTX2	Missense_Mutation	SNP	ENST00000542965.2	37	CCDS10687.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192656	0.38707	.	.	ENSG00000156858	ENST00000300835;ENST00000542965	T;T	0.44083	0.93;0.93	5.3	1.18	0.20946	.	0.936261	0.08886	N	0.879322	T	0.24547	0.0595	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.23691	-1.0181	10	0.20046	T	0.44	-0.876	4.7687	0.13144	0.2504:0.0:0.3196:0.43	.	86	Q9BWN1	PRR14_HUMAN	A	86	ENSP00000300835:V86A;ENSP00000441641:V86A	ENSP00000300835:V86A	V	+	2	0	PRR14	30571607	0.063000	0.20901	0.008000	0.14137	0.333000	0.28666	0.326000	0.19646	0.819000	0.34492	0.477000	0.44152	GTC		0.642	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		C	30664106	T	C	30664106	3	2	90	1	0	0	0	0	1	0	0	0	12620	1667	58	4	267	4	PRR14	16	30664106	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	47940	30664106	59690647	248	24835										
ABCC11	85320	hgsc.bcm.edu	37	chr16	48221275	48221275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cagctgttccaagtcccctgCgaagcagttcaaaagccggc	10	14	1	0	rs138453043		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:48221275C>T	ENST00000394747.1	-	20	3119	c.2770G>A	c.(2770-2772)Gca>Aca	p.A924T	ABCC11_ENST00000394748.1_Missense_Mutation_p.A924T|ABCC11_ENST00000565329.1_5'UTR|ABCC11_ENST00000537808.1_3'UTR|ABCC11_ENST00000356608.2_Missense_Mutation_p.A924T|ABCC11_ENST00000353782.5_Missense_Mutation_p.A924T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	924	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	AAGTCCCCTGCGAAGCAGTTC	0.522																																																0			16						C	THR/ALA,THR/ALA,THR/ALA	0,4402		0,0,2201	53	48	50		2770,2770,2770	-4.9	0	16	dbSNP_134	50	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	58,58,58	0,2,6499	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	924/1383,924/1383,924/1345	48221275	2,13000	2201	4300	6501	46778776	SO:0001583	missense	85320			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2770G>A	16.37:g.48221275C>T	ENSP00000378230:p.Ala924Thr		46778776	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119059	0.77323	0.0	2.33E-4	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.02	-4.87	0.03123	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.727994	0.13006	N	0.421300	T	0.72195	0.3430	N	0.11427	0.14	0.09310	N	0.999999	P;B	0.52170	0.951;0.042	B;B	0.40134	0.32;0.016	T	0.68059	-0.5509	10	0.52906	T	0.07	-3.6884	15.2142	0.73250	0.7913:0.2087:0.0:0.0	.	924;924	Q96J66-2;Q96J66	.;ABCCB_HUMAN	T	924	ENSP00000311326:A924T;ENSP00000349017:A924T;ENSP00000378231:A924T;ENSP00000378230:A924T	ENSP00000311326:A924T	A	-	1	0	ABCC11	46778776	0.005000	0.15991	0.004000	0.12327	0.860000	0.49131	-0.769000	0.04710	-0.377000	0.07930	0.563000	0.77884	GCA		0.522	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		T	48221275	C	T	48221275	3	4	90	1	0	0	0	0	1	0	0	0	51	768	27	1	1418	1	ABCC11	16	48221275	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	17557169	48221275	42133478	249	24836										
ADCY7	113	hgsc.bcm.edu	37	chr16	50346936	50346936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgctcaatgagatcattgccGacttcgacgaggtacagcct	10	11	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:50346936G>A	ENST00000394697.2	+	22	3080	c.2740G>A	c.(2740-2742)Gac>Aac	p.D914N	ADCY7_ENST00000254235.3_Missense_Mutation_p.D914N			P51828	ADCY7_HUMAN	adenylate cyclase 7	914	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		GATCATTGCCGACTTCGACGA	0.567																																																0			16											162	122	135					16																	50346936		2198	4300	6498	48904437	SO:0001583	missense	113			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2740G>A	16.37:g.50346936G>A	ENSP00000378187:p.Asp914Asn		48904437	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	37	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798834	0.90538	.	.	ENSG00000121281	ENST00000394697;ENST00000254235	T;T	0.81415	-1.49;-1.49	5.39	4.44	0.53790	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.46145	U	0.000305	D	0.89132	0.6628	M	0.77712	2.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90388	0.4393	10	0.87932	D	0	.	14.1413	0.65322	0.0722:0.0:0.9278:0.0	.	914	P51828	ADCY7_HUMAN	N	914	ENSP00000378187:D914N;ENSP00000254235:D914N	ENSP00000254235:D914N	D	+	1	0	ADCY7	48904437	1.000000	0.71417	0.712000	0.30502	0.793000	0.44817	9.828000	0.99408	1.276000	0.44395	0.491000	0.48974	GAC		0.567	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			A	50346936	G	A	50346936	3	1	90	1	0	0	0	0	1	0	0	0	299	1058	37	1	2822	1	ADCY7	16	50346936	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2125661	50346936	40007817	250	24837										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67979683	67979683	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgacttctcgctcccgctcaGtcttggtcagtctcatctgc	8	15	6	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:67979683G>A	ENST00000316341.3	-	21	2971	c.2831C>T	c.(2830-2832)aCt>aTt	p.T944I	CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000422611.2_Missense_Mutation_p.T946I|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000572037.1_Missense_Mutation_p.T896I|SLC12A4_ENST00000338335.3_3'UTR|SLC12A4_ENST00000576616.1_Missense_Mutation_p.T944I|SLC12A4_ENST00000537830.2_Missense_Mutation_p.T938I|SLC12A4_ENST00000541864.2_Missense_Mutation_p.T913I	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	944					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CTCCCGCTCAGTCTTGGTCAG	0.602																																																0			16											92	68	76					16																	67979683		2198	4300	6498	66537184	SO:0001583	missense	6560				CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.2831C>T	16.37:g.67979683G>A	ENSP00000318557:p.Thr944Ile		66537184	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486167	0.63962	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000316341	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.43	4.46	0.54185	.	0.055231	0.64402	D	0.000001	T	0.40297	0.1111	L	0.29908	0.895	0.80722	D	1	B;P;P;P;P;B	0.48230	0.391;0.711;0.907;0.809;0.713;0.291	B;B;P;B;B;B	0.48141	0.257;0.19;0.568;0.35;0.35;0.125	T	0.21075	-1.0256	10	0.40728	T	0.16	.	15.3799	0.74648	0.0:0.0:0.8595:0.1405	.	946;938;913;938;944;944	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	I	946;913;938;944	ENSP00000395983:T946I;ENSP00000438334:T913I;ENSP00000445962:T938I;ENSP00000318557:T944I	ENSP00000318557:T944I	T	-	2	0	SLC12A4	66537184	1.000000	0.71417	0.898000	0.35279	0.959000	0.62525	6.627000	0.74258	1.257000	0.44085	0.557000	0.71058	ACT		0.602	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		A	67979683	G	A	67979683	3	1	90	1	0	0	0	0	1	0	0	0	14422	1029	36	3	442	3	SLC12A4	16	67979683	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	17632747	67979683	22375070	251	24838										
WWOX	51741	hgsc.bcm.edu	37	chr16	78466521	78466521	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tctccaacgagctgcaccgtCgcctctccccacgcggggtc	10	19	2	0	rs193001955	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:78466521C>G	ENST00000566780.1	+	8	1294	c.928C>G	c.(928-930)Cgc>Ggc	p.R310G	WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.R310G|WWOX_ENST00000539474.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	310	Interaction with MAPT. {ECO:0000250}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		GCTGCACCGTCGCCTCTCCCC	0.532																																																0			16											121	124	123					16																	78466521		2070	4204	6274	77024022	SO:0001583	missense	51741			AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	12799	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 41C, member 1"	605131	"WW domain-containing oxidoreductase"			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.928C>G	16.37:g.78466521C>G	ENSP00000457230:p.Arg310Gly		77024022	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.585471	0.86748	.	.	ENSG00000186153	ENST00000408984	D	0.90133	-2.62	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.106718	0.64402	D	0.000003	D	0.97263	0.9105	H	0.98218	4.175	0.80722	D	1	D	0.67145	0.996	D	0.63192	0.912	D	0.98030	1.0376	10	0.87932	D	0	.	20.3261	0.98701	0.0:1.0:0.0:0.0	.	310	Q9NZC7	WWOX_HUMAN	G	310	ENSP00000386161:R310G	ENSP00000386161:R310G	R	+	1	0	WWOX	77024022	1.000000	0.71417	0.974000	0.42286	0.423000	0.31445	7.487000	0.81328	2.814000	0.96858	0.655000	0.94253	CGC		0.532	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			G	78466521	C	G	78466521	3	3	90	1	0	0	0	0	1	0	0	0	17454	884	31	5	1020	5	WWOX	16	78466521	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10486838	78466521	11888232	252	24839										
MAF	4094	hgsc.bcm.edu	37	chr16	79628417	79628417	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttccaaaatgtggcgtatccCactgatggctccaacttgcg	9	12	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr16:79628417C>T	ENST00000393350.1	-	0	6194				MAF_ENST00000569649.1_Intron|MAF_ENST00000326043.4_Silent_p.V384V	NM_001031804.2	NP_001026974.1	O75444	MAF_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog						cell development (GO:0048468)|cytokine production (GO:0001816)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of chondrocyte differentiation (GO:0032330)|transcription from RNA polymerase II promoter (GO:0006366)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)	10		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)		TGGCGTATCCCACTGATGGCT	0.398			T	IGH@	MM																																		Dom	yes		16	16q22-q23	4094	v-maf musculoaponeurotic fibrosarcoma oncogene homolog		L	0			16											53	45	48					16																	79628417		2198	4293	6491	78185918	SO:0001624	3_prime_UTR_variant	4094				CCDS10928.1, CCDS42198.1	16q22-q23	2013-07-09	2013-07-09		ENSG00000178573	ENSG00000178573			6776	protein-coding gene	gene with protein product		177075				14998484	Standard	NM_005360		Approved	c-MAF	uc002ffm.3	O75444	OTTHUMG00000137621	ENST00000393350.1:c.*4261G>A	16.37:g.79628417C>T			78185918	Q66I47|Q9UP93	Silent	SNP	ENST00000393350.1	37	CCDS42198.1																																																																																				0.398	MAF-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317037.1			T	79628417	C	T	79628417	1	4	90	0	1	0	0	0	0	0	0	0	9185	581	21	3		3	MAF	16	79628417	3'UTR	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1161896	79628417	10726336	253	24840										
NUP88	4927	hgsc.bcm.edu	37	chr17	5298291	5298291	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agttcctgtaaactatccttAtcttcttcatctaccatgga	4	11	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:5298291A>C	ENST00000573584.1	-	9	1811	c.1302T>G	c.(1300-1302)gaT>gaG	p.D434E		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	434					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						AACTATCCTTATCTTCTTCAT	0.388																																																0			17											148	136	140					17																	5298291		2203	4300	6503	5239015	SO:0001583	missense	4927			Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1302T>G	17.37:g.5298291A>C	ENSP00000458954:p.Asp434Glu		5239015	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.582247	0.65992	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	5.16	1.64	0.23874	.	0.050355	0.85682	D	0.000000	T	0.64505	0.2604	M	0.71581	2.175	0.48632	D	0.999688	P;P;D	0.71674	0.775;0.817;0.998	B;B;D	0.67725	0.428;0.284;0.953	T	0.67292	-0.5707	9	0.05436	T	0.98	9.6813	9.5368	0.39226	0.7131:0.0:0.2869:0.0	.	434;303;434	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	E	434;303	.	ENSP00000225696:D434E	D	-	3	2	NUP88	5239015	0.932000	0.31603	1.000000	0.80357	0.994000	0.84299	0.086000	0.14935	0.144000	0.18951	0.528000	0.53228	GAT		0.388	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		C	5298291	A	C	5298291	3	2	90	1	0	0	0	0	1	0	0	0	10802	446	16	4	959	4	NUP88	17	5298291	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10		5298291	75896919	254	24841										
FXR2	9513	hgsc.bcm.edu	37	chr17	7496124	7496124	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cggcgcctggcacttgctggGgggggttccccaggttctga	17	12	1	1	rs138143492	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:7496124G>C	ENST00000250113.7	-	14	1951	c.1617C>G	c.(1615-1617)ccC>ccG	p.P539P	FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000538513.2_5'Flank|SOX15_ENST00000570788.1_5'Flank|SOX15_ENST00000250055.2_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	539						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		CACTTGCTGGGGGGGGTTCCC	0.612																																																0			17											21	23	22					17																	7496124		1813	4065	5878	7436849	SO:0001819	synonymous_variant	9513			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1617C>G	17.37:g.7496124G>C			7436849	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Silent	SNP	ENST00000250113.7	37	CCDS45604.1																																																																																				0.612	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			C	7496124	G	C	7496124	2	2	90	1	0	0	0	0	0	0	0	1	6135	1219	43	5		5	FXR2	17	7496124	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2197833	7496124	73699086	255	24842										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	90	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	82282	7578406	73616804	256	24843										
MYH1	4619	hgsc.bcm.edu	37	chr17	10401992	10401992	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gatggcatctgtctcatattTggtcctccactgggcaacct	9	12	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:10401992T>G	ENST00000226207.5	-	30	4226	c.4132A>C	c.(4132-4134)Aaa>Caa	p.K1378Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1378					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GTCTCATATTTGGTCCTCCAC	0.517																																																0			17											159	140	146					17																	10401992		2203	4300	6503	10342717	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.4132A>C	17.37:g.10401992T>G	ENSP00000226207:p.Lys1378Gln		10342717	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.872306	0.91587	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	D	0.84589	-1.87	5.41	5.41	0.78517	Myosin tail (1);	0.000000	0.45867	U	0.000322	D	0.94817	0.8326	H	0.95917	3.74	0.58432	D	0.999993	D	0.76494	0.999	D	0.76071	0.987	D	0.96402	0.9297	10	0.87932	D	0	.	15.7287	0.77784	0.0:0.0:0.0:1.0	.	1378	P12882	MYH1_HUMAN	Q	1378;467	ENSP00000226207:K1378Q	ENSP00000226207:K1378Q	K	-	1	0	MYH1	10342717	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.993000	0.88291	2.177000	0.69029	0.533000	0.62120	AAA		0.517	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10401992	T	G	10401992	3	3	90	1	0	0	0	0	1	0	0	0	10059	1821	63	4	1731	4	MYH1	17	10401992	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2823586	10401992	70793218	257	24844										
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19552331	19552331	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acaggcgttcctgtccggccGgtcgcgacctctgcggtttc	13	15	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:19552331G>T	ENST00000176643.6	+	1	493	c.47G>T	c.(46-48)cGg>cTg	p.R16L	ALDH3A2_ENST00000581518.1_Missense_Mutation_p.R16L|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.R16L|Y_RNA_ENST00000578640.1_RNA|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.R16L|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.R16L			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	16					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					CTGTCCGGCCGGTCGCGACCT	0.701																																																0			17											10	12	11					17																	19552331		2164	4256	6420	19492923	SO:0001583	missense	224			L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"Aldehyde dehydrogenases"	403	protein-coding gene	gene with protein product	"fatty aldehyde dehydrogenase"	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.47G>T	17.37:g.19552331G>T	ENSP00000176643:p.Arg16Leu		19492923	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099397	0.56183	.	.	ENSG00000072210	ENST00000446398;ENST00000176643;ENST00000395575;ENST00000339618	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.28	5.28	0.74379	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.170384	0.48767	D	0.000162	T	0.80270	0.4592	M	0.71296	2.17	0.80722	D	1	P;P	0.50943	0.915;0.94	P;P	0.46076	0.46;0.503	T	0.82748	-0.0304	10	0.54805	T	0.06	-14.5518	16.0554	0.80798	0.0:0.0:1.0:0.0	.	16;16	P51648;P51648-2	AL3A2_HUMAN;.	L	16	ENSP00000395845:R16L;ENSP00000176643:R16L;ENSP00000378942:R16L;ENSP00000345774:R16L	ENSP00000176643:R16L	R	+	2	0	ALDH3A2	19492923	0.949000	0.32298	0.974000	0.42286	0.741000	0.42261	1.657000	0.37366	2.457000	0.83068	0.585000	0.79938	CGG		0.701	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			T	19552331	G	T	19552331	3	4	90	1	0	0	0	0	1	0	0	0	498	1116	39	2	49	2	ALDH3A2	17	19552331	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	9150339	19552331	61642879	258	24845										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29204470	29204470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgaacagaaacaaattactcAgactaaatctacaaatgcaa	4	8	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:29204470A>G	ENST00000321990.4	+	16	4199	c.3821A>G	c.(3820-3822)cAg>cGg	p.Q1274R		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1274					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CAAATTACTCAGACTAAATCT	0.303																																																0			17											52	56	55					17																	29204470		2203	4298	6501	26228596	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3821A>G	17.37:g.29204470A>G	ENSP00000313171:p.Gln1274Arg		26228596	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.494112	0.26774	.	.	ENSG00000176208	ENST00000321990	T	0.06608	3.28	5.09	1.58	0.23477	ATPase, AAA+ type, core (1);	2.948060	0.00890	N	0.002224	T	0.05960	0.0155	L	0.31294	0.92	0.09310	N	1	B	0.22414	0.069	B	0.12837	0.008	T	0.35151	-0.9800	10	0.28530	T	0.3	.	4.7657	0.13130	0.6665:0.1619:0.1717:0.0	.	1274	Q96QE3	ATAD5_HUMAN	R	1274	ENSP00000313171:Q1274R	ENSP00000313171:Q1274R	Q	+	2	0	ATAD5	26228596	0.113000	0.22115	0.046000	0.18839	0.939000	0.58152	0.686000	0.25392	0.341000	0.23771	0.397000	0.26171	CAG		0.303	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29204470	A	G	29204470	3	3	90	1	0	0	0	0	1	0	0	0	1077	188	7	4	3883	4	ATAD5	17	29204470	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	9652139	29204470	51990740	259	24846										
NF1	4763	hgsc.bcm.edu	37	chr17	29546045	29546045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tccaagaaaacaggggcccgAaacccaaggcagtacagcag	11	12	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:29546045A>G	ENST00000358273.4	+	14	1933	c.1550A>G	c.(1549-1551)gAa>gGa	p.E517G	NF1_ENST00000431387.4_Missense_Mutation_p.E517G|NF1_ENST00000356175.3_Missense_Mutation_p.E517G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	517					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)|p.N510_E547del(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CAGGGGCCCGAAACCCAAGGC	0.428			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	14	Whole gene deletion(8)|Unknown(5)|Deletion - In frame(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(2)|lung(1)	17											61	59	59					17																	29546045		2203	4300	6503	26570171	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1550A>G	17.37:g.29546045A>G	ENSP00000351015:p.Glu517Gly		26570171	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833390	0.71258	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	T;T;T;T	0.12039	2.72;2.97;3.11;2.81	5.65	5.65	0.86999	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.21062	0.0507	M	0.69823	2.125	0.80722	D	1	B;B;B;P;B	0.42692	0.425;0.081;0.258;0.787;0.361	B;B;B;B;B	0.40199	0.125;0.068;0.11;0.322;0.244	T	0.01757	-1.1280	10	0.72032	D	0.01	.	15.8667	0.79071	1.0:0.0:0.0:0.0	.	517;517;517;517;517	E1P657;P21359-2;P21359;Q14931;P21359-3	.;.;NF1_HUMAN;.;.	G	517;517;517;183	ENSP00000412921:E517G;ENSP00000351015:E517G;ENSP00000348498:E517G;ENSP00000389907:E183G	ENSP00000348498:E517G	E	+	2	0	NF1	26570171	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	8.645000	0.91049	2.152000	0.67230	0.477000	0.44152	GAA		0.428	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29546045	A	G	29546045	3	3	90	1	0	0	0	0	1	0	0	0	10387	246	9	4	1604	4	NF1	17	29546045	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	341575	29546045	51649165	260	24847										
ACCN1	40	hgsc.bcm.edu	37	chr17	31618780	31618780	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctccactcgcggtgcacccgCgtgtgtgacgggaagctgag	15	13	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:31618780C>T	ENST00000359872.6	-	2	1317				ASIC2_ENST00000225823.2_Silent_p.T118T|ASIC2_ENST00000448983.1_5'Flank	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GGTGCACCCGCGTGTGTGACG	0.657																																																0			17											31	31	31					17																	31618780		2203	4296	6499	28642893	SO:0001627	intron_variant	40			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179695G>A	17.37:g.31618780C>T			28642893	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																				0.657	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		T	31618780	C	T	31618780	1	4	90	0	1	0	0	0	0	0	0	0	128	755	27	1		1	ACCN1	17	31618780	Intron	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2072735	31618780	49576430	261	24848										
MED1	5469	hgsc.bcm.edu	37	chr17	37566376	37566376	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atcttcagtctggtgctttgGtttctcaggtggtaatcttg	11	7	5	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:37566376G>T	ENST00000300651.6	-	17	2321	c.2098C>A	c.(2098-2100)Cca>Aca	p.P700T	MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		TGGTGCTTTGGTTTCTCAGGT	0.463										HNSCC(31;0.082)																											Pancreas(21;279 768 2492 4877 24026)											0			17											141	147	145					17																	37566376		2203	4300	6503	34819902	SO:0001583	missense	8930			L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.2098C>A	17.37:g.37566376G>T	ENSP00000300651:p.Pro700Thr		34819902	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000300651.6	37	CCDS11336.1	.	.	.	.	.	.	.	.	.	.	G	3.733	-0.055237	0.07362	.	.	ENSG00000125686	ENST00000300651	T	0.44083	0.93	5.8	5.8	0.92144	.	.	.	.	.	T	0.26702	0.0653	N	0.14661	0.345	0.44485	D	0.997424	B	0.18461	0.028	B	0.13407	0.009	T	0.09465	-1.0673	9	0.16420	T	0.52	-8.3344	14.8426	0.70237	0.0:0.0:0.8562:0.1438	.	700	Q15648	MED1_HUMAN	T	700	ENSP00000300651:P700T	ENSP00000300651:P700T	P	-	1	0	MED1	34819902	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	4.989000	0.63870	2.739000	0.93911	0.561000	0.74099	CCA		0.463	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		T	37566376	G	T	37566376	3	4	90	1	0	0	0	0	1	0	0	0	9455	1261	44	2	2651	2	MED1	17	37566376	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	5947596	37566376	43628834	262	24849										
CBX1	10951	hgsc.bcm.edu	37	chr17	46148800	46148800	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gctggtactcaggagcgttaGttcttgtcatcttttttgtc	10	8	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:46148800G>T	ENST00000393408.3	-	5	1035	c.555C>A	c.(553-555)aaC>aaA	p.N185K	CBX1_ENST00000225603.4_Missense_Mutation_p.N185K	NM_006807.4	NP_006798.1	P83916	CBX1_HUMAN	chromobox homolog 1	185					negative regulation of transcription, DNA-templated (GO:0045892)	chromatin (GO:0000785)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|pericentric heterochromatin (GO:0005721)|spindle (GO:0005819)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)			breast(1)|central_nervous_system(1)|kidney(1)|prostate(1)	4						AGGAGCGTTAGTTCTTGTCAT	0.493																																					NSCLC(136;694 2497 38792 39034)											0			17											111	98	103					17																	46148800		2203	4300	6503	43503799	SO:0001583	missense	10951			U35451	CCDS11525.1	17q21.32	2010-07-06	2010-06-24		ENSG00000108468	ENSG00000108468			1551	protein-coding gene	gene with protein product	"HP1 beta homolog (Drosophila )"	604511	"chromobox homolog 1 (Drosophila HP1 beta)"			9169582	Standard	NM_001127228		Approved	HP1Hs-beta, M31, MOD1, CBX, HP1-BETA	uc002ind.4	P83916	OTTHUMG00000150417	ENST00000393408.3:c.555C>A	17.37:g.46148800G>T	ENSP00000377060:p.Asn185Lys		43503799	P23197	Missense_Mutation	SNP	ENST00000393408.3	37	CCDS11525.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.353344	0.61293	.	.	ENSG00000108468	ENST00000225603;ENST00000393408	.	.	.	5.17	1.75	0.24633	.	0.168352	0.37348	U	0.002129	T	0.45796	0.1360	N	0.08118	0	0.80722	D	1	P	0.51653	0.947	D	0.65140	0.932	T	0.47129	-0.9141	9	0.72032	D	0.01	.	7.2394	0.26088	0.5769:0.0:0.4231:0.0	.	185	P83916	CBX1_HUMAN	K	185	.	ENSP00000225603:N185K	N	-	3	2	CBX1	43503799	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.180000	0.42537	0.392000	0.25172	-0.427000	0.05922	AAC		0.493	CBX1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318016.1	NM_006807		T	46148800	G	T	46148800	3	4	90	1	0	0	0	0	1	0	0	0	2723	1020	36	2	6	2	CBX1	17	46148800	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	8582424	46148800	35046410	263	24850										
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247304	56247304	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aaaaccatctcttaccagggCtgcatgggtcagatcttctt	8	11	4	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:56247304C>T	ENST00000545221.1	+	1	288	c.288C>T	c.(286-288)ggC>ggT	p.G96G		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						CTTACCAGGGCTGCATGGGTC	0.527																																																0			17											113	104	107					17																	56247304		2203	4300	6503	53602303	SO:0001819	synonymous_variant	124538				CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"GPCR / Class A : Olfactory receptors"	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.288C>T	17.37:g.56247304C>T			53602303	Q6IFN8|Q96R75	Silent	SNP	ENST00000545221.1	37	CCDS32688.1																																																																																				0.527	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			T	56247304	C	T	56247304	2	4	90	1	0	0	0	0	0	0	0	1	11087	784	28	3		3	OR4D2	17	56247304	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10098504	56247304	24947906	264	24851										
TEX14	56155	hgsc.bcm.edu	37	chr17	56642287	56642287	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acaaaagcatactactatctTcttttttactgtcagtttct	3	9	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:56642287T>G	ENST00000240361.8	-	29	4230	c.4145A>C	c.(4144-4146)gAa>gCa	p.E1382A	TEX14_ENST00000584699.1_5'Flank|TEX14_ENST00000349033.5_Missense_Mutation_p.E1336A|TEX14_ENST00000389934.3_Missense_Mutation_p.E1376A			Q8IWB6	TEX14_HUMAN	testis expressed 14	1382					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTACTATCTTCTTTTTTACT	0.323																																																0			17											133	125	127					17																	56642287		2202	4297	6499	53997286	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.4145A>C	17.37:g.56642287T>G	ENSP00000240361:p.Glu1382Ala		53997286	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.789798	0.50102	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.26067	1.76;1.76;1.76	4.58	1.16	0.20824	.	0.433332	0.21616	N	0.071714	T	0.28532	0.0706	L	0.54323	1.7	0.22280	N	0.999238	P;P;P	0.51791	0.792;0.948;0.868	B;P;B	0.50490	0.257;0.642;0.443	T	0.09818	-1.0657	10	0.52906	T	0.07	-3.1646	6.0873	0.19975	0.0:0.3217:0.0:0.6783	.	1382;1336;1376	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	A	1382;1376;1336	ENSP00000240361:E1382A;ENSP00000374584:E1376A;ENSP00000268910:E1336A	ENSP00000240361:E1382A	E	-	2	0	TEX14	53997286	1.000000	0.71417	0.913000	0.36048	0.832000	0.47134	0.650000	0.24858	0.013000	0.14918	0.477000	0.44152	GAA		0.323	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			G	56642287	T	G	56642287	3	3	90	1	0	0	0	0	1	0	0	0	15817	1783	62	4	368	4	TEX14	17	56642287	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	394983	56642287	24552923	265	24852										
DUS1L	64118	hgsc.bcm.edu	37	chr17	80017882	80017882	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agctgcttcttttgcttgttCttggacaggacctccgtgcc	10	12	2	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr17:80017882C>T	ENST00000354321.7	-	10	1595	c.1110G>A	c.(1108-1110)aaG>aaA	p.K370K	DUS1L_ENST00000306796.5_Silent_p.K370K			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	370							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	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)			TTTGCTTGTTCTTGGACAGGA	0.632																																																0			17											143	128	133					17																	80017882		2203	4300	6503	77611171	SO:0001819	synonymous_variant	64118				CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.1110G>A	17.37:g.80017882C>T			77611171	A6NHV4|Q96AI3	Silent	SNP	ENST00000354321.7	37	CCDS32775.1																																																																																				0.632	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156		T	80017882	C	T	80017882	2	4	90	1	0	0	0	0	0	0	0	1	4816	912	32	3		3	DUS1L	17	80017882	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	23375595	80017882	1177328	266	24853										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21897130	21897130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	taccgtgcatactgcttgagTcaggtgtttgcatccctggc	11	11	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr18:21897130T>C	ENST00000319481.3	-	11	1059	c.853A>G	c.(853-855)Act>Gct	p.T285A		NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	285	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)	p.T285P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ACTGCTTGAGTCAGGTGTTTG	0.368																																																1	Substitution - Missense(1)	ovary(1)	18											109	106	107					18																	21897130		2203	4300	6503	20151128	SO:0001583	missense	114876			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.853A>G	18.37:g.21897130T>C	ENSP00000320291:p.Thr285Ala		20151128	B7Z7D3|Q9BZF5|Q9NW87	Missense_Mutation	SNP	ENST00000319481.3	37	CCDS11884.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211954	0.79240	.	.	ENSG00000141447	ENST00000319481	T	0.40225	1.04	5.73	5.73	0.89815	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.048710	0.85682	D	0.000000	T	0.55737	0.1939	L	0.50333	1.59	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.75020	0.985;0.97	T	0.49041	-0.8980	10	0.11794	T	0.64	-23.2478	16.0013	0.80294	0.0:0.0:0.0:1.0	.	285;285	B0YJ56;Q9BXW6	.;OSBL1_HUMAN	A	285	ENSP00000320291:T285A	ENSP00000320291:T285A	T	-	1	0	OSBPL1A	20151128	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.896000	0.75665	2.180000	0.69256	0.528000	0.53228	ACT		0.368	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		C	21897130	T	C	21897130	3	2	90	1	0	0	0	0	1	0	0	0	11308	1667	58	4	2071	4	OSBPL1A	18	21897130	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10		21897130	56180118	267	24854										
STK11	6794	hgsc.bcm.edu	37	chr19	1207091	1207091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctgctgggggaaggctcttAcggcaaggtgaaggaggtgc	18	8	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:1207091A>G	ENST00000326873.7	+	1	1352	c.179A>G	c.(178-180)tAc>tGc	p.Y60C	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	60	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGGCTCTTACGGCAAGGTG	0.627		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																												yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(3)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19	GRCh37	CI055775	STK11	I							43	47	45					19																	1207091		2089	4197	6286	1158091	SO:0001583	missense	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.179A>G	19.37:g.1207091A>G	ENSP00000324856:p.Tyr60Cys		1158091	B2RBX7|E7EW76	Missense_Mutation	SNP	ENST00000326873.7	37	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558907	0.86231	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	D	0.84146	-1.81	3.9	3.9	0.45041	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91310	0.7260	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92010	0.5617	10	0.87932	D	0	-28.0487	11.9419	0.52905	1.0:0.0:0.0:0.0	.	60	Q15831	STK11_HUMAN	C	60	ENSP00000324856:Y60C	ENSP00000324856:Y60C	Y	+	2	0	STK11	1158091	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.018000	0.93657	1.416000	0.47057	0.379000	0.24179	TAC		0.627	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		G	1207091	A	G	1207091	3	3	90	1	0	0	0	0	1	0	0	0	15326	391	14	4	181	4	STK11	19	1207091	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10		1207091	57921892	268	24855										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2217862	2217862	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	caccgtgcagcccaacaagcTcccggtcagcattcccctgg	9	18	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:2217862T>C	ENST00000398665.3	+	22	2672	c.2636T>C	c.(2635-2637)cTc>cCc	p.L879P	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	879					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		CCCAACAAGCTCCCGGTCAGC	0.697																																																0			19											18	24	22					19																	2217862		2155	4250	6405	2168862	SO:0001583	missense	84444			AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2636T>C	19.37:g.2217862T>C	ENSP00000381657:p.Leu879Pro		2168862	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.1|23.1	4.370572|4.370572	0.82573|0.82573	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|.	0.46451|.	0.87|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71426|0.71426	0.3338|0.3338	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.976|.	D;P|.	0.87578|.	0.998;0.877|.	T|T	0.71424|0.71424	-0.4597|-0.4597	10|5	0.87932|.	D|.	0|.	-26.054|-26.054	14.2588|14.2588	0.66070|0.66070	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	879;879|.	Q8TEK3;Q8TEK3-2|.	DOT1L_HUMAN;.|.	P|P	879|666	ENSP00000381657:L879P|.	ENSP00000221482:L879P|.	L|S	+|+	2|1	0|0	DOT1L|DOT1L	2168862|2168862	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.879000|0.879000	0.50718|0.50718	7.337000|7.337000	0.79256|0.79256	1.964000|1.964000	0.57103|0.57103	0.334000|0.334000	0.21626|0.21626	CTC|TCC		0.697	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		C	2217862	T	C	2217862	3	2	90	1	0	0	0	0	1	0	0	0	4720	1551	54	4	2722	4	DOT1L	19	2217862	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1010771	2217862	56911121	269	24856										
BRD4	23476	hgsc.bcm.edu	37	chr19	15376429	15376429	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gcttgagttgtgtttggtacCgtggaaacgccaggttttgc	14	7	0	1	rs183675300		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:15376429C>A	ENST00000263377.2	-	5	806	c.585G>T	c.(583-585)acG>acT	p.T195T	BRD4_ENST00000602230.1_5'Flank|BRD4_ENST00000371835.4_Silent_p.T195T|BRD4_ENST00000360016.5_Silent_p.T195T	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	195					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)	p.T195T(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TGTTTGGTACCGTGGAAACGC	0.567			T	C15orf55	lethal midline carcinoma of young people																																		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	2	Substitution - coding silent(2)	ovary(2)	19											293	291	292					19																	15376429		2203	4300	6503	15237429	SO:0001819	synonymous_variant	23476			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.585G>T	19.37:g.15376429C>A			15237429	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																				0.567	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15376429	C	A	15376429	2	1	90	1	0	0	0	0	0	0	0	1	1507	639	23	2		2	BRD4	19	15376429	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	13158567	15376429	43752554	270	24857										
ZNF85	7639	hgsc.bcm.edu	37	chr19	21131694	21131694	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tgaaagtatggatgagtgtaAgatgcacaaaggaggttgta	14	2	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:21131694A>G	ENST00000328178.8	+	4	487	c.374A>G	c.(373-375)aAg>aGg	p.K125R	ZNF85_ENST00000597314.1_3'UTR|ZNF85_ENST00000601023.1_Missense_Mutation_p.K66R|ZNF85_ENST00000345030.6_Missense_Mutation_p.K92R	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	125					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						GATGAGTGTAAGATGCACAAA	0.323																																																0			19											63	65	64					19																	21131694		2203	4299	6502	20923534	SO:0001583	missense	7639			U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.374A>G	19.37:g.21131694A>G	ENSP00000329793:p.Lys125Arg		20923534	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	5.778	0.327924	0.10956	.	.	ENSG00000105750	ENST00000328178;ENST00000345030	T;T	0.05996	3.44;3.36	0.421	0.421	0.16451	.	.	.	.	.	T	0.18841	0.0452	M	0.87269	2.87	0.09310	N	1	B;B;D	0.69078	0.074;0.014;0.997	B;B;P	0.60682	0.085;0.004;0.878	T	0.09796	-1.0658	9	0.56958	D	0.05	.	2.6241	0.04924	0.6069:0.0:0.3931:0.0	.	92;66;125	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	R	125;92	ENSP00000329793:K125R;ENSP00000342340:K92R	ENSP00000329793:K125R	K	+	2	0	ZNF85	20923534	0.000000	0.05858	0.059000	0.19551	0.057000	0.15508	0.077000	0.14738	0.383000	0.24910	0.374000	0.22700	AAG		0.323	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		G	21131694	A	G	21131694	3	3	90	1	0	0	0	0	1	0	0	0	18232	72	3	4	388	4	ZNF85	19	21131694	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	5755265	21131694	37997289	271	24858										
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35504576	35504576	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gcccaacctttcccgagccaGcagcgacgcagaccatgggg	12	16	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:35504576G>T	ENST00000317991.5	+	9	1043	c.851G>T	c.(850-852)aGc>aTc	p.S284I	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.S277I|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.S371I|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.S50I	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	284						integral component of membrane (GO:0016021)		p.S284I(1)|p.S284V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	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)			TCCCGAGCCAGCAGCGACGCA	0.652																																																2	Substitution - Missense(2)	lung(2)	19											31	36	34					19																	35504576		2063	4198	6261	40196416	SO:0001583	missense	57655			AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.851G>T	19.37:g.35504576G>T	ENSP00000441032:p.Ser284Ile		40196416	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.637841	0.47049	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.51574	0.7;1.64;1.66	4.86	4.86	0.63082	.	0.308060	0.28257	N	0.016004	T	0.42675	0.1213	N	0.14661	0.345	0.31455	N	0.670231	P;D;D;P;P	0.64830	0.919;0.989;0.994;0.551;0.889	B;P;P;B;P	0.56960	0.316;0.651;0.81;0.444;0.726	T	0.49263	-0.8958	10	0.56958	D	0.05	.	9.0309	0.36258	0.0982:0.0:0.9018:0.0	.	284;284;50;277;371	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	I	371;50;284;277	ENSP00000423728:S50I;ENSP00000441032:S284I;ENSP00000439267:S277I	ENSP00000441032:S284I	S	+	2	0	GRAMD1A	40196416	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	3.706000	0.54830	2.538000	0.85594	0.485000	0.47835	AGC		0.652	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35504576	G	T	35504576	3	4	90	1	0	0	0	0	1	0	0	0	6768	971	34	2	885	2	GRAMD1A	19	35504576	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	14372882	35504576	23624407	272	24859										
CD22	933	hgsc.bcm.edu	37	chr19	35823643	35823643	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aagtttgatgggacaagactCtatgaaagcacaaaggatgg	12	5	1	3	rs139372163	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:35823643C>T	ENST00000085219.5	+	3	294	c.228C>T	c.(226-228)ctC>ctT	p.L76L	CD22_ENST00000341773.6_Silent_p.L76L|CD22_ENST00000544992.2_Silent_p.L76L|CD22_ENST00000594250.1_Silent_p.L76L|CD22_ENST00000270311.6_5'UTR|CD22_ENST00000536635.2_Silent_p.L76L|U62631.5_ENST00000597110.1_RNA|CD22_ENST00000595419.1_3'UTR|CD22_ENST00000419549.2_5'UTR	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	76	Ig-like V-type.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GGACAAGACTCTATGAAAGCA	0.483																																					Ovarian(42;1009 1133 23674 26041)											0			19						C	,,,	2,4404	4.2+/-10.8	0,2,2201	100	95	97		228,228,228,228	-3	0.1	19	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,,	76/760,76/752,76/671,76/848	35823643	2,13004	2203	4300	6503	40515483	SO:0001819	synonymous_variant	933			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.228C>T	19.37:g.35823643C>T			40515483	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																				0.483	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		T	35823643	C	T	35823643	2	4	90	1	0	0	0	0	0	0	0	1	2991	900	32	3		3	CD22	19	35823643	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	319067	35823643	23305340	273	24860										
ZNF570	148268	hgsc.bcm.edu	37	chr19	37976014	37976014	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aattcatactggagagagacCctatgaatgtaaggaatgca	10	6	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:37976014C>G	ENST00000330173.1	+	5	2019	c.1490C>G	c.(1489-1491)cCc>cGc	p.P497R	CTD-2086O20.3_ENST00000591976.1_lincRNA|ZNF570_ENST00000388801.3_Missense_Mutation_p.P294R|ZNF570_ENST00000586475.1_Missense_Mutation_p.P553R	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P497L(1)		endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAGAGAGACCCTATGAATGT	0.448																																																1	Substitution - Missense(1)	ovary(1)	19											111	114	113					19																	37976014		2203	4300	6503	42667854	SO:0001583	missense	148268			AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.1490C>G	19.37:g.37976014C>G	ENSP00000331540:p.Pro497Arg		42667854	A1L472|B4DMP1	Missense_Mutation	SNP	ENST00000330173.1	37	CCDS12504.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.702627	0.48307	.	.	ENSG00000171827	ENST00000330173;ENST00000388801	T;T	0.17213	2.29;2.29	4.25	4.25	0.50352	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41294	D	0.000910	T	0.38665	0.1049	M	0.62016	1.91	0.41698	D	0.989383	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.25082	-1.0142	10	0.72032	D	0.01	.	14.532	0.67934	0.0:1.0:0.0:0.0	.	294;497	B4DMP1;Q96NI8	.;ZN570_HUMAN	R	497;294	ENSP00000331540:P497R;ENSP00000373453:P294R	ENSP00000331540:P497R	P	+	2	0	ZNF570	42667854	0.985000	0.35326	1.000000	0.80357	0.996000	0.88848	2.814000	0.48010	2.351000	0.79841	0.563000	0.77884	CCC		0.448	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		G	37976014	C	G	37976014	3	3	90	1	0	0	0	0	1	0	0	0	18041	623	22	5	1504	5	ZNF570	19	37976014	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2152371	37976014	21152969	274	24861										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40433812	40433812	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aaactccttgacattcctggCtgaggtgccggggggtgtga	15	9	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:40433812C>A	ENST00000221347.6	-	2	464	c.457G>T	c.(457-459)Gcc>Tcc	p.A153S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	153	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			ACATTCCTGGCTGAGGTGCCG	0.602																																																0			19											51	50	51					19																	40433812		2203	4300	6503	45125652	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.457G>T	19.37:g.40433812C>A	ENSP00000221347:p.Ala153Ser		45125652	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	0.375	-0.932050	0.02359	.	.	ENSG00000090920	ENST00000221347	T	0.18016	2.24	4.37	-5.29	0.02747	.	1.961470	0.02998	N	0.147695	T	0.03520	0.0101	N	0.00707	-1.245	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.27434	-1.0074	10	0.12430	T	0.62	.	1.2234	0.01929	0.442:0.1665:0.1033:0.2883	.	153	Q9Y6R7	FCGBP_HUMAN	S	153	ENSP00000221347:A153S	ENSP00000221347:A153S	A	-	1	0	FCGBP	45125652	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.620000	0.00879	-0.796000	0.04456	-0.150000	0.13652	GCC		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40433812	C	A	40433812	3	1	90	1	0	0	0	0	1	0	0	0	5797	797	28	2	15900	2	FCGBP	19	40433812	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2457798	40433812	18695171	275	24862										
CEACAM1	634	hgsc.bcm.edu	37	chr19	43025455	43025455	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cttgactgtggtcctgttgcAgccagtgactgagttattgg	13	8	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:43025455A>G	ENST00000161559.6	-	4	1056	c.922T>C	c.(922-924)Tgc>Cgc	p.C308R	LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000599389.1_Missense_Mutation_p.C308R|CEACAM1_ENST00000351134.3_Intron|CEACAM1_ENST00000358394.3_Missense_Mutation_p.C308R|CEACAM1_ENST00000308072.4_Missense_Mutation_p.C268R|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000403444.3_Missense_Mutation_p.C308R|CEACAM1_ENST00000352591.5_Missense_Mutation_p.C308R|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.C308R	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	308	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.C308G(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	GTCCTGTTGCAGCCAGTGACT	0.443																																																1	Substitution - Missense(1)	ovary(1)	19											207	187	194					19																	43025455		2203	4300	6503	47717295	SO:0001583	missense	634			M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.922T>C	19.37:g.43025455A>G	ENSP00000161559:p.Cys308Arg		47717295	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	g	0.040	-1.290482	0.01387	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.13657	2.74;2.74;2.74;2.74;2.74;2.57	5.24	3.06	0.35304	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02688	0.0081	N	0.00116	-2.08	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.40813	-0.9543	9	0.22109	T	0.4	.	7.8353	0.29365	0.2631:0.0:0.7369:0.0	.	308;308;308;308;308;308;308;308;308	P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;CEAM1_HUMAN	R	308;308;335;268;308;308;308;268;308;308;308	ENSP00000161559:C308R;ENSP00000351165:C308R;ENSP00000244291:C308R;ENSP00000384709:C308R;ENSP00000384083:C308R;ENSP00000312184:C268R	ENSP00000161559:C308R	C	-	1	0	CEACAM1	47717295	0.002000	0.14202	0.009000	0.14445	0.102000	0.19082	0.507000	0.22675	0.803000	0.34113	-0.227000	0.12334	TGC		0.443	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		G	43025455	A	G	43025455	3	3	90	1	0	0	0	0	1	0	0	0	3193	188	7	4	779	4	CEACAM1	19	43025455	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	2591643	43025455	16103528	276	24863										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44934173	44934173	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttacttttcaagccattctcTccagggttaatgcgatgaag	8	9	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:44934173T>C	ENST00000588931.1	-	6	1216	c.783A>G	c.(781-783)ggA>ggG	p.G261G	ZNF229_ENST00000291187.4_Silent_p.G255G|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G261G(1)		breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AGCCATTCTCTCCAGGGTTAA	0.423																																																1	Substitution - coding silent(1)	ovary(1)	19											101	94	96					19																	44934173		1910	4107	6017	49626013	SO:0001819	synonymous_variant	7772			AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.783A>G	19.37:g.44934173T>C			49626013	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	37	CCDS42574.1																																																																																				0.423	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		C	44934173	T	C	44934173	2	2	90	1	0	0	0	0	0	0	0	1	17821	1538	54	4		4	ZNF229	19	44934173	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	1908718	44934173	14194810	277	24864										
EML2	24139	hgsc.bcm.edu	37	chr19	46128003	46128003	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cccaaacatagaggttccccCcagagtcccccgtgaccacg	8	18	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:46128003C>A	ENST00000245925.3	-	9	865	c.815G>T	c.(814-816)gGg>gTg	p.G272V	EML2_ENST00000587152.1_Missense_Mutation_p.G473V|EML2_ENST00000536630.1_Missense_Mutation_p.G419V|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000589876.1_Missense_Mutation_p.G272V	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	272	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		GAGGTTCCCCCCAGAGTCCCC	0.537																																																0			19											85	63	71					19																	46128003		2203	4300	6503	50819843	SO:0001583	missense	24139			AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"WD repeat domain containing"	18035	protein-coding gene	gene with protein product	"echinoderm MT-associated protein (EMAP)-like protein 70", "microtubule-associated protein like echinoderm EMAP"					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.815G>T	19.37:g.46128003C>A	ENSP00000245925:p.Gly272Val		50819843	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.813421	0.70912	.	.	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.46819	0.86;0.86;4.96	4.09	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.110120	0.64402	D	0.000011	T	0.43986	0.1272	L	0.29908	0.895	0.58432	D	0.999996	D;P;P;P	0.52996	0.957;0.849;0.779;0.554	P;P;B;B	0.52823	0.71;0.467;0.299;0.424	T	0.43147	-0.9409	10	0.87932	D	0	-16.4938	7.6226	0.28193	0.0:0.8844:0.0:0.1156	.	272;438;419;272	B7Z918;B7Z3Q9;B7Z3I2;O95834	.;.;.;EMAL2_HUMAN	V	419;272;473;430	ENSP00000442365:G419V;ENSP00000245925:G272V;ENSP00000382503:G430V	ENSP00000245925:G272V	G	-	2	0	EML2	50819843	0.997000	0.39634	1.000000	0.80357	0.977000	0.68977	2.847000	0.48270	2.117000	0.64856	0.650000	0.86243	GGG		0.537	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		A	46128003	C	A	46128003	3	1	90	1	0	0	0	0	1	0	0	0	5110	623	22	2	1178	2	EML2	19	46128003	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	1193830	46128003	13000980	278	24865										
SPIB	6689	hgsc.bcm.edu	37	chr19	50931488	50931488	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	atgacctaccagaagctggcGcgcgccctccgaaactacgc	10	16	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr19:50931488G>A	ENST00000595883.1	+	6	709	c.684G>A	c.(682-684)gcG>gcA	p.A228A	SPIB_ENST00000439922.2_Silent_p.A137A|SPIB_ENST00000270632.7_3'UTR|CTD-2545M3.6_ENST00000599632.1_Missense_Mutation_p.A363T|SPIB_ENST00000596074.1_3'UTR	NM_001243999.1|NM_001244000.1|NM_003121.4	NP_001230928.1|NP_001230929.1|NP_003112.2	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	228					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)	14		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		AGAAGCTGGCGCGCGCCCTCC	0.662																																																0			19											29	24	26					19																	50931488		2175	4253	6428	55623300	SO:0001819	synonymous_variant	6689				CCDS33080.1, CCDS58674.1, CCDS59412.1	19q13.3-q13.4	2008-07-22				ENSG00000269404			11242	protein-coding gene	gene with protein product		606802				1406622	Standard	NM_003121		Approved	SPI-B	uc002psd.3	Q01892		ENST00000595883.1:c.684G>A	19.37:g.50931488G>A			55623300	A8K9C9|B4DUG6|Q15359	Silent	SNP	ENST00000595883.1	37	CCDS33080.1																																																																																				0.662	SPIB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464744.1	NM_003121		A	50931488	G	A	50931488	2	1	90	1	0	0	0	0	0	0	0	1	15089	1074	38	1		1	SPIB	19	50931488	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	4803485	50931488	8197495	279	24866										
HAO1	54363	hgsc.bcm.edu	37	chr20	7886843	7886843	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aattggcaatgatgtcagtcTtctcagccatttgatatctt	7	8	4	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:7886843T>G	ENST00000378789.3	-	4	730	c.679A>C	c.(679-681)Aga>Cga	p.R227R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	227	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GATGTCAGTCTTCTCAGCCAT	0.408																																																0			20											163	154	157					20																	7886843		2203	4300	6503	7834843	SO:0001819	synonymous_variant	54363			AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.679A>C	20.37:g.7886843T>G			7834843	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																				0.408	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			G	7886843	T	G	7886843	2	3	90	1	0	0	0	0	0	0	0	1	6972	1617	56	4		4	HAO1	20	7886843	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10		7886843	55138677	280	24867										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41076870	41076870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acctccttacctcgtagagcGtgatgaccccattggtctca	8	14	1	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:41076870G>A	ENST00000373187.1	-	9	1549	c.1550C>T	c.(1549-1551)aCg>aTg	p.T517M	PTPRT_ENST00000373193.3_Missense_Mutation_p.T517M|PTPRT_ENST00000373190.1_Missense_Mutation_p.T517M|PTPRT_ENST00000373184.1_Missense_Mutation_p.T517M|PTPRT_ENST00000356100.2_Missense_Mutation_p.T517M|PTPRT_ENST00000373198.4_Missense_Mutation_p.T517M|PTPRT_ENST00000373201.1_Missense_Mutation_p.T517M			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	517	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CTCGTAGAGCGTGATGACCCC	0.502																																																0			20											219	209	212					20																	41076870		1949	4151	6100	40510284	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1550C>T	20.37:g.41076870G>A	ENSP00000362283:p.Thr517Met		40510284	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500049	0.85176	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21;0.21	5.88	5.88	0.94601	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.109581	0.64402	D	0.000009	T	0.78451	0.4285	M	0.87758	2.905	0.58432	D	0.999999	D;D	0.76494	0.996;0.999	P;D	0.63703	0.865;0.917	T	0.81514	-0.0898	10	0.72032	D	0.01	.	17.159	0.86799	0.0:0.0:1.0:0.0	.	517;517	O14522-1;O14522	.;PTPRT_HUMAN	M	517	ENSP00000362286:T517M;ENSP00000362283:T517M;ENSP00000362289:T517M;ENSP00000348408:T517M;ENSP00000362294:T517M;ENSP00000362280:T517M;ENSP00000362297:T517M	ENSP00000348408:T517M	T	-	2	0	PTPRT	40510284	1.000000	0.71417	0.979000	0.43373	0.973000	0.67179	6.746000	0.74866	2.782000	0.95742	0.655000	0.94253	ACG		0.502	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41076870	G	A	41076870	3	1	90	1	0	0	0	0	1	0	0	0	12849	1145	40	1	2928	1	PTPRT	20	41076870	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	33190027	41076870	21948650	281	24868										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45194900	45194900	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaccggcaggaagatgatgaTggtcgccgtgttgctggcaa	16	8	0	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:45194900T>C	ENST00000279027.4	-	11	1480	c.1462A>G	c.(1462-1464)Atc>Gtc	p.I488V	SLC13A3_ENST00000495082.1_Missense_Mutation_p.I441V|SLC13A3_ENST00000396360.1_Missense_Mutation_p.I406V|SLC13A3_ENST00000290317.5_Missense_Mutation_p.I441V|SLC13A3_ENST00000472148.1_Missense_Mutation_p.I406V|SLC13A3_ENST00000435032.1_Missense_Mutation_p.I73V|SLC13A3_ENST00000413164.2_Missense_Mutation_p.I438V	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	488					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AAGATGATGATGGTCGCCGTG	0.617																																																0			20											94	96	95					20																	45194900		2203	4300	6503	44628307	SO:0001583	missense	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1462A>G	20.37:g.45194900T>C	ENSP00000279027:p.Ile488Val		44628307	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.145051	0.57044	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000435032;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082	T;T;T;T;T;T;T	0.02916	4.11;4.11;4.11;4.11;4.11;4.11;4.11	5.25	4.14	0.48551	.	0.159490	0.56097	N	0.000039	T	0.06917	0.0176	L	0.49778	1.585	0.80722	D	1	P;P;P;B;B;P	0.43392	0.603;0.684;0.545;0.395;0.45;0.805	P;P;B;B;P;P	0.52031	0.491;0.453;0.442;0.442;0.578;0.688	T	0.38802	-0.9644	10	0.33141	T	0.24	-17.2953	11.036	0.47802	0.0:0.0736:0.0:0.9264	.	438;73;406;441;390;488	B4DIR8;B4E181;Q8WWT9-3;F6WI18;B4DF27;Q8WWT9	.;.;.;.;.;S13A3_HUMAN	V	441;406;73;488;406;438;441	ENSP00000290317:I441V;ENSP00000379648:I406V;ENSP00000403394:I73V;ENSP00000279027:I488V;ENSP00000420177:I406V;ENSP00000415852:I438V;ENSP00000419621:I441V	ENSP00000279027:I488V	I	-	1	0	SLC13A3	44628307	1.000000	0.71417	0.991000	0.47740	0.686000	0.39977	6.153000	0.71819	0.825000	0.34637	-0.441000	0.05720	ATC		0.617	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			C	45194900	T	C	45194900	3	2	90	1	0	0	0	0	1	0	0	0	14430	1464	51	4	358	4	SLC13A3	20	45194900	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	4118030	45194900	17830620	282	24869										
EYA2	2139	hgsc.bcm.edu	37	chr20	45801436	45801436	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ggctctggcgtgcacggcggCgtggactggatgaggaagct	19	9	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:45801436C>A	ENST00000327619.5	+	12	1493	c.1119C>A	c.(1117-1119)ggC>ggA	p.G373G	EYA2_ENST00000357410.3_Silent_p.G373G|EYA2_ENST00000317304.6_Silent_p.G343G	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	373					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				TGCACGGCGGCGTGGACTGGA	0.607																																					Pancreas(120;56 1725 18501 25218 43520)											0			20											109	88	95					20																	45801436		2203	4300	6503	45234843	SO:0001819	synonymous_variant	2139				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.1119C>A	20.37:g.45801436C>A			45234843	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																				0.607	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244		A	45801436	C	A	45801436	2	1	90	1	0	0	0	0	0	0	0	1	5342	755	27	2		2	EYA2	20	45801436	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	606536	45801436	17224084	283	24870										
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47874091	47874091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ccgccgctggggcctcaccaCctcttcctcctcaatcaccc	6	22	4	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:47874091C>T	ENST00000396105.1	-	8	2773	c.2527G>A	c.(2527-2529)Gtg>Atg	p.V843M	ZNFX1_ENST00000371752.1_Missense_Mutation_p.V843M|ZNFX1_ENST00000371754.4_Missense_Mutation_p.V843M	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	843							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GGCCTCACCACCTCTTCCTCC	0.567																																																0			20											157	141	146					20																	47874091		2203	4300	6503	47307498	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.2527G>A	20.37:g.47874091C>T	ENSP00000379412:p.Val843Met		47307498	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.134012	0.37630	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744;ENST00000455070	D;D;D;T;T	0.86562	-1.85;-2.14;-2.14;-0.77;-1.48	5.87	4.92	0.64577	.	0.832431	0.10823	N	0.630267	D	0.83092	0.5179	L	0.34521	1.04	0.26474	N	0.97524	B	0.33826	0.427	B	0.37601	0.254	T	0.74490	-0.3648	10	0.48119	T	0.1	-7.7614	11.5259	0.50580	0.1405:0.724:0.1355:0.0	.	843	Q9P2E3	ZNFX1_HUMAN	M	843;843;843;843;843;647	ENSP00000360819:V843M;ENSP00000360817:V843M;ENSP00000379412:V843M;ENSP00000360809:V843M;ENSP00000413800:V647M	ENSP00000360809:V843M	V	-	1	0	ZNFX1	47307498	0.933000	0.31639	1.000000	0.80357	0.982000	0.71751	1.426000	0.34870	1.478000	0.48253	0.655000	0.94253	GTG		0.567	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		T	47874091	C	T	47874091	3	4	90	1	0	0	0	0	1	0	0	0	18244	507	18	3	3257	3	ZNFX1	20	47874091	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2072655	47874091	15151429	284	24871										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58467684	58467684	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttattacatagttcaatgttTgttacaggtgtccaacatgc	7	7	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:58467684T>C	ENST00000357552.3	-	23	2091	c.1866A>G	c.(1864-1866)acA>acG	p.T622T	SYCP2_ENST00000371001.2_Silent_p.T622T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	622					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GTTCAATGTTTGTTACAGGTG	0.323																																																0			20											143	132	135					20																	58467684		2202	4298	6500	57901079	SO:0001819	synonymous_variant	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1866A>G	20.37:g.58467684T>C			57901079	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																				0.323	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		C	58467684	T	C	58467684	2	2	90	1	0	0	0	0	0	0	0	1	15471	1799	63	4		4	SYCP2	20	58467684	Silent	SNP	T	TCGA-CI-6624-01C-11D-1826-10	10593593	58467684	4557836	285	24872										
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62378349	62378349	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgcggccgcggcgagtcttcCtcatccttgtcgtccgccaa	11	17	2	0	rs5019252	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:62378349C>T	ENST00000245663.4	-	5	1854	c.1704G>A	c.(1702-1704)gaG>gaA	p.E568E	ZBTB46_ENST00000395104.1_Silent_p.E568E|ZBTB46_ENST00000302995.2_Silent_p.E568E|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	568					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCGAGTCTTCCTCATCCTTGT	0.726													c|||	1350	0.269569	0.1498	0.379	5008	,	,		10337	0.3472		0.336	False		,,,				2504	0.2055															0			20						T		770,3626		79,612,1507	25	24	25		1704	-7.5	0	20	dbSNP_113	25	2820,5768		445,1930,1919	no	coding-synonymous	ZBTB46	NM_025224.3		524,2542,3426	TT,TC,CC		32.8365,17.5159,27.6494		568/590	62378349	3590,9394	2198	4294	6492	61848793	SO:0001819	synonymous_variant	140685			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1704G>A	20.37:g.62378349C>T			61848793	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																				0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62378349	C	T	62378349	2	4	90	1	0	0	0	0	0	0	0	1	17586	680	24	3		3	ZBTB46	20	62378349	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	3910665	62378349	647171	286	24873										
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62378364	62378364	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcttcctcatccttgtcgtcCgccaacagcgcatcctcagg	7	17	3	0	rs12625387	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:62378364C>T	ENST00000245663.4	-	5	1839	c.1689G>A	c.(1687-1689)gcG>gcA	p.A563A	ZBTB46_ENST00000395104.1_Silent_p.A563A|ZBTB46_ENST00000302995.2_Silent_p.A563A|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	563					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCTTGTCGTCCGCCAACAGCG	0.721													C|||	1350	0.269569	0.1392	0.3804	5008	,	,		10252	0.3452		0.3499	False		,,,				2504	0.2065															0			20						C		746,3652		73,600,1526	30	29	29		1689	-0.2	0.3	20	dbSNP_120	29	2911,5675		480,1951,1862	no	coding-synonymous	ZBTB46	NM_025224.3		553,2551,3388	TT,TC,CC		33.904,16.9623,28.1654		563/590	62378364	3657,9327	2199	4293	6492	61848808	SO:0001819	synonymous_variant	140685			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1689G>A	20.37:g.62378364C>T			61848808	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																				0.721	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62378364	C	T	62378364	2	4	90	1	0	0	0	0	0	0	0	1	17586	639	23	1		1	ZBTB46	20	62378364	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	15	62378364	647156	287	24874										
SAMD10	140700	hgsc.bcm.edu	37	chr20	62607160	62607160	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cccatccgctgcagcttctcCgcattcagccgcagcagtgc	9	18	2	0	rs817343	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr20:62607160C>T	ENST00000369886.3	-	4	645	c.471G>A	c.(469-471)gcG>gcA	p.A157A	ZNF512B_ENST00000450537.1_Intron|ZNF512B_ENST00000217130.3_Intron|SAMD10_ENST00000498830.1_5'UTR	NM_080621.4	NP_542188.1	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10	157	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	7	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GCAGCTTCTCCGCATTCAGCC	0.682													C|||	1301	0.259784	0.469	0.17	5008	,	,		18212	0.0456		0.1769	False		,,,				2504	0.3466															0			20						C		1825,2553		410,1005,774	15	18	17		471	-6	0.8	20	dbSNP_86	17	1455,7105		123,1209,2948	no	coding-synonymous	SAMD10	NM_080621.4		533,2214,3722	TT,TC,CC		16.9977,41.6857,25.3517		157/203	62607160	3280,9658	2189	4280	6469	62077604	SO:0001819	synonymous_variant	140700				CCDS13549.1	20q13.33	2013-01-10	2004-07-15	2004-07-16	ENSG00000130590	ENSG00000130590		"Sterile alpha motif (SAM) domain containing"	16129	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 136"	C20orf136			Standard	NM_080621		Approved		uc002yhm.2	Q9BYL1	OTTHUMG00000033011	ENST00000369886.3:c.471G>A	20.37:g.62607160C>T			62077604		Silent	SNP	ENST00000369886.3	37	CCDS13549.1																																																																																				0.682	SAMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080255.1	NM_080621		T	62607160	C	T	62607160	2	4	90	1	0	0	0	0	0	0	0	1	13852	639	23	1		1	SAMD10	20	62607160	Silent	SNP	C	TCGA-CI-6624-01C-11D-1826-10	228796	62607160	418360	288	24875										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41559867	41559867	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tcctccccataagaattaatAgcatggcaggaaaagaaacc	7	10	0	2	rs367614504		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr21:41559867A>G	ENST00000400454.1	-	13	3078	c.2601T>C	c.(2599-2601)gcT>gcC	p.A867A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	867	Ig-like C2-type 9.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AAGAATTAATAGCATGGCAGG	0.398																																					Melanoma(134;970 1778 1785 21664 32388)											0			21						A		0,3730		0,0,1865	113	103	106		2601	-0.6	1	21		106	1,8203		0,1,4101	no	coding-synonymous	DSCAM	NM_001389.3		0,1,5966	GG,GA,AA		0.0122,0.0,0.0084		867/2013	41559867	1,11933	1865	4102	5967	40481737	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.2601T>C	21.37:g.41559867A>G			40481737	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.398	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		G	41559867	A	G	41559867	2	3	90	1	0	0	0	0	0	0	0	1	4779	407	15	4		4	DSCAM	21	41559867	Silent	SNP	A	TCGA-CI-6624-01C-11D-1826-10		41559867	6570028	289	24876										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43802319	43802319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gaaactagacccacctggatGgtccatgacttggggaggta	13	9	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr21:43802319G>A	ENST00000291532.3	-	9	1762	c.807C>T	c.(805-807)acC>acT	p.T269T	TMPRSS3_ENST00000380399.1_Silent_p.T353T|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Silent_p.T269T|TMPRSS3_ENST00000433957.2_Silent_p.T269T|TMPRSS3_ENST00000398405.1_Silent_p.T267T	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	269	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						CCACCTGGATGGTCCATGACT	0.502																																																0			21											82	61	69					21																	43802319		2203	4300	6503	42675388	SO:0001819	synonymous_variant	64699			AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.807C>T	21.37:g.43802319G>A			42675388	D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	37	CCDS13686.1																																																																																				0.502	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			A	43802319	G	A	43802319	2	1	90	1	0	0	0	0	0	0	0	1	16287	1335	47	3		3	TMPRSS3	21	43802319	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	2242452	43802319	4327576	290	24877										
SIK1	150094	hgsc.bcm.edu	37	chr21	44845357	44845357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cctcacgatagattttctccAaattgcttgaatctaatcgt	5	10	3	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr21:44845357A>G	ENST00000270162.6	-	3	335	c.203T>C	c.(202-204)tTg>tCg	p.L68S		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	68	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	GATTTTCTCCAAATTGCTTGA	0.333																																																0			21											83	76	78					21																	44845357		2203	4300	6503	43669785	SO:0001583	missense	150094			BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.203T>C	21.37:g.44845357A>G	ENSP00000270162:p.Leu68Ser		43669785	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716809	0.89205	.	.	ENSG00000142178	ENST00000270162	T	0.64438	-0.1	5.0	5.0	0.66597	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.71160	0.3307	L	0.37800	1.135	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74833	-0.3530	10	0.87932	D	0	.	14.7308	0.69379	1.0:0.0:0.0:0.0	.	68	P57059	SIK1_HUMAN	S	68	ENSP00000270162:L68S	ENSP00000270162:L68S	L	-	2	0	SIK1	43669785	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.804000	0.91921	1.871000	0.54225	0.533000	0.62120	TTG		0.333	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		G	44845357	A	G	44845357	3	3	90	1	0	0	0	0	1	0	0	0	14354	131	5	4	2196	4	SIK1	21	44845357	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	1043038	44845357	3284538	291	24878										
RASD2	23551	hgsc.bcm.edu	37	chr22	35947724	35947724	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	cgaccacggcgagctgtgccGccaggtgcccaccaccgagg	14	17	0	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr22:35947724G>A	ENST00000216127.4	+	3	1088	c.446G>A	c.(445-447)cGc>cAc	p.R149H		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	149					locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						GAGCTGTGCCGCCAGGTGCCC	0.622																																																0			22											53	46	49					22																	35947724		2203	4300	6503	34277670	SO:0001583	missense	23551			AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"tumor endothelial marker 2", "Ras homolog enriched in striatum"	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.446G>A	22.37:g.35947724G>A	ENSP00000216127:p.Arg149His		34277670	O95520|Q5THY8	Missense_Mutation	SNP	ENST00000216127.4	37	CCDS13916.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.560690	0.86335	.	.	ENSG00000100302	ENST00000216127	T	0.80304	-1.36	5.57	5.57	0.84162	Small GTP-binding protein domain (1);	0.047201	0.85682	D	0.000000	D	0.92466	0.7608	M	0.92317	3.295	0.51482	D	0.999923	D	0.89917	1.0	D	0.80764	0.994	D	0.93779	0.7082	10	0.87932	D	0	.	19.5383	0.95264	0.0:0.0:1.0:0.0	.	149	Q96D21	RHES_HUMAN	H	149	ENSP00000216127:R149H	ENSP00000216127:R149H	R	+	2	0	RASD2	34277670	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	6.437000	0.73421	2.632000	0.89209	0.561000	0.74099	CGC		0.622	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310		A	35947724	G	A	35947724	3	1	90	1	0	0	0	0	1	0	0	0	13104	1087	38	1	452	1	RASD2	22	35947724	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10		35947724	15356842	292	24879										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46654759	46654759	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gggtgcaccttagcagtttcGtaagcatgccactttctcaa	9	11	1	0	rs141748832	byFrequency	TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chr22:46654759G>T	ENST00000253255.5	-	1	4460	c.4461C>A	c.(4459-4461)taC>taA	p.Y1487*		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1487					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.Y1487Y(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TAGCAGTTTCGTAAGCATGCC	0.488																																																1	Substitution - coding silent(1)	endometrium(1)	22											152	147	149					22																	46654759		2203	4300	6503	45033423	SO:0001587	stop_gained	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4461C>A	22.37:g.46654759G>T	ENSP00000253255:p.Tyr1487*		45033423	B1AJY3|O95850	Nonsense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	g	37	6.553462	0.97658	.	.	ENSG00000130943	ENST00000253255	.	.	.	5.05	-10.1	0.00402	.	2.461340	0.02328	U	0.073668	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.016	5.5277	0.16967	0.1295:0.3034:0.4453:0.1218	.	.	.	.	X	1487	.	ENSP00000253255:Y1487X	Y	-	3	2	PKDREJ	45033423	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.631000	0.00206	-4.657000	0.00037	-1.241000	0.01538	TAC		0.488	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46654759	G	T	46654759	4	4	90	1	0	0	0	0	0	1	0	0	12001	1140	40	2	2304	2	PKDREJ	22	46654759	Nonsense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	10707035	46654759	4649807	293	24880										
PHKA2	5256	hgsc.bcm.edu	37	chrX	19002035	19002035	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gtccaagcggaccccggaatTgctcctgctccgcatctccc	9	18	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:19002035T>G	ENST00000379942.4	-	1	681	c.16A>C	c.(16-18)Aat>Cat	p.N6H		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	6					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					ACCCCGGAATTGCTCCTGCTC	0.692																																																0			X											67	56	60					X																	19002035		2203	4300	6503	18911956	SO:0001583	missense	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.16A>C	X.37:g.19002035T>G	ENSP00000369274:p.Asn6His		18911956	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.804453	0.90623	.	.	ENSG00000044446	ENST00000379942	D	0.91740	-2.9	4.82	4.82	0.62117	Six-hairpin glycosidase-like (1);	0.215520	0.53938	D	0.000042	D	0.93213	0.7838	M	0.80847	2.515	0.52099	D	0.999949	P	0.43885	0.82	P	0.47470	0.548	D	0.93693	0.7009	10	0.72032	D	0.01	-15.3368	11.4302	0.50036	0.0:0.0:0.0:1.0	.	6	P46019	KPB2_HUMAN	H	6	ENSP00000369274:N6H	ENSP00000369274:N6H	N	-	1	0	PHKA2	18911956	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.844000	0.62846	1.908000	0.55244	0.441000	0.28932	AAT		0.692	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		G	19002035	T	G	19002035	3	3	90	1	0	0	0	0	1	0	0	0	11875	1812	63	4	3823	4	PHKA2	23	19002035	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10		19002035	136268525	294	24881										
TAB3	257397	hgsc.bcm.edu	37	chrX	30877657	30877657	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aatttcagggaaacgttgtcGaagatcatggagaacctgaa	11	6	2	3			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:30877657G>A	ENST00000378933.1	-	2	226	c.49C>T	c.(49-51)Cga>Tga	p.R17*	TAB3_ENST00000378932.2_Nonsense_Mutation_p.R17*|TAB3_ENST00000288422.2_Nonsense_Mutation_p.R17*|TAB3_ENST00000378930.3_Nonsense_Mutation_p.R17*	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	17	CUE. {ECO:0000255|PROSITE- ProRule:PRU00468}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						AAACGTTGTCGAAGATCATGG	0.453																																					Pancreas(164;1598 1985 29022 43301 49529)											0			X											98	76	84					X																	30877657		2202	4300	6502	30787578	SO:0001587	stop_gained	257397			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.49C>T	X.37:g.30877657G>A	ENSP00000368215:p.Arg17*		30787578	A6NDD9|Q6VQR0	Nonsense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	G	42	9.311963	0.99133	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	.	.	.	5.36	5.36	0.76844	.	0.118609	0.56097	D	0.000025	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8473	18.178	0.89767	0.0:0.0:1.0:0.0	.	.	.	.	X	17	.	ENSP00000288422:R17X	R	-	1	2	TAB3	30787578	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.046000	0.76592	2.229000	0.72834	0.506000	0.49869	CGA		0.453	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		A	30877657	G	A	30877657	4	1	90	1	0	0	0	0	0	1	0	0	15536	1066	37	1	2117	1	TAB3	23	30877657	Nonsense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	11875622	30877657	124392903	295	24882										
CASK	8573	hgsc.bcm.edu	37	chrX	41446234	41446234	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agggtaacatgaaatttcttCcaatacctaaaaaataaaca	4	7	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:41446234C>A	ENST00000378163.1	-	14	1714	c.1240G>T	c.(1240-1242)Gaa>Taa	p.E414*	CASK_ENST00000378158.1_Nonsense_Mutation_p.E414*|CASK_ENST00000361962.4_Nonsense_Mutation_p.E414*|CASK_ENST00000318588.9_Nonsense_Mutation_p.E414*|CASK_ENST00000421587.2_Nonsense_Mutation_p.E408*|CASK_ENST00000442742.2_Nonsense_Mutation_p.E414*|CASK_ENST00000378154.1_Nonsense_Mutation_p.E414*|CASK_ENST00000378166.4_Nonsense_Mutation_p.E414*			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	414	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)	p.E414*(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						GAAATTTCTTCCAATACCTAA	0.264																																					NSCLC(42;104 1086 3090 27189 35040)											1	Substitution - Nonsense(1)	ovary(1)	X											75	68	70					X																	41446234		2202	4294	6496	41331178	SO:0001587	stop_gained	8573			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1240G>T	X.37:g.41446234C>A	ENSP00000367405:p.Glu414*		41331178	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Nonsense_Mutation	SNP	ENST00000378163.1	37		.	.	.	.	.	.	.	.	.	.	C	39	7.620493	0.98393	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378179;ENST00000378158;ENST00000378166;ENST00000442742;ENST00000378154	.	.	.	5.33	5.33	0.75918	.	0.000000	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	18.0832	0.89449	0.0:1.0:0.0:0.0	.	.	.	.	X	408;414;414;414;29;414;414;414;414	.	ENSP00000322727:E414X	E	-	1	0	CASK	41331178	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.408000	0.80041	2.206000	0.71126	0.506000	0.49869	GAA		0.264	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		A	41446234	C	A	41446234	4	1	90	1	0	0	0	0	0	1	0	0	2671	864	30	2	1596	2	CASK	23	41446234	Nonsense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	10568577	41446234	113824326	296	24883										
AR	367	hgsc.bcm.edu	37	chrX	66765576	66765576	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	accatgcaactccttcagcaAcagcagcaggaagcagtatc	8	13	1	0			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:66765576A>C	ENST00000374690.3	+	1	1112	c.588A>C	c.(586-588)caA>caC	p.Q196H	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q196H|AR_ENST00000504326.1_Missense_Mutation_p.Q196H	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	194	Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	TCCTTCAGCAACAGCAGCAGG	0.607									Androgen Insensitivity Syndrome																																							0			X											26	26	26					X																	66765576		2203	4300	6503	66682301	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.588A>C	X.37:g.66765576A>C	ENSP00000363822:p.Gln196His		66682301	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.95	2.092505	0.36952	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78481	-1.18;-1.18;-1.18	5.04	-0.138	0.13464	.	0.180204	0.37857	N	0.001902	T	0.72827	0.3509	L	0.57130	1.785	0.26175	N	0.979816	B;B;B	0.25272	0.067;0.106;0.122	B;B;B	0.35813	0.092;0.211;0.069	T	0.65170	-0.6233	10	0.54805	T	0.06	.	7.738	0.28825	0.6116:0.0:0.3884:0.0	.	196;196;194	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	H	6;196;196;196;188	ENSP00000363822:Q196H;ENSP00000421155:Q196H;ENSP00000379359:Q196H	ENSP00000363822:Q196H	Q	+	3	2	AR	66682301	0.967000	0.33354	0.864000	0.33941	0.971000	0.66376	-0.113000	0.10774	-0.394000	0.07727	0.414000	0.27820	CAA		0.607	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66765576	A	C	66765576	3	2	90	1	0	0	0	0	1	0	0	0	836	40	2	4	590	4	AR	23	66765576	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	25319342	66765576	88504984	297	24884										
EDA	1896	hgsc.bcm.edu	37	chrX	69176977	69176977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	aagcaaaagcaatgaaggagCagatggtaagtctactcagt	11	6	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:69176977C>T	ENST00000374552.4	+	2	739	c.497C>T	c.(496-498)gCa>gTa	p.A166V	EDA_ENST00000524573.1_Missense_Mutation_p.A166V|EDA_ENST00000502251.1_3'UTR|EDA_ENST00000374553.2_Missense_Mutation_p.A166V	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	166					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.A166E(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						AATGAAGGAGCAGATGGTAAG	0.398																																																2	Substitution - Missense(2)	kidney(2)	X											121	114	117					X																	69176977		2203	4300	6503	69093702	SO:0001583	missense	1896			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.497C>T	X.37:g.69176977C>T	ENSP00000363680:p.Ala166Val		69093702	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467275	0.43839	.	.	ENSG00000158813	ENST00000513754;ENST00000374552;ENST00000374553;ENST00000524573;ENST00000503592	T;T;T;D	0.91792	-0.55;-0.55;-0.55;-2.91	4.85	4.85	0.62838	.	0.629040	0.15696	N	0.249183	D	0.84019	0.5380	N	0.08118	0	0.80722	D	1	B;B;B	0.22851	0.062;0.076;0.062	B;B;B	0.28011	0.051;0.085;0.051	T	0.80279	-0.1449	10	0.42905	T	0.14	-0.3066	12.2378	0.54526	0.0:1.0:0.0:0.0	.	166;166;166	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	V	166;166;166;166;34	ENSP00000363680:A166V;ENSP00000363681:A166V;ENSP00000432585:A166V;ENSP00000423037:A34V	ENSP00000363680:A166V	A	+	2	0	EDA	69093702	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.515000	0.45512	2.378000	0.81104	0.594000	0.82650	GCA		0.398	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		T	69176977	C	T	69176977	3	4	90	1	0	0	0	0	1	0	0	0	4914	710	25	3	604	3	EDA	23	69176977	Missense_Mutation	SNP	C	TCGA-CI-6624-01C-11D-1826-10	2411401	69176977	86093583	298	24885										
POU3F4	5456	hgsc.bcm.edu	37	chrX	82764016	82764016	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ctgtatggtaacgtgttctcGcagaccaccatctgcaggtt	10	11	2	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:82764016G>A	ENST00000373200.2	+	1	748	c.684G>A	c.(682-684)tcG>tcA	p.S228S	RP3-326L13.2_ENST00000607095.1_RNA|RP3-326L13.3_ENST00000607789.1_lincRNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	228	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						ACGTGTTCTCGCAGACCACCA	0.527																																																0			X											81	62	68					X																	82764016		2203	4300	6503	82650672	SO:0001819	synonymous_variant	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.684G>A	X.37:g.82764016G>A			82650672	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	37	CCDS14450.1																																																																																				0.527	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		A	82764016	G	A	82764016	2	1	90	1	0	0	0	0	0	0	0	1	12308	1074	38	1		1	POU3F4	23	82764016	Silent	SNP	G	TCGA-CI-6624-01C-11D-1826-10	13587039	82764016	72506544	299	24886										
NRK	203447	hgsc.bcm.edu	37	chrX	105190320	105190320	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	ttcacaggtatttccaacacTtgatcataagccagtgacag	7	10	2	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:105190320T>A	ENST00000243300.9	+	26	4520	c.4217T>A	c.(4216-4218)cTt>cAt	p.L1406H	NRK_ENST00000428173.2_Missense_Mutation_p.L1407H|NRK_ENST00000540278.1_5'Flank	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1406	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						TTTCCAACACTTGATCATAAG	0.378										HNSCC(51;0.14)																																						0			X											64	54	57					X																	105190320		1839	4080	5919	105076976	SO:0001583	missense	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.4217T>A	X.37:g.105190320T>A	ENSP00000434830:p.Leu1406His		105076976	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	T	12.45	1.942487	0.34283	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.06449	3.3;3.3	5.98	2.21	0.28008	Citron-like (2);	3.348890	0.00861	N	0.001928	T	0.06917	0.0176	L	0.29908	0.895	0.80722	D	1	B	0.17038	0.02	B	0.19946	0.027	T	0.28073	-1.0055	10	0.87932	D	0	.	3.6777	0.08298	0.1327:0.0727:0.1355:0.6591	.	1406	Q7Z2Y5	NRK_HUMAN	H	1406;1407	ENSP00000434830:L1406H;ENSP00000438378:L1407H	ENSP00000434830:L1406H	L	+	2	0	NRK	105076976	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	1.748000	0.38308	0.026000	0.15269	0.486000	0.48141	CTT		0.378	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105190320	T	A	105190320	3	1	90	1	0	0	0	0	1	0	0	0	10686	1609	56	5	4319	5	NRK	23	105190320	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	22426304	105190320	50080240	300	24887										
RBMX	27316	hgsc.bcm.edu	37	chrX	135956571	135956572	+	Frame_Shift_Ins	INS	-	-	GG													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	gactgcttccaccataagatINSggcgggggccctcgtgtagg					rs369155856		TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:135956571_135956572insGG	ENST00000320676.7	-	9	1059_1060	c.905_906insCC	c.(904-906)ccafs	p.P302fs	RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Frame_Shift_Ins_p.P174fs|RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000570135.1_Frame_Shift_Ins_p.P167fs	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	302					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CACCATAAGATGGCGGGGGCCC	0.465																																																0			X																																								135784238	SO:0001589	frameshift_variant	27316				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"RNA binding motif (RRM) containing"	9910	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G"	300199	"RNA binding motif protein, X chromosome"			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.904_905dupCC	X.37:g.135956572_135956573dupGG	ENSP00000359645:p.Pro302fs		135784237	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Frame_Shift_Ins	INS	ENST00000320676.7	37	CCDS14661.1																																																																																				0.465	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139		GG	135956572	-	GG	135956571	7	5	90	1	0	1	1	0	0	0	0	0	13188	1451	51	0	328	0	RBMX	23	135956571	Frame_Shift_Ins	INS	-	TCGA-CI-6624-01C-11D-1826-10	30766251	135956571	19313989	301	24888										
GPR101	83550	hgsc.bcm.edu	37	chrX	136113264	136113265	+	Missense_Mutation	DNP	GG	GG	CA													0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acgctgagaatagtgtagctGgggctggccccccagatcat							TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:136113264_136113265GG>CA	ENST00000298110.1	-	1	568_569	c.569_570CC>TG	c.(568-570)cCC>cTG	p.P190L		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					TAGTGTAGCTGGGGCTGGCCCC	0.579																																																0			X																																								135940930|135940931	SO:0001583	missense	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.569_570delinsCA	X.37:g.136113264_136113265delinsCA	ENSP00000298110:p.Pro190Leu		135940930|135940931	Q5JSM8|Q8NG93	Silent|Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1																																																																																				0.579	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			CA	136113265	GG	CA	136113264	3	2	90	1	0	0	0	0	1	0	0	0	6642	1335	47	5	959	5	GPR101	23	136113264	Missense_Mutation	DNP	GG	TCGA-CI-6624-01C-11D-1826-10	156693	136113264	19157296	302	24889										
F9	2158	hgsc.bcm.edu	37	chrX	138623283	138623283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	tttaaatggcggcagttgcaAggatgacattaattcctatg	10	6	0	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:138623283A>G	ENST00000218099.2	+	4	333	c.326A>G	c.(325-327)aAg>aGg	p.K109R	F9_ENST00000479617.2_3'UTR|F9_ENST00000394090.2_Intron	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	109	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	GGCAGTTGCAAGGATGACATT	0.373																																																0			X											219	175	190					X																	138623283		2203	4300	6503	138450949	SO:0001583	missense	2158			M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"Factor IX", "plasma thromboplastic component", "Christmas disease", "hemophilia B"	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.326A>G	X.37:g.138623283A>G	ENSP00000218099:p.Lys109Arg		138450949	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Missense_Mutation	SNP	ENST00000218099.2	37	CCDS14666.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053995	0.55218	.	.	ENSG00000101981	ENST00000218099	D	0.91843	-2.92	5.81	4.65	0.58169	Gamma-carboxyglutamic acid-rich (GLA) domain (1);EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.142348	0.64402	N	0.000007	D	0.84488	0.5483	N	0.11818	0.18	0.80722	D	1	P	0.39520	0.676	B	0.41619	0.361	T	0.82293	-0.0529	10	0.46703	T	0.11	.	9.0347	0.36280	0.9123:0.0:0.0877:0.0	.	109	P00740	FA9_HUMAN	R	109	ENSP00000218099:K109R	ENSP00000218099:K109R	K	+	2	0	F9	138450949	1.000000	0.71417	0.998000	0.56505	0.755000	0.42902	5.171000	0.64996	0.818000	0.34468	-0.321000	0.08615	AAG		0.373	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1			G	138623283	A	G	138623283	3	3	90	1	0	0	0	0	1	0	0	0	5367	72	3	4	340	4	F9	23	138623283	Missense_Mutation	SNP	A	TCGA-CI-6624-01C-11D-1826-10	2510019	138623283	16647277	303	24890										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140996485	140996485	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	agaataccgtccctattaccTttccatcctcttacaaggat	4	13	1	1			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:140996485T>A	ENST00000285879.4	+	4	3581	c.3295T>A	c.(3295-3297)Ttt>Att	p.F1099I	MAGEC1_ENST00000406005.2_Missense_Mutation_p.F166I	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	1099	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCCTATTACCTTTCCATCCTC	0.448										HNSCC(15;0.026)																																						0			X											137	125	129					X																	140996485		2203	4300	6503	140824151	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.3295T>A	X.37:g.140996485T>A	ENSP00000285879:p.Phe1099Ile		140824151	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	t	9.879	1.201140	0.22121	.	.	ENSG00000155495	ENST00000285879;ENST00000406005	T;T	0.08546	3.93;3.08	1.06	1.06	0.20224	.	.	.	.	.	T	0.18299	0.0439	M	0.88031	2.925	0.09310	N	1	P	0.48350	0.909	P	0.48704	0.587	T	0.12656	-1.0539	9	0.87932	D	0	.	4.0185	0.09655	0.0:0.0:0.0:1.0	.	1099	O60732	MAGC1_HUMAN	I	1099;166	ENSP00000285879:F1099I;ENSP00000385500:F166I	ENSP00000285879:F1099I	F	+	1	0	MAGEC1	140824151	0.002000	0.14202	0.001000	0.08648	0.008000	0.06430	1.390000	0.34464	0.667000	0.31107	0.231000	0.17811	TTT		0.448	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		A	140996485	T	A	140996485	3	1	90	1	0	0	0	0	1	0	0	0	9210	1609	56	5	3301	5	MAGEC1	23	140996485	Missense_Mutation	SNP	T	TCGA-CI-6624-01C-11D-1826-10	2373202	140996485	14274075	304	24891										
FLNA	2316	hgsc.bcm.edu	37	chrX	153588464	153588464	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0789473684210526	24	1	1.38774384236453	2.4913306122449	0.910885361552028	0.792494242590731	1	0	acgggctggccgccgtacttGatggtgacggtgtaggcccc	16	12	0	2			TCGA-CI-6624-01C-11D-1826-10	TCGA-CI-6624-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f21d2a2f-8a5e-48a5-8564-102056db359f	4eabf26b-7ad4-4126-9f2d-fb6f20b3deea	g.chrX:153588464G>C	ENST00000369850.3	-	22	3935	c.3699C>G	c.(3697-3699)atC>atG	p.I1233M	FLNA_ENST00000344736.4_Missense_Mutation_p.I1233M|FLNA_ENST00000360319.4_Missense_Mutation_p.I1233M|FLNA_ENST00000422373.1_Missense_Mutation_p.I1233M|FLNA_ENST00000369856.3_5'Flank	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1233					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGCCGTACTTGATGGTGACGG	0.637																																																0			X											34	40	38					X																	153588464		2052	4152	6204	153241658	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.3699C>G	X.37:g.153588464G>C	ENSP00000358866:p.Ile1233Met		153241658	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	G	7.353	0.623309	0.14193	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41	4.8	4.8	0.61643	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90813	0.7115	L	0.56199	1.76	0.80722	D	1	B;D	0.60575	0.08;0.988	B;D	0.73708	0.053;0.981	D	0.88221	0.2897	10	0.25751	T	0.34	.	7.8035	0.29189	0.0931:0.1748:0.7321:0.0	.	1233;1233	P21333-2;P21333	.;FLNA_HUMAN	M	1233;1206;1233;1233;1233	ENSP00000353467:I1233M;ENSP00000416926:I1233M;ENSP00000358866:I1233M;ENSP00000358863:I1233M	ENSP00000358863:I1233M	I	-	3	3	FLNA	153241658	1.000000	0.71417	1.000000	0.80357	0.610000	0.37248	0.819000	0.27308	1.981000	0.57761	0.436000	0.28706	ATC		0.637	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			C	153588464	G	C	153588464	3	2	90	1	0	0	0	0	1	0	0	0	5952	1280	45	5	4352	5	FLNA	23	153588464	Missense_Mutation	SNP	G	TCGA-CI-6624-01C-11D-1826-10	12591979	153588464	1682096	305	24892										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10431271	10431271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtgccaccctcactccctccTccacctgtccctctctggta	5	21	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:10431271T>C	ENST00000377086.1	+	45	5099	c.4897T>C	c.(4897-4899)Tcc>Ccc	p.S1633P	KIF1B_ENST00000377081.1_Missense_Mutation_p.S1633P|KIF1B_ENST00000263934.6_Missense_Mutation_p.S1587P			O60333	KIF1B_HUMAN	kinesin family member 1B	1633					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CACTCCCTCCTCCACCTGTCC	0.478																																																0			1											116	105	109					1																	10431271		2203	4300	6503	10353858	SO:0001583	missense	23095			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.4897T>C	1.37:g.10431271T>C	ENSP00000366290:p.Ser1633Pro		10353858	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	T	33	5.239646	0.95240	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.12879	2.64;2.64;2.64	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	L	0.61218	1.895	0.80722	D	1	P;D;D;D;D;D	0.89917	0.714;0.999;1.0;0.998;0.967;0.981	B;D;D;D;D;D	0.85130	0.263;0.994;0.997;0.995;0.91;0.959	T	0.02214	-1.1194	10	0.42905	T	0.14	.	15.9546	0.79876	0.0:0.0:0.0:1.0	.	1619;1593;1633;1607;1633;1587	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	P	1633;1587;1633;1633	ENSP00000263934:S1587P;ENSP00000366290:S1633P;ENSP00000366284:S1633P	ENSP00000263934:S1587P	S	+	1	0	KIF1B	10353858	1.000000	0.71417	0.987000	0.45799	0.975000	0.68041	7.655000	0.83696	2.227000	0.72691	0.528000	0.53228	TCC		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10431271	T	C	10431271	3	2	91	1	0	0	0	0	1	0	0	0	8305	1551	54	4	6414	4	KIF1B	1	10431271	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10		10431271	238819350	1	24893										
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47407091	47407091	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aggagtctgctggggctcagCacagagacactcatggtgca	14	10	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:47407091C>G	ENST00000310638.4	-	1	46	c.15G>C	c.(13-15)gtG>gtC	p.V5V	CYP4A11_ENST00000371905.1_Silent_p.V5V|CYP4A11_ENST00000371904.4_Silent_p.V5V|CYP4A11_ENST00000462347.1_Silent_p.V5V|CYP4A11_ENST00000457840.2_5'UTR	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	5				V -> A (in Ref. 8; AA sequence). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	TGGGGCTCAGCACAGAGACAC	0.587																																																0			1											83	83	83					1																	47407091		2203	4300	6503	47179678	SO:0001819	synonymous_variant	1579			L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.15G>C	1.37:g.47407091C>G			47179678	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Silent	SNP	ENST00000310638.4	37	CCDS543.1																																																																																				0.587	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		G	47407091	C	G	47407091	2	3	91	1	0	0	0	0	0	0	0	1	4189	697	25	5		5	CYP4A11	1	47407091	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	36975820	47407091	201843530	2	24894										
USP24	23358	hgsc.bcm.edu	37	chr1	55613373	55613373	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtcgagccacttaagcctccAggcccggccacagcagctgc	11	17	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:55613373A>G	ENST00000294383.6	-	18	2066	c.2067T>C	c.(2065-2067)ccT>ccC	p.P689P	USP24_ENST00000407756.1_Silent_p.P529P	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	689					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TTAAGCCTCCAGGCCCGGCCA	0.458																																																0			1											23	26	25					1																	55613373		1931	4148	6079	55385961	SO:0001819	synonymous_variant	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2067T>C	1.37:g.55613373A>G			55385961	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																				0.458	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55613373	A	G	55613373	2	3	91	1	0	0	0	0	0	0	0	1	17095	175	7	4		4	USP24	1	55613373	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	8206282	55613373	193637248	3	24895										
SGIP1	84251	hgsc.bcm.edu	37	chr1	67109400	67109400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcgcactttccccatcaccaGtggtgagtgttgtgtgtgtg	12	10	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:67109400G>A	ENST00000371037.4	+	7	534	c.457G>A	c.(457-459)Gtg>Atg	p.V153M	SGIP1_ENST00000371036.3_Missense_Mutation_p.V128M|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000371035.3_Missense_Mutation_p.V110M|SGIP1_ENST00000237247.6_Missense_Mutation_p.V157M|SGIP1_ENST00000371039.1_Missense_Mutation_p.V129M	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	153					endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						CCCATCACCAGTGGTGAGTGT	0.388																																																0			1											154	150	151					1																	67109400		2203	4300	6503	66881988	SO:0001583	missense	84251			AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.457G>A	1.37:g.67109400G>A	ENSP00000360076:p.Val153Met		66881988	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.401276	0.62288	.	.	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000424320;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037	T;T;T;T;T;T	0.03242	4.0;4.0;4.0;4.0;4.0;4.0	5.37	5.37	0.77165	.	0.262306	0.38778	N	0.001571	T	0.02848	0.0085	L	0.59436	1.845	0.23806	N	0.996797	B	0.22800	0.075	B	0.17098	0.017	T	0.19778	-1.0295	10	0.44086	T	0.13	-7.801	19.4728	0.94969	0.0:0.0:1.0:0.0	.	153	Q9BQI5	SGIP1_HUMAN	M	157;129;153;110;156;156;128;153	ENSP00000237247:V157M;ENSP00000360078:V129M;ENSP00000410439:V153M;ENSP00000360074:V110M;ENSP00000360075:V128M;ENSP00000360076:V153M	ENSP00000237247:V157M	V	+	1	0	SGIP1	66881988	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	3.479000	0.53165	2.668000	0.90789	0.563000	0.77884	GTG		0.388	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		A	67109400	G	A	67109400	3	1	91	1	0	0	0	0	1	0	0	0	14243	1029	36	3	483	3	SGIP1	1	67109400	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	11496027	67109400	182141221	4	24896										
PIGK	10026	hgsc.bcm.edu	37	chr1	77634995	77634995	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atctccatacacatttagttCcatattcttgtgactaaaca	3	10	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:77634995C>A	ENST00000370812.3	-	4	348	c.325G>T	c.(325-327)Gaa>Taa	p.E109*	PIGK_ENST00000478391.1_Intron|PIGK_ENST00000370813.5_Intron|PIGK_ENST00000359130.1_Nonsense_Mutation_p.E109*|PIGK_ENST00000445065.1_Intron	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	109					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)			endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						ACATTTAGTTCCATATTCTTG	0.348																																																0			1											112	96	101					1																	77634995		2203	4299	6502	77407583	SO:0001587	stop_gained	10026			AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"Phosphatidylinositol glycan anchor biosynthesis"	8965	protein-coding gene	gene with protein product	"GPI transamidase subunit"	605087	"phosphatidylinositol glycan, class K"			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.325G>T	1.37:g.77634995C>A	ENSP00000359848:p.Glu109*		77407583	B2R7K3|B4E2M3|O14822|Q5TG77	Nonsense_Mutation	SNP	ENST00000370812.3	37	CCDS674.1	.	.	.	.	.	.	.	.	.	.	C	38	7.244242	0.98161	.	.	ENSG00000142892	ENST00000370812;ENST00000359130	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-11.744	19.3214	0.94243	0.0:1.0:0.0:0.0	.	.	.	.	X	109	.	ENSP00000352041:E109X	E	-	1	0	PIGK	77407583	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.350000	0.79385	2.631000	0.89168	0.655000	0.94253	GAA		0.348	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482		A	77634995	C	A	77634995	4	1	91	1	0	0	0	0	0	1	0	0	11921	864	30	2	894	2	PIGK	1	77634995	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	10525595	77634995	171615626	5	24897										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060811	111060811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	caaagaggagccagaactgaCggtggatgtcattggtgggt	16	6	1	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:111060811C>T	ENST00000369771.2	-	1	986	c.599G>A	c.(598-600)cGt>cAt	p.R200H		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	200			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.R200H(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	CCAGAACTGACGGTGGATGTC	0.547																																																2	Substitution - Missense(2)	large_intestine(1)|lung(1)	1											120	121	120					1																	111060811		2203	4300	6503	110862334	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.599G>A	1.37:g.111060811C>T	ENSP00000358786:p.Arg200His		110862334		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071551	0.76301	.	.	ENSG00000143105	ENST00000369771	T	0.67698	-0.28	5.93	5.02	0.67125	.	0.050482	0.64402	D	0.000001	T	0.68467	0.3004	M	0.91872	3.25	0.46458	D	0.999051	D	0.61697	0.99	P	0.47528	0.549	T	0.77302	-0.2638	10	0.87932	D	0	.	10.0313	0.42103	0.0:0.8466:0.0:0.1534	.	200	Q16322	KCA10_HUMAN	H	200	ENSP00000358786:R200H	ENSP00000358786:R200H	R	-	2	0	KCNA10	110862334	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.088000	0.57678	1.510000	0.48803	0.655000	0.94253	CGT		0.547	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060811	C	T	111060811	3	4	91	1	0	0	0	0	1	0	0	0	8023	536	19	1	940	1	KCNA10	1	111060811	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	33425816	111060811	138189810	6	24898										
CEP350	9857	hgsc.bcm.edu	37	chr1	180012241	180012241	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gatgctgtcgtggcttcaggAgctccccttgcaatactgta	11	11	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:180012241A>G	ENST00000367607.3	+	20	4831	c.4413A>G	c.(4411-4413)ggA>ggG	p.G1471G		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1471					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TGGCTTCAGGAGCTCCCCTTG	0.433																																																0			1											173	160	164					1																	180012241		2203	4300	6503	178278864	SO:0001819	synonymous_variant	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4413A>G	1.37:g.180012241A>G			178278864	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	4.248	0.044922	0.08196	.	.	ENSG00000135837	ENST00000418229	.	.	.	5.9	4.74	0.60224	.	.	.	.	.	T	0.56292	0.1975	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53129	-0.8482	4	.	.	.	.	6.7619	0.23546	0.69:0.1584:0.0:0.1516	.	.	.	.	G	80	.	.	S	+	1	0	CEP350	178278864	1.000000	0.71417	0.996000	0.52242	0.205000	0.24178	2.601000	0.46249	1.002000	0.39104	0.459000	0.35465	AGC		0.433	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		G	180012241	A	G	180012241	2	3	91	1	0	0	0	0	0	0	0	1	3260	291	11	4		4	CEP350	1	180012241	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	68951430	180012241	69238380	7	24899										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228467032	228467032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggggggaacgtgggcctggAgcaggagggcacggtgcacc	21	9	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:228467032A>G	ENST00000422127.1	+	27	7327	c.7283A>G	c.(7282-7284)gAg>gGg	p.E2428G	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.E2857G|OBSCN_ENST00000284548.11_Missense_Mutation_p.E2428G|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000359599.6_Missense_Mutation_p.E1275G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2428					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGGGCCTGGAGCAGGAGGGC	0.677																																																0			1											58	69	65					1																	228467032		2121	4221	6342	226533655	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7283A>G	1.37:g.228467032A>G	ENSP00000409493:p.Glu2428Gly		226533655	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.553876	0.45487	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706	T;T;T	0.43294	0.95;0.95;0.95	4.4	4.4	0.53042	Immunoglobulin-like fold (1);	0.076099	0.50627	D	0.000104	T	0.62122	0.2402	M	0.80183	2.485	0.80722	D	1	B;D;P	0.76494	0.142;0.999;0.454	B;D;B	0.67382	0.043;0.951;0.137	T	0.62469	-0.6848	10	0.23302	T	0.38	.	13.9062	0.63836	1.0:0.0:0.0:0.0	.	2428;2428;2428	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	G	2428;2428;1275;127	ENSP00000284548:E2428G;ENSP00000409493:E2428G;ENSP00000352613:E1275G	ENSP00000284548:E2428G	E	+	2	0	OBSCN	226533655	1.000000	0.71417	0.999000	0.59377	0.633000	0.38033	9.040000	0.93783	1.767000	0.52121	0.454000	0.30748	GAG		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228467032	A	G	228467032	3	3	91	1	0	0	0	0	1	0	0	0	10843	304	11	4	7385	4	OBSCN	1	228467032	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	48454791	228467032	20783589	8	24900										
GPR137B	7107	hgsc.bcm.edu	37	chr1	236306210	236306212	+	In_Frame_Del	DEL	CTC	CTC	-													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tccctgcggaccgtcctcttCtccttctacttcaaagactt							TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:236306210_236306212delCTC	ENST00000366592.3	+	1	379_381	c.288_290delCTC	c.(286-291)ttctcc>ttc	p.S97del	GPR137B_ENST00000366591.4_In_Frame_Del_p.S97del	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	97						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			CCGTCCTCTTCTCCTTCTACTTC	0.586																																																0			1																																								234372835	SO:0001651	inframe_deletion	7107			AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.288_290delCTC	1.37:g.236306210_236306212delCTC	ENSP00000355551:p.Ser97del		234372833	Q53EK7|Q5TAE6|Q6FHI3	In_Frame_Del	DEL	ENST00000366592.3	37	CCDS1609.1																																																																																				0.586	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		-	236306212	CTC	-	236306210	7	5	91	1	0	1	0	1	0	0	0	0	6666	912	32	0	290	0	GPR137B	1	236306210	In_Frame_Del	DEL	CTC	TCGA-CL-5917-01A-11D-1657-10	7839178	236306210	12944411	9	24901										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	91	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-CL-5917-01A-11D-1657-10	4064704	240370914	8879707	10	24902										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804575	27804575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tctgagagaagacatcacagTccctctaagagaagccatcg	9	11	3	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:27804575T>C	ENST00000408964.2	+	1	5187	c.5136T>C	c.(5134-5136)agT>agC	p.S1712S	ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1712	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GACATCACAGTCCCTCTAAGA	0.577																																																0			2											169	171	170					2																	27804575		1920	4135	6055	27658079	SO:0001819	synonymous_variant	84226			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5136T>C	2.37:g.27804575T>C			27658079	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																				0.577	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27804575	T	C	27804575	2	2	91	1	0	0	0	0	0	0	0	1	2163	1664	58	4		4	C2orf16	2	27804575	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10		27804575	215394798	11	24903										
RASGRP3	25780	hgsc.bcm.edu	37	chr2	33748952	33748952	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcttcctttcctagttcactGattaccaaagctatgtcatc	4	12	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:33748952G>A	ENST00000403687.3	+	8	1263	c.523G>A	c.(523-525)Gat>Aat	p.D175N	RASGRP3_ENST00000402538.3_Missense_Mutation_p.D175N|RASGRP3_ENST00000407811.1_Missense_Mutation_p.D175N	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	175	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.D175N(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					CTAGTTCACTGATTACCAAAG	0.353																																																1	Substitution - Missense(1)	lung(1)	2											119	111	114					2																	33748952		1828	4082	5910	33602456	SO:0001583	missense	25780			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.523G>A	2.37:g.33748952G>A	ENSP00000384192:p.Asp175Asn		33602456	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	33	5.287655	0.95517	.	.	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.37058	1.22;1.22;1.22	5.4	5.4	0.78164	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.70046	0.3179	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76844	-0.2809	10	0.72032	D	0.01	-19.2033	19.5444	0.95285	0.0:0.0:1.0:0.0	.	175;175	D6W583;Q8IV61	.;GRP3_HUMAN	N	175	ENSP00000385886:D175N;ENSP00000384192:D175N;ENSP00000383917:D175N	ENSP00000385886:D175N	D	+	1	0	RASGRP3	33602456	1.000000	0.71417	0.995000	0.50966	0.938000	0.57974	9.864000	0.99589	2.683000	0.91414	0.655000	0.94253	GAT		0.353	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		A	33748952	G	A	33748952	3	1	91	1	0	0	0	0	1	0	0	0	13113	1290	45	3	545	3	RASGRP3	2	33748952	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	5944377	33748952	209450421	12	24904										
FAM98A	25940	hgsc.bcm.edu	37	chr2	33810660	33810660	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cttgtccttaaaatctttgaCaagtcctgccttgcagccaa	6	12	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:33810660C>T	ENST00000238823.8	-	7	965	c.825G>A	c.(823-825)ttG>ttA	p.L275L	FAM98A_ENST00000403368.1_Silent_p.L275L|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000441530.2_Silent_p.L80L			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	276							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					AAATCTTTGACAAGTCCTGCC	0.398																																																0			2											70	71	71					2																	33810660		2203	4300	6503	33664164	SO:0001819	synonymous_variant	25940				CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.825G>A	2.37:g.33810660C>T			33664164	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																				0.398	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		T	33810660	C	T	33810660	2	4	91	1	0	0	0	0	0	0	0	1	5675	477	17	3		3	FAM98A	2	33810660	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	61708	33810660	209388713	13	24905										
MSH2	4436	hgsc.bcm.edu	37	chr2	47637472	47637472	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccaaaggaatgtgttttaccCggaggagagactgctggaga	14	7	0	2	rs63750600		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:47637472C>A	ENST00000233146.2	+	3	829	c.606C>A	c.(604-606)ccC>ccA	p.P202P	MSH2_ENST00000406134.1_Silent_p.P202P|MSH2_ENST00000543555.1_Silent_p.P136P	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	202					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)|p.P202P(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTGTTTTACCCGGAGGAGAGA	0.453			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	4	Whole gene deletion(2)|Substitution - coding silent(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)	2											125	124	124					2																	47637472		2203	4300	6503	47490976	SO:0001819	synonymous_variant	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.606C>A	2.37:g.47637472C>A			47490976	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																				0.453	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			A	47637472	C	A	47637472	2	1	91	1	0	0	0	0	0	0	0	1	9900	639	23	2		2	MSH2	2	47637472	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	13826812	47637472	195561901	14	24906										
MSH6	2956	hgsc.bcm.edu	37	chr2	48032103	48032103	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gttacgtccctgctgaagtgTgcaggctcacaccaattgat	10	11	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:48032103T>C	ENST00000234420.5	+	6	3645	c.3493T>C	c.(3493-3495)Tgc>Cgc	p.C1165R	MSH6_ENST00000540021.1_Missense_Mutation_p.C1035R|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.C863R	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	1165					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCTGAAGTGTGCAGGCTCAC	0.438			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	2											167	144	152					2																	48032103		2203	4300	6503	47885607	SO:0001583	missense	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.3493T>C	2.37:g.48032103T>C	ENSP00000234420:p.Cys1165Arg		47885607	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	T	19.19	3.779535	0.70107	.	.	ENSG00000116062	ENST00000234420;ENST00000543270;ENST00000540021;ENST00000538136	D;D;D	0.85411	-1.98;-1.98;-1.98	5.23	5.23	0.72850	DNA mismatch repair protein MutS, C-terminal (2);	0.104988	0.64402	D	0.000002	D	0.93442	0.7908	M	0.89715	3.055	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.75484	0.986;0.981	D	0.94682	0.7866	10	0.72032	D	0.01	-16.2284	15.1229	0.72460	0.0:0.0:0.0:1.0	.	1035;1165	B4DF41;P52701	.;MSH6_HUMAN	R	1165;131;1035;863	ENSP00000234420:C1165R;ENSP00000446475:C1035R;ENSP00000438580:C863R	ENSP00000234420:C1165R	C	+	1	0	MSH6	47885607	1.000000	0.71417	0.949000	0.38748	0.960000	0.62799	4.692000	0.61746	1.975000	0.57531	0.374000	0.22700	TGC		0.438	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		C	48032103	T	C	48032103	3	2	91	1	0	0	0	0	1	0	0	0	9904	1696	59	4	3515	4	MSH6	2	48032103	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	394631	48032103	195167270	15	24907										
DYSF	8291	hgsc.bcm.edu	37	chr2	71753472	71753472	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttccgggccgaggacttgccGcagagtgcgtggggcgcgcc	18	13	0	1	rs544769503		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:71753472G>A	ENST00000258104.3	+	12	1453	c.1176G>A	c.(1174-1176)ccG>ccA	p.P392P	DYSF_ENST00000409366.1_Silent_p.P393P|DYSF_ENST00000394120.2_Silent_p.P393P|DYSF_ENST00000409651.1_Silent_p.P424P|DYSF_ENST00000409762.1_Silent_p.P423P|DYSF_ENST00000410041.1_Silent_p.P424P|DYSF_ENST00000409744.1_Silent_p.P393P|DYSF_ENST00000413539.2_Silent_p.P423P|DYSF_ENST00000410020.3_Silent_p.P424P|DYSF_ENST00000409582.3_Silent_p.P423P|DYSF_ENST00000429174.2_Silent_p.P392P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	392	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						AGGACTTGCCGCAGAGTGCGT	0.692																																																0			2											65	73	70					2																	71753472		2203	4300	6503	71606980	SO:0001819	synonymous_variant	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1176G>A	2.37:g.71753472G>A			71606980	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																				0.692	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71753472	G	A	71753472	2	1	91	1	0	0	0	0	0	0	0	1	4870	1074	38	1		1	DYSF	2	71753472	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	23721369	71753472	171445901	16	24908										
HK2	3099	hgsc.bcm.edu	37	chr2	75113773	75113773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atttgatgtggctgtggatgAgctttcactcaaccccggca	11	10	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:75113773A>G	ENST00000290573.2	+	15	2792	c.2192A>G	c.(2191-2193)gAg>gGg	p.E731G	HK2_ENST00000409174.1_Missense_Mutation_p.E703G	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	731	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						GCTGTGGATGAGCTTTCACTC	0.547																																																0			2											81	85	83					2																	75113773		2203	4300	6503	74967281	SO:0001583	missense	29911				CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2192A>G	2.37:g.75113773A>G	ENSP00000290573:p.Glu731Gly		74967281	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763915	0.69878	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.96856	-4.15;-4.15	5.49	5.49	0.81192	Hexokinase, C-terminal (1);	0.270076	0.47093	D	0.000242	D	0.95937	0.8677	M	0.63843	1.955	0.80722	D	1	D	0.54397	0.966	P	0.48795	0.59	D	0.96038	0.9022	10	0.72032	D	0.01	-22.5475	13.5962	0.61991	1.0:0.0:0.0:0.0	.	731	P52789	HXK2_HUMAN	G	731;731;703	ENSP00000290573:E731G;ENSP00000387140:E703G	ENSP00000290573:E731G	E	+	2	0	HK2	74967281	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.884000	0.63135	2.311000	0.77944	0.533000	0.62120	GAG		0.547	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		G	75113773	A	G	75113773	3	3	91	1	0	0	0	0	1	0	0	0	7212	304	11	4	2250	4	HK2	2	75113773	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	3360301	75113773	168085600	17	24909										
REEP1	65055	hgsc.bcm.edu	37	chr2	86459916	86459916	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccgcagtctctccgataaggCaccctgtccctggatacaac	8	16	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:86459916C>A	ENST00000165698.5	-	6	570	c.427G>T	c.(427-429)Gcc>Tcc	p.A143S	REEP1_ENST00000535845.1_Missense_Mutation_p.A116S|REEP1_ENST00000473407.1_5'UTR|REEP1_ENST00000541910.1_Silent_p.V64V|REEP1_ENST00000540790.1_Missense_Mutation_p.A122S|REEP1_ENST00000538924.1_Missense_Mutation_p.A150S	NM_022912.2	NP_075063.1	Q9H902	REEP1_HUMAN	receptor accessory protein 1	143					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein insertion into membrane (GO:0051205)|regulation of intracellular transport (GO:0032386)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	microtubule binding (GO:0008017)|olfactory receptor binding (GO:0031849)			breast(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	13						TCCGATAAGGCACCCTGTCCC	0.642																																																0			2											38	32	34					2																	86459916		2203	4300	6503	86313427	SO:0001583	missense	65055			AK023172	CCDS1989.1, CCDS54372.1, CCDS54373.1, CCDS54374.1	2p11.2	2014-09-17	2006-02-07	2006-02-07	ENSG00000068615	ENSG00000068615		"Receptor accessory proteins"	25786	protein-coding gene	gene with protein product	"receptor expression enhancing protein 1"	609139	"chromosome 2 open reading frame 23"	C2orf23		16271481, 15550249	Standard	NM_022912		Approved	FLJ13110, SPG31	uc002srh.4	Q9H902	OTTHUMG00000130205	ENST00000165698.5:c.427G>T	2.37:g.86459916C>A	ENSP00000165698:p.Ala143Ser		86313427	B7Z4D7|B7Z4F2|B7Z5R9|D6W5M2|Q53TI0	Missense_Mutation	SNP	ENST00000165698.5	37	CCDS1989.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984215	0.74474	.	.	ENSG00000068615	ENST00000165698;ENST00000538924;ENST00000535845;ENST00000540790;ENST00000453231;ENST00000428491	D;D;D;D;D;T	0.88124	-2.32;-2.34;-1.5;-1.5;-2.28;-1.41	5.66	5.66	0.87406	.	0.053192	0.85682	D	0.000000	D	0.84325	0.5447	.	.	.	0.46028	D	0.998822	B;B;B	0.24675	0.066;0.109;0.054	B;B;B	0.33042	0.075;0.157;0.027	T	0.78715	-0.2096	9	0.25106	T	0.35	.	17.0395	0.86484	0.0:1.0:0.0:0.0	.	116;122;143	B7Z5R9;F5H7Z9;Q9H902	.;.;REEP1_HUMAN	S	143;150;116;122;150;116	ENSP00000165698:A143S;ENSP00000438346:A150S;ENSP00000437567:A116S;ENSP00000443831:A122S;ENSP00000392197:A150S;ENSP00000400607:A116S	ENSP00000165698:A143S	A	-	1	0	REEP1	86313427	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.588000	0.67517	2.832000	0.97577	0.655000	0.94253	GCC		0.642	REEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252523.2	NM_022912		A	86459916	C	A	86459916	3	1	91	1	0	0	0	0	1	0	0	0	13241	710	25	2	247	2	REEP1	2	86459916	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	11346143	86459916	156739457	18	24910										
GLI2	2736	hgsc.bcm.edu	37	chr2	121726346	121726346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgagccgcaagcgggcgctgTccatctccccactctcagac	10	17	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:121726346T>C	ENST00000452319.1	+	6	760	c.700T>C	c.(700-702)Tcc>Ccc	p.S234P	GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.S234P					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GCGGGCGCTGTCCATCTCCCC	0.627																																																0			2											78	73	74					2																	121726346		2203	4300	6503	121442816	SO:0001583	missense	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.700T>C	2.37:g.121726346T>C	ENSP00000390436:p.Ser234Pro		121442816		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.5|29.5	5.007495|5.007495	0.93287|0.93287	.|.	.|.	ENSG00000074047|ENSG00000074047	ENST00000452319;ENST00000361492|ENST00000440937;ENST00000360874	T;T|.	0.70986|.	-0.53;-0.53|.	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62901|0.62901	0.2466|0.2466	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D;D|P	0.76494|0.49559	0.999;0.999|0.925	D;D|P	0.83275|0.47162	0.996;0.994|0.54	T|T	0.69628|0.69628	-0.5094|-0.5094	10|8	0.56958|0.87932	D|D	0.05|0	.|.	14.7053|14.7053	0.69186|0.69186	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	234;234|104	P10070;Q0VGA0|F5H4D9	GLI2_HUMAN;.|.	P|A	234|104;96	ENSP00000390436:S234P;ENSP00000354586:S234P|.	ENSP00000354586:S234P|ENSP00000441454:V96A	S|V	+|+	1|2	0|0	GLI2|GLI2	121442816|121442816	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.825000|7.825000	0.86693|0.86693	2.068000|2.068000	0.61886|0.61886	0.533000|0.533000	0.62120|0.62120	TCC|GTC		0.627	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		C	121726346	T	C	121726346	3	2	91	1	0	0	0	0	1	0	0	0	6458	1667	58	4	718	4	GLI2	2	121726346	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	35266430	121726346	121473027	19	24911										
ACVR1C	130399	hgsc.bcm.edu	37	chr2	158406686	158406686	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggaaatacctttgttgtcagCagcaatgaaaccaaggatgt	10	7	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:158406686C>T	ENST00000243349.8	-	4	1123	c.763G>A	c.(763-765)Gct>Act	p.A255T	ACVR1C_ENST00000348328.5_Intron|ACVR1C_ENST00000335450.7_Missense_Mutation_p.A175T|ACVR1C_ENST00000409680.3_Missense_Mutation_p.A205T	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						TTGTTGTCAGCAGCAATGAAA	0.383																																																0			2											101	100	101					2																	158406686		2203	4300	6503	158114932	SO:0001583	missense	130399			BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.763G>A	2.37:g.158406686C>T	ENSP00000243349:p.Ala255Thr		158114932		Missense_Mutation	SNP	ENST00000243349.8	37	CCDS2205.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.326152	0.81580	.	.	ENSG00000123612	ENST00000243349;ENST00000409680;ENST00000335450	T;T;T	0.66460	-0.21;-0.21;-0.21	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.245011	0.28371	N	0.015587	D	0.84410	0.5466	M	0.83692	2.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.992;0.998	D	0.85404	0.1133	10	0.87932	D	0	.	19.9557	0.97216	0.0:1.0:0.0:0.0	.	175;255	Q8NER5-3;Q8NER5	.;ACV1C_HUMAN	T	255;205;175	ENSP00000243349:A255T;ENSP00000387168:A205T;ENSP00000335178:A175T	ENSP00000243349:A255T	A	-	1	0	ACVR1C	158114932	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	7.818000	0.86416	2.817000	0.96982	0.557000	0.71058	GCT		0.383	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		T	158406686	C	T	158406686	3	4	91	1	0	0	0	0	1	0	0	0	222	710	25	3	742	3	ACVR1C	2	158406686	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	36680340	158406686	84792687	20	24912										
SP3	6670	hgsc.bcm.edu	37	chr2	174774706	174774706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttccagaaactgtgacaagcTgtaaaggtatttcagtgttg	10	6	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:174774706T>C	ENST00000310015.6	-	7	2839	c.2309A>G	c.(2308-2310)cAg>cGg	p.Q770R	SP3_ENST00000418194.2_Missense_Mutation_p.Q702R|SP3_ENST00000455789.2_Missense_Mutation_p.Q717R	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	770					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			TGTGACAAGCTGTAAAGGTAT	0.348																																																0			2											99	95	97					2																	174774706		2203	4300	6503	174482952	SO:0001583	missense	6670			M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.2309A>G	2.37:g.174774706T>C	ENSP00000310301:p.Gln770Arg		174482952	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.67|15.67	2.903526|2.903526	0.52333|0.52333	.|.	.|.	ENSG00000172845|ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194|ENST00000416195	T;T;T|.	0.06142|.	3.34;3.35;3.34|.	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.63058|0.63058	0.2479|0.2479	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	D;D;D|.	0.63046|.	0.987;0.987;0.992|.	D;D;D|.	0.72982|.	0.953;0.953;0.979|.	T|T	0.60388|0.60388	-0.7273|-0.7273	10|5	0.87932|.	D|.	0|.	.|.	15.7391|15.7391	0.77870|0.77870	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	767;770;717|.	B7ZLN9;Q02447;Q02447-6|.	.;SP3_HUMAN;.|.	R|G	770;717;702|727	ENSP00000310301:Q770R;ENSP00000388903:Q717R;ENSP00000406140:Q702R|.	ENSP00000310301:Q770R|.	Q|S	-|-	2|1	0|0	SP3|SP3	174482952|174482952	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.589000|7.589000	0.82641|0.82641	2.124000|2.124000	0.65301|0.65301	0.528000|0.528000	0.53228|0.53228	CAG|AGC		0.348	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		C	174774706	T	C	174774706	3	2	91	1	0	0	0	0	1	0	0	0	15002	1580	55	4	40	4	SP3	2	174774706	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	16368020	174774706	68424667	21	24913										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178494179	178494179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cataacactggcaggggaggAtgaggcagttgaggccagca	16	8	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:178494179A>G	ENST00000286063.6	-	20	3075	c.2758T>C	c.(2758-2760)Tcc>Ccc	p.S920P	PDE11A_ENST00000449286.2_Missense_Mutation_p.S562P|PDE11A_ENST00000358450.4_Missense_Mutation_p.S670P|PDE11A_ENST00000389683.3_Missense_Mutation_p.S476P|PDE11A_ENST00000450799.2_Missense_Mutation_p.S111P|PDE11A_ENST00000409504.1_Missense_Mutation_p.S562P	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	920					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GCAGGGGAGGATGAGGCAGTT	0.498									Primary Pigmented Nodular Adrenocortical Disease, Familial																																							0			2											251	202	218					2																	178494179		2203	4300	6503	178202425	SO:0001583	missense	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2758T>C	2.37:g.178494179A>G	ENSP00000286063:p.Ser920Pro		178202425	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.81|11.81	1.748334|1.748334	0.30955|0.30955	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000436700|ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286	.|T;T;T;T;T;T	.|0.72615	.|-0.28;-0.07;-0.09;-0.2;-0.67;-0.2	5.52|5.52	-1.21|-1.21	0.09524|0.09524	.|5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	.|2.024110	.|0.03038	.|N	.|0.153007	T|T	0.41305|0.41305	0.1153|0.1153	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.21930|0.21930	-1.0231|-1.0231	5|10	.|0.34782	.|T	.|0.22	.|.	1.2467|1.2467	0.01974|0.01974	0.2786:0.2943:0.2904:0.1367|0.2786:0.2943:0.2904:0.1367	.|.	.|670;920	.|Q9HCR9-2;Q9HCR9	.|.;PDE11_HUMAN	T|P	122|920;670;111;562;476;562	.|ENSP00000286063:S920P;ENSP00000351232:S670P;ENSP00000387964:S111P;ENSP00000386539:S562P;ENSP00000374333:S476P;ENSP00000390599:S562P	.|ENSP00000286063:S920P	I|S	-|-	2|1	0|0	PDE11A|PDE11A	178202425|178202425	0.036000|0.036000	0.19791|0.19791	0.006000|0.006000	0.13384|0.13384	0.054000|0.054000	0.15201|0.15201	0.168000|0.168000	0.16622|0.16622	-0.087000|-0.087000	0.12528|0.12528	-0.326000|-0.326000	0.08463|0.08463	ATC|TCC		0.498	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			G	178494179	A	G	178494179	3	3	91	1	0	0	0	0	1	0	0	0	11662	333	12	4	47	4	PDE11A	2	178494179	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	3719473	178494179	64705194	22	24914										
TTN	7273	hgsc.bcm.edu	37	chr2	179474209	179474209	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tttatccatgtaatagttggGtaaggtgatccagaaatact	9	5	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:179474209G>A	ENST00000591111.1	-	223	47129	c.46905C>T	c.(46903-46905)taC>taT	p.Y15635Y	TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.Y17276Y|TTN_ENST00000460472.2_Silent_p.Y8211Y|TTN_ENST00000359218.5_Silent_p.Y8336Y|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Silent_p.Y8403Y|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.Y14708Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15635	Ig-like 98.		Y -> C (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAATAGTTGGGTAAGGTGATC	0.413																																																0			2											105	98	100					2																	179474209		1893	4119	6012	179182454	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46905C>T	2.37:g.179474209G>A			179182454	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179474209	G	A	179474209	2	1	91	1	0	0	0	0	0	0	0	1	16775	1256	44	3		3	TTN	2	179474209	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	980030	179474209	63725164	23	24915										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191302144	191302144	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atgggttttggatatggcttCgtgttcacctttctctactg	10	8	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:191302144C>T	ENST00000392328.1	+	3	1713	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	MFSD6_ENST00000281416.7_Silent_p.F463F	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	463					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						GATATGGCTTCGTGTTCACCT	0.493																																																0			2											310	251	271					2																	191302144		2203	4300	6503	191010389	SO:0001819	synonymous_variant	54842				CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.1389C>T	2.37:g.191302144C>T			191010389	D3KSZ4|Q86TH2|Q9NXM3	Silent	SNP	ENST00000392328.1	37	CCDS2306.1																																																																																				0.493	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			T	191302144	C	T	191302144	2	4	91	1	0	0	0	0	0	0	0	1	9565	883	31	1		1	MFSD6	2	191302144	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	11827935	191302144	51897229	24	24916										
CPO	130749	hgsc.bcm.edu	37	chr2	207827159	207827159	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttggtgcctctagaaactgcCaagatcaaacattctgtggg	10	9	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:207827159C>T	ENST00000272852.3	+	7	644	c.598C>T	c.(598-600)Caa>Taa	p.Q200*		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	200						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		TAGAAACTGCCAAGATCAAAC	0.443																																																0			2											171	168	169					2																	207827159		2203	4300	6503	207535404	SO:0001587	stop_gained	130749				CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"metallocarboxypeptidase O", "metallocarboxypeptidase C"	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.598C>T	2.37:g.207827159C>T	ENSP00000272852:p.Gln200*		207535404	Q2M277|Q7RTW7	Nonsense_Mutation	SNP	ENST00000272852.3	37	CCDS2372.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286364	0.23478	.	.	ENSG00000144410	ENST00000272852	.	.	.	5.5	-1.38	0.09027	.	0.924814	0.09294	N	0.821866	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3377	0.43860	0.3295:0.2356:0.4349:0.0	.	.	.	.	X	200	.	ENSP00000272852:Q200X	Q	+	1	0	CPO	207535404	0.000000	0.05858	0.219000	0.23793	0.017000	0.09413	-0.716000	0.04991	-0.115000	0.11915	-0.324000	0.08512	CAA		0.443	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		T	207827159	C	T	207827159	4	4	91	1	0	0	0	0	0	1	0	0	3826	595	21	3	624	3	CPO	2	207827159	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	16525015	207827159	35372214	25	24917										
TNS1	7145	hgsc.bcm.edu	37	chr2	218750499	218750499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cttcaagagcagtcctggctCgatggtgatgcagacgctag	13	10	1	3	rs370385101		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:218750499C>T	ENST00000171887.4	-	13	1161	c.709G>A	c.(709-711)Gag>Aag	p.E237K	TNS1_ENST00000310858.6_Missense_Mutation_p.E268K|TNS1_ENST00000419504.1_Missense_Mutation_p.E237K|TNS1_ENST00000430930.1_Missense_Mutation_p.E237K	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	237	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		AGTCCTGGCTCGATGGTGATG	0.527																																																0			2						C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	148	127	134		709	3.9	1	2		134	0,8600		0,0,4300	no	missense	TNS1	NM_022648.4	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	237/1736	218750499	1,13005	2203	4300	6503	218458744	SO:0001583	missense	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.709G>A	2.37:g.218750499C>T	ENSP00000171887:p.Glu237Lys		218458744	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.892663|4.892663	0.91889|0.91889	2.27E-4|2.27E-4	0.0|0.0	ENSG00000079308|ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858|ENST00000453356	D;D;D;D;D;D|.	0.85773|.	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03|.	4.77|4.77	3.89|3.89	0.44902|0.44902	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71108|0.71108	0.3301|0.3301	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.992;0.996;1.0;1.0;1.0;1.0|.	P;D;D;D;D;D|.	0.91635|.	0.814;0.977;0.999;0.998;0.995;0.996|.	T|T	0.71283|0.71283	-0.4639|-0.4639	10|5	0.51188|.	T|.	0.08|.	.|.	12.9162|12.9162	0.58207|0.58207	0.0:0.92:0.0:0.08|0.0:0.92:0.0:0.08	.|.	237;291;268;237;237;237|.	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55|.	.;.;.;TENS1_HUMAN;.;.|.	K|Q	237;237;237;362;305;268|12	ENSP00000171887:E237K;ENSP00000408724:E237K;ENSP00000406016:E237K;ENSP00000405460:E362K;ENSP00000400383:E305K;ENSP00000308321:E268K|.	ENSP00000171887:E237K|.	E|R	-|-	1|2	0|0	TNS1|TNS1	218458744|218458744	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.903000|0.903000	0.53119|0.53119	5.787000|5.787000	0.69013|0.69013	1.218000|1.218000	0.43458|0.43458	0.462000|0.462000	0.41574|0.41574	GAG|CGA		0.527	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218750499	C	T	218750499	3	4	91	1	0	0	0	0	1	0	0	0	16382	893	31	1	4582	1	TNS1	2	218750499	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	10923340	218750499	24448874	26	24918										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347195	222347195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agctaggaggtcagtgatggAgactttggtggtcttcaagc	15	6	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:222347195A>G	ENST00000281821.2	-	5	1236	c.1195T>C	c.(1195-1197)Tcc>Ccc	p.S399P	EPHA4_ENST00000409938.1_Missense_Mutation_p.S399P|EPHA4_ENST00000409854.1_Missense_Mutation_p.S399P|EPHA4_ENST00000392071.4_Missense_Mutation_p.S348P	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	399	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> F (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TCAGTGATGGAGACTTTGGTG	0.498																																																0			2											274	277	276					2																	222347195		2203	4300	6503	222055439	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1195T>C	2.37:g.222347195A>G	ENSP00000281821:p.Ser399Pro		222055439	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361851	0.82353	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38	6.06	6.06	0.98353	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.66086	0.2754	L	0.59436	1.845	0.80722	D	1	P	0.52316	0.952	P	0.57846	0.828	T	0.65965	-0.6040	10	0.49607	T	0.09	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	399	P54764	EPHA4_HUMAN	P	399;399;399;348;103	ENSP00000281821:S399P;ENSP00000386276:S399P;ENSP00000386829:S399P;ENSP00000375923:S348P;ENSP00000395917:S103P	ENSP00000281821:S399P	S	-	1	0	EPHA4	222055439	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.053000	0.71089	2.324000	0.78689	0.533000	0.62120	TCC		0.498	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			G	222347195	A	G	222347195	3	3	91	1	0	0	0	0	1	0	0	0	5182	304	11	4	1817	4	EPHA4	2	222347195	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	3596696	222347195	20852178	27	24919										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238289624	238289624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cagcatgccttgcaatggggCggctcggaactcagctggga	15	11	1	0	rs372255458		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr2:238289624C>T	ENST00000295550.4	-	5	2283	c.1831G>A	c.(1831-1833)Gcc>Acc	p.A611T	COL6A3_ENST00000353578.4_Missense_Mutation_p.A405T|COL6A3_ENST00000392004.3_Missense_Mutation_p.A405T|COL6A3_ENST00000472056.1_Missense_Mutation_p.A204T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A410T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A405T|COL6A3_ENST00000392003.2_Missense_Mutation_p.A204T|COL6A3_ENST00000346358.4_Missense_Mutation_p.A611T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	611	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A611T(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		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)		TGCAATGGGGCGGCTCGGAAC	0.582																																																1	Substitution - Missense(1)	large_intestine(1)	2						C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	61	53	56		1213,610,1213,610,1831	4.4	0	2		56	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_057165.4,NM_057164.4,NM_004369.3	58,58,58,58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	405/2972,204/2571,405/1238,204/1037,611/3178	238289624	1,13005	2203	4300	6503	237954363	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1831G>A	2.37:g.238289624C>T	ENSP00000295550:p.Ala611Thr		237954363	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	6.522	0.464485	0.12402	0.0	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;T;T;T	0.88586	-2.4;-2.37;-2.35;-2.36;-2.35;-2.35;0.15;0.02;0.17	5.27	4.4	0.53042	von Willebrand factor, type A (2);	0.839591	0.10116	N	0.714003	T	0.81837	0.4907	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B;B	0.38535	0.106;0.635;0.03;0.03;0.407;0.039	B;B;B;B;B;B	0.38458	0.04;0.274;0.025;0.041;0.065;0.013	T	0.67829	-0.5569	10	0.15066	T	0.55	.	9.1507	0.36962	0.0:0.6557:0.2607:0.0836	.	611;204;204;405;405;611	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	T	611;410;405;204;405;611;405;204;611	ENSP00000295550:A611T;ENSP00000315609:A410T;ENSP00000315873:A405T;ENSP00000418285:A204T;ENSP00000386844:A405T;ENSP00000295546:A611T;ENSP00000375861:A405T;ENSP00000375860:A204T;ENSP00000389539:A611T	ENSP00000295550:A611T	A	-	1	0	COL6A3	237954363	0.000000	0.05858	0.010000	0.14722	0.022000	0.10575	0.127000	0.15790	1.362000	0.46000	0.655000	0.94253	GCC		0.582	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238289624	C	T	238289624	3	4	91	1	0	0	0	0	1	0	0	0	3707	768	27	1	7909	1	COL6A3	2	238289624	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	15942429	238289624	4909749	28	24920										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266167	41266167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	taaaggcaatcctgaggaagAggatgtggatacctcccaag	12	8	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:41266167A>G	ENST00000349496.5	+	3	444	c.164A>G	c.(163-165)gAg>gGg	p.E55G	CTNNB1_ENST00000405570.1_Missense_Mutation_p.E55G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.E55G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.E48G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.E55G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	55					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.E55G(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCTGAGGAAGAGGATGTGGAT	0.468		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	110	Deletion - In frame(87)|Complex - deletion inframe(15)|Unknown(7)|Substitution - Missense(1)	liver(80)|large_intestine(16)|stomach(8)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											73	67	69					3																	41266167		2203	4300	6503	41241171	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.164A>G	3.37:g.41266167A>G	ENSP00000344456:p.Glu55Gly		41241171	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.019915	0.35606	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.91	5.91	0.95273	.	0.090529	0.85682	D	0.000000	T	0.34948	0.0915	N	0.14661	0.345	0.58432	D	0.999999	B	0.18968	0.032	B	0.22753	0.041	T	0.10683	-1.0619	10	0.40728	T	0.16	-12.7154	16.3453	0.83126	1.0:0.0:0.0:0.0	.	55	P35222	CTNB1_HUMAN	G	48;55;55;55;55;48;55;55;55	ENSP00000400508:E48G;ENSP00000385604:E55G;ENSP00000412219:E55G;ENSP00000379486:E55G;ENSP00000344456:E55G;ENSP00000411226:E48G;ENSP00000379488:E55G;ENSP00000409302:E55G;ENSP00000401599:E55G	ENSP00000344456:E55G	E	+	2	0	CTNNB1	41241171	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	7.576000	0.82467	2.261000	0.74972	0.533000	0.62120	GAG		0.468	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266167	A	G	41266167	3	3	91	1	0	0	0	0	1	0	0	0	4022	304	11	4	170	4	CTNNB1	3	41266167	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10		41266167	156756263	29	24921										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266878	41266878	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cagctttctaaaaaggaagcTtccagacacgctatcatgcg	8	11	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:41266878T>C	ENST00000349496.5	+	5	829	c.549T>C	c.(547-549)gcT>gcC	p.A183A	CTNNB1_ENST00000405570.1_Silent_p.A183A|CTNNB1_ENST00000396183.3_Silent_p.A183A|CTNNB1_ENST00000453024.1_Silent_p.A176A|CTNNB1_ENST00000396185.3_Silent_p.A183A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	183					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		AAAAGGAAGCTTCCAGACACG	0.428		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	0			3											70	71	71					3																	41266878		2203	4300	6503	41241882	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.549T>C	3.37:g.41266878T>C			41241882	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.428	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266878	T	C	41266878	2	2	91	1	0	0	0	0	0	0	0	1	4022	1596	56	4		4	CTNNB1	3	41266878	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	711	41266878	156755552	30	24922										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52830591	52830591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	caccatgagagccgtcaaccGtgcagacacggccaaggagg	13	13	1	2	rs192350744		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:52830591G>A	ENST00000449956.2	+	3	215	c.209G>A	c.(208-210)cGt>cAt	p.R70H	ITIH3_ENST00000416872.2_Missense_Mutation_p.R70H	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	70	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		GCCGTCAACCGTGCAGACACG	0.542													G|||	1	0.000199681	0	0	5008	,	,		21786	0.001		0	False		,,,				2504	0															0			3						G	HIS/ARG	1,4249		0,1,2124	77	84	81		209	1.7	0.2	3		81	0,8536		0,0,4268	no	missense	ITIH3	NM_002217.3	29	0,1,6392	AA,AG,GG		0.0,0.0235,0.0078	benign	70/891	52830591	1,12785	2125	4268	6393	52805631	SO:0001583	missense	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.209G>A	3.37:g.52830591G>A	ENSP00000415769:p.Arg70His		52805631	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	5.978	0.364374	0.11296	2.35E-4	0.0	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.24151	1.87;1.87	4.54	1.68	0.24146	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.276116	0.36268	N	0.002689	T	0.20088	0.0483	L	0.56124	1.755	0.21675	N	0.999599	B;B	0.19200	0.008;0.034	B;B	0.16289	0.008;0.015	T	0.17077	-1.0381	10	0.39692	T	0.17	-5.6454	5.3115	0.15833	0.1941:0.1659:0.6399:0.0	.	70;70	E7ET33;Q06033	.;ITIH3_HUMAN	H	70;70;65;70;70	ENSP00000413922:R70H;ENSP00000415769:R70H	ENSP00000273291:R65H	R	+	2	0	ITIH3	52805631	0.012000	0.17670	0.235000	0.24058	0.209000	0.24338	0.816000	0.27267	0.157000	0.19338	-0.194000	0.12790	CGT		0.542	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		A	52830591	G	A	52830591	3	1	91	1	0	0	0	0	1	0	0	0	7926	1145	40	1	219	1	ITIH3	3	52830591	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	11563713	52830591	145191839	31	24923										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89259543	89259543	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctggtggaggttagagggtcTtgtgtcaacaattctaagga	14	5	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:89259543T>C	ENST00000336596.2	+	3	912	c.687T>C	c.(685-687)tcT>tcC	p.S229S	EPHA3_ENST00000494014.1_Silent_p.S229S|EPHA3_ENST00000452448.2_Silent_p.S229S	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	229	Cys-rich.		S -> Y (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TTAGAGGGTCTTGTGTCAACA	0.483										TSP Lung(6;0.00050)																																						0			3											157	150	152					3																	89259543		2203	4300	6503	89342233	SO:0001819	synonymous_variant	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.687T>C	3.37:g.89259543T>C			89342233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																				0.483	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89259543	T	C	89259543	2	2	91	1	0	0	0	0	0	0	0	1	5181	1596	56	4		4	EPHA3	3	89259543	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	36428952	89259543	108762887	32	24924										
OR5H15	403274	hgsc.bcm.edu	37	chr3	97888302	97888302	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tctgtctgtttatactatggCccccttctcttaatgtatgt	6	10	3	0	rs115424559	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:97888302C>A	ENST00000356526.2	+	1	759	c.759C>A	c.(757-759)ggC>ggA	p.G253G		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						TATACTATGGCCCCCTTCTCT	0.433													C|||	51	0.0101837	8e-04	0.0043	5008	,	,		15699	0		0.0427	False		,,,				2504	0.0041															0			3						C		31,4373		1,29,2172	96	100	98		759	-2.5	0.1	3	dbSNP_132	98	212,8388		3,206,4091	no	coding-synonymous	OR5H15	NM_001005515.1		4,235,6263	AA,AC,CC		2.4651,0.7039,1.8687		253/314	97888302	243,12761	2202	4300	6502	99370992	SO:0001819	synonymous_variant	403274				CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.759C>A	3.37:g.97888302C>A			99370992		Silent	SNP	ENST00000356526.2	37	CCDS33799.1																																																																																				0.433	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			A	97888302	C	A	97888302	2	1	91	1	0	0	0	0	0	0	0	1	11192	726	26	2		2	OR5H15	3	97888302	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	8628759	97888302	100134128	33	24925										
OR5H6	79295	hgsc.bcm.edu	37	chr3	97983497	97983497	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tttttttcccttgtaaccacTgtaaccacagaatgttttct	4	10	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:97983497T>A	ENST00000383696.2	+	1	410	c.369T>A	c.(367-369)acT>acA	p.T123T	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTGTAACCACTGTAACCACAG	0.383																																																0			3											103	83	89					3																	97983497		2203	4294	6497	99466187	SO:0001819	synonymous_variant	79295			BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"GPCR / Class A : Olfactory receptors"	14767	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily H, member 6"				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.369T>A	3.37:g.97983497T>A			99466187	Q6IF88	Silent	SNP	ENST00000383696.2	37	CCDS33800.1																																																																																				0.383	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			A	97983497	T	A	97983497	2	1	91	1	0	0	0	0	0	0	0	1	11194	1567	55	5		5	OR5H6	3	97983497	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	95195	97983497	100038933	34	24926										
C3orf52	79669	hgsc.bcm.edu	37	chr3	111805273	111805273	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acatggacctggcccaacccTcacagccagtagacgagctg	10	15	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:111805273T>C	ENST00000264848.5	+	1	78	c.19T>C	c.(19-21)Tca>Cca	p.S7P	C3orf52_ENST00000430855.1_Missense_Mutation_p.S7P|C3orf52_ENST00000431717.2_Missense_Mutation_p.S7P	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52	7						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						GGCCCAACCCTCACAGCCAGT	0.652																																																0			3											49	52	51					3																	111805273		692	1591	2283	113287963	SO:0001583	missense	79669			AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"TPA induced trans-membrane protein"	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.19T>C	3.37:g.111805273T>C	ENSP00000264848:p.Ser7Pro		113287963	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Missense_Mutation	SNP	ENST00000264848.5	37	CCDS46887.1	.	.	.	.	.	.	.	.	.	.	T	1.957	-0.439802	0.04636	.	.	ENSG00000114529	ENST00000430855;ENST00000431717;ENST00000264848	T;T;T	0.30981	1.53;1.51;1.97	4.07	2.27	0.28462	.	0.620541	0.15155	N	0.277494	T	0.07638	0.0192	N	0.01109	-1.01	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.37865	-0.9687	10	0.02654	T	1	-4.112	6.1666	0.20394	0.0:0.7701:0.0:0.2299	.	7;7;7	Q5BVD1-2;Q5BVD1-3;Q5BVD1	.;.;TTMP_HUMAN	P	7	ENSP00000390333:S7P;ENSP00000399392:S7P;ENSP00000264848:S7P	ENSP00000264848:S7P	S	+	1	0	C3orf52	113287963	0.000000	0.05858	0.019000	0.16419	0.003000	0.03518	-0.559000	0.05971	0.681000	0.31386	-0.534000	0.04291	TCA		0.652	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616		C	111805273	T	C	111805273	3	2	91	1	0	0	0	0	1	0	0	0	2238	1551	54	4	21	4	C3orf52	3	111805273	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	13821776	111805273	86217157	35	24927										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376113	113376113	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcttgttgttgttgctgttgCtgctgctgctgctgctgctg	14	9	0	0	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000316407.4_Silent_p.Q1472Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgctgttgctgctgctgct	0.502																																																0			3											68	71	70					3																	113376113		2188	4274	6462	114858803	SO:0001819	synonymous_variant	205717			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4416G>A	3.37:g.113376113C>T			114858803	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																				0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376113	C	T	113376113	2	4	91	1	0	0	0	0	0	0	0	1	8289	796	28	3		3	KIAA2018	3	113376113	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	1570840	113376113	84646317	36	24928										
MBD4	8930	hgsc.bcm.edu	37	chr3	129152970	129152970	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tttctatctgtgttcgtgggAtggtatcttctgaaaaggaa	11	5	4	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:129152970A>G	ENST00000249910.1	-	4	1386	c.1211T>C	c.(1210-1212)aTc>aCc	p.I404T	MBD4_ENST00000507208.1_Missense_Mutation_p.I404T|MBD4_ENST00000393278.2_Missense_Mutation_p.I86T|MBD4_ENST00000509587.1_5'UTR|MBD4_ENST00000429544.2_Missense_Mutation_p.I398T|MBD4_ENST00000503197.1_Missense_Mutation_p.I404T	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	404					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						TGTTCGTGGGATGGTATCTTC	0.333								Base excision repair (BER), DNA glycosylases																																								0			3											142	139	140					3																	129152970		2203	4300	6503	130635660	SO:0001583	missense	8930			AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.1211T>C	3.37:g.129152970A>G	ENSP00000249910:p.Ile404Thr		130635660	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	37	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235343	0.39498	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000393278;ENST00000507208	D;D;D;T;D	0.94184	-3.26;-3.16;-3.37;1.03;-3.36	5.57	4.41	0.53225	.	1.033840	0.07554	N	0.915929	D	0.93074	0.7795	M	0.62723	1.935	0.35672	D	0.813367	P;P;P;P;P	0.46142	0.799;0.488;0.763;0.873;0.651	B;B;B;P;B	0.44990	0.276;0.108;0.242;0.466;0.122	D	0.87789	0.2617	10	0.39692	T	0.17	-0.343	10.9443	0.47292	0.9263:0.0:0.0737:0.0	.	404;86;398;404;404	E9PEE4;Q2MD36;O95243-2;O95243-3;O95243	.;.;.;.;MBD4_HUMAN	T	398;404;404;86;404	ENSP00000394080:I398T;ENSP00000249910:I404T;ENSP00000424873:I404T;ENSP00000376959:I86T;ENSP00000422327:I404T	ENSP00000249910:I404T	I	-	2	0	MBD4	130635660	0.806000	0.28996	0.574000	0.28523	0.984000	0.73092	1.082000	0.30803	0.966000	0.38159	0.529000	0.55759	ATC		0.333	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		G	129152970	A	G	129152970	3	3	91	1	0	0	0	0	1	0	0	0	9376	333	12	4	551	4	MBD4	3	129152970	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	15776857	129152970	68869460	37	24929										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140409973	140409973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cctgacccccaacacagaatAcgtgtttaaagttagagcca	7	12	0	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:140409973A>T	ENST00000286349.3	+	4	2215	c.2024A>T	c.(2023-2025)tAc>tTc	p.Y675F		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	675	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AACACAGAATACGTGTTTAAA	0.423																																																0			3											153	148	150					3																	140409973		2203	4300	6503	141892663	SO:0001583	missense	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.2024A>T	3.37:g.140409973A>T	ENSP00000286349:p.Tyr675Phe		141892663	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214740	0.79352	.	.	ENSG00000155890	ENST00000286349	D	0.88664	-2.41	5.65	5.65	0.86999	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000037	D	0.89763	0.6809	N	0.24115	0.695	0.33734	D	0.61862	D	0.69078	0.997	D	0.80764	0.994	D	0.92936	0.6368	10	0.87932	D	0	-11.3208	12.2736	0.54721	1.0:0.0:0.0:0.0	.	675	Q8IWZ5	TRI42_HUMAN	F	675	ENSP00000286349:Y675F	ENSP00000286349:Y675F	Y	+	2	0	TRIM42	141892663	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	5.754000	0.68743	2.158000	0.67659	0.528000	0.53228	TAC		0.423	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140409973	A	T	140409973	3	4	91	1	0	0	0	0	1	0	0	0	16557	391	14	5	2038	5	TRIM42	3	140409973	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	11257003	140409973	57612457	38	24930										
ATR	545	hgsc.bcm.edu	37	chr3	142176490	142176490	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cgcatcagcctcattgtaacTtcacatgctcttcgaaaaag	6	12	4	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:142176490T>C	ENST00000350721.4	-	45	7732	c.7611A>G	c.(7609-7611)gaA>gaG	p.E2537E	ATR_ENST00000383101.3_Silent_p.E2473E	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2537	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		E -> Q (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TCATTGTAACTTCACATGCTC	0.393								Other conserved DNA damage response genes																																								0			3											106	99	101					3																	142176490		2203	4300	6503	143659180	SO:0001819	synonymous_variant	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7611A>G	3.37:g.142176490T>C			143659180	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	9.425	1.084057	0.20309	.	.	ENSG00000175054	ENST00000513291	.	.	.	5.2	4.04	0.47022	.	.	.	.	.	T	0.60971	0.2310	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59139	-0.7510	4	.	.	.	-20.4584	10.6321	0.45543	0.0:0.0757:0.0:0.9243	.	.	.	.	G	384	.	.	S	-	1	0	ATR	143659180	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.788000	0.55446	2.102000	0.63906	0.397000	0.26171	AGT		0.393	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142176490	T	C	142176490	2	2	91	1	0	0	0	0	0	0	0	1	1205	1606	56	4		4	ATR	3	142176490	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	1766517	142176490	55845940	39	24931										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178922365	178922365	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aacactcaaagagtaccttgTtccaatcccaggtaaggaag	8	10	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:178922365T>C	ENST00000263967.3	+	6	1291	c.1134T>C	c.(1132-1134)tgT>tgC	p.C378C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	378	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		C -> Y (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAGTACCTTGTTCCAATCCCA	0.333		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											188	149	161					3																	178922365		1836	4093	5929	180405059	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1134T>C	3.37:g.178922365T>C			180405059	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178922365	T	C	178922365	2	2	91	1	0	0	0	0	0	0	0	1	11944	1731	60	4		4	PIK3CA	3	178922365	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	36745875	178922365	19100065	40	24932										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951890	178951890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tattacttataggtttcaggAgatgtgttacaaggcttatc	9	5	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:178951890A>G	ENST00000263967.3	+	21	3102	c.2945A>G	c.(2944-2946)gAg>gGg	p.E982G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	982	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E982G(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGGTTTCAGGAGATGTGTTAC	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	thyroid(1)	3											116	106	109					3																	178951890		1859	4091	5950	180434584	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2945A>G	3.37:g.178951890A>G	ENSP00000263967:p.Glu982Gly		180434584	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.702741	0.48307	.	.	ENSG00000121879	ENST00000263967	T	0.78003	-1.14	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.74943	0.3783	L	0.59436	1.845	0.80722	D	1	P	0.36086	0.536	B	0.34873	0.191	T	0.73500	-0.3963	10	0.32370	T	0.25	-16.0253	16.635	0.85050	1.0:0.0:0.0:0.0	.	982	P42336	PK3CA_HUMAN	G	982	ENSP00000263967:E982G	ENSP00000263967:E982G	E	+	2	0	PIK3CA	180434584	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.859000	0.92264	2.330000	0.79161	0.477000	0.44152	GAG		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951890	A	G	178951890	3	3	91	1	0	0	0	0	1	0	0	0	11944	304	11	4	3023	4	PIK3CA	3	178951890	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	29525	178951890	19070540	41	24933										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910848	184910848	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggggaagagtattggctgggAataacctctaacaacttcat	11	7	2	1	rs200718927		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:184910848A>G	ENST00000231887.3	-	7	1413	c.1338T>C	c.(1336-1338)atT>atC	p.I446I	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Silent_p.I350I	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	446	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			ATTGGCTGGGAATAACCTCTA	0.423																																																0			3											98	100	100					3																	184910848		2203	4300	6503	186393542	SO:0001819	synonymous_variant	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1338T>C	3.37:g.184910848A>G			186393542	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	37	CCDS33901.1																																																																																				0.423	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			G	184910848	A	G	184910848	2	3	91	1	0	0	0	0	0	0	0	1	4993	242	9	4		4	EHHADH	3	184910848	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	5958958	184910848	13111582	42	24934										
RFC4	5984	hgsc.bcm.edu	37	chr3	186507806	186507806	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acagttgcacaaaggctgatGagttgcaaatgttcatcagc	10	8	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:186507806G>A	ENST00000392481.2	-	11	1325	c.1044C>T	c.(1042-1044)ctC>ctT	p.L348L	RFC4_ENST00000433496.1_Silent_p.L321L|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000296273.2_Silent_p.L348L|SNORA63_ENST00000363450.1_RNA	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	348					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		AAAGGCTGATGAGTTGCAAAT	0.358																																																0			3											88	84	85					3																	186507806		2203	4300	6503	187990500	SO:0001819	synonymous_variant	5984				CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"ATPases / AAA-type"	9972	protein-coding gene	gene with protein product	"A1 37 kDa subunit", "activator 1 37 kDa subunit", "RFC 37 kDa subunit"	102577	"replication factor C (activator 1) 4 (37kD)"			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.1044C>T	3.37:g.186507806G>A			187990500	B4DM41|D3DNV2|Q6FHX7	Silent	SNP	ENST00000392481.2	37	CCDS3283.1																																																																																				0.358	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		A	186507806	G	A	186507806	2	1	91	1	0	0	0	0	0	0	0	1	13284	1277	45	3		3	RFC4	3	186507806	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	1596958	186507806	11514624	43	24935										
TNK2	10188	hgsc.bcm.edu	37	chr3	195611887	195611887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggtgggaactcagcctccagTcgctttccactgaacacctg	10	14	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr3:195611887T>C	ENST00000333602.6	-	4	869	c.252A>G	c.(250-252)cgA>cgG	p.R84R	TNK2_ENST00000316664.3_Silent_p.R84R|TNK2_ENST00000392400.1_Silent_p.R84R|TNK2_ENST00000428187.1_Silent_p.R116R|TNK2_ENST00000468819.1_5'UTR|TNK2_ENST00000381916.2_Silent_p.R147R	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	84	SAM-like domain.				cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CAGCCTCCAGTCGCTTTCCAC	0.652																																																0			3											47	42	44					3																	195611887		2203	4300	6503	197096284	SO:0001819	synonymous_variant	10188			L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.252A>G	3.37:g.195611887T>C			197096284	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																				0.652	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		C	195611887	T	C	195611887	2	2	91	1	0	0	0	0	0	0	0	1	16357	1654	58	4		4	TNK2	3	195611887	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	9104081	195611887	2410543	44	24936										
DOK7	285489	hgsc.bcm.edu	37	chr4	3495129	3495129	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctgcctggccctgcccctggCgagccctgggaagcaggcgg	16	16	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:3495129C>T	ENST00000340083.5	+	7	1481	c.1416C>T	c.(1414-1416)ggC>ggT	p.G472G	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.G472G|DOK7_ENST00000507039.1_3'UTR	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	472					neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CTGCCCCTGGCGAGCCCTGGG	0.716																																																0			4											5	6	6					4																	3495129		2078	4093	6171	3464927	SO:0001819	synonymous_variant	285489			AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"chromosome 4 open reading frame 25"	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1416C>T	4.37:g.3495129C>T			3464927	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																				0.716	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		T	3495129	C	T	3495129	2	4	91	1	0	0	0	0	0	0	0	1	4713	755	27	1		1	DOK7	4	3495129	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10		3495129	187659147	45	24937										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602576	13602576	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gactgtcactttgatcagatGcagcactagtcataggaccc	9	11	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:13602576G>T	ENST00000040738.5	-	10	6083	c.5948C>A	c.(5947-5949)gCa>gAa	p.A1983E		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1983						nucleus (GO:0005634)	DNA binding (GO:0003677)										TTGATCAGATGCAGCACTAGT	0.478																																																0			4											132	125	128					4																	13602576		2203	4300	6503	13211674	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5948C>A	4.37:g.13602576G>T	ENSP00000040738:p.Ala1983Glu		13211674	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094165	0.36952	.	.	ENSG00000038219	ENST00000040738	T	0.07567	3.18	5.09	3.32	0.38043	.	0.409091	0.20800	N	0.085444	T	0.05593	0.0147	L	0.27053	0.805	0.09310	N	1	P	0.44877	0.845	B	0.39379	0.298	T	0.32903	-0.9889	10	0.36615	T	0.2	-2.6419	6.4077	0.21674	0.1666:0.153:0.6804:0.0	.	1983	Q8NFC6	BOD1L_HUMAN	E	1983	ENSP00000040738:A1983E	ENSP00000040738:A1983E	A	-	2	0	BOD1L	13211674	0.034000	0.19679	0.177000	0.23020	0.898000	0.52572	2.105000	0.41825	0.686000	0.31488	0.561000	0.74099	GCA		0.478	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13602576	G	T	13602576	3	4	91	1	0	0	0	0	1	0	0	0	1484	1319	46	2	3275	2	BOD1L	4	13602576	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	10107447	13602576	177551700	46	24938										
AFM	173	hgsc.bcm.edu	37	chr4	74351752	74351752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctggatcccgaagagaaatgCcaggcttatgaaagtaacag	11	8	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:74351752C>T	ENST00000226355.3	+	4	537	c.444C>T	c.(442-444)tgC>tgT	p.C148C		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	148	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAGAGAAATGCCAGGCTTATG	0.368																																																0			4											81	83	82					4																	74351752		2203	4300	6503	74570616	SO:0001819	synonymous_variant	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.444C>T	4.37:g.74351752C>T			74570616	A8K3E1|Q32MR3|Q4W5C5	Silent	SNP	ENST00000226355.3	37	CCDS3557.1																																																																																				0.368	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			T	74351752	C	T	74351752	2	4	91	1	0	0	0	0	0	0	0	1	361	747	26	3		3	AFM	4	74351752	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	60749176	74351752	116802524	47	24939										
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99214663	99214663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgcttcaagccctggctcaaAatagtaagtttcattatgtt	7	8	3	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:99214663A>T	ENST00000408927.3	+	2	222	c.109A>T	c.(109-111)Aat>Tat	p.N37Y	RAP1GDS1_ENST00000453712.2_Missense_Mutation_p.N38Y|RAP1GDS1_ENST00000408900.3_Missense_Mutation_p.N37Y|RAP1GDS1_ENST00000512857.1_3'UTR|RAP1GDS1_ENST00000380158.4_Missense_Mutation_p.N38Y|RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.N38Y|RAP1GDS1_ENST00000264572.7_Missense_Mutation_p.N38Y	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	37					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		CCTGGCTCAAAATAGTAAGTT	0.358			T	NUP98	T-ALL																																		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	0			4											61	56	58					4																	99214663		1847	4092	5939	99433686	SO:0001583	missense	5910				CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.109A>T	4.37:g.99214663A>T	ENSP00000386153:p.Asn37Tyr		99433686	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	ENST00000408927.3	37	CCDS43253.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.931474	0.52866	.	.	ENSG00000138698	ENST00000509011;ENST00000380158;ENST00000264572;ENST00000508213;ENST00000408927;ENST00000514122;ENST00000453712;ENST00000511212;ENST00000408900;ENST00000339360	T;T;T;T;T;T;T;T;T;T	0.56611	1.45;0.78;1.42;0.45;1.42;1.22;1.42;0.57;0.78;1.41	5.54	5.54	0.83059	Armadillo-like helical (1);	0.114500	0.56097	D	0.000040	T	0.67439	0.2893	L	0.54323	1.7	0.49483	D	0.999793	D;D;D;D;D;D;D	0.69078	0.997;0.997;0.995;0.989;0.997;0.996;0.997	D;D;D;P;D;D;D	0.80764	0.984;0.994;0.986;0.903;0.926;0.935;0.926	T	0.69654	-0.5087	10	0.62326	D	0.03	-7.7096	13.889	0.63726	1.0:0.0:0.0:0.0	.	38;37;38;37;38;38;37	E9PH06;P52306-2;Q499L7;P52306;Q4QQI8;G5E9P9;B3KNU0	.;.;.;GDS1_HUMAN;.;.;.	Y	37;38;38;37;37;37;38;38;37;38	ENSP00000425992:N37Y;ENSP00000369503:N38Y;ENSP00000264572:N38Y;ENSP00000426096:N37Y;ENSP00000386153:N37Y;ENSP00000424324:N37Y;ENSP00000407157:N38Y;ENSP00000421599:N38Y;ENSP00000386223:N37Y;ENSP00000340454:N38Y	ENSP00000264572:N38Y	N	+	1	0	RAP1GDS1	99433686	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.641000	0.74324	2.101000	0.63845	0.455000	0.32223	AAT		0.358	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		T	99214663	A	T	99214663	3	4	91	1	0	0	0	0	1	0	0	0	13076	14	1	5	118	5	RAP1GDS1	4	99214663	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	24862911	99214663	91939613	48	24940										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155244425	155244425	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtttgtttgtttgtttgtttGttttttgcacgactgcttcc	9	6	0	0	rs79509145		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:155244425G>T	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Missense_Mutation_p.Q1359K	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ttgtttgtttgttttttgCAC	0.368																																																0			4											84	63	69					4																	155244425		692	1591	2283	155463875	SO:0001627	intron_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2654-785C>A	4.37:g.155244425G>T			155463875	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.665839	0.00765	.	.	ENSG00000197410	ENST00000339452	T	0.55930	0.49	1.06	-2.12	0.07165	.	.	.	.	.	T	0.25158	0.0611	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	9	0.06099	T	0.92	.	0.0385	0.00007	0.2541:0.2052:0.2285:0.3121	.	1359	E9PC11	.	K	1359	ENSP00000345062:Q1359K	ENSP00000345062:Q1359K	Q	-	1	0	DCHS2	155463875	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.354000	0.02614	-2.047000	0.00908	-1.973000	0.00462	CAA		0.368	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155244425	G	T	155244425	1	4	91	0	1	0	0	0	0	0	0	0	4294	1386	48	2		2	DCHS2	4	155244425	Intron	SNP	G	TCGA-CL-5917-01A-11D-1657-10	56029762	155244425	35909851	49	24941										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167983666	167983666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gatcgaagggttttcctggaCtccaagtgcggaaataatca	11	8	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:167983666C>A	ENST00000357154.3	-	4	358	c.221G>T	c.(220-222)aGt>aTt	p.S74I	SPOCK3_ENST00000421836.2_Missense_Mutation_p.S23I|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Missense_Mutation_p.S71I|SPOCK3_ENST00000511269.1_Missense_Mutation_p.S71I|SPOCK3_ENST00000534949.1_Intron|SPOCK3_ENST00000506886.1_Missense_Mutation_p.S74I|SPOCK3_ENST00000541637.1_Intron|SPOCK3_ENST00000512648.1_Missense_Mutation_p.S71I|SPOCK3_ENST00000510741.1_Missense_Mutation_p.S71I|SPOCK3_ENST00000511531.1_Missense_Mutation_p.S74I|SPOCK3_ENST00000512681.1_Intron|SPOCK3_ENST00000535728.1_5'UTR|SPOCK3_ENST00000504953.1_Missense_Mutation_p.S71I|SPOCK3_ENST00000502330.1_Missense_Mutation_p.S74I|SPOCK3_ENST00000541354.1_5'UTR	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	74					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		TTTTCCTGGACTCCAAGTGCG	0.294																																																0			4											61	65	63					4																	167983666		2200	4297	6497	168220241	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.221G>T	4.37:g.167983666C>A	ENSP00000349677:p.Ser74Ile		168220241	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.246970	0.39697	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000511269;ENST00000421836;ENST00000512648;ENST00000510403;ENST00000509854;ENST00000506697;ENST00000512042	T;T;T;T;T;T;T;T;T;T;T;T;T	0.46451	1.49;1.47;1.47;1.49;1.49;1.49;1.46;1.47;1.27;2.2;0.89;0.87;0.87	4.61	2.53	0.30540	.	0.416166	0.24516	N	0.037852	T	0.40272	0.1110	L	0.50333	1.59	0.80722	D	1	P;P;P;P;P;P	0.47409	0.713;0.877;0.877;0.789;0.874;0.895	B;B;B;P;P;P	0.47470	0.434;0.276;0.276;0.452;0.466;0.548	T	0.15723	-1.0427	10	0.56958	D	0.05	-5.9505	6.9794	0.24694	0.0:0.661:0.0:0.339	.	23;83;71;74;71;74	B4DHB4;B4DFW5;E7EP61;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;TICN3_HUMAN	I	74;71;71;74;74;74;71;71;23;71;71;71;74;74	ENSP00000349677:S74I;ENSP00000350153:S71I;ENSP00000425570:S71I;ENSP00000420920:S74I;ENSP00000423421:S74I;ENSP00000423606:S74I;ENSP00000426716:S71I;ENSP00000425502:S71I;ENSP00000411344:S23I;ENSP00000426177:S71I;ENSP00000423367:S71I;ENSP00000424168:S74I;ENSP00000425407:S74I	ENSP00000349677:S74I	S	-	2	0	SPOCK3	168220241	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.288000	0.33296	0.306000	0.22856	0.585000	0.79938	AGT		0.294	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			A	167983666	C	A	167983666	3	1	91	1	0	0	0	0	1	0	0	0	15120	565	20	2	1125	2	SPOCK3	4	167983666	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	12739241	167983666	23170610	50	24942										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186598556	186598556	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctggaagctgctggtagtggAttagtgattttttgtgtata	13	3	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr4:186598556A>G	ENST00000284776.7	-	4	465				SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000437304.2_Silent_p.N29N|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000431808.1_Intron|RP11-626E13.1_ENST00000447277.1_RNA	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2						actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		CTGGTAGTGGATTAGTGATTT	0.423																																					Esophageal Squamous(153;41 2433 9491 36028)											0			4											366	314	330					4																	186598556		692	1591	2283	186835550	SO:0001627	intron_variant	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.44+1020T>C	4.37:g.186598556A>G			186835550	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																				0.423	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		G	186598556	A	G	186598556	1	3	91	0	1	0	0	0	0	0	0	0	14965	330	12	4		4	SORBS2	4	186598556	Intron	SNP	A	TCGA-CL-5917-01A-11D-1657-10	18614890	186598556	4555720	51	24943										
MARCH11	441061	hgsc.bcm.edu	37	chr5	16067614	16067614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctctcatcacaacctcccccGagctgttatcttctgataag	5	15	4	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:16067614G>A	ENST00000332432.8	-	4	1374	c.1175C>T	c.(1174-1176)tCg>tTg	p.S392L		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	392					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						AACCTCCCCCGAGCTGTTATC	0.463																																																0			5											182	177	179					5																	16067614		1943	4147	6090	16120614	SO:0001583	missense	441061			BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.1175C>T	5.37:g.16067614G>A	ENSP00000333181:p.Ser392Leu		16120614	A7E2S6	Missense_Mutation	SNP	ENST00000332432.8	37	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332104	0.81801	.	.	ENSG00000183654	ENST00000332432	T	0.22134	1.97	5.12	5.12	0.69794	.	0.135742	0.50627	D	0.000113	T	0.26919	0.0659	L	0.43152	1.355	0.80722	D	1	D	0.61080	0.989	P	0.46320	0.512	T	0.02505	-1.1149	10	0.62326	D	0.03	-14.7453	18.9417	0.92608	0.0:0.0:1.0:0.0	.	392	A6NNE9	MARHB_HUMAN	L	392	ENSP00000333181:S392L	ENSP00000333181:S392L	S	-	2	0	MARCH11	16120614	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	6.707000	0.74654	2.525000	0.85131	0.655000	0.94253	TCG		0.463	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		A	16067614	G	A	16067614	3	1	91	1	0	0	0	0	1	0	0	0	9330	1059	37	1	37	1	MARCH11	5	16067614	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10		16067614	164847646	52	24944										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527555	23527555	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gagtgtgggcggggctttagAgataagtcaaacctcctcag	14	8	2	1	rs200853373		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:23527555A>C	ENST00000296682.3	+	11	2540	c.2358A>C	c.(2356-2358)agA>agC	p.R786S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	786					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R786S(3)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGGCTTTAGAGATAAGTCAA	0.577										HNSCC(3;0.000094)																																						3	Substitution - Missense(3)	endometrium(2)|NS(1)	5											100	92	95					5																	23527555		2196	4292	6488	23563312	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2358A>C	5.37:g.23527555A>C	ENSP00000296682:p.Arg786Ser		23563312	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	a	0.001	-3.314329	0.00018	.	.	ENSG00000164256	ENST00000296682	T	0.35048	1.33	3.09	-6.17	0.02091	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10035	0.0246	N	0.05050	-0.12	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24728	-1.0152	9	0.02654	T	1	.	0.9381	0.01349	0.3133:0.2619:0.0944:0.3304	.	786	Q9NQV7	PRDM9_HUMAN	S	786	ENSP00000296682:R786S	ENSP00000296682:R786S	R	+	3	2	PRDM9	23563312	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-10.885000	0.00005	-2.669000	0.00415	-1.528000	0.00924	AGA		0.577	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		C	23527555	A	C	23527555	3	2	91	1	0	0	0	0	1	0	0	0	12497	301	11	4	2396	4	PRDM9	5	23527555	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	7459941	23527555	157387705	53	24945										
ZFR	51663	hgsc.bcm.edu	37	chr5	32400255	32400255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aggagtacttttaacacattCggttccttttatgtcttctg	7	8	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:32400255C>T	ENST00000265069.8	-	9	1672	c.1570G>A	c.(1570-1572)Gaa>Aaa	p.E524K		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	524					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		TTAACACATTCGGTTCCTTTT	0.358																																																0			5											141	127	132					5																	32400255		2203	4300	6503	32436012	SO:0001583	missense	51663			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1570G>A	5.37:g.32400255C>T	ENSP00000265069:p.Glu524Lys		32436012	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613796	0.66672	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.05081	3.5	6.16	6.16	0.99307	.	0.131135	0.64402	D	0.000001	T	0.03564	0.0102	N	0.14661	0.345	0.54753	D	0.999985	P	0.47545	0.897	B	0.27500	0.08	T	0.55798	-0.8084	10	0.09338	T	0.73	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	524	Q96KR1	ZFR_HUMAN	K	524;502	ENSP00000265069:E524K	ENSP00000265069:E524K	E	-	1	0	ZFR	32436012	0.998000	0.40836	0.970000	0.41538	0.996000	0.88848	3.994000	0.56994	2.937000	0.99478	0.650000	0.86243	GAA		0.358	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			T	32400255	C	T	32400255	3	4	91	1	0	0	0	0	1	0	0	0	17698	893	31	1	1702	1	ZFR	5	32400255	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	8872700	32400255	148515005	54	24946										
DDX4	54514	hgsc.bcm.edu	37	chr5	55056044	55056044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttagaaatggatgatggaccTtctcgaagagatcatttcat	9	6	3	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:55056044T>C	ENST00000505374.1	+	4	236	c.144T>C	c.(142-144)ccT>ccC	p.P48P	DDX4_ENST00000508580.1_3'UTR|DDX4_ENST00000354991.5_Silent_p.P48P|DDX4_ENST00000353507.5_Silent_p.P48P|DDX4_ENST00000514278.2_Silent_p.P48P|SLC38A9_ENST00000504880.1_Intron	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	48					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGATGGACCTTCTCGAAGAG	0.383																																																0			5											186	183	184					5																	55056044		2203	4300	6503	55091801	SO:0001819	synonymous_variant	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.144T>C	5.37:g.55056044T>C			55091801	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Silent	SNP	ENST00000505374.1	37	CCDS3969.1																																																																																				0.383	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		C	55056044	T	C	55056044	2	2	91	1	0	0	0	0	0	0	0	1	4366	1596	56	4		4	DDX4	5	55056044	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	22655789	55056044	125859216	55	24947										
IPO11	51194	hgsc.bcm.edu	37	chr5	61766116	61766116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	taatggatttgtggaacctcAtaagaatatggaggtgatgg	13	3	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:61766116A>G	ENST00000325324.6	+	7	858	c.689A>G	c.(688-690)cAt>cGt	p.H230R	IPO11_ENST00000409296.3_Missense_Mutation_p.H270R|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	230					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GTGGAACCTCATAAGAATATG	0.343																																																0			5											160	158	159					5																	61766116		2203	4300	6503	61801873	SO:0001583	missense	51194			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.689A>G	5.37:g.61766116A>G	ENSP00000316651:p.His230Arg		61801873	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.909763	0.52439	.	.	ENSG00000086200	ENST00000325324;ENST00000409296	T;T	0.66280	-0.2;-0.2	5.22	5.22	0.72569	Armadillo-like helical (1);Armadillo-type fold (1);	0.051516	0.85682	D	0.000000	T	0.56093	0.1962	L	0.53249	1.67	0.80722	D	1	B;B	0.29909	0.261;0.164	B;B	0.30105	0.111;0.052	T	0.52909	-0.8512	10	0.14252	T	0.57	.	14.7626	0.69617	1.0:0.0:0.0:0.0	.	270;230	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	R	230;270	ENSP00000316651:H230R;ENSP00000386992:H270R	ENSP00000316651:H230R	H	+	2	0	IPO11	61801873	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.724000	0.84798	1.964000	0.57103	0.519000	0.50382	CAT		0.343	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		G	61766116	A	G	61766116	3	3	91	1	0	0	0	0	1	0	0	0	7814	217	8	4	835	4	IPO11	5	61766116	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	6710072	61766116	119149144	56	24948										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64625279	64625279	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttaatgctgcagctcctttcAggctcacacattccagccac	6	15	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:64625279A>G	ENST00000536360.1	-	9	1962	c.1149T>C	c.(1147-1149)ccT>ccC	p.P383P				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	383	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		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)		AGCTCCTTTCAGGCTCACACA	0.413																																																0			5											66	58	61					5																	64625279		2203	4299	6502	64661035	SO:0001819	synonymous_variant	11174			AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.1149T>C	5.37:g.64625279A>G			64661035	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000536360.1	37																																																																																					0.413	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		G	64625279	A	G	64625279	2	3	91	1	0	0	0	0	0	0	0	1	270	175	7	4		4	ADAMTS6	5	64625279	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	2859163	64625279	116289981	57	24949										
MAST4	375449	hgsc.bcm.edu	37	chr5	66461970	66461970	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccagcggaccagaaactgtcCgctgttggtgaaaagcaaac	11	11	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:66461970C>T	ENST00000403625.2	+	29	7258	c.6963C>T	c.(6961-6963)tcC>tcT	p.S2321S	MAST4_ENST00000403666.1_Silent_p.S2132S|MAST4_ENST00000261569.7_Silent_p.S2127S|MAST4_ENST00000405643.1_Silent_p.S2142S|MAST4_ENST00000404260.3_Silent_p.S2324S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2324						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGAAACTGTCCGCTGTTGGTG	0.587											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			5											22	30	27					5																	66461970		2014	4169	6183	66497726	SO:0001819	synonymous_variant	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6963C>T	5.37:g.66461970C>T		1092	66497726	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	3.452	-0.111742	0.06881	.	.	ENSG00000069020	ENST00000443808	.	.	.	4.7	2.87	0.33458	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	0.999993	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	-4.0801	4.4247	0.11497	0.0:0.4234:0.3464:0.2303	.	.	.	.	C	1378	.	.	R	+	1	0	MAST4	66497726	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.291000	0.08343	0.560000	0.29169	0.561000	0.74099	CGC		0.587	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66461970	C	T	66461970	2	4	91	1	0	0	0	0	0	0	0	1	9357	639	23	1		1	MAST4	5	66461970	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	1836691	66461970	114453290	58	24950										
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74676952	74676952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tccctgctaatttcctggttTccctctggtgggcttaccaa	8	13	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:74676952T>C	ENST00000405807.4	-	16	2113	c.1692A>G	c.(1690-1692)ggA>ggG	p.G564G	COL4A3BP_ENST00000508692.1_Intron|COL4A3BP_ENST00000380494.5_Silent_p.G692G|COL4A3BP_ENST00000261415.7_Silent_p.G538G	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	564	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTTCCTGGTTTCCCTCTGGTG	0.373																																																0			5											235	211	219					5																	74676952		2203	4300	6503	74712708	SO:0001819	synonymous_variant	10087			AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1692A>G	5.37:g.74676952T>C			74712708	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	T	9.686	1.150508	0.21371	.	.	ENSG00000113163	ENST00000508809	.	.	.	5.91	3.44	0.39384	.	.	.	.	.	T	0.58409	0.2120	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51568	-0.8689	4	.	.	.	-0.0355	8.8989	0.35481	0.0:0.0639:0.3599:0.5761	.	.	.	.	E	66	.	.	K	-	1	0	COL4A3BP	74712708	0.444000	0.25649	0.998000	0.56505	0.992000	0.81027	-0.474000	0.06607	0.440000	0.26502	-0.332000	0.08345	AAA		0.373	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		C	74676952	T	C	74676952	2	2	91	1	0	0	0	0	0	0	0	1	3698	1770	62	4		4	COL4A3BP	5	74676952	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	8214982	74676952	106238308	59	24951										
APC	324	hgsc.bcm.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	91	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	37496965	112173917	68741343	60	24952			1	16		5	5	1667	N	T_C_A	6.096675e-10
APC	324	hgsc.bcm.edu	37	chr5	112175107	112175107	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gatactccaatatgtttttcAagatgtagttcattatcatc	5	7	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:112175107A>G	ENST00000457016.1	+	16	4196	c.3816A>G	c.(3814-3816)tcA>tcG	p.S1272S	APC_ENST00000257430.4_Silent_p.S1272S|APC_ENST00000508376.2_Silent_p.S1272S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1272	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATGTTTTTCAAGATGTAGTT	0.378		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											53	55	54					5																	112175107		2202	4300	6502	112203006	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3816A>G	5.37:g.112175107A>G			112203006	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175107	A	G	112175107	2	3	91	1	0	0	0	0	0	0	0	1	763	117	5	4		4	APC	5	112175107	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	1190	112175107	68740153	61	24953			1	16		5	5	1667	N	T_C_A	6.096675e-10
APC	324	hgsc.bcm.edu	37	chr5	112175234	112175234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagaaaagattggaactaggTcagctgaagatcctgtgagc	12	6	1	5			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:112175234T>C	ENST00000457016.1	+	16	4323	c.3943T>C	c.(3943-3945)Tca>Cca	p.S1315P	APC_ENST00000257430.4_Missense_Mutation_p.S1315P|APC_ENST00000508376.2_Missense_Mutation_p.S1315P|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1315	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1315fs*3(2)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGAACTAGGTCAGCTGAAGA	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Insertion - Frameshift(2)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											59	61	60					5																	112175234		2202	4300	6502	112203133	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3943T>C	5.37:g.112175234T>C	ENSP00000413133:p.Ser1315Pro		112203133	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	3.336	-0.135598	0.06711	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89681	-2.55;-2.55;-2.55	6.03	0.514	0.17007	.	0.642461	0.16403	N	0.215929	T	0.77003	0.4067	L	0.29908	0.895	0.35708	D	0.816143	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.62158	-0.6913	9	.	.	.	-3.6185	2.9424	0.05835	0.221:0.0622:0.2297:0.4871	.	1317;1315	Q4LE70;P25054	.;APC_HUMAN	P	1315	ENSP00000413133:S1315P;ENSP00000257430:S1315P;ENSP00000427089:S1315P	.	S	+	1	0	APC	112203133	0.120000	0.22244	0.003000	0.11579	0.060000	0.15804	0.357000	0.20199	-0.126000	0.11682	0.533000	0.62120	TCA		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175234	T	C	112175234	3	2	91	1	0	0	0	0	1	0	0	0	763	1667	58	4	4001	4	APC	5	112175234	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	127	112175234	68740026	62	24954			1	16		5	5	1667	N	T_C_A	6.096675e-10
APC	324	hgsc.bcm.edu	37	chr5	112175539	112175539	+	Frame_Shift_Del	DEL	C	C	-													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgcagtggaatggtaagtggCattataagccccagtgatct							TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:112175539delC	ENST00000457016.1	+	16	4628	c.4248delC	c.(4246-4248)ggcfs	p.G1416fs	APC_ENST00000257430.4_Frame_Shift_Del_p.G1416fs|APC_ENST00000508376.2_Frame_Shift_Del_p.G1416fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1416	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.I1417fs*2(3)|p.S1411fs*41(1)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGTAAGTGGCATTATAAGCC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Deletion - Frameshift(6)|Unknown(1)	large_intestine(5)|soft_tissue(1)|skin(1)	5	GRCh37	CD972011	APC	D							113	103	107					5																	112175539		2202	4300	6502	112203438	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4248delC	5.37:g.112175539delC	ENSP00000413133:p.Gly1416fs		112203438	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175539	C	-	112175539	7	5	91	1	0	1	0	1	0	0	0	0	763	697	25	0	4306	0	APC	5	112175539	Frame_Shift_Del	DEL	C	TCGA-CL-5917-01A-11D-1657-10	305	112175539	68739721	63	24955			1	16		5	5	1667	N	T_C_A	6.096675e-10
APC	324	hgsc.bcm.edu	37	chr5	112175583	112175583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agatagccctggacaaaccaTgccaccaagcagaagtaaaa	8	11	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:112175583T>C	ENST00000457016.1	+	16	4672	c.4292T>C	c.(4291-4293)aTg>aCg	p.M1431T	APC_ENST00000257430.4_Missense_Mutation_p.M1431T|APC_ENST00000508376.2_Missense_Mutation_p.M1431T|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1431	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.M1431fs*42(1)|p.Y1376fs*41(1)|p.?(1)|p.P1424fs*19(1)|p.S1411fs*41(1)|p.K1192fs*3(1)|p.Q1429fs*41(1)|p.M1431R(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGACAAACCATGCCACCAAGC	0.478		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	8	Deletion - Frameshift(6)|Substitution - Missense(1)|Unknown(1)	large_intestine(6)|soft_tissue(1)|skin(1)	5											111	99	103					5																	112175583		2202	4300	6502	112203482	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4292T>C	5.37:g.112175583T>C	ENSP00000413133:p.Met1431Thr		112203482	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.539084	0.65085	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.92299	-3.01;-3.01;-3.01	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.94935	0.8362	M	0.64404	1.975	0.80722	D	1	D;D	0.60160	0.987;0.987	D;D	0.66196	0.942;0.942	D	0.94360	0.7587	9	.	.	.	-15.2106	16.6288	0.85011	0.0:0.0:0.0:1.0	.	1433;1431	Q4LE70;P25054	.;APC_HUMAN	T	1431	ENSP00000413133:M1431T;ENSP00000257430:M1431T;ENSP00000427089:M1431T	.	M	+	2	0	APC	112203482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.326000	0.78906	0.533000	0.62120	ATG		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175583	T	C	112175583	3	2	91	1	0	0	0	0	1	0	0	0	763	1464	51	4	4350	4	APC	5	112175583	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	44	112175583	68739677	64	24956			1	16		5	5	1667	N	T_C_A	6.096675e-10
HARS2	23438	hgsc.bcm.edu	37	chr5	140073238	140073238	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gagaaaccaaattttattatCaagaccccaaaggtaatact	5	8	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:140073238C>T	ENST00000230771.3	+	2	394	c.171C>T	c.(169-171)atC>atT	p.I57I	HARS_ENST00000457527.2_5'Flank|HARS_ENST00000504156.1_5'Flank|HARS2_ENST00000448069.2_Intron|HARS_ENST00000307633.3_5'Flank|HARS2_ENST00000508522.1_Intron|HARS_ENST00000431330.2_5'Flank|HARS_ENST00000438307.2_5'Flank|HARS2_ENST00000432671.2_Silent_p.I57I|HARS_ENST00000415192.2_5'Flank|HARS2_ENST00000437649.2_Silent_p.I57I|HARS_ENST00000448240.1_5'Flank|HARS2_ENST00000502303.1_3'UTR|HARS2_ENST00000435019.2_Silent_p.I57I	NM_012208.2	NP_036340.1	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2, mitochondrial	57					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|large_intestine(5)|lung(10)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTTTATTATCAAGACCCCAA	0.443																																																0			5											131	127	128					5																	140073238		2203	4300	6503	140053422	SO:0001819	synonymous_variant	92675			U18937	CCDS4238.1, CCDS64267.1	5q31.3	2012-07-20	2012-07-20	2007-02-23	ENSG00000112855	ENSG00000112855	6.1.1.21	"Aminoacyl tRNA synthetases / Class II"	4817	protein-coding gene	gene with protein product	"histidine tRNA ligase 2, mitochondrial (putative)"	600783	"histidyl-tRNA synthetase-like"	HARSL		7755634, 21464306	Standard	NM_012208		Approved	HO3, HARSR	uc003lgx.3	P49590	OTTHUMG00000129500	ENST00000230771.3:c.171C>T	5.37:g.140073238C>T			140053422	B4DDY8	Silent	SNP	ENST00000230771.3	37	CCDS4238.1																																																																																				0.443	HARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251670.2	NM_012208		T	140073238	C	T	140073238	2	4	91	1	0	0	0	0	0	0	0	1	6981	816	29	3		3	HARS2	5	140073238	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	27897655	140073238	40842022	65	24957										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140799105	140799105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cgaccgtaacgacaacgcacCgcgggtgctgtaccctgcgc	12	16	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:140799105C>T	ENST00000398594.2	+	1	1679	c.1679C>T	c.(1678-1680)cCg>cTg	p.P560L	PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	560	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACAACGCACCGCGGGTGCTG	0.711																																																0			5											28	35	33					5																	140799105		2121	4234	6355	140779289	SO:0001583	missense	56099			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1679C>T	5.37:g.140799105C>T	ENSP00000381594:p.Pro560Leu		140779289	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.989543	0.74589	.	.	ENSG00000254122	ENST00000398594	D	0.81499	-1.5	5.38	5.38	0.77491	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.32852	U	0.005578	D	0.95095	0.8411	H	0.99789	4.78	0.50313	D	0.999864	D;D	0.89917	1.0;1.0	D;D	0.75020	0.98;0.985	D	0.97684	1.0174	10	0.87932	D	0	.	18.7253	0.91711	0.0:1.0:0.0:0.0	.	560;560	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	L	560	ENSP00000381594:P560L	ENSP00000381594:P560L	P	+	2	0	PCDHGB7	140779289	0.996000	0.38824	0.953000	0.39169	0.853000	0.48598	3.758000	0.55220	2.513000	0.84729	0.491000	0.48974	CCG		0.711	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		T	140799105	C	T	140799105	3	4	91	1	0	0	0	0	1	0	0	0	11599	652	23	1	1681	1	PCDHGB7	5	140799105	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	725867	140799105	40116155	66	24958										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150704916	150704916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	accgcaggtagcccagagccGccatgccaatgtatagggaa	12	12	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:150704916G>A	ENST00000335244.4	-	8	1070	c.941C>T	c.(940-942)gCg>gTg	p.A314V	SLC36A2_ENST00000450886.1_Missense_Mutation_p.A38V|SLC36A2_ENST00000521967.1_Missense_Mutation_p.A314V	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	314					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GCCCAGAGCCGCCATGCCAAT	0.532																																																0			5											89	75	80					5																	150704916		2203	4300	6503	150685109	SO:0001583	missense	153201			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.941C>T	5.37:g.150704916G>A	ENSP00000334223:p.Ala314Val		150685109	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.50|12.50	1.955218|1.955218	0.34471|0.34471	.|.	.|.	ENSG00000186335|ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967|ENST00000523044	T;T;T|.	0.03524|.	3.9;3.9;3.9|.	4.82|4.82	1.93|1.93	0.25924|0.25924	.|.	0.266898|.	0.41712|.	D|.	0.000838|.	T|T	0.55593|0.55593	0.1930|0.1930	M|M	0.62723|0.62723	1.935|1.935	0.23421|0.23421	N|N	0.997714|0.997714	P;P|.	0.50528|.	0.936;0.802|.	P;B|.	0.54499|.	0.754;0.382|.	T|T	0.51068|0.51068	-0.8752|-0.8752	10|5	0.87932|.	D|.	0|.	-5.8456|-5.8456	15.7582|15.7582	0.78054|0.78054	0.0:0.6081:0.3919:0.0|0.0:0.6081:0.3919:0.0	.|.	314;314|.	E5RJJ5;Q495M3|.	.;S36A2_HUMAN|.	V|W	314;38;314|67	ENSP00000334223:A314V;ENSP00000399479:A38V;ENSP00000430535:A314V|.	ENSP00000334223:A314V|.	A|R	-|-	2|1	0|2	SLC36A2|SLC36A2	150685109|150685109	0.530000|0.530000	0.26330|0.26330	0.003000|0.003000	0.11579|0.11579	0.035000|0.035000	0.12851|0.12851	2.346000|2.346000	0.44027|0.44027	0.283000|0.283000	0.22279|0.22279	-0.378000|-0.378000	0.06908|0.06908	GCG|CGG		0.532	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			A	150704916	G	A	150704916	3	1	91	1	0	0	0	0	1	0	0	0	14631	1087	38	1	522	1	SLC36A2	5	150704916	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	9905811	150704916	30210344	67	24959										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153026610	153026610	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcattacgccgagctttcccGttgatacatccaatcagttt	6	12	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:153026610G>A	ENST00000285900.5	+	3	686	c.343G>A	c.(343-345)Gtt>Att	p.V115I	GRIA1_ENST00000448073.4_Missense_Mutation_p.V125I|GRIA1_ENST00000518142.1_Intron|GRIA1_ENST00000340592.5_Missense_Mutation_p.V115I|GRIA1_ENST00000518783.1_Missense_Mutation_p.V125I|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000521843.2_Missense_Mutation_p.V46I	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	115					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAGCTTTCCCGTTGATACATC	0.483																																																0			5											167	153	158					5																	153026610		2203	4300	6503	153006803	SO:0001583	missense	2890				CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.343G>A	5.37:g.153026610G>A	ENSP00000285900:p.Val115Ile		153006803	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.511874	0.27036	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.55	4.69	0.59074	Extracellular ligand-binding receptor (1);	0.171743	0.51477	D	0.000100	T	0.68256	0.2981	N	0.12746	0.255	0.42504	D	0.992949	B;B;B;B;B	0.16802	0.019;0.019;0.019;0.015;0.003	B;B;B;B;B	0.18561	0.013;0.022;0.013;0.007;0.002	T	0.61959	-0.6955	10	0.16420	T	0.52	.	13.4589	0.61214	0.0753:0.0:0.9247:0.0	.	125;125;125;115;115	E7ESV8;B7Z9G9;B7Z2W8;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	I	115;115;69;115;46;46;125;125	ENSP00000285900:V115I;ENSP00000339343:V115I;ENSP00000427864:V46I;ENSP00000442108:V46I;ENSP00000428994:V125I;ENSP00000415569:V125I	ENSP00000285900:V115I	V	+	1	0	GRIA1	153006803	1.000000	0.71417	0.355000	0.25773	0.551000	0.35334	3.585000	0.53943	1.354000	0.45846	-0.136000	0.14681	GTT		0.483	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			A	153026610	G	A	153026610	3	1	91	1	0	0	0	0	1	0	0	0	6788	1145	40	1	353	1	GRIA1	5	153026610	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	2321694	153026610	27888650	68	24960										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172336688	172336688	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agtgtgaacgagctctatgtCgatgacccagacaaggacag	12	9	1	3	rs146725470	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr5:172336688C>T	ENST00000393784.3	+	4	313	c.174C>T	c.(172-174)gtC>gtT	p.V58V	ERGIC1_ENST00000523291.1_Silent_p.V58V|ERGIC1_ENST00000326654.2_Silent_p.V13V	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	58					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGCTCTATGTCGATGACCCAG	0.542													C|||	6	0.00119808	0.0045	0	5008	,	,		22510	0		0	False		,,,				2504	0															0			5						C		15,4391	22.3+/-47.3	0,15,2188	224	171	189		174	-1.2	1	5	dbSNP_134	189	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ERGIC1	NM_001031711.2		0,16,6487	TT,TC,CC		0.0116,0.3404,0.123		58/291	172336688	16,12990	2203	4300	6503	172269294	SO:0001819	synonymous_variant	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.174C>T	5.37:g.172336688C>T			172269294	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	37	CCDS34292.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.355	0.831742	0.16820	0.003404	1.16E-4	ENSG00000113719	ENST00000519567	.	.	.	5.11	-1.19	0.09585	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40175	-0.9577	4	.	.	.	-47.4619	6.4816	0.22065	0.0:0.2981:0.2703:0.4316	.	.	.	.	L	47	.	.	S	+	2	0	ERGIC1	172269294	0.823000	0.29233	0.991000	0.47740	0.788000	0.44548	-0.227000	0.09126	-0.310000	0.08766	-0.251000	0.11542	TCG		0.542	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		T	172336688	C	T	172336688	2	4	91	1	0	0	0	0	0	0	0	1	5236	871	31	1		1	ERGIC1	5	172336688	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	19310078	172336688	8578572	69	24961										
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834820	27834820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cctttttgacgccagccgccGcgggcttcttcgccttcttc	9	17	2	1	rs200387249		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr6:27834820G>T	ENST00000331442.3	-	1	539	c.488C>A	c.(487-489)gCg>gAg	p.A163E		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	163					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						GCCAGCCGCCGCGGGCTTCTT	0.592																																																0			6											73	84	80					6																	27834820		2202	4300	6502	27942799	SO:0001583	missense	3009			AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"Histones / Replication-dependent"	4719	protein-coding gene	gene with protein product		142711	"H1 histone family, member 5", "histone 1, H1b"	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.488C>A	6.37:g.27834820G>T	ENSP00000330074:p.Ala163Glu		27942799	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106399	0.56291	.	.	ENSG00000184357	ENST00000331442	T	0.25579	1.79	4.96	4.96	0.65561	.	0.346611	0.28635	N	0.014660	T	0.08447	0.0210	N	0.08118	0	0.80722	D	1	P	0.35923	0.528	B	0.36030	0.216	T	0.17289	-1.0374	10	0.36615	T	0.2	-8.7579	17.6043	0.88034	0.0:0.0:1.0:0.0	.	163	P16401	H15_HUMAN	E	163	ENSP00000330074:A163E	ENSP00000330074:A163E	A	-	2	0	HIST1H1B	27942799	0.992000	0.36948	0.074000	0.20217	0.507000	0.33981	4.773000	0.62331	2.487000	0.83934	0.655000	0.94253	GCG		0.592	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		T	27834820	G	T	27834820	3	4	91	1	0	0	0	0	1	0	0	0	7144	1087	38	2	196	2	HIST1H1B	6	27834820	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10		27834820	143280247	70	24962										
TREM2	54209	hgsc.bcm.edu	37	chr6	41129105	41129105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggggttgtagattccgcagcGtaatggtgagagtgccaccc	15	9	0	2	rs2234253	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr6:41129105G>A	ENST00000373113.3	-	2	380	c.287C>T	c.(286-288)aCg>aTg	p.T96M	TREM2_ENST00000338469.3_Missense_Mutation_p.T96M|TREM2_ENST00000373122.4_Missense_Mutation_p.T96M	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	96	Ig-like V-type.		T -> K (in dbSNP:rs2234253).|T -> R (in dbSNP:rs2234253).		axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					ATTCCGCAGCGTAATGGTGAG	0.592																																																0			6											134	121	125					6																	41129105		2203	4300	6503	41237083	SO:0001583	missense	54209			AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"Immunoglobulin superfamily / V-set domain containing"	17761	protein-coding gene	gene with protein product		605086	"triggering receptor expressed on myeloid cells 2a"			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.287C>T	6.37:g.41129105G>A	ENSP00000362205:p.Thr96Met		41237083	Q8N5H8|Q8WYN6	Missense_Mutation	SNP	ENST00000373113.3	37	CCDS4852.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.205554	0.39003	.	.	ENSG00000095970	ENST00000373113;ENST00000338469;ENST00000373122	T;T;T	0.69685	-0.42;-0.42;-0.42	5.51	5.51	0.81932	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	T	0.81375	0.4809	M	0.86178	2.8	0.23661	P	0.99717216	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.84144	0.0419	9	0.87932	D	0	-13.5737	16.5755	0.84635	0.0:0.0:1.0:0.0	.	96;96;96	Q9NZC2-2;Q9NZC2-3;Q9NZC2	.;.;TREM2_HUMAN	M	96	ENSP00000362205:T96M;ENSP00000342651:T96M;ENSP00000362214:T96M	ENSP00000342651:T96M	T	-	2	0	TREM2	41237083	0.996000	0.38824	0.075000	0.20258	0.034000	0.12701	5.140000	0.64807	2.599000	0.87857	0.561000	0.74099	ACG		0.592	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965		A	41129105	G	A	41129105	3	1	91	1	0	0	0	0	1	0	0	0	16511	1145	40	1	421	1	TREM2	6	41129105	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	13294285	41129105	129985962	71	24963										
T	6862	hgsc.bcm.edu	37	chr6	166580264	166580264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tccagcggtggttgtccgccGccacgaagtccagcaggaag	14	13	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr6:166580264G>A	ENST00000296946.2	-	3	755	c.287C>T	c.(286-288)gCg>gTg	p.A96V	T_ENST00000366871.3_Missense_Mutation_p.A96V	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	96					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		GTTGTCCGCCGCCACGAAGTC	0.657									Chordoma, Familial Clustering of																																							0			6											60	54	56					6																	166580264		2203	4300	6503	166500254	SO:0001583	missense	6862	Familial Cancer Database		AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.287C>T	6.37:g.166580264G>A	ENSP00000296946:p.Ala96Val		166500254	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	37	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.942177	0.92526	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	T;T;T	0.80033	-1.33;-1.33;-1.33	4.62	4.62	0.57501	p53-like transcription factor, DNA-binding (1);	0.187296	0.46758	D	0.000270	T	0.80576	0.4649	M	0.90082	3.085	0.47476	D	0.99943	P;P;P	0.45283	0.727;0.855;0.561	B;B;B	0.39660	0.158;0.306;0.111	D	0.86500	0.1803	10	0.72032	D	0.01	.	16.8408	0.85968	0.0:0.0:1.0:0.0	.	96;96;96	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	V	96	ENSP00000355841:A96V;ENSP00000296946:A96V;ENSP00000355836:A96V	ENSP00000296946:A96V	A	-	2	0	T	166500254	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.095000	0.94175	2.290000	0.77057	0.655000	0.94253	GCG		0.657	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		A	166580264	G	A	166580264	3	1	91	1	0	0	0	0	1	0	0	0	15527	1087	38	1	1048	1	T	6	166580264	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	125451159	166580264	4534803	72	24964										
GET4	51608	hgsc.bcm.edu	37	chr7	926225	926225	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcaaaacagtgcagcagactTgtccatgctggtcctggagt	12	10	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:926225T>C	ENST00000265857.3	+	3	348	c.254T>C	c.(253-255)tTg>tCg	p.L85S	RP11-449P15.2_ENST00000609998.1_RNA|GET4_ENST00000407192.1_Missense_Mutation_p.L32S	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	85					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GCAGCAGACTTGTCCATGCTG	0.562																																																0			7											144	136	139					7																	926225		2203	4300	6503	892751	SO:0001583	missense	0			AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"CGI-20 protein", "conserved edge protein", "transmembrane domain recognition complex, 35kDa"	612056	"chromosome 7 open reading frame 20"	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.254T>C	7.37:g.926225T>C	ENSP00000265857:p.Leu85Ser		892751	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Missense_Mutation	SNP	ENST00000265857.3	37	CCDS5317.1	.	.	.	.	.	.	.	.	.	.	t	26.2	4.717465	0.89205	.	.	ENSG00000239857	ENST00000265857;ENST00000412734;ENST00000407192;ENST00000441491	T	0.76186	-1.0	5.58	5.58	0.84498	.	0.069705	0.64402	D	0.000013	D	0.88306	0.6401	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90571	0.4522	10	0.87932	D	0	-17.0699	15.7423	0.77910	0.0:0.0:0.0:1.0	.	85	Q7L5D6	GET4_HUMAN	S	85;39;32;97	ENSP00000265857:L85S	ENSP00000265857:L85S	L	+	2	0	GET4	892751	1.000000	0.71417	0.688000	0.30117	0.918000	0.54935	7.781000	0.85668	2.116000	0.64780	0.529000	0.55759	TTG		0.562	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949		C	926225	T	C	926225	3	2	91	1	0	0	0	0	1	0	0	0	6356	1821	63	4	264	4	GET4	7	926225	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10		926225	158212438	73	24965										
BLVRA	644	hgsc.bcm.edu	37	chr7	43832380	43832380	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acactgtcattggcggccgcTcaggaactgtgggagctggc	15	11	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:43832380T>C	ENST00000402924.1	+	6	484	c.321T>C	c.(319-321)gcT>gcC	p.A107A	BLVRA_ENST00000265523.4_Silent_p.A107A	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	107					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						TGGCGGCCGCTCAGGAACTGT	0.453																																																0			7											70	64	66					7																	43832380		2203	4300	6503	43798905	SO:0001819	synonymous_variant	644			BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.321T>C	7.37:g.43832380T>C			43798905	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																				0.453	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712		C	43832380	T	C	43832380	2	2	91	1	0	0	0	0	0	0	0	1	1452	1538	54	4		4	BLVRA	7	43832380	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	42906155	43832380	115306283	74	24966										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72891434	72891434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctctcttcttatcattttctTccttcaacacagcaagccgt	3	14	5	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:72891434T>C	ENST00000339594.4	-	7	2695	c.2357A>G	c.(2356-2358)gAa>gGa	p.E786G	BAZ1B_ENST00000404251.1_Missense_Mutation_p.E786G	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	786					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				atcattttcttccttCAACAC	0.433																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											0			7											71	65	67					7																	72891434		2203	4300	6503	72529370	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2357A>G	7.37:g.72891434T>C	ENSP00000342434:p.Glu786Gly		72529370	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.718204	0.48622	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.62105	0.05;0.05	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.67748	0.2926	M	0.65498	2.005	0.58432	D	0.999999	D	0.59767	0.986	P	0.50970	0.655	T	0.65463	-0.6162	10	0.20046	T	0.44	-26.8675	14.9553	0.71107	0.0:0.0:0.0:1.0	.	786	Q9UIG0	BAZ1B_HUMAN	G	786	ENSP00000342434:E786G;ENSP00000385442:E786G	ENSP00000342434:E786G	E	-	2	0	BAZ1B	72529370	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.639000	0.83342	2.219000	0.72066	0.459000	0.35465	GAA		0.433	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72891434	T	C	72891434	3	2	91	1	0	0	0	0	1	0	0	0	1331	1783	62	4	2146	4	BAZ1B	7	72891434	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	29059054	72891434	86247229	75	24967										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77247821	77247821	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaattaacactgaaaacatgGtcagctccatagagcctgaa	7	9	1	3	rs9640663	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:77247821G>A	ENST00000248594.6	+	12	1236	c.964G>A	c.(964-966)Gtc>Atc	p.V322I	PTPN12_ENST00000415482.2_Missense_Mutation_p.V203I|PTPN12_ENST00000435495.2_Missense_Mutation_p.V192I	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	322			V -> I (in dbSNP:rs9640663). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1472029, ECO:0000269|PubMed:18669648, ECO:0000269|Ref.5}.		protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TGAAAACATGGTCAGCTCCAT	0.353													G|||	3943	0.78734	0.8729	0.7695	5008	,	,		15802	0.9048		0.6252	False		,,,				2504	0.7301															0			7						G	ILE/VAL,ILE/VAL,ILE/VAL	3643,763	755.1+/-412.5	1510,623,70	115	119	118		607,574,964	3.4	1	7	dbSNP_119	118	5049,3551	629.9+/-398.3	1521,2007,772	yes	missense,missense,missense	PTPN12	NM_001131008.1,NM_001131009.1,NM_002835.3	29,29,29	3031,2630,842	AA,AG,GG		41.2907,17.3173,33.1693	benign,benign,benign	203/662,192/651,322/781	77247821	8692,4314	2203	4300	6503	77085757	SO:0001583	missense	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.964G>A	7.37:g.77247821G>A	ENSP00000248594:p.Val322Ile		77085757	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	1661	0.7605311355311355	424	0.8617886178861789	266	0.7348066298342542	508	0.8881118881118881	463	0.6108179419525066	G	12.04	1.817478	0.32145	0.826827	0.587093	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.34472	1.36;1.36;1.36	5.21	3.41	0.39046	.	0.432581	0.24759	N	0.035823	T	0.00012	0.0000	N	0.17674	0.51	0.39781	P	0.027707000000000037	B	0.02656	0.0	B	0.06405	0.002	T	0.23048	-1.0199	9	0.15066	T	0.55	.	9.1932	0.37211	0.2234:0.0:0.7766:0.0	rs9640663;rs17382002;rs17854591;rs58031922;rs9640663	322	Q05209	PTN12_HUMAN	I	322;203;203;192	ENSP00000248594:V322I;ENSP00000392429:V203I;ENSP00000397991:V192I	ENSP00000248594:V322I	V	+	1	0	PTPN12	77085757	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	2.143000	0.42187	0.696000	0.31696	0.467000	0.42956	GTC		0.353	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			A	77247821	G	A	77247821	3	1	91	1	0	0	0	0	1	0	0	0	12816	1261	44	3	1010	3	PTPN12	7	77247821	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	4356387	77247821	81890842	76	24968										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87160636	87160636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agaaccttctagttctttctTatctttcagtgcttgtccag	6	10	5	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:87160636T>C	ENST00000265724.3	-	22	3076	c.2659A>G	c.(2659-2661)Aag>Gag	p.K887E	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Missense_Mutation_p.K823E	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	887	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		K -> N (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	AGTTCTTTCTTATCTTTCAGT	0.348																																																0			7											131	132	132					7																	87160636		2203	4300	6503	86998572	SO:0001583	missense	5243			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2659A>G	7.37:g.87160636T>C	ENSP00000265724:p.Lys887Glu		86998572	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852941	0.71719	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.91686	-2.89;-2.89	5.67	5.67	0.87782	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96237	0.8773	M	0.83012	2.62	0.58432	D	0.999999	P;D	0.89917	0.467;1.0	B;D	0.87578	0.084;0.998	D	0.96771	0.9568	10	0.87932	D	0	-14.596	16.1924	0.82000	0.0:0.0:0.0:1.0	.	823;887	B5AK60;P08183	.;MDR1_HUMAN	E	668;887;823	ENSP00000265724:K887E;ENSP00000444095:K823E	ENSP00000265724:K887E	K	-	1	0	ABCB1	86998572	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.113000	0.77095	2.287000	0.76781	0.482000	0.46254	AAG		0.348	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		C	87160636	T	C	87160636	3	2	91	1	0	0	0	0	1	0	0	0	40	1763	61	4	1215	4	ABCB1	7	87160636	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	9912815	87160636	71978027	77	24969										
FAM200A	221786	hgsc.bcm.edu	37	chr7	99145377	99145377	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtaagtctgctgtgttttccGgtcatatttgctgttccatc	9	9	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:99145377G>A	ENST00000449309.1	-	2	1033	c.654C>T	c.(652-654)acC>acT	p.T218T		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	218						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						tgtgttttccggtcatatttg	0.343																																																0			7											70	68	69					7																	99145377		1556	2754	4310	98983313	SO:0001819	synonymous_variant	0				CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 38"	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.654C>T	7.37:g.99145377G>A			98983313	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Silent	SNP	ENST00000449309.1	37	CCDS5668.1																																																																																				0.343	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111		A	99145377	G	A	99145377	2	1	91	1	0	0	0	0	0	0	0	1	5552	1103	39	1		1	FAM200A	7	99145377	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	11984741	99145377	59993286	78	24970										
MUC17	140453	hgsc.bcm.edu	37	chr7	100681303	100681303	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	actgaagcccgttcatctccTacaacttctgaaggtaccag	7	13	3	2	rs143516283		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:100681303T>C	ENST00000306151.4	+	3	6670	c.6606T>C	c.(6604-6606)ccT>ccC	p.P2202P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2202	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GTTCATCTCCTACAACTTCTG	0.507																																																0			7											311	311	311					7																	100681303		2203	4300	6503	100468023	SO:0001819	synonymous_variant	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6606T>C	7.37:g.100681303T>C			100468023	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																				0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100681303	T	C	100681303	2	2	91	1	0	0	0	0	0	0	0	1	10004	1509	53	4		4	MUC17	7	100681303	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	1535926	100681303	58457360	79	24971										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107315423	107315423	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcttgcagattggattcataGtgaggtacttggcagatcct	12	7	1	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:107315423G>C	ENST00000265715.3	+	6	858	c.634G>C	c.(634-636)Gtg>Ctg	p.V212L		NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	212					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TGGATTCATAGTGAGGTACTT	0.413									Pendred syndrome																																							0			7											271	249	256					7																	107315423		2203	4300	6503	107102659	SO:0001583	missense	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.634G>C	7.37:g.107315423G>C	ENSP00000265715:p.Val212Leu		107102659	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070310	0.93950	.	.	ENSG00000091137	ENST00000265715	D	0.94138	-3.36	5.61	5.61	0.85477	Sulphate transporter (1);	0.000000	0.64402	D	0.000002	D	0.96275	0.8785	M	0.76727	2.345	0.80722	D	1	D	0.64830	0.994	P	0.62382	0.901	D	0.96096	0.9065	10	0.59425	D	0.04	.	19.6254	0.95676	0.0:0.0:1.0:0.0	.	212	O43511	S26A4_HUMAN	L	212	ENSP00000265715:V212L	ENSP00000265715:V212L	V	+	1	0	SLC26A4	107102659	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.313000	0.96297	2.642000	0.89623	0.650000	0.86243	GTG		0.413	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		C	107315423	G	C	107315423	3	2	91	1	0	0	0	0	1	0	0	0	14556	1029	36	5	652	5	SLC26A4	7	107315423	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	6634120	107315423	51823240	80	24972										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518304	113518304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tacaaatattttctgatttcGtagaaataggttggctagcc	8	6	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:113518304G>A	ENST00000284601.3	-	4	2911	c.2843C>T	c.(2842-2844)aCg>aTg	p.T948M		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	948					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.T948M(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTCTGATTTCGTAGAAATAGG	0.383																																																1	Substitution - Missense(1)	prostate(1)	7											89	89	89					7																	113518304		2203	4299	6502	113305540	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2843C>T	7.37:g.113518304G>A	ENSP00000284601:p.Thr948Met		113305540	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	G	6.104	0.387372	0.11581	.	.	ENSG00000154415	ENST00000284601	T	0.21191	2.02	5.71	3.89	0.44902	.	0.636589	0.15483	N	0.259983	T	0.28101	0.0693	L	0.53249	1.67	0.09310	N	1	D	0.67145	0.996	P	0.50490	0.642	T	0.07927	-1.0747	10	0.54805	T	0.06	0.2371	9.2831	0.37740	0.0728:0.0:0.7829:0.1443	.	948	Q16821	PPR3A_HUMAN	M	948	ENSP00000284601:T948M	ENSP00000284601:T948M	T	-	2	0	PPP1R3A	113305540	0.000000	0.05858	0.002000	0.10522	0.103000	0.19146	0.270000	0.18607	0.746000	0.32786	0.650000	0.86243	ACG		0.383	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		A	113518304	G	A	113518304	3	1	91	1	0	0	0	0	1	0	0	0	12405	1145	40	1	529	1	PPP1R3A	7	113518304	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	6202881	113518304	45620359	81	24973										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117431428	117431428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttttggtggcagctgaggggAggatgacttaggaaggttct	17	4	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:117431428A>G	ENST00000160373.3	-	4	1913	c.1822T>C	c.(1822-1824)Tcc>Ccc	p.S608P	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	608					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGCTGAGGGGAGGATGACTTA	0.547																																																0			7											68	65	66					7																	117431428		2203	4300	6503	117218664	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1822T>C	7.37:g.117431428A>G	ENSP00000160373:p.Ser608Pro		117218664	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.56|18.56	3.650327|3.650327	0.67472|0.67472	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000160373	.|T	.|0.68624	.|-0.34	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.047019	.|0.85682	.|D	.|0.000000	T|T	0.73760|0.73760	0.3628|0.3628	M|M	0.75447|0.75447	2.3|2.3	0.44214|0.44214	D|D	0.997046|0.997046	.|D	.|0.56746	.|0.977	.|P	.|0.48738	.|0.588	T|T	0.77490|0.77490	-0.2568|-0.2568	5|10	.|0.56958	.|D	.|0.05	0.0257|0.0257	16.3426|16.3426	0.83092|0.83092	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|608	.|Q8WZ74	.|CTTB2_HUMAN	P|P	136|608	.|ENSP00000160373:S608P	.|ENSP00000160373:S608P	L|S	-|-	2|1	0|0	CTTNBP2|CTTNBP2	117218664|117218664	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	5.286000|5.286000	0.65639|0.65639	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	CTC|TCC		0.547	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117431428	A	G	117431428	3	3	91	1	0	0	0	0	1	0	0	0	4051	304	11	4	3249	4	CTTNBP2	7	117431428	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	3913124	117431428	41707235	82	24974										
C7orf58	79974	hgsc.bcm.edu	37	chr7	120629709	120629709	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cagtgttcccttgtcgtcggCgattttgcccccgacccttc	9	16	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:120629709C>T	ENST00000310396.5	+	2	501	c.34C>T	c.(34-36)Cga>Tga	p.R12*	CPED1_ENST00000340646.5_Nonsense_Mutation_p.R12*|CPED1_ENST00000450913.2_Nonsense_Mutation_p.R12*|CPED1_ENST00000495036.1_3'UTR	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	12						endoplasmic reticulum (GO:0005783)		p.R12*(1)									TTGTCGTCGGCGATTTTGCCC	0.562																																																1	Substitution - Nonsense(1)	large_intestine(1)	7											128	114	119					7																	120629709		2203	4300	6503	120416945	SO:0001587	stop_gained	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.34C>T	7.37:g.120629709C>T	ENSP00000309772:p.Arg12*		120416945	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Nonsense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	37	6.496659	0.97616	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000340646	.	.	.	5.64	4.75	0.60458	.	0.198839	0.33057	N	0.005338	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3463	0.49563	0.0:0.9173:0.0:0.0827	.	.	.	.	X	12	.	ENSP00000309772:R12X	R	+	1	2	C7orf58	120416945	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.247000	0.51422	2.662000	0.90505	0.655000	0.94253	CGA		0.562	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120629709	C	T	120629709	4	4	91	1	0	0	0	0	0	1	0	0	2411	760	27	1	36	1	C7orf58	7	120629709	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	3198281	120629709	38508954	83	24975										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139299047	139299047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cttaccttggaagccgggggGacacacgatgagagcttgct	14	10	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:139299047G>A	ENST00000406875.3	-	8	2069	c.1975C>T	c.(1975-1977)Ccc>Tcc	p.P659S	HIPK2_ENST00000342645.6_Missense_Mutation_p.P659S|HIPK2_ENST00000428878.2_Missense_Mutation_p.P632S	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	659	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					AAGCCGGGGGGACACACGATG	0.612																																																0			7											27	33	31					7																	139299047		1968	4149	6117	138949587	SO:0001583	missense	28996			AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1975C>T	7.37:g.139299047G>A	ENSP00000385571:p.Pro659Ser		138949587	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	37		.	.	.	.	.	.	.	.	.	.	G	27.5	4.839292	0.91117	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.61158	0.3;0.13;0.36	5.48	5.48	0.80851	.	.	.	.	.	T	0.78855	0.4349	.	.	.	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.986;0.998	T	0.80266	-0.1454	8	0.62326	D	0.03	.	19.7173	0.96127	0.0:0.0:1.0:0.0	.	659;632	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	S	659;632;659	ENSP00000385571:P659S;ENSP00000413724:P632S;ENSP00000343108:P659S	ENSP00000343108:P659S	P	-	1	0	HIPK2	138949587	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.724000	0.93272	0.563000	0.77884	CCC		0.612	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		A	139299047	G	A	139299047	3	1	91	1	0	0	0	0	1	0	0	0	7138	1174	41	3	1653	3	HIPK2	7	139299047	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	18669338	139299047	19839616	84	24976										
ZNF786	136051	hgsc.bcm.edu	37	chr7	148767801	148767801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gatggctgagcagctgcgccTtcaggcggaaactcttgtca	13	11	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:148767801T>C	ENST00000491431.1	-	4	2127	c.2063A>G	c.(2062-2064)aAg>aGg	p.K688R	ZNF786_ENST00000451334.3_Missense_Mutation_p.K651R|ZNF786_ENST00000316286.9_Missense_Mutation_p.K602R	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CAGCTGCGCCTTCAGGCGGAA	0.552																																																0			7											84	92	90					7																	148767801		2120	4253	6373	148398734	SO:0001583	missense	136051			AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2063A>G	7.37:g.148767801T>C	ENSP00000417470:p.Lys688Arg		148398734	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.380656	0.24944	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.15834	2.39;2.39;2.39	4.56	3.41	0.39046	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.199618	0.25052	N	0.033518	T	0.08044	0.0201	N	0.17872	0.535	0.09310	N	1	B	0.26120	0.142	B	0.15870	0.014	T	0.35847	-0.9772	10	0.11794	T	0.64	-16.9546	5.832	0.18586	0.0:0.2043:0.0:0.7957	.	688	Q8N393	ZN786_HUMAN	R	602;688;651	ENSP00000313516:K602R;ENSP00000417470:K688R;ENSP00000404984:K651R	ENSP00000313516:K602R	K	-	2	0	ZNF786	148398734	0.000000	0.05858	0.195000	0.23364	0.023000	0.10783	-0.538000	0.06120	0.800000	0.34041	0.533000	0.62120	AAG		0.552	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		C	148767801	T	C	148767801	3	2	91	1	0	0	0	0	1	0	0	0	18197	1609	56	4	289	4	ZNF786	7	148767801	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	9468754	148767801	10370862	85	24977										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149129870	149129870	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcggggggctctcctcgcccTcgggggacatctccccgggc	16	17	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr7:149129870T>C	ENST00000247930.4	-	6	1816	c.1493A>G	c.(1492-1494)gAg>gGg	p.E498G		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTCCTCGCCCTCGGGGGACAT	0.677																																																0			7											16	19	18					7																	149129870		1936	4122	6058	148760803	SO:0001583	missense	27153			AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1493A>G	7.37:g.149129870T>C	ENSP00000247930:p.Glu498Gly		148760803	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	37	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	T	9.872	1.199146	0.22121	.	.	ENSG00000196453	ENST00000247930;ENST00000314683	T	0.06068	3.35	4.44	4.44	0.53790	.	0.120556	0.36854	N	0.002367	T	0.04952	0.0133	N	0.19112	0.55	0.19300	N	0.99998	B	0.18310	0.027	B	0.19391	0.025	T	0.31861	-0.9928	10	0.46703	T	0.11	-7.9914	10.039	0.42146	0.0:0.0:0.0:1.0	.	498	Q9ULD5-2	.	G	498;241	ENSP00000247930:E498G	ENSP00000247930:E498G	E	-	2	0	ZNF777	148760803	0.000000	0.05858	0.558000	0.28319	0.893000	0.52053	0.176000	0.16782	1.868000	0.54150	0.383000	0.25322	GAG		0.677	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		C	149129870	T	C	149129870	3	2	91	1	0	0	0	0	1	0	0	0	18189	1551	54	4	1006	4	ZNF777	7	149129870	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	362069	149129870	10008793	86	24978										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20110684	20110684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cgtccgtggagatgggggagCggacacacgaggggcccttg	19	10	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr8:20110684C>T	ENST00000381569.1	-	3	1115	c.758G>A	c.(757-759)cGc>cAc	p.R253H	LZTS1_ENST00000265801.6_Missense_Mutation_p.R253H|LZTS1_ENST00000522290.1_Missense_Mutation_p.R253H			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	253					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GATGGGGGAGCGGACACACGA	0.622																																																0			8											68	58	62					8																	20110684		2197	4289	6486	20154964	SO:0001583	missense	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.758G>A	8.37:g.20110684C>T	ENSP00000370981:p.Arg253His		20154964	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368200	0.82463	.	.	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.25749	2.1;2.1;1.78	5.78	5.78	0.91487	.	0.160907	0.56097	D	0.000027	T	0.44329	0.1288	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.78314	0.781;0.991	T	0.07233	-1.0783	10	0.12430	T	0.62	-31.5626	18.5689	0.91128	0.0:1.0:0.0:0.0	.	253;253	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	H	253	ENSP00000370981:R253H;ENSP00000265801:R253H;ENSP00000429263:R253H	ENSP00000265801:R253H	R	-	2	0	LZTS1	20154964	1.000000	0.71417	0.980000	0.43619	0.752000	0.42762	4.496000	0.60360	2.739000	0.93911	0.561000	0.74099	CGC		0.622	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		T	20110684	C	T	20110684	3	4	91	1	0	0	0	0	1	0	0	0	9168	768	27	1	1040	1	LZTS1	8	20110684	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10		20110684	126253338	87	24979										
RP1	6101	hgsc.bcm.edu	37	chr8	55534077	55534077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccagagcttcgaggcatttcTacagcacctgacagaggtca	10	12	2	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr8:55534077T>C	ENST00000220676.1	+	2	699	c.551T>C	c.(550-552)cTa>cCa	p.L184P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	184	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			GAGGCATTTCTACAGCACCTG	0.622																																					Colon(91;1014 1389 7634 14542 40420)											0			8											119	122	121					8																	55534077		2203	4300	6503	55696630	SO:0001583	missense	10982			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.551T>C	8.37:g.55534077T>C	ENSP00000220676:p.Leu184Pro		55696630		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.823096	0.71143	.	.	ENSG00000104237	ENST00000220676	D	0.97328	-4.34	5.14	5.14	0.70334	Doublecortin domain (5);	0.000000	0.42548	D	0.000699	D	0.98551	0.9516	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.99741	1.1015	10	0.87932	D	0	-6.0059	14.9895	0.71374	0.0:0.0:0.0:1.0	.	184	P56715	RP1_HUMAN	P	184	ENSP00000220676:L184P	ENSP00000220676:L184P	L	+	2	0	RP1	55696630	1.000000	0.71417	0.902000	0.35471	0.391000	0.30476	6.162000	0.71874	1.946000	0.56461	0.528000	0.53228	CTA		0.622	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		C	55534077	T	C	55534077	3	2	91	1	0	0	0	0	1	0	0	0	13569	1522	53	4	553	4	RP1	8	55534077	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	35423393	55534077	90829945	88	24980										
UBR5	51366	hgsc.bcm.edu	37	chr8	103266662	103266662	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggaagatgttggtcatctggTggtcttattgtgattgaggg	16	3	3	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr8:103266662T>G	ENST00000520539.1	-	59	8874	c.8268A>C	c.(8266-8268)ccA>ccC	p.P2756P	KB-431C1.4_ENST00000520820.1_RNA|KB-431C1.5_ENST00000606361.1_RNA|UBR5_ENST00000521922.1_Silent_p.P2749P|KB-431C1.4_ENST00000499653.1_RNA|UBR5_ENST00000220959.4_Silent_p.P2755P|UBR5_ENST00000518205.1_Silent_p.P484P	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2756	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.|Pro-rich.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			GGTCATCTGGTGGTCTTATTG	0.428																																					Ovarian(131;96 1741 5634 7352 27489)											0			8											207	187	194					8																	103266662		2203	4300	6503	103335838	SO:0001819	synonymous_variant	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.8268A>C	8.37:g.103266662T>G			103335838	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																				0.428	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		G	103266662	T	G	103266662	2	3	91	1	0	0	0	0	0	0	0	1	16945	1683	59	4		4	UBR5	8	103266662	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	47732585	103266662	43097360	89	24981										
CSMD3	114788	hgsc.bcm.edu	37	chr8	114290849	114290849	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tataccttaaatccatgagcActaactgcaaaatcactggt	5	10	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr8:114290849A>G	ENST00000297405.5	-	3	730	c.486T>C	c.(484-486)agT>agC	p.S162S	CSMD3_ENST00000343508.3_Silent_p.S122S|CSMD3_ENST00000352409.3_Silent_p.S162S|CSMD3_ENST00000455883.2_Silent_p.S162S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	162	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATCCATGAGCACTAACTGCAA	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											123	106	112					8																	114290849		2203	4300	6503	114360025	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.486T>C	8.37:g.114290849A>G			114360025	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.378	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	114290849	A	G	114290849	2	3	91	1	0	0	0	0	0	0	0	1	3952	156	6	4		4	CSMD3	8	114290849	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	11024187	114290849	32073173	90	24982										
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4544601	4544601	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtcttggttcgagaacacagCaacctctcaactctagagaa	8	11	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:4544601C>A	ENST00000262352.3	+	2	362	c.126C>A	c.(124-126)agC>agA	p.S42R		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	42					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	GAGAACACAGCAACCTCTCAA	0.388																																																0			9											154	153	153					9																	4544601		2203	4300	6503	4534601	SO:0001583	missense	6505				CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.126C>A	9.37:g.4544601C>A	ENSP00000262352:p.Ser42Arg		4534601	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	37	CCDS6452.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444795	0.43429	.	.	ENSG00000106688	ENST00000262352	T	0.58652	0.32	5.47	4.57	0.56435	.	0.609592	0.19507	N	0.112605	T	0.40247	0.1109	N	0.17723	0.515	0.35555	D	0.804227	B	0.14805	0.011	B	0.18871	0.023	T	0.43734	-0.9373	10	0.38643	T	0.18	.	8.1134	0.30928	0.1578:0.757:0.0:0.0852	.	42	P43005	EAA3_HUMAN	R	42	ENSP00000262352:S42R	ENSP00000262352:S42R	S	+	3	2	SLC1A1	4534601	0.321000	0.24625	0.989000	0.46669	0.759000	0.43091	0.556000	0.23438	1.297000	0.44761	0.555000	0.69702	AGC		0.388	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			A	4544601	C	A	4544601	3	1	91	1	0	0	0	0	1	0	0	0	14468	709	25	2	132	2	SLC1A1	9	4544601	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10		4544601	136668830	91	24983										
TEK	7010	hgsc.bcm.edu	37	chr9	27158125	27158125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	caatcaggatacgaaccatgAagatgcgtcaacaaggtaac	9	9	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:27158125A>G	ENST00000380036.4	+	2	791	c.349A>G	c.(349-351)Aag>Gag	p.K117E	TEK_ENST00000406359.4_Missense_Mutation_p.K117E|TEK_ENST00000519097.1_Intron	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	117	Ig-like C2-type 1.		K -> N (in breast cancer samples; infiltrating ductal carcinoma; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ACGAACCATGAAGATGCGTCA	0.483																																																0			9											158	128	138					9																	27158125		2203	4300	6503	27148125	SO:0001583	missense	7010			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.349A>G	9.37:g.27158125A>G	ENSP00000369375:p.Lys117Glu		27148125	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.169259	0.78339	.	.	ENSG00000120156	ENST00000380036;ENST00000346448;ENST00000406359	T;T	0.74209	-0.76;-0.82	5.74	5.74	0.90152	Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000083	T	0.74816	0.3766	N	0.24115	0.695	0.53688	D	0.999977	P;D;D;D	0.69078	0.951;0.993;0.997;0.997	P;D;D;D	0.80764	0.666;0.982;0.994;0.988	T	0.69135	-0.5225	10	0.05959	T	0.93	.	16.0351	0.80621	1.0:0.0:0.0:0.0	.	150;117;117;117	Q59HG2;B5A953;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	E	117	ENSP00000369375:K117E;ENSP00000383977:K117E	ENSP00000343716:K117E	K	+	1	0	TEK	27148125	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.306000	0.72810	2.186000	0.69663	0.533000	0.62120	AAG		0.483	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27158125	A	G	27158125	3	3	91	1	0	0	0	0	1	0	0	0	15790	247	9	4	355	4	TEK	9	27158125	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	22613524	27158125	114055306	92	24984										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119033668	119033668	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atggctgctcccttttctgcCgacaagaagtctccttcaat	7	13	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:119033668C>T	ENST00000328252.3	+	9	3295	c.2926C>T	c.(2926-2928)Cga>Tga	p.R976*	PAPPA_ENST00000534838.1_Nonsense_Mutation_p.R14*	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	976					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CCTTTTCTGCCGACAAGAAGT	0.423																																																0			9											263	227	239					9																	119033668		2203	4300	6503	118073489	SO:0001587	stop_gained	5069				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2926C>T	9.37:g.119033668C>T	ENSP00000330658:p.Arg976*		118073489	B1AMF9|Q08371|Q68G52|Q9UDK7	Nonsense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	44	10.879788	0.99483	.	.	ENSG00000182752	ENST00000328252;ENST00000443904;ENST00000534838	.	.	.	4.78	1.77	0.24775	.	0.571091	0.18891	N	0.128313	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	0.0311	13.1465	0.59465	0.5577:0.4423:0.0:0.0	.	.	.	.	X	976;420;14	.	ENSP00000330658:R976X	R	+	1	2	PAPPA	118073489	0.015000	0.18098	0.572000	0.28498	0.885000	0.51271	0.198000	0.17217	0.264000	0.21851	0.563000	0.77884	CGA		0.423	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	119033668	C	T	119033668	4	4	91	1	0	0	0	0	0	1	0	0	11463	644	23	1	2960	1	PAPPA	9	119033668	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	91875543	119033668	22179763	93	24985										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123210312	123210312	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagatctggctctgcagctgCgtcaccacctcctgggtggc	12	14	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:123210312C>T	ENST00000349780.4	-	22	3065	c.2886G>A	c.(2884-2886)acG>acA	p.T962T	CDK5RAP2_ENST00000359309.3_Silent_p.T962T|CDK5RAP2_ENST00000360822.3_Silent_p.T930T|CDK5RAP2_ENST00000360190.4_Silent_p.T962T	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	962	Interaction with MAPRE1.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TCTGCAGCTGCGTCACCACCT	0.483																																																0			9											102	104	104					9																	123210312		2203	4300	6503	122250133	SO:0001819	synonymous_variant	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2886G>A	9.37:g.123210312C>T			122250133	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																				0.483	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123210312	C	T	123210312	2	4	91	1	0	0	0	0	0	0	0	1	3152	755	27	1		1	CDK5RAP2	9	123210312	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	4176644	123210312	18003119	94	24986										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124528809	124528809	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttgaaagaggtgtttgcctcGtggaggcaggagtgcagcag	17	6	0	2	rs371966536		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:124528809G>A	ENST00000408936.3	+	9	1679	c.1497G>A	c.(1495-1497)tcG>tcA	p.S499S	DAB2IP_ENST00000259371.2_Silent_p.S471S|DAB2IP_ENST00000309989.1_Silent_p.S375S			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	499	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.S375S(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						TGTTTGCCTCGTGGAGGCAGG	0.632																																																1	Substitution - coding silent(1)	central_nervous_system(1)	9						G	,	1,4405	2.1+/-5.4	0,1,2202	56	52	54		1413,1125	-9.2	0.3	9		54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DAB2IP	NM_032552.2,NM_138709.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	471/1133,375/1066	124528809	1,13005	2203	4300	6503	123568630	SO:0001819	synonymous_variant	153090			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.1497G>A	9.37:g.124528809G>A			123568630	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	37																																																																																					0.632	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		A	124528809	G	A	124528809	2	1	91	1	0	0	0	0	0	0	0	1	4225	1132	40	1		1	DAB2IP	9	124528809	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	1318497	124528809	16684622	95	24987										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130027259	130027259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cggaagacctaggctgtagaCgtggggatttcagtaggaaa	15	6	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:130027259C>T	ENST00000373387.4	+	1	455	c.103C>T	c.(103-105)Cgt>Tgt	p.R35C	GARNL3_ENST00000314904.5_Missense_Mutation_p.R35C|GARNL3_ENST00000435213.2_Missense_Mutation_p.R13C	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	35					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGGCTGTAGACGTGGGGATTT	0.423																																																0			9											257	244	248					9																	130027259		2203	4300	6503	129067080	SO:0001583	missense	84253			BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.103C>T	9.37:g.130027259C>T	ENSP00000362485:p.Arg35Cys		129067080	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	37	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786249	0.70337	.	.	ENSG00000136895	ENST00000439286;ENST00000444677;ENST00000446764;ENST00000373399;ENST00000425970;ENST00000435213;ENST00000314904;ENST00000373387	T;T;T;D;D;D	0.91740	1.2;0.14;0.24;-2.84;-2.8;-2.9	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.92980	0.7766	L	0.27053	0.805	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	D	0.91947	0.5568	9	.	.	.	.	17.9864	0.89157	0.0:1.0:0.0:0.0	.	35;13	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	C	58;58;58;58;13;13;35;35	ENSP00000400579:R58C;ENSP00000411160:R58C;ENSP00000411329:R13C;ENSP00000396205:R13C;ENSP00000313970:R35C;ENSP00000362485:R35C	.	R	+	1	0	GARNL3	129067080	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.539000	0.60657	2.656000	0.90262	0.650000	0.86243	CGT		0.423	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		T	130027259	C	T	130027259	3	4	91	1	0	0	0	0	1	0	0	0	6261	536	19	1	105	1	GARNL3	9	130027259	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	5498450	130027259	11186172	96	24988										
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138586279	138586279	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agcaggaaggacgtcccatcGtccacatcagaccccaacgc	9	16	1	1	rs369773381		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:138586279G>A	ENST00000298466.5	-	7	960	c.900C>T	c.(898-900)gaC>gaT	p.D300D	SOHLH1_ENST00000425225.1_Silent_p.D300D	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	300					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		ACGTCCCATCGTCCACATCAG	0.617																																																0			9						G	,	1,4403	2.1+/-5.4	0,1,2201	79	65	70		900,900	-0.2	0	9		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SOHLH1	NM_001012415.2,NM_001101677.1	,	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	,	300/329,300/388	138586279	2,13002	2202	4300	6502	137726100	SO:0001819	synonymous_variant	402381			BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915	ENST00000298466.5:c.900C>T	9.37:g.138586279G>A			137726100	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	37	CCDS35174.1																																																																																				0.617	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		A	138586279	G	A	138586279	2	1	91	1	0	0	0	0	0	0	0	1	14960	1136	40	1		1	SOHLH1	9	138586279	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	8559020	138586279	2627152	97	24989										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138678150	138678150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcccagggccgccacacgggCggcggtgaccccgcagagca	15	17	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr9:138678150C>T	ENST00000263604.3	+	28	3207	c.3207C>T	c.(3205-3207)ggC>ggT	p.G1069G	KCNT1_ENST00000487664.1_Silent_p.G1050G|KCNT1_ENST00000488444.2_Silent_p.G1074G|KCNT1_ENST00000298480.5_Silent_p.G1095G|KCNT1_ENST00000371757.2_Silent_p.G1095G|KCNT1_ENST00000486577.2_Silent_p.G1052G|KCNT1_ENST00000490355.2_Silent_p.G1073G|KCNT1_ENST00000491806.2_Silent_p.G1060G			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	1069					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GCCACACGGGCGGCGGTGACC	0.736																																																0			9											5	8	7					9																	138678150		1914	3779	5693	137817971	SO:0001819	synonymous_variant	57582			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.3207C>T	9.37:g.138678150C>T			137817971	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																					0.736	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		T	138678150	C	T	138678150	2	4	91	1	0	0	0	0	0	0	0	1	8112	755	27	1		1	KCNT1	9	138678150	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	91871	138678150	2535281	98	24990										
ZNF25	219749	hgsc.bcm.edu	37	chr10	38245971	38245971	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggaagccccgatgtggaaatTctacttctaatatccatggc	9	10	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:38245971T>C	ENST00000302609.7	-	4	427	c.215A>G	c.(214-216)gAa>gGa	p.E72G	ZNF25_ENST00000374633.1_5'UTR|AL117337.1_ENST00000582458.1_RNA	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ATGTGGAAATTCTACTTCTAA	0.403																																																0			10											127	118	121					10																	38245971		2203	4300	6503	38285977	SO:0001583	missense	219749			AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"Zinc fingers, C2H2-type", "-"	13043	protein-coding gene	gene with protein product		194528	"zinc finger protein 25 (KOX 19)"			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.215A>G	10.37:g.38245971T>C	ENSP00000302222:p.Glu72Gly		38285977	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	37	CCDS7195.1	.	.	.	.	.	.	.	.	.	.	T	11.70	1.717332	0.30413	.	.	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.50277	0.75	4.83	4.83	0.62350	Krueppel-associated box (1);	0.162448	0.29376	N	0.012324	T	0.40040	0.1101	L	0.55213	1.73	0.29128	N	0.87986	B	0.31318	0.319	B	0.27170	0.077	T	0.35500	-0.9786	10	0.28530	T	0.3	-24.9725	10.9615	0.47387	0.0:0.0:0.0:1.0	.	72	P17030	ZNF25_HUMAN	G	72;36	ENSP00000302222:E72G	ENSP00000302222:E72G	E	-	2	0	ZNF25	38285977	0.923000	0.31300	0.591000	0.28745	0.269000	0.26545	1.654000	0.37334	2.162000	0.67917	0.454000	0.30748	GAA		0.403	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966		C	38245971	T	C	38245971	3	2	91	1	0	0	0	0	1	0	0	0	17833	1783	62	4	1167	4	ZNF25	10	38245971	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10		38245971	97288776	99	24991										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61432595	61432595	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaactgctcaacatcaggccTccagccaccatgaagccact	6	16	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:61432595T>C	ENST00000395348.3	-	3	909	c.273A>G	c.(271-273)ggA>ggG	p.G91G	SLC16A9_ENST00000395347.1_Silent_p.G91G	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	91					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						ACATCAGGCCTCCAGCCACCA	0.433																																																0			10											83	79	80					10																	61432595		2203	4300	6503	61102601	SO:0001819	synonymous_variant	220963			AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.273A>G	10.37:g.61432595T>C			61102601	Q6ZMI2|Q9UFH8	Silent	SNP	ENST00000395348.3	37	CCDS7256.1																																																																																				0.433	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		C	61432595	T	C	61432595	2	2	91	1	0	0	0	0	0	0	0	1	14452	1538	54	4		4	SLC16A9	10	61432595	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	23186624	61432595	74102152	100	24992										
OIT3	170392	hgsc.bcm.edu	37	chr10	74673223	74673223	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagacatgtggtacagtggtCgatgtaggttcctcctggag	14	7	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:74673223C>T	ENST00000334011.5	+	6	1166	c.948C>T	c.(946-948)gtC>gtT	p.V316V		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	316	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					GTACAGTGGTCGATGTAGGTT	0.547																																					Colon(7;19 345 13446 17537)											0			10											102	83	89					10																	74673223		2203	4300	6503	74343229	SO:0001819	synonymous_variant	170392				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.948C>T	10.37:g.74673223C>T			74343229	A0AVP3|Q8N1M8	Silent	SNP	ENST00000334011.5	37	CCDS7318.1																																																																																				0.547	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		T	74673223	C	T	74673223	2	4	91	1	0	0	0	0	0	0	0	1	10880	871	31	1		1	OIT3	10	74673223	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	13240628	74673223	60861524	101	24993										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624279	89624279	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaacaaaaggagatatcaagAggatggattcgacttagact	10	5	1	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:89624279A>G	ENST00000371953.3	+	1	1410	c.53A>G	c.(52-54)gAg>gGg	p.E18G	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	18	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.R15fs*23(1)|p.Y16fs*21(1)|p.N12fs*6(1)|p.R14_D22del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGATATCAAGAGGATGGATTC	0.468		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	54	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(3)|Deletion - In frame(1)	prostate(14)|central_nervous_system(10)|skin(7)|lung(6)|endometrium(3)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10	GRCh37	CD033224	PTEN	D							182	174	177					10																	89624279		2203	4300	6503	89614259	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.53A>G	10.37:g.89624279A>G	ENSP00000361021:p.Glu18Gly		89614259	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465988	0.63625	.	.	ENSG00000171862	ENST00000371953	D	0.95377	-3.69	5.05	5.05	0.67936	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.93485	0.7921	M	0.62266	1.93	0.80722	D	1	B	0.31383	0.321	B	0.30943	0.122	D	0.91956	0.5575	9	.	.	.	-8.2513	13.7609	0.62966	1.0:0.0:0.0:0.0	.	18	P60484	PTEN_HUMAN	G	18	ENSP00000361021:E18G	.	E	+	2	0	PTEN	89614259	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.375000	0.90135	1.891000	0.54761	0.459000	0.35465	GAG		0.468	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89624279	A	G	89624279	3	3	91	1	0	0	0	0	1	0	0	0	12772	304	11	4	55	4	PTEN	10	89624279	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	14951056	89624279	45910468	102	24994										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717688	89717688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cacacgacgggaagacaagtTcatgtactttgagttccctc	9	11	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:89717688T>C	ENST00000371953.3	+	7	2070	c.713T>C	c.(712-714)tTc>tCc	p.F238S	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	238	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.M239fs*4(1)|p.R234fs*9(1)|p.K237_Y240>N(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GAAGACAAGTTCATGTACTTT	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	51	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(1)|Insertion - Frameshift(1)|Complex - deletion inframe(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|breast(4)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	10											153	131	138					10																	89717688		2203	4300	6503	89707668	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.713T>C	10.37:g.89717688T>C	ENSP00000361021:p.Phe238Ser		89707668	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.796292	0.31777	.	.	ENSG00000171862	ENST00000371953	D	0.84070	-1.8	5.15	2.6	0.31112	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.528864	0.22235	N	0.062762	T	0.61800	0.2376	N	0.03608	-0.345	0.32629	N	0.522217	B	0.27316	0.175	B	0.30943	0.122	T	0.60762	-0.7199	9	.	.	.	-0.3376	9.245	0.37520	0.4267:0.0:0.0:0.5733	.	238	P60484	PTEN_HUMAN	S	238	ENSP00000361021:F238S	.	F	+	2	0	PTEN	89707668	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.911000	0.48774	0.752000	0.32923	0.477000	0.44152	TTC		0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89717688	T	C	89717688	3	2	91	1	0	0	0	0	1	0	0	0	12772	1783	62	4	739	4	PTEN	10	89717688	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	93409	89717688	45817059	103	24995										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116245112	116245112	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acttttggaataaaagaaatCggatgaagaacgccgaatgt	10	5	0	3	rs139090722	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:116245112C>T	ENST00000277895.5	-	8	1139				ABLIM1_ENST00000369252.4_Intron|ABLIM1_ENST00000392952.3_Missense_Mutation_p.D41N|ABLIM1_ENST00000533213.2_Intron|ABLIM1_ENST00000369253.2_Intron|ABLIM1_ENST00000369266.3_Missense_Mutation_p.D41N	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1						axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		TAAAAGAAATCGGATGAAGAA	0.458													C|||	4	0.000798722	0	0	5008	,	,		19258	0		0.004	False		,,,				2504	0															0			10						C	,ASN/ASP,,ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	48	46	46		,889,,121	5.3	0.9	10	dbSNP_134	46	9,8591	6.4+/-24.3	0,9,4291	yes	intron,missense,intron,missense	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5,NM_006720.3	,23,,23	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	,,,	,297/747,,41/456	116245112	11,12995	2203	4300	6503	116235102	SO:0001627	intron_variant	3983			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1041+2604G>A	10.37:g.116245112C>T			116235102	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	14.56	2.572463	0.45798	4.54E-4	0.001047	ENSG00000099204	ENST00000392952;ENST00000369267;ENST00000369262;ENST00000369266;ENST00000277895;ENST00000369253	T;T	0.30448	1.53;1.53	6.17	5.28	0.74379	.	0.399231	0.25813	N	0.028139	T	0.18173	0.0436	L	0.33485	1.01	0.22435	N	0.999108	B;P;B	0.34546	0.327;0.456;0.327	B;B;B	0.26864	0.034;0.074;0.034	T	0.20472	-1.0274	10	0.02654	T	1	.	13.0295	0.58835	0.0:0.925:0.0:0.075	.	297;41;297	A6NKJ2;O14639-5;B3KVH2	.;.;.	N	41;297;357;41;357;41	ENSP00000376679:D41N;ENSP00000358270:D41N	ENSP00000277895:D357N	D	-	1	0	ABLIM1	116235102	0.996000	0.38824	0.923000	0.36655	0.727000	0.41649	2.724000	0.47285	1.633000	0.50488	-0.137000	0.14449	GAT		0.458	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			T	116245112	C	T	116245112	1	4	91	0	1	0	0	0	0	0	0	0	94	884	31	1		1	ABLIM1	10	116245112	Intron	SNP	C	TCGA-CL-5917-01A-11D-1657-10	26527424	116245112	19289635	104	24996										
CTBP2	1488	hgsc.bcm.edu	37	chr10	126715114	126715114	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgagatggtgcgctggagggAcggcgagccgggtctccagc	19	10	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr10:126715114A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Silent_p.R405R|CTBP2_ENST00000494626.2_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CGCTGGAGGGACGGCGAGCCG	0.667																																																0			10											18	16	17					10																	126715114		2172	4264	6436	126705104	SO:0001627	intron_variant	1488			AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12451T>C	10.37:g.126715114A>G			126705104	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	37	CCDS7643.1																																																																																				0.667	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		G	126715114	A	G	126715114	1	3	91	0	1	0	0	0	0	0	0	0	4004	262	10	4		4	CTBP2	10	126715114	Intron	SNP	A	TCGA-CL-5917-01A-11D-1657-10	10470002	126715114	8819633	105	24997										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5530318	5530318	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acagacacatgctgccgcatCagggagcttggctggtcagg	14	11	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:5530318C>A	ENST00000311659.4	-	2	618	c.471G>T	c.(469-471)ctG>ctT	p.L157L	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	157										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTGCCGCATCAGGGAGCTTG	0.597																																					Ovarian(72;684 1260 12332 41642 52180)											0			11											45	42	43					11																	5530318		2201	4297	6498	5486894	SO:0001819	synonymous_variant	50613			AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.471G>T	11.37:g.5530318C>A			5486894	Q9NRE0	Silent	SNP	ENST00000311659.4	37	CCDS7758.1																																																																																				0.597	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		A	5530318	C	A	5530318	2	1	91	1	0	0	0	0	0	0	0	1	16938	813	29	2		2	UBQLN3	11	5530318	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10		5530318	129476198	106	24998										
LDHA	3939	hgsc.bcm.edu	37	chr11	18421030	18421030	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	catcgaagacaaattgaaggGagagatgatggatctccaac	11	7	1	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:18421030G>A	ENST00000422447.3	+	3	452	c.179G>A	c.(178-180)gGa>gAa	p.G60E	LDHA_ENST00000227157.4_Missense_Mutation_p.G60E|LDHA_ENST00000379412.5_Missense_Mutation_p.G60E|LDHA_ENST00000396222.2_Missense_Mutation_p.G60E|LDHA_ENST00000540430.1_Missense_Mutation_p.G89E|LDHA_ENST00000430553.2_Missense_Mutation_p.G60E|LDHA_ENST00000542179.1_Missense_Mutation_p.G60E	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	60					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						AAATTGAAGGGAGAGATGATG	0.373																																																0			11											136	126	129					11																	18421030		2199	4293	6492	18377606	SO:0001583	missense	3939			X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.179G>A	11.37:g.18421030G>A	ENSP00000395337:p.Gly60Glu		18377606	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	G	33	5.239884	0.95240	.	.	ENSG00000134333	ENST00000422447;ENST00000543445;ENST00000430553;ENST00000396222;ENST00000535451;ENST00000227157;ENST00000478970;ENST00000495052;ENST00000540430;ENST00000379412;ENST00000542179	D;D;D;D;D;D;D;D;D;D;D	0.95069	-3.6;-3.6;-3.6;-3.6;-3.6;-3.6;-3.6;-3.6;-3.6;-3.6;-3.6	5.03	5.03	0.67393	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98667	0.9553	H	0.99391	4.545	0.80722	D	1	D;P;P;D	0.69078	0.997;0.803;0.955;0.994	D;P;P;D	0.69824	0.966;0.539;0.747;0.945	D	0.99239	1.0884	10	0.72032	D	0.01	-4.5663	18.9079	0.92471	0.0:0.0:1.0:0.0	.	89;60;60;60	B7Z5E3;B4DKQ2;F8W819;P00338	.;.;.;LDHA_HUMAN	E	60;60;60;60;60;60;60;60;89;60;60	ENSP00000395337:G60E;ENSP00000440161:G60E;ENSP00000406172:G60E;ENSP00000379524:G60E;ENSP00000444292:G60E;ENSP00000227157:G60E;ENSP00000441241:G60E;ENSP00000446415:G60E;ENSP00000445175:G89E;ENSP00000368722:G60E;ENSP00000445331:G60E	ENSP00000227157:G60E	G	+	2	0	LDHA	18377606	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.490000	0.97952	2.768000	0.95171	0.655000	0.94253	GGA		0.373	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		A	18421030	G	A	18421030	3	1	91	1	0	0	0	0	1	0	0	0	8720	1174	41	3	276	3	LDHA	11	18421030	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	12890712	18421030	116585486	107	24999										
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18956124	18956124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gaggaagaggaagtctgctgCggccaagttgaggatgtaga	17	5	1	3	rs567589026		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:18956124C>T	ENST00000302797.3	-	1	432	c.208G>A	c.(208-210)Gca>Aca	p.A70T	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	70					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AAGTCTGCTGCGGCCAAGTTG	0.532																																																0			11											130	129	130					11																	18956124		2194	4285	6479	18912700	SO:0001583	missense	259249				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.208G>A	11.37:g.18956124C>T	ENSP00000305766:p.Ala70Thr		18912700	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	8.032	0.762028	0.15914	.	.	ENSG00000170255	ENST00000302797	T	0.19938	2.11	2.43	-2.54	0.06307	GPCR, rhodopsin-like superfamily (1);	2.339570	0.01866	N	0.036909	T	0.28995	0.0720	M	0.80422	2.495	0.09310	N	1	P	0.44260	0.83	B	0.42386	0.386	T	0.34976	-0.9807	10	0.52906	T	0.07	.	5.023	0.14370	0.0:0.3685:0.2965:0.335	.	70	Q96LB2	MRGX1_HUMAN	T	70	ENSP00000305766:A70T	ENSP00000305766:A70T	A	-	1	0	MRGPRX1	18912700	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.567000	0.05916	-1.096000	0.03046	-1.579000	0.00862	GCA		0.532	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18956124	C	T	18956124	3	4	91	1	0	0	0	0	1	0	0	0	9796	768	27	1	764	1	MRGPRX1	11	18956124	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	535094	18956124	116050392	108	25000										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22399217	22399217	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggcctagtggttgggaaaaGaaagaggaatttgtacaagg	15	3	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:22399217G>A	ENST00000263160.3	+	12	2117	c.1680G>A	c.(1678-1680)aaG>aaA	p.K560K		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	560					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						GTTGGGAAAAGAAAGAGGAAT	0.368																																																0			11											43	44	44					11																	22399217		2203	4300	6503	22355793	SO:0001819	synonymous_variant	57084			AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.1680G>A	11.37:g.22399217G>A			22355793	A6NKS2	Silent	SNP	ENST00000263160.3	37	CCDS7856.1																																																																																				0.368	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		A	22399217	G	A	22399217	2	1	91	1	0	0	0	0	0	0	0	1	14458	933	33	3		3	SLC17A6	11	22399217	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	3443093	22399217	112607299	109	25001										
WT1	7490	hgsc.bcm.edu	37	chr11	32456369	32456369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	accgaagggcccgtagcgacAggctccggctgtgccagtga	15	13	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:32456369A>G	ENST00000332351.3	-	1	807	c.523T>C	c.(523-525)Tgt>Cgt	p.C175R	WT1-AS_ENST00000478367.1_RNA|WT1_ENST00000448076.3_Missense_Mutation_p.C175R|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000395900.1_RNA|WT1-AS_ENST00000459866.1_RNA|WT1-AS_ENST00000525436.1_RNA	NM_024424.3|NM_024426.4	NP_077742.2|NP_077744	P19544	WT1_HUMAN	Wilms tumor 1	107					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C107S(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CCGTAGCGACAGGCTCCGGCT	0.687			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	1	Substitution - Missense(1)	kidney(1)	11											18	19	19					11																	32456369		2198	4290	6488	32412945	SO:0001583	missense	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000332351.3:c.523T>C	11.37:g.32456369A>G	ENSP00000331327:p.Cys175Arg		32412945	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000332351.3	37	CCDS7878.2	.	.	.	.	.	.	.	.	.	.	A	18.95	3.731432	0.69189	.	.	ENSG00000184937	ENST00000332351;ENST00000452863;ENST00000448076	D;D;D	0.89552	-2.53;-2.53;-2.53	3.24	2.09	0.27110	Wilm&apos (1);s tumour protein, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.90964	0.7159	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.88858	0.3324	10	0.87932	D	0	.	6.9551	0.24565	0.8901:0.0:0.1099:0.0	.	180;107;180	P19544-8;P19544;P19544-7	.;WT1_HUMAN;.	R	175	ENSP00000331327:C175R;ENSP00000415516:C175R;ENSP00000413452:C175R	ENSP00000331327:C175R	C	-	1	0	WT1	32412945	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.834000	0.75339	0.438000	0.26450	0.379000	0.24179	TGT		0.687	WT1-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000095436.2	NM_000378		G	32456369	A	G	32456369	3	3	91	1	0	0	0	0	1	0	0	0	17448	188	7	4	1070	4	WT1	11	32456369	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	10057152	32456369	102550147	110	25002										
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62910956	62910956	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggaaggtcccgttcaggtgaAggagctgccactggggatgg	18	8	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:62910956A>G	ENST00000417740.1	-	1	737	c.296T>C	c.(295-297)cTt>cCt	p.L99P	SLC22A10_ENST00000525620.1_Intron|SLC22A24_ENST00000326192.5_Missense_Mutation_p.L99P	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	99					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						GTTCAGGTGAAGGAGCTGCCA	0.562																																																0			11											89	93	92					11																	62910956		692	1591	2283	62667532	SO:0001583	missense	283238				CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"Solute carriers"	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.296T>C	11.37:g.62910956A>G	ENSP00000396586:p.Leu99Pro		62667532		Missense_Mutation	SNP	ENST00000417740.1	37		.	.	.	.	.	.	.	.	.	.	A	14.72	2.619706	0.46736	.	.	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	T;T	0.35421	1.31;1.31	2.29	2.29	0.28610	.	0.701952	0.11826	U	0.525720	T	0.60130	0.2245	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.59021	-0.7532	10	0.49607	T	0.09	.	8.2441	0.31677	1.0:0.0:0.0:0.0	.	99	C9JC66	.	P	99	ENSP00000396586:L99P;ENSP00000321549:L99P	ENSP00000321549:L99P	L	-	2	0	SLC22A24	62667532	0.998000	0.40836	0.818000	0.32626	0.755000	0.42902	4.247000	0.58750	1.081000	0.41110	0.315000	0.21342	CTT		0.562	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		G	62910956	A	G	62910956	3	3	91	1	0	0	0	0	1	0	0	0	14490	72	3	4	1397	4	SLC22A24	11	62910956	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	30454587	62910956	72095560	111	25003										
ALDH3B1	221	hgsc.bcm.edu	37	chr11	67786316	67786316	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atcattgcgccctggaactaTccgctgaacctgacgctggt	10	13	1	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:67786316T>C	ENST00000539229.1	+	5	461	c.345T>C	c.(343-345)taT>taC	p.Y115Y	ALDH3B1_ENST00000316367.6_Silent_p.Y115Y|ALDH3B1_ENST00000007633.8_Silent_p.Y115Y|ALDH3B1_ENST00000342456.6_Silent_p.Y79Y|ALDH3B1_ENST00000434449.1_3'UTR	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	116					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										CCTGGAACTATCCGCTGAACC	0.667																																																0			11											23	25	25					11																	67786316		2166	4258	6424	67542892	SO:0001819	synonymous_variant	221			U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.345T>C	11.37:g.67786316T>C			67542892	A3FMP9|Q53XL5|Q8N515|Q96CK8	Missense_Mutation	SNP	ENST00000539229.1	37																																																																																					0.667	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694		C	67786316	T	C	67786316	2	2	91	1	0	0	0	0	0	0	0	1	499	1442	50	4		4	ALDH3B1	11	67786316	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	4875360	67786316	67220200	112	25004										
ARAP1	116985	hgsc.bcm.edu	37	chr11	72437883	72437883	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtgggcagcggctcgggtggAgtggcaggcacaggtggtga	22	7	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:72437883A>G	ENST00000393609.3	-	3	493	c.291T>C	c.(289-291)acT>acC	p.T97T	ARAP1_ENST00000455638.2_Silent_p.T97T|ARAP1_ENST00000359373.5_Silent_p.T97T	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	97					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GCTCGGGTGGAGTGGCAGGCA	0.706																																					Ovarian(102;1198 1520 13195 17913 37529)											0			11											7	11	9					11																	72437883		1947	4029	5976	72115531	SO:0001819	synonymous_variant	116985			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.291T>C	11.37:g.72437883A>G			72115531	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	37	CCDS41687.1																																																																																				0.706	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		G	72437883	A	G	72437883	2	3	91	1	0	0	0	0	0	0	0	1	838	291	11	4		4	ARAP1	11	72437883	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	4651567	72437883	62568633	113	25005										
CAPN5	726	hgsc.bcm.edu	37	chr11	76834878	76834878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acctgccaggcactgtggccGtgcacattctcagcagcacc	10	16	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:76834878G>A	ENST00000278559.3	+	13	2074	c.1885G>A	c.(1885-1887)Gtg>Atg	p.V629M	CAPN5_ENST00000456580.2_Missense_Mutation_p.V669M|CAPN5_ENST00000529629.1_Missense_Mutation_p.V629M|CAPN5_ENST00000531028.1_3'UTR	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	629					proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						CACTGTGGCCGTGCACATTCT	0.637																																																0			11											92	75	81					11																	76834878		2200	4292	6492	76512526	SO:0001583	missense	726				CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1885G>A	11.37:g.76834878G>A	ENSP00000278559:p.Val629Met		76512526	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797232	0.70567	.	.	ENSG00000149260	ENST00000278559;ENST00000360841;ENST00000529629;ENST00000456580	D;D;D	0.90197	-2.53;-2.53;-2.63	5.87	4.94	0.65067	.	0.189458	0.46145	D	0.000319	D	0.93022	0.7779	L	0.55481	1.735	0.51482	D	0.999925	D;D;D;D	0.76494	0.994;0.998;0.999;0.994	P;P;P;P	0.62089	0.742;0.898;0.898;0.742	D	0.93184	0.6577	10	0.66056	D	0.02	.	15.319	0.74105	0.0:0.2301:0.7699:0.0	.	667;669;669;629	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	M	629;669;629;669	ENSP00000278559:V629M;ENSP00000432332:V629M;ENSP00000409996:V669M	ENSP00000278559:V629M	V	+	1	0	CAPN5	76512526	0.996000	0.38824	0.154000	0.22540	0.006000	0.05464	2.387000	0.44389	2.780000	0.95670	0.655000	0.94253	GTG		0.637	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		A	76834878	G	A	76834878	3	1	91	1	0	0	0	0	1	0	0	0	2635	1145	40	1	1931	1	CAPN5	11	76834878	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	4396995	76834878	58171638	114	25006										
ATM	472	hgsc.bcm.edu	37	chr11	108199840	108199840	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctctcattagcccggttttcAgatactcaataccaaagaat	5	11	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:108199840A>T	ENST00000452508.2	+	50	7371	c.7182A>T	c.(7180-7182)tcA>tcT	p.S2394S	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.S2394S			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2394	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CCCGGTTTTCAGATACTCAAT	0.378			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											75	77	76					11																	108199840		2201	4298	6499	107705050	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7182A>T	11.37:g.108199840A>T			107705050	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.378	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108199840	A	T	108199840	2	4	91	1	0	0	0	0	0	0	0	1	1110	175	7	5		5	ATM	11	108199840	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	31364962	108199840	26806676	115	25007										
ATM	472	hgsc.bcm.edu	37	chr11	108216486	108216486	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaaggaggtgcaaaaaaagtCttttgaagagaaatatgaag	11	2	1	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:108216486C>A	ENST00000452508.2	+	59	8624	c.8435C>A	c.(8434-8436)tCt>tAt	p.S2812Y	C11orf65_ENST00000525729.1_Intron|C11orf65_ENST00000526725.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.S2812Y			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2812	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.K2810fs*1(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CAAAAAAAGTCTTTTGAAGAG	0.269			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	11											88	93	91					11																	108216486		2200	4298	6498	107721696	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8435C>A	11.37:g.108216486C>A	ENSP00000388058:p.Ser2812Tyr		107721696	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627613	0.46944	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.01787	4.64;4.64	5.56	5.56	0.83823	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.417785	0.26556	N	0.023704	T	0.02012	0.0063	L	0.31120	0.905	0.80722	D	1	B	0.31705	0.336	B	0.33846	0.171	T	0.60167	-0.7316	10	0.52906	T	0.07	.	9.7325	0.40370	0.1489:0.6089:0.2422:0.0	.	2812	Q13315	ATM_HUMAN	Y	2812	ENSP00000278616:S2812Y;ENSP00000388058:S2812Y	ENSP00000278616:S2812Y	S	+	2	0	ATM	107721696	0.998000	0.40836	1.000000	0.80357	0.856000	0.48823	1.388000	0.34442	2.619000	0.88677	0.650000	0.86243	TCT		0.269	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108216486	C	A	108216486	3	1	91	1	0	0	0	0	1	0	0	0	1110	913	32	2	8661	2	ATM	11	108216486	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	16646	108216486	26790030	116	25008										
DLAT	1737	hgsc.bcm.edu	37	chr11	111896434	111896434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tactgctgcagcttttggggTcgcccggccgccgctattac	12	14	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr11:111896434T>C	ENST00000280346.6	+	1	897	c.238T>C	c.(238-240)Tcg>Ccg	p.S80P	DLAT_ENST00000393051.1_Missense_Mutation_p.S80P|DLAT_ENST00000537636.1_5'UTR	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	80					cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		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)		GCTTTTGGGGTCGCCCGGCCG	0.657																																																0			11											20	23	22					11																	111896434		2194	4283	6477	111401644	SO:0001583	missense	1737			Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"E2 component of pyruvate dehydrogenase complex"	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.238T>C	11.37:g.111896434T>C	ENSP00000280346:p.Ser80Pro		111401644	Q16783|Q53EP3	Missense_Mutation	SNP	ENST00000280346.6	37	CCDS8354.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229444	0.39399	.	.	ENSG00000150768	ENST00000280346;ENST00000534998;ENST00000393051;ENST00000531306	T;T;T	0.16324	2.35;2.44;2.35	4.85	-2.55	0.06288	.	0.636785	0.14050	N	0.344834	T	0.07999	0.0200	N	0.19112	0.55	0.20489	N	0.999891	P;B	0.45283	0.855;0.412	B;B	0.41571	0.36;0.143	T	0.19712	-1.0297	10	0.52906	T	0.07	2.7444	1.1947	0.01872	0.1288:0.2075:0.2624:0.4013	.	80;80	E9PEJ4;P10515	.;ODP2_HUMAN	P	80;80;80;39	ENSP00000280346:S80P;ENSP00000376771:S80P;ENSP00000433432:S39P	ENSP00000280346:S80P	S	+	1	0	DLAT	111401644	0.000000	0.05858	0.000000	0.03702	0.581000	0.36288	-0.331000	0.07914	-0.047000	0.13423	0.533000	0.62120	TCG		0.657	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931		C	111896434	T	C	111896434	3	2	91	1	0	0	0	0	1	0	0	0	4560	1667	58	4	240	4	DLAT	11	111896434	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	3679948	111896434	23110082	117	25009										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14577964	14577964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgaaaatgaaaagaaggtagAggaagatattatcacagagc	11	3	1	6			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:14577964A>G	ENST00000540793.1	+	1	1270	c.1115A>G	c.(1114-1116)gAg>gGg	p.E372G	ATF7IP_ENST00000261168.4_Missense_Mutation_p.E372G|ATF7IP_ENST00000544627.1_Missense_Mutation_p.E380G|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000536444.1_Missense_Mutation_p.E372G|ATF7IP_ENST00000543189.1_Missense_Mutation_p.E372G			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	372	Glu-rich.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AAGAAGGTAGAGGAAGATATT	0.343																																																0			12											80	88	85					12																	14577964		2202	4300	6502	14469231	SO:0001583	missense	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1115A>G	12.37:g.14577964A>G	ENSP00000444589:p.Glu372Gly		14469231	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	A	6.373	0.436874	0.12104	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.26957	2.06;2.05;2.06;2.06;1.7;2.06	4.93	2.51	0.30379	.	0.578922	0.16345	N	0.218463	T	0.17152	0.0412	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.14438	0.002;0.01;0.001;0.001;0.001	B;B;B;B;B	0.14023	0.004;0.01;0.003;0.003;0.004	T	0.22521	-1.0214	10	0.27785	T	0.31	-0.6014	5.7635	0.18213	0.5919:0.2637:0.1444:0.0	.	380;372;372;372;372	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	G	372;372;372;380;372;372	ENSP00000261168:E372G;ENSP00000443179:E372G;ENSP00000445955:E372G;ENSP00000440440:E380G;ENSP00000379575:E372G;ENSP00000444589:E372G	ENSP00000261168:E372G	E	+	2	0	ATF7IP	14469231	0.549000	0.26481	0.058000	0.19502	0.712000	0.41017	0.714000	0.25808	0.418000	0.25898	0.482000	0.46254	GAG		0.343	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		G	14577964	A	G	14577964	3	3	91	1	0	0	0	0	1	0	0	0	1088	304	11	4	1117	4	ATF7IP	12	14577964	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10		14577964	119273931	118	25010										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	91	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	10820320	25398284	108453611	119	25011										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39713817	39713817	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tagagatgactgcctggaacTaaagtaaaagaagattcttt	9	5	1	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:39713817T>C	ENST00000361418.5	-	28	3687		c.e28-2		KIF21A_ENST00000541463.2_Splice_Site|KIF21A_ENST00000544797.2_Splice_Site|KIF21A_ENST00000547745.1_Splice_Site|KIF21A_ENST00000361961.3_Splice_Site|KIF21A_ENST00000395670.3_Splice_Site			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A						ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TGCCTGGAACTAAAGTAAAAG	0.333																																																0			12											53	48	50					12																	39713817		2201	4300	6501	38000084	SO:0001630	splice_region_variant	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3672-2A>G	12.37:g.39713817T>C			38000084	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Splice_Site	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	T	14.35	2.507826	0.44558	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000552961;ENST00000544797;ENST00000361418;ENST00000541463	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0707	0.80928	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIF21A	38000084	1.000000	0.71417	0.987000	0.45799	0.632000	0.37999	3.886000	0.56190	2.194000	0.70268	0.533000	0.62120	.		0.333	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	Intron	C	39713817	T	C	39713817	5	2	91	1	0	0	0	0	0	0	1	0	8309	1536	53	4	1398	4	KIF21A	12	39713817	Splice_Site	SNP	T	TCGA-CL-5917-01A-11D-1657-10	14315533	39713817	94138078	120	25012										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41957421	41957421	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aacgatgagtgtaagagaatCgtgctgcttgttgcaaggcc	13	7	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:41957421C>T	ENST00000402685.2	+	8	1445	c.1437C>T	c.(1435-1437)atC>atT	p.I479I	PDZRN4_ENST00000298919.7_Silent_p.I219I|PDZRN4_ENST00000539469.2_Silent_p.I221I	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	479	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GTAAGAGAATCGTGCTGCTTG	0.413																																																0			12											125	116	119					12																	41957421		2203	4300	6503	40243688	SO:0001819	synonymous_variant	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1437C>T	12.37:g.41957421C>T			40243688	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																				0.413	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41957421	C	T	41957421	2	4	91	1	0	0	0	0	0	0	0	1	11741	874	31	1		1	PDZRN4	12	41957421	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	2243604	41957421	91894474	121	25013										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46757532	46757532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaaatgttaggtatccaaagAgggcggcaagcagatacatg	12	6	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:46757532A>G	ENST00000256689.5	-	12	1475	c.1031T>C	c.(1030-1032)cTc>cCc	p.L344P	SLC38A2_ENST00000547252.1_5'Flank|SLC38A2_ENST00000551374.1_Missense_Mutation_p.L182P	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	344					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		GTATCCAAAGAGGGCGGCAAG	0.358																																					Ovarian(9;448 492 8335 28722 40361)											0			12											99	97	98					12																	46757532		2203	4298	6501	45043799	SO:0001583	missense	54407			AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1031T>C	12.37:g.46757532A>G	ENSP00000256689:p.Leu344Pro		45043799	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	37	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.787539	0.90367	.	.	ENSG00000134294	ENST00000256689;ENST00000551374	T;T	0.03065	4.06;4.06	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	M	0.91038	3.17	0.80722	D	1	D;D;D	0.76494	0.991;0.999;0.996	D;D;D	0.78314	0.944;0.991;0.961	T	0.08269	-1.0730	10	0.72032	D	0.01	-11.6708	15.7363	0.77846	1.0:0.0:0.0:0.0	.	182;244;344	F8VQW8;Q96QD8-2;Q96QD8	.;.;S38A2_HUMAN	P	344;182	ENSP00000256689:L344P;ENSP00000450406:L182P	ENSP00000256689:L344P	L	-	2	0	SLC38A2	45043799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.226000	0.95229	2.189000	0.69895	0.460000	0.39030	CTC		0.358	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			G	46757532	A	G	46757532	3	3	91	1	0	0	0	0	1	0	0	0	14641	304	11	4	509	4	SLC38A2	12	46757532	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	4800111	46757532	87094363	122	25014										
MLL2	8085	hgsc.bcm.edu	37	chr12	49421885	49421885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggagttggggatcttcatgcTcagcagctccgccactgcca	12	13	3	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:49421885T>C	ENST00000301067.7	-	46	14421	c.14422A>G	c.(14422-14424)Agc>Ggc	p.S4808G		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4808					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										ATCTTCATGCTCAGCAGCTCC	0.592																																																0			12											45	49	48					12																	49421885		2145	4240	6385	47708152	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.14422A>G	12.37:g.49421885T>C	ENSP00000301067:p.Ser4808Gly		47708152	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.378484	0.24944	.	.	ENSG00000167548	ENST00000301067	T	0.79749	-1.3	5.04	3.86	0.44501	.	0.000000	0.45867	D	0.000321	T	0.71904	0.3395	L	0.34521	1.04	0.26315	N	0.977768	B	0.23377	0.084	B	0.26310	0.068	T	0.65837	-0.6071	10	0.87932	D	0	.	11.1782	0.48612	0.0:0.0:0.1547:0.8453	.	4808	O14686	MLL2_HUMAN	G	4808	ENSP00000301067:S4808G	ENSP00000301067:S4808G	S	-	1	0	MLL2	47708152	0.995000	0.38212	0.958000	0.39756	0.898000	0.52572	2.333000	0.43912	0.850000	0.35239	0.459000	0.35465	AGC		0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49421885	T	C	49421885	3	2	91	1	0	0	0	0	1	0	0	0	9651	1551	54	4	2227	4	MLL2	12	49421885	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	2664353	49421885	84430010	123	25015										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045642	53045653	+	In_Frame_Del	DEL	ACCACCTCCTCT	ACCACCTCCTCT	-													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagctgctgccgcctccaaaAccacctcctctgccaccaaa							TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	ACCACCTCCTCT	ACCACCTCCTCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:53045642_53045653delACCACCTCCTCT	ENST00000309680.3	-	1	295_306	c.274_285delAGAGGAGGTGGT	c.(274-285)agaggaggtggtdel	p.RGGG92del		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	92	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		cgcctccaaaaccacctcctctgccaccaaat	0.618																																																0			12																																								51331920	SO:0001651	inframe_deletion	3849				CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.274_285delAGAGGAGGTGGT	12.37:g.53045642_53045653delACCACCTCCTCT	ENSP00000310861:p.Arg92_Gly95del		51331909	Q4VAQ2	In_Frame_Del	DEL	ENST00000309680.3	37	CCDS8835.1																																																																																				0.618	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		-	53045653	ACCACCTCCTCT	-	53045642	7	5	91	1	0	1	0	1	0	0	0	0	8478	30	2	0	1670	0	KRT2	12	53045642	In_Frame_Del	DEL	ACCACCTCCTCT	TCGA-CL-5917-01A-11D-1657-10	3623757	53045642	80806253	124	25016										
DDIT3	1649	hgsc.bcm.edu	37	chr12	57910757	57910757	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tccttcatgcgctgctttccAgcccgggctggggaatgacc	12	14	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:57910757A>G	ENST00000346473.3	-	4	524	c.345T>C	c.(343-345)gcT>gcC	p.A115A	MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000552740.1_Silent_p.A138A|RN7SL312P_ENST00000582079.1_RNA|DDIT3_ENST00000547303.1_Silent_p.A115A|DDIT3_ENST00000551116.1_Silent_p.A138A	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	115	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A115A(1)	EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						GCTGCTTTCCAGCCCGGGCTG	0.542			T	FUS	liposarcoma																																GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	1	Substitution - coding silent(1)	large_intestine(1)	12											142	151	148					12																	57910757		2203	4300	6503	56197024	SO:0001819	synonymous_variant	1649			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"C/EBP zeta"	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.345T>C	12.37:g.57910757A>G			56197024	F8VS99	Silent	SNP	ENST00000346473.3	37	CCDS8943.1																																																																																				0.542	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083		G	57910757	A	G	57910757	2	3	91	1	0	0	0	0	0	0	0	1	4336	175	7	4		4	DDIT3	12	57910757	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	4865115	57910757	75941138	125	25017										
E2F7	144455	hgsc.bcm.edu	37	chr12	77439991	77439991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctagtctctggaggttcctcAgggtttttggcaggctgtgc	14	9	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:77439991A>G	ENST00000322886.7	-	5	891	c.656T>C	c.(655-657)cTg>cCg	p.L219P	E2F7_ENST00000416496.2_Missense_Mutation_p.L219P	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	219					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GAGGTTCCTCAGGGTTTTTGG	0.483																																																0			12											137	130	132					12																	77439991		2203	4300	6503	75964122	SO:0001583	missense	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.656T>C	12.37:g.77439991A>G	ENSP00000323246:p.Leu219Pro		75964122	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.9|26.9	4.785584|4.785584	0.90282|0.90282	.|.	.|.	ENSG00000165891|ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669|ENST00000551058	T;T;T|.	0.30182|.	1.79;1.54;1.55|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.76666|.	0.4019|.	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	T|.	0.76955|.	-0.2767|.	10|.	0.87932|.	D|.	0|.	-14.1737|-14.1737	16.0034|16.0034	0.80327|0.80327	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	219;219|.	F8VSE7;Q96AV8|.	.;E2F7_HUMAN|.	P|R	219|97	ENSP00000323246:L219P;ENSP00000393639:L219P;ENSP00000448245:L219P|.	ENSP00000323246:L219P|.	L|X	-|-	2|1	0|0	E2F7|E2F7	75964122|75964122	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.997000|0.997000	0.91878|0.91878	9.339000|9.339000	0.96797|0.96797	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	CTG|TGA		0.483	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		G	77439991	A	G	77439991	3	3	91	1	0	0	0	0	1	0	0	0	4883	188	7	4	2115	4	E2F7	12	77439991	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	19529234	77439991	56411904	126	25018										
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108686442	108686442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aacccagtggtagtccatggCggcataggtgatatggattg	14	7	0	1	rs370635582		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:108686442C>T	ENST00000312143.7	-	3	661	c.298G>A	c.(298-300)Gcc>Acc	p.A100T	CMKLR1_ENST00000412676.1_Missense_Mutation_p.A100T|CMKLR1_ENST00000550402.1_Missense_Mutation_p.A100T|CMKLR1_ENST00000552995.1_Missense_Mutation_p.A98T|CMKLR1_ENST00000397688.2_Missense_Mutation_p.A98T	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	100					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						TAGTCCATGGCGGCATAGGTG	0.498																																																0			12											142	145	144					12																	108686442		2104	4218	6322	107210572	SO:0001583	missense	1240			U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"GPCR / Class A : Resolvin receptors"	2121	protein-coding gene	gene with protein product	"resolvin E1 receptor", "chemerin receptor"	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.298G>A	12.37:g.108686442C>T	ENSP00000311733:p.Ala100Thr		107210572	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	37	CCDS44965.1	.	.	.	.	.	.	.	.	.	.	c	17.42	3.383900	0.61845	.	.	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402;ENST00000550573;ENST00000549466	T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.23	5.23	0.72850	GPCR, rhodopsin-like superfamily (1);	0.365028	0.30347	N	0.009837	T	0.57814	0.2079	M	0.72479	2.2	0.42683	D	0.993557	D	0.71674	0.998	P	0.62184	0.899	T	0.61574	-0.7035	10	0.59425	D	0.04	.	17.3636	0.87358	0.0:1.0:0.0:0.0	.	100	Q99788	CML1_HUMAN	T	100;100;98;98;100;100;100	ENSP00000311733:A100T;ENSP00000401293:A100T;ENSP00000380803:A98T;ENSP00000447579:A98T;ENSP00000449716:A100T;ENSP00000448925:A100T;ENSP00000448362:A100T	ENSP00000311733:A100T	A	-	1	0	CMKLR1	107210572	0.998000	0.40836	0.935000	0.37517	0.364000	0.29643	3.866000	0.56040	2.448000	0.82819	0.486000	0.48141	GCC		0.498	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			T	108686442	C	T	108686442	3	4	91	1	0	0	0	0	1	0	0	0	3585	768	27	1	827	1	CMKLR1	12	108686442	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	31246451	108686442	25165453	127	25019										
CORO1C	23603	hgsc.bcm.edu	37	chr12	109042533	109042533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cttcaaggagatgaggattgGgtctgcattcttgccttcga	12	8	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr12:109042533G>A	ENST00000261401.3	-	10	1325	c.1153C>T	c.(1153-1155)Cca>Tca	p.P385S	CORO1C_ENST00000421578.2_Missense_Mutation_p.P280S|CORO1C_ENST00000420959.2_Missense_Mutation_p.P438S|CORO1C_ENST00000549772.1_Missense_Mutation_p.P391S|CORO1C_ENST00000541050.1_Missense_Mutation_p.P385S|CORO1C_ENST00000549384.1_5'UTR	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	385					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.P385S(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						ATGAGGATTGGGTCTGCATTC	0.517																																																1	Substitution - Missense(1)	skin(1)	12											214	160	178					12																	109042533		2203	4300	6503	107566662	SO:0001583	missense	23603			BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"Coronins", "WD repeat domain containing"	2254	protein-coding gene	gene with protein product		605269	"coronin, actin-binding protein, 1C"			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.1153C>T	12.37:g.109042533G>A	ENSP00000261401:p.Pro385Ser		107566662	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Missense_Mutation	SNP	ENST00000261401.3	37	CCDS9120.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958955	0.92726	.	.	ENSG00000110880	ENST00000261401;ENST00000541050;ENST00000546705;ENST00000421578;ENST00000549772;ENST00000420959	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	5.46	5.46	0.80206	Domain of unknown function DUF1900 (1);	0.000000	0.85682	D	0.000000	T	0.68851	0.3046	M	0.92026	3.265	0.80722	D	1	D;D;D	0.55172	0.965;0.965;0.97	P;D;P	0.65573	0.831;0.936;0.769	T	0.76479	-0.2944	10	0.87932	D	0	-9.0299	19.2975	0.94129	0.0:0.0:1.0:0.0	.	348;438;385	B4DMH3;A7MAP1;Q9ULV4	.;.;COR1C_HUMAN	S	385;385;76;280;391;438	ENSP00000261401:P385S;ENSP00000438341:P385S;ENSP00000447337:P76S;ENSP00000415554:P280S;ENSP00000447534:P391S;ENSP00000394496:P438S	ENSP00000261401:P385S	P	-	1	0	CORO1C	107566662	1.000000	0.71417	0.493000	0.27502	0.730000	0.41778	9.819000	0.99357	2.547000	0.85894	0.591000	0.81541	CCA		0.517	CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325		A	109042533	G	A	109042533	3	1	91	1	0	0	0	0	1	0	0	0	3761	1232	43	3	279	3	CORO1C	12	109042533	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	356091	109042533	24809362	128	25020										
MTUS2	23281	hgsc.bcm.edu	37	chr13	29599667	29599667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtgagcacacatcacattccGcccatccagagcctgctctg	8	16	2	2	rs573356096		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr13:29599667G>A	ENST00000431530.3	+	1	920	c.862G>A	c.(862-864)Gcc>Acc	p.A288T		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	278						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						ATCACATTCCGCCCATCCAGA	0.512													G|||	1	0.000199681	0	0	5008	,	,		20846	0		0.001	False		,,,				2504	0															0			13											42	43	42					13																	29599667		2115	4237	6352	28497667	SO:0001583	missense	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.862G>A	13.37:g.29599667G>A	ENSP00000392057:p.Ala288Thr		28497667	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	9.611	1.131226	0.21041	.	.	ENSG00000132938	ENST00000431530	T	0.14391	2.51	5.49	0.549	0.17213	.	0.878294	0.09712	N	0.765567	T	0.11452	0.0279	L	0.57536	1.79	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.41342	-0.9514	9	.	.	.	.	0.8684	0.01209	0.2788:0.1111:0.3601:0.2501	.	278	Q5JR59	MTUS2_HUMAN	T	288	ENSP00000392057:A288T	.	A	+	1	0	MTUS2	28497667	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.265000	0.08644	-0.228000	0.09869	-1.010000	0.02471	GCC		0.512	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		A	29599667	G	A	29599667	3	1	91	1	0	0	0	0	1	0	0	0	9996	1087	38	1	864	1	MTUS2	13	29599667	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10		29599667	85570211	129	25021										
SMAD9	4093	hgsc.bcm.edu	37	chr13	37427671	37427671	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gctggttgttgaagaccttgAggctgcagccgctggggatc	16	9	0	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr13:37427671A>G	ENST00000399275.2	-	5	1284	c.1145T>C	c.(1144-1146)cTc>cCc	p.L382P	SMAD9_ENST00000379826.4_Missense_Mutation_p.L382P|SMAD9_ENST00000350148.5_Missense_Mutation_p.L345P			O15198	SMAD9_HUMAN	SMAD family member 9	382	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		GAAGACCTTGAGGCTGCAGCC	0.552																																																0			13											128	85	99					13																	37427671		2203	4300	6503	36325671	SO:0001583	missense	4093				CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.1145T>C	13.37:g.37427671A>G	ENSP00000382216:p.Leu382Pro		36325671	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.591036	0.86851	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	D;D;D	0.99292	-5.7;-5.7;-5.7	5.42	5.42	0.78866	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99513	0.9826	M	0.93016	3.37	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.74348	0.919;0.983	D	0.98229	1.0482	10	0.87932	D	0	.	14.6354	0.68686	1.0:0.0:0.0:0.0	.	345;382	O15198-2;O15198	.;SMAD9_HUMAN	P	382;345;382	ENSP00000382216:L382P;ENSP00000239885:L345P;ENSP00000369154:L382P	ENSP00000239885:L345P	L	-	2	0	SMAD9	36325671	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.051000	0.93849	2.050000	0.60909	0.533000	0.62120	CTC		0.552	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		G	37427671	A	G	37427671	3	3	91	1	0	0	0	0	1	0	0	0	14801	304	11	4	266	4	SMAD9	13	37427671	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	7828004	37427671	77742207	130	25022										
LCP1	3936	hgsc.bcm.edu	37	chr13	46717468	46717468	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggggtatggcggtttgtttActctgttccagtcaacagga	13	7	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr13:46717468A>T	ENST00000398576.2	-	15	1713	c.1325T>A	c.(1324-1326)gTa>gAa	p.V442E	LCP1_ENST00000435666.2_5'Flank|LCP1_ENST00000323076.2_Missense_Mutation_p.V442E			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	442	Actin-binding 2.|CH 3. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|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;5.39e-05)		CGGTTTGTTTACTCTGTTCCA	0.433			T	BCL6	NHL																																		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	0			13											169	141	150					13																	46717468		2203	4300	6503	45615469	SO:0001583	missense	9878			M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"EF-hand domain containing"	6528	protein-coding gene	gene with protein product	"plastin 2"	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1325T>A	13.37:g.46717468A>T	ENSP00000381581:p.Val442Glu		45615469	B2R613|B4DUA0|Q5TBN4	Missense_Mutation	SNP	ENST00000398576.2	37	CCDS9403.1	.	.	.	.	.	.	.	.	.	.	A	35	5.448561	0.96205	.	.	ENSG00000136167	ENST00000323076;ENST00000398576	D;D	0.95918	-3.85;-3.85	5.65	5.65	0.86999	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97511	0.9185	M	0.82056	2.57	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	D	0.98220	1.0477	10	0.87932	D	0	-12.6547	15.0545	0.71904	1.0:0.0:0.0:0.0	.	442	P13796	PLSL_HUMAN	E	442	ENSP00000315757:V442E;ENSP00000381581:V442E	ENSP00000315757:V442E	V	-	2	0	LCP1	45615469	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.149000	0.67028	0.454000	0.30748	GTA		0.433	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298		T	46717468	A	T	46717468	3	4	91	1	0	0	0	0	1	0	0	0	8713	391	14	5	578	5	LCP1	13	46717468	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	9289797	46717468	68452410	131	25023										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111111246	111111246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaggggacagaggagaccccGgccaacacggcctccctggg	15	14	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr13:111111246G>A	ENST00000360467.5	+	22	1867	c.1561G>A	c.(1561-1563)Ggc>Agc	p.G521S	COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	521	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AGGAGACCCCGGCCAACACGG	0.617																																																0			13											33	38	36					13																	111111246		1911	4118	6029	109909247	SO:0001583	missense	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1561G>A	13.37:g.111111246G>A	ENSP00000353654:p.Gly521Ser		109909247	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.698065	0.48307	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.99607	-6.27	5.37	5.37	0.77165	.	0.000000	0.56097	D	0.000027	D	0.99667	0.9876	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97885	1.0294	10	0.62326	D	0.03	.	17.9069	0.88921	0.0:0.0:1.0:0.0	.	521	P08572	CO4A2_HUMAN	S	521	ENSP00000353654:G521S	ENSP00000257309:G521S	G	+	1	0	COL4A2	109909247	1.000000	0.71417	0.489000	0.27452	0.226000	0.24999	5.486000	0.66856	2.518000	0.84900	0.655000	0.94253	GGC		0.617	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111111246	G	A	111111246	3	1	91	1	0	0	0	0	1	0	0	0	3696	1116	39	1	1643	1	COL4A2	13	111111246	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	64393778	111111246	4058632	132	25024										
TEP1	7011	hgsc.bcm.edu	37	chr14	20859205	20859205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agcacgacgtccacctgctcCgccctcgtgatcatcatccc	7	19	2	1	rs872074	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:20859205C>T	ENST00000262715.5	-	14	2188	c.2148G>A	c.(2146-2148)gcG>gcA	p.A716A	TEP1_ENST00000556935.1_Silent_p.A608A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	716					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.A716A(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CCACCTGCTCCGCCCTCGTGA	0.537													C|||	802	0.160144	0.2685	0.1297	5008	,	,		21203	0.0317		0.1819	False		,,,				2504	0.1452															1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	14						C		1066,3340	389.6+/-327.4	114,838,1251	114	92	100		2148	-11	0.1	14	dbSNP_86	100	1515,7085	285.1+/-297.0	135,1245,2920	no	coding-synonymous	TEP1	NM_007110.4		249,2083,4171	TT,TC,CC		17.6163,24.1943,19.8447		716/2628	20859205	2581,10425	2203	4300	6503	19929045	SO:0001819	synonymous_variant	7011				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.2148G>A	14.37:g.20859205C>T			19929045	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																				0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20859205	C	T	20859205	2	4	91	1	0	0	0	0	0	0	0	1	15798	639	23	1		1	TEP1	14	20859205	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10		20859205	86490335	133	25025										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24525548	24525548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccggggtgtttggggagaacGggagctgtgtgctgcatgcc	19	8	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:24525548G>A	ENST00000342740.5	+	11	965	c.811G>A	c.(811-813)Ggg>Agg	p.G271R	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	271						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TGGGGAGAACGGGAGCTGTGT	0.622																																																0			14											105	83	91					14																	24525548		2203	4300	6503	23595388	SO:0001583	missense	90668			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.811G>A	14.37:g.24525548G>A	ENSP00000340467:p.Gly271Arg		23595388	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356751	0.41801	.	.	ENSG00000186648	ENST00000342740	T	0.52057	0.68	5.58	2.79	0.32731	.	0.192452	0.47455	N	0.000221	T	0.25158	0.0611	N	0.11789	0.175	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.04294	-1.0962	10	0.21014	T	0.42	-23.3373	7.8653	0.29533	0.2581:0.0:0.7419:0.0	.	271	Q8ND23	LR16B_HUMAN	R	271	ENSP00000340467:G271R	ENSP00000340467:G271R	G	+	1	0	LRRC16B	23595388	0.444000	0.25649	1.000000	0.80357	0.997000	0.91878	0.344000	0.19962	0.317000	0.23160	0.563000	0.77884	GGG		0.622	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		A	24525548	G	A	24525548	3	1	91	1	0	0	0	0	1	0	0	0	9001	1116	39	1	853	1	LRRC16B	14	24525548	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	3666343	24525548	82823992	134	25026										
CHMP4A	29082	hgsc.bcm.edu	37	chr14	24682618	24682618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gtcccaccctggctcaccctTcccgaagagcctgccgagac	9	19	1	2	rs533438540		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:24682618T>C	ENST00000609024.1	-	1	76	c.28A>G	c.(28-30)Aag>Gag	p.K10E	TM9SF1_ENST00000556387.1_Missense_Mutation_p.K10E|CHMP4A_ENST00000530996.1_5'UTR|MDP1_ENST00000532557.1_5'Flank|TM9SF1_ENST00000530611.1_Missense_Mutation_p.K10E|NEDD8-MDP1_ENST00000604306.1_5'Flank|AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000347519.6_Missense_Mutation_p.K53E|CHMP4A_ENST00000542700.2_5'Flank			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	10	Interaction with phosphoinosides.|Intramolecular interaction with C- terminus. {ECO:0000250}.				endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		GGCTCACCCTTCCCGAAGAGC	0.706																																																0			14											35	38	37					14																	24682618		2203	4300	6503	23752458	SO:0001583	missense	128866			AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"Charged multivesicular body proteins"	20274	protein-coding gene	gene with protein product		610051	"chromosome 14 open reading frame 123", "chromatin modifying protein 4A"	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.28A>G	14.37:g.24682618T>C	ENSP00000476412:p.Lys10Glu		23752458	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.4|20.4	3.979765|3.979765	0.74360|0.74360	.|.	.|.	ENSG00000254505|ENSG00000100926;ENSG00000254692;ENSG00000254505	ENST00000548308|ENST00000556387;ENST00000530611;ENST00000347519	.|T;T;T	.|0.59638	.|0.89;0.89;0.25	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|1.221540	.|0.06115	.|N	.|0.667896	T|T	0.60117|0.60117	0.2244|0.2244	M|M	0.66297|0.66297	2.02|2.02	0.25155|0.25155	N|N	0.990391|0.990391	.|B;B	.|0.20261	.|0.002;0.043	.|B;B	.|0.16722	.|0.007;0.016	T|T	0.51052|0.51052	-0.8754|-0.8754	5|10	.|0.56958	.|D	.|0.05	.|.	11.0407|11.0407	0.47829|0.47829	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|10;53	.|Q9BY43;Q14D22	.|CHM4A_HUMAN;.	G|E	29|10;10;53	.|ENSP00000451949:K10E;ENSP00000433967:K10E;ENSP00000324205:K53E	.|ENSP00000324205:K53E	E|K	-|-	2|1	0|0	AL096870.1|TM9SF1;AL096870.1;RP11-468E2.1	23752458|23752458	0.982000|0.982000	0.34865|0.34865	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	1.697000|1.697000	0.37784|0.37784	2.106000|2.106000	0.64143|0.64143	0.460000|0.460000	0.39030|0.39030	GAA|AAG		0.706	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169		C	24682618	T	C	24682618	3	2	91	1	0	0	0	0	1	0	0	0	3362	1792	62	4	664	4	CHMP4A	14	24682618	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	157070	24682618	82666922	135	25027										
SPTB	6710	hgsc.bcm.edu	37	chr14	65241858	65241858	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cagaccttggggatctcatcGgagatgacgtagagctcctg	13	10	1	4	rs187631599	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:65241858G>A	ENST00000389721.5	-	22	4859	c.4827C>T	c.(4825-4827)tcC>tcT	p.S1609S	SPTB_ENST00000389722.3_Silent_p.S1609S|SPTB_ENST00000389720.3_Silent_p.S1609S|SPTB_ENST00000556626.1_Silent_p.S1609S|SPTB_ENST00000542895.1_Silent_p.S1609S	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1609					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GGATCTCATCGGAGATGACGT	0.612													G|||	2	0.000399361	0	0.0029	5008	,	,		20285	0		0	False		,,,				2504	0															0			14						G	,	1,4405	2.1+/-5.4	0,1,2202	141	115	124		4827,4827	-5.4	0	14		124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	1609/2138,1609/2329	65241858	2,13004	2203	4300	6503	64311611	SO:0001819	synonymous_variant	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4827C>T	14.37:g.65241858G>A			64311611	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																				0.612	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			A	65241858	G	A	65241858	2	1	91	1	0	0	0	0	0	0	0	1	15157	1103	39	1		1	SPTB	14	65241858	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	40559240	65241858	42107682	136	25028										
PCNX	22990	hgsc.bcm.edu	37	chr14	71543080	71543080	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggcaggcatatctagggagAgtttctgtgtgatttacctc	12	7	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:71543080A>G	ENST00000304743.2	+	28	5727	c.5281A>G	c.(5281-5283)Agt>Ggt	p.S1761G	PCNX_ENST00000439984.3_Missense_Mutation_p.S1650G|PCNX_ENST00000238570.5_Missense_Mutation_p.S1689G	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1761						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		ATCTAGGGAGAGTTTCTGTGT	0.428																																																0			14											120	109	113					14																	71543080		2203	4300	6503	70612833	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.5281A>G	14.37:g.71543080A>G	ENSP00000304192:p.Ser1761Gly		70612833	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.389680	0.82902	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.12255	3.09;3.14;2.7	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	M	0.85041	2.73	0.32824	D	0.503199	D;D;D	0.58268	0.974;0.974;0.982	D;P;D	0.70487	0.969;0.695;0.952	T	0.58278	-0.7664	10	0.51188	T	0.08	.	15.3459	0.74337	1.0:0.0:0.0:0.0	.	1689;1650;1761	Q96RV3-3;B2RTR6;Q96RV3	.;.;PCX1_HUMAN	G	1761;1689;1650	ENSP00000304192:S1761G;ENSP00000238570:S1689G;ENSP00000396617:S1650G	ENSP00000238570:S1689G	S	+	1	0	PCNX	70612833	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.710000	0.61873	2.277000	0.76020	0.528000	0.53228	AGT		0.428	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71543080	A	G	71543080	3	3	91	1	0	0	0	0	1	0	0	0	11622	304	11	4	5391	4	PCNX	14	71543080	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	6301222	71543080	35806460	137	25029										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81964333	81964333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttcctggattttccacttcaTcaggcagccgtattctctgt	7	12	3	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:81964333T>C	ENST00000336735.4	-	10	1147	c.1031A>G	c.(1030-1032)gAt>gGt	p.D344G		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	344	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TTCCACTTCATCAGGCAGCCG	0.403																																																0			14											90	79	82					14																	81964333		2203	4300	6503	81034086	SO:0001583	missense	6400				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1031A>G	14.37:g.81964333T>C	ENSP00000337053:p.Asp344Gly		81034086	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	37	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847129	0.91277	.	.	ENSG00000071537	ENST00000336735	T	0.34667	1.35	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.65615	-0.6125	10	0.62326	D	0.03	-18.7479	15.8527	0.78947	0.0:0.0:0.0:1.0	.	344	Q9UBV2	SE1L1_HUMAN	G	344	ENSP00000337053:D344G	ENSP00000337053:D344G	D	-	2	0	SEL1L	81034086	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.525000	0.81892	2.330000	0.79161	0.477000	0.44152	GAT		0.403	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	81964333	T	C	81964333	3	2	91	1	0	0	0	0	1	0	0	0	14047	1435	50	4	1401	4	SEL1L	14	81964333	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	10421253	81964333	25385207	138	25030										
C14orf184	0	hgsc.bcm.edu	37	chr14	92040590	92040590	+	Frame_Shift_Del	DEL	C	C	-													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gacggaccactcgggcgcctCcgccccgcgccctgcctcgg					rs34650717	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:92040590delC	ENST00000596306.1	-	1	793	c.367delG	c.(367-369)gagfs	p.E123fs																								Tcgggcgcctccgccccgcgc	0.736													CC|CC|C|deletion	2499	0.499002	0.4493	0.621	5008	,	,		12978	0.5179		0.4881	False		,,,				2504	0.4714															0			14								991,1125		318,355,385	3	4	3			0.5	0	14	dbSNP_126	5	2231,2317		695,841,738	no	intergenic				1013,1196,1123	A1A1,A1R,RR		49.0545,46.8336,48.3493			92040590	3222,3442	890	1912	2802	91110343	SO:0001589	frameshift_variant	0																														ENST00000596306.1:c.367delG	14.37:g.92040590delC	ENSP00000472226:p.Glu123fs		91110343		Frame_Shift_Del	DEL	ENST00000596306.1	37																																																																																					0.736	AL133373.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding				-	92040590	C	-	92040590	7	5	91	1	0	1	0	1	0	0	0	0	1771	864	30	0	83	0	C14orf184	14	92040590	Frame_Shift_Del	DEL	C	TCGA-CL-5917-01A-11D-1657-10	10076257	92040590	15308950	139	25031										
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94756517	94756517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagagggaaggcaggagcccGggcttggtgggcttcagggc	20	8	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr14:94756517G>A	ENST00000393096.1	-	2	879	c.414C>T	c.(412-414)ccC>ccT	p.P138P	SERPINA10_ENST00000554723.1_Silent_p.P178P|SERPINA10_ENST00000261994.4_Silent_p.P138P|SERPINA10_ENST00000554173.1_Silent_p.P138P	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	138	Heparin-binding.				blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GCAGGAGCCCGGGCTTGGTGG	0.597																																																0			14											47	52	51					14																	94756517		2203	4300	6503	93826270	SO:0001819	synonymous_variant	51156			AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"Serine (or cysteine) peptidase inhibitors"	15996	protein-coding gene	gene with protein product		605271	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.414C>T	14.37:g.94756517G>A			93826270	A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	37	CCDS9923.1																																																																																				0.597	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		A	94756517	G	A	94756517	2	1	91	1	0	0	0	0	0	0	0	1	14124	1103	39	1		1	SERPINA10	14	94756517	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	2715927	94756517	12593023	140	25032										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43820822	43820823	+	Frame_Shift_Ins	INS	-	-	T													0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gaaaatgaagaggctgcggcINSttgccctgcctgggaacgtg							TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr15:43820822_43820823insT	ENST00000300231.5	+	4	7601_7602	c.7151_7152insT	c.(7150-7155)gcttgcfs	p.C2385fs	MAP1A_ENST00000399453.1_Frame_Shift_Ins_p.C2385fs|MAP1A_ENST00000382031.1_Frame_Shift_Ins_p.C2623fs			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2385					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAGGCTGCGGCTTGCCCTGCCT	0.639																																																0			15																																								41608115	SO:0001589	frameshift_variant	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7153dupT	15.37:g.43820824_43820824dupT	ENSP00000300231:p.Cys2385fs		41608114	O95643|Q12973|Q15882|Q9UJT4	Frame_Shift_Ins	INS	ENST00000300231.5	37	CCDS42031.1																																																																																				0.639	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43820823	-	T	43820822	7	5	91	1	0	1	1	0	0	0	0	0	9257	797	28	0	7153	0	MAP1A	15	43820822	Frame_Shift_Ins	INS	-	TCGA-CL-5917-01A-11D-1657-10		43820822	58710570	141	25033										
SMG1	23049	hgsc.bcm.edu	37	chr16	18839377	18839377	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	actgttgcaatagaagtttcAatctggctcagggtatgcag	11	7	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:18839377A>G	ENST00000446231.2	-	55	10129	c.9717T>C	c.(9715-9717)atT>atC	p.I3239I	SMG1_ENST00000389467.3_Silent_p.I3240I			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3239			I -> T (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TAGAAGTTTCAATCTGGCTCA	0.423																																																0			16											71	74	73					16																	18839377		1922	4121	6043	18746878	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9717T>C	16.37:g.18839377A>G			18746878	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.423	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18839377	A	G	18839377	2	3	91	1	0	0	0	0	0	0	0	1	14832	126	5	4		4	SMG1	16	18839377	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10		18839377	71515376	142	25034										
OTOA	146183	hgsc.bcm.edu	37	chr16	21696609	21696609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gccccagaagctgctggaggAcctgaggaagacagacgccc	14	13	0	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:21696609A>G	ENST00000286149.4	+	6	327	c.326A>G	c.(325-327)gAc>gGc	p.D109G	OTOA_ENST00000388958.3_Missense_Mutation_p.D109G|OTOA_ENST00000388956.4_Missense_Mutation_p.D30G			Q7RTW8	OTOAN_HUMAN	otoancorin	109					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CTGCTGGAGGACCTGAGGAAG	0.582																																																0			16											64	59	60					16																	21696609		2199	4300	6499	21604110	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.326A>G	16.37:g.21696609A>G	ENSP00000286149:p.Asp109Gly		21604110	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	A	20.5	3.994262	0.74703	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.12569	2.67;2.67;2.67	5.84	4.73	0.59995	.	0.337294	0.30159	N	0.010266	T	0.18509	0.0444	L	0.60455	1.87	0.80722	D	1	P;P	0.52316	0.908;0.952	B;P	0.45753	0.436;0.492	T	0.00907	-1.1519	10	0.72032	D	0.01	-9.3632	10.4233	0.44363	0.8537:0.0:0.0:0.1463	.	30;109	B3KWU3;E9PF51	.;.	G	109;109;30	ENSP00000373610:D109G;ENSP00000286149:D109G;ENSP00000373608:D30G	ENSP00000286149:D109G	D	+	2	0	OTOA	21604110	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.506000	0.53364	0.996000	0.38943	0.533000	0.62120	GAC		0.582	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			G	21696609	A	G	21696609	3	3	91	1	0	0	0	0	1	0	0	0	11333	275	10	4	382	4	OTOA	16	21696609	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	2857232	21696609	68658144	143	25035										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48139124	48139124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gaagacgaagcctttggtgaCgccaaacaccagcatgaaca	10	11	0	3	rs61742619	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:48139124C>T	ENST00000311303.3	-	19	2944	c.2599G>A	c.(2599-2601)Gtc>Atc	p.V867I	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Missense_Mutation_p.V864I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	867	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CCTTTGGTGACGCCAAACACC	0.547													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		20069	0		0	False		,,,				2504	0															0			16						C	ILE/VAL	5,4397	9.9+/-24.2	0,5,2196	242	170	194		2599	-0.9	0	16	dbSNP_129	194	0,8600		0,0,4300	yes	missense	ABCC12	NM_033226.2	29	0,5,6496	TT,TC,CC		0.0,0.1136,0.0385	benign	867/1360	48139124	5,12997	2201	4300	6501	46696625	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2599G>A	16.37:g.48139124C>T	ENSP00000311030:p.Val867Ile		46696625	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	0.007	-1.983659	0.00443	0.001136	0.0	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	D;D	0.91631	-2.62;-2.88	5.21	-0.92	0.10475	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.559617	0.19035	N	0.124457	T	0.67411	0.2890	N	0.03029	-0.43	0.09310	N	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.62006	-0.6945	10	0.12430	T	0.62	.	5.6322	0.17516	0.1513:0.4527:0.0:0.396	.	867	Q96J65	MRP9_HUMAN	I	867;864;785	ENSP00000311030:V867I;ENSP00000401855:V864I	ENSP00000311030:V867I	V	-	1	0	ABCC12	46696625	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.045000	0.14013	-0.229000	0.09854	-0.302000	0.09304	GTC		0.547	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48139124	C	T	48139124	3	4	91	1	0	0	0	0	1	0	0	0	52	536	19	1	1524	1	ABCC12	16	48139124	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	26442515	48139124	42215629	144	25036										
NOD2	64127	hgsc.bcm.edu	37	chr16	50733516	50733516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggactggctgctgtcctgggAggtcctctcctgggaggact	16	11	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:50733516A>G	ENST00000300589.2	+	2	296	c.191A>G	c.(190-192)gAg>gGg	p.E64G	NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	64	CARD 1. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CTGTCCTGGGAGGTCCTCTCC	0.627																																																0			16											56	61	59					16																	50733516		2198	4300	6498	49291017	SO:0001583	missense	64127			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.191A>G	16.37:g.50733516A>G	ENSP00000300589:p.Glu64Gly		49291017	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887214	0.33348	.	.	ENSG00000167207	ENST00000526417;ENST00000531674;ENST00000300589	T;T	0.21031	2.03;2.03	5.34	4.24	0.50183	DEATH-like (2);Caspase Recruitment (3);	0.886526	0.09693	N	0.768130	T	0.14743	0.0356	N	0.20685	0.6	0.31293	N	0.689235	P	0.43938	0.822	B	0.40825	0.341	T	0.08146	-1.0736	10	0.35671	T	0.21	.	7.8228	0.29296	0.9054:0.0:0.0946:0.0	.	64	Q9HC29	NOD2_HUMAN	G	37;37;64	ENSP00000431681:E37G;ENSP00000300589:E64G	ENSP00000300589:E64G	E	+	2	0	NOD2	49291017	0.978000	0.34361	0.931000	0.37212	0.894000	0.52154	2.494000	0.45329	0.874000	0.35823	0.533000	0.62120	GAG		0.627	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		G	50733516	A	G	50733516	3	3	91	1	0	0	0	0	1	0	0	0	10548	304	11	4	197	4	NOD2	16	50733516	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	2594392	50733516	39621237	145	25037										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687702	61687702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggagtcatatggcggggccGtgggatcattatctgcctca	14	9	4	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:61687702G>A	ENST00000577390.1	-	12	3164	c.2210C>T	c.(2209-2211)aCg>aTg	p.T737M	CDH8_ENST00000299345.6_Intron|CDH8_ENST00000577730.1_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	737					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TGGCGGGGCCGTGGGATCATT	0.502																																																0			16											67	73	71					16																	61687702		2203	4300	6503	60245203	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2210C>T	16.37:g.61687702G>A	ENSP00000462701:p.Thr737Met		60245203	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949902	0.53186	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.052664	0.85682	D	0.000000	T	0.74390	0.3710	M	0.68728	2.09	0.80722	D	1	P	0.50819	0.939	P	0.55161	0.77	T	0.75314	-0.3361	9	0.56958	D	0.05	.	18.8311	0.92139	0.0:0.0:1.0:0.0	.	737	P55286	CADH8_HUMAN	M	737	.	ENSP00000299345:T737M	T	-	2	0	CDH8	60245203	1.000000	0.71417	0.932000	0.37286	0.979000	0.70002	7.803000	0.85983	2.679000	0.91253	0.655000	0.94253	ACG		0.502	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		A	61687702	G	A	61687702	3	1	91	1	0	0	0	0	1	0	0	0	3122	1145	40	1	193	1	CDH8	16	61687702	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	10954186	61687702	28667051	146	25038										
IRF8	3394	hgsc.bcm.edu	37	chr16	85953744	85953744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agttctataacagccagggcCggcttcctgacggcagggtg	14	11	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr16:85953744C>T	ENST00000268638.5	+	8	1440	c.1018C>T	c.(1018-1020)Cgg>Tgg	p.R340W	IRF8_ENST00000562492.1_Missense_Mutation_p.R136W	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	340					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAGCCAGGGCCGGCTTCCTGA	0.587																																																0			16											59	53	55					16																	85953744		2198	4300	6498	84511245	SO:0001583	missense	3394			M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1018C>T	16.37:g.85953744C>T	ENSP00000268638:p.Arg340Trp		84511245	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909429	0.72868	.	.	ENSG00000140968	ENST00000268638	D	0.95447	-3.71	5.15	5.15	0.70609	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.130208	0.53938	D	0.000054	D	0.97090	0.9049	M	0.70595	2.14	0.58432	D	0.999995	D	0.69078	0.997	P	0.61658	0.892	D	0.97562	1.0099	10	0.66056	D	0.02	-40.0654	18.248	0.89993	0.0:1.0:0.0:0.0	.	340	Q02556	IRF8_HUMAN	W	340	ENSP00000268638:R340W	ENSP00000268638:R340W	R	+	1	2	IRF8	84511245	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	4.229000	0.58625	2.397000	0.81536	0.655000	0.94253	CGG		0.587	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		T	85953744	C	T	85953744	3	4	91	1	0	0	0	0	1	0	0	0	7857	643	23	1	1044	1	IRF8	16	85953744	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	24266042	85953744	4401009	147	25039										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5462052	5462052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ttccatatgcttctagcgtcTtttccaaatctatgatgcaa	5	10	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:5462052T>C	ENST00000572272.1	-	4	1963	c.1964A>G	c.(1963-1965)aAg>aGg	p.K655R	NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Missense_Mutation_p.K655R|NLRP1_ENST00000269280.4_Missense_Mutation_p.K655R|NLRP1_ENST00000262467.5_Missense_Mutation_p.K655R|NLRP1_ENST00000354411.3_Missense_Mutation_p.K655R|NLRP1_ENST00000345221.3_Missense_Mutation_p.K655R			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	655					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTCTAGCGTCTTTTCCAAATC	0.448																																																0			17											145	127	133					17																	5462052		2203	4300	6503	5402776	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1964A>G	17.37:g.5462052T>C	ENSP00000460475:p.Lys655Arg		5402776	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	7.850	0.723828	0.15439	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.72394	-0.65;-0.65;-0.63;-0.61;-0.63	4.11	-5.56	0.02529	.	1.319690	0.05449	N	0.549209	T	0.49762	0.1576	L	0.37897	1.145	0.09310	N	1	B;B;B;B;B	0.28880	0.2;0.2;0.126;0.2;0.226	B;B;B;B;B	0.30179	0.112;0.112;0.035;0.112;0.063	T	0.37197	-0.9716	10	0.13108	T	0.6	.	0.5195	0.00609	0.4144:0.214:0.15:0.2215	.	655;655;655;655;655	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	R	655	ENSP00000442029:K655R;ENSP00000262467:K655R;ENSP00000269280:K655R;ENSP00000346390:K655R;ENSP00000324366:K655R	ENSP00000262467:K655R	K	-	2	0	NLRP1	5402776	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.006000	0.12833	-1.289000	0.02375	-0.417000	0.06048	AAG		0.448	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		C	5462052	T	C	5462052	3	2	91	1	0	0	0	0	1	0	0	0	10502	1609	56	4	2588	4	NLRP1	17	5462052	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10		5462052	75733158	148	25040										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	91	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	2115068	7577120	73618090	149	25041										
FLII	2314	hgsc.bcm.edu	37	chr17	18149086	18149086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acgtgtgtgtttcatgtactCggcatcgtcatcatagggct	11	9	3	0	rs200966684		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:18149086C>T	ENST00000327031.4	-	27	3700	c.3475G>A	c.(3475-3477)Gag>Aag	p.E1159K	FLII_ENST00000578558.1_Intron|FLII_ENST00000579294.1_Missense_Mutation_p.E1148K|FLII_ENST00000545457.2_Missense_Mutation_p.E1104K|FLII_ENST00000379450.4_Missense_Mutation_p.E1073K	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1159					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.E1159K(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					TTCATGTACTCGGCATCGTCA	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	17						C	LYS/GLU	0,4406		0,0,2203	190	164	173		3475	5.7	0.9	17		173	1,8599	1.2+/-3.3	0,1,4299	no	missense	FLII	NM_002018.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1159/1270	18149086	1,13005	2203	4300	6503	18089811	SO:0001583	missense	2314			U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3475G>A	17.37:g.18149086C>T	ENSP00000324573:p.Glu1159Lys		18089811	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	17.26	3.344587	0.61073	0.0	1.16E-4	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T;T	0.37058	1.95;1.22;1.95	5.69	5.69	0.88448	.	0.151487	0.64402	D	0.000019	T	0.39410	0.1077	M	0.68317	2.08	0.80722	D	1	P;P;P;B	0.40230	0.477;0.477;0.708;0.308	B;B;B;B	0.33121	0.085;0.085;0.158;0.048	T	0.41484	-0.9506	10	0.54805	T	0.06	-21.1352	19.7945	0.96474	0.0:1.0:0.0:0.0	.	1073;1073;1159;1128	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	K	1159;1038;1073	ENSP00000324573:E1159K;ENSP00000438536:E1038K;ENSP00000368763:E1073K	ENSP00000324573:E1159K	E	-	1	0	FLII	18089811	1.000000	0.71417	0.946000	0.38457	0.290000	0.27261	7.456000	0.80751	2.690000	0.91761	0.655000	0.94253	GAG		0.587	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		T	18149086	C	T	18149086	3	4	91	1	0	0	0	0	1	0	0	0	5944	893	31	1	350	1	FLII	17	18149086	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	10571966	18149086	63046124	150	25042										
SARM1	23098	hgsc.bcm.edu	37	chr17	26711901	26711901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcttctgcggctcacggaggAggaactccagaccgacctgg	14	13	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:26711901A>G	ENST00000457710.3	+	4	1715	c.1244A>G	c.(1243-1245)gAg>gGg	p.E415G	SARM1_ENST00000379061.4_3'UTR	NM_015077.2	NP_055892.2	Q6SZW1	SARM1_HUMAN	sterile alpha and TIR motif containing 1	449	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of apoptotic process (GO:0042981)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron death (GO:1901214)|response to glucose (GO:0009749)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of mitochondrial outer membrane (GO:0031315)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|synapse (GO:0045202)				cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		CTCACGGAGGAGGAACTCCAG	0.647																																																0			17											38	33	35					17																	26711901		2178	4242	6420	23736028	SO:0001583	missense	23098			AB011096		17q11	2013-01-10			ENSG00000004139	ENSG00000004139		"Sterile alpha motif (SAM) domain containing"	17074	protein-coding gene	gene with protein product		607732				9628581	Standard	NM_015077		Approved	SARM, SAMD2, KIAA0524	uc010crl.1	Q6SZW1	OTTHUMG00000132499	ENST00000457710.3:c.1244A>G	17.37:g.26711901A>G	ENSP00000406738:p.Glu415Gly		23736028	O60277|Q7LGG3|Q9NXY5	Silent	SNP	ENST00000457710.3	37		.	.	.	.	.	.	.	.	.	.	A	14.17	2.456767	0.43634	.	.	ENSG00000004139	ENST00000457710;ENST00000003834	.	.	.	4.87	4.87	0.63330	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (1);Sterile alpha motif, type 2 (1);Armadillo-type fold (1);	0.063893	0.64402	D	0.000005	T	0.47210	0.1433	.	.	.	0.37841	D	0.929068	B	0.28820	0.224	B	0.28916	0.096	T	0.54682	-0.8257	8	0.62326	D	0.03	-22.7285	7.2179	0.25969	0.7068:0.1496:0.0:0.1436	.	449	Q6SZW1	SARM1_HUMAN	G	447;415	.	ENSP00000003834:E415G	E	+	2	0	SARM1	23736028	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.610000	0.54125	1.803000	0.52742	0.402000	0.26972	GAG		0.647	SARM1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000255679.3	NM_015077		G	26711901	A	G	26711901	3	3	91	1	0	0	0	0	1	0	0	0	13879	304	11	4	1358	4	SARM1	17	26711901	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	8562815	26711901	54483309	151	25043										
NF1	4763	hgsc.bcm.edu	37	chr17	29562981	29562981	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aactcctggatcctttattaCgaattgtgatcacatcctct	5	11	2	1	rs376576925		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:29562981C>T	ENST00000358273.4	+	29	4299	c.3916C>T	c.(3916-3918)Cga>Tga	p.R1306*	NF1_ENST00000356175.3_Nonsense_Mutation_p.R1306*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1306	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.R1306*(5)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCCTTTATTACGAATTGTGAT	0.363			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	17	Whole gene deletion(8)|Substitution - Nonsense(5)|Unknown(4)	soft_tissue(9)|haematopoietic_and_lymphoid_tissue(3)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17	GRCh37	CM981381	NF1	M							140	130	134					17																	29562981		2203	4300	6503	26587107	SO:0001587	stop_gained	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3916C>T	17.37:g.29562981C>T	ENSP00000351015:p.Arg1306*		26587107	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	46	12.668907	0.99687	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.94	2.6	0.31112	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4146	0.74956	0.589:0.411:0.0:0.0	.	.	.	.	X	1306;1306;972	.	ENSP00000348498:R1306X	R	+	1	2	NF1	26587107	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.385000	0.52485	0.763000	0.33175	0.557000	0.71058	CGA		0.363	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29562981	C	T	29562981	4	4	91	1	0	0	0	0	0	1	0	0	10387	528	19	1	4091	1	NF1	17	29562981	Nonsense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	2851080	29562981	51632229	152	25044										
NF1	4763	hgsc.bcm.edu	37	chr17	29662003	29662003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aatgaccatcaatgaaaaacAgatgtacccatctattcaag	5	9	3	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:29662003A>G	ENST00000358273.4	+	40	6343	c.5960A>G	c.(5959-5961)cAg>cGg	p.Q1987R	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Missense_Mutation_p.Q1966R|NF1_ENST00000444181.2_5'Flank|NF1_ENST00000417592.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1987					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AATGAAAAACAGATGTACCCA	0.358			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											104	92	96					17																	29662003		2203	4300	6503	26686129	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5960A>G	17.37:g.29662003A>G	ENSP00000351015:p.Gln1987Arg		26686129	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.870606	0.91587	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;T;D	0.91894	-2.93;-0.12;-2.93	5.54	5.54	0.83059	Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	D	0.92567	0.7639	N	0.24115	0.695	0.80722	D	1	P;B	0.48294	0.908;0.157	D;B	0.64144	0.922;0.073	D	0.93827	0.7124	10	0.72032	D	0.01	.	15.6824	0.77381	1.0:0.0:0.0:0.0	.	1966;1987	P21359-2;P21359	.;NF1_HUMAN	R	1987;1966;1632	ENSP00000351015:Q1987R;ENSP00000348498:Q1966R;ENSP00000389907:Q1632R	ENSP00000348498:Q1966R	Q	+	2	0	NF1	26686129	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.760000	0.91671	2.117000	0.64856	0.455000	0.32223	CAG		0.358	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29662003	A	G	29662003	3	3	91	1	0	0	0	0	1	0	0	0	10387	188	7	4	6179	4	NF1	17	29662003	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	99022	29662003	51533207	153	25045										
DHX58	79132	hgsc.bcm.edu	37	chr17	40257861	40257861	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctggagccagagcaggagggAgtgtgcgctttggcgggtgc	20	8	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:40257861A>G	ENST00000251642.3	-	9	1366	c.1144T>C	c.(1144-1146)Tcc>Ccc	p.S382P		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	382	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		AGCAGGAGGGAGTGTGCGCTT	0.592																																																0			17											84	83	83					17																	40257861		2203	4300	6503	37511387	SO:0001583	missense	79132			BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1144T>C	17.37:g.40257861A>G	ENSP00000251642:p.Ser382Pro		37511387	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.581443	0.46006	.	.	ENSG00000108771	ENST00000251642;ENST00000423748	T	0.43294	0.95	5.17	4.08	0.47627	Helicase, C-terminal (2);	0.136494	0.49305	D	0.000143	T	0.51143	0.1657	M	0.79258	2.445	0.23899	N	0.996521	D;D	0.56035	0.974;0.974	P;P	0.53861	0.736;0.451	T	0.46076	-0.9217	10	0.36615	T	0.2	.	6.4083	0.21676	0.6749:0.1851:0.0:0.14	.	375;382	B7Z455;Q96C10	.;DHX58_HUMAN	P	382;345	ENSP00000251642:S382P	ENSP00000251642:S382P	S	-	1	0	DHX58	37511387	0.999000	0.42202	0.564000	0.28396	0.455000	0.32408	1.328000	0.33758	1.962000	0.57031	0.374000	0.22700	TCC		0.592	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		G	40257861	A	G	40257861	3	3	91	1	0	0	0	0	1	0	0	0	4525	304	11	4	916	4	DHX58	17	40257861	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	10595858	40257861	40937349	154	25046										
PYY	5697	hgsc.bcm.edu	37	chr17	42030685	42030685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gctgccgggtgaccaggttgAggtagtggcgcagggaggcg	21	8	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:42030685A>G	ENST00000360085.2	-	5	707	c.167T>C	c.(166-168)cTc>cCc	p.L56P	PYY_ENST00000592796.1_Missense_Mutation_p.L56P	NM_004160.4	NP_004151	P10082	PYY_HUMAN	peptide YY	56					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|digestion (GO:0007586)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			endometrium(1)|ovary(1)	2		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GACCAGGTTGAGGTAGTGGCG	0.721																																																0			17											17	19	18					17																	42030685		2201	4298	6499	39386211	SO:0001583	missense	5697				CCDS32662.1	17q21.1	2013-02-28				ENSG00000131096		"Endogenous ligands"	9748	protein-coding gene	gene with protein product	"prepro-PYY"	600781				7782089	Standard	NM_004160		Approved	PYY1	uc002ieq.3	P10082		ENST00000360085.2:c.167T>C	17.37:g.42030685A>G	ENSP00000353198:p.Leu56Pro		39386211	Q5U5Q6|Q6FGH8	Missense_Mutation	SNP	ENST00000360085.2	37	CCDS32662.1	.	.	.	.	.	.	.	.	.	.	.	27.4	4.824649	0.90955	.	.	ENSG00000131096	ENST00000360085	T	0.50277	0.75	4.64	4.64	0.57946	Pancreatic hormone-like, conserved site (1);	.	.	.	.	T	0.66626	0.2808	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.70673	-0.4807	8	0.87932	D	0	-1.5578	10.4366	0.44439	1.0:0.0:0.0:0.0	.	56	P10082	PYY_HUMAN	P	56	ENSP00000353198:L56P	ENSP00000353198:L56P	L	-	2	0	PYY	39386211	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.187000	0.65087	1.714000	0.51371	0.448000	0.29417	CTC		0.721	PYY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000457658.1	NM_004160		G	42030685	A	G	42030685	3	3	91	1	0	0	0	0	1	0	0	0	12905	304	11	4	138	4	PYY	17	42030685	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	1772824	42030685	39164525	155	25047										
TEX14	56155	hgsc.bcm.edu	37	chr17	56688589	56688589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gatgatatggacagcataggAgctgagggagcggtggataa	17	4	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:56688589A>G	ENST00000240361.8	-	10	1220	c.1135T>C	c.(1135-1137)Tcc>Ccc	p.S379P	TEX14_ENST00000389934.3_Missense_Mutation_p.S373P|TEX14_ENST00000349033.5_Missense_Mutation_p.S373P			Q8IWB6	TEX14_HUMAN	testis expressed 14	379	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACAGCATAGGAGCTGAGGGAG	0.537																																																0			17											162	139	147					17																	56688589		2203	4300	6503	54043588	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1135T>C	17.37:g.56688589A>G	ENSP00000240361:p.Ser379Pro		54043588	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.340380	0.81911	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.30182	1.54;1.54;1.54	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.49558	0.1564	L	0.52759	1.655	0.44966	D	0.997983	D;D;D	0.69078	0.997;0.993;0.993	D;D;D	0.78314	0.991;0.985;0.985	T	0.51164	-0.8740	10	0.87932	D	0	-9.8832	14.1467	0.65355	1.0:0.0:0.0:0.0	.	379;373;373	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	P	379;373;373	ENSP00000240361:S379P;ENSP00000374584:S373P;ENSP00000268910:S373P	ENSP00000240361:S379P	S	-	1	0	TEX14	54043588	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.689000	0.74562	2.034000	0.60081	0.379000	0.24179	TCC		0.537	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			G	56688589	A	G	56688589	3	3	91	1	0	0	0	0	1	0	0	0	15817	304	11	4	3454	4	TEX14	17	56688589	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	14657904	56688589	24506621	156	25048										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67047246	67047246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agcccatgtttgctgacccaCgctcatgcgtctcttgctca	8	15	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:67047246C>T	ENST00000340001.4	-	2	233	c.22G>A	c.(22-24)Gtg>Atg	p.V8M	ABCA9_ENST00000370732.2_Missense_Mutation_p.V8M|ABCA9_ENST00000453985.2_Missense_Mutation_p.V8M|ABCA9_ENST00000495634.1_Missense_Mutation_p.V8M	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	8					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TGCTGACCCACGCTCATGCGT	0.393																																																0			17											132	123	126					17																	67047246		2203	4300	6503	64558841	SO:0001583	missense	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.22G>A	17.37:g.67047246C>T	ENSP00000342216:p.Val8Met		64558841	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.529110	0.27387	.	.	ENSG00000154258	ENST00000340001;ENST00000370732;ENST00000453749	D;D	0.89875	-2.44;-2.58	5.03	-6.34	0.01982	.	0.870603	0.09346	N	0.814786	D	0.89921	0.6855	M	0.79805	2.47	0.09310	N	1	D;D	0.76494	0.999;0.992	P;P	0.61397	0.888;0.776	T	0.80248	-0.1461	10	0.87932	D	0	.	0.2482	0.00201	0.2346:0.1857:0.2439:0.3359	.	8;8	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	M	8;8;3	ENSP00000342216:V8M;ENSP00000359767:V8M	ENSP00000342216:V8M	V	-	1	0	ABCA9	64558841	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.409000	0.07160	-0.934000	0.03733	0.655000	0.94253	GTG		0.393	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	67047246	C	T	67047246	3	4	91	1	0	0	0	0	1	0	0	0	39	536	19	1	5004	1	ABCA9	17	67047246	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	10358657	67047246	14147964	157	25049										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76094557	76094557	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccacctccagggttaaccaaTcccaagccctcctccacctg	5	20	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:76094557T>C	ENST00000588061.1	+	19	5167	c.4440T>C	c.(4438-4440)aaT>aaC	p.N1480N	TNRC6C_ENST00000544502.1_Silent_p.N1516N|TNRC6C_ENST00000588847.1_Silent_p.N1516N|TNRC6C_ENST00000541771.1_Silent_p.N1480N|TNRC6C_ENST00000301624.4_Silent_p.N1480N|TNRC6C_ENST00000335749.4_Silent_p.N1516N			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1480	Silencing domain; interaction with CNOT1 and PAN3.|Sufficient for translational repression when tethered to a target mRNA.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGTTAACCAATCCCAAGCCCT	0.617																																																0			17											78	84	82					17																	76094557		1989	4157	6146	73606152	SO:0001819	synonymous_variant	57690			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4440T>C	17.37:g.76094557T>C			73606152	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																				0.617	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		C	76094557	T	C	76094557	2	2	91	1	0	0	0	0	0	0	0	1	16381	1432	50	4		4	TNRC6C	17	76094557	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	9047311	76094557	5100653	158	25050										
AATK	9625	hgsc.bcm.edu	37	chr17	79094057	79094057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggacacggccttcttcttgcGttccaggtcctcgcagaagg	12	13	2	1	rs374195702		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:79094057G>A	ENST00000326724.4	-	11	3703	c.3679C>T	c.(3679-3681)Cgc>Tgc	p.R1227C	AATK_ENST00000417379.1_Missense_Mutation_p.R1124C	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1227					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TTCTTCTTGCGTTCCAGGTCC	0.682																																																0			17						G	CYS/ARG,CYS/ARG	0,4228		0,0,2114	29	34	32		3679,3370	4	1	17		32	1,8449		0,1,4224	no	missense,missense	AATK	NM_001080395.2,NM_004920.2	180,180	0,1,6338	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging,probably-damaging	1227/1375,1124/1272	79094057	1,12677	2114	4225	6339	76708652	SO:0001583	missense	9625			AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3679C>T	17.37:g.79094057G>A	ENSP00000324196:p.Arg1227Cys		76708652	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193269	0.58017	0.0	1.18E-4	ENSG00000181409	ENST00000326724	T	0.12465	2.68	3.98	3.98	0.46160	.	0.205235	0.39407	N	0.001366	T	0.34716	0.0907	M	0.77103	2.36	0.39345	D	0.965657	D	0.89917	1.0	D	0.68621	0.959	T	0.26155	-1.0111	10	0.87932	D	0	.	11.1426	0.48411	0.0:0.0:0.8153:0.1847	.	1227	Q6ZMQ8	LMTK1_HUMAN	C	1227	ENSP00000324196:R1227C	ENSP00000324196:R1227C	R	-	1	0	AATK	76708652	0.999000	0.42202	0.998000	0.56505	0.680000	0.39746	1.856000	0.39389	2.042000	0.60477	0.313000	0.20887	CGC		0.682	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		A	79094057	G	A	79094057	3	1	91	1	0	0	0	0	1	0	0	0	26	1145	40	1	461	1	AATK	17	79094057	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	2999500	79094057	2101153	159	25051										
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79219806	79219806	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agccggtggccctgctgtccAccctgctcgccatcagagat	11	16	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr17:79219806A>C	ENST00000374759.3	-	16	3293	c.2910T>G	c.(2908-2910)ggT>ggG	p.G970G		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	970					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCTGCTGTCCACCCTGCTCGC	0.687																																																0			17											23	27	26					17																	79219806		1990	4155	6145	76834401	SO:0001819	synonymous_variant	124565			BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2910T>G	17.37:g.79219806A>C			76834401	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																				0.687	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		C	79219806	A	C	79219806	2	2	91	1	0	0	0	0	0	0	0	1	14639	146	6	4		4	SLC38A10	17	79219806	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	125749	79219806	1975404	160	25052										
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9887416	9887416	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tccagcccaaggagggtgacAtccccaagtccccagaagaa	10	14	0	3	rs2240909		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr18:9887416A>C	ENST00000306084.6	+	2	1139	c.940A>C	c.(940-942)Atc>Ctc	p.I314L	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Missense_Mutation_p.I247L	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	314	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		I -> L (in dbSNP:rs2240909).		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)	p.I247L(2)|p.I314L(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GGAGGGTGACATCCCCAAGTC	0.597																																																3	Substitution - Missense(3)	kidney(2)|skin(1)	18											121	118	119					18																	9887416		2203	4299	6502	9877416	SO:0001583	missense	84203			AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.940A>C	18.37:g.9887416A>C	ENSP00000304908:p.Ile314Leu		9877416	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	-	10.84	1.464454	0.26335	.	.	ENSG00000168454	ENST00000357775;ENST00000306084	T;T	0.16324	2.35;2.35	4.52	-1.32	0.09201	.	0.746371	0.11489	N	0.558962	T	0.12263	0.0298	L	0.49778	1.585	0.09310	N	1	B	0.26547	0.152	B	0.29440	0.102	T	0.34502	-0.9826	9	.	.	.	0.3059	1.0808	0.01642	0.4266:0.1509:0.2759:0.1465	rs2240909;rs2240909	314	Q86VQ3	TXND2_HUMAN	L	247;314	ENSP00000350419:I247L;ENSP00000304908:I314L	.	I	+	1	0	TXNDC2	9877416	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.727000	0.04931	0.021000	0.15133	0.529000	0.55759	ATC		0.597	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			C	9887416	A	C	9887416	3	2	91	1	0	0	0	0	1	0	0	0	16837	217	8	4	946	4	TXNDC2	18	9887416	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10		9887416	68189832	161	25053										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575211	48575211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aatccatatcactacgaacgAgttgtatcacctggaattgg	8	9	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr18:48575211A>G	ENST00000342988.3	+	3	943	c.405A>G	c.(403-405)cgA>cgG	p.R135R	SMAD4_ENST00000452201.2_Silent_p.R135R|SMAD4_ENST00000588745.1_Silent_p.R135R|SMAD4_ENST00000398417.2_Silent_p.R135R|RP11-729L2.2_ENST00000590722.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	135	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ACTACGAACGAGTTGTATCAC	0.318																																																40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											122	110	114					18																	48575211		2203	4300	6503	46829209	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.405A>G	18.37:g.48575211A>G			46829209	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.318	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48575211	A	G	48575211	2	3	91	1	0	0	0	0	0	0	0	1	14797	291	11	4		4	SMAD4	18	48575211	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	38687795	48575211	29502037	162	25054										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591809	48591809	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	atagctcctgagtattggtgTtccattgcttactttgaaat	8	7	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr18:48591809T>C	ENST00000342988.3	+	9	1510	c.972T>C	c.(970-972)tgT>tgC	p.C324C	SMAD4_ENST00000588745.1_Silent_p.C228C|SMAD4_ENST00000398417.2_Silent_p.C324C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	324	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.W323fs*11(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGTATTGGTGTTCCATTGCTT	0.413																																																39	Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|small_intestine(1)|oesophagus(1)	18											248	214	225					18																	48591809		2203	4300	6503	46845807	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.972T>C	18.37:g.48591809T>C			46845807	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48591809	T	C	48591809	2	2	91	1	0	0	0	0	0	0	0	1	14797	1731	60	4		4	SMAD4	18	48591809	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	16598	48591809	29485439	163	25055										
NACC1	112939	hgsc.bcm.edu	37	chr19	13246330	13246330	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cagttcctgctcatgtacacGgctggcttcctgcagatcca	9	14	1	1	rs138480405		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:13246330G>A	ENST00000292431.4	+	2	435	c.309G>A	c.(307-309)acG>acA	p.T103T		NM_052876.3	NP_443108.1	Q96RE7	NACC1_HUMAN	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	103					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear body (GO:0016604)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(3)|skin(1)	9						TCATGTACACGGCTGGCTTCC	0.627													G|||	1	0.000199681	8e-04	0	5008	,	,		16927	0		0	False		,,,				2504	0															0			19						G		10,4396	12.9+/-30.5	0,10,2193	36	35	35		309	-8.8	0.9	19	dbSNP_134	35	0,8600		0,0,4300	no	coding-synonymous	NACC1	NM_052876.2		0,10,6493	AA,AG,GG		0.0,0.227,0.0769		103/528	13246330	10,12996	2203	4300	6503	13107330	SO:0001819	synonymous_variant	112939			AF395817	CCDS12294.1	19p13.13	2013-01-09	2008-10-03	2008-10-03		ENSG00000160877		"BEN domain containing", "BTB/POZ domain containing"	20967	protein-coding gene	gene with protein product	"nucleus accumbens associated 1", "BEN domain containing 8"	610672	"BTB (POZ) domain containing 14B"	BTBD14B		12477932	Standard	NM_052876		Approved	NAC1, NAC-1, BEND8, BTBD30	uc002mwm.4	Q96RE7		ENST00000292431.4:c.309G>A	19.37:g.13246330G>A			13107330		Silent	SNP	ENST00000292431.4	37	CCDS12294.1																																																																																				0.627	NACC1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452879.1	NM_052876		A	13246330	G	A	13246330	2	1	91	1	0	0	0	0	0	0	0	1	10165	1103	39	1		1	NACC1	19	13246330	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10		13246330	45882653	164	25056										
C19orf57	79173	hgsc.bcm.edu	37	chr19	14003622	14003622	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gctaaaggccccactcccacGgtcctcatccttcatctctt	5	18	3	0	rs146539987	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:14003622G>C	ENST00000586783.1	-	4	369	c.370C>G	c.(370-372)Cgt>Ggt	p.R124G	C19orf57_ENST00000346736.2_Missense_Mutation_p.R124G|C19orf57_ENST00000591586.1_Missense_Mutation_p.R124G|C19orf57_ENST00000454313.1_Missense_Mutation_p.R124G			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	124					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CCACTCCCACGGTCCTCATCC	0.537																																																0			19											124	113	116					19																	14003622		2203	4300	6503	13864622	SO:0001583	missense	79173			BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.370C>G	19.37:g.14003622G>C	ENSP00000465822:p.Arg124Gly		13864622	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		.	.	.	.	.	.	.	.	.	.	G	5.760	0.324668	0.10900	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.30981	1.51;1.51	4.64	-3.01	0.05463	.	2.199780	0.02650	N	0.106314	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.18871	0.023;0.023	T	0.19976	-1.0289	10	0.38643	T	0.18	1.1436	4.6506	0.12592	0.0953:0.4951:0.2371:0.1725	.	124;124	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	G	124	ENSP00000404382:R124G;ENSP00000254336:R124G	ENSP00000254336:R124G	R	-	1	0	C19orf57	13864622	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-0.059000	0.11731	-0.281000	0.09141	0.561000	0.74099	CGT		0.537	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		C	14003622	G	C	14003622	3	2	91	1	0	0	0	0	1	0	0	0	1945	1116	39	5	1559	5	C19orf57	19	14003622	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	757292	14003622	45125361	165	25057										
NWD1	284434	hgsc.bcm.edu	37	chr19	16918475	16918475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcagcgcaagctcctatttaCgggcctcgtgtcgggggtcg	15	12	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:16918475C>T	ENST00000552788.1	+	16	3815	c.3815C>T	c.(3814-3816)aCg>aTg	p.T1272M	NWD1_ENST00000549814.1_Missense_Mutation_p.T1230M|NWD1_ENST00000523826.1_Missense_Mutation_p.T1066M|NWD1_ENST00000339803.6_Missense_Mutation_p.T1137M|NWD1_ENST00000379808.3_Missense_Mutation_p.T1272M|NWD1_ENST00000524140.2_Missense_Mutation_p.T1272M			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1272							ATP binding (GO:0005524)	p.T1272M(1)|p.T1137M(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTCCTATTTACGGGCCTCGTG	0.567																																																2	Substitution - Missense(2)	endometrium(2)	19											81	84	83					19																	16918475		2203	4300	6503	16779475	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3815C>T	19.37:g.16918475C>T	ENSP00000447224:p.Thr1272Met		16779475	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	C	10.56	1.385067	0.25031	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.74002	-0.45;-0.8;-0.45;1.9;1.3;1.9	5.27	5.27	0.74061	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.411545	0.25964	N	0.027180	T	0.78444	0.4284	L	0.43152	1.355	0.09310	N	1	D;D;D	0.76494	0.998;0.999;0.998	P;D;P	0.63703	0.732;0.917;0.828	T	0.70741	-0.4789	10	0.72032	D	0.01	-10.5953	9.9171	0.41442	0.0:0.906:0.0:0.094	.	1272;1272;1137	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	M	1137;1272;1230;1272;1066;1272;1137	ENSP00000428579:T1272M;ENSP00000447548:T1230M;ENSP00000369136:T1272M;ENSP00000428955:T1066M;ENSP00000447224:T1272M;ENSP00000340159:T1137M	ENSP00000340159:T1137M	T	+	2	0	NWD1	16779475	0.047000	0.20315	0.014000	0.15608	0.005000	0.04900	2.135000	0.42112	2.457000	0.83068	0.655000	0.94253	ACG		0.567	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16918475	C	T	16918475	3	4	91	1	0	0	0	0	1	0	0	0	10812	536	19	1	3464	1	NWD1	19	16918475	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	2914853	16918475	42210508	166	25058										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363448	22363448	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggtttctctccagtatgaatAatcttatgtttagtaaggat	8	5	2	1	rs200452805		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:22363448A>T	ENST00000397121.2	-	3	1388	c.1071T>A	c.(1069-1071)atT>atA	p.I357I		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CAGTATGAATAATCTTATGTT	0.383																																																0			19											68	74	72					19																	22363448		2162	4271	6433	22155288	SO:0001819	synonymous_variant	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1071T>A	19.37:g.22363448A>T			22155288	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																				0.383	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		T	22363448	A	T	22363448	2	4	91	1	0	0	0	0	0	0	0	1	18122	358	13	5		5	ZNF676	19	22363448	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	5444973	22363448	36765535	167	25059										
DMKN	93099	hgsc.bcm.edu	37	chr19	35996856	35996856	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctcaccttccagaaagtgtcAaagttaaacatcccaggaga	7	11	2	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:35996856A>G	ENST00000339686.3	-	8	1247	c.1071T>C	c.(1069-1071)ttT>ttC	p.F357F	DMKN_ENST00000474928.1_Silent_p.F4F|DMKN_ENST00000458071.1_Silent_p.F102F|DMKN_ENST00000418261.1_Silent_p.F357F|DMKN_ENST00000467637.1_Silent_p.F82F|DMKN_ENST00000602781.1_Silent_p.F70F|DMKN_ENST00000451297.2_Silent_p.F340F|DMKN_ENST00000392206.2_Silent_p.F70F|DMKN_ENST00000414866.2_Silent_p.F70F|DMKN_ENST00000436012.1_Silent_p.F53F|DMKN_ENST00000447113.2_Silent_p.F407F|DMKN_ENST00000488892.1_Silent_p.F53F|DMKN_ENST00000472252.2_Silent_p.F4F|DMKN_ENST00000402589.2_Silent_p.F70F|DMKN_ENST00000480502.1_Silent_p.F70F|DMKN_ENST00000419602.1_Silent_p.F346F|DMKN_ENST00000443640.1_Silent_p.F120F|DMKN_ENST00000461300.1_Silent_p.F4F|DMKN_ENST00000424570.2_Silent_p.F369F|DMKN_ENST00000429837.1_Silent_p.F316F|DMKN_ENST00000462126.1_5'UTR|DMKN_ENST00000440396.1_Silent_p.F387F|DMKN_ENST00000492341.2_Silent_p.F4F	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	357						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	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)			AGAAAGTGTCAAAGTTAAACA	0.507																																																0			19											158	155	156					19																	35996856		2203	4300	6503	40688696	SO:0001819	synonymous_variant	93099			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1071T>C	19.37:g.35996856A>G			40688696	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.169|4.169	0.029835|0.029835	0.08101|0.08101	.|.	.|.	ENSG00000161249|ENSG00000161249	ENST00000443857|ENST00000434389	.|.	.|.	.|.	4.55|4.55	-9.11|-9.11	0.00711|0.00711	.|.	.|.	.|.	.|.	.|.	T|.	0.47358|.	0.1441|.	.|.	.|.	.|.	0.44627|0.44627	D|D	0.997607|0.997607	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.55786|.	-0.8086|.	4|.	.|.	.|.	.|.	-5.8847|-5.8847	8.8525|8.8525	0.35208|0.35208	0.6617:0.2093:0.129:0.0|0.6617:0.2093:0.129:0.0	.|.	.|.	.|.	.|.	S|R	61|68	.|.	.|.	L|X	-|-	2|1	0|0	DMKN|DMKN	40688696|40688696	0.742000|0.742000	0.28228|0.28228	0.505000|0.505000	0.27651|0.27651	0.508000|0.508000	0.34012|0.34012	-0.706000|-0.706000	0.05047|0.05047	-1.746000|-1.746000	0.01335|0.01335	-0.182000|-0.182000	0.12963|0.12963	TTG|TGA		0.507	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		G	35996856	A	G	35996856	2	3	91	1	0	0	0	0	0	0	0	1	4593	127	5	4		4	DMKN	19	35996856	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	13633408	35996856	23132127	168	25060										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36279026	36279026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cacctgcctcttcctcctccTcttcccctcctgcccacccc	2	26	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:36279026T>C	ENST00000007510.4	+	21	3703	c.3559T>C	c.(3559-3561)Tct>Cct	p.S1187P	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.S1026P|AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.S1023P			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1187	Poly-Ser.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TTCCTCCTCCTCTTCCCCTCC	0.692																																																0			19											29	33	32					19																	36279026		2195	4285	6480	40970866	SO:0001583	missense	0			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3559T>C	19.37:g.36279026T>C	ENSP00000007510:p.Ser1187Pro		40970866	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	37		.	.	.	.	.	.	.	.	.	.	t	15.99	2.994667	0.54041	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.13901	3.04;2.55;2.79	4.68	3.57	0.40892	.	0.000000	0.44285	D	0.000467	T	0.08179	0.0204	N	0.19112	0.55	0.34985	D	0.754435	B;B	0.27229	0.172;0.172	B;B	0.25987	0.065;0.065	T	0.26710	-1.0095	10	0.17832	T	0.49	.	10.3193	0.43756	0.0:0.0:0.1651:0.8349	.	1023;1026	O14559-10;O14559-11	.;.	P	1187;1026;1023	ENSP00000007510:S1187P;ENSP00000320038:S1026P;ENSP00000368227:S1023P	ENSP00000007510:S1187P	S	+	1	0	ARHGAP33	40970866	0.252000	0.23972	0.999000	0.59377	0.907000	0.53573	1.133000	0.31430	1.883000	0.54544	0.330000	0.21533	TCT		0.692	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		C	36279026	T	C	36279026	3	2	91	1	0	0	0	0	1	0	0	0	882	1551	54	4	3641	4	ARHGAP33	19	36279026	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	282170	36279026	22849957	169	25061										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44732645	44732645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tgtggtcttctccagggaggAactgcgactgctcgatctta	12	10	3	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:44732645A>G	ENST00000313040.7	+	4	312	c.107A>G	c.(106-108)gAa>gGa	p.E36G	ZNF227_ENST00000589237.1_3'UTR|ZNF227_ENST00000391961.2_5'UTR|ZNF227_ENST00000589005.1_5'UTR|ZNF227_ENST00000589707.1_5'UTR|ZNF227_ENST00000586228.1_Silent_p.G22G	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				TCCAGGGAGGAACTGCGACTG	0.493																																																0			19											243	211	222					19																	44732645		2203	4300	6503	49424485	SO:0001583	missense	7770			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.107A>G	19.37:g.44732645A>G	ENSP00000321049:p.Glu36Gly		49424485	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	14.06	2.423246	0.43020	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000418980	T	0.12255	2.7	3.84	3.84	0.44239	Krueppel-associated box (4);	.	.	.	.	T	0.52869	0.1761	H	0.98901	4.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.69457	-0.5140	9	0.87932	D	0	.	10.9005	0.47049	1.0:0.0:0.0:0.0	.	22;16;36	Q658S5;Q9NS43;Q86WZ6	.;.;ZN227_HUMAN	G	36;21;22	ENSP00000321049:E36G	ENSP00000321049:E36G	E	+	2	0	ZNF227	49424485	1.000000	0.71417	0.966000	0.40874	0.085000	0.17905	5.335000	0.65929	1.746000	0.51805	0.402000	0.26972	GAA		0.493	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44732645	A	G	44732645	3	3	91	1	0	0	0	0	1	0	0	0	17820	246	9	4	113	4	ZNF227	19	44732645	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	8453619	44732645	14396338	170	25062										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44933209	44933209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gctgtgaaggtctgaattccGccggaagcccttcccacact	10	14	1	2	rs370451566		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:44933209G>A	ENST00000588931.1	-	6	2180	c.1747C>T	c.(1747-1749)Cgg>Tgg	p.R583W	ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Missense_Mutation_p.R577W|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				TCTGAATTCCGCCGGAAGCCC	0.582																																																0			19						G	TRP/ARG	1,4375	2.1+/-5.4	0,1,2187	50	55	53		1747	-1.9	0	19		53	0,8590		0,0,4295	no	missense	ZNF229	NM_014518.2	101	0,1,6482	AA,AG,GG		0.0,0.0229,0.0077	probably-damaging	583/826	44933209	1,12965	2188	4295	6483	49625049	SO:0001583	missense	7772			AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1747C>T	19.37:g.44933209G>A	ENSP00000466519:p.Arg583Trp		49625049	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.348499	0.24426	2.29E-4	0.0	ENSG00000167383	ENST00000291187	.	.	.	3.5	-1.87	0.07737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36054	0.0953	M	0.64630	1.985	0.09310	N	1	D	0.67145	0.996	P	0.50192	0.634	T	0.25363	-1.0134	8	0.33940	T	0.23	.	4.2277	0.10589	0.1873:0.0:0.3716:0.441	.	583	Q9UJW7	ZN229_HUMAN	W	583	.	ENSP00000291187:R583W	R	-	1	2	ZNF229	49625049	0.000000	0.05858	0.001000	0.08648	0.513000	0.34164	-1.166000	0.03129	-0.203000	0.10251	-0.227000	0.12334	CGG		0.582	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		A	44933209	G	A	44933209	3	1	91	1	0	0	0	0	1	0	0	0	17821	1086	38	1	734	1	ZNF229	19	44933209	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	200564	44933209	14195774	171	25063										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52004795	52004795	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcttacatggtcccctgcccGgaaccagtagccatgaactg	10	14	0	1	rs61742108|rs371016684	byFrequency	TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:52004795G>C	ENST00000291707.3	-	1	248	c.193C>G	c.(193-195)Cgg>Ggg	p.R65G	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	65	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TCCCCTGCCCGGAACCAGTAG	0.597																																																0			19											83	71	75					19																	52004795		2203	4300	6503	56696607	SO:0001583	missense	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.193C>G	19.37:g.52004795G>C	ENSP00000291707:p.Arg65Gly		56696607	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	10.38	1.334254	0.24253	.	.	ENSG00000254521	ENST00000291707	T	0.70749	-0.51	2.28	-4.56	0.03431	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66147	0.2760	M	0.92555	3.32	0.09310	N	1	P	0.45986	0.87	B	0.33620	0.167	T	0.56774	-0.7923	9	0.72032	D	0.01	.	3.2272	0.06736	0.3003:0.0:0.3814:0.3183	.	65	Q96PQ1	SIG12_HUMAN	G	65	ENSP00000291707:R65G	ENSP00000291707:R65G	R	-	1	2	SIGLEC12	56696607	0.003000	0.15002	0.003000	0.11579	0.117000	0.20001	-0.338000	0.07842	-2.056000	0.00898	-1.151000	0.01829	CGG		0.597	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	52004795	G	C	52004795	3	2	91	1	0	0	0	0	1	0	0	0	14345	1115	39	5	1699	5	SIGLEC12	19	52004795	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	7071586	52004795	7124188	172	25064										
U2AF2	11338	hgsc.bcm.edu	37	chr19	56185420	56185420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	accccgactcttatcaccgcCgggacttctggtagaggcgg	12	14	3	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:56185420C>T	ENST00000308924.4	+	12	1454	c.1414C>T	c.(1414-1416)Cgg>Tgg	p.R472W	U2AF2_ENST00000590551.1_Missense_Mutation_p.R304W|CTD-2537I9.12_ENST00000589456.1_RNA|EPN1_ENST00000270460.6_5'Flank|U2AF2_ENST00000450554.2_Missense_Mutation_p.R468W|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|EPN1_ENST00000411543.2_5'Flank|EPN1_ENST00000085079.7_5'Flank			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	472					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TTATCACCGCCGGGACTTCTG	0.632																																																0			19											34	39	37					19																	56185420		2203	4299	6502	60877232	SO:0001583	missense	11338			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1414C>T	19.37:g.56185420C>T	ENSP00000307863:p.Arg472Trp		60877232	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.745599	0.69418	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.12147	2.73;2.71	3.94	1.64	0.23874	.	0.074951	0.53938	U	0.000052	T	0.36608	0.0973	M	0.86502	2.82	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	D;D	0.70935	0.957;0.971	T	0.17715	-1.0360	10	0.72032	D	0.01	-24.1686	9.1308	0.36843	0.1666:0.6725:0.1609:0.0	.	472;468	P26368;P26368-2	U2AF2_HUMAN;.	W	472;468	ENSP00000307863:R472W;ENSP00000388475:R468W	ENSP00000307863:R472W	R	+	1	2	U2AF2	60877232	1.000000	0.71417	0.769000	0.31535	0.625000	0.37756	2.390000	0.44416	0.378000	0.24764	0.478000	0.44815	CGG		0.632	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56185420	C	T	56185420	3	4	91	1	0	0	0	0	1	0	0	0	16863	643	23	1	1460	1	U2AF2	19	56185420	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	4180625	56185420	2943563	173	25065										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244788	56244788	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	agccgcagcagtatatgcgtCattcaattctttatactcat	6	10	4	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:56244788C>T	ENST00000332836.2	-	2	436	c.409G>A	c.(409-411)Gac>Aac	p.D137N		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	137						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		GTATATGCGTCATTCAATTCT	0.423																																																0			19											102	101	101					19																	56244788		2203	4300	6503	60936600	SO:0001583	missense	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.409G>A	19.37:g.56244788C>T	ENSP00000331857:p.Asp137Asn		60936600	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	3.476	-0.107006	0.06924	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.62788	-0.0	3.31	-1.43	0.08884	.	.	.	.	.	T	0.36663	0.0975	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.20840	-1.0263	9	0.09338	T	0.73	.	3.3459	0.07134	0.0:0.4171:0.2068:0.376	.	137	Q7RTR0	NALP9_HUMAN	N	137	ENSP00000331857:D137N	ENSP00000331857:D137N	D	-	1	0	NLRP9	60936600	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.211000	0.09332	-0.028000	0.13850	-0.232000	0.12228	GAC		0.423	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56244788	C	T	56244788	3	4	91	1	0	0	0	0	1	0	0	0	10515	826	29	3	2598	3	NLRP9	19	56244788	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	59368	56244788	2884195	174	25066										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57647192	57647192	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gaactgaataactttctacaGgcattacatttcagttgttg	7	7	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:57647192G>A	ENST00000269834.1	-	5	898	c.513C>T	c.(511-513)gcC>gcT	p.A171A	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACTTTCTACAGGCATTACATT	0.378																																																0			19											147	142	144					19																	57647192		2203	4300	6503	62339004	SO:0001819	synonymous_variant	114026			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.513C>T	19.37:g.57647192G>A			62339004	Q14CA6	Silent	SNP	ENST00000269834.1	37	CCDS33125.1																																																																																				0.378	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			A	57647192	G	A	57647192	2	1	91	1	0	0	0	0	0	0	0	1	17724	987	35	3		3	ZIM3	19	57647192	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	1402404	57647192	1481791	175	25067										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58549367	58549367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggcgagcgggccgcacctcGcgctgggccagctctggacg	17	15	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr19:58549367G>A	ENST00000282326.1	+	3	410	c.163G>A	c.(163-165)Gcg>Acg	p.A55T	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.A55T|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.A55T	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	55	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		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)		GCCGCACCTCGCGCTGGGCCA	0.706																																																0			19											14	15	15					19																	58549367		2182	4283	6465	63241179	SO:0001583	missense	284312			AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.163G>A	19.37:g.58549367G>A	ENSP00000282326:p.Ala55Thr		63241179	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.567425	0.45694	.	.	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.06142	3.34;3.34	1.97	0.863	0.19062	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.17916	0.0430	M	0.76002	2.32	0.09310	N	1	D;P	0.69078	0.997;0.939	D;B	0.67382	0.951;0.315	T	0.08617	-1.0713	9	0.87932	D	0	.	4.3852	0.11312	0.2187:0.0:0.7813:0.0	.	55;55	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	T	55	ENSP00000375581:A55T;ENSP00000282326:A55T	ENSP00000282326:A55T	A	+	1	0	ZSCAN1	63241179	0.000000	0.05858	0.002000	0.10522	0.067000	0.16453	0.526000	0.22971	0.160000	0.19432	0.205000	0.17691	GCG		0.706	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58549367	G	A	58549367	3	1	91	1	0	0	0	0	1	0	0	0	18265	1087	38	1	165	1	ZSCAN1	19	58549367	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	902175	58549367	579616	176	25068										
DEFB126	81623	hgsc.bcm.edu	37	chr20	126160	126160	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gttgggcaatgtgcggcaaaCaaagggactgctgtgttcca	14	8	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:126160C>G	ENST00000382398.3	+	2	423	c.163C>G	c.(163-165)Caa>Gaa	p.Q55E	DEFB126_ENST00000542572.1_Intron	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	55					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			GTGCGGCAAACAAAGGGACTG	0.423																																																0			20											198	173	181					20																	126160		2203	4300	6503	74160	SO:0001583	missense	81623				CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"Defensins, beta"	15900	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 8"	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.163C>G	20.37:g.126160C>G	ENSP00000371835:p.Gln55Glu		74160	Q562G3|Q9H1M5	Missense_Mutation	SNP	ENST00000382398.3	37	CCDS12990.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.809865	0.00606	.	.	ENSG00000125788	ENST00000382398	T	0.11063	2.81	3.66	-7.22	0.01485	.	4.295760	0.00447	N	0.000089	T	0.03220	0.0094	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34403	-0.9830	10	0.06236	T	0.91	-0.006	3.6146	0.08073	0.1986:0.4947:0.1739:0.1328	.	55	Q9BYW3	DB126_HUMAN	E	55	ENSP00000371835:Q55E	ENSP00000371835:Q55E	Q	+	1	0	DEFB126	74160	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.131000	0.03238	-1.402000	0.02056	-1.224000	0.01588	CAA		0.423	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931		G	126160	C	G	126160	3	3	91	1	0	0	0	0	1	0	0	0	4422	479	17	5	169	5	DEFB126	20	126160	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10		126160	62899360	177	25069										
FKBP1A	2280	hgsc.bcm.edu	37	chr20	1356217	1356217	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcttgtttctgtcccgggagGaatcaaatttctttccatct	8	10	4	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:1356217G>C	ENST00000400137.4	-	3	279	c.116C>G	c.(115-117)tCc>tGc	p.S39C	SDCBP2-AS1_ENST00000609470.1_RNA|SDCBP2-AS1_ENST00000609285.1_RNA|FKBP1A_ENST00000381719.3_Missense_Mutation_p.S39C|FKBP1A_ENST00000439640.2_Missense_Mutation_p.S23C|FKBP1A_ENST00000381715.1_Missense_Mutation_p.S34C|FKBP1A_ENST00000381724.3_Missense_Mutation_p.S34C|SDCBP2-AS1_ENST00000446423.1_RNA	NM_000801.4	NP_000792.1	P62942	FKB1A_HUMAN	FK506 binding protein 1A, 12kDa	39	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				'de novo' protein folding (GO:0006458)|amyloid fibril formation (GO:1990000)|calcium ion transmembrane transport (GO:0070588)|chaperone-mediated protein folding (GO:0061077)|extracellular fibril organization (GO:0043206)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of amyloid precursor protein catabolic process (GO:1902991)|regulation of immune response (GO:0050776)|regulation of protein localization (GO:0032880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|SMAD protein complex assembly (GO:0007183)|T cell activation (GO:0042110)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|terminal cisterna (GO:0014802)|Z disc (GO:0030018)	activin binding (GO:0048185)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|macrolide binding (GO:0005527)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|type I transforming growth factor beta receptor binding (GO:0034713)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	GTCCCGGGAGGAATCAAATTT	0.473																																																0			20											68	63	65					20																	1356217		2203	4300	6503	1304217	SO:0001583	missense	2280			M92423	CCDS13014.1, CCDS74688.1	20p13	2013-03-20	2002-08-29		ENSG00000088832	ENSG00000088832			3711	protein-coding gene	gene with protein product	"calstabin 1"	186945	"FK506-binding protein 1A (12kD)"	FKBP1		1930186	Standard	NM_000801		Approved	FKBP-12, FKBP12, PKC12, PPIASE, FKBP12C	uc002wey.3	P62942	OTTHUMG00000031666	ENST00000400137.4:c.116C>G	20.37:g.1356217G>C	ENSP00000383003:p.Ser39Cys		1304217	D3DVW6|P20071|Q4VC47|Q6FGD9|Q6LEU3|Q9H103|Q9H566	Missense_Mutation	SNP	ENST00000400137.4	37	CCDS13014.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192995	0.78902	.	.	ENSG00000088832	ENST00000400137;ENST00000381724;ENST00000381719;ENST00000381715;ENST00000439640	T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5	4.99	4.02	0.46733	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.000000	0.47093	D	0.000248	T	0.80265	0.4591	H	0.96365	3.81	0.54753	D	0.999982	D;D	0.71674	0.994;0.998	D;D	0.73708	0.959;0.981	D	0.87114	0.2187	10	0.87932	D	0	.	14.6542	0.68820	0.0:0.0:0.8533:0.1467	.	23;39	Q1JUQ5;P62942	.;FKB1A_HUMAN	C	39;34;39;34;23	ENSP00000383003:S39C;ENSP00000371143:S34C;ENSP00000371138:S39C;ENSP00000371134:S34C;ENSP00000409863:S23C	ENSP00000371134:S34C	S	-	2	0	FKBP1A	1304217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.493000	0.97960	1.425000	0.47237	0.561000	0.74099	TCC		0.473	FKBP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077534.2			C	1356217	G	C	1356217	3	2	91	1	0	0	0	0	1	0	0	0	5925	1174	41	5	218	5	FKBP1A	20	1356217	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	1230057	1356217	61669303	178	25070										
ACSS1	84532	hgsc.bcm.edu	37	chr20	24993471	24993471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggcgtcctcaatctctgcggTccccagccggtggccactga	12	16	2	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:24993471T>C	ENST00000323482.4	-	11	1763	c.1684A>G	c.(1684-1686)Acc>Gcc	p.T562A	ACSS1_ENST00000542618.1_Missense_Mutation_p.T441A|ACSS1_ENST00000432802.2_Intron|ACSS1_ENST00000484396.1_5'Flank|ACSS1_ENST00000537502.1_Missense_Mutation_p.T479A	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	562					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ATCTCTGCGGTCCCCAGCCGG	0.592																																																0			20											127	110	116					20																	24993471		2203	4300	6503	24941471	SO:0001583	missense	84532				CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"Acyl-CoA synthetase family"	16091	protein-coding gene	gene with protein product		614355	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.1684A>G	20.37:g.24993471T>C	ENSP00000316924:p.Thr562Ala		24941471	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	37	CCDS13167.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.390804	0.82902	.	.	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000537502;ENST00000542618	T;T;T	0.50548	0.74;0.74;0.74	4.84	4.84	0.62591	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.87328	2.875	0.80722	D	1	D;P;P;P	0.89917	1.0;0.857;0.882;0.911	D;P;P;P	0.87578	0.998;0.773;0.855;0.768	T	0.77840	-0.2438	10	0.87932	D	0	-29.933	13.5653	0.61815	0.0:0.0:0.0:1.0	.	357;560;562;479	E9PC79;Q9NUB1-2;Q9NUB1;Q6ZV30	.;.;ACS2L_HUMAN;.	A	562;357;479;441	ENSP00000316924:T562A;ENSP00000439304:T479A;ENSP00000437657:T441A	ENSP00000316924:T562A	T	-	1	0	ACSS1	24941471	1.000000	0.71417	0.945000	0.38365	0.969000	0.65631	7.538000	0.82048	1.928000	0.55862	0.533000	0.62120	ACC		0.592	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		C	24993471	T	C	24993471	3	2	91	1	0	0	0	0	1	0	0	0	188	1667	58	4	401	4	ACSS1	20	24993471	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	23637254	24993471	38032049	179	25071										
NINL	22981	hgsc.bcm.edu	37	chr20	25457076	25457076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	catccgtggctgggtttgcgAggcgtctctctctgttccca	12	13	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:25457076A>G	ENST00000278886.6	-	17	2924	c.2851T>C	c.(2851-2853)Tcg>Ccg	p.S951P	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	951					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TGGGTTTGCGAGGCGTCTCTC	0.667																																																0			20											16	17	17					20																	25457076		2182	4270	6452	25405076	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2851T>C	20.37:g.25457076A>G	ENSP00000278886:p.Ser951Pro		25405076	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	A	7.141	0.581822	0.13749	.	.	ENSG00000101004	ENST00000278886	T	0.26518	1.73	2.99	-5.36	0.02689	.	7.181740	0.00166	N	0.000000	T	0.11410	0.0278	N	0.14661	0.345	0.09310	N	1	B	0.30068	0.267	B	0.23018	0.043	T	0.10428	-1.0630	10	0.56958	D	0.05	4.4313	0.2947	0.00264	0.2226:0.1712:0.2674:0.3388	.	951	Q9Y2I6	NINL_HUMAN	P	951	ENSP00000278886:S951P	ENSP00000278886:S951P	S	-	1	0	NINL	25405076	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.273000	0.08548	-0.854000	0.04131	-0.516000	0.04426	TCG		0.667	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		G	25457076	A	G	25457076	3	3	91	1	0	0	0	0	1	0	0	0	10451	304	11	4	1329	4	NINL	20	25457076	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	463605	25457076	37568444	180	25072										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31024481	31024481	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cgccccaggcctgcggacccGatgcctcttcctgctgagat	11	17	1	1	rs147326327		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:31024481G>A	ENST00000375687.4	+	13	4390	c.3966G>A	c.(3964-3966)ccG>ccA	p.P1322P	ASXL1_ENST00000306058.5_Silent_p.P1317P	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1322					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CTGCGGACCCGATGCCTCTTC	0.572			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20						G		1,4405	2.1+/-5.4	0,1,2202	41	44	43		3966	-9.1	0	20	dbSNP_134	43	0,8600		0,0,4300	no	coding-synonymous	ASXL1	NM_015338.5		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1322/1542	31024481	1,13005	2203	4300	6503	30488142	SO:0001819	synonymous_variant	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3966G>A	20.37:g.31024481G>A			30488142	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																				0.572	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31024481	G	A	31024481	2	1	91	1	0	0	0	0	0	0	0	1	1067	1045	37	1		1	ASXL1	20	31024481	Silent	SNP	G	TCGA-CL-5917-01A-11D-1657-10	5567405	31024481	32001039	181	25073										
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31388033	31388033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aagtgtgtgaggagtccattGctgttggaaccgtgaagcac	14	7	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:31388033G>A	ENST00000328111.2	+	17	2155	c.1834G>A	c.(1834-1836)Gct>Act	p.A612T	DNMT3B_ENST00000348286.2_Missense_Mutation_p.A592T|DNMT3B_ENST00000443239.3_Missense_Mutation_p.A550T|DNMT3B_ENST00000344505.4_Missense_Mutation_p.A592T|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000201963.3_Missense_Mutation_p.A604T|DNMT3B_ENST00000353855.2_Missense_Mutation_p.A592T|DNMT3B_ENST00000456297.2_Missense_Mutation_p.A516T	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	612	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGAGTCCATTGCTGTTGGAAC	0.507																																																0			20											245	211	222					20																	31388033		2203	4300	6503	30851694	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1834G>A	20.37:g.31388033G>A	ENSP00000328547:p.Ala612Thr		30851694	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	9.382	1.073340	0.20147	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	T;T;T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99;-0.99;-0.99	5.65	4.69	0.59074	.	0.057077	0.64402	D	0.000001	T	0.60586	0.2280	N	0.25426	0.745	0.80722	D	1	B;B;B;B;B;B;B	0.25441	0.022;0.126;0.04;0.049;0.009;0.018;0.118	B;B;B;B;B;B;B	0.36092	0.173;0.145;0.1;0.024;0.061;0.024;0.217	T	0.51733	-0.8668	10	0.02654	T	1	-20.6388	10.9376	0.47253	0.1466:0.0:0.8534:0.0	.	516;550;311;604;592;592;612	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	T	612;592;592;550;516;592;604	ENSP00000328547:A612T;ENSP00000313397:A592T;ENSP00000337764:A592T;ENSP00000403169:A550T;ENSP00000412305:A516T;ENSP00000345105:A592T;ENSP00000201963:A604T	ENSP00000201963:A604T	A	+	1	0	DNMT3B	30851694	0.997000	0.39634	0.530000	0.27963	0.817000	0.46193	2.718000	0.47236	2.810000	0.96702	0.650000	0.86243	GCT		0.507	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31388033	G	A	31388033	3	1	91	1	0	0	0	0	1	0	0	0	4688	1319	46	3	1936	3	DNMT3B	20	31388033	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	363552	31388033	31637487	182	25074										
DHX35	60625	hgsc.bcm.edu	37	chr20	37597768	37597768	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tctctgaagagagacaaagtCtggctgaaaactctgggaca	11	8	3	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:37597768C>G	ENST00000252011.3	+	2	118	c.85C>G	c.(85-87)Ctg>Gtg	p.L29V	DHX35_ENST00000373323.4_Missense_Mutation_p.L29V|DHX35_ENST00000373325.2_Missense_Mutation_p.L29V	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	29					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				GAGACAAAGTCTGGCTGAAAA	0.453																																																0			20											83	66	72					20																	37597768		2203	4300	6503	37031182	SO:0001583	missense	60625			AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.85C>G	20.37:g.37597768C>G	ENSP00000252011:p.Leu29Val		37031182	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	37	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	C	3.352	-0.132404	0.06753	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000441485	T;T;T;T	0.09445	4.15;4.22;4.15;2.98	5.57	-1.56	0.08532	.	0.664334	0.14829	N	0.295966	T	0.03739	0.0106	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41805	-0.9488	10	0.20046	T	0.44	.	3.4908	0.07637	0.3731:0.3268:0.2218:0.0784	.	29;29	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	V	29;29;29;25	ENSP00000362422:L29V;ENSP00000252011:L29V;ENSP00000362420:L29V;ENSP00000414630:L25V	ENSP00000252011:L29V	L	+	1	2	DHX35	37031182	0.028000	0.19301	0.507000	0.27676	0.685000	0.39939	0.191000	0.17076	0.038000	0.15604	-0.169000	0.13324	CTG		0.453	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		G	37597768	C	G	37597768	3	3	91	1	0	0	0	0	1	0	0	0	4519	912	32	5	91	5	DHX35	20	37597768	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	6209735	37597768	25427752	183	25075										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39793965	39793965	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gagaacgacatcagcaactcTatcaagaatggcatcctcta	7	11	4	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:39793965T>C	ENST00000373271.1	+	14	1872	c.1467T>C	c.(1465-1467)tcT>tcC	p.S489S	PLCG1_ENST00000373272.2_Silent_p.S489S|PLCG1_ENST00000244007.3_Silent_p.S489S	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	489	PH 2; first part. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TCAGCAACTCTATCAAGAATG	0.577																																																0			20											105	96	99					20																	39793965		2203	4300	6503	39227379	SO:0001819	synonymous_variant	5335			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.1467T>C	20.37:g.39793965T>C			39227379	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																				0.577	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		C	39793965	T	C	39793965	2	2	91	1	0	0	0	0	0	0	0	1	12066	1509	53	4		4	PLCG1	20	39793965	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	2196197	39793965	23231555	184	25076										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47585760	47585760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggatgccttccttgtgttccGctccctgtgcaagctgtcca	10	14	0	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:47585760G>A	ENST00000371917.4	+	9	1136	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	379					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			CTTGTGTTCCGCTCCCTGTGC	0.532																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)											0			20											213	147	169					20																	47585760		2203	4300	6503	47019167	SO:0001583	missense	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1136G>A	20.37:g.47585760G>A	ENSP00000360985:p.Arg379His		47019167	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	35	5.590521	0.96590	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.50001	0.76	5.91	5.91	0.95273	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.85766	0.1352	10	0.87932	D	0	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	379	Q9Y6D5	BIG2_HUMAN	H	379	ENSP00000360985:R379H	ENSP00000360985:R379H	R	+	2	0	ARFGEF2	47019167	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	CGC		0.532	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47585760	G	A	47585760	3	1	91	1	0	0	0	0	1	0	0	0	853	1087	38	1	1170	1	ARFGEF2	20	47585760	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10	7791795	47585760	15439760	185	25077										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50310553	50310553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggaaagctactcacggcggcCgtggggagcctctgcgtgca	16	12	2	0	rs150864262		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:50310553C>T	ENST00000338821.5	-	7	900	c.636G>A	c.(634-636)acG>acA	p.T212T	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	212					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TCACGGCGGCCGTGGGGAGCC	0.617																																																0			20						C		0,4398		0,0,2199	40	44	43		636	-10.1	0	20	dbSNP_134	43	1,8597		0,1,4298	no	coding-synonymous	ATP9A	NM_006045.1		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		212/1048	50310553	1,12995	2199	4299	6498	49743960	SO:0001819	synonymous_variant	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.636G>A	20.37:g.50310553C>T			49743960	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																				0.617	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50310553	C	T	50310553	2	4	91	1	0	0	0	0	0	0	0	1	1199	639	23	1		1	ATP9A	20	50310553	Silent	SNP	C	TCGA-CL-5917-01A-11D-1657-10	2724793	50310553	12714967	186	25078										
TPD52L2	7165	hgsc.bcm.edu	37	chr20	62500732	62500732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acacaggtgtggctgcccggActcctgctgttgagggtctg	15	11	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:62500732A>G	ENST00000346249.4	+	2	179	c.103A>G	c.(103-105)Act>Gct	p.T35A	TPD52L2_ENST00000348257.5_Missense_Mutation_p.T35A|TPD52L2_ENST00000351424.4_Missense_Mutation_p.T35A|TPD52L2_ENST00000352482.4_Missense_Mutation_p.T35A|TPD52L2_ENST00000369927.4_Missense_Mutation_p.T12A|TPD52L2_ENST00000217121.5_Missense_Mutation_p.T35A|TPD52L2_ENST00000358548.4_Missense_Mutation_p.T35A	NM_001243891.1|NM_003288.3	NP_001230820.1|NP_003279.2	O43399	TPD54_HUMAN	tumor protein D52-like 2	35					regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)					GGCTGCCCGGACTCCTGCTGT	0.547																																																0			20											96	94	95					20																	62500732		2203	4300	6503	61971176	SO:0001583	missense	7165			AF004430	CCDS13540.1, CCDS13541.1, CCDS13542.1, CCDS13543.1, CCDS13544.1, CCDS13545.1, CCDS58785.1, CCDS74752.1, CCDS74753.1	20q13.2-q13.3	2007-12-19			ENSG00000101150	ENSG00000101150			12007	protein-coding gene	gene with protein product		603747				9484778	Standard	NM_199360		Approved	D54, hD54	uc002ygy.3	O43399	OTTHUMG00000033009	ENST00000346249.4:c.103A>G	20.37:g.62500732A>G	ENSP00000343547:p.Thr35Ala		61971176	B4DPJ6|E1P5G7|O43398|Q5JWU5|Q5JWU6|Q5JWU8|Q5U0E0|Q9H3Z6	Missense_Mutation	SNP	ENST00000346249.4	37	CCDS13540.1	.	.	.	.	.	.	.	.	.	.	A	9.436	1.086832	0.20390	.	.	ENSG00000101150	ENST00000369927;ENST00000346249;ENST00000348257;ENST00000352482;ENST00000351424;ENST00000217121;ENST00000358548	T;T;T;T;T;T;T	0.29917	1.55;2.03;2.03;2.03;2.03;2.03;2.03	5.62	0.846	0.18955	.	0.496506	0.22016	N	0.065787	T	0.17195	0.0413	L	0.29908	0.895	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001;0.001;0.001	B;B;B;B;B;B;B	0.15052	0.003;0.008;0.007;0.007;0.002;0.005;0.012	T	0.33954	-0.9848	10	0.08381	T	0.77	-1.6331	8.9132	0.35565	0.5532:0.0:0.4468:0.0	.	12;35;35;35;35;35;35	B4DPJ6;Q68E05;O43399;O43399-4;O43399-3;Q5U0E0;Q5JWU6	.;.;TPD54_HUMAN;.;.;.;.	A	12;35;35;35;35;35;35	ENSP00000358943:T12A;ENSP00000343547:T35A;ENSP00000343554:T35A;ENSP00000344647:T35A;ENSP00000340006:T35A;ENSP00000217121:T35A;ENSP00000351350:T35A	ENSP00000217121:T35A	T	+	1	0	TPD52L2	61971176	0.004000	0.15560	0.822000	0.32727	0.991000	0.79684	0.733000	0.26087	-0.108000	0.12066	0.529000	0.55759	ACT		0.547	TPD52L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080248.1			G	62500732	A	G	62500732	3	3	91	1	0	0	0	0	1	0	0	0	16439	275	10	4	109	4	TPD52L2	20	62500732	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	12190179	62500732	524788	187	25079										
OPRL1	4987	hgsc.bcm.edu	37	chr20	62729803	62729803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctcgggctcccgagagaaggAccggaacctgcggcgcatca	14	14	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr20:62729803A>G	ENST00000349451.3	+	6	1176	c.764A>G	c.(763-765)gAc>gGc	p.D255G	OPRL1_ENST00000336866.2_Missense_Mutation_p.D255G|OPRL1_ENST00000355631.4_Missense_Mutation_p.D255G	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	255					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					CGAGAGAAGGACCGGAACCTG	0.647																																																0			20											124	110	115					20																	62729803		2203	4299	6502	62200247	SO:0001583	missense	4987				CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"GPCR / Class A : Opioid receptors"	8155	protein-coding gene	gene with protein product	"LC132 receptor-like", "orphanin FQ receptor", "kappa3-related opioid receptor"	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.764A>G	20.37:g.62729803A>G	ENSP00000336764:p.Asp255Gly		62200247	Q8TD34|Q8WYH9|Q9H4K4	Missense_Mutation	SNP	ENST00000349451.3	37	CCDS13556.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394930	0.83011	.	.	ENSG00000125510	ENST00000336866;ENST00000355631;ENST00000349451	T;T;T	0.72051	-0.62;-0.62;-0.62	4.63	4.63	0.57726	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.79907	0.4527	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.81984	-0.0682	10	0.72032	D	0.01	.	14.0556	0.64767	1.0:0.0:0.0:0.0	.	250;255	P41146-2;P41146	.;OPRX_HUMAN	G	255	ENSP00000336843:D255G;ENSP00000347848:D255G;ENSP00000336764:D255G	ENSP00000336843:D255G	D	+	2	0	OPRL1	62200247	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	9.096000	0.94182	1.727000	0.51537	0.409000	0.27619	GAC		0.647	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		G	62729803	A	G	62729803	3	3	91	1	0	0	0	0	1	0	0	0	10917	275	10	4	774	4	OPRL1	20	62729803	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	229071	62729803	295717	188	25080										
PIGP	51227	hgsc.bcm.edu	37	chr21	38444871	38444871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acacaatcagcgccagcgatGtgctccgtggcaccattgat	10	13	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr21:38444871G>A	ENST00000464265.1	-	1	240	c.17C>T	c.(16-18)aCa>aTa	p.T6I	TTC3_ENST00000355666.1_5'Flank|PIGP_ENST00000360525.4_Intron|PIGP_ENST00000399103.1_Intron|PIGP_ENST00000399098.1_Intron|TTC3_ENST00000540756.1_5'Flank|PIGP_ENST00000399102.1_Intron|TTC3_ENST00000399010.1_5'Flank|PIGP_ENST00000329667.3_5'Flank	NM_153681.2	NP_710148.1	P57054	PIGP_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class P	6					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			kidney(1)|urinary_tract(1)	2		Myeloproliferative disorder(46;0.0412)				CGCCAGCGATGTGCTCCGTGG	0.602																																																0			21											144	145	145					21																	38444871		2203	4300	6503	37366741	SO:0001583	missense	51227			AB037162	CCDS13649.1, CCDS13650.1	21q22.2	2013-02-26	2006-06-28	2005-11-10	ENSG00000185808	ENSG00000185808	2.4.1.198	"Phosphatidylinositol glycan anchor biosynthesis"	3046	protein-coding gene	gene with protein product	"phosphatidylinositol-n-acetylglucosaminyltranferase subunit"	605938	"Down syndrome critical region gene 5", "phosphatidylinositol glycan, class P"	DSCR5		10814524, 15221505	Standard	NR_028352		Approved	DCRC, DSRC	uc002yvw.1	P57054	OTTHUMG00000086653	ENST00000464265.1:c.17C>T	21.37:g.38444871G>A	ENSP00000420037:p.Thr6Ile		37366741	B2RB18|B2RE99|B5BU92|D3DSG7|J3KR75|Q53Y28|Q96KI1|Q9NZA6	Missense_Mutation	SNP	ENST00000464265.1	37	CCDS13649.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.685887	0.29962	.	.	ENSG00000185808	ENST00000464265	T	0.22336	1.96	4.9	-8.2	0.01045	.	3.218240	0.00901	N	0.002353	T	0.11836	0.0288	N	0.14661	0.345	0.09310	N	0.999992	B	0.20368	0.044	B	0.15484	0.013	T	0.26121	-1.0112	10	0.72032	D	0.01	12.9914	8.47	0.32980	0.0:0.3292:0.4791:0.1917	.	6	P57054	PIGP_HUMAN	I	6	ENSP00000420037:T6I	ENSP00000420037:T6I	T	-	2	0	PIGP	37366741	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.502000	0.00965	-2.038000	0.00918	-0.457000	0.05445	ACA		0.602	PIGP-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194769.2	NM_153681		A	38444871	G	A	38444871	3	1	91	1	0	0	0	0	1	0	0	0	11926	1377	48	3	475	3	PIGP	21	38444871	Missense_Mutation	SNP	G	TCGA-CL-5917-01A-11D-1657-10		38444871	9685024	189	25081										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41385060	41385060	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ctgctcattttagctgcctgTcccagctctgctccctcccg	7	18	2	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr21:41385060T>C	ENST00000400454.1	-	33	6417	c.5940A>G	c.(5938-5940)ggA>ggG	p.G1980G		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1980				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TAGCTGCCTGTCCCAGCTCTG	0.582																																					Melanoma(134;970 1778 1785 21664 32388)											0			21											50	50	50					21																	41385060		1957	4152	6109	40306930	SO:0001819	synonymous_variant	1826			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5940A>G	21.37:g.41385060T>C			40306930	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.582	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41385060	T	C	41385060	2	2	91	1	0	0	0	0	0	0	0	1	4779	1654	58	4		4	DSCAM	21	41385060	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	2940189	41385060	6744835	190	25082										
USP18	11274	hgsc.bcm.edu	37	chr22	18656570	18656570	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tggcttccaggtgtcctgggAagacatccagtgtacctacg	12	11	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr22:18656570A>G	ENST00000215794.7	+	10	1464	c.1034A>G	c.(1033-1035)gAa>gGa	p.E345G		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	345	USP.				cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GTGTCCTGGGAAGACATCCAG	0.507																																																0			22											45	41	43					22																	18656570		2203	4293	6496	17036570	SO:0001583	missense	11274			AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"Ubiquitin-specific peptidases"	12616	protein-coding gene	gene with protein product		607057	"ubiquitin specific protease 18"			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.1034A>G	22.37:g.18656570A>G	ENSP00000215794:p.Glu345Gly		17036570	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	.	.	.	.	.	.	.	.	.	.	.	18.99	3.740748	0.69304	.	.	ENSG00000184979	ENST00000215794;ENST00000441683	T	0.37411	1.2	4.8	4.8	0.61643	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.221459	0.46442	D	0.000283	T	0.46776	0.1410	M	0.75884	2.315	0.26583	N	0.973331	P	0.44521	0.837	P	0.47299	0.543	T	0.50250	-0.8850	10	0.66056	D	0.02	.	12.5678	0.56320	1.0:0.0:0.0:0.0	.	345	Q9UMW8	UBP18_HUMAN	G	345;177	ENSP00000215794:E345G	ENSP00000215794:E345G	E	+	2	0	USP18	17036570	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	5.441000	0.66569	1.905000	0.55150	0.519000	0.50382	GAA		0.507	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1			G	18656570	A	G	18656570	3	3	91	1	0	0	0	0	1	0	0	0	17089	246	9	4	1068	4	USP18	22	18656570	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10		18656570	32647996	191	25083										
AP1B1	162	hgsc.bcm.edu	37	chr22	29750810	29750810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcaccttcacagcagagagcAccacagcggagttggcatgg	13	12	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chr22:29750810A>G	ENST00000405198.1	-	6	798	c.767T>C	c.(766-768)gTg>gCg	p.V256A	AP1B1_ENST00000415447.1_Missense_Mutation_p.V256A|AP1B1_ENST00000402502.1_Missense_Mutation_p.V256A|AP1B1_ENST00000357586.2_Missense_Mutation_p.V256A|AP1B1_ENST00000356015.2_Missense_Mutation_p.V256A|AP1B1_ENST00000432560.2_Missense_Mutation_p.V256A|AP1B1_ENST00000317368.7_Missense_Mutation_p.V256A			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	256					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AGCAGAGAGCACCACAGCGGA	0.572																																																0			22											94	77	83					22																	29750810		2203	4300	6503	28080810	SO:0001583	missense	162			L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.767T>C	22.37:g.29750810A>G	ENSP00000384194:p.Val256Ala		28080810	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Missense_Mutation	SNP	ENST00000405198.1	37	CCDS13855.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.942725	0.92526	.	.	ENSG00000100280	ENST00000357586;ENST00000356015;ENST00000432560;ENST00000405198;ENST00000317368;ENST00000402502;ENST00000415447;ENST00000421126	T;T;T;T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62;2.62;2.62;2.62	5.29	5.29	0.74685	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.050738	0.85682	D	0.000000	T	0.47544	0.1451	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.76494	0.976;0.999;0.996;0.999	P;D;D;D	0.91635	0.875;0.955;0.977;0.999	T	0.60429	-0.7265	10	0.87932	D	0	-24.4229	15.0492	0.71854	1.0:0.0:0.0:0.0	.	256;256;256;256	F8WDL0;Q10567-2;Q10567;Q10567-3	.;.;AP1B1_HUMAN;.	A	256	ENSP00000350199:V256A;ENSP00000348297:V256A;ENSP00000400065:V256A;ENSP00000384194:V256A;ENSP00000319361:V256A;ENSP00000386071:V256A;ENSP00000387612:V256A;ENSP00000400022:V256A	ENSP00000319361:V256A	V	-	2	0	AP1B1	28080810	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.139000	0.94554	2.228000	0.72767	0.533000	0.62120	GTG		0.572	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127		G	29750810	A	G	29750810	3	3	91	1	0	0	0	0	1	0	0	0	731	159	6	4	2150	4	AP1B1	22	29750810	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	11094240	29750810	21553756	192	25084										
KLHL34	257240	hgsc.bcm.edu	37	chrX	21674619	21674619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcccgcacccaggcccccgaCggccaggagcctctcgccca	11	22	1	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:21674619C>T	ENST00000379499.2	-	1	1829	c.1288G>A	c.(1288-1290)Gtc>Atc	p.V430I		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	430						extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						AGGCCCCCGACGGCCAGGAGC	0.736																																																0			X											4	5	5					X																	21674619		1925	3721	5646	21584540	SO:0001583	missense	257240			AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"Kelch-like", "BTB/POZ domain containing"	26634	protein-coding gene	gene with protein product			"kelch-like 34 (Drosophila)"				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.1288G>A	X.37:g.21674619C>T	ENSP00000368813:p.Val430Ile		21584540		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	C	2.779	-0.253869	0.05829	.	.	ENSG00000185915	ENST00000379499	T	0.46063	0.88	4.3	4.3	0.51218	Kelch-type beta propeller (1);	0.134936	0.49305	D	0.000156	T	0.31040	0.0784	L	0.43554	1.36	0.30998	N	0.720687	P	0.37955	0.612	B	0.37015	0.239	T	0.42344	-0.9457	10	0.54805	T	0.06	.	4.5832	0.12269	0.0:0.6884:0.0:0.3116	.	430	Q8N239	KLH34_HUMAN	I	430	ENSP00000368813:V430I	ENSP00000368813:V430I	V	-	1	0	KLHL34	21584540	1.000000	0.71417	0.985000	0.45067	0.033000	0.12548	4.258000	0.58822	1.974000	0.57490	0.415000	0.27848	GTC		0.736	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		T	21674619	C	T	21674619	3	4	91	1	0	0	0	0	1	0	0	0	8408	536	19	1	650	1	KLHL34	23	21674619	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10		21674619	133595941	193	25085										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24593379	24593379	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	tcctttgatctttcctccacAttcttgactttttccttcat	2	13	3	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:24593379A>G	ENST00000379144.2	-	7	895	c.765T>C	c.(763-765)aaT>aaC	p.N255N	PCYT1B_ENST00000379145.1_Silent_p.N237N|PCYT1B_ENST00000356768.4_Silent_p.N255N	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	255					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TTTCCTCCACATTCTTGACTT	0.378																																																0			X											210	171	184					X																	24593379		2203	4300	6503	24503300	SO:0001819	synonymous_variant	9468			AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.765T>C	X.37:g.24593379A>G			24503300	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Silent	SNP	ENST00000379144.2	37	CCDS14213.1																																																																																				0.378	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		G	24593379	A	G	24593379	2	3	91	1	0	0	0	0	0	0	0	1	11642	214	8	4		4	PCYT1B	23	24593379	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	2918760	24593379	130677181	194	25086										
CYBB	1536	hgsc.bcm.edu	37	chrX	37663245	37663245	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ggtgtccaagctggagtggcAcccttttacactgacatccg	11	12	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:37663245A>C	ENST00000378588.4	+	9	1080	c.1013A>C	c.(1012-1014)cAc>cCc	p.H338P	CYBB_ENST00000492288.1_3'UTR|CYBB_ENST00000545017.1_Missense_Mutation_p.H306P|TM4SF2_ENST00000465127.1_Intron|CYBB_ENST00000536160.1_Missense_Mutation_p.H71P	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	338	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		H -> D (in CGD). {ECO:0000269|PubMed:23910690}.|H -> Y (in CGD; dbSNP:rs151344484). {ECO:0000269|PubMed:10089913, ECO:0000269|PubMed:10914676}.		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	CTGGAGTGGCACCCTTTTACA	0.483																																																0			X											113	102	105					X																	37663245		2202	4300	6502	37548189	SO:0001583	missense	1536			X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"Cytochrome b genes"	2578	protein-coding gene	gene with protein product		300481	"chronic granulomatous disease"	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1013A>C	X.37:g.37663245A>C	ENSP00000367851:p.His338Pro		37548189	A8K138|Q2PP16	Missense_Mutation	SNP	ENST00000378588.4	37	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330388	0.81690	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	D;D;D	0.98807	-5.15;-5.15;-5.15	5.77	5.77	0.91146	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	H	0.98351	4.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97892	1.0298	10	0.72032	D	0.01	.	15.0692	0.72021	1.0:0.0:0.0:0.0	.	306;338	F5GWD2;P04839	.;CY24B_HUMAN	P	338;306;71	ENSP00000367851:H338P;ENSP00000441896:H306P;ENSP00000441958:H71P	ENSP00000367851:H338P	H	+	2	0	CYBB	37548189	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	8.962000	0.93254	1.941000	0.56285	0.441000	0.28932	CAC		0.483	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			C	37663245	A	C	37663245	3	2	91	1	0	0	0	0	1	0	0	0	4139	159	6	4	1047	4	CYBB	23	37663245	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	13069866	37663245	117607315	195	25087										
GPKOW	27238	hgsc.bcm.edu	37	chrX	48979963	48979963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccggagatggccccgcgccgTctcccgagtcggccagccgc	14	19	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:48979963T>C	ENST00000156109.5	-	1	188	c.110A>G	c.(109-111)gAc>gGc	p.D37G		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	37						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						CCCCGCGCCGTCTCCCGAGTC	0.617																																																0			X											20	20	20					X																	48979963		2202	4297	6499	48866907	SO:0001583	missense	27238			U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"G patch domain containing"	30677	protein-coding gene	gene with protein product	"G patch domain containing 5"					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.110A>G	X.37:g.48979963T>C	ENSP00000156109:p.Asp37Gly		48866907	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	37	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.843538	0.32606	.	.	ENSG00000068394	ENST00000156109	.	.	.	5.26	2.83	0.33086	.	0.527244	0.17101	N	0.186999	T	0.15912	0.0383	L	0.28740	0.885	0.09310	N	1	P	0.43788	0.817	B	0.36092	0.217	T	0.12630	-1.0540	9	0.39692	T	0.17	.	2.2467	0.04033	0.0:0.2352:0.2976:0.4672	.	37	Q92917	GPKOW_HUMAN	G	37	.	ENSP00000156109:D37G	D	-	2	0	GPKOW	48866907	0.005000	0.15991	0.003000	0.11579	0.261000	0.26267	0.651000	0.24873	0.626000	0.30322	0.338000	0.21704	GAC		0.617	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		C	48979963	T	C	48979963	3	2	91	1	0	0	0	0	1	0	0	0	6633	1667	58	4	1364	4	GPKOW	23	48979963	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	11316718	48979963	106290597	196	25088										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54987346	54987346	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	cgtcgatactggcctaaattAaacactgaaagcagggagtg	11	8	0	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:54987346A>T	ENST00000375006.3	-	3	298	c.228T>A	c.(226-228)ttT>ttA	p.F76L	PFKFB1_ENST00000374992.2_Intron|PFKFB1_ENST00000545676.1_Missense_Mutation_p.F11L	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	76	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						GGCCTAAATTAAACACTGAAA	0.468																																																0			X											87	73	78					X																	54987346		2203	4300	6503	55004071	SO:0001583	missense	5207				CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.228T>A	X.37:g.54987346A>T	ENSP00000364145:p.Phe76Leu		55004071	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	37	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137825	0.77775	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	.	.	.	4.89	3.57	0.40892	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	D	0.82930	0.5144	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.83914	0.0297	9	0.87932	D	0	-10.7484	5.3206	0.15879	0.7622:0.0:0.2378:0.0	.	11;76	B4DUN5;P16118	.;F261_HUMAN	L	76;11	.	ENSP00000364145:F76L	F	-	3	2	PFKFB1	55004071	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.406000	0.34646	1.743000	0.51761	0.481000	0.45027	TTT		0.468	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			T	54987346	A	T	54987346	3	4	91	1	0	0	0	0	1	0	0	0	11791	359	13	5	1235	5	PFKFB1	23	54987346	Missense_Mutation	SNP	A	TCGA-CL-5917-01A-11D-1657-10	6007383	54987346	100283214	197	25089										
ACRC	93953	hgsc.bcm.edu	37	chrX	70823980	70823980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcagtgatgattcggaagctTccgacgacagcagtgatgat	13	8	0	4	rs199853865		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:70823980T>C	ENST00000373695.1	+	7	1390	c.853T>C	c.(853-855)Tcc>Ccc	p.S285P	ACRC_ENST00000373696.3_Missense_Mutation_p.S285P			Q96QF7	ACRC_HUMAN	acidic repeat containing	285	Asp/Ser-rich.					nucleus (GO:0005634)		p.S285P(1)		autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					TTCGGAAGCTTCCGACGACAG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	X											111	107	109					X																	70823980		2203	4300	6503	70740705	SO:0001583	missense	93953			AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.853T>C	X.37:g.70823980T>C	ENSP00000362799:p.Ser285Pro		70740705	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	37	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.795474	0.00076	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.29917	1.55;1.55	0.14	-0.28	0.12886	.	.	.	.	.	T	0.13157	0.0319	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22695	-1.0209	9	0.30078	T	0.28	.	4.6957	0.12802	0.0:0.6866:0.0:0.3134	.	285	Q96QF7	ACRC_HUMAN	P	285	ENSP00000362800:S285P;ENSP00000362799:S285P	ENSP00000362799:S285P	S	+	1	0	ACRC	70740705	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.107000	0.01337	-1.694000	0.01425	-1.727000	0.00703	TCC		0.542	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			C	70823980	T	C	70823980	3	2	91	1	0	0	0	0	1	0	0	0	171	1783	62	4	879	4	ACRC	23	70823980	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	15836634	70823980	84446580	198	25090										
ACRC	93953	hgsc.bcm.edu	37	chrX	70824010	70824010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gcagtgatgattcggaagctTccgacgacagcagtgatgat	13	8	0	4			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:70824010T>C	ENST00000373695.1	+	7	1420	c.883T>C	c.(883-885)Tcc>Ccc	p.S295P	ACRC_ENST00000373696.3_Missense_Mutation_p.S295P			Q96QF7	ACRC_HUMAN	acidic repeat containing	295	Asp/Ser-rich.					nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					TTCGGAAGCTTCCGACGACAG	0.527																																																0			X											132	124	127					X																	70824010		2203	4300	6503	70740735	SO:0001583	missense	93953			AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.883T>C	X.37:g.70824010T>C	ENSP00000362799:p.Ser295Pro		70740735	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	37	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	T	2.597	-0.293877	0.05568	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.29397	1.57;1.57	0.14	-0.28	0.12886	.	.	.	.	.	T	0.09642	0.0237	N	0.01874	-0.695	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.30268	-0.9984	9	0.20519	T	0.43	.	4.4172	0.11463	0.0:0.6635:0.0:0.3365	.	295	Q96QF7	ACRC_HUMAN	P	295	ENSP00000362800:S295P;ENSP00000362799:S295P	ENSP00000362799:S295P	S	+	1	0	ACRC	70740735	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-1.504000	0.02275	-1.219000	0.02597	-1.215000	0.01618	TCC		0.527	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			C	70824010	T	C	70824010	3	2	91	1	0	0	0	0	1	0	0	0	171	1783	62	4	909	4	ACRC	23	70824010	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	30	70824010	84446550	199	25091										
THOC2	57187	hgsc.bcm.edu	37	chrX	122767822	122767822	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acctcagcttttagctgctcTccaccagtcatagcctctag	6	15	4	0			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:122767822T>C	ENST00000245838.8	-	20	2149	c.2118A>G	c.(2116-2118)ggA>ggG	p.G706G	THOC2_ENST00000491737.1_Silent_p.G591G|THOC2_ENST00000355725.4_Silent_p.G706G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	706					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TTAGCTGCTCTCCACCAGTCA	0.348																																																0			X											149	135	139					X																	122767822		1859	4078	5937	122595503	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2118A>G	X.37:g.122767822T>C			122595503	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122767822	T	C	122767822	2	2	91	1	0	0	0	0	0	0	0	1	15904	1538	54	4		4	THOC2	23	122767822	Silent	SNP	T	TCGA-CL-5917-01A-11D-1657-10	51943812	122767822	32502738	200	25092										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123630874	123630874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	gagaagacttaccttaattcCaaaatactaacggagtttcc	6	9	0	2			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:123630874C>A	ENST00000371130.3	-	20	3750	c.3687G>T	c.(3685-3687)ttG>ttT	p.L1229F	TENM1_ENST00000422452.2_Missense_Mutation_p.L1229F|TENM1_ENST00000461429.1_5'UTR	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1229					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ACCTTAATTCCAAAATACTAA	0.398																																																0			X											47	49	48					X																	123630874		2203	4299	6502	123458555	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.3687G>T	X.37:g.123630874C>A	ENSP00000360171:p.Leu1229Phe		123458555	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.081583	0.55753	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.90504	-2.68;-2.67	5.67	4.81	0.61882	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000005	D	0.92831	0.7720	L	0.55481	1.735	0.58432	D	0.999999	D;P;P	0.76494	0.999;0.675;0.93	D;B;P	0.80764	0.994;0.157;0.496	D	0.91814	0.5462	10	0.48119	T	0.1	.	9.5671	0.39405	0.0:0.7725:0.0:0.2275	.	1228;1229;1229	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	F	1229	ENSP00000360171:L1229F;ENSP00000403954:L1229F	ENSP00000360171:L1229F	L	-	3	2	ODZ1	123458555	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.124000	0.31320	1.156000	0.42514	-0.190000	0.12839	TTG		0.398	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123630874	C	A	123630874	3	1	91	1	0	0	0	0	1	0	0	0	10865	593	21	2	4563	2	ODZ1	23	123630874	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	863052	123630874	31639686	201	25093										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129377582	129377582	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	acagagctttgtgaagatttAgatacaagatgaaatctagg	10	4	1	6			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:129377582A>T	ENST00000370978.4	-	5	489	c.336T>A	c.(334-336)tcT>tcA	p.S112S		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	112	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						GTGAAGATTTAGATACAAGAT	0.378																																																0			X											79	79	79					X																	129377582		2203	4300	6503	129205263	SO:0001819	synonymous_variant	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.336T>A	X.37:g.129377582A>T			129205263	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																				0.378	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129377582	A	T	129377582	2	4	91	1	0	0	0	0	0	0	0	1	17855	407	15	5		5	ZNF280C	23	129377582	Silent	SNP	A	TCGA-CL-5917-01A-11D-1657-10	5746708	129377582	25892978	202	25094										
GABRE	2564	hgsc.bcm.edu	37	chrX	151123285	151123285	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	catggatgcagaggcggcccTgctgccaggtactgccctca	13	14	1	1			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:151123285T>C	ENST00000370328.3	-	9	1462	c.1409A>G	c.(1408-1410)cAg>cGg	p.Q470R	AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000370325.1_3'UTR|GABRE_ENST00000483564.1_5'UTR	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	470					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GAGGCGGCCCTGCTGCCAGGT	0.542																																																0			X											43	43	43					X																	151123285		2203	4300	6503	150873941	SO:0001583	missense	2564			Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4085	protein-coding gene	gene with protein product	"GABA(A) receptor, epsilon"	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.1409A>G	X.37:g.151123285T>C	ENSP00000359353:p.Gln470Arg		150873941	E7ET93|O15345|O15346|Q6PCD2|Q99520	Missense_Mutation	SNP	ENST00000370328.3	37	CCDS14703.1	.	.	.	.	.	.	.	.	.	.	T	5.548	0.285999	0.10513	.	.	ENSG00000102287	ENST00000370328	D	0.85258	-1.96	5.68	1.33	0.21861	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.128570	0.06734	N	0.777187	T	0.70002	0.3174	N	0.12831	0.26	0.28387	N	0.919279	B	0.09022	0.002	B	0.08055	0.003	T	0.53788	-0.8389	10	0.13108	T	0.6	.	6.9498	0.24538	0.0:0.3573:0.0:0.6427	.	470	P78334	GBRE_HUMAN	R	470	ENSP00000359353:Q470R	ENSP00000359353:Q470R	Q	-	2	0	GABRE	150873941	0.015000	0.18098	0.893000	0.35052	0.845000	0.48019	1.636000	0.37144	-0.102000	0.12197	0.486000	0.48141	CAG		0.542	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984		C	151123285	T	C	151123285	3	2	91	1	0	0	0	0	1	0	0	0	6189	1580	55	4	115	4	GABRE	23	151123285	Missense_Mutation	SNP	T	TCGA-CL-5917-01A-11D-1657-10	21745703	151123285	4147275	203	25095										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153041435	153041435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	ccgtgacaggcaaggccaaaCggaccctgaatgatagccgc	12	13	0	3			TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:153041435C>T	ENST00000361971.5	+	27	4609	c.4495C>T	c.(4495-4497)Cgg>Tgg	p.R1499W	PLXNB3_ENST00000538776.1_Missense_Mutation_p.R1152W|SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538966.1_Missense_Mutation_p.R1522W	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1499					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	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)					CAAGGCCAAACGGACCCTGAA	0.662																																																0			X											50	40	43					X																	153041435		2195	4297	6492	152694629	SO:0001583	missense	5365			AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4495C>T	X.37:g.153041435C>T	ENSP00000355378:p.Arg1499Trp		152694629	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	17.80|17.80	3.477859|3.477859	0.63849|0.63849	.|.	.|.	ENSG00000198753|ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776|ENST00000455214	T;T;T|.	0.11930|.	2.73;2.73;2.73|.	4.82|4.82	2.87|2.87	0.33458|0.33458	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61388|0.61388	0.2343|0.2343	L|L	0.57536|0.57536	1.79|1.79	0.41491|0.41491	D|D	0.988224|0.988224	D;D;D|.	0.76494|.	0.999;0.999;0.999|.	D;D;D|.	0.70935|.	0.956;0.91;0.971|.	T|T	0.59273|0.59273	-0.7485|-0.7485	10|5	0.87932|.	D|.	0|.	.|.	11.1678|11.1678	0.48554|0.48554	0.4336:0.5664:0.0:0.0|0.4336:0.5664:0.0:0.0	.|.	1152;1522;1499|.	B7Z3H9;F5H773;Q9ULL4|.	.;.;PLXB3_HUMAN|.	W|M	1522;1499;1152|2	ENSP00000442736:R1522W;ENSP00000355378:R1499W;ENSP00000445569:R1152W|.	ENSP00000355378:R1499W|.	R|T	+|+	1|2	2|0	PLXNB3|PLXNB3	152694629|152694629	0.358000|0.358000	0.24947|0.24947	0.992000|0.992000	0.48379|0.48379	0.993000|0.993000	0.82548|0.82548	0.082000|0.082000	0.14847|0.14847	0.922000|0.922000	0.37019|0.37019	0.525000|0.525000	0.51046|0.51046	CGG|ACG		0.662	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153041435	C	T	153041435	3	4	91	1	0	0	0	0	1	0	0	0	12156	527	19	1	4715	1	PLXNB3	23	153041435	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	1918150	153041435	2229125	204	25096										
FLNA	2316	hgsc.bcm.edu	37	chrX	153593246	153593246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292682926829268	6	1	0.565913865546218	1.13182773109244	0.514467150496562	0.118881118881119	0.500120569086087	0	aaagtctgctgacttgccaaCgacgccgccctccagcccag	9	17	1	1	rs200673062		TCGA-CL-5917-01A-11D-1657-10	TCGA-CL-5917-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	0253e8de-943f-450c-ac93-6ead3669dca4	f6aff8fa-b2c3-49cb-8408-cca274cc7d28	g.chrX:153593246C>T	ENST00000369850.3	-	12	2007	c.1771G>A	c.(1771-1773)Gtt>Att	p.V591I	FLNA_ENST00000344736.4_Missense_Mutation_p.V591I|FLNA_ENST00000360319.4_Missense_Mutation_p.V591I|FLNA_ENST00000422373.1_Missense_Mutation_p.V591I	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	591					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)	p.V591I(1)		breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GACTTGCCAACGACGCCGCCC	0.632													C|||	2	0.000529801	0	0.0029	3775	,	,		14037	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	kidney(1)	X											108	123	118					X																	153593246		2134	4223	6357	153246440	SO:0001583	missense	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1771G>A	X.37:g.153593246C>T	ENSP00000358866:p.Val591Ile		153246440	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	1	6.027727546714888E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.78	2.636253	0.47049	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93	4.34	4.34	0.51931	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000019	D	0.92652	0.7665	M	0.87547	2.89	0.80722	D	1	D;D	0.65815	0.978;0.995	P;D	0.67725	0.761;0.953	D	0.93650	0.6972	10	0.52906	T	0.07	.	16.2589	0.82530	0.0:1.0:0.0:0.0	.	591;591	P21333-2;P21333	.;FLNA_HUMAN	I	591;564;591;591;591	ENSP00000353467:V591I;ENSP00000416926:V591I;ENSP00000358866:V591I;ENSP00000358863:V591I	ENSP00000358863:V591I	V	-	1	0	FLNA	153246440	0.853000	0.29707	0.674000	0.29902	0.952000	0.60782	3.354000	0.52254	1.741000	0.51731	0.464000	0.42555	GTT		0.632	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153593246	C	T	153593246	3	4	91	1	0	0	0	0	1	0	0	0	5952	536	19	1	6320	1	FLNA	23	153593246	Missense_Mutation	SNP	C	TCGA-CL-5917-01A-11D-1657-10	551811	153593246	1677314	205	25097										
RUNX3	864	hgsc.bcm.edu	37	chr1	25245749	25245749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acgtctgggctcccggggtcCgtccacggtcaccttgatgg	14	14	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:25245749C>T	ENST00000308873.6	-	3	534	c.526G>A	c.(526-528)Gga>Aga	p.G176R	RUNX3_ENST00000338888.3_Missense_Mutation_p.G190R|RUNX3_ENST00000496967.1_5'UTR|RUNX3_ENST00000399916.1_Missense_Mutation_p.G190R|RUNX3_ENST00000540420.1_Missense_Mutation_p.G83R	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	176	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		TCCCGGGGTCCGTCCACGGTC	0.647																																																0			1											72	64	67					1																	25245749		2203	4300	6503	25118336	SO:0001583	missense	864			BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.526G>A	1.37:g.25245749C>T	ENSP00000308051:p.Gly176Arg		25118336	B1AJV5|Q12969|Q13760	Missense_Mutation	SNP	ENST00000308873.6	37	CCDS257.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067471	0.76301	.	.	ENSG00000020633	ENST00000399916;ENST00000308873;ENST00000338888;ENST00000540420;ENST00000428150	D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21	5.07	5.07	0.68467	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96366	0.9270	10	0.72032	D	0.01	-7.2297	18.4912	0.90848	0.0:1.0:0.0:0.0	.	176;190;176	E9PH34;B1AJV5;Q13761	.;.;RUNX3_HUMAN	R	190;176;190;83;176	ENSP00000382800:G190R;ENSP00000308051:G176R;ENSP00000343477:G190R;ENSP00000444872:G83R	ENSP00000308051:G176R	G	-	1	0	RUNX3	25118336	1.000000	0.71417	1.000000	0.80357	0.312000	0.27988	7.802000	0.85969	2.368000	0.80403	0.655000	0.94253	GGA		0.647	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350		T	25245749	C	T	25245749	3	4	92	1	0	0	0	0	1	0	0	0	13786	661	23	1	733	1	RUNX3	1	25245749	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		25245749	224004872	1	25098										
SDC3	9672	hgsc.bcm.edu	37	chr1	31346158	31346158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cctcatcctttttcttcataCgatagatgagcagtgtgacc	7	11	3	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:31346158C>T	ENST00000339394.6	-	5	1403	c.1229G>A	c.(1228-1230)cGt>cAt	p.R410H	SDC3_ENST00000336798.7_Missense_Mutation_p.R352H	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	410					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R410H(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		TTTCTTCATACGATAGATGAG	0.562																																																1	Substitution - Missense(1)	urinary_tract(1)	1											123	104	111					1																	31346158		2203	4300	6503	31118745	SO:0001583	missense	9672			AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"Proteoglycans / Cell Surface : Syndecans"	10660	protein-coding gene	gene with protein product	"syndecan proteoglycan 3"	186357	"syndecan 3 (N-syndecan)"			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.1229G>A	1.37:g.31346158C>T	ENSP00000344468:p.Arg410His		31118745	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	.	.	.	.	.	.	.	.	.	.	C	36	5.883757	0.97062	.	.	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.81415	-1.45;-1.49	5.3	5.3	0.74995	Neurexin/syndecan/glycophorin C (1);	0.000000	0.64402	D	0.000014	D	0.85128	0.5626	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87038	0.2139	10	0.87932	D	0	-10.5787	18.5454	0.91044	0.0:1.0:0.0:0.0	.	410;352	O75056;D3DPN2	SDC3_HUMAN;.	H	352;410	ENSP00000338346:R352H;ENSP00000344468:R410H	ENSP00000338346:R352H	R	-	2	0	SDC3	31118745	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.818000	0.86416	2.502000	0.84385	0.462000	0.41574	CGT		0.562	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		T	31346158	C	T	31346158	3	4	92	1	0	0	0	0	1	0	0	0	13990	536	19	1	103	1	SDC3	1	31346158	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	6100409	31346158	217904463	2	25099										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34204921	34204921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aacgccaggatccgggcactCgttgtgtcggaaggctgtgt	15	10	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:34204921C>T	ENST00000373381.4	-	15	2364	c.2188G>A	c.(2188-2190)Gag>Aag	p.E730K		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	690	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCCGGGCACTCGTTGTGTCGG	0.517																																																0			1											79	82	81					1																	34204921		2203	4300	6503	33977508	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2188G>A	1.37:g.34204921C>T	ENSP00000362479:p.Glu730Lys		33977508	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	C	36	5.824190	0.96989	.	.	ENSG00000121904	ENST00000373381	T	0.26660	1.72	6.17	6.17	0.99709	Complement control module (2);Sushi/SCR/CCP (1);	0.000000	0.85682	D	0.000000	T	0.39911	0.1096	N	0.25380	0.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.02683	-1.1124	10	0.22109	T	0.4	.	19.8676	0.96824	0.0:1.0:0.0:0.0	.	690;730	Q7Z408;E7EUA6	CSMD2_HUMAN;.	K	730	ENSP00000362479:E730K	ENSP00000241312:E690K	E	-	1	0	CSMD2	33977508	1.000000	0.71417	0.980000	0.43619	0.988000	0.76386	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	GAG		0.517	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34204921	C	T	34204921	3	4	92	1	0	0	0	0	1	0	0	0	3951	893	31	1	8615	1	CSMD2	1	34204921	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2858763	34204921	215045700	3	25100										
KDM4A	9682	hgsc.bcm.edu	37	chr1	44121267	44121267	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttgtgttcccttcaggttgtTcctccaaaagagtggaagcc	10	10	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:44121267T>C	ENST00000372396.3	+	3	278	c.144T>C	c.(142-144)gtT>gtC	p.V48V	KDM4A_ENST00000463151.1_3'UTR	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	48	JmjN. {ECO:0000255|PROSITE- ProRule:PRU00537}.				cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						TTCAGGTTGTTCCTCCAAAAG	0.493																																																0			1											109	103	105					1																	44121267		2203	4300	6503	43893854	SO:0001819	synonymous_variant	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.144T>C	1.37:g.44121267T>C			43893854	Q5VVB1	Silent	SNP	ENST00000372396.3	37	CCDS491.1																																																																																				0.493	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		C	44121267	T	C	44121267	2	2	92	1	0	0	0	0	0	0	0	1	8149	1770	62	4		4	KDM4A	1	44121267	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	9916346	44121267	205129354	4	25101										
DPH2	1802	hgsc.bcm.edu	37	chr1	44435855	44435855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	caagctgtgcctcatggagtCgatgtttagcagccctgccg	12	12	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:44435855C>T	ENST00000255108.3	+	1	180	c.8C>T	c.(7-9)tCg>tTg	p.S3L	DPH2_ENST00000396758.2_Missense_Mutation_p.S3L|DPH2_ENST00000529729.1_3'UTR|DPH2_ENST00000412950.2_5'UTR	NM_001384.4	NP_001375.2	Q9BQC3	DPH2_HUMAN	DPH2 homolog (S. cerevisiae)	3					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)	cytoplasm (GO:0005737)				autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(2)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				CTCATGGAGTCGATGTTTAGC	0.642																																																0			1											45	45	45					1																	44435855		2203	4300	6503	44208442	SO:0001583	missense	1802			AF053003	CCDS504.1, CCDS41314.1	1p34	2008-02-05	2005-06-03	2005-06-03	ENSG00000132768	ENSG00000132768			3004	protein-coding gene	gene with protein product		603456	"diptheria toxin resistance protein required for diphthamide biosynthesis-like 2 (S. cerevisiae)", "DPH2-like 2 (S. cerevisiae)"	DPH2L2		9782084, 15485916	Standard	XM_005270559		Approved		uc001ckz.3	Q9BQC3	OTTHUMG00000008295	ENST00000255108.3:c.8C>T	1.37:g.44435855C>T	ENSP00000255108:p.Ser3Leu		44208442	A8MVC9|B2RDE3|B4DNI8|O60623	Missense_Mutation	SNP	ENST00000255108.3	37	CCDS504.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358781	0.24598	.	.	ENSG00000132768	ENST00000255108;ENST00000396758	.	.	.	5.24	4.27	0.50696	.	0.237190	0.41938	D	0.000794	T	0.49592	0.1566	L	0.59436	1.845	0.80722	D	1	B;B	0.32731	0.382;0.382	B;B	0.25884	0.064;0.04	T	0.50625	-0.8806	9	0.33940	T	0.23	-14.1764	12.8783	0.58001	0.1615:0.8384:0.0:0.0	.	3;3	A8MVC9;Q9BQC3	.;DPH2_HUMAN	L	3	.	ENSP00000255108:S3L	S	+	2	0	DPH2	44208442	0.949000	0.32298	0.968000	0.41197	0.061000	0.15899	2.359000	0.44142	2.608000	0.88229	0.461000	0.40582	TCG		0.642	DPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022832.1	NM_001384		T	44435855	C	T	44435855	3	4	92	1	0	0	0	0	1	0	0	0	4731	893	31	1	10	1	DPH2	1	44435855	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	314588	44435855	204814766	5	25102										
CYP4X1	260293	hgsc.bcm.edu	37	chr1	47512207	47512207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgccgattgattcctgcagTcccgtccatttccagagatc	9	13	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:47512207T>C	ENST00000371901.3	+	9	1392	c.1142T>C	c.(1141-1143)gTc>gCc	p.V381A	CYP4X1_ENST00000538609.1_Missense_Mutation_p.V380A	NM_178033.1	NP_828847.1	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X, polypeptide 1	381						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	17						ATTCCTGCAGTCCCGTCCATT	0.512																																																0			1											182	154	164					1																	47512207		2203	4300	6503	47284794	SO:0001583	missense	260293			AK091806	CCDS544.1	1p33	2008-02-05			ENSG00000186377	ENSG00000186377		"Cytochrome P450s"	20244	protein-coding gene	gene with protein product		614999				12176035	Standard	NM_178033		Approved	MGC40051	uc001cqt.3	Q8N118	OTTHUMG00000008017	ENST00000371901.3:c.1142T>C	1.37:g.47512207T>C	ENSP00000360968:p.Val381Ala		47284794	G3V1U1|Q5VVE5|Q6ZN67|Q8NAZ3	Missense_Mutation	SNP	ENST00000371901.3	37	CCDS544.1	.	.	.	.	.	.	.	.	.	.	t	13.73	2.324650	0.41197	.	.	ENSG00000186377	ENST00000538609;ENST00000371901	T;T	0.70749	-0.51;-0.51	6.08	1.17	0.20885	.	0.536034	0.20317	N	0.094714	T	0.69378	0.3104	L	0.58302	1.8	0.20403	N	0.999905	P;P	0.44044	0.678;0.825	P;P	0.47162	0.536;0.54	T	0.62105	-0.6924	10	0.62326	D	0.03	.	9.7957	0.40733	0.0:0.2694:0.0:0.7306	.	381;380	Q8N118;G3V1U1	CP4X1_HUMAN;.	A	380;381	ENSP00000445965:V380A;ENSP00000360968:V381A	ENSP00000360968:V381A	V	+	2	0	CYP4X1	47284794	0.441000	0.25626	0.000000	0.03702	0.017000	0.09413	2.106000	0.41835	0.192000	0.20272	0.482000	0.46254	GTC		0.512	CYP4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022017.1	NM_178033		C	47512207	T	C	47512207	3	2	92	1	0	0	0	0	1	0	0	0	4199	1667	58	4	1176	4	CYP4X1	1	47512207	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	3076352	47512207	201738414	6	25103										
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52991354	52991354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcagagcacatttttctcccCctacagcttcaatattcact	4	14	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:52991354C>T	ENST00000371544.3	-	2	861	c.599G>A	c.(598-600)gGg>gAg	p.G200E	ZCCHC11_ENST00000371541.1_5'UTR|ZCCHC11_ENST00000257177.4_Missense_Mutation_p.G200E|ZCCHC11_ENST00000355809.4_Missense_Mutation_p.G200E	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	200					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						TTTTTCTCCCCCTACAGCTTC	0.388																																																0			1											189	193	192					1																	52991354		2203	4300	6503	52763942	SO:0001583	missense	23318			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.599G>A	1.37:g.52991354C>T	ENSP00000360599:p.Gly200Glu		52763942	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.917535	0.00055	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000355809	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	5.07	2.43	0.29744	.	0.797363	0.10968	N	0.614121	T	0.47985	0.1475	N	0.00707	-1.245	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.48234	-0.9053	10	0.02654	T	1	.	3.6401	0.08163	0.1624:0.3192:0.0:0.5184	.	200;200;200;200	E9PKY2;Q5TAX3-2;E9PRG2;Q5TAX3	.;.;.;TUT4_HUMAN	E	200	ENSP00000257177:G200E;ENSP00000360599:G200E;ENSP00000433486:G200E;ENSP00000348063:G200E	ENSP00000257177:G200E	G	-	2	0	ZCCHC11	52763942	0.057000	0.20700	0.000000	0.03702	0.004000	0.04260	1.356000	0.34079	-0.023000	0.13963	-0.254000	0.11334	GGG		0.388	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		T	52991354	C	T	52991354	3	4	92	1	0	0	0	0	1	0	0	0	17619	623	22	3	4454	3	ZCCHC11	1	52991354	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5479147	52991354	196259267	7	25104										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95310926	95310926	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aataaagccatcagcagtgcTcccttcctgctgttccagcc	7	15	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:95310926T>C	ENST00000271227.6	+	9	1080	c.978T>C	c.(976-978)gcT>gcC	p.A326A	RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000446120.2_Silent_p.A290A|SLC44A3_ENST00000529450.1_Silent_p.A294A|SLC44A3_ENST00000467909.1_Silent_p.A278A|SLC44A3_ENST00000527077.1_Silent_p.A258A|SLC44A3_ENST00000532427.1_Silent_p.A246A|SLC44A3_ENST00000530397.1_3'UTR	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	326					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	TCAGCAGTGCTCCCTTCCTGC	0.488																																																0			1											116	121	119					1																	95310926		2203	4300	6503	95083514	SO:0001819	synonymous_variant	126969			BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.978T>C	1.37:g.95310926T>C			95083514	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																				0.488	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		C	95310926	T	C	95310926	2	2	92	1	0	0	0	0	0	0	0	1	14674	1538	54	4		4	SLC44A3	1	95310926	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	42319572	95310926	153939695	8	25105										
SNX7	51375	hgsc.bcm.edu	37	chr1	99161077	99161078	+	Frame_Shift_Del	DEL	CT	CT	-													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggttttttgtttctaggaaCtctcttctcacaagaagcaa							TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:99161077_99161078delCT	ENST00000306121.3	+	5	652_653	c.643_644delCT	c.(643-645)ctcfs	p.L215fs	SNX7_ENST00000370189.5_Frame_Shift_Del_p.L151fs|SNX7_ENST00000529992.1_Frame_Shift_Del_p.L160fs	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	151					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTTCTAGGAACTCTCTTCTCAC	0.406																																																0			1																																								98933666	SO:0001589	frameshift_variant	51375			AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"Sorting nexins"	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.643_644delCT	1.37:g.99161081_99161082delCT	ENSP00000304429:p.Leu215fs		98933665	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Frame_Shift_Del	DEL	ENST00000306121.3	37	CCDS755.2																																																																																				0.406	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			-	99161078	CT	-	99161077	7	5	92	1	0	1	0	1	0	0	0	0	14944	565	20	0	661	0	SNX7	1	99161077	Frame_Shift_Del	DEL	CT	TCGA-CL-5918-01A-11D-1657-10	3850151	99161077	150089544	9	25106										
AGL	178	hgsc.bcm.edu	37	chr1	100343240	100343240	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaacttatttgctggggagaCagtgttaaattacgctatgg	12	5	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:100343240C>T	ENST00000294724.4	+	12	1945	c.1467C>T	c.(1465-1467)gaC>gaT	p.D489D	AGL_ENST00000361522.4_Silent_p.D472D|AGL_ENST00000370161.2_Silent_p.D473D|AGL_ENST00000370163.3_Silent_p.D489D|AGL_ENST00000361302.3_Silent_p.D473D|AGL_ENST00000370165.3_Silent_p.D489D|AGL_ENST00000361915.3_Silent_p.D489D	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GCTGGGGAGACAGTGTTAAAT	0.368																																																0			1											103	100	101					1																	100343240		2203	4300	6503	100115828	SO:0001819	synonymous_variant	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1467C>T	1.37:g.100343240C>T			100115828	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																				0.368	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		T	100343240	C	T	100343240	2	4	92	1	0	0	0	0	0	0	0	1	384	477	17	3		3	AGL	1	100343240	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1182163	100343240	148907381	10	25107										
GPR61	83873	hgsc.bcm.edu	37	chr1	110086198	110086198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gttgggaagggtctcctgggAggaaggagctcccagtgtcc	17	9	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:110086198A>G	ENST00000527748.1	+	2	1237	c.554A>G	c.(553-555)gAg>gGg	p.E185G	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		GTCTCCTGGGAGGAAGGAGCT	0.602																																																0			1											160	143	149					1																	110086198		2203	4300	6503	109887721	SO:0001583	missense	83873			AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"GPCR / Class A : Orphans"	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.554A>G	1.37:g.110086198A>G	ENSP00000432456:p.Glu185Gly		109887721	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	37	CCDS801.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.676939	0.29783	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.36520	1.25	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.392321	0.25836	N	0.027985	T	0.09113	0.0225	N	0.04132	-0.27	0.42656	D	0.993467	B	0.06786	0.001	B	0.04013	0.001	T	0.07888	-1.0749	10	0.35671	T	0.21	-5.4885	13.618	0.62120	1.0:0.0:0.0:0.0	.	185	Q9BZJ8	GPR61_HUMAN	G	185;313	ENSP00000432456:E185G	ENSP00000286603:E313G	E	+	2	0	GPR61	109887721	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.406000	0.52637	2.089000	0.63090	0.533000	0.62120	GAG		0.602	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1			G	110086198	A	G	110086198	3	3	92	1	0	0	0	0	1	0	0	0	6722	304	11	4	556	4	GPR61	1	110086198	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	9742958	110086198	139164423	11	25108										
KCNC4	3749	hgsc.bcm.edu	37	chr1	110754500	110754500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acgtgtgcgggccgctcttcGaagaggagctcaccttctgg	14	12	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:110754500G>A	ENST00000369787.3	+	1	406	c.379G>A	c.(379-381)Gaa>Aaa	p.E127K	KCNC4-AS1_ENST00000455967.1_RNA|KCNC4_ENST00000438661.2_Missense_Mutation_p.E127K|KCNC4_ENST00000413138.3_Missense_Mutation_p.E127K	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	127					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCCGCTCTTCGAAGAGGAGCT	0.657																																																0			1											45	51	49					1																	110754500		2203	4300	6503	110556023	SO:0001583	missense	3749			BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.379G>A	1.37:g.110754500G>A	ENSP00000358802:p.Glu127Lys		110556023	Q3MIM4|Q5TBI6	Missense_Mutation	SNP	ENST00000369787.3	37	CCDS821.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.102919	0.76983	.	.	ENSG00000116396	ENST00000369787;ENST00000413138;ENST00000438661	T;T;T	0.75938	-0.98;-0.98;-0.98	3.84	3.84	0.44239	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.72153	0.3425	L	0.46947	1.48	0.80722	D	1	P;B;D	0.53745	0.539;0.282;0.962	P;B;P	0.54706	0.501;0.264;0.759	T	0.77161	-0.2689	10	0.72032	D	0.01	.	15.5439	0.76077	0.0:0.0:1.0:0.0	.	127;127;127	Q03721;Q03721-3;Q03721-2	KCNC4_HUMAN;.;.	K	127	ENSP00000358802:E127K;ENSP00000388029:E127K;ENSP00000393655:E127K	ENSP00000358802:E127K	E	+	1	0	KCNC4	110556023	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.560000	0.98139	1.984000	0.57885	0.561000	0.74099	GAA		0.657	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110754500	G	A	110754500	3	1	92	1	0	0	0	0	1	0	0	0	8038	1059	37	1	381	1	KCNC4	1	110754500	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	668302	110754500	138496121	12	25109										
CTTNBP2NL	55917	hgsc.bcm.edu	37	chr1	112999695	112999695	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccagtctctcccaacagctcTccctttggcacagactatcg	6	17	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:112999695T>C	ENST00000271277.6	+	6	1806	c.1581T>C	c.(1579-1581)tcT>tcC	p.S527S	CTTNBP2NL_ENST00000607039.1_3'UTR	NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	527					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCAACAGCTCTCCCTTTGGCA	0.547																																																0			1											133	120	125					1																	112999695		2203	4300	6503	112801218	SO:0001819	synonymous_variant	55917			AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1581T>C	1.37:g.112999695T>C			112801218	B3KMS5|Q96B40	Silent	SNP	ENST00000271277.6	37	CCDS845.1																																																																																				0.547	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		C	112999695	T	C	112999695	2	2	92	1	0	0	0	0	0	0	0	1	4052	1538	54	4		4	CTTNBP2NL	1	112999695	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	2245195	112999695	136250926	13	25110										
RSBN1	54665	hgsc.bcm.edu	37	chr1	114354942	114354942	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	accgcccccccgtccgcgcaTcgcgcaagcgccgcccgcgc	11	24	0	0	rs3789604	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:114354942T>G	ENST00000261441.5	-	1	156	c.93A>C	c.(91-93)cgA>cgC	p.R31R	RP5-1073O3.2_ENST00000418238.1_RNA|RP5-1073O3.2_ENST00000429398.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	31						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		CGTCCGCGCATCGCGCAAGCG	0.672													T|||	670	0.133786	0.0461	0.1369	5008	,	,		12587	0.2282		0.1879	False		,,,				2504	0.0971															0			1	GRCh37	CR053507	PTPN22	R	rs3789604	T		350,4042		13,324,1859	21	29	27	http://omim.org/entry/177900	93	-10.1	0.1	1	dbSNP_107	27	1581,7007		145,1291,2858	yes	coding-synonymous	RSBN1	NM_018364.3		158,1615,4717	GG,GT,TT		18.4094,7.969,14.8767		31/803	114354942	1931,11049	2196	4294	6490	114156465	SO:0001819	synonymous_variant	54665			AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.93A>C	1.37:g.114354942T>G			114156465	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Silent	SNP	ENST00000261441.5	37	CCDS862.1																																																																																				0.672	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		G	114354942	T	G	114354942	2	3	92	1	0	0	0	0	0	0	0	1	13733	1422	50	4		4	RSBN1	1	114354942	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	1355247	114354942	134895679	14	25111										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117142868	117142868	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atgtcaccgacacggggaccCaggcagggtagtggggtttg	17	9	1	0	rs61730489	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:117142868C>T	ENST00000369486.3	-	7	2489	c.1724G>A	c.(1723-1725)tGg>tAg	p.W575*	IGSF3_ENST00000318837.6_Nonsense_Mutation_p.W595*|IGSF3_ENST00000369483.1_Nonsense_Mutation_p.W595*	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	575	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		CACGGGGACCCAGGCAGGGTA	0.627																																																0			1											34	39	37					1																	117142868		2203	4300	6503	116944391	SO:0001587	stop_gained	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1724G>A	1.37:g.117142868C>T	ENSP00000358498:p.Trp575*		116944391	A6NJZ6|A6NMC7	Nonsense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	35	5.418054	0.96092	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	.	.	.	4.57	4.57	0.56435	.	0.219347	0.41712	D	0.000829	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-31.603	14.8995	0.70666	0.0:1.0:0.0:0.0	.	.	.	.	X	575;595;595	.	ENSP00000321184:W595X	W	-	2	0	IGSF3	116944391	1.000000	0.71417	0.937000	0.37676	0.211000	0.24417	3.382000	0.52463	2.354000	0.79902	0.455000	0.32223	TGG		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117142868	C	T	117142868	4	4	92	1	0	0	0	0	0	1	0	0	7622	595	21	3	1880	3	IGSF3	1	117142868	Nonsense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2787926	117142868	132107753	15	25112										
FLG	2312	hgsc.bcm.edu	37	chr1	152280433	152280433	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atgcagcctgtccaccagagGaattctctgcatgatgagtg	11	10	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:152280433G>C	ENST00000368799.1	-	3	6964	c.6929C>G	c.(6928-6930)tCc>tGc	p.S2310C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2310	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCACCAGAGGAATTCTCTGC	0.567									Ichthyosis																																							0			1											236	271	259					1																	152280433		2203	4297	6500	150547057	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6929C>G	1.37:g.152280433G>C	ENSP00000357789:p.Ser2310Cys		150547057	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	2.736	-0.263323	0.05754	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.00695	5.83	1.74	1.74	0.24563	.	.	.	.	.	T	0.00936	0.0031	M	0.73598	2.24	0.09310	N	1	D	0.67145	0.996	P	0.53954	0.738	T	0.52064	-0.8625	9	0.59425	D	0.04	.	7.0128	0.24871	0.0:0.0:1.0:0.0	.	2310	P20930	FILA_HUMAN	C	2310;220	ENSP00000357789:S2310C	ENSP00000271820:S220C	S	-	2	0	FLG	150547057	0.042000	0.20092	0.001000	0.08648	0.006000	0.05464	0.711000	0.25764	1.292000	0.44672	0.194000	0.17425	TCC		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152280433	G	C	152280433	3	2	92	1	0	0	0	0	1	0	0	0	5941	1174	41	5	5260	5	FLG	1	152280433	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	35137565	152280433	96970188	16	25113										
PVRL4	81607	hgsc.bcm.edu	37	chr1	161044047	161044047	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggccttgcgccgatggtatcGggacatgagcaccaccacca	12	14	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:161044047G>A	ENST00000368012.3	-	6	1419	c.1117C>T	c.(1117-1119)Cga>Tga	p.R373*	PVRL4_ENST00000453926.2_Nonsense_Mutation_p.R107*|PVRL4_ENST00000486694.1_5'UTR	NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	373					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CGATGGTATCGGGACATGAGC	0.567																																					NSCLC(76;1160 1387 14476 16172 29359)											0			1											184	164	171					1																	161044047		2203	4300	6503	159310671	SO:0001587	stop_gained	81607			AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.1117C>T	1.37:g.161044047G>A	ENSP00000356991:p.Arg373*		159310671	B4DQW3|Q96K15	Nonsense_Mutation	SNP	ENST00000368012.3	37	CCDS1216.1	.	.	.	.	.	.	.	.	.	.	G	41	8.975002	0.99023	.	.	ENSG00000143217	ENST00000368012;ENST00000453926	.	.	.	4.99	2.81	0.32909	.	0.158137	0.28533	N	0.015009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	10.7829	0.46388	0.0:0.0:0.6447:0.3553	.	.	.	.	X	373;107	.	ENSP00000356991:R373X	R	-	1	2	PVRL4	159310671	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.675000	0.46875	1.041000	0.40125	0.462000	0.41574	CGA		0.567	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916		A	161044047	G	A	161044047	4	1	92	1	0	0	0	0	0	1	0	0	12879	1124	39	1	431	1	PVRL4	1	161044047	Nonsense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	8763614	161044047	88206574	17	25114										
LHX4	89884	hgsc.bcm.edu	37	chr1	180241067	180241067	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	taagagcgtcaagaggagccGgggcagcagcaagcaggaga	17	8	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:180241067G>A	ENST00000263726.2	+	5	948	c.704G>A	c.(703-705)cGg>cAg	p.R235Q	RP5-1180C10.2_ENST00000415414.1_RNA|RP5-1180C10.2_ENST00000440959.2_RNA	NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	235					medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						AAGAGGAGCCGGGGCAGCAGC	0.602																																																0			1											70	80	77					1																	180241067		2203	4300	6503	178507690	SO:0001583	missense	89884			AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"Homeoboxes / LIM class"	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	ENST00000263726.2:c.704G>A	1.37:g.180241067G>A	ENSP00000263726:p.Arg235Gln		178507690	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Missense_Mutation	SNP	ENST00000263726.2	37	CCDS1338.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003899	0.74932	.	.	ENSG00000121454	ENST00000263726	D	0.88975	-2.45	5.59	5.59	0.84812	.	0.123365	0.56097	D	0.000032	D	0.84552	0.5497	L	0.49126	1.545	0.54753	D	0.999984	D	0.54601	0.967	B	0.39503	0.301	D	0.86091	0.1550	10	0.62326	D	0.03	.	11.8035	0.52141	0.0814:0.0:0.9186:0.0	.	235	Q969G2	LHX4_HUMAN	Q	235	ENSP00000263726:R235Q	ENSP00000263726:R235Q	R	+	2	0	LHX4	178507690	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.902000	0.87389	2.631000	0.89168	0.561000	0.74099	CGG		0.602	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343		A	180241067	G	A	180241067	3	1	92	1	0	0	0	0	1	0	0	0	8796	1116	39	1	722	1	LHX4	1	180241067	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	19197020	180241067	69009554	18	25115										
CHIT1	1118	hgsc.bcm.edu	37	chr1	203192643	203192643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgtaccagggttgtgaagcGctccttgtctacggcagggc	14	11	1	1	rs142999142		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:203192643G>A	ENST00000367229.1	-	5	494	c.460C>T	c.(460-462)Cgc>Tgc	p.R154C	CHIT1_ENST00000484834.1_5'UTR|CHIT1_ENST00000535569.1_Missense_Mutation_p.R145C|CHIT1_ENST00000255427.3_Missense_Mutation_p.R135C	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	154					chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						GTTGTGAAGCGCTCCTTGTCT	0.622																																																0			1						G	CYS/ARG	0,4406		0,0,2203	78	79	79		460	2.9	0	1	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	no	missense	CHIT1	NM_003465.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	154/467	203192643	1,13005	2203	4300	6503	201459266	SO:0001583	missense	1118			U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.460C>T	1.37:g.203192643G>A	ENSP00000356198:p.Arg154Cys		201459266	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Missense_Mutation	SNP	ENST00000367229.1	37	CCDS1436.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.659179	0.29515	0.0	1.16E-4	ENSG00000133063	ENST00000367229;ENST00000255427;ENST00000535569	T;T;T	0.05649	3.41;3.41;3.41	4.83	2.87	0.33458	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.652347	0.13255	N	0.401787	T	0.24967	0.0606	M	0.91818	3.245	0.09310	N	0.999999	P;D	0.89917	0.946;1.0	B;D	0.63381	0.24;0.914	T	0.08764	-1.0706	10	0.51188	T	0.08	-9.8786	6.0552	0.19807	0.091:0.0:0.5682:0.3408	.	145;154	G5EA51;Q13231	.;CHIT1_HUMAN	C	154;135;145	ENSP00000356198:R154C;ENSP00000255427:R135C;ENSP00000438078:R145C	ENSP00000255427:R135C	R	-	1	0	CHIT1	201459266	0.025000	0.19082	0.001000	0.08648	0.168000	0.22595	2.137000	0.42130	0.491000	0.27793	0.655000	0.94253	CGC		0.622	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465		A	203192643	G	A	203192643	3	1	92	1	0	0	0	0	1	0	0	0	3352	1087	38	1	968	1	CHIT1	1	203192643	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	22951576	203192643	46057978	19	25116										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208211813	208211813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cccgggcgatccggccttggCgccactctgggtggaggggg	19	13	1	0	rs200636622		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:208211813C>T	ENST00000367033.3	-	26	5424	c.4667G>A	c.(4666-4668)cGc>cAc	p.R1556H		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1556					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCGGCCTTGGCGCCACTCTGG	0.612																																																0			1						C	HIS/ARG	0,4406		0,0,2203	82	71	75		4667	4.8	1	1		75	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLXNA2	NM_025179.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1556/1895	208211813	1,13005	2203	4300	6503	206278436	SO:0001583	missense	5362			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4667G>A	1.37:g.208211813C>T	ENSP00000356000:p.Arg1556His		206278436	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	35	5.520674	0.96416	0.0	1.16E-4	ENSG00000076356	ENST00000367033	T	0.13901	2.55	4.81	4.81	0.61882	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.44871	0.1314	M	0.87328	2.875	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.54951	-0.8216	10	0.87932	D	0	.	18.2659	0.90052	0.0:1.0:0.0:0.0	.	1556	O75051	PLXA2_HUMAN	H	1556	ENSP00000356000:R1556H	ENSP00000356000:R1556H	R	-	2	0	PLXNA2	206278436	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.486000	0.81215	2.372000	0.80975	0.455000	0.32223	CGC		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208211813	C	T	208211813	3	4	92	1	0	0	0	0	1	0	0	0	12151	768	27	1	1045	1	PLXNA2	1	208211813	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5019170	208211813	41038808	20	25117										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212538603	212538603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctcttcttttaaggtatctcTttctaattttgatcatccat	3	9	5	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:212538603T>C	ENST00000261455.4	-	8	1144	c.1007A>G	c.(1006-1008)aAg>aGg	p.K336R	TMEM206_ENST00000535273.1_Missense_Mutation_p.K397R	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	336			K -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		AAGGTATCTCTTTCTAATTTT	0.428																																																0			1											222	213	216					1																	212538603		2203	4300	6503	210605226	SO:0001583	missense	55248			AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.1007A>G	1.37:g.212538603T>C	ENSP00000261455:p.Lys336Arg		210605226	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.090053	0.36855	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.91	1.08	0.20341	.	0.175979	0.64402	N	0.000010	T	0.35248	0.0925	N	0.20986	0.625	0.35576	D	0.805866	B;B	0.14805	0.011;0.0	B;B	0.16722	0.016;0.004	T	0.22836	-1.0205	9	0.33940	T	0.23	-27.1738	10.6969	0.45905	0.0:0.3769:0.0:0.6231	.	397;336	B7Z4D6;Q9H813	.;TM206_HUMAN	R	336;397	.	ENSP00000261455:K336R	K	-	2	0	TMEM206	210605226	1.000000	0.71417	0.023000	0.16930	0.994000	0.84299	1.695000	0.37763	-0.054000	0.13266	0.528000	0.53228	AAG		0.428	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		C	212538603	T	C	212538603	3	2	92	1	0	0	0	0	1	0	0	0	16170	1609	56	4	49	4	TMEM206	1	212538603	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	4326790	212538603	36712018	21	25118										
PSEN2	5664	hgsc.bcm.edu	37	chr1	227073296	227073296	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggccagcgcctcctcaactcCgtgctgaacaccctcatcat	7	18	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:227073296C>T	ENST00000366783.3	+	6	850	c.414C>T	c.(412-414)tcC>tcT	p.S138S	PSEN2_ENST00000340188.4_Silent_p.S138S|PSEN2_ENST00000422240.2_Silent_p.S138S|PSEN2_ENST00000366782.1_Silent_p.S171S|PSEN2_ENST00000472139.2_5'UTR|PSEN2_ENST00000391872.2_Silent_p.S171S	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	138					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				TCCTCAACTCCGTGCTGAACA	0.587																																																0			1											200	133	156					1																	227073296		2203	4300	6503	225139919	SO:0001819	synonymous_variant	5664			BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"Alzheimer disease 4"	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.414C>T	1.37:g.227073296C>T			225139919	A8K8D4|B1AP21|Q96P32	Silent	SNP	ENST00000366783.3	37	CCDS1556.1																																																																																				0.587	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447		T	227073296	C	T	227073296	2	4	92	1	0	0	0	0	0	0	0	1	12685	639	23	1		1	PSEN2	1	227073296	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	14534693	227073296	22177325	22	25119										
RYR2	6262	hgsc.bcm.edu	37	chr1	237993876	237993876	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	caatgattacttcgacacagTgccacatggctttgaaaccc	7	12	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:237993876T>G	ENST00000366574.2	+	103	15019	c.14702T>G	c.(14701-14703)gTg>gGg	p.V4901G	RYR2_ENST00000360064.6_Missense_Mutation_p.V4907G|RYR2_ENST00000542537.1_Missense_Mutation_p.V4885G	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4901					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCGACACAGTGCCACATGGC	0.433																																																0			1											217	204	208					1																	237993876		1970	4169	6139	236060499	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14702T>G	1.37:g.237993876T>G	ENSP00000355533:p.Val4901Gly		236060499	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.264174	0.59431	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96774	-4.12;-4.08;-4.11	5.39	5.39	0.77823	.	0.000000	0.56097	D	0.000037	D	0.93877	0.8041	L	0.49455	1.56	0.80722	D	1	P	0.37781	0.608	B	0.37943	0.261	D	0.93539	0.6876	10	0.87932	D	0	-16.0718	9.8549	0.41079	0.0:0.0765:0.0:0.9235	.	4901	Q92736	RYR2_HUMAN	G	4901;4907;4885	ENSP00000355533:V4901G;ENSP00000353174:V4907G;ENSP00000443798:V4885G	ENSP00000353174:V4907G	V	+	2	0	RYR2	236060499	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.805000	0.47939	2.030000	0.59900	0.459000	0.35465	GTG		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237993876	T	G	237993876	3	3	92	1	0	0	0	0	1	0	0	0	13806	1696	59	4	15112	4	RYR2	1	237993876	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	10920580	237993876	11256745	23	25120										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371484	240371484	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ataccccctcctccccctctAcccggagcgggcataccccc	6	23	1	0	rs202006855	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr1:240371484A>T	ENST00000319653.9	+	5	3602	c.3372A>T	c.(3370-3372)ctA>ctT	p.L1124L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1124	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCCCCTCTACCCGGAGCGG	0.711																																																0			1											8	10	9					1																	240371484		2106	4139	6245	238438107	SO:0001819	synonymous_variant	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3372A>T	1.37:g.240371484A>T			238438107	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371484	A	T	240371484	2	4	92	1	0	0	0	0	0	0	0	1	5969	378	14	5		5	FMN2	1	240371484	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	2377608	240371484	8879137	24	25121										
TPO	7173	hgsc.bcm.edu	37	chr2	1497656	1497656	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acagccatcgccagcaggagCgtggccgacaagatcctgga	13	13	0	1	rs368276909		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:1497656C>A	ENST00000345913.4	+	11	1942	c.1851C>A	c.(1849-1851)agC>agA	p.S617R	TPO_ENST00000329066.4_Missense_Mutation_p.S617R|TPO_ENST00000337415.3_Missense_Mutation_p.S617R|TPO_ENST00000349624.3_Missense_Mutation_p.S444R|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382198.1_Missense_Mutation_p.S444R|TPO_ENST00000346956.3_Missense_Mutation_p.S617R|TPO_ENST00000382201.3_Missense_Mutation_p.S560R	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	617					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CCAGCAGGAGCGTGGCCGACA	0.612																																																0			2											71	66	68					2																	1497656		2203	4300	6503	1476663	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1851C>A	2.37:g.1497656C>A	ENSP00000318820:p.Ser617Arg		1476663	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.220|1.220	-0.627105|-0.627105	0.03610|0.03610	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000446278|ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	.|T;T;T;T;T;T;T;T;T	.|0.72835	.|-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69	4.84|4.84	1.63|1.63	0.23807|0.23807	.|.	.|0.674836	.|0.17460	.|N	.|0.173487	T|T	0.53449|0.53449	0.1797|0.1797	L|L	0.37561|0.37561	1.115|1.115	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.17465	.|0.018;0.007;0.018;0.022	.|B;B;B;B	.|0.26202	.|0.027;0.016;0.027;0.067	T|T	0.40905|0.40905	-0.9538|-0.9538	5|10	.|0.34782	.|T	.|0.22	-16.956|-16.956	0.8034|0.8034	0.01079|0.01079	0.2552:0.1702:0.1313:0.4432|0.2552:0.1702:0.1313:0.4432	.|.	.|617;444;560;617	.|P07202-4;P07202-5;P07202-2;P07202	.|.;.;.;PERT_HUMAN	E|R	92|617;617;617;444;617;560;444;546;91	.|ENSP00000337263:S617R;ENSP00000318820:S617R;ENSP00000263886:S617R;ENSP00000332044:S444R;ENSP00000329869:S617R;ENSP00000371636:S560R;ENSP00000371633:S444R;ENSP00000405788:S546R;ENSP00000419461:S91R	.|ENSP00000329869:S617R	A|S	+|+	2|3	0|2	TPO|TPO	1476663|1476663	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.141000|0.141000	0.21300|0.21300	-2.004000|-2.004000	0.01461|0.01461	0.109000|0.109000	0.17891|0.17891	0.561000|0.561000	0.74099|0.74099	GCG|AGC		0.612	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1497656	C	A	1497656	3	1	92	1	0	0	0	0	1	0	0	0	16450	767	27	2	1889	2	TPO	2	1497656	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		1497656	241701717	25	25122										
ZNF513	130557	hgsc.bcm.edu	37	chr2	27601843	27601843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gctcctcaacttcactctccGcacttagtgcccggccgccc	7	20	3	0	rs35554630	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:27601843G>A	ENST00000323703.6	-	3	488	c.290C>T	c.(289-291)gCg>gTg	p.A97V	ZNF513_ENST00000407879.1_Missense_Mutation_p.A35V|ZNF513_ENST00000491924.1_5'UTR	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	97	Gly-rich.				regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCACTCTCCGCACTTAGTGC	0.662													G|||	3	0.000599042	8e-04	0	5008	,	,		13575	0		0.001	False		,,,				2504	0.001															0			2						G	VAL/ALA,VAL/ALA	2,4294		0,2,2146	16	19	18		104,290	3.6	0.9	2	dbSNP_126	18	13,8387		0,13,4187	yes	missense,missense	ZNF513	NM_001201459.1,NM_144631.5	64,64	0,15,6333	AA,AG,GG		0.1548,0.0466,0.1181	probably-damaging,probably-damaging	35/480,97/542	27601843	15,12681	2148	4200	6348	27455347	SO:0001583	missense	130557			AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795		"Zinc fingers, C2H2-type"	26498	protein-coding gene	gene with protein product		613598				12477932	Standard	NM_001201459		Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.290C>T	2.37:g.27601843G>A	ENSP00000318373:p.Ala97Val		27455347	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	Missense_Mutation	SNP	ENST00000323703.6	37	CCDS1751.1	.	.	.	.	.	.	.	.	.	.	G	9.223	1.033866	0.19590	4.66E-4	0.001548	ENSG00000163795	ENST00000323703;ENST00000407879;ENST00000436006	T;T;T	0.54675	3.35;3.3;0.56	4.48	3.59	0.41128	.	0.000000	0.47455	D	0.000227	T	0.27419	0.0673	N	0.12182	0.205	0.28258	N	0.92495	P	0.52577	0.954	B	0.33521	0.165	T	0.10382	-1.0632	10	0.27082	T	0.32	-5.7578	12.6059	0.56523	0.0:0.0:0.8328:0.1672	rs35554630	97	Q8N8E2	ZN513_HUMAN	V	97;35;35	ENSP00000318373:A97V;ENSP00000384874:A35V;ENSP00000394226:A35V	ENSP00000318373:A97V	A	-	2	0	ZNF513	27455347	0.943000	0.32029	0.907000	0.35723	0.970000	0.65996	1.644000	0.37228	1.099000	0.41499	0.561000	0.74099	GCG		0.662	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215026.2	NM_144631		A	27601843	G	A	27601843	3	1	92	1	0	0	0	0	1	0	0	0	17997	1087	38	1	1343	1	ZNF513	2	27601843	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	26104187	27601843	215597530	26	25123										
EHD3	30845	hgsc.bcm.edu	37	chr2	31483747	31483747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgccccgaaatgctgccctgCgcaagctcaacgacctcatc	8	17	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:31483747C>T	ENST00000322054.5	+	4	1159	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	EHD3_ENST00000541626.1_Intron	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	292					blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					TGCTGCCCTGCGCAAGCTCAA	0.627																																																0			2											62	66	65					2																	31483747		2203	4300	6503	31337251	SO:0001583	missense	30845			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"EF-hand domain containing"	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.874C>T	2.37:g.31483747C>T	ENSP00000327116:p.Arg292Cys		31337251	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703193	0.68501	.	.	ENSG00000013016	ENST00000322054	D	0.95656	-3.77	4.77	4.77	0.60923	.	0.050153	0.85682	D	0.000000	D	0.98134	0.9384	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.98648	1.0678	10	0.87932	D	0	-19.4058	12.3523	0.55155	0.2731:0.7269:0.0:0.0	.	292	Q9NZN3	EHD3_HUMAN	C	292	ENSP00000327116:R292C	ENSP00000327116:R292C	R	+	1	0	EHD3	31337251	0.767000	0.28508	1.000000	0.80357	0.990000	0.78478	1.330000	0.33781	2.478000	0.83669	0.561000	0.74099	CGC		0.627	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600		T	31483747	C	T	31483747	3	4	92	1	0	0	0	0	1	0	0	0	4990	768	27	1	888	1	EHD3	2	31483747	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	3881904	31483747	211715626	27	25124										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33588553	33588553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atgctactgtaagcaagggaCgtactatgatcctgtgaaac	10	8	0	2	rs374132100		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:33588553C>T	ENST00000404816.2	+	29	4720	c.4367C>T	c.(4366-4368)aCg>aTg	p.T1456M	LTBP1_ENST00000272273.5_Missense_Mutation_p.T354M|LTBP1_ENST00000404525.1_Missense_Mutation_p.T1077M|LTBP1_ENST00000390003.4_Missense_Mutation_p.T1131M|LTBP1_ENST00000407925.1_Missense_Mutation_p.T1130M|LTBP1_ENST00000402934.1_Missense_Mutation_p.T1075M|LTBP1_ENST00000354476.3_Missense_Mutation_p.T1457M|LTBP1_ENST00000418533.2_Missense_Mutation_p.T1088M			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1456	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAGCAAGGGACGTACTATGAT	0.393																																																0			2											173	161	165					2																	33588553		2203	4300	6503	33442057	SO:0001583	missense	4052				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4367C>T	2.37:g.33588553C>T	ENSP00000386043:p.Thr1456Met		33442057	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	C	15.38	2.817253	0.50633	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	D;D;D;D;D;D;D;D	0.95554	-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-2.94	5.34	5.34	0.76211	Epidermal growth factor-like (1);	.	.	.	.	D	0.95909	0.8668	N	0.21097	0.63	0.39922	D	0.974176	D;D;D;D;D;D;D	0.89917	0.994;1.0;1.0;0.998;1.0;1.0;1.0	P;D;D;P;D;D;D	0.91635	0.821;0.964;0.999;0.902;0.987;0.999;0.984	D	0.97401	0.9996	9	0.72032	D	0.01	.	19.0478	0.93028	0.0:1.0:0.0:0.0	.	354;1456;1088;1077;1130;1131;1457	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	M	1456;1457;1131;1088;1075;1077;1130;354	ENSP00000386043:T1456M;ENSP00000346467:T1457M;ENSP00000374653:T1131M;ENSP00000393057:T1088M;ENSP00000384373:T1075M;ENSP00000385359:T1077M;ENSP00000384091:T1130M;ENSP00000272273:T354M	ENSP00000272273:T354M	T	+	2	0	LTBP1	33442057	0.634000	0.27190	1.000000	0.80357	0.890000	0.51754	2.354000	0.44098	2.502000	0.84385	0.563000	0.77884	ACG		0.393	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33588553	C	T	33588553	3	4	92	1	0	0	0	0	1	0	0	0	9102	536	19	1	4536	1	LTBP1	2	33588553	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2104806	33588553	209610820	28	25125										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85536328	85536328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cggagcaagcccagcccctcTccctcaccaccaaaccagaa	6	20	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:85536328T>C	ENST00000282111.3	+	12	1785	c.1510T>C	c.(1510-1512)Tcc>Ccc	p.S504P		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	504					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CCAGCCCCTCTCCCTCACCAC	0.672																																																0			2											48	52	50					2																	85536328		2203	4300	6503	85389839	SO:0001583	missense	83439			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.1510T>C	2.37:g.85536328T>C	ENSP00000282111:p.Ser504Pro		85389839	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.799714	0.90538	.	.	ENSG00000152284	ENST00000282111	T	0.37411	1.2	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.56949	0.2020	M	0.66939	2.045	0.53688	D	0.99997	D	0.65815	0.995	D	0.72982	0.979	T	0.58875	-0.7559	10	0.56958	D	0.05	.	13.3188	0.60421	0.0:0.0:0.0:1.0	.	504	Q9HCS4	TF7L1_HUMAN	P	504	ENSP00000282111:S504P	ENSP00000282111:S504P	S	+	1	0	TCF7L1	85389839	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	5.563000	0.67352	2.239000	0.73571	0.523000	0.50628	TCC		0.672	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		C	85536328	T	C	85536328	3	2	92	1	0	0	0	0	1	0	0	0	15736	1551	54	4	1556	4	TCF7L1	2	85536328	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	51947775	85536328	157663045	29	25126										
CYP27C1	339761	hgsc.bcm.edu	37	chr2	127950851	127950851	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	catcctggtacgatgtggcaTagtggcaaagggccagctgg	15	9	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:127950851T>G	ENST00000335247.7	-	7	951	c.821A>C	c.(820-822)tAt>tCt	p.Y274S	CYP27C1_ENST00000409327.1_Missense_Mutation_p.Y274S	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	274						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		CGATGTGGCATAGTGGCAAAG	0.557																																																0			2											80	76	77					2																	127950851		2203	4300	6503	127667321	SO:0001583	missense	339761			AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"Cytochrome P450s"	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.821A>C	2.37:g.127950851T>G	ENSP00000334128:p.Tyr274Ser		127667321	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	37	CCDS33285.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.839098	0.51057	.	.	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.47869	0.83;0.83	3.87	2.71	0.32032	.	0.000000	0.64402	D	0.000002	T	0.65228	0.2671	M	0.77103	2.36	0.44181	D	0.996992	D	0.89917	1.0	D	0.91635	0.999	T	0.65158	-0.6236	10	0.72032	D	0.01	-7.6457	9.0495	0.36367	0.0:0.0902:0.0:0.9098	.	274	Q4G0S4	C27C1_HUMAN	S	274	ENSP00000334128:Y274S;ENSP00000387198:Y274S	ENSP00000334128:Y274S	Y	-	2	0	CYP27C1	127667321	1.000000	0.71417	0.970000	0.41538	0.596000	0.36781	4.243000	0.58721	0.485000	0.27652	-0.425000	0.05940	TAT		0.557	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		G	127950851	T	G	127950851	3	3	92	1	0	0	0	0	1	0	0	0	4166	1406	49	4	305	4	CYP27C1	2	127950851	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	42414523	127950851	115248522	30	25127										
RAB3GAP1	22930	hgsc.bcm.edu	37	chr2	135884178	135884178	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggatcctattcaagctccaCattggtctgttagagttcga	9	9	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:135884178C>T	ENST00000264158.8	+	11	968	c.925C>T	c.(925-927)Cat>Tat	p.H309Y	RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.H309Y|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.H265Y	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	309					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		TCAAGCTCCACATTGGTCTGT	0.353																																																0			2											228	222	224					2																	135884178		2203	4300	6503	135600648	SO:0001583	missense	22930			D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.925C>T	2.37:g.135884178C>T	ENSP00000264158:p.His309Tyr		135600648	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028259	0.54790	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.61392	0.11;0.11;0.11	5.72	5.72	0.89469	.	0.142487	0.64402	D	0.000005	T	0.50377	0.1612	L	0.36672	1.1	0.47778	D	0.999511	B;B	0.31730	0.337;0.337	B;B	0.25614	0.062;0.062	T	0.49542	-0.8929	10	0.51188	T	0.08	-15.615	19.88	0.96892	0.0:1.0:0.0:0.0	.	309;309	C9J837;Q15042	.;RB3GP_HUMAN	Y	309;265;309	ENSP00000264158:H309Y;ENSP00000444306:H265Y;ENSP00000411418:H309Y	ENSP00000264158:H309Y	H	+	1	0	RAB3GAP1	135600648	1.000000	0.71417	0.984000	0.44739	0.973000	0.67179	7.386000	0.79775	2.703000	0.92315	0.655000	0.94253	CAT		0.353	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		T	135884178	C	T	135884178	3	4	92	1	0	0	0	0	1	0	0	0	12972	478	17	3	967	3	RAB3GAP1	2	135884178	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	7933327	135884178	107315195	31	25128										
ACVR1	90	hgsc.bcm.edu	37	chr2	158626989	158626989	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acggcaacattctccccttgCcagctgcccctccacacctc	5	21	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:158626989C>A	ENST00000263640.3	-	7	1110	c.681G>T	c.(679-681)tgG>tgT	p.W227C	ACVR1_ENST00000434821.1_Missense_Mutation_p.W227C|ACVR1_ENST00000410057.2_Missense_Mutation_p.W227C|ACVR1_ENST00000409283.2_Missense_Mutation_p.W227C	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	227	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	TCTCCCCTTGCCAGCTGCCCC	0.498																																																0			2											131	103	113					2																	158626989		2203	4300	6503	158335235	SO:0001583	missense	90				CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.681G>T	2.37:g.158626989C>A	ENSP00000263640:p.Trp227Cys		158335235		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564989	0.86439	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76821	0.4041	L	0.55990	1.75	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.76672	-0.2873	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	227	Q04771	ACVR1_HUMAN	C	227	ENSP00000263640:W227C;ENSP00000387273:W227C;ENSP00000405004:W227C;ENSP00000387127:W227C	ENSP00000263640:W227C	W	-	3	0	ACVR1	158335235	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	TGG		0.498	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		A	158626989	C	A	158626989	3	1	92	1	0	0	0	0	1	0	0	0	220	740	26	2	868	2	ACVR1	2	158626989	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	22742811	158626989	84572384	32	25129										
TTN	7273	hgsc.bcm.edu	37	chr2	179407928	179407928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aacagtgtgctctaggactgTgggttttaaggtgacaacct	12	7	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:179407928T>C	ENST00000591111.1	-	297	92073	c.91849A>G	c.(91849-91851)Aca>Gca	p.T30617A	TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T32258A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T23385A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T29690A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T23318A|TTN_ENST00000460472.2_Missense_Mutation_p.T23193A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30617	Fibronectin type-III 123. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> S (in a renal chromophobe cancer sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T23193S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTAGGACTGTGGGTTTTAAG	0.443																																																1	Substitution - Missense(1)	kidney(1)	2											230	220	223					2																	179407928		1947	4143	6090	179116174	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.91849A>G	2.37:g.179407928T>C	ENSP00000465570:p.Thr30617Ala		179116174	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.98	2.399056	0.42512	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.61	5.61	0.85477	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.47930	0.1472	N	0.25992	0.78	0.32961	D	0.521033	P;P;P;P	0.34462	0.454;0.454;0.454;0.454	B;B;B;B	0.38156	0.266;0.266;0.266;0.266	T	0.63175	-0.6696	9	0.87932	D	0	.	10.45	0.44516	0.0:0.0725:0.0:0.9275	.	23193;23318;23385;30617	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	29690;23193;23385;23318;23190	ENSP00000343764:T29690A;ENSP00000434586:T23193A;ENSP00000340554:T23385A;ENSP00000352154:T23318A	ENSP00000340554:T23385A	T	-	1	0	TTN	179116174	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	3.288000	0.51739	2.254000	0.74563	0.533000	0.62120	ACA		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179407928	T	C	179407928	3	2	92	1	0	0	0	0	1	0	0	0	16775	1696	59	4	11271	4	TTN	2	179407928	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	20780939	179407928	63791445	33	25130										
TTN	7273	hgsc.bcm.edu	37	chr2	179482201	179482201	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgaactgatgactgagtctGatctgaggaagttaggttta	12	5	2	6			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:179482201G>T	ENST00000591111.1	-	204	42912	c.42688C>A	c.(42688-42690)Cag>Aag	p.Q14230K	TTN_ENST00000589042.1_Missense_Mutation_p.Q15871K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q6998K|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q13303K|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q6931K|TTN_ENST00000460472.2_Missense_Mutation_p.Q6806K|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14230	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACTGAGTCTGATCTGAGGAA	0.413																																																0			2											71	64	66					2																	179482201		1872	4104	5976	179190446	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42688C>A	2.37:g.179482201G>T	ENSP00000465570:p.Gln14230Lys		179190446	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	15.70	2.910612	0.52439	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	6.08	6.08	0.98989	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59729	0.2215	N	0.12471	0.22	0.80722	D	1	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.76071	0.987;0.987;0.987;0.987	T	0.65977	-0.6037	9	0.87932	D	0	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	6806;6931;6998;14230	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	13303;6806;6998;6931;6806	ENSP00000343764:Q13303K;ENSP00000434586:Q6806K;ENSP00000340554:Q6998K;ENSP00000352154:Q6931K	ENSP00000340554:Q6998K	Q	-	1	0	TTN	179190446	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.807000	0.99171	2.894000	0.99253	0.655000	0.94253	CAG		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179482201	G	T	179482201	3	4	92	1	0	0	0	0	1	0	0	0	16775	1299	45	2	60518	2	TTN	2	179482201	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	74273	179482201	63717172	34	25131										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671833	186671833	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	actatggatctcaagactctAtttggaagaatataaacagt	7	6	2	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:186671833A>T	ENST00000424728.1	+	17	17800	c.17800A>T	c.(17800-17802)Att>Ttt	p.I5934F	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6023F			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5934										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TCAAGACTCTATTTGGAAGAA	0.303																																																0			2											85	84	84					2																	186671833		1806	4075	5881	186380078	SO:0001583	missense	285135			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17800A>T	2.37:g.186671833A>T	ENSP00000401306:p.Ile5934Phe		186380078	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	A	15.11	2.736010	0.49045	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.57752	0.38;0.38	4.8	3.61	0.41365	.	0.123830	0.36591	N	0.002516	T	0.48768	0.1518	L	0.36672	1.1	0.35443	D	0.795034	.	.	.	.	.	.	T	0.59862	-0.7374	8	0.72032	D	0.01	.	8.2774	0.31881	0.7986:0.2014:0.0:0.0	.	.	.	.	F	6023;5934	ENSP00000344403:I6023F;ENSP00000401306:I5934F	ENSP00000344403:I6023F	I	+	1	0	FSIP2	186380078	0.789000	0.28775	0.990000	0.47175	0.799000	0.45148	0.954000	0.29175	0.817000	0.34445	0.402000	0.26972	ATT		0.303	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186671833	A	T	186671833	3	4	92	1	0	0	0	0	1	0	0	0	6094	449	16	5	18133	5	FSIP2	2	186671833	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	7189632	186671833	56527540	35	25132										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196913042	196913042	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgggactgttcatttttaacActaaatggttctggactctc	8	8	3	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:196913042A>T	ENST00000312428.6	-	4	328	c.228T>A	c.(226-228)agT>agA	p.S76R	DNAH7_ENST00000410072.1_Missense_Mutation_p.S76R	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	76	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CATTTTTAACACTAAATGGTT	0.358																																																0			2											123	113	116					2																	196913042		1852	4107	5959	196621287	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.228T>A	2.37:g.196913042A>T	ENSP00000311273:p.Ser76Arg		196621287	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.505822	0.44558	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	T;T	0.21734	1.99;2.92	4.81	-0.591	0.11675	.	0.606619	0.16245	N	0.222967	T	0.08044	0.0201	N	0.14661	0.345	0.09310	N	1	B	0.23735	0.09	B	0.16289	0.015	T	0.32161	-0.9917	10	0.15952	T	0.53	.	3.2497	0.06810	0.5361:0.0:0.2911:0.1728	.	76	Q8WXX0	DYH7_HUMAN	R	76;76;76;51	ENSP00000311273:S76R;ENSP00000386260:S76R	ENSP00000311273:S76R	S	-	3	2	DNAH7	196621287	0.000000	0.05858	0.129000	0.21949	0.664000	0.39144	-0.100000	0.10990	0.097000	0.17492	0.477000	0.44152	AGT		0.358	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196913042	A	T	196913042	3	4	92	1	0	0	0	0	1	0	0	0	4617	156	6	5	12094	5	DNAH7	2	196913042	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	10241209	196913042	46286331	36	25133										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201440162	201440162	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaaggtgtactcctttctatTttaaagagccaagcctcaga	8	9	2	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:201440162T>G	ENST00000357799.4	+	8	3858	c.3760T>G	c.(3760-3762)Ttt>Gtt	p.F1254V		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	1254					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TCCTTTCTATTTTAAAGAGCC	0.318																																																0			2											88	84	85					2																	201440162		1812	4069	5881	201148407	SO:0001583	missense	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.3760T>G	2.37:g.201440162T>G	ENSP00000350447:p.Phe1254Val		201148407	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.573779	0.28092	.	.	ENSG00000163535	ENST00000357799	T	0.12672	2.66	5.23	0.258	0.15578	.	0.643075	0.12886	N	0.430980	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B;B	0.19706	0.038;0.038	B;B	0.18871	0.023;0.023	T	0.33599	-0.9862	10	0.62326	D	0.03	0.1065	7.8546	0.29474	0.0:0.3419:0.0:0.6581	.	1254;1254	Q562F6-2;Q562F6	.;SGOL2_HUMAN	V	1254	ENSP00000350447:F1254V	ENSP00000350447:F1254V	F	+	1	0	SGOL2	201148407	0.008000	0.16893	0.000000	0.03702	0.012000	0.07955	0.775000	0.26689	-0.028000	0.13850	0.467000	0.42956	TTT		0.318	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201440162	T	G	201440162	3	3	92	1	0	0	0	0	1	0	0	0	14254	1841	64	4	3786	4	SGOL2	2	201440162	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	4527120	201440162	41759211	37	25134										
USP37	57695	hgsc.bcm.edu	37	chr2	219330870	219330870	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttctttattctcatcacagtCtttagttatctcagtaaaac	3	9	5	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:219330870C>A	ENST00000258399.3	-	21	2741	c.2329G>T	c.(2329-2331)Gac>Tac	p.D777Y	USP37_ENST00000454775.1_Missense_Mutation_p.D777Y|USP37_ENST00000415516.1_Missense_Mutation_p.D683Y|USP37_ENST00000418019.1_Missense_Mutation_p.D777Y	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	777	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TCATCACAGTCTTTAGTTATC	0.388																																																0			2											136	132	133					2																	219330870		2203	4300	6503	219039114	SO:0001583	missense	57695			AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.2329G>T	2.37:g.219330870C>A	ENSP00000258399:p.Asp777Tyr		219039114	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Missense_Mutation	SNP	ENST00000258399.3	37	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983165	0.74474	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	T;T;T;T	0.51817	0.72;0.72;0.69;0.72	5.46	4.57	0.56435	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.155351	0.56097	D	0.000023	T	0.63248	0.2495	L	0.52573	1.65	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.964;0.989	T	0.65508	-0.6151	10	0.52906	T	0.07	-14.0062	16.1909	0.81987	0.0:0.8668:0.1332:0.0	.	683;777	Q86T82-2;Q86T82	.;UBP37_HUMAN	Y	777;777;683;777	ENSP00000258399:D777Y;ENSP00000393662:D777Y;ENSP00000400902:D683Y;ENSP00000396585:D777Y	ENSP00000258399:D777Y	D	-	1	0	USP37	219039114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.819000	0.69243	1.499000	0.48617	0.655000	0.94253	GAC		0.388	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		A	219330870	C	A	219330870	3	1	92	1	0	0	0	0	1	0	0	0	17108	913	32	2	634	2	USP37	2	219330870	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	17890708	219330870	23868503	38	25135										
CHPF	79586	hgsc.bcm.edu	37	chr2	220404219	220404219	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tacaggtcctcactgagcctCgcgctgcacgtctgggcccg	12	16	2	1	rs143397847	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:220404219C>T	ENST00000243776.6	-	4	2462	c.2214G>A	c.(2212-2214)gcG>gcA	p.A738A	CHPF_ENST00000535926.1_Silent_p.A576A	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	738					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CACTGAGCCTCGCGCTGCACG	0.652													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		17369	0		0	False		,,,				2504	0															0			2						C	,	8,4396	14.3+/-33.2	0,8,2194	46	41	43		1728,2214	-9.1	0	2	dbSNP_134	43	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	0,8,6493	TT,TC,CC		0.0,0.1817,0.0615	,	576/614,738/776	220404219	8,12994	2202	4299	6501	220112463	SO:0001819	synonymous_variant	79586			BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.2214G>A	2.37:g.220404219C>T			220112463	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																				0.652	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220404219	C	T	220404219	2	4	92	1	0	0	0	0	0	0	0	1	3374	871	31	1		1	CHPF	2	220404219	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1073349	220404219	22795154	39	25136										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228128656	228128656	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tcaccgggacctccaggaccGccaggtaaagatgtggaagg	14	11	1	1	rs369557944		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr2:228128656G>A	ENST00000396578.3	+	21	1473	c.1311G>A	c.(1309-1311)ccG>ccA	p.P437P	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	437	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CTCCAGGACCGCCAGGTAAAG	0.587																																																0			2						T		0,3862		0,0,1931	61	65	64		1311	0.8	1	2		64	1,8237		0,1,4118	no	coding-synonymous	COL4A3	NM_000091.4		0,1,6049	AA,AG,GG		0.0121,0.0,0.0083		437/1671	228128656	1,12099	1931	4119	6050	227836900	SO:0001819	synonymous_variant	1285				CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1311G>A	2.37:g.228128656G>A			227836900	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																				0.587	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		A	228128656	G	A	228128656	2	1	92	1	0	0	0	0	0	0	0	1	3697	1074	38	1		1	COL4A3	2	228128656	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	7724437	228128656	15070717	40	25137										
VHL	7428	hgsc.bcm.edu	37	chr3	10188274	10188274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	actgaattatttgtgccatcTctcaatgttgacggacagcc	8	10	2	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:10188274T>C	ENST00000256474.2	+	2	1257	c.417T>C	c.(415-417)tcT>tcC	p.S139S	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	139	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.S139fs*2(2)|p.P138fs*1(2)|p.S139S(2)|p.S139fs*5(1)|p.L140fs*4(1)|p.N141fs*19(1)|p.S139fs*12(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTGTGCCATCTCTCAATGTTG	0.423		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	10	Deletion - Frameshift(5)|Substitution - coding silent(2)|Insertion - Frameshift(2)|Complex - frameshift(1)	kidney(10)	3											218	202	207					3																	10188274		2203	4300	6503	10163274	SO:0001819	synonymous_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.417T>C	3.37:g.10188274T>C			10163274	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.423	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188274	T	C	10188274	2	2	92	1	0	0	0	0	0	0	0	1	17202	1538	54	4		4	VHL	3	10188274	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10		10188274	187834156	41	25138										
OXSM	54995	hgsc.bcm.edu	37	chr3	25832827	25832827	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtcagttcaatgaacaaaacTttgtgtccaaatcagatatc	6	8	3	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:25832827T>C	ENST00000280701.3	+	2	415	c.316T>C	c.(316-318)Ttt>Ctt	p.F106L	NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Missense_Mutation_p.F106L|OXSM_ENST00000449808.1_Intron	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	106			F -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)	p.F106I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TGAACAAAACTTTGTGTCCAA	0.448																																																1	Substitution - Missense(1)	breast(1)	3											170	144	153					3																	25832827		2203	4300	6503	25807831	SO:0001583	missense	54995			BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.316T>C	3.37:g.25832827T>C	ENSP00000280701:p.Phe106Leu		25807831		Missense_Mutation	SNP	ENST00000280701.3	37	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021443	0.75275	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	5.93	5.93	0.95920	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.39633	1.23	0.80722	D	1	D;B	0.55385	0.971;0.023	P;B	0.48189	0.57;0.012	T	0.62969	-0.6741	9	0.87932	D	0	-21.5264	16.379	0.83439	0.0:0.0:0.0:1.0	.	106;106	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	L	106	.	ENSP00000280701:F106L	F	+	1	0	OXSM	25807831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.991000	0.88244	2.268000	0.75426	0.455000	0.32223	TTT		0.448	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		C	25832827	T	C	25832827	3	2	92	1	0	0	0	0	1	0	0	0	11366	1609	56	4	318	4	OXSM	3	25832827	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	15644553	25832827	172189603	42	25139										
TGFBR2	7048	hgsc.bcm.edu	37	chr3	30729948	30729948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgtcgaaagcatgaaggacaAcgtgttgagagatcgagggc	15	6	0	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:30729948A>G	ENST00000295754.5	+	6	1851	c.1469A>G	c.(1468-1470)aAc>aGc	p.N490S	TGFBR2_ENST00000359013.4_Missense_Mutation_p.N515S	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	490	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> S (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)	p.N490S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						ATGAAGGACAACGTGTTGAGA	0.483																																																1	Substitution - Missense(1)	stomach(1)	3											126	117	120					3																	30729948		2203	4300	6503	30704952	SO:0001583	missense	7048				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"transforming growth factor, beta receptor II (70-80kD)"	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1469A>G	3.37:g.30729948A>G	ENSP00000295754:p.Asn490Ser		30704952	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.406586	0.42715	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	T;T	0.64260	-0.09;-0.09	5.38	4.18	0.49190	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.239102	0.48767	N	0.000176	T	0.43389	0.1245	N	0.12471	0.22	0.43130	D	0.994861	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29150	-1.0021	10	0.48119	T	0.1	.	11.7219	0.51688	0.9292:0.0:0.0708:0.0	.	490;515	P37173;D2JYI1	TGFR2_HUMAN;.	S	490;515;320	ENSP00000295754:N490S;ENSP00000351905:N515S	ENSP00000295754:N490S	N	+	2	0	TGFBR2	30704952	0.632000	0.27172	0.900000	0.35374	0.993000	0.82548	1.345000	0.33953	0.937000	0.37394	0.482000	0.46254	AAC		0.483	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2			G	30729948	A	G	30729948	3	3	92	1	0	0	0	0	1	0	0	0	15861	43	2	4	1570	4	TGFBR2	3	30729948	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	4897121	30729948	167292482	43	25140										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37151154	37151154	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aagtactaaccctgtcactcTtatatgttgccagagggtca	8	10	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:37151154T>A	ENST00000336686.4	-	10	634	c.554A>T	c.(553-555)aAg>aTg	p.K185M	LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.K185M			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	185	DVL3-binding.|Ser-rich.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CCTGTCACTCTTATATGTTGC	0.378																																																1	Whole gene deletion(1)	ovary(1)	3											115	118	117					3																	37151154		2203	4300	6503	37126158	SO:0001583	missense	9209			AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.554A>T	3.37:g.37151154T>A	ENSP00000338727:p.Lys185Met		37126158	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.634045	0.47049	.	.	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.51071	0.72;0.72	5.49	1.74	0.24563	.	0.434964	0.23704	N	0.045381	T	0.35653	0.0939	N	0.08118	0	0.20764	N	0.999858	D	0.69078	0.997	P	0.54401	0.751	T	0.18808	-1.0325	10	0.48119	T	0.1	-7.188	9.0529	0.36387	0.0:0.3516:0.0:0.6484	.	185	Q9Y608	LRRF2_HUMAN	M	185	ENSP00000392217:K185M;ENSP00000338727:K185M	ENSP00000338727:K185M	K	-	2	0	LRRFIP2	37126158	1.000000	0.71417	0.994000	0.49952	0.835000	0.47333	0.427000	0.21379	0.519000	0.28406	0.533000	0.62120	AAG		0.378	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37151154	T	A	37151154	3	1	92	1	0	0	0	0	1	0	0	0	9057	1609	56	5	1687	5	LRRFIP2	3	37151154	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	6421206	37151154	160871276	44	25141										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37783309	37783309	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aggtggacacgtccatcaccGggtgagtagcctggtcctgg	15	11	1	1	rs369201522		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:37783309G>A	ENST00000264741.5	+	21	2579	c.2323G>A	c.(2323-2325)Gga>Aga	p.G775R		NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	775					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GTCCATCACCGGGTGAGTAGC	0.582																																																0			3						G	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	74	57	63		2323	5.6	1	3		63	0,8600		0,0,4300	no	missense-near-splice	ITGA9	NM_002207.2	125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	775/1036	37783309	1,13005	2203	4300	6503	37758313	SO:0001630	splice_region_variant	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2324+1G>A	3.37:g.37783309G>A			37758313	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	32	5.121674	0.94385	2.27E-4	0.0	ENSG00000144668	ENST00000264741	T	0.64085	-0.08	5.55	5.55	0.83447	Integrin alpha-2 (1);	0.049975	0.85682	D	0.000000	T	0.80560	0.4646	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82559	-0.0397	10	0.87932	D	0	.	18.2896	0.90124	0.0:0.0:1.0:0.0	.	775	Q13797	ITA9_HUMAN	R	775	ENSP00000264741:G775R	ENSP00000264741:G775R	G	+	1	0	ITGA9	37758313	1.000000	0.71417	0.983000	0.44433	0.978000	0.69477	8.067000	0.89488	2.603000	0.88011	0.655000	0.94253	GGA		0.582	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	Missense_Mutation	A	37783309	G	A	37783309	5	1	92	1	0	0	0	0	0	0	1	0	7904	1130	39	1	2405	1	ITGA9	3	37783309	Splice_Site	SNP	G	TCGA-CL-5918-01A-11D-1657-10	632155	37783309	160239121	45	25142										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38523730	38523730	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gctcctgaggtgctcgagggAgccatcaacttccagagaga	13	11	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:38523730A>G	ENST00000352511.4	+	9	1588	c.1116A>G	c.(1114-1116)ggA>ggG	p.G372G		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		TGCTCGAGGGAGCCATCAACT	0.567																																																0			3											117	88	98					3																	38523730		2203	4300	6503	38498734	SO:0001819	synonymous_variant	93			X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.1116A>G	3.37:g.38523730A>G			38498734	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																				0.567	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		G	38523730	A	G	38523730	2	3	92	1	0	0	0	0	0	0	0	1	224	291	11	4		4	ACVR2B	3	38523730	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	740421	38523730	159498700	46	25143										
CCR1	1230	hgsc.bcm.edu	37	chr3	46244753	46244753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgagtcagaacccagcagagAgttcatgctcccctgtggag	12	11	2	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:46244753A>G	ENST00000296140.3	-	2	1177	c.1052T>C	c.(1051-1053)cTc>cCc	p.L351P	CCR3_ENST00000357422.2_Intron	NM_001295.2	NP_001286.1	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1	351					calcium ion transport (GO:0006816)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|exocytosis (GO:0006887)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of osteoclast differentiation (GO:0045672)|response to wounding (GO:0009611)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine (C-C motif) ligand 7 binding (GO:0035717)|chemokine receptor activity (GO:0004950)|phosphatidylinositol phospholipase C activity (GO:0004435)			autonomic_ganglia(1)|large_intestine(6)|lung(6)|pancreas(1)|skin(3)	17				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CCCAGCAGAGAGTTCATGCTC	0.607																																																0			3											50	48	48					3																	46244753		2203	4300	6503	46219757	SO:0001583	missense	1230				CCDS2737.1	3p21	2012-08-08			ENSG00000163823	ENSG00000163823		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1602	protein-coding gene	gene with protein product		601159		SCYAR1, CMKBR1		7679328	Standard	NM_001295		Approved	CKR-1, MIP1aR, CD191	uc003cph.1	P32246	OTTHUMG00000133451	ENST00000296140.3:c.1052T>C	3.37:g.46244753A>G	ENSP00000296140:p.Leu351Pro		46219757	Q86VA9	Missense_Mutation	SNP	ENST00000296140.3	37	CCDS2737.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.668036	0.47677	.	.	ENSG00000163823	ENST00000296140	T	0.69040	-0.37	4.76	4.76	0.60689	.	0.121404	0.34828	N	0.003652	T	0.81259	0.4785	M	0.89601	3.045	0.51482	D	0.999922	D	0.53462	0.96	P	0.56514	0.8	D	0.85599	0.1251	10	0.87932	D	0	.	13.2892	0.60262	1.0:0.0:0.0:0.0	.	351	P32246	CCR1_HUMAN	P	351	ENSP00000296140:L351P	ENSP00000296140:L351P	L	-	2	0	CCR1	46219757	0.336000	0.24757	0.272000	0.24630	0.514000	0.34195	5.026000	0.64103	2.131000	0.65755	0.448000	0.29417	CTC		0.607	CCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257325.2	NM_001295		G	46244753	A	G	46244753	3	3	92	1	0	0	0	0	1	0	0	0	2945	304	11	4	19	4	CCR1	3	46244753	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	7721023	46244753	151777677	47	25144										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48613082	48613082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cttgcctggggggccctgttCgcctgagtcccccttggggc	15	15	0	1	rs144208360	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:48613082C>T	ENST00000328333.8	-	72	6063	c.5956G>A	c.(5956-5958)Gaa>Aaa	p.E1986K	COL7A1_ENST00000454817.1_Missense_Mutation_p.E1954K	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1986	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGGCCCTGTTCGCCTGAGTCC	0.642													C|||	2	0.000399361	0.0015	0	5008	,	,		15468	0		0	False		,,,				2504	0															0			3						C	LYS/GLU	4,4402	8.1+/-20.4	0,4,2199	55	57	56		5956	3.6	0.2	3	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL7A1	NM_000094.3	56	0,5,6498	TT,TC,CC		0.0116,0.0908,0.0384	probably-damaging	1986/2945	48613082	5,13001	2203	4300	6503	48588086	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.5956G>A	3.37:g.48613082C>T	ENSP00000332371:p.Glu1986Lys		48588086	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	8.641	0.896083	0.17686	9.08E-4	1.16E-4	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.94184	-3.37;-3.37	4.51	3.62	0.41486	.	0.171274	0.26571	N	0.023621	D	0.93167	0.7824	L	0.52823	1.66	0.18873	N	0.999983	D	0.69078	0.997	P	0.57911	0.829	D	0.85156	0.0989	10	0.06494	T	0.89	.	14.3848	0.66938	0.0:0.8511:0.1489:0.0	.	1986	Q02388	CO7A1_HUMAN	K	1986;1954	ENSP00000332371:E1986K;ENSP00000412569:E1954K	ENSP00000332371:E1986K	E	-	1	0	COL7A1	48588086	0.978000	0.34361	0.174000	0.22961	0.007000	0.05969	4.093000	0.57714	1.065000	0.40693	0.563000	0.77884	GAA		0.642	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48613082	C	T	48613082	3	4	92	1	0	0	0	0	1	0	0	0	3710	893	31	1	3066	1	COL7A1	3	48613082	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2368329	48613082	149409348	48	25145										
MST1	327	hgsc.bcm.edu	37	chr3	49723379	49723379	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgccgcggtactgctccccTgcgccgtggtagcagtctgt	14	14	1	0	rs4052580		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:49723379T>C	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000449682.2_Silent_p.A388A|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000494828.2_5'Flank	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACTGCTCCCCTGCGCCGTGGT	0.711																																																0			3											14	16	15					3																	49723379		2180	4265	6445	49698383	SO:0001628	intergenic_variant	6789			D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723379T>C			49698383	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																				0.711	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			C	49723379	T	C	49723379	1	2	92	0	1	0	0	0	0	0	0	0	9920	1567	55	4		4	MST1	3	49723379	IGR	SNP	T	TCGA-CL-5918-01A-11D-1657-10	1110297	49723379	148299051	49	25146										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376119	113376119	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgttgttgctgttgctgctgCtgctgctgctgctgctgctg	14	10	0	0	rs62265538|rs112313093|rs59601191		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:113376119C>T	ENST00000478658.1	-	5	4427	c.4410G>A	c.(4408-4410)caG>caA	p.Q1470Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1470Q			Q68DE3	K2018_HUMAN	KIAA2018	1470	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgctgctgctgctgctgct	0.493																																																0			3											58	65	63					3																	113376119		2185	4279	6464	114858809	SO:0001819	synonymous_variant	205717			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4410G>A	3.37:g.113376119C>T			114858809	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																				0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376119	C	T	113376119	2	4	92	1	0	0	0	0	0	0	0	1	8289	796	28	3		3	KIAA2018	3	113376119	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	63652740	113376119	84646311	50	25147										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865609	118865609	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cagtctgagagaagagcttcCgagcagatggaccgcagaat	13	9	1	5	rs10934483	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:118865609C>T	ENST00000295622.1	+	1	613	c.573C>T	c.(571-573)tcC>tcT	p.S191S	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	191										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		GAAGAGCTTCCGAGCAGATGG	0.517													c|||	717	0.143171	0.1331	0.0663	5008	,	,		22755	0.2361		0.1531	False		,,,				2504	0.1053															0			3						T		519,3887	239.3+/-250.5	28,463,1712	91	94	93		573	-8.2	0	3	dbSNP_120	93	1187,7413	242.1+/-272.2	73,1041,3186	no	coding-synonymous	C3orf30	NM_152539.2		101,1504,4898	TT,TC,CC		13.8023,11.7794,13.117		191/537	118865609	1706,11300	2203	4300	6503	120348299	SO:0001819	synonymous_variant	152405			AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.573C>T	3.37:g.118865609C>T			120348299	A1L4B7	Silent	SNP	ENST00000295622.1	37	CCDS2984.1	359	0.16437728937728938	79	0.16056910569105692	22	0.06077348066298342	131	0.229020979020979	127	0.16754617414248021	c	4.219	0.039534	0.08148	0.117794	0.138023	ENSG00000163424	ENST00000460150	.	.	.	4.09	-8.17	0.01057	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.7772	9.1284	0.36830	0.0:0.4138:0.1026:0.4836	rs10934483;rs10934483	.	.	.	X	155	.	.	R	+	1	2	C3orf30	120348299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.657000	0.01979	-1.809000	0.01232	-1.402000	0.01139	CGA		0.517	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		T	118865609	C	T	118865609	2	4	92	1	0	0	0	0	0	0	0	1	2226	639	23	1		1	C3orf30	3	118865609	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5489490	118865609	79156821	51	25148										
PTPLB	201562	hgsc.bcm.edu	37	chr3	123303821	123303821	+	Silent	SNP	G	G	C													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcgtccccggccccggccctGccaccgccgcccccattccc					rs1271004	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:123303821G>C	ENST00000383657.5	-	1	211	c.54C>G	c.(52-54)ggC>ggG	p.G18G	MYLK-AS1_ENST00000463408.1_RNA|MYLK-AS1_ENST00000485162.1_RNA|MYLK-AS1_ENST00000470449.1_RNA	NM_198402.3	NP_940684.1	Q6Y1H2	HACD2_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b	18	Poly-Gly.				fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			kidney(2)	2				GBM - Glioblastoma multiforme(114;0.1)		ccccggccctgccaccgccgc	0.726													G|||	2032	0.405751	0.4811	0.3818	5008	,	,		9442	0.629		0.1779	False		,,,				2504	0.3252															0			3						G		746,2176		89,568,804	3	4	4		54	1.6	0.6	3	dbSNP_87	4	847,6001		60,727,2637	no	coding-synonymous	PTPLB	NM_198402.3		149,1295,3441	CC,CG,GG		12.3686,25.5305,16.305		18/255	123303821	1593,8177	1461	3424	4885	124786511	SO:0001819	synonymous_variant	201562			AK074605	CCDS46895.1	3q21.1	2010-04-30			ENSG00000206527	ENSG00000206527			9640	protein-coding gene	gene with protein product		615939				15024066	Standard	NM_198402		Approved		uc003egj.2	Q6Y1H2	OTTHUMG00000159529	ENST00000383657.5:c.54C>G	3.37:g.123303821G>C			124786511		Silent	SNP	ENST00000383657.5	37	CCDS46895.1																																																																																				0.726	PTPLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356021.3	NM_198402		C	123303821	G	C	123303821	2	2	92	1	0	0	0	0	0	0	0	1	12812	1306	46	5		5	PTPLB	3	123303821	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	4438212	123303821	74718609	52	25149	30	2								
PTPLB	201562	hgsc.bcm.edu	37	chr3	123303824	123303824	+	Silent	SNP	A	A	G													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tccccggccccggccctgccAccgccgcccccattcccctt					rs112371142	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:123303824A>G	ENST00000383657.5	-	1	208	c.51T>C	c.(49-51)ggT>ggC	p.G17G	MYLK-AS1_ENST00000463408.1_RNA|MYLK-AS1_ENST00000485162.1_RNA|MYLK-AS1_ENST00000470449.1_RNA	NM_198402.3	NP_940684.1	Q6Y1H2	HACD2_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b	17	Poly-Gly.				fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			kidney(2)	2				GBM - Glioblastoma multiforme(114;0.1)		cggccctgccaccgccgcccc	0.716													A|||	948	0.189297	0.211	0.2349	5008	,	,		9329	0.372		0.007	False		,,,				2504	0.1268															0			3						A		201,2695		1,199,1248	2	4	4		51	-0.6	0.4	3	dbSNP_132	4	22,6828		0,22,3403	no	coding-synonymous	PTPLB	NM_198402.3		1,221,4651	GG,GA,AA		0.3212,6.9406,2.2881		17/255	123303824	223,9523	1448	3425	4873	124786514	SO:0001819	synonymous_variant	201562			AK074605	CCDS46895.1	3q21.1	2010-04-30			ENSG00000206527	ENSG00000206527			9640	protein-coding gene	gene with protein product		615939				15024066	Standard	NM_198402		Approved		uc003egj.2	Q6Y1H2	OTTHUMG00000159529	ENST00000383657.5:c.51T>C	3.37:g.123303824A>G			124786514		Silent	SNP	ENST00000383657.5	37	CCDS46895.1																																																																																				0.716	PTPLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356021.3	NM_198402		G	123303824	A	G	123303824	2	3	92	1	0	0	0	0	0	0	0	1	12812	146	6	4		4	PTPLB	3	123303824	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	3	123303824	74718606	53	25150	30	2								
BCHE	590	hgsc.bcm.edu	37	chr3	165548173	165548173	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aaagagagttacacttttagGatttccaccaaaggctgcta	8	8	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:165548173G>T	ENST00000264381.3	-	2	815	c.649C>A	c.(649-651)Cct>Act	p.P217T	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	217					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	ACACTTTTAGGATTTCCACCA	0.443																																																0			3											80	85	84					3																	165548173		2203	4300	6503	167030867	SO:0001583	missense	590			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.649C>A	3.37:g.165548173G>T	ENSP00000264381:p.Pro217Thr		167030867	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911488	0.52439	.	.	ENSG00000114200	ENST00000264381	D	0.97303	-4.33	5.71	4.83	0.62350	Carboxylesterase, type B (1);	0.051366	0.85682	D	0.000000	D	0.98918	0.9633	H	0.97852	4.09	0.80722	D	1	D	0.67145	0.996	D	0.63597	0.916	D	0.98951	1.0794	10	0.87932	D	0	.	14.222	0.65833	0.0729:0.0:0.9271:0.0	.	217	P06276	CHLE_HUMAN	T	217	ENSP00000264381:P217T	ENSP00000264381:P217T	P	-	1	0	BCHE	167030867	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.513000	0.53414	2.699000	0.92147	0.655000	0.94253	CCT		0.443	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			T	165548173	G	T	165548173	3	4	92	1	0	0	0	0	1	0	0	0	1359	1174	41	2	1171	2	BCHE	3	165548173	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	42244349	165548173	32474257	54	25151										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952055	178952055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aactgagcaagaggctttggAgtatttcatgaaacaaatga	10	5	1	4			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:178952055A>G	ENST00000263967.3	+	21	3267	c.3110A>G	c.(3109-3111)gAg>gGg	p.E1037G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1037	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E1037G(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAGGCTTTGGAGTATTTCATG	0.388		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	lung(1)	3											96	85	88					3																	178952055		1890	4125	6015	180434749	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3110A>G	3.37:g.178952055A>G	ENSP00000263967:p.Glu1037Gly		180434749	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754595	0.49362	.	.	ENSG00000121879	ENST00000263967	D	0.81579	-1.51	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.052942	0.85682	D	0.000000	T	0.76521	0.3999	L	0.50333	1.59	0.80722	D	1	B	0.28713	0.22	B	0.21151	0.033	T	0.73855	-0.3851	10	0.46703	T	0.11	-21.2643	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1037	P42336	PK3CA_HUMAN	G	1037	ENSP00000263967:E1037G	ENSP00000263967:E1037G	E	+	2	0	PIK3CA	180434749	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	GAG		0.388	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952055	A	G	178952055	3	3	92	1	0	0	0	0	1	0	0	0	11944	304	11	4	3188	4	PIK3CA	3	178952055	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	13403882	178952055	19070375	55	25152										
HTR3E	285242	hgsc.bcm.edu	37	chr3	183824299	183824299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggcagatgccgggccctgcgGaggcagagctgacagggggc	20	11	0	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:183824299G>A	ENST00000415389.2	+	9	1655	c.1189G>A	c.(1189-1191)Gag>Aag	p.E397K	HTR3E_ENST00000425359.2_Missense_Mutation_p.E382K|HTR3E_ENST00000440596.2_Missense_Mutation_p.E423K|HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000436361.2_Missense_Mutation_p.E397K|HTR3E_ENST00000335304.2_Missense_Mutation_p.E412K	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	397					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GGGCCCTGCGGAGGCAGAGCT	0.612																																					Melanoma(7;227 727 6634 44770)											0			3											55	54	54					3																	183824299		2203	4300	6503	185306993	SO:0001583	missense	285242			AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24005	protein-coding gene	gene with protein product		610123	"5-hydroxytryptamine (serotonin) receptor 3, family member E"			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.1189G>A	3.37:g.183824299G>A	ENSP00000401444:p.Glu397Lys		185306993	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	.	.	.	.	.	.	.	.	.	.	g	10.40	1.340854	0.24339	.	.	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	4.07	-0.979	0.10276	Neurotransmitter-gated ion-channel transmembrane domain (1);	1.143130	0.07064	N	0.834192	T	0.80093	0.4560	L	0.53729	1.69	0.09310	N	1	B;B;B;B;B	0.26120	0.018;0.102;0.142;0.083;0.142	B;B;B;B;B	0.37550	0.055;0.252;0.253;0.163;0.163	T	0.66712	-0.5854	10	0.39692	T	0.17	.	5.0498	0.14503	0.3542:0.0:0.505:0.1408	.	423;397;397;412;382	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	K	397;382;412;397;423	ENSP00000401444:E397K;ENSP00000401900:E382K;ENSP00000335511:E412K;ENSP00000395833:E397K;ENSP00000406050:E423K	ENSP00000335511:E412K	E	+	1	0	HTR3E	185306993	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.300000	0.08243	-0.371000	0.08004	-1.731000	0.00696	GAG		0.612	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589		A	183824299	G	A	183824299	3	1	92	1	0	0	0	0	1	0	0	0	7469	1175	41	3	1264	3	HTR3E	3	183824299	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	4872244	183824299	14198131	56	25153										
KNG1	3827	hgsc.bcm.edu	37	chr3	186445055	186445055	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggattgaactttcgaattacCtactcaattgtgcaaacgaa	7	8	1	1	rs148661420		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:186445055C>T	ENST00000265023.4	+	5	806	c.594C>T	c.(592-594)acC>acT	p.T198T	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Silent_p.T198T	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	198	Cystatin kininogen-type 2. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		TTCGAATTACCTACTCAATTG	0.358																																																0			3											104	107	106					3																	186445055		2203	4300	6503	187927749	SO:0001819	synonymous_variant	3827				CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.594C>T	3.37:g.186445055C>T			187927749	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																				0.358	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		T	186445055	C	T	186445055	2	4	92	1	0	0	0	0	0	0	0	1	8448	668	24	3		3	KNG1	3	186445055	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2620756	186445055	11577375	57	25154										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10447326	10447326	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gccctttcatgtactctcttCgtgtgtttgacaatataatc	6	10	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:10447326C>A	ENST00000326756.3	-	3	1065	c.627G>T	c.(625-627)acG>acT	p.T209T		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	209					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.T209T(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GTACTCTCTTCGTGTGTTTGA	0.428																																																1	Substitution - coding silent(1)	large_intestine(1)	4											175	180	178					4																	10447326		2203	4300	6503	10056424	SO:0001819	synonymous_variant	85460			AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.627G>T	4.37:g.10447326C>A			10056424	Q96LN8	Silent	SNP	ENST00000326756.3	37	CCDS33960.1																																																																																				0.428	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		A	10447326	C	A	10447326	2	1	92	1	0	0	0	0	0	0	0	1	18002	871	31	2		2	ZNF518B	4	10447326	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10		10447326	180706950	58	25155										
SPINK2	6691	hgsc.bcm.edu	37	chr4	57677869	57677869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acctgattttcatgcacagaGtacattcattggcataagtg	8	8	2	2	rs368929102		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:57677869G>T	ENST00000248701.4	-	3	270	c.191C>A	c.(190-192)aCt>aAt	p.T64N	SPINK2_ENST00000506738.1_Missense_Mutation_p.T114N|SPINK2_ENST00000504762.1_Missense_Mutation_p.T99N	NM_021114.2	NP_066937.1	P20155	ISK2_HUMAN	serine peptidase inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)	64	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(1)|lung(2)	4	Glioma(25;0.08)|all_neural(26;0.181)					CATGCACAGAGTACATTCATT	0.378																																																0			4											135	131	132					4																	57677869		2203	4300	6503	57372626	SO:0001583	missense	6691			BC022514	CCDS3508.1, CCDS63971.1, CCDS63972.1, CCDS75128.1	4q12	2011-08-31	2005-08-17		ENSG00000128040	ENSG00000128040		"Serine peptidase inhibitors, Kazal type"	11245	protein-coding gene	gene with protein product		605753	"serine protease inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)"			8428671	Standard	NM_001271718		Approved	HUSI-II	uc031sep.1	P20155	OTTHUMG00000128769	ENST00000248701.4:c.191C>A	4.37:g.57677869G>T	ENSP00000248701:p.Thr64Asn		57372626	Q6FGH2	Missense_Mutation	SNP	ENST00000248701.4	37	CCDS3508.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788921	0.49997	.	.	ENSG00000128040	ENST00000248701;ENST00000506738;ENST00000504762	T;T;T	0.74947	-0.89;-0.89;-0.89	5.35	4.51	0.55191	Proteinase inhibitor I1, Kazal (3);	0.524458	0.19632	N	0.109649	T	0.78880	0.4353	.	.	.	0.22629	N	0.998911	D	0.69078	0.997	P	0.62740	0.906	T	0.67608	-0.5627	9	0.25751	T	0.34	-11.6224	9.7116	0.40249	0.0925:0.0:0.9075:0.0	.	64	P20155	ISK2_HUMAN	N	64;114;99	ENSP00000248701:T64N;ENSP00000425961:T114N;ENSP00000423858:T99N	ENSP00000248701:T64N	T	-	2	0	SPINK2	57372626	0.000000	0.05858	0.764000	0.31436	0.916000	0.54674	-0.216000	0.09266	1.514000	0.48869	0.644000	0.83932	ACT		0.378	SPINK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250690.2	NM_021114		T	57677869	G	T	57677869	3	4	92	1	0	0	0	0	1	0	0	0	15099	1029	36	2	71	2	SPINK2	4	57677869	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	47230543	57677869	133476407	59	25156										
ABCG2	9429	hgsc.bcm.edu	37	chr4	89039396	89039396	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aatggagaagatgattgttcGtccctgcttagacatcctaa	9	8	0	4	rs140207606		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:89039396G>A	ENST00000237612.3	-	7	1251	c.706C>T	c.(706-708)Cga>Tga	p.R236*	ABCG2_ENST00000515655.1_Nonsense_Mutation_p.R236*	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	236	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.R236R(2)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	ATGATTGTTCGTCCCTGCTTA	0.383													G|||	1	0.000199681	0	0	5008	,	,		20066	0		0	False		,,,				2504	0.001															2	Substitution - coding silent(2)	lung(2)	4						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	127	113	118		706	3.4	0.7	4	dbSNP_134	118	4,8596	3.0+/-9.4	0,4,4296	yes	stop-gained	ABCG2	NM_004827.2		0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384		236/656	89039396	5,13001	2203	4300	6503	89258420	SO:0001587	stop_gained	9429			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.706C>T	4.37:g.89039396G>A	ENSP00000237612:p.Arg236*		89258420	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Nonsense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	40	8.135799	0.98670	2.27E-4	4.65E-4	ENSG00000118777	ENST00000515655;ENST00000237612	.	.	.	5.45	3.42	0.39159	.	0.104263	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8846	11.8864	0.52604	0.0:0.0:0.4387:0.5613	.	.	.	.	X	236	.	ENSP00000237612:R236X	R	-	1	2	ABCG2	89258420	0.977000	0.34250	0.716000	0.30569	0.992000	0.81027	1.715000	0.37971	1.409000	0.46915	0.655000	0.94253	CGA		0.383	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		A	89039396	G	A	89039396	4	1	92	1	0	0	0	0	0	1	0	0	69	1153	40	1	1301	1	ABCG2	4	89039396	Nonsense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	31361527	89039396	102114880	60	25157										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153244185	153244185	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctccaatgtgactaggtttcGaataaattcacccgttttca	6	10	2	1	rs144247898		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:153244185G>A	ENST00000281708.4	-	12	3201	c.1972C>T	c.(1972-1974)Cga>Tga	p.R658*	RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R658*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.R578*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.R482*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.R540*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R658*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	658					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R658*(3)|p.R578*(1)|p.?(1)|p.R419*(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTAGGTTTCGAATAAATTCA	0.473			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	6	Substitution - Nonsense(5)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	4											167	164	165					4																	153244185		2203	4300	6503	153463635	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1972C>T	4.37:g.153244185G>A	ENSP00000281708:p.Arg658*		153463635	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.698056	0.88830	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	5.67	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7715	15.907	0.79439	0.0:0.0:0.8635:0.1365	.	.	.	.	X	658;540;578;482	.	ENSP00000263981:R578X	R	-	1	2	FBXW7	153463635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.632000	0.74281	1.377000	0.46286	0.655000	0.94253	CGA		0.473	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153244185	G	A	153244185	4	1	92	1	0	0	0	0	0	1	0	0	5788	1066	37	1	155	1	FBXW7	4	153244185	Nonsense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	64204789	153244185	37910091	61	25158										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156377	155156377	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agtttccccagataggcaggAgagctggtctgagtccctcg	13	11	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:155156377A>G	ENST00000357232.4	-	25	8061	c.8062T>C	c.(8062-8064)Tcc>Ccc	p.S2688P		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2688					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GATAGGCAGGAGAGCTGGTCT	0.552																																																0			4											82	73	76					4																	155156377		2203	4300	6503	155375827	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8062T>C	4.37:g.155156377A>G	ENSP00000349768:p.Ser2688Pro		155375827	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.429414	0.83776	.	.	ENSG00000197410	ENST00000357232	T	0.63255	-0.03	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000002	T	0.80182	0.4576	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82566	-0.0393	10	0.59425	D	0.04	.	15.6877	0.77424	1.0:0.0:0.0:0.0	.	2688	Q6V1P9	PCD23_HUMAN	P	2688	ENSP00000349768:S2688P	ENSP00000349768:S2688P	S	-	1	0	DCHS2	155375827	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.369000	0.79578	2.101000	0.63845	0.377000	0.23210	TCC		0.552	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155156377	A	G	155156377	3	3	92	1	0	0	0	0	1	0	0	0	4294	304	11	4	692	4	DCHS2	4	155156377	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	1912192	155156377	35997899	62	25159										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67589614	67589614	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aacactcagtttcaagaaaaAagtcgagaatatgatagatt	7	5	2	4			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:67589614A>G	ENST00000521381.1	+	11	1993	c.1377A>G	c.(1375-1377)aaA>aaG	p.K459K	PIK3R1_ENST00000396611.1_Silent_p.K459K|PIK3R1_ENST00000521657.1_Silent_p.K459K|PIK3R1_ENST00000523872.1_Silent_p.K96K|PIK3R1_ENST00000336483.5_Silent_p.K189K|PIK3R1_ENST00000320694.8_Silent_p.K159K|PIK3R1_ENST00000274335.5_Silent_p.K459K	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	459					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.K459_S460>N(1)|p.0?(1)|p.?(1)|p.F456_R461>S(1)|p.F456_R461del(1)|p.Q457_R461del(1)|p.T454_D464del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTCAAGAAAAAAGTCGAGAAT	0.274			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	7	Deletion - In frame(3)|Complex - deletion inframe(2)|Whole gene deletion(1)|Unknown(1)	endometrium(4)|large_intestine(1)|lung(1)|central_nervous_system(1)	5											45	49	48					5																	67589614		2186	4266	6452	67625370	SO:0001819	synonymous_variant	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1377A>G	5.37:g.67589614A>G			67625370	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																				0.274	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67589614	A	G	67589614	2	3	92	1	0	0	0	0	0	0	0	1	11949	11	1	4		4	PIK3R1	5	67589614	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10		67589614	113325646	63	25160										
NAIP	4671	hgsc.bcm.edu	37	chr5	70308329	70308329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agattcttcacccttatgtcGtacttggcaatgttaccaac	6	11	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:70308329G>A	ENST00000517649.1	-	4	704	c.414C>T	c.(412-414)taC>taT	p.Y138Y	NAIP_ENST00000508426.2_Silent_p.Y138Y|NAIP_ENST00000194097.4_Silent_p.Y138Y|NAIP_ENST00000503719.2_Intron|NAIP_ENST00000523981.1_Intron	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	138					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)	p.Y138Y(1)		central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CCCTTATGTCGTACTTGGCAA	0.483																																																1	Substitution - coding silent(1)	central_nervous_system(1)	5											213	174	187					5																	70308329		2202	4296	6498	70344085	SO:0001819	synonymous_variant	4671			U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.414C>T	5.37:g.70308329G>A			70344085	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Silent	SNP	ENST00000517649.1	37	CCDS4009.1																																																																																				0.483	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		A	70308329	G	A	70308329	2	1	92	1	0	0	0	0	0	0	0	1	10177	1140	40	1		1	NAIP	5	70308329	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	2718715	70308329	110606931	64	25161										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96130819	96130819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gagtcaccgcagcatccagtGcataatctgcttgatttatc	8	11	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:96130819G>A	ENST00000443439.2	-	5	911	c.845C>T	c.(844-846)gCa>gTa	p.A282V	ERAP1_ENST00000296754.3_Missense_Mutation_p.A282V	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	282					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		AGCATCCAGTGCATAATCTGC	0.403																																																0			5											76	70	72					5																	96130819		2203	4300	6503	96156575	SO:0001583	missense	51752			AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.845C>T	5.37:g.96130819G>A	ENSP00000406304:p.Ala282Val		96156575	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	G	35	5.545215	0.96488	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.03580	3.88;3.88	5.91	5.91	0.95273	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.27349	0.0671	M	0.91090	3.175	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.75484	0.986;0.971;0.95	T	0.05007	-1.0912	10	0.87932	D	0	.	19.8836	0.96906	0.0:0.0:1.0:0.0	.	282;282;282	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	V	282	ENSP00000296754:A282V;ENSP00000406304:A282V	ENSP00000296754:A282V	A	-	2	0	ERAP1	96156575	1.000000	0.71417	0.990000	0.47175	0.977000	0.68977	9.261000	0.95576	2.791000	0.96007	0.650000	0.86243	GCA		0.403	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		A	96130819	G	A	96130819	3	1	92	1	0	0	0	0	1	0	0	0	5216	1319	46	3	2073	3	ERAP1	5	96130819	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	25822490	96130819	84784441	65	25162										
APC	324	hgsc.bcm.edu	37	chr5	112174633	112174633	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aatggttcagaaacaaatcgAgtgggttctaatcatggaat	10	5	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:112174633A>G	ENST00000457016.1	+	16	3722	c.3342A>G	c.(3340-3342)cgA>cgG	p.R1114R	APC_ENST00000508376.2_Silent_p.R1114R|APC_ENST00000257430.4_Silent_p.R1114R|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAACAAATCGAGTGGGTTCTA	0.403		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											90	82	85					5																	112174633		2202	4300	6502	112202532	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3342A>G	5.37:g.112174633A>G			112202532	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174633	A	G	112174633	2	3	92	1	0	0	0	0	0	0	0	1	763	291	11	4		4	APC	5	112174633	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	16043814	112174633	68740627	66	25163										
APC	324	hgsc.bcm.edu	37	chr5	112175271	112175271	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gagcgaagttccagcagtgtCacagcaccctagaaccaaat	9	12	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:112175271C>A	ENST00000457016.1	+	16	4360	c.3980C>A	c.(3979-3981)tCa>tAa	p.S1327*	APC_ENST00000508376.2_Nonsense_Mutation_p.S1327*|APC_ENST00000257430.4_Nonsense_Mutation_p.S1327*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1327	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			AVSQHPR -> SSVHSTLE (in Ref. 1; AAA60353/ AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1327*(4)|p.K1192fs*3(1)|p.?(1)|p.V1326fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCAGCAGTGTCACAGCACCCT	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Substitution - Nonsense(4)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(5)|soft_tissue(1)|skin(1)	5											61	64	63					5																	112175271		2202	4300	6502	112203170	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3980C>A	5.37:g.112175271C>A	ENSP00000413133:p.Ser1327*		112203170	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	34	5.366503	0.95900	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.312416	0.32518	N	0.005998	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.4033	13.3889	0.60811	0.0:0.9279:0.0:0.0721	.	.	.	.	X	1327	.	.	S	+	2	0	APC	112203170	0.701000	0.27806	0.185000	0.23176	0.118000	0.20060	5.764000	0.68826	2.861000	0.98227	0.655000	0.94253	TCA		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175271	C	A	112175271	4	1	92	1	0	0	0	0	0	1	0	0	763	838	29	2	4038	2	APC	5	112175271	Nonsense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	638	112175271	68739989	67	25164										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480582	140480582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgcaaaaccctttgcaattcGttacaaacgagctccgtatc	6	12	0	0	rs374613377		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:140480582G>A	ENST00000231130.2	+	1	349	c.349G>A	c.(349-351)Gtt>Att	p.V117I	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	117	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTTGCAATTCGTTACAAACGA	0.423																																																0			5						G	ILE/VAL	0,4406		0,0,2203	81	84	83		349	-6.6	0	5		83	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCDHB3	NM_018937.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	117/797	140480582	1,13005	2203	4300	6503	140460766	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.349G>A	5.37:g.140480582G>A	ENSP00000231130:p.Val117Ile		140460766	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927671	0.34002	0.0	1.16E-4	ENSG00000113205	ENST00000231130	T	0.46451	0.87	5.08	-6.6	0.01824	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.12092	0.0294	N	0.01284	-0.91	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20505	-1.0273	9	0.46703	T	0.11	.	3.9707	0.09452	0.1568:0.0926:0.0977:0.6529	.	117	Q9Y5E6	PCDB3_HUMAN	I	117	ENSP00000231130:V117I	ENSP00000231130:V117I	V	+	1	0	PCDHB3	140460766	0.000000	0.05858	0.010000	0.14722	0.960000	0.62799	-0.691000	0.05133	-0.738000	0.04817	0.655000	0.94253	GTT		0.423	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		A	140480582	G	A	140480582	3	1	92	1	0	0	0	0	1	0	0	0	11574	1145	40	1	351	1	PCDHB3	5	140480582	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	28305311	140480582	40434678	68	25165										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140564370	140564370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	taagcggcaccgggaccctgTcccagagctaccaatacgag	11	14	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:140564370T>C	ENST00000361016.2	+	1	3391	c.2236T>C	c.(2236-2238)Tcc>Ccc	p.S746P		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	746					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGGACCCTGTCCCAGAGCTA	0.612																																																0			5											95	100	98					5																	140564370		2203	4300	6503	140544554	SO:0001583	missense	57717			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2236T>C	5.37:g.140564370T>C	ENSP00000354293:p.Ser746Pro		140544554	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	t	12.62	1.993511	0.35131	.	.	ENSG00000196963	ENST00000361016	T	0.55760	0.5	4.12	1.48	0.22813	.	0.000000	0.33364	N	0.004990	T	0.62392	0.2424	M	0.77406	2.37	0.25780	N	0.984734	P	0.52842	0.956	P	0.58266	0.836	T	0.54397	-0.8300	10	0.48119	T	0.1	.	6.2109	0.20628	0.0:0.0871:0.2935:0.6194	.	746	Q9NRJ7	PCDBG_HUMAN	P	746	ENSP00000354293:S746P	ENSP00000354293:S746P	S	+	1	0	PCDHB16	140544554	0.004000	0.15560	0.894000	0.35097	0.104000	0.19210	1.084000	0.30828	0.001000	0.14605	0.397000	0.26171	TCC		0.612	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		C	140564370	T	C	140564370	3	2	92	1	0	0	0	0	1	0	0	0	11572	1667	58	4	2238	4	PCDHB16	5	140564370	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	83788	140564370	40350890	69	25166										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140774316	140774316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agcagagcctcgtggtggccGtccaggaccatggccagccc	14	15	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:140774316G>A	ENST00000398604.2	+	1	1936	c.1936G>A	c.(1936-1938)Gtc>Atc	p.V646I	PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	646	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGGTGGCCGTCCAGGACCA	0.672																																																0			5											29	36	34					5																	140774316		2200	4295	6495	140754500	SO:0001583	missense	9708			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1936G>A	5.37:g.140774316G>A	ENSP00000381605:p.Val646Ile		140754500	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	17.36	3.370726	0.61624	.	.	ENSG00000253767	ENST00000398604	T	0.17370	2.28	4.99	4.12	0.48240	Cadherin (4);Cadherin-like (1);	0.000000	0.28624	U	0.014696	T	0.27900	0.0687	M	0.81112	2.525	0.28986	N	0.888349	P;P	0.52692	0.861;0.955	P;P	0.47118	0.477;0.538	T	0.27773	-1.0064	10	0.72032	D	0.01	.	9.7231	0.40315	0.0786:0.1415:0.7799:0.0	.	646;646	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	I	646	ENSP00000381605:V646I	ENSP00000381605:V646I	V	+	1	0	PCDHGA8	140754500	1.000000	0.71417	0.616000	0.29078	0.885000	0.51271	3.206000	0.51098	1.129000	0.42072	0.650000	0.86243	GTC		0.672	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		A	140774316	G	A	140774316	3	1	92	1	0	0	0	0	1	0	0	0	11591	1145	40	1	1938	1	PCDHGA8	5	140774316	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	209946	140774316	40140944	70	25167										
MAPK9	5601	hgsc.bcm.edu	37	chr5	179696366	179696366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgaaaaggacggcttagttTcttgactgcaacatttatcc	8	9	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr5:179696366T>C	ENST00000452135.2	-	3	464	c.166A>G	c.(166-168)Aaa>Gaa	p.K56E	MAPK9_ENST00000347470.4_Missense_Mutation_p.K56E|MAPK9_ENST00000425491.2_Missense_Mutation_p.K56E|MAPK9_ENST00000397072.3_3'UTR|MAPK9_ENST00000539014.1_Missense_Mutation_p.K56E|MAPK9_ENST00000343111.6_Missense_Mutation_p.K56E|MAPK9_ENST00000455781.1_Missense_Mutation_p.K56E|MAPK9_ENST00000393360.3_Missense_Mutation_p.K56E			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	56	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> N (in a head & Neck squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGGCTTAGTTTCTTGACTGCA	0.348																																																0			5											108	99	102					5																	179696366		2203	4300	6503	179628972	SO:0001583	missense	5601			U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.166A>G	5.37:g.179696366T>C	ENSP00000394560:p.Lys56Glu		179628972	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Missense_Mutation	SNP	ENST00000452135.2	37	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	T	32	5.171215	0.94807	.	.	ENSG00000050748	ENST00000452135;ENST00000393360;ENST00000455781;ENST00000343111;ENST00000347470;ENST00000425491;ENST00000539014;ENST00000523583	D;D;D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89670	0.6782	M	0.64676	1.99	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0	D	0.89256	0.3594	9	.	.	.	-29.4922	16.1773	0.81862	0.0:0.0:0.0:1.0	.	56;56;56;56;56	P45984-5;P45984-4;P45984-3;P45984-2;P45984	.;.;.;.;MK09_HUMAN	E	56	ENSP00000394560:K56E;ENSP00000377028:K56E;ENSP00000389338:K56E;ENSP00000345524:K56E;ENSP00000321410:K56E;ENSP00000397422:K56E;ENSP00000443149:K56E;ENSP00000430608:K56E	.	K	-	1	0	MAPK9	179628972	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.930000	0.87610	2.217000	0.71921	0.482000	0.46254	AAA		0.348	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			C	179696366	T	C	179696366	3	2	92	1	0	0	0	0	1	0	0	0	9317	1792	62	4	1270	4	MAPK9	5	179696366	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	38922050	179696366	1218894	71	25168										
ACOT13	55856	hgsc.bcm.edu	37	chr6	24698112	24698112	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttcttttttttacacttagaTtactcttgtctctgctgctc	4	10	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:24698112T>A	ENST00000230048.4	+	2	276	c.83T>A	c.(82-84)aTt>aAt	p.I28N	ACOT13_ENST00000537591.1_Splice_Site_p.I5N|ACOT13_ENST00000476436.1_3'UTR	NM_018473.3	NP_060943.1	Q9NPJ3	ACO13_HUMAN	acyl-CoA thioesterase 13	28					metabolic process (GO:0008152)|protein homotetramerization (GO:0051289)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA hydrolase activity (GO:0047617)			large_intestine(1)	1						TACACTTAGATTACTCTTGTC	0.383																																																0			6											62	63	63					6																	24698112		2203	4300	6503	24806091	SO:0001630	splice_region_variant	55856			AF220186	CCDS4558.1, CCDS54972.1	6p22.1	2009-11-20	2009-05-05	2009-05-05	ENSG00000112304	ENSG00000112304		"Acyl CoA thioesterases"	20999	protein-coding gene	gene with protein product		615652	"thioesterase superfamily member 2"	THEM2		16934754, 19405909	Standard	NM_018473		Approved	HT012	uc003nek.3	Q9NPJ3	OTTHUMG00000014359	ENST00000230048.4:c.82-1T>A	6.37:g.24698112T>A			24806091	F5H2L4|O95549	Missense_Mutation	SNP	ENST00000230048.4	37	CCDS4558.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.034990	0.35893	.	.	ENSG00000112304	ENST00000537591;ENST00000230048	.	.	.	5.03	5.03	0.67393	Phenylacetic acid degradation-related protein (1);	0.207799	0.42821	D	0.000653	T	0.33527	0.0866	L	0.29908	0.895	0.34975	D	0.753482	P;B	0.47545	0.897;0.296	B;B	0.43990	0.438;0.1	T	0.43686	-0.9376	9	0.87932	D	0	-14.6569	14.9189	0.70818	0.0:0.0:0.0:1.0	.	5;28	F5H2L4;Q9NPJ3	.;ACO13_HUMAN	N	5;28	.	ENSP00000230048:I28N	I	+	2	0	ACOT13	24806091	1.000000	0.71417	0.872000	0.34217	0.399000	0.30720	6.978000	0.76147	2.107000	0.64212	0.533000	0.62120	ATT		0.383	ACOT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040010.2	NM_018473	Missense_Mutation	A	24698112	T	A	24698112	5	1	92	1	0	0	0	0	0	0	1	0	151	1507	52	5	105	5	ACOT13	6	24698112	Splice_Site	SNP	T	TCGA-CL-5918-01A-11D-1657-10		24698112	146416955	72	25169										
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054978	29054978	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agccaagccctatctgagaaGccaagtagtataaactcttt	7	10	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:29054978G>T	ENST00000377173.2	-	1	112	c.48C>A	c.(46-48)ggC>ggA	p.G16G		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						TATCTGAGAAGCCAAGTAGTA	0.393																																																0			6											77	75	76					6																	29054978		2203	4300	6503	29162957	SO:0001819	synonymous_variant	442184				CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"GPCR / Class A : Olfactory receptors"	8238	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 3 pseudogene"	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.48C>A	6.37:g.29054978G>T			29162957	B0UYQ1|Q5ST41|Q96R13	Silent	SNP	ENST00000377173.2	37	CCDS34358.1																																																																																				0.393	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			T	29054978	G	T	29054978	2	4	92	1	0	0	0	0	0	0	0	1	11021	958	34	2		2	OR2B3	6	29054978	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	4356866	29054978	142060089	73	25170										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954870	30954870	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gccaccaactctgagtccagTacgacctccagtggggccaa	10	15	1	1	rs9262377		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:30954870T>C	ENST00000376296.3	+	2	1159	c.918T>C	c.(916-918)agT>agC	p.S306S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	306	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTGAGTCCAGTACGACCTCCA	0.597																																																0			6											171	164	167					6																	30954870		2203	4300	6503	31062849	SO:0001819	synonymous_variant	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.918T>C	6.37:g.30954870T>C			31062849	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																				0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954870	T	C	30954870	2	2	92	1	0	0	0	0	0	0	0	1	10007	1635	57	4		4	MUC21	6	30954870	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	1899892	30954870	140160197	74	25171										
DAXX	1616	hgsc.bcm.edu	37	chr6	33287445	33287445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccagggtcagctcctcaggcTgttctccattgctttcagca	9	14	4	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:33287445T>C	ENST00000374542.5	-	6	1856	c.1652A>G	c.(1651-1653)cAg>cGg	p.Q551R	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000414083.2_Missense_Mutation_p.Q476R|DAXX_ENST00000266000.6_Missense_Mutation_p.Q551R|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	551	Asp/Glu-rich (acidic).|Interaction with MAP3K5.|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						CTCCTCAGGCTGTTCTCCATT	0.537			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	0			6											102	96	98					6																	33287445		2203	4300	6503	33395423	SO:0001583	missense	1616			AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1652A>G	6.37:g.33287445T>C	ENSP00000363668:p.Gln551Arg		33395423	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	37	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	T	6.196	0.404265	0.11754	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083	.	.	.	4.69	-0.474	0.12108	.	1.119060	0.06748	N	0.779578	T	0.06325	0.0163	N	0.13043	0.29	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.35126	-0.9801	9	0.29301	T	0.29	-4.0E-4	4.1187	0.10095	0.0:0.2832:0.1748:0.5421	.	563;551	B4E1C1;Q9UER7	.;DAXX_HUMAN	R	551;551;476	.	ENSP00000266000:Q551R	Q	-	2	0	DAXX	33395423	0.001000	0.12720	0.000000	0.03702	0.731000	0.41821	-0.082000	0.11304	-0.223000	0.09943	-0.432000	0.05891	CAG		0.537	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			C	33287445	T	C	33287445	3	2	92	1	0	0	0	0	1	0	0	0	4249	1580	55	4	582	4	DAXX	6	33287445	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	2332575	33287445	137827622	75	25172										
TULP1	7287	hgsc.bcm.edu	37	chr6	35480009	35480009	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cagggggattcgggggcctcCgtcctcttcttccttagcct	12	14	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:35480009C>T	ENST00000229771.6	-	3	217	c.138G>A	c.(136-138)acG>acA	p.T46T	TULP1_ENST00000322263.4_Silent_p.T46T	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	46					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						CGGGGGCCTCCGTCCTCTTCT	0.726																																					GBM(55;1027 1091 11115 23439)											0			6											4	5	5					6																	35480009		1925	3932	5857	35587987	SO:0001819	synonymous_variant	7287			U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.138G>A	6.37:g.35480009C>T			35587987	O43536|Q5TGM5|Q8N571	Silent	SNP	ENST00000229771.6	37	CCDS4807.1																																																																																				0.726	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			T	35480009	C	T	35480009	2	4	92	1	0	0	0	0	0	0	0	1	16813	639	23	1		1	TULP1	6	35480009	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2192564	35480009	135635058	76	25173										
C6orf222	389384	hgsc.bcm.edu	37	chr6	36298051	36298051	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttcctgagggctggctccccTgctgcttccaggggctccgg	14	15	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:36298051T>C	ENST00000437635.2	-	2	594	c.417A>G	c.(415-417)gcA>gcG	p.A139A		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	139										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						CTGGCTCCCCTGCTGCTTCCA	0.627																																																0			6											76	66	69					6																	36298051		2203	4300	6503	36406029	SO:0001819	synonymous_variant	389384				CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.417A>G	6.37:g.36298051T>C			36406029	B2RTY8	Silent	SNP	ENST00000437635.2	37	CCDS34439.1																																																																																				0.627	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		C	36298051	T	C	36298051	2	2	92	1	0	0	0	0	0	0	0	1	2362	1567	55	4		4	C6orf222	6	36298051	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	818042	36298051	134817016	77	25174										
TFEB	7942	hgsc.bcm.edu	37	chr6	41658889	41658889	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgttgctgcatgcgctcccgCtgctcctcctgctgcgcctg	11	17	0	0	rs1015149	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:41658889C>T	ENST00000230323.4	-	3	364	c.63G>A	c.(61-63)caG>caA	p.Q21Q	TFEB_ENST00000358871.2_Silent_p.Q35Q|TFEB_ENST00000420312.1_Silent_p.Q21Q|TFEB_ENST00000394283.1_Silent_p.Q21Q|TFEB_ENST00000373033.1_Silent_p.Q21Q|TFEB_ENST00000403298.4_Silent_p.Q21Q	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	21	Gln-rich.				autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TGCGCTCCCGCTGCTCCTCCT	0.652			T	ALPHA	renal (childhood epithelioid)						OREG0004069	type=REGULATORY REGION|Gene=TFEB|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2313	0.461861	0.5703	0.4496	5008	,	,		17967	0.4355		0.4722	False		,,,				2504	0.3405						Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	0			6						C	,	2462,1932		701,1060,436	16	14	15		63,63	5.1	1	6	dbSNP_86	15	4095,4487		987,2121,1183	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	1688,3181,1619	TT,TC,CC		47.7162,43.969,49.4682	,	21/477,21/477	41658889	6557,6419	2197	4291	6488	41766867	SO:0001819	synonymous_variant	7942			M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.63G>A	6.37:g.41658889C>T		902	41766867	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																				0.652	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			T	41658889	C	T	41658889	2	4	92	1	0	0	0	0	0	0	0	1	15840	796	28	3		3	TFEB	6	41658889	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5360838	41658889	129456178	78	25175										
MYO6	4646	hgsc.bcm.edu	37	chr6	76527363	76527363	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gacagcttaacaattgaaccCttgaatcagaaaggcaaggt	9	8	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:76527363C>G	ENST00000369977.3	+	2	238	c.99C>G	c.(97-99)ccC>ccG	p.P33P	MYO6_ENST00000369975.1_Silent_p.P33P|MYO6_ENST00000369985.4_Silent_p.P33P|MYO6_ENST00000369981.3_Silent_p.P33P	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	33					actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CAATTGAACCCTTGAATCAGA	0.408																																																0			6											74	72	72					6																	76527363		2203	4300	6503	76584083	SO:0001819	synonymous_variant	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.99C>G	6.37:g.76527363C>G			76584083	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																				0.408	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76527363	C	G	76527363	2	3	92	1	0	0	0	0	0	0	0	1	10111	668	24	5		5	MYO6	6	76527363	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	34868474	76527363	94587704	79	25176										
MRAP2	112609	hgsc.bcm.edu	37	chr6	84799159	84799159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aaccacctattgttctggaaActaagccactttcccagacc	5	14	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:84799159A>G	ENST00000257776.4	+	4	712	c.577A>G	c.(577-579)Act>Gct	p.T193A		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	193					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						TGTTCTGGAAACTAAGCCACT	0.433																																																0			6											106	112	110					6																	84799159		2203	4300	6503	84855878	SO:0001583	missense	112609			AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"chromosome 6 open reading frame 117"	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.577A>G	6.37:g.84799159A>G	ENSP00000257776:p.Thr193Ala		84855878	A8K9M1|Q8IXM9|Q8N2D1	Missense_Mutation	SNP	ENST00000257776.4	37	CCDS5001.1	.	.	.	.	.	.	.	.	.	.	A	9.769	1.172145	0.21704	.	.	ENSG00000135324	ENST00000257776	D	0.82081	-1.57	5.54	4.38	0.52667	.	0.222907	0.45867	D	0.000326	T	0.50274	0.1606	N	0.08118	0	0.23346	N	0.997867	B	0.06786	0.001	B	0.09377	0.004	T	0.49978	-0.8881	10	0.62326	D	0.03	-3.991	11.6491	0.51277	0.9304:0.0:0.0696:0.0	.	193	Q96G30	MRAP2_HUMAN	A	193	ENSP00000257776:T193A	ENSP00000257776:T193A	T	+	1	0	MRAP2	84855878	1.000000	0.71417	1.000000	0.80357	0.182000	0.23217	6.361000	0.73070	1.054000	0.40438	0.533000	0.62120	ACT		0.433	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409		G	84799159	A	G	84799159	3	3	92	1	0	0	0	0	1	0	0	0	9784	43	2	4	587	4	MRAP2	6	84799159	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	8271796	84799159	86315908	80	25177										
LATS1	9113	hgsc.bcm.edu	37	chr6	149983274	149983274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cagcaccattcttgcctaagCgatcttcgggtcctcggcaa	9	14	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:149983274C>T	ENST00000543571.1	-	8	3531	c.2984G>A	c.(2983-2985)cGc>cAc	p.R995H	LATS1_ENST00000253339.5_Missense_Mutation_p.R995H	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CTTGCCTAAGCGATCTTCGGG	0.408																																																0			6											117	121	120					6																	149983274		2203	4300	6503	150024967	SO:0001583	missense	9113			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2984G>A	6.37:g.149983274C>T	ENSP00000437550:p.Arg995His		150024967		Missense_Mutation	SNP	ENST00000543571.1	37	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529913	0.85706	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.50277	0.75;0.75	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000074	T	0.74779	0.3761	M	0.93550	3.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81673	-0.0826	9	.	.	.	.	19.2848	0.94066	0.0:1.0:0.0:0.0	.	995	O95835	LATS1_HUMAN	H	995	ENSP00000437550:R995H;ENSP00000253339:R995H	.	R	-	2	0	LATS1	150024967	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.442000	0.80503	2.562000	0.86427	0.591000	0.81541	CGC		0.408	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		T	149983274	C	T	149983274	3	4	92	1	0	0	0	0	1	0	0	0	8668	768	27	1	412	1	LATS1	6	149983274	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	65184115	149983274	21131793	81	25178										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151672224	151672224	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cagcagctgtcgctgacgggAcgagggcagctaccattatt	13	11	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:151672224A>G	ENST00000253332.1	+	3	2887	c.2698A>G	c.(2698-2700)Acg>Gcg	p.T900A	AKAP12_ENST00000402676.2_Missense_Mutation_p.T900A|AKAP12_ENST00000354675.6_Missense_Mutation_p.T802A|AKAP12_ENST00000359755.5_Missense_Mutation_p.T795A			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	900					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		CGCTGACGGGACGAGGGCAGC	0.522																																					Melanoma(141;1616 1805 10049 24534 51979)											0			6											58	65	63					6																	151672224		2203	4300	6503	151713917	SO:0001583	missense	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2698A>G	6.37:g.151672224A>G	ENSP00000253332:p.Thr900Ala		151713917	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	A	6.393	0.440613	0.12104	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07216	3.21;3.21;3.22;3.22	4.98	-6.38	0.01957	.	1.482540	0.04470	N	0.375820	T	0.01353	0.0044	N	0.25890	0.77	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.003;0.001	T	0.41858	-0.9485	10	0.10902	T	0.67	.	9.984	0.41830	0.1287:0.2388:0.6325:0.0	.	795;802;900	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	A	900;900;802;795	ENSP00000384537:T900A;ENSP00000253332:T900A;ENSP00000346702:T802A;ENSP00000352794:T795A	ENSP00000253332:T900A	T	+	1	0	AKAP12	151713917	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.071000	0.14594	-1.175000	0.02751	0.459000	0.35465	ACG		0.522	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			G	151672224	A	G	151672224	3	3	92	1	0	0	0	0	1	0	0	0	448	275	10	4	2737	4	AKAP12	6	151672224	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	1688950	151672224	19442843	82	25179										
TCP1	6950	hgsc.bcm.edu	37	chr6	160209100	160209100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgtacttacaccaatatcaTccaccaacattttatccaag	3	12	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:160209100T>C	ENST00000321394.7	-	2	420	c.140A>G	c.(139-141)gAt>gGt	p.D47G	TCP1_ENST00000546023.1_5'Flank|TCP1_ENST00000420894.2_Missense_Mutation_p.D47G|SNORA29_ENST00000384183.1_RNA|TCP1_ENST00000544255.1_Intron|MRPL18_ENST00000367034.4_5'Flank|TCP1_ENST00000392168.2_Intron	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	47					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		ACCAATATCATCCACCAACAT	0.333																																																0			6											93	91	92					6																	160209100		2203	4300	6503	160129090	SO:0001583	missense	6950			X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"Heat Shock Proteins / Chaperonins"	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.140A>G	6.37:g.160209100T>C	ENSP00000317334:p.Asp47Gly		160129090	E1P5B2|Q15556|Q5TCM3	Missense_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561752	0.86335	.	.	ENSG00000120438	ENST00000321394;ENST00000420894;ENST00000539948;ENST00000537390;ENST00000536394	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.90086	0.6903	M	0.91717	3.235	0.80722	D	1	D;D	0.71674	0.998;0.97	D;P	0.85130	0.997;0.854	D	0.92499	0.6007	10	0.87932	D	0	-22.6907	14.722	0.69314	0.0:0.0:0.0:1.0	.	47;47	E7ERF2;P17987	.;TCPA_HUMAN	G	47;47;25;25;25	ENSP00000317334:D47G;ENSP00000390159:D47G;ENSP00000439671:D25G;ENSP00000437840:D25G;ENSP00000442856:D25G	ENSP00000317334:D47G	D	-	2	0	TCP1	160129090	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.907000	0.69908	1.936000	0.56123	0.528000	0.53228	GAT		0.333	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		C	160209100	T	C	160209100	3	2	92	1	0	0	0	0	1	0	0	0	15748	1435	50	4	1574	4	TCP1	6	160209100	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	8536876	160209100	10905967	83	25180										
FRMD1	79981	hgsc.bcm.edu	37	chr6	168459845	168459845	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctggcctctggtcctgacctGggtgcagggctcctgacgag	15	13	1	2	rs1548349	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr6:168459845G>C	ENST00000283309.6	-	10	1430	c.1366C>G	c.(1366-1368)Cag>Gag	p.Q456E	FRMD1_ENST00000440994.2_Missense_Mutation_p.Q388E|FRMD1_ENST00000537786.1_Missense_Mutation_p.Q227E|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	456			Q -> E (in dbSNP:rs1548349). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GTCCTGACCTGGGTGCAGGGC	0.687													C|||	4350	0.86861	0.8502	0.817	5008	,	,		15650	0.8482		0.8926	False		,,,				2504	0.9264				GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)											0			6						C	GLU/GLN,GLU/GLN	3786,592		1644,498,47	35	36	36		1162,1366	0.2	0	6	dbSNP_88	36	7717,869		3478,761,54	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	29,29	5122,1259,101	CC,CG,GG		10.1211,13.5222,11.2697	benign,benign	388/482,456/550	168459845	11503,1461	2189	4293	6482	168202694	SO:0001583	missense	79981				CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1366C>G	6.37:g.168459845G>C	ENSP00000283309:p.Gln456Glu		168202694	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	1903	0.8713369963369964	438	0.8902439024390244	286	0.7900552486187845	500	0.8741258741258742	679	0.895778364116095	C	0.003	-2.433115	0.00182	0.864778	0.898789	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.43294	0.95;0.95;0.95	2.22	0.236	0.15471	.	4.707320	0.01420	N	0.014329	T	0.03915	0.0110	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19484	-1.0304	9	0.05525	T	0.97	.	6.59	0.22642	0.0:0.3346:0.5398:0.1256	rs1548349;rs1548349	456;388;351	Q8N878;Q8N878-2;Q5SZU5	FRMD1_HUMAN;.;.	E	456;388;227	ENSP00000283309:Q456E;ENSP00000414115:Q388E;ENSP00000440078:Q227E	ENSP00000283309:Q456E	Q	-	1	0	FRMD1	168202694	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.638000	0.05452	-0.917000	0.03813	-3.273000	0.00048	CAG		0.687	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		C	168459845	G	C	168459845	3	2	92	1	0	0	0	0	1	0	0	0	6068	1357	47	5	291	5	FRMD1	6	168459845	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	8250745	168459845	2655222	84	25181										
MIOS	54468	hgsc.bcm.edu	37	chr7	7622772	7622772	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggtggaaagcagcagacatAattggagtgggttggataag	16	3	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:7622772A>C	ENST00000340080.4	+	6	1838	c.1417A>C	c.(1417-1419)Aat>Cat	p.N473H	MIOS_ENST00000461907.2_3'UTR|MIOS_ENST00000405785.1_Missense_Mutation_p.N473H	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	473						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CAGCAGACATAATTGGAGTGG	0.313																																																0			7											105	106	105					7																	7622772		1823	4075	5898	7589297	SO:0001583	missense	54468				CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.1417A>C	7.37:g.7622772A>C	ENSP00000339881:p.Asn473His		7589297	B2RTV6|O75216|Q7L551|Q9H092	Missense_Mutation	SNP	ENST00000340080.4	37	CCDS43554.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.287359	0.23478	.	.	ENSG00000164654	ENST00000340080;ENST00000405785	T;T	0.44083	0.93;0.93	5.77	4.62	0.57501	.	0.309294	0.40385	N	0.001119	T	0.20251	0.0487	N	0.11560	0.145	0.32288	N	0.566713	B	0.31910	0.346	B	0.24848	0.056	T	0.19778	-1.0295	10	0.14656	T	0.56	-15.0788	11.5201	0.50546	0.9302:0.0:0.0698:0.0	.	473	Q9NXC5	MIO_HUMAN	H	473	ENSP00000339881:N473H;ENSP00000384088:N473H	ENSP00000339881:N473H	N	+	1	0	MIOS	7589297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.622000	0.61240	2.340000	0.79590	0.528000	0.53228	AAT		0.313	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		C	7622772	A	C	7622772	3	2	92	1	0	0	0	0	1	0	0	0	9619	362	13	4	1427	4	MIOS	7	7622772	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10		7622772	151515891	85	25182										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11676072	11676072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	attggcacacctggaactccGtcaggtttggacagccagag	12	11	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:11676072G>A	ENST00000423059.4	-	2	958	c.707C>T	c.(706-708)aCg>aTg	p.T236M	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	236	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTGGAACTCCGTCAGGTTTGG	0.657										HNSCC(18;0.044)																																						0			7											32	32	32					7																	11676072		2060	4207	6267	11642597	SO:0001583	missense	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.707C>T	7.37:g.11676072G>A	ENSP00000406482:p.Thr236Met		11642597		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932674	0.73442	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.54675	0.56	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	M	0.67569	2.06	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.68379	-0.5424	10	0.40728	T	0.16	.	20.0333	0.97547	0.0:0.0:1.0:0.0	.	236	Q9UPZ6	THS7A_HUMAN	M	236	ENSP00000406482:T236M	ENSP00000262042:T236M	T	-	2	0	THSD7A	11642597	1.000000	0.71417	0.991000	0.47740	0.330000	0.28571	9.813000	0.99286	2.810000	0.96702	0.585000	0.79938	ACG		0.657	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11676072	G	A	11676072	3	1	92	1	0	0	0	0	1	0	0	0	15918	1145	40	1	4370	1	THSD7A	7	11676072	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	4053300	11676072	147462591	86	25183										
GLI3	2737	hgsc.bcm.edu	37	chr7	42004065	42004065	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccgaggcgtggtgaggcgggAggagctatgggaaaggttct	20	6	1	1	rs75313224		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:42004065A>G	ENST00000395925.3	-	15	4690	c.4606T>C	c.(4606-4608)Tcc>Ccc	p.S1536P	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1536					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GTGAGGCGGGAGGAGCTATGG	0.582									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											101	97	98					7																	42004065		2203	4300	6503	41970590	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4606T>C	7.37:g.42004065A>G	ENSP00000379258:p.Ser1536Pro		41970590	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.792335	0.90453	.	.	ENSG00000106571	ENST00000395925	T	0.51574	0.7	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.66597	0.2805	L	0.60067	1.865	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.68754	-0.5325	10	0.87932	D	0	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	1536	P10071	GLI3_HUMAN	P	1536	ENSP00000379258:S1536P	ENSP00000379258:S1536P	S	-	1	0	GLI3	41970590	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.291000	0.96070	2.308000	0.77769	0.533000	0.62120	TCC		0.582	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		G	42004065	A	G	42004065	3	3	92	1	0	0	0	0	1	0	0	0	6459	304	11	4	140	4	GLI3	7	42004065	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	30327993	42004065	117134598	87	25184										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47937659	47937659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggtctgtctgtgagtgtccaCagcagcagggagggagacag	17	8	2	2	rs372022624		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:47937659C>T	ENST00000289672.2	-	14	2247	c.2197G>A	c.(2197-2199)Gtg>Atg	p.V733M		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	733	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TGAGTGTCCACAGCAGCAGGG	0.537																																																0			7						C	MET/VAL	0,4406		0,0,2203	99	87	91		2197	-1.8	0	7		91	1,8599	1.2+/-3.3	0,1,4299	no	missense	PKD1L1	NM_138295.3	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	733/2850	47937659	1,13005	2203	4300	6503	47904184	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2197G>A	7.37:g.47937659C>T	ENSP00000289672:p.Val733Met		47904184	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.397358	0.25205	0.0	1.16E-4	ENSG00000158683	ENST00000289672	T	0.69561	-0.41	4.76	-1.79	0.07932	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.700458	0.12892	N	0.430501	T	0.70876	0.3274	L	0.51422	1.61	0.09310	N	1	D	0.71674	0.998	D	0.74348	0.983	T	0.60475	-0.7256	10	0.72032	D	0.01	-16.8495	6.1924	0.20532	0.0:0.2909:0.1555:0.5537	.	733	Q8TDX9	PK1L1_HUMAN	M	733	ENSP00000289672:V733M	ENSP00000289672:V733M	V	-	1	0	PKD1L1	47904184	0.000000	0.05858	0.002000	0.10522	0.177000	0.22998	-0.588000	0.05774	-0.216000	0.10048	-0.154000	0.13518	GTG		0.537	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47937659	C	T	47937659	3	4	92	1	0	0	0	0	1	0	0	0	11995	478	17	3	6528	3	PKD1L1	7	47937659	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5933594	47937659	111201004	88	25185										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103958	53103958	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttcgacgggccgttgtggttCgaggtctcagacagcaaggg	16	9	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:53103958C>T	ENST00000408890.4	+	1	610	c.594C>T	c.(592-594)ttC>ttT	p.F198F		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	198								p.F198F(2)		endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CGTTGTGGTTCGAGGTCTCAG	0.667																																																2	Substitution - coding silent(2)	prostate(1)|kidney(1)	7											49	58	55					7																	53103958		1981	4145	6126	53071452	SO:0001819	synonymous_variant	285877				CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.594C>T	7.37:g.53103958C>T			53071452	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																				0.667	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53103958	C	T	53103958	2	4	92	1	0	0	0	0	0	0	0	1	12272	883	31	1		1	POM121L12	7	53103958	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5166299	53103958	106034705	89	25186										
FZD9	8326	hgsc.bcm.edu	37	chr7	72848698	72848698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgtgcgagcaggcgcgcctgCgctgcgcgcccatcatggag	16	14	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:72848698C>T	ENST00000344575.3	+	1	590	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	121	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				GGCGCGCCTGCGCTGCGCGCC	0.701																																					Pancreas(144;909 1878 36867 38226 39554)											0			7											7	7	7					7																	72848698		2044	4035	6079	72486634	SO:0001583	missense	8326			U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"GPCR / Class F : Frizzled receptors", "CD molecules"	4047	protein-coding gene	gene with protein product		601766	"frizzled (Drosophila) homolog 9", "frizzled homolog 9 (Drosophila)", "frizzled 9, seven transmembrane spanning receptor", "frizzled family receptor 9"			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.361C>T	7.37:g.72848698C>T	ENSP00000345785:p.Arg121Cys		72486634		Missense_Mutation	SNP	ENST00000344575.3	37	CCDS5548.1	.	.	.	.	.	.	.	.	.	.	c	14.87	2.665581	0.47677	.	.	ENSG00000188763	ENST00000344575	T	0.80304	-1.36	3.2	2.19	0.27852	Frizzled domain (5);	0.748628	0.11925	U	0.516296	D	0.85309	0.5667	M	0.75447	2.3	0.41406	D	0.9877	D	0.76494	0.999	P	0.61658	0.892	D	0.84166	0.0431	10	0.72032	D	0.01	.	5.3982	0.16281	0.3501:0.4657:0.1842:0.0	.	121	O00144	FZD9_HUMAN	C	121	ENSP00000345785:R121C	ENSP00000345785:R121C	R	+	1	0	FZD9	72486634	0.976000	0.34144	1.000000	0.80357	0.868000	0.49771	2.301000	0.43628	1.527000	0.49086	0.177000	0.17058	CGC		0.701	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			T	72848698	C	T	72848698	3	4	92	1	0	0	0	0	1	0	0	0	6156	768	27	1	363	1	FZD9	7	72848698	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	19744740	72848698	86289965	90	25187										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726163	91726163	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agaacaaggtcgaaacttagAgcttcaggtacttcttgaat	9	7	2	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:91726163A>G	ENST00000359028.2	+	41	10127	c.9902A>G	c.(9901-9903)gAg>gGg	p.E3301G	AKAP9_ENST00000358100.2_Missense_Mutation_p.E3247G|AKAP9_ENST00000356239.3_Missense_Mutation_p.E3297G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3301			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CGAAACTTAGAGCTTCAGGTA	0.433			T	BRAF	papillary thyroid																																		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											107	104	105					7																	91726163		2203	4300	6503	91564099	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9902A>G	7.37:g.91726163A>G	ENSP00000351922:p.Glu3301Gly		91564099	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	15.36	2.811806	0.50527	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.05580	3.52;3.52;3.59;3.42	5.56	3.21	0.36854	.	0.170707	0.28192	N	0.016253	T	0.06416	0.0165	L	0.42245	1.32	0.40521	D	0.98083	B;B;B;B;B	0.30542	0.284;0.197;0.125;0.197;0.197	B;B;B;B;B	0.30251	0.113;0.09;0.041;0.09;0.09	T	0.37009	-0.9724	10	0.33141	T	0.24	.	9.4705	0.38839	0.8543:0.0:0.1457:0.0	.	572;3301;3301;3297;3289	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	G	3297;3301;3247;3301;1143	ENSP00000348573:E3297G;ENSP00000351922:E3301G;ENSP00000350813:E3247G;ENSP00000378042:E1143G	ENSP00000348573:E3297G	E	+	2	0	AKAP9	91564099	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.894000	0.63206	0.496000	0.27904	0.533000	0.62120	GAG		0.433	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91726163	A	G	91726163	3	3	92	1	0	0	0	0	1	0	0	0	459	304	11	4	10052	4	AKAP9	7	91726163	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	18877465	91726163	67412500	91	25188										
PON3	5446	hgsc.bcm.edu	37	chr7	95001483	95001483	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tccctaaacatacaggttttAcctttgtcgatgaaaatact	5	9	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:95001483A>G	ENST00000265627.5	-	4	378		c.e4+1		PON3_ENST00000451904.1_Splice_Site|PON3_ENST00000427422.1_Splice_Site|PON1_ENST00000542556.1_Intron	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3						aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TACAGGTTTTACCTTTGTCGA	0.383																																																0			7											123	119	120					7																	95001483		2203	4299	6502	94839419	SO:0001630	splice_region_variant	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.367+1T>C	7.37:g.95001483A>G			94839419	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Splice_Site	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.283829	0.40394	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7385	0.62833	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PON3	94839419	1.000000	0.71417	1.000000	0.80357	0.330000	0.28571	7.856000	0.86956	1.989000	0.58080	0.454000	0.30748	.		0.383	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	Intron	G	95001483	A	G	95001483	5	3	92	1	0	0	0	0	0	0	1	0	12281	405	14	4	719	4	PON3	7	95001483	Splice_Site	SNP	A	TCGA-CL-5918-01A-11D-1657-10	3275320	95001483	64137180	92	25189										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98592257	98592257	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcgaaatgttactccgtggcGtttgagaaaagtggagcggt	15	6	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:98592257G>A	ENST00000359863.4	+	66	10262	c.10053G>A	c.(10051-10053)gcG>gcA	p.A3351A	TRRAP_ENST00000446306.3_Silent_p.A3340A|TRRAP_ENST00000355540.3_Silent_p.A3322A	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3351					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ACTCCGTGGCGTTTGAGAAAA	0.527																																																0			7											181	174	176					7																	98592257		2203	4300	6503	98430193	SO:0001819	synonymous_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.10053G>A	7.37:g.98592257G>A			98430193	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	6.354	0.433410	0.12045	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.11	-10.2	0.00374	.	.	.	.	.	T	0.43144	0.1234	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51601	-0.8685	4	.	.	.	.	6.1587	0.20352	0.1559:0.2906:0.4618:0.0917	.	.	.	.	H	3080	.	.	R	+	2	0	TRRAP	98430193	0.035000	0.19736	0.442000	0.26870	0.663000	0.39108	-1.009000	0.03660	-1.455000	0.01923	-0.390000	0.06520	CGT		0.527	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98592257	G	A	98592257	2	1	92	1	0	0	0	0	0	0	0	1	16641	1132	40	1		1	TRRAP	7	98592257	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	3590774	98592257	60546406	93	25190										
COG5	10466	hgsc.bcm.edu	37	chr7	106964917	106964917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tatgaaattgagaagaaagtGcctgagtaactgaattccaa	9	5	0	5			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:106964917G>A	ENST00000347053.3	-	11	1219	c.1169C>T	c.(1168-1170)gCa>gTa	p.A390V	COG5_ENST00000297135.3_Missense_Mutation_p.A390V|COG5_ENST00000393603.2_Missense_Mutation_p.A390V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	390					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						AGAAGAAAGTGCCTGAGTAAC	0.254																																																0			7											49	58	55					7																	106964917		2203	4292	6495	106752153	SO:0001583	missense	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1169C>T	7.37:g.106964917G>A	ENSP00000334703:p.Ala390Val		106752153	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	G	7.846	0.722902	0.15439	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.54479	0.57;0.57;0.57	4.71	4.71	0.59529	.	0.160698	0.53938	D	0.000042	T	0.32734	0.0839	N	0.22421	0.69	0.25924	N	0.983077	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.09143	-1.0688	10	0.17369	T	0.5	-8.122	7.2498	0.26142	0.1816:0.0:0.8184:0.0	.	390;390	Q9UP83;Q9UP83-2	COG5_HUMAN;.	V	390	ENSP00000334703:A390V;ENSP00000297135:A390V;ENSP00000377228:A390V	ENSP00000297135:A390V	A	-	2	0	COG5	106752153	0.999000	0.42202	1.000000	0.80357	0.504000	0.33889	2.474000	0.45154	2.598000	0.87819	0.650000	0.86243	GCA		0.254	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			A	106964917	G	A	106964917	3	1	92	1	0	0	0	0	1	0	0	0	3667	1319	46	3	1465	3	COG5	7	106964917	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	8372660	106964917	52173746	94	25191										
MET	4233	hgsc.bcm.edu	37	chr7	116423415	116423415	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggtcttgccagagacatgtaTgataaagaatactatagtgt	10	5	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:116423415T>C	ENST00000318493.6	+	19	3931	c.3744T>C	c.(3742-3744)taT>taC	p.Y1248Y	MET_ENST00000397752.3_Silent_p.Y1230Y|MET_ENST00000539704.1_Silent_p.Y100Y			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GAGACATGTATGATAAAGAAT	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											105	98	100					7																	116423415		1843	4094	5937	116210651	SO:0001819	synonymous_variant	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3744T>C	7.37:g.116423415T>C			116210651	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																				0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423415	T	C	116423415	2	2	92	1	0	0	0	0	0	0	0	1	9515	1471	51	4		4	MET	7	116423415	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	9458498	116423415	42715248	95	25192										
CLEC2L	154790	hgsc.bcm.edu	37	chr7	139225207	139225207	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	acacccacgaggcggtgctgGctgtgattcagagccagaag	14	11	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:139225207G>C	ENST00000422142.2	+	3	478	c.406G>C	c.(406-408)Gct>Cct	p.A136P		NM_001080511.2	NP_001073980.2	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	136	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|kidney(2)|lung(1)	5	Melanoma(164;0.233)					GGCGGTGCTGGCTGTGATTCA	0.607																																																0			7											13	17	15					7																	139225207		2001	4174	6175	138875747	SO:0001583	missense	154790			AK057548	CCDS47724.1	7q34	2011-05-18			ENSG00000236279	ENSG00000236279		"C-type lectin domain containing"	21969	protein-coding gene	gene with protein product							Standard	NM_001080511		Approved	FLJ32986	uc010lnd.3	P0C7M8	OTTHUMG00000164900	ENST00000422142.2:c.406G>C	7.37:g.139225207G>C	ENSP00000390661:p.Ala136Pro		138875747		Missense_Mutation	SNP	ENST00000422142.2	37	CCDS47724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.16|14.16	2.451577|2.451577	0.43531|0.43531	.|.	.|.	ENSG00000236279|ENSG00000236279	ENST00000422142|ENST00000521281	T|.	0.22743|.	1.94|.	4.81|4.81	3.7|3.7	0.42460|0.42460	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);|.	.|.	.|.	.|.	.|.	T|T	0.51483|0.51483	0.1677|0.1677	L|L	0.61387|0.61387	1.9|1.9	0.28061|0.28061	N|N	0.932979|0.932979	P|.	0.46142|.	0.873|.	P|.	0.54431|.	0.752|.	T|T	0.45659|0.45659	-0.9246|-0.9246	9|5	0.44086|.	T|.	0.13|.	-14.2563|-14.2563	8.867|8.867	0.35291|0.35291	0.1223:0.0:0.8777:0.0|0.1223:0.0:0.8777:0.0	.|.	136|.	P0C7M8|.	CLC2L_HUMAN|.	P|C	136|59	ENSP00000390661:A136P|.	ENSP00000390661:A136P|.	A|W	+|+	1|3	0|0	CLEC2L|CLEC2L	138875747|138875747	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.902000|0.902000	0.53008|0.53008	2.312000|2.312000	0.43726|0.43726	2.200000|2.200000	0.70718|0.70718	0.563000|0.563000	0.77884|0.77884	GCT|TGG		0.607	CLEC2L-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380878.1	NM_001080511		C	139225207	G	C	139225207	3	2	92	1	0	0	0	0	1	0	0	0	3515	1203	42	5	416	5	CLEC2L	7	139225207	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	22801792	139225207	19913456	96	25193										
BRAF	673	hgsc.bcm.edu	37	chr7	140453105	140453105	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atggatccagacaactgttcAaactgatgggacccactcca	8	12	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:140453105A>G	ENST00000288602.6	-	15	1890	c.1830T>C	c.(1828-1830)ttT>ttC	p.F610F		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAACTGTTCAAACTGATGGG	0.393		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											101	93	95					7																	140453105		2203	4300	6503	140099574	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1830T>C	7.37:g.140453105A>G			140099574	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.329577	0.24167	.	.	ENSG00000157764	ENST00000496384	.	.	.	5.65	4.51	0.55191	.	.	.	.	.	T	0.61476	0.2350	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59857	-0.7375	4	.	.	.	.	11.0818	0.48064	0.9281:0.0:0.0719:0.0	.	.	.	.	S	218	.	.	L	-	2	0	BRAF	140099574	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.309000	0.43699	2.169000	0.68431	0.529000	0.55759	TTG		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		G	140453105	A	G	140453105	2	3	92	1	0	0	0	0	0	0	0	1	1499	127	5	4		4	BRAF	7	140453105	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	1227898	140453105	18685558	97	25194										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142566734	142566734	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cccttcccctcagcagcgggAgggccagttcagcagcctgc	12	17	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:142566734A>G	ENST00000392957.2	+	16	3078	c.2291A>G	c.(2290-2292)gAg>gGg	p.E764G	EPHB6_ENST00000442129.1_Missense_Mutation_p.E764G|EPHB6_ENST00000411471.2_Missense_Mutation_p.E487G	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	764	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CAGCAGCGGGAGGGCCAGTTC	0.637																																																0			7											35	32	33					7																	142566734		2203	4300	6503	142276856	SO:0001583	missense	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.2291A>G	7.37:g.142566734A>G	ENSP00000376684:p.Glu764Gly		142276856	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	A	28.6	4.935087	0.92458	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.61627	0.09;0.09;0.09	5.56	5.56	0.83823	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47455	D	0.000239	T	0.63616	0.2526	N	0.20766	0.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69131	-0.5226	10	0.87932	D	0	.	14.8971	0.70651	1.0:0.0:0.0:0.0	.	764;487	O15197;O15197-2	EPHB6_HUMAN;.	G	764;764;487	ENSP00000376684:E764G;ENSP00000410789:E764G;ENSP00000409061:E487G	ENSP00000376684:E764G	E	+	2	0	EPHB6	142276856	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.297000	0.96120	2.112000	0.64535	0.379000	0.24179	GAG		0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			G	142566734	A	G	142566734	3	3	92	1	0	0	0	0	1	0	0	0	5191	304	11	4	2337	4	EPHB6	7	142566734	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	2113629	142566734	16571929	98	25195										
SSPO	23145	hgsc.bcm.edu	37	chr7	149482248	149482248	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgtgtgcctcctgacctctgTccctgccgtcacagtgggca	11	15	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:149482248T>C	ENST00000378016.2	+	0	2922							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTGACCTCTGTCCCTGCCGTC	0.627																																																0			7											99	106	103					7																	149482248		2183	4282	6465	149113181			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149482248T>C			149113181	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149482248	T	C	149482248	1	2	92	0	1	0	0	0	0	0	0	0	15228	1673	58	4		4	SSPO	7	149482248	RNA	SNP	T	TCGA-CL-5918-01A-11D-1657-10	6915514	149482248	9656415	99	25196										
LRRC61	65999	hgsc.bcm.edu	37	chr7	150034184	150034184	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcctccttgcgccagctagcTgtgctcaatgtctccaacaa	8	15	2	0	rs3735170	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:150034184T>C	ENST00000359623.4	+	3	822	c.234T>C	c.(232-234)gcT>gcC	p.A78A	LRRC61_ENST00000493307.1_Silent_p.A78A|LRRC61_ENST00000323078.7_Silent_p.A78A	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	78										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCAGCTAGCTGTGCTCAATG	0.647													C|||	1295	0.258586	0.2625	0.1571	5008	,	,		17325	0.2907		0.2455	False		,,,				2504	0.3057															0			7						C	,	1062,3342	697.3+/-406.2	129,804,1269	49	46	47		234,234	-7.1	0	7	dbSNP_107	47	2188,6412	681.9+/-403.8	286,1616,2398	no	coding-synonymous,coding-synonymous	LRRC61	NM_001142928.1,NM_023942.2	,	415,2420,3667	CC,CT,TT		25.4419,24.1144,24.9923	,	78/260,78/260	150034184	3250,9754	2202	4300	6502	149665117	SO:0001819	synonymous_variant	65999			BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.234T>C	7.37:g.150034184T>C			149665117	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																				0.647	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942		C	150034184	T	C	150034184	2	2	92	1	0	0	0	0	0	0	0	1	9046	1567	55	4		4	LRRC61	7	150034184	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	551936	150034184	9104479	100	25197										
ABCF2	10061	hgsc.bcm.edu	37	chr7	150921028	150921028	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggagccctaccatcctcatgAgccagccgctctgcctcttt	8	17	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr7:150921028A>G	ENST00000287844.2	-	4	649	c.540T>C	c.(538-540)gcT>gcC	p.A180A	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.A180A	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	180	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATCCTCATGAGCCAGCCGCT	0.602																																																0			7											77	71	73					7																	150921028		2203	4300	6503	150551961	SO:0001819	synonymous_variant	10061			AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.540T>C	7.37:g.150921028A>G			150551961	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																				0.602	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		G	150921028	A	G	150921028	2	3	92	1	0	0	0	0	0	0	0	1	66	291	11	4		4	ABCF2	7	150921028	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	886844	150921028	8217635	101	25198										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2807758	2807758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tacacatgtacttacataacCatctagtccccagttgtcat	4	12	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:2807758C>T	ENST00000520002.1	-	68	10867	c.10312G>A	c.(10312-10314)Ggt>Agt	p.G3438S	CSMD1_ENST00000602723.1_Missense_Mutation_p.G3261S|CSMD1_ENST00000400186.3_Missense_Mutation_p.G3261S|CSMD1_ENST00000602557.1_Missense_Mutation_p.G3438S|CSMD1_ENST00000542608.1_Missense_Mutation_p.G3260S|CSMD1_ENST00000537824.1_Missense_Mutation_p.G3437S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3438						integral component of membrane (GO:0016021)				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)		CTTACATAACCATCTAGTCCC	0.438																																																0			8											156	158	157					8																	2807758		1881	4097	5978	2795165	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10312G>A	8.37:g.2807758C>T	ENSP00000430733:p.Gly3438Ser		2795165	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.63|18.63	3.666041|3.666041	0.67700|0.67700	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.60797|.	0.16;0.82;0.84;0.16|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.74612|.	0.3739|.	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D;P;D|.	0.89917|.	1.0;0.589;1.0|.	D;B;D|.	0.87578|.	0.998;0.222;0.994|.	T|.	0.73981|.	-0.3811|.	10|.	0.87932|.	D|.	0|.	.|.	18.5955|18.5955	0.91228|0.91228	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3438;3438;3260|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	S|X	3261;3438;3299;3437;3260|2839	ENSP00000383047:G3261S;ENSP00000430733:G3438S;ENSP00000441462:G3437S;ENSP00000446243:G3260S|.	ENSP00000320445:G3299S|.	G|W	-|-	1|2	0|0	CSMD1|CSMD1	2795165|2795165	1.000000|1.000000	0.71417|0.71417	0.919000|0.919000	0.36401|0.36401	0.489000|0.489000	0.33432|0.33432	7.578000|7.578000	0.82498|0.82498	2.375000|2.375000	0.81037|0.81037	0.643000|0.643000	0.83706|0.83706	GGT|TGG		0.438	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2807758	C	T	2807758	3	4	92	1	0	0	0	0	1	0	0	0	3950	594	21	3	401	3	CSMD1	8	2807758	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		2807758	143556264	102	25199										
BLK	640	hgsc.bcm.edu	37	chr8	11420487	11420487	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cttgcatggcttttcccacaGgggccaagttccccatcaag	9	14	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:11420487G>A	ENST00000259089.4	+	12	1772		c.e12-1		RP11-148O21.2_ENST00000533322.1_RNA|BLK_ENST00000529894.1_Splice_Site	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase						B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.?(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		TTTTCCCACAGGGGCCAAGTT	0.612																																																1	Unknown(1)	lung(1)	8											67	59	62					8																	11420487		2203	4300	6503	11457896	SO:0001630	splice_region_variant	640			BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"SH2 domain containing"	1057	protein-coding gene	gene with protein product		191305	"B lymphoid tyrosine kinase"			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.1181-1G>A	8.37:g.11420487G>A			11457896	Q16291|Q96IN1	Splice_Site	SNP	ENST00000259089.4	37	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460413	0.63401	.	.	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894;ENST00000526097	.	.	.	4.22	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1153	0.81302	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BLK	11457896	1.000000	0.71417	0.962000	0.40283	0.699000	0.40488	9.312000	0.96287	2.325000	0.78763	0.455000	0.32223	.		0.612	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		Intron	A	11420487	G	A	11420487	5	1	92	1	0	0	0	0	0	0	1	0	1445	1014	35	3	1222	3	BLK	8	11420487	Splice_Site	SNP	G	TCGA-CL-5918-01A-11D-1657-10	8612729	11420487	134943535	103	25200										
NEIL2	252969	hgsc.bcm.edu	37	chr8	11637447	11637447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	caagaggggggactggagggAcccttccccgaggtaatggt	17	9	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:11637447A>G	ENST00000284503.6	+	3	1078	c.479A>G	c.(478-480)gAc>gGc	p.D160G	NEIL2_ENST00000436750.3_Missense_Mutation_p.D160G|NEIL2_ENST00000455213.2_Missense_Mutation_p.D160G|NEIL2_ENST00000403422.3_Missense_Mutation_p.D99G|NEIL2_ENST00000528323.1_Intron	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	160					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GACTGGAGGGACCCTTCCCCG	0.562								Base excision repair (BER), DNA glycosylases																																								0			8											55	58	57					8																	11637447		2203	4300	6503	11674856	SO:0001583	missense	252969			AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"nei like 2 (E. coli)"			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.479A>G	8.37:g.11637447A>G	ENSP00000284503:p.Asp160Gly		11674856	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Missense_Mutation	SNP	ENST00000284503.6	37	CCDS5984.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.771213	0.49680	.	.	ENSG00000154328	ENST00000530433;ENST00000455213;ENST00000403422;ENST00000436750;ENST00000284503;ENST00000382309	T;T;T;T	0.12879	2.64;3.42;2.64;2.64	4.72	4.72	0.59763	DNA glycosylase/AP lyase, catalytic domain (1);	0.107037	0.64402	D	0.000008	T	0.34658	0.0905	M	0.77820	2.39	0.48632	D	0.99968	D	0.89917	1.0	D	0.80764	0.994	T	0.15607	-1.0431	10	0.15952	T	0.53	-7.3673	13.8341	0.63400	1.0:0.0:0.0:0.0	.	160	Q969S2	NEIL2_HUMAN	G	160;160;99;160;160;145	ENSP00000397538:D160G;ENSP00000384070:D99G;ENSP00000394023:D160G;ENSP00000284503:D160G	ENSP00000284503:D160G	D	+	2	0	NEIL2	11674856	1.000000	0.71417	0.998000	0.56505	0.011000	0.07611	5.573000	0.67417	2.112000	0.64535	0.459000	0.35465	GAC		0.562	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		G	11637447	A	G	11637447	3	3	92	1	0	0	0	0	1	0	0	0	10350	275	10	4	490	4	NEIL2	8	11637447	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	216960	11637447	134726575	104	25201										
FGF17	8822	hgsc.bcm.edu	37	chr8	21903639	21903639	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcaaagggggagaatcacccGtctcctaattttaaccagta	9	10	2	1	rs552877908		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:21903639G>A	ENST00000359441.3	+	3	590	c.87G>A	c.(85-87)ccG>ccA	p.P29P	FGF17_ENST00000518533.1_Intron|FGF17_ENST00000521709.1_Intron	NM_003867.2	NP_003858.1	O60258	FGF17_HUMAN	fibroblast growth factor 17	29					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)	p.P29P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	8				Colorectal(74;8.48e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0618)		AGAATCACCCGTCTCCTAATT	0.557																																																1	Substitution - coding silent(1)	lung(1)	8											60	64	63					8																	21903639		2203	4300	6503	21959585	SO:0001819	synonymous_variant	8822			AB009249	CCDS6019.1	8p21.3	2005-10-30			ENSG00000158815	ENSG00000158815			3673	protein-coding gene	gene with protein product		603725				9514906, 9751161	Standard	XM_005273675		Approved	FGF-13	uc003xag.3	O60258	OTTHUMG00000097051	ENST00000359441.3:c.87G>A	8.37:g.21903639G>A			21959585	B7ZLG4|Q2M2W1	Silent	SNP	ENST00000359441.3	37	CCDS6019.1																																																																																				0.557	FGF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214154.2	NM_003867		A	21903639	G	A	21903639	2	1	92	1	0	0	0	0	0	0	0	1	5864	1132	40	1		1	FGF17	8	21903639	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	10266192	21903639	124460383	105	25202										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27650248	27650248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agcaagttgttcctaaatgtCcaaacaaaataaaaactttt	4	7	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:27650248C>T	ENST00000305188.8	+	9	1655	c.1417C>T	c.(1417-1419)Cca>Tca	p.P473S	ESCO2_ENST00000397418.2_Missense_Mutation_p.P121S	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	473					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)	p.P473S(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		TCCTAAATGTCCAAACAAAAT	0.313									SC Phocomelia syndrome																																							1	Substitution - Missense(1)	central_nervous_system(1)	8											56	56	56					8																	27650248		2203	4293	6496	27706167	SO:0001583	missense	157570	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1417C>T	8.37:g.27650248C>T	ENSP00000306999:p.Pro473Ser		27706167	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	37	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.795400	0.31777	.	.	ENSG00000171320	ENST00000305188;ENST00000397418	T;T	0.72051	-0.2;-0.62	5.82	3.08	0.35506	.	0.099413	0.64402	N	0.000001	T	0.65333	0.2681	M	0.67625	2.065	0.54753	D	0.999988	B	0.17038	0.02	B	0.15052	0.012	T	0.61317	-0.7087	10	0.87932	D	0	-2.1446	7.6757	0.28484	0.0:0.7146:0.1358:0.1497	.	473	Q56NI9	ESCO2_HUMAN	S	473;121	ENSP00000306999:P473S;ENSP00000380563:P121S	ENSP00000306999:P473S	P	+	1	0	ESCO2	27706167	1.000000	0.71417	0.814000	0.32528	0.372000	0.29890	2.756000	0.47549	0.392000	0.25172	-0.189000	0.12847	CCA		0.313	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		T	27650248	C	T	27650248	3	4	92	1	0	0	0	0	1	0	0	0	5262	855	30	3	1447	3	ESCO2	8	27650248	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5746609	27650248	118713774	106	25203										
DDHD2	23259	hgsc.bcm.edu	37	chr8	38109742	38109747	+	In_Frame_Del	DEL	AAAAAG	AAAAAG	-													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttccttactgtccgaggactAaaaagaattgatcccaacta							TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	AAAAAG	AAAAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:38109742_38109747delAAAAAG	ENST00000397166.2	+	13	2079_2084	c.1554_1559delAAAAAG	c.(1552-1560)ctaaaaaga>cta	p.KR519del	DDHD2_ENST00000529845.1_5'UTR|DDHD2_ENST00000520272.2_In_Frame_Del_p.KR519del|DDHD2_ENST00000517385.1_In_Frame_Del_p.KR138del	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	519	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TCCGAGGACTAAAAAGAATTGATCCC	0.403																																																0			8																																								38228904	SO:0001651	inframe_deletion	23259			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"Sterile alpha motif (SAM) domain containing"	29106	protein-coding gene	gene with protein product		615003	"SAM, WWE and DDHD domain containing 1"	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.1554_1559delAAAAAG	8.37:g.38109742_38109747delAAAAAG	ENSP00000380352:p.Lys519_Arg520del		38228899	B3KWV2|B3KXB5|Q9H8X7	In_Frame_Del	DEL	ENST00000397166.2	37	CCDS34883.1																																																																																				0.403	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291		-	38109747	AAAAAG	-	38109742	7	5	92	1	0	1	0	1	0	0	0	0	4333	349	13	0	1662	0	DDHD2	8	38109742	In_Frame_Del	DEL	AAAAAG	TCGA-CL-5918-01A-11D-1657-10	10459494	38109742	108254280	107	25204										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48805818	48805818	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aggctgaatggcccccgaagTacaagagggtgggctgggcc	17	10	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:48805818T>G	ENST00000314191.2	-	31	3784	c.3728A>C	c.(3727-3729)tAc>tCc	p.Y1243S	PRKDC_ENST00000338368.3_Splice_Site_p.Y1243S|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	1243					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GCCCCCGAAGTACAAGAGGGT	0.592								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											0			8											27	28	28					8																	48805818		1925	4122	6047	48968371	SO:0001630	splice_region_variant	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.3729+1A>C	8.37:g.48805818T>G			48968371	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	T	2.860	-0.236295	0.05944	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.02085	4.53;4.46	5.82	5.82	0.92795	.	0.339639	0.29376	N	0.012340	T	0.02727	0.0082	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.52320	-0.8591	7	0.19590	T	0.45	.	12.0105	0.53284	0.0:0.0691:0.0:0.9309	rs33914855	.	.	.	S	1243	ENSP00000313420:Y1243S;ENSP00000345182:Y1243S	ENSP00000313420:Y1243S	Y	-	2	0	PRKDC	48968371	0.407000	0.25352	0.006000	0.13384	0.004000	0.04260	2.872000	0.48467	2.225000	0.72522	0.477000	0.44152	TAC		0.592	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640	Missense_Mutation	G	48805818	T	G	48805818	5	3	92	1	0	0	0	0	0	0	1	0	12555	1638	57	4	8881	4	PRKDC	8	48805818	Splice_Site	SNP	T	TCGA-CL-5918-01A-11D-1657-10	10696076	48805818	97558204	108	25205										
XKR4	114786	hgsc.bcm.edu	37	chr8	56435861	56435861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tttcacagcggcagcttcccTcgtgtccctggcctgggcct	11	16	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:56435861T>C	ENST00000327381.6	+	3	1128	c.1028T>C	c.(1027-1029)cTc>cCc	p.L343P	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	343						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCAGCTTCCCTCGTGTCCCTG	0.577																																																0			8											50	48	49					8																	56435861		2203	4300	6503	56598415	SO:0001583	missense	114786			AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1028T>C	8.37:g.56435861T>C	ENSP00000328326:p.Leu343Pro		56598415	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	37	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901679	0.72754	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.70631	-0.5	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.83367	0.5239	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85064	0.0936	10	0.66056	D	0.02	-0.0365	15.9501	0.79827	0.0:0.0:0.0:1.0	.	343	Q5GH76	XKR4_HUMAN	P	343	ENSP00000328326:L343P	ENSP00000328326:L343P	L	+	2	0	XKR4	56598415	1.000000	0.71417	0.950000	0.38849	0.993000	0.82548	8.040000	0.89188	2.167000	0.68274	0.528000	0.53228	CTC		0.577	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		C	56435861	T	C	56435861	3	2	92	1	0	0	0	0	1	0	0	0	17473	1551	54	4	1038	4	XKR4	8	56435861	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	7630043	56435861	89928161	109	25206										
CA3	761	hgsc.bcm.edu	37	chr8	86358404	86358404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccttcacaaagtttgacccaTcctgcctgttcccggcatgc	7	16	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:86358404T>C	ENST00000285381.2	+	6	624	c.541T>C	c.(541-543)Tcc>Ccc	p.S181P	RP11-317J10.2_ENST00000517697.1_RNA|RP11-317J10.2_ENST00000521761.1_RNA	NM_005181.3	NP_005172.1	P07451	CAH3_HUMAN	carbonic anhydrase III, muscle specific	181					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|response to ethanol (GO:0045471)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|nickel cation binding (GO:0016151)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23					Acetazolamide(DB00819)|Zonisamide(DB00909)	GTTTGACCCATCCTGCCTGTT	0.612																																																0			8											42	35	37					8																	86358404		2203	4300	6503	86545656	SO:0001583	missense	761			AJ006473	CCDS6238.1	8q21.2	2012-10-02					4.2.1.1	"Carbonic anhydrases"	1374	protein-coding gene	gene with protein product		114750				6221502	Standard	NM_005181		Approved	Car3, CAIII	uc003ydj.3	P07451		ENST00000285381.2:c.541T>C	8.37:g.86358404T>C	ENSP00000285381:p.Ser181Pro		86545656	B2R867|B3KUC8|O60842	Missense_Mutation	SNP	ENST00000285381.2	37	CCDS6238.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711907	0.68730	.	.	ENSG00000164879	ENST00000285381;ENST00000426378	T	0.68903	-0.36	6.07	6.07	0.98685	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.208574	0.50627	D	0.000108	D	0.83376	0.5241	M	0.90977	3.165	0.41181	D	0.986237	D	0.76494	0.999	D	0.67231	0.95	D	0.86446	0.1770	10	0.59425	D	0.04	-32.084	10.9649	0.47406	0.1393:0.0:0.0:0.8607	.	181	P07451	CAH3_HUMAN	P	181;165	ENSP00000285381:S181P	ENSP00000285381:S181P	S	+	1	0	CA3	86545656	0.007000	0.16637	0.986000	0.45419	0.807000	0.45602	0.915000	0.28638	2.330000	0.79161	0.528000	0.53228	TCC		0.612	CA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381090.1	NM_005181		C	86358404	T	C	86358404	3	2	92	1	0	0	0	0	1	0	0	0	2523	1435	50	4	563	4	CA3	8	86358404	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	29922543	86358404	60005618	110	25207										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93004062	93004062	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgggctaatagtgcatggtcGcttgcttggatgttctgagt	14	6	1	1	rs200629809		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:93004062G>A	ENST00000523629.1	-	7	1250	c.796C>T	c.(796-798)Cga>Tga	p.R266*	RUNX1T1_ENST00000518844.1_Nonsense_Mutation_p.R239*|RUNX1T1_ENST00000520724.1_Nonsense_Mutation_p.R229*|RUNX1T1_ENST00000360348.2_Nonsense_Mutation_p.R229*|RUNX1T1_ENST00000436581.2_Nonsense_Mutation_p.R277*|RUNX1T1_ENST00000265814.3_Nonsense_Mutation_p.R266*|RUNX1T1_ENST00000422361.2_Nonsense_Mutation_p.R229*|RUNX1T1_ENST00000396218.1_Nonsense_Mutation_p.R239*	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	266					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GTGCATGGTCGCTTGCTTGGA	0.488																																																0			8											168	140	150					8																	93004062		2203	4300	6503	93073238	SO:0001587	stop_gained	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.796C>T	8.37:g.93004062G>A	ENSP00000428543:p.Arg266*		93073238	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Nonsense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	35	5.505842	0.96371	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7919	20.2159	0.98296	0.0:0.0:1.0:0.0	.	.	.	.	X	266;239;266;229;229;229;277;239	.	ENSP00000265814:R266X	R	-	1	2	RUNX1T1	93073238	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.256000	0.58810	2.882000	0.98803	0.655000	0.94253	CGA		0.488	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93004062	G	A	93004062	4	1	92	1	0	0	0	0	0	1	0	0	13784	1095	38	1	1042	1	RUNX1T1	8	93004062	Nonsense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	6645658	93004062	53359960	111	25208										
LAPTM4B	55353	hgsc.bcm.edu	37	chr8	98788261	98788261	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aagatggtcgcgccctggacGcggttctactccaacagctg	12	13	1	1	rs2449508	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:98788261G>T	ENST00000521545.2	+	1	258	c.24G>T	c.(22-24)acG>acT	p.T8T	RNU7-177P_ENST00000517101.1_RNA|LAPTM4B_ENST00000445593.2_Silent_p.T99T			Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta	152					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			CGCCCTGGACGCGGTTCTACT	0.716													G|||	419	0.0836661	0.0598	0.0908	5008	,	,		10836	0		0.1471	False		,,,				2504	0.1319															0			8						G		258,4118		11,236,1941	18	20	19		297	0.8	1	8	dbSNP_100	19	1359,7205		99,1161,3022	no	coding-synonymous	LAPTM4B	NM_018407.4		110,1397,4963	TT,TG,GG		15.8688,5.8958,12.4961		99/318	98788261	1617,11323	2188	4282	6470	98857437	SO:0001819	synonymous_variant	55353			AF317417	CCDS6275.1	8q22.1	2008-08-11	2008-08-11		ENSG00000104341	ENSG00000104341			13646	protein-coding gene	gene with protein product		613296					Standard	NM_018407		Approved	LC27	uc003yia.3	Q86VI4	OTTHUMG00000164740	ENST00000521545.2:c.24G>T	8.37:g.98788261G>T			98857437	Q3ZCV5|Q7L909|Q86VH8|Q9H060	Silent	SNP	ENST00000521545.2	37		168	0.07692307692307693	26	0.052845528455284556	37	0.10220994475138122	0	0.0	105	0.13852242744063326	G	4.659	0.122439	0.08931	0.058958	0.158688	ENSG00000104341	ENST00000517924	.	.	.	4.29	0.755	0.18415	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.999999999869745	.	.	.	.	.	.	T	0.15694	-1.0428	3	.	.	.	-7.5416	2.1512	0.03800	0.098:0.2843:0.2599:0.3577	rs2449508;rs4397375;rs61112322;rs2449508	.	.	.	L	62	.	.	R	+	2	0	LAPTM4B	98857437	1.000000	0.71417	0.996000	0.52242	0.001000	0.01503	0.802000	0.27069	0.269000	0.21961	-0.179000	0.13096	CGC		0.716	LAPTM4B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000380016.2			T	98788261	G	T	98788261	2	4	92	1	0	0	0	0	0	0	0	1	8647	1074	38	2		2	LAPTM4B	8	98788261	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	5784199	98788261	47575761	112	25209										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121322277	121322277	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggactccgaggaccaaagggCcagcaaggtgaaccgggtcc	15	12	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:121322277C>A	ENST00000297848.3	+	37	4701	c.4431C>A	c.(4429-4431)ggC>ggA	p.G1477G	COL14A1_ENST00000309791.4_Silent_p.G1477G|COL14A1_ENST00000247781.3_Silent_p.G1382G	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.?(1)|p.G1477G(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			GACCAAAGGGCCAGCAAGGTG	0.433																																																2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	8											154	137	143					8																	121322277		2203	4300	6503	121391458	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4431C>A	8.37:g.121322277C>A			121391458		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.433	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121322277	C	A	121322277	2	1	92	1	0	0	0	0	0	0	0	1	3677	726	26	2		2	COL14A1	8	121322277	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	22534016	121322277	25041745	113	25210										
GRINA	2907	hgsc.bcm.edu	37	chr8	145065646	145065646	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tacccacagggcccctacccAcaagagggctacccacaggg	10	17	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr8:145065646A>C	ENST00000313269.5	+	2	533	c.255A>C	c.(253-255)ccA>ccC	p.P85P	GRINA_ENST00000395068.4_Silent_p.P85P	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	85	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCCCTACCCACAAGAGGGCT	0.701																																																0			8											3	4	4					8																	145065646		1938	3792	5730	145137634	SO:0001819	synonymous_variant	2907			NM_001009184	CCDS34961.1	8q24.3	2010-03-18	2008-04-01						4589	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 3"	138251		NMDARA1		1719427, 8406459	Standard	XM_005250899		Approved	HNRGW, TMBIM3, LFG1	uc003zao.1	Q7Z429		ENST00000313269.5:c.255A>C	8.37:g.145065646A>C			145137634	B3KXM7|O43836|Q8IVW7	Silent	SNP	ENST00000313269.5	37	CCDS34961.1	.	.	.	.	.	.	.	.	.	.	a	1.503	-0.551643	0.03996	.	.	ENSG00000178719	ENST00000534791	.	.	.	4.71	-1.66	0.08265	.	.	.	.	.	T	0.48466	0.1501	.	.	.	0.51767	D	0.999938	.	.	.	.	.	.	T	0.36625	-0.9740	4	.	.	.	.	4.9489	0.14004	0.5239:0.3085:0.0:0.1676	.	.	.	.	P	9	.	.	T	+	1	0	GRINA	145137634	0.007000	0.16637	0.397000	0.26308	0.332000	0.28634	-0.637000	0.05459	-0.284000	0.09102	-2.471000	0.00202	ACA		0.701	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	NM_001009184		C	145065646	A	C	145065646	2	2	92	1	0	0	0	0	0	0	0	1	6806	146	6	4		4	GRINA	8	145065646	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	23743369	145065646	1298376	114	25211										
GLDC	2731	hgsc.bcm.edu	37	chr9	6558671	6558671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggtcccatgtgctgatttcGgaatgaggcaaacctacaga	11	9	0	3	rs201135624		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:6558671G>A	ENST00000321612.6	-	17	2090	c.1940C>T	c.(1939-1941)cCg>cTg	p.P647L	GLDC_ENST00000460457.1_5'UTR	NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	647					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TGCTGATTTCGGAATGAGGCA	0.433													G|||	1	0.000199681	0	0.0014	5008	,	,		20942	0		0	False		,,,				2504	0															0			9						G	LEU/PRO	0,4406		0,0,2203	112	100	104		1940	5.9	1	9		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	GLDC	NM_000170.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	647/1021	6558671	1,13005	2203	4300	6503	6548671	SO:0001583	missense	2731			D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1940C>T	9.37:g.6558671G>A	ENSP00000370737:p.Pro647Leu		6548671	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	37	CCDS34987.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	29.4	5.002896	0.93287	0.0	1.16E-4	ENSG00000178445	ENST00000321612	D	0.98400	-4.91	5.86	5.86	0.93980	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aromatic amino acid beta-eliminating lyase/threonine aldolase (1);	0.000000	0.85682	D	0.000000	D	0.99510	0.9825	H	0.98802	4.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98008	1.0364	10	0.87932	D	0	-17.5618	20.5632	0.99335	0.0:0.0:1.0:0.0	.	647	P23378	GCSP_HUMAN	L	647	ENSP00000370737:P647L	ENSP00000370737:P647L	P	-	2	0	GLDC	6548671	1.000000	0.71417	0.975000	0.42487	0.941000	0.58515	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	CCG		0.433	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6558671	G	A	6558671	3	1	92	1	0	0	0	0	1	0	0	0	6453	1116	39	1	1158	1	GLDC	9	6558671	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10		6558671	134654760	115	25212										
NPR2	4882	hgsc.bcm.edu	37	chr9	35801945	35801945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gggatccagttacggctcgcTcatgacagcccatgggaaat	12	11	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:35801945T>C	ENST00000342694.2	+	9	1835	c.1580T>C	c.(1579-1581)cTc>cCc	p.L527P		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	527	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TACGGCTCGCTCATGACAGCC	0.522																																																0			9											145	130	135					9																	35801945		2203	4300	6503	35791945	SO:0001583	missense	4882			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.1580T>C	9.37:g.35801945T>C	ENSP00000341083:p.Leu527Pro		35791945	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.345468	0.82022	.	.	ENSG00000159899	ENST00000342694	T	0.53423	0.62	5.51	5.51	0.81932	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38837	N	0.001547	T	0.66489	0.2794	M	0.72894	2.215	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.72075	0.976;0.968	T	0.66217	-0.5979	10	0.39692	T	0.17	.	14.7531	0.69543	0.0:0.0:0.0:1.0	.	527;527	P20594-2;P20594	.;ANPRB_HUMAN	P	527	ENSP00000341083:L527P	ENSP00000341083:L527P	L	+	2	0	NPR2	35791945	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.103000	0.71492	2.230000	0.72887	0.528000	0.53228	CTC		0.522	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			C	35801945	T	C	35801945	3	2	92	1	0	0	0	0	1	0	0	0	10626	1551	54	4	1614	4	NPR2	9	35801945	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	29243274	35801945	105411486	116	25213										
GNE	10020	hgsc.bcm.edu	37	chr9	36246115	36246115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcagcctgccaaaaggatgcGatcatggtcctcacacatgg	11	12	2	0	rs539332585	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:36246115G>A	ENST00000539815.1	-	2	569	c.529C>T	c.(529-531)Cgc>Tgc	p.R177C	GNE_ENST00000543356.2_Missense_Mutation_p.R172C|GNE_ENST00000396594.3_Missense_Mutation_p.R208C|GNE_ENST00000447283.2_Missense_Mutation_p.R177C|GNE_ENST00000377902.5_Missense_Mutation_p.R177C|GNE_ENST00000539208.1_Missense_Mutation_p.R118C			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	177			R -> C (in NM). {ECO:0000269|PubMed:12473753}.		carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			AAAAGGATGCGATCATGGTCC	0.483													G|||	2	0.000399361	0.0015	0	5008	,	,		23136	0		0	False		,,,				2504	0				GBM(184;106 2118 20004 35750 50727)											0			9											172	140	151					9																	36246115		2203	4300	6503	36236115	SO:0001583	missense	10020			AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.529C>T	9.37:g.36246115G>A	ENSP00000439155:p.Arg177Cys		36236115	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	37	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051988	0.75960	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208;ENST00000447283	D;D;D;D;D	0.99167	-5.51;-5.51;-5.51;-5.51;-5.51	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.98931	0.9637	M	0.64404	1.975	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;P;D;D	0.75484	0.917;0.942;0.851;0.966;0.986	D	0.98771	1.0728	10	0.66056	D	0.02	-24.3334	12.2485	0.54585	0.0:0.0:0.8302:0.1698	.	118;136;208;177;177	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223;A7UNU7	.;.;.;GLCNE_HUMAN;.	C	177;208;172;177;149;118;177	ENSP00000367134:R177C;ENSP00000379839:R208C;ENSP00000439155:R177C;ENSP00000445117:R118C;ENSP00000414760:R177C	ENSP00000340770:R172C	R	-	1	0	GNE	36236115	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.748000	0.62148	2.682000	0.91365	0.467000	0.42956	CGC		0.483	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		A	36246115	G	A	36246115	3	1	92	1	0	0	0	0	1	0	0	0	6542	1058	37	1	1679	1	GNE	9	36246115	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	444170	36246115	104967316	117	25214										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90301542	90301542	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cgcagcatgatgttcgagccGggtcttaccaaagggatgct	13	10	1	1	rs371530974		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:90301542G>A	ENST00000408954.3	+	21	2636	c.2301G>A	c.(2299-2301)ccG>ccA	p.P767P	DAPK1_ENST00000469640.2_Silent_p.P767P|DAPK1_ENST00000472284.1_Silent_p.P767P|DAPK1_ENST00000358077.5_Silent_p.P767P|DAPK1_ENST00000491893.1_Silent_p.P767P	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	767					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TGTTCGAGCCGGGTCTTACCA	0.587									Chronic Lymphocytic Leukemia, Familial Clustering of																																							0			9						G		0,4252		0,0,2126	80	95	90		2301	-10.3	0.2	9		90	1,8475		0,1,4237	no	coding-synonymous	DAPK1	NM_004938.2		0,1,6363	AA,AG,GG		0.0118,0.0,0.0079		767/1431	90301542	1,12727	2126	4238	6364	89491362	SO:0001819	synonymous_variant	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2301G>A	9.37:g.90301542G>A			89491362	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																				0.587	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		A	90301542	G	A	90301542	2	1	92	1	0	0	0	0	0	0	0	1	4241	1103	39	1		1	DAPK1	9	90301542	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	54055427	90301542	50911889	118	25215										
BICD2	23299	hgsc.bcm.edu	37	chr9	95484999	95484999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgttctcctcctccagttccGagtagtcctgcagcagacga	9	14	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:95484999G>A	ENST00000375512.3	-	3	612	c.545C>T	c.(544-546)tCg>tTg	p.S182L	BICD2_ENST00000356884.6_Missense_Mutation_p.S182L	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	182					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTCCAGTTCCGAGTAGTCCTG	0.577																																																0			9											133	114	120					9																	95484999		2203	4300	6503	94524820	SO:0001583	missense	23299			AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.545C>T	9.37:g.95484999G>A	ENSP00000364662:p.Ser182Leu		94524820	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Missense_Mutation	SNP	ENST00000375512.3	37	CCDS6700.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086832	0.76642	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	T;T	0.53857	0.6;0.6	4.66	4.66	0.58398	.	0.194394	0.43110	D	0.000620	T	0.52208	0.1720	L	0.56199	1.76	0.51233	D	0.999914	P;P	0.47962	0.882;0.903	B;B	0.43838	0.307;0.433	T	0.57849	-0.7740	10	0.51188	T	0.08	-7.9084	15.4221	0.75022	0.0:0.0:1.0:0.0	.	182;182	Q8TD16-2;Q8TD16	.;BICD2_HUMAN	L	182	ENSP00000349351:S182L;ENSP00000364662:S182L	ENSP00000349351:S182L	S	-	2	0	BICD2	94524820	1.000000	0.71417	0.989000	0.46669	0.926000	0.56050	5.929000	0.70096	2.319000	0.78375	0.561000	0.74099	TCG		0.577	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250		A	95484999	G	A	95484999	3	1	92	1	0	0	0	0	1	0	0	0	1430	1059	37	1	2052	1	BICD2	9	95484999	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	5183457	95484999	45728432	119	25216										
WNK2	65268	hgsc.bcm.edu	37	chr9	96021423	96021423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgtgaagctgccccaccccCctggggcgcccctggccatg	12	19	0	1	rs45534637	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:96021423C>T	ENST00000297954.4	+	11	2593	c.2593C>T	c.(2593-2595)Cct>Tct	p.P865S	WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.P477S|WNK2_ENST00000349097.3_Missense_Mutation_p.P477S|WNK2_ENST00000395477.2_Missense_Mutation_p.P865S|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	865					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GCCCCACCCCCCTGGGGCGCC	0.692													c|||	201	0.0401358	8e-04	0.17	5008	,	,		9409	0.0456		0.0338	False		,,,				2504	0.002															0			9						T	SER/PRO	32,4362		0,32,2165	15	18	17		2593	-10.2	0	9	dbSNP_127	17	207,8383		4,199,4092	yes	missense	WNK2	NM_006648.3	74	4,231,6257	TT,TC,CC		2.4098,0.7283,1.8407	benign	865/2218	96021423	239,12745	2197	4295	6492	95061244	SO:0001583	missense	65268			AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.2593C>T	9.37:g.96021423C>T	ENSP00000297954:p.Pro865Ser		95061244	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		95|95	0.043498168498168496|0.043498168498168496	1|1	0.0020325203252032522|0.0020325203252032522	44|44	0.12154696132596685|0.12154696132596685	25|25	0.043706293706293704|0.043706293706293704	25|25	0.032981530343007916|0.032981530343007916	c|c	0.011|0.011	-1.733102|-1.733102	0.00687|0.00687	0.007283|0.007283	0.024098|0.024098	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	T|T;T;T;T	0.61040|0.67698	0.14|-0.28;-0.25;0.29;0.34	5.11|5.11	-10.2|-10.2	0.00374|0.00374	.|.	1.715750|1.715750	0.03147|0.03147	N|N	0.167463|0.167463	T|T	0.00608|0.00608	0.0020|0.0020	N|N	0.08118|0.08118	0|0	0.46376|0.46376	P|P	9.900000000000464E-4|9.900000000000464E-4	.|B;B;P;B;B	.|0.41008	.|0.002;0.001;0.735;0.002;0.005	.|B;B;P;B;B	.|0.44772	.|0.001;0.001;0.46;0.001;0.003	T|T	0.46978|0.46978	-0.9152|-0.9152	6|8	.|.	.|.	.|.	.|.	0.327|0.327	0.00312|0.00312	0.3423:0.1608:0.1722:0.3246|0.3423:0.1608:0.1722:0.3246	rs45534637|rs45534637	.|865;865;468;865;865	.|Q9Y3S1-2;Q9Y3S1-4;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;.;WNK2_HUMAN	L|S	468|865;865;477;477	ENSP00000414622:P468L|ENSP00000297954:P865S;ENSP00000378860:P865S;ENSP00000297876:P477S;ENSP00000411181:P477S	.|.	P|P	+|+	2|1	0|0	WNK2|WNK2	95061244|95061244	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.112000|0.112000	0.19704|0.19704	-1.710000|-1.710000	0.01888|0.01888	-3.130000|-3.130000	0.00236|0.00236	-1.472000|-1.472000	0.01007|0.01007	CCC|CCT		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96021423	C	T	96021423	3	4	92	1	0	0	0	0	1	0	0	0	17418	623	22	3	2635	3	WNK2	9	96021423	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	536424	96021423	45192008	120	25217										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101073478	101073478	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gatggagatatcccgtcctgCtgggtccggctgtgcaaaga	14	10	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:101073478C>G	ENST00000259455.2	-	14	2362	c.1903G>C	c.(1903-1905)Gca>Cca	p.A635P		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	635					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TCCCGTCCTGCTGGGTCCGGC	0.542																																																0			9											98	79	85					9																	101073478		2203	4300	6503	100113299	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1903G>C	9.37:g.101073478C>G	ENSP00000259455:p.Ala635Pro		100113299	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.878650	0.72294	.	.	ENSG00000136928	ENST00000259455	T	0.78246	-1.16	5.39	5.39	0.77823	GPCR, family 3, C-terminal (2);	0.101929	0.64402	D	0.000002	T	0.76723	0.4027	L	0.29908	0.895	0.50313	D	0.999865	P	0.48998	0.918	P	0.52386	0.697	T	0.74830	-0.3531	10	0.31617	T	0.26	.	16.6677	0.85257	0.0:1.0:0.0:0.0	.	635	O75899	GABR2_HUMAN	P	635	ENSP00000259455:A635P	ENSP00000259455:A635P	A	-	1	0	GABBR2	100113299	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.957000	0.63652	2.526000	0.85167	0.561000	0.74099	GCA		0.542	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			G	101073478	C	G	101073478	3	3	92	1	0	0	0	0	1	0	0	0	6175	797	28	5	946	5	GABBR2	9	101073478	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	5052055	101073478	40139953	121	25218										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130075823	130075823	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtccctcaataccgtgcaatTctttggagaaaaacagtaag	8	9	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr9:130075823T>C	ENST00000373387.4	+	4	775	c.423T>C	c.(421-423)atT>atC	p.I141I	GARNL3_ENST00000435213.2_Silent_p.I119I|GARNL3_ENST00000314904.5_Silent_p.I141I	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	141					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						ACCGTGCAATTCTTTGGAGAA	0.433																																																0			9											173	157	162					9																	130075823		2203	4300	6503	129115644	SO:0001819	synonymous_variant	84253			BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.423T>C	9.37:g.130075823T>C			129115644	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Silent	SNP	ENST00000373387.4	37	CCDS6869.2																																																																																				0.433	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		C	130075823	T	C	130075823	2	2	92	1	0	0	0	0	0	0	0	1	6261	1771	62	4		4	GARNL3	9	130075823	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	29002345	130075823	11137608	122	25219										
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20357162	20357162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tacgtgaaatcactgtggcaAccgggggtaagtggttttct	13	7	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:20357162A>G	ENST00000377252.4	+	4	1376	c.535A>G	c.(535-537)Acc>Gcc	p.T179A	PLXDC2_ENST00000377242.3_Missense_Mutation_p.T130A|RP11-575A19.2_ENST00000451584.1_RNA|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	179					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						CACTGTGGCAACCGGGGGTAA	0.358																																																0			10											81	76	77					10																	20357162		2203	4300	6503	20397168	SO:0001583	missense	84898			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.535A>G	10.37:g.20357162A>G	ENSP00000366460:p.Thr179Ala		20397168	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211204	0.58343	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	T;T	0.79653	-1.29;-1.29	5.85	5.85	0.93711	.	0.086767	0.85682	D	0.000000	T	0.81297	0.4793	M	0.75150	2.29	0.80722	D	1	B;B	0.32620	0.378;0.26	B;B	0.32928	0.155;0.08	T	0.81267	-0.1010	10	0.52906	T	0.07	.	16.2948	0.82765	1.0:0.0:0.0:0.0	.	130;179	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	A	179;130;42;165	ENSP00000366460:T179A;ENSP00000366450:T130A	ENSP00000366446:T42A	T	+	1	0	PLXDC2	20397168	1.000000	0.71417	1.000000	0.80357	0.527000	0.34593	8.404000	0.90210	2.253000	0.74438	0.456000	0.33151	ACC		0.358	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		G	20357162	A	G	20357162	3	3	92	1	0	0	0	0	1	0	0	0	12149	43	2	4	549	4	PLXDC2	10	20357162	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10		20357162	115177585	123	25220										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999030	46999030	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agcagcaccgtgtggcaggcCcagctgggcgaggccagcac	16	14	0	0	rs4925989	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:46999030C>T	ENST00000374317.1	+	3	423	c.150C>T	c.(148-150)gcC>gcT	p.A50A	GPRIN2_ENST00000374314.4_Silent_p.A50A	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	50										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TGTGGCAGGCCCAGCTGGGCG	0.697																																																0			10											29	37	35					10																	46999030		2199	4292	6491	46419036	SO:0001819	synonymous_variant	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.150C>T	10.37:g.46999030C>T			46419036	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																				0.697	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		T	46999030	C	T	46999030	2	4	92	1	0	0	0	0	0	0	0	1	6751	610	22	3		3	GPRIN2	10	46999030	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	26641868	46999030	88535717	124	25221										
MAPK8	5599	hgsc.bcm.edu	37	chr10	49628294	49628294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	caggaacgagttttatgatgAcgccttatgtagtgactcgc	11	8	0	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:49628294A>G	ENST00000374189.1	+	6	728	c.547A>G	c.(547-549)Acg>Gcg	p.T183A	MAPK8_ENST00000374174.1_Missense_Mutation_p.T183A|MAPK8_ENST00000374182.3_Missense_Mutation_p.T183A|MAPK8_ENST00000360332.3_Missense_Mutation_p.T183A|MAPK8_ENST00000395611.3_Missense_Mutation_p.T183A			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	183	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		TTTTATGATGACGCCTTATGT	0.428																																																0			10											153	144	147					10																	49628294		2203	4300	6503	49298300	SO:0001583	missense	5599			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.547A>G	10.37:g.49628294A>G	ENSP00000363304:p.Thr183Ala		49298300	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195707	0.78902	.	.	ENSG00000107643	ENST00000374189;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000374174;ENST00000395611	T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	5.47	5.47	0.80525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73560	0.3602	M	0.85373	2.75	0.80722	D	1	B;B;B;B;B	0.33103	0.397;0.072;0.088;0.037;0.029	B;B;B;B;B	0.38327	0.271;0.135;0.212;0.212;0.135	T	0.74349	-0.3694	9	.	.	.	.	15.8531	0.78952	1.0:0.0:0.0:0.0	.	183;183;183;183;183	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	A	183	ENSP00000363304:T183A;ENSP00000363297:T183A;ENSP00000363294:T183A;ENSP00000353483:T183A;ENSP00000363291:T183A;ENSP00000363289:T183A;ENSP00000378974:T183A	.	T	+	1	0	MAPK8	49298300	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.203000	0.70933	0.533000	0.62120	ACG		0.428	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			G	49628294	A	G	49628294	3	3	92	1	0	0	0	0	1	0	0	0	9313	275	10	4	565	4	MAPK8	10	49628294	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	2629264	49628294	85906453	125	25222										
CCDC6	8030	hgsc.bcm.edu	37	chr10	61552765	61552765	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgggctgcatgggtggcggAggtggaggcggaggtggctg	25	5	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:61552765A>G	ENST00000263102.6	-	9	1566	c.1335T>C	c.(1333-1335)ccT>ccC	p.P445P		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	445	Poly-Pro.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TGGGTGGCGGAGGTGGAGGCG	0.627			T	RET	NSCLC																																		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	0			10											151	141	145					10																	61552765		2203	4300	6503	61222771	SO:0001819	synonymous_variant	8030			S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"	601985	"DNA segment on chromosome 10 (unique) 170"	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1335T>C	10.37:g.61552765A>G			61222771	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																				0.627	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		G	61552765	A	G	61552765	2	3	92	1	0	0	0	0	0	0	0	1	2836	291	11	4		4	CCDC6	10	61552765	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	11924471	61552765	73981982	126	25223										
CHUK	1147	hgsc.bcm.edu	37	chr10	101980420	101980420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	attttgttttcatgcaaataTcgaatcccagaccctaaata	4	9	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:101980420T>C	ENST00000370397.7	-	5	485	c.399A>G	c.(397-399)cgA>cgG	p.R133R		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CATGCAAATATCGAATCCCAG	0.303																																					Ovarian(159;52 1904 10536 35305 37148)											0			10											79	78	78					10																	101980420		2203	4298	6501	101970410	SO:0001819	synonymous_variant	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.399A>G	10.37:g.101980420T>C			101970410	O14666|Q13132|Q5W0I4|Q92467	Silent	SNP	ENST00000370397.7	37	CCDS7488.1																																																																																				0.303	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101980420	T	C	101980420	2	2	92	1	0	0	0	0	0	0	0	1	3422	1422	50	4		4	CHUK	10	101980420	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	40427655	101980420	33554327	127	25224										
PSD	5662	hgsc.bcm.edu	37	chr10	104176584	104176584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cacggggtgagggggggccaCgcagaggtgtacagggtgct	21	8	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:104176584C>T	ENST00000020673.5	-	2	738	c.212G>A	c.(211-213)cGt>cAt	p.R71H	PSD_ENST00000406432.1_Missense_Mutation_p.R71H|PSD_ENST00000492902.2_5'UTR|FBXL15_ENST00000224862.3_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	71	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		GGGGGGGCCACGCAGAGGTGT	0.672																																																0			10											39	43	42					10																	104176584		2197	4288	6485	104166574	SO:0001583	missense	79176			X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.212G>A	10.37:g.104176584C>T	ENSP00000020673:p.Arg71His		104166574	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	37	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452370	0.63290	.	.	ENSG00000059915	ENST00000020673;ENST00000406432	T;T	0.26810	1.71;1.71	5.08	3.14	0.36123	.	0.205230	0.27876	N	0.017489	T	0.17280	0.0415	N	0.08118	0	0.27662	N	0.947057	D	0.54047	0.964	P	0.47744	0.556	T	0.05500	-1.0881	10	0.66056	D	0.02	.	10.5792	0.45246	0.1505:0.7046:0.1449:0.0	.	71	A5PKW4	PSD1_HUMAN	H	71	ENSP00000020673:R71H;ENSP00000384830:R71H	ENSP00000020673:R71H	R	-	2	0	PSD	104166574	1.000000	0.71417	0.880000	0.34516	0.986000	0.74619	3.738000	0.55067	0.495000	0.27882	0.561000	0.74099	CGT		0.672	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			T	104176584	C	T	104176584	3	4	92	1	0	0	0	0	1	0	0	0	12680	536	19	1	2926	1	PSD	10	104176584	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2196164	104176584	31358163	128	25225										
GSTO1	9446	hgsc.bcm.edu	37	chr10	106022834	106022834	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agaatttaccaagctagaggAggtaattatttctcctagct	8	7	1	2	rs200549805		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:106022834A>T	ENST00000369713.5	+	4	658	c.464A>T	c.(463-465)gAg>gTg	p.E155V	GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000369710.4_Intron|GSTO1_ENST00000539281.1_Splice_Site_p.E127V	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	155	GST C-terminal.		Missing (in allele GSTO1*B; decreased protein stability). {ECO:0000269|PubMed:12618591, ECO:0000269|PubMed:12928150}.		cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	AAGCTAGAGGAGGTAATTATT	0.363																																																0			10	GRCh37	CD056814	GSTO1	D	rs11509437						72	67	69					10																	106022834		2203	4300	6503	106012824	SO:0001630	splice_region_variant	9446			AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.465+1A>T	10.37:g.106022834A>T			106012824	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Missense_Mutation	SNP	ENST00000369713.5	37	CCDS7555.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.016783	0.75161	.	.	ENSG00000148834	ENST00000539281;ENST00000369713;ENST00000445155	T;T;T	0.02763	4.17;4.17;4.17	4.9	4.9	0.64082	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.146062	0.64402	D	0.000008	T	0.13798	0.0334	M	0.89287	3.02	0.80722	D	1	D	0.56287	0.975	P	0.55749	0.783	T	0.00785	-1.1567	10	0.49607	T	0.09	-30.9763	13.768	0.63006	1.0:0.0:0.0:0.0	.	155	P78417	GSTO1_HUMAN	V	127;155;127	ENSP00000441488:E127V;ENSP00000358727:E155V;ENSP00000406708:E127V	ENSP00000358727:E155V	E	+	2	0	GSTO1	106012824	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	4.977000	0.63792	2.183000	0.69458	0.533000	0.62120	GAG		0.363	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832	Missense_Mutation	T	106022834	A	T	106022834	5	4	92	1	0	0	0	0	0	0	1	0	6863	318	11	5	478	5	GSTO1	10	106022834	Splice_Site	SNP	A	TCGA-CL-5918-01A-11D-1657-10	1846250	106022834	29511913	129	25226										
EBF3	253738	hgsc.bcm.edu	37	chr10	131639129	131639129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gccgtagggagagttagcggAggagccattaagaaatccag	15	7	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:131639129A>G	ENST00000355311.5	-	14	1612	c.1540T>C	c.(1540-1542)Tcc>Ccc	p.S514P	MIR4297_ENST00000579857.1_RNA|EBF3_ENST00000368648.3_Missense_Mutation_p.S505P			Q9H4W6	COE3_HUMAN	early B-cell factor 3	514	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		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)		GAGTTAGCGGAGGAGCCATTA	0.502																																																0			10											107	105	106					10																	131639129		2203	4300	6503	131529119	SO:0001583	missense	253738				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.1540T>C	10.37:g.131639129A>G	ENSP00000347463:p.Ser514Pro		131529119	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.96|13.96	2.391856|2.391856	0.42410|0.42410	.|.	.|.	ENSG00000108001|ENSG00000108001	ENST00000440978|ENST00000355311;ENST00000368648	.|T;T	.|0.44482	.|0.92;0.92	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.104089	.|0.64402	.|D	.|0.000002	T|T	0.26195|0.26195	0.0639|0.0639	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.07271|0.07271	-1.0781|-1.0781	5|10	.|0.16420	.|T	.|0.52	-19.6946|-19.6946	14.6874|14.6874	0.69059|0.69059	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|505	.|Q9H4W6-2	.|.	P|P	75|514;505	.|ENSP00000347463:S514P;ENSP00000357637:S505P	.|ENSP00000347463:S514P	L|S	-|-	2|1	0|0	EBF3|EBF3	131529119|131529119	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.725000|5.725000	0.68507|0.68507	2.042000|2.042000	0.60477|0.60477	0.533000|0.533000	0.62120|0.62120	CTC|TCC		0.502	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		G	131639129	A	G	131639129	3	3	92	1	0	0	0	0	1	0	0	0	4893	304	11	4	154	4	EBF3	10	131639129	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	25616295	131639129	3895618	130	25227										
NKX6-2	84504	hgsc.bcm.edu	37	chr10	134598560	134598560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtattcgtcgtcgtcctccgCgtccgagccgcccaccttca	9	18	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr10:134598560C>T	ENST00000368592.5	-	3	797	c.694G>A	c.(694-696)Gcg>Acg	p.A232T	RP11-288G11.3_ENST00000441365.2_lincRNA	NM_177400.2	NP_796374	Q9C056	NKX62_HUMAN	NK6 homeobox 2	232					central nervous system myelination (GO:0022010)|endocrine pancreas development (GO:0031018)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of glial cell differentiation (GO:0045687)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(2)	3		all_cancers(35;2.79e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0584)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;4.06e-05)|Epithelial(32;5.53e-05)|all cancers(32;5.99e-05)		TCGTCCTCCGCGTCCGAGCCG	0.652																																																0			10											86	63	70					10																	134598560		2196	4299	6495	134448550	SO:0001583	missense	84504			AF184215	CCDS7670.1	10q26.3	2012-03-09	2007-07-09		ENSG00000148826	ENSG00000148826		"Homeoboxes / ANTP class : NKL subclass"	19321	protein-coding gene	gene with protein product		605955	"NK6 transcription factor related, locus 2 (Drosophila)"			11210186	Standard	NM_177400		Approved	NKX6B, GTX, NKX6.1	uc001llr.2	Q9C056	OTTHUMG00000019294	ENST00000368592.5:c.694G>A	10.37:g.134598560C>T	ENSP00000357581:p.Ala232Thr		134448550	Q5JSF3	Missense_Mutation	SNP	ENST00000368592.5	37	CCDS7670.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.244094	0.39697	.	.	ENSG00000148826	ENST00000368592	T	0.55234	0.53	3.83	2.8	0.32819	.	0.122356	0.52532	D	0.000078	T	0.22003	0.0530	N	0.08118	0	0.31229	N	0.696563	B	0.26744	0.158	B	0.18871	0.023	T	0.07065	-1.0792	10	0.17832	T	0.49	-12.8769	2.0526	0.03574	0.2819:0.4556:0.0:0.2625	.	232	Q9C056	NKX62_HUMAN	T	232	ENSP00000357581:A232T	ENSP00000357581:A232T	A	-	1	0	NKX6-2	134448550	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.806000	0.47947	2.072000	0.62099	0.305000	0.20034	GCG		0.652	NKX6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051093.2			T	134598560	C	T	134598560	3	4	92	1	0	0	0	0	1	0	0	0	10489	768	27	1	143	1	NKX6-2	10	134598560	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2959431	134598560	936187	131	25228										
NLRP6	171389	hgsc.bcm.edu	37	chr11	280790	280790	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgcgcggcttctccgacaaGgacaagaagaagtatttcta	11	9	2	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:280790G>T	ENST00000312165.5	+	4	1056	c.1056G>T	c.(1054-1056)aaG>aaT	p.K352N	NLRP6_ENST00000534750.1_Missense_Mutation_p.K352N	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	352	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)	p.K352K(1)		breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		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)		TCTCCGACAAGGACAAGAAGA	0.662																																																1	Substitution - coding silent(1)	skin(1)	11											48	51	50					11																	280790		2202	4300	6502	270790	SO:0001583	missense	171389			AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1056G>T	11.37:g.280790G>T	ENSP00000309767:p.Lys352Asn		270790	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636261	0.29068	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.81330	-1.48;-1.48	3.7	-1.24	0.09435	NACHT nucleoside triphosphatase (1);	0.584077	0.13391	N	0.391416	T	0.80076	0.4557	L	0.42686	1.345	0.25072	N	0.990987	D;D	0.71674	0.98;0.998	D;D	0.68483	0.929;0.958	T	0.68500	-0.5392	10	0.21014	T	0.42	.	5.8007	0.18412	0.2086:0.4756:0.3158:0.0	.	352;352	E9PJZ8;P59044	.;NALP6_HUMAN	N	352	ENSP00000433617:K352N;ENSP00000309767:K352N	ENSP00000309767:K352N	K	+	3	2	NLRP6	270790	0.000000	0.05858	0.053000	0.19242	0.756000	0.42949	-1.457000	0.02374	-0.354000	0.08212	0.455000	0.32223	AAG		0.662	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		T	280790	G	T	280790	3	4	92	1	0	0	0	0	1	0	0	0	10512	991	35	2	1070	2	NLRP6	11	280790	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10		280790	134725726	132	25229										
PHRF1	57661	hgsc.bcm.edu	37	chr11	609068	609068	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtgagggaggcttccccagcGccccttgcacagggggagcc	16	14	0	1	rs7928902	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:609068G>A	ENST00000264555.5	+	14	3740	c.3612G>A	c.(3610-3612)gcG>gcA	p.A1204A	PHRF1_ENST00000416188.2_Silent_p.A1203A|PHRF1_ENST00000533464.1_Silent_p.A1200A|PHRF1_ENST00000413872.2_Silent_p.A1202A	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1204					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CTTCCCCAGCGCCCCTTGCAC	0.701													G|||	940	0.1877	0.3359	0.2522	5008	,	,		15187	0.0198		0.2147	False		,,,				2504	0.0869															0			11						G		1208,2732		183,842,945	9	11	10		3609	-9.3	0	11	dbSNP_116	10	1939,6289		225,1489,2400	no	coding-synonymous	PHRF1	NM_020901.2		408,2331,3345	AA,AG,GG		23.5659,30.6599,25.8629		1203/1649	609068	3147,9021	1970	4114	6084	599068	SO:0001819	synonymous_variant	57661			BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3612G>A	11.37:g.609068G>A			599068	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																					0.701	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	609068	G	A	609068	2	1	92	1	0	0	0	0	0	0	0	1	11892	1074	38	1		1	PHRF1	11	609068	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	328278	609068	134397448	133	25230										
EFCAB4A	283229	hgsc.bcm.edu	37	chr11	830670	830670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tctggagctggagctgcagaGccgcgagcaggacctggaac	16	11	1	1	rs4075289	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:830670G>T	ENST00000525077.1	+	6	844	c.743G>T	c.(742-744)aGc>aTc	p.S248I	EFCAB4A_ENST00000528542.2_Missense_Mutation_p.S248I|AP006621.8_ENST00000532946.1_RNA|CD151_ENST00000397421.1_5'Flank|CD151_ENST00000322008.4_5'Flank|CD151_ENST00000397420.3_5'Flank|EFCAB4A_ENST00000450448.1_Missense_Mutation_p.S248I			Q8N4Y2	EFC4A_HUMAN		248			S -> I (in dbSNP:rs4075289). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		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)		GAGCTGCAGAGCCGCGAGCAG	0.731													g|||	3267	0.652356	0.5431	0.7767	5008	,	,		12723	0.8909		0.667	False		,,,				2504	0.4509															0			11							ILE/SER	2006,1190		678,650,270	3	5	5		743	1	1	11	dbSNP_108	5	4900,1892		1837,1226,333	yes	missense	EFCAB4A	NM_173584.3	142	2515,1876,603	TT,TG,GG		27.8563,37.234,30.857	benign	248/295	830670	6906,3082	1598	3396	4994	820670	SO:0001583	missense	283229																														ENST00000525077.1:c.743G>T	11.37:g.830670G>T	ENSP00000435299:p.Ser248Ile		820670	D5LPR2|Q8NBW8	Missense_Mutation	SNP	ENST00000525077.1	37		1580	0.7234432234432234	263	0.5345528455284553	280	0.7734806629834254	526	0.9195804195804196	511	0.6741424802110818	g	14.69	2.610896	0.46527	0.62766	0.721437	ENSG00000177685	ENST00000528542;ENST00000450448;ENST00000321883;ENST00000525077	T;T;T	0.07567	3.18;3.18;3.33	4.2	1.03	0.20045	.	.	.	.	.	T	0.00012	0.0000	L	0.47190	1.495	0.53688	P	2.999999999997449E-5	P;P	0.39782	0.688;0.513	B;B	0.34385	0.178;0.181	T	0.18587	-1.0332	8	0.30854	T	0.27	-6.4116	7.0862	0.25259	0.1002:0.3462:0.5536:0.0	rs4075289;rs58579267;rs4075289	248;248	Q8N4Y2-3;Q8N4Y2	.;EFC4A_HUMAN	I	248	ENSP00000432334:S248I;ENSP00000409256:S248I;ENSP00000435299:S248I	ENSP00000324024:S248I	S	+	2	0	EFCAB4A	820670	0.000000	0.05858	0.977000	0.42913	0.793000	0.44817	0.210000	0.17455	0.029000	0.15352	0.457000	0.33378	AGC		0.731	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1			T	830670	G	T	830670	3	4	92	1	0	0	0	0	1	0	0	0	4947	971	34	2	765	2	EFCAB4A	11	830670	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	221602	830670	134175846	134	25231										
RRP8	23378	hgsc.bcm.edu	37	chr11	6621754	6621754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcctagcttggtcacagcccGcagaaaggttcgaacatcct	10	13	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:6621754G>A	ENST00000254605.6	-	6	1330	c.1213C>T	c.(1213-1215)Cgg>Tgg	p.R405W	RRP8_ENST00000534343.1_Missense_Mutation_p.R89W	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	405					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						GTCACAGCCCGCAGAAAGGTT	0.512																																																0			11											43	44	44					11																	6621754		2201	4296	6497	6578330	SO:0001583	missense	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.1213C>T	11.37:g.6621754G>A	ENSP00000254605:p.Arg405Trp		6578330	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.783166	0.31593	.	.	ENSG00000132275	ENST00000254605;ENST00000534343	T;T	0.51325	0.71;0.71	5.89	4.03	0.46877	.	0.469319	0.23307	N	0.049617	T	0.50086	0.1595	L	0.55481	1.735	0.34318	D	0.686287	D	0.69078	0.997	P	0.53689	0.732	T	0.63125	-0.6707	10	0.72032	D	0.01	-0.5171	5.3368	0.15961	0.0:0.6101:0.1609:0.2289	.	405	O43159	RRP8_HUMAN	W	405;89	ENSP00000254605:R405W;ENSP00000436960:R89W	ENSP00000254605:R405W	R	-	1	2	RRP8	6578330	0.549000	0.26481	0.858000	0.33744	0.065000	0.16274	1.439000	0.35013	0.834000	0.34852	-0.311000	0.09066	CGG		0.512	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		A	6621754	G	A	6621754	3	1	92	1	0	0	0	0	1	0	0	0	13727	1086	38	1	165	1	RRP8	11	6621754	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	5791084	6621754	128384762	135	25232										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12281386	12281386	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaagcccctcggagagacacTcccaccgaaagttcttgcgc	10	15	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:12281386T>C	ENST00000256194.4	+	26	3564	c.3276T>C	c.(3274-3276)acT>acC	p.T1092T	MICAL2_ENST00000537344.1_Silent_p.T902T|MICAL2_ENST00000527546.1_Silent_p.T902T|MICAL2_ENST00000342902.5_Silent_p.T1071T|RP11-265D17.2_ENST00000527288.1_RNA|MICAL2_ENST00000379612.3_Silent_p.T866T	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1092					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		GGAGAGACACTCCCACCGAAA	0.572																																																0			11											54	54	54					11																	12281386		2201	4294	6495	12237962	SO:0001819	synonymous_variant	9645			AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.3276T>C	11.37:g.12281386T>C			12237962	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																				0.572	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		C	12281386	T	C	12281386	2	2	92	1	0	0	0	0	0	0	0	1	9600	1538	54	4		4	MICAL2	11	12281386	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	5659632	12281386	122725130	136	25233										
RRAS2	22800	hgsc.bcm.edu	37	chr11	14303176	14303176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccggacaagttcatggaaagCttgatctacattcatcctaa	7	10	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:14303176C>T	ENST00000256196.4	-	5	812	c.499G>A	c.(499-501)Gct>Act	p.A167T	RRAS2_ENST00000529237.1_Missense_Mutation_p.A90T|RRAS2_ENST00000545643.1_Missense_Mutation_p.A173T|RRAS2_ENST00000534746.1_Missense_Mutation_p.A90T|RRAS2_ENST00000532814.1_Missense_Mutation_p.A90T|RRAS2_ENST00000414023.2_Missense_Mutation_p.A90T|RRAS2_ENST00000526063.1_Missense_Mutation_p.A90T|RRAS2_ENST00000537760.1_Missense_Mutation_p.A132T			P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2	167					osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|endometrium(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	12				Epithelial(150;0.203)		TCATGGAAAGCTTGATCTACA	0.353																																																0			11											258	215	230					11																	14303176		2200	4294	6494	14259752	SO:0001583	missense	22800			M31468	CCDS7814.1, CCDS44544.1, CCDS53603.1	11p15.2	2014-05-09			ENSG00000133818	ENSG00000133818			17271	protein-coding gene	gene with protein product		600098				2108320, 8052619	Standard	NM_012250		Approved	TC21	uc001mlf.4	P62070	OTTHUMG00000165756	ENST00000256196.4:c.499G>A	11.37:g.14303176C>T	ENSP00000256196:p.Ala167Thr		14259752	B2R9Z3|B7Z5Z2|B7Z6C4|B7Z7H6|P17082	Missense_Mutation	SNP	ENST00000256196.4	37	CCDS7814.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.032920	0.93575	.	.	ENSG00000133818	ENST00000537760;ENST00000545643;ENST00000414023;ENST00000529237;ENST00000256196;ENST00000534746;ENST00000526063;ENST00000532814;ENST00000531807	T;T;T;T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.07	5.07	0.68467	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.86435	0.5932	L	0.53617	1.68	0.80722	D	1	D;D	0.67145	0.996;0.995	D;P	0.68483	0.958;0.895	D	0.87290	0.2298	10	0.66056	D	0.02	.	14.5283	0.67905	0.1471:0.8529:0.0:0.0	.	173;167	B7Z5Z2;P62070	.;RRAS2_HUMAN	T	132;173;90;90;167;90;90;90;148	ENSP00000437547:A132T;ENSP00000441722:A173T;ENSP00000403282:A90T;ENSP00000433230:A90T;ENSP00000256196:A167T;ENSP00000437083:A90T;ENSP00000434104:A90T;ENSP00000431954:A90T;ENSP00000435453:A148T	ENSP00000256196:A167T	A	-	1	0	RRAS2	14259752	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.605000	0.61119	2.525000	0.85131	0.650000	0.86243	GCT		0.353	RRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386035.1	NM_012250		T	14303176	C	T	14303176	3	4	92	1	0	0	0	0	1	0	0	0	13714	797	28	3	123	3	RRAS2	11	14303176	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2021790	14303176	120703340	137	25234										
LDHA	3939	hgsc.bcm.edu	37	chr11	18425274	18425274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggaatgaatgttgctggtgTctctctgaagactctgcacc	11	9	3	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:18425274T>C	ENST00000422447.3	+	6	899	c.626T>C	c.(625-627)gTc>gCc	p.V209A	LDHA_ENST00000430553.2_Missense_Mutation_p.V151A|LDHA_ENST00000379412.5_Missense_Mutation_p.V209A|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000396222.2_Missense_Mutation_p.V209A|LDHA_ENST00000542179.1_Missense_Mutation_p.V209A|LDHA_ENST00000227157.4_Missense_Mutation_p.V209A|LDHA_ENST00000540430.1_Missense_Mutation_p.V238A	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	209					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)	p.V209A(1)		central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						GTTGCTGGTGTCTCTCTGAAG	0.373																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											158	151	153					11																	18425274		2199	4293	6492	18381850	SO:0001583	missense	3939			X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.626T>C	11.37:g.18425274T>C	ENSP00000395337:p.Val209Ala		18381850	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	T	34	5.302139	0.95601	.	.	ENSG00000134333	ENST00000422447;ENST00000430553;ENST00000396222;ENST00000541620;ENST00000445376;ENST00000227157;ENST00000540430;ENST00000379412;ENST00000542179	T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	5.34	5.34	0.76211	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.64402	D	0.000001	D	0.83289	0.5222	M	0.88775	2.98	0.80722	D	1	B;B;P;B;B	0.50272	0.167;0.032;0.933;0.452;0.148	B;B;P;B;B	0.61874	0.335;0.093;0.895;0.411;0.313	D	0.86479	0.1790	10	0.66056	D	0.02	-3.6877	15.6155	0.76764	0.0:0.0:0.0:1.0	.	238;151;182;209;209	B7Z5E3;B4DKQ2;B4DJI1;F8W819;P00338	.;.;.;.;LDHA_HUMAN	A	209;151;209;181;182;209;238;209;209	ENSP00000395337:V209A;ENSP00000406172:V151A;ENSP00000379524:V209A;ENSP00000227157:V209A;ENSP00000445175:V238A;ENSP00000368722:V209A;ENSP00000445331:V209A	ENSP00000227157:V209A	V	+	2	0	LDHA	18381850	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.876000	0.87215	2.142000	0.66516	0.477000	0.44152	GTC		0.373	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		C	18425274	T	C	18425274	3	2	92	1	0	0	0	0	1	0	0	0	8720	1667	58	4	735	4	LDHA	11	18425274	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	4122098	18425274	116581242	138	25235										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18764922	18764922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agaggagacgaggtttgtggCgttctgtgaccagatgtggc	17	6	1	4			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:18764922C>T	ENST00000358540.2	-	5	776	c.346G>A	c.(346-348)Gcc>Acc	p.A116T	PTPN5_ENST00000396167.2_Intron|PTPN5_ENST00000396168.1_Missense_Mutation_p.A92T|PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396171.4_Missense_Mutation_p.A116T|PTPN5_ENST00000396170.1_Intron|PTPN5_ENST00000496201.2_5'UTR|RP11-1081L13.4_ENST00000527285.1_RNA	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	116					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						AGGTTTGTGGCGTTCTGTGAC	0.602																																																0			11											137	130	132					11																	18764922		2199	4293	6492	18721498	SO:0001583	missense	84867			BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.346G>A	11.37:g.18764922C>T	ENSP00000351342:p.Ala116Thr		18721498	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	37	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	c	5.779	0.327996	0.10956	.	.	ENSG00000110786	ENST00000358540;ENST00000396171;ENST00000396168	T;T;T	0.04360	3.64;3.64;3.66	3.86	0.891	0.19224	.	0.515938	0.17650	N	0.166708	T	0.02267	0.0070	N	0.08118	0	0.24615	N	0.993703	B	0.09022	0.002	B	0.04013	0.001	T	0.46062	-0.9218	10	0.25751	T	0.34	-10.9848	5.7064	0.17911	0.0:0.6279:0.0:0.3721	.	116	P54829	PTN5_HUMAN	T	116;116;92	ENSP00000351342:A116T;ENSP00000379474:A116T;ENSP00000379471:A92T	ENSP00000351342:A116T	A	-	1	0	PTPN5	18721498	0.733000	0.28132	0.888000	0.34837	0.067000	0.16453	0.333000	0.19768	0.088000	0.17205	-0.215000	0.12644	GCC		0.602	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		T	18764922	C	T	18764922	3	4	92	1	0	0	0	0	1	0	0	0	12828	768	27	1	1395	1	PTPN5	11	18764922	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	339648	18764922	116241594	139	25236										
BDNF	627	hgsc.bcm.edu	37	chr11	27695763	27695763	+	5'UTR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgcaaccctttctgtagaaaCtcagcattctgagtagtaac	7	10	3	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:27695763C>A	ENST00000420794.1	-	0	209				BDNF_ENST00000525950.1_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000530861.1_Intron|BDNF_ENST00000395986.2_Intron|BDNF-AS_ENST00000501663.2_RNA|BDNF_ENST00000584049.1_Intron|BDNF_ENST00000533246.1_Intron|BDNF_ENST00000356660.4_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000314915.6_Intron|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000395978.3_Intron|BDNF_ENST00000532997.1_Intron|BDNF_ENST00000533131.1_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000438929.1_Missense_Mutation_p.E23D|BDNF_ENST00000418212.1_Intron	NM_001143811.1	NP_001137283.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						TCTGTAGAAACTCAGCATTCT	0.483																																																0			11											83	77	79					11																	27695763		1567	3581	5148	27652339	SO:0001623	5_prime_UTR_variant	627			AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"Endogenous ligands"	1033	protein-coding gene	gene with protein product	"neurotrophin"	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000420794.1:c.-295G>T	11.37:g.27695763C>A			27652339	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000420794.1	37	CCDS7866.1	.	.	.	.	.	.	.	.	.	.	C	9.844	1.191715	0.21954	.	.	ENSG00000176697	ENST00000438929	T	0.57907	0.37	5.92	5.92	0.95590	.	.	.	.	.	T	0.48768	0.1518	.	.	.	0.80722	D	1	B	0.18310	0.027	B	0.16289	0.015	T	0.41233	-0.9520	8	0.66056	D	0.02	.	17.0462	0.86504	0.0:1.0:0.0:0.0	.	23	P23560-4	.	D	23	ENSP00000414303:E23D	ENSP00000414303:E23D	E	-	3	2	BDNF	27652339	0.962000	0.33011	0.979000	0.43373	0.088000	0.18126	0.925000	0.28791	2.794000	0.96219	0.650000	0.86243	GAG		0.483	BDNF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_170735		A	27695763	C	A	27695763	1	1	92	0	1	0	0	0	0	0	0	0	1395	564	20	2		2	BDNF	11	27695763	5'UTR	SNP	C	TCGA-CL-5918-01A-11D-1657-10	8930841	27695763	107310753	140	25237										
SLC39A13	91252	hgsc.bcm.edu	37	chr11	47435016	47435016	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggccactgtctggcccagccGgctgcagagcccggcctcgg	15	17	1	1	rs372236399		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:47435016G>A	ENST00000362021.4	+	5	645	c.603G>A	c.(601-603)ccG>ccA	p.P201P	SLC39A13_ENST00000529740.1_3'UTR|SLC39A13_ENST00000524928.1_Silent_p.P201P|SLC39A13_ENST00000354884.4_Silent_p.P201P|SLC39A13_ENST00000533076.1_Silent_p.P201P	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	201					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		TGGCCCAGCCGGCTGCAGAGC	0.677																																																0			11						G	,	0,4402		0,0,2201	26	30	29		603,603	0	1	11		29	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	SLC39A13	NM_001128225.2,NM_152264.4	,	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	,	201/372,201/365	47435016	1,12995	2201	4297	6498	47391592	SO:0001819	synonymous_variant	91252				CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"Solute carriers"	20859	protein-coding gene	gene with protein product		608735	"solute carrier family 39 (metal ion transporter), member 13"			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.603G>A	11.37:g.47435016G>A			47391592	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Silent	SNP	ENST00000362021.4	37	CCDS44592.1																																																																																				0.677	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264		A	47435016	G	A	47435016	2	1	92	1	0	0	0	0	0	0	0	1	14653	1103	39	1		1	SLC39A13	11	47435016	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	19739253	47435016	87571500	141	25238										
CD6	923	hgsc.bcm.edu	37	chr11	60777073	60777073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cctggcgcctgacagggggcGctgaccgctgcgaggggcag	19	13	0	2	rs12360861	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:60777073G>A	ENST00000313421.7	+	5	997	c.811G>A	c.(811-813)Gct>Act	p.A271T	CD6_ENST00000545105.1_Intron|CD6_ENST00000352009.5_Missense_Mutation_p.A271T|CD6_ENST00000346437.4_Missense_Mutation_p.A271T|CD6_ENST00000452451.2_Missense_Mutation_p.A271T|CD6_ENST00000344028.5_Missense_Mutation_p.A271T	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	271	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.		A -> T (in dbSNP:rs12360861).		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GACAGGGGGCGCTGACCGCTG	0.637													G|||	384	0.0766773	0.0401	0.121	5008	,	,		19148	0.001		0.1938	False		,,,				2504	0.0521				Pancreas(169;904 2017 4767 38890 42505)											0			11						G	THR/ALA	267,4139	145.0+/-179.8	8,251,1944	40	38	38		811	-9.8	0	11	dbSNP_120	38	1562,7036	285.1+/-297.0	144,1274,2881	yes	missense	CD6	NM_006725.3	58	152,1525,4825	AA,AG,GG		18.167,6.0599,14.0649	benign	271/669	60777073	1829,11175	2203	4299	6502	60533649	SO:0001583	missense	923				CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.811G>A	11.37:g.60777073G>A	ENSP00000323280:p.Ala271Thr		60533649	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	221	0.10119047619047619	19	0.03861788617886179	51	0.1408839779005525	1	0.0017482517482517483	150	0.19788918205804748	G	1.521	-0.546883	0.04024	0.060599	0.18167	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	4.9	-9.81	0.00487	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.748670	0.02962	N	0.143237	T	0.00012	0.0000	N	0.11284	0.12	0.80722	P	0.0	B;B;B;B	0.22414	0.055;0.069;0.041;0.054	B;B;B;B	0.15484	0.01;0.01;0.011;0.013	T	0.04495	-1.0947	9	0.12766	T	0.61	.	5.9428	0.19201	0.6054:0.0724:0.1293:0.1929	rs12360861	271;271;271;271	P30203-5;P30203-4;P30203;Q8N4Q7	.;.;CD6_HUMAN;.	T	271	ENSP00000344108:A271T;ENSP00000345566:A271T;ENSP00000323280:A271T;ENSP00000390676:A271T;ENSP00000340628:A271T	ENSP00000323280:A271T	A	+	1	0	CD6	60533649	0.000000	0.05858	0.000000	0.03702	0.346000	0.29079	-7.571000	0.00034	-2.169000	0.00777	-0.266000	0.10368	GCT		0.637	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		A	60777073	G	A	60777073	3	1	92	1	0	0	0	0	1	0	0	0	3034	1087	38	1	829	1	CD6	11	60777073	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	13342057	60777073	74229443	142	25239										
INCENP	3619	hgsc.bcm.edu	37	chr11	61897359	61897359	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtcggggagaacggctccgtCctgcggcgtgtgacccgtgc	17	13	0	2	rs1675133	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:61897359C>T	ENST00000394818.3	+	4	562	c.360C>T	c.(358-360)gtC>gtT	p.V120V	INCENP_ENST00000278849.4_Silent_p.V120V	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	120					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ACGGCTCCGTCCTGCGGCGTG	0.647													C|||	1731	0.345647	0.32	0.379	5008	,	,		15888	0.1181		0.6859	False		,,,				2504	0.2413															0			11						C	,	1583,2819	474.8+/-357.1	304,975,922	49	51	50		360,360	2.2	0.1	11	dbSNP_89	50	5875,2723	660.2+/-401.7	2026,1823,450	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	2330,2798,1372	TT,TC,CC		31.6702,35.9609,42.6308	,	120/919,120/915	61897359	7458,5542	2201	4299	6500	61653935	SO:0001819	synonymous_variant	3619			AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.360C>T	11.37:g.61897359C>T			61653935	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																				0.647	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		T	61897359	C	T	61897359	2	4	92	1	0	0	0	0	0	0	0	1	7754	842	30	3		3	INCENP	11	61897359	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1120286	61897359	73109157	143	25240										
ALDH3B1	221	hgsc.bcm.edu	37	chr11	67789295	67789295	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gggcattgctgggctgcggcGtgtggccattgggggccaga	20	9	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:67789295G>C	ENST00000539229.1	+	9	1015	c.899G>C	c.(898-900)cGt>cCt	p.R300P	RP5-901A4.1_ENST00000532296.1_RNA|ALDH3B1_ENST00000316367.6_Intron|ALDH3B1_ENST00000007633.8_Splice_Site_p.R300P|ALDH3B1_ENST00000434449.1_3'UTR|ALDH3B1_ENST00000342456.6_Splice_Site_p.R264P	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	302					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										GGGCTGCGGCGTGTGGCCATT	0.642																																																0			11											34	40	38					11																	67789295		2200	4293	6493	67545871	SO:0001630	splice_region_variant	221			U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.898-1G>C	11.37:g.67789295G>C			67545871	A3FMP9|Q53XL5|Q8N515|Q96CK8	Missense_Mutation	SNP	ENST00000539229.1	37																																																																																					0.642	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694	Missense_Mutation	C	67789295	G	C	67789295	5	2	92	1	0	0	0	0	0	0	1	0	499	1145	40	5	925	5	ALDH3B1	11	67789295	Splice_Site	SNP	G	TCGA-CL-5918-01A-11D-1657-10	5891936	67789295	67217221	144	25241										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825407	95825407	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgctgctgctgctgctgctgCtgctgctgttgctgctgttg	14	11	0	0	rs61901862		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	1	Substitution - coding silent(1)	kidney(1)	11											28	35	33					11																	95825407		2119	4148	6267	95465055	SO:0001819	synonymous_variant	84441			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T			95465055	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																				0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825407	C	T	95825407	2	4	92	1	0	0	0	0	0	0	0	1	9236	796	28	3		3	MAML2	11	95825407	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	28036112	95825407	39181109	145	25242										
HTR3B	9177	hgsc.bcm.edu	37	chr11	113815341	113815341	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttcttggttctcagcttagcTaagtccatcgtgttggtcaa	9	9	3	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:113815341T>G	ENST00000260191.2	+	8	1211	c.954T>G	c.(952-954)gcT>gcG	p.A318A	HTR3B_ENST00000537778.1_Silent_p.A307A	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	318					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	TCAGCTTAGCTAAGTCCATCG	0.537																																																0			11											225	177	193					11																	113815341		2201	4296	6497	113320551	SO:0001819	synonymous_variant	9177			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.954T>G	11.37:g.113815341T>G			113320551	B0YJ23|Q0VJC3	Silent	SNP	ENST00000260191.2	37	CCDS8364.1																																																																																				0.537	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		G	113815341	T	G	113815341	2	3	92	1	0	0	0	0	0	0	0	1	7466	1509	53	4		4	HTR3B	11	113815341	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	17989934	113815341	21191175	146	25243										
MPZL3	196264	hgsc.bcm.edu	37	chr11	118107936	118107936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aatccgatcccgaaatgtgcCtgctgtggttgggtactgga	13	9	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:118107936C>T	ENST00000278949.4	-	3	335	c.280G>A	c.(280-282)Ggc>Agc	p.G94S	MPZL3_ENST00000525386.1_Intron|MPZL3_ENST00000527472.1_Missense_Mutation_p.G82S			Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3	94	Ig-like V-type.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|hair cycle (GO:0042633)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		CGAAATGTGCCTGCTGTGGTT	0.393																																																0			11											142	138	140					11																	118107936		2200	4296	6496	117613146	SO:0001583	missense	196264			AK095399	CCDS8392.1, CCDS66241.1	11q23.3	2013-01-11			ENSG00000160588	ENSG00000160588		"Immunoglobulin superfamily / V-set domain containing"	27279	protein-coding gene	gene with protein product		611707				17273165	Standard	NM_198275		Approved		uc001psm.3	Q6UWV2	OTTHUMG00000166966	ENST00000278949.4:c.280G>A	11.37:g.118107936C>T	ENSP00000278949:p.Gly94Ser		117613146	A8K025|B4DLD5|B4E2I8	Missense_Mutation	SNP	ENST00000278949.4	37	CCDS8392.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145675	0.94603	.	.	ENSG00000160588	ENST00000278949;ENST00000527472	T;T	0.64991	-0.13;-0.13	5.98	5.98	0.97165	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79161	0.4399	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.75099	-0.3437	10	0.34782	T	0.22	.	19.4443	0.94840	0.0:1.0:0.0:0.0	.	82;94	B4E2I8;Q6UWV2	.;MPZL3_HUMAN	S	94;82	ENSP00000278949:G94S;ENSP00000432106:G82S	ENSP00000278949:G94S	G	-	1	0	MPZL3	117613146	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	5.007000	0.63984	2.847000	0.97988	0.591000	0.81541	GGC		0.393	MPZL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392109.1	NM_198275		T	118107936	C	T	118107936	3	4	92	1	0	0	0	0	1	0	0	0	9781	681	24	3	443	3	MPZL3	11	118107936	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	4292595	118107936	16898580	147	25244										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124766530	124766530	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gctcacccaccacagccaccAtgtcccgaggctggatctgg	10	17	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:124766530A>G	ENST00000306534.3	-	3	922	c.437T>C	c.(436-438)aTg>aCg	p.M146T	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Start_Codon_SNP_p.M1T	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	146	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CACAGCCACCATGTCCCGAGG	0.617																																																0			11											34	38	37					11																	124766530		2201	4299	6500	124271740	SO:0001583	missense	54538			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.437T>C	11.37:g.124766530A>G	ENSP00000304945:p.Met146Thr		124271740	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.339113	0.24253	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.66460	-0.21;0.31	5.82	-2.1	0.07210	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.744885	0.11393	N	0.568570	T	0.23410	0.0566	N	0.00313	-1.665	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08868	-1.0701	10	0.21014	T	0.42	.	4.1309	0.10149	0.4238:0.0:0.3251:0.2511	.	36;146	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	T	146;36;1	ENSP00000304945:M146T;ENSP00000437129:M1T	ENSP00000304945:M146T	M	-	2	0	ROBO4	124271740	0.746000	0.28272	0.073000	0.20177	0.251000	0.25915	1.882000	0.39648	-0.167000	0.10871	-0.349000	0.07799	ATG		0.617	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		G	124766530	A	G	124766530	3	3	92	1	0	0	0	0	1	0	0	0	13553	217	8	4	2650	4	ROBO4	11	124766530	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	6658594	124766530	10239986	148	25245										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125503113	125503113	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtatttcggtataataatcgTgagcgtttgttgaacaagat	10	4	0	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:125503113T>C	ENST00000534070.1	+	6	735	c.480T>C	c.(478-480)cgT>cgC	p.R160R	CHEK1_ENST00000427383.2_Silent_p.R176R|CHEK1_ENST00000278916.3_Silent_p.R160R|CHEK1_ENST00000524737.1_Silent_p.R160R|CHEK1_ENST00000438015.1_Silent_p.R160R|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000428830.2_Silent_p.R160R|CHEK1_ENST00000544373.1_Silent_p.R160R	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	160	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		ATAATAATCGTGAGCGTTTGT	0.363								Other conserved DNA damage response genes																																								0			11											109	109	109					11																	125503113		2201	4299	6500	125008323	SO:0001819	synonymous_variant	1111			AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.480T>C	11.37:g.125503113T>C			125008323	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Silent	SNP	ENST00000534070.1	37	CCDS8459.1																																																																																				0.363	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		C	125503113	T	C	125503113	2	2	92	1	0	0	0	0	0	0	0	1	3340	1683	59	4		4	CHEK1	11	125503113	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	736583	125503113	9503403	149	25246										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133806008	133806008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aggtgaggttgcccggatacGcctctgcccggcaggtgagc	16	12	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr11:133806008G>A	ENST00000321016.8	-	6	991	c.761C>T	c.(760-762)gCg>gTg	p.A254V	IGSF9B_ENST00000533871.2_Missense_Mutation_p.A254V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	254	Ig-like 3.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GCCCGGATACGCCTCTGCCCG	0.582																																																0			11											58	67	64					11																	133806008		2119	4230	6349	133311218	SO:0001583	missense	22997			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.761C>T	11.37:g.133806008G>A	ENSP00000317980:p.Ala254Val		133311218	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	29.6	5.019995	0.93462	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.68025	-0.3;-0.3;-0.3	5.22	4.24	0.50183	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Fibronectin, type III (2);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.81536	0.4843	M	0.81497	2.545	0.54753	D	0.999981	D	0.89917	1.0	D	0.77557	0.99	D	0.84451	0.0588	9	0.87932	D	0	.	14.5366	0.67966	0.0:0.0:0.8529:0.1471	.	254	Q9UPX0	TUTLB_HUMAN	V	254;96;254	ENSP00000317980:A254V;ENSP00000436552:A96V;ENSP00000436576:A254V	ENSP00000317980:A254V	A	-	2	0	IGSF9B	133311218	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.512000	0.81728	2.449000	0.82847	0.561000	0.74099	GCG		0.582	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133806008	G	A	133806008	3	1	92	1	0	0	0	0	1	0	0	0	7627	1087	38	1	3344	1	IGSF9B	11	133806008	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	8302895	133806008	1200508	150	25247										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56092682	56092682	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tctgcacgcaccagacctttCcccgagtcaatagagaagcc	8	15	2	2	rs3847675	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr12:56092682C>T	ENST00000555728.1	-	7	970	c.942G>A	c.(940-942)ggG>ggA	p.G314G	ITGA7_ENST00000452168.2_Silent_p.G177G|ITGA7_ENST00000394230.2_Silent_p.G274G|ITGA7_ENST00000394229.2_Silent_p.G270G|ITGA7_ENST00000257879.6_Silent_p.G270G|ITGA7_ENST00000347027.6_Silent_p.G270G|ITGA7_ENST00000257880.7_Silent_p.G314G|ITGA7_ENST00000553804.1_Silent_p.G274G			Q13683	ITA7_HUMAN	integrin, alpha 7	314					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCAGACCTTTCCCCGAGTCAA	0.617													C|||	175	0.0349441	0.0023	0.0648	5008	,	,		15771	0		0.0994	False		,,,				2504	0.0276															0			12						C	,,	63,4343		0,63,2140	19	20	20		822,531,810	4.5	1	12	dbSNP_108	20	710,7890		38,634,3628	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGA7	NM_001144996.1,NM_001144997.1,NM_002206.2	,,	38,697,5768	TT,TC,CC		8.2558,1.4299,5.9434	,,	274/1142,177/1045,270/1138	56092682	773,12233	2203	4300	6503	54378949	SO:0001819	synonymous_variant	3679				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.942G>A	12.37:g.56092682C>T			54378949	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																					0.617	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		T	56092682	C	T	56092682	2	4	92	1	0	0	0	0	0	0	0	1	7902	842	30	3		3	ITGA7	12	56092682	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10		56092682	77759213	151	25248										
RBMS2	5939	hgsc.bcm.edu	37	chr12	56975619	56975619	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgtgttctttctttatagggCgtcatggccttgacctatga	10	8	3	2	rs148057149		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr12:56975619C>T	ENST00000262031.5	+	8	830	c.735C>T	c.(733-735)ggC>ggT	p.G245G	RBMS2_ENST00000542360.1_Silent_p.G100G|RBMS2_ENST00000550726.1_Silent_p.G120G|RBMS2_ENST00000552247.2_Silent_p.G245G	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	245					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						CTTTATAGGGCGTCATGGCCT	0.453													C|||	1	0.000199681	0	0	5008	,	,		21428	0		0	False		,,,				2504	0.001															0			12						C		1,4405	2.1+/-5.4	0,1,2202	146	138	141		735	-6.4	0.9	12	dbSNP_134	141	0,8600		0,0,4300	no	coding-synonymous	RBMS2	NM_002898.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		245/408	56975619	1,13005	2203	4300	6503	55261886	SO:0001819	synonymous_variant	5939			D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"RNA binding motif (RRM) containing"	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	ENST00000262031.5:c.735C>T	12.37:g.56975619C>T			55261886		Silent	SNP	ENST00000262031.5	37	CCDS8923.1																																																																																				0.453	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898		T	56975619	C	T	56975619	2	4	92	1	0	0	0	0	0	0	0	1	13186	755	27	1		1	RBMS2	12	56975619	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	882937	56975619	76876276	152	25249										
MDM2	4193	hgsc.bcm.edu	37	chr12	69230472	69230472	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtatatcaagttactgtgtaTcaggcaggggagagtgatac	13	5	2	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr12:69230472T>C	ENST00000350057.5	+	8	768	c.768T>C	c.(766-768)taT>taC	p.Y256Y	MDM2_ENST00000356290.4_Silent_p.Y111Y|MDM2_ENST00000393413.3_Intron|MDM2_ENST00000540827.1_Silent_p.Y86Y|MDM2_ENST00000393412.3_Intron|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000462284.1_Silent_p.Y287Y|MDM2_ENST00000299252.4_Silent_p.Y111Y|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000360430.2_Silent_p.Y86Y|MDM2_ENST00000258148.7_Silent_p.Y232Y|MDM2_ENST00000348801.2_Intron|MDM2_ENST00000258149.5_Silent_p.Y226Y|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000478070.1_Intron|MDM2_ENST00000428863.2_Intron|MDM2_ENST00000393410.1_Intron			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	281	ARF-binding.|Asp/Glu-rich (acidic).|Interaction with MTBP. {ECO:0000250}.|Region II.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTACTGTGTATCAGGCAGGGG	0.323			A		"sarcoma, glioma, colorectal, other"																																		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"M, O, E, L"	0			12											174	167	169					12																	69230472		1852	4095	5947	67516739	SO:0001819	synonymous_variant	4193				CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"mouse double minute 2, human homolog of; p53-binding protein", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)", "Mdm2 p53 binding protein homolog (mouse)"			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.768T>C	12.37:g.69230472T>C			67516739	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000350057.5	37																																																																																					0.323	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880		C	69230472	T	C	69230472	2	2	92	1	0	0	0	0	0	0	0	1	9443	1442	50	4		4	MDM2	12	69230472	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	12254853	69230472	64621423	153	25250										
NAV3	89795	hgsc.bcm.edu	37	chr12	78388626	78388626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agtctaatcacagtggaattGcaaccagtcaaaaaaagcct	7	9	3	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr12:78388626G>A	ENST00000397909.2	+	6	888	c.715G>A	c.(715-717)Gca>Aca	p.A239T	NAV3_ENST00000228327.6_Missense_Mutation_p.A239T|NAV3_ENST00000536525.2_Missense_Mutation_p.A239T|NAV3_ENST00000266692.7_Missense_Mutation_p.A239T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	239						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CAGTGGAATTGCAACCAGTCA	0.343										HNSCC(70;0.22)																																						0			12											136	128	131					12																	78388626		1821	4091	5912	76912757	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.715G>A	12.37:g.78388626G>A	ENSP00000381007:p.Ala239Thr		76912757	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	17.02	3.281838	0.59758	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.95	5.01	0.66863	.	0.193276	0.24200	U	0.040630	T	0.23210	0.0561	N	0.08118	0	0.80722	D	1	B;P	0.38827	0.045;0.649	B;B	0.34536	0.013;0.185	T	0.07635	-1.0762	10	0.25106	T	0.35	-19.1809	15.9842	0.80138	0.0:0.0:0.8648:0.1352	.	239;239	Q8IVL0;Q8IVL0-2	NAV3_HUMAN;.	T	239	ENSP00000446628:A239T;ENSP00000446132:A239T;ENSP00000381007:A239T;ENSP00000228327:A239T;ENSP00000266692:A239T	ENSP00000228327:A239T	A	+	1	0	NAV3	76912757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.584000	0.67490	2.824000	0.97209	0.655000	0.94253	GCA		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78388626	G	A	78388626	3	1	92	1	0	0	0	0	1	0	0	0	10215	1319	46	3	737	3	NAV3	12	78388626	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	9158154	78388626	55463269	154	25251										
VSIG10	54621	hgsc.bcm.edu	37	chr12	118520062	118520062	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aagttgactgtcaggttgtgGccaaaggactcgctgctgga	14	8	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr12:118520062G>C	ENST00000359236.5	-	3	810	c.534C>G	c.(532-534)ggC>ggG	p.G178G	VSIG10_ENST00000536905.1_5'Flank	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	178	Ig-like C2-type 2.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						TCAGGTTGTGGCCAAAGGACT	0.537																																																0			12											124	126	125					12																	118520062		2017	4177	6194	117004445	SO:0001819	synonymous_variant	0				CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.534C>G	12.37:g.118520062G>C			117004445	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																				0.537	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		C	118520062	G	C	118520062	2	2	92	1	0	0	0	0	0	0	0	1	17263	1190	42	5		5	VSIG10	12	118520062	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	40131436	118520062	15331833	155	25252										
NBEA	26960	hgsc.bcm.edu	37	chr13	36223948	36223948	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggtgacagtgacttgcagcCgactctttgcagtgaataga	12	8	1	4			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr13:36223948C>T	ENST00000400445.3	+	51	8398	c.7864C>T	c.(7864-7866)Cga>Tga	p.R2622*	NBEA_ENST00000379922.3_Nonsense_Mutation_p.R200*|NBEA_ENST00000540320.1_Nonsense_Mutation_p.R2622*|NBEA_ENST00000537702.1_Nonsense_Mutation_p.R415*|NBEA_ENST00000310336.4_Nonsense_Mutation_p.R2622*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.R2619*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2622					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GACTTGCAGCCGACTCTTTGC	0.443																																																0			13											103	103	103					13																	36223948		2047	4188	6235	35121948	SO:0001587	stop_gained	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.7864C>T	13.37:g.36223948C>T	ENSP00000383295:p.Arg2622*		35121948	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	40	8.365577	0.98779	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	.	.	.	5.4	0.701	0.18104	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4671	0.75409	0.5776:0.4224:0.0:0.0	.	.	.	.	X	2622;2622;2619;2622;1249;200;415;200	.	ENSP00000308534:R2622X	R	+	1	2	NBEA	35121948	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	1.023000	0.30065	-0.106000	0.12110	0.563000	0.77884	CGA		0.443	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	36223948	C	T	36223948	4	4	92	1	0	0	0	0	0	1	0	0	10217	644	23	1	8066	1	NBEA	13	36223948	Nonsense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		36223948	78945930	156	25253										
ZNF828	283489	hgsc.bcm.edu	37	chr13	115090225	115090225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctccccagagcctaggagacCagcccccgctgtgtcaccag	10	18	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr13:115090225C>T	ENST00000361283.1	+	3	1217	c.908C>T	c.(907-909)cCa>cTa	p.P303L		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	303	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CCTAGGAGACCAGCCCCCGCT	0.602																																																0			13											47	53	51					13																	115090225		2203	4300	6503	114108327	SO:0001583	missense	283489			AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.908C>T	13.37:g.115090225C>T	ENSP00000354730:p.Pro303Leu		114108327	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	37	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323733	0.60634	.	.	ENSG00000198824	ENST00000361283	T	0.01172	5.23	5.92	5.92	0.95590	.	0.000000	0.56097	D	0.000027	T	0.04634	0.0126	M	0.68593	2.085	0.46874	D	0.999238	D	0.69078	0.997	D	0.63033	0.91	T	0.33954	-0.9848	9	.	.	.	-13.4284	10.8522	0.46777	0.1321:0.7996:0.0:0.0683	.	303	Q96JM3	ZN828_HUMAN	L	303	ENSP00000354730:P303L	.	P	+	2	0	ZNF828	114108327	0.136000	0.22515	1.000000	0.80357	0.995000	0.86356	0.700000	0.25601	2.805000	0.96524	0.655000	0.94253	CCA		0.602	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		T	115090225	C	T	115090225	3	4	92	1	0	0	0	0	1	0	0	0	18220	594	21	3	910	3	ZNF828	13	115090225	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	78866277	115090225	79653	157	25254										
MIA2	117153	hgsc.bcm.edu	37	chr14	39717088	39717088	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aaaaattatagaaacagaagAtcaaatagacaagaaaccag	6	5	1	5			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr14:39717088A>G	ENST00000280082.3	+	4	1509	c.1310A>G	c.(1309-1311)gAt>gGt	p.D437G	MIA2_ENST00000556784.1_Missense_Mutation_p.D436G|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.D437G	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	437			D -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		GAAACAGAAGATCAAATAGAC	0.333																																																0			14											58	65	62					14																	39717088		2202	4298	6500	38786839	SO:0001583	missense	117153			BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1310A>G	14.37:g.39717088A>G	ENSP00000280082:p.Asp437Gly		38786839	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.011432	0.35511	.	.	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.49720	0.77;0.79;3.15	5.53	3.17	0.36434	.	0.156215	0.30118	N	0.010373	T	0.40862	0.1134	L	0.59436	1.845	0.29096	N	0.881756	B;B	0.27997	0.125;0.197	B;B	0.28465	0.041;0.09	T	0.32851	-0.9891	9	.	.	.	-1.2413	8.9308	0.35668	0.8432:0.0:0.1568:0.0	.	437;437	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	G	437;436;437	ENSP00000280082:D437G;ENSP00000451934:D436G;ENSP00000452252:D437G	.	D	+	2	0	MIA2;RP11-407N17.3	38786839	0.966000	0.33281	0.848000	0.33437	0.452000	0.32318	1.102000	0.31050	0.909000	0.36697	0.533000	0.62120	GAT		0.333	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39717088	A	G	39717088	3	3	92	1	0	0	0	0	1	0	0	0	9594	333	12	4	1324	4	MIA2	14	39717088	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10		39717088	67632452	158	25255										
C14orf169	399671	hgsc.bcm.edu	37	chr14	73959403	73959403	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gatagctcggctggtgggtgAggggggccatttgtttctct	17	7	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr14:73959403A>G	ENST00000553558.1	-	17	3166				C14orf169_ENST00000531973.1_RNA|HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4											breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		CTGGTGGGTGAGGGGGGCCAT	0.517																																																0			14											55	61	59					14																	73959403		1883	4110	5993	73029156	SO:0001627	intron_variant	79697			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2844+366T>C	14.37:g.73959403A>G			73029156	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2																																																																																				0.517	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		G	73959403	A	G	73959403	1	3	92	0	1	0	0	0	0	0	0	0	1762	295	11	4		4	C14orf169	14	73959403	Intron	SNP	A	TCGA-CL-5918-01A-11D-1657-10	34242315	73959403	33390137	159	25256										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610293	81610293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agaggatggctgtgttgatcTtcaccgacttcatatgcatg	11	8	3	2	rs121908861		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr14:81610293T>C	ENST00000541158.2	+	11	2213	c.1891T>C	c.(1891-1893)Ttc>Ctc	p.F631L	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Missense_Mutation_p.F631L			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	631			F -> C (in hyperthyroidism; associated with hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:8045989}.|F -> L (in HTNA; gain of function; found in toxic thyroid nodules and hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:11434721, ECO:0000269|PubMed:7800007, ECO:0000269|PubMed:9253356}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.F631L(3)|p.F631I(2)|p.F631V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGTGTTGATCTTCACCGACTT	0.458			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	6	Substitution - Missense(6)	thyroid(6)	14	GRCh37	CM056416|CM941336	TSHR	M	rs121908861						214	189	197					14																	81610293		2203	4300	6503	80680046	SO:0001583	missense	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1891T>C	14.37:g.81610293T>C	ENSP00000441235:p.Phe631Leu		80680046	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409258	0.83340	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.32023	1.47;1.47	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.59649	0.2209	M	0.83312	2.635	0.80722	A	1	D	0.76494	0.999	D	0.85130	0.997	T	0.70128	-0.4957	9	0.87932	D	0	.	15.3712	0.74568	0.0:0.0:0.0:1.0	.	631	F5GYU5	.	L	631;278;631	ENSP00000441235:F631L;ENSP00000298171:F631L	ENSP00000298171:F631L	F	+	1	0	TSHR	80680046	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	8.040000	0.89188	2.042000	0.60477	0.459000	0.35465	TTC		0.458	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		C	81610293	T	C	81610293	3	2	92	1	0	0	0	0	1	0	0	0	16662	1609	56	4	2066	4	TSHR	14	81610293	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	7650890	81610293	25739247	160	25257										
PRIMA1	145270	hgsc.bcm.edu	37	chr14	94245652	94245652	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gacttctggggctcaccatgCgtcacctgtacacatgggca	11	13	3	0	rs4900195	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr14:94245652C>T	ENST00000393140.1	-	3	201	c.99G>A	c.(97-99)acG>acA	p.T33T	PRIMA1_ENST00000393143.1_Silent_p.T33T|PRIMA1_ENST00000316227.3_Silent_p.T33T	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	33					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		GCTCACCATGCGTCACCTGTA	0.647													C|||	1818	0.363019	0.3949	0.3573	5008	,	,		9432	0.2302		0.4692	False		,,,				2504	0.3517															0			14						C		1764,2638		367,1030,804	40	34	36		99	-8.8	0.2	14	dbSNP_111	36	4098,4500		978,2142,1179	no	coding-synonymous	PRIMA1	NM_178013.3		1345,3172,1983	TT,TC,CC		47.6622,40.0727,45.0923		33/154	94245652	5862,7138	2201	4299	6500	93315405	SO:0001819	synonymous_variant	145270				CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"membrane anchor of acetylcholinesterase"	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.99G>A	14.37:g.94245652C>T			93315405	Q86XR6	Silent	SNP	ENST00000393140.1	37	CCDS9912.1																																																																																				0.647	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013		T	94245652	C	T	94245652	2	4	92	1	0	0	0	0	0	0	0	1	12526	755	27	1		1	PRIMA1	14	94245652	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	12635359	94245652	13103888	161	25258										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23811330	23811330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cactgagggtggcgtttcgcCgcctggggcctctgcaggtg	17	12	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr15:23811330C>T	ENST00000314520.3	+	1	877	c.401C>T	c.(400-402)cCg>cTg	p.P134L	MKRN3_ENST00000564592.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	134					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		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)		GGCGTTTCGCCGCCTGGGGCC	0.632																																																0			15											41	44	43					15																	23811330		2203	4300	6503	21362423	SO:0001583	missense	7681			U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.401C>T	15.37:g.23811330C>T	ENSP00000313881:p.Pro134Leu		21362423		Missense_Mutation	SNP	ENST00000314520.3	37	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	C	7.925	0.739472	0.15642	.	.	ENSG00000179455	ENST00000314520	T	0.31247	1.5	3.47	-6.93	0.01638	.	0.309525	0.30392	N	0.009721	T	0.06325	0.0163	N	0.01668	-0.77	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.11941	-1.0567	10	0.26408	T	0.33	.	1.5294	0.02532	0.4863:0.152:0.1054:0.2563	.	134	Q13064	MKRN3_HUMAN	L	134	ENSP00000313881:P134L	ENSP00000313881:P134L	P	+	2	0	MKRN3	21362423	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.678000	0.05209	-2.070000	0.00881	-1.114000	0.02060	CCG		0.632	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		T	23811330	C	T	23811330	3	4	92	1	0	0	0	0	1	0	0	0	9638	652	23	1	403	1	MKRN3	15	23811330	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		23811330	78720062	162	25259										
RFX7	64864	hgsc.bcm.edu	37	chr15	56385633	56385633	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttcatggattcactgcaaatTtgttgaaataatgggtcatt	8	5	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr15:56385633T>C	ENST00000559447.2	-	9	4273	c.4002A>G	c.(4000-4002)caA>caG	p.Q1334Q	RFX7_ENST00000422057.1_Intron|RFX7_ENST00000317318.6_Intron|RFX7_ENST00000423270.1_Silent_p.Q1431Q			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	1334					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CACTGCAAATTTGTTGAAATA	0.373																																																0			15											111	101	104					15																	56385633		1872	4103	5975	54172925	SO:0001819	synonymous_variant	64864					15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.4002A>G	15.37:g.56385633T>C			54172925	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																					0.373	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56385633	T	C	56385633	2	2	92	1	0	0	0	0	0	0	0	1	13305	1838	64	4		4	RFX7	15	56385633	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	32574303	56385633	46145759	163	25260										
ANXA2	302	hgsc.bcm.edu	37	chr15	60690089	60690089	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cccttcttcccagcgtctccAcaccccgctagctggcggcc	8	21	2	0	rs12904657	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr15:60690089A>G	ENST00000396024.3	-	1	44				ANXA2_ENST00000332680.4_Silent_p.C8C|ANXA2_ENST00000421017.2_Intron|ANXA2_ENST00000451270.2_Intron|ANXA2_ENST00000557937.1_Intron	NM_001136015.2	NP_001129487.1	P07355	ANXA2_HUMAN	annexin A2						angiogenesis (GO:0001525)|body fluid secretion (GO:0007589)|cellular response to acid chemical (GO:0071229)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|membrane budding (GO:0006900)|membrane raft assembly (GO:0001765)|negative regulation of catalytic activity (GO:0043086)|osteoclast development (GO:0036035)|positive regulation of binding (GO:0051099)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vesicle fusion (GO:0031340)|protein heterotetramerization (GO:0051290)|protein targeting to plasma membrane (GO:0072661)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell surface (GO:0009986)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|late endosome membrane (GO:0031902)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)|midbody (GO:0030496)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|sarcolemma (GO:0042383)|Schmidt-Lanterman incisure (GO:0043220)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phospholipase A2 inhibitor activity (GO:0019834)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)	p.C8C(1)		kidney(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9					Tenecteplase(DB00031)	CAGCGTCTCCACACCCCGCTA	0.741													g|||	3978	0.794329	0.7859	0.7752	5008	,	,		7804	0.9087		0.7187	False		,,,				2504	0.7791															1	Substitution - coding silent(1)	prostate(1)	15							,,,	3229,943		1289,651,146	5	7	6		,24,,	-5.9	0	15	dbSNP_121	6	5975,2181		2248,1479,351	no	intron,coding-synonymous,intron,intron	ANXA2	NM_001002857.1,NM_001002858.2,NM_001136015.2,NM_004039.2	,,,	3537,2130,497	GG,GA,AA		26.741,22.6031,25.3407	,,,	,8/358,,	60690089	9204,3124	2086	4078	6164	58477381	SO:0001627	intron_variant	302			D00017	CCDS10175.1, CCDS32256.1	15q22.2	2012-10-02			ENSG00000182718	ENSG00000182718		"Annexins"	537	protein-coding gene	gene with protein product	"annexin II"	151740		ANX2, ANX2L4, CAL1H, LPC2D		7961821	Standard	NM_001136015		Approved	LIP2	uc002agm.3	P07355	OTTHUMG00000132763	ENST00000396024.3:c.115+52T>C	15.37:g.60690089A>G			58477381	Q567R4|Q6N0B3|Q8TBV2|Q96DD5|Q9UDH8	Silent	SNP	ENST00000396024.3	37	CCDS10175.1																																																																																				0.741	ANXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256135.1	NM_001002857		G	60690089	A	G	60690089	1	3	92	0	1	0	0	0	0	0	0	0	718	157	6	4		4	ANXA2	15	60690089	Intron	SNP	A	TCGA-CL-5918-01A-11D-1657-10	4304456	60690089	41841303	164	25261										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982275	75982275	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tcctccagcctgcagccggcTgccatgttgcgcgtcagcaa	11	16	1	0	rs146234778		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr15:75982275T>C	ENST00000308508.5	-	3	1223	c.1131A>G	c.(1129-1131)gcA>gcG	p.A377A		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	377	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGCAGCCGGCTGCCATGTTGC	0.622																																																0			15											10	12	12					15																	75982275		2044	4033	6077	73769330	SO:0001819	synonymous_variant	1464			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1131A>G	15.37:g.75982275T>C			73769330	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																				0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75982275	T	C	75982275	2	2	92	1	0	0	0	0	0	0	0	1	3966	1567	55	4		4	CSPG4	15	75982275	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	15292186	75982275	26549117	165	25262										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982565	75982565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gacctcatggggctgcccatCggccacaggcacactgttgt	12	14	1	0	rs140241379		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr15:75982565C>T	ENST00000308508.5	-	3	933	c.841G>A	c.(841-843)Gat>Aat	p.D281N		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	281	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GGCTGCCCATCGGCCACAGGC	0.582													C|||	1	0.000199681	0	0.0014	5008	,	,		20761	0		0	False		,,,				2504	0															0			15						C	ASN/ASP	1,4393		0,1,2196	51	45	47		841	5	0.9	15	dbSNP_134	47	0,8584		0,0,4292	no	missense	CSPG4	NM_001897.4	23	0,1,6488	TT,TC,CC		0.0,0.0228,0.0077	probably-damaging	281/2323	75982565	1,12977	2197	4292	6489	73769620	SO:0001583	missense	1464			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.841G>A	15.37:g.75982565C>T	ENSP00000312506:p.Asp281Asn		73769620	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	21.2	4.120267	0.77323	2.28E-4	0.0	ENSG00000173546	ENST00000308508	T	0.78126	-1.15	5.04	5.04	0.67666	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	D	0.000002	D	0.86814	0.6023	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86604	0.1868	10	0.44086	T	0.13	.	17.3697	0.87373	0.0:1.0:0.0:0.0	.	281	Q6UVK1	CSPG4_HUMAN	N	281	ENSP00000312506:D281N	ENSP00000312506:D281N	D	-	1	0	CSPG4	73769620	1.000000	0.71417	0.933000	0.37362	0.297000	0.27493	5.771000	0.68881	2.345000	0.79718	0.555000	0.69702	GAT		0.582	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75982565	C	T	75982565	3	4	92	1	0	0	0	0	1	0	0	0	3966	884	31	1	6159	1	CSPG4	15	75982565	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	290	75982565	26548827	166	25263										
CHTF18	63922	hgsc.bcm.edu	37	chr16	847845	847845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgtggccccgcaggggacaCggccccggagcaggactcag	16	15	1	0	rs2294453	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:847845C>T	ENST00000262315.9	+	22	2861	c.2798C>T	c.(2797-2799)aCg>aTg	p.T933M	CHTF18_ENST00000455171.2_Missense_Mutation_p.T961M|CHTF18_ENST00000317063.6_Missense_Mutation_p.T1142M	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	933					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GCAGGGGACACGGCCCCGGAG	0.692													C|||	2	0.000399361	8e-04	0	5008	,	,		7547	0.001		0	False		,,,				2504	0															0			16											14	19	17					16																	847845		1975	4148	6123	787846	SO:0001583	missense	63922			BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.2798C>T	16.37:g.847845C>T	ENSP00000262315:p.Thr933Met		787846	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.61	1.399220	0.25291	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.10573	2.86;2.88;2.89	4.58	-1.61	0.08399	.	1.381520	0.04134	N	0.318414	T	0.05135	0.0137	N	0.08118	0	0.09310	N	1	D;D	0.56746	0.977;0.961	B;B	0.41619	0.361;0.198	T	0.10474	-1.0628	10	0.48119	T	0.1	-1.2312	1.9355	0.03336	0.4258:0.2998:0.1068:0.1676	rs2294453	961;933	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	M	1142;961;933	ENSP00000313029:T1142M;ENSP00000406252:T961M;ENSP00000262315:T933M	ENSP00000262315:T933M	T	+	2	0	CHTF18	787846	0.003000	0.15002	0.000000	0.03702	0.026000	0.11368	-0.037000	0.12164	-0.518000	0.06452	-0.369000	0.07265	ACG		0.692	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		T	847845	C	T	847845	3	4	92	1	0	0	0	0	1	0	0	0	3420	536	19	1	2884	1	CHTF18	16	847845	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		847845	89506908	167	25264										
TBL3	10607	hgsc.bcm.edu	37	chr16	2025189	2025189	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gttgccgttgctccttcagcTccggccgtgacaagatatgt	11	12	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:2025189T>C	ENST00000568546.1	+	8	765	c.637T>C	c.(637-639)Tcc>Ccc	p.S213P		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	213					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						CTCCTTCAGCTCCGGCCGTGA	0.612																																					Melanoma(118;616 1651 35077 38081 48633)											0			16											86	91	89					16																	2025189		2198	4300	6498	1965190	SO:0001630	splice_region_variant	10607			U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.636-1T>C	16.37:g.2025189T>C			1965190	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	37	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.854730	0.51376	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.581723	0.19220	N	0.119693	T	0.78748	0.4332	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80797	-0.1222	9	0.72032	D	0.01	-19.8228	14.6831	0.69031	0.0:0.0:0.0:1.0	.	213	Q12788	TBL3_HUMAN	P	213	.	ENSP00000331815:S213P	S	+	1	0	TBL3	1965190	1.000000	0.71417	0.998000	0.56505	0.789000	0.44602	3.200000	0.51051	2.063000	0.61619	0.533000	0.62120	TCC		0.612	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	Missense_Mutation	C	2025189	T	C	2025189	5	2	92	1	0	0	0	0	0	0	1	0	15682	1565	54	4	667	4	TBL3	16	2025189	Splice_Site	SNP	T	TCGA-CL-5918-01A-11D-1657-10	1177344	2025189	88329564	168	25265										
ZNF500	26048	hgsc.bcm.edu	37	chr16	4802838	4802838	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaagcctttgccacattcggGgcaggtgtacggcttgtcag	14	10	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:4802838G>C	ENST00000219478.6	-	6	1281	c.982C>G	c.(982-984)Ccc>Gcc	p.P328A	ZNF500_ENST00000545009.1_Missense_Mutation_p.P328A|ZNF500_ENST00000591026.1_5'UTR|RP11-127I20.7_ENST00000588099.1_RNA			O60304	ZN500_HUMAN	zinc finger protein 500	328					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						CCACATTCGGGGCAGGTGTAC	0.642																																																0			16											94	81	85					16																	4802838		2197	4300	6497	4742839	SO:0001583	missense	26048			AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"Zinc fingers, C2H2-type", "-", "-", "-"	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.982C>G	16.37:g.4802838G>C	ENSP00000219478:p.Pro328Ala		4742839	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Missense_Mutation	SNP	ENST00000219478.6	37	CCDS32383.1	.	.	.	.	.	.	.	.	.	.	G	0.824	-0.747682	0.03065	.	.	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.06933	3.24;3.24	4.07	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32687	N	0.005775	T	0.04679	0.0127	N	0.26130	0.795	0.09310	N	0.999999	B;B	0.20780	0.048;0.048	B;B	0.21151	0.033;0.033	T	0.43877	-0.9364	10	0.09590	T	0.72	.	5.0747	0.14625	0.1119:0.0:0.6833:0.2048	.	328;328	B4DNN9;O60304	.;ZN500_HUMAN	A	328	ENSP00000445714:P328A;ENSP00000219478:P328A	ENSP00000219478:P328A	P	-	1	0	ZNF500	4742839	0.000000	0.05858	0.140000	0.22221	0.070000	0.16714	-3.234000	0.00546	0.698000	0.31739	0.655000	0.94253	CCC		0.642	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507		C	4802838	G	C	4802838	3	2	92	1	0	0	0	0	1	0	0	0	17987	1232	43	5	464	5	ZNF500	16	4802838	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	2777649	4802838	85551915	169	25266										
RABEP2	79874	hgsc.bcm.edu	37	chr16	28926022	28926022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgaatcagctcctcggcccTcagcagcttcgccttcagct	8	17	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:28926022T>C	ENST00000358201.4	-	4	1102	c.514A>G	c.(514-516)Agg>Ggg	p.R172G	RABEP2_ENST00000561803.1_5'Flank|RABEP2_ENST00000544477.1_Missense_Mutation_p.R101G|RABEP2_ENST00000357573.6_Missense_Mutation_p.R172G	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	172					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						TCCTCGGCCCTCAGCAGCTTC	0.667																																					Pancreas(66;639 1284 10093 31061 49099)											0			16											105	116	112					16																	28926022		2052	4177	6229	28833523	SO:0001583	missense	79874			AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.514A>G	16.37:g.28926022T>C	ENSP00000350934:p.Arg172Gly		28833523		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	9.909	1.209030	0.22205	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.47869	0.86;0.84;0.83	4.84	2.43	0.29744	.	0.492397	0.21112	N	0.079980	T	0.29126	0.0724	N	0.24115	0.695	0.09310	N	1	P;B;B;P	0.36282	0.546;0.152;0.094;0.546	B;B;B;B	0.32980	0.156;0.116;0.054;0.156	T	0.14227	-1.0480	10	0.72032	D	0.01	-12.4765	6.8533	0.24026	0.0:0.0844:0.4663:0.4493	.	101;172;172;172	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	G	172;172;101	ENSP00000350934:R172G;ENSP00000350186:R172G;ENSP00000442798:R101G	ENSP00000350186:R172G	R	-	1	2	RABEP2	28833523	0.000000	0.05858	0.981000	0.43875	0.361000	0.29550	0.082000	0.14847	0.243000	0.21327	0.379000	0.24179	AGG		0.667	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		C	28926022	T	C	28926022	3	2	92	1	0	0	0	0	1	0	0	0	12999	1550	54	4	1235	4	RABEP2	16	28926022	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	24123184	28926022	61428731	170	25267										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30735131	30735131	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	accatccccatctcagccccCttgactgtttctgcttcggg	7	17	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:30735131C>T	ENST00000262518.4	+	25	4771	c.4386C>T	c.(4384-4386)ccC>ccT	p.P1462P	SRCAP_ENST00000344771.4_Silent_p.P1304P|SRCAP_ENST00000395059.2_Silent_p.P1400P	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1462	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCTCAGCCCCCTTGACTGTTT	0.592																																																0			16											218	184	195					16																	30735131		2197	4300	6497	30642632	SO:0001819	synonymous_variant	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4386C>T	16.37:g.30735131C>T			30642632	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																				0.592	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30735131	C	T	30735131	2	4	92	1	0	0	0	0	0	0	0	1	15174	668	24	3		3	SRCAP	16	30735131	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1809109	30735131	59619622	171	25268										
CALB2	794	hgsc.bcm.edu	37	chr16	71411591	71411591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tggcgcagatcctgccaaccGaagagaacttccttctgtgc	10	13	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:71411591G>A	ENST00000302628.4	+	4	360	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	CALB2_ENST00000349553.5_Missense_Mutation_p.E95K	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	95	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				CCTGCCAACCGAAGAGAACTT	0.542																																																0			16											109	98	101					16																	71411591		2198	4300	6498	69969092	SO:0001583	missense	794			X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"EF-hand domain containing"	1435	protein-coding gene	gene with protein product	"calretinin"	114051	"calbindin 2, 29kDa (calretinin)"			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.283G>A	16.37:g.71411591G>A	ENSP00000307508:p.Glu95Lys		69969092	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	ENST00000302628.4	37	CCDS10899.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488449	0.84854	.	.	ENSG00000172137	ENST00000349553;ENST00000302628	T;T	0.81163	-1.39;-1.46	5.48	5.48	0.80851	EF-hand-like domain (1);	0.094703	0.64402	D	0.000001	T	0.79240	0.4412	M	0.72894	2.215	0.80722	D	1	P;B	0.47253	0.892;0.174	B;B	0.38428	0.273;0.128	T	0.80841	-0.1202	10	0.40728	T	0.16	-26.6497	17.2874	0.87146	0.0:0.0:1.0:0.0	.	95;95	A6NER6;P22676	.;CALB2_HUMAN	K	95	ENSP00000340294:E95K;ENSP00000307508:E95K	ENSP00000307508:E95K	E	+	1	0	CALB2	69969092	1.000000	0.71417	0.966000	0.40874	0.913000	0.54294	8.619000	0.90938	2.754000	0.94517	0.603000	0.83216	GAA		0.542	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740		A	71411591	G	A	71411591	3	1	92	1	0	0	0	0	1	0	0	0	2580	1059	37	1	297	1	CALB2	16	71411591	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	40676460	71411591	18943162	172	25269										
DHX38	9785	hgsc.bcm.edu	37	chr16	72135085	72135085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcacagggagcagaaggagcGcaagaaggttggtttcttgg	17	6	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:72135085G>A	ENST00000268482.3	+	10	1888	c.1379G>A	c.(1378-1380)cGc>cAc	p.R460H	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	460					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CAGAAGGAGCGCAAGAAGGTT	0.483																																					Melanoma(97;711 1442 7855 13832 28836)											0			16											117	125	122					16																	72135085		2198	4300	6498	70692586	SO:0001583	missense	9785			AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1379G>A	16.37:g.72135085G>A	ENSP00000268482:p.Arg460His		70692586	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	33	5.280204	0.95489	.	.	ENSG00000140829	ENST00000268482	T	0.48836	0.8	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.86740	2.835	0.80722	D	1	D	0.89917	1.0	D	0.63877	0.919	T	0.77864	-0.2429	10	0.72032	D	0.01	.	19.387	0.94560	0.0:0.0:1.0:0.0	.	460	Q92620	PRP16_HUMAN	H	460	ENSP00000268482:R460H	ENSP00000268482:R460H	R	+	2	0	DHX38	70692586	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.125000	0.94402	2.572000	0.86782	0.655000	0.94253	CGC		0.483	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72135085	G	A	72135085	3	1	92	1	0	0	0	0	1	0	0	0	4522	1087	38	1	1413	1	DHX38	16	72135085	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	723494	72135085	18219668	173	25270										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72993831	72993831	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctccttgctggcgggctcggAggggggcccggccgacgcgg	20	14	0	0	rs7193297	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:72993831A>C	ENST00000268489.5	-	2	886	c.214T>G	c.(214-216)Tcc>Gcc	p.S72A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	72			S -> A (in dbSNP:rs7193297). {ECO:0000269|PubMed:7592926}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GCGGGCTCGGAGGGGGGCCCG	0.701													C|||	2356	0.470447	0.7663	0.3127	5008	,	,		11554	0.2599		0.3946	False		,,,				2504	0.4775															0			16						C	,ALA/SER	2955,1417		1030,895,261	12	16	15		,214	5.1	1	16	dbSNP_116	15	3183,5397		642,1899,1749	yes	intron,missense	ZFHX3	NM_001164766.1,NM_006885.3	,99	1672,2794,2010	CC,CA,AA		37.0979,32.4108,47.3904	,benign	,72/3704	72993831	6138,6814	2186	4290	6476	71551332	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.214T>G	16.37:g.72993831A>C	ENSP00000268489:p.Ser72Ala		71551332	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	948	0.4340659340659341	384	0.7804878048780488	117	0.32320441988950277	150	0.26223776223776224	297	0.391820580474934	C	5.272	0.235641	0.10023	0.675892	0.370979	ENSG00000140836	ENST00000268489	T	0.72505	-0.66	5.11	5.11	0.69529	.	0.000000	0.49916	N	0.000135	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999936893	B	0.12630	0.006	B	0.09377	0.004	T	0.39014	-0.9634	9	0.02654	T	1	.	13.1969	0.59743	0.4111:0.5889:0.0:0.0	rs7193297;rs61311017;rs7193297	72	Q15911	ZFHX3_HUMAN	A	72	ENSP00000268489:S72A	ENSP00000268489:S72A	S	-	1	0	ZFHX3	71551332	0.038000	0.19896	0.980000	0.43619	0.194000	0.23727	0.375000	0.20518	1.168000	0.42723	-0.358000	0.07595	TCC		0.701	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72993831	A	C	72993831	3	2	92	1	0	0	0	0	1	0	0	0	17673	304	11	4	10933	4	ZFHX3	16	72993831	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	858746	72993831	17360922	174	25271										
MPHOSPH6	10200	hgsc.bcm.edu	37	chr16	82203768	82203768	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cttggacaaccttgtctttcGctcggccgccatggtagctt	10	13	1	0	rs2303261	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr16:82203768G>T	ENST00000258169.4	-	1	63	c.13C>A	c.(13-15)Cga>Aga	p.R5R	CTD-2588J6.2_ENST00000563841.1_lincRNA|MPHOSPH6_ENST00000567729.1_5'UTR|MPHOSPH6_ENST00000563504.1_5'UTR|MPHOSPH6_ENST00000569021.1_Silent_p.R5R	NM_005792.2	NP_005783.2	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	5					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(3)	5						CTTGTCTTTCGCTCGGCCGCC	0.692													G|||	3218	0.642572	0.4054	0.8112	5008	,	,		11750	0.7649		0.7475	False		,,,				2504	0.6094															0			16						G		2089,2305		521,1047,629	27	19	22		13	1.4	0.3	16	dbSNP_100	22	6264,2328		2340,1584,372	no	coding-synonymous	MPHOSPH6	NM_005792.2		2861,2631,1001	TT,TG,GG		27.095,47.5421,35.6769		5/161	82203768	8353,4633	2197	4296	6493	80761269	SO:0001819	synonymous_variant	10200			X98263	CCDS10937.1	16q23.3	2008-03-03			ENSG00000135698	ENSG00000135698			7214	protein-coding gene	gene with protein product		605500				8885239	Standard	NM_005792		Approved	MPP6	uc002fgw.3	Q99547	OTTHUMG00000137632	ENST00000258169.4:c.13C>A	16.37:g.82203768G>T			80761269	B2RAF0	Silent	SNP	ENST00000258169.4	37	CCDS10937.1																																																																																				0.692	MPHOSPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269058.1	NM_005792		T	82203768	G	T	82203768	2	4	92	1	0	0	0	0	0	0	0	1	9756	1095	38	2		2	MPHOSPH6	16	82203768	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	9209937	82203768	8150985	175	25272										
YWHAE	7531	hgsc.bcm.edu	37	chr17	1264493	1264493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggaagttctgtcattgcaatAtcactagcagctttataagc	8	8	3	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:1264493A>G	ENST00000264335.8	-	4	738	c.471T>C	c.(469-471)gaT>gaC	p.D157D	YWHAE_ENST00000573026.1_Intron|YWHAE_ENST00000575977.1_Intron|YWHAE_ENST00000571732.1_Silent_p.D135D	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon	157					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)			kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		TCATTGCAATATCACTAGCAG	0.468			T	"FAM22a, FAM22B"	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome																																Dom	yes		17	17p13.3	7531	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)"	yes	M	0			17											134	127	129					17																	1264493		2203	4300	6503	1211243	SO:0001819	synonymous_variant	7531			U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953			12851	protein-coding gene	gene with protein product	"14-3-3 epsilon"	605066	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"			9371399	Standard	NM_006761		Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.471T>C	17.37:g.1264493A>G			1211243	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	Silent	SNP	ENST00000264335.8	37	CCDS11001.1																																																																																				0.468	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259354.3	NM_006761		G	1264493	A	G	1264493	2	3	92	1	0	0	0	0	0	0	0	1	17542	446	16	4		4	YWHAE	17	1264493	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10		1264493	79930717	176	25273										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	92	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	6312601	7577094	73618116	177	25274										
NF1	4763	hgsc.bcm.edu	37	chr17	29562747	29562747	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctccatgcagactctcttccGaggcaacagcttggccagta	9	14	1	1	rs137854556		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:29562747G>T	ENST00000358273.4	+	28	4210	c.3827G>T	c.(3826-3828)cGa>cTa	p.R1276L	NF1_ENST00000356175.3_Missense_Mutation_p.R1276L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1276	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.		R -> G (in NF1; dbSNP:rs199474742). {ECO:0000269|PubMed:15060124}.|R -> P (in NF1; complete loss of GAP activity; dbSNP:rs137854556). {ECO:0000269|PubMed:10712197, ECO:0000269|PubMed:9668168}.|R -> Q (in NF1 and mismatch repair deficient cancer cells; dbSNP:rs137854556). {ECO:0000269|PubMed:10712197, ECO:0000269|PubMed:12522551, ECO:0000269|PubMed:15060124}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.R1276Q(2)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ACTCTCTTCCGAGGCAACAGC	0.398			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	14	Whole gene deletion(8)|Unknown(4)|Substitution - Missense(2)	soft_tissue(7)|large_intestine(2)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17	GRCh37	CM000802|CM983421	NF1	M	rs137854556						165	161	163					17																	29562747		2203	4300	6503	26586873	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3827G>T	17.37:g.29562747G>T	ENSP00000351015:p.Arg1276Leu		26586873	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	35	5.446474	0.96187	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.93426	-3.22;-3.22;-3.22	6.16	6.16	0.99307	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (3);	0.000000	0.85682	D	0.000000	D	0.98321	0.9443	H	0.97829	4.085	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.992;1.0	D;D;D;D	0.97110	1.0;1.0;0.979;1.0	D	0.98581	1.0650	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1276;326;1276;1276	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	L	1276;1276;942	ENSP00000351015:R1276L;ENSP00000348498:R1276L;ENSP00000389907:R942L	ENSP00000348498:R1276L	R	+	2	0	NF1	26586873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.212000	0.95126	2.937000	0.99478	0.650000	0.86243	CGA		0.398	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29562747	G	T	29562747	3	4	92	1	0	0	0	0	1	0	0	0	10387	1058	37	2	3998	2	NF1	17	29562747	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	21985653	29562747	51632463	178	25275										
XYLT2	64132	hgsc.bcm.edu	37	chr17	48437547	48437547	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgtgtgccataggcccctcTccctgcccctccctggagcc	9	20	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:48437547T>C	ENST00000017003.2	+	11	2542	c.2493T>C	c.(2491-2493)tcT>tcC	p.S831S	XYLT2_ENST00000507602.1_Intron	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	831					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					TAGGCCCCTCTCCCTGCCCCT	0.652																																																0			17											41	38	39					17																	48437547		2203	4300	6503	45792546	SO:0001819	synonymous_variant	64132			AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"protein xylosyltransferase 2"	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.2493T>C	17.37:g.48437547T>C			45792546	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	37	CCDS11563.1																																																																																				0.652	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167		C	48437547	T	C	48437547	2	2	92	1	0	0	0	0	0	0	0	1	17504	1538	54	4		4	XYLT2	17	48437547	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	18874800	48437547	32757663	179	25276										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48678509	48678509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcatcaccatcgccatggagCgccccaaaattgacccccac	7	18	1	1	rs376210592		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:48678509C>T	ENST00000359106.5	+	19	3889	c.3889C>T	c.(3889-3891)Cgc>Tgc	p.R1297C	CACNA1G_ENST00000510366.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R1274C|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R1274C|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R1274C|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R1274C|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R1297C|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R1274C|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R1274C|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R1297C|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R1274C|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R1297C|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R1297C|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R1274C|CACNA1G_ENST00000515411.1_Missense_Mutation_p.R1297C|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R1297C	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1297					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CGCCATGGAGCGCCCCAAAAT	0.592																																																0			17						C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4202		0,0,2101	79	78	79		3889,3820,3820,3889,3820,3889,3820,3820,3889,3889,3889,3820,3820,3820,3889	4.8	1	17		79	1,8421		0,1,4210	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1,NM_198397.1	180,180,180,180,180,180,180,180,180,180,180,180,180,180,180	0,1,6311	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1297/2378,1274/2172,1274/2355,1297/2274,1274/2299,1297/2322,1274/2262,1274/2307,1297/2285,1297/2333,1297/2267,1274/2251,1274/2244,1274/2344,1297/1556	48678509	1,12623	2101	4211	6312	46033508	SO:0001583	missense	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.3889C>T	17.37:g.48678509C>T	ENSP00000352011:p.Arg1297Cys		46033508	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.024057	0.75390	0.0	1.19E-4	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896;ENST00000506520	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97553	-4.2;-4.2;-4.33;-4.16;-4.19;-4.19;-4.21;-4.29;-4.28;-4.27;-4.28;-4.15;-4.16;-4.23;-4.17;-4.15;-4.21;-4.16;-4.15;-4.21;-4.2;-4.16;-4.21;-4.15;-4.2;-4.21;-4.43	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.98273	0.9428	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.99;0.986;1.0;0.998;0.996;0.999;0.997;0.994;0.999;0.996;1.0;0.999;0.998;0.996;0.999;0.998;0.999;0.998;0.994;0.999;1.0;0.994;0.996;0.999;1.0;0.974;0.999	D	0.98799	1.0739	10	0.72032	D	0.01	.	13.3255	0.60457	0.158:0.842:0.0:0.0	.	327;1274;1297;1297;1297;1297;1297;1297;1297;1297;1297;1297;1274;1297;1297;1297;1297;1297;1274;1297;1274;1274;1274;1274;1297;1274;1297	B4DKD3;Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	C	1274;1274;1297;1274;1274;1274;1297;1297;1274;1297;1297;1297;1297;1297;1297;1274;1297;1297;1297;1297;1274;1297;1297;1297;1297;1297;112	ENSP00000353990:R1274C;ENSP00000339302:R1274C;ENSP00000392390:R1297C;ENSP00000347078:R1274C;ENSP00000409759:R1274C;ENSP00000425522:R1274C;ENSP00000426261:R1297C;ENSP00000425451:R1297C;ENSP00000422407:R1274C;ENSP00000426814:R1297C;ENSP00000427238:R1297C;ENSP00000423112:R1297C;ENSP00000420918:R1297C;ENSP00000426172:R1297C;ENSP00000423045:R1297C;ENSP00000427173:R1274C;ENSP00000426098:R1297C;ENSP00000425698:R1297C;ENSP00000426232:R1297C;ENSP00000423317:R1297C;ENSP00000350979:R1274C;ENSP00000352011:R1297C;ENSP00000414388:R1297C;ENSP00000423155:R1297C;ENSP00000422268:R1297C;ENSP00000421518:R1297C;ENSP00000427697:R112C	ENSP00000339302:R1274C	R	+	1	0	CACNA1G	46033508	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.822000	0.48073	2.409000	0.81822	0.655000	0.94253	CGC		0.592	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48678509	C	T	48678509	3	4	92	1	0	0	0	0	1	0	0	0	2550	768	27	1	3963	1	CACNA1G	17	48678509	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	240962	48678509	32516701	180	25277										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66871863	66871863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccgtgtttctaaaggtggccCggatggcctgcctataatgt	12	10	1	0	rs146930637		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:66871863C>T	ENST00000269080.2	-	34	4399	c.4262G>A	c.(4261-4263)cGg>cAg	p.R1421Q	ABCA8_ENST00000586539.1_Missense_Mutation_p.R1461Q|ABCA8_ENST00000430352.2_Missense_Mutation_p.R1461Q	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1421	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					AAAGGTGGCCCGGATGGCCTG	0.473													C|||	1	0.000199681	8e-04	0	5008	,	,		19623	0		0	False		,,,				2504	0															0			17						C	GLN/ARG	5,4401	8.1+/-20.4	0,5,2198	64	52	56		4262	2.4	1	17	dbSNP_134	56	0,8600		0,0,4300	no	missense	ABCA8	NM_007168.2	43	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign	1421/1582	66871863	5,13001	2203	4300	6503	64383458	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.4262G>A	17.37:g.66871863C>T	ENSP00000269080:p.Arg1421Gln		64383458	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.755506	0.31046	0.001135	0.0	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.95588	-3.75;-3.75	4.36	2.37	0.29283	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.468940	0.17679	N	0.165687	D	0.87103	0.6094	N	0.21545	0.675	0.29142	N	0.878978	B;B;P	0.34639	0.087;0.157;0.461	B;B;B	0.28784	0.017;0.084;0.094	T	0.78917	-0.2015	10	0.06365	T	0.9	.	9.2127	0.37328	0.0:0.7493:0.0:0.2507	.	1461;1461;1421	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	Q	1421;1461	ENSP00000269080:R1421Q;ENSP00000402814:R1461Q	ENSP00000269080:R1421Q	R	-	2	0	ABCA8	64383458	0.063000	0.20901	0.998000	0.56505	0.711000	0.40976	0.542000	0.23222	0.609000	0.30018	-0.142000	0.14014	CGG		0.473	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66871863	C	T	66871863	3	4	92	1	0	0	0	0	1	0	0	0	38	652	23	1	503	1	ABCA8	17	66871863	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	18193354	66871863	14323347	181	25278										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccgagcggagaatggatgagCctgtgcgggcagagcagggt	19	8	0	3	rs1661715	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:73567846C>T	ENST00000392550.3	+	18	2392	c.2275C>T	c.(2275-2277)Cct>Tct	p.P759S	LLGL2_ENST00000577200.1_Missense_Mutation_p.P759S|LLGL2_ENST00000167462.5_Missense_Mutation_p.P759S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	759			P -> S (in dbSNP:rs1661715). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			AATGGATGAGCCTGTGCGGGC	0.697													C|||	1552	0.309904	0.5915	0.2435	5008	,	,		17459	0.1508		0.2823	False		,,,				2504	0.1687															0			17						C	SER/PRO,SER/PRO	2440,1962		693,1054,454	29	31	30		2275,2275	4.4	0.8	17	dbSNP_89	30	2542,6054		397,1748,2153	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1090,2802,2607	TT,TC,CC		29.5719,44.5706,38.329	benign,benign	759/1021,759/1016	73567846	4982,8016	2201	4298	6499	71079441	SO:0001583	missense	3993			X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2275C>T	17.37:g.73567846C>T	ENSP00000376333:p.Pro759Ser		71079441	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	711	0.32554945054945056	322	0.6544715447154471	87	0.24033149171270718	81	0.14160839160839161	221	0.29155672823219	C	12.78	2.039977	0.35989	0.554294	0.295719	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.08008	3.14;3.26	5.4	4.41	0.53225	.	0.209202	0.51477	D	0.000100	T	0.00012	0.0000	L	0.57536	1.79	0.27633	P	0.947969	B;P;B;B	0.36789	0.434;0.57;0.01;0.003	B;B;B;B	0.39904	0.166;0.313;0.015;0.004	T	0.06516	-1.0822	9	0.33141	T	0.24	-0.6264	10.9596	0.47376	0.1462:0.713:0.1408:0.0	rs1661715;rs17855941;rs60583153;rs1661715	748;748;759;759	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	S	759;759;748	ENSP00000167462:P759S;ENSP00000376333:P759S	ENSP00000167462:P759S	P	+	1	0	LLGL2	71079441	0.854000	0.29725	0.840000	0.33206	0.932000	0.56968	2.448000	0.44926	1.245000	0.43885	0.549000	0.68633	CCT		0.697	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		T	73567846	C	T	73567846	3	4	92	1	0	0	0	0	1	0	0	0	8858	739	26	3	2376	3	LLGL2	17	73567846	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	6695983	73567846	7627364	182	25279										
TBCD	6904	hgsc.bcm.edu	37	chr17	80710099	80710099	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agcgacgaaccggccgcgggCggccccgaggaggaggcgga	20	13	0	0	rs11550067	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:80710099C>T	ENST00000355528.4	+	1	160	c.30C>T	c.(28-30)ggC>ggT	p.G10G	TBCD_ENST00000539345.2_Silent_p.G10G|TBCD_ENST00000397466.2_5'UTR	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	10					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CGGCCGCGGGCGGCCCCGAGG	0.741													C|||	37	0.00738818	0.003	0.0058	5008	,	,		8998	0.0169		0.008	False		,,,				2504	0.0041															0			17						C		9,2997		0,9,1494	3	4	4		30	1.4	0	17	dbSNP_120	4	98,6474		0,98,3188	no	coding-synonymous	TBCD	NM_005993.4		0,107,4682	TT,TC,CC		1.4912,0.2994,1.1171		10/1193	80710099	107,9471	1503	3286	4789	78303388	SO:0001819	synonymous_variant	6904			BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.30C>T	17.37:g.80710099C>T			78303388	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																				0.741	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		T	80710099	C	T	80710099	2	4	92	1	0	0	0	0	0	0	0	1	15672	755	27	1		1	TBCD	17	80710099	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	7142253	80710099	485111	183	25280										
POLRMT	5442	hgsc.bcm.edu	37	chr19	622336	622336	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gggcctcgggcgcccccagcTcctcccagtactgccgcggc	13	20	0	0	rs2238549	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:622336T>G	ENST00000588649.2	-	9	1748	c.1664A>C	c.(1663-1665)gAg>gCg	p.E555A	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	555			E -> A (in dbSNP:rs2238549).		gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|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)		CGCCCCCAGCTCCTCCCAGTA	0.736													G|||	3107	0.620407	0.7421	0.3905	5008	,	,		13238	0.5804		0.505	False		,,,				2504	0.7791															0			19						G	ALA/GLU	2180,1784		674,832,476	3	4	4		1664	0.8	0.2	19	dbSNP_98	4	3162,4714		735,1692,1511	no	missense	POLRMT	NM_005035.3	107	1409,2524,1987	GG,GT,TT		40.1473,45.005,45.1182	benign	555/1231	622336	5342,6498	1982	3938	5920	573336	SO:0001583	missense	5442				CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1664A>C	19.37:g.622336T>G	ENSP00000465759:p.Glu555Ala		573336	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	1206	0.5521978021978022	355	0.7215447154471545	157	0.43370165745856354	311	0.5437062937062938	383	0.5052770448548812	.	0.101	-1.151710	0.01700	0.54995	0.401473	ENSG00000099821	ENST00000215591	T	0.38887	1.11	4.15	0.782	0.18567	.	1.028080	0.07721	N	0.943661	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39563	-0.9608	9	0.07175	T	0.84	-7.4541	3.713	0.08427	0.2656:0.0:0.3311:0.4033	rs2238549;rs60424827	555	O00411	RPOM_HUMAN	A	555	ENSP00000215591:E555A	ENSP00000215591:E555A	E	-	2	0	POLRMT	573336	0.000000	0.05858	0.177000	0.23020	0.499000	0.33736	0.188000	0.17018	-0.062000	0.13088	-0.217000	0.12591	GAG		0.736	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		G	622336	T	G	622336	3	3	92	1	0	0	0	0	1	0	0	0	12269	1551	54	4	2080	4	POLRMT	19	622336	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10		622336	58506647	184	25281										
SPPL2B	56928	hgsc.bcm.edu	37	chr19	2344022	2344022	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atcttcttcgtgttcatcacGcccttcctgaccaaggtagg	8	13	4	1	rs1128392	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:2344022G>A	ENST00000452401.2	+	0	1175							Q8TCT7	SPP2B_HUMAN	signal peptide peptidase like 2B						membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	endosome membrane (GO:0010008)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)						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)		TGTTCATCACGCCCTTCCTGA	0.697													.|||	521	0.104034	0.0303	0.1225	5008	,	,		6412	0.2262		0.0656	False		,,,				2504	0.1043															0			19						G	,	99,3655		3,93,1781	33	36	35		1097,1097	-8.4	0.9	19	dbSNP_86	35	311,7143		7,297,3423	yes	coding-synonymous,coding-synonymous	SPPL2B	NM_001077238.1,NM_152988.2	,	10,390,5204	AA,AG,GG		4.1723,2.6372,3.6581	,	366/512,366/593	2344022	410,10798	1877	3727	5604	2295022			56928				CCDS74252.1, CCDS74253.1	19p13.3	2012-02-21			ENSG00000005206	ENSG00000005206			30627	protein-coding gene	gene with protein product	"intramembrane protease 4"	608239				10819331	Standard	NM_001077238		Approved	IMP4, PSL1, KIAA1532	uc002lvs.3	Q8TCT7			19.37:g.2344022G>A			2295022	D6W609|O60365|Q567S3|Q8IUH9|Q9BUY6|Q9H3M4|Q9NPN2|Q9P1Z6	Missense_Mutation	SNP	ENST00000452401.2	37																																																																																					0.697	SPPL2B-202	KNOWN	basic	processed_transcript	processed_transcript		NM_020172		A	2344022	G	A	2344022	1	1	92	0	1	0	0	0	0	0	0	0	15128	1074	38	1		1	SPPL2B	19	2344022	RNA	SNP	G	TCGA-CL-5918-01A-11D-1657-10	1721686	2344022	56784961	185	25282										
C19orf28	126321	hgsc.bcm.edu	37	chr19	3547269	3547269	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccccggtccccgcccactcaCgttcctcccaatgcacttgt	6	21	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:3547269C>T	ENST00000355415.2	-	6	1193		c.e6+1		MFSD12_ENST00000389395.3_Splice_Site|MFSD12_ENST00000398558.4_Splice_Site|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000591878.1_5'Flank	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12						transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						CGCCCACTCACGTTCCTCCCA	0.627																																																0			19											62	66	64					19																	3547269		1982	4154	6136	3498269	SO:0001630	splice_region_variant	126321			AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 28"	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1023+1G>A	19.37:g.3547269C>T			3498269	A8MXP7|D6W615|E9PAJ8|Q8N459	Splice_Site	SNP	ENST00000355415.2	37	CCDS42465.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995157	0.35226	.	.	ENSG00000161091	ENST00000389395;ENST00000398558;ENST00000355415	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5211	0.87787	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf28	3498269	1.000000	0.71417	0.780000	0.31762	0.005000	0.04900	6.994000	0.76251	2.367000	0.80283	0.555000	0.69702	.		0.627	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	Intron	T	3547269	C	T	3547269	5	4	92	1	0	0	0	0	0	0	1	0	1923	550	19	1	645	1	C19orf28	19	3547269	Splice_Site	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1203247	3547269	55581714	186	25283										
KRI1	1032	hgsc.bcm.edu	37	chr19	10676423	10676423	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tcgcttgagtccgactcggaGctggagtcgctgctgctgtc	14	12	0	1	rs3745245	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:10676423G>A	ENST00000393599.2	-	0	1422				KRI1_ENST00000312962.6_Silent_p.S52S|KRI1_ENST00000361821.5_Silent_p.S48S|KRI1_ENST00000537964.1_5'UTR	NM_001800.3|NM_079421.2	NP_001791.1|NP_524145.1	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)						autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to retinoic acid (GO:0032526)|response to UV (GO:0009411)|response to vitamin D (GO:0033280)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)			endometrium(3)|lung(2)|ovary(1)	6			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			CCGACTCGGAGCTGGAGTCGC	0.716													g|||	3035	0.60603	0.7474	0.4726	5008	,	,		11812	0.3472		0.7773	False		,,,				2504	0.6002															0			19								3281,1103		1238,805,149	17	18	18		156	2.1	1	19	dbSNP_107	18	6392,2178		2405,1582,298	no	coding-synonymous	KRI1	NM_023008.3		3643,2387,447	AA,AG,GG		25.4142,25.1597,25.3281		52/710	10676423	9673,3281	2192	4285	6477	10537423	SO:0001628	intergenic_variant	65095				CCDS12244.1	19p13	2013-01-10				ENSG00000129355		"Ankyrin repeat domain containing"	1790	protein-coding gene	gene with protein product		600927				8575754	Standard	NM_079421		Approved	INK4D, p19	uc002mpa.3	P55273			19.37:g.10676423G>A			10537423	Q13102|Q6FGE9	Silent	SNP	ENST00000393599.2	37	CCDS12244.1																																																																																				0.716	CDKN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452030.1	NM_079421		A	10676423	G	A	10676423	1	1	92	0	1	0	0	0	0	0	0	0	8465	962	34	3		3	KRI1	19	10676423	IGR	SNP	G	TCGA-CL-5918-01A-11D-1657-10	7129154	10676423	48452560	187	25284										
DNM2	1785	hgsc.bcm.edu	37	chr19	10906754	10906754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	caggaccgggcttttcacccCggacttggcattcgaggcca	12	14	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:10906754C>T	ENST00000355667.6	+	10	1294	c.1214C>T	c.(1213-1215)cCg>cTg	p.P405L	DNM2_ENST00000314646.5_Intron|DNM2_ENST00000408974.4_Intron|DNM2_ENST00000585892.1_Missense_Mutation_p.P405L|DNM2_ENST00000359692.6_Missense_Mutation_p.P405L|DNM2_ENST00000389253.4_Intron	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	405					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CTTTTCACCCCGGACTTGGCA	0.532			"F, N, Splice, Mis, O"		ETP ALL																																		Rec	yes		19	19p13.2	1785	dynamin 2		L	0			19											118	118	118					19																	10906754		2203	4300	6503	10767754	SO:0001583	missense	1785				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1214C>T	19.37:g.10906754C>T	ENSP00000347890:p.Pro405Leu		10767754	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.783730	0.90282	.	.	ENSG00000079805	ENST00000355667;ENST00000359692	T;T	0.75260	-0.92;-0.92	4.7	4.7	0.59300	Dynamin central domain (1);	.	.	.	.	D	0.90625	0.7060	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.74348	0.927;0.983	D	0.93996	0.7271	9	0.87932	D	0	.	16.4349	0.83872	0.0:1.0:0.0:0.0	.	405;405	P50570-2;P50570	.;DYN2_HUMAN	L	405	ENSP00000347890:P405L;ENSP00000352721:P405L	ENSP00000347890:P405L	P	+	2	0	DNM2	10767754	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.792000	0.85828	2.174000	0.68829	0.561000	0.74099	CCG		0.532	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		T	10906754	C	T	10906754	3	4	92	1	0	0	0	0	1	0	0	0	4683	652	23	1	1252	1	DNM2	19	10906754	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	230331	10906754	48222229	188	25285										
RGL3	57139	hgsc.bcm.edu	37	chr19	11527625	11527625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaagctggggtcctgctcacGgtctccaaacaccaactctc	9	15	3	0	rs149175134		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:11527625G>A	ENST00000380456.3	-	3	319	c.256C>T	c.(256-258)Cgt>Tgt	p.R86C	RGL3_ENST00000393423.3_Missense_Mutation_p.R86C	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	86	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						TCCTGCTCACGGTCTCCAAAC	0.627																																					GBM(174;751 2067 17998 27979 33959)											0			19						G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	72	69	70		256,256	4.2	0.6	19	dbSNP_134	70	0,8600		0,0,4300	no	missense,missense	RGL3	NM_001035223.2,NM_001161616.1	180,180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging	86/711,86/717	11527625	2,13004	2203	4300	6503	11388625	SO:0001583	missense	57139			BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.256C>T	19.37:g.11527625G>A	ENSP00000369823:p.Arg86Cys		11388625	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155455	0.38021	4.54E-4	0.0	ENSG00000205517	ENST00000393423;ENST00000380456;ENST00000453604	T;T	0.53857	0.6;0.6	4.2	4.2	0.49525	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.945929	0.08909	N	0.876194	T	0.52613	0.1745	M	0.63843	1.955	0.21020	N	0.9998	B;B;B	0.23377	0.081;0.084;0.083	B;B;B	0.24701	0.017;0.055;0.013	T	0.47636	-0.9102	10	0.56958	D	0.05	.	10.5043	0.44823	0.0:0.1979:0.8021:0.0	.	86;86;86	B4DPC9;Q3MIN7;B5ME84	.;RGL3_HUMAN;.	C	86	ENSP00000377075:R86C;ENSP00000369823:R86C	ENSP00000369823:R86C	R	-	1	0	RGL3	11388625	0.470000	0.25854	0.592000	0.28758	0.846000	0.48090	1.971000	0.40530	2.046000	0.60703	0.561000	0.74099	CGT		0.627	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		A	11527625	G	A	11527625	3	1	92	1	0	0	0	0	1	0	0	0	13315	1116	39	1	1962	1	RGL3	19	11527625	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	620871	11527625	47601358	189	25286										
BEST2	54831	hgsc.bcm.edu	37	chr19	12866196	12866196	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cctgtatccacccccaggagCtgaatgtttttcggggcaaa	10	12	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:12866196C>A	ENST00000549706.1	+	6	964	c.640C>A	c.(640-642)Ctg>Atg	p.L214M	BEST2_ENST00000553030.1_Missense_Mutation_p.L214M|BEST2_ENST00000042931.1_Missense_Mutation_p.L214M			Q8NFU1	BEST2_HUMAN	bestrophin 2	214					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						CCCCCAGGAGCTGAATGTTTT	0.507																																																0			19											114	113	114					19																	12866196		1976	4142	6118	12727196	SO:0001583	missense	54831			AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17107	protein-coding gene	gene with protein product		607335	"vitelliform macular dystrophy 2-like 1"	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.640C>A	19.37:g.12866196C>A	ENSP00000448310:p.Leu214Met		12727196	Q53YQ8|Q9NXP0	Missense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935476	0.52866	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	D;D;D	0.99259	-5.64;-5.64;-5.64	4.13	4.13	0.48395	.	0.000000	0.56097	D	0.000021	D	0.98516	0.9505	L	0.42529	1.33	0.80722	D	1	B	0.33379	0.41	P	0.48488	0.579	D	0.99044	1.0825	10	0.19147	T	0.46	-20.8582	15.6627	0.77199	0.0:1.0:0.0:0.0	.	214	Q8NFU1	BEST2_HUMAN	M	214	ENSP00000448310:L214M;ENSP00000447203:L214M;ENSP00000042931:L214M	ENSP00000042931:L214M	L	+	1	2	BEST2	12727196	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.333000	0.43912	2.283000	0.76528	0.544000	0.68410	CTG		0.507	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682		A	12866196	C	A	12866196	3	1	92	1	0	0	0	0	1	0	0	0	1406	796	28	2	658	2	BEST2	19	12866196	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1338571	12866196	46262787	190	25287										
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15807034	15807034	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aactgtgtggccggatcctgAggtgctgccttccccattca	11	13	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:15807034A>G	ENST00000550308.1	+	11	1693	c.1313A>G	c.(1312-1314)gAg>gGg	p.E438G	CYP4F12_ENST00000324632.10_Splice_Site_p.E438G	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	438					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CCGGATCCTGAGGTGCTGCCT	0.542																																																0			19											101	104	103					19																	15807034		2194	4298	6492	15668034	SO:0001630	splice_region_variant	66002			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"Cytochrome P450s"	18857	protein-coding gene	gene with protein product		611485	"cytochrome P450, subfamily IVF, polypeptide 12"			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1314+1A>G	19.37:g.15807034A>G			15668034	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	.	.	.	.	.	.	.	.	.	.	.	19.15	3.771364	0.69992	.	.	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.73897	-0.79;-0.79	2.31	2.31	0.28768	.	0.282260	0.28403	U	0.015479	D	0.86393	0.5922	M	0.92122	3.275	0.32839	D	0.505115	P	0.36944	0.574	P	0.56563	0.801	D	0.88966	0.3397	10	0.87932	D	0	.	8.4933	0.33112	1.0:0.0:0.0:0.0	.	438	Q9HCS2	CP4FC_HUMAN	G	438	ENSP00000448998:E438G;ENSP00000321821:E438G	ENSP00000321821:E438G	E	+	2	0	CYP4F12	15668034	1.000000	0.71417	0.996000	0.52242	0.489000	0.33432	3.310000	0.51911	1.308000	0.44962	0.260000	0.18958	GAG		0.542	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		Missense_Mutation	G	15807034	A	G	15807034	5	3	92	1	0	0	0	0	0	0	1	0	4193	318	11	4	1351	4	CYP4F12	19	15807034	Splice_Site	SNP	A	TCGA-CL-5918-01A-11D-1657-10	2940838	15807034	43321949	191	25288										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18377048	18377048	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aggctcttcatgatggaagcCagaagggaaacctgaggtcg	14	8	2	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:18377048C>G	ENST00000600328.3	-	3	1495	c.1302G>C	c.(1300-1302)ctG>ctC	p.L434L	KIAA1683_ENST00000600359.3_Silent_p.L388L|KIAA1683_ENST00000392413.4_Silent_p.L434L			Q9H0B3	K1683_HUMAN	KIAA1683	434						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TGATGGAAGCCAGAAGGGAAA	0.617																																																0			19											86	80	82					19																	18377048		2203	4300	6503	18238048	SO:0001819	synonymous_variant	80726			AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1302G>C	19.37:g.18377048C>G			18238048	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																				0.617	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			G	18377048	C	G	18377048	2	3	92	1	0	0	0	0	0	0	0	1	8272	581	21	5		5	KIAA1683	19	18377048	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	2570014	18377048	40751935	192	25289										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363649	22363649	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	atgagctttgaggacgagttGgaagctttgccacattcttc	11	8	1	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:22363649G>T	ENST00000397121.2	-	3	1187	c.870C>A	c.(868-870)tcC>tcA	p.S290S		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				AGGACGAGTTGGAAGCTTTGC	0.438																																																0			19											98	103	102					19																	22363649		2155	4281	6436	22155489	SO:0001819	synonymous_variant	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.870C>A	19.37:g.22363649G>T			22155489	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																				0.438	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		T	22363649	G	T	22363649	2	4	92	1	0	0	0	0	0	0	0	1	18122	1335	47	2		2	ZNF676	19	22363649	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	3986601	22363649	36765334	193	25290										
ZNF574	64763	hgsc.bcm.edu	37	chr19	42583249	42583249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgcccctgttgtcctggggtCcccagttgttctagggcctc	12	14	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:42583249C>T	ENST00000600245.1	+	2	1146	c.491C>T	c.(490-492)tCc>tTc	p.S164F	ZNF574_ENST00000359044.4_Missense_Mutation_p.S164F|CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000222339.7_Missense_Mutation_p.S254F			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				GTCCTGGGGTCCCCAGTTGTT	0.647																																																0			19											52	61	58					19																	42583249		2203	4300	6503	47275089	SO:0001583	missense	64763			AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"Zinc fingers, C2H2-type"	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.491C>T	19.37:g.42583249C>T	ENSP00000469029:p.Ser164Phe		47275089	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352390	0.41700	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.06933	3.24;3.26	4.49	4.49	0.54785	.	0.732373	0.12350	N	0.476665	T	0.14056	0.0340	N	0.08118	0	0.28916	N	0.892436	D;D	0.69078	0.984;0.997	D;D	0.80764	0.979;0.994	T	0.31971	-0.9924	10	0.87932	D	0	-20.8679	14.7029	0.69168	0.0:1.0:0.0:0.0	.	164;253	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	F	254;164	ENSP00000222339:S254F;ENSP00000351939:S164F	ENSP00000222339:S254F	S	+	2	0	ZNF574	47275089	0.825000	0.29262	1.000000	0.80357	0.964000	0.63967	-0.229000	0.09098	2.322000	0.78497	0.591000	0.81541	TCC		0.647	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752		T	42583249	C	T	42583249	3	4	92	1	0	0	0	0	1	0	0	0	18045	855	30	3	493	3	ZNF574	19	42583249	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	20219600	42583249	16545734	194	25291										
ZNF574	64763	hgsc.bcm.edu	37	chr19	42584961	42584961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cccctgcggcccctgcccgcCgccggggtctagagtgcagc	14	19	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:42584961C>T	ENST00000600245.1	+	2	2858	c.2203C>T	c.(2203-2205)Cgc>Tgc	p.R735C	ZNF574_ENST00000359044.4_Missense_Mutation_p.R735C|CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000222339.7_Missense_Mutation_p.R825C			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	735					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				CCCTGCCCGCCGCCGGGGTCT	0.672																																																0			19											71	81	78					19																	42584961		2203	4300	6503	47276801	SO:0001583	missense	64763			AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"Zinc fingers, C2H2-type"	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.2203C>T	19.37:g.42584961C>T	ENSP00000469029:p.Arg735Cys		47276801	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.753815	0.31046	.	.	ENSG00000105732	ENST00000222339;ENST00000359044;ENST00000535775	T;T	0.07444	3.19;3.21	5.5	4.47	0.54385	.	0.000000	0.46442	D	0.000296	T	0.06188	0.0160	N	0.24115	0.695	0.44937	D	0.997951	B;B	0.14805	0.002;0.011	B;B	0.06405	0.0;0.002	T	0.21109	-1.0255	10	0.87932	D	0	-24.5143	7.8923	0.29686	0.0:0.7518:0.1619:0.0863	.	735;824	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	C	825;735;342	ENSP00000222339:R825C;ENSP00000351939:R735C	ENSP00000222339:R825C	R	+	1	0	ZNF574	47276801	0.000000	0.05858	0.985000	0.45067	0.271000	0.26615	-0.098000	0.11024	1.326000	0.45319	-0.142000	0.14014	CGC		0.672	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752		T	42584961	C	T	42584961	3	4	92	1	0	0	0	0	1	0	0	0	18045	652	23	1	2205	1	ZNF574	19	42584961	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1712	42584961	16544022	195	25292										
ZNF234	10780	hgsc.bcm.edu	37	chr19	44652970	44652970	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgtggtcttcactgaggaggAgctggggctgctggaccctg	17	9	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:44652970A>G	ENST00000426739.2	+	4	320	c.62A>G	c.(61-63)gAg>gGg	p.E21G	ZNF234_ENST00000592437.1_Missense_Mutation_p.E21G	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				ACTGAGGAGGAGCTGGGGCTG	0.483																																																0			19											199	198	198					19																	44652970		2203	4300	6503	49344810	SO:0001583	missense	10780			X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"Zinc fingers, C2H2-type", "-"	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.62A>G	19.37:g.44652970A>G	ENSP00000400878:p.Glu21Gly		49344810	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084950	0.76642	.	.	ENSG00000167380	ENST00000426739	T	0.12255	2.7	3.85	3.85	0.44370	Krueppel-associated box (4);	.	.	.	.	T	0.51398	0.1672	H	0.98883	4.36	0.30918	N	0.728353	D	0.61080	0.989	P	0.62298	0.9	T	0.68996	-0.5262	9	0.87932	D	0	.	12.0495	0.53500	1.0:0.0:0.0:0.0	.	21	Q14588	ZN234_HUMAN	G	21	ENSP00000400878:E21G	ENSP00000400878:E21G	E	+	2	0	ZNF226	49344810	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.534000	0.53568	1.725000	0.51514	0.459000	0.35465	GAG		0.483	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			G	44652970	A	G	44652970	3	3	92	1	0	0	0	0	1	0	0	0	17826	304	11	4	68	4	ZNF234	19	44652970	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	2068009	44652970	14476013	196	25293										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55098716	55098716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cacagtggagaatctcatccGcatgggtgtggctggcttgg	15	9	1	1	rs199988092		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:55098716G>A	ENST00000251377.3	+	9	1488	c.1355G>A	c.(1354-1356)cGc>cAc	p.R452H	LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.R435H|LILRB1_ENST00000448689.1_Intron|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391737.1_Missense_Mutation_p.R423H|LILRA2_ENST00000391738.3_Missense_Mutation_p.R452H			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	452					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		AATCTCATCCGCATGGGTGTG	0.577													g|||	1	0.000199681	0	0	5008	,	,		20282	0		0.001	False		,,,				2504	0															0			19											122	106	111					19																	55098716		2203	4300	6503	59790528	SO:0001583	missense	11027			U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1355G>A	19.37:g.55098716G>A	ENSP00000251377:p.Arg452His		59790528	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.074	0.997650	0.19043	.	.	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00571	6.52;6.52;6.6;6.5	2.74	-0.133	0.13485	.	24.497700	0.00610	U	0.000408	T	0.00815	0.0027	M	0.84219	2.685	0.09310	N	1	P;B;B	0.36535	0.557;0.196;0.012	B;B;B	0.26693	0.072;0.04;0.008	T	0.50074	-0.8870	10	0.66056	D	0.02	.	4.6957	0.12802	0.4472:0.0:0.5528:0.0	.	423;452;435	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	H	452;452;435;423	ENSP00000251377:R452H;ENSP00000375618:R452H;ENSP00000251376:R435H;ENSP00000375617:R423H	ENSP00000251376:R435H	R	+	2	0	LILRA2	59790528	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.211000	0.17474	-0.100000	0.12241	-0.192000	0.12808	CGC		0.577	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			A	55098716	G	A	55098716	3	1	92	1	0	0	0	0	1	0	0	0	8808	1087	38	1	1385	1	LILRA2	19	55098716	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	10445746	55098716	4030267	197	25294										
CCDC106	29903	hgsc.bcm.edu	37	chr19	56162681	56162681	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggatgaagcctgggcccaggCggatggagggggacagccgt	20	9	0	1	rs371292659		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:56162681C>T	ENST00000586790.1	+	4	1250	c.346C>T	c.(346-348)Cgg>Tgg	p.R116W	CCDC106_ENST00000308964.3_Missense_Mutation_p.R116W|CCDC106_ENST00000588740.1_Missense_Mutation_p.R116W|CCDC106_ENST00000591578.1_Missense_Mutation_p.R116W|U2AF2_ENST00000450554.2_5'Flank|CCDC106_ENST00000591241.1_Missense_Mutation_p.R81W			Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106	116						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|lung(5)|skin(1)	11		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		TGGGCCCAGGCGGATGGAGGG	0.667																																																0			19						C	TRP/ARG	0,4406		0,0,2203	28	32	30		346	-4.3	0.4	19		30	1,8599		0,1,4299	no	missense	CCDC106	NM_013301.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	116/281	56162681	1,13005	2203	4300	6503	60854493	SO:0001583	missense	29903			AF054984	CCDS33118.1	19q13.42	2013-09-20			ENSG00000173581	ENSG00000173581			30181	protein-coding gene	gene with protein product		613478				8619474, 9110174	Standard	XM_005258827		Approved	HSU79303	uc002qlr.3	Q9BWC9	OTTHUMG00000180907	ENST00000586790.1:c.346C>T	19.37:g.56162681C>T	ENSP00000465757:p.Arg116Trp		60854493	B3KUF9|D3K183|Q99786	Missense_Mutation	SNP	ENST00000586790.1	37	CCDS33118.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434644	0.43224	0.0	1.16E-4	ENSG00000173581	ENST00000308964	.	.	.	3.77	-4.3	0.03710	.	0.479059	0.20020	N	0.100923	T	0.61311	0.2337	L	0.38175	1.15	0.39273	D	0.96441	D	0.89917	1.0	D	0.69654	0.965	T	0.65335	-0.6193	9	0.72032	D	0.01	-20.4128	14.9371	0.70964	0.6349:0.3651:0.0:0.0	.	116	Q9BWC9	CC106_HUMAN	W	116	.	ENSP00000309681:R116W	R	+	1	2	CCDC106	60854493	0.993000	0.37304	0.367000	0.25926	0.333000	0.28666	0.052000	0.14163	-0.680000	0.05211	0.655000	0.94253	CGG		0.667	CCDC106-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453593.1	NM_013301		T	56162681	C	T	56162681	3	4	92	1	0	0	0	0	1	0	0	0	2747	759	27	1	360	1	CCDC106	19	56162681	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1063965	56162681	2966302	198	25295										
ZNF471	57573	hgsc.bcm.edu	37	chr19	57036518	57036518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ttttaggtataacacatcttTtattcgtcactggaggagtt	8	6	2	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:57036518T>C	ENST00000308031.5	+	5	1215	c.1082T>C	c.(1081-1083)tTt>tCt	p.F361S	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Silent_p.L221L	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	361			F -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F361C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AACACATCTTTTATTCGTCAC	0.418																																					Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)											1	Substitution - Missense(1)	large_intestine(1)	19											73	78	76					19																	57036518		2203	4300	6503	61728330	SO:0001583	missense	57573			AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1082T>C	19.37:g.57036518T>C	ENSP00000309161:p.Phe361Ser		61728330	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	T	9.110	1.006341	0.19199	.	.	ENSG00000196263	ENST00000308031	T	0.15487	2.42	3.63	2.52	0.30459	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12050	0.0293	L	0.35487	1.065	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19063	-1.0317	9	0.87932	D	0	.	4.2908	0.10878	0.1974:0.0:0.2035:0.5991	.	361	Q9BX82	ZN471_HUMAN	S	361	ENSP00000309161:F361S	ENSP00000309161:F361S	F	+	2	0	ZNF471	61728330	0.067000	0.21026	0.010000	0.14722	0.919000	0.55068	2.707000	0.47143	1.515000	0.48885	0.379000	0.24179	TTT		0.418	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57036518	T	C	57036518	3	2	92	1	0	0	0	0	1	0	0	0	17969	1841	64	4	1096	4	ZNF471	19	57036518	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	873837	57036518	2092465	199	25296										
ZNF154	7710	hgsc.bcm.edu	37	chr19	58216252	58216252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aaaagagccaagttctccagCatcacatcacggtacaggca	8	12	3	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:58216252C>T	ENST00000512439.2	-	2	325	c.129G>A	c.(127-129)atG>atA	p.M43I	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron|ZNF154_ENST00000426889.1_Missense_Mutation_p.M43I			Q13106	ZN154_HUMAN	zinc finger protein 154	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		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;0.0257)		AGTTCTCCAGCATCACATCAC	0.512																																																0			19											174	166	168					19																	58216252		2203	4300	6503	62908064	SO:0001583	missense	7710			U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"Zinc fingers, C2H2-type", "-"	12939	protein-coding gene	gene with protein product		604085	"zinc finger protein 154 (pHZ-92)"			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.129G>A	19.37:g.58216252C>T	ENSP00000421258:p.Met43Ile		62908064	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361406	0.61403	.	.	ENSG00000179909	ENST00000512439;ENST00000426889	T;T	0.03035	4.07;4.07	2.95	2.95	0.34219	Krueppel-associated box (4);	.	.	.	.	T	0.21631	0.0521	M	0.93898	3.47	0.23876	N	0.996598	D	0.62365	0.991	D	0.74023	0.982	T	0.04090	-1.0978	9	0.38643	T	0.18	.	9.5678	0.39409	0.0:1.0:0.0:0.0	.	43	Q13106	ZN154_HUMAN	I	43	ENSP00000421258:M43I;ENSP00000442370:M43I	ENSP00000442370:M43I	M	-	3	0	ZNF154	62908064	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.509000	0.45459	1.966000	0.57179	0.313000	0.20887	ATG		0.512	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			T	58216252	C	T	58216252	3	4	92	1	0	0	0	0	1	0	0	0	17774	710	25	3	1192	3	ZNF154	19	58216252	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	1179734	58216252	912731	200	25297										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59011992	59011992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gatccgaataggaccgaagcGctgctggaaggtctcccaca	12	12	1	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr19:59011992G>A	ENST00000263093.2	-	5	1373	c.1264C>T	c.(1264-1266)Cgc>Tgc	p.R422C	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.R338C|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	422					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GGACCGAAGCGCTGCTGGAAG	0.587																																																0			19											97	91	93					19																	59011992		2203	4300	6503	63703804	SO:0001583	missense	10998			AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1264C>T	19.37:g.59011992G>A	ENSP00000263093:p.Arg422Cys		63703804	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.567790	0.86439	.	.	ENSG00000083807	ENST00000263093	T	0.43688	0.94	5.22	4.18	0.49190	AMP-dependent synthetase/ligase (1);	0.054019	0.64402	D	0.000001	T	0.72590	0.3479	H	0.96015	3.755	0.52501	D	0.99995	D	0.89917	1.0	D	0.97110	1.0	T	0.79137	-0.1927	10	0.87932	D	0	-20.0313	10.0668	0.42308	0.0941:0.0:0.9059:0.0	.	422	Q9Y2P5	S27A5_HUMAN	C	422	ENSP00000263093:R422C	ENSP00000263093:R422C	R	-	1	0	SLC27A5	63703804	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	8.709000	0.91379	1.342000	0.45619	0.563000	0.77884	CGC		0.587	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		A	59011992	G	A	59011992	3	1	92	1	0	0	0	0	1	0	0	0	14566	1087	38	1	832	1	SLC27A5	19	59011992	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	795740	59011992	116991	201	25298										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36845803	36845803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggaactctgcacgttctgccTccccagcccctctggctgta	9	17	3	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:36845803T>C	ENST00000279024.4	-	13	3024	c.2753A>G	c.(2752-2754)gAg>gGg	p.E918G		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	918										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				ACGTTCTGCCTCCCCAGCCCC	0.672																																																0			20											35	30	32					20																	36845803		2203	4300	6503	36279217	SO:0001583	missense	85449			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2753A>G	20.37:g.36845803T>C	ENSP00000279024:p.Glu918Gly		36279217	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.351886	0.24512	.	.	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.25250	3.21;1.81	3.0	1.89	0.25635	.	0.374441	0.19560	N	0.111347	T	0.22282	0.0537	M	0.62723	1.935	0.09310	N	1	P;P	0.43094	0.799;0.557	B;B	0.38562	0.276;0.172	T	0.16571	-1.0398	10	0.72032	D	0.01	.	5.1215	0.14862	0.0:0.1381:0.0:0.8619	.	918;426	Q5JYT7;E9PFS1	K1755_HUMAN;.	G	918;426;217	ENSP00000279024:E918G;ENSP00000393503:E217G	ENSP00000279024:E918G	E	-	2	0	KIAA1755	36279217	0.005000	0.15991	0.008000	0.14137	0.001000	0.01503	0.584000	0.23864	0.552000	0.29026	-0.378000	0.06908	GAG		0.672	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36845803	T	C	36845803	3	2	92	1	0	0	0	0	1	0	0	0	8278	1551	54	4	857	4	KIAA1755	20	36845803	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10		36845803	26179717	202	25299										
TP53TG5	27296	hgsc.bcm.edu	37	chr20	44004158	44004158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gatctcctggaactcttcatTattttgttttgttttattgc	6	7	3	0	rs562359566|rs76663890|rs10546815	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:44004158T>C	ENST00000372726.3	-	4	445	c.289A>G	c.(289-291)Aat>Gat	p.N97D	SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000537995.1_Missense_Mutation_p.N81D|TP53TG5_ENST00000494455.1_5'UTR|SYS1_ENST00000426004.1_3'UTR|SYS1-DBNDD2_ENST00000452133.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	97					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						AACTCTTCATTATTTTGTTTT	0.493																																																0			20											65	37	46					20																	44004158		2179	4104	6283	43437572	SO:0001583	missense	27296			AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.289A>G	20.37:g.44004158T>C	ENSP00000361811:p.Asn97Asp		43437572		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.688512	0.29962	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.15603	2.41;2.41	4.26	-0.689	0.11313	.	0.985537	0.08305	N	0.966325	T	0.11707	0.0285	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.35968	-0.9767	10	0.45353	T	0.12	0.0023	4.23	0.10599	0.0:0.19:0.3451:0.4649	.	97	Q9Y2B4	T53G5_HUMAN	D	97;81	ENSP00000361811:N97D;ENSP00000438374:N81D	ENSP00000361811:N97D	N	-	1	0	TP53TG5	43437572	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.373000	0.07494	-0.143000	0.11334	-0.313000	0.08912	AAT		0.493	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		C	44004158	T	C	44004158	3	2	92	1	0	0	0	0	1	0	0	0	16431	1754	61	4	591	4	TP53TG5	20	44004158	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	7158355	44004158	19021362	203	25300										
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57289017	57289017	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gccgcggtgctcaccaacagCgctgagtgggaggccgcctg	16	14	1	1	rs35104993	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:57289017C>T	ENST00000356091.6	+	10	1458	c.1170C>T	c.(1168-1170)agC>agT	p.S390S	STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.S362S|RP11-261P9.4_ENST00000530479.1_RNA|NPEPL1_ENST00000525817.1_Silent_p.S342S	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	390						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TCACCAACAGCGCTGAGTGGG	0.667													C|||	393	0.0784744	0.0847	0.0749	5008	,	,		15687	0.006		0.0924	False		,,,				2504	0.1329															0			20						C	,,	279,3447		5,269,1589	13	20	18		1086,1026,1170	-2.9	1	20	dbSNP_126	18	656,6926		26,604,3161	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	31,873,4750	TT,TC,CC		8.6521,7.4879,8.2685	,,	362/496,342/476,390/524	57289017	935,10373	1863	3791	5654	56722424	SO:0001819	synonymous_variant	79716			AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1170C>T	20.37:g.57289017C>T			56722424	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																				0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		T	57289017	C	T	57289017	2	4	92	1	0	0	0	0	0	0	0	1	10605	767	27	1		1	NPEPL1	20	57289017	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	13284859	57289017	5736503	204	25301										
SS18L1	26039	hgsc.bcm.edu	37	chr20	60738562	60738562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gtcgcactacagctcggcgcAgggcggcagccagcactacc	13	16	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:60738562A>G	ENST00000331758.3	+	6	631	c.605A>G	c.(604-606)cAg>cGg	p.Q202R	SS18L1_ENST00000370848.4_Missense_Mutation_p.Q205R|SS18L1_ENST00000491916.1_3'UTR|SS18L1_ENST00000421564.1_Missense_Mutation_p.Q202R	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	202	Gln-rich.|Methionine-rich intra-molecular domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			AGCTCGGCGCAGGGCGGCAGC	0.692			T	SSX1	synovial sarcoma																																		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	0			20											31	34	33					20																	60738562		2201	4296	6497	60171957	SO:0001583	missense	26039			AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.605A>G	20.37:g.60738562A>G	ENSP00000333012:p.Gln202Arg		60171957	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Missense_Mutation	SNP	ENST00000331758.3	37	CCDS13491.1	.	.	.	.	.	.	.	.	.	.	A	5.243	0.230363	0.09969	.	.	ENSG00000184402	ENST00000421564;ENST00000331758;ENST00000370848	T;T;T	0.36157	1.38;1.38;1.27	5.32	4.21	0.49690	.	0.060333	0.64402	D	0.000002	T	0.37945	0.1022	M	0.66939	2.045	0.32469	N	0.543017	B;B	0.16166	0.016;0.016	B;B	0.14023	0.01;0.01	T	0.49113	-0.8973	10	0.87932	D	0	-5.6896	12.2977	0.54857	0.858:0.142:0.0:0.0	.	202;202	B4DSR7;O75177	.;CREST_HUMAN	R	202;202;205	ENSP00000393999:Q202R;ENSP00000333012:Q202R;ENSP00000359885:Q205R	ENSP00000333012:Q202R	Q	+	2	0	SS18L1	60171957	1.000000	0.71417	0.991000	0.47740	0.208000	0.24298	2.737000	0.47393	0.839000	0.34971	0.383000	0.25322	CAG		0.692	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			G	60738562	A	G	60738562	3	3	92	1	0	0	0	0	1	0	0	0	15215	188	7	4	627	4	SS18L1	20	60738562	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	3449545	60738562	2286958	205	25302										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60898720	60898720	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gggttcccaaagaatccgggCgcacacctgggagcagggtg	16	11	0	1	rs146904037	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:60898720C>T	ENST00000252999.3	-	45	5922	c.5856G>A	c.(5854-5856)gcG>gcA	p.A1952A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1952	Laminin EGF-like 18. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGAATCCGGGCGCACACCTGG	0.682													.|||	39	0.00778754	0	0.0115	5008	,	,		14154	0		0.0288	False		,,,				2504	0.002															0			20						C		31,4353		0,31,2161	18	25	22		5856	-6.5	0.6	20	dbSNP_134	22	232,8348		5,222,4063	no	coding-synonymous	LAMA5	NM_005560.3		5,253,6224	TT,TC,CC		2.704,0.7071,2.0287		1952/3696	60898720	263,12701	2192	4290	6482	60332115	SO:0001819	synonymous_variant	3911			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5856G>A	20.37:g.60898720C>T			60332115	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																				0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60898720	C	T	60898720	2	4	92	1	0	0	0	0	0	0	0	1	8631	755	27	1		1	LAMA5	20	60898720	Silent	SNP	C	TCGA-CL-5918-01A-11D-1657-10	160158	60898720	2126800	206	25303										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60909381	60909381	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggtggtgcaggtccgggaggTagtggtccctcgcaggcctg	19	10	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:60909381T>A	ENST00000252999.3	-	22	2666	c.2600A>T	c.(2599-2601)tAc>tTc	p.Y867F	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	867	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GTCCGGGAGGTAGTGGTCCCT	0.682																																																0			20											26	27	26					20																	60909381		2194	4296	6490	60342776	SO:0001583	missense	3911			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2600A>T	20.37:g.60909381T>A	ENSP00000252999:p.Tyr867Phe		60342776	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	16.40	3.111762	0.56398	.	.	ENSG00000130702	ENST00000252999	T	0.61859	0.07	4.49	3.36	0.38483	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	T	0.43612	0.1255	L	0.31664	0.95	0.80722	D	1	P	0.34757	0.467	B	0.34824	0.19	T	0.27806	-1.0063	10	0.39692	T	0.17	.	10.5583	0.45131	0.1449:0.0:0.0:0.8551	.	867	O15230	LAMA5_HUMAN	F	867	ENSP00000252999:Y867F	ENSP00000252999:Y867F	Y	-	2	0	LAMA5	60342776	1.000000	0.71417	0.987000	0.45799	0.336000	0.28762	3.260000	0.51523	0.653000	0.30826	0.454000	0.30748	TAC		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60909381	T	A	60909381	3	1	92	1	0	0	0	0	1	0	0	0	8631	1638	57	5	8723	5	LAMA5	20	60909381	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	10661	60909381	2116139	207	25304										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61513408	61513408	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcagacgaagcggtggaggaAgctgccgtggaggctgccgc	19	10	0	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr20:61513408A>G	ENST00000266070.4	-	16	4225	c.3900T>C	c.(3898-3900)gcT>gcC	p.A1300A	DIDO1_ENST00000395343.1_Silent_p.A1300A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1300					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CGGTGGAGGAAGCTGCCGTGG	0.582																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0			20											70	77	74					20																	61513408		2203	4298	6501	60983853	SO:0001819	synonymous_variant	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3900T>C	20.37:g.61513408A>G			60983853	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																				0.582	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		G	61513408	A	G	61513408	2	3	92	1	0	0	0	0	0	0	0	1	4533	59	3	4		4	DIDO1	20	61513408	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	604027	61513408	1512112	208	25305										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15889299	15889299	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tctcatttttttacccaaacCgcctccattatttgaagttt	3	11	1	1	rs377428221		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr21:15889299C>T	ENST00000400566.1	-	3	274	c.193G>A	c.(193-195)Ggt>Agt	p.G65S	SAMSN1_ENST00000285670.2_Missense_Mutation_p.G133S|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	65					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TTACCCAAACCGCCTCCATTA	0.338																																																0			21						C	SER/GLY	0,3582		0,0,1791	131	113	119		193	-4.9	0.3	21		119	2,8140		0,2,4069	no	missense	SAMSN1	NM_022136.3	56	0,2,5860	TT,TC,CC		0.0246,0.0,0.0171	benign	65/374	15889299	2,11722	1791	4071	5862	14811170	SO:0001583	missense	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.193G>A	21.37:g.15889299C>T	ENSP00000383411:p.Gly65Ser		14811170	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	C	8.744	0.919770	0.17982	0.0	2.46E-4	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.37584	1.19;1.19	4.32	-4.9	0.03094	.	0.343767	0.33438	N	0.004915	T	0.07593	0.0191	N	0.00436	-1.5	0.28629	N	0.907753	B;B	0.17852	0.008;0.024	B;B	0.12837	0.003;0.008	T	0.31530	-0.9940	10	0.05351	T	0.99	-36.3547	14.6637	0.68891	0.0:0.1201:0.0:0.8799	.	133;65	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	S	133;65	ENSP00000285670:G133S;ENSP00000383411:G65S	ENSP00000285670:G133S	G	-	1	0	SAMSN1	14811170	0.006000	0.16342	0.267000	0.24556	0.562000	0.35680	-0.056000	0.11787	-0.821000	0.04312	0.655000	0.94253	GGT		0.338	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			T	15889299	C	T	15889299	3	4	92	1	0	0	0	0	1	0	0	0	13867	652	23	1	952	1	SAMSN1	21	15889299	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10		15889299	32240596	209	25306										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45924706	45924706	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaaggtacgcccatcgaaggAgttggccaccaccaggaaat	12	11	0	0			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr21:45924706A>G	ENST00000323084.4	-	11	1878	c.1813T>C	c.(1813-1815)Tcc>Ccc	p.S605P	TSPEAR-AS1_ENST00000451035.1_RNA	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	605					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)		p.S605T(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CCATCGAAGGAGTTGGCCACC	0.537																																																1	Substitution - Missense(1)	central_nervous_system(1)	21											89	84	86					21																	45924706		2203	4300	6503	44749134	SO:0001583	missense	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1813T>C	21.37:g.45924706A>G	ENSP00000321987:p.Ser605Pro		44749134		Missense_Mutation	SNP	ENST00000323084.4	37	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.270735	0.59540	.	.	ENSG00000175894	ENST00000323084;ENST00000397918	T	0.80824	-1.42	4.72	4.72	0.59763	.	0.000000	0.85682	U	0.000000	D	0.88768	0.6526	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.90301	0.4330	10	0.87932	D	0	-23.5591	14.5571	0.68109	1.0:0.0:0.0:0.0	.	605	Q8WU66	TSEAR_HUMAN	P	605;458	ENSP00000321987:S605P	ENSP00000321987:S605P	S	-	1	0	TSPEAR	44749134	1.000000	0.71417	1.000000	0.80357	0.145000	0.21501	8.161000	0.89655	1.915000	0.55452	0.529000	0.55759	TCC		0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		G	45924706	A	G	45924706	3	3	92	1	0	0	0	0	1	0	0	0	2130	304	11	4	204	4	C21orf29	21	45924706	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	30035407	45924706	2205189	210	25307										
KRTAP10-11	386678	hgsc.bcm.edu	37	chr21	46066922	46066922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cagcttgctgcacctcctccTcctaccagcaggcctgctgc	8	19	0	0	rs587745520	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr21:46066922T>C	ENST00000334670.8	+	1	592	c.547T>C	c.(547-549)Tcc>Ccc	p.S183P	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	183	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CACCTCCTCCTCCTACCAGCA	0.597													T|||	7	0.00139776	0.0015	0	5008	,	,		24573	0.001		0	False		,,,				2504	0.0041															0			21											169	173	172					21																	46066922		2203	4300	6503	44891350	SO:0001583	missense	386678			AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"Keratin associated proteins"	20528	protein-coding gene	gene with protein product			"keratin associated protein 10-11"	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.547T>C	21.37:g.46066922T>C	ENSP00000334197:p.Ser183Pro		44891350	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	t	0.007	-1.994820	0.00435	.	.	ENSG00000243489	ENST00000334670	T	0.01430	4.9	3.09	-5.26	0.02772	.	.	.	.	.	T	0.00356	0.0011	N	0.00093	-2.17	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47129	-0.9141	9	0.11485	T	0.65	.	6.5173	0.22254	0.1305:0.2633:0.0:0.6062	.	183	P60412	KR10B_HUMAN	P	183	ENSP00000334197:S183P	ENSP00000334197:S183P	S	+	1	0	KRTAP10-11	44891350	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.524000	0.06222	-1.265000	0.02449	-0.404000	0.06349	TCC		0.597	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		C	46066922	T	C	46066922	3	2	92	1	0	0	0	0	1	0	0	0	8528	1551	54	4	549	4	KRTAP10-11	21	46066922	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	142216	46066922	2062973	211	25308										
ZDHHC8	29801	hgsc.bcm.edu	37	chr22	20134739	20134739	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gcctccagtcttttccccagCctctcggggccctagcagga	10	17	2	0	rs9605070	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:20134739C>T	ENST00000334554.7	+	0	4255				ZDHHC8_ENST00000405930.3_Silent_p.S774S	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8						locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					TTTTCCCCAGCCTCTCGGGGC	0.721													C|||	674	0.134585	0.0129	0.1138	5008	,	,		13169	0.0873		0.2207	False		,,,				2504	0.274															0			22																																								18514739	SO:0001624	3_prime_UTR_variant	29801			AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.*1816C>T	22.37:g.20134739C>T			18514739	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																				0.721	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20134739	C	T	20134739	1	4	92	0	1	0	0	0	0	0	0	0	17660	738	26	3		3	ZDHHC8	22	20134739	3'UTR	SNP	C	TCGA-CL-5918-01A-11D-1657-10		20134739	31169827	212	25309										
YDJC	150223	hgsc.bcm.edu	37	chr22	21984205	21984205	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agcagggacacgctggtcacAgccccggccagaaaggcctc	13	15	1	1	rs710177	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:21984205A>G	ENST00000292778.6	-	1	148	c.99T>C	c.(97-99)gcT>gcC	p.A33A	CCDC116_ENST00000607942.1_5'Flank|CCDC116_ENST00000292779.3_5'Flank|YDJC_ENST00000398873.3_Silent_p.A33A	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	33					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					CGCTGGTCACAGCCCCGGCCA	0.706													-|||	2301	0.459465	0.3926	0.4986	5008	,	,		13664	0.5109		0.3887	False		,,,				2504	0.5419															0			22								1688,2672		342,1004,834	18	17	17		99	-8.9	0	22	dbSNP_86	17	3196,5354		640,1916,1719	no	coding-synonymous	YDJC	NM_001017964.1		982,2920,2553	GG,GA,AA		37.3801,38.7156,37.8311		33/324	21984205	4884,8026	2180	4275	6455	20314205	SO:0001819	synonymous_variant	150223				CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.99T>C	22.37:g.21984205A>G			20314205	Q2YDT4|Q4V9R7	Silent	SNP	ENST00000292778.6	37	CCDS33613.1																																																																																				0.706	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1			G	21984205	A	G	21984205	2	3	92	1	0	0	0	0	0	0	0	1	17511	175	7	4		4	YDJC	22	21984205	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	1849466	21984205	29320361	213	25310										
YPEL1	29799	hgsc.bcm.edu	37	chr22	22064927	22064927	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	agccacttgccttggagatgAgctcgtcatgattggccagg	13	10	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:22064927A>T	ENST00000339468.3	-	2	490	c.107T>A	c.(106-108)cTc>cAc	p.L36H	YPEL1_ENST00000403503.1_Missense_Mutation_p.L36H	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)	36						nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					CTTGGAGATGAGCTCGTCATG	0.433																																																0			22											312	265	281					22																	22064927		2203	4300	6503	20394927	SO:0001583	missense	29799			AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"yippee (Drosophila) homolog-like 1"			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830	ENST00000339468.3:c.107T>A	22.37:g.22064927A>T	ENSP00000342832:p.Leu36His		20394927	Q65ZA1|Q6GLI6	Missense_Mutation	SNP	ENST00000339468.3	37	CCDS13794.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.636667	0.87760	.	.	ENSG00000100027	ENST00000339468;ENST00000403503	.	.	.	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	D	0.85873	0.5798	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89744	0.3935	9	0.87932	D	0	.	14.929	0.70900	1.0:0.0:0.0:0.0	.	36	O60688	YPEL1_HUMAN	H	36	.	ENSP00000342832:L36H	L	-	2	0	YPEL1	20394927	1.000000	0.71417	0.981000	0.43875	0.949000	0.60115	9.033000	0.93741	2.184000	0.69523	0.459000	0.35465	CTC		0.433	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313		T	22064927	A	T	22064927	3	4	92	1	0	0	0	0	1	0	0	0	17529	304	11	5	268	5	YPEL1	22	22064927	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	80722	22064927	29239639	214	25311										
ADRBK2	157	hgsc.bcm.edu	37	chr22	26091119	26091119	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	gaggtgctgcagaaggggacGgcctatgacagcagtgccga	17	9	0	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:26091119G>A	ENST00000324198.6	+	13	1290	c.1098G>A	c.(1096-1098)acG>acA	p.T366T		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	AGAAGGGGACGGCCTATGACA	0.517																																																0			22											181	158	166					22																	26091119		2203	4300	6503	24421119	SO:0001819	synonymous_variant	157			X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1098G>A	22.37:g.26091119G>A			24421119	Q9UGW9	Silent	SNP	ENST00000324198.6	37	CCDS13832.1																																																																																				0.517	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		A	26091119	G	A	26091119	2	1	92	1	0	0	0	0	0	0	0	1	344	1103	39	1		1	ADRBK2	22	26091119	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	4026192	26091119	25213447	215	25312										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32853314	32853314	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	taaatggtctgagaggatgaGacatagagattccacaggag	13	5	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:32853314G>A	ENST00000397452.1	-	2	170	c.60C>T	c.(58-60)gtC>gtT	p.V20V	BPIFC_ENST00000534972.1_5'UTR|BPIFC_ENST00000397450.1_Silent_p.V20V|BPIFC_ENST00000300399.3_Silent_p.V20V|BPIFC_ENST00000432451.2_5'UTR			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	20						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GAGAGGATGAGACATAGAGAT	0.443											OREG0003513	type=REGULATORY REGION|Gene=BPIL2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			22											130	120	123					22																	32853314		2203	4300	6503	31183314	SO:0001819	synonymous_variant	254240			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.60C>T	22.37:g.32853314G>A		835	31183314	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																				0.443	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32853314	G	A	32853314	2	1	92	1	0	0	0	0	0	0	0	1	1495	929	33	3		3	BPIL2	22	32853314	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	6762195	32853314	18451252	216	25313										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138182	8138182	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccacctcgctctcctgactcAgggggtcgtgctgggtcccc	12	17	2	1	rs41305169		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:8138182A>G	ENST00000317103.4	-	3	617	c.311T>C	c.(310-312)cTg>cCg	p.L104P		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	104	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		L -> P (in dbSNP:rs41305169). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CTCCTGACTCAGGGGGTCGTG	0.667																																																0			X											27	34	32					X																	8138182		2157	4235	6392	8098182	SO:0001583	missense	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.311T>C	X.37:g.8138182A>G	ENSP00000321309:p.Leu104Pro		8098182	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	798	0.4810126582278481	89	0.21394230769230768	103	0.3759124087591241	195	0.5158730158730159	169	0.2725806451612903	A	3.519	-0.098106	0.07010	.	.	ENSG00000177504	ENST00000317103	T	0.34859	1.34	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.09310	N	0.999999	D	0.54397	0.966	P	0.61070	0.883	T	0.47649	-0.9101	8	0.51188	T	0.08	.	.	.	.	rs41305169	104	Q9H322	VCX2_HUMAN	P	104	ENSP00000321309:L104P	ENSP00000321309:L104P	L	-	2	0	VCX2	8098182	0.001000	0.12720	0.014000	0.15608	0.015000	0.08874	-0.143000	0.10296	0.105000	0.17753	0.104000	0.15600	CTG		0.667	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		G	8138182	A	G	8138182	3	3	92	1	0	0	0	0	1	0	0	0	17183	188	7	4	112	4	VCX2	23	8138182	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10		8138182	147132378	217	25314										
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30260498	30260498	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tcatgcactggatctgataaAggcgacgagagccaagatga	12	8	2	4			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:30260498A>G	ENST00000378982.2	+	1	442	c.246A>G	c.(244-246)aaA>aaG	p.K82K	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	82										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						GATCTGATAAAGGCGACGAGA	0.527																																																0			X											58	46	50					X																	30260498		2202	4300	6502	30170419	SO:0001819	synonymous_variant	4115				CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.246A>G	X.37:g.30260498A>G			30170419	B2R9G0|Q6FHH4|Q8IZ00	Silent	SNP	ENST00000378982.2	37	CCDS14221.1																																																																																				0.527	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		G	30260498	A	G	30260498	2	3	92	1	0	0	0	0	0	0	0	1	9208	69	3	4		4	MAGEB4	23	30260498	Silent	SNP	A	TCGA-CL-5918-01A-11D-1657-10	22122316	30260498	125010062	218	25315										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccgacgagtcttgggaggctCcgagcggagactggacgtcc	16	12	1	1	rs5973088		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:34148877C>G	ENST00000346193.3	-	1	1570	c.1519G>C	c.(1519-1521)Gag>Cag	p.E507Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	507			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.					p.E507Q(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TTGGGAGGCTCCGAGCGGAGA	0.647																																																1	Substitution - Missense(1)	kidney(1)	X											29	29	29					X																	34148877		2181	4247	6428	34058798	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1519G>C	X.37:g.34148877C>G	ENSP00000345029:p.Glu507Gln		34058798	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	6	0.003616636528028933	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	9.299	1.052687	0.19907	.	.	ENSG00000185448	ENST00000346193	T	0.14391	2.51	0.226	0.226	0.15353	.	.	.	.	.	T	0.05227	0.0139	L	0.27053	0.805	0.09310	N	1	B	0.24483	0.104	B	0.16722	0.016	T	0.41466	-0.9507	8	0.17832	T	0.49	.	.	.	.	rs5973088	507	Q5JRC9	FA47A_HUMAN	Q	507	ENSP00000345029:E507Q	ENSP00000345029:E507Q	E	-	1	0	FAM47A	34058798	0.053000	0.20554	0.000000	0.03702	0.001000	0.01503	1.713000	0.37951	0.283000	0.22279	0.287000	0.19450	GAG		0.647	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		G	34148877	C	G	34148877	3	3	92	1	0	0	0	0	1	0	0	0	5588	864	30	5	860	5	FAM47A	23	34148877	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	3888379	34148877	121121683	219	25316										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961532	34961532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cccgcggcctcccgagactcCggtgtcccgtctccgtcctc	10	21	1	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:34961532C>T	ENST00000329357.5	+	1	620	c.584C>T	c.(583-585)cCg>cTg	p.P195L		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	195	Pro-rich.									breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						CCCGAGACTCCGGTGTCCCGT	0.657																																																0			X											27	31	30					X																	34961532		2201	4292	6493	34871453	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.584C>T	X.37:g.34961532C>T	ENSP00000328307:p.Pro195Leu		34871453	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	1.235	-0.623067	0.03636	.	.	ENSG00000189132	ENST00000329357	T	0.14516	2.5	0.602	-0.568	0.11760	.	.	.	.	.	T	0.08980	0.0222	L	0.35723	1.085	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.35674	-0.9779	9	0.56958	D	0.05	.	1.7333	0.02936	0.3153:0.4106:0.0:0.2741	.	195	Q8NA70	FA47B_HUMAN	L	195	ENSP00000328307:P195L	ENSP00000328307:P195L	P	+	2	0	FAM47B	34871453	0.000000	0.05858	0.008000	0.14137	0.005000	0.04900	-2.154000	0.01285	-0.405000	0.07599	-0.713000	0.03633	CCG		0.657	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34961532	C	T	34961532	3	4	92	1	0	0	0	0	1	0	0	0	5589	652	23	1	586	1	FAM47B	23	34961532	Missense_Mutation	SNP	C	TCGA-CL-5918-01A-11D-1657-10	812655	34961532	120309028	220	25317										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37027472	37027472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tgagactggagtgtcccatcTccacccagagcctcccaaga	9	15	1	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:37027472T>C	ENST00000358047.3	+	1	1041	c.989T>C	c.(988-990)cTc>cCc	p.L330P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	330										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTGTCCCATCTCCACCCAGAG	0.612																																																0			X											84	77	80					X																	37027472		2202	4299	6501	36937393	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.989T>C	X.37:g.37027472T>C	ENSP00000367913:p.Leu330Pro		36937393	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	t	10.17	1.276764	0.23307	.	.	ENSG00000198173	ENST00000358047	T	0.23348	1.91	0.95	-1.9	0.07665	.	.	.	.	.	T	0.32255	0.0823	L	0.49126	1.545	0.40143	D	0.976856	D	0.89917	1.0	D	0.80764	0.994	T	0.47275	-0.9130	9	0.21540	T	0.41	.	3.4413	0.07465	0.3453:1.0E-4:0.0:0.6546	.	330	Q5HY64	FA47C_HUMAN	P	330	ENSP00000367913:L330P	ENSP00000367913:L330P	L	+	2	0	FAM47C	36937393	0.011000	0.17503	0.010000	0.14722	0.010000	0.07245	-0.274000	0.08537	0.152000	0.19188	0.150000	0.16122	CTC		0.612	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		C	37027472	T	C	37027472	3	2	92	1	0	0	0	0	1	0	0	0	5590	1551	54	4	991	4	FAM47C	23	37027472	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	2065940	37027472	118243088	221	25318										
LANCL3	347404	hgsc.bcm.edu	37	chrX	37431229	37431229	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ccttggtcaccgccaccatcGagcgcatcctccaggagctt	9	17	1	0	rs35466136		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:37431229G>C	ENST00000378619.3	+	1	325	c.106G>C	c.(106-108)Gag>Cag	p.E36Q	LANCL3_ENST00000378621.3_Missense_Mutation_p.E36Q|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	36							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						CGCCACCATCGAGCGCATCCT	0.721																																																0			X											7	7	7					X																	37431229		2096	4100	6196	37316148	SO:0001583	missense	347404			AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.106G>C	X.37:g.37431229G>C	ENSP00000367882:p.Glu36Gln		37316148	A6NHE3	Missense_Mutation	SNP	ENST00000378619.3	37	CCDS55398.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018621	0.35606	.	.	ENSG00000147036	ENST00000378621;ENST00000378619	.	.	.	4.83	2.92	0.33932	.	0.128164	0.50627	D	0.000108	T	0.34337	0.0894	N	0.14661	0.345	0.43238	D	0.995145	B;P	0.35226	0.18;0.491	B;B	0.40982	0.052;0.345	T	0.04752	-1.0929	9	0.15066	T	0.55	-12.0193	8.7053	0.34351	0.0876:0.1485:0.7639:0.0	rs35466136	36;36	Q6ZV70;Q6ZV70-2	LANC3_HUMAN;.	Q	36	.	ENSP00000367882:E36Q	E	+	1	0	LANCL3	37316148	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.227000	0.58612	0.825000	0.34637	0.476000	0.43555	GAG		0.721	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511		C	37431229	G	C	37431229	3	2	92	1	0	0	0	0	1	0	0	0	8644	1059	37	5	108	5	LANCL3	23	37431229	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	403757	37431229	117839331	222	25319										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350752	50350752	+	Silent	SNP	T	T	C													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tcctcctcctcctcctcctgTtgcttctgctgctgctgttg					rs534812379		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:50350752T>C	ENST00000289292.7	-	6	3673	c.3390A>G	c.(3388-3390)caA>caG	p.Q1130Q	SHROOM4_ENST00000460112.3_Silent_p.Q1014Q|SHROOM4_ENST00000376020.2_Silent_p.Q1130Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1130	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctgttgcttctgct	0.582																																																0			X											15	15	15					X																	50350752		2198	4291	6489	50367492	SO:0001819	synonymous_variant	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3390A>G	X.37:g.50350752T>C			50367492	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																				0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350752	T	C	50350752	2	2	92	1	0	0	0	0	0	0	0	1	14333	1722	60	4		4	SHROOM4	23	50350752	Silent	SNP	T	TCGA-CL-5918-01A-11D-1657-10	12919523	50350752	104919808	223	25320	31	3								
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350757	50350758	+	Missense_Mutation	DNP	TC	TC	GT													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctcctcctcctcctgttgctTctgctgctgctgttgctgct					rs201922875|rs199502054|rs553160982		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T|C	T|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:50350757_50350758TC>GT	ENST00000289292.7	-	6	3667_3668	c.3384_3385GA>AC	c.(3382-3387)caGAag>caACag	p.K1129Q	SHROOM4_ENST00000460112.3_Missense_Mutation_p.K1013Q|SHROOM4_ENST00000376020.2_Missense_Mutation_p.K1129Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1129	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tcctgttgcttctgctgctgct	0.589																																																0			X																																								50367497|50367498	SO:0001583	missense	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3384_3385delinsGT	X.37:g.50350757_50350758delinsGT	ENSP00000289292:p.Lys1129Gln		50367497|50367498	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation|Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		GT	50350758	TC	GT	50350757	3	3	92	1	0	0	0	0	1	0	0	0	14333	1792	62	4	1112	4	SHROOM4	23	50350757	Missense_Mutation	DNP	TC	TCGA-CL-5918-01A-11D-1657-10	5	50350757	104919803	224	25321	31	3								
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	92	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-CL-5918-01A-11D-1657-10	1	50350758	104919802	225	25322	31	3								
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350778	50350778	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctgctgctgctgttgctgctTctgctgctgggctgcacgaa	13	12	1	0	rs112781654		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:50350778T>G	ENST00000289292.7	-	6	3647	c.3364A>C	c.(3364-3366)Aag>Cag	p.K1122Q	SHROOM4_ENST00000460112.3_Missense_Mutation_p.K1006Q|SHROOM4_ENST00000376020.2_Missense_Mutation_p.K1122Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1122	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tgttgctgcttctgctgctgG	0.582																																																0			X											22	20	21					X																	50350778		2201	4295	6496	50367518	SO:0001583	missense	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3364A>C	X.37:g.50350778T>G	ENSP00000289292:p.Lys1122Gln		50367518	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	1.804	-0.476250	0.04414	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.09073	3.02;3.02;3.02	4.36	1.23	0.21249	.	0.932286	0.08995	N	0.863864	T	0.02304	0.0071	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45071	-0.9286	10	0.06099	T	0.92	.	5.8974	0.18947	0.0:0.1611:0.3673:0.4717	.	1122	Q9ULL8	SHRM4_HUMAN	Q	1122;1122;1006	ENSP00000289292:K1122Q;ENSP00000365188:K1122Q;ENSP00000421450:K1006Q	ENSP00000289292:K1122Q	K	-	1	0	SHROOM4	50367518	0.007000	0.16637	0.012000	0.15200	0.528000	0.34623	0.084000	0.14891	0.088000	0.17205	0.417000	0.27973	AAG		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		G	50350778	T	G	50350778	3	3	92	1	0	0	0	0	1	0	0	0	14333	1792	62	4	1133	4	SHROOM4	23	50350778	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	20	50350778	104919782	226	25323										
ARHGEF9	23229	hgsc.bcm.edu	37	chrX	62885786	62885786	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	cttcttgcagaggaccatctGgtggtcaaacaggaagaaga	12	8	3	3			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:62885786G>T	ENST00000253401.6	-	7	1836	c.1036C>A	c.(1036-1038)Cag>Aag	p.Q346K	ARHGEF9_ENST00000374872.1_Missense_Mutation_p.Q325K|ARHGEF9_ENST00000374870.4_Missense_Mutation_p.Q244K|ARHGEF9_ENST00000437457.2_Missense_Mutation_p.Q293K|ARHGEF9_ENST00000495564.1_Intron|ARHGEF9_ENST00000374878.1_Missense_Mutation_p.Q344K|ARHGEF9_ENST00000433323.2_Intron	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	346	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						AGGACCATCTGGTGGTCAAAC	0.592																																																0			X											102	80	88					X																	62885786		2203	4300	6503	62802511	SO:0001583	missense	23229			AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.1036C>A	X.37:g.62885786G>T	ENSP00000253401:p.Gln346Lys		62802511	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Missense_Mutation	SNP	ENST00000253401.6	37	CCDS35315.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.784462	0.90282	.	.	ENSG00000131089	ENST00000253401;ENST00000374878;ENST00000437457;ENST00000374870;ENST00000374872	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.08	5.08	0.68730	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.86843	0.6030	M	0.92026	3.265	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.86509	0.1808	10	0.05959	T	0.93	.	16.1104	0.81259	0.0:0.0:1.0:0.0	.	293;344;346	B4DHC7;B1AMR4;O43307	.;.;ARHG9_HUMAN	K	346;344;293;244;325	ENSP00000253401:Q346K;ENSP00000364012:Q344K;ENSP00000399994:Q293K;ENSP00000364004:Q244K;ENSP00000364006:Q325K	ENSP00000253401:Q346K	Q	-	1	0	ARHGEF9	62802511	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.229000	0.95273	2.103000	0.63969	0.600000	0.82982	CAG		0.592	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			T	62885786	G	T	62885786	3	4	92	1	0	0	0	0	1	0	0	0	912	1357	47	2	530	2	ARHGEF9	23	62885786	Missense_Mutation	SNP	G	TCGA-CL-5918-01A-11D-1657-10	12535008	62885786	92384774	227	25324										
TEX11	56159	hgsc.bcm.edu	37	chrX	69825277	69825277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	aaaagctgttgaagcttttcTcccttgctctagatcaactg	7	10	3	2			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:69825277T>C	ENST00000395889.2	-	25	2241	c.2086A>G	c.(2086-2088)Aga>Gga	p.R696G	TEX11_ENST00000374333.2_Missense_Mutation_p.R681G|TEX11_ENST00000374320.2_Missense_Mutation_p.R371G|TEX11_ENST00000344304.3_Missense_Mutation_p.R696G	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	696					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GAAGCTTTTCTCCCTTGCTCT	0.393																																																0			X											126	106	113					X																	69825277		2203	4300	6503	69742002	SO:0001583	missense	56159			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2086A>G	X.37:g.69825277T>C	ENSP00000379226:p.Arg696Gly		69742002	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.365118	0.61513	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.58940	1.0;1.03;0.3;1.03	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.71533	0.3351	M	0.71581	2.175	0.30992	N	0.721329	D;D	0.89917	0.992;1.0	P;D	0.80764	0.906;0.994	T	0.73711	-0.3897	9	.	.	.	-7.6838	9.6229	0.39732	0.0:0.0:0.0:1.0	.	681;696	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	G	681;696;371;696	ENSP00000363453:R681G;ENSP00000379226:R696G;ENSP00000363440:R371G;ENSP00000340995:R696G	.	R	-	1	2	TEX11	69742002	0.998000	0.40836	1.000000	0.80357	0.980000	0.70556	3.300000	0.51834	1.794000	0.52575	0.441000	0.28932	AGA		0.393	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			C	69825277	T	C	69825277	3	2	92	1	0	0	0	0	1	0	0	0	15813	1559	54	4	764	4	TEX11	23	69825277	Missense_Mutation	SNP	T	TCGA-CL-5918-01A-11D-1657-10	6939491	69825277	85445283	228	25325										
IRS4	8471	hgsc.bcm.edu	37	chrX	107979263	107979263	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	tattccagccgagctggggcGtcagcagtctcgagtttgag	14	10	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:107979263G>A	ENST00000372129.2	-	1	388	c.312C>T	c.(310-312)gaC>gaT	p.D104D	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	104	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GAGCTGGGGCGTCAGCAGTCT	0.657																																																0			X											64	55	58					X																	107979263		2203	4297	6500	107865919	SO:0001819	synonymous_variant	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.312C>T	X.37:g.107979263G>A			107865919		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																				0.657	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107979263	G	A	107979263	2	1	92	1	0	0	0	0	0	0	0	1	7863	1136	40	1		1	IRS4	23	107979263	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	38153986	107979263	47291297	229	25326										
SPANXN2	494119	hgsc.bcm.edu	37	chrX	142795459	142795459	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ggattgatggagttctctcgGgactggtccttctccagttg	13	9	2	1			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:142795459G>T	ENST00000370498.1	-	2	972	c.219C>A	c.(217-219)tcC>tcA	p.S73S		NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN	SPANX family, member N2	73										NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)					AGTTCTCTCGGGACTGGTCCT	0.433																																																0			X											298	267	278					X																	142795459		2203	4300	6503	142623125	SO:0001819	synonymous_variant	494119				CCDS35419.1	Xq27.3	2012-06-12			ENSG00000203924	ENSG00000268988			33175	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 7"	300665				14973187, 17012309	Standard	NM_001009615		Approved	SPANX-N2, CT11.7	uc004fbz.3	Q5MJ10	OTTHUMG00000022583	ENST00000370498.1:c.219C>A	X.37:g.142795459G>T			142623125	Q0ZNM2	Silent	SNP	ENST00000370498.1	37	CCDS35419.1																																																																																				0.433	SPANXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058621.2	NM_001009615		T	142795459	G	T	142795459	2	4	92	1	0	0	0	0	0	0	0	1	15030	1219	43	2		2	SPANXN2	23	142795459	Silent	SNP	G	TCGA-CL-5918-01A-11D-1657-10	34816196	142795459	12475101	230	25327										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153220360	153220360	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0043859649122807	1	1	0.0849478390461997	0	0.0943864878291108	1	1	0	ctggcgggtttggcactgggActtagagccctgggctgcct	16	11	0	1	rs1051152		TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrX:153220360A>G	ENST00000310441.7	-	17	4456	c.3490T>C	c.(3490-3492)Tcc>Ccc	p.S1164P	HCFC1_ENST00000354233.3_Missense_Mutation_p.S1095P|HCFC1_ENST00000369984.4_Missense_Mutation_p.S1164P	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1164			S -> P (in dbSNP:rs1051152). {ECO:0000269|PubMed:7829097}.		cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGCACTGGGACTTAGAGCCC	0.701													G|||	2212	0.58596	0.5605	0.402	3775	,	,		10315	0.5893		0.1491	False		,,,				2504	0.4581															0			X						G	PRO/SER	2283,1298		636,633,378,251,163	9	13	12		3490	-0.3	0	X	dbSNP_86	12	1169,5332		86,662,335,1623,1424	yes	missense	HCFC1	NM_005334.2	74	722,1295,713,1874,1587	GG,GA,G,AA,A		17.9818,36.2469,34.2392	benign	1164/2036	153220360	3452,6630	2061	4130	6191	152873554	SO:0001583	missense	3054				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.3490T>C	X.37:g.153220360A>G	ENSP00000309555:p.Ser1164Pro		152873554	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	37	CCDS44020.1	829	0.49969861362266427	184	0.5411764705882353	91	0.30743243243243246	219	0.6329479768786127	79	0.1144927536231884	g	0.179	-1.063977	0.01934	0.637531	0.179818	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.02606	4.25;4.23;4.26	4.91	-0.339	0.12647	.	0.285881	0.32190	N	0.006441	T	0.00012	0.0000	N	0.01576	-0.805	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.21109	-1.0255	9	0.02654	T	1	.	6.7272	0.23363	0.2171:0.3413:0.4417:0.0	rs1051152	1164	P51610	HCFC1_HUMAN	P	1164;1164;1095	ENSP00000309555:S1164P;ENSP00000359001:S1164P;ENSP00000346174:S1095P	ENSP00000309555:S1164P	S	-	1	0	HCFC1	152873554	0.999000	0.42202	0.005000	0.12908	0.582000	0.36321	1.020000	0.30027	-0.527000	0.06374	-1.185000	0.01705	TCC		0.701	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		G	153220360	A	G	153220360	3	3	92	1	0	0	0	0	1	0	0	0	7012	275	10	4	2657	4	HCFC1	23	153220360	Missense_Mutation	SNP	A	TCGA-CL-5918-01A-11D-1657-10	10424901	153220360	2050200	231	25328										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7798261	7798261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggacttcagccgggaactcTcccctcccactccagagact	9	17	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:7798261T>C	ENST00000303635.7	+	16	4108	c.3901T>C	c.(3901-3903)Tcc>Ccc	p.S1301P	CAMTA1_ENST00000439411.2_Missense_Mutation_p.S1301P	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CCGGGAACTCTCCCCTCCCAC	0.512			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0			1											48	50	50					1																	7798261		2203	4300	6503	7720848	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3901T>C	1.37:g.7798261T>C	ENSP00000306522:p.Ser1301Pro		7720848	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.671293	0.29693	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646	T;T	0.21734	1.99;1.99	5.06	3.91	0.45181	.	0.319538	0.34110	N	0.004242	T	0.11067	0.0270	N	0.16478	0.41	0.25593	N	0.986673	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.20672	-1.0268	10	0.33141	T	0.24	-14.1043	5.3735	0.16152	0.0:0.1483:0.1517:0.7	.	1301;388;257;1301	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1	.;.;.;CMTA1_HUMAN	P	1301;1301;388;257	ENSP00000306522:S1301P;ENSP00000402561:S1301P	ENSP00000306522:S1301P	S	+	1	0	CAMTA1	7720848	0.996000	0.38824	0.947000	0.38551	0.998000	0.95712	1.903000	0.39858	0.837000	0.34925	0.533000	0.62120	TCC		0.512	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7798261	T	C	7798261	3	2	93	1	0	0	0	0	1	0	0	0	2619	1551	54	4	3963	4	CAMTA1	1	7798261	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10		7798261	241452360	1	25329										
UBR4	23352	hgsc.bcm.edu	37	chr1	19436959	19436959	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcatactgcaggctacttgcCtagaaggcaatgggaagaga	12	8	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:19436959C>A	ENST00000375254.3	-	80	11920		c.e80-1		UBR4_ENST00000375217.2_Splice_Site|UBR4_ENST00000375226.2_Splice_Site|UBR4_ENST00000375267.2_Splice_Site	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4						protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGCTACTTGCCTAGAAGGCAA	0.512																																																0			1											47	45	46					1																	19436959		2203	4300	6503	19309546	SO:0001630	splice_region_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.11893-1G>T	1.37:g.19436959C>A			19309546	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Splice_Site	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495468	0.85069	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8256	0.92117	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBR4	19309546	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.298000	0.78815	2.793000	0.96121	0.655000	0.94253	.		0.512	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	Intron	A	19436959	C	A	19436959	5	1	93	1	0	0	0	0	0	0	1	0	16944	695	24	2	3767	2	UBR4	1	19436959	Splice_Site	SNP	C	TCGA-DC-5337-01A-01D-1657-10	11638698	19436959	229813662	2	25330										
UBR4	23352	hgsc.bcm.edu	37	chr1	19487468	19487468	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cggcagaggctgctcttcttGggcttctcttcgtcagcaac	11	13	4	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:19487468G>T	ENST00000375254.3	-	38	5376	c.5349C>A	c.(5347-5349)ccC>ccA	p.P1783P	UBR4_ENST00000375217.2_Silent_p.P1783P|UBR4_ENST00000375226.2_Silent_p.P1783P|UBR4_ENST00000375267.2_Silent_p.P1783P	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1783					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGCTCTTCTTGGGCTTCTCTT	0.547																																																0			1											74	68	70					1																	19487468		2203	4300	6503	19360055	SO:0001819	synonymous_variant	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.5349C>A	1.37:g.19487468G>T			19360055	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.547	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19487468	G	T	19487468	2	4	93	1	0	0	0	0	0	0	0	1	16944	1335	47	2		2	UBR4	1	19487468	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	50509	19487468	229763153	3	25331										
YTHDF2	51441	hgsc.bcm.edu	37	chr1	29069170	29069170	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atttctttcccagtgggattGacttctcagcatggggaaat	10	8	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:29069170G>A	ENST00000373812.3	+	4	750	c.388G>A	c.(388-390)Gac>Aac	p.D130N	YTHDF2_ENST00000478283.1_3'UTR|YTHDF2_ENST00000541996.1_Missense_Mutation_p.D80N|YTHDF2_ENST00000542507.1_Missense_Mutation_p.D130N	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	130	Localization to mRNA processing bodies (P-bodies).				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)	p.D130N(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		CAGTGGGATTGACTTCTCAGC	0.478																																																1	Substitution - Missense(1)	kidney(1)	1											168	156	160					1																	29069170		1895	4132	6027	28941757	SO:0001583	missense	51441			AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"YTH domain family 2"			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.388G>A	1.37:g.29069170G>A	ENSP00000362918:p.Asp130Asn		28941757	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Missense_Mutation	SNP	ENST00000373812.3	37	CCDS41296.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124810	0.56613	.	.	ENSG00000198492	ENST00000542507;ENST00000373812;ENST00000541996;ENST00000396232	T;T;T	0.41065	1.01;1.01;1.01	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	M	0.66939	2.045	0.80722	D	1	P;P	0.49358	0.857;0.923	P;P	0.44811	0.461;0.461	T	0.56353	-0.7993	10	0.66056	D	0.02	-11.7442	17.9052	0.88916	0.0:0.0:1.0:0.0	.	130;130	B5BU99;Q9Y5A9	.;YTHD2_HUMAN	N	130;130;80;130	ENSP00000444660:D130N;ENSP00000362918:D130N;ENSP00000439394:D80N	ENSP00000362918:D130N	D	+	1	0	YTHDF2	28941757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.714000	0.98744	2.594000	0.87642	0.585000	0.79938	GAC		0.478	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258		A	29069170	G	A	29069170	3	1	93	1	0	0	0	0	1	0	0	0	17539	1290	45	3	402	3	YTHDF2	1	29069170	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	9581702	29069170	220181451	4	25332										
KDM4A	9682	hgsc.bcm.edu	37	chr1	44132642	44132642	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caggtgactcaagaggctggAgagtttatgatcactttccc	11	9	2	4	rs558421747		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:44132642A>G	ENST00000372396.3	+	8	929	c.795A>G	c.(793-795)ggA>ggG	p.G265G	KDM4A_ENST00000463151.1_3'UTR	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	265	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						AAGAGGCTGGAGAGTTTATGA	0.473																																																0			1											157	149	152					1																	44132642		2203	4300	6503	43905229	SO:0001819	synonymous_variant	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.795A>G	1.37:g.44132642A>G			43905229	Q5VVB1	Silent	SNP	ENST00000372396.3	37	CCDS491.1																																																																																				0.473	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		G	44132642	A	G	44132642	2	3	93	1	0	0	0	0	0	0	0	1	8149	291	11	4		4	KDM4A	1	44132642	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	15063472	44132642	205117979	5	25333										
IPP	3652	hgsc.bcm.edu	37	chr1	46206743	46206743	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gctcttcacttcgcaaaattTtgatcagctgatctttcgta	6	10	4	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:46206743T>A	ENST00000396478.3	-	3	656	c.554A>T	c.(553-555)aAa>aTa	p.K185I		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	185						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TCGCAAAATTTTGATCAGCTG	0.388																																																0			1											165	161	162					1																	46206743		2203	4300	6503	45979330	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.554A>T	1.37:g.46206743T>A	ENSP00000379739:p.Lys185Ile		45979330	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529406	0.64860	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.70282	-0.47;-0.47	5.19	2.79	0.32731	BTB/Kelch-associated (2);	0.213218	0.51477	D	0.000100	T	0.75781	0.3896	M	0.81682	2.555	0.45747	D	0.998642	B;P	0.43633	0.019;0.813	B;P	0.48552	0.099;0.581	T	0.75238	-0.3388	10	0.62326	D	0.03	.	9.903	0.41359	0.0:0.1364:0.0:0.8636	.	185;185	Q9Y573;A2A6V3	IPP_HUMAN;.	I	185	ENSP00000353024:K185I;ENSP00000379739:K185I	ENSP00000353024:K185I	K	-	2	0	IPP	45979330	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.904000	0.39868	0.355000	0.24131	0.533000	0.62120	AAA		0.388	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		A	46206743	T	A	46206743	3	1	93	1	0	0	0	0	1	0	0	0	7821	1841	64	5	1330	5	IPP	1	46206743	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2074101	46206743	203043878	6	25334										
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48713127	48713127	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acagaagctgacaagcattgAggaggagccactctggagac	13	9	1	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:48713127A>G	ENST00000438567.2	+	14	2010	c.1958A>G	c.(1957-1959)gAg>gGg	p.E653G	SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000533824.1_Missense_Mutation_p.E674G|SLC5A9_ENST00000236495.5_Missense_Mutation_p.E678G	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	653					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						ACAAGCATTGAGGAGGAGCCA	0.542																																																0			1											94	88	90					1																	48713127		2203	4300	6503	48485714	SO:0001583	missense	200010			BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1958A>G	1.37:g.48713127A>G	ENSP00000401730:p.Glu653Gly		48485714	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	A	12.44	1.939476	0.34189	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.88509	-2.33;-2.32;-2.39	5.04	1.41	0.22369	.	0.780772	0.12462	N	0.466782	D	0.85592	0.5732	M	0.72118	2.19	0.80722	D	1	B;B;B	0.29862	0.104;0.259;0.259	B;B;B	0.24701	0.024;0.034;0.055	T	0.78553	-0.2160	10	0.52906	T	0.07	.	7.0929	0.25293	0.6252:0.2995:0.0753:0.0	.	674;653;678	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	G	674;653;678	ENSP00000431900:E674G;ENSP00000401730:E653G;ENSP00000236495:E678G	ENSP00000236495:E678G	E	+	2	0	SLC5A9	48485714	0.019000	0.18553	0.228000	0.23943	0.538000	0.34931	1.135000	0.31454	0.072000	0.16694	0.533000	0.62120	GAG		0.542	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		G	48713127	A	G	48713127	3	3	93	1	0	0	0	0	1	0	0	0	14709	304	11	4	2091	4	SLC5A9	1	48713127	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	2506384	48713127	200537494	7	25335										
DMRTB1	63948	hgsc.bcm.edu	37	chr1	53927246	53927246	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttcccgctgggctacctggaCgcccctcctggcgtccccct	10	20	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:53927246C>T	ENST00000371445.3	+	2	733	c.678C>T	c.(676-678)gaC>gaT	p.D226D	DMRTB1_ENST00000463126.1_3'UTR	NM_033067.1	NP_149056.1	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal, 1	226	Pro-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(5)|ovary(1)|skin(1)	10						GCTACCTGGACGCCCCTCCTG	0.672																																																0			1											74	65	68					1																	53927246		2203	4300	6503	53699834	SO:0001819	synonymous_variant	63948			AJ291671	CCDS581.1	1p32	2008-08-29			ENSG00000143006	ENSG00000143006			13913	protein-coding gene	gene with protein product		614805					Standard	NM_033067		Approved		uc001cvq.1	Q96MA1	OTTHUMG00000008080	ENST00000371445.3:c.678C>T	1.37:g.53927246C>T			53699834	Q96SD2	Silent	SNP	ENST00000371445.3	37	CCDS581.1																																																																																				0.672	DMRTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022110.1			T	53927246	C	T	53927246	2	4	93	1	0	0	0	0	0	0	0	1	4601	535	19	1		1	DMRTB1	1	53927246	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	5214119	53927246	195323375	8	25336										
AK3L1	205	hgsc.bcm.edu	37	chr1	65691814	65691814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctggccctacgtttacacacTtttctcaaacaagatcacac	4	14	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:65691814T>C	ENST00000327299.7	+	5	831	c.626T>C	c.(625-627)cTt>cCt	p.L209P	AK4_ENST00000546702.1_Missense_Mutation_p.L157P|AK4_ENST00000395334.2_Missense_Mutation_p.L209P|AK4_ENST00000545314.1_Missense_Mutation_p.L209P	NM_013410.3	NP_037542.1			adenylate kinase 4									p.L209P(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						GTTTACACACTTTTCTCAAAC	0.443																																																1	Substitution - Missense(1)	kidney(1)	1											35	34	34					1																	65691814		2203	4296	6499	65464402	SO:0001583	missense	205			AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"Adenylate kinases"	363	protein-coding gene	gene with protein product		103030	"adenylate kinase 3", "adenylate kinase 3-like 1"	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.626T>C	1.37:g.65691814T>C	ENSP00000322175:p.Leu209Pro		65464402		Missense_Mutation	SNP	ENST00000327299.7	37	CCDS629.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.926582	0.92319	.	.	ENSG00000162433	ENST00000545314;ENST00000546702;ENST00000395334;ENST00000327299	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.2	5.2	0.72013	.	0.059484	0.64402	D	0.000002	T	0.53254	0.1785	M	0.64997	1.995	0.80722	D	1	D	0.58268	0.982	P	0.60541	0.876	T	0.53906	-0.8372	9	.	.	.	-18.5637	14.8945	0.70633	0.0:0.0:0.0:1.0	.	209	P27144	KAD4_HUMAN	P	209;157;209;209	ENSP00000445912:L209P;ENSP00000448458:L157P;ENSP00000378743:L209P;ENSP00000322175:L209P	.	L	+	2	0	AK4	65464402	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	7.176000	0.77643	2.187000	0.69744	0.528000	0.53228	CTT		0.443	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410		C	65691814	T	C	65691814	3	2	93	1	0	0	0	0	1	0	0	0	442	1609	56	4	644	4	AK3L1	1	65691814	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	11764568	65691814	183558807	9	25337										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103468327	103468328	+	Frame_Shift_Ins	INS	-	-	C													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcccttttggtcctggggggINSccatctacacctgccatacc							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:103468327_103468328insC	ENST00000370096.3	-	22	2330_2331	c.2018_2019insG	c.(2017-2019)ggcfs	p.G673fs	COL11A1_ENST00000353414.4_Frame_Shift_Ins_p.G634fs|COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000358392.2_Frame_Shift_Ins_p.G685fs|COL11A1_ENST00000512756.1_Frame_Shift_Ins_p.G557fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	673	Collagen-like 4.|Collagen-like 5.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		GTCCTGGGGGGCCATCTACACC	0.322																																																0			1																																								103240916	SO:0001589	frameshift_variant	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2019dupG	1.37:g.103468329_103468329dupC	ENSP00000359114:p.Gly673fs		103240915	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Ins	INS	ENST00000370096.3	37	CCDS778.1																																																																																				0.322	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103468328	-	C	103468327	7	5	93	1	0	1	1	0	0	0	0	0	3673	1190	42	0	3585	0	COL11A1	1	103468327	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	37776513	103468327	145782294	10	25338										
NRAS	4893	hgsc.bcm.edu	37	chr1	115258748	115258748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgcgcttttcccaacaccacCtgctccaaccaccaccagtt	4	19	0	0	rs121913250		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:115258748C>A	ENST00000369535.4	-	2	287	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	12			G -> C (in leukemia). {ECO:0000269|PubMed:2998510}.|G -> D (in KNEN). {ECO:0000269|PubMed:22499344}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12S(133)|p.G12C(81)|p.G12R(18)|p.G12N(2)|p.G12P(1)|p.G12Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		CCAACACCACCTGCTCCAACC	0.493	G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	236	Substitution - Missense(236)	haematopoietic_and_lymphoid_tissue(149)|skin(29)|upper_aerodigestive_tract(21)|large_intestine(13)|thyroid(8)|prostate(6)|lung(4)|soft_tissue(2)|urinary_tract(1)|NS(1)|kidney(1)|pancreas(1)	1											203	181	189					1																	115258748		2203	4300	6503	115060271	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.34G>T	1.37:g.115258748C>A	ENSP00000358548:p.Gly12Cys		115060271	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208516	0.95069	.	.	ENSG00000213281	ENST00000369535	T	0.79141	-1.24	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000025	D	0.85826	0.5787	M	0.89904	3.07	0.80722	D	1	P	0.39480	0.675	P	0.49276	0.605	D	0.87171	0.2221	10	0.72032	D	0.01	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	12	P01111	RASN_HUMAN	C	12	ENSP00000358548:G12C	ENSP00000358548:G12C	G	-	1	0	NRAS	115060271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT		0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		A	115258748	C	A	115258748	3	1	93	1	0	0	0	0	1	0	0	0	10671	681	24	2	551	2	NRAS	1	115258748	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	11790421	115258748	133991873	11	25339										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117146629	117146629	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgctggcattgctggccaccTccacggagatgctgctctct	11	15	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:117146629T>C	ENST00000369486.3	-	6	2006	c.1241A>G	c.(1240-1242)gAg>gGg	p.E414G	IGSF3_ENST00000318837.6_Missense_Mutation_p.E434G|IGSF3_ENST00000369483.1_Missense_Mutation_p.E434G	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	414	Ig-like C2-type 4.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		GCTGGCCACCTCCACGGAGAT	0.617																																																0			1											11	13	12					1																	117146629		2149	4191	6340	116948152	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1241A>G	1.37:g.117146629T>C	ENSP00000358498:p.Glu414Gly		116948152	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.372751	0.42003	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03330	3.97;4.0;4.0	4.89	4.89	0.63831	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.220320	0.38605	N	0.001623	T	0.01627	0.0052	N	0.22421	0.69	0.39864	D	0.973426	B;P;B	0.41131	0.127;0.739;0.154	B;B;B	0.42959	0.075;0.403;0.122	T	0.64232	-0.6456	10	0.31617	T	0.26	-29.1479	10.8148	0.46569	0.0:0.0:0.0:1.0	.	434;414;434	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	G	414;434;434	ENSP00000358498:E414G;ENSP00000358495:E434G;ENSP00000321184:E434G	ENSP00000321184:E434G	E	-	2	0	IGSF3	116948152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.782000	0.62396	2.043000	0.60533	0.455000	0.32223	GAG		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117146629	T	C	117146629	3	2	93	1	0	0	0	0	1	0	0	0	7622	1551	54	4	2367	4	IGSF3	1	117146629	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1887881	117146629	132103992	12	25340										
LCE4A	199834	hgsc.bcm.edu	37	chr1	152681679	152681680	+	Missense_Mutation	DNP	CC	CC	GT													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aatctcttcctgctgtggctCcagctctgggggctgtggtt					rs6143428|rs11269814|rs200890315	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:152681679_152681680CC>GT	ENST00000368777.1	+	2	384_385	c.128_129CC>GT	c.(127-129)tCC>tGT	p.S43C	LCE4A_ENST00000335535.3_Missense_Mutation_p.S43C			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	43	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			TGCTGTGGCTCCAGCTCTGGGG	0.599																																																0			1																																								150948303|150948304	SO:0001583	missense	199834			BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"Late cornified envelopes"	16613	protein-coding gene	gene with protein product		612618	"small proline rich-like (epidermal differentiation complex) 4A"	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	1.37:g.152681679_152681680delinsGT	ENSP00000357766:p.Ser43Cys		150948303|150948304	Q14D97	Missense_Mutation|Silent	SNP	ENST00000368777.1	37	CCDS1022.1																																																																																				0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356		GT	152681680	CC	GT	152681679	3	3	93	1	0	0	0	0	1	0	0	0	8696	855	30	5	130	5	LCE4A	1	152681679	Missense_Mutation	DNP	CC	TCGA-DC-5337-01A-01D-1657-10	35535050	152681679	96568942	13	25341										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153905205	153905205	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggccaggaccaccagggacAggagcatctttgctgccact	13	13	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:153905205A>G	ENST00000361217.4	-	23	4090	c.3672T>C	c.(3670-3672)ccT>ccC	p.P1224P	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1224					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CACCAGGGACAGGAGCATCTT	0.622																																																0			1											42	49	47					1																	153905205		2060	4190	6250	152171829	SO:0001819	synonymous_variant	9909			AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.3672T>C	1.37:g.153905205A>G			152171829	Q5T4K0	Silent	SNP	ENST00000361217.4	37	CCDS44228.1																																																																																				0.622	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		G	153905205	A	G	153905205	2	3	93	1	0	0	0	0	0	0	0	1	4445	175	7	4		4	DENND4B	1	153905205	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1223526	153905205	95345416	14	25342										
SEMA4A	64218	hgsc.bcm.edu	37	chr1	156146478	156146478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	actggcaggcatcccccgggAgcatgtgaaggtcccgttga	14	12	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:156146478A>G	ENST00000368285.3	+	15	2243	c.1976A>G	c.(1975-1977)gAg>gGg	p.E659G	SEMA4A_ENST00000368282.1_Missense_Mutation_p.E659G|SEMA4A_ENST00000355014.2_Missense_Mutation_p.E659G|SEMA4A_ENST00000368286.2_Missense_Mutation_p.E527G|SEMA4A_ENST00000368284.1_Missense_Mutation_p.E527G	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	659					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					ATCCCCCGGGAGCATGTGAAG	0.612																																																0			1											67	65	66					1																	156146478		2203	4300	6503	154413102	SO:0001583	missense	64218			AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"Semaphorins"	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.1976A>G	1.37:g.156146478A>G	ENSP00000357268:p.Glu659Gly		154413102	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Missense_Mutation	SNP	ENST00000368285.3	37	CCDS1132.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.019593	0.35606	.	.	ENSG00000196189	ENST00000355014;ENST00000368285;ENST00000368284;ENST00000368283;ENST00000544376;ENST00000368286;ENST00000368282	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.48	4.48	0.54585	.	0.413927	0.23461	N	0.047929	T	0.27967	0.0689	M	0.63428	1.95	0.37954	D	0.932764	B;B	0.25441	0.126;0.126	B;B	0.24701	0.055;0.055	T	0.12167	-1.0558	10	0.23891	T	0.37	.	11.7721	0.51965	1.0:0.0:0.0:0.0	.	527;659	Q5TCJ6;Q9H3S1	.;SEM4A_HUMAN	G	659;659;527;621;621;527;659	ENSP00000347117:E659G;ENSP00000357268:E659G;ENSP00000357267:E527G;ENSP00000357269:E527G;ENSP00000357265:E659G	ENSP00000347117:E659G	E	+	2	0	SEMA4A	154413102	1.000000	0.71417	0.997000	0.53966	0.814000	0.46013	3.666000	0.54540	1.893000	0.54813	0.260000	0.18958	GAG		0.612	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367		G	156146478	A	G	156146478	3	3	93	1	0	0	0	0	1	0	0	0	14068	304	11	4	2030	4	SEMA4A	1	156146478	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	2241273	156146478	93104143	15	25343										
CD84	8832	hgsc.bcm.edu	37	chr1	160535464	160535464	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggttcttggatatttacagGgaaagtgactgactctccca	10	8	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:160535464G>T	ENST00000311224.4	-	2	184	c.118C>A	c.(118-120)Cct>Act	p.P40T	CD84_ENST00000534968.1_Intron|CD84_ENST00000368047.3_5'UTR|RP11-528G1.2_ENST00000446952.1_RNA|CD84_ENST00000368048.3_Missense_Mutation_p.P40T|CD84_ENST00000368051.3_Missense_Mutation_p.P40T|CD84_ENST00000368054.3_Missense_Mutation_p.P40T	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	40	Ig-like V-type.				blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.P40S(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ATATTTACAGGGAAAGTGACT	0.433																																																1	Substitution - Missense(1)	central_nervous_system(1)	1											63	61	62					1																	160535464		2203	4300	6503	158802088	SO:0001583	missense	8832			AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1704	protein-coding gene	gene with protein product		604513	"CD84 antigen (leukocyte antigen)", "CD84 molecule "			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.118C>A	1.37:g.160535464G>T	ENSP00000312367:p.Pro40Thr		158802088	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	37	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.904504	0.52333	.	.	ENSG00000066294	ENST00000368054;ENST00000368048;ENST00000311224;ENST00000368051;ENST00000360056;ENST00000368047	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	5.11	4.16	0.48862	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.495500	0.22792	N	0.055595	T	0.34221	0.0890	M	0.84511	2.7	0.80722	D	1	D;D;D;D;D;D	0.71674	0.995;0.995;0.998;0.989;0.994;0.994	P;P;D;P;D;D	0.66979	0.905;0.871;0.948;0.82;0.913;0.913	T	0.25293	-1.0136	10	0.54805	T	0.06	-3.8381	8.3564	0.32333	0.1141:0.0:0.8859:0.0	.	40;40;40;40;40;40	Q9UIB8-5;Q9UIB8-6;Q9UIB8-4;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;.;.;SLAF5_HUMAN;.;.	T	40	ENSP00000357033:P40T;ENSP00000357027:P40T;ENSP00000312367:P40T;ENSP00000357030:P40T;ENSP00000353163:P40T;ENSP00000357026:P40T	ENSP00000312367:P40T	P	-	1	0	CD84	158802088	0.799000	0.28903	0.928000	0.36995	0.611000	0.37282	0.925000	0.28791	1.434000	0.47414	0.591000	0.81541	CCT		0.433	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874		T	160535464	G	T	160535464	3	4	93	1	0	0	0	0	1	0	0	0	3048	1232	43	2	947	2	CD84	1	160535464	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	4388986	160535464	88715157	16	25344										
ADAMTS4	9507	hgsc.bcm.edu	37	chr1	161168189	161168189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcacaacagcctggcaggggCgcccgagccaggcaggacgc	16	15	0	0	rs34448954	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:161168189C>T	ENST00000367996.5	-	1	657	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Missense_Mutation_p.A77T|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	77			A -> T (in dbSNP:rs34448954). {ECO:0000269|PubMed:9734811}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CTGGCAGGGGCGCCCGAGCCA	0.677													C|||	257	0.0513179	0.0068	0.0418	5008	,	,		15569	0.0099		0.1113	False		,,,				2504	0.0992															0			1						C	THR/ALA	82,4276		4,74,2101	12	12	12		229	-6.9	0	1	dbSNP_126	12	831,7711		48,735,3488	yes	missense	ADAMTS4	NM_005099.4	58	52,809,5589	TT,TC,CC		9.7284,1.8816,7.0775	benign	77/838	161168189	913,11987	2179	4271	6450	159434813	SO:0001583	missense	9507			AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.229G>A	1.37:g.161168189C>T	ENSP00000356975:p.Ala77Thr		159434813	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	117	0.05357142857142857	7	0.014227642276422764	17	0.04696132596685083	6	0.01048951048951049	87	0.11477572559366754	C	11.17	1.560306	0.27827	0.018816	0.097284	ENSG00000158859	ENST00000367996;ENST00000367995	T;T	0.07021	3.23;3.23	5.48	-6.94	0.01633	Peptidase M12B, propeptide (1);	1.266050	0.05430	N	0.545706	T	0.00936	0.0031	N	0.08118	0	0.09310	N	0.999995	B;B	0.22346	0.004;0.068	B;B	0.27887	0.003;0.084	T	0.47018	-0.9149	10	0.28530	T	0.3	.	2.4191	0.04444	0.4451:0.2678:0.082:0.2051	rs34448954	77;77	Q5VTW1;O75173	.;ATS4_HUMAN	T	77	ENSP00000356975:A77T;ENSP00000356974:A77T	ENSP00000356974:A77T	A	-	1	0	ADAMTS4	159434813	0.000000	0.05858	0.000000	0.03702	0.828000	0.46876	-1.501000	0.02281	-0.961000	0.03609	0.491000	0.48974	GCC		0.677	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		T	161168189	C	T	161168189	3	4	93	1	0	0	0	0	1	0	0	0	268	768	27	1	2320	1	ADAMTS4	1	161168189	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	632725	161168189	88082432	17	25345										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183909896	183909896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgctttctctggctcctttaCttgcatcctcttcctaccaa	4	15	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:183909896C>T	ENST00000361927.4	-	11	1794	c.1423G>A	c.(1423-1425)Gta>Ata	p.V475I	COLGALT2_ENST00000486375.1_5'Flank|COLGALT2_ENST00000546159.1_Missense_Mutation_p.V475I|COLGALT2_ENST00000367521.1_Missense_Mutation_p.V83I|COLGALT2_ENST00000367520.3_Missense_Mutation_p.V212I	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	475			V -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.V475I(1)									GGCTCCTTTACTTGCATCCTC	0.473																																																1	Substitution - Missense(1)	breast(1)	1											127	118	121					1																	183909896		2203	4300	6503	182176519	SO:0001583	missense	23127			AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.1423G>A	1.37:g.183909896C>T	ENSP00000354960:p.Val475Ile		182176519	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	37	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.847287	0.51164	.	.	ENSG00000198756	ENST00000546159;ENST00000361927;ENST00000367521;ENST00000367520	T;T	0.77358	-1.07;-1.09	5.54	3.65	0.41850	.	0.000000	0.85682	D	0.000000	T	0.75910	0.3914	M	0.68952	2.095	0.54753	D	0.999986	P;B;B	0.47302	0.893;0.179;0.364	B;B;B	0.42692	0.332;0.395;0.3	T	0.74484	-0.3650	9	.	.	.	-25.1966	12.9148	0.58200	0.1294:0.7464:0.1242:0.0	.	475;475;212	F5H3T5;Q8IYK4;Q5SXQ3	.;GT252_HUMAN;.	I	475;475;83;212	ENSP00000439112:V475I;ENSP00000354960:V475I	.	V	-	1	0	GLT25D2	182176519	1.000000	0.71417	0.985000	0.45067	0.714000	0.41099	3.870000	0.56070	0.681000	0.31386	0.655000	0.94253	GTA		0.473	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		T	183909896	C	T	183909896	3	4	93	1	0	0	0	0	1	0	0	0	6487	565	20	3	465	3	GLT25D2	1	183909896	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	22741707	183909896	65340725	18	25346										
CR2	1380	hgsc.bcm.edu	37	chr1	207646451	207646451	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aagtgttatagtggatttacTttgaagggcagtagtcagat	12	3	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:207646451T>C	ENST00000367058.3	+	10	2094	c.1905T>C	c.(1903-1905)acT>acC	p.T635T	CR2_ENST00000458541.2_Silent_p.T608T|CR2_ENST00000367057.3_Silent_p.T635T|CR2_ENST00000367059.3_Silent_p.T635T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	635	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						GTGGATTTACTTTGAAGGGCA	0.398																																																0			1											93	92	92					1																	207646451		2203	4300	6503	205713074	SO:0001819	synonymous_variant	1380			M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1905T>C	1.37:g.207646451T>C			205713074	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	37	CCDS1478.1																																																																																				0.398	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		C	207646451	T	C	207646451	2	2	93	1	0	0	0	0	0	0	0	1	3848	1596	56	4		4	CR2	1	207646451	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	23736555	207646451	41604170	19	25347										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220344349	220344349	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgaagcagagtctgaagtatGagacaatcctccagctgttt	10	8	1	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:220344349G>A	ENST00000358951.2	-	24	2807	c.2691C>T	c.(2689-2691)ctC>ctT	p.L897L		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	897					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TCTGAAGTATGAGACAATCCT	0.473																																																0			1											148	139	142					1																	220344349		2203	4300	6503	218410972	SO:0001819	synonymous_variant	25782			AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.2691C>T	1.37:g.220344349G>A			218410972	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	37	CCDS31028.1																																																																																				0.473	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		A	220344349	G	A	220344349	2	1	93	1	0	0	0	0	0	0	0	1	12973	1277	45	3		3	RAB3GAP2	1	220344349	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	12697898	220344349	28906272	20	25348										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228553825	228553825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgtgcaggcacagacaggcGgaacggcccaattcgaggct	14	11	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:228553825G>A	ENST00000422127.1	+	83	19158	c.19114G>A	c.(19114-19116)Gga>Aga	p.G6372R	OBSCN_ENST00000366707.4_Missense_Mutation_p.G4006R|OBSCN_ENST00000570156.2_Missense_Mutation_p.G7329R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6372	Ig-like 54.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACAGACAGGCGGAACGGCCCA	0.622																																																0			1											80	86	84					1																	228553825		2091	4207	6298	226620448	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.19114G>A	1.37:g.228553825G>A	ENSP00000409493:p.Gly6372Arg		226620448	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.79|10.79	1.450620|1.450620	0.26074|0.26074	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.74002|.	-0.8;-0.8|.	5.41|5.41	1.13|1.13	0.20643|0.20643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.35451|0.35451	0.0932|0.0932	L|L	0.28504|0.28504	0.86|0.86	0.09310|0.09310	N|N	1|1	B|.	0.29552|.	0.248|.	B|.	0.30029|.	0.11|.	T|T	0.24693|0.24693	-1.0153|-1.0153	9|5	0.34782|.	T|.	0.22|.	.|.	13.6422|13.6422	0.62257|0.62257	0.1429:0.0:0.8571:0.0|0.1429:0.0:0.8571:0.0	.|.	6372|.	Q5VST9|.	OBSCN_HUMAN|.	R|Q	6372;4006|988	ENSP00000409493:G6372R;ENSP00000355668:G4006R|.	ENSP00000355668:G4006R|.	G|R	+|+	1|2	0|0	OBSCN|OBSCN	226620448|226620448	0.007000|0.007000	0.16637|0.16637	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.470000|0.470000	0.22084|0.22084	-0.078000|-0.078000	0.12730|0.12730	-0.752000|-0.752000	0.03492|0.03492	GGA|CGG		0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228553825	G	A	228553825	3	1	93	1	0	0	0	0	1	0	0	0	10843	1117	39	1	20650	1	OBSCN	1	228553825	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	8209476	228553825	20696796	21	25349										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228560700	228560700	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggaggcacctgccgctggaTgagcctgcagagctggggct	18	11	0	2	rs512253	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:228560700T>C	ENST00000422127.1	+	94	22265	c.22221T>C	c.(22219-22221)gaT>gaC	p.D7407D	OBSCN_ENST00000366707.4_Silent_p.D5041D|OBSCN_ENST00000570156.2_Silent_p.D8364D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7407					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGCCGCTGGATGAGCCTGCAG	0.677													C|||	3796	0.757987	0.9365	0.6398	5008	,	,		15865	0.752		0.5636	False		,,,				2504	0.8067															0			1						C		3642,576		1602,438,69	16	22	20		22221	-7.7	0.1	1	dbSNP_83	20	4624,3806		1316,1992,907	no	coding-synonymous	OBSCN	NM_001098623.1		2918,2430,976	CC,CT,TT		45.1483,13.6558,34.6458		7407/7969	228560700	8266,4382	2109	4215	6324	226627323	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.22221T>C	1.37:g.228560700T>C			226627323	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	6.371	0.436557	0.12104	0.863442	0.548517	ENSG00000154358	ENST00000441106	.	.	.	5.31	-7.65	0.01281	.	.	.	.	.	.	.	.	.	.	.	0.26408	P	0.9763186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.4422	0.16515	0.1714:0.5044:0.1553:0.1689	rs512253;rs3795815	.	.	.	R	2024	.	.	X	+	1	0	OBSCN	226627323	0.942000	0.31987	0.072000	0.20136	0.009000	0.06853	-0.247000	0.08866	-1.794000	0.01256	-3.149000	0.00058	TGA		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228560700	T	C	228560700	2	2	93	1	0	0	0	0	0	0	0	1	10843	1461	51	4		4	OBSCN	1	228560700	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6875	228560700	20689921	22	25350										
LYST	1130	hgsc.bcm.edu	37	chr1	235850291	235850291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtgtaggctgtgatgacaccGcatttgcttccagtaaacag	11	9	0	2	rs145136281		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr1:235850291G>A	ENST00000389794.3	-	48	10932	c.10758C>T	c.(10756-10758)tgC>tgT	p.C3586C	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Silent_p.C3586C			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3586					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TGATGACACCGCATTTGCTTC	0.443																																																0			1						G		0,4406		0,0,2203	145	134	138		10758	-1.7	1	1	dbSNP_134	138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LYST	NM_000081.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		3586/3802	235850291	1,13005	2203	4300	6503	233916914	SO:0001819	synonymous_variant	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10758C>T	1.37:g.235850291G>A			233916914	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																				0.443	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235850291	G	A	235850291	2	1	93	1	0	0	0	0	0	0	0	1	9158	1079	38	1		1	LYST	1	235850291	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	7289591	235850291	13400330	23	25351										
DDX1	1653	hgsc.bcm.edu	37	chr2	15760412	15760412	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgcattttcctacatgggtTgacttaaaaggagaagactc	9	7	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:15760412T>C	ENST00000381341.2	+	18	1676	c.1287T>C	c.(1285-1287)gtT>gtC	p.V429V	DDX1_ENST00000233084.3_Silent_p.V429V			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	429	Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		CTACATGGGTTGACTTAAAAG	0.428																																																0			2											128	121	124					2																	15760412		2203	4300	6503	15677863	SO:0001819	synonymous_variant	1653			X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1287T>C	2.37:g.15760412T>C			15677863	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	37	CCDS1686.1																																																																																				0.428	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		C	15760412	T	C	15760412	2	2	93	1	0	0	0	0	0	0	0	1	4347	1799	63	4		4	DDX1	2	15760412	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10		15760412	227438961	24	25352										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51254947	51254947	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agttccgggggcagccccccGacgaaaaggccgctgaacac	13	15	0	1	rs531571569		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:51254947G>A	ENST00000406316.2	-	2	1941	c.465C>T	c.(463-465)gtC>gtT	p.V155V	NRXN1_ENST00000405581.1_Silent_p.V155V|NRXN1_ENST00000405472.3_Silent_p.V155V|NRXN1_ENST00000404971.1_Silent_p.V155V|NRXN1_ENST00000406859.3_Silent_p.V155V|NRXN1_ENST00000402717.3_Silent_p.V155V|NRXN1_ENST00000401669.2_Silent_p.V155V	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	155	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCAGCCCCCCGACGAAAAGGC	0.662													G|||	1	0.000199681	0	0	5008	,	,		13090	0		0	False		,,,				2504	0.001															0			2											22	29	27					2																	51254947		2117	4229	6346	51108451	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.465C>T	2.37:g.51254947G>A			51108451	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.662	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	51254947	G	A	51254947	2	1	93	1	0	0	0	0	0	0	0	1	10696	1045	37	1		1	NRXN1	2	51254947	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	35494535	51254947	191944426	25	25353										
MCEE	84693	hgsc.bcm.edu	37	chr2	71351574	71351574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctatggctacatggttgagtCgacccaggttccacacagaa	10	11	0	2	rs377624743		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:71351574C>T	ENST00000244217.5	-	2	157	c.140G>A	c.(139-141)cGa>cAa	p.R47Q	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	47					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						ATGGTTGAGTCGACCCAGGTT	0.493																																																0			2						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	112	121	118		140	1.6	0.6	2		118	0,8600		0,0,4300	no	missense	MCEE	NM_032601.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	47/177	71351574	1,13005	2203	4300	6503	71205082	SO:0001583	missense	84693			AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"glyoxalase domain containing 2"	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.140G>A	2.37:g.71351574C>T	ENSP00000244217:p.Arg47Gln		71205082	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488190	0.44249	2.27E-4	0.0	ENSG00000124370	ENST00000413592;ENST00000244217	T;T	0.70631	-0.5;-0.18	5.39	1.62	0.23740	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.172827	0.49916	N	0.000133	T	0.54967	0.1891	L	0.55481	1.735	0.47547	D	0.999459	P	0.43633	0.813	B	0.26693	0.072	T	0.53121	-0.8483	10	0.62326	D	0.03	-11.1457	8.9191	0.35601	0.0:0.6934:0.0:0.3066	.	47	Q96PE7	MCEE_HUMAN	Q	3;47	ENSP00000391140:R3Q;ENSP00000244217:R47Q	ENSP00000244217:R47Q	R	-	2	0	MCEE	71205082	0.996000	0.38824	0.621000	0.29145	0.639000	0.38242	1.502000	0.35704	0.087000	0.17167	0.650000	0.86243	CGA		0.493	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601		T	71351574	C	T	71351574	3	4	93	1	0	0	0	0	1	0	0	0	9407	884	31	1	398	1	MCEE	2	71351574	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	20096627	71351574	171847799	26	25354										
CD8A	925	hgsc.bcm.edu	37	chr2	87015672	87015672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccggggacatttgcaaacacGtcttcggttccctggataag	11	11	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:87015672G>A	ENST00000409511.2	-	8	1667	c.637C>T	c.(637-639)Cgt>Tgt	p.R213C	CD8A_ENST00000456996.2_Missense_Mutation_p.R176C|CD8A_ENST00000352580.3_Missense_Mutation_p.R176C|CD8A_ENST00000409781.1_Missense_Mutation_p.R176C|CD8A_ENST00000538832.1_Missense_Mutation_p.R254C|CD8A_ENST00000283635.3_Missense_Mutation_p.R213C	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	213					antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TTGCAAACACGTCTTCGGTTC	0.502																																																0			2											57	56	56					2																	87015672		2203	4300	6503	86869183	SO:0001583	missense	925				CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1706	protein-coding gene	gene with protein product		186910	"CD8 antigen, alpha polypeptide (p32)", "T-cell surface glycoprotein CD8 alpha chain"	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.637C>T	2.37:g.87015672G>A	ENSP00000386559:p.Arg213Cys		86869183	B4DT80|D6W5M8|Q13970|Q4ZG17	Missense_Mutation	SNP	ENST00000409511.2	37	CCDS1992.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953904	0.73902	.	.	ENSG00000153563	ENST00000456996;ENST00000352580;ENST00000283635;ENST00000409511;ENST00000442577;ENST00000538832;ENST00000409781	D;D;D;D;D;D	0.89810	-1.5;-1.5;-2.46;-2.46;-2.57;-2.32	4.95	4.04	0.47022	.	0.053858	0.64402	D	0.000001	D	0.94265	0.8158	M	0.87682	2.9	0.49582	D	0.999806	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.996	D	0.94438	0.7656	10	0.87932	D	0	-14.2863	10.5401	0.45029	0.0:0.0:0.8072:0.1928	.	254;176;213	B4DT80;P01732-2;P01732	.;.;CD8A_HUMAN	C	176;176;213;213;198;254;176	ENSP00000398868:R176C;ENSP00000321631:R176C;ENSP00000283635:R213C;ENSP00000386559:R213C;ENSP00000438371:R254C;ENSP00000387314:R176C	ENSP00000283635:R213C	R	-	1	0	CD8A	86869183	0.618000	0.27051	0.617000	0.29091	0.971000	0.66376	2.663000	0.46774	1.383000	0.46405	0.561000	0.74099	CGT		0.502	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768		A	87015672	G	A	87015672	3	1	93	1	0	0	0	0	1	0	0	0	3050	1145	40	1	78	1	CD8A	2	87015672	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	15664098	87015672	156183701	27	25355										
TEKT4	150483	hgsc.bcm.edu	37	chr2	95542490	95542490	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgtactcgctaccccaccatCctgcagctggctggctacca	8	18	0	0	rs76856825		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:95542490C>T	ENST00000295201.4	+	6	1421	c.1284C>T	c.(1282-1284)atC>atT	p.I428I	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	428					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						ACCCCACCATCCTGCAGCTGG	0.582																																																0			2											69	48	55					2																	95542490		2203	4300	6503	94906217	SO:0001819	synonymous_variant	150483			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1284C>T	2.37:g.95542490C>T			94906217		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																				0.582	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		T	95542490	C	T	95542490	2	4	93	1	0	0	0	0	0	0	0	1	15794	845	30	3		3	TEKT4	2	95542490	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	8526818	95542490	147656883	28	25356										
FAHD2B	151313	hgsc.bcm.edu	37	chr2	97751497	97751497	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagaaggtgtcgaaggttttTcccagcagccactgtttccc	10	12	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:97751497T>C	ENST00000414820.1	-	6	894	c.624A>G	c.(622-624)ggA>ggG	p.G208G	FAHD2B_ENST00000468548.1_5'Flank|FAHD2B_ENST00000440566.2_Silent_p.G208G|FAHD2B_ENST00000272610.3_Silent_p.G208G			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	208							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						CGAAGGTTTTTCCCAGCAGCC	0.597																																																0			2											98	86	90					2																	97751497		2203	4300	6503	97115224	SO:0001819	synonymous_variant	151313				CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.624A>G	2.37:g.97751497T>C			97115224	D3DXH7|Q8NDK1	Silent	SNP	ENST00000414820.1	37	CCDS2030.1																																																																																				0.597	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336		C	97751497	T	C	97751497	2	2	93	1	0	0	0	0	0	0	0	1	5390	1770	62	4		4	FAHD2B	2	97751497	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2209007	97751497	145447876	29	25357										
GPR45	11250	hgsc.bcm.edu	37	chr2	105858361	105858361	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggcttacacatacctgctgCtgaacaccagcaacgcctca	7	15	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:105858361C>T	ENST00000258456.1	+	1	162	c.46C>T	c.(46-48)Ctg>Ttg	p.L16L		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						ATACCTGCTGCTGAACACCAG	0.612																																																0			2											88	84	85					2																	105858361		2203	4300	6503	105224793	SO:0001819	synonymous_variant	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.46C>T	2.37:g.105858361C>T			105224793	Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	37	CCDS2066.1																																																																																				0.612	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		T	105858361	C	T	105858361	2	4	93	1	0	0	0	0	0	0	0	1	6716	796	28	3		3	GPR45	2	105858361	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	8106864	105858361	137341012	30	25358										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125405504	125405504	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gagcaggaggtggcctaccaCtgcaggaggtcccgcctgct	15	13	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:125405504C>T	ENST00000431078.1	+	13	2407	c.2043C>T	c.(2041-2043)caC>caT	p.H681H		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	681	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGGCCTACCACTGCAGGAGGT	0.607																																																0			2											22	26	25					2																	125405504		2053	4193	6246	125121974	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2043C>T	2.37:g.125405504C>T			125121974	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.607	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125405504	C	T	125405504	2	4	93	1	0	0	0	0	0	0	0	1	3656	564	20	3		3	CNTNAP5	2	125405504	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	19547143	125405504	117793869	31	25359										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149799245	149799245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	catggatgtaatagatgaagGcaaagcaaaccgacacgtgg	12	7	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:149799245G>A	ENST00000435030.1	+	7	928	c.560G>A	c.(559-561)gGc>gAc	p.G187D	KIF5C_ENST00000414838.2_Missense_Mutation_p.G92D			O60282	KIF5C_HUMAN	kinesin family member 5C	187	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		ATAGATGAAGGCAAAGCAAAC	0.532																																																0			2											75	73	74					2																	149799245		1979	4159	6138	149507491	SO:0001583	missense	3800			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.560G>A	2.37:g.149799245G>A	ENSP00000393379:p.Gly187Asp		149507491	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	G	27.1	4.799309	0.90538	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436	D;D	0.83837	-1.77;-1.77	5.48	5.48	0.80851	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.91848	0.7420	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92194	0.5762	9	0.87932	D	0	.	19.5489	0.95310	0.0:0.0:1.0:0.0	.	187	O60282	KIF5C_HUMAN	D	187;92;90	ENSP00000393379:G187D;ENSP00000410115:G92D	ENSP00000334176:G90D	G	+	2	0	KIF5C	149507491	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	9.564000	0.98151	2.850000	0.98022	0.655000	0.94253	GGC		0.532	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149799245	G	A	149799245	3	1	93	1	0	0	0	0	1	0	0	0	8328	1203	42	3	508	3	KIF5C	2	149799245	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	24393741	149799245	93400128	32	25360										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158156137	158156137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggaacatacgaccctggccTtgatgtttggggtggggaaa	15	7	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:158156137T>C	ENST00000259056.4	+	6	2560	c.2075T>C	c.(2074-2076)cTt>cCt	p.L692P	RN7SKP281_ENST00000410472.1_RNA	NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	692	Catalytic subdomain B.		L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GACCCTGGCCTTGATGTTTGG	0.373																																																0			2											90	86	87					2																	158156137		2203	4300	6503	157864383	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.2075T>C	2.37:g.158156137T>C	ENSP00000259056:p.Leu692Pro		157864383	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801379	0.90538	.	.	ENSG00000136542	ENST00000259056	T	0.74209	-0.82	5.85	5.85	0.93711	.	0.065901	0.64402	D	0.000008	D	0.88994	0.6589	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.91351	0.5104	10	0.87932	D	0	.	15.9098	0.79463	0.0:0.0:0.0:1.0	.	692	Q7Z7M9	GALT5_HUMAN	P	692	ENSP00000259056:L692P	ENSP00000259056:L692P	L	+	2	0	GALNT5	157864383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.237000	0.73441	0.459000	0.35465	CTT		0.373	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		C	158156137	T	C	158156137	3	2	93	1	0	0	0	0	1	0	0	0	6236	1609	56	4	2097	4	GALNT5	2	158156137	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	8356892	158156137	85043236	33	25361										
CIR1	9541	hgsc.bcm.edu	37	chr2	175213553	175213553	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgctgtcctccctagaactcTcgtgttttaagaacctgggc	9	12	1	2	rs200766128		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:175213553T>C	ENST00000342016.3	-	10	1117	c.1025A>G	c.(1024-1026)gAg>gGg	p.E342G	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	342	Lys/Ser-rich.				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E342G(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						CCTAGAACTCTCGTGTTTTAA	0.443																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											159	159	159					2																	175213553		2203	4300	6503	174921799	SO:0001583	missense	7335			AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"recepin", "CBF1 interacting corepressor"	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.1025A>G	2.37:g.175213553T>C	ENSP00000339723:p.Glu342Gly		174921799	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Missense_Mutation	SNP	ENST00000342016.3	37	CCDS2256.1	.	.	.	.	.	.	.	.	.	.	T	9.932	1.215039	0.22373	.	.	ENSG00000138433	ENST00000342016	.	.	.	6.16	5.01	0.66863	.	0.277370	0.34531	N	0.003885	T	0.53384	0.1793	L	0.56769	1.78	0.34740	D	0.730643	B;B	0.17465	0.022;0.012	B;B	0.17433	0.018;0.005	T	0.61173	-0.7116	9	0.59425	D	0.04	.	10.7341	0.46115	0.0:0.0721:0.0:0.9279	.	342;342	A0PJI7;Q86X95	.;CIR1_HUMAN	G	342	.	ENSP00000339723:E342G	E	-	2	0	CIR1	174921799	1.000000	0.71417	0.425000	0.26659	0.026000	0.11368	2.277000	0.43417	1.152000	0.42452	0.528000	0.53228	GAG		0.443	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882		C	175213553	T	C	175213553	3	2	93	1	0	0	0	0	1	0	0	0	3438	1551	54	4	331	4	CIR1	2	175213553	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	17057416	175213553	67985820	34	25362										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347300	222347300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tccacatttcttgcataccaCattataggaaatgtcctggc	6	11	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:222347300C>T	ENST00000281821.2	-	5	1131	c.1090G>A	c.(1090-1092)Gtg>Atg	p.V364M	EPHA4_ENST00000409938.1_Missense_Mutation_p.V364M|EPHA4_ENST00000392071.4_Missense_Mutation_p.V313M|EPHA4_ENST00000409854.1_Missense_Mutation_p.V364M	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	364	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TTGCATACCACATTATAGGAA	0.512																																																0			2											164	177	173					2																	222347300		2203	4300	6503	222055544	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1090G>A	2.37:g.222347300C>T	ENSP00000281821:p.Val364Met		222055544	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.8|22.8	4.332682|4.332682	0.81801|0.81801	.|.	.|.	ENSG00000116106|ENSG00000116106	ENST00000441679|ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	.|T;T;T;T;T	.|0.68765	.|-0.35;-0.35;-0.35;-0.35;-0.35	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.056865	.|0.64402	.|D	.|0.000001	T|T	0.81059|0.81059	0.4744|0.4744	M|M	0.90309|0.90309	3.105|3.105	0.58432|0.58432	D|D	0.999994|0.999994	.|P	.|0.40619	.|0.724	.|P	.|0.50049	.|0.629	D|D	0.83646|0.83646	0.0153|0.0153	5|10	.|0.87932	.|D	.|0	.|.	15.3505|15.3505	0.74380|0.74380	0.1395:0.8605:0.0:0.0|0.1395:0.8605:0.0:0.0	.|.	.|364	.|P54764	.|EPHA4_HUMAN	I|M	100|364;364;364;313;68	.|ENSP00000281821:V364M;ENSP00000386276:V364M;ENSP00000386829:V364M;ENSP00000375923:V313M;ENSP00000395917:V68M	.|ENSP00000281821:V364M	M|V	-|-	3|1	0|0	EPHA4|EPHA4	222055544|222055544	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.906000|0.906000	0.53458|0.53458	4.748000|4.748000	0.62148|0.62148	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	ATG|GTG		0.512	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222347300	C	T	222347300	3	4	93	1	0	0	0	0	1	0	0	0	5182	478	17	3	1922	3	EPHA4	2	222347300	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	47133747	222347300	20852073	35	25363										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240024515	240024515	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttctgccggttgagggggttCgtgccatacaggagggtgtg	18	7	1	1	rs149067286	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr2:240024515C>T	ENST00000345617.3	-	16	2966	c.2175G>A	c.(2173-2175)acG>acA	p.T725T	HDAC4_ENST00000543185.1_Silent_p.T309T|HDAC4_ENST00000541256.1_Silent_p.T699T	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	725	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGAGGGGGTTCGTGCCATACA	0.567													C|||	2	0.000399361	0.0015	0	5008	,	,		16836	0		0	False		,,,				2504	0															0			2						C		6,4396	11.4+/-27.6	0,6,2195	120	100	107		2175	-9.5	0.1	2	dbSNP_134	107	0,8600		0,0,4300	no	coding-synonymous	HDAC4	NM_006037.3		0,6,6495	TT,TC,CC		0.0,0.1363,0.0461		725/1085	240024515	6,12996	2201	4300	6501	239689452	SO:0001819	synonymous_variant	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2175G>A	2.37:g.240024515C>T			239689452	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																				0.567	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		T	240024515	C	T	240024515	2	4	93	1	0	0	0	0	0	0	0	1	7030	871	31	1		1	HDAC4	2	240024515	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	17677215	240024515	3174858	36	25364										
VHL	7428	hgsc.bcm.edu	37	chr3	10188243	10188243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agggacacacgatgggcttcTggttaaccaaactgaattat	10	8	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:10188243T>C	ENST00000256474.2	+	2	1226	c.386T>C	c.(385-387)cTg>cCg	p.L129P	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	129	Involved in binding to CCT complex.		L -> LE (in VHLD).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.H125fs*27(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATGGGCTTCTGGTTAACCAA	0.473		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	1	Deletion - Frameshift(1)	kidney(1)	3	GRCh37	CI024081	VHL	I							202	186	192					3																	10188243		2203	4300	6503	10163243	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.386T>C	3.37:g.10188243T>C	ENSP00000256474:p.Leu129Pro		10163243	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.212082	0.39102	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	5.07	3.89	0.44902	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.332531	0.28977	N	0.013530	D	0.99591	0.9852	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.98141	1.0436	10	0.51188	T	0.08	-18.8889	10.4626	0.44590	0.0:0.0:0.1639:0.8361	.	129	P40337	VHL_HUMAN	P	129;47	ENSP00000256474:L129P	ENSP00000256474:L129P	L	+	2	0	VHL	10163243	1.000000	0.71417	0.998000	0.56505	0.189000	0.23516	3.266000	0.51569	0.869000	0.35703	-0.460000	0.05396	CTG		0.473	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188243	T	C	10188243	3	2	93	1	0	0	0	0	1	0	0	0	17202	1580	55	4	392	4	VHL	3	10188243	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10		10188243	187834187	37	25365										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266114	41266114	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctggactctggaatccattcTggtgccactaccacagctcc	8	15	2	0	rs121913416		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:41266114T>C	ENST00000349496.5	+	3	391	c.111T>C	c.(109-111)tcT>tcC	p.S37S	CTNNB1_ENST00000405570.1_Silent_p.S37S|CTNNB1_ENST00000396183.3_Silent_p.S37S|CTNNB1_ENST00000453024.1_Silent_p.S30S|CTNNB1_ENST00000396185.3_Silent_p.S37S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S37S(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.S37_A39>S(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GAATCCATTCTGGTGCCACTA	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	132	Deletion - In frame(102)|Complex - deletion inframe(19)|Unknown(7)|Deletion - Frameshift(3)|Substitution - coding silent(1)	liver(98)|large_intestine(19)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|kidney(1)	3											92	78	82					3																	41266114		2203	4300	6503	41241118	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.111T>C	3.37:g.41266114T>C			41241118	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266114	T	C	41266114	2	2	93	1	0	0	0	0	0	0	0	1	4022	1567	55	4		4	CTNNB1	3	41266114	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	31077871	41266114	156756316	38	25366										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266181	41266181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggaagaggatgtggataccTcccaagtcctgtatgagtgg	14	7	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:41266181T>C	ENST00000349496.5	+	3	458	c.178T>C	c.(178-180)Tcc>Ccc	p.S60P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S60P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S60P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S53P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S60P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	60					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGTGGATACCTCCCAAGTCCT	0.458		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	108	Deletion - In frame(86)|Complex - deletion inframe(15)|Unknown(7)	liver(79)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											65	62	63					3																	41266181		2203	4300	6503	41241185	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.178T>C	3.37:g.41266181T>C	ENSP00000344456:p.Ser60Pro		41241185	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.871453	0.33069	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.91	3.48	0.39840	.	0.154766	0.56097	D	0.000040	T	0.28466	0.0704	L	0.35854	1.095	0.29701	N	0.840169	B	0.02656	0.0	B	0.04013	0.001	T	0.17107	-1.0380	10	0.29301	T	0.29	-3.6161	6.1112	0.20102	0.71:0.0:0.0846:0.2053	.	60	P35222	CTNB1_HUMAN	P	53;60;60;60;60;53;60;60;60	ENSP00000400508:S53P;ENSP00000385604:S60P;ENSP00000412219:S60P;ENSP00000379486:S60P;ENSP00000344456:S60P;ENSP00000411226:S53P;ENSP00000379488:S60P;ENSP00000409302:S60P;ENSP00000401599:S60P	ENSP00000344456:S60P	S	+	1	0	CTNNB1	41241185	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.318000	0.79029	0.464000	0.27142	0.533000	0.62120	TCC		0.458	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266181	T	C	41266181	3	2	93	1	0	0	0	0	1	0	0	0	4022	1551	54	4	184	4	CTNNB1	3	41266181	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	67	41266181	156756249	39	25367										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46016794	46016794	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccaacctctggtgcaccaagGagtagcgaataaatgctctt	9	11	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:46016794G>A	ENST00000296137.2	-	5	537	c.332C>T	c.(331-333)tCc>tTc	p.S111F	FYCO1_ENST00000535325.1_Missense_Mutation_p.S111F	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	111	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		GTGCACCAAGGAGTAGCGAAT	0.488																																																0			3											164	130	142					3																	46016794		2203	4300	6503	45991798	SO:0001583	missense	79443			AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.332C>T	3.37:g.46016794G>A	ENSP00000296137:p.Ser111Phe		45991798	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.572571	0.86542	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.30182	1.54;1.54	5.69	5.69	0.88448	RUN (2);	0.000000	0.85682	D	0.000000	T	0.49287	0.1548	L	0.40543	1.245	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.46219	-0.9207	10	0.87932	D	0	-19.6544	17.9818	0.89144	0.0:0.0:1.0:0.0	.	111;111	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	F	111	ENSP00000296137:S111F;ENSP00000441178:S111F	ENSP00000296137:S111F	S	-	2	0	FYCO1	45991798	1.000000	0.71417	0.977000	0.42913	0.983000	0.72400	9.352000	0.97076	2.684000	0.91462	0.557000	0.71058	TCC		0.488	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		A	46016794	G	A	46016794	3	1	93	1	0	0	0	0	1	0	0	0	6144	1174	41	3	4160	3	FYCO1	3	46016794	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	4750613	46016794	152005636	40	25368										
LTF	4057	hgsc.bcm.edu	37	chr3	46501175	46501175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctggatacactggatgggggAgtctctctttatgcagctga	13	8	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:46501175A>G	ENST00000231751.4	-	2	473	c.178T>C	c.(178-180)Tcc>Ccc	p.S60P	LTF_ENST00000426532.2_Missense_Mutation_p.S16P|LTF_ENST00000417439.1_Missense_Mutation_p.S60P	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	60	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TGGATGGGGGAGTCTCTCTTT	0.522																																																0			3											124	115	118					3																	46501175		2203	4300	6503	46476179	SO:0001583	missense	4057				CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.178T>C	3.37:g.46501175A>G	ENSP00000231751:p.Ser60Pro		46476179	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.799070	0.50208	.	.	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496;ENST00000443743;ENST00000431944;ENST00000415180	T;T;T;T;T;T	0.36878	2.25;2.25;2.25;2.25;1.23;1.23	4.62	3.42	0.39159	.	0.334073	0.32769	N	0.005661	T	0.64583	0.2611	M	0.93898	3.47	0.09310	N	1	D;D;D	0.65815	0.994;0.995;0.994	D;D;D	0.72625	0.978;0.946;0.978	T	0.59064	-0.7524	10	0.72032	D	0.01	-23.6303	8.032	0.30470	0.8192:0.0:0.0:0.1808	.	60;47;60	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	P	60;16;60;47;60;71;16	ENSP00000231751:S60P;ENSP00000405719:S16P;ENSP00000405546:S60P;ENSP00000397427:S47P;ENSP00000395234:S71P;ENSP00000400254:S16P	ENSP00000231751:S60P	S	-	1	0	LTF	46476179	0.136000	0.22515	0.002000	0.10522	0.006000	0.05464	1.447000	0.35101	0.839000	0.34971	0.528000	0.53228	TCC		0.522	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		G	46501175	A	G	46501175	3	3	93	1	0	0	0	0	1	0	0	0	9108	304	11	4	2018	4	LTF	3	46501175	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	484381	46501175	151521255	41	25369										
DHX30	22907	hgsc.bcm.edu	37	chr3	47889438	47889438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggaagaacgctatgacctgAagaccaaggtggcacctacc	11	11	0	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:47889438A>G	ENST00000445061.1	+	14	2685	c.2278A>G	c.(2278-2280)Aag>Gag	p.K760E	DHX30_ENST00000348968.4_Missense_Mutation_p.K732E|MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000457607.1_Missense_Mutation_p.K788E|DHX30_ENST00000446256.2_Missense_Mutation_p.K721E	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	760	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CTATGACCTGAAGACCAAGGT	0.557																																																0			3											125	109	114					3																	47889438		2203	4300	6503	47864442	SO:0001583	missense	22907			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.2278A>G	3.37:g.47889438A>G	ENSP00000405620:p.Lys760Glu		47864442	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	37	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	A	8.657	0.899565	0.17686	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.03152	4.04;4.03;4.03;4.03	5.73	4.57	0.56435	Helicase, C-terminal (3);	0.123853	0.52532	D	0.000073	T	0.02727	0.0082	N	0.16166	0.38	0.39555	D	0.96903	B;B	0.18968	0.032;0.005	B;B	0.21151	0.033;0.012	T	0.52518	-0.8565	10	0.20519	T	0.43	.	10.9223	0.47171	0.9268:0.0:0.0732:0.0	.	760;721	Q7L2E3;Q7L2E3-3	DHX30_HUMAN;.	E	721;760;732;788	ENSP00000392601:K721E;ENSP00000405620:K760E;ENSP00000343442:K732E;ENSP00000394682:K788E	ENSP00000343442:K732E	K	+	1	0	DHX30	47864442	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	4.418000	0.59828	1.002000	0.39104	0.460000	0.39030	AAG		0.557	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		G	47889438	A	G	47889438	3	3	93	1	0	0	0	0	1	0	0	0	4515	247	9	4	2335	4	DHX30	3	47889438	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1388263	47889438	150132992	42	25370										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48616674	48616674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcctggtttcccatccagtcCgctccggccatccagcccag	8	19	0	0	rs374718902		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:48616674C>T	ENST00000328333.8	-	61	5451	c.5344G>A	c.(5344-5346)Gga>Aga	p.G1782R	COL7A1_ENST00000454817.1_Missense_Mutation_p.G1782R|MIR711_ENST00000390201.1_RNA	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1782	Triple-helical region.		G -> R (in RDEB; mitis type). {ECO:0000269|PubMed:8618018}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCATCCAGTCCGCTCCGGCCA	0.612																																																0			3	GRCh37	CM960407	COL7A1	M		C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	40	45	43		5344	5.2	0.5	3		43	0,8600		0,0,4300	no	missense	COL7A1	NM_000094.3	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1782/2945	48616674	1,13005	2203	4300	6503	48591678	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.5344G>A	3.37:g.48616674C>T	ENSP00000332371:p.Gly1782Arg		48591678	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.629473	0.46944	2.27E-4	0.0	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.99353	-5.53;-5.77	5.16	5.16	0.70880	.	0.000000	0.46442	D	0.000285	D	0.99694	0.9884	H	0.98276	4.19	0.50632	D	0.999888	D	0.89917	1.0	D	0.97110	1.0	D	0.97210	0.9870	10	0.87932	D	0	.	17.2107	0.86929	0.0:1.0:0.0:0.0	.	1782	Q02388	CO7A1_HUMAN	R	1782	ENSP00000332371:G1782R;ENSP00000412569:G1782R	ENSP00000332371:G1782R	G	-	1	0	COL7A1	48591678	1.000000	0.71417	0.474000	0.27266	0.238000	0.25445	6.331000	0.72929	2.418000	0.82041	0.655000	0.94253	GGA		0.612	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48616674	C	T	48616674	3	4	93	1	0	0	0	0	1	0	0	0	3710	661	23	1	3722	1	COL7A1	3	48616674	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	727236	48616674	149405756	43	25371										
BSN	8927	hgsc.bcm.edu	37	chr3	49690353	49690353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggaggagctacaccgctccTcctgctctgagtactcaccc	9	16	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:49690353T>C	ENST00000296452.4	+	5	3478	c.3364T>C	c.(3364-3366)Tcc>Ccc	p.S1122P		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1122					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACACCGCTCCTCCTGCTCTGA	0.612																																																0			3											71	71	71					3																	49690353		2203	4300	6503	49665357	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3364T>C	3.37:g.49690353T>C	ENSP00000296452:p.Ser1122Pro		49665357	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.018151	0.54576	.	.	ENSG00000164061	ENST00000296452	T	0.34275	1.37	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	M	0.78049	2.395	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.65335	-0.6193	10	0.54805	T	0.06	.	15.1481	0.72674	0.0:0.0:0.0:1.0	.	1122	Q9UPA5	BSN_HUMAN	P	1122	ENSP00000296452:S1122P	ENSP00000296452:S1122P	S	+	1	0	BSN	49665357	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.013000	0.88655	1.998000	0.58463	0.459000	0.35465	TCC		0.612	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		C	49690353	T	C	49690353	3	2	93	1	0	0	0	0	1	0	0	0	1533	1551	54	4	3382	4	BSN	3	49690353	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1073679	49690353	148332077	44	25372										
ERC2	26059	hgsc.bcm.edu	37	chr3	55922427	55922427	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggtactcacttcatctccaGgatctcctccagctgtttcc	7	15	4	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:55922427G>A	ENST00000288221.6	-	14	2809	c.2554C>T	c.(2554-2556)Ctg>Ttg	p.L852L		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	852						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		TTCATCTCCAGGATCTCCTCC	0.537																																																0			3											139	145	143					3																	55922427		2000	4167	6167	55897467	SO:0001819	synonymous_variant	26059			AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2554C>T	3.37:g.55922427G>A			55897467	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1																																																																																				0.537	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	55922427	G	A	55922427	2	1	93	1	0	0	0	0	0	0	0	1	5224	991	35	3		3	ERC2	3	55922427	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	6232074	55922427	142100003	45	25373										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706662	96706662	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aacttggccatgtttcctgaTaccattccaagggttgattc	8	10	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:96706662T>C	ENST00000389672.5	+	3	977	c.939T>C	c.(937-939)gaT>gaC	p.D313D	EPHA6_ENST00000470610.2_Silent_p.D313D|EPHA6_ENST00000542517.1_Silent_p.D219D	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	219						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						TGTTTCCTGATACCATTCCAA	0.478																																																0			3											215	217	216					3																	96706662		1983	4178	6161	98189352	SO:0001819	synonymous_variant	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.939T>C	3.37:g.96706662T>C			98189352	D6RAL5	Silent	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	T	7.882	0.730493	0.15507	.	.	ENSG00000080224	ENST00000506569	.	.	.	5.47	1.9	0.25705	.	.	.	.	.	T	0.57140	0.2033	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47959	-0.9076	4	.	.	.	.	8.408	0.32627	0.0:0.4357:0.0:0.5643	.	.	.	.	H	258	.	.	Y	+	1	0	EPHA6	98189352	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.566000	0.36396	0.097000	0.17492	0.528000	0.53228	TAC		0.478	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		C	96706662	T	C	96706662	2	2	93	1	0	0	0	0	0	0	0	1	5184	1403	49	4		4	EPHA6	3	96706662	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	40784235	96706662	101315768	46	25374										
ATG3	64422	hgsc.bcm.edu	37	chr3	112272143	112272143	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttaccattgccatgttggacAgtggtggactaggtgatctc	12	8	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:112272143A>G	ENST00000283290.5	-	3	582	c.148T>C	c.(148-150)Tgt>Cgt	p.C50R	ATG3_ENST00000402314.2_Missense_Mutation_p.C50R|ATG3_ENST00000495756.1_5'UTR	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	50					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						CATGTTGGACAGTGGTGGACT	0.323																																																0			3											80	84	82					3																	112272143		2203	4300	6503	113754833	SO:0001583	missense	64422				CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"APG3 autophagy 3-like (S. cerevisiae)", "ATG3 autophagy related 3 homolog (S. cerevisiae)"	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.148T>C	3.37:g.112272143A>G	ENSP00000283290:p.Cys50Arg		113754833	Q6PKC5|Q9H6L9	Missense_Mutation	SNP	ENST00000283290.5	37	CCDS2966.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990307	0.74589	.	.	ENSG00000144848	ENST00000283290;ENST00000402314	.	.	.	5.38	5.38	0.77491	Autophagy-related protein 3, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	M	0.90309	3.105	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	D	0.86704	0.1931	9	0.51188	T	0.08	-8.5266	14.6589	0.68855	1.0:0.0:0.0:0.0	.	50;50	Q9NT62;Q9NT62-2	ATG3_HUMAN;.	R	50	.	ENSP00000283290:C50R	C	-	1	0	ATG3	113754833	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.321000	0.89997	2.152000	0.67230	0.528000	0.53228	TGT		0.323	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488		G	112272143	A	G	112272143	3	3	93	1	0	0	0	0	1	0	0	0	1096	188	7	4	836	4	ATG3	3	112272143	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	15565481	112272143	85750287	47	25375										
SIDT1	54847	hgsc.bcm.edu	37	chr3	113329935	113329935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acccagacatcaatgccagcGcctactctgcctatgcctcc	6	18	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:113329935G>A	ENST00000264852.4	+	18	2527	c.1801G>A	c.(1801-1803)Gcc>Acc	p.A601T	SIDT1_ENST00000463226.1_3'UTR|SIDT1_ENST00000393830.3_Missense_Mutation_p.A601T	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	601					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						CAATGCCAGCGCCTACTCTGC	0.577																																																0			3											191	163	172					3																	113329935		2203	4300	6503	114812625	SO:0001583	missense	54847			AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1801G>A	3.37:g.113329935G>A	ENSP00000264852:p.Ala601Thr		114812625	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	.	.	.	.	.	.	.	.	.	.	G	36	5.730561	0.96856	.	.	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.46451	0.87;0.87	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000003	T	0.72244	0.3436	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.988;0.989	T	0.76553	-0.2917	10	0.72032	D	0.01	-18.3682	20.0396	0.97574	0.0:0.0:1.0:0.0	.	601;601	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	T	601	ENSP00000264852:A601T;ENSP00000377416:A601T	ENSP00000264852:A601T	A	+	1	0	SIDT1	114812625	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.776000	0.99001	2.728000	0.93425	0.643000	0.83706	GCC		0.577	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		A	113329935	G	A	113329935	3	1	93	1	0	0	0	0	1	0	0	0	14339	1087	38	1	1871	1	SIDT1	3	113329935	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1057792	113329935	84692495	48	25376										
CPNE4	131034	hgsc.bcm.edu	37	chr3	131293954	131293954	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccacccatgatgtagtccaaGaaagaatgcatcttgtgaat	8	9	1	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:131293954G>T	ENST00000512055.1	-	14	3014	c.888C>A	c.(886-888)ttC>ttA	p.F296L	CPNE4_ENST00000429747.1_Missense_Mutation_p.F296L|CPNE4_ENST00000511604.1_Missense_Mutation_p.F296L|CPNE4_ENST00000502818.1_Missense_Mutation_p.F314L|CPNE4_ENST00000512332.1_Missense_Mutation_p.F314L			Q96A23	CPNE4_HUMAN	copine IV	296						extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						TGTAGTCCAAGAAAGAATGCA	0.423																																																0			3											132	117	122					3																	131293954		2203	4300	6503	132776644	SO:0001583	missense	131034			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.888C>A	3.37:g.131293954G>T	ENSP00000421705:p.Phe296Leu		132776644	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643822	0.67244	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.66099	-0.16;-0.16;-0.19;-0.16;-0.19	5.73	5.73	0.89815	.	0.045928	0.85682	D	0.000000	T	0.70465	0.3227	M	0.92784	3.345	0.80722	D	1	B;B	0.32071	0.164;0.355	B;B	0.32211	0.028;0.142	T	0.75169	-0.3412	10	0.87932	D	0	-25.5422	12.3863	0.55335	0.0781:0.0:0.9219:0.0	.	314;296	Q96A23-2;Q96A23	.;CPNE4_HUMAN	L	296;296;314;296;314	ENSP00000421705:F296L;ENSP00000411904:F296L;ENSP00000424853:F314L;ENSP00000423811:F296L;ENSP00000421646:F314L	ENSP00000411904:F296L	F	-	3	2	CPNE4	132776644	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.567000	0.67378	2.861000	0.98227	0.655000	0.94253	TTC		0.423	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		T	131293954	G	T	131293954	3	4	93	1	0	0	0	0	1	0	0	0	3820	933	33	2	813	2	CPNE4	3	131293954	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	17964019	131293954	66728476	49	25377										
PRR23B	389151	hgsc.bcm.edu	37	chr3	138738751	138738751	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gccttgcacggagggcgttcCgggagcggcgagcgcgcgtg	20	12	0	0	rs182603479		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:138738751C>T	ENST00000329447.5	-	1	1017	c.753G>A	c.(751-753)ccG>ccA	p.P251P	MRPS22_ENST00000495075.1_Intron	NM_001013650.2	NP_001013672.1	Q6ZRT6	PR23B_HUMAN	proline rich 23B	251	Pro-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GAGGGCGTTCCGGGAGCGGCG	0.667													C|||	1	0.000199681	0	0.0014	5008	,	,		14179	0		0	False		,,,				2504	0															0			3											19	23	22					3																	138738751		2182	4274	6456	140221441	SO:0001819	synonymous_variant	0			BC137146	CCDS33868.1	3q22.3	2014-06-03			ENSG00000184814	ENSG00000184814			33764	protein-coding gene	gene with protein product							Standard	NM_001013650		Approved	FLJ46116	uc003esy.1	Q6ZRT6	OTTHUMG00000160633	ENST00000329447.5:c.753G>A	3.37:g.138738751C>T			140221441	B2RNV9	Silent	SNP	ENST00000329447.5	37	CCDS33868.1																																																																																				0.667	PRR23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361501.1	NM_001013650		T	138738751	C	T	138738751	2	4	93	1	0	0	0	0	0	0	0	1	12629	639	23	1		1	PRR23B	3	138738751	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	7444797	138738751	59283679	50	25378										
XRN1	54464	hgsc.bcm.edu	37	chr3	142151541	142151541	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgctggttcatttttgctcgAggagccacaccatctacagc	9	12	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:142151541A>G	ENST00000264951.4	-	2	387	c.270T>C	c.(268-270)ccT>ccC	p.P90P	XRN1_ENST00000392981.2_Silent_p.P90P|XRN1_ENST00000544157.1_5'UTR|XRN1_ENST00000465074.1_5'Flank|XRN1_ENST00000463916.1_Silent_p.P90P	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	90					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TTTTTGCTCGAGGAGCCACAC	0.333																																																0			3											43	40	41					3																	142151541		2203	4299	6502	143634231	SO:0001819	synonymous_variant	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.270T>C	3.37:g.142151541A>G			143634231	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																				0.333	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		G	142151541	A	G	142151541	2	3	93	1	0	0	0	0	0	0	0	1	17499	291	11	4		4	XRN1	3	142151541	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	3412790	142151541	55870889	51	25379										
ATR	545	hgsc.bcm.edu	37	chr3	142176504	142176504	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgtaacttcacatgctcttcGaaaaagaccctctgttccca	5	13	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:142176504G>A	ENST00000350721.4	-	45	7718	c.7597C>T	c.(7597-7599)Cga>Tga	p.R2533*	ATR_ENST00000383101.3_Nonsense_Mutation_p.R2469*	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2533	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R2533*(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATGCTCTTCGAAAAAGACCC	0.403								Other conserved DNA damage response genes																																								1	Substitution - Nonsense(1)	central_nervous_system(1)	3											103	96	99					3																	142176504		2203	4300	6503	143659194	SO:0001587	stop_gained	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7597C>T	3.37:g.142176504G>A	ENSP00000343741:p.Arg2533*		143659194	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Nonsense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.275224|5.275224	0.95459|0.95459	.|.	.|.	ENSG00000175054|ENSG00000175054	ENST00000350721;ENST00000383101|ENST00000513291	.|.	.|.	.|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75087	.|0.3802	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73694	.|-0.3902	.|3	0.02654|.	T|.	1|.	-9.8182|-9.8182	19.0895|19.0895	0.93221|0.93221	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	2533;2469|379	.|.	ENSP00000343741:R2533X|.	R|S	-|-	1|2	2|0	ATR|ATR	143659194|143659194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.147000|4.147000	0.58078|0.58078	2.600000|2.600000	0.87896|0.87896	0.484000|0.484000	0.47621|0.47621	CGA|TCG		0.403	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142176504	G	A	142176504	4	1	93	1	0	0	0	0	0	1	0	0	1205	1066	37	1	349	1	ATR	3	142176504	Nonsense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	24963	142176504	55845926	52	25380										
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080475	194080475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcaggagccagttgcggagcGgaaggatgtctgagtcacac	16	9	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:194080475G>A	ENST00000347624.3	-	2	1383	c.1298C>T	c.(1297-1299)cCg>cTg	p.P433L	LRRC15_ENST00000439944.2_Missense_Mutation_p.P439L|LRRC15_ENST00000428839.1_Missense_Mutation_p.P439L	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	433	LRRCT.				negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GTTGCGGAGCGGAAGGATGTC	0.572																																																0			3											69	60	63					3																	194080475		2203	4300	6503	195561770	SO:0001583	missense	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1298C>T	3.37:g.194080475G>A	ENSP00000306276:p.Pro433Leu		195561770	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626363	0.66901	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.23552	1.9;1.9;1.9	5.35	5.35	0.76521	Cysteine-rich flanking region, C-terminal (1);	0.084010	0.51477	D	0.000093	T	0.50446	0.1616	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.72338	0.607;0.977	T	0.48703	-0.9012	10	0.10636	T	0.68	.	15.7791	0.78246	0.0:0.1363:0.8637:0.0	.	433;439	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	L	433;439;439	ENSP00000306276:P433L;ENSP00000389128:P439L;ENSP00000413707:P439L	ENSP00000306276:P433L	P	-	2	0	LRRC15	195561770	1.000000	0.71417	0.654000	0.29608	0.748000	0.42578	5.572000	0.67411	2.680000	0.91292	0.655000	0.94253	CCG		0.572	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			A	194080475	G	A	194080475	3	1	93	1	0	0	0	0	1	0	0	0	8999	1116	39	1	451	1	LRRC15	3	194080475	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	51903971	194080475	3941955	53	25381										
MUC4	4585	hgsc.bcm.edu	37	chr3	195475799	195475799	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cggggcccactgggcaggtgCtggcactggcctccatggtc	16	14	0	0	rs3205933	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:195475799C>T	ENST00000346145.4	-	23	3339	c.3300G>A	c.(3298-3300)caG>caA	p.Q1100Q	MUC4_ENST00000475231.1_Silent_p.Q5284Q|MUC4_ENST00000349607.4_Silent_p.Q1049Q|MUC4_ENST00000463781.3_Silent_p.Q5336Q	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2093					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	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)		TGGGCAGGTGCTGGCACTGGC	0.652													.|||	266	0.053115	0.0151	0.072	5008	,	,		26136	0.001		0.1382	False		,,,				2504	0.0573															0			3						C	,,	128,4278		0,128,2075	57	54	55		3300,16008,3147	3.2	1	3	dbSNP_105	55	1093,7507		7,1079,3214	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	7,1207,5289	TT,TC,CC		12.7093,2.9051,9.388	,,	1100/1177,5336/5413,1049/1126	195475799	1221,11785	2203	4300	6503	196961470	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3300G>A	3.37:g.195475799C>T			196961470	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																				0.652	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195475799	C	T	195475799	2	4	93	1	0	0	0	0	0	0	0	1	10008	796	28	3		3	MUC4	3	195475799	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1395324	195475799	2546631	54	25382										
TNK2	10188	hgsc.bcm.edu	37	chr3	195611844	195611844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggggcgggcgaggtcttccGgaaggtgctctgagagtgat	19	7	2	2	rs3747673	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr3:195611844G>A	ENST00000333602.6	-	4	912	c.295C>T	c.(295-297)Cgg>Tgg	p.R99W	TNK2_ENST00000381916.2_Missense_Mutation_p.R162W|TNK2_ENST00000428187.1_Missense_Mutation_p.R131W|TNK2_ENST00000316664.3_Missense_Mutation_p.R99W|TNK2_ENST00000392400.1_Missense_Mutation_p.R99W|TNK2_ENST00000468819.1_5'UTR	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	99	SAM-like domain.		R -> Q (in an ovarian mucinous carcinoma sample; somatic mutation; undergoes autoactivation and causes phosphorylation on Tyr-284 leading to activation of AKT1). {ECO:0000269|PubMed:17344846}.|R -> W (in dbSNP:rs3747673). {ECO:0000269|PubMed:17344846}.		cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	GAGGTCTTCCGGAAGGTGCTC	0.642													G|||	89	0.0177716	0	0	5008	,	,		14138	0.0853		0	False		,,,				2504	0.0031															0			3						G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	47	46	46		484,295	3	1	3	dbSNP_107	46	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TNK2	NM_001010938.1,NM_005781.4	101,101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	162/1087,99/1039	195611844	2,13004	2203	4300	6503	197096241	SO:0001583	missense	10188			L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.295C>T	3.37:g.195611844G>A	ENSP00000329425:p.Arg99Trp		197096241	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	67	0.030677655677655676	0	0.0	0	0.0	67	0.11713286713286714	0	0.0	G	16.63	3.175765	0.57692	0.0	2.33E-4	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664	T;T;T;T;T	0.76060	-0.96;-0.99;-0.97;-0.96;-0.96	4.92	2.99	0.34606	Protein kinase-like domain (1);	0.237632	0.34507	N	0.003909	T	0.02727	0.0082	L	0.29908	0.895	0.22531	P	0.999015041	D;B;B;B	0.63880	0.993;0.005;0.083;0.009	P;B;B;B	0.56751	0.805;0.0;0.011;0.003	T	0.53019	-0.8497	9	0.66056	D	0.02	.	9.0651	0.36458	0.083:0.0:0.7713:0.1457	rs3747673;rs3747673	99;99;162;131	Q07912-2;Q07912;Q07912-3;C9J1X3	.;ACK1_HUMAN;.;.	W	99;162;131;99;99	ENSP00000329425:R99W;ENSP00000371341:R162W;ENSP00000392546:R131W;ENSP00000376201:R99W;ENSP00000323216:R99W	ENSP00000323216:R99W	R	-	1	2	TNK2	197096241	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.234000	0.51320	1.198000	0.43158	0.407000	0.27541	CGG		0.642	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		A	195611844	G	A	195611844	3	1	93	1	0	0	0	0	1	0	0	0	16357	1115	39	1	2918	1	TNK2	3	195611844	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	136045	195611844	2410586	55	25383										
STIM2	57620	hgsc.bcm.edu	37	chr4	27010417	27010417	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctgagttgacaacttgtttaCgagaacgactttttcgctgg	10	8	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:27010417C>T	ENST00000467011.1	+	10	1707	c.1282C>T	c.(1282-1284)Cga>Tga	p.R428*	STIM2_ENST00000467087.1_Nonsense_Mutation_p.R428*|STIM2_ENST00000237364.5_Nonsense_Mutation_p.R515*|STIM2_ENST00000382009.3_Nonsense_Mutation_p.R523*|STIM2_ENST00000465503.1_Nonsense_Mutation_p.R436*|STIM2_ENST00000412829.2_Nonsense_Mutation_p.R515*	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	428					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AACTTGTTTACGAGAACGACT	0.413																																																0			4											71	73	72					4																	27010417		2203	4300	6503	26619515	SO:0001587	stop_gained	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.1282C>T	4.37:g.27010417C>T	ENSP00000419383:p.Arg428*		26619515	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Nonsense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	C	43	9.836158	0.99276	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503;ENST00000473519;ENST00000477474	.	.	.	5.95	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8551	0.63522	0.3926:0.6074:0.0:0.0	.	.	.	.	X	428;523;515;428;515;436;136;30	.	ENSP00000237364:R515X	R	+	1	2	STIM2	26619515	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.254000	0.32897	1.507000	0.48752	0.563000	0.77884	CGA		0.413	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		T	27010417	C	T	27010417	4	4	93	1	0	0	0	0	0	1	0	0	15323	528	19	1	1348	1	STIM2	4	27010417	Nonsense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10		27010417	164143859	56	25384										
KIT	3815	hgsc.bcm.edu	37	chr4	55593631	55593631	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgttgaggagataaatggaaAcaattatgtttacatagacc	9	4	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:55593631A>G	ENST00000288135.5	+	11	1794	c.1697A>G	c.(1696-1698)aAc>aGc	p.N566S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	566					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V560_L576del(4)|p.Y553_T574>S(3)|p.V555_I571del(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.W557_P573>S(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I563_D572del(1)|p.E562_V569>D(1)|p.E562_P573del(1)|p.N564_T574del(1)|p.E554_I571del(1)|p.K558_Q575del(1)|p.V555_Y570del(1)|p.M552_T574>TESA(1)|p.Q556_T574del(1)|p.Q556_D572>PS(1)|p.E561_P577del(1)|p.Q556_D572del(1)|p.N564_P573>T(1)|p.K558_L576>NV(1)|p.V559_P573>A(1)|p.V560_I571del(1)|p.W557_I571del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.K558_D572del(1)|p.N566S(1)|p.Q556_D572>H(1)|p.K558_Y570>N(1)|p.M552_D572del(1)|p.V559_I571del(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.N564_P573>TS(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATAAATGGAAACAATTATGTT	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	53	Deletion - In frame(38)|Complex - deletion inframe(14)|Substitution - Missense(1)	soft_tissue(52)|testis(1)	4											80	81	81					4																	55593631		2203	4300	6503	55288388	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1697A>G	4.37:g.55593631A>G	ENSP00000288135:p.Asn566Ser		55288388	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.731555	0.69189	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.96774	-4.12;-4.12	6.06	4.86	0.63082	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	D	0.98137	0.9385	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.997	D;D;D	0.85130	0.928;0.997;0.958	D	0.98455	1.0593	10	0.72032	D	0.01	.	13.5246	0.61586	0.8698:0.1302:0.0:0.0	.	73;562;566	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	S	566;562	ENSP00000288135:N566S;ENSP00000390987:N562S	ENSP00000288135:N566S	N	+	2	0	KIT	55288388	1.000000	0.71417	0.998000	0.56505	0.682000	0.39822	9.150000	0.94667	1.088000	0.41272	-0.316000	0.08728	AAC		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55593631	A	G	55593631	3	3	93	1	0	0	0	0	1	0	0	0	8350	43	2	4	1739	4	KIT	4	55593631	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	28583214	55593631	135560645	57	25385										
KIT	3815	hgsc.bcm.edu	37	chr4	55599284	55599284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atatcctccttactcatggtCggatcacaaagatttgtgat	7	9	2	2	rs145602440		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:55599284C>T	ENST00000288135.5	+	17	2507	c.2410C>T	c.(2410-2412)Cgg>Tgg	p.R804W		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	804	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> W (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R804W(3)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACTCATGGTCGGATCACAAA	0.373		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				C|||	1	0.000199681	0	0	5008	,	,		16804	0		0	False		,,,				2504	0.001					yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	3	Substitution - Missense(3)	large_intestine(1)|eye(1)|endometrium(1)	4						C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	123	123	123		2410,2398	4.8	1	4	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KIT	NM_000222.2,NM_001093772.1	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	804/977,800/973	55599284	1,13005	2203	4300	6503	55294041	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2410C>T	4.37:g.55599284C>T	ENSP00000288135:p.Arg804Trp		55294041	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159350	0.78226	0.0	1.16E-4	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.89123	-2.47;-2.47	5.62	4.76	0.60689	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45867	D	0.000327	D	0.88614	0.6484	N	0.10760	0.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91565	0.5267	10	0.87932	D	0	.	16.4042	0.83652	0.0:0.8682:0.1318:0.0	.	800;804	P10721-2;P10721	.;KIT_HUMAN	W	804;800	ENSP00000288135:R804W;ENSP00000390987:R800W	ENSP00000288135:R804W	R	+	1	2	KIT	55294041	1.000000	0.71417	0.957000	0.39632	0.992000	0.81027	3.958000	0.56737	1.336000	0.45506	0.585000	0.79938	CGG		0.373	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55599284	C	T	55599284	3	4	93	1	0	0	0	0	1	0	0	0	8350	875	31	1	2476	1	KIT	4	55599284	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	5653	55599284	135554992	58	25386										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537150	88537150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agcgatagcagtgacagcagCgatagcagtgacagcagtga	14	8	0	3	rs529175881	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:88537150C>T	ENST00000282478.7	+	4	3369	c.3336C>T	c.(3334-3336)agC>agT	p.S1112S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1112S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1112	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcgatagcagtg	0.542													c|||	951	0.189896	0.1339	0.1888	5008	,	,		14858	0.2054		0.2356	False		,,,				2504	0.2035															0			4											15	21	19					4																	88537150		1245	2342	3587	88756174	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3336C>T	4.37:g.88537150C>T			88756174	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88537150	C	T	88537150	2	4	93	1	0	0	0	0	0	0	0	1	4793	767	27	1		1	DSPP	4	88537150	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	32937866	88537150	102617126	59	25387										
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95496959	95496959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgaccacctcatcacatgctTccccttcacccgtggctgcc	6	20	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:95496959T>C	ENST00000317968.4	+	5	620	c.484T>C	c.(484-486)Tcc>Ccc	p.S162P	PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.S40P|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000514743.1_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	162					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		ATCACATGCTTCCCCTTCACC	0.557																																																0			4											256	211	226					4																	95496959		2203	4300	6503	95715982	SO:0001583	missense	10611			AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.484T>C	4.37:g.95496959T>C	ENSP00000321746:p.Ser162Pro		95715982	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.740315	0.49045	.	.	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.61274	0.55;0.12	4.75	4.75	0.60458	.	0.451479	0.23305	N	0.049635	T	0.47967	0.1474	L	0.41236	1.265	0.37801	D	0.927701	P	0.48503	0.911	B	0.39503	0.301	T	0.57189	-0.7854	10	0.44086	T	0.13	.	14.0951	0.65016	0.0:0.0:0.0:1.0	.	162	Q96HC4	PDLI5_HUMAN	P	162;40	ENSP00000321746:S162P;ENSP00000442187:S40P	ENSP00000321746:S162P	S	+	1	0	PDLIM5	95715982	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	2.569000	0.45973	1.983000	0.57843	0.533000	0.62120	TCC		0.557	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			C	95496959	T	C	95496959	3	2	93	1	0	0	0	0	1	0	0	0	11714	1783	62	4	498	4	PDLIM5	4	95496959	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6959809	95496959	95657317	60	25388										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005713	118005713	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcatcaggattccgattctgCgatccagccaggtgaaaccc	10	13	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:118005713C>T	ENST00000310754.4	-	1	1023	c.837G>A	c.(835-837)tcG>tcA	p.S279S		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	279	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S279S(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						TCCGATTCTGCGATCCAGCCA	0.453																																																1	Substitution - coding silent(1)	central_nervous_system(1)	4											82	74	77					4																	118005713		2203	4300	6503	118225161	SO:0001819	synonymous_variant	133022			AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.837G>A	4.37:g.118005713C>T			118225161	Q8N2L7	Silent	SNP	ENST00000310754.4	37	CCDS3707.1																																																																																				0.453	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		T	118005713	C	T	118005713	2	4	93	1	0	0	0	0	0	0	0	1	16492	755	27	1		1	TRAM1L1	4	118005713	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	22508754	118005713	73148563	61	25389										
FAT4	79633	hgsc.bcm.edu	37	chr4	126411849	126411849	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gagcactatgacattgacaaCgccagcagcatcgccccttc	8	15	0	2	rs369989432		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:126411849C>T	ENST00000394329.3	+	17	13885	c.13872C>T	c.(13870-13872)aaC>aaT	p.N4624N	FAT4_ENST00000335110.5_Silent_p.N2865N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4624					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ACATTGACAACGCCAGCAGCA	0.493													C|||	1	0.000199681	0	0	5008	,	,		19514	0		0	False		,,,				2504	0.001															0			4											76	76	76					4																	126411849		2203	4300	6503	126631299	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13872C>T	4.37:g.126411849C>T			126631299	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.493	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126411849	C	T	126411849	2	4	93	1	0	0	0	0	0	0	0	1	5711	535	19	1		1	FAT4	4	126411849	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	8406136	126411849	64742427	62	25390										
USP38	84640	hgsc.bcm.edu	37	chr4	144135946	144135946	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acgagcaggtttccaaaggaCacagcttatgtgcttttgta	10	8	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:144135946C>T	ENST00000307017.4	+	9	3323	c.2817C>T	c.(2815-2817)gaC>gaT	p.D939D	USP38_ENST00000510377.1_Silent_p.D939D	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	939	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TTCCAAAGGACACAGCTTATG	0.363																																																0			4											69	73	71					4																	144135946		2203	4300	6503	144355396	SO:0001819	synonymous_variant	84640			AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2817C>T	4.37:g.144135946C>T			144355396	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	37	CCDS3758.1																																																																																				0.363	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		T	144135946	C	T	144135946	2	4	93	1	0	0	0	0	0	0	0	1	17109	477	17	3		3	USP38	4	144135946	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	17724097	144135946	47018330	63	25391										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247169	153247169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agatcttacctgtaatgaatAgactctattagtatgcccct	6	9	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:153247169A>G	ENST00000281708.4	-	10	2862	c.1633T>C	c.(1633-1635)Tat>Cat	p.Y545H	FBXW7_ENST00000296555.5_Missense_Mutation_p.Y427H|FBXW7_ENST00000263981.5_Missense_Mutation_p.Y465H|FBXW7_ENST00000603841.1_Missense_Mutation_p.Y545H|FBXW7_ENST00000603548.1_Missense_Mutation_p.Y545H|FBXW7_ENST00000393956.3_Missense_Mutation_p.Y369H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	545					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGTAATGAATAGACTCTATTA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											152	149	150					4																	153247169		2203	4300	6503	153466619	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1633T>C	4.37:g.153247169A>G	ENSP00000281708:p.Tyr545His		153466619	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.493997	0.84962	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.54271	0.1848	L	0.31371	0.925	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.58047	-0.7705	10	0.87932	D	0	-20.3253	16.2962	0.82776	1.0:0.0:0.0:0.0	.	369;545;427;465	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	545;427;465;369	ENSP00000281708:Y545H;ENSP00000296555:Y427H;ENSP00000263981:Y465H;ENSP00000377528:Y369H	ENSP00000263981:Y465H	Y	-	1	0	FBXW7	153466619	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.304000	0.77564	0.528000	0.53228	TAT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153247169	A	G	153247169	3	3	93	1	0	0	0	0	1	0	0	0	5788	420	15	4	502	4	FBXW7	4	153247169	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	9111223	153247169	37907107	64	25392										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898442	175898442	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gagtactgattaccatttggGgatgaagggacctgatattg	13	5	0	3	rs267600094		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr4:175898442G>T	ENST00000359240.3	+	5	2436	c.1766G>T	c.(1765-1767)gGg>gTg	p.G589V	ADAM29_ENST00000445694.1_Missense_Mutation_p.G589V|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.G589V|ADAM29_ENST00000404450.4_Missense_Mutation_p.G589V	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	589	Cys-rich.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.G589E(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TACCATTTGGGGATGAAGGGA	0.418																																					Ovarian(140;1727 1835 21805 25838 41440)											2	Substitution - Missense(2)	skin(2)	4											202	184	190					4																	175898442		2203	4300	6503	176135017	SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1766G>T	4.37:g.175898442G>T	ENSP00000352177:p.Gly589Val		176135017	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921489	0.52653	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	3.69	3.69	0.42338	ADAM, cysteine-rich (2);	0.000000	0.36665	U	0.002476	T	0.55577	0.1929	M	0.88241	2.94	0.27388	N	0.955239	D	0.89917	1.0	D	0.91635	0.999	T	0.53851	-0.8380	9	.	.	.	.	13.721	0.62728	0.0:0.0:1.0:0.0	.	589	Q9UKF5	ADA29_HUMAN	V	589	ENSP00000352177:G589V;ENSP00000414544:G589V;ENSP00000384229:G589V;ENSP00000423517:G589V	.	G	+	2	0	ADAM29	176135017	1.000000	0.71417	0.078000	0.20375	0.054000	0.15201	6.123000	0.71614	2.351000	0.79841	0.643000	0.83706	GGG		0.418	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				T	175898442	G	T	175898442	3	4	93	1	0	0	0	0	1	0	0	0	247	1232	43	2	1768	2	ADAM29	4	175898442	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	22651273	175898442	15255834	65	25393										
C5orf34	375444	hgsc.bcm.edu	37	chr5	43505984	43505984	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcatcaattttagacatattGctgattttattatgaaaatg	6	4	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:43505984G>T	ENST00000306862.2	-	4	1173	c.798C>A	c.(796-798)agC>agA	p.S266R	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	266			S -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.					p.S266R(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					TAGACATATTGCTGATTTTAT	0.393																																																1	Substitution - Missense(1)	breast(1)	5											94	97	96					5																	43505984		2203	4300	6503	43541741	SO:0001583	missense	375444			AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.798C>A	5.37:g.43505984G>T	ENSP00000303490:p.Ser266Arg		43541741		Missense_Mutation	SNP	ENST00000306862.2	37	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	G	1.647	-0.515035	0.04200	.	.	ENSG00000172244	ENST00000306862;ENST00000509489	T	0.46819	0.86	5.03	-0.617	0.11579	.	0.813217	0.11639	N	0.544023	T	0.28466	0.0704	L	0.31926	0.97	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.23048	-1.0199	10	0.13853	T	0.58	0.5877	4.4403	0.11570	0.5555:0.188:0.2565:0.0	.	266	Q96MH7	CE034_HUMAN	R	266;152	ENSP00000303490:S266R	ENSP00000303490:S266R	S	-	3	2	C5orf34	43541741	0.000000	0.05858	0.000000	0.03702	0.203000	0.24098	-0.010000	0.12743	0.166000	0.19597	0.591000	0.81541	AGC		0.393	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566		T	43505984	G	T	43505984	3	4	93	1	0	0	0	0	1	0	0	0	2299	1310	46	2	1158	2	C5orf34	5	43505984	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10		43505984	137409276	66	25394										
IPO11	51194	hgsc.bcm.edu	37	chr5	61826559	61826559	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agtaactttggaaaacagtcCatgtattacaccagagttgc	8	8	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:61826559C>A	ENST00000325324.6	+	22	2205	c.2036C>A	c.(2035-2037)cCa>cAa	p.P679Q	IPO11_ENST00000409296.3_Missense_Mutation_p.P719Q|KIF2A_ENST00000509663.2_3'UTR	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	679					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.P679>?(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GAAAACAGTCCATGTATTACA	0.318																																																1	Complex(1)	skin(1)	5											124	118	120					5																	61826559		2202	4299	6501	61862316	SO:0001583	missense	51194			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.2036C>A	5.37:g.61826559C>A	ENSP00000316651:p.Pro679Gln		61862316	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.581867	0.86748	.	.	ENSG00000086200	ENST00000325324;ENST00000409296;ENST00000540553	T;T	0.70399	-0.48;-0.48	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.105429	0.64402	D	0.000003	T	0.80994	0.4731	M	0.83483	2.645	0.80722	D	1	P;P	0.48230	0.905;0.907	P;P	0.51516	0.672;0.472	T	0.81839	-0.0748	10	0.39692	T	0.17	.	18.6774	0.91534	0.0:1.0:0.0:0.0	.	719;679	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	Q	679;719;249	ENSP00000316651:P679Q;ENSP00000386992:P719Q	ENSP00000316651:P679Q	P	+	2	0	IPO11	61862316	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.023000	0.76437	2.507000	0.84556	0.650000	0.86243	CCA		0.318	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		A	61826559	C	A	61826559	3	1	93	1	0	0	0	0	1	0	0	0	7814	594	21	2	2242	2	IPO11	5	61826559	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	18320575	61826559	119088701	67	25395										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71490301	71490301	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aatccagagccaaacatcaaGatgaagagaagcatagaaga	9	7	1	6			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:71490301G>A	ENST00000296755.7	+	5	1417	c.1119G>A	c.(1117-1119)aaG>aaA	p.K373K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	373					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		CAAACATCAAGATGAAGAGAA	0.398																																					Melanoma(17;367 822 11631 31730 47712)											0			5											67	64	65					5																	71490301		2203	4300	6503	71526057	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.1119G>A	5.37:g.71490301G>A			71526057	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.398	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71490301	G	A	71490301	2	1	93	1	0	0	0	0	0	0	0	1	9258	933	33	3		3	MAP1B	5	71490301	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	9663742	71490301	109424959	68	25396										
SPZ1	84654	hgsc.bcm.edu	37	chr5	79616672	79616672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgcaagagatttggtaaatcGtttagaagaaaaaaaagtcc	9	4	0	3	rs562377054		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:79616672G>A	ENST00000296739.4	+	1	883	c.638G>A	c.(637-639)cGt>cAt	p.R213H		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	213	Basic motif. {ECO:0000255}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TTGGTAAATCGTTTAGAAGAA	0.348																																																0			5											59	54	56					5																	79616672		1823	4073	5896	79652428	SO:0001583	missense	84654				CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.638G>A	5.37:g.79616672G>A	ENSP00000369611:p.Arg213His		79652428	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	3.940	-0.014351	0.07681	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.42900	0.96;1.55	4.08	-8.15	0.01065	.	2.001320	0.02385	N	0.079180	T	0.26521	0.0648	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11867	-1.0570	10	0.15499	T	0.54	-8.6677	9.3814	0.38316	0.4377:0.1017:0.4606:0.0	.	213	Q9BXG8	SPZ1_HUMAN	H	213	ENSP00000426530:R213H;ENSP00000369611:R213H	ENSP00000369611:R213H	R	+	2	0	SPZ1	79652428	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-1.126000	0.03254	-1.994000	0.00972	-1.311000	0.01308	CGT		0.348	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		A	79616672	G	A	79616672	3	1	93	1	0	0	0	0	1	0	0	0	15166	1145	40	1	640	1	SPZ1	5	79616672	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	8126371	79616672	101298588	69	25397										
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	93	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	32558967	112175639	68739621	70	25398										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182324	140182324	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtgtcggtacacgcggagagCggcaaggtgtacgcgctgca	17	10	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140182324C>T	ENST00000522353.2	+	1	1542	c.1542C>T	c.(1540-1542)agC>agT	p.S514S	PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.S514S	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	514	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCGGAGAGCGGCAAGGTGT	0.697																																																0			5											77	79	79					5																	140182324		2203	4299	6502	140162508	SO:0001819	synonymous_variant	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1542C>T	5.37:g.140182324C>T			140162508	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																				0.697	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		T	140182324	C	T	140182324	2	4	93	1	0	0	0	0	0	0	0	1	11556	767	27	1		1	PCDHA3	5	140182324	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	28006685	140182324	40732936	71	25399										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237891	140237891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtcttactcgcagcagaggcGgcagagggtgtgttctgggg	18	8	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140237891G>A	ENST00000307360.5	+	1	2258	c.2258G>A	c.(2257-2259)cGg>cAg	p.R753Q	PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	753	6 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCAGAGGCGGCAGAGGGTG	0.672																																																0			5											50	57	54					5																	140237891		1322	2289	3611	140218075	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.2258G>A	5.37:g.140237891G>A	ENSP00000304234:p.Arg753Gln		140218075	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	5.800	0.331998	0.10956	.	.	ENSG00000250120	ENST00000307360	T	0.14022	2.54	3.79	0.935	0.19483	.	.	.	.	.	T	0.07369	0.0186	L	0.28776	0.89	0.09310	N	0.999999	B;B	0.31413	0.322;0.216	B;B	0.21708	0.036;0.024	T	0.38286	-0.9668	9	0.21014	T	0.42	.	4.4399	0.11568	0.3879:0.1603:0.4518:0.0	.	753;753	Q9Y5I2-3;Q9Y5I2	.;PCDAA_HUMAN	Q	753	ENSP00000304234:R753Q	ENSP00000304234:R753Q	R	+	2	0	PCDHA10	140218075	0.000000	0.05858	0.761000	0.31378	0.599000	0.36880	0.435000	0.21510	0.059000	0.16252	0.462000	0.41574	CGG		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140237891	G	A	140237891	3	1	93	1	0	0	0	0	1	0	0	0	11551	1116	39	1	2260	1	PCDHA10	5	140237891	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	55567	140237891	40677369	72	25400										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263141	140263141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggtggtgaccgcgcgggacGggggctcgccttcgctgtgg	20	11	0	1	rs144498761		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140263141G>A	ENST00000289272.2	+	1	1288	c.1288G>A	c.(1288-1290)Ggg>Agg	p.G430R	PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.G430R|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	430	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCGGGACGGGGGCTCGCC	0.657																																					Melanoma(147;1739 1852 5500 27947 37288)											0			5											91	96	94					5																	140263141		2203	4300	6503	140243325	SO:0001583	missense	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1288G>A	5.37:g.140263141G>A	ENSP00000289272:p.Gly430Arg		140243325	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	5.077	0.199804	0.09652	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.51071	0.72;0.72	5.19	2.35	0.29111	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.44871	0.1314	L	0.55834	1.745	0.20307	N	0.999913	B;B;B	0.30741	0.293;0.178;0.27	B;B;B	0.42188	0.379;0.1;0.075	T	0.42766	-0.9432	9	0.25106	T	0.35	.	3.4178	0.07382	0.2153:0.1134:0.5552:0.1161	.	430;430;430	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	R	430	ENSP00000386821:G430R;ENSP00000289272:G430R	ENSP00000289272:G430R	G	+	1	0	PCDHA13	140243325	0.000000	0.05858	0.094000	0.20943	0.446000	0.32137	-0.790000	0.04604	0.536000	0.28733	0.561000	0.74099	GGG		0.657	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263141	G	A	140263141	3	1	93	1	0	0	0	0	1	0	0	0	11554	1116	39	1	1290	1	PCDHA13	5	140263141	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	25250	140263141	40652119	73	25401										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140725113	140725113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggcgcccctgtcctccttcGtctctatcaactccaacact	6	18	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140725113G>A	ENST00000253812.6	+	1	1513	c.1513G>A	c.(1513-1515)Gtc>Atc	p.V505I	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	505	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V505I(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCTCCTTCGTCTCTATCAA	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	5											70	79	76					5																	140725113		2115	4263	6378	140705297	SO:0001583	missense	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1513G>A	5.37:g.140725113G>A	ENSP00000253812:p.Val505Ile		140705297	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	7.652	0.683080	0.14907	.	.	ENSG00000254245	ENST00000253812	T	0.60920	0.15	5.36	-3.5	0.04710	Cadherin (4);Cadherin-like (1);	0.000000	0.30338	U	0.009846	T	0.28167	0.0695	N	0.13198	0.31	0.09310	N	1	B;B	0.23891	0.093;0.051	B;B	0.23716	0.048;0.044	T	0.07751	-1.0756	10	0.27785	T	0.31	.	2.5247	0.04689	0.3725:0.1919:0.3386:0.0969	.	505;505	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	I	505	ENSP00000253812:V505I	ENSP00000253812:V505I	V	+	1	0	PCDHGA3	140705297	0.000000	0.05858	0.006000	0.13384	0.858000	0.48976	-0.554000	0.06006	-1.035000	0.03291	0.563000	0.77884	GTC		0.552	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		A	140725113	G	A	140725113	3	1	93	1	0	0	0	0	1	0	0	0	11586	1145	40	1	1515	1	PCDHGA3	5	140725113	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	461972	140725113	40190147	74	25402										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745765	140745765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctttgcggttgggctgcacaCgggcgaggtgcgcacagcgc	17	12	0	0	rs187196267		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140745765C>T	ENST00000518069.1	+	1	1868	c.1868C>T	c.(1867-1869)aCg>aTg	p.T623M	PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	623	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCTGCACACGGGCGAGGTG	0.652													.|||	1	0.000199681	0	0	5008	,	,		18951	0		0.001	False		,,,				2504	0															0			5						C	,,,,MET/THR,,,MET/THR	0,4406		0,0,2203	60	69	66		,,,,1868,,,1868	4.6	0.9	5		66	1,8599		0,1,4299	no	intron,intron,intron,intron,missense,intron,intron,missense	PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_032054.1	,,,,81,,,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,	,,,,623/932,,,623/814	140745765	1,13005	2203	4300	6503	140725949	SO:0001583	missense	56110			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.1868C>T	5.37:g.140745765C>T	ENSP00000429834:p.Thr623Met		140725949	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	9.681	1.149258	0.21288	0.0	1.16E-4	ENSG00000253485	ENST00000518069	T	0.58060	0.36	4.58	4.58	0.56647	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.81351	0.4804	H	0.96748	3.875	0.22888	N	0.998603	D;D	0.89917	1.0;1.0	D;D	0.79108	0.987;0.992	T	0.75836	-0.3177	9	0.87932	D	0	.	14.1717	0.65514	0.0:0.849:0.151:0.0	.	623;623	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	M	623	ENSP00000429834:T623M	ENSP00000429834:T623M	T	+	2	0	PCDHGA5	140725949	0.000000	0.05858	0.945000	0.38365	0.049000	0.14656	-0.467000	0.06664	2.266000	0.75297	0.563000	0.77884	ACG		0.652	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140745765	C	T	140745765	3	4	93	1	0	0	0	0	1	0	0	0	11588	536	19	1	1870	1	PCDHGA5	5	140745765	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	20652	140745765	40169495	75	25403										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140750565	140750565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tactgaaagcacccctggacAgggaagagcagccacatcac	10	13	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140750565A>G	ENST00000576222.1	+	1	735	c.604A>G	c.(604-606)Agg>Ggg	p.R202G	PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	202	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCCCTGGACAGGGAAGAGCA	0.562																																																0			5											58	62	60					5																	140750565		2043	4212	6255	140730749	SO:0001583	missense	56102			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.604A>G	5.37:g.140750565A>G	ENSP00000461862:p.Arg202Gly		140730749	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.562	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		G	140750565	A	G	140750565	3	3	93	1	0	0	0	0	1	0	0	0	11595	179	7	4	606	4	PCDHGB3	5	140750565	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	4800	140750565	40164695	76	25404										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140772816	140772816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aagtaaaaattaacgaaatcGcggttcctggagcacgttat	9	7	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:140772816G>A	ENST00000398604.2	+	1	436	c.436G>A	c.(436-438)Gcg>Acg	p.A146T	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	146	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A146T(1)		endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAACGAAATCGCGGTTCCTGG	0.443																																																1	Substitution - Missense(1)	lung(1)	5											51	56	54					5																	140772816		1933	4151	6084	140753000	SO:0001583	missense	9708			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.436G>A	5.37:g.140772816G>A	ENSP00000381605:p.Ala146Thr		140753000	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	6.133	0.392706	0.11638	.	.	ENSG00000253767	ENST00000398604	T	0.55413	0.52	5.41	2.63	0.31362	Cadherin (3);Cadherin-like (1);	0.699665	0.10826	U	0.629889	T	0.32255	0.0823	N	0.20807	0.61	0.23287	N	0.99798	B;B	0.17852	0.014;0.024	B;B	0.17979	0.02;0.016	T	0.24905	-1.0147	10	0.20519	T	0.43	.	4.0745	0.09897	0.3461:0.0:0.5014:0.1526	.	146;146	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	T	146	ENSP00000381605:A146T	ENSP00000381605:A146T	A	+	1	0	PCDHGA8	140753000	0.005000	0.15991	0.889000	0.34880	0.695000	0.40330	0.445000	0.21677	0.258000	0.21686	0.655000	0.94253	GCG		0.443	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		A	140772816	G	A	140772816	3	1	93	1	0	0	0	0	1	0	0	0	11591	1087	38	1	438	1	PCDHGA8	5	140772816	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	22251	140772816	40142444	77	25405										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145887490	145887490	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaatcattaaggaagatcctCgatgtattaagttctcctcc	6	9	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:145887490C>T	ENST00000296702.5	+	20	3003	c.2965C>T	c.(2965-2967)Cga>Tga	p.R989*	TCERG1_ENST00000394421.2_Nonsense_Mutation_p.R968*	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	989	FF 5.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAAGATCCTCGATGTATTAA	0.343																																																0			5											99	93	95					5																	145887490		2203	4300	6503	145867683	SO:0001587	stop_gained	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.2965C>T	5.37:g.145887490C>T	ENSP00000296702:p.Arg989*		145867683	Q2NKN2|Q59EA1	Nonsense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	C	40	8.332635	0.98764	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.484	14.9707	0.71232	0.1761:0.8239:0.0:0.0	.	.	.	.	X	989;968	.	ENSP00000296702:R989X	R	+	1	2	TCERG1	145867683	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.888000	0.63164	2.810000	0.96702	0.585000	0.79938	CGA		0.343	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145887490	C	T	145887490	4	4	93	1	0	0	0	0	0	1	0	0	15724	876	31	1	3043	1	TCERG1	5	145887490	Nonsense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	5114674	145887490	35027770	78	25406										
SYNPO	11346	hgsc.bcm.edu	37	chr5	150028323	150028323	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctaattgacaaggtatcaacTccagctaccaccaccagcac	5	15	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr5:150028323T>C	ENST00000394243.1	+	3	1592	c.1218T>C	c.(1216-1218)acT>acC	p.T406T	SYNPO_ENST00000519664.1_Silent_p.T162T|SYNPO_ENST00000518872.1_3'UTR|SYNPO_ENST00000307662.4_Silent_p.T162T|SYNPO_ENST00000522122.1_Silent_p.T406T	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	406					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGTATCAACTCCAGCTACCA	0.582																																																0			5											169	177	174					5																	150028323		2203	4300	6503	150008516	SO:0001819	synonymous_variant	11346			AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.1218T>C	5.37:g.150028323T>C			150008516	A5PKZ8|D3DQG8|O15271|Q9UPX1	Silent	SNP	ENST00000394243.1	37	CCDS54937.1																																																																																				0.582	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		C	150028323	T	C	150028323	2	2	93	1	0	0	0	0	0	0	0	1	15495	1538	54	4		4	SYNPO	5	150028323	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	4140833	150028323	30886937	79	25407										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25581618	25581618	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaagaagctggaacactttaCcaagttaaggccaaaaagga	10	7	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:25581618C>G	ENST00000329474.6	+	31	3325	c.2957C>G	c.(2956-2958)aCc>aGc	p.T986S		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	986	Inhibits capping activity of CAPZA2. {ECO:0000250}.				actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.T986I(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						GAACACTTTACCAAGTTAAGG	0.537																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											38	39	39					6																	25581618		1882	4097	5979	25689597	SO:0001583	missense	55604			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2957C>G	6.37:g.25581618C>G	ENSP00000331983:p.Thr986Ser		25689597	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.736419	0.89482	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.56611	0.45	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	M	0.69823	2.125	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.85130	0.993;0.993;0.997	T	0.70200	-0.4937	10	0.62326	D	0.03	.	19.9628	0.97258	0.0:1.0:0.0:0.0	.	986;986;986	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	S	986	ENSP00000331983:T986S	ENSP00000331983:T986S	T	+	2	0	LRRC16A	25689597	1.000000	0.71417	0.992000	0.48379	0.931000	0.56810	7.166000	0.77553	2.695000	0.91970	0.563000	0.77884	ACC		0.537	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		G	25581618	C	G	25581618	3	3	93	1	0	0	0	0	1	0	0	0	9000	507	18	5	3079	5	LRRC16A	6	25581618	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10		25581618	145533449	80	25408										
BAT2	7916	hgsc.bcm.edu	37	chr6	31599709	31599709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaggccgcactgccagcgagAcacggagcgagggttcagag	17	11	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:31599709A>G	ENST00000376033.2	+	16	3493	c.3259A>G	c.(3259-3261)Aca>Gca	p.T1087A	PRRC2A_ENST00000376007.4_Missense_Mutation_p.T1087A	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1087	4 X 57 AA type A repeats.		T -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGCCAGCGAGACACGGAGCGA	0.627																																																0			6											29	33	31					6																	31599709		1508	2706	4214	31707688	SO:0001583	missense	0			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3259A>G	6.37:g.31599709A>G	ENSP00000365201:p.Thr1087Ala		31707688	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.872097	0.33069	.	.	ENSG00000204469	ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01981	4.52;4.52	4.88	4.88	0.63580	.	0.000000	0.53938	D	0.000046	T	0.05547	0.0146	L	0.59436	1.845	0.53005	D	0.999961	D	0.69078	0.997	D	0.75020	0.985	T	0.15321	-1.0441	10	0.87932	D	0	-9.5316	13.6117	0.62083	1.0:0.0:0.0:0.0	.	1087	P48634	PRC2A_HUMAN	A	1087;1087;312	ENSP00000365175:T1087A;ENSP00000365201:T1087A	ENSP00000365175:T1087A	T	+	1	0	PRRC2A	31707688	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.754000	0.91642	2.071000	0.62044	0.533000	0.62120	ACA		0.627	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		G	31599709	A	G	31599709	3	3	93	1	0	0	0	0	1	0	0	0	1320	275	10	4	3317	4	BAT2	6	31599709	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6018091	31599709	139515358	81	25409										
RING1	6015	hgsc.bcm.edu	37	chr6	33177820	33177820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atacgaggcccatcaagaccGagtgcttatccgcctgagcc	10	14	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:33177820G>A	ENST00000374656.4	+	4	576	c.368G>A	c.(367-369)cGa>cAa	p.R123Q	MIR219-1_ENST00000362166.1_RNA|RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	123	Necessary for transcriptional repression. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						CATCAAGACCGAGTGCTTATC	0.582																																																0			6											67	58	61					6																	33177820		2203	4300	6503	33285798	SO:0001583	missense	6015				CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"RING-type (C3HC4) zinc fingers"	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.368G>A	6.37:g.33177820G>A	ENSP00000363787:p.Arg123Gln		33285798	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	37	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.360473	0.61403	.	.	ENSG00000204227	ENST00000374656	D	0.83837	-1.77	4.37	4.37	0.52481	.	0.078879	0.51477	D	0.000099	T	0.63710	0.2534	L	0.31294	0.92	0.45580	D	0.998528	P	0.47604	0.898	B	0.38106	0.265	T	0.69723	-0.5068	10	0.41790	T	0.15	-32.2537	14.4589	0.67435	0.0:0.0:1.0:0.0	.	123	Q06587	RING1_HUMAN	Q	123	ENSP00000363787:R123Q	ENSP00000363787:R123Q	R	+	2	0	RING1	33285798	0.998000	0.40836	0.961000	0.40146	0.905000	0.53344	7.357000	0.79456	2.269000	0.75478	0.542000	0.68232	CGA		0.582	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2			A	33177820	G	A	33177820	3	1	93	1	0	0	0	0	1	0	0	0	13411	1058	37	1	378	1	RING1	6	33177820	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1578111	33177820	137937247	82	25410										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33650367	33650367	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcctcgagtgtccgtggctaCagcagcagcacaagggctcc	12	14	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:33650367C>A	ENST00000374316.5	+	35	5603	c.4543C>A	c.(4543-4545)Cag>Aag	p.Q1515K	ITPR3_ENST00000605930.1_Missense_Mutation_p.Q1515K			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1515					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TCCGTGGCTACAGCAGCAGCA	0.652																																																0			6											49	47	48					6																	33650367		2203	4300	6503	33758345	SO:0001583	missense	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4543C>A	6.37:g.33650367C>A	ENSP00000363435:p.Gln1515Lys		33758345	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	8.689	0.907068	0.17833	.	.	ENSG00000096433	ENST00000374316	T	0.62232	0.04	5.29	5.29	0.74685	.	0.121419	0.56097	D	0.000021	T	0.34483	0.0899	L	0.36672	1.1	0.45415	D	0.998392	B	0.22683	0.073	B	0.24701	0.055	T	0.42999	-0.9418	10	0.02654	T	1	-32.1764	18.9236	0.92536	0.0:1.0:0.0:0.0	.	1515	Q14573	ITPR3_HUMAN	K	1515	ENSP00000363435:Q1515K	ENSP00000363435:Q1515K	Q	+	1	0	ITPR3	33758345	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	4.774000	0.62339	2.474000	0.83562	0.462000	0.41574	CAG		0.652	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33650367	C	A	33650367	3	1	93	1	0	0	0	0	1	0	0	0	7943	479	17	2	4677	2	ITPR3	6	33650367	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	472547	33650367	137464700	83	25411										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73102485	73102485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaccagcccagcttgttggcCgccaaacccttgccacccct	8	19	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:73102485C>T	ENST00000521978.1	+	31	4591	c.4591C>T	c.(4591-4593)Cgc>Tgc	p.R1531C	RIMS1_ENST00000522291.1_Missense_Mutation_p.R1130C|RIMS1_ENST00000520567.1_Missense_Mutation_p.R1181C|RIMS1_ENST00000517827.1_Missense_Mutation_p.R665C|RIMS1_ENST00000414192.2_Missense_Mutation_p.R58C|RIMS1_ENST00000491071.2_Missense_Mutation_p.R1354C|RIMS1_ENST00000538414.1_Missense_Mutation_p.R337C|RIMS1_ENST00000523963.1_Missense_Mutation_p.R656C|RIMS1_ENST00000264839.7_Missense_Mutation_p.R1380C|RIMS1_ENST00000348717.5_Missense_Mutation_p.R1314C|RIMS1_ENST00000517960.1_Missense_Mutation_p.R1314C|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000425662.2_Missense_Mutation_p.R599C|RIMS1_ENST00000518273.1_Missense_Mutation_p.R1210C|RIMS1_ENST00000401910.3_Missense_Mutation_p.R851C	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1531					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCTTGTTGGCCGCCAAACCCT	0.388																																																0			6											86	82	83					6																	73102485		1840	4103	5943	73159206	SO:0001583	missense	22999			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4591C>T	6.37:g.73102485C>T	ENSP00000428417:p.Arg1531Cys		73159206	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.72|18.72	3.683389|3.683389	0.68157|0.68157	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.43294	.|0.95;2.12;2.05;2.13;2.32;2.35;2.35;2.0;2.07;2.34;2.26;1.41;2.26;1.71;1.67;1.96	5.5|5.5	2.56|2.56	0.30785|0.30785	.|.	.|0.000000	.|0.64402	.|D	.|0.000020	T|T	0.58552|0.58552	0.2130|0.2130	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.996;0.992;0.969;0.996;0.998;0.994;1.0;0.995;0.996;0.979;0.998;0.979	T|T	0.69000|0.69000	-0.5261|-0.5261	5|10	.|0.87932	.|D	.|0	-10.7348|-10.7348	14.3795|14.3795	0.66902|0.66902	0.467:0.533:0.0:0.0|0.467:0.533:0.0:0.0	.|.	.|155;337;665;656;1380;851;1130;434;1210;1314;607;1354;1531	.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	L|C	876|1354;1380;1354;1314;1210;1130;1380;1314;1210;1181;1130;1531;851;656;599;696;665;579;337;58	.|ENSP00000430101:R1354C;ENSP00000275037:R1314C;ENSP00000264839:R1380C;ENSP00000429959:R1314C;ENSP00000430408:R1210C;ENSP00000430502:R1181C;ENSP00000430932:R1130C;ENSP00000428417:R1531C;ENSP00000385649:R851C;ENSP00000428328:R656C;ENSP00000411235:R599C;ENSP00000389503:R696C;ENSP00000428367:R665C;ENSP00000359448:R579C;ENSP00000439730:R337C;ENSP00000402273:R58C	.|ENSP00000264839:R1380C	P|R	+|+	2|1	0|0	RIMS1|RIMS1	73159206|73159206	0.877000|0.877000	0.30153|0.30153	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	1.520000|1.520000	0.35899|0.35899	0.646000|0.646000	0.30693|0.30693	0.591000|0.591000	0.81541|0.81541	CCG|CGC		0.388	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			T	73102485	C	T	73102485	3	4	93	1	0	0	0	0	1	0	0	0	13404	652	23	1	4876	1	RIMS1	6	73102485	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	39452118	73102485	98012582	84	25412										
PHIP	55023	hgsc.bcm.edu	37	chr6	79726343	79726343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aatacgtgctgtcccatcacGactgccacttacaaacctgt	6	14	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:79726343G>A	ENST00000275034.4	-	13	1320	c.1153C>T	c.(1153-1155)Cgt>Tgt	p.R385C		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	385					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GTCCCATCACGACTGCCACTT	0.403																																																0			6											139	137	137					6																	79726343		2203	4300	6503	79783062	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1153C>T	6.37:g.79726343G>A	ENSP00000275034:p.Arg385Cys		79783062	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	g	15.59	2.878102	0.51801	.	.	ENSG00000146247	ENST00000275034	T	0.63096	-0.02	5.62	4.76	0.60689	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.069892	0.64402	N	0.000011	T	0.37046	0.0989	N	0.03084	-0.415	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.63033	0.91;0.91	T	0.43925	-0.9361	9	.	.	.	-5.8313	8.3257	0.32156	0.0736:0.0:0.6686:0.2578	.	385;385	A7J992;Q8WWQ0	.;PHIP_HUMAN	C	385	ENSP00000275034:R385C	.	R	-	1	0	PHIP	79783062	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	2.256000	0.43231	1.391000	0.46566	-0.119000	0.15052	CGT		0.403	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79726343	G	A	79726343	3	1	93	1	0	0	0	0	1	0	0	0	11873	1058	37	1	4424	1	PHIP	6	79726343	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	6623858	79726343	91388724	85	25413										
DCBLD1	285761	hgsc.bcm.edu	37	chr6	117859999	117859999	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggagaaaaagaaaataacagGtgcagaaaataacacaagtg	10	4	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:117859999G>T	ENST00000338728.5	+	8	1096		c.e8+1		GOPC_ENST00000467125.1_Intron|DCBLD1_ENST00000296955.8_Splice_Site|DCBLD1_ENST00000368503.4_Intron			Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)		AAAATAACAGGTGCAGAAAAT	0.453																																																0			6											19	19	19					6																	117859999		2203	4299	6502	117966692	SO:0001630	splice_region_variant	285761			AK055462	CCDS34522.1	6q22.31	2003-06-20			ENSG00000164465	ENSG00000164465			21479	protein-coding gene	gene with protein product							Standard	NM_173674		Approved	MGC46341, dJ94G16.1	uc003pxs.3	Q8N8Z6	OTTHUMG00000015455	ENST00000338728.5:c.976+1G>T	6.37:g.117859999G>T			117966692	Q5H992|Q8IYK5|Q8N7L9|Q96NH2	Splice_Site	SNP	ENST00000338728.5	37		.	.	.	.	.	.	.	.	.	.	G	17.97	3.517840	0.64634	.	.	ENSG00000164465	ENST00000296955;ENST00000338728	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7101	0.85383	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCBLD1	117966692	1.000000	0.71417	0.997000	0.53966	0.932000	0.56968	7.335000	0.79234	2.166000	0.68216	0.555000	0.69702	.		0.453	DCBLD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000041979.2	NM_173674	Intron	T	117859999	G	T	117859999	5	4	93	1	0	0	0	0	0	0	1	0	4286	1275	44	2	1007	2	DCBLD1	6	117859999	Splice_Site	SNP	G	TCGA-DC-5337-01A-01D-1657-10	38133656	117859999	53255068	86	25414										
AHI1	54806	hgsc.bcm.edu	37	chr6	135769531	135769531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgcctcaacaacacttaatGgggatcgaggcttagtaggt	11	8	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:135769531G>A	ENST00000367800.4	-	10	1739	c.1523C>T	c.(1522-1524)cCa>cTa	p.P508L	AHI1_ENST00000457866.2_Missense_Mutation_p.P508L|AHI1_ENST00000327035.6_Missense_Mutation_p.P508L	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	508					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		AACACTTAATGGGGATCGAGG	0.403																																																0			6											140	132	134					6																	135769531		1885	4108	5993	135811224	SO:0001583	missense	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.1523C>T	6.37:g.135769531G>A	ENSP00000356774:p.Pro508Leu		135811224	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.88|10.88	1.475277|1.475277	0.26511|0.26511	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367799|ENST00000367800;ENST00000457866;ENST00000265602;ENST00000327035;ENST00000367801	.|T;T;T;T	.|0.58210	.|0.4;0.4;0.4;0.35	5.89|5.89	4.7|4.7	0.59300|0.59300	.|.	.|0.641721	.|0.16893	.|N	.|0.195247	T|T	0.12050|0.12050	0.0293|0.0293	N|N	0.08118|0.08118	0|0	0.44380|0.44380	D|D	0.997286|0.997286	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.11792|0.11792	-1.0573|-1.0573	5|10	.|0.30078	.|T	.|0.28	-3.728|-3.728	3.9684|3.9684	0.09443|0.09443	0.1188:0.0648:0.2475:0.5689|0.1188:0.0648:0.2475:0.5689	.|.	.|508;508	.|Q8N157-2;Q8N157	.|.;AHI1_HUMAN	Y|L	8|508	.|ENSP00000356774:P508L;ENSP00000388650:P508L;ENSP00000265602:P508L;ENSP00000322478:P508L	.|ENSP00000265602:P508L	H|P	-|-	1|2	0|0	AHI1|AHI1	135811224|135811224	0.803000|0.803000	0.28956|0.28956	0.019000|0.019000	0.16419|0.16419	0.036000|0.036000	0.12997|0.12997	1.109000|1.109000	0.31135|0.31135	0.462000|0.462000	0.27095|0.27095	-0.346000|-0.346000	0.07831|0.07831	CAT|CCA		0.403	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		A	135769531	G	A	135769531	3	1	93	1	0	0	0	0	1	0	0	0	413	1348	47	3	2196	3	AHI1	6	135769531	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	17909532	135769531	35345536	87	25415										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654180	159654180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctcaggtatccatggagacgAggaggatgagaagccgcttc	14	9	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr6:159654180A>G	ENST00000297267.9	+	11	2836	c.2636A>G	c.(2635-2637)gAg>gGg	p.E879G	FNDC1_ENST00000340366.6_Missense_Mutation_p.E816G	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	879					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CATGGAGACGAGGAGGATGAG	0.612																																																0			6											25	32	30					6																	159654180		1974	4155	6129	159574170	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2636A>G	6.37:g.159654180A>G	ENSP00000297267:p.Glu879Gly		159574170	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.835360	0.32421	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.08896	3.04;3.85	5.33	-3.39	0.04868	.	1.342850	0.04820	N	0.436847	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.46652	-0.9176	10	0.13108	T	0.6	0.0395	2.3807	0.04353	0.574:0.1233:0.1076:0.1951	.	816;879	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	G	879;816	ENSP00000297267:E879G;ENSP00000342460:E816G	ENSP00000297267:E879G	E	+	2	0	FNDC1	159574170	0.000000	0.05858	0.000000	0.03702	0.305000	0.27757	0.146000	0.16180	-0.941000	0.03700	-0.912000	0.02778	GAG		0.612	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		G	159654180	A	G	159654180	3	3	93	1	0	0	0	0	1	0	0	0	5987	304	11	4	2678	4	FNDC1	6	159654180	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	23884649	159654180	11460887	88	25416										
ETV1	2115	hgsc.bcm.edu	37	chr7	13971264	13971264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcttaaagccttgtggtgggAaggggatgtttggctcagac	16	6	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:13971264A>G	ENST00000430479.1	-	9	1332	c.665T>C	c.(664-666)tTc>tCc	p.F222S	ETV1_ENST00000242066.5_Missense_Mutation_p.F204S|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000399357.3_Missense_Mutation_p.F119S|ETV1_ENST00000403527.1_Missense_Mutation_p.F182S|ETV1_ENST00000403685.1_Missense_Mutation_p.F204S|ETV1_ENST00000343495.5_Missense_Mutation_p.F204S|ETV1_ENST00000405192.2_Missense_Mutation_p.F222S|ETV1_ENST00000405218.2_Missense_Mutation_p.F222S|ETV1_ENST00000420159.2_Missense_Mutation_p.F164S|ETV1_ENST00000405358.4_Missense_Mutation_p.F236S	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	222					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						TTGTGGTGGGAAGGGGATGTT	0.542			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	0			7											140	138	138					7																	13971264		2018	4191	6209	13937789	SO:0001583	missense	2115				CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"ets variant gene 1"			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.665T>C	7.37:g.13971264A>G	ENSP00000405327:p.Phe222Ser		13937789	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.745711	0.89663	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956;ENST00000443608	T;T;T;T;T;T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0	6.13	6.13	0.99165	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.43500	0.1250	L	0.56769	1.78	0.80722	D	1	D;B;P;P;D;D;B;B	0.76494	0.999;0.059;0.891;0.867;0.993;0.994;0.026;0.015	D;B;P;P;D;D;B;B	0.83275	0.958;0.039;0.492;0.544;0.996;0.989;0.029;0.026	T	0.08932	-1.0698	10	0.30078	T	0.28	.	16.7898	0.85586	1.0:0.0:0.0:0.0	.	233;204;236;164;119;182;164;222	Q59GA7;P50549-2;B5MCT2;F5GXR2;B7Z9P2;E9PHB1;B7Z618;P50549	.;.;.;.;.;.;.;ETV1_HUMAN	S	222;204;204;164;119;222;236;182;222;204;164;119	ENSP00000405327:F222S;ENSP00000242066:F204S;ENSP00000340853:F204S;ENSP00000411626:F164S;ENSP00000382293:F119S;ENSP00000385381:F222S;ENSP00000384085:F236S;ENSP00000384138:F182S;ENSP00000385551:F222S;ENSP00000385686:F204S;ENSP00000393078:F164S;ENSP00000394710:F119S	ENSP00000242066:F204S	F	-	2	0	ETV1	13937789	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.725000	0.91468	2.364000	0.80123	0.524000	0.50904	TTC		0.542	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		G	13971264	A	G	13971264	3	3	93	1	0	0	0	0	1	0	0	0	5290	246	9	4	792	4	ETV1	7	13971264	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10		13971264	145167399	89	25417										
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27832791	27832791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agaaaaatttaaggaatgccAaaggctccaaaaacaaataa	6	6	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:27832791A>G	ENST00000396319.2	+	10	1458	c.1370A>G	c.(1369-1371)cAa>cGa	p.Q457R	TAX1BP1_ENST00000543117.1_Missense_Mutation_p.Q457R|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.Q457R|TAX1BP1_ENST00000433216.2_Missense_Mutation_p.Q300R|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.Q457R	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	457			Q -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.Q457R(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			AAGGAATGCCAAAGGCTCCAA	0.323																																																1	Substitution - Missense(1)	breast(1)	7											37	38	37					7																	27832791		2203	4300	6503	27799316	SO:0001583	missense	8887			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1370A>G	7.37:g.27832791A>G	ENSP00000379612:p.Gln457Arg		27799316	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277984	0.80692	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	T;T;T;T;T	0.10099	2.91;2.91;2.91;2.91;2.91	5.9	5.9	0.94986	.	0.000000	0.50627	D	0.000109	T	0.29158	0.0725	L	0.59436	1.845	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.85130	0.997;0.997;0.99	T	0.01283	-1.1396	10	0.24483	T	0.36	-11.514	16.3291	0.83001	1.0:0.0:0.0:0.0	.	300;457;457	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	R	457;457;457;300;457;12	ENSP00000444811:Q457R;ENSP00000265393:Q457R;ENSP00000386515:Q457R;ENSP00000391907:Q300R;ENSP00000379612:Q457R	ENSP00000265393:Q457R	Q	+	2	0	TAX1BP1	27799316	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	8.770000	0.91746	2.257000	0.74773	0.528000	0.53228	CAA		0.323	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		G	27832791	A	G	27832791	3	3	93	1	0	0	0	0	1	0	0	0	15633	130	5	4	1404	4	TAX1BP1	7	27832791	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	13861527	27832791	131305872	90	25418										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70885988	70885988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggacaactttgaggtgcagCggtacgagaactcggcccac	13	11	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:70885988C>T	ENST00000333538.5	+	5	1493	c.859C>T	c.(859-861)Cgg>Tgg	p.R287W	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	287					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TGAGGTGCAGCGGTACGAGAA	0.577																																																0			7											149	137	141					7																	70885988		2203	4300	6503	70523924	SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.859C>T	7.37:g.70885988C>T	ENSP00000329654:p.Arg287Trp		70523924	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.469957	0.84533	.	.	ENSG00000185274	ENST00000333538	T	0.64438	-0.1	5.32	5.32	0.75619	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.73218	0.3559	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.75391	-0.3334	10	0.87932	D	0	.	13.0276	0.58825	0.1609:0.8391:0.0:0.0	.	287	Q6IS24	GLTL3_HUMAN	W	287	ENSP00000329654:R287W	ENSP00000329654:R287W	R	+	1	2	WBSCR17	70523924	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.621000	0.67743	2.490000	0.84030	0.557000	0.71058	CGG		0.577	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	70885988	C	T	70885988	3	4	93	1	0	0	0	0	1	0	0	0	17304	759	27	1	877	1	WBSCR17	7	70885988	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	43053197	70885988	88252675	91	25419										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77538204	77538204	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggctgatgctgctcctgggAactgtgcattgccagattgt	13	9	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:77538204A>G	ENST00000248550.7	+	7	616	c.540A>G	c.(538-540)ggA>ggG	p.G180G	PHTF2_ENST00000307305.8_Silent_p.G142G|PHTF2_ENST00000415251.2_Silent_p.G142G|PHTF2_ENST00000450574.1_Silent_p.G146G|PHTF2_ENST00000275575.7_Silent_p.G142G|PHTF2_ENST00000422959.2_Silent_p.G146G|PHTF2_ENST00000416283.2_Silent_p.G146G|PHTF2_ENST00000424760.1_Silent_p.G142G|PHTF2_ENST00000454592.1_3'UTR			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TGCTCCTGGGAACTGTGCATT	0.433																																																0			7											88	86	86					7																	77538204		1941	4146	6087	77376140	SO:0001819	synonymous_variant	57157			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.540A>G	7.37:g.77538204A>G			77376140	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	37																																																																																					0.433	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77538204	A	G	77538204	2	3	93	1	0	0	0	0	0	0	0	1	11894	233	9	4		4	PHTF2	7	77538204	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6652216	77538204	81600459	92	25420										
HGF	3082	hgsc.bcm.edu	37	chr7	81334975	81334975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tagcttacatccagtgtagcCccagccataaacactgcaac	6	14	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:81334975C>T	ENST00000222390.5	-	16	2078	c.1852G>A	c.(1852-1854)Ggc>Agc	p.G618S	HGF_ENST00000457544.2_Missense_Mutation_p.G613S	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	618	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CCAGTGTAGCCCCAGCCATAA	0.353																																																0			7											92	84	87					7																	81334975		2203	4300	6503	81172911	SO:0001583	missense	6654				CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1852G>A	7.37:g.81334975C>T	ENSP00000222390:p.Gly618Ser		81172911	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	37	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.608225	0.87258	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	D;D	0.93953	-3.32;-3.32	4.74	4.74	0.60224	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.97739	0.9258	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99038	1.0823	10	0.72032	D	0.01	.	17.0863	0.86611	0.0:1.0:0.0:0.0	.	613;618	P14210-3;P14210	.;HGF_HUMAN	S	618;613	ENSP00000222390:G618S;ENSP00000391238:G613S	ENSP00000222390:G618S	G	-	1	0	HGF	81172911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.782000	0.68973	2.331000	0.79229	0.585000	0.79938	GGC		0.353	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81334975	C	T	81334975	3	4	93	1	0	0	0	0	1	0	0	0	7106	623	22	3	346	3	HGF	7	81334975	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	3796771	81334975	77803688	93	25421										
PCLO	27445	hgsc.bcm.edu	37	chr7	82578912	82578912	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtcttaggacttgctgggggAactttagccatatctggatg	13	7	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:82578912A>G	ENST00000333891.9	-	6	11329	c.10992T>C	c.(10990-10992)gtT>gtC	p.V3664V	PCLO_ENST00000423517.2_Silent_p.V3664V|PCLO_ENST00000437081.1_Silent_p.V384V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGCTGGGGGAACTTTAGCCA	0.483																																																0			7											199	193	195					7																	82578912		1921	4143	6064	82416848	SO:0001819	synonymous_variant	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.10992T>C	7.37:g.82578912A>G			82416848		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82578912	A	G	82578912	2	3	93	1	0	0	0	0	0	0	0	1	11614	233	9	4		4	PCLO	7	82578912	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1243937	82578912	76559751	94	25422										
TSC22D4	81628	hgsc.bcm.edu	37	chr7	100064784	100064784	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caaacatgaggtgggacttcAccaagtcctgggggccccgg	14	12	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:100064784A>G	ENST00000300181.2	-	5	1740	c.986T>C	c.(985-987)gTg>gCg	p.V329A	C7orf61_ENST00000332375.3_5'Flank|TSC22D4_ENST00000496728.1_Intron|TSC22D4_ENST00000393991.1_Missense_Mutation_p.V90A	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	329			V -> M (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V329del(1)		breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTGGGACTTCACCAAGTCCTG	0.657																																																1	Deletion - In frame(1)	breast(1)	7											38	41	40					7																	100064784		2203	4300	6503	99902720	SO:0001583	missense	81628			BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.986T>C	7.37:g.100064784A>G	ENSP00000300181:p.Val329Ala		99902720	A4D2C3|A8MWR6|D6W5V9	Missense_Mutation	SNP	ENST00000300181.2	37	CCDS5695.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.41|12.41	1.931094|1.931094	0.34096|0.34096	.|.	.|.	ENSG00000166925|ENSG00000166925	ENST00000300181;ENST00000393991|ENST00000423266	.|.	.|.	.|.	4.16|4.16	4.16|4.16	0.48862|0.48862	.|.	0.212946|.	0.24134|.	N|.	0.041232|.	T|.	0.77718|.	0.4172|.	M|M	0.88241|0.88241	2.94|2.94	0.45541|0.45541	D|D	0.998497|0.998497	D|.	0.69078|.	0.997|.	D|.	0.79108|.	0.992|.	T|.	0.81046|.	-0.1110|.	9|.	0.87932|.	D|.	0|.	-15.7728|-15.7728	11.2055|11.2055	0.48767|0.48767	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	329|.	Q9Y3Q8|.	T22D4_HUMAN|.	A|R	329;90|145	.|.	ENSP00000300181:V329A|.	V|X	-|-	2|1	0|0	TSC22D4|TSC22D4	99902720|99902720	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.183000|0.183000	0.23260|0.23260	8.779000|8.779000	0.91792|0.91792	1.732000|1.732000	0.51606|0.51606	0.482000|0.482000	0.46254|0.46254	GTG|TGA		0.657	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1	NM_030935		G	100064784	A	G	100064784	3	3	93	1	0	0	0	0	1	0	0	0	16650	159	6	4	205	4	TSC22D4	7	100064784	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	17485872	100064784	59073879	95	25423										
MET	4233	hgsc.bcm.edu	37	chr7	116339625	116339625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cggaggttcactgcatattcTccccacagatagaagagccc	9	13	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:116339625T>C	ENST00000318493.6	+	2	674	c.487T>C	c.(487-489)Tcc>Ccc	p.S163P	MET_ENST00000436117.2_Missense_Mutation_p.S163P|MET_ENST00000397752.3_Missense_Mutation_p.S163P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CTGCATATTCTCCCCACAGAT	0.522			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											113	113	113					7																	116339625		2010	4175	6185	116126861	SO:0001583	missense	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.487T>C	7.37:g.116339625T>C	ENSP00000317272:p.Ser163Pro		116126861	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.273435	0.40194	.	.	ENSG00000105976	ENST00000437703;ENST00000456159;ENST00000397752;ENST00000318493;ENST00000436117	T;T;T;T	0.05025	3.51;3.51;3.51;3.51	5.76	4.58	0.56647	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.228945	0.46145	D	0.000319	T	0.27900	0.0687	M	0.87900	2.915	0.80722	D	1	D;P;D;P;P;P;D;P;P;P;P;P;P	0.63880	0.984;0.94;0.993;0.94;0.94;0.94;0.966;0.94;0.947;0.927;0.94;0.953;0.953	P;D;D;P;D;D;D;D;P;P;P;P;P	0.72075	0.825;0.919;0.976;0.901;0.919;0.919;0.919;0.919;0.865;0.697;0.873;0.85;0.85	T	0.03993	-1.0986	10	0.66056	D	0.02	.	12.3811	0.55307	0.1263:0.0:0.0:0.8737	.	163;163;163;163;163;163;163;163;163;163;163;163;163	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	P	182;182;163;163;163	ENSP00000413857:S182P;ENSP00000380860:S163P;ENSP00000317272:S163P;ENSP00000410980:S163P	ENSP00000317272:S163P	S	+	1	0	MET	116126861	1.000000	0.71417	0.995000	0.50966	0.547000	0.35210	5.445000	0.66594	1.066000	0.40716	0.533000	0.62120	TCC		0.522	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116339625	T	C	116339625	3	2	93	1	0	0	0	0	1	0	0	0	9515	1551	54	4	489	4	MET	7	116339625	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	16274841	116339625	42799038	96	25424										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138604032	138604032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgtatcaaaagtagtggcagAcggcggggctgtgacatgga	16	6	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:138604032A>G	ENST00000422774.1	-	2	388	c.340T>C	c.(340-342)Tct>Cct	p.S114P	KIAA1549_ENST00000242365.4_Missense_Mutation_p.S64P|KIAA1549_ENST00000440172.1_Missense_Mutation_p.S114P			Q9HCM3	K1549_HUMAN	KIAA1549	114						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GTAGTGGCAGACGGCGGGGCT	0.522			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	0			7											112	111	111					7																	138604032		1967	4173	6140	138254572	SO:0001583	missense	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.340T>C	7.37:g.138604032A>G	ENSP00000416040:p.Ser114Pro		138254572	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	A	5.541	0.284707	0.10513	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.32515	1.45;1.45;1.45	4.66	0.587	0.17439	.	0.531595	0.15874	N	0.240384	T	0.18467	0.0443	L	0.29908	0.895	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.09377	0.002;0.004	T	0.16600	-1.0397	10	0.54805	T	0.06	.	4.5502	0.12108	0.4355:0.3532:0.2113:0.0	.	114;114	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	P	114;64;114	ENSP00000406661:S114P;ENSP00000242365:S64P;ENSP00000416040:S114P	ENSP00000242365:S64P	S	-	1	0	KIAA1549	138254572	0.017000	0.18338	0.002000	0.10522	0.063000	0.16089	-0.352000	0.07701	-0.019000	0.14055	0.459000	0.35465	TCT		0.522	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			G	138604032	A	G	138604032	3	3	93	1	0	0	0	0	1	0	0	0	8265	275	10	4	5588	4	KIAA1549	7	138604032	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	22264407	138604032	20534631	97	25425										
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150174492	150174492	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggacgattcactgaagaggAcaaaacagctgtggcgaaac	13	8	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr7:150174492A>G	ENST00000307271.3	+	5	2196	c.1622A>G	c.(1621-1623)gAc>gGc	p.D541G		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	541	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ACTGAAGAGGACAAAACAGCT	0.512																																																0			7											79	76	77					7																	150174492		2203	4300	6503	149805425	SO:0001583	missense	155038			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1622A>G	7.37:g.150174492A>G	ENSP00000305107:p.Asp541Gly		149805425		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032996	0.75504	.	.	ENSG00000171115	ENST00000307271	T	0.10288	2.89	4.44	4.44	0.53790	AIG1 (1);	0.154035	0.29799	N	0.011174	T	0.35941	0.0949	M	0.89353	3.025	0.41576	D	0.988711	D	0.89917	1.0	D	0.78314	0.991	T	0.31779	-0.9931	10	0.72032	D	0.01	.	10.012	0.41992	1.0:0.0:0.0:0.0	.	541	Q8ND71	GIMA8_HUMAN	G	541	ENSP00000305107:D541G	ENSP00000305107:D541G	D	+	2	0	GIMAP8	149805425	1.000000	0.71417	0.047000	0.18901	0.044000	0.14063	6.727000	0.74764	1.881000	0.54492	0.533000	0.62120	GAC		0.512	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		G	150174492	A	G	150174492	3	3	93	1	0	0	0	0	1	0	0	0	6405	275	10	4	1636	4	GIMAP8	7	150174492	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	11570460	150174492	8964171	98	25426										
NEFM	4741	hgsc.bcm.edu	37	chr8	24772212	24772212	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tacgccaagctcaccgaggcGgccgagcagaacaaggaggc	14	13	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:24772212G>A	ENST00000221166.5	+	1	1688	c.906G>A	c.(904-906)gcG>gcA	p.A302A	NEFM_ENST00000433454.2_5'Flank|NEFM_ENST00000518131.1_Silent_p.A302A|RP11-624C23.1_ENST00000519689.1_RNA|NEFM_ENST00000437366.2_Silent_p.A302A|NEFM_ENST00000521540.1_3'UTR|GS1-72M22.1_ENST00000607058.1_RNA			P07197	NFM_HUMAN	neurofilament, medium polypeptide	302	Coil 2B.|Rod.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		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)		TCACCGAGGCGGCCGAGCAGA	0.617																																																0			8											65	56	59					8																	24772212		2203	4300	6503	24828117	SO:0001819	synonymous_variant	4741			BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"Intermediate filaments type IV"	7734	protein-coding gene	gene with protein product		162250	"neurofilament, medium polypeptide 150kDa"	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.906G>A	8.37:g.24772212G>A			24828117	B4DGN2|E9PBF7|Q4QRK6	Silent	SNP	ENST00000221166.5	37	CCDS6046.1																																																																																				0.617	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		A	24772212	G	A	24772212	2	1	93	1	0	0	0	0	0	0	0	1	10347	1103	39	1		1	NEFM	8	24772212	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10		24772212	121591810	99	25427										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27650248	27650248	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agcaagttgttcctaaatgtCcaaacaaaataaaaactttt	4	7	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:27650248C>A	ENST00000305188.8	+	9	1655	c.1417C>A	c.(1417-1419)Cca>Aca	p.P473T	ESCO2_ENST00000397418.2_Missense_Mutation_p.P121T	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	473					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)	p.P473S(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		TCCTAAATGTCCAAACAAAAT	0.313									SC Phocomelia syndrome																																							1	Substitution - Missense(1)	central_nervous_system(1)	8											56	56	56					8																	27650248		2203	4293	6496	27706167	SO:0001583	missense	157570	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1417C>A	8.37:g.27650248C>A	ENSP00000306999:p.Pro473Thr		27706167	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	37	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.605358	0.28623	.	.	ENSG00000171320	ENST00000305188;ENST00000397418	T;T	0.72282	-0.22;-0.64	5.82	3.08	0.35506	.	0.099413	0.64402	D	0.000001	T	0.68165	0.2971	M	0.74546	2.27	0.54753	D	0.999988	P	0.35982	0.531	B	0.37387	0.248	T	0.66384	-0.5937	10	0.87932	D	0	-2.1446	7.6757	0.28484	0.0:0.7146:0.1358:0.1497	.	473	Q56NI9	ESCO2_HUMAN	T	473;121	ENSP00000306999:P473T;ENSP00000380563:P121T	ENSP00000306999:P473T	P	+	1	0	ESCO2	27706167	1.000000	0.71417	0.814000	0.32528	0.372000	0.29890	2.756000	0.47549	0.392000	0.25172	-0.189000	0.12847	CCA		0.313	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		A	27650248	C	A	27650248	3	1	93	1	0	0	0	0	1	0	0	0	5262	855	30	2	1447	2	ESCO2	8	27650248	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	2878036	27650248	118713774	100	25428										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27650324	27650324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tttaattgcagaacccatcaAacaggtatggtatatttgtt	7	6	1	1	rs143530690		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:27650324A>G	ENST00000305188.8	+	9	1731	c.1493A>G	c.(1492-1494)aAa>aGa	p.K498R	ESCO2_ENST00000397418.2_Missense_Mutation_p.K146R	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	498					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		GAACCCATCAAACAGGTATGG	0.313									SC Phocomelia syndrome																																							0			8											40	42	42					8																	27650324		2203	4291	6494	27706243	SO:0001583	missense	157570	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1493A>G	8.37:g.27650324A>G	ENSP00000306999:p.Lys498Arg		27706243	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	37	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.799379	0.31869	.	.	ENSG00000171320	ENST00000305188;ENST00000397418	T;T	0.72505	-0.16;-0.66	5.82	4.63	0.57726	.	0.200678	0.50627	D	0.000116	T	0.46718	0.1407	N	0.17594	0.5	0.37016	D	0.895968	B	0.29988	0.264	B	0.23150	0.044	T	0.42899	-0.9424	10	0.16420	T	0.52	-9.9823	5.9393	0.19184	0.7485:0.1682:0.0833:0.0	.	498	Q56NI9	ESCO2_HUMAN	R	498;146	ENSP00000306999:K498R;ENSP00000380563:K146R	ENSP00000306999:K498R	K	+	2	0	ESCO2	27706243	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.698000	0.37794	0.982000	0.38575	0.482000	0.46254	AAA		0.313	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		G	27650324	A	G	27650324	3	3	93	1	0	0	0	0	1	0	0	0	5262	14	1	4	1523	4	ESCO2	8	27650324	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	76	27650324	118713698	101	25429										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48752648	48752648	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gttgtagaaggatgggaaacGaattccacaacggggttcag	14	6	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:48752648G>A	ENST00000314191.2	-	56	7436	c.7380C>T	c.(7378-7380)ttC>ttT	p.F2460F	PRKDC_ENST00000338368.3_Silent_p.F2460F|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2461	KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GATGGGAAACGAATTCCACAA	0.333								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											0			8											68	70	69					8																	48752648		1834	4079	5913	48915201	SO:0001819	synonymous_variant	5591				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.7380C>T	8.37:g.48752648G>A			48915201	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37																																																																																					0.333	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		A	48752648	G	A	48752648	2	1	93	1	0	0	0	0	0	0	0	1	12555	1049	37	1		1	PRKDC	8	48752648	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	21102324	48752648	97611374	102	25430										
SULF1	23213	hgsc.bcm.edu	37	chr8	70498635	70498635	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaatataatggcagctacatCccccctgggtggcgagaatg	12	10	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:70498635C>T	ENST00000260128.4	+	7	1173	c.456C>T	c.(454-456)atC>atT	p.I152I	SULF1_ENST00000402687.4_Silent_p.I152I|SULF1_ENST00000419716.3_Silent_p.I152I|SULF1_ENST00000458141.2_Silent_p.I152I	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	152					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GCAGCTACATCCCCCCTGGGT	0.348																																																0			8											57	63	61					8																	70498635		2203	4300	6503	70661189	SO:0001819	synonymous_variant	23213			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.456C>T	8.37:g.70498635C>T			70661189	Q86YV8|Q8NCA2|Q9UPS5	Silent	SNP	ENST00000260128.4	37	CCDS6204.1																																																																																				0.348	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70498635	C	T	70498635	2	4	93	1	0	0	0	0	0	0	0	1	15409	845	30	3		3	SULF1	8	70498635	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	21745987	70498635	75865387	103	25431										
PKIA	5569	hgsc.bcm.edu	37	chr8	79514030	79514030	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aacaaagtggggaagcccagGgagaagcagcaaaatctgaa	13	7	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:79514030G>A	ENST00000396418.2	+	4	691	c.205G>A	c.(205-207)Gga>Aga	p.G69R	PKIA_ENST00000518467.1_Missense_Mutation_p.G69R|PKIA_ENST00000352966.5_Missense_Mutation_p.G69R	NM_006823.3|NM_181839.2	NP_006814.1|NP_862822.1	P61925	IPKA_HUMAN	protein kinase (cAMP-dependent, catalytic) inhibitor alpha	69					negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP-dependent protein kinase inhibitor activity (GO:0004862)|protein kinase A catalytic subunit binding (GO:0034236)	p.G69R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6						GGAAGCCCAGGGAGAAGCAGC	0.413																																																1	Substitution - Missense(1)	central_nervous_system(1)	8											129	114	119					8																	79514030		2203	4300	6503	79676585	SO:0001583	missense	5569			S76965	CCDS6222.1	8q21.13	2014-08-12			ENSG00000171033	ENSG00000171033			9017	protein-coding gene	gene with protein product		606059		PRKACN1		1770951	Standard	NM_006823		Approved		uc003ybb.3	P61925	OTTHUMG00000164618	ENST00000396418.2:c.205G>A	8.37:g.79514030G>A	ENSP00000379696:p.Gly69Arg		79676585	P04541|Q6IAV2	Missense_Mutation	SNP	ENST00000396418.2	37	CCDS6222.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702467	0.30232	.	.	ENSG00000171033	ENST00000396418;ENST00000352966;ENST00000518467	.	.	.	5.38	5.38	0.77491	.	0.440893	0.22463	N	0.059739	T	0.75451	0.3851	.	.	.	0.40100	D	0.976362	D	0.58268	0.982	D	0.66351	0.943	T	0.76255	-0.3026	7	.	.	.	.	12.4752	0.55809	0.0767:0.0:0.9233:0.0	.	69	P61925	IPKA_HUMAN	R	69	.	.	G	+	1	0	PKIA	79676585	1.000000	0.71417	0.999000	0.59377	1.000000	0.99986	5.102000	0.64572	2.523000	0.85059	0.655000	0.94253	GGA		0.413	PKIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379420.1			A	79514030	G	A	79514030	3	1	93	1	0	0	0	0	1	0	0	0	12004	1233	43	3	211	3	PKIA	8	79514030	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	9015395	79514030	66849992	104	25432										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113240986	113240986	+	Splice_Site	DEL	T	T	-													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	taaaaatcaatgagcttaccTttgtttataaagataaaatc							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:113240986delT	ENST00000297405.5	-	70	11207	c.10963delA	c.(10963-10965)agg>gg	p.R3655fs	CSMD3_ENST00000343508.3_Splice_Site_p.R3615fs|CSMD3_ENST00000455883.2_Splice_Site_p.R3486fs|CSMD3_ENST00000352409.3_Splice_Site_p.R3585fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3655						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGAGCTTACCTTTGTTTATAA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											63	69	67					8																	113240986		2203	4295	6498	113310162	SO:0001630	splice_region_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10964+1A>-	8.37:g.113240986delT			113310162	Q96PZ3	Frame_Shift_Del	DEL	ENST00000297405.5	37	CCDS6315.1																																																																																				0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Frame_Shift_Del	-	113240986	T	-	113240986	8	5	93	1	0	1	0	1	0	0	1	0	3952	1623	56	0	168	0	CSMD3	8	113240986	Splice_Site	DEL	T	TCGA-DC-5337-01A-01D-1657-10	33726956	113240986	33123036	105	25433										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113349921	113349921	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	taccaattacaaaaccatttCgaaacgggcgtggatcagga	9	9	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:113349921C>A	ENST00000297405.5	-	43	6936	c.6692G>T	c.(6691-6693)cGa>cTa	p.R2231L	CSMD3_ENST00000343508.3_Missense_Mutation_p.R2191L|CSMD3_ENST00000455883.2_Missense_Mutation_p.R2127L|CSMD3_ENST00000352409.3_Missense_Mutation_p.R2161L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2231	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2231Q(2)|p.R2191Q(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAAACCATTTCGAAACGGGCG	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						3	Substitution - Missense(3)	kidney(3)	8											92	94	93					8																	113349921		2203	4300	6503	113419097	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6692G>T	8.37:g.113349921C>A	ENSP00000297405:p.Arg2231Leu		113419097	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429064	0.62844	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.64	5.64	0.86602	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000008	T	0.65004	0.2650	N	0.11845	0.185	0.48830	D	0.999712	D;P;B	0.76494	0.999;0.895;0.05	D;P;B	0.70227	0.968;0.723;0.033	T	0.63377	-0.6651	10	0.27785	T	0.31	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2127;2231;2191	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	L	2191;2231;1501;2127;2161	ENSP00000345799:R2191L;ENSP00000297405:R2231L;ENSP00000341558:R1501L;ENSP00000412263:R2127L;ENSP00000343124:R2161L	ENSP00000297405:R2231L	R	-	2	0	CSMD3	113419097	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.750000	0.62162	2.937000	0.99478	0.650000	0.86243	CGA		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113349921	C	A	113349921	3	1	93	1	0	0	0	0	1	0	0	0	3952	884	31	2	4547	2	CSMD3	8	113349921	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	108935	113349921	33014101	106	25434										
CSMD3	114788	hgsc.bcm.edu	37	chr8	114290849	114290849	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tataccttaaatccatgagcActaactgcaaaatcactggt	5	10	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:114290849A>G	ENST00000297405.5	-	3	730	c.486T>C	c.(484-486)agT>agC	p.S162S	CSMD3_ENST00000343508.3_Silent_p.S122S|CSMD3_ENST00000455883.2_Silent_p.S162S|CSMD3_ENST00000352409.3_Silent_p.S162S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	162	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATCCATGAGCACTAACTGCAA	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											123	106	112					8																	114290849		2203	4300	6503	114360025	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.486T>C	8.37:g.114290849A>G			114360025	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.378	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	114290849	A	G	114290849	2	3	93	1	0	0	0	0	0	0	0	1	3952	156	6	4		4	CSMD3	8	114290849	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	940928	114290849	32073173	107	25435										
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128429032	128429032	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggtctcctttctcagggggAccagtgtcctttcctccggc	12	14	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:128429032A>G	ENST00000465342.2	+	2	2078	c.921A>G	c.(919-921)ggA>ggG	p.G307G	CASC8_ENST00000502082.1_RNA|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000523825.1_RNA|POU5F1B_ENST00000391675.1_Silent_p.G307G			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						TCTCAGGGGGACCAGTGTCCT	0.587																																																0			8											14	14	14					8																	128429032		692	1591	2283	128498214	SO:0001819	synonymous_variant	5462			AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"Homeoboxes / POU class"	9223	protein-coding gene	gene with protein product		615739	"POU domain class 5, transcription factor 1 pseudogene 1", "POU class 5 homeobox 1 pseudogene 1"	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.921A>G	8.37:g.128429032A>G			128498214	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Silent	SNP	ENST00000465342.2	37	CCDS55274.1																																																																																				0.587	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		G	128429032	A	G	128429032	2	3	93	1	0	0	0	0	0	0	0	1	12313	262	10	4		4	POU5F1B	8	128429032	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	14138183	128429032	17934990	108	25436										
LYPD2	137797	hgsc.bcm.edu	37	chr8	143831749	143831749	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agcgtgagggccccgcagtgGaggctgttcagagcgggcgc	19	11	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:143831749G>A	ENST00000359228.3	-	3	412	c.330C>T	c.(328-330)ctC>ctT	p.L110L		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	110						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CCCCGCAGTGGAGGCTGTTCA	0.652																																																0			8											28	25	26					8																	143831749		2175	4252	6427	143828751	SO:0001819	synonymous_variant	137797			AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.330C>T	8.37:g.143831749G>A			143828751	A8K2R6|Q0VD64|Q0VF31	Silent	SNP	ENST00000359228.3	37	CCDS6388.1																																																																																				0.652	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545		A	143831749	G	A	143831749	2	1	93	1	0	0	0	0	0	0	0	1	9140	1161	41	3		3	LYPD2	8	143831749	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	15402717	143831749	2532273	109	25437										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144663283	144663283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cttctccagcacgttcagccGggcctccagcttggagatgg	12	14	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:144663283G>A	ENST00000529272.1	-	5	731	c.331C>T	c.(331-333)Cgg>Tgg	p.R111W	EEF1D_ENST00000526838.1_Missense_Mutation_p.R92W|EEF1D_ENST00000442189.2_Missense_Mutation_p.R477W|NAPRT1_ENST00000426292.3_5'Flank|NAPRT1_ENST00000449291.2_5'Flank|NAPRT1_ENST00000435154.3_5'Flank|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000423316.2_Missense_Mutation_p.R477W|EEF1D_ENST00000532741.1_Missense_Mutation_p.R527W|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000528610.1_Missense_Mutation_p.R87W|EEF1D_ENST00000419152.2_Missense_Mutation_p.R111W|EEF1D_ENST00000524624.1_Missense_Mutation_p.R87W|EEF1D_ENST00000317198.6_Missense_Mutation_p.R111W|EEF1D_ENST00000531621.1_Missense_Mutation_p.R68W|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000395119.3_Missense_Mutation_p.R111W			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	111	Leucine-zipper.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			ACGTTCAGCCGGGCCTCCAGC	0.677																																																0			8											42	43	43					8																	144663283		2203	4298	6501	144734426	SO:0001583	missense	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.331C>T	8.37:g.144663283G>A	ENSP00000434872:p.Arg111Trp		144734426	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512686	0.85389	.	.	ENSG00000104529	ENST00000419152;ENST00000532741;ENST00000526838;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000337369;ENST00000531621;ENST00000524624;ENST00000534380;ENST00000534377;ENST00000533204;ENST00000530191;ENST00000531218;ENST00000533494;ENST00000530445;ENST00000529516;ENST00000533749	.	.	.	4.8	2.78	0.32641	.	0.000000	0.85682	D	0.000000	T	0.79311	0.4424	M	0.87827	2.91	0.80722	D	1	P;D;D;B;D;D	0.89917	0.877;1.0;0.999;0.203;1.0;1.0	B;D;P;B;D;D	0.97110	0.232;0.997;0.908;0.022;1.0;0.999	T	0.81988	-0.0680	9	0.87932	D	0	.	10.9683	0.47424	0.0:0.0:0.6466:0.3533	.	92;477;405;111;527;477	E9PBQ9;D3DWK1;F8W934;P29692;E9PRY8;P29692-2	.;.;.;EF1D_HUMAN;.;.	W	111;527;92;477;87;111;111;477;405;111;477;68;87;111;87;111;111;111;111;111;92;127	.	ENSP00000317399:R111W	R	-	1	2	EEF1D	144734426	0.987000	0.35691	1.000000	0.80357	0.926000	0.56050	1.877000	0.39598	1.110000	0.41699	0.455000	0.32223	CGG		0.677	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		A	144663283	G	A	144663283	3	1	93	1	0	0	0	0	1	0	0	0	4937	1115	39	1	530	1	EEF1D	8	144663283	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	831534	144663283	1700739	110	25438										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144663457	144663457	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atccggacgacgagctcaccGtggtctccgctggtgccgct	13	15	2	0	rs370722668		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:144663457G>A	ENST00000529272.1	-	4	631	c.231C>T	c.(229-231)caC>caT	p.H77H	EEF1D_ENST00000526838.1_Splice_Site_p.H77H|EEF1D_ENST00000442189.2_Silent_p.H443H|NAPRT1_ENST00000426292.3_5'Flank|NAPRT1_ENST00000449291.2_5'Flank|NAPRT1_ENST00000435154.3_5'Flank|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000423316.2_Silent_p.H443H|EEF1D_ENST00000532741.1_Silent_p.H493H|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000528610.1_Silent_p.H53H|EEF1D_ENST00000419152.2_Silent_p.H77H|EEF1D_ENST00000524624.1_Silent_p.H53H|EEF1D_ENST00000317198.6_Silent_p.H77H|EEF1D_ENST00000531621.1_Splice_Site_p.H53H|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000395119.3_Silent_p.H77H			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	77					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CGAGCTCACCGTGGTCTCCGC	0.706																																																0			8											25	25	25					8																	144663457		2202	4293	6495	144734600	SO:0001819	synonymous_variant	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.231C>T	8.37:g.144663457G>A			144734600	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																				0.706	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		A	144663457	G	A	144663457	2	1	93	1	0	0	0	0	0	0	0	1	4937	1136	40	1		1	EEF1D	8	144663457	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	174	144663457	1700565	111	25439										
PARP10	84875	hgsc.bcm.edu	37	chr8	145057910	145057910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaggcccttcctcctccagcTcccgaggcagccagtcctcc	9	20	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr8:145057910T>C	ENST00000313028.7	-	8	1941	c.1847A>G	c.(1846-1848)gAg>gGg	p.E616G	PARP10_ENST00000533665.1_5'Flank|PARP10_ENST00000524918.1_Missense_Mutation_p.E607G|PARP10_ENST00000525773.1_Missense_Mutation_p.E628G	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	616	Glu-rich.				negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTCCTCCAGCTCCCGAGGCAG	0.687																																																0			8											17	16	16					8																	145057910		2155	4200	6355	145129898	SO:0001583	missense	84875			AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"Poly (ADP-ribose) polymerases"	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.1847A>G	8.37:g.145057910T>C	ENSP00000325618:p.Glu616Gly		145129898	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	T	9.032	0.987461	0.18889	.	.	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.12984	2.69;2.63;2.63	4.34	3.16	0.36331	.	0.000000	0.48286	D	0.000198	T	0.09158	0.0226	L	0.27053	0.805	0.31845	N	0.623006	B;B	0.12630	0.006;0.006	B;B	0.12837	0.008;0.008	T	0.06427	-1.0827	10	0.54805	T	0.06	.	6.6558	0.22986	0.0:0.1137:0.0:0.8863	.	628;616	E9PNI7;Q53GL7	.;PAR10_HUMAN	G	607;322;616;628	ENSP00000431620:E607G;ENSP00000325618:E616G;ENSP00000434776:E628G	ENSP00000325618:E616G	E	-	2	0	PARP10	145129898	0.000000	0.05858	0.315000	0.25238	0.101000	0.19017	-0.235000	0.09016	0.540000	0.28808	0.393000	0.25936	GAG		0.687	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		C	145057910	T	C	145057910	3	2	93	1	0	0	0	0	1	0	0	0	11486	1551	54	4	1246	4	PARP10	8	145057910	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	394453	145057910	1306112	112	25440										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5988413	5988413	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	accattatagattcaaaaacTccacttgtcaagcctgccaa	4	12	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:5988413T>C	ENST00000399933.3	-	2	725	c.726A>G	c.(724-726)ggA>ggG	p.G242G	KIAA2026_ENST00000381461.2_Silent_p.G242G	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	242										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ATTCAAAAACTCCACTTGTCA	0.398																																																0			9											111	109	109					9																	5988413		1889	4102	5991	5978413	SO:0001819	synonymous_variant	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.726A>G	9.37:g.5988413T>C			5978413	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																					0.398	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	5988413	T	C	5988413	2	2	93	1	0	0	0	0	0	0	0	1	8291	1538	54	4		4	KIAA2026	9	5988413	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10		5988413	135225018	113	25441										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8404560	8404560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctatagctgataggagaaccCgggaatgatcatatgcgatt	11	7	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:8404560C>T	ENST00000381196.4	-	33	4730	c.4187G>A	c.(4186-4188)cGg>cAg	p.R1396Q	PTPRD_ENST00000397611.3_Missense_Mutation_p.R986Q|PTPRD_ENST00000355233.5_Missense_Mutation_p.R990Q|PTPRD_ENST00000356435.5_Missense_Mutation_p.R1396Q|PTPRD_ENST00000397617.3_Missense_Mutation_p.R989Q|PTPRD_ENST00000540109.1_Missense_Mutation_p.R1396Q|PTPRD_ENST00000358503.5_Missense_Mutation_p.R1374Q|PTPRD_ENST00000537002.1_Missense_Mutation_p.R986Q|PTPRD_ENST00000397606.3_Missense_Mutation_p.R989Q|PTPRD_ENST00000360074.4_Missense_Mutation_p.R1383Q|PTPRD_ENST00000486161.1_Missense_Mutation_p.R989Q	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1396	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		TAGGAGAACCCGGGAATGATC	0.388										TSP Lung(15;0.13)																																						0			9											159	131	140					9																	8404560		2203	4300	6503	8394560	SO:0001583	missense	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4187G>A	9.37:g.8404560C>T	ENSP00000370593:p.Arg1396Gln		8394560	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	36	5.798171	0.96952	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.92	5.92	0.95590	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.84768	0.5545	H	0.98407	4.225	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.973;0.985;0.985;0.985;0.995;0.975;0.999;0.999;0.999	D	0.89990	0.4107	9	.	.	.	.	20.327	0.98704	0.0:1.0:0.0:0.0	.	989;980;989;990;986;986;1383;1396;1396	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	Q	1396;1396;1383;1374;990;989;986;986;867;1396;989;989	ENSP00000370593:R1396Q;ENSP00000348812:R1396Q;ENSP00000353187:R1383Q;ENSP00000351293:R1374Q;ENSP00000347373:R990Q;ENSP00000380741:R989Q;ENSP00000380735:R986Q;ENSP00000440515:R986Q;ENSP00000438164:R1396Q;ENSP00000417093:R989Q;ENSP00000380731:R989Q	.	R	-	2	0	PTPRD	8394560	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.770000	0.85390	2.794000	0.96219	0.650000	0.86243	CGG		0.388	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8404560	C	T	8404560	3	4	93	1	0	0	0	0	1	0	0	0	12836	652	23	1	1595	1	PTPRD	9	8404560	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	2416147	8404560	132808871	114	25442										
C9orf150	286343	hgsc.bcm.edu	37	chr9	12821518	12821518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagcagcctcagtggcagccTgtgcagtttgttggagagtc	14	10	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:12821518T>C	ENST00000319264.3	+	2	1141	c.446T>C	c.(445-447)cTg>cCg	p.L149P		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	152																	AGTGGCAGCCTGTGCAGTTTG	0.522																																																0			9											85	83	83					9																	12821518		2203	4300	6503	12811518	SO:0001583	missense	286343			AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"		"chromosome 9 open reading frame 150"	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.446T>C	9.37:g.12821518T>C	ENSP00000321026:p.Leu149Pro		12811518	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.247237	0.59103	.	.	ENSG00000153714	ENST00000319264	T	0.50813	0.73	5.59	5.59	0.84812	.	0.197315	0.32134	N	0.006530	T	0.62575	0.2439	L	0.48642	1.525	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.64905	-0.6297	10	0.66056	D	0.02	.	15.7718	0.78176	0.0:0.0:0.0:1.0	.	152	Q8IV03	CI150_HUMAN	P	149	ENSP00000321026:L149P	ENSP00000321026:L149P	L	+	2	0	C9orf150	12811518	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.986000	0.49370	2.130000	0.65690	0.460000	0.39030	CTG		0.522	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403		C	12821518	T	C	12821518	3	2	93	1	0	0	0	0	1	0	0	0	2468	1580	55	4	452	4	C9orf150	9	12821518	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	4416958	12821518	128391913	115	25443										
CER1	9350	hgsc.bcm.edu	37	chr9	14722340	14722340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atctatcggctggatgagggActgggtcccaggtgggaagg	18	7	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:14722340A>G	ENST00000380911.3	-	1	375	c.331T>C	c.(331-333)Tcc>Ccc	p.S111P		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	111					anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		TGGATGAGGGACTGGGTCCCA	0.502																																																0			9											66	69	68					9																	14722340		2203	4300	6503	14712340	SO:0001583	missense	23739			AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)", "cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.331T>C	9.37:g.14722340A>G	ENSP00000370297:p.Ser111Pro		14712340	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	37	CCDS6476.1	.	.	.	.	.	.	.	.	.	.	A	0.097	-1.158441	0.01686	.	.	ENSG00000147869	ENST00000380911	T	0.16597	2.33	4.29	1.35	0.21983	.	0.551296	0.17694	N	0.165150	T	0.07458	0.0188	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33904	-0.9850	10	0.30078	T	0.28	-0.0883	7.2036	0.25895	0.3521:0.368:0.2799:0.0	.	111	O95813	CER1_HUMAN	P	111	ENSP00000370297:S111P	ENSP00000370297:S111P	S	-	1	0	CER1	14712340	0.011000	0.17503	0.000000	0.03702	0.001000	0.01503	0.722000	0.25925	0.309000	0.22966	-1.642000	0.00770	TCC		0.502	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454		G	14722340	A	G	14722340	3	3	93	1	0	0	0	0	1	0	0	0	3271	275	10	4	480	4	CER1	9	14722340	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1900822	14722340	126491091	116	25444										
FREM1	158326	hgsc.bcm.edu	37	chr9	14805124	14805124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cacatagttaatgtgaaaagCgttcatgtctttccactgaa	7	8	2	2	rs369918312		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:14805124C>T	ENST00000380880.3	-	19	4084	c.3301G>A	c.(3301-3303)Gct>Act	p.A1101T	FREM1_ENST00000422223.2_Missense_Mutation_p.A1101T|FREM1_ENST00000380881.4_Missense_Mutation_p.A1102T			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1101					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATGTGAAAAGCGTTCATGTCT	0.413																																																0			9						C	THR/ALA	0,3842		0,0,1921	146	138	140		3301	3.5	1	9		140	1,8275		0,1,4137	no	missense	FREM1	NM_144966.5	58	0,1,6058	TT,TC,CC		0.0121,0.0,0.0083	benign	1101/2180	14805124	1,12117	1921	4138	6059	14795124	SO:0001583	missense	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3301G>A	9.37:g.14805124C>T	ENSP00000370262:p.Ala1101Thr		14795124	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.424773	0.43020	0.0	1.21E-4	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.30182	1.54;1.54;1.54	5.42	3.55	0.40652	.	0.227951	0.44285	D	0.000469	T	0.18257	0.0438	L	0.45352	1.415	0.38638	D	0.95153	P	0.43607	0.812	B	0.30401	0.115	T	0.09885	-1.0654	10	0.22109	T	0.4	-7.9858	8.1751	0.31276	0.28:0.6486:0.0:0.0714	.	1101	Q5H8C1	FREM1_HUMAN	T	1102;1101;1101	ENSP00000370263:A1102T;ENSP00000412940:A1101T;ENSP00000370262:A1101T	ENSP00000370257:A1104T	A	-	1	0	FREM1	14795124	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	1.210000	0.32370	0.639000	0.30564	0.650000	0.86243	GCT		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14805124	C	T	14805124	3	4	93	1	0	0	0	0	1	0	0	0	6063	768	27	1	3364	1	FREM1	9	14805124	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	82784	14805124	126408307	117	25445										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20953057	20953057	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggcttcttcattacaggaggAaaaaaaggcaagtgagcaca	11	7	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:20953057A>G	ENST00000380249.1	+	37	4489	c.4125A>G	c.(4123-4125)ggA>ggG	p.G1375G	FOCAD_ENST00000605086.1_Silent_p.G811G|FOCAD_ENST00000338382.6_Silent_p.G1375G	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1375						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TTACAGGAGGAAAAAAAGGCA	0.368																																																0			9											113	111	112					9																	20953057		2203	4300	6503	20943057	SO:0001819	synonymous_variant	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4125A>G	9.37:g.20953057A>G			20943057	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																				0.368	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		G	20953057	A	G	20953057	2	3	93	1	0	0	0	0	0	0	0	1	8279	233	9	4		4	KIAA1797	9	20953057	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6147933	20953057	120260374	118	25446										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35396474	35396474	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctttctccctaccactagaGcatgagaaagaccacctgtg	7	14	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:35396474G>A	ENST00000378495.3	+	26	3285	c.3063G>A	c.(3061-3063)gaG>gaA	p.E1021E	UNC13B_ENST00000378496.4_Splice_Site_p.E1021E|UNC13B_ENST00000396787.1_Splice_Site_p.E1033E	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1021	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TACCACTAGAGCATGAGAAAG	0.537																																																0			9											93	77	83					9																	35396474		2203	4300	6503	35386474	SO:0001630	splice_region_variant	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3062-1G>A	9.37:g.35396474G>A			35386474	Q5VYM8	Silent	SNP	ENST00000378495.3	37	CCDS6579.1																																																																																				0.537	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	Silent	A	35396474	G	A	35396474	5	1	93	1	0	0	0	0	0	0	1	0	17025	985	34	3	3165	3	UNC13B	9	35396474	Splice_Site	SNP	G	TCGA-DC-5337-01A-01D-1657-10	14443417	35396474	105816957	119	25447										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73213399	73213399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgccgaagatgtctaggagaCggatataccagtaaatgatg	12	7	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:73213399C>T	ENST00000377111.2	-	20	3191	c.2948G>A	c.(2947-2949)cGt>cAt	p.R983H	TRPM3_ENST00000377105.1_Missense_Mutation_p.R842H|TRPM3_ENST00000377110.3_Missense_Mutation_p.R983H|TRPM3_ENST00000396280.5_Missense_Mutation_p.R832H|TRPM3_ENST00000360823.2_Missense_Mutation_p.R845H|TRPM3_ENST00000408909.2_Missense_Mutation_p.R842H|TRPM3_ENST00000358082.3_Missense_Mutation_p.R845H|TRPM3_ENST00000357533.2_Missense_Mutation_p.R987H|TRPM3_ENST00000396285.1_Missense_Mutation_p.R830H|TRPM3_ENST00000423814.3_Missense_Mutation_p.R1010H|TRPM3_ENST00000377106.1_Missense_Mutation_p.R855H|TRPM3_ENST00000396292.4_Missense_Mutation_p.R855H	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1008					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GTCTAGGAGACGGATATACCA	0.448																																																0			9											132	129	130					9																	73213399		2203	4300	6503	72403219	SO:0001583	missense	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2948G>A	9.37:g.73213399C>T	ENSP00000366315:p.Arg983His		72403219	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	C	24.1	4.497307	0.85069	.	.	ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	D;D;D;D;D;D;D;D;D;D;D	0.99591	-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24	4.87	3.97	0.46021	.	0.000000	0.85682	D	0.000000	D	0.99569	0.9845	M	0.85859	2.78	0.49798	D	0.999822	D;D;D;D;P;B;D;P	0.89917	1.0;0.993;1.0;0.998;0.75;0.152;0.999;0.862	D;P;D;D;B;B;P;P	0.91635	0.997;0.809;0.999;0.949;0.386;0.056;0.837;0.581	D	0.98216	1.0475	10	0.66056	D	0.02	-7.615	13.3904	0.60821	0.0:0.923:0.0:0.077	.	983;983;973;987;845;842;955;830	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.;.	H	983;983;855;845;842;987;842;830;855;845;1010	ENSP00000366315:R983H;ENSP00000366314:R983H;ENSP00000366310:R855H;ENSP00000354066:R845H;ENSP00000366309:R842H;ENSP00000350140:R987H;ENSP00000386127:R842H;ENSP00000379581:R830H;ENSP00000379587:R855H;ENSP00000350791:R845H;ENSP00000389542:R1010H	ENSP00000350140:R987H	R	-	2	0	TRPM3	72403219	1.000000	0.71417	0.992000	0.48379	0.962000	0.63368	7.810000	0.86072	1.178000	0.42870	0.573000	0.79308	CGT		0.448	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73213399	C	T	73213399	3	4	93	1	0	0	0	0	1	0	0	0	16627	536	19	1	2199	1	TRPM3	9	73213399	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	37816925	73213399	68000032	120	25448										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87635212	87635212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggaaagcgacgtctggagccTgggggtcgtgttgtgggaga	20	6	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:87635212T>C	ENST00000323115.4	+	16	2569	c.2216T>C	c.(2215-2217)cTg>cCg	p.L739P	NTRK2_ENST00000376214.1_Missense_Mutation_p.L755P|NTRK2_ENST00000376213.1_Missense_Mutation_p.L739P|NTRK2_ENST00000277120.3_Missense_Mutation_p.L755P			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	739	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	GTCTGGAGCCTGGGGGTCGTG	0.562										TSP Lung(25;0.17)																																						0			9											137	127	130					9																	87635212		2203	4300	6503	86825032	SO:0001583	missense	4915			AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.2216T>C	9.37:g.87635212T>C	ENSP00000314586:p.Leu739Pro		86825032	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	37	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	T	31	5.090520	0.94149	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000277120;ENST00000323115	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	6.17	6.17	0.99709	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92374	0.7580	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.93373	0.6737	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	739;755	Q16620;Q16620-4	NTRK2_HUMAN;.	P	755;739;755;739	ENSP00000365387:L755P;ENSP00000365386:L739P;ENSP00000277120:L755P;ENSP00000314586:L739P	ENSP00000277120:L755P	L	+	2	0	NTRK2	86825032	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.033000	0.88852	2.371000	0.80710	0.533000	0.62120	CTG		0.562	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			C	87635212	T	C	87635212	3	2	93	1	0	0	0	0	1	0	0	0	10738	1580	55	4	2405	4	NTRK2	9	87635212	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	14421813	87635212	53578219	121	25449										
ROR2	4920	hgsc.bcm.edu	37	chr9	94495608	94495608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagctcacgcggcttgggtgTccgggagcgcgcgtcgcaca	16	14	1	0	rs10820900	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:94495608T>C	ENST00000375708.3	-	6	931	c.733A>G	c.(733-735)Aca>Gca	p.T245A	ROR2_ENST00000375715.1_Missense_Mutation_p.T105A|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	245	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		T -> A (in dbSNP:rs10820900). {ECO:0000269|PubMed:10700182, ECO:0000269|PubMed:10986040, ECO:0000269|PubMed:1334494, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.3}.		cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GGCTTGGGTGTCCGGGAGCGC	0.647													C|||	3230	0.644968	0.7587	0.5159	5008	,	,		11431	0.5268		0.659	False		,,,				2504	0.6902															0			9						C	ALA/THR	3275,1131	391.0+/-327.9	1215,845,143	41	39	39		733	3.5	1	9	dbSNP_120	39	5554,3046	459.5+/-364.9	1804,1946,550	yes	missense	ROR2	NM_004560.3	58	3019,2791,693	CC,CT,TT		35.4186,25.6695,32.1159	benign	245/944	94495608	8829,4177	2203	4300	6503	93535429	SO:0001583	missense	6095			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.733A>G	9.37:g.94495608T>C	ENSP00000364860:p.Thr245Ala		93535429	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	1366	0.6254578754578755	384	0.7804878048780488	192	0.5303867403314917	291	0.5087412587412588	499	0.658311345646438	C	5.817	0.334936	0.11013	0.743305	0.645814	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.74947	-0.89;-0.89	4.44	3.45	0.39498	Frizzled domain (2);Kringle (1);	0.182670	0.26334	N	0.024971	T	0.00012	0.0000	N	0.16656	0.425	0.52501	P	4.300000000001525E-5	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.45542	-0.9254	9	0.02654	T	1	.	4.1846	0.10392	0.0:0.5303:0.0:0.4697	rs10820900;rs10820900	245;105	Q01974;B1APY4	ROR2_HUMAN;.	A	105;245	ENSP00000364867:T105A;ENSP00000364860:T245A	ENSP00000364860:T245A	T	-	1	0	ROR2	93535429	0.000000	0.05858	0.998000	0.56505	0.714000	0.41099	0.861000	0.27885	1.109000	0.41680	-0.215000	0.12644	ACA		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			C	94495608	T	C	94495608	3	2	93	1	0	0	0	0	1	0	0	0	13564	1667	58	4	2114	4	ROR2	9	94495608	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6860396	94495608	46717823	122	25450										
FAM120A	23196	hgsc.bcm.edu	37	chr9	96318751	96318751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgtttgcaaatgatgcatgcGgacagccaatcccctgggaa	11	10	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:96318751G>A	ENST00000277165.6	+	13	2556	c.2362G>A	c.(2362-2364)Gga>Aga	p.G788R	FAM120A_ENST00000333936.5_Missense_Mutation_p.G816R|FAM120A_ENST00000340893.4_Missense_Mutation_p.G788R	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	788						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TGATGCATGCGGACAGCCAAT	0.468																																																0			9											187	185	186					9																	96318751		2203	4300	6503	95358572	SO:0001583	missense	23196			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.2362G>A	9.37:g.96318751G>A	ENSP00000277165:p.Gly788Arg		95358572	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	G	34	5.371218	0.95923	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.74921	0.3780	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.75900	-0.3154	10	0.87932	D	0	-15.5675	20.3214	0.98679	0.0:0.0:1.0:0.0	.	788;816;788	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	R	788;816;788;210	ENSP00000277165:G788R;ENSP00000334918:G816R;ENSP00000344698:G788R;ENSP00000412440:G210R	ENSP00000277165:G788R	G	+	1	0	FAM120A	95358572	1.000000	0.71417	0.975000	0.42487	0.987000	0.75469	9.772000	0.98984	2.804000	0.96469	0.655000	0.94253	GGA		0.468	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		A	96318751	G	A	96318751	3	1	93	1	0	0	0	0	1	0	0	0	5431	1117	39	1	2412	1	FAM120A	9	96318751	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1823143	96318751	44894680	123	25451										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98220497	98220497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tccttactttttcaattgccTccacaaagtctgaggtgtcc	6	12	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:98220497T>C	ENST00000331920.6	-	18	3265	c.2966A>G	c.(2965-2967)gAg>gGg	p.E989G	PTCH1_ENST00000418258.1_Missense_Mutation_p.E838G|PTCH1_ENST00000437951.1_Missense_Mutation_p.E923G|PTCH1_ENST00000421141.1_Missense_Mutation_p.E838G|PTCH1_ENST00000430669.2_Missense_Mutation_p.E923G|PTCH1_ENST00000375274.2_Missense_Mutation_p.E988G|PTCH1_ENST00000429896.2_Missense_Mutation_p.E838G	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	989					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.I963fs*2(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TTCAATTGCCTCCACAAAGTC	0.557																																																1	Deletion - Frameshift(1)	central_nervous_system(1)	9											58	50	53					9																	98220497		2203	4300	6503	97260318	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2966A>G	9.37:g.98220497T>C	ENSP00000332353:p.Glu989Gly		97260318	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429110	0.83667	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	5.74	5.74	0.90152	.	0.044263	0.85682	D	0.000000	D	0.88407	0.6428	L	0.56199	1.76	0.80722	D	1	P;D;P	0.54601	0.941;0.967;0.943	P;P;P	0.55222	0.66;0.692;0.771	D	0.88829	0.3304	10	0.54805	T	0.06	-22.187	16.3305	0.83010	0.0:0.0:0.0:1.0	.	923;988;989	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	G	989;923;838;838;425;923;838;988	ENSP00000332353:E989G;ENSP00000389744:E923G;ENSP00000399981:E838G;ENSP00000396135:E838G;ENSP00000410287:E923G;ENSP00000414823:E838G;ENSP00000364423:E988G	ENSP00000332353:E989G	E	-	2	0	PTCH1	97260318	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	7.655000	0.83696	2.317000	0.78254	0.459000	0.35465	GAG		0.557	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98220497	T	C	98220497	3	2	93	1	0	0	0	0	1	0	0	0	12764	1551	54	4	1401	4	PTCH1	9	98220497	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1901746	98220497	42992934	124	25452										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100090391	100090391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caactcctacagctctgcccTcagccaatacttctttgtgc	5	16	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:100090391T>C	ENST00000357054.1	+	30	3235	c.2300T>C	c.(2299-2301)cTc>cCc	p.L767P	CCDC180_ENST00000411667.2_Missense_Mutation_p.L625P|CCDC180_ENST00000375202.2_Missense_Mutation_p.L628P|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.L628P			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	767						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AGCTCTGCCCTCAGCCAATAC	0.483																																																0			9											168	148	155					9																	100090391		2203	4300	6503	99130212	SO:0001583	missense	0			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2300T>C	9.37:g.100090391T>C	ENSP00000349562:p.Leu767Pro		99130212	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	T	13.00	2.105240	0.37145	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.18	5.18	0.71444	.	0.000000	0.56097	D	0.000033	T	0.57577	0.2063	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.56805	-0.7918	10	0.36615	T	0.2	-17.1407	11.9967	0.53208	0.0:0.0:0.0:1.0	.	625;767;628;767	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	P	767;628;625;651;628	ENSP00000349562:L767P;ENSP00000364348:L628P;ENSP00000414000:L625P;ENSP00000434727:L628P	ENSP00000349562:L767P	L	+	2	0	C9orf174	99130212	0.997000	0.39634	1.000000	0.80357	0.263000	0.26337	3.928000	0.56506	2.269000	0.75478	0.533000	0.62120	CTC		0.483	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		C	100090391	T	C	100090391	3	2	93	1	0	0	0	0	1	0	0	0	8261	1551	54	4	2374	4	KIAA1529	9	100090391	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1869894	100090391	41123040	125	25453										
RGS3	5998	hgsc.bcm.edu	37	chr9	116224396	116224396	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggatggagtggctaagcccTgatatcgctctgcccagaag	13	10	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:116224396T>C	ENST00000374140.2	+	4	539	c.330T>C	c.(328-330)ccT>ccC	p.P110P	RGS3_ENST00000350696.5_Silent_p.P110P|RGS3_ENST00000317613.6_5'Flank	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	110					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGCTAAGCCCTGATATCGCTC	0.552																																																0			9											115	116	116					9																	116224396		2108	4227	6335	115264217	SO:0001819	synonymous_variant	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.330T>C	9.37:g.116224396T>C			115264217	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																				0.552	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		C	116224396	T	C	116224396	2	2	93	1	0	0	0	0	0	0	0	1	13343	1567	55	4		4	RGS3	9	116224396	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	16134005	116224396	24989035	126	25454										
AK1	203	hgsc.bcm.edu	37	chr9	130630695	130630695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tttgatggtctcctcattgtCgtccacacgcccgctggtct	9	14	3	1	rs387906582		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:130630695C>T	ENST00000373176.1	-	6	573	c.421G>A	c.(421-423)Gac>Aac	p.D141N	AK1_ENST00000223836.10_Missense_Mutation_p.D157N|RP11-203J24.9_ENST00000476274.2_RNA|MIR4672_ENST00000583126.1_RNA|AK1_ENST00000373156.1_Missense_Mutation_p.D141N	NM_000476.2	NP_000467.1			adenylate kinase 1											endometrium(1)|prostate(1)	2						TCCTCATTGTCGTCCACACGC	0.567																																																0			9											92	68	76					9																	130630695		2203	4300	6503	129670516	SO:0001583	missense	203			J04809	CCDS6881.1	9q34.1	2008-02-05			ENSG00000106992	ENSG00000106992	2.7.4.3	"Adenylate kinases"	361	protein-coding gene	gene with protein product		103000					Standard	NM_000476		Approved		uc004bsm.4	P00568	OTTHUMG00000020722	ENST00000373176.1:c.421G>A	9.37:g.130630695C>T	ENSP00000362271:p.Asp141Asn		129670516		Missense_Mutation	SNP	ENST00000373176.1	37	CCDS6881.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.587369	0.86851	.	.	ENSG00000106992	ENST00000373176;ENST00000373156;ENST00000223836	D;D;D	0.87179	-2.22;-2.22;-2.22	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.96938	0.9000	H	0.99842	4.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99218	1.0878	10	0.87932	D	0	-14.3136	16.8189	0.85740	0.0:1.0:0.0:0.0	.	141	P00568	KAD1_HUMAN	N	141;141;157	ENSP00000362271:D141N;ENSP00000362249:D141N;ENSP00000223836:D157N	ENSP00000223836:D157N	D	-	1	0	AK1	129670516	1.000000	0.71417	0.993000	0.49108	0.493000	0.33554	5.693000	0.68264	2.301000	0.77427	0.561000	0.74099	GAC		0.567	AK1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054307.1			T	130630695	C	T	130630695	3	4	93	1	0	0	0	0	1	0	0	0	439	884	31	1	171	1	AK1	9	130630695	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	14406299	130630695	10582736	127	25455										
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011365	138011365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cacaggtgtggtacatggacGgctatcacaacaaccgcttc	10	12	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:138011365G>A	ENST00000371793.3	+	6	1050	c.799G>A	c.(799-801)Ggc>Agc	p.G267S	OLFM1_ENST00000371796.3_Missense_Mutation_p.G240S|OLFM1_ENST00000252854.4_Missense_Mutation_p.G249S	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	267	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		GTACATGGACGGCTATCACAA	0.547																																																0			9											113	100	104					9																	138011365		2203	4300	6503	137151186	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.799G>A	9.37:g.138011365G>A	ENSP00000360858:p.Gly267Ser		137151186	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	G	11.91	1.778618	0.31502	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793;ENST00000539877	D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46	5.07	5.07	0.68467	Olfactomedin-like (3);	0.048847	0.85682	D	0.000000	T	0.79868	0.4520	L	0.38531	1.155	0.58432	D	0.999999	B;B	0.34290	0.447;0.115	B;B	0.27887	0.082;0.084	T	0.75671	-0.3237	10	0.15499	T	0.54	.	9.7722	0.40595	0.1293:0.0:0.8707:0.0	.	267;249	Q99784;Q6IMJ8	NOE1_HUMAN;.	S	249;240;267;164	ENSP00000252854:G249S;ENSP00000360861:G240S;ENSP00000360858:G267S;ENSP00000443806:G164S	ENSP00000252854:G249S	G	+	1	0	OLFM1	137151186	1.000000	0.71417	0.997000	0.53966	0.902000	0.53008	6.271000	0.72569	2.357000	0.79964	0.561000	0.74099	GGC		0.547	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		A	138011365	G	A	138011365	3	1	93	1	0	0	0	0	1	0	0	0	10883	1116	39	1	777	1	OLFM1	9	138011365	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	7380670	138011365	3202066	128	25456										
NOXA1	10811	hgsc.bcm.edu	37	chr9	140322556	140322556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccacgctgccatcgactacaCgcagctgggcctgcggttca	11	16	1	0	rs145080773		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr9:140322556C>T	ENST00000341349.2	+	3	512	c.332C>T	c.(331-333)aCg>aTg	p.T111M	NOXA1_ENST00000392815.2_Missense_Mutation_p.T111M	NM_001256067.1|NM_006647.1	NP_001242996.1|NP_006638.1	Q86UR1	NOXA1_HUMAN	NADPH oxidase activator 1	111	Mediates interaction with RAC1.				positive regulation of catalytic activity (GO:0043085)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|Rac GTPase binding (GO:0048365)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|large_intestine(2)|lung(2)|skin(3)|upper_aerodigestive_tract(1)	9	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000238)|Epithelial(140;0.000982)		ATCGACTACACGCAGCTGGGC	0.687																																																0			9							MET/THR	1,4339		0,1,2169	20	16	18		332	2.1	0.8	9	dbSNP_134	18	2,8554		0,2,4276	no	missense	NOXA1	NM_006647.1	81	0,3,6445	TT,TC,CC		0.0234,0.023,0.0233	probably-damaging	111/484	140322556	3,12893	2170	4278	6448	139442377	SO:0001583	missense	10811			AF039697	CCDS7042.1, CCDS59157.1	9q34.3	2013-09-20	2002-12-09	2002-12-13	ENSG00000188747	ENSG00000188747			10668	protein-coding gene	gene with protein product		611255	"serologically defined colon cancer antigen 31"	SDCCAG31		9610721	Standard	NM_001256067		Approved	NY-CO-31, FLJ25475	uc004cmu.3	Q86UR1	OTTHUMG00000131781	ENST00000341349.2:c.332C>T	9.37:g.140322556C>T	ENSP00000342848:p.Thr111Met		139442377	O60533|Q29VU9|Q29VV0|Q2TAM1|Q8IUS3	Missense_Mutation	SNP	ENST00000341349.2	37	CCDS7042.1	.	.	.	.	.	.	.	.	.	.	c	16.11	3.028763	0.54790	2.3E-4	2.34E-4	ENSG00000188747	ENST00000341349;ENST00000392815	T;T	0.66280	-0.2;1.17	4.32	2.1	0.27182	Tetratricopeptide-like helical (1);	0.263356	0.35495	N	0.003167	T	0.73048	0.3537	M	0.78916	2.43	0.24340	N	0.994965	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.967;0.95;0.977	T	0.61242	-0.7102	10	0.62326	D	0.03	.	5.2715	0.15627	0.3077:0.5067:0.1856:0.0	.	111;111;111	Q86UR1-3;Q86UR1;Q86UR1-2	.;NOXA1_HUMAN;.	M	111	ENSP00000342848:T111M;ENSP00000376562:T111M	ENSP00000342848:T111M	T	+	2	0	NOXA1	139442377	0.004000	0.15560	0.825000	0.32803	0.881000	0.50899	0.119000	0.15626	0.755000	0.32990	0.556000	0.70494	ACG		0.687	NOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254713.1			T	140322556	C	T	140322556	3	4	93	1	0	0	0	0	1	0	0	0	10591	536	19	1	342	1	NOXA1	9	140322556	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	2311191	140322556	890875	129	25457										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27311604	27311604	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttctttcttgtcatttttaaGaggttcttaaatctgcagga	7	6	5	1	rs535737907		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:27311604G>A	ENST00000376087.4	-	29	4263	c.4098C>T	c.(4096-4098)ctC>ctT	p.L1366L	ANKRD26_ENST00000376070.3_Silent_p.L923L|ANKRD26_ENST00000436985.2_Silent_p.L1382L	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1365					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCATTTTTAAGAGGTTCTTAA	0.254													G|||	1	0.000199681	8e-04	0	5008	,	,		14422	0		0	False		,,,				2504	0															0			10											48	48	48					10																	27311604		1778	4026	5804	27351610	SO:0001819	synonymous_variant	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4098C>T	10.37:g.27311604G>A			27351610	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	37	CCDS41499.1																																																																																				0.254	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27311604	G	A	27311604	2	1	93	1	0	0	0	0	0	0	0	1	654	929	33	3		3	ANKRD26	10	27311604	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10		27311604	108223143	130	25458										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28229554	28229554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	catgttttcatgagaagtctTcagcagccgagccaacagag	10	10	3	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:28229554T>C	ENST00000305242.5	-	13	2016	c.1924A>G	c.(1924-1926)Aag>Gag	p.K642E	ARMC4_ENST00000537576.1_Missense_Mutation_p.K334E|ARMC4_ENST00000545014.1_Missense_Mutation_p.K167E	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	642					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						TGAGAAGTCTTCAGCAGCCGA	0.522																																																0			10											109	94	99					10																	28229554		2203	4300	6503	28269560	SO:0001583	missense	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1924A>G	10.37:g.28229554T>C	ENSP00000306410:p.Lys642Glu		28269560	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811284	0.50527	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	T;T;T	0.66280	-0.2;-0.2;-0.2	5.39	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (2);	0.042785	0.85682	D	0.000000	T	0.66674	0.2813	L	0.52364	1.645	0.80722	D	1	P;P	0.45078	0.536;0.85	B;P	0.53722	0.398;0.733	T	0.64952	-0.6286	10	0.42905	T	0.14	-30.7743	11.5334	0.50624	0.0:0.0709:0.0:0.9291	.	167;642	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	E	334;642;167	ENSP00000443208:K334E;ENSP00000306410:K642E;ENSP00000441076:K167E	ENSP00000306410:K642E	K	-	1	0	ARMC4	28269560	1.000000	0.71417	0.998000	0.56505	0.108000	0.19459	7.702000	0.84576	0.968000	0.38212	0.533000	0.62120	AAG		0.522	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		C	28229554	T	C	28229554	3	2	93	1	0	0	0	0	1	0	0	0	954	1792	62	4	1242	4	ARMC4	10	28229554	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	917950	28229554	107305193	131	25459										
PTEN	5728	hgsc.bcm.edu	37	chr10	89690820	89690820	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tagttgtgctgaaagacattAtgacaccgccaaatttaatt	7	7	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:89690820A>G	ENST00000371953.3	+	4	1584	c.227A>G	c.(226-228)tAt>tGt	p.Y76C		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	76	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.Y76fs*1(12)|p.?(6)|p.R55fs*1(5)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y76del(2)|p.Y27fs*1(2)|p.H75_T78del(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GAAAGACATTATGACACCGCC	0.303		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	72	Whole gene deletion(37)|Deletion - Frameshift(26)|Unknown(6)|Deletion - In frame(3)	central_nervous_system(21)|prostate(17)|endometrium(7)|breast(6)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|stomach(1)|soft_tissue(1)|urinary_tract(1)	10											81	75	77					10																	89690820		2202	4295	6497	89680800	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.227A>G	10.37:g.89690820A>G	ENSP00000361021:p.Tyr76Cys		89680800	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.562909	0.86335	.	.	ENSG00000171862	ENST00000371953	D	0.98822	-5.16	5.62	5.62	0.85841	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99524	0.9830	H	0.98577	4.27	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97896	1.0300	9	.	.	.	-12.1246	16.1135	0.81278	1.0:0.0:0.0:0.0	.	76	P60484	PTEN_HUMAN	C	76	ENSP00000361021:Y76C	.	Y	+	2	0	PTEN	89680800	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.827000	0.92041	2.267000	0.75376	0.383000	0.25322	TAT		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89690820	A	G	89690820	3	3	93	1	0	0	0	0	1	0	0	0	12772	449	16	4	241	4	PTEN	10	89690820	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	61461266	89690820	45843927	132	25460										
PTEN	5728	hgsc.bcm.edu	37	chr10	89711972	89711972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agtggcactgttgtttcacaAgatgatgtttgaaactattc	9	6	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:89711972A>G	ENST00000371953.3	+	6	1947	c.590A>G	c.(589-591)aAg>aGg	p.K197R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	197	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(4)|p.G165fs*9(3)|p.Y27fs*1(2)|p.K197fs*2(1)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTGTTTCACAAGATGATGTTT	0.388		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Deletion - Frameshift(11)|Unknown(4)|Deletion - In frame(1)	prostate(16)|central_nervous_system(13)|skin(8)|lung(4)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											154	152	153					10																	89711972		2203	4300	6503	89701952	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.590A>G	10.37:g.89711972A>G	ENSP00000361021:p.Lys197Arg		89701952	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588954	0.66105	.	.	ENSG00000171862	ENST00000371953	D	0.85411	-1.98	5.85	5.85	0.93711	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.87629	0.6225	L	0.43152	1.355	0.80722	D	1	D	0.57257	0.979	P	0.57846	0.828	D	0.86619	0.1878	9	.	.	.	-2.989	16.2416	0.82411	1.0:0.0:0.0:0.0	.	197	P60484	PTEN_HUMAN	R	197	ENSP00000361021:K197R	.	K	+	2	0	PTEN	89701952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.862000	0.92283	2.241000	0.73720	0.477000	0.44152	AAG		0.388	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89711972	A	G	89711972	3	3	93	1	0	0	0	0	1	0	0	0	12772	72	3	4	612	4	PTEN	10	89711972	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	21152	89711972	45822775	133	25461										
PANK1	53354	hgsc.bcm.edu	37	chr10	91404388	91404388	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tttctccccgagtccatcctCctccgcagccggcatttctt	6	18	2	0	rs201927435	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:91404388C>T	ENST00000307534.4	-	1	827	c.672G>A	c.(670-672)agG>agA	p.R224R	PANK1_ENST00000371774.2_5'Flank|RP11-80H5.2_ENST00000451733.1_RNA|PANK1_ENST00000342512.3_5'Flank|RP11-80H5.6_ENST00000428166.1_lincRNA|PANK1_ENST00000488482.1_5'Flank|RP11-80H5.2_ENST00000454174.1_RNA|PANK1_ENST00000322191.6_5'Flank	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	224					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						AGTCCATCCTCCTCCGCAGCC	0.731													C|||	12	0.00239617	0	0.0043	5008	,	,		12183	0		0.0089	False		,,,				2504	0															0			10						C		10,4124		0,10,2057	7	8	8		672	4.9	1	10		8	115,8265		0,115,4075	yes	coding-synonymous	PANK1	NM_148977.2		0,125,6132	TT,TC,CC		1.3723,0.2419,0.9989		224/599	91404388	125,12389	2067	4190	6257	91394368	SO:0001819	synonymous_variant	53354			AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"pantothenate kinase"	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.672G>A	10.37:g.91404388C>T			91394368	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																				0.731	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	91404388	C	T	91404388	2	4	93	1	0	0	0	0	0	0	0	1	11447	854	30	3		3	PANK1	10	91404388	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1692416	91404388	44130359	134	25462										
UBTD1	80019	hgsc.bcm.edu	37	chr10	99329964	99329964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	catctactgcctgtcaccgcCggtgaacctgctgctggagc	11	15	2	1	rs146047099		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:99329964C>T	ENST00000370664.3	+	3	704	c.368C>T	c.(367-369)cCg>cTg	p.P123L	ANKRD2_ENST00000298808.5_5'Flank|ANKRD2_ENST00000455090.1_5'Flank|ANKRD2_ENST00000307518.5_5'Flank|ANKRD2_ENST00000370655.1_5'Flank	NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	123										central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		CTGTCACCGCCGGTGAACCTG	0.652																																					Pancreas(100;169 2668 32720)											0			10						C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	64	72	69		368	5.3	0.4	10	dbSNP_134	69	0,8600		0,0,4300	no	missense	UBTD1	NM_024954.3	98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	123/228	99329964	1,13005	2203	4300	6503	99319954	SO:0001583	missense	80019			BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886			25683	protein-coding gene	gene with protein product						12477932	Standard	NM_024954		Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.368C>T	10.37:g.99329964C>T	ENSP00000359698:p.Pro123Leu		99319954	D3DR57|Q53HI3	Missense_Mutation	SNP	ENST00000370664.3	37	CCDS7465.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.439660	0.63067	2.27E-4	0.0	ENSG00000165886	ENST00000370664	D	0.86769	-2.17	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.94928	0.8360	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95507	0.8582	10	0.87932	D	0	-20.7268	19.0508	0.93043	0.0:1.0:0.0:0.0	.	123	Q9HAC8	UBTD1_HUMAN	L	123	ENSP00000359698:P123L	ENSP00000359698:P123L	P	+	2	0	UBTD1	99319954	1.000000	0.71417	0.385000	0.26158	0.010000	0.07245	7.818000	0.86416	2.687000	0.91594	0.655000	0.94253	CCG		0.652	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049701.1	NM_024954		T	99329964	C	T	99329964	3	4	93	1	0	0	0	0	1	0	0	0	16947	652	23	1	378	1	UBTD1	10	99329964	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	7925576	99329964	36204783	135	25463										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108432721	108432721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaccagctgccattcagagcGgtggctgaagtgtccaaaca	12	11	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:108432721G>A	ENST00000263054.6	-	15	1970	c.1963C>T	c.(1963-1965)Cgc>Tgc	p.R655C	SORCS1_ENST00000344440.6_Missense_Mutation_p.R655C|SORCS1_ENST00000369698.1_Missense_Mutation_p.R190C	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	655					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CATTCAGAGCGGTGGCTGAAG	0.438																																																0			10											65	53	57					10																	108432721		2203	4300	6503	108422711	SO:0001583	missense	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.1963C>T	10.37:g.108432721G>A	ENSP00000263054:p.Arg655Cys		108422711	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919886	0.92249	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.32515	1.45;1.45;1.45	5.56	5.56	0.83823	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.62612	0.2442	M	0.85630	2.765	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.996;0.998;0.996;0.996;0.998	T	0.65615	-0.6125	9	.	.	.	-14.4438	19.5164	0.95167	0.0:0.0:1.0:0.0	.	655;655;655;655;655	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	C	190;655;655	ENSP00000358712:R190C;ENSP00000263054:R655C;ENSP00000345964:R655C	.	R	-	1	0	SORCS1	108422711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.450000	0.97607	2.630000	0.89119	0.561000	0.74099	CGC		0.438	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108432721	G	A	108432721	3	1	93	1	0	0	0	0	1	0	0	0	14967	1116	39	1	1825	1	SORCS1	10	108432721	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	9102757	108432721	27102026	136	25464										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135012652	135012652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctctgtctgccctgcgtggaTgcctcgccactcccagggag	12	16	2	0	rs3008388	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr10:135012652T>C	ENST00000304613.3	+	14	2661	c.2640T>C	c.(2638-2640)gaT>gaC	p.D880D	KNDC1_ENST00000368572.2_Silent_p.D880D|KNDC1_ENST00000368571.2_Silent_p.D815D			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	880	Pro-rich.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCTGCGTGGATGCCTCGCCAC	0.687													C|||	2060	0.411342	0.1203	0.4049	5008	,	,		11469	0.6091		0.4384	False		,,,				2504	0.5777															0			10											9	9	9					10																	135012652		2159	4223	6382	134862642	SO:0001819	synonymous_variant	85442			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2640T>C	10.37:g.135012652T>C			134862642	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																				0.687	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		C	135012652	T	C	135012652	2	2	93	1	0	0	0	0	0	0	0	1	8447	1461	51	4		4	KNDC1	10	135012652	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	26579931	135012652	522095	137	25465										
ANO9	338440	hgsc.bcm.edu	37	chr11	428385	428385	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acaaagcttcagggccacgcAcctgttgatctgcggaggag	13	11	2	1	rs10794323	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:428385A>G	ENST00000332826.6	-	14	1279	c.1195T>C	c.(1195-1197)Tgc>Cgc	p.C399R		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	399			C -> R (in dbSNP:rs10794323). {ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						AGGGCCACGCACCTGTTGATC	0.682													g|||	4616	0.921725	0.9894	0.7464	5008	,	,		16428	0.996		0.832	False		,,,				2504	0.9703															0			11							ARG/CYS	4223,177	114.6+/-152.6	2028,167,5	30	34	33		1195	-8.9	0	11	dbSNP_120	33	6798,1782	317.8+/-313.4	2686,1426,178	yes	missense	ANO9	NM_001012302.2	180	4714,1593,183	GG,GA,AA		20.7692,4.0227,15.0924	benign	399/783	428385	11021,1959	2200	4290	6490	418385	SO:0001583	missense	338440			U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1195T>C	11.37:g.428385A>G	ENSP00000332788:p.Cys399Arg		418385	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	1956	0.8956043956043956	485	0.9857723577235772	267	0.7375690607734806	572	1.0	632	0.8337730870712401	G	1.290	-0.607879	0.03717	0.959773	0.792308	ENSG00000185101	ENST00000332826	T	0.61392	0.11	4.43	-8.87	0.00792	.	3.473430	0.00846	N	0.001795	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.34700	-0.9818	9	0.10636	T	0.68	.	2.2513	0.04044	0.197:0.0952:0.3631:0.3447	rs10794323;rs59985239;rs10794323	100;399	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	R	399	ENSP00000332788:C399R	ENSP00000332788:C399R	C	-	1	0	ANO9	418385	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.497000	0.00969	-2.020000	0.00940	-4.222000	0.00009	TGC		0.682	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		G	428385	A	G	428385	3	3	93	1	0	0	0	0	1	0	0	0	704	159	6	4	1193	4	ANO9	11	428385	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10		428385	134578131	138	25466										
CDHR5	53841	hgsc.bcm.edu	37	chr11	617420	617420	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctccccgcgccctcgccctcAtcgccgctgccggagtcact	9	22	2	0	rs61877857	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:617420A>G	ENST00000358353.3	-	16	2791	c.2469T>C	c.(2467-2469)gaT>gaC	p.D823D	CDHR5_ENST00000349570.7_Silent_p.D629D|IRF7_ENST00000397574.2_5'Flank|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000348655.6_5'Flank|CDHR5_ENST00000397542.2_Silent_p.D823D|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000330243.5_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	823					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CCTCGCCCTCATCGCCGCTGC	0.687													G|||	1385	0.276558	0.5855	0.3026	5008	,	,		11465	0.0208		0.2684	False		,,,				2504	0.1125															0			11						-	,,	2269,2129		587,1095,517	30	28	29		2451,2469,1887	-1.4	0	11	dbSNP_129	29	2475,6121		360,1755,2183	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	947,2850,2700	GG,GA,AA		28.7925,48.4084,36.5092	,,	817/840,823/846,629/652	617420	4744,8250	2199	4298	6497	607420	SO:0001819	synonymous_variant	0			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2469T>C	11.37:g.617420A>G			607420	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																				0.687	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		G	617420	A	G	617420	2	3	93	1	0	0	0	0	0	0	0	1	3128	214	8	4		4	CDHR5	11	617420	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	189035	617420	134389096	139	25467										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1271178	1271178	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acaatccacccctcctccacTccggagaccacccacacctc	3	23	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:1271178T>C	ENST00000529681.1	+	31	13126	c.13068T>C	c.(13066-13068)acT>acC	p.T4356T	MUC5B_ENST00000447027.1_Silent_p.T4359T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4356	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CCTCCTCCACTCCGGAGACCA	0.652																																																0			11											92	114	107					11																	1271178		2139	4228	6367	1227754	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13068T>C	11.37:g.1271178T>C			1227754	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1271178	T	C	1271178	2	2	93	1	0	0	0	0	0	0	0	1	10009	1538	54	4		4	MUC5B	11	1271178	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	653758	1271178	133735338	140	25468										
USP47	55031	hgsc.bcm.edu	37	chr11	11941794	11941794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	taagaagaagtgtgatgcacGgaaggtaaatgccatgtaga	13	4	0	4	rs374867647		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:11941794G>T	ENST00000399455.2	+	10	1241	c.1121G>T	c.(1120-1122)cGg>cTg	p.R374L	USP47_ENST00000339865.5_Missense_Mutation_p.R286L|USP47_ENST00000527733.1_Missense_Mutation_p.R354L|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	374	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)	p.R286Q(1)		breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TGTGATGCACGGAAGGTAAAT	0.373																																																1	Substitution - Missense(1)	skin(1)	11											118	108	111					11																	11941794		1839	4074	5913	11898370	SO:0001583	missense	55031			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1121G>T	11.37:g.11941794G>T	ENSP00000382382:p.Arg374Leu		11898370	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	G	19.53	3.844873	0.71603	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000535588	T;T;T	0.05081	3.5;3.5;3.5	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.04724	0.0128	N	0.04116	-0.275	0.80722	D	1	B;B	0.18968	0.032;0.026	B;B	0.22753	0.041;0.024	T	0.51764	-0.8664	10	0.40728	T	0.16	.	18.7283	0.91724	0.0:0.0:1.0:0.0	.	354;286	E9PM46;Q96K76-2	.;.	L	286;354;374;374	ENSP00000339957:R286L;ENSP00000433146:R354L;ENSP00000382382:R374L	ENSP00000339957:R286L	R	+	2	0	USP47	11898370	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.476000	0.97823	2.532000	0.85374	0.563000	0.77884	CGG		0.373	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		T	11941794	G	T	11941794	3	4	93	1	0	0	0	0	1	0	0	0	17118	1116	39	2	887	2	USP47	11	11941794	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	10670616	11941794	123064722	141	25469										
RCN1	5954	hgsc.bcm.edu	37	chr11	32118743	32118743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggctttgtcactactgaggAgctgaaaacctggatcaaac	10	9	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:32118743A>G	ENST00000054950.3	+	2	601	c.308A>G	c.(307-309)gAg>gGg	p.E103G	RCN1_ENST00000532942.1_Missense_Mutation_p.E52G|RP1-65P5.3_ENST00000533009.1_RNA	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	103	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					ACTACTGAGGAGCTGAAAACC	0.408																																																0			11											49	46	47					11																	32118743		2202	4299	6501	32075319	SO:0001583	missense	5954			D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"EF-hand domain containing"	9934	protein-coding gene	gene with protein product	"proliferation-inducing gene 20"	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.308A>G	11.37:g.32118743A>G	ENSP00000054950:p.Glu103Gly		32075319	B7Z1M1|D3DR00	Missense_Mutation	SNP	ENST00000054950.3	37	CCDS7876.1	.	.	.	.	.	.	.	.	.	.	a	20.3	3.964045	0.74131	.	.	ENSG00000049449	ENST00000532942;ENST00000054950;ENST00000400416	T;T	0.80393	-1.37;-1.37	5.03	5.03	0.67393	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92107	0.7498	H	0.94582	3.555	0.80722	D	1	D;D	0.67145	0.996;0.96	D;P	0.74674	0.984;0.859	D	0.94249	0.7492	10	0.87932	D	0	-24.4942	14.7623	0.69614	1.0:0.0:0.0:0.0	.	103;52	Q15293;B7Z1M1	RCN1_HUMAN;.	G	52;103;103	ENSP00000436422:E52G;ENSP00000054950:E103G	ENSP00000054950:E103G	E	+	2	0	RCN1	32075319	1.000000	0.71417	0.994000	0.49952	0.482000	0.33219	9.297000	0.96120	1.886000	0.54624	0.528000	0.53228	GAG		0.408	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901		G	32118743	A	G	32118743	3	3	93	1	0	0	0	0	1	0	0	0	13216	304	11	4	314	4	RCN1	11	32118743	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	20176949	32118743	102887773	142	25470										
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33065440	33065440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aagccttacaaaaagcaataAagtcagactcctccagcccc	5	14	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:33065440A>G	ENST00000334274.4	+	2	521	c.121A>G	c.(121-123)Aag>Gag	p.K41E	TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000432887.1_Missense_Mutation_p.K41E|TCP11L1_ENST00000531632.2_Missense_Mutation_p.K41E	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	41						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AAAAGCAATAAAGTCAGACTC	0.423																																																0			11											185	186	186					11																	33065440		2202	4298	6500	33022016	SO:0001583	missense	55346			BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.121A>G	11.37:g.33065440A>G	ENSP00000335595:p.Lys41Glu		33022016	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	A	9.445	1.088961	0.20390	.	.	ENSG00000176148	ENST00000530419;ENST00000334274;ENST00000531632;ENST00000432887;ENST00000528898	T;T;T;T	0.22336	1.96;2.97;2.97;2.97	5.5	2.94	0.34122	.	1.173460	0.06142	N	0.672587	T	0.22704	0.0548	L	0.57536	1.79	0.09310	N	0.999999	B	0.23442	0.085	B	0.19666	0.026	T	0.38672	-0.9650	10	0.13108	T	0.6	-6.0409	10.9222	0.47171	0.6282:0.3718:0.0:0.0	.	41	Q9NUJ3	T11L1_HUMAN	E	41	ENSP00000436428:K41E;ENSP00000335595:K41E;ENSP00000433067:K41E;ENSP00000395070:K41E	ENSP00000335595:K41E	K	+	1	0	TCP11L1	33022016	0.042000	0.20092	0.002000	0.10522	0.451000	0.32288	1.674000	0.37544	0.891000	0.36235	0.402000	0.26972	AAG		0.423	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		G	33065440	A	G	33065440	3	3	93	1	0	0	0	0	1	0	0	0	15753	15	1	4	123	4	TCP11L1	11	33065440	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	946697	33065440	101941076	143	25471										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45967427	45967427	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctgggcagggacacaggctgAacaggtgcagggaaagtgaa	17	7	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:45967427A>G	ENST00000418153.2	-	14	1612	c.1413T>C	c.(1411-1413)gtT>gtC	p.V471V	PHF21A_ENST00000527753.1_Intron|PHF21A_ENST00000257821.4_Silent_p.V472V|PHF21A_ENST00000323180.6_Intron			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	471					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						ACACAGGCTGAACAGGTGCAG	0.502																																																0			11											91	109	103					11																	45967427		2149	4262	6411	45924003	SO:0001819	synonymous_variant	51317			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1413T>C	11.37:g.45967427A>G			45924003	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1																																																																																				0.502	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		G	45967427	A	G	45967427	2	3	93	1	0	0	0	0	0	0	0	1	11864	233	9	4		4	PHF21A	11	45967427	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	12901987	45967427	89039089	144	25472										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46564857	46564857	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggaaattgtggaggagaggcGtccggcgaactggctgtgat	18	6	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:46564857G>A	ENST00000458649.2	-	7	1128	c.710C>T	c.(709-711)aCg>aTg	p.T237M	AMBRA1_ENST00000528950.1_Missense_Mutation_p.T237M|AMBRA1_ENST00000298834.3_Missense_Mutation_p.T237M|AMBRA1_ENST00000314845.3_Missense_Mutation_p.T237M|AMBRA1_ENST00000534300.1_Missense_Mutation_p.T237M|AMBRA1_ENST00000426438.1_Missense_Mutation_p.T237M|AMBRA1_ENST00000533727.1_Missense_Mutation_p.T237M			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	237					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GAGGAGAGGCGTCCGGCGAAC	0.567																																																0			11											104	83	90					11																	46564857		2201	4299	6500	46521433	SO:0001583	missense	55626			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.710C>T	11.37:g.46564857G>A	ENSP00000415327:p.Thr237Met		46521433	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	G	16.06	3.014914	0.54468	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.71461	-0.42;-0.57;-0.34;-0.47;-0.34;-0.47;-0.47	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.79435	0.4445	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.76071	0.972;0.987;0.987;0.982;0.987;0.982	T	0.80056	-0.1542	10	0.72032	D	0.01	.	20.3593	0.98849	0.0:0.0:1.0:0.0	.	237;237;237;237;237;237	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	M	237	ENSP00000318313:T237M;ENSP00000433372:T237M;ENSP00000431926:T237M;ENSP00000410899:T237M;ENSP00000298834:T237M;ENSP00000415327:T237M;ENSP00000433945:T237M	ENSP00000298834:T237M	T	-	2	0	AMBRA1	46521433	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	9.706000	0.98722	2.822000	0.97130	0.557000	0.71058	ACG		0.567	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		A	46564857	G	A	46564857	3	1	93	1	0	0	0	0	1	0	0	0	565	1145	40	1	2968	1	AMBRA1	11	46564857	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	597430	46564857	88441659	145	25473										
VWCE	220001	hgsc.bcm.edu	37	chr11	61040722	61040723	+	Frame_Shift_Ins	INS	-	-	C													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caacactgcccagggcccagINSccgccactcttctcgggggc							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:61040722_61040723insC	ENST00000335613.5	-	13	2033_2034	c.1647_1648insG	c.(1645-1650)cggctgfs	p.L550fs	VWCE_ENST00000535710.1_Frame_Shift_Ins_p.L15fs	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	550	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CCAGGGCCCAGCCGCCACTCTT	0.653																																																0			11																																								60797299	SO:0001589	frameshift_variant	220001			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1648dupG	11.37:g.61040724_61040724dupC	ENSP00000334186:p.Leu550fs		60797298	A5PKV0|Q7Z7L6|Q86WK8	Frame_Shift_Ins	INS	ENST00000335613.5	37	CCDS8002.1																																																																																				0.653	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		C	61040723	-	C	61040722	7	5	93	1	0	1	1	0	0	0	0	0	17285	962	34	0	1251	0	VWCE	11	61040722	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	14475865	61040722	73965794	146	25474										
VWCE	220001	hgsc.bcm.edu	37	chr11	61050287	61050287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggagtgccggttgccatgaAggtggaagccagttcgacag	16	8	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:61050287A>G	ENST00000335613.5	-	6	1018	c.632T>C	c.(631-633)cTt>cCt	p.L211P		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	211	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GTTGCCATGAAGGTGGAAGCC	0.567																																																0			11											300	256	271					11																	61050287		2203	4299	6502	60806863	SO:0001583	missense	220001			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.632T>C	11.37:g.61050287A>G	ENSP00000334186:p.Leu211Pro		60806863	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284398	0.80803	.	.	ENSG00000167992	ENST00000335613	D	0.91631	-2.88	5.5	5.5	0.81552	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.48767	D	0.000167	D	0.94198	0.8138	L	0.42632	1.34	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94828	0.7993	10	0.72032	D	0.01	.	15.2875	0.73838	1.0:0.0:0.0:0.0	.	211	Q96DN2	VWCE_HUMAN	P	211	ENSP00000334186:L211P	ENSP00000301770:L211P	L	-	2	0	VWCE	60806863	1.000000	0.71417	0.992000	0.48379	0.979000	0.70002	6.704000	0.74639	2.082000	0.62665	0.533000	0.62120	CTT		0.567	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		G	61050287	A	G	61050287	3	3	93	1	0	0	0	0	1	0	0	0	17285	72	3	4	2295	4	VWCE	11	61050287	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	9565	61050287	73956229	147	25475										
MEN1	4221	hgsc.bcm.edu	37	chr11	64571985	64571985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	catcttctcactctggaaagTgagcactggaccctccggcg	10	14	3	1	rs121913035		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:64571985T>C	ENST00000337652.1	-	10	2172	c.1669A>G	c.(1669-1671)Act>Gct	p.T557A	MEN1_ENST00000377316.2_Missense_Mutation_p.T497A|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000312049.6_Missense_Mutation_p.T552A|MEN1_ENST00000315422.4_Missense_Mutation_p.T552A|MEN1_ENST00000478548.1_5'UTR|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000394374.2_Missense_Mutation_p.T557A|MEN1_ENST00000377326.3_Missense_Mutation_p.T552A|MEN1_ENST00000394376.1_Missense_Mutation_p.T557A|MEN1_ENST00000443283.1_Missense_Mutation_p.T557A|MEN1_ENST00000377321.1_Missense_Mutation_p.T517A|MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000377313.1_Missense_Mutation_p.T557A	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	557			T -> S (in adrenal adenoma; somatic). {ECO:0000269|PubMed:10647896}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.T552S(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CTCTGGAAAGTGAGCACTGGA	0.617			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	adrenal_gland(1)	11											131	112	119					11																	64571985		2201	4297	6498	64328561	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1669A>G	11.37:g.64571985T>C	ENSP00000337088:p.Thr557Ala		64328561	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622022	0.46840	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313	D;D;D;D;D;D;D;D;D;D	0.99409	-5.85;-5.85;-5.85;-5.85;-5.85;-5.85;-5.85;-5.85;-5.85;-5.85	4.35	4.35	0.52113	.	0.302605	0.32041	N	0.006671	D	0.97517	0.9187	L	0.38175	1.15	0.33262	D	0.559896	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	D	0.99948	1.1492	10	0.18276	T	0.48	-5.9355	11.8603	0.52461	0.0:0.0:0.0:1.0	.	552;517;557	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	A	497;517;552;552;552;557;557;557;557;557	ENSP00000366533:T497A;ENSP00000366538:T517A;ENSP00000366543:T552A;ENSP00000308975:T552A;ENSP00000323747:T552A;ENSP00000337088:T557A;ENSP00000377901:T557A;ENSP00000377899:T557A;ENSP00000396940:T557A;ENSP00000366530:T557A	ENSP00000308975:T552A	T	-	1	0	MEN1	64328561	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.645000	0.37238	1.749000	0.51849	0.374000	0.22700	ACT		0.617	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			C	64571985	T	C	64571985	3	2	93	1	0	0	0	0	1	0	0	0	9502	1696	59	4	182	4	MEN1	11	64571985	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	3521698	64571985	70434531	148	25476										
SSSCA1	10534	hgsc.bcm.edu	37	chr11	65339171	65339171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccttatccgcgcatgtgcggAggccctgcgcagcctgcagc	13	16	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:65339171A>G	ENST00000309328.3	+	4	628	c.566A>G	c.(565-567)gAg>gGg	p.E189G	SSSCA1_ENST00000527920.1_Intron|FAM89B_ENST00000449319.2_5'Flank|FAM89B_ENST00000530349.1_5'Flank|SSSCA1-AS1_ENST00000567594.1_RNA|SSSCA1_ENST00000526877.1_3'UTR|SSSCA1_ENST00000531405.1_Missense_Mutation_p.E152G|FAM89B_ENST00000316409.2_5'Flank	NM_006396.1	NP_006387.1	O60232	SSA27_HUMAN	Sjogren syndrome/scleroderma autoantigen 1	189					mitotic nuclear division (GO:0007067)					kidney(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8						GCATGTGCGGAGGCCCTGCGC	0.562																																																0			11											32	27	29					11																	65339171		2201	4296	6497	65095747	SO:0001583	missense	10534			AB001740	CCDS8104.1	11q13.1	2007-10-04	2007-10-04			ENSG00000173465			11328	protein-coding gene	gene with protein product		606044	"Sjogren's syndrome/scleroderma autoantigen 1"			9486406	Standard	NM_006396		Approved	p27	uc001oek.3	O60232		ENST00000309328.3:c.566A>G	11.37:g.65339171A>G	ENSP00000312318:p.Glu189Gly		65095747		Missense_Mutation	SNP	ENST00000309328.3	37	CCDS8104.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.794149	0.70452	.	.	ENSG00000173465	ENST00000309328;ENST00000531405;ENST00000533115	T;T	0.54279	0.58;0.63	4.35	4.35	0.52113	.	0.257192	0.39759	N	0.001270	T	0.43590	0.1254	L	0.55481	1.735	0.80722	D	1	P	0.34662	0.462	B	0.23275	0.045	T	0.51379	-0.8713	10	0.72032	D	0.01	-15.081	11.55	0.50715	1.0:0.0:0.0:0.0	.	189	O60232	SSA27_HUMAN	G	189;152;183	ENSP00000312318:E189G;ENSP00000435432:E183G	ENSP00000312318:E189G	E	+	2	0	SSSCA1	65095747	1.000000	0.71417	0.976000	0.42696	0.881000	0.50899	5.674000	0.68117	1.838000	0.53458	0.459000	0.35465	GAG		0.562	SSSCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389511.1	NM_006396		G	65339171	A	G	65339171	3	3	93	1	0	0	0	0	1	0	0	0	15234	304	11	4	580	4	SSSCA1	11	65339171	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	767186	65339171	69667345	149	25477										
ATM	472	hgsc.bcm.edu	37	chr11	108180981	108180981	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agtcttgtgctgctcactttAcagctttactctatgcagaa	7	10	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:108180981A>G	ENST00000452508.2	+	40	6046	c.5857A>G	c.(5857-5859)Aca>Gca	p.T1953A	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.T1953A			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1953			T -> R (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10397742}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.T1953A(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGCTCACTTTACAGCTTTACT	0.328			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											83	85	85					11																	108180981		2201	4298	6499	107686191	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5857A>G	11.37:g.108180981A>G	ENSP00000388058:p.Thr1953Ala		107686191	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889566	0.91889	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.77358	-1.09;-1.09	5.7	5.7	0.88788	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.88153	0.2852	10	0.46703	T	0.11	.	15.9668	0.79979	1.0:0.0:0.0:0.0	.	605;1953	E9PFP9;Q13315	.;ATM_HUMAN	A	1953	ENSP00000278616:T1953A;ENSP00000388058:T1953A	ENSP00000278616:T1953A	T	+	1	0	ATM	107686191	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.608000	0.90895	2.173000	0.68751	0.455000	0.32223	ACA		0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108180981	A	G	108180981	3	3	93	1	0	0	0	0	1	0	0	0	1110	391	14	4	6007	4	ATM	11	108180981	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	42841810	108180981	26825535	150	25478										
BSX	390259	hgsc.bcm.edu	37	chr11	122848537	122848537	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccgtctggtgctttgggttcGtcttggcttttccgcagttg	13	10	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr11:122848537G>A	ENST00000343035.2	-	3	570	c.522C>T	c.(520-522)gaC>gaT	p.D174D		NM_001098169.1	NP_001091639.1	Q3C1V8	BSH_HUMAN	brain-specific homeobox	174					eating behavior (GO:0042755)|locomotory behavior (GO:0007626)|mammary gland involution (GO:0060056)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D174D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	10		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)		CTTTGGGTTCGTCTTGGCTTT	0.592																																																1	Substitution - coding silent(1)	large_intestine(1)	11											63	64	64					11																	122848537		1893	4127	6020	122353747	SO:0001819	synonymous_variant	390259				CCDS41728.1	11q24.1	2011-07-19			ENSG00000188909	ENSG00000188909		"Homeoboxes / ANTP class : NKL subclass"	20450	protein-coding gene	gene with protein product		611074					Standard	NM_001098169		Approved	BSX1	uc010rzs.2	Q3C1V8	OTTHUMG00000150247	ENST00000343035.2:c.522C>T	11.37:g.122848537G>A			122353747		Silent	SNP	ENST00000343035.2	37	CCDS41728.1																																																																																				0.592	BSX-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317076.1	NM_001098169		A	122848537	G	A	122848537	2	1	93	1	0	0	0	0	0	0	0	1	1538	1136	40	1		1	BSX	11	122848537	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	14667556	122848537	12157979	151	25479										
KDM5A	5927	hgsc.bcm.edu	37	chr12	394797	394797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaacttgatgaaaccactcaTcacagccaccatcacattgt	4	13	3	2	rs79230839		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:394797T>C	ENST00000399788.2	-	28	5260	c.4898A>G	c.(4897-4899)gAt>gGt	p.D1633G	KDM5A_ENST00000540838.1_5'UTR	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1633	Interaction with LMO2. {ECO:0000269|PubMed:9129143}.				chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						AAACCACTCATCACAGCCACC	0.403			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	0			12											119	112	114					12																	394797		2003	4175	6178	265058	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4898A>G	12.37:g.394797T>C	ENSP00000382688:p.Asp1633Gly		265058	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739468	0.69304	.	.	ENSG00000073614	ENST00000399788	T	0.63913	-0.07	5.09	5.09	0.68999	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.109676	0.64402	D	0.000014	T	0.49898	0.1584	L	0.37850	1.14	0.80722	D	1	P	0.46784	0.884	B	0.35114	0.196	T	0.57997	-0.7714	10	0.56958	D	0.05	-18.1611	15.166	0.72825	0.0:0.0:0.0:1.0	.	1633	P29375	KDM5A_HUMAN	G	1633	ENSP00000382688:D1633G	ENSP00000382688:D1633G	D	-	2	0	KDM5A	265058	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.049000	0.60858	0.460000	0.39030	GAT		0.403	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		C	394797	T	C	394797	3	2	93	1	0	0	0	0	1	0	0	0	8154	1435	50	4	178	4	KDM5A	12	394797	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10		394797	133457098	152	25480										
GYS2	2998	hgsc.bcm.edu	37	chr12	21693450	21693450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaaatccatagagaaacttaGtcagctgattgcaagaatca	7	7	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:21693450G>A	ENST00000261195.2	-	14	1957	c.1703C>T	c.(1702-1704)aCt>aTt	p.T568I		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	568					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GAGAAACTTAGTCAGCTGATT	0.428																																					Colon(149;9 1820 3690 10544 50424)											0			12											128	131	130					12																	21693450		2203	4300	6503	21584717	SO:0001583	missense	2998				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1703C>T	12.37:g.21693450G>A	ENSP00000261195:p.Thr568Ile		21584717	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.784949	0.90282	.	.	ENSG00000111713	ENST00000261195	T	0.66099	-0.19	5.1	5.1	0.69264	.	0.052363	0.85682	N	0.000000	T	0.76630	0.4014	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78513	-0.2175	10	0.87932	D	0	-15.1571	18.6922	0.91588	0.0:0.0:1.0:0.0	.	568	P54840	GYS2_HUMAN	I	568	ENSP00000261195:T568I	ENSP00000261195:T568I	T	-	2	0	GYS2	21584717	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	9.640000	0.98453	2.641000	0.89580	0.650000	0.86243	ACT		0.428	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		A	21693450	G	A	21693450	3	1	93	1	0	0	0	0	1	0	0	0	6934	1029	36	3	420	3	GYS2	12	21693450	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	21298653	21693450	112158445	153	25481										
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27809550	27809550	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgaatttgtaacttgtaggAtgaactggcatctttaaaag	9	4	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:27809550A>G	ENST00000318304.8	+	10	1074	c.791A>G	c.(790-792)gAt>gGt	p.D264G	PPFIBP1_ENST00000228425.6_Splice_Site_p.D233G|PPFIBP1_ENST00000542629.1_Splice_Site_p.D233G|PPFIBP1_ENST00000537927.1_Splice_Site_p.D111G	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	264					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AACTTGTAGGATGAACTGGCA	0.318																																																0			12											54	57	56					12																	27809550		2203	4299	6502	27700817	SO:0001630	splice_region_variant	8496			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.790-1A>G	12.37:g.27809550A>G			27700817	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.272027	0.40194	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	T;T;T;T;T;T	0.32515	2.1;1.47;1.45;1.87;2.1;1.9	5.05	5.05	0.67936	.	0.463445	0.15765	U	0.245738	T	0.30417	0.0764	L	0.36672	1.1	0.44117	D	0.996891	B;B;P;B	0.39920	0.101;0.43;0.695;0.411	B;B;B;B	0.42319	0.12;0.193;0.383;0.354	T	0.06463	-1.0825	10	0.52906	T	0.07	-5.6884	13.3332	0.60500	1.0:0.0:0.0:0.0	.	111;264;233;233	Q86W92-3;Q86W92;Q86W92-2;Q86W92-4	.;LIPB1_HUMAN;.;.	G	235;233;92;111;264;233;233	ENSP00000445822:D233G;ENSP00000444304:D92G;ENSP00000445425:D111G;ENSP00000314724:D264G;ENSP00000443442:D233G;ENSP00000228425:D233G	ENSP00000228425:D233G	D	+	2	0	PPFIBP1	27700817	1.000000	0.71417	0.977000	0.42913	0.812000	0.45895	6.463000	0.73530	2.022000	0.59522	0.533000	0.62120	GAT		0.318	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	Missense_Mutation	G	27809550	A	G	27809550	5	3	93	1	0	0	0	0	0	0	1	0	12344	347	12	4	766	4	PPFIBP1	12	27809550	Splice_Site	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6116100	27809550	106042345	154	25482										
IPO8	10526	hgsc.bcm.edu	37	chr12	30822191	30822192	+	Frame_Shift_Ins	INS	-	-	A													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atctttataacacatcacagINSaaaaaatcacatcttcagag							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:30822191_30822192insA	ENST00000256079.4	-	10	1407_1408	c.1069_1070insT	c.(1069-1071)tctfs	p.S357fs	IPO8_ENST00000544829.1_Frame_Shift_Ins_p.S152fs	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	357					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ACACATCACAGAAAAAATCACA	0.297																																																0			12																																								30713459	SO:0001589	frameshift_variant	10526			U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1070dupT	12.37:g.30822197_30822197dupA	ENSP00000256079:p.Ser357fs		30713458	B7Z7M3	Frame_Shift_Ins	INS	ENST00000256079.4	37	CCDS8719.1																																																																																				0.297	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		A	30822192	-	A	30822191	7	5	93	1	0	1	1	0	0	0	0	0	7819	942	33	0	2107	0	IPO8	12	30822191	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	3012641	30822191	103029704	155	25483										
DDX23	9416	hgsc.bcm.edu	37	chr12	49231064	49231065	+	Splice_Site	DNP	AG	AG	GT													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcaggcctgaagccactcacAgggggttgtagtcaatggat							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A|G	A|G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:49231064_49231065AG>GT	ENST00000308025.3	-	8	944_945	c.865_866CT>AC	c.(865-867)CTg>ACg	p.L289T	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	289					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						AGCCACTCACAGGGGGTTGTAG	0.505																																																0			12																																								47517331|47517332	SO:0001630	splice_region_variant	9416			AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.865_866delinsGT	12.37:g.49231064_49231065delinsGT			47517331|47517332	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1																																																																																				0.505	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818	Missense_Mutation	GT	49231065	AG	GT	49231064	5	3	93	1	0	0	0	0	0	0	1	0	4356	202	7	4	1636	4	DDX23	12	49231064	Splice_Site	DNP	AG	TCGA-DC-5337-01A-01D-1657-10	18408873	49231064	84620831	156	25484										
ITGB7	3695	hgsc.bcm.edu	37	chr12	53586991	53587029	+	In_Frame_Del	DEL	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	-													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcgcacagatgcccagagctCtgtccactgcagctgcagcg					rs61730604|rs201186200|rs371662481|rs112135194|rs367794294	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:53586991_53587029delCTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	ENST00000267082.5	-	12	1852_1890	c.1621_1659delGGTCACTGTCAATGTGGACGCTGCAGCTGCAGTGGACAG	c.(1621-1659)ggtcactgtcaatgtggacgctgcagctgcagtggacagdel	p.GHCQCGRCSCSGQ541del	ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_In_Frame_Del_p.GHCQCGRCSCSGQ541del|ITGB7_ENST00000550743.2_Intron	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	541	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCCAGAGCTCTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACCCTTTCCACTG	0.628																																																0			12																																								51873296	SO:0001651	inframe_deletion	3695				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1621_1659delGGTCACTGTCAATGTGGACGCTGCAGCTGCAGTGGACAG	12.37:g.53586991_53587029delCTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	ENSP00000267082:p.Gly541_Gln553del		51873258	Q9UCP7|Q9UCS7	In_Frame_Del	DEL	ENST00000267082.5	37	CCDS8849.1																																																																																				0.628	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			-	53587029	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	-	53586991	7	5	93	1	0	1	0	1	0	0	0	0	7921	912	32	0	757	0	ITGB7	12	53586991	In_Frame_Del	DEL	CTGTCCACTGCAGCTGCAGCGTCCACATTGACAGTGACC	TCGA-DC-5337-01A-01D-1657-10	4355927	53586991	80264904	157	25485	32	2								
ITGB7	3695	hgsc.bcm.edu	37	chr12	53586993	53586993	+	Missense_Mutation	SNP	G	G	T													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcacagatgcccagagctctGtccactgcagctgcagcgtc							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:53586993G>T	ENST00000267082.5	-	12	1888	c.1657C>A	c.(1657-1659)Cag>Aag	p.Q553K	ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_Missense_Mutation_p.Q553K|ITGB7_ENST00000550743.2_Intron	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	553	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCAGAGCTCTGTCCACTGCAG	0.632																																																0			12											59	53	55					12																	53586993		2203	4300	6503	51873260	SO:0001583	missense	3695				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1657C>A	12.37:g.53586993G>T	ENSP00000267082:p.Gln553Lys		51873260	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	G	9.650	1.141417	0.21205	.	.	ENSG00000139626	ENST00000422257;ENST00000267082	D;D	0.89810	-2.57;-2.57	4.59	4.59	0.56863	.	0.185362	0.26700	N	0.022950	T	0.74397	0.3711	N	0.04746	-0.17	0.80722	D	1	B	0.17038	0.02	B	0.14023	0.01	T	0.68743	-0.5328	10	0.17369	T	0.5	.	10.3408	0.43877	0.0917:0.0:0.9083:0.0	.	553	P26010	ITB7_HUMAN	K	553	ENSP00000408741:Q553K;ENSP00000267082:Q553K	ENSP00000267082:Q553K	Q	-	1	0	ITGB7	51873260	0.001000	0.12720	1.000000	0.80357	0.754000	0.42855	0.386000	0.20702	2.542000	0.85734	0.563000	0.77884	CAG		0.632	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			T	53586993	G	T	53586993	3	4	93	1	0	0	0	0	1	0	0	0	7921	1386	48	2	759	2	ITGB7	12	53586993	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	2	53586993	80264902	158	25486	32	2								
COPZ1	22818	hgsc.bcm.edu	37	chr12	54741610	54741610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggggctgttcttggctgtggAtgaaattgtagatggagggt	18	3	1	2	rs76187942		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:54741610A>G	ENST00000262061.2	+	6	414	c.377A>G	c.(376-378)gAt>gGt	p.D126G	COPZ1_ENST00000548281.1_3'UTR|RP11-968A15.8_ENST00000553061.1_RNA|RN7SL744P_ENST00000577604.1_RNA|COPZ1_ENST00000553231.1_Missense_Mutation_p.D103G|COPZ1_ENST00000455864.2_Missense_Mutation_p.D103G|COPZ1_ENST00000549116.1_Missense_Mutation_p.D68G|COPZ1_ENST00000549043.1_Missense_Mutation_p.D134G|COPZ1_ENST00000416254.2_Missense_Mutation_p.D75G|COPZ1_ENST00000552218.1_Missense_Mutation_p.D147G|COPZ1_ENST00000551779.1_Missense_Mutation_p.D126G|COPZ1_ENST00000552362.1_Missense_Mutation_p.D126G|COPZ1_ENST00000548753.1_Missense_Mutation_p.D38G	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1	126					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						TTGGCTGTGGATGAAATTGTA	0.498																																																0			12											207	203	205					12																	54741610		2203	4300	6503	53027877	SO:0001583	missense	22818			AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"coatomer protein complex, subunit zeta"	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.377A>G	12.37:g.54741610A>G	ENSP00000262061:p.Asp126Gly		53027877	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	37	CCDS8877.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.704924	0.30232	.	.	ENSG00000111481	ENST00000262061;ENST00000549043;ENST00000552218;ENST00000553231;ENST00000552362;ENST00000455864;ENST00000416254;ENST00000549116;ENST00000551779;ENST00000548753;ENST00000550713	.	.	.	5.24	4.1	0.47936	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.86041	0.5838	H	0.97023	3.925	0.80722	D	1	B;B;D;B	0.89917	0.005;0.209;1.0;0.006	B;P;D;B	0.97110	0.011;0.674;1.0;0.021	D	0.87386	0.2360	9	0.72032	D	0.01	-4.0602	9.3988	0.38420	0.9147:0.0:0.0853:0.0	.	103;134;75;126	B4DDX8;F8VWL5;B4DHZ0;P61923	.;.;.;COPZ1_HUMAN	G	126;134;147;103;126;103;75;68;126;38;134	.	ENSP00000262061:D126G	D	+	2	0	COPZ1	53027877	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	8.476000	0.90421	0.941000	0.37499	-0.250000	0.11733	GAT		0.498	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057		G	54741610	A	G	54741610	3	3	93	1	0	0	0	0	1	0	0	0	3747	333	12	4	399	4	COPZ1	12	54741610	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1154617	54741610	79110285	159	25487										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54792386	54792386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggccctagactcacctgacGctctttttggggcagctgcc	11	14	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:54792386G>A	ENST00000293379.4	-	28	3199	c.2938C>T	c.(2938-2940)Cgt>Tgt	p.R980C	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	980					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R980S(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						CTCACCTGACGCTCTTTTTGG	0.582																																																1	Substitution - Missense(1)	lung(1)	12											76	66	70					12																	54792386		2203	4300	6503	53078653	SO:0001583	missense	3678				CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.2938C>T	12.37:g.54792386G>A	ENSP00000293379:p.Arg980Cys		53078653	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	37	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	G	7.962	0.747141	0.15710	.	.	ENSG00000161638	ENST00000293379	T	0.24908	1.83	5.27	4.38	0.52667	.	0.410669	0.25798	N	0.028221	T	0.18045	0.0433	L	0.34521	1.04	0.09310	N	0.999999	P	0.44816	0.844	B	0.36418	0.224	T	0.08764	-1.0706	10	0.44086	T	0.13	.	12.2137	0.54394	0.0838:0.0:0.9162:0.0	.	980	P08648	ITA5_HUMAN	C	980	ENSP00000293379:R980C	ENSP00000293379:R980C	R	-	1	0	ITGA5	53078653	0.052000	0.20516	0.101000	0.21167	0.441000	0.31987	1.385000	0.34408	1.378000	0.46305	-0.137000	0.14449	CGT		0.582	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			A	54792386	G	A	54792386	3	1	93	1	0	0	0	0	1	0	0	0	7900	1087	38	1	223	1	ITGA5	12	54792386	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	50776	54792386	79059509	160	25488										
MMP19	4327	hgsc.bcm.edu	37	chr12	56234594	56234594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggcttgacgcagggctgccCgggctgtgtggggtggaagg	21	8	0	1	rs151295753	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:56234594C>T	ENST00000322569.4	-	4	468	c.377G>A	c.(376-378)cGg>cAg	p.R126Q	MMP19_ENST00000409200.3_Missense_Mutation_p.R126Q|MMP19_ENST00000548629.1_Missense_Mutation_p.R103Q|MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000547487.1_5'Flank	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	126					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	CAGGGCTGCCCGGGCTGTGTG	0.577																																																0			12						C	GLN/ARG	0,4406		0,0,2203	95	88	91		377	4	1	12	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MMP19	NM_002429.4	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	126/509	56234594	1,13005	2203	4300	6503	54520861	SO:0001583	missense	4327			X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.377G>A	12.37:g.56234594C>T	ENSP00000313437:p.Arg126Gln		54520861	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	37	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815820	0.50527	0.0	1.16E-4	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	T;T;T	0.21932	2.5;1.98;2.5	5.8	3.97	0.46021	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.395949	0.28659	N	0.014561	T	0.13072	0.0317	L	0.41356	1.27	0.31688	N	0.642258	P;P	0.44478	0.836;0.473	B;B	0.29716	0.106;0.072	T	0.14144	-1.0483	10	0.30078	T	0.28	.	11.2207	0.48853	0.0:0.8459:0.0:0.1541	.	126;126	B4E030;Q99542	.;MMP19_HUMAN	Q	126;103;126	ENSP00000313437:R126Q;ENSP00000446979:R103Q;ENSP00000386625:R126Q	ENSP00000313437:R126Q	R	-	2	0	MMP19	54520861	0.014000	0.17966	0.960000	0.40013	0.766000	0.43426	1.117000	0.31234	1.468000	0.48064	-0.137000	0.14449	CGG		0.577	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		T	56234594	C	T	56234594	3	4	93	1	0	0	0	0	1	0	0	0	9687	652	23	1	1173	1	MMP19	12	56234594	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1442208	56234594	77617301	161	25489										
GLI1	2735	hgsc.bcm.edu	37	chr12	57859575	57859575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcctctcttgccctaggatcCcctgttggggatgctggatg	13	12	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:57859575C>T	ENST00000228682.2	+	7	720	c.629C>T	c.(628-630)cCc>cTc	p.P210L	GLI1_ENST00000543426.1_Missense_Mutation_p.P82L|GLI1_ENST00000546141.1_Missense_Mutation_p.P169L	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	210			P -> A (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CCCTAGGATCCCCTGTTGGGG	0.562																																					Pancreas(157;841 1936 10503 41495 50368)											0			12											97	95	96					12																	57859575		2203	4300	6503	56145842	SO:0001583	missense	2735				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.629C>T	12.37:g.57859575C>T	ENSP00000228682:p.Pro210Leu		56145842	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.541800	0.45280	.	.	ENSG00000111087	ENST00000532291;ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T;T	0.73575	-0.76;2.66;2.56;2.65;2.65	4.45	2.36	0.29203	.	0.249501	0.28021	N	0.016919	T	0.60340	0.2261	L	0.39898	1.24	0.45378	D	0.998362	B	0.20164	0.042	B	0.22601	0.04	T	0.45571	-0.9252	10	0.17369	T	0.5	.	7.6743	0.28476	0.2072:0.7052:0.0:0.0877	.	210	P08151	GLI1_HUMAN	L	82;82;210;169;169;82	ENSP00000436671:P82L;ENSP00000437607:P82L;ENSP00000228682:P210L;ENSP00000441006:P169L;ENSP00000434408:P169L	ENSP00000228682:P210L	P	+	2	0	GLI1	56145842	0.981000	0.34729	0.928000	0.36995	0.948000	0.59901	2.161000	0.42358	0.437000	0.26423	0.591000	0.81541	CCC		0.562	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		T	57859575	C	T	57859575	3	4	93	1	0	0	0	0	1	0	0	0	6457	623	22	3	651	3	GLI1	12	57859575	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1624981	57859575	75992320	162	25490										
CAND1	55832	hgsc.bcm.edu	37	chr12	67692814	67692814	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tatgatccaaattataattaCgatgatgaagatgaagatga	8	3	0	7	rs367644026		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:67692814C>T	ENST00000545606.1	+	7	1376	c.939C>T	c.(937-939)taC>taT	p.Y313Y		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	313					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		ATTATAATTACgatgatgaag	0.294																																																0			12						C		1,4397	2.1+/-5.4	0,1,2198	56	54	55		939	0.3	1	12		55	0,8598		0,0,4299	no	coding-synonymous	CAND1	NM_018448.3		0,1,6497	TT,TC,CC		0.0,0.0227,0.0077		313/1231	67692814	1,12995	2199	4299	6498	65979081	SO:0001819	synonymous_variant	55832				CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.939C>T	12.37:g.67692814C>T			65979081	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																				0.294	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		T	67692814	C	T	67692814	2	4	93	1	0	0	0	0	0	0	0	1	2621	547	19	1		1	CAND1	12	67692814	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	9833239	67692814	66159081	163	25491										
PTPRR	5801	hgsc.bcm.edu	37	chr12	71050577	71050577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggatgtagcaataaaacacCctgttctacctattcctgca	6	11	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:71050577C>T	ENST00000283228.2	-	13	2239	c.1787G>A	c.(1786-1788)gGg>gAg	p.G596E	PTPRR_ENST00000537619.2_5'UTR|PTPRR_ENST00000440835.2_Missense_Mutation_p.G351E|PTPRR_ENST00000549308.1_Missense_Mutation_p.G351E|PTPRR_ENST00000342084.4_Missense_Mutation_p.G484E|PTPRR_ENST00000378778.1_Missense_Mutation_p.G390E	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	596	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AATAAAACACCCTGTTCTACC	0.383																																																0			12											179	152	161					12																	71050577		2203	4300	6503	69336844	SO:0001583	missense	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1787G>A	12.37:g.71050577C>T	ENSP00000283228:p.Gly596Glu		69336844	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.805795	0.90623	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37	5.48	5.48	0.80851	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.53938	D	0.000055	D	0.86171	0.5869	H	0.99682	4.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.92537	0.6038	10	0.87932	D	0	-13.5374	19.3521	0.94393	0.0:1.0:0.0:0.0	.	484;390;596	F5GXR7;Q15256-4;Q15256	.;.;PTPRR_HUMAN	E	351;596;390;484;351	ENSP00000391750:G351E;ENSP00000283228:G596E;ENSP00000368054:G390E;ENSP00000339605:G484E;ENSP00000446943:G351E	ENSP00000283228:G596E	G	-	2	0	PTPRR	69336844	1.000000	0.71417	0.855000	0.33649	0.972000	0.66771	7.125000	0.77193	2.573000	0.86826	0.655000	0.94253	GGG		0.383	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		T	71050577	C	T	71050577	3	4	93	1	0	0	0	0	1	0	0	0	12847	623	22	3	194	3	PTPRR	12	71050577	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	3357763	71050577	62801318	164	25492										
POLR3B	55703	hgsc.bcm.edu	37	chr12	106804719	106804719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agattattatggtaacaagcGactggaattggcaggacagg	13	5	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:106804719G>A	ENST00000228347.4	+	12	1304	c.1082G>A	c.(1081-1083)cGa>cAa	p.R361Q	POLR3B_ENST00000539066.1_Missense_Mutation_p.R303Q|POLR3B_ENST00000549195.1_3'UTR	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	361					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.R361Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GGTAACAAGCGACTGGAATTG	0.348																																																1	Substitution - Missense(1)	large_intestine(1)	12											91	92	92					12																	106804719		2203	4300	6503	105328849	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1082G>A	12.37:g.106804719G>A	ENSP00000228347:p.Arg361Gln		105328849	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532310	0.85812	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066;ENST00000549569;ENST00000549195	T;T;T	0.77489	-1.1;-1.1;-1.1	5.42	4.53	0.55603	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.90635	0.7063	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92986	0.6410	10	0.87932	D	0	-12.2144	14.5055	0.67750	0.0711:0.0:0.9289:0.0	.	361	Q9NW08	RPC2_HUMAN	Q	361;361;303;119;24	ENSP00000228347:R361Q;ENSP00000445721:R303Q;ENSP00000448398:R119Q	ENSP00000228347:R361Q	R	+	2	0	POLR3B	105328849	1.000000	0.71417	0.992000	0.48379	0.758000	0.43043	9.368000	0.97152	1.430000	0.47334	-0.266000	0.10368	CGA		0.348	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		A	106804719	G	A	106804719	3	1	93	1	0	0	0	0	1	0	0	0	12260	1058	37	1	1128	1	POLR3B	12	106804719	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	35754142	106804719	27047176	165	25493										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113266158	113266158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gttcagcaacagttctaaccGttggatgtaccccagtgacc	9	12	2	1	rs139903605		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:113266158G>A	ENST00000389385.4	+	3	532	c.35G>A	c.(34-36)cGt>cAt	p.R12H	RPH3A_ENST00000420983.2_Missense_Mutation_p.R12H|RPH3A_ENST00000447659.2_Missense_Mutation_p.R12H|RPH3A_ENST00000543106.2_Missense_Mutation_p.R12H|RPH3A_ENST00000551052.1_Missense_Mutation_p.R12H|RPH3A_ENST00000548866.1_Missense_Mutation_p.R12H|RPH3A_ENST00000415485.3_Missense_Mutation_p.R12H	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	12					intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		AGTTCTAACCGTTGGATGTAC	0.473																																																0			12						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	185	159	168		35,35	5.7	0.7	12	dbSNP_134	168	0,8600		0,0,4300	no	missense,missense	RPH3A	NM_001143854.1,NM_014954.3	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	12/695,12/691	113266158	1,13005	2203	4300	6503	111750541	SO:0001583	missense	22895			AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.35G>A	12.37:g.113266158G>A	ENSP00000374036:p.Arg12His		111750541	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.943641	0.73672	2.27E-4	0.0	ENSG00000089169	ENST00000549736;ENST00000548197;ENST00000547686;ENST00000543106;ENST00000551593;ENST00000546426;ENST00000551748;ENST00000546703;ENST00000547840;ENST00000547728;ENST00000549769;ENST00000552667;ENST00000389385;ENST00000447659;ENST00000551198;ENST00000551052;ENST00000415485;ENST00000553114;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.77750	-0.2;-0.2;-1.12;-0.15;-0.2;-0.58;-0.2	5.7	5.7	0.88788	Rabphilin-3A effector, zinc-binding (1);	0.248756	0.28606	N	0.014742	D	0.86222	0.5881	M	0.63843	1.955	0.51233	D	0.999911	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.85130	0.994;0.997;0.997;0.994	D	0.86144	0.1583	10	0.54805	T	0.06	.	15.3248	0.74150	0.0:0.0:1.0:0.0	.	12;12;12;12	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	H	12	ENSP00000440384:R12H;ENSP00000374036:R12H;ENSP00000413254:R12H;ENSP00000448297:R12H;ENSP00000405357:R12H;ENSP00000450347:R12H;ENSP00000408889:R12H	ENSP00000374036:R12H	R	+	2	0	RPH3A	111750541	0.998000	0.40836	0.690000	0.30148	0.403000	0.30841	4.419000	0.59835	2.696000	0.92011	0.655000	0.94253	CGT		0.473	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113266158	G	A	113266158	3	1	93	1	0	0	0	0	1	0	0	0	13588	1145	40	1	37	1	RPH3A	12	113266158	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	6461439	113266158	20585737	166	25494										
RNF10	9921	hgsc.bcm.edu	37	chr12	120998652	120998652	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agaggagaagcacactcccgAgtcctgctttattgaggcag	12	10	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:120998652A>G	ENST00000325954.4	+	7	1552	c.1091A>G	c.(1090-1092)gAg>gGg	p.E364G	RNF10_ENST00000413266.2_Missense_Mutation_p.E364G	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	364					negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACACTCCCGAGTCCTGCTTT	0.527																																																0			12											74	67	69					12																	120998652		2203	4300	6503	119483035	SO:0001583	missense	9921			AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"RING-type (C3HC4) zinc fingers"	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.1091A>G	12.37:g.120998652A>G	ENSP00000322242:p.Glu364Gly		119483035	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	37	CCDS9201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.2|21.2	4.112575|4.112575	0.77210|0.77210	.|.	.|.	ENSG00000022840|ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000542438;ENST00000413266|ENST00000542207;ENST00000537740	D;D|.	0.91011|.	-2.77;-2.73|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.047268|.	0.85682|.	D|.	0.000000|.	T|T	0.76263|0.76263	0.3963|0.3963	M|M	0.75615|0.75615	2.305|2.305	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.996;0.983|.	D;P|.	0.63283|.	0.913;0.765|.	T|T	0.75952|0.75952	-0.3136|-0.3136	10|5	0.87932|.	D|.	0|.	.|.	16.8222|16.8222	0.85835|0.85835	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	364;364|.	Q8N5U6-2;Q8N5U6|.	.;RNF10_HUMAN|.	G|G	364;364;94;364|162;42	ENSP00000322242:E364G;ENSP00000415682:E364G|.	ENSP00000322242:E364G|.	E|S	+|+	2|1	0|0	RNF10|RNF10	119483035|119483035	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.735000|8.735000	0.91549|0.91549	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAG|AGT		0.527	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			G	120998652	A	G	120998652	3	3	93	1	0	0	0	0	1	0	0	0	13459	304	11	4	1117	4	RNF10	12	120998652	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	7732494	120998652	12853243	167	25495										
AACS	65985	hgsc.bcm.edu	37	chr12	125591727	125591727	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caggccccgcagctggagttCgagcagctgcccttcagcca	12	16	1	0	rs140471021	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr12:125591727C>G	ENST00000316519.6	+	8	1034	c.828C>G	c.(826-828)ttC>ttG	p.F276L	AACS_ENST00000261686.6_Missense_Mutation_p.F276L|AACS_ENST00000316543.10_5'UTR	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	276					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	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)		AGCTGGAGTTCGAGCAGCTGC	0.612																																																0			12											82	72	76					12																	125591727		2203	4300	6503	124157680	SO:0001583	missense	65985			AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"Acyl-CoA synthetase family"	21298	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 1"	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.828C>G	12.37:g.125591727C>G	ENSP00000324842:p.Phe276Leu		124157680	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	ENST00000316519.6	37	CCDS9263.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593044	0.86953	.	.	ENSG00000081760	ENST00000316519;ENST00000261686;ENST00000535001;ENST00000537564;ENST00000441247	T;T;T;T	0.46451	2.93;2.93;1.05;0.87	5.45	-2.17	0.07059	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.68118	0.2966	H	0.94503	3.545	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.74348	0.979;0.983	T	0.72312	-0.4331	10	0.72032	D	0.01	.	12.0299	0.53392	0.0:0.3172:0.0:0.6828	.	276;276	Q86V21-2;Q86V21	.;AACS_HUMAN	L	276;276;132;57;95	ENSP00000324842:F276L;ENSP00000261686:F276L;ENSP00000442956:F57L;ENSP00000392967:F95L	ENSP00000261686:F276L	F	+	3	2	AACS	124157680	0.620000	0.27068	0.984000	0.44739	0.963000	0.63663	-0.330000	0.07925	-0.704000	0.05042	0.561000	0.74099	TTC		0.612	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928		G	125591727	C	G	125591727	3	3	93	1	0	0	0	0	1	0	0	0	9	883	31	5	858	5	AACS	12	125591727	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	4593075	125591727	8260168	168	25496										
PARP4	143	hgsc.bcm.edu	37	chr13	25066720	25066720	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tactagaaggagaatcccctCtgccttgctcacctttcaac	6	14	3	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:25066720C>T	ENST00000381989.3	-	9	997	c.892G>A	c.(892-894)Gag>Aag	p.E298K		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	298	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGAATCCCCTCTGCCTTGCTC	0.358																																																0			13											195	186	189					13																	25066720		2203	4300	6503	23964720	SO:0001583	missense	143			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.892G>A	13.37:g.25066720C>T	ENSP00000371419:p.Glu298Lys		23964720	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783940	0.70222	.	.	ENSG00000102699	ENST00000381989	T	0.46451	0.87	4.59	4.59	0.56863	Poly(ADP-ribose) polymerase, regulatory domain (3);	0.139055	0.46442	D	0.000295	T	0.63988	0.2558	M	0.76328	2.33	0.44048	D	0.996782	D	0.76494	0.999	D	0.78314	0.991	T	0.68546	-0.5380	10	0.72032	D	0.01	-21.6396	14.9206	0.70835	0.0:1.0:0.0:0.0	.	298	Q9UKK3	PARP4_HUMAN	K	298	ENSP00000371419:E298K	ENSP00000371419:E298K	E	-	1	0	PARP4	23964720	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	4.294000	0.59043	2.362000	0.80069	0.643000	0.83706	GAG		0.358	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		T	25066720	C	T	25066720	3	4	93	1	0	0	0	0	1	0	0	0	11494	922	32	3	4386	3	PARP4	13	25066720	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10		25066720	90103158	169	25497										
NBEA	26960	hgsc.bcm.edu	37	chr13	35733400	35733401	+	Frame_Shift_Ins	INS	-	-	A													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgagacttactcatgtcaacINSaaaagtgtcagatgatattc					rs376327034		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:35733400_35733401insA	ENST00000400445.3	+	22	3626_3627	c.3092_3093insA	c.(3091-3096)acaaaafs	p.TK1031fs	NBEA_ENST00000379939.2_Frame_Shift_Ins_p.TK1031fs|NBEA_ENST00000540320.1_Frame_Shift_Ins_p.TK1031fs|NBEA_ENST00000310336.4_Frame_Shift_Ins_p.TK1031fs	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1031					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CTCATGTCAACAAAAGTGTCAG	0.401																																																0			13																																								34631401	SO:0001589	frameshift_variant	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.3096dupA	13.37:g.35733404_35733404dupA	ENSP00000383295:p.Thr1031fs		34631400	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Frame_Shift_Ins	INS	ENST00000400445.3	37	CCDS45026.1																																																																																				0.401	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35733401	-	A	35733400	7	5	93	1	0	1	1	0	0	0	0	0	10217	478	17	0	3178	0	NBEA	13	35733400	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	10666680	35733400	79436478	170	25498										
SUCLA2	8803	hgsc.bcm.edu	37	chr13	48542867	48542867	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaaatcccatcttctgtgcaAgctgaaatcaatatgtcttt	6	9	4	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:48542867A>G	ENST00000378654.3	-	6	721	c.665T>C	c.(664-666)cTt>cCt	p.L222P	SUCLA2_ENST00000534875.1_Splice_Site_p.L164P|SUCLA2_ENST00000544100.1_Splice_Site_p.L88P|SUCLA2_ENST00000543413.1_Splice_Site_p.L164P|SUCLA2_ENST00000497202.1_5'UTR	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	222	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		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)	CTTCTGTGCAAGCTGAAATCA	0.323																																																0			13											46	42	43					13																	48542867		2202	4300	6502	47440868	SO:0001630	splice_region_variant	8803			AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.664-1T>C	13.37:g.48542867A>G			47440868	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Missense_Mutation	SNP	ENST00000378654.3	37	CCDS9406.1	.	.	.	.	.	.	.	.	.	.	a	22.5	4.303976	0.81136	.	.	ENSG00000136143	ENST00000378654;ENST00000378645;ENST00000378642;ENST00000331052;ENST00000544100;ENST00000534875;ENST00000543413;ENST00000541732;ENST00000434484;ENST00000433022	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	6.08	6.08	0.98989	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.112739	0.64402	D	0.000010	D	0.83464	0.5260	M	0.88906	2.99	0.80722	D	1	D	0.63880	0.993	P	0.62649	0.905	D	0.86649	0.1897	10	0.87932	D	0	-10.3648	15.825	0.78698	1.0:0.0:0.0:0.0	.	222	Q9P2R7	SUCB1_HUMAN	P	222;200;152;74;88;164;164;50;152;74	ENSP00000367923:L222P;ENSP00000443412:L88P;ENSP00000438182:L164P;ENSP00000441056:L164P;ENSP00000392771:L152P;ENSP00000415091:L74P	ENSP00000367898:L74P	L	-	2	0	SUCLA2	47440868	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.515000	0.90548	2.333000	0.79357	0.533000	0.62120	CTT		0.323	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1		Missense_Mutation	G	48542867	A	G	48542867	5	3	93	1	0	0	0	0	0	0	1	0	15402	86	3	4	750	4	SUCLA2	13	48542867	Splice_Site	SNP	A	TCGA-DC-5337-01A-01D-1657-10	12809467	48542867	66627011	171	25499										
RB1	5925	hgsc.bcm.edu	37	chr13	48881536	48881536	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaagtttcatctgtggatggAgtattggtaaggattttctt	11	3	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:48881536A>G	ENST00000267163.4	+	2	396	c.258A>G	c.(256-258)ggA>ggG	p.G86G		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	86					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CTGTGGATGGAGTATTGGTAA	0.289		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	18	Whole gene deletion(15)|Unknown(3)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|stomach(1)	13											122	123	123					13																	48881536		2203	4299	6502	47779537	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.258A>G	13.37:g.48881536A>G			47779537	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.289	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48881536	A	G	48881536	2	3	93	1	0	0	0	0	0	0	0	1	13135	291	11	4		4	RB1	13	48881536	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	338669	48881536	66288342	172	25500										
TBC1D4	9882	hgsc.bcm.edu	37	chr13	76055518	76055518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggtcgtggctgttgtggatgAagcgcgagatatgctgcgcc	17	8	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:76055518A>G	ENST00000377636.3	-	1	732	c.386T>C	c.(385-387)tTc>tCc	p.F129S	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Missense_Mutation_p.F129S|TBC1D4_ENST00000431480.2_Missense_Mutation_p.F129S	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	129	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTTGTGGATGAAGCGCGAGAT	0.657																																																0			13											94	111	105					13																	76055518		2160	4271	6431	74953519	SO:0001583	missense	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.386T>C	13.37:g.76055518A>G	ENSP00000366863:p.Phe129Ser		74953519	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.769319	0.90020	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.19105	2.17;2.17;2.17	4.16	4.16	0.48862	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.52532	D	0.000061	T	0.39708	0.1088	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.91635	0.964;0.997;0.999	T	0.28235	-1.0050	10	0.87932	D	0	-12.4786	13.3507	0.60601	1.0:0.0:0.0:0.0	.	129;129;129	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	S	129	ENSP00000366863:F129S;ENSP00000395986:F129S;ENSP00000366852:F129S	ENSP00000366852:F129S	F	-	2	0	TBC1D4	74953519	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.626000	0.90969	1.732000	0.51606	0.459000	0.35465	TTC		0.657	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		G	76055518	A	G	76055518	3	3	93	1	0	0	0	0	1	0	0	0	15661	246	9	4	3594	4	TBC1D4	13	76055518	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	27173982	76055518	39114360	173	25501										
DAOA	267012	hgsc.bcm.edu	37	chr13	106142254	106142254	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccggatctccttacaggcttGaagaagtaagcagccatgtt	10	10	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr13:106142254G>T	ENST00000375936.3	+	4	332	c.286G>T	c.(286-288)Gaa>Taa	p.E96*	DAOA_ENST00000329625.5_Nonsense_Mutation_p.E25*|DAOA-AS1_ENST00000448407.1_RNA	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator	96					negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					ttacaggcttgaagaagtaag	0.483																																																0			13											71	77	75					13																	106142254		2174	4281	6455	104940255	SO:0001587	stop_gained	267012			AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"G72 transcript"	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.286G>T	13.37:g.106142254G>T	ENSP00000365103:p.Glu96*		104940255	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Nonsense_Mutation	SNP	ENST00000375936.3	37	CCDS41905.1	.	.	.	.	.	.	.	.	.	.	g	23.6	4.432547	0.83776	.	.	ENSG00000182346	ENST00000375936;ENST00000329625	.	.	.	2.34	-1.65	0.08291	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	0.3512	0.00349	0.2714:0.2011:0.3229:0.2047	.	.	.	.	X	96;25	.	ENSP00000329951:E25X	E	+	1	0	DAOA	104940255	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.156000	0.10100	-0.534000	0.06315	-0.216000	0.12614	GAA		0.483	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370		T	106142254	G	T	106142254	4	4	93	1	0	0	0	0	0	1	0	0	4238	1291	45	2	409	2	DAOA	13	106142254	Nonsense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	30086736	106142254	9027624	174	25502										
NRL	4901	hgsc.bcm.edu	37	chr14	24550505	24550505	+	Frame_Shift_Del	DEL	G	G	-													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctcgaggttagccggtcacaGcgagccttgtagagatcgcg					rs12883914		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:24550505delG	ENST00000561028.1	-	3	973	c.654delC	c.(652-654)cgcfs	p.R218fs	NRL_ENST00000396997.1_Frame_Shift_Del_p.R218fs|NRL_ENST00000396995.1_Frame_Shift_Del_p.R79fs|NRL_ENST00000397002.2_Frame_Shift_Del_p.R218fs|NRL_ENST00000560550.1_Frame_Shift_Del_p.R79fs			P54845	NRL_HUMAN	neural retina leucine zipper	218	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of rhodopsin gene expression (GO:0007468)|response to stimulus (GO:0050896)|retinal rod cell development (GO:0046548)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(2)	2				GBM - Glioblastoma multiforme(265;0.0181)		GCCGGTCACAGCGAGCCTTGT	0.741																																																0			14											3	4	4					14																	24550505		1953	3896	5849	23620345	SO:0001589	frameshift_variant	4901				CCDS9608.1	14q11.1-q11.2	2013-01-08			ENSG00000129535	ENSG00000129535			8002	protein-coding gene	gene with protein product		162080				1427865, 10192380	Standard	NM_006177		Approved	D14S46E, RP27, NRL-MAF	uc021rrk.1	P54845	OTTHUMG00000028789	ENST00000561028.1:c.654delC	14.37:g.24550505delG	ENSP00000454062:p.Arg218fs		23620345	A8MX14|Q53XD0	Frame_Shift_Del	DEL	ENST00000561028.1	37	CCDS9608.1																																																																																				0.741	NRL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415595.1			-	24550505	G	-	24550505	7	5	93	1	0	1	0	1	0	0	0	0	10687	958	34	0	63	0	NRL	14	24550505	Frame_Shift_Del	DEL	G	TCGA-DC-5337-01A-01D-1657-10		24550505	82799035	175	25503										
TGM1	7051	hgsc.bcm.edu	37	chr14	24724656	24724656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgagtgtgccgatggccttcTcctccacataaacaatcttg	8	12	2	1	rs142404759	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:24724656T>C	ENST00000206765.6	-	11	1682	c.1559A>G	c.(1558-1560)gAg>gGg	p.E520G	TGM1_ENST00000544573.1_Missense_Mutation_p.E78G	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	520			E -> G (in ARCI1; dbSNP:rs142404759).		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GATGGCCTTCTCCTCCACATA	0.537													T|||	8	0.00159744	0	0	5008	,	,		21003	0		0.008	False		,,,				2504	0															0			14	GRCh37	CM012197	TGM1	M	rs142404759	T	GLY/GLU	12,4394	19.1+/-41.9	0,12,2191	133	106	115		1559	5.4	1	14	dbSNP_134	115	67,8533	38.8+/-94.9	1,65,4234	yes	missense	TGM1	NM_000359.2	98	1,77,6425	CC,CT,TT		0.7791,0.2724,0.6074	probably-damaging	520/818	24724656	79,12927	2203	4300	6503	23794496	SO:0001583	missense	7051			D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.1559A>G	14.37:g.24724656T>C	ENSP00000206765:p.Glu520Gly		23794496	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	37	CCDS9622.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	20.1	3.936211	0.73442	0.002724	0.007791	ENSG00000092295	ENST00000206765;ENST00000544573	T;T	0.73897	-0.79;-0.79	5.42	5.42	0.78866	.	0.048871	0.85682	D	0.000000	T	0.58652	0.2137	L	0.33485	1.01	0.35147	D	0.76944	P	0.52842	0.956	B	0.44224	0.444	T	0.72194	-0.4364	10	0.34782	T	0.22	-34.6757	13.4085	0.60929	0.0:0.0:0.0:1.0	.	520	P22735	TGM1_HUMAN	G	520;78	ENSP00000206765:E520G;ENSP00000439446:E78G	ENSP00000206765:E520G	E	-	2	0	TGM1	23794496	0.251000	0.23961	1.000000	0.80357	0.994000	0.84299	2.134000	0.42102	2.046000	0.60703	0.533000	0.62120	GAG		0.537	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		C	24724656	T	C	24724656	3	2	93	1	0	0	0	0	1	0	0	0	15868	1551	54	4	914	4	TGM1	14	24724656	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	174151	24724656	82624884	176	25504										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33293351	33293351	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gagaaaaggggacttttattCgtacttatctctctcatctc	7	9	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:33293351C>T	ENST00000280979.4	+	13	6502	c.6332C>T	c.(6331-6333)tCg>tTg	p.S2111L	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2111					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GACTTTTATTCGTACTTATCT	0.463																																					Melanoma(49;821 1200 7288 13647 42351)											0			14											97	96	96					14																	33293351		2203	4300	6503	32363102	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6332C>T	14.37:g.33293351C>T	ENSP00000280979:p.Ser2111Leu		32363102	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103418	0.94245	.	.	ENSG00000151320	ENST00000280979	T	0.53857	0.6	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.74099	0.3672	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74456	-0.3659	10	0.87932	D	0	-9.1485	20.5568	0.99304	0.0:1.0:0.0:0.0	.	2111	Q13023	AKAP6_HUMAN	L	2111	ENSP00000280979:S2111L	ENSP00000280979:S2111L	S	+	2	0	AKAP6	32363102	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.851000	0.69481	2.861000	0.98227	0.655000	0.94253	TCG		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33293351	C	T	33293351	3	4	93	1	0	0	0	0	1	0	0	0	455	893	31	1	6378	1	AKAP6	14	33293351	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	8568695	33293351	74056189	177	25505										
RAD51L1	5890	hgsc.bcm.edu	37	chr14	68301901	68301901	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	catggtggtgtggcttgtggAtccctcacagaggtaaagga	15	7	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:68301901A>G	ENST00000487270.1	+	4	351	c.303A>G	c.(301-303)ggA>ggG	p.G101G	RAD51B_ENST00000487861.1_Silent_p.G101G|RAD51B_ENST00000390683.3_Silent_p.G101G|RAD51B_ENST00000488612.1_Silent_p.G101G|RAD51B_ENST00000471583.1_Silent_p.G101G	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	101					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						TGGCTTGTGGATCCCTCACAG	0.398								Direct reversal of damage																																								0			14											98	97	97					14																	68301901		2203	4300	6503	67371654	SO:0001819	synonymous_variant	5890			U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"RAD51 (S. cerevisiae)-like 1", "RAD51-like 1 (S. cerevisiae)", "RAD51 homolog B (S. cerevisiae)"	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.303A>G	14.37:g.68301901A>G			67371654	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Silent	SNP	ENST00000487270.1	37	CCDS9789.1																																																																																				0.398	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1			G	68301901	A	G	68301901	2	3	93	1	0	0	0	0	0	0	0	1	13026	320	12	4		4	RAD51L1	14	68301901	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	35008550	68301901	39047639	178	25506										
PCNX	22990	hgsc.bcm.edu	37	chr14	71444183	71444183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcttgaggagcctgagcacaCggagtagtgggtcaacagaa	15	8	1	3	rs371108639		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:71444183C>T	ENST00000304743.2	+	6	1575	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	PCNX_ENST00000238570.5_Missense_Mutation_p.R377W|PCNX_ENST00000439984.3_Missense_Mutation_p.R377W	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	377						integral component of membrane (GO:0016021)		p.R377W(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CCTGAGCACACGGAGTAGTGG	0.478																																																1	Substitution - Missense(1)	prostate(1)	14						C	TRP/ARG	0,4406		0,0,2203	69	74	72		1129	5	1	14		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCNX	NM_014982.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	377/2342	71444183	1,13005	2203	4300	6503	70513936	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.1129C>T	14.37:g.71444183C>T	ENSP00000304192:p.Arg377Trp		70513936	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791386	0.50102	0.0	1.16E-4	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.12255	3.16;3.16;2.7	5.93	5.01	0.66863	.	0.000000	0.64402	D	0.000001	T	0.23492	0.0568	N	0.24115	0.695	0.50813	D	0.99989	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.79108	0.893;0.936;0.992	T	0.00888	-1.1526	10	0.66056	D	0.02	.	13.9508	0.64116	0.2597:0.7403:0.0:0.0	.	377;377;377	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	W	377	ENSP00000304192:R377W;ENSP00000238570:R377W;ENSP00000396617:R377W	ENSP00000238570:R377W	R	+	1	2	PCNX	70513936	0.942000	0.31987	0.971000	0.41717	0.938000	0.57974	2.124000	0.42006	2.816000	0.96949	0.650000	0.86243	CGG		0.478	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71444183	C	T	71444183	3	4	93	1	0	0	0	0	1	0	0	0	11622	527	19	1	1151	1	PCNX	14	71444183	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	3142282	71444183	35905357	179	25507										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77844697	77844697	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gagcggactaaaccagacttTccagaccacaagccaagaaa	8	12	0	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr14:77844697T>C	ENST00000216471.4	+	1	1222	c.936T>C	c.(934-936)ttT>ttC	p.F312F	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	312										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AACCAGACTTTCCAGACCACA	0.453																																																0			14											80	81	80					14																	77844697		2203	4300	6503	76914450	SO:0001819	synonymous_variant	0			AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.936T>C	14.37:g.77844697T>C			76914450	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																				0.453	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		C	77844697	T	C	77844697	2	2	93	1	0	0	0	0	0	0	0	1	1763	1780	62	4		4	C14orf174	14	77844697	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6400514	77844697	29504843	180	25508										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42144501	42144501	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gctcctgtggctgcagcaggAgctcctgttccatcttgggg	14	12	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:42144501A>G	ENST00000320955.6	-	62	10690	c.10463T>C	c.(10462-10464)cTc>cCc	p.L3488P	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3488					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTGCAGCAGGAGCTCCTGTTC	0.647																																																0			15											15	19	18					15																	42144501		2085	4222	6307	39931793	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.10463T>C	15.37:g.42144501A>G	ENSP00000317790:p.Leu3488Pro		39931793		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	8.499	0.863884	0.17250	.	.	ENSG00000137877	ENST00000320955	T	0.65732	-0.17	2.9	-2.77	0.05877	.	3.444720	0.01989	U	0.045349	T	0.47875	0.1469	L	0.34521	1.04	0.22858	N	0.998645	B	0.14438	0.01	B	0.14023	0.01	T	0.18304	-1.0341	10	0.45353	T	0.12	.	3.2084	0.06674	0.3948:0.0:0.3995:0.2057	.	3488	Q9NRC6	SPTN5_HUMAN	P	3488	ENSP00000317790:L3488P	ENSP00000317790:L3488P	L	-	2	0	SPTBN5	39931793	0.002000	0.14202	0.001000	0.08648	0.085000	0.17905	0.273000	0.18662	-0.805000	0.04404	0.533000	0.62120	CTC		0.647	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42144501	A	G	42144501	3	3	93	1	0	0	0	0	1	0	0	0	15161	304	11	4	589	4	SPTBN5	15	42144501	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10		42144501	60386891	181	25509										
USP8	9101	hgsc.bcm.edu	37	chr15	50782647	50782647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaagcgctcctactcctcccCagatataacccaggctattc	6	16	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:50782647C>A	ENST00000396444.3	+	14	2497	c.2159C>A	c.(2158-2160)cCa>cAa	p.P720Q	USP8_ENST00000425032.3_Missense_Mutation_p.P614Q|USP8_ENST00000433963.1_Missense_Mutation_p.P720Q|USP8_ENST00000307179.4_Missense_Mutation_p.P720Q	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	720					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.P720Q(2)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TACTCCTCCCCAGATATAACC	0.478																																																2	Substitution - Missense(2)	urinary_tract(1)|lung(1)	15											114	114	114					15																	50782647		2196	4294	6490	48569939	SO:0001583	missense	9101			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2159C>A	15.37:g.50782647C>A	ENSP00000379721:p.Pro720Gln		48569939	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145451	0.94603	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.02323	4.34;4.34;4.34;4.34	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.10852	0.0265	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.984;0.994	T	0.03463	-1.1034	10	0.52906	T	0.07	-13.2942	19.9733	0.97292	0.0:1.0:0.0:0.0	.	614;720	B4DKA8;P40818	.;UBP8_HUMAN	Q	720;720;720;614	ENSP00000379721:P720Q;ENSP00000405537:P720Q;ENSP00000302239:P720Q;ENSP00000412682:P614Q	ENSP00000302239:P720Q	P	+	2	0	USP8	48569939	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.442000	0.80503	2.790000	0.95986	0.650000	0.86243	CCA		0.478	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		A	50782647	C	A	50782647	3	1	93	1	0	0	0	0	1	0	0	0	17129	594	21	2	2209	2	USP8	15	50782647	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	8638146	50782647	51748745	182	25510										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52667589	52667589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	taatcttgtacctcctgcggAccacatacatgcgccagtac	7	14	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:52667589A>G	ENST00000399231.3	-	20	2732	c.2489T>C	c.(2488-2490)gTc>gCc	p.V830A	MYO5A_ENST00000553916.1_Missense_Mutation_p.V830A|MYO5A_ENST00000356338.6_Missense_Mutation_p.V830A|MYO5A_ENST00000399233.2_Missense_Mutation_p.V830A|MYO5A_ENST00000358212.6_Missense_Mutation_p.V830A	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	830	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CCTCCTGCGGACCACATACAT	0.458																																																0			15											107	101	103					15																	52667589		1928	4126	6054	50454881	SO:0001583	missense	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.2489T>C	15.37:g.52667589A>G	ENSP00000382177:p.Val830Ala		50454881	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	A	4.425	0.078562	0.08533	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4	5.38	1.82	0.25136	.	0.471910	0.22334	N	0.061423	T	0.04724	0.0128	N	0.02129	-0.67	0.20307	N	0.999912	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.43523	-0.9386	10	0.02654	T	1	.	8.9123	0.35561	0.7143:0.0:0.2857:0.0	.	830;830	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	A	830;364;830;830;830;460;830	ENSP00000382177:V830A;ENSP00000382179:V830A;ENSP00000348693:V830A;ENSP00000350945:V830A;ENSP00000451109:V830A	ENSP00000348693:V830A	V	-	2	0	MYO5A	50454881	0.004000	0.15560	0.133000	0.22050	0.892000	0.51952	1.104000	0.31074	0.341000	0.23771	0.450000	0.29827	GTC		0.458	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		G	52667589	A	G	52667589	3	3	93	1	0	0	0	0	1	0	0	0	10108	275	10	4	3166	4	MYO5A	15	52667589	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1884942	52667589	49863803	183	25511										
RNF111	54778	hgsc.bcm.edu	37	chr15	59373358	59373358	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcaccaatccctcagcatctTcctcctacacaccagccaat	3	19	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:59373358T>C	ENST00000557998.1	+	8	2459	c.2172T>C	c.(2170-2172)ctT>ctC	p.L724L	RNF111_ENST00000348370.4_Silent_p.L724L|RNF111_ENST00000561186.1_Silent_p.L724L|RNF111_ENST00000434298.1_Silent_p.L724L|RNF111_ENST00000559209.1_Silent_p.L724L	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	724	Pro-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CTCAGCATCTTCCTCCTACAC	0.498																																					NSCLC(72;983 1365 10746 34387 47081)											0			15											297	241	260					15																	59373358		2192	4291	6483	57160650	SO:0001819	synonymous_variant	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2172T>C	15.37:g.59373358T>C			57160650	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																				0.498	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		C	59373358	T	C	59373358	2	2	93	1	0	0	0	0	0	0	0	1	13462	1770	62	4		4	RNF111	15	59373358	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6705769	59373358	43158034	184	25512										
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65219113	65219113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cggccagctggggaggacggCgtttcacagggcagctgagc	18	11	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:65219113C>T	ENST00000380230.3	+	6	514	c.485C>T	c.(484-486)gCg>gTg	p.A162V	ANKDD1A_ENST00000319580.8_3'UTR|ANKDD1A_ENST00000496660.1_Missense_Mutation_p.A71V|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.A71V|ANKDD1A_ENST00000395720.1_Missense_Mutation_p.A162V|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.A162V|AC069368.3_ENST00000437723.1_Intron|ANKDD1A_ENST00000491145.1_3'UTR	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	162					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						GGGAGGACGGCGTTTCACAGG	0.622																																																0			15											119	107	111					15																	65219113		2202	4299	6501	63006166	SO:0001583	missense	348094				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.485C>T	15.37:g.65219113C>T	ENSP00000369579:p.Ala162Val		63006166	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	C	13.89	2.373391	0.42105	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000496660;ENST00000395723	T;T;T;T;T	0.74106	2.16;2.16;2.16;-0.81;2.13	4.23	4.23	0.50019	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000015	T	0.81456	0.4826	L	0.56199	1.76	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.991;0.996;0.998;0.984	T	0.80139	-0.1507	10	0.39692	T	0.17	-21.6654	12.2937	0.54833	0.0:1.0:0.0:0.0	.	162;68;162;162	Q495B1;A4QMR4;Q495B1-2;Q495B1-1	AKD1A_HUMAN;.;.;.	V	162;162;162;71;71	ENSP00000369579:A162V;ENSP00000350329:A162V;ENSP00000379070:A162V;ENSP00000420999:A71V;ENSP00000379073:A71V	ENSP00000350329:A162V	A	+	2	0	ANKDD1A	63006166	0.994000	0.37717	0.949000	0.38748	0.882000	0.50991	3.727000	0.54984	2.363000	0.80096	0.561000	0.74099	GCG		0.622	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65219113	C	T	65219113	3	4	93	1	0	0	0	0	1	0	0	0	624	768	27	1	507	1	ANKDD1A	15	65219113	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	5845755	65219113	37312279	185	25513										
IQCH	64799	hgsc.bcm.edu	37	chr15	67664873	67664873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaaattcttcctcttttatcGccagcagaagtgggcatcag	8	10	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:67664873G>A	ENST00000335894.4	+	9	1244	c.1178G>A	c.(1177-1179)cGc>cAc	p.R393H	IQCH_ENST00000358767.3_Missense_Mutation_p.R220H|IQCH_ENST00000360277.4_Missense_Mutation_p.R145H|IQCH_ENST00000546225.1_Missense_Mutation_p.R141H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	393	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.									NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		CTCTTTTATCGCCAGCAGAAG	0.458																																																0			15											104	106	105					15																	67664873		2201	4299	6500	65451927	SO:0001583	missense	128153			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1178G>A	15.37:g.67664873G>A	ENSP00000336861:p.Arg393His		65451927	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002111	0.35320	.	.	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.74002	0.65;0.7;0.65;-0.8	6.03	2.11	0.27256	.	0.181773	0.46442	D	0.000293	T	0.82199	0.4985	M	0.78801	2.425	0.09310	N	1	B;B;B;D;D	0.89917	0.257;0.139;0.083;1.0;1.0	B;B;B;D;D	0.81914	0.037;0.018;0.018;0.983;0.995	T	0.70285	-0.4914	10	0.37606	T	0.19	-6.1117	7.3491	0.26680	0.19:0.0:0.69:0.12	.	220;141;145;393;220	F8WAL8;Q86VS3-2;Q86VS3-4;Q86VS3;Q86VS3-3	.;.;.;IQCH_HUMAN;.	H	220;141;393;145	ENSP00000351617:R220H;ENSP00000444118:R141H;ENSP00000336861:R393H;ENSP00000353419:R145H	ENSP00000336861:R393H	R	+	2	0	IQCH	65451927	0.651000	0.27340	0.034000	0.17996	0.571000	0.35966	1.879000	0.39618	0.440000	0.26502	0.655000	0.94253	CGC		0.458	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		A	67664873	G	A	67664873	3	1	93	1	0	0	0	0	1	0	0	0	7832	1087	38	1	1340	1	IQCH	15	67664873	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	2445760	67664873	34866519	186	25514										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68613809	68613809	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acaaggtcagggacacagtgCtcatcctcattgcagccgtt	10	12	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:68613809C>T	ENST00000315757.7	-	19	2441	c.2355G>A	c.(2353-2355)gaG>gaA	p.E785E	ITGA11_ENST00000423218.2_Silent_p.E785E	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	785					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GGACACAGTGCTCATCCTCAT	0.647																																																0			15											49	61	57					15																	68613809		2126	4230	6356	66400863	SO:0001819	synonymous_variant	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.2355G>A	15.37:g.68613809C>T			66400863	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																				0.647	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68613809	C	T	68613809	2	4	93	1	0	0	0	0	0	0	0	1	7895	796	28	3		3	ITGA11	15	68613809	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	948936	68613809	33917583	187	25515										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91017851	91017851	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcaccctcattcgttctaacCagcagctggagaatgacctc	7	14	3	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:91017851C>A	ENST00000268182.5	+	23	2834	c.2710C>A	c.(2710-2712)Cag>Aag	p.Q904K	IQGAP1_ENST00000560020.1_3'UTR|IQGAP1_ENST00000560738.1_Missense_Mutation_p.Q332K	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	904					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TCGTTCTAACCAGCAGCTGGA	0.473																																																0			15											113	100	104					15																	91017851		2198	4298	6496	88818855	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2710C>A	15.37:g.91017851C>A	ENSP00000268182:p.Gln904Lys		88818855	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.531393	0.85706	.	.	ENSG00000140575	ENST00000268182	T	0.02606	4.23	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.09642	0.0237	M	0.76574	2.34	0.80722	D	1	P	0.47841	0.901	P	0.49953	0.627	T	0.03818	-1.1001	10	0.42905	T	0.14	-22.6016	16.9844	0.86336	0.0:1.0:0.0:0.0	.	904	P46940	IQGA1_HUMAN	K	904	ENSP00000268182:Q904K	ENSP00000268182:Q904K	Q	+	1	0	IQGAP1	88818855	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.773000	0.68898	2.548000	0.85928	0.591000	0.81541	CAG		0.473	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		A	91017851	C	A	91017851	3	1	93	1	0	0	0	0	1	0	0	0	7835	595	21	2	2800	2	IQGAP1	15	91017851	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	22404042	91017851	11513541	188	25516										
PRC1	9055	hgsc.bcm.edu	37	chr15	91523594	91523594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgttttgcattttcagttctTccaaccgatccacttctaat	4	11	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:91523594T>C	ENST00000361188.5	-	7	2059	c.848A>G	c.(847-849)gAa>gGa	p.E283G	PRC1_ENST00000394249.3_Missense_Mutation_p.E283G|PRC1_ENST00000442656.2_Missense_Mutation_p.E242G|PRC1_ENST00000361919.3_Missense_Mutation_p.E283G|PRC1-AS1_ENST00000554388.1_RNA					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					TTTCAGTTCTTCCAACCGATC	0.433																																																0			15											165	138	147					15																	91523594		2198	4298	6496	89324598	SO:0001583	missense	9055			AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.848A>G	15.37:g.91523594T>C	ENSP00000354679:p.Glu283Gly		89324598		Missense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.782459	0.90282	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000442656;ENST00000556982	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	6.04	6.04	0.98038	.	0.048488	0.85682	D	0.000000	T	0.63010	0.2475	M	0.81341	2.54	0.58432	D	0.999997	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.76071	0.978;0.978;0.984;0.987	T	0.64935	-0.6290	10	0.48119	T	0.1	.	16.2378	0.82389	0.0:0.0:0.0:1.0	.	242;283;283;283	O43663-3;F8W9B5;O43663-2;O43663	.;.;.;PRC1_HUMAN	G	283;283;283;242;57	ENSP00000377793:E283G;ENSP00000354618:E283G;ENSP00000354679:E283G;ENSP00000409549:E242G	ENSP00000354679:E283G	E	-	2	0	PRC1	89324598	1.000000	0.71417	0.994000	0.49952	0.954000	0.61252	5.799000	0.69101	2.317000	0.78254	0.459000	0.35465	GAA		0.433	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		C	91523594	T	C	91523594	3	2	93	1	0	0	0	0	1	0	0	0	12480	1783	62	4	1050	4	PRC1	15	91523594	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	505743	91523594	11007798	189	25517										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92671650	92671650	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgtgaatgccaaaccgattcCttcactccagtgtgtggggc	11	11	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:92671650C>A	ENST00000318445.6	+	7	1657	c.1443C>A	c.(1441-1443)tcC>tcA	p.S481S	SLCO3A1_ENST00000424469.2_Silent_p.S481S|SLCO3A1_ENST00000555549.1_3'UTR	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	481	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	AAACCGATTCCTTCACTCCAG	0.562																																																0			15											195	153	167					15																	92671650		2198	4298	6496	90472654	SO:0001819	synonymous_variant	28232			AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.1443C>A	15.37:g.92671650C>A			90472654	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Silent	SNP	ENST00000318445.6	37	CCDS10371.1																																																																																				0.562	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		A	92671650	C	A	92671650	2	1	93	1	0	0	0	0	0	0	0	1	14765	668	24	2		2	SLCO3A1	15	92671650	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1148056	92671650	9859742	190	25518										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99491855	99491855	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cactggccgagcagccctacCagggcttgtccaacgagcaa	11	15	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr15:99491855C>A	ENST00000268035.6	+	20	4251	c.3640C>A	c.(3640-3642)Cag>Aag	p.Q1214K	IGF1R_ENST00000558762.1_Missense_Mutation_p.Q1213K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.Q1214*(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCAGCCCTACCAGGGCTTGTC	0.577																																																1	Substitution - Nonsense(1)	kidney(1)	15											110	106	107					15																	99491855		2197	4297	6494	97309378	SO:0001583	missense	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3640C>A	15.37:g.99491855C>A	ENSP00000268035:p.Gln1214Lys		97309378	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280850	0.95489	.	.	ENSG00000140443	ENST00000268035	D	0.81996	-1.56	5.83	4.92	0.64577	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000038	T	0.80924	0.4717	N	0.10916	0.065	0.80722	D	1	D;P	0.67145	0.996;0.888	P;P	0.60345	0.873;0.596	D	0.85003	0.0901	10	0.72032	D	0.01	.	14.9914	0.71390	0.0:0.9319:0.0:0.0681	.	1213;1214	C9J5X1;P08069	.;IGF1R_HUMAN	K	1214	ENSP00000268035:Q1214K	ENSP00000268035:Q1214K	Q	+	1	0	IGF1R	97309378	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	1.483000	0.48342	0.561000	0.74099	CAG		0.577	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99491855	C	A	99491855	3	1	93	1	0	0	0	0	1	0	0	0	7592	595	21	2	3718	2	IGF1R	15	99491855	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	6820205	99491855	3039537	191	25519										
TPSB2	64499	hgsc.bcm.edu	37	chr16	1279714	1279714	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctgacccccaacgatgcccActcgctgcagggcctggcct	10	19	0	1	rs192643610	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:1279714A>G	ENST00000339687.6	-	0	108				TPSB2_ENST00000430512.2_RNA|TPSB2_ENST00000445910.1_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				AACGATGCCCACTCGCTGCAG	0.711																																																0			16											25	32	29					16																	1279714		2180	4295	6475	1219715			64499			AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"tryptase beta II", "tryptase beta III"	191081	"tryptase beta 2"			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279714A>G			1219715	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Missense_Mutation	SNP	ENST00000339687.6	37		171	0.0782967032967033	39	0.07926829268292683	28	0.07734806629834254	44	0.07692307692307693	60	0.079155672823219	a	8.603	0.887339	0.17540	.	.	ENSG00000197253	ENST00000430512	T	0.81078	-1.45	4.02	-8.04	0.01110	.	1.382050	0.04868	N	0.445430	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32375	-0.9909	9	0.07644	T	0.81	.	3.7543	0.08579	0.5801:0.1008:0.1165:0.2027	.	29	P20231	TRYB2_HUMAN	A	29	ENSP00000412409:V29A	ENSP00000412409:V29A	V	-	2	0	TPSB2	1219715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.520000	0.00221	-2.364000	0.00607	-1.306000	0.01317	GTG		0.711	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164		G	1279714	A	G	1279714	1	3	93	0	1	0	0	0	0	0	0	0	16464	159	6	4		4	TPSB2	16	1279714	RNA	SNP	A	TCGA-DC-5337-01A-01D-1657-10		1279714	89075039	192	25520										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1306346	1306346	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gctgcccgtcctggcgagccCggcctacgtggcccctggtg	15	17	0	0	rs3865205	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:1306346C>G	ENST00000211076.3	+	1	213	c.65C>G	c.(64-66)cCg>cGg	p.P22R	TPSD1_ENST00000397534.2_Missense_Mutation_p.P15R|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	22			P -> R (in dbSNP:rs3865205). {ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTGGCGAGCCCGGCCTACGTG	0.721													-|||	1100	0.219649	0.112	0.1571	5008	,	,		14799	0.3641		0.1938	False		,,,				2504	0.2873															0			16											32	40	37					16																	1306346		2197	4298	6495	1246347	SO:0001583	missense	23430			AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.65C>G	16.37:g.1306346C>G	ENSP00000211076:p.Pro22Arg		1246347	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	3.814	-0.039033	0.07497	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.81579	-1.51;-1.51	2.55	0.112	0.14623	.	2.133630	0.02279	N	0.069280	T	0.64571	0.2610	N	0.08118	0	0.09310	N	1	B	0.22003	0.063	B	0.26693	0.072	T	0.51317	-0.8721	10	0.20046	T	0.44	.	6.9607	0.24595	0.0:0.3788:0.0:0.6212	rs3865205;rs3891050	22	Q9BZJ3	TRYD_HUMAN	R	15;22	ENSP00000380668:P15R;ENSP00000211076:P22R	ENSP00000211076:P22R	P	+	2	0	TPSD1	1246347	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	-2.678000	0.00839	-0.544000	0.06232	-2.646000	0.00150	CCG		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			G	1306346	C	G	1306346	3	3	93	1	0	0	0	0	1	0	0	0	16465	652	23	5	67	5	TPSD1	16	1306346	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	26632	1306346	89048407	193	25521										
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1396237	1396237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggcaggccttgaagggcctgGcatggccagagggggccacg	19	11	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:1396237G>T	ENST00000324385.5	+	25	2631	c.2473G>T	c.(2473-2475)Gca>Tca	p.A825S	BAIAP3_ENST00000421665.2_Missense_Mutation_p.A754S|BAIAP3_ENST00000397489.1_Missense_Mutation_p.A807S|BAIAP3_ENST00000568887.1_Missense_Mutation_p.A762S|BAIAP3_ENST00000562208.1_Missense_Mutation_p.A767S|BAIAP3_ENST00000426824.3_Missense_Mutation_p.A790S|BAIAP3_ENST00000397488.2_Missense_Mutation_p.A807S	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	825					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GAAGGGCCTGGCATGGCCAGA	0.687																																																0			16											22	27	26					16																	1396237		2191	4297	6488	1336238	SO:0001583	missense	8938			AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.2473G>T	16.37:g.1396237G>T	ENSP00000324510:p.Ala825Ser		1336238	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.319853	0.23994	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.71341	-0.55;-0.55;-0.56;-0.55;-0.55	3.98	3.98	0.46160	.	0.205916	0.40144	N	0.001171	T	0.60090	0.2242	L	0.47716	1.5	0.40836	D	0.983632	B;B;B;B	0.33000	0.393;0.229;0.229;0.229	B;B;B;B	0.26864	0.07;0.046;0.074;0.046	T	0.64833	-0.6314	10	0.49607	T	0.09	-16.7218	11.397	0.49847	0.0:0.0:1.0:0.0	.	754;767;825;807	E7EUB9;B4DIK3;O94812;A2A2B2	.;.;BAIP3_HUMAN;.	S	790;807;825;807;754	ENSP00000407242:A790S;ENSP00000380625:A807S;ENSP00000324510:A825S;ENSP00000380626:A807S;ENSP00000409533:A754S	ENSP00000324510:A825S	A	+	1	0	BAIAP3	1336238	0.321000	0.24625	0.986000	0.45419	0.174000	0.22865	0.732000	0.26072	2.046000	0.60703	0.491000	0.48974	GCA		0.687	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			T	1396237	G	T	1396237	3	4	93	1	0	0	0	0	1	0	0	0	1305	1203	42	2	2571	2	BAIAP3	16	1396237	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	89891	1396237	88958516	194	25522										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11214596	11214596	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtgtccaggcttggctggggAgtggtcaagtttgcaggcct	17	8	1	0	rs201350159		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:11214596A>G	ENST00000409790.1	+	20	2471	c.2241A>G	c.(2239-2241)ggA>ggG	p.G747G	CLEC16A_ENST00000409552.3_Silent_p.G729G|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TTGGCTGGGGAGTGGTCAAGT	0.532																																																1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	16											110	113	112					16																	11214596		2056	4200	6256	11122097	SO:0001819	synonymous_variant	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2241A>G	16.37:g.11214596A>G			11122097		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																				0.532	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		G	11214596	A	G	11214596	2	3	93	1	0	0	0	0	0	0	0	1	3506	291	11	4		4	CLEC16A	16	11214596	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	9818359	11214596	79140157	195	25523										
ABCC6	368	hgsc.bcm.edu	37	chr16	16248824	16248824	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcccaccctcagctgcctccTggagccgcagcagcccactg	9	20	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:16248824T>G	ENST00000205557.7	-	28	3976	c.3947A>C	c.(3946-3948)cAg>cCg	p.Q1316P		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1316	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AGCTGCCTCCTGGAGCCGCAG	0.677																																																0			16											20	17	18					16																	16248824		2189	4296	6485	16156325	SO:0001583	missense	368			AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3947A>C	16.37:g.16248824T>G	ENSP00000205557:p.Gln1316Pro		16156325	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.590438	0.28357	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.90324	-2.65	3.15	0.784	0.18578	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.238580	0.06176	U	0.678571	D	0.87442	0.6178	L	0.41824	1.3	0.09310	N	1	P;P	0.44877	0.845;0.845	P;P	0.44811	0.461;0.461	T	0.76602	-0.2899	10	0.62326	D	0.03	.	6.3105	0.21163	0.3172:0.0:0.0:0.6828	.	1316;1316	O95255;A8Y988	MRP6_HUMAN;.	P	1316;254	ENSP00000205557:Q1316P	ENSP00000205557:Q1316P	Q	-	2	0	ABCC6	16156325	0.400000	0.25295	0.764000	0.31436	0.668000	0.39293	4.144000	0.58057	0.125000	0.18397	0.386000	0.25728	CAG		0.677	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			G	16248824	T	G	16248824	3	3	93	1	0	0	0	0	1	0	0	0	57	1580	55	4	580	4	ABCC6	16	16248824	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	5034228	16248824	74105929	196	25524										
NOMO3	408050	hgsc.bcm.edu	37	chr16	16357002	16357002	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acatttcctcttactgtgacCgacaggcctgtgatggatgt	10	10	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:16357002C>T	ENST00000399336.4	+	13	1639	c.1467C>T	c.(1465-1467)acC>acT	p.T489T	NOMO3_ENST00000263012.6_Silent_p.T489T|NOMO3_ENST00000538468.1_Silent_p.T322T	NM_001004067.3	NP_001004067.1	P69849	NOMO3_HUMAN	NODAL modulator 3	489						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	8				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		TTACTGTGACCGACAGGCCTG	0.488																																																0			16											167	210	196					16																	16357002		2073	4295	6368	16264503	SO:0001819	synonymous_variant	408050			AK125530	CCDS42123.1	16p13	2004-11-24				ENSG00000103226			25242	protein-coding gene	gene with protein product		609159				15257293	Standard	NM_001004067		Approved		uc002deq.3	P69849	OTTHUMG00000170525	ENST00000399336.4:c.1467C>T	16.37:g.16357002C>T			16264503		Silent	SNP	ENST00000399336.4	37	CCDS42123.1																																																																																				0.488	NOMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409528.13	NM_001004067		T	16357002	C	T	16357002	2	4	93	1	0	0	0	0	0	0	0	1	10564	639	23	1		1	NOMO3	16	16357002	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	108178	16357002	73997751	197	25525										
ARL6IP1	23204	hgsc.bcm.edu	37	chr16	18804649	18804649	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	attccaatgtacttcaaaatGattccatgttggtttagtcc	6	8	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:18804649G>T	ENST00000304414.7	-	6	748	c.537C>A	c.(535-537)atC>atA	p.I179I	ARL6IP1_ENST00000546206.2_Silent_p.I150I|ARL6IP1_ENST00000562819.1_Silent_p.I64I|RPS15A_ENST00000322989.4_5'Flank|RPS15A_ENST00000563390.1_5'Flank|RP11-1035H13.3_ENST00000567078.2_Intron	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	179					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						ACTTCAAAATGATTCCATGTT	0.338																																																0			16											85	80	81					16																	18804649		2197	4300	6497	18712150	SO:0001819	synonymous_variant	23204			BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.537C>A	16.37:g.18804649G>T			18712150		Silent	SNP	ENST00000304414.7	37	CCDS10572.1																																																																																				0.338	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161		T	18804649	G	T	18804649	2	4	93	1	0	0	0	0	0	0	0	1	943	1280	45	2		2	ARL6IP1	16	18804649	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	2447647	18804649	71550104	198	25526										
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21968588	21968588	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctcaaagttgcccccaaagtTaaagccacagctgcgcctgc	8	15	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:21968588T>A	ENST00000268379.4	+	2	830	c.66T>A	c.(64-66)gtT>gtA	p.V22V	UQCRC2_ENST00000561553.1_Silent_p.V22V	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	22					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		CCCCCAAAGTTAAAGCCACAG	0.448																																					Colon(123;450 1645 12841 25393 45623)											0			16											69	71	70					16																	21968588		2198	4300	6498	21876089	SO:0001819	synonymous_variant	7385			J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.66T>A	16.37:g.21968588T>A			21876089	B3KSN4|Q9BQ05	Silent	SNP	ENST00000268379.4	37	CCDS10601.1																																																																																				0.448	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366		A	21968588	T	A	21968588	2	1	93	1	0	0	0	0	0	0	0	1	17060	1741	61	5		5	UQCRC2	16	21968588	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	3163939	21968588	68386165	199	25527										
PLK1	5347	hgsc.bcm.edu	37	chr16	23700038	23700038	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atcttctgggtcagcaagtgGgtggactattcggacaagta	13	7	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:23700038G>A	ENST00000300093.4	+	7	1353	c.1242G>A	c.(1240-1242)tgG>tgA	p.W414*	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	414					activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		TCAGCAAGTGGGTGGACTATT	0.542																																					Colon(12;240 564 27038 33155)											0			16											186	162	170					16																	23700038		2197	4300	6497	23607539	SO:0001587	stop_gained	5347				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.1242G>A	16.37:g.23700038G>A	ENSP00000300093:p.Trp414*		23607539	Q15153|Q99746	Nonsense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	G	38	6.717120	0.97784	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.469	16.9903	0.86352	0.0:0.0:1.0:0.0	.	.	.	.	X	414;317	.	ENSP00000300093:W414X	W	+	3	0	PLK1	23607539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.391000	0.97249	2.610000	0.88304	0.655000	0.94253	TGG		0.542	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		A	23700038	G	A	23700038	4	1	93	1	0	0	0	0	0	1	0	0	12125	1241	43	3	1268	3	PLK1	16	23700038	Nonsense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1731450	23700038	66654715	200	25528										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57059793	57059793	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgatgggctagatgaggcccTccagcctatgggtcctgatg	14	10	0	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:57059793T>C	ENST00000262510.6	+	6	1163	c.938T>C	c.(937-939)cTc>cCc	p.L313P	NLRC5_ENST00000308149.7_Missense_Mutation_p.L313P|NLRC5_ENST00000539144.1_Missense_Mutation_p.L313P|NLRC5_ENST00000436936.1_Missense_Mutation_p.L313P	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	313	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GATGAGGCCCTCCAGCCTATG	0.592																																																0			16											91	89	90					16																	57059793		2198	4300	6498	55617294	SO:0001583	missense	84166			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.938T>C	16.37:g.57059793T>C	ENSP00000262510:p.Leu313Pro		55617294	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.666611	0.29604	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.63	5.63	0.86233	NACHT nucleoside triphosphatase (1);	0.000000	0.27613	N	0.018589	D	0.85788	0.5778	M	0.68317	2.08	0.43435	D	0.995607	D;D;D;D	0.76494	0.998;0.999;0.959;0.997	D;D;D;D	0.70227	0.956;0.953;0.915;0.968	D	0.85869	0.1415	10	0.46703	T	0.11	.	13.7941	0.63160	0.0:0.0:0.0:1.0	.	313;313;313;313	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	P	313	ENSP00000262510:L313P;ENSP00000308886:L313P;ENSP00000389739:L313P;ENSP00000441727:L313P	ENSP00000262510:L313P	L	+	2	0	NLRC5	55617294	0.212000	0.23540	0.599000	0.28851	0.078000	0.17371	2.077000	0.41557	2.144000	0.66660	0.459000	0.35465	CTC		0.592	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57059793	T	C	57059793	3	2	93	1	0	0	0	0	1	0	0	0	10501	1551	54	4	952	4	NLRC5	16	57059793	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	33359755	57059793	33294960	201	25529										
CDH1	999	hgsc.bcm.edu	37	chr16	68849464	68849464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtacattctacacgtagcagTgacgaatgtggtaccttttg	10	8	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:68849464T>C	ENST00000261769.5	+	10	1558	c.1367T>C	c.(1366-1368)gTg>gCg	p.V456A	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Missense_Mutation_p.V395A|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	456	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.G441_E463del(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACGTAGCAGTGACGAATGTG	0.468			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	2	Unknown(1)|Deletion - In frame(1)	stomach(1)|breast(1)	16											157	130	139					16																	68849464		2198	4300	6498	67406965	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1367T>C	16.37:g.68849464T>C	ENSP00000261769:p.Val456Ala		67406965	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	T	7.361	0.624767	0.14193	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.55052	1.69;0.54	5.7	2.2	0.27929	Cadherin (5);Cadherin-like (1);	0.151709	0.30428	N	0.009659	T	0.32255	0.0823	N	0.13371	0.34	0.46298	D	0.99897	P;B	0.40250	0.709;0.213	B;B	0.43360	0.217;0.417	T	0.13335	-1.0513	10	0.06236	T	0.91	.	9.5778	0.39468	0.0:0.2058:0.0:0.7942	.	395;456	Q9UII8;P12830	.;CADH1_HUMAN	A	456;474;456;395	ENSP00000261769:V456A;ENSP00000414946:V395A	ENSP00000261769:V456A	V	+	2	0	CDH1	67406965	0.619000	0.27059	0.011000	0.14972	0.128000	0.20619	0.910000	0.28571	0.439000	0.26476	0.454000	0.30748	GTG		0.468	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		C	68849464	T	C	68849464	3	2	93	1	0	0	0	0	1	0	0	0	3101	1696	59	4	1405	4	CDH1	16	68849464	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	11789671	68849464	21505289	202	25530										
SLC7A5	8140	hgsc.bcm.edu	37	chr16	87870233	87870233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aagatgtccttggagaaggcGtagagcagcgtcatcacaca	12	9	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr16:87870233G>A	ENST00000261622.4	-	8	1226	c.1161C>T	c.(1159-1161)taC>taT	p.Y387Y	SLC7A5_ENST00000565644.1_Silent_p.Y121Y|RP4-536B24.2_ENST00000563687.1_RNA	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	387					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	TGGAGAAGGCGTAGAGCAGCG	0.622																																																0			16											87	81	83					16																	87870233		2198	4300	6498	86427734	SO:0001819	synonymous_variant	8140			AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"CD molecules", "Solute carriers"	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.1161C>T	16.37:g.87870233G>A			86427734	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Silent	SNP	ENST00000261622.4	37	CCDS10964.1																																																																																				0.622	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486		A	87870233	G	A	87870233	2	1	93	1	0	0	0	0	0	0	0	1	14737	1140	40	1		1	SLC7A5	16	87870233	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	19020769	87870233	2484520	203	25531										
VPS53	55275	hgsc.bcm.edu	37	chr17	617942	617942	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgaactccagttcctcctccTccatcattccgccacccggc	5	21	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:617942T>C	ENST00000571805.1	-	1	144	c.8A>G	c.(7-9)gAg>gGg	p.E3G	VPS53_ENST00000291074.5_Missense_Mutation_p.E3G|VPS53_ENST00000437048.2_Missense_Mutation_p.E3G|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000401468.3_Missense_Mutation_p.E3G|VPS53_ENST00000574029.1_Missense_Mutation_p.E3G			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	3					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TTCCTCCTCCTCCATCATTCC	0.701																																																0			17											58	60	59					17																	617942		2203	4300	6503	564692	SO:0001583	missense	55275				CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.8A>G	17.37:g.617942T>C	ENSP00000459312:p.Glu3Gly		564692	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		.	.	.	.	.	.	.	.	.	.	T	23.6	4.434824	0.83885	.	.	ENSG00000141252	ENST00000437048;ENST00000291074;ENST00000401468;ENST00000389040	T;T;T;T	0.54675	1.31;1.16;0.56;1.27	5.31	5.31	0.75309	.	0.092655	0.64402	D	0.000001	T	0.44603	0.1301	L	0.43152	1.355	0.80722	D	1	P;P;P;P	0.40731	0.608;0.728;0.608;0.728	B;B;B;B	0.36186	0.109;0.16;0.109;0.219	T	0.50676	-0.8800	10	0.66056	D	0.02	-24.931	13.2127	0.59834	0.0:0.0:0.0:1.0	.	3;3;3;3	E7EVT8;Q5VIR6-4;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	G	3	ENSP00000401435:E3G;ENSP00000291074:E3G;ENSP00000384294:E3G;ENSP00000373692:E3G	ENSP00000291074:E3G	E	-	2	0	VPS53	564692	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.536000	0.73842	2.002000	0.58637	0.482000	0.46254	GAG		0.701	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		C	617942	T	C	617942	3	2	93	1	0	0	0	0	1	0	0	0	17255	1551	54	4	2593	4	VPS53	17	617942	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10		617942	80577268	204	25532										
OR1G1	8390	hgsc.bcm.edu	37	chr17	3030389	3030389	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtgtagaagggagtggagggCattcatgatccaggatgcag	17	5	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:3030389C>G	ENST00000328890.2	-	1	486	c.457G>C	c.(457-459)Gcc>Ccc	p.A153P		NM_003555.1	NP_003546.1	P47890	OR1G1_HUMAN	olfactory receptor, family 1, subfamily G, member 1	153					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(3)|skin(3)	11						GAGTGGAGGGCATTCATGATC	0.512																																					Colon(127;1481 1654 8243 19426 50557)											0			17											141	125	130					17																	3030389		2203	4300	6503	2977139	SO:0001583	missense	8390			U04689	CCDS11020.1	17p13.3	2012-08-09			ENSG00000183024	ENSG00000183024		"GPCR / Class A : Olfactory receptors"	8204	protein-coding gene	gene with protein product				OR1G2		8004088, 9500546	Standard	NM_003555		Approved	OR17-209	uc002fvc.1	P47890	OTTHUMG00000090618	ENST00000328890.2:c.457G>C	17.37:g.3030389C>G	ENSP00000331545:p.Ala153Pro		2977139	Q4VBM1|Q6IFL9|Q9UM76	Missense_Mutation	SNP	ENST00000328890.2	37	CCDS11020.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.718075	0.48622	.	.	ENSG00000183024	ENST00000328890	T	0.00137	8.68	4.54	-2.52	0.06346	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	M	0.64170	1.965	0.09310	N	1	P	0.42941	0.794	P	0.45998	0.5	T	0.22871	-1.0204	9	0.52906	T	0.07	.	3.1808	0.06584	0.1297:0.1719:0.1279:0.5705	.	153	P47890	OR1G1_HUMAN	P	153	ENSP00000331545:A153P	ENSP00000331545:A153P	A	-	1	0	OR1G1	2977139	0.000000	0.05858	0.000000	0.03702	0.991000	0.79684	-0.446000	0.06837	-0.249000	0.09569	0.530000	0.56133	GCC		0.512	OR1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207206.2			G	3030389	C	G	3030389	3	3	93	1	0	0	0	0	1	0	0	0	10988	710	25	5	488	5	OR1G1	17	3030389	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	2412447	3030389	78164821	205	25533										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5462052	5462052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttccatatgcttctagcgtcTtttccaaatctatgatgcaa	5	10	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:5462052T>C	ENST00000572272.1	-	4	1963	c.1964A>G	c.(1963-1965)aAg>aGg	p.K655R	NLRP1_ENST00000262467.5_Missense_Mutation_p.K655R|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Missense_Mutation_p.K655R|NLRP1_ENST00000269280.4_Missense_Mutation_p.K655R|NLRP1_ENST00000345221.3_Missense_Mutation_p.K655R|NLRP1_ENST00000354411.3_Missense_Mutation_p.K655R			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	655					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTCTAGCGTCTTTTCCAAATC	0.448																																																0			17											145	127	133					17																	5462052		2203	4300	6503	5402776	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1964A>G	17.37:g.5462052T>C	ENSP00000460475:p.Lys655Arg		5402776	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	7.850	0.723828	0.15439	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.72394	-0.65;-0.65;-0.63;-0.61;-0.63	4.11	-5.56	0.02529	.	1.319690	0.05449	N	0.549209	T	0.49762	0.1576	L	0.37897	1.145	0.09310	N	1	B;B;B;B;B	0.28880	0.2;0.2;0.126;0.2;0.226	B;B;B;B;B	0.30179	0.112;0.112;0.035;0.112;0.063	T	0.37197	-0.9716	10	0.13108	T	0.6	.	0.5195	0.00609	0.4144:0.214:0.15:0.2215	.	655;655;655;655;655	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	R	655	ENSP00000442029:K655R;ENSP00000262467:K655R;ENSP00000269280:K655R;ENSP00000346390:K655R;ENSP00000324366:K655R	ENSP00000262467:K655R	K	-	2	0	NLRP1	5402776	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.006000	0.12833	-1.289000	0.02375	-0.417000	0.06048	AAG		0.448	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		C	5462052	T	C	5462052	3	2	93	1	0	0	0	0	1	0	0	0	10502	1609	56	4	2588	4	NLRP1	17	5462052	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2431663	5462052	75733158	206	25534										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6377779	6377779	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cccaggcagcaccgtcctccGcatggccaggaccaggccca	11	19	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:6377779G>A	ENST00000262483.8	-	10	1318	c.1231C>T	c.(1231-1233)Cgg>Tgg	p.R411W	PITPNM3_ENST00000576664.1_5'Flank|PITPNM3_ENST00000421306.3_Missense_Mutation_p.R375W	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	411	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		ACCGTCCTCCGCATGGCCAGG	0.667																																																0			17											40	35	36					17																	6377779		2203	4299	6502	6318503	SO:0001583	missense	83394			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1231C>T	17.37:g.6377779G>A	ENSP00000262483:p.Arg411Trp		6318503	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.266868	0.80469	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.63580	-0.02;-0.05	5.13	1.59	0.23543	DDHD (2);	0.000000	0.85682	D	0.000000	T	0.80248	0.4588	M	0.90082	3.085	0.50813	D	0.999893	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82348	-0.0502	10	0.87932	D	0	-19.2105	11.3745	0.49719	0.0:0.0:0.3342:0.6658	.	375;411	F8WEW5;Q9BZ71	.;PITM3_HUMAN	W	411;375	ENSP00000262483:R411W;ENSP00000407882:R375W	ENSP00000262483:R411W	R	-	1	2	PITPNM3	6318503	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.285000	0.43487	0.487000	0.27698	0.563000	0.77884	CGG		0.667	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		A	6377779	G	A	6377779	3	1	93	1	0	0	0	0	1	0	0	0	11983	1086	38	1	1737	1	PITPNM3	17	6377779	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	915727	6377779	74817431	207	25535										
C17orf49	124944	hgsc.bcm.edu	37	chr17	6919186	6919186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atcagctgtgtcatcaaggaAcggacagtgtgagggagggt	16	6	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:6919186A>G	ENST00000439424.2	+	3	286	c.210A>G	c.(208-210)gaA>gaG	p.E70E	C17orf49_ENST00000546495.1_Silent_p.E70E|MIR497HG_ENST00000572453.1_RNA|AC040977.1_ENST00000593646.1_5'Flank|MIR497HG_ENST00000443997.1_RNA|RP11-589P10.7_ENST00000572547.1_RNA|RNASEK-C17orf49_ENST00000547302.2_Missense_Mutation_p.N111S|C17orf49_ENST00000552402.1_Intron|C17orf49_ENST00000552775.1_Silent_p.E44E|C17orf49_ENST00000546760.1_Silent_p.E70E|MIR497HG_ENST00000385194.1_RNA|MIR497HG_ENST00000385056.1_RNA	NM_001142798.2|NM_174893.3	NP_001136270.1|NP_777553.1	Q8IXM2	BAP18_HUMAN	chromosome 17 open reading frame 49	70	SANT.				chromatin modification (GO:0016568)	MLL1 complex (GO:0071339)|NURF complex (GO:0016589)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|ovary(1)	4						TCATCAAGGAACGGACAGTGT	0.552																																																0			17											93	74	81					17																	6919186		2203	4300	6503	6859910	SO:0001819	synonymous_variant	124944			AK055800	CCDS32542.1, CCDS45595.1, CCDS45596.1	17p13.1	2013-02-11			ENSG00000258315	ENSG00000258315			28737	protein-coding gene	gene with protein product	"BPTF associated protein of 18 kDa", "human embryo lung cellular protein interacting with SARS-CoV nsp-10"						Standard	NM_174893		Approved	MGC49942, BAP18, HEPIS		Q8IXM2	OTTHUMG00000170147	ENST00000439424.2:c.210A>G	17.37:g.6919186A>G			6859910	B4DIV3|C9J4G0|E9PB29	Silent	SNP	ENST00000439424.2	37	CCDS32542.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577282	0.28092	.	.	ENSG00000161939	ENST00000547302	.	.	.	4.57	3.45	0.39498	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.31099	N	0.710612	.	.	.	.	.	.	T	0.37934	-0.9684	3	.	.	.	-3.1867	4.3385	0.11097	0.6672:0.2235:0.1093:0.0	.	.	.	.	S	111	.	.	N	+	2	0	C17orf49	6859910	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.602000	0.36783	1.900000	0.55004	0.460000	0.39030	AAC		0.552	C17orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407666.1	NM_174893		G	6919186	A	G	6919186	2	3	93	1	0	0	0	0	0	0	0	1	1865	40	2	4		4	C17orf49	17	6919186	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	541407	6919186	74276024	208	25536										
TP53	7157	hgsc.bcm.edu	37	chr17	7578224	7578224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	actatgtcgaaaagtgtttcTgtcatccaaatactccacac	5	11	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:7578224T>C	ENST00000269305.4	-	6	814	c.625A>G	c.(625-627)Aga>Gga	p.R209G	TP53_ENST00000455263.2_Missense_Mutation_p.R209G|TP53_ENST00000359597.4_Missense_Mutation_p.R209G|TP53_ENST00000445888.2_Missense_Mutation_p.R209G|TP53_ENST00000420246.2_Missense_Mutation_p.R209G|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.R209G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	209	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> I (in sporadic cancers; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).|R -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R209fs*6(27)|p.R209*(18)|p.0?(8)|p.?(5)|p.R77*(2)|p.R209fs*35(2)|p.D207fs*6(2)|p.R116*(2)|p.D208fs*1(1)|p.D208fs*38(1)|p.R209_R213delRNTFR(1)|p.D207_R213delDDRNTFR(1)|p.R209R(1)|p.D207_V216del10(1)|p.R116fs*6(1)|p.R209fs*5(1)|p.R209fs*36(1)|p.E204_N210delEYLDDRN(1)|p.R209fs*7(1)|p.R77fs*6(1)|p.D208_V216delDRNTFRHSV(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AAAGTGTTTCTGTCATCCAAA	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	79	Deletion - Frameshift(37)|Substitution - Nonsense(22)|Whole gene deletion(8)|Deletion - In frame(5)|Unknown(5)|Insertion - Frameshift(1)|Substitution - coding silent(1)	lung(17)|oesophagus(7)|upper_aerodigestive_tract(6)|biliary_tract(6)|prostate(5)|breast(5)|urinary_tract(4)|bone(4)|stomach(3)|soft_tissue(3)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|ovary(3)|salivary_gland(2)|pancreas(2)|thyroid(1)|liver(1)|skin(1)	17	GRCh37	CM971504	TP53	M							143	127	132					17																	7578224		2203	4300	6503	7518949	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.625A>G	17.37:g.7578224T>C	ENSP00000269305:p.Arg209Gly		7518949	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.205485	0.39003	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99719	-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52	5.41	-4.11	0.03928	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	1.073180	0.07006	N	0.824273	D	0.97848	0.9293	L	0.35487	1.065	0.23445	N	0.997664	B;B;B;B;B;B;B	0.19583	0.037;0.0;0.021;0.0;0.0;0.0;0.001	B;B;B;B;B;B;B	0.24848	0.056;0.002;0.035;0.002;0.003;0.006;0.002	D	0.99568	1.0970	10	0.30078	T	0.28	0.8848	2.5858	0.04830	0.1366:0.275:0.4156:0.1728	.	170;209;209;116;209;209;209	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	G	209;209;209;209;209;209;198;116;77;116;77	ENSP00000410739:R209G;ENSP00000352610:R209G;ENSP00000269305:R209G;ENSP00000398846:R209G;ENSP00000391127:R209G;ENSP00000391478:R209G;ENSP00000425104:R77G;ENSP00000423862:R116G	ENSP00000269305:R209G	R	-	1	2	TP53	7518949	0.000000	0.05858	0.005000	0.12908	0.450000	0.32258	-0.245000	0.08890	-0.585000	0.05905	0.533000	0.62120	AGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578224	T	C	7578224	3	2	93	1	0	0	0	0	1	0	0	0	16421	1588	55	4	669	4	TP53	17	7578224	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	659038	7578224	73616986	209	25537										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12028633	12028633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgaaagaatagacccaagcgCatcacgacaaggatatgatg	10	8	1	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:12028633C>T	ENST00000353533.5	+	8	899	c.836C>T	c.(835-837)gCa>gTa	p.A279V	MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Missense_Mutation_p.A290V	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(3)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		GACCCAAGCGCATCACGACAA	0.428			"D, Mis, N"		"pancreatic, breast, colorectal"																																		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	13	Whole gene deletion(10)|Unknown(3)	breast(4)|ovary(4)|lung(2)|biliary_tract(1)|large_intestine(1)|pancreas(1)	17											229	180	196					17																	12028633		2203	4300	6503	11969358	SO:0001583	missense	6416			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.836C>T	17.37:g.12028633C>T	ENSP00000262445:p.Ala279Val		11969358	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.386846	0.61956	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.73047	-0.64;-0.71	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	N	0.20845	0.615	0.80722	D	1	B;B;B	0.32365	0.367;0.067;0.082	B;B;B	0.37550	0.253;0.039;0.065	T	0.58053	-0.7704	10	0.28530	T	0.3	.	17.8064	0.88602	0.0:1.0:0.0:0.0	.	151;290;279	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	V	279;290;256;151	ENSP00000262445:A279V;ENSP00000410402:A290V	ENSP00000262445:A279V	A	+	2	0	MAP2K4	11969358	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.578000	0.82498	2.814000	0.96858	0.563000	0.77884	GCA		0.428	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	12028633	C	T	12028633	3	4	93	1	0	0	0	0	1	0	0	0	9269	710	25	3	866	3	MAP2K4	17	12028633	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	4450409	12028633	69166577	210	25538										
HS3ST3A1	9955	hgsc.bcm.edu	37	chr17	13400068	13400068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gatgcgcgcgggggcctcccGcgtgacgaagtaactgggcg	18	12	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:13400068G>A	ENST00000284110.1	-	2	1464	c.667C>T	c.(667-669)Cgg>Tgg	p.R223W	HS3ST3A1_ENST00000578576.1_Missense_Mutation_p.R21W	NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	223					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGGGCCTCCCGCGTGACGAAG	0.617																																																0			17											68	84	79					17																	13400068		2202	4300	6502	13340793	SO:0001583	missense	9955			AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"Sulfotransferases, membrane-bound"	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.667C>T	17.37:g.13400068G>A	ENSP00000284110:p.Arg223Trp		13340793	A8K7N2	Missense_Mutation	SNP	ENST00000284110.1	37	CCDS11165.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040396	0.55003	.	.	ENSG00000153976	ENST00000284110	T	0.44482	0.92	5.32	4.27	0.50696	Sulfotransferase domain (1);	0.138859	0.42682	U	0.000680	T	0.56863	0.2014	M	0.69358	2.11	0.44702	D	0.997697	D	0.89917	1.0	P	0.62491	0.903	T	0.58864	-0.7561	10	0.87932	D	0	.	11.3364	0.49507	0.0:0.0:0.6674:0.3326	.	223	Q9Y663	HS3SA_HUMAN	W	223	ENSP00000284110:R223W	ENSP00000284110:R223W	R	-	1	2	HS3ST3A1	13340793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.053000	0.49901	2.873000	0.98535	0.563000	0.77884	CGG		0.617	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042		A	13400068	G	A	13400068	3	1	93	1	0	0	0	0	1	0	0	0	7386	1086	38	1	557	1	HS3ST3A1	17	13400068	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1371435	13400068	67795142	211	25539										
SLC13A2	9058	hgsc.bcm.edu	37	chr17	26824244	26824244	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acagtccaacaccacagcccAgtgcctgccaagcctggcca	8	18	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:26824244A>G	ENST00000314669.5	+	12	2156	c.1736A>G	c.(1735-1737)cAg>cGg	p.Q579R	SLC13A2_ENST00000545060.1_Missense_Mutation_p.Q536R|SLC13A2_ENST00000444914.3_Missense_Mutation_p.Q628R|SLC13A2_ENST00000537681.1_Missense_Mutation_p.Q508R	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	579					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	ACCACAGCCCAGTGCCTGCCA	0.627																																																0			17											107	96	100					17																	26824244		2203	4300	6503	23848371	SO:0001583	missense	9058			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1736A>G	17.37:g.26824244A>G	ENSP00000316202:p.Gln579Arg		23848371	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	A	7.327	0.618102	0.14129	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000537681	T;T;T;T	0.70399	-0.17;-0.18;-0.47;-0.48	5.72	1.89	0.25635	.	3.689560	0.00508	N	0.000179	T	0.61123	0.2322	L	0.38175	1.15	0.09310	N	1	B;B;B;B	0.20988	0.05;0.017;0.05;0.029	B;B;B;B	0.20767	0.031;0.028;0.031;0.015	T	0.35674	-0.9779	10	0.15952	T	0.53	-7.3383	7.1411	0.25556	0.5439:0.3307:0.0:0.1254	.	536;628;508;579	F5GWV6;E7ETH5;G3V1L2;Q13183	.;.;.;S13A2_HUMAN	R	579;628;536;508	ENSP00000316202:Q579R;ENSP00000392411:Q628R;ENSP00000441935:Q536R;ENSP00000440802:Q508R	ENSP00000316202:Q579R	Q	+	2	0	SLC13A2	23848371	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.758000	0.04766	0.411000	0.25702	0.459000	0.35465	CAG		0.627	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		G	26824244	A	G	26824244	3	3	93	1	0	0	0	0	1	0	0	0	14429	188	7	4	1929	4	SLC13A2	17	26824244	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	13424176	26824244	54370966	212	25540										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27416980	27416980	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggagaagtgtgaacccaccTccagccgtttcacttgcgtc	11	13	1	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:27416980T>C	ENST00000527372.1	-	37	5705	c.5525A>G	c.(5524-5526)gAg>gGg	p.E1842G	MYO18A_ENST00000531253.1_Splice_Site_p.E1842G|MYO18A_ENST00000354329.4_Splice_Site_p.E1842G|MYO18A_ENST00000533112.1_Splice_Site_p.E1805G|TIAF1_ENST00000408971.2_5'UTR|MYO18A_ENST00000529578.1_5'UTR	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1842					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TGAACCCACCTCCAGCCGTTT	0.627																																					Esophageal Squamous(182;472 2015 7001 15270 22562)											0			17											57	64	62					17																	27416980		2049	4175	6224	24441106	SO:0001630	splice_region_variant	399687			D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.5526+1A>G	17.37:g.27416980T>C			24441106	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.0|26.0	4.699537|4.699537	0.88830|0.88830	.|.	.|.	ENSG00000196535|ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428;ENST00000546105|ENST00000527859	D;D;D;D|.	0.91011|.	-2.45;-2.77;-2.43;-2.45|.	4.79|4.79	4.79|4.79	0.61399|0.61399	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75391|0.75391	0.3843|0.3843	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.85130|.	0.997;0.997;0.997;0.997|.	T|T	0.77151|0.77151	-0.2693|-0.2693	10|5	0.87932|.	D|.	0|.	.|.	15.0476|15.0476	0.71838|0.71838	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1445;1805;1842;1842|.	F8W6Y3;Q92614-3;Q92614-4;Q92614|.	.;.;.;MY18A_HUMAN|.	G|G	1842;1805;1805;1842;1842;738;738;1445;123|105	ENSP00000346291:E1842G;ENSP00000435932:E1805G;ENSP00000434228:E1842G;ENSP00000437073:E1842G|.	ENSP00000346291:E1842G|.	E|R	-|-	2|1	0|2	MYO18A|MYO18A	24441106|24441106	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.894000|0.894000	0.52154|0.52154	5.870000|5.870000	0.69620|0.69620	2.104000|2.104000	0.64026|0.64026	0.528000|0.528000	0.53228|0.53228	GAG|AGA		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	Missense_Mutation	C	27416980	T	C	27416980	5	2	93	1	0	0	0	0	0	0	1	0	10095	1565	54	4	663	4	MYO18A	17	27416980	Splice_Site	SNP	T	TCGA-DC-5337-01A-01D-1657-10	592736	27416980	53778230	213	25541										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27448723	27448723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggccagatcctccagacggtCgcaggagggagcattagcct	14	12	0	2	rs373037295		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:27448723C>T	ENST00000527372.1	-	5	1393	c.1213G>A	c.(1213-1215)Gac>Aac	p.D405N	MYO18A_ENST00000531253.1_Missense_Mutation_p.D405N|MYO18A_ENST00000354329.4_Missense_Mutation_p.D405N|MYO18A_ENST00000533112.1_Missense_Mutation_p.D405N	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	405	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TCCAGACGGTCGCAGGAGGGA	0.632																																					Esophageal Squamous(182;472 2015 7001 15270 22562)											0			17						C	ASN/ASP,ASN/ASP	1,4289		0,1,2144	16	20	19		1213,1213	5.4	1	17		19	0,8440		0,0,4220	no	missense,missense	MYO18A	NM_078471.3,NM_203318.1	23,23	0,1,6364	TT,TC,CC		0.0,0.0233,0.0079	benign,benign	405/2055,405/2040	27448723	1,12729	2145	4220	6365	24472849	SO:0001583	missense	399687			D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.1213G>A	17.37:g.27448723C>T	ENSP00000437073:p.Asp405Asn		24472849	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.30|19.30	3.800250|3.800250	0.70567|0.70567	2.33E-4|2.33E-4	0.0|0.0	ENSG00000196535|ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000531686|ENST00000528564	T;T;T;T|.	0.72282|.	-0.64;-0.64;-0.64;-0.64|.	5.37|5.37	5.37|5.37	0.77165|0.77165	Myosin head, motor domain (1);|.	0.185478|.	0.56097|.	D|.	0.000026|.	T|T	0.78729|0.78729	0.4329|0.4329	M|M	0.80616|0.80616	2.505|2.505	0.48185|0.48185	D|D	0.999608|0.999608	P;B;B;B|.	0.40909|.	0.732;0.054;0.054;0.171|.	B;B;B;B|.	0.39876|.	0.312;0.014;0.014;0.019|.	T|T	0.79470|0.79470	-0.1790|-0.1790	10|5	0.87932|.	D|.	0|.	.|.	18.7332|18.7332	0.91744|0.91744	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	74;405;405;405|.	Q92614-2;Q92614-3;Q92614-4;Q92614|.	.;.;.;MY18A_HUMAN|.	N|Q	405;405;405;405;405;85|110	ENSP00000346291:D405N;ENSP00000435932:D405N;ENSP00000434228:D405N;ENSP00000437073:D405N|.	ENSP00000346291:D405N|.	D|R	-|-	1|2	0|0	MYO18A|MYO18A	24472849|24472849	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.993000|0.993000	0.82548|0.82548	5.626000|5.626000	0.67777|0.67777	2.505000|2.505000	0.84491|0.84491	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.632	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27448723	C	T	27448723	3	4	93	1	0	0	0	0	1	0	0	0	10095	884	31	1	5103	1	MYO18A	17	27448723	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	31743	27448723	53746487	214	25542										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33491061	33491061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggcaggttccagatctgccaTcctgcctgcccctgactgac	10	16	1	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:33491061T>C	ENST00000268876.5	+	9	1124	c.1027T>C	c.(1027-1029)Tcc>Ccc	p.S343P	RP11-799D4.3_ENST00000585646.1_RNA|UNC45B_ENST00000378449.1_Missense_Mutation_p.S343P|UNC45B_ENST00000394570.2_Missense_Mutation_p.S343P|UNC45B_ENST00000591048.1_Missense_Mutation_p.S343P|UNC45B_ENST00000433649.1_Missense_Mutation_p.S343P	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	343					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				AGATCTGCCATCCTGCCTGCC	0.577																																																0			17											160	148	152					17																	33491061		2203	4300	6503	30515174	SO:0001583	missense	146862			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1027T>C	17.37:g.33491061T>C	ENSP00000268876:p.Ser343Pro		30515174	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115605	0.37339	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	4.54	3.44	0.39384	.	0.350601	0.32488	N	0.006037	T	0.03477	0.0100	N	0.03608	-0.345	0.21220	N	0.999759	B;B;B	0.32467	0.053;0.372;0.0	B;B;B	0.34346	0.03;0.18;0.006	T	0.36089	-0.9762	10	0.39692	T	0.17	-9.3985	4.9553	0.14036	0.3006:0.0:0.1789:0.5205	.	343;343;343	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	P	343	ENSP00000378071:S343P;ENSP00000268876:S343P;ENSP00000412840:S343P;ENSP00000367710:S343P	ENSP00000268876:S343P	S	+	1	0	UNC45B	30515174	1.000000	0.71417	0.961000	0.40146	0.951000	0.60555	3.288000	0.51739	0.854000	0.35336	0.459000	0.35465	TCC		0.577	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		C	33491061	T	C	33491061	3	2	93	1	0	0	0	0	1	0	0	0	17029	1435	50	4	1057	4	UNC45B	17	33491061	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	6042338	33491061	47704149	215	25543										
ACACA	31	hgsc.bcm.edu	37	chr17	35445945	35445945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctattaccgagtgaacaccaTcctcctctgtcagctgtttc	6	14	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:35445945T>C	ENST00000394406.2	-	55	7035	c.6845A>G	c.(6844-6846)gAt>gGt	p.D2282G	ACACA_ENST00000335166.5_Missense_Mutation_p.D2204G|ACACA_ENST00000360679.3_Missense_Mutation_p.D2224G|ACACA_ENST00000361253.5_Missense_Mutation_p.D408G|ACACA_ENST00000353139.5_Missense_Mutation_p.D2319G	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2282					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GTGAACACCATCCTCCTCTGT	0.488																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											0			17											228	196	207					17																	35445945		2203	4300	6503	32520058	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6845A>G	17.37:g.35445945T>C	ENSP00000377928:p.Asp2282Gly		32520058	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.591580	0.66219	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330;ENST00000361253	T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54	5.77	5.77	0.91146	.	0.052073	0.85682	D	0.000000	T	0.53433	0.1796	M	0.65498	2.005	0.80722	D	1	B;B;B;B;B	0.10296	0.003;0.0;0.002;0.0;0.0	B;B;B;B;B	0.13407	0.003;0.002;0.009;0.001;0.003	T	0.49399	-0.8944	10	0.36615	T	0.2	-19.3572	16.089	0.81080	0.0:0.0:0.0:1.0	.	320;981;2319;2282;2224	B4DIG6;F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;.;ACACA_HUMAN;.	G	2319;2224;2282;2306;2204;981;408	ENSP00000344789:D2319G;ENSP00000353898:D2224G;ENSP00000377928:D2282G;ENSP00000335323:D2204G;ENSP00000354565:D408G	ENSP00000335323:D2204G	D	-	2	0	ACACA	32520058	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	8.021000	0.88750	2.205000	0.71048	0.533000	0.62120	GAT		0.488	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35445945	T	C	35445945	3	2	93	1	0	0	0	0	1	0	0	0	106	1435	50	4	203	4	ACACA	17	35445945	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1954884	35445945	45749265	216	25544										
SMARCE1	6605	hgsc.bcm.edu	37	chr17	38785137	38785137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tactatcactggttccttccTctgccatactgtcgaccccc	5	17	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:38785137T>C	ENST00000348513.6	-	11	1916	c.1136A>G	c.(1135-1137)gAg>gGg	p.E379G	SMARCE1_ENST00000578044.1_Missense_Mutation_p.E309G|SMARCE1_ENST00000431889.2_Missense_Mutation_p.E361G|SMARCE1_ENST00000377808.4_3'UTR|SMARCE1_ENST00000400122.3_3'UTR|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.E344G|SMARCE1_ENST00000544009.1_Missense_Mutation_p.E309G	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	379	Glu-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)			large_intestine(1)	1		Breast(137;0.000812)				GGTTCCTTCCTCTGCCATACT	0.502																																																0			17											137	116	123					17																	38785137		2203	4300	6503	36038663	SO:0001583	missense	6605			AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.1136A>G	17.37:g.38785137T>C	ENSP00000323967:p.Glu379Gly		36038663	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	Missense_Mutation	SNP	ENST00000348513.6	37	CCDS11370.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.006137	0.54361	.	.	ENSG00000073584	ENST00000348513;ENST00000544009;ENST00000431889	T;T	0.20738	2.05;2.05	4.99	3.87	0.44632	.	0.344315	0.37053	N	0.002278	T	0.13329	0.0323	N	0.19112	0.55	0.32623	N	0.523127	B;B	0.17667	0.023;0.023	B;B	0.17722	0.015;0.019	T	0.11817	-1.0572	10	0.26408	T	0.33	.	11.2013	0.48743	0.1376:0.0:0.0:0.8624	.	344;379	C0IMW4;Q969G3	.;SMCE1_HUMAN	G	379;309;361	ENSP00000323967:E379G;ENSP00000445370:E361G	ENSP00000323967:E379G	E	-	2	0	SMARCE1	36038663	1.000000	0.71417	0.926000	0.36857	0.992000	0.81027	5.385000	0.66231	0.971000	0.38288	0.533000	0.62120	GAG		0.502	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1	NM_003079		C	38785137	T	C	38785137	3	2	93	1	0	0	0	0	1	0	0	0	14817	1551	54	4	103	4	SMARCE1	17	38785137	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	3339192	38785137	42410073	217	25545										
KRT222	125113	hgsc.bcm.edu	37	chr17	38818214	38818214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cttgcaggtggtgccactggCgtcgggcctccttgagttct	14	12	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:38818214C>A	ENST00000476049.1	-	2	220	c.179G>T	c.(178-180)cGc>cTc	p.R60L	KRT222_ENST00000394052.3_Missense_Mutation_p.R60L			Q8N1A0	KT222_HUMAN	keratin 222	60						intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1)	15						GTGCCACTGGCGTCGGGCCTC	0.463																																																0			17											205	197	200					17																	38818214		2203	4300	6503	36071740	SO:0001583	missense	0			AK092967	CCDS11371.1	17q21.2	2013-06-25	2009-08-25	2009-08-25	ENSG00000213424	ENSG00000213424		"-"	28695	protein-coding gene	gene with protein product			"keratin 222 pseudogene"	KRT222P		16831889	Standard	NM_152349		Approved	KA21, MGC45562	uc002hvc.2	Q8N1A0	OTTHUMG00000133374	ENST00000476049.1:c.179G>T	17.37:g.38818214C>A	ENSP00000463483:p.Arg60Leu		36071740	Q7Z368	Missense_Mutation	SNP	ENST00000476049.1	37	CCDS11371.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.855712	0.91355	.	.	ENSG00000213424	ENST00000394049;ENST00000394052	D	0.90197	-2.63	5.8	5.8	0.92144	Filament (1);	0.236574	0.34178	U	0.004199	D	0.96259	0.8780	M	0.89840	3.065	0.49582	D	0.999804	D;D	0.61697	0.988;0.99	P;D	0.65573	0.895;0.936	D	0.96430	0.9318	10	0.87932	D	0	-9.0565	20.0553	0.97649	0.0:1.0:0.0:0.0	.	20;60	Q8N1A0-2;Q8N1A0	.;KT222_HUMAN	L	20;60	ENSP00000377616:R60L	ENSP00000377613:R20L	R	-	2	0	KRT222	36071740	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.302000	0.59092	2.754000	0.94517	0.585000	0.79938	CGC		0.463	KRT222-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000447539.1	NM_152349		A	38818214	C	A	38818214	3	1	93	1	0	0	0	0	1	0	0	0	8480	768	27	2	728	2	KRT222	17	38818214	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	33077	38818214	42376996	218	25546										
KRT23	25984	hgsc.bcm.edu	37	chr17	39084583	39084583	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctgctctgcacagtggctggActggctgcctcctgggacat	13	13	1	0	rs532163182	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:39084583A>G	ENST00000209718.3	-	6	1252	c.828T>C	c.(826-828)agT>agC	p.S276S	KRT23_ENST00000436344.3_Silent_p.S139S|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	276	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				CAGTGGCTGGACTGGCTGCCT	0.562													A|||	735	0.146765	0.0658	0.1657	5008	,	,		20886	0.2917		0.2296	False		,,,				2504	0.0082															0			17											173	142	153					17																	39084583		2203	4300	6503	36338109	SO:0001819	synonymous_variant	25984			AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"-", "Intermediate filaments type I, keratins (acidic)"	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.828T>C	17.37:g.39084583A>G			36338109	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Silent	SNP	ENST00000209718.3	37	CCDS11380.1																																																																																				0.562	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1			G	39084583	A	G	39084583	2	3	93	1	0	0	0	0	0	0	0	1	8481	272	10	4		4	KRT23	17	39084583	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	266369	39084583	42110627	219	25547										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51900732	51900732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagggaccagcgtaccgccaCgaaatgggttgcgatgatcc	13	12	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:51900732C>T	ENST00000268919.4	+	1	494	c.338C>T	c.(337-339)aCg>aTg	p.T113M		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	113					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T113M(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CGTACCGCCACGAAATGGGTT	0.592																																																1	Substitution - Missense(1)	endometrium(1)	17											76	82	80					17																	51900732		2203	4300	6503	49255731	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.338C>T	17.37:g.51900732C>T	ENSP00000268919:p.Thr113Met		49255731	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	2.969	-0.212944	0.06140	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.74315	-0.83	5.11	4.14	0.48551	.	0.928117	0.08888	N	0.878962	T	0.62270	0.2414	L	0.42245	1.32	0.09310	N	1	P	0.37731	0.607	B	0.26416	0.069	T	0.49808	-0.8900	10	0.30078	T	0.28	.	9.5255	0.39162	0.0:0.9047:0.0:0.0953	.	113	Q8N4N8	KIF2B_HUMAN	M	113;36	ENSP00000268919:T113M	ENSP00000268919:T113M	T	+	2	0	KIF2B	49255731	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.167000	0.16602	1.504000	0.48704	0.655000	0.94253	ACG		0.592	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51900732	C	T	51900732	3	4	93	1	0	0	0	0	1	0	0	0	8319	536	19	1	340	1	KIF2B	17	51900732	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	12816149	51900732	29294478	220	25548										
TEX14	56155	hgsc.bcm.edu	37	chr17	56676375	56676376	+	Frame_Shift_Del	DEL	CT	CT	-													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aacttgtaggcatttgtaaaCtctcttgaagtggcccataa							TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:56676375_56676376delCT	ENST00000240361.8	-	14	2433_2434	c.2348_2349delAG	c.(2347-2349)gagfs	p.E783fs	TEX14_ENST00000389934.3_Frame_Shift_Del_p.E777fs|TEX14_ENST00000349033.5_Frame_Shift_Del_p.E777fs			Q8IWB6	TEX14_HUMAN	testis expressed 14	783					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CATTTGTAAACTCTCTTGAAGT	0.46																																																0			17																																								54031375	SO:0001589	frameshift_variant	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2348_2349delAG	17.37:g.56676379_56676380delCT	ENSP00000240361:p.Glu783fs		54031374	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Frame_Shift_Del	DEL	ENST00000240361.8	37	CCDS56042.1																																																																																				0.46	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			-	56676376	CT	-	56676375	7	5	93	1	0	1	0	1	0	0	0	0	15817	564	20	0	2224	0	TEX14	17	56676375	Frame_Shift_Del	DEL	CT	TCGA-DC-5337-01A-01D-1657-10	4775643	56676375	24518835	221	25549										
ICAM2	3384	hgsc.bcm.edu	37	chr17	62081108	62081108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agaagttgcggtggccatccTctctgtcagccgtgctgttg	13	11	2	1	rs56285713		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:62081108T>C	ENST00000412356.1	-	5	899	c.545A>G	c.(544-546)gAg>gGg	p.E182G	ICAM2_ENST00000579788.1_Missense_Mutation_p.E182G|ICAM2_ENST00000581417.1_5'UTR|ICAM2_ENST00000578892.1_Missense_Mutation_p.E158G|C17orf72_ENST00000412177.1_3'UTR|ICAM2_ENST00000578379.1_Missense_Mutation_p.E81G|ICAM2_ENST00000579687.1_Missense_Mutation_p.E182G|ICAM2_ENST00000449662.2_Missense_Mutation_p.E182G|ICAM2_ENST00000418105.1_Missense_Mutation_p.E182G	NM_001099786.1	NP_001093256.1	P13598	ICAM2_HUMAN	intercellular adhesion molecule 2	182	Ig-like C2-type 2.				extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|uropod (GO:0001931)	integrin binding (GO:0005178)			large_intestine(1)|lung(2)|ovary(1)|skin(2)	6						GTGGCCATCCTCTCTGTCAGC	0.577																																																0			17											71	60	64					17																	62081108		2203	4300	6503	59434840	SO:0001583	missense	3384				CCDS11657.1	17q23.3	2014-01-30			ENSG00000108622	ENSG00000108622		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5345	protein-coding gene	gene with protein product		146630				1769660	Standard	NM_001099786		Approved	CD102	uc002jdx.4	P13598		ENST00000412356.1:c.545A>G	17.37:g.62081108T>C	ENSP00000415283:p.Glu182Gly		59434840	Q14600	Missense_Mutation	SNP	ENST00000412356.1	37	CCDS11657.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.126571	0.37533	.	.	ENSG00000108622	ENST00000412356;ENST00000418105;ENST00000449662	T;T;T	0.04194	3.68;3.68;3.68	5.54	3.36	0.38483	Immunoglobulin-like fold (1);	0.548756	0.19238	N	0.119223	T	0.05640	0.0148	L	0.52126	1.63	0.09310	N	1	B	0.18863	0.031	B	0.17433	0.018	T	0.32587	-0.9901	10	0.48119	T	0.1	-12.4187	6.9022	0.24288	0.0:0.1815:0.0:0.8185	.	182	P13598	ICAM2_HUMAN	G	182	ENSP00000415283:E182G;ENSP00000388666:E182G;ENSP00000392634:E182G	ENSP00000415283:E182G	E	-	2	0	ICAM2	59434840	0.002000	0.14202	0.001000	0.08648	0.010000	0.07245	0.960000	0.29253	0.410000	0.25675	0.459000	0.35465	GAG		0.577	ICAM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443687.1			C	62081108	T	C	62081108	3	2	93	1	0	0	0	0	1	0	0	0	7501	1551	54	4	290	4	ICAM2	17	62081108	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	5404733	62081108	19114102	222	25550										
SOX9	6662	hgsc.bcm.edu	37	chr17	70119814	70119815	+	Frame_Shift_Ins	INS	-	-	GT													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cccctatcgacttccgcgacINSgtggacatcggcgagctgag					rs201477430		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:70119814_70119815insGT	ENST00000245479.2	+	3	1188_1189	c.816_817insGT	c.(817-819)gtgfs	p.V273fs		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	273					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			ACTTCCGCGACGTGGACATCGG	0.653																																					Pancreas(42;83 1041 2320 35205 39456)											0			17																																								67631410	SO:0001589	frameshift_variant	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.817_818dupGT	17.37:g.70119815_70119816dupGT	ENSP00000245479:p.Val273fs		67631409	Q53Y80	Frame_Shift_Ins	INS	ENST00000245479.2	37	CCDS11689.1																																																																																				0.653	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		GT	70119815	-	GT	70119814	7	5	93	1	0	1	1	0	0	0	0	0	14995	535	19	0	826	0	SOX9	17	70119814	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	8038706	70119814	11075396	223	25551										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76506523	76506523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgttgcggacctcatcctcGtaactgtggaggttcagctg	12	10	2	0	rs200358276	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:76506523G>A	ENST00000585328.1	-	27	4294	c.4170C>T	c.(4168-4170)taC>taT	p.Y1390Y	DNAH17_ENST00000389840.5_Silent_p.Y1389Y	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1389	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCTCATCCTCGTAACTGTGGA	0.517													G|||	2	0.000399361	8e-04	0	5008	,	,		17339	0		0.001	False		,,,				2504	0															0			17						G		0,4080		0,0,2040	162	159	160		4179	-5.5	0.1	17		160	2,8396		0,2,4197	no	coding-synonymous	DNAH17	NM_173628.3		0,2,6237	AA,AG,GG		0.0238,0.0,0.016		1393/4463	76506523	2,12476	2040	4199	6239	74018118	SO:0001819	synonymous_variant	8632			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4170C>T	17.37:g.76506523G>A			74018118	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																					0.517	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76506523	G	A	76506523	2	1	93	1	0	0	0	0	0	0	0	1	4612	1140	40	1		1	DNAH17	17	76506523	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	6386709	76506523	4688687	224	25552										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77079184	77079184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgagtgtctggagaagaaggAtttcttccagaaccaggaca	12	7	2	4			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:77079184A>G	ENST00000579016.1	+	8	1121	c.1121A>G	c.(1120-1122)gAt>gGt	p.D374G	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	374	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.					cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GAGAAGAAGGATTTCTTCCAG	0.547											OREG0024792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			17											108	112	111					17																	77079184		2011	4173	6184	74590779	SO:0001583	missense	64772			AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1121A>G	17.37:g.77079184A>G	ENSP00000462333:p.Asp374Gly	1173	74590779	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.325598	0.41197	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.51	4.44	0.53790	Glycoside hydrolase, family 85 (1);BRCT (1);	0.704894	0.14860	N	0.294124	T	0.60470	0.2271	M	0.63428	1.95	0.80722	D	1	B	0.30870	0.298	B	0.34093	0.175	T	0.55915	-0.8065	9	0.41790	T	0.15	-18.6628	10.8586	0.46812	0.9254:0.0:0.0746:0.0	.	374	Q8NFI3	ENASE_HUMAN	G	374	.	ENSP00000438577:D374G	D	+	2	0	ENGASE	74590779	0.020000	0.18652	0.009000	0.14445	0.475000	0.33008	2.907000	0.48743	0.935000	0.37341	0.459000	0.35465	GAT		0.547	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		G	77079184	A	G	77079184	3	3	93	1	0	0	0	0	1	0	0	0	5131	333	12	4	1151	4	ENGASE	17	77079184	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	572661	77079184	4116026	225	25553										
TSPAN10	83882	hgsc.bcm.edu	37	chr17	79612397	79612397	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgcagtgagcctggctggctAcctgggcgccctctgtgaga	15	13	1	2	rs6420484	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:79612397A>G	ENST00000572675.1	+	0	416				TSPAN10_ENST00000328585.4_RNA			Q9H1Z9	TSN10_HUMAN	tetraspanin 10						establishment of protein localization to organelle (GO:0072594)	integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CTGGCTGGCTACCTGGGCGCC	0.687													G|||	4230	0.844649	0.947	0.7781	5008	,	,		17743	0.997		0.6431	False		,,,				2504	0.8037															0			17						G	CYS/TYR	3632,438		1624,384,27	29	38	35		416	4.2	1	17	dbSNP_116	35	5469,2911		1796,1877,517	yes	missense	TSPAN10	NM_031945.3	194	3420,2261,544	GG,GA,AA		34.7375,10.7617,26.8996	probably-damaging	139/356	79612397	9101,3349	2035	4190	6225	77222802			83882			BC032802		17q25.3	2013-10-02			ENSG00000182612	ENSG00000182612		"Tetraspanins"	29942	protein-coding gene	gene with protein product	"oculospanin"					12107410	Standard	NM_031945		Approved	OCSP	uc010die.3	Q9H1Z9	OTTHUMG00000178037		17.37:g.79612397A>G			77222802	Q8N548	Missense_Mutation	SNP	ENST00000572675.1	37		1779	0.8145604395604396	463	0.9410569105691057	270	0.7458563535911602	570	0.9965034965034965	476	0.6279683377308707	G	0.317	-0.964059	0.02249	0.892383	0.652625	ENSG00000182612	ENST00000328585;ENST00000540189	T	0.73789	-0.78	4.15	4.15	0.48705	.	0.058357	0.64402	N	0.000001	T	0.00012	0.0000	.	.	.	0.34577	P	0.28596200000000005	B	0.02656	0.0	B	0.01281	0.0	T	0.45338	-0.9268	8	0.02654	T	1	-13.6114	12.1229	0.53902	0.0847:0.0:0.9152:0.0	rs6420484;rs17846019;rs17859003;rs59590586	139	Q6PJ65	.	C	139	ENSP00000331620:Y139C	ENSP00000331620:Y139C	Y	+	2	0	TSPAN10	77222802	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	4.684000	0.61686	0.980000	0.38523	-0.355000	0.07637	TAC		0.687	TSPAN10-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000440313.1	NM_031945		G	79612397	A	G	79612397	1	3	93	0	1	0	0	0	0	0	0	0	16674	391	14	4		4	TSPAN10	17	79612397	RNA	SNP	A	TCGA-DC-5337-01A-01D-1657-10	2533213	79612397	1582813	226	25554										
P4HB	5034	hgsc.bcm.edu	37	chr17	79813416	79813416	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agggtggtggcagccgggccCgtgcgcttcttcagccagtt	16	12	2	0	rs370423809		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr17:79813416C>T	ENST00000331483.4	-	3	621	c.399G>A	c.(397-399)acG>acA	p.T133T	P4HB_ENST00000439918.2_Intron|P4HB_ENST00000472244.1_5'UTR|P4HB_ENST00000576390.1_Intron	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	133	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			CAGCCGGGCCCGTGCGCTTCT	0.597																																					Colon(49;444 983 1296 7887 42561)											0			17						C		1,4405		0,1,2202	47	49	48		399	-8.8	0.2	17		48	0,8600		0,0,4300	no	coding-synonymous	P4HB	NM_000918.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		133/509	79813416	1,13005	2203	4300	6503	77406705	SO:0001819	synonymous_variant	5034			J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"Protein disulfide isomerases"	8548	protein-coding gene	gene with protein product	"protein disulfide isomerase-associated 1", "protein disulfide isomerase family A, member 1", "collagen prolyl 4-hydroxylase beta"	176790	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.399G>A	17.37:g.79813416C>T			77406705	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Silent	SNP	ENST00000331483.4	37	CCDS11787.1																																																																																				0.597	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918		T	79813416	C	T	79813416	2	4	93	1	0	0	0	0	0	0	0	1	11390	639	23	1		1	P4HB	17	79813416	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	201019	79813416	1381794	227	25555										
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6138291	6138291	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggaaggatcttcaggtcattCgttccttcaggaagtaaaag	11	7	4	0	rs541961038		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:6138291C>T	ENST00000284898.6	-	14	1301	c.1101G>A	c.(1099-1101)acG>acA	p.T367T	L3MBTL4_ENST00000317931.7_Silent_p.T367T|L3MBTL4_ENST00000400104.3_Silent_p.T367T|L3MBTL4_ENST00000400105.2_Silent_p.T367T|L3MBTL4_ENST00000535782.1_Silent_p.T180T	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	367					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T367T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				TCAGGTCATTCGTTCCTTCAG	0.433																																					Esophageal Squamous(41;748 902 17366 28959 43175)											1	Substitution - coding silent(1)	central_nervous_system(1)	18											59	51	53					18																	6138291		2203	4300	6503	6128291	SO:0001819	synonymous_variant	91133			BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.1101G>A	18.37:g.6138291C>T			6128291	A8MTL8|Q8IXS3	Silent	SNP	ENST00000284898.6	37	CCDS11839.2																																																																																				0.433	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		T	6138291	C	T	6138291	2	4	93	1	0	0	0	0	0	0	0	1	8616	871	31	1		1	L3MBTL4	18	6138291	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10		6138291	71938957	228	25556										
PPP4R1	9989	hgsc.bcm.edu	37	chr18	9553342	9553342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agccagttcagctcgaaaccGccaatttctactattatctg	6	12	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:9553342G>A	ENST00000400556.3	-	16	2342	c.2269C>T	c.(2269-2271)Cgg>Tgg	p.R757W	PPP4R1_ENST00000400555.3_Missense_Mutation_p.R740W	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	757					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GCTCGAAACCGCCAATTTCTA	0.303																																					Melanoma(188;1232 2082 5061 11948 35994)											0			18											76	72	73					18																	9553342		1807	4073	5880	9543342	SO:0001583	missense	9989			AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2269C>T	18.37:g.9553342G>A	ENSP00000383402:p.Arg757Trp		9543342	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	37	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952157	0.73787	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.35421	1.31;1.31	5.38	5.38	0.77491	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60483	0.2272	M	0.76170	2.325	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;P;D	0.64776	0.92;0.777;0.929	T	0.60860	-0.7179	9	.	.	.	-9.9361	19.1356	0.93426	0.0:0.0:1.0:0.0	.	740;757;740	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	W	757;740	ENSP00000383402:R757W;ENSP00000383401:R740W	.	R	-	1	2	PPP4R1	9543342	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.377000	0.59562	2.527000	0.85204	0.655000	0.94253	CGG		0.303	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		A	9553342	G	A	9553342	3	1	93	1	0	0	0	0	1	0	0	0	12437	1086	38	1	603	1	PPP4R1	18	9553342	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	3415051	9553342	68523906	229	25557										
DSC1	1823	hgsc.bcm.edu	37	chr18	28711744	28711744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttccctggccaccaacagtaCcaacagacatgcttgtgtca	7	14	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:28711744C>T	ENST00000257198.5	-	15	2561	c.2300G>A	c.(2299-2301)gGt>gAt	p.G767D	RP11-408H20.3_ENST00000582307.1_RNA|RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Missense_Mutation_p.G767D	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	767					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			ACCAACAGTACCAACAGACAT	0.413																																																0			18											140	123	128					18																	28711744		2203	4300	6503	26965742	SO:0001583	missense	1827			AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"Cadherins / Major cadherins"	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2300G>A	18.37:g.28711744C>T	ENSP00000257198:p.Gly767Asp		26965742	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.629961	0.67015	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.56941	0.45;0.43	5.59	5.59	0.84812	.	0.000000	0.53938	D	0.000044	T	0.73528	0.3598	M	0.75777	2.31	0.36692	D	0.879624	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78001	-0.2375	10	0.52906	T	0.07	.	18.3478	0.90328	0.0:1.0:0.0:0.0	.	767;767	Q08554;Q9HB00	DSC1_HUMAN;.	D	767	ENSP00000257197:G767D;ENSP00000257198:G767D	ENSP00000257197:G767D	G	-	2	0	DSC1	26965742	0.959000	0.32827	0.490000	0.27465	0.683000	0.39861	1.929000	0.40114	2.646000	0.89796	0.655000	0.94253	GGT		0.413	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		T	28711744	C	T	28711744	3	4	93	1	0	0	0	0	1	0	0	0	4776	507	18	3	432	3	DSC1	18	28711744	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	19158402	28711744	49365504	230	25558										
DSG4	147409	hgsc.bcm.edu	37	chr18	28983486	28983486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaaccatctgcattgactctCcatcagtccttatctctgtt	5	13	4	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:28983486C>T	ENST00000308128.4	+	11	1660	c.1525C>T	c.(1525-1527)Cca>Tca	p.P509S	RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.P509S|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	509					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P509S(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CATTGACTCTCCATCAGTCCT	0.398																																																1	Substitution - Missense(1)	central_nervous_system(1)	18											156	144	148					18																	28983486		2203	4300	6503	27237484	SO:0001583	missense	147409			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1525C>T	18.37:g.28983486C>T	ENSP00000311859:p.Pro509Ser		27237484	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.419265	0.25552	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.61158	0.21;0.13	6.01	4.19	0.49359	Cadherin-like (1);	0.248030	0.21238	N	0.077878	T	0.48314	0.1493	L	0.47016	1.485	0.34894	D	0.745838	B;B	0.15141	0.006;0.012	B;B	0.16289	0.007;0.015	T	0.52823	-0.8524	10	0.38643	T	0.18	.	9.1737	0.37098	0.0:0.7604:0.1601:0.0794	.	509;509	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	S	509	ENSP00000311859:P509S;ENSP00000352785:P509S	ENSP00000311859:P509S	P	+	1	0	DSG4	27237484	0.457000	0.25752	0.843000	0.33291	0.356000	0.29392	1.384000	0.34396	0.826000	0.34661	0.655000	0.94253	CCA		0.398	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28983486	C	T	28983486	3	4	93	1	0	0	0	0	1	0	0	0	4790	855	30	3	1567	3	DSG4	18	28983486	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	271742	28983486	49093762	231	25559										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575195	48575195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgatagtgtctgtgtgaatcCatatcactacgaacgagttg	10	7	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:48575195C>T	ENST00000342988.3	+	3	927	c.389C>T	c.(388-390)cCa>cTa	p.P130L	SMAD4_ENST00000588745.1_Missense_Mutation_p.P130L|SMAD4_ENST00000398417.2_Missense_Mutation_p.P130L|SMAD4_ENST00000452201.2_Missense_Mutation_p.P130L|RP11-729L2.2_ENST00000590722.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	130	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.		P -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)|p.P130L(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TGTGTGAATCCATATCACTAC	0.363																																																41	Whole gene deletion(36)|Unknown(4)|Substitution - Missense(1)	pancreas(27)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											147	131	137					18																	48575195		2203	4300	6503	46829193	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.389C>T	18.37:g.48575195C>T	ENSP00000341551:p.Pro130Leu		46829193	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146268	0.94603	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	D;D;D	0.92965	-3.14;-3.14;-3.14	5.48	5.48	0.80851	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.97427	0.9158	H	0.95079	3.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98481	1.0605	10	0.87932	D	0	.	18.1041	0.89515	0.0:1.0:0.0:0.0	.	130	Q13485	SMAD4_HUMAN	L	130	ENSP00000409551:P130L;ENSP00000341551:P130L;ENSP00000381452:P130L	ENSP00000341551:P130L	P	+	2	0	SMAD4	46829193	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.793000	0.85851	2.540000	0.85666	0.585000	0.79938	CCA		0.363	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48575195	C	T	48575195	3	4	93	1	0	0	0	0	1	0	0	0	14797	594	21	3	395	3	SMAD4	18	48575195	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	19591709	48575195	29502053	232	25560										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48586282	48586282	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagcctcccatttccaatcaTcctggtaagtgtatttcaaa	5	12	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr18:48586282T>C	ENST00000342988.3	+	8	1489	c.951T>C	c.(949-951)caT>caC	p.H317H	SMAD4_ENST00000588745.1_Intron|SMAD4_ENST00000398417.2_Silent_p.H317H	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	317	SAD.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)|p.H317Q(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TTTCCAATCATCCTGGTAAGT	0.353																																																40	Whole gene deletion(36)|Unknown(3)|Substitution - Missense(1)	pancreas(27)|stomach(3)|breast(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|thyroid(1)|oesophagus(1)	18											113	108	110					18																	48586282		2202	4300	6502	46840280	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.951T>C	18.37:g.48586282T>C			46840280	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.353	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48586282	T	C	48586282	2	2	93	1	0	0	0	0	0	0	0	1	14797	1432	50	4		4	SMAD4	18	48586282	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	11087	48586282	29490966	233	25561										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1047523	1047523	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctggaggagcagggcgagggCgcgcagtggcacaacgtggg	21	9	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:1047523C>T	ENST00000263094.6	+	16	2370	c.2139C>T	c.(2137-2139)ggC>ggT	p.G713G	ABCA7_ENST00000435683.2_Silent_p.G575G|ABCA7_ENST00000433129.1_Silent_p.G713G|ABCA7_ENST00000533574.1_3'UTR	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	713					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		AGGGCGAGGGCGCGCAGTGGC	0.706																																																0			19											15	19	18					19																	1047523		2190	4287	6477	998523	SO:0001819	synonymous_variant	10347			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2139C>T	19.37:g.1047523C>T			998523	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																				0.706	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1047523	C	T	1047523	2	4	93	1	0	0	0	0	0	0	0	1	37	755	27	1		1	ABCA7	19	1047523	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10		1047523	58081460	234	25562										
STK11	6794	hgsc.bcm.edu	37	chr19	1207057	1207057	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggccaagctcatcggcaagTacctgatgggggacctgctg	15	11	1	1	rs137853080		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:1207057T>C	ENST00000326873.7	+	1	1318	c.145T>C	c.(145-147)Tac>Cac	p.Y49H	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	49	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.		Y -> D (in melanoma; sporadic malignant; somatic mutation). {ECO:0000269|PubMed:10201537}.		activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)|p.Y49D(1)|p.A43_L50del(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CATCGGCAAGTACCTGATGGG	0.617		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																												yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	25	Whole gene deletion(20)|Unknown(2)|Substitution - Missense(1)|Deletion - Frameshift(1)|Deletion - In frame(1)	cervix(15)|lung(4)|skin(2)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19											37	42	40					19																	1207057		2072	4191	6263	1158057	SO:0001583	missense	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.145T>C	19.37:g.1207057T>C	ENSP00000324856:p.Tyr49His		1158057	B2RBX7|E7EW76	Missense_Mutation	SNP	ENST00000326873.7	37	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.930988	0.92389	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	D	0.90004	-2.6	3.9	3.9	0.45041	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.069625	0.64402	D	0.000012	D	0.96150	0.8745	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96732	0.9540	10	0.87932	D	0	-29.1932	11.9419	0.52905	0.0:0.0:0.0:1.0	.	49	Q15831	STK11_HUMAN	H	49	ENSP00000324856:Y49H	ENSP00000324856:Y49H	Y	+	1	0	STK11	1158057	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.615000	0.83006	1.416000	0.47057	0.379000	0.24179	TAC		0.617	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		C	1207057	T	C	1207057	3	2	93	1	0	0	0	0	1	0	0	0	15326	1638	57	4	147	4	STK11	19	1207057	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	159534	1207057	57921926	235	25563										
ZGLP1	100125288	hgsc.bcm.edu	37	chr19	10415835	10415835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctcttgggctggacattttTcctgggcaccagccagcagc	11	14	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:10415835T>C	ENST00000403903.3	-	4	1946	c.748A>G	c.(748-750)Aaa>Gaa	p.K250E	ZGLP1_ENST00000403352.1_Missense_Mutation_p.K166E	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	250					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						TGGACATTTTTCCTGGGCACC	0.567																																																0			19											63	67	66					19																	10415835		2021	4188	6209	10276835	SO:0001583	missense	0			AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"GATA zinc finger domain containing"	37245	protein-coding gene	gene with protein product	"GATA like protein 1", "GATA zinc finger domain containing 3"	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.748A>G	19.37:g.10415835T>C	ENSP00000384434:p.Lys250Glu		10276835		Missense_Mutation	SNP	ENST00000403903.3	37	CCDS45959.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.408224	0.83340	.	.	ENSG00000220201	ENST00000403903;ENST00000403352	D;D	0.99023	-5.3;-5.34	5.67	4.59	0.56863	Zinc finger, GATA-type (1);	.	.	.	.	D	0.98080	0.9367	N	0.19112	0.55	0.35807	D	0.823597	D	0.76494	0.999	D	0.71414	0.973	D	0.99888	1.1128	9	0.72032	D	0.01	-10.0425	10.6295	0.45527	0.0:0.0:0.1608:0.8391	.	250	P0C6A0	ZGLP1_HUMAN	E	250;166	ENSP00000384434:K250E;ENSP00000385403:K166E	ENSP00000385403:K166E	K	-	1	0	ZGLP1	10276835	1.000000	0.71417	0.994000	0.49952	0.754000	0.42855	3.595000	0.54016	2.169000	0.68431	0.459000	0.35465	AAA		0.567	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167		C	10415835	T	C	10415835	3	2	93	1	0	0	0	0	1	0	0	0	17712	1792	62	4	71	4	ZGLP1	19	10415835	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	9208778	10415835	48713148	236	25564										
TMED1	11018	hgsc.bcm.edu	37	chr19	10945724	10945724	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atcagttcaaagaacaccagCttctcggagatggtgctgaa	10	9	3	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:10945724C>A	ENST00000214869.2	-	3	449	c.351G>T	c.(349-351)aaG>aaT	p.K117N	C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000588289.1_5'UTR|TMED1_ENST00000591695.1_Intron	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	117	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.K117K(1)		breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						AGAACACCAGCTTCTCGGAGA	0.557																																																1	Substitution - coding silent(1)	central_nervous_system(1)	19											117	114	115					19																	10945724		2203	4300	6503	10806724	SO:0001583	missense	11018			U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.351G>T	19.37:g.10945724C>A	ENSP00000214869:p.Lys117Asn		10806724		Missense_Mutation	SNP	ENST00000214869.2	37	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584417	0.86748	.	.	ENSG00000099203	ENST00000214869	T	0.67345	-0.26	5.15	4.09	0.47781	GOLD (3);	0.046316	0.85682	D	0.000000	D	0.84768	0.5545	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85869	0.1415	10	0.87932	D	0	-30.0631	8.0593	0.30623	0.0:0.8018:0.0:0.1982	.	117	Q13445	TMED1_HUMAN	N	117	ENSP00000214869:K117N	ENSP00000214869:K117N	K	-	3	2	TMED1	10806724	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	2.503000	0.45407	1.091000	0.41335	0.561000	0.74099	AAG		0.557	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		A	10945724	C	A	10945724	3	1	93	1	0	0	0	0	1	0	0	0	16041	796	28	2	340	2	TMED1	19	10945724	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	529889	10945724	48183259	237	25565										
DNASE2	1777	hgsc.bcm.edu	37	chr19	12992140	12992140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cggagtccccgtagcaggtcAgggccccggcggggacgcac	17	15	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:12992140A>G	ENST00000222219.3	-	1	142	c.50T>C	c.(49-51)cTg>cCg	p.L17P	DNASE2_ENST00000538460.1_Missense_Mutation_p.L17P|CTD-2265O21.7_ENST00000592400.1_RNA	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	17					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						GTAGCAGGTCAGGGCCCCGGC	0.697																																																0			19											7	8	8					19																	12992140		2164	4232	6396	12853140	SO:0001583	missense	1777			AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.50T>C	19.37:g.12992140A>G	ENSP00000222219:p.Leu17Pro		12853140	B2RD06|B7Z4K6|O43910	Missense_Mutation	SNP	ENST00000222219.3	37	CCDS12284.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858683	0.51376	.	.	ENSG00000105612	ENST00000222219;ENST00000538460	T;T	0.16457	2.35;2.34	5.37	4.35	0.52113	.	0.141241	0.45867	D	0.000328	T	0.22044	0.0531	M	0.83118	2.625	0.25731	N	0.985264	B;B	0.34161	0.439;0.439	B;B	0.33846	0.171;0.171	T	0.26121	-1.0112	10	0.54805	T	0.06	.	7.1526	0.25618	0.9014:0.0:0.0986:0.0	.	17;17	B7Z4K6;O00115	.;DNS2A_HUMAN	P	17	ENSP00000222219:L17P;ENSP00000445988:L17P	ENSP00000222219:L17P	L	-	2	0	DNASE2	12853140	0.966000	0.33281	0.679000	0.29978	0.192000	0.23643	2.546000	0.45778	2.045000	0.60652	0.459000	0.35465	CTG		0.697	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			G	12992140	A	G	12992140	3	3	93	1	0	0	0	0	1	0	0	0	4675	188	7	4	1056	4	DNASE2	19	12992140	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	2046416	12992140	46136843	238	25566										
NWD1	284434	hgsc.bcm.edu	37	chr19	16884050	16884050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agagctggttccagttgtgcGcacaccctgtgctggtgccc	13	13	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:16884050G>A	ENST00000552788.1	+	9	2524	c.2524G>A	c.(2524-2526)Gca>Aca	p.A842T	NWD1_ENST00000523826.1_Missense_Mutation_p.A636T|NWD1_ENST00000339803.6_Missense_Mutation_p.A707T|NWD1_ENST00000379808.3_Missense_Mutation_p.A842T|NWD1_ENST00000524140.2_Missense_Mutation_p.A842T|NWD1_ENST00000549814.1_Missense_Mutation_p.A842T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	842							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CCAGTTGTGCGCACACCCTGT	0.622																																																0			19											59	56	57					19																	16884050		2203	4299	6502	16745050	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2524G>A	19.37:g.16884050G>A	ENSP00000447224:p.Ala842Thr		16745050	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	-	2.846	-0.239371	0.05944	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57752	0.38;0.44;0.38;0.38;0.43;0.43	4.04	1.84	0.25277	.	0.486738	0.20217	U	0.096761	T	0.25791	0.0628	N	0.08118	0	0.09310	N	1	B;B;B	0.15719	0.008;0.006;0.014	B;B;B	0.08055	0.002;0.003;0.002	T	0.17992	-1.0351	10	0.15499	T	0.54	-4.5338	6.9503	0.24542	0.1883:0.5547:0.257:0.0	.	842;842;707	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	T	707;842;842;842;636;842;707	ENSP00000428579:A842T;ENSP00000447548:A842T;ENSP00000369136:A842T;ENSP00000428955:A636T;ENSP00000447224:A842T;ENSP00000340159:A707T	ENSP00000340159:A707T	A	+	1	0	NWD1	16745050	0.285000	0.24296	0.001000	0.08648	0.060000	0.15804	0.447000	0.21710	0.129000	0.18514	-2.490000	0.00194	GCA		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16884050	G	A	16884050	3	1	93	1	0	0	0	0	1	0	0	0	10812	1087	38	1	2145	1	NWD1	19	16884050	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	3891910	16884050	42244933	239	25567										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17844122	17844122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggatgaggagttcttccagcGcgtgcgcgcgctctgctacg	15	12	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:17844122G>A	ENST00000324096.4	+	6	3060	c.2909G>A	c.(2908-2910)cGc>cAc	p.R970H	MAP1S_ENST00000544059.2_Missense_Mutation_p.R944H|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	970	Necessary for association with actin. {ECO:0000250}.|Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for the mitochondrial aggregation and genome destruction.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						TTCTTCCAGCGCGTGCGCGCG	0.677																																																0			19											38	30	33					19																	17844122		2196	4297	6493	17705122	SO:0001583	missense	55201			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2909G>A	19.37:g.17844122G>A	ENSP00000325313:p.Arg970His		17705122	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.739690	0.49045	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.20463	2.07;2.07	4.54	4.54	0.55810	.	0.000000	0.44483	D	0.000442	T	0.39911	0.1096	M	0.67397	2.05	0.21950	N	0.999453	D;D	0.89917	1.0;1.0	D;D	0.71414	0.968;0.973	T	0.18493	-1.0335	10	0.87932	D	0	-26.2893	8.596	0.33716	0.1079:0.0:0.8921:0.0	.	944;970	B4DH53;Q66K74	.;MAP1S_HUMAN	H	970;944	ENSP00000325313:R970H;ENSP00000439243:R944H	ENSP00000325313:R970H	R	+	2	0	MAP1S	17705122	0.972000	0.33761	0.070000	0.20053	0.004000	0.04260	5.618000	0.67722	2.064000	0.61679	0.591000	0.81541	CGC		0.677	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		A	17844122	G	A	17844122	3	1	93	1	0	0	0	0	1	0	0	0	9264	1087	38	1	2931	1	MAP1S	19	17844122	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	960072	17844122	41284861	240	25568										
GDF15	9518	hgsc.bcm.edu	37	chr19	18497015	18497015	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagccatgcccgggcaagaaCtcaggacggtgaatggctct	13	12	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:18497015C>A	ENST00000252809.3	+	1	48	c.16C>A	c.(16-18)Ctc>Atc	p.L6I	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	6					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CGGGCAAGAACTCAGGACGGT	0.652																																																0			19											47	50	49					19																	18497015		2203	4300	6503	18358015	SO:0001583	missense	9518			BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.16C>A	19.37:g.18497015C>A	ENSP00000252809:p.Leu6Ile		18358015	O14629|P78360|Q9BWA0|Q9NRT0	Missense_Mutation	SNP	ENST00000252809.3	37	CCDS12376.1	.	.	.	.	.	.	.	.	.	.	C	8.838	0.941436	0.18281	.	.	ENSG00000130513	ENST00000252809	D	0.82803	-1.65	3.74	-2.03	0.07365	.	1.094490	0.07257	N	0.866871	T	0.67664	0.2917	N	0.22421	0.69	0.09310	N	1	B	0.20550	0.046	B	0.15870	0.014	T	0.51220	-0.8733	10	0.33940	T	0.23	-0.8063	4.5679	0.12196	0.0:0.3827:0.3525:0.2648	.	6	Q99988	GDF15_HUMAN	I	6	ENSP00000252809:L6I	ENSP00000252809:L6I	L	+	1	0	GDF15	18358015	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.050000	0.14120	-0.206000	0.10203	0.313000	0.20887	CTC		0.652	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		A	18497015	C	A	18497015	3	1	93	1	0	0	0	0	1	0	0	0	6333	565	20	2	18	2	GDF15	19	18497015	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	652893	18497015	40631968	241	25569										
PBX4	80714	hgsc.bcm.edu	37	chr19	19675818	19675818	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtatccacagccgttttaccCgtgtaaatggtagcctcttc	8	12	1	0	rs145467560		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:19675818C>T	ENST00000251203.9	-	6	1135	c.849G>A	c.(847-849)acG>acA	p.T283T		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	283			T -> M (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						CCGTTTTACCCGTGTAAATGG	0.532													C|||	1	0.000199681	8e-04	0	5008	,	,		19441	0		0	False		,,,				2504	0															0			19						C		6,4400	11.4+/-27.6	0,6,2197	313	317	316		849	-5.8	0	19	dbSNP_134	316	0,8600		0,0,4300	no	coding-synonymous	PBX4	NM_025245.2		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		283/375	19675818	6,13000	2203	4300	6503	19536818	SO:0001819	synonymous_variant	80714			AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"Homeoboxes / TALE class"	13403	protein-coding gene	gene with protein product		608127	"pre-B-cell leukemia transcription factor 4"				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.849G>A	19.37:g.19675818C>T			19536818	A5D8Y0|B3KUK9	Silent	SNP	ENST00000251203.9	37	CCDS12406.1																																																																																				0.532	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			T	19675818	C	T	19675818	2	4	93	1	0	0	0	0	0	0	0	1	11526	639	23	1		1	PBX4	19	19675818	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1178803	19675818	39453165	242	25570										
LRP3	4037	hgsc.bcm.edu	37	chr19	33696897	33696897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggtggcattgtgccagcggCcgagacgagcagggctgccc	17	12	0	1	rs11084712	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:33696897C>T	ENST00000253193.7	+	5	1423	c.1221C>T	c.(1219-1221)ggC>ggT	p.G407G	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	407					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					GTGCCAGCGGCCGAGACGAGC	0.682													C|||	1298	0.259185	0.1672	0.3761	5008	,	,		13617	0.2262		0.2207	False		,,,				2504	0.3742															0			19						C		667,3667		52,563,1552	9	9	9		1221	3	1	19	dbSNP_120	9	1559,6947		146,1267,2840	no	coding-synonymous	LRP3	NM_002333.3		198,1830,4392	TT,TC,CC		18.3282,15.3899,17.3364		407/771	33696897	2226,10614	2167	4253	6420	38388737	SO:0001819	synonymous_variant	4037			AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"Low density lipoprotein receptors"	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.1221C>T	19.37:g.33696897C>T			38388737	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																				0.682	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4			T	33696897	C	T	33696897	2	4	93	1	0	0	0	0	0	0	0	1	8987	726	26	3		3	LRP3	19	33696897	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	14021079	33696897	25432086	243	25571										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792390	33792390	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cagctccagcaccttctgctGcgtctccacgttgcgctgct	9	17	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:33792390G>T	ENST00000498907.2	-	1	1080	c.931C>A	c.(931-933)Cag>Aag	p.Q311K	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	311	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R306fs*48(3)|p.T310_Q311insS(2)|p.T310_Q311insT(2)|p.T310_Q311insV(2)|p.T310_Q311insET(2)|p.Q311*(1)|p.H200_K352>Q(1)|p.?(1)|p.T310_Q312>K(1)|p.Q311>PQ(1)|p.T310_Q311insGGQT(1)|p.N307_Q312del(1)|p.Q311del(1)|p.T310_Q311del(1)|p.T310_Q311insKQ(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					ACCTTCTGCTGCGTCTCCACG	0.647			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																														Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	21	Insertion - In frame(10)|Complex - deletion inframe(5)|Deletion - In frame(3)|Substitution - Nonsense(1)|Unknown(1)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(21)	19											53	54	54					19																	33792390		2203	4300	6503	38484230	SO:0001583	missense	1050	Familial Cancer Database	Familial AML	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.931C>A	19.37:g.33792390G>T	ENSP00000427514:p.Gln311Lys		38484230	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	37	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.853532	0.91355	.	.	ENSG00000245848	ENST00000498907	T	0.43688	0.94	4.7	4.7	0.59300	Basic-leucine zipper (bZIP) transcription factor (2);Basic leucine zipper (1);	.	.	.	.	T	0.66107	0.2756	M	0.78049	2.395	0.80722	D	1	D	0.65815	0.995	D	0.78314	0.991	T	0.72023	-0.4415	9	0.87932	D	0	.	16.6187	0.84924	0.0:0.0:1.0:0.0	.	311	P49715	CEBPA_HUMAN	K	311	ENSP00000427514:Q311K	ENSP00000427514:Q311K	Q	-	1	0	CEBPA	38484230	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.914000	0.87478	2.133000	0.65898	0.462000	0.41574	CAG		0.647	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33792390	G	T	33792390	3	4	93	1	0	0	0	0	1	0	0	0	3205	1328	46	2	149	2	CEBPA	19	33792390	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	95493	33792390	25336593	244	25572										
MLL4	9757	hgsc.bcm.edu	37	chr19	36210763	36210764	+	Frame_Shift_Ins	INS	-	-	C													0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctagcagatgtggctcctaINScccccccaaagacccctgcc					rs532152042|rs60207923	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:36210763_36210764insC	ENST00000222270.7	+	3	514_515	c.514_515insC	c.(514-516)accfs	p.T172fs	KMT2B_ENST00000420124.1_Frame_Shift_Ins_p.T172fs|KMT2B_ENST00000341701.1_Frame_Shift_Ins_p.T172fs|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	172			T -> I (in dbSNP:rs60207923).		chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGTGGCTCCTACCCCCCCAAAG	0.634																																																0			19								23,3623		0,23,1800						0.3	1			50	30,7828		1,28,3900	no	frameshift	MLL4	NM_014727.1		1,51,5700	A1A1,A1R,RR		0.3818,0.6308,0.4607				53,11451				40902604	SO:0001589	frameshift_variant	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.521dupC	19.37:g.36210770_36210770dupC	ENSP00000222270:p.Thr172fs		40902603	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Ins	INS	ENST00000222270.7	37	CCDS46055.1																																																																																				0.634	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36210764	-	C	36210763	7	5	93	1	0	1	1	0	0	0	0	0	9653	391	14	0	524	0	MLL4	19	36210763	Frame_Shift_Ins	INS	-	TCGA-DC-5337-01A-01D-1657-10	2418373	36210763	22918220	245	25573										
ZNF607	84775	hgsc.bcm.edu	37	chr19	38189363	38189363	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acattcgtagggtttctcagCgctatgaatattctgatggg	11	7	2	2	rs376563408		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:38189363C>T	ENST00000355202.4	-	5	2264	c.1669G>A	c.(1669-1671)Gct>Act	p.A557T	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.A556T	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	557					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			GGTTTCTCAGCGCTATGAATA	0.423																																																0			19						C	THR/ALA,THR/ALA	0,4406		0,0,2203	44	42	43		1666,1669	2	0.1	19		43	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	556/696,557/697	38189363	1,13005	2203	4300	6503	42881203	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1669G>A	19.37:g.38189363C>T	ENSP00000347338:p.Ala557Thr		42881203	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.849261	0.71603	0.0	1.16E-4	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.17854	2.25;2.25	1.97	1.97	0.26223	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17874	0.0429	L	0.31526	0.94	0.31359	N	0.681558	P;D	0.57571	0.527;0.98	B;P	0.49451	0.127;0.611	T	0.15636	-1.0430	9	0.72032	D	0.01	.	10.9265	0.47193	0.0:1.0:0.0:0.0	.	557;556	Q96SK3;F5H141	ZN607_HUMAN;.	T	557;556	ENSP00000347338:A557T;ENSP00000438015:A556T	ENSP00000347338:A557T	A	-	1	0	ZNF607	42881203	0.058000	0.20735	0.112000	0.21494	0.048000	0.14542	3.629000	0.54266	1.080000	0.41073	0.561000	0.74099	GCT		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		T	38189363	C	T	38189363	3	4	93	1	0	0	0	0	1	0	0	0	18072	768	27	1	425	1	ZNF607	19	38189363	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	1978600	38189363	20939620	246	25574										
RYR1	6261	hgsc.bcm.edu	37	chr19	38980821	38980821	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	acaagctccaggccaaccagCggagccgctatggcctcctc	10	17	0	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:38980821C>T	ENST00000359596.3	+	36	5920	c.5920C>T	c.(5920-5922)Cgg>Tgg	p.R1974W	RYR1_ENST00000360985.3_Missense_Mutation_p.R1974W|RYR1_ENST00000355481.4_Missense_Mutation_p.R1974W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1974	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R1974W(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCCAACCAGCGGAGCCGCTA	0.602																																																1	Substitution - Missense(1)	ovary(1)	19											60	53	55					19																	38980821		2203	4300	6503	43672661	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5920C>T	19.37:g.38980821C>T	ENSP00000352608:p.Arg1974Trp		43672661	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859942	0.32884	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73897	-0.79;-0.79;-0.79	4.61	-0.288	0.12855	.	0.000000	0.64402	U	0.000014	D	0.84620	0.5512	M	0.83483	2.645	0.30899	N	0.729433	D;D	0.89917	1.0;1.0	D;P	0.66084	0.941;0.874	D	0.85554	0.1223	10	0.66056	D	0.02	.	15.5957	0.76578	0.7178:0.2821:0.0:0.0	.	1974;1974	P21817-2;P21817	.;RYR1_HUMAN	W	1974	ENSP00000352608:R1974W;ENSP00000347667:R1974W;ENSP00000354254:R1974W	ENSP00000347667:R1974W	R	+	1	2	RYR1	43672661	0.978000	0.34361	0.953000	0.39169	0.498000	0.33706	0.101000	0.15251	-0.104000	0.12154	-0.270000	0.10280	CGG		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38980821	C	T	38980821	3	4	93	1	0	0	0	0	1	0	0	0	13805	759	27	1	6062	1	RYR1	19	38980821	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	791458	38980821	20148162	247	25575										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44732645	44732645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgtggtcttctccagggaggAactgcgactgctcgatctta	12	10	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:44732645A>G	ENST00000313040.7	+	4	312	c.107A>G	c.(106-108)gAa>gGa	p.E36G	ZNF227_ENST00000589707.1_5'UTR|ZNF227_ENST00000586228.1_Silent_p.G22G|ZNF227_ENST00000589005.1_5'UTR|ZNF227_ENST00000391961.2_5'UTR|ZNF227_ENST00000589237.1_3'UTR	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				TCCAGGGAGGAACTGCGACTG	0.493																																																0			19											243	211	222					19																	44732645		2203	4300	6503	49424485	SO:0001583	missense	7770			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.107A>G	19.37:g.44732645A>G	ENSP00000321049:p.Glu36Gly		49424485	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	14.06	2.423246	0.43020	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000418980	T	0.12255	2.7	3.84	3.84	0.44239	Krueppel-associated box (4);	.	.	.	.	T	0.52869	0.1761	H	0.98901	4.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.69457	-0.5140	9	0.87932	D	0	.	10.9005	0.47049	1.0:0.0:0.0:0.0	.	22;16;36	Q658S5;Q9NS43;Q86WZ6	.;.;ZN227_HUMAN	G	36;21;22	ENSP00000321049:E36G	ENSP00000321049:E36G	E	+	2	0	ZNF227	49424485	1.000000	0.71417	0.966000	0.40874	0.085000	0.17905	5.335000	0.65929	1.746000	0.51805	0.402000	0.26972	GAA		0.493	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44732645	A	G	44732645	3	3	93	1	0	0	0	0	1	0	0	0	17820	246	9	4	113	4	ZNF227	19	44732645	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	5751824	44732645	14396338	248	25576										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45495656	45495656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccggatcggctgcctgcgggAcggtgaggcccggtgggcag	20	12	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:45495656A>G	ENST00000337392.5	+	13	1871	c.1721A>G	c.(1720-1722)gAc>gGc	p.D574G	CLPTM1_ENST00000546079.1_Missense_Mutation_p.D472G|CLPTM1_ENST00000541297.2_Missense_Mutation_p.D560G	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	574					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		TGCCTGCGGGACGGTGAGGCC	0.647																																																0			19											130	126	127					19																	45495656		2203	4300	6503	50187496	SO:0001583	missense	1209			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1721A>G	19.37:g.45495656A>G	ENSP00000336994:p.Asp574Gly		50187496	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535841	0.85812	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.21	5.21	0.72293	.	0.054132	0.64402	D	0.000001	T	0.77850	0.4192	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80600	-0.1310	9	0.87932	D	0	-45.3221	11.4443	0.50114	1.0:0.0:0.0:0.0	.	560;574	F5H8J3;O96005	.;CLPT1_HUMAN	G	472;560;574;574	.	ENSP00000336994:D574G	D	+	2	0	CLPTM1	50187496	1.000000	0.71417	0.996000	0.52242	0.896000	0.52359	8.381000	0.90152	2.202000	0.70862	0.529000	0.55759	GAC		0.647	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		G	45495656	A	G	45495656	3	3	93	1	0	0	0	0	1	0	0	0	3560	275	10	4	1771	4	CLPTM1	19	45495656	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	763011	45495656	13633327	249	25577										
MARK4	57787	hgsc.bcm.edu	37	chr19	45783968	45783968	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gttcctcttccacctaccacCgccagcgcaggcatagcgat	8	17	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:45783968C>A	ENST00000262891.4	+	12	1583	c.1252C>A	c.(1252-1254)Cgc>Agc	p.R418S	MARK4_ENST00000300843.4_Missense_Mutation_p.R418S	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	418			R -> C (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)	p.R418C(1)		NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CACCTACCACCGCCAGCGCAG	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	19											104	83	90					19																	45783968		2203	4300	6503	50475808	SO:0001583	missense	57787			AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1252C>A	19.37:g.45783968C>A	ENSP00000262891:p.Arg418Ser		50475808	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	37	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052942	0.75960	.	.	ENSG00000007047	ENST00000262891;ENST00000300843	T;T	0.71934	-0.55;-0.61	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000001	T	0.79913	0.4528	L	0.53249	1.67	0.58432	D	0.999994	D;D;D	0.69078	0.978;0.997;0.996	P;D;D	0.79108	0.717;0.987;0.992	T	0.79281	-0.1868	10	0.51188	T	0.08	.	12.6992	0.57022	0.1645:0.8355:0.0:0.0	.	284;418;418	Q8N2N5;Q96L34;Q96L34-2	.;MARK4_HUMAN;.	S	418	ENSP00000262891:R418S;ENSP00000300843:R418S	ENSP00000262891:R418S	R	+	1	0	MARK4	50475808	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.183000	0.42565	2.804000	0.96469	0.462000	0.41574	CGC		0.612	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		A	45783968	C	A	45783968	3	1	93	1	0	0	0	0	1	0	0	0	9345	652	23	2	1298	2	MARK4	19	45783968	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	288312	45783968	13345015	250	25578										
BAX	581	hgsc.bcm.edu	37	chr19	49458976	49458976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcgagcagggcgaatgggggGggaggcacccgagctggccc	20	11	0	0	rs398122842		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:49458976G>A	ENST00000345358.7	+	3	171	c.119G>A	c.(118-120)gGg>gAg	p.G40E	BAX_ENST00000293288.8_Missense_Mutation_p.G40E|BAX_ENST00000354470.3_Intron|BAX_ENST00000415969.2_Missense_Mutation_p.G40E|BAX_ENST00000391871.3_Missense_Mutation_p.G23R|BAX_ENST00000539787.1_Missense_Mutation_p.G40E	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	40					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		CGAATGGGGGGGGAGGCACCC	0.597																																																0			19											58	56	57					19																	49458976		2203	4300	6503	54150788	SO:0001583	missense	581				CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.119G>A	19.37:g.49458976G>A	ENSP00000263262:p.Gly40Glu		54150788	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	37	CCDS12742.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.595|5.595	0.294558|0.294558	0.10567|0.10567	.|.	.|.	ENSG00000087088|ENSG00000087088	ENST00000539787;ENST00000345358;ENST00000415969;ENST00000293288|ENST00000391871	T;T;T;T|.	0.28255|.	2.84;1.62;3.03;2.98|.	4.21|4.21	2.07|2.07	0.26955|0.26955	.|.	0.354000|0.354000	0.30244|0.30244	N|N	0.010067|0.010067	T|T	0.34193|0.34193	0.0889|0.0889	L|L	0.34521|0.34521	1.04|1.04	0.19300|0.19300	N|N	0.999973|0.999973	B;B;B|.	0.16396|.	0.0;0.002;0.017|.	B;B;B|.	0.15052|.	0.001;0.006;0.012|.	T|T	0.21449|0.21449	-1.0245|-1.0245	10|7	0.06236|0.87932	T|D	0.91|0	-2.542|-2.542	6.5948|6.5948	0.22666|0.22666	0.2156:0.0:0.7844:0.0|0.2156:0.0:0.7844:0.0	.|.	40;40;40|.	Q07812;Q07812-8;Q07812-2|.	BAX_HUMAN;.;.|.	E|R	40|23	ENSP00000441413:G40E;ENSP00000263262:G40E;ENSP00000389971:G40E;ENSP00000293288:G40E|.	ENSP00000293288:G40E|ENSP00000375744:G23R	G|G	+|+	2|1	0|0	BAX|BAX	54150788|54150788	1.000000|1.000000	0.71417|0.71417	0.224000|0.224000	0.23877|0.23877	0.093000|0.093000	0.18481|0.18481	1.921000|1.921000	0.40035|0.40035	0.733000|0.733000	0.32492|0.32492	0.557000|0.557000	0.71058|0.71058	GGG|GGG		0.597	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		A	49458976	G	A	49458976	3	1	93	1	0	0	0	0	1	0	0	0	1329	1232	43	3	129	3	BAX	19	49458976	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	3675008	49458976	9670007	251	25579										
TRPM4	54795	hgsc.bcm.edu	37	chr19	49671933	49671933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cacacggctgcctggggggcGagaaccgcttccgcttgcgc	15	15	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:49671933G>A	ENST00000252826.5	+	6	862	c.736G>A	c.(736-738)Gag>Aag	p.E246K	TRPM4_ENST00000601347.1_3'UTR|TRPM4_ENST00000355712.5_5'UTR|TRPM4_ENST00000427978.2_Missense_Mutation_p.E246K	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	246					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		CCTGGGGGGCGAGAACCGCTT	0.647																																																0			19											31	28	29					19																	49671933		2203	4300	6503	54363745	SO:0001583	missense	54795			AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.736G>A	19.37:g.49671933G>A	ENSP00000252826:p.Glu246Lys		54363745	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Missense_Mutation	SNP	ENST00000252826.5	37	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974562	0.53720	.	.	ENSG00000130529	ENST00000252826;ENST00000427978	T;T	0.09630	2.96;2.96	4.49	4.49	0.54785	.	0.213774	0.37623	N	0.002005	T	0.38295	0.1035	M	0.86343	2.81	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.75020	0.915;0.915;0.985	T	0.40327	-0.9569	10	0.59425	D	0.04	-21.487	16.5383	0.84377	0.0:0.0:1.0:0.0	.	72;246;246	Q8TD43-2;Q8TD43-3;Q8TD43	.;.;TRPM4_HUMAN	K	246	ENSP00000252826:E246K;ENSP00000407492:E246K	ENSP00000252826:E246K	E	+	1	0	TRPM4	54363745	1.000000	0.71417	0.997000	0.53966	0.294000	0.27393	5.543000	0.67225	2.531000	0.85337	0.555000	0.69702	GAG		0.647	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		A	49671933	G	A	49671933	3	1	93	1	0	0	0	0	1	0	0	0	16628	1059	37	1	758	1	TRPM4	19	49671933	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	212957	49671933	9457050	252	25580										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51961585	51961585	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ccatccccatattgtctgtcTccctccatcccctttgtccc	3	20	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:51961585T>C	ENST00000321424.3	-	1	123	c.57A>G	c.(55-57)ggA>ggG	p.G19G	SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Silent_p.G19G|SIGLEC8_ENST00000430817.1_Silent_p.G19G	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	19					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		ATTGTCTGTCTCCCTCCATCC	0.622																																																0			19											86	83	84					19																	51961585		2203	4300	6503	56653397	SO:0001819	synonymous_variant	27181			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.57A>G	19.37:g.51961585T>C			56653397	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																				0.622	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		C	51961585	T	C	51961585	2	2	93	1	0	0	0	0	0	0	0	1	14351	1538	54	4		4	SIGLEC8	19	51961585	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2289652	51961585	7167398	253	25581										
MYADM	91663	hgsc.bcm.edu	37	chr19	54377532	54377532	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggccttgctgtctgtcctccTctatgccaccgcccttgttc	8	17	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:54377532T>C	ENST00000391769.2	+	3	1029	c.749T>C	c.(748-750)cTc>cCc	p.L250P	MYADM_ENST00000391770.4_Missense_Mutation_p.L250P|MYADM_ENST00000336967.3_Missense_Mutation_p.L250P|AC008440.5_ENST00000413496.2_RNA|MYADM_ENST00000391768.2_Missense_Mutation_p.L250P|MYADM_ENST00000391771.1_Missense_Mutation_p.L250P	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	250	MARVEL 2. {ECO:0000255|PROSITE- ProRule:PRU00581}.				establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		TCTGTCCTCCTCTATGCCACC	0.632																																																0			19											92	85	88					19																	54377532		2203	4300	6503	59069344	SO:0001583	missense	91663			AF087882	CCDS12866.1	19q13.33-q13.4	2004-07-23			ENSG00000179820	ENSG00000179820			7544	protein-coding gene	gene with protein product		609959				10733104, 12075932	Standard	NM_001020818		Approved		uc002qcl.3	Q96S97	OTTHUMG00000060775	ENST00000391769.2:c.749T>C	19.37:g.54377532T>C	ENSP00000375649:p.Leu250Pro		59069344	B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9	Missense_Mutation	SNP	ENST00000391769.2	37	CCDS12866.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030436	0.35797	.	.	ENSG00000179820	ENST00000336967;ENST00000391770;ENST00000439000;ENST00000391771;ENST00000415619;ENST00000391769;ENST00000391768	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	4.3	3.27	0.37495	Marvel (1);MARVEL-like domain (1);	0.418686	0.17771	N	0.162589	T	0.52773	0.1755	M	0.78344	2.41	0.41002	D	0.984934	D	0.58620	0.983	P	0.60541	0.876	T	0.57562	-0.7790	10	0.72032	D	0.01	-16.1523	7.4697	0.27342	0.0:0.1058:0.0:0.8942	.	250	Q96S97	MYADM_HUMAN	P	250;250;250;250;213;250;250	ENSP00000337222:L250P;ENSP00000375650:L250P;ENSP00000416919:L250P;ENSP00000375651:L250P;ENSP00000375649:L250P;ENSP00000375648:L250P	ENSP00000337222:L250P	L	+	2	0	MYADM	59069344	0.919000	0.31177	0.038000	0.18304	0.385000	0.30292	3.405000	0.52630	1.734000	0.51633	0.254000	0.18369	CTC		0.632	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	NM_138373		C	54377532	T	C	54377532	3	2	93	1	0	0	0	0	1	0	0	0	10036	1551	54	4	751	4	MYADM	19	54377532	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2415947	54377532	4751451	254	25582										
KIR3DL1	3811	hgsc.bcm.edu	37	chr19	55341633	55341633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cacacagagaaaaatcactcGcccttctcagaggcccaaga	7	14	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:55341633G>A	ENST00000391728.4	+	9	1271	c.1238G>A	c.(1237-1239)cGc>cAc	p.R413H	KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.R318H|KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R396H|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R413H|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R396H	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	413					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		AAAATCACTCGCCCTTCTCAG	0.502																																																0			19											250	238	242					19																	55341633		2174	4168	6342	60033445	SO:0001583	missense	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1238G>A	19.37:g.55341633G>A	ENSP00000375608:p.Arg413His		60033445	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	-	0.945	-0.708423	0.03230	.	.	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00479	7.21;7.12;7.21;7.12;7.25	0.569	-1.14	0.09741	.	.	.	.	.	T	0.00328	0.0010	L	0.48174	1.505	0.09310	N	1	B;B;B	0.15719	0.014;0.007;0.004	B;B;B	0.13407	0.009;0.004;0.004	T	0.48387	-0.9040	8	0.49607	T	0.09	.	.	.	.	.	396;318;413	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	H	413;396;391;413;396;318	ENSP00000443350:R413H;ENSP00000442355:R396H;ENSP00000375608:R413H;ENSP00000326868:R396H;ENSP00000350901:R318H	ENSP00000326868:R396H	R	+	2	0	KIR3DL1	60033445	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.469000	0.06648	-1.579000	0.01646	-1.121000	0.02013	CGC		0.502	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		A	55341633	G	A	55341633	3	1	93	1	0	0	0	0	1	0	0	0	8341	1087	38	1	1272	1	KIR3DL1	19	55341633	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	964101	55341633	3787350	255	25583										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369203	56369203	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aaggaagctgggaaacagccAcgtacagtgatcattcaagg	12	8	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:56369203A>G	ENST00000301295.6	+	3	866	c.444A>G	c.(442-444)ccA>ccG	p.P148P	NLRP4_ENST00000587891.1_Silent_p.P73P|NLRP4_ENST00000346986.5_Silent_p.P148P	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	148					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GGAAACAGCCACGTACAGTGA	0.473																																																0			19											137	124	128					19																	56369203		2203	4300	6503	61061015	SO:0001819	synonymous_variant	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.444A>G	19.37:g.56369203A>G			61061015	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																				0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		G	56369203	A	G	56369203	2	3	93	1	0	0	0	0	0	0	0	1	10510	146	6	4		4	NLRP4	19	56369203	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1027570	56369203	2759780	256	25584										
ZNF547	284306	hgsc.bcm.edu	37	chr19	57889115	57889115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggagttccacactcattacAcatcagagggttcacactgg	9	11	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr19:57889115A>G	ENST00000282282.3	+	4	921	c.771A>G	c.(769-771)acA>acG	p.T257T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	257					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CACTCATTACACATCAGAGGG	0.433																																																0			19											125	114	118					19																	57889115		2203	4300	6503	62580927	SO:0001819	synonymous_variant	284306			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.771A>G	19.37:g.57889115A>G			62580927	A8K5Z9|Q96NC4	Silent	SNP	ENST00000282282.3	37	CCDS33131.1																																																																																				0.433	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		G	57889115	A	G	57889115	2	3	93	1	0	0	0	0	0	0	0	1	18018	146	6	4		4	ZNF547	19	57889115	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	1519912	57889115	1239868	257	25585										
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3209659	3209659	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ggcagtgcccttcaccagccTgcagcagacgggcactcgtg	13	15	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:3209659T>C	ENST00000380056.3	-	16	2114		c.e16-2		SLC4A11_ENST00000380059.3_Splice_Site|SLC4A11_ENST00000539553.2_Splice_Site|SLC4A11_ENST00000488544.1_Splice_Site	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11						bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TTCACCAGCCTGCAGCAGACG	0.652																																					NSCLC(190;922 2139 10266 10292 38692)											0			20											82	69	73					20																	3209659		2202	4300	6502	3157659	SO:0001630	splice_region_variant	83959			AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2067-2A>G	20.37:g.3209659T>C			3157659	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Splice_Site	SNP	ENST00000380056.3	37	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581901	0.65992	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8866	0.70572	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC4A11	3157659	1.000000	0.71417	0.968000	0.41197	0.911000	0.54048	7.929000	0.87595	1.989000	0.58080	0.379000	0.24179	.		0.652	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		Intron	C	3209659	T	C	3209659	5	2	93	1	0	0	0	0	0	0	1	0	14689	1594	55	4	626	4	SLC4A11	20	3209659	Splice_Site	SNP	T	TCGA-DC-5337-01A-01D-1657-10		3209659	59815861	258	25586										
PAK7	57144	hgsc.bcm.edu	37	chr20	9520157	9520157	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gggacgatgcaagacggtggAcctgctagttttaagaatgg	15	6	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:9520157A>G	ENST00000378429.3	-	11	2658	c.2112T>C	c.(2110-2112)ggT>ggC	p.G704G	PAK7_ENST00000378423.1_Silent_p.G704G|PAK7_ENST00000353224.5_Silent_p.G704G	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	704			G -> S (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			AAGACGGTGGACCTGCTAGTT	0.512																																																0			20											242	220	227					20																	9520157		2203	4300	6503	9468157	SO:0001819	synonymous_variant	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.2112T>C	20.37:g.9520157A>G			9468157	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	37	CCDS13107.1																																																																																				0.512	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9520157	A	G	9520157	2	3	93	1	0	0	0	0	0	0	0	1	11436	262	10	4		4	PAK7	20	9520157	Silent	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6310498	9520157	53505363	259	25587										
CD93	22918	hgsc.bcm.edu	37	chr20	23066686	23066686	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tggttgcagtggttctgggcCtcggcagcgctcagcttgcc	15	12	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:23066686C>T	ENST00000246006.4	-	1	291	c.144G>A	c.(142-144)gaG>gaA	p.E48E		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	48	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GGTTCTGGGCCTCGGCAGCGC	0.697																																																0			20											33	28	29					20																	23066686		2203	4299	6502	23014686	SO:0001819	synonymous_variant	22918			U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.144G>A	20.37:g.23066686C>T			23014686	O00274	Silent	SNP	ENST00000246006.4	37	CCDS13149.1																																																																																				0.697	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23066686	C	T	23066686	2	4	93	1	0	0	0	0	0	0	0	1	3053	680	24	3		3	CD93	20	23066686	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	13546529	23066686	39958834	260	25588										
NINL	22981	hgsc.bcm.edu	37	chr20	25456790	25456790	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tctccagcgctattttggtcTccccctcttctggggcagca	9	15	4	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:25456790T>C	ENST00000278886.6	-	17	3210	c.3137A>G	c.(3136-3138)gAg>gGg	p.E1046G	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1046					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TATTTTGGTCTCCCCCTCTTC	0.562																																																0			20											97	89	92					20																	25456790		2203	4300	6503	25404790	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3137A>G	20.37:g.25456790T>C	ENSP00000278886:p.Glu1046Gly		25404790	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.638240	0.47153	.	.	ENSG00000101004	ENST00000278886	T	0.05382	3.45	4.58	3.46	0.39613	.	2.778030	0.01856	N	0.036254	T	0.06005	0.0156	N	0.24115	0.695	0.19575	N	0.999966	B	0.29162	0.235	B	0.23018	0.043	T	0.35871	-0.9771	10	0.34782	T	0.22	-1.9895	7.0151	0.24883	0.0:0.1067:0.0:0.8933	.	1046	Q9Y2I6	NINL_HUMAN	G	1046	ENSP00000278886:E1046G	ENSP00000278886:E1046G	E	-	2	0	NINL	25404790	0.665000	0.27466	0.005000	0.12908	0.003000	0.03518	1.980000	0.40618	0.604000	0.29930	0.459000	0.35465	GAG		0.562	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		C	25456790	T	C	25456790	3	2	93	1	0	0	0	0	1	0	0	0	10451	1551	54	4	1043	4	NINL	20	25456790	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	2390104	25456790	37568730	261	25589										
NINL	22981	hgsc.bcm.edu	37	chr20	25457588	25457588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcttcagtgccctctccagcTccagctgctccgacctctgg	9	18	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:25457588T>C	ENST00000278886.6	-	17	2412	c.2339A>G	c.(2338-2340)gAg>gGg	p.E780G	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	780					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CCTCTCCAGCTCCAGCTGCTC	0.697																																																0			20											31	27	28					20																	25457588		2203	4300	6503	25405588	SO:0001583	missense	22981				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2339A>G	20.37:g.25457588T>C	ENSP00000278886:p.Glu780Gly		25405588	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	T	5.842	0.339565	0.11069	.	.	ENSG00000101004	ENST00000278886	T	0.28069	1.63	3.07	1.95	0.26073	.	17.581000	0.00166	N	0.000000	T	0.19248	0.0462	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14727	-1.0462	10	0.23891	T	0.37	-2.3897	4.8558	0.13559	0.0:0.1492:0.0:0.8508	.	780	Q9Y2I6	NINL_HUMAN	G	780	ENSP00000278886:E780G	ENSP00000278886:E780G	E	-	2	0	NINL	25405588	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.062000	0.11674	0.414000	0.25790	0.379000	0.24179	GAG		0.697	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		C	25457588	T	C	25457588	3	2	93	1	0	0	0	0	1	0	0	0	10451	1551	54	4	1841	4	NINL	20	25457588	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	798	25457588	37567932	262	25590										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31022343	31022343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctcctgccggggttggactGgcgccaggaccctcgcagac	14	16	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:31022343G>A	ENST00000375687.4	+	13	2252	c.1828G>A	c.(1828-1830)Ggc>Agc	p.G610S	ASXL1_ENST00000306058.5_Missense_Mutation_p.G605S	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	610	Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.Q592fs*5(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GGGTTGGACTGGCGCCAGGAC	0.622			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	20											29	32	31					20																	31022343		2203	4300	6503	30486004	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1828G>A	20.37:g.31022343G>A	ENSP00000364839:p.Gly610Ser		30486004	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935515	0.52866	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.56776	0.44;0.44	5.41	2.44	0.29823	.	0.157000	0.56097	N	0.000023	T	0.41719	0.1171	M	0.65975	2.015	0.44181	D	0.996992	P;P	0.46220	0.874;0.794	B;B	0.35114	0.163;0.196	T	0.25950	-1.0117	10	0.42905	T	0.14	-8.2302	6.3002	0.21109	0.2138:0.1326:0.6535:0.0	.	605;610	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	S	610;610;610;549;605	ENSP00000364839:G610S;ENSP00000305119:G605S	ENSP00000305119:G605S	G	+	1	0	ASXL1	30486004	1.000000	0.71417	0.692000	0.30179	0.952000	0.60782	4.072000	0.57563	0.421000	0.25980	0.561000	0.74099	GGC		0.622	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31022343	G	A	31022343	3	1	93	1	0	0	0	0	1	0	0	0	1067	1348	47	3	1884	3	ASXL1	20	31022343	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	5564755	31022343	32003177	263	25591										
SNTA1	6640	hgsc.bcm.edu	37	chr20	32026745	32026745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cattcacagacaggatggcaTcccccacaaaaagggcctct	8	14	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:32026745T>C	ENST00000217381.2	-	2	669	c.398A>G	c.(397-399)gAt>gGt	p.D133G		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	133	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						CAGGATGGCATCCCCCACAAA	0.552																																																0			20											144	135	138					20																	32026745		2203	4300	6503	31490406	SO:0001583	missense	6640			U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"pro-TGF-alpha cytoplasmic domain-interacting protein 1", "dystrophin-associated protein A1, 59kDa, acidic component"	601017	"syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.398A>G	20.37:g.32026745T>C	ENSP00000217381:p.Asp133Gly		31490406	A8K7H9|B4DX40|E1P5N1|Q16438	Missense_Mutation	SNP	ENST00000217381.2	37	CCDS13220.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303050	0.81136	.	.	ENSG00000101400	ENST00000217381	T	0.74106	-0.81	5.03	5.03	0.67393	PDZ/DHR/GLGF (4);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.91975	0.7458	H	0.99249	4.485	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;1.0	D	0.95094	0.8224	10	0.87932	D	0	-13.1829	14.6168	0.68556	0.0:0.0:0.0:1.0	.	133;133	B4DX40;Q13424	.;SNTA1_HUMAN	G	133	ENSP00000217381:D133G	ENSP00000217381:D133G	D	-	2	0	SNTA1	31490406	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.512000	0.81728	2.114000	0.64651	0.459000	0.35465	GAT		0.552	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098		C	32026745	T	C	32026745	3	2	93	1	0	0	0	0	1	0	0	0	14908	1435	50	4	1147	4	SNTA1	20	32026745	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1004402	32026745	30998775	264	25592										
TUBB1	81027	hgsc.bcm.edu	37	chr20	57599243	57599243	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cgcagacctgcgcaagctggCggtgaacatggtccccttcc	12	15	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:57599243C>T	ENST00000217133.1	+	4	1030	c.761C>T	c.(760-762)gCg>gTg	p.A254V		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	254					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	CGCAAGCTGGCGGTGAACATG	0.637																																																0			20											76	66	70					20																	57599243		2203	4300	6503	57032638	SO:0001583	missense	203068			AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.761C>T	20.37:g.57599243C>T	ENSP00000217133:p.Ala254Val		57032638		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	C	34	5.364845	0.95877	.	.	ENSG00000101162	ENST00000217133	D	0.83914	-1.78	5.19	5.19	0.71726	Tubulin/FtsZ, 2-layer sandwich domain (1);Tubulin/FtsZ, GTPase domain (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90848	0.7125	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.91907	0.5536	10	0.87932	D	0	.	17.6651	0.88201	0.0:1.0:0.0:0.0	.	254	Q9H4B7	TBB1_HUMAN	V	254	ENSP00000217133:A254V	ENSP00000217133:A254V	A	+	2	0	TUBB1	57032638	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.818000	0.86416	2.431000	0.82371	0.561000	0.74099	GCG		0.637	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		T	57599243	C	T	57599243	3	4	93	1	0	0	0	0	1	0	0	0	16793	768	27	1	775	1	TUBB1	20	57599243	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	25572498	57599243	5426277	265	25593										
GTPBP5	26164	hgsc.bcm.edu	37	chr20	60775780	60775780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tacgaggcgcccaccagaacAggggtctggggtccgccttc	14	14	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:60775780A>G	ENST00000370823.3	+	7	886	c.868A>G	c.(868-870)Agg>Ggg	p.R290G	MTG2_ENST00000436421.2_Missense_Mutation_p.R132G|MTG2_ENST00000536470.1_Missense_Mutation_p.R62G	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	290	Localized in the mitochondria.|Not localized in the mitochondria.|OBG-type G.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)										CCACCAGAACAGGGGTCTGGG	0.622																																																0			20											81	89	86					20																	60775780		2203	4300	6503	60209175	SO:0001583	missense	26164			AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"GTP-binding protein 5 (putative)", "GTP binding protein 5 (putative)"	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.868A>G	20.37:g.60775780A>G	ENSP00000359859:p.Arg290Gly		60209175	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Missense_Mutation	SNP	ENST00000370823.3	37	CCDS13492.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.092043	0.76756	.	.	ENSG00000101181	ENST00000536470;ENST00000436421;ENST00000370823	T;T;T	0.18810	2.19;2.19;2.19	5.67	-5.71	0.02413	Small GTP-binding protein domain (1);GTP1/OBG (1);GTP-binding domain, HSR1-related (1);	0.101891	0.64402	D	0.000007	T	0.52419	0.1733	H	0.94925	3.6	0.41307	D	0.987089	D;P	0.55385	0.971;0.607	D;P	0.64506	0.926;0.579	T	0.73547	-0.3948	10	0.62326	D	0.03	-28.0314	20.5547	0.99287	0.5786:0.4214:0.0:0.0	.	132;290	E7EU10;Q9H4K7	.;GTPB5_HUMAN	G	62;132;290	ENSP00000445056:R62G;ENSP00000392267:R132G;ENSP00000359859:R290G	ENSP00000359859:R290G	R	+	1	2	GTPBP5	60209175	0.907000	0.30839	0.405000	0.26409	0.704000	0.40688	0.089000	0.15002	-0.746000	0.04766	-0.396000	0.06452	AGG		0.622	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666		G	60775780	A	G	60775780	3	3	93	1	0	0	0	0	1	0	0	0	6904	179	7	4	890	4	GTPBP5	20	60775780	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	3176537	60775780	2249740	266	25594										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62039789	62039789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cttctccaccttcccgagccGtcccatcatgctggggtcct	8	18	2	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr20:62039789G>A	ENST00000359125.2	-	16	2038	c.1864C>T	c.(1864-1866)Cgg>Tgg	p.R622W	KCNQ2_ENST00000354587.3_Missense_Mutation_p.R630W|KCNQ2_ENST00000370224.1_Missense_Mutation_p.R630W|KCNQ2_ENST00000344462.4_Missense_Mutation_p.R591W|KCNQ2_ENST00000360480.3_Missense_Mutation_p.R594W|KCNQ2_ENST00000357249.2_Missense_Mutation_p.R604W|KCNQ2_ENST00000359689.1_Missense_Mutation_p.R622W	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	622					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TTCCCGAGCCGTCCCATCATG	0.706																																																0			20											30	24	26					20																	62039789		2189	4289	6478	61510233	SO:0001583	missense	3785			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1864C>T	20.37:g.62039789G>A	ENSP00000352035:p.Arg622Trp		61510233	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372308	0.82573	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224	D;D;D;D;D;D;D;D;D	0.99885	-7.51;-7.51;-7.51;-7.51;-7.51;-7.51;-7.51;-7.51;-7.51	4.87	2.74	0.32292	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.065173	0.64402	D	0.000016	D	0.99864	0.9936	M	0.86502	2.82	0.53688	D	0.99997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.70716	0.949;0.931;0.949;0.97	D	0.96612	0.9453	10	0.87932	D	0	-28.7771	12.5655	0.56308	0.0:0.0:0.5796:0.4204	.	594;604;591;622	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	W	604;622;592;630;622;591;594;618;630	ENSP00000349789:R604W;ENSP00000352035:R622W;ENSP00000359246:R592W;ENSP00000346601:R630W;ENSP00000352718:R622W;ENSP00000399612:R591W;ENSP00000353668:R594W;ENSP00000339611:R618W;ENSP00000359244:R630W	ENSP00000339611:R618W	R	-	1	2	KCNQ2	61510233	0.998000	0.40836	0.948000	0.38648	0.863000	0.49368	2.533000	0.45667	1.027000	0.39758	0.491000	0.48974	CGG		0.706	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62039789	G	A	62039789	3	1	93	1	0	0	0	0	1	0	0	0	8104	1144	40	1	762	1	KCNQ2	20	62039789	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	1264009	62039789	985731	267	25595										
GART	2618	hgsc.bcm.edu	37	chr21	34876605	34876605	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gcttcttgcaaaataatctgTccagcatccacatcttcctg	5	13	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr21:34876605T>C	ENST00000381831.3	-	22	3122	c.2859A>G	c.(2857-2859)ggA>ggG	p.G953G	GART_ENST00000381839.3_Silent_p.G953G|GART_ENST00000381815.4_Silent_p.G953G|GART_ENST00000543717.1_Silent_p.G505G	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	953	GART.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	AAATAATCTGTCCAGCATCCA	0.373																																																0			21											59	59	59					21																	34876605		2203	4300	6503	33798475	SO:0001819	synonymous_variant	2618			M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2859A>G	21.37:g.34876605T>C			33798475	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Silent	SNP	ENST00000381831.3	37	CCDS13627.1																																																																																				0.373	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		C	34876605	T	C	34876605	2	2	93	1	0	0	0	0	0	0	0	1	6263	1654	58	4		4	GART	21	34876605	Silent	SNP	T	TCGA-DC-5337-01A-01D-1657-10		34876605	13253290	268	25596										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37583900	37583900	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctcaaatgttcttgtgcaaaGaaataatctggaaatcgttc	7	7	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr21:37583900G>T	ENST00000399151.3	+	6	816	c.731G>T	c.(730-732)aGa>aTa	p.R244I	RN7SL73P_ENST00000585239.1_RNA|DOPEY2_ENST00000492760.1_3'UTR	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	244					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CTTGTGCAAAGAAATAATCTG	0.418																																																0			21											221	188	199					21																	37583900		2203	4300	6503	36505770	SO:0001583	missense	9980			AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.731G>T	21.37:g.37583900G>T	ENSP00000382104:p.Arg244Ile		36505770	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	G	32	5.109878	0.94292	.	.	ENSG00000142197	ENST00000399151	T	0.38240	1.15	5.23	5.23	0.72850	Dopey, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	H	0.94385	3.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81295	-0.0997	10	0.87932	D	0	.	18.8324	0.92145	0.0:0.0:1.0:0.0	.	244;244	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	I	244	ENSP00000382104:R244I	ENSP00000382104:R244I	R	+	2	0	DOPEY2	36505770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.535000	0.90623	2.448000	0.82819	0.655000	0.94253	AGA		0.418	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37583900	G	T	37583900	3	4	93	1	0	0	0	0	1	0	0	0	4719	942	33	2	749	2	DOPEY2	21	37583900	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	2707295	37583900	10545995	269	25597										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47684123	47684123	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	atgagctcgtccaccacctgCgccaggtcctgtggagagac	12	14	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr21:47684123C>T	ENST00000397708.1	-	14	3497	c.3243G>A	c.(3241-3243)gcG>gcA	p.A1081A	MCM3AP_ENST00000291688.1_Silent_p.A1081A			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1081					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CCACCACCTGCGCCAGGTCCT	0.632																																																0			21											45	37	40					21																	47684123		2202	4300	6502	46508551	SO:0001819	synonymous_variant	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3243G>A	21.37:g.47684123C>T			46508551	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																				0.632	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		T	47684123	C	T	47684123	2	4	93	1	0	0	0	0	0	0	0	1	9418	755	27	1		1	MCM3AP	21	47684123	Silent	SNP	C	TCGA-DC-5337-01A-01D-1657-10	10100223	47684123	445772	270	25598										
MMP11	4320	hgsc.bcm.edu	37	chr22	24121515	24121515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ctccccgctgtggcgtgcccGacccatctgatgggctgagt	13	15	1	2	rs376901794		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr22:24121515G>A	ENST00000215743.3	+	2	302	c.250G>A	c.(250-252)Gac>Aac	p.D84N	MMP11_ENST00000477567.1_3'UTR	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	84					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	TGGCGTGCCCGACCCATCTGA	0.697																																																0			22						G	ASN/ASP	0,4406		0,0,2203	19	21	20		250	2	1	22		20	1,8599		0,1,4299	no	missense	MMP11	NM_005940.3	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	84/489	24121515	1,13005	2203	4300	6503	22451515	SO:0001583	missense	4320				CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.250G>A	22.37:g.24121515G>A	ENSP00000215743:p.Asp84Asn		22451515	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.822964	0.50739	0.0	1.16E-4	ENSG00000099953	ENST00000215743	T	0.16324	2.35	4.18	2.04	0.26737	Metallopeptidase, catalytic domain (1);	0.101382	0.64402	D	0.000004	T	0.23611	0.0571	L	0.32530	0.975	0.45354	D	0.998344	D	0.76494	0.999	D	0.63033	0.91	T	0.01874	-1.1256	10	0.87932	D	0	.	8.4586	0.32915	0.0872:0.0:0.7558:0.157	.	84	P24347	MMP11_HUMAN	N	84	ENSP00000215743:D84N	ENSP00000215743:D84N	D	+	1	0	MMP11	22451515	1.000000	0.71417	0.993000	0.49108	0.086000	0.17979	4.060000	0.57477	1.080000	0.41073	0.549000	0.68633	GAC		0.697	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		A	24121515	G	A	24121515	3	1	93	1	0	0	0	0	1	0	0	0	9680	1058	37	1	256	1	MMP11	22	24121515	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10		24121515	27183051	271	25599										
NF2	4771	hgsc.bcm.edu	37	chr22	30035170	30035170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tgctgaagaggagctggttcAggagatcacacaacatttat	11	7	2	3			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr22:30035170A>G	ENST00000338641.4	+	3	773	c.332A>G	c.(331-333)cAg>cGg	p.Q111R	NF2_ENST00000353887.4_Intron|NF2_ENST00000413209.2_Missense_Mutation_p.Q111R|NF2_ENST00000403999.3_Missense_Mutation_p.Q111R|NF2_ENST00000361676.4_Missense_Mutation_p.Q69R|NF2_ENST00000403435.1_Missense_Mutation_p.Q111R|NF2_ENST00000361452.4_Intron|NF2_ENST00000361166.4_Missense_Mutation_p.Q111R|NF2_ENST00000347330.5_Intron|NF2_ENST00000397789.3_Missense_Mutation_p.Q111R|NF2_ENST00000334961.7_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	111	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.H95fs*3(1)|p.L97fs*17(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GAGCTGGTTCAGGAGATCACA	0.458			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	5	Unknown(3)|Deletion - Frameshift(2)	soft_tissue(2)|stomach(1)|large_intestine(1)|lung(1)	22											137	120	126					22																	30035170		2203	4300	6503	28365170	SO:0001583	missense	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.332A>G	22.37:g.30035170A>G	ENSP00000344666:p.Gln111Arg		28365170	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	33	5.249779	0.95305	.	.	ENSG00000186575	ENST00000413209;ENST00000338641;ENST00000403435;ENST00000397822;ENST00000403999;ENST00000397789;ENST00000361676;ENST00000361166	T;D;D;D;D;D;D	0.83506	-1.18;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	6.03	6.03	0.97812	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.054166	0.85682	D	0.000000	D	0.93019	0.7778	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.995;0.999;0.999;0.998;1.0	D	0.94160	0.7413	9	.	.	.	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	111;111;111;69;111	P35240-9;P35240;P35240-2;P35240-6;P35240-3	.;MERL_HUMAN;.;.;.	R	111;111;111;111;111;111;69;111	ENSP00000409921:Q111R;ENSP00000344666:Q111R;ENSP00000384029:Q111R;ENSP00000384797:Q111R;ENSP00000380891:Q111R;ENSP00000355183:Q69R;ENSP00000354529:Q111R	.	Q	+	2	0	NF2	28365170	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.228000	0.95250	2.302000	0.77476	0.533000	0.62120	CAG		0.458	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		G	30035170	A	G	30035170	3	3	93	1	0	0	0	0	1	0	0	0	10388	188	7	4	342	4	NF2	22	30035170	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	5913655	30035170	21269396	272	25600										
RNF215	200312	hgsc.bcm.edu	37	chr22	30781916	30781916	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agcaatgcatccaacagcttGgtgacattggaggaataatg	11	7	0	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr22:30781916G>A	ENST00000382363.3	-	4	638	c.564C>T	c.(562-564)acC>acT	p.T188T		NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	188						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.T188T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						CCAACAGCTTGGTGACATTGG	0.557																																																1	Substitution - coding silent(1)	central_nervous_system(1)	22											172	157	162					22																	30781916		2203	4300	6503	29111916	SO:0001819	synonymous_variant	200312				CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999		"RING-type (C3HC4) zinc fingers"	33434	protein-coding gene	gene with protein product							Standard	NM_001017981		Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.564C>T	22.37:g.30781916G>A			29111916	A6NEL1	Silent	SNP	ENST00000382363.3	37	CCDS33633.1	.	.	.	.	.	.	.	.	.	.	G	9.776	1.174003	0.21704	.	.	ENSG00000099999	ENST00000215798	.	.	.	4.87	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.3352	10.3648	0.44017	0.1904:0.0:0.8096:0.0	.	.	.	.	X	126	.	.	Q	-	1	0	RNF215	29111916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.564000	0.45931	1.030000	0.39839	0.650000	0.86243	CAA		0.557	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320960.1	NM_001017981		A	30781916	G	A	30781916	2	1	93	1	0	0	0	0	0	0	0	1	13516	1335	47	3		3	RNF215	22	30781916	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	746746	30781916	20522650	273	25601										
RBM9	23543	hgsc.bcm.edu	37	chr22	36156005	36156005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tactgtccgccctctgccccTcaaatgggctcctctgaaag	8	16	3	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr22:36156005T>C	ENST00000438146.2	-	10	1038	c.1039A>G	c.(1039-1041)Agg>Ggg	p.R347G	RBFOX2_ENST00000416721.2_Missense_Mutation_p.R272G|RBFOX2_ENST00000397303.2_Missense_Mutation_p.R253G|RBFOX2_ENST00000359369.4_Missense_Mutation_p.R252G|RBFOX2_ENST00000405409.2_Missense_Mutation_p.R273G|RBFOX2_ENST00000449924.2_Missense_Mutation_p.R276G|RBFOX2_ENST00000262829.7_Missense_Mutation_p.R254G|RBFOX2_ENST00000414461.2_Missense_Mutation_p.R276G	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	286	Ala-rich.				dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						CCTCTGCCCCTCAAATGGGCT	0.522																																																0			22											73	72	72					22																	36156005		2203	4300	6503	34485951	SO:0001583	missense	0			AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"RNA binding motif (RRM) containing"	9906	protein-coding gene	gene with protein product	"hexaribonucleotide binding protein 2"	612149	"RNA binding motif protein 9"	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.1039A>G	22.37:g.36156005T>C	ENSP00000413035:p.Arg347Gly		34485951	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Missense_Mutation	SNP	ENST00000438146.2	37	CCDS43013.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154077	0.57259	.	.	ENSG00000100320	ENST00000405409;ENST00000338644;ENST00000414461;ENST00000449924;ENST00000262829;ENST00000397303;ENST00000359369;ENST00000416721;ENST00000438146	T;T;T;T;T;T;T	0.58210	1.2;0.92;0.42;0.77;1.12;0.77;0.35	5.48	3.16	0.36331	.	0.000000	0.85682	D	0.000000	T	0.68924	0.3054	M	0.70275	2.135	0.50467	D	0.999876	D;D;D;D;D;D;D;D;D	0.89917	0.997;0.996;1.0;0.989;0.996;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.996;0.99;0.996;0.985;0.99;0.999;0.999;0.999;0.999	T	0.71646	-0.4530	10	0.87932	D	0	.	11.8334	0.52309	0.0:0.0:0.2771:0.7229	.	252;346;347;254;272;273;276;276;253	B0QYY4;O43251-6;O43251-8;O43251-3;O43251-5;O43251-9;O43251-10;O43251-4;B0QYV1	.;.;.;.;.;.;.;.;.	G	273;282;276;276;254;253;252;272;347	ENSP00000384944:R273G;ENSP00000407855:R276G;ENSP00000391670:R276G;ENSP00000380470:R253G;ENSP00000352328:R252G;ENSP00000405651:R272G;ENSP00000413035:R347G	ENSP00000262829:R254G	R	-	1	2	RBFOX2	34485951	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.932000	0.40143	0.871000	0.35750	0.460000	0.39030	AGG		0.522	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3			C	36156005	T	C	36156005	3	2	93	1	0	0	0	0	1	0	0	0	13184	1550	54	4	346	4	RBM9	22	36156005	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	5374089	36156005	15148561	274	25602										
SBF1	6305	hgsc.bcm.edu	37	chr22	50893974	50893974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	aggagcctgaatccaggagcTccaccaccagcacagacacc	9	16	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chr22:50893974T>C	ENST00000390679.3	-	31	4410	c.4226A>G	c.(4225-4227)gAg>gGg	p.E1409G	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000348911.6_Missense_Mutation_p.E1410G|SBF1_ENST00000380817.3_Missense_Mutation_p.E1435G			O95248	MTMR5_HUMAN	SET binding factor 1	1409	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-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)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		ATCCAGGAGCTCCACCACCAG	0.692																																																0			22											19	27	24					22																	50893974		2148	4252	6400	49240840	SO:0001583	missense	6305			U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.4226A>G	22.37:g.50893974T>C	ENSP00000375097:p.Glu1409Gly		49240840	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	T	20.6	4.017845	0.75161	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	D;D;D	0.90444	-2.67;-2.67;-2.67	4.4	3.37	0.38596	Myotubularin phosphatase domain (1);	0.173570	0.49916	D	0.000134	D	0.92522	0.7625	L	0.49126	1.545	0.58432	D	0.999999	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.986	D	0.91544	0.5252	10	0.72032	D	0.01	.	9.3143	0.37924	0.0:0.0865:0.0:0.9135	.	1409;1435	O95248;O95248-4	MTMR5_HUMAN;.	G	1435;1410;1445;1409	ENSP00000370196:E1435G;ENSP00000252027:E1410G;ENSP00000375097:E1409G	ENSP00000336522:E1445G	E	-	2	0	SBF1	49240840	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.792000	0.69052	0.741000	0.32674	0.533000	0.62120	GAG		0.692	SBF1-201	KNOWN	basic	protein_coding	protein_coding				C	50893974	T	C	50893974	3	2	93	1	0	0	0	0	1	0	0	0	13895	1551	54	4	1417	4	SBF1	22	50893974	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	14737969	50893974	410592	275	25603										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3235262	3235262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gtacctgacgtccgtcctccGcggggaggtgcccgtgatgc	15	14	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:3235262G>A	ENST00000217939.6	-	6	6614	c.6460C>T	c.(6460-6462)Cgg>Tgg	p.R2154W		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2154	Ig-like C2-type 6.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCCGTCCTCCGCGGGGAGGTG	0.697																																																0			X											27	22	24					X																	3235262		2203	4298	6501	3245262	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6460C>T	X.37:g.3235262G>A	ENSP00000217939:p.Arg2154Trp		3245262	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752682	0.49362	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.69040	-0.37	3.48	3.48	0.39840	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.662716	0.11741	U	0.533982	T	0.76371	0.3978	L	0.52759	1.655	0.39658	D	0.970568	D	0.89917	1.0	D	0.63033	0.91	T	0.77536	-0.2551	10	0.87932	D	0	.	14.7878	0.69816	0.0:0.0:1.0:0.0	.	2154	Q9NR99	MXRA5_HUMAN	W	2154	ENSP00000217939:R2154W	ENSP00000217939:R2154W	R	-	1	2	MXRA5	3245262	0.762000	0.28451	0.004000	0.12327	0.002000	0.02628	3.451000	0.52964	1.354000	0.45846	0.597000	0.82753	CGG		0.697	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3235262	G	A	3235262	3	1	93	1	0	0	0	0	1	0	0	0	10033	1086	38	1	2034	1	MXRA5	23	3235262	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10		3235262	152035298	276	25604										
RBBP7	5931	hgsc.bcm.edu	37	chrX	16870190	16870190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	ttaaatcccacacattcaggCggcggtcagtaccacttgaa	8	12	2	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:16870190C>T	ENST00000380087.2	-	9	1379	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	RBBP7_ENST00000404022.1_Missense_Mutation_p.R331H|RBBP7_ENST00000380084.4_Missense_Mutation_p.R384H			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	340					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)	p.R340H(1)		biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					CACATTCAGGCGGCGGTCAGT	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	X											226	193	204					X																	16870190		2203	4300	6503	16780111	SO:0001583	missense	5931			U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"WD repeat domain containing"	9890	protein-coding gene	gene with protein product	"G1/S transition control protein-binding protein RbAp46", "retinoblastoma-binding protein 7", "retinoblastoma-binding protein RbAp46", "histone acetyltransferase type B subunit 2", "retinoblastoma-binding protein p46"	300825	"retinoblastoma-binding protein 7"			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.1019G>A	X.37:g.16870190C>T	ENSP00000369427:p.Arg340His		16780111	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	.	.	.	.	.	.	.	.	.	.	C	34	5.332239	0.95733	.	.	ENSG00000102054	ENST00000380087;ENST00000380084;ENST00000404022;ENST00000444437;ENST00000416035	T;T;T;T;T	0.64085	0.21;0.21;0.21;0.21;-0.08	5.46	5.46	0.80206	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.79924	0.4530	M	0.76938	2.355	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.91635	0.935;0.999;0.935	T	0.80594	-0.1313	9	.	.	.	-10.0579	17.4651	0.87630	0.0:1.0:0.0:0.0	.	331;340;384	E9PC52;Q16576;Q5JP00	.;RBBP7_HUMAN;.	H	340;384;331;144;279	ENSP00000369427:R340H;ENSP00000369424:R384H;ENSP00000386068:R331H;ENSP00000402796:R144H;ENSP00000392714:R279H	.	R	-	2	0	RBBP7	16780111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.039000	0.70972	2.426000	0.82243	0.538000	0.68166	CGC		0.378	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		T	16870190	C	T	16870190	3	4	93	1	0	0	0	0	1	0	0	0	13141	768	27	1	274	1	RBBP7	23	16870190	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	13634928	16870190	138400370	277	25605										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24625952	24625952	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gaagaggtcaaatattccatCggcgtatactctgacaggcc	10	10	2	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:24625952C>T	ENST00000379144.2	-	3	374	c.244G>A	c.(244-246)Gat>Aat	p.D82N	PCYT1B_ENST00000356768.4_Missense_Mutation_p.D82N|PCYT1B_ENST00000379145.1_Missense_Mutation_p.D64N	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	82					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	AATATTCCATCGGCGTATACT	0.453																																																0			X											82	75	77					X																	24625952		2203	4300	6503	24535873	SO:0001583	missense	9468			AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.244G>A	X.37:g.24625952C>T	ENSP00000368439:p.Asp82Asn		24535873	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	37	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	C	32	5.154598	0.94686	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	D;D;D	0.96685	-4.09;-4.09;-4.09	5.19	5.19	0.71726	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1);	0.000000	0.85682	D	0.000000	D	0.97346	0.9132	L	0.50919	1.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.99;0.99	D	0.98290	1.0513	10	0.87932	D	0	0.3713	17.8268	0.88668	0.0:1.0:0.0:0.0	.	82;64;82	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	N	64;82;82	ENSP00000368440:D64N;ENSP00000368439:D82N;ENSP00000349211:D82N	ENSP00000349211:D82N	D	-	1	0	PCYT1B	24535873	1.000000	0.71417	0.982000	0.44146	0.987000	0.75469	7.320000	0.79064	2.398000	0.81561	0.544000	0.68410	GAT		0.453	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		T	24625952	C	T	24625952	3	4	93	1	0	0	0	0	1	0	0	0	11642	884	31	1	926	1	PCYT1B	23	24625952	Missense_Mutation	SNP	C	TCGA-DC-5337-01A-01D-1657-10	7755762	24625952	130644608	278	25606										
ASB12	142689	hgsc.bcm.edu	37	chrX	63444307	63444307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	agcctggcacaaggctctgcGgacgactaaacggacctgtg	13	12	1	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:63444307G>A	ENST00000396130.2	-	2	837	c.838C>T	c.(838-840)Cgc>Tgc	p.R280C	ASB12_ENST00000362002.2_Missense_Mutation_p.R289C|MTMR8_ENST00000453546.1_Missense_Mutation_p.R664C			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	280	SOCS box.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)|p.R664G(1)|p.R289G(1)|p.R280G(1)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						AAGGCTCTGCGGACGACTAAA	0.493																																																5	Substitution - Missense(3)|Whole gene deletion(2)	lung(3)|ovary(1)|large_intestine(1)	X											106	86	92					X																	63444307		2203	4300	6503	63361032	SO:0001583	missense	142689			AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705	ENST00000396130.2:c.838C>T	X.37:g.63444307G>A	ENSP00000379435:p.Arg280Cys		63361032	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	37		.	.	.	.	.	.	.	.	.	.	G	13.20	2.166569	0.38217	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.64438	-0.1;-0.1;-0.1	3.73	2.87	0.33458	SOCS protein, C-terminal (2);	0.183804	0.45606	D	0.000342	T	0.62146	0.2404	M	0.85630	2.765	0.28306	N	0.922896	P;B	0.48294	0.908;0.019	B;B	0.43413	0.419;0.021	T	0.64127	-0.6480	10	0.87932	D	0	-15.3868	4.0617	0.09841	0.1227:0.0:0.5263:0.3509	.	664;280	B4DQL0;Q8WXK4	.;ASB12_HUMAN	C	289;280;257;664	ENSP00000355195:R289C;ENSP00000379435:R280C;ENSP00000394003:R664C	ENSP00000354626:R257C	R	-	1	0	ASB12;MTMR8	63361032	1.000000	0.71417	0.997000	0.53966	0.283000	0.27025	2.172000	0.42463	0.940000	0.37473	0.529000	0.55759	CGC		0.493	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	63444307	G	A	63444307	3	1	93	1	0	0	0	0	1	0	0	0	1017	1116	39	1	95	1	ASB12	23	63444307	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	38818355	63444307	91826253	279	25607										
MED12	9968	hgsc.bcm.edu	37	chrX	70338702	70338702	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	tcaggaccccaaacagaaggAggtgcgttcgaaaatcgggg	14	9	1	1			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:70338702A>G	ENST00000374080.3	+	1	130	c.98A>G	c.(97-99)gAg>gGg	p.E33G	MED12_ENST00000333646.6_Splice_Site_p.E33G|MED12_ENST00000374102.1_Splice_Site_p.E33G			Q93074	MED12_HUMAN	mediator complex subunit 12	33					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					AAACAGAAGGAGGTGCGTTCG	0.672			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																																Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	0			X											13	14	14					X																	70338702		1811	4045	5856	70255427	SO:0001630	splice_region_variant	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.99+1A>G	X.37:g.70338702A>G			70255427	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	20.5	3.998398	0.74818	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.73575	-0.75;-0.75;-0.76;-0.27	4.13	4.13	0.48395	.	0.148358	0.43747	D	0.000535	D	0.83454	0.5258	M	0.68317	2.08	0.80722	D	1	D;D;D	0.76494	0.999;0.992;0.999	D;P;D	0.72075	0.976;0.893;0.971	D	0.85501	0.1191	10	0.87932	D	0	-9.9108	13.06	0.59002	1.0:0.0:0.0:0.0	.	33;33;33	F5H3Y1;Q93074-3;Q93074	.;.;MED12_HUMAN	G	33;33;33;33;1	ENSP00000333125:E33G;ENSP00000363215:E33G;ENSP00000363193:E33G;ENSP00000414203:E1G	ENSP00000333125:E33G	E	+	2	0	MED12	70255427	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	8.036000	0.88901	1.611000	0.50210	0.352000	0.21897	GAG		0.672	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	Missense_Mutation	G	70338702	A	G	70338702	5	3	93	1	0	0	0	0	0	0	1	0	9458	318	11	4	100	4	MED12	23	70338702	Splice_Site	SNP	A	TCGA-DC-5337-01A-01D-1657-10	6894395	70338702	84931858	280	25608										
RPS4X	6191	hgsc.bcm.edu	37	chrX	71496026	71496026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	caaacacaccggtcaatttaTccagcatccaatgctttgga	6	12	1	0	rs113410562		TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:71496026T>C	ENST00000316084.6	-	2	166	c.62A>G	c.(61-63)gAt>gGt	p.D21G	RPS4X_ENST00000373626.3_Missense_Mutation_p.D21G|RPS4X_ENST00000486733.1_5'UTR	NM_001007.4	NP_000998.1	P62701	RS4X_HUMAN	ribosomal protein S4, X-linked	21					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			NS(1)|large_intestine(1)	2	Renal(35;0.156)					GGTCAATTTATCCAGCATCCA	0.453																																																0			X											40	38	38					X																	71496026		2203	4300	6503	71412751	SO:0001583	missense	6191				CCDS14418.1	Xq13.1	2011-04-05			ENSG00000198034	ENSG00000198034		"S ribosomal proteins"	10424	protein-coding gene	gene with protein product	"40S ribosomal protein S4, X isoform", "ribosomal protein S4X isoform", "single-copy abundant mRNA", "cell cycle gene 2"	312760				1795030, 8139551	Standard	NM_001007		Approved	DXS306, CCG2, SCAR, SCR10, FLJ40595, RPS4, S4	uc004ear.3	P62701	OTTHUMG00000021813	ENST00000316084.6:c.62A>G	X.37:g.71496026T>C	ENSP00000362744:p.Asp21Gly		71412751	P12631|P12750|P27576|P55831|Q14727|Q6IPY4	Missense_Mutation	SNP	ENST00000316084.6	37	CCDS14418.1	.	.	.	.	.	.	.	.	.	.	T	16.76	3.213451	0.58452	.	.	ENSG00000198034	ENST00000316084;ENST00000373626	.	.	.	4.59	4.59	0.56863	Ribosomal protein S4e, N-terminal, conserved site (1);Ribosomal protein S4e, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70064	0.3181	M	0.82823	2.61	0.80722	D	1	B;B	0.33073	0.094;0.396	B;B	0.42422	0.085;0.387	T	0.72802	-0.4183	9	0.54805	T	0.06	.	11.1874	0.48664	0.0:0.0:0.0:1.0	.	21;21	B7Z1M6;P62701	.;RS4X_HUMAN	G	21	.	ENSP00000362744:D21G	D	-	2	0	RPS4X	71412751	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.704000	0.84595	1.608000	0.50180	0.481000	0.45027	GAT		0.453	RPS4X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057188.1	NM_001007		C	71496026	T	C	71496026	3	2	93	1	0	0	0	0	1	0	0	0	13682	1435	50	4	753	4	RPS4X	23	71496026	Missense_Mutation	SNP	T	TCGA-DC-5337-01A-01D-1657-10	1157324	71496026	83774534	281	25609										
CAPN6	827	hgsc.bcm.edu	37	chrX	110489922	110489922	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	gacttcagatcacggcagtcGctggggtcagcatccagagt	13	11	3	2	rs147112567	byFrequency	TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:110489922G>A	ENST00000324068.1	-	13	1976	c.1809C>T	c.(1807-1809)agC>agT	p.S603S	CAPN6_ENST00000541758.1_Silent_p.S348S	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	603	C2.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						CACGGCAGTCGCTGGGGTCAG	0.512																																																0			X						G		1,3834		0,1,0,1631,571	128	96	107		1809	-2.8	0.9	X	dbSNP_134	107	6,6722		0,5,1,2423,1871	no	coding-synonymous	CAPN6	NM_014289.3		0,6,1,4054,2442	AA,AG,A,GG,G		0.0892,0.0261,0.0663		603/642	110489922	7,10556	2203	4300	6503	110376578	SO:0001819	synonymous_variant	827			AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1809C>T	X.37:g.110489922G>A			110376578	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	37	CCDS14555.1																																																																																				0.512	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			A	110489922	G	A	110489922	2	1	93	1	0	0	0	0	0	0	0	1	2636	1078	38	1		1	CAPN6	23	110489922	Silent	SNP	G	TCGA-DC-5337-01A-01D-1657-10	38993896	110489922	44780638	282	25610										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123554280	123554280	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	actcttttcaggactccattGctgcttatagtcagccagta	7	11	3	0			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:123554280G>T	ENST00000371130.3	-	24	4905	c.4842C>A	c.(4840-4842)agC>agA	p.S1614R	TENM1_ENST00000422452.2_Missense_Mutation_p.S1621R|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1614					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGACTCCATTGCTGCTTATAG	0.502																																																0			X											86	68	74					X																	123554280		2203	4300	6503	123381961	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4842C>A	X.37:g.123554280G>T	ENSP00000360171:p.Ser1614Arg		123381961	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	g	15.03	2.712475	0.48517	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85171	-1.95;-1.91	5.49	4.63	0.57726	Six-bladed beta-propeller, TolB-like (1);	0.045387	0.85682	D	0.000000	T	0.78502	0.4293	L	0.28556	0.865	0.40948	D	0.984524	P;P;P	0.45902	0.842;0.704;0.868	B;B;P	0.45474	0.273;0.236;0.482	T	0.74247	-0.3727	10	0.10111	T	0.7	.	13.4236	0.61011	0.0773:0.0:0.9227:0.0	.	1620;1621;1614	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	R	1614;1621	ENSP00000360171:S1614R;ENSP00000403954:S1621R	ENSP00000360171:S1614R	S	-	3	2	ODZ1	123381961	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.537000	0.60643	1.094000	0.41399	0.597000	0.82753	AGC		0.502	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123554280	G	T	123554280	3	4	93	1	0	0	0	0	1	0	0	0	10865	1310	46	2	3367	2	ODZ1	23	123554280	Missense_Mutation	SNP	G	TCGA-DC-5337-01A-01D-1657-10	13064358	123554280	31716280	283	25611										
DNASE1L1	1774	hgsc.bcm.edu	37	chrX	153633878	153633878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0176678445229682	5	1	0.368180037222059	0	0.380555836792548	0.0294117647058824	0.211072664359862	0	cctgggccccattggccaggAtgaggaagaggagtgcagtt	16	9	0	2			TCGA-DC-5337-01A-01D-1657-10	TCGA-DC-5337-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	70c26b7f-b356-415f-bdcb-5e15e2f0c42c	50d7d9b0-542b-4a97-9ed3-296874e16a49	g.chrX:153633878A>G	ENST00000393638.1	-	2	318	c.32T>C	c.(31-33)aTc>aCc	p.I11T	DNASE1L1_ENST00000369809.1_Missense_Mutation_p.I11T	NM_001009934.1	NP_001009934.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1	11					DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATTGGCCAGGATGAGGAAGAG	0.627																																																0			X											92	66	75					X																	153633878		2201	4299	6500	153287072	SO:0001583	missense	1774			L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"DNase X"	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000393638.1:c.32T>C	X.37:g.153633878A>G	ENSP00000377255:p.Ile11Thr		153287072	D3DWW7|Q5HY41	Missense_Mutation	SNP	ENST00000393638.1	37	CCDS14747.1	.	.	.	.	.	.	.	.	.	.	A	1.999	-0.429972	0.04701	.	.	ENSG00000013563	ENST00000369809;ENST00000393638;ENST00000014935;ENST00000369808;ENST00000369807;ENST00000309585;ENST00000447892;ENST00000451865;ENST00000412184;ENST00000424626;ENST00000432135	T;T;T;T;T;T;T;T	0.42900	1.45;1.45;1.45;1.45;1.45;1.45;0.96;1.96	3.65	3.65	0.41850	.	0.252152	0.23343	N	0.049219	T	0.21550	0.0519	N	0.08118	0	0.24173	N	0.995612	B	0.09022	0.002	B	0.01281	0.0	T	0.13019	-1.0525	10	0.51188	T	0.08	0.3941	7.9544	0.30033	1.0:0.0:0.0:0.0	.	11	P49184	DNSL1_HUMAN	T	11	ENSP00000358824:I11T;ENSP00000377255:I11T;ENSP00000014935:I11T;ENSP00000358823:I11T;ENSP00000358822:I11T;ENSP00000309168:I11T;ENSP00000393346:I11T;ENSP00000393000:I11T	ENSP00000014935:I11T	I	-	2	0	DNASE1L1	153287072	0.999000	0.42202	0.196000	0.23383	0.038000	0.13279	5.475000	0.66787	1.465000	0.48006	0.477000	0.44152	ATC		0.627	DNASE1L1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080928.2			G	153633878	A	G	153633878	3	3	93	1	0	0	0	0	1	0	0	0	4672	333	12	4	904	4	DNASE1L1	23	153633878	Missense_Mutation	SNP	A	TCGA-DC-5337-01A-01D-1657-10	30079598	153633878	1636682	284	25612										
KAZ	23254	hgsc.bcm.edu	37	chr1	15420804	15420804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cccactggaaggcgggcaccGtccaggcctggctggaggtg	17	13	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:15420804G>A	ENST00000376030.2	+	9	1645	c.1351G>A	c.(1351-1353)Gtc>Atc	p.V451I		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	451	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						GGCGGGCACCGTCCAGGCCTG	0.647																																																0			1											34	43	40					1																	15420804		2131	4237	6368	15293391	SO:0001583	missense	0			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1351G>A	1.37:g.15420804G>A	ENSP00000365198:p.Val451Ile		15293391	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986718	0.74589	.	.	ENSG00000189337	ENST00000376030	T	0.44881	0.91	4.68	4.68	0.58851	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.266713	0.23569	N	0.046771	T	0.46639	0.1403	M	0.67517	2.055	0.80722	D	1	D	0.57899	0.981	P	0.45753	0.492	T	0.54323	-0.8311	10	0.66056	D	0.02	-32.2833	13.4568	0.61204	0.0:0.0:1.0:0.0	.	451	Q674X7	KAZRN_HUMAN	I	451	ENSP00000365198:V451I	ENSP00000365198:V451I	V	+	1	0	KAZN	15293391	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	6.531000	0.73820	2.322000	0.78497	0.561000	0.74099	GTC		0.647	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		A	15420804	G	A	15420804	3	1	94	1	0	0	0	0	1	0	0	0	8009	1145	40	1	1641	1	KAZ	1	15420804	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10		15420804	233829817	1	25613										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24997999	24997999	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aaggctgtggctgcagctgcTgcagctgctgtgacccctgc	14	13	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:24997999T>C	ENST00000323848.9	+	16	2838	c.2523T>C	c.(2521-2523)gcT>gcC	p.A841A	SRRM1_ENST00000374389.4_Silent_p.A850A|SRRM1_ENST00000447431.2_Silent_p.A853A|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	841	Ala-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		ctgcagctgctgcagctgctg	0.473																																					Ovarian(68;897 1494 3282 17478)											0			1											31	31	31					1																	24997999		2203	4291	6494	24870586	SO:0001819	synonymous_variant	10250			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2523T>C	1.37:g.24997999T>C			24870586	O60585|Q5VVN4	Silent	SNP	ENST00000323848.9	37	CCDS255.1																																																																																				0.473	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		C	24997999	T	C	24997999	2	2	94	1	0	0	0	0	0	0	0	1	15207	1567	55	4		4	SRRM1	1	24997999	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	9577195	24997999	224252622	2	25614										
OPRD1	4985	hgsc.bcm.edu	37	chr1	29189597	29189597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cacctgtgcatcgcgctgggCtacgccaatagcagcctcaa	10	15	1	0	rs2234918	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:29189597C>T	ENST00000234961.2	+	3	1163	c.921C>T	c.(919-921)ggC>ggT	p.G307G		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	307					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	TCGCGCTGGGCTACGCCAATA	0.667													C|||	2911	0.58127	0.3056	0.7032	5008	,	,		15581	0.754		0.5726	False		,,,				2504	0.6984															0			1						C		1507,2897		274,959,969	29	26	27	http://www.ncbi.nlm.nih.gov/omim/103780,165195|http://omim.org/entry/165195|http://omim.org/entry/103780	921	3.2	1	1	dbSNP_98	27	4618,3982		1248,2122,930	no	coding-synonymous	OPRD1	NM_000911.3		1522,3081,1899	TT,TC,CC		46.3023,34.2189,47.1009		307/373	29189597	6125,6879	2202	4300	6502	29062184	SO:0001819	synonymous_variant	4985			U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"GPCR / Class A : Opioid receptors"	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.921C>T	1.37:g.29189597C>T			29062184	B5B0B8	Silent	SNP	ENST00000234961.2	37	CCDS329.1																																																																																				0.667	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	NM_000911		T	29189597	C	T	29189597	2	4	94	1	0	0	0	0	0	0	0	1	10915	784	28	3		3	OPRD1	1	29189597	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4191598	29189597	220061024	3	25615										
CLSPN	63967	hgsc.bcm.edu	37	chr1	36226207	36226207	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aacctgacattcctcactgtGattgttcccgaggaagttgg	10	10	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:36226207G>A	ENST00000318121.3	-	8	1372	c.1315C>T	c.(1315-1317)Cac>Tac	p.H439Y	CLSPN_ENST00000520551.1_Missense_Mutation_p.H439Y|CLSPN_ENST00000373220.3_Missense_Mutation_p.H439Y|CLSPN_ENST00000251195.5_Missense_Mutation_p.H439Y	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	439			H -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCCTCACTGTGATTGTTCCCG	0.488																																																0			1											170	154	160					1																	36226207		2203	4300	6503	35998794	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.1315C>T	1.37:g.36226207G>A	ENSP00000312995:p.His439Tyr		35998794	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.300172	0.01364	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551;ENST00000544356	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.19	3.31	0.37934	.	1.421980	0.03724	N	0.252254	T	0.12860	0.0312	N	0.08118	0	0.09310	N	1	B;B	0.29085	0.037;0.232	B;B	0.31495	0.04;0.131	T	0.26189	-1.0110	10	0.49607	T	0.09	-0.374	3.8322	0.08879	0.1591:0.5763:0.1718:0.0928	.	439;439	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Y	439	ENSP00000251195:H439Y;ENSP00000312995:H439Y;ENSP00000362317:H439Y;ENSP00000428848:H439Y	ENSP00000251195:H439Y	H	-	1	0	CLSPN	35998794	0.000000	0.05858	0.011000	0.14972	0.712000	0.41017	0.195000	0.17155	0.681000	0.31386	0.591000	0.81541	CAC		0.488	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		A	36226207	G	A	36226207	3	1	94	1	0	0	0	0	1	0	0	0	3566	1290	45	3	2776	3	CLSPN	1	36226207	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	7036610	36226207	213024414	4	25616										
C1orf109	54955	hgsc.bcm.edu	37	chr1	38155293	38155293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cttacagcctttcccctagcTtgtccaggacgatgtcacca	7	15	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:38155293T>C	ENST00000358011.4	-	2	449	c.260A>G	c.(259-261)aAg>aGg	p.K87R	CDCA8_ENST00000327331.2_5'Flank|C1orf109_ENST00000464085.1_Missense_Mutation_p.K87R|CDCA8_ENST00000373055.1_5'Flank	NM_017850.1	NP_060320.1	Q9NX04	CA109_HUMAN	chromosome 1 open reading frame 109	87										lung(2)|prostate(2)	4		Myeloproliferative disorder(586;0.0393)				TTCCCCTAGCTTGTCCAGGAC	0.522																																																0			1											106	111	109					1																	38155293		2203	4300	6503	37927880	SO:0001583	missense	54955			AK000515	CCDS423.1	1p34.3	2012-06-21			ENSG00000116922	ENSG00000116922			26039	protein-coding gene	gene with protein product		614799				22548824	Standard	XM_005270979		Approved	FLJ20508	uc001cbp.3	Q9NX04	OTTHUMG00000004323	ENST00000358011.4:c.260A>G	1.37:g.38155293T>C	ENSP00000350704:p.Lys87Arg		37927880	D3DPT1|Q8WVD1	Missense_Mutation	SNP	ENST00000358011.4	37	CCDS423.1	.	.	.	.	.	.	.	.	.	.	T	11.03	1.519998	0.27211	.	.	ENSG00000116922	ENST00000358011	.	.	.	5.62	4.49	0.54785	.	0.365437	0.32430	N	0.006107	T	0.41558	0.1164	M	0.70275	2.135	0.24205	N	0.995499	P;B;P	0.42296	0.775;0.29;0.775	B;B;B	0.42282	0.382;0.202;0.382	T	0.40627	-0.9553	9	0.44086	T	0.13	-18.6144	6.1916	0.20528	0.1417:0.077:0.0:0.7812	.	150;87;149	B7Z9X8;Q9NX04;B4DRQ5	.;CA109_HUMAN;.	R	87	.	ENSP00000350704:K87R	K	-	2	0	C1orf109	37927880	1.000000	0.71417	0.959000	0.39883	0.195000	0.23768	1.474000	0.35398	0.950000	0.37743	0.533000	0.62120	AAG		0.522	C1orf109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012486.1	NM_017850		C	38155293	T	C	38155293	3	2	94	1	0	0	0	0	1	0	0	0	1988	1609	56	4	367	4	C1orf109	1	38155293	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	1929086	38155293	211095328	5	25617										
ZNF684	127396	hgsc.bcm.edu	37	chr1	41012779	41012779	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	actcctcatttaatcaacacGtgaaatctcatacacttgag	4	11	3	2	rs201288463		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:41012779G>A	ENST00000372699.3	+	5	1035	c.784G>A	c.(784-786)Gtg>Atg	p.V262M	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			TAATCAACACGTGAAATCTCA	0.408													G|||	1	0.000199681	0	0.0014	5008	,	,		20967	0		0	False		,,,				2504	0															0			1											52	53	53					1																	41012779		2203	4300	6503	40785366	SO:0001583	missense	127396				CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"Zinc fingers, C2H2-type", "-"	28418	protein-coding gene	gene with protein product	"hypothetical protein MGC27466"					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.784G>A	1.37:g.41012779G>A	ENSP00000361784:p.Val262Met		40785366	Q2NKY4	Missense_Mutation	SNP	ENST00000372699.3	37	CCDS454.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	9.798	1.179637	0.21787	.	.	ENSG00000117010	ENST00000372699	T	0.16457	2.34	4.28	1.03	0.20045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.255793	0.20583	N	0.089500	T	0.06462	0.0166	N	0.03281	-0.365	0.26453	N	0.975577	B	0.26672	0.156	B	0.19946	0.027	T	0.27971	-1.0058	10	0.72032	D	0.01	.	7.0998	0.25330	0.1029:0.4656:0.4315:0.0	.	262	Q5T5D7	ZN684_HUMAN	M	262	ENSP00000361784:V262M	ENSP00000361784:V262M	V	+	1	0	ZNF684	40785366	0.016000	0.18221	0.934000	0.37439	0.951000	0.60555	0.639000	0.24690	0.530000	0.28619	0.585000	0.79938	GTG		0.408	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		A	41012779	G	A	41012779	3	1	94	1	0	0	0	0	1	0	0	0	18130	1145	40	1	798	1	ZNF684	1	41012779	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	2857486	41012779	208237842	6	25618										
LHX8	431707	hgsc.bcm.edu	37	chr1	75622741	75622741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agatggaacgatgttaactgCgctgcatagttatatggatg	12	5	0	1	rs34889650	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:75622741C>T	ENST00000294638.5	+	9	1638	c.974C>T	c.(973-975)gCg>gTg	p.A325V	LHX8_ENST00000356261.3_Missense_Mutation_p.A315V	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	325					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						ATGTTAACTGCGCTGCATAGT	0.453													C|||	7	0.00139776	8e-04	0.0014	5008	,	,		19239	0		0.003	False		,,,				2504	0.002															0			1						C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	189	170	176		974	5.4	1	1	dbSNP_126	176	18,8582	13.3+/-46.6	0,18,4282	yes	missense	LHX8	NM_001001933.1	64	0,20,6483	TT,TC,CC		0.2093,0.0454,0.1538	possibly-damaging	325/357	75622741	20,12986	2203	4300	6503	75395329	SO:0001583	missense	431707			AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.974C>T	1.37:g.75622741C>T	ENSP00000294638:p.Ala325Val		75395329	E9PGE3	Missense_Mutation	SNP	ENST00000294638.5	37	CCDS30756.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	25.0	4.594322	0.86953	4.54E-4	0.002093	ENSG00000162624	ENST00000294638;ENST00000356261	D;D	0.86956	-2.19;-2.17	5.36	5.36	0.76844	.	0.046555	0.85682	D	0.000000	D	0.88522	0.6459	L	0.50333	1.59	0.58432	D	0.999995	D	0.71674	0.998	P	0.57679	0.825	D	0.87195	0.2237	10	0.42905	T	0.14	.	19.4798	0.95005	0.0:1.0:0.0:0.0	rs34889650	325	Q68G74	LHX8_HUMAN	V	325;315	ENSP00000294638:A325V;ENSP00000348597:A315V	ENSP00000294638:A325V	A	+	2	0	LHX8	75395329	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	7.263000	0.78421	2.683000	0.91414	0.557000	0.71058	GCG		0.453	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		T	75622741	C	T	75622741	3	4	94	1	0	0	0	0	1	0	0	0	8799	768	27	1	1004	1	LHX8	1	75622741	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	34609962	75622741	173627880	7	25619										
ASB17	127247	hgsc.bcm.edu	37	chr1	76397610	76397610	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	caggttacaacttctgtcttGaacatagtcttttgtcttct	6	9	5	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:76397610G>A	ENST00000284142.6	-	1	506	c.367C>T	c.(367-369)Caa>Taa	p.Q123*		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	123					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						CTTCTGTCTTGAACATAGTCT	0.348																																																0			1											57	56	56					1																	76397610		2203	4299	6502	76170198	SO:0001587	stop_gained	127247			AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"Ankyrin repeat domain containing"	19769	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 17"			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.367C>T	1.37:g.76397610G>A	ENSP00000284142:p.Gln123*		76170198	B1APB8|Q8N0X5	Nonsense_Mutation	SNP	ENST00000284142.6	37	CCDS671.1	.	.	.	.	.	.	.	.	.	.	G	37	6.448354	0.97577	.	.	ENSG00000154007	ENST00000284142	.	.	.	5.97	5.97	0.96955	.	0.000000	0.52532	D	0.000080	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.9063	0.79433	0.0:0.0:1.0:0.0	.	.	.	.	X	123	.	ENSP00000284142:Q123X	Q	-	1	0	ASB17	76170198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.427000	0.52785	2.831000	0.97527	0.655000	0.94253	CAA		0.348	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		A	76397610	G	A	76397610	4	1	94	1	0	0	0	0	0	1	0	0	1022	1299	45	3	532	3	ASB17	1	76397610	Nonsense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	774869	76397610	172853011	8	25620										
RPTN	126638	hgsc.bcm.edu	37	chr1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cttgtctctcaggctgactgTggtgggaatctctgtcttgt					rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152129101	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	152129066	7	5	94	1	0	1	0	1	0	0	0	0	13701	1696	59	0	1849	0	RPTN	1	152129066	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TCGA-DC-5869-01A-01D-1657-10	75731456	152129066	97121555	9	25621										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158589083	158589083	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgacacatctcaaagttcttGacctgtcttgcctcttcctt	5	13	4	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:158589083G>T	ENST00000368147.4	-	45	6639	c.6459C>A	c.(6457-6459)gtC>gtA	p.V2153V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2153					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAAAGTTCTTGACCTGTCTTG	0.473																																																0			1											286	278	281					1																	158589083		2013	4176	6189	156855707	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6459C>A	1.37:g.158589083G>T			156855707	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158589083	G	T	158589083	2	4	94	1	0	0	0	0	0	0	0	1	15155	1277	45	2		2	SPTA1	1	158589083	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	6460017	158589083	90661538	10	25622										
MPZ	4359	hgsc.bcm.edu	37	chr1	161276172	161276172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agccagcagtaccgaaccacGtagaaaagcagcagcagcaa	10	12	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:161276172G>A	ENST00000533357.1	-	4	597	c.531C>T	c.(529-531)taC>taT	p.Y177Y	MPZ_ENST00000526189.1_5'UTR|MPZ_ENST00000491222.2_De_novo_Start_OutOfFrame|MPZ_ENST00000360451.6_Silent_p.Y187Y|MPZ_ENST00000336559.4_Silent_p.Y177Y	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	177					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			ACCGAACCACGTAGAAAAGCA	0.642																																																0			1											110	98	102					1																	161276172		2203	4300	6503	159542796	SO:0001819	synonymous_variant	4359			BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"Immunoglobulin superfamily / V-set domain containing"	7225	protein-coding gene	gene with protein product		159440	"Charcot-Marie-Tooth neuropathy 1B"	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.531C>T	1.37:g.161276172G>A			159542796	Q16072|Q5VTH4|Q92677|Q9BR67	Silent	SNP	ENST00000533357.1	37	CCDS1229.2																																																																																				0.642	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530		A	161276172	G	A	161276172	2	1	94	1	0	0	0	0	0	0	0	1	9778	1140	40	1		1	MPZ	1	161276172	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	2687089	161276172	87974449	11	25623										
TNR	7143	hgsc.bcm.edu	37	chr1	175355235	175355235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	acggcactgactgacacctcGtatcgggagccaggccgcag	13	14	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:175355235G>A	ENST00000367674.2	-	8	2418	c.1710C>T	c.(1708-1710)taC>taT	p.Y570Y	TNR_ENST00000263525.2_Silent_p.Y570Y			Q92752	TENR_HUMAN	tenascin R	570	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CTGACACCTCGTATCGGGAGC	0.632																																																0			1											74	70	72					1																	175355235		2203	4300	6503	173621858	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1710C>T	1.37:g.175355235G>A			173621858	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.632	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175355235	G	A	175355235	2	1	94	1	0	0	0	0	0	0	0	1	16377	1140	40	1		1	TNR	1	175355235	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	14079063	175355235	73895386	12	25624										
AVPR1B	553	hgsc.bcm.edu	37	chr1	206230986	206230986	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctctccgacggcagcctctcGagccgccacaccacgctgct	9	20	2	0	rs28676508	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:206230986G>A	ENST00000367126.4	+	2	1584	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S		NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	373					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	GCAGCCTCTCGAGCCGCCACA	0.701													G|||	1203	0.240216	0.4962	0.1225	5008	,	,		12235	0.0923		0.1312	False		,,,				2504	0.2423															0			1						G		1866,2526		424,1018,754	13	15	14		1119	-4.5	0.2	1	dbSNP_125	14	1019,7549		71,877,3336	no	coding-synonymous	AVPR1B	NM_000707.3		495,1895,4090	AA,AG,GG		11.8931,42.4863,22.2608		373/425	206230986	2885,10075	2196	4284	6480	204397609	SO:0001819	synonymous_variant	553			D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"GPCR / Class A : Vasopressin and oxytocin receptors"	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.1119G>A	1.37:g.206230986G>A			204397609	B0M0J6|Q5TZ00	Silent	SNP	ENST00000367126.4	37	CCDS30994.1																																																																																				0.701	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707		A	206230986	G	A	206230986	2	1	94	1	0	0	0	0	0	0	0	1	1233	1045	37	1		1	AVPR1B	1	206230986	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	30875751	206230986	43019635	13	25625										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227279611	227279611	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcaagttcactcgtcagcttTttattttcttcagttaacaa	4	9	5	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:227279611T>C	ENST00000366769.3	-	16	3622	c.2331A>G	c.(2329-2331)aaA>aaG	p.K777K	CDC42BPA_ENST00000366765.3_Silent_p.K777K|CDC42BPA_ENST00000366767.3_Silent_p.K696K|CDC42BPA_ENST00000366764.2_Silent_p.K777K|CDC42BPA_ENST00000334218.5_Silent_p.K777K|CDC42BPA_ENST00000535525.1_Silent_p.K777K|CDC42BPA_ENST00000366766.2_Silent_p.K777K	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCGTCAGCTTTTTATTTTCTT	0.328																																																0			1											190	179	183					1																	227279611		2201	4296	6497	225346234	SO:0001819	synonymous_variant	8476			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.2331A>G	1.37:g.227279611T>C			225346234		Silent	SNP	ENST00000366769.3	37	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	T	9.506	1.104396	0.20632	.	.	ENSG00000143776	ENST00000442054	T	0.46819	0.86	5.09	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.39410	0.1077	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06075	-1.0847	7	0.15499	T	0.54	.	9.4197	0.38544	0.0:0.213:0.0:0.7869	.	.	.	.	E	71	ENSP00000401051:K71E	ENSP00000401051:K71E	K	-	1	0	CDC42BPA	225346234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.530000	0.23036	0.357000	0.24183	0.455000	0.32223	AAA		0.328	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227279611	T	C	227279611	2	2	94	1	0	0	0	0	0	0	0	1	3078	1838	64	4		4	CDC42BPA	1	227279611	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	21048625	227279611	21971010	14	25626										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	94	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-DC-5869-01A-01D-1657-10	13091303	240370914	8879707	15	25627			1	17		3	3	513	N	T_GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	4.763661e-06
FMN2	56776	hgsc.bcm.edu	37	chr1	240371304	240371304	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cttcccggagcgggcataccTcctccaccccctctacccgg	8	21	1	0	rs71646894		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:240371304T>C	ENST00000319653.9	+	5	3422	c.3192T>C	c.(3190-3192)ccT>ccC	p.P1064P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1064	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCTCCTCCACCCC	0.741																																																0			1											1	1	1					1																	240371304		861	1841	2702	238437927	SO:0001819	synonymous_variant	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3192T>C	1.37:g.240371304T>C			238437927	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.741	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240371304	T	C	240371304	2	2	94	1	0	0	0	0	0	0	0	1	5969	1538	54	4		4	FMN2	1	240371304	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	390	240371304	8879317	16	25628			1	17		3	3	513	N	T_GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	4.763661e-06
FMN2	56776	hgsc.bcm.edu	37	chr1	240371426	240371426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tccgccccctctacccggagTgggcatacctcctccgcccc	8	22	1	0	rs200640213	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr1:240371426T>C	ENST00000319653.9	+	5	3544	c.3314T>C	c.(3313-3315)gTg>gCg	p.V1105A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1105	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTACCCGGAGTGGGCATACCT	0.736													-|||	349	0.0696885	0.0605	0.049	5008	,	,		2970	0.0724		0.0974	False		,,,				2504	0.0654															0			1						C	ALA/VAL	89,4025		0,89,1968	8	11	10		3314	-4.6	0	1		10	380,7864		4,372,3746	no	missense	FMN2	NM_020066.4	64	4,461,5714	CC,CT,TT		4.6094,2.1633,3.7951	benign	1105/1723	240371426	469,11889	2057	4122	6179	238438049	SO:0001583	missense	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3314T>C	1.37:g.240371426T>C	ENSP00000318884:p.Val1105Ala		238438049	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	t	6.825	0.521456	0.13005	0.021633	0.046094	ENSG00000155816	ENST00000319653	T	0.54071	0.59	3.44	-4.56	0.03431	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	2.607690	0.02057	N	0.050513	T	0.04363	0.0120	N	0.04335	-0.225	0.09310	N	1	B	0.23650	0.089	B	0.25614	0.062	T	0.03576	-1.1023	9	.	.	.	.	4.0237	0.09677	0.2447:0.3179:0.0:0.4374	.	1105	Q9NZ56	FMN2_HUMAN	A	1105	ENSP00000318884:V1105A	.	V	+	2	0	FMN2	238438049	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.925000	0.01564	-1.108000	0.03000	-2.277000	0.00273	GTG		0.736	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240371426	T	C	240371426	3	2	94	1	0	0	0	0	1	0	0	0	5969	1696	59	4	3332	4	FMN2	1	240371426	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	122	240371426	8879195	17	25629			1	17		3	3	513	N	T_GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	4.763661e-06
C2orf79	391356	hgsc.bcm.edu	37	chr2	25016051	25016078	+	Frame_Shift_Del	DEL	GGTGGTCGCGGTGAGTGTGCAAGGCCGC	GGTGGTCGCGGTGAGTGTGCAAGGCCGC	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaggtaagcggctgtgtgcgGgtggtcgcggtgagtgtgca					rs374244884|rs140217300|rs553276736|rs555151619	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	GGTGGTCGCGGTGAGTGTGCAAGGCCGC	GGTGGTCGCGGTGAGTGTGCAAGGCCGC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:25016051_25016078delGGTGGTCGCGGTGAGTGTGCAAGGCCGC	ENST00000328379.5	-	1	173_200	c.169_196delGCGGCCTTGCACACTCACCGCGACCACC	c.(169-198)gcggccttgcacactcaccgcgaccacccgfs	p.AALHTHRDHP57fs	CENPO_ENST00000473706.1_5'UTR|PTRHD1_ENST00000487316.1_5'Flank|CENPO_ENST00000260662.1_5'Flank|CENPO_ENST00000380834.2_5'UTR	NM_001013663.1	NP_001013685.1	Q6GMV3	PTRD1_HUMAN	peptidyl-tRNA hydrolase domain containing 1	57						extracellular vesicular exosome (GO:0070062)	aminoacyl-tRNA hydrolase activity (GO:0004045)	p.H62Y(1)		autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|skin(1)	6						GCTGTGTGCGGGTGGTCGCGGTGAGTGTGCAAGGCCGCGGTGGCCGCG	0.645														3	0.000599042	0.0023	0	5008	,	,		17592	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	2																																								24869582	SO:0001589	frameshift_variant	391356				CCDS33156.1	2p23.3	2011-05-09	2011-05-09	2011-05-09	ENSG00000184924	ENSG00000184924			33782	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 79"	C2orf79		12477932	Standard	NM_001013663		Approved	LOC391356	uc002rfm.3	Q6GMV3	OTTHUMG00000151978	ENST00000328379.5:c.169_196delGCGGCCTTGCACACTCACCGCGACCACC	2.37:g.25016051_25016078delGGTGGTCGCGGTGAGTGTGCAAGGCCGC	ENSP00000330389:p.Ala57fs		24869555		Frame_Shift_Del	DEL	ENST00000328379.5	37	CCDS33156.1																																																																																				0.645	PTRHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324626.3	NM_001013663		-	25016078	GGTGGTCGCGGTGAGTGTGCAAGGCCGC	-	25016051	7	5	94	1	0	1	0	1	0	0	0	0	2202	1232	43	0	234	0	C2orf79	2	25016051	Frame_Shift_Del	DEL	GGTGGTCGCGGTGAGTGTGCAAGGCCGC	TCGA-DC-5869-01A-01D-1657-10		25016051	218183322	18	25630	33	2								
C2orf79	391356	hgsc.bcm.edu	37	chr2	25016056	25016056	+	Missense_Mutation	SNP	T	T	C													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aagcggctgtgtgcgggtggTcgcggtgagtgtgcaaggcc					rs374244884|rs553276736	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:25016056T>C	ENST00000328379.5	-	1	195	c.191A>G	c.(190-192)gAc>gGc	p.D64G	CENPO_ENST00000473706.1_5'UTR|PTRHD1_ENST00000487316.1_5'Flank|CENPO_ENST00000260662.1_5'Flank|CENPO_ENST00000380834.2_5'UTR	NM_001013663.1	NP_001013685.1	Q6GMV3	PTRD1_HUMAN	peptidyl-tRNA hydrolase domain containing 1	64						extracellular vesicular exosome (GO:0070062)	aminoacyl-tRNA hydrolase activity (GO:0004045)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|skin(1)	6						GTGCGGGTGGTCGCGGTGAGT	0.657													T|||	3	0.000599042	0.0023	0	5008	,	,		13746	0		0	False		,,,				2504	0															0			2						T	GLY/ASP	1,4403		0,1,2201	37	41	39		191	4.7	1	2		39	2,8598		0,2,4298	no	missense	PTRHD1	NM_001013663.1	94	0,3,6499	CC,CT,TT		0.0233,0.0227,0.0231	benign	64/141	25016056	3,13001	2202	4300	6502	24869560	SO:0001583	missense	391356				CCDS33156.1	2p23.3	2011-05-09	2011-05-09	2011-05-09	ENSG00000184924	ENSG00000184924			33782	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 79"	C2orf79		12477932	Standard	NM_001013663		Approved	LOC391356	uc002rfm.3	Q6GMV3	OTTHUMG00000151978	ENST00000328379.5:c.191A>G	2.37:g.25016056T>C	ENSP00000330389:p.Asp64Gly		24869560		Missense_Mutation	SNP	ENST00000328379.5	37	CCDS33156.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.994805	0.54041	2.27E-4	2.33E-4	ENSG00000184924	ENST00000328379	T	0.10382	2.88	5.91	4.69	0.59074	Peptidyl-tRNA hydrolase II domain (2);	0.356851	0.31612	N	0.007359	T	0.12220	0.0297	L	0.55743	1.74	0.80722	D	1	B	0.11235	0.004	B	0.09377	0.004	T	0.02991	-1.1085	10	0.46703	T	0.11	.	11.4704	0.50266	0.0:0.0:0.2309:0.769	.	64	Q6GMV3	PTRD1_HUMAN	G	64	ENSP00000330389:D64G	ENSP00000330389:D64G	D	-	2	0	PTRHD1	24869560	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	0.931000	0.28871	2.261000	0.74972	0.533000	0.62120	GAC		0.657	PTRHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324626.3	NM_001013663		C	25016056	T	C	25016056	3	2	94	1	0	0	0	0	1	0	0	0	2202	1667	58	4	239	4	C2orf79	2	25016056	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	5	25016056	218183317	19	25631	33	2								
BRE	9577	hgsc.bcm.edu	37	chr2	28268640	28268640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgaagctgcccgtagatttcAgcaatatccccacatacctt	6	13	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:28268640A>G	ENST00000342045.2	+	7	685	c.544A>G	c.(544-546)Agc>Ggc	p.S182G	BRE_ENST00000361704.2_Missense_Mutation_p.S182G|BRE_ENST00000379632.2_Missense_Mutation_p.S182G|BRE_ENST00000344773.2_Missense_Mutation_p.S182G|BRE_ENST00000379624.1_Missense_Mutation_p.S182G	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					CGTAGATTTCAGCAATATCCC	0.279																																																0			2											41	42	42					2																	28268640		2202	4299	6501	28122144	SO:0001583	missense	9577			AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 4"	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.544A>G	2.37:g.28268640A>G	ENSP00000339371:p.Ser182Gly		28122144		Missense_Mutation	SNP	ENST00000342045.2	37	CCDS1763.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.156967	0.78114	.	.	ENSG00000158019	ENST00000344773;ENST00000379624;ENST00000342045;ENST00000379632;ENST00000361704;ENST00000379629;ENST00000379623	.	.	.	5.42	5.42	0.78866	.	0.040403	0.85682	D	0.000000	T	0.67268	0.2875	L	0.58101	1.795	0.54753	D	0.999981	P;D;D;B	0.59767	0.75;0.986;0.982;0.341	B;P;P;B	0.55923	0.4;0.787;0.681;0.201	T	0.70557	-0.4839	9	0.62326	D	0.03	-5.9715	14.4558	0.67416	1.0:0.0:0.0:0.0	.	182;182;182;182	Q9NXR7-1;Q9NXR7;Q9NXR7-4;Q9NXR7-3	.;BRE_HUMAN;.;.	G	182;182;182;182;182;182;84	.	ENSP00000339371:S182G	S	+	1	0	BRE	28122144	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.142000	0.77339	2.058000	0.61347	0.533000	0.62120	AGC		0.279	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1			G	28268640	A	G	28268640	3	3	94	1	0	0	0	0	1	0	0	0	1512	188	7	4	562	4	BRE	2	28268640	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	3252584	28268640	214930733	20	25632										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60689480	60689480	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cttaatccatgagtgttctgTgcgtgttgcaagagaaacca	10	8	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:60689480T>C	ENST00000335712.6	-	4	794	c.567A>G	c.(565-567)gcA>gcG	p.A189A	BCL11A_ENST00000356842.4_Silent_p.A189A|BCL11A_ENST00000538214.1_Silent_p.A155A|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000359629.5_Silent_p.A189A|BCL11A_ENST00000537768.1_Silent_p.A37A|BCL11A_ENST00000358510.4_Silent_p.A155A	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	189	Required for nuclear body formation and for SUMO1 recruitment. {ECO:0000250}.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GAGTGTTCTGTGCGTGTTGCA	0.473			T	IGH@	B-CLL																																		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	0			2											95	95	95					2																	60689480		2203	4300	6503	60542984	SO:0001819	synonymous_variant	53335			AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.567A>G	2.37:g.60689480T>C			60542984	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Silent	SNP	ENST00000335712.6	37	CCDS1862.1																																																																																				0.473	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		C	60689480	T	C	60689480	2	2	94	1	0	0	0	0	0	0	0	1	1364	1683	59	4		4	BCL11A	2	60689480	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	32420840	60689480	182509893	21	25633										
DYSF	8291	hgsc.bcm.edu	37	chr2	71766338	71766338	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	accacctacctgagtatgtcGaaaatctctgcccctggagg	9	13	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:71766338G>A	ENST00000258104.3	+	16	1726	c.1449G>A	c.(1447-1449)tcG>tcA	p.S483S	DYSF_ENST00000394120.2_Silent_p.S484S|DYSF_ENST00000409651.1_Silent_p.S515S|DYSF_ENST00000410020.3_Silent_p.S515S|DYSF_ENST00000410041.1_Silent_p.S515S|DYSF_ENST00000409582.3_Silent_p.S514S|DYSF_ENST00000413539.2_Silent_p.S514S|DYSF_ENST00000429174.2_Silent_p.S483S|DYSF_ENST00000409366.1_Silent_p.S484S|DYSF_ENST00000409762.1_Silent_p.S514S|DYSF_ENST00000409744.1_Silent_p.S484S	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	483					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TGAGTATGTCGAAAATCTCTG	0.552																																																0			2											166	139	148					2																	71766338		2203	4300	6503	71619846	SO:0001819	synonymous_variant	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1449G>A	2.37:g.71766338G>A			71619846	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																				0.552	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71766338	G	A	71766338	2	1	94	1	0	0	0	0	0	0	0	1	4870	1045	37	1		1	DYSF	2	71766338	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	11076858	71766338	171433035	22	25634										
ATOH8	84913	hgsc.bcm.edu	37	chr2	85991208	85991208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctggcgcggctggctgaccTtgactacagtgccgaccaca	12	15	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:85991208T>C	ENST00000306279.3	+	2	1159	c.863T>C	c.(862-864)cTt>cCt	p.L288P	ATOH8_ENST00000463422.1_3'UTR	NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)	288					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CTGGCTGACCTTGACTACAGT	0.612																																																0			2											70	56	61					2																	85991208		2203	4300	6503	85844719	SO:0001583	missense	84913			AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"Basic helix-loop-helix proteins"	24126	protein-coding gene	gene with protein product	"basic helix loop helix transcription factor 6"					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.863T>C	2.37:g.85991208T>C	ENSP00000304676:p.Leu288Pro		85844719	Q504S2|Q659B0	Missense_Mutation	SNP	ENST00000306279.3	37	CCDS1985.1	.	.	.	.	.	.	.	.	.	.	t	15.66	2.898588	0.52227	.	.	ENSG00000168874	ENST00000306279	D	0.88818	-2.43	5.02	5.02	0.67125	Helix-loop-helix DNA-binding (2);	0.000000	0.64402	D	0.000003	D	0.82838	0.5124	L	0.36672	1.1	0.80722	D	1	P;B	0.37731	0.607;0.446	B;B	0.34180	0.177;0.128	T	0.82082	-0.0633	10	0.31617	T	0.26	-1.9355	14.2471	0.65995	0.0:0.0:0.0:1.0	.	288;288	Q96SQ7;Q96SQ7-2	ATOH8_HUMAN;.	P	288	ENSP00000304676:L288P	ENSP00000304676:L288P	L	+	2	0	ATOH8	85844719	1.000000	0.71417	0.926000	0.36857	0.873000	0.50193	5.669000	0.68081	2.028000	0.59812	0.529000	0.55759	CTT		0.612	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252496.1	NM_032827		C	85991208	T	C	85991208	3	2	94	1	0	0	0	0	1	0	0	0	1115	1609	56	4	869	4	ATOH8	2	85991208	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	14224870	85991208	157208165	23	25635										
C2orf51	200523	hgsc.bcm.edu	37	chr2	88825975	88825975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccacatggtcgactatcagcCctacaggaagcacaaatact	7	13	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:88825975C>T	ENST00000303254.3	+	3	222	c.80C>T	c.(79-81)cCc>cTc	p.P27L		NM_152670.2	NP_689883.1	Q96LM6	TEX37_HUMAN	testis expressed 37	27						nucleus (GO:0005634)											GACTATCAGCCCTACAGGAAG	0.483																																																0			2											125	104	111					2																	88825975		2203	4300	6503	88607090	SO:0001583	missense	200523			AK058098	CCDS2003.1	2p11.2	2014-01-28	2012-09-14	2012-09-14	ENSG00000172073	ENSG00000172073			26341	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 21kDa"		"chromosome 2 open reading frame 51"	C2orf51		17091336	Standard	NM_152670		Approved	FLJ25369, TSC21	uc002stb.2	Q96LM6	OTTHUMG00000130332	ENST00000303254.3:c.80C>T	2.37:g.88825975C>T	ENSP00000307142:p.Pro27Leu		88607090		Missense_Mutation	SNP	ENST00000303254.3	37	CCDS2003.1	.	.	.	.	.	.	.	.	.	.	C	6.790	0.514817	0.12944	.	.	ENSG00000172073	ENST00000303254	T	0.59638	0.25	3.92	3.03	0.35002	.	0.180160	0.27349	N	0.019766	T	0.60157	0.2247	L	0.34521	1.04	0.18873	N	0.999985	D	0.67145	0.996	D	0.64877	0.93	T	0.49588	-0.8924	10	0.62326	D	0.03	-13.6596	8.9441	0.35747	0.2216:0.7784:0.0:0.0	.	27	Q96LM6	TSC21_HUMAN	L	27	ENSP00000307142:P27L	ENSP00000307142:P27L	P	+	2	0	C2orf51	88607090	0.002000	0.14202	0.042000	0.18584	0.037000	0.13140	0.075000	0.14686	1.199000	0.43173	0.462000	0.41574	CCC		0.483	TEX37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252682.1	NM_152670		T	88825975	C	T	88825975	3	4	94	1	0	0	0	0	1	0	0	0	2179	623	22	3	86	3	C2orf51	2	88825975	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	2834767	88825975	154373398	24	25636										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110015096	110015096	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atggacaagccatgcccagcCgctgcatccagctgcaatgc	10	15	0	0	rs537361444		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:110015096C>T	ENST00000309415.6	+	4	996	c.996C>T	c.(994-996)gcC>gcT	p.A332A		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	332							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CATGCCCAGCCGCTGCATCCA	0.602																																																0			2											29	31	30					2																	110015096		2202	4300	6502	109381528	SO:0001819	synonymous_variant	344558			AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.996C>T	2.37:g.110015096C>T			109381528	A0SDZ7|A8MPR1|Q8NDU1	Silent	SNP	ENST00000309415.6	37																																																																																					0.602	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		T	110015096	C	T	110015096	2	4	94	1	0	0	0	0	0	0	0	1	14297	639	23	1		1	SH3RF3	2	110015096	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	21189121	110015096	133184277	25	25637										
BIN1	274	hgsc.bcm.edu	37	chr2	127816682	127816682	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctcgggggtggcggcaggggAgccatctggaggcgaagggc	22	9	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:127816682A>G	ENST00000316724.5	-	11	1318	c.907T>C	c.(907-909)Tcc>Ccc	p.S303P	BIN1_ENST00000357970.3_Missense_Mutation_p.S303P|BIN1_ENST00000409400.1_Missense_Mutation_p.S272P|BIN1_ENST00000393040.3_Missense_Mutation_p.S272P|BIN1_ENST00000352848.3_Missense_Mutation_p.S287P|BIN1_ENST00000393041.3_Missense_Mutation_p.S272P|BIN1_ENST00000346226.3_Missense_Mutation_p.S272P|BIN1_ENST00000259238.4_Missense_Mutation_p.S287P|BIN1_ENST00000348750.4_Missense_Mutation_p.S272P|BIN1_ENST00000376113.2_Missense_Mutation_p.S287P|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000351659.3_Missense_Mutation_p.S303P	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	303					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GCGGCAGGGGAGCCATCTGGA	0.677																																																0			2											21	27	25					2																	127816682		2201	4296	6497	127533152	SO:0001583	missense	274			U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.907T>C	2.37:g.127816682A>G	ENSP00000316779:p.Ser303Pro		127533152	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.407352	0.42715	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.67523	0.38;-0.27;1.04;0.41;1.04;1.04;0.4;0.33;0.33;1.04;0.33	4.95	4.95	0.65309	.	0.536199	0.20330	N	0.094454	T	0.61776	0.2374	N	0.16743	0.435	0.47476	D	0.999434	B;B;B;B;B;B;B;B;B;B;B;B;D	0.63046	0.009;0.0;0.001;0.001;0.001;0.004;0.001;0.005;0.001;0.044;0.001;0.002;0.992	B;B;B;B;B;B;B;B;B;B;B;B;P	0.60949	0.008;0.002;0.006;0.012;0.005;0.012;0.003;0.009;0.005;0.03;0.004;0.002;0.881	T	0.57883	-0.7734	10	0.24483	T	0.36	-31.5721	8.1649	0.31220	0.8214:0.0:0.0:0.1786	.	303;248;272;272;272;272;303;287;287;303;287;272;303	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	P	287;303;272;272;287;272;272;303;287;303;272	ENSP00000365281:S287P;ENSP00000350654:S303P;ENSP00000376760:S272P;ENSP00000259237:S272P;ENSP00000259238:S287P;ENSP00000315411:S272P;ENSP00000376761:S272P;ENSP00000315388:S303P;ENSP00000315284:S287P;ENSP00000316779:S303P;ENSP00000386797:S272P	ENSP00000259238:S287P	S	-	1	0	BIN1	127533152	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.120000	0.41968	1.858000	0.53909	0.459000	0.35465	TCC		0.677	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		G	127816682	A	G	127816682	3	3	94	1	0	0	0	0	1	0	0	0	1433	304	11	4	910	4	BIN1	2	127816682	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	17801586	127816682	115382691	26	25638										
WIPF1	7456	hgsc.bcm.edu	37	chr2	175436915	175436915	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggctgcctggggcctccgggCactggtggggacccccggtt	18	14	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:175436915C>A	ENST00000392547.2	-	5	717	c.618G>T	c.(616-618)gtG>gtT	p.V206V	AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Silent_p.V206V|WIPF1_ENST00000359761.3_Silent_p.V206V|WIPF1_ENST00000409891.1_Silent_p.V206V|WIPF1_ENST00000272746.5_Silent_p.V206V|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000467149.1_5'Flank|WIPF1_ENST00000392546.2_Silent_p.V206V	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	206					actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						GGCCTCCGGGCACTGGTGGGG	0.642																																																0			2											41	50	47					2																	175436915		2201	4291	6492	175145161	SO:0001819	synonymous_variant	7456			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.618G>T	2.37:g.175436915C>A			175145161	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Silent	SNP	ENST00000392547.2	37	CCDS2260.1																																																																																				0.642	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		A	175436915	C	A	175436915	2	1	94	1	0	0	0	0	0	0	0	1	17407	697	25	2		2	WIPF1	2	175436915	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	47620233	175436915	67762458	27	25639										
TTN	7273	hgsc.bcm.edu	37	chr2	179429588	179429588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cactggctcatgccattgcaCaagcatctgatcttttgaga	8	11	3	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:179429588C>T	ENST00000591111.1	-	276	76572	c.76348G>A	c.(76348-76350)Gtg>Atg	p.V25450M	TTN_ENST00000342992.6_Missense_Mutation_p.V24523M|TTN_ENST00000589042.1_Missense_Mutation_p.V27091M|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V18218M|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V18026M|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V18151M|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25450	Fibronectin type-III 85. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCCATTGCACAAGCATCTGA	0.388																																																0			2											65	62	63					2																	179429588		1878	4116	5994	179137834	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76348G>A	2.37:g.179429588C>T	ENSP00000465570:p.Val25450Met		179137834	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.12	1.544641	0.27563	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	6.02	5.14	0.70334	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76835	0.4043	M	0.81239	2.535	0.41908	D	0.990454	D;D;D;D	0.62365	0.991;0.991;0.991;0.983	D;D;D;D	0.64687	0.928;0.928;0.928;0.924	T	0.81568	-0.0873	9	0.87932	D	0	.	17.5501	0.87873	0.0:0.8766:0.1234:0.0	.	18026;18151;18218;25450	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	24523;18026;18218;18151;18024	ENSP00000343764:V24523M;ENSP00000434586:V18026M;ENSP00000340554:V18218M;ENSP00000352154:V18151M	ENSP00000340554:V18218M	V	-	1	0	TTN	179137834	1.000000	0.71417	0.707000	0.30419	0.951000	0.60555	1.989000	0.40707	1.529000	0.49120	0.650000	0.86243	GTG		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179429588	C	T	179429588	3	4	94	1	0	0	0	0	1	0	0	0	16775	478	17	3	26856	3	TTN	2	179429588	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	3992673	179429588	63769785	28	25640										
TTN	7273	hgsc.bcm.edu	37	chr2	179434584	179434584	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcatatattggtttgctccaAgaaaggaatactgaagatct	8	6	2	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:179434584A>G	ENST00000591111.1	-	276	71576	c.71352T>C	c.(71350-71352)tcT>tcC	p.S23784S	TTN_ENST00000342992.6_Silent_p.S22857S|TTN_ENST00000589042.1_Silent_p.S25425S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Silent_p.S16552S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Silent_p.S16360S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Silent_p.S16485S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23784	Fibronectin type-III 73. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTTGCTCCAAGAAAGGAATA	0.408																																																0			2											154	141	145					2																	179434584		1857	4112	5969	179142830	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71352T>C	2.37:g.179434584A>G			179142830	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179434584	A	G	179434584	2	3	94	1	0	0	0	0	0	0	0	1	16775	59	3	4		4	TTN	2	179434584	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	4996	179434584	63764789	29	25641										
TTN	7273	hgsc.bcm.edu	37	chr2	179479018	179479018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtggtgggttccatgttagaAgacatgactcattggttaca	12	6	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:179479018A>G	ENST00000591111.1	-	212	44407	c.44183T>C	c.(44182-44184)cTt>cCt	p.L14728P	TTN_ENST00000342992.6_Missense_Mutation_p.L13801P|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000589042.1_Missense_Mutation_p.L16369P|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L7496P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L7304P|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L7429P			Q8WZ42	TITIN_HUMAN	titin	14728	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		L -> V (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATGTTAGAAGACATGACTC	0.443																																																0			2											99	92	94					2																	179479018		1990	4176	6166	179187263	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44183T>C	2.37:g.179479018A>G	ENSP00000465570:p.Leu14728Pro		179187263	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.29	2.192736	0.38707	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.55	5.55	0.83447	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55641	0.1933	L	0.52266	1.64	0.58432	D	0.99999	P;P;P;P	0.41188	0.741;0.741;0.741;0.741	P;P;P;P	0.47528	0.549;0.549;0.549;0.549	T	0.59984	-0.7351	9	0.87932	D	0	.	11.716	0.51653	0.8678:0.0:0.0:0.1322	.	7304;7429;7496;14728	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	13801;7304;7496;7429;7304	ENSP00000343764:L13801P;ENSP00000434586:L7304P;ENSP00000340554:L7496P;ENSP00000352154:L7429P	ENSP00000340554:L7496P	L	-	2	0	TTN	179187263	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.077000	0.71275	2.234000	0.73211	0.533000	0.62120	CTT		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179479018	A	G	179479018	3	3	94	1	0	0	0	0	1	0	0	0	16775	72	3	4	58991	4	TTN	2	179479018	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	44434	179479018	63720355	30	25642										
CERKL	375298	hgsc.bcm.edu	37	chr2	182402917	182402917	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaaacaattacatgttacttTggaatcatttcttccatgct	5	8	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:182402917T>C	ENST00000339098.5	-	14	1670	c.1671A>G	c.(1669-1671)ccA>ccG	p.P557P	CERKL_ENST00000374970.2_Silent_p.P462P|CERKL_ENST00000410087.3_Silent_p.P531P|CERKL_ENST00000409440.3_Silent_p.P513P|CERKL_ENST00000374969.2_Silent_p.P418P			Q49MI3	CERKL_HUMAN	ceramide kinase-like	557					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CATGTTACTTTGGAATCATTT	0.318																																																0			2											55	57	56					2																	182402917		2201	4294	6495	182111162	SO:0001819	synonymous_variant	375298			BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.1671A>G	2.37:g.182402917T>C			182111162	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Silent	SNP	ENST00000339098.5	37	CCDS42789.1																																																																																				0.318	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			C	182402917	T	C	182402917	2	2	94	1	0	0	0	0	0	0	0	1	3274	1799	63	4		4	CERKL	2	182402917	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	2923899	182402917	60796456	31	25643										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347396	222347396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atttgaaatcaagttcagggGagcagatggtggacctggag	15	5	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:222347396G>A	ENST00000281821.2	-	5	1035	c.994C>T	c.(994-996)Ccc>Tcc	p.P332S	EPHA4_ENST00000392071.4_Missense_Mutation_p.P281S|EPHA4_ENST00000409854.1_Missense_Mutation_p.P332S|EPHA4_ENST00000409938.1_Missense_Mutation_p.P332S	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	332	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		AAGTTCAGGGGAGCAGATGGT	0.443																																																0			2											79	88	85					2																	222347396		2203	4300	6503	222055640	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.994C>T	2.37:g.222347396G>A	ENSP00000281821:p.Pro332Ser		222055640	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405049	0.83230	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93413	0.7899	H	0.95780	3.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94480	0.7692	10	0.87932	D	0	.	20.2983	0.98569	0.0:0.0:1.0:0.0	.	332	P54764	EPHA4_HUMAN	S	332;332;332;281;36	ENSP00000281821:P332S;ENSP00000386276:P332S;ENSP00000386829:P332S;ENSP00000375923:P281S;ENSP00000395917:P36S	ENSP00000281821:P332S	P	-	1	0	EPHA4	222055640	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.876000	0.87215	2.802000	0.96397	0.655000	0.94253	CCC		0.443	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			A	222347396	G	A	222347396	3	1	94	1	0	0	0	0	1	0	0	0	5182	1174	41	3	2018	3	EPHA4	2	222347396	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	39944479	222347396	20851977	32	25644										
SP100	6672	hgsc.bcm.edu	37	chr2	231368941	231368941	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaaaatattaattttaaacaAtctgaacttcctgtgacctg	5	7	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:231368941A>G	ENST00000264052.5	+	21	2161	c.1806A>G	c.(1804-1806)caA>caG	p.Q602Q	SP100_ENST00000340126.4_Silent_p.Q602Q|RN7SL834P_ENST00000461450.2_RNA|SP100_ENST00000409112.1_Silent_p.Q602Q	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	602	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATTTTAAACAATCTGAACTTC	0.398																																																0			2											139	146	144					2																	231368941		2203	4300	6503	231077185	SO:0001819	synonymous_variant	6672			AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"Zinc fingers, PHD-type"	11206	protein-coding gene	gene with protein product		604585	"nuclear antigen Sp100"			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1806A>G	2.37:g.231368941A>G			231077185	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	37	CCDS2477.1																																																																																				0.398	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		G	231368941	A	G	231368941	2	3	94	1	0	0	0	0	0	0	0	1	14997	98	4	4		4	SP100	2	231368941	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	9021545	231368941	11830432	33	25645										
UGT1A4	54657	hgsc.bcm.edu	37	chr2	234627587	234627587	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgcccactgatggcagccccTggctcagcatgcgggaggcc	14	15	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:234627587T>C	ENST00000373409.3	+	1	164	c.121T>C	c.(121-123)Tgg>Cgg	p.W41R	UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	41					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	TGGCAGCCCCTGGCTCAGCAT	0.627																																					Melanoma(99;1011 1962 13201 26492)											0			2											52	51	51					2																	234627587		2203	4300	6503	234292326	SO:0001583	missense	54657			M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"UDP glucuronosyltransferases"	12536	other	complex locus constituent		606429	"UDP glycosyltransferase 1 family, polypeptide A4"			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.121T>C	2.37:g.234627587T>C	ENSP00000362508:p.Trp41Arg		234292326	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	37	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659380	0.47467	.	.	ENSG00000244474	ENST00000373409	T	0.64618	-0.11	4.16	4.16	0.48862	.	.	.	.	.	D	0.85457	0.5701	H	0.97611	4.04	0.52099	D	0.999943	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89897	0.4041	9	0.66056	D	0.02	.	13.201	0.59767	0.0:0.0:0.0:1.0	.	41;41	B8K288;P22310	.;UD14_HUMAN	R	41	ENSP00000362508:W41R	ENSP00000362508:W41R	W	+	1	0	UGT1A4	234292326	1.000000	0.71417	1.000000	0.80357	0.094000	0.18550	7.912000	0.87465	1.506000	0.48736	0.402000	0.26972	TGG		0.627	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1	NM_007120		C	234627587	T	C	234627587	3	2	94	1	0	0	0	0	1	0	0	0	16987	1580	55	4	123	4	UGT1A4	2	234627587	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	3258646	234627587	8571786	34	25646										
PRR21	643905	hgsc.bcm.edu	37	chr2	240981487	240981487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agggccgtgggtgaagaggcAtggacgaagggccgtgggtg	22	6	0	2	rs60617721	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:240981487A>G	ENST00000408934.1	-	1	912	c.913T>C	c.(913-915)Tgc>Cgc	p.C305R		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	305	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGGCATGGACGAAGG	0.632													a|||	2078	0.414936	0.4455	0.3775	5008	,	,		16158	0.5744		0.332	False		,,,				2504	0.3211															0			2											25	21	23					2																	240981487		1766	3570	5336	240630160	SO:0001583	missense	643905			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.913T>C	2.37:g.240981487A>G	ENSP00000386166:p.Cys305Arg		240630160		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.707321	0.00096	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	0.623	-1.25	0.09405	.	.	.	.	.	T	0.04452	0.0122	N	0.08118	0	0.80722	P	0.0	B	0.19073	0.033	B	0.08055	0.003	T	0.43360	-0.9396	8	0.08381	T	0.77	.	2.6586	0.05019	0.2679:0.4862:0.0:0.2459	rs60617721;rs62184584	305	Q8WXC7	PRR21_HUMAN	R	305	ENSP00000386166:C305R;ENSP00000418240:C305R	ENSP00000386166:C305R	C	-	1	0	PRR21	240630160	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.193000	0.01244	-1.350000	0.02199	-1.198000	0.01671	TGC		0.632	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		G	240981487	A	G	240981487	3	3	94	1	0	0	0	0	1	0	0	0	12626	217	8	4	259	4	PRR21	2	240981487	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	6353900	240981487	2217886	35	25647										
C2orf54	79919	hgsc.bcm.edu	37	chr2	241835379	241835379	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgccacaggggcacctgcacGgccatggctgaggtggggag	18	11	0	1	rs12105122	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:241835379G>A	ENST00000388934.4	-	1	194	c.36C>T	c.(34-36)gcC>gcT	p.A12A		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	12										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GCACCTGCACGGCCATGGCTG	0.697													G|||	2624	0.523962	0.7685	0.3487	5008	,	,		17050	0.4415		0.5159	False		,,,				2504	0.411															0			2						G		2920,1058		1120,680,189	5	6	6		36	-10.5	0	2	dbSNP_120	6	4133,4053		1141,1851,1101	no	coding-synonymous	C2orf54	NM_001085437.1		2261,2531,1290	AA,AG,GG		49.5114,26.5963,42.0174		12/448	241835379	7053,5111	1989	4093	6082	241484052	SO:0001819	synonymous_variant	79919			AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.36C>T	2.37:g.241835379G>A			241484052	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																				0.697	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		A	241835379	G	A	241835379	2	1	94	1	0	0	0	0	0	0	0	1	2181	1103	39	1		1	C2orf54	2	241835379	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	853892	241835379	1363994	36	25648										
NEU4	129807	hgsc.bcm.edu	37	chr2	242758326	242758326	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aacgtgcccgccagccccaaGccgcccaaccttggggacaa	10	18	0	0	rs2293761	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr2:242758326G>A	ENST00000391969.2	+	5	2118	c.1407G>A	c.(1405-1407)aaG>aaA	p.K469K	NEU4_ENST00000407683.1_Silent_p.K469K|NEU4_ENST00000325935.6_Silent_p.K482K|NEU4_ENST00000404257.1_Silent_p.K481K|NEU4_ENST00000405370.1_Silent_p.K469K	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	469					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCAGCCCCAAGCCGCCCAACC	0.657													G|||	2224	0.444089	0.4864	0.3458	5008	,	,		12711	0.4216		0.3847	False		,,,				2504	0.5409															0			2							,,,,	1448,1946		319,810,568	12	14	13		1446,1407,1407,1407,1443	3.7	0	2	dbSNP_100	13	2170,4686		383,1404,1641	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	702,2214,2209	AA,AG,GG		31.6511,42.6635,35.2976	,,,,	482/498,469/485,469/485,469/485,481/497	242758326	3618,6632	1697	3428	5125	242406999	SO:0001819	synonymous_variant	129807			BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1407G>A	2.37:g.242758326G>A			242406999	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																				0.657	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741		A	242758326	G	A	242758326	2	1	94	1	0	0	0	0	0	0	0	1	10375	962	34	3		3	NEU4	2	242758326	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	922947	242758326	441047	37	25649										
LRRN1	57633	hgsc.bcm.edu	37	chr3	3887423	3887423	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctccccaatctgcgtgagatCagtatccatagcaatcccct	6	15	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:3887423C>A	ENST00000319331.3	+	2	1859	c.1098C>A	c.(1096-1098)atC>atA	p.I366I	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	366						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TGCGTGAGATCAGTATCCATA	0.488																																																0			3											96	89	92					3																	3887423		2203	4300	6503	3862423	SO:0001819	synonymous_variant	57633			AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.1098C>A	3.37:g.3887423C>A			3862423	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																				0.488	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		A	3887423	C	A	3887423	2	1	94	1	0	0	0	0	0	0	0	1	9063	816	29	2		2	LRRN1	3	3887423	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10		3887423	194135007	38	25650										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47454350	47454350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccctgcagagcccccaggccTcccgccagccagcctcccag	9	23	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:47454350T>C	ENST00000265562.4	+	25	4663	c.4586T>C	c.(4585-4587)cTc>cCc	p.L1529P	PTPN23_ENST00000431726.1_Missense_Mutation_p.L1403P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1529	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCCCAGGCCTCCCGCCAGCC	0.677																																																0			3											29	35	33					3																	47454350		2203	4299	6502	47429354	SO:0001583	missense	25930			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4586T>C	3.37:g.47454350T>C	ENSP00000265562:p.Leu1529Pro		47429354	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	T	1.294	-0.606896	0.03717	.	.	ENSG00000076201	ENST00000265562	T	0.02763	4.17	4.35	-1.1	0.09872	.	0.493490	0.17116	N	0.186425	T	0.01454	0.0047	N	0.12182	0.205	0.20703	N	0.999868	B	0.02656	0.0	B	0.01281	0.0	T	0.44772	-0.9306	10	0.33141	T	0.24	-5.0099	2.8191	0.05467	0.3201:0.2437:0.0:0.4362	.	1529	Q9H3S7	PTN23_HUMAN	P	1529	ENSP00000265562:L1529P	ENSP00000265562:L1529P	L	+	2	0	PTPN23	47429354	0.000000	0.05858	0.002000	0.10522	0.092000	0.18411	-0.738000	0.04871	-0.086000	0.12550	-0.490000	0.04691	CTC		0.677	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		C	47454350	T	C	47454350	3	2	94	1	0	0	0	0	1	0	0	0	12825	1551	54	4	4684	4	PTPN23	3	47454350	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	43566927	47454350	150568080	39	25651										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52420860	52420860	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ttccttgagagcctcttcaaGtttgacaaggtaagcatgcc	9	10	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:52420860G>A	ENST00000420323.2	+	56	9255	c.8994G>A	c.(8992-8994)aaG>aaA	p.K2998K		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2998	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		GCCTCTTCAAGTTTGACAAGG	0.627																																																0			3											10	12	11					3																	52420860		2030	4173	6203	52395900	SO:0001819	synonymous_variant	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.8994G>A	3.37:g.52420860G>A			52395900	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																				0.627	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52420860	G	A	52420860	2	1	94	1	0	0	0	0	0	0	0	1	4608	1020	36	3		3	DNAH1	3	52420860	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	4966510	52420860	145601570	40	25652										
STAB1	23166	hgsc.bcm.edu	37	chr3	52541958	52541958	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccaccctaggacatcttcccCaaggagtgtgtctacatcca	7	15	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:52541958C>T	ENST00000321725.6	+	20	2140	c.2064C>T	c.(2062-2064)ccC>ccT	p.P688P		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	688					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ACATCTTCCCCAAGGAGTGTG	0.582																																																0			3											134	119	124					3																	52541958		2203	4300	6503	52516998	SO:0001819	synonymous_variant	23166			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2064C>T	3.37:g.52541958C>T			52516998	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																				0.582	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52541958	C	T	52541958	2	4	94	1	0	0	0	0	0	0	0	1	15276	581	21	3		3	STAB1	3	52541958	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	121098	52541958	145480472	41	25653										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78663931	78663931	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtgggcctagggcactgagaCgcatgaaaatgtcgacggcc	15	10	0	2	rs558087386		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:78663931C>T	ENST00000464233.1	-	28	4415	c.4302G>A	c.(4300-4302)gcG>gcA	p.A1434A	ROBO1_ENST00000436010.2_Silent_p.A1395A|ROBO1_ENST00000495273.1_Silent_p.A1389A|ROBO1_ENST00000467549.1_Silent_p.A1334A	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1434					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGCACTGAGACGCATGAAAAT	0.433													C|||	1	0.000199681	8e-04	0	5008	,	,		12693	0		0	False		,,,				2504	0															0			3											75	71	72					3																	78663931		1895	4108	6003	78746621	SO:0001819	synonymous_variant	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4302G>A	3.37:g.78663931C>T			78746621	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																				0.433	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78663931	C	T	78663931	2	4	94	1	0	0	0	0	0	0	0	1	13550	523	19	1		1	ROBO1	3	78663931	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	26121973	78663931	119358499	42	25654										
MORC1	27136	hgsc.bcm.edu	37	chr3	108836866	108836866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tggcgtggatgaaatccagaCgcagctgggcccgctgaagc	15	11	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:108836866C>T	ENST00000483760.1	-	1	84	c.41G>A	c.(40-42)cGt>cAt	p.R14H	MORC1_ENST00000232603.5_Missense_Mutation_p.R14H					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GAAATCCAGACGCAGCTGGGC	0.652																																																0			3											31	25	27					3																	108836866		2203	4300	6503	110319556	SO:0001583	missense	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.41G>A	3.37:g.108836866C>T	ENSP00000417282:p.Arg14His		110319556		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	C	8.281	0.815520	0.16607	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.04502	3.61;3.62	4.86	0.976	0.19727	.	0.563324	0.16155	N	0.227065	T	0.00815	0.0027	N	0.00045	-2.445	0.21290	N	0.999739	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46816	-0.9164	10	0.23302	T	0.38	-2.338	3.4087	0.07351	0.1666:0.187:0.0:0.6464	.	14;14	E7ERX1;Q86VD1	.;MORC1_HUMAN	H	14	ENSP00000232603:R14H;ENSP00000417282:R14H	ENSP00000232603:R14H	R	-	2	0	MORC1	110319556	0.893000	0.30496	0.849000	0.33467	0.280000	0.26924	0.690000	0.25451	0.073000	0.16731	-0.415000	0.06103	CGT		0.652	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108836866	C	T	108836866	3	4	94	1	0	0	0	0	1	0	0	0	9731	536	19	1	3025	1	MORC1	3	108836866	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	30172935	108836866	89185564	43	25655										
DRD3	1814	hgsc.bcm.edu	37	chr3	113878601	113878601	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaaggggaattgcagccctaCctgtctatgctgatggcaca	12	10	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:113878601C>T	ENST00000460779.1	-	4	673		c.e4+1		DRD3_ENST00000295881.7_Splice_Site|DRD3_ENST00000467632.1_Splice_Site|DRD3_ENST00000383673.2_Splice_Site	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3						acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGCAGCCCTACCTGTCTATGC	0.507																																																0			3											104	92	96					3																	113878601		2203	4300	6503	115361291	SO:0001630	splice_region_variant	1814				CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"GPCR / Class A : Dopamine receptors"	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.383+1G>A	3.37:g.113878601C>T			115361291	A1A4V5|Q4VBM8	Splice_Site	SNP	ENST00000460779.1	37	CCDS2978.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.217108	0.79352	.	.	ENSG00000151577	ENST00000460779;ENST00000467632;ENST00000383673;ENST00000281274;ENST00000295881	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2952	0.82767	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DRD3	115361291	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.301000	0.78850	2.384000	0.81235	0.555000	0.69702	.		0.507	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3	Intron	T	113878601	C	T	113878601	5	4	94	1	0	0	0	0	0	0	1	0	4769	521	18	3	838	3	DRD3	3	113878601	Splice_Site	SNP	C	TCGA-DC-5869-01A-01D-1657-10	5041735	113878601	84143829	44	25656										
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133374273	133374276	+	Frame_Shift_Del	DEL	AAGA	AAGA	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtcacacagattatgcaaccAagaaaaataggacacttgaa					rs374437816	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	AAGA	AAGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:133374273_133374276delAAGA	ENST00000260810.5	-	6	731_734	c.600_603delTCTT	c.(598-603)tttcttfs	p.FL200fs	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	200	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTATGCAACCAAGAAAAATAGGAC	0.338								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)											0			3																																								134856966	SO:0001589	frameshift_variant	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.600_603delTCTT	3.37:g.133374273_133374276delAAGA	ENSP00000260810:p.Phe200fs		134856963	B7Z7W8|Q7LGC1|Q9UEB9	Frame_Shift_Del	DEL	ENST00000260810.5	37	CCDS46919.1																																																																																				0.338	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		-	133374276	AAGA	-	133374273	7	5	94	1	0	1	0	1	0	0	0	0	16409	117	5	0	4057	0	TOPBP1	3	133374273	Frame_Shift_Del	DEL	AAGA	TCGA-DC-5869-01A-01D-1657-10	19495672	133374273	64648157	45	25657										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155303880	155303880	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	catttgtctgacttttcttcGgggcagattaacattcagtt	8	8	3	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:155303880G>A	ENST00000340059.7	-	4	537	c.538C>T	c.(538-540)Cga>Tga	p.R180*	PLCH1_ENST00000447496.2_Nonsense_Mutation_p.R180*|PLCH1_ENST00000414191.1_Nonsense_Mutation_p.R162*|PLCH1_ENST00000334686.6_Nonsense_Mutation_p.R162*|PLCH1_ENST00000460012.1_Nonsense_Mutation_p.R162*|PLCH1_ENST00000494598.1_Nonsense_Mutation_p.R180*	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	180	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ACTTTTCTTCGGGGCAGATTA	0.363																																																0			3											127	124	125					3																	155303880		2203	4300	6503	156786574	SO:0001587	stop_gained	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.538C>T	3.37:g.155303880G>A	ENSP00000345988:p.Arg180*		156786574	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Nonsense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	G	37	6.516100	0.97629	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	.	.	.	5.51	3.69	0.42338	.	0.080716	0.49305	D	0.000154	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8514	0.70300	0.0:0.0:0.7385:0.2615	.	.	.	.	X	180;162;180;180;162;162	.	ENSP00000335469:R162X	R	-	1	2	PLCH1	156786574	1.000000	0.71417	0.982000	0.44146	0.994000	0.84299	4.657000	0.61490	0.652000	0.30806	0.655000	0.94253	CGA		0.363	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		A	155303880	G	A	155303880	4	1	94	1	0	0	0	0	0	1	0	0	12068	1124	39	1	4638	1	PLCH1	3	155303880	Nonsense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	21929607	155303880	42718550	46	25658										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936047	178936047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aagggaaaatgacaaagaacAgctcaaagcaatttctacac	7	8	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:178936047A>G	ENST00000263967.3	+	10	1746	c.1589A>G	c.(1588-1590)cAg>cGg	p.Q530R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	530	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q530R(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GACAAAGAACAGCTCAAAGCA	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	ovary(1)	3											42	42	42					3																	178936047		1798	4059	5857	180418741	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1589A>G	3.37:g.178936047A>G	ENSP00000263967:p.Gln530Arg		180418741	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	13.04	2.116959	0.37339	.	.	ENSG00000121879	ENST00000263967	T	0.63580	-0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.127006	0.53938	D	0.000047	T	0.50086	0.1595	L	0.28192	0.835	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.42599	-0.9442	10	0.21014	T	0.42	-0.5103	16.1026	0.81194	1.0:0.0:0.0:0.0	.	530	P42336	PK3CA_HUMAN	R	530	ENSP00000263967:Q530R	ENSP00000263967:Q530R	Q	+	2	0	PIK3CA	180418741	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	CAG		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936047	A	G	178936047	3	3	94	1	0	0	0	0	1	0	0	0	11944	188	7	4	1623	4	PIK3CA	3	178936047	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	23632167	178936047	19086383	47	25659										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936093	178936093	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctctctctgaaatcactgaGcaggagaaagattttctatg	8	9	4	4	rs121913275		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:178936093G>T	ENST00000263967.3	+	10	1792	c.1635G>T	c.(1633-1635)gaG>gaT	p.E545D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545D(25)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAATCACTGAGCAGGAGAAAG	0.358		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	25	Substitution - Missense(25)	endometrium(9)|large_intestine(7)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|stomach(1)|oesophagus(1)	3											61	61	61					3																	178936093		1813	4072	5885	180418787	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1635G>T	3.37:g.178936093G>T	ENSP00000263967:p.Glu545Asp		180418787	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.718256	0.68844	.	.	ENSG00000121879	ENST00000263967	T	0.64438	-0.1	5.78	2.7	0.31948	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65626	0.2709	L	0.41027	1.25	0.80722	D	1	D	0.67145	0.996	D	0.69479	0.964	T	0.58696	-0.7591	10	0.29301	T	0.29	-25.7963	8.8586	0.35242	0.374:0.0:0.626:0.0	.	545	P42336	PK3CA_HUMAN	D	545	ENSP00000263967:E545D	ENSP00000263967:E545D	E	+	3	2	PIK3CA	180418787	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.952000	0.56691	0.236000	0.21180	0.467000	0.42956	GAG		0.358	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178936093	G	T	178936093	3	4	94	1	0	0	0	0	1	0	0	0	11944	962	34	2	1669	2	PIK3CA	3	178936093	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	46	178936093	19086337	48	25660										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951991	178951991	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaatgccagaactacaatctTttgatgacattgcatacatt	6	8	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr3:178951991T>C	ENST00000263967.3	+	21	3203	c.3046T>C	c.(3046-3048)Ttt>Ctt	p.F1016L	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1016	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.F1016L(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ACTACAATCTTTTGATGACAT	0.388		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	thyroid(1)	3											107	95	99					3																	178951991		1877	4115	5992	180434685	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3046T>C	3.37:g.178951991T>C	ENSP00000263967:p.Phe1016Leu		180434685	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	7.994	0.753863	0.15778	.	.	ENSG00000121879	ENST00000263967	T	0.80566	-1.39	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	N	0.17631	0.505	0.80722	D	1	P	0.36577	0.558	B	0.35931	0.214	T	0.68372	-0.5426	10	0.23302	T	0.38	-21.1775	16.635	0.85050	0.0:0.0:0.0:1.0	.	1016	P42336	PK3CA_HUMAN	L	1016	ENSP00000263967:F1016L	ENSP00000263967:F1016L	F	+	1	0	PIK3CA	180434685	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.560000	0.82277	2.330000	0.79161	0.477000	0.44152	TTT		0.388	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178951991	T	C	178951991	3	2	94	1	0	0	0	0	1	0	0	0	11944	1841	64	4	3124	4	PIK3CA	3	178951991	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	15898	178951991	19070439	49	25661										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cccgcctgctcacacacgtgTccatgtggagtgcccacctg	10	17	1	0	rs55703801		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:1388508T>C	ENST00000324803.4	+	1	3169	c.209T>C	c.(208-210)gTc>gCc	p.V70A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	70					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACACGTGTCCATGTGGAG	0.632																																																0			4											283	245	257					4																	1388508		2203	4300	6503	1378508	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.209T>C	4.37:g.1388508T>C	ENSP00000323978:p.Val70Ala		1378508	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	8.717	0.913380	0.17907	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.09	-2.19	0.07015	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.25257	-1.0137	9	0.16896	T	0.51	.	0.4342	0.00476	0.19:0.3247:0.1898:0.2955	rs55703801	70	Q8N1N5	CRPAK_HUMAN	A	70;63	ENSP00000323978:V70A	ENSP00000323978:V70A	V	+	2	0	CRIPAK	1378508	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-1.991000	0.01478	-2.302000	0.00657	-1.823000	0.00598	GTC		0.632	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1388508	T	C	1388508	3	2	94	1	0	0	0	0	1	0	0	0	3883	1667	58	4	211	4	CRIPAK	4	1388508	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10		1388508	189765768	50	25662										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77700013	77700013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctggtcagcatgaggatgccCgggagctgaaggagaacctg	16	9	1	3	rs186156427		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:77700013C>T	ENST00000296043.6	+	11	6627	c.5674C>T	c.(5674-5676)Cgg>Tgg	p.R1892W	RP11-359D14.3_ENST00000449007.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1892	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TGAGGATGCCCGGGAGCTGAA	0.537													C|||	1	0.000199681	0	0.0014	5008	,	,		18188	0		0	False		,,,				2504	0															0			4						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	66	62	63		5674	4.2	1	4		63	0,8600		0,0,4300	no	missense	SHROOM3	NM_020859.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1892/1997	77700013	1,13005	2203	4300	6503	77919037	SO:0001583	missense	57619			AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.5674C>T	4.37:g.77700013C>T	ENSP00000296043:p.Arg1892Trp		77919037	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	16.15	3.041037	0.55003	2.27E-4	0.0	ENSG00000138771	ENST00000296043	T	0.33216	1.42	5.01	4.16	0.48862	Apx/shroom, ASD2 (2);	0.105837	0.42548	D	0.000691	T	0.46483	0.1395	L	0.56769	1.78	0.45439	D	0.998418	D	0.89917	1.0	D	0.85130	0.997	T	0.43925	-0.9361	10	0.66056	D	0.02	-14.5715	6.5431	0.22390	0.0:0.6938:0.1543:0.1519	.	1892	Q8TF72	SHRM3_HUMAN	W	1892	ENSP00000296043:R1892W	ENSP00000296043:R1892W	R	+	1	2	SHROOM3	77919037	0.887000	0.30362	0.998000	0.56505	0.589000	0.36550	1.653000	0.37323	1.332000	0.45431	0.313000	0.20887	CGG		0.537	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		T	77700013	C	T	77700013	3	4	94	1	0	0	0	0	1	0	0	0	14332	643	23	1	5716	1	SHROOM3	4	77700013	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	76311505	77700013	113454263	51	25663										
PRDM8	56978	hgsc.bcm.edu	37	chr4	81123603	81123603	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggcggcggtggcgctggtctGgtagggggccggggccgctt	23	10	1	0	rs6831357	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:81123603G>T	ENST00000504452.1	+	8	1826	c.987G>T	c.(985-987)ctG>ctT	p.L329L	PRDM8_ENST00000339711.4_Silent_p.L329L|PRDM8_ENST00000415738.2_Silent_p.L329L			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	329	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GCGCTGGTCTGGTAGGGGGCC	0.706													G|||	309	0.0617013	0.2216	0.0231	5008	,	,		9086	0		0	False		,,,				2504	0															0			4						G	,	274,1802		1,272,765	2	2	2		987,987	4	0.9	4	dbSNP_116	2	7,5213		0,7,2603	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	1,279,3368	TT,TG,GG		0.1341,13.1985,3.8514	,	329/690,329/690	81123603	281,7015	1038	2610	3648	81342627	SO:0001819	synonymous_variant	56978			AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.987G>T	4.37:g.81123603G>T			81342627	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																				0.706	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			T	81123603	G	T	81123603	2	4	94	1	0	0	0	0	0	0	0	1	12496	1335	47	2		2	PRDM8	4	81123603	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	3423590	81123603	110030673	52	25664										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146030352	146030352	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tggtattggaaagtcaactgCtttaaaaattttagcaggaa	9	4	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:146030352C>G	ENST00000296577.4	+	5	871	c.356C>G	c.(355-357)gCt>gGt	p.A119G	OTUD4_ENST00000455611.2_5'Flank|ABCE1_ENST00000502803.1_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	119	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					AAGTCAACTGCTTTAAAAATT	0.328																																																0			4											96	98	97					4																	146030352		2203	4300	6503	146249802	SO:0001583	missense	6059			X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.356C>G	4.37:g.146030352C>G	ENSP00000296577:p.Ala119Gly		146249802	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	37	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	C	34	5.336655	0.95758	.	.	ENSG00000164163	ENST00000296577;ENST00000502586	D;D	0.93811	-3.29;-3.29	5.86	5.86	0.93980	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.97961	0.9329	H	0.95328	3.655	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.98227	1.0481	10	0.87932	D	0	-27.1952	20.5632	0.99335	0.0:1.0:0.0:0.0	.	119	P61221	ABCE1_HUMAN	G	119	ENSP00000296577:A119G;ENSP00000421250:A119G	ENSP00000296577:A119G	A	+	2	0	ABCE1	146249802	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.616000	0.83018	2.937000	0.99478	0.650000	0.86243	GCT		0.328	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		G	146030352	C	G	146030352	3	3	94	1	0	0	0	0	1	0	0	0	64	797	28	5	370	5	ABCE1	4	146030352	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	64906749	146030352	45123924	53	25665										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245453	153245453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tccacttgttaacgactggtGccctgttaacgtgtgaatgc	10	10	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:153245453G>A	ENST00000281708.4	-	11	2967	c.1738C>T	c.(1738-1740)Cac>Tac	p.H580Y	FBXW7_ENST00000603548.1_Missense_Mutation_p.H580Y|FBXW7_ENST00000296555.5_Missense_Mutation_p.H462Y|FBXW7_ENST00000263981.5_Missense_Mutation_p.H500Y|FBXW7_ENST00000393956.3_Missense_Mutation_p.H404Y|FBXW7_ENST00000603841.1_Missense_Mutation_p.H580Y	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	580					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.G579_Q581>E(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AACGACTGGTGCCCTGTTAAC	0.418			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	2	Unknown(1)|Complex - deletion inframe(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4											152	125	134					4																	153245453		2203	4300	6503	153464903	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1738C>T	4.37:g.153245453G>A	ENSP00000281708:p.His580Tyr		153464903	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.270761	0.59540	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.93494	0.7924	H	0.95917	3.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.94595	0.7791	10	0.59425	D	0.04	-16.0333	19.838	0.96666	0.0:0.0:1.0:0.0	.	404;580;462;500	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	Y	580;462;500;404	ENSP00000281708:H580Y;ENSP00000296555:H462Y;ENSP00000263981:H500Y;ENSP00000377528:H404Y	ENSP00000263981:H500Y	H	-	1	0	FBXW7	153464903	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.692000	0.91855	0.650000	0.86243	CAC		0.418	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153245453	G	A	153245453	3	1	94	1	0	0	0	0	1	0	0	0	5788	1319	46	3	393	3	FBXW7	4	153245453	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	7215101	153245453	37908823	54	25666										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249451	153249451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctctgcattccacactttgaGtgtccgatctgtagatccac	7	13	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:153249451G>A	ENST00000281708.4	-	9	2556	c.1327C>T	c.(1327-1329)Ctc>Ttc	p.L443F	FBXW7_ENST00000603548.1_Missense_Mutation_p.L443F|FBXW7_ENST00000296555.5_Missense_Mutation_p.L325F|FBXW7_ENST00000263981.5_Missense_Mutation_p.L363F|FBXW7_ENST00000393956.3_Missense_Mutation_p.L267F|FBXW7_ENST00000603841.1_Missense_Mutation_p.L443F	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	443					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CACACTTTGAGTGTCCGATCT	0.418			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											306	259	275					4																	153249451		2203	4300	6503	153468901	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1327C>T	4.37:g.153249451G>A	ENSP00000281708:p.Leu443Phe		153468901	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.109998	0.77210	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	L	0.52823	1.66	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.995;0.997;0.992;0.992	T	0.74386	-0.3682	10	0.72032	D	0.01	-10.502	10.5379	0.45016	0.1463:0.0:0.8537:0.0	.	267;443;325;363	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	F	443;325;363;267	ENSP00000281708:L443F;ENSP00000296555:L325F;ENSP00000263981:L363F;ENSP00000377528:L267F	ENSP00000263981:L363F	L	-	1	0	FBXW7	153468901	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.795000	0.69074	2.878000	0.98634	0.650000	0.86243	CTC		0.418	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249451	G	A	153249451	3	1	94	1	0	0	0	0	1	0	0	0	5788	1029	36	3	812	3	FBXW7	4	153249451	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	3998	153249451	37904825	55	25667										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153332917	153332917	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctcagagagcctccagttcgTcgtcttttgctgcccacaga	9	14	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:153332917T>C	ENST00000281708.4	-	2	1268	c.39A>G	c.(37-39)cgA>cgG	p.R13R	FBXW7_ENST00000603548.1_Silent_p.R13R|FBXW7_ENST00000604872.1_Silent_p.R13R|FBXW7_ENST00000603841.1_Silent_p.R13R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	13					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)			NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTCCAGTTCGTCGTCTTTTGC	0.483			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	0			4											79	69	73					4																	153332917		2203	4300	6503	153552367	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.39A>G	4.37:g.153332917T>C			153552367	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.483	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153332917	T	C	153332917	2	2	94	1	0	0	0	0	0	0	0	1	5788	1654	58	4		4	FBXW7	4	153332917	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	83466	153332917	37821359	56	25668										
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187476414	187476414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gatgtccaccacgatggtgaAgatgaggacgcaggccaggg	16	9	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr4:187476414A>G	ENST00000307161.5	-	1	307	c.106T>C	c.(106-108)Ttc>Ctc	p.F36L	RP11-215A19.2_ENST00000509111.1_Silent_p.S17S	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	36					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	ACGATGGTGAAGATGAGGACG	0.706																																																0			4											26	19	22					4																	187476414		2187	4276	6463	187713408	SO:0001583	missense	4543				CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"GPCR / Class A : Melatonin receptors"	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.106T>C	4.37:g.187476414A>G	ENSP00000302811:p.Phe36Leu		187713408	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	37	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	a	17.42	3.384043	0.61845	.	.	ENSG00000168412	ENST00000307161	T	0.33865	1.39	4.66	0.192	0.15134	.	0.288270	0.32273	U	0.006327	T	0.31104	0.0786	M	0.68952	2.095	0.54753	D	0.999982	B	0.06786	0.001	B	0.06405	0.002	T	0.20140	-1.0284	10	0.13108	T	0.6	-10.2532	11.6768	0.51434	0.5668:0.4332:0.0:0.0	.	36	P48039	MTR1A_HUMAN	L	36	ENSP00000302811:F36L	ENSP00000302811:F36L	F	-	1	0	MTNR1A	187713408	0.999000	0.42202	1.000000	0.80357	0.966000	0.64601	0.875000	0.28079	0.121000	0.18284	0.454000	0.30748	TTC		0.706	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			G	187476414	A	G	187476414	3	3	94	1	0	0	0	0	1	0	0	0	9981	72	3	4	954	4	MTNR1A	4	187476414	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	34143497	187476414	3677862	57	25669										
CEP72	55722	hgsc.bcm.edu	37	chr5	635610	635610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggagaagatgccttggagccAgctctgtggagagcttccgc	15	10	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:635610A>G	ENST00000264935.5	+	6	905	c.815A>G	c.(814-816)cAg>cGg	p.Q272R	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	272					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CCTTGGAGCCAGCTCTGTGGA	0.632																																																0			5											64	62	63					5																	635610		2203	4300	6503	688610	SO:0001583	missense	55722			BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.815A>G	5.37:g.635610A>G	ENSP00000264935:p.Gln272Arg		688610	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	.	.	.	.	.	.	.	.	.	.	A	0.184	-1.059610	0.01950	.	.	ENSG00000112877	ENST00000264935	T	0.08896	3.04	4.24	-1.52	0.08637	.	0.831662	0.10377	N	0.681943	T	0.05135	0.0137	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47636	-0.9102	10	0.07325	T	0.83	-3.35	5.4897	0.16769	0.5792:0.1424:0.2784:0.0	.	272	Q9P209	CEP72_HUMAN	R	272	ENSP00000264935:Q272R	ENSP00000264935:Q272R	Q	+	2	0	CEP72	688610	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.134000	0.10436	-0.341000	0.08376	-0.765000	0.03448	CAG		0.632	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140		G	635610	A	G	635610	3	3	94	1	0	0	0	0	1	0	0	0	3266	188	7	4	837	4	CEP72	5	635610	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10		635610	180279650	58	25670										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13866368	13866369	+	Frame_Shift_Ins	INS	-	-	A													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cactggcttcctggggcttcINSaagccgctagccattggacc					rs201366196		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:13866368_13866369insA	ENST00000265104.4	-	26	4180_4181	c.4076_4077insT	c.(4075-4077)ttgfs	p.L1359fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1359	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTGGGGCTTCAAGCCGCTAGC	0.332									Kartagener syndrome																																							0			5																																								13919369	SO:0001589	frameshift_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4077dupT	5.37:g.13866370_13866370dupA	ENSP00000265104:p.Leu1359fs		13919368	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Ins	INS	ENST00000265104.4	37	CCDS3882.1																																																																																				0.332	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13866369	-	A	13866368	7	5	94	1	0	1	1	0	0	0	0	0	4615	825	29	0	10013	0	DNAH5	5	13866368	Frame_Shift_Ins	INS	-	TCGA-DC-5869-01A-01D-1657-10	13230758	13866368	167048892	59	25671										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527387	23527387	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gagtgtgggcggggctttagCaataagtcacacctcctcag	13	10	2	0	rs56256550		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:23527387C>A	ENST00000296682.3	+	11	2372	c.2190C>A	c.(2188-2190)agC>agA	p.S730R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	730					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGGCTTTAGCAATAAGTCAC	0.597										HNSCC(3;0.000094)																																						0			5											23	25	24					5																	23527387		2067	4181	6248	23563144	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2190C>A	5.37:g.23527387C>A	ENSP00000296682:p.Ser730Arg		23563144	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.348632	0.01266	.	.	ENSG00000164256	ENST00000296682	T	0.19669	2.13	2.79	-5.57	0.02521	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10165	0.0249	L	0.27944	0.81	0.09310	N	1	P	0.47350	0.894	B	0.38880	0.284	T	0.03818	-1.1001	9	0.44086	T	0.13	.	3.9896	0.09532	0.4241:0.2776:0.0:0.2983	.	730	Q9NQV7	PRDM9_HUMAN	R	730	ENSP00000296682:S730R	ENSP00000296682:S730R	S	+	3	2	PRDM9	23563144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.778000	0.00099	-2.704000	0.00397	-0.350000	0.07774	AGC		0.597	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23527387	C	A	23527387	3	1	94	1	0	0	0	0	1	0	0	0	12497	709	25	2	2228	2	PRDM9	5	23527387	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	9661019	23527387	157387873	60	25672										
MRPS30	10884	hgsc.bcm.edu	37	chr5	44809451	44809451	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gcggagcccgagcccgagccCgaacccgaacctgaacctgc	12	18	0	1	rs372322665		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:44809451C>T	ENST00000507110.1	+	1	425	c.387C>T	c.(385-387)ccC>ccT	p.P129P	RP11-53O19.1_ENST00000505637.1_RNA|RP11-53O19.1_ENST00000508945.1_RNA|RP11-53O19.1_ENST00000508123.1_RNA|RP11-53O19.1_ENST00000505302.1_RNA|RP11-53O19.1_ENST00000505401.1_RNA|RP11-53O19.1_ENST00000514597.1_RNA|RP11-53O19.1_ENST00000503179.1_RNA|RP11-53O19.1_ENST00000503452.1_RNA	NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	129					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					agcccgagcccgaacccgaac	0.701																																																0			5						C		0,4392		0,0,2196	13	15	14		387	0.2	0	5		14	1,8589		0,1,4294	no	coding-synonymous	MRPS30	NM_016640.3		0,1,6490	TT,TC,CC		0.0116,0.0,0.0077		129/440	44809451	1,12981	2196	4295	6491	44845208	SO:0001819	synonymous_variant	10884			AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"Mitochondrial ribosomal proteins / small subunits"	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.387C>T	5.37:g.44809451C>T			44845208	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Silent	SNP	ENST00000507110.1	37	CCDS3951.1																																																																																				0.701	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640		T	44809451	C	T	44809451	2	4	94	1	0	0	0	0	0	0	0	1	9870	639	23	1		1	MRPS30	5	44809451	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	21282064	44809451	136105809	61	25673										
PARP8	79668	hgsc.bcm.edu	37	chr5	50091241	50091241	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	accatcttcatcttcatcttCtcagcttgctgtgcgtaaat	5	12	6	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:50091241C>T	ENST00000281631.5	+	12	1576	c.1418C>T	c.(1417-1419)tCt>tTt	p.S473F	PARP8_ENST00000505697.2_Missense_Mutation_p.S473F|PARP8_ENST00000514342.2_Missense_Mutation_p.S226F|PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000514067.2_Missense_Mutation_p.S473F|PARP8_ENST00000503750.2_Missense_Mutation_p.S473F|PARP8_ENST00000505554.1_Missense_Mutation_p.S452F	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	473	Poly-Ser.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				TCTTCATCTTCTCAGCTTGCT	0.393																																																0			5											48	51	50					5																	50091241		2203	4300	6503	50126998	SO:0001583	missense	79668			AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.1418C>T	5.37:g.50091241C>T	ENSP00000281631:p.Ser473Phe		50126998	Q3KRB7|Q6DHZ1|Q9H754	Missense_Mutation	SNP	ENST00000281631.5	37	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.946399	0.34377	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000514342;ENST00000281631;ENST00000514067;ENST00000505554;ENST00000503561;ENST00000423185	.	.	.	5.29	5.29	0.74685	.	0.676716	0.14351	N	0.325063	T	0.43809	0.1264	N	0.14661	0.345	0.45806	D	0.998688	B;P;B	0.34826	0.291;0.471;0.412	B;B;B	0.35278	0.087;0.199;0.133	T	0.34354	-0.9832	8	.	.	.	-6.3692	17.4702	0.87643	0.0:1.0:0.0:0.0	.	365;473;473	B4DQ81;Q8N3A8-2;Q8N3A8	.;.;PARP8_HUMAN	F	473;473;226;473;473;452;226;226	.	.	S	+	2	0	PARP8	50126998	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.088000	0.41663	2.601000	0.87937	0.655000	0.94253	TCT		0.393	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		T	50091241	C	T	50091241	3	4	94	1	0	0	0	0	1	0	0	0	11496	913	32	3	1464	3	PARP8	5	50091241	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	5281790	50091241	130824019	62	25674										
DDX4	54514	hgsc.bcm.edu	37	chr5	55056042	55056042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctttagaaatggatgatggaCcttctcgaagagatcatttc	9	7	2	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:55056042C>T	ENST00000505374.1	+	4	234	c.142C>T	c.(142-144)Cct>Tct	p.P48S	DDX4_ENST00000514278.2_Missense_Mutation_p.P48S|DDX4_ENST00000354991.5_Missense_Mutation_p.P48S|DDX4_ENST00000353507.5_Missense_Mutation_p.P48S|SLC38A9_ENST00000504880.1_Intron|DDX4_ENST00000508580.1_3'UTR	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	48					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.P48S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GGATGATGGACCTTCTCGAAG	0.388																																																1	Substitution - Missense(1)	skin(1)	5											186	182	184					5																	55056042		2203	4300	6503	55091799	SO:0001583	missense	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.142C>T	5.37:g.55056042C>T	ENSP00000424838:p.Pro48Ser		55091799	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	37	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.400691	0.25291	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000506848;ENST00000514679;ENST00000354991;ENST00000511491	T;T;T;T;T;T;T	0.59364	2.03;2.0;2.08;3.5;0.41;2.03;0.27	5.04	0.0983	0.14497	.	1.085870	0.06982	N	0.820163	T	0.39384	0.1076	N	0.19112	0.55	0.23215	N	0.998103	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.20739	-1.0266	10	0.24483	T	0.36	-22.046	7.4785	0.27391	0.0:0.5023:0.0:0.4977	.	48;48;48	D6RDK4;Q9NQI0-2;Q9NQI0	.;.;DDX4_HUMAN	S	48	ENSP00000334167:P48S;ENSP00000425359:P48S;ENSP00000424838:P48S;ENSP00000427167:P48S;ENSP00000424112:P48S;ENSP00000347087:P48S;ENSP00000427522:P48S	ENSP00000334167:P48S	P	+	1	0	DDX4	55091799	0.732000	0.28121	0.324000	0.25361	0.826000	0.46750	0.299000	0.19138	-0.187000	0.10516	0.563000	0.77884	CCT		0.388	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		T	55056042	C	T	55056042	3	4	94	1	0	0	0	0	1	0	0	0	4366	507	18	3	152	3	DDX4	5	55056042	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4964801	55056042	125859218	63	25675										
APC	324	hgsc.bcm.edu	37	chr5	112170821	112170824	+	Frame_Shift_Del	DEL	ACGG	ACGG	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaaagtggaggtgggatattAcggaatgtgtccagcttgat							TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	ACGG	ACGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:112170821_112170824delACGG	ENST00000457016.1	+	15	2297_2300	c.1917_1920delACGG	c.(1915-1920)ttacggfs	p.LR639fs	APC_ENST00000508376.2_Frame_Shift_Del_p.LR639fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.LR639fs			P25054	APC_HUMAN	adenomatous polyposis coli	639	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.N641fs*5(1)|p.R640W(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTGGGATATTACGGAATGTGTCCA	0.377		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Missense(1)|Unknown(1)|Deletion - Frameshift(1)	thyroid(1)|large_intestine(1)|skin(1)	5	GRCh37	CD991576|CI972531|CS090535	APC	D|I|S																																				112198723	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1917_1920delACGG	5.37:g.112170821_112170824delACGG	ENSP00000413133:p.Leu639fs		112198720	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.377	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112170824	ACGG	-	112170821	7	5	94	1	0	1	0	1	0	0	0	0	763	388	14	0	1971	0	APC	5	112170821	Frame_Shift_Del	DEL	ACGG	TCGA-DC-5869-01A-01D-1657-10	57114779	112170821	68744439	64	25676										
IRF1	3659	hgsc.bcm.edu	37	chr5	131822771	131822771	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agttcatggcacagcgaaagTtggccttccacgtcttggga	12	10	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:131822771T>C	ENST00000245414.4	-	4	497	c.239A>G	c.(238-240)aAc>aGc	p.N80S	IRF1_ENST00000463784.1_5'UTR|IRF1_ENST00000405885.2_Missense_Mutation_p.N80S	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	80					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		ACAGCGAAAGTTGGCCTTCCA	0.557																																																0			5											436	403	414					5																	131822771		2203	4300	6503	131850670	SO:0001583	missense	3659				CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"interferon regulatory factor-1"	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.239A>G	5.37:g.131822771T>C	ENSP00000245414:p.Asn80Ser		131850670	Q96GG7	Missense_Mutation	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761865	0.89932	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	D;D;D;D	0.97976	-4.64;-4.64;-4.64;-4.64	5.7	5.7	0.88788	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.99032	0.9669	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.77004	0.96;0.989	D	0.99505	1.0954	10	0.72032	D	0.01	-46.2621	15.9631	0.79945	0.0:0.0:0.0:1.0	.	80;80	Q5FBX3;P10914	.;IRF1_HUMAN	S	80	ENSP00000245414:N80S;ENSP00000384406:N80S;ENSP00000405655:N80S;ENSP00000396318:N80S	ENSP00000245414:N80S	N	-	2	0	IRF1	131850670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.161000	0.67846	0.533000	0.62120	AAC		0.557	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198		C	131822771	T	C	131822771	3	2	94	1	0	0	0	0	1	0	0	0	7848	1725	60	4	766	4	IRF1	5	131822771	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	19651950	131822771	49092489	65	25677										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140772810	140772810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atctagaagtaaaaattaacGaaatcgcggttcctggagca	9	7	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:140772810G>A	ENST00000398604.2	+	1	430	c.430G>A	c.(430-432)Gaa>Aaa	p.E144K	PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	144	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAAATTAACGAAATCGCGGT	0.443																																																0			5											51	55	54					5																	140772810		1911	4137	6048	140752994	SO:0001583	missense	9708			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.430G>A	5.37:g.140772810G>A	ENSP00000381605:p.Glu144Lys		140752994	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	23.8	4.455484	0.84209	.	.	ENSG00000253767	ENST00000398604	T	0.76316	-1.01	5.41	5.41	0.78517	Cadherin (3);Cadherin-like (1);	0.000000	0.31484	U	0.007564	D	0.94355	0.8185	H	0.99847	4.84	0.46437	D	0.999045	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97143	0.9826	10	0.87932	D	0	.	18.8047	0.92032	0.0:0.0:1.0:0.0	.	144;144	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	K	144	ENSP00000381605:E144K	ENSP00000381605:E144K	E	+	1	0	PCDHGA8	140752994	1.000000	0.71417	0.986000	0.45419	0.728000	0.41692	9.777000	0.99008	2.552000	0.86080	0.655000	0.94253	GAA		0.443	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		A	140772810	G	A	140772810	3	1	94	1	0	0	0	0	1	0	0	0	11591	1059	37	1	432	1	PCDHGA8	5	140772810	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	8950039	140772810	40142450	66	25678										
EBF1	1879	hgsc.bcm.edu	37	chr5	158139268	158139268	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atgctcgtggtgacggagttAtagttggtctgctggggagt	17	5	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:158139268A>G	ENST00000313708.6	-	14	1725	c.1443T>C	c.(1441-1443)taT>taC	p.Y481Y	EBF1_ENST00000380654.4_Silent_p.Y450Y|EBF1_ENST00000517373.1_Intron|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	481	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGACGGAGTTATAGTTGGTCT	0.612			T	HMGA2	lipoma																																		Dom	yes		5	5q34	1879	early B-cell factor 1		M	0			5											120	89	99					5																	158139268		2203	4300	6503	158071846	SO:0001819	synonymous_variant	1879			AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1443T>C	5.37:g.158139268A>G			158071846	Q8IW11	Silent	SNP	ENST00000313708.6	37	CCDS4343.1																																																																																				0.612	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		G	158139268	A	G	158139268	2	3	94	1	0	0	0	0	0	0	0	1	4891	456	16	4		4	EBF1	5	158139268	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	17366458	158139268	22775992	67	25679										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173316925	173316925	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gggtcagcttggctttttccTgctccagctacccataacat	8	13	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr5:173316925T>C	ENST00000265085.5	+	1	1643	c.189T>C	c.(187-189)ccT>ccC	p.P63P	CPEB4_ENST00000520867.1_Silent_p.P63P|CPEB4_ENST00000519835.1_Silent_p.P63P|CPEB4_ENST00000334035.5_Silent_p.P63P	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	63					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCTTTTTCCTGCTCCAGCTA	0.483																																																0			5											106	117	113					5																	173316925		2203	4300	6503	173249531	SO:0001819	synonymous_variant	80315			BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.189T>C	5.37:g.173316925T>C			173249531	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Silent	SNP	ENST00000265085.5	37	CCDS4390.1																																																																																				0.483	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		C	173316925	T	C	173316925	2	2	94	1	0	0	0	0	0	0	0	1	3809	1567	55	4		4	CPEB4	5	173316925	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	15177657	173316925	7598335	68	25680										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954434	30954434	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctccagcacaacctccagtgAggccagcacagccaccaact	7	18	0	1	rs9262337	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:30954434A>G	ENST00000376296.3	+	2	723	c.482A>G	c.(481-483)gAg>gGg	p.E161G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	161	28 X 15 AA approximate tandem repeats.|Ser-rich.		E -> G (in dbSNP:rs9262337). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E161G(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCTCCAGTGAGGCCAGCACA	0.617													G|||	458	0.0914537	0.093	0.1383	5008	,	,		25853	0.0685		0.0845	False		,,,				2504	0.0869															1	Substitution - Missense(1)	prostate(1)	6											144	135	138					6																	30954434		2202	4300	6502	31062413	SO:0001583	missense	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.482A>G	6.37:g.30954434A>G	ENSP00000365473:p.Glu161Gly		31062413	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	2.769	-0.256080	0.05829	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01178	5.22	3.76	-7.51	0.01346	.	.	.	.	.	T	0.00178	0.0005	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43015	-0.9417	8	.	.	.	3.8375	8.9823	0.35972	0.4863:0.3865:0.1271:0.0	rs9262337	161	Q5SSG8	MUC21_HUMAN	G	161	ENSP00000365473:E161G	.	E	+	2	0	MUC21	31062413	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-3.965000	0.00324	-2.460000	0.00537	-0.330000	0.08379	GAG		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		G	30954434	A	G	30954434	3	3	94	1	0	0	0	0	1	0	0	0	10007	304	11	4	488	4	MUC21	6	30954434	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10		30954434	140160633	69	25681										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43400662	43400662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	actggtgggcttcctggaagAggggcaggagccactaagcc	16	10	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:43400662A>G	ENST00000372530.4	+	3	1159	c.944A>G	c.(943-945)gAg>gGg	p.E315G	ABCC10_ENST00000244533.3_Missense_Mutation_p.E272G|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	315	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	TTCCTGGAAGAGGGGCAGGAG	0.607																																																0			6											45	48	47					6																	43400662		2203	4300	6503	43508640	SO:0001583	missense	89845			U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.944A>G	6.37:g.43400662A>G	ENSP00000361608:p.Glu315Gly		43508640	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853814	0.32791	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	D;D	0.89746	-2.56;-2.56	5.44	5.44	0.79542	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.424385	0.25869	N	0.027777	T	0.74283	0.3696	L	0.28694	0.88	0.27590	N	0.94931	B;B	0.30146	0.202;0.27	B;B	0.35550	0.205;0.192	T	0.66304	-0.5957	10	0.33141	T	0.24	-19.7313	11.1288	0.48334	0.7168:0.2832:0.0:0.0	.	272;315	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	G	315;272	ENSP00000361608:E315G;ENSP00000244533:E272G	ENSP00000244533:E272G	E	+	2	0	ABCC10	43508640	0.997000	0.39634	1.000000	0.80357	0.733000	0.41908	3.695000	0.54749	2.071000	0.62044	0.459000	0.35465	GAG		0.607	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		G	43400662	A	G	43400662	3	3	94	1	0	0	0	0	1	0	0	0	50	304	11	4	817	4	ABCC10	6	43400662	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	12446228	43400662	127714405	70	25682										
RIPPLY2	134701	hgsc.bcm.edu	37	chr6	84563147	84563147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgcggcgtcatggagaacgcGggaggcgcagagggtacaga	19	8	1	3	rs9353143	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:84563147G>A	ENST00000369689.1	+	1	163	c.12G>A	c.(10-12)gcG>gcA	p.A4A	RIPPLY2_ENST00000369687.1_5'Flank	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	4					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGGAGAACGCGGGAGGCGCAG	0.697													A|||	1469	0.293331	0.6596	0.2752	5008	,	,		13517	0.2619		0.0825	False		,,,				2504	0.0603															0			6						A		1259,1859		244,771,544	3	4	4		12	-3.7	0	6	dbSNP_119	4	433,5751		28,377,2687	no	coding-synonymous	RIPPLY2	NM_001009994.1		272,1148,3231	AA,AG,GG		7.0019,40.3784,18.1896		4/129	84563147	1692,7610	1559	3092	4651	84619866	SO:0001819	synonymous_variant	134701			BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"chromosome 6 open reading frame 159", "ripply2 homolog (zebrafish)"	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.12G>A	6.37:g.84563147G>A			84619866	Q5TAB6	Silent	SNP	ENST00000369689.1	37	CCDS34493.1																																																																																				0.697	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994		A	84563147	G	A	84563147	2	1	94	1	0	0	0	0	0	0	0	1	13422	1103	39	1		1	RIPPLY2	6	84563147	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	41162485	84563147	86551920	71	25683										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128841478	128841478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agagcgccacaaaagcaggcAgcgccgccgccgcagtcgta	13	15	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:128841478A>G	ENST00000368215.3	-	1	25	c.26T>C	c.(25-27)cTg>cCg	p.L9P	PTPRK_ENST00000368226.4_Missense_Mutation_p.L9P|PTPRK_ENST00000532331.1_Missense_Mutation_p.L9P|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368207.3_Missense_Mutation_p.L9P|PTPRK_ENST00000368210.3_Missense_Mutation_p.L9P|PTPRK_ENST00000525459.1_Missense_Mutation_p.L9P|PTPRK_ENST00000368227.3_Missense_Mutation_p.L9P|PTPRK_ENST00000368213.5_Missense_Mutation_p.L9P			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	9				L -> V (in Ref. 2; AAC37599). {ECO:0000305}.	cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		AAAAGCAGGCAGCGCCGCCGC	0.652																																																0			6											24	31	28					6																	128841478		2189	4289	6478	128883171	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.26T>C	6.37:g.128841478A>G	ENSP00000357198:p.Leu9Pro		128883171	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	A	11.29	1.596252	0.28445	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000525459	T;T;T;T;T;T;T;T	0.10960	3.07;3.08;3.08;3.07;3.08;3.07;3.08;2.82	4.56	3.4	0.38934	.	0.138146	0.28754	N	0.014246	T	0.06508	0.0167	N	0.14661	0.345	0.44061	D	0.996801	B;P;D;P;D	0.54397	0.0;0.943;0.966;0.943;0.966	B;P;P;P;P	0.61070	0.0;0.766;0.883;0.766;0.883	T	0.15292	-1.0442	10	0.72032	D	0.01	.	6.0271	0.19660	0.8842:0.0:0.1158:0.0	.	9;9;9;9;9	B4DHC3;B7ZMG0;Q15262-3;Q15262;Q15262-2	.;.;.;PTPRK_HUMAN;.	P	9	ENSP00000357209:L9P;ENSP00000357210:L9P;ENSP00000432973:L9P;ENSP00000357196:L9P;ENSP00000357193:L9P;ENSP00000357198:L9P;ENSP00000357190:L9P;ENSP00000434116:L9P	ENSP00000357190:L9P	L	-	2	0	PTPRK	128883171	1.000000	0.71417	0.995000	0.50966	0.836000	0.47400	1.952000	0.40343	1.675000	0.50919	0.459000	0.35465	CTG		0.652	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			G	128841478	A	G	128841478	3	3	94	1	0	0	0	0	1	0	0	0	12842	188	7	4	4438	4	PTPRK	6	128841478	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	44278331	128841478	42273589	72	25684										
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245447	137245447	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctgttcattgccggcgtggtGgtgaacaccctgggctctat	13	11	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:137245447G>T	ENST00000331858.4	+	2	1029	c.864G>T	c.(862-864)gtG>gtT	p.V288V		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	288					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		CCGGCGTGGTGGTGAACACCC	0.597																																																0			6											74	68	70					6																	137245447		2203	4300	6503	137287140	SO:0001819	synonymous_variant	340146				CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.864G>T	6.37:g.137245447G>T			137287140	B4DI58|Q5QNZ6|Q6NX71	Silent	SNP	ENST00000331858.4	37	CCDS34544.1																																																																																				0.597	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		T	137245447	G	T	137245447	2	4	94	1	0	0	0	0	0	0	0	1	14620	1335	47	2		2	SLC35D3	6	137245447	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	8403969	137245447	33869620	73	25685										
UTRN	7402	hgsc.bcm.edu	37	chr6	144758846	144758846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctgctgaatgctagatgggAggctcttagggtggagagta	16	6	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:144758846A>G	ENST00000367545.3	+	10	1205	c.1205A>G	c.(1204-1206)gAg>gGg	p.E402G		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	402	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GCTAGATGGGAGGCTCTTAGG	0.488																																																0			6											116	101	106					6																	144758846		2203	4300	6503	144800539	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1205A>G	6.37:g.144758846A>G	ENSP00000356515:p.Glu402Gly		144800539	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.755333	0.89843	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.55234	0.53	5.36	5.36	0.76844	.	0.000000	0.50627	D	0.000120	T	0.66973	0.2844	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71097	-0.4691	10	0.52906	T	0.07	.	15.3449	0.74327	1.0:0.0:0.0:0.0	.	402	P46939	UTRO_HUMAN	G	402	ENSP00000356515:E402G	ENSP00000356499:E402G	E	+	2	0	UTRN	144800539	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.339000	0.96797	2.034000	0.60081	0.533000	0.62120	GAG		0.488	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144758846	A	G	144758846	3	3	94	1	0	0	0	0	1	0	0	0	17143	304	11	4	1243	4	UTRN	6	144758846	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	7513399	144758846	26356221	74	25686										
MRPL18	29074	hgsc.bcm.edu	37	chr6	160211636	160211636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agcgatggcgcttcggtcgcGgttttgggggttgttctcgg	18	8	1	0	rs1128670	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr6:160211636G>A	ENST00000367034.4	+	1	139	c.17G>A	c.(16-18)cGg>cAg	p.R6Q	TCP1_ENST00000544255.1_5'Flank|MRPL18_ENST00000480842.1_3'UTR|TCP1_ENST00000392168.2_5'Flank|TCP1_ENST00000420894.2_5'Flank|TCP1_ENST00000321394.7_5'Flank|TCP1_ENST00000546023.1_5'Flank	NM_014161.3	NP_054880.2	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18	6			R -> Q (in dbSNP:rs1128670). {ECO:0000269|PubMed:11042152}.		rRNA import into mitochondrion (GO:0035928)|translation (GO:0006412)	extracellular space (GO:0005615)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	11		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		CTTCGGTCGCGGTTTTGGGGG	0.567													G|||	3330	0.664936	0.4818	0.8285	5008	,	,		16901	0.5873		0.7575	False		,,,				2504	0.7812															0			6						G	GLN/ARG	2293,2113	598.3+/-389.1	603,1087,513	108	95	100		17	4.5	0.2	6	dbSNP_86	100	6421,2179	711.0+/-405.8	2432,1557,311	yes	missense	MRPL18	NM_014161.3	43	3035,2644,824	AA,AG,GG		25.3372,47.9573,33.0002	probably-damaging	6/181	160211636	8714,4292	2203	4300	6503	160131626	SO:0001583	missense	29074			AF161556	CCDS5270.1	6q25.3	2012-09-13			ENSG00000112110	ENSG00000112110		"Mitochondrial ribosomal proteins / large subunits"	14477	protein-coding gene	gene with protein product		611831				11042152, 11551941	Standard	NM_014161		Approved	HSPC071	uc003qsw.4	Q9H0U6	OTTHUMG00000015942	ENST00000367034.4:c.17G>A	6.37:g.160211636G>A	ENSP00000356001:p.Arg6Gln		160131626	Q5TAP9|Q9NZW8	Missense_Mutation	SNP	ENST00000367034.4	37	CCDS5270.1	1445	0.6616300366300366	246	0.5	295	0.8149171270718232	324	0.5664335664335665	580	0.7651715039577837	G	14.16	2.452584	0.43531	0.520427	0.746628	ENSG00000112110	ENST00000367034	T	0.48522	0.81	5.32	4.46	0.54185	.	0.336411	0.26769	N	0.022593	T	0.28267	0.0698	M	0.67953	2.075	0.80722	P	0.0	B	0.22851	0.076	B	0.10450	0.005	T	0.27806	-1.0063	9	0.54805	T	0.06	-12.246	9.8104	0.40820	0.0921:0.0:0.9079:0.0	rs1128670;rs2273821;rs3177363;rs61436974;rs2273821	6	Q9H0U6	RM18_HUMAN	Q	6	ENSP00000356001:R6Q	ENSP00000356001:R6Q	R	+	2	0	MRPL18	160131626	0.116000	0.22171	0.193000	0.23327	0.127000	0.20565	1.266000	0.33039	1.482000	0.48325	-0.140000	0.14226	CGG		0.567	MRPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042925.1			A	160211636	G	A	160211636	3	1	94	1	0	0	0	0	1	0	0	0	9813	1116	39	1	19	1	MRPL18	6	160211636	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	15452790	160211636	10903431	75	25687										
ADAP1	11033	hgsc.bcm.edu	37	chr7	943860	943860	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggccgatcttggccggctggAaggtggcgttcaggtgctcg	18	10	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:943860A>G	ENST00000265846.5	-	6	770	c.551T>C	c.(550-552)tTc>tCc	p.F184S	ADAP1_ENST00000539900.1_Missense_Mutation_p.F195S|ADAP1_ENST00000449296.2_Missense_Mutation_p.F112S|ADAP1_ENST00000463358.1_5'UTR	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	184	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						GGCCGGCTGGAAGGTGGCGTT	0.612																																																0			7											148	121	130					7																	943860		2202	4297	6499	910386	SO:0001583	missense	11033			AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16486	protein-coding gene	gene with protein product		608114	"centaurin, alpha 1"	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.551T>C	7.37:g.943860A>G	ENSP00000265846:p.Phe184Ser		910386	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	37	CCDS5318.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	19.78|19.78	3.891149|3.891149	0.72524|0.72524	.|.	.|.	ENSG00000105963|ENSG00000105963	ENST00000265846;ENST00000449296;ENST00000449929;ENST00000539900;ENST00000453175|ENST00000446141;ENST00000437486;ENST00000453823	T;T;T|.	0.28255|.	1.62;1.62;1.62|.	4.29|4.29	4.29|4.29	0.51040|0.51040	Pleckstrin homology-type (1);Pleckstrin homology domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78368|0.78368	0.4272|0.4272	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.983;1.0|.	T|T	0.81982|0.81982	-0.0683|-0.0683	10|5	0.42905|.	T|.	0.14|.	-30.6721|-30.6721	13.5666|13.5666	0.61822|0.61822	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	89;184|.	B4DUZ7;O75689|.	.;ADAP1_HUMAN|.	S|P	184;112;10;195;17|167;118;127	ENSP00000265846:F184S;ENSP00000407267:F112S;ENSP00000442682:F195S|.	ENSP00000265846:F184S|.	F|S	-|-	2|1	0|0	ADAP1|ADAP1	910386|910386	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.548000|0.548000	0.35241|0.35241	6.906000|6.906000	0.75719|0.75719	1.797000|1.797000	0.52628|0.52628	0.454000|0.454000	0.30748|0.30748	TTC|TCC		0.612	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869		G	943860	A	G	943860	3	3	94	1	0	0	0	0	1	0	0	0	279	246	9	4	597	4	ADAP1	7	943860	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10		943860	158194803	76	25688										
C7orf27	221927	hgsc.bcm.edu	37	chr7	2578974	2578974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agccaagagtgcgcatctgaAgtcagcctgtcctgggggtc	14	11	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:2578974A>G	ENST00000340611.4	-	13	1865	c.1609T>C	c.(1609-1611)Ttc>Ctc	p.F537L	BRAT1_ENST00000473879.1_Intron	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	537					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GCGCATCTGAAGTCAGCCTGT	0.642																																																0			7											25	26	26					7																	2578974		2203	4299	6502	2545500	SO:0001583	missense	221927			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"BRCA1-associated protein required for ATM activation protein 1"	614506	"chromosome 7 open reading frame 27"	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1609T>C	7.37:g.2578974A>G	ENSP00000339637:p.Phe537Leu		2545500	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266857	0.59540	.	.	ENSG00000106009	ENST00000340611	T	0.34667	1.35	5.74	5.74	0.90152	Armadillo-like helical (1);Armadillo-type fold (1);	0.099224	0.64402	D	0.000002	T	0.62282	0.2415	M	0.79475	2.455	0.54753	D	0.999987	D	0.76494	0.999	D	0.80764	0.994	T	0.66709	-0.5855	10	0.72032	D	0.01	-32.5052	16.0213	0.80499	1.0:0.0:0.0:0.0	.	537	Q6PJG6	BRAT1_HUMAN	L	537	ENSP00000339637:F537L	ENSP00000339637:F537L	F	-	1	0	BRAT1	2545500	1.000000	0.71417	0.555000	0.28281	0.008000	0.06430	5.692000	0.68256	2.190000	0.69967	0.459000	0.35465	TTC		0.642	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		G	2578974	A	G	2578974	3	3	94	1	0	0	0	0	1	0	0	0	2388	72	3	4	864	4	C7orf27	7	2578974	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	1635114	2578974	156559689	77	25689										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4827330	4827330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctcctcccggccctggtggaCgctggcacagccctggagat	13	16	0	1	rs17135128	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:4827330C>T	ENST00000348624.4	+	11	1471	c.1377C>T	c.(1375-1377)gaC>gaT	p.D459D	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Silent_p.D459D	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	459					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGGTGGACGCTGGCACAG	0.692													C|||	408	0.0814696	0.0401	0.036	5008	,	,		15883	0.0496		0.0736	False		,,,				2504	0.2106															0			7						C		189,3981		5,179,1901	25	31	29		1377	-3.7	0	7	dbSNP_123	29	532,7742		19,494,3624	no	coding-synonymous	KIAA0415	NM_014855.2		24,673,5525	TT,TC,CC		6.4298,4.5324,5.794		459/808	4827330	721,11723	2085	4137	6222	4793856	SO:0001819	synonymous_variant	9907			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1377C>T	7.37:g.4827330C>T			4793856	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																				0.692	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4827330	C	T	4827330	2	4	94	1	0	0	0	0	0	0	0	1	8196	535	19	1		1	KIAA0415	7	4827330	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	2248356	4827330	154311333	78	25690										
SUN3	256979	hgsc.bcm.edu	37	chr7	48046774	48046774	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tccaggacctctgtgtggtcCgggtcctccacagggtctcc	12	15	2	0	rs150352113	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:48046774C>T	ENST00000297325.4	-	5	639	c.480G>A	c.(478-480)ccG>ccA	p.P160P	SUN3_ENST00000453192.2_Silent_p.P148P|SUN3_ENST00000395572.2_Silent_p.P160P|SUN3_ENST00000412142.1_Silent_p.P60P	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	160						integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTGTGTGGTCCGGGTCCTCCA	0.552													C|||	2	0.000399361	0	0.0014	5008	,	,		16503	0.001		0	False		,,,				2504	0															0			7						C	,	1,4405	2.1+/-5.4	0,1,2202	102	100	100		480,480	0.5	0	7	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SUN3	NM_001030019.1,NM_152782.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	160/358,160/358	48046774	1,13005	2203	4300	6503	48013299	SO:0001819	synonymous_variant	0			AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.480G>A	7.37:g.48046774C>T			48013299	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Silent	SNP	ENST00000297325.4	37	CCDS34636.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	3.303	-0.142565	0.06669	2.27E-4	0.0	ENSG00000164744	ENST00000453071	.	.	.	5.45	0.472	0.16758	.	.	.	.	.	T	0.34513	0.0900	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29488	-1.0010	4	.	.	.	.	9.2277	0.37416	0.0:0.6636:0.0:0.3364	.	.	.	.	Q	80	.	.	R	-	2	0	SUN3	48013299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.166000	0.09954	0.268000	0.21939	-1.063000	0.02288	CGG		0.552	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		T	48046774	C	T	48046774	2	4	94	1	0	0	0	0	0	0	0	1	15432	639	23	1		1	SUN3	7	48046774	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	43219444	48046774	111091889	79	25691										
C7orf64	84060	hgsc.bcm.edu	37	chr7	92158147	92158147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gatggcgtcgagcggcggggAgctagggagtttatttgatc	18	6	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:92158147A>G	ENST00000265732.5	+	1	61	c.20A>G	c.(19-21)gAg>gGg	p.E7G	RBM48_ENST00000481551.1_Missense_Mutation_p.E7G|PEX1_ENST00000248633.4_5'Flank|PEX1_ENST00000438045.1_5'Flank|PEX1_ENST00000428214.1_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	7						nucleus (GO:0005634)	RNA binding (GO:0003723)										AGCGGCGGGGAGCTAGGGAGT	0.557																																																0			7											61	65	64					7																	92158147		1963	4135	6098	91996083	SO:0001583	missense	84060			AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.20A>G	7.37:g.92158147A>G	ENSP00000265732:p.Glu7Gly		91996083	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Missense_Mutation	SNP	ENST00000265732.5	37	CCDS43615.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669555	0.47677	.	.	ENSG00000127993	ENST00000509224;ENST00000265732;ENST00000481551;ENST00000450580	.	.	.	4.77	4.77	0.60923	.	0.865247	0.10543	N	0.662413	T	0.27313	0.0670	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31125	0.255;0.003;0.309	B;B;B	0.27608	0.037;0.003;0.081	T	0.27226	-1.0080	9	0.54805	T	0.06	-3.2874	2.9757	0.05936	0.6301:0.1482:0.0792:0.1424	.	7;7;7	B4DGJ6;B7Z2K5;Q5RL73	.;.;CG064_HUMAN	G	9;7;7;7	.	ENSP00000265732:E7G	E	+	2	0	C7orf64	91996083	0.000000	0.05858	0.005000	0.12908	0.018000	0.09664	0.745000	0.26259	2.127000	0.65507	0.459000	0.35465	GAG		0.557	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		G	92158147	A	G	92158147	3	3	94	1	0	0	0	0	1	0	0	0	2416	304	11	4	22	4	C7orf64	7	92158147	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	44111373	92158147	66980516	80	25692										
PILRB	29990	hgsc.bcm.edu	37	chr7	99955934	99955934	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aagaacaaggccatgggtcgGcccctgctgctgcccctgct	12	15	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:99955934G>C	ENST00000452089.1	+	6	1068	c.9G>C	c.(7-9)cgG>cgC	p.R3R	PILRB_ENST00000610247.1_Silent_p.R3R|PILRB_ENST00000444073.1_Silent_p.R3R|PILRB_ENST00000448382.1_Silent_p.R125R|STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA|PILRB_ENST00000609309.1_Silent_p.R3R			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	3					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCATGGGTCGGCCCCTGCTGC	0.662																																																0			7											57	69	65					7																	99955934		2203	4300	6503	99793870	SO:0001819	synonymous_variant	29990			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"Immunoglobulin superfamily / V-set domain containing"	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.9G>C	7.37:g.99955934G>C			99793870	Q69YF9|Q9HBS0	Silent	SNP	ENST00000452089.1	37	CCDS43622.1																																																																																				0.662	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238		C	99955934	G	C	99955934	2	2	94	1	0	0	0	0	0	0	0	1	11957	1190	42	5		5	PILRB	7	99955934	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	7797787	99955934	59182729	81	25693										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100148130	100148130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aggaaaaatatgagaagaagAgatggtaaggagtaggaaag	15	0	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:100148130A>G	ENST00000300176.4	+	3	549	c.427A>G	c.(427-429)Aga>Gga	p.R143G	AGFG2_ENST00000474713.1_3'UTR|AGFG2_ENST00000262935.4_Missense_Mutation_p.R143G	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	143	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TGAGAAGAAGAGATGGTAAGG	0.418																																																0			7											85	85	85					7																	100148130		2203	4300	6503	99986066	SO:0001583	missense	3268			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.427A>G	7.37:g.100148130A>G	ENSP00000300176:p.Arg143Gly		99986066	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.022174	0.75275	.	.	ENSG00000106351	ENST00000300176;ENST00000262935	T;T	0.45668	0.89;0.89	6.14	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.66177	0.2763	M	0.88105	2.93	0.36632	D	0.876369	D;D	0.63046	0.992;0.991	P;D	0.66602	0.859;0.945	T	0.77046	-0.2733	10	0.87932	D	0	-17.6728	11.6632	0.51358	0.6685:0.3315:0.0:0.0	.	143;143	O95081-2;O95081	.;AGFG2_HUMAN	G	143	ENSP00000300176:R143G;ENSP00000262935:R143G	ENSP00000262935:R143G	R	+	1	2	AGFG2	99986066	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.598000	0.36740	1.107000	0.41642	0.529000	0.55759	AGA		0.418	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		G	100148130	A	G	100148130	3	3	94	1	0	0	0	0	1	0	0	0	381	296	11	4	437	4	AGFG2	7	100148130	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	192196	100148130	58990533	82	25694										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113517815	113517815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	actctttttgtctaccctctTcccaggatagccaggacaat	6	13	3	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:113517815T>C	ENST00000284601.3	-	4	3400	c.3332A>G	c.(3331-3333)gAa>gGa	p.E1111G		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	1111					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TCTACCCTCTTCCCAGGATAG	0.353																																																0			7											91	91	91					7																	113517815		2203	4299	6502	113305051	SO:0001583	missense	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.3332A>G	7.37:g.113517815T>C	ENSP00000284601:p.Glu1111Gly		113305051	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.085961	0.55861	.	.	ENSG00000154415	ENST00000284601	T	0.27402	1.67	5.85	3.36	0.38483	.	0.576432	0.16992	N	0.191244	T	0.51466	0.1676	M	0.72894	2.215	0.33582	D	0.59999	D	0.89917	1.0	D	0.85130	0.997	T	0.62025	-0.6941	10	0.87932	D	0	-2.5981	9.0262	0.36232	0.1247:0.0:0.1308:0.7445	.	1111	Q16821	PPR3A_HUMAN	G	1111	ENSP00000284601:E1111G	ENSP00000284601:E1111G	E	-	2	0	PPP1R3A	113305051	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.710000	0.47169	0.404000	0.25506	0.528000	0.53228	GAA		0.353	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113517815	T	C	113517815	3	2	94	1	0	0	0	0	1	0	0	0	12405	1783	62	4	40	4	PPP1R3A	7	113517815	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	13369685	113517815	45620848	83	25695										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122255279	122255279	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tctgtctgaagtttttctccTtccacttccattgtacagta	5	11	3	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:122255279T>G	ENST00000449022.2	-	6	1198	c.1179A>C	c.(1177-1179)gaA>gaC	p.E393D	CADPS2_ENST00000334010.7_Missense_Mutation_p.E393D|CADPS2_ENST00000412584.2_Missense_Mutation_p.E393D|CADPS2_ENST00000313070.7_Missense_Mutation_p.E393D	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	393	C2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GTTTTTCTCCTTCCACTTCCA	0.373																																																0			7											74	69	71					7																	122255279		1872	4100	5972	122042515	SO:0001583	missense	93664				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.1179A>C	7.37:g.122255279T>G	ENSP00000398481:p.Glu393Asp		122042515	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.245889	0.59103	.	.	ENSG00000081803	ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.59	3.27	0.37495	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	N	0.20401	0.57	0.40204	D	0.977544	B;D;D	0.64830	0.04;0.994;0.99	B;D;D	0.73380	0.016;0.97;0.98	T	0.60826	-0.7186	10	0.25106	T	0.35	-21.1829	9.2601	0.37608	0.0:0.2082:0.0:0.7918	.	393;393;393	Q86UW7-2;Q86UW7;Q86UW7-3	.;CAPS2_HUMAN;.	D	393;393;393;360;393;393	ENSP00000325581:E393D;ENSP00000333940:E393D;ENSP00000400401:E393D;ENSP00000398481:E393D	ENSP00000325581:E393D	E	-	3	2	CADPS2	122042515	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.360000	0.34125	0.972000	0.38314	0.533000	0.62120	GAA		0.373	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		G	122255279	T	G	122255279	3	3	94	1	0	0	0	0	1	0	0	0	2577	1606	56	4	2855	4	CADPS2	7	122255279	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	8737464	122255279	36883384	84	25696										
AKR1B1	231	hgsc.bcm.edu	37	chr7	134136461	134136461	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcgatgtggcggtacccgacGtcaatggccaccttcacggc	12	14	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:134136461G>A	ENST00000285930.4	-	2	190	c.111C>T	c.(109-111)gaC>gaT	p.D37D	AKR1B1_ENST00000489022.1_5'UTR	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	37					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	GGTACCCGACGTCAATGGCCA	0.592																																																0			7											70	56	61					7																	134136461		2203	4300	6503	133787001	SO:0001819	synonymous_variant	231			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.111C>T	7.37:g.134136461G>A			133787001	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Silent	SNP	ENST00000285930.4	37	CCDS5831.1																																																																																				0.592	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		A	134136461	G	A	134136461	2	1	94	1	0	0	0	0	0	0	0	1	466	1136	40	1		1	AKR1B1	7	134136461	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	11881182	134136461	25002202	85	25697										
CDK5	1020	hgsc.bcm.edu	37	chr7	150752165	150752165	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cattgccgggaaaaagaggcCgcccagcattggccagctct	12	13	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr7:150752165C>T	ENST00000485972.1	-	9	1280	c.599G>A	c.(598-600)cGg>cAg	p.R200Q	CDK5_ENST00000297518.4_Missense_Mutation_p.R168Q	NM_004935.3	NP_004926.1	Q00535	CDK5_HUMAN	cyclin-dependent kinase 5	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|behavioral response to cocaine (GO:0048148)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|central nervous system neuron development (GO:0021954)|cerebellar cortex formation (GO:0021697)|corpus callosum development (GO:0022038)|cortical actin cytoskeleton organization (GO:0030866)|dendrite morphogenesis (GO:0048813)|embryo development (GO:0009790)|hippocampus development (GO:0021766)|intracellular protein transport (GO:0006886)|layer formation in cerebral cortex (GO:0021819)|motor neuron axon guidance (GO:0008045)|negative regulation of axon extension (GO:0030517)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of proteolysis (GO:0045861)|negative regulation of synaptic plasticity (GO:0031914)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|nucleocytoplasmic transport (GO:0006913)|oligodendrocyte differentiation (GO:0048709)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphorylation (GO:0016310)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein targeting to membrane (GO:0090314)|protein autophosphorylation (GO:0046777)|protein localization to synapse (GO:0035418)|receptor catabolic process (GO:0032801)|receptor clustering (GO:0043113)|regulated secretory pathway (GO:0045055)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|rhythmic process (GO:0048511)|Schwann cell development (GO:0014044)|sensory perception of pain (GO:0019233)|serine phosphorylation of STAT3 protein (GO:0033136)|skeletal muscle tissue development (GO:0007519)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)|visual learning (GO:0008542)	axon (GO:0030424)|cell junction (GO:0030054)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activator activity (GO:0030549)|ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|ErbB-2 class receptor binding (GO:0005176)|ErbB-3 class receptor binding (GO:0043125)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			central_nervous_system(1)|endometrium(2)|lung(5)|urinary_tract(1)	9		Breast(660;0.159)|Ovarian(593;0.182)	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.008)|Lung(243;0.00942)|BRCA - Breast invasive adenocarcinoma(188;0.242)		AAAAAGAGGCCGCCCAGCATT	0.567																																																0			7											44	47	46					7																	150752165		1969	4148	6117	150383098	SO:0001583	missense	1020			X66364	CCDS47748.1, CCDS55184.1	7q36	2011-11-08			ENSG00000164885	ENSG00000164885		"Cyclin-dependent kinases"	1774	protein-coding gene	gene with protein product		123831				8275715, 1639063	Standard	NM_001164410		Approved	PSSALRE	uc003wir.2	Q00535	OTTHUMG00000158414	ENST00000485972.1:c.599G>A	7.37:g.150752165C>T	ENSP00000419782:p.Arg200Gln		150383098	A1XKG3	Missense_Mutation	SNP	ENST00000485972.1	37	CCDS47748.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.780274	0.70222	.	.	ENSG00000164885	ENST00000485972;ENST00000297518	T;T	0.66280	-0.2;-0.2	5.06	5.06	0.68205	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52224	0.1721	L	0.35414	1.06	0.58432	D	0.999997	B;B	0.23990	0.095;0.062	B;B	0.16289	0.015;0.015	T	0.51647	-0.8679	10	0.52906	T	0.07	-18.7595	15.9676	0.79985	0.0:1.0:0.0:0.0	.	168;200	Q00535-2;Q00535	.;CDK5_HUMAN	Q	200;168	ENSP00000419782:R200Q;ENSP00000297518:R168Q	ENSP00000297518:R168Q	R	-	2	0	CDK5	150383098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.341000	0.72977	2.619000	0.88677	0.655000	0.94253	CGG		0.567	CDK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350965.3			T	150752165	C	T	150752165	3	4	94	1	0	0	0	0	1	0	0	0	3148	652	23	1	295	1	CDK5	7	150752165	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	16615704	150752165	8386498	86	25698										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77765319	77765319	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctcctcctcctcctcctccTccccccccacctcctccacc	0	30	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr8:77765319T>C	ENST00000521891.2	+	10	6610	c.6162T>C	c.(6160-6162)ccT>ccC	p.P2054P	ZFHX4_ENST00000455469.2_Silent_p.P2009P|ZFHX4_ENST00000518282.1_Silent_p.P2028P|ZFHX4_ENST00000050961.6_Silent_p.P2009P	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2009					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ctcctcctcctccccccccac	0.592										HNSCC(33;0.089)																																						0			8											3	3	3					8																	77765319		1385	3182	4567	77927874	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6162T>C	8.37:g.77765319T>C			77927874	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.592	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77765319	T	C	77765319	2	2	94	1	0	0	0	0	0	0	0	1	17674	1538	54	4		4	ZFHX4	8	77765319	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10		77765319	68598703	87	25699										
NBN	4683	hgsc.bcm.edu	37	chr8	90990528	90990528	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tctggctttacaattggacgTccacaaatgagtgcacatat	8	9	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr8:90990528T>C	ENST00000265433.3	-	5	658	c.504A>G	c.(502-504)ggA>ggG	p.G168G	NBN_ENST00000409330.1_Silent_p.G86G	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	168	BRCT.|Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)	p.G168G(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			CAATTGGACGTCCACAAATGA	0.299								Homologous recombination																																								1	Substitution - coding silent(1)	central_nervous_system(1)	8											79	78	79					8																	90990528		2203	4300	6503	91059704	SO:0001819	synonymous_variant	9048			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.504A>G	8.37:g.90990528T>C			91059704	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	37	CCDS6249.1																																																																																				0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90990528	T	C	90990528	2	2	94	1	0	0	0	0	0	0	0	1	10221	1654	58	4		4	NBN	8	90990528	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	13225209	90990528	55373494	88	25700										
PGCP	10404	hgsc.bcm.edu	37	chr8	97797188	97797188	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ttatccctgtgctctgggaaAgctatatgcaagaatggcat	10	8	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr8:97797188A>G	ENST00000220763.5	+	2	273	c.63A>G	c.(61-63)aaA>aaG	p.K21K		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	21					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										GCTCTGGGAAAGCTATATGCA	0.373																																																0			8											94	96	95					8																	97797188		2203	4300	6503	97866364	SO:0001819	synonymous_variant	10404			AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.63A>G	8.37:g.97797188A>G			97866364	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Silent	SNP	ENST00000220763.5	37	CCDS6273.1																																																																																				0.373	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		G	97797188	A	G	97797188	2	3	94	1	0	0	0	0	0	0	0	1	11817	69	3	4		4	PGCP	8	97797188	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	6806660	97797188	48566834	89	25701										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125131953	125131953	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atcattgctttcattctcatCatcctcatcatcttcctcgt	2	14	7	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr8:125131953C>T	ENST00000522917.1	+	41	5702	c.5496C>T	c.(5494-5496)atC>atT	p.I1832I	FER1L6_ENST00000399018.1_Silent_p.I1832I|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1832						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			tcattctcatcatcctcatca	0.468																																																0			8											230	244	239					8																	125131953		2083	4204	6287	125201134	SO:0001819	synonymous_variant	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.5496C>T	8.37:g.125131953C>T			125201134		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																				0.468	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125131953	C	T	125131953	2	4	94	1	0	0	0	0	0	0	0	1	5834	816	29	3		3	FER1L6	8	125131953	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	27334765	125131953	21232069	90	25702										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144671244	144671244	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gcttcgaggcaccaggccacCcgcagggcctcggcagcgtg	15	16	0	0	rs4874160	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr8:144671244C>A	ENST00000529272.1	-	2	397				EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000442189.2_Silent_p.R336R|EEF1D_ENST00000423316.2_Silent_p.R336R|EEF1D_ENST00000532741.1_Silent_p.R386R|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000395119.3_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			ACCAGGCCACCCGCAGGGCCT	0.662													G|||	3218	0.642572	0.4879	0.7536	5008	,	,		16212	0.5149		0.8499	False		,,,				2504	0.6912															0			8						G	,,,,,,	2422,1970		730,962,504	22	21	22		1008,,,,,,1008	2.6	1	8	dbSNP_111	22	7854,740		3631,592,74	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	EEF1D	NM_001130053.2,NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1,NM_001960.4,NM_032378.4	,,,,,,	4361,1554,578	AA,AC,CC		8.6107,44.8543,20.8686	,,,,,,	336/648,,,,,,336/648	144671244	10276,2710	2196	4297	6493	144742387	SO:0001627	intron_variant	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.4-2225G>T	8.37:g.144671244C>A			144742387	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																				0.662	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		A	144671244	C	A	144671244	1	1	94	0	1	0	0	0	0	0	0	0	4937	610	22	2		2	EEF1D	8	144671244	Intron	SNP	C	TCGA-DC-5869-01A-01D-1657-10	19539291	144671244	1692778	91	25703										
JAK2	3717	hgsc.bcm.edu	37	chr9	5077468	5077468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgcagatattctggttcaggAgtttgtaaaatttggatcac	10	5	3	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:5077468A>G	ENST00000381652.3	+	15	2374	c.1880A>G	c.(1879-1881)gAg>gGg	p.E627G	AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000539801.1_Missense_Mutation_p.E627G|JAK2_ENST00000544510.1_Missense_Mutation_p.E478G	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	627	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTGGTTCAGGAGTTTGTAAAA	0.239		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											9	10	10					9																	5077468		2019	4157	6176	5067468	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1880A>G	9.37:g.5077468A>G	ENSP00000371067:p.Glu627Gly		5067468	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545734	0.86022	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.59083	0.29;0.29;0.29	5.98	5.98	0.97165	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84911	0.5577	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90262	0.4301	10	0.87932	D	0	-18.9686	16.4696	0.84102	1.0:0.0:0.0:0.0	.	627	O60674	JAK2_HUMAN	G	627;627;478	ENSP00000440387:E627G;ENSP00000371067:E627G;ENSP00000443103:E478G	ENSP00000371067:E627G	E	+	2	0	JAK2	5067468	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.878000	0.92393	2.289000	0.77006	0.482000	0.46254	GAG		0.239	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5077468	A	G	5077468	3	3	94	1	0	0	0	0	1	0	0	0	7959	304	11	4	1930	4	JAK2	9	5077468	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10		5077468	136135963	92	25704										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32541758	32541758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tattgtcacattctgtatccTcctttacttcagaatcctta	3	11	3	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:32541758T>C	ENST00000360538.2	-	3	2881	c.2765A>G	c.(2764-2766)gAg>gGg	p.E922G	TOPORS_ENST00000379858.1_Missense_Mutation_p.E857G	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	922				E -> G (in Ref. 1; AAD23379). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TTCTGTATCCTCCTTTACTTC	0.383																																																0			9											206	189	195					9																	32541758		2203	4300	6503	32531758	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2765A>G	9.37:g.32541758T>C	ENSP00000353735:p.Glu922Gly		32531758	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.208130	0.39003	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.17054	2.3;2.31	5.81	4.72	0.59763	.	0.145335	0.32328	N	0.006256	T	0.11410	0.0278	N	0.14661	0.345	0.23126	N	0.998251	B	0.24186	0.099	B	0.24155	0.051	T	0.21008	-1.0258	10	0.72032	D	0.01	-5.9919	11.6529	0.51299	0.0:0.0:0.1833:0.8167	.	922	Q9NS56	TOPRS_HUMAN	G	922;857	ENSP00000353735:E922G;ENSP00000369187:E857G	ENSP00000353735:E922G	E	-	2	0	TOPORS	32531758	0.944000	0.32072	0.883000	0.34634	0.402000	0.30811	1.312000	0.33574	1.115000	0.41800	0.528000	0.53228	GAG		0.383	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32541758	T	C	32541758	3	2	94	1	0	0	0	0	1	0	0	0	16410	1551	54	4	376	4	TOPORS	9	32541758	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	27464290	32541758	108671673	93	25705										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72840712	72840712	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atcaataagaagtgatattgCcattgatgatgttaaatttc	7	4	1	4			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:72840712C>A	ENST00000377182.4	+	13	2575	c.1958C>A	c.(1957-1959)gCc>gAc	p.A653D	SMC5-AS1_ENST00000594708.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	653	MAM 4. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						AGTGATATTGCCATTGATGAT	0.333																																																0			9											81	82	82					9																	72840712		2202	4299	6501	72030532	SO:0001583	missense	256691			BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.1958C>A	9.37:g.72840712C>A	ENSP00000366387:p.Ala653Asp		72030532	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	37	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705201	0.68615	.	.	ENSG00000165072	ENST00000377182	T	0.03441	3.93	6.08	6.08	0.98989	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.046059	0.85682	D	0.000000	T	0.28001	0.0690	H	0.94964	3.605	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.11717	-1.0576	10	0.87932	D	0	-17.1594	16.0688	0.80909	0.0:0.8668:0.1332:0.0	.	653	Q7Z304	MAMC2_HUMAN	D	653	ENSP00000366387:A653D	ENSP00000366387:A653D	A	+	2	0	MAMDC2	72030532	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	4.375000	0.59549	2.894000	0.99253	0.655000	0.94253	GCC		0.333	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		A	72840712	C	A	72840712	3	1	94	1	0	0	0	0	1	0	0	0	9233	739	26	2	2008	2	MAMDC2	9	72840712	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	40298954	72840712	68372719	94	25706										
SMC2	10592	hgsc.bcm.edu	37	chr9	106889739	106889739	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	catcagcaaacataaacgggAggctgaagatggtgctgcaa	12	8	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:106889739A>G	ENST00000286398.7	+	20	3056	c.2768A>G	c.(2767-2769)gAg>gGg	p.E923G	SMC2_ENST00000303219.8_Missense_Mutation_p.E923G|SMC2_ENST00000374787.3_Missense_Mutation_p.E923G|SMC2_ENST00000374793.3_Missense_Mutation_p.E923G	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	923					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						CATAAACGGGAGGCTGAAGAT	0.343																																																0			9											131	123	126					9																	106889739		2203	4300	6503	105929560	SO:0001583	missense	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2768A>G	9.37:g.106889739A>G	ENSP00000286398:p.Glu923Gly		105929560	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265727	0.59540	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.84	5.84	0.93424	RecF/RecN/SMC (1);	0.094159	0.64402	D	0.000001	T	0.80444	0.4624	M	0.82132	2.575	0.50813	D	0.999896	B	0.21309	0.054	B	0.30316	0.114	T	0.76650	-0.2881	10	0.33940	T	0.23	-9.511	15.0453	0.71822	1.0:0.0:0.0:0.0	.	923	O95347	SMC2_HUMAN	G	923	ENSP00000286398:E923G;ENSP00000363925:E923G;ENSP00000306152:E923G;ENSP00000363919:E923G	ENSP00000286398:E923G	E	+	2	0	SMC2	105929560	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.801000	0.75170	2.229000	0.72834	0.528000	0.53228	GAG		0.343	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			G	106889739	A	G	106889739	3	3	94	1	0	0	0	0	1	0	0	0	14820	304	11	4	2842	4	SMC2	9	106889739	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	34049027	106889739	34323692	95	25707										
SETX	23064	hgsc.bcm.edu	37	chr9	135150792	135150792	+	Silent	SNP	A	A	G													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atcaccagttttatttcttgAacatttatatatgagctaaa							TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:135150792A>G	ENST00000224140.5	-	23	7133	c.6951T>C	c.(6949-6951)gtT>gtC	p.V2317V	SETX_ENST00000393220.1_Silent_p.V2317V|SETX_ENST00000372169.2_Silent_p.V2317V|SETX_ENST00000477049.1_5'Flank	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2317					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTATTTCTTGAACATTTATAT	0.308																																																0			9											81	78	79					9																	135150792		2203	4298	6501	134140613	SO:0001819	synonymous_variant	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.6951T>C	9.37:g.135150792A>G			134140613	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																				0.308	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135150792	A	G	135150792	2	3	94	1	0	0	0	0	0	0	0	1	14178	233	9	4		4	SETX	9	135150792	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	28261053	135150792	6062639	96	25708	34	2								
SETX	23064	hgsc.bcm.edu	37	chr9	135150794	135150794	+	Missense_Mutation	SNP	C	C	A													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	caccagttttatttcttgaaCatttatatatgagctaaaca							TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:135150794C>A	ENST00000224140.5	-	23	7131	c.6949G>T	c.(6949-6951)Gtt>Ttt	p.V2317F	SETX_ENST00000393220.1_Missense_Mutation_p.V2317F|SETX_ENST00000372169.2_Missense_Mutation_p.V2317F|SETX_ENST00000477049.1_5'Flank	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2317					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATTTCTTGAACATTTATATAT	0.308																																																0			9											81	78	79					9																	135150794		2203	4298	6501	134140615	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.6949G>T	9.37:g.135150794C>A	ENSP00000224140:p.Val2317Phe		134140615	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	9.582	1.123934	0.20959	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.76	-2.82	0.05787	.	0.755427	0.12249	N	0.485788	D	0.84037	0.5384	L	0.46741	1.465	0.30635	N	0.757027	B;P;P	0.45634	0.231;0.863;0.646	B;B;B	0.43990	0.325;0.438;0.363	T	0.78173	-0.2307	10	0.09590	T	0.72	.	0.7862	0.01049	0.2032:0.2108:0.179:0.4069	.	2317;2317;2317	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	F	2317;559;2317;2317	ENSP00000224140:V2317F;ENSP00000409143:V559F;ENSP00000361242:V2317F;ENSP00000376913:V2317F	ENSP00000224140:V2317F	V	-	1	0	SETX	134140615	0.988000	0.35896	0.870000	0.34147	0.826000	0.46750	0.142000	0.16096	-0.482000	0.06782	0.555000	0.69702	GTT		0.308	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		A	135150794	C	A	135150794	3	1	94	1	0	0	0	0	1	0	0	0	14178	478	17	2	1100	2	SETX	9	135150794	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	2	135150794	6062637	97	25709	34	2								
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139273295	139273295	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	caggggctgtgccctcggccTctgagaagacaggagcgagg	17	11	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr9:139273295T>C	ENST00000298532.2	-	21	3352	c.2984A>G	c.(2983-2985)gAg>gGg	p.E995G		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GCCCTCGGCCTCTGAGAAGAC	0.652																																																0			9											17	21	20					9																	139273295		2193	4296	6489	138393116	SO:0001583	missense	6621			AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2984A>G	9.37:g.139273295T>C	ENSP00000298532:p.Glu995Gly		138393116		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	T	0.197	-1.048232	0.01981	.	.	ENSG00000165684	ENST00000298532	T	0.23754	1.89	2.5	-1.25	0.09405	.	7.452280	0.00166	N	0.000003	T	0.06735	0.0172	N	0.00483	-1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18304	-1.0341	10	0.15952	T	0.53	-0.3848	2.5239	0.04687	0.2517:0.4333:0.0:0.315	.	995	Q5SXM2	SNPC4_HUMAN	G	995	ENSP00000298532:E995G	ENSP00000298532:E995G	E	-	2	0	SNAPC4	138393116	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.589000	0.05767	-0.190000	0.10465	-0.696000	0.03686	GAG		0.652	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		C	139273295	T	C	139273295	3	2	94	1	0	0	0	0	1	0	0	0	14874	1551	54	4	1433	4	SNAPC4	9	139273295	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	4122501	139273295	1940136	98	25710										
ADARB2	105	hgsc.bcm.edu	37	chr10	1230968	1230968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccccggctggcgcgcctcggCgtcactcacgcctgtcgggg	15	18	2	0	rs2271275	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:1230968C>T	ENST00000381312.1	-	9	2201	c.1876G>A	c.(1876-1878)Gcc>Acc	p.A626T	ADARB2_ENST00000381305.1_Missense_Mutation_p.A28T|ADARB2_ENST00000381310.3_Missense_Mutation_p.A135T	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	626	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.		A -> T (in dbSNP:rs2271275). {ECO:0000269|PubMed:15489334}.		mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CGCGCCTCGGCGTCACTCACG	0.667													C|||	2720	0.543131	0.2504	0.5115	5008	,	,		15505	0.6696		0.6809	False		,,,				2504	0.6892															0			10						C	THR/ALA	1422,2984		224,974,1005	22	23	23		1876	4.8	0	10	dbSNP_100	23	5866,2730		2007,1852,439	yes	missense	ADARB2	NM_018702.3	58	2231,2826,1444	TT,TC,CC		31.759,32.2742,43.9471	benign	626/740	1230968	7288,5714	2203	4298	6501	1220968	SO:0001583	missense	105			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1876G>A	10.37:g.1230968C>T	ENSP00000370713:p.Ala626Thr		1220968	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	1213	0.5554029304029304	119	0.241869918699187	203	0.5607734806629834	372	0.6503496503496503	519	0.6846965699208444	C	13.59	2.281430	0.40394	0.322742	0.68241	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.93859	-3.3;-3.3;-3.3	4.81	4.81	0.61882	Adenosine deaminase/editase (3);	0.168400	0.51477	D	0.000099	T	0.00012	0.0000	L	0.53617	1.68	0.09310	P	0.99999836182	B;B;P	0.38223	0.158;0.416;0.623	B;B;B	0.42112	0.098;0.08;0.376	T	0.45454	-0.9260	9	0.34782	T	0.22	-20.7549	17.8992	0.88898	0.0:1.0:0.0:0.0	rs2271275;rs57620546;rs2271275	626;28;135	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	T	626;135;28	ENSP00000370713:A626T;ENSP00000370711:A135T;ENSP00000370706:A28T	ENSP00000370706:A28T	A	-	1	0	ADARB2	1220968	0.631000	0.27164	0.046000	0.18839	0.138000	0.21146	1.502000	0.35704	2.220000	0.72140	0.561000	0.74099	GCC		0.667	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		T	1230968	C	T	1230968	3	4	94	1	0	0	0	0	1	0	0	0	283	768	27	1	351	1	ADARB2	10	1230968	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10		1230968	134303779	99	25711										
IL2RA	3559	hgsc.bcm.edu	37	chr10	6067847	6067847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aggacgagtggctagagtttCctgtacagagcatatagagt	13	6	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:6067847C>T	ENST00000379959.3	-	2	379	c.206G>A	c.(205-207)gGa>gAa	p.G69E	IL2RA_ENST00000256876.6_Missense_Mutation_p.G69E|RP11-536K7.5_ENST00000440436.1_RNA|IL2RA_ENST00000379954.1_Missense_Mutation_p.G69E	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	69	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GCTAGAGTTTCCTGTACAGAG	0.463																																																0			10											114	106	109					10																	6067847		2203	4300	6503	6107853	SO:0001583	missense	3559			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.206G>A	10.37:g.6067847C>T	ENSP00000369293:p.Gly69Glu		6107853	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	37	CCDS7076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.21|16.21	3.058078|3.058078	0.55325|0.55325	.|.	.|.	ENSG00000134460|ENSG00000134460	ENST00000447847|ENST00000379959;ENST00000397240;ENST00000379954;ENST00000256876	.|T;T;T	.|0.63096	.|-0.02;-0.02;-0.02	4.72|4.72	2.8|2.8	0.32819|0.32819	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.474816	.|0.18682	.|N	.|0.134136	T|T	0.65729|0.65729	0.2719|0.2719	L|L	0.49126|0.49126	1.545|1.545	0.09310|0.09310	N|N	1|1	.|P;D;D	.|0.59357	.|0.715;0.985;0.977	.|B;P;P	.|0.58928	.|0.313;0.848;0.666	T|T	0.54702|0.54702	-0.8254|-0.8254	5|10	.|0.56958	.|D	.|0.05	-31.3022|-31.3022	6.313|6.313	0.21174|0.21174	0.0:0.7127:0.187:0.1003|0.0:0.7127:0.187:0.1003	.|.	.|69;55;69	.|Q5W005;E9PF94;P01589	.|.;.;IL2RA_HUMAN	K|E	40|69;55;69;69	.|ENSP00000369293:G69E;ENSP00000369287:G69E;ENSP00000256876:G69E	.|ENSP00000256876:G69E	E|G	-|-	1|2	0|0	IL2RA|IL2RA	6107853|6107853	0.002000|0.002000	0.14202|0.14202	0.011000|0.011000	0.14972|0.14972	0.129000|0.129000	0.20672|0.20672	0.172000|0.172000	0.16704|0.16704	0.672000|0.672000	0.31204|0.31204	0.585000|0.585000	0.79938|0.79938	GAA|GGA		0.463	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		T	6067847	C	T	6067847	3	4	94	1	0	0	0	0	1	0	0	0	7707	855	30	3	640	3	IL2RA	10	6067847	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4836879	6067847	129466900	100	25712										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17369026	17369026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtcttacctaaaaacgaagtCggatttatctatttcagttc	6	8	3	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:17369026C>T	ENST00000377602.4	-	6	696	c.622G>A	c.(622-624)Gac>Aac	p.D208N		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	208					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						AAAACGAAGTCGGATTTATCT	0.393																																																0			10											97	94	95					10																	17369026		2203	4300	6503	17409032	SO:0001583	missense	338596				CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.622G>A	10.37:g.17369026C>T	ENSP00000366827:p.Asp208Asn		17409032	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.52|19.52	3.842802|3.842802	0.71488|0.71488	.|.	.|.	ENSG00000148488|ENSG00000148488	ENST00000377610;ENST00000377602|ENST00000440449	T|.	0.55413|.	0.52|.	4.95|4.95	4.03|4.03	0.46877|0.46877	.|.	0.201547|.	0.52532|.	D|.	0.000065|.	T|T	0.79251|0.79251	0.4414|0.4414	M|M	0.86953|0.86953	2.85|2.85	0.51233|0.51233	D|D	0.999916|0.999916	D|.	0.64830|.	0.994|.	P|.	0.48795|.	0.59|.	T|T	0.83074|0.83074	-0.0141|-0.0141	10|5	0.48119|.	T|.	0.1|.	-14.449|-14.449	15.6336|15.6336	0.76933|0.76933	0.0:0.8622:0.1378:0.0|0.0:0.8622:0.1378:0.0	.|.	208|.	P61647|.	SIA8F_HUMAN|.	N|Q	38;208|28	ENSP00000366827:D208N|.	ENSP00000366827:D208N|.	D|R	-|-	1|2	0|0	ST8SIA6|ST8SIA6	17409032|17409032	0.998000|0.998000	0.40836|0.40836	0.878000|0.878000	0.34440|0.34440	0.987000|0.987000	0.75469|0.75469	4.064000|4.064000	0.57506|0.57506	1.398000|1.398000	0.46701|0.46701	0.655000|0.655000	0.94253|0.94253	GAC|CGA		0.393	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17369026	C	T	17369026	3	4	94	1	0	0	0	0	1	0	0	0	15275	884	31	1	586	1	ST8SIA6	10	17369026	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	11301179	17369026	118165721	101	25713										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24809079	24809081	+	In_Frame_Del	DEL	GAA	GAA	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaagactttgttgaagacttGaagaaggactccacggcagc					rs543352000	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:24809079_24809081delGAA	ENST00000376454.3	+	11	2235_2237	c.2205_2207delGAA	c.(2203-2208)ttgaag>ttg	p.K737del	KIAA1217_ENST00000396446.1_In_Frame_Del_p.K420del|KIAA1217_ENST00000376462.1_In_Frame_Del_p.K657del|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000458595.1_In_Frame_Del_p.K702del|KIAA1217_ENST00000307544.6_In_Frame_Del_p.K420del|KIAA1217_ENST00000376451.2_In_Frame_Del_p.K420del|KIAA1217_ENST00000376452.3_In_Frame_Del_p.K702del|KIAA1217_ENST00000396445.1_In_Frame_Del_p.K420del	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	737					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TTGAAGACTTGAAGAAGGACTCC	0.567														4	0.000798722	0.003	0	5008	,	,		17393	0		0	False		,,,				2504	0															0			10							,,	47,4217		17,13,2102					,,	4.9	0.9			139	30,8224		15,0,4112	no	coding,coding,coding	KIAA1217	NM_019590.3,NM_001098501.1,NM_001098500.1	,,	32,13,6214	A1A1,A1R,RR		0.3635,1.1023,0.6151	,,	,,		77,12441				24849087	SO:0001651	inframe_deletion	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2205_2207delGAA	10.37:g.24809082_24809084delGAA	ENSP00000365637:p.Lys737del		24849085	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	In_Frame_Del	DEL	ENST00000376454.3	37	CCDS31165.1																																																																																				0.567	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		-	24809081	GAA	-	24809079	7	5	94	1	0	1	0	1	0	0	0	0	8237	1281	45	0	2247	0	KIAA1217	10	24809079	In_Frame_Del	DEL	GAA	TCGA-DC-5869-01A-01D-1657-10	7440053	24809079	110725668	102	25714										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26463233	26463233	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	acaggcccaggaggaagaagAtaaagcagcggtattcattc	12	8	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:26463233A>G	ENST00000265944.5	+	30	4206	c.4040A>G	c.(4039-4041)gAt>gGt	p.D1347G	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1347	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.		D -> H (in a renal clear cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GAGGAAGAAGATAAAGCAGCG	0.502																																																0			10											127	126	126					10																	26463233		2203	4300	6503	26503239	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4040A>G	10.37:g.26463233A>G	ENSP00000265944:p.Asp1347Gly		26503239	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.504989	0.44558	.	.	ENSG00000095777	ENST00000265944	T	0.79141	-1.24	1.34	-2.69	0.06022	.	0.406068	0.30791	N	0.008878	T	0.62490	0.2432	L	0.27053	0.805	0.36413	D	0.863826	P	0.43938	0.822	P	0.45998	0.5	T	0.59952	-0.7357	10	0.62326	D	0.03	.	3.391	0.07289	0.6171:0.231:0.1519:0.0	.	1347	Q8NEV4	MYO3A_HUMAN	G	1347	ENSP00000265944:D1347G	ENSP00000265944:D1347G	D	+	2	0	MYO3A	26503239	0.951000	0.32395	0.001000	0.08648	0.672000	0.39443	2.249000	0.43169	-1.303000	0.02332	-0.538000	0.04264	GAT		0.502	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26463233	A	G	26463233	3	3	94	1	0	0	0	0	1	0	0	0	10106	333	12	4	4150	4	MYO3A	10	26463233	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	1654154	26463233	109071514	103	25715										
RET	5979	hgsc.bcm.edu	37	chr10	43601939	43601939	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggacacctgggcccagcagaCcttccgggtggaacactggc	14	14	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:43601939C>G	ENST00000355710.3	+	5	1215	c.983C>G	c.(982-984)aCc>aGc	p.T328S	RET_ENST00000340058.5_Missense_Mutation_p.T328S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	328					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GCCCAGCAGACCTTCCGGGTG	0.642		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	0			10											55	47	50					10																	43601939		2202	4300	6502	42921945	SO:0001583	missense	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.983C>G	10.37:g.43601939C>G	ENSP00000347942:p.Thr328Ser		42921945	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.888955	0.52014	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	T;T	0.80214	-1.23;-1.35	5.32	2.21	0.28008	.	0.450964	0.26003	N	0.026933	T	0.67822	0.2934	L	0.56769	1.78	0.28953	N	0.890311	B;B;P	0.40875	0.075;0.393;0.731	B;B;B	0.33620	0.08;0.08;0.167	T	0.61023	-0.7146	10	0.30854	T	0.27	.	3.4583	0.07523	0.3571:0.4503:0.0:0.1926	.	74;328;328	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	328	ENSP00000347942:T328S;ENSP00000344798:T328S	ENSP00000344798:T328S	T	+	2	0	RET	42921945	0.840000	0.29493	0.998000	0.56505	0.976000	0.68499	0.253000	0.18296	0.790000	0.33803	0.563000	0.77884	ACC		0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		G	43601939	C	G	43601939	3	3	94	1	0	0	0	0	1	0	0	0	13272	507	18	5	1001	5	RET	10	43601939	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	17138706	43601939	91932808	104	25716										
SYT15	83849	hgsc.bcm.edu	37	chr10	46968630	46968630	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agctctgatgccgggcagggGtcccatggggcatcggccca	16	13	1	1	rs201674590	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:46968630G>C	ENST00000374321.4	-	3	372	c.306C>G	c.(304-306)gaC>gaG	p.D102E	SYT15_ENST00000374323.4_Missense_Mutation_p.D155E|SYT15_ENST00000503753.1_Missense_Mutation_p.D102E|SYT15_ENST00000374325.3_Missense_Mutation_p.D102E|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CCGGGCAGGGGTCCCATGGGG	0.677													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		34486	0		0	False		,,,				2504	0				Ovarian(57;1152 1428 19651 37745)											0			10						G	GLU/ASP,GLU/ASP	24,4180		0,24,2078	37	47	44		306,306	2.7	0.1	10		44	0,8438		0,0,4219	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	45,45	0,24,6297	CC,CG,GG		0.0,0.5709,0.1898	benign,benign	102/422,102/391	46968630	24,12618	2102	4219	6321	46388636	SO:0001583	missense	83849			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.306C>G	10.37:g.46968630G>C	ENSP00000363441:p.Asp102Glu		46388636	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	7.693	0.691560	0.15039	0.005709	0.0	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374323;ENST00000374321	T;T;T;T	0.13420	2.59;2.59;2.95;2.82	4.59	2.69	0.31865	.	0.296665	0.32175	N	0.006477	T	0.07999	0.0200	L	0.56769	1.78	0.27051	N	0.963789	B;B	0.17667	0.013;0.023	B;B	0.16289	0.006;0.015	T	0.23084	-1.0198	10	0.15066	T	0.55	.	6.5028	0.22178	0.0975:0.3568:0.5456:0.0	.	102;102	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	E	102;102;102;155;102	ENSP00000363445:D102E;ENSP00000427607:D102E;ENSP00000363443:D155E;ENSP00000363441:D102E	ENSP00000363441:D102E	D	-	3	2	SYT15	46388636	0.977000	0.34250	0.091000	0.20842	0.015000	0.08874	0.925000	0.28791	1.279000	0.44446	0.555000	0.69702	GAC		0.677	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		C	46968630	G	C	46968630	3	2	94	1	0	0	0	0	1	0	0	0	15510	1252	44	5	1037	5	SYT15	10	46968630	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	3366691	46968630	88566117	105	25717										
SYT15	83849	hgsc.bcm.edu	37	chr10	46968668	46968668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccactctccactgtgcagggGcacccaatctcggccttgaa	9	16	2	1	rs199526536	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:46968668G>A	ENST00000374321.4	-	3	334	c.268C>T	c.(268-270)Ccc>Tcc	p.P90S	SYT15_ENST00000374323.4_Missense_Mutation_p.P143S|SYT15_ENST00000503753.1_Missense_Mutation_p.P90S|SYT15_ENST00000374325.3_Missense_Mutation_p.P90S|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CTGTGCAGGGGCACCCAATCT	0.632													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		35581	0		0	False		,,,				2504	0				Ovarian(57;1152 1428 19651 37745)											0			10						G	SER/PRO,SER/PRO	23,4245		0,23,2111	56	67	63		268,268	3.6	0.5	10		63	1,8499		0,1,4249	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	74,74	0,24,6360	AA,AG,GG		0.0118,0.5389,0.188	benign,benign	90/422,90/391	46968668	24,12744	2134	4250	6384	46388674	SO:0001583	missense	83849			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.268C>T	10.37:g.46968668G>A	ENSP00000363441:p.Pro90Ser		46388674	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	11.26	1.587092	0.28268	0.005389	1.18E-4	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374323;ENST00000374321	T;T;T;T	0.13420	2.59;2.59;2.6;2.81	4.59	3.61	0.41365	.	0.753114	0.12981	N	0.423316	T	0.08670	0.0215	L	0.60455	1.87	0.18873	N	0.999985	B;B	0.27559	0.179;0.181	B;B	0.26693	0.052;0.072	T	0.26224	-1.0109	10	0.11485	T	0.65	.	7.3993	0.26954	0.0:0.1803:0.6332:0.1865	.	90;90	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	S	90;90;90;143;90	ENSP00000363445:P90S;ENSP00000427607:P90S;ENSP00000363443:P143S;ENSP00000363441:P90S	ENSP00000363441:P90S	P	-	1	0	SYT15	46388674	0.365000	0.25006	0.458000	0.27068	0.459000	0.32528	0.287000	0.18920	2.569000	0.86673	0.555000	0.69702	CCC		0.632	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		A	46968668	G	A	46968668	3	1	94	1	0	0	0	0	1	0	0	0	15510	1203	42	3	1075	3	SYT15	10	46968668	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	38	46968668	88566079	106	25718										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123279631	123279631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	acgtctcctccgaccactgtGgaggcatttgccggcagtcc	11	15	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:123279631G>A	ENST00000358487.5	-	7	1073	c.801C>T	c.(799-801)tcC>tcT	p.S267S	FGFR2_ENST00000356226.4_Silent_p.S152S|FGFR2_ENST00000369059.1_Silent_p.S152S|FGFR2_ENST00000369060.4_Silent_p.S267S|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000478859.1_Silent_p.S39S|FGFR2_ENST00000457416.2_Silent_p.S267S|FGFR2_ENST00000357555.5_Silent_p.S178S|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000346997.2_Silent_p.S267S|FGFR2_ENST00000351936.6_Silent_p.S267S|FGFR2_ENST00000360144.3_Silent_p.S178S|FGFR2_ENST00000369056.1_Silent_p.S267S	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	267	Ig-like C2-type 3.		S -> P (in CS). {ECO:0000269|PubMed:11781872}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	CGACCACTGTGGAGGCATTTG	0.567		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											90	75	80					10																	123279631		2203	4300	6503	123269621	SO:0001819	synonymous_variant	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.801C>T	10.37:g.123279631G>A			123269621	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																				0.567	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123279631	G	A	123279631	2	1	94	1	0	0	0	0	0	0	0	1	5885	1335	47	3		3	FGFR2	10	123279631	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	76310963	123279631	12255116	107	25719										
CPXM2	119587	hgsc.bcm.edu	37	chr10	125651150	125651150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggagcaccagggccagcgctGgggtagcggtccccgggcgg	20	13	0	0	rs112027854	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:125651150G>A	ENST00000241305.3	-	1	180	c.26C>T	c.(25-27)cCa>cTa	p.P9L	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	9					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GGCCAGCGCTGGGGTAGCGGT	0.751													g|||	131	0.0261581	0.0938	0.0101	5008	,	,		8004	0		0	False		,,,				2504	0															0			10							LEU/PRO	153,2681		2,149,1266	4	6	5		26	-2.5	0	10	dbSNP_132	5	3,5397		0,3,2697	no	missense	CPXM2	NM_198148.2	98	2,152,3963	AA,AG,GG		0.0556,5.3987,1.8946	benign	9/757	125651150	156,8078	1417	2700	4117	125641140	SO:0001583	missense	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.26C>T	10.37:g.125651150G>A	ENSP00000241305:p.Pro9Leu		125641140	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	g	12.37	1.916952	0.33815	0.053987	5.56E-4	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96716	-4.1	3.45	-2.48	0.06423	.	3.521810	0.01155	N	0.006503	T	0.66406	0.2786	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.78841	-0.2045	10	0.30078	T	0.28	0.0228	7.7622	0.28959	0.6768:0.0:0.3232:0.0	.	9	Q8N436	CPXM2_HUMAN	L	9	ENSP00000241305:P9L	ENSP00000241305:P9L	P	-	2	0	CPXM2	125641140	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.090000	0.11163	-0.418000	0.07450	-0.701000	0.03672	CCA		0.751	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125651150	G	A	125651150	3	1	94	1	0	0	0	0	1	0	0	0	3844	1348	47	3	2300	3	CPXM2	10	125651150	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	2371519	125651150	9883597	108	25720										
CTBP2	1488	hgsc.bcm.edu	37	chr10	126727615	126727615	+	Frame_Shift_Del	DEL	A	A	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ttgactttgtgcttatccacAagggccattctttatggaac					rs144283283		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr10:126727615delA	ENST00000337195.5	-	3	408	c.9delT	c.(7-9)cttfs	p.L3fs	CTBP2_ENST00000531469.1_Frame_Shift_Del_p.L3fs|CTBP2_ENST00000494626.2_Frame_Shift_Del_p.L3fs|CTBP2_ENST00000476817.1_5'UTR|CTBP2_ENST00000411419.2_Frame_Shift_Del_p.L3fs	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2	3					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GCTTATCCACAAGGGCCATTC	0.458																																																0			10											114	105	108					10																	126727615		2203	4300	6503	126717605	SO:0001589	frameshift_variant	1488			AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.9delT	10.37:g.126727615delA	ENSP00000338615:p.Leu3fs		126717605	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Frame_Shift_Del	DEL	ENST00000337195.5	37	CCDS7643.1																																																																																				0.458	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		-	126727615	A	-	126727615	7	5	94	1	0	1	0	1	0	0	0	0	4004	117	5	0	3046	0	CTBP2	10	126727615	Frame_Shift_Del	DEL	A	TCGA-DC-5869-01A-01D-1657-10	1076465	126727615	8807132	109	25721										
IFITM2	10581	hgsc.bcm.edu	37	chr11	308314	308314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccacaaccctgctcccccgaTgtccaccgtgatccacatcc	5	21	0	1	rs14408	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:308314T>C	ENST00000399817.4	+	1	152	c.122T>C	c.(121-123)aTg>aCg	p.M41T	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000533141.1_Missense_Mutation_p.M21T|IFITM2_ENST00000602569.1_Missense_Mutation_p.M21T	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	41			M -> T (in dbSNP:rs14408). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCTCCCCCGATGTCCACCGTG	0.607													t|||	3531	0.705072	0.7617	0.6657	5008	,	,		14037	0.9593		0.3787	False		,,,				2504	0.7301															0			11						T	THR/MET	2520,1396		857,806,295	63	88	80		122	-2.8	0	11	dbSNP_52	80	3019,5275		590,1839,1718	no	missense	IFITM2	NM_006435.2	81	1447,2645,2013	CC,CT,TT		36.3998,35.6486,45.3645	benign	41/133	308314	5539,6671	1958	4147	6105	298314	SO:0001583	missense	10581			X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"interferon induced transmembrane protein 2 (1-8D)"			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.122T>C	11.37:g.308314T>C	ENSP00000382714:p.Met41Thr		298314	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1298	0.5943223443223443	337	0.6849593495934959	199	0.5497237569060773	523	0.9143356643356644	239	0.3153034300791557	T	0.004	-2.266536	0.00259	0.643514	0.363998	ENSG00000185201	ENST00000533141;ENST00000399817;ENST00000327366	T;T	0.76709	-1.04;-0.8	2.59	-2.76	0.05896	.	1.327100	0.06148	N	0.673694	T	0.00012	0.0000	N	0.00010	-3.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45644	-0.9247	9	0.02654	T	1	2.4836	3.407	0.07344	0.3221:0.496:0.0:0.1819	rs14408;rs3179090;rs17850538;rs58885107;rs14408	41	Q01629	IFM2_HUMAN	T	21;41;41	ENSP00000434443:M21T;ENSP00000382714:M41T	ENSP00000327996:M41T	M	+	2	0	IFITM2	298314	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.620000	0.00879	-0.998000	0.03446	-3.056000	0.00068	ATG		0.607	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435		C	308314	T	C	308314	3	2	94	1	0	0	0	0	1	0	0	0	7548	1464	51	4	124	4	IFITM2	11	308314	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10		308314	134698202	110	25722										
CDHR5	53841	hgsc.bcm.edu	37	chr11	618971	618971	+	Frame_Shift_Del	DEL	G	G	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	accgggagtggctggttggtGggaggtgctgttttctgcac							TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:618971delG	ENST00000358353.3	-	14	1910	c.1588delC	c.(1588-1590)cacfs	p.H530fs	CDHR5_ENST00000397542.2_Frame_Shift_Del_p.H530fs|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	530					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						GCTGGTTGGTGGGAGGTGCTG	0.672																																																0			11											72	87	82					11																	618971		2203	4300	6503	608971	SO:0001589	frameshift_variant	0			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1588delC	11.37:g.618971delG	ENSP00000351118:p.His530fs		608971	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Del	DEL	ENST00000358353.3	37	CCDS7707.1																																																																																				0.672	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		-	618971	G	-	618971	7	5	94	1	0	1	0	1	0	0	0	0	3128	1348	47	0	961	0	CDHR5	11	618971	Frame_Shift_Del	DEL	G	TCGA-DC-5869-01A-01D-1657-10	310657	618971	134387545	111	25723										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092928	1092928	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccggcacacagaccccaacaTcgacacccatcaccaccacc	4	22	1	1	rs12791677		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:1092928T>A	ENST00000441003.2	+	30	4774	c.4747T>A	c.(4747-4749)Tcg>Acg	p.S1583T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.S1584T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaacatcgacacccat	0.632																																																0			11																																								1082928	SO:0001583	missense	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4747T>A	11.37:g.1092928T>A	ENSP00000415183:p.Ser1583Thr		1082928	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	0.629	-0.817927	0.02776	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12255	2.7;3.41	1.75	-3.51	0.04696	.	3.022220	0.02729	N	0.114829	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29119	-1.0022	9	0.12766	T	0.61	.	0.5592	0.00676	0.2873:0.3401:0.1565:0.2162	.	1583	E7EUV1	.	T	1583;1584	ENSP00000415183:S1583T;ENSP00000351956:S1584T	ENSP00000351956:S1584T	S	+	1	0	MUC2	1082928	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.679000	0.00395	-2.640000	0.00429	-1.550000	0.00899	TCG		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092928	T	A	1092928	3	1	94	1	0	0	0	0	1	0	0	0	10005	1435	50	5	4865	5	MUC2	11	1092928	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	473957	1092928	133913588	112	25724										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272035	1272035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cacggtgaccccctcctccaTcccggggaccacccacaccg	8	22	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:1272035T>C	ENST00000529681.1	+	31	13983	c.13925T>C	c.(13924-13926)aTc>aCc	p.I4642T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.I4645T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4642	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		ccctcctccatcccggggacc	0.627																																																0			11											118	147	138					11																	1272035		2126	4210	6336	1228611	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13925T>C	11.37:g.1272035T>C	ENSP00000436812:p.Ile4642Thr		1228611	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	3.318	-0.139430	0.06669	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637	T;T	0.15718	2.4;2.58	1.53	-0.671	0.11381	.	.	.	.	.	T	0.07999	0.0200	N	0.11201	0.11	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.32161	-0.9917	9	0.87932	D	0	.	4.3731	0.11258	0.0:0.358:0.0:0.642	.	4645	E9PBJ0	.	T	4642;4645;4586	ENSP00000436812:I4642T;ENSP00000415793:I4645T	ENSP00000343037:I4586T	I	+	2	0	MUC5B	1228611	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.321000	0.02697	-0.012000	0.14223	0.155000	0.16302	ATC		0.627	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1272035	T	C	1272035	3	2	94	1	0	0	0	0	1	0	0	0	10009	1435	50	4	14056	4	MUC5B	11	1272035	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	179107	1272035	133734481	113	25725										
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651169	1651169	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggctgtggaggctgtggctcTggctgtgggggctgtggctc	21	8	1	0	rs71454095	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:1651169T>C	ENST00000399676.2	+	1	137	c.99T>C	c.(97-99)tcT>tcC	p.S33S		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	33						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gctgtggctctggctgtgggg	0.721													N|||	2639	0.526957	0.643	0.4827	5008	,	,		7432	0.4018		0.5527	False		,,,				2504	0.5041															0			11						C		2322,1648		759,804,422	20	30	27		99	-1.5	0	11	dbSNP_130	27	4372,3646		1321,1730,958	no	coding-synonymous	KRTAP5-5	NM_001001480.2		2080,2534,1380	CC,CT,TT		45.4727,41.5113,44.1608		33/238	1651169	6694,5294	1985	4009	5994	1607745	SO:0001819	synonymous_variant	440051			AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"Keratin associated proteins"	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.99T>C	11.37:g.1651169T>C			1607745	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																				0.721	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			C	1651169	T	C	1651169	2	2	94	1	0	0	0	0	0	0	0	1	8586	1567	55	4		4	KRTAP5-5	11	1651169	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	379134	1651169	133355347	114	25726										
ST5	6764	hgsc.bcm.edu	37	chr11	8751577	8751577	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gctggggtggagggcaagggAggtggagcagcaggtgtggg	25	4	0	0	rs200801002	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:8751577A>G	ENST00000534127.1	-	6	1645	c.1260T>C	c.(1258-1260)ccT>ccC	p.P420P	ST5_ENST00000526757.1_Intron|ST5_ENST00000357665.1_Silent_p.P420P|ST5_ENST00000530438.1_Intron|ST5_ENST00000313726.6_Silent_p.P420P	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	420	Interaction with ABL1.|Pro-rich.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		AGGGCAAGGGAGGTGGAGCAG	0.602													G|||	24	0.00479233	0	0.0014	5008	,	,		16036	0		0	False		,,,				2504	0.0235															0			11											238	223	228					11																	8751577		2201	4296	6497	8708153	SO:0001819	synonymous_variant	6764			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1260T>C	11.37:g.8751577A>G			8708153	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Silent	SNP	ENST00000534127.1	37	CCDS7791.1																																																																																				0.602	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		G	8751577	A	G	8751577	2	3	94	1	0	0	0	0	0	0	0	1	15259	291	11	4		4	ST5	11	8751577	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	7100408	8751577	126254939	115	25727										
TBC1D10C	374403	hgsc.bcm.edu	37	chr11	67176971	67176971	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccgcgccgggacccccgcccCggccacaggtccgcctcgcc	12	24	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:67176971C>T	ENST00000542590.1	+	9	1101	c.1087C>T	c.(1087-1089)Cgg>Tgg	p.R363W	TBC1D10C_ENST00000526387.1_Missense_Mutation_p.P298L|TBC1D10C_ENST00000312390.5_Missense_Mutation_p.R363W			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	363					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			ACCCCCGCCCCGGCCACAGGT	0.711																																																0			11											3	4	3					11																	67176971		1723	3399	5122	66933547	SO:0001583	missense	374403			BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.1087C>T	11.37:g.67176971C>T	ENSP00000443654:p.Arg363Trp		66933547	G3V1D6	Missense_Mutation	SNP	ENST00000542590.1	37	CCDS8162.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.551|9.551	1.115972|1.115972	0.20795|0.20795	.|.	.|.	ENSG00000175463|ENSG00000175463	ENST00000526387|ENST00000312390;ENST00000542590	.|T;T	.|0.07908	.|3.15;3.15	4.92|4.92	1.65|1.65	0.23941|0.23941	.|.	.|0.688838	.|0.12377	.|N	.|0.474252	T|T	0.10680|0.10680	0.0261|0.0261	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	B|D	0.31680|0.56746	0.335|0.977	B|P	0.19148|0.44860	0.024|0.462	T|T	0.19484|0.19484	-1.0304|-1.0304	8|10	0.87932|0.87932	D|D	0|0	.|.	11.4415|11.4415	0.50100|0.50100	0.662:0.3379:0.0:0.0|0.662:0.3379:0.0:0.0	.|.	298|363	G3V1D6|Q8IV04	.|TB10C_HUMAN	L|W	298|363	.|ENSP00000310193:R363W;ENSP00000443654:R363W	ENSP00000435543:P298L|ENSP00000310193:R363W	P|R	+|+	2|1	0|2	TBC1D10C|TBC1D10C	66933547|66933547	0.001000|0.001000	0.12720|0.12720	0.004000|0.004000	0.12327|0.12327	0.032000|0.032000	0.12392|0.12392	0.736000|0.736000	0.26130|0.26130	0.618000|0.618000	0.30179|0.30179	0.462000|0.462000	0.41574|0.41574	CCG|CGG		0.711	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517		T	67176971	C	T	67176971	3	4	94	1	0	0	0	0	1	0	0	0	15639	643	23	1	1121	1	TBC1D10C	11	67176971	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	58425394	67176971	67829545	116	25728										
GPR152	390212	hgsc.bcm.edu	37	chr11	67219263	67219263	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cagagagctgccgcgaaggaCgagagcacggagcgcagcag	17	11	0	2	rs148579956		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:67219263C>T	ENST00000312457.2	-	1	937	c.933G>A	c.(931-933)tcG>tcA	p.S311S	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CCGCGAAGGACGAGAGCACGG	0.642																																					Pancreas(102;800 1581 2723 7382 33622)											0			11						C		0,4400		0,0,2200	54	53	53		933	2.7	1	11	dbSNP_134	53	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	GPR152	NM_206997.1		0,1,6494	TT,TC,CC		0.0116,0.0,0.0077		311/471	67219263	1,12989	2200	4295	6495	66975839	SO:0001819	synonymous_variant	390212			AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.933G>A	11.37:g.67219263C>T			66975839	Q0VD88|Q86SM0	Silent	SNP	ENST00000312457.2	37	CCDS8165.1																																																																																				0.642	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			T	67219263	C	T	67219263	2	4	94	1	0	0	0	0	0	0	0	1	6678	523	19	1		1	GPR152	11	67219263	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	42292	67219263	67787253	117	25729										
MRGPRF	116535	hgsc.bcm.edu	37	chr11	68772923	68772923	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aagtagacgatgggcttggcGctgctgttgatgcagatgca	15	7	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:68772923G>A	ENST00000309099.6	-	3	1237	c.855C>T	c.(853-855)agC>agT	p.S285S	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Silent_p.S285S	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	285						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGGGCTTGGCGCTGCTGTTGA	0.642																																																0			11											33	26	29					11																	68772923		2195	4289	6484	68529499	SO:0001819	synonymous_variant	116535			AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"GPCR / Class A : Orphans"	24828	protein-coding gene	gene with protein product		607233	"G protein-coupled receptor 168", "G protein-coupled receptor 140"	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.855C>T	11.37:g.68772923G>A			68529499	B3KV43|Q8NBK8	Silent	SNP	ENST00000309099.6	37	CCDS8188.1																																																																																				0.642	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015		A	68772923	G	A	68772923	2	1	94	1	0	0	0	0	0	0	0	1	9795	1078	38	1		1	MRGPRF	11	68772923	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	1553660	68772923	66233593	118	25730										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249125	71249125	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggctgctgtggctgctctggAggctgtggctccggctgtgg	19	10	1	0	rs537752041|rs113379698|rs55848980	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:71249125A>G	ENST00000398534.3	+	1	55	c.24A>G	c.(22-24)ggA>ggG	p.G8G		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	8						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GCTGCTCTGGAGGCTGTGGCT	0.652																																																0			11											47	66	60					11																	71249125		2189	4280	6469	70926773	SO:0001819	synonymous_variant	440021			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.24A>G	11.37:g.71249125A>G			70926773	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																				0.652	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249125	A	G	71249125	2	3	94	1	0	0	0	0	0	0	0	1	8589	291	11	4		4	KRTAP5-8	11	71249125	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	2476202	71249125	63757391	119	25731										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249569	71249569	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aagccctgctgctgctcttcAggctgtgggtcatcctgctg	12	13	3	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:71249569A>G	ENST00000398534.3	+	1	499	c.468A>G	c.(466-468)tcA>tcG	p.S156S		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	156	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GCTGCTCTTCAGGCTGTGGGT	0.607																																																0			11											158	164	162					11																	71249569		2200	4294	6494	70927217	SO:0001819	synonymous_variant	440021			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.468A>G	11.37:g.71249569A>G			70927217	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																				0.607	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249569	A	G	71249569	2	3	94	1	0	0	0	0	0	0	0	1	8589	175	7	4		4	KRTAP5-8	11	71249569	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	444	71249569	63756947	120	25732										
ATM	472	hgsc.bcm.edu	37	chr11	108117839	108117839	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aatttgattgaattgatggcAgatatctgtcaccaggtaca	9	6	2	4			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:108117839A>G	ENST00000452508.2	+	9	1239	c.1050A>G	c.(1048-1050)gcA>gcG	p.A350A	ATM_ENST00000278616.4_Silent_p.A350A			Q13315	ATM_HUMAN	ATM serine/threonine kinase	350			A -> T (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10023947}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AATTGATGGCAGATATCTGTC	0.338			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											60	61	60					11																	108117839		2201	4297	6498	107623049	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.1050A>G	11.37:g.108117839A>G			107623049	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.338	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108117839	A	G	108117839	2	3	94	1	0	0	0	0	0	0	0	1	1110	175	7	4		4	ATM	11	108117839	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	36868270	108117839	26888677	121	25733										
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118514625	118514625	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcctcctcctcccagctcagCgtggctaccctggggcgtag	11	17	1	0	rs11216938	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:118514625C>T	ENST00000361417.2	+	15	3396	c.2985C>T	c.(2983-2985)agC>agT	p.S995S	PHLDB1_ENST00000527898.1_Silent_p.S31S|PHLDB1_ENST00000356063.5_Silent_p.S948S|PHLDB1_ENST00000524713.1_Silent_p.S138S|PHLDB1_ENST00000534672.1_3'UTR	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	995										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ccCAGCTCAGCGTGGCTACCC	0.692													C|||	1104	0.220447	0.1082	0.2118	5008	,	,		13682	0.2302		0.2157	False		,,,				2504	0.3732															0			11						C	,,	533,3867	223.3+/-239.8	32,469,1699	25	29	28		2985,2844,2985	-1.7	1	11	dbSNP_120	28	1851,6737	307.6+/-308.5	197,1457,2640	no	coding-synonymous,coding-synonymous,coding-synonymous	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	,,	229,1926,4339	TT,TC,CC		21.5533,12.1136,18.3554	,,	995/1378,948/1320,995/1378	118514625	2384,10604	2200	4294	6494	118019835	SO:0001819	synonymous_variant	23187				CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2985C>T	11.37:g.118514625C>T			118019835	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	37	CCDS8401.1																																																																																				0.692	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118514625	C	T	118514625	2	4	94	1	0	0	0	0	0	0	0	1	11882	767	27	1		1	PHLDB1	11	118514625	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	10396786	118514625	16491891	122	25734										
PRDM10	56980	hgsc.bcm.edu	37	chr11	129788540	129788540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgaacgtcttggagcggctgAtgcggtcggctttcttggcc	15	10	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr11:129788540A>G	ENST00000360871.3	-	14	2339	c.2108T>C	c.(2107-2109)aTc>aCc	p.I703T	PRDM10_ENST00000528746.1_Missense_Mutation_p.I677T|PRDM10_ENST00000423662.2_Missense_Mutation_p.I621T|PRDM10_ENST00000304538.6_Missense_Mutation_p.I617T|PRDM10_ENST00000526082.1_Missense_Mutation_p.I621T|PRDM10_ENST00000358825.5_Missense_Mutation_p.I707T	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	707					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		GGAGCGGCTGATGCGGTCGGC	0.552																																																0			11											257	236	243					11																	129788540		2201	4297	6498	129293750	SO:0001583	missense	56980			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2108T>C	11.37:g.129788540A>G	ENSP00000354118:p.Ile703Thr		129293750	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281797	0.40394	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	T;T;T;T;T;T;T	0.10477	2.89;2.89;2.9;2.87;2.93;2.87;2.96	5.79	4.65	0.58169	.	0.167749	0.52532	D	0.000079	T	0.05318	0.0141	N	0.08118	0	0.39721	D	0.971476	B;B;B;B;B;B	0.16396	0.001;0.001;0.001;0.001;0.017;0.001	B;B;B;B;B;B	0.14578	0.001;0.003;0.001;0.003;0.011;0.003	T	0.38672	-0.9650	10	0.29301	T	0.29	-13.2586	7.6159	0.28158	0.7875:0.1426:0.0698:0.0	.	617;703;707;621;617;621	B7ZL72;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;PRD10_HUMAN;.;.;.	T	707;617;703;621;677;621;420	ENSP00000351686:I707T;ENSP00000302669:I617T;ENSP00000354118:I703T;ENSP00000398431:I621T;ENSP00000431262:I677T;ENSP00000432237:I621T;ENSP00000435940:I420T	ENSP00000302669:I617T	I	-	2	0	PRDM10	129293750	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.189000	0.58358	1.001000	0.39076	0.533000	0.62120	ATC		0.552	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		G	129788540	A	G	129788540	3	3	94	1	0	0	0	0	1	0	0	0	12485	333	12	4	1394	4	PRDM10	11	129788540	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	11273915	129788540	5217976	123	25735										
KDM5A	5927	hgsc.bcm.edu	37	chr12	438067	438067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agagtcaattctttgcagacCatggcagccagccccacatc	8	14	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:438067C>T	ENST00000399788.2	-	14	2264	c.1902G>A	c.(1900-1902)atG>atA	p.M634I	KDM5A_ENST00000382815.4_Missense_Mutation_p.M634I	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	634					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CTTTGCAGACCATGGCAGCCA	0.443			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	0			12											103	97	99					12																	438067		1945	4152	6097	308328	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1902G>A	12.37:g.438067C>T	ENSP00000382688:p.Met634Ile		308328	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.347926	0.41599	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.70164	-0.46;-0.46;-0.46	5.27	4.37	0.52481	.	0.164014	0.64402	D	0.000017	T	0.42944	0.1225	N	0.03608	-0.345	0.36347	D	0.859843	B;B;B;B	0.25105	0.118;0.005;0.006;0.108	B;B;B;B	0.28385	0.016;0.017;0.017;0.089	T	0.51348	-0.8717	10	0.66056	D	0.02	-18.2113	9.0003	0.36077	0.1489:0.7772:0.0:0.0739	.	253;634;634;634	B4DVX3;F5H1F7;P29375;P29375-2	.;.;KDM5A_HUMAN;.	I	253;593;634;634;253	ENSP00000382688:M634I;ENSP00000372265:M634I;ENSP00000440622:M253I	ENSP00000261253:M253I	M	-	3	0	KDM5A	308328	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.732000	0.38146	1.338000	0.45544	0.462000	0.41574	ATG		0.443	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		T	438067	C	T	438067	3	4	94	1	0	0	0	0	1	0	0	0	8154	594	21	3	3230	3	KDM5A	12	438067	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10		438067	133413828	124	25736										
TUBA1B	10376	hgsc.bcm.edu	37	chr12	49521809	49521809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	accaacctcctcataatcctTctcaagggcagccatatctt	4	15	3	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:49521809T>C	ENST00000336023.5	-	4	1382	c.1288A>G	c.(1288-1290)Aag>Gag	p.K430E	RP11-386G11.10_ENST00000552893.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	430					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						TCATAATCCTTCTCAAGGGCA	0.507																																																0			12											120	128	125					12																	49521809		2203	4300	6503	47808076	SO:0001583	missense	10376			AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"Tubulins"	18809	protein-coding gene	gene with protein product	"tubulin, alpha, ubiquitous"	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.1288A>G	12.37:g.49521809T>C	ENSP00000336799:p.Lys430Glu		47808076	P04687|P05209|Q27I68|Q8WU19	Missense_Mutation	SNP	ENST00000336023.5	37	CCDS31792.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503766	0.44558	.	.	ENSG00000123416	ENST00000336023;ENST00000429203	D	0.83673	-1.75	5.45	4.29	0.51040	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.47093	U	0.000247	D	0.85609	0.5736	M	0.79614	2.46	0.80722	D	1	P	0.36959	0.575	B	0.44085	0.44	D	0.85519	0.1202	10	0.87932	D	0	.	11.7799	0.52008	0.0:0.0:0.1473:0.8527	.	430	P68363	TBA1B_HUMAN	E	430;161	ENSP00000336799:K430E	ENSP00000336799:K430E	K	-	1	0	TUBA1B	47808076	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.878000	0.87231	0.895000	0.36342	0.528000	0.53228	AAG		0.507	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082		C	49521809	T	C	49521809	3	2	94	1	0	0	0	0	1	0	0	0	16784	1792	62	4	71	4	TUBA1B	12	49521809	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	49083742	49521809	84330086	125	25737										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50190653	50190653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gactctgtgtcctcaaggagCtggcccaggttcaactgtct	11	12	4	0	rs3741555	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:50190653C>T	ENST00000335999.6	-	8	1191	c.990G>A	c.(988-990)caG>caA	p.Q330Q		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	326	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCTCAAGGAGCTGGCCCAGGT	0.652													C|||	1382	0.275958	0.23	0.3847	5008	,	,		16740	0.5466		0.0537	False		,,,				2504	0.2106															0			12						C		818,3146		97,624,1261	16	19	18		990	2.2	1	12	dbSNP_107	18	394,7876		9,376,3750	no	coding-synonymous	NCKAP5L	NM_001037806.3		106,1000,5011	TT,TC,CC		4.7642,20.6357,9.9068		330/1335	50190653	1212,11022	1982	4135	6117	48476920	SO:0001819	synonymous_variant	0			AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.990G>A	12.37:g.50190653C>T			48476920	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	602	0.27564102564102566	118	0.23983739837398374	126	0.34806629834254144	319	0.5576923076923077	39	0.051451187335092345	C	8.398	0.841268	0.16891	0.206357	0.047642	ENSG00000167566	ENST00000433948	.	.	.	4.12	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999738904	.	.	.	.	.	.	T	0.48007	-0.9072	3	.	.	.	-6.4151	7.0432	0.25031	0.0:0.6158:0.0:0.3842	rs3741555;rs58965238;rs3741555	.	.	.	T	45	.	.	A	-	1	0	NCKAP5L	48476920	0.992000	0.36948	0.993000	0.49108	0.963000	0.63663	0.922000	0.28734	0.299000	0.22661	0.462000	0.41574	GCT		0.652	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		T	50190653	C	T	50190653	2	4	94	1	0	0	0	0	0	0	0	1	10255	796	28	3		3	NCKAP5L	12	50190653	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	668844	50190653	83661242	126	25738										
LEMD3	23592	hgsc.bcm.edu	37	chr12	65564798	65564798	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ttcagtgcccactacttgtcGatgtttctcttaactgctgc	7	12	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:65564798G>A	ENST00000308330.2	+	1	1448	c.1422G>A	c.(1420-1422)tcG>tcA	p.S474S	LEMD3_ENST00000541171.1_Intron	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	474					negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		ACTACTTGTCGATGTTTCTCT	0.478																																																0			12											102	82	89					12																	65564798		2203	4300	6503	63851065	SO:0001819	synonymous_variant	23592			AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.1422G>A	12.37:g.65564798G>A			63851065	Q9NT47|Q9NYA5	Silent	SNP	ENST00000308330.2	37	CCDS8972.1																																																																																				0.478	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			A	65564798	G	A	65564798	2	1	94	1	0	0	0	0	0	0	0	1	8743	1045	37	1		1	LEMD3	12	65564798	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	15374145	65564798	68287097	127	25739										
MSRB3	253827	hgsc.bcm.edu	37	chr12	65672594	65672594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gccccctctcgctctgcctcTccctctgcctctgcctctgc	6	23	6	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:65672594T>C	ENST00000355192.3	+	1	172	c.46T>C	c.(46-48)Tcc>Ccc	p.S16P	MSRB3_ENST00000538725.1_3'UTR|MSRB3_ENST00000535664.1_5'UTR|MSRB3_ENST00000308259.5_5'UTR|RP11-305O6.3_ENST00000545709.1_RNA|MSRB3_ENST00000540804.1_Missense_Mutation_p.S16P	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	16					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		gctctgcctctccctctgcct	0.736																																																0			12											19	18	18					12																	65672594		2154	4231	6385	63958861	SO:0001583	missense	253827			BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"deafness, autosomal recessive 74"	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.46T>C	12.37:g.65672594T>C	ENSP00000347324:p.Ser16Pro		63958861	B4DR19|B7ZAQ0|Q6UXS2	Missense_Mutation	SNP	ENST00000355192.3	37	CCDS8973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.81|13.81	2.348869|2.348869	0.41599|0.41599	.|.	.|.	ENSG00000174099|ENSG00000174099	ENST00000541189|ENST00000355192;ENST00000540804	T|T;T	0.65916|0.64260	-0.18|-0.09;-0.09	.|.	.|.	.|.	.|.	.|9.681730	.|0.00397	.|N	.|0.000046	T|T	0.41096|0.41096	0.1144|0.1144	N|N	0.08118|0.08118	0|0	0.50039|0.50039	D|D	0.999842|0.999842	.|B	.|0.09022	.|0.002	.|B	.|0.01281	.|0.0	T|T	0.27839|0.27839	-1.0062|-1.0062	4|7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|16	.|Q8IXL7	.|MSRB3_HUMAN	P|P	24|16	ENSP00000440722:L24P|ENSP00000347324:S16P;ENSP00000437623:S16P	.|.	L|S	+|+	2|1	0|0	MSRB3|MSRB3	63958861|63958861	0.960000|0.960000	0.32886|0.32886	0.882000|0.882000	0.34594|0.34594	0.826000|0.826000	0.46750|0.46750	-0.339000|-0.339000	0.07832|0.07832	0.056000|0.056000	0.16144|0.16144	0.055000|0.055000	0.15244|0.15244	CTC|TCC		0.736	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		C	65672594	T	C	65672594	3	2	94	1	0	0	0	0	1	0	0	0	9919	1551	54	4	48	4	MSRB3	12	65672594	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	107796	65672594	68179301	128	25740										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100476887	100476887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aatactgaaggtgttctgcaTgtccctttcagagggtagtc	11	8	2	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:100476887T>C	ENST00000279907.7	-	11	1526	c.1314A>G	c.(1312-1314)acA>acG	p.T438T	UHRF1BP1L_ENST00000545232.2_Silent_p.T88T|UHRF1BP1L_ENST00000356828.3_Silent_p.T438T	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	438										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GTGTTCTGCATGTCCCTTTCA	0.348																																																0			12											156	141	146					12																	100476887		2203	4300	6503	99001018	SO:0001819	synonymous_variant	23074				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1314A>G	12.37:g.100476887T>C			99001018	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	37	CCDS31882.1																																																																																				0.348	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		C	100476887	T	C	100476887	2	2	94	1	0	0	0	0	0	0	0	1	17009	1451	51	4		4	UHRF1BP1L	12	100476887	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	34804293	100476887	33375008	129	25741										
KDM2B	84678	hgsc.bcm.edu	37	chr12	121880495	121880495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cccttcggtgctgggtcccgCggtgggggagctggagcggg	21	11	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr12:121880495C>T	ENST00000377071.4	-	19	2821	c.2749G>A	c.(2749-2751)Gcg>Acg	p.A917T	KDM2B_ENST00000377069.4_Missense_Mutation_p.A848T|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Missense_Mutation_p.A285T	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	917					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CTGGGTCCCGCGGTGGGGGAG	0.692																																																0			12											14	14	14					12																	121880495		1872	4081	5953	120364878	SO:0001583	missense	84678			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2749G>A	12.37:g.121880495C>T	ENSP00000366271:p.Ala917Thr		120364878	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640192	0.67244	.	.	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.25912	2.07;2.38;1.77	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000014	T	0.49355	0.1552	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	P;P;D;P	0.67103	0.819;0.87;0.949;0.902	T	0.26087	-1.0113	10	0.48119	T	0.1	-26.0179	20.3928	0.98949	0.0:1.0:0.0:0.0	.	357;917;848;360	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	T	905;285;848;917;360;920	ENSP00000437821:A285T;ENSP00000366269:A848T;ENSP00000366271:A917T	ENSP00000261824:A920T	A	-	1	0	KDM2B	120364878	1.000000	0.71417	0.214000	0.23707	0.051000	0.14879	7.750000	0.85110	2.813000	0.96785	0.655000	0.94253	GCG		0.692	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121880495	C	T	121880495	3	4	94	1	0	0	0	0	1	0	0	0	8146	768	27	1	1333	1	KDM2B	12	121880495	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	21403608	121880495	11971400	130	25742										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36445372	36445372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctgctttacctgagctggtgGaggcaggggacttgctacgc	15	10	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr13:36445372G>A	ENST00000360631.3	-	5	1140	c.929C>T	c.(928-930)tCc>tTc	p.S310F	DCLK1_ENST00000379892.4_Missense_Mutation_p.S310F|DCLK1_ENST00000255448.4_Missense_Mutation_p.S310F			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	310	Pro/Ser-rich.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TGAGCTGGTGGAGGCAGGGGA	0.527																																																0			13											175	166	169					13																	36445372		2203	4300	6503	35343372	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.929C>T	13.37:g.36445372G>A	ENSP00000353846:p.Ser310Phe		35343372	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.193711	0.78902	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.69435	-0.4;-0.4;1.74	5.43	5.43	0.79202	.	0.075461	0.53938	D	0.000041	T	0.68265	0.2982	N	0.19112	0.55	0.53005	D	0.999968	P	0.51791	0.948	P	0.56514	0.8	T	0.69978	-0.4998	10	0.48119	T	0.1	.	19.5966	0.95541	0.0:0.0:1.0:0.0	.	310	O15075-2	.	F	310	ENSP00000255448:S310F;ENSP00000353846:S310F;ENSP00000369222:S310F	ENSP00000255448:S310F	S	-	2	0	DCLK1	35343372	1.000000	0.71417	0.844000	0.33320	0.985000	0.73830	6.879000	0.75572	2.698000	0.92095	0.655000	0.94253	TCC		0.527	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36445372	G	A	36445372	3	1	94	1	0	0	0	0	1	0	0	0	4297	1174	41	3	1316	3	DCLK1	13	36445372	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10		36445372	78724506	131	25743										
ATP7B	540	hgsc.bcm.edu	37	chr13	52532539	52532539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cacagggctcctctccgcctTctcagccacagcaaccacca	6	20	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr13:52532539T>C	ENST00000242839.4	-	8	2419	c.2263A>G	c.(2263-2265)Aag>Gag	p.K755E	ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000417240.2_Missense_Mutation_p.K27E|ATP7B_ENST00000542656.1_3'UTR|ATP7B_ENST00000418097.2_Missense_Mutation_p.K755E|ATP7B_ENST00000448424.2_Intron|ATP7B_ENST00000400366.3_Missense_Mutation_p.K644E|ATP7B_ENST00000344297.5_Intron|ATP7B_ENST00000482841.1_Intron	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	755					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTCTCCGCCTTCTCAGCCACA	0.552									Wilson disease																																							0			13											112	118	116					13																	52532539		2081	4217	6298	51430540	SO:0001583	missense	540	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.2263A>G	13.37:g.52532539T>C	ENSP00000242839:p.Lys755Glu		51430540	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380353	0.61845	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000417240;ENST00000418097	D;D;D;D	0.95137	-3.62;-3.62;-3.62;-3.62	5.54	3.12	0.35913	ATPase,  P-type, cytoplasmic transduction domain A (1);	0.340362	0.34986	N	0.003532	D	0.90693	0.7080	L	0.38692	1.165	0.80722	D	1	P;B;B;P	0.38129	0.619;0.0;0.103;0.491	B;B;B;B	0.44108	0.441;0.001;0.024;0.184	D	0.84076	0.0382	10	0.19590	T	0.45	-7.6007	8.1175	0.30953	0.0:0.071:0.1469:0.782	.	755;27;644;755	F5H748;E7EQQ2;P35670-3;P35670	.;.;.;ATP7B_HUMAN	E	755;644;27;755	ENSP00000242839:K755E;ENSP00000383217:K644E;ENSP00000390360:K27E;ENSP00000393343:K755E	ENSP00000242839:K755E	K	-	1	0	ATP7B	51430540	1.000000	0.71417	0.984000	0.44739	0.884000	0.51177	2.560000	0.45896	0.386000	0.24997	0.460000	0.39030	AAG		0.552	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		C	52532539	T	C	52532539	3	2	94	1	0	0	0	0	1	0	0	0	1192	1792	62	4	2190	4	ATP7B	13	52532539	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	16087167	52532539	62637339	132	25744										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99554620	99554620	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgcccactgccattcatcagCgccggggacgtggtggcgag	15	13	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr13:99554620C>T	ENST00000376460.1	-	12	1382	c.1302G>A	c.(1300-1302)gcG>gcA	p.A434A	DOCK9_ENST00000339416.2_Silent_p.A435A|DOCK9_ENST00000448493.2_Silent_p.A446A|DOCK9_ENST00000442173.1_Silent_p.A434A	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	435					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CATTCATCAGCGCCGGGGACG	0.542																																																0			13											70	75	73					13																	99554620		2128	4243	6371	98352621	SO:0001819	synonymous_variant	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.1302G>A	13.37:g.99554620C>T			98352621	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	37	CCDS45062.1																																																																																				0.542	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		T	99554620	C	T	99554620	2	4	94	1	0	0	0	0	0	0	0	1	4705	755	27	1		1	DOCK9	13	99554620	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	47022081	99554620	15615258	133	25745										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113699587	113699587	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtctcttcctcactgcagccTgcaggacgctggcatcggat	11	14	2	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr13:113699587T>C	ENST00000375608.3	+	5	429	c.371T>C	c.(370-372)cTg>cCg	p.L124P	MCF2L_ENST00000397021.1_Missense_Mutation_p.L56P|MCF2L_ENST00000421756.1_Missense_Mutation_p.L98P|MCF2L_ENST00000375604.2_Missense_Mutation_p.L151P|MCF2L_ENST00000442652.2_Missense_Mutation_p.L124P|MCF2L_ENST00000434480.2_Missense_Mutation_p.L100P|MCF2L_ENST00000397030.1_Missense_Mutation_p.L127P|MCF2L_ENST00000480321.1_3'UTR|MCF2L_ENST00000423482.2_Missense_Mutation_p.L92P|MCF2L_ENST00000375597.4_Missense_Mutation_p.L92P|MCF2L_ENST00000375601.3_Missense_Mutation_p.L98P|MCF2L_ENST00000535094.2_Missense_Mutation_p.L94P			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	124	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	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;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CACTGCAGCCTGCAGGACGCT	0.607																																																0			13											61	59	59					13																	113699587		2203	4300	6503	112747588	SO:0001583	missense	23263			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.371T>C	13.37:g.113699587T>C	ENSP00000364758:p.Leu124Pro		112747588	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	T	15.17	2.754318	0.49362	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000430480;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000409954;ENST00000423482;ENST00000375597;ENST00000397021;ENST00000423251	T;T;T;T;T;T;T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;0.99	4.44	4.44	0.53790	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.000000	0.64402	D	0.000001	T	0.70902	0.3277	L	0.46885	1.475	0.58432	D	0.999997	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.998;0.999	D;D;D;D;D;D	0.85130	0.987;0.987;0.993;0.997;0.987;0.992	T	0.73052	-0.4104	10	0.72032	D	0.01	.	10.2484	0.43354	0.0:0.0:0.0:1.0	.	92;94;151;56;92;124	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	P	124;124;151;127;94;94;98;98;100;65;92;92;56;14	ENSP00000364758:L124P;ENSP00000401422:L124P;ENSP00000364754:L151P;ENSP00000380225:L127P;ENSP00000440374:L94P;ENSP00000397285:L98P;ENSP00000364751:L98P;ENSP00000407722:L100P;ENSP00000386551:L65P;ENSP00000405639:L92P;ENSP00000364747:L92P;ENSP00000405996:L14P	ENSP00000364747:L92P	L	+	2	0	MCF2L	112747588	0.969000	0.33509	0.478000	0.27316	0.301000	0.27625	3.491000	0.53252	1.983000	0.57843	0.459000	0.35465	CTG		0.607	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			C	113699587	T	C	113699587	3	2	94	1	0	0	0	0	1	0	0	0	9409	1580	55	4	561	4	MCF2L	13	113699587	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	14144967	113699587	1470291	134	25746										
IFI27	3429	hgsc.bcm.edu	37	chr14	94578076	94578076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gcagtgaccagtgtggccaaAgtggtcagggtggcctctgg	17	9	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr14:94578076A>G	ENST00000555744.1	+	2	236	c.48A>G	c.(46-48)aaA>aaG	p.K16K	IFI27_ENST00000298902.5_Silent_p.K16K|IFI27_ENST00000448882.1_Silent_p.K16K|IFI27_ENST00000557098.1_Intron|IFI27_ENST00000557634.1_Silent_p.K16K|IFI27_ENST00000444961.1_Silent_p.K16K			P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27	16					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)				breast(1)|lung(3)	4				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)		GTGTGGCCAAAGTGGTCAGGG	0.622																																					GBM(128;797 1667 20895 29868 47129)											0			14											140	112	122					14																	94578076		2203	4300	6503	93647829	SO:0001819	synonymous_variant	3429			X67325	CCDS32148.1	14q32.12	2012-10-02			ENSG00000165949	ENSG00000165949			5397	protein-coding gene	gene with protein product		600009				8358738	Standard	NM_005532		Approved	P27, FAM14D	uc021sba.1	P40305	OTTHUMG00000171303	ENST00000555744.1:c.48A>G	14.37:g.94578076A>G			93647829	Q53YA6|Q6IEC1|Q96BK3	Silent	SNP	ENST00000555744.1	37	CCDS32148.1																																																																																				0.622	IFI27-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412889.1	NM_005532		G	94578076	A	G	94578076	2	3	94	1	0	0	0	0	0	0	0	1	7533	69	3	4		4	IFI27	14	94578076	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10		94578076	12771464	135	25747										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102482766	102482766	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gcagagctgggtgaatacatCagaagaatcacgaccgtgcc	12	10	2	4			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr14:102482766C>G	ENST00000360184.4	+	37	7718	c.7554C>G	c.(7552-7554)atC>atG	p.I2518M		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2518					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GTGAATACATCAGAAGAATCA	0.483																																																0			14											85	80	82					14																	102482766		2203	4300	6503	101552519	SO:0001583	missense	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.7554C>G	14.37:g.102482766C>G	ENSP00000348965:p.Ile2518Met		101552519	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252053	0.59212	.	.	ENSG00000197102	ENST00000360184	T	0.25579	1.79	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.30293	0.0760	M	0.76838	2.35	0.58432	D	0.999999	B	0.32573	0.376	B	0.33454	0.164	T	0.12041	-1.0563	10	0.52906	T	0.07	.	8.7974	0.34887	0.1512:0.7683:0.0:0.0805	.	2518	Q14204	DYHC1_HUMAN	M	2518	ENSP00000348965:I2518M	ENSP00000348965:I2518M	I	+	3	3	DYNC1H1	101552519	1.000000	0.71417	0.988000	0.46212	0.910000	0.53928	1.739000	0.38217	2.837000	0.97791	0.655000	0.94253	ATC		0.483	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102482766	C	G	102482766	3	3	94	1	0	0	0	0	1	0	0	0	4852	816	29	5	7700	5	DYNC1H1	14	102482766	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	7904690	102482766	4866774	136	25748										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27126103	27126103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctacgacaacagacttcggcCcgggctgggaggtgagtgtg	16	10	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:27126103C>T	ENST00000335625.5	+	4	1085	c.197C>T	c.(196-198)cCc>cTc	p.P66L	GABRA5_ENST00000400081.3_Missense_Mutation_p.P66L|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000557449.1_3'UTR|GABRA5_ENST00000355395.5_Missense_Mutation_p.P66L	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	66					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	AGACTTCGGCCCGGGCTGGGA	0.512																																																0			15											70	70	70					15																	27126103		2002	4172	6174	24677196	SO:0001583	missense	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.197C>T	15.37:g.27126103C>T	ENSP00000335592:p.Pro66Leu		24677196	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974144	0.92919	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599;ENST00000554083	D;D;D;D;D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57	5.55	5.55	0.83447	Neurotransmitter-gated ion-channel ligand-binding (3);	0.105687	0.64402	D	0.000003	D	0.98204	0.9406	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.99253	1.0888	10	0.87932	D	0	.	18.5045	0.90892	0.0:1.0:0.0:0.0	.	66	P31644	GBRA5_HUMAN	L	66;66;34;66;66;66;66;34	ENSP00000335592:P66L;ENSP00000347557:P66L;ENSP00000450653:P34L;ENSP00000382953:P66L;ENSP00000451527:P66L;ENSP00000450806:P66L;ENSP00000450717:P66L;ENSP00000450529:P34L	ENSP00000335592:P66L	P	+	2	0	GABRA5	24677196	1.000000	0.71417	0.961000	0.40146	0.844000	0.47949	7.617000	0.83032	2.614000	0.88457	0.561000	0.74099	CCC		0.512	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27126103	C	T	27126103	3	4	94	1	0	0	0	0	1	0	0	0	6183	623	22	3	203	3	GABRA5	15	27126103	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10		27126103	75405289	137	25749										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31319180	31319180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcctgcagcggccgctgagaCgcataatgatgatgtagatg	13	9	0	4	rs200369359		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:31319180C>T	ENST00000256552.6	-	26	3581	c.3434G>A	c.(3433-3435)cGt>cAt	p.R1145H	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.R1162H|TRPM1_ENST00000397795.2_Missense_Mutation_p.R1123H	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1									p.R1123H(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GCCGCTGAGACGCATAATGAT	0.488																																																1	Substitution - Missense(1)	large_intestine(1)	15											129	124	125					15																	31319180		1937	4154	6091	29106472	SO:0001583	missense	4308			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3434G>A	15.37:g.31319180C>T	ENSP00000256552:p.Arg1145His		29106472		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509850	0.27036	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.55234	0.55;0.53;0.55	5.6	4.68	0.58851	.	0.049694	0.85682	N	0.000000	T	0.38295	0.1035	L	0.31926	0.97	0.50632	D	0.999882	B;B	0.28760	0.221;0.141	B;B	0.26202	0.067;0.018	T	0.17018	-1.0383	10	0.07325	T	0.83	-17.3962	14.2219	0.65833	0.0:0.9284:0.0:0.0716	.	1117;1123	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	H	1123;1162;1145;1123	ENSP00000380897:R1123H;ENSP00000437849:R1162H;ENSP00000256552:R1145H	ENSP00000256552:R1145H	R	-	2	0	TRPM1	29106472	0.994000	0.37717	0.781000	0.31783	0.137000	0.21094	3.330000	0.52068	1.364000	0.46038	0.655000	0.94253	CGT		0.488	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31319180	C	T	31319180	3	4	94	1	0	0	0	0	1	0	0	0	16625	536	19	1	1455	1	TRPM1	15	31319180	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4193077	31319180	71212212	138	25750										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40289214	40289214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cttctttgagatgtcctatcAccccatggtcacggcttcag	8	13	4	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:40289214A>G	ENST00000263791.5	+	19	2859	c.2816A>G	c.(2815-2817)cAc>cGc	p.H939R	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.H911R	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	939	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> Y (in a lung neuroendocrine carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATGTCCTATCACCCCATGGTC	0.403																																																0			15											241	224	229					15																	40289214		1856	4101	5957	38076506	SO:0001583	missense	440275			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.2816A>G	15.37:g.40289214A>G	ENSP00000263791:p.His939Arg		38076506	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	6.794	0.515425	0.12944	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.22945	1.93;1.93	5.98	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.177555	0.51477	D	0.000095	T	0.11281	0.0275	N	0.11255	0.115	0.33784	D	0.624643	B	0.02656	0.0	B	0.08055	0.003	T	0.19192	-1.0313	10	0.07990	T	0.79	-18.3238	8.7718	0.34737	0.8595:0.0:0.1405:0.0	.	939	Q9P2K8	E2AK4_HUMAN	R	939;911	ENSP00000263791:H939R;ENSP00000372174:H911R	ENSP00000263791:H939R	H	+	2	0	EIF2AK4	38076506	0.994000	0.37717	1.000000	0.80357	0.983000	0.72400	2.766000	0.47629	2.293000	0.77203	0.477000	0.44152	CAC		0.403	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40289214	A	G	40289214	3	3	94	1	0	0	0	0	1	0	0	0	5010	159	6	4	2890	4	EIF2AK4	15	40289214	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	8970034	40289214	62242178	139	25751										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54590047	54590047	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cagctgtatctggggccataCgattgaaaatcaatgtggag	12	7	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:54590047C>T	ENST00000260323.11	+	11	4027	c.4027C>T	c.(4027-4029)Cga>Tga	p.R1343*	UNC13C_ENST00000537900.1_Nonsense_Mutation_p.R1341*|UNC13C_ENST00000545554.1_Nonsense_Mutation_p.R1343*	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1343					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.R1343*(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TGGGGCCATACGATTGAAAAT	0.348																																																1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	15											71	69	70					15																	54590047		1857	4087	5944	52377339	SO:0001587	stop_gained	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4027C>T	15.37:g.54590047C>T	ENSP00000260323:p.Arg1343*		52377339	Q0P613|Q8ND48|Q96NP3	Nonsense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	43	10.396393	0.99397	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	.	.	.	5.59	2.46	0.29980	.	0.169417	0.49916	D	0.000125	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.329	0.66541	0.6135:0.3865:0.0:0.0	.	.	.	.	X	1343;1343;1341	.	ENSP00000260323:R1343X	R	+	1	2	UNC13C	52377339	0.566000	0.26618	0.824000	0.32777	0.978000	0.69477	0.394000	0.20834	0.648000	0.30732	0.650000	0.86243	CGA		0.348	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54590047	C	T	54590047	4	4	94	1	0	0	0	0	0	1	0	0	17026	528	19	1	4065	1	UNC13C	15	54590047	Nonsense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	14300833	54590047	47941345	140	25752										
PKM2	5315	hgsc.bcm.edu	37	chr15	72499525	72499525	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	caccgtccaatcatcatcttCtgagcaaggaagaccttctc	6	14	5	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:72499525C>T	ENST00000335181.5	-	7	1033	c.930G>A	c.(928-930)caG>caA	p.Q310Q	PKM_ENST00000565184.1_Silent_p.Q310Q|PKM_ENST00000568459.1_Silent_p.Q310Q|PKM_ENST00000389093.3_Silent_p.Q310Q|PKM_ENST00000449901.2_Silent_p.Q295Q|PKM_ENST00000565154.1_Silent_p.Q310Q|PKM_ENST00000319622.6_Silent_p.Q310Q|PKM_ENST00000568883.1_Silent_p.Q145Q	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	310	Interaction with POU5F1.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	TCATCATCTTCTGAGCAAGGA	0.532																																																0			15											116	84	95					15																	72499525		2199	4297	6496	70286579	SO:0001819	synonymous_variant	5315			M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.930G>A	15.37:g.72499525C>T			70286579	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																				0.532	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1			T	72499525	C	T	72499525	2	4	94	1	0	0	0	0	0	0	0	1	12008	912	32	3		3	PKM2	15	72499525	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	17909478	72499525	30031867	141	25753										
BNC1	646	hgsc.bcm.edu	37	chr15	83926804	83926804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctttcagaaggtaagctgcaCggaaatgatcttcactactc	8	10	3	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr15:83926804C>T	ENST00000345382.2	-	5	2460	c.2375G>A	c.(2374-2376)cGt>cAt	p.R792H	BNC1_ENST00000569704.1_Missense_Mutation_p.R785H|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	792					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						GTAAGCTGCACGGAAATGATC	0.443																																																0			15											152	135	141					15																	83926804		2203	4300	6503	81717808	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.2375G>A	15.37:g.83926804C>T	ENSP00000307041:p.Arg792His		81717808	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903640	0.33628	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.44083	0.93	5.73	-5.78	0.02362	.	0.862781	0.10360	N	0.684096	T	0.23330	0.0564	L	0.29908	0.895	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.29971	-0.9994	10	0.16420	T	0.52	-0.537	8.9029	0.35505	0.0:0.1291:0.3009:0.57	.	785;792	F5GY04;Q01954	.;BNC1_HUMAN	H	792;785	ENSP00000307041:R792H	ENSP00000307041:R792H	R	-	2	0	BNC1	81717808	0.000000	0.05858	0.009000	0.14445	0.902000	0.53008	-0.580000	0.05827	-1.041000	0.03266	0.563000	0.77884	CGT		0.443	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		T	83926804	C	T	83926804	3	4	94	1	0	0	0	0	1	0	0	0	1475	536	19	1	613	1	BNC1	15	83926804	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	11427279	83926804	18604588	142	25754										
MSLNL	401827	hgsc.bcm.edu	37	chr16	820888	820888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggtcccgctgctgccgaaggTctcatgggccttggtgtaga	15	11	1	1	rs12599339	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:820888T>C	ENST00000442466.1	-	12	1443	c.1444A>G	c.(1444-1446)Acc>Gcc	p.T482A	MSLNL_ENST00000293892.3_Missense_Mutation_p.T833A|MIR662_ENST00000384847.1_RNA			Q96KJ4	MSLNL_HUMAN	mesothelin-like	482					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.T833A(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(15)|ovary(2)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	36						CTGCCGAAGGTCTCATGGGCC	0.692													.|||	1855	0.370407	0.5802	0.3055	5008	,	,		10426	0.3284		0.2028	False		,,,				2504	0.3487															1	Substitution - Missense(1)	prostate(1)	16						C	ALA/THR	1768,2122		439,890,616	13	20	18		2497	4.8	1	16	dbSNP_120	18	1782,6484		216,1350,2567	yes	missense	MSLNL	NM_001025190.1	58	655,2240,3183	CC,CT,TT		21.5582,45.4499,29.2037	benign	833/1054	820888	3550,8606	1945	4133	6078	760889	SO:0001583	missense	401827					16p13.3	2008-08-06	2008-07-04	2008-07-04	ENSG00000162006	ENSG00000162006			14170	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 37"	C16orf37			Standard	NG_032123		Approved	MPFL		Q96KJ4		ENST00000442466.1:c.1444A>G	16.37:g.820888T>C	ENSP00000415767:p.Thr482Ala		760889		Missense_Mutation	SNP	ENST00000442466.1	37		719	0.3292124542124542	282	0.573170731707317	96	0.26519337016574585	188	0.32867132867132864	153	0.20184696569920843	C	0.767	-0.767001	0.02974	0.454499	0.215582	ENSG00000162006	ENST00000543963;ENST00000442466;ENST00000293892	T;T;T	0.05996	3.36;3.36;3.36	4.84	4.84	0.62591	.	0.141777	0.46145	N	0.000319	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35351	-0.9792	8	0.02654	T	1	-20.6114	10.7083	0.45969	0.0:0.9089:0.0:0.0911	rs12599339	482	Q96KJ4	MSLNL_HUMAN	A	532;482;833	ENSP00000441381:T532A;ENSP00000415767:T482A;ENSP00000293892:T833A	ENSP00000293892:T833A	T	-	1	0	MSLNL	760889	0.999000	0.42202	0.982000	0.44146	0.011000	0.07611	3.393000	0.52544	1.170000	0.42753	-0.215000	0.12644	ACC		0.692	MSLNL-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001025190		C	820888	T	C	820888	3	2	94	1	0	0	0	0	1	0	0	0	9912	1667	58	4	680	4	MSLNL	16	820888	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10		820888	89533865	143	25755										
MSLNL	401827	hgsc.bcm.edu	37	chr16	830710	830732	+	Intron	DEL	GGGTAGGTGACAGCTGTGTGCAC	GGGTAGGTGACAGCTGTGTGCAC	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gggtaggttacagtgtgcatGggtaggtgacagctgtgtgc					rs199603320|rs377530828|rs200443343	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	GGGTAGGTGACAGCTGTGTGCAC	GGGTAGGTGACAGCTGTGTGCAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:830710_830732delGGGTAGGTGACAGCTGTGTGCAC	ENST00000442466.1	-	2	37				MSLNL_ENST00000293892.3_Frame_Shift_Del_p.RAHSCHLP90fs			Q96KJ4	MSLNL_HUMAN	mesothelin-like						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(15)|ovary(2)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	36						CAGTGTGCATGGGTAGGTGACAGCTGTGTGCACGGGTAGGTGA	0.583																																																0			16																																								770733	SO:0001627	intron_variant	401827					16p13.3	2008-08-06	2008-07-04	2008-07-04	ENSG00000162006	ENSG00000162006			14170	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 37"	C16orf37			Standard	NG_032123		Approved	MPFL		Q96KJ4		ENST00000442466.1:c.38-548GTGCACACAGCTGTCACCTACCC>-	16.37:g.830710_830732delGGGTAGGTGACAGCTGTGTGCAC			770711		Frame_Shift_Del	DEL	ENST00000442466.1	37																																																																																					0.583	MSLNL-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001025190		-	830732	GGGTAGGTGACAGCTGTGTGCAC	-	830710	6	5	94	0	1	1	0	1	0	0	0	0	9912	1335	47	0		0	MSLNL	16	830710	Intron	DEL	GGGTAGGTGACAGCTGTGTGCAC	TCGA-DC-5869-01A-01D-1657-10	9822	830710	89524043	144	25756										
PRR25	388199	hgsc.bcm.edu	37	chr16	855717	855717	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctgcatttctgagctcccaaCcagctcaggaacagcgcagc	9	15	2	1	rs1005190	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:855717C>G	ENST00000301698.1	+	1	275	c.275C>G	c.(274-276)aCc>aGc	p.T92S		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	92			T -> S (in dbSNP:rs1005190).							large_intestine(1)|lung(1)|skin(1)	3						GAGCTCCCAACCAGCTCAGGA	0.647													A|||	2821	0.563299	0.8525	0.4726	5008	,	,		17560	0.4494		0.2833	False		,,,				2504	0.6421															0			16						A	SER/THR	2833,1047		1053,727,160	21	29	27		275	0.4	0	16	dbSNP_86	27	2410,5858		335,1740,2059	yes	missense	PRR25	NM_001013638.1	58	1388,2467,2219	GG,GC,CC		29.1485,26.9845,43.1594	benign	92/403	855717	5243,6905	1940	4134	6074	795718	SO:0001583	missense	0			BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.275C>G	16.37:g.855717C>G	ENSP00000301698:p.Thr92Ser		795718		Missense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	1043	0.4775641025641026	417	0.8475609756097561	159	0.43922651933701656	268	0.46853146853146854	199	0.262532981530343	A	0	-2.773183	0.00081	0.730155	0.291485	ENSG00000167945	ENST00000301698	T	0.36157	1.27	0.364	0.364	0.16124	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14309	-1.0477	8	0.87932	D	0	.	5.1656	0.15084	0.3575:0.6424:0.0:0.0	rs1005190;rs59369772;rs1005190	92	Q96S07	PRR25_HUMAN	S	92	ENSP00000301698:T92S	ENSP00000301698:T92S	T	+	2	0	PRR25	795718	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.151000	0.03175	-0.656000	0.05380	-0.694000	0.03704	ACC		0.647	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638		G	855717	C	G	855717	3	3	94	1	0	0	0	0	1	0	0	0	12631	507	18	5	277	5	PRR25	16	855717	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	25007	855717	89499036	145	25757										
TOX3	27324	hgsc.bcm.edu	37	chr16	52473381	52473383	+	In_Frame_Del	DEL	TGC	TGC	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gattaatttgctgctggagaTgctgctgctgctgctgcagg					rs376306249		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	TGC	TGC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:52473381_52473383delTGC	ENST00000219746.9	-	7	1769_1771	c.1485_1487delGCA	c.(1483-1488)cagcat>cat	p.Q495del	TOX3_ENST00000407228.3_In_Frame_Del_p.Q490del	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	495	Gln-rich.				apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						ctgctggagatgctgctgctgct	0.567																																																0			16							,	29,3881		2,25,1928					,	-11	0			19	64,7602		8,48,3777	no	coding,coding	TOX3	NM_001146188.1,NM_001080430.2	,	10,73,5705	A1A1,A1R,RR		0.8349,0.7417,0.8034	,	,		93,11483				51030884	SO:0001651	inframe_deletion	27324			U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"Trinucleotide (CAG) repeat containing"	11972	protein-coding gene	gene with protein product		611416	"trinucleotide repeat containing 9"	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.1485_1487delGCA	16.37:g.52473390_52473392delTGC	ENSP00000219746:p.Gln495del		51030882	B4DRD0|B5MCW4	In_Frame_Del	DEL	ENST00000219746.9	37	CCDS54009.1																																																																																				0.567	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037		-	52473383	TGC	-	52473381	7	5	94	1	0	1	0	1	0	0	0	0	16419	1464	51	0	247	0	TOX3	16	52473381	In_Frame_Del	DEL	TGC	TCGA-DC-5869-01A-01D-1657-10	51617664	52473381	37881372	146	25758										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81248745	81248745	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggacctggatgacctgccccAagccacagtgcacggtggca	13	14	0	1	rs8060294	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:81248745A>G	ENST00000525539.1	-	0	517				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GACCTGCCCCAAGCCACAGTG	0.627											OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1954	0.390176	0.5454	0.3473	5008	,	,		17841	0.4345		0.2962	False		,,,				2504	0.2618															0			16						G	SER/LEU,SER/LEU	1980,1928		535,910,509	17	22	20		518,518	3.8	0.5	16	dbSNP_116	20	2300,5980		328,1644,2168	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	145,145	863,2554,2677	GG,GA,AA		27.7778,49.3347,35.1165	benign,benign	173/992,173/2460	81248745	4280,7908	1954	4140	6094	79806246			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81248745A>G		1204	79806246	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		863	0.39514652014652013	269	0.5467479674796748	124	0.3425414364640884	233	0.40734265734265734	237	0.31266490765171506	G	11.07	1.529240	0.27387	0.506653	0.277778	ENSG00000166473	ENST00000337114	T	0.15487	2.42	4.76	3.79	0.43588	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.357637	0.26183	N	0.025853	T	0.00012	0.0000	.	.	.	0.39104	P	0.038654999999999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45220	-0.9276	8	0.02654	T	1	-0.5244	10.2659	0.43455	0.0742:0.1356:0.7902:0.0	rs8060294;rs52836656;rs8060294	173;173	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	S	173	ENSP00000337397:L173S	ENSP00000337397:L173S	L	-	2	0	PKD1L2	79806246	1.000000	0.71417	0.457000	0.27056	0.360000	0.29518	5.197000	0.65141	0.438000	0.26450	-0.134000	0.14843	TTG		0.627	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			G	81248745	A	G	81248745	1	3	94	0	1	0	0	0	0	0	0	0	11996	131	5	4		4	PKD1L2	16	81248745	RNA	SNP	A	TCGA-DC-5869-01A-01D-1657-10	28775364	81248745	9106008	147	25759										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84209864	84209864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgctgcaccactcacttccaGtggagacagggacagcgact	11	13	1	1	rs2288023	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:84209864G>C	ENST00000378553.5	+	11	2148	c.2024G>C	c.(2023-2025)aGt>aCt	p.S675T	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	675			S -> T (in dbSNP:rs2288023). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CTCACTTCCAGTGGAGACAGG	0.627													G|||	1340	0.267572	0.0613	0.4063	5008	,	,		17997	0.376		0.3439	False		,,,				2504	0.2577															0			16						G	THR/SER	491,3909	225.2+/-241.2	32,427,1741	46	42	43		2024	-1.7	0	16	dbSNP_100	43	3062,5538	457.8+/-364.4	561,1940,1799	yes	missense	DNAAF1	NM_178452.4	58	593,2367,3540	CC,CG,GG		35.6047,11.1591,27.3308	benign	675/726	84209864	3553,9447	2200	4300	6500	82767365	SO:0001583	missense	123872			BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.2024G>C	16.37:g.84209864G>C	ENSP00000367815:p.Ser675Thr		82767365	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	659	0.3017399267399267	36	0.07317073170731707	125	0.3453038674033149	237	0.4143356643356643	261	0.34432717678100266	G	9.612	1.131548	0.21041	0.111591	0.356047	ENSG00000154099	ENST00000378553	T	0.32023	1.47	4.34	-1.74	0.08056	.	1.806150	0.03273	N	0.185064	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	2.9999999999752447E-6	B;B	0.20988	0.05;0.021	B;B	0.20184	0.028;0.008	T	0.42666	-0.9438	9	0.15066	T	0.55	0.1543	5.967	0.19330	0.2144:0.5194:0.2662:0.0	rs2288023;rs17845738;rs17858688;rs2288023	439;675	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	T	675	ENSP00000367815:S675T	ENSP00000367815:S675T	S	+	2	0	DNAAF1	82767365	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.037000	0.12164	-0.128000	0.11641	0.563000	0.77884	AGT		0.627	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		C	84209864	G	C	84209864	3	2	94	1	0	0	0	0	1	0	0	0	9038	1029	36	5	2066	5	LRRC50	16	84209864	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	2961119	84209864	6144889	148	25760										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84402275	84402275	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aaactcggcttctcgggcggGggccgccagtaccaggcgct	15	14	1	0	rs62048787	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr16:84402275G>C	ENST00000262429.4	+	1	143	c.54G>C	c.(52-54)ggG>ggC	p.G18G	ATP2C2_ENST00000416219.2_Silent_p.G18G	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	18					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.G18G(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCTCGGGCGGGGGCCGCCAGT	0.706													G|||	2092	0.417732	0.5499	0.4856	5008	,	,		12564	0.4841		0.2714	False		,,,				2504	0.273															2	Substitution - coding silent(2)	prostate(2)	16						G		1340,2286		254,832,727	7	12	11		54	-6.1	0	16	dbSNP_129	11	1685,6367		219,1247,2560	no	coding-synonymous	ATP2C2	NM_014861.2		473,2079,3287	CC,CG,GG		20.9265,36.9553,25.9034		18/947	84402275	3025,8653	1813	4026	5839	82959776	SO:0001819	synonymous_variant	9914			AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.54G>C	16.37:g.84402275G>C			82959776	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																				0.706	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		C	84402275	G	C	84402275	2	2	94	1	0	0	0	0	0	0	0	1	1145	1219	43	5		5	ATP2C2	16	84402275	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	192411	84402275	5952478	149	25761										
SCARF1	8578	hgsc.bcm.edu	37	chr17	1548956	1548957	+	In_Frame_Ins	INS	-	-	AGC													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctgagtcccccgagtccagINSagcagcagcagcgggagcag					rs142617742|rs371158488	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:1548956_1548957insAGC	ENST00000263071.4	-	1	84_85	c.35_36insGCT	c.(34-36)ctc>ctGCTc	p.12_12L>LL	SCARF1_ENST00000348987.3_In_Frame_Ins_p.12_12L>LL|SCARF1_ENST00000571272.1_In_Frame_Ins_p.12_12L>LL|SCARF1_ENST00000574545.1_5'Flank	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	12					cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCGAGTCCAGAGCAGCAGCAG	0.698														199	0.0397364	0.0741	0.0115	5008	,	,		16590	0.001		0.0199	False		,,,				2504	0.0736															0			17							,,	296,3916		17,262,1827					,,	4	0.8		dbSNP_119	19	149,8047		4,141,3953	no	coding,coding,coding	SCARF1	NM_145352.2,NM_145350.1,NM_003693.2	,,	21,403,5780	A1A1,A1R,RR		1.818,7.0275,3.5864	,,	,,		445,11963				1495707	SO:0001652	inframe_insertion	8578			D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.33_35dupGCT	17.37:g.1548963_1548965dupAGC	ENSP00000263071:p.Leu12dup		1495706	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	In_Frame_Ins	INS	ENST00000263071.4	37	CCDS11007.1																																																																																				0.698	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		AGC	1548957	-	AGC	1548956	7	5	94	1	0	1	1	0	0	0	0	0	13920	929	33	0	2500	0	SCARF1	17	1548956	In_Frame_Ins	INS	-	TCGA-DC-5869-01A-01D-1657-10		1548956	79646254	150	25762										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	4020421	4020421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtatcattgacgagtgaataTcaaggccctccttcgactct	8	11	3	2	rs371226804		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:4020421T>C	ENST00000381638.2	-	3	663	c.539A>G	c.(538-540)gAt>gGt	p.D180G	ZZEF1_ENST00000574474.1_5'UTR|snoU13_ENST00000459263.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	180							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CGAGTGAATATCAAGGCCCTC	0.498																																																0			17						T	GLY/ASP	1,4405	2.1+/-5.4	0,1,2202	134	121	125		539	-6.3	0	17		125	0,8600		0,0,4300	no	missense	ZZEF1	NM_015113.3	94	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	180/2962	4020421	1,13005	2203	4300	6503	3967170	SO:0001583	missense	23140			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.539A>G	17.37:g.4020421T>C	ENSP00000371051:p.Asp180Gly		3967170	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.503123	0.00992	2.27E-4	0.0	ENSG00000074755	ENST00000381638	T	0.19105	2.17	5.76	-6.29	0.02013	.	0.413411	0.29106	N	0.013136	T	0.03651	0.0104	N	0.01048	-1.04	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31641	-0.9936	10	0.02654	T	1	-0.0349	8.1445	0.31104	0.0:0.4059:0.1019:0.4922	.	180;180	O43149-3;O43149	.;ZZEF1_HUMAN	G	180	ENSP00000371051:D180G	ENSP00000371051:D180G	D	-	2	0	ZZEF1	3967170	0.136000	0.22515	0.002000	0.10522	0.022000	0.10575	1.150000	0.31639	-0.980000	0.03524	-0.285000	0.09966	GAT		0.498	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	4020421	T	C	4020421	3	2	94	1	0	0	0	0	1	0	0	0	18294	1435	50	4	8558	4	ZZEF1	17	4020421	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	2471465	4020421	77174789	151	25763										
TP53	7157	hgsc.bcm.edu	37	chr17	7577508	7577508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tggctcctgacctggagtctTccagtgtgatgatggtgagg	15	8	1	4			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:7577508T>C	ENST00000269305.4	-	7	962	c.773A>G	c.(772-774)gAa>gGa	p.E258G	TP53_ENST00000455263.2_Missense_Mutation_p.E258G|TP53_ENST00000413465.2_Missense_Mutation_p.E258G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.E258G|TP53_ENST00000420246.2_Missense_Mutation_p.E258G|TP53_ENST00000445888.2_Missense_Mutation_p.E258G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.E258G(8)|p.E258V(5)|p.E258A(5)|p.?(1)|p.E258fs*85(1)|p.E258>XX(1)|p.E258fs*71(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)|p.E258L(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCTGGAGTCTTCCAGTGTGAT	0.582		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	34	Substitution - Missense(19)|Whole gene deletion(8)|Deletion - Frameshift(3)|Deletion - In frame(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(5)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|liver(3)|lung(3)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|ovary(2)|stomach(1)|soft_tissue(1)|biliary_tract(1)|breast(1)|testis(1)|urinary_tract(1)|pancreas(1)	17											136	97	110					17																	7577508		2203	4300	6503	7518233	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.773A>G	17.37:g.7577508T>C	ENSP00000269305:p.Glu258Gly		7518233	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.684597	0.68157	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99859	-7.24;-7.24;-7.24;-7.24;-7.24;-7.24;-7.24	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	M	0.92367	3.3	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0	D	0.96472	0.9349	10	0.72032	D	0.01	-21.9865	12.3101	0.54924	0.0:0.0:0.0:1.0	.	258;258;258;258;258	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	G	258;258;258;258;258;258;247;126	ENSP00000410739:E258G;ENSP00000352610:E258G;ENSP00000269305:E258G;ENSP00000398846:E258G;ENSP00000391127:E258G;ENSP00000391478:E258G;ENSP00000425104:E126G	ENSP00000269305:E258G	E	-	2	0	TP53	7518233	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	6.025000	0.70864	2.074000	0.62210	0.379000	0.24179	GAA		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577508	T	C	7577508	3	2	94	1	0	0	0	0	1	0	0	0	16421	1783	62	4	517	4	TP53	17	7577508	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	3557087	7577508	73617702	152	25764										
SOCS7	30837	hgsc.bcm.edu	37	chr17	36508688	36508688	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cagcagcagcagcagcagcaAcctcccccgcccccgcctcc	8	23	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:36508688A>G	ENST00000577233.1	+	1	561	c.561A>G	c.(559-561)caA>caG	p.Q187Q	SOCS7_ENST00000331159.5_Silent_p.Q187Q	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	187	Mediates interaction with SORBS3.|Poly-Gln.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					agcagcagcaACCTCCCCCGC	0.687																																																0			17											2	3	3					17																	36508688		1799	3725	5524	33762214	SO:0001819	synonymous_variant	122809			AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"Suppressors of cytokine signaling", "SH2 domain containing"	29846	protein-coding gene	gene with protein product	"Nck, Ash and phospholipase C binding protein", "NCK-associated protein 4"	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.561A>G	17.37:g.36508688A>G			33762214	A2VCU2|Q0IJ63	Silent	SNP	ENST00000577233.1	37	CCDS32637.1																																																																																				0.687	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052		G	36508688	A	G	36508688	2	3	94	1	0	0	0	0	0	0	0	1	14956	40	2	4		4	SOCS7	17	36508688	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	28931180	36508688	44686522	153	25765										
FMNL1	752	hgsc.bcm.edu	37	chr17	43323932	43323932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gacatcccggctcctctgtgAggccagcctgggagaagaga	14	12	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:43323932A>G	ENST00000331495.3	+	26	3608	c.3272A>G	c.(3271-3273)gAg>gGg	p.E1091G	FMNL1_ENST00000587489.1_Intron|MAP3K14-AS1_ENST00000588698.1_RNA|CTD-2020K17.4_ENST00000420431.2_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|CTD-2020K17.4_ENST00000591361.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA|FMNL1_ENST00000328118.3_Intron|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|CTD-2020K17.4_ENST00000589518.1_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	1091					actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CTCCTCTGTGAGGCCAGCCTG	0.647											OREG0024478	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(164;1247 1997 8702 11086 51972)											0			17											35	38	37					17																	43323932		2203	4298	6501	40679715	SO:0001583	missense	752			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.3272A>G	17.37:g.43323932A>G	ENSP00000329219:p.Glu1091Gly	915	40679715	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	37	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.002344	0.93227	.	.	ENSG00000184922	ENST00000331495	T	0.80738	-1.41	4.59	4.59	0.56863	.	.	.	.	.	T	0.80292	0.4596	N	0.22421	0.69	0.80722	D	1	D	0.67145	0.996	P	0.61477	0.889	T	0.80930	-0.1162	9	0.44086	T	0.13	.	13.2195	0.59879	1.0:0.0:0.0:0.0	.	1091	O95466	FMNL_HUMAN	G	1091	ENSP00000329219:E1091G	ENSP00000329219:E1091G	E	+	2	0	FMNL1	40679715	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.714000	0.91412	2.043000	0.60533	0.459000	0.35465	GAG		0.647	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		G	43323932	A	G	43323932	3	3	94	1	0	0	0	0	1	0	0	0	5970	304	11	4	3374	4	FMNL1	17	43323932	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	6815244	43323932	37871278	154	25766										
JMJD6	23210	hgsc.bcm.edu	37	chr17	74721622	74721623	+	Frame_Shift_Ins	INS	-	-	T													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	aactttggcaccttgtagtcINSttccaaaagtttccttcttt							TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr17:74721622_74721623insT	ENST00000397625.4	-	2	558_559	c.444_445insA	c.(442-447)gaagacfs	p.D149fs	JMJD6_ENST00000445478.2_Frame_Shift_Ins_p.D149fs|JMJD6_ENST00000585429.1_Frame_Shift_Ins_p.D149fs|METTL23_ENST00000586738.1_5'Flank|METTL23_ENST00000586200.1_5'Flank|METTL23_ENST00000591571.1_5'Flank|METTL23_ENST00000586752.1_5'Flank|METTL23_ENST00000588302.1_5'Flank|METTL23_ENST00000588822.1_5'Flank|METTL23_ENST00000590964.1_5'Flank|METTL23_ENST00000588783.1_5'Flank|METTL23_ENST00000589977.1_5'Flank|METTL23_ENST00000341249.6_5'Flank	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	149	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						ACCTTGTAGTCTTCCAAAAGTT	0.446																																																0			17																																								72233218	SO:0001589	frameshift_variant	23210			AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"phosphatidylserine receptor"	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.445dupA	17.37:g.74721624_74721624dupT	ENSP00000380750:p.Asp149fs		72233217	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Frame_Shift_Ins	INS	ENST00000397625.4	37	CCDS42384.1																																																																																				0.446	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167		T	74721623	-	T	74721622	7	5	94	1	0	1	1	0	0	0	0	0	7974	913	32	0	827	0	JMJD6	17	74721622	Frame_Shift_Ins	INS	-	TCGA-DC-5869-01A-01D-1657-10	31397690	74721622	6473588	155	25767										
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1004844	1004844	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gggcagctgtgcctggacccTggcaccaacgactcggccac	13	16	0	0	rs4806909	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:1004844T>C	ENST00000234389.3	+	3	1363	c.1344T>C	c.(1342-1344)ccT>ccC	p.P448P	GRIN3B_ENST00000588335.1_3'UTR|AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	448					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCCTGGACCCTGGCACCAACG	0.652													N|||	1605	0.320487	0.4213	0.2421	5008	,	,		15607	0.1667		0.3847	False		,,,				2504	0.3323															0			19						C		1841,2565	616.7+/-392.8	383,1075,745	51	50	50		1344	-9.2	0	19	dbSNP_111	50	3312,5280	623.5+/-397.5	640,2032,1624	no	coding-synonymous	GRIN3B	NM_138690.1		1023,3107,2369	CC,CT,TT		38.5475,41.7839,39.6446		448/1044	1004844	5153,7845	2203	4296	6499	955844	SO:0001819	synonymous_variant	116444				CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1344T>C	19.37:g.1004844T>C			955844	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																				0.652	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			C	1004844	T	C	1004844	2	2	94	1	0	0	0	0	0	0	0	1	6805	1567	55	4		4	GRIN3B	19	1004844	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10		1004844	58124139	156	25768										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36349690	36349690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaacctgacatgtcggagccGtggggatgcccgccctaccc	13	15	0	1	rs571708243		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:36349690G>A	ENST00000360202.5	+	4	644	c.446G>A	c.(445-447)cGt>cAt	p.R149H	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R99H|KIRREL2_ENST00000592409.1_Missense_Mutation_p.R149H|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R149H	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	149	Ig-like C2-type 2.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)		p.R149H(3)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGTCGGAGCCGTGGGGATGCC	0.612																																																3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	19											97	96	96					19																	36349690		2203	4300	6503	41041530	SO:0001583	missense	84063			AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.446G>A	19.37:g.36349690G>A	ENSP00000353331:p.Arg149His		41041530	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	G	1.470	-0.559959	0.03967	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.77620	-1.11;-1.11;-1.11	5.56	-1.45	0.08828	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.378405	0.18495	N	0.139527	T	0.60327	0.2260	L	0.28504	0.86	0.21416	N	0.999692	B;B;B;B;B	0.19331	0.008;0.007;0.018;0.035;0.035	B;B;B;B;B	0.16722	0.012;0.007;0.016;0.016;0.016	T	0.45731	-0.9241	10	0.26408	T	0.33	-3.9095	8.4803	0.33038	0.4985:0.0:0.5015:0.0	.	149;149;149;99;149	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	H	149;99;149;149	ENSP00000262625:R149H;ENSP00000345067:R99H;ENSP00000353331:R149H	ENSP00000262625:R149H	R	+	2	0	KIRREL2	41041530	0.000000	0.05858	0.591000	0.28745	0.031000	0.12232	-0.395000	0.07287	-0.058000	0.13177	-1.007000	0.02485	CGT		0.612	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36349690	G	A	36349690	3	1	94	1	0	0	0	0	1	0	0	0	8346	1145	40	1	460	1	KIRREL2	19	36349690	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	35344846	36349690	22779293	157	25769										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40366391	40366391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgcggggtcctggttgtagtTcccgcataagccacagagag	14	10	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:40366391T>C	ENST00000221347.6	-	30	13850	c.13843A>G	c.(13843-13845)Aac>Gac	p.N4615D		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4615	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			TGGTTGTAGTTCCCGCATAAG	0.677																																																0			19											47	54	52					19																	40366391		2202	4299	6501	45058231	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13843A>G	19.37:g.40366391T>C	ENSP00000221347:p.Asn4615Asp		45058231	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.697741	0.30142	.	.	ENSG00000090920	ENST00000221347	T	0.63096	-0.02	4.32	2.18	0.27775	von Willebrand factor, type D domain (3);	0.123851	0.50627	D	0.000106	T	0.50103	0.1596	L	0.41027	1.25	0.27172	N	0.960881	B	0.25048	0.117	B	0.31812	0.136	T	0.39542	-0.9609	10	0.26408	T	0.33	.	8.4372	0.32795	0.0:0.1816:0.0:0.8184	.	4615	Q9Y6R7	FCGBP_HUMAN	D	4615	ENSP00000221347:N4615D	ENSP00000221347:N4615D	N	-	1	0	FCGBP	45058231	0.997000	0.39634	1.000000	0.80357	0.301000	0.27625	2.629000	0.46485	0.767000	0.33267	0.254000	0.18369	AAC		0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		C	40366391	T	C	40366391	3	2	94	1	0	0	0	0	1	0	0	0	5797	1783	62	4	2402	4	FCGBP	19	40366391	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	4016701	40366391	18762592	158	25770										
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41354170	41354170	+	Frame_Shift_Del	DEL	C	C	-													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggaagattcctagcatcatgCgcaacagtgacaggaactct					rs145393137|rs28399445	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:41354170delC	ENST00000301141.5	-	4	628	c.608delG	c.(607-609)cgcfs	p.R203fs	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	203			R -> C (in allele CYP2A6*23; greatly reduced activity toward nicotine C- oxidation as well as reduced coumarin 7- hydroxylation; dbSNP:rs56256500). {ECO:0000269|PubMed:18216723, ECO:0000269|Ref.6}.|R -> S (in allele CYP2A6*16; dbSNP:rs56256500). {ECO:0000269|PubMed:15618701, ECO:0000269|PubMed:18216723}.		coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TAGCATCATGCGCAACAGTGA	0.562																																																0			19											173	150	158					19																	41354170		2203	4300	6503	46046010	SO:0001589	frameshift_variant	1548			AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.608delG	19.37:g.41354170delC	ENSP00000301141:p.Arg203fs		46046010	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Frame_Shift_Del	DEL	ENST00000301141.5	37	CCDS12568.1																																																																																				0.562	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		-	41354170	C	-	41354170	7	5	94	1	0	1	0	1	0	0	0	0	4168	768	27	0	900	0	CYP2A6	19	41354170	Frame_Shift_Del	DEL	C	TCGA-DC-5869-01A-01D-1657-10	987779	41354170	17774813	159	25771										
C19orf63	284361	hgsc.bcm.edu	37	chr19	50983930	50983930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtgtcggtggtgacgcacccCgggggctgccggggccatga	19	12	0	2	rs10409679	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:50983930C>T	ENST00000334976.6	+	5	541	c.495C>T	c.(493-495)ccC>ccT	p.P165P	CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000598585.1_Silent_p.P165P|EMC10_ENST00000376918.3_Silent_p.P165P	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	165						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGACGCACCCCGGGGGCTGCC	0.697													C|||	2712	0.541534	0.3389	0.6297	5008	,	,		13105	0.5556		0.5875	False		,,,				2504	0.6912															0			19						C	,	1652,2732		318,1016,858	24	25	25		495,495	-8.5	0.1	19	dbSNP_119	25	5033,3555		1498,2037,759	no	coding-synonymous,coding-synonymous	C19orf63	NM_175063.4,NM_206538.2	,	1816,3053,1617	TT,TC,CC		41.395,37.6825,48.4659	,	165/255,165/263	50983930	6685,6287	2192	4294	6486	55675742	SO:0001819	synonymous_variant	284361			BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.495C>T	19.37:g.50983930C>T			55675742	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Silent	SNP	ENST00000334976.6	37	CCDS12796.1																																																																																				0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		T	50983930	C	T	50983930	2	4	94	1	0	0	0	0	0	0	0	1	1951	639	23	1		1	C19orf63	19	50983930	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	9629760	50983930	8145053	160	25772										
KIR3DL1	3811	hgsc.bcm.edu	37	chr19	55327960	55327960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ctgcaccggcagcaccatgtCgctcatggtcgtcagcatgg	12	14	2	0	rs605219	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:55327960C>T	ENST00000391728.4	+	1	38	c.5C>T	c.(4-6)tCg>tTg	p.S2L	KIR3DL1_ENST00000326542.7_Missense_Mutation_p.S2L|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.S2L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	2			S -> L (in dbSNP:rs605219).		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		AGCACCATGTCGCTCATGGTC	0.597											OREG0003676	type=REGULATORY REGION|Gene=KIR3DL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	t|||	1829	0.365216	0.4327	0.3271	5008	,	,		7095	0.6002		0.174	False		,,,				2504	0.2556															0			19											30	39	36					19																	55327960		1107	3277	4384	60019772	SO:0001583	missense	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.5C>T	19.37:g.55327960C>T	ENSP00000375608:p.Ser2Leu	1007	60019772	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	C	9.183	1.024000	0.19433	.	.	ENSG00000167633	ENST00000391728;ENST00000326542;ENST00000358178	T;T;T	0.00493	7.08;7.14;7.0	0.388	0.388	0.16264	.	.	.	.	.	T	0.01061	0.0035	M	0.61703	1.905	0.29242	P	0.872557	B;D;B	0.61697	0.045;0.99;0.233	B;D;B	0.66847	0.008;0.947;0.039	T	0.55244	-0.8171	7	0.35671	T	0.21	.	.	.	.	rs605219;rs1049297;rs3189442;rs34986537	2;2;2	Q14946;F6QF33;P43629	.;.;KI3L1_HUMAN	L	2	ENSP00000375608:S2L;ENSP00000326868:S2L;ENSP00000350901:S2L	ENSP00000326868:S2L	S	+	2	0	KIR3DL1	60019772	0.000000	0.05858	0.069000	0.20011	0.070000	0.16714	-0.080000	0.11339	0.444000	0.26612	0.194000	0.17425	TCG		0.597	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		T	55327960	C	T	55327960	3	4	94	1	0	0	0	0	1	0	0	0	8341	893	31	1	7	1	KIR3DL1	19	55327960	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4344030	55327960	3801023	161	25773										
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55610394	55610394	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcctccacgccccagtgtgcCgctgcgtgcaggggagtcca	13	16	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:55610394C>T	ENST00000263433.3	-	5	816	c.801G>A	c.(799-801)gcG>gcA	p.A267A	PPP1R12C_ENST00000435544.2_Silent_p.A193A|PPP1R12C_ENST00000376393.2_Silent_p.A267A	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		CCCAGTGTGCCGCTGCGTGCA	0.711																																																0			19											16	15	15					19																	55610394		2134	4224	6358	60302206	SO:0001819	synonymous_variant	54776			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14947	protein-coding gene	gene with protein product	"myosin-binding subunit 85"	613245	"leukocyte receptor cluster (LRC) member 3", "protein phosphatase 1, regulatory (inhibitor) subunit 12C"	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.801G>A	19.37:g.55610394C>T			60302206		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																				0.711	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		T	55610394	C	T	55610394	2	4	94	1	0	0	0	0	0	0	0	1	12390	639	23	1		1	PPP1R12C	19	55610394	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	282434	55610394	3518589	162	25774										
C19orf51	352909	hgsc.bcm.edu	37	chr19	55672470	55672470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tgctcgtccgcaggaggctcTcgtcgtccgcttcgatgccg	13	15	1	0	rs2365725	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr19:55672470T>C	ENST00000524407.2	-	8	908	c.875A>G	c.(874-876)gAg>gGg	p.E292G	DNAAF3_ENST00000391720.4_Missense_Mutation_p.E339G|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000455045.1_Missense_Mutation_p.E238G|DNAAF3_ENST00000527223.2_Missense_Mutation_p.E360G|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	292			E -> G (in dbSNP:rs2365725).		axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CAGGAGGCTCTCGTCGTCCGC	0.716													t|||	1140	0.227636	0.5234	0.1455	5008	,	,		9834	0.0913		0.1421	False		,,,				2504	0.1145															0			19						T	GLY/GLU	1334,2304		255,824,740	4	7	6		1016	3.2	0.7	19	dbSNP_100	6	922,6602		75,772,2915	yes	missense	C19orf51	NM_178837.3	98	330,1596,3655	CC,CT,TT		12.2541,36.6685,20.2114	possibly-damaging	339/589	55672470	2256,8906	1819	3762	5581	60364282	SO:0001583	missense	352909			AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"chromosome 19 open reading frame 51", "ciliary dyskinesia, primary 2"	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.875A>G	19.37:g.55672470T>C	ENSP00000432046:p.Glu292Gly		60364282	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	37	CCDS59422.1	457	0.20924908424908426	260	0.5284552845528455	56	0.15469613259668508	45	0.07867132867132867	96	0.1266490765171504	T	13.36	2.213980	0.39102	0.366685	0.122541	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.22336	1.96;1.96	4.24	3.18	0.36537	.	0.812692	0.10927	N	0.618852	T	0.00012	0.0000	M	0.77486	2.375	0.51767	P	6.700000000003925E-5	P;P;B;P	0.41848	0.557;0.763;0.187;0.763	B;B;B;B	0.36845	0.234;0.229;0.073;0.229	T	0.43956	-0.9359	9	0.59425	D	0.04	-4.1385	8.5773	0.33605	0.0:0.0:0.3813:0.6186	rs2365725;rs2365725	360;238;313;292	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	G	360;238;339	ENSP00000394343:E238G;ENSP00000375600:E339G	ENSP00000301249:E360G	E	-	2	0	C19orf51	60364282	0.356000	0.24930	0.735000	0.30896	0.448000	0.32197	1.240000	0.32731	0.585000	0.29608	0.454000	0.30748	GAG		0.716	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837		C	55672470	T	C	55672470	3	2	94	1	0	0	0	0	1	0	0	0	1939	1551	54	4	770	4	C19orf51	19	55672470	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	62076	55672470	3456513	163	25775										
TBC1D20	128637	hgsc.bcm.edu	37	chr20	428640	428640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cactgatagccatgcgtctaAgggcagccacatcagtggga	12	11	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:428640A>G	ENST00000354200.4	-	2	296	c.149T>C	c.(148-150)cTt>cCt	p.L50P	Y_RNA_ENST00000384070.1_RNA	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	50					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				CATGCGTCTAAGGGCAGCCAC	0.493																																																0			20											170	128	143					20																	428640		2203	4300	6503	376640	SO:0001583	missense	128637			AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.149T>C	20.37:g.428640A>G	ENSP00000346139:p.Leu50Pro		376640	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	37	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379330	0.82682	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.04654	3.58	5.24	5.24	0.73138	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00142	-1.1997	10	0.87932	D	0	-16.212	14.4922	0.67660	1.0:0.0:0.0:0.0	.	50	Q96BZ9	TBC20_HUMAN	P	50;75	ENSP00000346139:L50P	ENSP00000246077:L75P	L	-	2	0	TBC1D20	376640	1.000000	0.71417	0.938000	0.37757	0.984000	0.73092	8.699000	0.91316	2.201000	0.70794	0.528000	0.53228	CTT		0.493	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		G	428640	A	G	428640	3	3	94	1	0	0	0	0	1	0	0	0	15648	72	3	4	1090	4	TBC1D20	20	428640	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10		428640	62596880	164	25776										
PRNP	5621	hgsc.bcm.edu	37	chr20	4680094	4680094	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggtggtggctgggggcagccCcatggtggtggctggggaca	22	8	0	0	rs138688873|rs112637437	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:4680094C>T	ENST00000379440.4	+	2	515	c.228C>T	c.(226-228)ccC>ccT	p.P76P	PRNP_ENST00000430350.2_Silent_p.P76P	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	7						integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)		p.P76P(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						GGGGGCAGCCCCATGGTGGTG	0.657													C|||	263	0.052516	0.1755	0.0274	5008	,	,		18121	0.001		0.0099	False		,,,				2504	0.001															1	Substitution - coding silent(1)	lung(1)	20						C	,,,,	28,4346		0,28,2159	20	21	21		228,228,228,228,228	-3.2	0.6	20	dbSNP_132	21	7,8561		0,7,4277	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRNP	NM_000311.3,NM_001080121.1,NM_001080122.1,NM_001080123.1,NM_183079.2	,,,,	0,35,6436	TT,TC,CC		0.0817,0.6401,0.2704	,,,,	76/254,76/254,76/254,76/254,76/254	4680094	35,12907	2187	4284	6471	4628094	SO:0001819	synonymous_variant	5621			M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"CD molecules"	9449	protein-coding gene	gene with protein product	"Creutzfeldt-Jakob disease", "Gerstmann-Strausler-Scheinker syndrome", "fatal familial insomnia", "p27-30"	176640	"prion protein (p27-30)"	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.228C>T	20.37:g.4680094C>T			4628094		Silent	SNP	ENST00000379440.4	37	CCDS13080.1																																																																																				0.657	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311		T	4680094	C	T	4680094	2	4	94	1	0	0	0	0	0	0	0	1	12578	610	22	3		3	PRNP	20	4680094	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4251454	4680094	58345426	165	25777										
SNX5	27131	hgsc.bcm.edu	37	chr20	17929564	17929564	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	tcaatgttgagcatgtagtaTcggaggagctctgttagctt	12	6	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:17929564T>C	ENST00000377768.3	-	11	1200	c.888A>G	c.(886-888)cgA>cgG	p.R296R	SNX5_ENST00000483485.1_5'UTR|SNX5_ENST00000377759.4_Silent_p.R296R	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	296	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						GCATGTAGTATCGGAGGAGCT	0.413																																																0			20											93	90	91					20																	17929564		2203	4300	6503	17877564	SO:0001819	synonymous_variant	27131			AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.888A>G	20.37:g.17929564T>C			17877564	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																				0.413	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			C	17929564	T	C	17929564	2	2	94	1	0	0	0	0	0	0	0	1	14942	1422	50	4		4	SNX5	20	17929564	Silent	SNP	T	TCGA-DC-5869-01A-01D-1657-10	13249470	17929564	45095956	166	25778										
FOXA2	3170	hgsc.bcm.edu	37	chr20	22563246	22563246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggagagcgagtggcggatggAgttctgccagcgctgctggt	19	8	1	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:22563246A>G	ENST00000377115.4	-	3	797	c.616T>C	c.(616-618)Tcc>Ccc	p.S206P	FOXA2_ENST00000419308.2_Missense_Mutation_p.S212P	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	206					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					TGGCGGATGGAGTTCTGCCAG	0.617																																																0			20											50	51	51					20																	22563246		2203	4300	6503	22511246	SO:0001583	missense	3170			AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"Forkhead boxes"	5022	protein-coding gene	gene with protein product		600288	"hepatocyte nuclear factor 3, beta"	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.616T>C	20.37:g.22563246A>G	ENSP00000366319:p.Ser206Pro		22511246	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745683	0.69418	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.97620	-4.46;-4.46;-4.46	4.98	4.98	0.66077	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);Transcription factor, fork head, conserved site (1);	0.000000	0.64402	U	0.000012	D	0.98943	0.9641	H	0.97829	4.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99097	1.0842	10	0.87932	D	0	.	10.4836	0.44708	0.8545:0.0:0.0:0.1455	.	206;212	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	P	206;206;212;92	ENSP00000366319:S206P;ENSP00000400341:S206P;ENSP00000315955:S212P	ENSP00000315955:S212P	S	-	1	0	FOXA2	22511246	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.063000	0.71162	1.867000	0.54127	0.468000	0.43344	TCC		0.617	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			G	22563246	A	G	22563246	3	3	94	1	0	0	0	0	1	0	0	0	6009	304	11	4	761	4	FOXA2	20	22563246	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	4633682	22563246	40462274	167	25779										
GDAP1L1	78997	hgsc.bcm.edu	37	chr20	42876150	42876150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gacccagtccttcagctcgcAgaaggtagagccgggccggg	15	13	1	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:42876150A>G	ENST00000342560.5	+	1	264	c.176A>G	c.(175-177)cAg>cGg	p.Q59R	GDAP1L1_ENST00000372952.3_Missense_Mutation_p.Q59R|GDAP1L1_ENST00000537864.1_5'UTR	NM_001256737.1|NM_024034.4	NP_001243666.1|NP_076939.3	Q96MZ0	GD1L1_HUMAN	ganglioside induced differentiation associated protein 1-like 1	59	GST N-terminal.									endometrium(1)|large_intestine(5)|lung(10)|pancreas(1)|prostate(1)	18		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TTCAGCTCGCAGAAGGTAGAG	0.706																																																0			20											7	9	8					20																	42876150		2074	4179	6253	42309564	SO:0001583	missense	78997				CCDS13328.1, CCDS74725.1, CCDS74726.1, CCDS74727.1	20q12	2012-02-09	2012-02-09		ENSG00000124194	ENSG00000124194			4213	protein-coding gene	gene with protein product							Standard	NM_024034		Approved		uc010zwl.3	Q96MZ0	OTTHUMG00000032530	ENST00000342560.5:c.176A>G	20.37:g.42876150A>G	ENSP00000341782:p.Gln59Arg		42309564	B7Z621|Q5TE60|Q68CW7|Q9BQJ7|Q9BQV4|Q9BWJ4|Q9H3Y2|Q9H4G5	Missense_Mutation	SNP	ENST00000342560.5	37	CCDS13328.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.192658	0.78902	.	.	ENSG00000124194	ENST00000342560;ENST00000372947;ENST00000372946;ENST00000545149;ENST00000438466;ENST00000372952	T;T;T	0.23754	1.89;1.89;1.89	4.2	4.2	0.49525	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.34948	0.0915	L	0.31065	0.9	0.80722	D	1	D;B;D;D	0.69078	0.985;0.379;0.997;0.993	D;B;D;D	0.74023	0.982;0.337;0.962;0.937	T	0.04255	-1.0965	10	0.23302	T	0.38	.	13.1148	0.59294	1.0:0.0:0.0:0.0	.	59;59;59;5	B7Z1I3;B7Z621;Q96MZ0;Q5JY50	.;.;GD1L1_HUMAN;.	R	59;57;59;28;59;59	ENSP00000341782:Q59R;ENSP00000392881:Q59R;ENSP00000362043:Q59R	ENSP00000341782:Q59R	Q	+	2	0	GDAP1L1	42309564	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	8.396000	0.90190	1.778000	0.52293	0.379000	0.24179	CAG		0.706	GDAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079356.1	NM_024034		G	42876150	A	G	42876150	3	3	94	1	0	0	0	0	1	0	0	0	6328	188	7	4	178	4	GDAP1L1	20	42876150	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	20312904	42876150	20149370	168	25780										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767043	57767043	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cggcagcaggcgacggcagcGgagaagccctgggatgccaa	17	12	0	1	rs259984	byFrequency	TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:57767043G>C	ENST00000371030.2	+	1	969	c.969G>C	c.(967-969)gcG>gcC	p.A323A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	323							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CGACGGCAGCGGAGAAGCCCT	0.716													.|||	1803	0.360024	0.5779	0.3141	5008	,	,		12009	0.3522		0.2356	False		,,,				2504	0.2342															0			20						C		1197,2125		240,717,704	11	14	13		969	-8.9	0	20	dbSNP_79	13	1317,6455		129,1059,2698	no	coding-synonymous	ZNF831	NM_178457.1		369,1776,3402	CC,CG,GG		16.9454,36.0325,22.6609		323/1678	57767043	2514,8580	1661	3886	5547	57200438	SO:0001819	synonymous_variant	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.969G>C	20.37:g.57767043G>C			57200438	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																				0.716	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57767043	G	C	57767043	2	2	94	1	0	0	0	0	0	0	0	1	18224	1103	39	5		5	ZNF831	20	57767043	Silent	SNP	G	TCGA-DC-5869-01A-01D-1657-10	14890893	57767043	5258477	169	25781										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62305428	62305428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agccccacccggagttcagcGcggactcccccagcccaggt	11	19	1	0	rs201365106		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr20:62305428G>A	ENST00000360203.5	+	10	1226	c.901G>A	c.(901-903)Gcg>Acg	p.A301T	RTEL1_ENST00000508582.2_Missense_Mutation_p.A325T|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.A301T|RTEL1_ENST00000318100.4_Missense_Mutation_p.A301T|RTEL1_ENST00000370018.3_Missense_Mutation_p.A301T					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			GGAGTTCAGCGCGGACTCCCC	0.662																																																0			20											61	61	61					20																	62305428		2203	4300	6503	61775872	SO:0001583	missense	51750			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.901G>A	20.37:g.62305428G>A	ENSP00000353332:p.Ala301Thr		61775872		Missense_Mutation	SNP	ENST00000360203.5	37		.	.	.	.	.	.	.	.	.	.	g	8.465	0.856265	0.17106	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000356810	D;D;T;D;T	0.81659	-1.51;-1.52;-1.46;-1.5;0.43	4.86	-1.31	0.09230	.	1.007960	0.07967	N	0.983347	T	0.64382	0.2593	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.10296	0.001;0.003;0.0;0.001	B;B;B;B	0.09377	0.004;0.001;0.001;0.002	T	0.45542	-0.9254	10	0.23302	T	0.38	0.1043	9.6182	0.39706	0.5928:0.0:0.4072:0.0	.	325;325;301;301	Q9NZ71-7;D6RBA3;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	T	301;301;325;301;351	ENSP00000359035:A301T;ENSP00000322287:A301T;ENSP00000424307:A325T;ENSP00000353332:A301T;ENSP00000349265:A351T	ENSP00000349265:A351T	A	+	1	0	AL353715.1	61775872	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.432000	0.21461	-0.207000	0.10187	-0.862000	0.03010	GCG		0.662	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62305428	G	A	62305428	3	1	94	1	0	0	0	0	1	0	0	0	13757	1087	38	1	935	1	RTEL1	20	62305428	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	4538385	62305428	720092	170	25782										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32639011	32639011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtctcaagcccatgtccactCggtccacccagatggggctc	10	16	1	1	rs371530269		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr21:32639011C>T	ENST00000286827.3	-	5	749	c.278G>A	c.(277-279)cGa>cAa	p.R93Q	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.R93Q	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	93					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CATGTCCACTCGGTCCACCCA	0.587																																																0			21						C	GLN/ARG	1,4405		0,1,2202	75	72	73		278	4.8	1	21		73	0,8600		0,0,4300	no	missense	TIAM1	NM_003253.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	93/1592	32639011	1,13005	2203	4300	6503	31560882	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.278G>A	21.37:g.32639011C>T	ENSP00000286827:p.Arg93Gln		31560882	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475275	0.84640	2.27E-4	0.0	ENSG00000156299	ENST00000286827;ENST00000541036;ENST00000455508	T;T	0.61510	0.25;0.1	4.83	4.83	0.62350	.	0.073583	0.56097	D	0.000035	T	0.68192	0.2974	L	0.46157	1.445	0.46678	D	0.999159	D;D;D	0.76494	0.999;0.999;0.999	P;P;P	0.60345	0.873;0.75;0.75	T	0.71968	-0.4432	10	0.87932	D	0	.	18.1054	0.89518	0.0:1.0:0.0:0.0	.	93;93;93	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	Q	93	ENSP00000286827:R93Q;ENSP00000441570:R93Q	ENSP00000286827:R93Q	R	-	2	0	TIAM1	31560882	1.000000	0.71417	0.989000	0.46669	0.990000	0.78478	5.365000	0.66116	2.505000	0.84491	0.591000	0.81541	CGA		0.587	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32639011	C	T	32639011	3	4	94	1	0	0	0	0	1	0	0	0	15929	884	31	1	4597	1	TIAM1	21	32639011	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10		32639011	15490884	171	25783										
C21orf33	8209	hgsc.bcm.edu	37	chr21	45560194	45560194	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agaagtggagcgtgtcctgaAggagttccaccaggccggga	16	9	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr21:45560194A>G	ENST00000291577.6	+	5	584	c.491A>G	c.(490-492)aAg>aGg	p.K164R	C21orf33_ENST00000427803.2_Missense_Mutation_p.K164R|C21orf33_ENST00000348499.5_Intron|C21orf33_ENST00000493883.1_3'UTR	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	164						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		CGTGTCCTGAAGGAGTTCCAC	0.622																																																0			21											106	102	103					21																	45560194		2203	4300	6503	44384622	SO:0001583	missense	8209			Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.491A>G	21.37:g.45560194A>G	ENSP00000291577:p.Lys164Arg		44384622	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	37	CCDS33580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.78|12.78	2.041999|2.041999	0.35989|0.35989	.|.	.|.	ENSG00000248354;ENSG00000160221;ENSG00000160221;ENSG00000160221|ENSG00000160221	ENST00000433711;ENST00000291577;ENST00000427803;ENST00000389690|ENST00000419699	T;T;T|.	0.80123|.	-1.34;-1.34;-1.34|.	4.29|4.29	1.55|1.55	0.23275|0.23275	ThiJ/PfpI (1);|.	0.276507|.	0.39083|.	N|.	0.001477|.	T|T	0.43233|0.43233	0.1238|0.1238	L|L	0.33245|0.33245	0.995|0.995	0.80722|0.80722	D|D	1|1	B|.	0.17038|.	0.02|.	B|.	0.20577|.	0.03|.	T|T	0.14868|0.14868	-1.0457|-1.0457	10|5	0.16896|.	T|.	0.51|.	-17.8592|-17.8592	7.2255|7.2255	0.26012|0.26012	0.751:0.0:0.249:0.0|0.751:0.0:0.249:0.0	.|.	164|.	P30042|.	ES1_HUMAN|.	R|G	143;164;164;137|80	ENSP00000291577:K164R;ENSP00000396655:K164R;ENSP00000374340:K137R|.	ENSP00000415634:K143R|.	K|R	+|+	2|1	0|2	C21orf33;AP001055.7|C21orf33	44384622|44384622	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.788000|0.788000	0.44548|0.44548	2.087000|2.087000	0.41653|0.41653	0.623000|0.623000	0.30267|0.30267	-0.379000|-0.379000	0.06801|0.06801	AAG|AGG		0.622	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649		G	45560194	A	G	45560194	3	3	94	1	0	0	0	0	1	0	0	0	2131	72	3	4	509	4	C21orf33	21	45560194	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	12921183	45560194	2569701	172	25784										
KCNJ4	3761	hgsc.bcm.edu	37	chr22	38823189	38823189	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gaagaccacaggctcaaagcGgtggccccacaggatctcgc	12	14	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr22:38823189G>A	ENST00000303592.3	-	2	1207	c.949C>T	c.(949-951)Cgc>Tgc	p.R317C	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	317					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					GGCTCAAAGCGGTGGCCCCAC	0.627																																																0			22											31	31	31					22																	38823189		2203	4300	6503	37153135	SO:0001583	missense	3761			U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.949C>T	22.37:g.38823189G>A	ENSP00000306497:p.Arg317Cys		37153135	Q14D44	Missense_Mutation	SNP	ENST00000303592.3	37	CCDS13971.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732631	0.69189	.	.	ENSG00000168135	ENST00000303592	D	0.95554	-3.74	4.83	4.83	0.62350	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97682	0.9240	M	0.90082	3.085	0.80722	D	1	D	0.67145	0.996	P	0.57244	0.816	D	0.98713	1.0705	10	0.87932	D	0	.	18.3485	0.90329	0.0:0.0:1.0:0.0	.	317	P48050	IRK4_HUMAN	C	317	ENSP00000306497:R317C	ENSP00000306497:R317C	R	-	1	0	KCNJ4	37153135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.625000	0.83145	2.401000	0.81631	0.555000	0.69702	CGC		0.627	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		A	38823189	G	A	38823189	3	1	94	1	0	0	0	0	1	0	0	0	8074	1116	39	1	392	1	KCNJ4	22	38823189	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10		38823189	12481377	173	25785										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43608506	43608506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccctccacaggggaagcagcCggtgcgcccgggctcaggct	15	16	1	0	rs550015784		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chr22:43608506C>T	ENST00000360835.4	-	17	2272	c.2146G>A	c.(2146-2148)Ggc>Agc	p.G716S	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	716					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GGGAAGCAGCCGGTGCGCCCG	0.652													C|||	1	0.000199681	0	0	5008	,	,		13011	0		0	False		,,,				2504	0.001															0			22											50	40	43					22																	43608506		2163	4233	6396	41938450	SO:0001583	missense	80274				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2146G>A	22.37:g.43608506C>T	ENSP00000354080:p.Gly716Ser		41938450	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	C	9.595	1.127122	0.20959	.	.	ENSG00000159307	ENST00000360835;ENST00000381243	T	0.12879	2.64	4.12	-8.24	0.01029	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.551444	0.20256	N	0.095975	T	0.01800	0.0057	N	0.00157	-1.96	0.24424	N	0.994607	B	0.02656	0.0	B	0.04013	0.001	T	0.42548	-0.9445	10	0.15952	T	0.53	.	9.1871	0.37176	0.0:0.2333:0.37:0.3967	.	716	Q8IWY4	SCUB1_HUMAN	S	716;346	ENSP00000354080:G716S	ENSP00000354080:G716S	G	-	1	0	SCUBE1	41938450	0.007000	0.16637	0.005000	0.12908	0.775000	0.43874	0.077000	0.14738	-1.908000	0.01086	-1.945000	0.00491	GGC		0.652	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		T	43608506	C	T	43608506	3	4	94	1	0	0	0	0	1	0	0	0	13981	652	23	1	844	1	SCUBE1	22	43608506	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4785317	43608506	7696060	174	25786										
SHROOM2	357	hgsc.bcm.edu	37	chrX	9900582	9900582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gcgcacctgctgacgcccccGtgggcgtcctcggcaggccc	14	19	0	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:9900582G>A	ENST00000380913.3	+	6	3349	c.3259G>A	c.(3259-3261)Gtg>Atg	p.V1087M	SHROOM2_ENST00000418909.2_5'UTR|SHROOM2_ENST00000493668.1_3'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1087					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				TGACGCCCCCGTGGGCGTCCT	0.692																																																0			X											32	31	31					X																	9900582		2202	4300	6502	9860582	SO:0001583	missense	357			X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.3259G>A	X.37:g.9900582G>A	ENSP00000370299:p.Val1087Met		9860582	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.103438	0.56291	.	.	ENSG00000146950	ENST00000380913	T	0.14516	2.5	4.27	-0.00577	0.14016	.	.	.	.	.	T	0.06554	0.0168	N	0.08118	0	0.09310	N	0.999998	B	0.06786	0.001	B	0.01281	0.0	T	0.40194	-0.9576	9	0.30078	T	0.28	.	8.6797	0.34201	0.0:0.4757:0.3896:0.1346	.	1087	Q13796	SHRM2_HUMAN	M	1087	ENSP00000370299:V1087M	ENSP00000370299:V1087M	V	+	1	0	SHROOM2	9860582	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.455000	0.21843	-0.117000	0.11872	-0.178000	0.13098	GTG		0.692	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		A	9900582	G	A	9900582	3	1	94	1	0	0	0	0	1	0	0	0	14331	1145	40	1	3281	1	SHROOM2	23	9900582	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10		9900582	145369978	175	25787										
MAGEB1	4112	hgsc.bcm.edu	37	chrX	30268764	30268764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	taggggatactcccacaagcTcccctgctgctggcattccc	9	16	0	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:30268764T>C	ENST00000378981.3	+	4	475	c.154T>C	c.(154-156)Tcc>Ccc	p.S52P	MAGEB1_ENST00000397548.2_Missense_Mutation_p.S52P|MAGEB1_ENST00000397550.1_Missense_Mutation_p.S52P	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	52										NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						TCCCACAAGCTCCCCTGCTGC	0.592																																																0			X											36	29	31					X																	30268764		2202	4299	6501	30178685	SO:0001583	missense	4112				CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 10", "cancer/testis antigen family 3, member 1"	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.154T>C	X.37:g.30268764T>C	ENSP00000368264:p.Ser52Pro		30178685	B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Missense_Mutation	SNP	ENST00000378981.3	37	CCDS14222.1	.	.	.	.	.	.	.	.	.	.	T	9.580	1.123272	0.20959	.	.	ENSG00000214107	ENST00000378981;ENST00000397550;ENST00000397548	T;T;T	0.05382	3.45;3.45;3.45	3.99	-2.03	0.07365	Melanoma associated antigen, MAGE, N-terminal (1);	0.874836	0.09509	N	0.792582	T	0.07773	0.0195	L	0.58428	1.81	0.09310	N	1	B	0.22276	0.067	B	0.33750	0.169	T	0.45920	-0.9228	10	0.33940	T	0.23	.	3.7609	0.08603	0.4993:0.1142:0.0:0.3865	.	52	P43366	MAGB1_HUMAN	P	52	ENSP00000368264:S52P;ENSP00000380683:S52P;ENSP00000380681:S52P	ENSP00000368264:S52P	S	+	1	0	MAGEB1	30178685	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.955000	0.03869	-0.475000	0.06852	-0.314000	0.08810	TCC		0.592	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363		C	30268764	T	C	30268764	3	2	94	1	0	0	0	0	1	0	0	0	9202	1551	54	4	156	4	MAGEB1	23	30268764	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	20368182	30268764	125001796	176	25788										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961413	34961413	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gtgctgaaacagctggatccCgagaggaagctggaggacgc	16	9	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:34961413C>T	ENST00000329357.5	+	1	501	c.465C>T	c.(463-465)ccC>ccT	p.P155P		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	155										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGCTGGATCCCGAGAGGAAGC	0.562																																																0			X											56	50	52					X																	34961413		2202	4300	6502	34871334	SO:0001819	synonymous_variant	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.465C>T	X.37:g.34961413C>T			34871334	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																				0.562	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34961413	C	T	34961413	2	4	94	1	0	0	0	0	0	0	0	1	5589	639	23	1		1	FAM47B	23	34961413	Silent	SNP	C	TCGA-DC-5869-01A-01D-1657-10	4692649	34961413	120309147	177	25789										
DGKK	139189	hgsc.bcm.edu	37	chrX	50111945	50111945	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccagctttcaagggctacagTtgagatctcgatggtgttag	12	8	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:50111945T>C	ENST00000376025.2	-	0	3868							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					AGGGCTACAGTTGAGATCTCG	0.393																																																0			X											173	142	152					X																	50111945		1886	4114	6000	50128685			139189			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50111945T>C			50128685	B2RP91	Missense_Mutation	SNP	ENST00000376025.2	37																																																																																					0.393	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742		C	50111945	T	C	50111945	1	2	94	0	1	0	0	0	0	0	0	0	4483	1722	60	4		4	DGKK	23	50111945	RNA	SNP	T	TCGA-DC-5869-01A-01D-1657-10	15150532	50111945	105158615	178	25790										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	94	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-DC-5869-01A-01D-1657-10	238813	50350758	104919802	179	25791										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53610679	53610679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	catggcatatttgtggtcccGggtgagcctcagacagagac	13	10	1	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:53610679G>A	ENST00000342160.3	-	41	5816	c.5359C>T	c.(5359-5361)Cgg>Tgg	p.R1787W	HUWE1_ENST00000262854.6_Missense_Mutation_p.R1787W			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1787					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTGTGGTCCCGGGTGAGCCTC	0.522																																																0			X											115	90	99					X																	53610679		2203	4300	6503	53627404	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.5359C>T	X.37:g.53610679G>A	ENSP00000340648:p.Arg1787Trp		53627404	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.9|20.9	4.069963|4.069963	0.76301|0.76301	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052|ENST00000342160;ENST00000262854	.|T;T	.|0.57107	.|0.42;0.42	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72653|0.72653	0.3487|0.3487	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	T|T	0.75806|0.75806	-0.3188|-0.3188	5|10	.|0.87932	.|D	.|0	.|.	17.2084|17.2084	0.86924|0.86924	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1787;1787	.|Q7Z6Z7;Q7Z6Z7-2	.|HUWE1_HUMAN;.	L|W	820|1787	.|ENSP00000340648:R1787W;ENSP00000262854:R1787W	.|ENSP00000262854:R1787W	P|R	-|-	2|1	0|2	HUWE1|HUWE1	53627404|53627404	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.589000|7.589000	0.82641|0.82641	2.329000|2.329000	0.79093|0.79093	0.600000|0.600000	0.82982|0.82982	CCG|CGG		0.522	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53610679	G	A	53610679	3	1	94	1	0	0	0	0	1	0	0	0	7482	1115	39	1	7937	1	HUWE1	23	53610679	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	3259921	53610679	101659881	180	25792										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54780087	54780087	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gttcttggggctcttacctgCctttgggtcctctatgagct	11	11	3	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:54780087C>A	ENST00000218436.6	-	11	3378	c.3349G>T	c.(3349-3351)Gca>Tca	p.A1117S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1117					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTCTTACCTGCCTTTGGGTCC	0.498																																																0			X											108	91	97					X																	54780087		2203	4300	6503	54796812	SO:0001583	missense	347365			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3349G>T	X.37:g.54780087C>A	ENSP00000218436:p.Ala1117Ser		54796812	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	C	5.610	0.297323	0.10622	.	.	ENSG00000102313	ENST00000218436	T	0.09445	2.98	3.25	3.25	0.37280	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	7739.210000	0.00582	N	0.000334	T	0.09818	0.0241	N	0.04787	-0.16	0.22171	N	0.999316	D	0.55605	0.972	P	0.51701	0.677	T	0.39165	-0.9627	10	0.11794	T	0.64	.	7.8874	0.29659	0.0:0.8665:0.0:0.1335	.	1117	Q6UXX5	ITH5L_HUMAN	S	1117	ENSP00000218436:A1117S	ENSP00000218436:A1117S	A	-	1	0	ITIH5L	54796812	0.017000	0.18338	0.987000	0.45799	0.261000	0.26267	0.023000	0.13533	1.208000	0.43306	0.417000	0.27973	GCA		0.498	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54780087	C	A	54780087	3	1	94	1	0	0	0	0	1	0	0	0	7929	739	26	2	604	2	ITIH5L	23	54780087	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	1169408	54780087	100490473	181	25793										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71360009	71360009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agagaaagacaaaacctcccGtagctgagaagcctccggtg	11	11	0	3	rs138074424		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:71360009G>A	ENST00000373677.1	+	2	2775	c.1513G>A	c.(1513-1515)Gta>Ata	p.V505I	NHSL2_ENST00000540800.1_Missense_Mutation_p.V871I|NHSL2_ENST00000510661.1_Missense_Mutation_p.V640I|NHSL2_ENST00000535692.1_Missense_Mutation_p.V505I			Q5HYW2	NHSL2_HUMAN	NHS-like 2	505										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					AAAACCTCCCGTAGCTGAGAA	0.537																																																0			X						G	ILE/VAL	0,3835		0,0,1632,571	50	44	46		2611	-2.6	0	X	dbSNP_134	46	1,6726		0,1,2427,1871	yes	missense	NHSL2	NM_001013627.2	29	0,1,4059,2442	AA,AG,GG,G		0.0149,0.0,0.0095	benign	871/1226	71360009	1,10561	2203	4299	6502	71276734	SO:0001583	missense	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1513G>A	X.37:g.71360009G>A	ENSP00000362781:p.Val505Ile		71276734	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	37		.	.	.	.	.	.	.	.	.	.	G	0.100	-1.154225	0.01700	0.0	1.49E-4	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.49139	1.4;0.81;0.79;0.81	5.65	-2.61	0.06171	.	0.338179	0.25723	N	0.028738	T	0.20618	0.0496	N	0.04959	-0.14	0.09310	N	0.999996	B;B;B	0.22211	0.066;0.066;0.066	B;B;B	0.17098	0.017;0.017;0.017	T	0.22068	-1.0227	10	0.09084	T	0.74	-0.0705	13.6317	0.62200	0.2087:0.0:0.7913:0.0	.	871;640;505	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	I	871;505;640;505	ENSP00000444617:V871I;ENSP00000362781:V505I;ENSP00000424079:V640I;ENSP00000444914:V505I	ENSP00000362781:V505I	V	+	1	0	NHSL2	71276734	0.930000	0.31532	0.031000	0.17742	0.929000	0.56500	1.131000	0.31406	-1.033000	0.03299	-0.380000	0.06706	GTA		0.537	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71360009	G	A	71360009	3	1	94	1	0	0	0	0	1	0	0	0	10443	1145	40	1	2633	1	NHSL2	23	71360009	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	16579922	71360009	83910551	182	25794										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104440214	104440214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	atacatggctttggcaggtgAaccagtccgagtgaaatgtg	13	7	0	2			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:104440214A>G	ENST00000372582.1	+	3	896	c.140A>G	c.(139-141)gAa>gGa	p.E47G	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.E47G	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	47	Ig-like C2-type 1.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TTGGCAGGTGAACCAGTCCGA	0.448																																																0			X											175	139	151					X																	104440214		2203	4300	6503	104326870	SO:0001583	missense	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.140A>G	X.37:g.104440214A>G	ENSP00000361663:p.Glu47Gly		104326870	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480357	0.84747	.	.	ENSG00000189108	ENST00000372582;ENST00000344799	T;T	0.78595	-1.19;-1.19	5.59	5.59	0.84812	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000018	D	0.89047	0.6604	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.90873	0.4747	10	0.87932	D	0	.	13.9029	0.63817	1.0:0.0:0.0:0.0	.	47	Q9NP60	IRPL2_HUMAN	G	47	ENSP00000361663:E47G;ENSP00000344976:E47G	ENSP00000344976:E47G	E	+	2	0	IL1RAPL2	104326870	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.907000	0.92634	1.880000	0.54463	0.486000	0.48141	GAA		0.448	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		G	104440214	A	G	104440214	3	3	94	1	0	0	0	0	1	0	0	0	7683	246	9	4	146	4	IL1RAPL2	23	104440214	Missense_Mutation	SNP	A	TCGA-DC-5869-01A-01D-1657-10	33080205	104440214	50830346	183	25795										
CLDN2	9075	hgsc.bcm.edu	37	chrX	106171824	106171824	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	agagtggcggtagcaggtggAgtctttttcatccttggagg	16	6	2	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:106171824A>G	ENST00000541806.1	+	2	885	c.366A>G	c.(364-366)ggA>ggG	p.G122G	CLDN2_ENST00000336803.1_Silent_p.G122G|CLDN2_ENST00000540876.1_Silent_p.G122G	NM_001171092.1	NP_001164563.1	P57739	CLD2_HUMAN	claudin 2	122					calcium-independent cell-cell adhesion (GO:0016338)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						TAGCAGGTGGAGTCTTTTTCA	0.542																																																0			X											127	109	115					X																	106171824		2203	4300	6503	106058480	SO:0001819	synonymous_variant	9075			AK075405	CCDS14524.1	Xq22.3-q23	2008-05-14			ENSG00000165376	ENSG00000165376		"Claudins"	2041	protein-coding gene	gene with protein product		300520				9892664	Standard	NM_020384		Approved		uc022ccc.1	P57739	OTTHUMG00000022154	ENST00000541806.1:c.366A>G	X.37:g.106171824A>G			106058480	B2R6B9	Silent	SNP	ENST00000541806.1	37	CCDS14524.1																																																																																				0.542	CLDN2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057815.1			G	106171824	A	G	106171824	2	3	94	1	0	0	0	0	0	0	0	1	3487	291	11	4		4	CLDN2	23	106171824	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	1731610	106171824	49098736	184	25796										
ALG13	79868	hgsc.bcm.edu	37	chrX	110987996	110987996	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ccaccaccaccaccaccaccAcctcctcctcctcctcctcc	0	28	0	0	rs56717389		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:110987996A>T	ENST00000394780.3	+	24	2808	c.2796A>T	c.(2794-2796)ccA>ccT	p.P932P	ALG13_ENST00000470971.1_3'UTR|ALG13_ENST00000251943.4_Intron	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	932	Pro-rich.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)	p.P932P(7)		endometrium(2)|lung(10)|skin(1)	13						caccaccaccacctcctcctc	0.567																																																7	Substitution - coding silent(7)	endometrium(7)	X											10	8	8					X																	110987996		1493	3408	4901	110874652	SO:0001819	synonymous_variant	79868			AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"Tudor domain containing", "OTU domain containing"	30881	protein-coding gene	gene with protein product	"tudor domain containing 13", "N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"	300776	"glycosyltransferase 28 domain containing 1", "chromosome X open reading frame 45", "asparagine-linked glycosylation 13 homolog (S. cerevisiae)"	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2796A>T	X.37:g.110987996A>T			110874652	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Silent	SNP	ENST00000394780.3	37	CCDS55477.1																																																																																				0.567	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466		T	110987996	A	T	110987996	2	4	94	1	0	0	0	0	0	0	0	1	515	146	6	5		5	ALG13	23	110987996	Silent	SNP	A	TCGA-DC-5869-01A-01D-1657-10	4816172	110987996	44282564	185	25797										
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130215773	130215773	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	cccaggacacaaccccgaccGcaggacgaagatggtatcga	11	14	0	1	rs368664815		TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:130215773G>T	ENST00000276211.5	+	2	479	c.134G>T	c.(133-135)cGc>cTc	p.R45L	ARHGAP36_ENST00000370921.1_5'Flank|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.R33L	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	45					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R45H(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						AACCCCGACCGCAGGACGAAG	0.552																																																1	Substitution - Missense(1)	prostate(1)	X						G	LEU/ARG	0,3835		0,0,1632,571	152	125	134		134	1.4	0	X		134	1,6727		0,1,2427,1872	no	missense	ARHGAP36	NM_144967.3	102	0,1,4059,2443	TT,TG,GG,G		0.0149,0.0,0.0095	probably-damaging	45/548	130215773	1,10562	2203	4300	6503	130043454	SO:0001583	missense	0				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.134G>T	X.37:g.130215773G>T	ENSP00000276211:p.Arg45Leu		130043454	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	G	3.610	-0.079756	0.07141	0.0	1.49E-4	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000412432	T;T;T	0.10382	2.88;2.88;2.9	4.16	1.4	0.22301	.	0.857059	0.09796	N	0.754700	T	0.06600	0.0169	N	0.19112	0.55	0.09310	N	1	B;B;B	0.34372	0.433;0.433;0.451	B;B;B	0.34536	0.185;0.185;0.127	T	0.37056	-0.9722	10	0.52906	T	0.07	.	2.9375	0.05819	0.2397:0.0:0.5418:0.2185	.	14;33;45	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	L	45;33;14	ENSP00000276211:R45L;ENSP00000359960:R33L;ENSP00000408515:R14L	ENSP00000276211:R45L	R	+	2	0	ARHGAP36	130043454	0.060000	0.20803	0.001000	0.08648	0.106000	0.19336	-0.006000	0.12833	0.156000	0.19299	-0.351000	0.07748	CGC		0.552	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130215773	G	T	130215773	3	4	94	1	0	0	0	0	1	0	0	0	883	1087	38	2	136	2	ARHGAP36	23	130215773	Missense_Mutation	SNP	G	TCGA-DC-5869-01A-01D-1657-10	19227777	130215773	25054787	186	25798										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140984899	140984899	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	gccagaaagtgaatccttgcCcaggtatgccctggatgaaa	11	10	0	3			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:140984899C>T	ENST00000298296.1	+	7	1355	c.1355C>T	c.(1354-1356)cCc>cTc	p.P452L	MAGEC3_ENST00000409007.1_Missense_Mutation_p.P154L|MAGEC3_ENST00000536088.1_Missense_Mutation_p.P154L|MAGEC3_ENST00000443323.2_Missense_Mutation_p.P74L|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000544766.1_Missense_Mutation_p.P154L	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	452										NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GAATCCTTGCCCAGGTATGCC	0.498																																																0			X											69	64	66					X																	140984899		2203	4300	6503	140812565	SO:0001583	missense	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1355C>T	X.37:g.140984899C>T	ENSP00000298296:p.Pro452Leu		140812565	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	c	0.540	-0.854203	0.02630	.	.	ENSG00000165509	ENST00000298296;ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T;T	0.03496	4.16;3.91;3.94;3.91;3.91	1.18	-0.485	0.12067	.	.	.	.	.	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B;B	0.18741	0.03;0.014	B;B	0.20384	0.029;0.014	T	0.49263	-0.8958	9	0.10902	T	0.67	.	3.3373	0.07106	0.0:0.4879:0.0:0.5121	.	452;154	Q8TD91;Q3SYA7	MAGC3_HUMAN;.	L	452;154;74;154;154	ENSP00000298296:P452L;ENSP00000441107:P154L;ENSP00000438254:P74L;ENSP00000440444:P154L;ENSP00000386566:P154L	ENSP00000298296:P452L	P	+	2	0	MAGEC3	140812565	0.000000	0.05858	0.000000	0.03702	0.545000	0.35147	-1.265000	0.02844	-0.234000	0.09782	0.179000	0.17066	CCC		0.498	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140984899	C	T	140984899	3	4	94	1	0	0	0	0	1	0	0	0	9212	623	22	3	1610	3	MAGEC3	23	140984899	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	10769126	140984899	14285661	187	25799										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140984944	140984944	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ggctgagttggtgcagtttcTtctcctcaaatatcaaacaa	8	9	4	1			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:140984944T>A	ENST00000298296.1	+	7	1400	c.1400T>A	c.(1399-1401)cTt>cAt	p.L467H	MAGEC3_ENST00000409007.1_Missense_Mutation_p.L169H|MAGEC3_ENST00000536088.1_Missense_Mutation_p.L169H|MAGEC3_ENST00000443323.2_Missense_Mutation_p.L89H|MAGEC3_ENST00000544766.1_Missense_Mutation_p.L169H	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	467	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GTGCAGTTTCTTCTCCTCAAA	0.458																																																0			X											96	89	91					X																	140984944		2203	4300	6503	140812610	SO:0001583	missense	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1400T>A	X.37:g.140984944T>A	ENSP00000298296:p.Leu467His		140812610	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	t	11.40	1.628972	0.28978	.	.	ENSG00000165509	ENST00000298296;ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T;T	0.07114	3.22;3.22;3.22;3.22;3.22	1.18	1.18	0.20946	.	.	.	.	.	T	0.32675	0.0837	H	0.94582	3.555	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.08229	-1.0732	9	0.87932	D	0	.	4.1545	0.10254	0.0:0.0:0.0:1.0	.	467;169	Q8TD91;Q3SYA7	MAGC3_HUMAN;.	H	467;169;89;169;169	ENSP00000298296:L467H;ENSP00000441107:L169H;ENSP00000438254:L89H;ENSP00000440444:L169H;ENSP00000386566:L169H	ENSP00000298296:L467H	L	+	2	0	MAGEC3	140812610	0.001000	0.12720	0.001000	0.08648	0.115000	0.19883	0.749000	0.26320	0.706000	0.31912	0.150000	0.16122	CTT		0.458	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		A	140984944	T	A	140984944	3	1	94	1	0	0	0	0	1	0	0	0	9212	1609	56	5	1655	5	MAGEC3	23	140984944	Missense_Mutation	SNP	T	TCGA-DC-5869-01A-01D-1657-10	45	140984944	14285616	188	25800										
AFF2	2334	hgsc.bcm.edu	37	chrX	147744068	147744068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.723687350835322	1.07212940864492	0.679518639281993	0.118881118881119	0.500120569086087	0	ttcaaaacttcccaccagggCtttactgcaaaacaagcatg	6	12	1	0			TCGA-DC-5869-01A-01D-1657-10	TCGA-DC-5869-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2a591f80-4da8-42e1-b6f6-a4b8e05bf084	33e9d02c-c3fb-403e-b626-b62da040983e	g.chrX:147744068C>A	ENST00000370460.2	+	3	1299	c.820C>A	c.(820-822)Ctt>Att	p.L274I	AFF2_ENST00000370457.5_Missense_Mutation_p.L270I|AFF2_ENST00000342251.3_Missense_Mutation_p.L270I|AFF2_ENST00000370458.1_Missense_Mutation_p.L270I	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	274					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CCCACCAGGGCTTTACTGCAA	0.532																																																0			X											91	92	91					X																	147744068		2203	4300	6503	147551760	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.820C>A	X.37:g.147744068C>A	ENSP00000359489:p.Leu274Ile		147551760	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507756	0.27036	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.71	3.92	0.45320	.	0.131543	0.51477	N	0.000082	T	0.73171	0.3553	L	0.46670	1.46	0.80722	D	1	B;B;B;B;B;B	0.20459	0.001;0.001;0.001;0.005;0.001;0.045	B;B;B;B;B;B	0.32864	0.005;0.005;0.005;0.01;0.009;0.154	T	0.67248	-0.5718	10	0.52906	T	0.07	.	10.2124	0.43150	0.2725:0.5988:0.1287:0.0	.	274;270;270;270;274;270	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	I	274;270;270;270	ENSP00000359489:L274I;ENSP00000359486:L270I;ENSP00000345459:L270I;ENSP00000359487:L270I	ENSP00000345459:L270I	L	+	1	0	AFF2	147551760	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.477000	0.53151	0.543000	0.28864	0.600000	0.82982	CTT		0.532	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	147744068	C	A	147744068	3	1	94	1	0	0	0	0	1	0	0	0	357	797	28	2	830	2	AFF2	23	147744068	Missense_Mutation	SNP	C	TCGA-DC-5869-01A-01D-1657-10	6759124	147744068	7526492	189	25801										
PRAMEF10	343071	hgsc.bcm.edu	37	chr1	12955474	12955474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cagatgaagtgtcttcatcaGggatcccagagggaggctga	14	8	3	4			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:12955474G>T	ENST00000235347.4	-	2	284	c.205C>A	c.(205-207)Ctg>Atg	p.L69M		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	69					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GTCTTCATCAGGGATCCCAGA	0.577																																																0			1											78	73	75					1																	12955474		2124	3827	5951	12878061	SO:0001583	missense	343071			AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"-"	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.205C>A	1.37:g.12955474G>T	ENSP00000235347:p.Leu69Met		12878061	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	11.77	1.737912	0.30774	.	.	ENSG00000187545	ENST00000235347	T	0.15487	2.42	1.99	1.99	0.26369	.	0.302894	0.27088	N	0.020983	T	0.38665	0.1049	M	0.82517	2.595	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.03695	-1.1012	10	0.56958	D	0.05	.	7.5431	0.27751	0.0:0.0:1.0:0.0	.	69	O60809	PRA10_HUMAN	M	69	ENSP00000235347:L69M	ENSP00000235347:L69M	L	-	1	2	PRAMEF10	12878061	0.518000	0.26234	0.018000	0.16275	0.034000	0.12701	0.646000	0.24797	1.431000	0.47355	0.400000	0.26472	CTG		0.577	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342		T	12955474	G	T	12955474	3	4	95	1	0	0	0	0	1	0	0	0	12460	991	35	2	1231	2	PRAMEF10	1	12955474	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10		12955474	236295147	1	25802			1	18		2	2	15	N	G_A	6.51211e-05
PRAMEF10	343071	hgsc.bcm.edu	37	chr1	12955488	12955488	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcatcagggatcccagagggAggctgaggaagggccaggcc	17	10	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:12955488A>T	ENST00000235347.4	-	2	270	c.191T>A	c.(190-192)cTc>cAc	p.L64H		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	64					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCAGAGGGAGGCTGAGGAA	0.582																																																0			1											83	76	79					1																	12955488		2125	3831	5956	12878075	SO:0001583	missense	343071			AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"-"	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.191T>A	1.37:g.12955488A>T	ENSP00000235347:p.Leu64His		12878075	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	12.20	1.865739	0.32977	.	.	ENSG00000187545	ENST00000235347	T	0.14516	2.5	1.99	1.99	0.26369	.	0.000000	0.64402	D	0.000003	T	0.41696	0.1170	H	0.94264	3.515	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.19418	-1.0306	10	0.87932	D	0	.	6.0147	0.19596	1.0:0.0:0.0:0.0	.	64	O60809	PRA10_HUMAN	H	64	ENSP00000235347:L64H	ENSP00000235347:L64H	L	-	2	0	PRAMEF10	12878075	0.831000	0.29352	0.054000	0.19295	0.012000	0.07955	1.654000	0.37334	1.174000	0.42811	0.329000	0.21502	CTC		0.582	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342		T	12955488	A	T	12955488	3	4	95	1	0	0	0	0	1	0	0	0	12460	304	11	5	1245	5	PRAMEF10	1	12955488	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	14	12955488	236295133	2	25803			1	18		2	2	15	N	G_A	6.51211e-05
WNT4	54361	hgsc.bcm.edu	37	chr1	22456337	22456337	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccccaccgacgacagcttggCcaggtacctggggagagggt	15	13	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:22456337C>T	ENST00000290167.6	-	2	128	c.85G>A	c.(85-87)Gcc>Acc	p.A29T	WNT4_ENST00000542383.1_5'UTR	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	29					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|embryonic epithelial tube formation (GO:0001838)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization to plasma membrane (GO:0090002)|female gonad development (GO:0008585)|female sex determination (GO:0030237)|immature T cell proliferation in thymus (GO:0033080)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|mammary gland epithelium development (GO:0061180)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric nephron morphogenesis (GO:0072273)|metanephric tubule formation (GO:0072174)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of gene expression (GO:0010629)|negative regulation of male gonad development (GO:2000019)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of testicular blood vessel morphogenesis (GO:0061369)|negative regulation of testosterone biosynthetic process (GO:2000225)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of wound healing (GO:0061045)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via MAPK cascade (GO:0038030)|oocyte development (GO:0048599)|paramesonephric duct development (GO:0061205)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cortisol biosynthetic process (GO:2000066)|positive regulation of dermatome development (GO:0061184)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of meiosis (GO:0045836)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|protein palmitoylation (GO:0018345)|regulation of cell-cell adhesion (GO:0022407)|renal vesicle formation (GO:0072033)|renal vesicle induction (GO:0072034)|smooth muscle cell differentiation (GO:0051145)|somatotropin secreting cell differentiation (GO:0060126)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	8		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-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;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GACAGCTTGGCCAGGTACCTG	0.627																																																0			1											130	125	127					1																	22456337		2203	4300	6503	22328924	SO:0001583	missense	54361			AL031281	CCDS223.1	1p36.23-p35.1	2013-02-28			ENSG00000162552	ENSG00000162552		"Wingless-type MMTV integration sites", "Endogenous ligands"	12783	protein-coding gene	gene with protein product		603490				8168088	Standard	NM_030761		Approved	WNT-4	uc001bfs.4	P56705	OTTHUMG00000002894	ENST00000290167.6:c.85G>A	1.37:g.22456337C>T	ENSP00000290167:p.Ala29Thr		22328924	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Missense_Mutation	SNP	ENST00000290167.6	37	CCDS223.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.030694|5.030694	0.93575|0.93575	.|.	.|.	ENSG00000162552|ENSG00000162552	ENST00000290167;ENST00000374655|ENST00000415567	T|.	0.77098|.	-1.07|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.348088|.	0.24599|.	U|.	0.037160|.	T|T	0.45296|0.45296	0.1335|0.1335	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.64237|.	0.923|.	T|T	0.42207|0.42207	-0.9465|-0.9465	10|5	0.87932|.	D|.	0|.	.|.	17.0573|17.0573	0.86537|0.86537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	29|.	P56705|.	WNT4_HUMAN|.	T|D	29|3	ENSP00000290167:A29T|.	ENSP00000290167:A29T|.	A|G	-|-	1|2	0|0	WNT4|WNT4	22328924|22328924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.896000|0.896000	0.52359|0.52359	7.810000|7.810000	0.86072|0.86072	2.360000|2.360000	0.80028|0.80028	0.462000|0.462000	0.41574|0.41574	GCC|GGC		0.627	WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2			T	22456337	C	T	22456337	3	4	95	1	0	0	0	0	1	0	0	0	17430	739	26	3	986	3	WNT4	1	22456337	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	9500849	22456337	226794284	3	25804										
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37949058	37949058	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtggggcagggcaggcagccTggccaaggagcaggccagcg	20	11	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:37949058T>C	ENST00000373087.6	+	6	1762	c.1646T>C	c.(1645-1647)cTg>cCg	p.L549P		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCAGGCAGCCTGGCCAAGGAG	0.662																																																0			1											49	59	55					1																	37949058		2203	4300	6503	37721645	SO:0001583	missense	80149				CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.1646T>C	1.37:g.37949058T>C	ENSP00000362179:p.Leu549Pro		37721645		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953790	0.34471	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.51574	0.7	5.15	5.15	0.70609	.	0.601634	0.14339	N	0.325840	T	0.43122	0.1233	L	0.51422	1.61	0.35754	D	0.819624	B;B	0.33637	0.42;0.003	B;B	0.29077	0.098;0.003	T	0.52548	-0.8561	10	0.35671	T	0.21	-20.9358	14.9753	0.71267	0.0:0.0:0.0:1.0	.	344;549	B3KSD3;Q5D1E8	.;ZC12A_HUMAN	P	549	ENSP00000362179:L549P	ENSP00000362174:L549P	L	+	2	0	ZC3H12A	37721645	0.285000	0.24296	0.999000	0.59377	0.976000	0.68499	1.842000	0.39250	1.938000	0.56188	0.459000	0.35465	CTG		0.662	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		C	37949058	T	C	37949058	3	2	95	1	0	0	0	0	1	0	0	0	17600	1580	55	4	1664	4	ZC3H12A	1	37949058	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	15492721	37949058	211301563	4	25805										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75039139	75039139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	attccttgtttgagttgattGctgctgtttcatccaccatg	8	9	1	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:75039139G>A	ENST00000326665.5	-	14	2473	c.2255C>T	c.(2254-2256)gCa>gTa	p.A752V	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		752	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGAGTTGATTGCTGCTGTTTC	0.408																																																0			1											85	87	87					1																	75039139		2203	4300	6503	74811727	SO:0001583	missense	127254																														ENST00000326665.5:c.2255C>T	1.37:g.75039139G>A	ENSP00000322609:p.Ala752Val		74811727	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.970181	0.34754	.	.	ENSG00000178965	ENST00000326665	T	0.13538	2.58	5.26	-0.176	0.13311	.	.	.	.	.	T	0.01730	0.0055	N	0.08118	0	0.09310	N	1	B	0.18310	0.027	B	0.15052	0.012	T	0.48068	-0.9067	9	0.19590	T	0.45	-0.3026	9.4689	0.38831	0.4148:0.0:0.5852:0.0	.	752	Q5RHP9	CA173_HUMAN	V	752	ENSP00000322609:A752V	ENSP00000322609:A752V	A	-	2	0	C1orf173	74811727	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.165000	0.16564	0.021000	0.15133	0.655000	0.94253	GCA		0.408	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75039139	G	A	75039139	3	1	95	1	0	0	0	0	1	0	0	0	2020	1319	46	3	2341	3	C1orf173	1	75039139	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	37090081	75039139	174211482	5	25806										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171526588	171526588	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccggcaaccttaactccagtTccagcctcaacctcagctcc	5	19	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:171526588T>C	ENST00000338920.4	+	19	5568	c.5331T>C	c.(5329-5331)gtT>gtC	p.V1777V	PRRC2C_ENST00000426496.2_Silent_p.V1777V|PRRC2C_ENST00000392078.3_Silent_p.V1779V|PRRC2C_ENST00000367742.3_Silent_p.V1779V	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1777	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										taactccagttccagcctcaa	0.557																																																0			1											104	89	94					1																	171526588		1693	3015	4708	169793212	SO:0001819	synonymous_variant	0			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.5331T>C	1.37:g.171526588T>C			169793212	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	T	12.22	1.874036	0.33069	.	.	ENSG00000117523	ENST00000495585	.	.	.	3.43	-5.74	0.02391	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29701	-1.0003	4	.	.	.	.	1.2787	0.02036	0.1468:0.2976:0.3001:0.2556	.	.	.	.	S	325	.	.	F	+	2	0	PRRC2C	169793212	0.000000	0.05858	0.000000	0.03702	0.917000	0.54804	-1.006000	0.03671	-1.295000	0.02357	0.449000	0.29647	TTC		0.557	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171526588	T	C	171526588	2	2	95	1	0	0	0	0	0	0	0	1	1322	1770	62	4		4	BAT2L2	1	171526588	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	96487449	171526588	77724033	6	25807										
IER5	51278	hgsc.bcm.edu	37	chr1	181058345	181058345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cggagaccgagccgcagccgGagcgctcctccgtctcagac	13	17	1	2	rs200142413	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:181058345G>A	ENST00000367577.4	+	1	708	c.307G>A	c.(307-309)Gag>Aag	p.E103K	RP11-309G3.3_ENST00000606938.1_lincRNA	NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	103										lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						GCCGCAGCCGGAGCGCTCCTC	0.776													G|||	29	0.00579073	8e-04	0.0029	5008	,	,		7139	0		0.0139	False		,,,				2504	0.0123															0			1						G	LYS/GLU	16,4268		0,16,2126	10	12	11		307	2	0	1		11	149,8269		1,147,4061	no	missense	IER5	NM_016545.4	56	1,163,6187	AA,AG,GG		1.77,0.3735,1.299	benign	103/328	181058345	165,12537	2142	4209	6351	179324968	SO:0001583	missense	51278			BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783			5393	protein-coding gene	gene with protein product		607177				10049588, 11102586	Standard	NM_016545		Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.307G>A	1.37:g.181058345G>A	ENSP00000356549:p.Glu103Lys		179324968	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	Missense_Mutation	SNP	ENST00000367577.4	37	CCDS1343.1	15	0.006868131868131868	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	8.592	0.884749	0.17540	0.003735	0.0177	ENSG00000162783	ENST00000367577;ENST00000545568	T	0.09255	3.0	3.0	2.02	0.26589	.	0.468679	0.17106	U	0.186814	T	0.04272	0.0118	L	0.46157	1.445	0.26327	N	0.97759	B	0.34181	0.44	B	0.32090	0.14	T	0.17653	-1.0362	10	0.48119	T	0.1	.	7.6479	0.28331	0.0:0.2819:0.7181:0.0	.	103	Q5VY09	IER5_HUMAN	K	103	ENSP00000356549:E103K	ENSP00000356549:E103K	E	+	1	0	IER5	179324968	0.005000	0.15991	0.008000	0.14137	0.033000	0.12548	0.899000	0.28417	0.535000	0.28714	0.448000	0.29417	GAG		0.776	IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085142.1	NM_016545		A	181058345	G	A	181058345	3	1	95	1	0	0	0	0	1	0	0	0	7529	1175	41	3	309	3	IER5	1	181058345	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	9531757	181058345	68192276	7	25808										
FAM129A	116496	hgsc.bcm.edu	37	chr1	184868326	184868326	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcttaccttggtcttcaaaaActgtgacgttaaatctcttt	6	9	3	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:184868326A>T	ENST00000367511.3	-	2	365	c.172T>A	c.(172-174)Ttt>Att	p.F58I		NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	58					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						GTCTTCAAAAACTGTGACGTT	0.393																																																0			1											183	165	171					1																	184868326		2203	4300	6503	183134949	SO:0001583	missense	116496			AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.172T>A	1.37:g.184868326A>T	ENSP00000356481:p.Phe58Ile		183134949	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	A	9.888	1.203482	0.22121	.	.	ENSG00000135842	ENST00000367511	T	0.13538	2.58	5.6	0.671	0.17929	.	0.296824	0.38605	N	0.001636	T	0.11281	0.0275	L	0.60455	1.87	0.22354	N	0.999176	B	0.10296	0.003	B	0.13407	0.009	T	0.23226	-1.0194	10	0.38643	T	0.18	-1.6788	3.5413	0.07812	0.5679:0.0:0.1534:0.2788	.	58	Q9BZQ8	NIBAN_HUMAN	I	58	ENSP00000356481:F58I	ENSP00000356481:F58I	F	-	1	0	FAM129A	183134949	0.048000	0.20356	0.028000	0.17463	0.368000	0.29767	0.265000	0.18515	-0.129000	0.11620	-0.309000	0.09137	TTT		0.393	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			T	184868326	A	T	184868326	3	4	95	1	0	0	0	0	1	0	0	0	5452	43	2	5	2666	5	FAM129A	1	184868326	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	3809981	184868326	64382295	8	25809										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228479800	228479800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctgtggcctggccatggcggAcgccggggagtacttgtgtg	18	10	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:228479800A>G	ENST00000422127.1	+	39	10585	c.10541A>G	c.(10540-10542)gAc>gGc	p.D3514G	OBSCN_ENST00000570156.2_Missense_Mutation_p.D3943G|OBSCN_ENST00000284548.11_Missense_Mutation_p.D3514G|OBSCN_ENST00000359599.6_Missense_Mutation_p.D2361G|OBSCN_ENST00000366709.4_Missense_Mutation_p.D633G|OBSCN_ENST00000366707.4_Missense_Mutation_p.D633G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3514	Ig-like 35.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCCATGGCGGACGCCGGGGAG	0.622																																																0			1											106	115	112					1																	228479800		2119	4210	6329	226546423	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10541A>G	1.37:g.228479800A>G	ENSP00000409493:p.Asp3514Gly		226546423	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.769011	0.69992	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.1	5.1	0.69264	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94351	0.8184	H	0.99507	4.6	0.58432	D	0.999996	D;D	0.89917	0.997;1.0	D;D	0.97110	0.999;1.0	D	0.96665	0.9492	10	0.72032	D	0.01	.	15.0425	0.71803	1.0:0.0:0.0:0.0	.	3514;3514	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3514;3514;633;633;2361	ENSP00000284548:D3514G;ENSP00000409493:D3514G;ENSP00000355668:D633G;ENSP00000355670:D633G;ENSP00000352613:D2361G	ENSP00000284548:D3514G	D	+	2	0	OBSCN	226546423	0.999000	0.42202	0.784000	0.31847	0.031000	0.12232	4.087000	0.57671	2.138000	0.66242	0.418000	0.28097	GAC		0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228479800	A	G	228479800	3	3	95	1	0	0	0	0	1	0	0	0	10843	275	10	4	10691	4	OBSCN	1	228479800	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	43611474	228479800	20770821	9	25810										
ACTA1	58	hgsc.bcm.edu	37	chr1	229567840	229567840	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctcgtagctcttttccagggAggaggaggaggcggccgtcg	17	10	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:229567840A>G	ENST00000366684.3	-	5	811	c.709T>C	c.(709-711)Tcc>Ccc	p.S237P	ACTA1_ENST00000366683.2_Missense_Mutation_p.S149P	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	237					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				TTTTCCAGGGAGGAGGAGGAG	0.642																																																0			1											37	32	34					1																	229567840		2203	4298	6501	227634463	SO:0001583	missense	58			J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"nemaline myopathy type 3"	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.709T>C	1.37:g.229567840A>G	ENSP00000355645:p.Ser237Pro		227634463	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	37	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.744528	0.30865	.	.	ENSG00000143632	ENST00000366684;ENST00000308794;ENST00000366683;ENST00000366682	D;D	0.94457	-3.43;-3.43	4.28	4.28	0.50868	.	0.150780	0.44902	D	0.000401	D	0.95059	0.8400	M	0.87827	2.91	0.58432	D	0.999997	B	0.21225	0.053	B	0.31191	0.125	D	0.94537	0.7741	10	0.87932	D	0	.	13.5673	0.61826	1.0:0.0:0.0:0.0	.	237	P68133	ACTS_HUMAN	P	237;147;149;202	ENSP00000355645:S237P;ENSP00000355644:S149P	ENSP00000312351:S147P	S	-	1	0	ACTA1	227634463	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	8.970000	0.93415	1.786000	0.52430	0.460000	0.39030	TCC		0.642	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		G	229567840	A	G	229567840	3	3	95	1	0	0	0	0	1	0	0	0	191	304	11	4	436	4	ACTA1	1	229567840	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	1088040	229567840	19682781	10	25811										
GALNT2	2590	hgsc.bcm.edu	37	chr1	230372463	230372463	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcgagttcttagaaatgatcGacgagaaggtaagattcttc	11	6	2	4	rs369808855		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:230372463G>A	ENST00000366672.4	+	6	671	c.599G>A	c.(598-600)cGa>cAa	p.R200Q	GALNT2_ENST00000543760.1_Missense_Mutation_p.R162Q|GALNT2_ENST00000541865.1_Missense_Mutation_p.R110Q	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	200	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGAAATGATCGACGAGAAGGT	0.398																																																0			1											98	99	99					1																	230372463		2203	4300	6503	228439086	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.599G>A	1.37:g.230372463G>A	ENSP00000355632:p.Arg200Gln		228439086	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.286606	0.40494	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.61158	0.13;0.13;0.13	5.3	5.3	0.74995	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.39009	0.1062	N	0.11698	0.16	0.80722	D	1	B;B	0.31274	0.317;0.11	B;B	0.16722	0.016;0.006	T	0.28427	-1.0044	10	0.34782	T	0.22	.	17.7155	0.88335	0.0:0.0:1.0:0.0	.	200;162	Q10471;G3V1S6	GALT2_HUMAN;.	Q	162;200;81;110	ENSP00000445017:R162Q;ENSP00000355632:R200Q;ENSP00000444346:R110Q	ENSP00000355632:R200Q	R	+	2	0	GALNT2	228439086	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	8.280000	0.89903	2.466000	0.83321	0.561000	0.74099	CGA		0.398	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		A	230372463	G	A	230372463	3	1	95	1	0	0	0	0	1	0	0	0	6233	1058	37	1	621	1	GALNT2	1	230372463	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	804623	230372463	18878158	11	25812										
KCNF1	3754	hgsc.bcm.edu	37	chr2	11053815	11053815	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aagcagcgcgtcctggagacCgcggccaagcacgagctgga	15	13	0	1	rs144040411	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:11053815C>T	ENST00000295082.1	+	1	1753	c.1263C>T	c.(1261-1263)acC>acT	p.T421T		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	421					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		TCCTGGAGACCGCGGCCAAGC	0.617																																																0			2											92	76	82					2																	11053815		2203	4300	6503	10971266	SO:0001819	synonymous_variant	3754			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1263C>T	2.37:g.11053815C>T			10971266	O43527|Q585L3	Silent	SNP	ENST00000295082.1	37	CCDS1676.1																																																																																				0.617	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		T	11053815	C	T	11053815	2	4	95	1	0	0	0	0	0	0	0	1	8047	639	23	1		1	KCNF1	2	11053815	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10		11053815	232145558	12	25813										
E2F6	1876	hgsc.bcm.edu	37	chr2	11587813	11587813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggtcccgacaccttcagaccTtttgttactggtctgaccct	8	14	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:11587813T>C	ENST00000381525.3	-	6	1008	c.739A>G	c.(739-741)Agg>Ggg	p.R247G	E2F6_ENST00000546212.1_Missense_Mutation_p.R172G|E2F6_ENST00000307236.4_Missense_Mutation_p.R215G|E2F6_ENST00000542100.1_Missense_Mutation_p.R172G|E2F6_ENST00000362009.4_3'UTR	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6	247	Transcription repression.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		CCTTCAGACCTTTTGTTACTG	0.458																																																0			2											102	93	96					2																	11587813		1880	4105	5985	11505264	SO:0001583	missense	1876			AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.739A>G	2.37:g.11587813T>C	ENSP00000370936:p.Arg247Gly		11505264	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Missense_Mutation	SNP	ENST00000381525.3	37	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	T	9.749	1.167010	0.21621	.	.	ENSG00000169016	ENST00000381525;ENST00000307236;ENST00000542100;ENST00000546212	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	4.88	-7.31	0.01441	.	3.278190	0.00654	N	0.000577	T	0.04048	0.0113	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34925	-0.9809	10	0.48119	T	0.1	17.3777	3.0861	0.06278	0.1853:0.1219:0.0931:0.5996	.	247;215	O75461;G5E936	E2F6_HUMAN;.	G	247;215;172;172	ENSP00000370936:R247G;ENSP00000302159:R215G;ENSP00000446315:R172G;ENSP00000438864:R172G	ENSP00000302159:R215G	R	-	1	2	E2F6	11505264	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.524000	0.06222	-1.305000	0.02327	0.533000	0.62120	AGG		0.458	E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952		C	11587813	T	C	11587813	3	2	95	1	0	0	0	0	1	0	0	0	4882	1608	56	4	114	4	E2F6	2	11587813	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	533998	11587813	231611560	13	25814										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24438977	24438977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctgctgtaacagagctgctcCattaagctggcagctgcaga	11	11	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:24438977C>T	ENST00000355123.4	-	32	4374	c.3931G>A	c.(3931-3933)Gga>Aga	p.G1311R	AC009228.1_ENST00000413254.1_RNA|ITSN2_ENST00000361999.3_Missense_Mutation_p.G1284R|AC009228.1_ENST00000413989.1_RNA|AC009228.1_ENST00000430105.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1311	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.G1310*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGCTGCTCCATTAAGCTGG	0.522																																																1	Substitution - Nonsense(1)	kidney(1)	2											79	79	79					2																	24438977		2203	4300	6503	24292481	SO:0001583	missense	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3931G>A	2.37:g.24438977C>T	ENSP00000347244:p.Gly1311Arg		24292481	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273906	0.80580	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.62788	0.0;0.0;0.0	5.38	5.38	0.77491	Dbl homology (DH) domain (5);	0.242049	0.20718	U	0.086974	T	0.78717	0.4327	L	0.61218	1.895	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79685	-0.1700	10	0.87932	D	0	.	19.5838	0.95484	0.0:1.0:0.0:0.0	.	1284;1311	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	R	1284;1311;1284	ENSP00000354561:G1284R;ENSP00000347244:G1311R;ENSP00000370250:G1284R	ENSP00000347244:G1311R	G	-	1	0	ITSN2	24292481	1.000000	0.71417	0.967000	0.41034	0.985000	0.73830	7.395000	0.79876	2.711000	0.92665	0.650000	0.86243	GGA		0.522	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		T	24438977	C	T	24438977	3	4	95	1	0	0	0	0	1	0	0	0	7948	603	21	3	1198	3	ITSN2	2	24438977	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	12851164	24438977	218760396	14	25815										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43927014	43927014	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtccagatgcacatccacccTctccagtcacacatctgagg	7	16	3	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:43927014T>C	ENST00000282406.4	+	8	1027	c.917T>C	c.(916-918)cTc>cCc	p.L306P		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	306					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ACATCCACCCTCTCCAGTCAC	0.517																																																0			2											68	62	64					2																	43927014		2203	4300	6503	43780518	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.917T>C	2.37:g.43927014T>C	ENSP00000282406:p.Leu306Pro		43780518	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	5.892	0.348670	0.11126	.	.	ENSG00000152527	ENST00000282406	T	0.74526	-0.85	5.54	5.54	0.83059	.	0.401318	0.25708	N	0.028821	T	0.66177	0.2763	L	0.50333	1.59	0.29250	N	0.872071	B;B	0.17667	0.004;0.023	B;B	0.18871	0.007;0.023	T	0.57562	-0.7790	10	0.21014	T	0.42	-5.8876	10.0883	0.42432	0.0:0.0748:0.0:0.9252	.	306;306	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	P	306	ENSP00000282406:L306P	ENSP00000282406:L306P	L	+	2	0	PLEKHH2	43780518	0.905000	0.30787	0.098000	0.21074	0.107000	0.19398	4.852000	0.62904	2.104000	0.64026	0.460000	0.39030	CTC		0.517	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		C	43927014	T	C	43927014	3	2	95	1	0	0	0	0	1	0	0	0	12108	1551	54	4	943	4	PLEKHH2	2	43927014	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	19488037	43927014	199272359	15	25816										
SLC1A4	6509	hgsc.bcm.edu	37	chr2	65243581	65243581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcttgtgccctaggtacgtaCctgtgggcatcatgttcctt	11	11	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:65243581C>T	ENST00000234256.3	+	5	1051	c.808C>T	c.(808-810)Cct>Tct	p.P270S	SLC1A4_ENST00000493121.1_3'UTR|SLC1A4_ENST00000531327.1_Intron	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	270					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	TAGGTACGTACCTGTGGGCAT	0.507																																																0			2											156	134	141					2																	65243581		2203	4300	6503	65097085	SO:0001583	missense	6509				CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"Solute carriers"	10942	protein-coding gene	gene with protein product	"alanine/serine/cysteine/threonine transporter"	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.808C>T	2.37:g.65243581C>T	ENSP00000234256:p.Pro270Ser		65097085	B7Z3C0|D6W5F0	Missense_Mutation	SNP	ENST00000234256.3	37	CCDS1879.1	.	.	.	.	.	.	.	.	.	.	C	33	5.283135	0.95489	.	.	ENSG00000115902	ENST00000448784;ENST00000234256	D	0.90844	-2.74	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.97639	0.9226	H	0.98612	4.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98231	1.0483	10	0.87932	D	0	-37.3515	20.5632	0.99335	0.0:1.0:0.0:0.0	.	270;270	P43007;B2R7N6	SATT_HUMAN;.	S	190;270	ENSP00000234256:P270S	ENSP00000234256:P270S	P	+	1	0	SLC1A4	65097085	0.999000	0.42202	0.680000	0.29994	0.942000	0.58702	7.773000	0.85462	2.937000	0.99478	0.650000	0.86243	CCT		0.507	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038		T	65243581	C	T	65243581	3	4	95	1	0	0	0	0	1	0	0	0	14471	507	18	3	826	3	SLC1A4	2	65243581	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	21316567	65243581	177955792	16	25817										
ANKRD53	79998	hgsc.bcm.edu	37	chr2	71209119	71209119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggcagcccgtgacggcttgcTggactgtgtgaaggtcctgg	17	10	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:71209119T>C	ENST00000360589.3	+	4	705	c.671T>C	c.(670-672)cTg>cCg	p.L224P	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000272421.6_Missense_Mutation_p.L224P|ANKRD53_ENST00000457410.1_Missense_Mutation_p.L190P|ANKRD53_ENST00000441349.1_Intron	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	224										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GACGGCTTGCTGGACTGTGTG	0.577																																																0			2											77	67	71					2																	71209119		2203	4300	6503	71062627	SO:0001583	missense	79998			BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"Ankyrin repeat domain containing"	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.671T>C	2.37:g.71209119T>C	ENSP00000353796:p.Leu224Pro		71062627	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392890	0.62066	.	.	ENSG00000144031	ENST00000272421;ENST00000457410;ENST00000360589	T;T;T	0.68903	-0.36;-0.36;-0.36	5.47	5.47	0.80525	Ankyrin repeat-containing domain (4);	0.000000	0.44902	D	0.000402	T	0.68824	0.3043	N	0.25286	0.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.71797	-0.4484	10	0.66056	D	0.02	-22.1427	9.1627	0.37032	0.1623:0.0:0.0:0.8377	.	224;224	Q8N9V6;Q8N9V6-2	ANR53_HUMAN;.	P	224;190;224	ENSP00000272421:L224P;ENSP00000407004:L190P;ENSP00000353796:L224P	ENSP00000272421:L224P	L	+	2	0	ANKRD53	71062627	1.000000	0.71417	0.985000	0.45067	0.514000	0.34195	2.701000	0.47094	2.216000	0.71823	0.459000	0.35465	CTG		0.577	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933		C	71209119	T	C	71209119	3	2	95	1	0	0	0	0	1	0	0	0	679	1580	55	4	685	4	ANKRD53	2	71209119	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	5965538	71209119	171990254	17	25818										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80101318	80101318	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctccgccacccagatgtcgcCgctacgagagccaaccgaga	10	17	0	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:80101318C>T	ENST00000402739.4	+	5	707	c.702C>T	c.(700-702)gcC>gcT	p.A234A	CTNNA2_ENST00000496558.1_Silent_p.A234A|CTNNA2_ENST00000540488.1_Silent_p.A234A|CTNNA2_ENST00000361291.4_Silent_p.A268A|CTNNA2_ENST00000466387.1_Silent_p.A234A|CTNNA2_ENST00000541047.1_Silent_p.A234A	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	234					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CAGATGTCGCCGCTACGAGAG	0.577																																																0			2											50	54	53					2																	80101318		2075	4219	6294	79954826	SO:0001819	synonymous_variant	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.702C>T	2.37:g.80101318C>T			79954826	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																					0.577	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80101318	C	T	80101318	2	4	95	1	0	0	0	0	0	0	0	1	4019	639	23	1		1	CTNNA2	2	80101318	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	8892199	80101318	163098055	18	25819										
GLI2	2736	hgsc.bcm.edu	37	chr2	121729540	121729540	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aagcagagcagtgagtcggcCgtcagcagcaccgtcaaccc	12	14	2	2	rs138680216		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:121729540C>T	ENST00000452319.1	+	8	1143	c.1083C>T	c.(1081-1083)gcC>gcT	p.A361A	GLI2_ENST00000361492.4_Silent_p.A361A|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Silent_p.A33A					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GTGAGTCGGCCGTCAGCAGCA	0.597																																																0			2						T		2,4404	4.2+/-10.8	0,2,2201	65	58	60		1083	-9.6	0.2	2	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous	GLI2	NM_005270.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		361/1587	121729540	2,13004	2203	4300	6503	121446010	SO:0001819	synonymous_variant	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1083C>T	2.37:g.121729540C>T			121446010		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																				0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121729540	C	T	121729540	2	4	95	1	0	0	0	0	0	0	0	1	6458	639	23	1		1	GLI2	2	121729540	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	41628222	121729540	121469833	19	25820										
SMPD4	55627	hgsc.bcm.edu	37	chr2	130911373	130911373	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtccaggtcgttggctgtgtAggagccattggtgtccatgg	16	8	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:130911373A>G	ENST00000409031.1	-	17	3060	c.1912T>C	c.(1912-1914)Tac>Cac	p.Y638H	SMPD4_ENST00000426662.2_Missense_Mutation_p.Y274H|SMPD4_ENST00000443958.2_Missense_Mutation_p.Y302H|SMPD4_ENST00000453750.1_Missense_Mutation_p.Y387H|SMPD4_ENST00000431183.2_Missense_Mutation_p.Y536H|SMPD4_ENST00000351288.6_Missense_Mutation_p.Y609H|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000339679.7_Missense_Mutation_p.Y496H|SMPD4_ENST00000452225.2_Missense_Mutation_p.Y379H	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	599					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	TTGGCTGTGTAGGAGCCATTG	0.587																																																0			2											82	81	81					2																	130911373		2203	4300	6503	130627843	SO:0001583	missense	55627			AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1912T>C	2.37:g.130911373A>G	ENSP00000386531:p.Tyr638His		130627843	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.	.	.	.	.	.	.	.	.	.	.	13.27	2.188058	0.38609	.	.	ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159	.	.	.	3.94	3.94	0.45596	.	0.466770	0.24152	N	0.041072	T	0.64000	0.2559	L	0.53249	1.67	0.38383	D	0.94518	P;B;D;D;D;D;D;D;P;D	0.58620	0.941;0.333;0.966;0.966;0.983;0.958;0.973;0.98;0.911;0.979	P;B;P;P;P;P;P;P;P;P	0.60886	0.735;0.08;0.735;0.735;0.731;0.487;0.751;0.861;0.563;0.88	T	0.62101	-0.6925	9	0.19147	T	0.46	.	10.7651	0.46288	1.0:0.0:0.0:0.0	.	274;379;536;496;387;570;599;638;645;170	B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4;Q9NXE4-5	.;.;.;.;.;.;NSMA3_HUMAN;.;.;.	H	609;638;536;387;302;496;379;274;235;148	.	ENSP00000339721:Y496H	Y	-	1	0	SMPD4	130627843	1.000000	0.71417	0.710000	0.30468	0.024000	0.10985	6.805000	0.75191	1.404000	0.46819	0.454000	0.30748	TAC		0.587	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		G	130911373	A	G	130911373	3	3	95	1	0	0	0	0	1	0	0	0	14844	420	15	4	704	4	SMPD4	2	130911373	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	9181833	130911373	112288000	20	25821										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133541426	133541426	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctctgcacttctgtcgtggcCggattagaagaaataactgg	11	9	2	2	rs189440819		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:133541426C>T	ENST00000409261.1	-	14	3331	c.2958G>A	c.(2956-2958)ccG>ccA	p.P986P	NCKAP5_ENST00000317721.6_Silent_p.P986P|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	986										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTGTCGTGGCCGGATTAGAAG	0.507													c|||	1	0.000199681	0	0	5008	,	,		17844	0.001		0	False		,,,				2504	0															0			2						T	,	1,3805		0,1,1902	31	34	33		2958,	-1.4	0	2		33	0,8240		0,0,4120	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	0,1,6022	TT,TC,CC		0.0,0.0263,0.0083	,	986/1910,	133541426	1,12045	1903	4120	6023	133257896	SO:0001819	synonymous_variant	0			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.2958G>A	2.37:g.133541426C>T			133257896	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				0.507	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133541426	C	T	133541426	2	4	95	1	0	0	0	0	0	0	0	1	10254	639	23	1		1	NCKAP5	2	133541426	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	2630053	133541426	109657947	21	25822										
TTN	7273	hgsc.bcm.edu	37	chr2	179497919	179497919	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctaatcttgacttacaggggAagctgtcaaaggctgtcctt	10	9	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:179497919A>G	ENST00000591111.1	-	183	38382	c.38158T>C	c.(38158-38160)Tcc>Ccc	p.S12720P	TTN_ENST00000342992.6_Missense_Mutation_p.S11793P|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S5421P|TTN_ENST00000460472.2_Missense_Mutation_p.S5296P|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S5488P|TTN_ENST00000589042.1_Missense_Mutation_p.S14361P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12720			S -> F (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTACAGGGGAAGCTGTCAAA	0.413																																																0			2											52	51	51					2																	179497919		1833	4086	5919	179206164	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.38158T>C	2.37:g.179497919A>G	ENSP00000465570:p.Ser12720Pro		179206164	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	12.77	2.037485	0.35989	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	6.17	6.17	0.99709	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72622	0.3483	M	0.91510	3.215	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.79230	-0.1889	9	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	5296;5421;5488;12720	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	11793;5296;5488;5421;5296	ENSP00000343764:S11793P;ENSP00000434586:S5296P;ENSP00000340554:S5488P;ENSP00000352154:S5421P	ENSP00000340554:S5488P	S	-	1	0	TTN	179206164	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	9.281000	0.95811	2.371000	0.80710	0.533000	0.62120	TCC		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179497919	A	G	179497919	3	3	95	1	0	0	0	0	1	0	0	0	16775	246	9	4	65132	4	TTN	2	179497919	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	45956493	179497919	63701454	22	25823										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220402397	220402397	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggtatggaggcgtcccaagaCccccctgcggacctccactg	12	16	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:220402397C>G	ENST00000347842.3	+	8	1783	c.1769C>G	c.(1768-1770)aCc>aGc	p.T590S	ASIC4_ENST00000358078.4_Missense_Mutation_p.T609S	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	590					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										CGTCCCAAGACCCCCCTGCGG	0.597																																																0			2											35	35	35					2																	220402397		2203	4300	6503	220110641	SO:0001583	missense	55515			AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1769C>G	2.37:g.220402397C>G	ENSP00000326627:p.Thr590Ser		220110641	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923549	0.33908	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.61274	0.12;0.12	4.76	4.76	0.60689	.	0.838767	0.10824	N	0.630143	T	0.28532	0.0706	N	0.00841	-1.15	0.38282	D	0.942445	B;B	0.16802	0.006;0.019	B;B	0.20955	0.002;0.032	T	0.17592	-1.0364	10	0.07482	T	0.82	-30.8304	16.5063	0.84273	0.0:1.0:0.0:0.0	.	590;609	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	S	590;609	ENSP00000326627:T590S;ENSP00000350786:T609S	ENSP00000326627:T590S	T	+	2	0	ACCN4	220110641	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	2.898000	0.48672	2.641000	0.89580	0.591000	0.81541	ACC		0.597	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		G	220402397	C	G	220402397	3	3	95	1	0	0	0	0	1	0	0	0	131	507	18	5	1860	5	ACCN4	2	220402397	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	40904478	220402397	22796976	23	25824										
HJURP	55355	hgsc.bcm.edu	37	chr2	234749731	234749731	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tggcctggcacttctttatcTgggactgaaagagttttgct	11	8	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:234749731T>C	ENST00000411486.2	-	8	1760	c.1695A>G	c.(1693-1695)ccA>ccG	p.P565P	HJURP_ENST00000441687.1_Silent_p.P480P|HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000432087.1_Silent_p.P511P	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	565					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		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)		CTTCTTTATCTGGGACTGAAA	0.448																																																0			2											96	100	99					2																	234749731		2203	4300	6503	234414470	SO:0001819	synonymous_variant	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1695A>G	2.37:g.234749731T>C			234414470	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Silent	SNP	ENST00000411486.2	37	CCDS33406.1																																																																																				0.448	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		C	234749731	T	C	234749731	2	2	95	1	0	0	0	0	0	0	0	1	7210	1567	55	4		4	HJURP	2	234749731	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	14347334	234749731	8449642	24	25825										
RAF1	5894	hgsc.bcm.edu	37	chr3	12641307	12641307	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atctctctgtccacgaggccTctgaaacaagtagagatcat	8	11	4	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:12641307T>C	ENST00000251849.4	-	10	1430	c.991A>G	c.(991-993)Agg>Ggg	p.R331G	RAF1_ENST00000442415.2_Splice_Site_p.R351G|RAF1_ENST00000542177.1_Splice_Site_p.R250G|RAF1_ENST00000534997.1_Splice_Site_p.R116G	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	331	Interaction with PEBP1/RKIP.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	CCACGAGGCCTCTGAAACAAG	0.408			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																														Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	0			3											78	79	78					3																	12641307		2203	4300	6503	12616307	SO:0001630	splice_region_variant	5894	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.991-1A>G	3.37:g.12641307T>C			12616307	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.018417	0.54576	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	T;T;T;T;T	0.75821	-0.93;-0.97;-0.91;-0.92;-0.92	5.17	3.99	0.46301	Protein kinase-like domain (1);	0.079450	0.85682	D	0.000000	T	0.74222	0.3688	M	0.69823	2.125	0.53688	D	0.999976	B;B;P	0.37233	0.019;0.133;0.588	B;B;B	0.40602	0.015;0.065;0.334	T	0.74697	-0.3578	10	0.62326	D	0.03	.	11.1273	0.48325	0.0:0.0:0.1548:0.8452	.	250;116;331	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	G	331;351;210;116;250	ENSP00000251849:R331G;ENSP00000401888:R351G;ENSP00000398591:R210G;ENSP00000441186:R116G;ENSP00000443567:R250G	ENSP00000251849:R331G	R	-	1	2	RAF1	12616307	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	4.887000	0.63156	0.890000	0.36211	-0.460000	0.05396	AGG		0.408	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880	Missense_Mutation	C	12641307	T	C	12641307	5	2	95	1	0	0	0	0	0	0	1	0	13039	1565	54	4	987	4	RAF1	3	12641307	Splice_Site	SNP	T	TCGA-DC-6155-01A-11D-1657-10		12641307	185381123	25	25826										
RBM6	10180	hgsc.bcm.edu	37	chr3	50098948	50098948	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctggctactattatgaccccTtggcaggaacttattatgac	8	10	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:50098948T>C	ENST00000266022.4	+	14	2666	c.2407T>C	c.(2407-2409)Ttg>Ctg	p.L803L	RBM6_ENST00000442092.1_Silent_p.L281L|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000539992.1_Silent_p.L145L|RBM6_ENST00000422955.1_Silent_p.L281L|RBM6_ENST00000443081.1_Silent_p.L671L	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	803					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TTATGACCCCTTGGCAGGAAC	0.373																																																0			3											163	154	157					3																	50098948		2203	4300	6503	50073952	SO:0001819	synonymous_variant	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2407T>C	3.37:g.50098948T>C			50073952	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																				0.373	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		C	50098948	T	C	50098948	2	2	95	1	0	0	0	0	0	0	0	1	13181	1606	56	4		4	RBM6	3	50098948	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	37457641	50098948	147923482	26	25827										
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52475665	52475665	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcggaagatcatggcctctcGccccaggaagtcagcagtga	12	12	3	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:52475665G>A	ENST00000231721.2	-	6	591	c.592C>T	c.(592-594)Cga>Tga	p.R198*		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	198	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		ATGGCCTCTCGCCCCAGGAAG	0.657																																																0			3											55	55	55					3																	52475665		2203	4300	6503	52450705	SO:0001587	stop_gained	56920				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.592C>T	3.37:g.52475665G>A	ENSP00000231721:p.Arg198*		52450705	Q7L9D9|Q9H7Q3	Nonsense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708207	0.48412	.	.	ENSG00000010319	ENST00000231721	.	.	.	4.84	4.84	0.62591	.	0.054016	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6002	0.50997	0.0:0.0:0.6927:0.3073	.	.	.	.	X	198	.	ENSP00000231721:R198X	R	-	1	2	SEMA3G	52450705	0.788000	0.28762	0.963000	0.40424	0.526000	0.34562	2.727000	0.47311	2.249000	0.74217	0.462000	0.41574	CGA		0.657	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52475665	G	A	52475665	4	1	95	1	0	0	0	0	0	1	0	0	14067	1095	38	1	1800	1	SEMA3G	3	52475665	Nonsense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	2376717	52475665	145546765	27	25828										
IMPG2	50939	hgsc.bcm.edu	37	chr3	101022988	101022988	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cttcctttgttgtgacacttAccttcatgattaagcttcta	5	10	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:101022988A>G	ENST00000193391.7	-	3	689		c.e3+1			NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TGTGACACTTACCTTCATGAT	0.393																																																0			3											148	143	145					3																	101022988		2203	4300	6503	102505678	SO:0001630	splice_region_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.501+1T>C	3.37:g.101022988A>G			102505678	A8MWT5|Q9UKD4|Q9UKK5	Splice_Site	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040918	0.75732	.	.	ENSG00000081148	ENST00000193391	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4459	0.75228	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IMPG2	102505678	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.815000	0.75242	2.137000	0.66172	0.528000	0.53228	.		0.393	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		Intron	G	101022988	A	G	101022988	5	3	95	1	0	0	0	0	0	0	1	0	7750	405	14	4	3290	4	IMPG2	3	101022988	Splice_Site	SNP	A	TCGA-DC-6155-01A-11D-1657-10	48547323	101022988	96999442	28	25829										
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137787047	137787047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agggtccatgcagtccggggCgtggagcgggggcggacacc	20	11	0	0	rs199606339|rs374045	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:137787047C>T	ENST00000327532.2	-	13	2140	c.1778G>A	c.(1777-1779)cGc>cAc	p.R593H	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	593			R -> H (in dbSNP:rs374045). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CAGTCCGGGGCGTGGAGCGGG	0.697													C|||	3149	0.628794	0.3094	0.7767	5008	,	,		14534	0.626		0.8608	False		,,,				2504	0.7198															0			3						C	HIS/ARG	1930,2476	539.0+/-375.1	417,1096,690	43	47	46		1778	2.2	0	3	dbSNP_80	46	7483,1117	760.0+/-407.6	3260,963,77	no	missense	DZIP1L	NM_173543.2	29	3677,2059,767	TT,TC,CC		12.9884,43.8039,27.6257	benign	593/768	137787047	9413,3593	2203	4300	6503	139269737	SO:0001583	missense	199221			AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1778G>A	3.37:g.137787047C>T	ENSP00000332148:p.Arg593His		139269737	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1465	0.6707875457875457	179	0.3638211382113821	271	0.7486187845303868	365	0.6381118881118881	650	0.8575197889182058	C	11.55	1.673457	0.29693	0.438039	0.870116	ENSG00000158163	ENST00000327532	T	0.38722	1.12	4.91	2.16	0.27623	.	0.815396	0.11163	N	0.592824	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B	0.19073	0.033	B	0.12156	0.007	T	0.22138	-1.0225	9	0.28530	T	0.3	-0.6235	6.6861	0.23146	0.0:0.7076:0.0:0.2924	rs374045;rs17853174;rs58860132	593	Q8IYY4	DZI1L_HUMAN	H	593	ENSP00000332148:R593H	ENSP00000332148:R593H	R	-	2	0	DZIP1L	139269737	0.001000	0.12720	0.002000	0.10522	0.043000	0.13939	0.080000	0.14802	0.268000	0.21939	0.650000	0.86243	CGC		0.697	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		T	137787047	C	T	137787047	3	4	95	1	0	0	0	0	1	0	0	0	4875	768	27	1	541	1	DZIP1L	3	137787047	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	36764059	137787047	60235383	29	25830										
ATR	545	hgsc.bcm.edu	37	chr3	142176502	142176502	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	attgtaacttcacatgctctTcgaaaaagaccctctgttcc	5	12	3	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:142176502T>C	ENST00000350721.4	-	45	7720	c.7599A>G	c.(7597-7599)cgA>cgG	p.R2533R	ATR_ENST00000383101.3_Silent_p.R2469R	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2533	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CACATGCTCTTCGAAAAAGAC	0.403								Other conserved DNA damage response genes																																								0			3											105	98	101					3																	142176502		2203	4300	6503	143659192	SO:0001819	synonymous_variant	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7599A>G	3.37:g.142176502T>C			143659192	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.473823	0.26423	.	.	ENSG00000175054	ENST00000513291	.	.	.	5.2	4.04	0.47022	.	.	.	.	.	T	0.60971	0.2310	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59139	-0.7510	4	.	.	.	-9.8182	10.6321	0.45543	0.0:0.0757:0.0:0.9243	.	.	.	.	E	380	.	.	K	-	1	0	ATR	143659192	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.301000	0.33447	2.102000	0.63906	0.397000	0.26171	AAG		0.403	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142176502	T	C	142176502	2	2	95	1	0	0	0	0	0	0	0	1	1205	1770	62	4		4	ATR	3	142176502	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	4389455	142176502	55845928	30	25831										
GPR149	344758	hgsc.bcm.edu	37	chr3	154056059	154056059	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tggcaagggcataaccggaaCgctggggacaaaaacaaaat	12	8	0	0	rs199967865		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:154056059C>T	ENST00000389740.2	-	4	1724	c.1625G>A	c.(1624-1626)cGt>cAt	p.R542H		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	542					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R542H(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATAACCGGAACGCTGGGGACA	0.413													C|||	1	0.000199681	0	0	5008	,	,		19095	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	3											76	77	77					3																	154056059		1876	4103	5979	155538753	SO:0001630	splice_region_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1624-1G>A	3.37:g.154056059C>T			155538753		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	24.3	4.519500	0.85495	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.77	4.89	0.63831	.	0.063289	0.64402	D	0.000006	T	0.74230	0.3689	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.76462	-0.2950	9	0.87932	D	0	-13.5998	15.0929	0.72211	0.0:0.9311:0.0:0.0689	.	542	Q86SP6	GP149_HUMAN	H	542	.	ENSP00000374390:R542H	R	-	2	0	GPR149	155538753	1.000000	0.71417	0.981000	0.43875	0.825000	0.46686	5.746000	0.68681	2.726000	0.93360	0.655000	0.94253	CGT		0.413	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	Missense_Mutation	T	154056059	C	T	154056059	5	4	95	1	0	0	0	0	0	0	1	0	6674	550	19	1	574	1	GPR149	3	154056059	Splice_Site	SNP	C	TCGA-DC-6155-01A-11D-1657-10	11879557	154056059	43966371	31	25832										
SI	6476	hgsc.bcm.edu	37	chr3	164716351	164716351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgattgatttgtccatgttgTcccatcgtgcatagttgtct	9	8	1	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:164716351T>C	ENST00000264382.3	-	38	4579	c.4517A>G	c.(4516-4518)gAc>gGc	p.D1506G		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1506	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GTCCATGTTGTCCCATCGTGC	0.398										HNSCC(35;0.089)																																						0			3											209	185	193					3																	164716351		2203	4300	6503	166199045	SO:0001583	missense	6490			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4517A>G	3.37:g.164716351T>C	ENSP00000264382:p.Asp1506Gly		166199045	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.474720	0.63737	.	.	ENSG00000090402	ENST00000264382	D	0.93763	-3.28	4.76	3.63	0.41609	Glycoside hydrolase, superfamily (1);	0.442401	0.25302	N	0.031646	D	0.94591	0.8257	L	0.56124	1.755	0.39636	D	0.970257	P	0.46859	0.885	D	0.64237	0.923	D	0.94513	0.7720	10	0.59425	D	0.04	.	10.6283	0.45521	0.0:0.0806:0.0:0.9194	.	1506	P14410	SUIS_HUMAN	G	1506	ENSP00000264382:D1506G	ENSP00000264382:D1506G	D	-	2	0	SI	166199045	1.000000	0.71417	0.995000	0.50966	0.634000	0.38068	3.092000	0.50207	2.127000	0.65507	0.528000	0.53228	GAC		0.398	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164716351	T	C	164716351	3	2	95	1	0	0	0	0	1	0	0	0	14334	1667	58	4	1010	4	SI	3	164716351	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	10660292	164716351	33306079	32	25833										
GNB4	59345	hgsc.bcm.edu	37	chr3	179132783	179132783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aggcaacataattaccagagGgagcataagcacaggtcatc	10	9	1	1	rs267599699		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:179132783G>A	ENST00000232564.3	-	6	606	c.320C>T	c.(319-321)cCc>cTc	p.P107L	GNB4_ENST00000465153.1_5'Flank|GNB4_ENST00000468623.1_Missense_Mutation_p.P107L	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	107					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)	p.P107L(2)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			ATTACCAGAGGGAGCATAAGC	0.458																																					Melanoma(105;1405 1491 7265 20440 33721)											2	Substitution - Missense(2)	skin(2)	3											121	119	120					3																	179132783		2203	4300	6503	180615477	SO:0001583	missense	59345			AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"WD repeat domain containing"	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.320C>T	3.37:g.179132783G>A	ENSP00000232564:p.Pro107Leu		180615477	B3KMH5|D3DNR8	Missense_Mutation	SNP	ENST00000232564.3	37	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.853706	0.71719	.	.	ENSG00000114450	ENST00000232564;ENST00000468623	T;T	0.71222	-0.55;-0.55	5.38	5.38	0.77491	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);G-protein, beta subunit (1);	0.000000	0.85682	D	0.000000	D	0.88901	0.6563	H	0.95611	3.695	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.65573	0.932;0.936	D	0.91898	0.5529	10	0.87932	D	0	-14.7066	19.4892	0.95044	0.0:0.0:1.0:0.0	.	107;107	Q9HAV0;A8K3F6	GBB4_HUMAN;.	L	107	ENSP00000232564:P107L;ENSP00000419693:P107L	ENSP00000232564:P107L	P	-	2	0	GNB4	180615477	1.000000	0.71417	0.979000	0.43373	0.133000	0.20885	9.717000	0.98755	2.663000	0.90544	0.655000	0.94253	CCC		0.458	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629		A	179132783	G	A	179132783	3	1	95	1	0	0	0	0	1	0	0	0	6540	1232	43	3	722	3	GNB4	3	179132783	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	14416432	179132783	18889647	33	25834										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cctgctcacacgtgcccatgCggagtgcccgcctgctcaca	10	18	2	0	rs112233131	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1388759C>T	ENST00000324803.4	+	1	3420	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	154					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R154W(2)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701																																																2	Substitution - Missense(2)	NS(1)|skin(1)	4											84	72	76					4																	1388759		2202	4282	6484	1378759	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.460C>T	4.37:g.1388759C>T	ENSP00000323978:p.Arg154Trp		1378759	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.074|0.074	-1.196289|-1.196289	0.01594|0.01594	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000382944|ENST00000324803	.|T	.|0.19806	.|2.12	0.948|0.948	-1.9|-1.9	0.07665|0.07665	.|.	.|.	.|.	.|.	.|.	T|T	0.07908|0.07908	0.0198|0.0198	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.22851	.|0.076	.|B	.|0.04013	.|0.001	T|T	0.18116|0.18116	-1.0347|-1.0347	6|9	0.02654|0.49607	T|T	1|0.09	.|.	0.8279|0.8279	0.01124|0.01124	0.1649:0.1747:0.3249:0.3355|0.1649:0.1747:0.3249:0.3355	.|.	.|154	.|Q8N1N5	.|CRPAK_HUMAN	V|W	137|154	.|ENSP00000323978:R154W	ENSP00000372402:A137V|ENSP00000323978:R154W	A|R	+|+	2|1	0|2	CRIPAK|CRIPAK	1378759|1378759	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-2.063000|-2.063000	0.01388|0.01388	-3.215000|-3.215000	0.00213|0.00213	-1.709000|-1.709000	0.00716|0.00716	GCG|CGG		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		T	1388759	C	T	1388759	3	4	95	1	0	0	0	0	1	0	0	0	3883	759	27	1	462	1	CRIPAK	4	1388759	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10		1388759	189765517	34	25835			2	19		3	3	626	N	T_C	4.211233e-06
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389156	1389156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cgcctgctcacatgtgccgaTgtggagtgcccgcctgctca	12	15	2	0	rs71614972	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1389156T>C	ENST00000324803.4	+	1	3817	c.857T>C	c.(856-858)aTg>aCg	p.M286T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	286					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CATGTGCCGATGTGGAGTGCC	0.677													T|||	3799	0.758586	0.9349	0.7954	5008	,	,		13659	0.7014		0.6392	False		,,,				2504	0.6759															0			4											131	131	131					4																	1389156		2202	4299	6501	1379156	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.857T>C	4.37:g.1389156T>C	ENSP00000323978:p.Met286Thr		1379156	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	T	0.854	-0.737538	0.03111	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.17691	2.26	0.815	-1.63	0.08345	Post-SET domain (1);	.	.	.	.	T	0.06826	0.0174	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.06405	0.002	T	0.38067	-0.9678	8	0.25106	T	0.35	.	5.1474	0.14993	0.0:0.3546:0.0:0.6454	.	286	Q8N1N5	CRPAK_HUMAN	T	286;228	ENSP00000323978:M286T	ENSP00000323978:M286T	M	+	2	0	CRIPAK	1379156	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.361000	0.01083	-0.674000	0.05253	-0.530000	0.04314	ATG		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1389156	T	C	1389156	3	2	95	1	0	0	0	0	1	0	0	0	3883	1464	51	4	859	4	CRIPAK	4	1389156	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	397	1389156	189765120	35	25836			2	19		3	3	626	N	T_C	4.211233e-06
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389384	1389384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	acgtgcccatgtggagtgccCgcctgctcacacacgtgccc	11	17	1	0	rs148729919		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1389384C>T	ENST00000324803.4	+	1	4045	c.1085C>T	c.(1084-1086)cCg>cTg	p.P362L		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	362					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GTGGAGTGCCCGCCTGCTCAC	0.672																																																0			4											173	178	176					4																	1389384		2203	4299	6502	1379384	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.1085C>T	4.37:g.1389384C>T	ENSP00000323978:p.Pro362Leu		1379384	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.247	0.231053	0.09969	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.33438	1.41	0.757	-0.648	0.11464	.	.	.	.	.	T	0.11281	0.0275	N	0.08118	0	0.09310	N	0.999993	B	0.18968	0.032	B	0.06405	0.002	T	0.28427	-1.0044	9	0.20519	T	0.43	.	1.6297	0.02730	0.3327:0.398:0.0:0.2693	.	362	Q8N1N5	CRPAK_HUMAN	L	362;304	ENSP00000323978:P362L	ENSP00000323978:P362L	P	+	2	0	CRIPAK	1379384	0.021000	0.18746	0.005000	0.12908	0.052000	0.14988	0.367000	0.20382	-0.286000	0.09076	0.205000	0.17691	CCG		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		T	1389384	C	T	1389384	3	4	95	1	0	0	0	0	1	0	0	0	3883	652	23	1	1087	1	CRIPAK	4	1389384	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	228	1389384	189764892	36	25837			2	19		3	3	626	N	T_C	4.211233e-06
FGFR3	2261	hgsc.bcm.edu	37	chr4	1807830	1807830	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gctggtgaccgaggacaacgTgatgaagatcgcagacttcg	14	9	0	5			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1807830T>C	ENST00000260795.2	+	13	1991	c.1889T>C	c.(1888-1890)gTg>gCg	p.V630A	FGFR3_ENST00000412135.2_Missense_Mutation_p.V518A|FGFR3_ENST00000440486.2_Missense_Mutation_p.V630A|FGFR3_ENST00000340107.4_Missense_Mutation_p.V632A|FGFR3_ENST00000481110.2_Missense_Mutation_p.V631A|FGFR3_ENST00000352904.1_Missense_Mutation_p.V518A			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	630	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GAGGACAACGTGATGAAGATC	0.657		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																														Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	0			4											47	46	46					4																	1807830		2202	4300	6502	1777628	SO:0001583	missense	2261	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1889T>C	4.37:g.1807830T>C	ENSP00000260795:p.Val630Ala		1777628	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	t	18.57	3.651523	0.67472	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	4.31	4.31	0.51392	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.063240	0.64402	D	0.000007	D	0.93311	0.7868	L	0.37466	1.105	0.80722	D	1	D;P;D;D	0.89917	0.995;0.72;0.996;1.0	D;B;D;D	0.77004	0.971;0.379;0.98;0.989	D	0.94015	0.7287	10	0.72032	D	0.01	.	13.7991	0.63188	0.0:0.0:0.0:1.0	.	632;518;630;631	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	A	631;632;630;518;630;518	ENSP00000420533:V631A;ENSP00000339824:V632A;ENSP00000414914:V630A;ENSP00000412903:V518A;ENSP00000260795:V630A;ENSP00000231803:V518A	ENSP00000260795:V630A	V	+	2	0	FGFR3	1777628	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.693000	0.84214	1.723000	0.51488	0.363000	0.22086	GTG		0.657	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		C	1807830	T	C	1807830	3	2	95	1	0	0	0	0	1	0	0	0	5886	1696	59	4	2094	4	FGFR3	4	1807830	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	418446	1807830	189346446	37	25838										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82065433	82065433	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttcaggtttgccacatatccTtcaaggtatttttgcagctc	7	10	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:82065433T>C	ENST00000395578.1	-	10	1322	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	PRKG2_ENST00000264399.1_Silent_p.E402E|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000418486.2_Silent_p.E402E			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	402					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CCACATATCCTTCAAGGTATT	0.408																																																0			4											173	160	164					4																	82065433		2203	4300	6503	82284457	SO:0001819	synonymous_variant	5593			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1206A>G	4.37:g.82065433T>C			82284457	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																				0.408	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		C	82065433	T	C	82065433	2	2	95	1	0	0	0	0	0	0	0	1	12557	1606	56	4		4	PRKG2	4	82065433	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	80257603	82065433	109088843	38	25839										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537435	88537435	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agcagcgatagtagtgatagCagtgacagcagtgacagcag	14	7	0	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:88537435C>T	ENST00000282478.7	+	4	3654	c.3621C>T	c.(3619-3621)agC>agT	p.S1207S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1207S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1207	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtagtgatagcagtgacagca	0.557																																																0			4																																								88756459	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3621C>T	4.37:g.88537435C>T			88756459	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88537435	C	T	88537435	2	4	95	1	0	0	0	0	0	0	0	1	4793	709	25	3		3	DSPP	4	88537435	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	6472002	88537435	102616841	39	25840										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183696105	183696105	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agctaccagattggttatgaCggctccctcagaattatcta	8	10	2	3	rs369200143		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:183696105C>T	ENST00000511685.1	+	24	5226	c.5103C>T	c.(5101-5103)gaC>gaT	p.D1701D	TENM3_ENST00000406950.2_Silent_p.D1701D|RP11-18D7.2_ENST00000513255.1_RNA			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1701					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TTGGTTATGACGGCTCCCTCA	0.468																																																0			4						C		0,3738		0,0,1869	35	35	35		5103	-9.5	0.2	4		35	1,8205		0,1,4102	no	coding-synonymous	ODZ3	NM_001080477.1		0,1,5971	TT,TC,CC		0.0122,0.0,0.0084		1701/2700	183696105	1,11943	1869	4103	5972	183933099	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5103C>T	4.37:g.183696105C>T			183933099	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				0.468	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183696105	C	T	183696105	2	4	95	1	0	0	0	0	0	0	0	1	10867	535	19	1		1	ODZ3	4	183696105	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	95158670	183696105	7458171	40	25841										
C5orf38	153571	hgsc.bcm.edu	37	chr5	2752437	2752437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcgcgcggctctcacttccaCggtcccggacctgctctgcc	11	19	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:2752437C>T	ENST00000334000.3	+	1	176	c.59C>T	c.(58-60)aCg>aTg	p.T20M	C5orf38_ENST00000515640.1_Missense_Mutation_p.T20M|C5orf38_ENST00000505778.1_Missense_Mutation_p.T20M|C5orf38_ENST00000397835.4_Missense_Mutation_p.T20M|C5orf38_ENST00000457752.2_Missense_Mutation_p.T20M|IRX2_ENST00000502957.1_Intron|IRX2_ENST00000302057.5_5'Flank|IRX2_ENST00000382611.6_5'Flank	NM_178569.2	NP_848664.1	Q86SI9	CEI_HUMAN	chromosome 5 open reading frame 38	20						extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(1)	4				GBM - Glioblastoma multiforme(108;0.205)		CTCACTTCCACGGTCCCGGAC	0.711																																																0			5											11	14	13					5																	2752437		2171	4249	6420	2805437	SO:0001583	missense	153571			AY249324	CCDS34131.1	5p15.33	2014-06-02			ENSG00000186493	ENSG00000186493			24226	protein-coding gene	gene with protein product	"coordinated expression to IRX2", "IRX2 neighbor"	610522				16515847, 16750006	Standard	XM_005248256		Approved	CEI, IRX2NB	uc003jdc.3	Q86SI9	OTTHUMG00000161741	ENST00000334000.3:c.59C>T	5.37:g.2752437C>T	ENSP00000334267:p.Thr20Met		2805437		Missense_Mutation	SNP	ENST00000334000.3	37	CCDS34131.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754433	0.31046	.	.	ENSG00000186493	ENST00000457752;ENST00000397835;ENST00000334000;ENST00000505778;ENST00000515640	.	.	.	2.02	2.02	0.26589	.	.	.	.	.	T	0.34308	0.0893	N	0.08118	0	0.09310	N	1	D	0.89917	1.0	D	0.68765	0.96	T	0.12192	-1.0557	8	0.87932	D	0	.	7.5672	0.27885	0.0:1.0:0.0:0.0	.	20	Q86SI9	CEI_HUMAN	M	20	.	ENSP00000334267:T20M	T	+	2	0	C5orf38	2805437	0.003000	0.15002	0.006000	0.13384	0.016000	0.09150	1.940000	0.40223	1.451000	0.47736	0.462000	0.41574	ACG		0.711	C5orf38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365956.2	NM_178569		T	2752437	C	T	2752437	3	4	95	1	0	0	0	0	1	0	0	0	2302	536	19	1	61	1	C5orf38	5	2752437	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10		2752437	178162823	41	25842										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9380001	9380001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	accctgggcctctgggtgggCgagtctccacagccccaggc	14	16	2	0	rs370176472		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:9380001C>T	ENST00000382496.5	-	3	723	c.58G>A	c.(58-60)Gcc>Acc	p.A20T	CTD-2201E9.4_ENST00000511310.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	20					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.A20T(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TCTGGGTGGGCGAGTCTCCAC	0.562																																																1	Substitution - Missense(1)	central_nervous_system(1)	5						C	THR/ALA	0,4406		0,0,2203	130	125	127		58	3.3	0	5		127	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA5A	NM_003966.2	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	20/1075	9380001	1,13005	2203	4300	6503	9433001	SO:0001583	missense	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.58G>A	5.37:g.9380001C>T	ENSP00000371936:p.Ala20Thr		9433001	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	9.263	1.043726	0.19748	0.0	1.16E-4	ENSG00000112902	ENST00000382496;ENST00000513968	T;T	0.36157	1.27;2.09	5.42	3.31	0.37934	.	0.585291	0.16361	N	0.217779	T	0.20251	0.0487	N	0.19112	0.55	0.09310	N	1	B	0.31837	0.342	B	0.21151	0.033	T	0.12218	-1.0556	10	0.52906	T	0.07	.	8.4262	0.32731	0.0:0.7917:0.0:0.2083	.	20	Q13591	SEM5A_HUMAN	T	20	ENSP00000371936:A20T;ENSP00000421961:A20T	ENSP00000371936:A20T	A	-	1	0	SEMA5A	9433001	0.000000	0.05858	0.008000	0.14137	0.195000	0.23768	0.600000	0.24104	1.299000	0.44798	-0.259000	0.10710	GCC		0.562	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9380001	C	T	9380001	3	4	95	1	0	0	0	0	1	0	0	0	14074	768	27	1	3250	1	SEMA5A	5	9380001	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	6627564	9380001	171535259	42	25843										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54424363	54424363	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atgttttcaatcccattgtgGttctccccattccagatgta	6	11	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:54424363G>C	ENST00000381375.2	-	7	925	c.780C>G	c.(778-780)aaC>aaG	p.N260K	CDC20B_ENST00000322374.6_Missense_Mutation_p.N260K|CDC20B_ENST00000334206.5_Missense_Mutation_p.N260K|CDC20B_ENST00000296733.1_Missense_Mutation_p.N260K			Q86Y33	CD20B_HUMAN	cell division cycle 20B	260										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TCCCATTGTGGTTCTCCCCAT	0.433																																																0			5											160	164	162					5																	54424363		2203	4300	6503	54460120	SO:0001583	missense	166979			AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.780C>G	5.37:g.54424363G>C	ENSP00000370781:p.Asn260Lys		54460120	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	G	6.880	0.531850	0.13127	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	4.49	0.267	0.15622	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.782162	0.11142	N	0.595219	T	0.66327	0.2778	M	0.68593	2.085	0.09310	N	1	P;P;P;P	0.46621	0.881;0.617;0.483;0.873	P;B;B;B	0.46299	0.511;0.242;0.122;0.306	T	0.58411	-0.7641	10	0.62326	D	0.03	-16.4791	0.9747	0.01423	0.2438:0.1242:0.3779:0.254	.	260;260;260;260	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	K	260	ENSP00000335664:N260K;ENSP00000296733:N260K;ENSP00000370781:N260K;ENSP00000315720:N260K	ENSP00000296733:N260K	N	-	3	2	CDC20B	54460120	0.000000	0.05858	0.001000	0.08648	0.168000	0.22595	0.182000	0.16900	-0.158000	0.11040	0.650000	0.86243	AAC		0.433	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		C	54424363	G	C	54424363	3	2	95	1	0	0	0	0	1	0	0	0	3066	1252	44	5	803	5	CDC20B	5	54424363	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	45044362	54424363	126490897	43	25844										
APC	324	hgsc.bcm.edu	37	chr5	112175205	112175205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgctaataccctgcaaatagCagaaataaaagaaaagattg	7	6	0	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:112175205C>A	ENST00000457016.1	+	16	4294	c.3914C>A	c.(3913-3915)gCa>gAa	p.A1305E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.A1305E|APC_ENST00000257430.4_Missense_Mutation_p.A1305E			P25054	APC_HUMAN	adenomatous polyposis coli	1305	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.A1305fs*3(1)|p.K1192fs*3(1)|p.?(1)|p.A1305G(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGCAAATAGCAGAAATAAAA	0.423		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											53	55	54					5																	112175205		2202	4300	6502	112203104	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3914C>A	5.37:g.112175205C>A	ENSP00000413133:p.Ala1305Glu		112203104	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	5.754	0.323594	0.10900	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89270	-2.49;-2.49;-2.49	5.73	4.84	0.62591	.	0.439882	0.27567	N	0.018787	T	0.80555	0.4645	N	0.24115	0.695	0.30596	N	0.761008	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.72431	-0.4296	9	.	.	.	-9.5709	12.2704	0.54702	0.1341:0.7366:0.1292:0.0	.	1307;1305	Q4LE70;P25054	.;APC_HUMAN	E	1305	ENSP00000413133:A1305E;ENSP00000257430:A1305E;ENSP00000427089:A1305E	.	A	+	2	0	APC	112203104	0.995000	0.38212	0.993000	0.49108	0.766000	0.43426	2.950000	0.49081	1.506000	0.48736	0.655000	0.94253	GCA		0.423	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175205	C	A	112175205	3	1	95	1	0	0	0	0	1	0	0	0	763	710	25	2	3972	2	APC	5	112175205	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	57750842	112175205	68740055	44	25845										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182270	140182270	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtgtcctactcgctggtggaAcggcgggtgggggagcgcgc	20	10	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:140182270A>G	ENST00000522353.2	+	1	1488	c.1488A>G	c.(1486-1488)gaA>gaG	p.E496E	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.E496E|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	496	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTGGTGGAACGGCGGGTGG	0.682																																																0			5											74	80	78					5																	140182270		2203	4299	6502	140162454	SO:0001819	synonymous_variant	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1488A>G	5.37:g.140182270A>G			140162454	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																				0.682	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		G	140182270	A	G	140182270	2	3	95	1	0	0	0	0	0	0	0	1	11556	40	2	4		4	PCDHA3	5	140182270	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	28007065	140182270	40732990	45	25846										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150722455	150722455	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	caagaacaggttaccttcccCagtgagcgtgattctggagc	11	11	1	3	rs143350420		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:150722455C>T	ENST00000335244.4	-	4	563	c.434G>A	c.(433-435)tGg>tAg	p.W145*	SLC36A2_ENST00000521967.1_Nonsense_Mutation_p.W145*	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	145					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	TTACCTTCCCCAGTGAGCGTG	0.532																																																0			5											159	123	135					5																	150722455		2203	4300	6503	150702648	SO:0001587	stop_gained	153201			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.434G>A	5.37:g.150722455C>T	ENSP00000334223:p.Trp145*		150702648	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Nonsense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	C	36	5.695920	0.96802	.	.	ENSG00000186335	ENST00000335244;ENST00000521967	.	.	.	4.77	4.77	0.60923	.	0.117155	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7126	17.9674	0.89103	0.0:1.0:0.0:0.0	.	.	.	.	X	145	.	ENSP00000334223:W145X	W	-	2	0	SLC36A2	150702648	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	3.894000	0.56250	2.636000	0.89361	0.655000	0.94253	TGG		0.532	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			T	150722455	C	T	150722455	4	4	95	1	0	0	0	0	0	1	0	0	14631	595	21	3	1045	3	SLC36A2	5	150722455	Nonsense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	10540185	150722455	30192805	46	25847										
PHIP	55023	hgsc.bcm.edu	37	chr6	79650577	79650577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcgaccttgatttctagttcTcatgtggggttcagagcctt	10	9	3	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:79650577T>C	ENST00000275034.4	-	40	5466	c.5299A>G	c.(5299-5301)Aga>Gga	p.R1767G	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1767			R -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTTCTAGTTCTCATGTGGGGT	0.408																																																0			6											554	545	548					6																	79650577		2203	4300	6503	79707296	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.5299A>G	6.37:g.79650577T>C	ENSP00000275034:p.Arg1767Gly		79707296	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.896101	0.52121	.	.	ENSG00000146247	ENST00000275034	T	0.47177	0.85	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.29908	0.895	0.58432	D	0.999993	P;P	0.44734	0.842;0.842	B;B	0.34536	0.185;0.185	T	0.03945	-1.0990	9	.	.	.	-19.0401	15.5447	0.76090	0.0:0.0:0.0:1.0	.	1767;1767	A7J992;Q8WWQ0	.;PHIP_HUMAN	G	1767	ENSP00000275034:R1767G	.	R	-	1	2	PHIP	79707296	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.084000	0.71335	2.267000	0.75376	0.528000	0.53228	AGA		0.408	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79650577	T	C	79650577	3	2	95	1	0	0	0	0	1	0	0	0	11873	1559	54	4	170	4	PHIP	6	79650577	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10		79650577	91464490	47	25848										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152477212	152477212	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcaacacctgtactgtgcttCtctatgtctctctgaagctc	7	13	3	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:152477212C>T	ENST00000367255.5	-	132	24412	c.23811G>A	c.(23809-23811)gaG>gaA	p.E7937E	SYNE1_ENST00000539504.1_Silent_p.E92E|SYNE1_ENST00000356820.4_Silent_p.E2461E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000354674.4_Silent_p.E92E|SYNE1_ENST00000423061.1_Silent_p.E7866E|SYNE1_ENST00000265368.4_Silent_p.E7937E|SYNE1_ENST00000448038.1_Silent_p.E7866E|SYNE1_ENST00000341594.5_Silent_p.E7549E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7937					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TACTGTGCTTCTCTATGTCTC	0.473										HNSCC(10;0.0054)																																						0			6											122	111	115					6																	152477212		2203	4300	6503	152518905	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23811G>A	6.37:g.152477212C>T			152518905	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152477212	C	T	152477212	2	4	95	1	0	0	0	0	0	0	0	1	15484	912	32	3		3	SYNE1	6	152477212	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	72826635	152477212	18637855	48	25849										
THBS2	7058	hgsc.bcm.edu	37	chr6	169620355	169620355	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gagagaagacaaatagacccAgccgcccgccagcgtaggtt	12	12	0	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:169620355A>G	ENST00000366787.3	-	22	3698	c.3449T>C	c.(3448-3450)cTg>cCg	p.L1150P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1150	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		AAATAGACCCAGCCGCCCGCC	0.458																																					Esophageal Squamous(91;219 1934 18562 44706)											0			6											131	136	134					6																	169620355		2203	4300	6503	169362280	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3449T>C	6.37:g.169620355A>G	ENSP00000355751:p.Leu1150Pro		169362280	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.920319	0.73098	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.97279	-4.32	4.64	4.64	0.57946	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.32161	U	0.006491	D	0.98210	0.9408	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99513	1.0956	10	0.87932	D	0	-24.657	14.078	0.64903	1.0:0.0:0.0:0.0	.	1150	P35442	TSP2_HUMAN	P	1150;408	ENSP00000355751:L1150P	ENSP00000355751:L1150P	L	-	2	0	THBS2	169362280	1.000000	0.71417	0.622000	0.29159	0.822000	0.46500	8.668000	0.91158	1.719000	0.51432	0.391000	0.25812	CTG		0.458	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		G	169620355	A	G	169620355	3	3	95	1	0	0	0	0	1	0	0	0	15893	188	7	4	77	4	THBS2	6	169620355	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	17143143	169620355	1494712	49	25850										
ICA1	3382	hgsc.bcm.edu	37	chr7	8268281	8268281	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctttcgataagtccagacagGttctctgaattgaatgaaac	8	8	1	4			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:8268281G>T	ENST00000402384.3	-	4	472	c.206C>A	c.(205-207)aCc>aAc	p.T69N	ICA1_ENST00000396675.3_Missense_Mutation_p.T69N|ICA1_ENST00000422063.2_Missense_Mutation_p.T69N|ICA1_ENST00000406470.2_Missense_Mutation_p.T69N|ICA1_ENST00000401396.1_Missense_Mutation_p.T57N|ICA1_ENST00000407906.1_Missense_Mutation_p.T69N|ICA1_ENST00000265577.7_Missense_Mutation_p.T68N			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	69	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		GTCCAGACAGGTTCTCTGAAT	0.303																																																0			7											89	84	86					7																	8268281		2202	4297	6499	8234806	SO:0001583	missense	3382				CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"islet cell autoantigen 1 (69kD)"			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.206C>A	7.37:g.8268281G>T	ENSP00000385570:p.Thr69Asn		8234806	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	37	CCDS34602.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.049382	0.93740	.	.	ENSG00000003147	ENST00000402384;ENST00000406470;ENST00000265577;ENST00000396675;ENST00000401396;ENST00000422063;ENST00000407906;ENST00000317367;ENST00000447326;ENST00000430867;ENST00000446305	T;T;T;T;T;T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	5.96	5.96	0.96718	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.88782	0.6530	M	0.76170	2.325	0.80722	D	1	P;D;D;D;D	0.89917	0.933;1.0;0.999;0.999;1.0	P;D;D;D;D	0.87578	0.718;0.99;0.976;0.976;0.998	D	0.88592	0.3144	10	0.72032	D	0.01	-16.0965	20.422	0.99049	0.0:0.0:1.0:0.0	.	69;69;68;69;57	B3FTQ2;E7ENI6;Q96HG3;Q05084;E9PDL4	.;.;.;ICA69_HUMAN;.	N	69;69;68;69;57;69;69;57;69;68;68	ENSP00000385570:T69N;ENSP00000385651:T69N;ENSP00000265577:T68N;ENSP00000379908:T69N;ENSP00000385305:T57N;ENSP00000403982:T69N;ENSP00000386021:T69N;ENSP00000316074:T57N;ENSP00000398435:T69N;ENSP00000397496:T68N;ENSP00000406722:T68N	ENSP00000265577:T68N	T	-	2	0	ICA1	8234806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.965000	0.93393	2.832000	0.97577	0.655000	0.94253	ACC		0.303	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968		T	8268281	G	T	8268281	3	4	95	1	0	0	0	0	1	0	0	0	7498	1261	44	2	1289	2	ICA1	7	8268281	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10		8268281	150870382	50	25851										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20768054	20768054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctatttaattcaagctggacGaatgaccccagagggcatgt	10	9	1	2	rs200559589		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:20768054G>A	ENST00000404938.2	+	23	3495	c.2843G>A	c.(2842-2844)cGa>cAa	p.R948Q	ABCB5_ENST00000258738.6_Missense_Mutation_p.R503Q	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	948	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CAAGCTGGACGAATGACCCCA	0.473																																																0			7											96	93	94					7																	20768054		2203	4300	6503	20734579	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2843G>A	7.37:g.20768054G>A	ENSP00000384881:p.Arg948Gln		20734579	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645459	0.67358	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.88741	-2.42;-2.42	3.91	3.91	0.45181	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	3.108400	0.02771	U	0.119757	D	0.90363	0.6984	L	0.36672	1.1	0.34459	D	0.701585	D;P;P	0.58268	0.982;0.892;0.928	P;B;P	0.53988	0.739;0.325;0.527	T	0.82786	-0.0285	10	0.29301	T	0.29	.	14.2264	0.65863	0.0:0.0:1.0:0.0	.	948;126;503	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	Q	948;503	ENSP00000384881:R948Q;ENSP00000258738:R503Q	ENSP00000258738:R503Q	R	+	2	0	ABCB5	20734579	0.545000	0.26449	1.000000	0.80357	0.998000	0.95712	1.544000	0.36158	2.472000	0.83506	0.655000	0.94253	CGA		0.473	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		A	20768054	G	A	20768054	3	1	95	1	0	0	0	0	1	0	0	0	44	1058	37	1	2970	1	ABCB5	7	20768054	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	12499773	20768054	138370609	51	25852										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21781775	21781775	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aatctgagagatttatcaaaCgtcttccaggtaccttgact	7	9	3	3	rs201592689		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:21781775C>T	ENST00000409508.3	+	49	8176	c.8145C>T	c.(8143-8145)aaC>aaT	p.N2715N	DNAH11_ENST00000328843.6_Silent_p.N2722N	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2722	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATTTATCAAACGTCTTCCAGG	0.353									Kartagener syndrome																																							0			7											92	85	87					7																	21781775		1840	4098	5938	21748300	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8145C>T	7.37:g.21781775C>T			21748300	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37																																																																																					0.353	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21781775	C	T	21781775	2	4	95	1	0	0	0	0	0	0	0	1	4610	535	19	1		1	DNAH11	7	21781775	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	1013721	21781775	137356888	52	25853										
TARP	6966	hgsc.bcm.edu	37	chr7	38299700	38299700	+	RNA	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	caccgtctgttatgatttctCtccattgcagcagaaagccg	8	12	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:38299700C>T	ENST00000443402.2	-	0	509					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											TATGATTTCTCTCCATTGCAG	0.473																																																0			7											43	45	45					7																	38299700		1813	4058	5871	38266225			445347			M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"T cell receptors / TRG locus"	12275	other	T cell receptor gene	"T-cell receptor, gamma, constant region C1"	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38299700C>T			38266225		Missense_Mutation	SNP	ENST00000443402.2	37																																																																																					0.473	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336		T	38299700	C	T	38299700	1	4	95	0	1	0	0	0	0	0	0	0	15597	922	32	3		3	TARP	7	38299700	RNA	SNP	C	TCGA-DC-6155-01A-11D-1657-10	16517925	38299700	120838963	53	25854										
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106781331	106781331	+	Frame_Shift_Del	DEL	T	T	-													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tagatgccatgtttgaaaaaTtggtcaaagatggggagcat							TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:106781331delT	ENST00000265717.4	+	5	779	c.520delT	c.(520-522)ttgfs	p.L174fs	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	174					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						GTTTGAAAAATTGGTCAAAGA	0.318																																																0			7											168	164	166					7																	106781331		2203	4300	6503	106568567	SO:0001589	frameshift_variant	5577				CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.520delT	7.37:g.106781331delT	ENSP00000265717:p.Leu174fs		106568567	A4D0R9	Frame_Shift_Del	DEL	ENST00000265717.4	37	CCDS5740.1																																																																																				0.318	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			-	106781331	T	-	106781331	7	5	95	1	0	1	0	1	0	0	0	0	12540	1490	52	0	538	0	PRKAR2B	7	106781331	Frame_Shift_Del	DEL	T	TCGA-DC-6155-01A-11D-1657-10	68481631	106781331	52357332	54	25855										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131864591	131864591	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atgaggaggccgccagccacTgcgatgctgacgatggcggg	17	11	0	2	rs3734989	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:131864591T>C	ENST00000359827.3	-	20	4691	c.3729A>G	c.(3727-3729)gcA>gcG	p.A1243A	PLXNA4_ENST00000321063.4_Silent_p.A1243A			Q9HCM2	PLXA4_HUMAN	plexin A4	1243					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CGCCAGCCACTGCGATGCTGA	0.632													C|||	3918	0.782348	0.9803	0.7305	5008	,	,		17133	0.6329		0.6133	False		,,,				2504	0.8793															0			7						C		4025,351		1855,315,18	15	20	18		3729	-9.8	0.1	7	dbSNP_107	18	5269,3299		1650,1969,665	no	coding-synonymous	PLXNA4	NM_020911.1		3505,2284,683	CC,CT,TT		38.5037,8.021,28.1984		1243/1895	131864591	9294,3650	2188	4284	6472	131515131	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3729A>G	7.37:g.131864591T>C			131515131	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.632	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	131864591	T	C	131864591	2	2	95	1	0	0	0	0	0	0	0	1	12153	1567	55	4		4	PLXNA4	7	131864591	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	25083260	131864591	27274072	55	25856										
SSPO	23145	hgsc.bcm.edu	37	chr7	149497386	149497386	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgcccacaggccagagcgtcGccccaggacccttcccacct	9	20	0	1	rs572771455	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:149497386G>A	ENST00000378016.2	+	0	7144							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCAGAGCGTCGCCCCAGGACC	0.672													G|||	2	0.000399361	0	0	5008	,	,		15894	0		0	False		,,,				2504	0.002															0			7											16	22	20					7																	149497386		2157	4243	6400	149128319			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149497386G>A			149128319	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149497386	G	A	149497386	1	1	95	0	1	0	0	0	0	0	0	0	15228	1087	38	1		1	SSPO	7	149497386	RNA	SNP	G	TCGA-DC-6155-01A-11D-1657-10	17632795	149497386	9641277	56	25857										
TCEA1	6917	hgsc.bcm.edu	37	chr8	54923039	54923039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcttaagctcctttagcaaaTccaatgctccagcctataaa	4	12	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:54923039T>C	ENST00000521604.2	-	2	480	c.77A>G	c.(76-78)gAt>gGt	p.D26G	TCEA1_ENST00000522635.1_Missense_Mutation_p.D26G|TCEA1_ENST00000518784.1_Missense_Mutation_p.D26G|TCEA1_ENST00000520534.1_Missense_Mutation_p.D26G|TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000396401.3_Intron	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	26	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			CTTTAGCAAATCCAATGCTCC	0.343			T	PLAG1	salivary adenoma																																		Dom	yes		8	8q11.2	6917	"transcription elongation factor A (SII), 1"		E	0			8											32	30	31					8																	54923039		1795	4063	5858	55085592	SO:0001583	missense	6917			X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"General transcription factors"	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.77A>G	8.37:g.54923039T>C	ENSP00000428426:p.Asp26Gly		55085592	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	37	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.750844	0.49257	.	.	ENSG00000187735	ENST00000521604;ENST00000522635;ENST00000520534;ENST00000518784;ENST00000519704	.	.	.	5.42	5.42	0.78866	Transcription factor IIS, N-terminal (4);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.000000	0.85682	U	0.000000	T	0.82107	0.4965	M	0.87381	2.88	0.54753	D	0.999989	P;P	0.43392	0.805;0.789	P;P	0.59424	0.857;0.833	D	0.84511	0.0622	9	0.62326	D	0.03	-22.1168	12.9809	0.58564	0.0:0.0:0.0:1.0	.	26;26	B7Z4S1;P23193	.;TCEA1_HUMAN	G	26	.	ENSP00000428868:D26G	D	-	2	0	TCEA1	55085592	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.413000	0.66399	2.063000	0.61619	0.459000	0.35465	GAT		0.343	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756		C	54923039	T	C	54923039	3	2	95	1	0	0	0	0	1	0	0	0	15706	1435	50	4	864	4	TCEA1	8	54923039	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10		54923039	91440983	57	25858										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100454774	100454774	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aacacttgtcctctgtttgcCtcaaataaagattattagtg	6	8	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:100454774C>A	ENST00000358544.2	+	23	3467	c.3356C>A	c.(3355-3357)cCt>cAt	p.P1119H	VPS13B_ENST00000357162.2_Missense_Mutation_p.P1119H|VPS13B_ENST00000395996.1_Missense_Mutation_p.P1119H	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1119					protein transport (GO:0015031)			p.P1119L(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTCTGTTTGCCTCAAATAAAG	0.438																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	skin(1)	8											122	114	116					8																	100454774		2203	4300	6503	100523950	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3356C>A	8.37:g.100454774C>A	ENSP00000351346:p.Pro1119His		100523950	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766807	0.90020	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.46063	0.88;0.88;0.88	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	L	0.36672	1.1	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.986;0.998;0.999	T	0.59573	-0.7429	10	0.87932	D	0	.	19.8633	0.96793	0.0:1.0:0.0:0.0	.	1118;1119;1119;1119	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	H	1119	ENSP00000349685:P1119H;ENSP00000351346:P1119H;ENSP00000379318:P1119H	ENSP00000349685:P1119H	P	+	2	0	VPS13B	100523950	1.000000	0.71417	0.991000	0.47740	0.966000	0.64601	7.216000	0.77974	2.697000	0.92050	0.591000	0.81541	CCT		0.438	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100454774	C	A	100454774	3	1	95	1	0	0	0	0	1	0	0	0	17230	681	24	2	3565	2	VPS13B	8	100454774	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	45531735	100454774	45909248	58	25859										
RAD21	5885	hgsc.bcm.edu	37	chr8	117864237	117864237	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agcttttcgcttaactccctGaggtggtggtggaggcatag	14	8	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:117864237G>A	ENST00000297338.2	-	11	1707	c.1420C>T	c.(1420-1422)Cag>Tag	p.Q474*	RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000518055.1_Nonsense_Mutation_p.Q19*	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	474	Pro-rich.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.Q474*(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TTAACTCCCTGAGGTGGTGGT	0.473																																																1	Substitution - Nonsense(1)	lung(1)	8											133	119	124					8																	117864237		2203	4300	6503	117933418	SO:0001587	stop_gained	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1420C>T	8.37:g.117864237G>A	ENSP00000297338:p.Gln474*		117933418	A8K0E0|Q15001|Q99568	Nonsense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	42	9.727148	0.99249	.	.	ENSG00000164754	ENST00000297338;ENST00000518055	.	.	.	5.71	5.71	0.89125	.	0.108239	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-21.6355	19.8625	0.96789	0.0:0.0:1.0:0.0	.	.	.	.	X	474;19	.	ENSP00000297338:Q474X	Q	-	1	0	RAD21	117933418	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.429000	0.97481	2.689000	0.91719	0.655000	0.94253	CAG		0.473	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117864237	G	A	117864237	4	1	95	1	0	0	0	0	0	1	0	0	13018	1299	45	3	491	3	RAD21	8	117864237	Nonsense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	17409463	117864237	28499785	59	25860										
NOV	4856	hgsc.bcm.edu	37	chr8	120428844	120428844	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctgaccttcctgcttctccaTctcctgggacaggtaagtgg	10	13	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:120428844T>C	ENST00000259526.3	+	1	299	c.72T>C	c.(70-72)caT>caC	p.H24H		NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TGCTTCTCCATCTCCTGGGAC	0.562											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			8											113	97	102					8																	120428844		2203	4300	6503	120498025	SO:0001819	synonymous_variant	6134			X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.72T>C	8.37:g.120428844T>C		1503	120498025		Silent	SNP	ENST00000259526.3	37	CCDS6328.1																																																																																				0.562	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		C	120428844	T	C	120428844	2	2	95	1	0	0	0	0	0	0	0	1	10584	1432	50	4		4	NOV	8	120428844	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	2564607	120428844	25935178	60	25861										
ZC3H3	23144	hgsc.bcm.edu	37	chr8	144550819	144550819	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cggctacagctgcctgcaggAtccagccggcctgtggggga	16	13	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:144550819A>G	ENST00000262577.5	-	6	1945	c.1914T>C	c.(1912-1914)gaT>gaC	p.D638D		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	638					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			TGCCTGCAGGATCCAGCCGGC	0.687																																																0			8											27	31	30					8																	144550819		2116	4172	6288	144621962	SO:0001819	synonymous_variant	23144			D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.1914T>C	8.37:g.144550819A>G			144621962	Q14163|Q8N4E2|Q9BUS4	Silent	SNP	ENST00000262577.5	37	CCDS6402.1																																																																																				0.687	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		G	144550819	A	G	144550819	2	3	95	1	0	0	0	0	0	0	0	1	17608	330	12	4		4	ZC3H3	8	144550819	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	24121975	144550819	1813203	61	25862										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145661320	145661320	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tccagctccagccagtccccGgccaggcactcctcctccgg	9	21	0	0	rs2721140	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:145661320G>A	ENST00000409379.3	-	17	2525	c.2496C>T	c.(2494-2496)gcC>gcT	p.A832A	AC084125.4_ENST00000442850.1_RNA|AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	832					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCCAGTCCCCGGCCAGGCACT	0.741													g|||	2347	0.46865	0.4115	0.438	5008	,	,		13786	0.4246		0.4662	False		,,,				2504	0.6155															0			8								1747,2459		402,943,758	8	11	10		2496	-8.9	0	8	dbSNP_100	10	3725,4593		923,1879,1357	no	coding-synonymous	TONSL	NM_013432.4		1325,2822,2115	AA,AG,GG		44.7824,41.5359,43.6921		832/1379	145661320	5472,7052	2103	4159	6262	145632128	SO:0001819	synonymous_variant	0				CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.2496C>T	8.37:g.145661320G>A			145632128	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	37	CCDS34968.2																																																																																				0.741	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		A	145661320	G	A	145661320	2	1	95	1	0	0	0	0	0	0	0	1	10413	1103	39	1		1	NFKBIL2	8	145661320	Silent	SNP	G	TCGA-DC-6155-01A-11D-1657-10	1110501	145661320	702702	62	25863										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145737816	145737816	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	actgcagctggcagagagccCgccgcacagaggccagctcc	13	16	0	2	rs4251691	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:145737816C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Missense_Mutation_p.R1005Q	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	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)			GCAGAGAGCCCGCCGCACAGA	0.667													C|||	1925	0.384385	0.0635	0.4899	5008	,	,		17898	0.4762		0.4543	False		,,,				2504	0.5767															0			8						C	GLN/ARG	543,3685		54,435,1625	22	31	28		3015	0.3	0.1	8	dbSNP_111	28	3802,4678		875,2052,1313	no	missense	RECQL4	NM_004260.3	43	929,2487,2938	TT,TC,CC		44.8349,12.843,34.1911	benign	1005/1209	145737816	4345,8363	2114	4240	6354	145708624	SO:0001628	intergenic_variant	9401				CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145737816C>T			145708624		Silent	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																				0.667	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145737816	C	T	145737816	1	4	95	0	1	0	0	0	0	0	0	0	13239	652	23	1		1	RECQL4	8	145737816	IGR	SNP	C	TCGA-DC-6155-01A-11D-1657-10	76496	145737816	626206	63	25864										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32630106	32630106	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcatgctttcttcattttccGtgcccatccttgtgttctcc	5	14	4	0	rs202147126		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:32630106G>T	ENST00000242310.4	-	1	5561	c.5472C>A	c.(5470-5472)caC>caA	p.H1824Q		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1824			H -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.H1824Q(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTCATTTTCCGTGCCCATCCT	0.493																																																2	Substitution - Missense(2)	lung(2)	9											191	138	156					9																	32630106		2203	4300	6503	32620106	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5472C>A	9.37:g.32630106G>T	ENSP00000418379:p.His1824Gln		32620106	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	9.056	0.993239	0.19043	.	.	ENSG00000122728	ENST00000242310	T	0.07114	3.22	0.479	0.479	0.16796	.	0.268520	0.39341	N	0.001400	T	0.02767	0.0083	N	0.08118	0	0.20563	N	0.999884	B	0.32245	0.361	B	0.17722	0.019	T	0.42832	-0.9428	10	0.31617	T	0.26	.	4.0672	0.09866	0.7251:0.0:0.2749:0.0	.	1824	Q8IZX4	TAF1L_HUMAN	Q	1824	ENSP00000418379:H1824Q	ENSP00000418379:H1824Q	H	-	3	2	TAF1L	32620106	1.000000	0.71417	0.981000	0.43875	0.132000	0.20833	3.993000	0.56987	-0.761000	0.04670	-1.298000	0.01336	CAC		0.493	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			T	32630106	G	T	32630106	3	4	95	1	0	0	0	0	1	0	0	0	15562	1136	40	2	12	2	TAF1L	9	32630106	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10		32630106	108583325	64	25865										
CDK20	23552	hgsc.bcm.edu	37	chr9	90586125	90586125	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agcagcatctgcaggtagctCttgacctgtgcctgggctag	13	11	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:90586125C>G	ENST00000325303.8	-	3	620	c.315G>C	c.(313-315)aaG>aaC	p.K105N	CDK20_ENST00000605159.1_Missense_Mutation_p.K105N|CDK20_ENST00000336654.5_Missense_Mutation_p.K118N|CDK20_ENST00000375883.3_Missense_Mutation_p.K105N|CDK20_ENST00000375871.4_Missense_Mutation_p.K105N	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						GCAGGTAGCTCTTGACCTGTG	0.602																																																0			9											104	75	85					9																	90586125		2203	4300	6503	89775945	SO:0001583	missense	0			AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"Cyclin-dependent kinases"	21420	protein-coding gene	gene with protein product		610076	"cell cycle related kinase"	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.315G>C	9.37:g.90586125C>G	ENSP00000322343:p.Lys105Asn		89775945	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	.	.	.	.	.	.	.	.	.	.	.	18.61	3.660113	0.67586	.	.	ENSG00000156345	ENST00000375883;ENST00000336654;ENST00000375871;ENST00000325303;ENST00000286878	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	3.93	3.93	0.45458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84777	0.5547	M	0.93763	3.455	0.54753	D	0.999983	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.87578	0.969;0.998;0.998;0.995	D	0.88231	0.2903	10	0.87932	D	0	-30.134	12.156	0.54077	0.0:1.0:0.0:0.0	.	105;118;105;105	Q8IZL9-2;A2A390;E7EQ88;Q8IZL9	.;.;.;CDK20_HUMAN	N	105;118;105;105;105	ENSP00000365043:K105N;ENSP00000338975:K118N;ENSP00000365031:K105N;ENSP00000322343:K105N	ENSP00000286878:K105N	K	-	3	2	CDK20	89775945	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.774000	0.26675	2.138000	0.66242	0.462000	0.41574	AAG		0.602	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119		G	90586125	C	G	90586125	3	3	95	1	0	0	0	0	1	0	0	0	3143	912	32	5	749	5	CDK20	9	90586125	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	57956019	90586125	50627306	65	25866										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98248057	98248057	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tggtcaggacattagcacctTcttctttaggggtctgtatc	10	9	4	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:98248057T>C	ENST00000331920.6	-	3	793	c.494A>G	c.(493-495)gAa>gGa	p.E165G	PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000468211.2_Missense_Mutation_p.E99G|PTCH1_ENST00000375274.2_Missense_Mutation_p.E164G|PTCH1_ENST00000418258.1_Missense_Mutation_p.E14G|PTCH1_ENST00000421141.1_Missense_Mutation_p.E14G|PTCH1_ENST00000437951.1_Missense_Mutation_p.E99G|PTCH1_ENST00000430669.2_Missense_Mutation_p.E99G|PTCH1_ENST00000429896.2_Missense_Mutation_p.E14G	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	165					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				ATTAGCACCTTCTTCTTTAGG	0.483																																																0			9											227	236	233					9																	98248057		2203	4300	6503	97287878	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.494A>G	9.37:g.98248057T>C	ENSP00000332353:p.Glu165Gly		97287878	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462250	0.43736	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000553011;ENST00000551845;ENST00000547672;ENST00000546820;ENST00000468211;ENST00000551630	D;D;D;D;D;D;D;D;D;D;D;D;T	0.91351	-1.83;-2.82;-2.81;-2.81;-2.82;-2.81;-2.83;-2.17;-2.17;-2.17;-2.17;-1.83;0.95	5.86	4.66	0.58398	.	0.263096	0.45867	D	0.000337	D	0.84902	0.5575	L	0.31926	0.97	0.45607	D	0.998548	B;B;B	0.15141	0.004;0.011;0.012	B;B;B	0.22386	0.014;0.039;0.006	T	0.79909	-0.1604	10	0.25106	T	0.35	-13.0371	12.7596	0.57356	0.0:0.0:0.1368:0.8632	.	99;164;165	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	G	165;99;14;14;99;14;164;14;14;14;14;99;14	ENSP00000332353:E165G;ENSP00000389744:E99G;ENSP00000399981:E14G;ENSP00000396135:E14G;ENSP00000410287:E99G;ENSP00000414823:E14G;ENSP00000364423:E164G;ENSP00000447797:E14G;ENSP00000447008:E14G;ENSP00000447878:E14G;ENSP00000448843:E14G;ENSP00000449745:E99G;ENSP00000450131:E14G	ENSP00000332353:E165G	E	-	2	0	PTCH1	97287878	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	5.919000	0.70005	2.241000	0.73720	0.482000	0.46254	GAA		0.483	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98248057	T	C	98248057	3	2	95	1	0	0	0	0	1	0	0	0	12764	1783	62	4	3933	4	PTCH1	9	98248057	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	7661932	98248057	42965374	66	25867										
SLC25A25	114789	hgsc.bcm.edu	37	chr9	130869700	130869700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tctacgagaacctgaagatcAccctgggcgtgcagtcgcgg	13	12	2	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:130869700A>G	ENST00000373064.5	+	10	1650	c.1387A>G	c.(1387-1389)Acc>Gcc	p.T463A	SLC25A25_ENST00000433501.1_Missense_Mutation_p.T360A|SLC25A25_ENST00000373066.5_Missense_Mutation_p.T495A|SLC25A25_ENST00000373068.2_Missense_Mutation_p.T497A|SLC25A25_ENST00000432073.2_Missense_Mutation_p.T483A|SLC25A25_ENST00000373069.5_Missense_Mutation_p.T509A|RP11-395P17.11_ENST00000602939.1_RNA	NM_052901.4	NP_443133.2	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	463					adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						CCTGAAGATCACCCTGGGCGT	0.652																																																0			9											73	79	77					9																	130869700		2203	4300	6503	129909521	SO:0001583	missense	114789			AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339		"Solute carriers", "EF-hand domain containing"	20663	protein-coding gene	gene with protein product		608745				15123600	Standard	NM_052901		Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373064.5:c.1387A>G	9.37:g.130869700A>G	ENSP00000362155:p.Thr463Ala		129909521	Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	Missense_Mutation	SNP	ENST00000373064.5	37	CCDS6890.1	.	.	.	.	.	.	.	.	.	.	A	8.262	0.811479	0.16537	.	.	ENSG00000148339	ENST00000373068;ENST00000373069;ENST00000432073;ENST00000373066;ENST00000373064;ENST00000433501	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.41	5.41	0.78517	.	0.163456	0.56097	D	0.000039	T	0.54711	0.1875	N	0.02751	-0.505	0.50813	D	0.999895	B;B;B;B	0.13594	0.002;0.0;0.001;0.008	B;B;B;B	0.14023	0.01;0.001;0.006;0.006	T	0.54043	-0.8352	10	0.13853	T	0.58	-44.8174	14.6343	0.68678	1.0:0.0:0.0:0.0	.	463;495;483;497	Q6KCM7;Q6KCM7-5;Q6KCM7-4;Q6KCM7-2	SCMC2_HUMAN;.;.;.	A	497;509;483;495;463;360	ENSP00000362159:T497A;ENSP00000362160:T509A;ENSP00000410053:T483A;ENSP00000362157:T495A;ENSP00000362155:T463A;ENSP00000401672:T360A	ENSP00000362155:T463A	T	+	1	0	SLC25A25	129909521	0.987000	0.35691	1.000000	0.80357	0.944000	0.59088	2.914000	0.48797	2.042000	0.60477	0.533000	0.62120	ACC		0.652	SLC25A25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054407.1	NM_052901		G	130869700	A	G	130869700	3	3	95	1	0	0	0	0	1	0	0	0	14525	159	6	4	1913	4	SLC25A25	9	130869700	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	32621643	130869700	10343731	67	25868										
NUP188	23511	hgsc.bcm.edu	37	chr9	131755942	131755942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atgctctgtggcaggatcggAgggacagtgccatgctggtc	16	9	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:131755942A>G	ENST00000372577.2	+	27	3007	c.2986A>G	c.(2986-2988)Agg>Ggg	p.R996G		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	996					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GCAGGATCGGAGGGACAGTGC	0.512																																																0			9											104	85	92					9																	131755942		2203	4300	6503	130795763	SO:0001583	missense	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2986A>G	9.37:g.131755942A>G	ENSP00000361658:p.Arg996Gly		130795763	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.730863	0.69074	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.34667	1.35	5.55	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.67953	2.075	0.58432	D	0.999998	D;D	0.89917	1.0;0.993	D;D	0.79784	0.993;0.977	T	0.60156	-0.7318	10	0.72032	D	0.01	-0.0024	13.7712	0.63026	0.3002:0.6998:0.0:0.0	.	329;996	E9PET9;Q5SRE5	.;NU188_HUMAN	G	885;996	ENSP00000361658:R996G	ENSP00000349125:R885G	R	+	1	2	NUP188	130795763	0.960000	0.32886	0.677000	0.29947	0.965000	0.64279	2.230000	0.42999	0.746000	0.32786	-0.213000	0.12676	AGG		0.512	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			G	131755942	A	G	131755942	3	3	95	1	0	0	0	0	1	0	0	0	10789	295	11	4	3092	4	NUP188	9	131755942	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	886242	131755942	9457489	68	25869										
GFI1B	8328	hgsc.bcm.edu	37	chr9	135865173	135865173	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgcggcaaggccttcaagcgCtcgtccacgctgtccaccca	10	17	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:135865173C>A	ENST00000339463.3	+	10	1512	c.693C>A	c.(691-693)cgC>cgA	p.R231R	GFI1B_ENST00000372122.1_Silent_p.R231R|GFI1B_ENST00000372124.1_Silent_p.R185R|GFI1B_ENST00000372123.1_Silent_p.R185R|GFI1B_ENST00000450530.1_Silent_p.R231R|GFI1B_ENST00000534944.1_Silent_p.R185R			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	231	Interaction with ARIH2.|Mediates interaction with GATA1.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		CCTTCAAGCGCTCGTCCACGC	0.652																																																0			9											73	60	64					9																	135865173		2203	4300	6503	134854994	SO:0001819	synonymous_variant	8328			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"Zinc fingers, C2H2-type"	4238	protein-coding gene	gene with protein product		604383	"growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.693C>A	9.37:g.135865173C>A			134854994	O95270|Q5VTD8|Q6FHZ2|Q6T888	Silent	SNP	ENST00000339463.3	37	CCDS6957.1																																																																																				0.652	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		A	135865173	C	A	135865173	2	1	95	1	0	0	0	0	0	0	0	1	6360	784	28	2		2	GFI1B	9	135865173	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	4109231	135865173	5348258	69	25870										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140852115	140852115	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	acgcagaggagggagaggacCggtttgcagatctctgtgct	16	8	1	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:140852115C>T	ENST00000371372.1	+	10	1454	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	CACNA1B_ENST00000371363.1_Missense_Mutation_p.R437W|CACNA1B_ENST00000277551.2_Missense_Mutation_p.R437W|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R438W|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371355.4_Missense_Mutation_p.R438W	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	437					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGGAGAGGACCGGTTTGCAGA	0.567																																																0			9											85	107	100					9																	140852115		2147	4251	6398	139971936	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1309C>T	9.37:g.140852115C>T	ENSP00000360423:p.Arg437Trp		139971936	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	c	22.7	4.318245	0.81469	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.96427	-4.0;-4.01;-4.0;-3.99;-3.99	4.93	4.93	0.64822	.	1.149610	0.06455	N	0.728365	D	0.96531	0.8868	L	0.47190	1.495	0.80722	D	1	D	0.69078	0.997	P	0.53313	0.723	D	0.91977	0.5591	10	0.66056	D	0.02	.	13.89	0.63733	0.0:0.8473:0.1526:0.0	.	437	B1AQK6	.	W	437;437;437;438;438	ENSP00000360423:R437W;ENSP00000277551:R437W;ENSP00000360414:R437W;ENSP00000360408:R438W;ENSP00000360406:R438W	ENSP00000277551:R437W	R	+	1	2	CACNA1B	139971936	1.000000	0.71417	0.987000	0.45799	0.944000	0.59088	5.238000	0.65366	2.311000	0.77944	0.299000	0.19835	CGG		0.567	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140852115	C	T	140852115	3	4	95	1	0	0	0	0	1	0	0	0	2545	643	23	1	1347	1	CACNA1B	9	140852115	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	4986942	140852115	361316	70	25871										
CALML5	51806	hgsc.bcm.edu	37	chr10	5541181	5541181	+	Missense_Mutation	SNP	T	T	C													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccaggccggccctggccttcTtcgccgccgtcaggaactcc					rs10904516|rs373657626|rs386740368	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:5541181T>C	ENST00000380332.3	-	1	352	c.221A>G	c.(220-222)aAg>aGg	p.K74R		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	74	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		K -> R (polymorphism confirmed at protein level; dbSNP:rs10904516). {ECO:0000269|PubMed:10777582, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105}.		epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.K74R(1)		biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						CCTGGCCTTCTTCGCCGCCGT	0.657													T|||	1769	0.353235	0.5121	0.2334	5008	,	,		16118	0.3046		0.3221	False		,,,				2504	0.3057				GBM(149;1055 3356 43077)											1	Substitution - Missense(1)	stomach(1)	10						T	ARG/LYS	530,3876		209,112,1882	42	45	44		221	-1.8	0	10	dbSNP_120	44	464,8136		175,114,4011	no	missense	CALML5	NM_017422.4	26	384,226,5893	CC,CT,TT		5.3953,12.0291,7.6426	possibly-damaging	74/147	5541181	994,12012	2203	4300	6503	5531181	SO:0001583	missense	51806			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"EF-hand domain containing"	18180	protein-coding gene	gene with protein product	"calmodulin-like skin protein"	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.221A>G	10.37:g.5541181T>C	ENSP00000369689:p.Lys74Arg		5531181	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	738	0.33791208791208793	245	0.49796747967479676	89	0.24585635359116023	165	0.28846153846153844	239	0.3153034300791557	T	3.065	-0.192375	0.06259	0.120291	0.053953	ENSG00000178372	ENST00000380332	T	0.37915	1.17	0.893	-1.79	0.07932	EF-hand-like domain (1);	0.809011	0.11132	N	0.596195	T	0.00012	0.0000	N	0.11023	0.085	0.80722	P	0.0	P	0.41710	0.76	B	0.32624	0.149	T	0.45205	-0.9277	9	0.66056	D	0.02	-3.9447	4.0258	0.09687	0.3917:0.0:0.0:0.6083	rs10904516;rs17846249;rs17859268;rs34351495	74	Q9NZT1	CALL5_HUMAN	R	74	ENSP00000369689:K74R	ENSP00000369689:K74R	K	-	2	0	CALML5	5531181	0.033000	0.19621	0.000000	0.03702	0.000000	0.00434	0.459000	0.21908	-1.160000	0.02804	-1.407000	0.01130	AAG		0.657	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422		C	5541181	T	C	5541181	3	2	95	1	0	0	0	0	1	0	0	0	2595	1609	56	4	223	4	CALML5	10	5541181	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10		5541181	129993566	71	25872	35	2								
CALML5	51806	hgsc.bcm.edu	37	chr10	5541183	5541183	+	Silent	SNP	C	C	T													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aggccggccctggccttcttCgccgccgtcaggaactcctg					rs10904517|rs202221308|rs373657626|rs386740368	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:5541183C>T	ENST00000380332.3	-	1	350	c.219G>A	c.(217-219)gcG>gcA	p.A73A		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	73	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						TGGCCTTCTTCGCCGCCGTCA	0.662													C|||	1780	0.355431	0.5182	0.2334	5008	,	,		16136	0.3065		0.3231	False		,,,				2504	0.3057				GBM(149;1055 3356 43077)											0			10						C		407,3999		128,151,1924	42	45	44		219	0.5	0	10	dbSNP_120	44	354,8246		109,136,4055	no	coding-synonymous	CALML5	NM_017422.4		237,287,5979	TT,TC,CC		4.1163,9.2374,5.8511		73/147	5541183	761,12245	2203	4300	6503	5531183	SO:0001819	synonymous_variant	51806			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"EF-hand domain containing"	18180	protein-coding gene	gene with protein product	"calmodulin-like skin protein"	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.219G>A	10.37:g.5541183C>T			5531183	Q5SQI3|Q8IXU8	Silent	SNP	ENST00000380332.3	37	CCDS7068.1																																																																																				0.662	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422		T	5541183	C	T	5541183	2	4	95	1	0	0	0	0	0	0	0	1	2595	871	31	1		1	CALML5	10	5541183	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	2	5541183	129993564	72	25873	35	2								
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46998999	46998999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggaacagaggccagagctccGcaagactgccagcagcaccg	13	14	0	3	rs3127818	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:46998999G>A	ENST00000374317.1	+	3	392	c.119G>A	c.(118-120)cGc>cAc	p.R40H	GPRIN2_ENST00000374314.4_Missense_Mutation_p.R40H	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	40			R -> H (in dbSNP:rs3127818). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CCAGAGCTCCGCAAGACTGCC	0.701																																																0			10																																								46419005	SO:0001583	missense	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.119G>A	10.37:g.46998999G>A	ENSP00000363436:p.Arg40His		46419005	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	1096	0.5018315018315018	248	0.5040650406504065	181	0.5	286	0.5	381	0.5026385224274407	G	10.65	1.410753	0.25465	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.07567	3.18;3.18	5.44	0.466	0.16716	.	0.310657	0.23676	N	0.045669	T	0.00012	0.0000	L	0.38531	1.155	0.26770	N	0.969813	B	0.25007	0.116	B	0.19391	0.025	T	0.51236	-0.8731	10	0.45353	T	0.12	-12.7811	5.8237	0.18542	0.2195:0.0:0.6423:0.1382	rs3127818	40	O60269	GRIN2_HUMAN	H	40	ENSP00000363436:R40H;ENSP00000363433:R40H	ENSP00000363433:R40H	R	+	2	0	GPRIN2	46419005	0.010000	0.17322	0.260000	0.24451	0.226000	0.24999	0.187000	0.16998	-0.022000	0.13986	-0.181000	0.13052	CGC		0.701	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46998999	G	A	46998999	3	1	95	1	0	0	0	0	1	0	0	0	6751	1087	38	1	121	1	GPRIN2	10	46998999	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	41457816	46998999	88535748	73	25874			3	20		2	2	21	G		9.302884e-05
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999019	46999019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcaagactgccagcagcaccGtgtggcaggcccagctgggc	15	14	0	1	rs3127819	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:46999019G>A	ENST00000374317.1	+	3	412	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	GPRIN2_ENST00000374314.4_Missense_Mutation_p.V47M	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	47			V -> M (in dbSNP:rs3127819). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CAGCAGCACCGTGTGGCAGGC	0.701																																																0			10																																								46419025	SO:0001583	missense	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.139G>A	10.37:g.46999019G>A	ENSP00000363436:p.Val47Met		46419025	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	1091	0.49954212454212454	246	0.5	181	0.5	286	0.5	378	0.49868073878627966	G	20.4	3.977383	0.74360	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.06687	3.27;3.27	5.43	5.43	0.79202	.	0.175186	0.27600	N	0.018643	T	0.00012	0.0000	M	0.64997	1.995	0.09310	N	0.999999	D	0.89917	1.0	P	0.61003	0.882	T	0.10567	-1.0624	10	0.48119	T	0.1	-7.7307	15.1094	0.72343	0.0:0.0:1.0:0.0	rs3127819;rs11499481	47	O60269	GRIN2_HUMAN	M	47	ENSP00000363436:V47M;ENSP00000363433:V47M	ENSP00000363433:V47M	V	+	1	0	GPRIN2	46419025	0.336000	0.24757	0.128000	0.21923	0.967000	0.64934	2.595000	0.46197	2.723000	0.93209	0.650000	0.86243	GTG		0.701	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46999019	G	A	46999019	3	1	95	1	0	0	0	0	1	0	0	0	6751	1145	40	1	141	1	GPRIN2	10	46999019	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	20	46999019	88535728	74	25875			3	20		2	2	21	G		9.302884e-05
HNRNPH3	3189	hgsc.bcm.edu	37	chr10	70101793	70101793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggcggcatgagtggaggtggAtggcgtgggatgtactgaaa	20	4	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:70101793A>G	ENST00000265866.7	+	10	1188	c.1023A>G	c.(1021-1023)ggA>ggG	p.G341G	HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000354695.5_Silent_p.G326G|HNRNPH3_ENST00000441000.2_Silent_p.G233G	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	341	Gly-rich.				epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GTGGAGGTGGATGGCGTGGGA	0.428																																																0			10											126	106	113					10																	70101793		2203	4300	6503	69771799	SO:0001819	synonymous_variant	3189				CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"RNA binding motif (RRM) containing"	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.1023A>G	10.37:g.70101793A>G			69771799	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Silent	SNP	ENST00000265866.7	37	CCDS7278.1																																																																																				0.428	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1			G	70101793	A	G	70101793	2	3	95	1	0	0	0	0	0	0	0	1	7289	320	12	4		4	HNRNPH3	10	70101793	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	23102774	70101793	65432954	75	25876										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	372700	372700	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gacatgctgtttcctgggggGgctgggaggctgccactgaa	17	9	0	1	rs35475866	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:372700G>C	ENST00000329962.6	+	3	294	c.294G>C	c.(292-294)ggG>ggC	p.G98G		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	98					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		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;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTCCTGGGGGGGCTGGGAGGC	0.647													.|||	1656	0.330671	0.3253	0.2997	5008	,	,		10061	0.3839		0.2952	False		,,,				2504	0.3415															0			11						G		1430,2946		245,940,1003	18	21	20		294	-1.3	0	11	dbSNP_126	20	2375,6187		331,1713,2237	no	coding-synonymous	B4GALNT4	NM_178537.4		576,2653,3240	CC,CG,GG		27.7388,32.6782,29.4095		98/1040	372700	3805,9133	2188	4281	6469	362700	SO:0001819	synonymous_variant	338707			AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.294G>C	11.37:g.372700G>C			362700	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																				0.647	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		C	372700	G	C	372700	2	2	95	1	0	0	0	0	0	0	0	1	1270	1219	43	5		5	B4GALNT4	11	372700	Silent	SNP	G	TCGA-DC-6155-01A-11D-1657-10		372700	134633816	76	25877										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092954	1092954	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cccatcaccaccaccactacGgtgaccccaaccccaacacc	3	23	1	1	rs56352686		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:1092954G>A	ENST00000359061.5	+	30	4776	c.4776G>A	c.(4774-4776)acG>acA	p.T1592T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000441003.2_Silent_p.T1591T			Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.627																																																0			11											52	85	74					11																	1092954		1812	3296	5108	1082954	SO:0001630	splice_region_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000359061.5:c.4776+1G>A	11.37:g.1092954G>A			1082954	Q14878	Silent	SNP	ENST00000359061.5	37																																																																																					0.627	MUC2-202	KNOWN	basic	protein_coding	protein_coding		NM_002457	Silent	A	1092954	G	A	1092954	5	1	95	1	0	0	0	0	0	0	1	0	10005	1103	39	1	4891	1	MUC2	11	1092954	Splice_Site	SNP	G	TCGA-DC-6155-01A-11D-1657-10	720254	1092954	133913562	77	25878										
LSP1	4046	hgsc.bcm.edu	37	chr11	1874404	1874404	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcttcgagtgacccgggtgcCgaggagcgggaagagttgct	18	9	0	2	rs2089910	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:1874404C>T	ENST00000311604.3	+	1	205	c.30C>T	c.(28-30)gcC>gcT	p.A10A		NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	10					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		ACCCGGGTGCCGAGGAGCGGG	0.657													C|||	1462	0.291933	0.2799	0.2795	5008	,	,		13920	0.4623		0.2654	False		,,,				2504	0.1687															0			11						C		1155,3241	375.1+/-321.5	150,855,1193	65	65	65		30	-5.1	0	11	dbSNP_96	65	1971,6619	325.8+/-317.1	236,1499,2560	no	coding-synonymous	LSP1	NM_002339.2		386,2354,3753	TT,TC,CC		22.9453,26.2739,24.0721		10/340	1874404	3126,9860	2198	4295	6493	1830980	SO:0001819	synonymous_variant	390387			M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.30C>T	11.37:g.1874404C>T			1830980	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																				0.657	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339		T	1874404	C	T	1874404	2	4	95	1	0	0	0	0	0	0	0	1	9092	639	23	1		1	LSP1	11	1874404	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	781450	1874404	133132112	78	25879										
TCIRG1	10312	hgsc.bcm.edu	37	chr11	67816592	67816592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gctgctggagacgctgccggAgctcaccttcctgctgggac	14	14	1	1	rs576389893	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:67816592A>G	ENST00000265686.3	+	15	1826	c.1718A>G	c.(1717-1719)gAg>gGg	p.E573G	RP11-802E16.3_ENST00000526897.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA|TCIRG1_ENST00000532635.1_Missense_Mutation_p.E357G	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	573					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						ACGCTGCCGGAGCTCACCTTC	0.662													A|||	5	0.000998403	0	0	5008	,	,		15878	0		0.001	False		,,,				2504	0.0041															0			11											103	94	97					11																	67816592		2200	4294	6494	67573168	SO:0001583	missense	10312			AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.1718A>G	11.37:g.67816592A>G	ENSP00000265686:p.Glu573Gly		67573168	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.693773	0.88735	.	.	ENSG00000110719	ENST00000265686;ENST00000532635	D;D	0.85773	-2.03;-2.03	4.53	4.53	0.55603	.	0.054616	0.64402	D	0.000001	D	0.87261	0.6133	L	0.37850	1.14	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85299	0.1072	10	0.29301	T	0.29	-23.7346	12.8543	0.57876	1.0:0.0:0.0:0.0	.	573	Q13488	VPP3_HUMAN	G	573;357	ENSP00000265686:E573G;ENSP00000434407:E357G	ENSP00000265686:E573G	E	+	2	0	TCIRG1	67573168	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	9.041000	0.93788	1.904000	0.55121	0.454000	0.30748	GAG		0.662	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019		G	67816592	A	G	67816592	3	3	95	1	0	0	0	0	1	0	0	0	15742	304	11	4	1772	4	TCIRG1	11	67816592	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	65942188	67816592	67189924	79	25880										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249452	71249452	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aaaccctgctgttcccagtcCagctgttgtaagccctgcag	9	14	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:71249452C>G	ENST00000398534.3	+	1	382	c.351C>G	c.(349-351)tcC>tcG	p.S117S		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	117	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GTTCCCAGTCCAGCTGTTGTA	0.607																																																0			11											166	178	174					11																	71249452		2200	4294	6494	70927100	SO:0001819	synonymous_variant	440021			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.351C>G	11.37:g.71249452C>G			70927100	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																				0.607	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249452	C	G	71249452	2	3	95	1	0	0	0	0	0	0	0	1	8589	581	21	5		5	KRTAP5-8	11	71249452	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	3432860	71249452	63757064	80	25881										
ATM	472	hgsc.bcm.edu	37	chr11	108199938	108199938	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	caaagaggaagtaggtctccTtagggaacataaaattcaga	10	6	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:108199938T>C	ENST00000452508.2	+	50	7469	c.7280T>C	c.(7279-7281)cTt>cCt	p.L2427P	ATM_ENST00000278616.4_Missense_Mutation_p.L2427P|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2427	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.		Missing (in AT; associated with T- prolymphocytic leukemia). {ECO:0000269|PubMed:7792600, ECO:0000269|PubMed:8845835, ECO:0000269|PubMed:9463314}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L2427R(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GTAGGTCTCCTTAGGGAACAT	0.358			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											61	61	61					11																	108199938		2201	4298	6499	107705148	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7280T>C	11.37:g.108199938T>C	ENSP00000388058:p.Leu2427Pro		107705148	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.314935	0.81358	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.74209	-0.82;-0.82	5.54	5.54	0.83059	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.266767	0.40302	N	0.001125	D	0.83936	0.5362	M	0.61703	1.905	0.80722	D	1	D	0.67145	0.996	D	0.71870	0.975	D	0.85217	0.1024	10	0.59425	D	0.04	.	15.6843	0.77396	0.0:0.0:0.0:1.0	.	2427	Q13315	ATM_HUMAN	P	2427	ENSP00000278616:L2427P;ENSP00000388058:L2427P	ENSP00000278616:L2427P	L	+	2	0	ATM	107705148	1.000000	0.71417	0.954000	0.39281	0.975000	0.68041	8.033000	0.88852	2.107000	0.64212	0.528000	0.53228	CTT		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108199938	T	C	108199938	3	2	95	1	0	0	0	0	1	0	0	0	1110	1609	56	4	7470	4	ATM	11	108199938	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	36950486	108199938	26806578	81	25882										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:25398285C>T	ENST00000256078.4	-	2	97	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	KRAS_ENST00000556131.1_Missense_Mutation_p.G12S|KRAS_ENST00000557334.1_Missense_Mutation_p.G12S|KRAS_ENST00000311936.3_Missense_Mutation_p.G12S	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>A	12.37:g.25398285C>T	ENSP00000256078:p.Gly12Ser		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441396	0.96187	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	L	0.28344	0.845	0.80722	D	1	P;P	0.39665	0.557;0.682	P;P	0.50570	0.525;0.644	T	0.80254	-0.1459	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	S	12	ENSP00000308495:G12S;ENSP00000452512:G12S;ENSP00000256078:G12S;ENSP00000451856:G12S	ENSP00000256078:G12S	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398285	C	T	25398285	3	4	95	1	0	0	0	0	1	0	0	0	8459	594	21	3	672	3	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10		25398285	108453610	82	25883										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42853901	42853901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gccataatcggaagtggcatGggcgtactgtccgtagagat	14	8	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:42853901G>T	ENST00000455697.1	-	8	2491	c.2206C>A	c.(2206-2208)Cat>Aat	p.H736N	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.H736N|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.H736N|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.H736N|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.H736N	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	736					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GAAGTGGCATGGGCGTACTGT	0.498																																																0			12											123	122	122					12																	42853901		2203	4300	6503	41140168	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.2206C>A	12.37:g.42853901G>T	ENSP00000401060:p.His736Asn		41140168	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.523436	0.27299	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	5.34	5.34	0.76211	.	0.076438	0.53938	D	0.000042	T	0.75087	0.3802	N	0.16478	0.41	0.27331	N	0.956786	B	0.06786	0.001	B	0.04013	0.001	T	0.65352	-0.6189	10	0.41790	T	0.15	-1.7478	14.2827	0.66224	0.0:0.0:0.8513:0.1486	.	736	Q96MT3	PRIC1_HUMAN	N	736	ENSP00000401060:H736N;ENSP00000398947:H736N;ENSP00000448359:H736N;ENSP00000345064:H736N;ENSP00000449819:H736N	ENSP00000345064:H736N	H	-	1	0	PRICKLE1	41140168	0.999000	0.42202	0.336000	0.25522	0.877000	0.50540	2.836000	0.48183	2.667000	0.90743	0.655000	0.94253	CAT		0.498	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			T	42853901	G	T	42853901	3	4	95	1	0	0	0	0	1	0	0	0	12520	1348	47	2	293	2	PRICKLE1	12	42853901	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	17455616	42853901	90997994	83	25884										
RAB21	23011	hgsc.bcm.edu	37	chr12	72149035	72149035	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtgctgcgctactgcgagaaCaagtttaacgacaagcacat	10	10	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:72149035C>T	ENST00000261263.3	+	1	382	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	42					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)	6						ACTGCGAGAACAAGTTTAACG	0.682																																																0			12											47	33	38					12																	72149035		2201	4295	6496	70435302	SO:0001819	synonymous_variant	23011			AF091035	CCDS9003.1	12q21.1	2014-09-04			ENSG00000080371	ENSG00000080371		"RAB, member RAS oncogene"	18263	protein-coding gene	gene with protein product		612398				10887961, 11697911, 16754960	Standard	NM_014999		Approved	KIAA0118	uc001swt.3	Q9UL25	OTTHUMG00000169572	ENST00000261263.3:c.126C>T	12.37:g.72149035C>T			70435302	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	37	CCDS9003.1																																																																																				0.682	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			T	72149035	C	T	72149035	2	4	95	1	0	0	0	0	0	0	0	1	12945	477	17	3		3	RAB21	12	72149035	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	29295134	72149035	61702860	84	25885										
APAF1	317	hgsc.bcm.edu	37	chr12	99043328	99043328	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgtttttgtcacaaggaagaAgctggtgaatgcaattcagc	11	6	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:99043328A>G	ENST00000551964.1	+	4	1128	c.392A>G	c.(391-393)aAg>aGg	p.K131R	APAF1_ENST00000339433.3_Missense_Mutation_p.K131R|APAF1_ENST00000547045.1_Missense_Mutation_p.K131R|APAF1_ENST00000550527.1_Missense_Mutation_p.K120R|APAF1_ENST00000333991.1_Missense_Mutation_p.K131R|APAF1_ENST00000359972.2_Missense_Mutation_p.K120R|APAF1_ENST00000357310.1_Missense_Mutation_p.K131R|APAF1_ENST00000552268.1_Missense_Mutation_p.K131R|APAF1_ENST00000549007.1_Missense_Mutation_p.K131R	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	131	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)	p.K131M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	ACAAGGAAGAAGCTGGTGAAT	0.438																																																1	Substitution - Missense(1)	lung(1)	12											128	120	122					12																	99043328		2203	4300	6503	97567459	SO:0001583	missense	317			AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.392A>G	12.37:g.99043328A>G	ENSP00000448165:p.Lys131Arg		97567459	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	37	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.634508	0.29068	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.55	5.55	0.83447	NB-ARC (1);	0.183845	0.64402	D	0.000019	T	0.72120	0.3421	L	0.36672	1.1	0.42714	D	0.993655	B;B;B;B;B	0.24317	0.017;0.09;0.007;0.096;0.101	B;B;B;B;B	0.32022	0.022;0.139;0.012;0.061;0.018	T	0.67821	-0.5571	10	0.27785	T	0.31	-13.726	15.676	0.77321	1.0:0.0:0.0:0.0	.	131;131;120;131;120	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	131;120;131;131;131;131;120;131;131	ENSP00000448165:K131R;ENSP00000353059:K120R;ENSP00000349862:K131R;ENSP00000341830:K131R;ENSP00000334558:K131R;ENSP00000448826:K131R;ENSP00000448449:K120R;ENSP00000449791:K131R;ENSP00000448161:K131R	ENSP00000334558:K131R	K	+	2	0	APAF1	97567459	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	5.715000	0.68430	2.109000	0.64355	0.533000	0.62120	AAG		0.438	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99043328	A	G	99043328	3	3	95	1	0	0	0	0	1	0	0	0	755	72	3	4	402	4	APAF1	12	99043328	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	26894293	99043328	34808567	85	25886										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121426689	121426689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtcctacctgcagcagcacaAcatcccacagcgggaggtgg	12	14	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:121426689A>G	ENST00000257555.6	+	2	606	c.380A>G	c.(379-381)aAc>aGc	p.N127S	HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.N127S|HNF1A_ENST00000402929.1_Missense_Mutation_p.N127S|HNF1A_ENST00000400024.2_Missense_Mutation_p.N127S|HNF1A_ENST00000543427.1_Missense_Mutation_p.N10S|HNF1A_ENST00000541395.1_Missense_Mutation_p.N127S			P20823	HNF1A_HUMAN	HNF1 homeobox A	127			N -> Y (in a hepatocellular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:12355088}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGCAGCACAACATCCCACAG	0.622									Hepatic Adenoma, Familial Clustering of																																							0			12	GRCh37	CD020597	HNF1A	D							163	124	138					12																	121426689		2203	4300	6503	119911072	SO:0001583	missense	6927	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.380A>G	12.37:g.121426689A>G	ENSP00000257555:p.Asn127Ser		119911072	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.807340	0.90623	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.99277	-5.67;-5.67;-5.67;-5.67	5.08	5.08	0.68730	Hepatocyte nuclear factor 1, N-terminal (1);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.99168	0.9712	M	0.63843	1.955	0.80722	D	1	D;P;D;P	0.89917	1.0;0.948;1.0;0.948	D;D;D;P	0.91635	0.999;0.917;0.999;0.797	D	0.99529	1.0960	10	0.62326	D	0.03	-37.6886	14.0164	0.64527	1.0:0.0:0.0:0.0	.	127;127;127;127	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	S	127;127;127;127;127;127;10;127;127;127;127;127	ENSP00000257555:N127S;ENSP00000439721:N10S;ENSP00000443112:N127S;ENSP00000438804:N127S	ENSP00000257555:N127S	N	+	2	0	HNF1A	119911072	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.889000	0.92470	1.902000	0.55061	0.433000	0.28618	AAC		0.622	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121426689	A	G	121426689	3	3	95	1	0	0	0	0	1	0	0	0	7272	43	2	4	386	4	HNF1A	12	121426689	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	22383361	121426689	12425206	86	25887										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25670801	25670802	+	Frame_Shift_Ins	INS	-	-	A													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	aagcagctgaaagagctattINSaaaaaaatgaacggaatgct							TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:25670801_25670802insA	ENST00000281589.3	+	1	502_503	c.465_466insA	c.(466-468)aaafs	p.K156fs		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	156	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAAGAGCTATTAAAAAAATGAA	0.396																																																0			13																																								24568802	SO:0001589	frameshift_variant	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.472dupA	13.37:g.25670808_25670808dupA	ENSP00000281589:p.Lys156fs		24568801	Q8NHV0|Q9H086	Frame_Shift_Ins	INS	ENST00000281589.3	37	CCDS9311.1																																																																																				0.396	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25670802	-	A	25670801	7	5	95	1	0	1	1	0	0	0	0	0	11396	1742	61	0	467	0	PABPC3	13	25670801	Frame_Shift_Ins	INS	-	TCGA-DC-6155-01A-11D-1657-10		25670801	89499077	87	25888										
BRCA2	675	hgsc.bcm.edu	37	chr13	32911252	32911252	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttgacttgtgtaaacgaaccCattttcaagaactctaccat	5	10	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:32911252C>T	ENST00000380152.3	+	11	2993	c.2760C>T	c.(2758-2760)ccC>ccT	p.P920P	BRCA2_ENST00000544455.1_Silent_p.P920P			P51587	BRCA2_HUMAN	breast cancer 2, early onset	920	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAAACGAACCCATTTTCAAGA	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13	GRCh37	CD031025	BRCA2	D	rs80359346						67	70	69					13																	32911252		2203	4297	6500	31809252	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2760C>T	13.37:g.32911252C>T			31809252	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32911252	C	T	32911252	2	4	95	1	0	0	0	0	0	0	0	1	1502	581	21	3		3	BRCA2	13	32911252	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	7240451	32911252	82258626	88	25889										
BRCA2	675	hgsc.bcm.edu	37	chr13	32913536	32913536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtagtagaaaaacttctgtgAgtcagacttcattacttgaa	8	6	3	4	rs397507756		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:32913536A>G	ENST00000380152.3	+	11	5277	c.5044A>G	c.(5044-5046)Agt>Ggt	p.S1682G	BRCA2_ENST00000544455.1_Missense_Mutation_p.S1682G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1682	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AACTTCTGTGAGTCAGACTTC	0.328			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											33	36	35					13																	32913536		2187	4287	6474	31811536	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5044A>G	13.37:g.32913536A>G	ENSP00000369497:p.Ser1682Gly		31811536	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	9.258	1.042569	0.19748	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.87650	-2.28;-2.28	5.76	3.22	0.36961	.	0.501323	0.22848	N	0.054886	T	0.79862	0.4519	L	0.35854	1.095	0.19300	N	0.999979	B	0.22909	0.077	B	0.23419	0.046	T	0.68435	-0.5409	10	0.49607	T	0.09	.	8.0637	0.30648	0.8122:0.0:0.0664:0.1214	.	1682	P51587	BRCA2_HUMAN	G	1682	ENSP00000369497:S1682G;ENSP00000439902:S1682G	ENSP00000369497:S1682G	S	+	1	0	BRCA2	31811536	0.216000	0.23585	0.037000	0.18230	0.241000	0.25554	2.109000	0.41863	0.400000	0.25396	0.533000	0.62120	AGT		0.328	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32913536	A	G	32913536	3	3	95	1	0	0	0	0	1	0	0	0	1502	304	11	4	5082	4	BRCA2	13	32913536	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	2284	32913536	82256342	89	25890										
DACH1	1602	hgsc.bcm.edu	37	chr13	72204807	72204807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcattgcttcagcaatagctGcattggtagcagcagcagct	10	10	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:72204807G>A	ENST00000359684.2	-	3	1012	c.1013C>T	c.(1012-1014)gCa>gTa	p.A338V	DACH1_ENST00000313174.7_Missense_Mutation_p.A338V|DACH1_ENST00000305425.4_Missense_Mutation_p.A338V|DACH1_ENST00000354591.4_Intron			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	338	Interaction with SIX6 and HDAC3. {ECO:0000250}.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		agcaatagctgcattggtagc	0.383																																																0			13											120	109	113					13																	72204807		1822	4075	5897	71102808	SO:0001583	missense	1602			AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.1013C>T	13.37:g.72204807G>A	ENSP00000352712:p.Ala338Val		71102808	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	37		.	.	.	.	.	.	.	.	.	.	G	26.0	4.696723	0.88830	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000359684;ENST00000377826	T;T;T	0.37058	1.26;1.38;1.22	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.54827	-0.8235	10	0.72032	D	0.01	-9.1643	20.3736	0.98901	0.0:0.0:1.0:0.0	.	336;336	Q9UI36-3;Q9UI36-2	.;.	V	338	ENSP00000304994:A338V;ENSP00000318506:A338V;ENSP00000352712:A338V	ENSP00000304994:A338V	A	-	2	0	DACH1	71102808	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.357000	0.97099	2.820000	0.97059	0.650000	0.86243	GCA		0.383	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		A	72204807	G	A	72204807	3	1	95	1	0	0	0	0	1	0	0	0	4226	1319	46	3	1149	3	DACH1	13	72204807	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	39291271	72204807	42965071	90	25891										
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21681138	21681138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cactttccagacttggaagaTccccgctgtccactcttaga	7	14	1	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:21681138T>C	ENST00000320084.7	-	5	782	c.543A>G	c.(541-543)ggA>ggG	p.G181G	HNRNPC_ENST00000554969.1_Silent_p.G168G|HNRNPC_ENST00000553300.1_Silent_p.G168G|HNRNPC_ENST00000449098.1_Silent_p.G168G|HNRNPC_ENST00000553753.1_Silent_p.G168G|HNRNPC_ENST00000555883.1_Intron|HNRNPC_ENST00000430246.2_Silent_p.G168G|HNRNPC_ENST00000554455.1_Silent_p.G181G|HNRNPC_ENST00000556142.1_Silent_p.G181G|HNRNPC_ENST00000555914.1_Silent_p.G168G|HNRNPC_ENST00000420743.2_Silent_p.G181G|HNRNPC_ENST00000556897.1_Silent_p.G168G|HNRNPC_ENST00000336053.6_Silent_p.G168G|HNRNPC_ENST00000556513.1_Silent_p.G181G|HNRNPC_ENST00000555309.1_Silent_p.G181G|HNRNPC_ENST00000556628.1_Silent_p.G101G|HNRNPC_ENST00000557201.1_Silent_p.G181G	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	181	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		ACTTGGAAGATCCCCGCTGTC	0.423																																					NSCLC(108;607 2244 12726 38757)											0			14											105	112	110					14																	21681138		2190	4289	6479	20750978	SO:0001819	synonymous_variant	3183				CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.543A>G	14.37:g.21681138T>C			20750978	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Silent	SNP	ENST00000320084.7	37	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	T	8.489	0.861496	0.17178	.	.	ENSG00000092199	ENST00000452166	.	.	.	4.53	0.232	0.15381	.	.	.	.	.	T	0.43299	0.1241	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23332	-1.0191	4	.	.	.	.	3.0517	0.06172	0.1324:0.0856:0.3985:0.3835	.	.	.	.	G	141	.	.	D	-	2	0	HNRNPC	20750978	0.870000	0.30015	0.998000	0.56505	0.985000	0.73830	-0.202000	0.09451	0.185000	0.20105	-0.490000	0.04691	GAT		0.423	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			C	21681138	T	C	21681138	2	2	95	1	0	0	0	0	0	0	0	1	7283	1422	50	4		4	HNRNPC	14	21681138	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10		21681138	85668402	91	25892										
ADCY4	196883	hgsc.bcm.edu	37	chr14	24793331	24793331	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtgcccaaggctattctcagTcctggtcgtgtggccaccag	12	13	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:24793331T>C	ENST00000310677.4	-	17	2096	c.1983A>G	c.(1981-1983)ggA>ggG	p.G661G	ADCY4_ENST00000554068.2_Silent_p.G661G|ADCY4_ENST00000396747.3_Silent_p.G354G|ADCY4_ENST00000418030.2_Silent_p.G661G	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	661					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CTATTCTCAGTCCTGGTCGTG	0.612																																																0			14											71	65	67					14																	24793331		2203	4300	6503	23863171	SO:0001819	synonymous_variant	196883			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.1983A>G	14.37:g.24793331T>C			23863171	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	37	CCDS9627.1																																																																																				0.612	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			C	24793331	T	C	24793331	2	2	95	1	0	0	0	0	0	0	0	1	296	1654	58	4		4	ADCY4	14	24793331	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	3112193	24793331	82556209	92	25893										
ACTN1	87	hgsc.bcm.edu	37	chr14	69387768	69387768	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gacgcctttgctggctatgaAatccagggccttgttgacgt	12	10	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:69387768A>C	ENST00000193403.6	-	3	678	c.295T>G	c.(295-297)Ttc>Gtc	p.F99V	ACTN1_ENST00000554508.1_5'Flank|ACTN1_ENST00000376839.3_Missense_Mutation_p.F34V|ACTN1_ENST00000394419.4_Missense_Mutation_p.F99V|ACTN1_ENST00000438964.2_Missense_Mutation_p.F99V|ACTN1_ENST00000538545.2_Missense_Mutation_p.F99V	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	99	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CTGGCTATGAAATCCAGGGCC	0.547																																																0			14											238	187	205					14																	69387768		2203	4300	6503	68457521	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.295T>G	14.37:g.69387768A>C	ENSP00000193403:p.Phe99Val		68457521	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834536	0.91036	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000555616;ENST00000556433;ENST00000553370;ENST00000553779;ENST00000556571	D;D;D;D;D;D;D;D;D;D	0.95949	-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86	4.9	4.9	0.64082	Calponin homology domain (5);	0.053778	0.85682	D	0.000000	D	0.97284	0.9112	M	0.80183	2.485	0.80722	D	1	D;P;P;P	0.61080	0.989;0.816;0.941;0.731	D;P;P;P	0.66084	0.941;0.808;0.855;0.72	D	0.97887	1.0295	10	0.87932	D	0	.	13.6324	0.62202	1.0:0.0:0.0:0.0	.	99;99;99;99	B7TY16;P12814-2;Q1HE25;P12814	.;.;.;ACTN1_HUMAN	V	99;99;99;34;99;34;78;34;34;76	ENSP00000193403:F99V;ENSP00000377941:F99V;ENSP00000414272:F99V;ENSP00000366035:F34V;ENSP00000439828:F99V;ENSP00000450903:F34V;ENSP00000450764:F78V;ENSP00000450925:F34V;ENSP00000450618:F34V;ENSP00000452423:F76V	ENSP00000193403:F99V	F	-	1	0	ACTN1	68457521	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.867000	0.92314	2.073000	0.62155	0.459000	0.35465	TTC		0.547	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		C	69387768	A	C	69387768	3	2	95	1	0	0	0	0	1	0	0	0	204	14	1	4	2529	4	ACTN1	14	69387768	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	44594437	69387768	37961772	93	25894										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73730428	73730428	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtgcggctctcctgctcagaCgacactgccccggaatccca	10	17	2	1	rs145397376	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:73730428C>T	ENST00000554301.1	+	19	2962	c.2799C>T	c.(2797-2799)gaC>gaT	p.D933D	PAPLN_ENST00000427855.1_Silent_p.D933D|PAPLN_ENST00000340738.5_Silent_p.D906D|PAPLN_ENST00000555445.1_Silent_p.D917D|PAPLN_ENST00000554314.1_Intron|PAPLN_ENST00000381166.3_Silent_p.D933D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	933	Ig-like C2-type 1.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.D906E(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CCTGCTCAGACGACACTGCCC	0.627													C|||	38	0.00758786	0	0.0014	5008	,	,		15881	0.0159		0.002	False		,,,				2504	0.0194															1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	14						C		4,4402	8.1+/-20.4	0,4,2199	68	63	64		2718	-9.8	0	14	dbSNP_134	64	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	PAPLN	NM_173462.3		0,24,6479	TT,TC,CC		0.2326,0.0908,0.1845		906/1252	73730428	24,12982	2203	4300	6503	72800181	SO:0001819	synonymous_variant	89932			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2799C>T	14.37:g.73730428C>T			72800181	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																					0.627	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		T	73730428	C	T	73730428	2	4	95	1	0	0	0	0	0	0	0	1	11459	535	19	1		1	PAPLN	14	73730428	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	4342660	73730428	33619112	94	25895										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81025624	81025624	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agaaaatgccccaacttaccGtttctaatgcaattacacgg	6	11	1	1	rs140154637	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:81025624G>A	ENST00000555265.1	-	21	3254	c.2879C>T	c.(2878-2880)aCg>aTg	p.T960M	CEP128_ENST00000281129.3_Splice_Site_p.T960M			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	960						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						CCAACTTACCGTTTCTAATGC	0.328													G|||	2	0.000399361	0	0.0014	5008	,	,		14809	0.001		0	False		,,,				2504	0															0			14						G	MET/THR	0,4406		0,0,2203	84	83	83		2879	1.8	1	14	dbSNP_134	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	CEP128	NM_152446.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	960/1095	81025624	1,13005	2203	4300	6503	80095377	SO:0001630	splice_region_variant	145508			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2880+1C>T	14.37:g.81025624G>A			80095377	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932072	0.34096	0.0	1.16E-4	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.30448	1.53;1.53	5.87	1.8	0.24995	.	0.440685	0.21369	N	0.075669	T	0.10423	0.0255	N	0.03608	-0.345	0.80722	D	1	B	0.30281	0.275	B	0.15870	0.014	T	0.12372	-1.0550	10	0.42905	T	0.14	.	5.5878	0.17283	0.2493:0.1462:0.6046:0.0	.	960	Q6ZU80	CE128_HUMAN	M	960	ENSP00000281129:T960M;ENSP00000451162:T960M	ENSP00000281129:T960M	T	-	2	0	CEP128	80095377	0.992000	0.36948	1.000000	0.80357	0.968000	0.65278	-0.042000	0.12063	0.473000	0.27368	0.655000	0.94253	ACG		0.328	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	Missense_Mutation	A	81025624	G	A	81025624	5	1	95	1	0	0	0	0	0	0	1	0	1753	1159	40	1	425	1	C14orf145	14	81025624	Splice_Site	SNP	G	TCGA-DC-6155-01A-11D-1657-10	7295196	81025624	26323916	95	25896										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86088994	86088994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agccccaagtacagcttctcCgaccactcagcctcccaccc	5	21	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:86088994C>T	ENST00000330753.4	+	2	1903	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	FLRT2_ENST00000554746.1_Missense_Mutation_p.P379L	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	379					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACAGCTTCTCCGACCACTCAG	0.562																																																0			14											83	88	87					14																	86088994		2203	4300	6503	85158747	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1136C>T	14.37:g.86088994C>T	ENSP00000332879:p.Pro379Leu		85158747	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	0.137	-1.106306	0.01828	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.58210	0.35;0.35	6.17	4.36	0.52297	.	0.108090	0.64402	D	0.000005	T	0.37865	0.1019	N	0.22421	0.69	0.46131	D	0.998888	D	0.61080	0.989	B	0.43413	0.419	T	0.07424	-1.0773	10	0.20519	T	0.43	-8.4603	11.8668	0.52499	0.1234:0.8137:0.0:0.063	.	379	O43155	FLRT2_HUMAN	L	379;379;32	ENSP00000332879:P379L;ENSP00000451050:P379L	ENSP00000332879:P379L	P	+	2	0	FLRT2	85158747	0.717000	0.27966	0.003000	0.11579	0.041000	0.13682	4.792000	0.62467	0.933000	0.37291	-0.150000	0.13652	CCG		0.562	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			T	86088994	C	T	86088994	3	4	95	1	0	0	0	0	1	0	0	0	5958	652	23	1	1138	1	FLRT2	14	86088994	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	5063370	86088994	21260546	96	25897										
DISP2	85455	hgsc.bcm.edu	37	chr15	40661726	40661726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atgggatgctggtactggggAccctggtggggagaaggcag	20	6	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr15:40661726A>G	ENST00000267889.3	+	8	3500	c.3413A>G	c.(3412-3414)gAc>gGc	p.D1138G	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	1138					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GGTACTGGGGACCCTGGTGGG	0.622																																																0			15											35	37	36					15																	40661726		2202	4300	6502	38449018	SO:0001583	missense	85455			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.3413A>G	15.37:g.40661726A>G	ENSP00000267889:p.Asp1138Gly		38449018	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.922967	0.73213	.	.	ENSG00000140323	ENST00000267889	T	0.12147	2.71	5.33	5.33	0.75918	.	0.807228	0.11440	N	0.563954	T	0.07728	0.0194	N	0.04508	-0.205	0.24000	N	0.996211	B	0.22211	0.066	B	0.24006	0.05	T	0.33420	-0.9869	10	0.24483	T	0.36	-10.5959	12.0949	0.53748	0.7379:0.2621:0.0:0.0	.	1138	A7MBM2	DISP2_HUMAN	G	1138	ENSP00000267889:D1138G	ENSP00000267889:D1138G	D	+	2	0	DISP2	38449018	0.999000	0.42202	0.896000	0.35187	0.812000	0.45895	4.145000	0.58065	2.237000	0.73441	0.459000	0.35465	GAC		0.622	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		G	40661726	A	G	40661726	3	3	95	1	0	0	0	0	1	0	0	0	4551	275	10	4	3443	4	DISP2	15	40661726	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10		40661726	61869666	97	25898										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91017007	91017007	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atcggttagcttacctgcgcTcccacaaagatgaagttgta	9	10	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr15:91017007T>C	ENST00000268182.5	+	20	2534	c.2410T>C	c.(2410-2412)Tcc>Ccc	p.S804P	IQGAP1_ENST00000560738.1_Missense_Mutation_p.S232P	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	804	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTACCTGCGCTCCCACAAAGA	0.433																																																0			15											95	84	88					15																	91017007		2198	4298	6496	88818011	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2410T>C	15.37:g.91017007T>C	ENSP00000268182:p.Ser804Pro		88818011	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148181	0.37923	.	.	ENSG00000140575	ENST00000268182	D	0.95238	-3.65	5.91	0.468	0.16732	.	0.298649	0.32357	N	0.006218	D	0.89354	0.6691	L	0.27053	0.805	0.28569	N	0.910734	B	0.26744	0.158	B	0.27262	0.078	T	0.78342	-0.2241	10	0.31617	T	0.26	-5.5698	16.4491	0.83973	0.0:0.0:0.7237:0.2762	.	804	P46940	IQGA1_HUMAN	P	804	ENSP00000268182:S804P	ENSP00000268182:S804P	S	+	1	0	IQGAP1	88818011	1.000000	0.71417	0.981000	0.43875	0.634000	0.38068	3.279000	0.51670	0.096000	0.17463	0.533000	0.62120	TCC		0.433	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		C	91017007	T	C	91017007	3	2	95	1	0	0	0	0	1	0	0	0	7835	1551	54	4	2488	4	IQGAP1	15	91017007	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	50355281	91017007	11514385	98	25899										
C16orf11	146325	hgsc.bcm.edu	37	chr16	615048	615048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcttggagaggcgtgggggcGgcccgagctgggtcccgtgt	20	10	1	1	rs113068385	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:615048G>A	ENST00000409413.3	+	3	1736	c.1457G>A	c.(1456-1458)cGg>cAg	p.R486Q	PIGQ_ENST00000409527.2_5'Flank|NHLRC4_ENST00000540585.1_5'Flank|NHLRC4_ENST00000424439.2_5'Flank	NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		486										central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						GCGTGGGGGCGGCCCGAGCTG	0.726													G|||	51	0.0101837	8e-04	0.0029	5008	,	,		11854	0		0.0447	False		,,,				2504	0.0031															0			16						G	GLN/ARG	21,3429		0,21,1704	5	7	7		1457	-7.7	0	16	dbSNP_132	7	278,7486		4,270,3608	no	missense	C16orf11	NM_145270.2	43	4,291,5312	AA,AG,GG		3.5806,0.6087,2.6663	benign	486/572	615048	299,10915	1725	3882	5607	555049	SO:0001583	missense	146325																														ENST00000409413.3:c.1457G>A	16.37:g.615048G>A	ENSP00000386499:p.Arg486Gln		555049	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	37	CCDS45365.1	35	0.016025641025641024	0	0.0	3	0.008287292817679558	0	0.0	32	0.04221635883905013	G	8.830	0.939587	0.18281	0.006087	0.035806	ENSG00000161992	ENST00000409413	.	.	.	3.84	-7.67	0.01272	.	3.460850	0.01504	N	0.017638	T	0.01558	0.0050	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15492	-1.0435	9	0.21540	T	0.41	.	1.6347	0.02740	0.3014:0.373:0.1849:0.1407	.	486	P0CG20	CP011_HUMAN	Q	486	.	ENSP00000386499:R486Q	R	+	2	0	C16orf11	555049	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.058000	0.14301	-1.772000	0.01292	-1.622000	0.00790	CGG		0.726	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1			A	615048	G	A	615048	3	1	95	1	0	0	0	0	1	0	0	0	1814	1116	39	1	1463	1	C16orf11	16	615048	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10		615048	89739705	99	25900										
WFIKKN1	117166	hgsc.bcm.edu	37	chr16	681284	681284	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tacgtccactcctgccgctcCtgctcctcctccggctgacc	7	21	0	1	rs8062289	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:681284C>T	ENST00000319070.2	+	1	353	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	11					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CCTGCCGCTCCTGCTCCTCCT	0.741													c|||	1093	0.218251	0.3986	0.0965	5008	,	,		11117	0.0357		0.1859	False		,,,				2504	0.2822															0			16								1488,2824		287,914,955	10	11	11		31	0.8	0	16	dbSNP_116	11	1579,6943		165,1249,2847	no	coding-synonymous	WFIKKN1	NM_053284.2		452,2163,3802	TT,TC,CC		18.5285,34.5083,23.8975		11/549	681284	3067,9767	2156	4261	6417	621285	SO:0001819	synonymous_variant	117166			AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30912	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20A"	608021	"chromosome 16 open reading frame 12"	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.31C>T	16.37:g.681284C>T			621285	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																				0.741	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284		T	681284	C	T	681284	2	4	95	1	0	0	0	0	0	0	0	1	17398	680	24	3		3	WFIKKN1	16	681284	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	66236	681284	89673469	100	25901										
FBXL16	146330	hgsc.bcm.edu	37	chr16	747029	747029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	acttgggctggtacagcacgCgccgccaggccttgcacacc	12	16	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:747029C>T	ENST00000397621.1	-	2	708	c.377G>A	c.(376-378)cGc>cAc	p.R126H	FBXL16_ENST00000562585.1_5'Flank|FBXL16_ENST00000324361.5_Missense_Mutation_p.R126H|FBXL16_ENST00000562563.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	126	F-box.									endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				GTACAGCACGCGCCGCCAGGC	0.632																																																0			16											36	34	35					16																	747029		2199	4299	6498	687030	SO:0001583	missense	146330			BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"F-boxes / Leucine-rich repeats"	14150	protein-coding gene	gene with protein product		609082	"chromosome 16 open reading frame 22"	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.377G>A	16.37:g.747029C>T	ENSP00000380746:p.Arg126His		687030	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Missense_Mutation	SNP	ENST00000397621.1	37	CCDS10421.1	.	.	.	.	.	.	.	.	.	.	c	13.76	2.332124	0.41297	.	.	ENSG00000127585	ENST00000397621;ENST00000324361	T;T	0.25579	1.79;1.79	4.01	4.01	0.46588	F-box domain, Skp2-like (1);	0.064020	0.64402	D	0.000011	T	0.24198	0.0586	L	0.47716	1.5	0.38375	D	0.944963	D	0.64830	0.994	B	0.41036	0.346	T	0.21008	-1.0258	10	0.44086	T	0.13	.	15.1067	0.72326	0.0:1.0:0.0:0.0	.	126	Q8N461	FXL16_HUMAN	H	126	ENSP00000380746:R126H;ENSP00000318674:R126H	ENSP00000318674:R126H	R	-	2	0	FBXL16	687030	1.000000	0.71417	0.997000	0.53966	0.879000	0.50718	5.607000	0.67648	1.798000	0.52647	0.313000	0.20887	CGC		0.632	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350		T	747029	C	T	747029	3	4	95	1	0	0	0	0	1	0	0	0	5731	768	27	1	1082	1	FBXL16	16	747029	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	65745	747029	89607724	101	25902										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55719134	55719134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggcagctcttgctctgtctgAtggtcgtcgtcatcgtcttg	12	11	5	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:55719134A>G	ENST00000379906.2	+	4	979	c.724A>G	c.(724-726)Atg>Gtg	p.M242V	SLC6A2_ENST00000566163.1_Missense_Mutation_p.M242V|SLC6A2_ENST00000567238.1_Missense_Mutation_p.M137V|SLC6A2_ENST00000561820.1_Missense_Mutation_p.M242V|SLC6A2_ENST00000414754.3_Missense_Mutation_p.M242V|SLC6A2_ENST00000219833.8_Missense_Mutation_p.M242V|SLC6A2_ENST00000568943.1_Missense_Mutation_p.M242V	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	242					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GCTCTGTCTGATGGTCGTCGT	0.532																																																0			16											135	123	127					16																	55719134		2198	4300	6498	54276635	SO:0001583	missense	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.724A>G	16.37:g.55719134A>G	ENSP00000369237:p.Met242Val		54276635	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	A	4.858	0.159443	0.09236	.	.	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833	T;T;T	0.72615	-0.67;-0.67;-0.67	5.65	-2.88	0.05682	.	0.445192	0.29133	N	0.013043	T	0.26412	0.0645	N	0.00504	-1.425	0.19575	N	0.999967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.002;0.001	T	0.30794	-0.9966	10	0.33141	T	0.24	.	1.5769	0.02626	0.3508:0.0973:0.1358:0.416	.	242;1;137;242	Q96KH8;F5H0T4;B4DX48;P23975	.;.;.;SC6A2_HUMAN	V	242;1;242;242	ENSP00000394956:M242V;ENSP00000369237:M242V;ENSP00000219833:M242V	ENSP00000219833:M242V	M	+	1	0	SLC6A2	54276635	0.810000	0.29049	0.082000	0.20525	0.494000	0.33585	1.169000	0.31871	-0.457000	0.07033	-1.407000	0.01130	ATG		0.532	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			G	55719134	A	G	55719134	3	3	95	1	0	0	0	0	1	0	0	0	14720	333	12	4	829	4	SLC6A2	16	55719134	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	54972105	55719134	34635619	102	25903										
SLC38A7	55238	hgsc.bcm.edu	37	chr16	58706132	58706132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccacagcagctccaaaggtcAggaagccacagatgcctgtg	11	13	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:58706132A>G	ENST00000570101.1	-	8	1782	c.899T>C	c.(898-900)cTg>cCg	p.L300P	SLC38A7_ENST00000219320.4_Missense_Mutation_p.L300P|SLC38A7_ENST00000564010.1_Missense_Mutation_p.L211P|SLC38A7_ENST00000564100.1_Intron|SLC38A7_ENST00000566953.1_5'UTR			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	300					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						TCCAAAGGTCAGGAAGCCACA	0.617																																																0			16											38	33	35					16																	58706132		2189	4294	6483	57263633	SO:0001583	missense	55238			BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.899T>C	16.37:g.58706132A>G	ENSP00000454646:p.Leu300Pro		57263633	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	37	CCDS10800.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.202928	0.58234	.	.	ENSG00000103042	ENST00000219320	T	0.03272	3.99	5.36	5.36	0.76844	.	0.067302	0.64402	N	0.000009	T	0.19005	0.0456	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00397	-1.1765	9	.	.	.	.	14.5336	0.67944	1.0:0.0:0.0:0.0	.	300	Q9NVC3	S38A7_HUMAN	P	300	ENSP00000219320:L300P	.	L	-	2	0	SLC38A7	57263633	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.853000	0.92222	2.020000	0.59435	0.482000	0.46254	CTG		0.617	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		G	58706132	A	G	58706132	3	3	95	1	0	0	0	0	1	0	0	0	14646	188	7	4	505	4	SLC38A7	16	58706132	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	2986998	58706132	31648621	103	25904										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70863708	70863708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tggtctgcgtgtgcttggagCgcacctggcacgtgaaattc	14	10	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:70863708C>T	ENST00000393567.2	-	81	14075	c.13925G>A	c.(13924-13926)cGc>cAc	p.R4642H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4642					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GTGCTTGGAGCGCACCTGGCA	0.577																																																0			16											2	2	2					16																	70863708		1419	3306	4725	69421209	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13925G>A	16.37:g.70863708C>T	ENSP00000377197:p.Arg4642His		69421209	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648491	0.87958	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01933	4.55	5.0	5.0	0.66597	.	0.000000	0.33813	U	0.004539	T	0.15825	0.0381	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01337	-1.1381	10	0.44086	T	0.13	.	17.9456	0.89036	0.0:1.0:0.0:0.0	.	4641	F8WD23	.	H	4642;4641	ENSP00000377197:R4642H	ENSP00000313052:R4641H	R	-	2	0	HYDIN	69421209	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	7.416000	0.80143	2.334000	0.79466	0.505000	0.49811	CGC		0.577	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70863708	C	T	70863708	3	4	95	1	0	0	0	0	1	0	0	0	7488	768	27	1	1464	1	HYDIN	16	70863708	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	12157576	70863708	19491045	104	25905										
HP	3240	hgsc.bcm.edu	37	chr16	72093037	72093037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gtacaccttaaacaatgagaAgcagtggataaataaggctg	10	6	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:72093037A>T	ENST00000355906.5	+	6	450	c.392A>T	c.(391-393)aAg>aTg	p.K131M	HP_ENST00000357763.4_Missense_Mutation_p.K167M|HP_ENST00000570083.1_Missense_Mutation_p.K72M|HP_ENST00000565574.1_Intron|HP_ENST00000569639.1_Missense_Mutation_p.K72M|HP_ENST00000562526.1_Missense_Mutation_p.K72M|HPR_ENST00000356967.5_Intron|HP_ENST00000398131.2_Missense_Mutation_p.K72M	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	131	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		AACAATGAGAAGCAGTGGATA	0.483																																																0			16											122	132	129					16																	72093037		1786	4080	5866	70650538	SO:0001583	missense	10395				CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.392A>T	16.37:g.72093037A>T	ENSP00000348170:p.Lys131Met		70650538	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Missense_Mutation	SNP	ENST00000355906.5	37	CCDS45524.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.754477	0.31046	.	.	ENSG00000257017	ENST00000355906;ENST00000398131	T;T	0.50548	0.74;0.74	4.24	4.24	0.50183	Complement control module (2);Sushi/SCR/CCP (2);	0.188909	0.35903	N	0.002917	T	0.68495	0.3007	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.73263	-0.4038	10	0.87932	D	0	.	9.8991	0.41338	1.0:0.0:0.0:0.0	.	131	P00738	HPT_HUMAN	M	131;72	ENSP00000348170:K131M;ENSP00000381199:K72M	ENSP00000348170:K131M	K	+	2	0	HP	70650538	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.473000	0.45145	1.902000	0.55061	0.482000	0.46254	AAG		0.483	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143		T	72093037	A	T	72093037	3	4	95	1	0	0	0	0	1	0	0	0	7348	72	3	5	414	5	HP	16	72093037	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	1229329	72093037	18261716	105	25906										
CMIP	80790	hgsc.bcm.edu	37	chr16	81478932	81478932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gctggggggcgacgtgtcggCccccgaaggcacgaagatgg	19	11	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:81478932C>T	ENST00000537098.3	+	1	158	c.86C>T	c.(85-87)gCc>gTc	p.A29V		NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	29						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						GACGTGTCGGCCCCCGAAGGC	0.701																																																0			16											14	16	15					16																	81478932		1900	4094	5994	80036433	SO:0001583	missense	80790			AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.86C>T	16.37:g.81478932C>T	ENSP00000446100:p.Ala29Val		80036433	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.794218	0.50102	.	.	ENSG00000153815	ENST00000537098	T	0.49432	0.78	3.02	2.01	0.26516	Pleckstrin homology domain (1);	.	.	.	.	T	0.27697	0.0681	N	0.08118	0	0.80722	D	1	B	0.15473	0.013	B	0.12156	0.007	T	0.05599	-1.0875	9	0.56958	D	0.05	.	11.5377	0.50648	0.0:0.8171:0.1829:0.0	.	29	Q8IY22	CMIP_HUMAN	V	29	ENSP00000446100:A29V	ENSP00000446100:A29V	A	+	2	0	CMIP	80036433	0.993000	0.37304	0.995000	0.50966	0.962000	0.63368	1.565000	0.36386	0.202000	0.20498	0.306000	0.20318	GCC		0.701	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		T	81478932	C	T	81478932	3	4	95	1	0	0	0	0	1	0	0	0	3584	739	26	3	88	3	CMIP	16	81478932	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	9385895	81478932	8875821	106	25907										
SGSM2	9905	hgsc.bcm.edu	37	chr17	2266812	2266812	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gaggacaggctggctgcctgTgcccgcgagtgtgtggagtc	18	10	0	0	rs2003968	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:2266812T>C	ENST00000426855.2	+	7	901	c.726T>C	c.(724-726)tgT>tgC	p.C242C	SGSM2_ENST00000268989.3_Silent_p.C242C|SGSM2_ENST00000574563.1_Silent_p.C242C	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	242					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TGGCTGCCTGTGCCCGCGAGT	0.642													C|||	2836	0.566294	0.5431	0.3444	5008	,	,		16364	0.7639		0.4314	False		,,,				2504	0.6902															0			17						C	,	2372,2034		640,1092,471	25	28	27		726,726	-11.5	0.1	17	dbSNP_92	27	3921,4677		893,2135,1271	yes	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	1533,3227,1742	CC,CT,TT		45.6036,46.1643,48.3928	,	242/1007,242/1052	2266812	6293,6711	2203	4299	6502	2213562	SO:0001819	synonymous_variant	9905			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.726T>C	17.37:g.2266812T>C			2213562	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																				0.642	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		C	2266812	T	C	2266812	2	2	95	1	0	0	0	0	0	0	0	1	14260	1702	59	4		4	SGSM2	17	2266812	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10		2266812	78928398	107	25908										
TP53	7157	hgsc.bcm.edu	37	chr17	7579470	7579471	+	Frame_Shift_Ins	INS	-	-	G													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gctgctggtgcaggggccacINSggggggagcagcctctggca					rs56275308|rs587782423		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:7579470_7579471insG	ENST00000269305.4	-	4	405_406	c.216_217insC	c.(214-219)cccgtgfs	p.V73fs	TP53_ENST00000359597.4_Frame_Shift_Ins_p.V73fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.V73fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	73	Interaction with HRMT1L2.|Interaction with WWOX.		V -> E (in a sporadic cancer; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V73fs*76(11)|p.0?(8)|p.V73L(3)|p.G59fs*23(3)|p.R72fs*51(2)|p.V73M(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.V73fs*50(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGGGCCACGGGGGGAGCAG	0.604		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	37	Insertion - Frameshift(11)|Deletion - Frameshift(9)|Whole gene deletion(8)|Substitution - Missense(5)|Complex - frameshift(3)|Deletion - In frame(1)	upper_aerodigestive_tract(6)|lung(6)|breast(4)|bone(4)|central_nervous_system(3)|biliary_tract(3)|urinary_tract(3)|large_intestine(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|ovary(1)|prostate(1)|liver(1)	17	GRCh37	CI920954	TP53	I																																				7520196	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.217dupC	17.37:g.7579476_7579476dupG	ENSP00000269305:p.Val73fs		7520195	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.604	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7579471	-	G	7579470	7	5	95	1	0	1	1	0	0	0	0	0	16421	536	19	0	1085	0	TP53	17	7579470	Frame_Shift_Ins	INS	-	TCGA-DC-6155-01A-11D-1657-10	5312658	7579470	73615740	108	25909										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319868	21319868	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccgaagccgggacggcctcaGcccccaggccaggcatgact	13	17	1	1	rs73979902	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:21319868G>T	ENST00000583088.1	+	3	2109	c.1214G>T	c.(1213-1215)aGc>aTc	p.S405I	KCNJ12_ENST00000331718.5_Missense_Mutation_p.S405I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	405				S -> I (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GACGGCCTCAGCCCCCAGGCC	0.662										Prostate(3;0.18)																																						0			17																																								21260461	SO:0001583	missense	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1214G>T	17.37:g.21319868G>T	ENSP00000463778:p.Ser405Ile		21260461	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252898	0.59212	.	.	ENSG00000184185	ENST00000331718	D	0.88354	-2.37	5.83	5.83	0.93111	.	1.356490	0.04362	N	0.357607	D	0.89410	0.6707	L	0.51422	1.61	0.09310	P	0.99999754014	B	0.23442	0.085	B	0.19946	0.027	T	0.74352	-0.3693	9	0.51188	T	0.08	.	18.3013	0.90164	0.0:0.0:1.0:0.0	.	405	Q14500	IRK12_HUMAN	I	405	ENSP00000328150:S405I	ENSP00000328150:S405I	S	+	2	0	KCNJ12	21260461	1.000000	0.71417	0.718000	0.30602	0.849000	0.48306	5.226000	0.65299	2.758000	0.94735	0.655000	0.94253	AGC		0.662	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21319868	G	T	21319868	3	4	95	1	0	0	0	0	1	0	0	0	8067	971	34	2	1216	2	KCNJ12	17	21319868	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	13740398	21319868	59875342	109	25910										
NF1	4763	hgsc.bcm.edu	37	chr17	29546136	29546136	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	attgctcaggaagcaatggaGgtaaggggaaaatgaattcc	13	5	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:29546136G>A	ENST00000358273.4	+	14	2024	c.1641G>A	c.(1639-1641)gaG>gaA	p.E547E	NF1_ENST00000431387.4_Splice_Site_p.E547E|NF1_ENST00000356175.3_Splice_Site_p.E547E	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	547					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.N510_E547del(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAGCAATGGAGGTAAGGGGAA	0.453			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	15	Whole gene deletion(8)|Unknown(6)|Deletion - In frame(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(2)|stomach(1)|lung(1)	17											63	57	59					17																	29546136		2203	4300	6503	26570262	SO:0001630	splice_region_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1641+1G>A	17.37:g.29546136G>A			26570262	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.453	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Silent	A	29546136	G	A	29546136	5	1	95	1	0	0	0	0	0	0	1	0	10387	1014	35	3	1695	3	NF1	17	29546136	Splice_Site	SNP	G	TCGA-DC-6155-01A-11D-1657-10	8226268	29546136	51649074	110	25911										
NF1	4763	hgsc.bcm.edu	37	chr17	29684030	29684030	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccacatttacgtaaagtttcAgtgtctgaatcaaatgttct	6	8	4	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:29684030A>G	ENST00000358273.4	+	53	8174	c.7791A>G	c.(7789-7791)tcA>tcG	p.S2597S	NF1_ENST00000444181.2_Silent_p.S390S|NF1_ENST00000356175.3_Silent_p.S2576S|NF1_ENST00000417592.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2597					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GTAAAGTTTCAGTGTCTGAAT	0.413			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											201	189	193					17																	29684030		2203	4300	6503	26708156	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7791A>G	17.37:g.29684030A>G			26708156	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29684030	A	G	29684030	2	3	95	1	0	0	0	0	0	0	0	1	10387	175	7	4		4	NF1	17	29684030	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	137894	29684030	51511180	111	25912										
DNAI2	64446	hgsc.bcm.edu	37	chr17	72295954	72295954	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggcaccatctggctgcagtcGaagacgggcaccgagtgctt	14	12	1	1	rs140295057		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:72295954G>A	ENST00000311014.6	+	7	889	c.822G>A	c.(820-822)tcG>tcA	p.S274S	DNAI2_ENST00000307504.5_Silent_p.S131S|DNAI2_ENST00000446837.2_Silent_p.S274S|DNAI2_ENST00000582036.1_Silent_p.S274S|DNAI2_ENST00000579490.1_Silent_p.S331S			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	274					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGCTGCAGTCGAAGACGGGCA	0.622									Kartagener syndrome				G|||	1	0.000199681	0	0.0014	5008	,	,		16985	0		0	False		,,,				2504	0															0			17						G	,	1,4405		0,1,2202	68	50	56		822,822	-10.3	0.2	17	dbSNP_134	56	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	274/594,274/606	72295954	1,13005	2203	4300	6503	69807549	SO:0001819	synonymous_variant	64446	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"Axonemal dyneins", "WD repeat domain containing"	18744	protein-coding gene	gene with protein product	"dynein intermediate chain 2"	605483	"dynein, axonemal, intermediate polypeptide 2"			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.822G>A	17.37:g.72295954G>A			69807549	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																				0.622	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		A	72295954	G	A	72295954	2	1	95	1	0	0	0	0	0	0	0	1	4621	1045	37	1		1	DNAI2	17	72295954	Silent	SNP	G	TCGA-DC-6155-01A-11D-1657-10	42611924	72295954	8899256	112	25913										
CASKIN2	57513	hgsc.bcm.edu	37	chr17	73498463	73498463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ccttcggggccctgtggcccCttccttgggccctgggctct	13	17	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:73498463C>T	ENST00000321617.3	-	18	3278	c.2692G>A	c.(2692-2694)Ggg>Agg	p.G898R	CASKIN2_ENST00000433559.2_Missense_Mutation_p.G816R	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	898	Pro-rich.					cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCTGTGGCCCCTTCCTTGGGC	0.731																																																0			17											4	5	4					17																	73498463		1921	3842	5763	71010058	SO:0001583	missense	57513			AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.2692G>A	17.37:g.73498463C>T	ENSP00000325355:p.Gly898Arg		71010058	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	37	CCDS11723.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548804	0.45383	.	.	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.72942	-0.7;-0.49	4.87	3.9	0.45041	.	0.000000	0.38897	N	0.001540	T	0.49389	0.1554	N	0.14661	0.345	0.22412	N	0.99912	B	0.14805	0.011	B	0.08055	0.003	T	0.44221	-0.9342	10	0.87932	D	0	.	5.5231	0.16943	0.0:0.6636:0.0:0.3364	.	898	Q8WXE0	CSKI2_HUMAN	R	898;816	ENSP00000325355:G898R;ENSP00000406963:G816R	ENSP00000325355:G898R	G	-	1	0	CASKIN2	71010058	.	.	0.936000	0.37596	0.810000	0.45777	.	.	1.290000	0.44636	0.491000	0.48974	GGG		0.731	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753		T	73498463	C	T	73498463	3	4	95	1	0	0	0	0	1	0	0	0	2673	681	24	3	928	3	CASKIN2	17	73498463	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	1202509	73498463	7696747	113	25914										
PRCD	768206	hgsc.bcm.edu	37	chr17	74536240	74536240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cgccatgtgcaccaccctttTcctgctcagcaccctggcca	7	19	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:74536240T>C	ENST00000586148.1	+	1	69	c.17T>C	c.(16-18)tTc>tCc	p.F6S	PRCD_ENST00000592014.1_Missense_Mutation_p.F6S|PRCD_ENST00000592432.1_Intron|CYGB_ENST00000589342.1_5'Flank|CYGB_ENST00000293230.5_5'Flank|CYGB_ENST00000589145.1_Intron			Q00LT1	PRCD_HUMAN	progressive rod-cone degeneration	6					response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											ACCACCCTTTTCCTGCTCAGC	0.662																																																0			17											18	21	20					17																	74536240		2022	4173	6195	72047835	SO:0001583	missense	768206			DQ390338	CCDS42382.1	17q25.1	2008-10-24			ENSG00000214140	ENSG00000214140			32528	protein-coding gene	gene with protein product		610598				16938425	Standard	NM_001077620		Approved	RP36	uc002jrw.1	Q00LT1	OTTHUMG00000132200	ENST00000586148.1:c.17T>C	17.37:g.74536240T>C	ENSP00000465932:p.Phe6Ser		72047835	B9EJD4	Missense_Mutation	SNP	ENST00000586148.1	37	CCDS42382.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686217	0.88639	.	.	ENSG00000214140	ENST00000397630	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.47911	0.1471	.	.	.	0.25118	N	0.990664	B	0.34015	0.435	B	0.41332	0.354	T	0.49753	-0.8906	7	0.87932	D	0	.	10.7494	0.46200	0.0:0.0:0.0:1.0	.	6	Q00LT1	PRCD_HUMAN	S	6	.	ENSP00000380754:F6S	F	+	2	0	PRCD	72047835	0.993000	0.37304	1.000000	0.80357	0.983000	0.72400	4.228000	0.58619	2.042000	0.60477	0.528000	0.53228	TTC		0.662	PRCD-008	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450598.1			C	74536240	T	C	74536240	3	2	95	1	0	0	0	0	1	0	0	0	12482	1783	62	4	19	4	PRCD	17	74536240	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	1037777	74536240	6658970	114	25915										
AZI1	22994	hgsc.bcm.edu	37	chr17	79176093	79176093	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctgggcaagcccgtgctgccCccagtattgttccgggctga	13	14	0	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:79176093C>T	ENST00000269392.4	-	7	982	c.735G>A	c.(733-735)ggG>ggA	p.G245G	AZI1_ENST00000450824.2_Silent_p.G245G|AZI1_ENST00000570482.2_5'UTR|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000575907.1_Silent_p.G245G|AZI1_ENST00000374782.3_Silent_p.G245G	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		245					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCGTGCTGCCCCCAGTATTGT	0.642																																																0			17											85	72	77					17																	79176093		2203	4300	6503	76790688	SO:0001819	synonymous_variant	22994																														ENST00000269392.4:c.735G>A	17.37:g.79176093C>T			76790688	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																					0.642	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			T	79176093	C	T	79176093	2	4	95	1	0	0	0	0	0	0	0	1	1241	610	22	3		3	AZI1	17	79176093	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	4639853	79176093	2019117	115	25916										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6958514	6958514	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tttttgatacagccatggaaCgatcttctcattgtgagcag	9	8	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:6958514C>T	ENST00000389658.3	-	55	8019	c.7926G>A	c.(7924-7926)tcG>tcA	p.S2642S	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2642	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGCCATGGAACGATCTTCTCA	0.463																																																0			18											164	122	137					18																	6958514		2203	4300	6503	6948514	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7926G>A	18.37:g.6958514C>T			6948514		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.463	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6958514	C	T	6958514	2	4	95	1	0	0	0	0	0	0	0	1	8627	523	19	1		1	LAMA1	18	6958514	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10		6958514	71118734	116	25917										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6985393	6985393	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tagcttatcctggtgatcctCtaagtgctacatggagaaat	9	8	1	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:6985393C>G	ENST00000389658.3	-	39	5596	c.5503G>C	c.(5503-5505)Gag>Cag	p.E1835Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1835	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGGTGATCCTCTAAGTGCTAC	0.378																																																0			18											125	118	120					18																	6985393		2203	4300	6503	6975393	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5503G>C	18.37:g.6985393C>G	ENSP00000374309:p.Glu1835Gln		6975393		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694868	0.48202	.	.	ENSG00000101680	ENST00000389658	T	0.18174	2.23	5.58	5.58	0.84498	.	0.126892	0.51477	D	0.000097	T	0.27098	0.0664	L	0.57536	1.79	0.45097	D	0.998119	D	0.59357	0.985	P	0.49887	0.625	T	0.01242	-1.1408	10	0.21014	T	0.42	.	17.741	0.88407	0.0:1.0:0.0:0.0	.	1835	P25391	LAMA1_HUMAN	Q	1835	ENSP00000374309:E1835Q	ENSP00000374309:E1835Q	E	-	1	0	LAMA1	6975393	1.000000	0.71417	0.484000	0.27391	0.195000	0.23768	6.149000	0.71795	2.631000	0.89168	0.655000	0.94253	GAG		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6985393	C	G	6985393	3	3	95	1	0	0	0	0	1	0	0	0	8627	922	32	5	3824	5	LAMA1	18	6985393	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	26879	6985393	71091855	117	25918										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591925	48591925	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttctggaggagatcgcttttGtttgggtcaactctccaatg	11	8	3	1	rs377767349		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:48591925G>A	ENST00000342988.3	+	9	1626	c.1088G>A	c.(1087-1089)tGt>tAt	p.C363Y	SMAD4_ENST00000588745.1_Missense_Mutation_p.C267Y|SMAD4_ENST00000398417.2_Missense_Mutation_p.C363Y	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	363	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GATCGCTTTTGTTTGGGTCAA	0.418																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18	GRCh37	CD064635	SMAD4	D							155	129	138					18																	48591925		2203	4300	6503	46845923	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1088G>A	18.37:g.48591925G>A	ENSP00000341551:p.Cys363Tyr		46845923	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.921255	0.92249	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99226	-5.59;-5.59	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97962	1.0338	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	363	Q13485	SMAD4_HUMAN	Y	363	ENSP00000341551:C363Y;ENSP00000381452:C363Y	ENSP00000341551:C363Y	C	+	2	0	SMAD4	46845923	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.676000	0.98643	2.771000	0.95319	0.563000	0.77884	TGT		0.418	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48591925	G	A	48591925	3	1	95	1	0	0	0	0	1	0	0	0	14797	1377	48	3	1118	3	SMAD4	18	48591925	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	41606532	48591925	29485323	118	25919										
AZU1	566	hgsc.bcm.edu	37	chr19	830820	830820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggccggctgggggagccagcGcagtggggggcgtctctccc	20	13	1	0	rs28626600	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:830820G>A	ENST00000233997.2	+	4	494	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		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)		GGGAGCCAGCGCAGTGGGGGG	0.657													G|||	285	0.0569089	0.0045	0.0576	5008	,	,		15019	0.0079		0.1223	False		,,,				2504	0.1104															0			19						G	HIS/ARG	73,4331	58.7+/-95.3	1,71,2130	29	28	29		473	-0.8	0	19	dbSNP_125	29	869,7731	189.1+/-236.0	48,773,3479	yes	missense	AZU1	NM_001700.3	29	49,844,5609	AA,AG,GG		10.1047,1.6576,7.2439	probably-damaging	158/252	830820	942,12062	2202	4300	6502	781820	SO:0001583	missense	566			X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"cationic antimicrobial protein 37", "heparin-binding protein", "neutrophil azurocidin"	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.473G>A	19.37:g.830820G>A	ENSP00000233997:p.Arg158His		781820	P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	124	0.056776556776556776	2	0.0040650406504065045	26	0.0718232044198895	3	0.005244755244755245	93	0.12269129287598944	G	10.53	1.374773	0.24857	0.016576	0.101047	ENSG00000172232	ENST00000334630;ENST00000233997	D	0.88896	-2.44	1.51	-0.763	0.11030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.04048	0.0113	N	0.16307	0.4	0.09310	N	1	D	0.65815	0.995	B	0.43950	0.437	T	0.40850	-0.9541	9	0.42905	T	0.14	.	3.9576	0.09396	0.4496:0.0:0.5504:0.0	rs28626600	158	P20160	CAP7_HUMAN	H	172;158	ENSP00000233997:R158H	ENSP00000233997:R158H	R	+	2	0	AZU1	781820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	-0.178000	0.10672	-0.258000	0.10820	CGC		0.657	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700		A	830820	G	A	830820	3	1	95	1	0	0	0	0	1	0	0	0	1244	1087	38	1	487	1	AZU1	19	830820	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10		830820	58298163	119	25920										
S1PR4	8698	hgsc.bcm.edu	37	chr19	3179472	3179472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gcctctatggggccatcttcCgcctggtgcaggccagcggg	15	14	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:3179472C>T	ENST00000246115.3	+	1	737	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C	S1PR4_ENST00000591346.1_3'UTR	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	228					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						GGCCATCTTCCGCCTGGTGCA	0.672																																					GBM(82;318 1638 33279 49708)											0			19											63	68	67					19																	3179472		2203	4296	6499	3130472	SO:0001583	missense	8698			AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3170	protein-coding gene	gene with protein product		603751	"endothelial differentiation, G-protein-coupled receptor 6", "endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.682C>T	19.37:g.3179472C>T	ENSP00000246115:p.Arg228Cys		3130472	D6W612	Missense_Mutation	SNP	ENST00000246115.3	37	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.252765	0.22965	.	.	ENSG00000125910	ENST00000246115	T	0.39406	1.08	4.23	1.94	0.25998	GPCR, rhodopsin-like superfamily (1);	0.307616	0.30219	N	0.010131	T	0.27765	0.0683	L	0.38838	1.175	0.42614	D	0.993321	B	0.15473	0.013	B	0.08055	0.003	T	0.05886	-1.0858	10	0.38643	T	0.18	.	5.4596	0.16610	0.3988:0.5025:0.0:0.0987	.	228	O95977	S1PR4_HUMAN	C	228	ENSP00000246115:R228C	ENSP00000246115:R228C	R	+	1	0	S1PR4	3130472	0.780000	0.28664	0.186000	0.23195	0.674000	0.39518	0.796000	0.26986	0.181000	0.19994	0.462000	0.41574	CGC		0.672	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775		T	3179472	C	T	3179472	3	4	95	1	0	0	0	0	1	0	0	0	13833	652	23	1	684	1	S1PR4	19	3179472	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	2348652	3179472	55949511	120	25921										
MUC16	94025	hgsc.bcm.edu	37	chr19	9047485	9047485	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gaagtggcttctgccccaggActggtggctattgatggtgt	15	8	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:9047485A>G	ENST00000397910.4	-	5	34349	c.34146T>C	c.(34144-34146)agT>agC	p.S11382S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11384	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGCCCCAGGACTGGTGGCTA	0.483																																																0			19											233	226	228					19																	9047485		1973	4157	6130	8908485	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34146T>C	19.37:g.9047485A>G			8908485	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9047485	A	G	9047485	2	3	95	1	0	0	0	0	0	0	0	1	10003	272	10	4		4	MUC16	19	9047485	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	5868013	9047485	50081498	121	25922										
SYDE1	85360	hgsc.bcm.edu	37	chr19	15220577	15220577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agtccccgggccccgccaggCgcctctccataaagatgaag	11	16	1	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:15220577C>T	ENST00000342784.2	+	3	524	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Missense_Mutation_p.R98C	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	165					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CCCCGCCAGGCGCCTCTCCAT	0.716																																																0			19											3	3	3					19																	15220577		1911	3773	5684	15081577	SO:0001583	missense	85360			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.493C>T	19.37:g.15220577C>T	ENSP00000341489:p.Arg165Cys		15081577	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	37	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940098	0.73557	.	.	ENSG00000105137	ENST00000342784	T	0.15718	2.4	3.98	3.98	0.46160	.	0.191857	0.35739	N	0.003015	T	0.29976	0.0750	L	0.47716	1.5	0.39881	D	0.973645	D;D	0.89917	1.0;1.0	D;D	0.67725	0.953;0.943	T	0.04678	-1.0934	10	0.72032	D	0.01	.	9.4437	0.38684	0.2123:0.7877:0.0:0.0	.	98;165	Q6ZW31-2;Q6ZW31	.;SYDE1_HUMAN	C	165	ENSP00000341489:R165C	ENSP00000341489:R165C	R	+	1	0	SYDE1	15081577	0.954000	0.32549	0.996000	0.52242	0.928000	0.56348	1.795000	0.38784	1.960000	0.56953	0.573000	0.79308	CGC		0.716	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15220577	C	T	15220577	3	4	95	1	0	0	0	0	1	0	0	0	15474	768	27	1	503	1	SYDE1	19	15220577	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	6173092	15220577	43908406	122	25923										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17014404	17014404	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cagccgtcccccttggcactCacaaacagccccgtggggag	11	17	1	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:17014404C>T	ENST00000443236.1	-	34	4609	c.4578G>A	c.(4576-4578)gtG>gtA	p.V1526V		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1479						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCTTGGCACTCACAAACAGCC	0.612																																																0			19											93	111	105					19																	17014404		2033	4177	6210	16875404	SO:0001819	synonymous_variant	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4578G>A	19.37:g.17014404C>T			16875404	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1																																																																																				0.612	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17014404	C	T	17014404	2	4	95	1	0	0	0	0	0	0	0	1	3801	813	29	3		3	CPAMD8	19	17014404	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	1793827	17014404	42114579	123	25924										
APLP1	333	hgsc.bcm.edu	37	chr19	36362573	36362573	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	atgctcttaccctgtggctcGgatcggttccgtggtgtgga	14	10	1	0	rs201024631	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:36362573G>A	ENST00000221891.4	+	5	789	c.597G>A	c.(595-597)tcG>tcA	p.S199S	NPHS1_ENST00000591817.1_5'Flank|APLP1_ENST00000586861.1_Silent_p.S193S|APLP1_ENST00000537454.2_Silent_p.S160S	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	199					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCTGTGGCTCGGATCGGTTCC	0.642													G|||	4	0.000798722	8e-04	0.0043	5008	,	,		15417	0		0	False		,,,				2504	0															0			19											114	104	107					19																	36362573		2203	4300	6503	41054413	SO:0001819	synonymous_variant	333			U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.597G>A	19.37:g.36362573G>A			41054413	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																				0.642	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		A	36362573	G	A	36362573	2	1	95	1	0	0	0	0	0	0	0	1	778	1103	39	1		1	APLP1	19	36362573	Silent	SNP	G	TCGA-DC-6155-01A-11D-1657-10	19348169	36362573	22766410	124	25925										
DMWD	1762	hgsc.bcm.edu	37	chr19	46289503	46289503	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gccttgggcagtggagagagCggggcgcccccggccgagcc	19	14	0	1	rs8109951	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:46289503C>T	ENST00000270223.6	-	3	1296	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000601370.1_5'Flank|DMWD_ENST00000377735.3_Silent_p.P417P	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	417										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GTGGAGAGAGCGGGGCGCCCC	0.692													C|||	1455	0.290535	0.3079	0.2291	5008	,	,		12564	0.2887		0.329	False		,,,				2504	0.273															0			19						C		1250,3120		209,832,1144	15	18	17		1251	-8.4	0	19	dbSNP_116	17	3086,5450		602,1882,1784	no	coding-synonymous	DMWD	NM_004943.1		811,2714,2928	TT,TC,CC		36.1528,28.6041,33.5968		417/675	46289503	4336,8570	2185	4268	6453	50981343	SO:0001819	synonymous_variant	1762			L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1251G>A	19.37:g.46289503C>T			50981343		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																				0.692	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		T	46289503	C	T	46289503	2	4	95	1	0	0	0	0	0	0	0	1	4604	755	27	1		1	DMWD	19	46289503	Silent	SNP	C	TCGA-DC-6155-01A-11D-1657-10	9926930	46289503	12839480	125	25926										
LIG1	3978	hgsc.bcm.edu	37	chr19	48657140	48657140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggggctcaccttcctcctccTtcttcctcttggcttctctg	7	17	4	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:48657140T>C	ENST00000263274.7	-	6	874	c.455A>G	c.(454-456)aAg>aGg	p.K152R	LIG1_ENST00000536218.1_Intron|LIG1_ENST00000599165.1_Intron|LIG1_ENST00000427526.2_Missense_Mutation_p.K122R	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	152			K -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ttcctcctccttcttcctctt	0.577								Nucleotide excision repair (NER)																																								0			19											196	113	141					19																	48657140		2203	4300	6503	53348952	SO:0001583	missense	26018				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.455A>G	19.37:g.48657140T>C	ENSP00000263274:p.Lys152Arg		53348952	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	6.386	0.439422	0.12104	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526	T;T	0.58506	0.44;0.33	3.99	2.94	0.34122	.	0.866238	0.10215	N	0.701604	T	0.48714	0.1515	L	0.54323	1.7	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.28839	-1.0031	10	0.18710	T	0.47	-18.4584	7.3918	0.26913	0.0:0.0:0.2229:0.7771	.	122;152	B4DTU4;P18858	.;DNLI1_HUMAN	R	152;184;122	ENSP00000263274:K152R;ENSP00000442841:K122R	ENSP00000263274:K152R	K	-	2	0	LIG1	53348952	0.292000	0.24362	0.892000	0.35008	0.244000	0.25665	1.067000	0.30616	0.837000	0.34925	0.496000	0.49642	AAG		0.577	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48657140	T	C	48657140	3	2	95	1	0	0	0	0	1	0	0	0	8804	1609	56	4	2396	4	LIG1	19	48657140	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10	2367637	48657140	10471843	126	25927										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612683	53612683	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctaatgcatgatttctgttcTtgtgtgagtaatgaagaaca	9	5	2	4			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:53612683T>C	ENST00000500065.4	-	4	948	c.615A>G	c.(613-615)caA>caG	p.Q205Q	ZNF415_ENST00000421033.1_Silent_p.Q217Q|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000440291.1_Silent_p.Q192Q|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000455735.2_Silent_p.Q253Q|ZNF415_ENST00000243643.4_Silent_p.Q205Q|ZNF415_ENST00000448501.1_Silent_p.Q253Q	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ATTTCTGTTCTTGTGTGAGTA	0.378																																																0			19											138	112	121					19																	53612683		2203	4300	6503	58304495	SO:0001819	synonymous_variant	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.615A>G	19.37:g.53612683T>C			58304495	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																				0.378	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		C	53612683	T	C	53612683	2	2	95	1	0	0	0	0	0	0	0	1	17931	1606	56	4		4	ZNF415	19	53612683	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	4955543	53612683	5516300	127	25928										
KIR2DS4	3811	hgsc.bcm.edu	37	chr19	55344246	55344246	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ctcatggtcatcatcatggcGtgtgttggtgagtcctggaa	13	8	4	1	rs374252476	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:55344246G>A	ENST00000391728.4	+	0	1871				KIR3DL1_ENST00000402254.2_Intron|KIR2DS4_ENST00000339924.8_RNA	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TCATCATGGCGTGTGTTGGTG	0.622													.|||	74	0.0147764	0.0038	0.013	5008	,	,		14966	0.0149		0.0169	False		,,,				2504	0.0286															0			19											180	165	170					19																	55344246		2172	4177	6349	60036058	SO:0001628	intergenic_variant	3809			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933		19.37:g.55344246G>A			60036058	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																				0.622	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		A	55344246	G	A	55344246	1	1	95	0	1	0	0	0	0	0	0	0	8340	1132	40	1		1	KIR2DS4	19	55344246	IGR	SNP	G	TCGA-DC-6155-01A-11D-1657-10	1731563	55344246	3784737	128	25929										
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20032998	20032998	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggccgccatgtctgcagcagTcgacctctggacacctgtcc	11	16	2	0	rs2255255	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:20032998T>C	ENST00000377340.2	-	2	503	c.472A>G	c.(472-474)Act>Gct	p.T158A	C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000245957.5_5'Flank|CRNKL1_ENST00000536226.1_5'UTR|C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000389656.3_5'Flank|CRNKL1_ENST00000377327.4_Missense_Mutation_p.T146A	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	158			T -> A (in dbSNP:rs2255255).		mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TCTGCAGCAGTCGACCTCTGG	0.607													C|||	2599	0.51897	0.4425	0.549	5008	,	,		18253	0.7024		0.4871	False		,,,				2504	0.4448															0			20						C	ALA/THR	1944,2462	615.9+/-392.7	429,1086,688	41	42	41		472	-0.5	0	20	dbSNP_100	41	4087,4513	587.3+/-392.2	963,2161,1176	yes	missense	CRNKL1	NM_016652.4	58	1392,3247,1864	CC,CT,TT		47.5233,44.1217,46.3709	benign	158/849	20032998	6031,6975	2203	4300	6503	19980998	SO:0001583	missense	51340			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.472A>G	20.37:g.20032998T>C	ENSP00000366557:p.Thr158Ala		19980998	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	1181	0.5407509157509157	216	0.43902439024390244	188	0.5193370165745856	402	0.7027972027972028	375	0.4947229551451187	C	3.383	-0.125925	0.06795	0.441217	0.475233	ENSG00000101343	ENST00000377327;ENST00000377340	T;T	0.28895	1.59;1.59	5.38	-0.469	0.12142	.	3.252220	0.01008	N	0.003785	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.500000000004725E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43458	-0.9390	9	0.02654	T	1	11.7577	2.5872	0.04833	0.3895:0.3588:0.1141:0.1376	rs2255255;rs61548236;rs2255255	146;158	Q5JY65;Q9BZJ0	.;CRNL1_HUMAN	A	146;158	ENSP00000366544:T146A;ENSP00000366557:T158A	ENSP00000366544:T146A	T	-	1	0	CRNKL1	19980998	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.451000	0.06795	-0.461000	0.06993	-0.119000	0.15052	ACT		0.607	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			C	20032998	T	C	20032998	3	2	95	1	0	0	0	0	1	0	0	0	3897	1667	58	4	2130	4	CRNKL1	20	20032998	Missense_Mutation	SNP	T	TCGA-DC-6155-01A-11D-1657-10		20032998	42992522	129	25930										
C20orf112	140688	hgsc.bcm.edu	37	chr20	31041518	31041518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggtcctcagggcagccgctgAcctcggtcttgatggaatcg	14	12	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:31041518A>G	ENST00000359676.5	-	4	576	c.434T>C	c.(433-435)gTc>gCc	p.V145A	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		145						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GCAGCCGCTGACCTCGGTCTT	0.602																																																0			20											56	45	49					20																	31041518		2181	4265	6446	30505179	SO:0001583	missense	140688																														ENST00000359676.5:c.434T>C	20.37:g.31041518A>G	ENSP00000352704:p.Val145Ala		30505179	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Missense_Mutation	SNP	ENST00000359676.5	37	CCDS13202.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242680	0.39598	.	.	ENSG00000197183	ENST00000359676;ENST00000397984	.	.	.	5.04	3.95	0.45737	.	0.369444	0.26190	N	0.025815	T	0.42223	0.1193	L	0.34521	1.04	0.80722	D	1	B	0.28998	0.23	B	0.20955	0.032	T	0.27020	-1.0086	9	0.38643	T	0.18	-19.865	9.5375	0.39231	0.8516:0.0:0.1484:0.0	.	145	Q96MY1	CT112_HUMAN	A	145	.	ENSP00000352704:V145A	V	-	2	0	C20orf112	30505179	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	6.713000	0.74686	0.944000	0.37579	0.379000	0.24179	GTC		0.602	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2			G	31041518	A	G	31041518	3	3	95	1	0	0	0	0	1	0	0	0	2087	275	10	4	896	4	C20orf112	20	31041518	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	11008520	31041518	31984002	130	25931										
ZNF341	84905	hgsc.bcm.edu	37	chr20	32379263	32379263	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gctctggcggagctgcaggcTggggccgagggcccatgtgc	19	12	1	0	rs2626551	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:32379263T>C	ENST00000375200.1	+	15	2870	c.2505T>C	c.(2503-2505)gcT>gcC	p.A835A	RP4-553F4.6_ENST00000443171.1_RNA|ZNF341_ENST00000342427.2_Silent_p.A828A|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	835					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						AGCTGCAGGCTGGGGCCGAGG	0.667													C|||	4074	0.813498	0.9743	0.7493	5008	,	,		15185	0.9355		0.6282	False		,,,				2504	0.7065															0			20						C		3999,403		1818,363,20	27	24	25		2484	-9.5	0.2	20	dbSNP_100	25	5544,3050		1820,1904,573	no	coding-synonymous	ZNF341	NM_032819.3		3638,2267,593	CC,CT,TT		35.4899,9.1549,26.5697		828/848	32379263	9543,3453	2201	4297	6498	31842924	SO:0001819	synonymous_variant	84905			AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.2505T>C	20.37:g.32379263T>C			31842924	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																					0.667	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32379263	T	C	32379263	2	2	95	1	0	0	0	0	0	0	0	1	17896	1567	55	4		4	ZNF341	20	32379263	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	1337745	32379263	30646257	131	25932										
LBP	3929	hgsc.bcm.edu	37	chr20	36982828	36982828	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gacgtggaggtggacatgtcGggagacttggggtaggtctc	19	6	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:36982828G>A	ENST00000217407.2	+	4	674	c.513G>A	c.(511-513)tcG>tcA	p.S171S		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	171					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TGGACATGTCGGGAGACTTGG	0.617																																																0			20											42	37	39					20																	36982828		2203	4300	6503	36416242	SO:0001819	synonymous_variant	3929				CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.513G>A	20.37:g.36982828G>A			36416242	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																				0.617	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		A	36982828	G	A	36982828	2	1	95	1	0	0	0	0	0	0	0	1	8673	1103	39	1		1	LBP	20	36982828	Silent	SNP	G	TCGA-DC-6155-01A-11D-1657-10	4603565	36982828	26042692	132	25933										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484420	57484420	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttcaggacctgcttcgctgcCgtgtcctgacttctggaatc	10	13	2	1	rs11554273		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:57484420C>A	ENST00000371085.3	+	8	1025	c.601C>A	c.(601-603)Cgt>Agt	p.R201S	GNAS_ENST00000306090.10_Missense_Mutation_p.R187S|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371102.4_Missense_Mutation_p.R830S|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844S|GNAS_ENST00000371095.3_Missense_Mutation_p.R187S|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202S|GNAS_ENST00000265620.7_Missense_Mutation_p.R186S	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	20											80	78	79					20																	57484420		2203	4300	6503	56917815	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>A	20.37:g.57484420C>A	ENSP00000360126:p.Arg201Ser		56917815	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	37	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420255	0.83559	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99458	-5.93;-5.93;-5.93;-5.93;-5.93;-2.93;-5.93	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	H	0.98256	4.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.997;0.995;0.984;1.0	D	0.97309	0.9936	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	.	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	S	844;830;187;201;202;186;187	ENSP00000360141:R844S;ENSP00000360143:R830S;ENSP00000360136:R187S;ENSP00000360126:R201S;ENSP00000346328:R202S;ENSP00000265620:R186S;ENSP00000304472:R187S	ENSP00000265620:R186S	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		A	57484420	C	A	57484420	3	1	95	1	0	0	0	0	1	0	0	0	6530	652	23	2	3448	2	GNAS	20	57484420	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	20501592	57484420	5541100	133	25934										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61982174	61982174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gaagtccagctggtccacgcGgctgtgcatgttcaccaggt	13	12	1	0	rs144716263		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:61982174G>A	ENST00000370263.4	-	5	810	c.589C>T	c.(589-591)Cgc>Tgc	p.R197C	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	197					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGGTCCACGCGGCTGTGCATG	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		17801	0		0	False		,,,				2504	0															0			20						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	130	107	115		589	4.9	1	20	dbSNP_134	115	1,8597	1.2+/-3.3	0,1,4298	no	missense	CHRNA4	NM_000744.5	180	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	197/628	61982174	2,13002	2203	4299	6502	61452618	SO:0001583	missense	1137				CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.589C>T	20.37:g.61982174G>A	ENSP00000359285:p.Arg197Cys		61452618	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	20.8	4.052353	0.75960	2.27E-4	1.16E-4	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.79749	-1.3	4.87	4.87	0.63330	Neurotransmitter-gated ion-channel ligand-binding (3);	0.098667	0.64402	D	0.000002	D	0.86096	0.5851	L	0.46157	1.445	0.51767	D	0.999933	D;D	0.76494	0.999;0.992	P;D	0.64776	0.892;0.929	D	0.87607	0.2501	10	0.66056	D	0.02	.	18.0032	0.89203	0.0:0.0:1.0:0.0	.	126;197	Q4VAQ5;P43681	.;ACHA4_HUMAN	C	103;197;126	ENSP00000359285:R197C	ENSP00000359280:R103C	R	-	1	0	CHRNA4	61452618	0.982000	0.34865	0.996000	0.52242	0.903000	0.53119	2.160000	0.42348	2.227000	0.72691	0.561000	0.74099	CGC		0.582	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61982174	G	A	61982174	3	1	95	1	0	0	0	0	1	0	0	0	3391	1116	39	1	1302	1	CHRNA4	20	61982174	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	4497754	61982174	1043346	134	25935										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32624330	32624330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agttctcgtacaccccctgaCgagccgcatccccggtggag	11	16	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr21:32624330C>T	ENST00000286827.3	-	6	1610	c.1139G>A	c.(1138-1140)cGt>cAt	p.R380H	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Missense_Mutation_p.R380H	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	380					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CACCCCCTGACGAGCCGCATC	0.662																																																0			21											55	62	60					21																	32624330		2203	4299	6502	31546201	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1139G>A	21.37:g.32624330C>T	ENSP00000286827:p.Arg380His		31546201	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222847	0.95139	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.50277	0.75;0.78	4.86	4.86	0.63082	.	0.304511	0.34879	N	0.003609	T	0.59500	0.2198	L	0.55481	1.735	0.58432	D	0.999991	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.55615	0.78;0.607;0.607	T	0.63915	-0.6529	10	0.72032	D	0.01	.	18.1782	0.89768	0.0:1.0:0.0:0.0	.	380;380;380	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	H	380;221;380	ENSP00000286827:R380H;ENSP00000441570:R380H	ENSP00000286827:R380H	R	-	2	0	TIAM1	31546201	0.998000	0.40836	0.981000	0.43875	0.990000	0.78478	4.187000	0.58344	2.497000	0.84241	0.655000	0.94253	CGT		0.662	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32624330	C	T	32624330	3	4	95	1	0	0	0	0	1	0	0	0	15929	536	19	1	3732	1	TIAM1	21	32624330	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10		32624330	15505565	135	25936										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765530	27765530	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ggaggatcaggcgctggaggAgtgggtttcctcagagacat	17	7	2	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:27765530A>G	ENST00000451261.2	+	5	917	c.518A>G	c.(517-519)gAg>gGg	p.E173G		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	173	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						GCGCTGGAGGAGTGGGTTTCC	0.602																																																0			X											47	41	43					X																	27765530		692	1591	2283	27675451	SO:0001583	missense	0				CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.518A>G	X.37:g.27765530A>G	ENSP00000462745:p.Glu173Gly		27675451	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																				0.602	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		G	27765530	A	G	27765530	3	3	95	1	0	0	0	0	1	0	0	0	4284	304	11	4	520	4	DCAF8L2	23	27765530	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10		27765530	127505030	136	25937										
TAB3	257397	hgsc.bcm.edu	37	chrX	30872751	30872751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gataggctactgaatggcttCcctgtttctgatagctagga	11	8	1	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:30872751C>T	ENST00000378933.1	-	3	1208	c.1031G>A	c.(1030-1032)gGa>gAa	p.G344E	TAB3-AS2_ENST00000445240.1_RNA|TAB3_ENST00000288422.2_Missense_Mutation_p.G344E|TAB3_ENST00000378932.2_Missense_Mutation_p.G344E|TAB3_ENST00000378930.3_Missense_Mutation_p.G344E|TAB3_ENST00000378928.1_5'Flank	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	344	Pro-rich.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TGAATGGCTTCCCTGTTTCTG	0.453																																					Pancreas(164;1598 1985 29022 43301 49529)											0			X											130	119	123					X																	30872751		2202	4300	6502	30782672	SO:0001583	missense	257397			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.1031G>A	X.37:g.30872751C>T	ENSP00000368215:p.Gly344Glu		30782672	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096596	0.56075	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	T;T;T;T	0.78364	-1.07;-1.07;-1.07;-1.17	5.06	5.06	0.68205	.	0.205851	0.48286	D	0.000192	T	0.75125	0.3807	N	0.24115	0.695	0.37805	D	0.927831	D;D	0.57257	0.979;0.964	P;P	0.51193	0.662;0.461	T	0.80388	-0.1403	10	0.52906	T	0.07	-3.8377	17.8235	0.88657	0.0:1.0:0.0:0.0	.	344;344	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	E	344	ENSP00000368215:G344E;ENSP00000368212:G344E;ENSP00000288422:G344E;ENSP00000368214:G344E	ENSP00000288422:G344E	G	-	2	0	TAB3	30782672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.804000	0.62554	2.229000	0.72834	0.538000	0.68166	GGA		0.453	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		T	30872751	C	T	30872751	3	4	95	1	0	0	0	0	1	0	0	0	15536	855	30	3	1131	3	TAB3	23	30872751	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	3107221	30872751	124397809	137	25938										
DMD	1756	hgsc.bcm.edu	37	chrX	32486674	32486674	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttgacaatgctcaaccagctGggaggagagcttcttccagc	11	11	2	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:32486674G>T	ENST00000357033.4	-	23	3309	c.3103C>A	c.(3103-3105)Cag>Aag	p.Q1035K	DMD_ENST00000378677.2_Missense_Mutation_p.Q1031K	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1035					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				TCAACCAGCTGGGAGGAGAGC	0.393																																																0			X											64	57	60					X																	32486674		2202	4300	6502	32396595	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3103C>A	X.37:g.32486674G>T	ENSP00000354923:p.Gln1035Lys		32396595	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	0.053	-1.243723	0.01481	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.49432	0.78;0.78	5.12	4.22	0.49857	.	0.000000	0.32503	U	0.006013	T	0.35451	0.0932	L	0.34521	1.04	0.80722	D	1	B;B;B	0.31383	0.002;0.321;0.002	B;B;B	0.35859	0.009;0.212;0.015	T	0.11084	-1.0602	10	0.02654	T	1	.	13.9995	0.64424	0.0:0.0:0.8474:0.1526	.	1027;1035;1031	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	K	1027;1031;1035;1035;912	ENSP00000367948:Q1031K;ENSP00000354923:Q1035K	ENSP00000354923:Q1035K	Q	-	1	0	DMD	32396595	1.000000	0.71417	0.189000	0.23252	0.024000	0.10985	5.718000	0.68455	0.974000	0.38366	0.538000	0.68166	CAG		0.393	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32486674	G	T	32486674	3	4	95	1	0	0	0	0	1	0	0	0	4591	1357	47	2	8425	2	DMD	23	32486674	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	1613923	32486674	122783886	138	25939										
GPKOW	27238	hgsc.bcm.edu	37	chrX	48978806	48978806	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tgggggtgcatcctttctggAtcatggggatagcgagcgtg	17	7	2	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:48978806A>T	ENST00000156109.5	-	3	476	c.398T>A	c.(397-399)aTc>aAc	p.I133N		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	133						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						TCCTTTCTGGATCATGGGGAT	0.587																																																0			X											49	42	44					X																	48978806		2203	4300	6503	48865750	SO:0001583	missense	27238			U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"G patch domain containing"	30677	protein-coding gene	gene with protein product	"G patch domain containing 5"					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.398T>A	X.37:g.48978806A>T	ENSP00000156109:p.Ile133Asn		48865750	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	37	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702460	0.68501	.	.	ENSG00000068394	ENST00000156109	.	.	.	4.17	4.17	0.49024	.	0.059284	0.64402	D	0.000004	T	0.60130	0.2245	L	0.51422	1.61	0.35377	D	0.789536	D	0.67145	0.996	P	0.61940	0.896	T	0.68530	-0.5384	9	0.45353	T	0.12	-2.347	9.2152	0.37342	1.0:0.0:0.0:0.0	.	133	Q92917	GPKOW_HUMAN	N	133	.	ENSP00000156109:I133N	I	-	2	0	GPKOW	48865750	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.091000	0.50199	1.630000	0.50440	0.413000	0.27773	ATC		0.587	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		T	48978806	A	T	48978806	3	4	95	1	0	0	0	0	1	0	0	0	6633	333	12	5	1068	5	GPKOW	23	48978806	Missense_Mutation	SNP	A	TCGA-DC-6155-01A-11D-1657-10	16492132	48978806	106291754	139	25940										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	95	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-DC-6155-01A-11D-1657-10	1371952	50350758	104919802	140	25941										
WNK3	65267	hgsc.bcm.edu	37	chrX	54328283	54328283	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	gactttattgaagctggctgGttttatgccctaggagaaaa	11	6	0	2			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:54328283G>T	ENST00000375159.2	-	5	1098	c.1099C>A	c.(1099-1101)Cca>Aca	p.P367T	WNK3_ENST00000375169.3_Missense_Mutation_p.P367T|WNK3_ENST00000354646.2_Missense_Mutation_p.P367T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	367	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AAGCTGGCTGGTTTTATGCCC	0.338																																																0			X											146	115	125					X																	54328283		2203	4300	6503	54345008	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1099C>A	X.37:g.54328283G>T	ENSP00000364301:p.Pro367Thr		54345008	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323725	0.81580	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.27256	1.68;1.68;1.68	5.04	5.04	0.67666	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000027	T	0.51432	0.1674	M	0.71036	2.16	0.53688	D	0.999971	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.56318	-0.7999	10	0.87932	D	0	-10.6732	16.2996	0.82804	0.0:0.0:1.0:0.0	.	367;367	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	T	367	ENSP00000364312:P367T;ENSP00000346667:P367T;ENSP00000364301:P367T	ENSP00000346667:P367T	P	-	1	0	WNK3	54345008	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.760000	0.98935	2.100000	0.63781	0.529000	0.55759	CCA		0.338	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54328283	G	T	54328283	3	4	95	1	0	0	0	0	1	0	0	0	17419	1261	44	2	4379	2	WNK3	23	54328283	Missense_Mutation	SNP	G	TCGA-DC-6155-01A-11D-1657-10	3977525	54328283	100942277	141	25942										
THOC2	57187	hgsc.bcm.edu	37	chrX	122820467	122820467	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tcacacatactcatgtaagaTtctaacaaagatataaagaa	4	7	3	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:122820467T>C	ENST00000245838.8	-	8	730	c.699A>G	c.(697-699)gaA>gaG	p.E233E	THOC2_ENST00000355725.4_Silent_p.E233E|THOC2_ENST00000491737.1_Silent_p.E118E	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	233					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TCATGTAAGATTCTAACAAAG	0.348																																																0			X											128	115	119					X																	122820467		1856	4089	5945	122648148	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.699A>G	X.37:g.122820467T>C			122648148	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122820467	T	C	122820467	2	2	95	1	0	0	0	0	0	0	0	1	15904	1490	52	4		4	THOC2	23	122820467	Silent	SNP	T	TCGA-DC-6155-01A-11D-1657-10	68492184	122820467	32450093	142	25943										
TFDP3	51270	hgsc.bcm.edu	37	chrX	132351846	132351846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	agctgactcgtttggtgaggCgtggttgctggcagctctga	16	8	1	3			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:132351846C>T	ENST00000310125.4	-	1	530	c.442G>A	c.(442-444)Gcc>Acc	p.A148T		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	148					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					TTTGGTGAGGCGTGGTTGCTG	0.537													C|||	1	0.000264901	8e-04	0	3775	,	,		15677	0		0	False		,,,				2504	0															0			X											96	87	90					X																	132351846		2202	4299	6501	132179512	SO:0001583	missense	51270			AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"E2F-like protein", "cancer/testis antigen 30"	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.442G>A	X.37:g.132351846C>T	ENSP00000385461:p.Ala148Thr		132179512	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	.	.	.	.	.	.	.	.	.	.	c	1.648	-0.514681	0.04200	.	.	ENSG00000183434	ENST00000310125	T	0.22336	1.96	0.208	-0.415	0.12355	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	.	.	.	.	T	0.07503	0.0189	N	0.04746	-0.17	0.22240	N	0.99927	B	0.06786	0.001	B	0.15484	0.013	T	0.37731	-0.9693	9	0.17369	T	0.5	.	2.1527	0.03804	0.0:0.3376:0.3429:0.3194	.	148	Q5H9I0	TFDP3_HUMAN	T	148	ENSP00000385461:A148T	ENSP00000385461:A148T	A	-	1	0	TFDP3	132179512	1.000000	0.71417	0.003000	0.11579	0.003000	0.03518	1.941000	0.40233	-0.952000	0.03649	-0.960000	0.02634	GCC		0.537	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		T	132351846	C	T	132351846	3	4	95	1	0	0	0	0	1	0	0	0	15838	768	27	1	779	1	TFDP3	23	132351846	Missense_Mutation	SNP	C	TCGA-DC-6155-01A-11D-1657-10	9531379	132351846	22918714	143	25944										
FLNA	2316	hgsc.bcm.edu	37	chrX	153585989	153585989	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	ttcttcggcttgccttcgggAtcctgtgtggcagaggcagg	15	10	1	1			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:153585989A>G	ENST00000369850.3	-	29	4994	c.4758T>C	c.(4756-4758)gaT>gaC	p.D1586D	FLNA_ENST00000344736.4_Silent_p.D1586D|FLNA_ENST00000369856.3_5'UTR|FLNA_ENST00000360319.4_Silent_p.D1586D|FLNA_ENST00000422373.1_Silent_p.D1586D	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1586	Interaction with furin. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCCTTCGGGATCCTGTGTGG	0.627																																																0			X											115	111	112					X																	153585989		2153	4228	6381	153239183	SO:0001819	synonymous_variant	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.4758T>C	X.37:g.153585989A>G			153239183	E9KL45|Q5HY53|Q5HY55|Q8NF52	Silent	SNP	ENST00000369850.3	37	CCDS48194.1																																																																																				0.627	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			G	153585989	A	G	153585989	2	3	95	1	0	0	0	0	0	0	0	1	5952	330	12	4		4	FLNA	23	153585989	Silent	SNP	A	TCGA-DC-6155-01A-11D-1657-10	21234143	153585989	1684571	144	25945										
FLNA	2316	hgsc.bcm.edu	37	chrX	153590348	153590348	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	6	1	0.787545787545788	3.06267806267806	0.574252136752137	0.567099567099567	1	0	tagtggagggtgtggctaccTgctggacaggcgtgtacttg	17	7	0	0			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:153590348T>C	ENST00000369850.3	-	19	3061	c.2825A>G	c.(2824-2826)cAg>cGg	p.Q942R	FLNA_ENST00000344736.4_Splice_Site_p.Q942R|FLNA_ENST00000360319.4_Splice_Site_p.Q942R|FLNA_ENST00000422373.1_Splice_Site_p.Q942R	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	942					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGTGGCTACCTGCTGGACAGG	0.572																																																0			X											70	79	76					X																	153590348		2162	4222	6384	153243542	SO:0001630	splice_region_variant	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.2826+1A>G	X.37:g.153590348T>C			153243542	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.025168	0.75390	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86	4.71	4.71	0.59529	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.073575	0.56097	D	0.000039	D	0.89343	0.6688	L	0.52126	1.63	0.80722	D	1	P;D	0.76494	0.833;0.999	P;D	0.70227	0.84;0.968	D	0.90157	0.4225	10	0.66056	D	0.02	.	13.624	0.62153	0.0:0.0:0.0:1.0	.	942;942	P21333-2;P21333	.;FLNA_HUMAN	R	942;915;942;942;942	ENSP00000353467:Q942R;ENSP00000416926:Q942R;ENSP00000358866:Q942R;ENSP00000358863:Q942R	ENSP00000358863:Q942R	Q	-	2	0	FLNA	153243542	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.934000	0.87649	1.659000	0.50751	0.425000	0.28330	CAG		0.572	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		Missense_Mutation	C	153590348	T	C	153590348	5	2	95	1	0	0	0	0	0	0	1	0	5952	1594	55	4	5238	4	FLNA	23	153590348	Splice_Site	SNP	T	TCGA-DC-6155-01A-11D-1657-10	4359	153590348	1680212	145	25946										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1887030	1887030	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cgaaggcctaggaaaattctCtactttccagccctcccctg	7	15	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:1887030C>T								TMEM52 (36318 upstream) : C1orf222 (32532 downstream)																							GGAAAATTCTCTACTTTCCAG	0.547																																																0			1											72	78	76					1																	1887030		1897	4098	5995	1876890	SO:0001628	intergenic_variant	85452																															1.37:g.1887030C>T			1876890		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	9.302	1.053256	0.19907	.	.	ENSG00000142609	ENST00000270720	.	.	.	1.45	-2.9	0.05648	.	0.942383	0.08525	U	0.932866	T	0.16085	0.0387	N	0.08118	0	0.09310	N	1	B	0.21309	0.054	B	0.11329	0.006	T	0.20472	-1.0274	9	0.87932	D	0	.	4.2188	0.10547	0.1916:0.4936:0.3147:0.0	.	759	Q9C0B2	K1751_HUMAN	K	759	.	ENSP00000270720:R759K	R	-	2	0	C1orf222	1876890	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.596000	0.02091	-0.853000	0.04136	-0.502000	0.04539	AGA	0	0.547									T	1887030	C	T	1887030	1	4	96	0	1	0	0	0	0	0	0	0	8277	913	32	3		3	KIAA1751	1	1887030	IGR	SNP	C	TCGA-DC-6157-01A-11D-1657-10		1887030	247363591	1	25947										
ZBTB17	7709	hgsc.bcm.edu	37	chr1	16274899	16274899	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gagccttaaagtgaacaccgTccaccacaaaggtgcagtca	9	12	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:16274899T>C	ENST00000375743.4	-	3	324	c.92A>G	c.(91-93)gAc>gGc	p.D31G	ZBTB17_ENST00000375733.2_Missense_Mutation_p.D31G|ZBTB17_ENST00000479282.1_5'UTR|ZBTB17_ENST00000537142.1_Intron|ZBTB17_ENST00000448462.2_Missense_Mutation_p.D31G	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	31	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|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;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GTGAACACCGTCCACCACAAA	0.562																																																0			1											82	76	78					1																	16274899		2203	4300	6503	16147486	SO:0001583	missense	7709			U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12936	protein-coding gene	gene with protein product		604084	"zinc finger protein 151 (pHZ-67)", "zinc finger protein 60"	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.92A>G	1.37:g.16274899T>C	ENSP00000364895:p.Asp31Gly		16147486	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	37	CCDS165.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.304579	0.81136	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000444654;ENST00000448462	T;T;T	0.68624	2.06;2.06;-0.34	5.3	5.3	0.74995	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.61375	0.2342	N	0.03084	-0.415	0.31954	N	0.609339	D;D;B;D;P;D	0.89917	1.0;1.0;0.143;1.0;0.85;0.998	D;D;B;D;P;D	0.91635	0.999;0.998;0.08;0.998;0.531;0.998	T	0.69899	-0.5020	10	0.87932	D	0	.	10.0476	0.42197	0.1501:0.0:0.0:0.8499	.	31;31;31;31;31;31	B4DGV6;E7EPQ4;Q13105-2;B4DSM7;B2RCP2;Q13105	.;.;.;.;.;ZBT17_HUMAN	G	31	ENSP00000364895:D31G;ENSP00000364885:D31G;ENSP00000391002:D31G	ENSP00000364885:D31G	D	-	2	0	ZBTB17	16147486	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	5.020000	0.64066	2.140000	0.66376	0.459000	0.35465	GAC		0.562	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443		C	16274899	T	C	16274899	3	2	96	1	0	0	0	0	1	0	0	0	17566	1667	58	4	2375	4	ZBTB17	1	16274899	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	14387869	16274899	232975722	2	25948										
PUM1	9698	hgsc.bcm.edu	37	chr1	31441275	31441275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cagctgccacaaggggatccGtttgctgtccctgctggttc	12	13	0	0	rs143359453		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:31441275G>A	ENST00000257075.5	-	11	1664	c.1571C>T	c.(1570-1572)aCg>aTg	p.T524M	PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000426105.2_Missense_Mutation_p.T524M|PUM1_ENST00000423018.2_Missense_Mutation_p.T428M|PUM1_ENST00000373742.2_Missense_Mutation_p.T465M|PUM1_ENST00000373747.3_Missense_Mutation_p.T525M|PUM1_ENST00000424085.2_Missense_Mutation_p.T282M|PUM1_ENST00000373741.4_Missense_Mutation_p.T560M|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000440538.2_Missense_Mutation_p.T525M	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	524	Ala-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		AAGGGGATCCGTTTGCTGTCC	0.532																																																0			1						G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	100	91	94		1571,1571	5.8	1	1	dbSNP_134	94	0,8600		0,0,4300	no	missense,missense	PUM1	NM_001020658.1,NM_014676.2	81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	524/1189,524/1187	31441275	1,13005	2203	4300	6503	31213862	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1571C>T	1.37:g.31441275G>A	ENSP00000257075:p.Thr524Met		31213862	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720374	0.89205	2.27E-4	0.0	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.18810	2.2;2.19;2.45;2.45;2.45;2.44;2.47;2.19	5.77	5.77	0.91146	.	0.086607	0.85682	D	0.000000	T	0.35856	0.0946	L	0.44542	1.39	0.49687	D	0.999813	D;P;D;P;D;D;D;D	0.71674	0.998;0.776;0.991;0.856;0.987;0.977;0.987;0.987	P;B;P;B;P;P;P;P	0.56216	0.794;0.253;0.614;0.316;0.614;0.614;0.614;0.614	T	0.00837	-1.1546	10	0.51188	T	0.08	-3.3636	20.3626	0.98863	0.0:0.0:1.0:0.0	.	465;428;560;525;524;524;525;524	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	M	282;524;525;262;524;525;560;428;465	ENSP00000400141:T282M;ENSP00000257075:T524M;ENSP00000362852:T525M;ENSP00000391723:T524M;ENSP00000401777:T525M;ENSP00000362846:T560M;ENSP00000399440:T428M;ENSP00000362847:T465M	ENSP00000257075:T524M	T	-	2	0	PUM1	31213862	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.401000	0.79962	2.885000	0.99019	0.655000	0.94253	ACG		0.532	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			A	31441275	G	A	31441275	3	1	96	1	0	0	0	0	1	0	0	0	12862	1145	40	1	2043	1	PUM1	1	31441275	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	15166376	31441275	217809346	3	25949										
TINAGL1	64129	hgsc.bcm.edu	37	chr1	32042921	32042921	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggacctgtgctgccgcggcCgtgccgacgactgtgccctg	15	15	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:32042921C>G	ENST00000271064.7	+	2	248	c.172C>G	c.(172-174)Cgt>Ggt	p.R58G	TINAGL1_ENST00000457433.2_Missense_Mutation_p.R58G|RP11-73M7.1_ENST00000435872.1_RNA|TINAGL1_ENST00000481165.1_3'UTR|TINAGL1_ENST00000537531.1_Missense_Mutation_p.R58G|TINAGL1_ENST00000441210.2_Missense_Mutation_p.R58G	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	58	SMB. {ECO:0000255|PROSITE- ProRule:PRU00350}.				endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		CTGCCGCGGCCGTGCCGACGA	0.692																																																0			1											69	55	60					1																	32042921		2203	4300	6503	31815508	SO:0001583	missense	64129			AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910			19168	protein-coding gene	gene with protein product			"lipocalin 7", "TINAG-like 1"	LCN7		11170462	Standard	NM_022164		Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.172C>G	1.37:g.32042921C>G	ENSP00000271064:p.Arg58Gly		31815508	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	Missense_Mutation	SNP	ENST00000271064.7	37	CCDS343.1	.	.	.	.	.	.	.	.	.	.	c	22.2	4.263601	0.80358	.	.	ENSG00000142910	ENST00000457433;ENST00000441210;ENST00000271064;ENST00000537531;ENST00000403321	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	4.71	4.71	0.59529	Somatomedin B domain (2);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	M	0.91406	3.205	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.995	T	0.51545	-0.8692	10	0.87932	D	0	.	11.8873	0.52610	0.2909:0.7091:0.0:0.0	.	58;58;58	B4DPK6;E7EUP2;Q9GZM7	.;.;TINAL_HUMAN	G	58	ENSP00000395137:R58G;ENSP00000411798:R58G;ENSP00000271064:R58G;ENSP00000445392:R58G	ENSP00000271064:R58G	R	+	1	0	TINAGL1	31815508	0.990000	0.36364	0.997000	0.53966	0.992000	0.81027	1.472000	0.35376	2.618000	0.88619	0.655000	0.94253	CGT		0.692	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011072.1	NM_022164		G	32042921	C	G	32042921	3	3	96	1	0	0	0	0	1	0	0	0	15961	652	23	5	174	5	TINAGL1	1	32042921	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	601646	32042921	217207700	4	25950										
BAI2	576	hgsc.bcm.edu	37	chr1	32207245	32207247	+	In_Frame_Del	DEL	TTG	TTG	-													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctgaggcattcggggggcacTtgttgtagatgatctcgcca							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	TTG	TTG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:32207245_32207247delTTG	ENST00000373658.3	-	10	2006_2008	c.1665_1667delCAA	c.(1663-1668)aacaag>aag	p.N555del	BAI2_ENST00000398538.1_In_Frame_Del_p.N543del|BAI2_ENST00000440175.2_In_Frame_Del_p.N197del|BAI2_ENST00000398547.1_In_Frame_Del_p.N488del|BAI2_ENST00000527361.1_In_Frame_Del_p.N555del|BAI2_ENST00000257070.4_In_Frame_Del_p.N555del|BAI2_ENST00000398556.3_In_Frame_Del_p.N503del|BAI2_ENST00000398542.1_In_Frame_Del_p.N488del|BAI2_ENST00000373655.2_In_Frame_Del_p.N555del	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	555					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CGGGGGGCACTTGTTGTAGATGA	0.596																																																0			1																																								31979834	SO:0001651	inframe_deletion	576			AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1665_1667delCAA	1.37:g.32207248_32207250delTTG	ENSP00000362762:p.Asn555del		31979832	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	In_Frame_Del	DEL	ENST00000373658.3	37	CCDS346.2																																																																																				0.596	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		-	32207247	TTG	-	32207245	7	5	96	1	0	1	0	1	0	0	0	0	1300	1609	56	0	3186	0	BAI2	1	32207245	In_Frame_Del	DEL	TTG	TCGA-DC-6157-01A-11D-1657-10	164324	32207245	217043376	5	25951										
SFPQ	6421	hgsc.bcm.edu	37	chr1	35656297	35656297	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ataaacaagacaacttacgtCgtcagtaagaaaacaccttc	5	10	1	2	rs140545880		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:35656297C>A	ENST00000357214.5	-	3	1415	c.1317G>T	c.(1315-1317)acG>acT	p.T439T		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	439	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				CAACTTACGTCGTCAGTAAGA	0.363			T	TFE3	papillary renal cell																																		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	0			1											99	99	99					1																	35656297		2203	4300	6503	35428884	SO:0001819	synonymous_variant	6421			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1317G>T	1.37:g.35656297C>A			35428884	P30808|Q5SZ71	Silent	SNP	ENST00000357214.5	37	CCDS388.1																																																																																				0.363	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		A	35656297	C	A	35656297	2	1	96	1	0	0	0	0	0	0	0	1	14197	871	31	2		2	SFPQ	1	35656297	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	3449052	35656297	213594324	6	25952										
PTPRF	5792	hgsc.bcm.edu	37	chr1	44085423	44085423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctgcaacaagttcaagaacCggctggtgaacatcatgccc	9	13	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:44085423C>T	ENST00000359947.4	+	29	5345	c.5005C>T	c.(5005-5007)Cgg>Tgg	p.R1669W	PTPRF_ENST00000372414.3_Missense_Mutation_p.R1669W|PTPRF_ENST00000422171.2_Missense_Mutation_p.R1028W|PTPRF_ENST00000372413.3_Missense_Mutation_p.R1660W|PTPRF_ENST00000438120.1_Missense_Mutation_p.R1660W|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1669	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTTCAAGAACCGGCTGGTGAA	0.582																																																0			1											130	108	116					1																	44085423		2203	4300	6503	43858010	SO:0001583	missense	5792			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.5005C>T	1.37:g.44085423C>T	ENSP00000353030:p.Arg1669Trp		43858010	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.293520|4.293520	0.80914|0.80914	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407	.|T;T;T;T;T;T	.|0.35973	.|1.28;1.28;1.28;1.28;1.28;1.28	5.2|5.2	5.2|5.2	0.72013|0.72013	.|Protein-tyrosine phosphatase, receptor/non-receptor type (3);	.|0.000000	.|0.34603	.|N	.|0.003835	T|T	0.75953|0.75953	0.3920|0.3920	H|H	0.99357|0.99357	4.53|4.53	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|1.0;1.0;1.0;0.999;1.0	D|D	0.85349|0.85349	0.1100|0.1100	5|10	.|0.87932	.|D	.|0	.|.	14.4696|14.4696	0.67506|0.67506	0.1473:0.8527:0.0:0.0|0.1473:0.8527:0.0:0.0	.|.	.|1314;1028;1246;1660;1669	.|Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586	.|.;.;.;.;PTPRF_HUMAN	L|W	1052;1093|1669;1660;1669;1660;1028;741	.|ENSP00000353030:R1669W;ENSP00000398822:R1660W;ENSP00000361491:R1669W;ENSP00000361490:R1660W;ENSP00000387885:R1028W;ENSP00000361484:R741W	.|ENSP00000353030:R1669W	P|R	+|+	2|1	0|2	PTPRF|PTPRF	43858010|43858010	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.662000|4.662000	0.61525|0.61525	2.811000|2.811000	0.96726|0.96726	0.555000|0.555000	0.69702|0.69702	CCG|CGG		0.582	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44085423	C	T	44085423	3	4	96	1	0	0	0	0	1	0	0	0	12838	643	23	1	5111	1	PTPRF	1	44085423	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	8429126	44085423	205165198	7	25953										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120491706	120491706	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caaacagcagcattctcacaAgggtttggggaacagggagc	13	9	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:120491706A>G	ENST00000256646.2	-	16	2742	c.2523T>C	c.(2521-2523)ccT>ccC	p.P841P		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	841	EGF-like 22. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATTCTCACAAGGGTTTGGGG	0.418			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome		OREG0013733	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0			1											144	142	143					1																	120491706		2203	4300	6503	120293229	SO:0001819	synonymous_variant	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.2523T>C	1.37:g.120491706A>G		1504	120293229	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																				0.418	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		G	120491706	A	G	120491706	2	3	96	1	0	0	0	0	0	0	0	1	10579	59	3	4		4	NOTCH2	1	120491706	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	76406283	120491706	128758915	8	25954										
FLG	2312	hgsc.bcm.edu	37	chr1	152277452	152277452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgctgactgctggtggcgggAtccgtgtctctctcctggac	14	12	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:152277452A>G	ENST00000368799.1	-	3	9945	c.9910T>C	c.(9910-9912)Tcc>Ccc	p.S3304P	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3304	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGTGGCGGGATCCGTGTCTC	0.572									Ichthyosis																																							0			1											380	373	375					1																	152277452		2203	4300	6503	150544076	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9910T>C	1.37:g.152277452A>G	ENSP00000357789:p.Ser3304Pro		150544076	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	A	7.126	0.578982	0.13686	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.10382	2.88	3.35	-6.7	0.01766	.	.	.	.	.	T	0.07324	0.0185	M	0.66939	2.045	0.09310	N	1	D	0.76494	0.999	D	0.91635	0.999	T	0.55121	-0.8190	9	0.62326	D	0.03	.	0.3179	0.00298	0.1976:0.2458:0.2603:0.2963	.	3304	P20930	FILA_HUMAN	P	3304;242	ENSP00000357789:S3304P	ENSP00000357786:S242P	S	-	1	0	FLG	150544076	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	-4.931000	0.00169	-4.671000	0.00037	0.248000	0.18094	TCC		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152277452	A	G	152277452	3	3	96	1	0	0	0	0	1	0	0	0	5941	333	12	4	2279	4	FLG	1	152277452	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	31785746	152277452	96973169	9	25955										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155491264	155491264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gactctttcttgaaaaacctTcggaatcagaacccaatcct	5	12	3	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:155491264T>C	ENST00000368346.3	-	2	686	c.47A>G	c.(46-48)gAa>gGa	p.E16G	ASH1L_ENST00000392403.3_Missense_Mutation_p.E16G|ASH1L_ENST00000548830.1_Missense_Mutation_p.E16G			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	16					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGAAAAACCTTCGGAATCAGA	0.398																																																0			1											169	165	166					1																	155491264		2203	4300	6503	153757888	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.47A>G	1.37:g.155491264T>C	ENSP00000357330:p.Glu16Gly		153757888	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	T	24.9	4.579297	0.86645	.	.	ENSG00000116539	ENST00000368346;ENST00000392403;ENST00000548830	D;D	0.91521	-2.86;-2.86	6.03	6.03	0.97812	.	0.064498	0.64402	D	0.000017	T	0.75874	0.3909	N	0.08118	0	0.43569	D	0.995899	P;P	0.37330	0.455;0.59	B;B	0.37239	0.123;0.244	T	0.83257	-0.0050	10	0.87932	D	0	.	14.8022	0.69924	0.0:0.0:0.0:1.0	.	16;16	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	16	ENSP00000357330:E16G;ENSP00000376204:E16G	ENSP00000357330:E16G	E	-	2	0	ASH1L	153757888	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.721000	0.68477	2.313000	0.78055	0.455000	0.32223	GAA		0.398	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155491264	T	C	155491264	3	2	96	1	0	0	0	0	1	0	0	0	1042	1783	62	4	8955	4	ASH1L	1	155491264	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	3213812	155491264	93759357	10	25956										
INSRR	3645	hgsc.bcm.edu	37	chr1	156811210	156811210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gaaggggacagccctccagcTcctccaggaccccgccatcc	10	19	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:156811210T>C	ENST00000368195.3	-	21	4034	c.3638A>G	c.(3637-3639)gAg>gGg	p.E1213G	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	1213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCCCTCCAGCTCCTCCAGGAC	0.602																																																0			1											55	56	56					1																	156811210		2203	4300	6503	155077834	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.3638A>G	1.37:g.156811210T>C	ENSP00000357178:p.Glu1213Gly		155077834	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.075279	0.36662	.	.	ENSG00000027644	ENST00000368195	D	0.83075	-1.68	4.89	3.76	0.43208	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44902	D	0.000415	T	0.62466	0.2430	.	.	.	0.33391	D	0.576087	B	0.09022	0.002	B	0.12156	0.007	T	0.60495	-0.7252	9	0.87932	D	0	.	7.7317	0.28791	0.0:0.1733:0.0:0.8267	.	1213	P14616	INSRR_HUMAN	G	1213	ENSP00000357178:E1213G	ENSP00000357178:E1213G	E	-	2	0	INSRR	155077834	0.029000	0.19370	1.000000	0.80357	0.739000	0.42172	0.770000	0.26618	0.886000	0.36113	0.459000	0.35465	GAG		0.602	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		C	156811210	T	C	156811210	3	2	96	1	0	0	0	0	1	0	0	0	7795	1551	54	4	262	4	INSRR	1	156811210	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1319946	156811210	92439411	11	25957										
RALGPS2	55103	hgsc.bcm.edu	37	chr1	178753557	178753557	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tctttcactttaacagaaaaGtagcagctctgaatccttaa	5	9	3	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:178753557G>C	ENST00000367635.3	+	3	400	c.62G>C	c.(61-63)aGt>aCt	p.S21T	RALGPS2_ENST00000367634.2_Missense_Mutation_p.S21T	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	21					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TAACAGAAAAGTAGCAGCTCT	0.363																																																0			1											101	97	99					1																	178753557		2203	4300	6503	177020180	SO:0001583	missense	55103			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.62G>C	1.37:g.178753557G>C	ENSP00000356607:p.Ser21Thr		177020180	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	37	CCDS1325.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117830	0.56505	.	.	ENSG00000116191	ENST00000367635;ENST00000367634	T;T	0.22336	1.96;1.99	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	L	0.59436	1.845	0.80722	D	1	B;P	0.38535	0.139;0.635	B;B	0.33339	0.051;0.162	T	0.03025	-1.1081	10	0.24483	T	0.36	.	18.0704	0.89404	0.0:0.0:1.0:0.0	.	21;21	B7Z7B1;Q86X27	.;RGPS2_HUMAN	T	21	ENSP00000356607:S21T;ENSP00000356606:S21T	ENSP00000356606:S21T	S	+	2	0	RALGPS2	177020180	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.898000	0.92538	2.567000	0.86603	0.467000	0.42956	AGT		0.363	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		C	178753557	G	C	178753557	3	2	96	1	0	0	0	0	1	0	0	0	13055	1029	36	5	68	5	RALGPS2	1	178753557	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	21942347	178753557	70497064	12	25958										
PRG4	10216	hgsc.bcm.edu	37	chr1	186276924	186276924	+	Frame_Shift_Del	DEL	T	T	-													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctaaggagcctgctccaacTacccctaaggagcctgctcc							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:186276924delT	ENST00000445192.2	+	7	2118	c.2073delT	c.(2071-2073)actfs	p.T692fs	PRG4_ENST00000367486.3_Frame_Shift_Del_p.T649fs|PRG4_ENST00000367483.4_Frame_Shift_Del_p.T651fs|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Frame_Shift_Del_p.T599fs	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	692	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTGCTCCAACTACCCCTAAGG	0.602																																																0			1											67	83	77					1																	186276924		2203	4297	6500	184543547	SO:0001589	frameshift_variant	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2073delT	1.37:g.186276924delT	ENSP00000399679:p.Thr692fs		184543547	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Frame_Shift_Del	DEL	ENST00000445192.2	37	CCDS1369.1																																																																																				0.602	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		-	186276924	T	-	186276924	7	5	96	1	0	1	0	1	0	0	0	0	12515	1509	53	0	2095	0	PRG4	1	186276924	Frame_Shift_Del	DEL	T	TCGA-DC-6157-01A-11D-1657-10	7523367	186276924	62973697	13	25959			1	21		3	2	14	N	T_C_A	7.684637e-05
PRG4	10216	hgsc.bcm.edu	37	chr1	186276935	186276935	+	Missense_Mutation	SNP	A	A	G													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgctccaactacccctaaggAgcctgctccaactaccccta					rs570889600	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:186276935A>G	ENST00000445192.2	+	7	2129	c.2084A>G	c.(2083-2085)gAg>gGg	p.E695G	PRG4_ENST00000367486.3_Missense_Mutation_p.E652G|PRG4_ENST00000367483.4_Missense_Mutation_p.E654G|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.E602G	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	695	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACCCCTAAGGAGCCTGCTCCA	0.592													-|||	6	0.00119808	0.0045	0	5008	,	,		13414	0		0	False		,,,				2504	0															0			1											85	101	96					1																	186276935		2203	4297	6500	184543558	SO:0001583	missense	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2084A>G	1.37:g.186276935A>G	ENSP00000399679:p.Glu695Gly		184543558	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	1.580	-0.531745	0.04112	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05382	3.45;3.57;3.46;3.58	2.63	-5.26	0.02772	.	0.454506	0.15898	U	0.239196	T	0.05410	0.0143	L	0.61218	1.895	0.09310	N	1	B;B;B;B	0.09022	0.002;0.002;0.001;0.002	B;B;B;B	0.08055	0.003;0.003;0.001;0.003	T	0.29822	-0.9999	9	.	.	.	.	4.0529	0.09803	0.6041:0.1814:0.1159:0.0986	.	561;602;695;654	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	G	652;561;654;602;695	ENSP00000356456:E652G;ENSP00000356453:E654G;ENSP00000356455:E602G;ENSP00000399679:E695G	.	E	+	2	0	PRG4	184543558	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.246000	0.01191	-2.875000	0.00321	-1.185000	0.01705	GAG		0.592	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186276935	A	G	186276935	3	3	96	1	0	0	0	0	1	0	0	0	12515	304	11	4	2106	4	PRG4	1	186276935	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	11	186276935	62973686	14	25960	36	2	1	21		3	2	14	N	T_C_A	7.684637e-05
PRG4	10216	hgsc.bcm.edu	37	chr1	186276937	186276937	+	Missense_Mutation	SNP	C	C	A													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctccaactacccctaaggagCctgctccaactacccctaag					rs199590878	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr1:186276937C>A	ENST00000445192.2	+	7	2131	c.2086C>A	c.(2086-2088)Cct>Act	p.P696T	PRG4_ENST00000367486.3_Missense_Mutation_p.P653T|PRG4_ENST00000367483.4_Missense_Mutation_p.P655T|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.P603T	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	696	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCCTAAGGAGCCTGCTCCAAC	0.597													-|||	6	0.00119808	0.0045	0	5008	,	,		13517	0		0	False		,,,				2504	0															0			1											90	106	100					1																	186276937		2203	4297	6500	184543560	SO:0001583	missense	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2086C>A	1.37:g.186276937C>A	ENSP00000399679:p.Pro696Thr		184543560	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	0.352	-0.944248	0.02322	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05319	3.5;3.61;3.46;3.56	2.63	-5.26	0.02772	.	0.368878	0.19612	N	0.110102	T	0.04952	0.0133	L	0.50333	1.59	0.18873	N	0.999986	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.32824	-0.9892	9	.	.	.	.	6.1241	0.20170	0.3826:0.4605:0.0:0.1569	.	562;603;696;655	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	T	653;562;655;603;696	ENSP00000356456:P653T;ENSP00000356453:P655T;ENSP00000356455:P603T;ENSP00000399679:P696T	.	P	+	1	0	PRG4	184543560	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.471000	0.06631	-4.461000	0.00047	-3.552000	0.00030	CCT		0.597	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186276937	C	A	186276937	3	1	96	1	0	0	0	0	1	0	0	0	12515	739	26	2	2108	2	PRG4	1	186276937	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	2	186276937	62973684	15	25961	36	2	1	21		3	2	14	N	T_C_A	7.684637e-05
NBAS	51594	hgsc.bcm.edu	37	chr2	15555785	15555785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caggcgactgtttctcacaaCgatgaagaaagggaaccatc	10	10	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:15555785C>T	ENST00000281513.5	-	25	2847	c.2822G>A	c.(2821-2823)cGt>cAt	p.R941H	NBAS_ENST00000441750.1_Intron	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	941					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TTTCTCACAACGATGAAGAAA	0.378																																																0			2											94	95	94					2																	15555785		2203	4300	6503	15473236	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.2822G>A	2.37:g.15555785C>T	ENSP00000281513:p.Arg941His		15473236	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	35	5.502774	0.96371	.	.	ENSG00000151779	ENST00000281513	T	0.18016	2.24	6.16	6.16	0.99307	Secretory pathway Sec39 (1);	0.000000	0.85682	D	0.000000	T	0.45836	0.1362	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.69479	0.964	T	0.25012	-1.0144	10	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	941	A2RRP1	NBAS_HUMAN	H	941	ENSP00000281513:R941H	ENSP00000281513:R941H	R	-	2	0	NBAS	15473236	1.000000	0.71417	0.989000	0.46669	0.987000	0.75469	7.323000	0.79105	2.937000	0.99478	0.650000	0.86243	CGT		0.378	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15555785	C	T	15555785	3	4	96	1	0	0	0	0	1	0	0	0	10216	536	19	1	4405	1	NBAS	2	15555785	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		15555785	227643588	16	25962										
MSH6	2956	hgsc.bcm.edu	37	chr2	48027959	48027959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agctcttgctgacataagagAaaatgaacagagcctcctgg	10	9	1	4			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:48027959A>G	ENST00000234420.5	+	4	2989	c.2837A>G	c.(2836-2838)gAa>gGa	p.E946G	MSH6_ENST00000540021.1_Missense_Mutation_p.E816G|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.E644G	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	946					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GACATAAGAGAAAATGAACAG	0.458			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	2											45	45	45					2																	48027959		2203	4300	6503	47881463	SO:0001583	missense	2956	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2837A>G	2.37:g.48027959A>G	ENSP00000234420:p.Glu946Gly		47881463	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	A	9.945	1.218515	0.22373	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.90788	-2.73;-2.73;-2.73	5.61	4.39	0.52855	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.538247	0.21758	N	0.069578	D	0.87317	0.6147	L	0.42632	1.34	0.80722	D	1	B;B;B	0.20459	0.02;0.009;0.045	B;B;B	0.28385	0.033;0.02;0.089	D	0.85095	0.0954	10	0.54805	T	0.06	-20.2924	12.1387	0.53986	0.7321:0.2679:0.0:0.0	.	816;946;946	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	G	946;944;816;644	ENSP00000234420:E946G;ENSP00000446475:E816G;ENSP00000438580:E644G	ENSP00000234420:E946G	E	+	2	0	MSH6	47881463	0.989000	0.36119	1.000000	0.80357	0.998000	0.95712	1.086000	0.30853	2.128000	0.65567	0.460000	0.39030	GAA		0.458	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48027959	A	G	48027959	3	3	96	1	0	0	0	0	1	0	0	0	9904	246	9	4	2851	4	MSH6	2	48027959	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	32472174	48027959	195171414	17	25963										
POTEF	728378	hgsc.bcm.edu	37	chr2	130869608	130869608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atttaaattcgcttttttctTaattaaaaatttcacgactt	2	6	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:130869608T>C	ENST00000409914.2	-	6	1276	c.877A>G	c.(877-879)Aag>Gag	p.K293E	POTEF_ENST00000357462.5_Missense_Mutation_p.K293E|AC018804.3_ENST00000433507.1_RNA|POTEF_ENST00000361163.4_Missense_Mutation_p.K303E|POTEF_ENST00000360967.5_Missense_Mutation_p.K293E|RNU6-1049P_ENST00000516414.1_RNA	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	293					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCTTTTTTCTTAATTAAAAAT	0.338																																																0			2											40	50	47					2																	130869608		1436	3451	4887	130586078	SO:0001583	missense	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.877A>G	2.37:g.130869608T>C	ENSP00000386786:p.Lys293Glu		130586078	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	9.633	1.136824	0.21123	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.61980	0.06;0.06;0.06;0.12	1.16	-0.0886	0.13672	Ankyrin repeat-containing domain (4);	0.193103	0.24547	U	0.037595	T	0.40222	0.1108	N	0.21282	0.65	0.09310	N	1	P	0.49961	0.93	B	0.41917	0.37	T	0.40001	-0.9586	10	0.87932	D	0	.	3.0851	0.06275	0.0:0.2815:0.0:0.7185	.	293	A5A3E0	POTEF_HUMAN	E	293;293;293;303	ENSP00000350052:K293E;ENSP00000386786:K293E;ENSP00000354232:K293E;ENSP00000355012:K303E	ENSP00000350052:K293E	K	-	1	0	POTEF	130586078	0.005000	0.15991	0.001000	0.08648	0.032000	0.12392	0.876000	0.28092	-0.027000	0.13873	0.136000	0.15936	AAG		0.338	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		C	130869608	T	C	130869608	3	2	96	1	0	0	0	0	1	0	0	0	12296	1763	61	4	2398	4	POTEF	2	130869608	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	82841649	130869608	112329765	18	25964										
FAP	2191	hgsc.bcm.edu	37	chr2	163055301	163055301	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcatagtacttggcgtagtcGctgaaacttgctgtgtaata	11	7	0	1	rs199889478		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:163055301G>A	ENST00000188790.4	-	16	1575	c.1368C>T	c.(1366-1368)agC>agT	p.S456S	FAP_ENST00000443424.1_Silent_p.S431S	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TGGCGTAGTCGCTGAAACTTG	0.468																																																0			2											248	203	219					2																	163055301		2203	4300	6503	162763547	SO:0001819	synonymous_variant	11146			U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1368C>T	2.37:g.163055301G>A			162763547		Silent	SNP	ENST00000188790.4	37	CCDS33311.1																																																																																				0.468	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			A	163055301	G	A	163055301	2	1	96	1	0	0	0	0	0	0	0	1	5692	1078	38	1		1	FAP	2	163055301	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	32185693	163055301	80144072	19	25965										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100233	168100233	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cggtggatgtttgaaacacaGccgttggacacaattaacaa	10	8	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:168100233G>T	ENST00000409195.1	+	9	2420	c.2331G>T	c.(2329-2331)caG>caT	p.Q777H	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q777H|XIRP2_ENST00000409273.1_Missense_Mutation_p.Q555H|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	602					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGAAACACAGCCGTTGGACA	0.413																																																0			2											71	66	68					2																	168100233		1866	4097	5963	167808479	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2331G>T	2.37:g.168100233G>T	ENSP00000386840:p.Gln777His		167808479	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.092898	0.36952	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.43688	0.94;0.94;0.94	5.92	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	M	0.71036	2.16	0.53688	D	0.999973	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.997	T	0.67417	-0.5676	10	0.72032	D	0.01	-9.7912	13.624	0.62153	0.1463:0.0:0.8537:0.0	.	602;602;555	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	H	777;777;555	ENSP00000386840:Q777H;ENSP00000295237:Q777H;ENSP00000387255:Q555H	ENSP00000295237:Q777H	Q	+	3	2	XIRP2	167808479	0.993000	0.37304	1.000000	0.80357	0.860000	0.49131	0.288000	0.18939	1.503000	0.48686	0.650000	0.86243	CAG		0.413	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168100233	G	T	168100233	3	4	96	1	0	0	0	0	1	0	0	0	17470	962	34	2	2361	2	XIRP2	2	168100233	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	5044932	168100233	75099140	20	25966										
TTN	7273	hgsc.bcm.edu	37	chr2	179437809	179437809	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccagtgatttctgaaccaccAtcatagataggtttattcca	6	10	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:179437809A>G	ENST00000591111.1	-	276	68351	c.68127T>C	c.(68125-68127)gaT>gaC	p.D22709D	TTN_ENST00000589042.1_Silent_p.D24350D|TTN_ENST00000342992.6_Silent_p.D21782D|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.D15410D|TTN_ENST00000460472.2_Silent_p.D15285D|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.D15477D|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22709	Fibronectin type-III 65. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D15285D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGAACCACCATCATAGATAG	0.463																																																1	Substitution - coding silent(1)	lung(1)	2											84	81	82					2																	179437809		1947	4146	6093	179146055	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.68127T>C	2.37:g.179437809A>G			179146055	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179437809	A	G	179437809	2	3	96	1	0	0	0	0	0	0	0	1	16775	214	8	4		4	TTN	2	179437809	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	11337576	179437809	63761564	21	25967										
ALS2	57679	hgsc.bcm.edu	37	chr2	202590171	202590171	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttgtttgggattctgtattcTccatacctgccatgaaaaag	8	8	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:202590171T>C	ENST00000264276.6	-	20	3627	c.3255A>G	c.(3253-3255)ggA>ggG	p.G1085G	ALS2_ENST00000457679.2_Silent_p.G397G	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1085					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTCTGTATTCTCCATACCTGC	0.353																																																0			2											176	176	176					2																	202590171		1858	4090	5948	202298416	SO:0001819	synonymous_variant	57679			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.3255A>G	2.37:g.202590171T>C			202298416	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	37	CCDS42800.1																																																																																				0.353	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		C	202590171	T	C	202590171	2	2	96	1	0	0	0	0	0	0	0	1	550	1538	54	4		4	ALS2	2	202590171	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	23152362	202590171	40609202	22	25968										
PNKD	25953	hgsc.bcm.edu	37	chr2	219204843	219204843	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctggctgtggctgtggacccTtcagaccctcgggctgtgca	14	13	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:219204843T>C	ENST00000273077.4	+	4	495	c.444T>C	c.(442-444)ccT>ccC	p.P148P	PNKD_ENST00000436005.2_Silent_p.P88P|PNKD_ENST00000258362.3_Silent_p.P124P|AC021016.8_ENST00000411433.1_RNA	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	148					glutathione biosynthetic process (GO:0006750)|neuromuscular process controlling posture (GO:0050884)|regulation of dopamine metabolic process (GO:0042053)|regulation of synaptic transmission, dopaminergic (GO:0032225)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGTGGACCCTTCAGACCCTC	0.632																																																0			2											69	61	64					2																	219204843		2203	4300	6503	218913087	SO:0001819	synonymous_variant	25953				CCDS2411.1, CCDS2413.1, CCDS42816.1	2q35	2011-01-21	2007-07-12		ENSG00000127838	ENSG00000127838			9153	protein-coding gene	gene with protein product	"myofibrillogenesis regulator 1"	609023	"paroxysmal nonkinesiogenic dyskinesia"			8659518	Standard	NM_015488		Approved	DYT8, PDC, DKFZp564N1362, FPD1, MR-1, BRP17, FKSG19, TAHCCP2, KIAA1184, KIPP1184, MGC31943, PKND1	uc002vhn.3	Q8N490	OTTHUMG00000133110	ENST00000273077.4:c.444T>C	2.37:g.219204843T>C			218913087	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Silent	SNP	ENST00000273077.4	37	CCDS2411.1																																																																																				0.632	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2			C	219204843	T	C	219204843	2	2	96	1	0	0	0	0	0	0	0	1	12177	1596	56	4		4	PNKD	2	219204843	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	16614672	219204843	23994530	23	25969										
STK36	27148	hgsc.bcm.edu	37	chr2	219563535	219563535	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctctgctggcccatactgccAgggtcctgtctcccagccac	9	18	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:219563535A>G	ENST00000295709.3	+	26	3547	c.3268A>G	c.(3268-3270)Agg>Ggg	p.R1090G	STK36_ENST00000392105.3_Missense_Mutation_p.R1069G|STK36_ENST00000392106.2_Missense_Mutation_p.R1069G|STK36_ENST00000440309.1_Missense_Mutation_p.R1090G	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CCATACTGCCAGGGTCCTGTC	0.587																																																0			2											106	94	98					2																	219563535		2203	4300	6503	219271779	SO:0001583	missense	27148			AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3268A>G	2.37:g.219563535A>G	ENSP00000295709:p.Arg1090Gly		219271779		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225133	0.39300	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	D;D;D;D	0.82803	-1.65;-1.64;-1.65;-1.65	6.06	4.08	0.47627	Armadillo-type fold (1);	0.000000	0.40728	N	0.001025	D	0.86020	0.5833	L	0.29908	0.895	0.46654	D	0.999146	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.996;0.994	D	0.88188	0.2875	10	0.87932	D	0	-26.3485	15.5365	0.76007	0.2656:0.7344:0.0:0.0	.	1069;1069;1090	A8MU99;Q9NRP7-2;Q9NRP7	.;.;STK36_HUMAN	G	1090;1069;1069;1090	ENSP00000295709:R1090G;ENSP00000375955:R1069G;ENSP00000375954:R1069G;ENSP00000394095:R1090G	ENSP00000295709:R1090G	R	+	1	2	STK36	219271779	0.981000	0.34729	0.931000	0.37212	0.018000	0.09664	1.372000	0.34261	1.565000	0.49641	-0.168000	0.13345	AGG		0.587	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			G	219563535	A	G	219563535	3	3	96	1	0	0	0	0	1	0	0	0	15341	179	7	4	3366	4	STK36	2	219563535	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	358692	219563535	23635838	24	25970										
KLHL30	377007	hgsc.bcm.edu	37	chr2	239049819	239049819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcctgggcatctgtgagttcGgggagcagcaagggctgctg	18	9	1	1	rs375543545		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:239049819G>A	ENST00000409223.1	+	2	531	c.424G>A	c.(424-426)Ggg>Agg	p.G142R	KLHL30_ENST00000305959.4_Missense_Mutation_p.G124R			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	142										lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CTGTGAGTTCGGGGAGCAGCA	0.657																																																0			2						G	ARG/GLY	0,4244		0,0,2122	17	22	20		424	5.8	1	2		20	1,8475		0,1,4237	no	missense	KLHL30	NM_198582.3	125	0,1,6359	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging	142/579	239049819	1,12719	2122	4238	6360	238714558	SO:0001583	missense	377007				CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"Kelch-like", "BTB/POZ domain containing"	24770	protein-coding gene	gene with protein product			"kelch-like 30 (Drosophila)"				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.424G>A	2.37:g.239049819G>A	ENSP00000386389:p.Gly142Arg		238714558	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	G	28.2	4.896027	0.91962	0.0	1.18E-4	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.69435	-0.4;-0.4	5.82	5.82	0.92795	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.83055	0.5171	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84270	0.0488	10	0.87932	D	0	.	18.8769	0.92341	0.0:0.0:1.0:0.0	.	142	Q0D2K2	KLH30_HUMAN	R	142;124	ENSP00000386389:G142R;ENSP00000302386:G124R	ENSP00000302386:G124R	G	+	1	0	KLHL30	238714558	1.000000	0.71417	0.956000	0.39512	0.900000	0.52787	9.649000	0.98487	2.757000	0.94681	0.655000	0.94253	GGG		0.657	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		A	239049819	G	A	239049819	3	1	96	1	0	0	0	0	1	0	0	0	8405	1116	39	1	426	1	KLHL30	2	239049819	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	19486284	239049819	4149554	25	25971										
PER2	8864	hgsc.bcm.edu	37	chr2	239170947	239170947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gttccgggcgcgaaaccgaaTgggagaatagtcgaaaggct	15	8	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr2:239170947T>C	ENST00000254657.3	-	11	1471	c.1192A>G	c.(1192-1194)Att>Gtt	p.I398V	PER2_ENST00000440245.1_Missense_Mutation_p.I398V|PER2_ENST00000355768.2_Missense_Mutation_p.H362R|PER2_ENST00000254658.3_Missense_Mutation_p.H362R	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	398	PAC.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		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)		CGAAACCGAATGGGAGAATAG	0.527																																																0			2											101	95	97					2																	239170947		2203	4300	6503	238835686	SO:0001583	missense	8864			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.1192A>G	2.37:g.239170947T>C	ENSP00000254657:p.Ile398Val		238835686	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.34|11.34	1.610646|1.610646	0.28712|0.28712	.|.	.|.	ENSG00000132326|ENSG00000132326	ENST00000254658;ENST00000355768|ENST00000254657;ENST00000440245	T;T|T;T	0.45276|0.15718	0.9;0.9|2.4;2.4	4.42|4.42	-1.58|-1.58	0.08479|0.08479	.|PAS fold-3 (1);	.|0.172839	.|0.50627	.|D	.|0.000107	T|T	0.14787|0.14787	0.0357|0.0357	L|L	0.37697|0.37697	1.125|1.125	0.21386|0.21386	N|N	0.99971|0.99971	B|B;B;B	0.29037|0.25743	0.231|0.008;0.022;0.133	B|B;B;B	0.29942|0.34824	0.109|0.023;0.018;0.19	T|T	0.27536|0.27536	-1.0071|-1.0071	9|10	0.87932|0.33141	D|T	0|0.24	-4.1172|-4.1172	13.1115|13.1115	0.59277|0.59277	0.0:0.0:0.61:0.39|0.0:0.0:0.61:0.39	.|.	362|398;398;398	O15055-2|F5GYD5;B4DH14;O15055	.|.;.;PER2_HUMAN	R|V	362|398	ENSP00000254658:H362R;ENSP00000348013:H362R|ENSP00000254657:I398V;ENSP00000397516:I398V	ENSP00000254658:H362R|ENSP00000254657:I398V	H|I	-|-	2|1	0|0	PER2|PER2	238835686|238835686	0.996000|0.996000	0.38824|0.38824	0.057000|0.057000	0.19452|0.19452	0.041000|0.041000	0.13682|0.13682	2.021000|2.021000	0.41020|0.41020	-0.473000|-0.473000	0.06871|0.06871	0.454000|0.454000	0.30748|0.30748	CAT|ATT		0.527	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		C	239170947	T	C	239170947	3	2	96	1	0	0	0	0	1	0	0	0	11761	1464	51	4	2627	4	PER2	2	239170947	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	121128	239170947	4028426	26	25972										
MLH1	4292	hgsc.bcm.edu	37	chr3	37089037	37089037	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caccgctctttgaccttgccAtgcttgccttagatagtcca	7	14	1	2	rs267607862		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:37089037A>G	ENST00000231790.2	+	16	1975	c.1759A>G	c.(1759-1761)Atg>Gtg	p.M587V	MLH1_ENST00000455445.2_Missense_Mutation_p.M346V|MLH1_ENST00000435176.1_Missense_Mutation_p.M489V|MLH1_ENST00000458205.2_Missense_Mutation_p.M346V|MLH1_ENST00000539477.1_Missense_Mutation_p.M346V|MLH1_ENST00000536378.1_Missense_Mutation_p.M346V	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	587	Interaction with EXO1.				ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.M587V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TGACCTTGCCATGCTTGCCTT	0.473		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|stomach(1)	3											113	104	107					3																	37089037		2203	4300	6503	37064041	SO:0001583	missense	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1759A>G	3.37:g.37089037A>G	ENSP00000231790:p.Met587Val		37064041	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284931	0.59867	.	.	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.92344	0.7571	M	0.67397	2.05	0.80722	D	1	P;B;B;B	0.37663	0.604;0.108;0.108;0.025	B;B;B;B	0.37780	0.258;0.157;0.157;0.104	D	0.91760	0.5419	10	0.39692	T	0.17	-26.2898	15.7458	0.77939	1.0:0.0:0.0:0.0	.	489;587;587;587	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	V	587;451;346;346;346;489;346	ENSP00000231790:M587V;ENSP00000402667:M346V;ENSP00000443665:M346V;ENSP00000398272:M346V;ENSP00000402564:M489V;ENSP00000444286:M346V	ENSP00000231790:M587V	M	+	1	0	MLH1	37064041	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	9.092000	0.94157	2.130000	0.65690	0.477000	0.44152	ATG		0.473	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37089037	A	G	37089037	3	3	96	1	0	0	0	0	1	0	0	0	9647	217	8	4	1821	4	MLH1	3	37089037	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10		37089037	160933393	27	25973										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37368886	37368886	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	acttggaaaatgtgtttgacGacgtccagaaaaccctccag	9	10	0	2	rs148910546		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:37368886G>A	ENST00000361924.2	+	14	5883	c.5509G>A	c.(5509-5511)Gac>Aac	p.D1837N	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.D1859N	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1837	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGTGTTTGACGACGTCCAGAA	0.383																																																0			3						G	ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	55	56	56		5575,5509	-1.5	0	3	dbSNP_134	56	0,8598		0,0,4299	no	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	23,23	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	1859/2244,1837/2231	37368886	1,13003	2203	4299	6502	37343890	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5509G>A	3.37:g.37368886G>A	ENSP00000354486:p.Asp1837Asn		37343890	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	5.791	0.330187	0.10956	2.27E-4	0.0	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.23754	1.9;1.89;1.9	5.17	-1.49	0.08718	.	1.413550	0.05130	N	0.492446	T	0.18087	0.0434	L	0.35723	1.085	0.09310	N	1	B;B;B;B	0.14438	0.008;0.008;0.008;0.01	B;B;B;B	0.08055	0.003;0.003;0.003;0.002	T	0.25882	-1.0119	10	0.24483	T	0.36	.	5.2699	0.15618	0.3916:0.0:0.4817:0.1267	.	1837;1837;1859;1837	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	N	1837;1859;1708	ENSP00000354486:D1837N;ENSP00000349305:D1859N;ENSP00000405842:D1708N	ENSP00000349305:D1859N	D	+	1	0	GOLGA4	37343890	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	-0.006000	0.12833	-0.393000	0.07739	-0.362000	0.07510	GAC		0.383	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37368886	G	A	37368886	3	1	96	1	0	0	0	0	1	0	0	0	6575	1058	37	1	5633	1	GOLGA4	3	37368886	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	279849	37368886	160653544	28	25974										
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47719762	47719762	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aaatactcttgggggtttagAcgatacgtgtcaatcataaa	9	6	3	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:47719762A>G	ENST00000254480.5	-	16	1616	c.1497T>C	c.(1495-1497)cgT>cgC	p.R499R	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	499	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		GGGGGTTTAGACGATACGTGT	0.388																																																0			3											143	137	139					3																	47719762		2203	4300	6503	47694766	SO:0001819	synonymous_variant	6599			U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1497T>C	3.37:g.47719762A>G			47694766	Q17RS0|Q6P172|Q8IWH2	Silent	SNP	ENST00000254480.5	37	CCDS2758.1																																																																																				0.388	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			G	47719762	A	G	47719762	2	3	96	1	0	0	0	0	0	0	0	1	14812	262	10	4		4	SMARCC1	3	47719762	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	10350876	47719762	150302668	29	25975										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49166570	49166570	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tggcggcagtggcattgaccTgtgccctcatcacacctgga	12	13	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:49166570T>C	ENST00000418109.1	-	14	1778	c.1614A>G	c.(1612-1614)acA>acG	p.T538T	LAMB2_ENST00000305544.4_Silent_p.T538T	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	538	Laminin EGF-like 5; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGCATTGACCTGTGCCCTCAT	0.572																																																0			3											72	66	68					3																	49166570		2203	4300	6503	49141574	SO:0001819	synonymous_variant	84823				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1614A>G	3.37:g.49166570T>C			49141574	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																				0.572	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49166570	T	C	49166570	2	2	96	1	0	0	0	0	0	0	0	1	8633	1567	55	4		4	LAMB2	3	49166570	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1446808	49166570	148855860	30	25976										
SPCS1	28972	hgsc.bcm.edu	37	chr3	52740182	52740182	+	5'UTR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	acgcgcagtgccagaccttaCccctcacggtccttaagtct	8	16	2	1	rs6617	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:52740182C>G	ENST00000602728.1	+	0	89				GLT8D1_ENST00000407584.3_5'Flank|GLT8D1_ENST00000394783.3_5'Flank|GLT8D1_ENST00000266014.5_5'Flank|SPCS1_ENST00000423431.1_Intron|GLT8D1_ENST00000491606.1_5'Flank|SPCS1_ENST00000233025.7_Missense_Mutation_p.P41A|GLT8D1_ENST00000478968.2_5'Flank			Q9Y6A9	SPCS1_HUMAN	signal peptidase complex subunit 1 homolog (S. cerevisiae)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6				BRCA - Breast invasive adenocarcinoma(193;6.51e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)|OV - Ovarian serous cystadenocarcinoma(275;0.0469)		CCAGACCTTACCCCTCACGGT	0.697													G|||	2230	0.445288	0.5575	0.5144	5008	,	,		13167	0.4286		0.4304	False		,,,				2504	0.2771															0			3											10	15	14					3																	52740182		687	1590	2277	52715222	SO:0001623	5_prime_UTR_variant	28972			AF092138	CCDS33769.2	3p21.31	2005-01-05			ENSG00000114902	ENSG00000114902			23401	protein-coding gene	gene with protein product		610358				8632014	Standard	NM_014041		Approved	SPC12, HSPC033, YJR010C-A, SPC1	uc011bei.2	Q9Y6A9	OTTHUMG00000154930	ENST00000602728.1:c.-81C>G	3.37:g.52740182C>G			52715222	B3KNF8|Q9BVW1	Missense_Mutation	SNP	ENST00000602728.1	37		1074	0.49175824175824173	273	0.5548780487804879	192	0.5303867403314917	280	0.48951048951048953	329	0.4340369393139842	G	1.062	-0.672572	0.03403	.	.	ENSG00000114902	ENST00000233025	.	.	.	3.96	-4.39	0.03611	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41716	-0.9493	7	0.02654	T	1	.	3.0659	0.06214	0.2759:0.4525:0.1602:0.1114	rs6617;rs1139798;rs3184127;rs17548630;rs6617	41	Q9Y6A9	SPCS1_HUMAN	A	41	.	ENSP00000233025:P41A	P	+	1	0	SPCS1	52715222	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.407000	0.02488	-1.177000	0.02744	-0.127000	0.14921	CCC		0.697	SPCS1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467759.1	NM_014041		G	52740182	C	G	52740182	1	3	96	0	1	0	0	0	0	0	0	0	15062	507	18	5		5	SPCS1	3	52740182	5'UTR	SNP	C	TCGA-DC-6157-01A-11D-1657-10	3573612	52740182	145282248	31	25977										
SNTN	132203	hgsc.bcm.edu	37	chr3	63638415	63638415	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aatctctccacttggaaggaGatcccaatccttctgcagcc	7	14	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:63638415G>C	ENST00000343837.3	+	1	72	c.52G>C	c.(52-54)Gat>Cat	p.D18H	SNTN_ENST00000496807.1_Missense_Mutation_p.D14H	NM_001080537.1	NP_001074006.1	A6NMZ2	SNTAN_HUMAN	sentan, cilia apical structure protein	18						cilium (GO:0005929)	calcium ion binding (GO:0005509)			endometrium(2)|ovary(1)	3						CTTGGAAGGAGATCCCAATCC	0.478																																																0			3											138	105	116					3																	63638415		2203	4300	6503	63613455	SO:0001583	missense	132203			AK126350	CCDS33779.1	3p14.2	2009-03-10	2009-03-10		ENSG00000188817	ENSG00000188817			33706	protein-coding gene	gene with protein product	"S100A-like protein"					18829862	Standard	NM_001080537		Approved	FLJ44379, S100AL	uc003dlr.3	A6NMZ2	OTTHUMG00000158766	ENST00000343837.3:c.52G>C	3.37:g.63638415G>C	ENSP00000341442:p.Asp18His		63613455	B7FF65	Missense_Mutation	SNP	ENST00000343837.3	37	CCDS33779.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.355103	0.24512	.	.	ENSG00000188817	ENST00000343837;ENST00000469440;ENST00000496807	T	0.45668	0.89	5.25	2.39	0.29439	.	0.615469	0.15218	N	0.274103	T	0.28764	0.0713	N	0.22421	0.69	0.09310	N	1	P	0.39624	0.681	B	0.41946	0.371	T	0.12116	-1.0560	10	0.62326	D	0.03	0.7398	4.8729	0.13642	0.1908:0.1781:0.6311:0.0	.	18	A6NMZ2	SNTAN_HUMAN	H	18;18;14	ENSP00000341442:D18H	ENSP00000341442:D18H	D	+	1	0	SNTN	63613455	0.037000	0.19845	0.062000	0.19696	0.182000	0.23217	0.176000	0.16782	0.682000	0.31407	0.591000	0.81541	GAT		0.478	SNTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352094.1	NM_001080537		C	63638415	G	C	63638415	3	2	96	1	0	0	0	0	1	0	0	0	14913	942	33	5	54	5	SNTN	3	63638415	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	10898233	63638415	134384015	32	25978										
ARL13B	200894	hgsc.bcm.edu	37	chr3	93755533	93755533	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caaaaagagacaacagagcaGcgtgctcttgaggaacaaga	11	8	1	4			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:93755533G>A	ENST00000394222.3	+	5	899	c.624G>A	c.(622-624)caG>caA	p.Q208Q	ARL13B_ENST00000486562.1_3'UTR|ARL13B_ENST00000303097.7_Silent_p.Q101Q|ARL13B_ENST00000471138.1_Silent_p.Q208Q|ARL13B_ENST00000535334.1_Silent_p.Q105Q|ARL13B_ENST00000539730.1_5'UTR	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	208					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						CAACAGAGCAGCGTGCTCTTG	0.388																																																0			3											72	70	71					3																	93755533		2203	4300	6503	95238223	SO:0001819	synonymous_variant	200894			AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.624G>A	3.37:g.93755533G>A			95238223	D3DN29|G3V1S8|Q504W8|Q8TCL5	Silent	SNP	ENST00000394222.3	37	CCDS2925.1																																																																																				0.388	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		A	93755533	G	A	93755533	2	1	96	1	0	0	0	0	0	0	0	1	929	962	34	3		3	ARL13B	3	93755533	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	30117118	93755533	104266897	33	25979										
CBLB	868	hgsc.bcm.edu	37	chr3	105470358	105470358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aaactgaaatgtaatcattgCaagttaaatcaattgttgat	6	4	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:105470358C>T	ENST00000264122.4	-	5	992	c.671G>A	c.(670-672)tGc>tAc	p.C224Y	CBLB_ENST00000403724.1_Missense_Mutation_p.C224Y|CBLB_ENST00000394027.3_Missense_Mutation_p.C246Y|CBLB_ENST00000545639.1_Missense_Mutation_p.C197Y|CBLB_ENST00000405772.1_Missense_Mutation_p.C224Y	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	224	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|EF-hand-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						GTAATCATTGCAAGTTAAATC	0.383			Mis S		AML																																GBM(93;588 1337 9788 29341 43499)		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	0			3											83	80	81					3																	105470358		2203	4300	6503	106953048	SO:0001583	missense	868			U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.671G>A	3.37:g.105470358C>T	ENSP00000264122:p.Cys224Tyr		106953048	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011465	0.75046	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772;ENST00000545639	D;D;D;D	0.85702	-1.96;-1.97;-2.01;-2.02	5.32	4.43	0.53597	Adaptor protein Cbl, PTB domain (1);EF-hand-like domain (1);Adaptor protein Cbl, EF hand-like (1);	0.000000	0.85682	D	0.000000	D	0.92954	0.7758	M	0.86573	2.825	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.993;0.988;0.995	D	0.94186	0.7436	10	0.87932	D	0	-6.5133	15.4627	0.75373	0.1398:0.8602:0.0:0.0	.	246;224;224	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	Y	224;246;224;224;197	ENSP00000264122:C224Y;ENSP00000377595:C246Y;ENSP00000384816:C224Y;ENSP00000384938:C224Y	ENSP00000264122:C224Y	C	-	2	0	CBLB	106953048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.830000	0.62745	1.335000	0.45486	0.650000	0.86243	TGC		0.383	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		T	105470358	C	T	105470358	3	4	96	1	0	0	0	0	1	0	0	0	2707	710	25	3	2337	3	CBLB	3	105470358	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	11714825	105470358	92552072	34	25980										
SIDT1	54847	hgsc.bcm.edu	37	chr3	113299554	113299554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttgtctcagtccagaatatcAtggtgagtgctgataacttg	10	7	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:113299554A>G	ENST00000264852.4	+	5	1387	c.661A>G	c.(661-663)Atg>Gtg	p.M221V	SIDT1_ENST00000393830.3_Missense_Mutation_p.M221V	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	221					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						CCAGAATATCATGGTGAGTGC	0.393																																																0			3											167	163	164					3																	113299554		2203	4300	6503	114782244	SO:0001583	missense	54847			AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.661A>G	3.37:g.113299554A>G	ENSP00000264852:p.Met221Val		114782244	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.422468	0.25639	.	.	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.21361	2.01;2.01	5.53	4.22	0.49857	.	0.074568	0.56097	D	0.000025	T	0.05318	0.0141	N	0.00926	-1.1	0.28079	N	0.932262	B	0.02656	0.0	B	0.09377	0.004	T	0.16660	-1.0395	10	0.28530	T	0.3	-12.5217	2.0146	0.03495	0.5702:0.0:0.174:0.2558	.	221	Q9NXL6	SIDT1_HUMAN	V	221	ENSP00000264852:M221V;ENSP00000377416:M221V	ENSP00000264852:M221V	M	+	1	0	SIDT1	114782244	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.773000	0.38563	2.232000	0.73038	0.402000	0.26972	ATG		0.393	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		G	113299554	A	G	113299554	3	3	96	1	0	0	0	0	1	0	0	0	14339	217	8	4	679	4	SIDT1	3	113299554	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	7829196	113299554	84722876	35	25981										
POLQ	10721	hgsc.bcm.edu	37	chr3	121230739	121230739	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	taaattctctcttacctccaGaatagctcgtatcatgctgc	5	12	3	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:121230739G>C	ENST00000264233.5	-	10	1734	c.1606C>G	c.(1606-1608)Ctg>Gtg	p.L536V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	536	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTTACCTCCAGAATAGCTCGT	0.353								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											0			3											108	105	106					3																	121230739		2203	4300	6503	122713429	SO:0001583	missense	51426			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1606C>G	3.37:g.121230739G>C	ENSP00000264233:p.Leu536Val		122713429	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.611246	0.46631	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.57107	0.42	5.32	2.54	0.30619	Helicase, C-terminal (1);	0.171732	0.39020	N	0.001499	T	0.62478	0.2431	M	0.91717	3.235	0.50171	D	0.999857	P	0.41748	0.761	B	0.43360	0.417	T	0.68078	-0.5504	10	0.87932	D	0	.	9.8229	0.40894	0.2221:0.0:0.7779:0.0	.	536	O75417	DPOLQ_HUMAN	V	159;536;672	ENSP00000264233:L536V	ENSP00000264233:L536V	L	-	1	2	POLQ	122713429	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.016000	0.49607	0.608000	0.30000	0.455000	0.32223	CTG		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121230739	G	C	121230739	3	2	96	1	0	0	0	0	1	0	0	0	12239	933	33	5	6250	5	POLQ	3	121230739	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	7931185	121230739	76791691	36	25982										
ZNF148	7707	hgsc.bcm.edu	37	chr3	125032392	125032392	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	acagtagactggccagacacTccacccattacaaccattgt	6	14	0	2	rs36112318		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:125032392T>C	ENST00000360647.4	-	4	578	c.93A>G	c.(91-93)ggA>ggG	p.G31G	ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000485866.1_Silent_p.G31G|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000492394.1_Silent_p.G31G|ZNF148_ENST00000484491.1_Silent_p.G31G	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	31					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						GGCCAGACACTCCACCCATTA	0.458																																																0			3											150	139	143					3																	125032392		2203	4300	6503	126515082	SO:0001819	synonymous_variant	7707			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.93A>G	3.37:g.125032392T>C			126515082	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Silent	SNP	ENST00000360647.4	37	CCDS3031.1																																																																																				0.458	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		C	125032392	T	C	125032392	2	2	96	1	0	0	0	0	0	0	0	1	17773	1538	54	4		4	ZNF148	3	125032392	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	3801653	125032392	72990038	37	25983										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134967347	134967347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agactgtggcaaccatcaccGccgtgtgagtctagtgaaac	11	11	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:134967347G>A	ENST00000398015.3	+	14	3056	c.2686G>A	c.(2686-2688)Gcc>Acc	p.A896T	EPHB1_ENST00000493838.1_Missense_Mutation_p.A457T	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	896					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						AACCATCACCGCCGTGTGAGT	0.522																																																0			3											16	19	18					3																	134967347		2120	4271	6391	136450037	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2686G>A	3.37:g.134967347G>A	ENSP00000381097:p.Ala896Thr		136450037	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.205643	0.58234	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.61980	0.06;0.06	5.35	5.35	0.76521	Protein kinase-like domain (1);	0.057386	0.64402	D	0.000002	T	0.52125	0.1715	L	0.36672	1.1	0.49915	D	0.999831	B	0.02656	0.0	B	0.01281	0.0	T	0.43180	-0.9407	10	0.37606	T	0.19	.	13.8532	0.63510	0.0728:0.0:0.9272:0.0	.	896	P54762	EPHB1_HUMAN	T	896;457	ENSP00000381097:A896T;ENSP00000419574:A457T	ENSP00000381097:A896T	A	+	1	0	EPHB1	136450037	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.892000	0.48625	2.941000	0.99782	0.655000	0.94253	GCC		0.522	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134967347	G	A	134967347	3	1	96	1	0	0	0	0	1	0	0	0	5187	1087	38	1	2740	1	EPHB1	3	134967347	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	9934955	134967347	63055083	38	25984										
TMEM22	80723	hgsc.bcm.edu	37	chr3	136573507	136573507	+	Missense_Mutation	SNP	T	T	C													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aaaaaaaagggagagctttcTttggaaccatggatacccta							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:136573507T>C	ENST00000446465.2	+	2	833	c.205T>C	c.(205-207)Ttt>Ctt	p.F69L	RP11-85F14.5_ENST00000474250.1_RNA|SLC35G2_ENST00000393079.3_Missense_Mutation_p.F69L|RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000470236.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2									p.A67_M72>V(1)									GAGAGCTTTCTTTGGAACCAT	0.383																																																1	Complex - deletion inframe(1)	ovary(1)	3											76	84	81					3																	136573507		2203	4300	6503	138056197	SO:0001583	missense	80723			BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"Solute carriers"	28480	protein-coding gene	gene with protein product			"transmembrane protein 22"	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.205T>C	3.37:g.136573507T>C	ENSP00000400839:p.Phe69Leu		138056197		Missense_Mutation	SNP	ENST00000446465.2	37	CCDS3091.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.802819	0.31869	.	.	ENSG00000168917	ENST00000446465;ENST00000393079	T;T	0.32515	1.45;1.45	5.33	5.33	0.75918	.	0.051201	0.85682	D	0.000000	T	0.30070	0.0753	L	0.50333	1.59	0.58432	D	0.999995	B	0.14012	0.009	B	0.12156	0.007	T	0.04551	-1.0943	10	0.36615	T	0.2	.	14.1289	0.65240	0.0:0.0:0.0:1.0	.	69	Q8TBE7	TMM22_HUMAN	L	69	ENSP00000400839:F69L;ENSP00000376794:F69L	ENSP00000376794:F69L	F	+	1	0	TMEM22	138056197	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	5.694000	0.68272	2.020000	0.59435	0.402000	0.26972	TTT		0.383	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		C	136573507	T	C	136573507	3	2	96	1	0	0	0	0	1	0	0	0	16182	1609	56	4	207	4	TMEM22	3	136573507	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1606160	136573507	61448923	39	25985	37	2								
TMEM22	80723	hgsc.bcm.edu	37	chr3	136573509	136573509	+	Missense_Mutation	SNP	T	T	A													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aaaaaagggagagctttcttTggaaccatggataccctacc							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:136573509T>A	ENST00000446465.2	+	2	835	c.207T>A	c.(205-207)ttT>ttA	p.F69L	RP11-85F14.5_ENST00000474250.1_RNA|SLC35G2_ENST00000393079.3_Missense_Mutation_p.F69L|RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000470236.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2									p.A67_M72>V(1)									GAGCTTTCTTTGGAACCATGG	0.378																																																1	Complex - deletion inframe(1)	ovary(1)	3											75	83	80					3																	136573509		2203	4300	6503	138056199	SO:0001583	missense	80723			BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"Solute carriers"	28480	protein-coding gene	gene with protein product			"transmembrane protein 22"	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.207T>A	3.37:g.136573509T>A	ENSP00000400839:p.Phe69Leu		138056199		Missense_Mutation	SNP	ENST00000446465.2	37	CCDS3091.1	.	.	.	.	.	.	.	.	.	.	T	11.28	1.593535	0.28357	.	.	ENSG00000168917	ENST00000446465;ENST00000393079	T;T	0.32515	1.45;1.45	5.33	4.19	0.49359	.	0.051201	0.85682	D	0.000000	T	0.25195	0.0612	L	0.50333	1.59	0.53005	D	0.999966	B	0.14012	0.009	B	0.12156	0.007	T	0.08472	-1.0720	10	0.36615	T	0.2	.	7.0869	0.25261	0.0:0.1701:0.0:0.8299	.	69	Q8TBE7	TMM22_HUMAN	L	69	ENSP00000400839:F69L;ENSP00000376794:F69L	ENSP00000376794:F69L	F	+	3	2	TMEM22	138056199	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	3.022000	0.49659	2.020000	0.59435	0.402000	0.26972	TTT		0.378	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		A	136573509	T	A	136573509	3	1	96	1	0	0	0	0	1	0	0	0	16182	1809	63	5	209	5	TMEM22	3	136573509	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	2	136573509	61448921	40	25986	37	2								
NMNAT3	349565	hgsc.bcm.edu	37	chr3	139280235	139280235	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aagcttcagctcaggcacagCtgcaaaaacaaggatggacc	10	11	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:139280235C>A	ENST00000296202.7	-	6	758		c.e6-1		RP11-319G6.1_ENST00000515247.1_RNA|NMNAT3_ENST00000413939.2_Splice_Site|NMNAT3_ENST00000507242.1_Splice_Site|NMNAT3_ENST00000511444.1_Splice_Site|RP11-319G6.1_ENST00000381790.3_RNA|NMNAT3_ENST00000406824.1_Splice_Site|NMNAT3_ENST00000512391.1_Splice_Site|NMNAT3_ENST00000339837.5_Splice_Site|NMNAT3_ENST00000406164.1_Splice_Site			Q96T66	NMNA3_HUMAN	nicotinamide nucleotide adenylyltransferase 3						NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)	9						TCAGGCACAGCTGCAAAAACA	0.483																																																0			3											43	47	46					3																	139280235		2203	4300	6503	140762925	SO:0001630	splice_region_variant	349565			AF345564	CCDS3111.1, CCDS56282.1	3q23	2013-09-20			ENSG00000163864	ENSG00000163864			20989	protein-coding gene	gene with protein product		608702				12574164	Standard	NM_178177		Approved	PNAT3	uc003etk.3	Q96T66	OTTHUMG00000159951	ENST00000296202.7:c.377-1G>T	3.37:g.139280235C>A			140762925	B3KVR6|D3DNF2|D3DNF3|Q8N4G1	Splice_Site	SNP	ENST00000296202.7	37		.	.	.	.	.	.	.	.	.	.	C	18.62	3.663041	0.67700	.	.	ENSG00000163864	ENST00000406164;ENST00000406824;ENST00000339837;ENST00000413939;ENST00000296202;ENST00000511444;ENST00000512391	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6495	0.91425	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NMNAT3	140762925	1.000000	0.71417	0.966000	0.40874	0.888000	0.51559	6.740000	0.74832	2.639000	0.89480	0.650000	0.86243	.		0.483	NMNAT3-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000358469.1	NM_178177	Intron	A	139280235	C	A	139280235	5	1	96	1	0	0	0	0	0	0	1	0	10531	811	28	2	386	2	NMNAT3	3	139280235	Splice_Site	SNP	C	TCGA-DC-6157-01A-11D-1657-10	2706726	139280235	58742195	41	25987										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951890	178951890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tattacttataggtttcaggAgatgtgttacaaggcttatc	9	5	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:178951890A>G	ENST00000263967.3	+	21	3102	c.2945A>G	c.(2944-2946)gAg>gGg	p.E982G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	982	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E982G(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGGTTTCAGGAGATGTGTTAC	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	thyroid(1)	3											116	106	109					3																	178951890		1859	4091	5950	180434584	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2945A>G	3.37:g.178951890A>G	ENSP00000263967:p.Glu982Gly		180434584	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.702741	0.48307	.	.	ENSG00000121879	ENST00000263967	T	0.78003	-1.14	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.74943	0.3783	L	0.59436	1.845	0.80722	D	1	P	0.36086	0.536	B	0.34873	0.191	T	0.73500	-0.3963	10	0.32370	T	0.25	-16.0253	16.635	0.85050	1.0:0.0:0.0:0.0	.	982	P42336	PK3CA_HUMAN	G	982	ENSP00000263967:E982G	ENSP00000263967:E982G	E	+	2	0	PIK3CA	180434584	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.859000	0.92264	2.330000	0.79161	0.477000	0.44152	GAG		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951890	A	G	178951890	3	3	96	1	0	0	0	0	1	0	0	0	11944	304	11	4	3023	4	PIK3CA	3	178951890	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	39671655	178951890	19070540	42	25988			2	22		3	3	179	A		5.501142e-07
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952046	178952046	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cttagataaaactgagcaagAggctttggagtatttcatga	10	5	1	4			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:178952046A>G	ENST00000263967.3	+	21	3258	c.3101A>G	c.(3100-3102)gAg>gGg	p.E1034G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1034	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E1034G(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ACTGAGCAAGAGGCTTTGGAG	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	liver(1)	3											97	86	89					3																	178952046		1886	4124	6010	180434740	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3101A>G	3.37:g.178952046A>G	ENSP00000263967:p.Glu1034Gly		180434740	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831404	0.71258	.	.	ENSG00000121879	ENST00000263967	D	0.83335	-1.71	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88306	0.6401	M	0.81682	2.555	0.80722	D	1	D	0.54601	0.967	P	0.50791	0.65	D	0.89905	0.4047	10	0.87932	D	0	-16.0336	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1034	P42336	PK3CA_HUMAN	G	1034	ENSP00000263967:E1034G	ENSP00000263967:E1034G	E	+	2	0	PIK3CA	180434740	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	GAG		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952046	A	G	178952046	3	3	96	1	0	0	0	0	1	0	0	0	11944	304	11	4	3179	4	PIK3CA	3	178952046	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	156	178952046	19070384	43	25989			2	22		3	3	179	A		5.501142e-07
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952068	178952068	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctttggagtatttcatgaaAcaaatgaatgatgcacatca	8	6	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:178952068A>G	ENST00000263967.3	+	21	3280	c.3123A>G	c.(3121-3123)aaA>aaG	p.K1041K	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1041	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.K1041N(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATTTCATGAAACAAATGAATG	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	thyroid(1)	3											95	85	88					3																	178952068		1902	4125	6027	180434762	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3123A>G	3.37:g.178952068A>G			180434762	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952068	A	G	178952068	2	3	96	1	0	0	0	0	0	0	0	1	11944	40	2	4		4	PIK3CA	3	178952068	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	22	178952068	19070362	44	25990			2	22		3	3	179	A		5.501142e-07
FXR1	8087	hgsc.bcm.edu	37	chr3	180675611	180675611	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttttctcttactaaaggaaaAgtaattggaaaaaatggcaa	7	4	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr3:180675611A>G	ENST00000357559.4	+	10	1269	c.885A>G	c.(883-885)aaA>aaG	p.K295K	FXR1_ENST00000468861.1_Silent_p.K210K|FXR1_ENST00000445140.2_Silent_p.K295K|FXR1_ENST00000480918.1_Silent_p.K282K|FXR1_ENST00000491062.1_Silent_p.K246K|FXR1_ENST00000305586.7_Silent_p.K210K	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	295	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			CTAAAGGAAAAGTAATTGGAA	0.333																																																0			3											74	82	79					3																	180675611		2203	4300	6503	182158305	SO:0001819	synonymous_variant	8087			M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.885A>G	3.37:g.180675611A>G			182158305	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	37	CCDS3238.1																																																																																				0.333	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			G	180675611	A	G	180675611	2	3	96	1	0	0	0	0	0	0	0	1	6134	69	3	4		4	FXR1	3	180675611	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	1723543	180675611	17346819	45	25991										
KIT	3815	hgsc.bcm.edu	37	chr4	55592159	55592159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cggttgaatgtaaggcttacAacgatgtgggcaagacttct	12	7	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr4:55592159A>G	ENST00000288135.5	+	9	1580	c.1483A>G	c.(1483-1485)Aac>Gac	p.N495D		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	495	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E490_F504>DHIVVSLTF(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TAAGGCTTACAACGATGTGGG	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Complex - deletion inframe(1)	soft_tissue(1)	4											136	122	127					4																	55592159		2203	4300	6503	55286916	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1483A>G	4.37:g.55592159A>G	ENSP00000288135:p.Asn495Asp		55286916	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796063	0.90453	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.08102	3.13;3.13	6.02	6.02	0.97574	Immunoglobulin-like fold (1);	0.080350	0.52532	D	0.000064	T	0.32496	0.0831	M	0.86028	2.79	0.48135	D	0.999595	P;P	0.40144	0.666;0.704	P;P	0.58928	0.695;0.848	T	0.01352	-1.1377	10	0.52906	T	0.07	.	15.1157	0.72401	1.0:0.0:0.0:0.0	.	495;495	P10721-2;P10721	.;KIT_HUMAN	D	495	ENSP00000288135:N495D;ENSP00000390987:N495D	ENSP00000288135:N495D	N	+	1	0	KIT	55286916	1.000000	0.71417	0.984000	0.44739	0.926000	0.56050	6.446000	0.73460	2.311000	0.77944	0.533000	0.62120	AAC		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55592159	A	G	55592159	3	3	96	1	0	0	0	0	1	0	0	0	8350	130	5	4	1517	4	KIT	4	55592159	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10		55592159	135562117	46	25992										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156634718	156634718	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcttcgaccagcagtgtggaGagctggatgtctacaaggta	14	8	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr4:156634718G>A	ENST00000296518.7	+	7	1764	c.1555G>A	c.(1555-1557)Gag>Aag	p.E519K	GUCY1A3_ENST00000455639.2_Missense_Mutation_p.E519K|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.E519K|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.E261K|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.E519K|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.E519K|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.E519K			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	519	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GCAGTGTGGAGAGCTGGATGT	0.507																																																0			4											43	38	40					4																	156634718		2203	4300	6503	156854168	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1555G>A	4.37:g.156634718G>A	ENSP00000296518:p.Glu519Lys		156854168	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353468	0.61293	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	T;T;T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42	5.78	4.94	0.65067	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.185786	0.37393	N	0.002105	T	0.70718	0.3256	N	0.25144	0.715	0.58432	D	0.999999	P;P	0.35328	0.495;0.495	B;B	0.40038	0.317;0.317	T	0.66771	-0.5839	10	0.06236	T	0.91	.	16.6755	0.85278	0.0:0.1373:0.8627:0.0	.	519;519	B3KU69;Q02108	.;GCYA3_HUMAN	K	519;519;519;519;261;519;519	ENSP00000424361:E519K;ENSP00000421493:E519K;ENSP00000426968:E519K;ENSP00000412201:E519K;ENSP00000377418:E261K;ENSP00000296518:E519K;ENSP00000426040:E519K	ENSP00000296518:E519K	E	+	1	0	GUCY1A3	156854168	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	5.570000	0.67398	1.420000	0.47138	0.655000	0.94253	GAG		0.507	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			A	156634718	G	A	156634718	3	1	96	1	0	0	0	0	1	0	0	0	6915	943	33	3	1588	3	GUCY1A3	4	156634718	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	101042559	156634718	34519558	47	25993										
TUBB4Q	56604	hgsc.bcm.edu	37	chr4	190906006	190906006	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttcccgcactgcccggtctgCgtgagcacaagctccctcgt	10	17	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr4:190906006C>T								FRG1 (21647 upstream) : RNA5SP174 (30286 downstream)																							GCCCGGTCTGCGTGAGCACAA	0.701																																																0			4											11	13	12					4																	190906006		2137	4191	6328	191143000	SO:0001628	intergenic_variant	56604																															4.37:g.190906006C>T			191143000		Missense_Mutation	SNP		37																																																																																				0	0.701									T	190906006	C	T	190906006	1	4	96	0	1	0	0	0	0	0	0	0	16799	768	27	1		1	TUBB4Q	4	190906006	IGR	SNP	C	TCGA-DC-6157-01A-11D-1657-10	34271288	190906006	248270	48	25994										
CDH18	1016	hgsc.bcm.edu	37	chr5	19838901	19838901	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgaggatctggtcccatatgTtcttctaaaacaaagaactg	8	8	3	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:19838901T>C	ENST00000507958.1	-	5	1185	c.195A>G	c.(193-195)gaA>gaG	p.E65E	CDH18_ENST00000274170.4_Silent_p.E65E|CDH18_ENST00000511273.1_Silent_p.E65E|CDH18_ENST00000506372.1_Silent_p.E65E|CDH18_ENST00000502796.1_Silent_p.E65E|CDH18_ENST00000382275.1_Silent_p.E65E			Q13634	CAD18_HUMAN	cadherin 18, type 2	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GTCCCATATGTTCTTCTAAAA	0.393																																																0			5											139	121	127					5																	19838901		2203	4300	6503	19874658	SO:0001819	synonymous_variant	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.195A>G	5.37:g.19838901T>C			19874658	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																				0.393	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		C	19838901	T	C	19838901	2	2	96	1	0	0	0	0	0	0	0	1	3109	1722	60	4		4	CDH18	5	19838901	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10		19838901	161076359	49	25995										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58270807	58270807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttgtgctctggtaccattcaCgattgtcctccaaagtgtcc	8	12	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:58270807C>T	ENST00000340635.6	-	15	2289	c.2114G>A	c.(2113-2115)cGt>cAt	p.R705H	PDE4D_ENST00000405755.2_Missense_Mutation_p.R583H|PDE4D_ENST00000507116.1_Missense_Mutation_p.R641H|PDE4D_ENST00000502484.2_Missense_Mutation_p.R644H|PDE4D_ENST00000358923.6_Missense_Mutation_p.R403H|PDE4D_ENST00000317118.8_Missense_Mutation_p.R414H|PDE4D_ENST00000360047.5_Missense_Mutation_p.R569H|PDE4D_ENST00000503258.1_Missense_Mutation_p.R575H|PDE4D_ENST00000546160.1_Missense_Mutation_p.R644H	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	705					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GTACCATTCACGATTGTCCTC	0.532																																																0			5											70	72	71					5																	58270807		2027	4204	6231	58306564	SO:0001583	missense	5144				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2114G>A	5.37:g.58270807C>T	ENSP00000345502:p.Arg705His		58306564	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	37	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.355466	0.82243	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000358923;ENST00000317118;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160;ENST00000505453	D;D;D;D;D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.08	5.08	0.68730	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.102683	0.64402	D	0.000005	D	0.93828	0.8026	H	0.94423	3.535	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.981;0.989;0.981;0.999;0.999;0.981;0.992;0.995	D	0.95258	0.8366	10	0.87932	D	0	.	18.6453	0.91408	0.0:1.0:0.0:0.0	.	644;705;641;568;583;575;480;414	Q08499-11;Q08499;Q08499-6;Q08499-2;Q08499-9;Q08499-10;Q08499-4;Q08499-8	.;PDE4D_HUMAN;.;.;.;.;.;.	H	705;574;569;641;403;414;575;583;644;644;403	ENSP00000345502:R705H;ENSP00000353152:R569H;ENSP00000424852:R641H;ENSP00000351800:R403H;ENSP00000321739:R414H;ENSP00000425605:R575H;ENSP00000384806:R583H;ENSP00000423094:R644H;ENSP00000442734:R644H;ENSP00000421013:R403H	ENSP00000321739:R414H	R	-	2	0	PDE4D	58306564	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	2.641000	0.89580	0.655000	0.94253	CGT		0.532	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			T	58270807	C	T	58270807	3	4	96	1	0	0	0	0	1	0	0	0	11673	536	19	1	319	1	PDE4D	5	58270807	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	38431906	58270807	122644453	50	25996										
DIMT1L	27292	hgsc.bcm.edu	37	chr5	61694694	61694694	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctactagccttgggtcaagTtcacaagcaacaacctaatt	7	11	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:61694694T>C	ENST00000199320.4	-	4	415	c.255A>G	c.(253-255)gaA>gaG	p.E85E	KIF2A_ENST00000509663.2_Intron|DIMT1_ENST00000506390.1_Silent_p.E85E	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	85						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)										TTGGGTCAAGTTCACAAGCAA	0.303																																																0			5											51	51	51					5																	61694694		2203	4300	6503	61730451	SO:0001819	synonymous_variant	27292			AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189			30217	protein-coding gene	gene with protein product		612499	"DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)"	DIMT1L		11124703	Standard	NM_014473		Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.255A>G	5.37:g.61694694T>C			61730451	O76025|Q9BU77|Q9UES1	Silent	SNP	ENST00000199320.4	37	CCDS3981.1																																																																																				0.303	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253967.1	NM_014473		C	61694694	T	C	61694694	2	2	96	1	0	0	0	0	0	0	0	1	4534	1722	60	4		4	DIMT1L	5	61694694	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	3423887	61694694	119220566	51	25997										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101724442	101724442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcttgttatatatccaacaaCgtcctgtgtgtccacattta	5	10	1	0	rs139236845	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:101724442C>T	ENST00000506729.1	-	12	2138	c.1967G>A	c.(1966-1968)cGt>cAt	p.R656H	SLCO6A1_ENST00000379810.1_Missense_Mutation_p.R403H|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.R403H|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.R656H|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.R594H			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	656						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R656H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TATCCAACAACGTCCTGTGTG	0.303													C|||	5	0.000998403	0.003	0	5008	,	,		14930	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	central_nervous_system(1)	5						C	HIS/ARG	3,4399	6.2+/-15.9	0,3,2198	69	69	69		1967	-10.1	0	5	dbSNP_134	69	0,8592		0,0,4296	no	missense	SLCO6A1	NM_173488.3	29	0,3,6494	TT,TC,CC		0.0,0.0682,0.0231	benign	656/720	101724442	3,12991	2201	4296	6497	101752341	SO:0001583	missense	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1967G>A	5.37:g.101724442C>T	ENSP00000421339:p.Arg656His		101752341	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	8.564	0.878400	0.17395	6.82E-4	0.0	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.06	-10.1	0.00402	Major facilitator superfamily domain, general substrate transporter (1);	1.363240	0.04835	N	0.439495	T	0.25344	0.0616	L	0.38175	1.15	0.09310	N	1	B;P;B	0.36010	0.36;0.532;0.285	B;B;B	0.30855	0.034;0.121;0.032	T	0.18053	-1.0349	10	0.39692	T	0.17	.	8.3098	0.32064	0.0743:0.1031:0.1838:0.6388	.	594;403;656	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	H	656;656;594;403;403	ENSP00000421339:R656H;ENSP00000369135:R656H;ENSP00000373671:R594H;ENSP00000421990:R403H;ENSP00000369138:R403H	ENSP00000369135:R656H	R	-	2	0	SLCO6A1	101752341	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.758000	0.00787	-3.320000	0.00188	-0.143000	0.13931	CGT		0.303	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		T	101724442	C	T	101724442	3	4	96	1	0	0	0	0	1	0	0	0	14769	536	19	1	200	1	SLCO6A1	5	101724442	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	40029748	101724442	79190818	52	25998										
FER	2241	hgsc.bcm.edu	37	chr5	108168541	108168541	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gacacatgcagaggacttgaActctggacctttacacaggc	10	11	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:108168541A>T	ENST00000281092.4	+	4	662	c.278A>T	c.(277-279)aAc>aTc	p.N93I	FER_ENST00000502752.1_3'UTR|FER_ENST00000536402.1_Missense_Mutation_p.N93I|CTD-2197I11.1_ENST00000510935.1_RNA|FER_ENST00000438717.2_Intron	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	93	Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		GAGGACTTGAACTCTGGACCT	0.383																																					Colon(146;1051 1799 9836 27344 47401)											0			5											144	131	136					5																	108168541		2202	4300	6502	108196440	SO:0001583	missense	2241			J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.278A>T	5.37:g.108168541A>T	ENSP00000281092:p.Asn93Ile		108196440	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182173	0.78677	.	.	ENSG00000151422	ENST00000281092;ENST00000536402	T;T	0.42900	0.96;0.96	6.0	6.0	0.97389	.	0.000000	0.85682	D	0.000000	T	0.48892	0.1525	L	0.55481	1.735	0.80722	D	1	P;B	0.41366	0.747;0.449	P;B	0.45971	0.499;0.373	T	0.45891	-0.9230	10	0.49607	T	0.09	-18.6913	16.5047	0.84268	1.0:0.0:0.0:0.0	.	93;93	Q6PEJ9;P16591	.;FER_HUMAN	I	93	ENSP00000281092:N93I;ENSP00000442627:N93I	ENSP00000281092:N93I	N	+	2	0	FER	108196440	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.513000	0.67037	2.297000	0.77311	0.533000	0.62120	AAC		0.383	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		T	108168541	A	T	108168541	3	4	96	1	0	0	0	0	1	0	0	0	5832	43	2	5	284	5	FER	5	108168541	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	6444099	108168541	72746719	53	25999										
APC	324	hgsc.bcm.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R876*			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	96	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	4005376	112173917	68741343	54	26000			3	23		3	3	1660	N	C_A	4.774818e-05
APC	324	hgsc.bcm.edu	37	chr5	112175400	112175400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aagtggtgctcagacacccaAaagtccacctgaacactatg	8	12	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:112175400A>G	ENST00000457016.1	+	16	4489	c.4109A>G	c.(4108-4110)aAa>aGa	p.K1370R	APC_ENST00000508376.2_Missense_Mutation_p.K1370R|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.K1370R			P25054	APC_HUMAN	adenomatous polyposis coli	1370	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)|p.P1372fs*2(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGACACCCAAAAGTCCACCT	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											79	76	77					5																	112175400		2202	4300	6502	112203299	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4109A>G	5.37:g.112175400A>G	ENSP00000413133:p.Lys1370Arg		112203299	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269525	0.80469	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	T;T;T	0.76448	-1.02;-1.02;-1.02	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.83059	0.5172	L	0.36672	1.1	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.81673	-0.0826	9	.	.	.	-27.6547	16.4957	0.84242	1.0:0.0:0.0:0.0	.	1372;1370	Q4LE70;P25054	.;APC_HUMAN	R	1370	ENSP00000413133:K1370R;ENSP00000257430:K1370R;ENSP00000427089:K1370R	.	K	+	2	0	APC	112203299	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.013000	0.76373	2.371000	0.80710	0.533000	0.62120	AAA		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175400	A	G	112175400	3	3	96	1	0	0	0	0	1	0	0	0	763	14	1	4	4167	4	APC	5	112175400	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	1483	112175400	68739860	55	26001			3	23		3	3	1660	N	C_A	4.774818e-05
APC	324	hgsc.bcm.edu	37	chr5	112175576	112175576	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atcttccagatagccctggaCaaaccatgccaccaagcaga	7	14	1	2	rs74535574		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:112175576C>T	ENST00000457016.1	+	16	4665	c.4285C>T	c.(4285-4287)Caa>Taa	p.Q1429*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1429*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1429*			P25054	APC_HUMAN	adenomatous polyposis coli	1429	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1429*(35)|p.Q1429fs*8(4)|p.Y1376fs*41(1)|p.?(1)|p.P1424fs*19(1)|p.S1411fs*41(1)|p.K1192fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGCCCTGGACAAACCATGCC	0.468	Q1429*(NCIH747_LARGE_INTESTINE)|Q1429*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	44	Substitution - Nonsense(35)|Deletion - Frameshift(8)|Unknown(1)	large_intestine(42)|soft_tissue(1)|skin(1)	5	GRCh37	HM050024	APC	M	rs74535574						109	98	102					5																	112175576		2202	4300	6502	112203475	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4285C>T	5.37:g.112175576C>T	ENSP00000413133:p.Gln1429*		112203475	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.799924	0.98958	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8813	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	1429	.	.	Q	+	1	0	APC	112203475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.884000	0.98904	0.655000	0.94253	CAA		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175576	C	T	112175576	4	4	96	1	0	0	0	0	0	1	0	0	763	479	17	3	4343	3	APC	5	112175576	Nonsense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	176	112175576	68739684	56	26002			3	23		3	3	1660	N	C_A	4.774818e-05
FEM1C	56929	hgsc.bcm.edu	37	chr5	114860474	114860474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tagtctgctttttgaaatggTcttgttctagagtacaagga	10	5	3	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:114860474T>C	ENST00000274457.3	-	3	1946	c.1385A>G	c.(1384-1386)gAc>gGc	p.D462G		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	462			D -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TTTGAAATGGTCTTGTTCTAG	0.388																																																0			5											129	131	130					5																	114860474		2202	4299	6501	114888373	SO:0001583	missense	56929				CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1385A>G	5.37:g.114860474T>C	ENSP00000274457:p.Asp462Gly		114888373	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	37	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495671	0.44352	.	.	ENSG00000145780	ENST00000274457	T	0.67171	-0.25	5.55	5.55	0.83447	Ankyrin repeat-containing domain (2);	0.095094	0.64402	D	0.000001	T	0.53916	0.1826	L	0.28556	0.865	0.58432	D	0.999998	B	0.27192	0.171	B	0.32724	0.151	T	0.50742	-0.8792	10	0.02654	T	1	-26.8312	15.6943	0.77481	0.0:0.0:0.0:1.0	.	462	Q96JP0	FEM1C_HUMAN	G	462	ENSP00000274457:D462G	ENSP00000274457:D462G	D	-	2	0	FEM1C	114888373	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.993000	0.88291	2.103000	0.63969	0.533000	0.62120	GAC		0.388	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		C	114860474	T	C	114860474	3	2	96	1	0	0	0	0	1	0	0	0	5830	1667	58	4	472	4	FEM1C	5	114860474	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	2684898	114860474	66054786	57	26003										
BRD8	10902	hgsc.bcm.edu	37	chr5	137500548	137500548	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctccatacttgtggctggaAcaactccagctactatttcg	8	12	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:137500548A>G	ENST00000254900.5	-	12	1957	c.1586T>C	c.(1585-1587)gTt>gCt	p.V529A	BRD8_ENST00000402931.1_Missense_Mutation_p.V529A|BRD8_ENST00000515014.1_5'UTR|BRD8_ENST00000230901.5_Missense_Mutation_p.V602A|BRD8_ENST00000455658.2_Missense_Mutation_p.V488A|BRD8_ENST00000411594.2_Missense_Mutation_p.V532A	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	529					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGTGGCTGGAACAACTCCAGC	0.517																																																0			5											117	111	113					5																	137500548		2203	4300	6503	137528447	SO:0001583	missense	10902			AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.1586T>C	5.37:g.137500548A>G	ENSP00000254900:p.Val529Ala		137528447	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.359|2.359	-0.346969|-0.346969	0.05208|0.05208	.|.	.|.	ENSG00000112983|ENSG00000112983	ENST00000441656|ENST00000254900;ENST00000454473;ENST00000418329;ENST00000230901;ENST00000402931;ENST00000411594;ENST00000239899;ENST00000455658	.|T;T;T;T;T;T;T	.|0.31510	.|1.87;1.5;1.49;1.64;1.62;1.49;1.61	5.38|5.38	2.92|2.92	0.33932|0.33932	.|.	.|0.482456	.|0.19559	.|N	.|0.111371	T|T	0.11750|0.11750	0.0286|0.0286	N|N	0.08118|0.08118	0|0	0.22842|0.22842	N|N	0.998669|0.998669	.|B;B;B;B;B;B;B;B	.|0.06786	.|0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.001	.|B;B;B;B;B;B;B;B	.|0.04013	.|0.001;0.0;0.001;0.0;0.001;0.001;0.0;0.001	T|T	0.35871|0.35871	-0.9771|-0.9771	5|10	.|0.02654	.|T	.|1	-0.852|-0.852	7.3575|7.3575	0.26727|0.26727	0.7322:0.1921:0.0757:0.0|0.7322:0.1921:0.0757:0.0	.|.	.|488;513;308;602;532;423;602;529	.|F8W820;B4DN43;B4DMS9;A8K1N6;Q9H0E9-4;Q9H0E9-3;Q9H0E9-2;Q9H0E9	.|.;.;.;.;.;.;.;BRD8_HUMAN	L|A	523|529;558;527;602;529;532;423;488	.|ENSP00000254900:V529A;ENSP00000398067:V558A;ENSP00000398873:V527A;ENSP00000230901:V602A;ENSP00000384845:V529A;ENSP00000394330:V532A;ENSP00000408396:V488A	.|ENSP00000230901:V602A	F|V	-|-	1|2	0|0	BRD8|BRD8	137528447|137528447	0.987000|0.987000	0.35691|0.35691	0.998000|0.998000	0.56505|0.56505	0.980000|0.980000	0.70556|0.70556	0.761000|0.761000	0.26489|0.26489	0.432000|0.432000	0.26286|0.26286	0.397000|0.397000	0.26171|0.26171	TTC|GTT		0.517	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		G	137500548	A	G	137500548	3	3	96	1	0	0	0	0	1	0	0	0	1509	43	2	4	2249	4	BRD8	5	137500548	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	22640074	137500548	43414712	58	26004										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229878	140229878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggtgcgcgcagtggacgccGactcgggctacaacgcgtgg	17	12	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:140229878G>A	ENST00000532602.1	+	1	2831	c.1798G>A	c.(1798-1800)Gac>Aac	p.D600N	PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.D600N|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	600	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGGACGCCGACTCGGGCTA	0.677																																					Melanoma(55;1800 1972 14909)											0			5											63	69	67					5																	140229878		2196	4268	6464	140210062	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1798G>A	5.37:g.140229878G>A	ENSP00000436042:p.Asp600Asn		140210062	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858484	0.71834	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.74002	-0.8;-0.8	3.36	3.36	0.38483	Cadherin (4);Cadherin-like (1);	0.000000	0.32753	U	0.005685	D	0.92286	0.7553	H	0.99659	4.685	0.42344	D	0.992349	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.95881	0.8899	10	0.87932	D	0	.	15.2417	0.73476	0.0:0.0:1.0:0.0	.	600;600	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	N	600	ENSP00000436042:D600N;ENSP00000367362:D600N	ENSP00000367362:D600N	D	+	1	0	PCDHA9	140210062	1.000000	0.71417	0.945000	0.38365	0.205000	0.24178	8.743000	0.91592	1.839000	0.53478	0.313000	0.20887	GAC		0.677	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229878	G	A	140229878	3	1	96	1	0	0	0	0	1	0	0	0	11562	1058	37	1	1800	1	PCDHA9	5	140229878	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	2729330	140229878	40685382	59	26005										
RBM27	54439	hgsc.bcm.edu	37	chr5	145631292	145631292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggacagcccatgtactctcGtgaacatggtgctgctgcat	11	11	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:145631292G>A	ENST00000265271.5	+	9	1464	c.1298G>A	c.(1297-1299)cGt>cAt	p.R433H	RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	433					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATGTACTCTCGTGAACATGGT	0.527																																																0			5											117	103	108					5																	145631292		1568	3582	5150	145611485	SO:0001583	missense	54439			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1298G>A	5.37:g.145631292G>A	ENSP00000265271:p.Arg433His		145611485	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.358685	0.61403	.	.	ENSG00000091009	ENST00000265271	T	0.46451	0.87	5.5	5.5	0.81552	.	0.000000	0.48767	D	0.000165	T	0.40297	0.1111	N	0.08118	0	0.27065	N	0.963466	D	0.71674	0.998	D	0.69479	0.964	T	0.29397	-1.0013	10	0.13853	T	0.58	-10.5245	14.7704	0.69671	0.0:0.0:1.0:0.0	.	433	Q9P2N5	RBM27_HUMAN	H	433	ENSP00000265271:R433H	ENSP00000265271:R433H	R	+	2	0	RBM27	145611485	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.235000	0.58666	2.861000	0.98227	0.655000	0.94253	CGT		0.527	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		A	145631292	G	A	145631292	3	1	96	1	0	0	0	0	1	0	0	0	13164	1145	40	1	1332	1	RBM27	5	145631292	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	5401414	145631292	35283968	60	26006										
CLTB	1212	hgsc.bcm.edu	37	chr5	175824681	175824681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctccaggtccttcttggcctTctcccgccattcctgttccg	7	18	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr5:175824681T>C	ENST00000310418.4	-	4	596	c.391A>G	c.(391-393)Aag>Gag	p.K131E	CLTB_ENST00000345807.2_Missense_Mutation_p.K131E	NM_007097.3	NP_009028.1	P09497	CLCB_HUMAN	clathrin, light chain B	131	Involved in binding clathrin heavy chain.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	ciliary membrane (GO:0060170)|clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|trans-Golgi network (GO:0005802)	peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			lung(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.098)		TTCTTGGCCTTCTCCCGCCAT	0.577																																																0			5											167	157	160					5																	175824681		2203	4300	6503	175757287	SO:0001583	missense	1212			M20470	CCDS4402.1, CCDS4403.1	5q35.2	2010-05-11	2010-05-11		ENSG00000175416	ENSG00000175416			2091	protein-coding gene	gene with protein product		118970	"clathrin, light polypeptide (Lcb)"			7713494	Standard	NM_007097		Approved	Lcb	uc003meh.4	P09497	OTTHUMG00000130662	ENST00000310418.4:c.391A>G	5.37:g.175824681T>C	ENSP00000309415:p.Lys131Glu		175757287	Q53Y37|Q6FHW1	Missense_Mutation	SNP	ENST00000310418.4	37	CCDS4403.1	.	.	.	.	.	.	.	.	.	.	t	16.56	3.156766	0.57259	.	.	ENSG00000175416	ENST00000310418;ENST00000345807	.	.	.	4.0	2.79	0.32731	.	0.000000	0.85682	U	0.000000	T	0.66655	0.2811	M	0.72118	2.19	0.51767	D	0.99993	D;D	0.63046	0.982;0.992	P;D	0.65010	0.767;0.931	T	0.63541	-0.6614	9	0.12766	T	0.61	.	9.4807	0.38900	0.1587:0.0:0.0:0.8413	.	131;131	P09497-2;P09497	.;CLCB_HUMAN	E	131	.	ENSP00000309415:K131E	K	-	1	0	CLTB	175757287	1.000000	0.71417	0.998000	0.56505	0.622000	0.37654	6.227000	0.72282	0.395000	0.25257	0.248000	0.18094	AAG		0.577	CLTB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253153.1			C	175824681	T	C	175824681	3	2	96	1	0	0	0	0	1	0	0	0	3571	1792	62	4	310	4	CLTB	5	175824681	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	30193389	175824681	5090579	61	26007										
MYLK4	340156	hgsc.bcm.edu	37	chr6	2749453	2749454	+	Frame_Shift_Ins	INS	-	-	A													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tccacctcttccctgcactgINSaaaaaaggccattttctcca							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:2749453_2749454insA	ENST00000274643.7	-	2	417_418	c.75_76insT	c.(73-78)tttcagfs	p.Q26fs	MYLK4_ENST00000268446.5_Frame_Shift_Ins_p.Q26fs	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	26						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				TCCCTGCACTGAAAAAAGGCCA	0.401																																																0			6																																								2694453	SO:0001589	frameshift_variant	340156				CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"caMLCK like"						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.76dupT	6.37:g.2749459_2749459dupA	ENSP00000274643:p.Gln26fs		2694452	A2RUC0|Q5TAW2	Frame_Shift_Ins	INS	ENST00000274643.7	37	CCDS34330.1																																																																																				0.401	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418		A	2749454	-	A	2749453	7	5	96	1	0	1	1	0	0	0	0	0	10089	1299	45	0	1134	0	MYLK4	6	2749453	Frame_Shift_Ins	INS	-	TCGA-DC-6157-01A-11D-1657-10		2749453	168365614	62	26008										
RREB1	6239	hgsc.bcm.edu	37	chr6	7231301	7231301	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggggcccagcggaatcctggAaagccccatggcccctgctc	13	16	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:7231301A>T	ENST00000349384.6	+	10	3283	c.2969A>T	c.(2968-2970)gAa>gTa	p.E990V	RREB1_ENST00000334984.6_Missense_Mutation_p.E990V|RREB1_ENST00000379933.3_Missense_Mutation_p.E990V|RREB1_ENST00000379938.2_Missense_Mutation_p.E990V	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	990	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGAATCCTGGAAAGCCCCATG	0.682																																																0			6											16	20	19					6																	7231301		2199	4293	6492	7176300	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2969A>T	6.37:g.7231301A>T	ENSP00000305560:p.Glu990Val		7176300	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.066712	0.76301	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.13089	2.75;2.7;2.75;2.62	5.74	4.58	0.56647	.	0.532999	0.17612	N	0.168044	T	0.11410	0.0278	L	0.50333	1.59	0.33069	D	0.535183	P;P;P	0.50710	0.912;0.938;0.879	P;P;P	0.51742	0.678;0.601;0.572	T	0.04153	-1.0973	10	0.44086	T	0.13	-9.4713	11.7947	0.52093	0.9313:0.0:0.0687:0.0	.	990;990;990	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	V	990	ENSP00000369265:E990V;ENSP00000369270:E990V;ENSP00000305560:E990V;ENSP00000335574:E990V	ENSP00000335574:E990V	E	+	2	0	RREB1	7176300	0.974000	0.33945	0.028000	0.17463	0.391000	0.30476	2.611000	0.46334	0.992000	0.38840	-0.290000	0.09829	GAA		0.682	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7231301	A	T	7231301	3	4	96	1	0	0	0	0	1	0	0	0	13716	246	9	5	2995	5	RREB1	6	7231301	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	4481848	7231301	163883766	63	26009										
MAK	4117	hgsc.bcm.edu	37	chr6	10764744	10764744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cccatgcactgagggaatggGctgtgcacggttcacaatat	12	10	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:10764744G>A	ENST00000313243.2	-	14	2195	c.1813C>T	c.(1813-1815)Ccc>Tcc	p.P605S	MAK_ENST00000354489.2_Missense_Mutation_p.P605S|MAK_ENST00000538030.1_3'UTR|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000474039.1_Missense_Mutation_p.P605S|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	605					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				GAGGGAATGGGCTGTGCACGG	0.488																																																0			6											89	88	88					6																	10764744		2203	4300	6503	10872730	SO:0001583	missense	57538				CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1813C>T	6.37:g.10764744G>A	ENSP00000313021:p.Pro605Ser		10872730	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.938538	0.34189	.	.	ENSG00000111837	ENST00000313243;ENST00000354489	T;T	0.73897	-0.79;-0.79	5.76	4.87	0.63330	.	0.234953	0.43579	D	0.000541	T	0.58666	0.2138	L	0.55103	1.725	0.80722	D	1	B	0.28439	0.212	B	0.28139	0.086	T	0.60444	-0.7262	10	0.37606	T	0.19	.	15.5767	0.76397	0.0:0.2604:0.7396:0.0	.	605	P20794	MAK_HUMAN	S	605	ENSP00000313021:P605S;ENSP00000346484:P605S	ENSP00000313021:P605S	P	-	1	0	MAK	10872730	1.000000	0.71417	0.975000	0.42487	0.437000	0.31866	2.289000	0.43523	1.373000	0.46208	0.655000	0.94253	CCC		0.488	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		A	10764744	G	A	10764744	3	1	96	1	0	0	0	0	1	0	0	0	9227	1203	42	3	62	3	MAK	6	10764744	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3533443	10764744	160350323	64	26010										
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24581175	24581175	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggcttaacagtgacattgaCaaatccttctccaaaggcgt	8	10	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:24581175C>A	ENST00000378214.3	-	7	1782	c.1258G>T	c.(1258-1260)Gtc>Ttc	p.V420F	KIAA0319_ENST00000537886.1_Missense_Mutation_p.V420F|KIAA0319_ENST00000535378.1_Missense_Mutation_p.V411F|KIAA0319_ENST00000430948.2_Missense_Mutation_p.V375F|KIAA0319_ENST00000543707.1_Missense_Mutation_p.V420F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	420	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						GTGACATTGACAAATCCTTCT	0.393											OREG0017229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			6											157	152	154					6																	24581175		2203	4300	6503	24689154	SO:0001583	missense	9856			AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1258G>T	6.37:g.24581175C>A	ENSP00000367459:p.Val420Phe	772	24689154	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.704095	0.68615	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.10382	2.92;2.88;2.93;2.89;2.89	4.53	2.56	0.30785	PKD/Chitinase domain (1);	0.114832	0.37095	N	0.002246	T	0.26231	0.0640	M	0.92555	3.32	0.48511	D	0.999668	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.06917	-1.0800	10	0.59425	D	0.04	-12.1434	8.6531	0.34046	0.0:0.7614:0.1493:0.0892	.	420;411;420	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	F	420;411;375;420;420	ENSP00000439700:V420F;ENSP00000442403:V411F;ENSP00000401086:V375F;ENSP00000367459:V420F;ENSP00000437656:V420F	ENSP00000367459:V420F	V	-	1	0	KIAA0319	24689154	1.000000	0.71417	0.993000	0.49108	0.943000	0.58893	2.988000	0.49386	0.411000	0.25702	-0.345000	0.07892	GTC		0.393	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		A	24581175	C	A	24581175	3	1	96	1	0	0	0	0	1	0	0	0	8189	478	17	2	2020	2	KIAA0319	6	24581175	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	13816431	24581175	146533892	65	26011										
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28219605	28219605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcctcggaagcgctggcgggAgcgttcggggccccgagcag	19	13	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:28219605A>G	ENST00000377294.2	-	1	397	c.154T>C	c.(154-156)Tcc>Ccc	p.S52P	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	52					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CGCTGGCGGGAGCGTTCGGGG	0.706																																																0			6											21	26	24					6																	28219605		2187	4279	6466	28327584	SO:0001583	missense	387032			AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"Zinc fingers, C2H2-type", "-", "-", "-"	13854	protein-coding gene	gene with protein product		611643	"zinc finger protein 307", "zinc finger protein 427"	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.154T>C	6.37:g.28219605A>G	ENSP00000366509:p.Ser52Pro		28327584	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.007432	0.54361	.	.	ENSG00000187626	ENST00000377294	T	0.04758	3.56	4.33	3.12	0.35913	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	.	.	.	.	T	0.11324	0.0276	M	0.93106	3.38	0.36851	D	0.887898	D	0.53885	0.963	P	0.58331	0.837	T	0.03863	-1.0997	9	0.33141	T	0.24	.	9.1724	0.37091	0.8158:0.1841:0.0:0.0	.	52	Q969J2	ZKSC4_HUMAN	P	52	ENSP00000366509:S52P	ENSP00000366509:S52P	S	-	1	0	ZKSCAN4	28327584	0.010000	0.17322	0.067000	0.19924	0.277000	0.26821	2.547000	0.45786	0.726000	0.32339	0.533000	0.62120	TCC		0.706	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		G	28219605	A	G	28219605	3	3	96	1	0	0	0	0	1	0	0	0	17728	304	11	4	1503	4	ZKSCAN4	6	28219605	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	3638430	28219605	142895462	66	26012										
DDR1	780	hgsc.bcm.edu	37	chr6	30866794	30866794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcgagaacgcgggggagttcTtccgggaccagggccggcag	18	11	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:30866794T>C	ENST00000324771.8	+	19	3129	c.2581T>C	c.(2581-2583)Ttc>Ctc	p.F861L	DDR1_ENST00000361741.4_Intron|DDR1_ENST00000508312.1_Missense_Mutation_p.F842L|DDR1_ENST00000376568.3_Missense_Mutation_p.F861L|DDR1_ENST00000376567.2_Missense_Mutation_p.F824L|DDR1_ENST00000376569.3_Missense_Mutation_p.F824L|DDR1_ENST00000376570.4_Missense_Mutation_p.F824L|DDR1_ENST00000454612.2_Missense_Mutation_p.F824L|DDR1_ENST00000513240.1_Missense_Mutation_p.F867L|DDR1_ENST00000452441.1_Missense_Mutation_p.F861L|DDR1_ENST00000376575.3_Missense_Mutation_p.F867L|DDR1_ENST00000418800.2_Missense_Mutation_p.F824L|DDR1_ENST00000446312.1_3'UTR			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	861	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			QLTDEQVIENAGEFFRDQGRQ -> SAHRRAGHRERGGVLP GPGPA (in Ref. 6; CAA66871). {ECO:0000305}.	branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	GGGGGAGTTCTTCCGGGACCA	0.617																																																0			6											61	58	59					6																	30866794		2203	4300	6503	30974773	SO:0001583	missense	780			X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.2581T>C	6.37:g.30866794T>C	ENSP00000318217:p.Phe861Leu		30974773	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098384	0.76870	.	.	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240	D;D;D;D;D;D;D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39;-2.39;-2.39;-2.39;-2.39;-2.39;-2.39	4.92	4.92	0.64577	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.78610	0.4310	N	0.04090	-0.28	0.80722	D	1	B;P;P;B	0.41848	0.089;0.675;0.763;0.174	B;P;P;B	0.51974	0.092;0.595;0.686;0.171	D	0.84908	0.0846	10	0.59425	D	0.04	.	12.5342	0.56133	0.0:0.0:0.0:1.0	.	842;325;867;861	B7Z2K0;A2ABL4;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	L	861;824;824;824;867;824;861;861;842;824;867	ENSP00000318217:F861L;ENSP00000407699:F824L;ENSP00000406091:F824L;ENSP00000365753:F824L;ENSP00000365759:F867L;ENSP00000365754:F824L;ENSP00000365752:F861L;ENSP00000405039:F861L;ENSP00000422442:F842L;ENSP00000365751:F824L;ENSP00000427552:F867L	ENSP00000318217:F861L	F	+	1	0	DDR1	30974773	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.942000	0.87708	1.856000	0.53863	0.383000	0.25322	TTC		0.617	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		C	30866794	T	C	30866794	3	2	96	1	0	0	0	0	1	0	0	0	4342	1609	56	4	2661	4	DDR1	6	30866794	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	2647189	30866794	140248273	67	26013										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30919230	30919230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccaatgagaacaccacaacaTccccaacagagtctacagaa	5	14	1	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:30919230T>C	ENST00000462446.1	+	2	3017	c.2989T>C	c.(2989-2991)Tcc>Ccc	p.S997P	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	348						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACCACAACATCCCCAACAGA	0.507																																																0			6											272	263	265					6																	30919230		692	1591	2283	31027209	SO:0001583	missense	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2989T>C	6.37:g.30919230T>C	ENSP00000417182:p.Ser997Pro		31027209	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	t	10.77	1.445242	0.25987	.	.	ENSG00000168631	ENST00000462446	T	0.50548	0.74	2.48	-4.97	0.03029	.	.	.	.	.	T	0.31167	0.0788	M	0.63428	1.95	0.09310	N	0.999997	D	0.57899	0.981	D	0.68621	0.959	T	0.35450	-0.9788	9	0.28530	T	0.3	.	0.3585	0.00361	0.3228:0.1277:0.1975:0.352	.	997	E9PEI6	.	P	997	ENSP00000417182:S997P	ENSP00000417182:S997P	S	+	1	0	DPCR1	31027209	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	-1.554000	0.02172	-2.625000	0.00437	0.227000	0.17789	TCC		0.507	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		C	30919230	T	C	30919230	3	2	96	1	0	0	0	0	1	0	0	0	4723	1435	50	4	2995	4	DPCR1	6	30919230	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	52436	30919230	140195837	68	26014										
HLA-B	3106	hgsc.bcm.edu	37	chr6	31324917	31324917	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gagcagcaggaggacggttcGgggcgccatgaccagcatct	16	11	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:31324917G>C	ENST00000412585.2	-	1	47	c.19C>G	c.(19-21)Cga>Gga	p.R7G		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	7					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						AGGACGGTTCGGGGCGCCATG	0.682									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																																							0			6											14	12	13					6																	31324917		2100	4078	6178	31432896	SO:0001583	missense	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.19C>G	6.37:g.31324917G>C	ENSP00000399168:p.Arg7Gly		31432896	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	11.58	1.681701	0.29872	.	.	ENSG00000234745	ENST00000412585	T	0.00633	6.08	3.34	0.474	0.16768	.	5.945680	0.01256	N	0.009039	T	0.00412	0.0013	M	0.66506	2.035	0.09310	N	1	P	0.38992	0.653	B	0.37989	0.262	T	0.44159	-0.9346	10	0.72032	D	0.01	.	3.23	0.06745	0.2623:0.227:0.5107:0.0	.	7	P01889	1B07_HUMAN	G	7	ENSP00000399168:R7G	ENSP00000399168:R7G	R	-	1	2	HLA-B	31432896	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-0.153000	0.10144	0.244000	0.21351	0.442000	0.29010	CGA		0.682	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		C	31324917	G	C	31324917	3	2	96	1	0	0	0	0	1	0	0	0	7217	1124	39	5	1097	5	HLA-B	6	31324917	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	405687	31324917	139790150	69	26015										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43221071	43221071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cattggctgtggcaggaacgAgaagtttaactatgtagtga	13	5	0	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:43221071A>G	ENST00000259750.4	+	4	382	c.299A>G	c.(298-300)gAg>gGg	p.E100G	TTBK1_ENST00000304139.5_Missense_Mutation_p.E49G	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GGCAGGAACGAGAAGTTTAAC	0.547																																																0			6											149	124	133					6																	43221071		2203	4300	6503	43329049	SO:0001583	missense	84630			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.299A>G	6.37:g.43221071A>G	ENSP00000259750:p.Glu100Gly		43329049	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.932631	0.52866	.	.	ENSG00000146216	ENST00000393984;ENST00000259750;ENST00000304139	T	0.66280	-0.2	4.76	3.57	0.40892	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063510	0.64402	D	0.000007	T	0.47488	0.1448	N	0.16368	0.405	0.50039	D	0.999841	D	0.71674	0.998	D	0.65443	0.935	T	0.45804	-0.9236	10	0.27082	T	0.32	.	9.7439	0.40435	0.9127:0.0:0.0873:0.0	.	100	Q5TCY1	TTBK1_HUMAN	G	49;100;49	ENSP00000259750:E100G	ENSP00000259750:E100G	E	+	2	0	TTBK1	43329049	1.000000	0.71417	0.917000	0.36280	0.966000	0.64601	8.795000	0.91872	1.766000	0.52107	0.379000	0.24179	GAG		0.547	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			G	43221071	A	G	43221071	3	3	96	1	0	0	0	0	1	0	0	0	16716	304	11	4	309	4	TTBK1	6	43221071	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	11896154	43221071	127893996	70	26016										
LRRC1	55227	hgsc.bcm.edu	37	chr6	53778763	53778763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atgtcctggatgtggcagggAacaggtaagcctgttgtagt	15	6	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:53778763A>G	ENST00000370888.1	+	11	1379	c.1102A>G	c.(1102-1104)Aac>Gac	p.N368D		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	368						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		TGTGGCAGGGAACAGGTAAGC	0.448																																																0			6											58	58	58					6																	53778763		1969	4163	6132	53886722	SO:0001583	missense	55227			AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1102A>G	6.37:g.53778763A>G	ENSP00000359925:p.Asn368Asp		53886722	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436751	0.83885	.	.	ENSG00000137269	ENST00000370888	D	0.89196	-2.48	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.95500	0.8538	H	0.96365	3.81	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.96616	0.9456	10	0.72032	D	0.01	.	13.5688	0.61834	1.0:0.0:0.0:0.0	.	368	Q9BTT6	LRRC1_HUMAN	D	368	ENSP00000359925:N368D	ENSP00000359925:N368D	N	+	1	0	LRRC1	53886722	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	8.687000	0.91255	1.996000	0.58369	0.533000	0.62120	AAC		0.448	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		G	53778763	A	G	53778763	3	3	96	1	0	0	0	0	1	0	0	0	8995	246	9	4	1144	4	LRRC1	6	53778763	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	10557692	53778763	117336304	71	26017										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70410693	70410693	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	catatgccaatatttcgaatTcctgccattgaagtaaaaat	5	8	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:70410693T>C	ENST00000370577.3	-	12	1381	c.1152A>G	c.(1150-1152)ggA>ggG	p.G384G	LMBRD1_ENST00000370570.1_Silent_p.G311G	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	384					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						TATTTCGAATTCCTGCCATTG	0.239																																																0			6											16	17	17					6																	70410693		2145	4228	6373	70467414	SO:0001819	synonymous_variant	55788			AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1152A>G	6.37:g.70410693T>C			70467414	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Silent	SNP	ENST00000370577.3	37	CCDS4969.1																																																																																				0.239	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		C	70410693	T	C	70410693	2	2	96	1	0	0	0	0	0	0	0	1	8866	1770	62	4		4	LMBRD1	6	70410693	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	16631930	70410693	100704374	72	26018										
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84913786	84913786	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gtcaacggtgcaccaacataCtcatcttcaaaatcatcact	4	13	6	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:84913786C>T	ENST00000403245.3	-	7	714	c.600G>A	c.(598-600)gaG>gaA	p.E200E	KIAA1009_ENST00000257766.4_Silent_p.E124E	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		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)		CACCAACATACTCATCTTCAA	0.328																																																0			6											99	101	100					6																	84913786		2203	4299	6502	84970505	SO:0001819	synonymous_variant	22832																														ENST00000403245.3:c.600G>A	6.37:g.84913786C>T			84970505		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																				0.328	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84913786	C	T	84913786	2	4	96	1	0	0	0	0	0	0	0	1	8224	564	20	3		3	KIAA1009	6	84913786	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	14503093	84913786	86201281	73	26019										
CDK19	23097	hgsc.bcm.edu	37	chr6	111136299	111136299	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caaacaaatcctccacccgcTcccgctccgccgccagcttc	5	22	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:111136299T>C	ENST00000368911.3	-	1	220	c.41A>G	c.(40-42)gAg>gGg	p.E14G	CDK19_ENST00000323817.3_Intron|CDK19_ENST00000497709.1_Intron	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	14							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						CTCCACCCGCTCCCGCTCCGC	0.627																																																0			6											94	83	87					6																	111136299		2203	4300	6503	111242992	SO:0001583	missense	0			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"Cyclin-dependent kinases"	19338	protein-coding gene	gene with protein product		614720	"cyclin-dependent kinase (CDC2-like) 11", "cell division cycle 2-like 6 (CDK8-like)"	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.41A>G	6.37:g.111136299T>C	ENSP00000357907:p.Glu14Gly		111242992	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897845	0.72639	.	.	ENSG00000155111	ENST00000368911	T	0.62498	0.02	3.43	3.43	0.39272	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40619	0.1124	L	0.52573	1.65	0.80722	D	1	B	0.34161	0.439	B	0.33521	0.165	T	0.45614	-0.9249	10	0.39692	T	0.17	-1.5891	12.0191	0.53333	0.0:0.0:0.0:1.0	.	14	Q9BWU1	CDK19_HUMAN	G	14	ENSP00000357907:E14G	ENSP00000357907:E14G	E	-	2	0	CDK19	111242992	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.761000	0.74945	1.560000	0.49568	0.454000	0.30748	GAG		0.627	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076		C	111136299	T	C	111136299	3	2	96	1	0	0	0	0	1	0	0	0	3141	1551	54	4	1519	4	CDK19	6	111136299	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	26222513	111136299	59978768	74	26020										
AHI1	54806	hgsc.bcm.edu	37	chr6	135644340	135644340	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctggaaaataaccttcctgTccctttcctatgctgccata	6	13	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:135644340T>C	ENST00000367800.4	-	23	3504	c.3288A>G	c.(3286-3288)ggA>ggG	p.G1096G	AHI1_ENST00000417892.2_Silent_p.G450G|AHI1_ENST00000457866.2_Silent_p.G1096G	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1096	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		AACCTTCCTGTCCCTTTCCTA	0.408																																																0			6											110	105	107					6																	135644340		1903	4098	6001	135686033	SO:0001819	synonymous_variant	54806			AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3288A>G	6.37:g.135644340T>C			135686033	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Silent	SNP	ENST00000367800.4	37	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	T	8.599	0.886436	0.17540	.	.	ENSG00000135541	ENST00000367799	.	.	.	6.06	2.24	0.28232	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15037	-1.0451	4	.	.	.	-20.8423	2.6852	0.05105	0.1199:0.1345:0.1248:0.6209	.	.	.	.	G	596	.	.	D	-	2	0	AHI1	135686033	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.770000	0.26618	0.150000	0.19136	0.533000	0.62120	GAC		0.408	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135644340	T	C	135644340	2	2	96	1	0	0	0	0	0	0	0	1	413	1654	58	4		4	AHI1	6	135644340	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	24508041	135644340	35470727	75	26021										
TXLNB	167838	hgsc.bcm.edu	37	chr6	139591742	139591742	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gaggagctttaacttcttttGctcagtacgatgttcatcca	8	9	3	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:139591742G>T	ENST00000358430.3	-	4	770	c.538C>A	c.(538-540)Caa>Aaa	p.Q180K	RP11-445F6.2_ENST00000441249.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	180						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		AACTTCTTTTGCTCAGTACGA	0.408																																																0			6											139	130	133					6																	139591742		2203	4300	6503	139633435	SO:0001583	missense	167838				CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.538C>A	6.37:g.139591742G>T	ENSP00000351206:p.Gln180Lys		139633435	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	37	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524009	0.85600	.	.	ENSG00000164440	ENST00000358430	T	0.27890	1.64	5.6	5.6	0.85130	.	0.048088	0.85682	D	0.000000	T	0.31575	0.0801	L	0.49126	1.545	0.53688	D	0.999978	P	0.48407	0.91	P	0.49999	0.628	T	0.00697	-1.1605	9	.	.	.	-20.7686	19.9884	0.97356	0.0:0.0:1.0:0.0	.	180	Q8N3L3	TXLNB_HUMAN	K	180	ENSP00000351206:Q180K	.	Q	-	1	0	TXLNB	139633435	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.874000	0.87199	2.809000	0.96659	0.655000	0.94253	CAA		0.408	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		T	139591742	G	T	139591742	3	4	96	1	0	0	0	0	1	0	0	0	16828	1328	46	2	1544	2	TXLNB	6	139591742	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3947402	139591742	31523325	76	26022										
GRM1	2911	hgsc.bcm.edu	37	chr6	146720306	146720306	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gggctcaggtgatcattgccTcaattctgattagtgtgcaa	11	8	4	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr6:146720306T>C	ENST00000282753.1	+	7	2366	c.2131T>C	c.(2131-2133)Tca>Cca	p.S711P	GRM1_ENST00000355289.4_Missense_Mutation_p.S711P|GRM1_ENST00000507907.1_Missense_Mutation_p.S711P|GRM1_ENST00000492807.2_Missense_Mutation_p.S711P|GRM1_ENST00000392299.2_Missense_Mutation_p.S711P|GRM1_ENST00000361719.2_Missense_Mutation_p.S711P			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	711					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GATCATTGCCTCAATTCTGAT	0.502																																																0			6											119	114	116					6																	146720306		2203	4300	6503	146761999	SO:0001583	missense	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2131T>C	6.37:g.146720306T>C	ENSP00000282753:p.Ser711Pro		146761999	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.363635	0.61513	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34;-2.34;-2.34	5.51	5.51	0.81932	GPCR, family 3, C-terminal (2);	0.105668	0.64402	D	0.000002	T	0.79701	0.4491	N	0.04705	-0.18	0.47862	D	0.999533	P;D;P	0.62365	0.94;0.991;0.892	P;P;P	0.60473	0.601;0.875;0.477	D	0.83848	0.0261	10	0.35671	T	0.21	.	15.6147	0.76756	0.0:0.0:0.0:1.0	.	711;711;711	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	P	711	ENSP00000354896:S711P;ENSP00000376119:S711P;ENSP00000424095:S711P;ENSP00000282753:S711P;ENSP00000347437:S711P;ENSP00000425599:S711P	ENSP00000282753:S711P	S	+	1	0	GRM1	146761999	1.000000	0.71417	0.971000	0.41717	0.890000	0.51754	6.289000	0.72696	2.104000	0.64026	0.477000	0.44152	TCA		0.502	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		C	146720306	T	C	146720306	3	2	96	1	0	0	0	0	1	0	0	0	6817	1551	54	4	2157	4	GRM1	6	146720306	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	7128564	146720306	24394761	77	26023										
LFNG	3955	hgsc.bcm.edu	37	chr7	2552885	2552885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggacggacagatggacagatGgatggatggatggatggatg	19	3	0	2	rs61564232		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:2552885G>A	ENST00000402506.1	+	2	268	c.142G>A	c.(142-144)Gga>Aga	p.G48R		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		atggacagatggatggatgga	0.567																																																0			7											116	119	118					7																	2552885		1568	3582	5150	2519411	SO:0001583	missense	3955			BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.142G>A	7.37:g.2552885G>A	ENSP00000385764:p.Gly48Arg		2519411	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	37	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.813490	0.32053	.	.	ENSG00000106003	ENST00000402506	T	0.39787	1.06	2.17	-0.389	0.12455	.	.	.	.	.	T	0.24392	0.0591	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.22695	-1.0209	7	0.30854	T	0.27	.	4.4118	0.11436	0.6437:0.0:0.3563:0.0	.	.	.	.	R	48	ENSP00000385764:G48R	ENSP00000385764:G48R	G	+	1	0	LFNG	2519411	0.015000	0.18098	0.002000	0.10522	0.006000	0.05464	0.517000	0.22832	-0.065000	0.13021	-0.458000	0.05436	GGA		0.567	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304		A	2552885	G	A	2552885	3	1	96	1	0	0	0	0	1	0	0	0	8759	1349	47	3	148	3	LFNG	7	2552885	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10		2552885	156585778	78	26024										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21639550	21639550	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gaagaatacagagaaacaatTgaaaccggcaccgttttttc	8	8	0	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:21639550T>G	ENST00000409508.3	+	15	2844	c.2813T>G	c.(2812-2814)tTg>tGg	p.L938W	DNAH11_ENST00000328843.6_Missense_Mutation_p.L938W	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	938	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GAGAAACAATTGAAACCGGCA	0.398									Kartagener syndrome																																							0			7											87	82	83					7																	21639550		1837	4076	5913	21606075	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.2813T>G	7.37:g.21639550T>G	ENSP00000475939:p.Leu938Trp		21606075	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	12.15	1.852563	0.32699	.	.	ENSG00000105877	ENST00000328843	T	0.24151	1.87	5.58	3.21	0.36854	.	0.618279	0.14917	N	0.290903	T	0.37156	0.0993	.	.	.	0.09310	N	0.999995	D	0.61697	0.99	P	0.54889	0.763	T	0.12218	-1.0556	9	0.51188	T	0.08	.	10.0773	0.42368	0.0:0.127:0.0:0.873	.	938	Q96DT5	DYH11_HUMAN	W	938	ENSP00000330671:L938W	ENSP00000330671:L938W	L	+	2	0	DNAH11	21606075	0.002000	0.14202	0.187000	0.23214	0.109000	0.19521	0.144000	0.16135	0.494000	0.27859	0.459000	0.35465	TTG		0.398	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21639550	T	G	21639550	3	3	96	1	0	0	0	0	1	0	0	0	4610	1821	63	4	2871	4	DNAH11	7	21639550	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	19086665	21639550	137499113	79	26025										
HOXA7	3204	hgsc.bcm.edu	37	chr7	27194724	27194724	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggcgctcggtgaggcagagcGcgtgggcgatttcaatgcgg	19	9	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:27194724G>A	ENST00000242159.3	-	2	630	c.497C>T	c.(496-498)gCg>gTg	p.A166V	HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000524304.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	166					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						GAGGCAGAGCGCGTGGGCGAT	0.617																																																0			7											92	101	98					7																	27194724		2203	4300	6503	27161249	SO:0001583	missense	23054				CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.497C>T	7.37:g.27194724G>A	ENSP00000242159:p.Ala166Val		27161249	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573742	0.86542	.	.	ENSG00000122592	ENST00000242159	D	0.96265	-3.96	4.96	4.96	0.65561	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96106	0.8731	L	0.42245	1.32	0.80722	D	1	P	0.42785	0.79	P	0.51229	0.663	D	0.96109	0.9075	10	0.48119	T	0.1	.	18.2675	0.90056	0.0:0.0:1.0:0.0	.	166	P31268	HXA7_HUMAN	V	166	ENSP00000242159:A166V	ENSP00000242159:A166V	A	-	2	0	HOXA7	27161249	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.697000	0.98697	2.324000	0.78689	0.456000	0.33151	GCG		0.617	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			A	27194724	G	A	27194724	3	1	96	1	0	0	0	0	1	0	0	0	7318	1087	38	1	199	1	HOXA7	7	27194724	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	5555174	27194724	131943939	80	26026										
ANLN	54443	hgsc.bcm.edu	37	chr7	36459854	36459854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tccaaaaccaggaaaattccAaagaactcgtgtccctcgag	7	12	0	1	rs267601502		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:36459854A>G	ENST00000265748.2	+	11	2167	c.1946A>G	c.(1945-1947)cAa>cGa	p.Q649R	ANLN_ENST00000396068.2_Missense_Mutation_p.Q612R	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	649	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.Q649R(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GGAAAATTCCAAAGAACTCGT	0.433																																																1	Substitution - Missense(1)	skin(1)	7											110	107	108					7																	36459854		2203	4300	6503	36426379	SO:0001583	missense	54443			AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.1946A>G	7.37:g.36459854A>G	ENSP00000265748:p.Gln649Arg		36426379	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	37	CCDS5447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.181919|4.181919	0.78677|0.78677	.|.	.|.	ENSG00000011426|ENSG00000011426	ENST00000446635|ENST00000265748;ENST00000396068	.|T;T	.|0.15256	.|2.44;2.55	5.84|5.84	3.35|3.35	0.38373|0.38373	.|.	.|0.049328	.|0.85682	.|D	.|0.000000	T|T	0.31918|0.31918	0.0812|0.0812	L|L	0.55481|0.55481	1.735|1.735	0.48236|0.48236	D|D	0.999617|0.999617	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.91635	.|0.959;0.998;0.999;0.998	T|T	0.02933|0.02933	-1.1092|-1.1092	5|10	.|0.72032	.|D	.|0.01	-9.0813|-9.0813	7.2941|7.2941	0.26383|0.26383	0.7823:0.1446:0.0731:0.0|0.7823:0.1446:0.0731:0.0	.|.	.|526;611;612;649	.|B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.|.;.;.;ANLN_HUMAN	E|R	8|649;612	.|ENSP00000265748:Q649R;ENSP00000379380:Q612R	.|ENSP00000265748:Q649R	K|Q	+|+	1|2	0|0	ANLN|ANLN	36426379|36426379	1.000000|1.000000	0.71417|0.71417	0.955000|0.955000	0.39395|0.39395	0.997000|0.997000	0.91878|0.91878	4.188000|4.188000	0.58351|0.58351	1.054000|1.054000	0.40438|0.40438	0.533000|0.533000	0.62120|0.62120	AAA|CAA		0.433	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		G	36459854	A	G	36459854	3	3	96	1	0	0	0	0	1	0	0	0	694	130	5	4	1988	4	ANLN	7	36459854	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	9265130	36459854	122678809	81	26027										
ELMO1	9844	hgsc.bcm.edu	37	chr7	36934508	36934508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gttcatcctctcggactggcGgattttcaggatctcagtgt	11	10	4	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:36934508G>A	ENST00000310758.4	-	17	2199	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	ELMO1_ENST00000442504.1_Missense_Mutation_p.R518C|ELMO1_ENST00000341056.3_Missense_Mutation_p.R220C|ELMO1_ENST00000396040.2_Missense_Mutation_p.R38C|ELMO1_ENST00000396045.3_Missense_Mutation_p.R38C|ELMO1_ENST00000448602.1_Missense_Mutation_p.R518C	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	518					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						TCGGACTGGCGGATTTTCAGG	0.478																																																0			7											188	168	175					7																	36934508		2203	4300	6503	36901033	SO:0001583	missense	9844			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1552C>T	7.37:g.36934508G>A	ENSP00000312185:p.Arg518Cys		36901033	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	37	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	G	34	5.394510	0.96009	.	.	ENSG00000155849	ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.71169	0.3308	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.72795	-0.4185	10	0.66056	D	0.02	.	20.0401	0.97581	0.0:0.0:1.0:0.0	.	518	Q92556	ELMO1_HUMAN	C	220;38;518;422;38;518;518	ENSP00000342142:R220C;ENSP00000379360:R38C;ENSP00000312185:R518C;ENSP00000379355:R38C;ENSP00000406952:R518C;ENSP00000394458:R518C	ENSP00000312185:R518C	R	-	1	0	ELMO1	36901033	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.813000	0.99286	2.805000	0.96524	0.655000	0.94253	CGC		0.478	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		A	36934508	G	A	36934508	3	1	96	1	0	0	0	0	1	0	0	0	5078	1116	39	1	655	1	ELMO1	7	36934508	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	474654	36934508	122204155	82	26028										
RFC2	5982	hgsc.bcm.edu	37	chr7	73668637	73668637	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggccggcgctgccgggggccTtgctgaaggcaggggcaggg	22	11	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:73668637T>C	ENST00000055077.3	-	1	137	c.77A>G	c.(76-78)aAg>aGg	p.K26R	RFC2_ENST00000352131.3_Missense_Mutation_p.K26R	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	26					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						GCCGGGGGCCTTGCTGAAGGC	0.701																																																0			7											26	23	24					7																	73668637		2201	4298	6499	73306573	SO:0001583	missense	5982				CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.77A>G	7.37:g.73668637T>C	ENSP00000055077:p.Lys26Arg		73306573	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	37	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990022	0.35131	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.18657	2.2;2.47	4.89	2.51	0.30379	.	0.697856	0.14749	N	0.300700	T	0.16085	0.0387	L	0.50333	1.59	0.26296	N	0.978049	B;B	0.26744	0.128;0.158	B;B	0.20384	0.01;0.029	T	0.24905	-1.0147	10	0.20519	T	0.43	-33.8697	6.489	0.22105	0.0:0.1927:0.0:0.8073	.	26;26	Q75MT5;P35250	.;RFC2_HUMAN	R	26	ENSP00000275627:K26R;ENSP00000055077:K26R	ENSP00000055077:K26R	K	-	2	0	RFC2	73306573	0.722000	0.28017	0.863000	0.33907	0.049000	0.14656	0.422000	0.21296	0.445000	0.26639	0.533000	0.62120	AAG		0.701	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		C	73668637	T	C	73668637	3	2	96	1	0	0	0	0	1	0	0	0	13282	1609	56	4	1031	4	RFC2	7	73668637	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	36734129	73668637	85470026	83	26029										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77583124	77583124	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agattatatgggcttacaatGaatccgctgctttataacat	7	7	0	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:77583124G>T	ENST00000248550.7	+	18	2326	c.2250G>T	c.(2248-2250)atG>atT	p.M750I	PHTF2_ENST00000422959.2_Missense_Mutation_p.M716I|PHTF2_ENST00000275575.7_Missense_Mutation_p.M660I|PHTF2_ENST00000416283.2_Missense_Mutation_p.M716I|PHTF2_ENST00000307305.8_Missense_Mutation_p.M712I			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	750					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						GGCTTACAATGAATCCGCTGC	0.373																																																0			7											175	165	168					7																	77583124		1840	4083	5923	77421060	SO:0001583	missense	57157			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.2250G>T	7.37:g.77583124G>T	ENSP00000248550:p.Met750Ile		77421060	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	G	29.6	5.020485	0.93462	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.72914	0.3520	L	0.42245	1.32	0.80722	D	1	P;D;P;D	0.64830	0.872;0.962;0.95;0.994	P;D;P;P	0.66716	0.611;0.946;0.621;0.85	T	0.70281	-0.4915	9	0.36615	T	0.2	-18.4938	19.1966	0.93691	0.0:0.0:1.0:0.0	.	660;716;750;712	Q8N3S3-4;Q8N3S3-2;Q8N3S3;Q8N3S3-3	.;.;PHTF2_HUMAN;.	I	716;716;712;660;716;750	.	ENSP00000248550:M750I	M	+	3	0	PHTF2	77421060	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.829000	0.86735	2.532000	0.85374	0.563000	0.77884	ATG		0.373	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		T	77583124	G	T	77583124	3	4	96	1	0	0	0	0	1	0	0	0	11894	1290	45	2	2268	2	PHTF2	7	77583124	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3914487	77583124	81555539	84	26030										
ALKBH4	54784	hgsc.bcm.edu	37	chr7	102100076	102100076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcctccgtccagactgggagAgcttccaggggtcacggtcc	13	14	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:102100076A>G	ENST00000292566.3	-	2	335	c.296T>C	c.(295-297)cTc>cCc	p.L99P		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	99					actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						AGACTGGGAGAGCTTCCAGGG	0.647																																																0			7											107	98	101					7																	102100076		2203	4300	6503	101887081	SO:0001583	missense	54784			BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"Alkylation repair homologs"	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.296T>C	7.37:g.102100076A>G	ENSP00000292566:p.Leu99Pro		101887081	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	37	CCDS5723.1	.	.	.	.	.	.	.	.	.	.	A	8.416	0.845354	0.16963	.	.	ENSG00000160993	ENST00000292566	T	0.43688	0.94	3.99	1.51	0.23008	.	0.712770	0.13565	N	0.378441	T	0.24470	0.0593	N	0.20401	0.57	0.58432	D	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.05007	-1.0912	10	0.27785	T	0.31	-23.1124	7.057	0.25106	0.6894:0.0:0.3106:0.0	.	99	Q9NXW9	ALKB4_HUMAN	P	99	ENSP00000292566:L99P	ENSP00000292566:L99P	L	-	2	0	ALKBH4	101887081	0.138000	0.22547	0.979000	0.43373	0.849000	0.48306	0.524000	0.22940	0.121000	0.18284	0.459000	0.35465	CTC		0.647	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621		G	102100076	A	G	102100076	3	3	96	1	0	0	0	0	1	0	0	0	529	304	11	4	620	4	ALKBH4	7	102100076	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	24516952	102100076	57038587	85	26031										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142566366	142566366	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgcagatgaccttcctgggcCgggccgcagtgctgggtcag	16	12	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:142566366C>A	ENST00000392957.2	+	15	2942	c.2155C>A	c.(2155-2157)Cgg>Agg	p.R719R	EPHB6_ENST00000442129.1_Silent_p.R719R|EPHB6_ENST00000411471.2_Silent_p.R442R	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	719	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.R704W(2)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CTTCCTGGGCCGGGCCGCAGT	0.692																																																2	Substitution - Missense(2)	pancreas(1)|skin(1)	7											26	27	27					7																	142566366		2203	4298	6501	142276488	SO:0001819	synonymous_variant	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.2155C>A	7.37:g.142566366C>A			142276488	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																				0.692	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			A	142566366	C	A	142566366	2	1	96	1	0	0	0	0	0	0	0	1	5191	643	23	2		2	EPHB6	7	142566366	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	40466290	142566366	16572297	86	26032										
SSPO	23145	hgsc.bcm.edu	37	chr7	149521570	149521570	+	RNA	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggcccctgcctccaggactgCcctagaggagcactggctcc	12	17	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:149521570C>G	ENST00000378016.2	+	0	13649							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCCAGGACTGCCCTAGAGGAG	0.687																																																0			7											24	29	28					7																	149521570		2034	4165	6199	149152503			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149521570C>G			149152503	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149521570	C	G	149521570	1	3	96	0	1	0	0	0	0	0	0	0	15228	739	26	5		5	SSPO	7	149521570	RNA	SNP	C	TCGA-DC-6157-01A-11D-1657-10	6955204	149521570	9617093	87	26033										
ABP1	26	hgsc.bcm.edu	37	chr7	150554581	150554581	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caggtcctgaacgtgcacttCggcggagagcgcattgccta	13	12	0	2	rs553084982		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:150554581C>T	ENST00000493429.1	+	4	1607	c.1023C>T	c.(1021-1023)ttC>ttT	p.F341F	AOC1_ENST00000360937.4_Silent_p.F341F|AOC1_ENST00000416793.2_Silent_p.F341F|AOC1_ENST00000467291.1_Silent_p.F341F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	341					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	ACGTGCACTTCGGCGGAGAGC	0.632																																																0			7											51	53	53					7																	150554581		2203	4299	6502	150185514	SO:0001819	synonymous_variant	28988			AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1023C>T	7.37:g.150554581C>T			150185514	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																				0.632	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		T	150554581	C	T	150554581	2	4	96	1	0	0	0	0	0	0	0	1	98	883	31	1		1	ABP1	7	150554581	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	1033011	150554581	8584082	88	26034										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154760440	154760440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cagggcatgctgctgctgaaAgggctggagctgctgctgag	17	9	0	2	rs550122265	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:154760440A>G	ENST00000404141.1	-	7	1625	c.1471T>C	c.(1471-1473)Ttt>Ctt	p.F491L	PAXIP1_ENST00000397192.1_Missense_Mutation_p.F491L|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	491	Gln-rich.			Missing (in Ref. 4; AAB91434). {ECO:0000305}.	adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		tgctgctgaaagggctggagc	0.597																																																0			7											31	37	35					7																	154760440		1807	3276	5083	154391373	SO:0001583	missense	22976			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1471T>C	7.37:g.154760440A>G	ENSP00000384048:p.Phe491Leu		154391373	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	A	3.265	-0.150294	0.06585	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000323199	D;D	0.89485	-2.52;-2.52	4.66	3.51	0.40186	.	0.000000	0.36066	U	0.002815	T	0.73024	0.3534	N	0.11201	0.11	0.24176	N	0.9956	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.55780	-0.8087	10	0.10377	T	0.69	-5.7397	6.5946	0.22666	0.7961:0.0:0.2039:0.0	.	444;400;457;491	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	L	491;491;444	ENSP00000384048:F491L;ENSP00000380376:F491L	ENSP00000319149:F444L	F	-	1	0	PAXIP1	154391373	0.974000	0.33945	0.106000	0.21319	0.868000	0.49771	2.004000	0.40854	0.645000	0.30675	0.528000	0.53228	TTT		0.597	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		G	154760440	A	G	154760440	3	3	96	1	0	0	0	0	1	0	0	0	11518	72	3	4	1798	4	PAXIP1	7	154760440	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	4205859	154760440	4378223	89	26035										
NOM1	64434	hgsc.bcm.edu	37	chr7	156762248	156762248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctgacaacccaaagctggggGtgttacgtgagggtttgaag	15	7	0	3	rs12919	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:156762248G>A	ENST00000275820.3	+	11	2449	c.2434G>A	c.(2434-2436)Gtg>Atg	p.V812M		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	812			V -> M (in dbSNP:rs12919).			nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAAGCTGGGGGTGTTACGTGA	0.512													A|||	2411	0.48143	0.556	0.536	5008	,	,		16487	0.2778		0.5706	False		,,,				2504	0.4601															0			7						A	MET/VAL	2437,1969	555.5+/-379.3	672,1093,438	107	109	108		2434	-3.1	0	7	dbSNP_52	108	4907,3693	529.1+/-381.5	1388,2131,781	yes	missense	NOM1	NM_138400.1	21	2060,3224,1219	AA,AG,GG		42.9419,44.6891,43.5338	benign	812/861	156762248	7344,5662	2203	4300	6503	156455009	SO:0001583	missense	64434			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2434G>A	7.37:g.156762248G>A	ENSP00000275820:p.Val812Met		156455009	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1047	0.4793956043956044	274	0.556910569105691	199	0.5497237569060773	154	0.2692307692307692	420	0.554089709762533	A	0.021	-1.421065	0.01126	0.553109	0.570581	ENSG00000146909	ENST00000275820	T	0.11169	2.8	5.41	-3.13	0.05266	.	0.201867	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.20009	-1.0288	9	0.15066	T	0.55	-9.8241	3.0886	0.06286	0.4413:0.1173:0.3376:0.1038	rs12919;rs17354962;rs56648938;rs61096186;rs12919	812	Q5C9Z4	NOM1_HUMAN	M	812	ENSP00000275820:V812M	ENSP00000275820:V812M	V	+	1	0	NOM1	156455009	0.011000	0.17503	0.001000	0.08648	0.280000	0.26924	-0.199000	0.09491	-1.325000	0.02269	-0.516000	0.04426	GTG		0.512	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		A	156762248	G	A	156762248	3	1	96	1	0	0	0	0	1	0	0	0	10561	1261	44	3	2476	3	NOM1	7	156762248	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	2001808	156762248	2376415	90	26036										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	158109546	158109546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tctgcaacgccacgcgcaggCgctgcagggccacgggcgac	15	16	1	0	rs145815332		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr7:158109546C>T	ENST00000389418.4	-	3	251	c.242G>A	c.(241-243)cGc>cAc	p.R81H	PTPRN2_ENST00000404321.2_Missense_Mutation_p.R104H|PTPRN2_ENST00000409483.1_Intron|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R64H|PTPRN2_ENST00000389413.3_Missense_Mutation_p.R81H	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	81					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R81L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	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)		CACGCGCAGGCGCTGCAGGGC	0.642																																																1	Substitution - Missense(1)	lung(1)	7							HIS/ARG,HIS/ARG,HIS/ARG	0,4404		0,0,2202	54	49	50		242,191,242	1.2	0.9	7	dbSNP_134	50	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	29,29,29	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign	81/1016,64/999,81/987	158109546	3,13001	2202	4300	6502	157802307	SO:0001583	missense	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.242G>A	7.37:g.158109546C>T	ENSP00000374069:p.Arg81His		157802307	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	2.554	-0.303442	0.05495	0.0	3.49E-4	ENSG00000155093	ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T	0.03035	4.09;4.07;4.08;4.09	4.88	1.21	0.21127	.	.	.	.	.	T	0.02848	0.0085	N	0.20574	0.59	0.25779	N	0.984756	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.44787	-0.9305	9	0.31617	T	0.26	.	9.0756	0.36519	0.0:0.4239:0.0:0.5761	.	104;81;64;81	Q92932-3;Q92932-2;E9PC57;Q92932	.;.;.;PTPR2_HUMAN	H	81;64;81;104	ENSP00000374064:R81H;ENSP00000374067:R64H;ENSP00000374069:R81H;ENSP00000385464:R104H	ENSP00000374064:R81H	R	-	2	0	PTPRN2	157802307	0.948000	0.32251	0.867000	0.34043	0.042000	0.13812	-0.013000	0.12678	-0.023000	0.13963	-0.312000	0.09012	CGC		0.642	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	158109546	C	T	158109546	3	4	96	1	0	0	0	0	1	0	0	0	12845	768	27	1	2889	1	PTPRN2	7	158109546	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	1347298	158109546	1029117	91	26037										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35542136	35542136	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttcctggacagagtggtcagCctgcaatgttcgctgtggta	13	9	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:35542136C>G	ENST00000404895.2	+	6	1116	c.788C>G	c.(787-789)gCc>gGc	p.A263G	UNC5D_ENST00000416672.1_Missense_Mutation_p.A263G|UNC5D_ENST00000287272.2_Intron|UNC5D_ENST00000420357.1_Intron|UNC5D_ENST00000453357.2_Missense_Mutation_p.A258G	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	263	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GAGTGGTCAGCCTGCAATGTT	0.517																																																0			8											138	128	131					8																	35542136		2203	4300	6503	35661678	SO:0001583	missense	137970			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.788C>G	8.37:g.35542136C>G	ENSP00000385143:p.Ala263Gly		35661678	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	37	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	C	14.24	2.475521	0.43942	.	.	ENSG00000156687	ENST00000404895;ENST00000416672;ENST00000453357	T;T;T	0.55234	0.53;0.53;0.53	5.06	5.06	0.68205	.	0.352028	0.33670	N	0.004667	T	0.31009	0.0783	N	0.10618	0.005	0.80722	D	1	B;B;B	0.25390	0.125;0.082;0.009	B;B;B	0.27887	0.084;0.058;0.025	T	0.15321	-1.0441	10	0.23891	T	0.37	-23.9131	10.4677	0.44618	0.2054:0.6697:0.1249:0.0	.	263;258;263	C9J2B6;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	G	263;263;258	ENSP00000385143:A263G;ENSP00000412652:A263G;ENSP00000394303:A258G	ENSP00000385143:A263G	A	+	2	0	UNC5D	35661678	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.837000	0.48191	2.520000	0.84964	0.655000	0.94253	GCC		0.517	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			G	35542136	C	G	35542136	3	3	96	1	0	0	0	0	1	0	0	0	17035	739	26	5	810	5	UNC5D	8	35542136	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		35542136	110821886	92	26038										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53598018	53598018	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccagtgttaaccagaaatacAtataacttcatgatgattta	5	7	1	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:53598018A>T	ENST00000025008.5	-	3	535	c.12T>A	c.(10-12)taT>taA	p.Y4*	RB1CC1_ENST00000435644.2_Nonsense_Mutation_p.Y4*|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Nonsense_Mutation_p.Y4*	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	4					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CCAGAAATACATATAACTTCA	0.333																																					GBM(180;1701 2102 13475 42023 52570)											0			8											80	72	75					8																	53598018		2195	4298	6493	53760571	SO:0001587	stop_gained	9821			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.12T>A	8.37:g.53598018A>T	ENSP00000025008:p.Tyr4*		53760571	Q86YR4|Q8WVU9|Q92601	Nonsense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	A	41	8.836438	0.98972	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297;ENST00000518468	.	.	.	5.61	4.44	0.53790	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.4779	11.3289	0.49465	0.9286:0.0:0.0714:0.0	.	.	.	.	X	4	.	ENSP00000025008:Y4X	Y	-	3	2	RB1CC1	53760571	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.028000	0.64115	0.948000	0.37687	0.477000	0.44152	TAT		0.333	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53598018	A	T	53598018	4	4	96	1	0	0	0	0	0	1	0	0	13136	224	8	5	4860	5	RB1CC1	8	53598018	Nonsense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	18055882	53598018	92766004	93	26039										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108296974	108296974	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgaataggctcggttcccttCccagtccattaactcaattc	6	13	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:108296974C>T	ENST00000520734.1	-	6	826	c.541G>A	c.(541-543)Gaa>Aaa	p.E181K	ANGPT1_ENST00000520052.1_Missense_Mutation_p.E180K|ANGPT1_ENST00000518386.1_Intron			Q15389	ANGP1_HUMAN	angiopoietin 1	381					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			CGGTTCCCTTCCCAGTCCATT	0.413																																																0			8											152	129	137					8																	108296974		2203	4300	6503	108366150	SO:0001583	missense	284			D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.541G>A	8.37:g.108296974C>T	ENSP00000430750:p.Glu181Lys		108366150	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.883762	0.97062	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000520734;ENST00000520052	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.73	5.73	0.89815	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.087053	0.85682	D	0.000000	T	0.55337	0.1914	M	0.73430	2.235	0.80722	D	1	P;D;D	0.59357	0.528;0.985;0.985	B;P;P	0.59948	0.341;0.866;0.866	T	0.54309	-0.8313	10	0.52906	T	0.07	.	19.8897	0.96925	0.0:1.0:0.0:0.0	.	180;381;381	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	K	381;380;181;180	ENSP00000428340:E381K;ENSP00000297450:E380K;ENSP00000430750:E181K;ENSP00000429349:E180K	ENSP00000297450:E380K	E	-	1	0	ANGPT1	108366150	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.037000	0.70956	2.709000	0.92574	0.650000	0.86243	GAA		0.413	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		T	108296974	C	T	108296974	3	4	96	1	0	0	0	0	1	0	0	0	610	864	30	3	367	3	ANGPT1	8	108296974	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	54698956	108296974	38067048	94	26040										
COLEC10	10584	hgsc.bcm.edu	37	chr8	120118131	120118131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccctaacccactgcaggattCggggtggaatgctagccatg	12	12	0	0	rs115273924	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:120118131C>T	ENST00000332843.2	+	6	576	c.535C>T	c.(535-537)Cgg>Tgg	p.R179W		NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	179	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.R179W(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			CTGCAGGATTCGGGGTGGAAT	0.502													C|||	15	0.00299521	0.0068	0	5008	,	,		19133	0		0	False		,,,				2504	0.0061															1	Substitution - Missense(1)	large_intestine(1)	8						C	TRP/ARG	14,4392	21.2+/-45.6	0,14,2189	104	82	89		535	5.4	1	8	dbSNP_132	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COLEC10	NM_006438.3	101	0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153	probably-damaging	179/278	120118131	15,12991	2203	4300	6503	120187312	SO:0001583	missense	10584			AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"Collectins"	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.535C>T	8.37:g.120118131C>T	ENSP00000332723:p.Arg179Trp		120187312	Q3SYH6|Q6UW19	Missense_Mutation	SNP	ENST00000332843.2	37	CCDS6327.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	19.52	3.842792	0.71488	0.003177	1.16E-4	ENSG00000184374	ENST00000332843	T	0.18174	2.23	5.39	5.39	0.77823	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.89968	3.075	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	T	0.52638	-0.8549	10	0.48119	T	0.1	-13.3309	13.5562	0.61761	0.2585:0.7415:0.0:0.0	.	179	Q9Y6Z7	COL10_HUMAN	W	179	ENSP00000332723:R179W	ENSP00000332723:R179W	R	+	1	2	COLEC10	120187312	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.341000	0.52151	2.692000	0.91855	0.555000	0.69702	CGG		0.502	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381225.1			T	120118131	C	T	120118131	3	4	96	1	0	0	0	0	1	0	0	0	3716	875	31	1	557	1	COLEC10	8	120118131	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	11821157	120118131	26245891	95	26041										
TAF2	6873	hgsc.bcm.edu	37	chr8	120810028	120810028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aaaattcaaagacttcatgaAggtatgatgtggtatgtttc	9	4	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:120810028A>G	ENST00000378164.2	-	7	1149	c.851T>C	c.(850-852)cTt>cCt	p.L284P		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	284					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.L284R(1)		NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GACTTCATGAAGGTATGATGT	0.358																																																1	Substitution - Missense(1)	kidney(1)	8											92	90	91					8																	120810028		2203	4299	6502	120879209	SO:0001583	missense	6873			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.851T>C	8.37:g.120810028A>G	ENSP00000367406:p.Leu284Pro		120879209	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.5|25.5	4.646498|4.646498	0.87958|0.87958	.|.	.|.	ENSG00000064313|ENSG00000064313	ENST00000523904|ENST00000378164	.|T	.|0.05925	.|3.37	6.07|6.07	6.07|6.07	0.98685|0.98685	.|Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	.|0.066316	.|0.64402	.|D	.|0.000007	T|T	0.27278|0.27278	0.0669|0.0669	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.74023	.|0.982	T|T	0.00681|0.00681	-1.1612|-1.1612	5|10	.|0.87932	.|D	.|0	-29.8087|-29.8087	16.6406|16.6406	0.85098|0.85098	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|284	.|Q6P1X5	.|TAF2_HUMAN	L|P	15|284	.|ENSP00000367406:L284P	.|ENSP00000367406:L284P	F|L	-|-	1|2	0|0	TAF2|TAF2	120879209|120879209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.288000|9.288000	0.96055|0.96055	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTC|CTT		0.358	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		G	120810028	A	G	120810028	3	3	96	1	0	0	0	0	1	0	0	0	15563	72	3	4	2828	4	TAF2	8	120810028	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	691897	120810028	25553994	96	26042										
OC90	729330	hgsc.bcm.edu	37	chr8	133051328	133051328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccaagcactctatggcagccTtatcacaggtacacagcagg	9	13	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:133051328T>C	ENST00000443356.2	-	7	586	c.500A>G	c.(499-501)aAg>aGg	p.K167R	OC90_ENST00000603859.1_Missense_Mutation_p.K167R|OC90_ENST00000262283.5_Missense_Mutation_p.K363R|OC90_ENST00000254627.3_Missense_Mutation_p.K167R			Q02509	OC90_HUMAN	otoconin 90	167	Phospholipase A2-like 1.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TATGGCAGCCTTATCACAGGT	0.527																																																0			8											74	81	79					8																	133051328		2043	4212	6255	133120510	SO:0001583	missense	729330			Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.500A>G	8.37:g.133051328T>C	ENSP00000390050:p.Lys167Arg		133120510	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	37		.	.	.	.	.	.	.	.	.	.	T	19.31	3.802411	0.70682	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.25749	1.78;1.78;1.78	4.61	4.61	0.57282	Phospholipase A2 (3);	0.234937	0.37348	N	0.002121	T	0.26484	0.0647	L	0.28649	0.875	0.38279	D	0.942365	P;D	0.56287	0.916;0.975	P;P	0.51079	0.527;0.658	T	0.06427	-1.0827	10	0.23891	T	0.37	-23.8859	13.209	0.59813	0.0:0.0:0.0:1.0	.	167;167	Q02509-2;Q02509	.;OC90_HUMAN	R	167;167;363	ENSP00000254627:K167R;ENSP00000390050:K167R;ENSP00000262283:K363R	ENSP00000254627:K167R	K	-	2	0	RP11-240B13.2;OC90	133120510	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.543000	0.67225	1.728000	0.51552	0.459000	0.35465	AAG		0.527	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		C	133051328	T	C	133051328	3	2	96	1	0	0	0	0	1	0	0	0	10845	1609	56	4	965	4	OC90	8	133051328	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	12241300	133051328	13312694	97	26043										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139160865	139160865	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atcagaagctagtacagttaAgtcactgtacagaaatcctt	7	8	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr8:139160865A>C	ENST00000395297.1	-	14	3516	c.3346T>G	c.(3346-3348)Tta>Gta	p.L1116V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1116										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGTACAGTTAAGTCACTGTAC	0.378										HNSCC(54;0.14)																																						0			8											94	85	88					8																	139160865		2203	4300	6503	139230047	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3346T>G	8.37:g.139160865A>C	ENSP00000378710:p.Leu1116Val		139230047	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	A	12.94	2.087593	0.36855	.	.	ENSG00000147724	ENST00000395297	T	0.15834	2.39	5.78	4.61	0.57282	.	0.168206	0.39274	N	0.001417	T	0.20536	0.0494	L	0.38531	1.155	0.34370	D	0.691972	B;D	0.76494	0.36;0.999	B;D	0.63793	0.22;0.918	T	0.24835	-1.0149	10	0.02654	T	1	-1.2126	7.002	0.24815	0.7751:0.1509:0.074:0.0	.	1116;1116	Q49AJ0-4;Q49AJ0	.;F135B_HUMAN	V	1116	ENSP00000378710:L1116V	ENSP00000378710:L1116V	L	-	1	2	FAM135B	139230047	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	2.665000	0.46791	0.994000	0.38892	-0.323000	0.08544	TTA		0.378	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139160865	A	C	139160865	3	2	96	1	0	0	0	0	1	0	0	0	5465	69	3	4	902	4	FAM135B	8	139160865	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	6109537	139160865	7203157	98	26044										
GLDC	2731	hgsc.bcm.edu	37	chr9	6565391	6565391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctttctggtttaagtaggctCggatagtggccagtccagca	12	9	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:6565391C>T	ENST00000321612.6	-	16	2039	c.1889G>A	c.(1888-1890)cGa>cAa	p.R630Q	snoU13_ENST00000516301.1_RNA|GLDC_ENST00000460457.1_5'UTR	NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	630					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TAAGTAGGCTCGGATAGTGGC	0.537																																																0			9											162	137	145					9																	6565391		2203	4300	6503	6555391	SO:0001583	missense	2731			D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1889G>A	9.37:g.6565391C>T	ENSP00000370737:p.Arg630Gln		6555391	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	37	CCDS34987.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424404	0.62733	.	.	ENSG00000178445	ENST00000321612	D	0.98455	-4.94	5.7	4.7	0.59300	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aromatic amino acid beta-eliminating lyase/threonine aldolase (1);	0.055776	0.64402	D	0.000001	D	0.95294	0.8473	L	0.47190	1.495	0.46874	D	0.999237	B	0.19200	0.034	B	0.24006	0.05	D	0.90128	0.4204	10	0.40728	T	0.16	-9.5588	3.7407	0.08528	0.0:0.664:0.0:0.336	.	630	P23378	GCSP_HUMAN	Q	630	ENSP00000370737:R630Q	ENSP00000370737:R630Q	R	-	2	0	GLDC	6555391	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.173000	0.58249	2.703000	0.92315	0.655000	0.94253	CGA		0.537	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		T	6565391	C	T	6565391	3	4	96	1	0	0	0	0	1	0	0	0	6453	884	31	1	1213	1	GLDC	9	6565391	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		6565391	134648040	99	26045										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73150980	73150980	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gacttgcttctctggaagggAtttcgcaggcttgctgtgtt	13	8	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:73150980A>G	ENST00000377110.3	-	25	5256	c.5013T>C	c.(5011-5013)aaT>aaC	p.N1671N	TRPM3_ENST00000396292.4_Silent_p.N1543N|TRPM3_ENST00000396280.5_Silent_p.N1520N|TRPM3_ENST00000408909.2_Silent_p.N1530N|TRPM3_ENST00000396285.1_Silent_p.N1530N|TRPM3_ENST00000423814.3_Silent_p.N1698N|TRPM3_ENST00000360823.2_Silent_p.N1533N|TRPM3_ENST00000357533.2_Silent_p.N1675N|TRPM3_ENST00000377105.1_Silent_p.N1530N|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000377106.1_Silent_p.N1543N|TRPM3_ENST00000358082.3_Silent_p.N1533N			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1696					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TCTGGAAGGGATTTCGCAGGC	0.562																																																0			9											165	160	162					9																	73150980		2203	4300	6503	72340800	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.5013T>C	9.37:g.73150980A>G			72340800	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377110.3	37	CCDS43835.1	.	.	.	.	.	.	.	.	.	.	A	4.330	0.060675	0.08339	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.77	-1.27	0.09347	.	.	.	.	.	T	0.65984	0.2744	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62258	-0.6892	4	.	.	.	-11.9705	14.5537	0.68086	0.2933:0.0:0.7067:0.0	.	.	.	.	P	1520	.	.	S	-	1	0	TRPM3	72340800	0.998000	0.40836	0.970000	0.41538	0.980000	0.70556	0.553000	0.23391	-0.594000	0.05836	0.533000	0.62120	TCC		0.562	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		G	73150980	A	G	73150980	2	3	96	1	0	0	0	0	0	0	0	1	16627	330	12	4		4	TRPM3	9	73150980	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	66585589	73150980	68062451	100	26046										
GNA14	9630	hgsc.bcm.edu	37	chr9	80144055	80144055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcatggcttgcatggcggtgAatatgttttggtaaaccagc	12	7	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:80144055A>G	ENST00000341700.6	-	2	752	c.239T>C	c.(238-240)tTc>tCc	p.F80S	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	80					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						CATGGCGGTGAATATGTTTTG	0.463																																																0			9											381	323	343					9																	80144055		2203	4300	6503	79333875	SO:0001583	missense	9630			AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.239T>C	9.37:g.80144055A>G	ENSP00000365807:p.Phe80Ser		79333875	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.947291	0.73672	.	.	ENSG00000156049	ENST00000341700	D	0.88509	-2.39	5.92	5.92	0.95590	G protein alpha subunit, helical insertion (2);	0.155416	0.64402	D	0.000019	D	0.94215	0.8143	M	0.86805	2.84	0.48135	D	0.999598	D	0.62365	0.991	D	0.63877	0.919	D	0.94839	0.8003	10	0.87932	D	0	.	12.0916	0.53730	0.8714:0.0:0.0:0.1286	.	80	O95837	GNA14_HUMAN	S	80	ENSP00000365807:F80S	ENSP00000365807:F80S	F	-	2	0	GNA14	79333875	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.226000	0.58606	2.282000	0.76494	0.529000	0.55759	TTC		0.463	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			G	80144055	A	G	80144055	3	3	96	1	0	0	0	0	1	0	0	0	6522	246	9	4	852	4	GNA14	9	80144055	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	6993075	80144055	61069376	101	26047										
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91964814	91964814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgctcccaatcacaccacctTccctaagatccacagccgca	4	19	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:91964814T>C	ENST00000375807.3	+	13	1933	c.1862T>C	c.(1861-1863)tTc>tCc	p.F621S	SECISBP2_ENST00000339901.4_Missense_Mutation_p.F548S|SECISBP2_ENST00000534113.2_Missense_Mutation_p.F553S	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	621					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						CACACCACCTTCCCTAAGATC	0.562																																																0			9											124	103	110					9																	91964814		2203	4300	6503	91154634	SO:0001583	missense	79048			AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.1862T>C	9.37:g.91964814T>C	ENSP00000364965:p.Phe621Ser		91154634	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.910998	0.33721	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.72615	-0.66;-0.67;-0.66	4.73	1.28	0.21552	.	0.848684	0.10780	N	0.634999	T	0.55593	0.1930	L	0.36672	1.1	0.09310	N	0.999995	B;B;B	0.21225	0.031;0.053;0.031	B;B;B	0.18561	0.006;0.022;0.006	T	0.41016	-0.9532	10	0.33940	T	0.23	-0.2525	4.8043	0.13312	0.0:0.1882:0.1981:0.6137	.	628;548;621	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	S	621;627;548;553	ENSP00000364965:F621S;ENSP00000364959:F548S;ENSP00000436650:F553S	ENSP00000364959:F548S	F	+	2	0	SECISBP2	91154634	0.639000	0.27234	0.720000	0.30636	0.884000	0.51177	0.965000	0.29319	0.072000	0.16694	0.533000	0.62120	TTC		0.562	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		C	91964814	T	C	91964814	3	2	96	1	0	0	0	0	1	0	0	0	14043	1783	62	4	1912	4	SECISBP2	9	91964814	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	11820759	91964814	49248617	102	26048										
ROR2	4920	hgsc.bcm.edu	37	chr9	94486946	94486946	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gccaggtccttgtgaaccacGtggtggctggataggtactc	14	10	0	1	rs138080280	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:94486946G>A	ENST00000375708.3	-	9	2028	c.1830C>T	c.(1828-1830)caC>caT	p.H610H	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Silent_p.H470H	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TGTGAACCACGTGGTGGCTGG	0.612																																																0			9						G		0,4406		0,0,2203	115	96	102		1830	-0.4	1	9	dbSNP_134	102	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ROR2	NM_004560.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		610/944	94486946	5,13001	2203	4300	6503	93526767	SO:0001819	synonymous_variant	6095			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1830C>T	9.37:g.94486946G>A			93526767	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																				0.612	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			A	94486946	G	A	94486946	2	1	96	1	0	0	0	0	0	0	0	1	13564	1136	40	1		1	ROR2	9	94486946	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	2522132	94486946	46726485	103	26049										
RGS3	5998	hgsc.bcm.edu	37	chr9	116246436	116246436	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agatttctttgatccctgaaGatagtagactacgccaccag	8	10	1	5			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:116246436G>C	ENST00000374140.2	+	7	753	c.544G>C	c.(544-546)Gat>Cat	p.D182H	RGS3_ENST00000350696.5_Missense_Mutation_p.D182H|RGS3_ENST00000317613.6_Missense_Mutation_p.D70H	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	182	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GATCCCTGAAGATAGTAGACT	0.512																																																0			9											73	72	72					9																	116246436		2203	4300	6503	115286257	SO:0001583	missense	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.544G>C	9.37:g.116246436G>C	ENSP00000363255:p.Asp182His		115286257	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.130123	0.77549	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613	T;T;T	0.77358	-1.09;-1.09;0.9	4.89	2.9	0.33743	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.816725	0.10606	N	0.655051	T	0.77903	0.4200	L	0.40543	1.245	0.34403	D	0.695498	D;P;P	0.55172	0.97;0.851;0.927	P;P;P	0.57679	0.825;0.529;0.762	T	0.78362	-0.2233	10	0.56958	D	0.05	.	5.8874	0.18888	0.2378:0.0:0.7622:0.0	.	72;70;182	B3KWG8;P49796-5;P49796	.;.;RGS3_HUMAN	H	182;182;70	ENSP00000363255:D182H;ENSP00000259406:D182H;ENSP00000312844:D70H	ENSP00000312844:D70H	D	+	1	0	RGS3	115286257	0.810000	0.29049	0.722000	0.30670	0.901000	0.52897	0.482000	0.22276	1.286000	0.44565	0.655000	0.94253	GAT		0.512	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		C	116246436	G	C	116246436	3	2	96	1	0	0	0	0	1	0	0	0	13343	942	33	5	649	5	RGS3	9	116246436	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	21759490	116246436	24966995	104	26050										
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666530	117666530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggaattggatcaccagattcCcatcctgatatctgactcca	7	12	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:117666530C>T	ENST00000223795.2	-	4	499	c.386G>A	c.(385-387)gGg>gAg	p.G129E	TNFSF8_ENST00000474301.1_5'UTR	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	129					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						CACCAGATTCCCATCCTGATA	0.403																																																0			9											149	144	146					9																	117666530		2203	4300	6503	116706351	SO:0001583	missense	944			L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.386G>A	9.37:g.117666530C>T	ENSP00000223795:p.Gly129Glu		116706351	O43404	Missense_Mutation	SNP	ENST00000223795.2	37	CCDS6810.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.388715	0.25118	.	.	ENSG00000106952	ENST00000223795	T	0.51325	0.71	5.63	3.81	0.43845	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.176137	0.40469	N	0.001088	T	0.27349	0.0671	N	0.12746	0.255	0.37923	D	0.931759	B	0.33739	0.422	B	0.36719	0.231	T	0.09818	-1.0657	10	0.10377	T	0.69	-7.5366	9.8813	0.41236	0.0:0.8385:0.0:0.1615	.	129	P32971	TNFL8_HUMAN	E	129	ENSP00000223795:G129E	ENSP00000223795:G129E	G	-	2	0	TNFSF8	116706351	0.992000	0.36948	0.930000	0.37139	0.992000	0.81027	1.723000	0.38053	0.748000	0.32831	0.655000	0.94253	GGG		0.403	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			T	117666530	C	T	117666530	3	4	96	1	0	0	0	0	1	0	0	0	16350	623	22	3	322	3	TNFSF8	9	117666530	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	1420094	117666530	23546901	105	26051										
C5	727	hgsc.bcm.edu	37	chr9	123792766	123792766	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gacagaaaaatgtggcaagaCtgaaaataaaaacaaacagg	9	5	0	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr9:123792766C>A	ENST00000223642.1	-	7	697		c.e7-1			NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5						activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TGTGGCAAGACTGAAAATAAA	0.318																																																0			9											19	19	19					9																	123792766		2132	4146	6278	122832587	SO:0001630	splice_region_variant	727			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.668-1G>T	9.37:g.123792766C>A			122832587	Q14CJ0|Q27I61	Splice_Site	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393396	0.42410	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.516	0.90936	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C5	122832587	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	4.856000	0.62932	2.725000	0.93324	0.655000	0.94253	.		0.318	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	Intron	A	123792766	C	A	123792766	5	1	96	1	0	0	0	0	0	0	1	0	2286	579	20	2	4503	2	C5	9	123792766	Splice_Site	SNP	C	TCGA-DC-6157-01A-11D-1657-10	6126236	123792766	17420665	106	26052										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7773950	7773950	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caaatagagagcgttatcacGgcgacttcggtacttccact	9	11	1	1	rs150260189		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr10:7773950G>A	ENST00000358415.4	+	13	1804	c.1638G>A	c.(1636-1638)acG>acA	p.T546T	ITIH2_ENST00000379587.4_Silent_p.T535T	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	546					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GCGTTATCACGGCGACTTCGG	0.438																																																0			10											127	119	122					10																	7773950		2203	4300	6503	7813956	SO:0001819	synonymous_variant	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1638G>A	10.37:g.7773950G>A			7813956	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.438	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		A	7773950	G	A	7773950	2	1	96	1	0	0	0	0	0	0	0	1	7925	1103	39	1		1	ITIH2	10	7773950	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10		7773950	127760797	107	26053										
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24873709	24873709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgagcattttggttttaaccGgtttacagctgaaagttcag	10	6	1	2	rs151326840		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr10:24873709G>A	ENST00000396432.2	-	26	5995	c.5509C>T	c.(5509-5511)Cgg>Tgg	p.R1837W		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1836	Interaction with CTNNA1.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						GGTTTTAACCGGTTTACAGCT	0.498																																																0			10						G	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	90	88	89		5509	2.5	0	10	dbSNP_134	89	0,8600		0,0,4300	no	missense	ARHGAP21	NM_020824.3	101	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	1837/1959	24873709	2,13004	2203	4300	6503	24913715	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5509C>T	10.37:g.24873709G>A	ENSP00000379709:p.Arg1837Trp		24913715	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	12.47	1.946163	0.34377	4.54E-4	0.0	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.15718	2.4	5.52	2.48	0.30137	.	0.111469	0.64402	D	0.000009	T	0.37812	0.1017	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12656	-1.0539	10	0.87932	D	0	.	9.394	0.38390	0.0678:0.0:0.6788:0.2534	.	1836	Q5T5U3	RHG21_HUMAN	W	1837;1286	ENSP00000379709:R1837W	ENSP00000379709:R1837W	R	-	1	2	ARHGAP21	24913715	1.000000	0.71417	0.009000	0.14445	0.010000	0.07245	3.853000	0.55941	0.604000	0.29930	0.655000	0.94253	CGG		0.498	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		A	24873709	G	A	24873709	3	1	96	1	0	0	0	0	1	0	0	0	871	1115	39	1	371	1	ARHGAP21	10	24873709	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	17099759	24873709	110661038	108	26054										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692776	89692776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tctttttaccacagttgcacAatatccttttgaagaccata	4	10	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr10:89692776A>G	ENST00000371953.3	+	5	1617	c.260A>G	c.(259-261)cAa>cGa	p.Q87R		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	87	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.Q87_P96del(1)|p.N82_P95del(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ACAGTTGCACAATATCCTTTT	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)|Deletion - In frame(2)	prostate(16)|central_nervous_system(11)|lung(6)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											107	98	101					10																	89692776		2203	4300	6503	89682756	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.260A>G	10.37:g.89692776A>G	ENSP00000361021:p.Gln87Arg		89682756	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	13.80	2.343964	0.41498	.	.	ENSG00000171862	ENST00000371953	D	0.85484	-1.99	5.07	5.07	0.68467	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72162	0.3426	N	0.01091	-1.02	0.80722	D	1	P	0.52692	0.955	P	0.52343	0.696	T	0.76342	-0.2994	9	.	.	.	-7.9828	14.8406	0.70220	1.0:0.0:0.0:0.0	.	87	P60484	PTEN_HUMAN	R	87	ENSP00000361021:Q87R	.	Q	+	2	0	PTEN	89682756	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.914000	0.92735	1.880000	0.54463	0.533000	0.62120	CAA		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692776	A	G	89692776	3	3	96	1	0	0	0	0	1	0	0	0	12772	130	5	4	278	4	PTEN	10	89692776	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	64819067	89692776	45841971	109	26055										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720849	89720849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aagcaaataaagacaaagccAaccgatacttttctccaaat	4	10	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr10:89720849A>G	ENST00000371953.3	+	8	2357	c.1000A>G	c.(1000-1002)Aac>Gac	p.N334D	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	334	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.N334Y(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGACAAAGCCAACCGATACTT	0.333		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(3)|Unknown(2)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|soft_tissue(2)|urinary_tract(2)|endometrium(1)	10											63	66	65					10																	89720849		2203	4298	6501	89710829	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1000A>G	10.37:g.89720849A>G	ENSP00000361021:p.Asn334Asp		89710829	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.748338	0.89663	.	.	ENSG00000171862	ENST00000371953	D	0.84730	-1.89	5.37	5.37	0.77165	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.91415	0.7291	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.91435	0.5169	9	.	.	.	-2.0279	15.3536	0.74409	1.0:0.0:0.0:0.0	.	334	P60484	PTEN_HUMAN	D	334	ENSP00000361021:N334D	.	N	+	1	0	PTEN	89710829	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.861000	0.92277	2.034000	0.60081	0.482000	0.46254	AAC		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720849	A	G	89720849	3	3	96	1	0	0	0	0	1	0	0	0	12772	130	5	4	1030	4	PTEN	10	89720849	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	28073	89720849	45813898	110	26056										
PKD2L1	9033	hgsc.bcm.edu	37	chr10	102089724	102089724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcttcttgggttggggctggAgaggccccgtgctggagatg	19	8	1	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr10:102089724A>G	ENST00000318222.3	-	1	519	c.137T>C	c.(136-138)cTc>cCc	p.L46P	PKD2L1_ENST00000353274.3_Missense_Mutation_p.L46P|PKD2L1_ENST00000338519.3_Missense_Mutation_p.L46P	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	46					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		TTGGGGCTGGAGAGGCCCCGT	0.617																																																0			10											78	83	81					10																	102089724		2203	4300	6503	102079714	SO:0001583	missense	9033			AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.137T>C	10.37:g.102089724A>G	ENSP00000325296:p.Leu46Pro		102079714	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	37	CCDS7492.1	.	.	.	.	.	.	.	.	.	.	A	8.081	0.772366	0.16051	.	.	ENSG00000107593	ENST00000338519;ENST00000353274;ENST00000318222;ENST00000339977	T;T;T	0.61742	0.27;0.08;0.15	5.57	1.89	0.25635	.	1.275030	0.05283	N	0.519747	T	0.22282	0.0537	N	0.00368	-1.59	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.14980	-1.0453	10	0.27082	T	0.32	-2.0943	5.7815	0.18310	0.2213:0.1584:0.6203:0.0	.	46	Q9P0L9	PK2L1_HUMAN	P	46	ENSP00000345068:L46P;ENSP00000266049:L46P;ENSP00000325296:L46P	ENSP00000325296:L46P	L	-	2	0	PKD2L1	102079714	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	1.116000	0.31221	1.360000	0.45960	-0.184000	0.12912	CTC		0.617	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		G	102089724	A	G	102089724	3	3	96	1	0	0	0	0	1	0	0	0	11998	304	11	4	2344	4	PKD2L1	10	102089724	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	12368875	102089724	33445023	111	26057										
PHRF1	57661	hgsc.bcm.edu	37	chr11	609553	609553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttccccggatgtggcgcctgCggggaaggaagacagcccct	15	13	0	1	rs201571276		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:609553C>T	ENST00000264555.5	+	14	4225	c.4097C>T	c.(4096-4098)gCg>gTg	p.A1366V	PHRF1_ENST00000413872.2_Missense_Mutation_p.A1364V|PHRF1_ENST00000416188.2_Missense_Mutation_p.A1365V|PHRF1_ENST00000533464.1_Missense_Mutation_p.A1362V	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1366					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GTGGCGCCTGCGGGGAAGGAA	0.697																																																0			11						C	VAL/ALA	2,4020		0,2,2009	16	22	20		4094	-9.7	0	11		20	1,8317		0,1,4158	yes	missense	PHRF1	NM_020901.2	64	0,3,6167	TT,TC,CC		0.012,0.0497,0.0243	benign	1365/1649	609553	3,12337	2011	4159	6170	599553	SO:0001583	missense	57661			BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4097C>T	11.37:g.609553C>T	ENSP00000264555:p.Ala1366Val		599553	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		.	.	.	.	.	.	.	.	.	.	C	9.117	1.008033	0.19199	4.97E-4	1.2E-4	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	4.84	-9.68	0.00528	.	2.573560	0.02008	N	0.046762	T	0.41143	0.1146	N	0.01576	-0.805	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47058	-0.9146	10	0.09590	T	0.72	.	3.2245	0.06728	0.1987:0.4227:0.1941:0.1846	.	1362;1364;1365;1366	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	V	1366;1364;1365;1362	ENSP00000264555:A1366V;ENSP00000388589:A1364V;ENSP00000410626:A1365V;ENSP00000431870:A1362V	ENSP00000264555:A1366V	A	+	2	0	PHRF1	599553	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.910000	0.00699	-2.153000	0.00793	-0.415000	0.06103	GCG		0.697	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	609553	C	T	609553	3	4	96	1	0	0	0	0	1	0	0	0	11892	768	27	1	4144	1	PHRF1	11	609553	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		609553	134396963	112	26058										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020476	5020476	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	accatgcttgctgtgttatgGttggatgctccagagatcca	11	9	0	1	rs199934313		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:5020476G>A	ENST00000321543.1	+	1	264	c.264G>A	c.(262-264)tgG>tgA	p.W88*		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTGTGTTATGGTTGGATGCTC	0.498																																																0			11											223	173	190					11																	5020476		2201	4298	6499	4977052	SO:0001587	stop_gained	119682			AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.264G>A	11.37:g.5020476G>A	ENSP00000322156:p.Trp88*		4977052	Q6IFE5	Nonsense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	G	9.455	1.091570	0.20471	.	.	ENSG00000176798	ENST00000321543	.	.	.	5.44	2.52	0.30459	.	0.658924	0.12780	N	0.439715	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9576	0.47366	0.0665:0.0:0.6874:0.2461	.	.	.	.	X	88	.	ENSP00000322156:W88X	W	+	3	0	OR51L1	4977052	0.170000	0.23016	0.025000	0.17156	0.087000	0.18053	0.454000	0.21827	0.118000	0.18165	-2.511000	0.00188	TGG		0.498	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		A	5020476	G	A	5020476	4	1	96	1	0	0	0	0	0	1	0	0	11133	1270	44	3	266	3	OR51L1	11	5020476	Nonsense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	4410923	5020476	129986040	113	26059										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7083736	7083736	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gtaacattcagaggctcgggTgagttcatagttttccatta	10	7	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:7083736T>G	ENST00000299481.4	+	10	3321		c.e10+2			NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GAGGCTCGGGTGAGTTCATAG	0.408																																																0			11											113	106	109					11																	7083736		2201	4296	6497	7040312	SO:0001630	splice_region_variant	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2975+2T>G	11.37:g.7083736T>G			7040312	Q7RTR6	Splice_Site	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.737484	0.49045	.	.	ENSG00000158077	ENST00000299481	.	.	.	4.84	3.68	0.42216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6353	0.33943	0.0:0.0:0.194:0.806	.	.	.	.	.	-1	.	.	.	+	.	.	NLRP14	7040312	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	4.383000	0.59600	0.957000	0.37930	0.533000	0.62120	.		0.408	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	Intron	G	7083736	T	G	7083736	5	3	96	1	0	0	0	0	0	0	1	0	10507	1710	59	4	3011	4	NLRP14	11	7083736	Splice_Site	SNP	T	TCGA-DC-6157-01A-11D-1657-10	2063260	7083736	127922780	114	26060										
IPO7	10527	hgsc.bcm.edu	37	chr11	9459625	9459625	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttttttttttttttttttttAggcttcatgacagaaagatg	6	3	1	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:9459625A>T	ENST00000379719.3	+	22	2631		c.e22-1			NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7						innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		ttttttttttAGGCTTCATGA	0.318																																																0			11											56	61	59					11																	9459625		2201	4294	6495	9416201	SO:0001630	splice_region_variant	10527			AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2490-1A>T	11.37:g.9459625A>T			9416201	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Splice_Site	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.163039	0.38217	.	.	ENSG00000205339	ENST00000379719	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0525	0.71885	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IPO7	9416201	1.000000	0.71417	0.975000	0.42487	0.219000	0.24729	8.945000	0.92985	1.960000	0.56953	0.377000	0.23210	.		0.318	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	Intron	T	9459625	A	T	9459625	5	4	96	1	0	0	0	0	0	0	1	0	7818	434	15	5	2574	5	IPO7	11	9459625	Splice_Site	SNP	A	TCGA-DC-6157-01A-11D-1657-10	2375889	9459625	125546891	115	26061										
SBF2	81846	hgsc.bcm.edu	37	chr11	9989940	9989940	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttttctattcgtgtggcaggAggtgcattctggttcttagc	12	7	3	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:9989940A>G	ENST00000256190.8	-	14	1685	c.1548T>C	c.(1546-1548)ccT>ccC	p.P516P		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	516					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GTGTGGCAGGAGGTGCATTCT	0.403																																																0			11											153	146	148					11																	9989940		2201	4294	6495	9946516	SO:0001819	synonymous_variant	81846			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.1548T>C	11.37:g.9989940A>G			9946516	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Silent	SNP	ENST00000256190.8	37	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	A	9.922	1.212442	0.22289	.	.	ENSG00000133812	ENST00000420722	.	.	.	5.21	2.86	0.33363	.	.	.	.	.	T	0.46639	0.1403	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28586	-1.0039	4	.	.	.	.	3.6958	0.08364	0.5286:0.0:0.1669:0.3045	.	.	.	.	P	123	.	.	S	-	1	0	SBF2	9946516	0.995000	0.38212	1.000000	0.80357	0.931000	0.56810	0.470000	0.22084	0.285000	0.22329	0.374000	0.22700	TCC		0.403	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		G	9989940	A	G	9989940	2	3	96	1	0	0	0	0	0	0	0	1	13896	291	11	4		4	SBF2	11	9989940	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	530315	9989940	125016576	116	26062										
POLA2	23649	hgsc.bcm.edu	37	chr11	65062101	65062101	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccacagatctgcttttccacCtgggggccgaggagatcagt	12	12	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:65062101C>A	ENST00000265465.3	+	15	1969	c.1438C>A	c.(1438-1440)Ctg>Atg	p.L480M	POLA2_ENST00000541089.1_Missense_Mutation_p.L272M|POLA2_ENST00000534785.1_3'UTR	NM_002689.2	NP_002680.2	Q14181	DPOA2_HUMAN	polymerase (DNA directed), alpha 2, accessory subunit	480					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein import into nucleus, translocation (GO:0000060)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|protein heterodimerization activity (GO:0046982)			endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	11					Dacarbazine(DB00851)	GCTTTTCCACCTGGGGGCCGA	0.522																																																0			11											94	90	91					11																	65062101		2201	4297	6498	64818677	SO:0001583	missense	23649			BC002990	CCDS8098.1	11q13	2012-05-18	2012-05-18		ENSG00000014138	ENSG00000014138		"DNA polymerases"	30073	protein-coding gene	gene with protein product	"DNA polymerase alpha subunit B", "DNA polymerase alpha 70 kDa subunit"		"polymerase (DNA directed), alpha 2 (70kD subunit)"			8223465, 11433027	Standard	NM_002689		Approved	FLJ21662	uc001odj.3	Q14181	OTTHUMG00000165951	ENST00000265465.3:c.1438C>A	11.37:g.65062101C>A	ENSP00000265465:p.Leu480Met		64818677	B4DNB4|Q9BPV3	Missense_Mutation	SNP	ENST00000265465.3	37	CCDS8098.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.303948	0.23736	.	.	ENSG00000014138	ENST00000265465;ENST00000541089	T;T	0.38560	1.13;1.13	5.58	4.45	0.53987	DNA polymerase alpha/epsilon, subunit B (1);	0.155374	0.64402	N	0.000001	T	0.35480	0.0933	N	0.21142	0.635	0.38743	D	0.953935	B;B	0.32753	0.383;0.063	B;B	0.42827	0.399;0.107	T	0.24190	-1.0167	10	0.27785	T	0.31	-22.6843	10.9093	0.47099	0.834:0.166:0.0:0.0	.	272;480	B4DNB4;Q14181	.;DPOA2_HUMAN	M	480;272	ENSP00000265465:L480M;ENSP00000443222:L272M	ENSP00000265465:L480M	L	+	1	2	POLA2	64818677	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	6.498000	0.73679	0.968000	0.38212	-0.397000	0.06425	CTG		0.522	POLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387223.1	NM_002689		A	65062101	C	A	65062101	3	1	96	1	0	0	0	0	1	0	0	0	12219	680	24	2	1496	2	POLA2	11	65062101	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	55072161	65062101	69944415	117	26063										
CHKA	1119	hgsc.bcm.edu	37	chr11	67842205	67842205	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gggatgaactgctccagtcgGccttggggaaagatgccata	14	9	0	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:67842205G>A	ENST00000265689.4	-	4	635	c.609C>T	c.(607-609)ggC>ggT	p.G203G	CHKA_ENST00000356135.5_Silent_p.G185G	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	203					CDP-choline pathway (GO:0006657)|choline metabolic process (GO:0019695)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline binding (GO:0033265)|choline kinase activity (GO:0004103)|cholinesterase activity (GO:0004104)|drug binding (GO:0008144)|ethanolamine kinase activity (GO:0004305)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13					Choline(DB00122)	GCTCCAGTCGGCCTTGGGGAA	0.488																																																0			11											125	119	121					11																	67842205		2200	4294	6494	67598781	SO:0001819	synonymous_variant	1119			D10704	CCDS8178.1, CCDS8179.1	11q13.1	2008-02-05	2004-04-19	2004-04-21	ENSG00000110721	ENSG00000110721	2.7.1.32		1937	protein-coding gene	gene with protein product		118491	"choline kinase"	CHK		1618328, 15003397	Standard	NM_001277		Approved	CKI	uc001onj.3	P35790	OTTHUMG00000167424	ENST00000265689.4:c.609C>T	11.37:g.67842205G>A			67598781	Q8NE29	Silent	SNP	ENST00000265689.4	37	CCDS8178.1																																																																																				0.488	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277		A	67842205	G	A	67842205	2	1	96	1	0	0	0	0	0	0	0	1	3353	1190	42	3		3	CHKA	11	67842205	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	2780104	67842205	67164311	118	26064										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67953362	67953362	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttccagaggatggtacatagCgactctgtccttcaaatccc	8	12	2	1	rs188627113		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr11:67953362C>T	ENST00000304363.4	-	3	547	c.194G>A	c.(193-195)cGc>cAc	p.R65H	SUV420H1_ENST00000405515.1_Missense_Mutation_p.R65H|SUV420H1_ENST00000401547.2_Missense_Mutation_p.R65H|SUV420H1_ENST00000402789.1_Missense_Mutation_p.R65H|SUV420H1_ENST00000402185.2_Missense_Mutation_p.R65H	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	65					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TGGTACATAGCGACTCTGTCC	0.383																																																0			11											125	119	121					11																	67953362		2200	4294	6494	67709938	SO:0001583	missense	51111			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.194G>A	11.37:g.67953362C>T	ENSP00000305899:p.Arg65His		67709938	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	37	CCDS31623.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	32	5.113794	0.94339	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000434573	T;T;T;T;T;T	0.58940	0.89;0.89;0.89;0.89;0.3;0.89	6.17	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.71921	0.3397	L	0.54323	1.7	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.975;1.0	D;D;P;P	0.68621	0.959;0.945;0.707;0.828	T	0.75357	-0.3346	10	0.87932	D	0	-13.8747	16.8679	0.86033	0.1295:0.8705:0.0:0.0	.	65;65;65;65	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	H	65	ENSP00000305899:R65H;ENSP00000385965:R65H;ENSP00000385640:R65H;ENSP00000385005:R65H;ENSP00000384724:R65H;ENSP00000402921:R65H	ENSP00000305899:R65H	R	-	2	0	SUV420H1	67709938	1.000000	0.71417	0.959000	0.39883	0.987000	0.75469	7.818000	0.86416	1.590000	0.49995	0.655000	0.94253	CGC		0.383	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		T	67953362	C	T	67953362	3	4	96	1	0	0	0	0	1	0	0	0	15453	768	27	1	2507	1	SUV420H1	11	67953362	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	111157	67953362	67053154	119	26065										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7549009	7549009	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctcaggccccatgttgcatCacctgcaccaagaacaatga	7	15	2	2	rs4072797	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr12:7549009C>T	ENST00000313599.3	-	8	1789	c.1732G>A	c.(1732-1734)Gat>Aat	p.D578N	CD163L1_ENST00000416109.2_Missense_Mutation_p.D588N|CD163L1_ENST00000396630.1_Missense_Mutation_p.D578N			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	578			D -> N (in dbSNP:rs4072797).			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATGTTGCATCACCTGCACCA	0.502													T|||	903	0.180312	0.3351	0.0937	5008	,	,		-128	0.2073		0.0328	False		,,,				2504	0.1564															0			12						T	ASN/ASP	1226,3180	696.3+/-406.1	159,908,1136	35	28	31		1732	-2.1	0	12	dbSNP_108	31	277,8323	795.1+/-407.5	4,269,4027	yes	missense	CD163L1	NM_174941.4	23	163,1177,5163	TT,TC,CC		3.2209,27.8257,11.5562	benign	578/1454	7549009	1503,11503	2203	4300	6503	7440276	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1732G>A	12.37:g.7549009C>T	ENSP00000315945:p.Asp578Asn		7440276	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	302	0.1382783882783883	146	0.2967479674796748	35	0.09668508287292818	97	0.16958041958041958	24	0.0316622691292876	T	3.722	-0.057248	0.07317	0.278257	0.032209	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630;ENST00000545926	T;T;T;T	0.27890	1.64;4.96;1.64;1.64	2.24	-2.14	0.07123	Speract/scavenger receptor-related (1);	3.118170	0.01912	N	0.039944	T	0.00012	0.0000	N	0.03084	-0.415	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34601	-0.9822	9	0.13470	T	0.59	.	10.8332	0.46673	0.0:0.8255:0.0:0.1745	rs4072797;rs52837880;rs57331676;rs4072797	588;578	E7EVK4;Q9NR16	.;C163B_HUMAN	N	578;588;578;117	ENSP00000315945:D578N;ENSP00000393474:D588N;ENSP00000379871:D578N;ENSP00000439921:D117N	ENSP00000315945:D578N	D	-	1	0	CD163L1	7440276	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.387000	0.07361	-1.048000	0.03238	-0.360000	0.07572	GAT		0.502	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7549009	C	T	7549009	3	4	96	1	0	0	0	0	1	0	0	0	2974	826	29	3	2677	3	CD163L1	12	7549009	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		7549009	126302886	120	26066										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48134780	48134780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cactcaccaggtccagccccTcagcagagcccacagtgggc	10	18	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr12:48134780T>C	ENST00000449771.2	-	20	2055	c.1967A>G	c.(1966-1968)gAg>gGg	p.E656G	RAPGEF3_ENST00000389212.3_Missense_Mutation_p.E656G|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.E614G|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.E614G|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.E614G|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.E565G			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	656					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GTCCAGCCCCTCAGCAGAGCC	0.647																																																0			12											24	23	23					12																	48134780		2203	4299	6502	46421047	SO:0001583	missense	10411			AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1967A>G	12.37:g.48134780T>C	ENSP00000395708:p.Glu656Gly		46421047	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.824561	0.50739	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	4.0	4.0	0.46444	Ras guanine nucleotide exchange factor, domain (1);	0.137262	0.47093	D	0.000259	T	0.13970	0.0338	N	0.08118	0	0.42006	D	0.990915	B	0.32573	0.376	B	0.26202	0.067	T	0.12941	-1.0528	10	0.20046	T	0.44	.	12.0726	0.53626	0.0:0.0:0.0:1.0	.	656	O95398	RPGF3_HUMAN	G	614;656;303;614;614;614;656;619;565	ENSP00000384521:E614G;ENSP00000395708:E656G;ENSP00000448619:E614G;ENSP00000171000:E614G;ENSP00000373864:E656G;ENSP00000448480:E565G	ENSP00000171000:E614G	E	-	2	0	RAPGEF3	46421047	0.075000	0.21258	1.000000	0.80357	0.997000	0.91878	1.156000	0.31712	1.609000	0.50190	0.459000	0.35465	GAG		0.647	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		C	48134780	T	C	48134780	3	2	96	1	0	0	0	0	1	0	0	0	13082	1551	54	4	840	4	RAPGEF3	12	48134780	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	40585771	48134780	85717115	121	26067										
FAM186B	84070	hgsc.bcm.edu	37	chr12	49993936	49993936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctgctgccacatctcctccTcctccagccacagctgcctc	6	21	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr12:49993936T>C	ENST00000257894.2	-	4	1648	c.1487A>G	c.(1486-1488)gAg>gGg	p.E496G	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.E406G	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	496						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CATCTCCTCCTCCTCCAGCCA	0.632																																																0			12											39	43	42					12																	49993936		2203	4300	6503	48280203	SO:0001583	missense	84070			AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1487A>G	12.37:g.49993936T>C	ENSP00000257894:p.Glu496Gly		48280203	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.324940	0.81580	.	.	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.19105	2.17;2.18;2.41	5.0	3.85	0.44370	.	0.000000	0.41001	D	0.000971	T	0.36963	0.0986	M	0.64997	1.995	0.30719	N	0.748411	D;D	0.71674	0.998;0.998	D;D	0.72338	0.948;0.977	T	0.28004	-1.0057	9	.	.	.	-22.9258	6.8677	0.24102	0.0:0.103:0.0:0.897	.	406;496	B4DZ15;Q8IYM0	.;F186B_HUMAN	G	406;109;496	ENSP00000438569:E406G;ENSP00000436995:E109G;ENSP00000257894:E496G	.	E	-	2	0	FAM186B	48280203	0.125000	0.22332	1.000000	0.80357	0.984000	0.73092	0.589000	0.23939	2.017000	0.59298	0.460000	0.39030	GAG		0.632	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		C	49993936	T	C	49993936	3	2	96	1	0	0	0	0	1	0	0	0	5528	1551	54	4	1210	4	FAM186B	12	49993936	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1859156	49993936	83857959	122	26068										
KRT85	3891	hgsc.bcm.edu	37	chr12	52756131	52756131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctggtactccttgagcaggCaggccatgtcctgcttggcc	12	14	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr12:52756131C>A	ENST00000257901.3	-	7	1277	c.1202G>T	c.(1201-1203)tGc>tTc	p.C401F	KRT85_ENST00000544265.1_Missense_Mutation_p.C189F	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	401	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTTGAGCAGGCAGGCCATGTC	0.657																																																0			12											83	76	79					12																	52756131		2203	4300	6503	51042398	SO:0001583	missense	3891			X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1202G>T	12.37:g.52756131C>A	ENSP00000257901:p.Cys401Phe		51042398	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239114	0.58995	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;D	0.88741	-2.42;-2.42	5.16	5.16	0.70880	Filament (1);	0.092459	0.48286	D	0.000181	D	0.91798	0.7405	M	0.87682	2.9	0.36967	D	0.893617	B	0.18310	0.027	B	0.30316	0.114	D	0.91900	0.5531	10	0.66056	D	0.02	.	18.6541	0.91441	0.0:1.0:0.0:0.0	.	401	P78386	KRT85_HUMAN	F	401;189	ENSP00000257901:C401F;ENSP00000440240:C189F	ENSP00000257901:C401F	C	-	2	0	KRT85	51042398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.199000	0.51043	2.420000	0.82092	0.561000	0.74099	TGC		0.657	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		A	52756131	C	A	52756131	3	1	96	1	0	0	0	0	1	0	0	0	8520	710	25	2	333	2	KRT85	12	52756131	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	2762195	52756131	81095764	123	26069										
SOCS2	8835	hgsc.bcm.edu	37	chr12	93966719	93966719	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccgggaatggcggggaagggAcgcggagccagtgggggacc	22	9	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr12:93966719A>G	ENST00000340600.2	+	2	644	c.46A>G	c.(46-48)Acg>Gcg	p.T16A	SOCS2_ENST00000551556.1_Missense_Mutation_p.T16A|SOCS2_ENST00000549206.1_Missense_Mutation_p.T16A|SOCS2_ENST00000536696.2_Missense_Mutation_p.T16A|SOCS2-AS1_ENST00000551626.1_RNA|SOCS2-AS1_ENST00000499137.2_RNA|SOCS2_ENST00000549122.1_Missense_Mutation_p.T16A|SOCS2_ENST00000548537.1_Missense_Mutation_p.T16A|SOCS2-AS1_ENST00000500986.1_RNA	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	O14508	SOCS2_HUMAN	suppressor of cytokine signaling 2	16					cellular response to hormone stimulus (GO:0032870)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of signal transduction (GO:0009967)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of signal transduction (GO:0009966)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	growth hormone receptor binding (GO:0005131)|insulin-like growth factor receptor binding (GO:0005159)|JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)	14						CGGGGAAGGGACGCGGAGCCA	0.711																																																0			12											8	9	9					12																	93966719		2161	4241	6402	92490850	SO:0001583	missense	8835			AF037989	CCDS9047.1	12q	2013-02-14			ENSG00000120833	ENSG00000120833		"Suppressors of cytokine signaling", "SH2 domain containing"	19382	protein-coding gene	gene with protein product	"STAT-induced STAT inhibitor-2"	605117				9344848, 9266833	Standard	NM_003877		Approved	STATI2, SSI2, SOCS-2, SSI-2, CIS2, Cish2	uc031qjc.1	O14508		ENST00000340600.2:c.46A>G	12.37:g.93966719A>G	ENSP00000339428:p.Thr16Ala		92490850	A8K3D1|O14542|O95102|Q9UKS5	Missense_Mutation	SNP	ENST00000340600.2	37	CCDS9047.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935540	0.73442	.	.	ENSG00000120833	ENST00000340600;ENST00000549206;ENST00000536696;ENST00000548091;ENST00000549122;ENST00000548537;ENST00000549887;ENST00000551556	T;T;T;T;T;T;T	0.32272	1.94;1.94;1.94;1.46;1.94;1.48;1.94	4.44	1.99	0.26369	.	1.108750	0.06722	N	0.775030	T	0.13114	0.0318	N	0.12182	0.205	0.23036	N	0.998394	B	0.32753	0.383	B	0.19946	0.027	T	0.20075	-1.0286	10	0.09843	T	0.71	-5.8584	5.283	0.15686	0.726:0.1788:0.0953:0.0	.	16	O14508	SOCS2_HUMAN	A	16	ENSP00000339428:T16A;ENSP00000448815:T16A;ENSP00000442898:T16A;ENSP00000447902:T16A;ENSP00000447161:T16A;ENSP00000448611:T16A;ENSP00000449227:T16A	ENSP00000339428:T16A	T	+	1	0	SOCS2	92490850	1.000000	0.71417	0.912000	0.35992	0.881000	0.50899	0.690000	0.25451	0.228000	0.21019	0.454000	0.30748	ACG		0.711	SOCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407731.2			G	93966719	A	G	93966719	3	3	96	1	0	0	0	0	1	0	0	0	14951	275	10	4	48	4	SOCS2	12	93966719	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	41210588	93966719	39885176	124	26070										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25672215	25672215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aagcagttaacagtgctaccGgtgttccaactgtttaaaat	8	8	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr13:25672215G>A	ENST00000281589.3	+	1	1916	c.1879G>A	c.(1879-1881)Ggt>Agt	p.G627S		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	627					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAGTGCTACCGGTGTTCCAAC	0.408																																																0			13											93	100	98					13																	25672215		2203	4298	6501	24570215	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1879G>A	13.37:g.25672215G>A	ENSP00000281589:p.Gly627Ser		24570215	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101887	0.37048	.	.	ENSG00000151846	ENST00000281589	T	0.38560	1.13	0.875	0.875	0.19130	Polyadenylate-binding protein/Hyperplastic disc protein (1);	.	.	.	.	T	0.29028	0.0721	L	0.31926	0.97	0.46678	D	0.999158	B	0.12013	0.005	B	0.18263	0.021	T	0.13656	-1.0501	9	0.51188	T	0.08	.	7.5489	0.27783	0.0:0.0:1.0:0.0	.	627	Q9H361	PABP3_HUMAN	S	627	ENSP00000281589:G627S	ENSP00000281589:G627S	G	+	1	0	PABPC3	24570215	0.719000	0.27986	0.806000	0.32338	0.149000	0.21700	1.439000	0.35013	0.759000	0.33084	0.313000	0.20887	GGT		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25672215	G	A	25672215	3	1	96	1	0	0	0	0	1	0	0	0	11396	1116	39	1	1881	1	PABPC3	13	25672215	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10		25672215	89497663	125	26071										
KLF12	11278	hgsc.bcm.edu	37	chr13	74420217	74420217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctggagttaatactgttgaCgaagatgacgctgaagatac	11	7	0	5			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr13:74420217C>T	ENST00000377669.2	-	3	443	c.417G>A	c.(415-417)tcG>tcA	p.S139S	KLF12_ENST00000377666.4_Silent_p.S139S|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	139					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		ATACTGTTGACGAAGATGACG	0.502																																																0			13											100	83	89					13																	74420217		2203	4300	6503	73318218	SO:0001819	synonymous_variant	11278			AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.417G>A	13.37:g.74420217C>T			73318218	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	37	CCDS9449.1																																																																																				0.502	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		T	74420217	C	T	74420217	2	4	96	1	0	0	0	0	0	0	0	1	8361	523	19	1		1	KLF12	13	74420217	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	48748002	74420217	40749661	126	26072										
TMTC4	84899	hgsc.bcm.edu	37	chr13	101289887	101289887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctccagcgcacgtagagcaTcccagcccctccagaggtga	10	17	0	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr13:101289887T>C	ENST00000376234.3	-	8	1036	c.847A>G	c.(847-849)Atg>Gtg	p.M283V	TMTC4_ENST00000328767.5_Missense_Mutation_p.M172V|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000342624.5_Missense_Mutation_p.M302V	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	283						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACGTAGAGCATCCCAGCCCCT	0.637																																																0			13											73	74	74					13																	101289887		2203	4300	6503	100087888	SO:0001583	missense	84899				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.847A>G	13.37:g.101289887T>C	ENSP00000365408:p.Met283Val		100087888	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	T	5.296	0.240030	0.10023	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.58210	0.36;0.35;1.24	5.6	-0.817	0.10836	.	0.389804	0.33477	N	0.004871	T	0.41026	0.1141	L	0.54323	1.7	0.21897	N	0.99949	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.29181	-1.0020	10	0.48119	T	0.1	.	6.9719	0.24654	0.0:0.2483:0.1205:0.6312	.	172;283;283;302	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	V	283;302;172	ENSP00000365408:M283V;ENSP00000343871:M302V;ENSP00000365409:M172V	ENSP00000365409:M172V	M	-	1	0	TMTC4	100087888	0.096000	0.21769	0.020000	0.16555	0.394000	0.30568	0.364000	0.20325	-0.385000	0.07833	0.533000	0.62120	ATG		0.637	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		C	101289887	T	C	101289887	3	2	96	1	0	0	0	0	1	0	0	0	16302	1435	50	4	1422	4	TMTC4	13	101289887	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	26869670	101289887	13879991	127	26073										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30105669	30105669	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcactcccttcttccatgacCacatcagactctgccccagg	5	18	4	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr14:30105669C>G	ENST00000331968.5	-	7	1246	c.1017G>C	c.(1015-1017)gtG>gtC	p.V339V	PRKD1_ENST00000415220.2_Silent_p.V347V|PRKD1_ENST00000551644.1_5'UTR	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	339					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CTTCCATGACCACATCAGACT	0.463																																																0			14											220	168	185					14																	30105669		2203	4300	6503	29175420	SO:0001819	synonymous_variant	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1017G>C	14.37:g.30105669C>G			29175420	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																				0.463	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		G	30105669	C	G	30105669	2	3	96	1	0	0	0	0	0	0	0	1	12552	581	21	5		5	PRKD1	14	30105669	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10		30105669	77243871	128	26074										
C14orf169	399671	hgsc.bcm.edu	37	chr14	73957772	73957772	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gttgaggcgcgggcggccgaAgcgccggcgcaagccccagc	18	15	0	1	rs10144469		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr14:73957772A>G	ENST00000553558.1	-	17	3166				HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron|C14orf169_ENST00000531973.1_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4											breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		GGGCGGCCGAAGCGCCGGCGC	0.687																																																0			14						G	,ARG/LYS,	3166,550		1357,452,49	18	22	21		,50,	2.9	0.9	14	dbSNP_119	21	5852,2314		2117,1618,348	no	intron,missense,intron	C14orf169,HEATR4	NM_001220484.1,NM_024644.2,NM_203309.2	,26,	3474,2070,397	GG,GA,AA		28.337,14.8009,24.1037	,benign,	,17/642,	73957772	9018,2864	1858	4083	5941	73027525	SO:0001627	intron_variant	79697			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2844+1997T>C	14.37:g.73957772A>G			73027525	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2																																																																																				0.687	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		G	73957772	A	G	73957772	1	3	96	0	1	0	0	0	0	0	0	0	1762	72	3	4		4	C14orf169	14	73957772	Intron	SNP	A	TCGA-DC-6157-01A-11D-1657-10	43852103	73957772	33391768	129	26075										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92480894	92480894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcatctcatagattttagagAgatcagtttctataactcca	6	8	3	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr14:92480894A>G	ENST00000267622.4	-	7	1224	c.851T>C	c.(850-852)cTc>cCc	p.L284P		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	284					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GATTTTAGAGAGATCAGTTTC	0.308			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											23	24	24					14																	92480894		2106	4229	6335	91550647	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.851T>C	14.37:g.92480894A>G	ENSP00000267622:p.Leu284Pro		91550647	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	A	0.349	-0.945740	0.02304	.	.	ENSG00000100815	ENST00000267622;ENST00000542257	T	0.59638	0.25	4.82	0.963	0.19649	.	1.479890	0.03688	N	0.246694	T	0.36413	0.0966	N	0.08118	0	0.20764	N	0.999859	B;B	0.17268	0.021;0.006	B;B	0.19148	0.024;0.005	T	0.20240	-1.0281	10	0.30854	T	0.27	.	5.0674	0.14589	0.2824:0.0806:0.0:0.637	.	49;284	F5H1Z0;Q15643	.;TRIPB_HUMAN	P	284;49	ENSP00000267622:L284P	ENSP00000267622:L284P	L	-	2	0	TRIP11	91550647	0.823000	0.29233	0.027000	0.17364	0.014000	0.08584	0.212000	0.17497	0.258000	0.21686	-1.847000	0.00572	CTC		0.308	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			G	92480894	A	G	92480894	3	3	96	1	0	0	0	0	1	0	0	0	16595	304	11	4	5148	4	TRIP11	14	92480894	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	18523122	92480894	14868646	130	26076										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22864299	22864299	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	taagagaaaaggaaacatggCagaatgtgtcttttcttaat	9	4	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:22864299C>A	ENST00000283645.4	+	16	2387	c.2257C>A	c.(2257-2259)Cag>Aag	p.Q753K	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.Q753K	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	753					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		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;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		GGAAACATGGCAGAATGTGTC	0.363																																																0			15											97	95	96					15																	22864299		2203	4300	6503	20415740	SO:0001583	missense	114791			AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.2257C>A	15.37:g.22864299C>A	ENSP00000283645:p.Gln753Lys		20415740	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	37	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	C	6.492	0.459005	0.12342	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.07327	3.2;3.2	5.0	3.07	0.35406	.	0.142426	0.48767	D	0.000180	T	0.06005	0.0156	L	0.38531	1.155	0.54753	D	0.999989	B;B	0.31026	0.304;0.304	B;B	0.33196	0.111;0.159	T	0.17018	-1.0383	10	0.06099	T	0.92	-4.7666	8.393	0.32540	0.1539:0.7677:0.0:0.0784	.	753;753	Q96RT8;E9PB12	GCP5_HUMAN;.	K	753	ENSP00000283645:Q753K;ENSP00000409217:Q753K	ENSP00000283645:Q753K	Q	+	1	0	TUBGCP5	20415740	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.159000	0.77483	0.776000	0.33473	0.591000	0.81541	CAG		0.363	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		A	22864299	C	A	22864299	3	1	96	1	0	0	0	0	1	0	0	0	16809	711	25	2	2319	2	TUBGCP5	15	22864299	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10		22864299	79667093	131	26077										
RYR3	6263	hgsc.bcm.edu	37	chr15	34130562	34130562	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcttacgtgttagaaattgcGggtgaagaggaagaagacgg	15	4	1	5	rs374756167		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:34130562G>A	ENST00000389232.4	+	89	12451	c.12381G>A	c.(12379-12381)gcG>gcA	p.A4127A	RYR3_ENST00000415757.3_Silent_p.A4122A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4127					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TAGAAATTGCGGGTGAAGAGG	0.483																																																0			15						G		0,3776		0,0,1888	145	144	144		12381	2.9	0.1	15		144	2,8190		0,2,4094	no	coding-synonymous	RYR3	NM_001036.3		0,2,5982	AA,AG,GG		0.0244,0.0,0.0167		4127/4871	34130562	2,11966	1888	4096	5984	31917854	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.12381G>A	15.37:g.34130562G>A			31917854	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34130562	G	A	34130562	2	1	96	1	0	0	0	0	0	0	0	1	13807	1103	39	1		1	RYR3	15	34130562	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	11266263	34130562	68400830	132	26078										
MFAP1	4236	hgsc.bcm.edu	37	chr15	44097662	44097662	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tgtatacttcttcatcctcaTcctgtataaaaaaaatctta	2	9	4	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:44097662T>C	ENST00000267812.3	-	8	1281	c.1049A>G	c.(1048-1050)gAt>gGt	p.D350G		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	350					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		TTCATCCTCATCCTGTATAAA	0.353																																																0			15											97	95	96					15																	44097662		2198	4298	6496	41884954	SO:0001630	splice_region_variant	4236				CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.1048-1A>G	15.37:g.44097662T>C			41884954	Q86TG6	Missense_Mutation	SNP	ENST00000267812.3	37	CCDS10105.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.364677	0.82463	.	.	ENSG00000140259	ENST00000267812	.	.	.	5.2	5.2	0.72013	.	0.047906	0.85682	D	0.000000	D	0.84028	0.5382	M	0.89214	3.015	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86812	0.1999	9	0.59425	D	0.04	-20.9749	14.8935	0.70627	0.0:0.0:0.0:1.0	.	350	P55081	MFAP1_HUMAN	G	350	.	ENSP00000267812:D350G	D	-	2	0	MFAP1	41884954	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	7.522000	0.81844	2.185000	0.69588	0.454000	0.30748	GAT		0.353	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926	Missense_Mutation	C	44097662	T	C	44097662	5	2	96	1	0	0	0	0	0	0	1	0	9543	1449	50	4	278	4	MFAP1	15	44097662	Splice_Site	SNP	T	TCGA-DC-6157-01A-11D-1657-10	9967100	44097662	58433730	133	26079										
USP8	9101	hgsc.bcm.edu	37	chr15	50784958	50784958	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcttctcagattcggaacctCaatcctgtttttggaggttc	9	10	2	1	rs138490617	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:50784958C>A	ENST00000396444.3	+	15	2633	c.2295C>A	c.(2293-2295)ctC>ctA	p.L765L	RP11-562A8.5_ENST00000560159.1_lincRNA|USP8_ENST00000425032.3_Silent_p.L659L|USP8_ENST00000433963.1_Silent_p.L765L|USP8_ENST00000307179.4_Silent_p.L765L	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	765					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TTCGGAACCTCAATCCTGTTT	0.408													C|||	56	0.0111821	0.0189	0.0144	5008	,	,		22644	0.004		0.002	False		,,,				2504	0.0153															0			15											136	121	126					15																	50784958		2196	4294	6490	48572250	SO:0001819	synonymous_variant	9101			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2295C>A	15.37:g.50784958C>A			48572250	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Silent	SNP	ENST00000396444.3	37	CCDS10137.1																																																																																				0.408	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		A	50784958	C	A	50784958	2	1	96	1	0	0	0	0	0	0	0	1	17129	813	29	2		2	USP8	15	50784958	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	6687296	50784958	51746434	134	26080										
CSNK1G1	53944	hgsc.bcm.edu	37	chr15	64506102	64506102	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aacacacctttgccaagatgCgtgttgatagacatatatct	7	9	1	3	rs139687499		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:64506102C>T	ENST00000303052.7	-	6	1089	c.666G>A	c.(664-666)acG>acA	p.T222T	CSNK1G1_ENST00000303032.6_Silent_p.T222T|CTD-2116N17.1_ENST00000606793.1_Silent_p.T204T|CSNK1G1_ENST00000607537.1_Silent_p.T222T	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	222	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						TGCCAAGATGCGTGTTGATAG	0.378																																																0			15						C		1,4405	2.1+/-5.4	0,1,2202	228	180	196		666	-0.5	1	15	dbSNP_134	196	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CSNK1G1	NM_022048.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		222/423	64506102	2,13004	2203	4300	6503	62293155	SO:0001819	synonymous_variant	53944			AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.666G>A	15.37:g.64506102C>T			62293155	Q5JPH1|Q96AE9|Q9HCP1	Silent	SNP	ENST00000303052.7	37	CCDS10192.2																																																																																				0.378	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048		T	64506102	C	T	64506102	2	4	96	1	0	0	0	0	0	0	0	1	3960	755	27	1		1	CSNK1G1	15	64506102	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	13721144	64506102	38025290	135	26081										
STARD5	80765	hgsc.bcm.edu	37	chr15	81611771	81611771	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agcttcatggcagcggagggAgtggaggttctgcttacaca	15	8	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr15:81611771A>G	ENST00000302824.6	-	4	334	c.309T>C	c.(307-309)acT>acC	p.T103T	STARD5_ENST00000559913.1_5'UTR	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	103	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						CAGCGGAGGGAGTGGAGGTTC	0.517																																																0			15											269	263	265					15																	81611771		2203	4300	6503	79398826	SO:0001819	synonymous_variant	80765			AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"StAR-related lipid transfer (START) domain containing"	18065	protein-coding gene	gene with protein product		607050	"START domain containing 5"			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.309T>C	15.37:g.81611771A>G			79398826	P59094	Silent	SNP	ENST00000302824.6	37	CCDS10318.1																																																																																				0.517	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2			G	81611771	A	G	81611771	2	3	96	1	0	0	0	0	0	0	0	1	15299	291	11	4		4	STARD5	15	81611771	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10	17105669	81611771	20919621	136	26082										
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24942331	24942331	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttctgttttcctaggggcggAgtactggggggcgttggagt	18	6	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr16:24942331A>G	ENST00000289968.6	-	19	2358	c.2289T>C	c.(2287-2289)acT>acC	p.T763T	ARHGAP17_ENST00000303665.5_Silent_p.T685T|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	763	Pro-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		CTAGGGGCGGAGTACTGGGGG	0.612																																																0			16											74	89	84					16																	24942331		2197	4300	6497	24849832	SO:0001819	synonymous_variant	55114			AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.2289T>C	16.37:g.24942331A>G			24849832	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	37	CCDS32409.1																																																																																				0.612	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		G	24942331	A	G	24942331	2	3	96	1	0	0	0	0	0	0	0	1	867	291	11	4		4	ARHGAP17	16	24942331	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10		24942331	65412422	137	26083										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57065327	57065327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atcctgcagggaggcggaccTcatcttccttctttccccgc	9	16	3	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr16:57065327T>C	ENST00000262510.6	+	11	2654	c.2429T>C	c.(2428-2430)cTc>cCc	p.L810P	NLRC5_ENST00000539144.1_Missense_Mutation_p.L810P|NLRC5_ENST00000436936.1_Missense_Mutation_p.L810P|NLRC5_ENST00000308149.7_Missense_Mutation_p.L810P	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	810				ADL -> RTI (in Ref. 1; AAO59377 and 2; ABO40479). {ECO:0000305}.	defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GAGGCGGACCTCATCTTCCTT	0.557																																																0			16											138	114	122					16																	57065327		2198	4300	6498	55622828	SO:0001583	missense	84166			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2429T>C	16.37:g.57065327T>C	ENSP00000262510:p.Leu810Pro		55622828	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138040	0.56936	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030	T;T;T;T;T;T	0.75260	-0.71;-0.74;-0.92;-0.74;2.26;0.24	4.18	4.18	0.49190	.	.	.	.	.	T	0.65811	0.2727	L	0.29908	0.895	0.54753	D	0.999983	B;B;B;B	0.31503	0.119;0.174;0.326;0.063	B;B;B;B	0.38458	0.072;0.143;0.274;0.068	T	0.68074	-0.5505	9	0.62326	D	0.03	.	9.9174	0.41444	0.0:0.0:0.0:1.0	.	810;810;810;810	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	P	810;810;810;284;810;317;109	ENSP00000262510:L810P;ENSP00000308886:L810P;ENSP00000389739:L810P;ENSP00000441727:L810P;ENSP00000441597:L317P;ENSP00000440153:L109P	ENSP00000262510:L810P	L	+	2	0	NLRC5	55622828	0.173000	0.23056	0.997000	0.53966	0.787000	0.44495	3.042000	0.49815	2.127000	0.65507	0.459000	0.35465	CTC		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57065327	T	C	57065327	3	2	96	1	0	0	0	0	1	0	0	0	10501	1551	54	4	2463	4	NLRC5	16	57065327	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	32122996	57065327	33289426	138	26084										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68191791	68191791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gctcctgggctataacgaaaAgccaataaatctacaaatgt	7	9	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr16:68191791A>G	ENST00000346183.3	+	4	1445	c.1421A>G	c.(1420-1422)aAg>aGg	p.K474R	NFATC3_ENST00000575270.1_Missense_Mutation_p.K474R|NFATC3_ENST00000329524.4_Missense_Mutation_p.K474R|NFATC3_ENST00000349223.5_Missense_Mutation_p.K474R|NFATC3_ENST00000535127.2_3'UTR	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	474	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TATAACGAAAAGCCAATAAAT	0.373																																																0			16											76	73	74					16																	68191791		2198	4300	6498	66749292	SO:0001583	missense	4775			L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1421A>G	16.37:g.68191791A>G	ENSP00000300659:p.Lys474Arg		66749292	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487086	0.84854	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.44482	0.92;0.92;0.92	4.99	4.99	0.66335	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.63379	0.2506	M	0.71581	2.175	0.58432	D	0.999997	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.81914	0.995;0.919;0.995;0.988	T	0.67852	-0.5563	10	0.72032	D	0.01	-6.3024	14.6788	0.69001	1.0:0.0:0.0:0.0	.	474;474;474;474	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	R	474	ENSP00000264008:K474R;ENSP00000300659:K474R;ENSP00000331324:K474R	ENSP00000331324:K474R	K	+	2	0	NFATC3	66749292	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	8.925000	0.92832	1.883000	0.54544	0.477000	0.44152	AAG		0.373	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		G	68191791	A	G	68191791	3	3	96	1	0	0	0	0	1	0	0	0	10395	72	3	4	1435	4	NFATC3	16	68191791	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	11126464	68191791	22162962	139	26085										
WDR81	124997	hgsc.bcm.edu	37	chr17	1628758	1628758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	acagtcacagccctgcccccTcagctgtccctgccttggac	8	19	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:1628758T>C	ENST00000409644.1	+	1	505	c.505T>C	c.(505-507)Tca>Cca	p.S169P	WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000419248.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	169					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCTGCCCCCTCAGCTGTCCC	0.587																																																0			17											31	30	30					17																	1628758		692	1590	2282	1575508	SO:0001583	missense	124997			AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.505T>C	17.37:g.1628758T>C	ENSP00000386609:p.Ser169Pro		1575508	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	T	8.228	0.804120	0.16467	.	.	ENSG00000167716	ENST00000409644	T	0.54675	0.56	5.64	-2.4	0.06583	.	.	.	.	.	T	0.28234	0.0697	.	.	.	0.19300	N	0.999976	.	.	.	.	.	.	T	0.20240	-1.0281	6	0.21540	T	0.41	.	1.5223	0.02518	0.1156:0.23:0.2568:0.3976	.	.	.	.	P	169	ENSP00000386609:S169P	ENSP00000386609:S169P	S	+	1	0	WDR81	1575508	0.037000	0.19845	0.003000	0.11579	0.031000	0.12232	0.592000	0.23984	-0.327000	0.08551	0.528000	0.53228	TCA		0.587	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		C	1628758	T	C	1628758	3	2	96	1	0	0	0	0	1	0	0	0	17370	1551	54	4	569	4	WDR81	17	1628758	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10		1628758	79566452	140	26086										
SPNS2	124976	hgsc.bcm.edu	37	chr17	4439611	4439611	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tccccgctctgggagttcctGagcctgggctacgcgctcat	12	15	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:4439611G>A	ENST00000329078.3	+	11	1707	c.1497G>A	c.(1495-1497)ctG>ctA	p.L499L		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	499					B cell homeostasis (GO:0001782)|bone development (GO:0060348)|lymph node development (GO:0048535)|lymphocyte migration (GO:0072676)|regulation of eye pigmentation (GO:0048073)|regulation of humoral immune response (GO:0002920)|sphingolipid metabolic process (GO:0006665)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell homeostasis (GO:0043029)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	sphingolipid transporter activity (GO:0046624)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6						GGGAGTTCCTGAGCCTGGGCT	0.637																																																0			17											94	80	84					17																	4439611		1568	3582	5150	4386360	SO:0001819	synonymous_variant	124976			BC041772	CCDS42237.1	17p13.2	2008-12-15				ENSG00000183018			26992	protein-coding gene	gene with protein product		612584				12815463	Standard	NM_001124758		Approved		uc002fxx.2	Q8IVW8		ENST00000329078.3:c.1497G>A	17.37:g.4439611G>A			4386360	B9A1T3	Silent	SNP	ENST00000329078.3	37	CCDS42237.1																																																																																				0.637	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1			A	4439611	G	A	4439611	2	1	96	1	0	0	0	0	0	0	0	1	15114	1277	45	3		3	SPNS2	17	4439611	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	2810853	4439611	76755599	141	26087										
TP53	7157	hgsc.bcm.edu	37	chr17	7578479	7578479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gacgcgggtgccgggcggggGtgtggaatcaacccacagct	18	11	1	0	rs28934874|rs137852790|rs137852791		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:7578479G>A	ENST00000269305.4	-	5	640	c.451C>T	c.(451-453)Ccc>Tcc	p.P151S	TP53_ENST00000420246.2_Missense_Mutation_p.P151S|TP53_ENST00000455263.2_Missense_Mutation_p.P151S|TP53_ENST00000359597.4_Missense_Mutation_p.P151S|TP53_ENST00000413465.2_Missense_Mutation_p.P151S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.P151S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	151	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934874). {ECO:0000269|PubMed:7682763}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P151S(68)|p.P151T(16)|p.P151A(13)|p.P152fs*18(9)|p.0?(8)|p.T150fs*16(6)|p.P151fs*30(6)|p.?(5)|p.P58A(2)|p.P58S(2)|p.P19A(2)|p.P19S(2)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.P151del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.P58T(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.Q144fs*16(1)|p.P19T(1)|p.P152fs*14(1)|p.T18fs*16(1)|p.T150_P151delTP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGGGCGGGGGTGTGGAATCA	0.612		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	156	Substitution - Missense(107)|Deletion - Frameshift(23)|Whole gene deletion(8)|Deletion - In frame(7)|Insertion - Frameshift(6)|Unknown(5)	upper_aerodigestive_tract(20)|large_intestine(17)|ovary(16)|lung(15)|oesophagus(12)|endometrium(11)|stomach(9)|breast(9)|central_nervous_system(7)|liver(7)|skin(7)|haematopoietic_and_lymphoid_tissue(5)|soft_tissue(4)|urinary_tract(4)|prostate(4)|bone(4)|vulva(2)|pancreas(2)|biliary_tract(1)	17	GRCh37	CM012662|CM941326	TP53	M	rs28934874						55	55	55					17																	7578479		2203	4300	6503	7519204	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.451C>T	17.37:g.7578479G>A	ENSP00000269305:p.Pro151Ser		7519204	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460739	0.63513	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99881	-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47	5.59	5.59	0.84812	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110207	0.64402	D	0.000007	D	0.99894	0.9949	M	0.87038	2.855	0.54753	D	0.999985	D;P;P;P;D;P;D	0.89917	0.99;0.941;0.92;0.835;0.98;0.953;1.0	P;P;P;P;P;P;D	0.97110	0.793;0.749;0.814;0.652;0.837;0.837;1.0	D	0.96419	0.9310	10	0.87932	D	0	-14.1156	17.4784	0.87667	0.0:0.0:1.0:0.0	rs28934874	112;151;151;58;151;151;151	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	151;151;151;151;151;151;140;58;19;58;19;151	ENSP00000410739:P151S;ENSP00000352610:P151S;ENSP00000269305:P151S;ENSP00000398846:P151S;ENSP00000391127:P151S;ENSP00000391478:P151S;ENSP00000425104:P19S;ENSP00000423862:P58S;ENSP00000424104:P151S	ENSP00000269305:P151S	P	-	1	0	TP53	7519204	1.000000	0.71417	0.971000	0.41717	0.067000	0.16453	7.823000	0.86660	2.804000	0.96469	0.655000	0.94253	CCC		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578479	G	A	7578479	3	1	96	1	0	0	0	0	1	0	0	0	16421	1261	44	3	847	3	TP53	17	7578479	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3138868	7578479	73616731	142	26088										
TP53	7157	hgsc.bcm.edu	37	chr17	7579591	7579591	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcttgggacggcaagggggaCtgtagatgggtgaaaagagc	19	5	0	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:7579591C>G	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	17	GRCh37	CS971912	TP53	S							141	137	138					17																	7579591		2203	4300	6503	7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>C	17.37:g.7579591C>G			7520316	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.036	0.374935	0.11409	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40870	D	0.9839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	G	7579591	C	G	7579591	5	3	96	1	0	0	0	0	0	0	1	0	16421	579	20	5	1206	5	TP53	17	7579591	Splice_Site	SNP	C	TCGA-DC-6157-01A-11D-1657-10	1112	7579591	73615619	143	26089										
FAM83G	644815	hgsc.bcm.edu	37	chr17	18875008	18875008	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctagggggtcctgggaagccGtctttatccctagtccctga	12	12	1	1	rs187116335		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:18875008G>A	ENST00000388995.6	-	6	2359	c.2136C>T	c.(2134-2136)gaC>gaT	p.D712D	SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Silent_p.D712D|FAM83G_ENST00000585154.2_Silent_p.D712D|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000317977.6_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	712					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CTGGGAAGCCGTCTTTATCCC	0.622													G|||	1	0.000199681	0	0	5008	,	,		17217	0.001		0	False		,,,				2504	0															0			17						G	,,	0,3986		0,0,1993	47	56	53		2136,,	-4.4	0.1	17		53	3,8305		0,3,4151	no	coding-synonymous,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	,,	0,3,6144	AA,AG,GG		0.0361,0.0,0.0244	,,	712/824,,	18875008	3,12291	1993	4154	6147	18815733	SO:0001819	synonymous_variant	644815			AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2136C>T	17.37:g.18875008G>A			18815733	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	37	CCDS42276.1																																																																																				0.622	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18875008	G	A	18875008	2	1	96	1	0	0	0	0	0	0	0	1	5658	1136	40	1		1	FAM83G	17	18875008	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	11295417	18875008	62320202	144	26090										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56386607	56386607	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctgacttctcctcctcctcGtcctcctcttcctcttcctc	2	22	3	1	rs148608257|rs200436316	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:56386607G>T	ENST00000343736.4	-	22	4189	c.4026C>A	c.(4024-4026)gaC>gaA	p.D1342E	BZRAP1_ENST00000355701.3_Missense_Mutation_p.D1342E|BZRAP1_ENST00000268893.6_Missense_Mutation_p.D1282E			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1342	Poly-Glu.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					cctcctcctcgtcctcctctt	0.602																																																0			17											66	68	68					17																	56386607		2203	4300	6503	53741606	SO:0001583	missense	9256			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4026C>A	17.37:g.56386607G>T	ENSP00000345824:p.Asp1342Glu		53741606	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.380184	0.00205	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	D;D;D	0.86865	-2.18;-2.18;-2.18	5.22	-10.1	0.00402	.	0.488446	0.24454	N	0.038383	T	0.49660	0.1570	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.65825	-0.6074	10	0.02654	T	1	.	0.8864	0.01245	0.273:0.3319:0.1809:0.2142	.	1342;1282;1342	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	E	1342;1342;1282	ENSP00000347929:D1342E;ENSP00000345824:D1342E;ENSP00000268893:D1282E	ENSP00000268893:D1282E	D	-	3	2	BZRAP1	53741606	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-2.513000	0.00957	-1.250000	0.02497	-1.482000	0.00985	GAC		0.602	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56386607	G	T	56386607	3	4	96	1	0	0	0	0	1	0	0	0	1580	1136	40	2	1587	2	BZRAP1	17	56386607	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	37511599	56386607	24808603	145	26091										
NOL11	25926	hgsc.bcm.edu	37	chr17	65716047	65716047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aagaatatggaataatgaagAtgtaaacctggataaagtat	9	2	0	3	rs547266367	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:65716047A>G	ENST00000253247.4	+	3	396	c.281A>G	c.(280-282)gAt>gGt	p.D94G	NOL11_ENST00000581966.1_3'UTR|NOL11_ENST00000535137.1_5'UTR	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	94					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			AATAATGAAGATGTAAACCTG	0.234																																																0			17											39	43	42					17																	65716047		2171	4245	6416	63146509	SO:0001583	missense	25926			AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.281A>G	17.37:g.65716047A>G	ENSP00000253247:p.Asp94Gly		63146509	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	37	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.892891	0.33442	.	.	ENSG00000130935	ENST00000253247	T	0.56611	0.45	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.65565	0.2703	M	0.68952	2.095	0.80722	D	1	D	0.62365	0.991	P	0.60541	0.876	T	0.69435	-0.5146	10	0.72032	D	0.01	-17.8901	11.5959	0.50972	1.0:0.0:0.0:0.0	.	94	Q9H8H0	NOL11_HUMAN	G	94	ENSP00000253247:D94G	ENSP00000253247:D94G	D	+	2	0	NOL11	63146509	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.095000	0.89535	1.808000	0.52836	0.379000	0.24179	GAT		0.234	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		G	65716047	A	G	65716047	3	3	96	1	0	0	0	0	1	0	0	0	10552	333	12	4	291	4	NOL11	17	65716047	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	9329440	65716047	15479163	146	26092										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66933106	66933106	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aattacctgtatggtccttgTgctccttctttgctggcatt	8	10	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr17:66933106T>A	ENST00000269080.2	-	4	589	c.452A>T	c.(451-453)cAc>cTc	p.H151L	ABCA8_ENST00000430352.2_Missense_Mutation_p.H151L|ABCA8_ENST00000586539.1_Missense_Mutation_p.H151L	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	151					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					ATGGTCCTTGTGCTCCTTCTT	0.353																																																0			17											148	123	132					17																	66933106		2203	4300	6503	64444701	SO:0001583	missense	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.452A>T	17.37:g.66933106T>A	ENSP00000269080:p.His151Leu		64444701	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	9.630	1.136035	0.21123	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.86432	-2.12;-2.12	4.8	0.914	0.19360	.	0.684095	0.13381	N	0.392142	T	0.80292	0.4596	L	0.49256	1.55	0.09310	N	1	B;B;B;B;B	0.17038	0.016;0.02;0.009;0.007;0.009	B;B;B;B;B	0.23852	0.017;0.049;0.029;0.029;0.02	T	0.61436	-0.7063	10	0.11794	T	0.64	.	7.7443	0.28860	0.5036:0.0:0.0:0.4963	.	90;151;151;151;151	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	L	151;151;90;151	ENSP00000269080:H151L;ENSP00000402814:H151L	ENSP00000269080:H151L	H	-	2	0	ABCA8	64444701	0.158000	0.22850	0.061000	0.19648	0.020000	0.10135	0.672000	0.25187	0.346000	0.23899	0.533000	0.62120	CAC		0.353	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66933106	T	A	66933106	3	1	96	1	0	0	0	0	1	0	0	0	38	1696	59	5	4433	5	ABCA8	17	66933106	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1217059	66933106	14262104	147	26093										
DCC	1630	hgsc.bcm.edu	37	chr18	50866179	50866179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcccttgaacccaaacatcgTggtgcgaggttatattatcg	9	10	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr18:50866179T>C	ENST00000442544.2	+	15	2877	c.2261T>C	c.(2260-2262)gTg>gCg	p.V754A	DCC_ENST00000581580.1_Missense_Mutation_p.V409A|DCC_ENST00000412726.1_Missense_Mutation_p.V602A	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	754	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCAAACATCGTGGTGCGAGGT	0.488																																																0			18											215	178	191					18																	50866179		2203	4300	6503	49120177	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2261T>C	18.37:g.50866179T>C	ENSP00000389140:p.Val754Ala		49120177		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889824	0.52014	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.56444	0.46;0.46	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.099300	0.42964	D	0.000635	T	0.71273	0.3320	M	0.68593	2.085	0.44702	D	0.997693	B;B;P	0.38223	0.26;0.26;0.623	P;P;P	0.62382	0.813;0.813;0.901	T	0.73357	-0.4008	10	0.72032	D	0.01	.	14.2812	0.66213	0.0:0.0:0.0:1.0	.	602;602;754	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	A	754;687;602	ENSP00000389140:V754A;ENSP00000397322:V602A	ENSP00000304146:V687A	V	+	2	0	DCC	49120177	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.755000	0.85180	2.074000	0.62210	0.533000	0.62120	GTG		0.488	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50866179	T	C	50866179	3	2	96	1	0	0	0	0	1	0	0	0	4288	1696	59	4	2319	4	DCC	18	50866179	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10		50866179	27211069	148	26094										
PIGN	23556	hgsc.bcm.edu	37	chr18	59815501	59815501	+	Frame_Shift_Del	DEL	A	A	-													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctattcctaataaatgtaagAaaaaaactattttctcttca							TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr18:59815501delA	ENST00000357637.5	-	8	1035	c.620delT	c.(619-621)ttcfs	p.F207fs	PIGN_ENST00000400334.3_Frame_Shift_Del_p.F207fs	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	207					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TAAATGTAAGAAAAAAACTAT	0.289																																																0			18											31	29	30					18																	59815501		1737	3902	5639	57966481	SO:0001589	frameshift_variant	23556			AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.620delT	18.37:g.59815501delA	ENSP00000350263:p.Phe207fs		57966481	Q7L8F8|Q8TC01|Q9NT05	Frame_Shift_Del	DEL	ENST00000357637.5	37	CCDS45879.1																																																																																				0.289	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		-	59815501	A	-	59815501	7	5	96	1	0	1	0	1	0	0	0	0	11924	246	9	0	2271	0	PIGN	18	59815501	Frame_Shift_Del	DEL	A	TCGA-DC-6157-01A-11D-1657-10	8949322	59815501	18261747	149	26095										
FSD1	79187	hgsc.bcm.edu	37	chr19	4318479	4318479	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gatggcaaggggcggacggcGtctcccatcaactccccagc	13	15	2	0	rs144756712		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:4318479G>A	ENST00000221856.6	+	9	1083	c.936G>A	c.(934-936)gcG>gcA	p.A312A	FSD1_ENST00000597590.1_Silent_p.A312A|FSD1_ENST00000598010.1_3'UTR	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	312	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGGACGGCGTCTCCCATCA	0.617													G|||	1	0.000199681	8e-04	0	5008	,	,		15740	0		0	False		,,,				2504	0															0			19											65	51	56					19																	4318479		2203	4300	6503	4269479	SO:0001819	synonymous_variant	79187			AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.936G>A	19.37:g.4318479G>A			4269479	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																				0.617	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		A	4318479	G	A	4318479	2	1	96	1	0	0	0	0	0	0	0	1	6089	1132	40	1		1	FSD1	19	4318479	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10		4318479	54810504	150	26096										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4512860	4512958	+	In_Frame_Del	DEL	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	-													0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cggcaccggtcaccccactgCagacagtgttcttggtgcca					rs139077831|rs199944112|rs79662071|rs111683150|rs183054734|rs61730750|rs61730751|rs187432849|rs80098309|rs75031432|rs543991052|rs139917681|rs200699570|rs560475123|rs201080851|rs112609940|rs375080147|rs200149931|rs61730749|rs61731458|rs61731459|rs199854884|rs201827810|rs377602894|rs576203663	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:4512860_4512958delCAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	ENST00000301286.3	-	3	971_1069	c.972_1070delTAGTGGGGTGACTGGTGCCATGAATGTGGCCAAAGGAACCATCCAGACCGGCGTGGACACCACCAAGACTGTCCTAACTGGCACCAAGAACACTGTCTG	c.(970-1071)tgtagtggggtgactggtgccatgaatgtggccaaaggaaccatccagaccggcgtggacaccaccaagactgtcctaactggcaccaagaacactgtctgc>tgc	p.324_357CSGVTGAMNVAKGTIQTGVDTTKTVLTGTKNTVC>C		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	324	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CACCCCACTGCAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGT	0.569																																																0			19																																								4463958	SO:0001651	inframe_deletion	0			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.972_1070delTAGTGGGGTGACTGGTGCCATGAATGTGGCCAAAGGAACCATCCAGACCGGCGTGGACACCACCAAGACTGTCCTAACTGGCACCAAGAACACTGTCTG	19.37:g.4512860_4512958delCAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	ENSP00000301286:p.Cys324_Val356del		4463860	A6NEI2	In_Frame_Del	DEL	ENST00000301286.3	37	CCDS45927.1																																																																																				0.569	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		-	4512958	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	-	4512860	7	5	96	1	0	1	0	1	0	0	0	0	12123	710	25	0	3019	0	PLIN4	19	4512860	In_Frame_Del	DEL	CAGACAGTGTTCTTGGTGCCAGTTAGGACAGTCTTGGTGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTA	TCGA-DC-6157-01A-11D-1657-10	194381	4512860	54616123	151	26097										
LRRC8E	80131	hgsc.bcm.edu	37	chr19	7964899	7964899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcaaatgcgaggagctccgcGaggtgccgctttgggtgttt	15	9	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:7964899G>A	ENST00000306708.6	+	3	1593	c.1492G>A	c.(1492-1494)Gag>Aag	p.E498K	RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_Missense_Mutation_p.S123L	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	498					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GGAGCTCCGCGAGGTGCCGCT	0.657																																																0			19											31	24	27					19																	7964899		2201	4298	6499	7870899	SO:0001583	missense	80131				CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1492G>A	19.37:g.7964899G>A	ENSP00000306524:p.Glu498Lys		7870899	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.78|15.78	2.935643|2.935643	0.52972|0.52972	.|.	.|.	ENSG00000171017|ENSG00000214248	ENST00000306708|ENST00000539278	T|.	0.20598|.	2.06|.	4.78|4.78	4.78|4.78	0.61160|0.61160	.|.	0.053877|.	0.64402|.	D|.	0.000001|.	T|T	0.69735|0.69735	0.3144|0.3144	L|L	0.52759|0.52759	1.655|1.655	0.45403|0.45403	D|D	0.998382|0.998382	P|.	0.39520|.	0.676|.	B|.	0.29077|.	0.098|.	T|T	0.73078|0.73078	-0.4096|-0.4096	10|6	0.23302|0.87932	T|D	0.38|0	.|.	15.3436|15.3436	0.74317|0.74317	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	498|.	Q6NSJ5|.	LRC8E_HUMAN|.	K|L	498|123	ENSP00000306524:E498K|.	ENSP00000306524:E498K|ENSP00000441047:S123L	E|S	+|-	1|2	0|0	LRRC8E|AC010336.2	7870899|7870899	1.000000|1.000000	0.71417|0.71417	0.917000|0.917000	0.36280|0.36280	0.957000|0.957000	0.61999|0.61999	7.800000|7.800000	0.85949|0.85949	2.491000|2.491000	0.84063|0.84063	0.650000|0.650000	0.86243|0.86243	GAG|TCG		0.657	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		A	7964899	G	A	7964899	3	1	96	1	0	0	0	0	1	0	0	0	9054	1059	37	1	1498	1	LRRC8E	19	7964899	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3452039	7964899	51164084	152	26098										
MUC16	94025	hgsc.bcm.edu	37	chr19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ctgtgtttatggaaggatgcGttgtctctatatctgtggtg	13	5	2	0	rs17000816	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:9072975G>A	ENST00000397910.4	-	3	14674	c.14471C>T	c.(14470-14472)aCg>aTg	p.T4824M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4826	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAAGGATGCGTTGTCTCTAT	0.448													G|||	936	0.186901	0.0923	0.2536	5008	,	,		23617	0.3254		0.1322	False		,,,				2504	0.181															0			19							MET/THR	399,3763		17,365,1699	165	153	157		14471	-1.5	0	19	dbSNP_123	157	1164,7258		73,1018,3120	yes	missense	MUC16	NM_024690.2	81	90,1383,4819	AA,AG,GG		13.8209,9.5867,12.4205	benign	4824/14508	9072975	1563,11021	2081	4211	6292	8933975	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14471C>T	19.37:g.9072975G>A	ENSP00000381008:p.Thr4824Met		8933975	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	1.725	-0.495688	0.04291	0.095867	0.138209	ENSG00000181143	ENST00000397910	T	0.20332	2.08	2.02	-1.54	0.08584	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.46005	-0.9222	8	0.87932	D	0	.	5.65	0.17610	0.644:0.0:0.356:0.0	rs17000816;rs56515928;rs17000816	4824	B5ME49	.	M	4824	ENSP00000381008:T4824M	ENSP00000381008:T4824M	T	-	2	0	MUC16	8933975	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.495000	0.02294	-0.474000	0.06862	-0.692000	0.03713	ACG		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9072975	G	A	9072975	3	1	96	1	0	0	0	0	1	0	0	0	10003	1145	40	1	29380	1	MUC16	19	9072975	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	1108076	9072975	50056008	153	26099										
TMED1	11018	hgsc.bcm.edu	37	chr19	10945726	10945726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cagttcaaagaacaccagctTctcggagatggtgctgaagg	12	9	2	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:10945726T>C	ENST00000214869.2	-	3	447	c.349A>G	c.(349-351)Aag>Gag	p.K117E	C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000588289.1_5'UTR|TMED1_ENST00000591695.1_Intron	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	117	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						AACACCAGCTTCTCGGAGATG	0.567																																																0			19											115	112	113					19																	10945726		2203	4300	6503	10806726	SO:0001583	missense	11018			U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.349A>G	19.37:g.10945726T>C	ENSP00000214869:p.Lys117Glu		10806726		Missense_Mutation	SNP	ENST00000214869.2	37	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.930171	0.92389	.	.	ENSG00000099203	ENST00000214869	T	0.67171	-0.25	5.15	4.13	0.48395	GOLD (3);	0.046316	0.85682	D	0.000000	D	0.85349	0.5676	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86728	0.1946	10	0.87932	D	0	-30.0631	9.8575	0.41094	0.0:0.0825:0.0:0.9175	.	117	Q13445	TMED1_HUMAN	E	117	ENSP00000214869:K117E	ENSP00000214869:K117E	K	-	1	0	TMED1	10806726	1.000000	0.71417	0.978000	0.43139	0.972000	0.66771	7.766000	0.85320	0.808000	0.34231	0.459000	0.35465	AAG		0.567	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		C	10945726	T	C	10945726	3	2	96	1	0	0	0	0	1	0	0	0	16041	1792	62	4	342	4	TMED1	19	10945726	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1872751	10945726	48183257	154	26100										
DHPS	1725	hgsc.bcm.edu	37	chr19	12790732	12790732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cagctgtggtcaccaatacgTccacctgcagccacaaggca	9	15	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:12790732T>C	ENST00000210060.7	-	3	512	c.377A>G	c.(376-378)gAc>gGc	p.D126G	CTD-2192J16.26_ENST00000593554.1_lincRNA|DHPS_ENST00000599481.1_5'UTR|DHPS_ENST00000351660.5_Missense_Mutation_p.D126G|DHPS_ENST00000594424.1_Missense_Mutation_p.D84G	NM_001930.3	NP_001921.1	P49366	DHYS_HUMAN	deoxyhypusine synthase	126					cellular protein metabolic process (GO:0044267)|deoxyhypusine biosynthetic process from spermidine (GO:0050983)|glucose homeostasis (GO:0042593)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell proliferation (GO:0042102)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|translation (GO:0006412)	cytosol (GO:0005829)	deoxyhypusine synthase activity (GO:0034038)			central_nervous_system(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)	8						CACCAATACGTCCACCTGCAG	0.572																																																0			19											40	40	40					19																	12790732		2203	4300	6503	12651732	SO:0001583	missense	1725			U79262	CCDS12276.1, CCDS12277.1, CCDS59354.1	19p13.2	2011-11-24			ENSG00000095059	ENSG00000095059			2869	protein-coding gene	gene with protein product	"migration-inducing gene 13"	600944				7673224	Standard	NM_001930		Approved	MIG13	uc002muh.2	P49366		ENST00000210060.7:c.377A>G	19.37:g.12790732T>C	ENSP00000210060:p.Asp126Gly		12651732	A8K688|M0R1I5|Q13184|Q13276|Q9UDG0	Missense_Mutation	SNP	ENST00000210060.7	37	CCDS12276.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.362954	0.82353	.	.	ENSG00000095059	ENST00000210060;ENST00000351660	T;T	0.54071	0.59;0.59	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.79919	0.4529	H	0.95260	3.645	0.80722	D	1	D;P;D	0.89917	1.0;0.688;0.993	D;P;P	0.73380	0.98;0.745;0.905	D	0.85866	0.1413	10	0.87932	D	0	-30.8443	13.7603	0.62961	0.0:0.0:0.0:1.0	.	126;126;126	Q5J8M5;P49366-2;P49366	.;.;DHYS_HUMAN	G	126	ENSP00000210060:D126G;ENSP00000221303:D126G	ENSP00000210060:D126G	D	-	2	0	DHPS	12651732	1.000000	0.71417	0.942000	0.38095	0.803000	0.45373	7.253000	0.78320	2.137000	0.66172	0.533000	0.62120	GAC		0.572	DHPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462708.1	NM_001930		C	12790732	T	C	12790732	3	2	96	1	0	0	0	0	1	0	0	0	4496	1667	58	4	760	4	DHPS	19	12790732	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1845006	12790732	46338251	155	26101										
MAST3	23031	hgsc.bcm.edu	37	chr19	18245673	18245673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ccccgaggtgatcttccgccAgggctatgggaagccagtgg	15	12	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:18245673A>G	ENST00000262811.6	+	16	1664	c.1664A>G	c.(1663-1665)cAg>cGg	p.Q555R		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	555	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						ATCTTCCGCCAGGGCTATGGG	0.632																																																0			19											86	91	90					19																	18245673		2031	4205	6236	18106673	SO:0001583	missense	23031			AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.1664A>G	19.37:g.18245673A>G	ENSP00000262811:p.Gln555Arg		18106673	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	37	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.318680	0.81469	.	.	ENSG00000099308	ENST00000262811	T	0.64803	-0.12	4.87	4.87	0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115003	0.64402	D	0.000008	T	0.61426	0.2346	L	0.31476	0.935	0.58432	D	0.999999	P	0.37423	0.594	P	0.48189	0.57	T	0.65240	-0.6216	10	0.59425	D	0.04	-38.4978	13.6275	0.62173	1.0:0.0:0.0:0.0	.	555	O60307	MAST3_HUMAN	R	555	ENSP00000262811:Q555R	ENSP00000262811:Q555R	Q	+	2	0	MAST3	18106673	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	9.209000	0.95087	1.830000	0.53286	0.260000	0.18958	CAG		0.632	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		G	18245673	A	G	18245673	3	3	96	1	0	0	0	0	1	0	0	0	9356	188	7	4	1726	4	MAST3	19	18245673	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	5454941	18245673	40883310	156	26102										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33424435	33424435	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cttaagttttaactgtagttCtttcattgcttgtttcattg	6	6	3	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:33424435C>A	ENST00000305768.5	-	8	896	c.808G>T	c.(808-810)Gaa>Taa	p.E270*	CEP89_ENST00000590597.2_Nonsense_Mutation_p.E270*	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	270					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						AACTGTAGTTCTTTCATTGCT	0.393																																																0			19											259	231	241					19																	33424435		2203	4300	6503	38116275	SO:0001587	stop_gained	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.808G>T	19.37:g.33424435C>A	ENSP00000306105:p.Glu270*		38116275	B9EGA6|Q8N5J8	Nonsense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815921	0.90790	.	.	ENSG00000121289	ENST00000305768	.	.	.	5.09	4.06	0.47325	.	1.156050	0.06054	N	0.657076	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-3.563	10.9047	0.47073	0.0:0.9107:0.0:0.0893	.	.	.	.	X	270	.	ENSP00000306105:E270X	E	-	1	0	CEP89	38116275	0.998000	0.40836	0.627000	0.29227	0.061000	0.15899	1.697000	0.37784	1.277000	0.44412	0.467000	0.42956	GAA		0.393	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33424435	C	A	33424435	4	1	96	1	0	0	0	0	0	1	0	0	2765	922	32	2	1591	2	CCDC123	19	33424435	Nonsense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	15178762	33424435	25704548	157	26103										
LSR	51599	hgsc.bcm.edu	37	chr19	35741361	35741361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggaagtacaagtctttctgcCgggaccgcatcgccgatgcc	12	13	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:35741361C>T	ENST00000361790.3	+	2	556	c.397C>T	c.(397-399)Cgg>Tgg	p.R133W	LSR_ENST00000360798.3_Missense_Mutation_p.R133W|LSR_ENST00000347609.4_Missense_Mutation_p.R96W|LSR_ENST00000354900.3_Missense_Mutation_p.R133W|AC002128.5_ENST00000604161.1_RNA|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000427250.1_Missense_Mutation_p.R85W|LSR_ENST00000602122.1_Missense_Mutation_p.R133W	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	133	Ig-like V-type.				embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTCTTTCTGCCGGGACCGCAT	0.617																																																0			19											180	149	159					19																	35741361		2203	4300	6503	40433201	SO:0001583	missense	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.397C>T	19.37:g.35741361C>T	ENSP00000354575:p.Arg133Trp		40433201	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	37	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075063	0.76415	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.69306	4.79;4.79;4.79;4.79;-0.39	4.88	3.79	0.43588	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.78375	0.4273	M	0.68952	2.095	0.30048	N	0.812031	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.991;0.999;0.997;1.0;0.991;0.991	T	0.75204	-0.3400	10	0.87932	D	0	-22.5233	12.4635	0.55745	0.1669:0.8331:0.0:0.0	.	90;96;133;133;133;133	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	W	133;133;133;96;85	ENSP00000354575:R133W;ENSP00000346976:R133W;ENSP00000354034:R133W;ENSP00000262627:R96W;ENSP00000394479:R85W	ENSP00000262627:R96W	R	+	1	2	LSR	40433201	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.149000	0.42244	2.548000	0.85928	0.655000	0.94253	CGG		0.617	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35741361	C	T	35741361	3	4	96	1	0	0	0	0	1	0	0	0	9093	643	23	1	403	1	LSR	19	35741361	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	2316926	35741361	23387622	158	26104										
MLL4	9757	hgsc.bcm.edu	37	chr19	36224680	36224680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcaggcccctccaggaacggTcccctttgctgccacttccg	10	18	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:36224680T>C	ENST00000222270.7	+	30	7066	c.7066T>C	c.(7066-7068)Tcc>Ccc	p.S2356P	KMT2B_ENST00000420124.1_Missense_Mutation_p.S2356P|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2356					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCAGGAACGGTCCCCTTTGCT	0.637																																																0			19											50	57	54					19																	36224680		1929	4125	6054	40916520	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7066T>C	19.37:g.36224680T>C	ENSP00000222270:p.Ser2356Pro		40916520	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	T	7.584	0.669352	0.14776	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.82984	-1.67;-1.67	5.46	2.27	0.28462	.	0.346769	0.21116	N	0.079899	T	0.55878	0.1948	N	0.01874	-0.695	0.22858	N	0.998648	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	10	0.23302	T	0.38	.	6.5152	0.22244	0.0:0.259:0.0:0.741	.	2356	Q9UMN6	MLL4_HUMAN	P	2356	ENSP00000222270:S2356P;ENSP00000398837:S2356P	ENSP00000222270:S2356P	S	+	1	0	AD000671.1	40916520	0.951000	0.32395	0.998000	0.56505	0.706000	0.40770	0.478000	0.22212	0.927000	0.37143	0.459000	0.35465	TCC		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36224680	T	C	36224680	3	2	96	1	0	0	0	0	1	0	0	0	9653	1667	58	4	7184	4	MLL4	19	36224680	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	483319	36224680	22904303	159	26105										
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40553361	40553361	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agtaatgtaatcacatctggCttagaaatggaacttcctgc	8	8	2	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:40553361C>T	ENST00000434248.1	-	4	218	c.153G>A	c.(151-153)aaG>aaA	p.K51K	ZNF780B_ENST00000598845.1_Silent_p.K52K|AC005614.5_ENST00000595508.1_RNA|ZNF780B_ENST00000221355.6_5'UTR	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TCACATCTGGCTTAGAAATGG	0.323																																																0			19											106	101	102					19																	40553361		2203	4300	6503	45245201	SO:0001819	synonymous_variant	163131			AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.153G>A	19.37:g.40553361C>T			45245201	B9EH00	Silent	SNP	ENST00000434248.1	37	CCDS46077.1																																																																																				0.323	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		T	40553361	C	T	40553361	2	4	96	1	0	0	0	0	0	0	0	1	18192	796	28	3		3	ZNF780B	19	40553361	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	4328681	40553361	18575622	160	26106										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41383816	41383816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	agcgcagggtggtgctgaccGtctcggtgcctgcaatgaag	16	10	1	2	rs373592664		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:41383816G>A	ENST00000301146.4	-	6	1455	c.914C>T	c.(913-915)aCg>aTg	p.T305M	CYP2A7_ENST00000291764.3_Missense_Mutation_p.T254M|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	305						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GGTGCTGACCGTCTCGGTGCC	0.592																																																0			19						G	MET/THR,MET/THR	0,4406		0,0,2203	135	104	115		914,761	2.2	0	19		115	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	81,81	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	305/495,254/444	41383816	1,13003	2203	4299	6502	46075656	SO:0001583	missense	1549			NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.914C>T	19.37:g.41383816G>A	ENSP00000301146:p.Thr305Met		46075656	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.849305	0.32699	0.0	1.16E-4	ENSG00000198077	ENST00000301146;ENST00000291764	D;D	0.87966	-2.32;-2.32	2.18	2.18	0.27775	.	0.000000	0.85682	U	0.000000	D	0.94407	0.8201	H	0.94542	3.55	0.32960	D	0.52085	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.933;0.957;0.998	D	0.95318	0.8418	10	0.87932	D	0	.	11.4495	0.50145	0.0:0.0:1.0:0.0	.	305;254;305	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	M	305;254	ENSP00000301146:T305M;ENSP00000291764:T254M	ENSP00000291764:T254M	T	-	2	0	CYP2A7	46075656	1.000000	0.71417	0.029000	0.17559	0.025000	0.11179	6.577000	0.74027	1.215000	0.43411	0.184000	0.17185	ACG		0.592	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		A	41383816	G	A	41383816	3	1	96	1	0	0	0	0	1	0	0	0	4169	1145	40	1	586	1	CYP2A7	19	41383816	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	830455	41383816	17745167	161	26107										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51217188	51217188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cagagccttcggtctgggccGccagtgtcaagggggtctct	15	12	3	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:51217188G>A	ENST00000293441.1	-	5	677	c.659C>T	c.(658-660)gCg>gTg	p.A220V	SHANK1_ENST00000359082.3_Missense_Mutation_p.A220V|SHANK1_ENST00000391814.1_Missense_Mutation_p.A220V	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	220					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GGTCTGGGCCGCCAGTGTCAA	0.617																																																0			19											33	34	34					19																	51217188		2203	4300	6503	55909000	SO:0001583	missense	50944			AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.659C>T	19.37:g.51217188G>A	ENSP00000293441:p.Ala220Val		55909000	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.823625	0.71143	.	.	ENSG00000161681	ENST00000293441;ENST00000359082;ENST00000391814	T;T;T	0.72615	-0.67;-0.67;-0.67	3.86	3.86	0.44501	Ankyrin repeat-containing domain (4);	0.094113	0.39407	U	0.001362	D	0.86768	0.6012	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90044	0.4144	10	0.87932	D	0	-21.0929	15.7532	0.78005	0.0:0.0:1.0:0.0	.	220	Q9Y566	SHAN1_HUMAN	V	220	ENSP00000293441:A220V;ENSP00000351984:A220V;ENSP00000375690:A220V	ENSP00000293441:A220V	A	-	2	0	SHANK1	55909000	1.000000	0.71417	0.981000	0.43875	0.954000	0.61252	9.205000	0.95048	2.459000	0.83118	0.561000	0.74099	GCG		0.617	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51217188	G	A	51217188	3	1	96	1	0	0	0	0	1	0	0	0	14301	1087	38	1	5902	1	SHANK1	19	51217188	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	9833372	51217188	7911795	162	26108										
KIR3DL2	3812	hgsc.bcm.edu	37	chr19	55365482	55365482	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttgtcagctcccagtgacccCctggacatcgtgatcacagg	10	14	2	2	rs140583928	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr19:55365482C>T	ENST00000326321.3	+	4	669	c.636C>T	c.(634-636)ccC>ccT	p.P212P	KIR3DL2_ENST00000270442.5_Silent_p.P212P|KIR3DL1_ENST00000402254.2_Intron	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	212					cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.P212P(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		CCAGTGACCCCCTGGACATCG	0.517																																																1	Substitution - coding silent(1)	skin(1)	19											12	11	11					19																	55365482		1639	3364	5003	60057294	SO:0001819	synonymous_variant	3812			L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.636C>T	19.37:g.55365482C>T			60057294	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Silent	SNP	ENST00000326321.3	37	CCDS12906.1																																																																																				0.517	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1			T	55365482	C	T	55365482	2	4	96	1	0	0	0	0	0	0	0	1	8342	610	22	3		3	KIR3DL2	19	55365482	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10	4148294	55365482	3763501	163	26109										
SNAP25	6616	hgsc.bcm.edu	37	chr20	10277601	10277601	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caagtgatgcttacaaaaaaGcctggggcaataatcaggac	10	8	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:10277601G>T	ENST00000254976.2	+	6	521	c.310G>T	c.(310-312)Gcc>Tcc	p.A104S	SNAP25_ENST00000304886.2_Missense_Mutation_p.A104S|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000495883.1_3'UTR	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	104					energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	TTACAAAAAAGCCTGGGGCAA	0.537																																																0			20											79	77	78					20																	10277601		2203	4300	6503	10225601	SO:0001583	missense	6616				CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"resistance to inhibitors of cholinesterase 4 homolog"	600322	"synaptosomal-associated protein, 25kD"	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.310G>T	20.37:g.10277601G>T	ENSP00000254976:p.Ala104Ser		10225601	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	37	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.785701	0.49997	.	.	ENSG00000132639	ENST00000254976;ENST00000304886	.	.	.	5.86	5.86	0.93980	SNAP-25 (1);	0.000000	0.85682	D	0.000000	T	0.58892	0.2154	L	0.50333	1.59	0.80722	D	1	B;B	0.19331	0.035;0.002	B;B	0.18871	0.023;0.011	T	0.53365	-0.8449	9	0.17369	T	0.5	-7.0596	20.1996	0.98256	0.0:0.0:1.0:0.0	.	104;104	P60880-2;P60880	.;SNP25_HUMAN	S	104	.	ENSP00000254976:A104S	A	+	1	0	SNAP25	10225601	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.776000	0.95493	0.650000	0.86243	GCC		0.537	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811		T	10277601	G	T	10277601	3	4	96	1	0	0	0	0	1	0	0	0	14867	971	34	2	450	2	SNAP25	20	10277601	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10		10277601	52747919	164	26110										
REM1	28954	hgsc.bcm.edu	37	chr20	30064410	30064410	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	caatcagcctccctcaacccTcccacccagaaaccttcacc	2	22	3	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:30064410T>C	ENST00000201979.2	+	2	455	c.162T>C	c.(160-162)ccT>ccC	p.P54P	DEFB124_ENST00000481595.1_Intron	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	54					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CCCTCAACCCTCCCACCCAGA	0.627																																																0			20											77	75	76					20																	30064410		2203	4300	6503	29528071	SO:0001819	synonymous_variant	28954			AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.162T>C	20.37:g.30064410T>C			29528071	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	37	CCDS13181.1																																																																																				0.627	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		C	30064410	T	C	30064410	2	2	96	1	0	0	0	0	0	0	0	1	13259	1538	54	4		4	REM1	20	30064410	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	19786809	30064410	32961110	165	26111										
GSS	2937	hgsc.bcm.edu	37	chr20	33529527	33529527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cacccttacttgggtgagccGtagagctcccaggctttggc	12	13	0	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:33529527G>A	ENST00000216951.2	-	6	695	c.597C>T	c.(595-597)taC>taT	p.Y199Y	GSS_ENST00000451957.2_Intron|GSS_ENST00000541098.1_Silent_p.Y71Y	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	199					aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	TGGGTGAGCCGTAGAGCTCCC	0.488																																																0			20											94	89	91					20																	33529527		2203	4300	6503	32993188	SO:0001819	synonymous_variant	5621				CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.597C>T	20.37:g.33529527G>A			32993188	B2R697|B6F210|E1P5P9|Q4TTD9	Silent	SNP	ENST00000216951.2	37	CCDS13245.1																																																																																				0.488	GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2			A	33529527	G	A	33529527	2	1	96	1	0	0	0	0	0	0	0	1	6850	1140	40	1		1	GSS	20	33529527	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	3465117	33529527	29495993	166	26112										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33568412	33568412	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cctcttctgtgtcaccatcaAcccctacaaatggctcccag	5	17	4	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:33568412A>T	ENST00000262873.7	+	6	592	c.500A>T	c.(499-501)aAc>aTc	p.N167I	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	125	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GTCACCATCAACCCCTACAAA	0.527																																																0			20											154	164	161					20																	33568412		2195	4300	6495	33032073	SO:0001583	missense	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.500A>T	20.37:g.33568412A>T	ENSP00000262873:p.Asn167Ile		33032073	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737901	0.89573	.	.	ENSG00000078814	ENST00000262873	D	0.96745	-4.11	4.46	4.46	0.54185	Myosin head, motor domain (3);	0.000000	0.41396	D	0.000883	D	0.99193	0.9720	H	0.99973	5.135	0.58432	D	0.999999	D	0.76494	0.999	D	0.81914	0.995	D	0.97964	1.0339	10	0.87932	D	0	.	14.1848	0.65598	1.0:0.0:0.0:0.0	.	125	A7E2Y1	MYH7B_HUMAN	I	167	ENSP00000262873:N167I	ENSP00000262873:N167I	N	+	2	0	MYH7B	33032073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.139000	0.94554	2.001000	0.58596	0.533000	0.62120	AAC		0.527	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33568412	A	T	33568412	3	4	96	1	0	0	0	0	1	0	0	0	10070	43	2	5	522	5	MYH7B	20	33568412	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	38885	33568412	29457108	167	26113										
BPI	671	hgsc.bcm.edu	37	chr20	36932648	36932648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggccaggggcccttgcaacgCgccgagatgggcgtccctga	16	14	0	2	rs5743498|rs397794979	byFrequency	TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:36932648C>T	ENST00000262865.4	+	1	124	c.35C>T	c.(34-36)gCg>gTg	p.A12V	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	12			A -> T (in dbSNP:rs5743497).|A -> V (in dbSNP:rs5743498).		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				CCTTGCAACGCGCCGAGATGG	0.622													C|||	15	0.00299521	0.0113	0	5008	,	,		16733	0		0	False		,,,				2504	0															0			20						C	VAL/ALA	51,4355	50.2+/-85.5	0,51,2152	73	73	73		35	-3.9	0	20	dbSNP_114	73	0,8600		0,0,4300	yes	missense	BPI	NM_001725.2	64	0,51,6452	TT,TC,CC		0.0,1.1575,0.3921	benign	12/488	36932648	51,12955	2203	4300	6503	36366062	SO:0001583	missense	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.35C>T	20.37:g.36932648C>T	ENSP00000262865:p.Ala12Val		36366062	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	2.080	-0.410868	0.04799	0.011575	0.0	ENSG00000101425	ENST00000418004;ENST00000262865	T;T	0.22539	1.95;3.34	3.16	-3.88	0.04205	.	2.211740	0.02188	N	0.061062	T	0.06826	0.0174	N	0.17674	0.51	0.09310	N	1	B	0.21905	0.062	B	0.08055	0.003	T	0.21586	-1.0241	10	0.02654	T	1	-0.003	4.7158	0.12894	0.1638:0.2728:0.0:0.5635	rs5743498;rs52790490;rs5743498	12	P17213	BPI_HUMAN	V	95;12	ENSP00000393126:A95V;ENSP00000262865:A12V	ENSP00000262865:A12V	A	+	2	0	BPI	36366062	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.810000	0.01729	-0.896000	0.03915	-0.816000	0.03127	GCG		0.622	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		T	36932648	C	T	36932648	3	4	96	1	0	0	0	0	1	0	0	0	1493	768	27	1	37	1	BPI	20	36932648	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	3364236	36932648	26092872	168	26114										
ZHX3	23051	hgsc.bcm.edu	37	chr20	39832940	39832940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cacccacaggctggctagggAcattctccttgagtgtatga	11	11	1	2	rs539008791		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:39832940A>G	ENST00000309060.3	-	4	1032	c.617T>C	c.(616-618)gTc>gCc	p.V206A	ZHX3_ENST00000558993.1_Missense_Mutation_p.V206A|ZHX3_ENST00000540170.1_Missense_Mutation_p.V206A|ZHX3_ENST00000559234.1_Missense_Mutation_p.V206A|ZHX3_ENST00000560361.1_Missense_Mutation_p.V206A|ZHX3_ENST00000432768.2_Missense_Mutation_p.V206A|ZHX3_ENST00000544979.2_Missense_Mutation_p.V206A|ZHX3_ENST00000557816.1_Missense_Mutation_p.V206A			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	206					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CTGGCTAGGGACATTCTCCTT	0.473													A|||	1	0.000199681	0	0	5008	,	,		20619	0		0.001	False		,,,				2504	0															0			20											123	115	118					20																	39832940		2203	4300	6503	39266354	SO:0001583	missense	23051			AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.617T>C	20.37:g.39832940A>G	ENSP00000312222:p.Val206Ala		39266354	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.254279	0.39896	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000432768	T;T;T;T;T	0.30714	1.52;2.92;2.92;2.7;1.52	6.07	1.18	0.20946	.	1.362780	0.04438	N	0.370301	T	0.16938	0.0407	N	0.16478	0.41	0.09310	N	1	B;B;B;B	0.11235	0.0;0.0;0.001;0.004	B;B;B;B	0.11329	0.001;0.001;0.004;0.006	T	0.20240	-1.0281	10	0.06891	T	0.86	-1.8098	5.6543	0.17635	0.6578:0.1306:0.2115:0.0	.	206;206;206;206	A8K8Q0;Q9H4I2;F5H820;F6R4Q5	.;ZHX3_HUMAN;.;.	A	206	ENSP00000312222:V206A;ENSP00000362360:V206A;ENSP00000442290:V206A;ENSP00000443783:V206A;ENSP00000415498:V206A	ENSP00000312222:V206A	V	-	2	0	ZHX3	39266354	0.018000	0.18449	0.000000	0.03702	0.993000	0.82548	1.549000	0.36212	0.169000	0.19679	0.533000	0.62120	GTC		0.473	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		G	39832940	A	G	39832940	3	3	96	1	0	0	0	0	1	0	0	0	17716	275	10	4	2261	4	ZHX3	20	39832940	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	2900292	39832940	23192580	169	26115										
TP53TG5	27296	hgsc.bcm.edu	37	chr20	44005966	44005966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcttgagtagcttcaagagcGacaagttttttaacacctgc	8	9	2	2			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:44005966G>A	ENST00000372726.3	-	3	296	c.140C>T	c.(139-141)tCg>tTg	p.S47L	SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000452133.1_Intron|TP53TG5_ENST00000537995.1_Missense_Mutation_p.S31L	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	47					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						CTTCAAGAGCGACAAGTTTTT	0.512																																																0			20											131	130	130					20																	44005966		2203	4300	6503	43439380	SO:0001583	missense	27296			AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.140C>T	20.37:g.44005966G>A	ENSP00000361811:p.Ser47Leu		43439380		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970101	0.74246	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.27104	1.69;1.69	5.52	4.56	0.56223	.	0.238705	0.30093	N	0.010430	T	0.26085	0.0636	L	0.47190	1.495	0.33948	D	0.644054	P	0.51791	0.948	B	0.43889	0.435	T	0.47005	-0.9150	10	0.87932	D	0	-4.5467	11.5749	0.50856	0.0836:0.0:0.9164:0.0	.	47	Q9Y2B4	T53G5_HUMAN	L	47;31	ENSP00000361811:S47L;ENSP00000438374:S31L	ENSP00000361811:S47L	S	-	2	0	TP53TG5	43439380	0.998000	0.40836	0.861000	0.33841	0.789000	0.44602	3.425000	0.52771	1.467000	0.48044	0.655000	0.94253	TCG		0.512	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		A	44005966	G	A	44005966	3	1	96	1	0	0	0	0	1	0	0	0	16431	1059	37	1	744	1	TP53TG5	20	44005966	Missense_Mutation	SNP	G	TCGA-DC-6157-01A-11D-1657-10	4173026	44005966	19019554	170	26116										
SLC2A10	81031	hgsc.bcm.edu	37	chr20	45354159	45354159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	atgcactggctggtacccccTggggatggaggcacatgttc	14	11	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:45354159T>C	ENST00000359271.2	+	2	734	c.484T>C	c.(484-486)Tgg>Cgg	p.W162R		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	162					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				TGGTACCCCCTGGGGATGGAG	0.617																																																0			20											90	72	78					20																	45354159		2203	4300	6503	44787566	SO:0001583	missense	81031			AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.484T>C	20.37:g.45354159T>C	ENSP00000352216:p.Trp162Arg		44787566	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	37	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.357100	0.01245	.	.	ENSG00000197496	ENST00000359271	T	0.81415	-1.49	5.58	-11.2	0.00127	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.053350	0.07345	N	0.881438	T	0.65491	0.2696	L	0.46157	1.445	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37842	-0.9688	10	0.23891	T	0.37	0.4064	7.1885	0.25813	0.1295:0.3713:0.4003:0.0989	.	162	O95528	GTR10_HUMAN	R	162	ENSP00000352216:W162R	ENSP00000352216:W162R	W	+	1	0	SLC2A10	44787566	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.793000	0.04589	-2.741000	0.00379	-0.969000	0.02612	TGG		0.617	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			C	45354159	T	C	45354159	3	2	96	1	0	0	0	0	1	0	0	0	14576	1580	55	4	490	4	SLC2A10	20	45354159	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1348193	45354159	17671361	171	26117										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484596	57484596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	catgtttgacgtgggtggccAgcgcgatgaacgccgcaagt	15	10	0	2	rs121913494		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr20:57484596A>G	ENST00000371085.3	+	9	1104	c.680A>G	c.(679-681)cAg>cGg	p.Q227R	GNAS_ENST00000265620.7_Missense_Mutation_p.Q212R|GNAS_ENST00000354359.7_Missense_Mutation_p.Q228R|GNAS_ENST00000306090.10_Missense_Mutation_p.Q213R|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.Q870R|GNAS_ENST00000371095.3_Missense_Mutation_p.Q213R|GNAS_ENST00000371102.4_Missense_Mutation_p.Q856R|GNAS_ENST00000313949.7_3'UTR	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	227			Q -> H (in pituitary adenoma; ACTH- secreting adenoma; in a patient with severe Cushing syndrome complicated by psychosis). {ECO:0000269|PubMed:7737262}.|Q -> R (in somatotrophinoma). {ECO:0000269|PubMed:2549426}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.Q227L(10)|p.Q227R(8)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GTGGGTGGCCAGCGCGATGAA	0.507			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	18	Substitution - Missense(18)	pituitary(17)|thyroid(1)	20											108	91	97					20																	57484596		2203	4300	6503	56917991	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.680A>G	20.37:g.57484596A>G	ENSP00000360126:p.Gln227Arg		56917991	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	37	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338864	0.60963	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.86030	-2.06;-2.06;-2.06;-2.06;-2.06;-2.06;-2.06	5.59	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.95201	0.8444	H	0.98466	4.24	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.996;1.0	D;D;D;D	0.79108	0.992;0.989;0.968;0.99	D	0.96067	0.9043	10	0.87932	D	0	.	13.0903	0.59164	0.8658:0.1342:0.0:0.0	.	227;228;212;870	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	R	870;856;213;227;228;212;213	ENSP00000360141:Q870R;ENSP00000360143:Q856R;ENSP00000360136:Q213R;ENSP00000360126:Q227R;ENSP00000346328:Q228R;ENSP00000265620:Q212R;ENSP00000304472:Q213R	ENSP00000265620:Q212R	Q	+	2	0	GNAS	56917991	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	8.784000	0.91818	1.044000	0.40200	-0.323000	0.08544	CAG		0.507	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		G	57484596	A	G	57484596	3	3	96	1	0	0	0	0	1	0	0	0	6530	188	7	4	3531	4	GNAS	20	57484596	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	12130437	57484596	5540924	172	26118										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32589977	32589977	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gatctggacatggcctgagtAcgtcttctcactccagtttc	9	12	3	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr21:32589977A>G	ENST00000286827.3	-	10	2505	c.2034T>C	c.(2032-2034)cgT>cgC	p.R678R	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Silent_p.R678R	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	678			R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						TGGCCTGAGTACGTCTTCTCA	0.557																																																0			21											154	125	135					21																	32589977		2203	4300	6503	31511848	SO:0001819	synonymous_variant	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.2034T>C	21.37:g.32589977A>G			31511848	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.557	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		G	32589977	A	G	32589977	2	3	96	1	0	0	0	0	0	0	0	1	15929	378	14	4		4	TIAM1	21	32589977	Silent	SNP	A	TCGA-DC-6157-01A-11D-1657-10		32589977	15539918	173	26119										
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117576	46117576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gtcaacagtcctgctgtgtgCccgtctgctgcaagcccatc	10	15	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr21:46117576C>T	ENST00000400365.3	+	1	490	c.460C>T	c.(460-462)Ccc>Tcc	p.P154S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	154	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CTGCTGTGTGCCCGTCTGCTG	0.617																																																0			21											177	182	180					21																	46117576		2203	4300	6503	44942004	SO:0001583	missense	386685			AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.460C>T	21.37:g.46117576C>T	ENSP00000383216:p.Pro154Ser		44942004	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	2.310	-0.358108	0.05138	.	.	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00648	5.99	3.7	1.73	0.24493	.	.	.	.	.	T	0.00815	0.0027	L	0.49778	1.585	0.09310	N	1	B	0.24963	0.115	B	0.25884	0.064	T	0.44360	-0.9333	9	0.15952	T	0.53	.	10.0177	0.42024	0.3626:0.6374:0.0:0.0	.	154	P60413	KR10C_HUMAN	S	154;62	ENSP00000383216:P154S	ENSP00000383216:P154S	P	+	1	0	KRTAP10-12	44942004	0.001000	0.12720	0.001000	0.08648	0.016000	0.09150	0.087000	0.14958	0.117000	0.18138	0.305000	0.20034	CCC		0.617	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117576	C	T	46117576	3	4	96	1	0	0	0	0	1	0	0	0	8529	739	26	3	462	3	KRTAP10-12	21	46117576	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	13527599	46117576	2012319	174	26120										
SNAP29	9342	hgsc.bcm.edu	37	chr22	21213410	21213410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gccggcaccatgtcagcttaCcctaaaagctacaatccgtt	7	14	1	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:21213410C>T	ENST00000215730.7	+	1	140	c.12C>T	c.(10-12)taC>taT	p.Y4Y	PI4KA_ENST00000255882.6_5'Flank|PI4KA_ENST00000572273.1_5'Flank	NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	4					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			TGTCAGCTTACCCTAAAAGCT	0.731																																																0			22											10	12	11					22																	21213410		2182	4263	6445	19543410	SO:0001819	synonymous_variant	9342			AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"soluble 29 kDa NSF attachment protein"	604202	"synaptosomal-associated protein, 29kD"			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.12C>T	22.37:g.21213410C>T			19543410		Silent	SNP	ENST00000215730.7	37	CCDS13784.1																																																																																				0.731	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782		T	21213410	C	T	21213410	2	4	96	1	0	0	0	0	0	0	0	1	14868	518	18	3		3	SNAP29	22	21213410	Silent	SNP	C	TCGA-DC-6157-01A-11D-1657-10		21213410	30091156	175	26121										
GNAZ	2781	hgsc.bcm.edu	37	chr22	23437925	23437925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggaaaaagaagcagcccggCggtcccggagaattgaccgc	14	11	0	3			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:23437925C>T	ENST00000248996.4	+	2	709	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	15					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)	p.R15W(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		AGCAGCCCGGCGGTCCCGGAG	0.637																																																1	Substitution - Missense(1)	lung(1)	22											27	30	29					22																	23437925		2202	4297	6499	21767925	SO:0001583	missense	2781				CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.43C>T	22.37:g.23437925C>T	ENSP00000248996:p.Arg15Trp		21767925	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	37	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728887	0.89390	.	.	ENSG00000128266	ENST00000248996	D	0.89123	-2.47	5.05	4.01	0.46588	.	0.000000	0.85682	D	0.000000	D	0.92309	0.7560	H	0.96301	3.8	0.80722	D	1	D	0.65815	0.995	B	0.42214	0.38	D	0.93852	0.7146	10	0.87932	D	0	.	14.035	0.64640	0.1523:0.8477:0.0:0.0	.	15	P19086	GNAZ_HUMAN	W	15	ENSP00000248996:R15W	ENSP00000248996:R15W	R	+	1	2	GNAZ	21767925	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	3.704000	0.54815	1.221000	0.43506	0.655000	0.94253	CGG		0.637	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		T	23437925	C	T	23437925	3	4	96	1	0	0	0	0	1	0	0	0	6534	759	27	1	45	1	GNAZ	22	23437925	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	2224515	23437925	27866641	176	26122										
RFPL1	5988	hgsc.bcm.edu	37	chr22	29837544	29837544	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ttcacagtggatatgaccttGgatgccgacacagccaacaa	9	11	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:29837544G>A	ENST00000354373.2	+	2	596	c.387G>A	c.(385-387)ttG>ttA	p.L129L	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	129	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						ATATGACCTTGGATGCCGACA	0.488																																																0			22											109	97	101					22																	29837544		2203	4300	6503	28167544	SO:0001819	synonymous_variant	5988			AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"RING-type (C3HC4) zinc fingers"	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.387G>A	22.37:g.29837544G>A			28167544	Q6IC06|Q9UJ97	Silent	SNP	ENST00000354373.2	37	CCDS13857.2																																																																																				0.488	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026		A	29837544	G	A	29837544	2	1	96	1	0	0	0	0	0	0	0	1	13290	1339	47	3		3	RFPL1	22	29837544	Silent	SNP	G	TCGA-DC-6157-01A-11D-1657-10	6399619	29837544	21467022	177	26123										
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30857429	30857429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	cttggtcttcaggaaaactcCgaagccgatgtccgcaccat	9	13	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:30857429C>T	ENST00000215812.4	-	11	1039	c.949G>A	c.(949-951)Gga>Aga	p.G317R	SEC14L3_ENST00000539629.1_Missense_Mutation_p.G258R|SEC14L3_ENST00000401751.1_Missense_Mutation_p.G258R|SEC14L3_ENST00000540910.1_Missense_Mutation_p.G240R|SEC14L3_ENST00000402286.1_Missense_Mutation_p.G240R|SEC14L3_ENST00000403066.1_Missense_Mutation_p.G258R|SEC14L3_ENST00000415957.2_Missense_Mutation_p.G258R	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	317	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	AGGAAAACTCCGAAGCCGATG	0.602																																					Esophageal Squamous(108;290 1516 3584 23771 37333)											0			22											58	52	54					22																	30857429		2203	4300	6503	29187429	SO:0001583	missense	266629			AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.949G>A	22.37:g.30857429C>T	ENSP00000215812:p.Gly317Arg		29187429	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145713	0.77888	.	.	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.52	5.52	0.82312	GOLD (2);	0.098933	0.64402	D	0.000001	T	0.67878	0.2940	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.71283	-0.4639	10	0.87932	D	0	-29.0971	19.0319	0.92960	0.0:1.0:0.0:0.0	.	240;317	E9PE57;Q9UDX4	.;S14L3_HUMAN	R	258;258;317;240;258;258;240	ENSP00000385941:G258R;ENSP00000401864:G258R;ENSP00000215812:G317R;ENSP00000385004:G240R;ENSP00000383896:G258R;ENSP00000444691:G258R;ENSP00000439752:G240R	ENSP00000215812:G317R	G	-	1	0	SEC14L3	29187429	1.000000	0.71417	0.636000	0.29352	0.338000	0.28826	7.297000	0.78799	2.599000	0.87857	0.655000	0.94253	GGA		0.602	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		T	30857429	C	T	30857429	3	4	96	1	0	0	0	0	1	0	0	0	14020	661	23	1	261	1	SEC14L3	22	30857429	Missense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	1019885	30857429	20447137	178	26124										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32242878	32242878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	catttccacgcattctctggAgtcaactgcacccccagtgg	8	15	2	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:32242878A>G	ENST00000382112.3	+	30	3123	c.3053A>G	c.(3052-3054)gAg>gGg	p.E1018G	DEPDC5_ENST00000382105.2_Missense_Mutation_p.E949G|DEPDC5_ENST00000266091.3_Missense_Mutation_p.E1027G|DEPDC5_ENST00000400249.2_Missense_Mutation_p.E1018G|DEPDC5_ENST00000400248.2_Missense_Mutation_p.E1018G|DEPDC5_ENST00000535622.1_Missense_Mutation_p.E949G|DEPDC5_ENST00000382111.2_Missense_Mutation_p.E1027G|DEPDC5_ENST00000400246.1_Missense_Mutation_p.E1027G	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1027					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CATTCTCTGGAGTCAACTGCA	0.552																																																0			22											83	83	83					22																	32242878		1989	4163	6152	30572878	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3053A>G	22.37:g.32242878A>G	ENSP00000371546:p.Glu1018Gly		30572878	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.322776	0.41096	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T	0.39056	1.34;1.78;1.78;1.63;1.1;1.67;1.63;1.78	5.31	3.12	0.35913	.	0.103999	0.64402	D	0.000005	T	0.48892	0.1525	L	0.29908	0.895	0.80722	D	1	D;P;D;B;D;P;P	0.76494	0.999;0.935;0.973;0.39;0.998;0.935;0.919	D;B;P;B;D;B;B	0.85130	0.997;0.34;0.658;0.281;0.937;0.34;0.253	T	0.41034	-0.9531	10	0.54805	T	0.06	.	10.1272	0.42656	0.7328:0.0:0.0:0.2671	.	348;1027;949;413;1027;1018;1018	B4DSS1;B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.;.;.;.;.;.;DEPD5_HUMAN	G	949;1027;1018;949;1027;949;1018;1027;1018	ENSP00000440210:E949G;ENSP00000266091:E1027G;ENSP00000383108:E1018G;ENSP00000383105:E1027G;ENSP00000371539:E949G;ENSP00000371546:E1018G;ENSP00000371545:E1027G;ENSP00000383107:E1018G	ENSP00000266091:E1027G	E	+	2	0	DEPDC5	30572878	1.000000	0.71417	0.018000	0.16275	0.001000	0.01503	8.063000	0.89482	0.386000	0.24997	-0.341000	0.08007	GAG		0.552	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32242878	A	G	32242878	3	3	96	1	0	0	0	0	1	0	0	0	4453	304	11	4	3189	4	DEPDC5	22	32242878	Missense_Mutation	SNP	A	TCGA-DC-6157-01A-11D-1657-10	1385449	32242878	19061688	179	26125										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40042683	40042683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggagcagcggcagcgctaccTgtcctccagcacggtggcca	14	15	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:40042683T>C	ENST00000402142.3	+	8	1259	c.1259T>C	c.(1258-1260)cTg>cCg	p.L420P	CACNA1I_ENST00000336649.4_Missense_Mutation_p.L420P|CACNA1I_ENST00000400164.3_Missense_Mutation_p.L420P|CACNA1I_ENST00000407673.1_Missense_Mutation_p.L420P|CACNA1I_ENST00000401624.1_Missense_Mutation_p.L420P|CACNA1I_ENST00000404898.1_Missense_Mutation_p.L420P	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	420					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGCGCTACCTGTCCTCCAGC	0.622																																																0			22											12	14	14					22																	40042683		2114	4229	6343	38372629	SO:0001583	missense	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.1259T>C	22.37:g.40042683T>C	ENSP00000385019:p.Leu420Pro		38372629	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.784023	0.49891	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97256	-4.27;-4.25;-4.26;-4.24;-4.31;-4.22	3.49	3.49	0.39957	.	1.630500	0.03490	N	0.216467	D	0.98356	0.9454	M	0.71581	2.175	0.80722	D	1	P;D;P;D	0.76494	0.649;0.998;0.849;0.999	B;D;B;D	0.85130	0.193;0.958;0.261;0.997	D	0.93418	0.6774	10	0.46703	T	0.11	.	12.7047	0.57054	0.0:0.0:0.0:1.0	.	420;420;420;420	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	P	420	ENSP00000385019:L420P;ENSP00000384093:L420P;ENSP00000383887:L420P;ENSP00000385680:L420P;ENSP00000337829:L420P;ENSP00000383028:L420P	ENSP00000337829:L420P	L	+	2	0	CACNA1I	38372629	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	3.004000	0.49513	1.547000	0.49401	0.254000	0.18369	CTG		0.622	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		C	40042683	T	C	40042683	3	2	96	1	0	0	0	0	1	0	0	0	2552	1580	55	4	1289	4	CACNA1I	22	40042683	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	7799805	40042683	11261883	180	26126										
SAMM50	25813	hgsc.bcm.edu	37	chr22	44371983	44371983	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	tcaagtgggaaggcgtatggCgagaactgggctgcctctca	15	9	2	1	rs143794573		TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:44371983C>T	ENST00000350028.4	+	8	854	c.697C>T	c.(697-699)Cga>Tga	p.R233*	SAMM50_ENST00000396202.3_Nonsense_Mutation_p.R23*	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	233					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AGGCGTATGGCGAGAACTGGG	0.483																																																0			22						C	stop/ARG	0,4406		0,0,2203	94	82	86		697	4.2	1	22	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	SAMM50	NM_015380.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		233/470	44371983	1,13005	2203	4300	6503	42703316	SO:0001587	stop_gained	25813			AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"sorting and assembly machinery component 50 homolog (S. cerevisiae)"			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.697C>T	22.37:g.44371983C>T	ENSP00000345445:p.Arg233*		42703316	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Nonsense_Mutation	SNP	ENST00000350028.4	37	CCDS14055.1	.	.	.	.	.	.	.	.	.	.	C	42	9.551304	0.99202	0.0	1.16E-4	ENSG00000100347	ENST00000350028;ENST00000396202	.	.	.	5.3	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.7185	10.9836	0.47510	0.2633:0.7367:0.0:0.0	.	.	.	.	X	233;23	.	ENSP00000345445:R233X	R	+	1	2	SAMM50	42703316	1.000000	0.71417	0.996000	0.52242	0.972000	0.66771	3.560000	0.53763	2.647000	0.89833	0.561000	0.74099	CGA		0.483	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380		T	44371983	C	T	44371983	4	4	96	1	0	0	0	0	0	1	0	0	13866	760	27	1	727	1	SAMM50	22	44371983	Nonsense_Mutation	SNP	C	TCGA-DC-6157-01A-11D-1657-10	4329300	44371983	6932583	181	26127										
NUP50	10762	hgsc.bcm.edu	37	chr22	45571915	45571915	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aacaacataaccagtgccccTcccttcgccagtgcaaaggc	7	16	0	0			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chr22:45571915T>C	ENST00000347635.4	+	4	760	c.294T>C	c.(292-294)ccT>ccC	p.P98P	NUP50_ENST00000407019.2_Silent_p.P70P|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000486184.1_3'UTR|NUP50_ENST00000396096.2_Silent_p.P70P|NUP50_ENST00000425733.2_Intron	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	98	5 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCAGTGCCCCTCCCTTCGCCA	0.532																																																0			22											69	65	67					22																	45571915		2203	4300	6503	43950579	SO:0001819	synonymous_variant	10762			AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"nucleoporin 50kD"	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.294T>C	22.37:g.45571915T>C			43950579	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Silent	SNP	ENST00000347635.4	37	CCDS14062.1																																																																																				0.532	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			C	45571915	T	C	45571915	2	2	96	1	0	0	0	0	0	0	0	1	10797	1538	54	4		4	NUP50	22	45571915	Silent	SNP	T	TCGA-DC-6157-01A-11D-1657-10	1199932	45571915	5732651	182	26128										
KCND1	3750	hgsc.bcm.edu	37	chrX	48819901	48819901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	aggggtacccaggctggagtTcctgagggtgctgccggccc	17	12	0	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chrX:48819901T>C	ENST00000218176.3	-	6	3182	c.1885A>G	c.(1885-1887)Aac>Gac	p.N629D	KCND1_ENST00000376477.1_Missense_Mutation_p.N252D	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	629					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	AGGCTGGAGTTCCTGAGGGTG	0.612																																																0			X											29	26	27					X																	48819901		2203	4300	6503	48704845	SO:0001583	missense	3750			AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1885A>G	X.37:g.48819901T>C	ENSP00000218176:p.Asn629Asp		48704845	A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	37	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	t	14.25	2.480597	0.44044	.	.	ENSG00000102057	ENST00000376477;ENST00000218176	D;D	0.96685	-3.72;-4.09	5.32	5.32	0.75619	.	0.071093	0.53938	D	0.000045	D	0.93370	0.7886	L	0.41236	1.265	0.44067	D	0.996811	B	0.25105	0.118	B	0.19666	0.026	D	0.91406	0.5147	10	0.66056	D	0.02	.	13.2815	0.60216	0.0:0.0:0.0:1.0	.	629	Q9NSA2	KCND1_HUMAN	D	252;629	ENSP00000365660:N252D;ENSP00000218176:N629D	ENSP00000218176:N629D	N	-	1	0	KCND1	48704845	1.000000	0.71417	0.999000	0.59377	0.907000	0.53573	2.777000	0.47717	1.778000	0.52293	0.352000	0.21897	AAC		0.612	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		C	48819901	T	C	48819901	3	2	96	1	0	0	0	0	1	0	0	0	8039	1783	62	4	62	4	KCND1	23	48819901	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10		48819901	106450659	183	26129										
ZC3H12B	340554	hgsc.bcm.edu	37	chrX	64722697	64722697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	ggatggatagcatttccgacTcccgcctctatgagagcaac	10	12	1	1			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chrX:64722697T>C	ENST00000338957.4	+	5	2186	c.2119T>C	c.(2119-2121)Tcc>Ccc	p.S707P	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.S696P	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	707							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CATTTCCGACTCCCGCCTCTA	0.617																																																0			X											41	44	43					X																	64722697		2119	4220	6339	64639422	SO:0001583	missense	340554			BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.2119T>C	X.37:g.64722697T>C	ENSP00000340839:p.Ser707Pro		64639422	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	37	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735311	0.69189	.	.	ENSG00000102053	ENST00000338957;ENST00000423889;ENST00000218172	T;T	0.39229	1.09;1.09	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.62792	0.2457	M	0.72894	2.215	0.58432	D	0.999991	D	0.76494	0.999	D	0.80764	0.994	T	0.63915	-0.6529	10	0.45353	T	0.12	-19.4828	13.7773	0.63062	0.0:0.0:0.0:1.0	.	696	Q5HYM0	ZC12B_HUMAN	P	707;696;643	ENSP00000340839:S707P;ENSP00000408077:S696P	ENSP00000218172:S643P	S	+	1	0	ZC3H12B	64639422	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.837000	0.69381	1.938000	0.56188	0.412000	0.27726	TCC		0.617	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		C	64722697	T	C	64722697	3	2	96	1	0	0	0	0	1	0	0	0	17601	1551	54	4	2137	4	ZC3H12B	23	64722697	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	15902796	64722697	90547863	184	26130										
ACRC	93953	hgsc.bcm.edu	37	chrX	70824010	70824010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0382513661202186	7	1	0.809669258299395	2.30282555282555	0.544754431851206	1	1	0	gcagtgatgattcggaagctTccgacgacagcagtgatgat	13	8	0	4			TCGA-DC-6157-01A-11D-1657-10	TCGA-DC-6157-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	3f20f4d7-029c-44bb-bc93-1ff5767a8e80	7f3e08e7-98d7-4cf5-9193-c0298d70926f	g.chrX:70824010T>C	ENST00000373695.1	+	7	1420	c.883T>C	c.(883-885)Tcc>Ccc	p.S295P	ACRC_ENST00000373696.3_Missense_Mutation_p.S295P			Q96QF7	ACRC_HUMAN	acidic repeat containing	295	Asp/Ser-rich.					nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					TTCGGAAGCTTCCGACGACAG	0.527																																																0			X											132	124	127					X																	70824010		2203	4300	6503	70740735	SO:0001583	missense	93953			AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.883T>C	X.37:g.70824010T>C	ENSP00000362799:p.Ser295Pro		70740735	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	37	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	T	2.597	-0.293877	0.05568	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.29397	1.57;1.57	0.14	-0.28	0.12886	.	.	.	.	.	T	0.09642	0.0237	N	0.01874	-0.695	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.30268	-0.9984	9	0.20519	T	0.43	.	4.4172	0.11463	0.0:0.6635:0.0:0.3365	.	295	Q96QF7	ACRC_HUMAN	P	295	ENSP00000362800:S295P;ENSP00000362799:S295P	ENSP00000362799:S295P	S	+	1	0	ACRC	70740735	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-1.504000	0.02275	-1.219000	0.02597	-1.215000	0.01618	TCC		0.527	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			C	70824010	T	C	70824010	3	2	96	1	0	0	0	0	1	0	0	0	171	1783	62	4	909	4	ACRC	23	70824010	Missense_Mutation	SNP	T	TCGA-DC-6157-01A-11D-1657-10	6101313	70824010	84446550	185	26131										
GPR157	80045	hgsc.bcm.edu	37	chr1	9165617	9165617	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agcacgaaccgcacggtgctCcagaccctgaggccgatgaa	12	14	0	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:9165617C>T	ENST00000377411.4	-	3	862	c.720G>A	c.(718-720)tgG>tgA	p.W240*	GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|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;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		GCACGGTGCTCCAGACCCTGA	0.667																																																0			1											54	54	54					1																	9165617		2202	4300	6502	9088204	SO:0001587	stop_gained	80045			AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"GPCR / Class B : Orphans"	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.720G>A	1.37:g.9165617C>T	ENSP00000366628:p.Trp240*		9088204	A2A334|Q8WWB8|Q9HA73	Nonsense_Mutation	SNP	ENST00000377411.4	37	CCDS100.2	.	.	.	.	.	.	.	.	.	.	C	38	6.733754	0.97796	.	.	ENSG00000180758	ENST00000377411	.	.	.	4.67	4.67	0.58626	.	0.110778	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.1932	17.0013	0.86382	0.0:1.0:0.0:0.0	.	.	.	.	X	240	.	ENSP00000366628:W240X	W	-	3	0	GPR157	9088204	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.898000	0.75676	2.314000	0.78098	0.549000	0.68633	TGG		0.667	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980		T	9165617	C	T	9165617	4	4	97	1	0	0	0	0	0	1	0	0	6682	856	30	3	295	3	GPR157	1	9165617	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10		9165617	240085004	1	26132										
MACF1	23499	hgsc.bcm.edu	37	chr1	39797858	39797858	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctcccaattacagatgccctAgaacaaggtattgtgtctac	7	11	1	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:39797858A>G	ENST00000372915.3	+	36	5700	c.5613A>G	c.(5611-5613)ctA>ctG	p.L1871L	MACF1_ENST00000564288.1_Silent_p.L1866L|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000289893.4_Silent_p.L306L|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000567887.1_Silent_p.L1903L|MACF1_ENST00000476350.1_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1871					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.L306L(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			CAGATGCCCTAGAACAAGGTA	0.458																																																1	Substitution - coding silent(1)	lung(1)	1											103	104	104					1																	39797858		2203	4300	6503	39570445	SO:0001819	synonymous_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.5613A>G	1.37:g.39797858A>G			39570445	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																					0.458	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39797858	A	G	39797858	2	3	97	1	0	0	0	0	0	0	0	1	9174	407	15	4		4	MACF1	1	39797858	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	30632241	39797858	209452763	2	26133										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214549632	214549632	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcagctctactcgattctccTcataggggacaacttcacgg	8	13	5	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:214549632T>C	ENST00000366956.5	-	15	3031	c.2837A>G	c.(2836-2838)gAg>gGg	p.E946G	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	946	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TCGATTCTCCTCATAGGGGAC	0.463																																					Colon(92;557 1424 24372 34121 40073)											0			1											184	177	180					1																	214549632		2203	4300	6503	212616255	SO:0001583	missense	5784			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2837A>G	1.37:g.214549632T>C	ENSP00000355923:p.Glu946Gly		212616255	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846616	0.91277	.	.	ENSG00000152104	ENST00000366956	D	0.85171	-1.95	5.29	5.29	0.74685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.93552	0.7942	M	0.89968	3.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94837	0.8001	10	0.87932	D	0	.	15.2459	0.73507	0.0:0.0:0.0:1.0	.	946	Q15678	PTN14_HUMAN	G	946	ENSP00000355923:E946G	ENSP00000355923:E946G	E	-	2	0	PTPN14	212616255	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	7.919000	0.87513	1.998000	0.58463	0.533000	0.62120	GAG		0.463	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		C	214549632	T	C	214549632	3	2	97	1	0	0	0	0	1	0	0	0	12818	1551	54	4	746	4	PTPN14	1	214549632	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	174751774	214549632	34700989	3	26134										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234565357	234565357	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aggaaagagaggcacacccaTtgatcatgaatatattgtgc	10	7	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:234565357T>C	ENST00000040877.1	-	16	2675	c.2676A>G	c.(2674-2676)caA>caG	p.Q892Q		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	892					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GGCACACCCATTGATCATGAA	0.393																																																0			1											98	98	98					1																	234565357		2203	4300	6503	232631980	SO:0001819	synonymous_variant	6894				CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2676A>G	1.37:g.234565357T>C			232631980	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																				0.393	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		C	234565357	T	C	234565357	2	2	97	1	0	0	0	0	0	0	0	1	15594	1490	52	4		4	TARBP1	1	234565357	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	20015725	234565357	14685264	4	26135										
RYR2	6262	hgsc.bcm.edu	37	chr1	237837513	237837513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcagatcaatggatatgctgTatccaggtaaaagtacacat	9	7	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:237837513T>C	ENST00000366574.2	+	59	9025	c.8708T>C	c.(8707-8709)gTa>gCa	p.V2903A	RYR2_ENST00000542537.1_Missense_Mutation_p.V2887A|RYR2_ENST00000360064.6_Missense_Mutation_p.V2901A	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2903	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGATATGCTGTATCCAGGTAA	0.378																																																0			1											76	74	75					1																	237837513		1926	4135	6061	235904136	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8708T>C	1.37:g.237837513T>C	ENSP00000355533:p.Val2903Ala		235904136	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816842	0.70912	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.92858	-3.12;-3.12;-3.12	5.17	5.17	0.71159	Ryanodine receptor Ryr (1);	0.000000	0.53938	D	0.000041	D	0.93051	0.7788	M	0.83603	2.65	0.80722	D	1	B	0.18741	0.03	B	0.29862	0.108	D	0.91760	0.5419	10	0.87932	D	0	.	15.0129	0.71562	0.0:0.0:0.0:1.0	.	2903	Q92736	RYR2_HUMAN	A	2903;2901;2887	ENSP00000355533:V2903A;ENSP00000353174:V2901A;ENSP00000443798:V2887A	ENSP00000353174:V2901A	V	+	2	0	RYR2	235904136	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	7.945000	0.87732	1.948000	0.56530	0.455000	0.32223	GTA		0.378	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237837513	T	C	237837513	3	2	97	1	0	0	0	0	1	0	0	0	13806	1638	57	4	8942	4	RYR2	1	237837513	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	3272156	237837513	11413108	5	26136										
CHML	1122	hgsc.bcm.edu	37	chr1	241797768	241797768	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggtaactgtcttccacaataAaatatttagcatttattctt	4	7	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:241797768A>C	ENST00000366553.1	-	1	1464	c.1301T>G	c.(1300-1302)tTt>tGt	p.F434C	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000331838.5_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	434					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TTCCACAATAAAATATTTAGC	0.353																																																0			1											80	84	83					1																	241797768		2203	4299	6502	239864391	SO:0001583	missense	1122			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1301T>G	1.37:g.241797768A>C	ENSP00000355511:p.Phe434Cys		239864391	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.206866	0.58343	.	.	ENSG00000203668	ENST00000366553	T	0.59224	0.28	4.93	4.93	0.64822	.	0.116646	0.64402	U	0.000012	T	0.75140	0.3809	.	.	.	0.49798	D	0.999827	D	0.89917	1.0	D	0.87578	0.998	T	0.78695	-0.2104	9	0.87932	D	0	-14.5002	12.8833	0.58030	1.0:0.0:0.0:0.0	.	434	P26374	RAE2_HUMAN	C	434	ENSP00000355511:F434C	ENSP00000355511:F434C	F	-	2	0	CHML	239864391	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.159000	0.71856	2.218000	0.71995	0.533000	0.62120	TTT		0.353	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		C	241797768	A	C	241797768	3	2	97	1	0	0	0	0	1	0	0	0	3357	14	1	4	673	4	CHML	1	241797768	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	3960255	241797768	7452853	6	26137										
OR2L2	26246	hgsc.bcm.edu	37	chr1	248201931	248201931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gacatcaatggcctatgatcGttatgtggccatttgctttc	9	9	1	1	rs144606855	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr1:248201931G>A	ENST00000366479.2	+	1	458	c.362G>A	c.(361-363)cGt>cAt	p.R121H	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			GCCTATGATCGTTATGTGGCC	0.433													g|||	74	0.0147764	0.0552	0.0014	5008	,	,		22925	0		0	False		,,,				2504	0															0			1						G	HIS/ARG,	194,4212		3,188,2012	158	139	145		362,	-1.8	0	1	dbSNP_134	145	1,8599		0,1,4299	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	29,	3,189,6311	AA,AG,GG		0.0116,4.4031,1.4993	benign,	121/313,	248201931	195,12811	2203	4300	6503	246268554	SO:0001583	missense	26246			X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"GPCR / Class A : Olfactory receptors"	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.362G>A	1.37:g.248201931G>A	ENSP00000355435:p.Arg121His		246268554	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	.	12.37	1.917347	0.33815	0.044031	1.16E-4	ENSG00000203663	ENST00000366479	T	0.77489	-1.1	1.9	-1.77	0.07982	GPCR, rhodopsin-like superfamily (1);	0.540487	0.13896	N	0.355267	T	0.35038	0.0918	M	0.87900	2.915	0.20307	N	0.999914	P	0.37955	0.612	B	0.31290	0.127	T	0.56086	-0.8037	10	0.62326	D	0.03	.	7.2486	0.26135	0.3467:0.0:0.6533:0.0	.	121	Q8NH16	OR2L2_HUMAN	H	121	ENSP00000355435:R121H	ENSP00000355435:R121H	R	+	2	0	OR2L2	246268554	0.723000	0.28027	0.042000	0.18584	0.309000	0.27889	4.115000	0.57865	-0.405000	0.07599	0.194000	0.17425	CGT		0.433	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		A	248201931	G	A	248201931	3	1	97	1	0	0	0	0	1	0	0	0	11038	1145	40	1	364	1	OR2L2	1	248201931	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	6404163	248201931	1048690	7	26138										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1893031	1893031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	acagtaatgtctttggactcGtcctcgtctatcctccgggg	10	12	2	0	rs562364952	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:1893031G>A	ENST00000399161.2	-	16	3249	c.2502C>T	c.(2500-2502)gaC>gaT	p.D834D	MYT1L_ENST00000428368.2_Silent_p.D832D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	834					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CTTTGGACTCGTCCTCGTCTA	0.507													G|||	2	0.000399361	0	0	5008	,	,		15924	0.002		0	False		,,,				2504	0															0			2											82	85	84					2																	1893031		1968	4134	6102	1872038	SO:0001819	synonymous_variant	23040			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2502C>T	2.37:g.1893031G>A			1872038	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																					0.507	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1893031	G	A	1893031	2	1	97	1	0	0	0	0	0	0	0	1	10137	1136	40	1		1	MYT1L	2	1893031	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10		1893031	241306342	8	26139										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39553323	39553323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaacataggaggctgaagcTctgcaagttctatggcagtg	12	8	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:39553323T>C	ENST00000263881.3	-	9	950	c.626A>G	c.(625-627)gAg>gGg	p.E209G	MAP4K3_ENST00000341681.5_Missense_Mutation_p.E209G|RP11-449G16.1_ENST00000609671.1_RNA|MAP4K3_ENST00000437545.1_Missense_Mutation_p.E146G|MAP4K3_ENST00000536018.1_5'Flank	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				AGGCTGAAGCTCTGCAAGTTC	0.458																																																0			2											125	123	124					2																	39553323		2203	4300	6503	39406827	SO:0001583	missense	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.626A>G	2.37:g.39553323T>C	ENSP00000263881:p.Glu209Gly		39406827	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	T	31	5.086554	0.94100	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	T;T;T	0.24350	1.86;2.55;1.86	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43700	0.1259	L	0.43923	1.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	T	0.16276	-1.0408	9	.	.	.	.	15.9136	0.79491	0.0:0.0:0.0:1.0	.	209;209	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	G	209;146;209	ENSP00000263881:E209G;ENSP00000416958:E146G;ENSP00000345434:E209G	.	E	-	2	0	MAP4K3	39406827	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	7.848000	0.86902	2.154000	0.67381	0.477000	0.44152	GAG		0.458	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		C	39553323	T	C	39553323	3	2	97	1	0	0	0	0	1	0	0	0	9291	1551	54	4	2162	4	MAP4K3	2	39553323	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	37660292	39553323	203646050	9	26140										
DYSF	8291	hgsc.bcm.edu	37	chr2	71892301	71892301	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttgctcctcagctctggaccGaaccagtggcgggaccagct	12	14	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:71892301G>A	ENST00000258104.3	+	46	5344	c.5067G>A	c.(5065-5067)ccG>ccA	p.P1689P	DYSF_ENST00000413539.2_Silent_p.P1720P|DYSF_ENST00000410020.3_Silent_p.P1728P|DYSF_ENST00000409762.1_Silent_p.P1706P|DYSF_ENST00000429174.2_Silent_p.P1710P|DYSF_ENST00000409366.1_Silent_p.P1711P|DYSF_ENST00000394120.2_Silent_p.P1690P|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409651.1_Silent_p.P1721P|DYSF_ENST00000409744.1_Silent_p.P1697P|DYSF_ENST00000410041.1_Silent_p.P1707P|DYSF_ENST00000409582.3_Silent_p.P1727P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1689					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCTCTGGACCGAACCAGTGGC	0.577																																																0			2											109	105	106					2																	71892301		2203	4300	6503	71745809	SO:0001819	synonymous_variant	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5067G>A	2.37:g.71892301G>A			71745809	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																				0.577	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71892301	G	A	71892301	2	1	97	1	0	0	0	0	0	0	0	1	4870	1045	37	1		1	DYSF	2	71892301	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	32338978	71892301	171307072	10	26141										
IL1F8	27177	hgsc.bcm.edu	37	chr2	113786565	113786565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tttctgcacagaagagacagAgatcttttcccttgattccc	7	11	2	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:113786565A>G	ENST00000259213.4	-	4	319	c.212T>C	c.(211-213)cTc>cCc	p.L71P	IL36B_ENST00000327407.2_Missense_Mutation_p.L71P	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta	71					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			kidney(1)|ovary(1)|pancreas(1)	3						GAAGAGACAGAGATCTTTTCC	0.418																																																0			2											187	164	172					2																	113786565		2203	4300	6503	113503036	SO:0001583	missense	27177			AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"Interleukins and interleukin receptors"	15564	protein-coding gene	gene with protein product		605508	"interleukin 1 family, member 8 (eta)"	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.212T>C	2.37:g.113786565A>G	ENSP00000259213:p.Leu71Pro		113503036	Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Missense_Mutation	SNP	ENST00000259213.4	37	CCDS2109.1	.	.	.	.	.	.	.	.	.	.	a	13.14	2.147042	0.37923	.	.	ENSG00000136696	ENST00000259213;ENST00000327407	T;T	0.29655	1.9;1.56	4.38	3.2	0.36748	.	0.333042	0.21766	N	0.069422	T	0.47021	0.1423	M	0.63843	1.955	0.09310	N	0.999999	D;D	0.76494	0.999;0.997	D;D	0.72075	0.976;0.952	T	0.26258	-1.0108	10	0.66056	D	0.02	.	7.3442	0.26654	0.8047:0.0:0.0:0.1953	.	71;71	Q9NZH7-2;Q9NZH7	.;IL36B_HUMAN	P	71	ENSP00000259213:L71P;ENSP00000328420:L71P	ENSP00000259213:L71P	L	-	2	0	IL36B	113503036	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.045000	0.30341	0.632000	0.30432	0.454000	0.30748	CTC		0.418	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438		G	113786565	A	G	113786565	3	3	97	1	0	0	0	0	1	0	0	0	7677	304	11	4	511	4	IL1F8	2	113786565	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	41894264	113786565	129412808	11	26142										
NEB	4703	hgsc.bcm.edu	37	chr2	152390749	152390749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctgactgatctggtcgcctgCggtcttagccagcagatgtc	12	12	2	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:152390749C>T	ENST00000172853.10	-	115	16441	c.16294G>A	c.(16294-16296)Gca>Aca	p.A5432T	NEB_ENST00000603639.1_Intron|NEB_ENST00000604864.1_Missense_Mutation_p.A7133T|NEB_ENST00000397345.3_Intron|NEB_ENST00000427231.2_Missense_Mutation_p.A7133T|NEB_ENST00000409198.1_Missense_Mutation_p.A5432T			P20929	NEBU_HUMAN	nebulin	5432				AG -> RS (in Ref. 1; CAA58788). {ECO:0000305}.	muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGTCGCCTGCGGTCTTAGCC	0.517																																																0			2											193	196	195					2																	152390749		1996	4177	6173	152098995	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16294G>A	2.37:g.152390749C>T	ENSP00000172853:p.Ala5432Thr		152098995	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	16.62	3.173137	0.57584	.	.	ENSG00000183091	ENST00000409198;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	6.03	5.16	0.70880	.	0.209030	0.49916	N	0.000129	T	0.33235	0.0856	N	0.21324	0.655	0.80722	D	1	B;D	0.53885	0.015;0.963	B;B	0.38264	0.014;0.269	T	0.28808	-1.0032	10	0.06236	T	0.91	.	15.3416	0.74303	0.0:0.9335:0.0:0.0665	.	5432;1863	P20929;Q14215	NEBU_HUMAN;.	T	5432;7133;1481;1863;5432	ENSP00000386259:A5432T;ENSP00000416578:A7133T;ENSP00000410961:A1863T;ENSP00000172853:A5432T	ENSP00000172853:A5432T	A	-	1	0	NEB	152098995	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.400000	0.59709	1.569000	0.49696	0.655000	0.94253	GCA		0.517	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152390749	C	T	152390749	3	4	97	1	0	0	0	0	1	0	0	0	10333	768	27	1	4449	1	NEB	2	152390749	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	38604184	152390749	90808624	12	26143										
TTN	7273	hgsc.bcm.edu	37	chr2	179458387	179458387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tccggaaaatataatcttttCcttcaagtagtttagaaact	5	7	2	1	rs374713701		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:179458387C>T	ENST00000591111.1	-	248	53941	c.53717G>A	c.(53716-53718)gGa>gAa	p.G17906E	TTN_ENST00000589042.1_Missense_Mutation_p.G19547E|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G10607E|TTN_ENST00000460472.2_Missense_Mutation_p.G10482E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G16979E|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G10674E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17906	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> E (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G10482E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAATCTTTTCCTTCAAGTAG	0.363																																																1	Substitution - Missense(1)	skin(1)	2						C	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	1,3691		0,1,1845	88	83	85		31445,50936,31820,32021	6	1	2		85	0,8182		0,0,4091	no	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	98,98,98,98	0,1,5936	TT,TC,CC		0.0,0.0271,0.0084	probably-damaging,probably-damaging,probably-damaging,probably-damaging	10482/26927,16979/33424,10607/27052,10674/27119	179458387	1,11873	1846	4091	5937	179166633	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53717G>A	2.37:g.179458387C>T	ENSP00000465570:p.Gly17906Glu		179166633	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.09	2.432583	0.43224	2.71E-4	0.0	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	6.02	6.02	0.97574	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82898	0.5137	M	0.85299	2.745	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.84089	0.0389	9	0.87932	D	0	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	10482;10607;10674;17906	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	16979;10482;10674;10607;10480	ENSP00000343764:G16979E;ENSP00000434586:G10482E;ENSP00000340554:G10674E;ENSP00000352154:G10607E	ENSP00000340554:G10674E	G	-	2	0	TTN	179166633	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.760000	0.85248	2.857000	0.98124	0.650000	0.86243	GGA		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179458387	C	T	179458387	3	4	97	1	0	0	0	0	1	0	0	0	16775	855	30	3	49599	3	TTN	2	179458387	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	27067638	179458387	63740986	13	26144										
STAT1	6772	hgsc.bcm.edu	37	chr2	191862953	191862953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aaataactacctttctcttaTtgtcaagcattaaatacatc	2	9	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:191862953T>C	ENST00000361099.3	-	8	1010	c.623A>G	c.(622-624)aAt>aGt	p.N208S	STAT1_ENST00000409465.1_Missense_Mutation_p.N208S|STAT1_ENST00000392322.3_Missense_Mutation_p.N208S|STAT1_ENST00000540176.1_Intron|STAT1_ENST00000392323.2_Missense_Mutation_p.N210S	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	208					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			CTTTCTCTTATTGTCAAGCAT	0.348																																																0			2											142	136	138					2																	191862953		2202	4297	6499	191571198	SO:0001583	missense	6772				CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.623A>G	2.37:g.191862953T>C	ENSP00000354394:p.Asn208Ser		191571198	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	T	3.207	-0.162535	0.06502	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323;ENST00000544783	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	4.89	-4.47	0.03525	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.954811	0.08908	N	0.876282	T	0.39963	0.1098	L	0.43152	1.355	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38415	-0.9662	10	0.12430	T	0.62	-8.1681	13.7575	0.62946	0.0:0.567:0.0:0.433	.	208;208	P42224-2;P42224	.;STAT1_HUMAN	S	208;208;208;210;116	ENSP00000354394:N208S;ENSP00000386244:N208S;ENSP00000376136:N208S;ENSP00000376137:N210S	ENSP00000354394:N208S	N	-	2	0	STAT1	191571198	0.000000	0.05858	0.521000	0.27850	0.758000	0.43043	-0.709000	0.05030	-1.145000	0.02858	-0.256000	0.11100	AAT		0.348	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		C	191862953	T	C	191862953	3	2	97	1	0	0	0	0	1	0	0	0	15303	1493	52	4	1705	4	STAT1	2	191862953	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	12404566	191862953	51336420	14	26145										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203817322	203817322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agaaaatggacaggtacttcGtgtaattccacctacccaga	8	10	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:203817322G>A	ENST00000402905.3	+	5	668	c.347G>A	c.(346-348)cGt>cAt	p.R116H	CARF_ENST00000320443.8_Missense_Mutation_p.R116H|CARF_ENST00000456821.2_Missense_Mutation_p.R104H|CARF_ENST00000428585.1_Missense_Mutation_p.R40H|CARF_ENST00000434998.1_Missense_Mutation_p.R14H|CARF_ENST00000438828.2_Missense_Mutation_p.R116H|CARF_ENST00000471271.1_3'UTR|CARF_ENST00000545253.1_Missense_Mutation_p.R28H|WDR12_ENST00000477723.1_Intron|CARF_ENST00000444724.1_Missense_Mutation_p.R116H|CARF_ENST00000545262.1_Missense_Mutation_p.R40H|CARF_ENST00000414439.1_Missense_Mutation_p.R14H	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	116					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CAGGTACTTCGTGTAATTCCA	0.408																																																0			2											143	128	133					2																	203817322		1863	4113	5976	203525567	SO:0001583	missense	79800			AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.347G>A	2.37:g.203817322G>A	ENSP00000384006:p.Arg116His		203525567	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	8.211	0.800380	0.16397	.	.	ENSG00000138380	ENST00000402905;ENST00000431787;ENST00000444724;ENST00000414857;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000447539;ENST00000456821;ENST00000434998;ENST00000320443;ENST00000438828	.	.	.	5.46	1.38	0.22167	.	0.366056	0.23222	N	0.050544	T	0.25901	0.0631	L	0.33137	0.985	0.25159	N	0.990366	B;B;B;B;B	0.11235	0.001;0.001;0.004;0.001;0.004	B;B;B;B;B	0.08055	0.001;0.001;0.003;0.001;0.002	T	0.25433	-1.0132	9	0.11485	T	0.65	-0.1921	8.6682	0.34134	0.8098:0.0:0.1901:0.0	.	28;40;116;116;116	B4DIA7;G3V1K7;B4DRP6;Q8N187;F6SXV3	.;.;.;AL2S8_HUMAN;.	H	116;86;116;116;14;40;28;40;40;104;14;116;116	.	ENSP00000316224:R116H	R	+	2	0	ALS2CR8	203525567	1.000000	0.71417	0.955000	0.39395	0.976000	0.68499	1.128000	0.31369	0.016000	0.14998	0.467000	0.42956	CGT		0.408	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		A	203817322	G	A	203817322	3	1	97	1	0	0	0	0	1	0	0	0	555	1145	40	1	357	1	ALS2CR8	2	203817322	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	11954369	203817322	39382051	15	26146										
TNS1	7145	hgsc.bcm.edu	37	chr2	218678420	218678420	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gaggttaccttttttattctGctgcatgatggttggaggtg	13	5	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:218678420G>A	ENST00000171887.4	-	26	4989	c.4537C>T	c.(4537-4539)Cag>Tag	p.Q1513*	TNS1_ENST00000419504.1_Nonsense_Mutation_p.Q1500*|TNS1_ENST00000430930.1_Nonsense_Mutation_p.Q1492*	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1513	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		TTTTTATTCTGCTGCATGATG	0.592																																																0			2											136	136	136					2																	218678420		2203	4300	6503	218386665	SO:0001587	stop_gained	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4537C>T	2.37:g.218678420G>A	ENSP00000171887:p.Gln1513*		218386665	Q4ZG71|Q6IPI5	Nonsense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	48	13.929793	0.99770	.	.	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	.	.	.	5.15	4.27	0.50696	.	0.070369	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	13.834	0.63398	0.0732:0.0:0.9268:0.0	.	.	.	.	X	1513;651;1500;1492	.	ENSP00000171887:Q1513X	Q	-	1	0	TNS1	218386665	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.757000	0.85209	1.410000	0.46936	0.561000	0.74099	CAG		0.592	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218678420	G	A	218678420	4	1	97	1	0	0	0	0	0	1	0	0	16382	1328	46	3	702	3	TNS1	2	218678420	Nonsense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	14861098	218678420	24520953	16	26147										
MRPL44	65080	hgsc.bcm.edu	37	chr2	224828575	224828575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aactgaagaaaaggaatgttTcagctcctgaatcaagactt	8	7	2	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:224828575T>C	ENST00000258383.3	+	3	820	c.751T>C	c.(751-753)Tca>Cca	p.S251P	AC073641.2_ENST00000425192.1_RNA	NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	251	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		AAGGAATGTTTCAGCTCCTGA	0.378																																																0			2											105	104	104					2																	224828575		2203	4300	6503	224536819	SO:0001583	missense	65080			AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.751T>C	2.37:g.224828575T>C	ENSP00000258383:p.Ser251Pro		224536819	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	37	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	T	2.841	-0.240394	0.05944	.	.	ENSG00000135900	ENST00000258383	T	0.78126	-1.15	5.7	0.417	0.16421	Double-stranded RNA-binding (1);Double-stranded RNA-binding-like (1);	0.415449	0.27393	N	0.019574	T	0.53351	0.1791	N	0.05414	-0.055	0.20926	N	0.999829	B	0.09022	0.002	B	0.06405	0.002	T	0.38628	-0.9652	10	0.27082	T	0.32	-6.2797	8.8421	0.35148	0.0:0.4993:0.0:0.5007	.	251	Q9H9J2	RM44_HUMAN	P	251	ENSP00000258383:S251P	ENSP00000258383:S251P	S	+	1	0	MRPL44	224536819	0.002000	0.14202	0.003000	0.11579	0.105000	0.19272	-0.043000	0.12043	0.045000	0.15804	0.482000	0.46254	TCA		0.378	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		C	224828575	T	C	224828575	3	2	97	1	0	0	0	0	1	0	0	0	9838	1783	62	4	761	4	MRPL44	2	224828575	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	6150155	224828575	18370798	17	26148										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226447285	226447285	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcgtcgccctccacgctgccGtcccacgtccccggccatgc	10	22	0	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:226447285G>A	ENST00000272907.6	+	4	1565	c.1152G>A	c.(1150-1152)ccG>ccA	p.P384P	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	384	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CCACGCTGCCGTCCCACGTCC	0.677																																																0			2											15	19	18					2																	226447285		1983	4138	6121	226155529	SO:0001819	synonymous_variant	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1152G>A	2.37:g.226447285G>A			226155529	A2RRN4|Q96NL2	Silent	SNP	ENST00000272907.6	37	CCDS46529.1																																																																																				0.677	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		A	226447285	G	A	226447285	2	1	97	1	0	0	0	0	0	0	0	1	8258	1132	40	1		1	KIAA1486	2	226447285	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	1618710	226447285	16752088	18	26149										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227872075	227872075	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cgcagacctggcaccggctgAttttctggcgttgggcctgg	15	12	1	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr2:227872075A>G	ENST00000396625.3	-	48	5246	c.5039T>C	c.(5038-5040)aTc>aCc	p.I1680T	COL4A4_ENST00000329662.7_Missense_Mutation_p.I1677T	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1680	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCACCGGCTGATTTTCTGGCG	0.502																																																0			2											350	350	350					2																	227872075		1963	4163	6126	227580319	SO:0001583	missense	1286				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.5039T>C	2.37:g.227872075A>G	ENSP00000379866:p.Ile1680Thr		227580319	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.058860	0.36277	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.95980	-3.87;-3.87	5.89	0.634	0.17718	C-type lectin fold (1);	.	.	.	.	D	0.93739	0.7999	M	0.78049	2.395	0.37026	D	0.896432	B	0.06786	0.001	B	0.14023	0.01	D	0.89443	0.3725	9	0.38643	T	0.18	.	10.7718	0.46327	0.6894:0.0:0.3106:0.0	.	1680	P53420	CO4A4_HUMAN	T	1680;1677	ENSP00000379866:I1680T;ENSP00000328553:I1677T	ENSP00000328553:I1677T	I	-	2	0	COL4A4	227580319	0.982000	0.34865	0.996000	0.52242	0.942000	0.58702	2.166000	0.42406	0.117000	0.18138	-1.151000	0.01829	ATC		0.502	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		G	227872075	A	G	227872075	3	3	97	1	0	0	0	0	1	0	0	0	3699	333	12	4	37	4	COL4A4	2	227872075	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	1424790	227872075	15327298	19	26150										
IL5RA	3568	hgsc.bcm.edu	37	chr3	3137079	3137079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttctcccattggatagagagAcgagttccttcaatctctgc	8	11	3	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:3137079A>G	ENST00000446632.2	-	8	1333	c.759T>C	c.(757-759)cgT>cgC	p.R253R	IL5RA_ENST00000438560.1_Silent_p.R253R|IL5RA_ENST00000383846.1_Silent_p.R253R|IL5RA_ENST00000456302.1_Silent_p.R253R|IL5RA_ENST00000418488.2_Intron|IL5RA_ENST00000256452.3_Silent_p.R253R|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000311981.8_Silent_p.R253R|IL5RA_ENST00000430514.2_Silent_p.R253R	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	253	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		GGATAGAGAGACGAGTTCCTT	0.358																																					GBM(169;430 2801 24955 28528)											0			3											101	100	100					3																	3137079		2203	4300	6503	3112079	SO:0001819	synonymous_variant	3568			M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.759T>C	3.37:g.3137079A>G			3112079	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Silent	SNP	ENST00000446632.2	37	CCDS2559.1																																																																																				0.358	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			G	3137079	A	G	3137079	2	3	97	1	0	0	0	0	0	0	0	1	7721	262	10	4		4	IL5RA	3	3137079	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10		3137079	194885351	20	26151										
GRM7	2917	hgsc.bcm.edu	37	chr3	7456805	7456805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aaaacttcaactgcaagttgAcgattagtgggtcaaaaaaa	8	6	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:7456805A>G	ENST00000357716.4	+	5	1403	c.1129A>G	c.(1129-1131)Acg>Gcg	p.T377A	GRM7_ENST00000403881.1_Missense_Mutation_p.T377A|GRM7_ENST00000389336.4_Missense_Mutation_p.T377A|GRM7_ENST00000402647.2_Missense_Mutation_p.T377A|GRM7_ENST00000486284.1_Missense_Mutation_p.T377A	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	377					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CTGCAAGTTGACGATTAGTGG	0.408																																																0			3											107	98	101					3																	7456805		2203	4300	6503	7431805	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1129A>G	3.37:g.7456805A>G	ENSP00000350348:p.Thr377Ala		7431805	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550880	0.27739	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492;ENST00000445087	D;D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02;-2.02	5.8	5.8	0.92144	Extracellular ligand-binding receptor (1);	0.184921	0.49305	D	0.000148	D	0.89079	0.6613	L	0.46885	1.475	0.45046	D	0.99806	D;P;B	0.56035	0.974;0.941;0.082	D;D;B	0.71414	0.953;0.973;0.036	D	0.86941	0.2079	10	0.27785	T	0.31	.	15.263	0.73640	1.0:0.0:0.0:0.0	.	377;377;377	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	A	377;377;377;377;377;377;377;34	ENSP00000350348:T377A;ENSP00000417536:T377A;ENSP00000373987:T377A;ENSP00000385664:T377A;ENSP00000384585:T377A;ENSP00000395035:T34A	ENSP00000350348:T377A	T	+	1	0	GRM7	7431805	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.713000	0.74686	2.340000	0.79590	0.528000	0.53228	ACG		0.408	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		G	7456805	A	G	7456805	3	3	97	1	0	0	0	0	1	0	0	0	6823	275	10	4	1147	4	GRM7	3	7456805	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	4319726	7456805	190565625	21	26152										
CPNE9	151835	hgsc.bcm.edu	37	chr3	9768379	9768379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgcccatgtctatcattatcGtcggtgtaggaccagccatg	10	11	2	0	rs566993609		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:9768379G>A	ENST00000383832.3	+	19	1565	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	CPNE9_ENST00000383831.3_Missense_Mutation_p.V459I	NM_153635.2	NP_705899.2	Q8IYJ1	CPNE9_HUMAN	copine family member IX	459	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.V459I(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16	Medulloblastoma(99;0.227)					TATCATTATCGTCGGTGTAGG	0.547																																																2	Substitution - Missense(2)	ovary(1)|prostate(1)	3											122	117	119					3																	9768379		1927	4145	6072	9743379	SO:0001583	missense	151835				CCDS2574.2	3p25.3	2008-10-30			ENSG00000144550	ENSG00000144550			24336	protein-coding gene	gene with protein product						9430674	Standard	XM_006712990		Approved	KIAA4217	uc003bsd.3	Q8IYJ1	OTTHUMG00000128418	ENST00000383832.3:c.1375G>A	3.37:g.9768379G>A	ENSP00000373343:p.Val459Ile		9743379	A1L430|A6NDX6|A8MSP8	Missense_Mutation	SNP	ENST00000383832.3	37	CCDS2574.2	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876822	0.72180	.	.	ENSG00000144550	ENST00000383832;ENST00000383831	T;T	0.22945	1.93;1.93	4.4	4.4	0.53042	von Willebrand factor, type A (2);Copine (1);	0.064498	0.64402	D	0.000011	T	0.37489	0.1005	M	0.62723	1.935	0.53688	D	0.999976	P	0.43857	0.819	P	0.48304	0.573	T	0.21759	-1.0236	10	0.45353	T	0.12	.	16.7977	0.85606	0.0:0.0:1.0:0.0	.	459	Q8IYJ1	CPNE9_HUMAN	I	459	ENSP00000373343:V459I;ENSP00000373342:V459I	ENSP00000373342:V459I	V	+	1	0	CPNE9	9743379	1.000000	0.71417	0.962000	0.40283	0.964000	0.63967	6.831000	0.75324	2.257000	0.74773	0.460000	0.39030	GTC		0.547	CPNE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250205.4	NM_001033755		A	9768379	G	A	9768379	3	1	97	1	0	0	0	0	1	0	0	0	3825	1145	40	1	1445	1	CPNE9	3	9768379	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	2311574	9768379	188254051	22	26153										
TSEN2	80746	hgsc.bcm.edu	37	chr3	12558136	12558136	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttcttggtctatgctctgggAtgtttaagtatttactatga	9	5	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:12558136A>G	ENST00000284995.6	+	7	1323	c.936A>G	c.(934-936)ggA>ggG	p.G312G	RNU6-377P_ENST00000515965.1_RNA|TSEN2_ENST00000454502.2_Silent_p.G253G|TSEN2_ENST00000314571.7_Silent_p.G286G|TSEN2_ENST00000415684.1_Silent_p.G286G|TSEN2_ENST00000444864.1_Silent_p.G286G|TSEN2_ENST00000402228.3_Silent_p.G312G|TSEN2_ENST00000383797.5_Intron|C3orf83_ENST00000567514.1_Intron	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	312					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						ATGCTCTGGGATGTTTAAGTA	0.328																																																0			3											158	133	141					3																	12558136		2203	4299	6502	12533136	SO:0001819	synonymous_variant	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"tRNA splicing endonuclease subunits"	28422	protein-coding gene	gene with protein product		608753	"tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)", "tRNA splicing endonuclease 2 homolog (S. cerevisiae)"			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.936A>G	3.37:g.12558136A>G			12533136	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Silent	SNP	ENST00000284995.6	37	CCDS2611.1																																																																																				0.328	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265		G	12558136	A	G	12558136	2	3	97	1	0	0	0	0	0	0	0	1	16652	320	12	4		4	TSEN2	3	12558136	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	2789757	12558136	185464294	23	26154										
SATB1	6304	hgsc.bcm.edu	37	chr3	18419722	18419722	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gacactttagcacgcttcatTtcctgctgaatctcatcata	5	12	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:18419722T>C	ENST00000338745.6	-	9	3249	c.1515A>G	c.(1513-1515)gaA>gaG	p.E505E	SATB1_ENST00000417717.2_Silent_p.E505E|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Silent_p.E505E	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	505					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CACGCTTCATTTCCTGCTGAA	0.413																																																0			3											198	188	192					3																	18419722		2203	4300	6503	18394726	SO:0001819	synonymous_variant	6304				CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1515A>G	3.37:g.18419722T>C			18394726	B3KXF1|C9JTR6|Q59EQ0	Silent	SNP	ENST00000338745.6	37	CCDS2631.1																																																																																				0.413	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18419722	T	C	18419722	2	2	97	1	0	0	0	0	0	0	0	1	13890	1838	64	4		4	SATB1	3	18419722	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	5861586	18419722	179602708	24	26155										
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21467073	21467073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcctgtgtttcctttattaaCaggtcctttgcctttcactc	6	12	1	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:21467073C>T	ENST00000281523.2	-	6	1281	c.763G>A	c.(763-765)Gtt>Att	p.V255I		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	255						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						CCTTTATTAACAGGTCCTTTG	0.438																																																0			3											149	137	141					3																	21467073		2203	4300	6503	21442077	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.763G>A	3.37:g.21467073C>T	ENSP00000281523:p.Val255Ile		21442077		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.908261	0.33721	.	.	ENSG00000151789	ENST00000281523	T	0.42900	0.96	5.59	3.77	0.43336	.	0.427365	0.21633	N	0.071460	T	0.22003	0.0530	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12889	-1.0530	10	0.37606	T	0.19	-18.7096	9.4481	0.38710	0.0:0.7237:0.0:0.2763	.	255	Q9H6B1	Z385D_HUMAN	I	255	ENSP00000281523:V255I	ENSP00000281523:V255I	V	-	1	0	ZNF385D	21442077	0.911000	0.30947	0.872000	0.34217	0.998000	0.95712	1.205000	0.32308	1.491000	0.48482	0.655000	0.94253	GTT		0.438	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		T	21467073	C	T	21467073	3	4	97	1	0	0	0	0	1	0	0	0	17917	478	17	3	436	3	ZNF385D	3	21467073	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	3047351	21467073	176555357	25	26156										
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27436595	27436595	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cttatgatccaccctctctcTggatgagtaggctgttaaaa	8	10	2	2	rs148520298	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:27436595T>C	ENST00000295736.5	-	19	2758	c.2688A>G	c.(2686-2688)ccA>ccG	p.P896P	SLC4A7_ENST00000445684.1_Silent_p.P892P|SLC4A7_ENST00000446700.1_Silent_p.P888P|SLC4A7_ENST00000428386.1_Silent_p.P772P|SLC4A7_ENST00000435667.2_Silent_p.P781P|SLC4A7_ENST00000454389.1_Silent_p.P905P|SLC4A7_ENST00000455077.1_Silent_p.P777P|SLC4A7_ENST00000388777.4_Silent_p.P446P|SLC4A7_ENST00000440156.1_Silent_p.P892P|SLC4A7_ENST00000437179.1_Silent_p.P777P|SLC4A7_ENST00000425128.2_3'UTR	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	896					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ACCCTCTCTCTGGATGAGTAG	0.368													T|||	11	0.00219649	0.0053	0.0058	5008	,	,		17897	0		0	False		,,,				2504	0															0			3						T		10,4396	17.9+/-39.9	0,10,2193	63	62	62		2688	4.9	0.9	3	dbSNP_134	62	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SLC4A7	NM_003615.3		0,15,6488	CC,CT,TT		0.0581,0.227,0.1153		896/1215	27436595	15,12991	2203	4300	6503	27411599	SO:0001819	synonymous_variant	9497			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2688A>G	3.37:g.27436595T>C			27411599	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																				0.368	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		C	27436595	T	C	27436595	2	2	97	1	0	0	0	0	0	0	0	1	14695	1567	55	4		4	SLC4A7	3	27436595	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	5969522	27436595	170585835	26	26157										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38134331	38134331	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcagagcagaccttcatcatCatgtgcgacaactgccagat	9	12	3	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:38134331C>T	ENST00000308059.6	+	11	1737	c.1716C>T	c.(1714-1716)atC>atT	p.I572I	DLEC1_ENST00000452631.2_Silent_p.I572I|DLEC1_ENST00000346219.3_Silent_p.I572I					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCTTCATCATCATGTGCGACA	0.567																																																0			3											101	102	102					3																	38134331		2039	4200	6239	38109335	SO:0001819	synonymous_variant	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1716C>T	3.37:g.38134331C>T			38109335		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																				0.567	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38134331	C	T	38134331	2	4	97	1	0	0	0	0	0	0	0	1	4563	816	29	3		3	DLEC1	3	38134331	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	10697736	38134331	159888099	27	26158										
DAG1	1605	hgsc.bcm.edu	37	chr3	49568627	49568627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcttcacaacatgaaattagTgccggtggtgaataacagac	10	8	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:49568627T>C	ENST00000539901.1	+	3	1241	c.683T>C	c.(682-684)gTg>gCg	p.V228A	DAG1_ENST00000515359.2_Missense_Mutation_p.V228A|DAG1_ENST00000541308.1_Missense_Mutation_p.V228A|DAG1_ENST00000308775.2_Missense_Mutation_p.V228A|DAG1_ENST00000545947.1_Missense_Mutation_p.V228A|DAG1_ENST00000538711.1_Missense_Mutation_p.V228A	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	228	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		ATGAAATTAGTGCCGGTGGTG	0.512																																																0			3											78	82	81					3																	49568627		2203	4300	6503	49543631	SO:0001583	missense	1605			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.683T>C	3.37:g.49568627T>C	ENSP00000439334:p.Val228Ala		49543631	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	37	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.249813	0.39797	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711;ENST00000415315	T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	5.92	5.92	0.95590	.	0.058901	0.64402	D	0.000003	T	0.81583	0.4853	L	0.34521	1.04	0.46823	D	0.999211	D	0.69078	0.997	D	0.68039	0.955	T	0.81280	-0.1004	10	0.40728	T	0.16	-17.7946	15.3474	0.74350	0.0:0.0:0.0:1.0	.	228	Q14118	DAG1_HUMAN	A	228;228;228;228;228;228;27	ENSP00000440705:V228A;ENSP00000312435:V228A;ENSP00000442600:V228A;ENSP00000440590:V228A;ENSP00000439334:V228A;ENSP00000438421:V228A	ENSP00000312435:V228A	V	+	2	0	DAG1	49543631	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	8.040000	0.89188	2.263000	0.75096	0.533000	0.62120	GTG		0.512	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			C	49568627	T	C	49568627	3	2	97	1	0	0	0	0	1	0	0	0	4231	1696	59	4	689	4	DAG1	3	49568627	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	11434296	49568627	148453803	28	26159										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52597433	52597433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atcatctccaccttctaactCggcaaatttagcttctagca	4	13	4	0	rs199643728		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:52597433C>T	ENST00000296302.7	-	24	3953	c.3952G>A	c.(3952-3954)Gag>Aag	p.E1318K	PBRM1_ENST00000409767.1_Missense_Mutation_p.E1333K|PBRM1_ENST00000410007.1_Missense_Mutation_p.E1293K|PBRM1_ENST00000356770.4_Missense_Mutation_p.E1286K|PBRM1_ENST00000409057.1_Missense_Mutation_p.E1318K|PBRM1_ENST00000409114.3_Missense_Mutation_p.E1333K|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000337303.4_Missense_Mutation_p.E1318K|RNU6ATAC16P_ENST00000408591.1_RNA|PBRM1_ENST00000394830.3_Missense_Mutation_p.E1293K			Q86U86	PB1_HUMAN	polybromo 1	1318					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CCTTCTAACTCGGCAAATTTA	0.438			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																		Rec	yes		3	3p21	55193	polybromo 1		E	0			3						C	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	149	132	137		3856,3877,3952	5.6	1	3		137	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	56,56,56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	1286/1603,1293/1583,1318/1583	52597433	2,13004	2203	4300	6503	52572473	SO:0001583	missense	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3952G>A	3.37:g.52597433C>T	ENSP00000296302:p.Glu1318Lys		52572473	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	20.6	4.019567	0.75275	0.0	2.33E-4	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	T;T;T;T;T;T;T;T;T	0.36157	1.29;1.38;1.31;1.27;1.29;1.3;1.74;1.27;1.27	5.63	5.63	0.86233	.	0.099948	0.64402	D	0.000002	T	0.23094	0.0558	N	0.22421	0.69	0.53005	D	0.999963	P;P;P;P;P;P;P;P	0.47106	0.769;0.564;0.769;0.876;0.89;0.846;0.769;0.564	B;B;B;B;B;B;B;B	0.33890	0.158;0.112;0.158;0.123;0.172;0.076;0.158;0.085	T	0.04041	-1.0982	10	0.21540	T	0.41	-17.2823	18.2115	0.89872	0.0:1.0:0.0:0.0	.	1293;1293;1318;1333;1333;1318;1286;1318	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	K	1286;1293;1318;1318;1318;1293;1333;1333;1317	ENSP00000349213:E1286K;ENSP00000378307:E1293K;ENSP00000296302:E1318K;ENSP00000338302:E1318K;ENSP00000386593:E1318K;ENSP00000386529:E1293K;ENSP00000386643:E1333K;ENSP00000386601:E1333K;ENSP00000387775:E1317K	ENSP00000296302:E1318K	E	-	1	0	PBRM1	52572473	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.772000	0.85439	2.802000	0.96397	0.561000	0.74099	GAG		0.438	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52597433	C	T	52597433	3	4	97	1	0	0	0	0	1	0	0	0	11522	893	31	1	976	1	PBRM1	3	52597433	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	3028806	52597433	145424997	29	26160										
B4GALT4	8702	hgsc.bcm.edu	37	chr3	118948710	118948710	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactgaggtaaggagacacAgaagggcagttgtcaagttc	13	6	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:118948710A>T	ENST00000483209.1	-	3	878	c.237T>A	c.(235-237)tcT>tcA	p.S79S	B4GALT4_ENST00000471675.1_Silent_p.S32S|B4GALT4_ENST00000467604.1_Silent_p.S79S|B4GALT4_ENST00000359213.3_Silent_p.S79S|B4GALT4_ENST00000393765.2_Silent_p.S79S|B4GALT4_ENST00000460321.1_Intron|B4GALT4-AS1_ENST00000470790.1_RNA			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	79					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	AAGGAGACACAGAAGGGCAGT	0.368																																																0			3											137	126	130					3																	118948710		2203	4300	6503	120431400	SO:0001819	synonymous_variant	8702			AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"Beta 4-glycosyltransferases"	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.237T>A	3.37:g.118948710A>T			120431400	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	37	CCDS2986.1																																																																																				0.368	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778		T	118948710	A	T	118948710	2	4	97	1	0	0	0	0	0	0	0	1	1274	175	7	5		5	B4GALT4	3	118948710	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	66351277	118948710	79073720	30	26161										
SEC61A1	29927	hgsc.bcm.edu	37	chr3	127788458	127788458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	accagtactttgagatcttcGttaaggagcaaagcgaggtt	11	7	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:127788458G>A	ENST00000243253.3	+	12	1568	c.1384G>A	c.(1384-1386)Gtt>Att	p.V462I	RUVBL1_ENST00000464873.1_Intron|SEC61A1_ENST00000464451.1_Missense_Mutation_p.V468I|SEC61A1_ENST00000483956.1_3'UTR|SEC61A1_ENST00000424880.2_Missense_Mutation_p.V342I	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	462					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)	p.V462F(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						TGAGATCTTCGTTAAGGAGCA	0.607																																																1	Substitution - Missense(1)	ovary(1)	3											103	111	108					3																	127788458		2203	4300	6503	129271148	SO:0001583	missense	29927			AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.1384G>A	3.37:g.127788458G>A	ENSP00000243253:p.Val462Ile		129271148	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	37	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.834435	0.50951	.	.	ENSG00000058262	ENST00000464451;ENST00000243253;ENST00000424880	.	.	.	5.96	5.96	0.96718	SecY subunit domain (2);	0.055610	0.64402	N	0.000001	T	0.68659	0.3025	M	0.66939	2.045	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.62728	-0.6793	9	0.46703	T	0.11	.	20.4084	0.99013	0.0:0.0:1.0:0.0	.	462	P61619	S61A1_HUMAN	I	468;462;342	.	ENSP00000243253:V462I	V	+	1	0	SEC61A1	129271148	1.000000	0.71417	0.986000	0.45419	0.008000	0.06430	9.869000	0.99810	2.833000	0.97629	0.650000	0.86243	GTT		0.607	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336		A	127788458	G	A	127788458	3	1	97	1	0	0	0	0	1	0	0	0	14037	1145	40	1	1430	1	SEC61A1	3	127788458	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	8839748	127788458	70233972	31	26162										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936094	178936094	+	Missense_Mutation	SNP	C	C	G													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctctctctgaaatcactgagCaggagaaagattttctatgg					rs121913286		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:178936094C>G	ENST00000263967.3	+	10	1793	c.1636C>G	c.(1636-1638)Cag>Gag	p.Q546E		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	546	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		Q -> E (in BC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> K (in OC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> P (found in an anaplastic astrocytoma sample; unknown pathological significance). {ECO:0000269|PubMed:15289301}.|Q -> R (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q546K(89)|p.Q546E(12)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATCACTGAGCAGGAGAAAGA	0.358		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	101	Substitution - Missense(101)	large_intestine(55)|breast(17)|endometrium(15)|central_nervous_system(3)|lung(3)|ovary(3)|skin(2)|cervix(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)	3											61	61	61					3																	178936094		1814	4072	5886	180418788	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1636C>G	3.37:g.178936094C>G	ENSP00000263967:p.Gln546Glu		180418788	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069293	0.55539	.	.	ENSG00000121879	ENST00000263967	T	0.61274	0.12	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35682	0.0940	N	0.05177	-0.1	0.80722	D	1	P	0.40282	0.711	B	0.38056	0.264	T	0.40478	-0.9561	10	0.02654	T	1	-14.2064	20.0024	0.97423	0.0:1.0:0.0:0.0	.	546	P42336	PK3CA_HUMAN	E	546	ENSP00000263967:Q546E	ENSP00000263967:Q546E	Q	+	1	0	PIK3CA	180418788	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.487000	0.81328	2.722000	0.93159	0.467000	0.42956	CAG		0.358	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936094	C	G	178936094	3	3	97	1	0	0	0	0	1	0	0	0	11944	711	25	5	1670	5	PIK3CA	3	178936094	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	51147636	178936094	19086336	32	26163	38	2								
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936098	178936098	+	Missense_Mutation	SNP	A	A	G													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctctgaaatcactgagcaggAgaaagattttctatggagtc							TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:178936098A>G	ENST00000263967.3	+	10	1797	c.1640A>G	c.(1639-1641)gAg>gGg	p.E547G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	547	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ACTGAGCAGGAGAAAGATTTT	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											62	62	62					3																	178936098		1812	4070	5882	180418792	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1640A>G	3.37:g.178936098A>G	ENSP00000263967:p.Glu547Gly		180418792	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543251	0.86022	.	.	ENSG00000121879	ENST00000263967	T	0.70399	-0.48	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85737	0.5766	M	0.87900	2.915	0.80722	D	1	D	0.67145	0.996	D	0.69479	0.964	D	0.88339	0.2973	10	0.87932	D	0	-14.9038	16.1026	0.81194	1.0:0.0:0.0:0.0	.	547	P42336	PK3CA_HUMAN	G	547	ENSP00000263967:E547G	ENSP00000263967:E547G	E	+	2	0	PIK3CA	180418792	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAG		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936098	A	G	178936098	3	3	97	1	0	0	0	0	1	0	0	0	11944	304	11	4	1674	4	PIK3CA	3	178936098	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	4	178936098	19086332	33	26164	38	2								
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951964	178951964	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atcttttctcaatgatgcttGgctctggaatgccagaacta	8	9	3	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:178951964G>C	ENST00000263967.3	+	21	3176	c.3019G>C	c.(3019-3021)Ggc>Cgc	p.G1007R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1007	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		G -> R (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.G1007R(8)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCTTGGCTCTGGAAT	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	8	Substitution - Missense(8)	lung(3)|endometrium(3)|urinary_tract(1)|large_intestine(1)	3											114	103	106					3																	178951964		1886	4108	5994	180434658	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3019G>C	3.37:g.178951964G>C	ENSP00000263967:p.Gly1007Arg		180434658	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.856328	0.71834	.	.	ENSG00000121879	ENST00000263967	T	0.79749	-1.3	5.8	5.8	0.92144	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.112145	0.64402	D	0.000010	D	0.84844	0.5562	L	0.46947	1.48	0.80722	D	1	D	0.62365	0.991	P	0.56398	0.797	D	0.83385	0.0014	10	0.41790	T	0.15	-8.1028	20.0716	0.97726	0.0:0.0:1.0:0.0	.	1007	P42336	PK3CA_HUMAN	R	1007	ENSP00000263967:G1007R	ENSP00000263967:G1007R	G	+	1	0	PIK3CA	180434658	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.237000	0.95368	2.741000	0.93983	0.585000	0.79938	GGC		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178951964	G	C	178951964	3	2	97	1	0	0	0	0	1	0	0	0	11944	1348	47	5	3097	5	PIK3CA	3	178951964	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	15866	178951964	19070466	34	26165										
RNF168	165918	hgsc.bcm.edu	37	chr3	196229996	196229996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gaggatttccatgcagatccCgcactggcactcggacagcg	12	13	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr3:196229996C>T	ENST00000318037.3	-	1	643	c.49G>A	c.(49-51)Ggg>Agg	p.G17R		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	17					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		ATGCAGATCCCGCACTGGCAC	0.527																																																0			3											97	87	90					3																	196229996		2203	4300	6503	197714393	SO:0001583	missense	165918			AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.49G>A	3.37:g.196229996C>T	ENSP00000320898:p.Gly17Arg		197714393	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	37	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	C	2.440	-0.328906	0.05314	.	.	ENSG00000163961	ENST00000318037	D	0.84223	-1.82	6.0	-0.514	0.11958	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	2.310530	0.01382	N	0.012942	T	0.81054	0.4743	L	0.39397	1.21	0.09310	N	0.999995	B	0.23891	0.093	B	0.17722	0.019	T	0.61222	-0.7106	10	0.18276	T	0.48	9.3621	14.6787	0.69001	0.0:0.5678:0.2498:0.1824	.	17	Q8IYW5	RN168_HUMAN	R	17	ENSP00000320898:G17R	ENSP00000320898:G17R	G	-	1	0	RNF168	197714393	0.966000	0.33281	0.010000	0.14722	0.023000	0.10783	1.589000	0.36644	-0.410000	0.07542	-0.321000	0.08615	GGG		0.527	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		T	196229996	C	T	196229996	3	4	97	1	0	0	0	0	1	0	0	0	13496	652	23	1	1690	1	RNF168	3	196229996	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	17278032	196229996	1792434	35	26166										
LDB2	9079	hgsc.bcm.edu	37	chr4	16597494	16597494	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cgggggatgagggtcctgccGatagctgggagagaaacaca	17	8	0	2	rs546170586	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr4:16597494G>A	ENST00000304523.5	-	3	563	c.240C>T	c.(238-240)atC>atT	p.I80I	LDB2_ENST00000503178.2_5'UTR|LDB2_ENST00000515064.1_Silent_p.I80I|LDB2_ENST00000502640.1_Silent_p.I80I|LDB2_ENST00000441778.2_Silent_p.I80I|LDB2_ENST00000503829.1_5'UTR	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	80					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						GGGTCCTGCCGATAGCTGGGA	0.473													G|||	2	0.000399361	8e-04	0	5008	,	,		16237	0.001		0	False		,,,				2504	0															0			4											49	46	47					4																	16597494		2203	4300	6503	16206592	SO:0001819	synonymous_variant	9079			AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.240C>T	4.37:g.16597494G>A			16206592	O60619|O75480	Silent	SNP	ENST00000304523.5	37	CCDS3420.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.931054	0.34096	.	.	ENSG00000169744	ENST00000507464	.	.	.	5.6	2.03	0.26663	.	.	.	.	.	T	0.52821	0.1758	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43147	-0.9409	4	.	.	.	-26.8944	5.9101	0.19023	0.5705:0.0:0.4295:0.0	.	.	.	.	L	2	.	.	S	-	2	0	LDB2	16206592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.164000	0.31810	0.641000	0.30601	0.563000	0.77884	TCG		0.473	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2			A	16597494	G	A	16597494	2	1	97	1	0	0	0	0	0	0	0	1	8718	1048	37	1		1	LDB2	4	16597494	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10		16597494	174556782	36	26167										
HPGDS	27306	hgsc.bcm.edu	37	chr4	95239101	95239101	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caacttccaaaatggggattTttccaaatgggagagcttaa	9	7	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr4:95239101T>C	ENST00000295256.5	-	3	239	c.149A>G	c.(148-150)aAa>aGa	p.K50R	HPGDS_ENST00000514774.1_5'UTR	NM_014485.2	NP_055300.1	O60760	HPGDS_HUMAN	hematopoietic prostaglandin D synthase	50	GST N-terminal.				arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|glutathione derivative biosynthetic process (GO:1901687)|locomotory behavior (GO:0007626)|prostaglandin metabolic process (GO:0006693)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	calcium ion binding (GO:0005509)|glutathione transferase activity (GO:0004364)|magnesium ion binding (GO:0000287)|prostaglandin-D synthase activity (GO:0004667)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|lung(3)|ovary(1)|urinary_tract(1)	7					Glutathione(DB00143)	AATGGGGATTTTTCCAAATGG	0.333																																					Colon(86;1802 1843 17863 46794)											0			4											79	79	79					4																	95239101		2203	4299	6502	95458124	SO:0001583	missense	0			D82073	CCDS3640.1	4q22.2	2012-06-21			ENSG00000163106	ENSG00000163106		"Glutathione S-transferases / Soluble"	17890	protein-coding gene	gene with protein product	"glutathione S-transferase sigma"	602598				9323136, 9353279, 11672424	Standard	XM_005262932		Approved	GSTS, PGDS, H-PGDS, PGD2, GSTS1-1	uc003hte.1	O60760	OTTHUMG00000130974	ENST00000295256.5:c.149A>G	4.37:g.95239101T>C	ENSP00000295256:p.Lys50Arg		95458124	Q6FHT9	Missense_Mutation	SNP	ENST00000295256.5	37	CCDS3640.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.245379	0.39697	.	.	ENSG00000163106	ENST00000295256	T	0.06142	3.34	5.48	5.48	0.80851	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.075249	0.56097	D	0.000037	T	0.18676	0.0448	L	0.49256	1.55	0.42258	D	0.992006	D	0.61080	0.989	D	0.77004	0.989	T	0.00321	-1.1819	10	0.62326	D	0.03	.	11.961	0.53009	0.0:0.0:0.0:1.0	.	50	O60760	HPGDS_HUMAN	R	50	ENSP00000295256:K50R	ENSP00000295256:K50R	K	-	2	0	HPGDS	95458124	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	4.849000	0.62882	2.081000	0.62600	0.528000	0.53228	AAA		0.333	HPGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253587.1	NM_014485		C	95239101	T	C	95239101	3	2	97	1	0	0	0	0	1	0	0	0	7356	1841	64	4	466	4	HPGDS	4	95239101	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	78641607	95239101	95915175	37	26168										
ANK2	287	hgsc.bcm.edu	37	chr4	114204004	114204004	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	accttgcttctggataagggAgccaatatccacatgtcaac	8	11	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr4:114204004A>G	ENST00000357077.4	+	18	2108	c.2055A>G	c.(2053-2055)ggA>ggG	p.G685G	ANK2_ENST00000394537.3_Silent_p.G685G|ANK2_ENST00000264366.6_Silent_p.G685G|ANK2_ENST00000506722.1_Silent_p.G664G	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	685			G -> E (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TGGATAAGGGAGCCAATATCC	0.458																																																0			4											134	97	110					4																	114204004		2203	4300	6503	114423453	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2055A>G	4.37:g.114204004A>G			114423453	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.458	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114204004	A	G	114204004	2	3	97	1	0	0	0	0	0	0	0	1	621	291	11	4		4	ANK2	4	114204004	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	18964903	114204004	76950272	38	26169										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249369	153249369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttttcccttaccttttttcaTgaagatgcatacaacgcaca	4	11	1	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr4:153249369T>C	ENST00000281708.4	-	9	2638	c.1409A>G	c.(1408-1410)cAt>cGt	p.H470R	FBXW7_ENST00000603841.1_Missense_Mutation_p.H470R|FBXW7_ENST00000393956.3_Missense_Mutation_p.H294R|FBXW7_ENST00000263981.5_Missense_Mutation_p.H390R|FBXW7_ENST00000296555.5_Missense_Mutation_p.H352R|FBXW7_ENST00000603548.1_Missense_Mutation_p.H470R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	470					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.H470P(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CCTTTTTTCATGAAGATGCAT	0.418			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	2	Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(2)	4											206	183	191					4																	153249369		2203	4300	6503	153468819	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1409A>G	4.37:g.153249369T>C	ENSP00000281708:p.His470Arg		153468819	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595946	0.28445	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49881	0.1583	L	0.39514	1.22	0.80722	D	1	B;B;B;B	0.29612	0.067;0.251;0.054;0.054	B;B;B;B	0.26517	0.023;0.07;0.013;0.024	T	0.45071	-0.9286	10	0.34782	T	0.22	-19.3583	16.2194	0.82247	0.0:0.0:0.0:1.0	.	294;470;352;390	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	R	470;352;390;294	ENSP00000281708:H470R;ENSP00000296555:H352R;ENSP00000263981:H390R;ENSP00000377528:H294R	ENSP00000263981:H390R	H	-	2	0	FBXW7	153468819	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.234000	0.73211	0.528000	0.53228	CAT		0.418	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153249369	T	C	153249369	3	2	97	1	0	0	0	0	1	0	0	0	5788	1464	51	4	730	4	FBXW7	4	153249369	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	39045365	153249369	37904907	39	26170										
FGB	2244	hgsc.bcm.edu	37	chr4	155491582	155491582	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttctttcaggttaacatcagAtcccagaaaacagtgttcta	6	9	4	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr4:155491582A>G	ENST00000302068.4	+	8	1319	c.1256A>G	c.(1255-1257)gAt>gGt	p.D419G	FGB_ENST00000509493.1_Missense_Mutation_p.D200G|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	419	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TTAACATCAGATCCCAGAAAA	0.423																																					NSCLC(106;1133 1613 21870 46110 52656)											0			4											92	82	85					4																	155491582		2203	4300	6503	155711032	SO:0001583	missense	2244				CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"Fibrinogen C domain containing", "Endogenous ligands"	3662	protein-coding gene	gene with protein product		134830	"fibrinogen, B beta polypeptide"				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.1256A>G	4.37:g.155491582A>G	ENSP00000306099:p.Asp419Gly		155711032	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	37	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.166697	0.57476	.	.	ENSG00000171564	ENST00000302068;ENST00000537843;ENST00000509493	T;T	0.81330	-1.48;-1.48	5.62	5.62	0.85841	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.043120	0.85682	D	0.000000	D	0.90000	0.6878	M	0.81179	2.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91209	0.4997	10	0.72032	D	0.01	.	16.1203	0.81346	1.0:0.0:0.0:0.0	.	402;419	B4E1D3;P02675	.;FIBB_HUMAN	G	419;402;200	ENSP00000306099:D419G;ENSP00000426757:D200G	ENSP00000306099:D419G	D	+	2	0	FGB	155711032	1.000000	0.71417	0.999000	0.59377	0.035000	0.12851	9.218000	0.95166	2.274000	0.75844	0.533000	0.62120	GAT		0.423	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141		G	155491582	A	G	155491582	3	3	97	1	0	0	0	0	1	0	0	0	5850	333	12	4	1286	4	FGB	4	155491582	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	2242213	155491582	35662694	40	26171										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5182370	5182370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ccctgcacagcagcgaccttCgcctgggactgccacaaaag	10	16	0	0	rs202209661		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr5:5182370C>T	ENST00000274181.7	+	4	853	c.715C>T	c.(715-717)Cgc>Tgc	p.R239C	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.R239C	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	239					branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						CAGCGACCTTCGCCTGGGACT	0.517																																																0			5						C	CYS/ARG	0,4186		0,0,2093	67	72	70		715	-0.9	0	5		70	2,8474		0,2,4236	yes	missense	ADAMTS16	NM_139056.2	180	0,2,6329	TT,TC,CC		0.0236,0.0,0.0158	possibly-damaging	239/1225	5182370	2,12660	2093	4238	6331	5235370	SO:0001583	missense	170690			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.715C>T	5.37:g.5182370C>T	ENSP00000274181:p.Arg239Cys		5235370	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606407	0.46527	0.0	2.36E-4	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.63255	0.06;-0.03	5.26	-0.905	0.10527	.	0.697943	0.13970	N	0.350256	T	0.48003	0.1476	N	0.14661	0.345	0.09310	N	1	P;P;P	0.47302	0.893;0.741;0.738	B;P;B	0.47162	0.27;0.54;0.276	T	0.47484	-0.9114	10	0.49607	T	0.09	.	11.0966	0.48147	0.3715:0.5514:0.0771:0.0	.	239;239;239	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	C	239	ENSP00000274181:R239C;ENSP00000421631:R239C	ENSP00000274181:R239C	R	+	1	0	ADAMTS16	5235370	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.768000	0.04715	-0.418000	0.07450	0.650000	0.86243	CGC		0.517	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		T	5182370	C	T	5182370	3	4	97	1	0	0	0	0	1	0	0	0	261	884	31	1	729	1	ADAMTS16	5	5182370	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10		5182370	175732890	41	26172										
APC	324	hgsc.bcm.edu	37	chr5	112175242	112175242	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	attggaactaggtcagctgaAgatcctgtgagcgaagttcc	12	8	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr5:112175242A>G	ENST00000457016.1	+	16	4331	c.3951A>G	c.(3949-3951)gaA>gaG	p.E1317E	APC_ENST00000257430.4_Silent_p.E1317E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Silent_p.E1317E			P25054	APC_HUMAN	adenomatous polyposis coli	1317	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		E -> Q (may contribute to colorectal tumor development; dbSNP:rs1801166). {ECO:0000269|PubMed:9724771}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.D1318fs*3(1)|p.K1192fs*3(1)|p.?(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGTCAGCTGAAGATCCTGTGA	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											60	62	61					5																	112175242		2202	4300	6502	112203141	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3951A>G	5.37:g.112175242A>G			112203141	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175242	A	G	112175242	2	3	97	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112175242	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	106992872	112175242	68740018	42	26173										
APC	324	hgsc.bcm.edu	37	chr5	112175324	112175324	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agggttctagtttatcttcaGaatcagccaggcacaaagct	9	9	4	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr5:112175324G>T	ENST00000457016.1	+	16	4413	c.4033G>T	c.(4033-4035)Gaa>Taa	p.E1345*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1345*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1345*			P25054	APC_HUMAN	adenomatous polyposis coli	1345	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1345*(3)|p.S1335fs*70(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATCTTCAGAATCAGCCAG	0.478		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Substitution - Nonsense(3)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5	GRCh37	CM994565	APC	M							58	62	60					5																	112175324		2202	4300	6502	112203223	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4033G>T	5.37:g.112175324G>T	ENSP00000413133:p.Glu1345*		112203223	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.442588	0.98813	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.216974	0.45867	D	0.000337	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.7885	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1345	.	.	E	+	1	0	APC	112203223	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	4.374000	0.59543	2.861000	0.98227	0.655000	0.94253	GAA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175324	G	T	112175324	4	4	97	1	0	0	0	0	0	1	0	0	763	943	33	2	4091	2	APC	5	112175324	Nonsense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	82	112175324	68739936	43	26174										
NRG2	9542	hgsc.bcm.edu	37	chr5	139245141	139245141	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcttcaaacatactttgcttAggatctggcatgtacaatcg	7	9	3	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr5:139245141A>G	ENST00000361474.1	-	5	1406	c.1182T>C	c.(1180-1182)ccT>ccC	p.P394P	NRG2_ENST00000289422.7_Silent_p.P394P|NRG2_ENST00000340391.3_Silent_p.P191P|NRG2_ENST00000358522.3_Intron|NRG2_ENST00000289409.4_Intron|NRG2_ENST00000545385.1_Intron|NRG2_ENST00000541337.1_Intron|NRG2_ENST00000394770.1_Silent_p.P394P	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	394					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTTTGCTTAGGATCTGGCA	0.468																																																0			5											102	98	99					5																	139245141		2203	4300	6503	139225325	SO:0001819	synonymous_variant	9542				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1182T>C	5.37:g.139245141A>G			139225325		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																				0.468	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		G	139245141	A	G	139245141	2	3	97	1	0	0	0	0	0	0	0	1	10679	407	15	4		4	NRG2	5	139245141	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	27069817	139245141	41670119	44	26175										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140737183	140737183	+	Frame_Shift_Del	DEL	C	C	-													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aaacaaaaggagaccctaatCttcaggtgagtcaatcttat							TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr5:140737183delC	ENST00000571252.1	+	1	2416	c.2416delC	c.(2416-2418)cttfs	p.L806fs	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	806					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGACCCTAATCTTCAGGTGAG	0.373																																																0			5											41	45	44					5																	140737183		2105	4228	6333	140717367	SO:0001589	frameshift_variant	56111			AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.2416delC	5.37:g.140737183delC	ENSP00000458570:p.Leu806fs		140717367	Q9Y5D3	Frame_Shift_Del	DEL	ENST00000571252.1	37	CCDS58979.1																																																																																				0.373	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		-	140737183	C	-	140737183	7	5	97	1	0	1	0	1	0	0	0	0	11587	913	32	0	2418	0	PCDHGA4	5	140737183	Frame_Shift_Del	DEL	C	TCGA-DC-6158-01A-11D-1657-10	1492042	140737183	40178077	45	26176										
DDX43	55510	hgsc.bcm.edu	37	chr6	74118978	74118978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tttgtcaatgcaggttttagAtgaagcagacaagatgttgg	12	4	1	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr6:74118978A>G	ENST00000370336.4	+	10	1345	c.1187A>G	c.(1186-1188)gAt>gGt	p.D396G	DDX43_ENST00000479773.1_3'UTR	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CAGGTTTTAGATGAAGCAGAC	0.383																																																0			6											180	171	174					6																	74118978		2203	4300	6503	74175699	SO:0001583	missense	55510				CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1187A>G	6.37:g.74118978A>G	ENSP00000359361:p.Asp396Gly		74175699	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	37	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214823	0.58452	.	.	ENSG00000080007	ENST00000370336	T	0.55413	0.52	4.82	4.82	0.62117	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.046925	0.85682	D	0.000000	D	0.82407	0.5030	H	0.99705	4.715	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.90266	0.4304	10	0.87932	D	0	-6.01	14.3102	0.66410	1.0:0.0:0.0:0.0	.	396	Q9NXZ2	DDX43_HUMAN	G	396	ENSP00000359361:D396G	ENSP00000359361:D396G	D	+	2	0	DDX43	74175699	1.000000	0.71417	1.000000	0.80357	0.298000	0.27526	8.703000	0.91344	1.926000	0.55796	0.374000	0.22700	GAT		0.383	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		G	74118978	A	G	74118978	3	3	97	1	0	0	0	0	1	0	0	0	4369	333	12	4	1225	4	DDX43	6	74118978	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10		74118978	96996089	46	26177										
PHIP	55023	hgsc.bcm.edu	37	chr6	79657465	79657465	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tctaacggtagcaaaatccaTtggagtgtcaatgatgtctc	9	8	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr6:79657465T>C	ENST00000275034.4	-	36	4248	c.4081A>G	c.(4081-4083)Atg>Gtg	p.M1361V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1361	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GCAAAATCCATTGGAGTGTCA	0.403																																																0			6											132	121	125					6																	79657465		2203	4300	6503	79714184	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4081A>G	6.37:g.79657465T>C	ENSP00000275034:p.Met1361Val		79714184	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	19.24	3.790162	0.70337	.	.	ENSG00000146247	ENST00000275034;ENST00000355098	T	0.26067	1.76	5.21	5.21	0.72293	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.56062	0.1960	H	0.96547	3.84	0.80722	D	1	D;D	0.60160	0.987;0.987	D;D	0.68039	0.955;0.955	T	0.72161	-0.4374	9	.	.	.	-14.0995	14.5571	0.68109	0.0:0.0:0.0:1.0	.	1361;1361	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	1361;87	ENSP00000275034:M1361V	.	M	-	1	0	PHIP	79714184	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.638000	0.83328	2.093000	0.63338	0.459000	0.35465	ATG		0.403	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79657465	T	C	79657465	3	2	97	1	0	0	0	0	1	0	0	0	11873	1493	52	4	1404	4	PHIP	6	79657465	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	5538487	79657465	91457602	47	26178										
BACH2	60468	hgsc.bcm.edu	37	chr6	90660281	90660281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agctggaagtcctggtcctgGtctccaaggggggtgagcga	17	9	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr6:90660281G>A	ENST00000257749.4	-	7	2251	c.1544C>T	c.(1543-1545)aCc>aTc	p.T515I	RP3-512E2.2_ENST00000445838.1_RNA|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000343122.3_Missense_Mutation_p.T515I|BACH2_ENST00000537989.1_Missense_Mutation_p.T515I	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	515						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		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)		CCTGGTCCTGGTCTCCAAGGG	0.642																																																0			6											52	58	56					6																	90660281		2203	4300	6503	90717002	SO:0001583	missense	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1544C>T	6.37:g.90660281G>A	ENSP00000257749:p.Thr515Ile		90717002	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	37	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760600	0.69763	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.47869	0.83;0.83;0.83	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.49167	0.1541	L	0.29908	0.895	0.54753	D	0.999986	D	0.89917	1.0	D	0.69307	0.963	T	0.45512	-0.9256	10	0.39692	T	0.17	-24.4385	19.0174	0.92900	0.0:0.0:1.0:0.0	.	515	Q9BYV9	BACH2_HUMAN	I	515	ENSP00000257749:T515I;ENSP00000437473:T515I;ENSP00000345642:T515I	ENSP00000257749:T515I	T	-	2	0	BACH2	90717002	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.230000	0.95299	2.499000	0.84300	0.557000	0.71058	ACC		0.642	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90660281	G	A	90660281	3	1	97	1	0	0	0	0	1	0	0	0	1285	1261	44	3	993	3	BACH2	6	90660281	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	11002816	90660281	80454786	48	26179										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146264622	146264622	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	catgatttagagattcagcaCagtcctctgtttcatgttct	7	9	4	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr6:146264622C>G	ENST00000367505.2	-	9	2159	c.1895G>C	c.(1894-1896)tGt>tCt	p.C632S	SHPRH_ENST00000275233.7_Missense_Mutation_p.C632S|SHPRH_ENST00000438092.2_Missense_Mutation_p.C632S|SHPRH_ENST00000367503.3_Missense_Mutation_p.C632S			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	632					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		AGATTCAGCACAGTCCTCTGT	0.408																																																0			6											183	173	176					6																	146264622		1966	4159	6125	146306315	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1895G>C	6.37:g.146264622C>G	ENSP00000356475:p.Cys632Ser		146306315	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	3.886	-0.024911	0.07589	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.72282	-0.64;-0.64;-0.63;-0.64	5.46	-0.871	0.10642	DEAD-like helicase (1);	1.724300	0.02669	N	0.108389	T	0.17746	0.0426	N	0.03608	-0.345	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.0;0.0;0.0;0.002	T	0.24368	-1.0162	10	0.05721	T	0.95	2.8985	7.355	0.26714	0.0:0.3979:0.1567:0.4454	.	521;632;632;521	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	S	632;632;632;632;521	ENSP00000356475:C632S;ENSP00000356473:C632S;ENSP00000412797:C632S;ENSP00000275233:C632S	ENSP00000275233:C632S	C	-	2	0	SHPRH	146306315	0.004000	0.15560	0.001000	0.08648	0.009000	0.06853	0.398000	0.20899	-0.075000	0.12798	-0.806000	0.03193	TGT		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146264622	C	G	146264622	3	3	97	1	0	0	0	0	1	0	0	0	14328	478	17	5	3288	5	SHPRH	6	146264622	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	55604341	146264622	24850445	49	26180										
SDK1	221935	hgsc.bcm.edu	37	chr7	4213858	4213858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgtgatgtctttgcagcctcCgagggacgaaagcctgaatg	13	9	1	2	rs539173474		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:4213858C>T	ENST00000404826.2	+	33	4944	c.4805C>T	c.(4804-4806)cCg>cTg	p.P1602L	SDK1_ENST00000389531.3_Missense_Mutation_p.P1602L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1602	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TTGCAGCCTCCGAGGGACGAA	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		19396	0		0	False		,,,				2504	0															0			7											204	196	198					7																	4213858		2203	4300	6503	4180384	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4805C>T	7.37:g.4213858C>T	ENSP00000385899:p.Pro1602Leu		4180384	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	9.521	1.108287	0.20714	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.74315	-0.83;-0.83	4.74	4.74	0.60224	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.84238	0.5428	M	0.84219	2.685	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.958;0.998;0.974	T	0.82621	-0.0367	10	0.02654	T	1	.	15.9147	0.79503	0.0:1.0:0.0:0.0	.	1602;89;1602	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	L	1602	ENSP00000385899:P1602L;ENSP00000374182:P1602L	ENSP00000374182:P1602L	P	+	2	0	SDK1	4180384	0.998000	0.40836	0.823000	0.32752	0.803000	0.45373	5.334000	0.65923	2.181000	0.69327	0.462000	0.41574	CCG		0.577	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4213858	C	T	4213858	3	4	97	1	0	0	0	0	1	0	0	0	14005	652	23	1	4935	1	SDK1	7	4213858	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10		4213858	154924805	50	26181										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84651728	84651728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgttccaagaaacattacatCgtactggccatcttctgcaa	6	11	2	1	rs202240375		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:84651728C>T	ENST00000284136.6	-	11	1436	c.1393G>A	c.(1393-1395)Gat>Aat	p.D465N	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	465	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						AACATTACATCGTACTGGCCA	0.363																																					Ovarian(63;442 1191 17318 29975 31528)											0			7											223	200	208					7																	84651728		2203	4300	6503	84489664	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1393G>A	7.37:g.84651728C>T	ENSP00000284136:p.Asp465Asn		84489664	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087733	0.94100	.	.	ENSG00000153993	ENST00000284136	T	0.24151	1.87	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.135696	0.64402	D	0.000003	T	0.50616	0.1626	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	P	0.62491	0.903	T	0.48864	-0.8997	10	0.59425	D	0.04	.	19.7762	0.96393	0.0:1.0:0.0:0.0	.	465	O95025	SEM3D_HUMAN	N	465	ENSP00000284136:D465N	ENSP00000284136:D465N	D	-	1	0	SEMA3D	84489664	1.000000	0.71417	0.859000	0.33776	0.801000	0.45260	4.842000	0.62831	2.664000	0.90586	0.557000	0.71058	GAT		0.363	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		T	84651728	C	T	84651728	3	4	97	1	0	0	0	0	1	0	0	0	14064	884	31	1	968	1	SEMA3D	7	84651728	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	80437870	84651728	74486935	51	26182										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98555602	98555602	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctgaaaggaggtccttttccAggtctttgggaggagccagt	14	8	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:98555602A>G	ENST00000359863.4	+	43	6419		c.e43-1		TRRAP_ENST00000446306.3_Splice_Site|TRRAP_ENST00000355540.3_Splice_Site	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein						chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTCCTTTTCCAGGTCTTTGGG	0.542																																																0			7											70	56	61					7																	98555602		2203	4300	6503	98393538	SO:0001630	splice_region_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.6211-1A>G	7.37:g.98555602A>G			98393538	A4D265|O75218|Q9Y631|Q9Y6H4	Splice_Site	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.887796	0.52014	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306;ENST00000456197	.	.	.	5.39	4.2	0.49525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3817	0.55311	0.8591:0.1409:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRRAP	98393538	1.000000	0.71417	0.783000	0.31826	0.515000	0.34225	9.228000	0.95250	0.845000	0.35118	0.533000	0.62120	.		0.542	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	Intron	G	98555602	A	G	98555602	5	3	97	1	0	0	0	0	0	0	1	0	16641	202	7	4	6317	4	TRRAP	7	98555602	Splice_Site	SNP	A	TCGA-DC-6158-01A-11D-1657-10	13903874	98555602	60583061	52	26183										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106523591	106523591	+	Frame_Shift_Del	DEL	T	T	-													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atcactggctcaaagaaaaaTcccctactgaagaaaaggtg							TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:106523591delT	ENST00000359195.3	+	8	3053	c.2743delT	c.(2743-2745)tccfs	p.S915fs	PIK3CG_ENST00000496166.1_Frame_Shift_Del_p.S915fs|PIK3CG_ENST00000440650.2_Frame_Shift_Del_p.S915fs	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	915	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CAAAGAAAAATCCCCTACTGA	0.423																																																0			7											111	108	109					7																	106523591		2203	4300	6503	106310827	SO:0001589	frameshift_variant	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2743delT	7.37:g.106523591delT	ENSP00000352121:p.Ser915fs		106310827	A4D0Q6|Q8IV23|Q9BZC8	Frame_Shift_Del	DEL	ENST00000359195.3	37	CCDS5739.1																																																																																				0.423	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			-	106523591	T	-	106523591	7	5	97	1	0	1	0	1	0	0	0	0	11947	1435	50	0	2769	0	PIK3CG	7	106523591	Frame_Shift_Del	DEL	T	TCGA-DC-6158-01A-11D-1657-10	7967989	106523591	52615072	53	26184										
CPA1	1357	hgsc.bcm.edu	37	chr7	130023569	130023569	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcagctttcaccgccattctCgacaccttggacatcttcct	6	16	3	0	rs377138792		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:130023569C>T	ENST00000011292.3	+	6	780	c.630C>T	c.(628-630)ctC>ctT	p.L210L	CPA1_ENST00000484324.1_Silent_p.L122L	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	210					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.L210L(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					CCGCCATTCTCGACACCTTGG	0.607																																																1	Substitution - coding silent(1)	ovary(1)	7						C		0,4406		0,0,2203	187	158	168		630	-9	0	7		168	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CPA1	NM_001868.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		210/420	130023569	1,13005	2203	4300	6503	129810805	SO:0001819	synonymous_variant	1357				CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase A"	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.630C>T	7.37:g.130023569C>T			129810805	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Silent	SNP	ENST00000011292.3	37	CCDS5820.1																																																																																				0.607	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868		T	130023569	C	T	130023569	2	4	97	1	0	0	0	0	0	0	0	1	3795	871	31	1		1	CPA1	7	130023569	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	23499978	130023569	29115094	54	26185										
BRAF	673	hgsc.bcm.edu	37	chr7	140453193	140453193	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggtcttcatgaagaaatataTctgaggtgtagtaagtaaag	11	3	3	3	rs121913370		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:140453193T>C	ENST00000288602.6	-	15	1802	c.1742A>G	c.(1741-1743)aAt>aGt	p.N581S		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	581	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> D (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|N -> S (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N581S(9)|p.N581I(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AAGAAATATATCTGAGGTGTA	0.358		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	10	Substitution - Missense(10)	large_intestine(3)|lung(3)|skin(2)|ovary(1)|soft_tissue(1)	7											86	83	84					7																	140453193		2203	4298	6501	140099662	SO:0001630	splice_region_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1742-1A>G	7.37:g.140453193T>C			140099662	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.68|17.68	3.450518|3.450518	0.63290|0.63290	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.99803	.|-6.82	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99864|0.99864	0.9936|0.9936	H|H	0.96970|0.96970	3.915|3.915	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.96655|0.96655	0.9484|0.9484	5|10	.|0.59425	.|D	.|0.04	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|581	.|P15056	.|BRAF_HUMAN	V|S	189|581	.|ENSP00000288602:N581S	.|ENSP00000288602:N581S	I|N	-|-	1|2	0|0	BRAF|BRAF	140099662|140099662	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	ATA|AAT		0.358	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	Missense_Mutation	C	140453193	T	C	140453193	5	2	97	1	0	0	0	0	0	0	1	0	1499	1449	50	4	574	4	BRAF	7	140453193	Splice_Site	SNP	T	TCGA-DC-6158-01A-11D-1657-10	10429624	140453193	18685470	55	26186										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142571892	142571892	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcgcatcaggtcgccaaaaaTcatctagaaggagcaggagg	12	9	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:142571892T>C	ENST00000359396.3	-	12	1701	c.1456A>G	c.(1456-1458)Att>Gtt	p.I486V	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	486					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					TCGCCAAAAATCATCTAGAAG	0.547																																																0			7											68	51	57					7																	142571892		2203	4300	6503	142282014	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1456A>G	7.37:g.142571892T>C	ENSP00000352358:p.Ile486Val		142282014	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.594587	0.46214	.	.	ENSG00000165125	ENST00000359396;ENST00000311470;ENST00000436401	D;D	0.98474	-4.95;-2.57	5.0	5.0	0.66597	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	M	0.71296	2.17	0.58432	D	0.999996	P	0.36171	0.541	P	0.45712	0.491	D	0.98048	1.0386	10	0.42905	T	0.14	-16.0181	14.171	0.65510	0.0:0.0:0.0:1.0	.	486	Q9H1D0	TRPV6_HUMAN	V	486;318;109	ENSP00000352358:I486V;ENSP00000411100:I109V	ENSP00000310825:I318V	I	-	1	0	TRPV6	142282014	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	5.187000	0.65087	1.996000	0.58369	0.533000	0.62120	ATT		0.547	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		C	142571892	T	C	142571892	3	2	97	1	0	0	0	0	1	0	0	0	16640	1435	50	4	737	4	TRPV6	7	142571892	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	2118699	142571892	16566771	56	26187										
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151478503	151478503	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttggaggggctgcccgggccGaaggggctgtccacctgcag	18	12	0	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr7:151478503G>A	ENST00000287878.4	-	3	705	c.201C>T	c.(199-201)ttC>ttT	p.F67F	PRKAG2_ENST00000392801.2_Silent_p.F23F|PRKAG2_ENST00000461529.1_5'UTR	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	67					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	TGCCCGGGCCGAAGGGGCTGT	0.627																																																0			7											16	14	15					7																	151478503		2197	4299	6496	151109436	SO:0001819	synonymous_variant	51422			AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.201C>T	7.37:g.151478503G>A			151109436	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	37	CCDS5928.1																																																																																				0.627	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		A	151478503	G	A	151478503	2	1	97	1	0	0	0	0	0	0	0	1	12535	1049	37	1		1	PRKAG2	7	151478503	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	8906611	151478503	7660160	57	26188										
TEX15	56154	hgsc.bcm.edu	37	chr8	30699868	30699868	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atgtgggccatttttcctaaAtctttcctaggggcagacat	9	9	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:30699868A>G	ENST00000256246.2	-	1	6740	c.6666T>C	c.(6664-6666)gaT>gaC	p.D2222D		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2222					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TTTTTCCTAAATCTTTCCTAG	0.343																																																0			8											86	86	86					8																	30699868		2203	4298	6501	30819410	SO:0001819	synonymous_variant	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.6666T>C	8.37:g.30699868A>G			30819410		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																				0.343	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30699868	A	G	30699868	2	3	97	1	0	0	0	0	0	0	0	1	15818	98	4	4		4	TEX15	8	30699868	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10		30699868	115664154	58	26189										
FGFR1	2260	hgsc.bcm.edu	37	chr8	38272133	38272133	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcctcgggtgccatccacttCacaggcagtcggccctgaaa	11	15	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:38272133C>T	ENST00000447712.2	-	15	2933	c.1992G>A	c.(1990-1992)gtG>gtA	p.V664V	FGFR1_ENST00000425967.3_Silent_p.V695V|FGFR1_ENST00000326324.6_Silent_p.V573V|FGFR1_ENST00000335922.5_Silent_p.V654V|FGFR1_ENST00000397091.5_Silent_p.V662V|FGFR1_ENST00000397103.1_Silent_p.V575V|FGFR1_ENST00000532791.1_Silent_p.V662V|FGFR1_ENST00000356207.5_Silent_p.V575V|FGFR1_ENST00000341462.5_Silent_p.V664V|FGFR1_ENST00000397113.2_Silent_p.V662V|FGFR1_ENST00000397108.4_Silent_p.V662V	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> L (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CCATCCACTTCACAGGCAGTC	0.587		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	0			8											57	60	59					8																	38272133		2092	4269	6361	38391290	SO:0001819	synonymous_variant	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.1992G>A	8.37:g.38272133C>T			38391290	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	37	CCDS6107.2																																																																																				0.587	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	38272133	C	T	38272133	2	4	97	1	0	0	0	0	0	0	0	1	5882	813	29	3		3	FGFR1	8	38272133	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	7572265	38272133	108091889	59	26190										
OPRK1	4986	hgsc.bcm.edu	37	chr8	54147372	54147372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cagagatgccaacagatgacGacagcagccagatgcagata	11	10	0	5	rs143457105		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:54147372G>A	ENST00000265572.3	-	3	854	c.557C>T	c.(556-558)tCg>tTg	p.S186L	OPRK1_ENST00000520287.1_Missense_Mutation_p.S186L|OPRK1_ENST00000524278.1_Missense_Mutation_p.S97L|RP11-162D9.3_ENST00000524425.1_RNA	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	186					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)	p.S186L(1)		NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	AACAGATGACGACAGCAGCCA	0.483																																																1	Substitution - Missense(1)	skin(1)	8						G	LEU/SER	0,4406		0,0,2203	113	103	106		557	5.7	1	8	dbSNP_134	106	2,8598	2.2+/-6.3	0,2,4298	no	missense	OPRK1	NM_000912.3	145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	186/381	54147372	2,13004	2203	4300	6503	54309925	SO:0001583	missense	4986				CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.557C>T	8.37:g.54147372G>A	ENSP00000265572:p.Ser186Leu		54309925	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	37	CCDS6152.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898286	0.91962	0.0	2.33E-4	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.46819	0.86;0.86;0.86	5.66	5.66	0.87406	GPCR, rhodopsin-like superfamily (1);	0.053050	0.85682	D	0.000000	T	0.73305	0.3570	H	0.94264	3.515	0.80722	D	1	P	0.52842	0.956	P	0.52823	0.71	T	0.81357	-0.0969	10	0.87932	D	0	.	20.0961	0.97843	0.0:0.0:1.0:0.0	.	186	P41145	OPRK_HUMAN	L	186;97;186;172	ENSP00000265572:S186L;ENSP00000430923:S97L;ENSP00000429706:S186L	ENSP00000265572:S186L	S	-	2	0	OPRK1	54309925	1.000000	0.71417	0.999000	0.59377	0.696000	0.40369	9.711000	0.98735	2.813000	0.96785	0.655000	0.94253	TCG		0.483	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			A	54147372	G	A	54147372	3	1	97	1	0	0	0	0	1	0	0	0	10916	1059	37	1	593	1	OPRK1	8	54147372	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	15875239	54147372	92216650	60	26191										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110457743	110457743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaccccaatgaagtctactGccgcactcccgctgggacca	8	17	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:110457743G>A	ENST00000378402.5	+	38	5749	c.5645G>A	c.(5644-5646)tGc>tAc	p.C1882Y		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1882	IPT/TIG 11.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.C1884Y(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAAGTCTACTGCCGCACTCCC	0.438										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	ovary(1)	8											48	48	48					8																	110457743		1918	4142	6060	110526919	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5645G>A	8.37:g.110457743G>A	ENSP00000367655:p.Cys1882Tyr		110526919	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967065	0.53507	.	.	ENSG00000205038	ENST00000378402	D	0.83163	-1.69	5.91	5.91	0.95273	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94476	0.8222	H	0.96633	3.855	0.50632	D	0.999887	D	0.89917	1.0	D	0.97110	1.0	D	0.95736	0.8779	10	0.87932	D	0	.	17.7921	0.88555	0.0:0.0:1.0:0.0	.	1882	Q86WI1	PKHL1_HUMAN	Y	1882	ENSP00000367655:C1882Y	ENSP00000367655:C1882Y	C	+	2	0	PKHD1L1	110526919	1.000000	0.71417	0.523000	0.27875	0.129000	0.20672	7.560000	0.82277	2.802000	0.96397	0.655000	0.94253	TGC		0.438	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110457743	G	A	110457743	3	1	97	1	0	0	0	0	1	0	0	0	12003	1319	46	3	5795	3	PKHD1L1	8	110457743	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	56310371	110457743	35906279	61	26192										
TG	7038	hgsc.bcm.edu	37	chr8	133925352	133925352	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agatctgatccagagtggctCattccagcttcatctggact	9	11	4	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:133925352C>T	ENST00000220616.4	+	20	4260	c.4220C>T	c.(4219-4221)tCa>tTa	p.S1407L	TG_ENST00000377869.1_Missense_Mutation_p.S1407L	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1407					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.S1407L(1)|p.S1407*(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		CAGAGTGGCTCATTCCAGCTT	0.557																																																2	Substitution - Nonsense(1)|Substitution - Missense(1)	breast(1)|skin(1)	8											112	94	100					8																	133925352		2203	4300	6503	133994534	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4220C>T	8.37:g.133925352C>T	ENSP00000220616:p.Ser1407Leu		133994534	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	7.805	0.714420	0.15306	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.63744	-0.06;-0.05	5.81	-11.2	0.00127	.	5.257790	0.00166	N	0.000008	T	0.37945	0.1022	N	0.14661	0.345	0.09310	N	1	B	0.23806	0.091	B	0.16722	0.016	T	0.21245	-1.0251	10	0.40728	T	0.16	.	7.809	0.29219	0.5717:0.0974:0.2702:0.0607	.	1407	P01266	THYG_HUMAN	L	1407;213;1407	ENSP00000367100:S1407L;ENSP00000220616:S1407L	ENSP00000220616:S1407L	S	+	2	0	TG	133994534	0.000000	0.05858	0.000000	0.03702	0.381000	0.30169	-1.940000	0.01543	-2.244000	0.00706	-0.873000	0.02984	TCA		0.557	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133925352	C	T	133925352	3	4	97	1	0	0	0	0	1	0	0	0	15852	838	29	3	4298	3	TG	8	133925352	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	23467609	133925352	12438670	62	26193										
EXOSC4	54512	hgsc.bcm.edu	37	chr8	145134985	145134985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgagatgggcctgcagctccGccagactttcgaagcagcca	12	13	0	2	rs201630396		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:145134985G>A	ENST00000316052.5	+	2	414	c.311G>A	c.(310-312)cGc>cAc	p.R104H	EXOSC4_ENST00000525936.1_Intron|GPAA1_ENST00000355091.4_5'Flank|GPAA1_ENST00000361036.6_5'Flank|CTD-3065J16.9_ENST00000524499.1_RNA	NM_019037.2	NP_061910.1	Q9NPD3	EXOS4_HUMAN	exosome component 4	104					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)			lung(4)|prostate(1)|upper_aerodigestive_tract(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTGCAGCTCCGCCAGACTTTC	0.577													G|||	1	0.000199681	0	0	5008	,	,		20906	0.001		0	False		,,,				2504	0															0			8											64	54	57					8																	145134985		2203	4300	6503	145206973	SO:0001583	missense	54512			AF281133	CCDS6414.1	8q24.3	2004-03-26			ENSG00000178896	ENSG00000178896			18189	protein-coding gene	gene with protein product	"exosome component Rrp41"	606491				11110791	Standard	NM_019037		Approved	hRrp41p, FLJ20591, Rrp41p, RRP41, RRP41A, Ski6p, SKI6, p12A	uc003zau.3	Q9NPD3	OTTHUMG00000165437	ENST00000316052.5:c.311G>A	8.37:g.145134985G>A	ENSP00000315476:p.Arg104His		145206973		Missense_Mutation	SNP	ENST00000316052.5	37	CCDS6414.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	24.4	4.527131	0.85706	.	.	ENSG00000178896	ENST00000316052;ENST00000527954	T;T	0.62232	0.04;0.04	5.05	4.17	0.49024	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.113654	0.56097	D	0.000027	T	0.72606	0.3481	M	0.78223	2.4	0.80722	D	1	D	0.71674	0.998	P	0.61201	0.885	T	0.75167	-0.3413	10	0.72032	D	0.01	-21.4364	6.7988	0.23740	0.1954:0.0:0.8046:0.0	.	104	Q9NPD3	EXOS4_HUMAN	H	104;127	ENSP00000315476:R104H;ENSP00000436539:R127H	ENSP00000315476:R104H	R	+	2	0	EXOSC4	145206973	1.000000	0.71417	0.976000	0.42696	0.961000	0.63080	5.720000	0.68470	2.345000	0.79718	0.561000	0.74099	CGC		0.577	EXOSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384065.1	NM_019037		A	145134985	G	A	145134985	3	1	97	1	0	0	0	0	1	0	0	0	5330	1087	38	1	317	1	EXOSC4	8	145134985	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	11209633	145134985	1229037	63	26194										
ZNF16	7564	hgsc.bcm.edu	37	chr8	146157290	146157290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggcttttccacattcattacAcatataaggcctctcactgc	5	13	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr8:146157290A>G	ENST00000276816.4	-	4	1069	c.883T>C	c.(883-885)Tgt>Cgt	p.C295R	ZNF16_ENST00000394909.2_Missense_Mutation_p.C295R	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	295	Required for nuclear localization.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		CATTCATTACACATATAAGGC	0.468																																																0			8											86	85	85					8																	146157290		2203	4300	6503	146128094	SO:0001583	missense	7564			X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"Zinc fingers, C2H2-type"	12947	protein-coding gene	gene with protein product		601262	"zinc finger protein 16 (KOX 9)"				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.883T>C	8.37:g.146157290A>G	ENSP00000276816:p.Cys295Arg		146128094	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	37	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.817876	0.32145	.	.	ENSG00000170631	ENST00000276816;ENST00000394909	D;D	0.85258	-1.96;-1.96	4.02	4.02	0.46733	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95385	0.8502	H	0.99347	4.525	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96323	0.9238	9	0.87932	D	0	.	12.0541	0.53524	1.0:0.0:0.0:0.0	.	295	P17020	ZNF16_HUMAN	R	295	ENSP00000276816:C295R;ENSP00000378369:C295R	ENSP00000276816:C295R	C	-	1	0	ZNF16	146128094	1.000000	0.71417	0.067000	0.19924	0.026000	0.11368	6.246000	0.72405	1.671000	0.50874	0.460000	0.39030	TGT		0.468	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		G	146157290	A	G	146157290	3	3	97	1	0	0	0	0	1	0	0	0	17777	159	6	4	1169	4	ZNF16	8	146157290	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	1022305	146157290	206732	64	26195										
JAK2	3717	hgsc.bcm.edu	37	chr9	5072518	5072518	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agccttggccaaggcactttTacaaagatttttaaaggcgt	9	8	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr9:5072518T>C	ENST00000381652.3	+	13	2162	c.1668T>C	c.(1666-1668)ttT>ttC	p.F556F	JAK2_ENST00000544510.1_Silent_p.F407F|JAK2_ENST00000539801.1_Silent_p.F556F	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	556	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.F556F(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	AAGGCACTTTTACAAAGATTT	0.358		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	9											53	55	54					9																	5072518		2203	4300	6503	5062518	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1668T>C	9.37:g.5072518T>C			5062518	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5072518	T	C	5072518	2	2	97	1	0	0	0	0	0	0	0	1	7959	1751	61	4		4	JAK2	9	5072518	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10		5072518	136140913	65	26196										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137707473	137707473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cccccggagagcctggccccGcggtaggtgctcaagagggc	16	15	1	2	rs147868179	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr9:137707473G>A	ENST00000371817.3	+	51	4480	c.4066G>A	c.(4066-4068)Gcg>Acg	p.A1356T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1356	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GCCTGGCCCCGCGGTAGGTGC	0.607													G|||	5	0.000998403	0.003	0.0014	5008	,	,		15983	0		0	False		,,,				2504	0															0			9						G	THR/ALA	9,4397	15.5+/-35.6	0,9,2194	44	46	46		4066	5.2	0.9	9	dbSNP_134	46	0,8600		0,0,4300	yes	missense	COL5A1	NM_000093.3	58	0,9,6494	AA,AG,GG		0.0,0.2043,0.0692	probably-damaging	1356/1839	137707473	9,12997	2203	4300	6503	136847294	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4066G>A	9.37:g.137707473G>A	ENSP00000360882:p.Ala1356Thr		136847294	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.13	2.741522	0.49151	0.002043	0.0	ENSG00000130635	ENST00000371817	D	0.93659	-3.26	5.2	5.2	0.72013	.	0.068615	0.64402	U	0.000020	D	0.84822	0.5557	N	0.16166	0.38	0.48040	D	0.999577	D	0.54772	0.968	B	0.34873	0.191	D	0.84904	0.0844	10	0.19147	T	0.46	.	18.7294	0.91730	0.0:0.0:1.0:0.0	.	1356	P20908	CO5A1_HUMAN	T	1356	ENSP00000360882:A1356T	ENSP00000360882:A1356T	A	+	1	0	COL5A1	136847294	1.000000	0.71417	0.940000	0.37924	0.732000	0.41865	4.329000	0.59260	2.404000	0.81709	0.551000	0.68910	GCG		0.607	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137707473	G	A	137707473	3	1	97	1	0	0	0	0	1	0	0	0	3702	1087	38	1	4268	1	COL5A1	9	137707473	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	132634955	137707473	3505958	66	26197										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15688877	15688877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cttggttcaggtctcctaagTgtgccatagcactaccgaat	9	11	2	0	rs139249793		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:15688877T>C	ENST00000378076.3	-	12	1528	c.1175A>G	c.(1174-1176)cAc>cGc	p.H392R		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	392					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GTCTCCTAAGTGTGCCATAGC	0.473													T|||	1	0.000199681	8e-04	0	5008	,	,		18125	0		0	False		,,,				2504	0															0			10						T	ARG/HIS	9,4397	15.5+/-35.6	0,9,2194	113	102	106		1175	3.9	0.4	10	dbSNP_134	106	0,8600		0,0,4300	yes	missense	ITGA8	NM_003638.1	29	0,9,6494	CC,CT,TT		0.0,0.2043,0.0692	possibly-damaging	392/1064	15688877	9,12997	2203	4300	6503	15728883	SO:0001583	missense	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1175A>G	10.37:g.15688877T>C	ENSP00000367316:p.His392Arg		15728883	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.664793	0.67700	0.002043	0.0	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.10960	2.82	5.09	3.93	0.45458	.	0.097154	0.64402	D	0.000001	T	0.14313	0.0346	N	0.20766	0.605	0.44500	D	0.997444	D;D	0.59357	0.981;0.985	P;P	0.58266	0.747;0.836	T	0.04708	-1.0932	10	0.33940	T	0.23	.	11.9624	0.53015	0.0:0.0:0.1455:0.8545	.	377;392	F5H818;P53708	.;ITA8_HUMAN	R	392;377	ENSP00000367316:H392R	ENSP00000367316:H392R	H	-	2	0	ITGA8	15728883	1.000000	0.71417	0.449000	0.26957	0.701000	0.40568	6.447000	0.73465	0.747000	0.32809	0.460000	0.39030	CAC		0.473	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		C	15688877	T	C	15688877	3	2	97	1	0	0	0	0	1	0	0	0	7903	1696	59	4	2092	4	ITGA8	10	15688877	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10		15688877	119845870	67	26198										
PTPLA	9200	hgsc.bcm.edu	37	chr10	17636292	17636292	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggaagtcttattgaaaacatTcctgttttcttcacatgcgg	8	8	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:17636292T>C	ENST00000361271.3	-	6	733	c.696A>G	c.(694-696)ggA>ggG	p.G232G		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	232					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						TTGAAAACATTCCTGTTTTCT	0.323																																																0			10											71	72	72					10																	17636292		2203	4295	6498	17676298	SO:0001819	synonymous_variant	9200			AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.696A>G	10.37:g.17636292T>C			17676298	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Silent	SNP	ENST00000361271.3	37	CCDS7121.1																																																																																				0.323	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		C	17636292	T	C	17636292	2	2	97	1	0	0	0	0	0	0	0	1	12809	1770	62	4		4	PTPLA	10	17636292	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	1947415	17636292	117898455	68	26199										
DNAJC1	64215	hgsc.bcm.edu	37	chr10	22055214	22055214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggagcaggtcactgaatcctTcagttgcttggctttggttg	13	8	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:22055214T>C	ENST00000376980.3	-	10	1413	c.1123A>G	c.(1123-1125)Aag>Gag	p.K375E	DNAJC1_ENST00000483085.1_5'UTR	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	375	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				ACTGAATCCTTCAGTTGCTTG	0.358																																																0			10											144	148	147					10																	22055214		2203	4300	6503	22095220	SO:0001583	missense	64215			AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.1123A>G	10.37:g.22055214T>C	ENSP00000366179:p.Lys375Glu		22095220	B0YIZ8|Q5VX89|Q9H6B8	Missense_Mutation	SNP	ENST00000376980.3	37	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.822405	0.90873	.	.	ENSG00000136770	ENST00000376980	T	0.22743	1.94	5.24	5.24	0.73138	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.050282	0.85682	D	0.000000	T	0.34542	0.0901	L	0.33624	1.015	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.65987	0.94;0.734	T	0.11446	-1.0587	10	0.87932	D	0	-9.6528	15.1573	0.72752	0.0:0.0:0.0:1.0	.	96;375	Q96NY3;Q96KC8	.;DNJC1_HUMAN	E	375	ENSP00000366179:K375E	ENSP00000366179:K375E	K	-	1	0	DNAJC1	22095220	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.486000	0.73629	1.982000	0.57802	0.482000	0.46254	AAG		0.358	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		C	22055214	T	C	22055214	3	2	97	1	0	0	0	0	1	0	0	0	4639	1792	62	4	553	4	DNAJC1	10	22055214	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	4418922	22055214	113479533	69	26200										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624235	89624235	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aggctcccagacatgacagcCatcatcaaagagatcgttag	9	11	2	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:89624235C>T	ENST00000371953.3	+	1	1366	c.9C>T	c.(7-9)gcC>gcT	p.A3A	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	3					activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.A3fs*21(2)|p.I4fs*6(1)|p.M1fs*24(1)|p.A3fs*14(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ACATGACAGCCATCATCAAAG	0.498		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	55	Whole gene deletion(37)|Unknown(13)|Complex - frameshift(3)|Deletion - Frameshift(2)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											150	149	149					10																	89624235		2203	4300	6503	89614215	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.9C>T	10.37:g.89624235C>T			89614215	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.498	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624235	C	T	89624235	2	4	97	1	0	0	0	0	0	0	0	1	12772	581	21	3		3	PTEN	10	89624235	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	67569021	89624235	45910512	70	26201										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116225564	116225564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcgtggaccgatggatcatcCgatcccgaacatcctggtac	10	13	1	0	rs375611769		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:116225564C>T	ENST00000277895.5	-	12	1431	c.1334G>A	c.(1333-1335)cGg>cAg	p.R445Q	ABLIM1_ENST00000369253.2_Missense_Mutation_p.R103Q|ABLIM1_ENST00000392952.3_Missense_Mutation_p.R157Q|ABLIM1_ENST00000369266.3_Missense_Mutation_p.R157Q|ABLIM1_ENST00000533213.2_Missense_Mutation_p.R385Q|ABLIM1_ENST00000369252.4_Missense_Mutation_p.R385Q	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	445					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		ATGGATCATCCGATCCCGAAC	0.557																																																0			10						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	209	187	195		1154,1238,1334,470	4.5	1	10		195	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5,NM_006720.3	43,43,43,43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging	385/719,413/747,445/779,157/456	116225564	2,13004	2203	4300	6503	116215554	SO:0001583	missense	3983			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1334G>A	10.37:g.116225564C>T	ENSP00000277895:p.Arg445Gln		116215554	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.386552|5.386552	0.95967|0.95967	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000099204|ENSG00000099204	ENST00000392955|ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000369260;ENST00000277895;ENST00000369253;ENST00000440467;ENST00000428430	.|T;T;T;T;T;T	.|0.72725	.|-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.41|5.41	4.51|4.51	0.55191|0.55191	.|.	.|0.246709	.|0.41500	.|D	.|0.000864	T|T	0.78349|0.78349	0.4269|0.4269	L|L	0.50919|0.50919	1.6|1.6	0.45567|0.45567	D|D	0.998515|0.998515	.|D;D;D;D;D;D;D;D;P	.|0.76494	.|0.995;0.988;0.999;0.989;0.961;0.999;0.998;0.981;0.937	.|P;B;D;P;B;D;D;P;P	.|0.85130	.|0.749;0.431;0.997;0.691;0.417;0.946;0.98;0.498;0.689	T|T	0.75659|0.75659	-0.3241|-0.3241	5|10	.|0.29301	.|T	.|0.29	.|.	12.7367|12.7367	0.57228|0.57228	0.0:0.9236:0.0:0.0764|0.0:0.9236:0.0:0.0764	.|.	.|369;129;385;413;445;157;413;369;103	.|B7Z4H1;B4DQA3;F8W8M4;A6NKJ2;O14639;O14639-5;B3KVH2;C9K0X4;O14639-4	.|.;.;.;.;ABLM1_HUMAN;.;.;.;.	R|Q	354|445;385;157;103;413;385;473;369;157;369;369;473;157;110;129	.|ENSP00000358256:R385Q;ENSP00000376679:R157Q;ENSP00000433629:R385Q;ENSP00000358270:R157Q;ENSP00000414154:R110Q;ENSP00000400934:R129Q	.|ENSP00000277895:R473Q	G|R	-|-	1|2	0|0	ABLIM1|ABLIM1	116215554|116215554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.719000|7.719000	0.84751|0.84751	1.432000|1.432000	0.47375|0.47375	0.650000|0.650000	0.86243|0.86243	GGA|CGG		0.557	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			T	116225564	C	T	116225564	3	4	97	1	0	0	0	0	1	0	0	0	94	652	23	1	1046	1	ABLIM1	10	116225564	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	26601329	116225564	19309183	71	26202										
FOXI2	399823	hgsc.bcm.edu	37	chr10	129537055	129537055	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctggctggcggccttggcacCttccccgggggcctggcggg	18	15	0	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr10:129537055C>T	ENST00000388920.4	+	2	822	c.783C>T	c.(781-783)acC>acT	p.T261T		NM_207426.2	NP_997309.2	Q6ZQN5	FOXI2_HUMAN	forkhead box I2	261					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(3)	4		all_epithelial(44;0.0021)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)				GCCTTGGCACCTTCCCCGGGG	0.697																																					Esophageal Squamous(54;1038 1280 2528 31583)											0			10											8	9	9					10																	129537055		2181	4264	6445	129427045	SO:0001819	synonymous_variant	399823			AK128865	CCDS7655.2	10q26.2	2008-04-10			ENSG00000186766	ENSG00000186766		"Forkhead boxes"	32448	protein-coding gene	gene with protein product							Standard	NM_207426		Approved	FLJ46831	uc009yas.2	Q6ZQN5	OTTHUMG00000019250	ENST00000388920.4:c.783C>T	10.37:g.129537055C>T			129427045		Silent	SNP	ENST00000388920.4	37	CCDS7655.2																																																																																				0.697	FOXI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050984.2	NM_207426		T	129537055	C	T	129537055	2	4	97	1	0	0	0	0	0	0	0	1	6029	668	24	3		3	FOXI2	10	129537055	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	13311491	129537055	5997692	72	26203										
OR56A4	120793	hgsc.bcm.edu	37	chr11	6024308	6024308	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ataaaaagtacattctagacGtagtagagtgtgggtttcca	10	5	1	2	rs116472611	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:6024308G>A	ENST00000330728.4	-	1	116	c.71C>T	c.(70-72)aCg>aTg	p.T24M		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTCTAGACGTAGTAGAGTG	0.393													.|||	22	0.00439297	0.003	0	5008	,	,		18639	0		0	False		,,,				2504	0.0184															0			11						G	MET/THR	12,4390	19.1+/-41.9	0,12,2189	118	128	125		71	-5.5	0	11	dbSNP_132	125	1,8591	1.2+/-3.3	0,1,4295	yes	missense	OR56A4	NM_001005179.2	81	0,13,6484	AA,AG,GG		0.0116,0.2726,0.1	benign	24/366	6024308	13,12981	2201	4296	6497	5980884	SO:0001583	missense	120793			BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"GPCR / Class A : Olfactory receptors"	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.71C>T	11.37:g.6024308G>A	ENSP00000328215:p.Thr24Met		5980884	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.16	1.557533	0.27827	0.002726	1.16E-4	ENSG00000183389	ENST00000330728	T	0.00608	6.25	3.36	-5.49	0.02584	.	.	.	.	.	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.46176	-0.9210	7	0.87932	D	0	.	8.4005	0.32583	0.6121:0.114:0.2738:0.0	.	.	.	.	M	24	ENSP00000328215:T24M	ENSP00000328215:T24M	T	-	2	0	OR56A4	5980884	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.447000	0.02396	-1.503000	0.01812	-1.164000	0.01763	ACG		0.393	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179		A	6024308	G	A	6024308	3	1	97	1	0	0	0	0	1	0	0	0	11166	1145	40	1	1028	1	OR56A4	11	6024308	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10		6024308	128982208	73	26204										
LDHA	3939	hgsc.bcm.edu	37	chr11	18424398	18424398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttttcatagtggatatcttgAcctacgtggcttggaagata	10	6	2	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:18424398A>G	ENST00000422447.3	+	5	703	c.430A>G	c.(430-432)Acc>Gcc	p.T144A	LDHA_ENST00000540430.1_Missense_Mutation_p.T173A|LDHA_ENST00000396222.2_Missense_Mutation_p.T144A|LDHA_ENST00000379412.5_Missense_Mutation_p.T144A|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000542179.1_Missense_Mutation_p.T144A|LDHA_ENST00000227157.4_Missense_Mutation_p.T144A|LDHA_ENST00000430553.2_Missense_Mutation_p.T86A	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	144					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						GGATATCTTGACCTACGTGGC	0.403																																																0			11											154	151	152					11																	18424398		2199	4293	6492	18380974	SO:0001583	missense	3939			X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.430A>G	11.37:g.18424398A>G	ENSP00000395337:p.Thr144Ala		18380974	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735880	0.69189	.	.	ENSG00000134333	ENST00000422447;ENST00000543445;ENST00000430553;ENST00000396222;ENST00000541620;ENST00000445376;ENST00000227157;ENST00000540430;ENST00000379412;ENST00000542179	D;D;D;D;D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97;-2.97;-2.97;-2.97;-2.97	5.35	5.35	0.76521	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.94679	0.8284	M	0.77486	2.375	0.80722	D	1	B;B;B;B;B	0.33841	0.256;0.118;0.373;0.428;0.153	B;B;P;B;B	0.47827	0.295;0.157;0.558;0.195;0.221	D	0.94959	0.8106	10	0.87932	D	0	-3.8613	15.79	0.78350	1.0:0.0:0.0:0.0	.	173;86;117;144;144	B7Z5E3;B4DKQ2;B4DJI1;F8W819;P00338	.;.;.;.;LDHA_HUMAN	A	144;144;86;144;116;117;144;173;144;144	ENSP00000395337:T144A;ENSP00000440161:T144A;ENSP00000406172:T86A;ENSP00000379524:T144A;ENSP00000227157:T144A;ENSP00000445175:T173A;ENSP00000368722:T144A;ENSP00000445331:T144A	ENSP00000227157:T144A	T	+	1	0	LDHA	18380974	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.930000	0.92872	2.371000	0.80710	0.533000	0.62120	ACC		0.403	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		G	18424398	A	G	18424398	3	3	97	1	0	0	0	0	1	0	0	0	8720	275	10	4	535	4	LDHA	11	18424398	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	12400090	18424398	116582118	74	26205										
FOSL1	8061	hgsc.bcm.edu	37	chr11	65661581	65661581	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	actcggcggcgctcctcttcCtccgggctgatctgggggtg	15	14	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:65661581C>T	ENST00000312562.2	-	3	495	c.309G>A	c.(307-309)gaG>gaA	p.E103E	FOSL1_ENST00000448083.2_Intron|FOSL1_ENST00000531493.1_Intron|FOSL1_ENST00000532401.1_Missense_Mutation_p.G102R	NM_005438.3	NP_005429.1	P15407	FOSL1_HUMAN	FOS-like antigen 1	103	Poly-Glu.				cellular defense response (GO:0006968)|cellular response to extracellular stimulus (GO:0031668)|chemotaxis (GO:0006935)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gravity (GO:0009629)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to virus (GO:0009615)|transcription from RNA polymerase II promoter (GO:0006366)|vitellogenesis (GO:0007296)	cytosol (GO:0005829)|neuron projection (GO:0043005)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	10				READ - Rectum adenocarcinoma(159;0.168)		GCTCCTCTTCCTCCGGGCTGA	0.667																																																0			11											26	24	24					11																	65661581		2201	4295	6496	65418157	SO:0001819	synonymous_variant	8061			BC016648	CCDS8121.1, CCDS73324.1	11q13	2013-01-10			ENSG00000175592	ENSG00000175592		"basic leucine zipper proteins"	13718	protein-coding gene	gene with protein product		136515				2107490	Standard	XM_005274311		Approved	fra-1	uc001ogg.1	P15407	OTTHUMG00000166715	ENST00000312562.2:c.309G>A	11.37:g.65661581C>T			65418157	B4DR11|Q6FG51	Silent	SNP	ENST00000312562.2	37	CCDS8121.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.853516	0.51270	.	.	ENSG00000175592	ENST00000532401	.	.	.	4.13	3.21	0.36854	.	.	.	.	.	T	0.50973	0.1647	.	.	.	0.28274	N	0.924293	.	.	.	.	.	.	T	0.50092	-0.8868	5	0.87932	D	0	-21.0119	9.7634	0.40545	0.0:0.8971:0.0:0.1029	.	.	.	.	R	102	.	ENSP00000431594:G102R	G	-	1	0	FOSL1	65418157	1.000000	0.71417	0.998000	0.56505	0.505000	0.33919	2.016000	0.40971	1.097000	0.41459	0.557000	0.71058	GGA		0.667	FOSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391168.2	NM_005438		T	65661581	C	T	65661581	2	4	97	1	0	0	0	0	0	0	0	1	6006	680	24	3		3	FOSL1	11	65661581	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	47237183	65661581	69344935	75	26206										
SYT12	91683	hgsc.bcm.edu	37	chr11	66812174	66812174	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctcatctggaccaacgacaaGaccacagcgggtaaggccca	10	14	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:66812174G>A	ENST00000393946.2	+	9	2110	c.948G>A	c.(946-948)aaG>aaA	p.K316K	SYT12_ENST00000525457.1_Silent_p.K316K|SYT12_ENST00000527043.1_Silent_p.K316K			Q8IV01	SYT12_HUMAN	synaptotagmin XII	316	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						CCAACGACAAGACCACAGCGG	0.657																																					Ovarian(65;2862 3307)											0			11											96	81	86					11																	66812174		2200	4295	6495	66568750	SO:0001819	synonymous_variant	91683			AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"Synaptotagmins"	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.948G>A	11.37:g.66812174G>A			66568750		Silent	SNP	ENST00000393946.2	37	CCDS8154.1																																																																																				0.657	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963		A	66812174	G	A	66812174	2	1	97	1	0	0	0	0	0	0	0	1	15507	933	33	3		3	SYT12	11	66812174	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	1150593	66812174	68194342	76	26207										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70332477	70332477	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	agcaggccagccgacttctgCtgggacgtgtccatgatgtc	13	12	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:70332477C>T	ENST00000423696.2	-	15	2820	c.2784G>A	c.(2782-2784)caG>caA	p.Q928Q	SHANK2_ENST00000449833.2_Silent_p.Q712Q|SHANK2_ENST00000338508.4_Silent_p.Q1308Q|SHANK2_ENST00000409161.1_Silent_p.Q711Q			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	928					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CCGACTTCTGCTGGGACGTGT	0.597																																																0			11											125	112	116					11																	70332477		2200	4294	6494	70010125	SO:0001819	synonymous_variant	22941			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2784G>A	11.37:g.70332477C>T			70010125	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37																																																																																					0.597	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		T	70332477	C	T	70332477	2	4	97	1	0	0	0	0	0	0	0	1	14302	796	28	3		3	SHANK2	11	70332477	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	3520303	70332477	64674039	77	26208										
KRTAP5-10	387273	hgsc.bcm.edu	37	chr11	71276909	71276909	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcctgtgggggctccaagggGggctgtggctcctgtggggg	21	9	0	0	rs71272260|rs12289712	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:71276909G>A	ENST00000398531.1	+	1	301	c.276G>A	c.(274-276)ggG>ggA	p.G92G	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	92	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GCTCCAAGGGGGGCTGTGGCT	0.677																																																0			11											35	54	47					11																	71276909		2068	4190	6258	70954557	SO:0001819	synonymous_variant	387273			AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"Keratin associated proteins"	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.276G>A	11.37:g.71276909G>A			70954557	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																				0.677	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2			A	71276909	G	A	71276909	2	1	97	1	0	0	0	0	0	0	0	1	8581	1219	43	3		3	KRTAP5-10	11	71276909	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	944432	71276909	63729607	78	26209										
P4HA3	283208	hgsc.bcm.edu	37	chr11	74015396	74015396	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tttgatgagagtaaatgcaaGcagagggttagccacagggg	15	5	0	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:74015396G>C	ENST00000331597.4	-	2	307	c.262C>G	c.(262-264)Ctt>Gtt	p.L88V	P4HA3_ENST00000427714.2_Missense_Mutation_p.L88V	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	88						endoplasmic reticulum (GO:0005783)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			NS(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(1)	15	Breast(11;2.31e-05)					GTAAATGCAAGCAGAGGGTTA	0.478																																																0			11											166	162	163					11																	74015396		2200	4293	6493	73693044	SO:0001583	missense	283208			AY327887	CCDS8230.1, CCDS73347.1	11q13	2008-12-09	2008-12-09			ENSG00000149380			30135	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(III)"	608987	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III"			14500733	Standard	XM_005273924		Approved	C-P4Halpha(III)	uc001ouz.3	Q7Z4N8		ENST00000331597.4:c.262C>G	11.37:g.74015396G>C	ENSP00000332170:p.Leu88Val		73693044	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Missense_Mutation	SNP	ENST00000331597.4	37	CCDS8230.1	.	.	.	.	.	.	.	.	.	.	G	6.361	0.434787	0.12045	.	.	ENSG00000149380	ENST00000331597;ENST00000427714	T;T	0.54675	0.58;0.56	5.79	4.87	0.63330	Prolyl 4-hydroxylase alpha-subunit, N-terminal (1);	0.212862	0.40144	N	0.001177	T	0.39306	0.1073	N	0.19112	0.55	0.29913	N	0.823395	P;B	0.42296	0.775;0.012	B;B	0.39660	0.306;0.036	T	0.36040	-0.9764	10	0.36615	T	0.2	-13.3992	14.6898	0.69076	0.0:0.1461:0.8539:0.0	.	88;88	B4DUD3;Q7Z4N8	.;P4HA3_HUMAN	V	88	ENSP00000332170:L88V;ENSP00000401749:L88V	ENSP00000332170:L88V	L	-	1	0	P4HA3	73693044	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	2.297000	0.43593	1.422000	0.47177	0.655000	0.94253	CTT		0.478	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		C	74015396	G	C	74015396	3	2	97	1	0	0	0	0	1	0	0	0	11389	971	34	5	1420	5	P4HA3	11	74015396	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	2738487	74015396	60991120	79	26210										
KCNJ1	3758	hgsc.bcm.edu	37	chr11	128709851	128709851	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	acacagggagtgtgattggcAgaaggatggaattccgggag	17	5	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr11:128709851A>G	ENST00000392664.2	-	2	461	c.345T>C	c.(343-345)tcT>tcC	p.S115S	KCNJ1_ENST00000392665.2_Silent_p.S96S|KCNJ1_ENST00000392666.1_Silent_p.S96S|KCNJ1_ENST00000324036.3_Silent_p.S96S|KCNJ1_ENST00000440599.2_Silent_p.S96S	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	115			S -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	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)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	TGTGATTGGCAGAAGGATGGA	0.458																																																0			11											89	88	88					11																	128709851		2201	4297	6498	128215061	SO:0001819	synonymous_variant	3758			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.345T>C	11.37:g.128709851A>G			128215061	B2RMR4|Q6LD67	Silent	SNP	ENST00000392664.2	37	CCDS8476.1																																																																																				0.458	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		G	128709851	A	G	128709851	2	3	97	1	0	0	0	0	0	0	0	1	8064	175	7	4		4	KCNJ1	11	128709851	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	54694455	128709851	6296665	80	26211										
A2M	2	hgsc.bcm.edu	37	chr12	9230353	9230354	+	Missense_Mutation	DNP	GC	GC	TT													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gaaacagccattgtccttctGcctctgggagagccatatga							TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:9230353_9230354GC>TT	ENST00000318602.7	-	26	3526_3527	c.3219_3220GC>AA	c.(3217-3222)agGCag>agAAag	p.Q1074K	A2M_ENST00000542567.1_5'Flank	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1074					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TTGTCCTTCTGCCTCTGGGAGA	0.47																																																0			12																																								9121620|9121621	SO:0001583	missense	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.3219_3220delinsTT	12.37:g.9230353_9230354delinsTT	ENSP00000323929:p.Gln1074Lys		9121620|9121621	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation|Silent	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																				0.47	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		TT	9230354	GC	TT	9230353	3	4	97	1	0	0	0	0	1	0	0	0	4	1328	46	2	1248	2	A2M	12	9230353	Missense_Mutation	DNP	GC	TCGA-DC-6158-01A-11D-1657-10		9230353	124621542	81	26212										
ABCD2	225	hgsc.bcm.edu	37	chr12	39979967	39979967	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	actttacctccttctctttgAactatgtgatagagatggac	7	9	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:39979967A>G	ENST00000308666.3	-	7	1914	c.1779T>C	c.(1777-1779)gtT>gtC	p.V593V		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	593	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CTTCTCTTTGAACTATGTGAT	0.333																																																0			12											163	139	147					12																	39979967		2203	4300	6503	38266234	SO:0001819	synonymous_variant	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1779T>C	12.37:g.39979967A>G			38266234	B2RAM3|Q13210|Q2M3H9	Silent	SNP	ENST00000308666.3	37	CCDS8734.1																																																																																				0.333	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		G	39979967	A	G	39979967	2	3	97	1	0	0	0	0	0	0	0	1	61	233	9	4		4	ABCD2	12	39979967	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	30749614	39979967	93871928	82	26213										
FAM113B	91523	hgsc.bcm.edu	37	chr12	47629015	47629015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaggggggagctgaacttcGaacaagatgagctggtggac	16	7	0	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:47629015G>A	ENST00000546455.1	+	4	900	c.169G>A	c.(169-171)Gaa>Aaa	p.E57K	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Missense_Mutation_p.E57K			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	57							hydrolase activity (GO:0016787)										GCTGAACTTCGAACAAGATGA	0.607																																																0			12											82	73	76					12																	47629015		2203	4300	6503	45915282	SO:0001583	missense	91523			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.169G>A	12.37:g.47629015G>A	ENSP00000446688:p.Glu57Lys		45915282	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598813	0.46318	.	.	ENSG00000179715	ENST00000546455;ENST00000432328;ENST00000549500;ENST00000549630;ENST00000551777	T;T;T;T;T	0.54866	1.4;1.4;0.9;0.9;0.55	3.79	3.79	0.43588	Esterase, SGNH hydrolase-type (1);	0.000000	0.64402	D	0.000006	T	0.68035	0.2957	M	0.76574	2.34	0.37806	D	0.927873	D	0.89917	1.0	D	0.72982	0.979	T	0.73808	-0.3866	10	0.87932	D	0	-23.3243	9.6404	0.39835	0.0:0.2128:0.7872:0.0	.	57	Q96HM7	F113B_HUMAN	K	57	ENSP00000446688:E57K;ENSP00000396040:E57K;ENSP00000449680:E57K;ENSP00000448000:E57K;ENSP00000448926:E57K	ENSP00000396040:E57K	E	+	1	0	FAM113B	45915282	1.000000	0.71417	0.056000	0.19401	0.019000	0.09904	6.112000	0.71547	2.417000	0.82017	0.655000	0.94253	GAA		0.607	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47629015	G	A	47629015	3	1	97	1	0	0	0	0	1	0	0	0	5418	1059	37	1	171	1	FAM113B	12	47629015	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	7649048	47629015	86222880	83	26214										
ACVR1B	91	hgsc.bcm.edu	37	chr12	52377794	52377794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tctctgcagataatggcaccTggacacagctgtggcttgtt	11	10	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:52377794T>C	ENST00000257963.4	+	5	900	c.823T>C	c.(823-825)Tgg>Cgg	p.W275R	ACVR1B_ENST00000415850.2_Missense_Mutation_p.W275R|ACVR1B_ENST00000541224.1_Missense_Mutation_p.W316R|ACVR1B_ENST00000542485.1_Missense_Mutation_p.W223R|ACVR1B_ENST00000426655.2_Missense_Mutation_p.W275R	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TAATGGCACCTGGACACAGCT	0.448																																																0			12											103	87	93					12																	52377794		2203	4300	6503	50664061	SO:0001583	missense	91				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.823T>C	12.37:g.52377794T>C	ENSP00000257963:p.Trp275Arg		50664061	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	37	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276883	0.80580	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73164	0.3552	L	0.45228	1.405	0.80722	D	1	D;D;D;D	0.89917	0.989;1.0;0.991;0.991	P;D;P;P	0.91635	0.888;0.999;0.903;0.852	T	0.76200	-0.3046	10	0.87932	D	0	.	15.4857	0.75564	0.0:0.0:0.0:1.0	.	316;275;275;275	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	R	275;316;275;275;223	ENSP00000257963:W275R;ENSP00000442656:W316R;ENSP00000390477:W275R;ENSP00000397550:W275R;ENSP00000442885:W223R	ENSP00000257963:W275R	W	+	1	0	ACVR1B	50664061	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.036000	0.88901	2.117000	0.64856	0.533000	0.62120	TGG		0.448	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		C	52377794	T	C	52377794	3	2	97	1	0	0	0	0	1	0	0	0	221	1580	55	4	968	4	ACVR1B	12	52377794	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	4748779	52377794	81474101	84	26215										
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54914544	54914544	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gaatctgccatgttgcgttaTgccattgctttccccctgat	8	12	1	1	rs540937692	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:54914544T>C	ENST00000293373.6	+	17	1771	c.1692T>C	c.(1690-1692)taT>taC	p.Y564Y	NCKAP1L_ENST00000545638.2_Silent_p.Y514Y	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	564					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TGTTGCGTTATGCCATTGCTT	0.458													T|||	2	0.000399361	0	0	5008	,	,		20187	0		0	False		,,,				2504	0.002															0			12											436	369	392					12																	54914544		2203	4300	6503	53200811	SO:0001819	synonymous_variant	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1692T>C	12.37:g.54914544T>C			53200811	B4DUT5|Q52LW0	Silent	SNP	ENST00000293373.6	37	CCDS31813.1																																																																																				0.458	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		C	54914544	T	C	54914544	2	2	97	1	0	0	0	0	0	0	0	1	10253	1471	51	4		4	NCKAP1L	12	54914544	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	2536750	54914544	78937351	85	26216										
NAV3	89795	hgsc.bcm.edu	37	chr12	78591083	78591083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgcagtgctgataataatggAgtggagctcccagttgtaat	12	6	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:78591083A>G	ENST00000397909.2	+	35	6521	c.6348A>G	c.(6346-6348)ggA>ggG	p.G2116G	NAV3_ENST00000228327.6_Silent_p.G2094G|NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000266692.7_Silent_p.G1917G|NAV3_ENST00000536525.2_Silent_p.G2094G			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2116						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ATAATAATGGAGTGGAGCTCC	0.343										HNSCC(70;0.22)																																						0			12											124	114	117					12																	78591083		1843	4088	5931	77115214	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6348A>G	12.37:g.78591083A>G			77115214	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	A	1.704	-0.500816	0.04261	.	.	ENSG00000067798	ENST00000552895	.	.	.	5.35	-7.35	0.01422	.	.	.	.	.	T	0.38026	0.1025	.	.	.	0.41356	D	0.987398	.	.	.	.	.	.	T	0.40440	-0.9563	4	.	.	.	-9.3769	3.9409	0.09326	0.113:0.4082:0.1151:0.3637	.	.	.	.	G	989	.	.	S	+	1	0	NAV3	77115214	0.020000	0.18652	0.003000	0.11579	0.410000	0.31052	-0.182000	0.09726	-1.686000	0.01439	-1.392000	0.01152	AGT		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78591083	A	G	78591083	2	3	97	1	0	0	0	0	0	0	0	1	10215	291	11	4		4	NAV3	12	78591083	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	23676539	78591083	55260812	86	26217										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100497707	100497707	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcaccaaacagatgggatgtGttttcagttttgtccatggg	11	7	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr12:100497707G>A	ENST00000279907.7	-	3	442	c.230C>T	c.(229-231)aCa>aTa	p.T77I	UHRF1BP1L_ENST00000356828.3_Missense_Mutation_p.T77I	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	77										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GATGGGATGTGTTTTCAGTTT	0.269																																																0			12											76	81	80					12																	100497707		2203	4294	6497	99021838	SO:0001583	missense	23074				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.230C>T	12.37:g.100497707G>A	ENSP00000279907:p.Thr77Ile		99021838	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.945006	0.92593	.	.	ENSG00000111647	ENST00000279907;ENST00000356828	D;D	0.83335	-1.71;-1.71	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.92113	0.7500	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.994;1.0	D	0.92715	0.6186	10	0.72032	D	0.01	-15.5275	19.437	0.94799	0.0:0.0:1.0:0.0	.	77;77	A0JNW5-2;A0JNW5	.;UH1BL_HUMAN	I	77	ENSP00000279907:T77I;ENSP00000349285:T77I	ENSP00000279907:T77I	T	-	2	0	UHRF1BP1L	99021838	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.638000	0.98445	2.587000	0.87381	0.591000	0.81541	ACA		0.269	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		A	100497707	G	A	100497707	3	1	97	1	0	0	0	0	1	0	0	0	17009	1377	48	3	4264	3	UHRF1BP1L	12	100497707	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	21906624	100497707	33354188	87	26218										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24871586	24871586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcaaggcaaaagccagcagcGgacgttcttcctgtttgacc	11	12	1	1	rs371749849	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr13:24871586G>A	ENST00000382095.4	+	10	1828	c.1421G>A	c.(1420-1422)cGg>cAg	p.R474Q	SPATA13_ENST00000382108.3_Missense_Mutation_p.R1099Q|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.R977Q|SPATA13_ENST00000409126.1_Missense_Mutation_p.R334Q|SPATA13_ENST00000399949.2_Missense_Mutation_p.R396Q|SPATA13_ENST00000424834.2_Missense_Mutation_p.R1099Q|SPATA13_ENST00000343003.6_Missense_Mutation_p.R418Q	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	474	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		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)		AGCCAGCAGCGGACGTTCTTC	0.517													G|||	2	0.000399361	0	0	5008	,	,		20924	0		0.002	False		,,,				2504	0															0			13						G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	80	78	79		3296,1421	5.1	0.9	13		79	0,8600		0,0,4300	no	missense,missense	SPATA13	NM_001166271.1,NM_153023.2	43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1099/1278,474/653	24871586	1,13005	2203	4300	6503	23769586	SO:0001583	missense	221178			AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.1421G>A	13.37:g.24871586G>A	ENSP00000371527:p.Arg474Gln		23769586	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	G	34	5.348915	0.95807	2.27E-4	0.0	ENSG00000182957	ENST00000382108;ENST00000382095;ENST00000434675;ENST00000438694;ENST00000399949;ENST00000409126;ENST00000343003	D;D;D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01;-3.01;-3.01	5.12	5.12	0.69794	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.97148	0.9068	M	0.94101	3.495	0.58432	D	0.999996	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.997;0.999;0.997;0.997;0.999	D	0.98134	1.0432	10	0.72032	D	0.01	.	17.5456	0.87860	0.0:0.0:1.0:0.0	.	334;418;358;420;396;474	E9PFR9;Q96N96-3;Q96N96-5;Q96N96-4;Q96N96-2;Q96N96	.;.;.;.;.;SPT13_HUMAN	Q	1099;474;372;420;396;334;418	ENSP00000371542:R1099Q;ENSP00000371527:R474Q;ENSP00000401605:R372Q;ENSP00000382830:R396Q;ENSP00000386471:R334Q;ENSP00000343631:R418Q	ENSP00000343631:R418Q	R	+	2	0	SPATA13	23769586	1.000000	0.71417	0.941000	0.38009	0.947000	0.59692	9.381000	0.97205	2.403000	0.81681	0.561000	0.74099	CGG		0.517	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		A	24871586	G	A	24871586	3	1	97	1	0	0	0	0	1	0	0	0	15039	1116	39	1	3334	1	SPATA13	13	24871586	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10		24871586	90298292	88	26219										
N4BP2L1	90634	hgsc.bcm.edu	37	chr13	32981406	32981406	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ccatgactgcatagggcttcAtttcccaggcgtggaggttg	13	10	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr13:32981406A>G	ENST00000380133.2	-	3	427	c.377T>C	c.(376-378)aTg>aCg	p.M126T	N4BP2L1_ENST00000530622.2_Missense_Mutation_p.M20T|N4BP2L1_ENST00000380139.4_Missense_Mutation_p.M126T|N4BP2L1_ENST00000380130.2_Missense_Mutation_p.M126T|N4BP2L1_ENST00000459716.1_5'UTR			Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1	126										large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		ATAGGGCTTCATTTCCCAGGC	0.383																																																0			13											179	160	166					13																	32981406		2203	4300	6503	31879406	SO:0001583	missense	90634			U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697	ENST00000380133.2:c.377T>C	13.37:g.32981406A>G	ENSP00000369476:p.Met126Thr		31879406	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380133.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	A	17.31	3.358312	0.61403	.	.	ENSG00000139597	ENST00000380130;ENST00000380139;ENST00000530622;ENST00000380133	T;T;T	0.42131	0.98;0.98;0.98	5.35	5.35	0.76521	Zeta toxin domain (1);	0.000000	0.85682	D	0.000000	T	0.60521	0.2275	L	0.53729	1.69	0.49582	D	0.999806	D;D	0.89917	1.0;0.994	D;D	0.83275	0.996;0.985	T	0.63883	-0.6536	10	0.87932	D	0	.	15.3353	0.74247	1.0:0.0:0.0:0.0	.	126;126	Q5TBK1-2;Q5TBK1	.;N42L1_HUMAN	T	126;126;20;126	ENSP00000369473:M126T;ENSP00000369484:M126T;ENSP00000369476:M126T	ENSP00000369473:M126T	M	-	2	0	N4BP2L1	31879406	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.461000	0.80834	2.041000	0.60428	0.533000	0.62120	ATG		0.383	N4BP2L1-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044412.2	NM_052818		G	32981406	A	G	32981406	3	3	97	1	0	0	0	0	1	0	0	0	10141	217	8	4	439	4	N4BP2L1	13	32981406	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	8109820	32981406	82188472	89	26220										
NOVA1	4857	hgsc.bcm.edu	37	chr14	27066568	27066568	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcttccagcggccttttccgCgagtccggcgggtccaggtc	14	15	0	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr14:27066568C>T	ENST00000344429.5	-	1	78	c.75G>A	c.(73-75)tcG>tcA	p.S25S	NOVA1-AS1_ENST00000547786.1_RNA|NOVA1_ENST00000539517.2_Silent_p.S25S|NOVA1_ENST00000551754.1_5'Flank|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000547619.1_Silent_p.S25S|NOVA1_ENST00000465357.2_Silent_p.S25S|RP11-483C6.1_ENST00000572358.1_RNA|NOVA1_ENST00000574031.1_Silent_p.S25S	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	25					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GCCTTTTCCGCGAGTCCGGCG	0.667																																																0			14											10	11	11					14																	27066568		2192	4281	6473	26136408	SO:0001819	synonymous_variant	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.75G>A	14.37:g.27066568C>T			26136408	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Silent	SNP	ENST00000344429.5	37	CCDS9635.1																																																																																				0.667	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		T	27066568	C	T	27066568	2	4	97	1	0	0	0	0	0	0	0	1	10585	755	27	1		1	NOVA1	14	27066568	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10		27066568	80282972	90	26221										
PYGL	5836	hgsc.bcm.edu	37	chr14	51411055	51411055	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cttcagctctgccacgttctCcacgcccacgatgccgcgga	9	18	3	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr14:51411055C>G	ENST00000216392.7	-	1	399	c.67G>C	c.(67-69)Gag>Cag	p.E23Q	PYGL_ENST00000532462.1_Missense_Mutation_p.E23Q|PYGL_ENST00000544180.2_Missense_Mutation_p.E23Q	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	23					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	GCCACGTTCTCCACGCCCACG	0.672																																																0			14											73	56	62					14																	51411055		2203	4300	6503	50480805	SO:0001583	missense	5836				CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"Glycogen phosphorylases"	9725	protein-coding gene	gene with protein product	"Hers disease", "glycogen storage disease type VI", "glycogen phosphorylase, liver form"	613741	"phosphorylase, glycogen; liver"			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.67G>C	14.37:g.51411055C>G	ENSP00000216392:p.Glu23Gln		50480805	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816067	0.70912	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.94376	-3.41;-3.16;-3.23	4.24	4.24	0.50183	.	0.000000	0.85682	D	0.000000	D	0.93429	0.7904	M	0.73372	2.23	0.80722	D	1	B;B;B	0.32731	0.369;0.382;0.055	B;B;B	0.42282	0.382;0.043;0.016	D	0.91540	0.5249	10	0.20046	T	0.44	.	15.7814	0.78264	0.0:1.0:0.0:0.0	.	23;45;23	F5H816;Q6P1L4;P06737	.;.;PYGL_HUMAN	Q	23	ENSP00000431657:E23Q;ENSP00000443787:E23Q;ENSP00000216392:E23Q	ENSP00000216392:E23Q	E	-	1	0	PYGL	50480805	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.307000	0.78920	2.206000	0.71126	0.561000	0.74099	GAG		0.672	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		G	51411055	C	G	51411055	3	3	97	1	0	0	0	0	1	0	0	0	12898	864	30	5	2556	5	PYGL	14	51411055	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	24344487	51411055	55938485	91	26222										
TNFAIP2	7127	hgsc.bcm.edu	37	chr14	103593950	103593950	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	acatgctgctgctctgggtgCagaacctctaccccaagtga	10	13	2	2	rs1132339	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr14:103593950C>G	ENST00000560869.1	+	3	1483	c.844C>G	c.(844-846)Cag>Gag	p.Q282E	TNFAIP2_ENST00000333007.1_Missense_Mutation_p.Q282E|TNFAIP2_ENST00000451723.2_5'UTR			Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	282			Q -> E (in dbSNP:rs1132339). {ECO:0000269|PubMed:1374453, ECO:0000269|Ref.3}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|exocytosis (GO:0006887)	exocyst (GO:0000145)|extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	11		Melanoma(154;0.155)	Epithelial(46;0.191)			GCTCTGGGTGCAGAACCTCTA	0.687													C|||	2617	0.522564	0.3971	0.5562	5008	,	,		11207	0.5556		0.6233	False		,,,				2504	0.5307															0			14						C	GLU/GLN	1760,2304		417,926,689	7	7	7		844	3.5	1	14	dbSNP_86	7	5280,2792		1829,1622,585	yes	missense	TNFAIP2	NM_006291.2	29	2246,2548,1274	GG,GC,CC		34.5887,43.3071,41.9908	probably-damaging	282/655	103593950	7040,5096	2032	4036	6068	102663703	SO:0001583	missense	7127				CCDS9979.1	14q32	2011-01-31				ENSG00000185215			11895	protein-coding gene	gene with protein product	"exocyst complex component 3-like 3"	603300				1374453	Standard	NM_006291		Approved	B94, EXOC3L3	uc001ymm.1	Q03169		ENST00000560869.1:c.844C>G	14.37:g.103593950C>G	ENSP00000452634:p.Gln282Glu		102663703	Q86VI0	Missense_Mutation	SNP	ENST00000560869.1	37	CCDS9979.1	1170	0.5357142857142857	211	0.42886178861788615	196	0.5414364640883977	307	0.5367132867132867	456	0.6015831134564644	C	13.60	2.284832	0.40394	0.433071	0.654113	ENSG00000185215	ENST00000333007	T	0.06371	3.31	4.42	3.5	0.40072	.	0.272836	0.38272	N	0.001756	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	1.0	D	0.56968	0.978	P	0.48227	0.571	T	0.07927	-1.0747	9	0.56958	D	0.05	-34.8346	10.7654	0.46291	0.1905:0.8095:0.0:0.0	rs1132339;rs3178152;rs3193023;rs3783389;rs11558552;rs57581835;rs3178152	282	Q03169	TNAP2_HUMAN	E	282	ENSP00000332326:Q282E	ENSP00000332326:Q282E	Q	+	1	0	TNFAIP2	102663703	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	1.263000	0.33004	0.794000	0.33899	0.289000	0.19496	CAG		0.687	TNFAIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415674.1	NM_006291		G	103593950	C	G	103593950	3	3	97	1	0	0	0	0	1	0	0	0	16312	711	25	5	850	5	TNFAIP2	14	103593950	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	52182895	103593950	3755590	92	26223										
IVD	3712	hgsc.bcm.edu	37	chr15	40699846	40699846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tctcctattagcttcgtcagAccatggctaagttccttcag	7	12	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr15:40699846A>G	ENST00000249760.2	+	2	497	c.154A>G	c.(154-156)Acc>Gcc	p.T52A	IVD_ENST00000487418.2_Missense_Mutation_p.T55A|IVD_ENST00000479013.2_Intron|IVD_ENST00000490194.1_3'UTR	NM_002225.3	NP_002216.2	P26440	IVD_HUMAN	isovaleryl-CoA dehydrogenase	52					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	flavin adenine dinucleotide binding (GO:0050660)|isovaleryl-CoA dehydrogenase activity (GO:0008470)	p.T52A(1)		kidney(1)|lung(5)|ovary(2)|prostate(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-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;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)	Flavin adenine dinucleotide(DB03147)	GCTTCGTCAGACCATGGCTAA	0.537																																					GBM(31;293 617 7486 32527 34655)											1	Substitution - Missense(1)	ovary(1)	15											140	128	132					15																	40699846		2203	4300	6503	38487138	SO:0001583	missense	3712			AF038317	CCDS10057.1, CCDS10057.2, CCDS53930.1	15q14-q15	2010-05-11	2010-05-11		ENSG00000128928	ENSG00000128928	1.3.99.10		6186	protein-coding gene	gene with protein product		607036	"isovaleryl Coenzyme A dehydrogenase", "isovaleryl CoA dehydrogenase"			2063866	Standard	NM_002225		Approved	ACAD2	uc001zls.3	P26440	OTTHUMG00000129984	ENST00000249760.2:c.154A>G	15.37:g.40699846A>G	ENSP00000249760:p.Thr52Ala		38487138	B2RCV5|B3KVI7|J3KR54|Q53XZ9|Q96AF6	Missense_Mutation	SNP	ENST00000249760.2	37		.	.	.	.	.	.	.	.	.	.	A	10.87	1.472625	0.26423	.	.	ENSG00000128928	ENST00000249760;ENST00000487418	D;D	0.99706	-6.47;-6.47	5.27	4.16	0.48862	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.049858	0.85682	D	0.000000	D	0.97654	0.9231	N	0.17345	0.48	0.58432	D	0.999994	B	0.06786	0.001	B	0.12156	0.007	D	0.97607	1.0127	10	0.13470	T	0.59	.	9.741	0.40418	0.9225:0.0:0.0775:0.0	.	52	P26440	IVD_HUMAN	A	52;55	ENSP00000249760:T52A;ENSP00000418397:T55A	ENSP00000249760:T52A	T	+	1	0	IVD	38487138	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	4.203000	0.58453	1.028000	0.39785	-0.250000	0.11733	ACC		0.537	IVD-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				G	40699846	A	G	40699846	3	3	97	1	0	0	0	0	1	0	0	0	7949	275	10	4	169	4	IVD	15	40699846	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10		40699846	61831546	93	26224										
RTF1	23168	hgsc.bcm.edu	37	chr15	41730613	41730613	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctcgtcagactcggagacgtCtgacagtgacgatgaggtgg	15	9	2	5			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr15:41730613C>T	ENST00000389629.4	+	2	305	c.293C>T	c.(292-294)tCt>tTt	p.S98F	RTF1_ENST00000462276.1_3'UTR	NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	98					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		TCGGAGACGTCTGACAGTGAC	0.577																																																0			15											56	55	55					15																	41730613		692	1591	2283	39517905	SO:0001583	missense	23168			D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.293C>T	15.37:g.41730613C>T	ENSP00000374280:p.Ser98Phe		39517905	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	37	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	C	22.2	4.256738	0.80246	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.1	5.1	0.69264	.	0.000000	0.64402	U	0.000001	T	0.77785	0.4182	M	0.67397	2.05	0.80722	D	1	D	0.61697	0.99	D	0.69142	0.962	T	0.80487	-0.1361	9	0.87932	D	0	-5.1711	18.1099	0.89532	0.0:1.0:0.0:0.0	.	98	Q92541	RTF1_HUMAN	F	98	.	ENSP00000374280:S98F	S	+	2	0	RTF1	39517905	1.000000	0.71417	0.239000	0.24122	0.647000	0.38526	6.929000	0.75852	2.381000	0.81170	0.462000	0.41574	TCT		0.577	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138		T	41730613	C	T	41730613	3	4	97	1	0	0	0	0	1	0	0	0	13758	913	32	3	299	3	RTF1	15	41730613	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	1030767	41730613	60800779	94	26225										
TCF12	6938	hgsc.bcm.edu	37	chr15	57543589	57543589	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctggagggcaagcaccttcaTccccaagctatgaaaactca	8	13	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr15:57543589T>C	ENST00000267811.5	+	14	1460	c.1156T>C	c.(1156-1158)Tcc>Ccc	p.S386P	TCF12_ENST00000343827.3_Missense_Mutation_p.S216P|TCF12_ENST00000559703.1_Missense_Mutation_p.S20P|TCF12_ENST00000559710.1_Missense_Mutation_p.S20P|TCF12_ENST00000452095.2_Missense_Mutation_p.S382P|TCF12_ENST00000543579.1_Missense_Mutation_p.S216P|TCF12_ENST00000557843.1_Missense_Mutation_p.S386P|TCF12_ENST00000560764.1_3'UTR|TCF12_ENST00000438423.2_Missense_Mutation_p.S386P|TCF12_ENST00000333725.5_Missense_Mutation_p.S386P|TCF12_ENST00000537840.1_Missense_Mutation_p.S150P	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	386					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AGCACCTTCATCCCCAAGCTA	0.443			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	0			15											146	118	128					15																	57543589		2192	4292	6484	55330881	SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1156T>C	15.37:g.57543589T>C	ENSP00000267811:p.Ser386Pro		55330881	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	T	31	5.088405	0.94100	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.81113	0.4755	M	0.83223	2.63	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.995;0.999;1.0;0.995;1.0;1.0;0.997;0.995;0.997	D;D;D;D;D;D;D;D;D	0.85130	0.979;0.993;0.997;0.992;0.997;0.997;0.991;0.979;0.991	D	0.84007	0.0346	10	0.87932	D	0	-20.4826	16.3265	0.82983	0.0:0.0:0.0:1.0	.	20;216;150;382;438;216;216;386;386	B4DZP2;B4DH96;B4E1W1;E9PGY0;F5H6Z6;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;.;.;HTF4_HUMAN;.	P	438;386;386;382;386;216;150;216	ENSP00000267811:S386P;ENSP00000388940:S386P;ENSP00000396881:S382P;ENSP00000331057:S386P;ENSP00000440017:S216P;ENSP00000444696:S150P;ENSP00000342459:S216P	ENSP00000267811:S386P	S	+	1	0	TCF12	55330881	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.973000	0.70456	2.313000	0.78055	0.455000	0.32223	TCC		0.443	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		C	57543589	T	C	57543589	3	2	97	1	0	0	0	0	1	0	0	0	15726	1435	50	4	1279	4	TCF12	15	57543589	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	15812976	57543589	44987803	95	26226										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77087666	77087666	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgtcattggtgggcaagactGggcgggtgttatttctgaag	16	5	2	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr15:77087666G>A	ENST00000563290.1	-	8	822	c.727C>T	c.(727-729)Cag>Tag	p.Q243*	SCAPER_ENST00000324767.7_Nonsense_Mutation_p.Q243*|SCAPER_ENST00000562890.1_5'UTR|SCAPER_ENST00000538941.2_5'UTR			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	243						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GGGCAAGACTGGGCGGGTGTT	0.488																																																0			15											135	133	133					15																	77087666		1926	4130	6056	74874721	SO:0001587	stop_gained	49855			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.727C>T	15.37:g.77087666G>A	ENSP00000454973:p.Gln243*		74874721	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Nonsense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035374	0.75617	.	.	ENSG00000140386	ENST00000324767;ENST00000303521	.	.	.	5.53	5.53	0.82687	.	0.157436	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	19.4467	0.94851	0.0:0.0:1.0:0.0	.	.	.	.	X	243;259	.	ENSP00000303560:Q259X	Q	-	1	0	SCAPER	74874721	1.000000	0.71417	0.054000	0.19295	0.306000	0.27790	6.676000	0.74498	2.612000	0.88384	0.484000	0.47621	CAG		0.488	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		A	77087666	G	A	77087666	4	1	97	1	0	0	0	0	0	1	0	0	13915	1357	47	3	3613	3	SCAPER	15	77087666	Nonsense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	19544077	77087666	25443726	96	26227										
CCDC78	124093	hgsc.bcm.edu	37	chr16	775123	775123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gggcctcctgatgctccagcGcccacttcacttccccctgc	8	20	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:775123G>A	ENST00000293889.6	-	6	620	c.515C>T	c.(514-516)gCg>gTg	p.A172V	HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000549114.1_5'Flank|HAGHL_ENST00000564537.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78	172					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				ATGCTCCAGCGCCCACTTCAC	0.657																																																0			16											52	57	56					16																	775123		2199	4294	6493	715124	SO:0001583	missense	124093			BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.515C>T	16.37:g.775123G>A	ENSP00000293889:p.Ala172Val		715124	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Missense_Mutation	SNP	ENST00000293889.6	37	CCDS32353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	3.041|3.041	-0.197575|-0.197575	0.06259|0.06259	.|.	.|.	ENSG00000162004|ENSG00000162004	ENST00000293889|ENST00000345165	T|.	0.27890|.	1.64|.	4.17|4.17	-6.84|-6.84	0.01687|0.01687	.|.	1.837330|.	0.02904|.	N|.	0.135830|.	T|T	0.11965|0.11965	0.0291|0.0291	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.19706|.	0.005;0.038|.	B;B|.	0.12837|.	0.001;0.008|.	T|T	0.32268|0.32268	-0.9913|-0.9913	10|5	0.02654|.	T|.	1|.	-0.0759|-0.0759	7.5652|7.5652	0.27874|0.27874	0.6999:0.0:0.168:0.1321|0.6999:0.0:0.168:0.1321	.|.	172;21|.	A2IDD5;D3DU61|.	CCD78_HUMAN;.|.	V|C	172|21	ENSP00000293889:A172V|.	ENSP00000293889:A172V|.	A|R	-|-	2|1	0|0	CCDC78|CCDC78	715124|715124	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.859000|-1.859000	0.01657|0.01657	-1.155000|-1.155000	0.02822|0.02822	-0.215000|-0.215000	0.12644|0.12644	GCG|CGC		0.657	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476		A	775123	G	A	775123	3	1	97	1	0	0	0	0	1	0	0	0	2858	1087	38	1	837	1	CCDC78	16	775123	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10		775123	89579630	97	26228										
PARN	5073	hgsc.bcm.edu	37	chr16	14693794	14693794	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcgtgaatgactctagaaaaTcccacagcatcattcagctc	7	12	3	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:14693794T>C	ENST00000437198.2	-	12	948	c.807A>G	c.(805-807)ggA>ggG	p.G269G	PARN_ENST00000420015.2_Silent_p.G223G|PARN_ENST00000341484.7_Silent_p.G208G|PARN_ENST00000539279.1_Silent_p.G94G|RN7SL274P_ENST00000492268.2_RNA	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	269					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						CTCTAGAAAATCCCACAGCAT	0.313																																																0			16											112	101	104					16																	14693794		1824	4081	5905	14601295	SO:0001819	synonymous_variant	5073			AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.807A>G	16.37:g.14693794T>C			14601295	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Silent	SNP	ENST00000437198.2	37	CCDS45419.1																																																																																				0.313	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582		C	14693794	T	C	14693794	2	2	97	1	0	0	0	0	0	0	0	1	11484	1422	50	4		4	PARN	16	14693794	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	13918671	14693794	75660959	98	26229										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21133399	21133399	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgatcatgattagctgaggtAtgaaaaacttcatctcttgg	9	6	3	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:21133399A>G	ENST00000261383.3	-	10	1450	c.1451T>C	c.(1450-1452)aTa>aCa	p.I484T	CTC-508F8.1_ENST00000575612.1_RNA|DNAH3_ENST00000415178.1_Missense_Mutation_p.I484T	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	484	Stem. {ECO:0000250}.		I -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TAGCTGAGGTATGAAAAACTT	0.408																																																0			16											126	127	127					16																	21133399		2201	4300	6501	21040900	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1451T>C	16.37:g.21133399A>G	ENSP00000261383:p.Ile484Thr		21040900	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	7.705	0.693921	0.15039	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.21543	2.0;2.15	5.36	4.06	0.47325	.	0.531714	0.19407	N	0.115022	T	0.13500	0.0327	L	0.32530	0.975	0.27506	N	0.951829	B;B	0.11235	0.0;0.004	B;B	0.11329	0.001;0.006	T	0.21759	-1.0236	10	0.11485	T	0.65	.	8.1586	0.31185	0.8297:0.0:0.1703:0.0	.	484;455	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	T	484;484;455	ENSP00000261383:I484T;ENSP00000394245:I484T	ENSP00000261383:I484T	I	-	2	0	DNAH3	21040900	0.002000	0.14202	0.998000	0.56505	0.957000	0.61999	0.629000	0.24538	2.032000	0.59987	0.533000	0.62120	ATA		0.408	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	21133399	A	G	21133399	3	3	97	1	0	0	0	0	1	0	0	0	4614	449	16	4	11110	4	DNAH3	16	21133399	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	6439605	21133399	69221354	99	26230										
SALL1	6299	hgsc.bcm.edu	37	chr16	51175936	51175936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttaaaactaattgatttttaGtacagttcttcttgtggagc	7	5	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:51175936G>A	ENST00000251020.4	-	2	230	c.197C>T	c.(196-198)aCt>aTt	p.T66I	SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000440970.1_5'UTR|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	66					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TTGATTTTTAGTACAGTTCTT	0.473																																					GBM(103;1352 1446 1855 4775 8890)											0			16											80	87	85					16																	51175936		2198	4300	6498	49733437	SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.197C>T	16.37:g.51175936G>A	ENSP00000251020:p.Thr66Ile		49733437	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735611	0.69189	.	.	ENSG00000103449	ENST00000251020;ENST00000457559	T	0.48522	0.81	5.37	5.37	0.77165	.	0.044847	0.85682	D	0.000000	T	0.51991	0.1707	M	0.74647	2.275	0.80722	D	1	P	0.39282	0.666	B	0.35859	0.212	T	0.61486	-0.7053	10	0.87932	D	0	.	19.1099	0.93313	0.0:0.0:1.0:0.0	.	66	Q9NSC2	SALL1_HUMAN	I	66	ENSP00000251020:T66I	ENSP00000251020:T66I	T	-	2	0	SALL1	49733437	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	8.044000	0.89434	2.499000	0.84300	0.555000	0.69702	ACT		0.473	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51175936	G	A	51175936	3	1	97	1	0	0	0	0	1	0	0	0	13847	1029	36	3	3785	3	SALL1	16	51175936	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	30042537	51175936	39178817	100	26231										
CHD9	80205	hgsc.bcm.edu	37	chr16	53358032	53358032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcctaaaagtggaattgcaaAggccacagcagcagcagctg	12	10	0	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:53358032A>G	ENST00000398510.3	+	38	8006	c.7919A>G	c.(7918-7920)aAg>aGg	p.K2640R	CHD9_ENST00000564845.1_Missense_Mutation_p.K2624R|CHD9_ENST00000447540.1_Missense_Mutation_p.K2625R|CHD9_ENST00000566029.1_Missense_Mutation_p.K2624R			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2640	Poly-Ala.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.K2641T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GGAATTGCAAAGGCCACAGCA	0.507																																																1	Substitution - Missense(1)	lung(1)	16											100	101	101					16																	53358032		1927	4138	6065	51915533	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.7919A>G	16.37:g.53358032A>G	ENSP00000381522:p.Lys2640Arg		51915533	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	A	14.95	2.687341	0.48097	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.88354	-2.37	5.23	5.23	0.72850	.	0.000000	0.56097	D	0.000034	D	0.91952	0.7451	L	0.49350	1.555	0.58432	D	0.999997	D;D;D;D	0.71674	0.997;0.996;0.997;0.998	D;D;D;D	0.78314	0.98;0.987;0.98;0.991	D	0.90043	0.4143	10	0.23891	T	0.37	-14.547	15.4199	0.75003	1.0:0.0:0.0:0.0	.	706;2625;2640;2624	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	R	2625;2624;706	ENSP00000396345:K2625R	ENSP00000381522:K2624R	K	+	2	0	CHD9	51915533	1.000000	0.71417	0.931000	0.37212	0.613000	0.37349	9.219000	0.95173	2.112000	0.64535	0.533000	0.62120	AAG		0.507	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53358032	A	G	53358032	3	3	97	1	0	0	0	0	1	0	0	0	3338	72	3	4	8021	4	CHD9	16	53358032	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	2182096	53358032	36996721	101	26232										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70954693	70954694	+	In_Frame_Ins	INS	-	-	CCC													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcgctcccgctccgccttctINSccctctccaggcgctccttc							TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:70954693_70954694insCCC	ENST00000393567.2	-	46	7735_7736	c.7585_7586insGGG	c.(7585-7587)gag>gGGGag	p.2528_2529insG		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2528					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ctccgccttctccctctccagg	0.698																																																0			16																																								69512195	SO:0001652	inframe_insertion	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7583_7585dupGGG	16.37:g.70954694_70954696dupCCC	ENSP00000377197:p.Arg2528_Glu2529insGly		69512194	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	In_Frame_Ins	INS	ENST00000393567.2	37	CCDS59269.1																																																																																				0.698	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			CCC	70954694	-	CCC	70954693	7	5	97	1	0	1	1	0	0	0	0	0	7488	1551	54	0	7943	0	HYDIN	16	70954693	In_Frame_Ins	INS	-	TCGA-DC-6158-01A-11D-1657-10	17596661	70954693	19400060	102	26233										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70954726	70954726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gctccttctccgtgcgctccTtctccaggcgctctctctcc	7	20	4	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr16:70954726T>C	ENST00000393567.2	-	46	7703	c.7553A>G	c.(7552-7554)aAg>aGg	p.K2518R		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2518					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				cgtgcgctccttctccaggcg	0.711																																																0			16											15	17	16					16																	70954726		1919	4093	6012	69512227	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7553A>G	16.37:g.70954726T>C	ENSP00000377197:p.Lys2518Arg		69512227	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.507932	0.27036	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01113	5.32	5.72	4.62	0.57501	.	0.000000	0.32314	U	0.006275	T	0.00906	0.0030	N	0.08118	0	0.80722	D	1	B	0.27997	0.197	B	0.30716	0.119	T	0.69960	-0.5003	10	0.35671	T	0.21	.	10.1791	0.42957	0.0:0.0766:0.0:0.9234	.	2517	F8WD23	.	R	2518;2517	ENSP00000377197:K2518R	ENSP00000313052:K2517R	K	-	2	0	HYDIN	69512227	0.978000	0.34361	1.000000	0.80357	0.094000	0.18550	1.128000	0.31369	0.986000	0.38683	-0.363000	0.07495	AAG		0.711	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	70954726	T	C	70954726	3	2	97	1	0	0	0	0	1	0	0	0	7488	1609	56	4	7976	4	HYDIN	16	70954726	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	33	70954726	19400027	103	26234										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	97	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10		7577094	73618116	104	26235										
TP53	7157	hgsc.bcm.edu	37	chr17	7578190	7578190	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	accagacctcaggcggctcaTagggcaccaccacactatgt	9	15	2	1	rs121912666		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr17:7578190T>A	ENST00000269305.4	-	6	848	c.659A>T	c.(658-660)tAt>tTt	p.Y220F	TP53_ENST00000420246.2_Missense_Mutation_p.Y220F|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y220F|TP53_ENST00000445888.2_Missense_Mutation_p.Y220F|TP53_ENST00000359597.4_Missense_Mutation_p.Y220F|TP53_ENST00000455263.2_Missense_Mutation_p.Y220F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	17	GRCh37	CM015378|CM951227	TP53	M	rs121912666						102	94	97					17																	7578190		2203	4300	6503	7518915	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>T	17.37:g.7578190T>A	ENSP00000269305:p.Tyr220Phe		7518915	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.763682	0.89932	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99818	-6.92;-6.92;-6.92;-6.92;-6.92;-6.92;-6.92;-6.92	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99648	0.9870	L	0.49640	1.575	0.58432	D	0.999996	D;D;B;D;D;P;D	0.89917	1.0;0.993;0.085;1.0;0.994;0.945;1.0	D;D;B;D;D;D;D	0.97110	0.999;0.978;0.32;1.0;0.991;0.975;0.999	D	0.97268	0.9909	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220F;ENSP00000352610:Y220F;ENSP00000269305:Y220F;ENSP00000398846:Y220F;ENSP00000391127:Y220F;ENSP00000391478:Y220F;ENSP00000425104:Y88F;ENSP00000423862:Y127F	ENSP00000269305:Y220F	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578190	T	A	7578190	3	1	97	1	0	0	0	0	1	0	0	0	16421	1406	49	5	635	5	TP53	17	7578190	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	1096	7578190	73617020	105	26236										
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21208416	21208416	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggctacaatgtcaagtccgaCgtctggagcctgggcatcac	12	12	3	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr17:21208416C>T	ENST00000342679.4	+	9	999	c.750C>T	c.(748-750)gaC>gaT	p.D250D	MAP2K3_ENST00000316920.6_Silent_p.D221D|MAP2K3_ENST00000361818.5_Silent_p.D221D	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	250	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TCAAGTCCGACGTCTGGAGCC	0.637																																																0			17											163	137	146					17																	21208416		2203	4300	6503	21149009	SO:0001819	synonymous_variant	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.750C>T	17.37:g.21208416C>T			21149009	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																				0.637	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		T	21208416	C	T	21208416	2	4	97	1	0	0	0	0	0	0	0	1	9268	535	19	1		1	MAP2K3	17	21208416	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	13630226	21208416	59986794	106	26237										
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9887389	9887433	+	In_Frame_Del	DEL	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	-													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	acctccccaagtccctagagGaagccatccagcccaaggag					rs148775952|rs2240910|rs368943432|rs2240909|rs2240908|rs191244385|rs2240907|rs371825355	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr18:9887389_9887433delGAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	ENST00000306084.6	+	2	1112_1156	c.913_957delGAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	c.(913-957)gaagccatccagcccaaggagggtgacatccccaagtccccagaadel	p.EAIQPKEGDIPKSPE305del	TXNDC2_ENST00000536353.2_Stop_Codon_Del|TXNDC2_ENST00000357775.5_In_Frame_Del_p.EAIQPKEGDIPKSPE238del	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	305	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)	p.I247L(2)|p.G245S(1)|p.I314L(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GTCCCTAGAGGAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAAGAAGCCATCC	0.6																																																4	Substitution - Missense(4)	kidney(2)|skin(2)	18																																								9877433	SO:0001651	inframe_deletion	84203			AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.913_957delGAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	18.37:g.9887389_9887433delGAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	ENSP00000304908:p.Glu305_Glu319del		9877389	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	In_Frame_Del	DEL	ENST00000306084.6	37	CCDS42414.1																																																																																				0.6	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			-	9887433	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	-	9887389	7	5	97	1	0	1	0	1	0	0	0	0	16837	1175	41	0	919	0	TXNDC2	18	9887389	In_Frame_Del	DEL	GAAGCCATCCAGCCCAAGGAGGGTGACATCCCCAAGTCCCCAGAA	TCGA-DC-6158-01A-11D-1657-10		9887389	68189859	107	26238										
DSG1	1828	hgsc.bcm.edu	37	chr18	28911805	28911805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aaatactggagaaattcgaaCgatgaataattttctagaca	7	5	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr18:28911805C>T	ENST00000257192.4	+	6	871	c.659C>T	c.(658-660)aCg>aTg	p.T220M		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	220	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.T220M(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			GAAATTCGAACGATGAATAAT	0.328																																																1	Substitution - Missense(1)	central_nervous_system(1)	18											68	70	69					18																	28911805		2203	4296	6499	27165803	SO:0001583	missense	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.659C>T	18.37:g.28911805C>T	ENSP00000257192:p.Thr220Met		27165803	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651199	0.67472	.	.	ENSG00000134760	ENST00000257192	T	0.56941	0.43	5.49	5.49	0.81192	Cadherin (4);Cadherin-like (1);	0.000000	0.53938	D	0.000053	T	0.76118	0.3943	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80652	-0.1287	10	0.87932	D	0	.	10.4937	0.44764	0.0:0.8817:0.0:0.1183	.	220	Q02413	DSG1_HUMAN	M	220	ENSP00000257192:T220M	ENSP00000257192:T220M	T	+	2	0	DSG1	27165803	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.485000	0.53208	2.584000	0.87258	0.655000	0.94253	ACG		0.328	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28911805	C	T	28911805	3	4	97	1	0	0	0	0	1	0	0	0	4787	536	19	1	681	1	DSG1	18	28911805	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	19024416	28911805	49165443	108	26239										
DCC	1630	hgsc.bcm.edu	37	chr18	50937002	50937002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	actctctgatcctatcctctTcaggactctgaaaggtttga	7	11	4	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr18:50937002T>C	ENST00000442544.2	+	20	3732	c.3116T>C	c.(3115-3117)tTc>tCc	p.F1039S	DCC_ENST00000412726.1_Missense_Mutation_p.F867S|DCC_ENST00000581580.1_Missense_Mutation_p.F674S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1039	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		F -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.F1039S(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCTATCCTCTTCAGGACTCTG	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	18											71	71	71					18																	50937002		2203	4299	6502	49191000	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3116T>C	18.37:g.50937002T>C	ENSP00000389140:p.Phe1039Ser		49191000		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.583330	0.46006	.	.	ENSG00000187323	ENST00000442544;ENST00000412726	T;T	0.56103	0.48;0.48	5.87	5.87	0.94306	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.67297	0.2878	M	0.68593	2.085	0.58432	D	0.999999	D;D;D	0.61697	0.99;0.99;0.982	D;D;D	0.64144	0.922;0.922;0.916	T	0.63161	-0.6699	10	0.21014	T	0.42	-11.3642	15.5573	0.76208	0.0:0.0:0.0:1.0	.	867;867;1039	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	S	1039;867	ENSP00000389140:F1039S;ENSP00000397322:F867S	ENSP00000397322:F867S	F	+	2	0	DCC	49191000	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.020000	0.70826	2.371000	0.80710	0.533000	0.62120	TTC		0.383	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50937002	T	C	50937002	3	2	97	1	0	0	0	0	1	0	0	0	4288	1783	62	4	3194	4	DCC	18	50937002	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	22025197	50937002	27140246	109	26240										
MUM1	84939	hgsc.bcm.edu	37	chr19	1362290	1362290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ccatggggtctaattccatgCgttctatcctggaggaagac	11	10	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:1362290C>T	ENST00000415183.3	+	5	1182	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C	MUM1_ENST00000591806.1_Missense_Mutation_p.R386C|MUM1_ENST00000311401.5_Missense_Mutation_p.R317C|MUM1_ENST00000344663.3_Missense_Mutation_p.R386C			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	385					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)		TAATTCCATGCGTTCTATCCT	0.498																																																0			19											85	73	77					19																	1362290		2203	4300	6503	1313290	SO:0001583	missense	84939			AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1156C>T	19.37:g.1362290C>T	ENSP00000394925:p.Arg386Cys		1313290	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		.	.	.	.	.	.	.	.	.	.	C	14.35	2.508946	0.44660	.	.	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.24151	1.89;1.89;1.87	4.56	-3.88	0.04205	.	2.083720	0.01962	N	0.043414	T	0.26085	0.0636	N	0.24115	0.695	0.09310	N	1	D;D;D;D	0.69078	0.989;0.996;0.997;0.987	B;B;P;B	0.49953	0.332;0.332;0.627;0.431	T	0.43048	-0.9415	10	0.54805	T	0.06	.	11.2883	0.49234	0.2274:0.6893:0.0833:0.0	.	386;386;317;385	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	C	386;317;386	ENSP00000345789:R386C;ENSP00000309135:R317C;ENSP00000394925:R386C	ENSP00000309135:R317C	R	+	1	0	MUM1	1313290	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.575000	0.05861	-1.476000	0.01874	-0.397000	0.06425	CGT		0.498	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		T	1362290	C	T	1362290	3	4	97	1	0	0	0	0	1	0	0	0	10015	768	27	1	1174	1	MUM1	19	1362290	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10		1362290	57766693	110	26241										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066448	9066448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tggcaaaactgtggactgagAagggccagggatggatgttc	16	6	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:9066448A>G	ENST00000397910.4	-	3	21201	c.20998T>C	c.(20998-21000)Tct>Cct	p.S7000P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7002	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGACTGAGAAGGGCCAGGG	0.493																																																0			19											263	245	251					19																	9066448		1993	4176	6169	8927448	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20998T>C	19.37:g.9066448A>G	ENSP00000381008:p.Ser7000Pro		8927448	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	2.881	-0.231868	0.05983	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	2.77	-5.53	0.02552	.	.	.	.	.	T	0.01592	0.0051	N	0.14661	0.345	.	.	.	B	0.09022	0.002	B	0.06405	0.002	T	0.46735	-0.9170	8	0.87932	D	0	.	1.9791	0.03422	0.1296:0.3491:0.1247:0.3966	.	7000	B5ME49	.	P	7000	ENSP00000381008:S7000P	ENSP00000381008:S7000P	S	-	1	0	MUC16	8927448	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.124000	0.00290	-2.060000	0.00893	-2.195000	0.00310	TCT		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9066448	A	G	9066448	3	3	97	1	0	0	0	0	1	0	0	0	10003	246	9	4	22853	4	MUC16	19	9066448	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	7704158	9066448	50062535	111	26242										
KANK2	25959	hgsc.bcm.edu	37	chr19	11304015	11304015	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcggggaggtccaggcagagCtcgctgcgaccccggcccgc	16	16	0	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:11304015C>T	ENST00000586659.1	-	4	1055	c.741G>A	c.(739-741)gaG>gaA	p.E247E	KANK2_ENST00000589894.1_Silent_p.E247E|KANK2_ENST00000355150.5_Silent_p.E247E|KANK2_ENST00000432929.2_Silent_p.E247E|KANK2_ENST00000589359.1_Silent_p.E247E			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	247					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCAGGCAGAGCTCGCTGCGAC	0.642																																																0			19											23	26	25					19																	11304015		2198	4292	6490	11165015	SO:0001819	synonymous_variant	25959			AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	29300	protein-coding gene	gene with protein product		614610	"matrix-remodelling associated 3", "ankyrin repeat domain 25"	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.741G>A	19.37:g.11304015C>T			11165015	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																				0.642	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11304015	C	T	11304015	2	4	97	1	0	0	0	0	0	0	0	1	7998	796	28	3		3	KANK2	19	11304015	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	2237567	11304015	47824968	112	26243										
GTPBP3	84705	hgsc.bcm.edu	37	chr19	17451981	17451981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ccccagtgacagcagccagcGcctcctcctggtgctgaaca	10	17	0	2	rs3745193	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:17451981G>A	ENST00000324894.8	+	8	1171	c.1103G>A	c.(1102-1104)cGc>cAc	p.R368H	GTPBP3_ENST00000598038.1_3'UTR|GTPBP3_ENST00000600625.1_Missense_Mutation_p.R347H|GTPBP3_ENST00000358792.7_Missense_Mutation_p.R400H|GTPBP3_ENST00000361619.5_Missense_Mutation_p.R390H	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	368	TrmE-type G.		R -> H (in dbSNP:rs3745193). {ECO:0000269|PubMed:15489334}.		tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						AGCAGCCAGCGCCTCCTCCTG	0.662													G|||	477	0.0952476	0.0023	0.111	5008	,	,		13930	0.2976		0.0189	False		,,,				2504	0.0798															0			19						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	30,4376	36.8+/-68.6	0,30,2173	46	43	44		1040,1169,1103,1199	1.8	1	19	dbSNP_107	44	245,8355	97.9+/-159.5	2,241,4057	yes	missense,missense,missense,missense	GTPBP3	NM_001128855.2,NM_001195422.1,NM_032620.3,NM_133644.3	29,29,29,29	2,271,6230	AA,AG,GG		2.8488,0.6809,2.1144	benign,benign,benign,benign	347/472,390/515,368/493,400/525	17451981	275,12731	2203	4300	6503	17312981	SO:0001583	missense	84705			AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.1103G>A	19.37:g.17451981G>A	ENSP00000313818:p.Arg368His		17312981	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Missense_Mutation	SNP	ENST00000324894.8	37	CCDS32951.1	270	0.12362637362637363	2	0.0040650406504065045	46	0.1270718232044199	202	0.3531468531468531	20	0.026385224274406333	G	15.21	2.767190	0.49574	0.006809	0.028488	ENSG00000130299	ENST00000361619;ENST00000324894;ENST00000358792	T;T;T	0.13657	2.57;2.57;2.57	5.31	1.84	0.25277	GTP-binding domain, HSR1-related (1);	0.321413	0.31531	N	0.007500	T	0.00012	0.0000	L	0.35414	1.06	0.22050	P	0.999397508	B;B;B;B	0.23377	0.028;0.059;0.084;0.069	B;B;B;B	0.22386	0.01;0.039;0.034;0.015	T	0.46624	-0.9178	9	0.59425	D	0.04	-15.2831	4.2285	0.10592	0.2754:0.17:0.5546:0.0	rs3745193;rs17851736;rs3745193	390;368;347;400	A6NIG5;Q969Y2;Q969Y2-3;Q969Y2-2	.;GTPB3_HUMAN;.;.	H	390;368;400	ENSP00000354598:R390H;ENSP00000313818:R368H;ENSP00000351644:R400H	ENSP00000313818:R368H	R	+	2	0	GTPBP3	17312981	0.100000	0.21855	1.000000	0.80357	0.600000	0.36913	1.530000	0.36007	0.631000	0.30412	0.484000	0.47621	CGC		0.662	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620		A	17451981	G	A	17451981	3	1	97	1	0	0	0	0	1	0	0	0	6902	1087	38	1	1225	1	GTPBP3	19	17451981	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	6147966	17451981	41677002	113	26244										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299951	21299951	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcatgcttttacacctacatCaacataaaagaattcatatt	3	9	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21299951C>T	ENST00000596143.1	+	5	806	c.481C>T	c.(481-483)Caa>Taa	p.Q161*	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ACACCTACATCAACATAAAAG	0.323																																																0			19											50	56	54					19																	21299951		2174	4278	6452	21091791	SO:0001587	stop_gained	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.481C>T	19.37:g.21299951C>T	ENSP00000472368:p.Gln161*		21091791	Q49AI1|Q86W65|Q8ND40	Nonsense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	16.16	3.045767	0.55110	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.889	-1.55	0.08558	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	7.4808	0.27404	0.0:0.7304:0.2696:0.0	.	.	.	.	X	161	.	ENSP00000291770:Q161X	Q	+	1	0	ZNF714	21091791	0.000000	0.05858	0.137000	0.22149	0.135000	0.20990	-0.245000	0.08890	0.300000	0.22699	0.306000	0.20318	CAA		0.323	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21299951	C	T	21299951	4	4	97	1	0	0	0	0	0	1	0	0	18157	827	29	3	491	3	ZNF714	19	21299951	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	3847970	21299951	37829032	114	26245			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300050	21300050	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactagacacaagagagttCatactggagagaaacccttc	8	9	1	3	rs377506115		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300050C>G	ENST00000596143.1	+	5	905	c.580C>G	c.(580-582)Cat>Gat	p.H194D	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						CAAGAGAGTTCATACTGGAGA	0.373																																																0			19						C	ASP/HIS	0,4342		0,0,2171	60	66	64		580	1	0	19		64	1,8563		0,1,4281	no	missense	ZNF714	NM_182515.3	81	0,1,6452	GG,GC,CC		0.0117,0.0,0.0077	probably-damaging	194/555	21300050	1,12905	2171	4282	6453	21091890	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.580C>G	19.37:g.21300050C>G	ENSP00000472368:p.His194Asp		21091890	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	12.26	1.883232	0.33255	0.0	1.17E-4	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.02	1.02	0.19986	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.77824	0.4188	H	0.97440	4.005	0.28978	N	0.888805	D;D;D	0.89917	0.982;1.0;1.0	D;D;D	0.91635	0.925;0.999;0.999	T	0.66913	-0.5803	8	0.72032	D	0.01	.	5.095	0.14729	0.0:0.7691:0.0:0.2309	.	195;194;195	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	D	194	.	ENSP00000291770:H194D	H	+	1	0	ZNF714	21091890	0.945000	0.32115	0.010000	0.14722	0.009000	0.06853	2.535000	0.45685	0.452000	0.26830	0.456000	0.33151	CAT		0.373	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21300050	C	G	21300050	3	3	97	1	0	0	0	0	1	0	0	0	18157	826	29	5	590	5	ZNF714	19	21300050	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	99	21300050	37828933	115	26246			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300108	21300108	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcttttaagcactcctCaacccttactacacataaga	3	13	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300108C>T	ENST00000596143.1	+	5	963	c.638C>T	c.(637-639)tCa>tTa	p.S213L	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	213					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAGCACTCCTCAACCCTTACT	0.413																																																0			19											53	56	55					19																	21300108		2188	4293	6481	21091948	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.638C>T	19.37:g.21300108C>T	ENSP00000472368:p.Ser213Leu		21091948	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	12.69	2.014228	0.35511	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.02	1.02	0.19986	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.64204	0.2577	M	0.76574	2.34	0.09310	N	1	D;P;D	0.89917	1.0;0.908;0.97	D;P;P	0.78314	0.991;0.521;0.715	T	0.51553	-0.8691	8	0.66056	D	0.02	.	8.8919	0.35439	0.0:1.0:0.0:0.0	.	214;213;214	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	L	213	.	ENSP00000291770:S213L	S	+	2	0	ZNF714	21091948	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-0.433000	0.06948	0.452000	0.26830	0.456000	0.33151	TCA		0.413	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21300108	C	T	21300108	3	4	97	1	0	0	0	0	1	0	0	0	18157	838	29	3	648	3	ZNF714	19	21300108	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	58	21300108	37828875	116	26247			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300150	21300150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gattcatactggagagaaacCctacagatgtgaagaatgtg	11	6	1	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300150C>T	ENST00000596143.1	+	5	1005	c.680C>T	c.(679-681)cCc>cTc	p.P227L	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						GGAGAGAAACCCTACAGATGT	0.403																																																0			19											45	47	47					19																	21300150		2183	4296	6479	21091990	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.680C>T	19.37:g.21300150C>T	ENSP00000472368:p.Pro227Leu		21091990	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	14.87	2.664644	0.47572	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.02	1.02	0.19986	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75591	0.3870	M	0.79805	2.47	0.51233	D	0.999918	D;D;D	0.89917	0.966;1.0;1.0	P;D;D	0.97110	0.717;0.992;1.0	T	0.73949	-0.3821	8	0.51188	T	0.08	.	8.8919	0.35439	0.0:1.0:0.0:0.0	.	228;227;228	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	L	227	.	ENSP00000291770:P227L	P	+	2	0	ZNF714	21091990	0.463000	0.25799	0.076000	0.20297	0.069000	0.16628	2.452000	0.44961	0.452000	0.26830	0.456000	0.33151	CCC		0.403	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21300150	C	T	21300150	3	4	97	1	0	0	0	0	1	0	0	0	18157	623	22	3	690	3	ZNF714	19	21300150	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	42	21300150	37828833	117	26248			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300365	21300365	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cttttaaccgattctcatacCttactaaacataagataatt	2	9	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300365C>G	ENST00000596143.1	+	5	1220	c.895C>G	c.(895-897)Ctt>Gtt	p.L299V	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ATTCTCATACCTTACTAAACA	0.343																																																0			19											23	25	24					19																	21300365		2176	4291	6467	21092205	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.895C>G	19.37:g.21300365C>G	ENSP00000472368:p.Leu299Val		21092205	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	4.885	0.164525	0.09287	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.70640	0.3247	M	0.90870	3.155	0.09310	N	0.999998	D;P;D	0.61697	0.99;0.931;0.962	D;P;D	0.75020	0.982;0.549;0.985	T	0.58267	-0.7666	8	0.72032	D	0.01	.	8.8708	0.35314	0.0:1.0:0.0:0.0	.	300;299;300	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	V	299	.	ENSP00000291770:L299V	L	+	1	0	ZNF714	21092205	0.005000	0.15991	0.021000	0.16686	0.019000	0.09904	0.338000	0.19858	0.446000	0.26666	0.449000	0.29647	CTT		0.343	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21300365	C	G	21300365	3	3	97	1	0	0	0	0	1	0	0	0	18157	681	24	5	905	5	ZNF714	19	21300365	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	215	21300365	37828618	118	26249			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300528	21300528	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcctttaatgtgtcttCacaccttactacacataaga	4	11	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300528C>G	ENST00000596143.1	+	5	1383	c.1058C>G	c.(1057-1059)tCa>tGa	p.S353*	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AATGTGTCTTCACACCTTACT	0.373																																																0			19											42	45	44					19																	21300528		2175	4288	6463	21092368	SO:0001587	stop_gained	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1058C>G	19.37:g.21300528C>G	ENSP00000472368:p.Ser353*		21092368	Q49AI1|Q86W65|Q8ND40	Nonsense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	16.77	3.213835	0.58452	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	8.8708	0.35314	0.0:1.0:0.0:0.0	.	.	.	.	X	353	.	ENSP00000291770:S353X	S	+	2	0	ZNF714	21092368	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.547000	0.23299	0.446000	0.26666	0.449000	0.29647	TCA		0.373	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21300528	C	G	21300528	4	3	97	1	0	0	0	0	0	1	0	0	18157	838	29	5	1068	5	ZNF714	19	21300528	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	163	21300528	37828455	119	26250			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300554	21300554	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactacacataagatgattCatactggagagaaaccctac	6	9	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300554C>T	ENST00000596143.1	+	5	1409	c.1084C>T	c.(1084-1086)Cat>Tat	p.H362Y	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H362N(1)		endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TAAGATGATTCATACTGGAGA	0.358																																																1	Substitution - Missense(1)	large_intestine(1)	19											41	44	43					19																	21300554		2169	4283	6452	21092394	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1084C>T	19.37:g.21300554C>T	ENSP00000472368:p.His362Tyr		21092394	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	11.18	1.561667	0.27915	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.76478	0.3993	H	0.95004	3.61	0.29908	N	0.823782	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.998	T	0.70557	-0.4839	8	0.66056	D	0.02	.	8.8708	0.35314	0.0:1.0:0.0:0.0	.	363;362;363	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	Y	362	.	ENSP00000291770:H362Y	H	+	1	0	ZNF714	21092394	0.999000	0.42202	0.441000	0.26858	0.428000	0.31595	5.289000	0.65656	0.446000	0.26666	0.449000	0.29647	CAT		0.358	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21300554	C	T	21300554	3	4	97	1	0	0	0	0	1	0	0	0	18157	826	29	3	1094	3	ZNF714	19	21300554	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	26	21300554	37828429	120	26251			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300696	21300696	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcttttaaccaatcctCaaaccttaccaaacataaga	2	12	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300696C>G	ENST00000596143.1	+	5	1551	c.1226C>G	c.(1225-1227)tCa>tGa	p.S409*	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AACCAATCCTCAAACCTTACC	0.353																																																0			19											36	39	38					19																	21300696		2149	4278	6427	21092536	SO:0001587	stop_gained	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1226C>G	19.37:g.21300696C>G	ENSP00000472368:p.Ser409*		21092536	Q49AI1|Q86W65|Q8ND40	Nonsense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	24.8	4.571314	0.86542	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	1.05	0.20165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	8.9116	0.35557	0.0:1.0:0.0:0.0	.	.	.	.	X	409	.	ENSP00000291770:S409X	S	+	2	0	ZNF714	21092536	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-0.590000	0.05760	0.459000	0.27016	0.462000	0.41574	TCA		0.353	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21300696	C	G	21300696	4	3	97	1	0	0	0	0	0	1	0	0	18157	838	29	5	1236	5	ZNF714	19	21300696	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	142	21300696	37828287	121	26252			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300765	21300765	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atgtgaagaatgtggcaaagCttttaaccgatcctcaaacc	8	9	1	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300765C>G	ENST00000596143.1	+	5	1620	c.1295C>G	c.(1294-1296)gCt>gGt	p.A432G	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	432					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TGTGGCAAAGCTTTTAACCGA	0.383																																																0			19											41	44	43					19																	21300765		2179	4293	6472	21092605	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1295C>G	19.37:g.21300765C>G	ENSP00000472368:p.Ala432Gly		21092605	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	6.963	0.547540	0.13312	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	-0.725	0.11174	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19248	0.0462	N	0.12471	0.22	0.24525	N	0.994144	B;B;B	0.22480	0.033;0.025;0.07	B;B;B	0.27796	0.036;0.055;0.083	T	0.25398	-1.0133	8	0.62326	D	0.03	.	4.8834	0.13690	0.0:0.5928:0.0:0.4072	.	433;432;433	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	G	432	.	ENSP00000291770:A432G	A	+	2	0	ZNF714	21092605	0.000000	0.05858	0.028000	0.17463	0.027000	0.11550	-0.049000	0.11924	-0.384000	0.07845	-0.379000	0.06801	GCT		0.383	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21300765	C	G	21300765	3	3	97	1	0	0	0	0	1	0	0	0	18157	797	28	5	1305	5	ZNF714	19	21300765	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	69	21300765	37828218	122	26253			1	24		10	10	827	C		8.777295e-28
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300777	21300777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tggcaaagcttttaaccgatCctcaaaccttactacacata	4	12	1	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21300777C>T	ENST00000596143.1	+	5	1632	c.1307C>T	c.(1306-1308)tCc>tTc	p.S436F	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	436					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TTTAACCGATCCTCAAACCTT	0.368																																																0			19											42	45	44					19																	21300777		2187	4290	6477	21092617	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1307C>T	19.37:g.21300777C>T	ENSP00000472368:p.Ser436Phe		21092617	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	6.271	0.418144	0.11870	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	-2.11	0.07187	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41143	0.1146	L	0.41415	1.275	0.09310	N	1	B;B;D	0.89917	0.033;0.016;1.0	B;B;D	0.87578	0.059;0.01;0.998	T	0.27536	-1.0071	8	0.38643	T	0.18	.	3.3998	0.07319	0.0:0.2151:0.2269:0.558	.	437;436;437	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	F	436	.	ENSP00000291770:S436F	S	+	2	0	ZNF714	21092617	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.734000	0.01848	-0.384000	0.07845	-0.379000	0.06801	TCC		0.368	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21300777	C	T	21300777	3	4	97	1	0	0	0	0	1	0	0	0	18157	855	30	3	1317	3	ZNF714	19	21300777	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	12	21300777	37828206	123	26254			1	24		10	10	827	C		8.777295e-28
ZNF493	284443	hgsc.bcm.edu	37	chr19	21605924	21605924	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ctacccagagcaaaatatttCaatgtgataaatatgtgaaa	6	6	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21605924C>T	ENST00000355504.4	+	2	345	c.79C>T	c.(79-81)Caa>Taa	p.Q27*	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Nonsense_Mutation_p.Q155*	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	27					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CAAAATATTTCAATGTGATAA	0.284																																																0			19											67	71	70					19																	21605924		2203	4287	6490	21397764	SO:0001587	stop_gained	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.79C>T	19.37:g.21605924C>T	ENSP00000347691:p.Gln27*		21397764	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Nonsense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	13.25	2.180440	0.38511	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	.	.	.	1.05	-1.67	0.08238	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.883	0.03232	0.3168:0.4406:0.0:0.2426	.	.	.	.	X	155;27	.	ENSP00000347691:Q27X	Q	+	1	0	ZNF493	21397764	0.057000	0.20700	0.008000	0.14137	0.007000	0.05969	0.741000	0.26202	-0.530000	0.06349	-0.535000	0.04281	CAA		0.284	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21605924	C	T	21605924	4	4	97	1	0	0	0	0	0	1	0	0	17983	827	29	3	540	3	ZNF493	19	21605924	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	305147	21605924	37523059	124	26255			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606037	21606037	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aaatgtggcaaatcattttgCatgcttttacacctatgtca	6	8	2	0	rs572127415	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606037C>T	ENST00000355504.4	+	2	458	c.192C>T	c.(190-192)tgC>tgT	p.C64C	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Silent_p.C192C	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	64					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AATCATTTTGCATGCTTTTAC	0.308													.|||	2	0.000399361	0	0	5008	,	,		19091	0		0	False		,,,				2504	0.002															0			19											50	56	54					19																	21606037		2203	4296	6499	21397877	SO:0001819	synonymous_variant	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.192C>T	19.37:g.21606037C>T			21397877	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Silent	SNP	ENST00000355504.4	37	CCDS12412.1																																																																																				0.308	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21606037	C	T	21606037	2	4	97	1	0	0	0	0	0	0	0	1	17983	718	25	3		3	ZNF493	19	21606037	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	113	21606037	37522946	125	26256			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606056	21606056	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gcatgcttttacacctatgtCagcataaaagaattcatatt	5	8	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606056C>T	ENST00000355504.4	+	2	477	c.211C>T	c.(211-213)Cag>Tag	p.Q71*	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Nonsense_Mutation_p.Q199*	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	71					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						ACACCTATGTCAGCATAAAAG	0.328																																																0			19											52	58	56					19																	21606056		2203	4293	6496	21397896	SO:0001587	stop_gained	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.211C>T	19.37:g.21606056C>T	ENSP00000347691:p.Gln71*		21397896	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Nonsense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	12.94	2.088962	0.36855	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	.	.	.	1.05	-2.1	0.07210	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	0.9385	0.01350	0.2944:0.3632:0.1734:0.1689	.	.	.	.	X	199;71	.	ENSP00000347691:Q71X	Q	+	1	0	ZNF493	21397896	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.132000	0.00288	-1.585000	0.01634	-1.613000	0.00800	CAG		0.328	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21606056	C	T	21606056	4	4	97	1	0	0	0	0	0	1	0	0	17983	827	29	3	672	3	ZNF493	19	21606056	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	19	21606056	37522927	126	26257			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606129	21606129	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcctttatctggttttCaacccttactagacacagga	6	11	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606129C>T	ENST00000355504.4	+	2	550	c.284C>T	c.(283-285)tCa>tTa	p.S95L	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.S223L	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	95					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						ATCTGGTTTTCAACCCTTACT	0.363																																																0			19											47	52	50					19																	21606129		2198	4296	6494	21397969	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.284C>T	19.37:g.21606129C>T	ENSP00000347691:p.Ser95Leu		21397969	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	11.19	1.564858	0.27915	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.58797	0.31;4.68	1.05	-0.842	0.10748	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.72700	0.3493	M	0.84511	2.7	0.09310	N	1	P;D	0.67145	0.955;0.996	D;D	0.77557	0.928;0.99	T	0.59096	-0.7518	9	0.72032	D	0.01	.	6.1953	0.20546	0.0:0.684:0.316:0.0	.	95;223	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	L	223;95	ENSP00000376110:S223L;ENSP00000347691:S95L	ENSP00000347691:S95L	S	+	2	0	ZNF493	21397969	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-0.043000	0.12043	0.452000	0.26830	0.460000	0.39030	TCA		0.363	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21606129	C	T	21606129	3	4	97	1	0	0	0	0	1	0	0	0	17983	838	29	3	745	3	ZNF493	19	21606129	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	73	21606129	37522854	127	26258			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606236	21606236	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactacacataagagaattCatactggacagaaaccctac	5	10	1	2	rs371368724		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606236C>G	ENST00000355504.4	+	2	657	c.391C>G	c.(391-393)Cat>Gat	p.H131D	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.H259D	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TAAGAGAATTCATACTGGACA	0.373																																																0			19						C	ASP/HIS,ASP/HIS	0,4406		0,0,2203	38	41	40		775,391	0.9	0.1	19		40	1,8593		0,1,4296	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	81,81	0,1,6499	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	259/775,131/647	21606236	1,12999	2203	4297	6500	21398076	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.391C>G	19.37:g.21606236C>G	ENSP00000347691:p.His131Asp		21398076	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	10.06	1.246144	0.22796	0.0	1.16E-4	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.67698	-0.28;-0.28	0.927	0.927	0.19437	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85048	0.5608	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;0.962	D;P	0.87578	0.998;0.63	D	0.84806	0.0787	9	0.87932	D	0	.	8.6978	0.34307	0.0:1.0:0.0:0.0	.	131;259	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	D	259;131	ENSP00000376110:H259D;ENSP00000347691:H131D	ENSP00000347691:H131D	H	+	1	0	ZNF493	21398076	0.980000	0.34600	0.138000	0.22173	0.132000	0.20833	2.615000	0.46368	0.378000	0.24764	0.384000	0.25694	CAT		0.373	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606236	C	G	21606236	3	3	97	1	0	0	0	0	1	0	0	0	17983	826	29	5	852	5	ZNF493	19	21606236	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	107	21606236	37522747	128	26259			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606336	21606336	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aattcatactagagagaaacCctataaatgtgaacaatatg	6	6	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606336C>A	ENST00000355504.4	+	2	757	c.491C>A	c.(490-492)cCc>cAc	p.P164H	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.P292H	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AGAGAGAAACCCTATAAATGT	0.343																																																0			19											57	59	58					19																	21606336		2203	4297	6500	21398176	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.491C>A	19.37:g.21606336C>A	ENSP00000347691:p.Pro164His		21398176	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	13.77	2.335922	0.41398	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.29397	1.57;1.57	0.927	0.927	0.19437	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.60090	0.2242	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.64002	-0.6509	9	0.87932	D	0	.	8.6978	0.34307	0.0:1.0:0.0:0.0	.	164;292	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	H	292;164	ENSP00000376110:P292H;ENSP00000347691:P164H	ENSP00000347691:P164H	P	+	2	0	ZNF493	21398176	0.002000	0.14202	0.222000	0.23844	0.219000	0.24729	0.930000	0.28858	0.378000	0.24764	0.384000	0.25694	CCC		0.343	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		A	21606336	C	A	21606336	3	1	97	1	0	0	0	0	1	0	0	0	17983	623	22	2	952	2	ZNF493	19	21606336	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	100	21606336	37522647	129	26260			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606392	21606392	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aatcttcaacccttactggaCataagataattcataatgga	5	8	3	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606392C>G	ENST00000355504.4	+	2	813	c.547C>G	c.(547-549)Cat>Gat	p.H183D	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.H311D	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CCTTACTGGACATAAGATAAT	0.333																																																0			19											40	43	42					19																	21606392		2203	4294	6497	21398232	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.547C>G	19.37:g.21606392C>G	ENSP00000347691:p.His183Asp		21398232	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	11.79	1.742260	0.30865	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	D;D	0.86769	-2.17;-2.17	0.985	-0.629	0.11533	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94732	0.8300	H	0.98218	4.175	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.97110	1.0;0.986	D	0.91457	0.5186	9	0.87932	D	0	.	7.5185	0.27614	0.0:0.7281:0.2719:0.0	.	183;311	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	D	311;183	ENSP00000376110:H311D;ENSP00000347691:H183D	ENSP00000347691:H183D	H	+	1	0	ZNF493	21398232	0.739000	0.28196	0.004000	0.12327	0.004000	0.04260	2.769000	0.47654	-0.522000	0.06417	-0.521000	0.04368	CAT		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606392	C	G	21606392	3	3	97	1	0	0	0	0	1	0	0	0	17983	478	17	5	1008	5	ZNF493	19	21606392	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	56	21606392	37522591	130	26261			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606462	21606462	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcctttagtattttctCaacccctactaaacataaga	3	11	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606462C>G	ENST00000355504.4	+	2	883	c.617C>G	c.(616-618)tCa>tGa	p.S206*	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Nonsense_Mutation_p.S334*	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AGTATTTTCTCAACCCCTACT	0.348																																																0			19											35	39	38					19																	21606462		2199	4296	6495	21398302	SO:0001587	stop_gained	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.617C>G	19.37:g.21606462C>G	ENSP00000347691:p.Ser206*		21398302	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Nonsense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	16.22	3.060371	0.55432	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	.	.	.	0.985	-1.07	0.09968	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	7.6352	0.28261	0.0:0.7353:0.2647:0.0	.	.	.	.	X	334;206	.	ENSP00000347691:S206X	S	+	2	0	ZNF493	21398302	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.948000	0.03897	0.399000	0.25367	0.404000	0.27445	TCA		0.348	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606462	C	G	21606462	4	3	97	1	0	0	0	0	0	1	0	0	17983	838	29	5	1078	5	ZNF493	19	21606462	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	70	21606462	37522521	131	26262			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606546	21606546	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	caaagcttataaggagtcctCacaccttactacacataaaa	4	11	1	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606546C>G	ENST00000355504.4	+	2	967	c.701C>G	c.(700-702)tCa>tGa	p.S234*	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Nonsense_Mutation_p.S362*	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AAGGAGTCCTCACACCTTACT	0.358																																																0			19											48	52	51					19																	21606546		2201	4296	6497	21398386	SO:0001587	stop_gained	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.701C>G	19.37:g.21606546C>G	ENSP00000347691:p.Ser234*		21398386	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Nonsense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	15.86	2.958898	0.53400	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	.	.	.	0.966	-1.15	0.09709	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	6.86	0.24062	0.2692:0.7308:0.0:0.0	.	.	.	.	X	362;234	.	ENSP00000347691:S234X	S	+	2	0	ZNF493	21398386	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	1.590000	0.36654	0.393000	0.25203	0.399000	0.26434	TCA		0.358	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606546	C	G	21606546	4	3	97	1	0	0	0	0	0	1	0	0	17983	838	29	5	1162	5	ZNF493	19	21606546	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	84	21606546	37522437	132	26263			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606656	21606656	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactaaacataagataattCacactgaagagaaatcccac	4	9	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606656C>G	ENST00000355504.4	+	2	1077	c.811C>G	c.(811-813)Cac>Gac	p.H271D	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.H399D	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TAAGATAATTCACACTGAAGA	0.358																																																0			19											36	39	38					19																	21606656		2197	4295	6492	21398496	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.811C>G	19.37:g.21606656C>G	ENSP00000347691:p.His271Asp		21398496	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	13.99	2.403328	0.42613	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.67698	-0.28;-0.28	1.03	1.03	0.20045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.83709	0.5313	H	0.95004	3.61	0.80722	D	1	D;D	0.76494	0.999;0.98	D;D	0.91635	0.999;0.969	D	0.83818	0.0245	9	0.87932	D	0	.	8.893	0.35446	0.0:1.0:0.0:0.0	.	271;399	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	D	399;271	ENSP00000376110:H399D;ENSP00000347691:H271D	ENSP00000347691:H271D	H	+	1	0	ZNF493	21398496	0.902000	0.30710	0.002000	0.10522	0.002000	0.02628	2.780000	0.47742	0.447000	0.26695	0.454000	0.30748	CAC		0.358	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606656	C	G	21606656	3	3	97	1	0	0	0	0	1	0	0	0	17983	826	29	5	1272	5	ZNF493	19	21606656	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	110	21606656	37522327	133	26264			2	25	305147	11	11	817	C		3.156183e-31
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606740	21606740	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttactacacataaaagaattCatactggagagaaaccctac	5	9	1	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21606740C>T	ENST00000355504.4	+	2	1161	c.895C>T	c.(895-897)Cat>Tat	p.H299Y	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.H427Y	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TAAAAGAATTCATACTGGAGA	0.333																																																0			19											31	34	33					19																	21606740		2185	4273	6458	21398580	SO:0001583	missense	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.895C>T	19.37:g.21606740C>T	ENSP00000347691:p.His299Tyr		21398580	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	12.07	1.828619	0.32329	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.67523	-0.27;-0.27	1.03	-0.51	0.11973	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.82815	0.5119	H	0.94423	3.535	0.80722	D	1	D;P	0.89917	1.0;0.849	D;B	0.97110	1.0;0.155	T	0.79572	-0.1748	9	0.87932	D	0	.	6.9519	0.24550	0.2753:0.7247:0.0:0.0	.	299;427	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	Y	427;299	ENSP00000376110:H427Y;ENSP00000347691:H299Y	ENSP00000347691:H299Y	H	+	1	0	ZNF493	21398580	0.080000	0.21391	0.026000	0.17262	0.026000	0.11368	1.514000	0.35834	-0.386000	0.07821	-0.377000	0.06932	CAT		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21606740	C	T	21606740	3	4	97	1	0	0	0	0	1	0	0	0	17983	826	29	3	1356	3	ZNF493	19	21606740	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	84	21606740	37522243	134	26265			2	25	305147	11	11	817	C		3.156183e-31
ZNF43	7594	hgsc.bcm.edu	37	chr19	21990501	21990501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tccagtatgaattttgttatGtgtagtaaggtttgaatatt	9	2	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:21990501G>A	ENST00000354959.4	-	4	2507	c.2338C>T	c.(2338-2340)Cat>Tat	p.H780Y	ZNF43_ENST00000598381.1_Missense_Mutation_p.H774Y|ZNF43_ENST00000594012.1_Missense_Mutation_p.H774Y|ZNF43_ENST00000595461.1_Missense_Mutation_p.H774Y	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	780					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		ATTTTGTTATGTGTAGTAAGG	0.318																																																0			19											61	62	62					19																	21990501		2203	4300	6503	21782341	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.2338C>T	19.37:g.21990501G>A	ENSP00000347045:p.His780Tyr		21782341	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227793	0.58668	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.59772	0.24	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75413	0.3846	M	0.84846	2.72	0.23855	N	0.996651	D	0.89917	1.0	D	0.72625	0.978	T	0.63010	-0.6732	9	0.87932	D	0	.	10.4707	0.44635	0.0:0.0:1.0:0.0	.	780	P17038	ZNF43_HUMAN	Y	779;780	ENSP00000347045:H780Y	ENSP00000347045:H780Y	H	-	1	0	ZNF43	21782341	1.000000	0.71417	0.004000	0.12327	0.890000	0.51754	4.867000	0.63013	0.976000	0.38417	0.305000	0.20034	CAT		0.318	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		A	21990501	G	A	21990501	3	1	97	1	0	0	0	0	1	0	0	0	17942	1377	48	3	95	3	ZNF43	19	21990501	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	383761	21990501	37138482	135	26266										
RHPN2	85415	hgsc.bcm.edu	37	chr19	33493200	33493201	+	Missense_Mutation	DNP	GC	GC	AT													0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tgaagtagtgggccagggccGcgtagtggtgggccttcacg					rs200623446|rs201601538	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:33493200_33493201GC>AT	ENST00000254260.3	-	9	1092_1093	c.1057_1058GC>AT	c.(1057-1059)GCg>ATg	p.A353M	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202M	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.A353T(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					GGCCAGGGCCGCGTAGTGGTGG	0.639																																																2	Substitution - Missense(2)	central_nervous_system(2)	19																																								38185040|38185041	SO:0001583	missense	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1057_1058delinsAT	19.37:g.33493200_33493201delinsAT	ENSP00000254260:p.Ala353Met		38185040|38185041	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																				0.639	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		AT	33493201	GC	AT	33493200	3	1	97	1	0	0	0	0	1	0	0	0	13388	1087	38	1	1030	1	RHPN2	19	33493200	Missense_Mutation	DNP	GC	TCGA-DC-6158-01A-11D-1657-10	11502699	33493200	25635783	136	26267										
IL28A	282616	hgsc.bcm.edu	37	chr19	39760612	39760612	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	acctcttccgcctcctcacgCgagacctgaattgtgttgcc	8	16	2	2	rs200581777	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:39760612C>T	ENST00000331982.5	+	6	617	c.562C>T	c.(562-564)Cga>Tga	p.R188*		NM_172138.1	NP_742150.1	Q8IZJ0	IFNL2_HUMAN	interferon, lambda 2	188					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|mucosal immune response (GO:0002385)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											CCTCCTCACGCGAGACCTGAA	0.547																																																0			19						C	stop/ARG	0,4406		0,0,2203	44	44	44		562	-0.4	0	19		44	4,8596		0,4,4296	no	stop-gained	IL28A	NM_172138.1		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		188/201	39760612	4,13002	2203	4300	6503	44452452	SO:0001587	stop_gained	282616			AY129148	CCDS42567.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000183709	ENSG00000183709		"Interferons"	18364	protein-coding gene	gene with protein product		607401	"interleukin 28A", "interleukin 28A (interferon, lambda 2)"	IL28A			Standard	NM_172138		Approved	IL-28A	uc002oku.1	Q8IZJ0		ENST00000331982.5:c.562C>T	19.37:g.39760612C>T	ENSP00000333639:p.Arg188*		44452452	Q45KQ8|Q6VN55|Q8IWL7	Nonsense_Mutation	SNP	ENST00000331982.5	37	CCDS42567.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.966635	0.34659	0.0	4.65E-4	ENSG00000183709	ENST00000331982	.	.	.	3.43	-0.385	0.12470	.	1.521050	0.03997	N	0.295834	.	.	.	.	.	.	0.31501	N	0.664808	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.5153	3.8264	0.08856	0.4234:0.4526:0.0:0.124	.	.	.	.	X	188	.	ENSP00000333639:R188X	R	+	1	2	IL28A	44452452	0.000000	0.05858	0.016000	0.15963	0.002000	0.02628	-1.115000	0.03289	0.270000	0.21984	0.580000	0.79431	CGA		0.547	IFNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463833.1	NM_172138		T	39760612	C	T	39760612	4	4	97	1	0	0	0	0	0	1	0	0	7703	760	27	1	584	1	IL28A	19	39760612	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	6267412	39760612	19368371	137	26268										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49342500	49342500	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cttctgagccatttctgggcTcccgagtgtcctacgacagg	11	13	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:49342500T>C	ENST00000263265.6	-	18	2481	c.1926A>G	c.(1924-1926)ggA>ggG	p.G642G	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_Intron|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	642						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		ATTTCTGGGCTCCCGAGTGTC	0.527																																																0			19											56	51	53					19																	49342500		2203	4300	6503	54034312	SO:0001819	synonymous_variant	57664			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1926A>G	19.37:g.49342500T>C			54034312	Q8N4M8|Q8N658	Silent	SNP	ENST00000263265.6	37	CCDS12737.1																																																																																				0.527	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			C	49342500	T	C	49342500	2	2	97	1	0	0	0	0	0	0	0	1	12089	1538	54	4		4	PLEKHA4	19	49342500	Silent	SNP	T	TCGA-DC-6158-01A-11D-1657-10	9581888	49342500	9786483	138	26269										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54395020	54395020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcccagaccctcggaacctgAcgaaacagaagacccgaacg	9	15	0	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:54395020A>G	ENST00000263431.3	+	6	904	c.622A>G	c.(622-624)Acg>Gcg	p.T208A	PRKCG_ENST00000542049.1_Missense_Mutation_p.T95A|PRKCG_ENST00000536044.1_Missense_Mutation_p.T208A|PRKCG_ENST00000540413.1_Missense_Mutation_p.T208A	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	208	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TCGGAACCTGACGAAACAGAA	0.527																																																0			19											142	116	125					19																	54395020		2203	4300	6503	59086832	SO:0001583	missense	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.622A>G	19.37:g.54395020A>G	ENSP00000263431:p.Thr208Ala		59086832	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392993	0.62066	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.25	5.25	0.73442	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.56187	0.1968	L	0.38838	1.175	0.45035	D	0.998055	B;B;B;B;B	0.18013	0.025;0.004;0.003;0.002;0.0	B;B;B;B;B	0.24701	0.055;0.027;0.014;0.007;0.006	T	0.51172	-0.8739	9	0.16420	T	0.52	.	13.4075	0.60922	1.0:0.0:0.0:0.0	.	95;208;208;208;208	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	A	208;208;208;95	ENSP00000440541:T208A;ENSP00000443493:T208A;ENSP00000263431:T208A;ENSP00000438090:T95A	ENSP00000263431:T208A	T	+	1	0	PRKCG	59086832	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.608000	0.67654	2.124000	0.65301	0.459000	0.35465	ACG		0.527	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		G	54395020	A	G	54395020	3	3	97	1	0	0	0	0	1	0	0	0	12546	275	10	4	644	4	PRKCG	19	54395020	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	5052520	54395020	4733963	139	26270										
CNOT3	4849	hgsc.bcm.edu	37	chr19	54657465	54657465	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cccccagggcactaaggcacAgtatctggcagccaaggccc	11	16	1	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:54657465A>G	ENST00000406403.1	+	16	3654	c.2051A>G	c.(2050-2052)cAg>cGg	p.Q684R	CNOT3_ENST00000496327.1_3'UTR|CNOT3_ENST00000221232.5_Missense_Mutation_p.Q684R			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	684	Repressor domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ACTAAGGCACAGTATCTGGCA	0.597																																																0			19											124	96	106					19																	54657465		2203	4300	6503	59349277	SO:0001583	missense	4849			AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"NOT3 (negative regulator of transcription 3, yeast) homolog"	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.2051A>G	19.37:g.54657465A>G	ENSP00000383954:p.Gln684Arg		59349277	Q9NZN7|Q9UF76	Missense_Mutation	SNP	ENST00000406403.1	37	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109584	0.77096	.	.	ENSG00000088038	ENST00000221232;ENST00000406403;ENST00000471126	T;T;T	0.59224	0.28;0.28;0.28	4.14	4.14	0.48551	NOT2/NOT3/NOT5 (1);	0.071575	0.64402	N	0.000017	T	0.80076	0.4557	M	0.94021	3.485	0.80722	D	1	D	0.59357	0.985	D	0.71414	0.973	D	0.83992	0.0338	10	0.48119	T	0.1	-15.9521	12.9889	0.58608	1.0:0.0:0.0:0.0	.	684	O75175	CNOT3_HUMAN	R	684;684;2	ENSP00000221232:Q684R;ENSP00000383954:Q684R;ENSP00000420064:Q2R	ENSP00000221232:Q684R	Q	+	2	0	CNOT3	59349277	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.763000	0.91715	1.869000	0.54173	0.449000	0.29647	CAG		0.597	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		G	54657465	A	G	54657465	3	3	97	1	0	0	0	0	1	0	0	0	3626	188	7	4	2113	4	CNOT3	19	54657465	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	262445	54657465	4471518	140	26271										
TNNI3	7137	hgsc.bcm.edu	37	chr19	55665544	55665544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ccgcttaaacttgcctcgaaGgtcaaagatcttctgagtca	8	11	4	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr19:55665544G>T	ENST00000344887.5	-	7	545	c.403C>A	c.(403-405)Ctt>Att	p.L135I	TNNI3_ENST00000588882.1_Missense_Mutation_p.L110I|TNNI3_ENST00000590463.1_5'Flank	NM_000363.4	NP_000354.4	P19429	TNNI3_HUMAN	troponin I type 3 (cardiac)	135	Involved in binding TNC and actin.				cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|heart contraction (GO:0060047)|heart development (GO:0007507)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|regulation of smooth muscle contraction (GO:0006940)|regulation of systemic arterial blood pressure by ischemic conditions (GO:0001980)|vasculogenesis (GO:0001570)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|troponin complex (GO:0005861)	actin binding (GO:0003779)|calcium channel inhibitor activity (GO:0019855)|calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|troponin C binding (GO:0030172)|troponin T binding (GO:0031014)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		TTGCCTCGAAGGTCAAAGATC	0.582																																																0			19											46	51	50					19																	55665544		2008	4155	6163	60357356	SO:0001583	missense	7137			M64247	CCDS42628.1	19q13.4	2014-09-17	2005-09-12			ENSG00000129991			11947	protein-coding gene	gene with protein product		191044	"troponin I, cardiac", "cardiomyopathy, dilated 2A (autosomal recessive)"	CMD2A		9605869, 9241277, 10806205	Standard	NM_000363		Approved	TNNC1, CMH7	uc002qjg.4	P19429		ENST00000344887.5:c.403C>A	19.37:g.55665544G>T	ENSP00000341838:p.Leu135Ile		60357356		Missense_Mutation	SNP	ENST00000344887.5	37	CCDS42628.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.320072	0.60634	.	.	ENSG00000129991	ENST00000344887	D	0.95307	-3.67	4.72	4.72	0.59763	.	0.000000	0.53938	D	0.000047	D	0.96629	0.8900	M	0.81497	2.545	0.58432	D	0.999991	P	0.39717	0.684	P	0.53518	0.728	D	0.97273	0.9912	10	0.66056	D	0.02	-21.9619	16.8019	0.85616	0.0:0.0:1.0:0.0	.	135	P19429	TNNI3_HUMAN	I	135	ENSP00000341838:L135I	ENSP00000341838:L135I	L	-	1	0	TNNI3	60357356	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.449000	0.73473	2.333000	0.79357	0.585000	0.79938	CTT		0.582	TNNI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452098.1			T	55665544	G	T	55665544	3	4	97	1	0	0	0	0	1	0	0	0	16367	1000	35	2	237	2	TNNI3	19	55665544	Missense_Mutation	SNP	G	TCGA-DC-6158-01A-11D-1657-10	1008079	55665544	3463439	141	26272										
CPXM1	56265	hgsc.bcm.edu	37	chr20	2775016	2775016	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gtcactgaatggtagccctcGgcactggcagtcaccatgta	11	12	2	1	rs150179711	byFrequency	TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr20:2775016G>A	ENST00000380605.2	-	14	2089	c.2025C>T	c.(2023-2025)gcC>gcT	p.A675A		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	675					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GGTAGCCCTCGGCACTGGCAG	0.582													g|||	2	0.000399361	0	0	5008	,	,		18776	0.001		0	False		,,,				2504	0.001															0			20							,	0,4406		0,0,2203	56	55	55		1803,2025	-9.6	0.8	20	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	CPXM1	NM_001184699.1,NM_019609.4	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	601/661,675/735	2775016	2,13004	2203	4300	6503	2723016	SO:0001819	synonymous_variant	56265			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.2025C>T	20.37:g.2775016G>A			2723016	Q6P4G8|Q6UW65|Q9NUB5	Silent	SNP	ENST00000380605.2	37	CCDS13033.1																																																																																				0.582	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2775016	G	A	2775016	2	1	97	1	0	0	0	0	0	0	0	1	3843	1103	39	1		1	CPXM1	20	2775016	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10		2775016	60250504	142	26273										
APCDD1L	164284	hgsc.bcm.edu	37	chr20	57036437	57036437	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tcccaggagcggctgtgcccGtggaaagtgaagagccgggt	17	10	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr20:57036437G>A	ENST00000371149.3	-	4	1145	c.915C>T	c.(913-915)caC>caT	p.H305H	APCDD1L_ENST00000491015.1_5'UTR|APCDD1L_ENST00000439429.1_Silent_p.H316H	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	305						integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			GGCTGTGCCCGTGGAAAGTGA	0.687																																																0			20											20	19	20					20																	57036437		2195	4295	6490	56469843	SO:0001819	synonymous_variant	164284			AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.915C>T	20.37:g.57036437G>A			56469843		Silent	SNP	ENST00000371149.3	37	CCDS13467.1																																																																																				0.687	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360		A	57036437	G	A	57036437	2	1	97	1	0	0	0	0	0	0	0	1	766	1136	40	1		1	APCDD1L	20	57036437	Silent	SNP	G	TCGA-DC-6158-01A-11D-1657-10	54261421	57036437	5989083	143	26274										
KRTAP24-1	643803	hgsc.bcm.edu	37	chr21	31654689	31654689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	aatataacataatggtgagaCgtagctgggtatgaagcaag	12	4	0	2	rs200135144		TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr21:31654689C>T	ENST00000340345.4	-	1	587	c.562G>A	c.(562-564)Gtc>Atc	p.V188I		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	188						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						AATGGTGAGACGTAGCTGGGT	0.418																																																0			21											130	126	127					21																	31654689		1872	4106	5978	30576560	SO:0001583	missense	643803			AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"Keratin associated proteins"	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.562G>A	21.37:g.31654689C>T	ENSP00000339238:p.Val188Ile		30576560	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	37	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	c	0.016	-1.524270	0.00959	.	.	ENSG00000188694	ENST00000340345	T	0.03889	3.77	4.8	0.977	0.19733	.	0.648359	0.14303	N	0.328131	T	0.02083	0.0065	N	0.08118	0	0.09310	N	1	B	0.21688	0.059	B	0.17722	0.019	T	0.46247	-0.9205	10	0.25106	T	0.35	-4.483	2.1659	0.03837	0.5894:0.1668:0.09:0.1539	.	188	Q3LI83	KR241_HUMAN	I	188	ENSP00000339238:V188I	ENSP00000339238:V188I	V	-	1	0	KRTAP24-1	30576560	0.766000	0.28496	0.020000	0.16555	0.034000	0.12701	0.517000	0.22832	0.070000	0.16634	-1.971000	0.00464	GTC		0.418	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455		T	31654689	C	T	31654689	3	4	97	1	0	0	0	0	1	0	0	0	8564	536	19	1	206	1	KRTAP24-1	21	31654689	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10		31654689	16475206	144	26275										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842615	22842615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ttttacagacagtagagggcTcctgggcagtgtggacattt	13	7	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr22:22842615T>C	ENST00000406426.1	-	4	1851	c.1109A>G	c.(1108-1110)gAg>gGg	p.E370G	ZNF280B_ENST00000360412.2_Missense_Mutation_p.E370G			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	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)		AGTAGAGGGCTCCTGGGCAGT	0.502																																																0			22											121	113	116					22																	22842615		2203	4300	6503	21172615	SO:0001583	missense	140883			AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1109A>G	22.37:g.22842615T>C	ENSP00000385998:p.Glu370Gly		21172615		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.447257	0.25987	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.03553	3.89;3.89	4.85	4.85	0.62838	Zinc finger, C2H2 (1);	.	.	.	.	T	0.03136	0.0092	N	0.14661	0.345	0.43095	D	0.994773	B	0.13145	0.007	B	0.12837	0.008	T	0.51148	-0.8742	9	0.49607	T	0.09	-3.6511	12.726	0.57170	0.0:0.0:0.0:1.0	.	370	Q86YH2	Z280B_HUMAN	G	370	ENSP00000385998:E370G;ENSP00000353586:E370G	ENSP00000353586:E370G	E	-	2	0	ZNF280B	21172615	1.000000	0.71417	0.818000	0.32626	0.218000	0.24690	3.357000	0.52277	2.172000	0.68678	0.533000	0.62120	GAG		0.502	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		C	22842615	T	C	22842615	3	2	97	1	0	0	0	0	1	0	0	0	17854	1551	54	4	526	4	ZNF280B	22	22842615	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10		22842615	28461951	145	26276										
TTLL12	23170	hgsc.bcm.edu	37	chr22	43570384	43570384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggggaactggttcagcagcaCgcctggcctctcctggctga	14	13	2	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chr22:43570384C>T	ENST00000216129.6	-	8	1123	c.1060G>A	c.(1060-1062)Gtg>Atg	p.V354M	TTLL12_ENST00000494035.1_5'Flank|TTLL12_ENST00000484118.1_5'UTR	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	354	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				TTCAGCAGCACGCCTGGCCTC	0.697																																																0			22											31	36	34					22																	43570384		2203	4299	6502	41900328	SO:0001583	missense	23170			D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"Tubulin tyrosine ligase-like family"	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.1060G>A	22.37:g.43570384C>T	ENSP00000216129:p.Val354Met		41900328	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842404	0.51057	.	.	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.05649	3.41	4.67	4.67	0.58626	.	0.068363	0.64402	D	0.000018	T	0.11153	0.0272	M	0.69248	2.105	0.58432	D	0.999999	P;P	0.47106	0.89;0.89	B;B	0.43445	0.42;0.42	T	0.02512	-1.1148	10	0.49607	T	0.09	-31.9055	13.3423	0.60551	0.0:0.8415:0.1585:0.0	.	354;354	B1AH89;Q14166	.;TTL12_HUMAN	M	354	ENSP00000216129:V354M	ENSP00000216129:V354M	V	-	1	0	TTLL12	41900328	1.000000	0.71417	0.908000	0.35775	0.333000	0.28666	4.506000	0.60428	2.119000	0.64992	0.655000	0.94253	GTG		0.697	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140		T	43570384	C	T	43570384	3	4	97	1	0	0	0	0	1	0	0	0	16765	536	19	1	902	1	TTLL12	22	43570384	Missense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	20727769	43570384	7734182	146	26277										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29972756	29972756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cctacctgatatgcttgaaaAgcattatggatataagttgt	8	6	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:29972756A>G	ENST00000378993.1	+	10	1992	c.1319A>G	c.(1318-1320)aAg>aGg	p.K440R	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.K440R	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	440	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						ATGCTTGAAAAGCATTATGGA	0.378																																																0			X											94	82	86					X																	29972756		2202	4300	6502	29882677	SO:0001583	missense	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1319A>G	X.37:g.29972756A>G	ENSP00000368278:p.Lys440Arg		29882677	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.670803	0.88348	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.08807	3.05;3.05	5.81	5.81	0.92471	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	L	0.48218	1.51	0.58432	D	0.999994	P	0.50443	0.935	P	0.62740	0.906	T	0.00523	-1.1690	9	.	.	.	.	15.1467	0.72657	1.0:0.0:0.0:0.0	.	440	Q9NZN1	IRPL1_HUMAN	R	440	ENSP00000368278:K440R;ENSP00000305200:K440R	.	K	+	2	0	IL1RAPL1	29882677	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	1.960000	0.56953	0.481000	0.45027	AAG		0.378	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		G	29972756	A	G	29972756	3	3	97	1	0	0	0	0	1	0	0	0	7682	72	3	4	1353	4	IL1RAPL1	23	29972756	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10		29972756	125297804	147	26278										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29972784	29972784	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggatataagttgtttataccAgatagagatttaatcccaac	7	6	0	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:29972784A>G	ENST00000378993.1	+	10	2020	c.1347A>G	c.(1345-1347)ccA>ccG	p.P449P	IL1RAPL1_ENST00000302196.4_Silent_p.P449P	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	449	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						TGTTTATACCAGATAGAGATT	0.368																																																0			X											78	73	75					X																	29972784		2202	4300	6502	29882705	SO:0001819	synonymous_variant	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1347A>G	X.37:g.29972784A>G			29882705	A0AVG4|Q9UJ53	Silent	SNP	ENST00000378993.1	37	CCDS14218.1																																																																																				0.368	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		G	29972784	A	G	29972784	2	3	97	1	0	0	0	0	0	0	0	1	7682	175	7	4		4	IL1RAPL1	23	29972784	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	28	29972784	125297776	148	26279										
USP11	8237	hgsc.bcm.edu	37	chrX	47102927	47102927	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	ggcctgatgctttttggacaCcccctcctggtatcagtgcc	10	14	1	1			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:47102927C>T	ENST00000218348.3	+	13	1845	c.1845C>T	c.(1843-1845)caC>caT	p.H615H	USP11_ENST00000377107.2_Silent_p.H572H	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	615	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						TTTTTGGACACCCCCTCCTGG	0.607																																																0			X											105	80	89					X																	47102927		2203	4300	6503	46987871	SO:0001819	synonymous_variant	8237			U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.1845C>T	X.37:g.47102927C>T			46987871	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	ENST00000218348.3	37	CCDS14277.1																																																																																				0.607	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		T	47102927	C	T	47102927	2	4	97	1	0	0	0	0	0	0	0	1	17082	506	18	3		3	USP11	23	47102927	Silent	SNP	C	TCGA-DC-6158-01A-11D-1657-10	17130143	47102927	108167633	149	26280										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49851179	49851179	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	atatttggtggtctgtggggAgcactgtttatccgcacaaa	12	7	1	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:49851179A>G	ENST00000307367.2	+	8	1290	c.999A>G	c.(997-999)ggA>ggG	p.G333G	CLCN5_ENST00000376108.3_Silent_p.G333G|CLCN5_ENST00000376091.3_Silent_p.G403G|CLCN5_ENST00000376088.3_Silent_p.G403G			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	333					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					GTCTGTGGGGAGCACTGTTTA	0.507																																																0			X											103	79	87					X																	49851179		2203	4300	6503	49737919	SO:0001819	synonymous_variant	1184			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.999A>G	X.37:g.49851179A>G			49737919	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	37	CCDS14328.1																																																																																				0.507	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			G	49851179	A	G	49851179	2	3	97	1	0	0	0	0	0	0	0	1	3472	291	11	4		4	CLCN5	23	49851179	Silent	SNP	A	TCGA-DC-6158-01A-11D-1657-10	2748252	49851179	105419381	150	26281										
CXCR3	2833	hgsc.bcm.edu	37	chrX	70836933	70836933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	cgtagaagttgatgttgaagAgggcacctgccactttgcag	13	8	0	4			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:70836933A>G	ENST00000373693.3	-	2	456	c.389T>C	c.(388-390)cTc>cCc	p.L130P	CXCR3_ENST00000373691.4_Missense_Mutation_p.L177P	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3	130					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					GATGTTGAAGAGGGCACCTGC	0.612																																																0			X											20	16	17					X																	70836933		2200	4292	6492	70753658	SO:0001583	missense	2833			U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	4540	protein-coding gene	gene with protein product		300574	"G protein-coupled receptor 9"	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.389T>C	X.37:g.70836933A>G	ENSP00000362797:p.Leu130Pro		70753658	B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	ENST00000373693.3	37	CCDS14416.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.640364	0.29157	.	.	ENSG00000186810	ENST00000373691;ENST00000373693;ENST00000373687	T;T	0.47177	0.85;0.85	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.326711	0.28225	N	0.016138	T	0.74306	0.3699	M	0.93106	3.38	0.54753	D	0.999982	D;D	0.76494	0.999;0.999	D;D	0.80764	0.964;0.994	T	0.80670	-0.1279	10	0.87932	D	0	.	12.1786	0.54199	1.0:0.0:0.0:0.0	.	177;130	P49682-2;P49682	.;CXCR3_HUMAN	P	177;130;130	ENSP00000362795:L177P;ENSP00000362797:L130P	ENSP00000362791:L130P	L	-	2	0	CXCR3	70753658	0.934000	0.31675	0.990000	0.47175	0.002000	0.02628	5.886000	0.69743	2.006000	0.58801	0.481000	0.45027	CTC		0.612	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144141.1			G	70836933	A	G	70836933	3	3	97	1	0	0	0	0	1	0	0	0	4098	304	11	4	721	4	CXCR3	23	70836933	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	20985754	70836933	84433627	151	26282										
THOC2	57187	hgsc.bcm.edu	37	chrX	122760389	122760389	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tacttgctaaaagccagttgTccttttccagtttcaatctc	5	11	2	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:122760389T>C	ENST00000245838.8	-	24	2913	c.2882A>G	c.(2881-2883)gAc>gGc	p.D961G	THOC2_ENST00000491737.1_Missense_Mutation_p.D846G|THOC2_ENST00000355725.4_Missense_Mutation_p.D961G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	961					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AAGCCAGTTGTCCTTTTCCAG	0.378																																																0			X											180	157	164					X																	122760389		1841	4083	5924	122588070	SO:0001583	missense	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2882A>G	X.37:g.122760389T>C	ENSP00000245838:p.Asp961Gly		122588070	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.989729	0.74589	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737	T;T;T	0.21932	1.98;1.98;1.98	5.83	5.83	0.93111	THO complex, subunitTHOC2, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.52025	0.1709	M	0.87038	2.855	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.56890	-0.7904	10	0.41790	T	0.15	-11.54	15.1686	0.72850	0.0:0.0:0.0:1.0	.	961	Q8NI27	THOC2_HUMAN	G	961;961;846	ENSP00000245838:D961G;ENSP00000347959:D961G;ENSP00000419795:D846G	ENSP00000245838:D961G	D	-	2	0	THOC2	122588070	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	GAC		0.378	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122760389	T	C	122760389	3	2	97	1	0	0	0	0	1	0	0	0	15904	1667	58	4	1959	4	THOC2	23	122760389	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	51923456	122760389	32510171	152	26283										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129377605	129377605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tacaagatgaaatctaggcgAggcagccactggatttgatg	12	7	1	3			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:129377605A>G	ENST00000370978.4	-	5	466	c.313T>C	c.(313-315)Tcg>Ccg	p.S105P		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	105	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						AATCTAGGCGAGGCAGCCACT	0.353																																																0			X											63	66	65					X																	129377605		2203	4300	6503	129205286	SO:0001583	missense	55609			AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.313T>C	X.37:g.129377605A>G	ENSP00000360017:p.Ser105Pro		129205286	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	37	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.581225	0.28180	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.25912	1.77;1.77	3.62	3.62	0.41486	.	.	.	.	.	T	0.29491	0.0735	L	0.39898	1.24	0.09310	N	1	B;P	0.42993	0.004;0.797	B;P	0.51101	0.021;0.659	T	0.07046	-1.0793	9	0.34782	T	0.22	.	7.8624	0.29517	1.0:0.0:0.0:0.0	.	105;105	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	P	105	ENSP00000360017:S105P;ENSP00000408521:S105P	ENSP00000066465:S105P	S	-	1	0	ZNF280C	129205286	0.006000	0.16342	0.013000	0.15412	0.011000	0.07611	1.588000	0.36633	1.441000	0.47550	0.412000	0.27726	TCG		0.353	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		G	129377605	A	G	129377605	3	3	97	1	0	0	0	0	1	0	0	0	17855	304	11	4	1960	4	ZNF280C	23	129377605	Missense_Mutation	SNP	A	TCGA-DC-6158-01A-11D-1657-10	6617216	129377605	25892955	153	26284										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135314029	135314029	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	gagtgcttctatgctcaactCgggggatgcgtccatgctca	12	11	3	0			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:135314029C>A	ENST00000316077.9	-	8	1307	c.1087G>T	c.(1087-1089)Gag>Tag	p.E363*	MAP7D3_ENST00000370663.5_Nonsense_Mutation_p.E345*|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370661.1_Nonsense_Mutation_p.E328*	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	363					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					ATGCTCAACTCGGGGGATGCG	0.592																																																0			X											69	72	71					X																	135314029		2155	4235	6390	135141695	SO:0001587	stop_gained	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1087G>T	X.37:g.135314029C>A	ENSP00000318086:p.Glu363*		135141695	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Nonsense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551129	0.86127	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	.	.	.	4.34	-1.84	0.07809	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	6.8805	9.6831	0.40082	0.0:0.4441:0.0:0.5559	.	.	.	.	X	328;363;345;322	.	ENSP00000318086:E363X	E	-	1	0	MAP7D3	135141695	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.605000	0.05661	-0.472000	0.06881	-1.050000	0.02344	GAG		0.592	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			A	135314029	C	A	135314029	4	1	97	1	0	0	0	0	0	1	0	0	9299	893	31	2	1587	2	MAP7D3	23	135314029	Nonsense_Mutation	SNP	C	TCGA-DC-6158-01A-11D-1657-10	5936424	135314029	19956531	154	26285										
SLC10A3	8273	hgsc.bcm.edu	37	chrX	153717032	153717032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.123376623376623	19	1	1.51444737420347	3.05015015015015	1.17063331988705	0.204927155190733	0.66867542651632	0	tggagatcacgatgatgcccTcactgtcctcaggaaactca	9	12	4	2			TCGA-DC-6158-01A-11D-1657-10	TCGA-DC-6158-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	989088f8-382e-4bc6-8c9f-edfcda3bdde5	5213f89c-4979-404a-88ff-16157531d747	g.chrX:153717032T>C	ENST00000393587.4	-	3	511	c.248A>G	c.(247-249)gAg>gGg	p.E83G	SLC10A3_ENST00000369649.4_Missense_Mutation_p.E83G|UBL4A_ENST00000477777.1_5'Flank|UBL4A_ENST00000369653.4_5'Flank|SLC10A3_ENST00000393586.1_Missense_Mutation_p.E138G|SLC10A3_ENST00000263512.4_Missense_Mutation_p.E83G|UBL4A_ENST00000369660.4_5'Flank	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	83					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GATGATGCCCTCACTGTCCTC	0.622																																																0			X											157	123	134					X																	153717032		2203	4300	6503	153370226	SO:0001583	missense	8273			X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"Solute carriers"	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.248A>G	X.37:g.153717032T>C	ENSP00000377212:p.Glu83Gly		153370226	Q5HY79|Q9BSL2	Missense_Mutation	SNP	ENST00000393587.4	37	CCDS14755.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.478121	0.63849	.	.	ENSG00000126903	ENST00000369649;ENST00000393586;ENST00000263512;ENST00000393587;ENST00000453912	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	4.88	4.88	0.63580	.	0.494750	0.19637	U	0.109527	T	0.28400	0.0702	M	0.68317	2.08	0.27945	N	0.937377	B;B	0.31026	0.255;0.304	B;B	0.26693	0.053;0.072	T	0.26744	-1.0094	10	0.72032	D	0.01	-14.4909	12.5528	0.56236	0.0:0.0:0.0:1.0	.	83;83	Q9BSL2;P09131	.;P3_HUMAN	G	83;138;83;83;83	ENSP00000358663:E83G;ENSP00000377211:E138G;ENSP00000263512:E83G;ENSP00000377212:E83G;ENSP00000395702:E83G	ENSP00000263512:E83G	E	-	2	0	SLC10A3	153370226	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	4.016000	0.57159	1.808000	0.52836	0.430000	0.28490	GAG		0.622	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3	NM_019848		C	153717032	T	C	153717032	3	2	97	1	0	0	0	0	1	0	0	0	14412	1551	54	4	1189	4	SLC10A3	23	153717032	Missense_Mutation	SNP	T	TCGA-DC-6158-01A-11D-1657-10	18403003	153717032	1553528	155	26286										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67795384	67795384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcttaatcgactcagatatcGgcccagtaacagcaggctct	9	12	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:67795384G>A	ENST00000262345.1	+	6	1419	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	IL12RB2_ENST00000544434.1_Missense_Mutation_p.R260Q|IL12RB2_ENST00000541374.1_Missense_Mutation_p.R260Q|IL12RB2_ENST00000371000.1_Missense_Mutation_p.R260Q	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	260	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CTCAGATATCGGCCCAGTAAC	0.423																																																0			1											119	114	116					1																	67795384		2203	4300	6503	67567972	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.779G>A	1.37:g.67795384G>A	ENSP00000262345:p.Arg260Gln		67567972	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189792	0.38707	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.2	4.28	0.50868	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.156761	0.53938	N	0.000047	T	0.40719	0.1128	L	0.51914	1.62	0.24901	N	0.992105	P;D;P;P	0.61697	0.915;0.99;0.885;0.887	B;P;B;B	0.50825	0.329;0.651;0.424;0.194	T	0.19844	-1.0293	10	0.29301	T	0.29	-20.6601	9.1957	0.37226	0.1031:0.0:0.8969:0.0	.	260;260;260;260	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	Q	260	ENSP00000262345:R260Q;ENSP00000360039:R260Q;ENSP00000445276:R260Q;ENSP00000442443:R260Q	ENSP00000262345:R260Q	R	+	2	0	IL12RB2	67567972	0.996000	0.38824	0.474000	0.27266	0.146000	0.21551	3.377000	0.52425	1.298000	0.44778	0.561000	0.74099	CGG		0.423	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		A	67795384	G	A	67795384	3	1	98	1	0	0	0	0	1	0	0	0	7648	1116	39	1	797	1	IL12RB2	1	67795384	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10		67795384	181455237	1	26287										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70257750	70257750	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgttcaactgtcaagctctaCgaaaactaagtattcctgat	6	9	3	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:70257750C>T	ENST00000035383.5	+	2	244	c.214C>T	c.(214-216)Cga>Tga	p.R72*	LRRC7_ENST00000415775.2_5'UTR|LRRC7_ENST00000370958.1_Nonsense_Mutation_p.R110*|LRRC7_ENST00000310961.5_Nonsense_Mutation_p.R77*	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	72						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.R72G(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TCAAGCTCTACGAAAACTAAG	0.294																																																1	Substitution - Missense(1)	ovary(1)	1											95	103	100					1																	70257750		2202	4295	6497	70030338	SO:0001587	stop_gained	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.214C>T	1.37:g.70257750C>T	ENSP00000035383:p.Arg72*		70030338	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Nonsense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	37	6.592986	0.97688	.	.	ENSG00000033122	ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298	.	.	.	5.68	2.7	0.31948	.	0.148908	0.46758	D	0.000280	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3006	0.60324	0.4547:0.5453:0.0:0.0	.	.	.	.	X	77;110;72;72	.	ENSP00000035383:R72X	R	+	1	2	LRRC7	70030338	0.999000	0.42202	0.999000	0.59377	0.997000	0.91878	2.305000	0.43664	0.277000	0.22141	0.561000	0.74099	CGA		0.294	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70257750	C	T	70257750	4	4	98	1	0	0	0	0	0	1	0	0	9049	528	19	1	220	1	LRRC7	1	70257750	Nonsense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	2462366	70257750	178992871	2	26288										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catggcactgtactcttcttGtccagctgtatccagtatgt	8	11	2	0	rs121913254		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:115256530G>T	ENST00000369535.4	-	3	434	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61K(595)|p.Q61E(9)|p.Q61L(3)|p.Q61R(2)|p.G60>?(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		TACTCTTCTTGTCCAGCTGTA	0.458	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	610	Substitution - Missense(609)|Complex(1)	skin(372)|haematopoietic_and_lymphoid_tissue(73)|thyroid(55)|NS(29)|large_intestine(28)|soft_tissue(16)|lung(12)|autonomic_ganglia(6)|liver(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|cervix(2)|endometrium(2)|pancreas(2)|meninges(1)|kidney(1)|biliary_tract(1)|stomach(1)|ovary(1)|bone(1)	1											180	156	164					1																	115256530		2203	4300	6503	115058053	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.181C>A	1.37:g.115256530G>T	ENSP00000358548:p.Gln61Lys		115058053	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	33	5.255564	0.95336	.	.	ENSG00000213281	ENST00000369535	D	0.83506	-1.73	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.91845	0.7419	H	0.95850	3.73	0.80722	D	1	P	0.51791	0.948	P	0.54759	0.76	D	0.93711	0.7024	10	0.62326	D	0.03	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	61	P01111	RASN_HUMAN	K	61	ENSP00000358548:Q61K	ENSP00000358548:Q61K	Q	-	1	0	NRAS	115058053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.520000	0.98027	2.624000	0.88883	0.655000	0.94253	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115256530	G	T	115256530	3	4	98	1	0	0	0	0	1	0	0	0	10671	1386	48	2	400	2	NRAS	1	115256530	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	44998780	115256530	133994091	3	26289										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115398116	115398116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaaagccctttgcattgttcGtaccaccgagatcaagcagc	8	12	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:115398116G>A	ENST00000369522.3	+	2	271	c.31G>A	c.(31-33)Gta>Ata	p.V11I	SYCP1_ENST00000369518.1_Missense_Mutation_p.V11I	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	11					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		TGCATTGTTCGTACCACCGAG	0.483																																																0			1											91	90	90					1																	115398116		2203	4300	6503	115199639	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.31G>A	1.37:g.115398116G>A	ENSP00000358535:p.Val11Ile		115199639	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	6.040	0.375815	0.11409	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.54866	1.12;0.55;1.12	5.16	-1.7	0.08159	.	0.149164	0.44097	N	0.000484	T	0.14013	0.0339	L	0.34521	1.04	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.14504	-1.0470	10	0.51188	T	0.08	-0.6391	2.1983	0.03916	0.2641:0.3133:0.3156:0.1071	.	11;11	B7ZLS9;Q15431	.;SYCP1_HUMAN	I	11	ENSP00000358535:V11I;ENSP00000410011:V11I;ENSP00000358531:V11I	ENSP00000358531:V11I	V	+	1	0	SYCP1	115199639	0.588000	0.26799	0.005000	0.12908	0.006000	0.05464	0.235000	0.17948	-0.285000	0.09089	-1.036000	0.02392	GTA		0.483	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		A	115398116	G	A	115398116	3	1	98	1	0	0	0	0	1	0	0	0	15470	1145	40	1	33	1	SYCP1	1	115398116	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	141586	115398116	133852505	4	26290										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154229840	154229840	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aggaaaagctcctcccaaccTccctcctggggtcccgccgt	9	18	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:154229840T>C	ENST00000361546.2	+	19	2414	c.2372T>C	c.(2371-2373)cTc>cCc	p.L791P	UBAP2L_ENST00000343815.6_Missense_Mutation_p.L791P|UBAP2L_ENST00000428931.1_Missense_Mutation_p.L791P|UBAP2L_ENST00000271877.7_Missense_Mutation_p.L802P|AL590431.1_ENST00000517008.1_RNA|SNORA58_ENST00000364259.1_RNA			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	791					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTCCCAACCTCCCTCCTGGG	0.468																																																0			1											78	82	81					1																	154229840		2203	4300	6503	152496464	SO:0001583	missense	9898			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.2372T>C	1.37:g.154229840T>C	ENSP00000355343:p.Leu791Pro		152496464	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.438082	0.62955	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.62660	0.2446	M	0.74647	2.275	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.998	D;D;D;D;D	0.87578	0.993;0.998;0.998;0.998;0.995	T	0.67948	-0.5538	10	0.87932	D	0	-10.2648	15.0308	0.71705	0.0:0.0:0.0:1.0	.	705;802;784;791;791	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	P	791;791;287;287;802;791	ENSP00000345308:L791P;ENSP00000389445:L791P;ENSP00000271877:L802P;ENSP00000355343:L791P	ENSP00000271877:L802P	L	+	2	0	UBAP2L	152496464	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.499000	0.81566	2.330000	0.79161	0.533000	0.62120	CTC		0.468	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		C	154229840	T	C	154229840	3	2	98	1	0	0	0	0	1	0	0	0	16878	1551	54	4	2446	4	UBAP2L	1	154229840	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	38831724	154229840	95020781	5	26291										
TMEM79	84283	hgsc.bcm.edu	37	chr1	156261301	156261301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catgttcgtggtggagccggAgcgcatgctcactgccaccg	14	13	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:156261301A>G	ENST00000405535.2	+	4	1268	c.1097A>G	c.(1096-1098)gAg>gGg	p.E366G	TMEM79_ENST00000357501.2_Silent_p.G127G|TMEM79_ENST00000295694.5_Missense_Mutation_p.E366G|TMEM79_ENST00000495881.1_3'UTR|C1orf85_ENST00000482579.1_5'Flank	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	366					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					GTGGAGCCGGAGCGCATGCTC	0.677																																																0			1											114	110	111					1																	156261301		2203	4300	6503	154527925	SO:0001583	missense	84283			BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.1097A>G	1.37:g.156261301A>G	ENSP00000384748:p.Glu366Gly		154527925	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	37	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.402841	0.62288	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.52526	0.66;0.66	5.7	5.7	0.88788	.	0.270193	0.37857	N	0.001904	T	0.32704	0.0838	L	0.34521	1.04	0.80722	D	1	P	0.51537	0.946	P	0.46253	0.509	T	0.26950	-1.0088	10	0.66056	D	0.02	-22.1261	14.8012	0.69916	1.0:0.0:0.0:0.0	.	366	Q9BSE2	TMM79_HUMAN	G	366	ENSP00000295694:E366G;ENSP00000384748:E366G	ENSP00000295694:E366G	E	+	2	0	TMEM79	154527925	1.000000	0.71417	0.996000	0.52242	0.033000	0.12548	3.231000	0.51294	2.170000	0.68504	0.533000	0.62120	GAG		0.677	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		G	156261301	A	G	156261301	3	3	98	1	0	0	0	0	1	0	0	0	16242	304	11	4	1107	4	TMEM79	1	156261301	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2031461	156261301	92989320	6	26292										
NES	10763	hgsc.bcm.edu	37	chr1	156646849	156646849	+	Frame_Shift_Del	DEL	G	G	-													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgcgtgcttctcccgccagcGttggtcaacgagggcccgca							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:156646849delG	ENST00000368223.3	-	1	340	c.208delC	c.(208-210)cgcfs	p.R70fs		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	70	Coil 1B.|Rod.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCCCGCCAGCGTTGGTCAACG	0.746																																																0			1											5	5	5					1																	156646849		1861	3825	5686	154913473	SO:0001589	frameshift_variant	10763			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.208delC	1.37:g.156646849delG	ENSP00000357206:p.Arg70fs		154913473	O00552|Q3LIF5|Q5SYZ6	Frame_Shift_Del	DEL	ENST00000368223.3	37	CCDS1151.1																																																																																				0.746	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		-	156646849	G	-	156646849	7	5	98	1	0	1	0	1	0	0	0	0	10368	1145	40	0	4673	0	NES	1	156646849	Frame_Shift_Del	DEL	G	TCGA-DC-6160-01A-11D-1657-10	385548	156646849	92603772	7	26293										
EPRS	2058	hgsc.bcm.edu	37	chr1	220156677	220156677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttcccaaatggcataggcccAgggacgaagaatataacagc	10	10	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:220156677A>G	ENST00000366923.3	-	22	3423	c.3154T>C	c.(3154-3156)Tgg>Cgg	p.W1052R		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1052	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	GCATAGGCCCAGGGACGAAGA	0.378																																																0			1											61	65	64					1																	220156677		2203	4300	6503	218223300	SO:0001583	missense	2058			X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3154T>C	1.37:g.220156677A>G	ENSP00000355890:p.Trp1052Arg		218223300	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528778	0.85706	.	.	ENSG00000136628	ENST00000366923	T	0.28666	1.6	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.56514	0.1990	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.61515	-0.7047	10	0.87932	D	0	-8.7816	15.5395	0.76031	1.0:0.0:0.0:0.0	.	1052	P07814	SYEP_HUMAN	R	1052	ENSP00000355890:W1052R	ENSP00000355890:W1052R	W	-	1	0	EPRS	218223300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.065000	0.93941	2.089000	0.63090	0.533000	0.62120	TGG		0.378	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		G	220156677	A	G	220156677	3	3	98	1	0	0	0	0	1	0	0	0	5204	188	7	4	1428	4	EPRS	1	220156677	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	63509828	220156677	29093944	8	26294										
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226046987	226046987	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggaaaaatagccccaggaagAgggtgaagttgatgcccagc	14	8	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:226046987A>G	ENST00000366835.3	-	15	1556	c.1286T>C	c.(1285-1287)cTc>cCc	p.L429P	TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	429					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					CCCCAGGAAGAGGGTGAAGTT	0.547																																																0			1											111	102	105					1																	226046987		2203	4300	6503	224113610	SO:0001583	missense	9725				CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"KIAA0792"	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.1286T>C	1.37:g.226046987A>G	ENSP00000355800:p.Leu429Pro		224113610	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472745	0.84640	.	.	ENSG00000196187	ENST00000366835	T	0.35973	1.28	5.07	5.07	0.68467	Domain of unknown function DUF221 (1);	0.000000	0.85682	D	0.000000	T	0.66771	0.2823	M	0.89785	3.06	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74648	-0.3595	10	0.62326	D	0.03	-40.5488	14.8201	0.70065	1.0:0.0:0.0:0.0	.	429	O94886	TM63A_HUMAN	P	429	ENSP00000355800:L429P	ENSP00000355800:L429P	L	-	2	0	TMEM63A	224113610	1.000000	0.71417	0.970000	0.41538	0.985000	0.73830	9.115000	0.94336	1.921000	0.55644	0.459000	0.35465	CTC		0.547	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		G	226046987	A	G	226046987	3	3	98	1	0	0	0	0	1	0	0	0	16229	304	11	4	1177	4	TMEM63A	1	226046987	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	5890310	226046987	23203634	9	26295										
RYR2	6262	hgsc.bcm.edu	37	chr1	237754050	237754050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atgttttatcgcctgagcatGccgatcgagtgcgcggaggt	14	9	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr1:237754050G>A	ENST00000366574.2	+	31	4235	c.3918G>A	c.(3916-3918)atG>atA	p.M1306I	RYR2_ENST00000360064.6_Missense_Mutation_p.M1304I|RYR2_ENST00000542537.1_Missense_Mutation_p.M1290I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1306	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GCCTGAGCATGCCGATCGAGT	0.512																																																0			1											207	197	200					1																	237754050		1963	4163	6126	235820673	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3918G>A	1.37:g.237754050G>A	ENSP00000355533:p.Met1306Ile		235820673	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	g	17.12	3.308760	0.60305	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96745	-4.11;-4.09;-4.1	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000001	D	0.95465	0.8527	M	0.66939	2.045	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	D	0.92722	0.6192	10	0.72032	D	0.01	.	18.915	0.92501	0.0:0.0:1.0:0.0	.	1306	Q92736	RYR2_HUMAN	I	1306;1304;1290	ENSP00000355533:M1306I;ENSP00000353174:M1304I;ENSP00000443798:M1290I	ENSP00000353174:M1304I	M	+	3	0	RYR2	235820673	1.000000	0.71417	1.000000	0.80357	0.612000	0.37316	9.597000	0.98273	2.777000	0.95525	0.655000	0.94253	ATG		0.512	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237754050	G	A	237754050	3	1	98	1	0	0	0	0	1	0	0	0	13806	1319	46	3	4040	3	RYR2	1	237754050	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	11707063	237754050	11496571	10	26296										
NBAS	51594	hgsc.bcm.edu	37	chr2	15307424	15307424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aggagcagggaaagaagttcTtggtcacaattggaatcatt	12	5	3	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:15307424T>A	ENST00000281513.5	-	52	6889	c.6864A>T	c.(6862-6864)caA>caT	p.Q2288H	NBAS_ENST00000441750.1_Missense_Mutation_p.Q2168H	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2288					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						AAAGAAGTTCTTGGTCACAAT	0.527																																																0			2											65	58	60					2																	15307424		2203	4300	6503	15224875	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6864A>T	2.37:g.15307424T>A	ENSP00000281513:p.Gln2288His		15224875	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.15|10.15	1.272018|1.272018	0.23221|0.23221	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000442506|ENST00000441750;ENST00000281513;ENST00000433283	.|T;T	.|0.33438	.|1.41;1.41	5.46|5.46	-10.9|-10.9	0.00192|0.00192	.|.	.|0.635313	.|0.15818	.|N	.|0.243144	T|T	0.34483|0.34483	0.0899|0.0899	L|L	0.47716|0.47716	1.5|1.5	0.20074|0.20074	N|N	0.999935|0.999935	.|D;P	.|0.69078	.|0.997;0.878	.|P;B	.|0.58820	.|0.846;0.192	T|T	0.68823|0.68823	-0.5307|-0.5307	5|10	.|0.87932	.|D	.|0	.|.	14.2516|14.2516	0.66023|0.66023	0.1654:0.5816:0.0:0.253|0.1654:0.5816:0.0:0.253	.|.	.|2168;2288	.|A2RRP1-2;A2RRP1	.|.;NBAS_HUMAN	M|H	1336|2168;2288;101	.|ENSP00000413201:Q2168H;ENSP00000281513:Q2288H	.|ENSP00000281513:Q2288H	K|Q	-|-	2|3	0|2	NBAS|NBAS	15224875|15224875	0.024000|0.024000	0.19004|0.19004	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.778000|-0.778000	0.04664|0.04664	-3.101000|-3.101000	0.00244|0.00244	-1.139000|-1.139000	0.01908|0.01908	AAG|CAA		0.527	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15307424	T	A	15307424	3	1	98	1	0	0	0	0	1	0	0	0	10216	1606	56	5	255	5	NBAS	2	15307424	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10		15307424	227891949	11	26297										
CD207	50489	hgsc.bcm.edu	37	chr2	71062833	71062833	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tctcagcagcgatgtggcttGctcggggccagagggagatg	17	9	1	2	rs397692276|rs11450450		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:71062833G>C	ENST00000410009.3	-	1	119		c.e1+1			NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						GATGTGGCTTGCTCGGGGCCA	0.547																																																0			2											71	84	80					2																	71062833		2133	4253	6386	70916341	SO:0001630	splice_region_variant	50489			AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.73+1C>G	2.37:g.71062833G>C			70916341		Splice_Site	SNP	ENST00000410009.3	37		.	.	.	.	.	.	.	.	.	.	G	8.781	0.928326	0.18131	.	.	ENSG00000116031	ENST00000410009	.	.	.	3.98	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8493	0.52401	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CD207	70916341	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	2.092000	0.41700	2.482000	0.83794	0.655000	0.94253	.		0.547	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	Intron	C	71062833	G	C	71062833	5	2	98	1	0	0	0	0	0	0	1	0	2989	1333	46	5	936	5	CD207	2	71062833	Splice_Site	SNP	G	TCGA-DC-6160-01A-11D-1657-10	55755409	71062833	172136540	12	26298										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84771470	84771470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgaaattgatcgatgggaacAggaatatctgtatcacagag	11	6	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:84771470A>T	ENST00000237449.6	+	4	784	c.776A>T	c.(775-777)cAg>cTg	p.Q259L	DNAH6_ENST00000398278.2_Missense_Mutation_p.Q259L|DNAH6_ENST00000389394.3_Missense_Mutation_p.Q259L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	259	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						CGATGGGAACAGGAATATCTG	0.368																																																0			2											78	64	68					2																	84771470		692	1590	2282	84624981	SO:0001583	missense	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.776A>T	2.37:g.84771470A>T	ENSP00000237449:p.Gln259Leu		84624981	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.306399	0.60305	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.25250	1.81;1.95;1.81	5.46	5.46	0.80206	.	.	.	.	.	T	0.25306	0.0615	L	0.49126	1.545	0.40308	D	0.978682	B	0.16166	0.016	B	0.12156	0.007	T	0.04930	-1.0917	8	.	.	.	.	14.8016	0.69922	1.0:0.0:0.0:0.0	.	259	Q9C0G6	DYH6_HUMAN	L	259	ENSP00000374045:Q259L;ENSP00000381326:Q259L;ENSP00000237449:Q259L	.	Q	+	2	0	DNAH6	84624981	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.621000	0.74228	2.185000	0.69588	0.482000	0.46254	CAG		0.368	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84771470	A	T	84771470	3	4	98	1	0	0	0	0	1	0	0	0	4616	188	7	5	790	5	DNAH6	2	84771470	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	13708637	84771470	158427903	13	26299										
CNGA3	1261	hgsc.bcm.edu	37	chr2	98996745	98996745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tttccgtggagccgagcttaAggaggtgtccagccaagaaa	13	9	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:98996745A>G	ENST00000272602.2	+	3	362	c.323A>G	c.(322-324)aAg>aGg	p.K108R	CNGA3_ENST00000409937.1_Missense_Mutation_p.K112R|CNGA3_ENST00000393504.1_Missense_Mutation_p.K108R|CNGA3_ENST00000436404.2_Missense_Mutation_p.K108R			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	108					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GCCGAGCTTAAGGAGGTGTCC	0.587																																																0			2											72	68	69					2																	98996745		2203	4300	6503	98363177	SO:0001583	missense	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.323A>G	2.37:g.98996745A>G	ENSP00000272602:p.Lys108Arg		98363177	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	37	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	A	9.791	1.177876	0.21787	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	5.28	2.91	0.33838	.	0.269175	0.41294	N	0.000919	T	0.37945	0.1022	M	0.64567	1.98	0.30327	N	0.787032	P;B;B	0.36086	0.536;0.44;0.001	B;B;B	0.30646	0.079;0.118;0.006	T	0.33879	-0.9851	10	0.32370	T	0.25	.	7.6602	0.28398	0.8302:0.0:0.1698:0.0	.	112;108;108	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	R	108;108;108;112	ENSP00000377140:K108R;ENSP00000410070:K108R;ENSP00000272602:K108R;ENSP00000386761:K112R	ENSP00000272602:K108R	K	+	2	0	CNGA3	98363177	1.000000	0.71417	0.983000	0.44433	0.050000	0.14768	2.204000	0.42761	0.471000	0.27319	-0.256000	0.11100	AAG		0.587	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		G	98996745	A	G	98996745	3	3	98	1	0	0	0	0	1	0	0	0	3604	72	3	4	333	4	CNGA3	2	98996745	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	14225275	98996745	144202628	14	26300										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165986523	165986523	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggccagcgacctccatacagTcccacatggtctctatccac	7	17	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:165986523T>C	ENST00000360093.3	-	17	3340	c.2849A>G	c.(2848-2850)gAc>gGc	p.D950G	SCN3A_ENST00000283254.7_Missense_Mutation_p.D950G|SCN3A_ENST00000409101.3_Missense_Mutation_p.D901G	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	950					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCATACAGTCCCACATGGT	0.483																																																0			2											181	173	175					2																	165986523		2203	4300	6503	165694769	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2849A>G	2.37:g.165986523T>C	ENSP00000353206:p.Asp950Gly		165694769	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	T	17.19	3.325377	0.60743	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66	5.49	5.49	0.81192	Ion transport (1);	0.000000	0.64402	D	0.000009	D	0.98372	0.9459	M	0.68728	2.09	0.80722	D	1	D;D;D;D;D	0.89917	0.971;0.991;0.988;0.988;1.0	D;P;P;P;D	0.97110	0.918;0.904;0.844;0.844;1.0	D	0.99620	1.0983	10	0.66056	D	0.02	.	15.5759	0.76387	0.0:0.0:0.0:1.0	.	950;901;901;901;950	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	G	950;950;901;901	ENSP00000353206:D950G;ENSP00000283254:D950G;ENSP00000386726:D901G;ENSP00000403348:D901G	ENSP00000283254:D950G	D	-	2	0	SCN3A	165694769	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.073000	0.62155	0.460000	0.39030	GAC		0.483	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165986523	T	C	165986523	3	2	98	1	0	0	0	0	1	0	0	0	13955	1667	58	4	3201	4	SCN3A	2	165986523	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	66989778	165986523	77212850	15	26301										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167133566	167133566	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gaccagcgacctccatacagTcccacatggtctctatccac	6	17	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:167133566T>C	ENST00000409435.1	-	15	2800	c.2801A>G	c.(2800-2802)gAc>gGc	p.D934G	SCN9A_ENST00000375387.4_Missense_Mutation_p.D935G|SCN9A_ENST00000303354.6_Missense_Mutation_p.D935G|SCN9A_ENST00000409672.1_Missense_Mutation_p.D923G|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	934					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCATACAGTCCCACATGGT	0.488																																																0			2											231	215	220					2																	167133566		2203	4300	6503	166841812	SO:0001583	missense	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.2801A>G	2.37:g.167133566T>C	ENSP00000386330:p.Asp934Gly		166841812	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.426004	0.83667	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000001	D	0.98083	0.9368	L	0.60455	1.87	0.54753	D	0.999982	D	0.60575	0.988	D	0.63488	0.915	D	0.98945	1.0792	10	0.62326	D	0.03	.	16.175	0.81844	0.0:0.0:0.0:1.0	.	923	E7EUN6	.	G	923;935;935;934	ENSP00000386306:D923G;ENSP00000364536:D935G;ENSP00000304748:D935G;ENSP00000386330:D934G	ENSP00000304748:D935G	D	-	2	0	SCN9A	166841812	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.947000	0.87758	2.274000	0.75844	0.528000	0.53228	GAC		0.488	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		C	167133566	T	C	167133566	3	2	98	1	0	0	0	0	1	0	0	0	13962	1667	58	4	3213	4	SCN9A	2	167133566	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	1147043	167133566	76065807	16	26302										
KBTBD10	10324	hgsc.bcm.edu	37	chr2	170374710	170374710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ctgtttacagaaaatgtacaAacagggtgtttatcttcaac	7	7	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:170374710A>G	ENST00000284669.1	+	4	1464	c.1387A>G	c.(1387-1389)Aac>Gac	p.N463D	KLHL41_ENST00000463400.1_3'UTR|BBS5_ENST00000554017.1_Missense_Mutation_p.N401D|RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.N401D	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	463					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)											AAAATGTACAAACAGGGTGTT	0.353																																																0			2											61	59	60					2																	170374710		2203	4300	6503	170082956	SO:0001583	missense	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1387A>G	2.37:g.170374710A>G	ENSP00000284669:p.Asn463Asp		170082956	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	37	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850802	0.71719	.	.	ENSG00000163093;ENSG00000251569;ENSG00000239474	ENST00000554017;ENST00000513963;ENST00000284669	T;T;T	0.79554	-1.28;-1.28;-1.28	5.82	5.82	0.92795	Kelch-type beta propeller (1);	0.129609	0.64402	D	0.000001	T	0.81254	0.4784	L	0.61036	1.89	0.44852	D	0.997868	P;B	0.35551	0.509;0.331	B;B	0.43103	0.4;0.408	T	0.81433	-0.0935	10	0.52906	T	0.07	.	10.8276	0.46643	0.9297:0.0:0.0703:0.0	.	401;463	E9PBE3;O60662	.;KBTBA_HUMAN	D	401;401;463	ENSP00000452313:N401D;ENSP00000424363:N401D;ENSP00000284669:N463D	ENSP00000284669:N463D	N	+	1	0	BBS5;RP11-724O16.1;KBTBD10	170082956	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.521000	0.81832	2.364000	0.80123	0.524000	0.50904	AAC		0.353	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		G	170374710	A	G	170374710	3	3	98	1	0	0	0	0	1	0	0	0	8011	14	1	4	1401	4	KBTBD10	2	170374710	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	3241144	170374710	72824663	17	26303										
GORASP2	26003	hgsc.bcm.edu	37	chr2	171822354	171822354	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cttacctggcattgcacctcTccccctgccatccgagttcc	6	19	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:171822354T>C	ENST00000234160.4	+	10	1888	c.1073T>C	c.(1072-1074)cTc>cCc	p.L358P	GORASP2_ENST00000452526.2_Missense_Mutation_p.L370P|GORASP2_ENST00000493692.1_3'UTR	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	358	Pro-rich.				mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						ATTGCACCTCTCCCCCTGCCA	0.572																																																0			2											186	137	154					2																	171822354		2203	4300	6503	171530600	SO:0001583	missense	26003				CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.1073T>C	2.37:g.171822354T>C	ENSP00000234160:p.Leu358Pro		171530600	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	37	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487884	0.64074	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.56611	0.54;0.45	5.85	5.85	0.93711	.	0.065917	0.64402	D	0.000008	T	0.42988	0.1227	L	0.41824	1.3	0.80722	D	1	B;B;B	0.25390	0.125;0.125;0.125	B;B;B	0.20184	0.028;0.028;0.028	T	0.30357	-0.9981	10	0.30854	T	0.27	-5.8666	12.0983	0.53767	0.0:0.0685:0.0:0.9315	.	314;370;358	B4DNR1;B4DKT0;Q9H8Y8	.;.;GORS2_HUMAN	P	358;370	ENSP00000234160:L358P;ENSP00000410208:L370P	ENSP00000234160:L358P	L	+	2	0	GORASP2	171530600	0.980000	0.34600	1.000000	0.80357	0.984000	0.73092	3.612000	0.54142	2.222000	0.72286	0.533000	0.62120	CTC		0.572	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			C	171822354	T	C	171822354	3	2	98	1	0	0	0	0	1	0	0	0	6596	1551	54	4	1111	4	GORASP2	2	171822354	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	1447644	171822354	71377019	18	26304										
HOXD1	3231	hgsc.bcm.edu	37	chr2	177054788	177054788	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggccattcctgtggctccccTccaacttcccctctctggaa	7	18	1	0	rs544403010	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:177054788T>C	ENST00000331462.4	+	2	1128	c.905T>C	c.(904-906)cTc>cCc	p.L302P	HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000436126.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	302					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		GTGGCTCCCCTCCAACTTCCC	0.557													T|||	447	0.0892572	0.031	0.1066	5008	,	,		15245	0.2004		0.1272	False		,,,				2504	0.002															0			2											95	103	100					2																	177054788		2203	4300	6503	176763034	SO:0001583	missense	3231				CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.905T>C	2.37:g.177054788T>C	ENSP00000328598:p.Leu302Pro		176763034	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	T	9.428	1.084673	0.20309	.	.	ENSG00000128645	ENST00000331462	D	0.90620	-2.7	5.66	5.66	0.87406	.	0.339551	0.21508	N	0.073420	D	0.84442	0.5473	L	0.27053	0.805	0.09310	N	0.999999	P;B	0.52842	0.956;0.083	P;B	0.44732	0.459;0.02	T	0.76642	-0.2884	10	0.30078	T	0.28	.	9.1882	0.37182	0.1619:0.0:0.0:0.8381	.	302;302	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	P	302	ENSP00000328598:L302P	ENSP00000328598:L302P	L	+	2	0	HOXD1	176763034	0.862000	0.29867	0.210000	0.23637	0.881000	0.50899	3.421000	0.52742	2.143000	0.66587	0.533000	0.62120	CTC		0.557	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			C	177054788	T	C	177054788	3	2	98	1	0	0	0	0	1	0	0	0	7339	1551	54	4	911	4	HOXD1	2	177054788	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	5232434	177054788	66144585	19	26305										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196718135	196718135	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggaaatgaggatatccccagTcaagttgatgtacagctgac	11	8	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:196718135T>C	ENST00000312428.6	-	46	8813	c.8713A>G	c.(8713-8715)Act>Gct	p.T2905A		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2905					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ATATCCCCAGTCAAGTTGATG	0.502																																																0			2											119	117	118					2																	196718135		2000	4181	6181	196426380	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.8713A>G	2.37:g.196718135T>C	ENSP00000311273:p.Thr2905Ala		196426380	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.166154	0.57476	.	.	ENSG00000118997	ENST00000312428	T	0.73469	-0.75	5.55	5.55	0.83447	Dynein heavy chain, coiled coil stalk (1);	0.055612	0.64402	D	0.000001	D	0.83709	0.5313	M	0.82433	2.59	0.80722	D	1	P	0.51791	0.948	P	0.56648	0.803	T	0.82436	-0.0458	10	0.24483	T	0.36	.	15.8615	0.79026	0.0:0.0:0.0:1.0	.	2905	Q8WXX0	DYH7_HUMAN	A	2905	ENSP00000311273:T2905A	ENSP00000311273:T2905A	T	-	1	0	DNAH7	196426380	1.000000	0.71417	0.998000	0.56505	0.096000	0.18686	7.793000	0.85851	2.333000	0.79357	0.533000	0.62120	ACT		0.502	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196718135	T	C	196718135	3	2	98	1	0	0	0	0	1	0	0	0	4617	1667	58	4	3441	4	DNAH7	2	196718135	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	19663347	196718135	46481238	20	26306										
ABI2	10152	hgsc.bcm.edu	37	chr2	204260401	204260401	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcagtgggagtagtggagggAgccacccaagtagtcggagc	18	8	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:204260401A>G	ENST00000422511.2	+	7	779	c.748A>G	c.(748-750)Agc>Ggc	p.S250G	RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000261017.5_Missense_Mutation_p.S244G|ABI2_ENST00000430418.1_Missense_Mutation_p.S195G|ABI2_ENST00000424558.1_Missense_Mutation_p.S244G|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000295851.5_Missense_Mutation_p.S250G|ABI2_ENST00000261016.6_Missense_Mutation_p.S199G|ABI2_ENST00000261018.7_Missense_Mutation_p.S36G			Q9NYB9	ABI2_HUMAN	abl-interactor 2	250	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						TAGTGGAGGGAGCCACCCAAG	0.483																																																0			2											171	149	157					2																	204260401		2203	4300	6503	203968646	SO:0001583	missense	10152			AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.748A>G	2.37:g.204260401A>G	ENSP00000396249:p.Ser250Gly		203968646	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	37		.	.	.	.	.	.	.	.	.	.	A	21.8	4.206513	0.79127	.	.	ENSG00000138443	ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511;ENST00000261018	T;T;T;T;T;T;T;T	0.55930	1.13;1.11;1.27;1.12;0.97;1.38;1.07;0.49	5.81	5.81	0.92471	.	0.111038	0.85682	D	0.000000	T	0.69033	0.3066	L	0.56769	1.78	0.80722	D	1	P;P;P;D;P;P;D;P;P	0.61080	0.924;0.924;0.805;0.989;0.954;0.924;0.982;0.924;0.725	P;P;P;D;D;P;D;P;P	0.74348	0.827;0.827;0.827;0.983;0.916;0.827;0.961;0.827;0.452	T	0.69168	-0.5216	10	0.48119	T	0.1	-3.4351	16.1713	0.81820	1.0:0.0:0.0:0.0	.	36;85;36;188;244;195;199;250;244	B7Z5L1;B7Z612;B4DMM5;B7Z836;Q9NYB9-4;E9PEZ7;Q9NYB9-3;Q9NYB9;Q9NYB9-2	.;.;.;.;.;.;.;ABI2_HUMAN;.	G	250;244;195;244;199;250;250;36	ENSP00000295851:S250G;ENSP00000261017:S244G;ENSP00000408898:S195G;ENSP00000391433:S244G;ENSP00000261016:S199G;ENSP00000414703:S250G;ENSP00000396249:S250G;ENSP00000261018:S36G	ENSP00000261016:S199G	S	+	1	0	ABI2	203968646	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.723000	0.91458	2.221000	0.72209	0.528000	0.53228	AGC		0.483	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		G	204260401	A	G	204260401	3	3	98	1	0	0	0	0	1	0	0	0	89	304	11	4	752	4	ABI2	2	204260401	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	7542266	204260401	38938972	21	26307										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220423001	220423001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgtggggcagggtcagggtgCgggtgggcccctcggcaccc	20	13	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:220423001C>T	ENST00000404537.1	-	10	3463	c.3407G>A	c.(3406-3408)cGc>cAc	p.R1136H	OBSL1_ENST00000265317.5_Missense_Mutation_p.R127H|OBSL1_ENST00000603926.1_Missense_Mutation_p.R1136H|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000373876.1_Missense_Mutation_p.R1136H|OBSL1_ENST00000265318.4_Intron	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1136	Ig-like 9.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGTCAGGGTGCGGGTGGGCCC	0.667																																																0			2																																								220131245	SO:0001583	missense	23363			BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.3407G>A	2.37:g.220423001C>T	ENSP00000385636:p.Arg1136His		220131245	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.78|16.78	3.217616|3.217616	0.58560|0.58560	.|.	.|.	ENSG00000124006|ENSG00000124006	ENST00000456147|ENST00000404537;ENST00000373876;ENST00000265317	.|T;T;T	.|0.66280	.|-0.2;-0.2;-0.2	4.47|4.47	4.47|4.47	0.54385|0.54385	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.54663|0.54663	0.1872|0.1872	L|L	0.38531|0.38531	1.155|1.155	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.45396	.|0.857;0.583;0.603	.|B;B;B	.|0.43251	.|0.326;0.394;0.413	T|T	0.51576|0.51576	-0.8688|-0.8688	5|9	.|0.17832	.|T	.|0.49	.|.	17.3271|17.3271	0.87252|0.87252	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1137;1136;127	.|A4KVA4;O75147;E7ER99	.|.;OBSL1_HUMAN;.	T|H	130|1136;1136;127	.|ENSP00000385636:R1136H;ENSP00000362983:R1136H;ENSP00000265317:R127H	.|ENSP00000265317:R127H	A|R	-|-	1|2	0|0	OBSL1|OBSL1	220131245|220131245	0.998000|0.998000	0.40836|0.40836	0.996000|0.996000	0.52242|0.52242	0.658000|0.658000	0.38924|0.38924	4.520000|4.520000	0.60524|0.60524	2.322000|2.322000	0.78497|0.78497	0.313000|0.313000	0.20887|0.20887	GCA|CGC		0.667	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			T	220423001	C	T	220423001	3	4	98	1	0	0	0	0	1	0	0	0	10844	768	27	1	2354	1	OBSL1	2	220423001	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	16162600	220423001	22776372	22	26308										
AGAP1	116987	hgsc.bcm.edu	37	chr2	237029022	237029022	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aacgagacctgcggggagggAgacggccgcacggcgctgca	18	12	0	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:237029022A>G	ENST00000304032.8	+	17	2881	c.2301A>G	c.(2299-2301)ggA>ggG	p.G767G	AGAP1_ENST00000336665.5_Silent_p.G714G|AGAP1_ENST00000409538.1_Silent_p.G979G|AGAP1_ENST00000428334.2_Silent_p.G606G	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	767					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						GCGGGGAGGGAGACGGCCGCA	0.711																																																0			2											39	43	42					2																	237029022		2194	4282	6476	236693761	SO:0001819	synonymous_variant	116987			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.2301A>G	2.37:g.237029022A>G			236693761	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Silent	SNP	ENST00000304032.8	37	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	A	8.425	0.847395	0.17034	.	.	ENSG00000157985	ENST00000453371	.	.	.	4.61	-9.23	0.00672	.	.	.	.	.	T	0.46927	0.1418	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59841	-0.7378	4	.	.	.	.	7.8321	0.29349	0.3675:0.1327:0.4434:0.0563	.	.	.	.	G	169	.	.	R	+	1	2	AGAP1	236693761	0.000000	0.05858	0.075000	0.20258	0.881000	0.50899	-6.347000	0.00069	-3.755000	0.00111	-0.425000	0.05940	AGA		0.711	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		G	237029022	A	G	237029022	2	3	98	1	0	0	0	0	0	0	0	1	366	291	11	4		4	AGAP1	2	237029022	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	16606021	237029022	6170351	23	26309										
C2orf54	79919	hgsc.bcm.edu	37	chr2	241827798	241827798	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgccttgagcccggagccgaTgcgcggcggggggctgcggc	20	14	0	1	rs11899555	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr2:241827798T>C	ENST00000388934.4	-	4	1320	c.1162A>G	c.(1162-1164)Atc>Gtc	p.I388V	C2orf54_ENST00000307486.8_Missense_Mutation_p.I239V|C2orf54_ENST00000402775.2_Missense_Mutation_p.I220V	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	388										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		CCGGAGCCGATGCGCGGCGGG	0.711													T|||	1192	0.238019	0.5356	0.0994	5008	,	,		10641	0.1766		0.0954	False		,,,				2504	0.1442															0			2						T	VAL/ILE,VAL/ILE	1174,2058		185,804,627	4	5	5		1162,658	-5.4	0	2	dbSNP_120	5	504,6652		22,460,3096	yes	missense,missense	C2orf54	NM_001085437.1,NM_024861.2	29,29	207,1264,3723	CC,CT,TT		7.043,36.3243,16.1533	benign,benign	388/448,220/280	241827798	1678,8710	1616	3578	5194	241476471	SO:0001583	missense	79919			AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.1162A>G	2.37:g.241827798T>C	ENSP00000373586:p.Ile388Val		241476471	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	37	CCDS42839.1	443	0.20283882783882784	254	0.516260162601626	34	0.09392265193370165	81	0.14160839160839161	74	0.09762532981530343	T	4.846	0.157297	0.09236	0.363243	0.07043	ENSG00000172478	ENST00000402775;ENST00000307486;ENST00000388934	T;T;T	0.42900	0.96;1.52;1.54	4.61	-5.43	0.02632	.	0.927650	0.08993	N	0.864092	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.48186	-0.9057	9	0.87932	D	0	0.0087	6.4354	0.21821	0.0:0.3174:0.3681:0.3145	rs11899555	388;239;220	Q08AI8;B3KU29;Q08AI8-3	CB054_HUMAN;.;.	V	220;239;388	ENSP00000385338:I220V;ENSP00000302779:I239V;ENSP00000373586:I388V	ENSP00000302779:I239V	I	-	1	0	C2orf54	241476471	0.000000	0.05858	0.013000	0.15412	0.076000	0.17211	-0.609000	0.05635	-0.841000	0.04200	0.477000	0.44152	ATC		0.711	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		C	241827798	T	C	241827798	3	2	98	1	0	0	0	0	1	0	0	0	2181	1464	51	4	189	4	C2orf54	2	241827798	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	4798776	241827798	1371575	24	26310										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4842276	4842276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccacgttgtttcttctgggcGctttcaatgtaagtgtgaat	10	8	3	1	rs201144431		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:4842276G>A	ENST00000443694.2	+	51	7054	c.7054G>A	c.(7054-7056)Gct>Act	p.A2352T	ITPR1_ENST00000456211.2_Missense_Mutation_p.A2304T|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000423119.2_Missense_Mutation_p.A2319T|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.A2352T|ITPR1_ENST00000302640.8_Missense_Mutation_p.A2352T|ITPR1_ENST00000357086.4_Missense_Mutation_p.A2319T			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2367					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.A2304T(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TCTTCTGGGCGCTTTCAATGT	0.478													G|||	0	0	0	0	5008	,	,		20301	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	3						G	THR/ALA,THR/ALA,THR/ALA	0,3800		0,0,1900	104	100	101		6955,7054,6910	5.1	1	3		101	10,8232		0,10,4111	yes	missense,missense,missense	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	58,58,58	0,10,6011	AA,AG,GG		0.1213,0.0,0.083	benign,benign,benign	2319/2711,2352/2744,2304/2696	4842276	10,12032	1900	4121	6021	4817276	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7054G>A	3.37:g.4842276G>A	ENSP00000401671:p.Ala2352Thr		4817276	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253886	0.59212	0.0	0.001213	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	5.1	5.1	0.69264	Ion transport (1);	0.053458	0.85682	D	0.000000	D	0.95667	0.8591	L	0.31476	0.935	0.80722	D	1	P;B	0.40180	0.705;0.053	B;B	0.38264	0.269;0.013	D	0.95034	0.8172	10	0.21540	T	0.41	.	18.8652	0.92289	0.0:0.0:1.0:0.0	.	2367;2319	Q14643;G5E9P1	ITPR1_HUMAN;.	T	2367;2352;2352;2319;813;2319;2304;2352	ENSP00000306253:A2352T;ENSP00000346595:A2352T;ENSP00000405934:A2319T;ENSP00000349597:A2319T;ENSP00000397885:A2304T;ENSP00000401671:A2352T	ENSP00000306253:A2352T	A	+	1	0	ITPR1	4817276	1.000000	0.71417	0.994000	0.49952	0.940000	0.58332	9.338000	0.96553	2.535000	0.85469	0.591000	0.81541	GCT		0.478	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4842276	G	A	4842276	3	1	98	1	0	0	0	0	1	0	0	0	7941	1087	38	1	7305	1	ITPR1	3	4842276	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10		4842276	193180154	25	26311										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10106487	10106487	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggatgggattgccataaaccTcctgccgctgctgttttctc	10	12	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:10106487T>C	ENST00000419585.1	+	23	2257	c.2096T>C	c.(2095-2097)cTc>cCc	p.L699P	FANCD2_ENST00000383807.1_Missense_Mutation_p.L699P|FANCD2_ENST00000383806.1_Missense_Mutation_p.L699P|FANCD2_ENST00000287647.3_Missense_Mutation_p.L699P			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	699					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCCATAAACCTCCTGCCGCTG	0.463			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	0			3											96	106	102					3																	10106487		2203	4300	6503	10081487	SO:0001583	missense	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2096T>C	3.37:g.10106487T>C	ENSP00000398754:p.Leu699Pro		10081487	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	T	15.64	2.892685	0.52121	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.62105	0.05;0.05;0.05;0.05	5.65	5.65	0.86999	.	0.059519	0.64402	D	0.000002	T	0.79587	0.4471	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.82481	-0.0436	10	0.87932	D	0	.	14.1569	0.65424	0.0:0.0:0.0:1.0	.	699;699	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	P	699	ENSP00000287647:L699P;ENSP00000373318:L699P;ENSP00000373317:L699P;ENSP00000398754:L699P	ENSP00000287647:L699P	L	+	2	0	FANCD2	10081487	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	6.697000	0.74603	2.293000	0.77203	0.477000	0.44152	CTC		0.463	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10106487	T	C	10106487	3	2	98	1	0	0	0	0	1	0	0	0	5684	1551	54	4	2182	4	FANCD2	3	10106487	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	5264211	10106487	187915943	26	26312										
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21706484	21706484	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaggaggggctggtggacggAcaagggccgggagagcagga	22	6	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:21706484A>G	ENST00000281523.2	-	2	577	c.59T>C	c.(58-60)gTc>gCc	p.V20A	ZNF385D_ENST00000494118.1_Intron	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	20						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						TGGTGGACGGACAAGGGCCGG	0.522																																																0			3											76	71	72					3																	21706484		2203	4300	6503	21681488	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.59T>C	3.37:g.21706484A>G	ENSP00000281523:p.Val20Ala		21681488		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.725243	0.30593	.	.	ENSG00000151789	ENST00000281523	T	0.33216	1.42	5.62	5.62	0.85841	.	0.130120	0.50627	D	0.000112	T	0.29620	0.0739	L	0.44542	1.39	0.36111	D	0.844831	B	0.22541	0.071	B	0.20184	0.028	T	0.26677	-1.0096	10	0.56958	D	0.05	2.3122	14.9882	0.71365	1.0:0.0:0.0:0.0	.	20	Q9H6B1	Z385D_HUMAN	A	20	ENSP00000281523:V20A	ENSP00000281523:V20A	V	-	2	0	ZNF385D	21681488	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.736000	0.74811	2.141000	0.66446	0.482000	0.46254	GTC		0.522	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		G	21706484	A	G	21706484	3	3	98	1	0	0	0	0	1	0	0	0	17917	275	10	4	1156	4	ZNF385D	3	21706484	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	11599997	21706484	176315946	27	26313										
QRICH1	54870	hgsc.bcm.edu	37	chr3	49094428	49094437	+	Frame_Shift_Del	DEL	ACAGCCTGCA	ACAGCCTGCA	-													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tattctggtacgtgcctgccAcagcctgcacagccactgga					rs576649534		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	ACAGCCTGCA	ACAGCCTGCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:49094428_49094437delACAGCCTGCA	ENST00000395443.2	-	3	1668_1677	c.1196_1205delTGCAGGCTGT	c.(1195-1206)gtgcaggctgtgfs	p.VQAV399fs	QRICH1_ENST00000424300.1_Frame_Shift_Del_p.VQAV399fs|QRICH1_ENST00000357496.2_Frame_Shift_Del_p.VQAV399fs|QRICH1_ENST00000479449.1_5'UTR	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	399	Gln-rich.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CGTGCCTGCCACAGCCTGCACAGCCACTGG	0.529																																																0			3																																								49069441	SO:0001589	frameshift_variant	54870				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1196_1205delTGCAGGCTGT	3.37:g.49094428_49094437delACAGCCTGCA	ENSP00000378830:p.Val399fs		49069432	Q4G0F7|Q7L621|Q8TEA5	Frame_Shift_Del	DEL	ENST00000395443.2	37	CCDS2787.1																																																																																				0.529	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		-	49094437	ACAGCCTGCA	-	49094428	7	5	98	1	0	1	0	1	0	0	0	0	12916	159	6	0	1157	0	QRICH1	3	49094428	Frame_Shift_Del	DEL	ACAGCCTGCA	TCGA-DC-6160-01A-11D-1657-10	27387944	49094428	148928002	28	26314										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52404598	52404598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgggtgccactggggacagcAgtggccgcaccagtttcagc	15	12	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:52404598A>G	ENST00000420323.2	+	40	6625	c.6364A>G	c.(6364-6366)Agt>Ggt	p.S2122G		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2122					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				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)		TGGGGACAGCAGTGGCCGCAC	0.587																																																0			3											31	34	33					3																	52404598		1978	4146	6124	52379638	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.6364A>G	3.37:g.52404598A>G	ENSP00000401514:p.Ser2122Gly		52379638	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	11.49	1.654667	0.29425	.	.	ENSG00000114841	ENST00000420323	T	0.23754	1.89	4.61	-7.43	0.01383	.	4.036830	0.00837	N	0.001703	T	0.18002	0.0432	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29882	-0.9997	10	0.45353	T	0.12	.	9.793	0.40717	0.4239:0.4361:0.14:0.0	.	2122	C9JXH6	.	G	2122	ENSP00000401514:S2122G	ENSP00000401514:S2122G	S	+	1	0	DNAH1	52379638	0.000000	0.05858	0.001000	0.08648	0.324000	0.28378	-1.762000	0.01803	-0.955000	0.03636	-0.415000	0.06103	AGT		0.587	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52404598	A	G	52404598	3	3	98	1	0	0	0	0	1	0	0	0	4608	188	7	4	6518	4	DNAH1	3	52404598	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	3310170	52404598	145617832	29	26315										
GXYLT2	727936	hgsc.bcm.edu	37	chr3	73016713	73016713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	accagagtgtctctatgtatTcccctgccagtggaactacc	8	13	1	1	rs78135180		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:73016713T>C	ENST00000389617.4	+	6	1153	c.992T>C	c.(991-993)tTc>tCc	p.F331S		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	331					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						CTCTATGTATTCCCCTGCCAG	0.493																																																0			3											78	76	76					3																	73016713		1995	4190	6185	73099403	SO:0001583	missense	0			AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"Glycosyltransferase family 8 domain containing"	33383	protein-coding gene	gene with protein product		613322	"glycosyltransferase 8 domain containing 4"	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.992T>C	3.37:g.73016713T>C	ENSP00000374268:p.Phe331Ser		73099403		Missense_Mutation	SNP	ENST00000389617.4	37	CCDS46870.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614776	0.87359	.	.	ENSG00000172986	ENST00000389617;ENST00000491839	T;T	0.22539	1.95;1.95	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.49643	0.1569	M	0.83692	2.655	0.80722	D	1	D	0.61697	0.99	D	0.67103	0.949	T	0.55842	-0.8077	10	0.72032	D	0.01	.	15.928	0.79635	0.0:0.0:0.0:1.0	.	331	A0PJZ3	GXLT2_HUMAN	S	331;92	ENSP00000374268:F331S;ENSP00000420426:F92S	ENSP00000374268:F331S	F	+	2	0	GXYLT2	73099403	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.800000	0.85949	2.221000	0.72209	0.455000	0.32223	TTC		0.493	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393		C	73016713	T	C	73016713	3	2	98	1	0	0	0	0	1	0	0	0	6925	1783	62	4	1014	4	GXYLT2	3	73016713	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	20612115	73016713	125005717	30	26316										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706487	96706487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgagagttttacccagatggAtttgggtgatcgcatcctca	11	8	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:96706487A>G	ENST00000389672.5	+	3	802	c.764A>G	c.(763-765)gAt>gGt	p.D255G	EPHA6_ENST00000542517.1_Missense_Mutation_p.D161G|EPHA6_ENST00000470610.2_Missense_Mutation_p.D255G	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	161						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						ACCCAGATGGATTTGGGTGAT	0.423																																																0			3											196	203	200					3																	96706487		1900	4131	6031	98189177	SO:0001583	missense	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.764A>G	3.37:g.96706487A>G	ENSP00000374323:p.Asp255Gly		98189177	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124470	0.77436	.	.	ENSG00000080224	ENST00000470610;ENST00000389672;ENST00000542517	T;T;T	0.10192	2.9;2.9;2.9	5.48	5.48	0.80851	.	0.000000	0.64402	U	0.000002	T	0.35913	0.0948	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.19516	-1.0303	10	0.87932	D	0	.	14.7559	0.69564	1.0:0.0:0.0:0.0	.	255;255	B3KS12;E7EU71	.;.	G	255;255;161	ENSP00000420598:D255G;ENSP00000374323:D255G;ENSP00000439758:D161G	ENSP00000374323:D255G	D	+	2	0	EPHA6	98189177	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	9.339000	0.96797	2.066000	0.61787	0.533000	0.62120	GAT		0.423	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		G	96706487	A	G	96706487	3	3	98	1	0	0	0	0	1	0	0	0	5184	333	12	4	774	4	EPHA6	3	96706487	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	23689774	96706487	101315943	31	26317										
TFG	10342	hgsc.bcm.edu	37	chr3	100467198	100467198	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cctactaattatactgtggcTcctgcctctcaacctggaat	6	13	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:100467198T>C	ENST00000240851.4	+	8	1366	c.1026T>C	c.(1024-1026)gcT>gcC	p.A342A	TFG_ENST00000490574.1_Silent_p.A342A|TFG_ENST00000418917.2_Silent_p.A338A|TFG_ENST00000481203.1_3'UTR|TFG_ENST00000476228.1_Silent_p.A338A	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	342					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						ATACTGTGGCTCCTGCCTCTC	0.517			T	"NTRK1, ALK"	"papillary thyroid, ALCL, NSCLC"																																		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"E, L"	0			3											76	78	77					3																	100467198		2203	4300	6503	101949888	SO:0001819	synonymous_variant	10342			BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.1026T>C	3.37:g.100467198T>C			101949888	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1	.	.	.	.	.	.	.	.	.	.	T	5.539	0.284441	0.10513	.	.	ENSG00000114354	ENST00000443578	.	.	.	6.16	4.36	0.52297	.	.	.	.	.	T	0.63153	0.2487	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64188	-0.6466	5	0.87932	D	0	0.0058	6.5823	0.22602	0.0:0.6542:0.1302:0.2156	.	.	.	.	P	338	.	ENSP00000409727:L338P	L	+	2	0	TFG	101949888	0.998000	0.40836	1.000000	0.80357	0.987000	0.75469	0.448000	0.21726	0.898000	0.36418	-0.248000	0.11899	CTC		0.517	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070		C	100467198	T	C	100467198	2	2	98	1	0	0	0	0	0	0	0	1	15845	1538	54	4		4	TFG	3	100467198	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	3760711	100467198	97555232	32	26318										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100988374	100988374	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tttacctaaattcaagtacaCgaatttccttgtagcctggt	6	9	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:100988374C>T	ENST00000193391.7	-	8	1059	c.872G>A	c.(871-873)cGt>cAt	p.R291H		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	291	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TTCAAGTACACGAATTTCCTT	0.269																																																0			3											70	69	69					3																	100988374		2203	4289	6492	102471064	SO:0001583	missense	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.872G>A	3.37:g.100988374C>T	ENSP00000193391:p.Arg291His		102471064	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	1.238	-0.622288	0.03636	.	.	ENSG00000081148	ENST00000193391	T	0.39406	1.08	5.96	-5.92	0.02261	SEA (2);	0.935231	0.09185	N	0.836948	T	0.22551	0.0544	N	0.17082	0.46	0.18873	N	0.999983	B;B	0.18610	0.029;0.029	B;B	0.10450	0.005;0.003	T	0.41574	-0.9501	10	0.07990	T	0.79	0.8834	15.6188	0.76790	0.0:0.3222:0.0:0.6778	.	291;291	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	H	291	ENSP00000193391:R291H	ENSP00000193391:R291H	R	-	2	0	IMPG2	102471064	0.535000	0.26370	0.027000	0.17364	0.778000	0.44026	-0.507000	0.06352	-1.186000	0.02713	0.655000	0.94253	CGT		0.269	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			T	100988374	C	T	100988374	3	4	98	1	0	0	0	0	1	0	0	0	7750	536	19	1	2901	1	IMPG2	3	100988374	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	521176	100988374	97034056	33	26319										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126142435	126142435	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tccagaacagccaggagacgGagaagaccctggaggagctg	15	10	0	4	rs140223152|rs398102320|rs35657615|rs200815085	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:126142435G>A	ENST00000352312.1	+	13	1333	c.1234G>A	c.(1234-1236)Gag>Aag	p.E412K	CCDC37_ENST00000505024.1_Missense_Mutation_p.E413K|CCDC37_ENST00000393425.1_Missense_Mutation_p.E413K	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	412				Missing (in Ref. 3; AAI01370/AAI01368). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		CCAGGAGACGGAGAAGACCCT	0.612													G|||	1	0.000199681	0	0.0014	5008	,	,		17029	0		0	False		,,,				2504	0															0			3											109	83	92					3																	126142435		2200	4257	6457	127625125	SO:0001583	missense	348807			AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1234G>A	3.37:g.126142435G>A	ENSP00000344749:p.Glu412Lys		127625125	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	37	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295376	0.81025	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.41400	1.0;1.0;1.0	4.93	4.93	0.64822	.	0.159668	0.53938	D	0.000054	T	0.66015	0.2747	M	0.83384	2.64	0.58432	D	0.999999	D;D	0.69078	0.997;0.996	D;P	0.66716	0.946;0.884	T	0.71137	-0.4680	10	0.56958	D	0.05	-35.5644	15.657	0.77144	0.0:0.0:1.0:0.0	.	413;412	Q494V2-2;Q494V2	.;CCD37_HUMAN	K	412;413;413	ENSP00000344749:E412K;ENSP00000377076:E413K;ENSP00000423046:E413K	ENSP00000344749:E412K	E	+	1	0	CCDC37	127625125	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	6.860000	0.75473	2.284000	0.76573	0.491000	0.48974	GAG		0.612	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126142435	G	A	126142435	3	1	98	1	0	0	0	0	1	0	0	0	2815	1175	41	3	1280	3	CCDC37	3	126142435	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	25154061	126142435	71879995	34	26320										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134851696	134851696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaaagtgccgggcagaccgcCggagctgctcccgctgtgac	14	14	0	2	rs576710309	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:134851696C>T	ENST00000398015.3	+	5	1472	c.1102C>T	c.(1102-1104)Cgg>Tgg	p.R368W	EPHB1_ENST00000493838.1_5'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	368	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GGCAGACCGCCGGAGCTGCTC	0.622													C|||	2	0.000399361	8e-04	0	5008	,	,		19081	0		0.001	False		,,,				2504	0															0			3											40	46	44					3																	134851696		2194	4291	6485	136334386	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1102C>T	3.37:g.134851696C>T	ENSP00000381097:p.Arg368Trp		136334386	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.662017	0.88251	.	.	ENSG00000154928	ENST00000398015	T	0.49432	0.78	5.41	3.55	0.40652	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.67655	0.2916	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71069	-0.4699	10	0.87932	D	0	.	14.2335	0.65908	0.2725:0.7275:0.0:0.0	.	368	P54762	EPHB1_HUMAN	W	368	ENSP00000381097:R368W	ENSP00000381097:R368W	R	+	1	2	EPHB1	136334386	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.374000	0.44274	0.587000	0.29643	0.655000	0.94253	CGG		0.622	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		T	134851696	C	T	134851696	3	4	98	1	0	0	0	0	1	0	0	0	5187	643	23	1	1120	1	EPHB1	3	134851696	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	8709261	134851696	63170734	35	26321										
ATR	545	hgsc.bcm.edu	37	chr3	142215235	142215235	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccactttgccctttccacgtAcagttcagcgagtcgtgatt	8	13	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:142215235A>G	ENST00000350721.4	-	34	5987	c.5866T>C	c.(5866-5868)Tac>Cac	p.Y1956H	ATR_ENST00000383101.3_Missense_Mutation_p.Y1892H	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1956	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTTTCCACGTACAGTTCAGCG	0.418								Other conserved DNA damage response genes																																								0			3											141	116	125					3																	142215235		2203	4300	6503	143697925	SO:0001583	missense	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5866T>C	3.37:g.142215235A>G	ENSP00000343741:p.Tyr1956His		143697925	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758042	0.31137	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.65916	-0.18;-0.18	5.78	4.63	0.57726	PIK-related kinase (1);Tetratricopeptide-like helical (1);PIK-related kinase, FAT (1);	0.343185	0.31279	N	0.007930	T	0.39886	0.1095	N	0.12637	0.245	0.37478	D	0.915864	B	0.15930	0.015	B	0.23716	0.048	T	0.26503	-1.0101	10	0.20046	T	0.44	-3.09	6.7266	0.23361	0.7934:0.0:0.0711:0.1355	.	1956	Q13535	ATR_HUMAN	H	1956;1892	ENSP00000343741:Y1956H;ENSP00000372581:Y1892H	ENSP00000343741:Y1956H	Y	-	1	0	ATR	143697925	0.999000	0.42202	0.886000	0.34754	0.990000	0.78478	4.137000	0.58010	1.024000	0.39682	0.533000	0.62120	TAC		0.418	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		G	142215235	A	G	142215235	3	3	98	1	0	0	0	0	1	0	0	0	1205	391	14	4	2124	4	ATR	3	142215235	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	7363539	142215235	55807195	36	26322										
WDR49	151790	hgsc.bcm.edu	37	chr3	167322162	167322162	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttgaaggatgtcatattaagAcgcttttttgatttctctct	7	6	3	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:167322162A>G	ENST00000308378.3	-	2	335	c.30T>C	c.(28-30)cgT>cgC	p.R10R	WDR49_ENST00000479765.1_Silent_p.R351R|WDR49_ENST00000453925.2_Silent_p.R63R	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	10			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.							breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TCATATTAAGACGCTTTTTTG	0.358																																																0			3											155	152	153					3																	167322162		2203	4300	6503	168804856	SO:0001819	synonymous_variant	151790			AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.30T>C	3.37:g.167322162A>G			168804856	Q8N297	Silent	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	A	0.201	-1.044951	0.01997	.	.	ENSG00000174776	ENST00000472600	.	.	.	5.36	1.31	0.21738	.	.	.	.	.	T	0.24509	0.0594	.	.	.	0.19300	N	0.999972	.	.	.	.	.	.	T	0.23119	-1.0197	4	.	.	.	.	4.2442	0.10663	0.6656:0.1361:0.0803:0.118	.	.	.	.	A	75	.	.	V	-	2	0	WDR49	168804856	0.038000	0.19896	0.917000	0.36280	0.006000	0.05464	0.238000	0.18004	0.343000	0.23821	0.533000	0.62120	GTC		0.358	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		G	167322162	A	G	167322162	2	3	98	1	0	0	0	0	0	0	0	1	17342	262	10	4		4	WDR49	3	167322162	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	25106927	167322162	30700268	37	26323										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952092	178952092	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atgaatgatgcacatcatggTggctggacaacaaaaatgga	11	6	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:178952092T>C	ENST00000263967.3	+	21	3304	c.3147T>C	c.(3145-3147)ggT>ggC	p.G1049G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1049	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		G -> S (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.G1049G(9)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CACATCATGGTGGCTGGACAA	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	9	Substitution - coding silent(9)	large_intestine(8)|ovary(1)	3											98	88	91					3																	178952092		1917	4132	6049	180434786	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3147T>C	3.37:g.178952092T>C			180434786	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178952092	T	C	178952092	2	2	98	1	0	0	0	0	0	0	0	1	11944	1683	59	4		4	PIK3CA	3	178952092	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	11629930	178952092	19070338	38	26324										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952152	178952152	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaacagcatgcattgaactgAaaagataactgagaaaatga	8	5	0	5			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:178952152A>G	ENST00000263967.3	+	21	3364	c.3207A>G	c.(3205-3207)tgA>tgG	p.*1069W	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	0					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.*1069_*1069insWKDN*(3)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CATTGAACTGAAAAGATAACT	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Insertion - In frame(3)	endometrium(2)|ovary(1)	3											79	71	74					3																	178952152		1897	4138	6035	180434846	SO:0001578	stop_lost	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3207A>G	3.37:g.178952152A>G	ENSP00000263967:p.*1069Trpext*4		180434846	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.351538	0.41700	.	.	ENSG00000121879	ENST00000263967	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.20563	N	0.999881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3945	0.83586	1.0:0.0:0.0:0.0	.	.	.	.	W	1069	.	.	X	+	3	0	PIK3CA	180434846	1.000000	0.71417	0.971000	0.41717	0.917000	0.54804	8.526000	0.90588	2.265000	0.75225	0.482000	0.46254	TGA		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952152	A	G	178952152	4	3	98	1	0	0	0	0	0	0	0	0	11944	259	9	4	3285	4	PIK3CA	3	178952152	Nonstop_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	60	178952152	19070278	39	26325										
FAM43A	131583	hgsc.bcm.edu	37	chr3	194408704	194408704	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgggtgacgcgcctgctgtcAggcgacagcacgggcagcga	17	13	1	1	rs4677673	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:194408704A>G	ENST00000329759.4	+	1	2083	c.1149A>G	c.(1147-1149)tcA>tcG	p.S383S		NM_153690.4	NP_710157.2	Q8N2R8	FA43A_HUMAN	family with sequence similarity 43, member A	383										breast(2)|central_nervous_system(1)|lung(6)|skin(1)	10	all_cancers(143;2.04e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.147)	OV - Ovarian serous cystadenocarcinoma(49;8.37e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.78e-05)		GCCTGCTGTCAGGCGACAGCA	0.711													G|||	3580	0.714856	0.8116	0.6282	5008	,	,		12995	0.7728		0.6262	False		,,,				2504	0.6769															0			3						G		3248,806		1308,632,87	10	11	10		1149	-6.1	0.5	3	dbSNP_111	10	5248,2772		1743,1762,505	no	coding-synonymous	FAM43A	NM_153690.4		3051,2394,592	GG,GA,AA		34.5636,19.8816,29.6339		383/424	194408704	8496,3578	2027	4010	6037	195889993	SO:0001819	synonymous_variant	131583			AK074503	CCDS33923.1	3q29	2004-07-28			ENSG00000185112	ENSG00000185112			26888	protein-coding gene	gene with protein product						12477932	Standard	NM_153690		Approved	FLJ90022	uc003fuj.3	Q8N2R8	OTTHUMG00000156016	ENST00000329759.4:c.1149A>G	3.37:g.194408704A>G			195889993	A3KME2|Q8IXP4|Q8WZ07	Silent	SNP	ENST00000329759.4	37	CCDS33923.1																																																																																				0.711	FAM43A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342734.1	NM_153690		G	194408704	A	G	194408704	2	3	98	1	0	0	0	0	0	0	0	1	5581	175	7	4		4	FAM43A	3	194408704	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	15456552	194408704	3613726	40	26326										
PAK2	5062	hgsc.bcm.edu	37	chr3	196530013	196530013	+	Silent	SNP	A	A	G													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tccaacacagtgaagcagaaAtatctgagctttactcctcc					rs73205842	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:196530013A>G	ENST00000327134.3	+	4	736	c.414A>G	c.(412-414)aaA>aaG	p.K138K		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	138					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	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)		TGAAGCAGAAATATCTGAGCT	0.418																																																0			3											92	84	87					3																	196530013		2203	4300	6503	198014410	SO:0001819	synonymous_variant	5586			U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.414A>G	3.37:g.196530013A>G			198014410	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																				0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		G	196530013	A	G	196530013	2	3	98	1	0	0	0	0	0	0	0	1	11432	98	4	4		4	PAK2	3	196530013	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2121309	196530013	1492417	41	26327	39	2								
PAK2	5062	hgsc.bcm.edu	37	chr3	196530022	196530022	+	Silent	SNP	C	C	T													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gtgaagcagaaatatctgagCtttactcctcctggtaagag					rs115224945	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr3:196530022C>T	ENST00000327134.3	+	4	745	c.423C>T	c.(421-423)agC>agT	p.S141S		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	141					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	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)		AATATCTGAGCTTTACTCCTC	0.418																																																0			3											85	79	81					3																	196530022		2203	4300	6503	198014419	SO:0001819	synonymous_variant	5586			U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.423C>T	3.37:g.196530022C>T			198014419	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																				0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		T	196530022	C	T	196530022	2	4	98	1	0	0	0	0	0	0	0	1	11432	796	28	3		3	PAK2	3	196530022	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	9	196530022	1492408	42	26328	39	2								
SLC2A9	56606	hgsc.bcm.edu	37	chr4	9836573	9836573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gacggtgcctgcaatgatgaAggcagccggccgctgagatt	15	10	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr4:9836573A>G	ENST00000264784.3	-	11	1404	c.1351T>C	c.(1351-1353)Ttc>Ctc	p.F451L	SLC2A9_ENST00000309065.3_Missense_Mutation_p.F422L|SLC2A9_ENST00000506583.1_Missense_Mutation_p.F422L	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	451					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	GCAATGATGAAGGCAGCCGGC	0.527																																																0			4											74	66	69					4																	9836573		2203	4300	6503	9445671	SO:0001583	missense	56606			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"Solute carriers"	13446	protein-coding gene	gene with protein product	"urate voltage-driven efflux transporter 1"	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.1351T>C	4.37:g.9836573A>G	ENSP00000264784:p.Phe451Leu		9445671	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833881	0.71258	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.44083	0.93;0.93;0.93	5.27	5.27	0.74061	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	M	0.64567	1.98	0.42479	D	0.992856	P;P	0.46578	0.498;0.88	B;P	0.56865	0.253;0.808	T	0.60131	-0.7323	10	0.62326	D	0.03	.	13.1238	0.59342	1.0:0.0:0.0:0.0	.	422;451	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	L	422;451;422	ENSP00000422209:F422L;ENSP00000264784:F451L;ENSP00000311383:F422L	ENSP00000264784:F451L	F	-	1	0	SLC2A9	9445671	1.000000	0.71417	0.794000	0.32065	0.079000	0.17450	8.502000	0.90505	1.982000	0.57802	0.477000	0.44152	TTC		0.527	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			G	9836573	A	G	9836573	3	3	98	1	0	0	0	0	1	0	0	0	14589	72	3	4	279	4	SLC2A9	4	9836573	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10		9836573	181317703	43	26329										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153332662	153332662	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcatgttcttcatcttcctcTtgttcttcttggtttcctga	6	11	6	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr4:153332662T>C	ENST00000281708.4	-	2	1523	c.294A>G	c.(292-294)caA>caG	p.Q98Q	FBXW7_ENST00000604872.1_Silent_p.Q98Q|FBXW7_ENST00000603841.1_Silent_p.Q98Q|FBXW7_ENST00000603548.1_Silent_p.Q98Q	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	98					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)			NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CATCTTCCTCTTGTTCTTCTT	0.443			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	0			4											277	241	253					4																	153332662		2203	4300	6503	153552112	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.294A>G	4.37:g.153332662T>C			153552112	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.443	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153332662	T	C	153332662	2	2	98	1	0	0	0	0	0	0	0	1	5788	1606	56	4		4	FBXW7	4	153332662	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	143496089	153332662	37821614	44	26330										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	182337	182337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catctgatatcagagcctgcGtcgaggaagatgagccagag	13	9	2	5	rs368497309		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:182337G>A	ENST00000283426.6	+	18	3765	c.3715G>A	c.(3715-3717)Gtc>Atc	p.V1239I		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1239							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CAGAGCCTGCGTCGAGGAAGA	0.662																																																0			5						G	ILE/VAL	0,4406		0,0,2203	35	38	37		3715	-0.8	0	5		37	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLEKHG4B	NM_052909.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1239/1272	182337	1,13005	2203	4300	6503	235337	SO:0001583	missense	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3715G>A	5.37:g.182337G>A	ENSP00000283426:p.Val1239Ile		235337		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.211487	0.00289	0.0	1.16E-4	ENSG00000153404	ENST00000283426	T	0.24350	1.86	3.55	-0.756	0.11057	.	.	.	.	.	T	0.09468	0.0233	N	0.14661	0.345	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.35450	-0.9788	9	0.02654	T	1	.	2.6075	0.04882	0.5403:0.0:0.2457:0.2139	.	1239	Q96PX9	PKH4B_HUMAN	I	1239	ENSP00000283426:V1239I	ENSP00000283426:V1239I	V	+	1	0	PLEKHG4B	235337	0.999000	0.42202	0.001000	0.08648	0.081000	0.17604	1.874000	0.39568	-0.510000	0.06523	-1.583000	0.00853	GTC		0.662	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	182337	G	A	182337	3	1	98	1	0	0	0	0	1	0	0	0	12103	1145	40	1	3785	1	PLEKHG4B	5	182337	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10		182337	180732923	45	26331										
ADCY2	108	hgsc.bcm.edu	37	chr5	7802363	7802363	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cagtcctatgactgcgtctgCgtcatgtttgcctccattcc	8	14	2	1	rs2290910	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:7802363C>T	ENST00000338316.4	+	21	2750	c.2661C>T	c.(2659-2661)tgC>tgT	p.C887C	ADCY2_ENST00000537121.1_Silent_p.C707C	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	887					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						ACTGCGTCTGCGTCATGTTTG	0.483													C|||	1169	0.233427	0.1203	0.4164	5008	,	,		20942	0.2768		0.2644	False		,,,				2504	0.18															0			5						C		684,3722	288.4+/-279.8	53,578,1572	82	77	79		2661	-2.6	1	5	dbSNP_100	79	2285,6315	385.4+/-341.5	289,1707,2304	no	coding-synonymous	ADCY2	NM_020546.2		342,2285,3876	TT,TC,CC		26.5698,15.5243,22.8279		887/1092	7802363	2969,10037	2203	4300	6503	7855363	SO:0001819	synonymous_variant	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2661C>T	5.37:g.7802363C>T			7855363	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																				0.483	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7802363	C	T	7802363	2	4	98	1	0	0	0	0	0	0	0	1	294	776	27	1		1	ADCY2	5	7802363	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	7620026	7802363	173112897	46	26332										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13792154	13792154	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttcagcattccctgccagacCcgagaaagatctcgtaggtt	9	12	2	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:13792154C>A	ENST00000265104.4	-	50	8501	c.8397G>T	c.(8395-8397)cgG>cgT	p.R2799R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2799	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTGCCAGACCCGAGAAAGAT	0.413									Kartagener syndrome																																							0			5											81	78	79					5																	13792154		2203	4300	6503	13845154	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8397G>T	5.37:g.13792154C>A			13845154	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13792154	C	A	13792154	2	1	98	1	0	0	0	0	0	0	0	1	4615	610	22	2		2	DNAH5	5	13792154	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	5989791	13792154	167123106	47	26333										
RAI14	26064	hgsc.bcm.edu	37	chr5	34803835	34803835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aggacacagcgccttacatcTcgcagccaagaacagccacc	8	16	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:34803835T>C	ENST00000265109.3	+	5	562	c.275T>C	c.(274-276)cTc>cCc	p.L92P	RAI14_ENST00000397449.1_Missense_Mutation_p.L85P|RAI14_ENST00000515799.1_Missense_Mutation_p.L95P|RAI14_ENST00000428746.2_Missense_Mutation_p.L92P|RAI14_ENST00000503673.1_Missense_Mutation_p.L92P|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000512629.1_Missense_Mutation_p.L92P|RAI14_ENST00000506376.1_Missense_Mutation_p.L84P	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	92						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GCCTTACATCTCGCAGCCAAG	0.343																																																0			5											51	48	49					5																	34803835		2203	4300	6503	34839592	SO:0001583	missense	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.275T>C	5.37:g.34803835T>C	ENSP00000265109:p.Leu92Pro		34839592	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945578	0.73672	.	.	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	5.93	5.93	0.95920	Ankyrin repeat-containing domain (4);	.	.	.	.	D	0.82291	0.5005	M	0.84082	2.675	0.80722	D	1	D;D;D;D	0.61697	0.988;0.99;0.99;0.99	P;D;D;D	0.66847	0.885;0.916;0.935;0.947	D	0.85022	0.0912	9	0.87932	D	0	-2.1695	14.9508	0.71071	0.0:0.0:0.0:1.0	.	84;92;95;92	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	P	92;92;92;92;92;92;92;92;92;92;95;92;92;84;85	ENSP00000265109:L92P;ENSP00000424879:L92P;ENSP00000422112:L92P;ENSP00000422377:L92P;ENSP00000388725:L92P;ENSP00000421424:L92P;ENSP00000422942:L92P;ENSP00000422515:L92P;ENSP00000422114:L92P;ENSP00000424502:L92P;ENSP00000427123:L95P;ENSP00000426770:L92P;ENSP00000425115:L92P;ENSP00000423854:L84P;ENSP00000380591:L85P	ENSP00000265109:L92P	L	+	2	0	RAI14	34839592	1.000000	0.71417	0.850000	0.33497	0.992000	0.81027	5.810000	0.69179	2.271000	0.75665	0.533000	0.62120	CTC		0.343	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		C	34803835	T	C	34803835	3	2	98	1	0	0	0	0	1	0	0	0	13045	1551	54	4	354	4	RAI14	5	34803835	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	21011681	34803835	146111425	48	26334										
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74676952	74676952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tccctgctaatttcctggttTccctctggtgggcttaccaa	8	13	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:74676952T>C	ENST00000405807.4	-	16	2113	c.1692A>G	c.(1690-1692)ggA>ggG	p.G564G	COL4A3BP_ENST00000380494.5_Silent_p.G692G|COL4A3BP_ENST00000261415.7_Silent_p.G538G|COL4A3BP_ENST00000508692.1_Intron	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	564	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTTCCTGGTTTCCCTCTGGTG	0.373																																																0			5											235	211	219					5																	74676952		2203	4300	6503	74712708	SO:0001819	synonymous_variant	10087			AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1692A>G	5.37:g.74676952T>C			74712708	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	T	9.686	1.150508	0.21371	.	.	ENSG00000113163	ENST00000508809	.	.	.	5.91	3.44	0.39384	.	.	.	.	.	T	0.58409	0.2120	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51568	-0.8689	4	.	.	.	-0.0355	8.8989	0.35481	0.0:0.0639:0.3599:0.5761	.	.	.	.	E	66	.	.	K	-	1	0	COL4A3BP	74712708	0.444000	0.25649	0.998000	0.56505	0.992000	0.81027	-0.474000	0.06607	0.440000	0.26502	-0.332000	0.08345	AAA		0.373	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		C	74676952	T	C	74676952	2	2	98	1	0	0	0	0	0	0	0	1	3698	1770	62	4		4	COL4A3BP	5	74676952	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	39873117	74676952	106238308	49	26335										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80408616	80408616	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atcgtattttcactactgccGctgtggtgctggggaaactc	11	10	1	0	rs376549001		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:80408616G>T	ENST00000265080.4	+	14	2093	c.2026G>T	c.(2026-2028)Gct>Tct	p.A676S	CTD-2193P3.2_ENST00000508993.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	676	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A676T(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CACTACTGCCGCTGTGGTGCT	0.493																																																1	Substitution - Missense(1)	lung(1)	5						G	SER/ALA	0,4406		0,0,2203	154	148	150		2026	4	0	5		150	1,8599	1.2+/-3.3	0,1,4299	no	missense	RASGRF2	NM_006909.1	99	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	676/1238	80408616	1,13005	2203	4300	6503	80444372	SO:0001583	missense	5924			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2026G>T	5.37:g.80408616G>T	ENSP00000265080:p.Ala676Ser		80444372	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621822	0.28889	0.0	1.16E-4	ENSG00000113319	ENST00000265080	T	0.49720	0.77	5.79	3.99	0.46301	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.381137	0.32430	N	0.006112	T	0.32526	0.0832	L	0.36672	1.1	0.09310	N	1	B	0.26445	0.149	B	0.31686	0.134	T	0.25012	-1.0144	10	0.09843	T	0.71	.	5.9208	0.19080	0.2119:0.0:0.6539:0.1342	.	676	O14827	RGRF2_HUMAN	S	676	ENSP00000265080:A676S	ENSP00000265080:A676S	A	+	1	0	RASGRF2	80444372	0.004000	0.15560	0.042000	0.18584	0.852000	0.48524	0.522000	0.22909	0.789000	0.33779	0.558000	0.71614	GCT		0.493	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		T	80408616	G	T	80408616	3	4	98	1	0	0	0	0	1	0	0	0	13110	1087	38	2	2080	2	RASGRF2	5	80408616	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	5731664	80408616	100506644	50	26336										
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	98	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	31766015	112174631	68740629	51	26337										
APC	324	hgsc.bcm.edu	37	chr5	112175305	112175305	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	accaaatccagcagactgcaGggttctagtttatcttcaga	8	10	3	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:112175305G>A	ENST00000457016.1	+	16	4394	c.4014G>A	c.(4012-4014)caG>caA	p.Q1338Q	APC_ENST00000508376.2_Silent_p.Q1338Q|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.Q1338Q			P25054	APC_HUMAN	adenomatous polyposis coli	1338	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.L1337fs*76(4)|p.S1335fs*70(1)|p.K1192fs*3(1)|p.?(1)|p.V1326fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCAGACTGCAGGGTTCTAGTT	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	8	Deletion - Frameshift(7)|Unknown(1)	large_intestine(6)|soft_tissue(1)|skin(1)	5											57	60	59					5																	112175305		2202	4300	6502	112203204	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4014G>A	5.37:g.112175305G>A			112203204	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175305	G	A	112175305	2	1	98	1	0	0	0	0	0	0	0	1	763	991	35	3		3	APC	5	112175305	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	674	112175305	68739955	52	26338										
APC	324	hgsc.bcm.edu	37	chr5	112177789	112177789	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acaagtaataaaggcccacgAattctaaaaccaggggagaa	9	8	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:112177789A>G	ENST00000457016.1	+	16	6878	c.6498A>G	c.(6496-6498)cgA>cgG	p.R2166R	APC_ENST00000508376.2_Silent_p.R2166R|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.R2166R			P25054	APC_HUMAN	adenomatous polyposis coli	2166	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGGCCCACGAATTCTAAAAC	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											45	51	49					5																	112177789		2193	4295	6488	112205688	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.6498A>G	5.37:g.112177789A>G			112205688	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112177789	A	G	112177789	2	3	98	1	0	0	0	0	0	0	0	1	763	233	9	4		4	APC	5	112177789	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2484	112177789	68737471	53	26339										
WDR55	54853	hgsc.bcm.edu	37	chr5	140049096	140049096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggtggtggatgactaccgtCggcgcaaaaaaaagggagga	16	6	0	1	rs138378618		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:140049096C>T	ENST00000358337.5	+	7	1246	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	337					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTACCGTCGGCGCAAAAA	0.592																																																0			5						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	41	44	43		1009	2.1	0.8	5	dbSNP_134	43	0,8600		0,0,4300	no	missense	WDR55	NM_017706.4	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	337/384	140049096	1,13005	2203	4300	6503	140029280	SO:0001583	missense	54853			AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.1009C>T	5.37:g.140049096C>T	ENSP00000351100:p.Arg337Trp		140029280	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741904	0.30865	2.27E-4	0.0	ENSG00000120314	ENST00000358337	T	0.31247	1.5	5.29	2.06	0.26882	.	1.205560	0.06196	N	0.682296	T	0.22975	0.0555	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29941	-0.9995	10	0.72032	D	0.01	-0.7715	8.1252	0.30995	0.4101:0.5048:0.0:0.0851	.	337	Q9H6Y2	WDR55_HUMAN	W	337	ENSP00000351100:R337W	ENSP00000351100:R337W	R	+	1	2	WDR55	140029280	0.564000	0.26602	0.777000	0.31699	0.904000	0.53231	1.258000	0.32944	0.561000	0.29186	0.467000	0.42956	CGG		0.592	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		T	140049096	C	T	140049096	3	4	98	1	0	0	0	0	1	0	0	0	17347	875	31	1	1035	1	WDR55	5	140049096	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	27871307	140049096	40866164	54	26340										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140502958	140502958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cctcctacaccctgttcgtcCgcgagaacaacagccccgcc	7	20	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:140502958C>T	ENST00000194152.1	+	1	1378	c.1378C>T	c.(1378-1380)Cgc>Tgc	p.R460C	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	460	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGTTCGTCCGCGAGAACAA	0.627																																																0			5											65	65	65					5																	140502958		2203	4296	6499	140483142	SO:0001583	missense	56131			AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1378C>T	5.37:g.140502958C>T	ENSP00000194152:p.Arg460Cys		140483142	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.643242	0.29246	.	.	ENSG00000081818	ENST00000194152	T	0.01767	4.65	4.1	4.1	0.47936	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.05593	0.0147	M	0.83953	2.67	0.20764	N	0.999857	B	0.22146	0.065	B	0.27715	0.082	T	0.06625	-1.0816	9	0.66056	D	0.02	.	16.5721	0.84615	0.0:1.0:0.0:0.0	.	460	Q9Y5E5	PCDB4_HUMAN	C	460	ENSP00000194152:R460C	ENSP00000194152:R460C	R	+	1	0	PCDHB4	140483142	0.000000	0.05858	0.792000	0.32020	0.752000	0.42762	0.221000	0.17680	2.307000	0.77673	0.650000	0.86243	CGC		0.627	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140502958	C	T	140502958	3	4	98	1	0	0	0	0	1	0	0	0	11575	652	23	1	1380	1	PCDHB4	5	140502958	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	453862	140502958	40412302	55	26341										
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148619347	148619347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ctacgagaacctggacctccGgcagagacgggcctccagcc	12	16	0	2	rs138526744		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:148619347G>A	ENST00000506113.1	+	12	1582	c.1100G>A	c.(1099-1101)cGg>cAg	p.R367Q	ABLIM3_ENST00000356541.3_Missense_Mutation_p.R305Q|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.R367Q|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000309868.7_Missense_Mutation_p.R367Q|ABLIM3_ENST00000519549.1_3'UTR|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000504238.1_Missense_Mutation_p.R305Q|ABLIM3_ENST00000326685.7_Missense_Mutation_p.R305Q			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	367					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGACCTCCGGCAGAGACGG	0.642																																																0			5						G	GLN/ARG	0,4406		0,0,2203	70	75	74		1100	5	1	5	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABLIM3	NM_014945.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	367/684	148619347	1,13005	2203	4300	6503	148599540	SO:0001583	missense	22885			AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1100G>A	5.37:g.148619347G>A	ENSP00000425394:p.Arg367Gln		148599540	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923022	0.92319	0.0	1.16E-4	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.0	5.0	0.66597	.	0.113050	0.64402	D	0.000018	T	0.55130	0.1901	L	0.43923	1.385	0.47065	D	0.999307	D;D;P	0.76494	0.999;0.999;0.943	D;D;B	0.74023	0.948;0.982;0.293	T	0.41645	-0.9497	10	0.15499	T	0.54	.	18.4763	0.90793	0.0:0.0:1.0:0.0	.	305;305;367	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	Q	305;305;367;367;305;367	ENSP00000315841:R305Q;ENSP00000348938:R305Q;ENSP00000310309:R367Q;ENSP00000425394:R367Q;ENSP00000421183:R305Q;ENSP00000420855:R367Q	ENSP00000310309:R367Q	R	+	2	0	ABLIM3	148599540	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.028000	0.76470	2.598000	0.87819	0.462000	0.41574	CGG		0.642	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		A	148619347	G	A	148619347	3	1	98	1	0	0	0	0	1	0	0	0	96	1116	39	1	1146	1	ABLIM3	5	148619347	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	8116389	148619347	32295913	56	26342										
RPS14	6208	hgsc.bcm.edu	37	chr5	149826426	149826426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gatacccagctccttgcaccTctgggccacatcctgggcag	10	16	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:149826426T>C	ENST00000401695.3	-	3	296	c.250A>G	c.(250-252)Agg>Ggg	p.R84G	RPS14_ENST00000312037.5_Missense_Mutation_p.R84G|RPS14_ENST00000407193.1_Missense_Mutation_p.R84G			P62263	RS14_HUMAN	ribosomal protein S14	84					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTTGCACCTCTGGGCCACA	0.562																																																0			5											100	81	87					5																	149826426		2203	4300	6503	149806619	SO:0001583	missense	6208				CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587		"S ribosomal proteins"	10387	protein-coding gene	gene with protein product	"emetine resistance", "40S ribosomal protein S14"	130620				3785212, 1549121	Standard	XM_006714790		Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.250A>G	5.37:g.149826426T>C	ENSP00000385958:p.Arg84Gly		149806619	B2R5G5|D3DQG5|P06366|Q5BJI0	Missense_Mutation	SNP	ENST00000401695.3	37	CCDS4307.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858429	0.51376	.	.	ENSG00000164587	ENST00000401695;ENST00000407193;ENST00000521466;ENST00000312037	.	.	.	4.96	3.8	0.43715	.	0.042711	0.85682	D	0.000000	T	0.76891	0.4051	M	0.86028	2.79	0.58432	D	0.999998	B	0.33637	0.42	P	0.47075	0.536	T	0.76200	-0.3046	9	0.49607	T	0.09	.	10.6943	0.45890	0.0:0.0759:0.0:0.9241	.	84	P62263	RS14_HUMAN	G	84	.	ENSP00000311028:R84G	R	-	1	2	RPS14	149806619	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.210000	0.51129	0.854000	0.35336	0.374000	0.22700	AGG		0.562	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252373.1	NM_001025071		C	149826426	T	C	149826426	3	2	98	1	0	0	0	0	1	0	0	0	13661	1550	54	4	217	4	RPS14	5	149826426	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	1207079	149826426	31088834	57	26343										
HNRNPAB	85007	hgsc.bcm.edu	37	chr5	177637603	177637604	+	Intron	INS	-	-	A													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	agcgacgtggtggccatcagINSaataactacaagccatactg							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr5:177637603_177637604insA	ENST00000308158.5	-	12	1619				HNRNPAB_ENST00000504898.1_Frame_Shift_Ins_p.N327fs|HNRNPAB_ENST00000514633.1_Frame_Shift_Ins_p.N278fs|HNRNPAB_ENST00000358344.3_Frame_Shift_Ins_p.N327fs|HNRNPAB_ENST00000355836.5_Frame_Shift_Ins_p.N280fs|HNRNPAB_ENST00000515193.1_Frame_Shift_Ins_p.N275fs|HNRNPAB_ENST00000506339.1_Frame_Shift_Ins_p.N322fs|HNRNPAB_ENST00000506259.1_Frame_Shift_Ins_p.N280fs|PHYKPL_ENST00000481811.1_Intron	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GTGGCCATCAGAATAACTACAA	0.47																																																0			5																																								177570210	SO:0001627	intron_variant	3182			BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1350+1286->T	5.37:g.177637605_177637605dupA			177570209	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Frame_Shift_Ins	INS	ENST00000308158.5	37	CCDS4434.1																																																																																				0.47	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		A	177637604	-	A	177637603	6	5	98	0	1	1	1	0	0	0	0	0	7282	933	33	0		0	HNRNPAB	5	177637603	Intron	INS	-	TCGA-DC-6160-01A-11D-1657-10	27811177	177637603	3277657	58	26344										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918390	30918390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccaatgagaacaccacactaTccccagcagagcctacagaa	6	15	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:30918390T>C	ENST00000462446.1	+	2	2177	c.2149T>C	c.(2149-2151)Tcc>Ccc	p.S717P	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	281						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACCACACTATCCCCAGCAGA	0.488																																																0			6											59	67	65					6																	30918390		692	1591	2283	31026369	SO:0001583	missense	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2149T>C	6.37:g.30918390T>C	ENSP00000417182:p.Ser717Pro		31026369	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	8.819	0.937133	0.18206	.	.	ENSG00000168631	ENST00000462446	T	0.59772	0.24	2.04	-2.24	0.06909	.	.	.	.	.	T	0.21509	0.0518	M	0.71581	2.175	0.09310	N	0.999999	P	0.46020	0.871	B	0.31812	0.136	T	0.13710	-1.0499	9	0.27785	T	0.31	.	3.0358	0.06122	0.2852:0.0:0.4414:0.2734	.	717	E9PEI6	.	P	717	ENSP00000417182:S717P	ENSP00000417182:S717P	S	+	1	0	DPCR1	31026369	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.904000	0.04080	-0.481000	0.06792	0.359000	0.22050	TCC		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		C	30918390	T	C	30918390	3	2	98	1	0	0	0	0	1	0	0	0	4723	1435	50	4	2155	4	DPCR1	6	30918390	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10		30918390	140196677	59	26345										
TNXB	7148	hgsc.bcm.edu	37	chr6	32029492	32029492	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggggctgggggtctcttcctCtgcagctgagaaaaagggac	16	9	2	1	rs56144119		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:32029492C>T	ENST00000375244.3	-	21	7375	c.7174G>A	c.(7174-7176)Gag>Aag	p.E2392K	TNXB_ENST00000375247.2_Missense_Mutation_p.E2392K			P22105	TENX_HUMAN	tenascin XB	2452	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GTCTCTTCCTCTGCAGCTGAG	0.617																																																0			6											41	51	48					6																	32029492		1224	2532	3756	32137470	SO:0001583	missense	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7174G>A	6.37:g.32029492C>T	ENSP00000364393:p.Glu2392Lys		32137470	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	6.972	0.549230	0.13374	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56444	0.63;0.46	4.45	4.45	0.53987	.	0.511078	0.17591	N	0.168773	T	0.37892	0.1020	M	0.82823	2.61	0.27403	N	0.954798	B	0.21147	0.052	B	0.22152	0.038	T	0.37911	-0.9685	10	0.17832	T	0.49	.	14.0182	0.64536	0.0:1.0:0.0:0.0	rs56144119	2392	P22105-3	.	K	2392	ENSP00000364393:E2392K;ENSP00000364396:E2392K	ENSP00000364393:E2392K	E	-	1	0	TNXB	32137470	0.027000	0.19231	0.805000	0.32314	0.071000	0.16799	0.580000	0.23803	2.010000	0.58986	0.650000	0.86243	GAG		0.617	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32029492	C	T	32029492	3	4	98	1	0	0	0	0	1	0	0	0	16385	922	32	3	7635	3	TNXB	6	32029492	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	1111102	32029492	139085575	60	26346										
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32497986	32497986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catgtaggaacctccagggaGcttcagacacaccatgctgg	11	12	1	1	rs200744795		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:32497986G>A	ENST00000374975.3	-	1	78	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCTCCAGGGAGCTTCAGACAC	0.577																																																0			6											55	61	59					6																	32497986		2203	4296	6499	32605964	SO:0001583	missense	3127				CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.16C>T	6.37:g.32497986G>A	ENSP00000364114:p.Leu6Phe		32605964		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	4.629	0.117010	0.08881	.	.	ENSG00000198502	ENST00000374975	T	0.00281	8.32	4.42	-2.83	0.05769	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.27975	0.815	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.28808	-1.0032	9	0.06891	T	0.86	.	5.2478	0.15506	0.2872:0.0:0.5657:0.1472	rs1059548;rs2308658;rs3200252;rs16822997	6	Q30154	DRB5_HUMAN	F	6	ENSP00000364114:L6F	ENSP00000364114:L6F	L	-	1	0	HLA-DRB5	32605964	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.163000	0.09997	-0.229000	0.09854	-0.350000	0.07774	CTC		0.577	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		A	32497986	G	A	32497986	3	1	98	1	0	0	0	0	1	0	0	0	7230	971	34	3	808	3	HLA-DRB5	6	32497986	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	468494	32497986	138617081	61	26347										
HLA-DMA	3108	hgsc.bcm.edu	37	chr6	32920741	32920741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cttaccttcagggacggcccAggagtggggtagcagccaca	14	12	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:32920741A>G	ENST00000374843.4	-	1	158	c.73T>C	c.(73-75)Tgg>Cgg	p.W25R	HLA-DMA_ENST00000395303.3_Missense_Mutation_p.W25R|XXbac-BPG181M17.5_ENST00000429234.1_Missense_Mutation_p.W25R|HLA-DMA_ENST00000464392.1_Intron|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.W25R	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	25					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						GGGACGGCCCAGGAGTGGGGT	0.527																																																0			6											199	196	197					6																	32920741		1511	2709	4220	33028719	SO:0001583	missense	3108				CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.73T>C	6.37:g.32920741A>G	ENSP00000363976:p.Trp25Arg		33028719	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	.	.	.	.	.	.	.	.	.	.	A	8.167	0.790886	0.16258	.	.	ENSG00000248993;ENSG00000204257;ENSG00000204257;ENSG00000204257;ENSG00000204257	ENST00000429234;ENST00000395305;ENST00000395303;ENST00000374843;ENST00000341486	T;T;T;T	0.31510	1.49;5.36;4.64;5.75	4.18	1.77	0.24775	.	0.825675	0.11036	N	0.606691	T	0.07999	0.0200	L	0.40543	1.245	0.28771	N	0.900391	B;B	0.15473	0.013;0.013	B;B	0.10450	0.005;0.005	T	0.33059	-0.9883	10	0.27082	T	0.32	.	4.463	0.11675	0.6703:0.2237:0.106:0.0	.	25;25	P28067;Q31604	DMA_HUMAN;.	R	25;25;25;25;17	ENSP00000412457:W25R;ENSP00000378716:W25R;ENSP00000378714:W25R;ENSP00000363976:W25R	ENSP00000345804:W17R	W	-	1	0	XXbac-BPG181M17.5;HLA-DMA	33028719	0.961000	0.32948	0.985000	0.45067	0.095000	0.18619	0.176000	0.16782	0.378000	0.24764	-0.350000	0.07774	TGG		0.527	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120		G	32920741	A	G	32920741	3	3	98	1	0	0	0	0	1	0	0	0	7219	188	7	4	732	4	HLA-DMA	6	32920741	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	422755	32920741	138194326	62	26348										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524215	51524215	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cccagcctttttctaagactGaaaccatcacagtgagggcc	8	13	2	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:51524215G>T	ENST00000371117.3	-	61	10984	c.10709C>A	c.(10708-10710)tCa>tAa	p.S3570*		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3570					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.S3570L(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TTCTAAGACTGAAACCATCAC	0.423																																																1	Substitution - Missense(1)	lung(1)	6	GRCh37	CM051187	PKHD1	M							71	72	72					6																	51524215		2203	4300	6503	51632174	SO:0001587	stop_gained	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10709C>A	6.37:g.51524215G>T	ENSP00000360158:p.Ser3570*		51632174	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Nonsense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	53	20.758359	0.99934	.	.	ENSG00000170927	ENST00000371117	.	.	.	5.92	5.92	0.95590	.	0.624961	0.15040	N	0.283950	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	15.8173	0.78612	0.0:0.0:1.0:0.0	.	.	.	.	X	3570	.	ENSP00000360158:S3570X	S	-	2	0	PKHD1	51632174	0.897000	0.30589	0.294000	0.24946	0.864000	0.49448	5.826000	0.69293	2.801000	0.96364	0.650000	0.86243	TCA		0.423	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51524215	G	T	51524215	4	4	98	1	0	0	0	0	0	1	0	0	12002	1294	45	2	1543	2	PKHD1	6	51524215	Nonsense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	18603474	51524215	119590852	63	26349										
ICK	22858	hgsc.bcm.edu	37	chr6	52878505	52878506	+	Missense_Mutation	DNP	TG	TG	AA													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gatgggaaaagcaacgggctTggcttgtcctcctggagatg					rs201964851	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T|G	T|G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:52878505_52878506TG>AA	ENST00000350082.5	-	9	1452_1453	c.1106_1107CA>TT	c.(1105-1107)cCA>cTT	p.P369L	ICK_ENST00000356971.3_Missense_Mutation_p.P369L	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	369					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GCAACGGGCTTGGCTTGTCCTC	0.559																																																0			6																																								52986464|52986465	SO:0001583	missense	22858			AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.1106_1107delinsAA	6.37:g.52878505_52878506delinsAA	ENSP00000263043:p.Pro369Leu		52986464|52986465	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Silent|Missense_Mutation	SNP	ENST00000350082.5	37	CCDS4949.1																																																																																				0.559	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513		AA	52878506	TG	AA	52878505	3	1	98	1	0	0	0	0	1	0	0	0	7505	1799	63	5	815	5	ICK	6	52878505	Missense_Mutation	DNP	TG	TCGA-DC-6160-01A-11D-1657-10	1354290	52878505	118236562	64	26350										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73904449	73904449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cagtgcccagactttctacgCgcttagccctactatgcaca	7	15	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:73904449C>T	ENST00000370398.1	+	14	2220	c.2111C>T	c.(2110-2112)gCg>gTg	p.A704V	KCNQ5_ENST00000414165.2_Missense_Mutation_p.A594V|KCNQ5_ENST00000355635.3_Missense_Mutation_p.A705V|KCNQ5_ENST00000355194.4_Missense_Mutation_p.A704V|KCNQ5_ENST00000342056.2_Missense_Mutation_p.A723V|KCNQ5_ENST00000403813.2_Missense_Mutation_p.A695V|KCNQ5_ENST00000402622.2_Missense_Mutation_p.A714V	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	704					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	ACTTTCTACGCGCTTAGCCCT	0.488																																					GBM(142;1375 1859 14391 23261 44706)											0			6											130	130	130					6																	73904449		2203	4300	6503	73961170	SO:0001583	missense	56479			AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2111C>T	6.37:g.73904449C>T	ENSP00000359425:p.Ala704Val		73961170	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499373	0.64298	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99637	-5.89;-5.9;-5.9;-5.89;-5.91;-5.94;-6.29	5.32	5.32	0.75619	.	0.140270	0.48286	D	0.000184	D	0.99309	0.9758	L	0.56769	1.78	0.25729	N	0.985295	D;D;P;D;D	0.76494	0.999;0.973;0.627;0.994;0.99	D;B;B;P;P	0.64506	0.926;0.439;0.053;0.752;0.734	D	0.98218	1.0476	10	0.39692	T	0.17	.	18.9881	0.92780	0.0:1.0:0.0:0.0	.	594;714;723;695;704	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	V	723;723;704;704;714;705;695;594	ENSP00000345055:A723V;ENSP00000347326:A704V;ENSP00000359425:A704V;ENSP00000385501:A714V;ENSP00000347853:A705V;ENSP00000384453:A695V;ENSP00000409861:A594V	ENSP00000345055:A723V	A	+	2	0	KCNQ5	73961170	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	2.588000	0.46137	2.486000	0.83907	0.561000	0.74099	GCG		0.488	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		T	73904449	C	T	73904449	3	4	98	1	0	0	0	0	1	0	0	0	8107	768	27	1	2226	1	KCNQ5	6	73904449	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	21025944	73904449	97210618	65	26351										
CD109	135228	hgsc.bcm.edu	37	chr6	74481166	74481166	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttttagataaagctatattgGagtaaagtgaaagctgaacc	9	4	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:74481166G>T	ENST00000287097.5	+	15	1801	c.1689G>T	c.(1687-1689)tgG>tgT	p.W563C	CD109_ENST00000437994.2_Missense_Mutation_p.W563C|CD109_ENST00000422508.2_Missense_Mutation_p.W486C			Q6YHK3	CD109_HUMAN	CD109 molecule	563					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGCTATATTGGAGTAAAGTGA	0.378																																																0			6											79	78	78					6																	74481166		2203	4300	6503	74537887	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.1689G>T	6.37:g.74481166G>T	ENSP00000287097:p.Trp563Cys		74537887	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.102886	0.56183	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.62941	-0.01;-0.01;-0.01	5.5	5.5	0.81552	Alpha-2-macroglobulin, N-terminal 2 (1);	0.000000	0.85682	D	0.000000	T	0.77505	0.4140	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.997;0.995;0.992	T	0.78954	-0.2000	10	0.87932	D	0	.	18.332	0.90272	0.0:0.0:1.0:0.0	.	486;563;563;563	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	C	563;486;563	ENSP00000388062:W563C;ENSP00000404475:W486C;ENSP00000287097:W563C	ENSP00000287097:W563C	W	+	3	0	CD109	74537887	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	5.979000	0.70508	2.861000	0.98227	0.655000	0.94253	TGG		0.378	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		T	74481166	G	T	74481166	3	4	98	1	0	0	0	0	1	0	0	0	2969	1183	41	2	1747	2	CD109	6	74481166	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	576717	74481166	96633901	66	26352										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75843057	75843057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cccatcaccttcagtataaaCgggaactacagtcacagtgt	7	12	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:75843057C>T	ENST00000322507.8	-	34	6055	c.5746G>A	c.(5746-5748)Gtt>Att	p.V1916I	COL12A1_ENST00000416123.2_Missense_Mutation_p.V1916I|COL12A1_ENST00000483888.2_Missense_Mutation_p.V1916I|COL12A1_ENST00000345356.6_Missense_Mutation_p.V752I	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1916	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCAGTATAAACGGGAACTACA	0.378																																																0			6											128	119	122					6																	75843057		1871	4100	5971	75899777	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5746G>A	6.37:g.75843057C>T	ENSP00000325146:p.Val1916Ile		75899777	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.033127	0.54896	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.61627	0.09;0.09;0.09;0.09	5.93	4.13	0.48395	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.089397	0.47455	D	0.000239	T	0.38665	0.1049	L	0.45744	1.44	0.36596	D	0.874378	D;P	0.53151	0.958;0.922	P;P	0.49192	0.602;0.506	T	0.32693	-0.9897	10	0.28530	T	0.3	.	6.9233	0.24401	0.133:0.6691:0.1283:0.0696	.	752;1916	Q99715-2;Q99715	.;COCA1_HUMAN	I	1916;1916;752;1916;1916	ENSP00000325146:V1916I;ENSP00000305147:V752I;ENSP00000412864:V1916I;ENSP00000421216:V1916I	ENSP00000325146:V1916I	V	-	1	0	COL12A1	75899777	0.995000	0.38212	0.982000	0.44146	0.060000	0.15804	2.808000	0.47963	1.496000	0.48567	0.650000	0.86243	GTT		0.378	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75843057	C	T	75843057	3	4	98	1	0	0	0	0	1	0	0	0	3675	536	19	1	3577	1	COL12A1	6	75843057	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	1361891	75843057	95272010	67	26353										
ME1	4199	hgsc.bcm.edu	37	chr6	83963402	83963402	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcgatacttgttcaggagacGaaatgcattcacattggcaa	9	8	2	1	rs267601137		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr6:83963402G>A	ENST00000369705.3	-	7	876	c.760C>T	c.(760-762)Cgt>Tgt	p.R254C	ME1_ENST00000541327.1_Missense_Mutation_p.R88C|ME1_ENST00000543031.1_Missense_Mutation_p.R179C	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	254					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)			NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		TTCAGGAGACGAAATGCATTC	0.328																																																0			6											150	135	140					6																	83963402		2203	4299	6502	84020121	SO:0001583	missense	57717			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.760C>T	6.37:g.83963402G>A	ENSP00000358719:p.Arg254Cys		84020121	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Missense_Mutation	SNP	ENST00000369705.3	37	CCDS34492.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663564	0.88251	.	.	ENSG00000065833	ENST00000369705;ENST00000541327;ENST00000543031	T;T;T	0.46451	0.87;0.87;0.87	5.53	5.53	0.82687	Malic enzyme, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.52125	0.1715	M	0.90977	3.165	0.80722	D	1	D	0.57899	0.981	P	0.45946	0.498	T	0.68044	-0.5513	10	0.87932	D	0	-12.6428	18.2288	0.89927	0.0:0.0:1.0:0.0	.	254	P48163	MAOX_HUMAN	C	254;88;179	ENSP00000358719:R254C;ENSP00000439912:R88C;ENSP00000446114:R179C	ENSP00000358719:R254C	R	-	1	0	ME1	84020121	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.969000	0.87988	2.602000	0.87976	0.460000	0.39030	CGT		0.328	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1			A	83963402	G	A	83963402	3	1	98	1	0	0	0	0	1	0	0	0	9447	1058	37	1	990	1	ME1	6	83963402	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	8120345	83963402	87151665	68	26354										
HOXA1	3198	hgsc.bcm.edu	37	chr7	27135338	27135338	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggtggtggtggtggtggtggTggggcgaaccgatctgcacc	21	7	1	0	rs146782650|rs533892779	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:27135338T>G	ENST00000343060.4	-	1	255	c.194A>C	c.(193-195)cAc>cCc	p.H65P	HOXA1_ENST00000355633.5_Missense_Mutation_p.H65P|HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	65	Poly-His.				abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						gtggtggtggtggGGCGAACC	0.637											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		11	0.00219649	0.0061	0	5008	,	,		10402	0		0.001	False		,,,				2504	0.002															0			7						T	PRO/HIS,PRO/HIS	0,4406		0,0,2203	35	38	37		194,194	4.1	1	7	dbSNP_134	37	4,8596	3.0+/-9.4	0,4,4296	no	missense,missense	HOXA1	NM_005522.4,NM_153620.2	77,77	0,4,6499	GG,GT,TT		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	65/336,65/138	27135338	4,13002	2203	4300	6503	27101863	SO:0001583	missense	3198				CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"Homeoboxes / ANTP class : HOXL subclass"	5099	protein-coding gene	gene with protein product		142955	"homeo box A1"	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.194A>C	7.37:g.27135338T>G	ENSP00000343246:p.His65Pro	792	27101863	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	37	CCDS5401.1	53	0.024267399267399268	11	0.022357723577235773	10	0.027624309392265192	14	0.024475524475524476	18	0.023746701846965697	T	6.238	0.411954	0.11812	0.0	4.65E-4	ENSG00000105991	ENST00000343060;ENST00000355633	D;T	0.90844	-2.74;0.83	5.26	4.12	0.48240	.	0.390179	0.22852	N	0.054849	T	0.66218	0.2767	N	0.17474	0.49	0.35904	D	0.830584	B;P	0.52316	0.277;0.952	B;P	0.47470	0.029;0.548	T	0.77143	-0.2696	10	0.24483	T	0.36	.	7.4412	0.27185	0.0:0.1595:0.0:0.8405	.	65;65	P49639;E7ERT8	HXA1_HUMAN;.	P	65	ENSP00000343246:H65P;ENSP00000347851:H65P	ENSP00000343246:H65P	H	-	2	0	HOXA1	27101863	1.000000	0.71417	1.000000	0.80357	0.164000	0.22412	1.515000	0.35845	1.998000	0.58463	0.247000	0.18012	CAC		0.637	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			G	27135338	T	G	27135338	3	3	98	1	0	0	0	0	1	0	0	0	7309	1696	59	4	821	4	HOXA1	7	27135338	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10		27135338	132003325	69	26355										
CHN2	1124	hgsc.bcm.edu	37	chr7	29539490	29539490	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tctttgtttacagactgtggAttgaacgtacacaaacagtg	9	7	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:29539490A>G	ENST00000222792.6	+	9	1277	c.747A>G	c.(745-747)ggA>ggG	p.G249G	CHN2_ENST00000409041.4_Silent_p.G113G|CHN2_ENST00000495789.2_Silent_p.G262G|CHN2_ENST00000421775.2_Intron|CHN2_ENST00000539406.1_Silent_p.G324G|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000410098.1_3'UTR|CHN2_ENST00000546235.1_Silent_p.G234G|CHN2_ENST00000424025.2_Silent_p.G68G|CHN2_ENST00000539389.1_Silent_p.G105G|CHN2_ENST00000439711.2_Silent_p.G113G	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	249					positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						CAGACTGTGGATTGAACGTAC	0.423																																					Ovarian(1;44 48 13232 18918 31480)											0			7											120	109	112					7																	29539490		2203	4300	6503	29506015	SO:0001819	synonymous_variant	1124			L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"Rho GTPase activating proteins", "SH2 domain containing"	1944	protein-coding gene	gene with protein product	"beta chimerin", "chimaerin 2"	602857	"chimerin (chimaerin) 2"			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.747A>G	7.37:g.29539490A>G			29506015	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Silent	SNP	ENST00000222792.6	37	CCDS5420.1																																																																																				0.423	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067		G	29539490	A	G	29539490	2	3	98	1	0	0	0	0	0	0	0	1	3369	320	12	4		4	CHN2	7	29539490	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2404152	29539490	129599173	70	26356										
SEPT7	989	hgsc.bcm.edu	37	chr7	35942737	35942737	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atttggaagcacagcacaaaGaattggaggaaaaacgtcgt	11	6	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:35942737G>T	ENST00000435235.1	+	12	1459	c.1027G>T	c.(1027-1029)Gaa>Taa	p.E343*	SEPT7_ENST00000350320.6_Nonsense_Mutation_p.E395*|SEPT7_ENST00000494488.2_3'UTR|SEPT7_ENST00000399034.2_Nonsense_Mutation_p.E397*|SEPT7_ENST00000432293.2_Nonsense_Mutation_p.E47*|SEPT7_ENST00000399035.3_Nonsense_Mutation_p.E395*			Q16181	SEPT7_HUMAN	septin 7	396					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ACAGCACAAAGAATTGGAGGA	0.378																																																0			7											42	43	42					7																	35942737		1838	4083	5921	35909262	SO:0001587	stop_gained	989			S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.1027G>T	7.37:g.35942737G>T	ENSP00000413507:p.Glu343*		35909262	Q52M76|Q6NX50	Nonsense_Mutation	SNP	ENST00000435235.1	37		.	.	.	.	.	.	.	.	.	.	G	38	6.659335	0.97743	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000432293	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	18.9185	0.92516	0.0:0.0:1.0:0.0	.	.	.	.	X	343;397;395;395;341;343;47	.	ENSP00000344868:E395X	E	+	1	0	SEPT7	35909262	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.813000	0.86123	2.538000	0.85594	0.609000	0.83330	GAA		0.378	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		T	35942737	G	T	35942737	4	4	98	1	0	0	0	0	0	1	0	0	14106	943	33	2	1230	2	SEPT7	7	35942737	Nonsense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	6403247	35942737	123195926	71	26357										
SFRP4	6424	hgsc.bcm.edu	37	chr7	37951856	37951856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acttgaagatctcttttacaTccaccaccgttgtgacctca	5	13	2	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:37951856T>C	ENST00000436072.2	-	4	1033	c.656A>G	c.(655-657)gAt>gGt	p.D219G	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	219	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CTCTTTTACATCCACCACCGT	0.433																																																0			7											191	172	179					7																	37951856		2203	4300	6503	37918381	SO:0001583	missense	6424			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.656A>G	7.37:g.37951856T>C	ENSP00000410715:p.Asp219Gly		37918381	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Missense_Mutation	SNP	ENST00000436072.2	37	CCDS5453.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.622309	0.87460	.	.	ENSG00000106483	ENST00000436072;ENST00000446575;ENST00000447200	T;T	0.22743	1.94;1.94	5.9	5.9	0.94986	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.106321	0.64402	D	0.000004	T	0.34019	0.0883	L	0.43152	1.355	0.51482	D	0.999926	P	0.52316	0.952	P	0.55824	0.785	T	0.03043	-1.1079	10	0.72032	D	0.01	.	15.3178	0.74095	0.0:0.0:0.0:1.0	.	219	Q6FHJ7	SFRP4_HUMAN	G	219;216;85	ENSP00000410715:D219G;ENSP00000402262:D85G	ENSP00000410715:D219G	D	-	2	0	SFRP4	37918381	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	7.376000	0.79658	2.248000	0.74166	0.528000	0.53228	GAT		0.433	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		C	37951856	T	C	37951856	3	2	98	1	0	0	0	0	1	0	0	0	14200	1435	50	4	396	4	SFRP4	7	37951856	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	2009119	37951856	121186807	72	26358										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45003711	45003711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggtccagcttgtagaggtgCtggtctgtgagcaggagggc	19	7	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:45003711C>T	ENST00000258787.7	-	20	2818	c.2682G>A	c.(2680-2682)caG>caA	p.Q894Q		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	894	Myosin tail. {ECO:0000255}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						TGTAGAGGTGCTGGTCTGTGA	0.652																																																0			7											95	86	89					7																	45003711		2202	4300	6502	44970236	SO:0001819	synonymous_variant	64005			AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2682G>A	7.37:g.45003711C>T			44970236	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	37	CCDS34629.1																																																																																				0.652	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45003711	C	T	45003711	2	4	98	1	0	0	0	0	0	0	0	1	10104	796	28	3		3	MYO1G	7	45003711	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	7051855	45003711	114134952	73	26359										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79833136	79833136	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aacccattttactttcaaagAtcttcattttaagtgagtag	5	7	3	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:79833136A>G	ENST00000351004.3	+	5	951	c.578A>G	c.(577-579)gAt>gGt	p.D193G	GNAI1_ENST00000457358.2_Missense_Mutation_p.D141G	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	193					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						ACTTTCAAAGATCTTCATTTT	0.289																																																0			7											49	47	48					7																	79833136		2199	4295	6494	79671072	SO:0001583	missense	2770			AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.578A>G	7.37:g.79833136A>G	ENSP00000343027:p.Asp193Gly		79671072	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	37	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.197905	0.58126	.	.	ENSG00000127955	ENST00000351004;ENST00000418742;ENST00000457358	T;D;T	0.87412	-0.38;-2.25;-0.38	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.75968	0.3922	N	0.11284	0.12	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.70908	-0.4744	9	.	.	.	.	16.2652	0.82574	1.0:0.0:0.0:0.0	.	193	P63096	GNAI1_HUMAN	G	193;141;141	ENSP00000343027:D193G;ENSP00000389435:D141G;ENSP00000410572:D141G	.	D	+	2	0	GNAI1	79671072	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.230000	0.95299	2.241000	0.73720	0.528000	0.53228	GAT		0.289	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		G	79833136	A	G	79833136	3	3	98	1	0	0	0	0	1	0	0	0	6524	333	12	4	596	4	GNAI1	7	79833136	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	34829425	79833136	79305527	74	26360										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98493411	98493411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atcattttctggattttgtgAaacagatttacaaggagctt	8	5	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:98493411A>G	ENST00000359863.4	+	7	684	c.475A>G	c.(475-477)Aaa>Gaa	p.K159E	TRRAP_ENST00000355540.3_Missense_Mutation_p.K159E|TRRAP_ENST00000446306.3_Missense_Mutation_p.K159E	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	159					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGATTTTGTGAAACAGATTTA	0.274																																																0			7											82	79	80					7																	98493411		2199	4298	6497	98331347	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.475A>G	7.37:g.98493411A>G	ENSP00000352925:p.Lys159Glu		98331347	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091903	0.76756	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.63913	3.6;-0.07	5.63	5.63	0.86233	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	M	0.68317	2.08	0.80722	D	1	B;B	0.16603	0.018;0.01	B;B	0.20767	0.031;0.014	T	0.57435	-0.7812	10	0.21540	T	0.41	.	16.1358	0.81487	1.0:0.0:0.0:0.0	.	159;159	Q9Y4A5-2;Q9Y4A5	.;TRRAP_HUMAN	E	159	ENSP00000352925:K159E;ENSP00000347733:K159E	ENSP00000347733:K159E	K	+	1	0	TRRAP	98331347	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.014000	0.93635	2.261000	0.74972	0.460000	0.39030	AAA		0.274	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98493411	A	G	98493411	3	3	98	1	0	0	0	0	1	0	0	0	16641	247	9	4	497	4	TRRAP	7	98493411	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	18660275	98493411	60645252	75	26361										
CUX1	1523	hgsc.bcm.edu	37	chr7	101837149	101837149	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aagtccatggagtttgcaccGtccgagggcgctgggacaca	14	11	0	0	rs11540899|rs2230104	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:101837149G>A	ENST00000292535.7	+	13	1142	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000547394.2_Silent_p.P363P|CUX1_ENST00000425244.2_Silent_p.P333P|CUX1_ENST00000556210.1_Silent_p.P368P|CUX1_ENST00000292538.4_Silent_p.P379P|CUX1_ENST00000393824.3_Silent_p.P340P|CUX1_ENST00000437600.4_Silent_p.P377P|CUX1_ENST00000360264.3_Silent_p.P379P|CUX1_ENST00000549414.2_Silent_p.P368P|CUX1_ENST00000546411.2_Silent_p.P368P|CUX1_ENST00000550008.2_Silent_p.P368P|SNORA48_ENST00000517015.1_RNA	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	368					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AGTTTGCACCGTCCGAGGGCG	0.527													G|||	1495	0.298522	0.3646	0.2738	5008	,	,		19932	0.0675		0.3857	False		,,,				2504	0.3753															0			7						G	,,,,,,	1667,2739	507.1+/-366.6	331,1005,867	82	69	73		1137,1089,999,1020,1137,1131,1104	-8.6	0	7	dbSNP_120	73	3374,5226	499.2+/-374.9	652,2070,1578	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	983,3075,2445	AA,AG,GG		39.2326,37.8348,38.759	,,,,,,	379/1517,363/663,333/633,340/640,379/679,377/677,368/1506	101837149	5041,7965	2203	4300	6503	101623869	SO:0001819	synonymous_variant	1523			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1104G>A	7.37:g.101837149G>A			101623869	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																				0.527	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101837149	G	A	101837149	2	1	98	1	0	0	0	0	0	0	0	1	4070	1132	40	1		1	CUX1	7	101837149	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	3343738	101837149	57301514	76	26362										
TNPO3	23534	hgsc.bcm.edu	37	chr7	128612495	128612495	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cttacatcattggctaccccTgtatgaatgaggtctcgtag	9	10	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:128612495T>C	ENST00000265388.5	-	19	2558	c.2415A>G	c.(2413-2415)acA>acG	p.T805T	TNPO3_ENST00000471234.1_Silent_p.T741T|TNPO3_ENST00000471166.1_Silent_p.T839T|TNPO3_ENST00000482320.1_Silent_p.T739T|RN7SL306P_ENST00000492941.2_RNA|TNPO3_ENST00000393245.1_Silent_p.T839T			Q9Y5L0	TNPO3_HUMAN	transportin 3	805					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TGGCTACCCCTGTATGAATGA	0.433																																					Pancreas(147;583 2585 39696 52331)											0			7											97	91	93					7																	128612495		2203	4300	6503	128399731	SO:0001819	synonymous_variant	23534			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2415A>G	7.37:g.128612495T>C			128399731	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	37	CCDS5809.1																																																																																				0.433	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		C	128612495	T	C	128612495	2	2	98	1	0	0	0	0	0	0	0	1	16376	1567	55	4		4	TNPO3	7	128612495	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	26775346	128612495	30526168	77	26363										
BRAF	673	hgsc.bcm.edu	37	chr7	140453133	140453133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggacccactccatcgagatTtcactgtagctagaccaaaa	8	12	1	2	rs397516897|rs121913226|rs397507484		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:140453133T>C	ENST00000288602.6	-	15	1862	c.1802A>G	c.(1801-1803)aAa>aGa	p.K601R		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	601	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CRC). {ECO:0000269|PubMed:12198537}.|K -> Q (in CFC1). {ECO:0000269|PubMed:19206169}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T599_R603>I(2)|p.K601del(1)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.K601I(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CCATCGAGATTTCACTGTAGC	0.373		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	7	Complex - deletion inframe(5)|Substitution - Missense(1)|Deletion - In frame(1)	thyroid(4)|skin(2)|ovary(1)	7											112	104	107					7																	140453133		2203	4300	6503	140099602	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1802A>G	7.37:g.140453133T>C	ENSP00000288602:p.Lys601Arg		140099602	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	31|31	5.099050|5.099050	0.94197|0.94197	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.82803|.	-1.65|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57504|0.57504	0.2058|0.2058	L|L	0.33710|0.33710	1.025|1.025	0.80722|0.80722	D|D	1|1	P|.	0.35307|.	0.494|.	B|.	0.42593|.	0.392|.	T|T	0.54084|0.54084	-0.8346|-0.8346	10|5	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601|.	P15056|.	BRAF_HUMAN|.	R|D	601|209	ENSP00000288602:K601R|.	ENSP00000288602:K601R|.	K|N	-|-	2|1	0|0	BRAF|BRAF	140099602|140099602	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	AAA|AAT		0.373	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140453133	T	C	140453133	3	2	98	1	0	0	0	0	1	0	0	0	1499	1841	64	4	514	4	BRAF	7	140453133	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	11840638	140453133	18685530	78	26364										
ASB10	136371	hgsc.bcm.edu	37	chr7	150878272	150878272	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcctggtccgcagcatcagcGtctgctccagctgaaagcag	11	14	2	1	rs371957185		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr7:150878272G>A	ENST00000420175.2	-	3	882	c.858C>T	c.(856-858)gaC>gaT	p.D286D	ASB10_ENST00000434669.1_Silent_p.D331D|ASB10_ENST00000422024.1_Silent_p.D331D|ASB10_ENST00000377867.3_Silent_p.D271D|ASB10_ENST00000275838.1_Silent_p.D286D			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	286					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCATCAGCGTCTGCTCCAG	0.672																																																0			7						G	,,	2,4400	2.1+/-5.4	0,2,2199	29	29	29		858,858,813	-8.1	0	7		29	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB10	NM_001142459.1,NM_001142460.1,NM_080871.3	,,	0,2,6496	AA,AG,GG		0.0,0.0454,0.0154	,,	286/468,286/430,271/453	150878272	2,12994	2201	4297	6498	150509205	SO:0001819	synonymous_variant	136371			AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.858C>T	7.37:g.150878272G>A			150509205	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																				0.672	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		A	150878272	G	A	150878272	2	1	98	1	0	0	0	0	0	0	0	1	1015	1136	40	1		1	ASB10	7	150878272	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	10425139	150878272	8260391	79	26365										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1905021	1905021	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaatccagggacagcctggcTcctggccccgagcctcagga	12	15	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:1905021T>C	ENST00000398564.1	+	29	3702	c.3702T>C	c.(3700-3702)gcT>gcC	p.A1234A	ARHGEF10_ENST00000262112.6_Silent_p.A1205A|ARHGEF10_ENST00000520359.1_Silent_p.A1171A|ARHGEF10_ENST00000518288.1_Silent_p.A1233A|ARHGEF10_ENST00000349830.3_Silent_p.A1209A|ARHGEF10_ENST00000521927.1_3'UTR			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1234					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		ACAGCCTGGCTCCTGGCCCCG	0.587																																																0			8											64	61	62					8																	1905021		2203	4300	6503	1892428	SO:0001819	synonymous_variant	9639			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3702T>C	8.37:g.1905021T>C			1892428	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																					0.587	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				C	1905021	T	C	1905021	2	2	98	1	0	0	0	0	0	0	0	1	894	1538	54	4		4	ARHGEF10	8	1905021	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10		1905021	144459001	80	26366										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20107850	20107850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cagctgctgcttcaggagggAgatctcgcctgacttctggc	13	12	3	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:20107850A>G	ENST00000381569.1	-	4	1531	c.1174T>C	c.(1174-1176)Tcc>Ccc	p.S392P	LZTS1_ENST00000265801.6_Missense_Mutation_p.S392P|LZTS1_ENST00000522290.1_Missense_Mutation_p.S392P			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	392					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		TTCAGGAGGGAGATCTCGCCT	0.607																																																0			8											40	42	42					8																	20107850		2203	4300	6503	20152130	SO:0001583	missense	11178			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1174T>C	8.37:g.20107850A>G	ENSP00000370981:p.Ser392Pro		20152130	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	a	22.2	4.253544	0.80135	.	.	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.61392	0.11;0.11;0.11	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81195	-0.1043	10	0.62326	D	0.03	-18.3908	13.3793	0.60759	1.0:0.0:0.0:0.0	.	392;392	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	P	392	ENSP00000370981:S392P;ENSP00000265801:S392P;ENSP00000429263:S392P	ENSP00000265801:S392P	S	-	1	0	LZTS1	20152130	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	7.336000	0.79245	1.842000	0.53543	0.454000	0.30748	TCC		0.607	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		G	20107850	A	G	20107850	3	3	98	1	0	0	0	0	1	0	0	0	9168	304	11	4	620	4	LZTS1	8	20107850	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	18202829	20107850	126256172	81	26367										
ENTPD4	9583	hgsc.bcm.edu	37	chr8	23290531	23290531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggagtgcgcctgtggatgcGccgcagccgcagcaggtaca	17	12	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:23290531G>A	ENST00000358689.4	-	13	1994	c.1759C>T	c.(1759-1761)Cgc>Tgc	p.R587C	ENTPD4_ENST00000417069.2_Missense_Mutation_p.R579C|ENTPD4_ENST00000356206.6_Intron|ENTPD4_ENST00000521321.1_Intron	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	587					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		CTGTGGATGCGCCGCAGCCGC	0.667																																																0			8											41	43	43					8																	23290531		2203	4300	6503	23346476	SO:0001583	missense	9583			AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"lysosomal apyrase-like 1"	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1759C>T	8.37:g.23290531G>A	ENSP00000351520:p.Arg587Cys		23346476	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267606	0.95399	.	.	ENSG00000197217	ENST00000358689;ENST00000417069	T;T	0.17054	2.3;2.3	5.58	5.58	0.84498	.	0.152106	0.64402	D	0.000009	T	0.43743	0.1261	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.977	T	0.31475	-0.9942	10	0.87932	D	0	-13.2634	18.1425	0.89644	0.0:0.0:1.0:0.0	.	579;587	Q9Y227-2;Q9Y227	.;ENTP4_HUMAN	C	587;579	ENSP00000351520:R587C;ENSP00000408573:R579C	ENSP00000351520:R587C	R	-	1	0	ENTPD4	23346476	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	7.903000	0.87398	2.631000	0.89168	0.563000	0.77884	CGC		0.667	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		A	23290531	G	A	23290531	3	1	98	1	0	0	0	0	1	0	0	0	5154	1087	38	1	95	1	ENTPD4	8	23290531	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	3182681	23290531	123073491	82	26368										
STAU2	27067	hgsc.bcm.edu	37	chr8	74464439	74464439	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ctgaagaaagagcttgaaggTtggttcatatctttgggtga	13	4	2	5	rs148124805		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:74464439T>C	ENST00000521451.1	-	8	1054	c.678A>G	c.(676-678)caA>caG	p.Q226Q	STAU2_ENST00000524300.1_Silent_p.Q446Q|STAU2_ENST00000522695.1_Silent_p.Q414Q|STAU2_ENST00000521210.1_Silent_p.Q342Q|STAU2_ENST00000519961.1_Silent_p.Q446Q|STAU2_ENST00000523558.1_Silent_p.Q274Q|STAU2_ENST00000522509.1_Silent_p.Q414Q|STAU2_ENST00000355780.5_Silent_p.Q414Q|STAU2_ENST00000517542.1_Silent_p.Q408Q|STAU2_ENST00000521727.1_Silent_p.Q426Q			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	446	DRBM 3. {ECO:0000255|PROSITE- ProRule:PRU00266}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			AGCTTGAAGGTTGGTTCATAT	0.428																																																0			8						T	,,,,,,	1,4405	2.1+/-5.4	0,1,2202	145	141	142		1338,1242,1026,822,1242,1224,1242	1	1	8	dbSNP_134	142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STAU2	NM_001164380.1,NM_001164381.1,NM_001164382.1,NM_001164383.1,NM_001164384.1,NM_001164385.1,NM_014393.2	,,,,,,	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	,,,,,,	446/571,414/539,342/505,274/399,414/480,408/474,414/480	74464439	2,13004	2203	4300	6503	74626993	SO:0001819	synonymous_variant	27067			Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"staufen (Drosophila, RNA-binding protein) homolog 2", "staufen, RNA binding protein, homolog 2 (Drosophila)"			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.678A>G	8.37:g.74464439T>C			74626993	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	37																																																																																					0.428	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380		C	74464439	T	C	74464439	2	2	98	1	0	0	0	0	0	0	0	1	15312	1722	60	4		4	STAU2	8	74464439	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	51173908	74464439	71899583	83	26369										
PSKH2	85481	hgsc.bcm.edu	37	chr8	87076699	87076699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctggacaatgtaacgatggCtaacccgccgcaggacgctc	12	13	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:87076699C>T	ENST00000276616.2	-	2	421	c.347G>A	c.(346-348)aGc>aAc	p.S116N	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	116	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S116I(1)		NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			GTAACGATGGCTAACCCGCCG	0.502																																																1	Substitution - Missense(1)	lung(1)	8											92	79	83					8																	87076699		2203	4300	6503	87145815	SO:0001583	missense	85481			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.347G>A	8.37:g.87076699C>T	ENSP00000276616:p.Ser116Asn		87145815	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223143	0.39300	.	.	ENSG00000147613	ENST00000276616	T	0.38240	1.15	5.59	3.78	0.43462	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.18087	0.0434	N	0.03294	-0.36	0.30624	N	0.758162	B	0.14012	0.009	B	0.14023	0.01	T	0.12116	-1.0560	9	0.40728	T	0.16	.	10.7921	0.46438	0.0:0.8544:0.0:0.1456	.	116	Q96QS6	KPSH2_HUMAN	N	116	ENSP00000276616:S116N	ENSP00000276616:S116N	S	-	2	0	PSKH2	87145815	0.983000	0.35010	0.030000	0.17652	0.822000	0.46500	4.605000	0.61119	0.681000	0.31386	0.655000	0.94253	AGC		0.502	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		T	87076699	C	T	87076699	3	4	98	1	0	0	0	0	1	0	0	0	12699	797	28	3	816	3	PSKH2	8	87076699	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	12612260	87076699	59287323	84	26370										
RGS22	26166	hgsc.bcm.edu	37	chr8	101076146	101076146	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aagagcttgagaaggagtgtCttgtagagatacagacacct	12	6	1	4			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:101076146C>G	ENST00000360863.6	-	8	1044	c.850G>C	c.(850-852)Gac>Cac	p.D284H	RGS22_ENST00000523437.1_Missense_Mutation_p.D272H|RGS22_ENST00000523287.1_Missense_Mutation_p.D103H	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	284					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			GAAGGAGTGTCTTGTAGAGAT	0.373																																																0			8											88	90	89					8																	101076146		1832	4075	5907	101145322	SO:0001583	missense	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.850G>C	8.37:g.101076146C>G	ENSP00000354109:p.Asp284His		101145322	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056275	0.76074	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.44482	0.95;0.92;0.95	5.86	5.86	0.93980	.	0.368863	0.27886	N	0.017441	T	0.65893	0.2735	M	0.66939	2.045	0.39401	D	0.966598	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.988;0.988;0.995	T	0.66779	-0.5837	10	0.87932	D	0	.	20.1735	0.98170	0.0:1.0:0.0:0.0	.	272;284;103	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	H	284;272;103;272	ENSP00000354109:D284H;ENSP00000429382:D103H;ENSP00000428212:D272H	ENSP00000354109:D284H	D	-	1	0	RGS22	101145322	1.000000	0.71417	0.703000	0.30354	0.722000	0.41435	4.957000	0.63652	2.937000	0.99478	0.650000	0.86243	GAC		0.373	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101076146	C	G	101076146	3	3	98	1	0	0	0	0	1	0	0	0	13342	913	32	5	3024	5	RGS22	8	101076146	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	13999447	101076146	45287876	85	26371										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616445	116616445	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggtgcttttctgggctgcaaAgtcctctgggacagaatgga	14	8	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:116616445A>T	ENST00000220888.5	-	3	1871	c.1712T>A	c.(1711-1713)cTt>cAt	p.L571H	TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000520276.1_Missense_Mutation_p.L575H|TRPS1_ENST00000395715.3_Missense_Mutation_p.L584H|TRPS1_ENST00000519674.1_Missense_Mutation_p.L571H			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	571					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			TGGGCTGCAAAGTCCTCTGGG	0.438									Langer-Giedion syndrome																																							0			8											71	71	71					8																	116616445		1903	4121	6024	116685620	SO:0001583	missense	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1712T>A	8.37:g.116616445A>T	ENSP00000220888:p.Leu571His		116685620	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	A	16.70	3.196179	0.58126	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.87	5.87	0.94306	.	0.193906	0.45606	D	0.000345	T	0.20088	0.0483	L	0.27053	0.805	0.53688	D	0.999977	P;B;P	0.45715	0.461;0.331;0.865	B;B;B	0.42555	0.303;0.159;0.391	T	0.01294	-1.1393	10	0.87932	D	0	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	575;571;584	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	H	584;571;575;571	ENSP00000379065:L584H;ENSP00000220888:L571H;ENSP00000428680:L575H;ENSP00000429174:L571H	ENSP00000220888:L571H	L	-	2	0	TRPS1	116685620	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.976000	0.76135	2.371000	0.80710	0.533000	0.62120	CTT		0.438	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116616445	A	T	116616445	3	4	98	1	0	0	0	0	1	0	0	0	16633	72	3	5	2149	5	TRPS1	8	116616445	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	15540299	116616445	29747577	86	26372										
EXT1	2131	hgsc.bcm.edu	37	chr8	118812009	118812009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tagagacctggtctttaaagAggacggggtcgagcctcatc	13	9	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr8:118812009A>G	ENST00000378204.2	-	11	2989	c.2183T>C	c.(2182-2184)cTc>cCc	p.L728P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	728					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			GTCTTTAAAGAGGACGGGGTC	0.537			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																													yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	0			8											86	83	84					8																	118812009		2203	4300	6503	118881190	SO:0001583	missense	2131	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.2183T>C	8.37:g.118812009A>G	ENSP00000367446:p.Leu728Pro		118881190	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	37	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638668	0.87760	.	.	ENSG00000182197	ENST00000378204	T	0.80653	-1.4	5.96	5.96	0.96718	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.91901	0.7436	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93497	0.6841	10	0.87932	D	0	-11.7954	16.4484	0.83959	1.0:0.0:0.0:0.0	.	728	Q16394	EXT1_HUMAN	P	728	ENSP00000367446:L728P	ENSP00000367446:L728P	L	-	2	0	EXT1	118881190	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.278000	0.95766	2.285000	0.76669	0.533000	0.62120	CTC		0.537	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		G	118812009	A	G	118812009	3	3	98	1	0	0	0	0	1	0	0	0	5336	304	11	4	61	4	EXT1	8	118812009	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2195564	118812009	27552013	87	26373										
UHRF2	115426	hgsc.bcm.edu	37	chr9	6504639	6504639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttttatgtgcgtttgctgtcAggagctagtttaccagcctg	11	8	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:6504639A>G	ENST00000276893.5	+	15	2378	c.2210A>G	c.(2209-2211)cAg>cGg	p.Q737R	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	737					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		GTTTGCTGTCAGGAGCTAGTT	0.383																																																0			9											95	87	90					9																	6504639		2203	4300	6503	6494639	SO:0001583	missense	115426			AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	12557	protein-coding gene	gene with protein product	"Np95-like ring finger protein"	615211	"ubiquitin-like with PHD and ring finger domains 2"			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.2210A>G	9.37:g.6504639A>G	ENSP00000276893:p.Gln737Arg		6494639	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.563252	0.86335	.	.	ENSG00000147854	ENST00000276893	T	0.76316	-1.01	5.81	5.81	0.92471	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.84447	0.5474	L	0.48218	1.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83707	0.0185	10	0.39692	T	0.17	-9.2324	16.1667	0.81768	1.0:0.0:0.0:0.0	.	737	Q96PU4	UHRF2_HUMAN	R	737	ENSP00000276893:Q737R	ENSP00000276893:Q737R	Q	+	2	0	UHRF2	6494639	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.210000	0.71456	0.533000	0.62120	CAG		0.383	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		G	6504639	A	G	6504639	3	3	98	1	0	0	0	0	1	0	0	0	17010	188	7	4	2268	4	UHRF2	9	6504639	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10		6504639	134708792	88	26374										
CER1	9350	hgsc.bcm.edu	37	chr9	14720358	14720358	+	Frame_Shift_Del	DEL	T	T	-													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aggttgttctgaacaactacTttttcacagccttcgtgggt					rs35706018	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:14720358delT	ENST00000380911.3	-	2	578	c.534delA	c.(532-534)aaafs	p.K178fs		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	178	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		GAACAACTACTTTTTCACAGC	0.423																																																0			9											65	57	60					9																	14720358		2203	4300	6503	14710358	SO:0001589	frameshift_variant	23739			AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)", "cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.534delA	9.37:g.14720358delT	ENSP00000370297:p.Lys178fs		14710358	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Frame_Shift_Del	DEL	ENST00000380911.3	37	CCDS6476.1																																																																																				0.423	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454		-	14720358	T	-	14720358	7	5	98	1	0	1	0	1	0	0	0	0	3271	1606	56	0	273	0	CER1	9	14720358	Frame_Shift_Del	DEL	T	TCGA-DC-6160-01A-11D-1657-10	8215719	14720358	126493073	89	26375										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632961	32632961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gtttgaatccatccctgtgcGtttgaagtcagcgcagagct	11	10	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:32632961G>A	ENST00000242310.4	-	1	2706	c.2617C>T	c.(2617-2619)Cgc>Tgc	p.R873C	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	873					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ATCCCTGTGCGTTTGAAGTCA	0.483																																																0			9											147	147	147					9																	32632961		2203	4300	6503	32622961	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2617C>T	9.37:g.32632961G>A	ENSP00000418379:p.Arg873Cys		32622961	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.548593	0.45383	.	.	ENSG00000122728	ENST00000242310	T	0.20332	2.08	1.19	1.19	0.21007	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	M	0.93462	3.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55231	-0.8173	10	0.87932	D	0	.	7.8312	0.29344	0.0:0.0:1.0:0.0	.	873	Q8IZX4	TAF1L_HUMAN	C	873	ENSP00000418379:R873C	ENSP00000418379:R873C	R	-	1	0	TAF1L	32622961	1.000000	0.71417	0.996000	0.52242	0.703000	0.40648	6.138000	0.71717	0.632000	0.30432	0.195000	0.17529	CGC		0.483	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32632961	G	A	32632961	3	1	98	1	0	0	0	0	1	0	0	0	15562	1145	40	1	2867	1	TAF1L	9	32632961	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	17912603	32632961	108580470	90	26376										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98239899	98239899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gtcctgcagccactgacagtGcaaccagcaggacgccagcc	11	16	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:98239899G>A	ENST00000331920.6	-	10	1732	c.1433C>T	c.(1432-1434)gCa>gTa	p.A478V	PTCH1_ENST00000429896.2_Missense_Mutation_p.A327V|PTCH1_ENST00000375274.2_Missense_Mutation_p.A477V|PTCH1_ENST00000430669.2_Missense_Mutation_p.A412V|PTCH1_ENST00000437951.1_Missense_Mutation_p.A412V|PTCH1_ENST00000421141.1_Missense_Mutation_p.A327V|PTCH1_ENST00000418258.1_Missense_Mutation_p.A327V|PTCH1_ENST00000548379.1_5'Flank	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	478	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.A478V(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CACTGACAGTGCAACCAGCAG	0.567																																																1	Substitution - Missense(1)	skin(1)	9											45	46	46					9																	98239899		2203	4300	6503	97279720	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1433C>T	9.37:g.98239899G>A	ENSP00000332353:p.Ala478Val		97279720	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259524	0.95368	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86	5.06	5.06	0.68205	Sterol-sensing domain (1);	0.051243	0.85682	D	0.000000	D	0.90003	0.6879	M	0.65975	2.015	0.58432	D	0.999991	B;B;B	0.31274	0.317;0.199;0.201	B;B;B	0.36092	0.193;0.196;0.217	D	0.86942	0.2080	10	0.13470	T	0.59	-18.342	18.6256	0.91336	0.0:0.0:1.0:0.0	.	412;477;478	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	V	478;412;327;327;412;327;477	ENSP00000332353:A478V;ENSP00000389744:A412V;ENSP00000399981:A327V;ENSP00000396135:A327V;ENSP00000410287:A412V;ENSP00000414823:A327V;ENSP00000364423:A477V	ENSP00000332353:A478V	A	-	2	0	PTCH1	97279720	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	9.263000	0.95617	2.619000	0.88677	0.655000	0.94253	GCA		0.567	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98239899	G	A	98239899	3	1	98	1	0	0	0	0	1	0	0	0	12764	1319	46	3	2966	3	PTCH1	9	98239899	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	65606938	98239899	42973532	91	26377										
OR13C3	138803	hgsc.bcm.edu	37	chr9	107298357	107298358	+	Frame_Shift_Ins	INS	-	-	A													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	agaggatgaacatataggagINSaaaaaaatgaccatcagtgg							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:107298357_107298358insA	ENST00000374781.2	-	1	779_780	c.737_738insT	c.(736-738)ttcfs	p.F246fs		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						ACATATAGGAGAAAAAAATGAC	0.45																																					GBM(86;1248 1274 14222 15028 46219)											0			9																																								106338179	SO:0001589	frameshift_variant	138803				CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"GPCR / Class A : Olfactory receptors"	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.738dupT	9.37:g.107298364_107298364dupA	ENSP00000363913:p.Phe246fs		106338178	Q5VVG1|Q6IF52	Frame_Shift_Ins	INS	ENST00000374781.2	37	CCDS35089.1																																																																																				0.45	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			A	107298358	-	A	107298357	7	5	98	1	0	1	1	0	0	0	0	0	10966	933	33	0	309	0	OR13C3	9	107298357	Frame_Shift_Ins	INS	-	TCGA-DC-6160-01A-11D-1657-10	9058458	107298357	33915074	92	26378										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114184267	114184267	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gccccttccaaagtactataCgctccaaccatcatagataa	4	14	1	1	rs188300073		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:114184267C>T	ENST00000338205.5	-	14	1608	c.1389G>A	c.(1387-1389)gcG>gcA	p.A463A	KIAA0368_ENST00000259335.4_Silent_p.A641A			Q5VYK3	ECM29_HUMAN	KIAA0368	469					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						AAGTACTATACGCTCCAACCA	0.448													C|||	1	0.000199681	8e-04	0	5008	,	,		18813	0		0	False		,,,				2504	0															0			9						C		0,3772		0,0,1886	81	75	77		1923	-11.1	0.1	9		77	1,8229		0,1,4114	no	coding-synonymous	KIAA0368	NM_001080398.1		0,1,6000	TT,TC,CC		0.0122,0.0,0.0083		641/2018	114184267	1,12001	1886	4115	6001	113224088	SO:0001819	synonymous_variant	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1389G>A	9.37:g.114184267C>T			113224088	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																					0.448	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		T	114184267	C	T	114184267	2	4	98	1	0	0	0	0	0	0	0	1	8192	523	19	1		1	KIAA0368	9	114184267	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	6885910	114184267	27029164	93	26379										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138676638	138676638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgagggcgacctgtggatccGcacgtacggccgcctcttcc	13	16	1	0	rs373365707		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr9:138676638G>A	ENST00000263604.3	+	27	3002	c.3002G>A	c.(3001-3003)cGc>cAc	p.R1001H	KCNT1_ENST00000371757.2_Missense_Mutation_p.R1020H|KCNT1_ENST00000488444.2_Missense_Mutation_p.R1001H|KCNT1_ENST00000486577.2_Missense_Mutation_p.R979H|KCNT1_ENST00000490355.2_Missense_Mutation_p.R999H|KCNT1_ENST00000487664.1_Missense_Mutation_p.R975H|KCNT1_ENST00000491806.2_Missense_Mutation_p.R987H|KCNT1_ENST00000298480.5_Missense_Mutation_p.R1020H			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	1001					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CTGTGGATCCGCACGTACGGC	0.627																																																0			9						G	HIS/ARG	0,4406		0,0,2203	67	71	70		3059	3.3	1	9		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNT1	NM_020822.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1020/1236	138676638	1,13005	2203	4300	6503	137816459	SO:0001583	missense	57582			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.3002G>A	9.37:g.138676638G>A	ENSP00000263604:p.Arg1001His		137816459	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	37		.	.	.	.	.	.	.	.	.	.	G	17.81	3.480466	0.63849	0.0	1.16E-4	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	4.19	3.29	0.37713	.	0.000000	0.85682	U	0.000000	T	0.75102	0.3804	M	0.79475	2.455	0.54753	D	0.999986	B;B;B;B	0.32507	0.218;0.373;0.325;0.373	B;B;B;B	0.26770	0.049;0.066;0.073;0.066	T	0.75130	-0.3426	10	0.72032	D	0.01	-6.0464	11.8036	0.52141	0.088:0.0:0.912:0.0	.	987;1020;975;1001	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	H	975;1020;1020;979;987;1001;999;1001	ENSP00000417851:R975H;ENSP00000298480:R1020H;ENSP00000360822:R1020H;ENSP00000263604:R1001H	ENSP00000263604:R1001H	R	+	2	0	KCNT1	137816459	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	7.357000	0.79456	0.743000	0.32719	0.462000	0.41574	CGC		0.627	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138676638	G	A	138676638	3	1	98	1	0	0	0	0	1	0	0	0	8112	1087	38	1	3165	1	KCNT1	9	138676638	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	24492371	138676638	2536793	94	26380										
IL15RA	3601	hgsc.bcm.edu	37	chr10	6002514	6002514	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctgtgttgtttgagctgggAgatgaagctgcgggctctgt	17	6	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:6002514A>G	ENST00000379977.3	-	4	496	c.399T>C	c.(397-399)tcT>tcC	p.S133S	IL15RA_ENST00000528354.1_Silent_p.S100S|IL15RA_ENST00000525219.2_Silent_p.S97S|IL15RA_ENST00000397255.3_Silent_p.S133S|IL15RA_ENST00000534292.1_5'UTR|IL15RA_ENST00000379971.1_Silent_p.S35S|IL15RA_ENST00000397248.2_Silent_p.S97S|IL15RA_ENST00000397250.2_Silent_p.S35S|IL15RA_ENST00000397251.3_Silent_p.S68S|IL15RA_ENST00000530685.1_Silent_p.S100S			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	133					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						TTGAGCTGGGAGATGAAGCTG	0.572																																																0			10											107	94	99					10																	6002514		2203	4300	6503	6042520	SO:0001819	synonymous_variant	3601			U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"Interleukins and interleukin receptors", "CD molecules"	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.399T>C	10.37:g.6002514A>G			6042520	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Silent	SNP	ENST00000379977.3	37	CCDS7074.1	.	.	.	.	.	.	.	.	.	.	A	2.449	-0.326725	0.05350	.	.	ENSG00000134470	ENST00000435171;ENST00000447291	.	.	.	4.19	1.62	0.23740	.	.	.	.	.	T	0.43612	0.1255	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29549	-1.0008	4	.	.	.	-31.9931	2.2847	0.04124	0.6078:0.0:0.1496:0.2425	.	.	.	.	P	9;36	.	.	L	-	2	0	IL15RA	6042520	0.979000	0.34478	0.899000	0.35326	0.228000	0.25075	0.841000	0.27613	0.758000	0.33059	0.459000	0.35465	CTC		0.572	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189		G	6002514	A	G	6002514	2	3	98	1	0	0	0	0	0	0	0	1	7653	291	11	4		4	IL15RA	10	6002514	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10		6002514	129532233	95	26381										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49791110	49791110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tctgcttcttcagccagcccGccttcagcacggggcccagc	10	18	4	0	rs138838300	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:49791110G>A	ENST00000249601.4	-	2	418	c.122C>T	c.(121-123)gCg>gTg	p.A41V	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.A41V|ARHGAP22_ENST00000491108.1_5'UTR|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.A47V	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	41	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CAGCCAGCCCGCCTTCAGCAC	0.607													G|||	11	0.00219649	0.0061	0	5008	,	,		22546	0.003		0	False		,,,				2504	0															0			10						G	VAL/ALA	19,4387	26.2+/-53.5	0,19,2184	141	140	141		122	4.4	1	10	dbSNP_134	141	0,8600		0,0,4300	yes	missense	ARHGAP22	NM_021226.2	64	0,19,6484	AA,AG,GG		0.0,0.4312,0.1461	benign	41/699	49791110	19,12987	2203	4300	6503	49461116	SO:0001583	missense	58504			AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.122C>T	10.37:g.49791110G>A	ENSP00000249601:p.Ala41Val		49461116	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	0	0.0	G	10.42	1.345667	0.24426	0.004312	0.0	ENSG00000128805	ENST00000249601;ENST00000435790;ENST00000417912	T;T;T	0.30714	1.52;1.52;1.52	5.28	4.36	0.52297	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.170854	0.36134	N	0.002770	T	0.35189	0.0923	L	0.56124	1.755	0.30067	N	0.810405	B;P;D;P	0.56287	0.253;0.915;0.975;0.915	B;P;P;P	0.49953	0.073;0.627;0.482;0.627	T	0.25745	-1.0123	10	0.29301	T	0.29	.	10.2564	0.43399	0.0:0.1411:0.6981:0.1608	.	47;41;41;41	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3	.;.;.;RHG22_HUMAN	V	41;47;41	ENSP00000249601:A41V;ENSP00000416701:A47V;ENSP00000412461:A41V	ENSP00000249601:A41V	A	-	2	0	ARHGAP22	49461116	0.993000	0.37304	0.992000	0.48379	0.846000	0.48090	2.192000	0.42649	1.196000	0.43129	0.655000	0.94253	GCG		0.607	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		A	49791110	G	A	49791110	3	1	98	1	0	0	0	0	1	0	0	0	872	1087	38	1	2010	1	ARHGAP22	10	49791110	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	43788596	49791110	85743637	96	26382										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61112139	61112139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgctgtccaccagcacggtcGcctctacattctgctgctgc	9	17	2	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:61112139G>A	ENST00000373868.2	-	3	302	c.215C>T	c.(214-216)gCg>gTg	p.A72V	FAM13C_ENST00000277705.6_Missense_Mutation_p.A72V|FAM13C_ENST00000435852.2_Missense_Mutation_p.A72V|FAM13C_ENST00000419214.2_Missense_Mutation_p.A72V|FAM13C_ENST00000442566.3_Missense_Mutation_p.A72V|FAM13C_ENST00000422313.2_Missense_Mutation_p.A72V|FAM13C_ENST00000468840.2_5'UTR|FAM13C_ENST00000373867.3_5'UTR	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	72										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAGCACGGTCGCCTCTACATT	0.577																																																0			10											47	49	48					10																	61112139		2203	4300	6503	60782145	SO:0001583	missense	220965			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.215C>T	10.37:g.61112139G>A	ENSP00000362975:p.Ala72Val		60782145	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	G	6.331	0.429254	0.11987	.	.	ENSG00000148541	ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000435852;ENST00000422313	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.93	0.743	0.18347	.	0.794133	0.11611	N	0.546791	T	0.40145	0.1105	N	0.08118	0	0.58432	D	0.999999	B;B;B	0.30526	0.0;0.283;0.0	B;B;B	0.23419	0.0;0.046;0.0	T	0.07947	-1.0746	10	0.37606	T	0.19	1.3955	13.692	0.62550	0.0:0.0:0.5363:0.4637	.	72;72;72	B7Z2K3;Q8NE31-3;Q8NE31	.;.;FA13C_HUMAN	V	72	ENSP00000362975:A72V;ENSP00000395661:A72V;ENSP00000277705:A72V;ENSP00000391993:A72V;ENSP00000392302:A72V;ENSP00000400241:A72V	ENSP00000277705:A72V	A	-	2	0	FAM13C	60782145	0.942000	0.31987	0.206000	0.23566	0.510000	0.34073	0.519000	0.22862	-0.097000	0.12307	-0.265000	0.10407	GCG		0.577	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			A	61112139	G	A	61112139	3	1	98	1	0	0	0	0	1	0	0	0	5470	1087	38	1	1590	1	FAM13C	10	61112139	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	11321029	61112139	74422608	97	26383										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75506596	75506596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggaatgctttcataatgaaCgtcaaccagtcagttccacc	8	11	3	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:75506596C>T	ENST00000339365.2	+	3	168	c.6C>T	c.(4-6)aaC>aaT	p.N2N	SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_5'UTR|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000345254.4_Silent_p.N2N	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	2					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCATAATGAACGTCAACCAGT	0.483																																																0			10											101	94	96					10																	75506596		2203	4300	6503	75176602	SO:0001819	synonymous_variant	9632			D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.6C>T	10.37:g.75506596C>T			75176602	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																				0.483	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			T	75506596	C	T	75506596	2	4	98	1	0	0	0	0	0	0	0	1	14033	535	19	1		1	SEC24C	10	75506596	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	14394457	75506596	60028151	98	26384										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78771791	78771791	+	Frame_Shift_Del	DEL	A	A	-													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atcatgacaggccttgcagtAaaaaaatgccctggagaaag							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:78771791delA	ENST00000286628.8	-	18	2025	c.2026delT	c.(2026-2028)tacfs	p.Y676fs	KCNMA1_ENST00000404857.1_Frame_Shift_Del_p.Y676fs|KCNMA1_ENST00000406533.3_Frame_Shift_Del_p.Y680fs|KCNMA1_ENST00000286627.5_Frame_Shift_Del_p.Y676fs|KCNMA1_ENST00000372440.1_Frame_Shift_Del_p.Y676fs|KCNMA1_ENST00000354353.5_Frame_Shift_Del_p.Y676fs|KCNMA1_ENST00000372443.1_Frame_Shift_Del_p.Y676fs|KCNMA1_ENST00000404771.3_Frame_Shift_Del_p.Y676fs	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	676					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GCCTTGCAGTAAAAAAATGCC	0.428																																																0			10											113	110	111					10																	78771791		2203	4300	6503	78441797	SO:0001589	frameshift_variant	3778			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.2026delT	10.37:g.78771791delA	ENSP00000286628:p.Tyr676fs		78441797	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Frame_Shift_Del	DEL	ENST00000286628.8	37																																																																																					0.428	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		-	78771791	A	-	78771791	7	5	98	1	0	1	0	1	0	0	0	0	8094	362	13	0	1884	0	KCNMA1	10	78771791	Frame_Shift_Del	DEL	A	TCGA-DC-6160-01A-11D-1657-10	3265195	78771791	56762956	99	26385										
LRIT2	340745	hgsc.bcm.edu	37	chr10	85984164	85984164	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctggcctgtgccaagcatcGcagggtcacattctgtcctg	12	13	2	0	rs139197166		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:85984164G>A	ENST00000372113.4	-	2	822	c.817C>T	c.(817-819)Cga>Tga	p.R273*	LRIT2_ENST00000538192.1_Nonsense_Mutation_p.R273*	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	273	Ig-like.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						GCCAAGCATCGCAGGGTCACA	0.522													G|||	1	0.000199681	0	0	5008	,	,		20625	0		0	False		,,,				2504	0.001															0			10											97	80	86					10																	85984164		2203	4300	6503	85974144	SO:0001587	stop_gained	340745				CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"Immunoglobulin superfamily / I-set domain containing"	23443	protein-coding gene	gene with protein product			"leucine rich repeat containing 22"	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.817C>T	10.37:g.85984164G>A	ENSP00000361185:p.Arg273*		85974144	B7ZME6	Nonsense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686962	0.88639	.	.	ENSG00000204033	ENST00000372113;ENST00000538192	.	.	.	5.44	-1.91	0.07641	.	0.556839	0.19341	N	0.116645	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9395	0.58335	0.0:0.0878:0.1425:0.7696	.	.	.	.	X	273	.	ENSP00000361185:R273X	R	-	1	2	LRIT2	85974144	0.033000	0.19621	0.411000	0.26484	0.991000	0.79684	0.360000	0.20250	-0.176000	0.10707	0.655000	0.94253	CGA		0.522	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		A	85984164	G	A	85984164	4	1	98	1	0	0	0	0	0	1	0	0	8977	1095	38	1	843	1	LRIT2	10	85984164	Nonsense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	7212373	85984164	49550583	100	26386										
PTEN	5728	hgsc.bcm.edu	37	chr10	89693003	89693003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggaagtaaggaccagagacAaaaaggtaagttattttttg	12	3	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:89693003A>G	ENST00000371953.3	+	5	1844	c.487A>G	c.(487-489)Aaa>Gaa	p.K163E		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	163	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.K163*(2)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GACCAGAGACAAAAAGGTAAG	0.348		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)|Substitution - Nonsense(2)	prostate(17)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											49	51	50					10																	89693003		2203	4300	6503	89682983	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.487A>G	10.37:g.89693003A>G	ENSP00000361021:p.Lys163Glu		89682983	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.261981	0.39995	.	.	ENSG00000171862	ENST00000371953	D	0.98550	-4.99	5.09	5.09	0.68999	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.93851	0.8033	N	0.08118	0	0.80722	D	1	B	0.25007	0.116	B	0.28011	0.085	D	0.92015	0.5621	9	.	.	.	-10.3599	14.8682	0.70434	1.0:0.0:0.0:0.0	.	163	P60484	PTEN_HUMAN	E	163	ENSP00000361021:K163E	.	K	+	1	0	PTEN	89682983	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.918000	0.92759	1.898000	0.54952	0.460000	0.39030	AAA		0.348	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89693003	A	G	89693003	3	3	98	1	0	0	0	0	1	0	0	0	12772	131	5	4	505	4	PTEN	10	89693003	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	3708839	89693003	45841744	101	26387										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93952314	93952314	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	agtgtttacctttcagaggtTcatgatcagtccttatcata	7	8	4	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:93952314T>G	ENST00000265997.4	-	3	1257	c.1085A>C	c.(1084-1086)gAa>gCa	p.E362A	CPEB3_ENST00000412050.4_Missense_Mutation_p.E362A	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	362					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				TTTCAGAGGTTCATGATCAGT	0.403																																																0			10											137	125	129					10																	93952314		2203	4300	6503	93942294	SO:0001583	missense	22849			AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1085A>C	10.37:g.93952314T>G	ENSP00000265997:p.Glu362Ala		93942294	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	37	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777039	0.70107	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.49139	0.8;0.79	6.06	6.06	0.98353	.	0.051048	0.85682	D	0.000000	T	0.50582	0.1624	N	0.08118	0	0.58432	D	0.999995	P;P;D	0.56035	0.779;0.956;0.974	B;D;D	0.70487	0.23;0.931;0.969	T	0.61603	-0.7029	10	0.72032	D	0.01	-14.9532	16.6175	0.84920	0.0:0.0:0.0:1.0	.	362;362;362	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	A	362	ENSP00000398310:E362A;ENSP00000265997:E362A	ENSP00000265997:E362A	E	-	2	0	CPEB3	93942294	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.599000	0.82757	2.326000	0.78906	0.472000	0.43445	GAA		0.403	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		G	93952314	T	G	93952314	3	3	98	1	0	0	0	0	1	0	0	0	3808	1783	62	4	1070	4	CPEB3	10	93952314	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	4259311	93952314	41582433	102	26388										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123258040	123258040	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	caggctccaagaagatttatGatattcttgtgtttcccaat	7	8	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr10:123258040G>T	ENST00000358487.5	-	12	1913	c.1641C>A	c.(1639-1641)atC>atA	p.I547I	FGFR2_ENST00000369059.1_Silent_p.I433I|FGFR2_ENST00000369061.4_Silent_p.I435I|FGFR2_ENST00000356226.4_Silent_p.I430I|FGFR2_ENST00000369060.4_Silent_p.I431I|FGFR2_ENST00000346997.2_Silent_p.I545I|FGFR2_ENST00000369056.1_Silent_p.I548I|FGFR2_ENST00000357555.5_Silent_p.I458I|FGFR2_ENST00000360144.3_Silent_p.I459I|FGFR2_ENST00000457416.2_Silent_p.I548I|FGFR2_ENST00000478859.1_Silent_p.I319I|FGFR2_ENST00000351936.6_Silent_p.I545I	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	547	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GAAGATTTATGATATTCTTGT	0.408		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											170	151	157					10																	123258040		2203	4300	6503	123248030	SO:0001819	synonymous_variant	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1641C>A	10.37:g.123258040G>T			123248030	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																				0.408	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123258040	G	T	123258040	2	4	98	1	0	0	0	0	0	0	0	1	5885	1280	45	2		2	FGFR2	10	123258040	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	29305726	123258040	12276707	103	26389										
TSPAN4	7106	hgsc.bcm.edu	37	chr11	864489	864489	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggaggccaccatcgccatccTcttcttcgcctacacggaca	8	17	2	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:864489T>C	ENST00000397404.1	+	5	567	c.308T>C	c.(307-309)cTc>cCc	p.L103P	TSPAN4_ENST00000397408.1_Missense_Mutation_p.L103P|TSPAN4_ENST00000409531.1_Missense_Mutation_p.L122P|TSPAN4_ENST00000397411.2_Missense_Mutation_p.L103P|TSPAN4_ENST00000346501.4_Missense_Mutation_p.L103P|TSPAN4_ENST00000397397.2_Missense_Mutation_p.L103P|TSPAN4_ENST00000525201.1_Missense_Mutation_p.L39P|TSPAN4_ENST00000397406.1_Missense_Mutation_p.L103P|TSPAN4_ENST00000409543.2_Missense_Mutation_p.L103P|TSPAN4_ENST00000397396.1_Missense_Mutation_p.L39P	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4	103					protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ATCGCCATCCTCTTCTTCGCC	0.662																																																0			11											102	92	95					11																	864489		2203	4299	6502	854489	SO:0001583	missense	7106			AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063		"Tetraspanins"	11859	protein-coding gene	gene with protein product		602644	"transmembrane 4 superfamily member 7"	TM4SF7		9360996	Standard	XM_005253102		Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.308T>C	11.37:g.864489T>C	ENSP00000380553:p.Leu103Pro		854489	Q6IAP6	Missense_Mutation	SNP	ENST00000397404.1	37	CCDS7721.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.840571	0.51057	.	.	ENSG00000214063	ENST00000397397;ENST00000397411;ENST00000397396;ENST00000397408;ENST00000525334;ENST00000397406;ENST00000409543;ENST00000525201;ENST00000397404;ENST00000532375;ENST00000346501;ENST00000409531;ENST00000527644	D;D;D;D;D;D;D;D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	2.9	2.9	0.33743	.	0.085006	0.48767	D	0.000170	D	0.91496	0.7315	H	0.97158	3.95	0.80722	D	1	D	0.61080	0.989	D	0.71184	0.972	D	0.91698	0.5371	10	0.72032	D	0.01	.	8.9426	0.35740	0.0:0.0:0.0:1.0	.	103	O14817	TSN4_HUMAN	P	103;103;39;103;39;103;103;39;103;39;103;122;103	ENSP00000380552:L103P;ENSP00000380558:L103P;ENSP00000380551:L39P;ENSP00000380555:L103P;ENSP00000433980:L39P;ENSP00000380554:L103P;ENSP00000386513:L103P;ENSP00000431943:L39P;ENSP00000380553:L103P;ENSP00000434818:L39P;ENSP00000324304:L103P;ENSP00000386899:L122P;ENSP00000436260:L103P	ENSP00000324304:L103P	L	+	2	0	TSPAN4	854489	1.000000	0.71417	0.942000	0.38095	0.388000	0.30384	5.650000	0.67944	1.202000	0.43218	0.260000	0.18958	CTC		0.662	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257102.2			C	864489	T	C	864489	3	2	98	1	0	0	0	0	1	0	0	0	16689	1551	54	4	318	4	TSPAN4	11	864489	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10		864489	134142027	104	26390										
TH	7054	hgsc.bcm.edu	37	chr11	2190907	2190907	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	accttcacagctcgggacagCgccgagggcttggtggccct	14	14	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:2190907C>T	ENST00000381178.1	-	3	396	c.378G>A	c.(376-378)gcG>gcA	p.A126A	TH_ENST00000381175.1_Silent_p.A122A|TH_ENST00000352909.3_Silent_p.A95A|TH_ENST00000333684.5_Silent_p.A99A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	126					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CTCGGGACAGCGCCGAGGGCT	0.657																																																0			11											63	70	67					11																	2190907		2202	4299	6501	2147483	SO:0001819	synonymous_variant	7054			X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"tyrosine 3-monooxygenase"	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.378G>A	11.37:g.2190907C>T			2147483	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																				0.657	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		T	2190907	C	T	2190907	2	4	98	1	0	0	0	0	0	0	0	1	15877	755	27	1		1	TH	11	2190907	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	1326418	2190907	132815609	105	26391										
MRVI1	10335	hgsc.bcm.edu	37	chr11	10647702	10647702	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcagggccactgtcccaggaGagccctcgcagcagcggggg	16	14	1	1	rs2241489	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:10647702G>A	ENST00000436272.1	-	8	1176	c.1098C>T	c.(1096-1098)ctC>ctT	p.L366L	MRVI1_ENST00000541483.1_Intron|MRVI1_ENST00000552103.1_Silent_p.L302L|MRVI1_ENST00000534266.2_Silent_p.L78L|MRVI1_ENST00000558540.1_Silent_p.L78L|MRVI1_ENST00000545852.1_Silent_p.L78L|MRVI1_ENST00000424001.1_Silent_p.L78L|MRVI1_ENST00000423302.2_Silent_p.L393L|MRVI1_ENST00000547195.1_Silent_p.L302L|MRVI1_ENST00000531107.1_Silent_p.L385L|MRVI1_ENST00000421747.1_Silent_p.L384L|MRVI1_ENST00000527509.2_Silent_p.L302L			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	366					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TGTCCCAGGAGAGCCCTCGCA	0.667													G|||	2230	0.445288	0.2557	0.4452	5008	,	,		16413	0.6915		0.4622	False		,,,				2504	0.4305															0			11						G	,,,,,	1053,2665		152,749,958	15	17	16		1155,906,234,,234,1179	-0.9	1	11	dbSNP_98	16	4000,4168		991,2018,1075	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	MRVI1	NM_001098579.2,NM_001100163.2,NM_001100167.2,NM_001206880.1,NM_001206881.1,NM_130385.3	,,,,,	1143,2767,2033	AA,AG,GG		48.9716,28.3217,42.5122	,,,,,	385/905,302/822,78/598,,78/598,393/913	10647702	5053,6833	1859	4084	5943	10604278	SO:0001819	synonymous_variant	10335			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1098C>T	11.37:g.10647702G>A			10604278	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	37																																																																																					0.667	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		A	10647702	G	A	10647702	2	1	98	1	0	0	0	0	0	0	0	1	9883	929	33	3		3	MRVI1	11	10647702	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	8456795	10647702	124358814	106	26392										
WT1	7490	hgsc.bcm.edu	37	chr11	32410610	32410610	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccgagggagacccctcaaagCgccagctggagtttggtcat	13	12	2	1	rs202118284		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:32410610C>T	ENST00000379079.2	-	10	1176	c.903G>A	c.(901-903)gcG>gcA	p.A301A	WT1_ENST00000530998.1_Silent_p.A287A|WT1_ENST00000332351.3_Silent_p.A516A|WT1_ENST00000448076.3_Silent_p.A513A	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	448					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A448A(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CCCCTCAAAGCGCCAGCTGGA	0.522			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome				C|||	1	0.000199681	0	0	5008	,	,		20200	0.001		0	False		,,,				2504	0					yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	1	Substitution - coding silent(1)	large_intestine(1)	11											174	151	159					11																	32410610		2202	4299	6501	32367186	SO:0001819	synonymous_variant	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.903G>A	11.37:g.32410610C>T			32367186	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000379079.2	37	CCDS55751.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	6.649	0.488294	0.12641	.	.	ENSG00000184937	ENST00000527882	T	0.05319	3.46	5.76	-5.59	0.02505	.	0.264865	0.30168	U	0.010254	T	0.06826	0.0174	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17715	-1.0360	7	0.34782	T	0.22	.	5.8858	0.18880	0.0721:0.3259:0.115:0.487	.	.	.	.	T	177	ENSP00000435624:A177T	ENSP00000435624:A177T	A	-	1	0	WT1	32367186	0.950000	0.32346	0.393000	0.26258	0.890000	0.51754	0.024000	0.13555	-1.024000	0.03338	-1.267000	0.01435	GCT		0.522	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		T	32410610	C	T	32410610	2	4	98	1	0	0	0	0	0	0	0	1	17448	755	27	1		1	WT1	11	32410610	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	21762908	32410610	102595906	107	26393										
LRP4	4038	hgsc.bcm.edu	37	chr11	46917461	46917461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acgtgtgcccatcctctgtgAgccggtagcctgtgtggcag	14	12	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:46917461A>G	ENST00000378623.1	-	10	1399	c.1157T>C	c.(1156-1158)cTc>cCc	p.L386P		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	386	EGF-like 1; calcium-binding. {ECO:0000255}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		ATCCTCTGTGAGCCGGTAGCC	0.607																																																0			11											73	61	65					11																	46917461		2201	4299	6500	46874037	SO:0001583	missense	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.1157T>C	11.37:g.46917461A>G	ENSP00000367888:p.Leu386Pro		46874037	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505119	0.85282	.	.	ENSG00000134569	ENST00000378623	D	0.96232	-3.95	5.8	5.8	0.92144	Growth factor, receptor (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.98185	0.9400	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98776	1.0730	10	0.54805	T	0.06	.	16.1432	0.81544	1.0:0.0:0.0:0.0	.	386	O75096	LRP4_HUMAN	P	386	ENSP00000367888:L386P	ENSP00000367888:L386P	L	-	2	0	LRP4	46874037	1.000000	0.71417	0.971000	0.41717	0.997000	0.91878	8.719000	0.91436	2.214000	0.71695	0.528000	0.53228	CTC		0.607	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		G	46917461	A	G	46917461	3	3	98	1	0	0	0	0	1	0	0	0	8988	304	11	4	4676	4	LRP4	11	46917461	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	14506851	46917461	88089055	108	26394										
P2RX3	5024	hgsc.bcm.edu	37	chr11	57135907	57135907	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcggcctttacttctgtgggAgtggtgagttcagcccctcc	13	12	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:57135907A>G	ENST00000263314.2	+	10	1033	c.999A>G	c.(997-999)ggA>ggG	p.G333G		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	333					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CTTCTGTGGGAGTGGTGAGTT	0.612																																																0			11											155	122	133					11																	57135907		2201	4296	6497	56892483	SO:0001819	synonymous_variant	5024			Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.999A>G	11.37:g.57135907A>G			56892483	Q6DK37|Q9UQB6	Silent	SNP	ENST00000263314.2	37	CCDS7953.1																																																																																				0.612	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559		G	57135907	A	G	57135907	2	3	98	1	0	0	0	0	0	0	0	1	11372	291	11	4		4	P2RX3	11	57135907	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	10218446	57135907	77870609	109	26395										
PRG3	10394	hgsc.bcm.edu	37	chr11	57147010	57147010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gagtccgcaccaataggtagCggcagatcttgcaccttgga	12	11	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:57147010C>T	ENST00000287143.2	-	3	441	c.332G>A	c.(331-333)cGc>cAc	p.R111H		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						CAATAGGTAGCGGCAGATCTT	0.532																																					Melanoma(154;1456 2519 19358 45229)											0			11											128	126	127					11																	57147010		2201	4296	6497	56903586	SO:0001583	missense	84883			AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.332G>A	11.37:g.57147010C>T	ENSP00000287143:p.Arg111His		56903586	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	37	CCDS7954.1	.	.	.	.	.	.	.	.	.	.	C	8.927	0.962469	0.18583	.	.	ENSG00000156575	ENST00000287143	T	0.39787	1.06	5.27	-10.5	0.00291	C-type lectin fold (1);C-type lectin (1);	1.246370	0.05475	N	0.553753	T	0.31009	0.0783	L	0.49455	1.56	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.23904	-1.0175	10	0.15066	T	0.55	-0.2423	12.365	0.55224	0.0:0.3303:0.0792:0.5905	.	111	Q9Y2Y8	PRG3_HUMAN	H	111	ENSP00000287143:R111H	ENSP00000287143:R111H	R	-	2	0	PRG3	56903586	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.435000	0.00234	-3.785000	0.00107	-2.153000	0.00332	CGC		0.532	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093		T	57147010	C	T	57147010	3	4	98	1	0	0	0	0	1	0	0	0	12514	768	27	1	361	1	PRG3	11	57147010	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	11103	57147010	77859506	110	26396										
MS4A6E	245802	hgsc.bcm.edu	37	chr11	60105330	60105330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcattgcagtgtaagttggaCgaaaaggatataccaaccag	10	7	1	0	rs150096314	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:60105330C>T	ENST00000300182.4	+	2	329	c.264C>T	c.(262-264)gaC>gaT	p.D88D		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	88						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						GTAAGTTGGACGAAAAGGATA	0.458													C|||	19	0.00379393	0.0144	0	5008	,	,		19295	0		0	False		,,,				2504	0															0			11						C		39,4367	43.1+/-76.7	1,37,2165	157	148	151		264	2	0	11	dbSNP_134	151	0,8600		0,0,4300	no	coding-synonymous	MS4A6E	NM_139249.2		1,37,6465	TT,TC,CC		0.0,0.8852,0.2999		88/148	60105330	39,12967	2203	4300	6503	59861906	SO:0001819	synonymous_variant	245802			AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.264C>T	11.37:g.60105330C>T			59861906	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Silent	SNP	ENST00000300182.4	37	CCDS7984.1																																																																																				0.458	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1			T	60105330	C	T	60105330	2	4	98	1	0	0	0	0	0	0	0	1	9895	535	19	1		1	MS4A6E	11	60105330	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	2958320	60105330	74901186	111	26397										
MLL	4297	hgsc.bcm.edu	37	chr11	118373628	118373628	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggccccacaggttcataacAcaacatctagagaactgaat	7	11	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr11:118373628A>T	ENST00000389506.5	+	27	7012	c.7012A>T	c.(7012-7014)Aca>Tca	p.T2338S	KMT2A_ENST00000534358.1_Missense_Mutation_p.T2341S|KMT2A_ENST00000354520.4_Missense_Mutation_p.T2300S			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2338					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.T2338S(1)									GGTTCATAACACAACATCTAG	0.478																																																1	Substitution - Missense(1)	kidney(1)	11											121	129	126					11																	118373628		2200	4296	6496	117878838	SO:0001583	missense	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7012A>T	11.37:g.118373628A>T	ENSP00000374157:p.Thr2338Ser		117878838	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	5.478	0.273182	0.10349	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.80994	-1.44;-1.44;-1.41	5.19	0.0287	0.14159	.	0.666605	0.16113	N	0.228971	T	0.52289	0.1725	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35871	-0.9771	10	0.05721	T	0.95	.	0.3153	0.00294	0.3599:0.2322:0.1574:0.2505	.	2341;2338	E9PQG7;Q03164	.;MLL1_HUMAN	S	2341;2338;2300;1248	ENSP00000436786:T2341S;ENSP00000374157:T2338S;ENSP00000346516:T2300S	ENSP00000346516:T2300S	T	+	1	0	MLL	117878838	0.000000	0.05858	0.022000	0.16811	0.891000	0.51852	0.081000	0.14823	-0.150000	0.11195	0.460000	0.39030	ACA		0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118373628	A	T	118373628	3	4	98	1	0	0	0	0	1	0	0	0	9650	159	6	5	7118	5	MLL	11	118373628	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	58268298	118373628	16632888	112	26398										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380283	25380283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	actgtactcctcttgacctgCtgtgtcgagaatatccaaga	8	11	1	3	rs121913528		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr12:25380283C>T	ENST00000256078.4	-	3	238	c.175G>A	c.(175-177)Gca>Aca	p.A59T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.A59T	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	59			A -> T (in bladder cancer and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:1553789}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A59T(10)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TCTTGACCTGCTGTGTCGAGA	0.423	A59T(143B_BONE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	10	Substitution - Missense(10)	stomach(5)|large_intestine(3)|urinary_tract(1)|haematopoietic_and_lymphoid_tissue(1)	12											107	95	99					12																	25380283		2203	4300	6503	25271550	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.175G>A	12.37:g.25380283C>T	ENSP00000256078:p.Ala59Thr		25271550	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	31	5.083391	0.94050	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.77	4.87	0.63330	Small GTP-binding protein domain (1);	0.046090	0.85682	D	0.000000	D	0.95201	0.8444	H	0.96333	3.805	0.80722	D	1	P;P	0.50528	0.635;0.936	B;P	0.54210	0.321;0.745	D	0.96531	0.9393	10	0.72032	D	0.01	.	16.1496	0.81605	0.0:0.8663:0.1337:0.0	.	59;59	P01116-2;P01116	.;RASK_HUMAN	T	59	ENSP00000308495:A59T;ENSP00000256078:A59T	ENSP00000256078:A59T	A	-	1	0	KRAS	25271550	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.763000	0.85283	1.544000	0.49359	0.655000	0.94253	GCA		0.423	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25380283	C	T	25380283	3	4	98	1	0	0	0	0	1	0	0	0	8459	797	28	3	527	3	KRAS	12	25380283	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10		25380283	108471612	113	26399										
LRP1	4035	hgsc.bcm.edu	37	chr12	57585235	57585235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcagcaacatgaagctgctgCgcgtggacatcccccagcag	12	14	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr12:57585235C>T	ENST00000243077.3	+	44	7835	c.7369C>T	c.(7369-7371)Cgc>Tgc	p.R2457C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2457					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GAAGCTGCTGCGCGTGGACAT	0.662																																																0			12											73	62	66					12																	57585235		2203	4298	6501	55871502	SO:0001583	missense	10438			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7369C>T	12.37:g.57585235C>T	ENSP00000243077:p.Arg2457Cys		55871502	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	c	17.26	3.343345	0.61073	.	.	ENSG00000123384	ENST00000243077	D	0.91631	-2.88	4.61	4.61	0.57282	Six-bladed beta-propeller, TolB-like (1);	0.150547	0.44285	D	0.000480	D	0.96049	0.8713	M	0.89214	3.015	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95923	0.8932	10	0.56958	D	0.05	.	11.6841	0.51474	0.1772:0.8228:0.0:0.0	.	2457	Q07954	LRP1_HUMAN	C	2457	ENSP00000243077:R2457C	ENSP00000243077:R2457C	R	+	1	0	LRP1	55871502	1.000000	0.71417	0.990000	0.47175	0.906000	0.53458	2.371000	0.44248	2.424000	0.82194	0.531000	0.56144	CGC		0.662	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57585235	C	T	57585235	3	4	98	1	0	0	0	0	1	0	0	0	8980	768	27	1	7543	1	LRP1	12	57585235	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	32204952	57585235	76266660	114	26400										
NUAK1	9891	hgsc.bcm.edu	37	chr12	106480539	106480539	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	caatagtgcacagcagagacGatctgccggaagaagtgccg	13	10	1	2	rs267603280		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr12:106480539G>A	ENST00000261402.2	-	3	1865	c.486C>T	c.(484-486)atC>atT	p.I162I		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	162	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						CAGCAGAGACGATCTGCCGGA	0.517																																																0			12											112	91	98					12																	106480539		2203	4300	6503	105004669	SO:0001819	synonymous_variant	9891			AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.486C>T	12.37:g.106480539G>A			105004669	A7MD39|Q96KA8	Silent	SNP	ENST00000261402.2	37	CCDS31892.1																																																																																				0.517	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		A	106480539	G	A	106480539	2	1	98	1	0	0	0	0	0	0	0	1	10743	1048	37	1		1	NUAK1	12	106480539	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	48895304	106480539	27371356	115	26401										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123055446	123055446	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	attcttgcaaaatggttggaAcaagcagccaggaaccttga	10	8	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr12:123055446A>G	ENST00000333479.7	+	23	2061	c.1884A>G	c.(1882-1884)gaA>gaG	p.E628E	KNTC1_ENST00000450485.2_Silent_p.E591E	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	628					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	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)		AATGGTTGGAACAAGCAGCCA	0.294																																																0			12											22	21	21					12																	123055446		1793	4059	5852	121621399	SO:0001819	synonymous_variant	9735				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.1884A>G	12.37:g.123055446A>G			121621399	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	37	CCDS45002.1																																																																																				0.294	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			G	123055446	A	G	123055446	2	3	98	1	0	0	0	0	0	0	0	1	8449	40	2	4		4	KNTC1	12	123055446	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	16574907	123055446	10796449	116	26402										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123810120	123810120	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tctaatgttctagcttctccTgtagactgcagaccaattac	6	11	3	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr12:123810120T>C	ENST00000602398.1	-	15	2029	c.1902A>G	c.(1900-1902)acA>acG	p.T634T	SBNO1_ENST00000267176.4_Silent_p.T633T|SBNO1_ENST00000420886.2_Silent_p.T634T|SBNO1_ENST00000602750.1_Silent_p.T633T			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	634			T -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TAGCTTCTCCTGTAGACTGCA	0.333																																																0			12											164	172	170					12																	123810120		2203	4300	6503	122376073	SO:0001819	synonymous_variant	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1902A>G	12.37:g.123810120T>C			122376073	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																				0.333	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123810120	T	C	123810120	2	2	98	1	0	0	0	0	0	0	0	1	13899	1567	55	4		4	SBNO1	12	123810120	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	754674	123810120	10041775	117	26403										
GJA3	2700	hgsc.bcm.edu	37	chr13	20716415	20716415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccgggtaagccttgagcgccGggggctgccgctcggccgcc	17	16	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr13:20716415G>A	ENST00000241125.3	-	2	1189	c.1013C>T	c.(1012-1014)cCg>cTg	p.P338L		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	338					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		CTTGAGCGCCGGGGGCTGCCG	0.736																																																0			13																																								19614415	SO:0001583	missense	2700			AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"Ion channels / Gap junction proteins (connexins)"	4277	protein-coding gene	gene with protein product	"connexin 46"	121015	"gap junction protein, alpha 3, 46kD (connexin 46)", "gap junction protein, alpha 3, 46kDa (connexin 46)"	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.1013C>T	13.37:g.20716415G>A	ENSP00000241125:p.Pro338Leu		19614415	Q0VAB7|Q9H537	Missense_Mutation	SNP	ENST00000241125.3	37	CCDS9289.1	.	.	.	.	.	.	.	.	.	.	G	0.524	-0.860729	0.02610	.	.	ENSG00000121743	ENST00000241125	D	0.97328	-4.34	4.55	2.44	0.29823	.	1.073180	0.07262	U	0.867626	D	0.91613	0.7350	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.81814	-0.0760	10	0.18276	T	0.48	.	8.7203	0.34436	0.1167:0.0:0.7315:0.1518	.	338	Q9Y6H8	CXA3_HUMAN	L	338	ENSP00000241125:P338L	ENSP00000241125:P338L	P	-	2	0	GJA3	19614415	0.221000	0.23642	0.000000	0.03702	0.000000	0.00434	1.425000	0.34859	0.369000	0.24510	-2.067000	0.00394	CCG		0.736	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954		A	20716415	G	A	20716415	3	1	98	1	0	0	0	0	1	0	0	0	6422	1116	39	1	298	1	GJA3	13	20716415	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10		20716415	94453463	118	26404										
TBC1D4	9882	hgsc.bcm.edu	37	chr13	76055525	76055525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctgttgtggatgaagcgcgAgatatgctgcgccttgtgct	15	8	0	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr13:76055525A>G	ENST00000377636.3	-	1	725	c.379T>C	c.(379-381)Tcg>Ccg	p.S127P	TBC1D4_ENST00000377625.2_Missense_Mutation_p.S127P|TBC1D4_ENST00000431480.2_Missense_Mutation_p.S127P|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	127	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		ATGAAGCGCGAGATATGCTGC	0.662																																																0			13											93	111	105					13																	76055525		2163	4277	6440	74953526	SO:0001583	missense	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.379T>C	13.37:g.76055525A>G	ENSP00000366863:p.Ser127Pro		74953526	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743823	0.69418	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.33216	1.42;1.42;1.42	4.16	1.51	0.23008	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.322546	0.20924	N	0.083230	T	0.43366	0.1244	L	0.44542	1.39	0.80722	D	1	P;D;D	0.76494	0.951;0.999;0.999	P;D;D	0.72338	0.786;0.943;0.977	T	0.11717	-1.0576	10	0.45353	T	0.12	-2.0935	11.9444	0.52920	0.4735:0.5265:0.0:0.0	.	127;127;127	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	P	127	ENSP00000366863:S127P;ENSP00000395986:S127P;ENSP00000366852:S127P	ENSP00000366852:S127P	S	-	1	0	TBC1D4	74953526	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.475000	0.53136	0.128000	0.18479	0.459000	0.35465	TCG		0.662	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		G	76055525	A	G	76055525	3	3	98	1	0	0	0	0	1	0	0	0	15661	304	11	4	3601	4	TBC1D4	13	76055525	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	55339110	76055525	39114353	119	26405										
LIG4	3981	hgsc.bcm.edu	37	chr13	108863441	108863441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gataaaaagagtctgtgacaTctttgtggttcttatgaaga	10	4	3	4			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr13:108863441T>C	ENST00000356922.4	-	2	448	c.176A>G	c.(175-177)gAt>gGt	p.D59G	LIG4_ENST00000442234.1_Missense_Mutation_p.D59G|LIG4_ENST00000405925.1_Missense_Mutation_p.D59G	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	59					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					GTCTGTGACATCTTTGTGGTT	0.358								Non-homologous end-joining																																								0			13											87	90	89					13																	108863441		2203	4300	6503	107661442	SO:0001583	missense	3981			X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.176A>G	13.37:g.108863441T>C	ENSP00000349393:p.Asp59Gly		107661442	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	T	4.549	0.101978	0.08731	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.23552	1.9;1.9;1.9	6.05	2.4	0.29515	DNA ligase, ATP-dependent, N-terminal (3);	0.537818	0.21212	N	0.078291	T	0.18087	0.0434	L	0.35793	1.09	0.09310	N	0.999993	B	0.10296	0.003	B	0.18871	0.023	T	0.14559	-1.0468	10	0.38643	T	0.18	.	7.3014	0.26422	0.0:0.1129:0.1296:0.7575	.	59	P49917	DNLI4_HUMAN	G	59	ENSP00000385955:D59G;ENSP00000402030:D59G;ENSP00000349393:D59G	ENSP00000349393:D59G	D	-	2	0	LIG4	107661442	0.526000	0.26298	0.619000	0.29118	0.990000	0.78478	1.898000	0.39809	1.087000	0.41251	0.523000	0.50628	GAT		0.358	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		C	108863441	T	C	108863441	3	2	98	1	0	0	0	0	1	0	0	0	8806	1435	50	4	2563	4	LIG4	13	108863441	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	32807916	108863441	6306437	120	26406										
PSMB11	122706	hgsc.bcm.edu	37	chr14	23512050	23512050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aggaagcctacgccctggctCgctgcgccgtggcccacgcc	13	18	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr14:23512050C>T	ENST00000408907.2	+	1	675	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	206					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		CGCCCTGGCTCGCTGCGCCGT	0.622																																																0			14											40	41	41					14																	23512050		2124	4240	6364	22581890	SO:0001583	missense	122706				CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.616C>T	14.37:g.23512050C>T	ENSP00000386212:p.Arg206Cys		22581890		Missense_Mutation	SNP	ENST00000408907.2	37	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	C	9.587	1.125031	0.20959	.	.	ENSG00000222028	ENST00000408907	T	0.23754	1.89	5.02	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.28200	0.0696	M	0.80028	2.48	0.52099	D	0.999941	P	0.39737	0.685	B	0.36092	0.217	T	0.08046	-1.0741	10	0.49607	T	0.09	-10.6153	7.4524	0.27246	0.1651:0.7488:0.0:0.0861	.	206	A5LHX3	PSB11_HUMAN	C	206	ENSP00000386212:R206C	ENSP00000386212:R206C	R	+	1	0	PSMB11	22581890	0.751000	0.28327	0.855000	0.33649	0.029000	0.11900	1.566000	0.36396	1.126000	0.42016	0.655000	0.94253	CGC		0.622	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		T	23512050	C	T	23512050	3	4	98	1	0	0	0	0	1	0	0	0	12710	884	31	1	618	1	PSMB11	14	23512050	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10		23512050	83837490	121	26407										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31675095	31675095	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atgtccctttcatctccctgTcccatctgtagccattccag	5	16	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr14:31675095T>C	ENST00000399332.1	-	2	536	c.48A>G	c.(46-48)ggA>ggG	p.G16G	HECTD1_ENST00000556474.1_5'UTR|HECTD1_ENST00000553700.1_Silent_p.G16G	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	16					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		CATCTCCCTGTCCCATCTGTA	0.418																																																0			14											173	161	165					14																	31675095		1959	4150	6109	30744846	SO:0001819	synonymous_variant	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.48A>G	14.37:g.31675095T>C			30744846	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																				0.418	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31675095	T	C	31675095	2	2	98	1	0	0	0	0	0	0	0	1	7060	1654	58	4		4	HECTD1	14	31675095	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	8163045	31675095	75674445	122	26408										
DDX24	57062	hgsc.bcm.edu	37	chr14	94517583	94517583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctgttccggctgtggctccTtcggcttctttgtcttcttc	10	13	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr14:94517583T>C	ENST00000330836.5	-	9	2665	c.2534A>G	c.(2533-2535)aAg>aGg	p.K845R	DDX24_ENST00000555054.1_Missense_Mutation_p.K802R|DDX24_ENST00000544005.1_Missense_Mutation_p.K595R|DDX24_ENST00000553400.1_5'UTR	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	845	Poly-Lys.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CTGTGGCTCCTTCGGCTTCTT	0.512											OREG0022891	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			14											84	88	87					14																	94517583		2203	4300	6503	93587336	SO:0001583	missense	57062			AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.2534A>G	14.37:g.94517583T>C	ENSP00000328690:p.Lys845Arg	1306	93587336	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	37	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237635	0.39598	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054	T;T;T	0.03607	3.96;3.87;3.96	4.6	2.11	0.27256	.	0.950586	0.08827	N	0.887933	T	0.04003	0.0112	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42982	-0.9419	10	0.46703	T	0.11	-0.1316	5.4214	0.16402	0.0:0.1008:0.1737:0.7255	.	845	Q9GZR7	DDX24_HUMAN	R	845;595;790;471;802	ENSP00000328690:K845R;ENSP00000440623:K595R;ENSP00000452145:K802R	ENSP00000328690:K845R	K	-	2	0	DDX24	93587336	0.005000	0.15991	0.000000	0.03702	0.165000	0.22458	1.211000	0.32382	0.330000	0.23485	0.459000	0.35465	AAG		0.512	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		C	94517583	T	C	94517583	3	2	98	1	0	0	0	0	1	0	0	0	4357	1609	56	4	49	4	DDX24	14	94517583	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	62842488	94517583	12831957	123	26409										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105420119	105420119	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgtcctctgtagtccttcctCtccatctccttcatccccct	3	19	4	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr14:105420119C>T	ENST00000333244.5	-	7	1788	c.1669G>A	c.(1669-1671)Gag>Aag	p.E557K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	557						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			AGTCCTTCCTCTCCATCTCCT	0.557																																																0			14											301	314	310					14																	105420119		2124	4246	6370	104491164	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.1669G>A	14.37:g.105420119C>T	ENSP00000353114:p.Glu557Lys		104491164	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	12.12	1.843403	0.32606	.	.	ENSG00000185567	ENST00000333244	T	0.02606	4.23	4.81	-1.37	0.09056	.	.	.	.	.	T	0.01454	0.0047	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.15870	0.014	T	0.48127	-0.9062	9	0.07325	T	0.83	.	9.4135	0.38507	0.0:0.3332:0.4909:0.1759	.	557	Q8IVF2	AHNK2_HUMAN	K	557	ENSP00000353114:E557K	ENSP00000353114:E557K	E	-	1	0	AHNAK2	104491164	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-0.892000	0.04131	-0.060000	0.13132	-1.259000	0.01468	GAG		0.557	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105420119	C	T	105420119	3	4	98	1	0	0	0	0	1	0	0	0	415	922	32	3	15722	3	AHNAK2	14	105420119	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	10902536	105420119	1929421	124	26410										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25972335	25972335	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atgacaatgccgacgactgcGtccgtgttcctaagggtgca	12	11	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:25972335G>A	ENST00000356865.6	-	4	930	c.819C>T	c.(817-819)gaC>gaT	p.D273D		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	273					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CGACGACTGCGTCCGTGTTCC	0.572																																																0			15											150	115	127					15																	25972335		2203	4300	6503	23523428	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.819C>T	15.37:g.25972335G>A			23523428	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.572	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25972335	G	A	25972335	2	1	98	1	0	0	0	0	0	0	0	1	1117	1136	40	1		1	ATP10A	15	25972335	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10		25972335	76559057	125	26411										
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41068792	41068792	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cctcttcctcctcactctccTgggcctgggcctgccgctcc	8	21	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:41068792T>C	ENST00000220496.4	-	5	359	c.329A>G	c.(328-330)cAg>cGg	p.Q110R		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	110					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTCACTCTCCTGGGCCTGGGC	0.632																																																0			15											105	94	98					15																	41068792		2203	4300	6503	38856084	SO:0001583	missense	55192			AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"Heat shock proteins / DNAJ (HSP40)", "RNA binding motif (RRM) containing"	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.329A>G	15.37:g.41068792T>C	ENSP00000220496:p.Gln110Arg		38856084		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	.	.	.	.	.	.	.	.	.	.	T	7.046	0.563433	0.13498	.	.	ENSG00000104129	ENST00000220496	T	0.18502	2.21	4.99	1.26	0.21427	.	0.988489	0.08264	N	0.972521	T	0.07683	0.0193	N	0.10809	0.05	0.19300	N	0.999973	B	0.02656	0.0	B	0.01281	0.0	T	0.43327	-0.9398	10	0.15952	T	0.53	.	3.7073	0.08405	0.3952:0.1507:0.0:0.4541	.	110	Q9NVM6	DJC17_HUMAN	R	110	ENSP00000220496:Q110R	ENSP00000220496:Q110R	Q	-	2	0	DNAJC17	38856084	0.930000	0.31532	0.218000	0.23776	0.992000	0.81027	1.403000	0.34612	-0.036000	0.13669	0.459000	0.35465	CAG		0.632	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		C	41068792	T	C	41068792	3	2	98	1	0	0	0	0	1	0	0	0	4647	1580	55	4	613	4	DNAJC17	15	41068792	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	15096457	41068792	61462600	126	26412										
MGA	23269	hgsc.bcm.edu	37	chr15	42042158	42042158	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgtgaaggtggaacagcagaAaggatttgacaatccagaag	13	5	0	4			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:42042158A>T	ENST00000570161.1	+	16	6353	c.6353A>T	c.(6352-6354)aAa>aTa	p.K2118I	MGA_ENST00000219905.7_Missense_Mutation_p.K2118I|MGA_ENST00000545763.1_Missense_Mutation_p.K1909I|MGA_ENST00000389936.4_Missense_Mutation_p.K2079I|MGA_ENST00000566586.1_Missense_Mutation_p.K1909I			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GAACAGCAGAAAGGATTTGAC	0.363																																																0			15											63	58	60					15																	42042158		1841	4100	5941	39829450	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.6353A>T	15.37:g.42042158A>T	ENSP00000457035:p.Lys2118Ile		39829450	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	6.335	0.429890	0.11987	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.86030	-2.06;-2.02;-2.04	4.53	-6.79E-4	0.14037	.	0.859224	0.09962	N	0.733244	T	0.71247	0.3317	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.31054	0.278;0.228;0.306;0.306	B;B;B;B	0.28305	0.088;0.082;0.054;0.054	T	0.60989	-0.7153	10	0.72032	D	0.01	.	4.9871	0.14196	0.4958:0.1578:0.3464:0.0	.	734;1909;2118;2079	B4DVS1;F5H7K2;E7ENI0;Q8IWI9	.;.;.;MGAP_HUMAN	I	2118;2079;1909	ENSP00000219905:K2118I;ENSP00000374586:K2079I;ENSP00000442467:K1909I	ENSP00000219905:K2118I	K	+	2	0	MGA	39829450	0.000000	0.05858	0.607000	0.28956	0.464000	0.32679	0.724000	0.25954	-0.004000	0.14419	0.383000	0.25322	AAA		0.363	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42042158	A	T	42042158	3	4	98	1	0	0	0	0	1	0	0	0	9570	14	1	5	6415	5	MGA	15	42042158	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	973366	42042158	60489234	127	26413										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42167185	42167185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tttctgcagcctctggctggAgcgcaggtcctgccctgttt	12	13	2	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:42167185A>G	ENST00000320955.6	-	23	4584	c.4357T>C	c.(4357-4359)Tcc>Ccc	p.S1453P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1453					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTCTGGCTGGAGCGCAGGTCC	0.637																																																0			15											36	40	39					15																	42167185		2046	4172	6218	39954477	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4357T>C	15.37:g.42167185A>G	ENSP00000317790:p.Ser1453Pro		39954477		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	8.280	0.815389	0.16607	.	.	ENSG00000137877	ENST00000320955	T	0.74842	-0.88	5.12	2.72	0.32119	.	0.000000	0.64402	D	0.000001	T	0.65186	0.2667	M	0.78637	2.42	0.09310	N	0.999999	P	0.43169	0.8	B	0.34180	0.177	T	0.64601	-0.6369	10	0.72032	D	0.01	.	2.1834	0.03880	0.5946:0.1622:0.0871:0.1562	.	1453	Q9NRC6	SPTN5_HUMAN	P	1453	ENSP00000317790:S1453P	ENSP00000317790:S1453P	S	-	1	0	SPTBN5	39954477	1.000000	0.71417	0.004000	0.12327	0.047000	0.14425	3.026000	0.49689	0.252000	0.21531	0.454000	0.30748	TCC		0.637	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42167185	A	G	42167185	3	3	98	1	0	0	0	0	1	0	0	0	15161	304	11	4	6851	4	SPTBN5	15	42167185	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	125027	42167185	60364207	128	26414										
SNX1	6642	hgsc.bcm.edu	37	chr15	64410395	64410395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaaacactcatttctcttccTcctcaggaagccacaaattc	3	14	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:64410395T>C	ENST00000559844.1	+	3	365	c.351T>C	c.(349-351)ccT>ccC	p.P117P	SNX1_ENST00000560829.1_5'UTR|SNX1_ENST00000353874.4_Silent_p.P117P|SNX1_ENST00000561026.1_Intron|SNX1_ENST00000261889.5_Silent_p.P117P			Q13596	SNX1_HUMAN	sorting nexin 1	117				P -> S (in Ref. 2; AAC17182). {ECO:0000305}.	early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						TTTCTCTTCCTCCTCAGGAAG	0.433																																																0			15											108	98	101					15																	64410395		2203	4300	6503	62197448	SO:0001819	synonymous_variant	6642			BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.351T>C	15.37:g.64410395T>C			62197448	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Silent	SNP	ENST00000559844.1	37	CCDS32266.1																																																																																				0.433	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		C	64410395	T	C	64410395	2	2	98	1	0	0	0	0	0	0	0	1	14917	1538	54	4		4	SNX1	15	64410395	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	22243210	64410395	38120997	129	26415										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65994657	65994657	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgttacctcatcaggtggatCcatcttctttgactgcattt	7	10	4	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:65994657C>A	ENST00000431932.2	-	17	2624	c.2416G>T	c.(2416-2418)Gat>Tat	p.D806Y	DENND4A_ENST00000443035.3_Missense_Mutation_p.D806Y	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	806					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TCAGGTGGATCCATCTTCTTT	0.388																																																0			15											44	37	39					15																	65994657		1775	3876	5651	63781711	SO:0001583	missense	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2416G>T	15.37:g.65994657C>A	ENSP00000396830:p.Asp806Tyr		63781711	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.788839	0.70337	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05258	3.47;3.49	5.49	5.49	0.81192	.	0.101162	0.64402	D	0.000002	T	0.19967	0.0480	L	0.48642	1.525	0.58432	D	0.999999	D;D	0.76494	0.999;0.998	D;D	0.66196	0.926;0.942	T	0.00096	-1.2074	10	0.59425	D	0.04	.	19.3483	0.94374	0.0:1.0:0.0:0.0	.	806;806	E7EPL3;Q7Z401	.;MYCPP_HUMAN	Y	806	ENSP00000391167:D806Y;ENSP00000396830:D806Y	ENSP00000396830:D806Y	D	-	1	0	DENND4A	63781711	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.676000	0.61627	2.577000	0.86979	0.585000	0.79938	GAT		0.388	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		A	65994657	C	A	65994657	3	1	98	1	0	0	0	0	1	0	0	0	4444	855	30	2	3372	2	DENND4A	15	65994657	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	1584262	65994657	36536735	130	26416										
IL16	3603	hgsc.bcm.edu	37	chr15	81595964	81595964	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggttcagcttggcaggaggAgcagatctagaaaacaaggt	15	6	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr15:81595964A>G	ENST00000302987.4	+	15	3393	c.3393A>G	c.(3391-3393)ggA>ggG	p.G1131G	IL16_ENST00000394652.2_Silent_p.G430G|RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Silent_p.G1131G			Q14005	IL16_HUMAN	interleukin 16	1131	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TGGCAGGAGGAGCAGATCTAG	0.517																																																0			15											170	152	158					15																	81595964		2203	4300	6503	79383019	SO:0001819	synonymous_variant	3603			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3393A>G	15.37:g.81595964A>G			79383019	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																				0.517	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81595964	A	G	81595964	2	3	98	1	0	0	0	0	0	0	0	1	7654	291	11	4		4	IL16	15	81595964	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	15601307	81595964	20935428	131	26417										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3632513	3632513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cagctctgcctgcagctcccGcagctcaaagggctggtaca	11	15	2	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr16:3632513G>A	ENST00000294008.3	-	15	5975	c.5335C>T	c.(5335-5337)Cgg>Tgg	p.R1779W	RP11-461A8.1_ENST00000573982.1_lincRNA	NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1779	Interaction with PLK1 and TERF2-TERF2IP.|Interaction with SLX1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGCAGCTCCCGCAGCTCAAAG	0.647								Direct reversal of damage																																								0			16											98	94	95					16																	3632513		2197	4300	6497	3572514	SO:0001583	missense	0			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.5335C>T	16.37:g.3632513G>A	ENSP00000294008:p.Arg1779Trp		3572514	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161122	0.38119	.	.	ENSG00000188827	ENST00000294008	T	0.01152	5.26	5.4	2.26	0.28386	.	0.763192	0.12400	N	0.472166	T	0.00967	0.0032	N	0.08118	0	0.24479	N	0.994355	D	0.53312	0.959	B	0.42653	0.394	T	0.58154	-0.7686	10	0.87932	D	0	.	10.8848	0.46960	0.2604:0.6133:0.1263:0.0	.	1779	Q8IY92	SLX4_HUMAN	W	1779	ENSP00000294008:R1779W	ENSP00000294008:R1779W	R	-	1	2	SLX4	3572514	1.000000	0.71417	0.805000	0.32314	0.824000	0.46624	0.868000	0.27982	0.670000	0.31165	-0.375000	0.07067	CGG		0.647	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3632513	G	A	3632513	3	1	98	1	0	0	0	0	1	0	0	0	1543	1086	38	1	173	1	BTBD12	16	3632513	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10		3632513	86722240	132	26418										
SPN	6693	hgsc.bcm.edu	37	chr16	29675991	29675991	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	caggtccctgaggagggggcCgtgacagtgaccgtgggagg	20	9	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr16:29675991C>T	ENST00000360121.3	+	2	1034	c.942C>T	c.(940-942)gcC>gcT	p.A314A	SPN_ENST00000395389.2_Silent_p.A314A	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						AGGAGGGGGCCGTGACAGTGA	0.701																																																0			16											6	7	6					16																	29675991		2137	4172	6309	29583492	SO:0001819	synonymous_variant	10522			J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.942C>T	16.37:g.29675991C>T			29583492	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000360121.3	37	CCDS10650.1																																																																																				0.701	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			T	29675991	C	T	29675991	2	4	98	1	0	0	0	0	0	0	0	1	15112	639	23	1		1	SPN	16	29675991	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	26043478	29675991	60678762	133	26419										
C16orf7	9605	hgsc.bcm.edu	37	chr16	89782980	89782980	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acacggcggtgtcggccggcAggctggggaatgggagcagc	20	10	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr16:89782980A>G	ENST00000389386.3	-	4	445	c.321T>C	c.(319-321)ccT>ccC	p.P107P	VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1-AS1_ENST00000562298.1_RNA|VPS9D1_ENST00000561976.1_Silent_p.P37P	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	107					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										GTCGGCCGGCAGGCTGGGGAA	0.592																																																0			16											105	123	117					16																	89782980		2022	4184	6206	88310481	SO:0001819	synonymous_variant	9605			AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.321T>C	16.37:g.89782980A>G			88310481		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																				0.592	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		G	89782980	A	G	89782980	2	3	98	1	0	0	0	0	0	0	0	1	1832	175	7	4		4	C16orf7	16	89782980	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	60106989	89782980	571773	134	26420										
C16orf3	2622	hgsc.bcm.edu	37	chr16	90095486	90095486	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	agcatgtgagctgctgcccgTctccctgtccgcttcccatt	9	16	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr16:90095486T>C	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.T89A	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		CTGCTGCCCGTCTCCCTGTCC	0.602																																																0			16											82	45	58					16																	90095486		2092	4114	6206	88622987	SO:0001627	intron_variant	750			AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"growth arrest-specific 11"	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1356T>C	16.37:g.90095486T>C			88622987	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	T	6.646	0.487636	0.12641	.	.	ENSG00000221819	ENST00000408886	T	0.50813	0.73	1.9	-3.61	0.04556	.	.	.	.	.	T	0.21509	0.0518	N	0.08118	0	0.09310	N	1	B	0.30068	0.267	B	0.33339	0.162	T	0.23119	-1.0197	8	.	.	.	.	4.2774	0.10815	0.0:0.4585:0.2177:0.3238	.	97	O95177	CP003_HUMAN	A	89	ENSP00000386218:T89A	.	T	-	1	0	C16orf3	88622987	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.290000	0.02777	-1.130000	0.02914	-0.609000	0.04063	ACG		0.602	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2			C	90095486	T	C	90095486	1	2	98	0	1	0	0	0	0	0	0	0	1816	1667	58	4		4	C16orf3	16	90095486	Intron	SNP	T	TCGA-DC-6160-01A-11D-1657-10	312506	90095486	259267	135	26421										
TP53	7157	hgsc.bcm.edu	37	chr17	7579353	7579363	+	Frame_Shift_Del	DEL	CCAGACGGAAA	CCAGACGGAAA	-													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgtcccagaatgcaagaagcCcagacggaaaccgtagctgc					rs587783063|rs587781371|rs11540654|rs587780066	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	CCAGACGGAAA	CCAGACGGAAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:7579353_7579363delCCAGACGGAAA	ENST00000269305.4	-	4	513_523	c.324_334delTTTCCGTCTGG	c.(322-336)ggtttccgtctgggcfs	p.GFRLG108fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Del_p.GFRLG108fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.GFRLG108fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.GFRLG108fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.GFRLG108fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.GFRLG108fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	108	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.		G -> D (in a sporadic cancer; somatic mutation).|G -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R110L(36)|p.R110fs*13(11)|p.L111R(11)|p.R110P(9)|p.0?(8)|p.R110C(7)|p.L111Q(7)|p.L111P(6)|p.F109C(4)|p.F109S(4)|p.Q100fs*37(3)|p.G59fs*23(3)|p.F109fs*16(3)|p.G108_F109delGF(2)|p.R110H(2)|p.L111L(2)|p.G108del(2)|p.F109_R110delFR(2)|p.G112S(1)|p.R110fs*18(1)|p.R110fs*39(1)|p.G112fs*9(1)|p.L111fs*10(1)|p.G108G(1)|p.V73fs*9(1)|p.Y107fs*38(1)|p.Y107fs*44(1)|p.L111M(1)|p.S33fs*23(1)|p.R110S(1)|p.?_?ins?(1)|p.F109F(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.G112fs*36(1)|p.F109V(1)|p.Y103_L111>L(1)|p.F109_R110insXX(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.W91fs*13(1)|p.G112_S116delGFLHS(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCAAGAAGCCCAGACGGAAACCGTAGCTGC	0.616		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	146	Substitution - Missense(90)|Deletion - Frameshift(25)|Deletion - In frame(9)|Whole gene deletion(8)|Insertion - Frameshift(5)|Substitution - coding silent(4)|Insertion - In frame(2)|Complex - deletion inframe(2)|Complex - frameshift(1)	lung(22)|breast(22)|upper_aerodigestive_tract(19)|large_intestine(14)|liver(12)|ovary(10)|urinary_tract(9)|haematopoietic_and_lymphoid_tissue(6)|stomach(4)|central_nervous_system(4)|oesophagus(4)|prostate(4)|bone(4)|NS(3)|soft_tissue(3)|skin(3)|autonomic_ganglia(1)|salivary_gland(1)|pancreas(1)	17	GRCh37	CM984590|CX942126	TP53	M|X	rs11540654																																			7520088	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.324_334delTTTCCGTCTGG	17.37:g.7579353_7579363delCCAGACGGAAA	ENSP00000269305:p.Gly108fs		7520078	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.616	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579363	CCAGACGGAAA	-	7579353	7	5	98	1	0	1	0	1	0	0	0	0	16421	623	22	0	968	0	TP53	17	7579353	Frame_Shift_Del	DEL	CCAGACGGAAA	TCGA-DC-6160-01A-11D-1657-10		7579353	73615857	136	26422										
SLC5A10	125206	hgsc.bcm.edu	37	chr17	18923704	18923704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggcttcaatgccatcctccTcatgtgtgtcaacatattct	6	12	4	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:18923704T>C	ENST00000395645.3	+	15	1769	c.1751T>C	c.(1750-1752)cTc>cCc	p.L584P	SLC5A10_ENST00000395647.2_Missense_Mutation_p.L600P|SLC5A10_ENST00000395643.2_Missense_Mutation_p.L557P|SLC5A10_ENST00000395642.1_Missense_Mutation_p.L554P|SLC5A10_ENST00000417251.2_Missense_Mutation_p.L548P|SLC5A10_ENST00000317977.6_Missense_Mutation_p.L554P	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	584					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						GCCATCCTCCTCATGTGTGTC	0.547																																																0			17											132	110	117					17																	18923704		2203	4300	6503	18864429	SO:0001583	missense	125206				CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1751T>C	17.37:g.18923704T>C	ENSP00000379007:p.Leu584Pro		18864429	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	37	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.476010	0.84640	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.94457	-3.43;-2.85;-3.43;-2.92;-2.74;-2.87	5.2	5.2	0.72013	.	0.066131	0.64402	D	0.000008	D	0.97501	0.9182	M	0.89095	3.005	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;0.998;0.999;1.0	D;D;D;D;D	0.79108	0.959;0.982;0.959;0.982;0.992	D	0.98385	1.0560	10	0.87932	D	0	.	15.2436	0.73490	0.0:0.0:0.0:1.0	.	548;557;584;600;554	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	P	554;600;554;548;584;557	ENSP00000324346:L554P;ENSP00000379008:L600P;ENSP00000379004:L554P;ENSP00000401875:L548P;ENSP00000379007:L584P;ENSP00000379005:L557P	ENSP00000324346:L554P	L	+	2	0	SLC5A10	18864429	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	5.091000	0.64505	2.191000	0.70037	0.529000	0.55759	CTC		0.547	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		C	18923704	T	C	18923704	3	2	98	1	0	0	0	0	1	0	0	0	14699	1551	54	4	1857	4	SLC5A10	17	18923704	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	11344351	18923704	62271506	137	26423										
PCGF2	7703	hgsc.bcm.edu	37	chr17	36895857	36895857	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acctgatgctcagcagcggcCgggttttatggacctgcacg	13	12	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:36895857C>T	ENST00000580830.1	-	5	892	c.191G>A	c.(190-192)cGg>cAg	p.R64Q	PCGF2_ENST00000581345.1_Missense_Mutation_p.R64Q|PCGF2_ENST00000579882.1_Missense_Mutation_p.R64Q|PCGF2_ENST00000578109.1_Missense_Mutation_p.R10Q|PCGF2_ENST00000585100.1_Missense_Mutation_p.R64Q|PCGF2_ENST00000360797.2_Missense_Mutation_p.R64Q			P35227	PCGF2_HUMAN	polycomb group ring finger 2	64					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CAGCAGCGGCCGGGTTTTATG	0.612																																																0			17											144	116	125					17																	36895857		2203	4300	6503	34149383	SO:0001583	missense	7703			D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.191G>A	17.37:g.36895857C>T	ENSP00000461961:p.Arg64Gln		34149383	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	37	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603293	0.46423	.	.	ENSG00000056661	ENST00000360797	T	0.41758	0.99	4.56	4.56	0.56223	Zinc finger, RING/FYVE/PHD-type (1);	0.070142	0.64402	D	0.000017	T	0.30103	0.0754	L	0.31578	0.945	0.38636	D	0.9515	B	0.27882	0.192	B	0.21546	0.035	T	0.13872	-1.0493	10	0.20046	T	0.44	-9.2425	14.8624	0.70392	0.0:1.0:0.0:0.0	.	64	P35227	PCGF2_HUMAN	Q	64	ENSP00000354033:R64Q	ENSP00000354033:R64Q	R	-	2	0	PCGF2	34149383	0.030000	0.19436	0.495000	0.27527	0.907000	0.53573	2.863000	0.48396	2.364000	0.80123	0.491000	0.48974	CGG		0.612	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		T	36895857	C	T	36895857	3	4	98	1	0	0	0	0	1	0	0	0	11606	652	23	1	875	1	PCGF2	17	36895857	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	17972153	36895857	44299353	138	26424										
KRT38	8687	hgsc.bcm.edu	37	chr17	39595539	39595539	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcggccttggccagggtcgcAtcatccaggagcttctgtgt	13	12	2	0	rs117668654	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:39595539A>G	ENST00000246646.3	-	3	647	c.648T>C	c.(646-648)gaT>gaC	p.D216D		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	216	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				CCAGGGTCGCATCATCCAGGA	0.632													G|||	58	0.0115815	8e-04	0.0043	5008	,	,		17656	0.0278		0.0089	False		,,,				2504	0.0174															0			17											85	77	79					17																	39595539		2203	4300	6503	36849065	SO:0001819	synonymous_variant	8687			Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.648T>C	17.37:g.39595539A>G			36849065	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																				0.632	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		G	39595539	A	G	39595539	2	3	98	1	0	0	0	0	0	0	0	1	8496	214	8	4		4	KRT38	17	39595539	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2699682	39595539	41599671	139	26425										
KRT17	3872	hgsc.bcm.edu	37	chr17	39780398	39780398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggcgggccccggggcctgccTctggtaccagtcacggatct	15	15	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:39780398T>C	ENST00000311208.8	-	1	431	c.364A>G	c.(364-366)Agg>Ggg	p.R122G	JUP_ENST00000540235.1_Intron|KRT42P_ENST00000438131.1_RNA	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	122	Linker 1.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				GGGGCCTGCCTCTGGTACCAG	0.637																																					Pancreas(92;1242 2086 39193 50508)											0			17											74	91	86					17																	39780398		2201	4295	6496	37033924	SO:0001583	missense	3872			X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"-", "Intermediate filaments type I, keratins (acidic)"	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.364A>G	17.37:g.39780398T>C	ENSP00000308452:p.Arg122Gly		37033924	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Missense_Mutation	SNP	ENST00000311208.8	37	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384977	0.61956	.	.	ENSG00000128422	ENST00000311208	D	0.89415	-2.51	4.95	4.95	0.65309	Filament (1);	0.327598	0.22028	N	0.065626	D	0.86347	0.5911	L	0.31294	0.92	0.80722	D	1	B	0.30104	0.268	B	0.39339	0.297	D	0.86120	0.1568	10	0.62326	D	0.03	.	15.0804	0.72110	0.0:0.0:0.0:1.0	.	122	Q04695	K1C17_HUMAN	G	122	ENSP00000308452:R122G	ENSP00000308452:R122G	R	-	1	2	KRT17	37033924	1.000000	0.71417	1.000000	0.80357	0.413000	0.31143	7.505000	0.81655	2.212000	0.71576	0.260000	0.18958	AGG		0.637	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		C	39780398	T	C	39780398	3	2	98	1	0	0	0	0	1	0	0	0	8475	1550	54	4	966	4	KRT17	17	39780398	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	184859	39780398	41414812	140	26426										
WNT3	7473	hgsc.bcm.edu	37	chr17	44845792	44845792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccttccgcttctccgtcctcGtgttgtggccccggccacag	10	18	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:44845792G>A	ENST00000225512.5	-	4	1124	c.962C>T	c.(961-963)aCg>aTg	p.T321M		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	321					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CTCCGTCCTCGTGTTGTGGCC	0.592																																																0			17											137	120	126					17																	44845792		2203	4300	6503	42200961	SO:0001583	missense	7473			AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.962C>T	17.37:g.44845792G>A	ENSP00000225512:p.Thr321Met		42200961	Q2M237|Q9H1J9	Missense_Mutation	SNP	ENST00000225512.5	37	CCDS11505.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.296462	0.81025	.	.	ENSG00000108379	ENST00000225512	T	0.77750	-1.12	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.88640	0.6491	M	0.84846	2.72	0.80722	D	1	D	0.71674	0.998	D	0.63192	0.912	D	0.90398	0.4400	10	0.87932	D	0	.	18.6237	0.91330	0.0:0.0:1.0:0.0	.	321	P56703	WNT3_HUMAN	M	321	ENSP00000225512:T321M	ENSP00000225512:T321M	T	-	2	0	WNT3	42200961	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.657000	0.98554	2.620000	0.88729	0.561000	0.74099	ACG		0.592	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		A	44845792	G	A	44845792	3	1	98	1	0	0	0	0	1	0	0	0	17428	1145	40	1	109	1	WNT3	17	44845792	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	5065394	44845792	36349418	141	26427										
PPM1E	4591	hgsc.bcm.edu	37	chr17	57057614	57057614	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catgaacaaagctgtaaatgTtagtgaggaatcagattgga	11	4	1	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:57057614T>C	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Missense_Mutation_p.V497A	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GCTGTAAATGTTAGTGAGGAA	0.463									Mulibrey Nanism																																							0			17											142	130	134					17																	57057614		2203	4300	6503	54412396	SO:0001628	intergenic_variant	22843	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			17.37:g.57057614T>C			54412396	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000393066.3	37	CCDS45746.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.625796	0.28889	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.19532	2.14	5.71	5.71	0.89125	.	0.416945	0.26546	N	0.023766	T	0.15739	0.0379	L	0.27053	0.805	0.35165	D	0.770993	B;B	0.25169	0.119;0.095	B;B	0.26202	0.067;0.015	T	0.16335	-1.0406	10	0.44086	T	0.13	-13.6967	10.0643	0.42295	0.0:0.0754:0.0:0.9246	.	506;497	Q8WY54-3;Q8WY54-2	.;.	A	497;348	ENSP00000312411:V497A	ENSP00000312411:V497A	V	+	2	0	PPM1E	54412396	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.850000	0.39328	2.189000	0.69895	0.402000	0.26972	GTT		0.463	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294		C	57057614	T	C	57057614	1	2	98	0	1	0	0	0	0	0	0	0	12372	1725	60	4		4	PPM1E	17	57057614	IGR	SNP	T	TCGA-DC-6160-01A-11D-1657-10	12211822	57057614	24137596	142	26428										
USP32	84669	hgsc.bcm.edu	37	chr17	58297087	58297087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggcaggctgctgtctcaggAagagaagatagcggggaaat	16	6	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:58297087A>G	ENST00000300896.4	-	16	2005	c.1811T>C	c.(1810-1812)tTc>tCc	p.F604S	USP32_ENST00000592339.1_Missense_Mutation_p.F274S	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	604					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTGTCTCAGGAAGAGAAGATA	0.428																																																0			17											44	47	46					17																	58297087		2201	4294	6495	55651869	SO:0001583	missense	84669			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.1811T>C	17.37:g.58297087A>G	ENSP00000300896:p.Phe604Ser		55651869	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503663	0.85176	.	.	ENSG00000170832	ENST00000300896	T	0.47528	0.84	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.40767	0.1130	L	0.29908	0.895	0.80722	D	1	D	0.54601	0.967	B	0.44044	0.439	T	0.43245	-0.9403	10	0.62326	D	0.03	.	14.9543	0.71101	1.0:0.0:0.0:0.0	.	604	Q8NFA0	UBP32_HUMAN	S	604	ENSP00000300896:F604S	ENSP00000300896:F604S	F	-	2	0	USP32	55651869	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.701000	0.91331	2.005000	0.58758	0.477000	0.44152	TTC		0.428	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		G	58297087	A	G	58297087	3	3	98	1	0	0	0	0	1	0	0	0	17103	246	9	4	3079	4	USP32	17	58297087	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	1239473	58297087	22898123	143	26429										
MARCH10	162333	hgsc.bcm.edu	37	chr17	60814611	60814611	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttctcagtcattggctgtgaCgatgggaccaagtttcttct	10	9	4	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:60814611C>T	ENST00000311269.5	-	6	892	c.618G>A	c.(616-618)tcG>tcA	p.S206S	RP11-156L14.1_ENST00000582564.1_RNA|RP11-156L14.1_ENST00000577270.1_RNA|MARCH10_ENST00000456609.2_Silent_p.S206S|RP11-156L14.1_ENST00000579201.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000544856.2_Silent_p.S205S|MARCH10_ENST00000583600.1_Silent_p.S244S	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	206					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						TTGGCTGTGACGATGGGACCA	0.502																																																0			17											253	244	247					17																	60814611		2203	4300	6503	58168343	SO:0001819	synonymous_variant	162333			AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.618G>A	17.37:g.60814611C>T			58168343	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																				0.502	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		T	60814611	C	T	60814611	2	4	98	1	0	0	0	0	0	0	0	1	9329	523	19	1		1	MARCH10	17	60814611	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	2517524	60814611	20380599	144	26430										
BPTF	2186	hgsc.bcm.edu	37	chr17	65900869	65900869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgacaggatatggtggttggAgctggattagtaaaactcat	13	4	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:65900869A>G	ENST00000321892.4	+	11	3164	c.3103A>G	c.(3103-3105)Agc>Ggc	p.S1035G	BPTF_ENST00000335221.5_Missense_Mutation_p.S1035G|BPTF_ENST00000424123.3_Missense_Mutation_p.S896G|BPTF_ENST00000306378.6_Missense_Mutation_p.S909G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1035					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGGTGGTTGGAGCTGGATTAG	0.328																																																0			17											140	140	140					17																	65900869		2203	4300	6503	63331331	SO:0001583	missense	2186			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.3103A>G	17.37:g.65900869A>G	ENSP00000315454:p.Ser1035Gly		63331331	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	A	12.20	1.865432	0.32977	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.63417	-0.02;-0.04;-0.03	5.78	5.78	0.91487	.	.	.	.	.	T	0.59500	0.2198	L	0.57536	1.79	0.45378	D	0.99836	B;P;P	0.51933	0.41;0.604;0.949	B;B;P	0.45881	0.138;0.387;0.496	T	0.57260	-0.7842	9	0.16896	T	0.51	-2.0167	11.2764	0.49170	0.8639:0.0:0.0:0.1361	.	1035;909;1035	Q12830;Q12830-2;Q12830-4	BPTF_HUMAN;.;.	G	909;1035;1035	ENSP00000307208:S909G;ENSP00000334351:S1035G;ENSP00000315454:S1035G	ENSP00000307208:S909G	S	+	1	0	BPTF	63331331	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.026000	0.64103	2.218000	0.71995	0.529000	0.55759	AGC		0.328	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65900869	A	G	65900869	3	3	98	1	0	0	0	0	1	0	0	0	1498	304	11	4	3145	4	BPTF	17	65900869	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	5086258	65900869	15294341	145	26431										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67102293	67102293	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	catttcagagaaggaagagtGagccagctccatttcattga	10	8	2	4			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:67102293G>A	ENST00000284425.2	-	19	2623	c.2449C>T	c.(2449-2451)Cac>Tac	p.H817Y		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	817					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AAGGAAGAGTGAGCCAGCTCC	0.418																																																0			17											115	102	107					17																	67102293		2203	4300	6503	64613888	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.2449C>T	17.37:g.67102293G>A	ENSP00000284425:p.His817Tyr		64613888	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.237869	0.22711	.	.	ENSG00000154262	ENST00000284425	D	0.86865	-2.18	4.74	-5.49	0.02584	.	3.282670	0.00654	N	0.000561	T	0.65291	0.2677	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.66881	-0.5811	10	0.07030	T	0.85	.	8.8765	0.35348	0.3623:0.1212:0.5165:0.0	.	817	Q8N139	ABCA6_HUMAN	Y	817	ENSP00000284425:H817Y	ENSP00000284425:H817Y	H	-	1	0	ABCA6	64613888	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.547000	0.02186	-1.162000	0.02797	0.561000	0.74099	CAC		0.418	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67102293	G	A	67102293	3	1	98	1	0	0	0	0	1	0	0	0	36	1290	45	3	2488	3	ABCA6	17	67102293	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	1201424	67102293	14092917	146	26432										
SDK2	54549	hgsc.bcm.edu	37	chr17	71395336	71395336	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	caccagccagcgggagatggAggttttcccatcgtagcctg	13	12	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:71395336A>G	ENST00000392650.3	-	22	3064	c.3064T>C	c.(3064-3066)Tcc>Ccc	p.S1022P	SDK2_ENST00000388726.3_Missense_Mutation_p.S1022P	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1022	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CGGGAGATGGAGGTTTTCCCA	0.632																																																0			17											27	27	27					17																	71395336		2203	4300	6503	68906931	SO:0001583	missense	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.3064T>C	17.37:g.71395336A>G	ENSP00000376421:p.Ser1022Pro		68906931	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.473340	0.63737	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.54071	0.59;0.59;0.59	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.44973	0.1319	N	0.25825	0.765	0.58432	D	0.999998	B;B;B	0.30741	0.245;0.293;0.134	B;B;B	0.39299	0.196;0.296;0.149	T	0.32745	-0.9895	10	0.18276	T	0.48	.	14.6241	0.68608	1.0:0.0:0.0:0.0	.	1022;1022;1022	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	P	646;1022;1022;198;1022	ENSP00000376421:S1022P;ENSP00000373378:S1022P;ENSP00000407098:S198P	ENSP00000324967:S1022P	S	-	1	0	SDK2	68906931	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.088000	0.94132	1.870000	0.54199	0.454000	0.30748	TCC		0.632	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		G	71395336	A	G	71395336	3	3	98	1	0	0	0	0	1	0	0	0	14006	304	11	4	3550	4	SDK2	17	71395336	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	4293043	71395336	9799874	147	26433										
UBE2O	63893	hgsc.bcm.edu	37	chr17	74396331	74396331	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggaagacatacagacagcgcTccccaagctgccgctgagca	11	14	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr17:74396331T>C	ENST00000319380.7	-	8	1116	c.1052A>G	c.(1051-1053)gAg>gGg	p.E351G	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	351					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						CAGACAGCGCTCCCCAAGCTG	0.602																																																0			17											44	43	44					17																	74396331		2203	4300	6503	71907926	SO:0001583	missense	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.1052A>G	17.37:g.74396331T>C	ENSP00000323687:p.Glu351Gly		71907926	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	37	CCDS32742.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.507549	0.85282	.	.	ENSG00000175931	ENST00000319380	T	0.75367	-0.93	4.96	4.96	0.65561	.	0.174864	0.38492	N	0.001666	T	0.80576	0.4649	L	0.40543	1.245	0.47905	D	0.999549	D	0.71674	0.998	D	0.70227	0.968	T	0.82910	-0.0223	10	0.87932	D	0	-23.2309	14.6319	0.68663	0.0:0.0:0.0:1.0	.	351	Q9C0C9	UBE2O_HUMAN	G	351	ENSP00000323687:E351G	ENSP00000323687:E351G	E	-	2	0	UBE2O	71907926	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.875000	0.54330	0.459000	0.35465	GAG		0.602	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		C	74396331	T	C	74396331	3	2	98	1	0	0	0	0	1	0	0	0	16908	1551	54	4	2870	4	UBE2O	17	74396331	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	3000995	74396331	6798879	148	26434										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61077591	61077591	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcttttttctctttatttttCaggtactcctttagtttttc	4	8	2	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr18:61077591C>T	ENST00000238497.5	-	3	431	c.228G>A	c.(226-228)ctG>ctA	p.L76L	VPS4B_ENST00000591519.1_Silent_p.L76L	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	76	MIT.				ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						CTTTATTTTTCAGGTACTCCT	0.388																																																0			18											189	175	180					18																	61077591		2203	4300	6503	59228571	SO:0001819	synonymous_variant	9525			AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.228G>A	18.37:g.61077591C>T			59228571	Q69HW4|Q9GZS7	Silent	SNP	ENST00000238497.5	37	CCDS11983.1																																																																																				0.388	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		T	61077591	C	T	61077591	2	4	98	1	0	0	0	0	0	0	0	1	17253	813	29	3		3	VPS4B	18	61077591	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10		61077591	16999657	149	26435										
CDH7	1005	hgsc.bcm.edu	37	chr18	63529943	63529943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccaggagaaacggcttccggAgacaggaacaatcagtttac	11	10	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr18:63529943A>G	ENST00000397968.2	+	11	2080	c.1654A>G	c.(1654-1656)Aga>Gga	p.R552G	CDH7_ENST00000536984.2_Missense_Mutation_p.R552G|CDH7_ENST00000323011.3_Missense_Mutation_p.R552G|RP11-389J22.1_ENST00000581987.1_RNA	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				CGGCTTCCGGAGACAGGAACA	0.463																																																0			18											134	114	121					18																	63529943		2203	4300	6503	61680923	SO:0001583	missense	28513			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1654A>G	18.37:g.63529943A>G	ENSP00000381058:p.Arg552Gly		61680923	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659343	0.67586	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.60040	0.22;0.22;0.22	5.37	4.19	0.49359	Cadherin (4);Cadherin-like (1);	0.050797	0.85682	D	0.000000	D	0.82783	0.5112	H	0.98005	4.125	0.58432	D	0.999999	D;D	0.61080	0.989;0.98	D;P	0.65010	0.931;0.721	D	0.87304	0.2307	10	0.72032	D	0.01	.	12.399	0.55402	0.8591:0.1409:0.0:0.0	.	552;552	F5H5X9;Q9ULB5	.;CADH7_HUMAN	G	552	ENSP00000319166:R552G;ENSP00000443030:R552G;ENSP00000381058:R552G	ENSP00000319166:R552G	R	+	1	2	CDH7	61680923	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	2.734000	0.47368	0.862000	0.35528	0.482000	0.46254	AGA		0.463	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		G	63529943	A	G	63529943	3	3	98	1	0	0	0	0	1	0	0	0	3121	296	11	4	1692	4	CDH7	18	63529943	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2452352	63529943	14547305	150	26436										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1119071	1119071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccagcgggatctcctcgatgCggaaggtgacgccggagaag	16	11	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:1119071C>T	ENST00000361757.3	-	14	1703	c.1466G>A	c.(1465-1467)cGc>cAc	p.R489H	SBNO2_ENST00000438103.2_Missense_Mutation_p.R432H|SBNO2_ENST00000587024.1_Missense_Mutation_p.R489H	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	489					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CTCCTCGATGCGGAAGGTGAC	0.667																																																0			19											32	42	38					19																	1119071		2195	4286	6481	1070071	SO:0001583	missense	22904			AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1466G>A	19.37:g.1119071C>T	ENSP00000354733:p.Arg489His		1070071	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374978	0.82573	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	.	.	.	3.89	2.85	0.33270	.	0.122741	0.56097	N	0.000034	T	0.70029	0.3177	M	0.64260	1.97	0.42720	D	0.993676	P;D;D	0.89917	0.902;1.0;1.0	P;D;D	0.97110	0.608;1.0;0.999	T	0.72054	-0.4406	9	0.72032	D	0.01	-31.8968	10.6025	0.45375	0.0:0.9041:0.0:0.0959	.	489;489;432	B4DV91;Q9Y2G9;Q9Y2G9-3	.;SBNO2_HUMAN;.	H	489;432;513	.	ENSP00000250872:R513H	R	-	2	0	SBNO2	1070071	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.707000	0.68370	0.972000	0.38314	0.462000	0.41574	CGC		0.667	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		T	1119071	C	T	1119071	3	4	98	1	0	0	0	0	1	0	0	0	13900	768	27	1	2710	1	SBNO2	19	1119071	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10		1119071	58009912	151	26437										
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881395	1881395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccgggtgcgcccgaggaggcTctcagggtccccaagggggc	18	14	1	0	rs199929215	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:1881395T>C	ENST00000292577.7	-	2	604	c.171A>G	c.(169-171)agA>agG	p.R57R	ABHD17A_ENST00000250974.9_Silent_p.R57R|ABHD17A_ENST00000590661.1_Silent_p.R57R	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	57						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.R57R(1)									CCGAGGAGGCTCTCAGGGTCC	0.726																																																1	Substitution - coding silent(1)	prostate(1)	19											7	10	9					19																	1881395		1880	3957	5837	1832395	SO:0001819	synonymous_variant	81926			BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.171A>G	19.37:g.1881395T>C			1832395	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Silent	SNP	ENST00000292577.7	37	CCDS45902.1																																																																																				0.726	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		C	1881395	T	C	1881395	2	2	98	1	0	0	0	0	0	0	0	1	5407	1548	54	4		4	FAM108A1	19	1881395	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10	762324	1881395	57247588	152	26438										
EMR1	2015	hgsc.bcm.edu	37	chr19	6906479	6906479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gtaaggaagatgtgatacccGataataagcagatccagcaa	10	7	0	3	rs151096072		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:6906479G>A	ENST00000312053.4	+	9	1022	c.985G>A	c.(985-987)Gat>Aat	p.D329N	EMR1_ENST00000250572.8_Missense_Mutation_p.D329N|EMR1_ENST00000381404.4_Missense_Mutation_p.D277N|EMR1_ENST00000381407.5_Missense_Mutation_p.D188N|EMR1_ENST00000450315.3_Missense_Mutation_p.D152N	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	329	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.D329Y(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					TGTGATACCCGATAATAAGCA	0.393																																																1	Substitution - Missense(1)	lung(1)	19						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	140	134	136		985	-4.2	0	19	dbSNP_134	136	0,8600		0,0,4300	no	missense	EMR1	NM_001974.3	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	329/887	6906479	1,13005	2203	4300	6503	6857479	SO:0001583	missense	2015			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.985G>A	19.37:g.6906479G>A	ENSP00000311545:p.Asp329Asn		6857479	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	1.146	-0.648008	0.03506	2.27E-4	0.0	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.77750	-1.09;-1.11;-1.12;0.05;0.39	2.98	-4.22	0.03800	.	.	.	.	.	T	0.48786	0.1519	N	0.04203	-0.255	0.09310	N	1	B;B;B;B;B	0.16396	0.017;0.008;0.011;0.017;0.006	B;B;B;B;B	0.11329	0.005;0.004;0.002;0.006;0.001	T	0.34279	-0.9835	9	0.17369	T	0.5	.	6.4188	0.21732	0.2627:0.1813:0.556:0.0	.	152;188;329;277;329	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	N	329;329;277;329;188;152	ENSP00000311545:D329N;ENSP00000370811:D277N;ENSP00000250572:D329N;ENSP00000370814:D188N;ENSP00000405974:D152N	ENSP00000250572:D329N	D	+	1	0	EMR1	6857479	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.398000	0.02509	-1.026000	0.03330	-1.267000	0.01435	GAT		0.393	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6906479	G	A	6906479	3	1	98	1	0	0	0	0	1	0	0	0	5117	1058	37	1	1019	1	EMR1	19	6906479	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	5025084	6906479	52222504	153	26439										
MCOLN1	57192	hgsc.bcm.edu	37	chr19	7593142	7593142	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	caccccagtgtcttccagcaCggtgagcccctgagccccag	10	18	1	2	rs199588225		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:7593142C>T	ENST00000264079.6	+	7	1001	c.876C>T	c.(874-876)caC>caT	p.H292H		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	292					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCTTCCAGCACGGTGAGCCCC	0.642													C|||	1	0.000199681	0	0	5008	,	,		16300	0.001		0	False		,,,				2504	0															0			19											71	64	67					19																	7593142		2203	4300	6503	7499142	SO:0001630	splice_region_variant	57192			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"Voltage-gated ion channels / Transient receptor potential cation channels"	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.877+1C>T	19.37:g.7593142C>T			7499142	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Silent	SNP	ENST00000264079.6	37	CCDS12180.1																																																																																				0.642	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533	Silent	T	7593142	C	T	7593142	5	4	98	1	0	0	0	0	0	0	1	0	9425	550	19	1	902	1	MCOLN1	19	7593142	Splice_Site	SNP	C	TCGA-DC-6160-01A-11D-1657-10	686663	7593142	51535841	154	26440										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10081347	10081347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctccccagaagctccaggcGgaccctggaggagacaagga	14	13	0	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:10081347G>A	ENST00000264828.3	-	54	3972	c.3887C>T	c.(3886-3888)cCg>cTg	p.P1296L		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1296	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			AGCTCCAGGCGGACCCTGGAG	0.617																																																0			19											9	11	10					19																	10081347		2168	4263	6431	9942347	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3887C>T	19.37:g.10081347G>A	ENSP00000264828:p.Pro1296Leu		9942347	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797707	0.31777	.	.	ENSG00000080573	ENST00000264828	D	0.96685	-4.09	3.28	3.28	0.37604	.	0.075383	0.53938	U	0.000050	D	0.95974	0.8689	L	0.39898	1.24	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93644	0.6967	10	0.27082	T	0.32	.	10.3456	0.43903	0.0:0.0:1.0:0.0	.	1296	P25940	CO5A3_HUMAN	L	1296	ENSP00000264828:P1296L	ENSP00000264828:P1296L	P	-	2	0	COL5A3	9942347	0.998000	0.40836	0.824000	0.32777	0.203000	0.24098	3.173000	0.50839	2.126000	0.65437	0.486000	0.48141	CCG		0.617	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10081347	G	A	10081347	3	1	98	1	0	0	0	0	1	0	0	0	3704	1116	39	1	1406	1	COL5A3	19	10081347	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	2488205	10081347	49047636	155	26441										
LYL1	4066	hgsc.bcm.edu	37	chr19	13211527	13211527	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcttcaaccggctgctagggAagatgctaaaaggtcctgct	12	10	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:13211527A>G	ENST00000264824.4	-	3	731	c.371T>C	c.(370-372)tTc>tCc	p.F124S		NM_005583.4	NP_005574.2	P12980	LYL1_HUMAN	lymphoblastic leukemia associated hematopoiesis regulator 1	124					B cell differentiation (GO:0030183)|blood vessel maturation (GO:0001955)|definitive hemopoiesis (GO:0060216)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)	7			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)			GCTGCTAGGGAAGATGCTAAA	0.577			T	TRB@	T-ALL																																		Dom	yes		19	19p13.2-p13.1	4066	lymphoblastic leukemia derived sequence 1		L	0			19											196	182	187					19																	13211527		2203	4300	6503	13072527	SO:0001583	missense	4066				CCDS12292.1	19p13.2	2014-01-20	2014-01-20			ENSG00000104903		"Basic helix-loop-helix proteins"	6734	protein-coding gene	gene with protein product		151440	"lymphoblastic leukemia derived sequence 1"			2752424	Standard	NM_005583		Approved	bHLHa18	uc002mwi.3	P12980		ENST00000264824.4:c.371T>C	19.37:g.13211527A>G	ENSP00000264824:p.Phe124Ser		13072527	O76102	Missense_Mutation	SNP	ENST00000264824.4	37	CCDS12292.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.728609	0.69074	.	.	ENSG00000104903	ENST00000264824	D	0.97906	-4.6	4.17	4.17	0.49024	.	0.097598	0.43579	D	0.000549	D	0.96144	0.8743	L	0.58101	1.795	0.30401	N	0.780008	P	0.48911	0.917	B	0.44315	0.446	D	0.94383	0.7606	10	0.51188	T	0.08	-6.8045	11.0377	0.47811	1.0:0.0:0.0:0.0	.	124	P12980	LYL1_HUMAN	S	124	ENSP00000264824:F124S	ENSP00000264824:F124S	F	-	2	0	LYL1	13072527	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	2.713000	0.47194	1.653000	0.50694	0.459000	0.35465	TTC		0.577	LYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452827.1	NM_005583		G	13211527	A	G	13211527	3	3	98	1	0	0	0	0	1	0	0	0	9136	246	9	4	479	4	LYL1	19	13211527	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	3130180	13211527	45917456	156	26442										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15272410	15272410	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcagtctctcctgggctacgTcccgcggcagcctgtccagg	13	16	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:15272410T>C	ENST00000263388.2	-	33	6104	c.6029A>G	c.(6028-6030)gAc>gGc	p.D2010G		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	2010					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CTGGGCTACGTCCCGCGGCAG	0.682																																																0			19											28	27	28					19																	15272410		2202	4298	6500	15133410	SO:0001583	missense	4855			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.6029A>G	19.37:g.15272410T>C	ENSP00000263388:p.Asp2010Gly		15133410	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.631081	0.67015	.	.	ENSG00000074181	ENST00000263388	T	0.57107	0.42	3.92	3.92	0.45320	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.66934	0.2840	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70382	-0.4887	9	0.87932	D	0	.	12.2215	0.54437	0.0:0.0:0.0:1.0	.	2010	Q9UM47	NOTC3_HUMAN	G	2010	ENSP00000263388:D2010G	ENSP00000263388:D2010G	D	-	2	0	NOTCH3	15133410	1.000000	0.71417	0.713000	0.30519	0.729000	0.41735	7.836000	0.86788	1.790000	0.52503	0.528000	0.53228	GAC		0.682	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15272410	T	C	15272410	3	2	98	1	0	0	0	0	1	0	0	0	10581	1667	58	4	940	4	NOTCH3	19	15272410	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	2060883	15272410	43856573	157	26443										
TMEM59L	25789	hgsc.bcm.edu	37	chr19	18724827	18724827	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccaaactgagtgtgaagcagGtgagggcccgccggcagggt	17	10	0	3			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:18724827G>A	ENST00000600490.1	+	3	501		c.e3+1		TMEM59L_ENST00000262817.3_Splice_Site			Q9UK28	TM59L_HUMAN	transmembrane protein 59-like							Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(2)	13						TGTGAAGCAGGTGAGGGCCCG	0.672																																																0			19											34	39	37					19																	18724827		2203	4300	6503	18585827	SO:0001630	splice_region_variant	25789			AF186264	CCDS12383.1	19p12	2008-02-05	2007-03-14	2007-03-14		ENSG00000105696			13237	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 4"	C19orf4		10527841	Standard	NM_012109		Approved	BSMAP	uc002njy.4	Q9UK28		ENST00000600490.1:c.316+1G>A	19.37:g.18724827G>A			18585827		Splice_Site	SNP	ENST00000600490.1	37	CCDS12383.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609583	0.66558	.	.	ENSG00000105696	ENST00000262817	.	.	.	4.54	3.5	0.40072	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5325	0.50618	0.0898:0.0:0.9102:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM59L	18585827	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.951000	0.63610	0.889000	0.36185	0.561000	0.74099	.		0.672	TMEM59L-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465143.2		Intron	A	18724827	G	A	18724827	5	1	98	1	0	0	0	0	0	0	1	0	16225	1275	44	3	323	3	TMEM59L	19	18724827	Splice_Site	SNP	G	TCGA-DC-6160-01A-11D-1657-10	3452417	18724827	40404156	158	26444										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155783	22155783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tttctctccagtatgaattaCcttatgtttagtaaggattg	7	6	1	1	rs199604702		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:22155783C>T	ENST00000397126.4	-	4	2201	c.2053G>A	c.(2053-2055)Gta>Ata	p.V685I	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	685					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GTATGAATTACCTTATGTTTA	0.383																																																0			19											37	38	37					19																	22155783		1986	4182	6168	21947623	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2053G>A	19.37:g.22155783C>T	ENSP00000380315:p.Val685Ile		21947623		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	4.480	0.089023	0.08583	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.17054	2.3	2.43	-4.86	0.03132	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11024	0.0269	.	.	.	0.09310	N	1	B	0.25441	0.126	B	0.24701	0.055	T	0.29852	-0.9998	8	0.42905	T	0.14	.	9.3378	0.38060	0.0:0.3337:0.0:0.6663	.	585	O43345	ZN208_HUMAN	I	685;585	ENSP00000380315:V685I	ENSP00000380315:V685I	V	-	1	0	ZNF208	21947623	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-6.732000	0.00055	-1.081000	0.03105	-1.169000	0.01745	GTA		0.383	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155783	C	T	22155783	3	4	98	1	0	0	0	0	1	0	0	0	17805	507	18	3	1793	3	ZNF208	19	22155783	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	3430956	22155783	36973200	159	26445										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363610	22363610	+	Silent	SNP	A	A	G													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ttgtagggtttctctccagtAtgaattctcttatgttccat					rs201622264	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:22363610A>G	ENST00000397121.2	-	3	1226	c.909T>C	c.(907-909)caT>caC	p.H303H		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TCTCTCCAGTATGAATTCTCT	0.443																																																0			19											81	83	83					19																	22363610		2112	4258	6370	22155450	SO:0001819	synonymous_variant	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.909T>C	19.37:g.22363610A>G			22155450	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																				0.443	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		G	22363610	A	G	22363610	2	3	98	1	0	0	0	0	0	0	0	1	18122	446	16	4		4	ZNF676	19	22363610	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10	207827	22363610	36765373	160	26446	40	2								
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363615	22363615	+	Missense_Mutation	SNP	T	T	C													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggtttctctccagtatgaaTtctcttatgttccatgagct					rs76328545	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:22363615T>C	ENST00000397121.2	-	3	1221	c.904A>G	c.(904-906)Att>Gtt	p.I302V		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CCAGTATGAATTCTCTTATGT	0.428																																																0			19											85	88	87					19																	22363615		2125	4266	6391	22155455	SO:0001583	missense	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.904A>G	19.37:g.22363615T>C	ENSP00000380310:p.Ile302Val		22155455	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.103	-1.149580	0.01714	.	.	ENSG00000196109	ENST00000397121	T	0.00986	5.47	0.85	-1.7	0.08159	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00580	0.0019	N	0.05534	-0.03	0.20196	N	0.999929	B	0.15930	0.015	B	0.18871	0.023	T	0.51004	-0.8760	9	0.62326	D	0.03	.	0.401	0.00426	0.2032:0.1668:0.2049:0.4252	.	302	Q8N7Q3	ZN676_HUMAN	V	302	ENSP00000380310:I302V	ENSP00000380310:I302V	I	-	1	0	ZNF676	22155455	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.149000	0.10204	-3.301000	0.00192	-3.318000	0.00044	ATT		0.428	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		C	22363615	T	C	22363615	3	2	98	1	0	0	0	0	1	0	0	0	18122	1493	52	4	866	4	ZNF676	19	22363615	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	5	22363615	36765368	161	26447	40	2								
ZNF99	7652	hgsc.bcm.edu	37	chr19	22951126	22951126	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cctgggggtttagttaccatCtcatgtctcttcatattcca	7	11	3	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:22951126C>A	ENST00000596209.1	-	3	297	c.207G>T	c.(205-207)gaG>gaT	p.E69D	ZNF99_ENST00000397104.3_Missense_Mutation_p.E90D	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TAGTTACCATCTCATGTCTCT	0.393																																																0			19											59	62	61					19																	22951126		2171	4292	6463	22742966	SO:0001583	missense	7652			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.207G>T	19.37:g.22951126C>A	ENSP00000472969:p.Glu69Asp		22742966	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	c	0.972	-0.699753	0.03279	.	.	ENSG00000213973	ENST00000397104	T	0.06371	3.31	0.195	0.195	0.15151	Krueppel-associated box (1);	.	.	.	.	T	0.04998	0.0134	L	0.41236	1.265	0.09310	N	1	B	0.21606	0.058	B	0.21151	0.033	T	0.46512	-0.9186	8	0.13853	T	0.58	.	.	.	.	.	90	A8MXY4	ZNF99_HUMAN	D	90	ENSP00000380293:E90D	ENSP00000380293:E90D	E	-	3	2	ZNF99	22742966	0.009000	0.17119	0.185000	0.23176	0.181000	0.23173	1.131000	0.31406	0.300000	0.22699	0.306000	0.20318	GAG		0.393	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22951126	C	A	22951126	3	1	98	1	0	0	0	0	1	0	0	0	18243	912	32	2	2862	2	ZNF99	19	22951126	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	587511	22951126	36177857	162	26448										
ATP4A	495	hgsc.bcm.edu	37	chr19	36051418	36051418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cgccaggatgcggatgtcggCgggcactctgtccccacctt	13	15	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:36051418C>T	ENST00000262623.3	-	6	662	c.634G>A	c.(634-636)Gcc>Acc	p.A212T		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	212					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGGATGTCGGCGGGCACTCTG	0.627																																																0			19											59	54	56					19																	36051418		2203	4300	6503	40743258	SO:0001583	missense	495				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.634G>A	19.37:g.36051418C>T	ENSP00000262623:p.Ala212Thr		40743258	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	c	18.94	3.729544	0.69074	.	.	ENSG00000105675	ENST00000262623	D	0.94184	-3.37	4.16	3.12	0.35913	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000005	D	0.97402	0.9150	H	0.96916	3.905	0.58432	D	0.99999	D	0.89917	1.0	D	0.81914	0.995	D	0.97089	0.9789	10	0.87932	D	0	.	9.8583	0.41098	0.0:0.8975:0.0:0.1025	.	212	P20648	ATP4A_HUMAN	T	212	ENSP00000262623:A212T	ENSP00000262623:A212T	A	-	1	0	ATP4A	40743258	1.000000	0.71417	0.306000	0.25113	0.536000	0.34869	5.844000	0.69430	1.103000	0.41568	-0.348000	0.07805	GCC		0.627	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36051418	C	T	36051418	3	4	98	1	0	0	0	0	1	0	0	0	1146	768	27	1	2541	1	ATP4A	19	36051418	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	13100292	36051418	23077565	163	26449										
ZNF607	84775	hgsc.bcm.edu	37	chr19	38190768	38190768	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	taaagctgcattttcccatcGctgattatttcacatcttga	5	10	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:38190768G>A	ENST00000355202.4	-	5	859	c.264C>T	c.(262-264)agC>agT	p.S88S	CTD-2528L19.4_ENST00000586606.2_Silent_p.S88S|ZNF607_ENST00000395835.3_Silent_p.S87S	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	88					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TTTTCCCATCGCTGATTATTT	0.313																																																0			19											53	56	55					19																	38190768		2203	4299	6502	42882608	SO:0001819	synonymous_variant	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.264C>T	19.37:g.38190768G>A			42882608	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Silent	SNP	ENST00000355202.4	37	CCDS33006.1																																																																																				0.313	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38190768	G	A	38190768	2	1	98	1	0	0	0	0	0	0	0	1	18072	1078	38	1		1	ZNF607	19	38190768	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10	2139350	38190768	20938215	164	26450										
RYR1	6261	hgsc.bcm.edu	37	chr19	38983253	38983253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	agagaaacctgaggaggagcGgtcagcagaggagagcaaac	16	7	1	4	rs143681974		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:38983253G>A	ENST00000359596.3	+	38	6251	c.6251G>A	c.(6250-6252)cGg>cAg	p.R2084Q	RYR1_ENST00000360985.3_Missense_Mutation_p.R2084Q|RYR1_ENST00000355481.4_Missense_Mutation_p.R2084Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2084	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R2084Q(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GAGGAGGAGCGGTCAGCAGAG	0.627																																																1	Substitution - Missense(1)	prostate(1)	19						G	GLN/ARG,GLN/ARG	2,4402	4.2+/-10.8	0,2,2200	44	40	41		6251,6251	-6.2	0	19	dbSNP_134	41	0,8600		0,0,4300	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	43,43	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	benign,benign	2084/5039,2084/5034	38983253	2,13002	2202	4300	6502	43675093	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6251G>A	19.37:g.38983253G>A	ENSP00000352608:p.Arg2084Gln		43675093	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	8.553	0.875924	0.17395	4.54E-4	0.0	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.72615	-0.67;-0.67;-0.67	4.52	-6.16	0.02098	.	0.262866	0.28921	U	0.013715	T	0.24160	0.0585	N	0.03608	-0.345	0.09310	N	1	B;P	0.37548	0.0;0.599	B;B	0.11329	0.0;0.006	T	0.55842	-0.8077	10	0.14252	T	0.57	.	0.5766	0.00704	0.2381:0.2735:0.1265:0.3618	.	2084;2084	P21817-2;P21817	.;RYR1_HUMAN	Q	2084	ENSP00000352608:R2084Q;ENSP00000347667:R2084Q;ENSP00000354254:R2084Q	ENSP00000347667:R2084Q	R	+	2	0	RYR1	43675093	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.297000	0.08276	-1.248000	0.02503	-1.713000	0.00713	CGG		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38983253	G	A	38983253	3	1	98	1	0	0	0	0	1	0	0	0	13805	1116	39	1	6401	1	RYR1	19	38983253	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	792485	38983253	20145730	165	26451										
GMFG	9535	hgsc.bcm.edu	37	chr19	39820258	39820258	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcacgtacttgtagctgtaaAccacgaacctaccgtgaaag	9	11	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:39820258A>C	ENST00000597595.1	-	5	417	c.209T>G	c.(208-210)gTt>gGt	p.V70G	GMFG_ENST00000602185.1_Missense_Mutation_p.V21G|GMFG_ENST00000601387.1_Missense_Mutation_p.V29G|GMFG_ENST00000598034.1_Missense_Mutation_p.V70G|GMFG_ENST00000600322.1_Missense_Mutation_p.V37G|GMFG_ENST00000253054.8_Missense_Mutation_p.V37G|GMFG_ENST00000595636.1_Intron|GMFG_ENST00000594700.1_Intron	NM_004877.2	NP_004868.1	O60234	GMFG_HUMAN	glia maturation factor, gamma	70	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				negative regulation of protein kinase activity (GO:0006469)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)			breast(1)|large_intestine(2)|liver(2)|lung(3)|skin(1)|stomach(1)	10	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.15e-27)|all cancers(26;1.3e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GTAGCTGTAAACCACGAACCT	0.517																																																0			19											177	122	141					19																	39820258		2203	4300	6503	44512098	SO:0001583	missense	9535			AB001993	CCDS12532.1, CCDS74364.1	19q13.2	2014-08-12			ENSG00000130755	ENSG00000130755			4374	protein-coding gene	gene with protein product		604104				9545571, 9653160, 17127212	Standard	XM_005259440		Approved		uc002okz.4	O60234	OTTHUMG00000182811	ENST00000597595.1:c.209T>G	19.37:g.39820258A>C	ENSP00000472249:p.Val70Gly		44512098	Q6IB37	Missense_Mutation	SNP	ENST00000597595.1	37	CCDS12532.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.154118	0.78114	.	.	ENSG00000130755	ENST00000253054	.	.	.	4.16	4.16	0.48862	Actin-binding, cofilin/tropomyosin type (3);	0.282664	0.25436	N	0.030698	T	0.80460	0.4627	M	0.88704	2.975	0.80722	D	1	D;D	0.71674	0.99;0.998	D;D	0.80764	0.982;0.994	D	0.83814	0.0243	9	0.87932	D	0	-16.0296	11.4702	0.50264	1.0:0.0:0.0:0.0	.	70;70	O60234;Q6IB37	GMFG_HUMAN;.	G	70	.	ENSP00000253054:V70G	V	-	2	0	GMFG	44512098	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.389000	0.66255	1.862000	0.54008	0.459000	0.35465	GTT		0.517	GMFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463839.1			C	39820258	A	C	39820258	3	2	98	1	0	0	0	0	1	0	0	0	6510	43	2	4	231	4	GMFG	19	39820258	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	837005	39820258	19308725	166	26452										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41386148	41386148	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaggtgggatcgatattggcGcctgcgggtgtggagggaga	20	5	0	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:41386148G>A	ENST00000301146.4	-	4	1036	c.495C>T	c.(493-495)ggC>ggT	p.G165G	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Splice_Site_p.G114G	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	165						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CGATATTGGCGCCTGCGGGTG	0.542																																																0			19											107	97	100					19																	41386148		2203	4300	6503	46077988	SO:0001630	splice_region_variant	1549			NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.494-1C>T	19.37:g.41386148G>A			46077988	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																				0.542	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	Silent	A	41386148	G	A	41386148	5	1	98	1	0	0	0	0	0	0	1	0	4169	1101	38	1	1013	1	CYP2A7	19	41386148	Splice_Site	SNP	G	TCGA-DC-6160-01A-11D-1657-10	1565890	41386148	17742835	167	26453										
PSG11	5680	hgsc.bcm.edu	37	chr19	43519316	43519316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gctttcctcgccagtggctgAgttacgagcagagcaagcat	12	11	0	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:43519316A>G	ENST00000401740.1	-	4	1019	c.916T>C	c.(916-918)Tca>Cca	p.S306P	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000403486.1_Missense_Mutation_p.S184P|PSG11_ENST00000320078.7_Missense_Mutation_p.S306P|PSG11_ENST00000306322.7_Missense_Mutation_p.S184P			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	315	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CCAGTGGCTGAGTTACGAGCA	0.453																																																0			19											148	142	144					19																	43519316		2199	4297	6496	48211156	SO:0001583	missense	5680			U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.916T>C	19.37:g.43519316A>G	ENSP00000384995:p.Ser306Pro		48211156	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	a	5.154	0.213959	0.09810	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.13089	2.62;2.62;2.62;2.62	0.976	-0.977	0.10282	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.21145	0.0509	L	0.41824	1.3	0.09310	N	1	B;B	0.32620	0.006;0.378	B;P	0.55260	0.054;0.772	T	0.51301	-0.8723	9	0.51188	T	0.08	.	3.291	0.06949	0.6621:0.0:0.3379:0.0	.	184;306	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	P	306;184;184;306	ENSP00000319140:S306P;ENSP00000385427:S184P;ENSP00000304913:S184P;ENSP00000384995:S306P	ENSP00000304913:S184P	S	-	1	0	PSG11	48211156	0.002000	0.14202	0.006000	0.13384	0.065000	0.16274	-0.588000	0.05774	-0.457000	0.07033	0.155000	0.16302	TCA		0.453	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		G	43519316	A	G	43519316	3	3	98	1	0	0	0	0	1	0	0	0	12688	304	11	4	99	4	PSG11	19	43519316	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	2133168	43519316	15609667	168	26454										
TULP2	7288	hgsc.bcm.edu	37	chr19	49385383	49385383	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acaccgttctccttgtcccaCgacggggttttgttgtgcaa	10	12	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:49385383C>T	ENST00000221399.3	-	12	1497	c.1353G>A	c.(1351-1353)tcG>tcA	p.S451S		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	451					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CCTTGTCCCACGACGGGGTTT	0.517																																																0			19											131	105	114					19																	49385383		2203	4300	6503	54077195	SO:0001819	synonymous_variant	7288			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1353G>A	19.37:g.49385383C>T			54077195	Q8TC50	Silent	SNP	ENST00000221399.3	37	CCDS12739.1																																																																																				0.517	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		T	49385383	C	T	49385383	2	4	98	1	0	0	0	0	0	0	0	1	16814	523	19	1		1	TULP2	19	49385383	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	5866067	49385383	9743600	169	26455										
NUCB1	4924	hgsc.bcm.edu	37	chr19	49425587	49425587	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	atttccagacgatgtacctgTcccagctccagccggtgacc	9	15	0	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:49425587T>C	ENST00000405315.4	+	13	1626	c.1292T>C	c.(1291-1293)gTc>gCc	p.V431A	NUCB1_ENST00000263273.5_Missense_Mutation_p.V431A|NUCB1_ENST00000485798.1_3'UTR|NUCB1_ENST00000407032.1_Missense_Mutation_p.V431A	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	431						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GATGTACCTGTCCCAGCTCCA	0.612																																																0			19											121	114	116					19																	49425587		2203	4300	6503	54117399	SO:0001583	missense	4924			BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.1292T>C	19.37:g.49425587T>C	ENSP00000385923:p.Val431Ala		54117399	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Missense_Mutation	SNP	ENST00000405315.4	37	CCDS12740.1	.	.	.	.	.	.	.	.	.	.	t	11.19	1.565779	0.27915	.	.	ENSG00000104805	ENST00000405315;ENST00000407032;ENST00000263273	T;T;T	0.18502	2.21;2.21;2.21	3.5	2.48	0.30137	.	0.490245	0.17947	N	0.156652	T	0.07503	0.0189	N	0.14661	0.345	0.28829	N	0.897252	B	0.06786	0.001	B	0.04013	0.001	T	0.36553	-0.9743	10	0.09843	T	0.71	.	5.5411	0.17038	0.0:0.1276:0.0:0.8724	.	431	Q02818	NUCB1_HUMAN	A	431	ENSP00000385923:V431A;ENSP00000385211:V431A;ENSP00000263273:V431A	ENSP00000263273:V431A	V	+	2	0	NUCB1	54117399	0.998000	0.40836	0.939000	0.37840	0.325000	0.28411	1.078000	0.30754	0.720000	0.32209	0.255000	0.18592	GTC		0.612	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		C	49425587	T	C	49425587	3	2	98	1	0	0	0	0	1	0	0	0	10749	1667	58	4	1338	4	NUCB1	19	49425587	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	40204	49425587	9703396	170	26456										
KCNA7	3743	hgsc.bcm.edu	37	chr19	49575304	49575304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcaccgggccggctgcggctGcagcagcaagccccgtgccg	15	17	1	0	rs77059600	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:49575304G>A	ENST00000221444.1	-	1	894	c.539C>T	c.(538-540)gCa>gTa	p.A180V		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	180				A -> V (in Ref. 3; AAX11186). {ECO:0000305}.	protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GGCTGCGGCTGCAGCAGCAAG	0.687													A|||	709	0.141573	0.2837	0.1398	5008	,	,		8486	0.0486		0.0885	False		,,,				2504	0.1012				Colon(74;686 1235 3793 23366 48562)											0			19						A	VAL/ALA	883,3133		82,719,1207	7	9	8		539	1.8	0	19	dbSNP_131	8	658,7272		33,592,3340	no	missense	KCNA7	NM_031886.2	64	115,1311,4547	AA,AG,GG		8.2976,21.9871,12.8997	benign	180/457	49575304	1541,10405	2008	3965	5973	54267116	SO:0001583	missense	3743			AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.539C>T	19.37:g.49575304G>A	ENSP00000221444:p.Ala180Val		54267116	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	322	0.14743589743589744	158	0.32113821138211385	62	0.1712707182320442	34	0.05944055944055944	68	0.08970976253298153	A	9.871	1.198847	0.22121	0.219871	0.082976	ENSG00000104848	ENST00000221444	D	0.97620	-4.46	4.28	1.79	0.24919	.	3.155100	0.01167	N	0.006767	T	0.00012	0.0000	N	0.03224	-0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.55503	-0.8131	9	0.27785	T	0.31	.	4.3707	0.11246	0.4332:0.237:0.3298:0.0	.	180	Q96RP8	KCNA7_HUMAN	V	180	ENSP00000221444:A180V	ENSP00000221444:A180V	A	-	2	0	KCNA7	54267116	0.034000	0.19679	0.006000	0.13384	0.002000	0.02628	-0.536000	0.06135	0.175000	0.19841	-0.504000	0.04507	GCA		0.687	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886		A	49575304	G	A	49575304	3	1	98	1	0	0	0	0	1	0	0	0	8029	1319	46	3	839	3	KCNA7	19	49575304	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	149717	49575304	9553679	171	26457										
MED25	81857	hgsc.bcm.edu	37	chr19	50333403	50333403	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cagccagtccccctgcctccCgccgcaccctcaggtgccac	8	23	1	0	rs111621037		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:50333403C>T	ENST00000312865.6	+	7	800	c.747C>T	c.(745-747)ccC>ccT	p.P249P	MED25_ENST00000538643.1_Intron	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	249	Pro-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		CCCTGCCTCCCGCCGCACCCT	0.667																																					GBM(51;894 1657 37868)											0			19											36	45	42					19																	50333403		2179	4273	6452	55025215	SO:0001819	synonymous_variant	81857			AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.747C>T	19.37:g.50333403C>T			55025215	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Silent	SNP	ENST00000312865.6	37	CCDS33075.1	.	.	.	.	.	.	.	.	.	.	C	3.583	-0.085295	0.07097	.	.	ENSG00000104973	ENST00000544580	.	.	.	4.98	-6.65	0.01795	.	.	.	.	.	T	0.49660	0.1570	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	T	0.56147	-0.8027	5	0.59425	D	0.04	.	2.3928	0.04382	0.3428:0.3804:0.1531:0.1238	.	.	.	.	C	249	.	ENSP00000444765:R249C	R	+	1	0	MED25	55025215	0.253000	0.23982	0.013000	0.15412	0.485000	0.33311	-0.636000	0.05465	-1.722000	0.01377	-0.940000	0.02684	CGC		0.667	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973		T	50333403	C	T	50333403	2	4	98	1	0	0	0	0	0	0	0	1	9473	639	23	1		1	MED25	19	50333403	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	758099	50333403	8795580	172	26458										
KLK8	11202	hgsc.bcm.edu	37	chr19	51503938	51503938	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggacacacggcaagttctccGcatacaacttagtgaggagg	12	10	1	1	rs111771104	byFrequency	TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:51503938G>A	ENST00000600767.1	-	4	560				KLK8_ENST00000320838.5_Intron|KLK8_ENST00000593490.1_Intron|KLK9_ENST00000376832.4_Intron|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000347619.4_Intron|KLK8_ENST00000391806.2_Missense_Mutation_p.A36V|KLK9_ENST00000250366.6_Intron|KLK8_ENST00000598195.1_5'Flank|KLK8_ENST00000291726.7_Intron			O60259	KLK8_HUMAN	kallikrein-related peptidase 8						cell death (GO:0008219)|keratinocyte proliferation (GO:0043616)|memory (GO:0007613)|negative regulation of axon regeneration (GO:0048681)|negative regulation of myelination (GO:0031642)|neuron projection morphogenesis (GO:0048812)|regulation of synapse organization (GO:0050807)|response to wounding (GO:0009611)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|prostate(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)		CAAGTTCTCCGCATACAACTT	0.567													G|||	2	0.000399361	8e-04	0.0014	5008	,	,		19096	0		0	False		,,,				2504	0															0			19						G	,VAL/ALA,,	4,4402	4.2+/-10.8	0,4,2199	71	72	72		,107,,	-3	0	19	dbSNP_132	72	0,8600		0,0,4300	yes	intron,missense,intron,intron	KLK8	NM_007196.2,NM_144505.1,NM_144506.1,NM_144507.1	,64,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,,,	,36/306,,	51503938	4,13002	2203	4300	6503	56195750	SO:0001627	intron_variant	284366			AB008390	CCDS12813.1, CCDS12814.1, CCDS12815.1, CCDS42600.1, CCDS74433.1	19q13	2011-09-07	2006-10-27			ENSG00000129455		"Kallikreins", "Serine peptidases / Serine peptidases"	6369	protein-coding gene	gene with protein product		605644	"kallikrein 8 (neuropsin/ovasin)"	PRSS19		10102990, 9714609, 16800724, 16800723	Standard	NM_144505		Approved	HNP, TADG14, neuropsin, ovasin	uc002pur.1	O60259		ENST00000600767.1:c.71-99C>T	19.37:g.51503938G>A			56195750	Q5V9X1|Q5V9X2|Q8IW69|Q9HCB3|Q9NR68|Q9NR69|Q9UIL9|Q9UQ47	Missense_Mutation	SNP	ENST00000600767.1	37	CCDS12813.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	14.69	2.612036	0.46631	9.08E-4	0.0	ENSG00000129455	ENST00000391806	D	0.88431	-2.38	3.74	-2.97	0.05530	.	.	.	.	.	T	0.76364	0.3977	N	0.19112	0.55	0.09310	N	0.999999	B	0.14012	0.009	B	0.10450	0.005	T	0.61412	-0.7068	9	0.44086	T	0.13	.	4.3826	0.11302	0.5207:0.1812:0.2981:0.0	.	36	O60259-2	.	V	36	ENSP00000375682:A36V	ENSP00000375682:A36V	A	-	2	0	KLK8	56195750	0.000000	0.05858	0.000000	0.03702	0.216000	0.24613	0.102000	0.15272	-0.356000	0.08187	0.561000	0.74099	GCG		0.567	KLK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465032.2	NM_007196		A	51503938	G	A	51503938	1	1	98	0	1	0	0	0	0	0	0	0	8431	1087	38	1		1	KLK8	19	51503938	Intron	SNP	G	TCGA-DC-6160-01A-11D-1657-10	1170535	51503938	7625045	173	26459										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53741069	53741069	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tctgatgcctagtgaggttcGaacactggttaaaggctttg	12	7	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:53741069G>A	ENST00000598513.1	-	5	1061	c.911C>T	c.(910-912)tCg>tTg	p.S304L	ZNF677_ENST00000333952.4_Missense_Mutation_p.S304L|CTD-2245F17.6_ENST00000596041.1_RNA	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		AGTGAGGTTCGAACACTGGTT	0.403																																																0			19											121	111	114					19																	53741069		2203	4300	6503	58432881	SO:0001583	missense	342926			BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.911C>T	19.37:g.53741069G>A	ENSP00000469391:p.Ser304Leu		58432881		Missense_Mutation	SNP	ENST00000598513.1	37	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.183588	0.38609	.	.	ENSG00000197928	ENST00000333952	T	0.36520	1.25	2.2	-0.0421	0.13865	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.29692	N	0.011454	T	0.26846	0.0657	M	0.69523	2.12	0.09310	N	1	B	0.29432	0.244	B	0.18561	0.022	T	0.25572	-1.0128	10	0.59425	D	0.04	.	1.0549	0.01588	0.1474:0.2289:0.3907:0.233	.	304	Q86XU0	ZN677_HUMAN	L	304	ENSP00000334394:S304L	ENSP00000334394:S304L	S	-	2	0	ZNF677	58432881	0.000000	0.05858	0.000000	0.03702	0.928000	0.56348	0.583000	0.23849	0.056000	0.16144	0.650000	0.86243	TCG		0.403	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		A	53741069	G	A	53741069	3	1	98	1	0	0	0	0	1	0	0	0	18123	1059	37	1	847	1	ZNF677	19	53741069	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	2237131	53741069	5387914	174	26460										
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58967438	58967438	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tgcttgcgcacagtgtggccGccgcttctgccgcaactcgc	12	16	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr19:58967438G>A	ENST00000336614.4	+	4	1234	c.1127G>A	c.(1126-1128)cGc>cAc	p.R376H	ZNF324B_ENST00000545523.1_Missense_Mutation_p.R376H|ZNF324B_ENST00000391696.1_Missense_Mutation_p.R366H	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		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;0.0164)|Lung(386;0.179)		CAGTGTGGCCGCCGCTTCTGC	0.662																																																0			19											22	22	22					19																	58967438		2199	4291	6490	63659250	SO:0001583	missense	388569			AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.1127G>A	19.37:g.58967438G>A	ENSP00000337473:p.Arg376His		63659250	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	37	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.361007	0.61403	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.03920	3.76;3.76;3.76	2.66	1.57	0.23409	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42053	D	0.000775	T	0.11196	0.0273	L	0.48218	1.51	0.09310	N	0.999999	D;D	0.89917	1.0;0.998	D;D	0.77557	0.99;0.914	T	0.04333	-1.0959	10	0.87932	D	0	.	5.1088	0.14798	0.2867:0.0:0.7133:0.0	.	376;366	Q6AW86;C9JTQ8	Z324B_HUMAN;.	H	376;376;366	ENSP00000337473:R376H;ENSP00000438930:R376H;ENSP00000375578:R366H	ENSP00000337473:R376H	R	+	2	0	ZNF324B	63659250	0.019000	0.18553	0.952000	0.39060	0.996000	0.88848	0.344000	0.19962	0.646000	0.30693	0.591000	0.81541	CGC		0.662	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		A	58967438	G	A	58967438	3	1	98	1	0	0	0	0	1	0	0	0	17884	1087	38	1	1137	1	ZNF324B	19	58967438	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	5226369	58967438	161545	175	26461										
CHD6	84181	hgsc.bcm.edu	37	chr20	40083356	40083356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaggaaatatctgttctgttTcctgaagccacaaagctagc	8	9	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr20:40083356T>C	ENST00000373233.3	-	20	3207	c.3030A>G	c.(3028-3030)ggA>ggG	p.G1010G	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1010					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CTGTTCTGTTTCCTGAAGCCA	0.358																																																0			20											122	118	119					20																	40083356		2203	4300	6503	39516770	SO:0001819	synonymous_variant	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3030A>G	20.37:g.40083356T>C			39516770	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																				0.358	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40083356	T	C	40083356	2	2	98	1	0	0	0	0	0	0	0	1	3335	1770	62	4		4	CHD6	20	40083356	Silent	SNP	T	TCGA-DC-6160-01A-11D-1657-10		40083356	22942164	176	26462										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50769674	50769674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gcgcagggcggccttgctggAgcaggagtagctgcattccg	17	11	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr20:50769674A>G	ENST00000216923.4	-	6	1406	c.1057T>C	c.(1057-1059)Tcc>Ccc	p.S353P	ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000346617.4_Missense_Mutation_p.S299P|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Missense_Mutation_p.S351P	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GCCTTGCTGGAGCAGGAGTAG	0.607																																																0			20											118	109	112					20																	50769674		2203	4300	6503	50203081	SO:0001583	missense	55734			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1057T>C	20.37:g.50769674A>G	ENSP00000216923:p.Ser353Pro		50203081	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	37	CCDS13440.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463391	0.43736	.	.	ENSG00000020256	ENST00000216923;ENST00000346617;ENST00000371515;ENST00000546083;ENST00000371516	T;T;T	0.09163	3.02;3.04;3.01	5.79	-1.29	0.09288	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.319355	0.27202	N	0.020455	T	0.08403	0.0209	L	0.45228	1.405	0.43756	D	0.996269	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.10450	0.005;0.001;0.001	T	0.13548	-1.0505	10	0.66056	D	0.02	-18.4798	7.0797	0.25223	0.5896:0.2214:0.189:0.0	.	299;351;353	Q9NPA5-2;Q5JWM1;Q9NPA5	.;.;ZF64A_HUMAN	P	353;299;351;195;506	ENSP00000216923:S353P;ENSP00000344615:S299P;ENSP00000360570:S351P	ENSP00000216923:S353P	S	-	1	0	ZFP64	50203081	1.000000	0.71417	0.979000	0.43373	0.981000	0.71138	1.220000	0.32491	-0.109000	0.12044	0.496000	0.49642	TCC		0.607	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		G	50769674	A	G	50769674	3	3	98	1	0	0	0	0	1	0	0	0	17691	304	11	4	2183	4	ZFP64	20	50769674	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	10686318	50769674	12255846	177	26463										
C20orf107	388799	hgsc.bcm.edu	37	chr20	55108569	55108569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	acacccaaggctggcttgggAgcaaatggctctggcttttg	13	10	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr20:55108569A>G	ENST00000371325.1	+	1	268	c.172A>G	c.(172-174)Agc>Ggc	p.S58G		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	58						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											CTGGCTTGGGAGCAAATGGCT	0.498																																																0			20											156	134	142					20																	55108569		2203	4300	6503	54541976	SO:0001583	missense	388799			AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 107"	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.172A>G	20.37:g.55108569A>G	ENSP00000360376:p.Ser58Gly		54541976	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	A	6.714	0.500344	0.12762	.	.	ENSG00000213714	ENST00000371325	T	0.10573	2.86	2.8	2.8	0.32819	.	0.323633	0.26213	N	0.025676	T	0.11879	0.0289	L	0.52573	1.65	0.23943	N	0.996395	P	0.39044	0.656	B	0.42138	0.377	T	0.09143	-1.0688	10	0.49607	T	0.09	-19.0876	7.3067	0.26451	1.0:0.0:0.0:0.0	.	58	Q5JX69	CT107_HUMAN	G	58	ENSP00000360376:S58G	ENSP00000360376:S58G	S	+	1	0	C20orf107	54541976	0.982000	0.34865	0.996000	0.52242	0.283000	0.27025	3.360000	0.52299	1.274000	0.44362	0.323000	0.21402	AGC		0.498	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1			G	55108569	A	G	55108569	3	3	98	1	0	0	0	0	1	0	0	0	2083	304	11	4	174	4	C20orf107	20	55108569	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	4338895	55108569	7916951	178	26464										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60893967	60893967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ccaggtcccgggcccgcatcTcccagagcagccgctccacc	10	21	1	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr20:60893967T>C	ENST00000252999.3	-	52	7040	c.6974A>G	c.(6973-6975)gAg>gGg	p.E2325G		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2325	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGCCCGCATCTCCCAGAGCAG	0.692																																																0			20											9	11	10					20																	60893967		2146	4238	6384	60327362	SO:0001583	missense	3911			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6974A>G	20.37:g.60893967T>C	ENSP00000252999:p.Glu2325Gly		60327362	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	-	16.42	3.118620	0.56505	.	.	ENSG00000130702	ENST00000252999	T	0.12984	2.63	4.25	3.11	0.35812	Laminin I (1);	0.170522	0.50627	U	0.000103	T	0.17789	0.0427	L	0.54323	1.7	0.80722	D	1	P	0.42078	0.77	P	0.44921	0.464	T	0.01021	-1.1478	10	0.72032	D	0.01	.	10.3799	0.44106	0.0:0.0:0.1654:0.8346	.	2325	O15230	LAMA5_HUMAN	G	2325	ENSP00000252999:E2325G	ENSP00000252999:E2325G	E	-	2	0	LAMA5	60327362	1.000000	0.71417	0.725000	0.30721	0.115000	0.19883	3.830000	0.55768	0.491000	0.27793	0.515000	0.50301	GAG		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60893967	T	C	60893967	3	2	98	1	0	0	0	0	1	0	0	0	8631	1551	54	4	4229	4	LAMA5	20	60893967	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	5785398	60893967	2131553	179	26465										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15889291	15889291	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gaaatagctctcatttttttAcccaaaccgcctccattatt	3	12	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr21:15889291A>C	ENST00000400566.1	-	3	282	c.201T>G	c.(199-201)ggT>ggG	p.G67G	SAMSN1_ENST00000285670.2_Silent_p.G135G|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	67					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TCATTTTTTTACCCAAACCGC	0.343																																																0			21											134	116	121					21																	15889291		1792	4073	5865	14811162	SO:0001819	synonymous_variant	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.201T>G	21.37:g.15889291A>C			14811162	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Silent	SNP	ENST00000400566.1	37	CCDS42906.1																																																																																				0.343	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			C	15889291	A	C	15889291	2	2	98	1	0	0	0	0	0	0	0	1	13867	378	14	4		4	SAMSN1	21	15889291	Silent	SNP	A	TCGA-DC-6160-01A-11D-1657-10		15889291	32240604	180	26466										
GABPA	2551	hgsc.bcm.edu	37	chr21	27136964	27136964	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gaacttcttactgataaggaCgctcgagactgcatttcttg	9	9	2	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr21:27136964C>T	ENST00000354828.3	+	9	1529	c.1002C>T	c.(1000-1002)gaC>gaT	p.D334D	GABPA_ENST00000400075.3_Silent_p.D334D	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	334					cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.D334D(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						CTGATAAGGACGCTCGAGACT	0.398																																																1	Substitution - coding silent(1)	large_intestine(1)	21											118	106	110					21																	27136964		2203	4299	6502	26058835	SO:0001819	synonymous_variant	2551				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"human nuclear respiratory factor-2 subunit alpha", "nuclear respiratory factor 2 alpha subunit"	600609	"GA-binding protein transcription factor, alpha subunit (60kD)"			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.1002C>T	21.37:g.27136964C>T			26058835	Q12939	Silent	SNP	ENST00000354828.3	37	CCDS13575.1																																																																																				0.398	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040		T	27136964	C	T	27136964	2	4	98	1	0	0	0	0	0	0	0	1	6176	535	19	1		1	GABPA	21	27136964	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	11247673	27136964	20992931	181	26467										
SLC7A4	6545	hgsc.bcm.edu	37	chr22	21384276	21384276	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	cctggctcagggacggaggcGtgtacagtgcccaccagctg	15	13	1	0	rs559055973		TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr22:21384276G>A	ENST00000382932.2	-	3	1414	c.1347C>T	c.(1345-1347)caC>caT	p.H449H	SLC7A4_ENST00000403586.1_Silent_p.H449H|AC002472.11_ENST00000450652.1_RNA	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	449					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	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)	GGACGGAGGCGTGTACAGTGC	0.662													G|||	1	0.000199681	0	0	5008	,	,		17842	0		0.001	False		,,,				2504	0															0			22											34	32	33					22																	21384276		2203	4300	6503	19714276	SO:0001819	synonymous_variant	6545			AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"Solute carriers"	11062	protein-coding gene	gene with protein product		603752	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 4", "solute carrier family 7 (orphan transporter), member 4"			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.1347C>T	22.37:g.21384276G>A			19714276	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Silent	SNP	ENST00000382932.2	37	CCDS33608.1																																																																																				0.662	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173		A	21384276	G	A	21384276	2	1	98	1	0	0	0	0	0	0	0	1	14736	1136	40	1		1	SLC7A4	22	21384276	Silent	SNP	G	TCGA-DC-6160-01A-11D-1657-10		21384276	29920290	182	26468										
PISD	23761	hgsc.bcm.edu	37	chr22	32017125	32017125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tcttgaaggagtcacacgacGcggctgtggagtaggagcag	16	8	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chr22:32017125G>A	ENST00000439502.2	-	6	924	c.701C>T	c.(700-702)gCg>gTg	p.A234V	PISD_ENST00000478893.1_5'UTR|PISD_ENST00000266095.5_Missense_Mutation_p.A200V|PISD_ENST00000397500.1_Missense_Mutation_p.A200V|PISD_ENST00000336566.4_Missense_Mutation_p.A233V|PISD_ENST00000382151.2_Missense_Mutation_p.A200V			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	234					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)			central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	GTCACACGACGCGGCTGTGGA	0.612											OREG0003530	type=REGULATORY REGION|Gene=PISD|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			22											98	92	94					22																	32017125		2203	4300	6503	30347125	SO:0001583	missense	23761				CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.701C>T	22.37:g.32017125G>A	ENSP00000391739:p.Ala234Val	829	30347125	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Missense_Mutation	SNP	ENST00000439502.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.26|15.26	2.782269|2.782269	0.49891|0.49891	.|.	.|.	ENSG00000241878|ENSG00000241878	ENST00000382151;ENST00000266095;ENST00000397500;ENST00000439502;ENST00000336566;ENST00000451635;ENST00000422020|ENST00000435900	.|.	.|.	.|.	5.03|5.03	5.03|5.03	0.67393|0.67393	.|.	1.031700|.	0.07641|.	N|.	0.930296|.	T|T	0.31670|0.31670	0.0804|0.0804	N|N	0.12637|0.12637	0.245|0.245	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.15719|.	0.0;0.002;0.007;0.014|.	B;B;B;B|.	0.15484|.	0.003;0.013;0.004;0.004|.	T|T	0.21793|0.21793	-1.0235|-1.0235	9|5	0.15952|.	T|.	0.53|.	-14.5644|-14.5644	15.5397|15.5397	0.76031|0.76031	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	224;234;200;200|.	B1AJZ0;Q9UG56;B1AKM6;Q9UG56-2|.	.;PISD_HUMAN;.;.|.	V|C	200;200;200;234;233;200;200|225	.|.	ENSP00000266095:A200V|.	A|R	-|-	2|1	0|0	PISD|PISD	30347125|30347125	0.434000|0.434000	0.25570|0.25570	0.012000|0.012000	0.15200|0.15200	0.107000|0.107000	0.19398|0.19398	3.735000|3.735000	0.55044|0.55044	2.330000|2.330000	0.79161|0.79161	0.563000|0.563000	0.77884|0.77884	GCG|CGT		0.612	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4			A	32017125	G	A	32017125	3	1	98	1	0	0	0	0	1	0	0	0	11977	1087	38	1	540	1	PISD	22	32017125	Missense_Mutation	SNP	G	TCGA-DC-6160-01A-11D-1657-10	10632849	32017125	19287441	183	26469										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148376	34148377	+	Frame_Shift_Ins	INS	-	-	G													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggaatttcctgccccagtaINStttttcctgtgagaagaatt							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:34148376_34148377insG	ENST00000346193.3	-	1	2070_2071	c.2019_2020insC	c.(2017-2022)aaatacfs	p.Y674fs		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	674										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CTGCCCCAGTATTTTTCCTGTG	0.431																																																0			X																																								34058298	SO:0001589	frameshift_variant	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.2019_2020insC	X.37:g.34148376_34148377insG	ENSP00000345029:p.Tyr674fs		34058297	A8K8I9|Q8TAA0	Frame_Shift_Ins	INS	ENST00000346193.3	37	CCDS43926.1																																																																																				0.431	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		G	34148377	-	G	34148376	7	5	98	1	0	1	1	0	0	0	0	0	5588	449	16	0	359	0	FAM47A	23	34148376	Frame_Shift_Ins	INS	-	TCGA-DC-6160-01A-11D-1657-10		34148376	121122184	184	26470	41	2								
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148377	34148377	+	Missense_Mutation	SNP	T	T	G													0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	tggaatttcctgccccagtaTttttcctgtgagaagaattt							TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:34148377T>G	ENST00000346193.3	-	1	2070	c.2019A>C	c.(2017-2019)aaA>aaC	p.K673N		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	673										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TGCCCCAGTATTTTTCCTGTG	0.433																																																0			X											84	84	84					X																	34148377		2199	4296	6495	34058298	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.2019A>C	X.37:g.34148377T>G	ENSP00000345029:p.Lys673Asn		34058298	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	T	6.898	0.535141	0.13188	.	.	ENSG00000185448	ENST00000346193	T	0.41758	0.99	1.49	0.148	0.14843	.	.	.	.	.	T	0.30696	0.0773	M	0.63428	1.95	0.09310	N	1	P	0.47253	0.892	B	0.37304	0.246	T	0.17592	-1.0364	9	0.25751	T	0.34	.	4.0088	0.09613	0.0:0.0:0.3786:0.6214	.	673	Q5JRC9	FA47A_HUMAN	N	673	ENSP00000345029:K673N	ENSP00000345029:K673N	K	-	3	2	FAM47A	34058298	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.405000	0.07196	-0.007000	0.14345	0.441000	0.28932	AAA		0.433	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		G	34148377	T	G	34148377	3	3	98	1	0	0	0	0	1	0	0	0	5588	1490	52	4	360	4	FAM47A	23	34148377	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	1	34148377	121122183	185	26471	41	2								
UBA1	7317	hgsc.bcm.edu	37	chrX	47069380	47069380	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	ggcaggcactcagcccttggAggtgctggaggctgtgcagc	17	11	1	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:47069380A>G	ENST00000335972.6	+	18	2240	c.2057A>G	c.(2056-2058)gAg>gGg	p.E686G	UBA1_ENST00000377351.4_Missense_Mutation_p.E686G|UBA1_ENST00000377269.3_Missense_Mutation_p.E134G	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	686					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CAGCCCTTGGAGGTGCTGGAG	0.612																																																0			X											64	60	62					X																	47069380		2202	4300	6502	46954324	SO:0001583	missense	7317			AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.2057A>G	X.37:g.47069380A>G	ENSP00000338413:p.Glu686Gly		46954324	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793156	0.50102	.	.	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.45276	0.9;0.9;0.9	4.5	4.5	0.54988	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.114984	0.64402	D	0.000016	T	0.44138	0.1279	L	0.56769	1.78	0.58432	D	0.999999	P;D	0.58620	0.794;0.983	B;P	0.48189	0.273;0.57	T	0.35943	-0.9768	10	0.35671	T	0.21	-27.4606	10.6844	0.45835	1.0:0.0:0.0:0.0	.	134;686	Q5JRR6;P22314	.;UBA1_HUMAN	G	686;686;134	ENSP00000366568:E686G;ENSP00000338413:E686G;ENSP00000366481:E134G	ENSP00000338413:E686G	E	+	2	0	UBA1	46954324	1.000000	0.71417	0.999000	0.59377	0.890000	0.51754	6.760000	0.74939	1.791000	0.52520	0.430000	0.28490	GAG		0.612	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		G	47069380	A	G	47069380	3	3	98	1	0	0	0	0	1	0	0	0	16867	304	11	4	2123	4	UBA1	23	47069380	Missense_Mutation	SNP	A	TCGA-DC-6160-01A-11D-1657-10	12921003	47069380	108201180	186	26472										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50377223	50377223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggtctcttccactggctccTtagtgtcacacagctgtgac	10	13	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:50377223T>C	ENST00000289292.7	-	4	2133	c.1850A>G	c.(1849-1851)aAg>aGg	p.K617R	SHROOM4_ENST00000460112.3_Missense_Mutation_p.K501R|SHROOM4_ENST00000376020.2_Missense_Mutation_p.K617R			Q9ULL8	SHRM4_HUMAN	shroom family member 4	617					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					CACTGGCTCCTTAGTGTCACA	0.507																																																0			X											49	50	50					X																	50377223		2203	4300	6503	50393963	SO:0001583	missense	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.1850A>G	X.37:g.50377223T>C	ENSP00000289292:p.Lys617Arg		50393963	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	5.769	0.326227	0.10900	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	D;D;D	0.88818	-2.43;-2.43;-2.43	6.06	4.89	0.63831	.	0.430862	0.24233	N	0.040330	D	0.83825	0.5338	L	0.51422	1.61	0.24462	N	0.994432	B	0.28713	0.22	B	0.25140	0.058	T	0.70124	-0.4958	10	0.23891	T	0.37	.	10.1172	0.42598	0.0:0.0798:0.0:0.9202	.	617	Q9ULL8	SHRM4_HUMAN	R	617;617;501	ENSP00000289292:K617R;ENSP00000365188:K617R;ENSP00000421450:K501R	ENSP00000289292:K617R	K	-	2	0	SHROOM4	50393963	1.000000	0.71417	0.965000	0.40720	0.569000	0.35902	7.100000	0.76989	0.893000	0.36288	0.486000	0.48141	AAG		0.507	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50377223	T	C	50377223	3	2	98	1	0	0	0	0	1	0	0	0	14333	1609	56	4	2655	4	SHROOM4	23	50377223	Missense_Mutation	SNP	T	TCGA-DC-6160-01A-11D-1657-10	3307843	50377223	104893337	187	26473										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63557191	63557191	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	aaaatggatctaggaggatgCtagccactgagcagacttgt	12	7	1	2			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:63557191C>T	ENST00000374852.3	-	9	1125	c.1058G>A	c.(1057-1059)aGc>aAc	p.S353N	MTMR8_ENST00000478487.1_5'UTR|MTMR8_ENST00000453546.1_Missense_Mutation_p.S353N	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	353	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TAGGAGGATGCTAGCCACTGA	0.443																																																1	Whole gene deletion(1)	ovary(1)	X											99	75	83					X																	63557191		2203	4300	6503	63473916	SO:0001583	missense	66036			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1058G>A	X.37:g.63557191C>T	ENSP00000363985:p.Ser353Asn		63473916	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.771651	0.49680	.	.	ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400	D;D	0.90133	-2.62;-2.62	2.66	2.66	0.31614	Myotubularin phosphatase domain (1);	0.096905	0.41823	U	0.000817	D	0.91821	0.7412	L	0.49571	1.57	0.28043	N	0.933651	P;D	0.61697	0.77;0.99	B;P	0.61800	0.216;0.894	D	0.86171	0.1600	10	0.59425	D	0.04	.	11.839	0.52342	0.0:1.0:0.0:0.0	.	353;353	B4DQL0;Q96EF0	.;MTMR8_HUMAN	N	353;353;239	ENSP00000394003:S353N;ENSP00000363985:S353N	ENSP00000247400:S239N	S	-	2	0	MTMR8	63473916	0.911000	0.30947	1.000000	0.80357	0.971000	0.66376	1.834000	0.39171	1.361000	0.45981	0.600000	0.82982	AGC		0.443	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63557191	C	T	63557191	3	4	98	1	0	0	0	0	1	0	0	0	9979	797	28	3	1080	3	MTMR8	23	63557191	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	13179968	63557191	91713369	188	26474										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107911595	107911595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gggattccaggaaatcctggCcttccaggtccaaagggcga	13	11	0	0			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:107911595C>T	ENST00000361603.2	+	41	3895	c.3651C>T	c.(3649-3651)ggC>ggT	p.G1217G	COL4A5_ENST00000328300.6_Silent_p.G1217G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1217	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.G1217G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GAAATCCTGGCCTTCCAGGTC	0.512									Alport syndrome with Diffuse Leiomyomatosis																																							1	Substitution - coding silent(1)	lung(1)	X											61	56	58					X																	107911595		2203	4300	6503	107798251	SO:0001819	synonymous_variant	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.3651C>T	X.37:g.107911595C>T			107798251	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1																																																																																				0.512	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107911595	C	T	107911595	2	4	98	1	0	0	0	0	0	0	0	1	3700	726	26	3		3	COL4A5	23	107911595	Silent	SNP	C	TCGA-DC-6160-01A-11D-1657-10	44354404	107911595	47358965	189	26475										
CDR1	1038	hgsc.bcm.edu	37	chrX	139866524	139866524	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0320855614973262	6	1	0.700391180654339	4.43581081081081	0.599433893352812	0.140866873065015	0.572858617131061	0	gaaaatccacgtcttccaacCaagccatgtcttccagaaaa	5	13	2	1			TCGA-DC-6160-01A-11D-1657-10	TCGA-DC-6160-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	902a8fff-7675-4b2c-8c43-077d1fcc6d7b	0af81acb-66b4-4a7c-951f-8b2ee8a82767	g.chrX:139866524C>A	ENST00000370532.2	-	1	199	c.8G>T	c.(7-9)tGg>tTg	p.W3L		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	3	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				GTCTTCCAACCAAGCCATGTC	0.428													C|||	45	0.0119205	0.0045	0.0101	3775	,	,		18061	0.0179		0.0139	False		,,,				2504	0															0			X											131	134	133					X																	139866524		2202	4299	6501	139694190	SO:0001583	missense	1038				CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.8G>T	X.37:g.139866524C>A	ENSP00000359563:p.Trp3Leu		139694190	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	C	7.642	0.681130	0.14907	.	.	ENSG00000184258	ENST00000370532	T	0.28666	1.6	4.24	-4.03	0.04021	.	.	.	.	.	T	0.10465	0.0256	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29488	-1.0010	8	.	.	.	.	1.2552	0.01990	0.2147:0.2808:0.0981:0.4064	.	3	P51861	CDR1_HUMAN	L	3	ENSP00000359563:W3L	.	W	-	2	0	CDR1	139694190	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.420000	0.07062	-0.546000	0.06216	-1.390000	0.01156	TGG		0.428	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		A	139866524	C	A	139866524	3	1	98	1	0	0	0	0	1	0	0	0	3177	595	21	2	784	2	CDR1	23	139866524	Missense_Mutation	SNP	C	TCGA-DC-6160-01A-11D-1657-10	31954929	139866524	15404036	190	26476										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10231208	10231208	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tttcctaggagcttggacccCgattggctgcaatgctgaac	11	11	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:10231208C>T	ENST00000253251.8	+	24	3798	c.2959C>T	c.(2959-2961)Cga>Tga	p.R987*	UBE4B_ENST00000377157.3_Nonsense_Mutation_p.R871*|UBE4B_ENST00000343090.6_Nonsense_Mutation_p.R1116*					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GCTTGGACCCCGATTGGCTGC	0.448																																																0			1											95	99	98					1																	10231208		2203	4300	6503	10153795	SO:0001587	stop_gained	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2959C>T	1.37:g.10231208C>T	ENSP00000253251:p.Arg987*		10153795		Nonsense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	C	49	16.040778	0.99852	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9686	15.0617	0.71961	0.1418:0.8582:0.0:0.0	.	.	.	.	X	987;871;1116	.	ENSP00000253251:R987X	R	+	1	2	UBE4B	10153795	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.930000	0.70104	2.793000	0.96121	0.655000	0.94253	CGA		0.448	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		T	10231208	C	T	10231208	4	4	99	1	0	0	0	0	0	1	0	0	16923	644	23	1	3444	1	UBE4B	1	10231208	Nonsense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		10231208	239019413	1	26477										
PPCS	79717	hgsc.bcm.edu	37	chr1	42922570	42922571	+	Frame_Shift_Ins	INS	-	-	TT													0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcggccttcgggcccagcccINStttcgggcttgctgagcctg							TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:42922570_42922571insTT	ENST00000372561.3	+	1	341_342	c.334_335insTT	c.(334-336)cttfs	p.L112fs	PPCS_ENST00000472013.1_3'UTR|ZMYND12_ENST00000433602.2_5'Flank|PPCS_ENST00000372562.1_Intron|PPCS_ENST00000372556.3_Intron|ZMYND12_ENST00000372565.3_5'Flank|PPCS_ENST00000455780.1_Intron|PPCS_ENST00000372560.3_Frame_Shift_Ins_p.L112fs	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	112					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGCCCAGCCCTTTCGGGCTTG	0.653																																																0			1																																								42695158	SO:0001589	frameshift_variant	79717			AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.335_336dupTT	1.37:g.42922571_42922572dupTT	ENSP00000361642:p.Leu112fs		42695157	Q3KQT2|Q5VVM0	Frame_Shift_Ins	INS	ENST00000372561.3	37	CCDS41311.1																																																																																				0.653	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		TT	42922571	-	TT	42922570	7	5	99	1	0	1	1	0	0	0	0	0	12336	681	24	0	336	0	PPCS	1	42922570	Frame_Shift_Ins	INS	-	TCGA-DC-6681-01A-11D-1826-10	32691362	42922570	206328051	2	26478										
ACADM	34	hgsc.bcm.edu	37	chr1	76205781	76205781	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aagatgtggataaccaacggAggaaaagctaattggtatgt	12	4	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:76205781A>G	ENST00000370841.4	+	7	1022	c.585A>G	c.(583-585)ggA>ggG	p.G195G	ACADM_ENST00000420607.2_Silent_p.G199G|ACADM_ENST00000370834.5_Silent_p.G228G|ACADM_ENST00000543667.1_Silent_p.G6G|ACADM_ENST00000541113.1_Silent_p.G159G	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	195			G -> R (in ACADMD). {ECO:0000269|PubMed:7929823}.		cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	TAACCAACGGAGGAAAAGCTA	0.328																																																0			1											104	107	106					1																	76205781		2203	4299	6502	75978369	SO:0001819	synonymous_variant	34			M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.585A>G	1.37:g.76205781A>G			75978369	Q5T4U4|Q9NYF1	Silent	SNP	ENST00000370841.4	37	CCDS668.1																																																																																				0.328	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			G	76205781	A	G	76205781	2	3	99	1	0	0	0	0	0	0	0	1	113	291	11	4		4	ACADM	1	76205781	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	33283211	76205781	173044840	3	26479										
CTBS	1486	hgsc.bcm.edu	37	chr1	85039955	85039955	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tggtggcgaatcgggcggcaGagctcaggctccgggcatgg	19	10	1	1	rs2303307	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:85039955G>A	ENST00000370630.5	-	1	192	c.144C>T	c.(142-144)ctC>ctT	p.L48L	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	48					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		TCGGGCGGCAGAGCTCAGGCT	0.687													G|||	1373	0.274161	0.2595	0.2464	5008	,	,		8005	0.2302		0.2475	False		,,,				2504	0.3865															0			1						G		1086,3252		157,772,1240	8	8	8		144	3	1	1	dbSNP_100	8	2129,6387		294,1541,2423	no	coding-synonymous	CTBS	NM_004388.2		451,2313,3663	AA,AG,GG		25.0,25.0346,25.0117		48/386	85039955	3215,9639	2169	4258	6427	84812543	SO:0001819	synonymous_variant	1486			M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.144C>T	1.37:g.85039955G>A			84812543	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																				0.687	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		A	85039955	G	A	85039955	2	1	99	1	0	0	0	0	0	0	0	1	4005	929	33	3		3	CTBS	1	85039955	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	8834174	85039955	164210666	4	26480										
CDC7	8317	hgsc.bcm.edu	37	chr1	91977399	91977399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tatgcttaatctgttcaaagCtttgaaacgcattcatcagt	6	8	4	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:91977399C>T	ENST00000428239.1	+	6	750	c.491C>T	c.(490-492)gCt>gTt	p.A164V	CDC7_ENST00000234626.6_Missense_Mutation_p.A164V|CDC7_ENST00000430031.2_Missense_Mutation_p.A136V	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	164	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		CTGTTCAAAGCTTTGAAACGC	0.328																																																0			1											92	90	91					1																	91977399		2203	4298	6501	91749987	SO:0001583	missense	8317			AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.491C>T	1.37:g.91977399C>T	ENSP00000393139:p.Ala164Val		91749987	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	37	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	36	5.630607	0.96682	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.12672	2.66;2.66;2.66	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37544	0.1007	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.97110	1.0;0.988	T	0.27157	-1.0082	10	0.87932	D	0	-8.5828	20.0114	0.97452	0.0:1.0:0.0:0.0	.	136;164	B7Z5H7;O00311	.;CDC7_HUMAN	V	136;164;164	ENSP00000407477:A136V;ENSP00000234626:A164V;ENSP00000393139:A164V	ENSP00000234626:A164V	A	+	2	0	CDC7	91749987	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.629000	0.83207	2.732000	0.93576	0.591000	0.81541	GCT		0.328	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		T	91977399	C	T	91977399	3	4	99	1	0	0	0	0	1	0	0	0	3090	797	28	3	509	3	CDC7	1	91977399	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	6937444	91977399	157273222	5	26481										
ABCA4	24	hgsc.bcm.edu	37	chr1	94512603	94512603	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atctttaccagattcttcacGcataccccaggaacccaccc	4	17	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:94512603G>A	ENST00000370225.3	-	19	2876	c.2790C>T	c.(2788-2790)tgC>tgT	p.C930C	ABCA4_ENST00000535735.1_Silent_p.C856C	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	930	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GATTCTTCACGCATACCCCAG	0.493																																																0			1											134	146	142					1																	94512603		2203	4300	6503	94285191	SO:0001819	synonymous_variant	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2790C>T	1.37:g.94512603G>A			94285191	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.493	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94512603	G	A	94512603	2	1	99	1	0	0	0	0	0	0	0	1	34	1079	38	1		1	ABCA4	1	94512603	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	2535204	94512603	154738018	6	26482										
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957411	111957411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggggacagtcaccttttcaCgggccacagccttccttcta	9	14	3	0	rs150120731	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:111957411C>T	ENST00000369732.3	-	11	1767	c.1712G>A	c.(1711-1713)cGt>cAt	p.R571H		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	571					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		CACCTTTTCACGGGCCACAGC	0.527													C|||	2	0.000399361	0	0.0014	5008	,	,		19331	0		0.001	False		,,,				2504	0															0			1						C	HIS/ARG	0,4406		0,0,2203	105	112	110		1712	-4.8	0	1	dbSNP_134	110	7,8593	5.7+/-21.5	0,7,4293	yes	missense	OVGP1	NM_002557.3	29	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	benign	571/679	111957411	7,12999	2203	4300	6503	111758934	SO:0001583	missense	5016			U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1712G>A	1.37:g.111957411C>T	ENSP00000358747:p.Arg571His		111758934	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.790	1.177629	0.21787	0.0	8.14E-4	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04275	3.66	4.08	-4.84	0.03151	.	8.718220	0.00357	N	0.000029	T	0.00580	0.0019	N	0.14661	0.345	0.19575	N	0.999964	P;B	0.46277	0.875;0.001	B;B	0.25759	0.063;0.001	T	0.45381	-0.9265	10	0.59425	D	0.04	0.035	0.2829	0.00247	0.3045:0.1398:0.2832:0.2726	.	571;635	Q12889;Q59HH5	OVGP1_HUMAN;.	H	571;635;379	ENSP00000358747:R571H	ENSP00000358743:R635H	R	-	2	0	OVGP1	111758934	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.400000	0.07241	-1.061000	0.03185	-1.696000	0.00724	CGT		0.527	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		T	111957411	C	T	111957411	3	4	99	1	0	0	0	0	1	0	0	0	11356	536	19	1	328	1	OVGP1	1	111957411	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	17444808	111957411	137293210	7	26483										
SLC16A1	6566	hgsc.bcm.edu	37	chr1	113460434	113460434	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gccttggttggcttgggcccGattggtcgcatgagggctcc	16	11	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:113460434G>A	ENST00000538576.1	-	4	1425	c.594C>T	c.(592-594)atC>atT	p.I198I	SLC16A1_ENST00000369626.3_Silent_p.I198I|SLC16A1_ENST00000433570.4_Silent_p.I198I	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	198					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	GCTTGGGCCCGATTGGTCGCA	0.463																																																0			1											89	87	88					1																	113460434		2203	4300	6503	113261957	SO:0001819	synonymous_variant	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.594C>T	1.37:g.113460434G>A			113261957	Q49A45|Q5T8R6|Q9NSJ9	Silent	SNP	ENST00000538576.1	37	CCDS858.1																																																																																				0.463	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		A	113460434	G	A	113460434	2	1	99	1	0	0	0	0	0	0	0	1	14439	1048	37	1		1	SLC16A1	1	113460434	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	1503023	113460434	135790187	8	26484										
AMPD1	270	hgsc.bcm.edu	37	chr1	115216605	115216605	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttctgaaggaaatccaaaaaAggatttttggcatactctag	8	6	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:115216605A>G	ENST00000520113.2	-	14	2013	c.1998T>C	c.(1996-1998)ccT>ccC	p.P666P	AMPD1_ENST00000353928.6_Silent_p.P633P|AMPD1_ENST00000369538.3_Silent_p.P662P			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	666			P -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	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)	AATCCAAAAAAGGATTTTTGG	0.408																																																0			1											94	95	95					1																	115216605		2203	4300	6503	115018128	SO:0001819	synonymous_variant	270			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1998T>C	1.37:g.115216605A>G			115018128	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Silent	SNP	ENST00000520113.2	37	CCDS876.2																																																																																				0.408	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			G	115216605	A	G	115216605	2	3	99	1	0	0	0	0	0	0	0	1	585	59	3	4		4	AMPD1	1	115216605	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1756171	115216605	134034016	9	26485										
SLC22A15	55356	hgsc.bcm.edu	37	chr1	116562223	116562223	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tggtttttaattgccaacagAtcctacaaagtcagtgcagc	8	9	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:116562223A>C	ENST00000369503.4	+	3	451	c.321A>C	c.(319-321)agA>agC	p.R107S	SLC22A15_ENST00000369502.1_Missense_Mutation_p.R107S|RP11-159M11.2_ENST00000453128.1_RNA	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	107					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGCCAACAGATCCTACAAAG	0.363																																																0			1											151	127	135					1																	116562223		1831	4087	5918	116363746	SO:0001583	missense	55356			AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.321A>C	1.37:g.116562223A>C	ENSP00000358515:p.Arg107Ser		116363746	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	37	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.719101	0.30503	.	.	ENSG00000163393	ENST00000369503;ENST00000369502	T;T	0.70749	-0.51;-0.51	5.26	1.56	0.23342	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.171366	0.56097	D	0.000037	T	0.31827	0.0809	N	0.25245	0.725	0.34526	D	0.708655	B;B	0.23650	0.039;0.089	B;B	0.27380	0.079;0.029	T	0.04320	-1.0960	10	0.14252	T	0.57	.	9.0626	0.36444	0.6897:0.0:0.3103:0.0	.	107;107	Q8IZD6;Q8IZD6-2	S22AF_HUMAN;.	S	107	ENSP00000358515:R107S;ENSP00000358514:R107S	ENSP00000358514:R107S	R	+	3	2	SLC22A15	116363746	0.980000	0.34600	1.000000	0.80357	0.954000	0.61252	0.223000	0.17719	0.431000	0.26258	0.533000	0.62120	AGA		0.363	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		C	116562223	A	C	116562223	3	2	99	1	0	0	0	0	1	0	0	0	14483	330	12	4	331	4	SLC22A15	1	116562223	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1345618	116562223	132688398	10	26486										
CGN	57530	hgsc.bcm.edu	37	chr1	151502427	151502427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggcaacagtgctggggcagCggcgggccgcagtggagacg	20	10	0	1	rs34834099	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:151502427C>T	ENST00000271636.7	+	12	2282	c.2149C>T	c.(2149-2151)Cgg>Tgg	p.R717W	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	711	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGGGGCAGCGGCGGGCCGC	0.652													C|||	78	0.0155751	8e-04	0.0231	5008	,	,		18157	0		0.0537	False		,,,				2504	0.0072															0			1						C	TRP/ARG	51,4353		0,51,2151	28	35	32		2149	3.2	1	1	dbSNP_126	32	536,8062		19,498,3782	yes	missense	CGN	NM_020770.2	101	19,549,5933	TT,TC,CC		6.234,1.158,4.5147	probably-damaging	717/1204	151502427	587,12415	2202	4299	6501	149769051	SO:0001583	missense	57530			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2149C>T	1.37:g.151502427C>T	ENSP00000271636:p.Arg717Trp		149769051	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	54	0.024725274725274724	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	46	0.06068601583113457	C	15.44	2.834621	0.50951	0.01158	0.06234	ENSG00000143375	ENST00000271636	T	0.66280	-0.2	5.27	3.25	0.37280	.	0.472495	0.21879	N	0.067773	T	0.59810	0.2221	M	0.63428	1.95	0.33704	P	0.385058	D	0.89917	1.0	D	0.70016	0.967	T	0.64002	-0.6509	9	0.87932	D	0	-10.0013	3.549	0.07839	0.1774:0.561:0.1711:0.0904	rs34834099	711	Q9P2M7	CING_HUMAN	W	717	ENSP00000271636:R717W	ENSP00000271636:R717W	R	+	1	2	CGN	149769051	0.893000	0.30496	0.984000	0.44739	0.362000	0.29581	0.142000	0.16096	1.184000	0.42957	-0.309000	0.09137	CGG		0.652	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151502427	C	T	151502427	3	4	99	1	0	0	0	0	1	0	0	0	3309	759	27	1	2191	1	CGN	1	151502427	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	34940204	151502427	97748194	11	26487										
DCST1	149095	hgsc.bcm.edu	37	chr1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgaaggtcgggggagactccAtgctagcccggcttcttcga	14	11	1	2	rs11264300	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:155019710A>C	ENST00000295542.1	+	14	1630	c.1534A>C	c.(1534-1536)Atg>Ctg	p.M512L	DCST1_ENST00000368419.2_Missense_Mutation_p.M512L|DCST1_ENST00000423025.2_Missense_Mutation_p.M487L|RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000392480.1_Missense_Mutation_p.M512L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	512			M -> L (in dbSNP:rs11264300). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGGAGACTCCATGCTAGCCCG	0.532													A|||	2777	0.554513	0.3858	0.5865	5008	,	,		18637	0.8849		0.3569	False		,,,				2504	0.6227															0			1						A	LEU/MET,LEU/MET	1798,2608	527.6+/-372.2	350,1098,755	88	86	87		1459,1534	3.7	1	1	dbSNP_120	87	2984,5616	462.0+/-365.6	524,1936,1840	yes	missense,missense	DCST1	NM_001143687.2,NM_152494.3	15,15	874,3034,2595	CC,CA,AA		34.6977,40.808,36.7676	benign,benign	487/682,512/707	155019710	4782,8224	2203	4300	6503	153286334	SO:0001583	missense	149095			AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1534A>C	1.37:g.155019710A>C	ENSP00000295542:p.Met512Leu		153286334	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	1163	0.5325091575091575	179	0.3638211382113821	193	0.5331491712707183	517	0.9038461538461539	274	0.36147757255936674	A	11.83	1.756878	0.31137	0.40808	0.346977	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	4.88	3.73	0.42828	Dendritic cell-specific transmembrane protein-like (1);	0.190127	0.51477	N	0.000086	T	0.06416	0.0165	L	0.31420	0.93	0.36215	P	0.148416	B;B	0.16166	0.016;0.016	B;B	0.18561	0.022;0.022	T	0.24048	-1.0171	9	0.06494	T	0.89	-31.4022	8.753	0.34629	0.8085:0.1915:0.0:0.0	rs11264300;rs52800761;rs60521342;rs11264300	487;512	E9PHV3;Q5T197	.;DCST1_HUMAN	L	512;512;487;512	ENSP00000295542:M512L;ENSP00000376271:M512L;ENSP00000387369:M487L;ENSP00000357404:M512L	ENSP00000295542:M512L	M	+	1	0	DCST1	153286334	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	3.293000	0.51779	0.960000	0.38005	0.533000	0.62120	ATG		0.532	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		C	155019710	A	C	155019710	3	2	99	1	0	0	0	0	1	0	0	0	4308	217	8	4	1584	4	DCST1	1	155019710	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	3517283	155019710	94230911	12	26488										
OR6N1	128372	hgsc.bcm.edu	37	chr1	158735892	158735892	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	caaaatctactaggacatttAtagacgtatcagtgcaagcc	7	9	2	1	rs857827	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:158735892A>G	ENST00000335094.2	-	1	600	c.581T>C	c.(580-582)aTa>aCa	p.I194T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	194			I -> T (in dbSNP:rs857827). {ECO:0000269|PubMed:12213199}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					TAGGACATTTATAGACGTATC	0.473													A|||	3345	0.667931	0.7784	0.7839	5008	,	,		20865	0.6171		0.7217	False		,,,				2504	0.4335															0			1						A	THR/ILE	3436,970	731.3+/-410.3	1329,778,96	105	111	109		581	3.7	0.8	1	dbSNP_86	109	6162,2438	697.1+/-404.9	2217,1728,355	yes	missense	OR6N1	NM_001005185.1	89	3546,2506,451	GG,GA,AA		28.3488,22.0154,26.2033	benign	194/313	158735892	9598,3408	2203	4300	6503	157002516	SO:0001583	missense	128372			BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"GPCR / Class A : Olfactory receptors"	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.581T>C	1.37:g.158735892A>G	ENSP00000335535:p.Ile194Thr		157002516	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	1561	0.7147435897435898	376	0.7642276422764228	286	0.7900552486187845	344	0.6013986013986014	555	0.7321899736147758	A	4.870	0.161768	0.09287	0.779846	0.716512	ENSG00000197403	ENST00000335094	T	0.00183	8.6	4.78	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.459103	0.18288	N	0.145796	T	0.00039	0.0001	L	0.27944	0.81	0.50632	P	1.1300000000002974E-4	B	0.06786	0.001	B	0.06405	0.002	T	0.13818	-1.0495	9	0.30078	T	0.28	-8.2149	4.054	0.09808	0.6369:0.1797:0.1834:0.0	rs857827;rs17698061;rs61135327;rs857827	194	Q8NGY5	OR6N1_HUMAN	T	194	ENSP00000335535:I194T	ENSP00000335535:I194T	I	-	2	0	OR6N1	157002516	0.000000	0.05858	0.805000	0.32314	0.908000	0.53690	0.391000	0.20784	0.836000	0.34901	0.533000	0.62120	ATA		0.473	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		G	158735892	A	G	158735892	3	3	99	1	0	0	0	0	1	0	0	0	11237	449	16	4	360	4	OR6N1	1	158735892	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	3716182	158735892	90514729	13	26489										
DPT	1805	hgsc.bcm.edu	37	chr1	168698173	168698173	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggttccccgaggctctgtggCgtgggcatgcaggcgtagtt	17	10	1	0	rs1052591	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:168698173C>T	ENST00000367817.3	-	1	329	c.240G>A	c.(238-240)acG>acA	p.T80T		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	80	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					GGCTCTGTGGCGTGGGCATGC	0.612													c|||	1590	0.317492	0.2519	0.3141	5008	,	,		21034	0.1637		0.5129	False		,,,				2504	0.3661															0			1						T		1438,2968	467.2+/-354.7	253,932,1018	158	126	137		240	-10	0.4	1	dbSNP_86	137	4658,3942	603.9+/-394.7	1281,2096,923	no	coding-synonymous	DPT	NM_001937.4		1534,3028,1941	TT,TC,CC		45.8372,32.6373,46.8707		80/202	168698173	6096,6910	2203	4300	6503	166964797	SO:0001819	synonymous_variant	1805			BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.240G>A	1.37:g.168698173C>T			166964797	A8K981|Q8N4R2|Q9UIX8	Silent	SNP	ENST00000367817.3	37	CCDS1275.1																																																																																				0.612	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937		T	168698173	C	T	168698173	2	4	99	1	0	0	0	0	0	0	0	1	4750	755	27	1		1	DPT	1	168698173	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	9962281	168698173	80552448	14	26490										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200972808	200972808	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgtcctggttcactaccaccTtgttcttgatgttgcgggcc	10	12	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:200972808T>C	ENST00000422435.2	-	8	1434	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	KIF21B_ENST00000360529.5_Missense_Mutation_p.K373R|KIF21B_ENST00000461742.2_Missense_Mutation_p.K373R|KIF21B_ENST00000332129.2_Missense_Mutation_p.K373R	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	373					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CACTACCACCTTGTTCTTGAT	0.542																																																0			1											193	148	163					1																	200972808		2203	4300	6503	199239431	SO:0001583	missense	23046			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1118A>G	1.37:g.200972808T>C	ENSP00000411831:p.Lys373Arg		199239431	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	t	16.77	3.215667	0.58452	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.19	5.19	0.71726	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.52573	1.65	0.52501	D	0.999952	D;D;B;D	0.56746	0.961;0.961;0.006;0.977	P;P;B;P	0.51974	0.489;0.489;0.005;0.686	T	0.73132	-0.4079	10	0.52906	T	0.07	.	9.5798	0.39481	0.0:0.0786:0.0:0.9214	.	373;373;373;373	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	R	373	ENSP00000328494:K373R;ENSP00000353724:K373R;ENSP00000433808:K373R;ENSP00000411831:K373R	ENSP00000328494:K373R	K	-	2	0	KIF21B	199239431	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.128000	0.64733	1.959000	0.56917	0.524000	0.50904	AAG		0.542	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200972808	T	C	200972808	3	2	99	1	0	0	0	0	1	0	0	0	8310	1609	56	4	3864	4	KIF21B	1	200972808	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	32274635	200972808	48277813	15	26491										
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213068595	213068595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cacagaccaagaaccaaaaaCggttatgttgtccaagcagt	8	10	0	2	rs3207090	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:213068595C>T	ENST00000366971.4	+	10	1829	c.1631C>T	c.(1630-1632)aCg>aTg	p.T544M	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	544			T -> M (in dbSNP:rs3207090). {ECO:0000269|PubMed:15489334}.		blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		GAACCAAAAACGGTTATGTTG	0.383													C|||	1900	0.379393	0.1316	0.2781	5008	,	,		18284	0.4583		0.5	False		,,,				2504	0.5808				Esophageal Squamous(199;2235 2952 19233 26256)											0			1						C	MET/THR	920,3486	351.6+/-311.3	102,716,1385	116	108	111		1631	-2.6	0	1	dbSNP_105	111	4086,4514	560.3+/-387.6	986,2114,1200	yes	missense	FLVCR1	NM_014053.3	81	1088,2830,2585	TT,TC,CC		47.5116,20.8806,38.4899	possibly-damaging	544/556	213068595	5006,8000	2203	4300	6503	211135218	SO:0001583	missense	28982			AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.1631C>T	1.37:g.213068595C>T	ENSP00000355938:p.Thr544Met		211135218	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	37	CCDS1510.1	848|848	0.3882783882783883|0.3882783882783883	85|85	0.17276422764227642|0.17276422764227642	120|120	0.3314917127071823|0.3314917127071823	273|273	0.4772727272727273|0.4772727272727273	370|370	0.48812664907651715|0.48812664907651715	C|C	5.834|5.834	0.338073|0.338073	0.11013|0.11013	0.208806|0.208806	0.475116|0.475116	ENSG00000162769|ENSG00000162769	ENST00000419102|ENST00000366971	.|D	.|0.82619	.|-1.63	4.88|4.88	-2.58|-2.58	0.06228|0.06228	.|.	.|1.686840	.|0.03088	.|N	.|0.159422	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.45634	.|0.863	.|B	.|0.35240	.|0.198	T|T	0.26883|0.26883	-1.0090|-1.0090	4|9	.|0.59425	.|D	.|0.04	-16.4378|-16.4378	3.3478|3.3478	0.07141|0.07141	0.3494:0.2632:0.0:0.3874|0.3494:0.2632:0.0:0.3874	rs3207090;rs17857350;rs52790363;rs60120981;rs3207090|rs3207090;rs17857350;rs52790363;rs60120981;rs3207090	.|544	.|Q9Y5Y0	.|FLVC1_HUMAN	W|M	343|544	.|ENSP00000355938:T544M	.|ENSP00000355938:T544M	R|T	+|+	1|2	2|0	FLVCR1|FLVCR1	211135218|211135218	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	-0.358000|-0.358000	0.07641|0.07641	-0.118000|-0.118000	0.11851|0.11851	-0.274000|-0.274000	0.10170|0.10170	CGG|ACG		0.383	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053		T	213068595	C	T	213068595	3	4	99	1	0	0	0	0	1	0	0	0	5964	536	19	1	1669	1	FLVCR1	1	213068595	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	12095787	213068595	36182026	16	26492										
AGT	183	hgsc.bcm.edu	37	chr1	230845794	230845794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgctgtccacactggctcccAtcagggagcagccagtcttc	10	15	2	0	rs699	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:230845794A>G	ENST00000366667.4	-	2	1017	c.803T>C	c.(802-804)aTg>aCg	p.M268T	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	268			M -> I (in dbSNP:rs11568053).|M -> T (associated with essential hypertension and pre-eclampsia; dbSNP:rs699). {ECO:0000269|PubMed:1394429, ECO:0000269|PubMed:8513325}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACTGGCTCCCATCAGGGAGCA	0.547													G|||	3531	0.705072	0.9032	0.6354	5008	,	,		18819	0.8532		0.4115	False		,,,				2504	0.636															0			1	GRCh37	CM920010	AGT	M	rs699	G	THR/MET	3643,763	308.8+/-290.8	1504,635,64	82	91	88	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	803	-0.4	0	1	dbSNP_36	88	3662,4938	620.8+/-397.1	801,2060,1439	yes	missense	AGT	NM_000029.3	81	2305,2695,1503	GG,GA,AA		42.5814,17.3173,43.8336	benign	268/486	230845794	7305,5701	2203	4300	6503	228912417	SO:0001583	missense	189			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.803T>C	1.37:g.230845794A>G	ENSP00000355627:p.Met268Thr		228912417	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	1446	0.6620879120879121	427	0.8678861788617886	230	0.6353591160220995	479	0.8374125874125874	310	0.40897097625329815	G	0.001	-2.932260	0.00053	0.826827	0.425814	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.86694	-2.16	5.1	-0.372	0.12520	Serpin domain (3);	0.941754	0.08896	N	0.877893	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32481	-0.9905	9	0.10636	T	0.68	.	5.2545	0.15540	0.2662:0.0:0.5073:0.2265	rs699;rs4714;rs3182295;rs17856353;rs61617185;rs699	268;268;268	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	T	268;186	ENSP00000355627:M268T	ENSP00000355627:M268T	M	-	2	0	AGT	228912417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.431000	0.21444	-0.242000	0.09667	-0.733000	0.03571	ATG		0.547	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		G	230845794	A	G	230845794	3	3	99	1	0	0	0	0	1	0	0	0	399	217	8	4	670	4	AGT	1	230845794	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	17777199	230845794	18404827	17	26493										
RYR2	6262	hgsc.bcm.edu	37	chr1	237811895	237811895	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tttctgccagatctccgggcGgctgcttctttagatacggt	11	11	3	2	rs533068485	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:237811895G>A	ENST00000366574.2	+	49	7811	c.7494G>A	c.(7492-7494)gcG>gcA	p.A2498A	RYR2_ENST00000542537.1_Silent_p.A2482A|RYR2_ENST00000360064.6_Silent_p.A2496A	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2498	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATCTCCGGGCGGCTGCTTCTT	0.463													g|||	2	0.000399361	0	0.0014	5008	,	,		17635	0		0.001	False		,,,				2504	0															0			1											65	60	61					1																	237811895		1900	4115	6015	235878518	SO:0001819	synonymous_variant	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7494G>A	1.37:g.237811895G>A			235878518	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237811895	G	A	237811895	2	1	99	1	0	0	0	0	0	0	0	1	13806	1103	39	1		1	RYR2	1	237811895	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	6966101	237811895	11438726	18	26494										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247014368	247014368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctttttgggacttttggtcaCtagttacggcagatggcaaa	11	7	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr1:247014368C>T	ENST00000391829.2	-	33	5063	c.4940G>A	c.(4939-4941)aGt>aAt	p.S1647N	AHCTF1_ENST00000366508.1_Missense_Mutation_p.S1682N|AHCTF1_ENST00000326225.3_Missense_Mutation_p.S1656N|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1647	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	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)			CTTTTGGTCACTAGTTACGGC	0.358																																					Colon(145;197 1800 4745 15099 26333)											0			1											118	116	116					1																	247014368		2203	4300	6503	245080991	SO:0001583	missense	25909				CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4940G>A	1.37:g.247014368C>T	ENSP00000375705:p.Ser1647Asn		245080991	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	C	7.793	0.711961	0.15306	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.34859	1.34;1.35;1.35	6.17	2.87	0.33458	.	0.338343	0.32918	N	0.005491	T	0.26810	0.0656	L	0.52364	1.645	0.21020	N	0.9998	P;B;B	0.39759	0.687;0.047;0.028	B;B;B	0.34779	0.189;0.032;0.014	T	0.10451	-1.0629	10	0.22109	T	0.4	-5.0371	9.6216	0.39725	0.0:0.7363:0.1205:0.1432	.	508;1682;1647	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	N	1682;1656;1647	ENSP00000355464:S1682N;ENSP00000355465:S1656N;ENSP00000375705:S1647N	ENSP00000355465:S1656N	S	-	2	0	AHCTF1	245080991	0.944000	0.32072	0.416000	0.26546	0.429000	0.31625	0.906000	0.28517	0.921000	0.36994	0.655000	0.94253	AGT		0.358	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247014368	C	T	247014368	3	4	99	1	0	0	0	0	1	0	0	0	408	565	20	3	1876	3	AHCTF1	1	247014368	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	9202473	247014368	2236253	19	26495										
SDC1	6382	hgsc.bcm.edu	37	chr2	20403740	20403740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggccaggctgcatgtccctgTgggggtgggaggtggcgggc	22	9	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:20403740T>C	ENST00000254351.4	-	3	705	c.461A>G	c.(460-462)cAc>cGc	p.H154R	SDC1_ENST00000381150.1_Missense_Mutation_p.H154R|SDC1_ENST00000403076.1_Missense_Mutation_p.H154R|SDC1_ENST00000482879.1_Intron	NM_002997.4	NP_002988	P18827	SDC1_HUMAN	syndecan 1	154					canonical Wnt signaling pathway (GO:0060070)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|myoblast development (GO:0048627)|odontogenesis (GO:0042476)|phototransduction, visible light (GO:0007603)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to toxic substance (GO:0009636)|retinoid metabolic process (GO:0001523)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|striated muscle cell development (GO:0055002)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2)	21	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		CATGTCCCTGTGGGGGTGGGA	0.667																																																0			2											88	88	88					2																	20403740		2203	4300	6503	20267221	SO:0001583	missense	6382			AJ551176	CCDS1697.1	2p24.1	2008-02-05			ENSG00000115884	ENSG00000115884		"CD molecules", "Proteoglycans / Cell Surface : Syndecans"	10658	protein-coding gene	gene with protein product	"syndecan proteoglycan 1"	186355		SDC			Standard	XM_005262621		Approved	CD138, syndecan, SYND1	uc002rdo.1	P18827	OTTHUMG00000090751	ENST00000254351.4:c.461A>G	2.37:g.20403740T>C	ENSP00000254351:p.His154Arg		20267221	D6W523|Q53QV0|Q546D3|Q96HB7	Missense_Mutation	SNP	ENST00000254351.4	37	CCDS1697.1	.	.	.	.	.	.	.	.	.	.	T	8.919	0.960494	0.18583	.	.	ENSG00000115884	ENST00000254351;ENST00000381150;ENST00000403076;ENST00000429035	T;T;T;T	0.34667	2.35;2.35;1.35;1.47	3.87	-1.85	0.07784	.	0.476710	0.19395	N	0.115308	T	0.41811	0.1175	M	0.73962	2.25	0.18873	N	0.999983	D;P	0.53462	0.96;0.918	P;P	0.51777	0.679;0.604	T	0.34900	-0.9810	10	0.87932	D	0	-8.6825	5.9793	0.19399	0.1553:0.0:0.4401:0.4046	.	154;154	E9PHH3;P18827	.;SDC1_HUMAN	R	154;154;154;162	ENSP00000254351:H154R;ENSP00000370542:H154R;ENSP00000384613:H154R;ENSP00000400773:H162R	ENSP00000254351:H154R	H	-	2	0	SDC1	20267221	0.924000	0.31332	0.230000	0.23976	0.083000	0.17756	0.438000	0.21559	-0.293000	0.08986	0.459000	0.35465	CAC		0.667	SDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207495.1	NM_001006946		C	20403740	T	C	20403740	3	2	99	1	0	0	0	0	1	0	0	0	13988	1696	59	4	483	4	SDC1	2	20403740	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10		20403740	222795633	20	26496										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27481175	27481175	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggctgtgtgccagatacccgCctgccagggtgaaatgatgg	15	10	0	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:27481175C>T	ENST00000233535.4	-	3	630	c.278G>A	c.(277-279)gGc>gAc	p.G93D	SLC30A3_ENST00000447008.2_Splice_Site_p.G88D	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	93					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGATACCCGCCTGCCAGGGT	0.507																																																0			2											32	34	33					2																	27481175		2203	4300	6503	27334679	SO:0001630	splice_region_variant	7781			U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.278-1G>A	2.37:g.27481175C>T			27334679	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	37	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998502	0.93227	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000432351;ENST00000426924;ENST00000424577;ENST00000450118;ENST00000426569	T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86715	0.5999	H	0.97465	4.01	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.81914	0.993;0.995	D	0.90954	0.4807	10	0.87932	D	0	.	17.2848	0.87138	0.0:1.0:0.0:0.0	.	88;93	F5H3B7;Q99726	.;ZNT3_HUMAN	D	93;88;44;80;71;44;44	ENSP00000233535:G93D;ENSP00000415226:G88D;ENSP00000414320:G44D;ENSP00000393545:G80D;ENSP00000403959:G71D;ENSP00000403912:G44D;ENSP00000392673:G44D	ENSP00000233535:G93D	G	-	2	0	SLC30A3	27334679	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.746000	0.85057	2.768000	0.95171	0.561000	0.74099	GGC		0.507	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2		Missense_Mutation	T	27481175	C	T	27481175	5	4	99	1	0	0	0	0	0	0	1	0	14593	753	26	3	912	3	SLC30A3	2	27481175	Splice_Site	SNP	C	TCGA-DC-6681-01A-11D-1826-10	7077435	27481175	215718198	21	26497										
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27565858	27565858	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcttaggcatgggggtggacAgagggttggattgatctaag	17	4	2	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:27565858A>C	ENST00000359541.2	-	3	833	c.404T>G	c.(403-405)cTg>cGg	p.L135R	AC109828.1_ENST00000587586.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000588707.1_RNA|GTF3C2_ENST00000264720.3_Missense_Mutation_p.L135R|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	135					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGGTGGACAGAGGGTTGGA	0.527																																																0			2											103	98	100					2																	27565858		2203	4300	6503	27419362	SO:0001583	missense	2976			D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.404T>G	2.37:g.27565858A>C	ENSP00000352536:p.Leu135Arg		27419362	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	37	CCDS1749.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.437576	0.62955	.	.	ENSG00000115207	ENST00000359541;ENST00000264720	T;T	0.74526	-0.85;-0.85	5.31	4.15	0.48705	.	0.195444	0.34025	N	0.004339	T	0.68044	0.2958	N	0.19112	0.55	0.34624	D	0.718937	D;P;D	0.61080	0.989;0.93;0.98	P;P;P	0.61201	0.885;0.462;0.804	T	0.68891	-0.5289	10	0.17369	T	0.5	-9.4886	6.3761	0.21509	0.89:0.0:0.11:0.0	.	135;135;135	Q8WUA4-2;Q8WUA4;Q53QN0	.;TF3C2_HUMAN;.	R	135	ENSP00000352536:L135R;ENSP00000264720:L135R	ENSP00000264720:L135R	L	-	2	0	GTF3C2	27419362	0.951000	0.32395	0.929000	0.37066	0.986000	0.74619	2.039000	0.41193	2.231000	0.72958	0.460000	0.39030	CTG		0.527	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			C	27565858	A	C	27565858	3	2	99	1	0	0	0	0	1	0	0	0	6894	188	7	4	2399	4	GTF3C2	2	27565858	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	84683	27565858	215633515	22	26498										
FSHR	2492	hgsc.bcm.edu	37	chr2	49381418	49381418	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tactcacagttcaatggcatTcctcgggaggtcagaaggaa	11	9	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:49381418T>C	ENST00000406846.2	-	1	258	c.139A>G	c.(139-141)Aat>Gat	p.N47D	FSHR_ENST00000346173.3_Missense_Mutation_p.N47D|FSHR_ENST00000304421.4_Missense_Mutation_p.N47D	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	47					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)	p.N47Y(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		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)|Suramin(DB04786)|Urofollitropin(DB00094)	TCAATGGCATTCCTCGGGAGG	0.468									Gonadal Dysgenesis, 46 XX																																							1	Substitution - Missense(1)	ovary(1)	2											69	69	69					2																	49381418		2203	4300	6503	49234922	SO:0001583	missense	2492	Familial Cancer Database			CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.139A>G	2.37:g.49381418T>C	ENSP00000384708:p.Asn47Asp		49234922	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	T	8.426	0.847606	0.17034	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000454032	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	5.46	4.31	0.51392	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75642	0.3877	L	0.39020	1.185	0.80722	D	1	B;B;B	0.13594	0.008;0.001;0.001	B;B;B	0.11329	0.006;0.006;0.002	T	0.66626	-0.5876	9	.	.	.	.	8.0138	0.30368	0.0:0.0895:0.0:0.9105	.	47;47;47	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	D	47	ENSP00000384708:N47D;ENSP00000333908:N47D;ENSP00000306780:N47D;ENSP00000415504:N47D	.	N	-	1	0	FSHR	49234922	1.000000	0.71417	0.989000	0.46669	0.288000	0.27193	2.765000	0.47621	1.092000	0.41356	0.533000	0.62120	AAT		0.468	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			C	49381418	T	C	49381418	3	2	99	1	0	0	0	0	1	0	0	0	6092	1783	62	4	1988	4	FSHR	2	49381418	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	21815560	49381418	193817955	23	26499										
ATP6V1B1	525	hgsc.bcm.edu	37	chr2	71163089	71163089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agctggggactgctccatggCcatggagatagacagcaggc	15	10	0	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:71163089C>T	ENST00000234396.4	+	1	78	c.5C>T	c.(4-6)gCc>gTc	p.A2V	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.A2V	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	2					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						TGCTCCATGGCCATGGAGATA	0.632																																																0			2											34	37	36					2																	71163089		2203	4300	6503	71016597	SO:0001583	missense	525			AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"ATPases / V-type"	853	protein-coding gene	gene with protein product	"Renal tubular acidosis with deafness"	192132	"vacuolar proton pump 3"	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.5C>T	2.37:g.71163089C>T	ENSP00000234396:p.Ala2Val		71016597	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300374	0.40694	.	.	ENSG00000116039	ENST00000234396;ENST00000412314	D;D	0.83075	-1.68;-1.68	4.9	4.9	0.64082	.	0.000000	0.39475	N	0.001355	T	0.79639	0.4480	N	0.14661	0.345	0.36812	D	0.885936	D;D	0.58268	0.982;0.982	P;P	0.53649	0.731;0.731	D	0.84951	0.0871	10	0.54805	T	0.06	-16.0861	15.5933	0.76558	0.0:1.0:0.0:0.0	.	2;2	C9JL73;P15313	.;VATB1_HUMAN	V	2	ENSP00000234396:A2V;ENSP00000388353:A2V	ENSP00000234396:A2V	A	+	2	0	ATP6V1B1	71016597	0.988000	0.35896	0.944000	0.38274	0.202000	0.24057	2.804000	0.47931	2.261000	0.74972	0.591000	0.81541	GCC		0.632	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692		T	71163089	C	T	71163089	3	4	99	1	0	0	0	0	1	0	0	0	1179	739	26	3	7	3	ATP6V1B1	2	71163089	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	21781671	71163089	172036284	24	26500										
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71365676	71365676	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttagaaaaaaagccgtggcaGcttcagggggaagtgacagc	14	7	1	2	rs357756	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:71365676G>A	ENST00000244230.2	+	5	1507	c.1155G>A	c.(1153-1155)caG>caA	p.Q385Q	MPHOSPH10_ENST00000498451.2_Silent_p.Q385Q	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	385					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						AGCCGTGGCAGCTTCAGGGGG	0.413													G|||	1532	0.305911	0.261	0.3934	5008	,	,		14422	0.2639		0.2942	False		,,,				2504	0.3599															0			2						G		1101,3305	393.3+/-328.8	137,827,1239	35	38	37		1155	-0.1	1	2	dbSNP_79	37	2544,6056	411.3+/-350.5	395,1754,2151	no	coding-synonymous	MPHOSPH10	NM_005791.2		532,2581,3390	AA,AG,GG		29.5814,24.9887,28.0255		385/682	71365676	3645,9361	2203	4300	6503	71219184	SO:0001819	synonymous_variant	10199			X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1155G>A	2.37:g.71365676G>A			71219184	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																				0.413	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		A	71365676	G	A	71365676	2	1	99	1	0	0	0	0	0	0	0	1	9755	962	34	3		3	MPHOSPH10	2	71365676	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	202587	71365676	171833697	25	26501										
PTCD3	55037	hgsc.bcm.edu	37	chr2	86333384	86333384	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atcaaagatggcggttgtatCtgctgttcgctggctgggcc	14	9	2	1	rs537889886		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:86333384C>G	ENST00000254630.7	+	1	80	c.14C>G	c.(13-15)tCt>tGt	p.S5C	PTCD3_ENST00000409277.3_Missense_Mutation_p.S5C|PTCD3_ENST00000465560.1_3'UTR|POLR1A_ENST00000263857.6_5'Flank|POLR1A_ENST00000409681.1_5'Flank	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	5					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						GCGGTTGTATCTGCTGTTCGC	0.632																																																0			2											50	52	52					2																	86333384		2203	4300	6503	86186895	SO:0001583	missense	55037				CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.14C>G	2.37:g.86333384C>G	ENSP00000254630:p.Ser5Cys		86186895	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.356157	0.41700	.	.	ENSG00000132300	ENST00000254630;ENST00000409783;ENST00000409277	T;T;T	0.52526	1.47;0.71;0.66	5.22	1.0	0.19881	.	0.797892	0.11833	N	0.525071	T	0.19805	0.0476	N	0.02539	-0.55	0.09310	N	1	B	0.28512	0.214	B	0.28305	0.088	T	0.17501	-1.0367	10	0.72032	D	0.01	2.592	3.7476	0.08554	0.1589:0.4446:0.3088:0.0877	.	5	Q96EY7	PTCD3_HUMAN	C	5	ENSP00000254630:S5C;ENSP00000386922:S5C;ENSP00000386462:S5C	ENSP00000254630:S5C	S	+	2	0	PTCD3	86186895	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.517000	0.02248	0.272000	0.22027	0.557000	0.71058	TCT		0.632	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		G	86333384	C	G	86333384	3	3	99	1	0	0	0	0	1	0	0	0	12763	913	32	5	16	5	PTCD3	2	86333384	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	14967708	86333384	156865989	26	26502										
UBR3	130507	hgsc.bcm.edu	37	chr2	170684455	170684455	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ccctgcatgtcgctgtgcgcCgagtgcttccaccagggcga	13	15	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:170684455C>T	ENST00000272793.5	+	1	488	c.438C>T	c.(436-438)gcC>gcT	p.A146A	UBR3_ENST00000418381.1_Silent_p.A146A			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	146					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CGCTGTGCGCCGAGTGCTTCC	0.692																																																0			2											10	10	10					2																	170684455		686	1587	2273	170392701	SO:0001819	synonymous_variant	130507			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.438C>T	2.37:g.170684455C>T			170392701	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																					0.692	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		T	170684455	C	T	170684455	2	4	99	1	0	0	0	0	0	0	0	1	16943	639	23	1		1	UBR3	2	170684455	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	84351071	170684455	72514918	27	26503										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171240249	171240249	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctttatcatggggtgaaacgCgcctccaatcccccccacat	7	16	1	1	rs11675394	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:171240249C>T	ENST00000408978.4	+	12	1358	c.1215C>T	c.(1213-1215)cgC>cgT	p.R405R	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.R414R|MYO3B_ENST00000409044.3_Silent_p.R405R	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	405	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.S397_A406del(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GGGTGAAACGCGCCTCCAATC	0.453													C|||	1079	0.215455	0.0303	0.2493	5008	,	,		20601	0.2887		0.325	False		,,,				2504	0.2536															1	Deletion - In frame(1)	ovary(1)	2						C	,,	327,3487		13,301,1593	120	112	114		1215,1215,1215	-2.5	1	2	dbSNP_120	114	2679,5543		437,1805,1869	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	450,2106,3462	TT,TC,CC		32.5833,8.5737,24.9751	,,	405/1315,405/1276,405/1342	171240249	3006,9030	1907	4111	6018	170948495	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1215C>T	2.37:g.171240249C>T			170948495	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																				0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171240249	C	T	171240249	2	4	99	1	0	0	0	0	0	0	0	1	10107	755	27	1		1	MYO3B	2	171240249	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	555794	171240249	71959124	28	26504										
STK36	27148	hgsc.bcm.edu	37	chr2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggatgctgacctccttatagGtgtcttggccgacctcaggg	13	11	2	1	rs1863704	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:219562675G>A	ENST00000295709.3	+	25	3287	c.3008G>A	c.(3007-3009)gGt>gAt	p.G1003D	STK36_ENST00000392105.3_Missense_Mutation_p.G982D|STK36_ENST00000440309.1_Missense_Mutation_p.G1003D|STK36_ENST00000392106.2_Missense_Mutation_p.G982D	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CTCCTTATAGGTGTCTTGGCC	0.557													G|||	950	0.189696	0.0212	0.3285	5008	,	,		21184	0.0556		0.3757	False		,,,				2504	0.2658															0			2						G	ASP/GLY	336,4070	178.7+/-207.4	11,314,1878	149	131	137		3008	2	0	2	dbSNP_92	137	3284,5316	492.8+/-373.4	656,1972,1672	yes	missense	STK36	NM_015690.4	94	667,2286,3550	AA,AG,GG		38.186,7.626,27.8333	possibly-damaging	1003/1316	219562675	3620,9386	2203	4300	6503	219270919	SO:0001583	missense	27148			AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3008G>A	2.37:g.219562675G>A	ENSP00000295709:p.Gly1003Asp		219270919		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	454|454	0.2078754578754579|0.2078754578754579	23|23	0.046747967479674794|0.046747967479674794	112|112	0.30939226519337015|0.30939226519337015	36|36	0.06293706293706294|0.06293706293706294	283|283	0.3733509234828496|0.3733509234828496	G|G	0.208|0.208	-1.039006|-1.039006	0.02013|0.02013	0.07626|0.07626	0.38186|0.38186	ENSG00000163482|ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309|ENST00000431040	T;T;T;T|.	0.69561|.	-0.4;-0.4;-0.41;-0.4|.	5.82|5.82	2.01|2.01	0.26516|0.26516	.|.	0.790460|.	0.11084|.	N|.	0.601535|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	B;P;B|.	0.39424|.	0.001;0.673;0.179|.	B;B;B|.	0.36464|.	0.001;0.225;0.077|.	T|T	0.47699|0.47699	-0.9097|-0.9097	9|4	0.32370|.	T|.	0.25|.	-0.0347|-0.0347	6.8511|6.8511	0.24014|0.24014	0.3342:0.0:0.5491:0.1167|0.3342:0.0:0.5491:0.1167	rs1863704;rs56519430;rs57906514;rs1863704|rs1863704;rs56519430;rs57906514;rs1863704	982;982;1003|.	A8MU99;Q9NRP7-2;Q9NRP7|.	.;.;STK36_HUMAN|.	D|M	1003;982;982;1003|196	ENSP00000295709:G1003D;ENSP00000375955:G982D;ENSP00000375954:G982D;ENSP00000394095:G1003D|.	ENSP00000295709:G1003D|.	G|V	+|+	2|1	0|0	STK36|STK36	219270919|219270919	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.823000|0.823000	0.27366|0.27366	0.122000|0.122000	0.18314|0.18314	-0.797000|-0.797000	0.03246|0.03246	GGT|GTG		0.557	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			A	219562675	G	A	219562675	3	1	99	1	0	0	0	0	1	0	0	0	15341	1261	44	3	3102	3	STK36	2	219562675	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	48322426	219562675	23636698	29	26505										
RHBDD1	84236	hgsc.bcm.edu	37	chr2	227778996	227778996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agaagcacccaggaactatgAcacgtacacagcaggactga	10	11	0	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr2:227778996A>G	ENST00000341329.3	+	6	1027	c.785A>G	c.(784-786)gAc>gGc	p.D262G	RHBDD1_ENST00000493526.1_3'UTR|RHBDD1_ENST00000392062.2_Missense_Mutation_p.D262G|RHBDD1_ENST00000409053.1_Missense_Mutation_p.D96G	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	262					apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.D262G(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		AGGAACTATGACACGTACACA	0.488																																																1	Substitution - Missense(1)	ovary(1)	2											123	119	121					2																	227778996		2203	4300	6503	227487240	SO:0001583	missense	84236			AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.785A>G	2.37:g.227778996A>G	ENSP00000344779:p.Asp262Gly		227487240	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Missense_Mutation	SNP	ENST00000341329.3	37	CCDS2464.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662232	0.29515	.	.	ENSG00000144468	ENST00000341329;ENST00000392062;ENST00000409053	T;T	0.45668	0.89;0.89	6.06	4.9	0.64082	.	0.326994	0.34676	N	0.003766	T	0.43366	0.1244	L	0.56769	1.78	0.23314	N	0.997922	P;B	0.51351	0.944;0.009	P;B	0.47075	0.536;0.005	T	0.31251	-0.9950	10	0.27082	T	0.32	-11.713	10.4493	0.44513	0.8366:0.1634:0.0:0.0	.	53;262	Q8TEB9-2;Q8TEB9	.;RHBD1_HUMAN	G	262;262;96	ENSP00000344779:D262G;ENSP00000375914:D262G	ENSP00000344779:D262G	D	+	2	0	RHBDD1	227487240	0.761000	0.28439	0.194000	0.23346	0.426000	0.31534	2.084000	0.41625	1.087000	0.41251	0.528000	0.53228	GAC		0.488	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			G	227778996	A	G	227778996	3	3	99	1	0	0	0	0	1	0	0	0	13353	275	10	4	803	4	RHBDD1	2	227778996	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	8216321	227778996	15420377	30	26506										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4704848	4704848	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtcttctccaagcccaacagAgaacggcagaaactgatgag	10	11	2	4			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:4704848A>G	ENST00000443694.2	+	13	1467	c.1467A>G	c.(1465-1467)agA>agG	p.R489R	ITPR1_ENST00000354582.6_Silent_p.R504R|ITPR1_ENST00000456211.2_Silent_p.R489R|ITPR1_ENST00000423119.2_Silent_p.R504R|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Silent_p.R504R|ITPR1_ENST00000302640.8_Silent_p.R489R			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	504					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGCCCAACAGAGAACGGCAGA	0.443																																																0			3											118	120	119					3																	4704848		1985	4181	6166	4679848	SO:0001819	synonymous_variant	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1467A>G	3.37:g.4704848A>G			4679848	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																				0.443	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		G	4704848	A	G	4704848	2	3	99	1	0	0	0	0	0	0	0	1	7941	301	11	4		4	ITPR1	3	4704848	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10		4704848	193317582	31	26507										
VHL	7428	hgsc.bcm.edu	37	chr3	10188208	10188208	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtcccgataggtcacctttgGctcttcagagatgcagggac	12	11	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:10188208G>A	ENST00000256474.2	+	2	1191	c.351G>A	c.(349-351)tgG>tgA	p.W117*	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	117	Involved in binding to CCT complex.		W -> C (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.W117C(4)|p.W117*(2)|p.?(1)|p.W117fs*40(1)|p.W117fs*42(1)|p.W117fs*1(1)|p.H115fs*41(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTCACCTTTGGCTCTTCAGAG	0.512		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	11	Substitution - Missense(4)|Deletion - Frameshift(4)|Substitution - Nonsense(2)|Unknown(1)	kidney(10)|upper_aerodigestive_tract(1)	3	GRCh37	CM951286|HM971481	VHL	M							178	165	169					3																	10188208		2203	4300	6503	10163208	SO:0001587	stop_gained	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.351G>A	3.37:g.10188208G>A	ENSP00000256474:p.Trp117*		10163208	B2RE45|Q13599|Q6PDA9	Nonsense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	42	9.265052	0.99118	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	.	.	.	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0021	16.3181	0.82935	0.0:0.0:1.0:0.0	.	.	.	.	X	117;35	.	ENSP00000256474:W117X	W	+	3	0	VHL	10163208	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	7.278000	0.78587	2.530000	0.85305	0.563000	0.77884	TGG		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10188208	G	A	10188208	4	1	99	1	0	0	0	0	0	1	0	0	17202	1212	42	3	357	3	VHL	3	10188208	Nonsense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	5483360	10188208	187834222	32	26508										
OXNAD1	92106	hgsc.bcm.edu	37	chr3	16312564	16312564	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	acactcagcactttgcgccaCcttactctaaccaggtgagt	7	14	2	1	rs842259	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:16312564C>T	ENST00000285083.5	+	3	570	c.105C>T	c.(103-105)caC>caT	p.H35H	OXNAD1_ENST00000435829.2_Silent_p.H53H|OXNAD1_ENST00000544043.1_Silent_p.H53H|OXNAD1_ENST00000606098.1_Silent_p.H35H|OXNAD1_ENST00000605932.1_Silent_p.H35H	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	35						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						CTTTGCGCCACCTTACTCTAA	0.483													C|||	2107	0.420727	0.2617	0.4654	5008	,	,		17886	0.4752		0.4324	False		,,,				2504	0.5358															0			3						C		1361,3045	450.8+/-349.5	221,919,1063	157	146	150		105	3	0.5	3	dbSNP_86	150	3655,4945	526.1+/-380.9	787,2081,1432	no	coding-synonymous	OXNAD1	NM_138381.3		1008,3000,2495	TT,TC,CC		42.5,30.8897,38.5668		35/313	16312564	5016,7990	2203	4300	6503	16287568	SO:0001819	synonymous_variant	92106			AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.105C>T	3.37:g.16312564C>T			16287568	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																				0.483	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381		T	16312564	C	T	16312564	2	4	99	1	0	0	0	0	0	0	0	1	11364	506	18	3		3	OXNAD1	3	16312564	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	6124356	16312564	181709866	33	26509										
SETD2	29072	hgsc.bcm.edu	37	chr3	47098748	47098748	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agggttgctgggatccacatAggcctgcatgggataacctg	14	9	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:47098748A>G	ENST00000409792.3	-	15	6568	c.6526T>C	c.(6526-6528)Tat>Cat	p.Y2176H		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2176	Low charge region.|Pro-rich.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GGATCCACATAGGCCTGCATG	0.537			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0			3											151	134	140					3																	47098748		2203	4300	6503	47073752	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6526T>C	3.37:g.47098748A>G	ENSP00000386759:p.Tyr2176His		47073752	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363142	0.82353	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.48836	0.8	5.25	5.25	0.73442	.	0.000000	0.53938	D	0.000057	T	0.53997	0.1831	L	0.40543	1.245	0.39312	D	0.965098	D;D	0.57257	0.979;0.979	P;P	0.55222	0.771;0.771	T	0.58885	-0.7557	10	0.62326	D	0.03	.	15.6116	0.76727	1.0:0.0:0.0:0.0	.	2176;2176	F2Z317;Q9BYW2	.;SETD2_HUMAN	H	2176	ENSP00000386759:Y2176H	ENSP00000386759:Y2176H	Y	-	1	0	SETD2	47073752	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	8.632000	0.90995	2.333000	0.79357	0.533000	0.62120	TAT		0.537	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47098748	A	G	47098748	3	3	99	1	0	0	0	0	1	0	0	0	14168	420	15	4	1196	4	SETD2	3	47098748	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	30786184	47098748	150923682	34	26510										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51246252	51246252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gatccacgagaacatcatccGaaagtccagtgccaagtact	8	12	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:51246252G>A	ENST00000266037.9	+	13	1108	c.1085G>A	c.(1084-1086)cGa>cAa	p.R362Q		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	362					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AACATCATCCGAAAGTCCAGT	0.458																																																0			3											98	103	101					3																	51246252		2039	4207	6246	51221292	SO:0001583	missense	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1085G>A	3.37:g.51246252G>A	ENSP00000266037:p.Arg362Gln		51221292	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	35	5.569967	0.96540	.	.	ENSG00000088538	ENST00000266037	T	0.04862	3.54	5.72	5.72	0.89469	.	0.096640	0.64402	D	0.000003	T	0.24586	0.0596	M	0.74881	2.28	0.58432	D	0.999995	D	0.76494	0.999	P	0.61874	0.895	T	0.00028	-1.2296	10	0.51188	T	0.08	.	19.0394	0.92992	0.0:0.0:1.0:0.0	.	362	Q8IZD9	DOCK3_HUMAN	Q	362	ENSP00000266037:R362Q	ENSP00000266037:R362Q	R	+	2	0	DOCK3	51221292	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.125000	0.94402	2.878000	0.98634	0.650000	0.86243	CGA		0.458	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51246252	G	A	51246252	3	1	99	1	0	0	0	0	1	0	0	0	4699	1058	37	1	1135	1	DOCK3	3	51246252	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	4147504	51246252	146776178	35	26511										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52643685	52643685	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaagactccggctcattgtaTgtacaggcattattaaacat	7	8	1	1	rs3755806	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:52643685T>C	ENST00000296302.7	-	16	2212	c.2211A>G	c.(2209-2211)acA>acG	p.T737T	PBRM1_ENST00000409767.1_Silent_p.T752T|PBRM1_ENST00000410007.1_Silent_p.T737T|PBRM1_ENST00000356770.4_Silent_p.T705T|PBRM1_ENST00000337303.4_Silent_p.T737T|PBRM1_ENST00000409114.3_Silent_p.T752T|PBRM1_ENST00000394830.3_Silent_p.T737T|PBRM1_ENST00000409057.1_Silent_p.T737T			Q86U86	PB1_HUMAN	polybromo 1	737	Bromo 5. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A735fs*7(2)|p.A703fs*7(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GCTCATTGTATGTACAGGCAT	0.423			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"								T|||	1615	0.322484	0.1483	0.4611	5008	,	,		22548	0.4276		0.4215	False		,,,				2504	0.2495						Rec	yes		3	3p21	55193	polybromo 1		E	3	Deletion - Frameshift(3)	kidney(3)	3						T	,,	771,3635	314.4+/-293.6	64,643,1496	141	135	137		2115,2211,2211	-2.2	1	3	dbSNP_107	137	3516,5084	512.1+/-377.9	737,2042,1521	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	801,2685,3017	CC,CT,TT		40.8837,17.4989,32.9617	,,	705/1603,737/1583,737/1583	52643685	4287,8719	2203	4300	6503	52618725	SO:0001819	synonymous_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2211A>G	3.37:g.52643685T>C			52618725	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																					0.423	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		C	52643685	T	C	52643685	2	2	99	1	0	0	0	0	0	0	0	1	11522	1451	51	4		4	PBRM1	3	52643685	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	1397433	52643685	145378745	36	26512										
ATXN7	6314	hgsc.bcm.edu	37	chr3	63982082	63982082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggttgccaaagtgccagccGtgaacaatgtccacatgaaa	10	10	0	2	rs3774729	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:63982082G>A	ENST00000295900.6	+	12	3134	c.2584G>A	c.(2584-2586)Gtg>Atg	p.V862M	ATXN7_ENST00000538065.1_Missense_Mutation_p.V862M|ATXN7_ENST00000487717.1_Missense_Mutation_p.V862M|ATXN7_ENST00000398590.3_Missense_Mutation_p.V862M|ATXN7_ENST00000484332.1_Missense_Mutation_p.V717M	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	862			V -> M (in dbSNP:rs3774729). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9425224}.		cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		AGTGCCAGCCGTGAACAATGT	0.507													A|||	2192	0.4377	0.6354	0.3429	5008	,	,		18405	0.4603		0.334	False		,,,				2504	0.3211															0			3						A	MET/VAL,MET/VAL,MET/VAL	2374,1882		676,1022,430	65	69	68		2584,2149,2584	-1.6	1	3	dbSNP_107	68	2612,5894		406,1800,2047	yes	missense,missense,missense	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	21,21,21	1082,2822,2477	AA,AG,GG		30.7077,44.2199,39.0691	benign,benign,benign	862/893,717/748,862/946	63982082	4986,7776	2128	4253	6381	63957122	SO:0001583	missense	6314			AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2584G>A	3.37:g.63982082G>A	ENSP00000295900:p.Val862Met		63957122	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	954	0.4368131868131868	288	0.5853658536585366	128	0.35359116022099446	284	0.4965034965034965	254	0.33509234828496043	A	1.225	-0.625811	0.03610	0.557801	0.307077	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332;ENST00000522345	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.07	-1.61	0.08399	.	0.335977	0.36893	N	0.002341	T	0.00012	0.0000	N	0.04746	-0.17	0.46798	P	7.989999999999942E-4	B;B;B	0.18461	0.006;0.028;0.005	B;B;B	0.08055	0.003;0.003;0.001	T	0.41342	-0.9514	9	0.02654	T	1	0.1485	9.2895	0.37778	0.2927:0.1299:0.5775:0.0	rs3774729;rs57082092;rs3774729	717;862;862	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	M	862;862;862;862;717;33	ENSP00000381590:V862M;ENSP00000295900:V862M;ENSP00000420234:V862M;ENSP00000439585:V862M;ENSP00000428277:V717M;ENSP00000428067:V33M	ENSP00000295900:V862M	V	+	1	0	ATXN7	63957122	0.000000	0.05858	0.983000	0.44433	0.990000	0.78478	-0.265000	0.08644	-0.467000	0.06932	-0.260000	0.10688	GTG		0.507	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		A	63982082	G	A	63982082	3	1	99	1	0	0	0	0	1	0	0	0	1216	1145	40	1	2690	1	ATXN7	3	63982082	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	11338397	63982082	134040348	37	26513										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64139008	64139008	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtgtttcatgtgccagtgtcGcccctcagcttctgtgcatt	10	12	3	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:64139008G>A	ENST00000295902.6	-	6	1222	c.637C>T	c.(637-639)Cga>Tga	p.R213*	PRICKLE2_ENST00000564377.1_Nonsense_Mutation_p.R269*	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	213	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		TGCCAGTGTCGCCCCTCAGCT	0.498																																																0			3											125	113	117					3																	64139008		2203	4300	6503	64114048	SO:0001587	stop_gained	166336			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.637C>T	3.37:g.64139008G>A	ENSP00000295902:p.Arg213*		64114048	Q0VF44	Nonsense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	G	41	9.070864	0.99055	.	.	ENSG00000163637	ENST00000295902	.	.	.	5.78	2.76	0.32466	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-36.5829	14.3734	0.66857	0.0:0.0:0.4938:0.5062	.	.	.	.	X	213	.	ENSP00000295902:R213X	R	-	1	2	PRICKLE2	64114048	0.993000	0.37304	0.997000	0.53966	0.593000	0.36681	2.279000	0.43435	0.856000	0.35383	-0.182000	0.12963	CGA		0.498	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64139008	G	A	64139008	4	1	99	1	0	0	0	0	0	1	0	0	12521	1095	38	1	1909	1	PRICKLE2	3	64139008	Nonsense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	156926	64139008	133883422	38	26514										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098806	133098806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgcagctcccatggcaacacCgacaccccgtgcagaggggc	12	16	0	1	rs34111099	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:133098806C>T	ENST00000321871.6	+	4	461	c.251C>T	c.(250-252)cCg>cTg	p.P84L	TMEM108_ENST00000515826.1_Missense_Mutation_p.P84L|TMEM108_ENST00000393130.3_Missense_Mutation_p.P84L|TMEM108_ENST00000508711.1_Intron	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	84	Pro-rich.		P -> L (in dbSNP:rs34111099). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12975309}.			integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ATGGCAACACCGACACCCCGT	0.627													c|||	145	0.0289537	0.0136	0.0173	5008	,	,		15503	0		0.0616	False		,,,				2504	0.0542															0			3							LEU/PRO,LEU/PRO	82,4324	68.7+/-106.4	2,78,2123	97	89	92		251,251	0.9	0	3	dbSNP_126	92	597,8003	157.7+/-211.4	23,551,3726	yes	missense,missense	TMEM108	NM_001136469.1,NM_023943.2	98,98	25,629,5849	TT,TC,CC		6.9419,1.8611,5.2207	benign,benign	84/576,84/576	133098806	679,12327	2203	4300	6503	134581496	SO:0001583	missense	66000			AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.251C>T	3.37:g.133098806C>T	ENSP00000324651:p.Pro84Leu		134581496	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	61	0.027930402930402932	12	0.024390243902439025	4	0.011049723756906077	0	0.0	45	0.059366754617414245	c	2.305	-0.359279	0.05138	0.018611	0.069419	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000514894;ENST00000512662;ENST00000512137;ENST00000515826;ENST00000510183	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	2.76	0.893	0.19236	.	0.467395	0.15982	N	0.235273	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B;B	0.29862	0.259;0.007	B;B	0.20384	0.029;0.004	T	0.08269	-1.0730	10	0.52906	T	0.07	0.0198	3.2014	0.06651	0.2607:0.5932:0.0:0.1461	rs34111099	84;84	E9PB58;Q6UXF1	.;TM108_HUMAN	L	84;84;35;35;84;84;84	ENSP00000324651:P84L;ENSP00000376838:P84L;ENSP00000422072:P35L;ENSP00000427447:P35L;ENSP00000426301:P84L;ENSP00000423338:P84L;ENSP00000421486:P84L	ENSP00000324651:P84L	P	+	2	0	TMEM108	134581496	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.106000	0.15354	0.219000	0.20840	0.457000	0.33378	CCG		0.627	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133098806	C	T	133098806	3	4	99	1	0	0	0	0	1	0	0	0	16063	652	23	1	257	1	TMEM108	3	133098806	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	68959798	133098806	64923624	39	26515										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670642	134670642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggattatggagcctgtatgTctcttctttctgtccgtgtc	10	9	3	0	rs373971290		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:134670642T>C	ENST00000398015.3	+	3	923	c.553T>C	c.(553-555)Tct>Cct	p.S185P	EPHB1_ENST00000488154.1_Intron	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	185	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.			S -> I (in Ref. 2; AAD02030/AAD02031/ AAB94627/AAB94628). {ECO:0000305}.	angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						AGCCTGTATGTCTCTTCTTTC	0.463																																																0			3											253	241	245					3																	134670642		1922	4136	6058	136153332	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.553T>C	3.37:g.134670642T>C	ENSP00000381097:p.Ser185Pro		136153332	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344404	0.82022	.	.	ENSG00000154928	ENST00000398015	T	0.04406	3.63	5.49	5.49	0.81192	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	M	0.86097	2.795	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.01725	-1.1287	9	.	.	.	.	15.6027	0.76636	0.0:0.0:0.0:1.0	.	185	P54762	EPHB1_HUMAN	P	185	ENSP00000381097:S185P	.	S	+	1	0	EPHB1	136153332	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.085000	0.62840	0.533000	0.62120	TCT		0.463	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		C	134670642	T	C	134670642	3	2	99	1	0	0	0	0	1	0	0	0	5187	1667	58	4	563	4	EPHB1	3	134670642	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	1571836	134670642	63351788	40	26516										
DGKG	1608	hgsc.bcm.edu	37	chr3	185990096	185990096	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgacacaaccaggaatgtttCtggacacacagcgttcgtgg	11	10	1	1	rs2193587	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:185990096C>T	ENST00000265022.3	-	11	1486	c.947G>A	c.(946-948)aGa>aAa	p.R316K	DGKG_ENST00000344484.4_Missense_Mutation_p.R316K|DGKG_ENST00000544847.1_Missense_Mutation_p.R316K|DGKG_ENST00000382164.4_Missense_Mutation_p.R316K	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	316			R -> K (in dbSNP:rs2193587). {ECO:0000269|PubMed:10071200, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8034597}.		blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	AGGAATGTTTCTGGACACACA	0.473													T|||	4051	0.808906	0.9191	0.8357	5008	,	,		24915	0.744		0.8002	False		,,,				2504	0.7168															0			3						T	LYS/ARG,LYS/ARG,LYS/ARG	3951,455	215.8+/-234.7	1777,397,29	247	199	216		947,947,947	3.9	1	3	dbSNP_96	216	6775,1825	328.5+/-318.3	2666,1443,191	yes	missense,missense,missense	DGKG	NM_001080744.1,NM_001080745.1,NM_001346.2	26,26,26	4443,1840,220	TT,TC,CC		21.2209,10.3268,17.5304	benign,benign,benign	316/767,316/753,316/792	185990096	10726,2280	2203	4300	6503	187472790	SO:0001583	missense	1608			AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.947G>A	3.37:g.185990096C>T	ENSP00000265022:p.Arg316Lys		187472790	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	1785	0.8173076923076923	446	0.9065040650406504	292	0.8066298342541437	429	0.75	618	0.8153034300791556	T	5.951	0.359433	0.11239	0.896732	0.787791	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691;ENST00000437018	D;D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01;-3.01	5.08	3.92	0.45320	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.057438	0.64402	N	0.000002	T	0.00012	0.0000	N	0.01446	-0.86	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.002;0.002;0.003	T	0.43621	-0.9380	9	0.02654	T	1	.	8.2693	0.31833	0.0:0.1642:0.0:0.8358	rs2193587;rs2228940;rs59009759;rs2193587	316;316;316;316	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	K	316;316;316;316;319;67	ENSP00000265022:R316K;ENSP00000339777:R316K;ENSP00000371599:R316K;ENSP00000440507:R316K;ENSP00000395526:R67K	ENSP00000265022:R316K	R	-	2	0	DGKG	187472790	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	0.838000	0.27572	0.471000	0.27319	-1.044000	0.02363	AGA		0.473	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			T	185990096	C	T	185990096	3	4	99	1	0	0	0	0	1	0	0	0	4480	913	32	3	1488	3	DGKG	3	185990096	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	51319454	185990096	12032334	41	26517										
LEPREL1	55214	hgsc.bcm.edu	37	chr3	189689720	189689720	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcaggaggctccttccagcaTtcgttggcctctggatccaa	11	13	1	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr3:189689720T>C	ENST00000319332.5	-	12	1973	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	LEPREL1_ENST00000427335.2_Silent_p.E411E	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	592	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CCTTCCAGCATTCGTTGGCCT	0.448																																																0			3											89	78	82					3																	189689720		2203	4300	6503	191172414	SO:0001819	synonymous_variant	55214				CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.1776A>G	3.37:g.189689720T>C			191172414	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																				0.448	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192		C	189689720	T	C	189689720	2	2	99	1	0	0	0	0	0	0	0	1	8752	1490	52	4		4	LEPREL1	3	189689720	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	3699624	189689720	8332710	42	26518										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6037713	6037713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tctgcctgaggatctgcctgCgcaccttttccacagcagcc	9	16	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:6037713C>T	ENST00000409021.3	-	19	2746	c.2297G>A	c.(2296-2298)cGc>cAc	p.R766H	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R581H	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	129					cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GATCTGCCTGCGCACCTTTTC	0.692																																																0			4											14	18	17					4																	6037713		2048	3998	6046	6088614	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.2297G>A	4.37:g.6037713C>T	ENSP00000386711:p.Arg766His		6088614	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	37	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733960	0.89482	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000425341	T;T	0.37584	1.61;1.19	4.79	4.79	0.61399	.	0.135010	0.26045	U	0.026666	T	0.53642	0.1809	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.63113	0.911;0.855	T	0.56727	-0.7931	9	0.62326	D	0.03	.	10.477	0.44670	0.0:0.9111:0.0:0.0889	.	581;766	Q96N16-5;Q96N16-2	.;.	H	766;581;504	ENSP00000386711:R766H;ENSP00000387042:R581H	ENSP00000386711:R766H	R	-	2	0	JAKMIP1	6088614	1.000000	0.71417	0.970000	0.41538	0.994000	0.84299	7.299000	0.78831	2.219000	0.72066	0.436000	0.28706	CGC		0.692	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		T	6037713	C	T	6037713	3	4	99	1	0	0	0	0	1	0	0	0	7961	768	27	1	210	1	JAKMIP1	4	6037713	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		6037713	185116563	43	26519										
NAAA	27163	hgsc.bcm.edu	37	chr4	76836137	76836137	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	taccgtagtataaattgtgaAgctgaaaattatgaggaaat	9	3	0	3	rs6823734	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:76836137A>G	ENST00000286733.4	-	10	1101	c.1000T>C	c.(1000-1002)Ttc>Ctc	p.F334L	NAAA_ENST00000511606.1_Intron|NAAA_ENST00000399497.3_Intron	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	334			F -> L (in dbSNP:rs6823734).		lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						TAAATTGTGAAGCTGAAAATT	0.413													G|||	3728	0.744409	0.975	0.6974	5008	,	,		16888	0.5387		0.7127	False		,,,				2504	0.7106															0			4						G	,LEU/PHE	3413,251		1591,231,10	109	101	103		,1000	-8	0	4	dbSNP_116	103	5712,2468		2006,1700,384	yes	intron,missense-near-splice	NAAA	NM_001042402.1,NM_014435.3	,22	3597,1931,394	GG,GA,AA		30.1711,6.8504,22.9568	,benign	,334/360	76836137	9125,2719	1832	4090	5922	77055161	SO:0001630	splice_region_variant	27163			M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.999-1T>C	4.37:g.76836137A>G			77055161	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	37	CCDS43239.1	1561	0.7147435897435898	477	0.9695121951219512	263	0.7265193370165746	293	0.5122377622377622	528	0.6965699208443272	G	12.72	2.021135	0.35701	0.931496	0.698289	ENSG00000138744	ENST00000286733	T	0.61392	0.11	5.38	-7.99	0.01131	.	2.715070	0.00780	N	0.001268	T	0.00012	0.0000	N	0.00188	-1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	9	0.11485	T	0.65	0.9122	5.4366	0.16484	0.2787:0.0:0.2699:0.4514	rs6823734;rs52832600;rs58370479;rs6823734	334	Q02083	NAAA_HUMAN	L	334	ENSP00000286733:F334L	ENSP00000286733:F334L	F	-	1	0	NAAA	77055161	0.000000	0.05858	0.001000	0.08648	0.073000	0.16967	-1.111000	0.03303	-1.179000	0.02737	-1.088000	0.02184	TTC		0.413	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4		Missense_Mutation	G	76836137	A	G	76836137	5	3	99	1	0	0	0	0	0	0	1	0	10157	86	3	4	90	4	NAAA	4	76836137	Splice_Site	SNP	A	TCGA-DC-6681-01A-11D-1826-10	70798424	76836137	114318139	44	26520										
PDHA2	5161	hgsc.bcm.edu	37	chr4	96761377	96761377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcagagtgctggtggcatccCgtaactcctcaaatgacgct	11	12	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:96761377C>T	ENST00000295266.4	+	1	139	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	26					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.R26S(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		GGTGGCATCCCGTAACTCCTC	0.522																																																1	Substitution - Missense(1)	lung(1)	4											56	56	56					4																	96761377		2203	4300	6503	96980400	SO:0001583	missense	5161				CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.76C>T	4.37:g.96761377C>T	ENSP00000295266:p.Arg26Cys		96980400	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	37	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404644	0.42613	.	.	ENSG00000163114	ENST00000295266	D	0.97553	-4.43	4.52	-4.39	0.03611	.	0.242826	0.40728	N	0.001028	D	0.90662	0.7071	L	0.35644	1.08	0.20703	N	0.999864	B	0.09022	0.002	B	0.01281	0.0	T	0.80529	-0.1342	10	0.45353	T	0.12	-3.6194	2.1172	0.03716	0.1577:0.4105:0.1615:0.2703	.	26	P29803	ODPAT_HUMAN	C	26	ENSP00000295266:R26C	ENSP00000295266:R26C	R	+	1	0	PDHA2	96980400	0.000000	0.05858	0.000000	0.03702	0.625000	0.37756	-0.660000	0.05317	-0.535000	0.06307	-0.670000	0.03821	CGT		0.522	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			T	96761377	C	T	96761377	3	4	99	1	0	0	0	0	1	0	0	0	11696	652	23	1	78	1	PDHA2	4	96761377	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	19925240	96761377	94392899	45	26521										
CLGN	1047	hgsc.bcm.edu	37	chr4	141321660	141321660	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aatcttctccacatttatctGgtccaaacataatgatatag	4	9	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:141321660G>T	ENST00000325617.5	-	7	985	c.545C>A	c.(544-546)cCa>cAa	p.P182Q	CLGN_ENST00000414773.1_Missense_Mutation_p.P182Q|CLGN_ENST00000537281.1_Missense_Mutation_p.P182Q	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	182					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)	p.P182R(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					ACATTTATCTGGTCCAAACAT	0.333																																																1	Substitution - Missense(1)	ovary(1)	4											78	82	81					4																	141321660		2203	4298	6501	141541110	SO:0001583	missense	4312			D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.545C>A	4.37:g.141321660G>T	ENSP00000326699:p.Pro182Gln		141541110	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	37	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919186	0.92249	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.62498	0.02;0.02;0.02	5.36	5.36	0.76844	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Calreticulin/calnexin, conserved site (1);	0.047867	0.85682	D	0.000000	D	0.85230	0.5649	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88749	0.3249	10	0.87932	D	0	-12.8213	19.4559	0.94889	0.0:0.0:1.0:0.0	.	182	O14967	CLGN_HUMAN	Q	182;182;182;99	ENSP00000326699:P182Q;ENSP00000392782:P182Q;ENSP00000439381:P182Q	ENSP00000326699:P182Q	P	-	2	0	CLGN	141541110	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.669000	0.90835	0.591000	0.81541	CCA		0.333	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362		T	141321660	G	T	141321660	3	4	99	1	0	0	0	0	1	0	0	0	3530	1348	47	2	1323	2	CLGN	4	141321660	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	44560283	141321660	49832616	46	26522										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158254091	158254091	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gagactgtctggcaaacccaGcagtgccctggggacaaggt	14	11	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:158254091G>C	ENST00000264426.9	+	7	1282	c.1003G>C	c.(1003-1005)Gca>Cca	p.A335P	GRIA2_ENST00000449365.1_Missense_Mutation_p.A288P|GRIA2_ENST00000296526.7_Missense_Mutation_p.A335P|GRIA2_ENST00000393815.2_Missense_Mutation_p.A288P|GRIA2_ENST00000507898.1_Missense_Mutation_p.A288P	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	335					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGCAAACCCAGCAGTGCCCTG	0.458																																																0			4											58	64	62					4																	158254091		2203	4299	6502	158473541	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1003G>C	4.37:g.158254091G>C	ENSP00000264426:p.Ala335Pro		158473541	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107046	0.56291	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.14391	2.51;2.51;2.56;2.56;2.51	5.09	5.09	0.68999	Extracellular ligand-binding receptor (1);	0.054918	0.64402	D	0.000001	T	0.30634	0.0771	L	0.39245	1.2	0.80722	D	1	D;B;D	0.89917	0.999;0.111;1.0	D;B;D	0.83275	0.929;0.027;0.996	T	0.01488	-1.1342	10	0.45353	T	0.12	.	18.4737	0.90783	0.0:0.0:1.0:0.0	.	335;335;288	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	P	288;288;335;335;288	ENSP00000426845:A288P;ENSP00000377403:A288P;ENSP00000296526:A335P;ENSP00000264426:A335P;ENSP00000389837:A288P	ENSP00000264426:A335P	A	+	1	0	GRIA2	158473541	1.000000	0.71417	0.997000	0.53966	0.876000	0.50452	9.869000	0.99810	2.341000	0.79615	0.557000	0.71058	GCA		0.458	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158254091	G	C	158254091	3	2	99	1	0	0	0	0	1	0	0	0	6789	971	34	5	1029	5	GRIA2	4	158254091	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	16932431	158254091	32900185	47	26523										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170608810	170608810	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	taaacatttctaatttcagaTcaacagcaaaaagaaagaat	4	6	3	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:170608810T>C	ENST00000513761.1	+	4	879	c.320T>C	c.(319-321)aTc>aCc	p.I107T	CLCN3_ENST00000360642.3_Splice_Site_p.I107T|CLCN3_ENST00000504131.2_Splice_Site_p.I90T|CLCN3_ENST00000347613.4_Splice_Site_p.I107T	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	107					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		TAATTTCAGATCAACAGCAAA	0.353																																																0			4											97	92	94					4																	170608810		2203	4300	6503	170845385	SO:0001630	splice_region_variant	1182			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.319-1T>C	4.37:g.170608810T>C			170845385	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.680351	0.88542	.	.	ENSG00000109572	ENST00000511092;ENST00000513761;ENST00000347613;ENST00000360642;ENST00000512813;ENST00000538301;ENST00000504131;ENST00000507875	D;D;D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93	5.29	5.29	0.74685	Chloride channel, core (1);	0.000000	0.85682	D	0.000000	D	0.93693	0.7985	L	0.48260	1.515	0.80722	D	1	D;P;P;D;D	0.61080	0.981;0.95;0.95;0.981;0.989	P;P;P;P;P	0.61201	0.844;0.77;0.77;0.844;0.885	D	0.94436	0.7654	10	0.87932	D	0	-7.2237	15.2291	0.73372	0.0:0.0:0.0:1.0	.	107;90;80;107;107	B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.;.;.;CLCN3_HUMAN;.	T	107;107;107;107;107;107;90;80	ENSP00000425160:I107T;ENSP00000424603:I107T;ENSP00000261514:I107T;ENSP00000353857:I107T;ENSP00000425823:I107T;ENSP00000424540:I90T;ENSP00000425323:I80T	ENSP00000261514:I107T	I	+	2	0	CLCN3	170845385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	1.998000	0.58463	0.455000	0.32223	ATC		0.353	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		Missense_Mutation	C	170608810	T	C	170608810	5	2	99	1	0	0	0	0	0	0	1	0	3470	1449	50	4	330	4	CLCN3	4	170608810	Splice_Site	SNP	T	TCGA-DC-6681-01A-11D-1826-10	12354719	170608810	20545466	48	26524										
SNX25	83891	hgsc.bcm.edu	37	chr4	186267729	186267729	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaagtccagttgccttctctTagcaagctgcctttcaaatc	6	12	2	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr4:186267729T>C	ENST00000504273.1	+	13	2028	c.1734T>C	c.(1732-1734)ctT>ctC	p.L578L	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Silent_p.L578L			Q9H3E2	SNX25_HUMAN	sorting nexin 25	578	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TGCCTTCTCTTAGCAAGCTGC	0.308																																																0			4											61	64	63					4																	186267729		2203	4298	6501	186504723	SO:0001819	synonymous_variant	83891			AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1734T>C	4.37:g.186267729T>C			186504723	Q3ZT30|Q8N6K3	Silent	SNP	ENST00000504273.1	37	CCDS34116.1																																																																																				0.308	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		C	186267729	T	C	186267729	2	2	99	1	0	0	0	0	0	0	0	1	14933	1741	61	4		4	SNX25	4	186267729	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	15658919	186267729	4886547	49	26525										
ZDHHC11	79844	hgsc.bcm.edu	37	chr5	843723	843723	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcggccacgtaccttcatacCtggggtccgtgcggagcacc	13	15	1	0	rs3863148		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:843723C>A	ENST00000283441.8	-	4	1003	c.620G>T	c.(619-621)aGg>aTg	p.R207M	ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.R207M|ZDHHC11_ENST00000511539.1_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	207						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ACCTTCATACCTGGGGTCCGT	0.657																																																0			5											56	47	50					5																	843723		2201	4290	6491	896723	SO:0001583	missense	79844			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"Zinc fingers, DHHC-type"	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.620G>T	5.37:g.843723C>A	ENSP00000283441:p.Arg207Met		896723	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	601	0.2751831501831502	211	0.42886178861788615	83	0.2292817679558011	121	0.21153846153846154	186	0.24538258575197888	t	11.12	1.543781	0.27563	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.25085	1.82;1.82	3.98	-2.98	0.05513	.	16.107500	0.01230	U	0.008323	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B	0.06786	0.001	B	0.14023	0.01	T	0.44143	-0.9347	9	0.36615	T	0.2	0.0249	3.3426	0.07124	0.353:0.2826:0.0:0.3644	rs3863148;rs4993147	207	Q9H8X9	ZDH11_HUMAN	M	207	ENSP00000397719:R207M;ENSP00000283441:R207M	ENSP00000283441:R207M	R	-	2	0	ZDHHC11	896723	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.765000	0.04730	-1.644000	0.01517	-0.858000	0.03015	AGG		0.657	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786		A	843723	C	A	843723	3	1	99	1	0	0	0	0	1	0	0	0	17640	681	24	2	654	2	ZDHHC11	5	843723	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		843723	180071537	50	26526										
ZDHHC11	79844	hgsc.bcm.edu	37	chr5	843815	843815	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cagagcatgccagctgtggcCgaggccacagtgctgaagaa	14	11	0	3	rs71591190	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:843815C>T	ENST00000283441.8	-	4	911	c.528G>A	c.(526-528)tcG>tcA	p.S176S	ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Silent_p.S176S|ZDHHC11_ENST00000511539.1_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	176						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CAGCTGTGGCCGAGGCCACAG	0.667																																																0			5											27	22	23					5																	843815		2199	4276	6475	896815	SO:0001819	synonymous_variant	79844			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"Zinc fingers, DHHC-type"	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.528G>A	5.37:g.843815C>T			896815	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																				0.667	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786		T	843815	C	T	843815	2	4	99	1	0	0	0	0	0	0	0	1	17640	639	23	1		1	ZDHHC11	5	843815	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	92	843815	180071445	51	26527										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33588803	33588803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggtgctggcagtctgtgggCgggagagcctgctcgtcaga	18	9	2	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:33588803C>T	ENST00000504830.1	-	18	3101	c.2766G>A	c.(2764-2766)ccG>ccA	p.P922P	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Silent_p.P837P	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	922	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P922P(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AGTCTGTGGGCGGGAGAGCCT	0.632										HNSCC(64;0.19)																																						1	Substitution - coding silent(1)	lung(1)	5											127	126	126					5																	33588803		2203	4300	6503	33624560	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2766G>A	5.37:g.33588803C>T			33624560	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.632	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33588803	C	T	33588803	2	4	99	1	0	0	0	0	0	0	0	1	257	755	27	1		1	ADAMTS12	5	33588803	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	32744988	33588803	147326457	52	26528										
C6	729	hgsc.bcm.edu	37	chr5	41153985	41153985	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	catgtgtaccttgatggcccAgcaacaacaaagcctttggg	10	11	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:41153985A>G	ENST00000263413.3	-	15	2481	c.2217T>C	c.(2215-2217)gcT>gcC	p.A739A	C6_ENST00000337836.5_Silent_p.A739A	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	739	C5b-binding domain.|CCP 2.|Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TTGATGGCCCAGCAACAACAA	0.473																																																0			5											124	107	112					5																	41153985		2203	4300	6503	41189742	SO:0001819	synonymous_variant	5688			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2217T>C	5.37:g.41153985A>G			41189742		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																				0.473	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			G	41153985	A	G	41153985	2	3	99	1	0	0	0	0	0	0	0	1	2321	175	7	4		4	C6	5	41153985	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	7565182	41153985	139761275	53	26529										
ARRDC3	57561	hgsc.bcm.edu	37	chr5	90678754	90678754	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cagcgtactttcgcatgtccTcttgcatgaattttaagaga	8	9	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:90678754T>C	ENST00000265138.3	-	1	422	c.156A>G	c.(154-156)agA>agG	p.R52R	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	52					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		TCGCATGTCCTCTTGCATGAA	0.413																																																0			5											134	136	135					5																	90678754		2203	4300	6503	90714510	SO:0001819	synonymous_variant	57561			AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.156A>G	5.37:g.90678754T>C			90714510	A8K6T8|Q9P2H1	Silent	SNP	ENST00000265138.3	37	CCDS34202.1																																																																																				0.413	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		C	90678754	T	C	90678754	2	2	99	1	0	0	0	0	0	0	0	1	985	1548	54	4		4	ARRDC3	5	90678754	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	49524769	90678754	90236506	54	26530										
APC	324	hgsc.bcm.edu	37	chr5	112151204	112151204	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atttttagggttcaactacaCgaatggaccatgaaacagcc	8	9	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:112151204C>T	ENST00000457016.1	+	9	1227	c.847C>T	c.(847-849)Cga>Tga	p.R283*	APC_ENST00000257430.4_Nonsense_Mutation_p.R283*|APC_ENST00000508376.2_Nonsense_Mutation_p.R283*			P25054	APC_HUMAN	adenomatous polyposis coli	283	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R283*(11)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCAACTACACGAATGGACCA	0.383		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	11	Substitution - Nonsense(11)	large_intestine(11)	5	GRCh37	CM920030	APC	M							108	98	102					5																	112151204		2202	4300	6502	112179103	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.847C>T	5.37:g.112151204C>T	ENSP00000413133:p.Arg283*		112179103	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381748	0.98786	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	4.22	0.49857	.	0.134048	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.044	12.9775	0.58546	0.2942:0.7058:0.0:0.0	.	.	.	.	X	283;265;283;283;283	.	ENSP00000257430:R283X	R	+	1	2	APC	112179103	1.000000	0.71417	0.953000	0.39169	0.976000	0.68499	5.216000	0.65246	1.244000	0.43870	0.650000	0.86243	CGA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112151204	C	T	112151204	4	4	99	1	0	0	0	0	0	1	0	0	763	528	19	1	877	1	APC	5	112151204	Nonsense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	21472450	112151204	68764056	55	26531										
APC	324	hgsc.bcm.edu	37	chr5	112154723	112154723	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atgataaggatgatatgtcgCgaactttgctagctatgtct	10	6	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:112154723C>T	ENST00000457016.1	+	10	1374	c.994C>T	c.(994-996)Cga>Tga	p.R332*	APC_ENST00000257430.4_Nonsense_Mutation_p.R332*|APC_ENST00000508376.2_Nonsense_Mutation_p.R332*			P25054	APC_HUMAN	adenomatous polyposis coli	332	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R332*(5)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATATGTCGCGAACTTTGCT	0.418		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Substitution - Nonsense(5)	large_intestine(4)|endometrium(1)	5	GRCh37	CM980087	APC	M							193	168	176					5																	112154723		2202	4300	6502	112182622	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.994C>T	5.37:g.112154723C>T	ENSP00000413133:p.Arg332*		112182622	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.980865	0.97979	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	4.84	0.62591	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.226	13.9957	0.64397	0.3296:0.6704:0.0:0.0	.	.	.	.	X	332;314;332;332;332	.	ENSP00000257430:R332X	R	+	1	2	APC	112182622	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	4.029000	0.57253	1.388000	0.46506	0.650000	0.86243	CGA		0.418	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112154723	C	T	112154723	4	4	99	1	0	0	0	0	0	1	0	0	763	760	27	1	1028	1	APC	5	112154723	Nonsense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	3519	112154723	68760537	56	26532										
APC	324	hgsc.bcm.edu	37	chr5	112175951	112175952	+	Frame_Shift_Ins	INS	-	-	A													0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaaccaagagaaagaggcagINSaaaaaactattgattctgaa					rs587783031		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:112175951_112175952insA	ENST00000457016.1	+	16	5040_5041	c.4660_4661insA	c.(4660-4662)gaafs	p.E1554fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Ins_p.E1554fs|APC_ENST00000508376.2_Frame_Shift_Ins_p.E1554fs			P25054	APC_HUMAN	adenomatous polyposis coli	1554	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1556fs*3(42)|p.E1554fs*5(2)|p.E1554fs*3(1)|p.?(1)|p.T1556fs*9(1)|p.?fs(1)|p.K1192fs*3(1)|p.E1554*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAGAGGCAGAAAAAACTATT	0.342		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	50	Insertion - Frameshift(45)|Deletion - Frameshift(3)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(45)|stomach(3)|soft_tissue(1)|skin(1)	5																																								112203851	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4666dupA	5.37:g.112175957_112175957dupA	ENSP00000413133:p.Glu1554fs		112203850	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.342	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175952	-	A	112175951	7	5	99	1	0	1	1	0	0	0	0	0	763	943	33	0	4718	0	APC	5	112175951	Frame_Shift_Ins	INS	-	TCGA-DC-6681-01A-11D-1826-10	21228	112175951	68739309	57	26533										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115341638	115341638	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gttattcacagactgcagttGattgatgatgccttttcctt	8	8	1	4	rs10078759	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:115341638G>C	ENST00000357872.4	+	13	2191	c.2067G>C	c.(2065-2067)ttG>ttC	p.L689F	AQPEP_ENST00000395528.2_Missense_Mutation_p.L206F	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		689			L -> F (in dbSNP:rs10078759). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										GACTGCAGTTGATTGATGATG	0.348																																																0			5						G	PHE/LEU	3518,884	742.0+/-411.3	1401,716,84	167	153	157		2067	3	0.7	5	dbSNP_119	157	7104,1494	747.4+/-407.3	2942,1220,137	yes	missense	AQPEP	NM_173800.4	22	4343,1936,221	CC,CG,GG		17.3761,20.0818,18.2923	probably-damaging	689/991	115341638	10622,2378	2201	4299	6500	115369537	SO:0001583	missense	0																														ENST00000357872.4:c.2067G>C	5.37:g.115341638G>C	ENSP00000350541:p.Leu689Phe		115369537	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	1747	0.799908424908425	404	0.8211382113821138	292	0.8066298342541437	438	0.7657342657342657	613	0.8087071240105541	G	13.83	2.354623	0.41700	0.799182	0.826239	ENSG00000172901	ENST00000395528;ENST00000357872;ENST00000379578	T;T	0.08896	3.04;3.04	6.06	2.97	0.34412	.	0.377447	0.22608	N	0.057874	T	0.00012	0.0000	M	0.66506	2.035	0.58432	P	9.000000000036756E-6	B	0.33477	0.413	B	0.32583	0.148	T	0.02797	-1.1109	9	0.40728	T	0.16	.	7.8749	0.29589	0.3166:0.0:0.6834:0.0	rs10078759;rs52814426;rs56611672;rs57021800;rs10078759	689	Q6Q4G3	AMPQ_HUMAN	F	206;689;678	ENSP00000378899:L206F;ENSP00000350541:L689F	ENSP00000350541:L689F	L	+	3	2	AC010282.1	115369537	0.995000	0.38212	0.683000	0.30040	0.997000	0.91878	0.924000	0.28777	0.898000	0.36418	0.655000	0.94253	TTG		0.348	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			C	115341638	G	C	115341638	3	2	99	1	0	0	0	0	1	0	0	0	834	1281	45	5	2117	5	AQPEP	5	115341638	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	3165687	115341638	65573622	58	26534										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132939653	132939653	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tccgagcagtgtgagatgcaGccaaaagcctcctggtttca	11	11	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:132939653G>A	ENST00000265342.7	-	2	271	c.22C>T	c.(22-24)Ctg>Ttg	p.L8L		NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	8						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTGAGATGCAGCCAAAAGCCT	0.507																																																0			5											55	62	59					5																	132939653		2203	4300	6503	132967552	SO:0001819	synonymous_variant	23105			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.22C>T	5.37:g.132939653G>A			132967552	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																				0.507	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		A	132939653	G	A	132939653	2	1	99	1	0	0	0	0	0	0	0	1	6098	962	34	3		3	FSTL4	5	132939653	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	17598015	132939653	47975607	59	26535										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236950	140236950	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ccgctgtgggccacggccagCgtgtctgtggaggtggccga	18	12	1	0	rs251362	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:140236950C>G	ENST00000307360.5	+	1	1317	c.1317C>G	c.(1315-1317)agC>agG	p.S439R	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.S439R|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> R (in dbSNP:rs251362). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGGCCAGCGTGTCTGTGG	0.682													.|||	2354	0.470048	0.3245	0.4582	5008	,	,		17119	0.4355		0.5288	False		,,,				2504	0.6503															0			5						C	,ARG/SER,,,,,,,,,,,ARG/SER,ARG/SER	1439,2955		285,869,1043	97	93	94		,1317,,,,,,,,,,,1317,1317	3.1	1	5	dbSNP_79	94	4670,3874		1455,1760,1057	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,110,,,,,,,,,,,110,110	1740,2629,2100	GG,GC,CC		45.3418,32.7492,47.2175	,,,,,,,,,,,,,	,439/949,,,,,,,,,,,439/845,439/686	140236950	6109,6829	2197	4272	6469	140217134	SO:0001583	missense	56139			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1317C>G	5.37:g.140236950C>G	ENSP00000304234:p.Ser439Arg		140217134	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	1037	0.4748168498168498	183	0.3719512195121951	193	0.5331491712707183	261	0.4562937062937063	400	0.5277044854881267	C	10.30	1.312597	0.23908	0.327492	0.546582	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.51574	4.64;0.7	3.96	3.09	0.35607	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.41710	1.295	0.80722	P	0.0	B;B;B	0.28258	0.205;0.059;0.001	B;B;B	0.32090	0.14;0.128;0.024	T	0.45659	-0.9246	8	0.36615	T	0.2	.	1.6641	0.02798	0.1571:0.4772:0.1751:0.1907	rs251362;rs3733702;rs17844342;rs56831346	439;439;439	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	R	439	ENSP00000421030:S439R;ENSP00000304234:S439R	ENSP00000304234:S439R	S	+	3	2	PCDHA10	140217134	0.004000	0.15560	1.000000	0.80357	0.985000	0.73830	1.204000	0.32296	1.006000	0.39211	0.556000	0.70494	AGC		0.682	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		G	140236950	C	G	140236950	3	3	99	1	0	0	0	0	1	0	0	0	11551	767	27	5	1319	5	PCDHA10	5	140236950	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	7297297	140236950	40678310	60	26536										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140744090	140744090	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agctggcggagcgcggagtcCgcatcgtctccagaggtagg	17	11	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:140744090C>T	ENST00000518069.1	+	1	193	c.193C>T	c.(193-195)Cgc>Tgc	p.R65C	PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGGAGTCCGCATCGTCTC	0.652																																																0			5											51	62	58					5																	140744090		2201	4297	6498	140724274	SO:0001583	missense	56110			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.193C>T	5.37:g.140744090C>T	ENSP00000429834:p.Arg65Cys		140724274	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	15.25	2.778908	0.49891	.	.	ENSG00000253485	ENST00000518069	T	0.38887	1.11	5.38	5.38	0.77491	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.79678	0.4487	H	0.99800	4.79	0.40411	D	0.979741	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.87108	0.2183	9	0.87932	D	0	.	11.0653	0.47972	0.0:0.8812:0.0:0.1188	.	65;65	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	C	65	ENSP00000429834:R65C	ENSP00000429834:R65C	R	+	1	0	PCDHGA5	140724274	0.994000	0.37717	1.000000	0.80357	0.421000	0.31385	3.141000	0.50593	2.694000	0.91930	0.558000	0.71614	CGC		0.652	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140744090	C	T	140744090	3	4	99	1	0	0	0	0	1	0	0	0	11588	652	23	1	195	1	PCDHGA5	5	140744090	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	507140	140744090	40171170	61	26537										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154278135	154278135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atggcagccaactctgcagcCgttctaagtgatgccgcatc	10	13	2	1	rs148426811		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:154278135C>T	ENST00000285873.7	-	23	3285	c.3210G>A	c.(3208-3210)acG>acA	p.T1070T		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1070					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACTCTGCAGCCGTTCTAAGTG	0.498													C|||	1	0.000199681	0	0	5008	,	,		19316	0		0.001	False		,,,				2504	0															0			5						C		0,4406		0,0,2203	85	77	79		3210	-11.8	0.1	5	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GEMIN5	NM_015465.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1070/1509	154278135	1,13005	2203	4300	6503	154258328	SO:0001819	synonymous_variant	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.3210G>A	5.37:g.154278135C>T			154258328	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																				0.498	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			T	154278135	C	T	154278135	2	4	99	1	0	0	0	0	0	0	0	1	6351	639	23	1		1	GEMIN5	5	154278135	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	13534045	154278135	26637125	62	26538										
RNF145	153830	hgsc.bcm.edu	37	chr5	158588284	158588284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaggagttacctgataacagAtggcacaaatatcattgtgt	9	6	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr5:158588284A>G	ENST00000424310.2	-	10	1975	c.1616T>C	c.(1615-1617)aTc>aCc	p.I539T	RNF145_ENST00000518802.1_Missense_Mutation_p.I569T|RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000520638.1_Missense_Mutation_p.I553T|RNF145_ENST00000519865.1_Missense_Mutation_p.I539T|RNF145_ENST00000274542.2_Missense_Mutation_p.I567T|RNF145_ENST00000521606.2_Missense_Mutation_p.I556T	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	539						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGATAACAGATGGCACAAAT	0.383																																																0			5											53	54	54					5																	158588284		2191	4262	6453	158520862	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1616T>C	5.37:g.158588284A>G	ENSP00000409064:p.Ile539Thr		158520862	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.482723	0.84747	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4;-1.4	6.07	6.07	0.98685	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.91680	0.7370	M	0.90650	3.135	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999	D	0.93129	0.6531	10	0.87932	D	0	-20.9594	16.6277	0.84984	1.0:0.0:0.0:0.0	.	556;553;569;539;567	B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;RN145_HUMAN;.	T	567;539;539;555;556;569;539;553	ENSP00000274542:I567T;ENSP00000430397:I539T;ENSP00000409064:I539T;ENSP00000430753:I555T;ENSP00000445115:I556T;ENSP00000430955:I569T;ENSP00000429071:I553T	ENSP00000274542:I567T	I	-	2	0	RNF145	158520862	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.210000	0.95106	2.330000	0.79161	0.528000	0.53228	ATC		0.383	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		G	158588284	A	G	158588284	3	3	99	1	0	0	0	0	1	0	0	0	13484	333	12	4	383	4	RNF145	5	158588284	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	4310149	158588284	22326976	63	26539										
BMP6	654	hgsc.bcm.edu	37	chr6	7845412	7845412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctcccctcgtcagcgacaccAcaaagagttcaagttcaact	6	15	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:7845412A>G	ENST00000283147.6	+	2	863	c.704A>G	c.(703-705)cAc>cGc	p.H235R		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	235					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)	p.H235R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					CAGCGACACCACAAAGAGTTC	0.458																																																1	Substitution - Missense(1)	ovary(1)	6											134	132	133					6																	7845412		2203	4300	6503	7790411	SO:0001583	missense	654			AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"Bone morphogenetic proteins", "Endogenous ligands"	1073	protein-coding gene	gene with protein product		112266	"vegetal related growth factor (TGFB-related)"	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.704A>G	6.37:g.7845412A>G	ENSP00000283147:p.His235Arg		7790411	Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	37	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.525973	0.44969	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	T	0.61859	0.07	5.41	5.41	0.78517	Transforming growth factor-beta, N-terminal (1);	0.048468	0.85682	D	0.000000	T	0.37237	0.0996	L	0.44542	1.39	0.80722	D	1	B	0.23442	0.085	B	0.29440	0.102	T	0.28808	-1.0032	10	0.25106	T	0.35	.	15.4422	0.75195	1.0:0.0:0.0:0.0	.	235	P22004	BMP6_HUMAN	R	157;235;198	ENSP00000283147:H235R	ENSP00000283147:H235R	H	+	2	0	BMP6	7790411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.735000	0.91549	2.044000	0.60594	0.455000	0.32223	CAC		0.458	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718		G	7845412	A	G	7845412	3	3	99	1	0	0	0	0	1	0	0	0	1465	159	6	4	710	4	BMP6	6	7845412	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10		7845412	163269655	64	26540										
GPLD1	2822	hgsc.bcm.edu	37	chr6	24462992	24462992	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttgctggccgccacatgcaaTgaacagagggttctcaggca	12	11	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:24462992T>A	ENST00000230036.1	-	11	963	c.853A>T	c.(853-855)Att>Ttt	p.I285F		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	285					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						CCACATGCAATGAACAGAGGG	0.453																																																0			6											139	137	138					6																	24462992		2203	4300	6503	24570971	SO:0001583	missense	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.853A>T	6.37:g.24462992T>A	ENSP00000230036:p.Ile285Phe		24570971	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.216202	0.39201	.	.	ENSG00000112293	ENST00000230036	T	0.68025	-0.3	5.92	5.92	0.95590	.	0.073640	0.53938	D	0.000055	T	0.68568	0.3015	M	0.78637	2.42	0.80722	D	1	D	0.61080	0.989	P	0.52856	0.711	T	0.70872	-0.4754	10	0.37606	T	0.19	-24.4559	13.8758	0.63651	0.0:0.0:0.0:1.0	.	285	P80108	PHLD_HUMAN	F	285	ENSP00000230036:I285F	ENSP00000230036:I285F	I	-	1	0	GPLD1	24570971	1.000000	0.71417	0.989000	0.46669	0.070000	0.16714	4.639000	0.61361	2.255000	0.74692	0.533000	0.62120	ATT		0.453	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		A	24462992	T	A	24462992	3	1	99	1	0	0	0	0	1	0	0	0	6634	1464	51	5	1729	5	GPLD1	6	24462992	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	16617580	24462992	146652075	65	26541										
OR2B2	81697	hgsc.bcm.edu	37	chr6	27879916	27879917	+	Frame_Shift_Ins	INS	-	-	C													0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgagagattgctaagaaaaaINSagtacataggggtgtggagt							TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:27879916_27879917insC	ENST00000303324.2	-	1	257_258	c.181_182insG	c.(181-183)tttfs	p.F61fs		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						GCTAAGAAAAAAGTACATAGGG	0.376																																																0			6																																								27987896	SO:0001589	frameshift_variant	81697			Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"GPCR / Class A : Olfactory receptors"	13966	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 9"	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.181_182insG	6.37:g.27879916_27879917insC	ENSP00000304419:p.Phe61fs		27987895	B2RNH2|Q9GZL2|Q9Y299	Frame_Shift_Ins	INS	ENST00000303324.2	37	CCDS4641.1																																																																																				0.376	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			C	27879917	-	C	27879916	7	5	99	1	0	1	1	0	0	0	0	0	11020	14	1	0	895	0	OR2B2	6	27879916	Frame_Shift_Ins	INS	-	TCGA-DC-6681-01A-11D-1826-10	3416924	27879916	143235151	66	26542										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32170369	32170369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgtggctgcaggtggggcctTcaaaaccctgtggaggggag	18	8	1	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:32170369T>C	ENST00000375023.3	-	21	3377	c.3239A>G	c.(3238-3240)gAa>gGa	p.E1080G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1080	EGF-like 27. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGTGGGGCCTTCAAAACCCTG	0.597																																																0			6											16	21	19					6																	32170369		1447	2648	4095	32278347	SO:0001583	missense	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3239A>G	6.37:g.32170369T>C	ENSP00000364163:p.Glu1080Gly		32278347	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.328321	0.60743	.	.	ENSG00000204301	ENST00000375023	D	0.87887	-2.31	5.14	5.14	0.70334	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.46145	D	0.000302	T	0.74076	0.3669	L	0.41356	1.27	0.80722	D	1	P	0.35107	0.484	B	0.32149	0.141	T	0.78316	-0.2251	10	0.49607	T	0.09	.	12.9575	0.58438	0.0:0.0:0.0:1.0	.	1080	Q99466	NOTC4_HUMAN	G	1080	ENSP00000364163:E1080G	ENSP00000364163:E1080G	E	-	2	0	NOTCH4	32278347	0.896000	0.30565	1.000000	0.80357	0.996000	0.88848	1.965000	0.40471	2.161000	0.67846	0.459000	0.35465	GAA		0.597	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32170369	T	C	32170369	3	2	99	1	0	0	0	0	1	0	0	0	10582	1783	62	4	2812	4	NOTCH4	6	32170369	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	4290453	32170369	138944698	67	26543										
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35923246	35923246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgagcagtgaatcaggttaaTggaggatgcttcgggatcca	14	6	1	2	rs2295852	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:35923246T>C	ENST00000490799.1	-	17	2268	c.1915A>G	c.(1915-1917)Att>Gtt	p.I639V	SLC26A8_ENST00000355574.2_Missense_Mutation_p.I639V|SLC26A8_ENST00000394602.2_Missense_Mutation_p.I534V	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						ATCAGGTTAATGGAGGATGCT	0.463													N|||	2041	0.407548	0.6967	0.2867	5008	,	,		21471	0.2758		0.3529	False		,,,				2504	0.2945															0			6						C	VAL/ILE,VAL/ILE,VAL/ILE	2807,1599	496.2+/-363.5	886,1035,282	198	191	193		1915,1915,1600	-5	0	6	dbSNP_100	193	3003,5597	664.5+/-402.2	551,1901,1848	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	29,29,29	1437,2936,2130	CC,CT,TT		34.9186,36.2914,44.6717	benign,benign,benign	639/971,639/971,534/866	35923246	5810,7196	2203	4300	6503	36031224	SO:0001583	missense	116369			AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.1915A>G	6.37:g.35923246T>C	ENSP00000417638:p.Ile639Val		36031224		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	835	0.3823260073260073	322	0.6544715447154471	106	0.292817679558011	152	0.26573426573426573	255	0.33641160949868076	C	3.950	-0.012529	0.07727	0.637086	0.349186	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	D;D;D	0.94862	-3.16;-3.54;-3.16	5.01	-4.99	0.03010	Sulphate transporter/antisigma-factor antagonist STAS (3);	1.172630	0.06260	N	0.693768	T	0.72581	0.3478	L	0.31752	0.955	0.80722	P	0.0	B;B;B	0.15141	0.0;0.012;0.0	B;B;B	0.14023	0.001;0.01;0.001	T	0.67166	-0.5739	9	0.11485	T	0.65	.	2.4043	0.04409	0.1092:0.3104:0.1431:0.4373	rs2295852;rs17706470;rs52831325;rs58070509;rs2295852	639;534;221	Q96RN1;Q96RN1-2;Q96RN1-3	S26A8_HUMAN;.;.	V	639;534;639	ENSP00000417638:I639V;ENSP00000378100:I534V;ENSP00000347778:I639V	ENSP00000347778:I639V	I	-	1	0	SLC26A8	36031224	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.320000	0.02700	-1.280000	0.02402	-2.418000	0.00219	ATT		0.463	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			C	35923246	T	C	35923246	3	2	99	1	0	0	0	0	1	0	0	0	14560	1464	51	4	1013	4	SLC26A8	6	35923246	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	3752877	35923246	135191821	68	26544										
GCM1	8521	hgsc.bcm.edu	37	chr6	52993290	52993290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tggctgcaggtggctccaatGgaagctgctggtaaaagggt	16	7	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:52993290G>A	ENST00000259803.7	-	6	1236	c.1025C>T	c.(1024-1026)cCa>cTa	p.P342L	RP11-506E9.3_ENST00000566420.1_RNA	NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	342					anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					TGGCTCCAATGGAAGCTGCTG	0.468																																																0			6											68	74	72					6																	52993290		2203	4300	6503	53101249	SO:0001583	missense	8521			D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270			4197	protein-coding gene	gene with protein product		603715	"glial cells missing (Drosophila) homolog a"	GCMA		8962155	Standard	NM_003643		Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.1025C>T	6.37:g.52993290G>A	ENSP00000259803:p.Pro342Leu		53101249	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	Missense_Mutation	SNP	ENST00000259803.7	37	CCDS4950.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.649173	0.67358	.	.	ENSG00000137270	ENST00000259803	T	0.77098	-1.07	5.73	4.86	0.63082	.	0.168763	0.41712	D	0.000834	T	0.55721	0.1938	L	0.36672	1.1	0.43133	D	0.994878	P	0.41673	0.759	B	0.38327	0.271	T	0.65121	-0.6245	10	0.72032	D	0.01	0.0486	10.2101	0.43136	0.1563:0.0:0.8437:0.0	.	342	Q9NP62	GCM1_HUMAN	L	342	ENSP00000259803:P342L	ENSP00000259803:P342L	P	-	2	0	GCM1	53101249	0.869000	0.29996	0.962000	0.40283	0.885000	0.51271	3.822000	0.55708	1.444000	0.47605	0.591000	0.81541	CCA		0.468	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040953.1			A	52993290	G	A	52993290	3	1	99	1	0	0	0	0	1	0	0	0	6317	1348	47	3	289	3	GCM1	6	52993290	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	17070044	52993290	118121777	69	26545										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90581037	90581037	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ccgggaaattttattggagtGtcagaaaagagggccatcat	12	6	2	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:90581037G>A	ENST00000551025.1	+	0	7259									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TTATTGGAGTGTCAGAAAAGA	0.343																																					Colon(187;1656 2025 17045 31481 39901)											0			6											85	81	82					6																	90581037		1796	4070	5866	90637758			9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90581037G>A			90637758		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.343	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90581037	G	A	90581037	1	1	99	0	1	0	0	0	0	0	0	0	2684	1377	48	3		3	CASP8AP2	6	90581037	RNA	SNP	G	TCGA-DC-6681-01A-11D-1826-10	37587747	90581037	80534030	70	26546										
RSPO3	84870	hgsc.bcm.edu	37	chr6	127476516	127476516	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ccttcagcaaagggtaacctGtgtcccccaacaaatgagac	8	13	1	1	rs1892172	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:127476516G>A	ENST00000356698.4	+	4	1156	c.567G>A	c.(565-567)ctG>ctA	p.L189L	RSPO3_ENST00000368317.3_Silent_p.L189L	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	189	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		AGGGTAACCTGTGTCCCCCAA	0.438													g|||	2668	0.532748	0.5983	0.5231	5008	,	,		20533	0.494		0.5	False		,,,				2504	0.5245															0			6						A		2614,1792	641.7+/-397.5	789,1036,378	110	99	103		567	4.6	1	6	dbSNP_92	103	4583,4017	597.8+/-393.8	1220,2143,937	yes	coding-synonymous	RSPO3	NM_032784.3		2009,3179,1315	AA,AG,GG		46.7093,40.6718,44.664		189/273	127476516	7197,5809	2203	4300	6503	127518209	SO:0001819	synonymous_variant	84870			BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"Endogenous ligands"	20866	protein-coding gene	gene with protein product		610574	"thrombospondin, type I, domain containing 2", "R-spondin 3 homolog (Xenopus laevis)"	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.567G>A	6.37:g.127476516G>A			127518209	B2RC27|Q5VTV4|Q96K87	Silent	SNP	ENST00000356698.4	37	CCDS5135.1																																																																																				0.438	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784		A	127476516	G	A	127476516	2	1	99	1	0	0	0	0	0	0	0	1	13748	1364	48	3		3	RSPO3	6	127476516	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	36895479	127476516	43638551	71	26547										
NMBR	4829	hgsc.bcm.edu	37	chr6	142400020	142400020	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctgacgtctgcatgtccatgGggttaacgatggctctgtac	12	10	2	1	rs138994608	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr6:142400020G>T	ENST00000258042.1	-	2	583	c.443C>A	c.(442-444)cCc>cAc	p.P148H	NMBR_ENST00000480652.1_5'Flank	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	148					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)	p.P148H(1)		breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		CATGTCCATGGGGTTAACGAT	0.463													G|||	39	0.00778754	8e-04	0.0058	5008	,	,		17607	0		0.0239	False		,,,				2504	0.0102															1	Substitution - Missense(1)	central_nervous_system(1)	6						G	HIS/PRO	34,4372	39.2+/-71.8	0,34,2169	58	49	52		443	5.6	1	6	dbSNP_134	52	281,8319	105.4+/-166.3	4,273,4023	yes	missense	NMBR	NM_002511.2	77	4,307,6192	TT,TG,GG		3.2674,0.7717,2.422	probably-damaging	148/391	142400020	315,12691	2203	4300	6503	142441713	SO:0001583	missense	4829				CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.443C>A	6.37:g.142400020G>T	ENSP00000258042:p.Pro148His		142441713	E9KL38|Q5VUK8	Missense_Mutation	SNP	ENST00000258042.1	37	CCDS5196.1	24	0.01098901098901099	0	0.0	1	0.0027624309392265192	0	0.0	23	0.030343007915567283	G	27.4	4.826244	0.90955	0.007717	0.032674	ENSG00000135577	ENST00000258042	T	0.61510	0.1	5.59	5.59	0.84812	GPCR, rhodopsin-like superfamily (1);	0.098715	0.64402	D	0.000001	T	0.76285	0.3966	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79242	-0.1884	10	0.87932	D	0	-22.3696	19.5708	0.95413	0.0:0.0:1.0:0.0	.	148	P28336	NMBR_HUMAN	H	148	ENSP00000258042:P148H	ENSP00000258042:P148H	P	-	2	0	NMBR	142441713	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.390000	0.97246	2.646000	0.89796	0.585000	0.79938	CCC		0.463	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			T	142400020	G	T	142400020	3	4	99	1	0	0	0	0	1	0	0	0	10518	1232	43	2	737	2	NMBR	6	142400020	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	14923504	142400020	28715047	72	26548										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21778449	21778449	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tatggcaccgttcagcctcaCaccctgatccggcagcatat	8	15	2	1	rs1109806	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:21778449C>T	ENST00000409508.3	+	47	7807	c.7776C>T	c.(7774-7776)caC>caT	p.H2592H	DNAH11_ENST00000328843.6_Silent_p.H2599H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2599	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTCAGCCTCACACCCTGATCC	0.373									Kartagener syndrome				C|||	2702	0.539537	0.5923	0.5677	5008	,	,		15729	0.244		0.7048	False		,,,				2504	0.5828															0			7						C		2660,1692		844,972,360	45	46	46		7798	2.6	0.9	7	dbSNP_86	46	5930,2640		2061,1808,416	yes	coding-synonymous	DNAH11	NM_003777.3		2905,2780,776	TT,TC,CC		30.8051,38.8787,33.5242		2599/4524	21778449	8590,4332	2176	4285	6461	21744974	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.7776C>T	7.37:g.21778449C>T			21744974	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37																																																																																					0.373	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21778449	C	T	21778449	2	4	99	1	0	0	0	0	0	0	0	1	4610	477	17	3		3	DNAH11	7	21778449	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10		21778449	137360214	73	26549										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34698057	34698057	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcacagagggcagcttcgaTtccagtgggaccgggcagac	14	11	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:34698057T>C	ENST00000360581.1	+	1	161	c.33T>C	c.(31-33)gaT>gaC	p.D11D	AC005493.1_ENST00000399077.1_Intron|NPSR1-AS1_ENST00000419766.1_RNA|NPSR1_ENST00000531252.1_Silent_p.D11D|NPSR1_ENST00000381553.3_Silent_p.D11D|NPSR1_ENST00000359791.1_Silent_p.D11D|NPSR1_ENST00000381542.1_Silent_p.D11D|NPSR1_ENST00000381539.3_Silent_p.D11D|NPSR1_ENST00000465305.1_Silent_p.D11D	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	11						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	GCAGCTTCGATTCCAGTGGGA	0.572																																																0			7											103	92	96					7																	34698057		2203	4300	6503	34664582	SO:0001819	synonymous_variant	387129			AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.33T>C	7.37:g.34698057T>C			34664582	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000360581.1	37	CCDS5444.1																																																																																				0.572	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		C	34698057	T	C	34698057	2	2	99	1	0	0	0	0	0	0	0	1	10631	1490	52	4		4	NPSR1	7	34698057	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	12919608	34698057	124440606	74	26550										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729983	41729983	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cctgtgtccaagctgccctgCgggtgcttctgctgctggaa	13	13	1	0	rs141733287		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:41729983C>T	ENST00000242208.4	-	3	792	c.546G>A	c.(544-546)ccG>ccA	p.P182P	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Silent_p.P182P	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	182					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						AGCTGCCCTGCGGGTGCTTCT	0.567										TSP Lung(11;0.080)																																						0			7											90	85	87					7																	41729983		2203	4300	6503	41696508	SO:0001819	synonymous_variant	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.546G>A	7.37:g.41729983C>T			41696508	Q14599	Silent	SNP	ENST00000242208.4	37	CCDS5464.1																																																																																				0.567	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			T	41729983	C	T	41729983	2	4	99	1	0	0	0	0	0	0	0	1	7762	755	27	1		1	INHBA	7	41729983	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	7031926	41729983	117408680	75	26551										
AUTS2	26053	hgsc.bcm.edu	37	chr7	69583190	69583190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gagaatccaagggcttccacCggagcagctctcgggaaagg	14	11	1	1	rs139132240		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:69583190C>T	ENST00000342771.4	+	3	916	c.595C>T	c.(595-597)Cgg>Tgg	p.R199W	AUTS2_ENST00000406775.2_Missense_Mutation_p.R199W|AUTS2_ENST00000403018.2_Missense_Mutation_p.R199W	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	199										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GGGCTTCCACCGGAGCAGCTC	0.433																																																0			7						C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	54	55	55		595,595,595	3.4	1	7	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	AUTS2	NM_001127231.1,NM_001127232.1,NM_015570.2	101,101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging	199/1236,199/267,199/1260	69583190	2,13004	2203	4300	6503	69221126	SO:0001583	missense	282553			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.595C>T	7.37:g.69583190C>T	ENSP00000344087:p.Arg199Trp		69221126	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360337	0.82353	2.27E-4	1.16E-4	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000403018	T;T	0.34472	1.36;1.37	5.33	3.38	0.38709	.	0.000000	0.50627	D	0.000109	T	0.42245	0.1194	N	0.19112	0.55	0.36443	D	0.865627	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	T	0.43442	-0.9391	9	.	.	.	-15.1367	13.2239	0.59905	0.3784:0.6216:0.0:0.0	.	199;199;199	Q8WXX7-2;Q8WXX7;Q6PJU5	.;AUTS2_HUMAN;.	W	199	ENSP00000385263:R199W;ENSP00000344087:R199W	.	R	+	1	2	AUTS2	69221126	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	1.395000	0.34520	0.671000	0.31185	0.655000	0.94253	CGG		0.433	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	69583190	C	T	69583190	3	4	99	1	0	0	0	0	1	0	0	0	1226	643	23	1	605	1	AUTS2	7	69583190	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	27853207	69583190	89555473	76	26552										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70233014	70233014	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tttgatccctttacagtttgAcaaataccctacaaaagttg	5	9	0	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:70233014A>C	ENST00000342771.4	+	10	2015	c.1694A>C	c.(1693-1695)gAc>gCc	p.D565A	AUTS2_ENST00000406775.2_Missense_Mutation_p.D565A	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	565										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TTACAGTTTGACAAATACCCT	0.413																																																0			7											200	179	186					7																	70233014		2203	4300	6503	69870950	SO:0001583	missense	282553			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1694A>C	7.37:g.70233014A>C	ENSP00000344087:p.Asp565Ala		69870950	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.469811	0.84533	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.51574	0.7;0.7	5.87	5.87	0.94306	.	0.226779	0.52532	D	0.000080	T	0.63604	0.2525	L	0.61036	1.89	0.80722	D	1	P;D;D	0.65815	0.925;0.995;0.995	P;P;P	0.61477	0.453;0.889;0.889	T	0.62690	-0.6801	9	.	.	.	-18.9418	16.2774	0.82651	1.0:0.0:0.0:0.0	.	17;565;565	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	A	565	ENSP00000385263:D565A;ENSP00000344087:D565A	.	D	+	2	0	AUTS2	69870950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.247000	0.74100	0.482000	0.46254	GAC		0.413	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			C	70233014	A	C	70233014	3	2	99	1	0	0	0	0	1	0	0	0	1226	275	10	4	1877	4	AUTS2	7	70233014	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	649824	70233014	88905649	77	26553										
HIP1	3092	hgsc.bcm.edu	37	chr7	75178262	75178262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgtccaccaggtcccccagcTcctcctgcttgatgtccagt	8	17	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:75178262T>C	ENST00000336926.6	-	23	2359	c.2333A>G	c.(2332-2334)gAg>gGg	p.E778G	HIP1_ENST00000434438.2_Missense_Mutation_p.E778G	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	778	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GTCCCCCAGCTCCTCCTGCTT	0.577			T	PDGFRB	CMML																																		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	0			7											170	160	163					7																	75178262		2203	4300	6503	75016198	SO:0001583	missense	3092			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2333A>G	7.37:g.75178262T>C	ENSP00000336747:p.Glu778Gly		75016198	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	37	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	t	23.5	4.425199	0.83667	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.34072	1.38;1.38	4.77	4.77	0.60923	I/LWEQ (1);	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	M	0.83118	2.625	0.58432	D	0.999995	D;B	0.58268	0.982;0.04	P;B	0.53224	0.721;0.035	T	0.62234	-0.6897	10	0.62326	D	0.03	-11.8227	13.1094	0.59265	0.0:0.0:0.0:1.0	.	778;778	E7ES17;O00291	.;HIP1_HUMAN	G	778	ENSP00000336747:E778G;ENSP00000410300:E778G	ENSP00000336747:E778G	E	-	2	0	HIP1	75016198	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.865000	0.69583	1.786000	0.52430	0.459000	0.35465	GAG		0.577	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		C	75178262	T	C	75178262	3	2	99	1	0	0	0	0	1	0	0	0	7135	1551	54	4	816	4	HIP1	7	75178262	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	4945248	75178262	83960401	78	26554										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84628989	84628989	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agccaatagatccttgacctTcccctcctcatgctctgccc	5	18	2	2	rs7800072	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:84628989T>G	ENST00000284136.6	-	17	2144	c.2101A>C	c.(2101-2103)Aag>Cag	p.K701Q	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	701			K -> Q (in dbSNP:rs7800072). {ECO:0000269|PubMed:12975309}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TCCTTGACCTTCCCCTCCTCA	0.473													G|||	1430	0.285543	0.351	0.2421	5008	,	,		17893	0.2718		0.3201	False		,,,				2504	0.2065				Ovarian(63;442 1191 17318 29975 31528)											0			7						G	GLN/LYS	1642,2764	659.1+/-400.5	314,1014,875	144	119	128		2101	3.8	1	7	dbSNP_116	128	2814,5786	676.5+/-403.3	459,1896,1945	yes	missense	SEMA3D	NM_152754.2	53	773,2910,2820	GG,GT,TT		32.7209,37.2674,34.2611	benign	701/778	84628989	4456,8550	2203	4300	6503	84466925	SO:0001583	missense	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2101A>C	7.37:g.84628989T>G	ENSP00000284136:p.Lys701Gln		84466925	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	667	0.30540293040293043	191	0.3882113821138211	94	0.2596685082872928	139	0.243006993006993	243	0.32058047493403696	G	5.817	0.334982	0.11013	0.372674	0.327209	ENSG00000153993	ENST00000284136	T	0.30981	1.51	5.73	3.82	0.43975	.	0.959042	0.08767	N	0.896847	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999611851	B	0.02656	0.0	B	0.01281	0.0	T	0.44620	-0.9316	9	0.13108	T	0.6	.	15.0253	0.71667	0.0:0.0:0.6279:0.3721	rs7800072;rs10365892;rs7800072	701	O95025	SEM3D_HUMAN	Q	701	ENSP00000284136:K701Q	ENSP00000284136:K701Q	K	-	1	0	SEMA3D	84466925	0.865000	0.29922	0.998000	0.56505	0.986000	0.74619	1.502000	0.35704	0.759000	0.33084	-0.121000	0.15023	AAG		0.473	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84628989	T	G	84628989	3	3	99	1	0	0	0	0	1	0	0	0	14064	1792	62	4	236	4	SEMA3D	7	84628989	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	9450727	84628989	74509674	79	26555										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84685072	84685072	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cgagaaaggatggttttatcGgaggtactgccttcttgaga	13	6	1	2	rs552162067	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:84685072G>A	ENST00000284136.6	-	7	865	c.822C>T	c.(820-822)tcC>tcT	p.S274S	SEMA3D_ENST00000444867.1_Silent_p.S274S	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	274	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TGGTTTTATCGGAGGTACTGC	0.274													G|||	10	0.00199681	0	0	5008	,	,		9233	0		0	False		,,,				2504	0.0102				Ovarian(63;442 1191 17318 29975 31528)											0			7											65	65	65					7																	84685072		2202	4300	6502	84523008	SO:0001819	synonymous_variant	223117			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.822C>T	7.37:g.84685072G>A			84523008	A6NK46|Q6UW77|Q8NCQ1	Silent	SNP	ENST00000284136.6	37	CCDS34676.1																																																																																				0.274	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		A	84685072	G	A	84685072	2	1	99	1	0	0	0	0	0	0	0	1	14064	1103	39	1		1	SEMA3D	7	84685072	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	56083	84685072	74453591	80	26556										
GRM3	2913	hgsc.bcm.edu	37	chr7	86415812	86415812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggccttcgagcaggaagcccGcctgcgcaacatctgcatcg	12	15	1	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:86415812G>A	ENST00000361669.2	+	3	1803	c.704G>A	c.(703-705)cGc>cAc	p.R235H	AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.R107H|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000439827.1_Missense_Mutation_p.R235H|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000394720.2_Missense_Mutation_p.R233H	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	235					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CAGGAAGCCCGCCTGCGCAAC	0.597																																					GBM(52;969 1098 3139 52280)											0			7											55	52	53					7																	86415812		2203	4300	6503	86253748	SO:0001583	missense	2913				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.704G>A	7.37:g.86415812G>A	ENSP00000355316:p.Arg235His		86253748	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619381	0.87460	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81	5.72	4.83	0.62350	Extracellular ligand-binding receptor (1);	0.051376	0.85682	D	0.000000	D	0.93223	0.7841	M	0.88775	2.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.75020	0.975;0.907;0.985	D	0.94386	0.7609	10	0.72032	D	0.01	.	15.8198	0.78631	0.0:0.1361:0.8639:0.0	.	107;235;235	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	H	235;107;107;235;233	ENSP00000355316:R235H;ENSP00000405427:R107H;ENSP00000441407:R107H;ENSP00000398767:R235H;ENSP00000378209:R233H	ENSP00000355316:R235H	R	+	2	0	GRM3	86253748	1.000000	0.71417	0.370000	0.25965	0.990000	0.78478	9.756000	0.98918	1.400000	0.46741	0.655000	0.94253	CGC		0.597	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			A	86415812	G	A	86415812	3	1	99	1	0	0	0	0	1	0	0	0	6819	1087	38	1	710	1	GRM3	7	86415812	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	1730740	86415812	72722851	81	26557										
CALCR	799	hgsc.bcm.edu	37	chr7	93108737	93108737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtgcatccatcatcttctttCgtcctacgacgtaaagaaat	6	11	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:93108737C>T	ENST00000394441.1	-	3	449	c.134G>A	c.(133-135)cGa>cAa	p.R45Q	CALCR_ENST00000359558.2_Missense_Mutation_p.R63Q|CALCR_ENST00000421592.1_Missense_Mutation_p.R45Q|CALCR_ENST00000360249.4_Missense_Mutation_p.R45Q|CALCR_ENST00000426151.1_Missense_Mutation_p.R45Q	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	63					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CATCTTCTTTCGTCCTACGAC	0.403																																																0			7											246	228	234					7																	93108737		2203	4300	6503	92946673	SO:0001583	missense	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.134G>A	7.37:g.93108737C>T	ENSP00000377959:p.Arg45Gln		92946673	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.176800	0.38413	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000535783;ENST00000394441;ENST00000426151	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.21	2.38	0.29361	.	.	.	.	.	T	0.40498	0.1119	L	0.56769	1.78	0.09310	N	0.999999	P;B	0.35982	0.531;0.396	B;B	0.30179	0.112;0.042	T	0.22173	-1.0224	9	0.30854	T	0.27	.	4.4219	0.11484	0.0:0.5602:0.1636:0.2763	.	63;45	F5H605;A4D1G6	.;.	Q	63;45;45;45;45;45	ENSP00000352561:R63Q;ENSP00000353385:R45Q;ENSP00000399552:R45Q;ENSP00000377959:R45Q;ENSP00000389295:R45Q	ENSP00000352561:R63Q	R	-	2	0	CALCR	92946673	0.009000	0.17119	0.001000	0.08648	0.040000	0.13550	1.047000	0.30367	0.426000	0.26116	0.650000	0.86243	CGA		0.403	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		T	93108737	C	T	93108737	3	4	99	1	0	0	0	0	1	0	0	0	2585	884	31	1	1386	1	CALCR	7	93108737	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	6692925	93108737	66029926	82	26558										
DLX5	1749	hgsc.bcm.edu	37	chr7	96653816	96653816	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tagtcagaatcggtagctgaAgactcgggcaaagttggcga	14	7	1	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:96653816A>G	ENST00000222598.4	-	1	593	c.120T>C	c.(118-120)tcT>tcC	p.S40S	DLX5_ENST00000486603.2_Silent_p.S40S|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	40					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CGGTAGCTGAAGACTCGGGCA	0.602																																																0			7											53	58	56					7																	96653816		2203	4300	6503	96491752	SO:0001819	synonymous_variant	1749				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.120T>C	7.37:g.96653816A>G			96491752	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																				0.602	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			G	96653816	A	G	96653816	2	3	99	1	0	0	0	0	0	0	0	1	4585	59	3	4		4	DLX5	7	96653816	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	3545079	96653816	62484847	83	26559										
ZAN	7455	hgsc.bcm.edu	37	chr7	100366320	100366320	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcagctgggggccgcctggaAgttacctgaatcctctgaac	13	12	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:100366320A>G	ENST00000348028.3	+	0	5294				ZAN_ENST00000542585.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000449052.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K1710M(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCCGCCTGGAAGTTACCTGAA	0.627																																																1	Substitution - Missense(1)	ovary(1)	7											19	19	19					7																	100366320		1863	4088	5951	100204256			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100366320A>G			100204256	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	A	13.75	2.330833	0.41297	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213	T;T;T;T	0.25912	2.32;2.31;2.29;1.77	4.62	0.246	0.15516	von Willebrand factor, type D domain (1);	0.657454	0.13404	N	0.390435	T	0.18593	0.0446	L	0.46157	1.445	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.21449	-1.0245	10	0.45353	T	0.12	.	4.0425	0.09758	0.3681:0.0:0.1049:0.527	.	1710;1710	F5H0T8;Q9Y493	.;ZAN_HUMAN	R	1710;1710;1710;287	ENSP00000445943:K1710R;ENSP00000445091:K1710R;ENSP00000444427:K1710R;ENSP00000441117:K287R	ENSP00000423579:K1710R	K	+	2	0	ZAN	100204256	0.047000	0.20315	0.267000	0.24556	0.029000	0.11900	0.023000	0.13533	0.025000	0.15241	-0.301000	0.09380	AAG		0.627	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		G	100366320	A	G	100366320	1	3	99	0	1	0	0	0	0	0	0	0	17553	72	3	4		4	ZAN	7	100366320	RNA	SNP	A	TCGA-DC-6681-01A-11D-1826-10	3712504	100366320	58772343	84	26560										
MUC17	140453	hgsc.bcm.edu	37	chr7	100679902	100679902	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcatctcctacaacttctgaAggtaccagcatgccaaactc	5	14	3	1	rs55974941	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:100679902A>G	ENST00000306151.4	+	3	5269	c.5205A>G	c.(5203-5205)gaA>gaG	p.E1735E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1735	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.E1735E(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACTTCTGAAGGTACCAGCA	0.512													a|||	1933	0.385982	0.1392	0.3372	5008	,	,		24828	0.5595		0.4861	False		,,,				2504	0.4724															1	Substitution - coding silent(1)	stomach(1)	7						A		858,3548	336.3+/-304.3	91,676,1436	252	259	256		5205	-1.6	0	7	dbSNP_129	256	4211,4389	570.1+/-389.3	1030,2151,1119	no	coding-synonymous	MUC17	NM_001040105.1		1121,2827,2555	GG,GA,AA		48.9651,19.4734,38.9743		1735/4494	100679902	5069,7937	2203	4300	6503	100466622	SO:0001819	synonymous_variant	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5205A>G	7.37:g.100679902A>G			100466622	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																				0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100679902	A	G	100679902	2	3	99	1	0	0	0	0	0	0	0	1	10004	69	3	4		4	MUC17	7	100679902	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	313582	100679902	58458761	85	26561										
TRIM56	81844	hgsc.bcm.edu	37	chr7	100731829	100731829	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggtggagtccagccccaggcTggagatggagcccagacccc	15	14	0	2	rs6948536	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:100731829T>C	ENST00000306085.6	+	3	1533	c.1236T>C	c.(1234-1236)gcT>gcC	p.A412A		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	412					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCCCCAGGCTGGAGATGGAG	0.632													C|||	3548	0.708466	0.9614	0.5418	5008	,	,		15987	0.5496		0.7455	False		,,,				2504	0.6104				Ovarian(89;1092 1379 22756 38989 39611)											0			7						C		3809,297		1776,257,20	50	67	62		1236	-7.1	0	7	dbSNP_116	62	6223,2179		2318,1587,296	no	coding-synonymous	TRIM56	NM_030961.1		4094,1844,316	CC,CT,TT		25.9343,7.2333,19.7953		412/756	100731829	10032,2476	2053	4201	6254	100518549	SO:0001819	synonymous_variant	81844			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1236T>C	7.37:g.100731829T>C			100518549	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																				0.632	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		C	100731829	T	C	100731829	2	2	99	1	0	0	0	0	0	0	0	1	16570	1567	55	4		4	TRIM56	7	100731829	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	51927	100731829	58406834	86	26562										
RELN	5649	hgsc.bcm.edu	37	chr7	103214611	103214611	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cattgaagtagagagatttgCcatcgttaagtgttccacag	10	7	0	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:103214611C>G	ENST00000428762.1	-	30	4598	c.4439G>C	c.(4438-4440)gGc>gCc	p.G1480A	RELN_ENST00000343529.5_Missense_Mutation_p.G1480A|RELN_ENST00000424685.2_Missense_Mutation_p.G1480A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1480					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GAGAGATTTGCCATCGTTAAG	0.483																																					NSCLC(146;835 1944 15585 22231 52158)											0			7											147	134	139					7																	103214611		2203	4300	6503	103001847	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.4439G>C	7.37:g.103214611C>G	ENSP00000392423:p.Gly1480Ala		103001847	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.853377	0.91355	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.43688	1.75;0.94;1.75	5.62	5.62	0.85841	.	0.105878	0.64402	D	0.000004	T	0.66519	0.2797	M	0.76170	2.325	0.80722	D	1	P;D	0.89917	0.782;1.0	P;D	0.72625	0.469;0.978	T	0.64719	-0.6341	10	0.46703	T	0.11	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	1480;1480	P78509-2;P78509	.;RELN_HUMAN	A	1480	ENSP00000392423:G1480A;ENSP00000345694:G1480A;ENSP00000388446:G1480A	ENSP00000345694:G1480A	G	-	2	0	RELN	103001847	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	5.717000	0.68446	2.809000	0.96659	0.655000	0.94253	GGC		0.483	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103214611	C	G	103214611	3	3	99	1	0	0	0	0	1	0	0	0	13257	739	26	5	6087	5	RELN	7	103214611	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	2482782	103214611	55924052	87	26563										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112112899	112112899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	caacgcttaaaacgatgaagAtttctcgtttcgaaagggta	9	7	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:112112899A>G	ENST00000403825.3	+	11	1510	c.1249A>G	c.(1249-1251)Att>Gtt	p.I417V	IFRD1_ENST00000005558.4_Missense_Mutation_p.I417V|IFRD1_ENST00000535603.1_Missense_Mutation_p.I367V	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	417					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						AACGATGAAGATTTCTCGTTT	0.378																																																0			7											122	125	124					7																	112112899		2203	4300	6503	111900135	SO:0001583	missense	3475			Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1249A>G	7.37:g.112112899A>G	ENSP00000384477:p.Ile417Val		111900135	B7Z5G1|O75234|Q5U013|Q9BVE4	Missense_Mutation	SNP	ENST00000403825.3	37	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.373053	0.42105	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000536259;ENST00000535603;ENST00000462155	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.81	5.81	0.92471	Interferon-related developmental regulator, C-terminal (1);	0.103669	0.64402	D	0.000003	T	0.37461	0.1004	L	0.47716	1.5	0.42674	D	0.993523	B;B	0.28713	0.22;0.22	B;B	0.33392	0.163;0.163	T	0.23297	-1.0192	10	0.30854	T	0.27	-32.4626	10.2108	0.43138	0.9251:0.0:0.0749:0.0	.	417;417	A4D0U1;O00458	.;IFRD1_HUMAN	V	417;417;152;367;80	ENSP00000005558:I417V;ENSP00000384477:I417V;ENSP00000439188:I367V;ENSP00000435635:I80V	ENSP00000005558:I417V	I	+	1	0	IFRD1	111900135	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.782000	0.75073	2.221000	0.72209	0.519000	0.50382	ATT		0.378	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		G	112112899	A	G	112112899	3	3	99	1	0	0	0	0	1	0	0	0	7574	333	12	4	1291	4	IFRD1	7	112112899	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	8898288	112112899	47025764	88	26564										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135406176	135406176	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aggactccgaagaacgggtaAaggaaggccggcaccagggc	16	10	0	1	rs4596594	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:135406176A>G	ENST00000354042.4	-	2	884	c.195T>C	c.(193-195)ctT>ctC	p.L65L		NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	65					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AGAACGGGTAAAGGAAGGCCG	0.617													G|||	2255	0.45028	0.5091	0.3184	5008	,	,		19216	0.4435		0.4553	False		,,,				2504	0.4663															0			7						G		2277,2129	577.0+/-384.4	599,1079,525	51	44	46		195	3.4	1	7	dbSNP_111	46	3942,4658	601.1+/-394.3	917,2108,1275	no	coding-synonymous	SLC13A4	NM_012450.2		1516,3187,1800	GG,GA,AA		45.8372,48.3205,47.8164		65/627	135406176	6219,6787	2203	4300	6503	135056716	SO:0001819	synonymous_variant	26266			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.195T>C	7.37:g.135406176A>G			135056716	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																				0.617	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		G	135406176	A	G	135406176	2	3	99	1	0	0	0	0	0	0	0	1	14431	1	1	4		4	SLC13A4	7	135406176	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	23293277	135406176	23732487	89	26565										
BRAF	673	hgsc.bcm.edu	37	chr7	140453170	140453170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaaatcacctatttttactgTgaggtcttcatgaagaaata	6	6	3	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:140453170T>C	ENST00000288602.6	-	15	1825	c.1765A>G	c.(1765-1767)Aca>Gca	p.T589A		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	589	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ATTTTTACTGTGAGGTCTTCA	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											98	94	95					7																	140453170		2203	4300	6503	140099639	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1765A>G	7.37:g.140453170T>C	ENSP00000288602:p.Thr589Ala		140099639	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.616302	0.87359	.	.	ENSG00000157764	ENST00000288602	D	0.98958	-5.27	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98451	0.9484	L	0.49640	1.575	0.80722	D	1	P	0.35780	0.52	P	0.51701	0.677	D	0.99846	1.1066	10	0.87932	D	0	.	15.9326	0.79675	0.0:0.0:0.0:1.0	.	589	P15056	BRAF_HUMAN	A	589	ENSP00000288602:T589A	ENSP00000288602:T589A	T	-	1	0	BRAF	140099639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.921000	0.87530	2.169000	0.68431	0.529000	0.55759	ACA		0.383	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140453170	T	C	140453170	3	2	99	1	0	0	0	0	1	0	0	0	1499	1696	59	4	551	4	BRAF	7	140453170	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	5046994	140453170	18685493	90	26566										
MLL3	58508	hgsc.bcm.edu	37	chr7	151962211	151962211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atccaggcacattccatgatAgtgctgaccacaagtagtac	8	11	0	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr7:151962211A>G	ENST00000262189.6	-	8	1314	c.1096T>C	c.(1096-1098)Tat>Cat	p.Y366H	KMT2C_ENST00000355193.2_Missense_Mutation_p.Y366H	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	366					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										ATTCCATGATAGTGCTGACCA	0.448																																																0			7											389	349	362					7																	151962211		2203	4300	6503	151593144	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1096T>C	7.37:g.151962211A>G	ENSP00000262189:p.Tyr366His		151593144	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.024678	0.35701	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.99089	-5.41;-5.41	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38111	U	0.001814	D	0.99180	0.9716	M	0.81682	2.555	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.99406	1.0929	10	0.87932	D	0	.	14.395	0.67005	1.0:0.0:0.0:0.0	.	366	Q8NEZ4	MLL3_HUMAN	H	366	ENSP00000262189:Y366H;ENSP00000347325:Y366H	ENSP00000262189:Y366H	Y	-	1	0	MLL3	151593144	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	9.287000	0.95975	1.843000	0.53566	0.455000	0.32223	TAT		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151962211	A	G	151962211	3	3	99	1	0	0	0	0	1	0	0	0	9652	420	15	4	13847	4	MLL3	7	151962211	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	11509041	151962211	7176452	91	26567										
MYST3	7994	hgsc.bcm.edu	37	chr8	41832338	41832338	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gccatcccagccatcctgatTgtctacatataaaaaaagag	6	11	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:41832338T>C	ENST00000396930.3	-	9	1909	c.1366A>G	c.(1366-1368)Aat>Gat	p.N456D	KAT6A_ENST00000485568.1_Missense_Mutation_p.N456D|KAT6A_ENST00000406337.1_Missense_Mutation_p.N456D|KAT6A_ENST00000265713.2_Missense_Mutation_p.N456D	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	456	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CCATCCTGATTGTCTACATAT	0.348																																																0			8											83	78	80					8																	41832338		2203	4300	6503	41951495	SO:0001583	missense	7994			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1366A>G	8.37:g.41832338T>C	ENSP00000380136:p.Asn456Asp		41951495	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300185	0.60195	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.83914	0.23;0.23;0.23;-1.78	5.68	5.68	0.88126	.	0.268590	0.37261	N	0.002177	D	0.87341	0.6153	L	0.42245	1.32	0.58432	D	0.999993	D;D	0.69078	0.993;0.997	D;D	0.75020	0.971;0.985	D	0.85871	0.1416	10	0.32370	T	0.25	-16.7418	15.9723	0.80031	0.0:0.0:0.0:1.0	.	456;456	A5PLL3;Q92794	.;KAT6A_HUMAN	D	456	ENSP00000265713:N456D;ENSP00000385888:N456D;ENSP00000380136:N456D;ENSP00000430606:N456D	ENSP00000265713:N456D	N	-	1	0	KAT6A	41951495	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.367000	0.79558	2.169000	0.68431	0.529000	0.55759	AAT		0.348	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		C	41832338	T	C	41832338	3	2	99	1	0	0	0	0	1	0	0	0	10134	1812	63	4	4688	4	MYST3	8	41832338	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10		41832338	104531684	92	26568										
FAM164A	51101	hgsc.bcm.edu	37	chr8	79610710	79610710	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggaaacaaacttcagaccttAtctccctctcataaagggat	6	11	3	1	rs1054283	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:79610710A>G	ENST00000263849.4	+	7	768	c.666A>G	c.(664-666)ttA>ttG	p.L222L		NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	222							metal ion binding (GO:0046872)										TTCAGACCTTATCTCCCTCTC	0.343													A|||	3592	0.717252	0.4985	0.7968	5008	,	,		16940	0.8978		0.7157	False		,,,				2504	0.772															0			8						A		2401,2005	615.4+/-392.6	668,1065,470	117	113	114		666	2	1	8	dbSNP_86	114	6317,2283	706.5+/-405.5	2325,1667,308	no	coding-synonymous	FAM164A	NM_016010.2		2993,2732,778	GG,GA,AA		26.5465,45.5061,32.9694		222/326	79610710	8718,4288	2203	4300	6503	79773265	SO:0001819	synonymous_variant	51101				CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"Zinc fingers, C2HC-type containing"	24277	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 70", "family with sequence similarity 164, member A"	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.666A>G	8.37:g.79610710A>G			79773265	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1	1586	0.7261904761904762	244	0.4959349593495935	291	0.8038674033149171	508	0.8881118881118881	543	0.716358839050132	A	6.349	0.432414	0.12045	0.544939	0.734535	ENSG00000104427	ENST00000519307	.	.	.	5.85	2.0	0.26442	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999973996	.	.	.	.	.	.	T	0.15122	-1.0448	3	.	.	.	-4.1446	5.4563	0.16592	0.641:0.1342:0.2248:0.0	rs1054283;rs3194797;rs13258774;rs17418488;rs17845203;rs17858015;rs1054283	.	.	.	V	55	.	.	I	+	1	0	FAM164A	79773265	0.992000	0.36948	0.996000	0.52242	0.666000	0.39218	0.371000	0.20450	0.096000	0.17463	-0.379000	0.06801	ATC		0.343	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		G	79610710	A	G	79610710	2	3	99	1	0	0	0	0	0	0	0	1	5494	446	16	4		4	FAM164A	8	79610710	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	37778372	79610710	66753312	93	26569										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121210069	121210069	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggtcttgcacagtatagtggTgaccccagaatagaatggca	12	8	1	3	rs2305598	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:121210069T>C	ENST00000297848.3	+	7	882	c.612T>C	c.(610-612)ggT>ggC	p.G204G	COL14A1_ENST00000247781.3_Intron|COL14A1_ENST00000537875.1_Silent_p.G204G|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.G204G	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			AGTATAGTGGTGACCCCAGAA	0.408													C|||	3177	0.634385	0.8192	0.6009	5008	,	,		16103	0.6597		0.4622	False		,,,				2504	0.5593															0			8						C		3359,1047	385.1+/-325.6	1310,739,154	122	125	124		612	-6.2	0.6	8	dbSNP_100	124	4124,4476	590.4+/-392.7	1002,2120,1178	no	coding-synonymous	COL14A1	NM_021110.1		2312,2859,1332	CC,CT,TT		47.9535,23.7631,42.465		204/1797	121210069	7483,5523	2203	4300	6503	121279250	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.612T>C	8.37:g.121210069T>C			121279250		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.408	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		C	121210069	T	C	121210069	2	2	99	1	0	0	0	0	0	0	0	1	3677	1683	59	4		4	COL14A1	8	121210069	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	41599359	121210069	25153953	94	26570										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121228679	121228679	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	acccaacttcaagacagatcAatggttatcgaattgtatat	6	8	2	2	rs4870723	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:121228679A>C	ENST00000297848.3	+	14	1957	c.1687A>C	c.(1687-1689)Aat>Cat	p.N563H	COL14A1_ENST00000247781.3_Missense_Mutation_p.N468H|COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.N563H	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			AAGACAGATCAATGGTTATCG	0.408													A|||	2955	0.590056	0.6286	0.5749	5008	,	,		17835	0.6687		0.4702	False		,,,				2504	0.591															0			8						A	HIS/ASN	2536,1870	632.1+/-395.8	757,1022,424	124	115	118		1687	2.8	0	8	dbSNP_111	118	4175,4425	567.4+/-388.8	1034,2107,1159	yes	missense	COL14A1	NM_021110.1	68	1791,3129,1583	CC,CA,AA		48.5465,42.4421,48.4007	benign	563/1797	121228679	6711,6295	2203	4300	6503	121297860	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1687A>C	8.37:g.121228679A>C	ENSP00000297848:p.Asn563His		121297860		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	1247|1247	0.5709706959706959|0.5709706959706959	306|306	0.6219512195121951|0.6219512195121951	212|212	0.585635359116022|0.585635359116022	381|381	0.666083916083916|0.666083916083916	348|348	0.45910290237467016|0.45910290237467016	A|A	10.79|10.79	1.450389|1.450389	0.26074|0.26074	0.575579|0.575579	0.485465|0.485465	ENSG00000187955|ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	T;T;T;T|.	0.57436|.	0.4;0.4;0.4;0.4|.	5.29|5.29	2.85|2.85	0.33270|0.33270	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	1.232880|.	0.05311|.	N|.	0.524871|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25647|0.25647	0.755|0.755	0.51012|0.51012	P|P	9.499999999995623E-5|9.499999999995623E-5	P;B|.	0.35050|.	0.482;0.295|.	P;B|.	0.46172|.	0.506;0.298|.	T|T	0.37820|0.37820	-0.9689|-0.9689	9|4	0.56958|.	D|.	0.05|.	.|.	7.3206|7.3206	0.26526|0.26526	0.8012:0.0:0.0701:0.1287|0.8012:0.0:0.0701:0.1287	rs4870723;rs59507382;rs4870723|rs4870723;rs59507382;rs4870723	563;563|.	Q05707-2;Q05707|.	.;COEA1_HUMAN|.	H|P	563;563;468;376|319	ENSP00000311809:N563H;ENSP00000297848:N563H;ENSP00000247781:N468H;ENSP00000409461:N376H|.	ENSP00000247781:N468H|.	N|Q	+|+	1|2	0|0	COL14A1|COL14A1	121297860|121297860	0.244000|0.244000	0.23889|0.23889	0.010000|0.010000	0.14722|0.14722	0.003000|0.003000	0.03518|0.03518	3.215000|3.215000	0.51169|0.51169	0.435000|0.435000	0.26365|0.26365	0.533000|0.533000	0.62120|0.62120	AAT|CAA		0.408	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		C	121228679	A	C	121228679	3	2	99	1	0	0	0	0	1	0	0	0	3677	130	5	4	1737	4	COL14A1	8	121228679	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	18610	121228679	25135343	95	26571										
EFR3A	23167	hgsc.bcm.edu	37	chr8	132999936	132999936	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agattgtcagttccgtatgtAccacaagtaacaggtaagag	10	7	1	2	rs2270875	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:132999936A>G	ENST00000254624.5	+	18	2277	c.2052A>G	c.(2050-2052)gtA>gtG	p.V684V	EFR3A_ENST00000334503.4_Silent_p.V684V|EFR3A_ENST00000519656.1_Silent_p.V648V	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	684						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.V684V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTCCGTATGTACCACAAGTAA	0.353													A|||	662	0.132188	0.034	0.1513	5008	,	,		15583	0.1587		0.1064	False		,,,				2504	0.2505															1	Substitution - coding silent(1)	stomach(1)	8						A		198,4204	115.4+/-153.4	6,186,2009	93	76	81		2052	-6.3	0.8	8	dbSNP_100	81	1013,7583	201.3+/-244.8	55,903,3340	no	coding-synonymous	EFR3A	NM_015137.4		61,1089,5349	GG,GA,AA		11.7846,4.498,9.3168		684/822	132999936	1211,11787	2201	4298	6499	133069118	SO:0001819	synonymous_variant	23167			D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.2052A>G	8.37:g.132999936A>G			133069118	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																				0.353	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		G	132999936	A	G	132999936	2	3	99	1	0	0	0	0	0	0	0	1	4969	378	14	4		4	EFR3A	8	132999936	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	11771257	132999936	13364086	96	26572										
TG	7038	hgsc.bcm.edu	37	chr8	133931748	133931748	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggcagaacgaccatttctgcTggagctttcagccagactca	10	12	3	2	rs853304	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:133931748T>C	ENST00000220616.4	+	21	4546	c.4506T>C	c.(4504-4506)gcT>gcC	p.A1502A	TG_ENST00000542445.1_5'UTR|TG_ENST00000377869.1_Silent_p.A1502A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1502					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.A1502A(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		CCATTTCTGCTGGAGCTTTCA	0.488													C|||	2373	0.473842	0.351	0.6052	5008	,	,		19290	0.3542		0.6074	False		,,,				2504	0.5327															1	Substitution - coding silent(1)	stomach(1)	8						C		1751,2655	647.4+/-398.5	372,1007,824	148	116	127		4506	-5.8	0	8	dbSNP_86	127	5271,3329	495.1+/-374.0	1638,1995,667	no	coding-synonymous	TG	NM_003235.4		2010,3002,1491	CC,CT,TT		38.7093,39.7413,46.0095		1502/2769	133931748	7022,5984	2203	4300	6503	134000930	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4506T>C	8.37:g.133931748T>C			134000930	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	1037	0.4748168498168498	162	0.32926829268292684	214	0.5911602209944752	195	0.3409090909090909	466	0.6147757255936676	C	0.377	-0.930702	0.02359	0.397413	0.612907	ENSG00000042832	ENST00000519178	.	.	.	5.39	-5.82	0.02333	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20926	P	0.99982814	.	.	.	.	.	.	T	0.38001	-0.9681	3	.	.	.	.	7.4268	0.27105	0.0:0.2113:0.4241:0.3646	rs853304;rs1140939;rs2069560;rs3739272;rs57557910;rs853304	.	.	.	R	22	.	.	W	+	1	0	TG	134000930	0.000000	0.05858	0.003000	0.11579	0.086000	0.17979	-0.618000	0.05578	-1.170000	0.02769	-3.029000	0.00073	TGG		0.488	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133931748	T	C	133931748	2	2	99	1	0	0	0	0	0	0	0	1	15852	1567	55	4		4	TG	8	133931748	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	931812	133931748	12432274	97	26573										
PSCA	8000	hgsc.bcm.edu	37	chr8	143763531	143763531	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgcactcggcctgctgctctGgggacccggccagctctagg	14	15	2	0	rs138377917	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:143763531G>A	ENST00000301258.4	+	3	409	c.326G>A	c.(325-327)tGg>tAg	p.W109*		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	118						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGCTGCTCTGGGGACCCGGC	0.706													G|||	38	0.00758786	8e-04	0.013	5008	,	,		14034	0		0.0258	False		,,,				2504	0.002															0			8						G	stop/TRP	29,4163		1,27,2068	19	22	21		326	3.2	1	8	dbSNP_134	21	287,8139		7,273,3933	yes	stop-gained	PSCA	NM_005672.4		8,300,6001	AA,AG,GG		3.4061,0.6918,2.5044		109/115	143763531	316,12302	2096	4213	6309	143760533	SO:0001587	stop_gained	8000			AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.326G>A	8.37:g.143763531G>A	ENSP00000301258:p.Trp109*		143760533	Q6UW92	Nonsense_Mutation	SNP	ENST00000301258.4	37	CCDS47925.2	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	G	17.42	3.384145	0.61845	0.006918	0.034061	ENSG00000167653	ENST00000301258	.	.	.	3.21	3.21	0.36854	.	0.705245	0.11876	N	0.520920	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1903	0.43021	0.0:0.0:1.0:0.0	.	.	.	.	X	118	.	ENSP00000301258:W118X	W	+	2	0	PSCA	143760533	0.999000	0.42202	0.953000	0.39169	0.012000	0.07955	1.837000	0.39201	2.096000	0.63516	0.563000	0.77884	TGG		0.706	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672		A	143763531	G	A	143763531	4	1	99	1	0	0	0	0	0	1	0	0	12679	1357	47	3	336	3	PSCA	8	143763531	Nonsense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	9831783	143763531	2600491	98	26574										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143996553	143996553	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcttcttcagggcctgggaGaagtccctggccactgcatc	11	13	3	1	rs4546	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:143996553G>A	ENST00000323110.2	-	3	506	c.504C>T	c.(502-504)ttC>ttT	p.F168F		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	168					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	GGGCCTGGGAGAAGTCCCTGG	0.622									Familial Hyperaldosteronism type I				.|||	1730	0.345447	0.1838	0.4697	5008	,	,		19590	0.2867		0.4841	False		,,,				2504	0.3937															0			8						G		1021,3385		122,777,1304	43	39	41		504	1.6	0	8	dbSNP_52	41	3861,4735		876,2109,1313	no	coding-synonymous	CYP11B2	NM_000498.3		998,2886,2617	AA,AG,GG		44.9162,23.1729,37.5481		168/504	143996553	4882,8120	2203	4298	6501	143993555	SO:0001819	synonymous_variant	1585	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.504C>T	8.37:g.143996553G>A			143993555	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																				0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			A	143996553	G	A	143996553	2	1	99	1	0	0	0	0	0	0	0	1	4152	933	33	3		3	CYP11B2	8	143996553	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	233022	143996553	2367469	99	26575										
ADCK5	203054	hgsc.bcm.edu	37	chr8	145603114	145603114	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cactctgctctgctgcacagAaggcagaagccctggccgtc	11	15	2	2	rs6599528	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr8:145603114A>C	ENST00000308860.6	+	2	95	c.51A>C	c.(49-51)agA>agC	p.R17S	ADCK5_ENST00000526231.2_3'UTR|ADCK5_ENST00000532190.1_Missense_Mutation_p.R17S	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	17			R -> S (in dbSNP:rs6599528). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)	p.R17S(1)		endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-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;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGCTGCACAGAAGGCAGAAGC	0.602													C|||	3167	0.632388	0.8101	0.5648	5008	,	,		20220	0.6577		0.4314	False		,,,				2504	0.6207															1	Substitution - Missense(1)	stomach(1)	8						C	SER/ARG	3290,1114	391.2+/-328.0	1218,854,130	64	54	57		51	3.7	0	8	dbSNP_116	57	3755,4845	613.8+/-396.1	826,2103,1371	yes	missense	ADCK5	NM_174922.3	110	2044,2957,1501	CC,CA,AA		43.6628,25.2952,45.8244	benign	17/581	145603114	7045,5959	2202	4300	6502	145573922	SO:0001583	missense	203054			BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.51A>C	8.37:g.145603114A>C	ENSP00000310547:p.Arg17Ser		145573922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Missense_Mutation	SNP	ENST00000308860.6	37	CCDS34965.1	1275	0.5837912087912088	387	0.7865853658536586	201	0.5552486187845304	369	0.6451048951048951	318	0.41952506596306066	C	0.157	-1.085760	0.01873	0.747048	0.436628	ENSG00000173137	ENST00000308860;ENST00000532190	T;T	0.74421	-0.84;0.92	4.55	3.68	0.42216	.	0.917523	0.09037	N	0.857810	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42582	-0.9443	9	0.07175	T	0.84	-5.5209	5.77	0.18247	0.1918:0.7078:0.0:0.1004	rs6599528;rs61015944;rs6599528	17	Q3MIX3	ADCK5_HUMAN	S	17	ENSP00000310547:R17S;ENSP00000435155:R17S	ENSP00000310547:R17S	R	+	3	2	ADCK5	145573922	0.127000	0.22367	0.001000	0.08648	0.279000	0.26890	2.275000	0.43399	0.389000	0.25086	-0.975000	0.02590	AGA		0.602	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922		C	145603114	A	C	145603114	3	2	99	1	0	0	0	0	1	0	0	0	291	243	9	4	57	4	ADCK5	8	145603114	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1606561	145603114	760908	100	26576										
IFNA5	3442	hgsc.bcm.edu	37	chr9	21304926	21304926	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcagctgctggtaaagttcAgtgtagaatttgtctagaag	11	5	3	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr9:21304926A>G	ENST00000259555.4	-	1	386	c.330T>C	c.(328-330)acT>acC	p.T110T		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	110					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GGTAAAGTTCAGTGTAGAATT	0.468																																																0			9											119	116	117					9																	21304926		2203	4300	6503	21294926	SO:0001819	synonymous_variant	3442				CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"Interferons"	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.330T>C	9.37:g.21304926A>G			21294926	Q52LX3	Silent	SNP	ENST00000259555.4	37	CCDS6502.1																																																																																				0.468	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169		G	21304926	A	G	21304926	2	3	99	1	0	0	0	0	0	0	0	1	7561	175	7	4		4	IFNA5	9	21304926	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10		21304926	119908505	101	26577										
AQP3	360	hgsc.bcm.edu	37	chr9	33447424	33447424	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cggctccctccactcaccacCaggatgagggtccccaggca	10	18	1	1	rs591810	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr9:33447424C>G	ENST00000297991.4	-	1	185	c.105G>C	c.(103-105)ctG>ctC	p.L35L	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	35					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CACTCACCACCAGGATGAGGG	0.647													G|||	3712	0.741214	0.7837	0.83	5008	,	,		13427	0.7629		0.7286	False		,,,				2504	0.6115															0			9						G		3484,898		1401,682,108	21	24	23		105	2.7	1	9	dbSNP_83	23	6151,2445		2244,1663,391	no	coding-synonymous	AQP3	NM_004925.4		3645,2345,499	GG,GC,CC		28.4435,20.4929,25.759		35/293	33447424	9635,3343	2191	4298	6489	33437424	SO:0001819	synonymous_variant	360				CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.105G>C	9.37:g.33447424C>G			33437424	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	37	CCDS6542.1																																																																																				0.647	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		G	33447424	C	G	33447424	2	3	99	1	0	0	0	0	0	0	0	1	827	581	21	5		5	AQP3	9	33447424	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	12142498	33447424	107766007	102	26578										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113275227	113275227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tctgcagtagctctctgaacCggaccacaaaccattgggta	9	12	2	1	rs10980419	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr9:113275227C>T	ENST00000401783.2	-	5	1618	c.1282G>A	c.(1282-1284)Ggt>Agt	p.G428S	SVEP1_ENST00000302728.8_Missense_Mutation_p.G428S|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.G405S|SVEP1_ENST00000374461.1_Missense_Mutation_p.G405S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	428	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		G -> S (in dbSNP:rs10980419).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CTCTCTGAACCGGACCACAAA	0.443													C|||	207	0.0413339	0.0023	0.0086	5008	,	,		17993	0.1071		0.0169	False		,,,				2504	0.0746															0			9						C	SER/GLY	22,3858		0,22,1918	99	94	96		1282	2.2	0.4	9	dbSNP_120	96	224,8054		3,218,3918	yes	missense	SVEP1	NM_153366.3	56	3,240,5836	TT,TC,CC		2.706,0.567,2.0234	benign	428/3572	113275227	246,11912	1940	4139	6079	112315048	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1282G>A	9.37:g.113275227C>T	ENSP00000384917:p.Gly428Ser		112315048	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	83	0.038003663003663	1	0.0020325203252032522	2	0.0055248618784530384	65	0.11363636363636363	15	0.01978891820580475	C	21.0	4.077805	0.76528	0.00567	0.02706	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.99	2.19	0.27852	Complement control module (2);Growth factor, receptor (1);Sushi/SCR/CCP (3);	0.097518	0.64402	N	0.000001	T	0.00784	0.0026	M	0.81682	2.555	0.41592	D	0.988807	P;P;D;B	0.55172	0.856;0.721;0.97;0.449	B;B;P;B	0.49922	0.333;0.234;0.626;0.15	T	0.00091	-1.2084	10	0.42905	T	0.14	.	10.2762	0.43512	0.0:0.7396:0.0:0.2604	rs10980419;rs52828370;rs10980419	428;428;428;428	E9PBN8;Q4LDE5;B3KV07;Q4LDE5-2	.;SVEP1_HUMAN;.;.	S	428;405;428;405	ENSP00000384917:G428S;ENSP00000363593:G405S;ENSP00000304118:G428S;ENSP00000363585:G405S	ENSP00000304118:G428S	G	-	1	0	SVEP1	112315048	0.993000	0.37304	0.429000	0.26710	0.916000	0.54674	3.077000	0.50089	0.152000	0.19188	-0.136000	0.14681	GGT		0.443	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113275227	C	T	113275227	3	4	99	1	0	0	0	0	1	0	0	0	15459	652	23	1	9609	1	SVEP1	9	113275227	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	79827803	113275227	27938204	103	26579										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22675815	22675815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaagcattctccagagttagCacagacagtagtggatgcag	11	8	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:22675815C>T	ENST00000376624.3	+	5	747	c.605C>T	c.(604-606)gCa>gTa	p.A202V	SPAG6_ENST00000376603.2_Missense_Mutation_p.A278V|SPAG6_ENST00000313311.6_Missense_Mutation_p.A202V|SPAG6_ENST00000376601.1_Intron|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Missense_Mutation_p.A177V	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	202					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						CCAGAGTTAGCACAGACAGTA	0.423																																																0			10											112	106	108					10																	22675815		2203	4300	6503	22715821	SO:0001583	missense	9576			AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.605C>T	10.37:g.22675815C>T	ENSP00000365811:p.Ala202Val		22715821	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	37	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980249	0.53827	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311	T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37	5.6	4.7	0.59300	Armadillo-like helical (1);Armadillo-type fold (1);	0.046053	0.85682	N	0.000000	D	0.84032	0.5383	M	0.88241	2.94	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.994;0.998;0.999	D	0.87380	0.2356	10	0.72032	D	0.01	-20.0511	14.7982	0.69894	0.0:0.9307:0.0:0.0693	.	177;278;202;202	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	V	202;278;177;202	ENSP00000365811:A202V;ENSP00000365788:A278V;ENSP00000441325:A177V;ENSP00000323599:A202V	ENSP00000323599:A202V	A	+	2	0	SPAG6	22715821	1.000000	0.71417	0.718000	0.30602	0.067000	0.16453	5.971000	0.70440	1.509000	0.48786	-0.253000	0.11424	GCA		0.423	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			T	22675815	C	T	22675815	3	4	99	1	0	0	0	0	1	0	0	0	15021	710	25	3	623	3	SPAG6	10	22675815	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		22675815	112858932	104	26580										
MYPN	84665	hgsc.bcm.edu	37	chr10	69955237	69955237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gctgttctggccacttgatgGtacaaagtttgcccattcgc	10	11	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:69955237G>A	ENST00000358913.5	+	15	3594	c.3106G>A	c.(3106-3108)Gta>Ata	p.V1036I	MYPN_ENST00000354393.2_Missense_Mutation_p.V761I|MYPN_ENST00000540630.1_Missense_Mutation_p.V1036I	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1036	Interaction with ACTN.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCACTTGATGGTACAAAGTTT	0.428																																																0			10											104	99	101					10																	69955237		2203	4300	6503	69625243	SO:0001583	missense	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.3106G>A	10.37:g.69955237G>A	ENSP00000351790:p.Val1036Ile		69625243	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.473457	0.84640	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.74209	-0.82;-0.82;-0.82	5.45	4.53	0.55603	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.069454	0.56097	D	0.000022	D	0.84279	0.5437	M	0.68728	2.09	0.80722	D	1	B;B;D	0.61080	0.403;0.403;0.989	B;B;D	0.79784	0.255;0.255;0.993	D	0.84611	0.0678	9	.	.	.	.	15.753	0.78001	0.0:0.0:0.8622:0.1378	.	1036;761;1036	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	I	761;761;1036;1036	ENSP00000346369:V761I;ENSP00000351790:V1036I;ENSP00000441668:V1036I	.	V	+	1	0	MYPN	69625243	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.514000	0.81750	1.401000	0.46761	0.655000	0.94253	GTA		0.428	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		A	69955237	G	A	69955237	3	1	99	1	0	0	0	0	1	0	0	0	10128	1261	44	3	3160	3	MYPN	10	69955237	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	47279422	69955237	65579510	105	26581										
CDH23	64072	hgsc.bcm.edu	37	chr10	73537647	73537647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcgtcaacaccttccgcatcGacagacacatggtcagcagc	8	15	2	1	rs373836924		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:73537647G>A	ENST00000224721.6	+	38	5076	c.5071G>A	c.(5071-5073)Gac>Aac	p.D1691N		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1686	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTTCCGCATCGACAGACACAT	0.572																																																0			10						G	ASN/ASP	2,4364		0,2,2181	68	62	64		5056	-11	0	10		64	0,8566		0,0,4283	no	missense	CDH23	NM_022124.5	23	0,2,6464	AA,AG,GG		0.0,0.0458,0.0155	benign	1686/3355	73537647	2,12930	2183	4283	6466	73207653	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5071G>A	10.37:g.73537647G>A	ENSP00000224721:p.Asp1691Asn		73207653	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	1.228	-0.624899	0.03636	4.58E-4	0.0	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.76	-11.0	0.00169	Cadherin (4);Cadherin-like (1);	0.771452	0.12391	N	0.472978	T	0.36276	0.0961	N	0.25957	0.775	0.36264	D	0.854752	B	0.02656	0.0	B	0.09377	0.004	T	0.31943	-0.9925	9	0.16420	T	0.52	.	17.3357	0.87280	0.7526:0.0767:0.1708:0.0	.	1686	Q9H251	CAD23_HUMAN	N	1691;1686;1689	.	ENSP00000224721:D1691N	D	+	1	0	CDH23	73207653	0.000000	0.05858	0.000000	0.03702	0.546000	0.35178	-0.837000	0.04377	-2.988000	0.00280	-1.202000	0.01658	GAC		0.572	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73537647	G	A	73537647	3	1	99	1	0	0	0	0	1	0	0	0	3114	1058	37	1	5551	1	CDH23	10	73537647	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	3582410	73537647	61997100	106	26582										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767717	73767717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cccgggccgtgctggcctcgCgcatggtggccttcgccggc	16	17	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:73767717C>T	ENST00000373115.4	+	3	1365	c.928C>T	c.(928-930)Cgc>Tgc	p.R310C		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	310					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GCTGGCCTCGCGCATGGTGGC	0.706																																																0			10											5	6	6					10																	73767717		1901	3742	5643	73437723	SO:0001583	missense	9469			AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.928C>T	10.37:g.73767717C>T	ENSP00000362207:p.Arg310Cys		73437723	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	37	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837978	0.91117	.	.	ENSG00000122863	ENST00000373115	T	0.81415	-1.49	5.55	5.55	0.83447	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.92374	0.7580	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93801	0.7101	10	0.87932	D	0	-27.1064	18.5034	0.90889	0.0:1.0:0.0:0.0	.	310	Q7LGC8	CHST3_HUMAN	C	310	ENSP00000362207:R310C	ENSP00000362207:R310C	R	+	1	0	CHST3	73437723	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.724000	0.61972	2.630000	0.89119	0.561000	0.74099	CGC		0.706	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		T	73767717	C	T	73767717	3	4	99	1	0	0	0	0	1	0	0	0	3411	768	27	1	934	1	CHST3	10	73767717	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	230070	73767717	61767030	107	26583										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624289	89624289	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agatatcaagaggatggattCgacttagacttgacctgtat	10	6	1	4			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:89624289C>T	ENST00000371953.3	+	1	1420	c.63C>T	c.(61-63)ttC>ttT	p.F21F	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	21	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Y16fs*21(1)|p.R14_D22del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGGATGGATTCGACTTAGACT	0.468		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Unknown(13)|Deletion - In frame(1)|Deletion - Frameshift(1)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|endometrium(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											177	168	171					10																	89624289		2203	4300	6503	89614269	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.63C>T	10.37:g.89624289C>T			89614269	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.468	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624289	C	T	89624289	2	4	99	1	0	0	0	0	0	0	0	1	12772	883	31	1		1	PTEN	10	89624289	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	15856572	89624289	45910458	108	26584										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692850	89692850	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtgaagatcttgaccaatggCtaagtgaagatgacaatcat	10	6	2	6			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:89692850C>T	ENST00000371953.3	+	5	1691	c.334C>T	c.(334-336)Cta>Tta	p.L112L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	112	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		L -> P (in CWS1 and LDD; loss of phosphatase activity towards Ins(1,3,4,5)P4). {ECO:0000269|PubMed:10051160, ECO:0000269|PubMed:9600246}.|L -> R (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.L112V(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TGACCAATGGCTAAGTGAAGA	0.388		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	55	Whole gene deletion(37)|Deletion - Frameshift(8)|Substitution - Missense(5)|Unknown(5)	prostate(16)|central_nervous_system(13)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10	GRCh37	CM031337	PTEN	S							128	118	121					10																	89692850		2203	4297	6500	89682830	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.334C>T	10.37:g.89692850C>T			89682830	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.388	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89692850	C	T	89692850	2	4	99	1	0	0	0	0	0	0	0	1	12772	796	28	3		3	PTEN	10	89692850	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	68561	89692850	45841897	109	26585										
CHUK	1147	hgsc.bcm.edu	37	chr10	101978563	101978563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaatatacactttggatcctTcttcttaatcttctcatgcc	3	11	4	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr10:101978563T>C	ENST00000370397.7	-	8	795	c.709A>G	c.(709-711)Aag>Gag	p.K237E		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.K237Q(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TTTGGATCCTTCTTCTTAATC	0.323																																					Ovarian(159;52 1904 10536 35305 37148)											1	Substitution - Missense(1)	ovary(1)	10											117	110	112					10																	101978563		2203	4300	6503	101968553	SO:0001583	missense	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.709A>G	10.37:g.101978563T>C	ENSP00000359424:p.Lys237Glu		101968553	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	37	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.509966	0.85282	.	.	ENSG00000213341	ENST00000370397	T	0.64618	-0.11	5.92	5.92	0.95590	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74473	0.3721	L	0.52364	1.645	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.76761	-0.2840	10	0.87932	D	0	-16.8521	14.3262	0.66523	0.0:0.0:0.0:1.0	.	237	O15111	IKKA_HUMAN	E	237	ENSP00000359424:K237E	ENSP00000359424:K237E	K	-	1	0	CHUK	101968553	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.661000	0.83786	2.263000	0.75096	0.533000	0.62120	AAG		0.323	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101978563	T	C	101978563	3	2	99	1	0	0	0	0	1	0	0	0	3422	1792	62	4	1584	4	CHUK	10	101978563	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	12285713	101978563	33556184	110	26586										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	720197	720197	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgcaggtgaacgaccagtcgCtgcggctgctggacatcgag	15	11	0	1	rs3087546	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:720197C>T	ENST00000533256.1	+	6	676	c.301C>T	c.(301-303)Ctg>Ttg	p.L101L	EPS8L2_ENST00000530636.1_Silent_p.L101L|EPS8L2_ENST00000526198.1_Silent_p.L101L|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Silent_p.L101L			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	101	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGACCAGTCGCTGCGGCTGCT	0.657													C|||	2463	0.491813	0.5651	0.647	5008	,	,		17050	0.2222		0.5457	False		,,,				2504	0.5051															0			11						C		2361,2045	601.6+/-389.7	622,1117,464	58	49	52		301	0.3	0.4	11	dbSNP_102	52	5037,3563	623.5+/-397.5	1480,2077,743	no	coding-synonymous	EPS8L2	NM_022772.3		2102,3194,1207	TT,TC,CC		41.4302,46.414,43.1186		101/716	720197	7398,5608	2203	4300	6503	710197	SO:0001819	synonymous_variant	64787			AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.301C>T	11.37:g.720197C>T			710197	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																				0.657	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		T	720197	C	T	720197	2	4	99	1	0	0	0	0	0	0	0	1	5209	796	28	3		3	EPS8L2	11	720197	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10		720197	134286319	111	26587										
OR51A7	119687	hgsc.bcm.edu	37	chr11	4928866	4928866	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agggtcttcttgttcaatgcCatgggaatttcacctaatgc	9	9	4	0	rs7941509	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:4928866C>T	ENST00000359350.4	+	1	267	c.267C>T	c.(265-267)gcC>gcT	p.A89A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTTCAATGCCATGGGAATTT	0.453													C|||	1995	0.398363	0.2625	0.3919	5008	,	,		21957	0.0804		0.6143	False		,,,				2504	0.6922															0			11						C		1333,3069	445.7+/-347.8	197,939,1065	153	131	138		267	-2.3	0.2	11	dbSNP_116	138	5302,3294	646.7+/-400.3	1637,2028,633	no	coding-synonymous	OR51A7	NM_001004749.1		1834,2967,1698	TT,TC,CC		38.3201,30.2817,48.9537		89/313	4928866	6635,6363	2201	4298	6499	4885442	SO:0001819	synonymous_variant	119687			AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.267C>T	11.37:g.4928866C>T			4885442	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																				0.453	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		T	4928866	C	T	4928866	2	4	99	1	0	0	0	0	0	0	0	1	11119	581	21	3		3	OR51A7	11	4928866	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	4208669	4928866	130077650	112	26588										
MUC15	143662	hgsc.bcm.edu	37	chr11	26584680	26584680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tacctggttcatttctgtcgTcataaagtcgccgatgggaa	10	9	3	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:26584680T>C	ENST00000455601.2	-	3	945	c.827A>G	c.(826-828)gAc>gGc	p.D276G	ANO3_ENST00000531568.1_Intron|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000529533.1_Missense_Mutation_p.D303G|ANO3_ENST00000529242.1_3'UTR|ANO3_ENST00000256737.3_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.D303G|MUC15_ENST00000281268.8_Intron|MUC15_ENST00000527569.1_Intron|ANO3_ENST00000537978.1_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	276					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						ATTTCTGTCGTCATAAAGTCG	0.403																																																0			11											91	92	92					11																	26584680		2203	4300	6503	26541256	SO:0001583	missense	143662			AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"Mucins"	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.827A>G	11.37:g.26584680T>C	ENSP00000397339:p.Asp276Gly		26541256	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.696186	0.68386	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000529533	T;T;T	0.47869	0.87;0.83;0.83	4.52	4.52	0.55395	.	0.000000	0.51477	D	0.000083	T	0.55386	0.1917	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.59820	-0.7382	10	0.72032	D	0.01	-5.892	13.1013	0.59222	0.0:0.0:0.0:1.0	.	276;303	Q8N387;E9PII6	MUC15_HUMAN;.	G	276;303;303	ENSP00000397339:D276G;ENSP00000416753:D303G;ENSP00000431983:D303G	ENSP00000416753:D303G	D	-	2	0	MUC15	26541256	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	4.557000	0.60782	1.787000	0.52448	0.528000	0.53228	GAC		0.403	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		C	26584680	T	C	26584680	3	2	99	1	0	0	0	0	1	0	0	0	10002	1667	58	4	185	4	MUC15	11	26584680	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	21655814	26584680	108421836	113	26589										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33596419	33596419	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttgtccttctgcaagctgacCgtaagggaatggtcttttta	10	8	2	1	rs558721492		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:33596419C>T	ENST00000321505.4	+	9	3691	c.3511C>T	c.(3511-3513)Ccc>Tcc	p.P1171S	KIAA1549L_ENST00000389726.3_Splice_Site_p.P1177S|KIAA1549L_ENST00000265654.5_Splice_Site_p.P1177S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1171						integral component of membrane (GO:0016021)											GCAAGCTGACCGTAAGGGAAT	0.433																																																0			11											138	131	133					11																	33596419		1991	4169	6160	33552995	SO:0001630	splice_region_variant	25758			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3511+1C>T	11.37:g.33596419C>T			33552995	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.503560	0.85176	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.	.	.	5.6	5.6	0.85130	.	0.049055	0.85682	D	0.000000	T	0.80444	0.4624	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81680	-0.0823	9	0.72032	D	0.01	-18.9313	19.6091	0.95594	0.0:1.0:0.0:0.0	.	1177;1177	E9PAT2;Q6ZVL6-2	.;.	S	1171;1177;1177;1010	.	ENSP00000265654:P1177S	P	+	1	0	C11orf41	33552995	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.602000	0.61098	2.650000	0.89964	0.655000	0.94253	CCC		0.433	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	Missense_Mutation	T	33596419	C	T	33596419	5	4	99	1	0	0	0	0	0	0	1	0	1644	666	23	1	3563	1	C11orf41	11	33596419	Splice_Site	SNP	C	TCGA-DC-6681-01A-11D-1826-10	7011739	33596419	101410097	114	26590										
VPS37C	55048	hgsc.bcm.edu	37	chr11	60899364	60899364	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcgggcccggggggataaggGggctgcaggggcactgaggg	24	8	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:60899364G>A	ENST00000301765.5	-	5	1228	c.996C>T	c.(994-996)ccC>ccT	p.P332P		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	332	Pro-rich.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						GGGGATAAGGGGGCTGCAGGG	0.682																																																0			11											20	19	19					11																	60899364		1951	3827	5778	60655940	SO:0001819	synonymous_variant	55048			AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.996C>T	11.37:g.60899364G>A			60655940	Q8N3K4	Silent	SNP	ENST00000301765.5	37	CCDS31573.1																																																																																				0.682	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966		A	60899364	G	A	60899364	2	1	99	1	0	0	0	0	0	0	0	1	17247	1219	43	3		3	VPS37C	11	60899364	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	27302945	60899364	74107152	115	26591										
ROM1	6094	hgsc.bcm.edu	37	chr11	62381808	62381808	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgcaacccccactcaccccgGccttgcctgcaaaaccgtct	6	20	2	0	rs1801144	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:62381808G>C	ENST00000278833.3	+	2	1210	c.669G>C	c.(667-669)cgG>cgC	p.R223R	EML3_ENST00000494176.2_5'Flank|EML3_ENST00000529309.1_5'Flank|ROM1_ENST00000534093.1_Missense_Mutation_p.G14A|EML3_ENST00000394773.2_5'Flank|EML3_ENST00000278845.4_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	223					camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						ACTCACCCCGGCCTTGCCTGC	0.597													G|||	863	0.172324	0.1203	0.1988	5008	,	,		17343	0.0427		0.3161	False		,,,				2504	0.2096															0			11						G		689,3715	287.8+/-279.5	51,587,1564	130	125	127		669	1.5	1	11	dbSNP_89	127	3096,5502	473.0+/-368.5	562,1972,1765	no	coding-synonymous	ROM1	NM_000327.3		613,2559,3329	CC,CG,GG		36.0084,15.6449,29.1109		223/352	62381808	3785,9217	2202	4299	6501	62138384	SO:0001819	synonymous_variant	6094			L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"Tetraspanins"	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.669G>C	11.37:g.62381808G>C			62138384	B2R978	Silent	SNP	ENST00000278833.3	37	CCDS8024.1	419	0.19184981684981686	69	0.1402439024390244	85	0.23480662983425415	28	0.04895104895104895	237	0.31266490765171506	G	11.13	1.548416	0.27652	0.156449	0.360084	ENSG00000149489	ENST00000525801;ENST00000534093;ENST00000525947	.	.	.	5.38	1.46	0.22682	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.29058	-1.0024	4	0.87932	D	0	-15.2781	8.048	0.30562	0.3405:0.0:0.6595:0.0	rs1801144;rs17845151;rs17857955;rs61654907;rs1801144	.	.	.	A	14	.	ENSP00000433566:G14A	G	+	2	0	ROM1	62138384	0.997000	0.39634	1.000000	0.80357	0.939000	0.58152	0.287000	0.18920	0.266000	0.21894	0.462000	0.41574	GGC		0.597	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327		C	62381808	G	C	62381808	2	2	99	1	0	0	0	0	0	0	0	1	13558	1190	42	5		5	ROM1	11	62381808	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	1482444	62381808	72624708	116	26592										
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64814952	64814952	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggggcgcctgctcacccggtCataggtataggcaatgtcca	13	12	2	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:64814952C>G	ENST00000358658.3	-	13	1621	c.1594G>C	c.(1594-1596)Gac>Cac	p.D532H	RN7SL114P_ENST00000582042.1_RNA|NAALADL1_ENST00000355721.3_Missense_Mutation_p.D491H|NAALADL1_ENST00000355369.2_Intron|NAALADL1_ENST00000528884.1_Intron|NAALADL1_ENST00000356632.3_Missense_Mutation_p.D497H|NAALADL1_ENST00000340252.4_Missense_Mutation_p.D583H|NAALADL1_ENST00000339885.2_Intron|NAALADL1_ENST00000526799.1_Intron	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	532	NAALADase.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						CTCACCCGGTCATAGGTATAG	0.602																																																0			11											49	41	44					11																	64814952		2193	4285	6478	64571528	SO:0001583	missense	10004			AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1594G>C	11.37:g.64814952C>G	ENSP00000351484:p.Asp532His		64571528	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	37	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152122	0.57259	.	.	ENSG00000168060	ENST00000358658;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632;ENST00000530139	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	4.25	4.25	0.50352	Peptidase M28 (1);	0.000000	0.85682	D	0.000000	T	0.61135	0.2323	M	0.67517	2.055	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.63765	-0.6563	10	0.52906	T	0.07	-26.5802	14.1727	0.65519	0.0:1.0:0.0:0.0	.	532	Q9UQQ1	NALDL_HUMAN	H	532;532;583;491;497;8	ENSP00000351484:D532H;ENSP00000344244:D583H;ENSP00000347955:D491H;ENSP00000349045:D497H;ENSP00000434233:D8H	ENSP00000344244:D583H	D	-	1	0	NAALADL1	64571528	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	6.376000	0.73141	2.203000	0.70933	0.455000	0.32223	GAC		0.602	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		G	64814952	C	G	64814952	3	3	99	1	0	0	0	0	1	0	0	0	10159	826	29	5	652	5	NAALADL1	11	64814952	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	2433144	64814952	70191564	117	26593										
RSF1	51773	hgsc.bcm.edu	37	chr11	77386126	77386126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcctcctcttcatcatcatCggaatattttttctttgggg	6	10	5	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:77386126C>T	ENST00000308488.6	-	14	3819	c.3517G>A	c.(3517-3519)Gat>Aat	p.D1173N	RSF1_ENST00000360355.2_Missense_Mutation_p.D1142N|RSF1_ENST00000480887.1_Missense_Mutation_p.D921N			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1173	Arg-rich.				CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	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)			TCATCATCATCGGAATATTTT	0.413																																																0			11											123	119	120					11																	77386126		2200	4292	6492	77063774	SO:0001583	missense	51773			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3517G>A	11.37:g.77386126C>T	ENSP00000311513:p.Asp1173Asn		77063774	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	C	31	5.094334	0.94149	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355	D;D;D	0.85411	-1.94;-1.98;-1.94	4.97	4.97	0.65823	.	0.000000	0.53938	D	0.000055	D	0.86112	0.5855	L	0.34521	1.04	0.51767	D	0.999935	D	0.71674	0.998	P	0.55011	0.766	D	0.87755	0.2594	10	0.66056	D	0.02	-17.5344	18.0282	0.89275	0.0:1.0:0.0:0.0	.	1173	Q96T23	RSF1_HUMAN	N	1173;921;1142	ENSP00000311513:D1173N;ENSP00000434509:D921N;ENSP00000353511:D1142N	ENSP00000311513:D1173N	D	-	1	0	RSF1	77063774	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	6.262000	0.72514	2.575000	0.86900	0.650000	0.86243	GAT		0.413	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		T	77386126	C	T	77386126	3	4	99	1	0	0	0	0	1	0	0	0	13736	884	31	1	820	1	RSF1	11	77386126	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	12571174	77386126	57620390	118	26594										
GAB2	9846	hgsc.bcm.edu	37	chr11	77930449	77930449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cttctcatcagaggtgacggAtgaagtagatggctgagggg	16	6	2	5			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:77930449A>G	ENST00000361507.4	-	10	1985	c.1900T>C	c.(1900-1902)Tcc>Ccc	p.S634P	GAB2_ENST00000340149.2_Missense_Mutation_p.S596P	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	634					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GAGGTGACGGATGAAGTAGAT	0.567																																																0			11											120	97	105					11																	77930449		2200	4292	6492	77608097	SO:0001583	missense	9846			AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1900T>C	11.37:g.77930449A>G	ENSP00000354952:p.Ser634Pro		77608097	A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	37	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	A	33	5.282382	0.95489	.	.	ENSG00000033327	ENST00000340149;ENST00000361507	T;T	0.25085	1.82;1.82	5.35	5.35	0.76521	.	0.000000	0.85682	U	0.000000	T	0.51822	0.1697	M	0.76328	2.33	0.58432	D	0.999999	D	0.76494	0.999	D	0.75484	0.986	T	0.55792	-0.8085	10	0.66056	D	0.02	-13.1684	15.6396	0.76984	1.0:0.0:0.0:0.0	.	634	Q9UQC2	GAB2_HUMAN	P	596;634	ENSP00000343959:S596P;ENSP00000354952:S634P	ENSP00000343959:S596P	S	-	1	0	GAB2	77608097	1.000000	0.71417	0.109000	0.21407	0.971000	0.66376	8.910000	0.92685	2.150000	0.67090	0.383000	0.25322	TCC		0.567	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		G	77930449	A	G	77930449	3	3	99	1	0	0	0	0	1	0	0	0	6168	333	12	4	134	4	GAB2	11	77930449	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	544323	77930449	57076067	119	26595										
ANKK1	255239	hgsc.bcm.edu	37	chr11	113270789	113270789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggacacccgcccacctggccGccctcaagggcaacacagcc	10	20	1	0	rs374434021		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:113270789G>A	ENST00000303941.3	+	8	2192	c.2098G>A	c.(2098-2100)Gcc>Acc	p.A700T		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	700							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		CCACCTGGCCGCCCTCAAGGG	0.627																																																0			11						G	THR/ALA	0,4036		0,0,2018	30	35	33		2098	1.6	0	11		33	1,8343		0,1,4171	no	missense	ANKK1	NM_178510.1	58	0,1,6189	AA,AG,GG		0.012,0.0,0.0081	probably-damaging	700/766	113270789	1,12379	2018	4172	6190	112775999	SO:0001583	missense	255239			AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.2098G>A	11.37:g.113270789G>A	ENSP00000306678:p.Ala700Thr		112775999		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	G	9.628	1.135634	0.21123	0.0	1.2E-4	ENSG00000170209	ENST00000303941	T	0.72051	-0.62	4.53	1.63	0.23807	Ankyrin repeat-containing domain (3);	0.122146	0.36444	N	0.002599	T	0.79064	0.4383	M	0.79926	2.475	0.09310	N	0.999998	D	0.89917	1.0	P	0.61070	0.883	T	0.69113	-0.5231	10	0.36615	T	0.2	-11.8511	9.5778	0.39468	0.0884:0.1289:0.7828:0.0	.	700	Q8NFD2	ANKK1_HUMAN	T	700	ENSP00000306678:A700T	ENSP00000306678:A700T	A	+	1	0	ANKK1	112775999	0.019000	0.18553	0.034000	0.17996	0.025000	0.11179	1.793000	0.38764	0.183000	0.20059	-1.130000	0.01982	GCC		0.627	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		A	113270789	G	A	113270789	3	1	99	1	0	0	0	0	1	0	0	0	631	1087	38	1	2128	1	ANKK1	11	113270789	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	35340340	113270789	21735727	120	26596										
APOA4	337	hgsc.bcm.edu	37	chr11	116691634	116691634	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgctcctgctgctgctcctgCtgctgttcctgctgttgctc	10	15	0	0	rs5110	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:116691634C>A	ENST00000357780.3	-	3	1254	c.1140G>T	c.(1138-1140)caG>caT	p.Q380H		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	380	Gln/Glu-rich.		Q -> H (in allele APOA-IV*2 and allele APOA-IV*0A; associated with E-187 in allele APOA-IV*0A; dbSNP:rs5110). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15108119, ECO:0000269|PubMed:1677358, ECO:0000269|PubMed:2065039, ECO:0000269|PubMed:2351649, ECO:0000269|PubMed:3036793, ECO:0000269|PubMed:3080432}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		gctgctcctgctgctgttcct	0.612													C|||	119	0.023762	0.0038	0.0418	5008	,	,		19562	0		0.0656	False		,,,				2504	0.0194															0			11	GRCh37	CM984162	APOA4	M	rs5110	C	HIS/GLN	78,4324	68.7+/-106.4	1,76,2124	54	47	50	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1140	0.1	0.1	11	dbSNP_52	50	712,7876	174.9+/-225.1	24,664,3606	yes	missense	APOA4	NM_000482.3	24	25,740,5730	AA,AC,CC		8.2906,1.7719,6.0816	benign	380/397	116691634	790,12200	2201	4294	6495	116196844	SO:0001583	missense	337				CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"Apolipoproteins"	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.1140G>T	11.37:g.116691634C>A	ENSP00000350425:p.Gln380His		116196844	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	72	0.03296703296703297	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	49	0.06464379947229551	C	4.510	0.094555	0.08632	0.017719	0.082906	ENSG00000110244	ENST00000357780	T	0.74106	-0.81	1.25	0.139	0.14798	.	.	.	.	.	T	0.05090	0.0136	N	0.22421	0.69	0.09310	N	1	B	0.24533	0.105	B	0.20955	0.032	T	0.02471	-1.1154	9	0.20046	T	0.44	.	4.2239	0.10572	0.4256:0.5744:0.0:0.0	rs5110;rs3181830;rs9282881;rs17250981;rs5110	380	P06727	APOA4_HUMAN	H	380	ENSP00000350425:Q380H	ENSP00000350425:Q380H	Q	-	3	2	APOA4	116196844	0.000000	0.05858	0.111000	0.21465	0.022000	0.10575	-0.722000	0.04958	0.041000	0.15688	0.460000	0.39030	CAG		0.612	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		A	116691634	C	A	116691634	3	1	99	1	0	0	0	0	1	0	0	0	783	796	28	2	54	2	APOA4	11	116691634	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	3420845	116691634	18314882	121	26597										
APOA4	337	hgsc.bcm.edu	37	chr11	116691861	116691861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cccgtagggctccacccggcGtcggaactcctccacctgct	10	19	0	0	rs150264487		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:116691861G>T	ENST00000357780.3	-	3	1027	c.913C>A	c.(913-915)Cgc>Agc	p.R305S		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	305	13 X 22 AA approximate tandem repeats.		R -> C (in Budapest-1). {ECO:0000269|PubMed:7728150}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		TCCACCCGGCGTCGGAACTCC	0.647																																																0			11											45	49	47					11																	116691861		2201	4292	6493	116197071	SO:0001583	missense	337				CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"Apolipoproteins"	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.913C>A	11.37:g.116691861G>T	ENSP00000350425:p.Arg305Ser		116197071	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	G	9.098	1.003367	0.19121	.	.	ENSG00000110244	ENST00000357780	T	0.72394	-0.65	4.95	1.65	0.23941	Apolipoprotein/apolipophorin (1);	0.641907	0.13771	N	0.363918	T	0.81955	0.4932	M	0.83312	2.635	0.09310	N	1	D	0.69078	0.997	D	0.66351	0.943	T	0.70223	-0.4931	10	0.54805	T	0.06	-11.18	10.0411	0.42158	0.0:0.1062:0.4824:0.4114	.	305	P06727	APOA4_HUMAN	S	305	ENSP00000350425:R305S	ENSP00000350425:R305S	R	-	1	0	APOA4	116197071	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.478000	0.06575	0.484000	0.27630	-0.233000	0.12211	CGC		0.647	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		T	116691861	G	T	116691861	3	4	99	1	0	0	0	0	1	0	0	0	783	1145	40	2	281	2	APOA4	11	116691861	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	227	116691861	18314655	122	26598										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126316659	126316659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gagctgcagcctcaccactcCggagccccgcttcatccaga	9	18	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:126316659C>T	ENST00000525144.2	-	9	1369	c.1120G>A	c.(1120-1122)Gga>Aga	p.G374R	KIRREL3_ENST00000525704.2_Missense_Mutation_p.G374R|KIRREL3_ENST00000529097.2_Missense_Mutation_p.G374R	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	374	Ig-like C2-type 4.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		CTCACCACTCCGGAGCCCCGC	0.632																																																0			11											22	25	24					11																	126316659		2000	4154	6154	125821869	SO:0001583	missense	84623			AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1120G>A	11.37:g.126316659C>T	ENSP00000435466:p.Gly374Arg		125821869	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.579106	0.28180	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.65916	-0.18;-0.18;-0.18	4.77	3.86	0.44501	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.60702	0.2289	N	0.10707	0.03	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.971	T	0.67309	-0.5703	10	0.66056	D	0.02	.	12.4402	0.55621	0.0:0.9167:0.0:0.0833	.	374;374;374	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	R	374	ENSP00000435466:G374R;ENSP00000434081:G374R;ENSP00000435094:G374R	ENSP00000435466:G374R	G	-	1	0	KIRREL3	125821869	0.767000	0.28508	0.082000	0.20525	0.106000	0.19336	2.703000	0.47110	0.997000	0.38969	0.297000	0.19635	GGA		0.632	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		T	126316659	C	T	126316659	3	4	99	1	0	0	0	0	1	0	0	0	8347	661	23	1	1359	1	KIRREL3	11	126316659	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	9624798	126316659	8689857	123	26599										
FLI1	2313	hgsc.bcm.edu	37	chr11	128680804	128680804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	acaatactggacctcccccaCggggggaatctaccccaacc	8	17	1	0	rs531254948		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr11:128680804C>T	ENST00000527786.2	+	9	1769	c.1280C>T	c.(1279-1281)aCg>aTg	p.T427M	FLI1_ENST00000534087.2_Missense_Mutation_p.T394M|FLI1_ENST00000525560.1_Missense_Mutation_p.T234M|FLI1_ENST00000281428.8_Missense_Mutation_p.T361M|FLI1_ENST00000344954.6_Missense_Mutation_p.T394M	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	427					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		ACCTCCCCCACGGGGGGAATC	0.567			T	EWSR1	Ewing sarcoma								C|||	1	0.000199681	0	0	5008	,	,		17766	0		0	False		,,,				2504	0.001						Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	0			11											104	105	105					11																	128680804		1968	4151	6119	128186014	SO:0001583	missense	2313			M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"Friend leukemia virus integration 1"			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.1280C>T	11.37:g.128680804C>T	ENSP00000433488:p.Thr427Met		128186014	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Missense_Mutation	SNP	ENST00000527786.2	37	CCDS44768.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.694545	0.68386	.	.	ENSG00000151702	ENST00000525560;ENST00000344954;ENST00000429175;ENST00000534087;ENST00000281428	T;T;T;T;T	0.25085	1.82;2.41;2.42;2.41;2.42	5.46	5.46	0.80206	.	0.153135	0.64402	D	0.000020	T	0.42877	0.1222	M	0.65498	2.005	0.50313	D	0.999869	P;D;D	0.69078	0.863;0.98;0.997	P;B;P	0.54965	0.587;0.346;0.765	T	0.30995	-0.9959	10	0.87932	D	0	.	15.0422	0.71799	0.0:0.8586:0.1414:0.0	.	427;234;361	Q01543;B4DFV4;Q01543-2	FLI1_HUMAN;.;.	M	234;394;427;394;361	ENSP00000437124:T234M;ENSP00000339627:T394M;ENSP00000399985:T427M;ENSP00000432950:T394M;ENSP00000281428:T361M	ENSP00000281428:T361M	T	+	2	0	FLI1	128186014	0.996000	0.38824	0.994000	0.49952	0.984000	0.73092	5.803000	0.69129	2.840000	0.97914	0.655000	0.94253	ACG		0.567	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017		T	128680804	C	T	128680804	3	4	99	1	0	0	0	0	1	0	0	0	5943	536	19	1	1314	1	FLI1	11	128680804	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	2364145	128680804	6325712	124	26600										
CD163	9332	hgsc.bcm.edu	37	chr12	7632575	7632575	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcagcagcactgaaatcagCtgactcatgggaattttctg	9	9	4	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:7632575C>A	ENST00000359156.4	-	16	3563	c.3361G>T	c.(3361-3363)Gct>Tct	p.A1121S	CD163_ENST00000541972.1_Intron|CD163_ENST00000396620.3_Intron|CD163_ENST00000432237.2_Intron	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	1121					acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CTGAAATCAGCTGACTCATGG	0.393																																																0			12											57	57	57					12																	7632575		2202	4300	6502	7523842	SO:0001583	missense	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.3361G>T	12.37:g.7632575C>A	ENSP00000352071:p.Ala1121Ser		7523842	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.012|0.012	-1.670623|-1.670623	0.00758|0.00758	.|.	.|.	ENSG00000177575|ENSG00000177575	ENST00000359156;ENST00000542280|ENST00000537626	T;T|.	0.01933|.	5.08;4.55|.	4.69|4.69	-4.73|-4.73	0.03259|0.03259	.|.	3.141460|.	0.01099|.	N|.	0.005334|.	T|T	0.09555|0.09555	0.0235|0.0235	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.14012|.	0.009|.	B|.	0.12156|.	0.007|.	T|T	0.26744|0.26744	-1.0094|-1.0094	9|5	.|.	.|.	.|.	.|.	0.1645|0.1645	0.00107|0.00107	0.2642:0.2573:0.2257:0.2528|0.2642:0.2573:0.2257:0.2528	.|.	1121|.	Q86VB7|.	C163A_HUMAN|.	S|H	1121;89|101	ENSP00000352071:A1121S;ENSP00000445438:A89S|.	.|.	A|Q	-|-	1|3	0|2	CD163|CD163	7523842|7523842	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.294000|0.294000	0.27393|0.27393	-0.078000|-0.078000	0.11375|0.11375	-0.824000|-0.824000	0.04295|0.04295	0.563000|0.563000	0.77884|0.77884	GCT|CAG		0.393	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7632575	C	A	7632575	3	1	99	1	0	0	0	0	1	0	0	0	2973	797	28	2	113	2	CD163	12	7632575	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		7632575	126219320	125	26601										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21329830	21329830	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcacctgagatagtgggaaaAggtaagaattaatattgaca	10	4	1	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:21329830A>G	ENST00000256958.2	+	5	576	c.480A>G	c.(478-480)aaA>aaG	p.K160K		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	160					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TAGTGGGAAAAGGTAAGAATT	0.259																																																0			12											62	63	63					12																	21329830		2203	4281	6484	21221097	SO:0001630	splice_region_variant	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.481+1A>G	12.37:g.21329830A>G			21221097	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																				0.259	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	Silent	G	21329830	A	G	21329830	5	3	99	1	0	0	0	0	0	0	1	0	14760	86	3	4	494	4	SLCO1B1	12	21329830	Splice_Site	SNP	A	TCGA-DC-6681-01A-11D-1826-10	13697255	21329830	112522065	126	26602										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26580929	26580929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tattgatacaagaaacggccGaatacccacaggcttggaga	10	9	0	3	rs61751236	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:26580929G>A	ENST00000381340.3	-	49	7278	c.6862C>T	c.(6862-6864)Cgg>Tgg	p.R2288W		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2288					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AGAAACGGCCGAATACCCACA	0.393													G|||	3	0.000599042	0	0	5008	,	,		15835	0		0.003	False		,,,				2504	0															0			12						G	TRP/ARG	1,3667		0,1,1833	96	88	91		6862	4.3	1	12	dbSNP_129	91	9,8181		0,9,4086	yes	missense	ITPR2	NM_002223.2	101	0,10,5919	AA,AG,GG		0.1099,0.0273,0.0843	probably-damaging	2288/2702	26580929	10,11848	1834	4095	5929	26472196	SO:0001583	missense	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.6862C>T	12.37:g.26580929G>A	ENSP00000370744:p.Arg2288Trp		26472196	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	21.2	4.112440	0.77210	2.73E-4	0.001099	ENSG00000123104	ENST00000381340	D	0.92545	-3.06	4.32	4.32	0.51571	.	0.191550	0.37219	N	0.002187	D	0.94870	0.8342	M	0.77486	2.375	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	D	0.93786	0.7088	10	0.35671	T	0.21	.	12.1523	0.54055	0.0:0.0:0.829:0.171	rs61751236	2288	Q14571	ITPR2_HUMAN	W	2288	ENSP00000370744:R2288W	ENSP00000370744:R2288W	R	-	1	2	ITPR2	26472196	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.631000	0.54280	2.246000	0.74042	0.585000	0.79938	CGG		0.393	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26580929	G	A	26580929	3	1	99	1	0	0	0	0	1	0	0	0	7942	1057	37	1	1279	1	ITPR2	12	26580929	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	5251099	26580929	107270966	127	26603										
BICD1	636	hgsc.bcm.edu	37	chr12	32481093	32481093	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cgattagccaggcggggtgtGtcatccccggtagaaacaag	14	10	1	1	rs3748275	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:32481093G>C	ENST00000281474.5	+	5	1807	c.1704G>C	c.(1702-1704)gtG>gtC	p.V568V	BICD1_ENST00000548411.1_Silent_p.V568V	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	568					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GGCGGGGTGTGTCATCCCCGG	0.537													G|||	1325	0.264577	0.1377	0.2118	5008	,	,		18566	0.5764		0.2296	False		,,,				2504	0.1881															0			12						G	,	651,3755	278.7+/-274.4	63,525,1615	112	110	111		1704,1704	3.2	1	12	dbSNP_107	111	1802,6798	324.1+/-316.3	192,1418,2690	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	255,1943,4305	CC,CG,GG		20.9535,14.7753,18.8605	,	568/836,568/976	32481093	2453,10553	2203	4300	6503	32372360	SO:0001819	synonymous_variant	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1704G>C	12.37:g.32481093G>C			32372360	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																				0.537	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		C	32481093	G	C	32481093	2	2	99	1	0	0	0	0	0	0	0	1	1429	1364	48	5		5	BICD1	12	32481093	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	5900164	32481093	101370802	128	26604										
ABCD2	225	hgsc.bcm.edu	37	chr12	39947933	39947933	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aataaatgtgtgtggtatttCctgcataattaaaatgaaat	7	3	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:39947933C>A	ENST00000308666.3	-	10	2139	c.2004G>T	c.(2002-2004)tgG>tgT	p.W668C		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	668	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TGTGGTATTTCCTGCATAATT	0.303																																																0			12											62	63	63					12																	39947933		2203	4300	6503	38234200	SO:0001630	splice_region_variant	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.2004-1G>T	12.37:g.39947933C>A			38234200	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.127433	0.77549	.	.	ENSG00000173208	ENST00000308666	D	0.99843	-7.11	5.1	5.1	0.69264	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.99806	0.9916	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.97344	0.9959	9	.	.	.	.	18.8712	0.92315	0.0:1.0:0.0:0.0	.	668	Q9UBJ2	ABCD2_HUMAN	C	668	ENSP00000310688:W668C	.	W	-	3	0	ABCD2	38234200	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.713000	0.84693	2.535000	0.85469	0.655000	0.94253	TGG		0.303	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	Missense_Mutation	A	39947933	C	A	39947933	5	1	99	1	0	0	0	0	0	0	1	0	61	869	30	2	222	2	ABCD2	12	39947933	Splice_Site	SNP	C	TCGA-DC-6681-01A-11D-1826-10	7466840	39947933	93903962	129	26605										
SSH1	54434	hgsc.bcm.edu	37	chr12	109185877	109185877	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tacgtacccaccagcagaatCaccctgtgaaagaaccctca	6	15	2	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:109185877C>T	ENST00000326495.5	-	14	1987				SSH1_ENST00000551165.1_Silent_p.*693*|SSH1_ENST00000360239.3_Intron|SSH1_ENST00000326470.5_Silent_p.*704*	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1						actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCAGCAGAATCACCCTGTGAA	0.498																																																0			12											27	27	27					12																	109185877		692	1591	2283	107710006	SO:0001627	intron_variant	54434			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1893+184G>A	12.37:g.109185877C>T			107710006	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1																																																																																				0.498	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		T	109185877	C	T	109185877	1	4	99	0	1	0	0	0	0	0	0	0	15223	837	29	3		3	SSH1	12	109185877	Intron	SNP	C	TCGA-DC-6681-01A-11D-1826-10	69237944	109185877	24666018	130	26606										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926886	112926886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atggtgcggtctcagaggtcAgggatggtccagacagaagc	16	8	2	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:112926886A>G	ENST00000351677.2	+	13	1704	c.1506A>G	c.(1504-1506)tcA>tcG	p.S502S		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	506	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		R -> L (in LEOPARD1). {ECO:0000269|PubMed:15121796}.|R -> W (in LEOPARD1; reduced phosphatase activity). {ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:24891296}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CTCAGAGGTCAGGGATGGTCC	0.463			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12											180	168	172					12																	112926886		2203	4300	6503	111411269	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1506A>G	12.37:g.112926886A>G			111411269	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.463	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112926886	A	G	112926886	2	3	99	1	0	0	0	0	0	0	0	1	12815	175	7	4		4	PTPN11	12	112926886	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	3741009	112926886	20925009	131	26607										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123471337	123471337	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttctgcatgtcgggccggccCgtcacgtagatgatgaggta	14	10	2	3			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr12:123471337C>T	ENST00000542749.1	-	22	3516	c.3453G>A	c.(3451-3453)acG>acA	p.T1151T	PITPNM2_ENST00000320201.4_Silent_p.T1151T|PITPNM2_ENST00000392428.1_Silent_p.T872T|PITPNM2_ENST00000280562.5_Silent_p.T1145T			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	1151					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CGGGCCGGCCCGTCACGTAGA	0.657																																																0			12											44	39	41					12																	123471337		2202	4300	6502	122037290	SO:0001819	synonymous_variant	57605			AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.3453G>A	12.37:g.123471337C>T			122037290	Q9P271	Silent	SNP	ENST00000542749.1	37	CCDS9242.1																																																																																				0.657	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123471337	C	T	123471337	2	4	99	1	0	0	0	0	0	0	0	1	11982	639	23	1		1	PITPNM2	12	123471337	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	10544451	123471337	10380558	132	26608										
ABHD13	84945	hgsc.bcm.edu	37	chr13	108882235	108882235	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aacacatttttaagcataccAcatatggccagcactttatt	4	10	0	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr13:108882235A>G	ENST00000375898.3	+	2	970	c.669A>G	c.(667-669)ccA>ccG	p.P223P		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	223						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.P223P(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TAAGCATACCACATATGGCCA	0.388																																					Pancreas(22;506 789 38166 45896 51596)											1	Substitution - coding silent(1)	ovary(1)	13											121	119	119					13																	108882235		2203	4300	6503	107680236	SO:0001819	synonymous_variant	84945			AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"Abhydrolase domain containing"	20293	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 6"	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	ENST00000375898.3:c.669A>G	13.37:g.108882235A>G			107680236	B3KWE7|Q8NBW1|Q96JX9	Silent	SNP	ENST00000375898.3	37	CCDS32007.1																																																																																				0.388	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045743.1	NM_032859		G	108882235	A	G	108882235	2	3	99	1	0	0	0	0	0	0	0	1	78	146	6	4		4	ABHD13	13	108882235	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10		108882235	6287643	133	26609										
KHNYN	23351	hgsc.bcm.edu	37	chr14	24901249	24901249	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tgtggagaaggagggagggaAacagggtggtcccagggaga	21	4	0	2	rs3742520	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:24901249A>C	ENST00000251343.5	+	3	921	c.782A>C	c.(781-783)aAa>aCa	p.K261T	KHNYN_ENST00000556842.1_Missense_Mutation_p.K261T|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Missense_Mutation_p.K261T|CBLN3_ENST00000555436.1_5'Flank|CBLN3_ENST00000267406.6_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	261			K -> T (in dbSNP:rs3742520). {ECO:0000269|PubMed:9205841}.				RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GAGGGAGGGAAACAGGGTGGT	0.617											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2029	0.405152	0.0552	0.5807	5008	,	,		19821	0.5208		0.5636	False		,,,				2504	0.4714															0			14						A	THR/LYS	573,3833	252.4+/-258.8	39,495,1669	95	92	93		782	2.3	0	14	dbSNP_107	93	4661,3939	600.9+/-394.3	1282,2097,921	yes	missense	KHNYN	NM_015299.2	78	1321,2592,2590	CC,CA,AA		45.8023,13.005,40.243	possibly-damaging	261/679	24901249	5234,7772	2203	4300	6503	23971089	SO:0001583	missense	0			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.782A>C	14.37:g.24901249A>C	ENSP00000251343:p.Lys261Thr	774	23971089	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	979	0.4482600732600733	43	0.08739837398373984	202	0.5580110497237569	301	0.5262237762237763	433	0.5712401055408971	A	5.982	0.365043	0.11296	0.13005	0.541977	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935	T;T;T	0.25414	1.8;1.8;1.8	4.7	2.28	0.28536	.	0.215138	0.14362	U	0.324384	T	0.00012	0.0000	L	0.27053	0.805	0.49915	P	1.6099999999996673E-4	B;B	0.18461	0.028;0.015	B;B	0.12156	0.007;0.007	T	0.39482	-0.9612	9	0.66056	D	0.02	.	3.8544	0.08968	0.711:0.0:0.1029:0.1861	rs3742520;rs57351660;rs3742520	302;261	D3DS77;O15037	.;KHNYN_HUMAN	T	261	ENSP00000251343:K261T;ENSP00000451106:K261T;ENSP00000450799:K261T	ENSP00000251343:K261T	K	+	2	0	KHNYN	23971089	0.887000	0.30362	0.048000	0.18961	0.168000	0.22595	1.941000	0.40233	0.182000	0.20032	0.460000	0.39030	AAA		0.617	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			C	24901249	A	C	24901249	3	2	99	1	0	0	0	0	1	0	0	0	8171	14	1	4	788	4	KHNYN	14	24901249	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10		24901249	82448291	134	26610										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31582526	31582526	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gggtcacttgcaactatataTagaatacgcagaagctgaag	10	7	1	3	rs2273483	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:31582526T>C	ENST00000399332.1	-	33	6509	c.6021A>G	c.(6019-6021)ctA>ctG	p.L2007L	HECTD1_ENST00000553700.1_Silent_p.L2007L	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2007					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	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)		CAACTATATATAGAATACGCA	0.373													C|||	2673	0.533746	0.7549	0.5	5008	,	,		14301	0.376		0.4215	False		,,,				2504	0.5368															0			14						C		2479,1217		830,819,199	123	118	119		6021	3	1	14	dbSNP_100	119	3329,4851		682,1965,1443	no	coding-synonymous	HECTD1	NM_015382.2		1512,2784,1642	CC,CT,TT		40.6968,32.9275,48.9054		2007/2611	31582526	5808,6068	1848	4090	5938	30652277	SO:0001819	synonymous_variant	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6021A>G	14.37:g.31582526T>C			30652277	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1	1078	0.4935897435897436	375	0.7621951219512195	183	0.505524861878453	206	0.36013986013986016	314	0.41424802110817943	C	0.183	-1.060382	0.01950	0.670725	0.406968	ENSG00000092148	ENST00000554882	.	.	.	5.94	3.05	0.35203	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25293	-1.0136	3	.	.	.	-4.2389	4.2472	0.10677	0.117:0.5125:0.2434:0.127	rs2273483;rs61584938;rs2273483	.	.	.	C	373	.	.	Y	-	2	0	HECTD1	30652277	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	0.790000	0.26900	0.424000	0.26061	-0.755000	0.03482	TAT		0.373	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31582526	T	C	31582526	2	2	99	1	0	0	0	0	0	0	0	1	7060	1393	49	4		4	HECTD1	14	31582526	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	6681277	31582526	75767014	135	26611										
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ttcctccacctcttgctccaAtcagaggtccattgtttcca	5	15	2	1	rs1140952	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:39818028A>G	ENST00000280083.3	+	23	2409	c.2095A>G	c.(2095-2097)Atc>Gtc	p.I699V	CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000341749.3_Missense_Mutation_p.I687V|CTAGE5_ENST00000556148.1_Missense_Mutation_p.I624V|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000553352.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000557038.1_Missense_Mutation_p.I619V|CTAGE5_ENST00000396165.4_Missense_Mutation_p.I670V|CTAGE5_ENST00000341502.5_Missense_Mutation_p.I699V|CTAGE5_ENST00000396158.2_Missense_Mutation_p.I704V|CTAGE5_ENST00000348007.3_Missense_Mutation_p.I656V|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I1234V			O15320	CTGE5_HUMAN	CTAGE family, member 5	699	Pro-rich.		I -> V (in dbSNP:rs1140952). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9356211}.		positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TCTTGCTCCAATCAGAGGTCC	0.493													A|||	1926	0.384585	0.2519	0.3415	5008	,	,		16436	0.5923		0.4115	False		,,,				2504	0.3528															0			14						A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1173,3233	412.2+/-336.0	151,871,1181	191	199	196		2095,2059,1966,2008	-2	0	14	dbSNP_86	196	3395,5205	500.7+/-375.3	671,2053,1576	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	29,29,29,29	822,2924,2757	GG,GA,AA		39.4767,26.6228,35.1223	benign,benign,benign,benign	699/805,687/793,656/762,670/776	39818028	4568,8438	2203	4300	6503	38887779	SO:0001583	missense	4253			U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"meningioma expressed antigen 6 (coiled-coil proline-rich)"	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2095A>G	14.37:g.39818028A>G	ENSP00000280083:p.Ile699Val		38887779	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	937	0.429029304029304	131	0.266260162601626	136	0.3756906077348066	359	0.6276223776223776	311	0.4102902374670185	A	0.004	-2.297832	0.00243	0.266228	0.394767	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.06528	3.49;3.33;3.33;3.29;3.55;3.58;3.58;3.33;3.83;3.29	5.41	-2.01	0.07410	.	1.206650	0.06423	N	0.722732	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.002;0.004;0.002;0.004;0.002	T	0.32241	-0.9914	8	.	.	.	.	8.1094	0.30905	0.1281:0.1851:0.6868:0.0	rs1140952;rs3204972;rs17846661;rs17859758;rs1140952	704;656;699;627;687	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	V	1234;687;619;670;699;704;699;624;656;670	ENSP00000452252:I1234V;ENSP00000343897:I687V;ENSP00000450869:I619V;ENSP00000379468:I670V;ENSP00000339286:I699V;ENSP00000379462:I704V;ENSP00000280083:I699V;ENSP00000452562:I624V;ENSP00000343912:I656V;ENSP00000450449:I670V	.	I	+	1	0	CTAGE5;RP11-407N17.3	38887779	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-1.436000	0.02421	-0.792000	0.04480	-0.316000	0.08728	ATC		0.493	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		G	39818028	A	G	39818028	3	3	99	1	0	0	0	0	1	0	0	0	4000	101	4	4	2216	4	CTAGE5	14	39818028	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	8235502	39818028	67531512	136	26612										
FANCM	57697	hgsc.bcm.edu	37	chr14	45658453	45658453	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gaatttaaaggatacaatttCcgaagtctcagacttcaaac	6	8	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:45658453C>G	ENST00000267430.5	+	20	5313	c.5228C>G	c.(5227-5229)tCc>tGc	p.S1743C	FANCM_ENST00000542564.2_Missense_Mutation_p.S1717C	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1743	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GATACAATTTCCGAAGTCTCA	0.418								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							0			14											123	127	125					14																	45658453		2203	4300	6503	44728203	SO:0001583	missense	57697	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5228C>G	14.37:g.45658453C>G	ENSP00000267430:p.Ser1743Cys		44728203	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.59|14.59	2.581325|2.581325	0.46006|0.46006	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000554809|ENST00000267430;ENST00000542564;ENST00000556250	.|T;T;T	.|0.78816	.|-1.21;-1.21;-1.21	5.26|5.26	4.33|4.33	0.51752|0.51752	.|.	.|1.125210	.|0.06380	.|N	.|0.715088	D|D	0.86619|0.86619	0.5976|0.5976	M|M	0.66939|0.66939	2.045|2.045	0.09310|0.09310	N|N	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.67231	.|0.95;0.95	T|T	0.69632|0.69632	-0.5093|-0.5093	5|10	.|0.72032	.|D	.|0.01	.|.	10.3121|10.3121	0.43714|0.43714	0.0:0.9006:0.0:0.0994|0.0:0.9006:0.0:0.0994	.|.	.|1717;1743	.|B2RTQ9;Q8IYD8	.|.;FANCM_HUMAN	L|C	675|1743;1717;1259	.|ENSP00000267430:S1743C;ENSP00000442493:S1717C;ENSP00000452033:S1259C	.|ENSP00000267430:S1743C	F|S	+|+	3|2	2|0	FANCM|FANCM	44728203|44728203	0.970000|0.970000	0.33590|0.33590	0.006000|0.006000	0.13384|0.13384	0.003000|0.003000	0.03518|0.03518	3.340000|3.340000	0.52143|0.52143	1.274000|1.274000	0.44362|0.44362	-0.355000|-0.355000	0.07637|0.07637	TTC|TCC		0.418	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45658453	C	G	45658453	3	3	99	1	0	0	0	0	1	0	0	0	5690	855	30	5	5306	5	FANCM	14	45658453	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	5840425	45658453	61691087	137	26613										
NDUFB1	4707	hgsc.bcm.edu	37	chr14	92588002	92588002	+	5'UTR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ccacctgcagcctcagcgccTacagcgaccccgagaccaag	9	19	1	1	rs3818263	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:92588002T>G	ENST00000553514.1	-	0	66				NDUFB1_ENST00000556555.1_5'UTR|NDUFB1_ENST00000555441.1_5'Flank|CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000329559.3_Silent_p.V40V|NDUFB1_ENST00000605997.1_5'UTR			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		CCTCAGCGCCTACAGCGACCC	0.711													G|||	2703	0.539736	0.5514	0.379	5008	,	,		10980	0.8552		0.334	False		,,,				2504	0.5245															0			14						G		2232,2174		573,1086,544	33	39	37		120	-7	0	14	dbSNP_107	37	2915,5681		489,1937,1872	no	coding-synonymous	NDUFB1	NM_004545.3		1062,3023,2416	GG,GT,TT		33.9111,49.3418,39.5862		40/106	92588002	5147,7855	2203	4298	6501	91657755	SO:0001623	5_prime_UTR_variant	4707			BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"Mitochondrial respiratory chain complex / Complex I"	7695	protein-coding gene	gene with protein product	"complex I MNLL subunit"	603837	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000553514.1:c.-140A>C	14.37:g.92588002T>G			91657755	A0AV68	Silent	SNP	ENST00000553514.1	37																																																																																					0.711	NDUFB1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412116.2	NM_004545		G	92588002	T	G	92588002	1	3	99	0	1	0	0	0	0	0	0	0	10309	1509	53	4		4	NDUFB1	14	92588002	5'UTR	SNP	T	TCGA-DC-6681-01A-11D-1826-10	46929549	92588002	14761538	138	26614										
RIN3	79890	hgsc.bcm.edu	37	chr14	93118669	93118669	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcagacggccctgaggacacGccccgggagagcacggagca	15	14	1	3	rs3742716	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:93118669G>A	ENST00000216487.7	+	6	1434	c.1275G>A	c.(1273-1275)acG>acA	p.T425T	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	425	Pro-rich.		T -> I (in dbSNP:rs3742717).|T -> M (in dbSNP:rs3742717). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CTGAGGACACGCCCCGGGAGA	0.652													g|||	1194	0.238419	0.0295	0.2594	5008	,	,		13370	0.4494		0.2883	False		,,,				2504	0.2372															0			14						A		330,4076	173.0+/-202.9	18,294,1891	56	64	62		1275	0.9	0	14	dbSNP_107	62	2738,5862	433.0+/-357.3	433,1872,1995	no	coding-synonymous	RIN3	NM_024832.3		451,2166,3886	AA,AG,GG		31.8372,7.4898,23.5891		425/986	93118669	3068,9938	2203	4300	6503	92188422	SO:0001819	synonymous_variant	79890			BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1275G>A	14.37:g.93118669G>A			92188422	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																				0.652	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			A	93118669	G	A	93118669	2	1	99	1	0	0	0	0	0	0	0	1	13410	1074	38	1		1	RIN3	14	93118669	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	530667	93118669	14230871	139	26615										
SERPINA4	5267	hgsc.bcm.edu	37	chr14	95034582	95034582	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tctgttctccaagtgggctgActtatccggcatcaccaaac	8	13	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:95034582A>G	ENST00000557004.1	+	4	1461	c.1040A>G	c.(1039-1041)gAc>gGc	p.D347G	SERPINA4_ENST00000555095.1_Missense_Mutation_p.D347G|SERPINA4_ENST00000298841.5_Missense_Mutation_p.D347G|SERPINA5_ENST00000553780.1_Intron			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	347					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		AAGTGGGCTGACTTATCCGGC	0.498																																																0			14											83	81	82					14																	95034582		2203	4300	6503	94104335	SO:0001583	missense	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.1040A>G	14.37:g.95034582A>G	ENSP00000450838:p.Asp347Gly		94104335	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	37	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	A	19.15	3.770868	0.69992	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.86097	-2.07;-2.07;-2.07	5.3	4.16	0.48862	Serpin domain (3);	0.320980	0.24481	N	0.038156	D	0.91092	0.7196	M	0.80746	2.51	0.80722	D	1	D;P	0.76494	0.999;0.898	D;P	0.69479	0.964;0.791	D	0.90694	0.4615	10	0.72032	D	0.01	.	10.2434	0.43326	0.9218:0.0:0.0782:0.0	.	347;347	B2R815;P29622	.;KAIN_HUMAN	G	347	ENSP00000450838:D347G;ENSP00000451172:D347G;ENSP00000298841:D347G	ENSP00000298841:D347G	D	+	2	0	SERPINA4	94104335	0.951000	0.32395	0.010000	0.14722	0.025000	0.11179	5.106000	0.64597	0.863000	0.35553	-0.250000	0.11733	GAC		0.498	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		G	95034582	A	G	95034582	3	3	99	1	0	0	0	0	1	0	0	0	14128	275	10	4	1050	4	SERPINA4	14	95034582	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1915913	95034582	12314958	140	26616										
JAG2	3714	hgsc.bcm.edu	37	chr14	105615648	105615648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggggcttggctcacaaaggtCgacatccacctgcagggtgg	15	11	1	0	rs9972231	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr14:105615648C>T	ENST00000331782.3	-	13	2015	c.1612G>A	c.(1612-1614)Gac>Aac	p.D538N	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Missense_Mutation_p.D500N	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	538	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.		D -> N (in dbSNP:rs9972231).		auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)	p.D538N(2)		breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TCACAAAGGTCGACATCCACC	0.622													c|||	601	0.120008	0.0053	0.1268	5008	,	,		11943	0.1687		0.1312	False		,,,				2504	0.2086															2	Substitution - Missense(2)	lung(1)|skin(1)	14							ASN/ASP,ASN/ASP	143,4261	98.9+/-137.6	2,139,2061	68	71	70		1612,1498	3.8	0	14	dbSNP_119	70	1119,7481	229.8+/-264.4	82,955,3263	yes	missense,missense	JAG2	NM_002226.3,NM_145159.1	23,23	84,1094,5324	TT,TC,CC		13.0116,3.247,9.7047	possibly-damaging,possibly-damaging	538/1239,500/1201	105615648	1262,11742	2202	4300	6502	104686693	SO:0001583	missense	3714			AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1612G>A	14.37:g.105615648C>T	ENSP00000328169:p.Asp538Asn		104686693	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	253	0.11584249084249085	5	0.01016260162601626	44	0.12154696132596685	104	0.18181818181818182	100	0.13192612137203166	C	12.41	1.928193	0.34002	0.03247	0.130116	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.83673	-1.75;-1.75	3.8	3.8	0.43715	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.056989	0.64402	D	0.000002	T	0.00412	0.0013	L	0.49455	1.56	0.21020	P	0.999805715	B;B	0.34147	0.438;0.202	B;B	0.29267	0.1;0.025	T	0.30238	-0.9985	9	0.20519	T	0.43	.	13.511	0.61513	0.0:1.0:0.0:0.0	rs9972231;rs57317492;rs9972231	500;538	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	N	538;500	ENSP00000328169:D538N;ENSP00000328566:D500N	ENSP00000328169:D538N	D	-	1	0	JAG2	104686693	0.269000	0.24143	0.038000	0.18304	0.038000	0.13279	0.959000	0.29240	1.830000	0.53286	0.556000	0.70494	GAC		0.622	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			T	105615648	C	T	105615648	3	4	99	1	0	0	0	0	1	0	0	0	7956	884	31	1	2160	1	JAG2	14	105615648	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	10581066	105615648	1733892	141	26617										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25940151	25940151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cgatcacgaggctgggtctgCggccagaggcagtggacgtg	18	10	2	1	rs150976669		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:25940151C>T	ENST00000356865.6	-	14	3014	c.2903G>A	c.(2902-2904)cGc>cAc	p.R968H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	968					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCTGGGTCTGCGGCCAGAGGC	0.602													C|||	1	0.000199681	0	0	5008	,	,		19196	0		0	False		,,,				2504	0.001															0			15						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	104	99	101		2903	0.6	0.1	15	dbSNP_134	101	0,8600		0,0,4300	no	missense	ATP10A	NM_024490.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	968/1500	25940151	1,13005	2203	4300	6503	23491244	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2903G>A	15.37:g.25940151C>T	ENSP00000349325:p.Arg968His		23491244	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	7.061	0.566312	0.13560	2.27E-4	0.0	ENSG00000206190	ENST00000356865	D	0.82803	-1.65	4.91	0.572	0.17357	HAD-like domain (1);	0.558796	0.21761	N	0.069517	T	0.53690	0.1812	N	0.11673	0.155	0.26036	N	0.98168	P	0.37500	0.597	B	0.20767	0.031	T	0.50898	-0.8773	10	0.22706	T	0.39	-14.3147	3.2727	0.06888	0.0847:0.1489:0.3249:0.4415	.	968	O60312	AT10A_HUMAN	H	968	ENSP00000349325:R968H	ENSP00000349325:R968H	R	-	2	0	ATP10A	23491244	0.982000	0.34865	0.077000	0.20336	0.005000	0.04900	0.525000	0.22956	-0.039000	0.13602	-0.256000	0.11100	CGC		0.602	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25940151	C	T	25940151	3	4	99	1	0	0	0	0	1	0	0	0	1117	768	27	1	1628	1	ATP10A	15	25940151	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10		25940151	76591241	142	26618										
INO80	54617	hgsc.bcm.edu	37	chr15	41276061	41276061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	catccacaatgaccagcatgTcactgctgctctcgtccagg	8	15	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:41276061T>C	ENST00000361937.3	-	34	4560	c.4136A>G	c.(4135-4137)gAc>gGc	p.D1379G	INO80_ENST00000401393.3_Missense_Mutation_p.D1379G|INO80_ENST00000561244.1_5'Flank			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1379	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GACCAGCATGTCACTGCTGCT	0.552																																																0			15											115	92	100					15																	41276061		2203	4300	6503	39063353	SO:0001583	missense	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.4136A>G	15.37:g.41276061T>C	ENSP00000355205:p.Asp1379Gly		39063353	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.864075	0.71949	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.92249	-3.0;-3.0	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.93164	0.7823	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.93510	0.6852	10	0.51188	T	0.08	.	14.7983	0.69894	0.0:0.0:0.0:1.0	.	1379	Q9ULG1	INO80_HUMAN	G	1379	ENSP00000355205:D1379G;ENSP00000384686:D1379G	ENSP00000355205:D1379G	D	-	2	0	INO80	39063353	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.669000	0.83911	2.084000	0.62774	0.533000	0.62120	GAC		0.552	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		C	41276061	T	C	41276061	3	2	99	1	0	0	0	0	1	0	0	0	7767	1667	58	4	546	4	INO80	15	41276061	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	15335910	41276061	61255331	143	26619										
FRMD5	84978	hgsc.bcm.edu	37	chr15	44166328	44166328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cttattcacctgttcctcctCgggcccgctgtgcccctgac	8	18	1	1	rs551307319		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:44166328C>T	ENST00000417257.1	-	14	1644	c.1468G>A	c.(1468-1470)Gag>Aag	p.E490K	FRMD5_ENST00000484674.1_Missense_Mutation_p.E396K|FRMD5_ENST00000402883.1_Missense_Mutation_p.E490K	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	490						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		TGTTCCTCCTCGGGCCCGCTG	0.562													.|||	1	0.000199681	0	0	5008	,	,		19810	0		0.001	False		,,,				2504	0															0			15											114	96	102					15																	44166328		2198	4298	6496	41953620	SO:0001583	missense	84978			BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.1468G>A	15.37:g.44166328C>T	ENSP00000403067:p.Glu490Lys		41953620	Q8NBG4	Missense_Mutation	SNP	ENST00000417257.1	37	CCDS10107.2	.	.	.	.	.	.	.	.	.	.	C	14.60	2.583679	0.46006	.	.	ENSG00000171877	ENST00000417257;ENST00000402883;ENST00000449926	D;D;D	0.84944	-1.68;-1.92;-1.89	6.03	6.03	0.97812	.	0.053243	0.64402	D	0.000001	D	0.84424	0.5469	M	0.62723	1.935	0.46725	D	0.999177	P;P;D;D	0.56968	0.854;0.772;0.978;0.966	B;B;P;P	0.45099	0.162;0.078;0.469;0.45	T	0.81129	-0.1073	10	0.09338	T	0.73	.	19.1447	0.93459	0.0:1.0:0.0:0.0	.	475;490;490;163	Q7Z6J6-2;Q7Z6J6;B5MC67;A8K1U8	.;FRMD5_HUMAN;.;.	K	490;490;456	ENSP00000403067:E490K;ENSP00000384142:E490K;ENSP00000399684:E456K	ENSP00000384142:E490K	E	-	1	0	FRMD5	41953620	0.997000	0.39634	0.998000	0.56505	0.961000	0.63080	3.655000	0.54460	2.854000	0.98071	0.655000	0.94253	GAG		0.562	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892		T	44166328	C	T	44166328	3	4	99	1	0	0	0	0	1	0	0	0	6072	893	31	1	248	1	FRMD5	15	44166328	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	2890267	44166328	58365064	144	26620										
SLC28A2	9153	hgsc.bcm.edu	37	chr15	45554232	45554232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggaggagtcggtggcctttcAgcaaagcaagaagtttctgc	14	8	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:45554232A>G	ENST00000347644.3	+	4	255	c.190A>G	c.(190-192)Agc>Ggc	p.S64G	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	64					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		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)	Mercaptopurine(DB01033)	GTGGCCTTTCAGCAAAGCAAG	0.398																																					NSCLC(92;493 1501 26361 28917 47116)											0			15											178	166	170					15																	45554232		2198	4298	6496	43341524	SO:0001583	missense	9153			U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"Solute carriers"	11002	protein-coding gene	gene with protein product		606208	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.190A>G	15.37:g.45554232A>G	ENSP00000315006:p.Ser64Gly		43341524	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	.	.	.	.	.	.	.	.	.	.	A	4.577	0.107255	0.08780	.	.	ENSG00000137860	ENST00000347644	D	0.82344	-1.6	5.64	-2.9	0.05648	.	1.424290	0.04030	N	0.301229	T	0.60637	0.2284	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45948	-0.9226	10	0.21014	T	0.42	0.1026	0.6462	0.00819	0.2713:0.1329:0.1718:0.424	.	64	O43868	S28A2_HUMAN	G	64	ENSP00000315006:S64G	ENSP00000315006:S64G	S	+	1	0	SLC28A2	43341524	0.000000	0.05858	0.005000	0.12908	0.382000	0.30200	-0.270000	0.08584	-0.156000	0.11079	0.377000	0.23210	AGC		0.398	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212		G	45554232	A	G	45554232	3	3	99	1	0	0	0	0	1	0	0	0	14569	188	7	4	200	4	SLC28A2	15	45554232	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1387904	45554232	56977160	145	26621										
RNF111	54778	hgsc.bcm.edu	37	chr15	59347929	59347929	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tctcattggagccagggttcCagttctcatgcaagtcggcc	11	12	2	0	rs1446239	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:59347929C>A	ENST00000557998.1	+	4	1343	c.1056C>A	c.(1054-1056)tcC>tcA	p.S352S	RNF111_ENST00000559209.1_Silent_p.S352S|RNF111_ENST00000348370.4_Silent_p.S352S|RNF111_ENST00000434298.1_Silent_p.S352S|RNF111_ENST00000561186.1_Silent_p.S352S	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	352	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		GCCAGGGTTCCAGTTCTCATG	0.433													A|||	2212	0.441693	0.6611	0.4986	5008	,	,		16383	0.4405		0.3161	False		,,,				2504	0.2352				NSCLC(72;983 1365 10746 34387 47081)											0			15						A		2723,1661	505.6+/-366.2	863,997,332	56	48	51		1056	0	1	15	dbSNP_88	51	3016,5566	661.7+/-401.9	560,1896,1835	yes	coding-synonymous	RNF111	NM_017610.6		1423,2893,2167	AA,AC,CC		35.1433,37.8878,44.2619		352/987	59347929	5739,7227	2192	4291	6483	57135221	SO:0001819	synonymous_variant	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1056C>A	15.37:g.59347929C>A			57135221	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																				0.433	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		A	59347929	C	A	59347929	2	1	99	1	0	0	0	0	0	0	0	1	13462	581	21	2		2	RNF111	15	59347929	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	13793697	59347929	43183463	146	26622										
LINGO1	84894	hgsc.bcm.edu	37	chr15	77907145	77907145	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cagtcgcaggccagcgggttGgagtccaggatgagtgtctc	16	10	1	1	rs3743481	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:77907145G>A	ENST00000355300.6	-	2	1278	c.1104C>T	c.(1102-1104)tcC>tcT	p.S368S	LINGO1_ENST00000561030.1_Silent_p.S362S	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	368					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						CCAGCGGGTTGGAGTCCAGGA	0.637													G|||	2604	0.519968	0.5666	0.4164	5008	,	,		17828	0.5952		0.4056	False		,,,				2504	0.5706															0			15						G		2162,2064		575,1012,526	42	45	44		1104	4.9	1	15	dbSNP_107	44	3157,5271		564,2029,1621	no	coding-synonymous	LINGO1	NM_032808.5		1139,3041,2147	AA,AG,GG		37.4585,48.8405,42.0341		368/621	77907145	5319,7335	2113	4214	6327	75694200	SO:0001819	synonymous_variant	84894			AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.1104C>T	15.37:g.77907145G>A			75694200	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																				0.637	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		A	77907145	G	A	77907145	2	1	99	1	0	0	0	0	0	0	0	1	8838	1335	47	3		3	LINGO1	15	77907145	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	18559216	77907145	24624247	147	26623										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99452112	99452112	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gacataaacaccaggaacaaCggggagagagcctcctgtga	12	10	0	2	rs537098180		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr15:99452112C>T	ENST00000268035.6	+	6	2057	c.1446C>T	c.(1444-1446)aaC>aaT	p.N482N	IGF1R_ENST00000558762.1_Silent_p.N482N	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	482					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CCAGGAACAACGGGGAGAGAG	0.512																																																0			15											96	76	82					15																	99452112		2196	4297	6493	97269635	SO:0001819	synonymous_variant	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1446C>T	15.37:g.99452112C>T			97269635	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																				0.512	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		T	99452112	C	T	99452112	2	4	99	1	0	0	0	0	0	0	0	1	7592	535	19	1		1	IGF1R	15	99452112	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	21544967	99452112	3079280	148	26624										
CLDN6	9074	hgsc.bcm.edu	37	chr16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gttatagaagtcccggatgaTggcatgcgccgtccagcaca	12	11	0	2	rs2257295	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr16:3065596T>C	ENST00000396925.1	-	3	855	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	TNFRSF12A_ENST00000573001.1_5'Flank|CLDN6_ENST00000572154.1_Intron|CLDN6_ENST00000328796.4_Missense_Mutation_p.I143V			P56747	CLD6_HUMAN	claudin 6	143			I -> V (in dbSNP:rs2257295). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TCCCGGATGATGGCATGCGCC	0.617													T|||	1497	0.298922	0.3548	0.3343	5008	,	,		18815	0.1925		0.3708	False		,,,				2504	0.2342															0			16						T	VAL/ILE	1631,2761		311,1009,876	23	25	25		427	2.5	0.9	16	dbSNP_100	25	3379,5217		688,2003,1607	no	missense	CLDN6	NM_021195.4	29	999,3012,2483	CC,CT,TT		39.309,37.1357,38.5741	benign	143/221	3065596	5010,7978	2196	4298	6494	3005597	SO:0001583	missense	9074			AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"Claudins"	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.427A>G	16.37:g.3065596T>C	ENSP00000380131:p.Ile143Val		3005597	B3KQP9|D3DUA5	Missense_Mutation	SNP	ENST00000396925.1	37	CCDS10488.1	695	0.3182234432234432	179	0.3638211382113821	122	0.3370165745856354	124	0.21678321678321677	270	0.3562005277044855	T	6.973	0.549571	0.13374	0.371357	0.39309	ENSG00000184697	ENST00000396925;ENST00000328796	D;D	0.89270	-2.49;-2.49	4.76	2.51	0.30379	.	0.125321	0.52532	N	0.000076	T	0.00012	0.0000	L	0.33245	0.995	0.32491	P	0.540211	B	0.22276	0.067	B	0.27500	0.08	T	0.10776	-1.0615	9	0.23302	T	0.38	.	7.5467	0.27770	0.0:0.1806:0.0:0.8194	rs2257295;rs17850428;rs61137178;rs2257295	143	P56747	CLD6_HUMAN	V	143	ENSP00000380131:I143V;ENSP00000328674:I143V	ENSP00000328674:I143V	I	-	1	0	CLDN6	3005597	1.000000	0.71417	0.941000	0.38009	0.114000	0.19823	1.726000	0.38085	0.423000	0.26033	0.533000	0.62120	ATC		0.617	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195		C	3065596	T	C	3065596	3	2	99	1	0	0	0	0	1	0	0	0	3495	1464	51	4	239	4	CLDN6	16	3065596	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10		3065596	87289157	149	26625										
FA2H	79152	hgsc.bcm.edu	37	chr16	74773946	74773946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cccaatccaccactttgaacCgtggttccatagcaggatct	7	14	1	1	rs147632811	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr16:74773946C>T	ENST00000219368.3	-	2	407	c.338G>A	c.(337-339)cGg>cAg	p.R113Q	FA2H_ENST00000544337.1_5'UTR	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	113					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R113Q(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CACTTTGAACCGTGGTTCCAT	0.537													C|||	2	0.000399361	0	0	5008	,	,		18815	0		0.001	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	16						C	GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	270	243	252		338	1.6	0.1	16	dbSNP_134	252	9,8591	7.1+/-27.0	0,9,4291	yes	missense	FA2H	NM_024306.4	43	0,10,6488	TT,TC,CC		0.1047,0.0227,0.0769	benign	113/373	74773946	10,12986	2198	4300	6498	73331447	SO:0001583	missense	79152			BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.338G>A	16.37:g.74773946C>T	ENSP00000219368:p.Arg113Gln		73331447	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	37	CCDS10911.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	12.93	2.085562	0.36758	2.27E-4	0.001047	ENSG00000103089	ENST00000219368	D	0.85702	-2.02	4.74	1.6	0.23607	.	0.580298	0.18201	N	0.148510	T	0.64260	0.2582	N	0.11201	0.11	0.46416	D	0.999035	B	0.20052	0.041	B	0.08055	0.003	T	0.46119	-0.9214	10	0.10902	T	0.67	-0.0465	5.3315	0.15936	0.0:0.5415:0.0:0.4585	.	113	Q7L5A8	FA2H_HUMAN	Q	113	ENSP00000219368:R113Q	ENSP00000219368:R113Q	R	-	2	0	FA2H	73331447	0.830000	0.29337	0.120000	0.21714	0.732000	0.41865	0.823000	0.27366	0.117000	0.18138	0.556000	0.70494	CGG		0.537	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		T	74773946	C	T	74773946	3	4	99	1	0	0	0	0	1	0	0	0	5368	652	23	1	804	1	FA2H	16	74773946	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	71708350	74773946	15580807	150	26626										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35956391	35956391	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gctgcatcggcatcaggcctGctgaaaatataaagacatta	9	9	1	2	rs12944821	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr17:35956391G>C	ENST00000339208.6	-	3	259	c.119C>G	c.(118-120)gCa>gGa	p.A40G	SYNRG_ENST00000394378.2_Splice_Site_p.A40G|SYNRG_ENST00000346661.4_Splice_Site_p.A40G|SYNRG_ENST00000345615.4_Splice_Site_p.A40G|SYNRG_ENST00000591288.1_Splice_Site_p.A40G|SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000502449.2_Splice_Site_p.A40G	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	40			A -> G (in dbSNP:rs12944821).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CATCAGGCCTGCTGAAAATAT	0.383													G|||	1009	0.201478	0.1203	0.3372	5008	,	,		21269	0.251		0.1789	False		,,,				2504	0.1871															0			17						G	GLY/ALA,,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	564,3842	251.8+/-258.4	39,486,1678	83	78	80		119,,119,119,119,119,119	3.7	1	17	dbSNP_121	80	1587,7013	295.7+/-302.5	151,1285,2864	yes	missense-near-splice,intron,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	60,,60,60,60,60,60	190,1771,4542	CC,CG,GG		18.4535,12.8007,16.5385	benign,,benign,benign,benign,benign,benign	40/1237,,40/1180,40/1109,40/1315,40/1225,40/1260	35956391	2151,10855	2203	4300	6503	33030504	SO:0001630	splice_region_variant	0			AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"gamma-synergin", "adaptor-related protein complex 1 gamma subunit-binding protein 1"	607291	"AP1 gamma subunit binding protein 1"	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.119-1C>G	17.37:g.35956391G>C			33030504	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	440	0.20146520146520147	55	0.11178861788617886	116	0.32044198895027626	139	0.243006993006993	130	0.17150395778364116	G	13.47	2.246510	0.39697	0.128007	0.184535	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.46451	1.53;1.53;0.87;0.87;0.87	6.07	3.74	0.42951	.	0.470274	0.20873	N	0.084129	T	0.00012	0.0000	L	0.27053	0.805	0.29416	P	0.860872	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001;0.001	T	0.34477	-0.9827	9	0.24483	T	0.36	.	12.9222	0.58239	0.0721:0.1192:0.8088:0.0	rs12944821;rs12944821	40;40;40;40;40;40;40	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	G	40	ENSP00000005279:A40G;ENSP00000343610:A40G;ENSP00000315722:A40G;ENSP00000424893:A40G;ENSP00000377903:A40G	ENSP00000343610:A40G	A	-	2	0	SYNRG	33030504	1.000000	0.71417	0.995000	0.50966	0.973000	0.67179	3.224000	0.51238	1.548000	0.49413	0.655000	0.94253	GCA		0.383	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	Missense_Mutation	C	35956391	G	C	35956391	5	2	99	1	0	0	0	0	0	0	1	0	15499	1333	46	5	3978	5	SYNRG	17	35956391	Splice_Site	SNP	G	TCGA-DC-6681-01A-11D-1826-10		35956391	45238819	151	26627										
KRT32	3882	hgsc.bcm.edu	37	chr17	39620399	39620399	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctcaggtcaatgatgtctgaCtggtagttctgaagctgctc	11	9	4	3	rs12948056	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr17:39620399C>T	ENST00000225899.3	-	5	1030	c.927G>A	c.(925-927)caG>caA	p.Q309Q		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	309	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				TGATGTCTGACTGGTAGTTCT	0.582													C|||	1523	0.304113	0.2095	0.3818	5008	,	,		21394	0.3145		0.4215	False		,,,				2504	0.2454															0			17						C		935,3471	357.1+/-313.8	98,739,1366	175	132	147		927	4.1	1	17	dbSNP_121	147	3179,5421	481.6+/-370.7	611,1957,1732	no	coding-synonymous	KRT32	NM_002278.3		709,2696,3098	TT,TC,CC		36.9651,21.2211,31.6316		309/449	39620399	4114,8892	2203	4300	6503	36873925	SO:0001819	synonymous_variant	3882			X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.927G>A	17.37:g.39620399C>T			36873925		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																				0.582	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		T	39620399	C	T	39620399	2	4	99	1	0	0	0	0	0	0	0	1	8489	564	20	3		3	KRT32	17	39620399	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	3664008	39620399	41574811	152	26628										
AARSD1	100885848	hgsc.bcm.edu	37	chr17	41131645	41131645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaaactccatgaacacatacCtgggcctgtcgtaccacaag	7	13	0	1	rs35444712	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr17:41131645C>A	ENST00000453594.1	-	2	518	c.173G>T	c.(172-174)aGg>aTg	p.R58M	PTGES3L-AARSD1_ENST00000421990.2_Missense_Mutation_p.R58M|PTGES3L-AARSD1_ENST00000409399.1_Missense_Mutation_p.R58M|PTGES3L-AARSD1_ENST00000360221.4_De_novo_Start_InFrame|RUNDC1_ENST00000361677.1_5'Flank|PTGES3L-AARSD1_ENST00000409103.1_De_novo_Start_InFrame|RP11-376M2.2_ENST00000587526.1_RNA|PTGES3L_ENST00000409446.3_Intron	NM_001142653.1|NM_001261430.1	NP_001136125.1|NP_001248359.1	E9PB15	PTG3L_HUMAN	prostaglandin E synthase 3 (cytosolic)-like	58	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.																GAACACATACCTGGGCCTGTC	0.557													C|||	522	0.104233	0.2625	0.0778	5008	,	,		19681	0		0.0954	False		,,,				2504	0.0256															0			17						C	MET/ARG,MET/ARG,,	1048,3358	386.3+/-326.1	126,796,1281	85	75	78		173,173,,	2.8	1	17	dbSNP_126	78	701,7899	172.9+/-223.5	30,641,3629	yes	missense,missense,intron,utr-5	AARSD1	NM_001136042.2,NM_001142653.1,NM_001142654.1,NM_025267.3	91,91,,	156,1437,4910	AA,AC,CC		8.1512,23.7857,13.4476	benign,benign,,	58/587,58/167,,	41131645	1749,11257	2203	4300	6503	38385171	SO:0001583	missense	80755				CCDS45692.1	17q21.31	2012-10-05				ENSG00000267060			43943	protein-coding gene	gene with protein product							Standard	NM_001142653		Approved			E9PB15	OTTHUMG00000180906	ENST00000453594.1:c.173G>T	17.37:g.41131645C>A	ENSP00000394415:p.Arg58Met		38385171		Missense_Mutation	SNP	ENST00000453594.1	37		249|249|249|249	0.11401098901098901|0.11401098901098901|0.11401098901098901|0.11401098901098901	144|144|144|144	0.2926829268292683|0.2926829268292683|0.2926829268292683|0.2926829268292683	31|31|31|31	0.0856353591160221|0.0856353591160221|0.0856353591160221|0.0856353591160221	0|0|0|0	0.0|0.0|0.0|0.0	74|74|74|74	0.09762532981530343|0.09762532981530343|0.09762532981530343|0.09762532981530343	C|C|C|C	20.7|20.7|20.7|20.7	4.031603|4.031603|4.031603|4.031603	0.75504|0.75504|0.75504|0.75504	0.237857|0.237857|0.237857|0.237857	0.081512|0.081512|0.081512|0.081512	ENSG00000108825|ENSG00000108825|ENSG00000108825|ENSG00000108825	ENST00000424284|ENST00000423601|ENST00000452752|ENST00000409399;ENST00000421990;ENST00000453594;ENST00000451885	.|.|.|T;T;T	.|.|.|0.30448	.|.|.|1.53;1.53;1.53	5.02|5.02|5.02|5.02	2.82|2.82|2.82|2.82	0.32997|0.32997|0.32997|0.32997	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	T|.|T|T	0.00012|.|0.00012|0.00012	0.0000|.|0.0000|0.0000	L|L|L|L	0.36672|0.36672|0.36672|0.36672	1.1|1.1|1.1|1.1	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|P;P	.|.|.|0.41188	.|.|.|0.741;0.741	.|.|.|B;P	.|.|.|0.47528	.|.|.|0.386;0.549	T|.|T|T	0.32295|.|0.32295|0.32295	-0.9912|.|-0.9912|-0.9912	4|.|4|8	.|0.87932|.|0.62326	.|D|.|D	.|0|.|0.03	-6.8848|-6.8848|-6.8848|-6.8848	7.3946|7.3946|7.3946|7.3946	0.26929|0.26929|0.26929|0.26929	0.0:0.3093:0.0:0.6907|0.0:0.3093:0.0:0.6907|0.0:0.3093:0.0:0.6907|0.0:0.3093:0.0:0.6907	rs35444712;rs57068522|rs35444712;rs57068522|rs35444712;rs57068522|rs35444712;rs57068522	.|.|.|58;58	.|.|.|E9PB15;B4DI73	.|.|.|.;.	S|X|H|M	13|31|12|58	.|.|.|ENSP00000386621:R58M;ENSP00000409924:R58M;ENSP00000394415:R58M	.|ENSP00000393780:E31X|.|ENSP00000386621:R58M	A|E|Q|R	-|-|-|-	1|1|3|2	0|0|2|0	AARSD1|AARSD1|AARSD1|AARSD1	38385171|38385171|38385171|38385171	0.991000|0.991000|0.991000|0.991000	0.36638|0.36638|0.36638|0.36638	1.000000|1.000000|1.000000|1.000000	0.80357|0.80357|0.80357|0.80357	0.989000|0.989000|0.989000|0.989000	0.77384|0.77384|0.77384|0.77384	0.833000|0.833000|0.833000|0.833000	0.27504|0.27504|0.27504|0.27504	0.397000|0.397000|0.397000|0.397000	0.25310|0.25310|0.25310|0.25310	-0.255000|-0.255000|-0.255000|-0.255000	0.11280|0.11280|0.11280|0.11280	GCT|GAG|CAG|AGG		0.557	PTGES3L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001142653		A	41131645	C	A	41131645	3	1	99	1	0	0	0	0	1	0	0	0	21	681	24	2	1694	2	AARSD1	17	41131645	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	1511246	41131645	40063565	153	26629										
SOX9	6662	hgsc.bcm.edu	37	chr17	70119696	70119697	+	Frame_Shift_Ins	INS	-	-	CC													0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tccacagggcaatcccagggINScccaccgaccccacccacca							TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr17:70119696_70119697insCC	ENST00000245479.2	+	3	1070_1071	c.698_699insCC	c.(697-702)ggcccafs	p.GP233fs		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	233					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CAATCCCAGGGCCCACCGACCC	0.644																																					Pancreas(42;83 1041 2320 35205 39456)											0			17																																								67631292	SO:0001589	frameshift_variant	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.699_700dupCC	17.37:g.70119697_70119698dupCC	ENSP00000245479:p.Gly233fs		67631291	Q53Y80	Frame_Shift_Ins	INS	ENST00000245479.2	37	CCDS11689.1																																																																																				0.644	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		CC	70119697	-	CC	70119696	7	5	99	1	0	1	1	0	0	0	0	0	14995	1203	42	0	708	0	SOX9	17	70119696	Frame_Shift_Ins	INS	-	TCGA-DC-6681-01A-11D-1826-10	28988051	70119696	11075514	154	26630										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48593406	48593406	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aaggttgcacataggcaaagGtgtgcagttggaatgtaaag	14	4	0	0	rs121912580		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr18:48593406G>A	ENST00000342988.3	+	10	1695	c.1157G>A	c.(1156-1158)gGt>gAt	p.G386D	SMAD4_ENST00000398417.2_Missense_Mutation_p.G386D|SMAD4_ENST00000588745.1_Missense_Mutation_p.G290D	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	386	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		G -> D (in JP/HHT; dbSNP:rs28936393). {ECO:0000269|PubMed:15031030}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ATAGGCAAAGGTGTGCAGTTG	0.368																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18	GRCh37	CM021284	SMAD4	M	rs121912580						202	166	178					18																	48593406		2203	4300	6503	46847404	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1157G>A	18.37:g.48593406G>A	ENSP00000341551:p.Gly386Asp		46847404	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.998838	0.93227	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99872	-7.37;-7.37	5.65	5.65	0.86999	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.046058	0.85682	D	0.000000	D	0.99910	0.9957	H	0.96080	3.765	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96369	0.9272	9	0.87932	D	0	.	18.5072	0.90901	0.0:0.0:1.0:0.0	rs28936393	386	Q13485	SMAD4_HUMAN	D	386	ENSP00000341551:G386D;ENSP00000381452:G386D	ENSP00000341551:G386D	G	+	2	0	SMAD4	46847404	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.759000	0.98931	2.662000	0.90505	0.563000	0.77884	GGT		0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48593406	G	A	48593406	3	1	99	1	0	0	0	0	1	0	0	0	14797	1261	44	3	1191	3	SMAD4	18	48593406	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10		48593406	29483842	155	26631										
OR10H5	284433	hgsc.bcm.edu	37	chr19	15905061	15905061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cttcctgtgtgccctctccaTcaccgagatcctctacaccg	6	18	3	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr19:15905061T>C	ENST00000308940.8	+	1	301	c.203T>C	c.(202-204)aTc>aCc	p.I68T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GCCCTCTCCATCACCGAGATC	0.622																																																0			19											206	164	178					19																	15905061		2203	4300	6503	15766061	SO:0001583	missense	284433			AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"GPCR / Class A : Olfactory receptors"	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.203T>C	19.37:g.15905061T>C	ENSP00000310704:p.Ile68Thr		15766061	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	.	.	.	.	.	.	.	.	.	.	.	0.039	-1.294597	0.01375	.	.	ENSG00000172519	ENST00000308940	T	0.00551	6.65	3.47	0.0127	0.14093	GPCR, rhodopsin-like superfamily (1);	0.635963	0.13822	N	0.360341	T	0.00328	0.0010	N	0.20610	0.595	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.38908	-0.9639	10	0.19590	T	0.45	.	4.1594	0.10277	0.0:0.3256:0.1792:0.4952	.	68	Q8NGA6	O10H5_HUMAN	T	68	ENSP00000310704:I68T	ENSP00000310704:I68T	I	+	2	0	OR10H5	15766061	0.000000	0.05858	0.110000	0.21437	0.036000	0.12997	0.488000	0.22371	-0.357000	0.08175	-0.356000	0.07607	ATC		0.622	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1			C	15905061	T	C	15905061	3	2	99	1	0	0	0	0	1	0	0	0	10940	1435	50	4	205	4	OR10H5	19	15905061	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10		15905061	43223922	156	26632										
NPAS1	4861	hgsc.bcm.edu	37	chr19	47543774	47543774	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	taccagtttgtccacggacaGgacgccacgaggatccgcca	11	14	0	0	rs3745615	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr19:47543774G>A	ENST00000602212.1	+	9	1255	c.1035G>A	c.(1033-1035)caG>caA	p.Q345Q	NPAS1_ENST00000449844.2_Silent_p.Q345Q|NPAS1_ENST00000439365.2_Silent_p.Q169Q|NPAS1_ENST00000602189.1_Silent_p.Q170Q			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	345	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		TCCACGGACAGGACGCCACGA	0.662													G|||	2878	0.574681	0.3177	0.6556	5008	,	,		12848	0.7192		0.7237	False		,,,				2504	0.5624															0			19						G		1638,2764		305,1028,868	45	38	40		1035	4.1	1	19	dbSNP_107	40	6193,2401		2239,1715,343	no	coding-synonymous	NPAS1	NM_002517.2		2544,2743,1211	AA,AG,GG		27.9381,37.2104,39.743		345/591	47543774	7831,5165	2201	4297	6498	52235614	SO:0001819	synonymous_variant	4861			U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"Basic helix-loop-helix proteins"	7894	protein-coding gene	gene with protein product	"neuronal PAS1", "member of PAS superfamily 5"	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1035G>A	19.37:g.47543774G>A			52235614	B4DR69|Q99632|Q9BY83	Silent	SNP	ENST00000602212.1	37	CCDS12694.1																																																																																				0.662	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517		A	47543774	G	A	47543774	2	1	99	1	0	0	0	0	0	0	0	1	10593	991	35	3		3	NPAS1	19	47543774	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	31638713	47543774	11585209	157	26633										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52033206	52033206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctggccctccaggacagggaGggacgaggtgttttgcagga	17	9	0	0	rs2005199	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr19:52033206G>A	ENST00000425629.3	-	5	938	c.784C>T	c.(784-786)Ctc>Ttc	p.L262F	SIGLEC6_ENST00000391797.3_Missense_Mutation_p.L251F|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.L210F|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.L273F|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.L262F|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.L246F	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	262	Ig-like C2-type 2.		L -> F (in dbSNP:rs2005199).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		AGGACAGGGAGGGACGAGGTG	0.607													G|||	354	0.0706869	0.0144	0.0648	5008	,	,		17592	0.0942		0.0686	False		,,,				2504	0.1288															0			19						G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	105,4301	79.9+/-118.3	1,103,2099	99	111	107		628,817,751,784,736,784	-2.2	0	19	dbSNP_92	107	577,8015	151.0+/-205.8	20,537,3739	yes	missense,missense,missense,missense,missense,missense	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	22,22,22,22,22,22	21,640,5838	AA,AG,GG		6.7155,2.3831,5.247	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	210/402,273/390,251/343,262/454,246/438,262/354	52033206	682,12316	2203	4296	6499	56725018	SO:0001583	missense	946			D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.784C>T	19.37:g.52033206G>A	ENSP00000401502:p.Leu262Phe		56725018	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	150	0.06868131868131869	13	0.026422764227642278	30	0.08287292817679558	58	0.10139860139860139	49	0.06464379947229551	G	12.86	2.065950	0.36470	0.023831	0.067155	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	3.71	-2.15	0.07102	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.482528	0.15384	N	0.265175	T	0.05364	0.0142	M	0.79926	2.475	0.80722	P	0.0	B;P;P;P;P;P	0.49635	0.451;0.759;0.839;0.839;0.926;0.701	P;P;P;P;P;P	0.55667	0.498;0.513;0.781;0.673;0.781;0.617	T	0.48305	-0.9047	9	0.52906	T	0.07	.	0.4643	0.00521	0.2894:0.1853:0.3361:0.1892	rs2005199;rs17305038;rs52789758;rs59181551;rs2005199	273;210;251;262;246;262	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	F	235;246;262;273;210;262	ENSP00000401502:L262F;ENSP00000353071:L273F;ENSP00000410679:L210F;ENSP00000345907:L262F	ENSP00000345907:L262F	L	-	1	0	SIGLEC6	56725018	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.232000	0.09055	-0.404000	0.07610	0.514000	0.50259	CTC		0.607	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		A	52033206	G	A	52033206	3	1	99	1	0	0	0	0	1	0	0	0	14349	1000	35	3	593	3	SIGLEC6	19	52033206	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	4489432	52033206	7095777	158	26634										
ZNF761	388561	hgsc.bcm.edu	37	chr19	53958126	53958126	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aatcaaaaagttgacaggtaTtacagaacgatatgatcaaa	7	5	2	3	rs2708743	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr19:53958126T>G	ENST00000454407.1	+	0	818							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TTGACAGGTATTACAGAACGA	0.358													N|||	3224	0.64377	0.6846	0.7666	5008	,	,		20267	0.5278		0.6899	False		,,,				2504	0.5736															0			19						G	SER/ILE	3076,1330	441.4+/-346.4	1090,896,217	95	94	94		366	-2	0	19	dbSNP_100	94	5864,2736	435.4+/-358.0	1984,1896,420	yes	missense	ZNF761	NM_001008401.3	142	3074,2792,637	GG,GT,TT		31.814,30.1861,31.2625	probably-damaging	122/747	53958126	8940,4066	2203	4300	6503	58649938			388561			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958126T>G			58649938	Q6ZNB9	Nonsense_Mutation	SNP	ENST00000454407.1	37																																																																																					0.358	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		G	53958126	T	G	53958126	1	3	99	0	1	0	0	0	0	0	0	0	18175	1493	52	4		4	ZNF761	19	53958126	RNA	SNP	T	TCGA-DC-6681-01A-11D-1826-10	1924920	53958126	5170857	159	26635										
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959568	53959568	+	RNA	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atcagaaaattcatactgaaGagaatccttacaagtgtaat	6	6	2	3	rs2617726	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr19:53959568G>C	ENST00000454407.1	+	0	2260							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TCATACTGAAGAGAATCCTTA	0.393													g|||	1936	0.386581	0.3964	0.5346	5008	,	,		24330	0.2401		0.3986	False		,,,				2504	0.407															0			19						G	GLN/GLU	1775,2631	521.7+/-370.6	392,991,820	116	121	119		1808	1.1	0.2	19	dbSNP_100	119	3494,5102	510.5+/-377.5	706,2082,1510	no	missense	ZNF761	NM_001008401.3	29	1098,3073,2330	CC,CG,GG		40.6468,40.286,40.5245	benign	603/747	53959568	5269,7733	2203	4298	6501	58651380			388561			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959568G>C			58651380	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																					0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		C	53959568	G	C	53959568	1	2	99	0	1	0	0	0	0	0	0	0	18175	943	33	5		5	ZNF761	19	53959568	RNA	SNP	G	TCGA-DC-6681-01A-11D-1826-10	1442	53959568	5169415	160	26636										
FAM110A	83541	hgsc.bcm.edu	37	chr20	825678	825678	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ctgtccaaacagccgctcttTagccctgagactcgccgcac	8	17	1	1	rs538094	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr20:825678T>C	ENST00000304189.2	+	3	612	c.231T>C	c.(229-231)ttT>ttC	p.F77F	FAM110A_ENST00000541082.1_Silent_p.F77F|FAM110A_ENST00000246100.3_Silent_p.F77F|FAM110A_ENST00000381939.1_Silent_p.F77F|FAM110A_ENST00000381941.3_Silent_p.F77F			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	77						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|lung(2)	3						AGCCGCTCTTTAGCCCTGAGA	0.682													T|||	4132	0.82508	0.7678	0.8934	5008	,	,		11354	0.8829		0.8708	False		,,,				2504	0.7474															0			20						T	,,	3401,977		1331,739,119	14	15	14		231,231,231	-0.4	1	20	dbSNP_83	14	7450,1122		3241,968,77	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM110A	NM_001042353.1,NM_031424.4,NM_207121.3	,,	4572,1707,196	CC,CT,TT		13.0891,22.3161,16.2085	,,	77/296,77/296,77/296	825678	10851,2099	2189	4286	6475	773678	SO:0001819	synonymous_variant	83541			BC012800	CCDS13008.1	20p13	2007-06-21	2007-03-21	2007-03-21	ENSG00000125898	ENSG00000125898			16188	protein-coding gene	gene with protein product		611393	"chromosome 20 open reading frame 55"	C20orf55		17499476	Standard	NM_001042353		Approved	bA371L19.3	uc002wef.1	Q9BQ89	OTTHUMG00000031649	ENST00000304189.2:c.231T>C	20.37:g.825678T>C			773678	D3DVW2|Q5R1M7	Silent	SNP	ENST00000304189.2	37	CCDS13008.1																																																																																				0.682	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424		C	825678	T	C	825678	2	2	99	1	0	0	0	0	0	0	0	1	5412	1751	61	4		4	FAM110A	20	825678	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10		825678	62199842	161	26637										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023710	31023710	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	atggttgctcctcagagctgGgtgtctcgagtatgtgcggt	15	8	2	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr20:31023710G>A	ENST00000375687.4	+	13	3619	c.3195G>A	c.(3193-3195)tgG>tgA	p.W1065*	ASXL1_ENST00000306058.5_Nonsense_Mutation_p.W1060*	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1065					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CTCAGAGCTGGGTGTCTCGAG	0.547			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20											179	143	155					20																	31023710		2203	4300	6503	30487371	SO:0001587	stop_gained	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3195G>A	20.37:g.31023710G>A	ENSP00000364839:p.Trp1065*		30487371	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Nonsense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	G	43	10.011113	0.99317	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	.	.	.	4.17	4.17	0.49024	.	0.295841	0.36778	N	0.002407	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-8.028	15.9282	0.79635	0.0:0.0:1.0:0.0	.	.	.	.	X	1065;1065;1065;986;1060	.	ENSP00000305119:W1060X	W	+	3	0	ASXL1	30487371	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.967000	0.49216	2.614000	0.88457	0.561000	0.74099	TGG		0.547	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		A	31023710	G	A	31023710	4	1	99	1	0	0	0	0	0	1	0	0	1067	1241	43	3	3251	3	ASXL1	20	31023710	Nonsense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	30198032	31023710	32001810	162	26638										
FAM83C	128876	hgsc.bcm.edu	37	chr20	33875030	33875030	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtcagggtctcccacttctcGggctctggggaaggggacaa	15	11	4	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr20:33875030G>A	ENST00000374408.3	-	4	1648	c.1552C>T	c.(1552-1554)Cga>Tga	p.R518*	EIF6_ENST00000374450.3_5'Flank|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374443.3_5'Flank|FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374436.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	518										central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			CCCACTTCTCGGGCTCTGGGG	0.637																																																0			20											47	47	47					20																	33875030		2123	4196	6319	33338444	SO:0001587	stop_gained	128876			AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 128"	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1552C>T	20.37:g.33875030G>A	ENSP00000363529:p.Arg518*		33338444	Q14D67|Q5JWN6|Q8N276	Nonsense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.800929	0.90538	.	.	ENSG00000125998	ENST00000374408	.	.	.	4.14	2.04	0.26737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-16.1375	6.5978	0.22683	0.0:0.1894:0.5881:0.2225	.	.	.	.	X	518	.	ENSP00000363529:R518X	R	-	1	2	FAM83C	33338444	0.994000	0.37717	0.986000	0.45419	0.772000	0.43724	1.735000	0.38176	0.433000	0.26313	0.561000	0.74099	CGA		0.637	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3			A	33875030	G	A	33875030	4	1	99	1	0	0	0	0	0	1	0	0	5654	1124	39	1	695	1	FAM83C	20	33875030	Nonsense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	2851320	33875030	29150490	163	26639										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50310638	50310638	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gatccgtccgcaagaagcatGaccctgtggaaggaagtcgg	14	10	0	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr20:50310638G>A	ENST00000338821.5	-	7	815	c.551C>T	c.(550-552)tCa>tTa	p.S184L	ATP9A_ENST00000402822.1_Intron|ATP9A_ENST00000311637.5_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	184					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.S184L(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CAAGAAGCATGACCCTGTGGA	0.632																																																1	Substitution - Missense(1)	ovary(1)	20											55	50	51					20																	50310638		2203	4300	6503	49744045	SO:0001583	missense	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.551C>T	20.37:g.50310638G>A	ENSP00000342481:p.Ser184Leu		49744045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140081	0.94560	.	.	ENSG00000054793	ENST00000338821	D	0.91631	-2.88	5.04	5.04	0.67666	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.90539	0.7035	N	0.17631	0.505	0.80722	D	1	D	0.56287	0.975	P	0.56088	0.791	D	0.88285	0.2939	10	0.17369	T	0.5	-21.8079	18.3987	0.90509	0.0:0.0:1.0:0.0	.	184	O75110	ATP9A_HUMAN	L	184	ENSP00000342481:S184L	ENSP00000342481:S184L	S	-	2	0	ATP9A	49744045	1.000000	0.71417	0.956000	0.39512	0.741000	0.42261	9.368000	0.97152	2.329000	0.79093	0.655000	0.94253	TCA		0.632	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50310638	G	A	50310638	3	1	99	1	0	0	0	0	1	0	0	0	1199	1294	45	3	2680	3	ATP9A	20	50310638	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	16435608	50310638	12714882	164	26640										
APP	351	hgsc.bcm.edu	37	chr21	27264060	27264060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cacaccatgatgaatggatgTgtactgtttcttcttcagca	8	9	3	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr21:27264060T>C	ENST00000346798.3	-	17	2218	c.2185A>G	c.(2185-2187)Aca>Gca	p.T729A	APP_ENST00000357903.3_Missense_Mutation_p.T710A|APP_ENST00000354192.3_Missense_Mutation_p.T598A|APP_ENST00000440126.3_Missense_Mutation_p.T705A|APP_ENST00000448388.2_Missense_Mutation_p.T619A|APP_ENST00000358918.3_Missense_Mutation_p.T711A|APP_ENST00000348990.5_Missense_Mutation_p.T654A|APP_ENST00000359726.3_Missense_Mutation_p.T673A|APP_ENST00000439274.2_Missense_Mutation_p.T673A	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	729					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TGAATGGATGTGTACTGTTTC	0.443																																																0			21											189	151	164					21																	27264060		2203	4300	6503	26185931	SO:0001583	missense	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.2185A>G	21.37:g.27264060T>C	ENSP00000284981:p.Thr729Ala		26185931	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.390570	0.62066	.	.	ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274;ENST00000456209	D;D;D;D;D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64	5.65	5.65	0.86999	Beta-amyloid precursor protein C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94026	0.8086	N	0.12182	0.205	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.979;0.999;0.974;0.974;0.999	D;D;D;D;D;D;D	0.87578	0.998;0.998;0.982;0.997;0.969;0.969;0.998	D	0.95403	0.8491	10	0.62326	D	0.03	-14.8557	15.8391	0.78831	0.0:0.0:0.0:1.0	.	619;673;705;598;654;710;729	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067	.;.;.;.;.;.;A4_HUMAN	A	729;598;654;710;711;673;619;705;673;298	ENSP00000284981:T729A;ENSP00000346129:T598A;ENSP00000345463:T654A;ENSP00000350578:T710A;ENSP00000351796:T711A;ENSP00000352760:T673A;ENSP00000388538:T619A;ENSP00000387483:T705A;ENSP00000398879:T673A	ENSP00000284981:T729A	T	-	1	0	APP	26185931	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.858000	0.69532	2.279000	0.76181	0.533000	0.62120	ACA		0.443	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27264060	T	C	27264060	3	2	99	1	0	0	0	0	1	0	0	0	815	1696	59	4	135	4	APP	21	27264060	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10		27264060	20865835	165	26641										
TCP10L	140290	hgsc.bcm.edu	37	chr21	33956579	33956579	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tcctctgggtgggtgccctcTttggggtccctggcctcgag	15	13	2	0	rs2017816	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr21:33956579T>C	ENST00000300258.3	-	2	149	c.36A>G	c.(34-36)aaA>aaG	p.K12K	AP000275.65_ENST00000553001.1_Intron|TCP10L_ENST00000472557.1_Intron	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	12					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						GGGTGCCCTCTTTGGGGTCCC	0.637													C|||	2175	0.434305	0.553	0.3703	5008	,	,		17914	0.3492		0.3767	False		,,,				2504	0.4663															0			21						C		2319,2087		596,1127,480	48	44	46		36	-0.9	0	21	dbSNP_92	46	3178,5422		607,1964,1729	no	coding-synonymous	TCP10L	NM_144659.5		1203,3091,2209	CC,CT,TT		36.9535,47.3672,42.2651		12/216	33956579	5497,7509	2203	4300	6503	32878450	SO:0001819	synonymous_variant	140290			AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"t-complex 10 (a murine tcp homolog)-like", "t-complex 10 (mouse)-like"			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.36A>G	21.37:g.33956579T>C			32878450	Q53EW0|Q96LN5	Silent	SNP	ENST00000300258.3	37	CCDS13616.1																																																																																				0.637	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659		C	33956579	T	C	33956579	2	2	99	1	0	0	0	0	0	0	0	1	15750	1606	56	4		4	TCP10L	21	33956579	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10	6692519	33956579	14173316	166	26642										
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gcagacggacatggtagacgTggccatgctggggtggggag	20	7	0	2	rs452472	byFrequency	TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr21:45978592T>C	ENST00000391620.1	-	1	51	c.7A>G	c.(7-9)Acg>Gcg	p.T3A	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	3			T -> A (in dbSNP:rs452472). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ATGGTAGACGTGGCCATGCTG	0.642													.|||	1067	0.213059	0.1483	0.2594	5008	,	,		17698	0.1964		0.337	False		,,,				2504	0.1575															0			21						T	,ALA/THR	730,3676	732.5+/-410.4	60,610,1533	59	59	59		,7	-3.7	0	21	dbSNP_80	59	2840,5760	661.1+/-401.8	475,1890,1935	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,58	535,2500,3468	CC,CT,TT		33.0233,16.5683,27.4489	,benign	,3/222	45978592	3570,9436	2203	4300	6503	44803020	SO:0001583	missense	386682			AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"Keratin associated proteins"	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.7A>G	21.37:g.45978592T>C	ENSP00000375478:p.Thr3Ala		44803020	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	482	0.2206959706959707	65	0.13211382113821138	91	0.2513812154696133	102	0.17832167832167833	224	0.2955145118733509	c	0.001	-2.986087	0.00046	0.165683	0.330233	ENSG00000212935	ENST00000391620	T	0.02863	4.13	3.32	-3.69	0.04450	.	.	.	.	.	T	0.00012	0.0000	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	8	0.02654	T	1	.	3.4126	0.07364	0.1224:0.5648:0.1215:0.1914	rs452472	3	P60369	KR103_HUMAN	A	3	ENSP00000375478:T3A	ENSP00000375478:T3A	T	-	1	0	KRTAP10-3	44803020	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.871000	0.04223	-1.132000	0.02907	-2.541000	0.00179	ACG		0.642	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			C	45978592	T	C	45978592	3	2	99	1	0	0	0	0	1	0	0	0	8531	1696	59	4	662	4	KRTAP10-3	21	45978592	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	12022013	45978592	2151303	167	26643										
KRTAP10-8	386681	hgsc.bcm.edu	37	chr21	46032564	46032564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gtgtgcctgtctgctctgggGcttcctctctgtgctgccag	13	13	3	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr21:46032564G>A	ENST00000334662.2	+	1	569	c.547G>A	c.(547-549)Gct>Act	p.A183T	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	183	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.A183S(2)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						CTGCTCTGGGGCTTCCTCTCT	0.632																																																2	Substitution - Missense(2)	lung(2)	21											189	190	190					21																	46032564		2203	4300	6503	44856992	SO:0001583	missense	386681			AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"Keratin associated proteins"	20525	protein-coding gene	gene with protein product			"keratin associated protein 18-8"	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.547G>A	21.37:g.46032564G>A	ENSP00000335565:p.Ala183Thr		44856992	A0JNW4	Missense_Mutation	SNP	ENST00000334662.2	37	CCDS13713.1	.	.	.	.	.	.	.	.	.	.	g	0.795	-0.757611	0.03019	.	.	ENSG00000187766	ENST00000334662	T	0.00824	5.65	2.75	-1.32	0.09201	.	.	.	.	.	T	0.01029	0.0034	L	0.33668	1.02	0.09310	N	1	B	0.19706	0.038	B	0.25291	0.059	T	0.42865	-0.9426	9	0.30854	T	0.27	.	10.8118	0.46551	0.0:0.0:0.6604:0.3396	.	183	P60410	KR108_HUMAN	T	183	ENSP00000335565:A183T	ENSP00000335565:A183T	A	+	1	0	KRTAP10-8	44856992	0.880000	0.30214	0.001000	0.08648	0.008000	0.06430	-0.279000	0.08479	-0.429000	0.07329	-0.520000	0.04383	GCT		0.632	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695		A	46032564	G	A	46032564	3	1	99	1	0	0	0	0	1	0	0	0	8536	1203	42	3	549	3	KRTAP10-8	21	46032564	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	53972	46032564	2097331	168	26644										
NF2	4771	hgsc.bcm.edu	37	chr22	30050666	30050666	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tatggtgactacgaccccagTgttcacaagcggggattttt	11	9	1	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr22:30050666T>C	ENST00000338641.4	+	5	909	c.468T>C	c.(466-468)agT>agC	p.S156S	NF2_ENST00000353887.4_Silent_p.S73S|NF2_ENST00000334961.7_Silent_p.S73S|NF2_ENST00000403435.1_Silent_p.S156S|NF2_ENST00000361166.4_Silent_p.S156S|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Silent_p.S115S|NF2_ENST00000361676.4_Silent_p.S114S|NF2_ENST00000403999.3_Silent_p.S156S|NF2_ENST00000413209.2_Intron|NF2_ENST00000397789.3_Silent_p.S156S	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	156	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.S156R(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ACGACCCCAGTGTTCACAAGC	0.433			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	4	Unknown(3)|Substitution - Missense(1)	meninges(1)|large_intestine(1)|stomach(1)|central_nervous_system(1)	22											156	158	158					22																	30050666		2203	4300	6503	28380666	SO:0001819	synonymous_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.468T>C	22.37:g.30050666T>C			28380666	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Silent	SNP	ENST00000338641.4	37	CCDS13861.1																																																																																				0.433	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		C	30050666	T	C	30050666	2	2	99	1	0	0	0	0	0	0	0	1	10388	1693	59	4		4	NF2	22	30050666	Silent	SNP	T	TCGA-DC-6681-01A-11D-1826-10		30050666	21253900	169	26645										
APOL6	80830	hgsc.bcm.edu	37	chr22	36055398	36055398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	ggaagcacctgaaggaaggaGcaaggacaaagtttgcggaa	15	6	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr22:36055398G>A	ENST00000409652.4	+	3	1063	c.787G>A	c.(787-789)Gca>Aca	p.A263T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	263					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						GAAGGAAGGAGCAAGGACAAA	0.527																																																0			22											80	76	77					22																	36055398		2203	4300	6503	34385344	SO:0001583	missense	80830			AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"Apolipoproteins"	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.787G>A	22.37:g.36055398G>A	ENSP00000386280:p.Ala263Thr		34385344	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	37	CCDS13919.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.855199	0.32791	.	.	ENSG00000221963	ENST00000409652	T	0.04917	3.53	4.38	0.475	0.16774	.	0.885835	0.09576	N	0.783573	T	0.09818	0.0241	M	0.76002	2.32	0.09310	N	1	B	0.14012	0.009	B	0.19666	0.026	T	0.30119	-0.9989	10	0.52906	T	0.07	-17.2031	7.1954	0.25849	0.3523:0.0:0.6477:0.0	.	263	Q9BWW8	APOL6_HUMAN	T	263	ENSP00000386280:A263T	ENSP00000386280:A263T	A	+	1	0	APOL6	34385344	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	0.231000	0.17872	0.073000	0.16731	-0.136000	0.14681	GCA		0.527	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		A	36055398	G	A	36055398	3	1	99	1	0	0	0	0	1	0	0	0	810	971	34	3	793	3	APOL6	22	36055398	Missense_Mutation	SNP	G	TCGA-DC-6681-01A-11D-1826-10	6004732	36055398	15249168	170	26646										
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37480817	37480817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	cgagtagtagctggggaagtAcggggtgctgaggacgccct	18	8	0	1			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr22:37480817A>G	ENST00000346753.3	-	9	1179	c.1063T>C	c.(1063-1065)Tac>Cac	p.Y355H	TMPRSS6_ENST00000406856.1_Missense_Mutation_p.Y346H|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.Y346H|RP5-1170K4.7_ENST00000414203.2_RNA|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.Y355H|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.Y346H	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	355	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CTGGGGAAGTACGGGGTGCTG	0.642																																																0			22											86	72	77					22																	37480817		2199	4290	6489	35810763	SO:0001583	missense	164656			AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1063T>C	22.37:g.37480817A>G	ENSP00000334962:p.Tyr355His		35810763	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	a	11.37	1.618980	0.28801	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000429068;ENST00000442782	T;T;T;T;T;T	0.19532	2.14;2.14;2.14;2.14;2.14;2.14	4.52	3.49	0.39957	CUB (4);	0.252955	0.33712	N	0.004638	T	0.16769	0.0403	L	0.43152	1.355	0.36265	D	0.854783	B;B;B	0.14438	0.01;0.003;0.001	B;B;B	0.13407	0.009;0.003;0.001	T	0.08638	-1.0712	10	0.45353	T	0.12	.	7.0904	0.25282	0.7963:0.0:0.2037:0.0	.	355;346;355	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	H	346;355;346;346;17;355	ENSP00000371211:Y346H;ENSP00000334962:Y355H;ENSP00000385453:Y346H;ENSP00000384964:Y346H;ENSP00000392433:Y17H;ENSP00000397691:Y355H	ENSP00000334962:Y355H	Y	-	1	0	TMPRSS6	35810763	0.996000	0.38824	0.740000	0.30986	0.652000	0.38707	3.384000	0.52478	0.597000	0.29811	0.456000	0.33151	TAC		0.642	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		G	37480817	A	G	37480817	3	3	99	1	0	0	0	0	1	0	0	0	16290	391	14	4	1412	4	TMPRSS6	22	37480817	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10	1425419	37480817	13823749	171	26647										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50437751	50437751	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gggcagatctggatccgcacCgcgtcaggggtcgcagacca	15	13	2	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chr22:50437751C>T	ENST00000389983.2	-	9	834	c.570G>A	c.(568-570)gcG>gcA	p.A190A	IL17REL_ENST00000341280.5_Silent_p.A190A	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	190										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GGATCCGCACCGCGTCAGGGG	0.667																																																0			22											63	65	64					22																	50437751		2203	4300	6503	48779878	SO:0001819	synonymous_variant	400935			AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.570G>A	22.37:g.50437751C>T			48779878	A6NCN4|A6PVC1	Silent	SNP	ENST00000389983.2	37	CCDS33679.1																																																																																				0.667	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		T	50437751	C	T	50437751	2	4	99	1	0	0	0	0	0	0	0	1	7665	639	23	1		1	IL17REL	22	50437751	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	12956934	50437751	866815	172	26648										
XG	7499	hgsc.bcm.edu	37	chrX	2729382	2729382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tctccactcctgcaggcaatAtggtagcaaaaatcgtgtct	8	11	2	0	rs201628009		TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:2729382A>G	ENST00000381174.5	+	9	640	c.415A>G	c.(415-417)Atg>Gtg	p.M139V	XG_ENST00000426774.1_Missense_Mutation_p.M140V|XG_ENST00000419513.2_Missense_Mutation_p.M154V|snoU13_ENST00000516039.1_RNA			P55808	XG_HUMAN	Xg blood group	139						integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TGCAGGCAATATGGTAGCAAA	0.433																																																0			X						A	VAL/MET,VAL/MET,VAL/MET	0,3835		0,0,1632,571	51	48	49		460,418,415	-0.7	0	X		49	2,6724		0,2,2426,1870	yes	missense,missense,missense	XG	NM_001141919.1,NM_001141920.1,NM_175569.2	21,21,21	0,2,4058,2441	GG,GA,AA,A		0.0297,0.0,0.0189	benign,benign,benign	154/196,140/182,139/181	2729382	2,10559	2203	4298	6501	2739382	SO:0001583	missense	100132596			AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"Blood group antigens", "Pseudoautosomal regions / PAR1"	12806	protein-coding gene	gene with protein product		300879	"Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.415A>G	X.37:g.2729382A>G	ENSP00000370566:p.Met139Val		2739382	E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Missense_Mutation	SNP	ENST00000381174.5	37	CCDS14120.1	.	.	.	.	.	.	.	.	.	.	A	5.638	0.302347	0.10678	0.0	2.97E-4	ENSG00000124343	ENST00000381174;ENST00000419513;ENST00000426774;ENST00000509484;ENST00000533923	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	3.58	-0.727	0.11166	.	2.178760	0.02607	U	0.101685	T	0.10895	0.0266	N	0.19112	0.55	0.09310	N	1	B;B	0.13145	0.007;0.006	B;B	0.14578	0.011;0.006	T	0.14392	-1.0474	10	0.06365	T	0.9	.	2.7504	0.05279	0.5324:0.0:0.2669:0.2008	.	139;154	P55808;P55808-3	XG_HUMAN;.	V	139;154;140;117;1	ENSP00000370566:M139V;ENSP00000411004:M154V;ENSP00000398503:M140V;ENSP00000430005:M117V	ENSP00000370566:M139V	M	+	1	0	XG	2739382	0.006000	0.16342	0.006000	0.13384	0.139000	0.21198	0.991000	0.29654	-0.038000	0.13624	0.303000	0.19852	ATG		0.433	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		G	2729382	A	G	2729382	3	3	99	1	0	0	0	0	1	0	0	0	17467	449	16	4	501	4	XG	23	2729382	Missense_Mutation	SNP	A	TCGA-DC-6681-01A-11D-1826-10		2729382	152541178	173	26649										
KDM6A	7403	hgsc.bcm.edu	37	chrX	44942737	44942737	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gctacatgagctgactaaacTtcctgcttttgtgcgtgtcg	10	10	0	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:44942737T>C	ENST00000377967.4	+	23	3358	c.3317T>C	c.(3316-3318)cTt>cCt	p.L1106P	KDM6A_ENST00000536777.1_Missense_Mutation_p.L1061P|KDM6A_ENST00000382899.4_Missense_Mutation_p.L1113P|KDM6A_ENST00000543216.1_Missense_Mutation_p.L1027P	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1106	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.		L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.L1106R(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						CTGACTAAACTTCCTGCTTTT	0.398			"D, N, F, S"		"renal, oesophageal SCC, MM"																																Colon(129;1273 1667 15230 27352 52914)		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	7	Whole gene deletion(6)|Substitution - Missense(1)	oesophagus(2)|breast(2)|pancreas(2)|large_intestine(1)	X											145	107	120					X																	44942737		2203	4300	6503	44827681	SO:0001583	missense	7403			AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3317T>C	X.37:g.44942737T>C	ENSP00000367203:p.Leu1106Pro		44827681	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363272	0.82353	.	.	ENSG00000147050	ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.24	5.24	0.73138	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	D	0.91707	0.7378	M	0.92833	3.35	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.997;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.993;0.994;1.0;0.999;0.999	D	0.93562	0.6896	10	0.87932	D	0	-12.5257	14.2463	0.65990	0.0:0.0:0.0:1.0	.	745;1113;1061;1158;1106	B4E0L8;F8W8R6;F5H6S1;B7ZKN5;O15550	.;.;.;.;KDM6A_HUMAN	P	803;1106;1061;1113;1027	ENSP00000367203:L1106P;ENSP00000437405:L1061P;ENSP00000372355:L1113P;ENSP00000443078:L1027P	ENSP00000334340:L803P	L	+	2	0	KDM6A	44827681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.603000	0.82811	1.742000	0.51746	0.472000	0.43445	CTT		0.398	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		C	44942737	T	C	44942737	3	2	99	1	0	0	0	0	1	0	0	0	8158	1609	56	4	3407	4	KDM6A	23	44942737	Missense_Mutation	SNP	T	TCGA-DC-6681-01A-11D-1826-10	42213355	44942737	110327823	174	26650										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71830999	71830999	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	gctctctcactgtagcactcCgttcattatacaattcagtg	6	12	4	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:71830999C>A	ENST00000373542.4	-	22	2564	c.2405G>T	c.(2404-2406)cGg>cTg	p.R802L	PHKA1_ENST00000339490.3_Missense_Mutation_p.R802L|PHKA1_ENST00000373539.3_Missense_Mutation_p.R802L|PHKA1_ENST00000373545.3_Missense_Mutation_p.R743L|PHKA1_ENST00000541944.1_Missense_Mutation_p.R743L	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	802					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R802Q(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TGTAGCACTCCGTTCATTATA	0.428																																																1	Substitution - Missense(1)	lung(1)	X											83	73	76					X																	71830999		2203	4300	6503	71747724	SO:0001583	missense	5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2405G>T	X.37:g.71830999C>A	ENSP00000362643:p.Arg802Leu		71747724	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287273	0.23478	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.90900	-2.75;-2.74;-2.75;-2.74;-2.75	5.85	0.493	0.16878	Glycoside hydrolase 15-related (1);	0.923503	0.09445	N	0.801259	D	0.83119	0.5185	L	0.33245	0.995	0.09310	N	1	B;B;B	0.19331	0.035;0.0;0.003	B;B;B	0.23852	0.031;0.009;0.049	T	0.66822	-0.5826	10	0.23891	T	0.37	-3.2086	6.0072	0.19553	0.0:0.4232:0.1325:0.4443	.	743;802;802	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	L	743;802;743;802;802	ENSP00000362646:R743L;ENSP00000362643:R802L;ENSP00000441251:R743L;ENSP00000342469:R802L;ENSP00000362640:R802L	ENSP00000342469:R802L	R	-	2	0	PHKA1	71747724	0.000000	0.05858	0.009000	0.14445	0.918000	0.54935	0.246000	0.18160	0.004000	0.14682	0.600000	0.82982	CGG		0.428	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71830999	C	A	71830999	3	1	99	1	0	0	0	0	1	0	0	0	11874	652	23	2	1310	2	PHKA1	23	71830999	Missense_Mutation	SNP	C	TCGA-DC-6681-01A-11D-1826-10	26888262	71830999	83439561	175	26651										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120182714	120182714	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	aagcagttgaccaaatccaaCgcacccagagtcaaagccaa	7	13	1	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:120182714C>T	ENST00000328078.1	+	1	1253	c.1176C>T	c.(1174-1176)aaC>aaT	p.N392N		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	392					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CCAAATCCAACGCACCCAGAG	0.493																																																0			X											195	178	184					X																	120182714		2203	4300	6503	120010395	SO:0001819	synonymous_variant	2747			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1176C>T	X.37:g.120182714C>T			120010395	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																				0.493	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		T	120182714	C	T	120182714	2	4	99	1	0	0	0	0	0	0	0	1	6497	535	19	1		1	GLUD2	23	120182714	Silent	SNP	C	TCGA-DC-6681-01A-11D-1826-10	48351715	120182714	35087846	176	26652										
CD40LG	959	hgsc.bcm.edu	37	chrX	135730440	135730440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	tacaaccaaacttctccccgAtctgcggccactggactgcc	7	17	2	0			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:135730440A>G	ENST00000370629.2	+	1	89	c.33A>G	c.(31-33)cgA>cgG	p.R11R	CD40LG_ENST00000370628.2_Silent_p.R11R	NM_000074.2	NP_000065.1	P29965	CD40L_HUMAN	CD40 ligand	11					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|immunoglobulin secretion (GO:0048305)|inflammatory response (GO:0006954)|isotype switching (GO:0045190)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of interleukin-12 production (GO:0032735)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CD40 receptor binding (GO:0005174)			endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|skin(1)|stomach(1)	26	Acute lymphoblastic leukemia(192;0.000127)					CTTCTCCCCGATCTGCGGCCA	0.433									Immune Deficiency with Hyper-IgM																																							0			X											148	138	141					X																	135730440		2203	4300	6503	135558106	SO:0001819	synonymous_variant	959	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	X67878	CCDS14659.1	Xq26	2014-09-17	2008-08-01	2005-01-14	ENSG00000102245	ENSG00000102245		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11935	protein-coding gene	gene with protein product	"CD40 antigen ligand", "tumor necrosis factor (ligand) superfamily member 5", "T-B cell-activating molecule", "TNF-related activation protein", "hyper-IgM syndrome"	300386	"tumor necrosis factor (ligand) superfamily, member 5 (hyper-IgM syndrome)"	HIGM1, IMD3, TNFSF5		1427881, 7678782	Standard	NM_000074		Approved	CD40L, TRAP, gp39, hCD40L, CD154	uc004faa.3	P29965	OTTHUMG00000022512	ENST00000370629.2:c.33A>G	X.37:g.135730440A>G			135558106		Silent	SNP	ENST00000370629.2	37	CCDS14659.1																																																																																				0.433	CD40LG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058501.1	NM_000074		G	135730440	A	G	135730440	2	3	99	1	0	0	0	0	0	0	0	1	3022	320	12	4		4	CD40LG	23	135730440	Silent	SNP	A	TCGA-DC-6681-01A-11D-1826-10	15547726	135730440	19540120	177	26653										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138886723	138886723	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.050561797752809	9	1	0.772580498453702	2.63249651324965	0.49359309623431	1	1	0	agaataagatcacagggaaaGgtttcatctgcctgtacttc	9	8	3	2			TCGA-DC-6681-01A-11D-1826-10	TCGA-DC-6681-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	821cef24-769d-4f2d-8006-819cda661112	ffc9adfb-e651-4424-a0a7-2ea6a0340f63	g.chrX:138886723G>T	ENST00000327569.3	-	6	569	c.471C>A	c.(469-471)acC>acA	p.T157T	ATP11C_ENST00000370557.1_Silent_p.T154T|ATP11C_ENST00000359686.2_Silent_p.T157T|ATP11C_ENST00000361648.2_Silent_p.T157T|ATP11C_ENST00000370543.1_Silent_p.T157T	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	157			T -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					CACAGGGAAAGGTTTCATCTG	0.368																																																0			X											187	162	171					X																	138886723		2203	4300	6503	138714389	SO:0001819	synonymous_variant	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.471C>A	X.37:g.138886723G>T			138714389	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Silent	SNP	ENST00000327569.3	37	CCDS14668.1																																																																																				0.368	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		T	138886723	G	T	138886723	2	4	99	1	0	0	0	0	0	0	0	1	1122	987	35	2		2	ATP11C	23	138886723	Silent	SNP	G	TCGA-DC-6681-01A-11D-1826-10	3156283	138886723	16383837	178	26654										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1412699	1412699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggcgcagatgcaggagcagaCgctgcagttggagcaacagt	16	9	0	2	rs144497634		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:1412699C>T	ENST00000308647.7	+	2	367	c.251C>T	c.(250-252)aCg>aTg	p.T84M	ATAD3B_ENST00000378741.3_5'UTR	NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	84						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CAGGAGCAGACGCTGCAGTTG	0.632																																																0			1						C	MET/THR	0,4406		0,0,2203	48	46	47		251	2.9	1	1	dbSNP_134	47	1,8589		0,1,4294	no	missense	ATAD3B	NM_031921.4	81	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	84/649	1412699	1,12995	2203	4295	6498	1402562	SO:0001583	missense	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.251C>T	1.37:g.1412699C>T	ENSP00000311766:p.Thr84Met		1402562	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	15.43	2.831351	0.50845	0.0	1.16E-4	ENSG00000160072	ENST00000360489;ENST00000308647	T	0.11385	2.78	2.9	2.9	0.33743	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.111372	0.64402	D	0.000011	T	0.40196	0.1107	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.55711	-0.8098	10	0.87932	D	0	.	12.9335	0.58301	0.0:1.0:0.0:0.0	.	84	Q5T9A4	ATD3B_HUMAN	M	84	ENSP00000311766:T84M	ENSP00000311766:T84M	T	+	2	0	ATAD3B	1402562	1.000000	0.71417	0.993000	0.49108	0.261000	0.26267	6.326000	0.72905	1.460000	0.47911	0.306000	0.20318	ACG		0.632	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1412699	C	T	1412699	3	4	100	1	0	0	0	0	1	0	0	0	1075	536	19	1	257	1	ATAD3B	1	1412699	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10		1412699	247837922	1	26655										
EIF3I	56063	hgsc.bcm.edu	37	chr1	32688149	32688149	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtccccacagaagccgatccTactgcagggccatgagcggt	12	14	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:32688149T>C	ENST00000344461.3	-	0	0				TMEM234_ENST00000309777.6_5'Flank|TMEM234_ENST00000545122.1_5'Flank|EIF3I_ENST00000373586.1_Missense_Mutation_p.L5P|EIF3I_ENST00000471486.1_3'UTR|TMEM234_ENST00000373593.1_5'Flank			Q8WY98	TM234_HUMAN	transmembrane protein 234							integral component of membrane (GO:0016021)				kidney(2)|lung(3)	5						AAGCCGATCCTACTGCAGGGC	0.562																																																0			1											77	78	78					1																	32688149		2203	4300	6503	32460736	SO:0001631	upstream_gene_variant	8668			AY358586	CCDS356.2	1p36.11-p34.2	2011-02-14	2011-02-14	2011-02-14	ENSG00000160055	ENSG00000160055			28837	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 91"	C1orf91		12477932	Standard	XM_005271045		Approved	RP4-622L5, dJ622L5.7, FLJ90779	uc001buq.4	Q8WY98	OTTHUMG00000005742		1.37:g.32688149T>C	Exception_encountered		32460736	B2R535|D3DPP7|Q6UWY9|Q8N2H6|Q9BSR2|Q9NU76	Missense_Mutation	SNP	ENST00000344461.3	37		.	.	.	.	.	.	.	.	.	.	T	24.6	4.554261	0.86231	.	.	ENSG00000084623	ENST00000355082;ENST00000373586	D;D	0.81739	-1.53;-1.53	4.1	4.1	0.47936	.	0.157358	0.43919	D	0.000514	D	0.89584	0.6757	M	0.87900	2.915	0.80722	D	1	D	0.59767	0.986	D	0.65573	0.936	D	0.91429	0.5164	10	0.72032	D	0.01	-9.9483	13.5493	0.61723	0.0:0.0:0.0:1.0	.	5	Q13347	EIF3I_HUMAN	P	5	ENSP00000347194:L5P;ENSP00000362688:L5P	ENSP00000347194:L5P	L	+	2	0	EIF3I	32460736	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.641000	0.67881	1.854000	0.53819	0.455000	0.32223	CTA		0.562	TMEM234-009	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000092260.2	NM_019118		C	32688149	T	C	32688149	1	2	100	0	1	0	0	0	0	0	0	0	5032	1522	53	4		4	EIF3I	1	32688149	5'Flank	SNP	T	TCGA-DC-6682-01A-11D-1826-10	31275450	32688149	216562472	2	26656										
IFI44	10561	hgsc.bcm.edu	37	chr1	79116110	79116110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggaaggaaagtatgcttccaTcatcctttttgcacttcaag	8	9	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:79116110T>C	ENST00000370747.4	+	2	315	c.230T>C	c.(229-231)aTc>aCc	p.I77T	IFI44_ENST00000495254.1_Intron|IFI44_ENST00000545124.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	77					response to virus (GO:0009615)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						TATGCTTCCATCATCCTTTTT	0.353																																																0			1											132	134	133					1																	79116110		2203	4300	6503	78888698	SO:0001583	missense	10561			D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 5"	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.230T>C	1.37:g.79116110T>C	ENSP00000359783:p.Ile77Thr		78888698	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	37	CCDS688.1	.	.	.	.	.	.	.	.	.	.	T	0.068	-1.209314	0.01568	.	.	ENSG00000137965	ENST00000370747	T	0.37058	1.22	3.03	-1.01	0.10169	TLDc (1);	0.948341	0.08700	N	0.906574	T	0.06872	0.0175	L	0.34521	1.04	0.09310	N	1	B;B	0.16396	0.017;0.017	B;B	0.14578	0.011;0.011	T	0.36553	-0.9743	10	0.15499	T	0.54	4.0E-4	2.3652	0.04317	0.2147:0.2611:0.0:0.5242	.	77;77	B7ZB11;Q8TCB0	.;IFI44_HUMAN	T	77	ENSP00000359783:I77T	ENSP00000359783:I77T	I	+	2	0	IFI44	78888698	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.317000	0.19487	-0.220000	0.09988	-0.467000	0.05162	ATC		0.353	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417		C	79116110	T	C	79116110	3	2	100	1	0	0	0	0	1	0	0	0	7538	1435	50	4	232	4	IFI44	1	79116110	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	46427961	79116110	170134511	3	26657										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86203133	86203133	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccaccagcactgaaattgcaGaaaacctcaatggcatctga	7	12	2	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:86203133G>C	ENST00000370571.2	-	58	5094	c.4728C>G	c.(4726-4728)ttC>ttG	p.F1576L	COL24A1_ENST00000436319.1_Missense_Mutation_p.F1555L	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1576	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TGAAATTGCAGAAAACCTCAA	0.353																																																0			1											71	69	70					1																	86203133		1890	4109	5999	85975721	SO:0001583	missense	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.4728C>G	1.37:g.86203133G>C	ENSP00000359603:p.Phe1576Leu		85975721	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209946	0.39003	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	T;T	0.74106	-0.81;-0.81	4.68	2.82	0.32997	Fibrillar collagen, C-terminal (3);	0.000000	0.38058	N	0.001827	T	0.69260	0.3091	M	0.82517	2.595	0.52099	D	0.999947	P;B	0.37548	0.599;0.39	P;B	0.45167	0.472;0.341	T	0.68123	-0.5492	10	0.34782	T	0.22	.	10.3121	0.43714	0.1582:0.0:0.8418:0.0	.	1576;1555	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	L	1576;1555	ENSP00000359603:F1576L;ENSP00000392531:F1555L	ENSP00000359603:F1576L	F	-	3	2	COL24A1	85975721	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.542000	0.60677	0.587000	0.29643	0.563000	0.77884	TTC		0.353	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		C	86203133	G	C	86203133	3	2	100	1	0	0	0	0	1	0	0	0	3689	933	33	5	428	5	COL24A1	1	86203133	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	7087023	86203133	163047488	4	26658										
DPYD	1806	hgsc.bcm.edu	37	chr1	97658647	97658647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtccatgagttcagctataCgtggaactggtttccctttc	9	10	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:97658647C>A	ENST00000370192.3	-	20	2700	c.2600G>T	c.(2599-2601)cGt>cTt	p.R867L	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	867					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TTCAGCTATACGTGGAACTGG	0.423																																																0			1											199	172	181					1																	97658647		2203	4300	6503	97431235	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2600G>T	1.37:g.97658647C>A	ENSP00000359211:p.Arg867Leu		97431235	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.891962	0.00522	.	.	ENSG00000188641	ENST00000370192	D	0.89552	-2.53	5.81	-4.47	0.03525	.	0.923471	0.09453	N	0.800145	T	0.51466	0.1676	N	0.12182	0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.49679	-0.8914	10	0.11182	T	0.66	0.1887	7.0875	0.25266	0.0:0.358:0.1962:0.4458	.	867	Q12882	DPYD_HUMAN	L	867	ENSP00000359211:R867L	ENSP00000359211:R867L	R	-	2	0	DPYD	97431235	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-2.800000	0.00761	-1.000000	0.03438	-0.759000	0.03464	CGT		0.423	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97658647	C	A	97658647	3	1	100	1	0	0	0	0	1	0	0	0	4756	536	19	2	493	2	DPYD	1	97658647	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	11455514	97658647	151591974	5	26659										
KCND3	3752	hgsc.bcm.edu	37	chr1	112525069	112525069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgtgcggtagaagttgagcaCgcagcggaacacctcggggt	16	10	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:112525069C>T	ENST00000315987.2	-	2	759	c.280G>A	c.(280-282)Gtg>Atg	p.V94M	KCND3_ENST00000369697.1_Missense_Mutation_p.V94M|KCND3_ENST00000302127.4_Missense_Mutation_p.V94M	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	94			V -> M (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.V94M(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AAGTTGAGCACGCAGCGGAAC	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	1											121	108	112					1																	112525069		2203	4300	6503	112326592	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.280G>A	1.37:g.112525069C>T	ENSP00000319591:p.Val94Met		112326592	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932725	0.52866	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	T;T;T	0.53423	0.62;0.62;0.62	5.74	5.74	0.90152	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.170734	0.52532	D	0.000073	T	0.52885	0.1762	M	0.81942	2.565	0.48236	D	0.999619	D;D	0.61697	0.966;0.99	P;P	0.56648	0.679;0.803	T	0.62982	-0.6738	10	0.87932	D	0	.	7.9086	0.29776	0.0:0.8064:0.0:0.1936	.	94;94	Q14D71;Q9UK17	.;KCND3_HUMAN	M	94	ENSP00000358711:V94M;ENSP00000319591:V94M;ENSP00000306923:V94M	ENSP00000306923:V94M	V	-	1	0	KCND3	112326592	0.961000	0.32948	0.996000	0.52242	0.997000	0.91878	2.002000	0.40835	2.717000	0.92951	0.655000	0.94253	GTG		0.612	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112525069	C	T	112525069	3	4	100	1	0	0	0	0	1	0	0	0	8041	536	19	1	1715	1	KCND3	1	112525069	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	14866422	112525069	136725552	6	26660										
NRAS	4893	hgsc.bcm.edu	37	chr1	115258747	115258747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtgcgcttttcccaacaccaCctgctccaaccaccaccagt	5	19	0	0	rs121913237		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:115258747C>T	ENST00000369535.4	-	2	288	c.35G>A	c.(34-36)gGt>gAt	p.G12D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	12			G -> C (in leukemia). {ECO:0000269|PubMed:2998510}.|G -> D (in KNEN). {ECO:0000269|PubMed:22499344}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(375)|p.G12V(59)|p.G12A(42)|p.G12N(2)|p.G12E(1)|p.G12P(1)|p.G12Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		CCCAACACCACCTGCTCCAAC	0.493	G12D(697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(HEC151_ENDOMETRIUM)|G12D(KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	481	Substitution - Missense(481)	haematopoietic_and_lymphoid_tissue(375)|skin(59)|large_intestine(21)|testis(5)|thyroid(4)|central_nervous_system(3)|endometrium(3)|biliary_tract(3)|ovary(3)|soft_tissue(2)|lung(2)|prostate(1)	1						C	ASP/GLY	0,4406		0,0,2203	206	184	191	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	35	5.6	1	1	dbSNP_133	191	1,8599	1.2+/-3.3	0,1,4299	no	missense	NRAS	NM_002524.4	94	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	12/190	115258747	1,13005	2203	4300	6503	115060270	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.35G>A	1.37:g.115258747C>T	ENSP00000358548:p.Gly12Asp		115060270	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	35	5.524414	0.96431	0.0	1.16E-4	ENSG00000213281	ENST00000369535	T	0.78595	-1.19	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000025	D	0.85252	0.5654	M	0.92604	3.325	0.80722	D	1	B	0.32467	0.372	B	0.42827	0.399	D	0.86173	0.1601	10	0.87932	D	0	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	12	P01111	RASN_HUMAN	D	12	ENSP00000358548:G12D	ENSP00000358548:G12D	G	-	2	0	NRAS	115060270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT		0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115258747	C	T	115258747	3	4	100	1	0	0	0	0	1	0	0	0	10671	507	18	3	550	3	NRAS	1	115258747	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	2733678	115258747	133991874	7	26661										
HRNR	388697	hgsc.bcm.edu	37	chr1	152192776	152192776	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaagatcgaccaaagccagtCccatgttggccggagctggg	14	11	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:152192776C>A	ENST00000368801.2	-	3	1404	c.1329G>T	c.(1327-1329)ggG>ggT	p.G443G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	443					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAAAGCCAGTCCCATGTTGGC	0.607																																																0			1											109	112	111					1																	152192776		2203	4300	6503	150459400	SO:0001819	synonymous_variant	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1329G>T	1.37:g.152192776C>A			150459400	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																				0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152192776	C	A	152192776	2	1	100	1	0	0	0	0	0	0	0	1	7380	842	30	2		2	HRNR	1	152192776	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	36934029	152192776	97057845	8	26662										
FLG	2312	hgsc.bcm.edu	37	chr1	152280792	152280792	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccttgtcatatgtttttctGcttgcacttctggatcctga	7	10	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:152280792G>T	ENST00000368799.1	-	3	6605	c.6570C>A	c.(6568-6570)agC>agA	p.S2190R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2190	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTTTTTCTGCTTGCACTTC	0.537									Ichthyosis																																							0			1											474	401	425					1																	152280792		2203	4300	6503	150547416	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6570C>A	1.37:g.152280792G>T	ENSP00000357789:p.Ser2190Arg		150547416	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	4.258	0.046981	0.08243	.	.	ENSG00000143631	ENST00000368799	T	0.01647	4.71	2.26	-3.39	0.04868	.	.	.	.	.	T	0.00608	0.0020	M	0.73962	2.25	0.09310	N	1	B	0.20164	0.042	B	0.11329	0.006	T	0.48479	-0.9032	9	0.15952	T	0.53	.	0.4443	0.00491	0.1797:0.2026:0.3058:0.3119	.	2190	P20930	FILA_HUMAN	R	2190	ENSP00000357789:S2190R	ENSP00000357789:S2190R	S	-	3	2	FLG	150547416	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.870000	0.01641	-0.230000	0.09840	0.485000	0.47835	AGC		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152280792	G	T	152280792	3	4	100	1	0	0	0	0	1	0	0	0	5941	1310	46	2	5619	2	FLG	1	152280792	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	88016	152280792	96969829	9	26663										
S100A7A	338324	hgsc.bcm.edu	37	chr1	153391729	153391729	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccttgctgggagacatagccGcagactaccacaagcagagc	11	13	0	3	rs3006414	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:153391729G>A	ENST00000368729.4	+	3	307	c.250G>A	c.(250-252)Gca>Aca	p.A84T	S100A7A_ENST00000329256.2_Missense_Mutation_p.A84T|S100A7A_ENST00000368728.2_Missense_Mutation_p.A84T	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	84	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		A -> T (in dbSNP:rs3006414).			cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)	p.A84T(1)		cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGACATAGCCGCAGACTACCA	0.527													a|||	1047	0.209065	0.4766	0.1686	5008	,	,		16030	0.1379		0.0835	False		,,,				2504	0.0787															1	Substitution - Missense(1)	stomach(1)	1						A	THR/ALA	1893,2513		408,1077,718	81	76	78		250	-2.9	0	1	dbSNP_101	78	765,7835		32,701,3567	no	missense	S100A7A	NM_176823.3	58	440,1778,4285	AA,AG,GG		8.8953,42.9641,20.4367	benign	84/102	153391729	2658,10348	2203	4300	6503	151658353	SO:0001583	missense	338324			AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"S100 calcium binding proteins", "EF-hand domain containing"	21657	protein-coding gene	gene with protein product			"S100 calcium binding protein A15", "S100 calcium binding protein A7-like 1"	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.250G>A	1.37:g.153391729G>A	ENSP00000357718:p.Ala84Thr		151658353	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	37	CCDS30872.1	436	0.19963369963369965	229	0.4654471544715447	55	0.15193370165745856	85	0.1486013986013986	67	0.08839050131926121	.	0.009	-1.820264	0.00595	0.429641	0.088953	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.06142	3.34;3.34;3.34	1.7	-2.9	0.05648	EF-hand-like domain (1);	.	.	.	.	T	0.00328	0.0010	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37798	-0.9690	8	0.09843	T	0.71	.	3.6925	0.08351	0.2976:0.0:0.4869:0.2155	rs3006414;rs57686181;rs3006414	84	Q86SG5	S1A7A_HUMAN	T	84	ENSP00000357718:A84T;ENSP00000357717:A84T;ENSP00000329008:A84T	ENSP00000329008:A84T	A	+	1	0	S100A7A	151658353	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.964000	0.01512	-1.503000	0.01812	-2.435000	0.00213	GCA		0.527	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823		A	153391729	G	A	153391729	3	1	100	1	0	0	0	0	1	0	0	0	13821	1087	38	1	256	1	S100A7A	1	153391729	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1110937	153391729	95858892	10	26664										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154218736	154218736	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tacaatggagaatgattcatCtaatctggatccgtctcagg	9	8	4	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:154218736C>G	ENST00000361546.2	+	10	941	c.899C>G	c.(898-900)tCt>tGt	p.S300C	UBAP2L_ENST00000271877.7_Missense_Mutation_p.S311C|UBAP2L_ENST00000428931.1_Missense_Mutation_p.S300C|UBAP2L_ENST00000343815.6_Missense_Mutation_p.S300C			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	300					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AATGATTCATCTAATCTGGAT	0.478																																																0			1											131	122	125					1																	154218736		2203	4300	6503	152485360	SO:0001583	missense	9898			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.899C>G	1.37:g.154218736C>G	ENSP00000355343:p.Ser300Cys		152485360	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.863738	0.91511	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000368504;ENST00000361546	T;T;T;T;T	0.48201	2.63;2.63;2.63;0.82;2.63	5.19	5.19	0.71726	.	0.238623	0.43579	D	0.000548	T	0.45337	0.1337	N	0.22421	0.69	0.50632	D	0.999882	P;D;P;P;B	0.71674	0.679;0.998;0.545;0.545;0.214	B;P;B;B;B	0.61328	0.174;0.887;0.326;0.326;0.241	T	0.49254	-0.8959	10	0.62326	D	0.03	-6.0519	17.8947	0.88883	0.0:1.0:0.0:0.0	.	214;311;293;300;300	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	C	300;300;311;311;300	ENSP00000345308:S300C;ENSP00000389445:S300C;ENSP00000271877:S311C;ENSP00000357490:S311C;ENSP00000355343:S300C	ENSP00000271877:S311C	S	+	2	0	UBAP2L	152485360	0.986000	0.35501	1.000000	0.80357	0.999000	0.98932	5.627000	0.67784	2.705000	0.92388	0.655000	0.94253	TCT		0.478	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		G	154218736	C	G	154218736	3	3	100	1	0	0	0	0	1	0	0	0	16878	913	32	5	937	5	UBAP2L	1	154218736	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	827007	154218736	95031885	11	26665										
ABL2	27	hgsc.bcm.edu	37	chr1	179084017	179084017	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	atgcaaaaatactcacatgcTctcataagttcataaacctt	3	10	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:179084017T>C	ENST00000502732.1	-	9	1760	c.1557A>G	c.(1555-1557)agA>agG	p.R519R	ABL2_ENST00000507173.1_Silent_p.R498R|ABL2_ENST00000344730.3_Silent_p.R504R|ABL2_ENST00000408940.3_Silent_p.R483R|ABL2_ENST00000392043.3_Silent_p.R498R|ABL2_ENST00000512653.1_Silent_p.R504R|ABL2_ENST00000511413.1_Silent_p.R519R|ABL2_ENST00000367623.4_Silent_p.R498R|ABL2_ENST00000504405.1_Silent_p.R483R	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	519	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> I (somatic mutation in a lung squamous cell carcinoma). {ECO:0000269|PubMed:17344846}.		actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ACTCACATGCTCTCATAAGTT	0.383			T	ETV6	AML																																		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	0			1											94	97	96					1																	179084017		2203	4300	6503	177350640	SO:0001819	synonymous_variant	27			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1557A>G	1.37:g.179084017T>C			177350640	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Silent	SNP	ENST00000502732.1	37	CCDS30947.1																																																																																				0.383	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		C	179084017	T	C	179084017	2	2	100	1	0	0	0	0	0	0	0	1	93	1548	54	4		4	ABL2	1	179084017	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	24865281	179084017	70166604	12	26666										
CRB1	23418	hgsc.bcm.edu	37	chr1	197396918	197396918	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggatttatttctgcttctacGtggaaaatcgaaaagggaga	11	5	2	1	rs375269970		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:197396918G>A	ENST00000367400.3	+	7	2598	c.2463G>A	c.(2461-2463)acG>acA	p.T821T	CRB1_ENST00000367399.2_Silent_p.T709T|CRB1_ENST00000367397.1_Silent_p.T202T|CRB1_ENST00000544212.1_Silent_p.T302T|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000535699.1_Silent_p.T752T	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	821	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> M. {ECO:0000269|PubMed:11389483}.		cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CTGCTTCTACGTGGAAAATCG	0.373																																																0			1						A	,	1,4405	824.2+/-416.5	0,1,2202	69	68	68		2127,2463	-9.9	0.1	1		68	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CRB1	NM_001193640.1,NM_201253.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	709/1295,821/1407	197396918	1,13005	2203	4300	6503	195663541	SO:0001819	synonymous_variant	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2463G>A	1.37:g.197396918G>A			195663541	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	37	CCDS1390.1																																																																																				0.373	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197396918	G	A	197396918	2	1	100	1	0	0	0	0	0	0	0	1	3854	1132	40	1		1	CRB1	1	197396918	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	18312901	197396918	51853703	13	26667										
HIST3H2A	92815	hgsc.bcm.edu	37	chr1	228645230	228645230	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gatggtcacgcggcccagcaGcttgttgagctcctcgtcgt	13	13	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:228645230G>T	ENST00000366695.2	-	1	330	c.289C>A	c.(289-291)Ctg>Atg	p.L97M	HIST3H2BB_ENST00000369160.2_5'Flank	NM_033445.2	NP_254280.1	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	97					nucleosome disassembly (GO:0006337)|UV-damage excision repair (GO:0070914)	extracellular vesicular exosome (GO:0070062)|nuclear nucleosome (GO:0000788)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)	5		Prostate(94;0.183)				CGGCCCAGCAGCTTGTTGAGC	0.662																																																0			1											83	77	79					1																	228645230		2203	4299	6502	226711853	SO:0001583	missense	92815			AY131974	CCDS1573.1	1q42.13	2011-01-27	2006-10-11		ENSG00000181218	ENSG00000181218		"Histones / Replication-dependent"	20507	protein-coding gene	gene with protein product		615015	"histone 3, H2a"			12408966	Standard	NM_033445		Approved	MGC3165	uc001hsy.3	Q7L7L0	OTTHUMG00000040046	ENST00000366695.2:c.289C>A	1.37:g.228645230G>T	ENSP00000355656:p.Leu97Met		226711853	B2R4S4	Missense_Mutation	SNP	ENST00000366695.2	37	CCDS1573.1	.	.	.	.	.	.	.	.	.	.	.	15.77	2.930245	0.52866	.	.	ENSG00000181218	ENST00000366695	T	0.67345	-0.26	3.86	2.94	0.34122	Histone-fold (2);Histone H2A (1);	0.000000	0.37715	N	0.001972	T	0.74604	0.3738	M	0.85462	2.755	0.30368	N	0.78318	D	0.53745	0.962	P	0.51324	0.666	T	0.76302	-0.3009	10	0.87932	D	0	.	9.8636	0.41129	0.1034:0.0:0.8966:0.0	.	97	Q7L7L0	H2A3_HUMAN	M	97	ENSP00000355656:L97M	ENSP00000355656:L97M	L	-	1	2	HIST3H2A	226711853	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.952000	0.63618	1.198000	0.43158	0.655000	0.94253	CTG		0.662	HIST3H2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096598.1	NM_033445		T	228645230	G	T	228645230	3	4	100	1	0	0	0	0	1	0	0	0	7203	962	34	2	107	2	HIST3H2A	1	228645230	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	31248312	228645230	20605391	14	26668										
RYR2	6262	hgsc.bcm.edu	37	chr1	237656264	237656264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcttttcaggttctggatgTcttgtgctcactctgtgttt	9	9	6	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:237656264T>C	ENST00000366574.2	+	19	2155	c.1838T>C	c.(1837-1839)gTc>gCc	p.V613A	RYR2_ENST00000542537.1_Missense_Mutation_p.V597A|RYR2_ENST00000360064.6_Missense_Mutation_p.V611A	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	613	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTTCTGGATGTCTTGTGCTCA	0.507																																																0			1											144	156	152					1																	237656264		1993	4165	6158	235722887	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1838T>C	1.37:g.237656264T>C	ENSP00000355533:p.Val613Ala		235722887	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.406025	0.42715	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96073	-3.9;-3.9;-3.9	6.06	6.06	0.98353	Intracellular calcium-release channel (1);B30.2/SPRY domain (1);	0.000000	0.56097	D	0.000028	D	0.95478	0.8531	M	0.81497	2.545	0.80722	D	1	B	0.20164	0.042	B	0.25506	0.061	D	0.93119	0.6523	10	0.52906	T	0.07	.	16.6127	0.84892	0.0:0.0:0.0:1.0	.	613	Q92736	RYR2_HUMAN	A	613;611;597	ENSP00000355533:V613A;ENSP00000353174:V611A;ENSP00000443798:V597A	ENSP00000353174:V611A	V	+	2	0	RYR2	235722887	1.000000	0.71417	0.323000	0.25347	0.006000	0.05464	7.980000	0.88113	2.322000	0.78497	0.528000	0.53228	GTC		0.507	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237656264	T	C	237656264	3	2	100	1	0	0	0	0	1	0	0	0	13806	1667	58	4	1912	4	RYR2	1	237656264	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	9011034	237656264	11594357	15	26669										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072443	240072444	+	Frame_Shift_Ins	INS	-	-	A													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgctgctgtgccagtgtgacINSaaaaaaaagaggcgcaagca							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:240072443_240072444insA	ENST00000255380.4	+	5	2471_2472	c.1692_1693insA	c.(1693-1695)aaafs	p.K565fs		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	565					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)	p.R568fs*>24(1)|p.K567fs*>24(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GCCAGTGTGACAAAAAAAAGAG	0.505																																																2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|breast(1)	1																																								238139067	SO:0001589	frameshift_variant	1131			U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1700dupA	1.37:g.240072451_240072451dupA	ENSP00000255380:p.Lys565fs		238139066	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Frame_Shift_Ins	INS	ENST00000255380.4	37	CCDS1616.1																																																																																				0.505	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		A	240072444	-	A	240072443	7	5	100	1	0	1	1	0	0	0	0	0	3384	477	17	0	1694	0	CHRM3	1	240072443	Frame_Shift_Ins	INS	-	TCGA-DC-6682-01A-11D-1826-10	2416179	240072443	9178178	16	26670										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	100	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-DC-6682-01A-11D-1826-10	298471	240370914	8879707	17	26671										
OR2M5	127059	hgsc.bcm.edu	37	chr1	248308552	248308552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tctttctggtcctggccatcTtttcagtggccttcatggga	10	11	5	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr1:248308552T>C	ENST00000366476.1	+	1	103	c.103T>C	c.(103-105)Ttt>Ctt	p.F35L		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F35I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CCTGGCCATCTTTTCAGTGGC	0.522																																																1	Substitution - Missense(1)	ovary(1)	1											239	237	237					1																	248308552		2203	4296	6499	246375175	SO:0001583	missense	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.103T>C	1.37:g.248308552T>C	ENSP00000355432:p.Phe35Leu		246375175		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	t	10.24	1.295534	0.23564	.	.	ENSG00000162727	ENST00000366476	T	0.00581	6.42	3.28	3.28	0.37604	.	0.250947	0.20653	U	0.088177	T	0.01092	0.0036	M	0.81497	2.545	0.09310	N	1	P	0.41546	0.754	B	0.39119	0.291	T	0.37731	-0.9693	10	0.72032	D	0.01	.	11.5465	0.50696	0.0:0.0:0.0:1.0	.	35	A3KFT3	OR2M5_HUMAN	L	35	ENSP00000355432:F35L	ENSP00000355432:F35L	F	+	1	0	OR2M5	246375175	0.022000	0.18835	0.140000	0.22221	0.115000	0.19883	2.033000	0.41136	1.250000	0.43966	0.403000	0.27427	TTT		0.522	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		C	248308552	T	C	248308552	3	2	100	1	0	0	0	0	1	0	0	0	11044	1609	56	4	105	4	OR2M5	1	248308552	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	7937638	248308552	942069	18	26672										
TTC15	51112	hgsc.bcm.edu	37	chr2	3469378	3469378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cttcccacaggattatgtgcTggccgtggaggcgtatcatt	12	10	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:3469378T>C	ENST00000324266.5	+	9	1883	c.1688T>C	c.(1687-1689)cTg>cCg	p.L563P	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Missense_Mutation_p.L563P	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	563					vesicle-mediated transport (GO:0016192)			p.L563P(1)									GATTATGTGCTGGCCGTGGAG	0.527																																																1	Substitution - Missense(1)	ovary(1)	2											115	108	111					2																	3469378		2203	4300	6503	3448385	SO:0001583	missense	51112			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1688T>C	2.37:g.3469378T>C	ENSP00000324318:p.Leu563Pro		3448385	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.028083	0.54790	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266;ENST00000415624	T;T;T	0.63744	-0.06;-0.06;-0.06	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.80909	0.4714	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.82741	-0.0307	10	0.48119	T	0.1	.	15.072	0.72046	0.0:0.0:0.0:1.0	.	552;563	E7ENL7;Q8WVT3	.;TPC12_HUMAN	P	563;552;563;61	ENSP00000371544:L563P;ENSP00000324318:L563P;ENSP00000396592:L61P	ENSP00000303612:L552P	L	+	2	0	TTC15	3448385	1.000000	0.71417	0.960000	0.40013	0.035000	0.12851	7.496000	0.81526	2.146000	0.66826	0.533000	0.62120	CTG		0.527	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		C	3469378	T	C	3469378	3	2	100	1	0	0	0	0	1	0	0	0	16722	1580	55	4	1718	4	TTC15	2	3469378	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10		3469378	239729995	19	26673										
DTNB	1838	hgsc.bcm.edu	37	chr2	25875497	25875497	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agctgcctcttctctgccatGgtcttccgcttgttcccact	7	16	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:25875497G>A	ENST00000406818.3	-	2	282	c.33C>T	c.(31-33)acC>acT	p.T11T	DTNB_ENST00000405222.1_Silent_p.T11T|DTNB_ENST00000496972.2_5'Flank|DTNB_ENST00000407038.3_Silent_p.T11T|DTNB_ENST00000404103.3_Silent_p.T11T|DTNB_ENST00000407186.1_Silent_p.T11T|DTNB_ENST00000407661.3_Silent_p.T11T|DTNB_ENST00000472690.1_5'Flank|DTNB_ENST00000288642.8_Silent_p.T11T|DTNB_ENST00000545439.1_5'UTR	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	11						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCTGCCATGGTCTTCCGCT	0.383																																																0			2											177	172	174					2																	25875497		1950	4146	6096	25729001	SO:0001819	synonymous_variant	1838			AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.33C>T	2.37:g.25875497G>A			25729001	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																				0.383	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		A	25875497	G	A	25875497	2	1	100	1	0	0	0	0	0	0	0	1	4800	1335	47	3		3	DTNB	2	25875497	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	22406119	25875497	217323876	20	26674										
SPDYA	245711	hgsc.bcm.edu	37	chr2	29039006	29039006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgtcctatttgtaaagataaTtggcaagcatttgaaaaaaa	7	5	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:29039006T>G	ENST00000334056.5	+	3	315	c.126T>G	c.(124-126)aaT>aaG	p.N42K	SPDYA_ENST00000462832.1_3'UTR|SPDYA_ENST00000379579.4_Missense_Mutation_p.N42K	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A									p.N42K(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					GTAAAGATAATTGGCAAGCAT	0.373																																																1	Substitution - Missense(1)	ovary(1)	2											112	111	111					2																	29039006		2203	4300	6503	28892510	SO:0001583	missense	245711			AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"Speedy homologs"	30613	protein-coding gene	gene with protein product		614029	"speedy homolog 1 (Drosophila)", "speedy homolog A (Xenopus laevis)"	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000334056.5:c.126T>G	2.37:g.29039006T>G	ENSP00000335628:p.Asn42Lys		28892510		Missense_Mutation	SNP	ENST00000334056.5	37	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	T	11.77	1.736850	0.30774	.	.	ENSG00000163806	ENST00000379579;ENST00000334056;ENST00000449210	.	.	.	4.89	2.51	0.30379	.	0.392314	0.21639	U	0.071364	T	0.23846	0.0577	N	0.19112	0.55	0.23893	N	0.996542	B;B	0.14012	0.002;0.009	B;B	0.15870	0.006;0.014	T	0.16394	-1.0404	9	0.19590	T	0.45	-34.7368	8.2118	0.31488	0.0:0.2299:0.0:0.77	.	42;42	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	K	42	.	ENSP00000335628:N42K	N	+	3	2	SPDYA	28892510	0.945000	0.32115	1.000000	0.80357	0.923000	0.55619	0.500000	0.22562	0.828000	0.34709	0.533000	0.62120	AAT		0.373	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	NM_182756		G	29039006	T	G	29039006	3	3	100	1	0	0	0	0	1	0	0	0	15066	1490	52	4	128	4	SPDYA	2	29039006	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	3163509	29039006	214160367	21	26675										
SOS1	6654	hgsc.bcm.edu	37	chr2	39249842	39249842	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagagtcaggctctgcaaatCtataaacatcagcactaggc	8	11	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:39249842C>T	ENST00000426016.1	-	11	1813	c.1727G>A	c.(1726-1728)aGa>aAa	p.R576K	SOS1_ENST00000472480.1_5'Flank|SOS1_ENST00000402219.2_Missense_Mutation_p.R576K|SOS1_ENST00000395038.2_Missense_Mutation_p.R576K			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	576					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				CTCTGCAAATCTATAAACATC	0.408									Noonan syndrome																																							0			2											148	144	145					2																	39249842		2203	4300	6503	39103346	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1727G>A	2.37:g.39249842C>T	ENSP00000387784:p.Arg576Lys		39103346	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.590954	0.66219	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.30714	1.52;1.52;1.52	5.78	5.78	0.91487	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.39462	0.1079	L	0.51914	1.62	0.80722	D	1	P;B	0.40431	0.717;0.326	P;B	0.46389	0.515;0.323	T	0.02437	-1.1159	10	0.18710	T	0.47	.	20.0039	0.97428	0.0:1.0:0.0:0.0	.	308;576	F5GX06;Q07889	.;SOS1_HUMAN	K	576;576;308;576;576	ENSP00000387784:R576K;ENSP00000384675:R576K;ENSP00000378479:R576K	ENSP00000263879:R576K	R	-	2	0	SOS1	39103346	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	5.971000	0.70440	2.722000	0.93159	0.557000	0.71058	AGA		0.408	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39249842	C	T	39249842	3	4	100	1	0	0	0	0	1	0	0	0	14973	913	32	3	2330	3	SOS1	2	39249842	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	10210836	39249842	203949531	22	26676										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55473531	55473531	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttccactggaccattgggatCtgctttcaattctaacattt	6	10	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:55473531C>T	ENST00000263629.4	-	10	1363	c.1048G>A	c.(1048-1050)Gat>Aat	p.D350N	MTIF2_ENST00000403721.1_Missense_Mutation_p.D350N|MTIF2_ENST00000394600.3_Missense_Mutation_p.D350N	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	350					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.D350Y(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CCATTGGGATCTGCTTTCAAT	0.388																																																1	Substitution - Missense(1)	ovary(1)	2											172	158	163					2																	55473531		2203	4300	6503	55327035	SO:0001583	missense	4528			L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1048G>A	2.37:g.55473531C>T	ENSP00000263629:p.Asp350Asn		55327035	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	C	34	5.302861	0.95601	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823;ENST00000535023	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.33	5.33	0.75918	.	0.105696	0.64402	D	0.000005	T	0.42944	0.1225	N	0.11845	0.185	0.80722	D	1	D	0.60160	0.987	D	0.70487	0.969	T	0.16630	-1.0396	10	0.02654	T	1	-17.6566	19.0262	0.92932	0.0:1.0:0.0:0.0	.	350	P46199	IF2M_HUMAN	N	350;350;350;70;350	ENSP00000384481:D350N;ENSP00000263629:D350N;ENSP00000378099:D350N;ENSP00000403492:D70N	ENSP00000263629:D350N	D	-	1	0	MTIF2	55327035	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.268000	0.78473	2.505000	0.84491	0.655000	0.94253	GAT		0.388	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		T	55473531	C	T	55473531	3	4	100	1	0	0	0	0	1	0	0	0	9964	913	32	3	1163	3	MTIF2	2	55473531	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	16223689	55473531	187725842	23	26677										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84886194	84886194	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctatgtcagacttttgtattCtgttatttgtggtctttggg	10	5	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:84886194C>A	ENST00000237449.6	+	36	5993	c.5985C>A	c.(5983-5985)ttC>ttA	p.F1995L	DNAH6_ENST00000602588.1_Missense_Mutation_p.F16L|DNAH6_ENST00000389394.3_Missense_Mutation_p.F1995L|DNAH6_ENST00000398278.2_Missense_Mutation_p.F1995L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1995					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						CTTTTGTATTCTGTTATTTGT	0.294																																																0			2											116	102	106					2																	84886194		692	1585	2277	84739705	SO:0001583	missense	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5985C>A	2.37:g.84886194C>A	ENSP00000237449:p.Phe1995Leu		84739705	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	19.79	3.893597	0.72639	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.33216	1.42;1.48;1.42	5.09	3.18	0.36537	.	.	.	.	.	T	0.54447	0.1859	M	0.87456	2.885	0.36632	D	0.87633	D;D	0.69078	0.997;0.988	D;D	0.66602	0.945;0.945	T	0.65467	-0.6161	9	0.72032	D	0.01	.	8.7628	0.34685	0.0:0.7381:0.0:0.2619	.	1995;1995	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	L	1995	ENSP00000374045:F1995L;ENSP00000381326:F1995L;ENSP00000237449:F1995L	ENSP00000237449:F1995L	F	+	3	2	DNAH6	84739705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.927000	0.40094	1.206000	0.43276	0.643000	0.83706	TTC		0.294	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84886194	C	A	84886194	3	1	100	1	0	0	0	0	1	0	0	0	4616	912	32	2	6127	2	DNAH6	2	84886194	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	29412663	84886194	158313179	24	26678										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103299862	103299862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcttcatgggtgtgtctaccGtgggcaagaaccacgagtgg	14	9	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:103299862G>A	ENST00000233969.2	+	4	1289	c.1147G>A	c.(1147-1149)Gtg>Atg	p.V383M		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	383					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.V383M(1)		breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TGTGTCTACCGTGGGCAAGAA	0.502																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											187	151	163					2																	103299862		2203	4300	6503	102666294	SO:0001583	missense	6549				CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1147G>A	2.37:g.103299862G>A	ENSP00000233969:p.Val383Met		102666294	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	37	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.896925	0.52121	.	.	ENSG00000115616	ENST00000233969	T	0.15718	2.4	5.67	5.67	0.87782	Cation/H+ exchanger (1);	0.120730	0.56097	D	0.000037	T	0.33498	0.0865	M	0.76838	2.35	0.44966	D	0.997985	D	0.53745	0.962	P	0.54060	0.741	T	0.07597	-1.0764	10	0.87932	D	0	.	10.2345	0.43275	0.1469:0.0:0.8531:0.0	.	383	Q9UBY0	SL9A2_HUMAN	M	383	ENSP00000233969:V383M	ENSP00000233969:V383M	V	+	1	0	SLC9A2	102666294	0.979000	0.34478	0.294000	0.24946	0.560000	0.35617	1.941000	0.40233	2.686000	0.91538	0.561000	0.74099	GTG		0.502	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			A	103299862	G	A	103299862	3	1	100	1	0	0	0	0	1	0	0	0	14749	1145	40	1	1161	1	SLC9A2	2	103299862	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	18413668	103299862	139899511	25	26679										
MFSD9	84804	hgsc.bcm.edu	37	chr2	103348857	103348857	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aaaggcacaaccatgctgacAccaaacaaatcctaaaacaa	4	12	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:103348857A>G	ENST00000258436.5	-	2	220	c.177T>C	c.(175-177)ggT>ggC	p.G59G		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	59			G -> A (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CCATGCTGACACCAAACAAAT	0.338																																																0			2											117	110	112					2																	103348857		2203	4300	6503	102715289	SO:0001819	synonymous_variant	84804				CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.177T>C	2.37:g.103348857A>G			102715289	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																				0.338	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		G	103348857	A	G	103348857	2	3	100	1	0	0	0	0	0	0	0	1	9569	146	6	4		4	MFSD9	2	103348857	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	48995	103348857	139850516	26	26680										
MERTK	10461	hgsc.bcm.edu	37	chr2	112779854	112779854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtgggcatttggcgtgaccaTgtgggaaatagctacgcggg	17	7	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:112779854T>C	ENST00000295408.4	+	18	2626	c.2369T>C	c.(2368-2370)aTg>aCg	p.M790T	MERTK_ENST00000421804.2_Missense_Mutation_p.M790T|MERTK_ENST00000409780.1_Missense_Mutation_p.M614T			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	790	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GGCGTGACCATGTGGGAAATA	0.493																																																0			2											136	119	125					2																	112779854		2203	4300	6503	112496325	SO:0001583	missense	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2369T>C	2.37:g.112779854T>C	ENSP00000295408:p.Met790Thr		112496325	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.206371	0.79127	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780;ENST00000449344	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.42	5.42	0.78866	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40469	U	0.001096	T	0.74876	0.3774	L	0.51853	1.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77496	-0.2566	10	0.87932	D	0	-39.568	15.7698	0.78157	0.0:0.0:0.0:1.0	.	790	Q12866	MERTK_HUMAN	T	790;790;426;614;114	ENSP00000295408:M790T;ENSP00000389152:M790T;ENSP00000387277:M614T;ENSP00000412660:M114T	ENSP00000295408:M790T	M	+	2	0	MERTK	112496325	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.997000	0.88414	2.189000	0.69895	0.533000	0.62120	ATG		0.493	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			C	112779854	T	C	112779854	3	2	100	1	0	0	0	0	1	0	0	0	9509	1464	51	4	2439	4	MERTK	2	112779854	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	9430997	112779854	130419519	27	26681										
NEB	4703	hgsc.bcm.edu	37	chr2	152402489	152402489	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttgtctcgcatcttccttgcCttatcagtgtataggtaatt	7	9	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:152402489C>T	ENST00000172853.10	-	107	15534	c.15387G>A	c.(15385-15387)aaG>aaA	p.K5129K	NEB_ENST00000604864.1_Silent_p.K6830K|NEB_ENST00000603639.1_Silent_p.K6830K|NEB_ENST00000409198.1_Silent_p.K5129K|NEB_ENST00000397345.3_Silent_p.K6830K|NEB_ENST00000427231.2_Silent_p.K6830K			P20929	NEBU_HUMAN	nebulin	5129					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTTCCTTGCCTTATCAGTGT	0.338																																																0			2											155	132	139					2																	152402489		1871	4104	5975	152110735	SO:0001819	synonymous_variant	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.15387G>A	2.37:g.152402489C>T			152110735	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.338	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152402489	C	T	152402489	2	4	100	1	0	0	0	0	0	0	0	1	10333	680	24	3		3	NEB	2	152402489	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	39622635	152402489	90796884	28	26682										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158115757	158115757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	taaccatgctttaactggagGgctagagccagcaaaaatca	9	9	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:158115757G>A	ENST00000259056.4	+	1	1648	c.1163G>A	c.(1162-1164)gGg>gAg	p.G388E		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	388					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						TTAACTGGAGGGCTAGAGCCA	0.443																																																0			2											94	92	93					2																	158115757		2203	4300	6503	157824003	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1163G>A	2.37:g.158115757G>A	ENSP00000259056:p.Gly388Glu		157824003	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.894018	0.33442	.	.	ENSG00000136542	ENST00000259056	T	0.59772	0.24	5.95	0.983	0.19767	.	0.963564	0.08591	N	0.922966	T	0.40719	0.1128	N	0.20986	0.625	0.09310	N	1	B	0.13145	0.007	B	0.11329	0.006	T	0.28839	-1.0031	10	0.46703	T	0.11	.	5.7524	0.18154	0.2709:0.2357:0.4933:0.0	.	388	Q7Z7M9	GALT5_HUMAN	E	388	ENSP00000259056:G388E	ENSP00000259056:G388E	G	+	2	0	GALNT5	157824003	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.552000	0.23376	-0.095000	0.12351	-0.157000	0.13467	GGG		0.443	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		A	158115757	G	A	158115757	3	1	100	1	0	0	0	0	1	0	0	0	6236	1232	43	3	1165	3	GALNT5	2	158115757	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	5713268	158115757	85083616	29	26683										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162813736	162813736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgggttcatcagtctttatgAccagtattctgaaggtaaca	9	7	4	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:162813736A>G	ENST00000446997.1	+	20	2872	c.2779A>G	c.(2779-2781)Acc>Gcc	p.T927A	SLC4A10_ENST00000272716.5_Missense_Mutation_p.T897A|SLC4A10_ENST00000415876.2_Missense_Mutation_p.T897A|SLC4A10_ENST00000375514.5_Missense_Mutation_p.T908A|SLC4A10_ENST00000421911.1_Missense_Mutation_p.T927A	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	927					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	AGTCTTTATGACCAGTATTCT	0.348																																																0			2											63	61	62					2																	162813736		1871	4116	5987	162521982	SO:0001583	missense	57282				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.2779A>G	2.37:g.162813736A>G	ENSP00000393066:p.Thr927Ala		162521982	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	37	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.661776	0.47572	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	5.42	5.42	0.78866	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80914	0.4715	L	0.48362	1.52	0.80722	D	1	D;D;B	0.53885	0.963;0.963;0.273	P;P;B	0.60886	0.88;0.88;0.254	T	0.76041	-0.3104	10	0.08837	T	0.75	.	15.7565	0.78030	1.0:0.0:0.0:0.0	.	908;897;927	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	A	908;897;897;896;927;927;926	ENSP00000364664:T908A;ENSP00000395797:T897A;ENSP00000272716:T897A;ENSP00000393066:T927A;ENSP00000404486:T927A	ENSP00000272716:T897A	T	+	1	0	SLC4A10	162521982	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.287000	0.95975	2.177000	0.69029	0.533000	0.62120	ACC		0.348	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		G	162813736	A	G	162813736	3	3	100	1	0	0	0	0	1	0	0	0	14688	275	10	4	2942	4	SLC4A10	2	162813736	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	4697979	162813736	80385637	30	26684										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165994389	165994389	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	taaacttcaaatgtacttacCaggtttcctacagtcaacac	4	11	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:165994389C>T	ENST00000360093.3	-	15	2882	c.2391G>A	c.(2389-2391)ctG>ctA	p.L797L	SCN3A_ENST00000409101.3_Splice_Site_p.L748L|SCN3A_ENST00000283254.7_Splice_Site_p.L797L	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	797					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGTACTTACCAGGTTTCCTA	0.383																																																0			2											104	100	102					2																	165994389		2203	4299	6502	165702635	SO:0001630	splice_region_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2391+1G>A	2.37:g.165994389C>T			165702635	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																					0.383	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	Silent	T	165994389	C	T	165994389	5	4	100	1	0	0	0	0	0	0	1	0	13955	608	21	3	3667	3	SCN3A	2	165994389	Splice_Site	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3180653	165994389	77204984	31	26685										
SP3	6670	hgsc.bcm.edu	37	chr2	174777881	174777881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccagttacaaacaaaagggCgttctccagaatgccaacgc	8	12	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:174777881C>T	ENST00000310015.6	-	6	2476	c.1946G>A	c.(1945-1947)cGc>cAc	p.R649H	SP3_ENST00000455789.2_Missense_Mutation_p.R596H|SP3_ENST00000418194.2_Missense_Mutation_p.R581H	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	649					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			AACAAAAGGGCGTTCTCCAGA	0.408																																																0			2											117	104	108					2																	174777881		2203	4300	6503	174486127	SO:0001583	missense	6670			M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.1946G>A	2.37:g.174777881C>T	ENSP00000310301:p.Arg649His		174486127	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.53|18.53	3.643666|3.643666	0.67244|0.67244	.|.	.|.	ENSG00000172845|ENSG00000172845	ENST00000416195|ENST00000310015;ENST00000455789;ENST00000418194	.|T;T;T	.|0.20332	.|2.08;2.08;2.08	5.41|5.41	5.41|5.41	0.78517|0.78517	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54029|0.54029	0.1833|0.1833	M|M	0.84511|0.84511	2.7|2.7	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.89917	.|0.772;1.0;1.0	.|P;D;D	.|0.91635	.|0.458;0.981;0.999	T|T	0.59910|0.59910	-0.7365|-0.7365	5|10	.|0.87932	.|D	.|0	.|.	19.5526|19.5526	0.95328|0.95328	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|646;649;596	.|B7ZLN9;Q02447;Q02447-6	.|.;SP3_HUMAN;.	T|H	606|649;596;581	.|ENSP00000310301:R649H;ENSP00000388903:R596H;ENSP00000406140:R581H	.|ENSP00000310301:R649H	A|R	-|-	1|2	0|0	SP3|SP3	174486127|174486127	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	7.776000|7.776000	0.85560|0.85560	2.701000|2.701000	0.92244|0.92244	0.563000|0.563000	0.77884|0.77884	GCC|CGC		0.408	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		T	174777881	C	T	174777881	3	4	100	1	0	0	0	0	1	0	0	0	15002	768	27	1	407	1	SP3	2	174777881	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	8783492	174777881	68421492	32	26686										
TTN	7273	hgsc.bcm.edu	37	chr2	179485250	179485250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cttcaccatttttggtccacTtcagtgttacattgagacga	7	10	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:179485250T>C	ENST00000591111.1	-	198	41299	c.41075A>G	c.(41074-41076)aAg>aGg	p.K13692R	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K6460R|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K6393R|TTN_ENST00000460472.2_Missense_Mutation_p.K6268R|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K15333R|TTN_ENST00000342992.6_Missense_Mutation_p.K12765R			Q8WZ42	TITIN_HUMAN	titin	13692	Ig-like 93.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K12765M(1)|p.K6268M(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTGGTCCACTTCAGTGTTAC	0.403																																																2	Substitution - Missense(2)	ovary(2)	2											136	128	130					2																	179485250		1938	4131	6069	179193495	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.41075A>G	2.37:g.179485250T>C	ENSP00000465570:p.Lys13692Arg		179193495	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	13.38	2.219334	0.39201	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.9	5.9	0.94986	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66934	0.2840	L	0.49256	1.55	0.31136	N	0.707199	B;B;B;B	0.32653	0.379;0.379;0.379;0.379	B;B;B;B	0.40825	0.341;0.341;0.341;0.341	T	0.72912	-0.4148	9	0.87932	D	0	.	11.4123	0.49933	0.1347:0.0:0.0:0.8653	.	6268;6393;6460;13692	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	12765;6268;6460;6393;6268	ENSP00000343764:K12765R;ENSP00000434586:K6268R;ENSP00000340554:K6460R;ENSP00000352154:K6393R	ENSP00000340554:K6460R	K	-	2	0	TTN	179193495	1.000000	0.71417	0.996000	0.52242	0.945000	0.59286	3.966000	0.56795	2.254000	0.74563	0.460000	0.39030	AAG		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179485250	T	C	179485250	3	2	100	1	0	0	0	0	1	0	0	0	16775	1609	56	4	62155	4	TTN	2	179485250	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	4707369	179485250	63714123	33	26687										
SDPR	8436	hgsc.bcm.edu	37	chr2	192711271	192711271	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctatccatgcgctctttgacCgcgcgcgtgtgggcgctgac	13	14	1	2	rs116535615	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:192711271C>A	ENST00000304141.4	-	1	710	c.381G>T	c.(379-381)gcG>gcT	p.A127A	AC098617.1_ENST00000424116.2_RNA	NM_004657.5	NP_004648.1			serum deprivation response									p.A127A(1)		NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			GCTCTTTGACCGCGCGCGTGT	0.597													C|||	11	0.00219649	8e-04	0	5008	,	,		20070	0.0099		0	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	2						C		4,4402	8.1+/-20.4	0,4,2199	70	63	66		381	-9.2	0.1	2	dbSNP_132	66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SDPR	NM_004657.5		0,5,6498	AA,AC,CC		0.0116,0.0908,0.0384		127/426	192711271	5,13001	2203	4300	6503	192419516	SO:0001819	synonymous_variant	8436			AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.381G>T	2.37:g.192711271C>A			192419516		Silent	SNP	ENST00000304141.4	37	CCDS2313.1																																																																																				0.597	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		A	192711271	C	A	192711271	2	1	100	1	0	0	0	0	0	0	0	1	14007	639	23	2		2	SDPR	2	192711271	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	13226021	192711271	50488102	34	26688										
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201281141	201281142	+	Frame_Shift_Ins	INS	-	-	A													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aaagaatggaatatgacaggINSaaaaaagaaggtaagattaa							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:201281141_201281142insA	ENST00000358677.5	+	5	435_436	c.188_189insA	c.(187-192)ggaaaafs	p.GK63fs	SPATS2L_ENST00000451764.2_Frame_Shift_Ins_p.GK63fs|SPATS2L_ENST00000409755.3_Frame_Shift_Ins_p.GK93fs|SPATS2L_ENST00000409151.1_Frame_Shift_Ins_p.GK71fs|SPATS2L_ENST00000360760.5_Frame_Shift_Ins_p.GK63fs|SPATS2L_ENST00000409385.1_Frame_Shift_Ins_p.GK3fs|SPATS2L_ENST00000409988.3_Frame_Shift_Ins_p.GK63fs|SPATS2L_ENST00000409140.3_Frame_Shift_Ins_p.GK63fs|SPATS2L_ENST00000409718.1_Frame_Shift_Ins_p.GK63fs	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	63						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						AATATGACAGGAAAAAAGAAGG	0.297																																																0			2																																								200989387	SO:0001589	frameshift_variant	26010			AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"DNA polymerase transactivated protein 6"	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.194dupA	2.37:g.201281147_201281147dupA	ENSP00000351503:p.Gly63fs		200989386	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Frame_Shift_Ins	INS	ENST00000358677.5	37	CCDS46483.1																																																																																				0.297	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		A	201281142	-	A	201281141	7	5	100	1	0	1	1	0	0	0	0	0	15059	1174	41	0	198	0	SPATS2L	2	201281141	Frame_Shift_Ins	INS	-	TCGA-DC-6682-01A-11D-1826-10	8569870	201281141	41918232	35	26689										
MYL1	4632	hgsc.bcm.edu	37	chr2	211163165	211163165	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttcattgctggggtttcccaGaactttcctgacctctgcat	8	12	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:211163165G>A	ENST00000352451.3	-	3	430	c.283C>T	c.(283-285)Ctg>Ttg	p.L95L	MYL1_ENST00000496436.1_5'UTR|MYL1_ENST00000341685.4_Silent_p.L51L	NM_079420.2	NP_524144.1	P05976	MYL1_HUMAN	myosin, light chain 1, alkali; skeletal, fast	95					cardiac muscle contraction (GO:0060048)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|sarcomere (GO:0030017)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	16				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		GGGTTTCCCAGAACTTTCCTG	0.483																																																0			2											164	155	158					2																	211163165		2203	4300	6503	210871410	SO:0001819	synonymous_variant	4632				CCDS2390.1, CCDS2391.1	2q33-q34	2013-01-10	2006-09-29		ENSG00000168530	ENSG00000168530		"Myosins / Light chain", "EF-hand domain containing"	7582	protein-coding gene	gene with protein product		160780	"myosin, light polypeptide 1, alkali; skeletal, fast"			2304459, 3422212	Standard	NM_079422		Approved		uc002vec.3	P05976	OTTHUMG00000132992	ENST00000352451.3:c.283C>T	2.37:g.211163165G>A			210871410	B2R4N6|B2R4T6|P06741|Q6IBD5	Silent	SNP	ENST00000352451.3	37	CCDS2390.1																																																																																				0.483	MYL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256566.2	NM_079420		A	211163165	G	A	211163165	2	1	100	1	0	0	0	0	0	0	0	1	10073	933	33	3		3	MYL1	2	211163165	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	9882024	211163165	32036208	36	26690										
FN1	2335	hgsc.bcm.edu	37	chr2	216298151	216298151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtcacccactcggtaagtgTtcccagtgtacttgtcaaag	9	11	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:216298151T>C	ENST00000359671.1	-	3	576	c.311A>G	c.(310-312)aAc>aGc	p.N104S	FN1_ENST00000357867.4_Missense_Mutation_p.N104S|FN1_ENST00000446046.1_Missense_Mutation_p.N104S|FN1_ENST00000421182.1_Missense_Mutation_p.N104S|FN1_ENST00000443816.1_Missense_Mutation_p.N104S|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000356005.4_Missense_Mutation_p.N104S|FN1_ENST00000354785.4_Missense_Mutation_p.N104S|FN1_ENST00000323926.6_Missense_Mutation_p.N104S|FN1_ENST00000432072.2_Missense_Mutation_p.N104S|FN1_ENST00000345488.5_Missense_Mutation_p.N104S|FN1_ENST00000426059.1_Missense_Mutation_p.N104S|FN1_ENST00000357009.2_Missense_Mutation_p.N104S|FN1_ENST00000336916.4_Missense_Mutation_p.N104S|FN1_ENST00000346544.3_Missense_Mutation_p.N104S			P02751	FINC_HUMAN	fibronectin 1	104	Fibrin- and heparin-binding 1.|Fibronectin type-I 2. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.N104S(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	TCGGTAAGTGTTCCCAGTGTA	0.498																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											121	99	106					2																	216298151		2203	4300	6503	216006396	SO:0001583	missense	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.311A>G	2.37:g.216298151T>C	ENSP00000352696:p.Asn104Ser		216006396	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	T	6.501	0.460622	0.12342	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	6.07	3.67	0.42095	.	0.408692	0.25836	N	0.027991	T	0.30262	0.0759	N	0.03608	-0.345	0.09310	N	0.999998	B;D;B;P;B;B;B;B;B;B;B	0.64830	0.005;0.994;0.004;0.885;0.001;0.002;0.013;0.035;0.003;0.001;0.014	B;D;B;P;B;B;B;B;B;B;B	0.79108	0.023;0.992;0.008;0.533;0.003;0.005;0.022;0.049;0.003;0.003;0.02	T	0.16867	-1.0388	10	0.15952	T	0.53	.	2.1799	0.03872	0.22:0.0716:0.2648:0.4435	.	104;104;104;104;104;104;104;104;104;104;104	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	S	104	ENSP00000394423:N104S;ENSP00000323534:N104S;ENSP00000338200:N104S;ENSP00000350534:N104S;ENSP00000346839:N104S;ENSP00000352696:N104S;ENSP00000265312:N104S;ENSP00000273049:N104S;ENSP00000349509:N104S;ENSP00000410422:N104S;ENSP00000415018:N104S;ENSP00000399538:N104S;ENSP00000348285:N104S;ENSP00000398907:N104S	ENSP00000265313:N104S	N	-	2	0	FN1	216006396	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	0.818000	0.27295	0.515000	0.28320	0.533000	0.62120	AAC		0.498	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216298151	T	C	216298151	3	2	100	1	0	0	0	0	1	0	0	0	5981	1725	60	4	7331	4	FN1	2	216298151	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	5134986	216298151	26901222	37	26691										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225639744	225639744	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcatttcgaaatctgtcttcCggtcttcgatttccttttcc	6	12	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr2:225639744C>A	ENST00000258390.7	-	52	5958	c.5891G>T	c.(5890-5892)cGg>cTg	p.R1964L	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1958L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1964	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		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)		ATCTGTCTTCCGGTCTTCGAT	0.517																																																0			2											88	91	90					2																	225639744		2017	4204	6221	225347988	SO:0001583	missense	55619			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5891G>T	2.37:g.225639744C>A	ENSP00000258390:p.Arg1964Leu		225347988	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558258	0.65538	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	T;T	0.24538	1.85;1.85	5.48	5.48	0.80851	.	0.056199	0.64402	D	0.000001	T	0.58148	0.2102	M	0.92970	3.365	0.53005	D	0.999968	P;P;P	0.47484	0.896;0.802;0.848	P;P;B	0.55391	0.775;0.588;0.394	T	0.67864	-0.5560	10	0.72032	D	0.01	.	19.7173	0.96127	0.0:1.0:0.0:0.0	.	1964;1958;626	Q96BY6;B3FL70;B4DEY4	DOC10_HUMAN;.;.	L	1958;1964;471	ENSP00000386694:R1958L;ENSP00000258390:R1964L	ENSP00000258390:R1964L	R	-	2	0	DOCK10	225347988	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	4.506000	0.60428	2.724000	0.93272	0.563000	0.77884	CGG		0.517	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225639744	C	A	225639744	3	1	100	1	0	0	0	0	1	0	0	0	4696	652	23	2	689	2	DOCK10	2	225639744	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	9341593	225639744	17559629	38	26692										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10452333	10452333	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcgccgggcgggtggtagaaGgacagccccagggagatgat	18	9	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:10452333G>A	ENST00000352432.4	-	2	435	c.366C>T	c.(364-366)tcC>tcT	p.S122S	ATP2B2_ENST00000360273.2_Silent_p.S122S|ATP2B2_ENST00000343816.4_Silent_p.S122S|ATP2B2_ENST00000383800.4_Silent_p.S122S|ATP2B2_ENST00000397077.1_Silent_p.S122S			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	122					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GGTGGTAGAAGGACAGCCCCA	0.642																																					Ovarian(125;1619 1709 15675 19819 38835)											0			3											145	153	151					3																	10452333		2203	4300	6503	10427333	SO:0001819	synonymous_variant	493			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.366C>T	3.37:g.10452333G>A			10427333	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																				0.642	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10452333	G	A	10452333	2	1	100	1	0	0	0	0	0	0	0	1	1141	987	35	3		3	ATP2B2	3	10452333	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10		10452333	187570097	39	26693										
CAPN7	23473	hgsc.bcm.edu	37	chr3	15282120	15282120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgaacagctcagaaaatagaCaacggtaaatatatcttttt	6	7	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:15282120C>T	ENST00000253693.2	+	13	1801	c.1548C>T	c.(1546-1548)gaC>gaT	p.D516D		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	516	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						AGAAAATAGACAACGGTAAAT	0.294																																																0			3											41	45	44					3																	15282120		2191	4298	6489	15257124	SO:0001819	synonymous_variant	23473			AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.1548C>T	3.37:g.15282120C>T			15257124		Silent	SNP	ENST00000253693.2	37	CCDS2624.1																																																																																				0.294	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		T	15282120	C	T	15282120	2	4	100	1	0	0	0	0	0	0	0	1	2637	477	17	3		3	CAPN7	3	15282120	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	4829787	15282120	182740310	40	26694										
OXSM	54995	hgsc.bcm.edu	37	chr3	25833044	25833045	+	Frame_Shift_Ins	INS	-	-	G													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tacaataaagttagcccattINSttttgtccctaagattctgg							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:25833044_25833045insG	ENST00000280701.3	+	2	632_633	c.533_534insG	c.(532-537)ttttttfs	p.F178fs	OXSM_ENST00000420173.2_Frame_Shift_Ins_p.F178fs|OXSM_ENST00000449808.1_Intron|NGLY1_ENST00000417874.2_5'Flank	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	178					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GTTAGCCCATTTTTTGTCCCTA	0.426																																																0			3																																								25808049	SO:0001589	frameshift_variant	54995			BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	Exception_encountered	3.37:g.25833044_25833045insG	ENSP00000280701:p.Phe178fs		25808048		Frame_Shift_Ins	INS	ENST00000280701.3	37	CCDS2643.1																																																																																				0.426	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		G	25833045	-	G	25833044	7	5	100	1	0	1	1	0	0	0	0	0	11366	1841	64	0	535	0	OXSM	3	25833044	Frame_Shift_Ins	INS	-	TCGA-DC-6682-01A-11D-1826-10	10550924	25833044	172189386	41	26695										
NEK10	152110	hgsc.bcm.edu	37	chr3	27343219	27343219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agaaagtattttcttgtattTccctagggctcaagtcttct	7	8	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:27343219T>C	ENST00000429845.2	-	14	1498	c.1136A>G	c.(1135-1137)gAa>gGa	p.E379G	NEK10_ENST00000341435.5_Missense_Mutation_p.E379G			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	379			E -> K (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TTCTTGTATTTCCCTAGGGCT	0.348																																																0			3											42	37	38					3																	27343219		1565	3577	5142	27318223	SO:0001583	missense	152110			AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1136A>G	3.37:g.27343219T>C	ENSP00000395849:p.Glu379Gly		27318223	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		.	.	.	.	.	.	.	.	.	.	T	16.39	3.110411	0.56398	.	.	ENSG00000163491	ENST00000341435;ENST00000396636	T	0.70631	-0.5	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.131196	0.49305	N	0.000159	T	0.65460	0.2693	L	0.44542	1.39	0.80722	D	1	D	0.59357	0.985	P	0.47206	0.541	T	0.63301	-0.6668	10	0.27082	T	0.32	.	11.1359	0.48375	0.0:0.0752:0.0:0.9248	.	379	Q6ZWH5	NEK10_HUMAN	G	379	ENSP00000343847:E379G	ENSP00000343847:E379G	E	-	2	0	NEK10	27318223	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.138000	0.64795	2.029000	0.59856	0.477000	0.44152	GAA		0.348	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		C	27343219	T	C	27343219	3	2	100	1	0	0	0	0	1	0	0	0	10353	1783	62	4	1050	4	NEK10	3	27343219	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	1510175	27343219	170679211	42	26696										
ARPP21	10777	hgsc.bcm.edu	37	chr3	35833957	35833957	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcagagtcagaacgtgataAataaccaacaaggaactccg	8	10	2	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:35833957A>G	ENST00000187397.4	+	19	2572	c.2116A>G	c.(2116-2118)Aat>Gat	p.N706D	ARPP21_ENST00000476052.1_3'UTR|ARPP21_ENST00000417925.1_Missense_Mutation_p.N707D|ARPP21_ENST00000444190.1_Missense_Mutation_p.N687D|ARPP21_ENST00000458225.1_Missense_Mutation_p.N707D|ARPP21_ENST00000337271.5_Missense_Mutation_p.N687D	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	706	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						GAACGTGATAAATAACCAACA	0.463																																																0			3											158	144	148					3																	35833957		2203	4300	6503	35808961	SO:0001583	missense	0			AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.2116A>G	3.37:g.35833957A>G	ENSP00000187397:p.Asn706Asp		35808961	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.011310	0.35511	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.71	3.33	0.38152	.	0.311061	0.33959	N	0.004391	T	0.33352	0.0860	L	0.40543	1.245	0.19775	N	0.999954	B;B;B;B	0.27679	0.027;0.185;0.016;0.027	B;B;B;B	0.31101	0.073;0.124;0.02;0.073	T	0.24764	-1.0151	10	0.51188	T	0.08	-3.3237	8.3883	0.32514	0.7874:0.0:0.2126:0.0	.	707;229;706;687	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	D	707;687;687;706;707	ENSP00000414351:N707D;ENSP00000337792:N687D;ENSP00000405276:N687D;ENSP00000187397:N706D;ENSP00000412326:N707D	ENSP00000187397:N706D	N	+	1	0	ARPP21	35808961	1.000000	0.71417	0.671000	0.29857	0.696000	0.40369	2.078000	0.41567	0.438000	0.26450	-0.256000	0.11100	AAT		0.463	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		G	35833957	A	G	35833957	3	3	100	1	0	0	0	0	1	0	0	0	979	14	1	4	2195	4	ARPP21	3	35833957	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	8490738	35833957	162188473	43	26697										
MLH1	4292	hgsc.bcm.edu	37	chr3	37053326	37053326	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccaggtattcagtacacaaTgcaggcattagtttctcagt	8	9	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:37053326T>C	ENST00000231790.2	+	7	777	c.561T>C	c.(559-561)aaT>aaC	p.N187N	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000492474.1_3'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000435176.1_Silent_p.N89N	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	187					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CAGTACACAATGCAGGCATTA	0.328		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	1	Whole gene deletion(1)	ovary(1)	3											184	200	195					3																	37053326		2203	4300	6503	37028330	SO:0001819	synonymous_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.561T>C	3.37:g.37053326T>C			37028330	B4DI13|B4DQ11|E9PCU2	Silent	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	T	9.070	0.996756	0.19043	.	.	ENSG00000076242	ENST00000456676	.	.	.	6.08	1.27	0.21489	.	.	.	.	.	T	0.56217	0.1970	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50440	-0.8828	4	.	.	.	-28.5752	8.9174	0.35590	0.0:0.4005:0.0:0.5995	.	.	.	.	T	179	.	.	M	+	2	0	MLH1	37028330	0.662000	0.27439	1.000000	0.80357	0.892000	0.51952	-0.205000	0.09411	0.547000	0.28938	0.533000	0.62120	ATG		0.328	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		C	37053326	T	C	37053326	2	2	100	1	0	0	0	0	0	0	0	1	9647	1461	51	4		4	MLH1	3	37053326	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	1219369	37053326	160969104	44	26698										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266679	41266679	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aatccctgaactgacaaaacTgctaaatgacgaggaccagg	9	10	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:41266679T>C	ENST00000349496.5	+	4	756	c.476T>C	c.(475-477)cTg>cCg	p.L159P	CTNNB1_ENST00000396183.3_Missense_Mutation_p.L159P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.L159P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.L152P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L159P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	159	Interaction with BCL9.				adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.M1_V173del(1)|p.I35_K170del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGACAAAACTGCTAAATGAC	0.413		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	2	Deletion - In frame(2)	liver(1)|skin(1)	3											121	113	116					3																	41266679		2203	4300	6503	41241683	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.476T>C	3.37:g.41266679T>C	ENSP00000344456:p.Leu159Pro		41241683	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.670370	0.67814	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80476	0.4630	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	D	0.83363	0.0003	10	0.87932	D	0	-18.4809	15.971	0.80019	0.0:0.0:0.0:1.0	.	87;159	B4DSW9;P35222	.;CTNB1_HUMAN	P	159;159;159;152;159	ENSP00000385604:L159P;ENSP00000379486:L159P;ENSP00000344456:L159P;ENSP00000411226:L152P;ENSP00000379488:L159P	ENSP00000344456:L159P	L	+	2	0	CTNNB1	41241683	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.040000	0.89188	2.175000	0.68902	0.533000	0.62120	CTG		0.413	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266679	T	C	41266679	3	2	100	1	0	0	0	0	1	0	0	0	4022	1580	55	4	486	4	CTNNB1	3	41266679	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	4213353	41266679	156755751	45	26699										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77147195	77147195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcgccaggaggactttccccCgcggattgtggagcatcctt	12	13	0	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:77147195C>T	ENST00000461745.1	+	2	992	c.92C>T	c.(91-93)cCg>cTg	p.P31L	ROBO2_ENST00000332191.8_Missense_Mutation_p.P31L|ROBO2_ENST00000487694.3_Missense_Mutation_p.P47L	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	31	Ig-like C2-type 1.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GACTTTCCCCCGCGGATTGTG	0.537																																																0			3											45	48	47					3																	77147195		1943	4128	6071	77229885	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.92C>T	3.37:g.77147195C>T	ENSP00000417164:p.Pro31Leu		77229885	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.694194	0.68386	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191	T;T;T	0.64803	-0.12;-0.12;-0.12	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.38605	U	0.001631	D	0.84938	0.5583	M	0.93462	3.42	0.48830	D	0.999710	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89231	0.3577	9	0.87932	D	0	.	18.541	0.91027	0.0:1.0:0.0:0.0	.	47;31;31	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	L	47;47;47;31;31	ENSP00000417335:P47L;ENSP00000417164:P31L;ENSP00000327536:P31L	ENSP00000327536:P31L	P	+	2	0	ROBO2	77229885	1.000000	0.71417	0.872000	0.34217	0.017000	0.09413	7.814000	0.86154	2.360000	0.80028	0.655000	0.94253	CCG		0.537	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77147195	C	T	77147195	3	4	100	1	0	0	0	0	1	0	0	0	13551	652	23	1	100	1	ROBO2	3	77147195	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	35880516	77147195	120875235	46	26700										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78987978	78987978	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgggtgtggggcggccttcaGctttgcagttcaaagttgca	15	8	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:78987978G>C	ENST00000464233.1	-	4	385	c.272C>G	c.(271-273)gCt>gGt	p.A91G	RN7SL751P_ENST00000473281.2_RNA|ROBO1_ENST00000467549.1_Missense_Mutation_p.A52G|ROBO1_ENST00000495273.1_Missense_Mutation_p.A52G|ROBO1_ENST00000436010.2_Missense_Mutation_p.A52G	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	91	Ig-like C2-type 1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GCGGCCTTCAGCTTTGCAGTT	0.517																																																0			3											113	106	108					3																	78987978		1883	4120	6003	79070668	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.272C>G	3.37:g.78987978G>C	ENSP00000420321:p.Ala91Gly		79070668	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983488	0.93044	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.53	5.53	0.82687	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84750	0.5541	M	0.86502	2.82	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.999;0.998	D;D;D;D	0.77004	0.984;0.989;0.977;0.961	D	0.86084	0.1546	9	.	.	.	.	19.4697	0.94958	0.0:0.0:1.0:0.0	.	91;52;52;52	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	G	52;52;91;52;52;91	ENSP00000406043:A52G;ENSP00000420321:A91G;ENSP00000420637:A52G;ENSP00000417992:A52G	.	A	-	2	0	ROBO1	79070668	1.000000	0.71417	0.976000	0.42696	0.894000	0.52154	9.835000	0.99442	2.611000	0.88343	0.462000	0.41574	GCT		0.517	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		C	78987978	G	C	78987978	3	2	100	1	0	0	0	0	1	0	0	0	13550	971	34	5	4808	5	ROBO1	3	78987978	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1840783	78987978	119034452	47	26701										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111432929	111432929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcacccccagagtgaagaccAttgcccggggcttggttggg	14	12	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:111432929A>G	ENST00000477665.1	+	3	1144	c.820A>G	c.(820-822)Att>Gtt	p.I274V	PLCXD2_ENST00000472215.1_3'UTR|PLCXD2_ENST00000393934.3_Missense_Mutation_p.I274V	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	274					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						AGTGAAGACCATTGCCCGGGG	0.517																																																0			3											40	40	40					3																	111432929		2203	4300	6503	112915619	SO:0001583	missense	257068			AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.820A>G	3.37:g.111432929A>G	ENSP00000420686:p.Ile274Val		112915619	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	37	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	A	4.927	0.172253	0.09391	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.5	5.5	0.81552	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.39489	0.1080	N	0.21617	0.685	0.52099	D	0.99994	B;B	0.30236	0.274;0.202	B;B	0.22386	0.026;0.039	T	0.29336	-1.0015	8	0.12103	T	0.63	-19.0346	13.5883	0.61944	1.0:0.0:0.0:0.0	.	274;274	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	V	274	.	ENSP00000377511:I274V	I	+	1	0	PLCXD2	112915619	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.819000	0.62664	2.090000	0.63153	0.460000	0.39030	ATT		0.517	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		G	111432929	A	G	111432929	3	3	100	1	0	0	0	0	1	0	0	0	12073	217	8	4	830	4	PLCXD2	3	111432929	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	32444951	111432929	86589501	48	26702										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111988836	111988836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcatcaccaaaaacagttgaCatccaaaattgaatcagttt	4	9	3	2	rs371705215		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:111988836C>T	ENST00000305815.5	-	7	954	c.702G>A	c.(700-702)atG>atA	p.M234I	SLC9C1_ENST00000487372.1_Missense_Mutation_p.M234I	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	234					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										AAACAGTTGACATCCAAAATT	0.328																																																0			3						C	ILE/MET	1,4405	2.1+/-5.4	0,1,2202	68	73	71		702	0.7	0.1	3		71	0,8590		0,0,4295	no	missense	SLC9A10	NM_183061.1	10	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	234/1178	111988836	1,12995	2203	4295	6498	113471526	SO:0001583	missense	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.702G>A	3.37:g.111988836C>T	ENSP00000306627:p.Met234Ile		113471526	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.262464	0.23051	2.27E-4	0.0	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.10668	2.85;2.85	5.9	0.686	0.18015	Cation/H+ exchanger (1);	0.307176	0.30940	N	0.008575	T	0.07143	0.0181	L	0.44542	1.39	0.09310	N	0.999996	P;P	0.40144	0.539;0.704	B;B	0.39217	0.195;0.294	T	0.21655	-1.0239	10	0.25751	T	0.34	-16.2819	1.7336	0.02937	0.3004:0.4079:0.1335:0.1582	.	234;234	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	I	234	ENSP00000306627:M234I;ENSP00000420688:M234I	ENSP00000306627:M234I	M	-	3	0	SLC9A10	113471526	0.094000	0.21725	0.134000	0.22075	0.382000	0.30200	0.186000	0.16978	0.086000	0.17137	0.505000	0.49811	ATG		0.328	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111988836	C	T	111988836	3	4	100	1	0	0	0	0	1	0	0	0	14747	478	17	3	2923	3	SLC9A10	3	111988836	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	555907	111988836	86033594	49	26703										
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133356882	133356882	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcacggaaagctttactctgAaagcggttcatatctaaagg	10	8	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:133356882A>G	ENST00000260810.5	-	14	2489	c.2358T>C	c.(2356-2358)ttT>ttC	p.F786F		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	786					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTTTACTCTGAAAGCGGTTCA	0.493								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)											0			3											262	262	262					3																	133356882		1994	4165	6159	134839572	SO:0001819	synonymous_variant	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.2358T>C	3.37:g.133356882A>G			134839572	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																				0.493	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		G	133356882	A	G	133356882	2	3	100	1	0	0	0	0	0	0	0	1	16409	243	9	4		4	TOPBP1	3	133356882	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	21368046	133356882	64665548	50	26704										
MSL2	55167	hgsc.bcm.edu	37	chr3	135871147	135871147	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccattataagtaggcaaaccAttgataacagaactgccaat	6	9	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:135871147A>G	ENST00000309993.2	-	2	1308	c.576T>C	c.(574-576)aaT>aaC	p.N192N	MSL2_ENST00000434835.2_Silent_p.N118N	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	192					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						TAGGCAAACCATTGATAACAG	0.378																																																0			3											64	64	64					3																	135871147		2203	4300	6503	137353837	SO:0001819	synonymous_variant	55167			AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"RING-type (C3HC4) zinc fingers"	25544	protein-coding gene	gene with protein product	"male-specific lethal-2 homolog (Drosophila)"	614802	"ring finger protein 184", "male-specific lethal 2-like 1 (Drosophila)"	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.576T>C	3.37:g.135871147A>G			137353837	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Silent	SNP	ENST00000309993.2	37	CCDS33861.1																																																																																				0.378	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		G	135871147	A	G	135871147	2	3	100	1	0	0	0	0	0	0	0	1	9908	214	8	4		4	MSL2	3	135871147	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	2514265	135871147	62151283	51	26705										
COPB2	9276	hgsc.bcm.edu	37	chr3	139077104	139077104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agtaggagaagcaggtttccCatcaagttcctgaaaccaca	9	10	1	2	rs560518160		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:139077104C>A	ENST00000333188.5	-	21	2744	c.2563G>T	c.(2563-2565)Ggg>Tgg	p.G855W	COPB2_ENST00000507777.1_Missense_Mutation_p.G826W	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	855					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.G855R(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						GCAGGTTTCCCATCAAGTTCC	0.433																																																1	Substitution - Missense(1)	ovary(1)	3											110	96	100					3																	139077104		2203	4300	6503	140559794	SO:0001583	missense	9276			BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.2563G>T	3.37:g.139077104C>A	ENSP00000329419:p.Gly855Trp		140559794	B4DZI8	Missense_Mutation	SNP	ENST00000333188.5	37	CCDS3108.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.78|13.78	2.338314|2.338314	0.41398|0.41398	.|.	.|.	ENSG00000184432|ENSG00000184432	ENST00000333188;ENST00000507777|ENST00000503326	T;T|.	0.62941|.	-0.01;0.1|.	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	0.717399|.	0.13055|.	N|.	0.417385|.	T|T	0.41259|0.41259	0.1151|0.1151	N|N	0.24115|0.24115	0.695|0.695	0.31506|0.31506	N|N	0.664213|0.664213	B|.	0.26147|.	0.143|.	B|.	0.23852|.	0.049|.	T|T	0.43015|0.43015	-0.9417|-0.9417	10|5	0.72032|.	D|.	0.01|.	-21.3713|-21.3713	13.8059|13.8059	0.63230|0.63230	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	855|.	P35606|.	COPB2_HUMAN|.	W|L	855;826|68	ENSP00000329419:G855W;ENSP00000422295:G826W|.	ENSP00000329419:G855W|.	G|W	-|-	1|2	0|0	COPB2|COPB2	140559794|140559794	0.797000|0.797000	0.28877|0.28877	0.936000|0.936000	0.37596|0.37596	0.765000|0.765000	0.43378|0.43378	3.232000|3.232000	0.51302|0.51302	2.634000|2.634000	0.89283|0.89283	0.650000|0.650000	0.86243|0.86243	GGG|TGG		0.433	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		A	139077104	C	A	139077104	3	1	100	1	0	0	0	0	1	0	0	0	3735	594	21	2	165	2	COPB2	3	139077104	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3205957	139077104	58945326	52	26706										
PCOLCE2	26577	hgsc.bcm.edu	37	chr3	142561849	142561849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccagttgggggttttaaaagAgccggaaggtctgtcaagga	15	6	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:142561849A>G	ENST00000295992.3	-	4	796	c.490T>C	c.(490-492)Tct>Cct	p.S164P	PCOLCE2_ENST00000485766.1_Missense_Mutation_p.S164P	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	164	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						GTTTTAAAAGAGCCGGAAGGT	0.473																																																0			3											82	84	83					3																	142561849		2203	4300	6503	144044539	SO:0001583	missense	26577			AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.490T>C	3.37:g.142561849A>G	ENSP00000295992:p.Ser164Pro		144044539	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.329004	0.24167	.	.	ENSG00000163710	ENST00000295992;ENST00000485766	T;T	0.29655	1.56;1.56	5.22	4.02	0.46733	CUB (5);	0.274051	0.42420	D	0.000709	T	0.42494	0.1205	L	0.52266	1.64	0.34220	D	0.675348	P	0.50272	0.933	P	0.57009	0.811	T	0.57837	-0.7742	10	0.66056	D	0.02	-24.3321	11.2896	0.49241	0.8633:0.0:0.0:0.1367	.	164	Q9UKZ9	PCOC2_HUMAN	P	164	ENSP00000295992:S164P;ENSP00000419842:S164P	ENSP00000295992:S164P	S	-	1	0	PCOLCE2	144044539	1.000000	0.71417	0.977000	0.42913	0.057000	0.15508	4.525000	0.60559	0.951000	0.37770	0.454000	0.30748	TCT		0.473	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		G	142561849	A	G	142561849	3	3	100	1	0	0	0	0	1	0	0	0	11626	304	11	4	781	4	PCOLCE2	3	142561849	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	3484745	142561849	55460581	53	26707										
SIAH2	6478	hgsc.bcm.edu	37	chr3	150460047	150460047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	catgatggccgcagccacacCgtcatgaatcgaacggggcg	13	13	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:150460047C>T	ENST00000312960.3	-	2	1383	c.856G>A	c.(856-858)Ggt>Agt	p.G286S		NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2	286	SBD.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|cellular protein catabolic process (GO:0044257)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|regulation of protein ubiquitination (GO:0031396)|regulation of RNA biosynthetic process (GO:2001141)|small GTPase mediated signal transduction (GO:0007264)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G286S(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)	16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GCAGCCACACCGTCATGAATC	0.527																																																1	Substitution - Missense(1)	ovary(1)	3											90	74	80					3																	150460047		2203	4300	6503	151942737	SO:0001583	missense	6478			U76248	CCDS3152.1	3q25	2012-02-23	2012-02-23		ENSG00000181788	ENSG00000181788	6.3.2.1		10858	protein-coding gene	gene with protein product		602213	"seven in absentia (Drosophila) homolog 2", "seven in absentia homolog 2 (Drosophila)"			9334332	Standard	NM_005067		Approved		uc003eyi.3	O43255	OTTHUMG00000159847	ENST00000312960.3:c.856G>A	3.37:g.150460047C>T	ENSP00000322457:p.Gly286Ser		151942737	O43270	Missense_Mutation	SNP	ENST00000312960.3	37	CCDS3152.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529817	0.64860	.	.	ENSG00000181788	ENST00000312960	T	0.24723	1.84	5.81	4.94	0.65067	TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);	0.000000	0.85682	D	0.000000	T	0.23330	0.0564	L	0.35793	1.09	0.80722	D	1	D	0.54601	0.967	P	0.47402	0.546	T	0.03025	-1.1081	10	0.05620	T	0.96	.	14.874	0.70481	0.0:0.9315:0.0:0.0685	.	286	O43255	SIAH2_HUMAN	S	286	ENSP00000322457:G286S	ENSP00000322457:G286S	G	-	1	0	SIAH2	151942737	1.000000	0.71417	0.896000	0.35187	0.390000	0.30446	7.802000	0.85969	1.468000	0.48064	-0.229000	0.12294	GGT		0.527	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	NM_005067		T	150460047	C	T	150460047	3	4	100	1	0	0	0	0	1	0	0	0	14337	652	23	1	122	1	SIAH2	3	150460047	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	7898198	150460047	47562383	54	26708										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178938860	178938860	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	atgtgggatgtatttgaagcAcctgaataggcaagtcgagg	14	5	0	2	rs121913282		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:178938860A>G	ENST00000263967.3	+	14	2259	c.2102A>G	c.(2101-2103)cAc>cGc	p.H701R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	701					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H701P(3)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TATTTGAAGCACCTGAATAGG	0.418		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Substitution - Missense(3)	breast(2)|central_nervous_system(1)	3											75	67	69					3																	178938860		1876	4094	5970	180421554	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2102A>G	3.37:g.178938860A>G	ENSP00000263967:p.His701Arg		180421554	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662705	0.47572	.	.	ENSG00000121879	ENST00000263967	T	0.62639	0.01	5.41	5.41	0.78517	Phosphoinositide 3-kinase, accessory (PIK) domain (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.55130	0.1901	L	0.44542	1.39	0.80722	D	1	P	0.37955	0.612	B	0.38264	0.269	T	0.52298	-0.8594	10	0.19590	T	0.45	-12.0205	15.4463	0.75232	1.0:0.0:0.0:0.0	.	701	P42336	PK3CA_HUMAN	R	701	ENSP00000263967:H701R	ENSP00000263967:H701R	H	+	2	0	PIK3CA	180421554	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.962000	0.93254	2.052000	0.61016	0.528000	0.53228	CAC		0.418	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178938860	A	G	178938860	3	3	100	1	0	0	0	0	1	0	0	0	11944	159	6	4	2152	4	PIK3CA	3	178938860	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	28478813	178938860	19083570	55	26709										
DGKG	1608	hgsc.bcm.edu	37	chr3	186024720	186024720	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcatattgtttgaggctcccAccctcattaaattcagtcaa	5	11	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr3:186024720A>G	ENST00000265022.3	-	3	653	c.114T>C	c.(112-114)ggT>ggC	p.G38G	DGKG_ENST00000544847.1_Silent_p.G38G|DGKG_ENST00000344484.4_Silent_p.G38G|DGKG_ENST00000382164.4_Silent_p.G38G	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	38					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TGAGGCTCCCACCCTCATTAA	0.388																																																0			3											155	152	153					3																	186024720		2203	4300	6503	187507414	SO:0001819	synonymous_variant	1608			AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.114T>C	3.37:g.186024720A>G			187507414	B2RAH4|Q2M1H4|Q5FWG1	Silent	SNP	ENST00000265022.3	37	CCDS3274.1																																																																																				0.388	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			G	186024720	A	G	186024720	2	3	100	1	0	0	0	0	0	0	0	1	4480	146	6	4		4	DGKG	3	186024720	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	7085860	186024720	11997710	56	26710										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228459	4228459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggcgcgcacaccgccccgccGgggggccggggattccgggg	20	16	0	0	rs553397205		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:4228459G>A	ENST00000296358.4	-	1	157	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	45					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ccgccccgccggggggccggg	0.736													G|||	1	0.000199681	0	0	5008	,	,		11547	0		0.001	False		,,,				2504	0															0			4											3	4	4					4																	4228459		1958	3835	5793	4279360	SO:0001583	missense	133060			BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.133C>T	4.37:g.4228459G>A	ENSP00000296358:p.Arg45Trp		4279360	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148239	0.37923	.	.	ENSG00000163982	ENST00000296358	T	0.09163	3.01	3.37	2.42	0.29668	.	0.633721	0.13992	U	0.348702	T	0.10078	0.0247	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	P	0.50378	0.639	T	0.19353	-1.0308	10	0.66056	D	0.02	.	10.4757	0.44663	0.0:0.1977:0.8023:0.0	.	45	Q7RTM1	OTOP1_HUMAN	W	45	ENSP00000296358:R45W	ENSP00000296358:R45W	R	-	1	2	OTOP1	4279360	0.017000	0.18338	0.009000	0.14445	0.117000	0.20001	1.053000	0.30442	1.626000	0.50381	0.430000	0.28490	CGG		0.736	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4228459	G	A	4228459	3	1	100	1	0	0	0	0	1	0	0	0	11336	1115	39	1	1729	1	OTOP1	4	4228459	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		4228459	186925817	57	26711										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8211522	8211522	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggcctgctgctgggacccctCcctgccagatgggggtttat	14	13	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:8211522C>G	ENST00000245105.3	+	3	287	c.220C>G	c.(220-222)Ccc>Gcc	p.P74A	SH3TC1_ENST00000539824.1_5'UTR	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	74										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TGGGACCCCTCCCTGCCAGAT	0.627																																					NSCLC(145;2298 2623 35616 37297)											0			4											37	36	37					4																	8211522		2203	4300	6503	8262422	SO:0001583	missense	54436			AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.220C>G	4.37:g.8211522C>G	ENSP00000245105:p.Pro74Ala		8262422	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	c	5.116	0.206961	0.09704	.	.	ENSG00000125089	ENST00000245105;ENST00000457650	T	0.74526	-0.85	2.32	0.395	0.16304	.	0.323947	0.18656	U	0.134842	T	0.57227	0.2039	L	0.48642	1.525	0.09310	N	0.999998	B	0.32101	0.356	B	0.30401	0.115	T	0.38394	-0.9663	10	0.14252	T	0.57	-2.2221	3.7639	0.08615	0.0:0.5883:0.2534:0.1583	.	74	Q8TE82	S3TC1_HUMAN	A	74	ENSP00000245105:P74A	ENSP00000245105:P74A	P	+	1	0	SH3TC1	8262422	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.269000	0.18589	0.066000	0.16515	0.556000	0.70494	CCC		0.627	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		G	8211522	C	G	8211522	3	3	100	1	0	0	0	0	1	0	0	0	14298	855	30	5	226	5	SH3TC1	4	8211522	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3983063	8211522	182942754	58	26712										
CEP135	9662	hgsc.bcm.edu	37	chr4	56865777	56865777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtagatgagaagacagaaaAgattgcaaatttgcaagaaa	10	3	0	6			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:56865777A>G	ENST00000257287.4	+	17	2370	c.2246A>G	c.(2245-2247)aAg>aGg	p.K749R		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	749					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AAGACAGAAAAGATTGCAAAT	0.333																																																0			4											70	78	75					4																	56865777		2203	4300	6503	56560534	SO:0001583	missense	9662			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2246A>G	4.37:g.56865777A>G	ENSP00000257287:p.Lys749Arg		56560534	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.280056	0.23392	.	.	ENSG00000174799	ENST00000257287	T	0.56941	0.43	5.18	2.73	0.32206	.	0.248856	0.47093	D	0.000257	T	0.30230	0.0758	N	0.17723	0.515	0.28411	N	0.9182	B	0.06786	0.001	B	0.12837	0.008	T	0.17623	-1.0363	10	0.10377	T	0.69	.	7.3434	0.26650	0.6558:0.0:0.3442:0.0	.	749	Q66GS9	CP135_HUMAN	R	749	ENSP00000257287:K749R	ENSP00000257287:K749R	K	+	2	0	CEP135	56560534	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	2.491000	0.45303	0.786000	0.33708	0.524000	0.50904	AAG		0.333	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56865777	A	G	56865777	3	3	100	1	0	0	0	0	1	0	0	0	3253	72	3	4	2308	4	CEP135	4	56865777	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	48654255	56865777	134288499	59	26713										
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95202679	95202679	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	atgctggatatcttagaggtTctattaaaacatcatcagca	7	7	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:95202679T>C	ENST00000354268.4	+	21	2737	c.2664T>C	c.(2662-2664)gtT>gtC	p.V888V	SMARCAD1_ENST00000457823.2_Silent_p.V890V|SMARCAD1_ENST00000509418.1_Silent_p.V458V			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	888	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TCTTAGAGGTTCTATTAAAAC	0.308																																																0			4											161	164	163					4																	95202679		2203	4297	6500	95421702	SO:0001819	synonymous_variant	56916			AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2664T>C	4.37:g.95202679T>C			95421702	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Silent	SNP	ENST00000354268.4	37	CCDS3639.1																																																																																				0.308	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		C	95202679	T	C	95202679	2	2	100	1	0	0	0	0	0	0	0	1	14809	1770	62	4		4	SMARCAD1	4	95202679	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	38336902	95202679	95951597	60	26714										
FAT4	79633	hgsc.bcm.edu	37	chr4	126238491	126238491	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgggacttatcacggtgcggGagcccctggacttcgaagct	14	12	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:126238491G>A	ENST00000394329.3	+	1	938	c.925G>A	c.(925-927)Gag>Aag	p.E309K		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	309	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CACGGTGCGGGAGCCCCTGGA	0.657											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4											25	31	29					4																	126238491		2015	4165	6180	126457941	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.925G>A	4.37:g.126238491G>A	ENSP00000377862:p.Glu309Lys	1548	126457941	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648997	0.29336	.	.	ENSG00000196159	ENST00000394329	T	0.44881	0.91	5.2	3.33	0.38152	Cadherin (4);Cadherin-like (1);	0.000000	0.34676	U	0.003761	T	0.31796	0.0808	N	0.01482	-0.84	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.19877	-1.0292	10	0.07990	T	0.79	.	14.7103	0.69225	0.0:0.412:0.5879:0.0	.	309	Q6V0I7	FAT4_HUMAN	K	309	ENSP00000377862:E309K	ENSP00000377862:E309K	E	+	1	0	FAT4	126457941	1.000000	0.71417	0.992000	0.48379	0.153000	0.21895	6.327000	0.72910	1.156000	0.42514	-0.175000	0.13238	GAG		0.657	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126238491	G	A	126238491	3	1	100	1	0	0	0	0	1	0	0	0	5711	1175	41	3	927	3	FAT4	4	126238491	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	31035812	126238491	64915785	61	26715										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153244079	153244079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcaccagcagcttggtttctTcagtcccattccgactccca	7	16	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:153244079T>C	ENST00000281708.4	-	12	3307	c.2078A>G	c.(2077-2079)gAa>gGa	p.E693G	FBXW7_ENST00000263981.5_Missense_Mutation_p.E613G|FBXW7_ENST00000393956.3_Missense_Mutation_p.E517G|FBXW7_ENST00000603841.1_Missense_Mutation_p.E693G|FBXW7_ENST00000296555.5_Missense_Mutation_p.E575G|RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000603548.1_Missense_Mutation_p.E693G	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	693					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTTGGTTTCTTCAGTCCCATT	0.502			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											164	159	161					4																	153244079		2203	4300	6503	153463529	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.2078A>G	4.37:g.153244079T>C	ENSP00000281708:p.Glu693Gly		153463529	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.673314	0.47781	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.56941	0.44;0.47;0.43;0.63	5.67	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.73481	0.3592	M	0.82923	2.615	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.77148	-0.2694	10	0.87932	D	0	-21.5342	13.079	0.59102	0.0:0.0:0.1338:0.8662	.	517;693;575;613	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	G	693;575;613;517	ENSP00000281708:E693G;ENSP00000296555:E575G;ENSP00000263981:E613G;ENSP00000377528:E517G	ENSP00000263981:E613G	E	-	2	0	FBXW7	153463529	1.000000	0.71417	0.587000	0.28692	0.998000	0.95712	8.015000	0.88690	0.948000	0.37687	0.533000	0.62120	GAA		0.502	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153244079	T	C	153244079	3	2	100	1	0	0	0	0	1	0	0	0	5788	1783	62	4	49	4	FBXW7	4	153244079	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	27005588	153244079	37910197	62	26716										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249383	153249383	+	Silent	SNP	A	A	G													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttttcatgaagatgcatacaAcgcacagtggaagtatgccc							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:153249383A>G	ENST00000281708.4	-	9	2624	c.1395T>C	c.(1393-1395)cgT>cgC	p.R465R	FBXW7_ENST00000263981.5_Silent_p.R385R|FBXW7_ENST00000393956.3_Silent_p.R289R|FBXW7_ENST00000603841.1_Silent_p.R465R|FBXW7_ENST00000296555.5_Silent_p.R347R|FBXW7_ENST00000603548.1_Silent_p.R465R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GATGCATACAACGCACAGTGG	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											253	218	230					4																	153249383		2203	4300	6503	153468833	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1395T>C	4.37:g.153249383A>G			153468833	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153249383	A	G	153249383	2	3	100	1	0	0	0	0	0	0	0	1	5788	30	2	4		4	FBXW7	4	153249383	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	5304	153249383	37904893	63	26717	42	2								
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249385	153249385	+	Missense_Mutation	SNP	G	G	A													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttcatgaagatgcatacaacGcacagtggaagtatgcccat							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:153249385G>A	ENST00000281708.4	-	9	2622	c.1393C>T	c.(1393-1395)Cgt>Tgt	p.R465C	FBXW7_ENST00000263981.5_Missense_Mutation_p.R385C|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289C|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465C|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347C|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465C	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465C(71)|p.R226C(11)|p.R385C(11)|p.R347C(3)|p.R465Y(2)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGCATACAACGCACAGTGGAA	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	99	Substitution - Missense(98)|Unknown(1)	haematopoietic_and_lymphoid_tissue(41)|large_intestine(27)|endometrium(20)|stomach(6)|biliary_tract(4)|pancreas(1)	4											260	223	235					4																	153249385		2203	4300	6503	153468835	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1393C>T	4.37:g.153249385G>A	ENSP00000281708:p.Arg465Cys		153468835	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909959	0.92107	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67287	0.2877	M	0.71206	2.165	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67130	-0.5748	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:0.0:1.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	C	465;347;385;289	ENSP00000281708:R465C;ENSP00000296555:R347C;ENSP00000263981:R385C;ENSP00000377528:R289C	ENSP00000263981:R385C	R	-	1	0	FBXW7	153468835	1.000000	0.71417	0.959000	0.39883	0.996000	0.88848	9.869000	0.99810	2.878000	0.98634	0.650000	0.86243	CGT		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249385	G	A	153249385	3	1	100	1	0	0	0	0	1	0	0	0	5788	1087	38	1	746	1	FBXW7	4	153249385	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	2	153249385	37904891	64	26718	42	2								
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154504794	154504794	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tacctacttctacaacaaacTttacaaaaattgcttctttt	1	10	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:154504794T>G	ENST00000409663.3	+	11	1082	c.1030T>G	c.(1030-1032)Ttt>Gtt	p.F344V	KIAA0922_ENST00000409959.3_Missense_Mutation_p.F344V|KIAA0922_ENST00000440693.1_Missense_Mutation_p.F344V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	344						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TACAACAAACTTTACAAAAAT	0.358																																																0			4											101	100	101					4																	154504794		2203	4300	6503	154724244	SO:0001583	missense	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1030T>G	4.37:g.154504794T>G	ENSP00000386574:p.Phe344Val		154724244	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469759	0.84533	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.19394	2.32;2.15;2.41;2.15	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.35970	0.0950	L	0.32530	0.975	0.33015	D	0.52805	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.42832	-0.9428	10	0.42905	T	0.14	-24.0989	15.1157	0.72401	0.0:0.0:0.0:1.0	.	344;344;344	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	V	344;344;344;205	ENSP00000386574:F344V;ENSP00000409663:F344V;ENSP00000386787:F344V;ENSP00000240487:F205V	ENSP00000240487:F205V	F	+	1	0	KIAA0922	154724244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.480000	0.66820	2.311000	0.77944	0.533000	0.62120	TTT		0.358	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		G	154504794	T	G	154504794	3	3	100	1	0	0	0	0	1	0	0	0	8222	1609	56	4	1072	4	KIAA0922	4	154504794	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	1255409	154504794	36649482	65	26719										
FAM198B	51313	hgsc.bcm.edu	37	chr4	159091911	159091911	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gggcgctctcgctgtagatcCtaatgttgctctccctggag	12	12	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:159091911C>A	ENST00000296530.8	-	2	1238	c.617G>T	c.(616-618)aGg>aTg	p.R206M	RP11-597D13.9_ENST00000503611.1_RNA|RP11-597D13.9_ENST00000514381.1_RNA|RP11-597D13.9_ENST00000505532.1_RNA|RP11-597D13.9_ENST00000509463.1_RNA|FAM198B_ENST00000592057.1_Missense_Mutation_p.R206M|FAM198B_ENST00000589306.1_Intron|FAM198B_ENST00000393807.5_Missense_Mutation_p.R206M|FAM198B_ENST00000585682.1_Missense_Mutation_p.R206M	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	206						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						GCTGTAGATCCTAATGTTGCT	0.637											OREG0016378	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4											53	57	56					4																	159091911		2203	4300	6503	159311361	SO:0001583	missense	0				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 18"	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.617G>T	4.37:g.159091911C>A	ENSP00000296530:p.Arg206Met	1798	159311361	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779122	0.90195	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.34859	1.34;1.34	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65405	-0.6176	10	0.87932	D	0	0.7848	18.341	0.90305	0.0:1.0:0.0:0.0	.	206;206;206	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	M	206	ENSP00000296530:R206M;ENSP00000377396:R206M	ENSP00000296530:R206M	R	-	2	0	FAM198B	159311361	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.780000	0.75063	2.550000	0.86006	0.563000	0.77884	AGG		0.637	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		A	159091911	C	A	159091911	3	1	100	1	0	0	0	0	1	0	0	0	5545	681	24	2	1063	2	FAM198B	4	159091911	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	4587117	159091911	32062365	66	26720										
KLKB1	3818	hgsc.bcm.edu	37	chr4	187177214	187177214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tttataccaactgttgggtaAccggatggggcttctcgaag	12	8	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr4:187177214A>G	ENST00000264690.6	+	13	1745	c.1558A>G	c.(1558-1560)Acc>Gcc	p.T520A	KLKB1_ENST00000513864.1_Missense_Mutation_p.T520A	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	520	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		CTGTTGGGTAACCGGATGGGG	0.383																																																0			4											68	70	70					4																	187177214		2203	4300	6503	187414208	SO:0001583	missense	3818			M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1558A>G	4.37:g.187177214A>G	ENSP00000264690:p.Thr520Ala		187414208	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182385	0.57800	.	.	ENSG00000164344	ENST00000264690;ENST00000513864;ENST00000418715	D;D	0.92752	-3.1;-3.1	5.77	5.77	0.91146	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.148919	0.46758	D	0.000278	D	0.90834	0.7121	N	0.20574	0.59	0.40217	D	0.977693	P;P;P	0.48350	0.909;0.847;0.866	P;P;P	0.55455	0.455;0.776;0.471	D	0.91157	0.4958	10	0.38643	T	0.18	.	15.2758	0.73739	1.0:0.0:0.0:0.0	.	482;520;520	E7EQA8;A8K9A9;P03952	.;.;KLKB1_HUMAN	A	520;520;482	ENSP00000264690:T520A;ENSP00000424469:T520A	ENSP00000264690:T520A	T	+	1	0	KLKB1	187414208	0.998000	0.40836	0.895000	0.35142	0.049000	0.14656	5.632000	0.67819	2.203000	0.70933	0.460000	0.39030	ACC		0.383	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		G	187177214	A	G	187177214	3	3	100	1	0	0	0	0	1	0	0	0	8433	43	2	4	1604	4	KLKB1	4	187177214	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	28085303	187177214	3977062	67	26721										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461211	5461211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tctggccattttcacagactAtctagagaattggaaaagga	9	7	3	2	rs374313250		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:5461211A>G	ENST00000296564.7	+	13	1986	c.1764A>G	c.(1762-1764)ctA>ctG	p.L588L		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		588					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TTCACAGACTATCTAGAGAAT	0.403																																																0			5						G		0,3702		0,0,1851	112	110	111		1764	-9.1	0	5		111	1,8207		0,1,4103	no	coding-synonymous	KIAA0947	NM_015325.1		0,1,5954	GG,GA,AA		0.0122,0.0,0.0084		588/2267	5461211	1,11909	1851	4104	5955	5514211	SO:0001819	synonymous_variant	23379																														ENST00000296564.7:c.1764A>G	5.37:g.5461211A>G			5514211	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																				0.403	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5461211	A	G	5461211	2	3	100	1	0	0	0	0	0	0	0	1	8223	436	16	4		4	KIAA0947	5	5461211	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10		5461211	175454049	68	26722										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11384790	11384790	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cctttacctgccaggctgccCggcctctggagggtggccgt	14	15	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:11384790C>T	ENST00000304623.8	-	7	1353	c.1164G>A	c.(1162-1164)ccG>ccA	p.P388P	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Silent_p.P297P|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000359640.2_Silent_p.P388P|CTNND2_ENST00000503622.1_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	388					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						CCAGGCTGCCCGGCCTCTGGA	0.697																																																0			5											20	19	19					5																	11384790		2201	4299	6500	11437790	SO:0001819	synonymous_variant	1501			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.1164G>A	5.37:g.11384790C>T			11437790	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1																																																																																				0.697	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11384790	C	T	11384790	2	4	100	1	0	0	0	0	0	0	0	1	4026	639	23	1		1	CTNND2	5	11384790	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	5923579	11384790	169530470	69	26723										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33549336	33549336	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctccaaggctccacctgccaCgcctcacagggctccgggtt	10	18	1	0	rs149971505		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:33549336C>T	ENST00000504830.1	-	21	4613	c.4278G>A	c.(4276-4278)gcG>gcA	p.A1426A	ADAMTS12_ENST00000352040.3_Silent_p.A1341A	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1426	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CCACCTGCCACGCCTCACAGG	0.587										HNSCC(64;0.19)			C|||	1	0.000199681	0	0	5008	,	,		18285	0.001		0	False		,,,				2504	0															0			5						C		0,4406		0,0,2203	53	52	52		4278	3.6	1	5	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS12	NM_030955.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1426/1595	33549336	1,13005	2203	4300	6503	33585093	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4278G>A	5.37:g.33549336C>T			33585093	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.587	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33549336	C	T	33549336	2	4	100	1	0	0	0	0	0	0	0	1	257	523	19	1		1	ADAMTS12	5	33549336	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	22164546	33549336	147365924	70	26724										
DNAJC21	134218	hgsc.bcm.edu	37	chr5	34945131	34945131	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaagatgcaccaaaacaaaaGtacttctaaatattaaatgt	5	6	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:34945131G>A	ENST00000342382.4	+	8	1369		c.e8+1		DNAJC21_ENST00000303525.7_Splice_Site|DNAJC21_ENST00000382021.2_Splice_Site			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21						protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			CAAAACAAAAGTACTTCTAAA	0.343																																																0			5											74	81	79					5																	34945131		2203	4300	6503	34980888	SO:0001630	splice_region_variant	134218				CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"Heat shock proteins / DNAJ (HSP40)"	27030	protein-coding gene	gene with protein product	"JJJ1 DnaJ domain protein homolog (S. cerevisiae)"					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.1142+1G>A	5.37:g.34945131G>A			34980888	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Splice_Site	SNP	ENST00000342382.4	37	CCDS34144.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476209	0.44044	.	.	ENSG00000168724	ENST00000342382;ENST00000382021;ENST00000303525	.	.	.	5.83	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3776	0.74621	0.0:0.1386:0.8614:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJC21	34980888	1.000000	0.71417	0.996000	0.52242	0.505000	0.33919	7.992000	0.88273	1.465000	0.48006	0.655000	0.94253	.		0.343	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	Intron	A	34945131	G	A	34945131	5	1	100	1	0	0	0	0	0	0	1	0	4651	1043	36	3	1173	3	DNAJC21	5	34945131	Splice_Site	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1395795	34945131	145970129	71	26725										
FYB	2533	hgsc.bcm.edu	37	chr5	39202368	39202368	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttaaagggccgcttttggacCtgactcccaggggagctggg	15	10	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:39202368C>A	ENST00000351578.6	-	2	885	c.695G>T	c.(694-696)aGg>aTg	p.R232M	FYB_ENST00000540520.1_Missense_Mutation_p.R242M|FYB_ENST00000512982.1_Missense_Mutation_p.R232M|FYB_ENST00000505428.1_Missense_Mutation_p.R232M|FYB_ENST00000515010.1_Missense_Mutation_p.R232M	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	232					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)	p.R232T(1)		endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			GCTTTTGGACCTGACTCCCAG	0.507																																																1	Substitution - Missense(1)	ovary(1)	5											78	78	78					5																	39202368		1837	4081	5918	39238125	SO:0001583	missense	2533			U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.695G>T	5.37:g.39202368C>A	ENSP00000316460:p.Arg232Met		39238125	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	C	7.201	0.593570	0.13875	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.26067	1.76;1.76;1.77;1.77;1.77	6.07	2.36	0.29203	.	0.863259	0.10719	N	0.642006	T	0.18759	0.0450	N	0.14661	0.345	0.09310	N	1	P;P	0.44877	0.845;0.845	B;P	0.44732	0.36;0.459	T	0.13522	-1.0506	10	0.54805	T	0.06	-2.9495	8.9822	0.35972	0.0:0.3638:0.0:0.6362	.	242;232	B4DLN2;O15117	.;FYB_HUMAN	M	232;232;232;232;242;232	ENSP00000316460:R232M;ENSP00000426346:R232M;ENSP00000425845:R232M;ENSP00000427114:R232M;ENSP00000442840:R242M	ENSP00000316460:R232M	R	-	2	0	FYB	39238125	0.819000	0.29175	0.018000	0.16275	0.201000	0.24016	0.986000	0.29590	0.175000	0.19841	0.655000	0.94253	AGG		0.507	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		A	39202368	C	A	39202368	3	1	100	1	0	0	0	0	1	0	0	0	6143	681	24	2	1866	2	FYB	5	39202368	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	4257237	39202368	141712892	72	26726										
TRIM23	373	hgsc.bcm.edu	37	chr5	64907524	64907524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agcaaacaaactcaatggcaTgcacctggtgctgagagcac	10	11	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:64907524T>C	ENST00000231524.9	-	4	922	c.551A>G	c.(550-552)cAt>cGt	p.H184R	TRIM23_ENST00000274327.7_Missense_Mutation_p.H184R|TRIM23_ENST00000381018.3_Missense_Mutation_p.H184R|TRIM23_ENST00000508808.1_5'Flank	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	184					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		CTCAATGGCATGCACCTGGTG	0.438																																																0			5											177	169	172					5																	64907524		2203	4300	6503	64943280	SO:0001583	missense	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.551A>G	5.37:g.64907524T>C	ENSP00000231524:p.His184Arg		64943280	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.596372	0.86953	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.55413	0.52;0.52;0.52	5.14	5.14	0.70334	Zinc finger, B-box (1);	0.000000	0.85682	D	0.000000	T	0.65678	0.2714	L	0.56769	1.78	0.80722	D	1	D;D;D	0.63880	0.982;0.993;0.99	P;P;P	0.59424	0.634;0.855;0.857	T	0.69807	-0.5045	10	0.87932	D	0	.	15.2441	0.73493	0.0:0.0:0.0:1.0	.	184;184;184	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	R	184	ENSP00000231524:H184R;ENSP00000370406:H184R;ENSP00000274327:H184R	ENSP00000231524:H184R	H	-	2	0	TRIM23	64943280	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.630000	0.83225	2.055000	0.61198	0.402000	0.26972	CAT		0.438	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		C	64907524	T	C	64907524	3	2	100	1	0	0	0	0	1	0	0	0	16537	1464	51	4	1272	4	TRIM23	5	64907524	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	25705156	64907524	116007736	73	26727										
NLN	57486	hgsc.bcm.edu	37	chr5	65105372	65105372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cacgatttagcggaacaaatGtggaaactgactttgtagag	11	6	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:65105372G>A	ENST00000380985.5	+	10	1736	c.1558G>A	c.(1558-1560)Gtg>Atg	p.V520M	NLN_ENST00000502464.1_Missense_Mutation_p.V416M	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	520						mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		CGGAACAAATGTGGAAACTGA	0.358																																																0			5											135	135	135					5																	65105372		2203	4300	6503	65141128	SO:0001583	missense	57486			AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"angiotensin binding protein"	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1558G>A	5.37:g.65105372G>A	ENSP00000370372:p.Val520Met		65141128	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.6|29.6	5.023205|5.023205	0.93462|0.93462	.|.	.|.	ENSG00000123213|ENSG00000123213	ENST00000509935|ENST00000380985;ENST00000502464;ENST00000340159;ENST00000511299	.|T;T;T	.|0.13657	.|2.57;2.57;2.57	5.66|5.66	5.66|5.66	0.87406|0.87406	.|Metallopeptidase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55497|0.55497	0.1924|0.1924	H|H	0.96861|0.96861	3.895|3.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.995	T|T	0.71344|0.71344	-0.4621|-0.4621	5|10	.|0.87932	.|D	.|0	-19.3343|-19.3343	19.7604|19.7604	0.96314|0.96314	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|197;520	.|Q96K48;Q9BYT8	.|.;NEUL_HUMAN	Y|M	116|520;416;520;230	.|ENSP00000370372:V520M;ENSP00000423214:V416M;ENSP00000427417:V230M	.|ENSP00000339283:V520M	C|V	+|+	2|1	0|0	NLN|NLN	65141128|65141128	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	9.209000|9.209000	0.95087|0.95087	2.675000|2.675000	0.91044|0.91044	0.655000|0.655000	0.94253|0.94253	TGT|GTG		0.358	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1			A	65105372	G	A	65105372	3	1	100	1	0	0	0	0	1	0	0	0	10498	1377	48	3	1596	3	NLN	5	65105372	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	197848	65105372	115809888	74	26728										
CD180	4064	hgsc.bcm.edu	37	chr5	66480370	66480370	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cacaagtgtgcttaattgatGatggctttgaaaagtgtctt	10	5	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:66480370G>A	ENST00000256447.4	-	3	458	c.301C>T	c.(301-303)Cat>Tat	p.H101Y		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	101					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		CTTAATTGATGATGGCTTTGA	0.338																																																0			5											99	100	99					5																	66480370		2202	4299	6501	66516126	SO:0001583	missense	4064			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.301C>T	5.37:g.66480370G>A	ENSP00000256447:p.His101Tyr		66516126	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	G	8.364	0.833783	0.16820	.	.	ENSG00000134061	ENST00000256447	T	0.57907	0.37	5.92	0.763	0.18459	.	1.321840	0.04670	N	0.410482	T	0.36496	0.0969	N	0.25485	0.75	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29212	-1.0019	10	0.56958	D	0.05	.	0.8682	0.01208	0.225:0.1353:0.2262:0.4136	.	101	Q99467	CD180_HUMAN	Y	101	ENSP00000256447:H101Y	ENSP00000256447:H101Y	H	-	1	0	CD180	66516126	0.000000	0.05858	0.002000	0.10522	0.654000	0.38779	-0.065000	0.11617	0.101000	0.17610	-0.169000	0.13324	CAT		0.338	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		A	66480370	G	A	66480370	3	1	100	1	0	0	0	0	1	0	0	0	2978	1290	45	3	1688	3	CD180	5	66480370	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1374998	66480370	114434890	75	26729										
PDE8B	8622	hgsc.bcm.edu	37	chr5	76621552	76621552	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttcgatgcagaagcagtgtgCaggtaccttctctaatttaa	9	8	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:76621552C>A	ENST00000264917.5	+	3	633	c.588C>A	c.(586-588)tgC>tgA	p.C196*	PDE8B_ENST00000333194.4_Nonsense_Mutation_p.C196*|PDE8B_ENST00000346042.3_Nonsense_Mutation_p.C196*|PDE8B_ENST00000340978.3_Nonsense_Mutation_p.C196*|PDE8B_ENST00000342343.4_Nonsense_Mutation_p.C176*	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	196					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	AAGCAGTGTGCAGGTACCTTC	0.308																																																0			5											62	64	64					5																	76621552		2201	4300	6501	76657308	SO:0001587	stop_gained	8622			AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.588C>A	5.37:g.76621552C>A	ENSP00000264917:p.Cys196*		76657308	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Nonsense_Mutation	SNP	ENST00000264917.5	37	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	C	37	6.421137	0.97555	.	.	ENSG00000113231	ENST00000505926;ENST00000340978;ENST00000346042;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000502945	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2628	0.66097	0.0:0.9291:0.0:0.0709	.	.	.	.	X	72;196;196;196;176;196;72	.	ENSP00000264917:C196X	C	+	3	2	PDE8B	76657308	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	3.761000	0.55242	2.743000	0.94032	0.650000	0.86243	TGC		0.308	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		A	76621552	C	A	76621552	4	1	100	1	0	0	0	0	0	1	0	0	11685	718	25	2	598	2	PDE8B	5	76621552	Nonsense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	10141182	76621552	104293708	76	26730										
PCSK1	5122	hgsc.bcm.edu	37	chr5	95729016	95729016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcatccctccggccccctaCgctgctgctgctggggcttt	10	18	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:95729016C>T	ENST00000311106.3	-	14	2188	c.1951G>A	c.(1951-1953)Gta>Ata	p.V651I	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.V604I	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	651					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CGGCCCCCTACGCTGCTGCTG	0.552																																																0			5											62	66	65					5																	95729016		2203	4300	6503	95754772	SO:0001583	missense	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1951G>A	5.37:g.95729016C>T	ENSP00000308024:p.Val651Ile		95754772	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	8.435	0.849546	0.17034	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.66460	-0.05;-0.21	5.62	0.0182	0.14116	.	1.317330	0.04858	N	0.443482	T	0.42698	0.1214	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16276	-1.0408	10	0.34782	T	0.22	-1.8736	2.6891	0.05116	0.1131:0.3695:0.1109:0.4065	.	604;651	E9PHA1;P29120	.;NEC1_HUMAN	I	651;604	ENSP00000308024:V651I;ENSP00000421600:V604I	ENSP00000308024:V651I	V	-	1	0	PCSK1	95754772	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.012000	0.13287	-0.329000	0.08527	-0.797000	0.03246	GTA		0.552	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		T	95729016	C	T	95729016	3	4	100	1	0	0	0	0	1	0	0	0	11631	536	19	1	314	1	PCSK1	5	95729016	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	19107464	95729016	85186244	77	26731										
APC	324	hgsc.bcm.edu	37	chr5	112163644	112163644	+	Frame_Shift_Del	DEL	A	A	-													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aggctacgctatgctctatgAaaggctgcatgagagcactt							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:112163644delA	ENST00000457016.1	+	13	1947	c.1567delA	c.(1567-1569)aaafs	p.K523fs	APC_ENST00000257430.4_Frame_Shift_Del_p.K523fs|CTC-554D6.1_ENST00000520401.1_Frame_Shift_Del_p.*18fs|APC_ENST00000508376.2_Frame_Shift_Del_p.K523fs			P25054	APC_HUMAN	adenomatous polyposis coli	523	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATGCTCTATGAAAGGCTGCAT	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											86	85	85					5																	112163644		2202	4300	6502	112191543	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1567delA	5.37:g.112163644delA	ENSP00000413133:p.Lys523fs		112191543	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112163644	A	-	112163644	7	5	100	1	0	1	0	1	0	0	0	0	763	247	9	0	1613	0	APC	5	112163644	Frame_Shift_Del	DEL	A	TCGA-DC-6682-01A-11D-1826-10	16434628	112163644	68751616	78	26732										
APC	324	hgsc.bcm.edu	37	chr5	112164588	112164588	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttgaggaatttgtcttggcgAgcagatgtaaatagtaaaaa	11	3	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:112164588A>G	ENST00000457016.1	+	14	2042	c.1662A>G	c.(1660-1662)cgA>cgG	p.R554R	APC_ENST00000257430.4_Silent_p.R554R|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.E50G|APC_ENST00000508376.2_Silent_p.R554R			P25054	APC_HUMAN	adenomatous polyposis coli	554	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGTCTTGGCGAGCAGATGTAA	0.303		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											123	130	128					5																	112164588		2202	4300	6502	112192487	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1662A>G	5.37:g.112164588A>G			112192487	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.303	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112164588	A	G	112164588	2	3	100	1	0	0	0	0	0	0	0	1	763	291	11	4		4	APC	5	112164588	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	944	112164588	68750672	79	26733										
APC	324	hgsc.bcm.edu	37	chr5	112175149	112175149	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttgtcatcagctgaagatgaAataggatgtaatcagacgac	10	6	3	4			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:112175149A>G	ENST00000457016.1	+	16	4238	c.3858A>G	c.(3856-3858)gaA>gaG	p.E1286E	APC_ENST00000257430.4_Silent_p.E1286E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Silent_p.E1286E			P25054	APC_HUMAN	adenomatous polyposis coli	1286	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGAAGATGAAATAGGATGTA	0.353		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											55	57	56					5																	112175149		2202	4300	6502	112203048	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3858A>G	5.37:g.112175149A>G			112203048	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.353	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175149	A	G	112175149	2	3	100	1	0	0	0	0	0	0	0	1	763	11	1	4		4	APC	5	112175149	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	10561	112175149	68740111	80	26734										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123984308	123984308	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccgagatcttgtcctcactgTcaggctcgaactccagcttg	9	14	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:123984308T>C	ENST00000306315.5	-	4	2204	c.1769A>G	c.(1768-1770)gAc>gGc	p.D590G	ZNF608_ENST00000504926.1_Missense_Mutation_p.D163G	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	590							metal ion binding (GO:0046872)	p.D590V(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		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)		GTCCTCACTGTCAGGCTCGAA	0.483																																																1	Substitution - Missense(1)	ovary(1)	5											234	199	210					5																	123984308		2203	4300	6503	124012207	SO:0001583	missense	57507			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1769A>G	5.37:g.123984308T>C	ENSP00000307746:p.Asp590Gly		124012207	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863838	0.71949	.	.	ENSG00000168916	ENST00000504926;ENST00000306315;ENST00000509799;ENST00000513986	T;T	0.61158	0.13;0.14	5.6	5.6	0.85130	.	0.196214	0.52532	D	0.000078	T	0.67804	0.2932	M	0.67397	2.05	0.80722	D	1	P	0.50272	0.933	P	0.52267	0.694	T	0.71755	-0.4497	10	0.66056	D	0.02	-28.9427	15.8007	0.78453	0.0:0.0:0.0:1.0	.	590	Q9ULD9	ZN608_HUMAN	G	163;590;590;590	ENSP00000427657:D163G;ENSP00000307746:D590G	ENSP00000307746:D590G	D	-	2	0	ZNF608	124012207	1.000000	0.71417	0.938000	0.37757	0.951000	0.60555	8.023000	0.88764	2.126000	0.65437	0.445000	0.29226	GAC		0.483	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		C	123984308	T	C	123984308	3	2	100	1	0	0	0	0	1	0	0	0	18073	1667	58	4	2793	4	ZNF608	5	123984308	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	11809159	123984308	56930952	81	26735										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811649	140811649	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaaactcatatctcgctgaaCgtggcagacaccaacgacaa	8	12	2	2	rs376415955		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:140811649C>T	ENST00000252085.3	+	1	1465	c.1323C>T	c.(1321-1323)aaC>aaT	p.N441N	PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA10_ENST00000398610.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	441	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCGCTGAACGTGGCAGACA	0.552																																																0			5						C	,,,,,,,,,,,,,,,,,,,,	0,4406		0,0,2203	63	70	67		1323,,,,,,,,,,,,,,,,,,,,1323	-9.6	0	5		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032092.1,NM_032094.1	,,,,,,,,,,,,,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,,,,,,,,,,,,,	441/933,,,,,,,,,,,,,,,,,,,,441/821	140811649	1,13005	2203	4300	6503	140791833	SO:0001819	synonymous_variant	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1323C>T	5.37:g.140811649C>T			140791833	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																				0.552	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140811649	C	T	140811649	2	4	100	1	0	0	0	0	0	0	0	1	11584	535	19	1		1	PCDHGA12	5	140811649	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	16827341	140811649	40103611	82	26736										
CCDC69	26112	hgsc.bcm.edu	37	chr5	150585026	150585026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtggctgttctggttctggtTcttggcgcttctggaagaaa	14	7	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:150585026T>C	ENST00000355417.2	-	2	233	c.59A>G	c.(58-60)gAa>gGa	p.E20G	CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	20										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTTCTGGTTCTTGGCGCTT	0.572																																																0			5											169	152	158					5																	150585026		2203	4300	6503	150565219	SO:0001583	missense	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.59A>G	5.37:g.150585026T>C	ENSP00000347586:p.Glu20Gly		150565219	A8K9X6	Missense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326242	0.41197	.	.	ENSG00000198624	ENST00000355417	T	0.24151	1.87	4.32	3.16	0.36331	.	1.077990	0.07209	N	0.858869	T	0.14013	0.0339	N	0.08118	0	0.21256	N	0.999746	B	0.34290	0.447	B	0.33254	0.16	T	0.24621	-1.0155	10	0.52906	T	0.07	-1.8048	6.2558	0.20874	0.0:0.1135:0.0:0.8865	.	20	A6NI79	CCD69_HUMAN	G	20	ENSP00000347586:E20G	ENSP00000347586:E20G	E	-	2	0	CCDC69	150565219	0.931000	0.31567	0.883000	0.34634	0.804000	0.45430	0.858000	0.27845	0.705000	0.31890	0.454000	0.30748	GAA		0.572	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		C	150585026	T	C	150585026	3	2	100	1	0	0	0	0	1	0	0	0	2847	1783	62	4	863	4	CCDC69	5	150585026	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	9773377	150585026	30330234	83	26737										
ITK	3702	hgsc.bcm.edu	37	chr5	156649962	156649962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaactcgcactgcggcgcaaCgaagagtactgcctgctgga	13	12	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr5:156649962C>T	ENST00000422843.3	+	6	737	c.585C>T	c.(583-585)aaC>aaT	p.N195N	CTB-4E7.1_ENST00000519375.1_RNA	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	195	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	TGCGGCGCAACGAAGAGTACT	0.522			T	SYK	peripheral T-cell lymphoma																																Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	0			5											134	124	128					5																	156649962		2203	4300	6503	156582540	SO:0001819	synonymous_variant	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.585C>T	5.37:g.156649962C>T			156582540	B2R752|Q32ML7	Silent	SNP	ENST00000422843.3	37	CCDS4336.1																																																																																				0.522	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156649962	C	T	156649962	2	4	100	1	0	0	0	0	0	0	0	1	7930	535	19	1		1	ITK	5	156649962	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	6064936	156649962	24265298	84	26738										
RNF182	221687	hgsc.bcm.edu	37	chr6	13978054	13978054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtatggtttttgccagtgtgTttgtcatgaatttctagact	10	5	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:13978054T>C	ENST00000488300.1	+	3	1227	c.704T>C	c.(703-705)gTt>gCt	p.V235A	RNF182_ENST00000544682.1_Missense_Mutation_p.V235A|RNF182_ENST00000537388.1_Missense_Mutation_p.V235A|RNF182_ENST00000537663.1_Missense_Mutation_p.V235A	NM_152737.3	NP_689950.1	Q8N6D2	RN182_HUMAN	ring finger protein 182	235					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|large_intestine(7)|liver(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			TGCCAGTGTGTTTGTCATGAA	0.418																																																0			6											170	159	162					6																	13978054		2203	4300	6503	14086033	SO:0001583	missense	221687			AK090576	CCDS4531.1	6p23	2013-01-09			ENSG00000180537	ENSG00000180537		"RING-type (C3HC4) zinc fingers"	28522	protein-coding gene	gene with protein product						12477932	Standard	NM_152737		Approved	MGC33993	uc003nbg.3	Q8N6D2	OTTHUMG00000014280	ENST00000488300.1:c.704T>C	6.37:g.13978054T>C	ENSP00000420465:p.Val235Ala		14086033	B2RDG2|Q8NBG3	Missense_Mutation	SNP	ENST00000488300.1	37	CCDS4531.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.555231	0.45487	.	.	ENSG00000180537	ENST00000537663;ENST00000488300;ENST00000544682;ENST00000537388	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	5.51	5.51	0.81932	.	0.595355	0.16295	N	0.220713	T	0.01905	0.0060	N	0.08118	0	0.36120	D	0.845408	B	0.19200	0.034	B	0.17098	0.017	T	0.48692	-0.9013	9	.	.	.	-5.5304	15.6376	0.76966	0.0:0.0:0.0:1.0	.	235	Q8N6D2	RN182_HUMAN	A	235	ENSP00000443228:V235A;ENSP00000420465:V235A;ENSP00000442021:V235A;ENSP00000441271:V235A	.	V	+	2	0	RNF182	14086033	1.000000	0.71417	0.866000	0.34008	0.985000	0.73830	5.902000	0.69869	2.090000	0.63153	0.460000	0.39030	GTT		0.418	RNF182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039911.2	NM_152737		C	13978054	T	C	13978054	3	2	100	1	0	0	0	0	1	0	0	0	13503	1725	60	4	706	4	RNF182	6	13978054	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10		13978054	157137013	85	26739										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323830	29323830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggtgtggatcagtcacagtcGtcaagataattaatatattt	9	5	3	1	rs150457685		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:29323830G>A	ENST00000377154.1	-	4	442	c.143C>T	c.(142-144)aCg>aTg	p.T48M	OR5V1_ENST00000543825.1_Missense_Mutation_p.T48M			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGTCACAGTCGTCAAGATAAT	0.388													A|||	1	0.000199681	0	0	5008	,	,		18339	0		0.001	False		,,,				2504	0				Ovarian(32;43 883 21137 32120 42650)											0			6											138	140	139					6																	29323830		2203	4300	6503	29431809	SO:0001583	missense	81696				CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.143C>T	6.37:g.29323830G>A	ENSP00000366359:p.Thr48Met		29431809	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	A	8.253	0.809510	0.16537	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.03124	4.04;4.04	4.36	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01320	0.0043	L	0.33792	1.035	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.46386	-0.9195	9	0.66056	D	0.02	-18.7518	9.9169	0.41439	0.9169:0.0:0.0831:0.0	.	48	Q9UGF6	OR5V1_HUMAN	M	48	ENSP00000366359:T48M;ENSP00000443309:T48M	ENSP00000366356:T48M	T	-	2	0	OR5V1	29431809	0.000000	0.05858	0.001000	0.08648	0.078000	0.17371	0.425000	0.21346	0.814000	0.34374	-0.434000	0.05882	ACG		0.388	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			A	29323830	G	A	29323830	3	1	100	1	0	0	0	0	1	0	0	0	11215	1145	40	1	825	1	OR5V1	6	29323830	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	15345776	29323830	141791237	86	26740										
SENP6	26054	hgsc.bcm.edu	37	chr6	76373129	76373129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	attgtgatgacagtaaacacActtatttacagactaatgga	7	6	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:76373129A>G	ENST00000447266.2	+	9	1367	c.889A>G	c.(889-891)Act>Gct	p.T297A	SENP6_ENST00000370010.2_Missense_Mutation_p.T290A|SENP6_ENST00000327284.8_Missense_Mutation_p.T290A|SENP6_ENST00000370014.3_Missense_Mutation_p.T297A	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	297					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CAGTAAACACACTTATTTACA	0.333																																																0			6											107	101	103					6																	76373129		1823	4090	5913	76429849	SO:0001583	missense	26054				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.889A>G	6.37:g.76373129A>G	ENSP00000402527:p.Thr297Ala		76429849	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	8.946	0.967055	0.18659	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.42131	2.79;2.77;1.55;2.78;0.98;1.56	5.35	4.16	0.48862	.	0.494197	0.21704	N	0.070370	T	0.07279	0.0184	N	0.02011	-0.69	0.80722	D	1	B;B;B	0.16802	0.019;0.011;0.019	B;B;B	0.15484	0.013;0.006;0.013	T	0.08086	-1.0739	10	0.52906	T	0.07	-8.6407	7.2468	0.26127	0.6018:0.2577:0.0:0.1405	.	290;297;290	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	A	290;297;290;297;187;187	ENSP00000359027:T290A;ENSP00000359031:T297A;ENSP00000321820:T290A;ENSP00000402527:T297A;ENSP00000426480:T187A;ENSP00000391426:T187A	ENSP00000321820:T290A	T	+	1	0	SENP6	76429849	1.000000	0.71417	0.980000	0.43619	0.197000	0.23852	3.130000	0.50508	0.942000	0.37525	0.533000	0.62120	ACT		0.333	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76373129	A	G	76373129	3	3	100	1	0	0	0	0	1	0	0	0	14087	159	6	4	923	4	SENP6	6	76373129	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	47049299	76373129	94741938	87	26741										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87928403	87928403	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	actggggtgtggaaaaacccGgtactgtgcactattctttc	11	9	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:87928403G>A	ENST00000369577.3	+	4	535	c.492G>A	c.(490-492)ccG>ccA	p.P164P	ZNF292_ENST00000339907.4_Silent_p.P164P|ZNF292_ENST00000369578.2_3'UTR	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	164						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GGAAAAACCCGGTACTGTGCA	0.368																																																0			6											41	41	41					6																	87928403		1822	4077	5899	87985122	SO:0001819	synonymous_variant	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.492G>A	6.37:g.87928403G>A			87985122	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	37	CCDS47457.1																																																																																				0.368	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87928403	G	A	87928403	2	1	100	1	0	0	0	0	0	0	0	1	17865	1103	39	1		1	ZNF292	6	87928403	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	11555274	87928403	83186664	88	26742										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87971463	87971463	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tacattcaaatgatccagatAtgtctgttatgaaagatatc	6	6	2	4			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:87971463A>T	ENST00000369577.3	+	8	8159	c.8116A>T	c.(8116-8118)Atg>Ttg	p.M2706L	ZNF292_ENST00000339907.4_Missense_Mutation_p.M2701L	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2706						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TGATCCAGATATGTCTGTTAT	0.323																																																0			6											51	50	50					6																	87971463		1826	4078	5904	88028182	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.8116A>T	6.37:g.87971463A>T	ENSP00000358590:p.Met2706Leu		88028182	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	3.620	-0.077838	0.07184	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.05258	3.47;3.48	6.05	0.766	0.18476	.	0.719989	0.13400	N	0.390739	T	0.00496	0.0016	N	0.01352	-0.895	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.46345	-0.9198	10	0.18276	T	0.48	.	1.574	0.02621	0.4371:0.2081:0.2329:0.1218	.	2706	O60281	ZN292_HUMAN	L	2706;2701	ENSP00000358590:M2706L;ENSP00000342847:M2701L	ENSP00000342847:M2701L	M	+	1	0	ZNF292	88028182	0.000000	0.05858	0.953000	0.39169	0.953000	0.61014	-0.102000	0.10956	0.705000	0.31890	0.528000	0.53228	ATG		0.323	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		T	87971463	A	T	87971463	3	4	100	1	0	0	0	0	1	0	0	0	17865	449	16	5	8146	5	ZNF292	6	87971463	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	43060	87971463	83143604	89	26743										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93965716	93965716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agcagcaattcctctcagcaTtcctactaactgaatgactg	6	12	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:93965716T>C	ENST00000369303.4	-	13	2396	c.2212A>G	c.(2212-2214)Atg>Gtg	p.M738V		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	738	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CCTCTCAGCATTCCTACTAAC	0.403																																																0			6											135	130	132					6																	93965716		2203	4300	6503	94022437	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2212A>G	6.37:g.93965716T>C	ENSP00000358309:p.Met738Val		94022437	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569161	0.86439	.	.	ENSG00000135333	ENST00000369303	T	0.61040	0.14	5.75	5.75	0.90469	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	L	0.29908	0.895	0.80722	D	1	P;D;D	0.55385	0.825;0.964;0.971	P;P;P	0.51615	0.629;0.546;0.675	T	0.56153	-0.8026	10	0.72032	D	0.01	.	16.0455	0.80717	0.0:0.0:0.0:1.0	.	734;733;738	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	V	738	ENSP00000358309:M738V	ENSP00000358309:M738V	M	-	1	0	EPHA7	94022437	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.189000	0.69895	0.460000	0.39030	ATG		0.403	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			C	93965716	T	C	93965716	3	2	100	1	0	0	0	0	1	0	0	0	5185	1493	52	4	804	4	EPHA7	6	93965716	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	5994253	93965716	77149351	90	26744										
FRK	2444	hgsc.bcm.edu	37	chr6	116263658	116263658	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttccaacgcagtgtctcaaaTgtaggtcgttccttaggctc	9	11	1	0	rs148599364	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr6:116263658T>C	ENST00000606080.1	-	8	1883	c.1437A>G	c.(1435-1437)acA>acG	p.T479T	FRK_ENST00000538210.1_Silent_p.T337T	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	479	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	GTGTCTCAAATGTAGGTCGTT	0.398																																																0			6											145	138	140					6																	116263658		2203	4300	6503	116370351	SO:0001819	synonymous_variant	2444			U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.1437A>G	6.37:g.116263658T>C			116370351	B4DY49|Q13128|Q9NTR5	Silent	SNP	ENST00000606080.1	37	CCDS5103.1																																																																																				0.398	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		C	116263658	T	C	116263658	2	2	100	1	0	0	0	0	0	0	0	1	6067	1451	51	4		4	FRK	6	116263658	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	22297942	116263658	54851409	91	26745										
INTS1	26173	hgsc.bcm.edu	37	chr7	1522322	1522322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaaaccagatgtccagcagcGcctggaactcgctgtcgtcg	12	13	0	1	rs543463656		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:1522322G>A	ENST00000404767.3	-	27	3648	c.3563C>T	c.(3562-3564)gCg>gTg	p.A1188V	INTS1_ENST00000389470.4_Missense_Mutation_p.A1350V	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1188					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCCAGCAGCGCCTGGAACTC	0.647													g|||	1	0.000199681	0	0.0014	5008	,	,		17964	0		0	False		,,,				2504	0															0			7											52	62	58					7																	1522322		2080	4205	6285	1488848	SO:0001583	missense	26173			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.3563C>T	7.37:g.1522322G>A	ENSP00000385722:p.Ala1188Val		1488848	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	37	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	G	6.695	0.496840	0.12762	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.42900	0.96;0.99	4.67	2.71	0.32032	.	0.612906	0.12290	U	0.482041	T	0.28566	0.0707	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.17107	-1.0380	10	0.28530	T	0.3	.	12.4981	0.55940	0.0:0.0:0.6387:0.3613	.	1188	Q8N201	INT1_HUMAN	V	1188;1350	ENSP00000385722:A1188V;ENSP00000374121:A1350V	ENSP00000374121:A1350V	A	-	2	0	INTS1	1488848	0.133000	0.22466	0.003000	0.11579	0.282000	0.26991	2.532000	0.45659	0.310000	0.22990	-0.314000	0.08810	GCG		0.647	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1522322	G	A	1522322	3	1	100	1	0	0	0	0	1	0	0	0	7796	1087	38	1	3097	1	INTS1	7	1522322	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		1522322	157616341	92	26746										
SDK1	221935	hgsc.bcm.edu	37	chr7	4014071	4014071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggatcgtggtggagaaggacGggtcccttctcatcagccag	15	10	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:4014071G>A	ENST00000404826.2	+	13	2027	c.1888G>A	c.(1888-1890)Ggg>Agg	p.G630R	SDK1_ENST00000389531.3_Missense_Mutation_p.G630R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	630	Ig-like C2-type 6.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGAGAAGGACGGGTCCCTTCT	0.567																																																0			7											150	115	127					7																	4014071		2203	4300	6503	3980597	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1888G>A	7.37:g.4014071G>A	ENSP00000385899:p.Gly630Arg		3980597	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.770546	0.90108	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	D;D	0.82255	-1.59;-1.59	5.35	5.35	0.76521	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000002	D	0.93501	0.7926	M	0.92122	3.275	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	D	0.94812	0.7979	10	0.87932	D	0	.	19.0581	0.93074	0.0:0.0:1.0:0.0	.	630	Q7Z5N4	SDK1_HUMAN	R	630	ENSP00000385899:G630R;ENSP00000374182:G630R	ENSP00000374182:G630R	G	+	1	0	SDK1	3980597	1.000000	0.71417	0.996000	0.52242	0.759000	0.43091	7.159000	0.77483	2.484000	0.83849	0.563000	0.77884	GGG		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4014071	G	A	4014071	3	1	100	1	0	0	0	0	1	0	0	0	14005	1116	39	1	1938	1	SDK1	7	4014071	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	2491749	4014071	155124592	93	26747										
HOXA2	3199	hgsc.bcm.edu	37	chr7	27140404	27140404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtctgtaaaaaagtctaagcTgtcagctgaaatatctacgg	9	7	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:27140404T>C	ENST00000222718.5	-	2	1382	c.1072A>G	c.(1072-1074)Agc>Ggc	p.S358G	HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000593300.1_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	358					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S358G(1)		breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						AAGTCTAAGCTGTCAGCTGAA	0.428																																																1	Substitution - Missense(1)	ovary(1)	7											93	92	92					7																	27140404		2203	4300	6503	27106929	SO:0001583	missense	3199				CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.1072A>G	7.37:g.27140404T>C	ENSP00000222718:p.Ser358Gly		27106929	A1L4K3|B2RMW3	Missense_Mutation	SNP	ENST00000222718.5	37	CCDS5403.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904289	0.33628	.	.	ENSG00000105996	ENST00000222718	T	0.10099	2.91	5.66	5.66	0.87406	.	0.178481	0.64402	D	0.000014	T	0.16342	0.0393	M	0.66506	2.035	0.44079	D	0.996839	B	0.28439	0.212	B	0.30316	0.114	T	0.01476	-1.1345	10	0.39692	T	0.17	.	15.5758	0.76380	0.0:0.0:0.0:1.0	.	358	O43364	HXA2_HUMAN	G	358	ENSP00000222718:S358G	ENSP00000222718:S358G	S	-	1	0	HOXA2	27106929	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.912000	0.69948	2.153000	0.67306	0.533000	0.62120	AGC		0.428	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			C	27140404	T	C	27140404	3	2	100	1	0	0	0	0	1	0	0	0	7313	1580	55	4	62	4	HOXA2	7	27140404	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	23126333	27140404	131998259	94	26748										
EGFR	1956	hgsc.bcm.edu	37	chr7	55249096	55249096	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcatgcccttcggctgcctCctggactatgtccgggaaca	10	15	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:55249096C>T	ENST00000275493.2	+	20	2571	c.2394C>T	c.(2392-2394)ctC>ctT	p.L798L	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000454757.2_Silent_p.L745L|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.L753L	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	798	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCGGCTGCCTCCTGGACTATG	0.592		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											93	81	85					7																	55249096		2203	4300	6503	55216590	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2394C>T	7.37:g.55249096C>T			55216590	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.592	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55249096	C	T	55249096	2	4	100	1	0	0	0	0	0	0	0	1	4978	842	30	3		3	EGFR	7	55249096	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	28108692	55249096	103889567	95	26749										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963859	88963859	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	caagtctcaggtttaactgaAgaccaacaaaaattgatcca	6	9	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:88963859A>C	ENST00000333190.4	+	4	2172	c.1563A>C	c.(1561-1563)gaA>gaC	p.E521D		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	521							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GTTTAACTGAAGACCAACAAA	0.373										HNSCC(36;0.09)																																						0			7											42	44	43					7																	88963859		2200	4300	6500	88801795	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1563A>C	7.37:g.88963859A>C	ENSP00000329638:p.Glu521Asp		88801795	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415772	0.25552	.	.	ENSG00000182348	ENST00000333190	T	0.05199	3.48	5.49	5.49	0.81192	.	0.158609	0.44902	D	0.000407	T	0.05044	0.0135	N	0.22421	0.69	0.22330	N	0.9992	B	0.19817	0.039	B	0.14023	0.01	T	0.31420	-0.9944	10	0.41790	T	0.15	-13.1276	9.532	0.39200	0.922:0.0:0.078:0.0	.	521	A4D1E1	Z804B_HUMAN	D	521	ENSP00000329638:E521D	ENSP00000329638:E521D	E	+	3	2	ZNF804B	88801795	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	3.260000	0.51523	2.311000	0.77944	0.533000	0.62120	GAA		0.373	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88963859	A	C	88963859	3	2	100	1	0	0	0	0	1	0	0	0	18210	69	3	4	1577	4	ZNF804B	7	88963859	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	33714763	88963859	70174804	96	26750										
FLNC	2318	hgsc.bcm.edu	37	chr7	128477225	128477225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cctctccaggtctctgccccGactgggaggcctgggacccc	12	18	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr7:128477225G>A	ENST00000325888.8	+	3	874	c.613G>A	c.(613-615)Gac>Aac	p.D205N	FLNC_ENST00000346177.6_Missense_Mutation_p.D205N	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	205	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.D205Y(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCTCTGCCCCGACTGGGAGGC	0.667																																																1	Substitution - Missense(1)	breast(1)	7											12	15	14					7																	128477225		1988	4151	6139	128264461	SO:0001583	missense	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.613G>A	7.37:g.128477225G>A	ENSP00000327145:p.Asp205Asn		128264461	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434164	0.62955	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.95412	-3.7;-3.7	6.08	5.1	0.69264	Calponin homology domain (5);	0.105384	0.64402	D	0.000006	D	0.93858	0.8035	M	0.63428	1.95	0.48571	D	0.999675	B;B	0.19331	0.03;0.035	B;B	0.24269	0.004;0.052	D	0.91065	0.4888	10	0.72032	D	0.01	.	12.7077	0.57070	0.1052:0.0:0.8948:0.0	.	205;205	Q14315-2;Q14315	.;FLNC_HUMAN	N	205	ENSP00000327145:D205N;ENSP00000344002:D205N	ENSP00000327145:D205N	D	+	1	0	FLNC	128264461	1.000000	0.71417	0.979000	0.43373	0.583000	0.36354	6.743000	0.74848	2.894000	0.99253	0.655000	0.94253	GAC		0.667	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128477225	G	A	128477225	3	1	100	1	0	0	0	0	1	0	0	0	5954	1058	37	1	623	1	FLNC	7	128477225	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	39513366	128477225	30661438	97	26751										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10469327	10469327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccccgcgtcccctgcccaccCggcagagggagcgttgtgcg	14	18	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:10469327C>T	ENST00000382483.3	-	4	2504	c.2281G>A	c.(2281-2283)Ggg>Agg	p.G761R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	761					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCTGCCCACCCGGCAGAGGGA	0.647																																																0			8											45	52	50					8																	10469327		1965	4148	6113	10506737	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2281G>A	8.37:g.10469327C>T	ENSP00000371923:p.Gly761Arg		10506737	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	5.753	0.323356	0.10900	.	.	ENSG00000183638	ENST00000382483	T	0.03772	3.81	5.11	3.19	0.36642	.	0.465537	0.15977	N	0.235503	T	0.02888	0.0086	N	0.14661	0.345	0.09310	N	1	B	0.30709	0.291	B	0.24701	0.055	T	0.41998	-0.9477	10	0.52906	T	0.07	-12.5422	6.3253	0.21240	0.0:0.7137:0.1862:0.1	.	761	A6NKC6	.	R	761	ENSP00000371923:G761R	ENSP00000371923:G761R	G	-	1	0	RP1L1	10506737	0.007000	0.16637	0.017000	0.16124	0.011000	0.07611	1.395000	0.34520	1.139000	0.42245	0.462000	0.41574	GGG		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10469327	C	T	10469327	3	4	100	1	0	0	0	0	1	0	0	0	13570	652	23	1	4925	1	RP1L1	8	10469327	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10		10469327	135894695	98	26752										
DLC1	10395	hgsc.bcm.edu	37	chr8	12957788	12957788	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	atcaaccccagctttgagggCgctttgtgcttgctgtgatg	12	10	1	2	rs372344109		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:12957788C>T	ENST00000276297.4	-	9	2467	c.2058G>A	c.(2056-2058)gcG>gcA	p.A686A	DLC1_ENST00000512044.2_Silent_p.A283A|DLC1_ENST00000520226.1_Silent_p.A175A|DLC1_ENST00000358919.2_Silent_p.A249A	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	686					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCTTTGAGGGCGCTTTGTGCT	0.557																																																0			8						C	,,	1,4405	2.1+/-5.4	0,1,2202	99	93	95		525,747,2058	-5.9	0.2	8		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,	175/1018,249/1092,686/1529	12957788	2,13004	2203	4300	6503	13002159	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2058G>A	8.37:g.12957788C>T			13002159	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.557	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	12957788	C	T	12957788	2	4	100	1	0	0	0	0	0	0	0	1	4561	755	27	1		1	DLC1	8	12957788	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	2488461	12957788	133406234	99	26753										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59500199	59500199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgacatcatgttccagctcgGccagcaagtcaaagtggtgt	11	10	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:59500199G>A	ENST00000038176.3	-	27	2485	c.2273C>T	c.(2272-2274)gCc>gTc	p.A758V	NSMAF_ENST00000427130.2_Missense_Mutation_p.A789V	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	758					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TTCCAGCTCGGCCAGCAAGTC	0.453																																																0			8											102	88	93					8																	59500199		2203	4300	6503	59662753	SO:0001583	missense	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.2273C>T	8.37:g.59500199G>A	ENSP00000038176:p.Ala758Val		59662753	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	G	35	5.488942	0.96323	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.30448	1.53;1.53	5.97	5.97	0.96955	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.55737	0.1939	M	0.71581	2.175	0.58432	D	0.999997	D;P	0.67145	0.996;0.5	D;B	0.64321	0.924;0.11	T	0.49133	-0.8971	9	.	.	.	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	789;758	Q92636-2;Q92636	.;FAN_HUMAN	V	758;789	ENSP00000038176:A758V;ENSP00000411012:A789V	.	A	-	2	0	NSMAF	59662753	1.000000	0.71417	0.993000	0.49108	0.926000	0.56050	7.072000	0.76777	2.828000	0.97474	0.655000	0.94253	GCC		0.453	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		A	59500199	G	A	59500199	3	1	100	1	0	0	0	0	1	0	0	0	10705	1203	42	3	500	3	NSMAF	8	59500199	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	46542411	59500199	86863823	100	26754										
CLVS1	157807	hgsc.bcm.edu	37	chr8	62370922	62370922	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagctaatacaccctgaattTttgccctctgaatttggagg	8	10	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:62370922T>G	ENST00000519846.1	+	6	1270	c.798T>G	c.(796-798)ttT>ttG	p.F266L	CLVS1_ENST00000325897.4_Missense_Mutation_p.F266L|CLVS1_ENST00000518592.1_5'UTR			Q8IUQ0	CLVS1_HUMAN	clavesin 1	266	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						ACCCTGAATTTTTGCCCTCTG	0.408																																																0			8											128	121	123					8																	62370922		2203	4300	6503	62533476	SO:0001583	missense	0			AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"retinaldehyde binding protein 1-like 1"	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.798T>G	8.37:g.62370922T>G	ENSP00000428402:p.Phe266Leu		62533476	B2R7M5|C8UZT3|Q8NB32	Missense_Mutation	SNP	ENST00000519846.1	37	CCDS6176.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139401	0.56936	.	.	ENSG00000177182	ENST00000519846;ENST00000325897	T;T	0.74526	-0.85;-0.85	5.43	2.97	0.34412	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.199783	0.52532	D	0.000078	T	0.45175	0.1329	N	0.02802	-0.49	0.27951	N	0.937135	B	0.06786	0.001	B	0.12156	0.007	T	0.29912	-0.9996	10	0.24483	T	0.36	-12.882	6.4378	0.21833	0.0:0.2656:0.0:0.7344	.	266	Q8IUQ0	CLVS1_HUMAN	L	266	ENSP00000428402:F266L;ENSP00000325506:F266L	ENSP00000325506:F266L	F	+	3	2	CLVS1	62533476	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.310000	0.33551	1.028000	0.39785	0.528000	0.53228	TTT		0.408	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519		G	62370922	T	G	62370922	3	3	100	1	0	0	0	0	1	0	0	0	3577	1838	64	4	812	4	CLVS1	8	62370922	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	2870723	62370922	83993100	101	26755										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88298882	88298882	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgcactccttaaatggaaaaAatttcctccaggtcatggta	7	9	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:88298882A>G	ENST00000518476.1	+	8	1076	c.1025A>G	c.(1024-1026)aAa>aGa	p.K342R		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	342										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AAATGGAAAAAATTTCCTCCA	0.289																																																0			8											51	47	48					8																	88298882		1713	3793	5506	88367998	SO:0001583	missense	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1025A>G	8.37:g.88298882A>G	ENSP00000430073:p.Lys342Arg		88367998		Missense_Mutation	SNP	ENST00000518476.1	37	CCDS55259.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.883|8.883	0.952064|0.952064	0.18431|0.18431	.|.	.|.	ENSG00000176571|ENSG00000176571	ENST00000518476|ENST00000523299	D|.	0.92348|.	-3.02|.	5.49|5.49	1.62|1.62	0.23740|0.23740	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);|.	0.414174|.	0.20817|.	N|.	0.085132|.	T|T	0.34395|0.34395	0.0896|0.0896	L|L	0.47716|0.47716	1.5|1.5	0.20403|0.20403	N|N	0.999904|0.999904	P|.	0.44429|.	0.835|.	B|.	0.37091|.	0.241|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|5	0.22109|.	T|.	0.4|.	-9.8488|-9.8488	2.7241|2.7241	0.05209|0.05209	0.6168:0.1526:0.0837:0.1469|0.6168:0.1526:0.0837:0.1469	.|.	342|.	Q8NA66|.	CNBD1_HUMAN|.	R|D	342|34	ENSP00000430073:K342R|.	ENSP00000430073:K342R|.	K|N	+|+	2|1	0|0	CNBD1|CNBD1	88367998|88367998	0.893000|0.893000	0.30496|0.30496	0.915000|0.915000	0.36163|0.36163	0.994000|0.994000	0.84299|0.84299	0.570000|0.570000	0.23653|0.23653	0.412000|0.412000	0.25729|0.25729	0.533000|0.533000	0.62120|0.62120	AAA|AAT		0.289	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		G	88298882	A	G	88298882	3	3	100	1	0	0	0	0	1	0	0	0	3597	14	1	4	1055	4	CNBD1	8	88298882	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	25927960	88298882	58065140	102	26756										
POP1	10940	hgsc.bcm.edu	37	chr8	99142441	99142441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctatcgagccatgacgaaccGgtgcctcctgcaggtgagct	12	13	0	2	rs148502433		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:99142441G>A	ENST00000401707.2	+	5	803	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	POP1_ENST00000349693.3_Missense_Mutation_p.R241Q	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	241					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			ATGACGAACCGGTGCCTCCTG	0.498													G|||	1	0.000199681	0	0	5008	,	,		15993	0		0.001	False		,,,				2504	0															0			8						G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	75	74	74		722,722,722	-1.7	0	8	dbSNP_134	74	2,8596		0,2,4297	yes	missense,missense,missense	POP1	NM_001145860.1,NM_001145861.1,NM_015029.2	43,43,43	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign	241/1025,241/1025,241/1025	99142441	2,13002	2203	4299	6502	99211617	SO:0001583	missense	260434			D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.722G>A	8.37:g.99142441G>A	ENSP00000385787:p.Arg241Gln		99211617	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.70	1.424994	0.25639	0.0	2.33E-4	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.41758	0.99;0.99	5.91	-1.73	0.08081	Ribonuclease P/MRP, subunit POP1 (1);	0.441265	0.23766	N	0.044766	T	0.20170	0.0485	L	0.28400	0.85	0.09310	N	1	B	0.22851	0.076	B	0.22753	0.041	T	0.06917	-1.0800	9	.	.	.	-14.9496	0.3734	0.00383	0.3481:0.131:0.2675:0.2534	.	241	Q99575	POP1_HUMAN	Q	241	ENSP00000385787:R241Q;ENSP00000339529:R241Q	.	R	+	2	0	POP1	99211617	0.044000	0.20184	0.001000	0.08648	0.221000	0.24807	1.582000	0.36568	-0.185000	0.10550	-0.176000	0.13171	CGG		0.498	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99142441	G	A	99142441	3	1	100	1	0	0	0	0	1	0	0	0	12282	1116	39	1	736	1	POP1	8	99142441	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	10843559	99142441	47221581	103	26757										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100454775	100454775	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acacttgtcctctgtttgccTcaaataaagattattagtgc	6	9	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr8:100454775T>C	ENST00000358544.2	+	23	3468	c.3357T>C	c.(3355-3357)ccT>ccC	p.P1119P	VPS13B_ENST00000357162.2_Silent_p.P1119P|VPS13B_ENST00000395996.1_Silent_p.P1119P	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1119					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TCTGTTTGCCTCAAATAAAGA	0.438																																					Colon(161;2205 2542 7338 31318)											0			8											121	113	116					8																	100454775		2203	4300	6503	100523951	SO:0001819	synonymous_variant	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3357T>C	8.37:g.100454775T>C			100523951	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.438	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100454775	T	C	100454775	2	2	100	1	0	0	0	0	0	0	0	1	17230	1538	54	4		4	VPS13B	8	100454775	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	1312334	100454775	45909247	104	26758										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17464557	17464557	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gatagaggacttgaaatttcGacagaaagtaaatttggaaa	10	3	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:17464557G>C	ENST00000380647.3	+	21	3551	c.3467G>C	c.(3466-3468)cGa>cCa	p.R1156P	CNTLN_ENST00000262360.5_Missense_Mutation_p.R1156P|CNTLN_ENST00000425824.1_Missense_Mutation_p.R1156P			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1156					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		TTGAAATTTCGACAGAAAGTA	0.289																																																0			9											76	80	79					9																	17464557		1797	4038	5835	17454557	SO:0001583	missense	54875			AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.3467G>C	9.37:g.17464557G>C	ENSP00000370021:p.Arg1156Pro		17454557	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659690	0.47572	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.32272	1.46;1.46;1.71	5.26	5.26	0.73747	.	.	.	.	.	T	0.57242	0.2040	M	0.75264	2.295	0.40012	D	0.975306	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.979;0.979	T	0.54146	-0.8337	9	0.32370	T	0.25	.	19.2495	0.93917	0.0:0.0:1.0:0.0	.	1156;1156;1156	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	P	1156	ENSP00000370021:R1156P;ENSP00000392798:R1156P;ENSP00000262360:R1156P	ENSP00000262360:R1156P	R	+	2	0	CNTLN	17454557	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	5.454000	0.66651	2.626000	0.88956	0.585000	0.79938	CGA		0.289	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17464557	G	C	17464557	3	2	100	1	0	0	0	0	1	0	0	0	3645	1058	37	5	3579	5	CNTLN	9	17464557	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		17464557	123748874	105	26759										
CTSL1	1514	hgsc.bcm.edu	37	chr9	90342638	90342638	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcgatgcacaacagattataCggcatggttagtgaaacttc	10	8	0	2	rs546059099		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:90342638C>T	ENST00000343150.5	+	2	1010	c.120C>T	c.(118-120)taC>taT	p.Y40Y	CTSL_ENST00000342020.5_Silent_p.Y40Y|CTSL_ENST00000340342.6_Silent_p.Y40Y|CTSL_ENST00000495822.1_Intron			P07711	CATL1_HUMAN	cathepsin L	40					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										ACAGATTATACGGCATGGTTA	0.453																																																0			9											83	75	77					9																	90342638		2203	4300	6503	89532458	SO:0001819	synonymous_variant	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.120C>T	9.37:g.90342638C>T			89532458	Q6IAV1|Q96QJ0	Silent	SNP	ENST00000343150.5	37	CCDS6675.1																																																																																				0.453	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		T	90342638	C	T	90342638	2	4	100	1	0	0	0	0	0	0	0	1	4044	547	19	1		1	CTSL1	9	90342638	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	72878081	90342638	50870793	106	26760										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98221883	98221883	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccgataaaacgctacttactTctcagccttgtttcaggcat	6	12	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:98221883T>C	ENST00000331920.6	-	17	3185	c.2886A>G	c.(2884-2886)agA>agG	p.R962R	PTCH1_ENST00000375274.2_Splice_Site_p.R961R|PTCH1_ENST00000429896.2_Splice_Site_p.R811R|PTCH1_ENST00000421141.1_Splice_Site_p.R811R|PTCH1_ENST00000437951.1_Splice_Site_p.R896R|PTCH1_ENST00000418258.1_Splice_Site_p.R811R|PTCH1_ENST00000430669.2_Splice_Site_p.R896R	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	962					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GCTACTTACTTCTCAGCCTTG	0.567																																																0			9											129	111	117					9																	98221883		2203	4300	6503	97261704	SO:0001630	splice_region_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2887+1A>G	9.37:g.98221883T>C			97261704	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.567	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	Silent	C	98221883	T	C	98221883	5	2	100	1	0	0	0	0	0	0	1	0	12764	1797	62	4	1485	4	PTCH1	9	98221883	Splice_Site	SNP	T	TCGA-DC-6682-01A-11D-1826-10	7879245	98221883	42991548	107	26761										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	111956583	111956583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cttgggggacggcagcggcaCggagacttgtgtggcggccg	20	10	0	1	rs201636849		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:111956583C>T	ENST00000374566.3	-	21	2657	c.2140G>A	c.(2140-2142)Gtg>Atg	p.V714M	RNU6-984P_ENST00000363236.1_RNA	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	714					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGCAGCGGCACGGAGACTTGT	0.612																																																0			9											123	146	138					9																	111956583		2037	4189	6226	110996404	SO:0001583	missense	54566			AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.2140G>A	9.37:g.111956583C>T	ENSP00000363694:p.Val714Met		110996404	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	37	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	C	13.14	2.149441	0.37923	.	.	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.85171	-1.95	5.49	4.6	0.57074	.	1.002150	0.08049	N	0.996398	T	0.76884	0.4050	N	0.24115	0.695	0.26290	N	0.978136	B	0.27286	0.174	B	0.20955	0.032	T	0.65257	-0.6212	10	0.45353	T	0.12	.	10.291	0.43596	0.0:0.9092:0.0:0.0908	.	714	Q9H329	E41LB_HUMAN	M	399;714	ENSP00000363694:V714M	ENSP00000262536:V399M	V	-	1	0	EPB41L4B	110996404	0.011000	0.17503	0.002000	0.10522	0.182000	0.23217	2.673000	0.46858	1.328000	0.45358	0.655000	0.94253	GTG		0.612	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		T	111956583	C	T	111956583	3	4	100	1	0	0	0	0	1	0	0	0	5169	536	19	1	586	1	EPB41L4B	9	111956583	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	13734700	111956583	29256848	108	26762										
CEP110	11064	hgsc.bcm.edu	37	chr9	123924138	123924138	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtttctatcccttagaactAaagaatattctggacatgtt	6	7	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:123924138A>T	ENST00000373855.1	+	33	5354	c.5094A>T	c.(5092-5094)ctA>ctT	p.L1698L	CNTRL_ENST00000373850.1_Silent_p.L1146L|CNTRL_ENST00000238341.5_Silent_p.L1698L|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	1698					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CCTTAGAACTAAAGAATATTC	0.348																																																0			9											67	70	69					9																	123924138		2203	4300	6503	122963959	SO:0001819	synonymous_variant	11064			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5094A>T	9.37:g.123924138A>T			122963959	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																				0.348	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		T	123924138	A	T	123924138	2	4	100	1	0	0	0	0	0	0	0	1	3251	349	13	5		5	CEP110	9	123924138	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	11967555	123924138	17289293	109	26763										
ARPC5L	81873	hgsc.bcm.edu	37	chr9	127637257	127637257	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctctttttcgtctgcaggagCgagcccagggcgtggtgctg	15	11	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr9:127637257C>T	ENST00000353214.2	+	5	1478	c.226C>T	c.(226-228)Cga>Tga	p.R76*	ARPC5L_ENST00000465124.1_3'UTR|ARPC5L_ENST00000259477.6_Nonsense_Mutation_p.R76*			Q9BPX5	ARP5L_HUMAN	actin related protein 2/3 complex, subunit 5-like	76					regulation of actin filament polymerization (GO:0030833)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)				large_intestine(2)|lung(1)	3						TCTGCAGGAGCGAGCCCAGGG	0.542																																																0			9											106	102	103					9																	127637257		2203	4300	6503	126677078	SO:0001587	stop_gained	81873			AF087842	CCDS6859.1	9q34.11	2011-07-06			ENSG00000136950	ENSG00000136950		"Actin related protein 2/3 complex subunits"	23366	protein-coding gene	gene with protein product							Standard	NM_030978		Approved	MGC3038, ARC16-2	uc004bpa.4	Q9BPX5	OTTHUMG00000020660	ENST00000353214.2:c.226C>T	9.37:g.127637257C>T	ENSP00000345361:p.Arg76*		126677078	Q7Z523	Nonsense_Mutation	SNP	ENST00000353214.2	37	CCDS6859.1	.	.	.	.	.	.	.	.	.	.	C	44	11.272936	0.99539	.	.	ENSG00000136950	ENST00000353214;ENST00000259477	.	.	.	5.97	0.769	0.18492	.	0.075178	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.1215	6.7622	0.23546	0.1679:0.5652:0.207:0.0599	.	.	.	.	X	76	.	ENSP00000259477:R76X	R	+	1	2	ARPC5L	126677078	0.995000	0.38212	0.705000	0.30386	0.275000	0.26752	3.281000	0.51685	0.131000	0.18576	-2.292000	0.00266	CGA		0.542	ARPC5L-002	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054041.1	NM_030978		T	127637257	C	T	127637257	4	4	100	1	0	0	0	0	0	1	0	0	976	760	27	1	236	1	ARPC5L	9	127637257	Nonsense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3713119	127637257	13576174	110	26764										
PFKP	5214	hgsc.bcm.edu	37	chr10	3175426	3175426	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcagtgaaaactacaccaccGacttcatttaccagctgtat	6	12	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr10:3175426G>A	ENST00000381125.4	+	19	2018	c.1942G>A	c.(1942-1944)Gac>Aac	p.D648N	PFKP_ENST00000381072.1_Missense_Mutation_p.D66N|PFKP_ENST00000381075.2_Missense_Mutation_p.D640N	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	648	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		CTACACCACCGACTTCATTTA	0.527																																																0			10											167	162	164					10																	3175426		2203	4300	6503	3165426	SO:0001583	missense	5214			AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1942G>A	10.37:g.3175426G>A	ENSP00000370517:p.Asp648Asn		3165426	B3KS15|Q5VSR7|Q5VSR8	Missense_Mutation	SNP	ENST00000381125.4	37	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	g	35	5.431723	0.96150	.	.	ENSG00000067057	ENST00000381125;ENST00000397834;ENST00000381075;ENST00000381072	T;T;T	0.76448	-1.02;-1.02;-1.02	5.15	5.15	0.70609	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.86703	0.5996	M	0.62266	1.93	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.71870	0.975;0.975;0.975	D	0.88057	0.2791	10	0.87932	D	0	.	18.664	0.91481	0.0:0.0:1.0:0.0	.	640;640;648	B3KS15;Q5VSR7;Q01813	.;.;K6PP_HUMAN	N	648;637;640;66	ENSP00000370517:D648N;ENSP00000370465:D640N;ENSP00000370462:D66N	ENSP00000370462:D66N	D	+	1	0	PFKP	3165426	1.000000	0.71417	0.992000	0.48379	0.904000	0.53231	9.436000	0.97532	2.409000	0.81822	0.563000	0.77884	GAC		0.527	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		A	3175426	G	A	3175426	3	1	100	1	0	0	0	0	1	0	0	0	11797	1058	37	1	2016	1	PFKP	10	3175426	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		3175426	132359321	111	26765										
CUBN	8029	hgsc.bcm.edu	37	chr10	16990490	16990490	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttcttacccgacactgatgcGgtgaccgtggtgtggaaacc	12	11	1	2	rs182162293	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr10:16990490G>A	ENST00000377833.4	-	35	5261	c.5196C>T	c.(5194-5196)acC>acT	p.T1732T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1732	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACACTGATGCGGTGACCGTGG	0.522													A|||	5	0.000998403	0.0038	0	5008	,	,		19037	0		0	False		,,,				2504	0															0			10						A		5,4401	825.8+/-416.5	0,5,2198	80	68	72		5196	-11.1	0	10		72	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	CUBN	NM_001081.3		0,7,6496	AA,AG,GG		0.0233,0.1135,0.0538		1732/3624	16990490	7,12999	2203	4300	6503	17030496	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5196C>T	10.37:g.16990490G>A			17030496	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16990490	G	A	16990490	2	1	100	1	0	0	0	0	0	0	0	1	4057	1103	39	1		1	CUBN	10	16990490	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	13815064	16990490	118544257	112	26766										
MKX	283078	hgsc.bcm.edu	37	chr10	28030376	28030376	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agccactgcttgaggggtcgCgccatgtcttgcagggcctg	15	12	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr10:28030376C>T	ENST00000375790.5	-	3	678	c.246G>A	c.(244-246)gcG>gcA	p.A82A	MKX_ENST00000419761.1_Silent_p.A82A			Q8IYA7	MKX_HUMAN	mohawk homeobox	82					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						TGAGGGGTCGCGCCATGTCTT	0.642																																																0			10											130	92	105					10																	28030376		2203	4300	6503	28070382	SO:0001819	synonymous_variant	283078			BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"Homeoboxes / TALE class"	23729	protein-coding gene	gene with protein product		601332	"chromosome 10 open reading frame 48", "iroquois homeobox protein-like 1"	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.246G>A	10.37:g.28030376C>T			28070382	B3KWM5	Silent	SNP	ENST00000375790.5	37	CCDS7156.1																																																																																				0.642	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576		T	28030376	C	T	28030376	2	4	100	1	0	0	0	0	0	0	0	1	9640	755	27	1		1	MKX	10	28030376	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	11039886	28030376	107504371	113	26767										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63850716	63850716	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gacatgaagaaaaaaatagaAgggtatcaggaattttcagc	10	4	2	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr10:63850716A>G	ENST00000279873.7	+	10	1904	c.1494A>G	c.(1492-1494)gaA>gaG	p.E498E	ARID5B_ENST00000309334.5_Silent_p.E255E	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	498					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					AAAAAATAGAAGGGTATCAGG	0.468																																																0			10											78	80	79					10																	63850716		2203	4300	6503	63520722	SO:0001819	synonymous_variant	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1494A>G	10.37:g.63850716A>G			63520722	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																				0.468	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63850716	A	G	63850716	2	3	100	1	0	0	0	0	0	0	0	1	922	69	3	4		4	ARID5B	10	63850716	Silent	SNP	A	TCGA-DC-6682-01A-11D-1826-10	35820340	63850716	71684031	114	26768										
ADRB1	153	hgsc.bcm.edu	37	chr10	115804357	115804357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtgtgtcattgccctggacCgctacctcgccatcacctcg	9	16	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr10:115804357C>T	ENST00000369295.2	+	1	552	c.466C>T	c.(466-468)Cgc>Tgc	p.R156C		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	156					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	TGCCCTGGACCGCTACCTCGC	0.682																																																0			10											86	94	91					10																	115804357		2203	4300	6503	115794347	SO:0001583	missense	153			J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"GPCR / Class A : Adrenoceptors : beta"	285	protein-coding gene	gene with protein product		109630	"adrenergic, beta-1-, receptor"	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.466C>T	10.37:g.115804357C>T	ENSP00000358301:p.Arg156Cys		115794347	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Missense_Mutation	SNP	ENST00000369295.2	37	CCDS7586.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.262950	0.59431	.	.	ENSG00000043591	ENST00000369295	D	0.97186	-4.28	4.27	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	D	0.99202	0.9723	H	0.99863	4.86	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.98078	1.0402	10	0.87932	D	0	.	11.9543	0.52973	0.1737:0.8263:0.0:0.0	.	156	P08588	ADRB1_HUMAN	C	156	ENSP00000358301:R156C	ENSP00000358301:R156C	R	+	1	0	ADRB1	115794347	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	2.284000	0.43478	1.937000	0.56155	0.549000	0.68633	CGC		0.682	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1			T	115804357	C	T	115804357	3	4	100	1	0	0	0	0	1	0	0	0	340	652	23	1	468	1	ADRB1	10	115804357	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	51953641	115804357	19730390	115	26769										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643183	1643203	+	In_Frame_Del	DEL	GGAGCCACAGCCCCCACAGCC	GGAGCCACAGCCCCCACAGCC	-													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagatgggcacacagcagctGgagccacagcccccacagcc					rs545892989	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	GGAGCCACAGCCCCCACAGCC	GGAGCCACAGCCCCCACAGCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:1643183_1643203delGGAGCCACAGCCCCCACAGCC	ENST00000399682.1	-	1	165_185	c.121_141delGGCTGTGGGGGCTGTGGCTCC	c.(121-141)ggctgtgggggctgtggctccdel	p.GCGGCGS41del		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CACAGCAGCTGGagccacagcccccacagccggagccacag	0.697																																																0			11																																								1599779	SO:0001651	inframe_deletion	387267			AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.121_141delGGCTGTGGGGGCTGTGGCTCC	11.37:g.1643183_1643203delGGAGCCACAGCCCCCACAGCC	ENSP00000382590:p.Gly41_Ser47del		1599759		In_Frame_Del	DEL	ENST00000399682.1	37																																																																																					0.697	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		-	1643203	GGAGCCACAGCCCCCACAGCC	-	1643183	7	5	100	1	0	1	0	1	0	0	0	0	8585	1335	47	0	549	0	KRTAP5-4	11	1643183	In_Frame_Del	DEL	GGAGCCACAGCCCCCACAGCC	TCGA-DC-6682-01A-11D-1826-10		1643183	133363333	116	26770										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3383053	3383053	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcccagcactttgggaggctGaggcaggcagatcgcttgag	15	10	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:3383053G>A	ENST00000399602.4	-	4	419	c.293C>T	c.(292-294)tCa>tTa	p.S98L	ZNF195_ENST00000429541.2_Intron|ZNF195_ENST00000343338.7_Intron|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000438262.2_Intron|ZNF195_ENST00000354599.6_Intron|ZNF195_ENST00000005082.9_Missense_Mutation_p.S98L|ZNF195_ENST00000526601.1_Missense_Mutation_p.S102L	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	98	Spacer.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		ttgggaggctgaggcaggcag	0.483																																																0			11											148	137	141					11																	3383053		692	1591	2283	3339629	SO:0001583	missense	7748				CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.293C>T	11.37:g.3383053G>A	ENSP00000382511:p.Ser98Leu		3339629	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	.	.	.	.	.	.	.	.	.	.	g	8.719	0.914003	0.17907	.	.	ENSG00000005801	ENST00000399602;ENST00000005082;ENST00000526601;ENST00000533036;ENST00000534569	T;T;T;T;T	0.62105	4.55;4.55;4.55;0.05;4.55	0.225	0.225	0.15325	.	.	.	.	.	T	0.50854	0.1640	L	0.27975	0.815	0.25757	N	0.984995	P;B;B	0.37500	0.597;0.0;0.0	P;B;B	0.46110	0.504;0.0;0.0	T	0.43972	-0.9358	8	0.21540	T	0.41	.	.	.	.	.	102;98;98	O14628-6;O14628-5;O14628	.;.;ZN195_HUMAN	L	98;98;102;117;102	ENSP00000382511:S98L;ENSP00000005082:S98L;ENSP00000435828:S102L;ENSP00000433911:S117L;ENSP00000437265:S102L	ENSP00000005082:S98L	S	-	2	0	ZNF195	3339629	0.002000	0.14202	0.433000	0.26760	0.448000	0.32197	-0.203000	0.09438	0.300000	0.22699	0.305000	0.20034	TCA		0.483	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			A	3383053	G	A	3383053	3	1	100	1	0	0	0	0	1	0	0	0	17797	1294	45	3	1608	3	ZNF195	11	3383053	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1739870	3383053	131623463	117	26771										
OR5P2	120065	hgsc.bcm.edu	37	chr11	7818452	7818452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agcccaataggatgaaccccGtcagagcggtgtgattcccg	12	12	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:7818452G>A	ENST00000329434.2	-	1	68	c.38C>T	c.(37-39)aCg>aTg	p.T13M	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GATGAACCCCGTCAGAGCGGT	0.408																																																0			11											55	63	60					11																	7818452		2098	4292	6390	7775028	SO:0001583	missense	120065			AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"GPCR / Class A : Olfactory receptors"	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.38C>T	11.37:g.7818452G>A	ENSP00000331823:p.Thr13Met		7775028	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	G	8.471	0.857629	0.17178	.	.	ENSG00000183303	ENST00000329434	T	0.00502	6.95	5.5	3.62	0.41486	.	0.088468	0.49305	D	0.000142	T	0.01353	0.0044	M	0.75777	2.31	0.09310	N	1	D	0.71674	0.998	P	0.62885	0.908	T	0.33317	-0.9873	10	0.72032	D	0.01	-13.9801	10.7387	0.46141	0.0:0.1426:0.7091:0.1483	.	13	Q8WZ92	OR5P2_HUMAN	M	13	ENSP00000331823:T13M	ENSP00000331823:T13M	T	-	2	0	OR5P2	7775028	0.170000	0.23016	0.477000	0.27303	0.000000	0.00434	2.361000	0.44160	0.861000	0.35504	-0.314000	0.08810	ACG		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		A	7818452	G	A	7818452	3	1	100	1	0	0	0	0	1	0	0	0	11209	1145	40	1	934	1	OR5P2	11	7818452	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	4435399	7818452	127188064	118	26772										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48171647	48171647	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgataagttttgttttcttaGatctaagttaatcagagtgg	9	3	3	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:48171647G>T	ENST00000418331.2	+	18	3402		c.e18-1			NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGTTTTCTTAGATCTAAGTTA	0.338																																																0			11											92	96	95					11																	48171647		2201	4298	6499	48128223	SO:0001630	splice_region_variant	5795			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.3051-1G>T	11.37:g.48171647G>T			48128223	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Splice_Site	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.430207	0.43122	.	.	ENSG00000149177	ENST00000418331	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1524	0.72709	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRJ	48128223	1.000000	0.71417	0.995000	0.50966	0.271000	0.26615	3.169000	0.50809	2.650000	0.89964	0.561000	0.74099	.		0.338	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		Intron	T	48171647	G	T	48171647	5	4	100	1	0	0	0	0	0	0	1	0	12841	956	33	2	3129	2	PTPRJ	11	48171647	Splice_Site	SNP	G	TCGA-DC-6682-01A-11D-1826-10	40353195	48171647	86834869	119	26773										
MAP3K11	399909	hgsc.bcm.edu	37	chr11	65380783	65380783	+	5'Flank	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	actgatgtcctcatcggggtCctggcgagctgccttcacag	12	13	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:65380783C>T	ENST00000355703.3	+	0	0				MAP3K11_ENST00000309100.3_Missense_Mutation_p.D149N|MAP3K11_ENST00000530153.1_5'Flank	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)							integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCATCGGGGTCCTGGCGAGCT	0.637																																																0			11											48	49	49					11																	65380783		2201	4297	6498	65137359	SO:0001631	upstream_gene_variant	4296			BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539		11.37:g.65380783C>T	Exception_encountered		65137359	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.704284	0.88924	.	.	ENSG00000173327	ENST00000309100	D	0.93659	-3.26	4.09	3.16	0.36331	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.081152	0.47852	D	0.000207	D	0.90383	0.6990	N	0.11651	0.15	0.80722	D	1	P	0.50943	0.94	P	0.57548	0.823	D	0.90812	0.4702	10	0.87932	D	0	.	11.4476	0.50134	0.0:0.816:0.184:0.0	.	149	Q16584	M3K11_HUMAN	N	149	ENSP00000309597:D149N	ENSP00000309597:D149N	D	-	1	0	MAP3K11	65137359	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.578000	0.82498	0.914000	0.36822	0.563000	0.77884	GAC		0.637	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65380783	C	T	65380783	1	4	100	0	1	0	0	0	0	0	0	0	9275	855	30	3		3	MAP3K11	11	65380783	5'Flank	SNP	C	TCGA-DC-6682-01A-11D-1826-10	17209136	65380783	69625733	120	26774										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249587	71249587	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcaggctgtgggtcatcctgCtgccagtccagctgctgcaa	12	13	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:71249587C>A	ENST00000398534.3	+	1	517	c.486C>A	c.(484-486)tgC>tgA	p.C162*		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	162	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GGTCATCCTGCTGCCAGTCCA	0.597																																																0			11											138	147	144					11																	71249587		2200	4290	6490	70927235	SO:0001587	stop_gained	440021			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.486C>A	11.37:g.71249587C>A	ENSP00000420723:p.Cys162*		70927235	Q6L8G7|Q6UTX6	Nonsense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	12.56	1.974479	0.34848	.	.	ENSG00000241233	ENST00000398534	.	.	.	1.77	0.825	0.18824	.	.	.	.	.	.	.	.	.	.	.	0.30988	N	0.721761	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9625	0.09417	0.0:0.6045:0.0:0.3955	.	.	.	.	X	162	.	ENSP00000420723:C162X	C	+	3	2	KRTAP5-8	70927235	0.037000	0.19845	0.285000	0.24819	0.073000	0.16967	0.811000	0.27198	0.304000	0.22809	0.655000	0.94253	TGC		0.597	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		A	71249587	C	A	71249587	4	1	100	1	0	0	0	0	0	1	0	0	8589	805	28	2	488	2	KRTAP5-8	11	71249587	Nonsense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	5868804	71249587	63756929	121	26775										
IL18BP	10068	hgsc.bcm.edu	37	chr11	71712581	71712581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aggttgtccagcgtcacgtcGtcctggcccagctctgggtg	14	13	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:71712581G>A	ENST00000393703.4	+	5	1027	c.490G>A	c.(490-492)Gtc>Atc	p.V164I	IL18BP_ENST00000497194.2_Missense_Mutation_p.V164I|IL18BP_ENST00000531053.1_Missense_Mutation_p.V164I|IL18BP_ENST00000260049.5_Missense_Mutation_p.V164I|IL18BP_ENST00000393707.4_Intron|IL18BP_ENST00000404792.1_Missense_Mutation_p.V164I|IL18BP_ENST00000393705.4_Missense_Mutation_p.V164I|IL18BP_ENST00000337131.5_Missense_Mutation_p.V164I	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	164	Ig-like C2-type.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						GCGTCACGTCGTCCTGGCCCA	0.627																																																0			11											27	29	28					11																	71712581		2062	4202	6264	71390229	SO:0001583	missense	10068			AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5987	protein-coding gene	gene with protein product	"MC51L-53L-54L homolog gene product"	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.490G>A	11.37:g.71712581G>A	ENSP00000377306:p.Val164Ile		71390229	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	G	6.744	0.506085	0.12883	.	.	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049	T;T;T;T;T;T;T	0.36340	1.29;1.26;1.29;1.29;1.26;1.29;1.29	4.2	-5.13	0.02884	Immunoglobulin-like (1);	1.611470	0.03838	N	0.270179	T	0.21509	0.0518	L	0.42245	1.32	0.09310	N	1	B;B	0.21821	0.045;0.061	B;B	0.15052	0.012;0.011	T	0.16541	-1.0399	10	0.09084	T	0.74	-2.5139	1.6323	0.02734	0.3039:0.2538:0.3248:0.1174	.	164;164	G3V1C5;O95998	.;I18BP_HUMAN	I	164	ENSP00000377306:V164I;ENSP00000434717:V164I;ENSP00000377308:V164I;ENSP00000338723:V164I;ENSP00000434835:V164I;ENSP00000384212:V164I;ENSP00000260049:V164I	ENSP00000260049:V164I	V	+	1	0	IL18BP	71390229	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.772000	0.00779	-1.182000	0.02727	-2.630000	0.00154	GTC		0.627	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		A	71712581	G	A	71712581	3	1	100	1	0	0	0	0	1	0	0	0	7667	1145	40	1	504	1	IL18BP	11	71712581	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	462994	71712581	63293935	122	26776										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105732755	105732755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttttttccccaataggatacTcgatactccaagctattatg	5	10	0	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:105732755T>C	ENST00000530497.1	+	4	493	c.493T>C	c.(493-495)Tcg>Ccg	p.S165P	GRIA4_ENST00000428631.2_Missense_Mutation_p.S165P|GRIA4_ENST00000525187.1_Missense_Mutation_p.S165P|GRIA4_ENST00000393127.2_Missense_Mutation_p.S165P|GRIA4_ENST00000282499.5_Missense_Mutation_p.S165P|GRIA4_ENST00000393125.2_Missense_Mutation_p.S165P			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	165					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AATAGGATACTCGATACTCCA	0.368																																																0			11											85	85	85					11																	105732755		2202	4299	6501	105237965	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.493T>C	11.37:g.105732755T>C	ENSP00000435775:p.Ser165Pro		105237965	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185673	0.57909	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.31	5.31	0.75309	Extracellular ligand-binding receptor (1);	0.000000	0.56097	D	0.000039	D	0.87010	0.6071	L	0.59436	1.845	0.53005	D	0.999964	B;P;D;P	0.54964	0.268;0.909;0.969;0.924	B;P;P;P	0.56398	0.128;0.547;0.676;0.797	D	0.87417	0.2379	10	0.49607	T	0.09	.	15.2545	0.73573	0.0:0.0:0.0:1.0	.	165;165;195;165	P48058;G3V164;Q59GL7;Q86XE8	GRIA4_HUMAN;.;.;.	P	165	ENSP00000376833:S165P;ENSP00000282499:S165P;ENSP00000376835:S165P;ENSP00000415551:S165P;ENSP00000435775:S165P;ENSP00000432180:S165P	ENSP00000282499:S165P	S	+	1	0	GRIA4	105237965	1.000000	0.71417	0.966000	0.40874	0.749000	0.42624	4.840000	0.62817	2.004000	0.58718	0.455000	0.32223	TCG		0.368	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			C	105732755	T	C	105732755	3	2	100	1	0	0	0	0	1	0	0	0	6791	1551	54	4	507	4	GRIA4	11	105732755	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	34020174	105732755	29273761	123	26777										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117374606	117374606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctgatgtcggtgcctacgccGttgctggcctggcagaggta	15	11	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:117374606G>A	ENST00000321322.6	-	11	2494	c.2493C>T	c.(2491-2493)aaC>aaT	p.N831N	DSCAML1_ENST00000527706.1_Silent_p.N561N	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	771	Ig-like C2-type 9.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	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)		TGCCTACGCCGTTGCTGGCCT	0.617																																																0			11											107	79	89					11																	117374606		2201	4296	6497	116879816	SO:0001819	synonymous_variant	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2493C>T	11.37:g.117374606G>A			116879816	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.617	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117374606	G	A	117374606	2	1	100	1	0	0	0	0	0	0	0	1	4780	1136	40	1		1	DSCAML1	11	117374606	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	11641851	117374606	17631910	124	26778										
NLRX1	79671	hgsc.bcm.edu	37	chr11	119045975	119045975	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctctgcctctgctcttcaacCtgatcaaggtaacatcccga	6	15	5	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:119045975C>T	ENST00000409109.1	+	6	2250	c.1663C>T	c.(1663-1665)Ctg>Ttg	p.L555L	NLRX1_ENST00000409991.1_Silent_p.L555L|NLRX1_ENST00000409265.4_Silent_p.L555L|NLRX1_ENST00000525863.1_Silent_p.L555L|NLRX1_ENST00000292199.2_Silent_p.L555L	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	555	Required for interaction with MAVS.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GCTCTTCAACCTGATCAAGGT	0.632																																																0			11											91	95	94					11																	119045975		2200	4295	6495	118551185	SO:0001819	synonymous_variant	79671			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.1663C>T	11.37:g.119045975C>T			118551185	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Silent	SNP	ENST00000409109.1	37	CCDS8416.1																																																																																				0.632	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		T	119045975	C	T	119045975	2	4	100	1	0	0	0	0	0	0	0	1	10516	680	24	3		3	NLRX1	11	119045975	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	1671369	119045975	15960541	125	26779										
MFRP	83552	hgsc.bcm.edu	37	chr11	119215650	119215650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttccacactgctgtcagagaCgaagaccaccaggaggtggc	12	12	1	2	rs147276252		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:119215650C>T	ENST00000530681.1	-	6	850	c.706G>A	c.(706-708)Gtc>Atc	p.V236I	C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000360167.4_Missense_Mutation_p.V236I|MFRP_ENST00000529147.1_5'UTR|MFRP_ENST00000555262.1_Missense_Mutation_p.V236I|MFRP_ENST00000449574.2_Missense_Mutation_p.V236I	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	236	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		CTGTCAGAGACGAAGACCACC	0.607													C|||	1	0.000199681	0	0	5008	,	,		19452	0		0.001	False		,,,				2504	0															0			11						C	,ILE/VAL	0,4394		0,0,2197	37	27	30		,706	2.2	1	11	dbSNP_134	30	1,8585	1.2+/-3.3	0,1,4292	no	utr-5,missense	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,29	0,1,6489	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging	,236/580	119215650	1,12979	2197	4293	6490	118720860	SO:0001583	missense	83552			AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"membrane-type frizzled-related protein", "complement C1q tumor necrosis factor-related protein 5 precursor variant 1"	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.706G>A	11.37:g.119215650C>T	ENSP00000456533:p.Val236Ile		118720860	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Missense_Mutation	SNP	ENST00000530681.1	37	CCDS8421.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	20.7	4.042036	0.75732	0.0	1.16E-4	ENSG00000235718	ENST00000555262;ENST00000449574;ENST00000360167	T;T;T	0.28666	1.6;1.6;1.6	5.1	2.24	0.28232	CUB (5);	0.362582	0.28784	N	0.014157	T	0.39172	0.1068	L	0.43923	1.385	0.24387	N	0.994768	D;D	0.71674	0.998;0.986	P;P	0.60609	0.877;0.759	T	0.17776	-1.0358	10	0.37606	T	0.19	-15.8509	10.6378	0.45575	0.0:0.7933:0.0:0.2067	.	236;236	B4DHN8;Q9BY79	.;MFRP_HUMAN	I	236	ENSP00000450509:V236I;ENSP00000391664:V236I;ENSP00000353291:V236I	ENSP00000353291:V236I	V	-	1	0	MFRP	118720860	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.948000	0.40303	0.283000	0.22279	-0.219000	0.12488	GTC		0.607	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433		T	119215650	C	T	119215650	3	4	100	1	0	0	0	0	1	0	0	0	9556	536	19	1	1065	1	MFRP	11	119215650	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	169675	119215650	15790866	126	26780										
TECTA	7007	hgsc.bcm.edu	37	chr11	121033054	121033054	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccttcgggatccttagcacCgagtggattgagaaggagaa	13	8	0	2	rs377599437		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr11:121033054C>T	ENST00000392793.1	+	16	5518	c.5247C>T	c.(5245-5247)acC>acT	p.T1749T	TECTA_ENST00000264037.2_Silent_p.T1749T			O75443	TECTA_HUMAN	tectorin alpha	1749					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TCCTTAGCACCGAGTGGATTG	0.507																																																0			11						C		0,4406		0,0,2203	26	29	28		5247	-6.1	0.9	11		28	1,8587		0,1,4293	no	coding-synonymous	TECTA	NM_005422.2		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		1749/2156	121033054	1,12993	2203	4294	6497	120538264	SO:0001819	synonymous_variant	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5247C>T	11.37:g.121033054C>T			120538264		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																				0.507	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121033054	C	T	121033054	2	4	100	1	0	0	0	0	0	0	0	1	15786	639	23	1		1	TECTA	11	121033054	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	1817404	121033054	13973462	127	26781										
HEBP1	50865	hgsc.bcm.edu	37	chr12	13128389	13128389	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcttgtgctacgtagtctgcTtccttggcataaccaccaaa	8	12	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:13128389T>G	ENST00000014930.4	-	4	581	c.423A>C	c.(421-423)gaA>gaC	p.E141D	RP11-392P7.6_ENST00000543515.2_RNA|HEBP1_ENST00000540916.1_5'UTR|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000545914.1_RNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	141					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CGTAGTCTGCTTCCTTGGCAT	0.562																																																0			12											78	58	65					12																	13128389		2203	4300	6503	13019656	SO:0001583	missense	50865			AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.423A>C	12.37:g.13128389T>G	ENSP00000014930:p.Glu141Asp		13019656	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	37	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.204962	0.58234	.	.	ENSG00000013583	ENST00000014930	T	0.23552	1.9	4.64	2.26	0.28386	Regulatory factor, effector, bacterial (1);	0.047689	0.85682	D	0.000000	T	0.25269	0.0614	L	0.47716	1.5	0.80722	D	1	P	0.36354	0.549	P	0.47891	0.56	T	0.12993	-1.0526	10	0.02654	T	1	-16.7636	8.3275	0.32167	0.0:0.1675:0.0:0.8325	.	141	Q9NRV9	HEBP1_HUMAN	D	141	ENSP00000014930:E141D	ENSP00000014930:E141D	E	-	3	2	HEBP1	13019656	1.000000	0.71417	0.969000	0.41365	0.950000	0.60333	1.247000	0.32815	0.377000	0.24735	0.460000	0.39030	GAA		0.562	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			G	13128389	T	G	13128389	3	3	100	1	0	0	0	0	1	0	0	0	7057	1606	56	4	150	4	HEBP1	12	13128389	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10		13128389	120723506	128	26782										
PTHLH	5744	hgsc.bcm.edu	37	chr12	28116381	28116381	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	taaccaggcagagcgagttcGccgttttttcttttcctgct	9	11	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:28116381G>A	ENST00000545234.1	-	5	964	c.424C>T	c.(424-426)Cga>Tga	p.R142*	PTHLH_ENST00000395868.3_Nonsense_Mutation_p.R142*|PTHLH_ENST00000535992.1_Nonsense_Mutation_p.R142*|PTHLH_ENST00000201015.4_Nonsense_Mutation_p.R142*|PTHLH_ENST00000395872.1_Nonsense_Mutation_p.R142*|PTHLH_ENST00000538310.1_Nonsense_Mutation_p.R142*|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000354417.3_Nonsense_Mutation_p.R142*|PTHLH_ENST00000539239.1_Nonsense_Mutation_p.R142*			P12272	PTHR_HUMAN	parathyroid hormone-like hormone	142					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|endochondral ossification (GO:0001958)|endoderm development (GO:0007492)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|lung alveolus development (GO:0048286)|mammary gland bud elongation (GO:0060649)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|nipple sheath formation (GO:0060659)|osteoblast development (GO:0002076)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|protein processing (GO:0016485)|regulation of gene expression (GO:0010468)|skeletal system development (GO:0001501)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	10	Lung SC(9;0.184)					GAGCGAGTTCGCCGTTTTTTC	0.547																																																0			12											174	151	159					12																	28116381		2203	4300	6503	28007648	SO:0001587	stop_gained	5744				CCDS8715.1, CCDS44853.1	12p12.1-p11.2	2014-01-07			ENSG00000087494	ENSG00000087494		"Endogenous ligands"	9607	protein-coding gene	gene with protein product	"osteostatin", "parathyroid hormone-like hormone preproprotein", "parathyroid hormone-related protein preproprotein"	168470				2708388	Standard	NM_002820		Approved	PTHRP, HHM, PLP, PTHR	uc001ril.3	P12272	OTTHUMG00000169221	ENST00000545234.1:c.424C>T	12.37:g.28116381G>A	ENSP00000441765:p.Arg142*		28007648	Q15251|Q6FH74	Nonsense_Mutation	SNP	ENST00000545234.1	37	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	G	37	6.489895	0.97607	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963	.	.	.	5.63	1.32	0.21799	.	0.059542	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6815	14.4297	0.67240	0.0:0.0:0.4939:0.5061	.	.	.	.	X	142	.	ENSP00000201015:R142X	R	-	1	2	PTHLH	28007648	0.991000	0.36638	0.873000	0.34254	0.994000	0.84299	0.449000	0.21744	0.251000	0.21505	0.591000	0.81541	CGA		0.547	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	NM_198965		A	28116381	G	A	28116381	4	1	100	1	0	0	0	0	0	1	0	0	12796	1095	38	1	121	1	PTHLH	12	28116381	Nonsense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	14987992	28116381	105735514	129	26783										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39695439	39695439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aactgggtggtctggcaccaCtcccagggcacagacccaat	11	14	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:39695439C>T	ENST00000361418.5	-	37	4789	c.4774G>A	c.(4774-4776)Gtg>Atg	p.V1592M	KIF21A_ENST00000541463.2_Missense_Mutation_p.V1539M|KIF21A_ENST00000395670.3_Missense_Mutation_p.V1593M|KIF21A_ENST00000544797.2_Missense_Mutation_p.V1555M|KIF21A_ENST00000361961.3_Missense_Mutation_p.V1579M			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1592					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TCTGGCACCACTCCCAGGGCA	0.463																																																0			12											132	137	135					12																	39695439		2203	4300	6503	37981706	SO:0001583	missense	55605			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.4774G>A	12.37:g.39695439C>T	ENSP00000354878:p.Val1592Met		37981706	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431488	0.25813	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14	4.43	-1.12	0.09808	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.919587	0.09011	N	0.861562	T	0.45438	0.1342	L	0.55990	1.75	0.09310	N	1	B;B;B;B;B;B	0.20052	0.001;0.0;0.003;0.0;0.009;0.041	B;B;B;B;B;B	0.26202	0.005;0.004;0.038;0.002;0.013;0.067	T	0.42258	-0.9462	10	0.35671	T	0.21	.	0.4703	0.00530	0.2284:0.1986:0.3043:0.2688	.	1555;1539;1592;1579;1545;579	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3;F5H0V8	.;.;KI21A_HUMAN;.;.;.	M	1579;1593;1545;579;573;1555;1592;1539	ENSP00000354851:V1579M;ENSP00000379029:V1593M;ENSP00000448792:V573M;ENSP00000445606:V1555M;ENSP00000354878:V1592M;ENSP00000438075:V1539M	ENSP00000344501:V1545M	V	-	1	0	KIF21A	37981706	0.000000	0.05858	0.968000	0.41197	0.934000	0.57294	-0.177000	0.09796	-0.090000	0.12462	0.650000	0.86243	GTG		0.463	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		T	39695439	C	T	39695439	3	4	100	1	0	0	0	0	1	0	0	0	8309	565	20	3	258	3	KIF21A	12	39695439	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	11579058	39695439	94156456	130	26784										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244130	46244130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gaggaggacctccacagagtTctgttgttcagaatcatagt	11	8	3	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:46244130T>C	ENST00000334344.6	+	15	2396	c.2224T>C	c.(2224-2226)Tct>Cct	p.S742P	ARID2_ENST00000444670.1_Missense_Mutation_p.S352P|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Missense_Mutation_p.S593P	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	742					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCACAGAGTTCTGTTGTTCA	0.438			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0			12											87	87	87					12																	46244130		2203	4300	6503	44530397	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2224T>C	12.37:g.46244130T>C	ENSP00000335044:p.Ser742Pro		44530397	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.698247	0.30142	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.36520	1.25	5.97	4.83	0.62350	.	0.294458	0.39146	N	0.001459	T	0.20373	0.0490	N	0.19112	0.55	0.80722	D	1	B;B;B	0.13145	0.003;0.001;0.007	B;B;B	0.11329	0.006;0.004;0.004	T	0.07233	-1.0783	10	0.02654	T	1	-9.5181	11.7793	0.52003	0.0:0.0682:0.0:0.9318	.	742;352;742	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	P	742;593;352	ENSP00000335044:S742P	ENSP00000335044:S742P	S	+	1	0	ARID2	44530397	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.430000	0.52807	1.092000	0.41356	0.533000	0.62120	TCT		0.438	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		C	46244130	T	C	46244130	3	2	100	1	0	0	0	0	1	0	0	0	915	1783	62	4	2282	4	ARID2	12	46244130	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	6548691	46244130	87607765	131	26785										
MLL2	8085	hgsc.bcm.edu	37	chr12	49427582	49427582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctgcagcccatggccagggaGcagctgaccagggagcttgg	16	12	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:49427582G>A	ENST00000301067.7	-	39	10905	c.10906C>T	c.(10906-10908)Ctc>Ttc	p.L3636F	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3636	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TGGCCAGGGAGCAGCTGACCA	0.662																																																0			12											11	14	13					12																	49427582		2142	4255	6397	47713849	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10906C>T	12.37:g.49427582G>A	ENSP00000301067:p.Leu3636Phe		47713849	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	8.906	0.957598	0.18507	.	.	ENSG00000167548	ENST00000301067	T	0.80653	-1.4	5.34	4.44	0.53790	.	0.000000	0.33127	N	0.005244	T	0.65217	0.2670	N	0.08118	0	0.24499	N	0.994261	P	0.44627	0.839	B	0.41236	0.351	T	0.63198	-0.6691	10	0.87932	D	0	.	12.556	0.56254	0.0:0.0:0.698:0.302	.	3636	O14686	MLL2_HUMAN	F	3636	ENSP00000301067:L3636F	ENSP00000301067:L3636F	L	-	1	0	MLL2	47713849	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.128000	0.50492	1.380000	0.46344	0.563000	0.77884	CTC		0.662	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49427582	G	A	49427582	3	1	100	1	0	0	0	0	1	0	0	0	9651	971	34	3	5771	3	MLL2	12	49427582	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	3183452	49427582	84424313	132	26786										
KRT73	319101	hgsc.bcm.edu	37	chr12	53012172	53012172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cccccaggctgtaaaggctcCgactgctgaagcctccactg	10	16	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:53012172C>T	ENST00000305748.3	-	1	171	c.137G>A	c.(136-138)cGg>cAg	p.R46Q		NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	46	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.R46Q(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		GTAAAGGCTCCGACTGCTGAA	0.662																																																1	Substitution - Missense(1)	endometrium(1)	12											53	62	59					12																	53012172		2203	4299	6502	51298439	SO:0001583	missense	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.137G>A	12.37:g.53012172C>T	ENSP00000307014:p.Arg46Gln		51298439	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129233	0.37533	.	.	ENSG00000186049	ENST00000305748	T	0.75260	-0.92	4.64	2.8	0.32819	.	0.137789	0.33040	N	0.005355	T	0.74366	0.3707	M	0.84846	2.72	0.09310	N	1	B	0.12630	0.006	B	0.15052	0.012	T	0.67515	-0.5651	10	0.54805	T	0.06	.	10.0316	0.42103	0.0:0.7116:0.0:0.2884	.	46	Q86Y46	K2C73_HUMAN	Q	46	ENSP00000307014:R46Q	ENSP00000307014:R46Q	R	-	2	0	KRT73	51298439	0.000000	0.05858	0.998000	0.56505	0.994000	0.84299	-0.446000	0.06837	0.645000	0.30675	-0.126000	0.14955	CGG		0.662	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		T	53012172	C	T	53012172	3	4	100	1	0	0	0	0	1	0	0	0	8507	652	23	1	1521	1	KRT73	12	53012172	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3584590	53012172	80839723	133	26787										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59270243	59270243	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttaccactactgtcatgttgTggtaagaaaaatccagcacc	7	10	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:59270243T>C	ENST00000320743.3	-	16	2965	c.2679A>G	c.(2677-2679)ccA>ccG	p.P893P	LRIG3_ENST00000379141.4_Silent_p.P833P	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	893					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TGTCATGTTGTGGTAAGAAAA	0.423			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0			12											101	89	93					12																	59270243		2203	4300	6503	57556510	SO:0001819	synonymous_variant	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2679A>G	12.37:g.59270243T>C			57556510	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																				0.423	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		C	59270243	T	C	59270243	2	2	100	1	0	0	0	0	0	0	0	1	8975	1683	59	4		4	LRIG3	12	59270243	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	6258071	59270243	74581652	134	26788										
CRY1	1407	hgsc.bcm.edu	37	chr12	107395140	107395140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagaggataagccatctgtaTcaaaacctacaagaaagaaa	7	8	2	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:107395140T>C	ENST00000008527.5	-	5	1469	c.602A>G	c.(601-603)gAt>gGt	p.D201G		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	201					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						GCCATCTGTATCAAAACCTAC	0.343																																																0			12											86	89	88					12																	107395140		2203	4300	6503	105919270	SO:0001583	missense	1407			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.602A>G	12.37:g.107395140T>C	ENSP00000008527:p.Asp201Gly		105919270		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360076	0.61403	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.72	5.72	0.89469	DNA photolyase, N-terminal (1);	0.043473	0.85682	D	0.000000	T	0.70815	0.3267	M	0.85299	2.745	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.68078	-0.5504	9	0.34782	T	0.22	-24.6757	15.9922	0.80214	0.0:0.0:0.0:1.0	.	201	Q16526	CRY1_HUMAN	G	201	.	ENSP00000008527:D201G	D	-	2	0	CRY1	105919270	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	4.102000	0.57776	2.176000	0.68965	0.455000	0.32223	GAT		0.343	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		C	107395140	T	C	107395140	3	2	100	1	0	0	0	0	1	0	0	0	3909	1435	50	4	1190	4	CRY1	12	107395140	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	48124897	107395140	26456755	135	26789										
MLEC	9761	hgsc.bcm.edu	37	chr12	121132653	121132653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gatgtacgattgaatggccaCgtcgtggtgaaggacttgga	15	6	0	2	rs368412650	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr12:121132653C>T	ENST00000228506.3	+	3	869	c.441C>T	c.(439-441)caC>caT	p.H147H	RP11-173P15.3_ENST00000541383.1_RNA|MLEC_ENST00000412616.2_Intron	NM_014730.2	NP_055545.1	Q14165	MLEC_HUMAN	malectin	147					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	16						TGAATGGCCACGTCGTGGTGA	0.428													C|||	10	0.00199681	0	0	5008	,	,		23550	0.003		0	False		,,,				2504	0.0072															0			12						C		0,4406		0,0,2203	223	202	209		441	-7.7	0.3	12		209	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MLEC	NM_014730.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		147/293	121132653	1,13005	2203	4300	6503	119617036	SO:0001819	synonymous_variant	9761			BC000371	CCDS9206.1	12q24.31	2013-03-06	2008-11-05	2008-11-05	ENSG00000110917	ENSG00000110917			28973	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	613802	"KIAA0152"	KIAA0152		18524852	Standard	NM_014730		Approved		uc001tyy.1	Q14165	OTTHUMG00000169187	ENST00000228506.3:c.441C>T	12.37:g.121132653C>T			119617036		Silent	SNP	ENST00000228506.3	37	CCDS9206.1	.	.	.	.	.	.	.	.	.	.	C	8.019	0.759301	0.15846	0.0	1.16E-4	ENSG00000110917	ENST00000535656	.	.	.	5.5	-7.67	0.01272	.	.	.	.	.	T	0.72969	0.3527	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74937	-0.3494	4	.	.	.	.	22.1983	0.99968	0.0:0.7455:0.0:0.2545	.	.	.	.	C	44	.	.	R	+	1	0	MLEC	119617036	0.007000	0.16637	0.343000	0.25615	0.996000	0.88848	-1.053000	0.03500	-1.442000	0.01955	-0.238000	0.12139	CGT		0.428	MLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402781.2	NM_014730		T	121132653	C	T	121132653	2	4	100	1	0	0	0	0	0	0	0	1	9643	535	19	1		1	MLEC	12	121132653	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	13737513	121132653	12719242	136	26790										
RXFP2	122042	hgsc.bcm.edu	37	chr13	32367190	32367190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttatgaccaaacagaagataTtggaagcaaagggtattctc	9	6	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr13:32367190T>C	ENST00000298386.2	+	16	1822	c.1751T>C	c.(1750-1752)aTt>aCt	p.I584T	RXFP2_ENST00000380314.1_Missense_Mutation_p.I560T	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	584					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		ACAGAAGATATTGGAAGCAAA	0.289																																																0			13											37	42	40					13																	32367190		2200	4299	6499	31265190	SO:0001583	missense	122042			AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1751T>C	13.37:g.32367190T>C	ENSP00000298386:p.Ile584Thr		31265190	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	T	0.314	-0.966210	0.02232	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.36157	1.27;1.27	5.73	-4.76	0.03229	GPCR, rhodopsin-like superfamily (1);	0.690463	0.15450	N	0.261736	T	0.13457	0.0326	N	0.03000	-0.44	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.21381	-1.0247	10	0.19147	T	0.46	.	14.1667	0.65480	0.0:0.5746:0.0:0.4254	.	560;584	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	T	560;584	ENSP00000369670:I560T;ENSP00000298386:I584T	ENSP00000298386:I584T	I	+	2	0	RXFP2	31265190	0.000000	0.05858	0.260000	0.24451	0.290000	0.27261	0.032000	0.13732	-1.115000	0.02973	-0.290000	0.09829	ATT		0.289	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		C	32367190	T	C	32367190	3	2	100	1	0	0	0	0	1	0	0	0	13797	1493	52	4	1813	4	RXFP2	13	32367190	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10		32367190	82802688	137	26791										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46549583	46549583	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcgttcccgttctcgctctCgctctctctcccgttctcgc	6	20	5	0	rs565588902	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr13:46549583C>A	ENST00000242848.4	-	12	2651	c.2303G>T	c.(2302-2304)cGa>cTa	p.R768L	ZC3H13_ENST00000282007.3_Missense_Mutation_p.R768L			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	768	Arg/Glu-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		ttctcgctctcgctctctctc	0.527																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											0			13											292	224	247					13																	46549583		2203	4299	6502	45447584	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.2303G>T	13.37:g.46549583C>A	ENSP00000242848:p.Arg768Leu		45447584	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	C	14.36	2.512985	0.44660	.	.	ENSG00000123200	ENST00000242848;ENST00000282007	T;T	0.39997	2.04;1.05	5.0	5.0	0.66597	.	0.000000	0.46145	D	0.000317	T	0.65439	0.2691	.	.	.	0.80722	D	1	D;D	0.67145	0.993;0.996	D;D	0.79108	0.982;0.992	T	0.66015	-0.6028	9	0.44086	T	0.13	.	18.2552	0.90017	0.0:1.0:0.0:0.0	.	768;768	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	L	768	ENSP00000242848:R768L;ENSP00000282007:R768L	ENSP00000242848:R768L	R	-	2	0	ZC3H13	45447584	0.400000	0.25295	0.726000	0.30738	0.979000	0.70002	6.177000	0.71961	2.483000	0.83821	0.563000	0.77884	CGA		0.527	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46549583	C	A	46549583	3	1	100	1	0	0	0	0	1	0	0	0	17604	884	31	2	2415	2	ZC3H13	13	46549583	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	14182393	46549583	68620295	138	26792										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26941584	26941584	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aggacttggtggtagttgggGaagatggcaatgtctgggaa	18	3	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr14:26941584G>T	ENST00000344429.5	-	4	464	c.461C>A	c.(460-462)tCc>tAc	p.S154Y	NOVA1_ENST00000465357.2_Intron|NOVA1_ENST00000547619.1_Missense_Mutation_p.S154Y|NOVA1_ENST00000267422.7_Missense_Mutation_p.S32Y|NOVA1_ENST00000539517.2_Missense_Mutation_p.S154Y	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	157					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GGTAGTTGGGGAAGATGGCAA	0.388																																																0			14											223	187	199					14																	26941584		2203	4300	6503	26011424	SO:0001583	missense	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.461C>A	14.37:g.26941584G>T	ENSP00000342387:p.Ser154Tyr		26011424	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	37	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781608	0.31502	.	.	ENSG00000139910	ENST00000539517;ENST00000267422;ENST00000449198;ENST00000549146;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T;T	0.48522	1.4;1.39;1.42;0.81;0.85;0.87;0.83	5.98	5.09	0.68999	.	0.220831	0.32028	N	0.006700	T	0.46073	0.1374	N	0.08118	0	0.42349	D	0.992364	P;P;D	0.56035	0.514;0.88;0.974	B;P;D	0.66979	0.354;0.608;0.948	T	0.55179	-0.8181	10	0.62326	D	0.03	-9.3152	11.0314	0.47774	0.1402:0.0:0.8598:0.0	.	154;157;154	P51513-2;P51513;P51513-4	.;NOVA1_HUMAN;.	Y	154;32;113;32;117;154;154	ENSP00000438875:S154Y;ENSP00000267422:S32Y;ENSP00000408914:S113Y;ENSP00000449113:S32Y;ENSP00000449185:S117Y;ENSP00000342387:S154Y;ENSP00000448157:S154Y	ENSP00000267422:S32Y	S	-	2	0	NOVA1	26011424	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.757000	0.62213	1.539000	0.49286	0.650000	0.86243	TCC		0.388	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		T	26941584	G	T	26941584	3	4	100	1	0	0	0	0	1	0	0	0	10585	1174	41	2	1101	2	NOVA1	14	26941584	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		26941584	80407956	139	26793										
FAM71D	161142	hgsc.bcm.edu	37	chr14	67669810	67669810	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tttcctgttttctgcactcaGgtcaacagaagaggtgaatc	9	9	3	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr14:67669810G>A	ENST00000556046.1	+	5	700		c.e5-1					Q8N9W8	FA71D_HUMAN	family with sequence similarity 71, member D							cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)	13		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		TCTGCACTCAGGTCAACAGAA	0.463																																																0			14											90	78	82					14																	67669810		2203	4300	6503	66739563	SO:0001630	splice_region_variant	161142				CCDS9778.1	14q23.3	2007-11-20	2007-11-20	2007-11-20		ENSG00000172717			20101	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 54"	C14orf54			Standard	NM_173526		Approved		uc001xja.2	Q8N9W8		ENST00000556046.1:c.259-1G>A	14.37:g.67669810G>A			66739563	Q86VN4	Splice_Site	SNP	ENST00000556046.1	37		.	.	.	.	.	.	.	.	.	.	G	19.59	3.856099	0.71834	.	.	ENSG00000172717	ENST00000524532;ENST00000530728	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9156	0.79512	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM71D	66739563	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	5.656000	0.67988	2.485000	0.83878	0.643000	0.83706	.		0.463	FAM71D-009	KNOWN	not_organism_supported|basic|appris_candidate	nonsense_mediated_decay	protein_coding	OTTHUMT00000412390.1	NM_173526	Intron	A	67669810	G	A	67669810	5	1	100	1	0	0	0	0	0	0	1	0	5629	1014	35	3	165	3	FAM71D	14	67669810	Splice_Site	SNP	G	TCGA-DC-6682-01A-11D-1826-10	40728226	67669810	39679730	140	26794										
SLC24A4	123041	hgsc.bcm.edu	37	chr14	92949084	92949084	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cctcatcttcctcctgtgcgTcaccattcccaactgcagca	5	18	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr14:92949084T>C	ENST00000532405.1	+	13	1542	c.1316T>C	c.(1315-1317)gTc>gCc	p.V439A	SLC24A4_ENST00000531433.1_Missense_Mutation_p.V420A|SLC24A4_ENST00000393265.2_Missense_Mutation_p.V375A|SLC24A4_ENST00000298877.1_Missense_Mutation_p.V422A|SLC24A4_ENST00000351924.5_Missense_Mutation_p.V403A			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	439					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.V422D(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		CTCCTGTGCGTCACCATTCCC	0.587																																					NSCLC(10;315 435 10383 28450 38798)											1	Substitution - Missense(1)	ovary(1)	14											129	108	115					14																	92949084		2203	4300	6503	92018837	SO:0001583	missense	123041			AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"Solute carriers"	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1316T>C	14.37:g.92949084T>C	ENSP00000431840:p.Val439Ala		92018837	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Missense_Mutation	SNP	ENST00000532405.1	37	CCDS9903.2	.	.	.	.	.	.	.	.	.	.	T	14.63	2.591704	0.46214	.	.	ENSG00000140090	ENST00000393265;ENST00000531433;ENST00000532405;ENST00000298877;ENST00000351924;ENST00000318079	T;T;T;T;T	0.67865	-0.28;0.13;0.14;-0.28;-0.29	5.74	4.59	0.56863	.	0.363088	0.33732	N	0.004619	T	0.53690	0.1812	L	0.41710	1.295	0.25217	N	0.989932	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.16722	0.016;0.016;0.004	T	0.44513	-0.9323	10	0.35671	T	0.21	.	6.7164	0.23306	0.0:0.1383:0.1302:0.7315	.	420;375;439	Q8NFF2-3;Q8NFF2-2;Q8NFF2	.;.;NCKX4_HUMAN	A	375;420;439;422;403;291	ENSP00000376948:V375A;ENSP00000433302:V420A;ENSP00000431840:V439A;ENSP00000298877:V422A;ENSP00000337789:V403A	ENSP00000298877:V422A	V	+	2	0	SLC24A4	92018837	0.999000	0.42202	0.793000	0.32043	0.910000	0.53928	4.003000	0.57061	1.002000	0.39104	0.459000	0.35465	GTC		0.587	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646		C	92949084	T	C	92949084	3	2	100	1	0	0	0	0	1	0	0	0	14505	1667	58	4	1315	4	SLC24A4	14	92949084	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	25279274	92949084	14400456	141	26795										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102476614	102476614	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tttttttcttcttttctagaCtatgcgatgagcagctctct	6	9	4	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr14:102476614C>G	ENST00000360184.4	+	31	6387	c.6223C>G	c.(6223-6225)Cta>Gta	p.L2075V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2075	AAA 1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CTTTTCTAGACTATGCGATGA	0.403																																																0			14											61	65	63					14																	102476614		2203	4300	6503	101546367	SO:0001630	splice_region_variant	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.6222-1C>G	14.37:g.102476614C>G			101546367	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.881227	0.51801	.	.	ENSG00000197102	ENST00000360184	T	0.14766	2.48	5.61	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.46908	0.1417	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53995	-0.8359	10	0.87932	D	0	.	8.4994	0.33148	0.0:0.7103:0.0:0.2897	.	2075	Q14204	DYHC1_HUMAN	V	2075	ENSP00000348965:L2075V	ENSP00000348965:L2075V	L	+	1	2	DYNC1H1	101546367	0.998000	0.40836	0.150000	0.22450	0.727000	0.41649	2.193000	0.42658	0.756000	0.33013	0.650000	0.86243	CTA		0.403	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	Missense_Mutation	G	102476614	C	G	102476614	5	3	100	1	0	0	0	0	0	0	1	0	4852	579	20	5	6345	5	DYNC1H1	14	102476614	Splice_Site	SNP	C	TCGA-DC-6682-01A-11D-1826-10	9527530	102476614	4872926	142	26796										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27182372	27182372	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gtcgtttacgtctggaccaaCggctccaccaagtcggtggt	12	12	1	0	rs200310381		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:27182372C>T	ENST00000335625.5	+	8	1509	c.621C>T	c.(619-621)aaC>aaT	p.N207N	GABRA5_ENST00000355395.5_Silent_p.N207N|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000400081.3_Silent_p.N207N	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	207					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	TCTGGACCAACGGCTCCACCA	0.532																																																0			15						C	,	1,4015		0,1,2007	120	121	121		621,621	-8.9	0.3	15		121	1,8359		0,1,4179	no	coding-synonymous,coding-synonymous	GABRA5	NM_000810.3,NM_001165037.1	,	0,2,6186	TT,TC,CC		0.012,0.0249,0.0162	,	207/463,207/463	27182372	2,12374	2008	4180	6188	24765118	SO:0001819	synonymous_variant	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.621C>T	15.37:g.27182372C>T			24765118	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	37	CCDS45194.1																																																																																				0.532	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27182372	C	T	27182372	2	4	100	1	0	0	0	0	0	0	0	1	6183	535	19	1		1	GABRA5	15	27182372	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10		27182372	75349020	143	26797										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40581105	40581105	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctggcctcgtactctgccagCgcctccttctggaactgtgg	11	15	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:40581105C>T	ENST00000260402.3	-	32	3618	c.3369G>A	c.(3367-3369)gcG>gcA	p.A1123A	PLCB2_ENST00000557821.1_Silent_p.A1119A|PLCB2_ENST00000456256.2_Silent_p.A1108A	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	1123					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		ACTCTGCCAGCGCCTCCTTCT	0.647																																																0			15											46	51	49					15																	40581105		2014	4182	6196	38368397	SO:0001819	synonymous_variant	5330				CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.3369G>A	15.37:g.40581105C>T			38368397	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																				0.647	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			T	40581105	C	T	40581105	2	4	100	1	0	0	0	0	0	0	0	1	12059	755	27	1		1	PLCB2	15	40581105	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	13398733	40581105	61950287	144	26798										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40751724	40751724	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccccacacctcagctgtcgcCgctgccgatgcctggcaacc	9	20	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:40751724C>T	ENST00000416165.1	+	2	1132	c.1061C>T	c.(1060-1062)cCg>cTg	p.P354L	BAHD1_ENST00000560846.1_Missense_Mutation_p.P354L|BAHD1_ENST00000561234.1_Missense_Mutation_p.P354L	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	354	Pro-rich.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		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)		CAGCTGTCGCCGCTGCCGATG	0.647																																																0			15											57	59	58					15																	40751724		2203	4300	6503	38539016	SO:0001583	missense	22893			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.1061C>T	15.37:g.40751724C>T	ENSP00000396976:p.Pro354Leu		38539016	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	37	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.831755	0.32421	.	.	ENSG00000140320	ENST00000416165	T	0.61392	0.11	5.97	3.99	0.46301	.	0.200830	0.43579	N	0.000560	T	0.33702	0.0872	N	0.24115	0.695	0.49389	D	0.999781	B;B;B	0.26081	0.141;0.087;0.141	B;B;B	0.19391	0.025;0.011;0.025	T	0.13764	-1.0497	10	0.05721	T	0.95	-8.0927	6.7758	0.23619	0.1387:0.7069:0.0:0.1543	.	354;354;354	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	L	354	ENSP00000396976:P354L	ENSP00000396976:P354L	P	+	2	0	BAHD1	38539016	0.634000	0.27190	0.404000	0.26397	0.848000	0.48234	2.736000	0.47385	0.756000	0.33013	0.655000	0.94253	CCG		0.647	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		T	40751724	C	T	40751724	3	4	100	1	0	0	0	0	1	0	0	0	1298	652	23	1	1063	1	BAHD1	15	40751724	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	170619	40751724	61779668	145	26799										
LTK	4058	hgsc.bcm.edu	37	chr15	41797016	41797016	+	Frame_Shift_Del	DEL	G	G	-													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgccctccaggaaggcctctGggggcatccacttgactggg							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:41797016delG	ENST00000263800.6	-	17	2171	c.2075delC	c.(2074-2076)ccafs	p.P692fs	LTK_ENST00000561619.1_Frame_Shift_Del_p.P390fs|LTK_ENST00000453182.2_Frame_Shift_Del_p.P562fs|LTK_ENST00000355166.5_Frame_Shift_Del_p.P631fs	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	692	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		GAAGGCCTCTGGGGGCATCCA	0.587										TSP Lung(18;0.14)																																						0			15							,,	3,4261		1,1,2130	51	56	55		,,	-1.7	1	15		55	3,8251		1,1,4125	no	frameshift,frameshift,frameshift	LTK	NM_206961.3,NM_002344.5,NM_001135685.1	,,	2,2,6255	A1A1,A1R,RR		0.0363,0.0704,0.0479	,,	,,	41797016	6,12512	2203	4300	6503	39584308	SO:0001589	frameshift_variant	4058			D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2075delC	15.37:g.41797016delG	ENSP00000263800:p.Pro692fs		39584308	A6NNJ8|B4DL89|E9PFX4	Frame_Shift_Del	DEL	ENST00000263800.6	37	CCDS10077.1																																																																																				0.587	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			-	41797016	G	-	41797016	7	5	100	1	0	1	0	1	0	0	0	0	9109	1348	47	0	535	0	LTK	15	41797016	Frame_Shift_Del	DEL	G	TCGA-DC-6682-01A-11D-1826-10	1045292	41797016	60734376	146	26800										
VPS39	23339	hgsc.bcm.edu	37	chr15	42479475	42479475	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	taataagattttacccttatTaggtagtagtctctcttgaa	6	6	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:42479475T>G	ENST00000348544.4	-	8	560	c.561A>C	c.(559-561)ctA>ctC	p.L187L	VPS39_ENST00000318006.5_Silent_p.L176L			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	187	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		TTACCCTTATTAGGTAGTAGT	0.403																																																0			15											64	63	63					15																	42479475		2203	4299	6502	40266767	SO:0001819	synonymous_variant	23339			AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.561A>C	15.37:g.42479475T>G			40266767	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	37	CCDS10083.1																																																																																				0.403	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		G	42479475	T	G	42479475	2	3	100	1	0	0	0	0	0	0	0	1	17249	1741	61	4		4	VPS39	15	42479475	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	682459	42479475	60051917	147	26801										
CCNDBP1	23582	hgsc.bcm.edu	37	chr15	43482525	43482525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	actgatttctttccccagccCtgagaacaatgaccttattt	5	12	1	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:43482525C>T	ENST00000300213.4	+	6	673	c.431C>T	c.(430-432)cCt>cTt	p.P144L	CCNDBP1_ENST00000356633.5_5'UTR|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	144	Interaction with RPLP0.|Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-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;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		TTCCCCAGCCCTGAGAACAAT	0.463																																																0			15											86	81	83					15																	43482525		2203	4299	6502	41269817	SO:0001583	missense	23582			AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.431C>T	15.37:g.43482525C>T	ENSP00000300213:p.Pro144Leu		41269817	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	37	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.502808	0.44558	.	.	ENSG00000166946	ENST00000300213;ENST00000444658	T	0.39997	1.05	5.32	3.31	0.37934	.	0.688366	0.14692	N	0.304139	T	0.21509	0.0518	N	0.10916	0.065	0.35430	D	0.793936	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.10450	0.003;0.005;0.003	T	0.16928	-1.0386	10	0.27785	T	0.31	-4.2758	6.694	0.23189	0.0:0.7882:0.0:0.2118	.	144;144;16	O95273-2;O95273;O95273-4	.;CCDB1_HUMAN;.	L	144;16	ENSP00000300213:P144L	ENSP00000300213:P144L	P	+	2	0	CCNDBP1	41269817	0.034000	0.19679	0.550000	0.28217	0.987000	0.75469	0.969000	0.29370	1.471000	0.48121	0.655000	0.94253	CCT		0.463	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142		T	43482525	C	T	43482525	3	4	100	1	0	0	0	0	1	0	0	0	2925	681	24	3	453	3	CCNDBP1	15	43482525	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	1003050	43482525	59048867	148	26802										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52652178	52652178	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	actgtacctctgtccttgatGgaatgtcttccatttctgca	7	11	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:52652178G>T	ENST00000399231.3	-	25	3653	c.3410C>A	c.(3409-3411)cCa>cAa	p.P1137Q	MYO5A_ENST00000553916.1_Missense_Mutation_p.P1137Q|MYO5A_ENST00000358212.6_Missense_Mutation_p.P1137Q|MYO5A_ENST00000356338.6_Missense_Mutation_p.P1137Q|MYO5A_ENST00000399233.2_Missense_Mutation_p.P1137Q	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1137					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		TGTCCTTGATGGAATGTCTTC	0.428																																																0			15											84	80	81					15																	52652178		1946	4152	6098	50439470	SO:0001583	missense	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3410C>A	15.37:g.52652178G>T	ENSP00000382177:p.Pro1137Gln		50439470	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	G	7.036	0.561554	0.13498	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.78	4.87	0.63330	.	0.163360	0.56097	D	0.000026	T	0.08223	0.0205	N	0.08118	0	0.34789	D	0.735544	B;B	0.09022	0.0;0.002	B;B	0.10450	0.002;0.005	T	0.23797	-1.0178	10	0.12430	T	0.62	.	10.4938	0.44766	0.0688:0.0:0.7977:0.1334	.	1137;1137	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	Q	1137;671;1137;1137;1137;767;1137	ENSP00000382177:P1137Q;ENSP00000382179:P1137Q;ENSP00000348693:P1137Q;ENSP00000350945:P1137Q;ENSP00000451109:P1137Q	ENSP00000348693:P1137Q	P	-	2	0	MYO5A	50439470	0.994000	0.37717	0.168000	0.22838	0.168000	0.22595	2.450000	0.44943	1.451000	0.47736	-0.140000	0.14226	CCA		0.428	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		T	52652178	G	T	52652178	3	4	100	1	0	0	0	0	1	0	0	0	10108	1348	47	2	2225	2	MYO5A	15	52652178	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	9169653	52652178	49879214	149	26803										
SEMA4B	10519	hgsc.bcm.edu	37	chr15	90771850	90771850	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gccccgggtccgccttggctCggagatccgtgactctgtgg	15	14	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr15:90771850C>T	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000332496.6_Missense_Mutation_p.S830L|SEMA4B_ENST00000411539.2_Missense_Mutation_p.S830L|SEMA4B_ENST00000379122.3_Intron	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)	p.C821fs*>1(1)		lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CGCCTTGGCTCGGAGATCCGT	0.622																																																1	Deletion - Frameshift(1)	breast(1)	15											34	40	38					15																	90771850		2142	4230	6372	88572854	SO:0001628	intergenic_variant	10509			U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"EF-hand domain containing"	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90771850C>T			88572854	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	37	CCDS10360.1	.	.	.	.	.	.	.	.	.	.	C	19.64	3.866063	0.71949	.	.	ENSG00000185033	ENST00000332496;ENST00000411539	T;T	0.29917	1.55;1.55	4.57	4.57	0.56435	.	0.300840	0.33023	N	0.005367	T	0.45895	0.1365	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.47661	-0.9100	10	0.87932	D	0	.	16.856	0.86006	0.0:1.0:0.0:0.0	.	830;825	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	L	830	ENSP00000332204:S830L;ENSP00000394720:S830L	ENSP00000332204:S830L	S	+	2	0	SEMA4B	88572854	1.000000	0.71417	0.968000	0.41197	0.251000	0.25915	6.964000	0.76061	2.522000	0.85027	0.561000	0.74099	TCG		0.622	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1			T	90771850	C	T	90771850	1	4	100	0	1	0	0	0	0	0	0	0	14069	893	31	1		1	SEMA4B	15	90771850	IGR	SNP	C	TCGA-DC-6682-01A-11D-1826-10	38119672	90771850	11759542	150	26804										
ABCC6	368	hgsc.bcm.edu	37	chr16	16263583	16263583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cacctactgcagggtcgtccGcccacaggctcagccagtag	11	16	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr16:16263583G>A	ENST00000205557.7	-	22	2944	c.2915C>T	c.(2914-2916)gCg>gTg	p.A972V		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	972	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AGGGTCGTCCGCCCACAGGCT	0.682																																																0			16											20	19	20					16																	16263583		2194	4298	6492	16171084	SO:0001583	missense	368			AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.2915C>T	16.37:g.16263583G>A	ENSP00000205557:p.Ala972Val		16171084	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910698	0.72983	.	.	ENSG00000091262	ENST00000205557	D	0.93019	-3.15	5.11	3.15	0.36227	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.297384	0.23626	U	0.046193	D	0.91345	0.7270	L	0.38838	1.175	0.80722	D	1	D	0.63880	0.993	P	0.51170	0.661	D	0.91051	0.4878	10	0.87932	D	0	.	10.8368	0.46692	0.1525:0.0:0.8475:0.0	.	972	O95255	MRP6_HUMAN	V	972	ENSP00000205557:A972V	ENSP00000205557:A972V	A	-	2	0	ABCC6	16171084	1.000000	0.71417	0.887000	0.34795	0.583000	0.36354	5.751000	0.68720	1.149000	0.42402	0.551000	0.68910	GCG		0.682	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			A	16263583	G	A	16263583	3	1	100	1	0	0	0	0	1	0	0	0	57	1087	38	1	1636	1	ABCC6	16	16263583	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		16263583	74091170	151	26805										
NUP93	9688	hgsc.bcm.edu	37	chr16	56866217	56866217	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggggatttagttgaaccaagTgtgttttgacgacgatggca	14	5	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr16:56866217T>C	ENST00000308159.5	+	12	1383	c.1262T>C	c.(1261-1263)gTg>gCg	p.V421A	NUP93_ENST00000569842.1_Missense_Mutation_p.V421A|NUP93_ENST00000564887.1_Missense_Mutation_p.V298A|NUP93_ENST00000542526.1_Missense_Mutation_p.V298A	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	421					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTGAACCAAGTGTGTTTTGAC	0.473																																					Colon(33;610 796 1305 1705 38917)											0			16											181	166	171					16																	56866217		2198	4300	6498	55423718	SO:0001583	missense	9688			D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1262T>C	16.37:g.56866217T>C	ENSP00000310668:p.Val421Ala		55423718	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	37	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	T	33	5.283572	0.95489	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.47528	0.84;0.84	6.03	6.03	0.97812	.	0.052556	0.85682	D	0.000000	T	0.64724	0.2624	M	0.74881	2.28	0.80722	D	1	D	0.60160	0.987	P	0.61003	0.882	T	0.61461	-0.7058	10	0.20046	T	0.44	-20.3252	16.5582	0.84512	0.0:0.0:0.0:1.0	.	421	Q8N1F7	NUP93_HUMAN	A	421;298	ENSP00000310668:V421A;ENSP00000440235:V298A	ENSP00000310668:V421A	V	+	2	0	NUP93	55423718	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.895000	0.87343	2.308000	0.77769	0.533000	0.62120	GTG		0.473	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		C	56866217	T	C	56866217	3	2	100	1	0	0	0	0	1	0	0	0	10803	1696	59	4	1304	4	NUP93	16	56866217	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	40602634	56866217	33488536	152	26806										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67440242	67440242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccacccattccggcgggatCgctggccctgcagctcaggg	13	16	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr16:67440242C>T	ENST00000348579.2	-	3	454	c.113G>A	c.(112-114)cGa>cAa	p.R38Q		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	38					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		CCGGCGGGATCGCTGGCCCTG	0.627																																																0			16											36	28	31					16																	67440242		2190	4292	6482	65997743	SO:0001583	missense	29800			U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.113G>A	16.37:g.67440242C>T	ENSP00000340299:p.Arg38Gln		65997743	O15461	Missense_Mutation	SNP	ENST00000348579.2	37	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.769939	0.90020	.	.	ENSG00000159714	ENST00000348579	T	0.36699	1.24	5.25	4.23	0.50019	.	0.093431	0.46758	D	0.000276	T	0.45677	0.1354	L	0.49126	1.545	0.35383	D	0.790061	D	0.89917	1.0	D	0.66196	0.942	T	0.49862	-0.8894	10	0.24483	T	0.36	.	8.1309	0.31027	0.0:0.756:0.1605:0.0835	.	38	Q8WTX9	ZDHC1_HUMAN	Q	38	ENSP00000340299:R38Q	ENSP00000340299:R38Q	R	-	2	0	ZDHHC1	65997743	0.448000	0.25681	0.993000	0.49108	0.902000	0.53008	1.482000	0.35486	2.463000	0.83235	0.561000	0.74099	CGA		0.627	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		T	67440242	C	T	67440242	3	4	100	1	0	0	0	0	1	0	0	0	17639	884	31	1	1380	1	ZDHHC1	16	67440242	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	10574025	67440242	22914511	153	26807										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89357573	89357573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gctccttcttaatcctcttcCgctcagggccctgcttctct	6	17	4	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr16:89357573C>T	ENST00000301030.4	-	5	705	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	ANKRD11_ENST00000378330.2_Missense_Mutation_p.R82Q	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	82					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		AATCCTCTTCCGCTCAGGGCC	0.607																																																0			16											46	52	50					16																	89357573		2198	4300	6498	87885074	SO:0001583	missense	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.245G>A	16.37:g.89357573C>T	ENSP00000301030:p.Arg82Gln		87885074	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	36	5.699436	0.96802	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000378332	T;T	0.48836	0.8;0.8	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.63082	0.2481	L	0.40543	1.245	0.80722	D	1	D;D;D	0.76494	0.999;0.992;0.998	D;P;D	0.74674	0.984;0.644;0.96	T	0.63756	-0.6565	10	0.72032	D	0.01	.	19.9197	0.97082	0.0:1.0:0.0:0.0	.	82;96;82	A8K4M9;Q59GC3;Q6UB99	.;.;ANR11_HUMAN	Q	82;82;96	ENSP00000301030:R82Q;ENSP00000367581:R82Q	ENSP00000301030:R82Q	R	-	2	0	ANKRD11	87885074	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.949000	0.70257	2.702000	0.92279	0.655000	0.94253	CGG		0.607	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89357573	C	T	89357573	3	4	100	1	0	0	0	0	1	0	0	0	639	652	23	1	7782	1	ANKRD11	16	89357573	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	21917331	89357573	997180	154	26808										
TUBB3	10381	hgsc.bcm.edu	37	chr16	90001587	90001587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	caccacctccttgcgcttccCgggccagctcaacgctgacc	8	20	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr16:90001587C>T	ENST00000315491.7	+	4	851	c.728C>T	c.(727-729)cCg>cTg	p.P243L	TUBB3_ENST00000554444.1_Missense_Mutation_p.P171L|TUBB3_ENST00000304984.5_Missense_Mutation_p.P171L|TUBB3_ENST00000556922.1_Missense_Mutation_p.P590L|TUBB3_ENST00000555576.1_Intron	NM_006086.3	NP_006077.2	Q13509	TBB3_HUMAN	tubulin, beta 3 class III	243					'de novo' posttranslational protein folding (GO:0051084)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.P243Q(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Ixabepilone(DB04845)	TTGCGCTTCCCGGGCCAGCTC	0.667																																																1	Substitution - Missense(1)	kidney(1)	16											58	52	54					16																	90001587		2198	4300	6498	88529088	SO:0001583	missense	10381			BC000748	CCDS10988.1, CCDS56012.1	16q24.3	2014-02-04	2011-10-10		ENSG00000198211	ENSG00000198211		"Tubulins"	20772	protein-coding gene	gene with protein product	"class III beta-tubulin"	602661	"tubulin, beta 3", "fibrosis of extraocular muscles, congenital, 3"	FEOM3		9473684, 8098743, 20074521	Standard	NM_006086		Approved	beta-4, CFEOM3, CFEOM3A	uc002fph.2	Q13509	OTTHUMG00000138985	ENST00000315491.7:c.728C>T	16.37:g.90001587C>T	ENSP00000320295:p.Pro243Leu		88529088	A8K854|Q9BTZ0|Q9BW10	Missense_Mutation	SNP	ENST00000315491.7	37	CCDS10988.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.705872	0.30232	.	.	ENSG00000258947;ENSG00000258947;ENSG00000258947;ENSG00000198211;ENSG00000198211;ENSG00000198211	ENST00000556922;ENST00000555399;ENST00000304984;ENST00000555810;ENST00000554444;ENST00000315491	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	4.67	4.67	0.58626	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.56097	D	0.000025	D	0.90686	0.7078	H	0.96547	3.84	0.80722	D	1	P;D	0.89917	0.949;1.0	B;D	0.97110	0.203;1.0	D	0.93867	0.7159	9	.	.	.	.	17.5189	0.87782	0.0:1.0:0.0:0.0	.	243;243	Q13509;B2RBD5	TBB3_HUMAN;.	L	590;243;171;171;171;243	ENSP00000451560:P590L;ENSP00000302777:P171L;ENSP00000450538:P171L;ENSP00000451617:P171L;ENSP00000320295:P243L	.	P	+	2	0	RP11-566K11.2;TUBB3	88529088	1.000000	0.71417	0.935000	0.37517	0.431000	0.31685	5.855000	0.69510	2.316000	0.78162	0.407000	0.27541	CCG		0.667	TUBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272874.1	NM_006086		T	90001587	C	T	90001587	3	4	100	1	0	0	0	0	1	0	0	0	16797	652	23	1	742	1	TUBB3	16	90001587	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	644014	90001587	353166	155	26809										
ABR	29	hgsc.bcm.edu	37	chr17	1028683	1028683	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttcccctctccgtcgtactcGtccgtcccgtagctgaagtc	8	17	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:1028683G>A	ENST00000302538.5	-	2	227	c.81C>T	c.(79-81)gaC>gaT	p.D27D	ABR_ENST00000574437.1_De_novo_Start_OutOfFrame|ABR_ENST00000544583.2_De_novo_Start_OutOfFrame	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	27					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CGTCGTACTCGTCCGTCCCGT	0.627																																					Esophageal Squamous(197;2016 2115 4129 29033 46447)											0			17											107	99	102					17																	1028683		2203	4300	6503	975433	SO:0001819	synonymous_variant	29			L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.81C>T	17.37:g.1028683G>A			975433	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																				0.627	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			A	1028683	G	A	1028683	2	1	100	1	0	0	0	0	0	0	0	1	99	1136	40	1		1	ABR	17	1028683	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10		1028683	80166527	156	26810										
OR3A2	4995	hgsc.bcm.edu	37	chr17	3182182	3182182	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agaatgaactcagcaacagcGgtcctattggtcccagcttc	9	12	1	2	rs376118398		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:3182182G>A	ENST00000408891.2	-	1	86	c.48C>T	c.(46-48)acC>acT	p.T16T	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	16					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			ovary(1)	1						CAGCAACAGCGGTCCTATTGG	0.483																																					GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)											0			17						T		3,4393		0,3,2195	24	27	26		48	-8.2	0	17		26	0,8548		0,0,4274	no	coding-synonymous	OR3A2	NM_002551.3		0,3,6469	AA,AG,GG		0.0,0.0682,0.0232		16/322	3182182	3,12941	2198	4274	6472	3128932	SO:0001819	synonymous_variant	4995			U04713	CCDS42233.1	17p13.3	2012-08-09				ENSG00000221882		"GPCR / Class A : Olfactory receptors"	8283	protein-coding gene	gene with protein product						8921386, 10673334	Standard	NM_002551		Approved	OLFRA04, OR228, OR17-228	uc002fvg.3	P47893		ENST00000408891.2:c.48C>T	17.37:g.3182182G>A			3128932	Q6IFM3|Q9P1Q3	Silent	SNP	ENST00000408891.2	37	CCDS42233.1																																																																																				0.483	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1			A	3182182	G	A	3182182	2	1	100	1	0	0	0	0	0	0	0	1	11069	1103	39	1		1	OR3A2	17	3182182	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	2153499	3182182	78013028	157	26811										
TP53	7157	hgsc.bcm.edu	37	chr17	7577548	7577548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gatgggcctccggttcatgcCgcccatgcaggaactgttac	12	13	1	0	rs28934575|rs397516437		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:7577548C>T	ENST00000269305.4	-	7	922	c.733G>A	c.(733-735)Ggc>Agc	p.G245S	TP53_ENST00000455263.2_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGGTTCATGCCGCCCATGCAG	0.577	G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	420	Substitution - Missense(390)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)|Insertion - Frameshift(1)	large_intestine(119)|lung(51)|breast(38)|ovary(29)|central_nervous_system(27)|upper_aerodigestive_tract(25)|stomach(25)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(22)|urinary_tract(14)|skin(9)|liver(7)|prostate(7)|biliary_tract(5)|bone(5)|pancreas(4)|soft_tissue(3)|vulva(2)|endometrium(2)|kidney(1)|cervix(1)|salivary_gland(1)	17	GRCh37	CM010463|CM900210|CM920674	TP53	M	rs28934575	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	149	112	125	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	733,733,733,733,337,337,337	4.6	1	17	dbSNP_125	125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	56,56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	245/394,245/394,245/347,245/342,113/262,113/210,113/215	7577548	1,13005	2203	4300	6503	7518273	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.733G>A	17.37:g.7577548C>T	ENSP00000269305:p.Gly245Ser		7518273	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	33	5.259904	0.95368	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99894	-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99878	0.9942	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.976;0.992;0.999;0.999;1.0	D	0.96039	0.9023	10	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	rs28934575	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245S;ENSP00000352610:G245S;ENSP00000269305:G245S;ENSP00000398846:G245S;ENSP00000391127:G245S;ENSP00000391478:G245S;ENSP00000425104:G113S;ENSP00000423862:G152S	ENSP00000269305:G245S	G	-	1	0	TP53	7518273	1.000000	0.71417	0.965000	0.40720	0.974000	0.67602	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577548	C	T	7577548	3	4	100	1	0	0	0	0	1	0	0	0	16421	652	23	1	557	1	TP53	17	7577548	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	4395366	7577548	73617662	158	26812										
TNFRSF13B	23495	hgsc.bcm.edu	37	chr17	16843766	16843767	+	Frame_Shift_Ins	INS	-	-	C													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aggacggcacacaggcagagINSccccagcgtgctgtagacca							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:16843766_16843767insC	ENST00000261652.2	-	4	516_517	c.504_505insG	c.(502-507)gggctcfs	p.L169fs	TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000583789.1_Frame_Shift_Ins_p.L123fs|TNFRSF13B_ENST00000437538.2_Frame_Shift_Ins_p.L123fs|TNFRSF13B_ENST00000581616.2_5'Flank	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	169					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						CACAGGCAGAGCCCCAGCGTGC	0.649									IgA Deficiency, Selective																																							0			17																																								16784492	SO:0001589	frameshift_variant	23495	Familial Cancer Database	IGAD1, IGAD2	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"Tumor necrosis factor receptor superfamily", "CD molecules"	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.505dupG	17.37:g.16843770_16843770dupC	ENSP00000261652:p.Leu169fs		16784491	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Frame_Shift_Ins	INS	ENST00000261652.2	37	CCDS11181.1																																																																																				0.649	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2			C	16843767	-	C	16843766	7	5	100	1	0	1	1	0	0	0	0	0	16326	971	34	0	384	0	TNFRSF13B	17	16843766	Frame_Shift_Ins	INS	-	TCGA-DC-6682-01A-11D-1826-10	9266218	16843766	64351444	159	26813										
AKAP10	11216	hgsc.bcm.edu	37	chr17	19839689	19839689	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagatattggattcaatttcTaatcgtacaacatcatcaaa	4	8	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:19839689T>C	ENST00000225737.6	-	9	1534	c.1377A>G	c.(1375-1377)ttA>ttG	p.L459L	AKAP10_ENST00000395536.3_Silent_p.L459L	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	459	RGS 2. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)		p.L459L(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					ATTCAATTTCTAATCGTACAA	0.438																																																1	Substitution - coding silent(1)	skin(1)	17											107	92	97					17																	19839689		2203	4300	6503	19780281	SO:0001819	synonymous_variant	11216			AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1377A>G	17.37:g.19839689T>C			19780281	B2R650|Q96AJ7	Silent	SNP	ENST00000225737.6	37	CCDS11214.1																																																																																				0.438	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		C	19839689	T	C	19839689	2	2	100	1	0	0	0	0	0	0	0	1	446	1519	53	4		4	AKAP10	17	19839689	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	2995923	19839689	61355521	160	26814										
NF1	4763	hgsc.bcm.edu	37	chr17	29509617	29509617	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccactacaaatcattctcctTatcttgtgtccagaaataat	3	11	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:29509617T>C	ENST00000358273.4	+	8	1205	c.822T>C	c.(820-822)ctT>ctC	p.L274L	NF1_ENST00000431387.4_Silent_p.L274L|NF1_ENST00000356175.3_Silent_p.L274L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	274					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCATTCTCCTTATCTTGTGTC	0.378			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	17											108	91	97					17																	29509617		2203	4300	6503	26533743	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.822T>C	17.37:g.29509617T>C			26533743	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.378	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29509617	T	C	29509617	2	2	100	1	0	0	0	0	0	0	0	1	10387	1741	61	4		4	NF1	17	29509617	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	9669928	29509617	51685593	161	26815										
NR1D1	9572	hgsc.bcm.edu	37	chr17	38249487	38249487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cccgaagagcccgcagcagcGtctcctggagctgctccacc	11	18	1	1	rs201684407		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:38249487G>A	ENST00000246672.3	-	8	2324	c.1694C>T	c.(1693-1695)aCg>aTg	p.T565M	THRA_ENST00000394121.4_Missense_Mutation_p.R442H|THRA_ENST00000584985.1_Missense_Mutation_p.R403H|THRA_ENST00000264637.4_Missense_Mutation_p.R442H	NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	565	Ligand-binding.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CCGCAGCAGCGTCTCCTGGAG	0.652																																																0			17											37	41	39					17																	38249487		2203	4300	6503	35503013	SO:0001583	missense	9572			X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"Nuclear hormone receptors"	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.1694C>T	17.37:g.38249487G>A	ENSP00000246672:p.Thr565Met		35503013	Q0P5Z4|Q15304	Missense_Mutation	SNP	ENST00000246672.3	37	CCDS11361.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.69|18.69	3.678832|3.678832	0.68042|0.68042	.|.	.|.	ENSG00000126351|ENSG00000126368	ENST00000394121;ENST00000264637|ENST00000246672	D;D|D	0.94613|0.96587	-3.47;-3.47|-4.06	5.05|5.05	5.05|5.05	0.67936|0.67936	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.077801	.|0.49916	.|D	.|0.000122	D|D	0.96172|0.96172	0.8752|0.8752	N|N	0.19112|0.19112	0.55|0.55	0.43703|0.43703	D|D	0.996161|0.996161	D;P|D	0.55800|0.89917	0.973;0.955|1.0	B;B|D	0.41723|0.79108	0.365;0.2|0.992	D|D	0.97103|0.97103	0.9799|0.9799	9|10	0.72032|0.66056	D|D	0.01|0.02	.|.	17.3484|17.3484	0.87316|0.87316	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	403;442|565	P10827-3;P10827|P20393	.;THA_HUMAN|NR1D1_HUMAN	H|M	442|565	ENSP00000377679:R442H;ENSP00000264637:R442H|ENSP00000246672:T565M	ENSP00000264637:R442H|ENSP00000246672:T565M	R|T	+|-	2|2	0|0	THRA|NR1D1	35503013|35503013	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.934000|1.934000	0.40163|0.40163	2.618000|2.618000	0.88619|0.88619	0.563000|0.563000	0.77884|0.77884	CGT|ACG		0.652	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			A	38249487	G	A	38249487	3	1	100	1	0	0	0	0	1	0	0	0	10646	1145	40	1	154	1	NR1D1	17	38249487	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	8739870	38249487	42945723	162	26816										
TUBG2	27175	hgsc.bcm.edu	37	chr17	40817777	40817777	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acctcatcggcctcatcgccTcgctcattcccaccccacgg	6	21	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:40817777T>C	ENST00000251412.7	+	8	974	c.775T>C	c.(775-777)Tcg>Ccg	p.S259P	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	259					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		CCTCATCGCCTCGCTCATTCC	0.622																																																0			17											222	180	194					17																	40817777		2203	4300	6503	38071303	SO:0001583	missense	27175			AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"Tubulins"	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.775T>C	17.37:g.40817777T>C	ENSP00000251412:p.Ser259Pro		38071303	A6NDI4|Q32NB2	Missense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.929278	0.52759	.	.	ENSG00000037042	ENST00000251412	D	0.84800	-1.9	4.63	4.63	0.57726	Tubulin/FtsZ, 2-layer sandwich domain (1);Tubulin/FtsZ, GTPase domain (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.78566	0.4303	L	0.37630	1.12	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.73300	-0.4026	10	0.29301	T	0.29	-8.3935	14.0672	0.64837	0.0:0.0:0.0:1.0	.	259	Q9NRH3	TBG2_HUMAN	P	259	ENSP00000251412:S259P	ENSP00000251412:S259P	S	+	1	0	TUBG2	38071303	1.000000	0.71417	0.993000	0.49108	0.871000	0.50021	7.917000	0.87498	1.728000	0.51552	0.379000	0.24179	TCG		0.622	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437		C	40817777	T	C	40817777	3	2	100	1	0	0	0	0	1	0	0	0	16805	1551	54	4	805	4	TUBG2	17	40817777	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	2568290	40817777	40377433	163	26817										
IGF2BP1	10642	hgsc.bcm.edu	37	chr17	47115649	47115649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccgagggggctttggctctcGgggtcagccccgccagggct	17	14	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:47115649G>A	ENST00000290341.3	+	6	855	c.521G>A	c.(520-522)cGg>cAg	p.R174Q	RNU6-826P_ENST00000516827.1_RNA|IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	174					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTTGGCTCTCGGGGTCAGCCC	0.657																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)											0			17											31	37	35					17																	47115649		2203	4300	6503	44470648	SO:0001583	missense	10642			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.521G>A	17.37:g.47115649G>A	ENSP00000290341:p.Arg174Gln		44470648	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	36	5.776025	0.96922	.	.	ENSG00000159217	ENST00000290341	T	0.21191	2.02	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	T	0.31071	0.0785	L	0.59436	1.845	0.80722	D	1	D	0.54397	0.966	P	0.47626	0.552	T	0.01472	-1.1346	10	0.31617	T	0.26	-22.2604	19.0998	0.93269	0.0:0.0:1.0:0.0	.	174	Q9NZI8	IF2B1_HUMAN	Q	174	ENSP00000290341:R174Q	ENSP00000290341:R174Q	R	+	2	0	IGF2BP1	44470648	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.491000	0.66887	2.585000	0.87301	0.655000	0.94253	CGG		0.657	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		A	47115649	G	A	47115649	3	1	100	1	0	0	0	0	1	0	0	0	7594	1116	39	1	543	1	IGF2BP1	17	47115649	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	6297872	47115649	34079561	164	26818										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56056657	56056657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctgctgcttttggttactggTctcttcactcatgcatgcta	8	11	3	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:56056657T>C	ENST00000581208.1	-	5	1034	c.994A>G	c.(994-996)Acc>Gcc	p.T332A	VEZF1_ENST00000584396.1_Missense_Mutation_p.T323A	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	332					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						TGGTTACTGGTCTCTTCACTC	0.438																																																0			17											96	100	99					17																	56056657		2203	4300	6503	53411656	SO:0001583	missense	7716			D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.994A>G	17.37:g.56056657T>C	ENSP00000462337:p.Thr332Ala		53411656		Missense_Mutation	SNP	ENST00000581208.1	37	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.577517	0.45902	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.61	5.61	0.85477	.	1.042020	0.07417	N	0.893314	T	0.42810	0.1219	N	0.08118	0	0.39888	D	0.973735	B	0.10296	0.003	B	0.08055	0.003	T	0.06679	-1.0813	9	0.35671	T	0.21	1.3406	14.3775	0.66889	0.0:0.0:0.0:1.0	.	332	Q14119	VEZF1_HUMAN	A	332	.	ENSP00000258963:T332A	T	-	1	0	VEZF1	53411656	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.381000	0.52455	2.143000	0.66587	0.533000	0.62120	ACC		0.438	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			C	56056657	T	C	56056657	3	2	100	1	0	0	0	0	1	0	0	0	17195	1667	58	4	579	4	VEZF1	17	56056657	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	8941008	56056657	25138553	165	26819										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57125156	57125156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcataaacaagatccagatCcagatctccatctgaaagct	5	12	3	4			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr17:57125156C>T	ENST00000262294.7	-	16	1814	c.1555G>A	c.(1555-1557)Gat>Aat	p.D519N	TRIM37_ENST00000393066.3_Missense_Mutation_p.D519N|TRIM37_ENST00000393065.2_Missense_Mutation_p.D485N|TRIM37_ENST00000376149.3_Missense_Mutation_p.D397N	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	519					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AGATCCAGATCCAGATCTCCA	0.413									Mulibrey Nanism																																							0			17											113	102	106					17																	57125156		2203	4300	6503	54479938	SO:0001583	missense	4591	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1555G>A	17.37:g.57125156C>T	ENSP00000262294:p.Asp519Asn		54479938	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	C	35	5.543314	0.96474	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.68624	1.42;1.42;-0.34;1.03	5.74	5.74	0.90152	.	0.053328	0.64402	D	0.000001	T	0.74283	0.3696	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.997;0.996	D;D;P	0.66196	0.942;0.942;0.877	T	0.76313	-0.3005	10	0.72032	D	0.01	-29.1409	19.9145	0.97053	0.0:1.0:0.0:0.0	.	485;397;519	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	N	519;519;397;485	ENSP00000376785:D519N;ENSP00000262294:D519N;ENSP00000365319:D397N;ENSP00000376784:D485N	ENSP00000262294:D519N	D	-	1	0	TRIM37	54479938	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.707000	0.92482	0.557000	0.71058	GAT		0.413	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		T	57125156	C	T	57125156	3	4	100	1	0	0	0	0	1	0	0	0	16551	855	30	3	1383	3	TRIM37	17	57125156	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	1068499	57125156	24070054	166	26820										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2891253	2891253	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggggagaaggaaacaagcctGagaaaagaaataaataacct	11	5	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr18:2891253G>T	ENST00000254528.3	+	4	1287	c.1128G>T	c.(1126-1128)ctG>ctT	p.L376L		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	376					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AAACAAGCCTGAGAAAAGAAA	0.502																																																0			18											44	51	48					18																	2891253		2203	4300	6503	2881253	SO:0001819	synonymous_variant	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1128G>T	18.37:g.2891253G>T			2881253	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																				0.502	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891253	G	T	2891253	2	4	100	1	0	0	0	0	0	0	0	1	5107	1277	45	2		2	EMILIN2	18	2891253	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10		2891253	75185995	167	26821										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3188780	3188780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acaggcgttctgccttttctCgaatcacaactttccttgac	6	13	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr18:3188780C>T	ENST00000356443.4	-	4	1070	c.737G>A	c.(736-738)cGa>cAa	p.R246Q	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000261606.7_Missense_Mutation_p.R246Q|MYOM1_ENST00000400569.3_Missense_Mutation_p.R246Q	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	246					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TGCCTTTTCTCGAATCACAAC	0.453																																																0			18											93	87	89					18																	3188780		1944	4137	6081	3178780	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.737G>A	18.37:g.3188780C>T	ENSP00000348821:p.Arg246Gln		3178780	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	34	5.356344	0.95854	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.49720	0.87;0.89;0.77	5.84	5.84	0.93424	.	0.071710	0.53938	D	0.000048	T	0.62429	0.2427	L	0.38175	1.15	0.44447	D	0.997374	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.61554	-0.7039	10	0.56958	D	0.05	.	19.7351	0.96200	0.0:1.0:0.0:0.0	.	246;246	P52179-2;P52179	.;MYOM1_HUMAN	Q	246	ENSP00000348821:R246Q;ENSP00000383413:R246Q;ENSP00000261606:R246Q	ENSP00000261606:R246Q	R	-	2	0	MYOM1	3178780	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.270000	0.58896	2.756000	0.94617	0.603000	0.83216	CGA		0.453	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3188780	C	T	3188780	3	4	100	1	0	0	0	0	1	0	0	0	10121	884	31	1	4460	1	MYOM1	18	3188780	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	297527	3188780	74888468	168	26822										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30903494	30903494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tttcatcctggtaaatatccTtatcaatctcttctttaatt	2	9	4	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr18:30903494T>C	ENST00000383096.3	-	11	1165	c.983A>G	c.(982-984)aAg>aGg	p.K328R	CCDC178_ENST00000579947.1_Missense_Mutation_p.K328R|CCDC178_ENST00000403303.1_Missense_Mutation_p.K328R|CCDC178_ENST00000583930.1_Missense_Mutation_p.K328R|CCDC178_ENST00000300227.8_Missense_Mutation_p.K328R|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000402325.1_Missense_Mutation_p.K328R|CCDC178_ENST00000406524.2_Missense_Mutation_p.K328R			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	328																	GTAAATATCCTTATCAATCTC	0.318																																																0			18											60	58	58					18																	30903494		2202	4295	6497	29157492	SO:0001583	missense	374864			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.983A>G	18.37:g.30903494T>C	ENSP00000372576:p.Lys328Arg		29157492	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	9.255	1.041781	0.19748	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	4.52	-5.23	0.02798	.	.	.	.	.	T	0.16171	0.0389	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.20550	0.011;0.046;0.011;0.011	B;B;B;B	0.17722	0.019;0.019;0.019;0.019	T	0.31641	-0.9936	9	0.13470	T	0.59	-8.9701	1.7952	0.03059	0.1362:0.2961:0.3495:0.2182	.	328;328;328;328	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	R	328	ENSP00000385591:K328R;ENSP00000372576:K328R;ENSP00000300227:K328R;ENSP00000385867:K328R;ENSP00000385234:K328R	ENSP00000300227:K328R	K	-	2	0	C18orf34	29157492	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.794000	0.01753	-0.620000	0.05641	0.528000	0.53228	AAG		0.318	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30903494	T	C	30903494	3	2	100	1	0	0	0	0	1	0	0	0	1908	1609	56	4	1672	4	C18orf34	18	30903494	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	27714714	30903494	47173754	169	26823										
ZNF426	79088	hgsc.bcm.edu	37	chr19	9641741	9641741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggtttcaagtcgcatttcccAtcctgaaataaaacagacaa	6	10	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:9641741A>G	ENST00000535489.1	-	5	664	c.328T>C	c.(328-330)Tgg>Cgg	p.W110R	ZNF426_ENST00000589289.1_Intron|ZNF426_ENST00000593003.1_Missense_Mutation_p.W72R|ZNF426_ENST00000253115.2_Missense_Mutation_p.W110R			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	110	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W110R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						CGCATTTCCCATCCTGAAATA	0.443																																																1	Substitution - Missense(1)	ovary(1)	19											96	90	92					19																	9641741		2203	4300	6503	9502741	SO:0001583	missense	79088			AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.328T>C	19.37:g.9641741A>G	ENSP00000439017:p.Trp110Arg		9502741	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	A	9.959	1.222209	0.22457	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.07021	3.23;3.23	1.53	1.53	0.23141	Krueppel-associated box (1);	.	.	.	.	T	0.07683	0.0193	N	0.08118	0	0.18873	N	0.999986	D;D	0.55605	0.972;0.972	P;P	0.59643	0.861;0.861	T	0.37407	-0.9707	9	0.21540	T	0.41	.	5.172	0.15114	1.0:0.0:0.0:0.0	.	97;110	Q59EH4;Q9BUY5	.;ZN426_HUMAN	R	97;110;110	ENSP00000253115:W110R;ENSP00000439017:W110R	ENSP00000253115:W110R	W	-	1	0	ZNF426	9502741	0.019000	0.18553	0.024000	0.17045	0.459000	0.32528	2.240000	0.43088	0.945000	0.37605	0.377000	0.23210	TGG		0.443	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		G	9641741	A	G	9641741	3	3	100	1	0	0	0	0	1	0	0	0	17939	217	8	4	1344	4	ZNF426	19	9641741	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10		9641741	49487242	170	26824										
ZNF564	163050	hgsc.bcm.edu	37	chr19	12638452	12638452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtgagttctttcatgtcttCgaaaggattgacaagaactg	10	6	3	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:12638452C>T	ENST00000339282.7	-	4	666	c.470G>A	c.(469-471)cGa>cAa	p.R157Q	ZNF709_ENST00000428311.1_Intron|CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						TTCATGTCTTCGAAAGGATTG	0.423																																																0			19											104	110	108					19																	12638452		2199	4299	6498	12499452	SO:0001583	missense	163050			BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.470G>A	19.37:g.12638452C>T	ENSP00000340004:p.Arg157Gln		12499452	B9EGT4|Q6P1K6	Missense_Mutation	SNP	ENST00000339282.7	37	CCDS42505.1	.	.	.	.	.	.	.	.	.	.	C	5.842	0.339547	0.11069	.	.	ENSG00000249709	ENST00000339282	T	0.04275	3.66	1.71	-2.31	0.06765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02888	0.0086	N	0.20483	0.58	0.09310	N	0.999998	B	0.19935	0.04	B	0.24155	0.051	T	0.49390	-0.8945	9	0.10111	T	0.7	.	8.0541	0.30596	0.0:0.2441:0.0:0.7559	.	157	Q8TBZ8	ZN564_HUMAN	Q	157	ENSP00000340004:R157Q	ENSP00000340004:R157Q	R	-	2	0	ZNF564	12499452	0.002000	0.14202	0.001000	0.08648	0.958000	0.62258	0.040000	0.13905	-0.568000	0.06038	0.643000	0.83706	CGA		0.423	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		T	12638452	C	T	12638452	3	4	100	1	0	0	0	0	1	0	0	0	18034	884	31	1	1195	1	ZNF564	19	12638452	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	2996711	12638452	46490531	171	26825										
AP1M1	8907	hgsc.bcm.edu	37	chr19	16338426	16338426	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgtgtgcggctatcacgcttCgagaatgaccgcaccatctc	10	13	2	2	rs142555840		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:16338426C>T	ENST00000291439.3	+	7	1190	c.741C>T	c.(739-741)ttC>ttT	p.F247F	AP1M1_ENST00000429941.2_Silent_p.F247F|AP1M1_ENST00000541844.1_Silent_p.F175F|AP1M1_ENST00000590756.1_Silent_p.F175F|AP1M1_ENST00000444449.2_Silent_p.F259F	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	247	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						TATCACGCTTCGAGAATGACC	0.607													C|||	1	0.000199681	0	0	5008	,	,		20242	0		0.001	False		,,,				2504	0															0			19						C	,	0,4406		0,0,2203	280	227	245		777,741	-3.6	0.8	19	dbSNP_134	245	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	259/436,247/424	16338426	1,13005	2203	4300	6503	16199426	SO:0001819	synonymous_variant	8907				CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.741C>T	19.37:g.16338426C>T			16199426	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																				0.607	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		T	16338426	C	T	16338426	2	4	100	1	0	0	0	0	0	0	0	1	734	883	31	1		1	AP1M1	19	16338426	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	3699974	16338426	42790557	172	26826										
ZNF43	7594	hgsc.bcm.edu	37	chr19	21990501	21990501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tccagtatgaattttgttatGtgtagtaaggtttgaatatt	9	2	0	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:21990501G>A	ENST00000354959.4	-	4	2507	c.2338C>T	c.(2338-2340)Cat>Tat	p.H780Y	ZNF43_ENST00000598381.1_Missense_Mutation_p.H774Y|ZNF43_ENST00000594012.1_Missense_Mutation_p.H774Y|ZNF43_ENST00000595461.1_Missense_Mutation_p.H774Y	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	780					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		ATTTTGTTATGTGTAGTAAGG	0.318																																																0			19											61	62	62					19																	21990501		2203	4300	6503	21782341	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.2338C>T	19.37:g.21990501G>A	ENSP00000347045:p.His780Tyr		21782341	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227793	0.58668	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.59772	0.24	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75413	0.3846	M	0.84846	2.72	0.23855	N	0.996651	D	0.89917	1.0	D	0.72625	0.978	T	0.63010	-0.6732	9	0.87932	D	0	.	10.4707	0.44635	0.0:0.0:1.0:0.0	.	780	P17038	ZNF43_HUMAN	Y	779;780	ENSP00000347045:H780Y	ENSP00000347045:H780Y	H	-	1	0	ZNF43	21782341	1.000000	0.71417	0.004000	0.12327	0.890000	0.51754	4.867000	0.63013	0.976000	0.38417	0.305000	0.20034	CAT		0.318	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		A	21990501	G	A	21990501	3	1	100	1	0	0	0	0	1	0	0	0	17942	1377	48	3	95	3	ZNF43	19	21990501	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	5652075	21990501	37138482	173	26827										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22270820	22270820	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aagacctttgcccagagcgaGacataaaatattttttccaa	6	9	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:22270820G>C	ENST00000594947.1	+	4	412	c.268G>C	c.(268-270)Gac>Cac	p.D90H	ZNF257_ENST00000600162.1_3'UTR	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	90					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				CCCAGAGCGAGACATAAAATA	0.313																																																0			19											54	56	55					19																	22270820		1971	4189	6160	22062660	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.268G>C	19.37:g.22270820G>C	ENSP00000470209:p.Asp90His		22062660	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	1.451	-0.564890	0.03939	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.1	1.1	0.20463	.	.	.	.	.	T	0.32675	0.0837	L	0.52364	1.645	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.29058	-1.0024	8	0.48119	T	0.1	.	4.3207	0.11016	0.0:0.0:0.6118:0.3882	.	90	Q9Y2Q1	ZN257_HUMAN	H	90	.	ENSP00000380312:D90H	D	+	1	0	ZNF257	22062660	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.063000	0.11655	0.512000	0.28257	0.305000	0.20034	GAC		0.313	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			C	22270820	G	C	22270820	3	2	100	1	0	0	0	0	1	0	0	0	17839	942	33	5	282	5	ZNF257	19	22270820	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	280319	22270820	36858163	174	26828										
PDCD5	9141	hgsc.bcm.edu	37	chr19	33076809	33076809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aagatatggacaactaagtgAgaaggtaagcttagacagcc	11	6	0	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:33076809A>G	ENST00000590247.2	+	4	448	c.254A>G	c.(253-255)gAg>gGg	p.E85G	PDCD5_ENST00000586035.1_Missense_Mutation_p.E47G|PDCD5_ENST00000592786.1_Intron|PDCD5_ENST00000379316.3_Intron|PDCD5_ENST00000419343.3_Missense_Mutation_p.E85G	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	85					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					CAACTAAGTGAGAAGGTAAGC	0.363																																																0			19											103	108	106					19																	33076809		2203	4300	6503	37768649	SO:0001583	missense	9141			AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"TFAR19 novel apoptosis-related", "TF1 cell apoptosis-related gene 19"	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.254A>G	19.37:g.33076809A>G	ENSP00000466214:p.Glu85Gly		37768649	B4DE64|Q53YC9|Q6IB70	Missense_Mutation	SNP	ENST00000590247.2	37	CCDS12423.1	.	.	.	.	.	.	.	.	.	.	A	5.109	0.205798	0.09704	.	.	ENSG00000105185	ENST00000419343;ENST00000221784	.	.	.	5.6	4.57	0.56435	.	0.148836	0.64402	N	0.000011	T	0.15262	0.0368	N	0.00690	-1.25	0.37085	D	0.899182	B;B	0.09022	0.0;0.002	B;B	0.09377	0.004;0.004	T	0.29058	-1.0024	9	0.02654	T	1	-14.8081	12.4858	0.55872	0.083:0.0:0.917:0.0	.	85;85	O14737;B4DE64	PDCD5_HUMAN;.	G	85	.	ENSP00000221784:E85G	E	+	2	0	PDCD5	37768649	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	6.533000	0.73829	1.325000	0.45301	-0.468000	0.05107	GAG		0.363	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708		G	33076809	A	G	33076809	3	3	100	1	0	0	0	0	1	0	0	0	11653	304	11	4	268	4	PDCD5	19	33076809	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	10805989	33076809	26052174	175	26829										
GGN	199720	hgsc.bcm.edu	37	chr19	38877875	38877875	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tttcgggagcccccgcccgcGgatggctccgactgcaagtt	13	15	0	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:38877875G>A	ENST00000334928.6	-	3	159	c.27C>T	c.(25-27)tcC>tcT	p.S9S	SPRED3_ENST00000587013.1_5'Flank|SPRED3_ENST00000586301.1_5'Flank|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000338502.4_5'Flank|GGN_ENST00000591809.1_Intron	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	9					cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCCCGCCCGCGGATGGCTCCG	0.667																																																0			19											5	6	5					19																	38877875		2059	4057	6116	43569715	SO:0001819	synonymous_variant	199720			AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.27C>T	19.37:g.38877875G>A			43569715	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	37	CCDS12516.1																																																																																				0.667	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		A	38877875	G	A	38877875	2	1	100	1	0	0	0	0	0	0	0	1	6378	1103	39	1		1	GGN	19	38877875	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	5801066	38877875	20251108	176	26830										
ZNF546	339327	hgsc.bcm.edu	37	chr19	40504277	40504277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgggcctccaaatgactttcTcatttttcaaatcattcctc	4	13	3	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:40504277T>C	ENST00000347077.4	+	3	260	c.44T>C	c.(43-45)cTc>cCc	p.L15P	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	15			L -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AATGACTTTCTCATTTTTCAA	0.408																																																0			19											99	96	97					19																	40504277		2203	4300	6503	45196117	SO:0001583	missense	339327			BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.44T>C	19.37:g.40504277T>C	ENSP00000339823:p.Leu15Pro		45196117	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	t	10.96	1.499748	0.26861	.	.	ENSG00000187187	ENST00000347077	T	0.08458	3.09	1.66	1.66	0.24008	.	.	.	.	.	T	0.05044	0.0135	N	0.08118	0	0.09310	N	0.999998	D	0.59357	0.985	P	0.45639	0.488	T	0.34850	-0.9812	9	0.66056	D	0.02	.	5.414	0.16363	0.0:0.0:0.0:1.0	.	15	Q86UE3	ZN546_HUMAN	P	15	ENSP00000339823:L15P	ENSP00000339823:L15P	L	+	2	0	ZNF546	45196117	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.005000	0.13129	1.033000	0.39918	0.528000	0.53228	CTC		0.408	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		C	40504277	T	C	40504277	3	2	100	1	0	0	0	0	1	0	0	0	18017	1551	54	4	46	4	ZNF546	19	40504277	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	1626402	40504277	18624706	177	26831										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44934175	44934175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acttttcaagccattctctcCagggttaatgcgatgaagta	8	9	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:44934175C>T	ENST00000588931.1	-	6	1214	c.781G>A	c.(781-783)Gga>Aga	p.G261R	ZNF229_ENST00000291187.4_Missense_Mutation_p.G255R|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				CCATTCTCTCCAGGGTTAATG	0.428																																																0			19											102	95	98					19																	44934175		1908	4108	6016	49626015	SO:0001583	missense	7772			AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.781G>A	19.37:g.44934175C>T	ENSP00000466519:p.Gly261Arg		49626015	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457632	0.26161	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.35	-0.334	0.12666	.	.	.	.	.	T	0.25082	0.0609	N	0.24115	0.695	0.09310	N	1	B	0.20368	0.044	B	0.17722	0.019	T	0.18366	-1.0339	8	0.49607	T	0.09	.	4.955	0.14035	0.0:0.6043:0.1714:0.2243	.	261	Q9UJW7	ZN229_HUMAN	R	261	.	ENSP00000291187:G261R	G	-	1	0	ZNF229	49626015	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	0.175000	0.16762	-0.390000	0.07774	0.609000	0.83330	GGA		0.428	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		T	44934175	C	T	44934175	3	4	100	1	0	0	0	0	1	0	0	0	17821	603	21	3	1700	3	ZNF229	19	44934175	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	4429898	44934175	14194808	178	26832										
RTN2	6253	hgsc.bcm.edu	37	chr19	45998253	45998253	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	agctctcgaaaatcagagtcGtcgttccctcctgcagtggg	11	12	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:45998253G>A	ENST00000245923.4	-	3	325	c.90C>T	c.(88-90)gaC>gaT	p.D30D	PPM1N_ENST00000401705.1_Intron|RTN2_ENST00000430715.2_5'Flank|RTN2_ENST00000590526.1_De_novo_Start_OutOfFrame|PPM1N_ENST00000456399.2_5'Flank|RTN2_ENST00000344680.4_Silent_p.D30D|PPM1N_ENST00000396737.2_5'Flank|RTN2_ENST00000589384.1_5'UTR	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	30					cell death (GO:0008219)|intracellular protein transmembrane transport (GO:0065002)|regulation of glucose import (GO:0046324)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(4)|skin(1)|urinary_tract(1)	20		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		AATCAGAGTCGTCGTTCCCTC	0.627																																																0			19											74	71	72					19																	45998253		2203	4300	6503	50690093	SO:0001819	synonymous_variant	6253			AF038540	CCDS12665.1, CCDS12666.1, CCDS46114.1	19q13.2-q13.3	2012-03-30				ENSG00000125744			10468	protein-coding gene	gene with protein product	"NSP-like protein 1", "Neuroendocrine-specific protein-like 1"	603183	"spastic paraplegia 12 (autosomal dominant)"	SPG12		8812484, 9530622, 22232211	Standard	NM_005619		Approved	NSP2, NSPL1	uc002pcb.4	O75298		ENST00000245923.4:c.90C>T	19.37:g.45998253G>A			50690093	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Silent	SNP	ENST00000245923.4	37	CCDS12665.1																																																																																				0.627	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619		A	45998253	G	A	45998253	2	1	100	1	0	0	0	0	0	0	0	1	13763	1136	40	1		1	RTN2	19	45998253	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	1064078	45998253	13130730	179	26833										
PNMAL2	57469	hgsc.bcm.edu	37	chr19	46997356	46997356	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cctccgccatgtcctgggcaGccaggagcgccaccagctcc	11	19	0	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:46997356G>T	ENST00000377655.2	-	1	734				PNMAL2_ENST00000594749.1_Intron|AC011484.1_ENST00000377652.3_5'Flank|PNMAL2_ENST00000599531.1_Missense_Mutation_p.A456D			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		GTCCTGGGCAGCCAGGAGCGC	0.627																																																0			19											61	70	67					19																	46997356		1973	4148	6121	51689196	SO:0001627	intron_variant	57469			AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+632C>A	19.37:g.46997356G>T			51689196	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37																																																																																					0.627	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		T	46997356	G	T	46997356	1	4	100	0	1	0	0	0	0	0	0	0	12189	971	34	2		2	PNMAL2	19	46997356	Intron	SNP	G	TCGA-DC-6682-01A-11D-1826-10	999103	46997356	12131627	180	26834										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54720983	54720983	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tagtggatggccagagtggcGtagatgctgggctcagctgg	18	7	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:54720983G>A	ENST00000391750.1	-	14	2011	c.1875C>T	c.(1873-1875)taC>taT	p.Y625Y	LILRA6_ENST00000270464.5_Silent_p.Y626Y|LILRB3_ENST00000346401.6_Silent_p.Y637Y|LILRA6_ENST00000419410.2_Silent_p.Y626Y|LILRB3_ENST00000407860.2_Silent_p.Y642Y|LILRA6_ENST00000440558.2_Silent_p.Y625Y|LILRB3_ENST00000424807.1_Silent_p.Y625Y|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000245620.9_Silent_p.Y626Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	625					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAGAGTGGCGTAGATGCTGG	0.627																																																0			19											102	95	97					19																	54720983		2203	4300	6503	59412795	SO:0001819	synonymous_variant	79168			U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1875C>T	19.37:g.54720983G>A			59412795	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																				0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		A	54720983	G	A	54720983	2	1	100	1	0	0	0	0	0	0	0	1	8815	1140	40	1		1	LILRB3	19	54720983	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	7723627	54720983	4408000	181	26835										
ZNF550	162972	hgsc.bcm.edu	37	chr19	58058834	58058834	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cttcccacactcaaggcactTgtatggtttctccccggtgt	8	14	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr19:58058834T>A	ENST00000457177.1	-	4	958	c.778A>T	c.(778-780)Aag>Tag	p.K260*	ZNF549_ENST00000594943.1_Intron|ZNF550_ENST00000325134.5_Nonsense_Mutation_p.K228*|ZNF550_ENST00000506609.2_Nonsense_Mutation_p.K219*|ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron			Q7Z398	ZN550_HUMAN	zinc finger protein 550	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	7		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)		TCAAGGCACTTGTATGGTTTC	0.502																																																0			19											124	91	102					19																	58058834		2203	4300	6503	62750646	SO:0001587	stop_gained	162972			AL833214	CCDS35500.1, CCDS35500.2	19q13.43	2013-05-22			ENSG00000251369	ENSG00000251369		"Zinc fingers, C2H2-type"	28643	protein-coding gene	gene with protein product						12477932	Standard	NM_001277090		Approved	MGC41917	uc002qpd.4	Q7Z398	OTTHUMG00000133709	ENST00000457177.1:c.778A>T	19.37:g.58058834T>A	ENSP00000469679:p.Lys260*		62750646	B3KVF6|O43337|Q7Z6D7|Q8NE45	Nonsense_Mutation	SNP	ENST00000457177.1	37		.	.	.	.	.	.	.	.	.	.	T	16.69	3.194529	0.58017	.	.	ENSG00000251369	ENST00000344222;ENST00000325134;ENST00000506609	.	.	.	3.5	-4.73	0.03259	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	2.4295	0.04468	0.1308:0.2794:0.3988:0.191	.	.	.	.	X	260;228;219	.	ENSP00000446224:K228X	K	-	1	0	AC003682.1	62750646	0.000000	0.05858	0.001000	0.08648	0.947000	0.59692	-2.794000	0.00765	-1.099000	0.03034	0.533000	0.62120	AAG		0.502	ZNF550-001	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000257992.2	NM_153231		A	58058834	T	A	58058834	4	1	100	1	0	0	0	0	0	1	0	0	18021	1821	63	5	494	5	ZNF550	19	58058834	Nonsense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	3337851	58058834	1070149	182	26836										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13867033	13867033	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ctcagattttcaggtctttcCgttagtctcactttttccac	5	12	4	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr20:13867033C>T	ENST00000284951.5	-	9	875	c.801G>A	c.(799-801)acG>acA	p.T267T	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Silent_p.T267T			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	267						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CAGGTCTTTCCGTTAGTCTCA	0.373																																																0			20											133	122	125					20																	13867033		1837	4094	5931	13815033	SO:0001819	synonymous_variant	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.801G>A	20.37:g.13867033C>T			13815033	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																					0.373	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		T	13867033	C	T	13867033	2	4	100	1	0	0	0	0	0	0	0	1	14048	639	23	1		1	SEL1L2	20	13867033	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10		13867033	49158487	183	26837										
BPIL1	80341	hgsc.bcm.edu	37	chr20	31606462	31606462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggctgttctcttcctgctggGcaagcccatcatcctgccca	9	16	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr20:31606462G>A	ENST00000170150.3	+	9	884	c.689G>A	c.(688-690)gGc>gAc	p.G230D		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	230						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										TTCCTGCTGGGCAAGCCCATC	0.637																																																0			20											122	120	121					20																	31606462		2203	4300	6503	31070123	SO:0001583	missense	80341			AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.689G>A	20.37:g.31606462G>A	ENSP00000170150:p.Gly230Asp		31070123	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.837505	0.71373	.	.	ENSG00000078898	ENST00000170150	T	0.08634	3.07	5.39	3.39	0.38822	.	0.117930	0.38663	N	0.001618	T	0.21186	0.0510	M	0.84585	2.705	0.43994	D	0.996694	P	0.52316	0.952	P	0.53593	0.73	T	0.00735	-1.1588	10	0.72032	D	0.01	-14.932	7.4039	0.26979	0.0908:0.1695:0.7398:0.0	.	230	Q8N4F0	BPIB2_HUMAN	D	230	ENSP00000170150:G230D	ENSP00000170150:G230D	G	+	2	0	BPIFB2	31070123	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.103000	0.50298	0.727000	0.32360	0.561000	0.74099	GGC		0.637	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		A	31606462	G	A	31606462	3	1	100	1	0	0	0	0	1	0	0	0	1494	1203	42	3	719	3	BPIL1	20	31606462	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	17739429	31606462	31419058	184	26838										
KCNK15	140730	hgsc.bcm.edu	37	chr20	43378887	43378887	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cctgggcgaacggctgaacgCggtggtgcggcgcctcctgt	17	13	0	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr20:43378887C>T	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.A134V	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CGGCTGAACGCGGTGGTGCGG	0.682																																																0			20											30	27	28					20																	43378887		2202	4299	6501	42812301	SO:0001628	intergenic_variant	60598				CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		20.37:g.43378887C>T			42812301	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309919	0.40895	.	.	ENSG00000124249	ENST00000372861	D	0.97256	-4.31	4.29	3.26	0.37387	.	0.432064	0.22167	U	0.063700	D	0.92890	0.7738	L	0.29908	0.895	0.23361	N	0.997832	B	0.12630	0.006	B	0.15484	0.013	D	0.86044	0.1521	10	0.42905	T	0.14	.	10.3317	0.43827	0.0:0.838:0.0:0.162	.	134	Q9H427	KCNKF_HUMAN	V	134	ENSP00000361952:A134V	ENSP00000361952:A134V	A	+	2	0	KCNK15	42812301	0.998000	0.40836	1.000000	0.80357	0.522000	0.34438	3.842000	0.55858	2.207000	0.71202	0.655000	0.94253	GCG		0.682	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		T	43378887	C	T	43378887	1	4	100	0	1	0	0	0	0	0	0	0	8083	768	27	1		1	KCNK15	20	43378887	IGR	SNP	C	TCGA-DC-6682-01A-11D-1826-10	11772425	43378887	19646633	185	26839										
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45874874	45874874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cagagtccaggcccaaatggActgttggggaatccgtctca	12	11	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr20:45874874A>G	ENST00000311275.7	-	14	2355	c.2102T>C	c.(2101-2103)gTc>gCc	p.V701A	ZMYND8_ENST00000352431.2_Missense_Mutation_p.V721A|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V696A|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V728A|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V696A|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V701A|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V721A|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V701A|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V696A|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V701A|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V649A|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V638A|ZMYND8_ENST00000471951.2_Missense_Mutation_p.V721A	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	701					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.V721G(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GCCCAAATGGACTGTTGGGGA	0.473																																																1	Substitution - Missense(1)	central_nervous_system(1)	20											173	163	166					20																	45874874		2203	4300	6503	45308281	SO:0001583	missense	23613			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.2102T>C	20.37:g.45874874A>G	ENSP00000312237:p.Val701Ala		45308281	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		.	.	.	.	.	.	.	.	.	.	A	13.78	2.340181	0.41398	.	.	ENSG00000101040	ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	T;T;T;T;T;T;T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.91	5.91	0.95273	.	0.265743	0.37012	N	0.002285	T	0.58047	0.2095	L	0.55103	1.725	0.32905	D	0.513734	B;B;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B	0.45768	0.041;0.036;0.011;0.011;0.036;0.011;0.866;0.042;0.035;0.035;0.042;0.011;0.025;0.025;0.025;0.023;0.036;0.011	B;B;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B	0.48815	0.018;0.051;0.023;0.01;0.008;0.01;0.591;0.023;0.012;0.012;0.023;0.01;0.008;0.008;0.034;0.011;0.008;0.007	T	0.66933	-0.5798	10	0.33141	T	0.24	-15.4966	16.3483	0.83171	1.0:0.0:0.0:0.0	.	696;728;696;696;676;695;721;701;696;721;721;701;638;696;649;721;649;701	B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	A	696;701;696;702;722;721;701;728;701;638;721;696;649	ENSP00000354166:V696A;ENSP00000312237:V701A;ENSP00000392964:V696A;ENSP00000335537:V721A;ENSP00000379577:V701A;ENSP00000439800:V728A;ENSP00000348246:V701A;ENSP00000396725:V638A;ENSP00000418210:V721A;ENSP00000361093:V696A;ENSP00000443086:V649A	ENSP00000262975:V702A	V	-	2	0	ZMYND8	45308281	1.000000	0.71417	0.222000	0.23844	0.691000	0.40173	7.079000	0.76829	2.254000	0.74563	0.533000	0.62120	GTC		0.473	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		G	45874874	A	G	45874874	3	3	100	1	0	0	0	0	1	0	0	0	17750	275	10	4	1444	4	ZMYND8	20	45874874	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	2495987	45874874	17150646	186	26840										
RNF160	26046	hgsc.bcm.edu	37	chr21	30358519	30358519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aactcctttcacagtttctgTgtctctctctgtacacatgg	6	12	4	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr21:30358519T>C	ENST00000361371.5	-	3	365	c.286A>G	c.(286-288)Aca>Gca	p.T96A	LTN1_ENST00000389195.2_Missense_Mutation_p.T142A|LTN1_ENST00000389194.2_Missense_Mutation_p.T142A			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	96					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						ACAGTTTCTGTGTCTCTCTCT	0.308																																																0			21											62	63	62					21																	30358519		2202	4298	6500	29280390	SO:0001583	missense	0			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.286A>G	21.37:g.30358519T>C	ENSP00000354977:p.Thr96Ala		29280390	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	T	7.844	0.722604	0.15439	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.65178	3.6;3.6;-0.14	4.2	3.03	0.35002	Armadillo-like helical (1);Armadillo-type fold (1);	0.154150	0.41396	D	0.000889	T	0.30230	0.0758	N	0.05306	-0.075	0.35507	D	0.800264	B	0.02656	0.0	B	0.04013	0.001	T	0.28004	-1.0057	10	0.06891	T	0.86	.	4.9027	0.13782	0.0:0.2187:0.0:0.7813	.	96	O94822	LTN1_HUMAN	A	142;96;98;142	ENSP00000373846:T142A;ENSP00000354977:T96A;ENSP00000373847:T142A	ENSP00000354977:T96A	T	-	1	0	LTN1	29280390	0.364000	0.24997	1.000000	0.80357	0.990000	0.78478	0.599000	0.24089	1.779000	0.52309	0.383000	0.25322	ACA		0.308	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		C	30358519	T	C	30358519	3	2	100	1	0	0	0	0	1	0	0	0	13492	1696	59	4	5126	4	RNF160	21	30358519	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10		30358519	17771376	187	26841										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40568294	40568294	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ttctcgtttttatttttgaaCgtcgaagaactcttttagat	6	6	2	3			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr21:40568294C>T	ENST00000333229.2	-	41	6899				BRWD1_ENST00000380800.3_Intron|BRWD1_ENST00000342449.3_Missense_Mutation_p.R2234H	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1						cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TATTTTTGAACGTCGAAGAAC	0.393																																					Melanoma(170;988 1986 4794 16843 39731)											0			21											195	190	191					21																	40568294		2203	4300	6503	39490164	SO:0001627	intron_variant	54014			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6571+129G>A	21.37:g.40568294C>T			39490164	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.912234	0.52439	.	.	ENSG00000185658	ENST00000342449	T	0.56275	0.47	5.53	4.64	0.57946	.	.	.	.	.	T	0.70263	0.3204	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.63703	0.917	T	0.73579	-0.3938	8	0.51188	T	0.08	.	15.9865	0.80157	0.1352:0.8648:0.0:0.0	.	2234	Q9NSI6-2	.	H	2234	ENSP00000344333:R2234H	ENSP00000344333:R2234H	R	-	2	0	BRWD1	39490164	0.301000	0.24444	0.999000	0.59377	0.998000	0.95712	2.019000	0.41001	1.307000	0.44944	0.655000	0.94253	CGT		0.393	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40568294	C	T	40568294	1	4	100	0	1	0	0	0	0	0	0	0	1528	536	19	1		1	BRWD1	21	40568294	Intron	SNP	C	TCGA-DC-6682-01A-11D-1826-10	10209775	40568294	7561601	188	26842										
HIRA	7290	hgsc.bcm.edu	37	chr22	19363215	19363215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acctggtgtggctttggaccGctctgtgaaccgggagtcaa	14	10	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr22:19363215G>A	ENST00000263208.5	-	15	1970	c.1714C>T	c.(1714-1716)Cgg>Tgg	p.R572W	HIRA_ENST00000546308.1_Missense_Mutation_p.R528W|HIRA_ENST00000340170.4_Missense_Mutation_p.R572W|HIRA_ENST00000541063.1_Missense_Mutation_p.R528W	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	572	Interaction with CCNA1.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GCTTTGGACCGCTCTGTGAAC	0.562																																																0			22											186	148	161					22																	19363215		2203	4300	6503	17743215	SO:0001583	missense	7290			X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.1714C>T	22.37:g.19363215G>A	ENSP00000263208:p.Arg572Trp		17743215	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	37	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713654	0.89112	.	.	ENSG00000100084	ENST00000340170;ENST00000263208;ENST00000541063;ENST00000539600;ENST00000546308	T;T;T;T	0.74421	-0.84;-0.77;-0.62;-0.62	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.80571	0.4648	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.965	T	0.82568	-0.0392	10	0.66056	D	0.02	-18.5411	18.5366	0.91013	0.0:0.0:1.0:0.0	.	528;572;572	F5H4M2;P54198-2;P54198	.;.;HIRA_HUMAN	W	572;572;528;81;528	ENSP00000345350:R572W;ENSP00000263208:R572W;ENSP00000446073:R528W;ENSP00000441870:R528W	ENSP00000263208:R572W	R	-	1	2	HIRA	17743215	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.501000	0.73691	2.616000	0.88540	0.655000	0.94253	CGG		0.562	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		A	19363215	G	A	19363215	3	1	100	1	0	0	0	0	1	0	0	0	7141	1086	38	1	1383	1	HIRA	22	19363215	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10		19363215	31941351	189	26843										
EP300	2033	hgsc.bcm.edu	37	chr22	41513646	41513646	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgttggctgcaggcaatggaCaagggataatgcctaatcaa	12	7	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr22:41513646C>T	ENST00000263253.7	+	2	1769	c.550C>T	c.(550-552)Caa>Taa	p.Q184*		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	184					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGGCAATGGACAAGGGATAAT	0.502			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											118	96	103					22																	41513646		2203	4300	6503	39843592	SO:0001587	stop_gained	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.550C>T	22.37:g.41513646C>T	ENSP00000263253:p.Gln184*		39843592	B1AKC2	Nonsense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	48	14.324288	0.99790	.	.	ENSG00000100393	ENST00000263253	.	.	.	6.11	6.11	0.99139	.	0.000000	0.46442	D	0.000296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-6.2198	20.731	0.99711	0.0:1.0:0.0:0.0	.	.	.	.	X	184	.	ENSP00000263253:Q184X	Q	+	1	0	EP300	39843592	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.585000	0.60977	2.907000	0.99374	0.609000	0.83330	CAA		0.502	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41513646	C	T	41513646	4	4	100	1	0	0	0	0	0	1	0	0	5161	479	17	3	556	3	EP300	22	41513646	Nonsense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	22150431	41513646	9790920	190	26844										
EP300	2033	hgsc.bcm.edu	37	chr22	41548253	41548253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggaatctaccgaaacagaagAgagaagcactgagttaaaaa	10	6	1	4			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr22:41548253A>G	ENST00000263253.7	+	16	4260	c.3041A>G	c.(3040-3042)gAg>gGg	p.E1014G		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1014					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GAAACAGAAGAGAGAAGCACT	0.383			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											41	44	43					22																	41548253		2203	4300	6503	39878199	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3041A>G	22.37:g.41548253A>G	ENSP00000263253:p.Glu1014Gly		39878199	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.322360	0.41096	.	.	ENSG00000100393	ENST00000263253	D	0.84516	-1.86	5.68	4.61	0.57282	.	0.000000	0.48767	D	0.000162	T	0.74504	0.3725	N	0.19112	0.55	0.44798	D	0.997804	P	0.34522	0.455	B	0.32465	0.146	T	0.72537	-0.4263	10	0.48119	T	0.1	-11.5398	11.8175	0.52220	0.8685:0.0:0.0:0.1315	.	1014	Q09472	EP300_HUMAN	G	1014	ENSP00000263253:E1014G	ENSP00000263253:E1014G	E	+	2	0	EP300	39878199	1.000000	0.71417	0.877000	0.34402	0.180000	0.23129	4.846000	0.62860	0.926000	0.37118	0.533000	0.62120	GAG		0.383	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41548253	A	G	41548253	3	3	100	1	0	0	0	0	1	0	0	0	5161	304	11	4	3103	4	EP300	22	41548253	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	34607	41548253	9756313	191	26845										
PANX2	56666	hgsc.bcm.edu	37	chr22	50617505	50617505	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ccagccagcctgggcaaggcGgagcccctcaccatcctgag	12	17	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr22:50617505G>A	ENST00000395842.2	+	3	1833	c.1833G>A	c.(1831-1833)gcG>gcA	p.A611A	PANX2_ENST00000159647.5_Silent_p.A611A	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	611					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		TGGGCAAGGCGGAGCCCCTCA	0.731																																																0			22											29	28	29					22																	50617505		2190	4297	6487	48959632	SO:0001819	synonymous_variant	56666				CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"Ion channels / Pannexins"	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.1833G>A	22.37:g.50617505G>A			48959632	B7Z684|Q96RD5|Q9UGX8	Silent	SNP	ENST00000395842.2	37	CCDS14085.2																																																																																				0.731	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		A	50617505	G	A	50617505	2	1	100	1	0	0	0	0	0	0	0	1	11452	1103	39	1		1	PANX2	22	50617505	Silent	SNP	G	TCGA-DC-6682-01A-11D-1826-10	9069252	50617505	687061	192	26846										
NCAPH2	29781	hgsc.bcm.edu	37	chr22	50946857	50946857	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tggacgtggcggcccagctgGgcgagtatctggaggaggta	19	8	1	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chr22:50946857G>T	ENST00000420993.2	+	1	213	c.91G>T	c.(91-93)Ggc>Tgc	p.G31C	NCAPH2_ENST00000299821.11_Missense_Mutation_p.G31C|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_5'Flank|LMF2_ENST00000474879.2_5'Flank|NCAPH2_ENST00000395701.3_Missense_Mutation_p.G31C|LMF2_ENST00000216080.5_5'Flank|NCAPH2_ENST00000395698.3_Missense_Mutation_p.G31C	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	31					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		GGCCCAGCTGGGCGAGTATCT	0.751																																																0			22											9	10	10					22																	50946857		1759	3927	5686	49293723	SO:0001583	missense	29781			BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"kleisin beta", "CAP-H2 subunit of the condensin II complex"	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.91G>T	22.37:g.50946857G>T	ENSP00000410088:p.Gly31Cys		49293723	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Missense_Mutation	SNP	ENST00000420993.2	37	CCDS14094.2	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713872	0.89112	.	.	ENSG00000025770	ENST00000420993;ENST00000395698;ENST00000395701;ENST00000523045;ENST00000299821	.	.	.	4.62	4.62	0.57501	.	0.192280	0.43747	D	0.000525	T	0.68467	0.3004	L	0.44542	1.39	0.54753	D	0.999989	D;D;D;D	0.76494	0.996;0.998;0.994;0.999	D;D;P;D	0.68483	0.919;0.919;0.831;0.958	T	0.70525	-0.4848	9	0.59425	D	0.04	-22.0299	16.5768	0.84704	0.0:0.0:1.0:0.0	.	31;31;31;31	Q6IBW4-4;Q6IBW4-2;Q6IBW4;Q6IBW4-5	.;.;CNDH2_HUMAN;.	C	31	.	ENSP00000299821:G31C	G	+	1	0	NCAPH2	49293723	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.540000	0.67205	2.580000	0.87095	0.555000	0.69702	GGC		0.751	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299		T	50946857	G	T	50946857	3	4	100	1	0	0	0	0	1	0	0	0	10241	1232	43	2	93	2	NCAPH2	22	50946857	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	329352	50946857	357709	193	26847										
ZNF157	7712	hgsc.bcm.edu	37	chrX	47272000	47272000	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	gcttactgtaggaagtcaaaCcttgttgaacatctgagaat	9	7	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:47272000C>A	ENST00000377073.3	+	4	614	c.528C>A	c.(526-528)aaC>aaA	p.N176K		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	176					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GGAAGTCAAACCTTGTTGAAC	0.408																																																0			X											74	63	66					X																	47272000		2203	4300	6503	47156944	SO:0001583	missense	7712			U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"Zinc fingers, C2H2-type", "-"	12942	protein-coding gene	gene with protein product		300024	"zinc finger protein 157 (HZF22)"			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.528C>A	X.37:g.47272000C>A	ENSP00000366273:p.Asn176Lys		47156944	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	.	.	.	.	.	.	.	.	.	.	C	2.407	-0.336139	0.05278	.	.	ENSG00000147117	ENST00000377073	T	0.07021	3.23	2.85	-2.77	0.05877	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08313	0.0207	L	0.36672	1.1	0.09310	N	1	D	0.53885	0.963	P	0.48368	0.575	T	0.25433	-1.0132	9	0.21540	T	0.41	.	8.9618	0.35851	0.0:0.4637:0.0:0.5363	.	176	P51786	ZN157_HUMAN	K	176	ENSP00000366273:N176K	ENSP00000366273:N176K	N	+	3	2	ZNF157	47156944	0.000000	0.05858	0.002000	0.10522	0.877000	0.50540	-0.652000	0.05366	-0.978000	0.03533	0.462000	0.41574	AAC		0.408	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		A	47272000	C	A	47272000	3	1	100	1	0	0	0	0	1	0	0	0	17776	506	18	2	542	2	ZNF157	23	47272000	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10		47272000	107998560	194	26848										
FGD1	2245	hgsc.bcm.edu	37	chrX	54472704	54472704	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	acagccatccagcgtcgctgTagttcctctgtctcagggct	10	14	2	0			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:54472704T>C	ENST00000375135.3	-	18	3457	c.2724A>G	c.(2722-2724)ctA>ctG	p.L908L		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	908	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AGCGTCGCTGTAGTTCCTCTG	0.657																																																0			X											52	40	44					X																	54472704		2203	4300	6503	54489429	SO:0001819	synonymous_variant	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.2724A>G	X.37:g.54472704T>C			54489429	Q5H999|Q8N4D9	Silent	SNP	ENST00000375135.3	37	CCDS14359.1																																																																																				0.657	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		C	54472704	T	C	54472704	2	2	100	1	0	0	0	0	0	0	0	1	5851	1625	57	4		4	FGD1	23	54472704	Silent	SNP	T	TCGA-DC-6682-01A-11D-1826-10	7200704	54472704	100797856	195	26849										
USP51	158880	hgsc.bcm.edu	37	chrX	55514071	55514071	+	Silent	SNP	C	C	G													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgttctgcatggatccatatCagatgcagtaacttataggg							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:55514071C>G	ENST00000500968.3	-	2	1384	c.1302G>C	c.(1300-1302)ctG>ctC	p.L434L	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	434	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						GGATCCATATCAGATGCAGTA	0.458																																																0			X											77	67	71					X																	55514071		2203	4300	6503	55530796	SO:0001819	synonymous_variant	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1302G>C	X.37:g.55514071C>G			55530796	Q8IWJ8	Silent	SNP	ENST00000500968.3	37	CCDS14370.1																																																																																				0.458	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		G	55514071	C	G	55514071	2	3	100	1	0	0	0	0	0	0	0	1	17123	813	29	5		5	USP51	23	55514071	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	1041367	55514071	99756489	196	26850	43	2								
USP51	158880	hgsc.bcm.edu	37	chrX	55514076	55514076	+	Missense_Mutation	SNP	G	G	T													0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgcatggatccatatcagatGcagtaacttatagggaatgt							TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:55514076G>T	ENST00000500968.3	-	2	1379	c.1297C>A	c.(1297-1299)Cat>Aat	p.H433N	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	433	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CATATCAGATGCAGTAACTTA	0.453																																																0			X											77	67	70					X																	55514076		2203	4300	6503	55530801	SO:0001583	missense	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1297C>A	X.37:g.55514076G>T	ENSP00000423333:p.His433Asn		55530801	Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	15.99	2.996398	0.54147	.	.	ENSG00000247746	ENST00000500968	T	0.27256	1.68	3.04	3.04	0.35103	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.29158	0.0725	L	0.31578	0.945	0.80722	D	1	P	0.46395	0.877	P	0.54664	0.758	T	0.02437	-1.1159	10	0.40728	T	0.16	.	11.3014	0.49309	0.0:0.0:1.0:0.0	.	433	Q70EK9	UBP51_HUMAN	N	433	ENSP00000423333:H433N	ENSP00000423333:H433N	H	-	1	0	USP51	55530801	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.709000	0.84645	1.796000	0.52611	0.508000	0.49915	CAT		0.453	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		T	55514076	G	T	55514076	3	4	100	1	0	0	0	0	1	0	0	0	17123	1319	46	2	842	2	USP51	23	55514076	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	5	55514076	99756484	197	26851	43	2								
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91873533	91873533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	attgtgccacagcccaccacCgatacaggtgtctgctctcc	8	16	2	0	rs140768648	byFrequency	TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:91873533C>T	ENST00000373094.1	+	7	4483	c.3638C>T	c.(3637-3639)cCg>cTg	p.P1213L	PCDH11X_ENST00000373097.1_Missense_Mutation_p.P1203L|PCDH11X_ENST00000373088.1_Missense_Mutation_p.P1176L|PCDH11X_ENST00000406881.1_Missense_Mutation_p.P1205L|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000298274.8_Missense_Mutation_p.P1176L|PCDH11X_ENST00000361655.2_Missense_Mutation_p.P1195L	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1213					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						AGCCCACCACCGATACAGGTG	0.597													C|||	28	0.00741722	0	0.0014	3775	,	,		14482	0.0258		0	False		,,,				2504	0.001				NSCLC(38;925 1092 2571 38200 45895)											0			X						C	LEU/PRO,,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,3829		0,4,2,1628,569	173	136	148		3614,,3527,3584,3638,3608	1.4	0	X	dbSNP_134	148	1,6723		0,0,1,2426,1871	no	missense,utr-3,missense,missense,missense,missense	PCDH11X	NM_001168360.1,NM_001168361.1,NM_001168362.1,NM_001168363.1,NM_032968.3,NM_032969.3	98,,98,98,98,98	0,4,3,4054,2440	TT,TC,T,CC,C		0.0149,0.1565,0.0663	possibly-damaging,,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1205/1340,,1176/1311,1195/1330,1213/1348,1203/1338	91873533	7,10552	2203	4298	6501	91760189	SO:0001583	missense	83259			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3638C>T	X.37:g.91873533C>T	ENSP00000362186:p.Pro1213Leu		91760189	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	16	0.009644364074743821	0	0.0	0	0.0	17	0.02972027972027972	0	0.0	C	7.533	0.659181	0.14645	0.001565	1.49E-4	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000373088;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T	0.47177	0.86;0.87;0.85;0.85;0.87;0.85	3.24	1.35	0.21983	.	.	.	.	.	T	0.10078	0.0247	N	0.19112	0.55	0.22401	N	0.999139	B;B;B;B;B	0.20780	0.048;0.048;0.048;0.048;0.028	B;B;B;B;B	0.11329	0.006;0.006;0.006;0.006;0.003	T	0.12553	-1.0543	9	0.45353	T	0.12	.	2.3462	0.04272	0.245:0.4752:0.0:0.2798	.	1176;1195;1205;1203;1213	Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7	.;.;.;.;PC11X_HUMAN	L	1213;1203;1176;1195;1205;1213;1176	ENSP00000362186:P1213L;ENSP00000362189:P1203L;ENSP00000362180:P1176L;ENSP00000355105:P1195L;ENSP00000384758:P1205L;ENSP00000298274:P1176L	ENSP00000298274:P1176L	P	+	2	0	PCDH11X	91760189	0.000000	0.05858	0.038000	0.18304	0.001000	0.01503	-0.376000	0.07465	0.207000	0.20607	-0.412000	0.06146	CCG		0.597	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91873533	C	T	91873533	3	4	100	1	0	0	0	0	1	0	0	0	11539	652	23	1	3786	1	PCDH11X	23	91873533	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	36359457	91873533	63397027	198	26852										
AMOT	154796	hgsc.bcm.edu	37	chrX	112022297	112022297	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	aggaccggtagctggacttgCaggaacctcagcctgagcca	13	12	1	1	rs373265985|rs147791784		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:112022297C>G	ENST00000524145.1	-	11	3159	c.3085G>C	c.(3085-3087)Gca>Cca	p.A1029P	AMOT_ENST00000371962.1_Missense_Mutation_p.A797P|AMOT_ENST00000304758.1_Missense_Mutation_p.A620P|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371959.3_Missense_Mutation_p.A1029P			Q4VCS5	AMOT_HUMAN	angiomotin	1029					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						GCTGGACTTGCAGGAACCTCA	0.522																																																0			X											110	101	104					X																	112022297		2203	4300	6503	111908953	SO:0001583	missense	154796			AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.3085G>C	X.37:g.112022297C>G	ENSP00000429013:p.Ala1029Pro		111908953	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060096	0.36373	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.37915	1.17;1.95;2.19;1.95	4.28	3.41	0.39046	.	0.230125	0.33938	N	0.004418	T	0.20820	0.0501	N	0.19112	0.55	0.80722	D	1	B	0.32693	0.38	B	0.32533	0.147	T	0.05037	-1.0910	10	0.38643	T	0.18	-1.2273	6.5512	0.22436	0.207:0.5962:0.1968:0.0	.	1029	Q4VCS5	AMOT_HUMAN	P	620;1029;797;1029	ENSP00000305557:A620P;ENSP00000361027:A1029P;ENSP00000361030:A797P;ENSP00000429013:A1029P	ENSP00000305557:A620P	A	-	1	0	AMOT	111908953	0.998000	0.40836	1.000000	0.80357	0.982000	0.71751	1.000000	0.29770	1.143000	0.42306	0.529000	0.55759	GCA		0.522	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112022297	C	G	112022297	3	3	100	1	0	0	0	0	1	0	0	0	582	710	25	5	177	5	AMOT	23	112022297	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	20148764	112022297	43248263	199	26853										
LONRF3	79836	hgsc.bcm.edu	37	chrX	118108844	118108844	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggcatcagcggcccaagtagAcatgggcccccacccaaagg	12	15	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:118108844A>G	ENST00000371628.3	+	1	132	c.101A>G	c.(100-102)gAc>gGc	p.D34G	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Missense_Mutation_p.D34G	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	34							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCCCAAGTAGACATGGGCCCC	0.652																																																0			X											21	19	20					X																	118108844		2197	4294	6491	117992872	SO:0001583	missense	79836			AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.101A>G	X.37:g.118108844A>G	ENSP00000360690:p.Asp34Gly		117992872	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	A	7.417	0.635942	0.14386	.	.	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628	D;D;T	0.81908	-1.55;-1.55;-1.28	4.79	2.34	0.29019	.	0.899845	0.09331	N	0.816843	T	0.73776	0.3630	L	0.36672	1.1	0.19575	N	0.999968	B;B	0.26809	0.16;0.099	B;B	0.25291	0.059;0.027	T	0.64972	-0.6281	10	0.62326	D	0.03	-9.6208	5.965	0.19320	0.6135:0.2493:0.0:0.1372	.	34;34	Q496Y0-2;Q496Y0	.;LONF3_HUMAN	G	34	ENSP00000360691:D34G;ENSP00000307732:D34G;ENSP00000360690:D34G	ENSP00000307732:D34G	D	+	2	0	LONRF3	117992872	0.001000	0.12720	0.004000	0.12327	0.020000	0.10135	0.864000	0.27926	1.774000	0.52232	0.430000	0.28490	GAC		0.652	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		G	118108844	A	G	118108844	3	3	100	1	0	0	0	0	1	0	0	0	8925	275	10	4	103	4	LONRF3	23	118108844	Missense_Mutation	SNP	A	TCGA-DC-6682-01A-11D-1826-10	6086547	118108844	37161716	200	26854										
UBE2A	7319	hgsc.bcm.edu	37	chrX	118716593	118716593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tctggacatacttcagaaccGttggagtccaacctatgatg	9	10	2	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:118716593G>A	ENST00000371558.2	+	5	458	c.284G>A	c.(283-285)cGt>cAt	p.R95H	UBE2A_ENST00000371569.5_Missense_Mutation_p.R20H|UBE2A_ENST00000346330.3_Missense_Mutation_p.R65H	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	95					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						CTTCAGAACCGTTGGAGTCCA	0.338								Rad6 pathway																																								0			X											208	185	193					X																	118716593		2203	4300	6503	118600621	SO:0001583	missense	7319			AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"Ubiquitin-conjugating enzymes E2"	12472	protein-coding gene	gene with protein product		312180	"ubiquitin-conjugating enzyme E2A (RAD6 homolog)"			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.284G>A	X.37:g.118716593G>A	ENSP00000360613:p.Arg95His		118600621	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Missense_Mutation	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.345104	0.61073	.	.	ENSG00000077721	ENST00000371558;ENST00000346330;ENST00000371569	T;T;T	0.72505	-0.66;-0.66;-0.66	5.85	4.99	0.66335	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	L	0.52266	1.64	0.80722	D	1	B;B	0.15473	0.013;0.002	B;B	0.17098	0.017;0.009	T	0.62732	-0.6792	10	0.56958	D	0.05	-1.5311	13.1282	0.59368	0.078:0.0:0.922:0.0	.	65;95	A6NGR2;P49459	.;UBE2A_HUMAN	H	95;65;20	ENSP00000360613:R95H;ENSP00000335027:R65H;ENSP00000360624:R20H	ENSP00000335027:R65H	R	+	2	0	UBE2A	118600621	1.000000	0.71417	0.985000	0.45067	0.937000	0.57800	9.858000	0.99539	1.235000	0.43724	-0.192000	0.12808	CGT		0.338	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336		A	118716593	G	A	118716593	3	1	100	1	0	0	0	0	1	0	0	0	16884	1145	40	1	302	1	UBE2A	23	118716593	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	607749	118716593	36553967	201	26855										
ZNF75D	7626	hgsc.bcm.edu	37	chrX	134421516	134421516	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tcctgacacttaaaaggtttCtcccctgtggggcctttccc	8	14	1	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:134421516C>G	ENST00000370766.3	-	7	3795	c.1086G>C	c.(1084-1086)gaG>gaC	p.E362D	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Missense_Mutation_p.E267D	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	362					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TAAAAGGTTTCTCCCCTGTGG	0.418																																																0			X											55	55	55					X																	134421516		2203	4298	6501	134249182	SO:0001583	missense	7626			S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"Zinc fingers, C2H2-type", "-", "-", "-"	13145	protein-coding gene	gene with protein product		314997	"zinc finger protein 75 (D8C6)"	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.1086G>C	X.37:g.134421516C>G	ENSP00000359802:p.Glu362Asp		134249182	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Missense_Mutation	SNP	ENST00000370766.3	37	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920730	0.33908	.	.	ENSG00000186376	ENST00000370766;ENST00000370764	T;T	0.01034	5.42;5.42	3.1	2.21	0.28008	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.219586	0.23176	N	0.051069	T	0.01061	0.0035	L	0.35723	1.085	0.24988	N	0.99155	B;B	0.14438	0.01;0.01	B;B	0.21546	0.035;0.021	T	0.44097	-0.9350	10	0.45353	T	0.12	.	8.7237	0.34456	0.2277:0.7723:0.0:0.0	.	362;267	P51815;A6NK62	ZN75D_HUMAN;.	D	362;267	ENSP00000359802:E362D;ENSP00000359800:E267D	ENSP00000359800:E267D	E	-	3	2	ZNF75D	134249182	0.974000	0.33945	0.018000	0.16275	0.281000	0.26958	0.135000	0.15952	0.675000	0.31264	0.422000	0.28245	GAG		0.418	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131		G	134421516	C	G	134421516	3	3	100	1	0	0	0	0	1	0	0	0	18173	912	32	5	450	5	ZNF75D	23	134421516	Missense_Mutation	SNP	C	TCGA-DC-6682-01A-11D-1826-10	15704923	134421516	20849044	202	26856										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153032489	153032489	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	cgaggcacactctatgtcggCgcagtgaaccgcctcttcca	10	15	2	1			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:153032489C>A	ENST00000361971.5	+	3	321	c.207C>A	c.(205-207)ggC>ggA	p.G69G	PLXNB3_ENST00000538282.1_Intron|U52111.14_ENST00000434284.1_RNA|U52111.14_ENST00000416854.1_RNA|PLXNB3_ENST00000538966.1_Silent_p.G92G|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Intron	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	69	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	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)					TCTATGTCGGCGCAGTGAACC	0.642																																																0			X											46	39	42					X																	153032489		2202	4300	6502	152685683	SO:0001819	synonymous_variant	5365			AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.207C>A	X.37:g.153032489C>A			152685683	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1																																																																																				0.642	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153032489	C	A	153032489	2	1	100	1	0	0	0	0	0	0	0	1	12156	755	27	2		2	PLXNB3	23	153032489	Silent	SNP	C	TCGA-DC-6682-01A-11D-1826-10	18610973	153032489	2238071	203	26857										
TAZ	6901	hgsc.bcm.edu	37	chrX	153648064	153648064	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	ggaaagtgaacatgagttccGaattcctgcgtttcaagtgg	12	7	1	2	rs375663114		TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:153648064G>A	ENST00000350743.4	+	6	761	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	TAZ_ENST00000299328.5_Missense_Mutation_p.E188K|TAZ_ENST00000369776.4_Intron|TAZ_ENST00000369790.4_Intron|TAZ_ENST00000351413.4_Intron|TAZ_ENST00000475699.1_Missense_Mutation_p.E161K	NM_181311.2	NP_851828.1	Q9GZV5	WWTR1_HUMAN	tafazzin	0					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			lung(1)	1	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CATGAGTTCCGAATTCCTGCG	0.647																																																0			X	GRCh37	CM022463	TAZ	M			LYS/GLU,LYS/GLU,,	1,3834		0,1,1631,571	82	69	73		562,472,,	5	0.9	X		73	0,6728		0,0,2428,1872	no	missense,missense,intron,intron	TAZ	NM_000116.3,NM_181311.2,NM_181312.2,NM_181313.2	56,56,,	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	probably-damaging,probably-damaging,,	188/293,158/263,,	153648064	1,10562	2203	4300	6503	153301258	SO:0001583	missense	25937			X92762	CCDS14748.1, CCDS14749.1, CCDS14750.1, CCDS35450.1	Xq28	2014-09-17	2008-07-29		ENSG00000102125	ENSG00000102125			11577	protein-coding gene	gene with protein product	"Barth syndrome"	300394	"endocardial fibroelastosis 2", "cardiomyopathy, dilated 3A (X-linked)"	CMD3A, EFE2, EFE		8042670	Standard	NM_000116		Approved	BTHS, XAP-2, G4.5	uc004fkx.3	Q16635	OTTHUMG00000033190	ENST00000350743.4:c.472G>A	X.37:g.153648064G>A	ENSP00000338891:p.Glu158Lys		153301258	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000350743.4	37	CCDS14749.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061804	0.76187	2.61E-4	0.0	ENSG00000102125	ENST00000299328;ENST00000350743;ENST00000454722;ENST00000439735;ENST00000475699	D;D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36;-3.19	5.04	5.04	0.67666	Phospholipid/glycerol acyltransferase (2);	0.112510	0.64402	D	0.000020	D	0.97235	0.9096	L	0.43646	1.37	0.80722	D	1	D;D	0.89917	0.963;1.0	B;D	0.81914	0.182;0.995	D	0.96538	0.9398	10	0.30078	T	0.28	.	14.8628	0.70394	0.0:0.0:1.0:0.0	.	158;188	Q16635-3;Q16635	.;TAZ_HUMAN	K	188;158;176;157;161	ENSP00000299328:E188K;ENSP00000338891:E158K;ENSP00000397388:E176K;ENSP00000398193:E157K;ENSP00000419854:E161K	ENSP00000299328:E188K	E	+	1	0	TAZ	153301258	1.000000	0.71417	0.919000	0.36401	0.520000	0.34377	6.323000	0.72891	2.093000	0.63338	0.525000	0.51046	GAA		0.647	TAZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080939.1			A	153648064	G	A	153648064	3	1	100	1	0	0	0	0	1	0	0	0	15635	1059	37	1	588	1	TAZ	23	153648064	Missense_Mutation	SNP	G	TCGA-DC-6682-01A-11D-1826-10	615575	153648064	1622496	204	26858										
MPP1	4354	hgsc.bcm.edu	37	chrX	154009975	154009975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0443349753694581	9	1	0.638144550016014	3.21435773341399	0.388833596783951	1	1	0	tgccttggtagctgccaaacTccaagaactcattggcagag	10	11	1	2			TCGA-DC-6682-01A-11D-1826-10	TCGA-DC-6682-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	d46cd6df-41f9-4872-9b7a-0dd025046a69	0e685c06-968a-45dd-90b0-ccd2ee41e816	g.chrX:154009975T>C	ENST00000369534.3	-	10	1196	c.1049A>G	c.(1048-1050)gAg>gGg	p.E350G	MPP1_ENST00000413259.3_Missense_Mutation_p.E320G|MPP1_ENST00000462825.1_5'Flank|MPP1_ENST00000393531.1_Missense_Mutation_p.E330G	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	350	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|Interaction with MPP5.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCTGCCAAACTCCAAGAACTC	0.488																																																0			X											346	248	281					X																	154009975		2203	4300	6503	153663169	SO:0001583	missense	9585				CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.1049A>G	X.37:g.154009975T>C	ENSP00000358547:p.Glu350Gly		153663169	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Missense_Mutation	SNP	ENST00000369534.3	37	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.878344	0.72294	.	.	ENSG00000130830	ENST00000369534;ENST00000413259;ENST00000393531	T;T;T	0.71934	-0.61;-0.61;-0.61	5.39	5.39	0.77823	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.85682	D	0.000000	D	0.89962	0.6867	H	0.98542	4.26	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.93261	0.6643	10	0.87932	D	0	.	13.2369	0.59974	0.0:0.0:0.0:1.0	.	333;320;330;350	B4E325;B4DZV5;G3XAI1;Q00013	.;.;.;EM55_HUMAN	G	350;320;330	ENSP00000358547:E350G;ENSP00000400155:E320G;ENSP00000377165:E330G	ENSP00000358547:E350G	E	-	2	0	MPP1	153663169	1.000000	0.71417	1.000000	0.80357	0.453000	0.32348	7.857000	0.86963	1.803000	0.52742	0.481000	0.45027	GAG		0.488	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		C	154009975	T	C	154009975	3	2	100	1	0	0	0	0	1	0	0	0	9763	1551	54	4	363	4	MPP1	23	154009975	Missense_Mutation	SNP	T	TCGA-DC-6682-01A-11D-1826-10	361911	154009975	1260585	205	26859										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117146492	117146492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atcccggtctagccacatgaTattgctgcggcggttctgcc	11	13	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:117146492T>C	ENST00000369486.3	-	6	2143	c.1378A>G	c.(1378-1380)Atc>Gtc	p.I460V	IGSF3_ENST00000318837.6_Missense_Mutation_p.I480V|IGSF3_ENST00000369483.1_Missense_Mutation_p.I480V	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	460	Ig-like C2-type 4.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	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)		AGCCACATGATATTGCTGCGG	0.647																																																0			1											71	68	69					1																	117146492		2202	4298	6500	116948015	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1378A>G	1.37:g.117146492T>C	ENSP00000358498:p.Ile460Val		116948015	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	2.598	-0.293562	0.05568	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.68765	-0.35;-0.35;-0.35	5.27	3.92	0.45320	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.201085	0.44688	N	0.000431	T	0.20981	0.0505	L	0.27053	0.805	0.30404	N	0.779707	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.13407	0.005;0.005;0.009	T	0.16897	-1.0387	10	0.02654	T	1	-35.2255	5.9085	0.19014	0.0:0.2589:0.0:0.7411	.	480;460;480	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	V	460;480;480	ENSP00000358498:I460V;ENSP00000358495:I480V;ENSP00000321184:I480V	ENSP00000321184:I480V	I	-	1	0	IGSF3	116948015	0.989000	0.36119	0.992000	0.48379	0.981000	0.71138	2.080000	0.41586	0.816000	0.34421	0.455000	0.32223	ATC		0.647	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117146492	T	C	117146492	3	2	101	1	0	0	0	0	1	0	0	0	7622	1406	49	4	2230	4	IGSF3	1	117146492	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10		117146492	132104129	1	26860										
S100A2	6273	hgsc.bcm.edu	37	chr1	153533948	153533948	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gggcagccctggaagaagtcAttgcacatgacagtgatgag	14	8	1	4			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:153533948A>G	ENST00000368708.3	-	3	633	c.261T>C	c.(259-261)aaT>aaC	p.N87N	S100A2_ENST00000368707.4_3'UTR|S100A2_ENST00000368709.1_Silent_p.N87N|S100A2_ENST00000487430.2_Silent_p.N87N|S100A2_ENST00000368710.1_Silent_p.N87N|S100A2_ENST00000497140.1_Silent_p.N54N	NM_005978.3	NP_005969.1	P29034	S10A2_HUMAN	S100 calcium binding protein A2	88					endothelial cell migration (GO:0043542)		calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Olopatadine(DB00768)	GGAAGAAGTCATTGCACATGA	0.532																																																0			1											191	183	185					1																	153533948		2203	4300	6503	151800572	SO:0001819	synonymous_variant	6273			BC002829	CCDS1044.1	1q21	2013-01-10	2001-11-28		ENSG00000196754	ENSG00000196754		"S100 calcium binding proteins", "EF-hand domain containing"	10492	protein-coding gene	gene with protein product		176993	"S100 calcium-binding protein A2"	S100L		8341667	Standard	NM_005978		Approved	CAN19	uc001fcb.3	P29034	OTTHUMG00000035031	ENST00000368708.3:c.261T>C	1.37:g.153533948A>G			151800572	O00266|Q3KRB9|Q5RHS8|Q9BU83	Silent	SNP	ENST00000368708.3	37	CCDS1044.1																																																																																				0.532	S100A2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084789.1	NM_005978		G	153533948	A	G	153533948	2	3	101	1	0	0	0	0	0	0	0	1	13815	214	8	4		4	S100A2	1	153533948	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	36387456	153533948	95716673	2	26861										
ACBD6	84320	hgsc.bcm.edu	37	chr1	180366655	180366655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tctttatcactcttacctgaCagttaatgtcagctctatgt	5	10	5	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:180366655C>T	ENST00000367595.3	-	6	1346	c.659G>A	c.(658-660)tGt>tAt	p.C220Y	ACBD6_ENST00000475338.2_5'UTR	NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	220						cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)		ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						TCTTACCTGACAGTTAATGTC	0.363																																																0			1											154	160	158					1																	180366655		2203	4300	6503	178633278	SO:0001583	missense	84320			BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847			"Ankyrin repeat domain containing"	23339	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 6"			18268358	Standard	NM_032360		Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.659G>A	1.37:g.180366655C>T	ENSP00000356567:p.Cys220Tyr		178633278		Missense_Mutation	SNP	ENST00000367595.3	37	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168997	0.38315	.	.	ENSG00000135847	ENST00000367595	T	0.64085	-0.08	5.67	4.75	0.60458	Ankyrin repeat-containing domain (4);	0.330869	0.37053	N	0.002262	T	0.61211	0.2329	L	0.28694	0.88	0.30074	N	0.809823	D	0.56287	0.975	P	0.51974	0.686	T	0.63919	-0.6528	10	0.54805	T	0.06	-4.4325	14.6262	0.68624	0.0:0.8544:0.1456:0.0	.	220	Q9BR61	ACBD6_HUMAN	Y	220	ENSP00000356567:C220Y	ENSP00000356567:C220Y	C	-	2	0	ACBD6	178633278	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.431000	0.34925	1.379000	0.46325	0.467000	0.42956	TGT		0.363	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	NM_032360		T	180366655	C	T	180366655	3	4	101	1	0	0	0	0	1	0	0	0	126	478	17	3	201	3	ACBD6	1	180366655	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	26832707	180366655	68883966	3	26862										
LGR6	59352	hgsc.bcm.edu	37	chr1	202273693	202273693	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tgttctccctgcaggaccctGacccgcgcaggcatccggct	11	17	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:202273693G>T	ENST00000367278.3	+	11	1094	c.1005G>T	c.(1003-1005)ctG>ctT	p.L335L	LGR6_ENST00000439764.2_Silent_p.L196L|LGR6_ENST00000308543.3_3'UTR|LGR6_ENST00000255432.7_Silent_p.L283L	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	335					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						GCAGGACCCTGACCCGCGCAG	0.632																																																0			1											39	42	41					1																	202273693		2203	4300	6503	200540316	SO:0001819	synonymous_variant	59352			AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1005G>T	1.37:g.202273693G>T			200540316	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																				0.632	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		T	202273693	G	T	202273693	2	4	101	1	0	0	0	0	0	0	0	1	8781	1277	45	2		2	LGR6	1	202273693	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	21907038	202273693	46976928	4	26863										
RYR2	6262	hgsc.bcm.edu	37	chr1	237666611	237666611	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tacgctttctgcttggagggCgacatggagaattcaaattt	11	7	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:237666611C>T	ENST00000366574.2	+	22	2736	c.2419C>T	c.(2419-2421)Cga>Tga	p.R807*	RYR2_ENST00000360064.6_Nonsense_Mutation_p.R805*|RYR2_ENST00000542537.1_Nonsense_Mutation_p.R791*	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	807	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GCTTGGAGGGCGACATGGAGA	0.403																																																0			1											67	63	64					1																	237666611		1905	4115	6020	235733234	SO:0001587	stop_gained	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2419C>T	1.37:g.237666611C>T	ENSP00000355533:p.Arg807*		235733234	Q15411|Q546N8|Q5T3P2	Nonsense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	40	8.491584	0.98834	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	.	.	.	5.73	0.569	0.17340	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6868	0.85310	0.3242:0.6758:0.0:0.0	.	.	.	.	X	807;805;791	.	ENSP00000353174:R805X	R	+	1	2	RYR2	235733234	0.997000	0.39634	0.997000	0.53966	0.978000	0.69477	3.518000	0.53451	0.242000	0.21303	0.655000	0.94253	CGA		0.403	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237666611	C	T	237666611	4	4	101	1	0	0	0	0	0	1	0	0	13806	760	27	1	2505	1	RYR2	1	237666611	Nonsense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	35392918	237666611	11584010	5	26864										
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343348	248343348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tccttggaatcttcaatcacAgcccaccacacacgttcctc	4	17	3	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr1:248343348A>G	ENST00000359682.2	+	1	61	c.61A>G	c.(61-63)Agc>Ggc	p.S21G		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CTTCAATCACAGCCCACCACA	0.468																																																0			1											240	235	237					1																	248343348		2203	4300	6503	246409971	SO:0001583	missense	391194			AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.61A>G	1.37:g.248343348A>G	ENSP00000352710:p.Ser21Gly		246409971	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	a	9.703	1.154939	0.21371	.	.	ENSG00000198601	ENST00000359682	T	0.02974	4.09	0.855	0.855	0.19013	.	0.215514	0.22966	U	0.053495	T	0.02610	0.0079	L	0.42632	1.34	0.09310	N	1	P	0.45672	0.864	B	0.41332	0.354	T	0.43458	-0.9390	10	0.62326	D	0.03	.	2.7475	0.05271	0.5408:0.2718:0.1873:0.0	.	21	Q96R28	OR2M2_HUMAN	G	21	ENSP00000352710:S21G	ENSP00000352710:S21G	S	+	1	0	OR2M2	246409971	0.000000	0.05858	0.034000	0.17996	0.248000	0.25809	0.054000	0.14205	0.651000	0.30788	0.248000	0.18094	AGC		0.468	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		G	248343348	A	G	248343348	3	3	101	1	0	0	0	0	1	0	0	0	11041	188	7	4	63	4	OR2M2	1	248343348	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	10676737	248343348	907273	6	26865										
TSSC1	7260	hgsc.bcm.edu	37	chr2	3358401	3358401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	agtttgaggtgttaaggcacGtgcctgcaggagggaagaaa	16	5	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:3358401G>A	ENST00000382125.4	-	2	238	c.46C>T	c.(46-48)Cgt>Tgt	p.R16C	TSSC1_ENST00000443925.2_Missense_Mutation_p.R16C|TSSC1_ENST00000398659.4_Missense_Mutation_p.R16C	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	16										breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		GTTAAGGCACGTGCCTGCAGG	0.363																																					Colon(140;1261 1762 4183 34270 49743)											0			2											81	79	80					2																	3358401		2203	4300	6503	3337408	SO:0001583	missense	7260			AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"WD repeat domain containing"	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.46C>T	2.37:g.3358401G>A	ENSP00000371559:p.Arg16Cys		3337408	D6W4Y1|O43179|Q53S19|Q53SG2	Missense_Mutation	SNP	ENST00000382125.4	37	CCDS1651.1	.	.	.	.	.	.	.	.	.	.	g	18.32	3.598686	0.66332	.	.	ENSG00000032389	ENST00000382125;ENST00000398659;ENST00000443925;ENST00000444776	D;D	0.97404	-3.52;-4.37	4.45	3.56	0.40772	.	0.000000	0.85682	D	0.000000	D	0.98273	0.9428	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98883	1.0770	10	0.87932	D	0	-0.4511	12.5121	0.56011	0.0:0.1696:0.8304:0.0	.	16	Q53HC9	TSSC1_HUMAN	C	16	ENSP00000371559:R16C;ENSP00000381652:R16C	ENSP00000371559:R16C	R	-	1	0	TSSC1	3337408	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	4.591000	0.61019	1.217000	0.43442	0.558000	0.71614	CGT		0.363	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		A	3358401	G	A	3358401	3	1	101	1	0	0	0	0	1	0	0	0	16706	1145	40	1	1149	1	TSSC1	2	3358401	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10		3358401	239840972	7	26866										
APOB	338	hgsc.bcm.edu	37	chr2	21235160	21235160	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttatctggttggtgccttggAggtaggaggagttaaacctc	14	6	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:21235160A>G	ENST00000233242.1	-	26	4707	c.4580T>C	c.(4579-4581)cTc>cCc	p.L1527P		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1527					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.L1527H(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTGCCTTGGAGGTAGGAGGA	0.488																																																1	Substitution - Missense(1)	ovary(1)	2											121	123	123					2																	21235160		2203	4300	6503	21088665	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4580T>C	2.37:g.21235160A>G	ENSP00000233242:p.Leu1527Pro		21088665	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286495	0.80803	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01076	5.37	5.88	5.88	0.94601	.	1.077840	0.07220	N	0.860701	T	0.01661	0.0053	L	0.29908	0.895	0.80722	D	1	B	0.34372	0.451	B	0.26517	0.07	T	0.65751	-0.6092	10	0.87932	D	0	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	1527	P04114	APOB_HUMAN	P	1527	ENSP00000233242:L1527P	ENSP00000233242:L1527P	L	-	2	0	APOB	21088665	1.000000	0.71417	0.908000	0.35775	0.994000	0.84299	8.842000	0.92136	2.246000	0.74042	0.533000	0.62120	CTC		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21235160	A	G	21235160	3	3	101	1	0	0	0	0	1	0	0	0	785	304	11	4	9127	4	APOB	2	21235160	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	17876759	21235160	221964213	8	26867										
CCT4	10575	hgsc.bcm.edu	37	chr2	62099332	62099332	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ctagtgtagatggaatgaccTccatagcatctgcaaaagca	9	9	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:62099332T>C	ENST00000394440.3	-	12	1672	c.1376A>G	c.(1375-1377)gAg>gGg	p.E459G	AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544185.1_Missense_Mutation_p.E309G|CCT4_ENST00000544079.1_Missense_Mutation_p.E429G|CCT4_ENST00000461540.2_Intron|CCT4_ENST00000538252.1_Missense_Mutation_p.E403G	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	459					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	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)			TGGAATGACCTCCATAGCATC	0.468																																																0			2											106	100	102					2																	62099332		2203	4300	6503	61952836	SO:0001583	missense	10575				CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.1376A>G	2.37:g.62099332T>C	ENSP00000377958:p.Glu459Gly		61952836	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	37	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.916421	0.92249	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000544185;ENST00000538252	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.94912	0.8355	H	0.99838	4.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97374	0.9978	10	0.87932	D	0	-19.2426	15.7401	0.77887	0.0:0.0:0.0:1.0	.	429;459	F5H5W3;P50991	.;TCPD_HUMAN	G	459;429;309;403	ENSP00000377958:E459G;ENSP00000443061:E429G;ENSP00000443451:E309G;ENSP00000442174:E403G	ENSP00000377958:E459G	E	-	2	0	CCT4	61952836	1.000000	0.71417	0.983000	0.44433	0.998000	0.95712	7.967000	0.87967	2.246000	0.74042	0.533000	0.62120	GAG		0.468	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62099332	T	C	62099332	3	2	101	1	0	0	0	0	1	0	0	0	2961	1551	54	4	255	4	CCT4	2	62099332	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	40864172	62099332	181100041	9	26868										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70064744	70064744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tttgaatggtgaaaacagtgAcattaagatttgtgctctag	10	4	1	4			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:70064744A>G	ENST00000282570.3	+	2	577	c.326A>G	c.(325-327)gAc>gGc	p.D109G	GMCL1_ENST00000468386.2_3'UTR	NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	109	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)		p.D109G(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						GAAAACAGTGACATTAAGATT	0.259																																																1	Substitution - Missense(1)	ovary(1)	2											42	44	44					2																	70064744		2192	4291	6483	69918248	SO:0001583	missense	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.326A>G	2.37:g.70064744A>G	ENSP00000282570:p.Asp109Gly		69918248	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	37	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281341	0.80692	.	.	ENSG00000087338	ENST00000282570	D	0.91351	-2.83	4.92	4.92	0.64577	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.96750	0.8939	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97655	1.0157	10	0.87932	D	0	-32.076	12.832	0.57750	1.0:0.0:0.0:0.0	.	109	Q96IK5	GMCL1_HUMAN	G	109	ENSP00000282570:D109G	ENSP00000282570:D109G	D	+	2	0	GMCL1	69918248	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.131000	0.89601	2.181000	0.69327	0.455000	0.32223	GAC		0.259	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70064744	A	G	70064744	3	3	101	1	0	0	0	0	1	0	0	0	6505	275	10	4	332	4	GMCL1	2	70064744	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	7965412	70064744	173134629	10	26869										
TSGA10	80705	hgsc.bcm.edu	37	chr2	99651815	99651815	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	agcggacactttttcaaactGaaccttctgaagctcctctt	6	12	3	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:99651815G>T	ENST00000393483.3	-	17	2336	c.1492C>A	c.(1492-1494)Cag>Aag	p.Q498K	TSGA10_ENST00000355053.4_Missense_Mutation_p.Q498K|TSGA10_ENST00000539964.1_Missense_Mutation_p.Q498K|TSGA10_ENST00000410001.1_Missense_Mutation_p.Q498K	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	498					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						TTTTCAAACTGAACCTTCTGA	0.378																																																0			2											66	67	66					2																	99651815		2203	4300	6503	99018247	SO:0001583	missense	80705			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.1492C>A	2.37:g.99651815G>T	ENSP00000377123:p.Gln498Lys		99018247	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	G	8.173	0.792210	0.16258	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000393482	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	5.13	5.13	0.70059	.	0.155039	0.45361	D	0.000376	T	0.07143	0.0181	N	0.14661	0.345	0.80722	D	1	B	0.20988	0.05	B	0.12837	0.008	T	0.11641	-1.0579	10	0.05525	T	0.97	-11.7912	12.7334	0.57210	0.0:0.0:0.8356:0.1643	.	498	Q9BZW7	TSG10_HUMAN	K	498	ENSP00000377123:Q498K;ENSP00000386956:Q498K;ENSP00000347161:Q498K;ENSP00000444419:Q498K;ENSP00000377122:Q498K	ENSP00000347161:Q498K	Q	-	1	0	TSGA10	99018247	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.186000	0.58337	2.827000	0.97445	0.655000	0.94253	CAG		0.378	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		T	99651815	G	T	99651815	3	4	101	1	0	0	0	0	1	0	0	0	16657	1299	45	2	624	2	TSGA10	2	99651815	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	29587071	99651815	143547558	11	26870										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125671767	125671767	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cacatcgtacgagccagatgAaggagaaggaatatccagaa	11	8	0	4			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:125671767A>G	ENST00000431078.1	+	24	4187	c.3823A>G	c.(3823-3825)Aag>Gag	p.K1275E		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1275					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GAGCCAGATGAAGGAGAAGGA	0.438																																																0			2											149	144	145					2																	125671767		1940	4157	6097	125388237	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3823A>G	2.37:g.125671767A>G	ENSP00000399013:p.Lys1275Glu		125388237	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.628181	0.46944	.	.	ENSG00000155052	ENST00000431078	D	0.92699	-3.09	6.14	4.98	0.66077	.	0.000000	0.52532	D	0.000080	D	0.96327	0.8802	M	0.90309	3.105	0.49915	D	0.999837	D	0.69078	0.997	D	0.75020	0.985	D	0.96219	0.9159	10	0.62326	D	0.03	.	12.2077	0.54361	0.8724:0.0:0.0:0.1276	.	1275	Q8WYK1	CNTP5_HUMAN	E	1275	ENSP00000399013:K1275E	ENSP00000399013:K1275E	K	+	1	0	CNTNAP5	125388237	1.000000	0.71417	1.000000	0.80357	0.309000	0.27889	6.638000	0.74309	1.125000	0.41998	-0.354000	0.07668	AAG		0.438	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125671767	A	G	125671767	3	3	101	1	0	0	0	0	1	0	0	0	3656	247	9	4	3917	4	CNTNAP5	2	125671767	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	26019952	125671767	117527606	12	26871										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128072395	128072395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	caccctccagaatctgacggGtgtatttcctagtcacattc	7	13	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:128072395G>A	ENST00000409947.1	-	15	1673	c.1391C>T	c.(1390-1392)aCc>aTc	p.T464I	MAP3K2_ENST00000344908.5_Missense_Mutation_p.T464I|RNU6-1147P_ENST00000363380.1_RNA			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	464	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.T465S(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	AATCTGACGGGTGTATTTCCT	0.343																																																1	Substitution - Missense(1)	ovary(1)	2											99	95	96					2																	128072395		1832	4074	5906	127788865	SO:0001583	missense	10746			AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1391C>T	2.37:g.128072395G>A	ENSP00000387246:p.Thr464Ile		127788865	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	37	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486083	0.84854	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.63417	-0.04;-0.04	5.22	5.22	0.72569	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.045018	0.85682	D	0.000000	T	0.61739	0.2371	N	0.20483	0.58	0.80722	D	1	P	0.40681	0.727	P	0.50570	0.644	T	0.63853	-0.6543	10	0.46703	T	0.11	.	18.7661	0.91873	0.0:0.0:1.0:0.0	.	464	Q9Y2U5	M3K2_HUMAN	I	464	ENSP00000387246:T464I;ENSP00000343463:T464I	ENSP00000343463:T464I	T	-	2	0	MAP3K2	127788865	1.000000	0.71417	0.995000	0.50966	0.929000	0.56500	7.844000	0.86867	2.452000	0.82932	0.591000	0.81541	ACC		0.343	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		A	128072395	G	A	128072395	3	1	101	1	0	0	0	0	1	0	0	0	9280	1261	44	3	480	3	MAP3K2	2	128072395	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	2400628	128072395	115126978	13	26872										
UGGT1	56886	hgsc.bcm.edu	37	chr2	128886624	128886624	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ctgtttgatgtgttgaggaaTgaagctcgggtaatggaggg	17	3	0	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:128886624T>C	ENST00000259253.6	+	13	1295	c.1248T>C	c.(1246-1248)aaT>aaC	p.N416N	UGGT1_ENST00000375990.3_Silent_p.N392N	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	416					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TGTTGAGGAATGAAGCTCGGG	0.383																																																0			2											123	127	125					2																	128886624		2203	4300	6503	128603094	SO:0001819	synonymous_variant	0			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1248T>C	2.37:g.128886624T>C			128603094	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																				0.383	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		C	128886624	T	C	128886624	2	2	101	1	0	0	0	0	0	0	0	1	16981	1461	51	4		4	UGGT1	2	128886624	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	814229	128886624	114312749	14	26873										
TTN	7273	hgsc.bcm.edu	37	chr2	179605073	179605073	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttttacctccttctgtgcatGagtgttctgaagggactagg	11	8	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:179605073G>C	ENST00000591111.1	-	46	12160	c.11936C>G	c.(11935-11937)tCa>tGa	p.S3979*	TTN_ENST00000342175.6_Nonsense_Mutation_p.S4125*|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.S3933*|TTN_ENST00000589042.1_Nonsense_Mutation_p.S4296*|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.S4058*|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGTGCATGAGTGTTCTGA	0.463																																																0			2											65	63	63					2																	179605073		1907	4121	6028	179313318	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11936C>G	2.37:g.179605073G>C	ENSP00000465570:p.Ser3979*		179313318	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	53	20.392664	0.99930	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.65	-1.25	0.09405	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.5059	0.50466	0.4675:0.0:0.5325:0.0	.	.	.	.	X	3933;4125;4058;3933	.	ENSP00000340554:S4125X	S	-	2	0	TTN	179313318	0.000000	0.05858	0.026000	0.17262	0.651000	0.38670	0.445000	0.21677	-0.134000	0.11516	0.655000	0.94253	TCA		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179605073	G	C	179605073	4	2	101	1	0	0	0	0	0	1	0	0	16775	1294	45	5	91902	5	TTN	2	179605073	Nonsense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	50718449	179605073	63594300	15	26874										
DNPEP	23549	hgsc.bcm.edu	37	chr2	220250689	220250689	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcagccctgccccagtctcaCagatgcatctctgtgttggg	11	14	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:220250689C>T	ENST00000273075.4	-	6	811		c.e6+1		DNPEP_ENST00000373972.1_Splice_Site|DNPEP_ENST00000523282.1_Splice_Site|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase						peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCAGTCTCACAGATGCATCT	0.537																																																0			2											67	75	73					2																	220250689		2033	4206	6239	219958933	SO:0001630	splice_region_variant	23549				CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.590+1G>A	2.37:g.220250689C>T			219958933	Q9BW44|Q9NUV5	Splice_Site	SNP	ENST00000273075.4	37	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003174	0.74932	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339	.	.	.	4.33	4.33	0.51752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3495	0.66691	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNPEP	219958933	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.222000	0.78025	2.124000	0.65301	0.561000	0.74099	.		0.537	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	Intron	T	220250689	C	T	220250689	5	4	101	1	0	0	0	0	0	0	1	0	4690	492	17	3	906	3	DNPEP	2	220250689	Splice_Site	SNP	C	TCGA-DC-6683-01A-11D-1826-10	40645616	220250689	22948684	16	26875										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882373	228882373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cgccactcagtaaccgattcCggggatagccctgcgcctgc	11	16	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:228882373C>T	ENST00000392056.3	-	7	3243	c.3197G>A	c.(3196-3198)cGg>cAg	p.R1066Q	SPHKAP_ENST00000344657.5_Missense_Mutation_p.R1066Q	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1066						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.R1066L(2)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		TAACCGATTCCGGGGATAGCC	0.562																																																2	Substitution - Missense(2)	lung(2)	2											50	52	52					2																	228882373		2203	4300	6503	228590617	SO:0001583	missense	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3197G>A	2.37:g.228882373C>T	ENSP00000375909:p.Arg1066Gln		228590617	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069431	0.93950	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.20463	2.1;2.07	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	L	0.32530	0.975	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	T	0.01062	-1.1464	10	0.25751	T	0.34	.	19.6516	0.95815	0.0:1.0:0.0:0.0	.	97;1066;1066	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	Q	1066	ENSP00000375909:R1066Q;ENSP00000339886:R1066Q	ENSP00000339886:R1066Q	R	-	2	0	SPHKAP	228590617	1.000000	0.71417	0.694000	0.30210	0.879000	0.50718	4.404000	0.59735	2.894000	0.99253	0.655000	0.94253	CGG		0.562	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228882373	C	T	228882373	3	4	101	1	0	0	0	0	1	0	0	0	15087	652	23	1	1929	1	SPHKAP	2	228882373	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	8631684	228882373	14317000	17	26876										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233344869	233344869	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcgggcagccaggctcaccaCacggaacacttgtgggcagg	15	13	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr2:233344869C>A	ENST00000304546.1	-	18	2532	c.2322G>T	c.(2320-2322)gtG>gtT	p.V774V	ECEL1_ENST00000409941.1_Silent_p.V772V	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	774					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		AGGCTCACCACACGGAACACT	0.672																																																0			2											78	66	70					2																	233344869		2203	4300	6503	233053113	SO:0001819	synonymous_variant	9427			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.2322G>T	2.37:g.233344869C>A			233053113	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.672	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233344869	C	A	233344869	2	1	101	1	0	0	0	0	0	0	0	1	4902	465	17	2		2	ECEL1	2	233344869	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	4462496	233344869	9854504	18	26877										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9036107	9036107	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcccaccagtcctccgaggcGcggtggtacaggagcagcga	14	14	0	0	rs138152185		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:9036107G>A	ENST00000383836.3	-	19	2755	c.2328C>T	c.(2326-2328)cgC>cgT	p.R776R	SRGAP3_ENST00000360413.3_Silent_p.R752R	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	776	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CCTCCGAGGCGCGGTGGTACA	0.587			T	RAF1	pilocytic astrocytoma																																		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	0			3											77	77	77					3																	9036107		2203	4300	6503	9011107	SO:0001819	synonymous_variant	9901			AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2328C>T	3.37:g.9036107G>A			9011107	Q8IX13|Q8IZV8	Silent	SNP	ENST00000383836.3	37	CCDS2572.1																																																																																				0.587	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			A	9036107	G	A	9036107	2	1	101	1	0	0	0	0	0	0	0	1	15186	1074	38	1		1	SRGAP3	3	9036107	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10		9036107	188986323	19	26878										
VHL	7428	hgsc.bcm.edu	37	chr3	10188287	10188287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tgccatctctcaatgttgacGgacagcctatttttgccaat	7	11	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:10188287G>A	ENST00000256474.2	+	2	1270	c.430G>A	c.(430-432)Gga>Aga	p.G144R	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	144	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.G144*(3)|p.G144R(1)|p.Q145fs*30(1)|p.G144fs*29(1)|p.G144fs*14(1)|p.D143fs*29(1)|p.N141fs*30(1)|p.S139fs*12(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAATGTTGACGGACAGCCTAT	0.423		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	11	Deletion - Frameshift(6)|Substitution - Nonsense(3)|Insertion - Frameshift(1)|Substitution - Missense(1)	kidney(10)|endometrium(1)	3	GRCh37	CM982008	VHL	M							217	200	206					3																	10188287		2203	4300	6503	10163287	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.430G>A	3.37:g.10188287G>A	ENSP00000256474:p.Gly144Arg		10163287	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677013	0.88445	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99857	-7.22	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99708	0.9888	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97587	1.0114	10	0.33940	T	0.23	-0.306	16.3181	0.82935	0.0:0.0:1.0:0.0	.	144	P40337	VHL_HUMAN	R	144;62	ENSP00000256474:G144R	ENSP00000256474:G144R	G	+	1	0	VHL	10163287	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	5.083000	0.64456	2.530000	0.85305	0.563000	0.77884	GGA		0.423	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10188287	G	A	10188287	3	1	101	1	0	0	0	0	1	0	0	0	17202	1117	39	1	436	1	VHL	3	10188287	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	1152180	10188287	187834143	20	26879										
EFHB	151651	hgsc.bcm.edu	37	chr3	19947113	19947113	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	acagtataattaaacttacaTttgtagttcatggagccaat	6	6	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:19947113T>A	ENST00000295824.9	-	6	1578	c.1417A>T	c.(1417-1419)Atg>Ttg	p.M473L	EFHB_ENST00000344838.4_Splice_Site_p.M343L|EFHB_ENST00000498089.1_5'UTR	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	473							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TAAACTTACATTTGTAGTTCA	0.333																																																0			3											110	116	114					3																	19947113		2203	4300	6503	19922117	SO:0001630	splice_region_variant	151651			AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.1418+1A>T	3.37:g.19947113T>A			19922117	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	T	1.205	-0.631396	0.03584	.	.	ENSG00000163576	ENST00000295824;ENST00000344838;ENST00000389256;ENST00000440022	T;T;T;T	0.28666	1.94;1.97;2.24;1.6	4.83	3.58	0.41010	.	0.139348	0.50627	D	0.000111	T	0.25158	0.0611	L	0.52573	1.65	0.34572	D	0.713495	B;B	0.16603	0.018;0.013	B;B	0.13407	0.009;0.002	T	0.23547	-1.0185	9	.	.	.	-11.919	9.3014	0.37847	0.0:0.0:0.1807:0.8193	.	343;473	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	L	473;343;473;210	ENSP00000295824:M473L;ENSP00000342263:M343L;ENSP00000373908:M473L;ENSP00000396778:M210L	.	M	-	1	0	EFHB	19922117	1.000000	0.71417	1.000000	0.80357	0.073000	0.16967	2.183000	0.42565	1.945000	0.56424	0.402000	0.26972	ATG		0.333	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	Missense_Mutation	A	19947113	T	A	19947113	5	1	101	1	0	0	0	0	0	0	1	0	4956	1507	52	5	1116	5	EFHB	3	19947113	Splice_Site	SNP	T	TCGA-DC-6683-01A-11D-1826-10	9758826	19947113	178075317	21	26880										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33855080	33855080	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	acatttacctggaaggatgcTttcgataaaggttcactttt	8	7	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:33855080T>C	ENST00000307296.3	+	3	671	c.294T>C	c.(292-294)gcT>gcC	p.A98A	PDCD6IP_ENST00000498147.1_3'UTR|PDCD6IP_ENST00000457054.2_Silent_p.A98A			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	98	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						GGAAGGATGCTTTCGATAAAG	0.318																																																0			3											161	165	164					3																	33855080		2203	4299	6502	33830084	SO:0001819	synonymous_variant	10015			BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.294T>C	3.37:g.33855080T>C			33830084	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	37	CCDS2660.1																																																																																				0.318	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			C	33855080	T	C	33855080	2	2	101	1	0	0	0	0	0	0	0	1	11655	1596	56	4		4	PDCD6IP	3	33855080	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	13907967	33855080	164167350	22	26881										
PCBP4	57060	hgsc.bcm.edu	37	chr3	51994283	51994283	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcagggatgacaaggcgcagGgtcactggaggcctggagac	18	9	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:51994283G>A	ENST00000461554.1	-	7	640	c.309C>T	c.(307-309)acC>acT	p.T103T	PCBP4_ENST00000322099.7_Silent_p.T103T|PCBP4_ENST00000471622.1_Silent_p.T103T|PCBP4_ENST00000395014.2_Silent_p.T69T|PCBP4_ENST00000395013.3_Silent_p.T26T|PCBP4_ENST00000355852.2_Silent_p.T103T|PCBP4_ENST00000484633.1_Silent_p.T103T|PCBP4_ENST00000428823.2_Silent_p.T103T|RP11-155D18.12_ENST00000488257.1_RNA	NM_001174100.1	NP_001167571.1	P57723	PCBP4_HUMAN	poly(rC) binding protein 4	103	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.					cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(2)|lung(2)|prostate(1)|stomach(1)	8				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAAGGCGCAGGGTCACTGGAG	0.582																																																0			3											46	46	46					3																	51994283		2203	4300	6503	51969323	SO:0001819	synonymous_variant	57060			AF176330	CCDS2839.1, CCDS2840.1, CCDS2840.2	3p21	2013-07-16	2001-11-28		ENSG00000090097	ENSG00000090097			8652	protein-coding gene	gene with protein product	"RNA binding protein MCG10", "LYST-interacting protein", "alphaCP-4 protein"	608503	"poly(rC)-binding protein 4"			10936052	Standard	NM_033008		Approved	MCG10, LIP4	uc003dch.2	P57723	OTTHUMG00000157366	ENST00000461554.1:c.309C>T	3.37:g.51994283G>A			51969323	Q96AH7	Silent	SNP	ENST00000461554.1	37	CCDS2839.1																																																																																				0.582	PCBP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348597.1	NM_020418		A	51994283	G	A	51994283	2	1	101	1	0	0	0	0	0	0	0	1	11534	1219	43	3		3	PCBP4	3	51994283	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	18139203	51994283	146028147	23	26882										
KIAA1524	57650	hgsc.bcm.edu	37	chr3	108271109	108271109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcaactcttttcttatctgtTctgttctgcttaattctttt	3	9	7	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:108271109T>C	ENST00000295746.8	-	20	2595	c.2519A>G	c.(2518-2520)gAa>gGa	p.E840G	KIAA1524_ENST00000491772.1_Missense_Mutation_p.E681G	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	840					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCTTATCTGTTCTGTTCTGCT	0.303																																																0			3											192	180	184					3																	108271109		2200	4298	6498	109753799	SO:0001583	missense	57650			AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.2519A>G	3.37:g.108271109T>C	ENSP00000295746:p.Glu840Gly		109753799	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164872	0.78339	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.31769	3.49;1.48	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.42675	0.1213	M	0.66939	2.045	0.58432	D	0.999991	P	0.51653	0.947	P	0.49477	0.612	T	0.47736	-0.9094	10	0.87932	D	0	-1.9254	14.5013	0.67724	0.0:0.0:0.0:1.0	.	840	Q8TCG1	CIP2A_HUMAN	G	681;840	ENSP00000419487:E681G;ENSP00000295746:E840G	ENSP00000295746:E840G	E	-	2	0	KIAA1524	109753799	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	6.819000	0.75262	1.816000	0.52996	0.455000	0.32223	GAA		0.303	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		C	108271109	T	C	108271109	3	2	101	1	0	0	0	0	1	0	0	0	8260	1783	62	4	206	4	KIAA1524	3	108271109	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	56276826	108271109	89751321	24	26883										
FOXL2	668	hgsc.bcm.edu	37	chr3	138664470	138664470	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gaatgcagcgcgccggtcttGctgtcgtggtcccagtaaga	14	11	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:138664470G>A	ENST00000330315.3	-	1	1512	c.1095C>T	c.(1093-1095)agC>agT	p.S365S	C3orf72_ENST00000383165.3_5'Flank|RP11-548O1.3_ENST00000495287.1_lincRNA	NM_023067.3	NP_075555.1	P58012	FOXL2_HUMAN	forkhead box L2	365					apoptotic DNA fragmentation (GO:0006309)|cell differentiation (GO:0030154)|embryonic eye morphogenesis (GO:0048048)|extraocular skeletal muscle development (GO:0002074)|female somatic sex determination (GO:0019101)|granulosa cell differentiation (GO:0060014)|menstruation (GO:0042703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	cysteine-type endopeptidase regulator activity involved in apoptotic process (GO:0043028)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin conjugating enzyme binding (GO:0031624)			large_intestine(1)|lung(1)|ovary(333)|skin(1)	336						CGCCGGTCTTGCTGTCGTGGT	0.711			Mis		granulosa-cell tumour of the ovary		"Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"																																Dom	yes		3	3q23	668	forkhead box L2	yes	O	0			3											29	30	29					3																	138664470		2200	4296	6496	140147160	SO:0001819	synonymous_variant	668			AF301906	CCDS3105.1	3q23	2008-04-10			ENSG00000183770	ENSG00000183770		"Forkhead boxes"	1092	protein-coding gene	gene with protein product		605597		BPES		1941972	Standard	NM_023067		Approved	BPES1	uc003esw.3	P58012	OTTHUMG00000159889	ENST00000330315.3:c.1095C>T	3.37:g.138664470G>A			140147160	Q4ZGJ3	Silent	SNP	ENST00000330315.3	37	CCDS3105.1																																																																																				0.711	FOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357999.1			A	138664470	G	A	138664470	2	1	101	1	0	0	0	0	0	0	0	1	6036	1310	46	3		3	FOXL2	3	138664470	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	30393361	138664470	59357960	25	26884										
GPR149	344758	hgsc.bcm.edu	37	chr3	154138852	154138852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cgaggggttctttctgatttActcctacaccactcccagtc	7	14	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:154138852A>T	ENST00000389740.2	-	3	1698	c.1599T>A	c.(1597-1599)agT>agA	p.S533R		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	533					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCTGATTTACTCCTACACC	0.373																																																0			3											68	61	63					3																	154138852		1829	4083	5912	155621546	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1599T>A	3.37:g.154138852A>T	ENSP00000374390:p.Ser533Arg		155621546		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.408937	0.62399	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.15	1.13	0.20643	.	0.081744	0.85682	D	0.000000	T	0.69663	0.3136	M	0.68952	2.095	0.47183	D	0.999345	D	0.89917	1.0	D	0.85130	0.997	T	0.69946	-0.5007	9	0.87932	D	0	-9.3452	9.9643	0.41715	0.6784:0.0:0.3216:0.0	.	533	Q86SP6	GP149_HUMAN	R	533	.	ENSP00000374390:S533R	S	-	3	2	GPR149	155621546	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.950000	0.29122	0.390000	0.25115	0.372000	0.22366	AGT		0.373	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154138852	A	T	154138852	3	4	101	1	0	0	0	0	1	0	0	0	6674	388	14	5	604	5	GPR149	3	154138852	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	15474382	154138852	43883578	26	26885										
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167750550	167750550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tgggggagcctgaaattctgCctccttatgggtgggagcat	15	8	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:167750550C>T	ENST00000470487.1	-	9	1623	c.934G>A	c.(934-936)Gca>Aca	p.A312T	GOLIM4_ENST00000309027.4_Missense_Mutation_p.A284T	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	312	Glu-rich.		A -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A312P(1)|p.A312>L(1)		breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TGAAATTCTGCCTCCTTATGG	0.517																																																2	Substitution - Missense(1)|Complex - compound substitution(1)	breast(2)	3											123	124	124					3																	167750550		2203	4300	6503	169233244	SO:0001583	missense	27333			U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.934G>A	3.37:g.167750550C>T	ENSP00000417354:p.Ala312Thr		169233244		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	C	8.245	0.807722	0.16467	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.1	1.25	0.21368	.	1.108700	0.06647	N	0.762100	T	0.33673	0.0871	L	0.57536	1.79	0.09310	N	1	P;P	0.36465	0.554;0.554	B;B	0.29785	0.107;0.107	T	0.18840	-1.0324	9	0.15952	T	0.53	-0.1128	7.3262	0.26557	0.1193:0.6479:0.0:0.2327	.	284;312	F8W785;O00461	.;GOLI4_HUMAN	T	312;284	.	ENSP00000309893:A284T	A	-	1	0	GOLIM4	169233244	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.397000	0.07269	0.184000	0.20083	-1.168000	0.01747	GCA		0.517	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			T	167750550	C	T	167750550	3	4	101	1	0	0	0	0	1	0	0	0	6586	739	26	3	1188	3	GOLIM4	3	167750550	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	13611698	167750550	30271880	27	26886										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951995	178951995	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gccagaactacaatcttttgAtgacattgcatacattcgaa	6	9	1	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:178951995A>G	ENST00000263967.3	+	21	3207	c.3050A>G	c.(3049-3051)gAt>gGt	p.D1017G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1017	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D1017V(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAATCTTTTGATGACATTGCA	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	lung(1)	3											107	95	98					3																	178951995		1879	4117	5996	180434689	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3050A>G	3.37:g.178951995A>G	ENSP00000263967:p.Asp1017Gly		180434689	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.897876	0.72639	.	.	ENSG00000121879	ENST00000263967	T	0.80824	-1.42	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.82098	0.4963	L	0.35288	1.05	0.80722	D	1	D	0.65815	0.995	P	0.56700	0.804	T	0.82131	-0.0609	10	0.42905	T	0.14	-22.9512	16.635	0.85050	1.0:0.0:0.0:0.0	.	1017	P42336	PK3CA_HUMAN	G	1017	ENSP00000263967:D1017G	ENSP00000263967:D1017G	D	+	2	0	PIK3CA	180434689	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.798000	0.91888	2.330000	0.79161	0.477000	0.44152	GAT		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951995	A	G	178951995	3	3	101	1	0	0	0	0	1	0	0	0	11944	333	12	4	3128	4	PIK3CA	3	178951995	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	11201445	178951995	19070435	28	26887										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952090	178952090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaatgaatgatgcacatcatGgtggctggacaacaaaaatg	10	6	1	2	rs121913277		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:178952090G>A	ENST00000263967.3	+	21	3302	c.3145G>A	c.(3145-3147)Ggt>Agt	p.G1049S	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1049	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		G -> S (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.G1049R(27)|p.G1049S(13)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGCACATCATGGTGGCTGGAC	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	40	Substitution - Missense(40)	breast(12)|endometrium(7)|lung(4)|thyroid(3)|large_intestine(3)|central_nervous_system(3)|upper_aerodigestive_tract(2)|urinary_tract(2)|kidney(2)|ovary(1)|pancreas(1)	3											98	88	91					3																	178952090		1919	4132	6051	180434784	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3145G>A	3.37:g.178952090G>A	ENSP00000263967:p.Gly1049Ser		180434784	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396096	0.83011	.	.	ENSG00000121879	ENST00000263967	T	0.78924	-1.22	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.75250	0.3824	N	0.17723	0.515	0.80722	D	1	D	0.53885	0.963	P	0.52627	0.704	T	0.69614	-0.5098	10	0.17369	T	0.5	-16.0151	20.6721	0.99693	0.0:0.0:1.0:0.0	.	1049	P42336	PK3CA_HUMAN	S	1049	ENSP00000263967:G1049S	ENSP00000263967:G1049S	G	+	1	0	PIK3CA	180434784	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.367000	0.97148	2.894000	0.99253	0.591000	0.81541	GGT		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178952090	G	A	178952090	3	1	101	1	0	0	0	0	1	0	0	0	11944	1348	47	3	3223	3	PIK3CA	3	178952090	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	95	178952090	19070340	29	26888										
DCUN1D1	54165	hgsc.bcm.edu	37	chr3	182681755	182681755	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttccacgcaataatcaacacActaatgctggctggatcgag	8	11	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:182681755A>G	ENST00000292782.4	-	3	456	c.303T>C	c.(301-303)agT>agC	p.S101S	DCUN1D1_ENST00000469954.1_Silent_p.S86S	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1	101	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					ubiquitin ligase complex (GO:0000151)		p.S101R(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TAATCAACACACTAATGCTGG	0.418																																																1	Substitution - Missense(1)	ovary(1)	3											152	125	134					3																	182681755		2203	4300	6503	184164449	SO:0001819	synonymous_variant	54165			AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"squamous cell carcinoma related oncogene"	605905	"DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.303T>C	3.37:g.182681755A>G			184164449	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Silent	SNP	ENST00000292782.4	37	CCDS3240.1																																																																																				0.418	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640		G	182681755	A	G	182681755	2	3	101	1	0	0	0	0	0	0	0	1	4319	156	6	4		4	DCUN1D1	3	182681755	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	3729665	182681755	15340675	30	26889										
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080827	194080827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	caggacctgcaactggcggaGgttgctgaagacattgtcgg	15	9	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr3:194080827G>A	ENST00000347624.3	-	2	1031	c.946C>T	c.(946-948)Ctc>Ttc	p.L316F	LRRC15_ENST00000428839.1_Missense_Mutation_p.L322F|LRRC15_ENST00000439944.2_Missense_Mutation_p.L322F	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	316					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		AACTGGCGGAGGTTGCTGAAG	0.582																																																0			3											52	54	53					3																	194080827		2203	4300	6503	195562122	SO:0001583	missense	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.946C>T	3.37:g.194080827G>A	ENSP00000306276:p.Leu316Phe		195562122	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006884	0.54361	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.70749	-0.51;-0.51;-0.51	5.09	4.22	0.49857	.	0.000000	0.64402	D	0.000019	T	0.81322	0.4798	L	0.61387	1.9	0.50632	D	0.999884	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.83121	-0.0118	10	0.72032	D	0.01	.	13.6329	0.62206	0.0751:0.0:0.9249:0.0	.	316;322	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	F	316;322;322	ENSP00000306276:L316F;ENSP00000389128:L322F;ENSP00000413707:L322F	ENSP00000306276:L316F	L	-	1	0	LRRC15	195562122	1.000000	0.71417	0.803000	0.32268	0.658000	0.38924	5.457000	0.66672	1.293000	0.44690	0.655000	0.94253	CTC		0.582	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			A	194080827	G	A	194080827	3	1	101	1	0	0	0	0	1	0	0	0	8999	1000	35	3	803	3	LRRC15	3	194080827	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	11399072	194080827	3941603	31	26890										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25156721	25156721	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcctccactgctttcaggtcTgtacgcagctcgtcaccttc	8	16	3	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr4:25156721T>A	ENST00000382103.2	-	5	672	c.600A>T	c.(598-600)acA>acT	p.T200T	SEPSECS_ENST00000302922.3_Silent_p.T121T	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	200					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				CTTTCAGGTCTGTACGCAGCT	0.428																																																0			4											141	121	128					4																	25156721		2203	4300	6503	24765819	SO:0001819	synonymous_variant	51091			AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.600A>T	4.37:g.25156721T>A			24765819	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Silent	SNP	ENST00000382103.2	37	CCDS3432.2																																																																																				0.428	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		A	25156721	T	A	25156721	2	1	101	1	0	0	0	0	0	0	0	1	14095	1567	55	5		5	SEPSECS	4	25156721	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10		25156721	165997555	32	26891										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138442723	138442723	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ggatgctgctgctggggttgCgttgggaattcttcccctgg	16	9	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr4:138442723C>T	ENST00000344876.4	-	4	3254	c.2868G>A	c.(2866-2868)acG>acA	p.T956T	PCDH18_ENST00000510305.1_Silent_p.T167T|PCDH18_ENST00000511115.1_Silent_p.T136T|PCDH18_ENST00000412923.2_Silent_p.T955T|PCDH18_ENST00000507846.1_Silent_p.T735T	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	956	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T956T(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GCTGGGGTTGCGTTGGGAATT	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	4											129	124	126					4																	138442723		2203	4300	6503	138662173	SO:0001819	synonymous_variant	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2868G>A	4.37:g.138442723C>T			138662173	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.517	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138442723	C	T	138442723	2	4	101	1	0	0	0	0	0	0	0	1	11544	755	27	1		1	PCDH18	4	138442723	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	113286002	138442723	52711553	33	26892										
EDNRA	1909	hgsc.bcm.edu	37	chr4	148406954	148406954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tggatgatttcaccacttttCgtggcacagagctcagcttc	9	11	2	2	rs139739379		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr4:148406954C>T	ENST00000324300.5	+	2	636	c.121C>T	c.(121-123)Cgt>Tgt	p.R41C	EDNRA_ENST00000506066.1_Missense_Mutation_p.R41C|EDNRA_ENST00000511804.1_Intron|EDNRA_ENST00000339690.5_Missense_Mutation_p.R41C|EDNRA_ENST00000358556.4_Missense_Mutation_p.R41C	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	41					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	CACCACTTTTCGTGGCACAGA	0.463													C|||	1	0.000199681	0	0.0014	5008	,	,		20105	0		0	False		,,,				2504	0															0			4						C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	156	131	140		121,121	6	0.1	4	dbSNP_134	140	0,8600		0,0,4300	no	missense,missense	EDNRA	NM_001166055.1,NM_001957.3	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	41/319,41/428	148406954	1,13005	2203	4300	6503	148626404	SO:0001583	missense	1909			D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"GPCR / Class A : Endothelin receptors"	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.121C>T	4.37:g.148406954C>T	ENSP00000315011:p.Arg41Cys		148626404	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Missense_Mutation	SNP	ENST00000324300.5	37	CCDS3769.1	.	.	.	.	.	.	.	.	.	.	C	9.961	1.222901	0.22457	2.27E-4	0.0	ENSG00000151617	ENST00000358556;ENST00000339690;ENST00000394047;ENST00000324300;ENST00000506066	T;D;T;T	0.82526	0.32;-1.62;-0.87;0.32	5.96	5.96	0.96718	.	1.356400	0.04488	N	0.379053	T	0.73560	0.3602	N	0.14661	0.345	0.09310	N	1	P;P;P	0.52842	0.566;0.956;0.476	B;B;B	0.42882	0.157;0.401;0.118	T	0.63242	-0.6681	10	0.56958	D	0.05	0.234	6.357	0.21406	0.1797:0.7129:0.0:0.1074	.	41;41;41	P25101-4;P25101-2;P25101	.;.;EDNRA_HUMAN	C	41	ENSP00000351359:R41C;ENSP00000341556:R41C;ENSP00000315011:R41C;ENSP00000425281:R41C	ENSP00000315011:R41C	R	+	1	0	EDNRA	148626404	0.005000	0.15991	0.113000	0.21522	0.052000	0.14988	2.046000	0.41260	2.832000	0.97577	0.655000	0.94253	CGT		0.463	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1			T	148406954	C	T	148406954	3	4	101	1	0	0	0	0	1	0	0	0	4930	884	31	1	123	1	EDNRA	4	148406954	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	9964231	148406954	42747322	34	26893										
FAM134B	54463	hgsc.bcm.edu	37	chr5	16478972	16478972	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tacctaccagatctctcacgTttcttctgattaatatattc	3	11	4	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:16478972T>C	ENST00000306320.9	-	6	881	c.795A>G	c.(793-795)aaA>aaG	p.K265K	FAM134B_ENST00000399793.2_Silent_p.K124K	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	265					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						ATCTCTCACGTTTCTTCTGAT	0.289																																																0			5											92	90	91					5																	16478972		1809	4066	5875	16531972	SO:0001819	synonymous_variant	54463			BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.795A>G	5.37:g.16478972T>C			16531972	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Silent	SNP	ENST00000306320.9	37	CCDS43304.1																																																																																				0.289	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		C	16478972	T	C	16478972	2	2	101	1	0	0	0	0	0	0	0	1	5462	1722	60	4		4	FAM134B	5	16478972	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10		16478972	164436288	35	26894										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75996929	75996929	+	Nonsense_Mutation	SNP	G	G	T													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ggagatcaattaaactagatGgaaaaggagaacccaaaggg							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:75996929G>T	ENST00000274364.6	+	34	4693	c.4396G>T	c.(4396-4398)Gga>Tga	p.G1466*	IQGAP2_ENST00000379730.3_Nonsense_Mutation_p.G968*|IQGAP2_ENST00000502745.1_Nonsense_Mutation_p.G962*|IQGAP2_ENST00000396234.3_Nonsense_Mutation_p.G962*|CTD-2384B11.2_ENST00000507514.1_RNA	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1466					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TAAACTAGATGGAAAAGGAGA	0.423																																																0			5											95	93	93					5																	75996929		2203	4300	6503	76032685	SO:0001587	stop_gained	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4396G>T	5.37:g.75996929G>T	ENSP00000274364:p.Gly1466*		76032685	A8K4V1|B7Z8A4|J3KR91	Nonsense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	44	11.085150	0.99513	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000396234;ENST00000502745	.	.	.	5.46	3.64	0.41730	.	0.466924	0.25052	N	0.033504	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-9.414	12.75	0.57304	0.1414:0.0:0.8586:0.0	.	.	.	.	X	1466;968;962;962	.	ENSP00000274364:G1466X	G	+	1	0	IQGAP2	76032685	1.000000	0.71417	0.395000	0.26283	0.215000	0.24574	3.468000	0.53086	1.427000	0.47276	0.655000	0.94253	GGA		0.423	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75996929	G	T	75996929	4	4	101	1	0	0	0	0	0	1	0	0	7836	1349	47	2	4530	2	IQGAP2	5	75996929	Nonsense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	59517957	75996929	104918331	36	26895	44	2								
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75996931	75996931	+	Silent	SNP	A	A	G													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	agatcaattaaactagatggAaaaggagaacccaaaggggc							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:75996931A>G	ENST00000274364.6	+	34	4695	c.4398A>G	c.(4396-4398)ggA>ggG	p.G1466G	IQGAP2_ENST00000379730.3_Silent_p.G968G|IQGAP2_ENST00000502745.1_Silent_p.G962G|IQGAP2_ENST00000396234.3_Silent_p.G962G|CTD-2384B11.2_ENST00000507514.1_RNA	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1466					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AACTAGATGGAAAAGGAGAAC	0.423																																																0			5											96	94	95					5																	75996931		2203	4300	6503	76032687	SO:0001819	synonymous_variant	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4398A>G	5.37:g.75996931A>G			76032687	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1																																																																																				0.423	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		G	75996931	A	G	75996931	2	3	101	1	0	0	0	0	0	0	0	1	7836	233	9	4		4	IQGAP2	5	75996931	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	2	75996931	104918329	37	26896	44	2								
APC	324	hgsc.bcm.edu	37	chr5	112164616	112164616	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	taaatagtaaaaagacgttgCgagaagttggaagtgtgaaa	12	2	0	3	rs137854574		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:112164616C>A	ENST00000457016.1	+	14	2070	c.1690C>A	c.(1690-1692)Cga>Aga	p.R564R	APC_ENST00000508376.2_Silent_p.R564R|CTC-554D6.1_ENST00000520401.1_Nonsense_Mutation_p.C59*|APC_ENST00000257430.4_Silent_p.R564R			P25054	APC_HUMAN	adenomatous polyposis coli	564	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R564*(14)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGACGTTGCGAGAAGTTGG	0.313		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(14)|Unknown(1)	large_intestine(14)|skin(1)	5	GRCh37	CM920035	APC	M	rs137854574						126	137	134					5																	112164616		2202	4300	6502	112192515	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1690C>A	5.37:g.112164616C>A			112192515	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112164616	C	A	112164616	2	1	101	1	0	0	0	0	0	0	0	1	763	760	27	2		2	APC	5	112164616	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	36167685	112164616	68750644	38	26897										
APC	324	hgsc.bcm.edu	37	chr5	112175123	112175123	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tttcaagatgtagttcattaTcatctttgtcatcagctgaa	6	7	6	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:112175123T>C	ENST00000457016.1	+	16	4212	c.3832T>C	c.(3832-3834)Tca>Cca	p.S1278P	APC_ENST00000508376.2_Missense_Mutation_p.S1278P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1278P			P25054	APC_HUMAN	adenomatous polyposis coli	1278	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1278P(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGTTCATTATCATCTTTGTC	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Missense(1)|Unknown(1)|Deletion - Frameshift(1)	urinary_tract(1)|soft_tissue(1)|skin(1)	5											53	56	55					5																	112175123		2202	4300	6502	112203022	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3832T>C	5.37:g.112175123T>C	ENSP00000413133:p.Ser1278Pro		112203022	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.468474	0.63625	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	6.03	6.03	0.97812	.	0.114891	0.64402	D	0.000010	D	0.93562	0.7945	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93608	0.6936	9	.	.	.	-13.7606	16.2316	0.82347	0.0:0.0:0.0:1.0	.	1280;1278	Q4LE70;P25054	.;APC_HUMAN	P	1278	ENSP00000413133:S1278P;ENSP00000257430:S1278P;ENSP00000427089:S1278P;ENSP00000423828:S1278P	.	S	+	1	0	APC	112203022	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.698000	0.84413	2.308000	0.77769	0.533000	0.62120	TCA		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175123	T	C	112175123	3	2	101	1	0	0	0	0	1	0	0	0	763	1435	50	4	3890	4	APC	5	112175123	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	10507	112175123	68740137	39	26898										
APC	324	hgsc.bcm.edu	37	chr5	112175752	112175752	+	Frame_Shift_Del	DEL	T	T	-													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gttcttccagatgctgatacTttattacattttgccacgga							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:112175752delT	ENST00000457016.1	+	16	4841	c.4461delT	c.(4459-4461)actfs	p.T1487fs	APC_ENST00000508376.2_Frame_Shift_Del_p.T1487fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.T1487fs			P25054	APC_HUMAN	adenomatous polyposis coli	1487	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1487fs*17(10)|p.L1488fs*19(7)|p.L1488fs*26(5)|p.L1488fs*18(1)|p.?(1)|p.K1454fs*3(1)|p.T1487fs*25(1)|p.T1487T(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*20(1)|p.L1488fs*21(1)|p.L1488fs*23(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATGCTGATACTTTATTACATT	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	32	Deletion - Frameshift(21)|Insertion - Frameshift(7)|Complex - frameshift(2)|Unknown(1)|Substitution - coding silent(1)	large_intestine(29)|thyroid(1)|soft_tissue(1)|skin(1)	5											69	70	70					5																	112175752		2202	4300	6502	112203651	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4461delT	5.37:g.112175752delT	ENSP00000413133:p.Thr1487fs		112203651	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175752	T	-	112175752	7	5	101	1	0	1	0	1	0	0	0	0	763	1596	56	0	4519	0	APC	5	112175752	Frame_Shift_Del	DEL	T	TCGA-DC-6683-01A-11D-1826-10	629	112175752	68739508	40	26899	45	2								
APC	324	hgsc.bcm.edu	37	chr5	112175756	112175756	+	Frame_Shift_Del	DEL	T	T	-													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttccagatgctgatactttaTtacattttgccacggaaagt							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:112175756delT	ENST00000457016.1	+	16	4845	c.4465delT	c.(4465-4467)ttafs	p.L1489fs	APC_ENST00000508376.2_Frame_Shift_Del_p.L1489fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.L1489fs			P25054	APC_HUMAN	adenomatous polyposis coli	1489	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.L1488fs*18(17)|p.T1487fs*17(10)|p.L1488fs*23(3)|p.L1489fs*19(2)|p.?(1)|p.K1454fs*3(1)|p.L1488fs*13(1)|p.L1489V(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*22(1)|p.L1488fs*25(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATACTTTATTACATTTTGC	0.443		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Deletion - Frameshift(34)|Complex - frameshift(2)|Insertion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(36)|thyroid(1)|lung(1)|soft_tissue(1)|skin(1)	5											69	70	70					5																	112175756		2202	4300	6502	112203655	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4465delT	5.37:g.112175756delT	ENSP00000413133:p.Leu1489fs		112203655	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175756	T	-	112175756	7	5	101	1	0	1	0	1	0	0	0	0	763	1490	52	0	4523	0	APC	5	112175756	Frame_Shift_Del	DEL	T	TCGA-DC-6683-01A-11D-1826-10	4	112175756	68739504	41	26900	45	2								
ADAM19	8728	hgsc.bcm.edu	37	chr5	156932761	156932761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	catgggtcatgccaaagttgTggcccatctcgtgggccatg	13	11	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr5:156932761T>C	ENST00000517905.1	-	11	1090	c.1046A>G	c.(1045-1047)cAc>cGc	p.H349R	ADAM19_ENST00000430702.2_Missense_Mutation_p.H82R|ADAM19_ENST00000257527.4_Missense_Mutation_p.H349R|ADAM19_ENST00000394020.1_Missense_Mutation_p.H351R			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	349	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	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)			GCCAAAGTTGTGGCCCATCTC	0.572																																																0			5											62	50	54					5																	156932761		2203	4300	6503	156865339	SO:0001583	missense	8728			AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"ADAM metallopeptidase domain containing"	197	protein-coding gene	gene with protein product	"meltrin beta"	603640	"a disintegrin and metalloproteinase domain 19 (meltrin beta)"			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.1046A>G	5.37:g.156932761T>C	ENSP00000428654:p.His349Arg		156865339	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		.	.	.	.	.	.	.	.	.	.	T	29.5	5.012675	0.93346	.	.	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;D;D;D	0.98684	1.66;-5.07;-5.07;-5.07	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000001	D	0.99554	0.9840	H	0.99026	4.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.97734	1.0204	10	0.87932	D	0	.	16.3483	0.83171	0.0:0.0:0.0:1.0	.	349;82	Q9H013-2;E9PD32	.;.	R	82;349;351;349	ENSP00000414088:H82R;ENSP00000257527:H349R;ENSP00000377588:H351R;ENSP00000428654:H349R	ENSP00000257527:H349R	H	-	2	0	ADAM19	156865339	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.254000	0.74563	0.533000	0.62120	CAC		0.572	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		C	156932761	T	C	156932761	3	2	101	1	0	0	0	0	1	0	0	0	240	1696	59	4	1762	4	ADAM19	5	156932761	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	44757005	156932761	23982499	42	26901										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51921513	51921513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cacctcgttcaaatccaagcCggagaaggatgttagaccaa	9	11	1	2	rs142896856	byFrequency	TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr6:51921513C>T	ENST00000371117.3	-	18	1951	c.1676G>A	c.(1675-1677)cGg>cAg	p.R559Q	PKHD1_ENST00000340994.4_Missense_Mutation_p.R559Q	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	559					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AAATCCAAGCCGGAGAAGGAT	0.398													C|||	2	0.000399361	0	0.0014	5008	,	,		20939	0		0.001	False		,,,				2504	0															0			6						C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	128	135	133		1676,1676	1.6	0	6	dbSNP_134	133	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	43,43	0,10,6493	TT,TC,CC		0.093,0.0454,0.0769	possibly-damaging,possibly-damaging	559/4075,559/3397	51921513	10,12996	2203	4300	6503	52029472	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1676G>A	6.37:g.51921513C>T	ENSP00000360158:p.Arg559Gln		52029472	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.780	0.512837	0.12944	4.54E-4	9.3E-4	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87571	-2.27;-2.27	5.4	1.6	0.23607	.	0.972088	0.08456	N	0.943106	T	0.71316	0.3325	L	0.40543	1.245	0.09310	N	1	D;D	0.56521	0.969;0.976	P;B	0.45474	0.482;0.289	T	0.59726	-0.7400	10	0.29301	T	0.29	.	8.3453	0.32270	0.0:0.674:0.0:0.326	.	559;559	P08F94-2;P08F94	.;PKHD1_HUMAN	Q	559	ENSP00000360158:R559Q;ENSP00000341097:R559Q	ENSP00000341097:R559Q	R	-	2	0	PKHD1	52029472	0.006000	0.16342	0.024000	0.17045	0.132000	0.20833	0.595000	0.24029	0.271000	0.22005	0.462000	0.41574	CGG		0.398	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51921513	C	T	51921513	3	4	101	1	0	0	0	0	1	0	0	0	12002	652	23	1	10787	1	PKHD1	6	51921513	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		51921513	119193554	43	26902										
GPR126	57211	hgsc.bcm.edu	37	chr6	142764633	142764633	+	3'UTR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tatcatgtcagacaccttcaGccacagcacaaagttttaat	5	11	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr6:142764633G>T	ENST00000230173.6	+	0	4256				GPR126_ENST00000367609.3_Missense_Mutation_p.S1245I|GPR126_ENST00000367608.2_Missense_Mutation_p.S1217I|GPR126_ENST00000296932.8_3'UTR	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GACACCTTCAGCCACAGCACA	0.358																																																0			6											97	93	95					6																	142764633		1877	4110	5987	142806326	SO:0001624	3_prime_UTR_variant	57211			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.*114G>T	6.37:g.142764633G>T			142806326	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577227	0.86645	.	.	ENSG00000112414	ENST00000367608;ENST00000367609	T;T	0.31247	1.5;1.5	6.17	6.17	0.99709	.	0.079820	0.53938	D	0.000051	T	0.22282	0.0537	N	0.22421	0.69	0.31184	N	0.70168	P;D;D	0.53885	0.883;0.963;0.963	B;P;P	0.48270	0.368;0.572;0.572	T	0.03354	-1.1045	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	305;1217;1245	B4DSK4;Q86SQ4-4;Q86SQ4-3	.;.;.	I	1217;1245	ENSP00000356580:S1217I;ENSP00000356581:S1245I	ENSP00000356580:S1217I	S	+	2	0	GPR126	142806326	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.956000	0.76013	2.941000	0.99782	0.655000	0.94253	AGC		0.358	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142764633	G	T	142764633	1	4	101	0	1	0	0	0	0	0	0	0	6660	971	34	2		2	GPR126	6	142764633	3'UTR	SNP	G	TCGA-DC-6683-01A-11D-1826-10	90843120	142764633	28350434	44	26903										
LTV1	84946	hgsc.bcm.edu	37	chr6	144171288	144171288	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	agcactggaattaagttgccTtcatcagtgtttgcttcaga	9	8	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr6:144171288T>C	ENST00000367576.5	+	4	464	c.330T>C	c.(328-330)ccT>ccC	p.P110P		NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	110						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		TTAAGTTGCCTTCATCAGTGT	0.363																																																0			6											173	171	172					6																	144171288		2203	4300	6503	144212981	SO:0001819	synonymous_variant	84946			BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 93", "LTV1 homolog (S. cerevisiae)"	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.330T>C	6.37:g.144171288T>C			144212981	Q96JX8	Silent	SNP	ENST00000367576.5	37	CCDS5201.1																																																																																				0.363	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860		C	144171288	T	C	144171288	2	2	101	1	0	0	0	0	0	0	0	1	9110	1596	56	4		4	LTV1	6	144171288	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	1406655	144171288	26943779	45	26904										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21609825	21609825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gaaaaaaattggcaagctacTttatgggaagaaagctgaga	11	4	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr7:21609825T>C	ENST00000409508.3	+	7	1364	c.1333T>C	c.(1333-1335)Ttt>Ctt	p.F445L	DNAH11_ENST00000328843.6_Missense_Mutation_p.F445L	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	445	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GGCAAGCTACTTTATGGGAAG	0.353									Kartagener syndrome																																							0			7											79	79	79					7																	21609825		1804	4073	5877	21576350	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.1333T>C	7.37:g.21609825T>C	ENSP00000475939:p.Phe445Leu		21576350	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	7.207	0.594589	0.13875	.	.	ENSG00000105877	ENST00000328843	T	0.22336	1.96	5.79	4.64	0.57946	Dynein heavy chain, domain-1 (1);	2.966790	0.01012	N	0.003845	T	0.30823	0.0777	M	0.75150	2.29	0.28473	N	0.915306	B	0.24317	0.101	B	0.25291	0.059	T	0.53258	-0.8464	10	0.10636	T	0.68	.	11.9496	0.52948	0.0:0.0:0.1585:0.8415	.	445	Q96DT5	DYH11_HUMAN	L	445	ENSP00000330671:F445L	ENSP00000330671:F445L	F	+	1	0	DNAH11	21576350	1.000000	0.71417	0.073000	0.20177	0.022000	0.10575	3.666000	0.54540	1.017000	0.39495	0.455000	0.32223	TTT		0.353	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		C	21609825	T	C	21609825	3	2	101	1	0	0	0	0	1	0	0	0	4610	1609	56	4	1359	4	DNAH11	7	21609825	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10		21609825	137528838	46	26905										
FLNC	2318	hgsc.bcm.edu	37	chr7	128496863	128496863	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tccatcgatgtcaagttcaaCggtgcccacatccctggaag	9	13	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr7:128496863C>T	ENST00000325888.8	+	45	7710	c.7449C>T	c.(7447-7449)aaC>aaT	p.N2483N	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.N2450N	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2483	Interaction with INPPL1.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.N2483N(2)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAGTTCAACGGTGCCCACA	0.597																																																2	Substitution - coding silent(2)	lung(1)|breast(1)	7											97	101	100					7																	128496863		2198	4296	6494	128284099	SO:0001819	synonymous_variant	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.7449C>T	7.37:g.128496863C>T			128284099	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																				0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128496863	C	T	128496863	2	4	101	1	0	0	0	0	0	0	0	1	5954	535	19	1		1	FLNC	7	128496863	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	106887038	128496863	30641800	47	26906										
UBE2H	7328	hgsc.bcm.edu	37	chr7	129479123	129479123	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ccattgagaggatctatgggGttaggataggccaataactg	13	6	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr7:129479123G>A	ENST00000355621.3	-	6	744	c.351C>T	c.(349-351)aaC>aaT	p.N117N	UBE2H_ENST00000473814.2_Silent_p.N86N	NM_001202498.1|NM_003344.3	NP_001189427.1|NP_003335.1	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H	117					protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)	p.N117N(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|skin(1)	10	Melanoma(18;0.0435)					GATCTATGGGGTTAGGATAGG	0.428																																																1	Substitution - coding silent(1)	skin(1)	7											150	136	141					7																	129479123		2203	4300	6503	129266359	SO:0001819	synonymous_variant	7328			BC006277	CCDS5814.1, CCDS47710.1	7q32	2012-07-20	2011-05-19		ENSG00000186591	ENSG00000186591	6.3.2.19	"Ubiquitin-conjugating enzymes E2"	12484	protein-coding gene	gene with protein product	"GID complex subunit 3, UBC8 homolog (S. cerevisiae)"	601082	"ubiquitin-conjugating enzyme E2H (homologous to yeast UBC8)", "ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast)"			8132613	Standard	NM_003344		Approved	UBCH, UBC8, GID3	uc003vpf.2	P62256	OTTHUMG00000157650	ENST00000355621.3:c.351C>T	7.37:g.129479123G>A			129266359	A4D1L6|C9JY93|P37286|Q7Z6F4	Silent	SNP	ENST00000355621.3	37	CCDS5814.1																																																																																				0.428	UBE2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349327.2	NM_003344		A	129479123	G	A	129479123	2	1	101	1	0	0	0	0	0	0	0	1	16898	1252	44	3		3	UBE2H	7	129479123	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	982260	129479123	29659540	48	26907										
BRAF	673	hgsc.bcm.edu	37	chr7	140449173	140449173	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaatgcatatacatctgactGaaagctgtatggatttttat	7	5	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr7:140449173G>A	ENST00000288602.6	-	16	1966	c.1906C>T	c.(1906-1908)Cag>Tag	p.Q636*		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q636E(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACATCTGACTGAAAGCTGTAT	0.333		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	1	Substitution - Missense(1)	lung(1)	7											106	110	109					7																	140449173		2202	4300	6502	140095642	SO:0001587	stop_gained	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1906C>T	7.37:g.140449173G>A	ENSP00000288602:p.Gln636*		140095642	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Nonsense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082683	0.94050	.	.	ENSG00000157764	ENST00000288602	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.7092	0.91649	0.0:0.0:1.0:0.0	.	.	.	.	X	636	.	ENSP00000288602:Q636X	Q	-	1	0	BRAF	140095642	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.502000	0.84385	0.462000	0.41574	CAG		0.333	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		A	140449173	G	A	140449173	4	1	101	1	0	0	0	0	0	1	0	0	1499	1299	45	3	406	3	BRAF	7	140449173	Nonsense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	10970050	140449173	18689490	49	26908										
EFCAB1	79645	hgsc.bcm.edu	37	chr8	49642320	49642320	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaccaaatctttaattccttCatcagggtcttcctcagatg	5	11	5	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:49642320C>T	ENST00000262103.3	-	4	510	c.430G>A	c.(430-432)Gaa>Aaa	p.E144K	EFCAB1_ENST00000433756.1_Missense_Mutation_p.E92K|EFCAB1_ENST00000523092.1_Missense_Mutation_p.E92K|EFCAB1_ENST00000521002.1_Intron	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	144							calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				TTAATTCCTTCATCAGGGTCT	0.358																																																0			8											106	102	103					8																	49642320		2202	4300	6502	49804873	SO:0001583	missense	79645				CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.430G>A	8.37:g.49642320C>T	ENSP00000262103:p.Glu144Lys		49804873	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	37	CCDS6145.1	.	.	.	.	.	.	.	.	.	.	C	35	5.472495	0.96274	.	.	ENSG00000034239	ENST00000433756;ENST00000262103;ENST00000450553;ENST00000523092	T;T;T	0.53423	0.62;0.62;0.62	5.46	5.46	0.80206	EF-hand-like domain (1);	0.041957	0.85682	D	0.000000	T	0.74176	0.3682	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.966;1.0	T	0.78661	-0.2117	10	0.87932	D	0	.	16.8609	0.86018	0.0:1.0:0.0:0.0	.	92;144	Q9HAE3-2;Q9HAE3	.;EFCB1_HUMAN	K	92;144;144;92	ENSP00000400873:E92K;ENSP00000262103:E144K;ENSP00000430765:E92K	ENSP00000262103:E144K	E	-	1	0	EFCAB1	49804873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.840000	0.97914	0.655000	0.94253	GAA		0.358	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		T	49642320	C	T	49642320	3	4	101	1	0	0	0	0	1	0	0	0	4944	835	29	3	217	3	EFCAB1	8	49642320	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		49642320	96721702	50	26909										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68087633	68087633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cctgctaagagagcagcagaAgaggctgaacagaataaaaa	11	7	0	5			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:68087633A>G	ENST00000262210.5	+	24	3087	c.3056A>G	c.(3055-3057)aAg>aGg	p.K1019R	CSPP1_ENST00000521168.1_3'UTR|ARFGEF1_ENST00000520381.1_3'UTR|CSPP1_ENST00000412460.1_Missense_Mutation_p.K674R	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1054					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GAGCAGCAGAAGAGGCTGAAC	0.428																																																0			8											56	55	55					8																	68087633		1907	4120	6027	68250187	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3056A>G	8.37:g.68087633A>G	ENSP00000262210:p.Lys1019Arg		68250187	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.060839	0.36373	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.33438	1.41;1.44;1.44	4.8	2.1	0.27182	.	0.232657	0.35291	N	0.003310	T	0.17959	0.0431	N	0.25380	0.74	0.80722	D	1	B;B;B;B	0.14805	0.011;0.008;0.011;0.004	B;B;B;B	0.16722	0.016;0.009;0.016;0.011	T	0.08513	-1.0718	10	0.20046	T	0.44	-13.3239	7.5124	0.27581	0.7184:0.0:0.2816:0.0	.	177;674;1019;1054	Q9H688;Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;.;CSPP1_HUMAN	R	1019;1054;674;674	ENSP00000262210:K1019R;ENSP00000415782:K674R;ENSP00000430092:K674R	ENSP00000262210:K1019R	K	+	2	0	CSPP1	68250187	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	1.380000	0.34351	0.203000	0.20529	0.482000	0.46254	AAG		0.428	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68087633	A	G	68087633	3	3	101	1	0	0	0	0	1	0	0	0	3968	72	3	4	3263	4	CSPP1	8	68087633	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	18445313	68087633	78276389	51	26910										
PREX2	80243	hgsc.bcm.edu	37	chr8	68989671	68989671	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aagaggcaatgatatttggcGttggactctgtgacaatgga	13	5	1	3	rs147538692	byFrequency	TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:68989671G>T	ENST00000288368.4	+	15	1886	c.1609G>T	c.(1609-1611)Gtt>Ttt	p.V537F	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	537	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.		V -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.V537I(1)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GATATTTGGCGTTGGACTCTG	0.443																																																1	Substitution - Missense(1)	large_intestine(1)	8											200	178	185					8																	68989671		2203	4300	6503	69152225	SO:0001583	missense	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1609G>T	8.37:g.68989671G>T	ENSP00000288368:p.Val537Phe		69152225	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.490851	0.64074	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.21932	1.98	5.58	-4.1	0.03940	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.486385	0.21108	N	0.080024	T	0.33352	0.0860	L	0.47716	1.5	0.36635	D	0.876542	D;P;D	0.89917	1.0;0.933;0.966	D;D;D	0.77557	0.99;0.915;0.936	T	0.09975	-1.0650	10	0.72032	D	0.01	.	13.6045	0.62039	0.6098:0.0:0.3902:0.0	.	537;537;537	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	F	537	ENSP00000288368:V537F	ENSP00000288368:V537F	V	+	1	0	PREX2	69152225	0.973000	0.33851	0.003000	0.11579	0.985000	0.73830	1.795000	0.38784	-1.201000	0.02659	-0.237000	0.12165	GTT		0.443	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68989671	G	T	68989671	3	4	101	1	0	0	0	0	1	0	0	0	12511	1145	40	2	1667	2	PREX2	8	68989671	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	902038	68989671	77374351	52	26911										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109240603	109240603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gttctctgctgaagagactgAagtggagaactcacagacta	11	8	2	5			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:109240603A>G	ENST00000220849.5	-	7	677	c.615T>C	c.(613-615)ctT>ctC	p.L205L	EIF3E_ENST00000519030.1_Silent_p.L112L|RP11-35G22.1_ENST00000520037.1_RNA|EIF3E_ENST00000519517.1_5'UTR	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			GAAGAGACTGAAGTGGAGAAC	0.348																																					GBM(15;360 410 8460 34179 52246)											0			8											75	75	75					8																	109240603		2203	4300	6503	109309779	SO:0001819	synonymous_variant	3646			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.615T>C	8.37:g.109240603A>G			109309779		Silent	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	8.734	0.917257	0.17982	.	.	ENSG00000104408	ENST00000522352	.	.	.	5.5	-3.03	0.05429	.	.	.	.	.	T	0.51126	0.1656	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44711	-0.9310	4	.	.	.	-11.5618	7.819	0.29276	0.2882:0.2755:0.4363:0.0	.	.	.	.	P	29	.	.	S	-	1	0	EIF3E	109309779	0.996000	0.38824	0.935000	0.37517	0.974000	0.67602	0.333000	0.19768	-0.844000	0.04184	-1.501000	0.00957	TCA		0.348	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		G	109240603	A	G	109240603	2	3	101	1	0	0	0	0	0	0	0	1	5028	233	9	4		4	EIF3E	8	109240603	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	40250932	109240603	37123419	53	26912										
NUDCD1	84955	hgsc.bcm.edu	37	chr8	110257626	110257626	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tggttgccagagtagggcatCaacatcatggcgcaaacaga	12	9	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:110257626C>A	ENST00000239690.4	-	9	1758	c.1384G>T	c.(1384-1386)Gat>Tat	p.D462Y	NUDCD1_ENST00000427660.2_Missense_Mutation_p.D433Y	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			AGTAGGGCATCAACATCATGG	0.413																																																0			8											161	143	149					8																	110257626		2203	4300	6503	110326802	SO:0001583	missense	84955			AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.1384G>T	8.37:g.110257626C>A	ENSP00000239690:p.Asp462Tyr		110326802		Missense_Mutation	SNP	ENST00000239690.4	37	CCDS6312.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796219	0.90453	.	.	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.54279	0.61;0.58	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.77384	0.4122	M	0.87180	2.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81479	-0.0914	10	0.87932	D	0	-3.9212	18.2178	0.89892	0.0:1.0:0.0:0.0	.	375;462;433	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	Y	462;433	ENSP00000239690:D462Y;ENSP00000410707:D433Y	ENSP00000239690:D462Y	D	-	1	0	NUDCD1	110326802	1.000000	0.71417	0.943000	0.38184	0.980000	0.70556	7.365000	0.79537	2.559000	0.86315	0.650000	0.86243	GAT		0.413	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		A	110257626	C	A	110257626	3	1	101	1	0	0	0	0	1	0	0	0	10753	826	29	2	375	2	NUDCD1	8	110257626	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	1017023	110257626	36106396	54	26913										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113349921	113349921	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	taccaattacaaaaccatttCgaaacgggcgtggatcagga	9	9	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:113349921C>A	ENST00000297405.5	-	43	6936	c.6692G>T	c.(6691-6693)cGa>cTa	p.R2231L	CSMD3_ENST00000455883.2_Missense_Mutation_p.R2127L|CSMD3_ENST00000343508.3_Missense_Mutation_p.R2191L|CSMD3_ENST00000352409.3_Missense_Mutation_p.R2161L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2231	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2231Q(2)|p.R2191Q(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAAACCATTTCGAAACGGGCG	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						3	Substitution - Missense(3)	kidney(3)	8											92	94	93					8																	113349921		2203	4300	6503	113419097	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6692G>T	8.37:g.113349921C>A	ENSP00000297405:p.Arg2231Leu		113419097	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429064	0.62844	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.64	5.64	0.86602	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000008	T	0.65004	0.2650	N	0.11845	0.185	0.48830	D	0.999712	D;P;B	0.76494	0.999;0.895;0.05	D;P;B	0.70227	0.968;0.723;0.033	T	0.63377	-0.6651	10	0.27785	T	0.31	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2127;2231;2191	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	L	2191;2231;1501;2127;2161	ENSP00000345799:R2191L;ENSP00000297405:R2231L;ENSP00000341558:R1501L;ENSP00000412263:R2127L;ENSP00000343124:R2161L	ENSP00000297405:R2231L	R	-	2	0	CSMD3	113419097	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.750000	0.62162	2.937000	0.99478	0.650000	0.86243	CGA		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113349921	C	A	113349921	3	1	101	1	0	0	0	0	1	0	0	0	3952	884	31	2	4547	2	CSMD3	8	113349921	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	3092295	113349921	33014101	55	26914										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116430676	116430676	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaaaaacaccggagcctctaCgcctctgaaacaggggaaaa	9	11	2	1	rs549374718		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr8:116430676C>G	ENST00000220888.5	-	5	2825	c.2666G>C	c.(2665-2667)cGt>cCt	p.R889P	TRPS1_ENST00000520276.1_Missense_Mutation_p.R893P|TRPS1_ENST00000395715.3_Missense_Mutation_p.R902P|TRPS1_ENST00000519076.1_Missense_Mutation_p.R643P			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	889					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GGAGCCTCTACGCCTCTGAAA	0.478									Langer-Giedion syndrome																																							0			8											91	93	92					8																	116430676		1913	4124	6037	116499852	SO:0001583	missense	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2666G>C	8.37:g.116430676C>G	ENSP00000220888:p.Arg889Pro		116499852	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	C	17.43	3.387411	0.61956	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	D;D;D;D	0.99663	-6.33;-6.33;-6.33;-6.33	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.99906	1.1179	10	0.87932	D	0	.	20.0805	0.97772	0.0:1.0:0.0:0.0	.	893;889;902	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	P	902;889;643;893	ENSP00000379065:R902P;ENSP00000220888:R889P;ENSP00000428910:R643P;ENSP00000428680:R893P	ENSP00000220888:R889P	R	-	2	0	TRPS1	116499852	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	4.899000	0.63245	2.755000	0.94549	0.650000	0.86243	CGT		0.478	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116430676	C	G	116430676	3	3	101	1	0	0	0	0	1	0	0	0	16633	536	19	5	1187	5	TRPS1	8	116430676	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	3080755	116430676	29933346	56	26915										
JAK2	3717	hgsc.bcm.edu	37	chr9	5069951	5069951	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	caaaccttctagtcttcagaAcgaatggtgtttctgatgta	8	8	4	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr9:5069951A>G	ENST00000381652.3	+	12	2034	c.1540A>G	c.(1540-1542)Acg>Gcg	p.T514A	JAK2_ENST00000539801.1_Missense_Mutation_p.T514A|JAK2_ENST00000544510.1_Missense_Mutation_p.T365A	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	514					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	AGTCTTCAGAACGAATGGTGT	0.318		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											80	74	76					9																	5069951		2203	4298	6501	5059951	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1540A>G	9.37:g.5069951A>G	ENSP00000371067:p.Thr514Ala		5059951	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.189261	0.38707	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.76709	-0.93;-0.93;-1.04	4.93	4.93	0.64822	.	0.176879	0.64402	D	0.000014	T	0.69043	0.3067	L	0.40543	1.245	0.40494	D	0.980571	B	0.13145	0.007	B	0.14578	0.011	T	0.64626	-0.6363	10	0.21014	T	0.42	-9.114	14.2363	0.65929	1.0:0.0:0.0:0.0	.	514	O60674	JAK2_HUMAN	A	514;514;365	ENSP00000440387:T514A;ENSP00000371067:T514A;ENSP00000443103:T365A	ENSP00000371067:T514A	T	+	1	0	JAK2	5059951	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.912000	0.92726	1.836000	0.53414	0.374000	0.22700	ACG		0.318	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5069951	A	G	5069951	3	3	101	1	0	0	0	0	1	0	0	0	7959	43	2	4	1578	4	JAK2	9	5069951	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10		5069951	136143480	57	26916										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632685	32632685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cccagtcacctctaggagacActtgcccttcatggcagcaa	8	15	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr9:32632685A>G	ENST00000242310.4	-	1	2982	c.2893T>C	c.(2893-2895)Tgt>Cgt	p.C965R	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	965					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCTAGGAGACACTTGCCCTTC	0.468																																																0			9											152	142	146					9																	32632685		2203	4300	6503	32622685	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2893T>C	9.37:g.32632685A>G	ENSP00000418379:p.Cys965Arg		32622685	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.340945	0.41498	.	.	ENSG00000122728	ENST00000242310	T	0.14391	2.51	1.04	1.04	0.20106	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.047285	0.85682	D	0.000000	T	0.31765	0.0807	M	0.81682	2.555	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.03630	-1.1018	10	0.87932	D	0	.	5.8599	0.18740	1.0:0.0:0.0:0.0	.	965	Q8IZX4	TAF1L_HUMAN	R	965	ENSP00000418379:C965R	ENSP00000418379:C965R	C	-	1	0	TAF1L	32622685	1.000000	0.71417	0.993000	0.49108	0.868000	0.49771	5.877000	0.69675	0.426000	0.26116	0.164000	0.16699	TGT		0.468	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32632685	A	G	32632685	3	3	101	1	0	0	0	0	1	0	0	0	15562	159	6	4	2591	4	TAF1L	9	32632685	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	27562734	32632685	108580746	58	26917										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98229453	98229453	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttgggaagctgtttgttttcTtccaacatgacatacttcac	7	9	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr9:98229453T>C	ENST00000331920.6	-	15	2804	c.2505A>G	c.(2503-2505)gaA>gaG	p.E835E	PTCH1_ENST00000429896.2_Silent_p.E684E|PTCH1_ENST00000421141.1_Silent_p.E684E|PTCH1_ENST00000418258.1_Silent_p.E684E|PTCH1_ENST00000430669.2_Silent_p.E769E|PTCH1_ENST00000375274.2_Silent_p.E834E|PTCH1_ENST00000437951.1_Silent_p.E769E	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	835					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GTTTGTTTTCTTCCAACATGA	0.468																																																0			9											150	136	141					9																	98229453		2203	4300	6503	97269274	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2505A>G	9.37:g.98229453T>C			97269274	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.468	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98229453	T	C	98229453	2	2	101	1	0	0	0	0	0	0	0	1	12764	1606	56	4		4	PTCH1	9	98229453	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	65596768	98229453	42983978	59	26918										
OR13C3	138803	hgsc.bcm.edu	37	chr9	107298658	107298658	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aacgatcaaatgccatcatgCcaagaagcagacattctgtt	7	10	3	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr9:107298658C>G	ENST00000374781.2	-	1	479	c.437G>C	c.(436-438)gGc>gCc	p.G146A		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						TGCCATCATGCCAAGAAGCAG	0.463																																					GBM(86;1248 1274 14222 15028 46219)											0			9											228	194	206					9																	107298658		2203	4300	6503	106338479	SO:0001583	missense	138803				CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"GPCR / Class A : Olfactory receptors"	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.437G>C	9.37:g.107298658C>G	ENSP00000363913:p.Gly146Ala		106338479	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	37	CCDS35089.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.214858	0.01555	.	.	ENSG00000204246	ENST00000374781	T	0.00949	5.51	4.72	3.75	0.43078	GPCR, rhodopsin-like superfamily (1);	0.153752	0.29868	N	0.010989	T	0.00300	0.0009	N	0.00525	-1.395	0.25407	N	0.988398	B	0.28636	0.218	B	0.15052	0.012	T	0.47886	-0.9082	10	0.02654	T	1	.	7.5769	0.27942	0.1837:0.6387:0.1775:0.0	.	146	Q8NGS6	O13C3_HUMAN	A	146	ENSP00000363913:G146A	ENSP00000363913:G146A	G	-	2	0	OR13C3	106338479	0.008000	0.16893	0.999000	0.59377	0.555000	0.35460	1.115000	0.31209	2.610000	0.88304	0.591000	0.81541	GGC		0.463	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			G	107298658	C	G	107298658	3	3	101	1	0	0	0	0	1	0	0	0	10966	739	26	5	610	5	OR13C3	9	107298658	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	9069205	107298658	33914773	60	26919										
RET	5979	hgsc.bcm.edu	37	chr10	43597981	43597981	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	caaggccctccttccgcattCgggagaaccgacccccaggc	10	18	0	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:43597981C>T	ENST00000355710.3	+	3	761	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	RET_ENST00000340058.5_Missense_Mutation_p.R177W	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	177	Cadherin. {ECO:0000255|PROSITE- ProRule:PRU00043}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTTCCGCATTCGGGAGAACCG	0.617		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	0			10											92	75	81					10																	43597981		2203	4300	6503	42917987	SO:0001583	missense	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.529C>T	10.37:g.43597981C>T	ENSP00000347942:p.Arg177Trp		42917987	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.588246	0.66105	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	T;T	0.53640	0.61;0.61	5.09	0.162	0.14981	Cadherin (3);Cadherin-like (1);	0.255981	0.37669	N	0.001990	T	0.58581	0.2132	L	0.47716	1.5	0.24263	N	0.995271	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.56884	-0.7905	10	0.62326	D	0.03	.	13.8849	0.63702	0.7797:0.2203:0.0:0.0	.	177;177	P07949;P07949-2	RET_HUMAN;.	W	177	ENSP00000347942:R177W;ENSP00000344798:R177W	ENSP00000344798:R177W	R	+	1	2	RET	42917987	0.971000	0.33674	0.197000	0.23402	0.955000	0.61496	1.157000	0.31724	0.100000	0.17581	0.655000	0.94253	CGG		0.617	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		T	43597981	C	T	43597981	3	4	101	1	0	0	0	0	1	0	0	0	13272	875	31	1	539	1	RET	10	43597981	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		43597981	91936766	61	26920										
RET	5979	hgsc.bcm.edu	37	chr10	43617396	43617396	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	attccatcttctctttagggTcggattccagttaaatggat	8	8	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:43617396T>C	ENST00000355710.3	+	16	2965	c.2733T>C	c.(2731-2733)ggT>ggC	p.G911G	RET_ENST00000340058.5_Silent_p.G911G	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	911	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCTTTAGGGTCGGATTCCAG	0.448		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	0			10											225	212	217					10																	43617396		2203	4300	6503	42937402	SO:0001819	synonymous_variant	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2733T>C	10.37:g.43617396T>C			42937402	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																				0.448	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		C	43617396	T	C	43617396	2	2	101	1	0	0	0	0	0	0	0	1	13272	1654	58	4		4	RET	10	43617396	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	19415	43617396	91917351	62	26921										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692797	89692797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atatccttttgaagaccataAcccaccacagctagaactta	4	12	0	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:89692797A>G	ENST00000371953.3	+	5	1638	c.281A>G	c.(280-282)aAc>aGc	p.N94S		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	94	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.H93fs*5(1)|p.Q87_P96del(1)|p.N82_P95del(1)|p.F56fs*2(1)|p.N94I(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GAAGACCATAACCCACCACAG	0.343		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	54	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)|Deletion - In frame(2)|Substitution - Missense(1)	prostate(16)|central_nervous_system(11)|lung(6)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|endometrium(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|urinary_tract(1)	10											111	102	106					10																	89692797		2203	4300	6503	89682777	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.281A>G	10.37:g.89692797A>G	ENSP00000361021:p.Asn94Ser		89682777	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487227	0.84854	.	.	ENSG00000171862	ENST00000371953	D	0.85171	-1.95	5.07	5.07	0.68467	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89329	0.6684	L	0.55990	1.75	0.80722	D	1	D	0.71674	0.998	D	0.64506	0.926	D	0.88938	0.3378	9	.	.	.	-6.8234	14.8406	0.70220	1.0:0.0:0.0:0.0	.	94	P60484	PTEN_HUMAN	S	94	ENSP00000361021:N94S	.	N	+	2	0	PTEN	89682777	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.914000	0.92735	1.880000	0.54463	0.533000	0.62120	AAC		0.343	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692797	A	G	89692797	3	3	101	1	0	0	0	0	1	0	0	0	12772	43	2	4	299	4	PTEN	10	89692797	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	46075401	89692797	45841950	63	26922										
PTEN	5728	hgsc.bcm.edu	37	chr10	89711925	89711925	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gtgtattattatagctacctGttaaagaatcatctggatta	7	5	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:89711925G>A	ENST00000371953.3	+	6	1900	c.543G>A	c.(541-543)ctG>ctA	p.L181L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	181	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(4)|p.V166fs*17(3)|p.G165fs*9(3)|p.Y27fs*1(2)|p.G165_*404del(1)|p.V175fs*3(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATAGCTACCTGTTAAAGAATC	0.383		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	56	Whole gene deletion(37)|Deletion - Frameshift(11)|Unknown(4)|Complex - frameshift(3)|Deletion - In frame(1)	prostate(16)|central_nervous_system(13)|skin(9)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											144	144	144					10																	89711925		2203	4300	6503	89701905	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.543G>A	10.37:g.89711925G>A			89701905	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.383	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89711925	G	A	89711925	2	1	101	1	0	0	0	0	0	0	0	1	12772	1364	48	3		3	PTEN	10	89711925	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	19128	89711925	45822822	64	26923										
PTEN	5728	hgsc.bcm.edu	37	chr10	89725043	89725043	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttttaaattttctttctctaGgtgaagctgtacttcacaaa	5	7	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:89725043G>T	ENST00000371953.3	+	9	2383		c.e9-1			NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(7)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TCTTTCTCTAGGTGAAGCTGT	0.333		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	54	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(7)|Deletion - In frame(1)	prostate(16)|central_nervous_system(12)|skin(5)|endometrium(4)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|kidney(1)	10											42	39	40					10																	89725043		2203	4300	6503	89715023	SO:0001630	splice_region_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1027-1G>T	10.37:g.89725043G>T			89715023	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Splice_Site	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972931	0.53614	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4116	0.94675	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTEN	89715023	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.426000	0.97469	2.652000	0.90054	0.586000	0.80456	.		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Intron	T	89725043	G	T	89725043	5	4	101	1	0	0	0	0	0	0	1	0	12772	1014	35	2	1060	2	PTEN	10	89725043	Splice_Site	SNP	G	TCGA-DC-6683-01A-11D-1826-10	13118	89725043	45809704	65	26924										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114912188	114912188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tgtaccccggctggtccgcgCgggataactatgtaggtgga	15	10	0	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:114912188C>T	ENST00000355995.4	+	11	1765	c.1258C>T	c.(1258-1260)Cgg>Tgg	p.R420W	TCF7L2_ENST00000355717.4_Missense_Mutation_p.R444W|TCF7L2_ENST00000534894.1_Missense_Mutation_p.R420W|TCF7L2_ENST00000538897.1_Missense_Mutation_p.R420W|TCF7L2_ENST00000542695.1_Missense_Mutation_p.R136W|TCF7L2_ENST00000543371.1_Missense_Mutation_p.R420W|TCF7L2_ENST00000369386.1_Missense_Mutation_p.R63W|TCF7L2_ENST00000545257.1_Missense_Mutation_p.R420W|TCF7L2_ENST00000369397.4_Missense_Mutation_p.R397W|TCF7L2_ENST00000369389.1_Missense_Mutation_p.R131W|TCF7L2_ENST00000352065.5_Missense_Mutation_p.R397W|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000536810.1_Missense_Mutation_p.R420W			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	420					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CTGGTCCGCGCGGGATAACTA	0.527			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											105	111	109					10																	114912188		2203	4300	6503	114902178	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1258C>T	10.37:g.114912188C>T	ENSP00000348274:p.Arg420Trp		114902178	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	c	22.3	4.269553	0.80469	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945;ENST00000369386	D;D;D;D;D;D;D;D;D;D;D;D	0.99519	-5.52;-5.55;-5.53;-5.57;-6.03;-6.07;-6.03;-5.54;-6.01;-5.47;-5.96;-5.96	5.66	3.75	0.43078	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.058760	0.64402	D	0.000003	D	0.99477	0.9814	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.998;0.999;0.994;0.999;0.999;0.999;0.998;0.999;0.997;0.999;0.999;0.999;0.999;0.998;0.996;0.999;1.0;1.0	D	0.98626	1.0669	10	0.87932	D	0	-7.2209	14.8202	0.70068	0.263:0.737:0.0:0.0	.	277;237;319;420;291;335;393;397;397;363;420;397;397;402;444;397;420;393;397	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	W	420;420;420;420;444;420;420;397;397;136;131;137;63	ENSP00000348274:R420W;ENSP00000440547:R420W;ENSP00000444972:R420W;ENSP00000446238:R420W;ENSP00000347949:R444W;ENSP00000446172:R420W;ENSP00000443626:R420W;ENSP00000358404:R397W;ENSP00000344823:R397W;ENSP00000443883:R136W;ENSP00000358396:R131W;ENSP00000277945:R137W	ENSP00000277945:R137W	R	+	1	2	TCF7L2	114902178	1.000000	0.71417	0.987000	0.45799	0.996000	0.88848	3.984000	0.56923	0.705000	0.31890	-0.169000	0.13324	CGG		0.527	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114912188	C	T	114912188	3	4	101	1	0	0	0	0	1	0	0	0	15737	759	27	1	1445	1	TCF7L2	10	114912188	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	25187145	114912188	20622559	66	26925										
MKI67	4288	hgsc.bcm.edu	37	chr10	129903300	129903300	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcacctcctgctggtttgggTgtgtccatagctttccctac	9	13	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr10:129903300T>C	ENST00000368654.3	-	13	7179	c.6804A>G	c.(6802-6804)acA>acG	p.T2268T	MKI67_ENST00000368653.3_Silent_p.T1908T	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2268	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTGGTTTGGGTGTGTCCATAG	0.468																																																0			10											298	271	280					10																	129903300		2203	4300	6503	129793290	SO:0001819	synonymous_variant	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6804A>G	10.37:g.129903300T>C			129793290	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																				0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129903300	T	C	129903300	2	2	101	1	0	0	0	0	0	0	0	1	9628	1683	59	4		4	MKI67	10	129903300	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	14991112	129903300	5631447	67	26926										
DKK3	27122	hgsc.bcm.edu	37	chr11	11988507	11988507	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gggaggccactcacctctctGgaaggcacagcacagccccg	12	16	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr11:11988507G>A	ENST00000396505.2	-	6	905	c.667C>T	c.(667-669)Cag>Tag	p.Q223*	DKK3_ENST00000527132.1_Intron|DKK3_ENST00000525493.1_Nonsense_Mutation_p.Q223*|DKK3_ENST00000450094.2_Nonsense_Mutation_p.Q195*|DKK3_ENST00000326932.4_Nonsense_Mutation_p.Q223*	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	223	DKK-type Cys-2.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		TCACCTCTCTGGAAGGCACAG	0.602											OREG0020766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			11											78	76	77					11																	11988507		2201	4294	6495	11945083	SO:0001587	stop_gained	27122			AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.667C>T	11.37:g.11988507G>A	ENSP00000379762:p.Gln223*	676	11945083	A8K1I2|D3DQW1|Q9ULB7	Nonsense_Mutation	SNP	ENST00000396505.2	37	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	G	37	6.264078	0.97426	.	.	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000450094;ENST00000326914;ENST00000533813	.	.	.	5.14	5.14	0.70334	.	0.164588	0.56097	D	0.000034	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-23.544	12.6624	0.56822	0.0805:0.0:0.9195:0.0	.	.	.	.	X	223;223;166;223;195;67;223	.	ENSP00000314730:Q67X	Q	-	1	0	DKK3	11945083	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	6.392000	0.73213	2.379000	0.81126	0.655000	0.94253	CAG		0.602	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		A	11988507	G	A	11988507	4	1	101	1	0	0	0	0	0	1	0	0	4557	1357	47	3	397	3	DKK3	11	11988507	Nonsense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10		11988507	123018009	68	26927										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190275	58190275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcccccaatgtggaatgaggCatttaggaagccacagacat	11	10	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr11:58190275C>T	ENST00000302581.2	-	1	511	c.460G>A	c.(460-462)Gcc>Acc	p.A154T		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGGAATGAGGCATTTAGGAAG	0.493																																																0			11											72	63	66					11																	58190275		2201	4295	6496	57946851	SO:0001583	missense	390190			AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.460G>A	11.37:g.58190275C>T	ENSP00000303076:p.Ala154Thr		57946851	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	C	9.723	1.160226	0.21454	.	.	ENSG00000172365	ENST00000302581	T	0.39056	1.1	3.73	-3.8	0.04307	GPCR, rhodopsin-like superfamily (1);	0.839861	0.09676	U	0.770413	T	0.41811	0.1175	L	0.58810	1.83	0.09310	N	1	P	0.40476	0.718	B	0.41813	0.367	T	0.51926	-0.8643	10	0.66056	D	0.02	-5.2047	14.3488	0.66685	0.7189:0.2811:0.0:0.0	.	154	Q96R09	OR5B2_HUMAN	T	154	ENSP00000303076:A154T	ENSP00000303076:A154T	A	-	1	0	OR5B2	57946851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.785000	0.00367	-0.382000	0.07870	-0.291000	0.09656	GCC		0.493	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		T	58190275	C	T	58190275	3	4	101	1	0	0	0	0	1	0	0	0	11181	710	25	3	473	3	OR5B2	11	58190275	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	46201768	58190275	76816241	69	26928										
GANAB	23193	hgsc.bcm.edu	37	chr11	62414063	62414063	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cgcgccgccactgccgctacCgccgccatcttgtgcagagt	11	18	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr11:62414063C>T	ENST00000356638.3	-	1	25	c.9G>A	c.(7-9)gcG>gcA	p.A3A	GANAB_ENST00000540933.1_5'UTR|GANAB_ENST00000346178.4_Silent_p.A3A|GANAB_ENST00000534779.1_Silent_p.A3A	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	3					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	CTGCCGCTACCGCCGCCATCT	0.682																																					Melanoma(23;1005 1074 15747 18937)											0			11											25	29	28					11																	62414063		2201	4298	6499	62170639	SO:0001819	synonymous_variant	23193			AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.9G>A	11.37:g.62414063C>T			62170639	A6NC20|Q8WTS9|Q9P0X0	Silent	SNP	ENST00000356638.3	37	CCDS8026.1																																																																																				0.682	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		T	62414063	C	T	62414063	2	4	101	1	0	0	0	0	0	0	0	1	6253	639	23	1		1	GANAB	11	62414063	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	4223788	62414063	72592453	70	26929										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73843994	73843994	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cttcaatgtggtctttaaacCgattcctagaaaaggctctg	8	9	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr11:73843994C>A	ENST00000334126.7	-	7	1338	c.1112G>T	c.(1111-1113)cGg>cTg	p.R371L	C2CD3_ENST00000539061.1_Missense_Mutation_p.R371L|C2CD3_ENST00000313663.7_Missense_Mutation_p.R371L			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	371					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.R371P(1)|p.R371Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GTCTTTAAACCGATTCCTAGA	0.388																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	11											171	155	160					11																	73843994		2200	4293	6493	73521642	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1112G>T	11.37:g.73843994C>A	ENSP00000334379:p.Arg371Leu		73521642	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.07|13.07	2.128638|2.128638	0.37533|0.37533	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000289350|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000539061	.|T;T	.|0.09163	.|3.01;3.02	5.2|5.2	-0.211|-0.211	0.13172|0.13172	.|.	.|1.109980	.|0.06889	.|N	.|0.803948	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|B;B	.|0.26512	.|0.015;0.151	.|B;B	.|0.19391	.|0.016;0.025	T|T	0.44112|0.44112	-0.9349|-0.9349	6|10	0.39692|0.11182	T|T	0.17|0.66	6.7573|6.7573	5.9902|5.9902	0.19456|0.19456	0.0:0.3639:0.2564:0.3797|0.0:0.3639:0.2564:0.3797	.|.	.|371;371	.|Q4AC94;Q4AC94-1	.|C2CD3_HUMAN;.	C|L	371|371	.|ENSP00000334379:R371L;ENSP00000323339:R371L	ENSP00000289350:G371C|ENSP00000323339:R371L	G|R	-|-	1|2	0|0	C2CD3|C2CD3	73521642|73521642	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.144000|0.144000	0.21451|0.21451	0.034000|0.034000	0.13776|0.13776	-0.270000|-0.270000	0.09285|0.09285	-0.254000|-0.254000	0.11334|0.11334	GGT|CGG		0.388	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73843994	C	A	73843994	3	1	101	1	0	0	0	0	1	0	0	0	2160	652	23	2	4879	2	C2CD3	11	73843994	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	11429931	73843994	61162522	71	26930										
ATM	472	hgsc.bcm.edu	37	chr11	108205780	108205780	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tagcaggaggtgtaaatttaCcaaaaataatagattgtgta	9	3	0	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr11:108205780C>A	ENST00000452508.2	+	56	8284	c.8095C>A	c.(8095-8097)Cca>Aca	p.P2699T	ATM_ENST00000278616.4_Missense_Mutation_p.P2699T|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2699					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.P2699S(2)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGTAAATTTACCAAAAATAAT	0.398			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	11											98	97	98					11																	108205780		2201	4298	6499	107710990	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8095C>A	11.37:g.108205780C>A	ENSP00000388058:p.Pro2699Thr		107710990	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642621	0.87859	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.94046	-3.34;-3.34	5.67	4.74	0.60224	Protein kinase-like domain (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.98052	0.9358	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99461	1.0943	10	0.87932	D	0	.	15.8575	0.78989	0.1367:0.8633:0.0:0.0	.	2699	Q13315	ATM_HUMAN	T	2699	ENSP00000278616:P2699T;ENSP00000388058:P2699T	ENSP00000278616:P2699T	P	+	1	0	ATM	107710990	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.230000	0.78097	1.351000	0.45789	0.655000	0.94253	CCA		0.398	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108205780	C	A	108205780	3	1	101	1	0	0	0	0	1	0	0	0	1110	507	18	2	8309	2	ATM	11	108205780	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	34361786	108205780	26800736	72	26931										
A2M	2	hgsc.bcm.edu	37	chr12	9251204	9251204	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gaggctgccaggaactcaccGaggacgccgagagctcagca	14	13	2	1	rs531579697		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:9251204G>A	ENST00000318602.7	-	15	2157	c.1850C>T	c.(1849-1851)tCg>tTg	p.S617L		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	617					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	GGAACTCACCGAGGACGCCGA	0.552																																																0			12											26	27	26					12																	9251204		2203	4298	6501	9142471	SO:0001630	splice_region_variant	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1851+1C>T	12.37:g.9251204G>A			9142471	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.128480	0.37533	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.29655	1.56	5.55	4.65	0.58169	.	0.682982	0.14032	N	0.346065	T	0.27027	0.0662	L	0.42529	1.33	0.80722	D	1	B	0.20988	0.05	B	0.12837	0.008	T	0.03651	-1.1016	10	0.40728	T	0.16	.	10.8266	0.46635	0.0896:0.0:0.9104:0.0	.	617	P01023	A2MG_HUMAN	L	617;632	ENSP00000323929:S617L	ENSP00000323929:S617L	S	-	2	0	A2M	9142471	0.732000	0.28121	0.763000	0.31416	0.279000	0.26890	2.166000	0.42406	1.457000	0.47850	0.655000	0.94253	TCG		0.552	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	Missense_Mutation	A	9251204	G	A	9251204	5	1	101	1	0	0	0	0	0	0	1	0	4	1072	37	1	2662	1	A2M	12	9251204	Splice_Site	SNP	G	TCGA-DC-6683-01A-11D-1826-10		9251204	124600691	73	26932										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000311936.3_Missense_Mutation_p.G12C|KRAS_ENST00000557334.1_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	12.37:g.25398285C>A	ENSP00000256078:p.Gly12Cys		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398285	C	A	25398285	3	1	101	1	0	0	0	0	1	0	0	0	8459	594	21	2	672	2	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	16147081	25398285	108453610	74	26933										
C12orf11	55726	hgsc.bcm.edu	37	chr12	27064184	27064184	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tttggaggttctggggaatcAggcgaatcttttataatctc	11	6	4	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:27064184A>G	ENST00000261191.7	-	15	2408	c.1872T>C	c.(1870-1872)ccT>ccC	p.P624P	ASUN_ENST00000539625.1_Silent_p.P523P	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	624					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTGGGGAATCAGGCGAATCTT	0.373																																																0			12											133	134	133					12																	27064184		2203	4300	6503	26955451	SO:0001819	synonymous_variant	55726			AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1872T>C	12.37:g.27064184A>G			26955451	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	37	CCDS8708.1																																																																																				0.373	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		G	27064184	A	G	27064184	2	3	101	1	0	0	0	0	0	0	0	1	1679	175	7	4		4	C12orf11	12	27064184	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	1665899	27064184	106787711	75	26934										
ARID2	196528	hgsc.bcm.edu	37	chr12	46123634	46123634	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaaataatggcaaactcgacGgggaaggcgcctccggacga	13	10	0	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:46123634G>A	ENST00000334344.6	+	1	187	c.15G>A	c.(13-15)acG>acA	p.T5T	LINC00938_ENST00000609803.1_lincRNA|ARID2_ENST00000422737.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	5					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAAACTCGACGGGGAAGGCGC	0.582			"N, S, F"		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0			12											15	20	18					12																	46123634		2189	4294	6483	44409901	SO:0001819	synonymous_variant	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.15G>A	12.37:g.46123634G>A			44409901	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																				0.582	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46123634	G	A	46123634	2	1	101	1	0	0	0	0	0	0	0	1	915	1103	39	1		1	ARID2	12	46123634	Silent	SNP	G	TCGA-DC-6683-01A-11D-1826-10	19059450	46123634	87728261	76	26935										
NAV3	89795	hgsc.bcm.edu	37	chr12	78583787	78583787	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tagaagaaaatagtttggacAgttttgtttttgatacgctg	10	3	0	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:78583787A>T	ENST00000397909.2	+	34	6252	c.6079A>T	c.(6079-6081)Agt>Tgt	p.S2027C	NAV3_ENST00000266692.7_Missense_Mutation_p.S1828C|NAV3_ENST00000536525.2_Missense_Mutation_p.S2005C|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000228327.6_Missense_Mutation_p.S2005C			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2027						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TAGTTTGGACAGTTTTGTTTT	0.338										HNSCC(70;0.22)																																						0			12											104	95	98					12																	78583787		1904	4143	6047	77107918	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6079A>T	12.37:g.78583787A>T	ENSP00000381007:p.Ser2027Cys		77107918	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.52|18.52	3.641227|3.641227	0.67244|0.67244	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000552895|ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	.|D;D;D;D;D	.|0.88664	.|-2.41;-2.41;-2.41;-2.41;-2.41	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	.|0.000000	.|0.47093	.|U	.|0.000249	D|D	0.91304|0.91304	0.7258|0.7258	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|B;D;D;D	.|0.89917	.|0.118;0.995;1.0;0.998	.|B;P;D;D	.|0.66497	.|0.159;0.821;0.944;0.924	D|D	0.91626|0.91626	0.5315|0.5315	5|10	.|0.51188	.|T	.|0.08	-2.6613|-2.6613	14.8066|14.8066	0.69962|0.69962	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2005;1828;2027;2005	.|E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.|.;.;NAV3_HUMAN;.	L|C	899|2005;2027;2005;1828;619;627	.|ENSP00000446132:S2005C;ENSP00000381007:S2027C;ENSP00000228327:S2005C;ENSP00000266692:S1828C;ENSP00000448303:S627C	.|ENSP00000228327:S2005C	Q|S	+|+	2|1	0|0	NAV3|NAV3	77107918|77107918	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.905000|5.905000	0.69893|0.69893	1.966000|1.966000	0.57179|0.57179	0.459000|0.459000	0.35465|0.35465	CAG|AGT		0.338	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78583787	A	T	78583787	3	4	101	1	0	0	0	0	1	0	0	0	10215	188	7	5	6143	5	NAV3	12	78583787	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	32460153	78583787	55268108	77	26936										
ARL6IP4	23457	hgsc.bcm.edu	37	chr12	123466587	123466587	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atgcccggcagagcatcatcCgcaaggtggtggaccctgag	14	12	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:123466587C>T	ENST00000542678.1	-	0	0				ARL6IP4_ENST00000454885.2_Missense_Mutation_p.R174C|ARL6IP4_ENST00000392435.2_Missense_Mutation_p.R289C|ARL6IP4_ENST00000357866.4_Missense_Mutation_p.R129C|ARL6IP4_ENST00000543566.1_Missense_Mutation_p.R289C|ARL6IP4_ENST00000439686.2_Missense_Mutation_p.R177C|ARL6IP4_ENST00000426960.2_Missense_Mutation_p.R166C|ARL6IP4_ENST00000453766.2_Missense_Mutation_p.R300C|ARL6IP4_ENST00000315580.5_Missense_Mutation_p.R308C|ARL6IP4_ENST00000412505.2_Missense_Mutation_p.R118C|RP11-197N18.2_ENST00000540866.2_RNA			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		GAGCATCATCCGCAAGGTGGT	0.602																																					Ovarian(49;786 1333 9175 38236)											0			12											60	59	60					12																	123466587		2203	4300	6503	122032540	SO:0001631	upstream_gene_variant	51329			U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78			12.37:g.123466587C>T	Exception_encountered		122032540	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925206	0.73213	.	.	ENSG00000182196	ENST00000544323;ENST00000543566;ENST00000315580;ENST00000542099;ENST00000392435;ENST00000413381;ENST00000426960;ENST00000453766;ENST00000454885;ENST00000412505;ENST00000439686;ENST00000456762;ENST00000357866	T;T;T;T;T;T;T;T;T;T;T;T;T	0.66460	0.93;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.82277	0.5002	M	0.83223	2.63	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.997;0.995;0.999;0.998;0.998;0.996	D	0.84799	0.0783	10	0.87932	D	0	.	13.5635	0.61804	0.2861:0.7139:0.0:0.0	.	174;252;289;289;308;300	B3V0L1;Q66PJ3-5;Q66PJ3-4;B3V0L0;Q66PJ3;Q66PJ3-2	.;.;.;.;AR6P4_HUMAN;.	C	241;289;308;297;289;177;166;300;174;118;177;167;129	ENSP00000445309:R241C;ENSP00000442718:R289C;ENSP00000313422:R308C;ENSP00000442200:R297C;ENSP00000376230:R289C;ENSP00000441406:R177C;ENSP00000406036:R166C;ENSP00000414847:R300C;ENSP00000396723:R174C;ENSP00000413132:R118C;ENSP00000396365:R177C;ENSP00000391598:R167C;ENSP00000350532:R129C	ENSP00000313422:R308C	R	+	1	0	ARL6IP4	122032540	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	2.971000	0.49248	2.475000	0.83589	0.561000	0.74099	CGC		0.602	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		T	123466587	C	T	123466587	1	4	101	0	1	0	0	0	0	0	0	0	944	652	23	1		1	ARL6IP4	12	123466587	5'Flank	SNP	C	TCGA-DC-6683-01A-11D-1826-10	44882800	123466587	10385308	78	26937										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124315193	124315193	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tggaactgcacaaacacacaGatgttctcaatgagattgtc	8	9	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:124315193G>C	ENST00000409039.3	+	25	4163	c.4138G>C	c.(4138-4140)Gat>Cat	p.D1380H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1380	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CAAACACACAGATGTTCTCAA	0.378																																																0			12											75	72	73					12																	124315193		1880	4111	5991	122881146	SO:0001583	missense	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4138G>C	12.37:g.124315193G>C	ENSP00000386770:p.Asp1380His		122881146	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	13.75	2.329822	0.41297	.	.	ENSG00000197653	ENST00000409039	T	0.62788	0.0	5.52	5.52	0.82312	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.82277	0.5002	M	0.88906	2.99	0.37576	D	0.919609	D	0.62365	0.991	D	0.63793	0.918	D	0.87111	0.2185	9	0.87932	D	0	.	19.4505	0.94865	0.0:0.0:1.0:0.0	.	1380	Q8IVF4	DYH10_HUMAN	H	1380	ENSP00000386770:D1380H	ENSP00000386770:D1380H	D	+	1	0	DNAH10	122881146	1.000000	0.71417	0.063000	0.19743	0.116000	0.19942	5.021000	0.64072	2.597000	0.87782	0.655000	0.94253	GAT		0.378	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124315193	G	C	124315193	3	2	101	1	0	0	0	0	1	0	0	0	4609	942	33	5	4236	5	DNAH10	12	124315193	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	848606	124315193	9536702	79	26938										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130851689	130851689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atttttaagccctagactaaCggtaattgtggtgaagaaaa	9	5	0	3	rs117506395		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr12:130851689C>T	ENST00000245255.3	+	19	2479	c.2207C>T	c.(2206-2208)aCg>aTg	p.T736M	PIWIL1_ENST00000541480.1_3'UTR	NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	736	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CCTAGACTAACGGTAATTGTG	0.388													C|||	1	0.000199681	0	0	5008	,	,		19889	0		0.001	False		,,,				2504	0															0			12						C	MET/THR,MET/THR	0,4406		0,0,2203	157	146	150		2207,2207	5.8	0.1	12	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	PIWIL1	NM_001190971.1,NM_004764.4	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	736/830,736/862	130851689	1,13005	2203	4300	6503	129417642	SO:0001583	missense	9271			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2207C>T	12.37:g.130851689C>T	ENSP00000245255:p.Thr736Met		129417642	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.83	3.899460	0.72754	0.0	1.16E-4	ENSG00000125207	ENST00000245255	T	0.14640	2.49	5.78	5.78	0.91487	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.154450	0.56097	D	0.000024	T	0.43010	0.1228	M	0.84082	2.675	0.54753	D	0.999989	D;D	0.76494	0.999;0.999	D;D	0.69654	0.965;0.931	T	0.37407	-0.9707	10	0.87932	D	0	-10.6778	18.9996	0.92828	0.0:1.0:0.0:0.0	.	736;736	Q96J94;Q96J94-2	PIWL1_HUMAN;.	M	736	ENSP00000245255:T736M	ENSP00000245255:T736M	T	+	2	0	PIWIL1	129417642	0.695000	0.27747	0.118000	0.21660	0.928000	0.56348	3.181000	0.50903	2.732000	0.93576	0.591000	0.81541	ACG		0.388	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			T	130851689	C	T	130851689	3	4	101	1	0	0	0	0	1	0	0	0	11988	536	19	1	2277	1	PIWIL1	12	130851689	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	6536496	130851689	3000206	80	26939										
FLT3	2322	hgsc.bcm.edu	37	chr13	28599079	28599079	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aacttctcttgaaccaggcaTgctattaaaaaattttgttt	5	7	1	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:28599079T>C	ENST00000241453.7	-	18	2290	c.2209A>G	c.(2209-2211)Atg>Gtg	p.M737V	FLT3_ENST00000537084.1_Splice_Site_p.M737V|FLT3_ENST00000380982.4_Splice_Site_p.M737V	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	737	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAACCAGGCATGCTATTAAAA	0.303			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13											97	105	102					13																	28599079		2203	4300	6503	27497079	SO:0001630	splice_region_variant	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2208-1A>G	13.37:g.28599079T>C			27497079	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	T	3.839	-0.034180	0.07543	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.76709	-0.97;-1.04;-0.75	5.67	4.48	0.54585	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.285052	0.36932	N	0.002328	T	0.60637	0.2284	N	0.16368	0.405	0.30284	N	0.791016	B;B	0.28350	0.017;0.208	B;B	0.27380	0.008;0.079	T	0.56944	-0.7895	10	0.27785	T	0.31	.	9.5515	0.39313	0.0:0.0812:0.0:0.9188	.	737;737	P36888-2;P36888	.;FLT3_HUMAN	V	737	ENSP00000241453:M737V;ENSP00000370369:M737V;ENSP00000438139:M737V	ENSP00000241453:M737V	M	-	1	0	FLT3	27497079	0.995000	0.38212	0.881000	0.34555	0.480000	0.33159	2.872000	0.48467	0.974000	0.38366	0.454000	0.30748	ATG		0.303	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		Missense_Mutation	C	28599079	T	C	28599079	5	2	101	1	0	0	0	0	0	0	1	0	5961	1478	51	4	800	4	FLT3	13	28599079	Splice_Site	SNP	T	TCGA-DC-6683-01A-11D-1826-10		28599079	86570799	81	26940										
BRCA2	675	hgsc.bcm.edu	37	chr13	32912506	32912506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cataacttagaatttgatggCagtgattcaagtaaaaatga	8	4	1	4	rs276174839		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:32912506C>T	ENST00000380152.3	+	11	4247	c.4014C>T	c.(4012-4014)ggC>ggT	p.G1338G	BRCA2_ENST00000544455.1_Silent_p.G1338G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1338	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.G1338G(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AATTTGATGGCAGTGATTCAA	0.303			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	1	Substitution - coding silent(1)	oesophagus(1)	13											33	33	33					13																	32912506		2202	4300	6502	31810506	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.4014C>T	13.37:g.32912506C>T			31810506	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.303	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32912506	C	T	32912506	2	4	101	1	0	0	0	0	0	0	0	1	1502	697	25	3		3	BRCA2	13	32912506	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	4313427	32912506	82257372	82	26941										
BRCA2	675	hgsc.bcm.edu	37	chr13	32968953	32968953	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcaagcaacctccagtggcgAccagaatccaaatcaggcct	9	14	1	1	rs80359758		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:32968953A>G	ENST00000380152.3	+	25	9617	c.9384A>G	c.(9382-9384)cgA>cgG	p.R3128R	BRCA2_ENST00000544455.1_Silent_p.R3128R			P51587	BRCA2_HUMAN	breast cancer 2, early onset	3128					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCCAGTGGCGACCAGAATCCA	0.383			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											100	93	95					13																	32968953		2203	4300	6503	31866953	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.9384A>G	13.37:g.32968953A>G			31866953	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.383	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32968953	A	G	32968953	2	3	101	1	0	0	0	0	0	0	0	1	1502	262	10	4		4	BRCA2	13	32968953	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	56447	32968953	82200925	83	26942										
CCNA1	8900	hgsc.bcm.edu	37	chr13	37011834	37011834	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ccagctggaaagaaagcactCcctgactgtggggtccaaga	12	11	0	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:37011834C>T	ENST00000255465.4	+	3	630	c.366C>T	c.(364-366)ctC>ctT	p.L122L	CCNA1_ENST00000440264.1_Silent_p.L78L|CCNA1_ENST00000449823.1_Silent_p.L78L|CCNA1_ENST00000418263.1_Silent_p.L121L|CCNA1_ENST00000463403.1_3'UTR			P78396	CCNA1_HUMAN	cyclin A1	122					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.L122L(1)|p.P123>S(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		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;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		AGAAAGCACTCCCTGACTGTG	0.498																																																2	Substitution - coding silent(1)|Complex - compound substitution(1)	lung(2)	13											86	93	91					13																	37011834		2203	4300	6503	35909834	SO:0001819	synonymous_variant	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.366C>T	13.37:g.37011834C>T			35909834	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Silent	SNP	ENST00000255465.4	37	CCDS9357.1																																																																																				0.498	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		T	37011834	C	T	37011834	2	4	101	1	0	0	0	0	0	0	0	1	2915	842	30	3		3	CCNA1	13	37011834	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	4042881	37011834	78158044	84	26943										
EXOSC8	11340	hgsc.bcm.edu	37	chr13	37578694	37578694	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gatgcccctgataaaggataCgttggtaagttaaatggttt	11	5	0	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:37578694C>T	ENST00000389704.3	+	5	499	c.234C>T	c.(232-234)taC>taT	p.Y78Y	EXOSC8_ENST00000489088.1_3'UTR	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	78					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		ATAAAGGATACGTTGGTAAGT	0.279																																																0			13											67	68	68					13																	37578694		2203	4300	6503	36476694	SO:0001819	synonymous_variant	11340			AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"CBP-interacting protein 3", "Opa interacting protein 2"	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.234C>T	13.37:g.37578694C>T			36476694	O43480|Q5TBA5	Silent	SNP	ENST00000389704.3	37	CCDS31958.1																																																																																				0.279	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503		T	37578694	C	T	37578694	2	4	101	1	0	0	0	0	0	0	0	1	5333	547	19	1		1	EXOSC8	13	37578694	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	566860	37578694	77591184	85	26944										
C13orf28	122258	hgsc.bcm.edu	37	chr13	113052451	113052451	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcaacattatcaacaccgttAcgtaaggagaaaagcaagca	7	9	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr13:113052451A>G	ENST00000283550.3	+	3	307	c.240A>G	c.(238-240)ttA>ttG	p.L80L	SPACA7_ENST00000375699.3_Splice_Site_p.L49L	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	80						acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						CAACACCGTTACGTAAGGAGA	0.423																																																0			13											162	139	147					13																	113052451		2203	4300	6503	112100452	SO:0001630	splice_region_variant	122258			BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 28"	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.241+1A>G	13.37:g.113052451A>G			112100452	Q5T8L1	Silent	SNP	ENST00000283550.3	37	CCDS9524.1																																																																																				0.423	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	Silent	G	113052451	A	G	113052451	5	3	101	1	0	0	0	0	0	0	1	0	1728	405	14	4	250	4	C13orf28	13	113052451	Splice_Site	SNP	A	TCGA-DC-6683-01A-11D-1826-10	75473757	113052451	2117427	86	26945										
MNAT1	4331	hgsc.bcm.edu	37	chr14	61285488	61285488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ttttggctcagcataaagatAgatctacccaattagaaatg	7	7	2	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr14:61285488A>G	ENST00000261245.4	+	6	711	c.610A>G	c.(610-612)Aga>Gga	p.R204G	MNAT1_ENST00000539616.2_Intron	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	204					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		GCATAAAGATAGATCTACCCA	0.363								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																																								0			14											77	77	77					14																	61285488		2203	4300	6503	60355241	SO:0001583	missense	4331			X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.610A>G	14.37:g.61285488A>G	ENSP00000261245:p.Arg204Gly		60355241	G3V1U8|Q15817|Q6ICQ7	Missense_Mutation	SNP	ENST00000261245.4	37	CCDS9750.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.988120	0.35036	.	.	ENSG00000020426	ENST00000261245;ENST00000554002;ENST00000557134	T;T	0.47869	0.87;0.83	5.87	4.75	0.60458	Cdk-activating kinase assembly factor MAT1, centre (1);	0.043838	0.85682	D	0.000000	T	0.43500	0.1250	L	0.58810	1.83	0.80722	D	1	P	0.38280	0.625	B	0.34536	0.185	T	0.41378	-0.9512	10	0.51188	T	0.08	-6.0627	12.8736	0.57978	0.563:0.437:0.0:0.0	.	204	P51948	MAT1_HUMAN	G	204;99;64	ENSP00000261245:R204G;ENSP00000451017:R64G	ENSP00000261245:R204G	R	+	1	2	MNAT1	60355241	0.999000	0.42202	0.982000	0.44146	0.543000	0.35085	1.655000	0.37345	1.182000	0.42928	0.533000	0.62120	AGA		0.363	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		G	61285488	A	G	61285488	3	3	101	1	0	0	0	0	1	0	0	0	9704	412	15	4	632	4	MNAT1	14	61285488	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10		61285488	46064052	87	26946										
RHOJ	57381	hgsc.bcm.edu	37	chr14	63747827	63747827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcaaggactgcatgcctcacGtgccttatgtcctcataggg	10	12	3	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr14:63747827G>A	ENST00000316754.3	+	3	838	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	RHOJ_ENST00000555125.1_Missense_Mutation_p.V126M	NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	126					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		CATGCCTCACGTGCCTTATGT	0.532																																																0			14											124	96	106					14																	63747827		2203	4300	6503	62817580	SO:0001583	missense	57381			AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"RAS-like, family 7, member B", "ras homolog gene family, member J"	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.376G>A	14.37:g.63747827G>A	ENSP00000316729:p.Val126Met		62817580	Q96KC1	Missense_Mutation	SNP	ENST00000316754.3	37	CCDS9757.1	.	.	.	.	.	.	.	.	.	.	G	34	5.305812	0.95629	.	.	ENSG00000126785	ENST00000316754;ENST00000555125	T;T	0.79141	-1.24;-1.24	5.87	5.87	0.94306	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84960	0.5588	M	0.85710	2.77	0.80722	D	1	P	0.51147	0.942	P	0.47162	0.54	D	0.87270	0.2285	10	0.87932	D	0	.	20.2147	0.98293	0.0:0.0:1.0:0.0	.	126	Q9H4E5	RHOJ_HUMAN	M	126	ENSP00000316729:V126M;ENSP00000451643:V126M	ENSP00000316729:V126M	V	+	1	0	RHOJ	62817580	1.000000	0.71417	0.972000	0.41901	0.942000	0.58702	9.844000	0.99494	2.785000	0.95823	0.591000	0.81541	GTG		0.532	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3			A	63747827	G	A	63747827	3	1	101	1	0	0	0	0	1	0	0	0	13378	1145	40	1	386	1	RHOJ	14	63747827	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	2462339	63747827	43601713	88	26947										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105352895	105352895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gacagcagacgcaggagcccCcaggaggggcccacgtggag	17	13	0	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr14:105352895C>T	ENST00000414716.3	+	12	2547	c.2319C>T	c.(2317-2319)ccC>ccT	p.P773P	CEP170B_ENST00000556508.1_Silent_p.P703P|CEP170B_ENST00000418279.1_Silent_p.P703P|CEP170B_ENST00000453495.1_Silent_p.P774P	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	773						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GCAGGAGCCCCCAGGAGGGGC	0.697																																																0			14											8	10	9					14																	105352895		1841	4028	5869	104423940	SO:0001819	synonymous_variant	283638			AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.2319C>T	14.37:g.105352895C>T			104423940	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																				0.697	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105352895	C	T	105352895	2	4	101	1	0	0	0	0	0	0	0	1	8187	610	22	3		3	KIAA0284	14	105352895	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	41605068	105352895	1996645	89	26948										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43817611	43817611	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gggcgatcacaagccctgatGaacacattctgacacctgat	9	12	2	4			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr15:43817611G>A	ENST00000300231.5	+	4	4390	c.3940G>A	c.(3940-3942)Gaa>Aaa	p.E1314K	MAP1A_ENST00000399453.1_Missense_Mutation_p.E1314K|MAP1A_ENST00000382031.1_Missense_Mutation_p.E1552K			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1314					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AAGCCCTGATGAACACATTCT	0.502																																																0			15											82	83	83					15																	43817611		2018	4183	6201	41604903	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3940G>A	15.37:g.43817611G>A	ENSP00000300231:p.Glu1314Lys		41604903	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.828609	0.32329	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01613	4.73;4.74;4.74	4.98	4.03	0.46877	.	.	.	.	.	T	0.02888	0.0086	M	0.62723	1.935	0.18873	N	0.999986	B	0.33612	0.419	B	0.33690	0.168	T	0.33317	-0.9873	9	0.40728	T	0.16	-8.2832	8.7091	0.34374	0.0899:0.1676:0.7425:0.0	.	1314	P78559	MAP1A_HUMAN	K	1552;1314;1314	ENSP00000371462:E1552K;ENSP00000382380:E1314K;ENSP00000300231:E1314K	ENSP00000300231:E1314K	E	+	1	0	MAP1A	41604903	0.181000	0.23161	0.989000	0.46669	0.669000	0.39330	1.450000	0.35134	2.605000	0.88082	0.563000	0.77884	GAA		0.502	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43817611	G	A	43817611	3	1	101	1	0	0	0	0	1	0	0	0	9257	1291	45	3	3942	3	MAP1A	15	43817611	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10		43817611	58713781	90	26949										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305356	54305356	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aagacgaggccagtaaagagTtttccctctcaccaacattc	7	12	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr15:54305356T>A	ENST00000260323.11	+	1	256	c.256T>A	c.(256-258)Ttt>Att	p.F86I	UNC13C_ENST00000537900.1_Missense_Mutation_p.F86I|UNC13C_ENST00000545554.1_Missense_Mutation_p.F86I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	86					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAGTAAAGAGTTTTCCCTCTC	0.403																																																0			15											62	61	61					15																	54305356		1895	4110	6005	52092648	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.256T>A	15.37:g.54305356T>A	ENSP00000260323:p.Phe86Ile		52092648	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766527	0.69878	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.79033	-1.23;-1.23;-1.23	5.09	2.76	0.32466	.	.	.	.	.	T	0.63710	0.2534	L	0.27053	0.805	0.30819	N	0.738001	B	0.24823	0.112	B	0.21708	0.036	T	0.62746	-0.6789	9	0.72032	D	0.01	.	6.7788	0.23634	0.0:0.0801:0.1541:0.7658	.	86	Q8NB66	UN13C_HUMAN	I	86	ENSP00000260323:F86I;ENSP00000438156:F86I;ENSP00000442569:F86I	ENSP00000260323:F86I	F	+	1	0	UNC13C	52092648	1.000000	0.71417	0.880000	0.34516	0.865000	0.49528	6.225000	0.72271	0.757000	0.33036	0.533000	0.62120	TTT		0.403	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54305356	T	A	54305356	3	1	101	1	0	0	0	0	1	0	0	0	17026	1725	60	5	258	5	UNC13C	15	54305356	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	10487745	54305356	48226036	91	26950										
LINGO1	84894	hgsc.bcm.edu	37	chr15	77907398	77907398	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	agcggagatagactaggtggCggacggccaggtagggcaca	18	8	0	2	rs202233236		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr15:77907398C>T	ENST00000355300.6	-	2	1025	c.851G>A	c.(850-852)cGc>cAc	p.R284H	LINGO1_ENST00000561030.1_Missense_Mutation_p.R278H	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	284					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						GACTAGGTGGCGGACGGCCAG	0.582													C|||	1	0.000199681	0	0.0014	5008	,	,		21171	0		0	False		,,,				2504	0															0			15											101	102	102					15																	77907398		2190	4285	6475	75694453	SO:0001583	missense	84894			AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.851G>A	15.37:g.77907398C>T	ENSP00000347451:p.Arg284His		75694453	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	37	CCDS45313.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	11.64	1.699149	0.30142	.	.	ENSG00000169783	ENST00000355300	T	0.79940	-1.32	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.77363	0.4119	L	0.51422	1.61	0.80722	D	1	B	0.21606	0.058	B	0.06405	0.002	T	0.72204	-0.4361	10	0.35671	T	0.21	.	19.0471	0.93025	0.0:1.0:0.0:0.0	.	284	Q96FE5	LIGO1_HUMAN	H	284	ENSP00000347451:R284H	ENSP00000347451:R284H	R	-	2	0	LINGO1	75694453	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.306000	0.51881	2.513000	0.84729	0.462000	0.41574	CGC		0.582	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		T	77907398	C	T	77907398	3	4	101	1	0	0	0	0	1	0	0	0	8838	768	27	1	1015	1	LINGO1	15	77907398	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	23602042	77907398	24623994	92	26951										
ASB7	140460	hgsc.bcm.edu	37	chr15	101188573	101188573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gtgccgaattaaaattcgacAatgtataggccttcaaaacc	7	9	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr15:101188573A>G	ENST00000332783.7	+	6	1648	c.863A>G	c.(862-864)cAa>cGa	p.Q288R	ASB7_ENST00000558747.1_Missense_Mutation_p.Q86R	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	288	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	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)			AAAATTCGACAATGTATAGGC	0.363																																																0			15											96	91	93					15																	101188573		2203	4300	6503	99006096	SO:0001583	missense	140460				CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"Ankyrin repeat domain containing"	17182	protein-coding gene	gene with protein product		615052	"ankyrin repeat and SOCS box-containing 7"				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.863A>G	15.37:g.101188573A>G	ENSP00000328327:p.Gln288Arg		99006096	A8K1E5|Q6GSJ6|Q7Z4S3	Missense_Mutation	SNP	ENST00000332783.7	37	CCDS10387.1	.	.	.	.	.	.	.	.	.	.	A	9.274	1.046295	0.19748	.	.	ENSG00000183475	ENST00000332783	T	0.38401	1.14	5.51	5.51	0.81932	SOCS protein, C-terminal (3);	0.159749	0.56097	D	0.000022	T	0.21022	0.0506	N	0.05574	-0.02	0.80722	D	1	B	0.14805	0.011	B	0.11329	0.006	T	0.08027	-1.0742	10	0.19147	T	0.46	-3.6355	15.657	0.77144	1.0:0.0:0.0:0.0	.	288	Q9H672	ASB7_HUMAN	R	288	ENSP00000328327:Q288R	ENSP00000328327:Q288R	Q	+	2	0	ASB7	99006096	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	8.738000	0.91569	2.097000	0.63578	0.533000	0.62120	CAA		0.363	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708		G	101188573	A	G	101188573	3	3	101	1	0	0	0	0	1	0	0	0	1029	130	5	4	881	4	ASB7	15	101188573	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	23281175	101188573	1342819	93	26952										
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21968795	21968795	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tggaaaactattctcctgtaTcaagaattggtttgttcatt	7	6	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr16:21968795T>C	ENST00000268379.4	+	3	939	c.175T>C	c.(175-177)Tca>Cca	p.S59P	UQCRC2_ENST00000561553.1_Missense_Mutation_p.S59P	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	59					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		TTCTCCTGTATCAAGAATTGG	0.363																																					Colon(123;450 1645 12841 25393 45623)											0			16											140	131	134					16																	21968795		2198	4300	6498	21876296	SO:0001583	missense	7385			J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.175T>C	16.37:g.21968795T>C	ENSP00000268379:p.Ser59Pro		21876296	B3KSN4|Q9BQ05	Missense_Mutation	SNP	ENST00000268379.4	37	CCDS10601.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.978180	0.74360	.	.	ENSG00000140740	ENST00000268379	T	0.26518	1.73	5.5	4.39	0.52855	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56352	0.1979	M	0.89715	3.055	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.64015	-0.6506	10	0.72032	D	0.01	-9.395	11.943	0.52911	0.0:0.0:0.1456:0.8544	.	59	P22695	QCR2_HUMAN	P	59	ENSP00000268379:S59P	ENSP00000268379:S59P	S	+	1	0	UQCRC2	21876296	1.000000	0.71417	0.727000	0.30756	0.830000	0.47004	4.647000	0.61418	0.994000	0.38892	0.533000	0.62120	TCA		0.363	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366		C	21968795	T	C	21968795	3	2	101	1	0	0	0	0	1	0	0	0	17060	1435	50	4	185	4	UQCRC2	16	21968795	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10		21968795	68385958	94	26953										
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25258106	25258106	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gatgcctatttcatcatcatCagaatcttctgcagcttcct	5	12	6	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr16:25258106C>G	ENST00000328086.7	-	5	2214	c.1411G>C	c.(1411-1413)Gat>Cat	p.D471H		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	471					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TCATCATCATCAGAATCTTCT	0.448																																																0			16											151	138	142					16																	25258106		2197	4300	6497	25165607	SO:0001583	missense	342357			AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1411G>C	16.37:g.25258106C>G	ENSP00000331626:p.Asp471His		25165607	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150788	0.78001	.	.	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.09630	2.96	5.57	5.57	0.84162	.	0.084342	0.51477	D	0.000089	T	0.21631	0.0521	M	0.64997	1.995	0.40950	D	0.984536	P;P;D	0.52996	0.898;0.925;0.957	P;P;P	0.50378	0.557;0.639;0.557	T	0.00211	-1.1915	10	0.72032	D	0.01	-15.5771	15.4129	0.74941	0.0:1.0:0.0:0.0	.	267;471;471	B4DYF0;Q63HK3-2;Q63HK3	.;.;ZKSC2_HUMAN	H	471	ENSP00000331626:D471H	ENSP00000331626:D471H	D	-	1	0	ZKSCAN2	25165607	0.997000	0.39634	0.917000	0.36280	0.982000	0.71751	3.839000	0.55835	2.780000	0.95670	0.655000	0.94253	GAT		0.448	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		G	25258106	C	G	25258106	3	3	101	1	0	0	0	0	1	0	0	0	17726	826	29	5	1504	5	ZKSCAN2	16	25258106	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	3289311	25258106	65096647	95	26954										
BCL7C	9274	hgsc.bcm.edu	37	chr16	30900209	30900209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ccagcagttctggaacaggcTcctccttggtcagcattggg	12	12	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr16:30900209T>C	ENST00000215115.4	-	5	1515	c.500A>G	c.(499-501)gAg>gGg	p.E167G	AC106782.20_ENST00000572471.1_RNA|MIR4519_ENST00000564901.1_RNA|MIR4519_ENST00000570025.1_RNA|BCL7C_ENST00000380317.4_Missense_Mutation_p.E167G|MIR4519_ENST00000565573.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	167	Pro-rich.				apoptotic process (GO:0006915)					large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			TGGAACAGGCTCCTCCTTGGT	0.587																																																0			16											95	82	86					16																	30900209		2197	4300	6497	30807710	SO:0001583	missense	9274			AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.500A>G	16.37:g.30900209T>C	ENSP00000215115:p.Glu167Gly		30807710	O43770|Q6PD89	Missense_Mutation	SNP	ENST00000215115.4	37	CCDS10693.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552899	0.65425	.	.	ENSG00000099385	ENST00000380317;ENST00000215115	T;T	0.56776	0.44;0.48	4.93	4.93	0.64822	.	0.000000	0.52532	D	0.000069	T	0.68988	0.3061	M	0.65498	2.005	0.37500	D	0.916731	D;D	0.76494	0.998;0.999	D;D	0.75484	0.968;0.986	T	0.75425	-0.3322	10	0.62326	D	0.03	-18.4412	12.8285	0.57733	0.0:0.0:0.0:1.0	.	167;167	Q8WUZ0;Q8WUZ0-2	BCL7C_HUMAN;.	G	167	ENSP00000369674:E167G;ENSP00000215115:E167G	ENSP00000215115:E167G	E	-	2	0	BCL7C	30807710	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.561000	0.60809	1.978000	0.57642	0.459000	0.35465	GAG		0.587	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765		C	30900209	T	C	30900209	3	2	101	1	0	0	0	0	1	0	0	0	1381	1551	54	4	161	4	BCL7C	16	30900209	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	5642103	30900209	59454544	96	26955										
SALL1	6299	hgsc.bcm.edu	37	chr16	51176035	51176035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tgctcttagtagggcgactcGgttgacccttttctgtgtct	11	10	3	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr16:51176035G>A	ENST00000251020.4	-	2	131	c.98C>T	c.(97-99)cCg>cTg	p.P33L	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_5'UTR	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	33					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AGGGCGACTCGGTTGACCCTT	0.463																																					GBM(103;1352 1446 1855 4775 8890)											0			16											84	86	85					16																	51176035		2197	4299	6496	49733536	SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.98C>T	16.37:g.51176035G>A	ENSP00000251020:p.Pro33Leu		49733536	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	7.983	0.751597	0.15778	.	.	ENSG00000103449	ENST00000251020;ENST00000457559	T	0.06528	3.29	5.6	5.6	0.85130	.	0.391386	0.31612	N	0.007360	T	0.04272	0.0118	N	0.14661	0.345	0.40593	D	0.981508	B	0.24426	0.103	B	0.11329	0.006	T	0.46275	-0.9203	10	0.40728	T	0.16	.	10.0977	0.42486	0.0723:0.1379:0.7899:0.0	.	33	Q9NSC2	SALL1_HUMAN	L	33	ENSP00000251020:P33L	ENSP00000251020:P33L	P	-	2	0	SALL1	49733536	1.000000	0.71417	0.807000	0.32361	0.771000	0.43674	4.273000	0.58914	2.615000	0.88500	0.650000	0.86243	CCG		0.463	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51176035	G	A	51176035	3	1	101	1	0	0	0	0	1	0	0	0	13847	1116	39	1	3884	1	SALL1	16	51176035	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10	20275826	51176035	39178718	97	26956										
KIFC3	3801	hgsc.bcm.edu	37	chr16	57799530	57799530	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tctttggtgactggccggacAcgagcaatcactcggatgtt	12	10	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr16:57799530A>G	ENST00000379655.4	-	11	1610	c.1353T>C	c.(1351-1353)cgT>cgC	p.R451R	KIFC3_ENST00000539578.1_Silent_p.R393R|KIFC3_ENST00000465878.2_Silent_p.R312R|KIFC3_ENST00000543930.1_Silent_p.R312R|KIFC3_ENST00000421376.2_Silent_p.R312R|KIFC3_ENST00000541240.1_Silent_p.R473R|KIFC3_ENST00000445690.2_Silent_p.R451R|KIFC3_ENST00000540079.2_Silent_p.R349R|KIFC3_ENST00000562903.1_Silent_p.R312R	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	451	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTGGCCGGACACGAGCAATCA	0.577																																																0			16											120	76	91					16																	57799530		2197	4300	6497	56357031	SO:0001819	synonymous_variant	3801			BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1353T>C	16.37:g.57799530A>G			56357031	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Silent	SNP	ENST00000379655.4	37	CCDS10789.2																																																																																				0.577	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		G	57799530	A	G	57799530	2	3	101	1	0	0	0	0	0	0	0	1	8335	146	6	4		4	KIFC3	16	57799530	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	6623495	57799530	32555223	98	26957										
SMG6	23293	hgsc.bcm.edu	37	chr17	2202717	2202717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gcctccacggccccaactccGagatcccttactaccagatc	6	19	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:2202717G>A	ENST00000263073.6	-	2	1380	c.1330C>T	c.(1330-1332)Cgg>Tgg	p.R444W	SMG6_ENST00000544865.1_Missense_Mutation_p.R413W	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	444	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCCCAACTCCGAGATCCCTTA	0.537																																					Melanoma(59;28 1088 11621 25887 46638 50814)											0			17											97	110	105					17																	2202717		2203	4299	6502	2149467	SO:0001583	missense	23293			AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1330C>T	17.37:g.2202717G>A	ENSP00000263073:p.Arg444Trp		2149467	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.208175	0.58343	.	.	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.13307	2.6;2.6	5.54	4.54	0.55810	.	0.132346	0.49305	D	0.000149	T	0.10337	0.0253	N	0.24115	0.695	0.50632	D	0.999883	B	0.30664	0.289	B	0.17722	0.019	T	0.07046	-1.0793	10	0.87932	D	0	-7.9807	15.4398	0.75173	0.0:0.0:0.8599:0.1401	.	444	Q86US8	EST1A_HUMAN	W	444;413	ENSP00000263073:R444W;ENSP00000443920:R413W	ENSP00000263073:R444W	R	-	1	2	SMG6	2149467	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	2.821000	0.48065	1.273000	0.44346	0.650000	0.86243	CGG		0.537	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			A	2202717	G	A	2202717	3	1	101	1	0	0	0	0	1	0	0	0	14834	1057	37	1	3001	1	SMG6	17	2202717	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10		2202717	78992493	99	26958										
TP53	7157	hgsc.bcm.edu	37	chr17	7577568	7577568	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cgcccatgcaggaactgttaCacatgtagttgtagtggatg	12	8	0	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:7577568C>T	ENST00000269305.4	-	7	902	c.713G>A	c.(712-714)tGt>tAt	p.C238Y	TP53_ENST00000413465.2_Missense_Mutation_p.C238Y|TP53_ENST00000455263.2_Missense_Mutation_p.C238Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.C238Y|TP53_ENST00000420246.2_Missense_Mutation_p.C238Y|TP53_ENST00000359597.4_Missense_Mutation_p.C238Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	238	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C238Y(65)|p.C238F(46)|p.C238S(9)|p.0?(8)|p.?(5)|p.C145F(5)|p.C145Y(5)|p.M237_N239delMCN(4)|p.C238fs*21(1)|p.M237fs*1(1)|p.M144_N146delMCN(1)|p.C238del(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.H233fs*6(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.N239_C242del(1)|p.C145S(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAACTGTTACACATGTAGTT	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	158	Substitution - Missense(131)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(4)	breast(22)|ovary(17)|large_intestine(14)|haematopoietic_and_lymphoid_tissue(13)|endometrium(13)|lung(12)|upper_aerodigestive_tract(9)|pancreas(8)|soft_tissue(7)|urinary_tract(7)|oesophagus(7)|biliary_tract(6)|central_nervous_system(6)|liver(5)|bone(5)|stomach(4)|skin(2)|meninges(1)	17	GRCh37	CM034930	TP53	M							132	103	113					17																	7577568		2203	4300	6503	7518293	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.713G>A	17.37:g.7577568C>T	ENSP00000269305:p.Cys238Tyr		7518293	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327056	0.81690	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99964	-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96	4.09	4.09	0.47781	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99972	0.9991	M	0.92970	3.365	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.95847	0.8871	10	0.87932	D	0	-18.536	14.6088	0.68501	0.0:1.0:0.0:0.0	.	238;238;145;238;238;238	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Y	238;238;238;238;238;238;227;145;106;145	ENSP00000410739:C238Y;ENSP00000352610:C238Y;ENSP00000269305:C238Y;ENSP00000398846:C238Y;ENSP00000391127:C238Y;ENSP00000391478:C238Y;ENSP00000425104:C106Y;ENSP00000423862:C145Y	ENSP00000269305:C238Y	C	-	2	0	TP53	7518293	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.556000	0.82233	2.564000	0.86499	0.462000	0.41574	TGT		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577568	C	T	7577568	3	4	101	1	0	0	0	0	1	0	0	0	16421	478	17	3	577	3	TP53	17	7577568	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	5374851	7577568	73617642	100	26959										
NF1	4763	hgsc.bcm.edu	37	chr17	29556851	29556851	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aatgtatttgttctttctttAggttttattgactgatacca	6	5	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:29556851A>T	ENST00000358273.4	+	22	3233		c.e22-1		NF1_ENST00000356175.3_Splice_Site	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1						actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTCTTTCTTTAGGTTTTATTG	0.363			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(5)	soft_tissue(8)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17	GRCh37	CS040850|CS062076	NF1	S							84	84	84					17																	29556851		2203	4300	6503	26580977	SO:0001630	splice_region_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2851-1A>T	17.37:g.29556851A>T			26580977	O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.236999	0.39498	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4896	0.75593	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF1	26580977	1.000000	0.71417	0.978000	0.43139	0.198000	0.23893	8.923000	0.92808	2.053000	0.61076	0.374000	0.22700	.		0.363	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Intron	T	29556851	A	T	29556851	5	4	101	1	0	0	0	0	0	0	1	0	10387	434	15	5	2996	5	NF1	17	29556851	Splice_Site	SNP	A	TCGA-DC-6683-01A-11D-1826-10	21979283	29556851	51638359	101	26960										
GPR179	440435	hgsc.bcm.edu	37	chr17	36483854	36483854	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atagtttcctgttgttgacaCagttttgccatcccttttga	7	9	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:36483854C>T	ENST00000342292.4	-	11	5618	c.5598G>A	c.(5596-5598)ctG>ctA	p.L1866L	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1866					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GTTGTTGACACAGTTTTGCCA	0.493																																																0			17											129	128	128					17																	36483854		1948	4145	6093	33737380	SO:0001819	synonymous_variant	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.5598G>A	17.37:g.36483854C>T			33737380		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																				0.493	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36483854	C	T	36483854	2	4	101	1	0	0	0	0	0	0	0	1	6694	465	17	3		3	GPR179	17	36483854	Silent	SNP	C	TCGA-DC-6683-01A-11D-1826-10	6927003	36483854	44711356	102	26961										
DHX8	1659	hgsc.bcm.edu	37	chr17	41571093	41571093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aagatctaaacccaaatagaCggcgaaatcttgtcggggag	11	8	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:41571093C>T	ENST00000262415.3	+	8	1123	c.1051C>T	c.(1051-1053)Cgg>Tgg	p.R351W	DHX8_ENST00000540306.1_Missense_Mutation_p.R351W	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	351					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CCCAAATAGACGGCGAAATCT	0.502																																					NSCLC(56;1548 1661 49258 49987)											0			17											210	211	210					17																	41571093		2203	4300	6503	38926619	SO:0001583	missense	1659			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1051C>T	17.37:g.41571093C>T	ENSP00000262415:p.Arg351Trp		38926619		Missense_Mutation	SNP	ENST00000262415.3	37	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.612982	0.66672	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.03524	3.9;3.9	5.79	5.79	0.91817	Nucleic acid-binding, OB-fold-like (1);	0.051774	0.64402	N	0.000001	T	0.16342	0.0393	M	0.80508	2.5	0.58432	D	0.999997	D;B	0.76494	0.999;0.194	P;B	0.59825	0.864;0.023	T	0.00015	-1.2399	10	0.87932	D	0	.	14.5075	0.67762	0.1558:0.8442:0.0:0.0	.	351;351	F5H658;Q14562	.;DHX8_HUMAN	W	351	ENSP00000437886:R351W;ENSP00000262415:R351W	ENSP00000262415:R351W	R	+	1	2	DHX8	38926619	1.000000	0.71417	0.961000	0.40146	0.992000	0.81027	4.911000	0.63328	2.746000	0.94184	0.561000	0.74099	CGG		0.502	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			T	41571093	C	T	41571093	3	4	101	1	0	0	0	0	1	0	0	0	4526	527	19	1	1081	1	DHX8	17	41571093	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	5087239	41571093	39624117	103	26962										
CACNG5	27091	hgsc.bcm.edu	37	chr17	64880888	64880888	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tccacaaccattttggacccCggaccacccactctacttcc	4	19	1	0	rs375595665		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:64880888C>T	ENST00000533854.1	+	5	807				CACNG5_ENST00000307139.3_Intron|CACNG5_ENST00000169565.3_Missense_Mutation_p.P227L			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			TTTTGGACCCCGGACCACCCA	0.597																																																0			17						C		0,4406		0,0,2203	106	94	98			-1.2	0	17		98	1,8599	1.2+/-3.3	0,1,4299	no	intron	CACNG5	NM_145811.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077			64880888	1,13005	2203	4300	6503	62311350	SO:0001627	intron_variant	140738			AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"Calcium channel subunits"	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.570+110C>T	17.37:g.64880888C>T			62311350	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Missense_Mutation	SNP	ENST00000533854.1	37	CCDS11665.1	.	.	.	.	.	.	.	.	.	.	C	2.263	-0.368852	0.05069	0.0	1.16E-4	ENSG00000075429	ENST00000169565	T	0.55588	0.51	2.65	-1.2	0.09554	.	0.794422	0.10542	N	0.662599	T	0.35278	0.0926	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27571	-1.0070	6	.	.	.	-2.1846	3.7815	0.08682	0.0:0.2482:0.2159:0.5359	.	.	.	.	L	227	ENSP00000169565:P227L	.	P	+	2	0	CACNG5	62311350	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.483000	0.06536	-0.284000	0.09102	-0.370000	0.07254	CCG		0.597	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811		T	64880888	C	T	64880888	1	4	101	0	1	0	0	0	0	0	0	0	2566	652	23	1		1	CACNG5	17	64880888	Intron	SNP	C	TCGA-DC-6683-01A-11D-1826-10	23309795	64880888	16314322	104	26963										
PRKAR1A	5573	hgsc.bcm.edu	37	chr17	66522010	66522010	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	caaagcaaagacaaatgtgaAattgtggggcatcgaccgag	12	7	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:66522010A>G	ENST00000589228.1	+	7	793	c.665A>G	c.(664-666)aAa>aGa	p.K222R	PRKAR1A_ENST00000586397.1_Missense_Mutation_p.K222R|PRKAR1A_ENST00000588188.2_Missense_Mutation_p.K222R|PRKAR1A_ENST00000392711.1_Missense_Mutation_p.K222R|PRKAR1A_ENST00000536854.2_Missense_Mutation_p.K222R|PRKAR1A_ENST00000358598.2_Missense_Mutation_p.K222R	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	222					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					ACAAATGTGAAATTGTGGGGC	0.448			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	0			17											115	103	107					17																	66522010		2203	4300	6503	64033605	SO:0001583	missense	5573	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.665A>G	17.37:g.66522010A>G	ENSP00000464977:p.Lys222Arg		64033605	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785302	0.90282	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	D;D;D	0.92446	-3.04;-3.04;-3.04	5.83	5.83	0.93111	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.88880	0.6557	N	0.25332	0.735	0.80722	D	1	B;B	0.27791	0.189;0.189	B;B	0.36719	0.231;0.231	D	0.85899	0.1433	10	0.32370	T	0.25	-35.6973	16.1801	0.81892	1.0:0.0:0.0:0.0	.	222;222	B2R5T5;P10644	.;KAP0_HUMAN	R	222	ENSP00000351410:K222R;ENSP00000376475:K222R;ENSP00000445625:K222R	ENSP00000351410:K222R	K	+	2	0	PRKAR1A	64033605	1.000000	0.71417	0.960000	0.40013	0.994000	0.84299	9.339000	0.96797	2.225000	0.72522	0.455000	0.32223	AAA		0.448	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			G	66522010	A	G	66522010	3	3	101	1	0	0	0	0	1	0	0	0	12537	14	1	4	687	4	PRKAR1A	17	66522010	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	1641122	66522010	14673200	105	26964										
NPTX1	4884	hgsc.bcm.edu	37	chr17	78444822	78444822	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ctgggtggcatcaaacccacCacccagagtgtccttcagag	10	14	2	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr17:78444822C>A	ENST00000306773.4	-	5	1247	c.1090G>T	c.(1090-1092)Ggt>Tgt	p.G364C	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	364	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			TCAAACCCACCACCCAGAGTG	0.617																																																0			17											55	53	54					17																	78444822		2203	4300	6503	76059417	SO:0001583	missense	4884			U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.1090G>T	17.37:g.78444822C>A	ENSP00000307549:p.Gly364Cys		76059417	B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	37	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864498	0.91511	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.23147	1.92	5.41	5.41	0.78517	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.69015	0.3064	H	0.97874	4.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82059	-0.0645	10	0.87932	D	0	-11.6184	18.7866	0.91957	0.0:1.0:0.0:0.0	.	364	Q15818	NPTX1_HUMAN	C	364;126	ENSP00000307549:G364C	ENSP00000307549:G364C	G	-	1	0	NPTX1	76059417	1.000000	0.71417	0.546000	0.28166	0.981000	0.71138	7.749000	0.85096	2.519000	0.84933	0.561000	0.74099	GGT		0.617	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			A	78444822	C	A	78444822	3	1	101	1	0	0	0	0	1	0	0	0	10633	594	21	2	212	2	NPTX1	17	78444822	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	11922812	78444822	2750388	106	26965										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29797058	29797058	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atgacggtgtctgcactgttCgagatggcaaagctgagtgc	14	8	1	3	rs201834412		TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr18:29797058C>T	ENST00000269202.6	+	13	1911	c.1864C>T	c.(1864-1866)Cga>Tga	p.R622*	MEP1B_ENST00000581447.1_Nonsense_Mutation_p.R622*	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	622	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CTGCACTGTTCGAGATGGCAA	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		13756	0		0	False		,,,				2504	0															0			18											115	108	111					18																	29797058		1954	4167	6121	28051056	SO:0001587	stop_gained	4225			X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.1864C>T	18.37:g.29797058C>T	ENSP00000269202:p.Arg622*		28051056	B7ZM35|B9EGL6|Q670J1	Nonsense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	38	7.228143	0.98150	.	.	ENSG00000141434	ENST00000269202	.	.	.	6.08	3.06	0.35304	.	0.809214	0.11285	N	0.579895	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	1.3491	8.2041	0.31443	0.3649:0.3833:0.2518:0.0	.	.	.	.	X	622	.	ENSP00000269202:R622X	R	+	1	2	MEP1B	28051056	0.000000	0.05858	0.009000	0.14445	0.851000	0.48451	0.831000	0.27476	0.809000	0.34255	0.655000	0.94253	CGA		0.398	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		T	29797058	C	T	29797058	4	4	101	1	0	0	0	0	0	1	0	0	9506	876	31	1	1914	1	MEP1B	18	29797058	Nonsense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		29797058	48280190	107	26966										
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130434	37130434	+	Frame_Shift_Del	DEL	T	T	-													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cattcgttacattcatagcgTttttcaccattatgaattct							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr19:37130434delT	ENST00000588268.1	-	6	1040	c.813delA	c.(811-813)aaafs	p.K271fs	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Frame_Shift_Del_p.K248fs	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATTCATAGCGTTTTTCACCAT	0.353																																																0			19											56	60	59					19																	37130434		2171	4280	6451	41822274	SO:0001589	frameshift_variant	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.813delA	19.37:g.37130434delT	ENSP00000467931:p.Lys271fs		41822274	A8K9W9|Q6VSF7|Q9ULZ8	Frame_Shift_Del	DEL	ENST00000588268.1	37	CCDS54257.1																																																																																				0.353	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		-	37130434	T	-	37130434	7	5	101	1	0	1	0	1	0	0	0	0	17964	1722	60	0	882	0	ZNF461	19	37130434	Frame_Shift_Del	DEL	T	TCGA-DC-6683-01A-11D-1826-10		37130434	21998549	108	26967	46	3								
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130437	37130437	+	Missense_Mutation	SNP	T	T	G													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tcgttacattcatagcgtttTtcaccattatgaattcttag							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr19:37130437T>G	ENST00000588268.1	-	6	1037	c.810A>C	c.(808-810)gaA>gaC	p.E270D	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Missense_Mutation_p.E247D	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CATAGCGTTTTTCACCATTAT	0.353																																																0			19											55	59	58					19																	37130437		2166	4275	6441	41822277	SO:0001583	missense	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.810A>C	19.37:g.37130437T>G	ENSP00000467931:p.Glu270Asp		41822277	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258760	0.39896	.	.	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605	T	0.26810	1.71	3.71	0.366	0.16136	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22589	0.0545	L	0.60904	1.88	0.22541	N	0.999004	B;B;B	0.31351	0.0;0.32;0.0	B;B;B	0.33620	0.003;0.167;0.005	T	0.32929	-0.9888	9	0.72032	D	0.01	.	2.7062	0.05163	0.2278:0.404:0.0:0.3682	.	247;192;270	B4DRP8;Q59G30;Q8TAF7	.;.;ZN461_HUMAN	D	270;1;247;143	ENSP00000353515:E247D	ENSP00000353515:E247D	E	-	3	2	ZNF461	41822277	0.955000	0.32602	0.980000	0.43619	0.935000	0.57460	0.070000	0.14573	0.132000	0.18615	0.477000	0.44152	GAA		0.353	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		G	37130437	T	G	37130437	3	3	101	1	0	0	0	0	1	0	0	0	17964	1838	64	4	885	4	ZNF461	19	37130437	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	3	37130437	21998546	109	26968	46	3								
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130439	37130439	+	Nonsense_Mutation	SNP	C	C	A													0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	gttacattcatagcgtttttCaccattatgaattcttagat							TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr19:37130439C>A	ENST00000588268.1	-	6	1035	c.808G>T	c.(808-810)Gaa>Taa	p.E270*	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Nonsense_Mutation_p.E247*	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TAGCGTTTTTCACCATTATGA	0.358																																																0			19											56	60	58					19																	37130439		2166	4277	6443	41822279	SO:0001587	stop_gained	92283			BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.808G>T	19.37:g.37130439C>A	ENSP00000467931:p.Glu270*		41822279	A8K9W9|Q6VSF7|Q9ULZ8	Nonsense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	C	37	6.564350	0.97667	.	.	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605	.	.	.	3.71	3.71	0.42584	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	5.8631	0.18760	0.0:0.7756:0.0:0.2244	.	.	.	.	X	270;1;247;143	.	ENSP00000353515:E247X	E	-	1	0	ZNF461	41822279	0.855000	0.29742	0.987000	0.45799	0.903000	0.53119	1.683000	0.37638	2.066000	0.61787	0.585000	0.79938	GAA		0.358	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		A	37130439	C	A	37130439	4	1	101	1	0	0	0	0	0	1	0	0	17964	835	29	2	887	2	ZNF461	19	37130439	Nonsense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	2	37130439	21998544	110	26969	46	3								
PSG3	5671	hgsc.bcm.edu	37	chr19	43233949	43233949	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cagaggacattcagggtgacTgggtaactgcggatgccacc	14	10	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr19:43233949T>A	ENST00000327495.5	-	4	1153	c.969A>T	c.(967-969)ccA>ccT	p.P323P	PSG3_ENST00000595140.1_Silent_p.P323P	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	323	Ig-like C2-type 2.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				TCAGGGTGACTGGGTAACTGC	0.488																																																0			19											156	141	147					19																	43233949		1511	2709	4220	47925789	SO:0001819	synonymous_variant	5671				CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.969A>T	19.37:g.43233949T>A			47925789	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Silent	SNP	ENST00000327495.5	37	CCDS12611.1																																																																																				0.488	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		A	43233949	T	A	43233949	2	1	101	1	0	0	0	0	0	0	0	1	12690	1567	55	5		5	PSG3	19	43233949	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	6103510	43233949	15895034	111	26970										
KIR2DL3	3804	hgsc.bcm.edu	37	chr19	55258812	55258812	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ccttcaaatagttggccttcAcccactgaaccaagctccga	6	15	2	1			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr19:55258812A>T	ENST00000342376.3	+	5	721	c.690A>T	c.(688-690)tcA>tcT	p.S230S	KIR2DL3_ENST00000434419.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	230					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		GTTGGCCTTCACCCACTGAAC	0.488																																																0			19											104	90	95					19																	55258812		1478	2618	4096	59950624	SO:0001819	synonymous_variant	3804			L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.690A>T	19.37:g.55258812A>T			59950624	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Silent	SNP	ENST00000342376.3	37	CCDS33107.1																																																																																				0.488	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1			T	55258812	A	T	55258812	2	4	101	1	0	0	0	0	0	0	0	1	8338	146	6	5		5	KIR2DL3	19	55258812	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	12024863	55258812	3870171	112	26971										
CPXM1	56265	hgsc.bcm.edu	37	chr20	2779441	2779441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cacaaggggcccggcagtcaCcagtggggtggggcgagtta	18	10	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr20:2779441C>T	ENST00000380605.2	-	2	335	c.271G>A	c.(271-273)Gtg>Atg	p.V91M		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	91					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCGGCAGTCACCAGTGGGGTG	0.567																																																0			20											107	114	112					20																	2779441		2203	4300	6503	2727441	SO:0001583	missense	56265			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.271G>A	20.37:g.2779441C>T	ENSP00000369979:p.Val91Met		2727441	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.888991	0.52014	.	.	ENSG00000088882	ENST00000380605	D	0.95622	-3.76	4.75	3.78	0.43462	.	0.427763	0.18639	N	0.135359	D	0.90421	0.7001	N	0.24115	0.695	0.09310	N	0.999999	B;B	0.34015	0.435;0.255	B;B	0.33799	0.17;0.088	D	0.84479	0.0604	10	0.56958	D	0.05	-8.1401	10.6563	0.45678	0.0:0.8062:0.1938:0.0	.	91;91	Q8N2E1;Q96SM3	.;CPXM1_HUMAN	M	91	ENSP00000369979:V91M	ENSP00000369979:V91M	V	-	1	0	CPXM1	2727441	0.194000	0.23325	0.602000	0.28890	0.225000	0.24961	3.665000	0.54532	1.194000	0.43101	0.563000	0.77884	GTG		0.567	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		T	2779441	C	T	2779441	3	4	101	1	0	0	0	0	1	0	0	0	3843	507	18	3	1985	3	CPXM1	20	2779441	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		2779441	60246079	113	26972										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9400473	9400473	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	ggtaccttctcaaaccagatTtcatgaggcggcctgatcga	10	11	2	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr20:9400473T>C	ENST00000378493.1	+	22	2050	c.2035T>C	c.(2035-2037)Ttc>Ctc	p.F679L	PLCB4_ENST00000278655.4_Missense_Mutation_p.F679L|PLCB4_ENST00000414679.2_Missense_Mutation_p.F691L|PLCB4_ENST00000378473.3_Missense_Mutation_p.F691L|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000334005.3_Missense_Mutation_p.F679L|PLCB4_ENST00000378501.2_Missense_Mutation_p.F679L			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	679	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CAAACCAGATTTCATGAGGCG	0.443																																																0			20											165	158	160					20																	9400473		2203	4300	6503	9348473	SO:0001583	missense	5332				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.2035T>C	20.37:g.9400473T>C	ENSP00000367754:p.Phe679Leu		9348473	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	T	33	5.212170	0.95069	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64	5.36	5.36	0.76844	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	M	0.71206	2.165	0.80722	D	1	D;P;D;D	0.76494	0.999;0.889;0.958;0.999	D;P;D;D	0.87578	0.993;0.511;0.983;0.998	T	0.70992	-0.4721	10	0.59425	D	0.04	.	15.6507	0.77091	0.0:0.0:0.0:1.0	.	691;526;679;679	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	L	679;691;679;679;679;527	ENSP00000334105:F679L;ENSP00000367734:F691L;ENSP00000278655:F679L;ENSP00000367754:F679L;ENSP00000367762:F679L;ENSP00000390616:F527L	ENSP00000278655:F679L	F	+	1	0	PLCB4	9348473	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.972000	0.88022	2.163000	0.67991	0.460000	0.39030	TTC		0.443	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			C	9400473	T	C	9400473	3	2	101	1	0	0	0	0	1	0	0	0	12061	1841	64	4	2161	4	PLCB4	20	9400473	Missense_Mutation	SNP	T	TCGA-DC-6683-01A-11D-1826-10	6621032	9400473	53625047	114	26973										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22710714	22710714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	atatattctttacagtacagCctcacataatacagcttaaa	3	9	2	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr21:22710714C>T	ENST00000400546.1	+	8	1153	c.904C>T	c.(904-906)Cct>Tct	p.P302S	NCAM2_ENST00000284894.7_Missense_Mutation_p.P160S|NCAM2_ENST00000535285.1_Missense_Mutation_p.P327S	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	302	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P302S(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TACAGTACAGCCTCACATAAT	0.358																																																1	Substitution - Missense(1)	ovary(1)	21											52	51	51					21																	22710714		1838	4079	5917	21632585	SO:0001583	missense	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.904C>T	21.37:g.22710714C>T	ENSP00000383392:p.Pro302Ser		21632585	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699806	0.88924	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.78126	-1.15;-1.08;0.63	5.8	5.8	0.92144	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.91788	0.7402	H	0.94771	3.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93456	0.6806	10	0.87932	D	0	-14.2816	18.6141	0.91296	0.0:1.0:0.0:0.0	.	327;160;302	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	S	302;160;327	ENSP00000383392:P302S;ENSP00000284894:P160S;ENSP00000441887:P327S	ENSP00000284894:P160S	P	+	1	0	NCAM2	21632585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.312000	0.65792	2.736000	0.93811	0.591000	0.81541	CCT		0.358	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22710714	C	T	22710714	3	4	101	1	0	0	0	0	1	0	0	0	10234	739	26	3	934	3	NCAM2	21	22710714	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10		22710714	25419181	115	26974										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28210258	28210258	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aaagtggggatagcattgaaAgattccttcttcttctttac	8	7	3	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr21:28210258A>G	ENST00000284984.3	-	9	2998	c.2544T>C	c.(2542-2544)tcT>tcC	p.S848S		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	848	Spacer.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TAGCATTGAAAGATTCCTTCT	0.453																																																0			21											95	94	94					21																	28210258		2203	4300	6503	27132129	SO:0001819	synonymous_variant	9510			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2544T>C	21.37:g.28210258A>G			27132129	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1																																																																																				0.453	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			G	28210258	A	G	28210258	2	3	101	1	0	0	0	0	0	0	0	1	255	59	3	4		4	ADAMTS1	21	28210258	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	5499544	28210258	19919637	116	26975										
C22orf42	150297	hgsc.bcm.edu	37	chr22	32547484	32547484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tacatcttacaatatctgacGttatattctcctccacaccg	3	13	3	1	rs72502004	byFrequency	TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr22:32547484G>A	ENST00000382097.3	-	5	527	c.455C>T	c.(454-456)aCg>aTg	p.T152M	C22orf42_ENST00000490640.1_5'Flank	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	152										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						AATATCTGACGTTATATTCTC	0.423													.|||	10	0.00199681	0	0	5008	,	,		20921	0.0099		0	False		,,,				2504	0															0			22						G	MET/THR	0,4406		0,0,2203	113	100	105		455	-0.7	0	22	dbSNP_130	105	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C22orf42	NM_001010859.1	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	152/252	32547484	2,13004	2203	4300	6503	30877484	SO:0001583	missense	150297			BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.455C>T	22.37:g.32547484G>A	ENSP00000371529:p.Thr152Met		30877484	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	G	1.118	-0.656166	0.03480	0.0	2.33E-4	ENSG00000205856	ENST00000382097	T	0.28895	1.59	0.579	-0.68	0.11346	.	.	.	.	.	T	0.19248	0.0462	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.62014	0.897	T	0.15093	-1.0449	8	0.66056	D	0.02	.	.	.	.	.	152	Q6IC83	CV042_HUMAN	M	152	ENSP00000371529:T152M	ENSP00000371529:T152M	T	-	2	0	C22orf42	30877484	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.212000	0.02994	-0.251000	0.09542	-1.592000	0.00843	ACG		0.423	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		A	32547484	G	A	32547484	3	1	101	1	0	0	0	0	1	0	0	0	2155	1145	40	1	320	1	C22orf42	22	32547484	Missense_Mutation	SNP	G	TCGA-DC-6683-01A-11D-1826-10		32547484	18757082	117	26976										
CPT1B	1375	hgsc.bcm.edu	37	chr22	51012953	51012953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cttcacggtccagtttacggCgatacatgatcatggcgtgg	12	10	2	1	rs141802871	byFrequency	TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chr22:51012953C>T	ENST00000360719.2	-	8	991	c.854G>A	c.(853-855)cGc>cAc	p.R285H	CPT1B_ENST00000405237.3_Missense_Mutation_p.R285H|CPT1B_ENST00000457250.1_Missense_Mutation_p.R251H|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000440709.1_Missense_Mutation_p.R285H|CPT1B_ENST00000312108.7_Missense_Mutation_p.R285H|CPT1B_ENST00000395650.2_Missense_Mutation_p.R285H|CPT1B_ENST00000434492.2_Missense_Mutation_p.R82H	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	285					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		CAGTTTACGGCGATACATGAT	0.572													C|||	2	0.000399361	0.0015	0	5008	,	,		19908	0		0	False		,,,				2504	0				Esophageal Squamous(170;988 1933 25577 30295 48163)											0			22						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	217	182	194		752,854,854,854,854,854,854	4.8	1	22	dbSNP_134	194	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	29,29,29,29,29,29,29	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	251/739,285/773,285/692,285/773,285/773,285/773,285/773	51012953	3,13003	2203	4300	6503	49359819	SO:0001583	missense	1375			U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.854G>A	22.37:g.51012953C>T	ENSP00000353945:p.Arg285His		49359819	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553335	0.96501	6.81E-4	0.0	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;T;D;T;D	0.89810	-2.57;-2.57;-2.57;-1.44;-2.57;-1.44;-2.57	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.94706	0.8292	M	0.85041	2.73	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.999;0.977;1.0;1.0	D	0.95343	0.8440	10	0.87932	D	0	-28.5979	15.3912	0.74744	0.0:1.0:0.0:0.0	.	285;251;82;285	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	H	285;285;285;251;285;82;285	ENSP00000385486:R285H;ENSP00000312189:R285H;ENSP00000353945:R285H;ENSP00000409342:R251H;ENSP00000414713:R285H;ENSP00000410966:R82H;ENSP00000379011:R285H	ENSP00000312189:R285H	R	-	2	0	CPT1B	49359819	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.196000	0.77805	2.503000	0.84419	0.561000	0.74099	CGC		0.572	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		T	51012953	C	T	51012953	3	4	101	1	0	0	0	0	1	0	0	0	3838	768	27	1	1512	1	CPT1B	22	51012953	Missense_Mutation	SNP	C	TCGA-DC-6683-01A-11D-1826-10	18465469	51012953	291613	118	26977										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820649	35820649	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	aggaatgtgcccgcagatgcTctcgaccagaaagtggcttt	12	10	1	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chrX:35820649T>C	ENST00000399989.1	+	2	615	c.336T>C	c.(334-336)gcT>gcC	p.A112A	MAGEB16_ENST00000399987.1_Silent_p.A112A|MAGEB16_ENST00000399992.1_Silent_p.A144A|MAGEB16_ENST00000399985.1_Silent_p.A112A|MAGEB16_ENST00000399988.1_Silent_p.A112A	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	112										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CCGCAGATGCTCTCGACCAGA	0.438																																																0			X											56	52	54					X																	35820649		1959	4153	6112	35730570	SO:0001819	synonymous_variant	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.336T>C	X.37:g.35820649T>C			35730570	A8MU30	Silent	SNP	ENST00000399989.1	37	CCDS43927.1																																																																																				0.438	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			C	35820649	T	C	35820649	2	2	101	1	0	0	0	0	0	0	0	1	9204	1538	54	4		4	MAGEB16	23	35820649	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10		35820649	119449911	119	26978										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75649956	75649956	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	cccacctggagtgcatttttAggtttgaattgagagaactt	10	7	0	3			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chrX:75649956A>C	ENST00000361470.2	+	1	1911	c.1633A>C	c.(1633-1635)Agg>Cgg	p.R545R		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	545	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						GTGCATTTTTAGGTTTGAATT	0.463																																																0			X											37	35	35					X																	75649956		2203	4300	6503	75566360	SO:0001819	synonymous_variant	728239			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1633A>C	X.37:g.75649956A>C			75566360	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																				0.463	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		C	75649956	A	C	75649956	2	2	101	1	0	0	0	0	0	0	0	1	9215	411	15	4		4	MAGEE1	23	75649956	Silent	SNP	A	TCGA-DC-6683-01A-11D-1826-10	39829307	75649956	79620604	120	26979										
ATRX	546	hgsc.bcm.edu	37	chrX	76814176	76814176	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	tatacataaacaggcttagtTtgtccaaagcgataaactct	6	8	1	0			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chrX:76814176T>C	ENST00000373344.5	-	29	6682	c.6468A>G	c.(6466-6468)caA>caG	p.Q2156Q	ATRX_ENST00000395603.3_Silent_p.Q2118Q|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2156	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.Q2156H(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CAGGCTTAGTTTGTCCAAAGC	0.318			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	2	Substitution - Missense(1)|Unknown(1)	bone(1)|pancreas(1)	X											86	84	85					X																	76814176		2203	4294	6497	76700832	SO:0001819	synonymous_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6468A>G	X.37:g.76814176T>C			76700832	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Silent	SNP	ENST00000373344.5	37	CCDS14434.1																																																																																				0.318	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		C	76814176	T	C	76814176	2	2	101	1	0	0	0	0	0	0	0	1	1209	1838	64	4		4	ATRX	23	76814176	Silent	SNP	T	TCGA-DC-6683-01A-11D-1826-10	1164220	76814176	78456384	121	26980										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96502831	96502831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.734372436423298	3.89217391304348	0.405434782608696	1	1	0	acacgataagtttgtggaaaAgatgaccatatcctttattt	7	6	0	2			TCGA-DC-6683-01A-11D-1826-10	TCGA-DC-6683-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	2fb4aebc-3a86-46ef-ab91-96db120cab15	a1f3b7da-3d32-4ca1-a81f-5515fa9fc811	g.chrX:96502831A>G	ENST00000324765.8	+	23	3184	c.2837A>G	c.(2836-2838)aAg>aGg	p.K946R	DIAPH2_ENST00000355827.4_Missense_Mutation_p.K946R|DIAPH2_ENST00000373049.4_Missense_Mutation_p.K946R|DIAPH2_ENST00000373054.4_Missense_Mutation_p.K942R|DIAPH2_ENST00000373061.3_Missense_Mutation_p.K946R			O60879	DIAP2_HUMAN	diaphanous-related formin 2	946	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)	p.K946M(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TTTGTGGAAAAGATGACCATA	0.348																																																1	Substitution - Missense(1)	ovary(1)	X											135	114	121					X																	96502831		2203	4300	6503	96389487	SO:0001583	missense	1730			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2837A>G	X.37:g.96502831A>G	ENSP00000321348:p.Lys946Arg		96389487	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	37	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094476	0.56075	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	T;T;T;T;T	0.19532	2.14;2.14;2.14;2.14;2.14	5.66	5.66	0.87406	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.183014	0.32802	U	0.005633	T	0.49270	0.1547	M	0.85373	2.75	0.48341	D	0.999632	D;D	0.67145	0.996;0.994	D;D	0.79784	0.993;0.988	T	0.50783	-0.8787	10	0.23891	T	0.37	.	15.0903	0.72188	1.0:0.0:0.0:0.0	.	946;946	O60879;O60879-2	DIAP2_HUMAN;.	R	946;942;946;946;946;953	ENSP00000362152:K946R;ENSP00000362145:K942R;ENSP00000348082:K946R;ENSP00000362140:K946R;ENSP00000321348:K946R	ENSP00000321348:K946R	K	+	2	0	DIAPH2	96389487	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.560000	0.90712	2.014000	0.59158	0.481000	0.45027	AAG		0.348	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		G	96502831	A	G	96502831	3	3	101	1	0	0	0	0	1	0	0	0	4530	72	3	4	2927	4	DIAPH2	23	96502831	Missense_Mutation	SNP	A	TCGA-DC-6683-01A-11D-1826-10	19688655	96502831	58767729	122	26981										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1417636	1417636	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gacatcatccgcgagcagatCcgcctgaaggcgtccgagca	12	14	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:1417636C>T	ENST00000308647.7	+	6	749	c.633C>T	c.(631-633)atC>atT	p.I211I	ATAD3B_ENST00000378736.3_3'UTR|ATAD3B_ENST00000378741.3_Silent_p.I43I	NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	211						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCGAGCAGATCCGCCTGAAGG	0.672																																																0			1											36	42	40					1																	1417636		2198	4296	6494	1407499	SO:0001819	synonymous_variant	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.633C>T	1.37:g.1417636C>T			1407499	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Silent	SNP	ENST00000308647.7	37	CCDS30.1																																																																																				0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1417636	C	T	1417636	2	4	102	1	0	0	0	0	0	0	0	1	1075	845	30	3		3	ATAD3B	1	1417636	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10		1417636	247832985	1	26982										
MTOR	2475	hgsc.bcm.edu	37	chr1	11184574	11184574	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cctgaggtttttccgaagagAtgttgggtcattggccagaa	13	7	1	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:11184574A>G	ENST00000361445.4	-	47	6719	c.6643T>C	c.(6643-6645)Tct>Cct	p.S2215P	MTOR_ENST00000376838.1_Missense_Mutation_p.S420P	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2215	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTCCGAAGAGATGTTGGGTCA	0.443																																																0			1											102	99	100					1																	11184574		2203	4300	6503	11107161	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6643T>C	1.37:g.11184574A>G	ENSP00000354558:p.Ser2215Pro		11107161	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	18.02	3.530226	0.64860	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.78364	-1.17;-1.17	5.8	5.8	0.92144	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.84678	0.5525	M	0.80183	2.485	0.80722	D	1	P	0.45078	0.85	P	0.51079	0.658	D	0.86737	0.1952	10	0.72032	D	0.01	-14.2436	14.7657	0.69637	1.0:0.0:0.0:0.0	.	2215	P42345	MTOR_HUMAN	P	2215;420	ENSP00000354558:S2215P;ENSP00000366034:S420P	ENSP00000354558:S2215P	S	-	1	0	MTOR	11107161	1.000000	0.71417	0.975000	0.42487	0.998000	0.95712	8.855000	0.92236	2.229000	0.72834	0.529000	0.55759	TCT		0.443	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		G	11184574	A	G	11184574	3	3	102	1	0	0	0	0	1	0	0	0	9984	333	12	4	1054	4	MTOR	1	11184574	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	9766938	11184574	238066047	2	26983										
UBR4	23352	hgsc.bcm.edu	37	chr1	19490883	19490883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gttggccagcatctctgttgCcatgggagtcagggtgccca	14	11	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:19490883C>T	ENST00000375254.3	-	33	4591	c.4564G>A	c.(4564-4566)Gca>Aca	p.A1522T	UBR4_ENST00000375267.2_Missense_Mutation_p.A1522T|UBR4_ENST00000375226.2_Missense_Mutation_p.A1522T|UBR4_ENST00000375217.2_Missense_Mutation_p.A1522T	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1522					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A1522T(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ATCTCTGTTGCCATGGGAGTC	0.522																																																1	Substitution - Missense(1)	kidney(1)	1											82	62	69					1																	19490883		2203	4300	6503	19363470	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.4564G>A	1.37:g.19490883C>T	ENSP00000364403:p.Ala1522Thr		19363470	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.628540	0.67015	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.87	5.87	0.94306	.	0.058098	0.64402	D	0.000002	T	0.72020	0.3409	N	0.19112	0.55	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.71227	-0.4655	10	0.38643	T	0.18	.	19.8177	0.96578	0.0:1.0:0.0:0.0	.	1522	Q5T4S7	UBR4_HUMAN	T	1522;1522;1522;1522;232;738	ENSP00000364403:A1522T;ENSP00000364416:A1522T;ENSP00000364365:A1522T;ENSP00000364374:A1522T	ENSP00000364365:A1522T	A	-	1	0	UBR4	19363470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.208000	0.77907	2.778000	0.95560	0.650000	0.86243	GCA		0.522	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19490883	C	T	19490883	3	4	102	1	0	0	0	0	1	0	0	0	16944	739	26	3	11283	3	UBR4	1	19490883	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	8306309	19490883	229759738	3	26984										
C1QB	713	hgsc.bcm.edu	37	chr1	22987486	22987486	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aaggccacccagaaaatcgcCttctctgccacaagaaccat	6	15	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:22987486C>T	ENST00000314933.6	+	3	501	c.369C>T	c.(367-369)gcC>gcT	p.A123A	C1QB_ENST00000509305.1_Silent_p.A121A	NM_000491.3	NP_000482.3	P02746	C1QB_HUMAN	complement component 1, q subcomponent, B chain	123	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|inner ear development (GO:0048839)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(1)|lung(9)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AGAAAATCGCCTTCTCTGCCA	0.617																																																0			1											119	111	114					1																	22987486		2203	4300	6503	22860073	SO:0001819	synonymous_variant	713			X03084	CCDS228.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173369	ENSG00000173369		"Complement system"	1242	protein-coding gene	gene with protein product		120570	"complement component 1, q subcomponent, beta polypeptide"			1537612	Standard	XM_005245982		Approved		uc001bgd.3	P02746	OTTHUMG00000002896	ENST00000314933.6:c.369C>T	1.37:g.22987486C>T			22860073	Q5T959|Q96H17	Silent	SNP	ENST00000314933.6	37	CCDS228.1																																																																																				0.617	C1QB-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000491		T	22987486	C	T	22987486	2	4	102	1	0	0	0	0	0	0	0	1	1961	668	24	3		3	C1QB	1	22987486	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	3496603	22987486	226263135	4	26985										
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27690729	27690729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tgtggcctccagcaggcgggCaagccggcccaccaggggag	17	14	0	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:27690729C>T	ENST00000493901.1	-	5	900	c.661G>A	c.(661-663)Gcc>Acc	p.A221T	MAP3K6_ENST00000374040.3_Missense_Mutation_p.A213T|MAP3K6_ENST00000357582.2_Missense_Mutation_p.A221T	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	221					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGCAGGCGGGCAAGCCGGCCC	0.687																																																0			1											30	36	34					1																	27690729		2203	4297	6500	27563316	SO:0001583	missense	9064			AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6858	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 2"	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.661G>A	1.37:g.27690729C>T	ENSP00000419591:p.Ala221Thr		27563316	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.537839	0.45176	.	.	ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000357582	T;T;T	0.09445	2.98;2.98;2.98	5.82	5.82	0.92795	.	.	.	.	.	T	0.08179	0.0204	N	0.14661	0.345	0.24761	N	0.992924	B;B	0.20459	0.037;0.045	B;B	0.18263	0.012;0.021	T	0.31668	-0.9935	9	0.12766	T	0.61	.	17.8623	0.88784	0.0:1.0:0.0:0.0	.	213;221	O95382-3;O95382	.;M3K6_HUMAN	T	213;221;221	ENSP00000363152:A213T;ENSP00000419591:A221T;ENSP00000350195:A221T	ENSP00000350195:A221T	A	-	1	0	MAP3K6	27563316	0.091000	0.21658	0.986000	0.45419	0.999000	0.98932	0.810000	0.27183	2.761000	0.94854	0.655000	0.94253	GCC		0.687	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		T	27690729	C	T	27690729	3	4	102	1	0	0	0	0	1	0	0	0	9284	710	25	3	3309	3	MAP3K6	1	27690729	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	4703243	27690729	221559892	5	26986										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70505259	70505259	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tacagagagttacggtgcctCccaaaccaggccagtttcag	10	12	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:70505259C>A	ENST00000035383.5	+	19	3668	c.3638C>A	c.(3637-3639)tCc>tAc	p.S1213Y	LRRC7_ENST00000310961.5_Missense_Mutation_p.S1218Y|LRRC7_ENST00000415775.2_Missense_Mutation_p.S497Y	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1213						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TACGGTGCCTCCCAAACCAGG	0.468																																																0			1											73	68	70					1																	70505259		2203	4300	6503	70277847	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3638C>A	1.37:g.70505259C>A	ENSP00000035383:p.Ser1213Tyr		70277847	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.988216	0.35036	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.49720	0.77;0.86;1.97	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	N	0.14661	0.345	0.43364	D	0.995444	D;D;D	0.71674	0.998;0.983;0.989	D;P;P	0.66351	0.943;0.837;0.768	T	0.54159	-0.8335	10	0.87932	D	0	.	19.848	0.96722	0.0:1.0:0.0:0.0	.	497;1213;1213	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	Y	1218;1213;497;1036	ENSP00000309245:S1218Y;ENSP00000035383:S1213Y;ENSP00000394867:S497Y	ENSP00000035383:S1213Y	S	+	2	0	LRRC7	70277847	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	5.715000	0.68430	2.937000	0.99478	0.650000	0.86243	TCC		0.468	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70505259	C	A	70505259	3	1	102	1	0	0	0	0	1	0	0	0	9049	855	30	2	3712	2	LRRC7	1	70505259	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	42814530	70505259	178745362	6	26987										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144864162	144864162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cgttttcctggagggaaagaCgttcctccctgaaatgcaag	11	10	0	2	rs145067181	byFrequency	TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:144864162C>T	ENST00000369354.3	-	36	6122	c.5933G>A	c.(5932-5934)cGt>cAt	p.R1978H	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R2063H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R1872H|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R2114H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R1978H			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1978					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAGGGAAAGACGTTCCTCCCT	0.483			T	PDGFRB	MPD								.|||	6	0.00119808	0	0.0014	5008	,	,		38654	0		0.003	False		,,,				2504	0.002						Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			1						C	HIS/ARG,HIS/ARG,HIS/ARG	7,4399	14.3+/-33.2	0,7,2196	301	319	313		5615,5933,5933	4.4	0.1	1	dbSNP_134	313	23,8577	15.3+/-51.7	0,23,4277	no	missense,missense,missense	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	29,29,29	0,30,6473	TT,TC,CC		0.2674,0.1589,0.2307	probably-damaging,probably-damaging,probably-damaging	1872/2241,1978/2363,1978/2347	144864162	30,12976	2203	4300	6503	143575519	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5933G>A	1.37:g.144864162C>T	ENSP00000358360:p.Arg1978His		143575519	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.01|17.01	3.280006|3.280006	0.59758|0.59758	0.001589|0.001589	0.002674|0.002674	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530130	T;T;T;T;T|.	0.02032|.	4.49;4.57;4.57;4.59;4.58|.	4.43|4.43	4.43|4.43	0.53597|0.53597	.|.	.|.	.|.	.|.	.|.	T|T	0.63780|0.63780	0.2540|0.2540	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.78314|.	0.73;0.991|.	T|T	0.63202|0.63202	-0.6690|-0.6690	9|5	0.27082|.	T|.	0.32|.	.|.	14.9219|14.9219	0.70843|0.70843	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1872;1978|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	H|I	1872;1978;1978;2063;2114|135	ENSP00000327209:R1872H;ENSP00000358360:R1978H;ENSP00000358363:R1978H;ENSP00000435654:R2063H;ENSP00000358366:R2114H|.	ENSP00000327209:R1872H|.	R|V	-|-	2|1	0|0	PDE4DIP|PDE4DIP	143575519|143575519	0.003000|0.003000	0.15002|0.15002	0.102000|0.102000	0.21198|0.21198	0.358000|0.358000	0.29455|0.29455	1.777000|1.777000	0.38604|0.38604	2.463000|2.463000	0.83235|0.83235	0.555000|0.555000	0.69702|0.69702	CGT|GTC		0.483	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144864162	C	T	144864162	3	4	102	1	0	0	0	0	1	0	0	0	11674	536	19	1	1143	1	PDE4DIP	1	144864162	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	74358903	144864162	104386459	7	26988										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144882867	144882867	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccgcattctcaaggcaaaggCtcagcatggtgttcctgcag	11	12	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:144882867C>A	ENST00000369354.3	-	24	3341	c.3152G>T	c.(3151-3153)aGc>aTc	p.S1051I	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.S1188I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.S1117I|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.S1188I|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.S1051I			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1051					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGGCAAAGGCTCAGCATGGT	0.502			T	PDGFRB	MPD																																		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			1											234	218	224					1																	144882867		2203	4296	6499	143594224	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3152G>T	1.37:g.144882867C>A	ENSP00000358360:p.Ser1051Ile		143594224	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689355	0.68271	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01963	4.53;4.66;4.66;4.67;4.66	5.9	4.99	0.66335	.	.	.	.	.	T	0.02342	0.0072	N	0.17082	0.46	0.80722	D	1	B;D	0.76494	0.02;0.999	B;D	0.80764	0.027;0.994	T	0.66376	-0.5939	9	0.38643	T	0.18	.	12.163	0.54115	0.3105:0.6895:0.0:0.0	.	1117;1051	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	I	1117;1051;1051;1188;1188	ENSP00000327209:S1117I;ENSP00000358360:S1051I;ENSP00000358363:S1051I;ENSP00000435654:S1188I;ENSP00000358366:S1188I	ENSP00000327209:S1117I	S	-	2	0	PDE4DIP	143594224	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.191000	0.50981	1.506000	0.48736	0.655000	0.94253	AGC		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144882867	C	A	144882867	3	1	102	1	0	0	0	0	1	0	0	0	11674	797	28	2	3972	2	PDE4DIP	1	144882867	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	18705	144882867	104367754	8	26989										
ADAMTS4	9507	hgsc.bcm.edu	37	chr1	161163136	161163136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agctcttgaagaggtcggtgCggtggttgtaggcagcacac	16	8	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:161163136C>T	ENST00000367996.5	-	7	2206	c.1778G>A	c.(1777-1779)cGc>cAc	p.R593H	ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	593	Cys-rich.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GAGGTCGGTGCGGTGGTTGTA	0.627																																																0			1											76	69	72					1																	161163136		2203	4300	6503	159429760	SO:0001583	missense	9507			AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.1778G>A	1.37:g.161163136C>T	ENSP00000356975:p.Arg593His		159429760	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.914070	0.33815	.	.	ENSG00000158859	ENST00000367996	T	0.03553	3.89	4.81	3.89	0.44902	.	0.000000	0.56097	D	0.000026	T	0.00784	0.0026	N	0.16567	0.415	0.80722	D	1	P	0.43542	0.81	B	0.31191	0.125	T	0.64445	-0.6406	10	0.15952	T	0.53	.	12.1591	0.54093	0.0:0.9155:0.0:0.0845	.	593	O75173	ATS4_HUMAN	H	593	ENSP00000356975:R593H	ENSP00000356975:R593H	R	-	2	0	ADAMTS4	159429760	0.218000	0.23608	1.000000	0.80357	0.994000	0.84299	1.029000	0.30140	1.238000	0.43771	0.557000	0.71058	CGC		0.627	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		T	161163136	C	T	161163136	3	4	102	1	0	0	0	0	1	0	0	0	268	768	27	1	747	1	ADAMTS4	1	161163136	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	16280269	161163136	88087485	9	26990										
ASTN1	460	hgsc.bcm.edu	37	chr1	177030287	177030287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gttcttcagtggggtcttgtCcaggaaggcttggggcacca	15	9	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:177030287C>A	ENST00000367654.3	-	2	609	c.398G>T	c.(397-399)gGa>gTa	p.G133V	ASTN1_ENST00000424564.2_Missense_Mutation_p.G133V|ASTN1_ENST00000361833.2_Missense_Mutation_p.G133V|ASTN1_ENST00000367657.3_Missense_Mutation_p.G133V|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	133					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.G133E(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GGGGTCTTGTCCAGGAAGGCT	0.532																																																1	Substitution - Missense(1)	lung(1)	1											248	234	239					1																	177030287		2203	4300	6503	175296910	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.398G>T	1.37:g.177030287C>A	ENSP00000356626:p.Gly133Val		175296910	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	C	18.85	3.711990	0.68730	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.15487	2.42;2.83;2.83;2.42	6.06	6.06	0.98353	.	0.081308	0.51477	D	0.000082	T	0.23014	0.0556	N	0.25647	0.755	0.80722	D	1	P;P;P	0.41393	0.748;0.748;0.748	P;P;P	0.47206	0.541;0.541;0.541	T	0.00448	-1.1733	10	0.72032	D	0.01	-9.3983	20.2159	0.98296	0.0:1.0:0.0:0.0	.	133;133;133	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	V	133	ENSP00000356629:G133V;ENSP00000354536:G133V;ENSP00000356626:G133V;ENSP00000395041:G133V	ENSP00000354536:G133V	G	-	2	0	ASTN1	175296910	0.999000	0.42202	0.998000	0.56505	0.984000	0.73092	3.733000	0.55029	2.882000	0.98803	0.655000	0.94253	GGA		0.532	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	177030287	C	A	177030287	3	1	102	1	0	0	0	0	1	0	0	0	1065	855	30	2	3578	2	ASTN1	1	177030287	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	15867151	177030287	72220334	10	26991										
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179886683	179886683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tgcctctgggagtttttggtTctttagtactcctgaggtag	12	7	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:179886683T>C	ENST00000606911.2	+	10	1252	c.1061T>C	c.(1060-1062)tTc>tCc	p.F354S	TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.F233S|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.F355S|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.F370S|TOR1AIP1_ENST00000474875.1_3'UTR			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	354					positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						AGTTTTTGGTTCTTTAGTACT	0.453																																																0			1											116	124	122					1																	179886683		2203	4300	6503	178153306	SO:0001583	missense	26092				CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"lamina associated polypeptide 1B"	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1061T>C	1.37:g.179886683T>C	ENSP00000476687:p.Phe354Ser		178153306	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.30|14.30	2.494951|2.494951	0.44352|0.44352	.|.	.|.	ENSG00000143337|ENSG00000143337	ENST00000528443;ENST00000271583;ENST00000435319|ENST00000447964	T;T;T|.	0.31247|.	1.5;1.5;1.5|.	5.96|5.96	-3.77|-3.77	0.04346|0.04346	.|.	1.146510|.	0.06179|.	N|.	0.679180|.	T|T	0.33731|0.33731	0.0873|0.0873	L|L	0.45581|0.45581	1.43|1.43	0.09310|0.09310	N|N	1|1	B|.	0.17667|.	0.023|.	B|.	0.12837|.	0.008|.	T|T	0.41893|0.41893	-0.9483|-0.9483	9|5	.|.	.|.	.|.	0.8852|0.8852	5.6542|5.6542	0.17633|0.17633	0.4952:0.1571:0.0:0.3478|0.4952:0.1571:0.0:0.3478	.|.	354|.	Q5JTV8|.	TOIP1_HUMAN|.	S|P	355;370;354|89	ENSP00000435365:F355S;ENSP00000271583:F370S;ENSP00000393292:F354S|.	.|.	F|S	+|+	2|1	0|0	TOR1AIP1|TOR1AIP1	178153306|178153306	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.404000|0.404000	0.30871|0.30871	-0.210000|-0.210000	0.09345|0.09345	-0.108000|-0.108000	0.12066|0.12066	0.533000|0.533000	0.62120|0.62120	TTC|TCT		0.453	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		C	179886683	T	C	179886683	3	2	102	1	0	0	0	0	1	0	0	0	16412	1783	62	4	1099	4	TOR1AIP1	1	179886683	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	2856396	179886683	69363938	11	26992										
KIF14	9928	hgsc.bcm.edu	37	chr1	200529955	200529955	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acagcttgttgtacaatttgGattgcattcttttgagcctc	8	8	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:200529955G>T	ENST00000367350.4	-	26	4563	c.4125C>A	c.(4123-4125)atC>atA	p.I1375I		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1375	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GTACAATTTGGATTGCATTCT	0.368																																																0			1											178	164	168					1																	200529955		2203	4300	6503	198796578	SO:0001819	synonymous_variant	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4125C>A	1.37:g.200529955G>T			198796578	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.368	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		T	200529955	G	T	200529955	2	4	102	1	0	0	0	0	0	0	0	1	8297	1164	41	2		2	KIF14	1	200529955	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	20643272	200529955	48720666	12	26993										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232579389	232579389	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctccagggtccgctcccgccGggtccagggtcgctggagga	16	15	0	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:232579389G>A	ENST00000366630.1	-	11	3754	c.3396C>T	c.(3394-3396)ccC>ccT	p.P1132P	SIPA1L2_ENST00000308942.4_Silent_p.P206P|SIPA1L2_ENST00000262861.4_Silent_p.P1132P			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1132					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CGCTCCCGCCGGGTCCAGGGT	0.522																																																0			1											77	89	85					1																	232579389		1936	4132	6068	230646012	SO:0001819	synonymous_variant	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3396C>T	1.37:g.232579389G>A			230646012	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																				0.522	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232579389	G	A	232579389	2	1	102	1	0	0	0	0	0	0	0	1	14367	1103	39	1		1	SIPA1L2	1	232579389	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	32049434	232579389	16671232	13	26994										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371635	240371667	+	In_Frame_Del	DEL	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	-													0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tacccggagcgggcatacccCctccgccccctctacctgga					rs267598447|rs183336748|rs142072223|rs528484073|rs549087270|rs76758921	byFrequency	TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr1:240371635_240371667delCCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	ENST00000319653.9	+	5	3753_3785	c.3523_3555delCCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	c.(3523-3555)cctccgccccctctacctggagtgggaatacctdel	p.PPPPLPGVGIP1186del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1186	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1319P(1)|p.P1319L(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGCATACCCCCTCCGCCCCCTCTACCTGGAGTGGGAATACCTCCTCCGCCCC	0.674																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(1)|prostate(1)	1																																								238438290	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3523_3555delCCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	1.37:g.240371635_240371667delCCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	ENSP00000318884:p.Pro1186_Pro1196del		238438258	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.674	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240371667	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	-	240371635	7	5	102	1	0	1	0	1	0	0	0	0	5969	623	22	0	3541	0	FMN2	1	240371635	In_Frame_Del	DEL	CCTCCGCCCCCTCTACCTGGAGTGGGAATACCT	TCGA-DT-5265-01A-21D-1826-10	7792246	240371635	8878986	14	26995										
PXDN	7837	hgsc.bcm.edu	37	chr2	1677555	1677555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	catcgtccagcaagtttaggCgggaatctgtcttcatgctc	10	11	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:1677555C>T	ENST00000252804.4	-	9	928	c.878G>A	c.(877-879)cGc>cAc	p.R293H	PXDN_ENST00000483018.1_5'UTR	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	293	Ig-like C2-type 1.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CAAGTTTAGGCGGGAATCTGT	0.507																																																0			2											124	126	125					2																	1677555		2055	4200	6255	1656562	SO:0001583	missense	7837			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.878G>A	2.37:g.1677555C>T	ENSP00000252804:p.Arg293His		1656562	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.0|23.0	4.356500|4.356500	0.82243|0.82243	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000433670|ENST00000252804	.|T	.|0.51574	.|0.7	5.25|5.25	5.25|5.25	0.73442|0.73442	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.056903	.|0.64402	.|D	.|0.000001	T|T	0.65637|0.65637	0.2710|0.2710	L|L	0.57536|0.57536	1.79|1.79	0.58432|0.58432	D|D	0.999998|0.999998	.|D;P	.|0.76494	.|0.999;0.58	.|D;B	.|0.70016	.|0.967;0.187	T|T	0.68078|0.68078	-0.5504|-0.5504	5|10	.|0.87932	.|D	.|0	-30.6332|-30.6332	17.3575|17.3575	0.87341|0.87341	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|293;293	.|Q92626-2;Q92626	.|.;PXDN_HUMAN	T|H	289|293	.|ENSP00000252804:R293H	.|ENSP00000252804:R293H	A|R	-|-	1|2	0|0	PXDN|PXDN	1656562|1656562	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.525000|0.525000	0.34531|0.34531	7.683000|7.683000	0.84093|0.84093	2.583000|2.583000	0.87209|0.87209	0.561000|0.561000	0.74099|0.74099	GCC|CGC		0.507	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1677555	C	T	1677555	3	4	102	1	0	0	0	0	1	0	0	0	12884	768	27	1	3621	1	PXDN	2	1677555	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		1677555	241521818	15	26996										
CHST10	9486	hgsc.bcm.edu	37	chr2	101009849	101009849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tgttatacacggtaatgcccGgagggatagtcgggtatgac	14	7	0	1	rs367887748		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:101009849G>A	ENST00000264249.3	-	7	1314	c.929C>T	c.(928-930)cCg>cTg	p.P310L	CHST10_ENST00000542617.1_Missense_Mutation_p.P358L|CHST10_ENST00000409701.1_Missense_Mutation_p.P310L	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	310					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						GGTAATGCCCGGAGGGATAGT	0.527																																																0			2											152	130	138					2																	101009849		2203	4300	6503	100376281	SO:0001583	missense	9486			BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.929C>T	2.37:g.101009849G>A	ENSP00000264249:p.Pro310Leu		100376281	Q53T18	Missense_Mutation	SNP	ENST00000264249.3	37	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213075	0.39102	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701	T;T;T	0.73047	1.92;-0.71;1.92	5.7	4.83	0.62350	.	0.138669	0.64402	N	0.000002	T	0.67664	0.2917	M	0.63843	1.955	0.80722	D	1	B	0.26258	0.145	B	0.23018	0.043	T	0.65199	-0.6226	10	0.38643	T	0.18	-14.4906	14.7123	0.69241	0.0695:0.0:0.9305:0.0	.	310	O43529	CHSTA_HUMAN	L	310;358;310	ENSP00000264249:P310L;ENSP00000438869:P358L;ENSP00000387309:P310L	ENSP00000264249:P310L	P	-	2	0	CHST10	100376281	1.000000	0.71417	0.175000	0.22980	0.376000	0.30014	6.793000	0.75130	1.430000	0.47334	0.655000	0.94253	CCG		0.527	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		A	101009849	G	A	101009849	3	1	102	1	0	0	0	0	1	0	0	0	3404	1116	39	1	145	1	CHST10	2	101009849	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	99332294	101009849	142189524	16	26997										
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194857	120194857	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctggtgtctttcgtcctctcCtccggcgggctcctgggttt	12	14	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:120194857C>T	ENST00000019103.5	-	0	1865				TMEM37_ENST00000409826.1_Silent_p.S150S|TMEM37_ENST00000306406.4_Silent_p.S138S|TMEM37_ENST00000465296.1_3'UTR	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	TCGTCCTCTCCTCCGGCGGGC	0.557																																																0			2											177	178	178					2																	120194857		2203	4300	6503	119911327	SO:0001628	intergenic_variant	140738				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"GPCR / Class B : Glucagon receptors"	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194857C>T			119911327	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																				0.557	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			T	120194857	C	T	120194857	1	4	102	0	1	0	0	0	0	0	0	0	16197	668	24	3		3	TMEM37	2	120194857	IGR	SNP	C	TCGA-DT-5265-01A-21D-1826-10	19185008	120194857	123004516	17	26998										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125521571	125521571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	caggacgcttctggaacgccGtctcattttatacagaagcc	9	12	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:125521571G>A	ENST00000431078.1	+	16	2741	c.2377G>A	c.(2377-2379)Gtc>Atc	p.V793I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	793	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.V793I(2)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTGGAACGCCGTCTCATTTTA	0.428																																																2	Substitution - Missense(2)	prostate(2)	2											128	121	123					2																	125521571		1867	4092	5959	125238041	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2377G>A	2.37:g.125521571G>A	ENSP00000399013:p.Val793Ile		125238041	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660591	0.67586	.	.	ENSG00000155052	ENST00000431078	T	0.49139	0.79	5.9	4.99	0.66335	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.142139	0.31601	N	0.007361	T	0.30510	0.0767	L	0.28556	0.865	0.36018	D	0.83852	P	0.43633	0.813	B	0.25405	0.06	T	0.45086	-0.9285	10	0.37606	T	0.19	.	16.2139	0.82191	0.0:0.1324:0.8676:0.0	.	793	Q8WYK1	CNTP5_HUMAN	I	793	ENSP00000399013:V793I	ENSP00000399013:V793I	V	+	1	0	CNTNAP5	125238041	1.000000	0.71417	0.976000	0.42696	0.983000	0.72400	7.857000	0.86963	2.804000	0.96469	0.655000	0.94253	GTC		0.428	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125521571	G	A	125521571	3	1	102	1	0	0	0	0	1	0	0	0	3656	1145	40	1	2439	1	CNTNAP5	2	125521571	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	5326714	125521571	117677802	18	26999										
NEB	4703	hgsc.bcm.edu	37	chr2	152582047	152582047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggcgtatggctgtccttttgTtttctcaaacttctccttgt	8	10	2	0	rs544069233		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:152582047T>C	ENST00000172853.10	-	6	469	c.322A>G	c.(322-324)Aca>Gca	p.T108A	NEB_ENST00000427231.2_Missense_Mutation_p.T108A|NEB_ENST00000397345.3_Missense_Mutation_p.T108A|NEB_ENST00000604864.1_Missense_Mutation_p.T108A|NEB_ENST00000603639.1_Missense_Mutation_p.T108A|NEB_ENST00000409198.1_Missense_Mutation_p.T108A			P20929	NEBU_HUMAN	nebulin	108					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGTCCTTTTGTTTTCTCAAAC	0.393													T|||	1	0.000199681	0	0	5008	,	,		17330	0		0	False		,,,				2504	0.001															0			2											205	196	199					2																	152582047		1881	4106	5987	152290293	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.322A>G	2.37:g.152582047T>C	ENSP00000172853:p.Thr108Ala		152290293	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	3.636	-0.074596	0.07184	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000439291	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	6.17	0.693	0.18056	.	0.505751	0.21446	N	0.074418	T	0.11793	0.0287	N	0.00890	-1.11	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16837	-1.0389	10	0.06757	T	0.87	.	3.4966	0.07657	0.1088:0.5147:0.1063:0.2701	.	108	P20929	NEBU_HUMAN	A	108	ENSP00000386259:T108A;ENSP00000380505:T108A;ENSP00000416578:T108A;ENSP00000172853:T108A	ENSP00000172853:T108A	T	-	1	0	NEB	152290293	0.996000	0.38824	0.995000	0.50966	0.978000	0.69477	0.440000	0.21592	0.166000	0.19597	-0.242000	0.12053	ACA		0.393	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152582047	T	C	152582047	3	2	102	1	0	0	0	0	1	0	0	0	10333	1725	60	4	26072	4	NEB	2	152582047	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	27060476	152582047	90617326	19	27000										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158156137	158156137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tggaacatacgaccctggccTtgatgtttggggtggggaaa	15	7	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:158156137T>C	ENST00000259056.4	+	6	2560	c.2075T>C	c.(2074-2076)cTt>cCt	p.L692P	RN7SKP281_ENST00000410472.1_RNA	NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	692	Catalytic subdomain B.		L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GACCCTGGCCTTGATGTTTGG	0.373																																																0			2											90	86	87					2																	158156137		2203	4300	6503	157864383	SO:0001583	missense	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.2075T>C	2.37:g.158156137T>C	ENSP00000259056:p.Leu692Pro		157864383	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801379	0.90538	.	.	ENSG00000136542	ENST00000259056	T	0.74209	-0.82	5.85	5.85	0.93711	.	0.065901	0.64402	D	0.000008	D	0.88994	0.6589	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.91351	0.5104	10	0.87932	D	0	.	15.9098	0.79463	0.0:0.0:0.0:1.0	.	692	Q7Z7M9	GALT5_HUMAN	P	692	ENSP00000259056:L692P	ENSP00000259056:L692P	L	+	2	0	GALNT5	157864383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.237000	0.73441	0.459000	0.35465	CTT		0.373	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		C	158156137	T	C	158156137	3	2	102	1	0	0	0	0	1	0	0	0	6236	1609	56	4	2097	4	GALNT5	2	158156137	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	5574090	158156137	85043236	20	27001										
SPEG	10290	hgsc.bcm.edu	37	chr2	220347992	220347992	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggaagagctgccctcagtgcCccgcccactgcagcccgagt	12	17	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:220347992C>T	ENST00000312358.7	+	30	5939	c.5807C>T	c.(5806-5808)cCc>cTc	p.P1936L	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1936					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CCCTCAGTGCCCCGCCCACTG	0.662																																																0			2											10	12	12					2																	220347992		1858	4078	5936	220056236	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5807C>T	2.37:g.220347992C>T	ENSP00000311684:p.Pro1936Leu		220056236	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.264238	0.39995	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.66099	-0.19	4.75	3.84	0.44239	.	0.000000	0.38663	N	0.001602	T	0.57989	0.2091	L	0.34521	1.04	0.80722	D	1	P	0.48503	0.911	P	0.46940	0.532	T	0.64019	-0.6505	10	0.87932	D	0	.	14.7333	0.69399	0.0:0.8543:0.1457:0.0	.	1936	Q15772	SPEG_HUMAN	L	1936	ENSP00000311684:P1936L	ENSP00000265327:P1936L	P	+	2	0	SPEG	220056236	1.000000	0.71417	0.759000	0.31340	0.759000	0.43091	5.829000	0.69316	1.173000	0.42796	0.455000	0.32223	CCC		0.662	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220347992	C	T	220347992	3	4	102	1	0	0	0	0	1	0	0	0	15075	623	22	3	5937	3	SPEG	2	220347992	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	62191855	220347992	22851381	21	27002										
PAX3	5077	hgsc.bcm.edu	37	chr2	223163317	223163317	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cgcatcatcctgggcacagcGccggccagcgtggtcatcct	12	16	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:223163317G>A	ENST00000350526.4	-	1	154	c.18C>T	c.(16-18)ggC>ggT	p.G6G	PAX3_ENST00000392070.2_Silent_p.G6G|PAX3_ENST00000409828.3_Silent_p.G6G|PAX3_ENST00000392069.2_Silent_p.G6G|PAX3_ENST00000336840.6_Silent_p.G6G|PAX3_ENST00000258387.5_Silent_p.G6G|CCDC140_ENST00000295226.1_Intron|PAX3_ENST00000409551.3_Silent_p.G6G|PAX3_ENST00000344493.4_Silent_p.G6G	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	6					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGGCACAGCGCCGGCCAGCG	0.677			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																Dom	yes		2	2q35	5077	paired box gene 3	yes	M	0			2											8	10	9					2																	223163317		2190	4282	6472	222871561	SO:0001819	synonymous_variant	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.18C>T	2.37:g.223163317G>A			222871561	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	37	CCDS42826.1																																																																																				0.677	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			A	223163317	G	A	223163317	2	1	102	1	0	0	0	0	0	0	0	1	11511	1074	38	1		1	PAX3	2	223163317	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	2815325	223163317	20036056	22	27003										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228102706	228102706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttgtgtctgtaaagacaaagGccagtgcttctgtgacgggg	14	7	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr2:228102706G>A	ENST00000396578.3	+	2	272	c.110G>A	c.(109-111)gGc>gAc	p.G37D	AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	37	7S domain.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AAAGACAAAGGCCAGTGCTTC	0.433																																																0			2											191	184	186					2																	228102706		1844	4085	5929	227810950	SO:0001583	missense	1285				CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.110G>A	2.37:g.228102706G>A	ENSP00000379823:p.Gly37Asp		227810950	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233567	0.79688	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.91068	-2.78	4.95	4.95	0.65309	.	0.207971	0.34178	N	0.004197	D	0.89269	0.6667	N	0.08118	0	0.38580	D	0.950155	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.90781	0.4679	10	0.44086	T	0.13	.	14.0362	0.64646	0.0:0.0:1.0:0.0	.	37;37;37;37	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	D	37	ENSP00000379823:G37D	ENSP00000323334:G37D	G	+	2	0	COL4A3	227810950	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.714000	0.61902	2.454000	0.82982	0.591000	0.81541	GGC		0.433	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		A	228102706	G	A	228102706	3	1	102	1	0	0	0	0	1	0	0	0	3697	1203	42	3	116	3	COL4A3	2	228102706	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	4939389	228102706	15096667	23	27004										
OXSM	54995	hgsc.bcm.edu	37	chr3	25832827	25832827	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gtcagttcaatgaacaaaacTttgtgtccaaatcagatatc	6	8	3	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:25832827T>C	ENST00000280701.3	+	2	415	c.316T>C	c.(316-318)Ttt>Ctt	p.F106L	OXSM_ENST00000420173.2_Missense_Mutation_p.F106L|OXSM_ENST00000449808.1_Intron|NGLY1_ENST00000417874.2_5'Flank	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	106			F -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)	p.F106I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TGAACAAAACTTTGTGTCCAA	0.448																																																1	Substitution - Missense(1)	breast(1)	3											170	144	153					3																	25832827		2203	4300	6503	25807831	SO:0001583	missense	54995			BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.316T>C	3.37:g.25832827T>C	ENSP00000280701:p.Phe106Leu		25807831		Missense_Mutation	SNP	ENST00000280701.3	37	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021443	0.75275	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	5.93	5.93	0.95920	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.39633	1.23	0.80722	D	1	D;B	0.55385	0.971;0.023	P;B	0.48189	0.57;0.012	T	0.62969	-0.6741	9	0.87932	D	0	-21.5264	16.379	0.83439	0.0:0.0:0.0:1.0	.	106;106	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	L	106	.	ENSP00000280701:F106L	F	+	1	0	OXSM	25807831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.991000	0.88244	2.268000	0.75426	0.455000	0.32223	TTT		0.448	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		C	25832827	T	C	25832827	3	2	102	1	0	0	0	0	1	0	0	0	11366	1609	56	4	318	4	OXSM	3	25832827	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10		25832827	172189603	24	27005										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54914866	54914866	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gtcatgggaaatatttcttcCgagggaatgtaaccatcgaa	10	7	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:54914866C>T	ENST00000474759.1	+	21	1936	c.1888C>T	c.(1888-1890)Cga>Tga	p.R630*	CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.R536*|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.R630*|CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.R630*	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	630						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	ATATTTCTTCCGAGGGAATGT	0.478																																																0			3											254	239	243					3																	54914866		1922	4132	6054	54889906	SO:0001587	stop_gained	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1888C>T	3.37:g.54914866C>T	ENSP00000419101:p.Arg630*		54889906	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.661944|7.661944	0.98419|0.98419	.|.	.|.	ENSG00000157445|ENSG00000157445	ENST00000438476|ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	.|.	.|.	.|.	5.88|5.88	4.94|4.94	0.65067|0.65067	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.40815|.	0.1132|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42155|.	-0.9468|.	4|.	0.51188|0.10377	T|T	0.08|0.69	-0.7754|-0.7754	11.1578|11.1578	0.48497|0.48497	0.305:0.695:0.0:0.0|0.305:0.695:0.0:0.0	.|.	.|.	.|.	.|.	L|X	508|630;630;630;536;536	.|.	ENSP00000391808:P508L|ENSP00000288197:R630X	P|R	+|+	2|1	0|2	CACNA2D3|CACNA2D3	54889906|54889906	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	6.539000|6.539000	0.73856|0.73856	2.788000|2.788000	0.95919|0.95919	0.637000|0.637000	0.83480|0.83480	CCG|CGA		0.478	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54914866	C	T	54914866	4	4	102	1	0	0	0	0	0	1	0	0	2556	644	23	1	1970	1	CACNA2D3	3	54914866	Nonsense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	29082039	54914866	143107564	25	27006										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121615292	121615292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	atccactgagcattgccttcAttgtggtgaatgaattctgc	9	9	2	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:121615292A>G	ENST00000489711.1	+	2	533	c.145A>G	c.(145-147)Att>Gtt	p.I49V	SLC15A2_ENST00000295605.2_Missense_Mutation_p.I49V	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	49					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CATTGCCTTCATTGTGGTGAA	0.438																																																0			3											168	155	159					3																	121615292		2203	4300	6503	123097982	SO:0001583	missense	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.145A>G	3.37:g.121615292A>G	ENSP00000417085:p.Ile49Val		123097982	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810758	0.90707	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.58060	0.36;0.36	5.52	5.52	0.82312	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.63920	0.2552	L	0.41124	1.26	0.80722	D	1	D;D	0.76494	0.999;0.989	D;D	0.81914	0.995;0.968	T	0.66654	-0.5869	10	0.87932	D	0	-18.0944	13.6447	0.62275	1.0:0.0:0.0:0.0	.	49;49	B4E2A7;Q16348	.;S15A2_HUMAN	V	49;42;49	ENSP00000417085:I49V;ENSP00000295605:I49V	ENSP00000295605:I49V	I	+	1	0	SLC15A2	123097982	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.605000	0.90883	2.320000	0.78422	0.528000	0.53228	ATT		0.438	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		G	121615292	A	G	121615292	3	3	102	1	0	0	0	0	1	0	0	0	14436	217	8	4	151	4	SLC15A2	3	121615292	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	66700426	121615292	76407138	26	27007										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178927982	178927982	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttgttttttaaggaacactgTccattggcatggggaaatat	10	5	0	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:178927982T>C	ENST00000263967.3	+	8	1417	c.1260T>C	c.(1258-1260)tgT>tgC	p.C420C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	420	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		C -> R (in CLOVE and CRC; shows an increase in lipid kinase activity; may increase the affinity for lipid membranes). {ECO:0000269|PubMed:22658544}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGGAACACTGTCCATTGGCAT	0.328		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											88	83	85					3																	178927982		1822	4079	5901	180410676	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1260T>C	3.37:g.178927982T>C			180410676	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.328	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178927982	T	C	178927982	2	2	102	1	0	0	0	0	0	0	0	1	11944	1673	58	4		4	PIK3CA	3	178927982	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	57312690	178927982	19094448	27	27008										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936092	178936092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcctctctctgaaatcactgAgcaggagaaagattttctat	7	9	4	4	rs121913274		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:178936092A>G	ENST00000263967.3	+	10	1791	c.1634A>G	c.(1633-1635)gAg>gGg	p.E545G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545A(96)|p.E545G(78)|p.E545V(4)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAAATCACTGAGCAGGAGAAA	0.353	E545A(AGS_STOMACH)|E545G(KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	178	Substitution - Missense(178)	breast(40)|large_intestine(39)|ovary(30)|endometrium(17)|skin(9)|urinary_tract(8)|upper_aerodigestive_tract(4)|central_nervous_system(4)|oesophagus(4)|stomach(4)|liver(4)|thyroid(3)|soft_tissue(3)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|NS(1)|eye(1)|pancreas(1)|prostate(1)|pituitary(1)	3											61	61	61					3																	178936092		1813	4072	5885	180418786	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1634A>G	3.37:g.178936092A>G	ENSP00000263967:p.Glu545Gly		180418786	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704887	0.88924	.	.	ENSG00000121879	ENST00000263967	T	0.64438	-0.1	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77046	0.4073	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.76675	-0.2872	10	0.41790	T	0.15	-25.7963	16.1026	0.81194	1.0:0.0:0.0:0.0	.	545	P42336	PK3CA_HUMAN	G	545	ENSP00000263967:E545G	ENSP00000263967:E545G	E	+	2	0	PIK3CA	180418786	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178936092	A	G	178936092	3	3	102	1	0	0	0	0	1	0	0	0	11944	304	11	4	1668	4	PIK3CA	3	178936092	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	8110	178936092	19086338	28	27009										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951901	178951901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggtttcaggagatgtgttacAaggcttatctagctattcga	11	6	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:178951901A>G	ENST00000263967.3	+	21	3113	c.2956A>G	c.(2956-2958)Aag>Gag	p.K986E	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	986	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GATGTGTTACAAGGCTTATCT	0.368		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											120	109	112					3																	178951901		1863	4096	5959	180434595	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2956A>G	3.37:g.178951901A>G	ENSP00000263967:p.Lys986Glu		180434595	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484726	0.44147	.	.	ENSG00000121879	ENST00000263967	T	0.74315	-0.83	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.74772	0.3760	N	0.21142	0.635	0.80722	D	1	D	0.64830	0.994	P	0.61397	0.888	T	0.70454	-0.4867	10	0.15066	T	0.55	-18.4827	16.635	0.85050	1.0:0.0:0.0:0.0	.	986	P42336	PK3CA_HUMAN	E	986	ENSP00000263967:K986E	ENSP00000263967:K986E	K	+	1	0	PIK3CA	180434595	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	2.330000	0.79161	0.477000	0.44152	AAG		0.368	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951901	A	G	178951901	3	3	102	1	0	0	0	0	1	0	0	0	11944	131	5	4	3034	4	PIK3CA	3	178951901	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	15809	178951901	19070529	29	27010										
DVL3	1857	hgsc.bcm.edu	37	chr3	183884627	183884627	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cctgcaggcgagcccatccgGcccattgaccctgcggcctg	12	18	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr3:183884627G>T	ENST00000313143.3	+	11	1310	c.1062G>T	c.(1060-1062)cgG>cgT	p.R354R	EIF2B5_ENST00000444495.1_Intron|DVL3_ENST00000431765.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	354					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			AGCCCATCCGGCCCATTGACC	0.637																																																0			3											76	73	74					3																	183884627		2203	4300	6503	185367321	SO:0001819	synonymous_variant	1857			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.1062G>T	3.37:g.183884627G>T			185367321	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Silent	SNP	ENST00000313143.3	37	CCDS3253.1																																																																																				0.637	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		T	183884627	G	T	183884627	2	4	102	1	0	0	0	0	0	0	0	1	4848	1190	42	2		2	DVL3	3	183884627	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	4932726	183884627	14137803	30	27011										
CPLX1	10815	hgsc.bcm.edu	37	chr4	780337	780337	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccgggcaggtacttgatgacGgtgtccaggatgctctcgtc	14	11	1	2	rs377036276		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:780337G>A	ENST00000304062.6	-	4	588	c.357C>T	c.(355-357)acC>acT	p.T119T	CPLX1_ENST00000505203.1_Silent_p.T98T	NM_006651.3	NP_006642.1	O14810	CPLX1_HUMAN	complexin 1	119					exocytosis (GO:0006887)|glutamate secretion (GO:0014047)|insulin secretion (GO:0030073)|neurotransmitter secretion (GO:0007269)|regulation of exocytosis (GO:0017157)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|synapse (GO:0045202)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex (GO:0070554)	neurotransmitter transporter activity (GO:0005326)			kidney(1)|lung(2)	3				Colorectal(103;0.187)		ACTTGATGACGGTGTCCAGGA	0.701																																																0			4											28	31	30					4																	780337		2201	4296	6497	770337	SO:0001819	synonymous_variant	10815			AF022383	CCDS46995.1	4p16.3	2008-08-07			ENSG00000168993	ENSG00000168993			2309	protein-coding gene	gene with protein product		605032				7553862	Standard	NM_006651		Approved	CPX-I	uc003gbi.3	O14810	OTTHUMG00000160005	ENST00000304062.6:c.357C>T	4.37:g.780337G>A			770337	A6NI80|B2R4R5|D3DVN3|F1T0G1	Silent	SNP	ENST00000304062.6	37	CCDS46995.1																																																																																				0.701	CPLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358830.1			A	780337	G	A	780337	2	1	102	1	0	0	0	0	0	0	0	1	3810	1103	39	1		1	CPLX1	4	780337	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10		780337	190373939	31	27012										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6037771	6037771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gccctcgctcagcgcctcacCggccctccgccccggctcct	9	24	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:6037771C>T	ENST00000409021.3	-	19	2688	c.2239G>A	c.(2239-2241)Ggt>Agt	p.G747S	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.G562S	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	103					cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGCGCCTCACCGGCCCTCCGC	0.642																																																0			4											10	13	12					4																	6037771		2067	4128	6195	6088672	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.2239G>A	4.37:g.6037771C>T	ENSP00000386711:p.Gly747Ser		6088672	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	37	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	C	5.571	0.290203	0.10567	.	.	ENSG00000152969	ENST00000409021;ENST00000409371	T;T	0.27890	2.07;1.64	4.79	0.36	0.16097	.	0.116804	0.31071	U	0.008301	T	0.14270	0.0345	.	.	.	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.12156	0.001;0.007	T	0.17379	-1.0371	9	0.09338	T	0.73	.	8.7426	0.34567	0.0:0.4719:0.0:0.5281	.	562;747	Q96N16-5;Q96N16-2	.;.	S	747;562	ENSP00000386711:G747S;ENSP00000387042:G562S	ENSP00000386711:G747S	G	-	1	0	JAKMIP1	6088672	0.998000	0.40836	0.776000	0.31678	0.438000	0.31896	1.588000	0.36633	0.089000	0.17243	0.436000	0.28706	GGT		0.642	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		T	6037771	C	T	6037771	3	4	102	1	0	0	0	0	1	0	0	0	7961	652	23	1	268	1	JAKMIP1	4	6037771	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	5257434	6037771	185116505	32	27013										
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83349484	83349484	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aaatccaaatcctcttgatcTcccagtgactggatctgttt	6	11	3	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:83349484T>G	ENST00000295470.5	-	2	734	c.559A>C	c.(559-561)Aga>Cga	p.R187R	HNRNPDL_ENST00000602300.1_Silent_p.R68R|ENOPH1_ENST00000509635.1_5'Flank|HNRNPDL_ENST00000349655.4_Silent_p.R68R|ENOPH1_ENST00000273920.3_5'Flank|HNRNPDL_ENST00000514511.1_Intron|HNRNPDL_ENST00000502762.1_Silent_p.R187R	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	187	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										CCTCTTGATCTCCCAGTGACT	0.408																																																0			4											138	134	135					4																	83349484		2203	4300	6503	83568508	SO:0001819	synonymous_variant	9987			D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.559A>C	4.37:g.83349484T>G			83568508	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Silent	SNP	ENST00000295470.5	37	CCDS3593.1																																																																																				0.408	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		G	83349484	T	G	83349484	2	3	102	1	0	0	0	0	0	0	0	1	7297	1559	54	4		4	HNRPDL	4	83349484	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	77311713	83349484	107804792	33	27014										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148800446	148800446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gtatcgaaaagcagcaaagaAgttcaacatgatcccatttg	8	8	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:148800446A>G	ENST00000336498.3	+	9	1135	c.896A>G	c.(895-897)aAg>aGg	p.K299R	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GCAGCAAAGAAGTTCAACATG	0.393																																																0			4											154	146	149					4																	148800446		2203	4300	6503	149019896	SO:0001583	missense	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.896A>G	4.37:g.148800446A>G	ENSP00000336923:p.Lys299Arg		149019896	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	37	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	A	8.749	0.920871	0.17982	.	.	ENSG00000071205	ENST00000336498	T	0.42513	0.97	5.1	3.86	0.44501	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.228786	0.47455	N	0.000240	T	0.25680	0.0625	L	0.31065	0.9	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06698	-1.0812	10	0.18710	T	0.47	.	5.7181	0.17972	0.7384:0.1637:0.0979:0.0	.	299	A1A4S6	RHG10_HUMAN	R	299	ENSP00000336923:K299R	ENSP00000336923:K299R	K	+	2	0	ARHGAP10	149019896	0.995000	0.38212	0.999000	0.59377	0.990000	0.78478	1.641000	0.37197	0.716000	0.32124	0.459000	0.35465	AAG		0.393	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		G	148800446	A	G	148800446	3	3	102	1	0	0	0	0	1	0	0	0	862	72	3	4	930	4	ARHGAP10	4	148800446	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	65450962	148800446	42353830	34	27015										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245445	153245445	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agttccattccacttgttaaCgactggtgccctgttaacgt	8	11	0	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:153245445C>T	ENST00000281708.4	-	11	2975	c.1746G>A	c.(1744-1746)tcG>tcA	p.S582S	FBXW7_ENST00000393956.3_Silent_p.S406S|FBXW7_ENST00000603548.1_Silent_p.S582S|FBXW7_ENST00000263981.5_Silent_p.S502S|FBXW7_ENST00000296555.5_Silent_p.S464S|FBXW7_ENST00000603841.1_Silent_p.S582S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	582			S -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CACTTGTTAACGACTGGTGCC	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											149	126	133					4																	153245445		2203	4300	6503	153464895	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1746G>A	4.37:g.153245445C>T			153464895	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153245445	C	T	153245445	2	4	102	1	0	0	0	0	0	0	0	1	5788	523	19	1		1	FBXW7	4	153245445	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	4444999	153245445	37908831	35	27016										
MARCH1	55016	hgsc.bcm.edu	37	chr4	164507069	164507069	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gggctctcttcatccccttcGcagtgacagattctgcagaa	9	13	3	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:164507069G>A	ENST00000503008.1	-	6	1231	c.255C>T	c.(253-255)tgC>tgT	p.C85C	MARCH1_ENST00000339875.5_Silent_p.C68C|MARCH1_ENST00000274056.7_Silent_p.C85C|MARCH1_ENST00000514618.1_Silent_p.C341C	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase	85					antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C68C(1)|p.C85C(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CATCCCCTTCGCAGTGACAGA	0.527																																																2	Substitution - coding silent(2)	lung(2)	4											55	54	54					4																	164507069		2203	4300	6503	164726519	SO:0001819	synonymous_variant	55016			AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.255C>T	4.37:g.164507069G>A			164726519	D3DP29|Q9NWR0	Silent	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																				0.527	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		A	164507069	G	A	164507069	2	1	102	1	0	0	0	0	0	0	0	1	9328	1079	38	1		1	MARCH1	4	164507069	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	11261624	164507069	26647207	36	27017										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186598368	186598368	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggggccttttgagaaatgacGgtacttcgacagatttggag	14	6	0	3	rs532231815		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr4:186598368G>A	ENST00000284776.7	-	4	465				SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000437304.2_Missense_Mutation_p.P92L|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000449407.2_Intron|RP11-626E13.1_ENST00000447277.1_RNA	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2						actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GAGAAATGACGGTACTTCGAC	0.483													G|||	1	0.000199681	8e-04	0	5008	,	,		19750	0		0	False		,,,				2504	0				Esophageal Squamous(153;41 2433 9491 36028)											0			4											143	128	133					4																	186598368		692	1591	2283	186835362	SO:0001627	intron_variant	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.44+1208C>T	4.37:g.186598368G>A			186835362	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	3.975	-0.007579	0.07773	.	.	ENSG00000154556	ENST00000437304	T	0.48836	0.8	5.91	5.07	0.68467	.	.	.	.	.	T	0.30103	0.0754	N	0.08118	0	0.45979	D	0.998795	B	0.11235	0.004	B	0.04013	0.001	T	0.09314	-1.0680	9	0.72032	D	0.01	.	13.3695	0.60705	0.0723:0.0:0.9277:0.0	.	92	E9PAW4	.	L	92	ENSP00000396008:P92L	ENSP00000396008:P92L	P	-	2	0	SORBS2	186835362	0.700000	0.27796	0.005000	0.12908	0.064000	0.16182	3.098000	0.50259	1.505000	0.48720	0.655000	0.94253	CCG		0.483	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		A	186598368	G	A	186598368	1	1	102	0	1	0	0	0	0	0	0	0	14965	1116	39	1		1	SORBS2	4	186598368	Intron	SNP	G	TCGA-DT-5265-01A-21D-1826-10	22091299	186598368	4555908	37	27018										
TRIO	7204	hgsc.bcm.edu	37	chr5	14419928	14419928	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acagtggtgatccatgacttCaccgcttgcaacagcaacga	9	12	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr5:14419928C>T	ENST00000344204.4	+	34	5025	c.5001C>T	c.(4999-5001)ttC>ttT	p.F1667F	TRIO_ENST00000537187.1_Silent_p.F1667F	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1667	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					TCCATGACTTCACCGCTTGCA	0.602																																																0			5											59	52	54					5																	14419928		2203	4300	6503	14472928	SO:0001819	synonymous_variant	7204			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.5001C>T	5.37:g.14419928C>T			14472928	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																				0.602	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		T	14419928	C	T	14419928	2	4	102	1	0	0	0	0	0	0	0	1	16592	825	29	3		3	TRIO	5	14419928	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10		14419928	166495332	38	27019										
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36035969	36035969	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	catagggcttgaggtgcgtcGcgccccctgtctggaggacg	16	12	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr5:36035969G>A	ENST00000282507.3	-	7	1504	c.1403C>T	c.(1402-1404)gCg>gTg	p.A468V	UGT3A2_ENST00000513300.1_Missense_Mutation_p.A434V|UGT3A2_ENST00000545528.1_Missense_Mutation_p.A166V	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	468					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAGGTGCGTCGCGCCCCCTGT	0.632																																																0			5											50	45	47					5																	36035969		2203	4300	6503	36071726	SO:0001583	missense	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.1403C>T	5.37:g.36035969G>A	ENSP00000282507:p.Ala468Val		36071726	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328942	0.24167	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.70749	-0.51;-0.51;-0.26	2.74	1.83	0.25207	.	0.364632	0.19685	U	0.108411	D	0.83613	0.5292	M	0.90759	3.145	0.09310	N	1	D;D	0.76494	0.978;0.999	P;D	0.64410	0.74;0.925	T	0.74677	-0.3585	10	0.87932	D	0	.	10.5339	0.44992	0.0:0.3944:0.6056:0.0	.	434;468	E9PFK7;Q3SY77	.;UD3A2_HUMAN	V	468;434;166	ENSP00000282507:A468V;ENSP00000427404:A434V;ENSP00000445367:A166V	ENSP00000282507:A468V	A	-	2	0	UGT3A2	36071726	0.003000	0.15002	0.003000	0.11579	0.001000	0.01503	0.774000	0.26675	0.670000	0.31165	0.563000	0.77884	GCG		0.632	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		A	36035969	G	A	36035969	3	1	102	1	0	0	0	0	1	0	0	0	17004	1087	38	1	172	1	UGT3A2	5	36035969	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	21616041	36035969	144879291	39	27020										
NNT	23530	hgsc.bcm.edu	37	chr5	43655960	43655960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aggattgacaattgccaaacGcatccagatttctgatttac	7	9	1	3	rs139987446		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr5:43655960G>A	ENST00000264663.5	+	15	2299	c.2078G>A	c.(2077-2079)cGc>cAc	p.R693H	NNT_ENST00000344920.4_Missense_Mutation_p.R693H|NNT_ENST00000512996.2_Missense_Mutation_p.R562H	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	693					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					ATTGCCAAACGCATCCAGATT	0.348																																																0			5						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	114	106	109		2078,2078	5.7	1	5	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NNT	NM_012343.3,NM_182977.2	29,29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	693/1087,693/1087	43655960	2,13004	2203	4300	6503	43691717	SO:0001583	missense	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2078G>A	5.37:g.43655960G>A	ENSP00000264663:p.Arg693His		43691717	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440831	0.83993	2.27E-4	1.16E-4	ENSG00000112992	ENST00000542759;ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.92397	-3.03;-3.03;-3.03	5.7	5.7	0.88788	.	0.088921	0.64402	D	0.000001	D	0.96753	0.8940	M	0.88310	2.945	0.58432	D	0.999995	D	0.76494	0.999	D	0.69654	0.965	D	0.97008	0.9734	10	0.87932	D	0	-11.1376	19.8361	0.96658	0.0:0.0:1.0:0.0	.	693	Q13423	NNTM_HUMAN	H	208;693;693;562	ENSP00000264663:R693H;ENSP00000343873:R693H;ENSP00000426343:R562H	ENSP00000264663:R693H	R	+	2	0	NNT	43691717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.428000	0.52792	2.692000	0.91855	0.655000	0.94253	CGC		0.348	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43655960	G	A	43655960	3	1	102	1	0	0	0	0	1	0	0	0	10541	1087	38	1	2132	1	NNT	5	43655960	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	7619991	43655960	137259300	40	27021										
C5orf30	90355	hgsc.bcm.edu	37	chr5	102611999	102611999	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cagctgtcaatggcaggaggCgaaggcggatgccaagctca	15	10	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr5:102611999C>T	ENST00000319933.2	+	3	687	c.379C>T	c.(379-381)Cga>Tga	p.R127*	C5orf30_ENST00000515669.1_Nonsense_Mutation_p.R127*|C5orf30_ENST00000510890.1_Nonsense_Mutation_p.R127*	NM_033211.2	NP_149988.1	Q96GV9	CE030_HUMAN	chromosome 5 open reading frame 30	127	Poly-Arg.				cilium morphogenesis (GO:0060271)|protein transport (GO:0015031)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9		all_cancers(142;2.22e-05)|all_epithelial(76;9.54e-08)|Prostate(80;0.0174)|Colorectal(57;0.0551)|Ovarian(225;0.11)|Lung NSC(167;0.136)|all_lung(232;0.18)		Epithelial(69;2.84e-14)|COAD - Colon adenocarcinoma(37;0.00762)		TGGCAGGAGGCGAAGGCGGAT	0.493																																																0			5											54	57	56					5																	102611999		2203	4300	6503	102639898	SO:0001587	stop_gained	90355				CCDS4095.1	5q21.1	2012-02-23			ENSG00000181751	ENSG00000181751			25052	protein-coding gene	gene with protein product						22085962	Standard	NM_033211		Approved	FLJ25291	uc003kog.1	Q96GV9	OTTHUMG00000128738	ENST00000319933.2:c.379C>T	5.37:g.102611999C>T	ENSP00000326110:p.Arg127*		102639898		Nonsense_Mutation	SNP	ENST00000319933.2	37	CCDS4095.1	.	.	.	.	.	.	.	.	.	.	C	37	6.171622	0.97348	.	.	ENSG00000181751	ENST00000319933;ENST00000515669;ENST00000510890	.	.	.	6.17	5.3	0.74995	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2029	14.9259	0.70878	0.3094:0.6906:0.0:0.0	.	.	.	.	X	127	.	ENSP00000326110:R127X	R	+	1	2	C5orf30	102639898	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.706000	0.47135	1.618000	0.50286	0.655000	0.94253	CGA		0.493	C5orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250649.1	NM_033211		T	102611999	C	T	102611999	4	4	102	1	0	0	0	0	0	1	0	0	2296	760	27	1	381	1	C5orf30	5	102611999	Nonsense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	58956039	102611999	78303261	41	27022										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121638667	121638667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	caatgatgaatcactatcagAgcaattgtctgtgcggtaac	9	8	3	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr6:121638667A>G	ENST00000398212.2	-	3	518	c.469T>C	c.(469-471)Tct>Cct	p.S157P	TBC1D32_ENST00000275159.6_Missense_Mutation_p.S157P	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	157					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCACTATCAGAGCAATTGTCT	0.318																																																0			6											296	270	278					6																	121638667		1862	4091	5953	121680366	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.469T>C	6.37:g.121638667A>G	ENSP00000381270:p.Ser157Pro		121680366	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870427	0.51588	.	.	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.25414	1.8;1.8;1.8	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	M	0.62016	1.91	0.54753	D	0.999987	P	0.47762	0.9	B	0.43194	0.411	T	0.02805	-1.1108	10	0.51188	T	0.08	-0.0535	15.0687	0.72017	1.0:0.0:0.0:0.0	.	157	Q96NH3	BROMI_HUMAN	P	157	ENSP00000275159:S157P;ENSP00000381270:S157P;ENSP00000397993:S157P	ENSP00000275159:S157P	S	-	1	0	C6orf170	121680366	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.050000	0.89445	2.013000	0.59113	0.533000	0.62120	TCT		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121638667	A	G	121638667	3	3	102	1	0	0	0	0	1	0	0	0	2350	304	11	4	3424	4	C6orf170	6	121638667	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10		121638667	49476400	42	27023										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138198312	138198312	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aaatgagatgaaggagaagcTcttaaaagagtacttaatgg	11	3	1	4			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr6:138198312T>C	ENST00000237289.4	+	6	971	c.905T>C	c.(904-906)cTc>cCc	p.L302P	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	302	2 X approximate repeats.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.L302P(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		AAGGAGAAGCTCTTAAAAGAG	0.423			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	26	Whole gene deletion(25)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(26)	6											93	98	96					6																	138198312		2203	4300	6503	138240005	SO:0001583	missense	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.905T>C	6.37:g.138198312T>C	ENSP00000237289:p.Leu302Pro		138240005	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.615533	0.87359	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.39787	1.06	6.08	6.08	0.98989	.	0.060900	0.64402	D	0.000002	T	0.46151	0.1378	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51980	-0.8636	10	0.87932	D	0	-14.2873	15.214	0.73250	0.0:0.0:0.0:1.0	.	302	P21580	TNAP3_HUMAN	P	302	ENSP00000237289:L302P	ENSP00000237289:L302P	L	+	2	0	TNFAIP3	138240005	1.000000	0.71417	0.923000	0.36655	0.924000	0.55760	7.375000	0.79646	2.330000	0.79161	0.533000	0.62120	CTC		0.423	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			C	138198312	T	C	138198312	3	2	102	1	0	0	0	0	1	0	0	0	16313	1551	54	4	923	4	TNFAIP3	6	138198312	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	16559645	138198312	32916755	43	27024										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165713889	165713889	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agatcaccaaatatcaaagaActgttacaaatatcttcaaa	3	8	4	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr6:165713889A>T	ENST00000230301.8	-	3	860	c.840T>A	c.(838-840)agT>agA	p.S280R	C6orf118_ENST00000543069.1_Missense_Mutation_p.S176R	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	280										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		ATATCAAAGAACTGTTACAAA	0.393																																																0			6											112	131	125					6																	165713889		2203	4300	6503	165633879	SO:0001583	missense	168090				CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.840T>A	6.37:g.165713889A>T	ENSP00000230301:p.Ser280Arg		165633879	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.422750	0.62733	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.13901	2.55;2.55	5.24	-0.952	0.10366	.	0.226301	0.38663	N	0.001608	T	0.17238	0.0414	L	0.61218	1.895	0.28469	N	0.915529	D	0.76494	0.999	D	0.72075	0.976	T	0.09143	-1.0688	10	0.56958	D	0.05	.	14.0096	0.64488	0.1648:0.0:0.8352:0.0	.	280	Q5T5N4	CF118_HUMAN	R	280;176	ENSP00000230301:S280R;ENSP00000439288:S176R	ENSP00000230301:S280R	S	-	3	2	C6orf118	165633879	0.961000	0.32948	0.784000	0.31847	0.787000	0.44495	-0.194000	0.09559	-0.517000	0.06461	0.533000	0.62120	AGT		0.393	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		T	165713889	A	T	165713889	3	4	102	1	0	0	0	0	1	0	0	0	2329	40	2	5	597	5	C6orf118	6	165713889	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	27515577	165713889	5401178	44	27025										
SFRP4	6424	hgsc.bcm.edu	37	chr7	37947203	37947203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gggattactacgactggtgcGcccggctgttttcttcttgt	12	10	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:37947203G>A	ENST00000436072.2	-	6	1296	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	307	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CGACTGGTGCGCCCGGCTGTT	0.493																																																0			7											120	119	119					7																	37947203		2203	4300	6503	37913728	SO:0001583	missense	6424			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.919C>T	7.37:g.37947203G>A	ENSP00000410715:p.Arg307Cys		37913728	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Missense_Mutation	SNP	ENST00000436072.2	37	CCDS5453.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150897	0.78001	.	.	ENSG00000106483	ENST00000436072;ENST00000446575	T	0.68331	-0.32	5.83	5.83	0.93111	Netrin domain (1);	0.000000	0.56097	D	0.000029	T	0.67942	0.2947	N	0.24115	0.695	0.54753	D	0.999985	D	0.89917	1.0	P	0.59221	0.854	T	0.71454	-0.4588	10	0.87932	D	0	.	14.4157	0.67148	0.0:0.0:0.8518:0.1481	.	307	Q6FHJ7	SFRP4_HUMAN	C	307;304	ENSP00000410715:R307C	ENSP00000410715:R307C	R	-	1	0	SFRP4	37913728	1.000000	0.71417	0.991000	0.47740	0.896000	0.52359	4.503000	0.60407	2.753000	0.94483	0.650000	0.86243	CGC		0.493	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		A	37947203	G	A	37947203	3	1	102	1	0	0	0	0	1	0	0	0	14200	1087	38	1	125	1	SFRP4	7	37947203	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10		37947203	121191460	45	27026										
ZNF735	0	hgsc.bcm.edu	37	chr7	63680313	63680313	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gagaattcatactggagagaGaccctacaaatgtgaagaat	10	6	1	5			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:63680313G>T								GUSBP6 (69214 upstream) : ZNF679 (8538 downstream)																							ACTGGAGAGAGACCCTACAAA	0.448																																																0			7											13	14	14					7																	63680313		692	1590	2282	63317748	SO:0001628	intergenic_variant	730291																															7.37:g.63680313G>T			63317748		Missense_Mutation	SNP		37																																																																																				0	0.448									T	63680313	G	T	63680313	1	4	102	0	1	0	0	0	0	0	0	0	18163	942	33	2		2	ZNF735	7	63680313	IGR	SNP	G	TCGA-DT-5265-01A-21D-1826-10	25733110	63680313	95458350	46	27027										
C7orf42	55069	hgsc.bcm.edu	37	chr7	66409968	66409968	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttcactttcccaaaggattgGaatacttttctgctacggtt	7	9	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:66409968G>A	ENST00000341567.4	+	3	420	c.165G>A	c.(163-165)tgG>tgA	p.W55*		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	55						integral component of membrane (GO:0016021)											CAAAGGATTGGAATACTTTTC	0.473																																																0			7											83	72	76					7																	66409968		2203	4300	6503	66047403	SO:0001587	stop_gained	55069				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.165G>A	7.37:g.66409968G>A	ENSP00000340668:p.Trp55*		66047403	Q53H07|Q96FR2	Nonsense_Mutation	SNP	ENST00000341567.4	37	CCDS5536.1	.	.	.	.	.	.	.	.	.	.	G	36	5.884498	0.97062	.	.	ENSG00000106609	ENST00000341567;ENST00000413593;ENST00000424964;ENST00000418375	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.8932	18.2626	0.90041	0.0:0.0:1.0:0.0	.	.	.	.	X	55	.	ENSP00000340668:W55X	W	+	3	0	C7orf42	66047403	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	9.324000	0.96373	2.569000	0.86673	0.561000	0.74099	TGG		0.473	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		A	66409968	G	A	66409968	4	1	102	1	0	0	0	0	0	1	0	0	2398	1183	41	3	171	3	C7orf42	7	66409968	Nonsense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	2729655	66409968	92728695	47	27028										
ZAN	7455	hgsc.bcm.edu	37	chr7	100377138	100377139	+	RNA	INS	-	-	GGGC													0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gaacccgagtggaaactgcaINSgggcggccgacctccgcagg					rs377520746|rs141127397	byFrequency	TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:100377138_100377139insGGGC	ENST00000348028.3	+	0	6552_6553				ZAN_ENST00000542585.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000349350.6_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TGGAAACTGCAGGGCGGCCGAC	0.634														282	0.0563099	0.0038	0.0245	5008	,	,		14335	0.1002		0.006	False		,,,				2504	0.1564															0			7							,	22,3824		2,18,1903					,	-2.9	0		dbSNP_134	31	35,7909		0,35,3937	no	frameshift,frameshift	ZAN	NM_173059.1,NM_003386.1	,	2,53,5840	A1A1,A1R,RR		0.4406,0.572,0.4835	,	,		57,11733				100215075			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100377139_100377142dupGGGC			100215074	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Frame_Shift_Ins	INS	ENST00000348028.3	37																																																																																					0.634	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		GGGC	100377139	-	GGGC	100377138	6	5	102	0	1	1	1	0	0	0	0	0	17553	179	7	0		0	ZAN	7	100377138	RNA	INS	-	TCGA-DT-5265-01A-21D-1826-10	33967170	100377138	58761525	48	27029										
BCAP29	55973	hgsc.bcm.edu	37	chr7	107258785	107258785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccttacaggatcgtttagaaAgaggcaacaagaaaagactg	10	7	0	4			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:107258785A>G	ENST00000005259.4	+	8	1042	c.703A>G	c.(703-705)Aga>Gga	p.R235G	BCAP29_ENST00000379117.2_Missense_Mutation_p.R235G|BCAP29_ENST00000465919.1_Missense_Mutation_p.R141G|BCAP29_ENST00000445771.2_Missense_Mutation_p.K261R|BCAP29_ENST00000379119.2_Missense_Mutation_p.K261R|BCAP29_ENST00000494086.1_3'UTR	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	235					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						TCGTTTAGAAAGAGGCAACAA	0.299																																																0			7											52	57	56					7																	107258785		2203	4293	6496	107046021	SO:0001583	missense	55973				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.703A>G	7.37:g.107258785A>G	ENSP00000005259:p.Arg235Gly		107046021	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.92|12.92	2.082220|2.082220	0.36758|0.36758	.|.	.|.	ENSG00000075790|ENSG00000075790	ENST00000445771;ENST00000379119|ENST00000005259;ENST00000465919;ENST00000379117	.|.	.|.	.|.	4.71|4.71	3.54|3.54	0.40534|0.40534	.|.	2.034270|.	0.02970|.	N|.	0.144229|.	T|T	0.17408|0.17408	0.0418|0.0418	N|N	0.11064|0.11064	0.09|0.09	0.09310|0.09310	N|N	0.999994|0.999994	P|B	0.37330|0.02656	0.59|0.0	B|B	0.33690|0.01281	0.168|0.0	T|T	0.27905|0.27905	-1.0060|-1.0060	9|8	0.87932|0.10111	D|T	0|0.7	.|.	8.3442|8.3442	0.32263|0.32263	0.8:0.2:0.0:0.0|0.8:0.2:0.0:0.0	.|.	261|235	G5E9L4|Q9UHQ4	.|BAP29_HUMAN	R|G	261|235;141;235	.|.	ENSP00000368414:K261R|ENSP00000005259:R235G	K|R	+|+	2|1	0|2	BCAP29|BCAP29	107046021|107046021	0.427000|0.427000	0.25514|0.25514	0.004000|0.004000	0.12327|0.12327	0.379000|0.379000	0.30106|0.30106	1.896000|1.896000	0.39789|0.39789	0.824000|0.824000	0.34613|0.34613	0.482000|0.482000	0.46254|0.46254	AAG|AGA		0.299	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844		G	107258785	A	G	107258785	3	3	102	1	0	0	0	0	1	0	0	0	1347	73	3	4	812	4	BCAP29	7	107258785	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	6881647	107258785	51879878	49	27030										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111484842	111484842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gacatcctggaactggaaccGcattgctgagctggatggct	13	10	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:111484842G>A	ENST00000437633.1	-	25	2969	c.2713C>T	c.(2713-2715)Cgg>Tgg	p.R905W	DOCK4_ENST00000428084.1_Missense_Mutation_p.R905W	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	905					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				AACTGGAACCGCATTGCTGAG	0.512																																																0			7											160	158	159					7																	111484842		2049	4201	6250	111272078	SO:0001583	missense	9732				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2713C>T	7.37:g.111484842G>A	ENSP00000404179:p.Arg905Trp		111272078	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086388	0.76642	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.72505	-0.66;-0.66	6.12	2.96	0.34315	.	0.000000	0.85682	D	0.000000	T	0.81749	0.4888	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;P;P	0.68765	0.96;0.735;0.784	D	0.84261	0.0483	10	0.62326	D	0.03	.	16.8359	0.85957	0.0:0.0:0.5766:0.4234	.	905;905;905	Q149N5;Q8N1I0;Q8N1I0-2	.;DOCK4_HUMAN;.	W	893;905;905;893;904	ENSP00000410746:R905W;ENSP00000404179:R905W	ENSP00000345432:R893W	R	-	1	2	DOCK4	111272078	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	1.935000	0.40173	0.871000	0.35750	0.644000	0.83932	CGG		0.512	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111484842	G	A	111484842	3	1	102	1	0	0	0	0	1	0	0	0	4700	1086	38	1	3299	1	DOCK4	7	111484842	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	4226057	111484842	47653821	50	27031										
POT1	25913	hgsc.bcm.edu	37	chr7	124467279	124467279	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gatacttacagaatccatgaGataggcttctagtactcctg	8	9	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:124467279G>A	ENST00000357628.3	-	17	2273	c.1675C>T	c.(1675-1677)Ctc>Ttc	p.L559F	POT1_ENST00000393329.1_Missense_Mutation_p.L428F	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	559					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						GAATCCATGAGATAGGCTTCT	0.303																																					Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)											0			7											72	70	71					7																	124467279		2203	4300	6503	124254515	SO:0001583	missense	25913			AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"protection of telomeres 1 homolog (S. pombe)"			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1675C>T	7.37:g.124467279G>A	ENSP00000350249:p.Leu559Phe		124254515	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	37	CCDS5793.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.79|18.79	3.698721|3.698721	0.68501|0.68501	.|.	.|.	ENSG00000128513|ENSG00000128513	ENST00000357628;ENST00000393329|ENST00000436534	T;T|.	0.66638|.	-0.22;0.22|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77685|0.77685	0.4167|0.4167	M|M	0.80183|0.80183	2.485|2.485	0.51482|0.51482	D|D	0.999928|0.999928	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.78523|0.78523	-0.2171|-0.2171	10|5	0.87932|.	D|.	0|.	-3.8836|-3.8836	16.7379|16.7379	0.85452|0.85452	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	559|.	Q9NUX5|.	POTE1_HUMAN|.	F|F	559;428|57	ENSP00000350249:L559F;ENSP00000377002:L428F|.	ENSP00000350249:L559F|.	L|S	-|-	1|2	0|0	POT1|POT1	124254515|124254515	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.731000|0.731000	0.41821|0.41821	6.346000|6.346000	0.72999|0.72999	2.548000|2.548000	0.85928|0.85928	0.655000|0.655000	0.94253|0.94253	CTC|TCT		0.303	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			A	124467279	G	A	124467279	3	1	102	1	0	0	0	0	1	0	0	0	12291	942	33	3	241	3	POT1	7	124467279	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	12982437	124467279	34671384	51	27032										
TNPO3	23534	hgsc.bcm.edu	37	chr7	128633897	128633897	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	atagaccctatcaagaaaatCaagtcctttaccaggtctga	6	10	3	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:128633897C>T	ENST00000265388.5	-	9	1373	c.1230G>A	c.(1228-1230)ttG>ttA	p.L410L	TNPO3_ENST00000482320.1_Silent_p.L344L|TNPO3_ENST00000471166.1_Silent_p.L410L|TNPO3_ENST00000393245.1_Silent_p.L410L|TNPO3_ENST00000471234.1_Silent_p.L410L			Q9Y5L0	TNPO3_HUMAN	transportin 3	410					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TCAAGAAAATCAAGTCCTTTA	0.413																																					Pancreas(147;583 2585 39696 52331)											0			7											118	109	112					7																	128633897		2203	4300	6503	128421133	SO:0001819	synonymous_variant	23534			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1230G>A	7.37:g.128633897C>T			128421133	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	37	CCDS5809.1																																																																																				0.413	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		T	128633897	C	T	128633897	2	4	102	1	0	0	0	0	0	0	0	1	16376	825	29	3		3	TNPO3	7	128633897	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	4166618	128633897	30504766	52	27033										
BRAF	673	hgsc.bcm.edu	37	chr7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acccactccatcgagatttcActgtagctagaccaaaatca	5	13	2	2	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	7											112	104	107					7																	140453136		2203	4300	6503	140099605	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu		140099605	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453136	A	T	140453136	3	4	102	1	0	0	0	0	1	0	0	0	1499	159	6	5	517	5	BRAF	7	140453136	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	11819239	140453136	18685527	53	27034										
CYHR1	50626	hgsc.bcm.edu	37	chr8	145689545	145689545	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gcgctgtgtatgcagggcccGgcagtaagcccagctgccta	14	13	0	0	rs543509475		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr8:145689545G>A	ENST00000438911.2	-	2	380				CYHR1_ENST00000306145.5_Missense_Mutation_p.R182W|CYHR1_ENST00000530374.1_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|KIFC2_ENST00000301332.2_5'Flank|CYHR1_ENST00000403000.2_Missense_Mutation_p.R182W|CYHR1_ENST00000424149.2_Missense_Mutation_p.R182W	NM_138496.1	NP_612505.1	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1							cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(3)|ovary(2)	7	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-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;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TGCAGGGCCCGGCAGTAAGCC	0.647											OREG0019056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		17925	0.001		0	False		,,,				2504	0															0			8											45	50	48					8																	145689545		2202	4299	6501	145660353	SO:0001627	intron_variant	50626			AB007965	CCDS6426.1, CCDS47943.1	8q24	2004-12-07	2005-07-24		ENSG00000187954	ENSG00000187954			17806	protein-coding gene	gene with protein product			"cysteine and histidine rich 1"			10745073	Standard	NM_138496		Approved	CHRP, KIAA0496, MGC13010	uc003zcv.2	Q6ZMK1	OTTHUMG00000165171	ENST00000438911.2:c.246+297C>T	8.37:g.145689545G>A		1696	145660353	B3KSX0|D3DWM3|Q9BSF6|Q9BSU6	Missense_Mutation	SNP	ENST00000438911.2	37	CCDS47943.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.873986	0.72180	.	.	ENSG00000187954	ENST00000403000;ENST00000424149;ENST00000306145	T;T;T	0.44881	0.91;0.91;0.91	4.79	-1.65	0.08291	.	0.511586	0.16788	N	0.199505	T	0.24547	0.0595	.	.	.	0.21184	N	0.999762	B	0.02656	0.0	B	0.01281	0.0	T	0.12477	-1.0546	9	0.54805	T	0.06	.	3.3555	0.07168	0.2385:0.0:0.2553:0.5062	.	182	Q6ZMK1-3	.	W	182	ENSP00000385962:R182W;ENSP00000414647:R182W;ENSP00000304826:R182W	ENSP00000304826:R182W	R	-	1	2	CYHR1	145660353	0.009000	0.17119	0.988000	0.46212	0.980000	0.70556	0.230000	0.17852	-0.180000	0.10637	0.462000	0.41574	CGG		0.647	CYHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382438.1	NM_032687		A	145689545	G	A	145689545	1	1	102	0	1	0	0	0	0	0	0	0	4146	1115	39	1		1	CYHR1	8	145689545	Intron	SNP	G	TCGA-DT-5265-01A-21D-1826-10		145689545	674477	54	27035										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5921603	5921604	+	Frame_Shift_Ins	INS	-	-	TACA													0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tgaactggagtcccactgatINStacatctccatttgttgctg							TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr9:5921603_5921604insTACA	ENST00000399933.3	-	8	4391_4392	c.4392_4393insTGTA	c.(4390-4395)gtaatcfs	p.I1465fs	KIAA2026_ENST00000381461.2_Frame_Shift_Ins_p.I1435fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1465										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GTCCCACTGATTACATCTCCAT	0.391																																																0			9																																								5911604	SO:0001589	frameshift_variant	158358			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4389_4392dupTGTA	9.37:g.5921604_5921607dupTACA	ENSP00000382815:p.Ile1465fs		5911603	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Ins	INS	ENST00000399933.3	37																																																																																					0.391	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		TACA	5921604	-	TACA	5921603	7	5	102	1	0	1	1	0	0	0	0	0	8291	1493	52	0	1922	0	KIAA2026	9	5921603	Frame_Shift_Ins	INS	-	TCGA-DT-5265-01A-21D-1826-10		5921603	135291828	55	27036										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100413599	100413599	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acactttttatagtgctgcaCagttagtgagctatccaggg	10	8	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr9:100413599C>T	ENST00000375147.3	+	10	1259	c.1003C>T	c.(1003-1005)Cag>Tag	p.Q335*		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	335					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TAGTGCTGCACAGTTAGTGAG	0.353																																					Ovarian(36;879 898 2893 44212 50307)											0			9											131	122	125					9																	100413599		2203	4300	6503	99453420	SO:0001587	stop_gained	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1003C>T	9.37:g.100413599C>T	ENSP00000364289:p.Gln335*		99453420	B2R718|Q59G76|Q5T1V0|Q5T7X2	Nonsense_Mutation	SNP	ENST00000375147.3	37	CCDS6728.1	.	.	.	.	.	.	.	.	.	.	C	38	7.035503	0.98017	.	.	ENSG00000136937	ENST00000375147	.	.	.	5.59	4.68	0.58851	.	0.056109	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-9.8878	15.6735	0.77297	0.1384:0.8616:0.0:0.0	.	.	.	.	X	335	.	ENSP00000364289:Q335X	Q	+	1	0	NCBP1	99453420	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	7.110000	0.77069	1.474000	0.48178	0.585000	0.79938	CAG		0.353	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		T	100413599	C	T	100413599	4	4	102	1	0	0	0	0	0	1	0	0	10242	479	17	3	1041	3	NCBP1	9	100413599	Nonsense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	94491996	100413599	40799832	56	27037										
C9orf156	51531	hgsc.bcm.edu	37	chr9	100672273	100672273	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agctgcccaaggtccatctcGgcatgaggagtaaaccgcac	11	13	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr9:100672273G>A	ENST00000375119.3	-	4	1111	c.1035C>T	c.(1033-1035)gcC>gcT	p.A345A	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	345					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				ggtcCATCTCGGCATGAGGAG	0.507																																																0			9											42	40	41					9																	100672273		2203	4300	6503	99712094	SO:0001819	synonymous_variant	51531			AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.1035C>T	9.37:g.100672273G>A			99712094	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	37	CCDS6730.1																																																																																				0.507	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		A	100672273	G	A	100672273	2	1	102	1	0	0	0	0	0	0	0	1	2471	1103	39	1		1	C9orf156	9	100672273	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	258674	100672273	40541158	57	27038										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130149570	130149570	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aattctcctcagacacccccGggccgagatactccagtatt	7	15	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr9:130149570G>A	ENST00000373387.4	+	25	2839	c.2487G>A	c.(2485-2487)ccG>ccA	p.P829P	GARNL3_ENST00000435213.2_Silent_p.P807P|GARNL3_ENST00000314904.5_Intron|GARNL3_ENST00000496711.1_3'UTR	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	829					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGACACCCCCGGGCCGAGATA	0.463																																																0			9											59	62	61					9																	130149570		2203	4300	6503	129189391	SO:0001819	synonymous_variant	84253			BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.2487G>A	9.37:g.130149570G>A			129189391	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Silent	SNP	ENST00000373387.4	37	CCDS6869.2																																																																																				0.463	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		A	130149570	G	A	130149570	2	1	102	1	0	0	0	0	0	0	0	1	6261	1103	39	1		1	GARNL3	9	130149570	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	29477297	130149570	11063861	58	27039										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55945014	55945014	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcattcagaaaaaggtgaagCtctgggtcttttgtctttga	10	6	5	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr10:55945014C>G	ENST00000320301.6	-	12	1714	c.1320G>C	c.(1318-1320)gaG>gaC	p.E440D	PCDH15_ENST00000361849.3_Missense_Mutation_p.E440D|PCDH15_ENST00000373955.1_Missense_Mutation_p.E440D|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.E403D|PCDH15_ENST00000414778.1_Missense_Mutation_p.E445D|PCDH15_ENST00000395433.1_Missense_Mutation_p.E418D|PCDH15_ENST00000395445.1_Missense_Mutation_p.E447D|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.E447D|PCDH15_ENST00000395446.1_Missense_Mutation_p.E440D|PCDH15_ENST00000437009.1_Missense_Mutation_p.E440D|PCDH15_ENST00000373957.3_Missense_Mutation_p.E418D|PCDH15_ENST00000409834.1_Missense_Mutation_p.E51D|PCDH15_ENST00000395438.1_Missense_Mutation_p.E440D|PCDH15_ENST00000395430.1_Missense_Mutation_p.E440D	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	440	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAAGGTGAAGCTCTGGGTCTT	0.373										HNSCC(58;0.16)																																						0			10											126	120	122					10																	55945014		2203	4300	6503	55615020	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1320G>C	10.37:g.55945014C>G	ENSP00000322604:p.Glu440Asp		55615020	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325119	0.41197	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60797	0.16;0.16;0.16;1.45;0.16;0.16;0.16;0.16;0.16;0.16;0.16;0.16;0.16;0.16	5.29	2.38	0.29361	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.60287	0.2257	L	0.36672	1.1	0.24819	N	0.992599	D;P;P;B;P;P;D;P;P;P;P;P;P;P;P	0.56287	0.975;0.772;0.772;0.157;0.702;0.891;0.975;0.542;0.61;0.61;0.542;0.741;0.486;0.542;0.772	P;P;P;B;P;P;P;B;B;B;B;P;B;B;P	0.57911	0.829;0.484;0.602;0.105;0.545;0.602;0.829;0.388;0.277;0.191;0.388;0.489;0.098;0.388;0.602	T	0.50617	-0.8807	9	0.49607	T	0.09	.	10.595	0.45331	0.0:0.7692:0.0:0.2308	.	418;440;440;445;440;403;440;440;447;447;440;445;440;418;440	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	D	447;445;440;440;51;447;440;403;440;418;418;440;440;445;440;440	ENSP00000363076:E447D;ENSP00000410304:E445D;ENSP00000378826:E440D;ENSP00000386693:E51D;ENSP00000378832:E447D;ENSP00000378833:E440D;ENSP00000378820:E403D;ENSP00000354950:E440D;ENSP00000378821:E418D;ENSP00000363068:E418D;ENSP00000322604:E440D;ENSP00000378818:E440D;ENSP00000412628:E440D;ENSP00000363066:E440D	ENSP00000322604:E440D	E	-	3	2	PCDH15	55615020	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.741000	0.26202	0.727000	0.32360	0.591000	0.81541	GAG		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55945014	C	G	55945014	3	3	102	1	0	0	0	0	1	0	0	0	11542	796	28	5	6254	5	PCDH15	10	55945014	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		55945014	79589733	59	27040										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624297	89624297	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agaggatggattcgacttagActtgacctgtatccatttct	9	8	1	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr10:89624297A>G	ENST00000371953.3	+	1	1428	c.71A>G	c.(70-72)gAc>gGc	p.D24G	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	24	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.D24G(4)|p.D24fs*19(2)|p.D24fs*20(2)|p.D24_L25del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTCGACTTAGACTTGACCTGT	0.463		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	59	Whole gene deletion(37)|Unknown(13)|Substitution - Missense(4)|Insertion - Frameshift(4)|Deletion - In frame(1)	prostate(14)|central_nervous_system(13)|skin(7)|lung(6)|endometrium(5)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											165	157	160					10																	89624297		2203	4300	6503	89614277	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.71A>G	10.37:g.89624297A>G	ENSP00000361021:p.Asp24Gly		89614277	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.686823	0.88639	.	.	ENSG00000171862	ENST00000371953	D	0.98849	-5.18	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.107942	0.64402	D	0.000010	D	0.98710	0.9567	H	0.97365	3.99	0.80722	D	1	P	0.36144	0.539	B	0.34991	0.193	D	0.99478	1.0947	9	.	.	.	-0.0364	14.1807	0.65572	1.0:0.0:0.0:0.0	.	24	P60484	PTEN_HUMAN	G	24	ENSP00000361021:D24G	.	D	+	2	0	PTEN	89614277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.379000	0.90146	1.996000	0.58369	0.459000	0.35465	GAC		0.463	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89624297	A	G	89624297	3	3	102	1	0	0	0	0	1	0	0	0	12772	275	10	4	73	4	PTEN	10	89624297	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	33679283	89624297	45910450	60	27041										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692999	89692999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tatggggaagtaaggaccagAgacaaaaaggtaagttattt	12	3	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr10:89692999A>G	ENST00000371953.3	+	5	1840	c.483A>G	c.(481-483)agA>agG	p.R161R		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	161	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(5)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TAAGGACCAGAGACAAAAAGG	0.363		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											50	52	51					10																	89692999		2203	4300	6503	89682979	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.483A>G	10.37:g.89692999A>G			89682979	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.363	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692999	A	G	89692999	2	3	102	1	0	0	0	0	0	0	0	1	12772	301	11	4		4	PTEN	10	89692999	Silent	SNP	A	TCGA-DT-5265-01A-21D-1826-10	68702	89692999	45841748	61	27042										
CYP2E1	1571	hgsc.bcm.edu	37	chr10	135352376	135352376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	attttaatttgaagcctctcGttgacccaaaggatatcgac	7	9	1	2	rs187941410		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr10:135352376G>A	ENST00000463117.2	+	11	1662	c.1390G>A	c.(1390-1392)Gtt>Att	p.V464I	CYP2E1_ENST00000252945.3_Missense_Mutation_p.V464I|SPRN_ENST00000541506.1_Intron			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	464					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	GAAGCCTCTCGTTGACCCAAA	0.473									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				G|||	1	0.000199681	0	0	5008	,	,		17902	0		0.001	False		,,,				2504	0															0			10						G	ILE/VAL	0,4406		0,0,2203	219	178	192		1390	5.1	0.2	10		192	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP2E1	NM_000773.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	464/494	135352376	1,13005	2203	4300	6503	135202366	SO:0001583	missense	1571	Familial Cancer Database	incl.: Familial Head and Neck Cancer	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"Cytochrome P450s"	2631	protein-coding gene	gene with protein product		124040	"cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.1390G>A	10.37:g.135352376G>A	ENSP00000440689:p.Val464Ile		135202366	Q5VZD5|Q6NWT9|Q9UK47	Missense_Mutation	SNP	ENST00000463117.2	37	CCDS7686.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.490	0.861845	0.17178	0.0	1.16E-4	ENSG00000130649	ENST00000463117;ENST00000252945	T;T	0.69561	-0.41;-0.41	5.1	5.1	0.69264	.	0.686916	0.14634	N	0.307614	T	0.59459	0.2195	L	0.49513	1.565	0.09310	N	1	B	0.20368	0.044	B	0.14578	0.011	T	0.50608	-0.8808	10	0.49607	T	0.09	.	9.7342	0.40377	0.0919:0.0:0.9081:0.0	.	464	P05181	CP2E1_HUMAN	I	464	ENSP00000440689:V464I;ENSP00000252945:V464I	ENSP00000252945:V464I	V	+	1	0	CYP2E1	135202366	0.002000	0.14202	0.163000	0.22734	0.209000	0.24338	0.750000	0.26334	2.831000	0.97527	0.561000	0.74099	GTT		0.473	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773		A	135352376	G	A	135352376	3	1	102	1	0	0	0	0	1	0	0	0	4176	1145	40	1	1424	1	CYP2E1	10	135352376	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	45659377	135352376	182371	62	27043										
MRGPRE	116534	hgsc.bcm.edu	37	chr11	3249228	3249228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	actgcccaggcagaagtagaCgacgggcttggccgcgcagt	15	12	0	2	rs199803545	byFrequency	TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:3249228C>T	ENST00000389832.5	-	2	1108	c.802G>A	c.(802-804)Gtc>Atc	p.V268I	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.V267I			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGAAGTAGACGACGGGCTTG	0.672													C|||	3	0.000599042	0.0023	0	5008	,	,		15434	0		0	False		,,,				2504	0															0			11						C	ILE/VAL	7,3777		0,7,1885	13	19	17		799	-7.2	0	11		17	1,8197		0,1,4098	yes	missense	MRGPRE	NM_001039165.2	29	0,8,5983	TT,TC,CC		0.0122,0.185,0.0668	benign	267/312	3249228	8,11974	1892	4099	5991	3205804	SO:0001583	missense	116534			AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"GPCR / Class A : Orphans"	30694	protein-coding gene	gene with protein product		607232	"G protein-coupled receptor 167"	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.802G>A	11.37:g.3249228C>T	ENSP00000374482:p.Val268Ile		3205804	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		.	.	.	.	.	.	.	.	.	.	c	0.015	-1.543006	0.00934	0.00185	1.22E-4	ENSG00000184350	ENST00000436689;ENST00000389832	T	0.32753	1.44	3.6	-7.21	0.01490	GPCR, rhodopsin-like superfamily (1);	0.164676	0.27366	N	0.019687	T	0.03434	0.0099	N	0.00123	-2.06	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21280	-1.0250	10	0.02654	T	1	-8.5808	6.769	0.23583	0.0:0.3357:0.3389:0.3253	.	267	Q86SM8	MRGRE_HUMAN	I	268;267	ENSP00000374482:V267I	ENSP00000374482:V267I	V	-	1	0	MRGPRE	3205804	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-1.674000	0.01949	-1.984000	0.00985	-2.646000	0.00150	GTC		0.672	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536		T	3249228	C	T	3249228	3	4	102	1	0	0	0	0	1	0	0	0	9794	536	19	1	140	1	MRGPRE	11	3249228	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		3249228	131757288	63	27044										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6530297	6530297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tctttaagtattgcctcttaCgcaagtcctttacctggtag	7	10	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:6530297C>T	ENST00000527990.2	+	3	1108	c.1108C>T	c.(1108-1110)Cgc>Tgc	p.R370C	DNHD1_ENST00000254579.6_Missense_Mutation_p.R370C|DNHD1_ENST00000354685.3_Missense_Mutation_p.R370C			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	370					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TTGCCTCTTACGCAAGTCCTT	0.453																																																0			11											190	175	180					11																	6530297		2201	4296	6497	6486873	SO:0001583	missense	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1108C>T	11.37:g.6530297C>T	ENSP00000436180:p.Arg370Cys		6486873	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680339	0.68042	.	.	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.17691	2.26;2.26;2.26	5.47	3.33	0.38152	.	0.523957	0.16861	N	0.196527	T	0.36853	0.0982	M	0.78801	2.425	0.38032	D	0.935202	D;D	0.89917	1.0;1.0	P;D	0.63597	0.877;0.916	T	0.31833	-0.9929	10	0.56958	D	0.05	.	8.7968	0.34885	0.1575:0.7492:0.0:0.0933	.	370;370	Q96M86;Q96M86-4	DNHD1_HUMAN;.	C	370	ENSP00000254579:R370C;ENSP00000346716:R370C;ENSP00000436180:R370C	ENSP00000254579:R370C	R	+	1	0	DNHD1	6486873	0.994000	0.37717	1.000000	0.80357	0.993000	0.82548	0.780000	0.26760	1.242000	0.43836	0.650000	0.86243	CGC		0.453	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6530297	C	T	6530297	3	4	102	1	0	0	0	0	1	0	0	0	4679	536	19	1	1118	1	DNHD1	11	6530297	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	3281069	6530297	128476219	64	27045										
ZFP91	80829	hgsc.bcm.edu	37	chr11	58384980	58384980	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cttgggaaactcaacctctgGagagtgcctactgttagaag	11	9	2	2	rs369678965		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:58384980G>C	ENST00000316059.6	+	11	1685	c.1514G>C	c.(1513-1515)gGa>gCa	p.G505A	ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.G505A	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	505					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TCAACCTCTGGAGAGTGCCTA	0.532																																																0			11											90	82	84					11																	58384980		2201	4295	6496	58141556	SO:0001583	missense	80829			AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1514G>C	11.37:g.58384980G>C	ENSP00000339030:p.Gly505Ala		58141556	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	37	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634266	0.47049	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.09911	2.93	6.16	5.21	0.72293	.	0.200181	0.34906	N	0.003582	T	0.07143	0.0181	N	0.08118	0	0.29716	N	0.839021	B;B	0.13594	0.008;0.002	B;B	0.14578	0.011;0.003	T	0.13656	-1.0501	10	0.38643	T	0.18	-19.368	16.4438	0.83909	0.0:0.1423:0.8577:0.0	.	505;505	Q96JP5-2;Q96JP5	.;ZFP91_HUMAN	A	505	ENSP00000339030:G505A	ENSP00000374569:G505A	G	+	2	0	ZFP91	58141556	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.026000	0.41069	2.937000	0.99478	0.650000	0.86243	GGA		0.532	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		C	58384980	G	C	58384980	3	2	102	1	0	0	0	0	1	0	0	0	17694	1174	41	5	1556	5	ZFP91	11	58384980	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	51854683	58384980	76621536	65	27046										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85436931	85436931	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttggttcaagcacttgttttCcatgaacttttccaccagag	7	10	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:85436931C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000354566.3_Missense_Mutation_p.G190E|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000525423.1_Missense_Mutation_p.G190E|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.G714E	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.G190V(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTGTTTTCCATGAACTTT	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	11											118	111	114					11																	85436931		2203	4299	6502	85114579	SO:0001627	intron_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2007G>A	11.37:g.85436931C>T			85114579	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	8.776	0.926992	0.18056	.	.	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.25579	1.79;1.81;1.81	6.17	-3.84	0.04256	.	1.580750	0.03505	N	0.218707	T	0.11623	0.0283	N	0.12746	0.255	0.09310	N	0.999997	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.08055	0.003;0.003;0.003	T	0.18493	-1.0335	9	.	.	.	1.7323	2.926	0.05784	0.12:0.3509:0.0956:0.4335	.	190;190;190	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	E	714;190;190	ENSP00000352065:G714E;ENSP00000346576:G190E;ENSP00000432694:G190E	.	G	-	2	0	SYTL2	85114579	0.000000	0.05858	0.001000	0.08648	0.686000	0.39977	-2.817000	0.00751	-0.200000	0.10300	0.655000	0.94253	GGA		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85436931	C	T	85436931	1	4	102	0	1	0	0	0	0	0	0	0	15522	855	30	3		3	SYTL2	11	85436931	Intron	SNP	C	TCGA-DT-5265-01A-21D-1826-10	27051951	85436931	49569585	66	27047										
DDX6	1656	hgsc.bcm.edu	37	chr11	118627889	118627889	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tttatactcacctgcctcatTttagcatgaatatagaagca	5	9	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:118627889T>C	ENST00000526070.2	-	10	1461	c.1101A>G	c.(1099-1101)aaA>aaG	p.K367K	DDX6_ENST00000264018.4_Silent_p.K367K|DDX6_ENST00000534980.1_Silent_p.K367K	NM_001257191.1	NP_001244120.1	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 6	367	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cytoplasmic mRNA processing body assembly (GO:0033962)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	13	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		CCTGCCTCATTTTAGCATGAA	0.323			T	IGH@	B-NHL																																		Dom	yes		11	11q23.3	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6		L	0			11											42	38	39					11																	118627889		1794	4061	5855	118133099	SO:0001819	synonymous_variant	1656			D17532	CCDS44751.1	11q23.3	2012-02-23	2012-02-23		ENSG00000110367	ENSG00000110367		"DEAD-boxes"	2747	protein-coding gene	gene with protein product		600326	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 6"	HLR2		1579499, 11839790	Standard	NM_004397		Approved	RCK	uc001pub.2	P26196	OTTHUMG00000166411	ENST00000526070.2:c.1101A>G	11.37:g.118627889T>C			118133099	Q5D048	Silent	SNP	ENST00000526070.2	37	CCDS44751.1																																																																																				0.323	DDX6-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389647.2	NM_004397		C	118627889	T	C	118627889	2	2	102	1	0	0	0	0	0	0	0	1	4383	1838	64	4		4	DDX6	11	118627889	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	33190958	118627889	16378627	67	27048										
DPAGT1	1798	hgsc.bcm.edu	37	chr11	118971414	118971414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcgtgttgccaaagttggtgAaatagaccatgaggagaggt	14	5	0	4	rs374406577		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:118971414A>G	ENST00000409993.2	-	5	1973	c.422T>C	c.(421-423)tTc>tCc	p.F141S	DPAGT1_ENST00000432443.2_Missense_Mutation_p.F34S|DPAGT1_ENST00000445653.1_5'UTR|DPAGT1_ENST00000354202.4_Missense_Mutation_p.F141S			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	141					cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		AAAGTTGGTGAAATAGACCAT	0.552											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			11						A	SER/PHE	0,4400		0,0,2200	75	60	65		422	5.5	1	11		65	1,8589	1.2+/-3.3	0,1,4294	no	missense	DPAGT1	NM_001382.3	155	0,1,6494	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging	141/409	118971414	1,12989	2200	4295	6495	118476624	SO:0001583	missense	1798			Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.422T>C	11.37:g.118971414A>G	ENSP00000386597:p.Phe141Ser	1492	118476624	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	A	32	5.137261	0.94517	0.0	1.16E-4	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.93366	-3.21;-3.21;-3.21	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93194	0.7832	L	0.60455	1.87	0.80722	D	1	P;P	0.47191	0.891;0.797	P;P	0.47346	0.544;0.544	D	0.93795	0.7096	10	0.72032	D	0.01	-25.9921	14.8174	0.70045	1.0:0.0:0.0:0.0	.	34;141	E7EW40;Q9H3H5	.;GPT_HUMAN	S	141;141;34	ENSP00000386597:F141S;ENSP00000346142:F141S;ENSP00000404036:F34S	ENSP00000346142:F141S	F	-	2	0	DPAGT1	118476624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.090000	0.63153	0.460000	0.39030	TTC		0.552	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		G	118971414	A	G	118971414	3	3	102	1	0	0	0	0	1	0	0	0	4721	246	9	4	832	4	DPAGT1	11	118971414	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	343525	118971414	16035102	68	27049										
BSX	390259	hgsc.bcm.edu	37	chr11	122850031	122850031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttctggcgtggacaggtagcGctggatctcgaacctcttct	12	11	4	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr11:122850031G>A	ENST00000343035.2	-	2	445	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C		NM_001098169.1	NP_001091639.1	Q3C1V8	BSH_HUMAN	brain-specific homeobox	133					eating behavior (GO:0042755)|locomotory behavior (GO:0007626)|mammary gland involution (GO:0060056)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	10		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)		GACAGGTAGCGCTGGATCTCG	0.672																																																0			11											59	71	67					11																	122850031		2074	4196	6270	122355241	SO:0001583	missense	390259				CCDS41728.1	11q24.1	2011-07-19			ENSG00000188909	ENSG00000188909		"Homeoboxes / ANTP class : NKL subclass"	20450	protein-coding gene	gene with protein product		611074					Standard	NM_001098169		Approved	BSX1	uc010rzs.2	Q3C1V8	OTTHUMG00000150247	ENST00000343035.2:c.397C>T	11.37:g.122850031G>A	ENSP00000344285:p.Arg133Cys		122355241		Missense_Mutation	SNP	ENST00000343035.2	37	CCDS41728.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.602929	0.87157	.	.	ENSG00000188909	ENST00000343035	D	0.96745	-4.11	5.22	4.25	0.50352	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.104648	0.64402	D	0.000005	D	0.97867	0.9299	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98350	1.0543	10	0.87932	D	0	.	14.546	0.68030	0.0:0.0:0.853:0.147	.	133	Q3C1V8	BSH_HUMAN	C	133	ENSP00000344285:R133C	ENSP00000344285:R133C	R	-	1	0	BSX	122355241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.404000	0.59735	2.454000	0.82982	0.655000	0.94253	CGC		0.672	BSX-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317076.1	NM_001098169		A	122850031	G	A	122850031	3	1	102	1	0	0	0	0	1	0	0	0	1538	1087	38	1	311	1	BSX	11	122850031	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	3878617	122850031	12156485	69	27050										
CD163	9332	hgsc.bcm.edu	37	chr12	7637927	7637927	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	atgctactcttgccaacagtGccccaagctccattgtaaaa	6	13	1	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:7637927G>T	ENST00000359156.4	-	11	2746	c.2544C>A	c.(2542-2544)ggC>ggA	p.G848G	CD163_ENST00000396620.3_Silent_p.G881G|CD163_ENST00000541972.1_Silent_p.G836G|CD163_ENST00000432237.2_Silent_p.G848G|CD163_ENST00000539632.1_5'UTR	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	848	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	TGCCAACAGTGCCCCAAGCTC	0.512																																																0			12											113	105	108					12																	7637927		2203	4300	6503	7529194	SO:0001819	synonymous_variant	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.2544C>A	12.37:g.7637927G>T			7529194	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																				0.512	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		T	7637927	G	T	7637927	2	4	102	1	0	0	0	0	0	0	0	1	2973	1306	46	2		2	CD163	12	7637927	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10		7637927	126213968	70	27051										
LDHB	3945	hgsc.bcm.edu	37	chr12	21796910	21796910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tgatgcaatcaggactgtacTtgacgatctgaggaataatg	11	6	2	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:21796910T>C	ENST00000396076.1	-	4	712	c.380A>G	c.(379-381)aAg>aGg	p.K127R	LDHB_ENST00000350669.1_Missense_Mutation_p.K127R	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	127					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						AGGACTGTACTTGACGATCTG	0.408																																																0			12											131	124	126					12																	21796910		2203	4300	6503	21688177	SO:0001583	missense	3945				CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.380A>G	12.37:g.21796910T>C	ENSP00000379386:p.Lys127Arg		21688177		Missense_Mutation	SNP	ENST00000396076.1	37	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.363460	0.61513	.	.	ENSG00000111716	ENST00000396076;ENST00000350669;ENST00000396075;ENST00000450584	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	5.69	5.69	0.88448	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.096535	0.64402	D	0.000002	D	0.88897	0.6562	L	0.60455	1.87	0.58432	D	0.999998	B	0.21821	0.061	B	0.32533	0.147	D	0.86298	0.1678	10	0.54805	T	0.06	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	127	P07195	LDHB_HUMAN	R	127	ENSP00000379386:K127R;ENSP00000229319:K127R;ENSP00000379385:K127R;ENSP00000398015:K127R	ENSP00000229319:K127R	K	-	2	0	LDHB	21688177	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.786000	0.62425	2.167000	0.68274	0.460000	0.39030	AAG		0.408	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300		C	21796910	T	C	21796910	3	2	102	1	0	0	0	0	1	0	0	0	8723	1609	56	4	644	4	LDHB	12	21796910	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	14158983	21796910	112054985	71	27052										
PKP2	5318	hgsc.bcm.edu	37	chr12	33031163	33031163	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccatgctggtactgtctgtgGtatgtgtcaaagtggcgctg	14	8	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:33031163G>T	ENST00000070846.6	-	3	675	c.651C>A	c.(649-651)taC>taA	p.Y217*	PKP2_ENST00000340811.4_Nonsense_Mutation_p.Y217*	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	217					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					ACTGTCTGTGGTATGTGTCAA	0.632																																																0			12											138	117	124					12																	33031163		2203	4300	6503	32922430	SO:0001587	stop_gained	5318			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.651C>A	12.37:g.33031163G>T	ENSP00000070846:p.Tyr217*		32922430	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Nonsense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	38	7.053094	0.98029	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	.	.	.	4.34	2.49	0.30216	.	1.300720	0.05181	N	0.501343	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.4173	6.4181	0.21728	0.3709:0.0:0.6291:0.0	.	.	.	.	X	217	.	ENSP00000070846:Y217X	Y	-	3	2	PKP2	32922430	0.002000	0.14202	0.063000	0.19743	0.968000	0.65278	0.424000	0.21330	0.308000	0.22923	0.650000	0.86243	TAC		0.632	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		T	33031163	G	T	33031163	4	4	102	1	0	0	0	0	0	1	0	0	12016	1256	44	2	2042	2	PKP2	12	33031163	Nonsense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	11234253	33031163	100820732	72	27053										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40715933	40715933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggtaggatctgaagtcttagAcaatcatccagagagtttct	10	7	4	3			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:40715933A>G	ENST00000298910.7	+	36	5325	c.5267A>G	c.(5266-5268)gAc>gGc	p.D1756G		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1756					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GAAGTCTTAGACAATCATCCA	0.348																																																0			12											74	77	76					12																	40715933		2203	4299	6502	39002200	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5267A>G	12.37:g.40715933A>G	ENSP00000298910:p.Asp1756Gly		39002200	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.473830	0.84640	.	.	ENSG00000188906	ENST00000298910	T	0.72051	-0.62	5.73	5.73	0.89815	.	0.153463	0.64402	D	0.000019	T	0.69700	0.3140	L	0.49778	1.585	0.58432	D	0.99999	P;P	0.48503	0.828;0.911	B;B	0.44163	0.272;0.443	T	0.74272	-0.3719	10	0.72032	D	0.01	.	16.0258	0.80545	1.0:0.0:0.0:0.0	.	1756;1756	Q17RV3;Q5S007	.;LRRK2_HUMAN	G	1756	ENSP00000298910:D1756G	ENSP00000298910:D1756G	D	+	2	0	LRRK2	39002200	1.000000	0.71417	0.884000	0.34674	0.987000	0.75469	6.806000	0.75195	2.184000	0.69523	0.454000	0.30748	GAC		0.348	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		G	40715933	A	G	40715933	3	3	102	1	0	0	0	0	1	0	0	0	9062	275	10	4	5409	4	LRRK2	12	40715933	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	7684770	40715933	93135962	73	27054										
TMPRSS12	283471	hgsc.bcm.edu	37	chr12	51237739	51237739	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cctgcagattaaatatggccGtgttcttgttcatgtatgtg	10	7	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:51237739G>A	ENST00000398458.3	+	2	334	c.302G>A	c.(301-303)cGt>cAt	p.R101H	TMPRSS12_ENST00000551456.1_Missense_Mutation_p.R101H|RN7SL519P_ENST00000497925.2_RNA	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	101	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	18						AAATATGGCCGTGTTCTTGTT	0.537																																																0			12											51	54	53					12																	51237739		2055	4195	6250	49524006	SO:0001583	missense	283471			BC048112	CCDS44881.1	12q13.12	2014-08-12	2010-04-21		ENSG00000186452	ENSG00000186452		"Serine peptidases / Transmembrane"	28779	protein-coding gene	gene with protein product			"transmembrane protease, serine 12"				Standard	NM_182559		Approved	MGC57341, CT151	uc001rwx.4	Q86WS5	OTTHUMG00000169483	ENST00000398458.3:c.302G>A	12.37:g.51237739G>A	ENSP00000381476:p.Arg101His		49524006	B9ZVX2	Missense_Mutation	SNP	ENST00000398458.3	37	CCDS44881.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.423768	0.25639	.	.	ENSG00000186452	ENST00000551456;ENST00000398458	T;T	0.60672	0.17;0.38	5.7	-9.64	0.00541	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.776020	0.02431	N	0.083571	T	0.39279	0.1072	N	0.19112	0.55	0.09310	N	1	B;B	0.13594	0.008;0.0	B;B	0.11329	0.006;0.001	T	0.28650	-1.0037	10	0.44086	T	0.13	-0.0302	11.5077	0.50476	0.6665:0.0925:0.2411:0.0	.	101;101	F8WBX2;Q86WS5	.;TMPSC_HUMAN	H	101	ENSP00000447259:R101H;ENSP00000381476:R101H	ENSP00000381476:R101H	R	+	2	0	TMPRSS12	49524006	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.453000	0.02383	-1.552000	0.01704	-2.395000	0.00226	CGT		0.537	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559		A	51237739	G	A	51237739	3	1	102	1	0	0	0	0	1	0	0	0	16283	1145	40	1	308	1	TMPRSS12	12	51237739	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	10521806	51237739	82614156	74	27055										
SP1	6667	hgsc.bcm.edu	37	chr12	53775987	53775987	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acaactcccagggcccgagtCagtcagggggaacaggtgag	15	11	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:53775987C>T	ENST00000327443.4	+	3	354	c.256C>T	c.(256-258)Cag>Tag	p.Q86*	SP1_ENST00000426431.2_Nonsense_Mutation_p.Q79*	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	86	Ser/Thr-rich.				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		GGGCCCGAGTCAGTCAGGGGG	0.582																																																0			12											67	66	66					12																	53775987		2203	4300	6503	52062254	SO:0001587	stop_gained	199699			J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11205	protein-coding gene	gene with protein product	"specificity protein 1"	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.256C>T	12.37:g.53775987C>T	ENSP00000329357:p.Gln86*		52062254	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Nonsense_Mutation	SNP	ENST00000327443.4	37	CCDS8857.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784565	0.49997	.	.	ENSG00000185591	ENST00000327443;ENST00000426431	.	.	.	4.13	4.13	0.48395	.	0.000000	0.52532	D	0.000073	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	13.7852	0.63105	0.0:1.0:0.0:0.0	.	.	.	.	X	86;79	.	ENSP00000329357:Q86X	Q	+	1	0	SP1	52062254	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.869000	0.48444	2.306000	0.77630	0.467000	0.42956	CAG		0.582	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1			T	53775987	C	T	53775987	4	4	102	1	0	0	0	0	0	1	0	0	14996	827	29	3	266	3	SP1	12	53775987	Nonsense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	2538248	53775987	80075908	75	27056										
DDIT3	1649	hgsc.bcm.edu	37	chr12	57911116	57911116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctgaagacaggacctcttgcAggtcctcataccaggcttcc	9	14	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:57911116A>G	ENST00000346473.3	-	3	253	c.74T>C	c.(73-75)cTg>cCg	p.L25P	DDIT3_ENST00000547303.1_Missense_Mutation_p.L25P|MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000551116.1_Missense_Mutation_p.L48P|DDIT3_ENST00000552740.1_Missense_Mutation_p.L48P	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	25	N-terminal.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.L25R(1)	EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						GACCTCTTGCAGGTCCTCATA	0.498			T	FUS	liposarcoma																																GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	1	Substitution - Missense(1)	ovary(1)	12											65	59	61					12																	57911116		2203	4300	6503	56197383	SO:0001583	missense	1649			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"C/EBP zeta"	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.74T>C	12.37:g.57911116A>G	ENSP00000340671:p.Leu25Pro		56197383	F8VS99	Missense_Mutation	SNP	ENST00000346473.3	37	CCDS8943.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.168545	0.78339	.	.	ENSG00000175197	ENST00000547303;ENST00000551116;ENST00000346473;ENST00000552740;ENST00000547526	T;T;T;T	0.70045	-0.36;-0.45;-0.36;-0.45	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000002	T	0.74215	0.3687	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.77159	-0.2690	10	0.87932	D	0	-2.6048	14.1539	0.65405	1.0:0.0:0.0:0.0	.	48;25	F8VS99;P35638	.;DDIT3_HUMAN	P	25;48;25;48;48	ENSP00000447188:L25P;ENSP00000448665:L48P;ENSP00000340671:L25P;ENSP00000447803:L48P	ENSP00000340671:L25P	L	-	2	0	DDIT3	56197383	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.141000	0.89618	2.240000	0.73641	0.533000	0.62120	CTG		0.498	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083		G	57911116	A	G	57911116	3	3	102	1	0	0	0	0	1	0	0	0	4336	188	7	4	443	4	DDIT3	12	57911116	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	4135129	57911116	75940779	76	27057										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63544123	63544123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cgatcatgaggcgcgagcggCgcgcgggctgttgcagagtc	18	11	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:63544123C>T	ENST00000299178.2	-	1	599	c.494G>A	c.(493-495)cGc>cAc	p.R165H		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	165					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GCGCGAGCGGCGCGCGGGCTG	0.622																																																0			12											39	45	43					12																	63544123		2203	4298	6501	61830390	SO:0001583	missense	552			L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.494G>A	12.37:g.63544123C>T	ENSP00000299178:p.Arg165His		61830390		Missense_Mutation	SNP	ENST00000299178.2	37	CCDS8965.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789019	0.70337	.	.	ENSG00000166148	ENST00000299178	T	0.42513	0.97	4.91	4.91	0.64330	GPCR, rhodopsin-like superfamily (1);	0.255608	0.41194	D	0.000935	T	0.56615	0.1997	M	0.72479	2.2	0.41131	D	0.985886	D	0.58268	0.982	D	0.65140	0.932	T	0.59161	-0.7506	9	.	.	.	-24.1646	7.1915	0.25828	0.0:0.8083:0.0:0.1917	.	165	P37288	V1AR_HUMAN	H	165	ENSP00000299178:R165H	.	R	-	2	0	AVPR1A	61830390	0.292000	0.24362	1.000000	0.80357	0.937000	0.57800	0.765000	0.26546	2.274000	0.75844	0.455000	0.32223	CGC		0.622	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			T	63544123	C	T	63544123	3	4	102	1	0	0	0	0	1	0	0	0	1232	768	27	1	770	1	AVPR1A	12	63544123	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	5633007	63544123	70307772	77	27058										
CDK17	5128	hgsc.bcm.edu	37	chr12	96688846	96688846	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tggtttcaagtctcgatgcaAtacctttcttctatggcaat	7	9	4	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr12:96688846A>G	ENST00000261211.3	-	10	1531	c.928T>C	c.(928-930)Ttg>Ctg	p.L310L	CDK17_ENST00000543119.2_Silent_p.L310L|CDK17_ENST00000553042.1_5'UTR|CDK17_ENST00000542666.1_Silent_p.L257L	NM_001170464.2|NM_002595.4	NP_001163935.1|NP_002586.2	Q00537	CDK17_HUMAN	cyclin-dependent kinase 17	310	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(11)|ovary(4)|prostate(2)|skin(1)	37						TCTCGATGCAATACCTTTCTT	0.338																																																0			12											133	126	128					12																	96688846		2203	4299	6502	95212977	SO:0001819	synonymous_variant	0				CCDS9061.1, CCDS53819.1	12q23.1	2011-11-08	2009-12-16	2009-12-16		ENSG00000059758		"Cyclin-dependent kinases"	8750	protein-coding gene	gene with protein product		603440	"PCTAIRE protein kinase 2"	PCTK2		9370357, 19884882	Standard	NM_001170464		Approved	PCTAIRE2	uc009ztk.3	Q00537		ENST00000261211.3:c.928T>C	12.37:g.96688846A>G			95212977	A8K1U6|B2RCQ2|Q8NEB8	Silent	SNP	ENST00000261211.3	37	CCDS9061.1																																																																																				0.338	CDK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408751.1	NM_002595		G	96688846	A	G	96688846	2	3	102	1	0	0	0	0	0	0	0	1	3139	98	4	4		4	CDK17	12	96688846	Silent	SNP	A	TCGA-DT-5265-01A-21D-1826-10	33144723	96688846	37163049	78	27059										
PSPC1	55269	hgsc.bcm.edu	37	chr13	20325440	20325440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttagcattaattggtgttcaTgcctagctgcttccatttct	7	9	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr13:20325440T>C	ENST00000338910.4	-	4	1097	c.938A>G	c.(937-939)cAt>cGt	p.H313R		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	313	Sufficient for paraspeckles localization.|Sufficient for perinucleolar caps localization and interaction with NONO.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TTGGTGTTCATGCCTAGCTGC	0.398																																																0			13											287	264	272					13																	20325440		1928	4127	6055	19223440	SO:0001583	missense	55269			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.938A>G	13.37:g.20325440T>C	ENSP00000343966:p.His313Arg		19223440	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313494	0.60414	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.16073	2.37	4.83	4.83	0.62350	.	0.112999	0.64402	D	0.000011	T	0.21347	0.0514	M	0.66297	2.02	0.53688	D	0.999977	P	0.45672	0.864	B	0.39299	0.296	T	0.04307	-1.0961	10	0.51188	T	0.08	-18.8568	14.705	0.69183	0.0:0.0:0.0:1.0	.	313	Q8WXF1	PSPC1_HUMAN	R	313;253	ENSP00000343966:H313R	ENSP00000343966:H313R	H	-	2	0	PSPC1	19223440	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	7.988000	0.88194	1.943000	0.56356	0.454000	0.30748	CAT		0.398	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			C	20325440	T	C	20325440	3	2	102	1	0	0	0	0	1	0	0	0	12750	1464	51	4	657	4	PSPC1	13	20325440	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10		20325440	94844438	79	27060										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25826045	25826045	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctgtaaatctgtgagattcgGaactgtagagaggatttaag	12	4	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr13:25826045G>T	ENST00000381801.5	-	12	2185	c.1424C>A	c.(1423-1425)tCc>tAc	p.S475Y	MTMR6_ENST00000540661.1_Missense_Mutation_p.S475Y	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	475	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)	p.S475F(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GTGAGATTCGGAACTGTAGAG	0.328																																																1	Substitution - Missense(1)	ovary(1)	13											116	132	127					13																	25826045		2203	4299	6502	24724045	SO:0001583	missense	9107			AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1424C>A	13.37:g.25826045G>T	ENSP00000371221:p.Ser475Tyr		24724045	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	37	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.498193	0.44455	.	.	ENSG00000139505	ENST00000540661;ENST00000541021;ENST00000381801;ENST00000319298	D;D	0.90444	-2.67;-2.67	5.51	5.51	0.81932	Myotubularin phosphatase domain (1);	0.315828	0.38959	N	0.001517	D	0.87249	0.6130	L	0.35644	1.08	0.50467	D	0.999877	B;B	0.18166	0.015;0.026	B;B	0.30251	0.053;0.113	D	0.83960	0.0321	10	0.59425	D	0.04	.	12.9901	0.58614	0.0:0.0:0.7174:0.2825	.	475;475	Q9Y217;Q9Y217-2	MTMR6_HUMAN;.	Y	475;475;475;43	ENSP00000443161:S475Y;ENSP00000371221:S475Y	ENSP00000317987:S43Y	S	-	2	0	MTMR6	24724045	0.883000	0.30277	0.447000	0.26932	0.876000	0.50452	3.735000	0.55044	2.578000	0.87016	0.585000	0.79938	TCC		0.328	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		T	25826045	G	T	25826045	3	4	102	1	0	0	0	0	1	0	0	0	9977	1174	41	2	453	2	MTMR6	13	25826045	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	5500605	25826045	89343833	80	27061										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96277049	96277049	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aatgctgaattcttcgaagtTaattctttaaattccttcat	4	7	3	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr13:96277049T>C	ENST00000376829.2	-	8	1796	c.945A>G	c.(943-945)ttA>ttG	p.L315L	DZIP1_ENST00000347108.3_Silent_p.L315L|DZIP1_ENST00000361396.2_Silent_p.L315L|DZIP1_ENST00000361156.3_Silent_p.L315L	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	315					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TCTTCGAAGTTAATTCTTTAA	0.333																																																0			13											99	93	95					13																	96277049		2194	4300	6494	95075050	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.945A>G	13.37:g.96277049T>C			95075050	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.333	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		C	96277049	T	C	96277049	2	2	102	1	0	0	0	0	0	0	0	1	4874	1751	61	4		4	DZIP1	13	96277049	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	70451004	96277049	18892829	81	27062										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24529216	24529216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcatgtccttccccgtgagcGacatctcccaagcctatcgc	7	17	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr14:24529216G>A	ENST00000342740.5	+	23	2060	c.1906G>A	c.(1906-1908)Gac>Aac	p.D636N	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	636						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CCCCGTGAGCGACATCTCCCA	0.652																																																0			14											152	130	138					14																	24529216		2203	4300	6503	23599056	SO:0001583	missense	90668			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1906G>A	14.37:g.24529216G>A	ENSP00000340467:p.Asp636Asn		23599056	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444161	0.83993	.	.	ENSG00000186648	ENST00000342740	T	0.61274	0.12	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.74412	0.3713	M	0.76574	2.34	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.77686	-0.2495	10	0.62326	D	0.03	-13.6603	14.7808	0.69766	0.0:0.0:1.0:0.0	.	636	Q8ND23	LR16B_HUMAN	N	636	ENSP00000340467:D636N	ENSP00000340467:D636N	D	+	1	0	LRRC16B	23599056	1.000000	0.71417	0.996000	0.52242	0.950000	0.60333	6.001000	0.70685	2.331000	0.79229	0.561000	0.74099	GAC		0.652	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		A	24529216	G	A	24529216	3	1	102	1	0	0	0	0	1	0	0	0	9001	1058	37	1	1996	1	LRRC16B	14	24529216	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10		24529216	82820324	82	27063										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42361064	42361064	+	Frame_Shift_Del	DEL	A	A	-													0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cgtcacaaatgttgaatcccAaaacactaacaggaacaact							TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr14:42361064delA	ENST00000298119.4	+	4	3186	c.1997delA	c.(1996-1998)caafs	p.Q666fs	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	666						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		GTTGAATCCCAAAACACTAAC	0.468										HNSCC(30;0.082)																																						0			14											101	84	90					14																	42361064		2203	4300	6503	41430814	SO:0001589	frameshift_variant	145581			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1997delA	14.37:g.42361064delA	ENSP00000298119:p.Gln666fs		41430814	B3KU78|Q86XL2	Frame_Shift_Del	DEL	ENST00000298119.4	37	CCDS9678.1																																																																																				0.468	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		-	42361064	A	-	42361064	7	5	102	1	0	1	0	1	0	0	0	0	8970	130	5	0	2003	0	LRFN5	14	42361064	Frame_Shift_Del	DEL	A	TCGA-DT-5265-01A-21D-1826-10	17831848	42361064	64988476	83	27064										
TRMT5	57570	hgsc.bcm.edu	37	chr14	61442484	61442484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttttgctggcaagttcatgaCaacgtgcacagagggttttc	11	8	1	2	rs549009711		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr14:61442484C>T	ENST00000261249.6	-	4	1537	c.1153G>A	c.(1153-1155)Gtc>Atc	p.V385I	RP11-193F5.1_ENST00000553946.1_RNA|RNU6-398P_ENST00000384143.1_RNA	NM_020810.2	NP_065861.2			tRNA methyltransferase 5									p.V385I(1)		NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(1)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0873)		AAGTTCATGACAACGTGCACA	0.458													C|||	1	0.000199681	8e-04	0	5008	,	,		20734	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	central_nervous_system(1)	14											93	91	92					14																	61442484		2203	4300	6503	60512237	SO:0001583	missense	57570			AB037814	CCDS32092.1	14q23.1	2013-06-05	2013-06-05	2005-08-11		ENSG00000126814	2.1.1.228		23141	protein-coding gene	gene with protein product	"tRNA (guanine(37)-N1)-methyltransferase"	611023	"KIAA1393", "tRNA methyltransferase 5 homolog (S. cerevisiae)"	KIAA1393		15248782	Standard	XM_005267916		Approved	TRM5	uc001xff.4	Q32P41		ENST00000261249.6:c.1153G>A	14.37:g.61442484C>T	ENSP00000261249:p.Val385Ile		60512237		Missense_Mutation	SNP	ENST00000261249.6	37	CCDS32092.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.933878	0.52866	.	.	ENSG00000126814	ENST00000261249	T	0.23147	1.92	6.17	4.38	0.52667	.	0.110226	0.64402	N	0.000008	T	0.15565	0.0375	N	0.16016	0.355	0.48571	D	0.999679	B	0.12013	0.005	B	0.22880	0.042	T	0.06023	-1.0850	10	0.17369	T	0.5	-6.5099	12.8575	0.57894	0.0:0.8698:0.0:0.1302	.	385	Q32P41	TRM5_HUMAN	I	385	ENSP00000261249:V385I	ENSP00000261249:V385I	V	-	1	0	TRMT5	60512237	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.661000	0.61518	0.955000	0.37878	-0.136000	0.14681	GTC		0.458	TRMT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412831.1	NM_02081		T	61442484	C	T	61442484	3	4	102	1	0	0	0	0	1	0	0	0	16607	478	17	3	384	3	TRMT5	14	61442484	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	19081420	61442484	45907056	84	27065										
EXD2	55218	hgsc.bcm.edu	37	chr14	69695623	69695623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tggttcgcctgcccaagctaAtctgtggaggaaaaacacta	10	10	1	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr14:69695623A>G	ENST00000409018.3	+	3	552	c.424A>G	c.(424-426)Atc>Gtc	p.I142V	EXD2_ENST00000409014.1_Missense_Mutation_p.I17V|EXD2_ENST00000449989.1_Missense_Mutation_p.I17V|EXD2_ENST00000409242.1_Missense_Mutation_p.I17V|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000312994.5_Missense_Mutation_p.I142V|EXD2_ENST00000409949.1_Missense_Mutation_p.I17V|EXD2_ENST00000409675.1_Missense_Mutation_p.I17V	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	142							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						GCCCAAGCTAATCTGTGGAGG	0.483																																																0			14											109	103	105					14																	69695623		2203	4300	6503	68765376	SO:0001583	missense	55218			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.424A>G	14.37:g.69695623A>G	ENSP00000387331:p.Ile142Val		68765376	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	37	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	A	1.636	-0.517711	0.04171	.	.	ENSG00000081177	ENST00000409018;ENST00000193422;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000413191;ENST00000449989	T;T;T;T;T;T;T;T	0.62941	-0.01;0.06;0.06;0.06;0.06;-0.01;0.06;0.06	5.74	2.21	0.28008	Ribonuclease H-like (1);	0.564835	0.21759	N	0.069553	T	0.32763	0.0840	N	0.08118	0	0.24745	N	0.993019	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25293	-1.0136	10	0.02654	T	1	-0.8965	8.8378	0.35123	0.7049:0.0:0.2951:0.0	.	142;17	G5E947;Q9NVH0	.;EXD2_HUMAN	V	142;142;17;17;17;17;142;17;17	ENSP00000387331:I142V;ENSP00000386915:I17V;ENSP00000386762:I17V;ENSP00000386632:I17V;ENSP00000386839:I17V;ENSP00000313140:I142V;ENSP00000409089:I17V;ENSP00000392177:I17V	ENSP00000193422:I142V	I	+	1	0	EXD2	68765376	0.994000	0.37717	0.993000	0.49108	0.842000	0.47809	2.077000	0.41557	0.466000	0.27193	0.460000	0.39030	ATC		0.483	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			G	69695623	A	G	69695623	3	3	102	1	0	0	0	0	1	0	0	0	5311	101	4	4	51	4	EXD2	14	69695623	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	8253139	69695623	37653917	85	27066										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610398	81610398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccaaaatcttgctggtactcTtctatccacttaactcctgt	4	13	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr14:81610398T>C	ENST00000541158.2	+	11	2318	c.1996T>C	c.(1996-1998)Ttc>Ctc	p.F666L	TSHR_ENST00000298171.2_Missense_Mutation_p.F666L|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	666					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.F666L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	GCTGGTACTCTTCTATCCACT	0.453			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	1	Substitution - Missense(1)	thyroid(1)	14											187	184	185					14																	81610398		2203	4300	6503	80680151	SO:0001583	missense	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1996T>C	14.37:g.81610398T>C	ENSP00000441235:p.Phe666Leu		80680151	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.220933	0.79464	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	D;D	0.94687	-3.49;-3.49	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	M	0.80746	2.51	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.97796	1.0241	10	0.87932	D	0	.	14.8175	0.70045	0.0:0.0:0.0:1.0	.	666	F5GYU5	.	L	666;313;666	ENSP00000441235:F666L;ENSP00000298171:F666L	ENSP00000298171:F666L	F	+	1	0	TSHR	80680151	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.040000	0.89188	1.906000	0.55180	0.459000	0.35465	TTC		0.453	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		C	81610398	T	C	81610398	3	2	102	1	0	0	0	0	1	0	0	0	16662	1609	56	4	2171	4	TSHR	14	81610398	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	11914775	81610398	25739142	86	27067										
GABRG3	2567	hgsc.bcm.edu	37	chr15	27572176	27572176	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gaaaatcctttacactttgaGgtaagatgctgcatcgatct	8	8	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr15:27572176G>C	ENST00000333743.6	+	4	745	c.491G>C	c.(490-492)aGg>aCg	p.R164T	GABRG3_ENST00000555083.1_Splice_Site_p.R164T	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	164					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R164M(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TACACTTTGAGGTAAGATGCT	0.423																																					NSCLC(114;800 1656 7410 37729 45293)											1	Substitution - Missense(1)	lung(1)	15											35	34	34					15																	27572176		1920	4157	6077	25154922	SO:0001630	splice_region_variant	2567				CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4088	protein-coding gene	gene with protein product	"GABA(G) receptor, gamma 3"	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.491+1G>C	15.37:g.27572176G>C			25154922	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529233	0.64860	.	.	ENSG00000182256	ENST00000333743;ENST00000555083;ENST00000554696	D;D;D	0.81821	-1.54;-1.54;-1.54	5.69	5.69	0.88448	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.93491	0.7923	H	0.97131	3.945	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.74023	0.982;0.966	D	0.95249	0.8358	10	0.87932	D	0	.	18.8001	0.92013	0.0:0.0:1.0:0.0	.	164;164	Q99928;G3V594	GBRG3_HUMAN;.	T	164;164;106	ENSP00000331912:R164T;ENSP00000452244:R164T;ENSP00000451862:R106T	ENSP00000331912:R164T	R	+	2	0	GABRG3	25154922	1.000000	0.71417	0.978000	0.43139	0.066000	0.16364	9.539000	0.98076	2.664000	0.90586	0.655000	0.94253	AGG		0.423	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		Missense_Mutation	C	27572176	G	C	27572176	5	2	102	1	0	0	0	0	0	0	1	0	6192	1014	35	5	505	5	GABRG3	15	27572176	Splice_Site	SNP	G	TCGA-DT-5265-01A-21D-1826-10		27572176	74959216	87	27068										
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43940168	43940168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cttggctcaagccttgcaaaTgctcaatgagagagaaagta	10	8	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr15:43940168T>C	ENST00000321596.5	-	2	291	c.92A>G	c.(91-93)cAt>cGt	p.H31R	CATSPER2_ENST00000381761.1_Missense_Mutation_p.H37R|CATSPER2_ENST00000396879.1_Missense_Mutation_p.H31R|CATSPER2_ENST00000355438.2_Missense_Mutation_p.H31R|CATSPER2_ENST00000464721.1_Intron|CATSPER2_ENST00000354127.4_Missense_Mutation_p.H31R|STRC_ENST00000541030.1_Intron			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	31					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.H31L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GCCTTGCAAATGCTCAATGAG	0.473																																																1	Substitution - Missense(1)	ovary(1)	15											183	181	182					15																	43940168		2199	4296	6495	41727460	SO:0001583	missense	117155			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.92A>G	15.37:g.43940168T>C	ENSP00000321463:p.His31Arg		41727460	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694243	0.48202	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438;ENST00000432420;ENST00000409481;ENST00000419473	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	2.64	2.64	0.31445	.	2.597920	0.01853	N	0.036089	T	0.60157	0.2247	M	0.73598	2.24	0.29336	N	0.866362	D;D;D	0.76494	0.999;0.998;0.997	D;D;P	0.71184	0.972;0.935;0.863	T	0.18053	-1.0349	10	0.48119	T	0.1	.	7.0877	0.25267	0.0:0.0:0.0:1.0	.	31;37;31	Q96P56-4;F8W9H2;Q96P56	.;.;CTSR2_HUMAN	R	31;31;37;31;31;31;31;31;31	ENSP00000380088:H31R;ENSP00000371180:H37R;ENSP00000321463:H31R;ENSP00000339137:H31R;ENSP00000347613:H31R;ENSP00000407694:H31R;ENSP00000386595:H31R	ENSP00000299989:H31R	H	-	2	0	CATSPER2	41727460	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	3.580000	0.53907	1.219000	0.43474	0.155000	0.16302	CAT		0.473	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		C	43940168	T	C	43940168	3	2	102	1	0	0	0	0	1	0	0	0	2694	1464	51	4	1587	4	CATSPER2	15	43940168	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	16367992	43940168	58591224	88	27069										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51829848	51829848	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	caagcagaaccgtaggcagtGgcattggtacactaagtcgt	12	9	0	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr15:51829848G>T	ENST00000251076.5	-	11	1741	c.1454C>A	c.(1453-1455)cCa>cAa	p.P485Q	DMXL2_ENST00000543779.2_Missense_Mutation_p.P485Q|DMXL2_ENST00000449909.3_Missense_Mutation_p.P485Q	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	485						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CGTAGGCAGTGGCATTGGTAC	0.433																																																0			15											238	196	210					15																	51829848		2195	4293	6488	49617140	SO:0001583	missense	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.1454C>A	15.37:g.51829848G>T	ENSP00000251076:p.Pro485Gln		49617140	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713118	0.89112	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.38722	1.12;1.12;1.12	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.64997	1.995	0.38600	D	0.950631	D;D;D	0.89917	0.993;1.0;0.969	P;D;P	0.83275	0.876;0.996;0.656	T	0.67082	-0.5760	10	0.51188	T	0.08	.	18.3459	0.90322	0.0:0.0:1.0:0.0	.	485;485;485	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	Q	485	ENSP00000251076:P485Q;ENSP00000441858:P485Q;ENSP00000400855:P485Q	ENSP00000251076:P485Q	P	-	2	0	DMXL2	49617140	1.000000	0.71417	0.971000	0.41717	0.960000	0.62799	9.386000	0.97228	2.337000	0.79520	0.650000	0.86243	CCA		0.433	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51829848	G	T	51829848	3	4	102	1	0	0	0	0	1	0	0	0	4606	1348	47	2	7791	2	DMXL2	15	51829848	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	7889680	51829848	50701544	89	27070										
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52905979	52905979	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttacagaacattcaggtgttCgtccttctgttatcagcaag	8	9	3	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr15:52905979C>T	ENST00000261844.7	-	3	244	c.92G>A	c.(91-93)cGa>cAa	p.R31Q	FAM214A_ENST00000546305.2_Missense_Mutation_p.R38Q	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	31																	TTCAGGTGTTCGTCCTTCTGT	0.413																																																0			15											129	121	123					15																	52905979		1916	4119	6035	50693271	SO:0001583	missense	56204			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.92G>A	15.37:g.52905979C>T	ENSP00000261844:p.Arg31Gln		50693271	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	C	36	5.704274	0.96812	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.66099	-0.17;-0.19	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	L	0.59436	1.845	0.49798	D	0.999827	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.78481	-0.2187	10	0.87932	D	0	-9.2382	20.3186	0.98660	0.0:1.0:0.0:0.0	.	38;31	F5H8G0;Q32MH5	.;K1370_HUMAN	Q	31;31;30;38	ENSP00000261844:R31Q;ENSP00000443598:R38Q	ENSP00000261844:R31Q	R	-	2	0	KIAA1370	50693271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.294000	0.78760	2.798000	0.96311	0.579000	0.79373	CGA		0.413	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		T	52905979	C	T	52905979	3	4	102	1	0	0	0	0	1	0	0	0	8247	884	31	1	3182	1	KIAA1370	15	52905979	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	1076131	52905979	49625413	90	27071										
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57910379	57910379	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gaaagaagagatgaactacaTcaaagatgtgagccatttaa	9	5	1	5			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr15:57910379T>C	ENST00000267853.5	+	3	405	c.311T>C	c.(310-312)aTc>aCc	p.I104T	GCOM1_ENST00000574161.1_Missense_Mutation_p.I104T|GCOM1_ENST00000572390.1_Missense_Mutation_p.I104T|GCOM1_ENST00000380569.2_Missense_Mutation_p.I104T|GCOM1_ENST00000380560.2_Missense_Mutation_p.I104T|MYZAP_ENST00000380565.4_Missense_Mutation_p.I104T|GCOM1_ENST00000587652.1_Missense_Mutation_p.I104T|GCOM1_ENST00000380568.3_Missense_Mutation_p.I104T|GCOM1_ENST00000380561.2_Missense_Mutation_p.I104T|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000396180.1_Missense_Mutation_p.I104T			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	104					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											ATGAACTACATCAAAGATGTG	0.418																																																0			15											165	148	154					15																	57910379		2192	4292	6484	55697671	SO:0001583	missense	145781			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.311T>C	15.37:g.57910379T>C	ENSP00000267853:p.Ile104Thr		55697671	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.023186	0.75275	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.36340	1.26;1.36;1.41;1.63;1.26;1.26;1.26	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.58352	0.2116	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	T	0.57394	-0.7819	10	0.49607	T	0.09	-21.5521	15.8048	0.78491	0.0:0.0:0.0:1.0	.	104;104;104;104	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	T	104	ENSP00000369943:I104T;ENSP00000369935:I104T;ENSP00000379483:I104T;ENSP00000369933:I104T;ENSP00000267853:I104T;ENSP00000369939:I104T;ENSP00000369942:I104T	ENSP00000267853:I104T	I	+	2	0	GCOM1	55697671	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	6.068000	0.71201	2.371000	0.80710	0.533000	0.62120	ATC		0.418	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		C	57910379	T	C	57910379	3	2	102	1	0	0	0	0	1	0	0	0	6324	1435	50	4	321	4	GCOM1	15	57910379	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	5004400	57910379	44621013	91	27072										
TP53	7157	hgsc.bcm.edu	37	chr17	7577079	7577079	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccctttcttgcggagattctCttcctctgtgcgccggtctc	9	15	4	1	rs587782006		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr17:7577079C>A	ENST00000269305.4	-	8	1048	c.859G>T	c.(859-861)Gag>Tag	p.E287*	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.E287*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E287*|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.E287*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E287*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	287	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in a sporadic cancer; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.N288fs*13(17)|p.E287*(13)|p.0?(8)|p.E287K(6)|p.?(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.E287fs*17(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGGAGATTCTCTTCCTCTGTG	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	60	Deletion - Frameshift(25)|Substitution - Nonsense(13)|Whole gene deletion(8)|Deletion - In frame(6)|Substitution - Missense(6)|Unknown(2)	upper_aerodigestive_tract(20)|breast(6)|lung(6)|large_intestine(4)|bone(4)|liver(4)|stomach(3)|urinary_tract(3)|oesophagus(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|skin(2)|pancreas(1)	17	GRCh37	CM044948	TP53	M							97	83	88					17																	7577079		2203	4300	6503	7517804	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.859G>T	17.37:g.7577079C>A	ENSP00000269305:p.Glu287*		7517804	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.403327	0.83230	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.12	4.15	0.48705	.	0.602197	0.18632	N	0.135543	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-7.7207	11.4307	0.50038	0.0:0.9127:0.0:0.0873	.	.	.	.	X	287;287;287;287;287;276;155	.	ENSP00000269305:E287X	E	-	1	0	TP53	7517804	1.000000	0.71417	0.955000	0.39395	0.167000	0.22549	4.360000	0.59455	1.381000	0.46364	-0.258000	0.10820	GAG		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577079	C	A	7577079	4	1	102	1	0	0	0	0	0	1	0	0	16421	922	32	2	427	2	TP53	17	7577079	Nonsense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		7577079	73618131	92	27073										
FKBP10	60681	hgsc.bcm.edu	37	chr17	39977328	39977328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gtgcccccgcacctggcccaCggggagagtggaggtgaggg	19	12	0	2	rs571808781	byFrequency	TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr17:39977328C>T	ENST00000321562.4	+	8	1490	c.1386C>T	c.(1384-1386)caC>caT	p.H462H	FKBP10_ENST00000544340.1_Silent_p.H235H	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	462	PPIase FKBP-type 4. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		ACCTGGCCCACGGGGAGAGTG	0.552													C|||	2	0.000399361	8e-04	0	5008	,	,		13628	0		0	False		,,,				2504	0.001															0			17											12	13	12					17																	39977328		2183	4271	6454	37230854	SO:0001819	synonymous_variant	60681			AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"EF-hand domain containing"	18169	protein-coding gene	gene with protein product		607063	"FK506 binding protein 10 (65 kDa)"			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.1386C>T	17.37:g.39977328C>T			37230854	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Silent	SNP	ENST00000321562.4	37	CCDS11409.1	.	.	.	.	.	.	.	.	.	.	C	6.777	0.512306	0.12944	.	.	ENSG00000141756	ENST00000455106	.	.	.	5.38	-5.25	0.02781	.	.	.	.	.	T	0.62804	0.2458	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64394	-0.6418	4	.	.	.	-22.9653	14.7979	0.69891	0.0:0.4266:0.0:0.5734	.	.	.	.	M	266	.	.	T	+	2	0	FKBP10	37230854	0.001000	0.12720	0.645000	0.29479	0.923000	0.55619	-1.651000	0.01989	-0.860000	0.04099	-1.036000	0.02392	ACG		0.552	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		T	39977328	C	T	39977328	2	4	102	1	0	0	0	0	0	0	0	1	5921	535	19	1		1	FKBP10	17	39977328	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	32400249	39977328	41217882	93	27074										
STAT5A	6776	hgsc.bcm.edu	37	chr17	40453361	40453361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	caagtttgcagccaccgtacGcctgctggtgggcgggaagc	15	12	0	0	rs372745237		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr17:40453361G>A	ENST00000345506.4	+	10	1700	c.1058G>A	c.(1057-1059)cGc>cAc	p.R353H	STAT5A_ENST00000588868.1_Missense_Mutation_p.R353H|STAT5A_ENST00000546010.2_Missense_Mutation_p.R323H|STAT5A_ENST00000590949.1_Missense_Mutation_p.R353H|STAT5A_ENST00000452307.2_Missense_Mutation_p.R353H	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	353					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GCCACCGTACGCCTGCTGGTG	0.557																																																0			17						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	154	133	140		1058	4.6	1	17		140	0,8600		0,0,4300	no	missense	STAT5A	NM_003152.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	353/795	40453361	1,13005	2203	4300	6503	37706887	SO:0001583	missense	6776			U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1058G>A	17.37:g.40453361G>A	ENSP00000341208:p.Arg353His		37706887	Q1KLZ6	Missense_Mutation	SNP	ENST00000345506.4	37	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818980	0.90873	2.27E-4	0.0	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	D;D;D	0.94184	-3.37;-3.37;-3.37	4.6	4.6	0.57074	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97278	0.9110	M	0.89601	3.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98413	1.0573	10	0.87932	D	0	-13.3349	17.4923	0.87708	0.0:0.0:1.0:0.0	.	323;355;353	Q1KLZ6;Q59GY7;P42229	.;.;STA5A_HUMAN	H	353;323;355;353	ENSP00000341208:R353H;ENSP00000443107:R323H;ENSP00000400320:R353H	ENSP00000341208:R353H	R	+	2	0	STAT5A	37706887	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	9.698000	0.98700	2.122000	0.65172	0.306000	0.20318	CGC		0.557	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		A	40453361	G	A	40453361	3	1	102	1	0	0	0	0	1	0	0	0	15307	1087	38	1	1088	1	STAT5A	17	40453361	Missense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	476033	40453361	40741849	94	27075										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59886067	59886067	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	aatggtattcgatgactcttGactgtttccttgtttagtag	9	6	1	2	rs45459799		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr17:59886067G>A	ENST00000259008.2	-	7	946	c.679C>T	c.(679-681)Caa>Taa	p.Q227*	BRIP1_ENST00000577598.1_Nonsense_Mutation_p.Q227*	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	227	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						GATGACTCTTGACTGTTTCCT	0.388			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	0			17											85	80	82					17																	59886067		2203	4300	6503	57240849	SO:0001587	stop_gained	83990			AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.679C>T	17.37:g.59886067G>A	ENSP00000259008:p.Gln227*		57240849	Q3MJE2|Q8NCI5	Nonsense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	G	34	5.353297	0.95830	.	.	ENSG00000136492	ENST00000259008	.	.	.	5.29	0.53	0.17102	.	0.576431	0.19352	N	0.116363	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.4737	3.4205	0.07392	0.0767:0.2361:0.321:0.3662	.	.	.	.	X	227	.	.	Q	-	1	0	BRIP1	57240849	0.967000	0.33354	0.980000	0.43619	0.899000	0.52679	1.517000	0.35867	0.279000	0.22186	-0.292000	0.09595	CAA		0.388	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		A	59886067	G	A	59886067	4	1	102	1	0	0	0	0	0	1	0	0	1517	1299	45	3	3126	3	BRIP1	17	59886067	Nonsense_Mutation	SNP	G	TCGA-DT-5265-01A-21D-1826-10	19432706	59886067	21309143	95	27076										
NOL11	25926	hgsc.bcm.edu	37	chr17	65732801	65732801	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggaactcatgtcgtgtcccaTtttgtaaactgggagacacc	10	10	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr17:65732801T>C	ENST00000253247.4	+	10	1189	c.1074T>C	c.(1072-1074)caT>caC	p.H358H	NOL11_ENST00000535137.1_Silent_p.H176H	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	358					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TCGTGTCCCATTTTGTAAACT	0.363																																																0			17											87	81	83					17																	65732801		2203	4300	6503	63163263	SO:0001819	synonymous_variant	25926			AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1074T>C	17.37:g.65732801T>C			63163263	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																				0.363	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		C	65732801	T	C	65732801	2	2	102	1	0	0	0	0	0	0	0	1	10552	1490	52	4		4	NOL11	17	65732801	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	5846734	65732801	15462409	96	27077										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8247843	8247843	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agcctctcttttatttacagCtgtgtcttcaccatcgtcct	5	13	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr18:8247843C>G	ENST00000332175.8	+	16	3490	c.2453C>G	c.(2452-2454)tCt>tGt	p.S818C	PTPRM_ENST00000400053.4_Splice_Site_p.S756C|PTPRM_ENST00000444013.1_Splice_Site_p.S605C|PTPRM_ENST00000580170.1_Splice_Site_p.S818C|PTPRM_ENST00000400060.4_Splice_Site_p.S818C	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	818					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TTATTTACAGCTGTGTCTTCA	0.468																																																0			18											145	131	136					18																	8247843		2203	4300	6503	8237843	SO:0001630	splice_region_variant	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2453-1C>G	18.37:g.8247843C>G			8237843	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069916	0.55539	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.49432	1.1;1.09;0.92;0.78	6.17	6.17	0.99709	.	0.245924	0.45126	D	0.000399	T	0.58133	0.2101	M	0.63843	1.955	0.80722	D	1	P;D;D	0.58620	0.809;0.983;0.983	B;P;P	0.49561	0.345;0.615;0.615	T	0.53244	-0.8466	9	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	605;818;818	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	C	818;818;756;605	ENSP00000331418:S818C;ENSP00000382933:S818C;ENSP00000382927:S756C;ENSP00000387608:S605C	.	S	+	2	0	PTPRM	8237843	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.175000	0.77632	2.941000	0.99782	0.655000	0.94253	TCT		0.468	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Missense_Mutation	G	8247843	C	G	8247843	5	3	102	1	0	0	0	0	0	0	1	0	12843	811	28	5	2515	5	PTPRM	18	8247843	Splice_Site	SNP	C	TCGA-DT-5265-01A-21D-1826-10		8247843	69829405	97	27078										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44559563	44559563	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctgctgtctctgccaccgccGctgctgctctggctggaggg	14	15	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr18:44559563G>A	ENST00000332567.4	-	1	2425	c.2073C>T	c.(2071-2073)agC>agT	p.S691S	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	691					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						tgccaccgccgctgctgctCT	0.662																																																0			18											33	38	36					18																	44559563		2201	4299	6500	42813561	SO:0001819	synonymous_variant	51224			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.2073C>T	18.37:g.44559563G>A			42813561	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																				0.662	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		A	44559563	G	A	44559563	2	1	102	1	0	0	0	0	0	0	0	1	15721	1078	38	1		1	TCEB3B	18	44559563	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	36311720	44559563	33517685	98	27079										
SERPINB5	5268	hgsc.bcm.edu	37	chr18	61170746	61170746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acacatctgatttctctggaAtgtcagagaccaagggagtg	11	8	3	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr18:61170746A>G	ENST00000382771.4	+	7	1211	c.919A>G	c.(919-921)Atg>Gtg	p.M307V		NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	307					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.M307L(1)		kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						TTTCTCTGGAATGTCAGAGAC	0.433																																																1	Substitution - Missense(1)	ovary(1)	18											96	82	87					18																	61170746		2203	4300	6503	59321726	SO:0001583	missense	5268			U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"Serine (or cysteine) peptidase inhibitors"	8949	protein-coding gene	gene with protein product	"protease inhibitor 5 (maspin)"	154790	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.919A>G	18.37:g.61170746A>G	ENSP00000372221:p.Met307Val		59321726	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.534268	0.45073	.	.	ENSG00000206075	ENST00000382771	D	0.85171	-1.95	5.95	3.42	0.39159	Serpin domain (3);	0.211041	0.49305	D	0.000145	D	0.84737	0.5538	M	0.85710	2.77	0.80722	D	1	B	0.17268	0.021	B	0.15052	0.012	D	0.84628	0.0688	10	0.66056	D	0.02	.	9.64	0.39833	0.7218:0.1722:0.0:0.1059	.	307	P36952	SPB5_HUMAN	V	307	ENSP00000372221:M307V	ENSP00000372221:M307V	M	+	1	0	SERPINB5	59321726	0.995000	0.38212	1.000000	0.80357	0.970000	0.65996	3.365000	0.52335	2.285000	0.76669	0.533000	0.62120	ATG		0.433	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639		G	61170746	A	G	61170746	3	3	102	1	0	0	0	0	1	0	0	0	14141	101	4	4	941	4	SERPINB5	18	61170746	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	16611183	61170746	16906502	99	27080										
OR7C1	26664	hgsc.bcm.edu	37	chr19	14910336	14910336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gaaggaaatcacacccaggaCgccagttgcaaagtatatca	9	10	2	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:14910336C>T	ENST00000248073.2	-	1	687	c.613G>A	c.(613-615)Gtc>Atc	p.V205I	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	205					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						ACACCCAGGACGCCAGTTGCA	0.393																																																0			19											68	69	69					19																	14910336		2203	4300	6503	14771336	SO:0001583	missense	26664			X89676	CCDS12317.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.613G>A	19.37:g.14910336C>T	ENSP00000248073:p.Val205Ile		14771336	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	.	.	.	.	.	.	.	.	.	.	c	5.029	0.191024	0.09547	.	.	ENSG00000127530	ENST00000248073	T	0.37058	1.22	3.55	-5.04	0.02964	GPCR, rhodopsin-like superfamily (1);	1.048770	0.07733	U	0.945483	T	0.11750	0.0286	N	0.03253	-0.375	0.09310	N	1	B	0.17268	0.021	B	0.18263	0.021	T	0.17319	-1.0373	10	0.30854	T	0.27	.	0.4666	0.00525	0.2686:0.3149:0.1971:0.2194	.	205	O76099	OR7C1_HUMAN	I	205	ENSP00000248073:V205I	ENSP00000248073:V205I	V	-	1	0	OR7C1	14771336	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-10.568000	0.00006	-1.040000	0.03271	-3.246000	0.00050	GTC		0.393	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			T	14910336	C	T	14910336	3	4	102	1	0	0	0	0	1	0	0	0	11248	536	19	1	351	1	OR7C1	19	14910336	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		14910336	44218647	100	27081										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18378120	18378120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	cccggaggcgtgggacgcggCgggacgccgtcttgccttcg	18	14	1	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:18378120C>T	ENST00000600328.3	-	3	423	c.230G>A	c.(229-231)cGc>cAc	p.R77H	KIAA1683_ENST00000392413.4_Missense_Mutation_p.R77H|KIAA1683_ENST00000600359.3_Missense_Mutation_p.R31H			Q9H0B3	K1683_HUMAN	KIAA1683	77						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TGGGACGCGGCGGGACGCCGT	0.632																																																0			19											60	62	61					19																	18378120		2203	4299	6502	18239120	SO:0001583	missense	80726			AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.230G>A	19.37:g.18378120C>T	ENSP00000470780:p.Arg77His		18239120	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.983092	0.34942	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422;ENST00000411671	T;T;T	0.03663	3.93;3.94;3.85	1.41	-2.83	0.05769	.	.	.	.	.	T	0.01800	0.0057	N	0.20986	0.625	0.09310	N	1	P;B	0.37864	0.61;0.025	B;B	0.21917	0.037;0.003	T	0.41520	-0.9504	9	0.48119	T	0.1	-0.2358	2.8698	0.05613	0.0:0.4068:0.2415:0.3517	.	77;77	E9PDE0;Q9H0B3	.;K1683_HUMAN	H	77;77;31;76;77	ENSP00000376213:R77H;ENSP00000352774:R77H;ENSP00000404501:R31H	ENSP00000351198:R76H	R	-	2	0	KIAA1683	18239120	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-4.719000	0.00194	-0.765000	0.04645	0.313000	0.20887	CGC		0.632	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			T	18378120	C	T	18378120	3	4	102	1	0	0	0	0	1	0	0	0	8272	768	27	1	3881	1	KIAA1683	19	18378120	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	3467784	18378120	40750863	101	27082										
LSR	51599	hgsc.bcm.edu	37	chr19	35741411	35741411	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gccagcgtcgacaaccagctCaatgcccagctggcagccgg	12	16	1	0	rs542223511		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:35741411C>T	ENST00000361790.3	+	2	606	c.447C>T	c.(445-447)ctC>ctT	p.L149L	LSR_ENST00000347609.4_Silent_p.L112L|LSR_ENST00000427250.1_Silent_p.L101L|AC002128.5_ENST00000604161.1_RNA|LSR_ENST00000354900.3_Silent_p.L149L|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000360798.3_Silent_p.L149L|LSR_ENST00000602122.1_Silent_p.L149L	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	149	Ig-like V-type.				embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ACAACCAGCTCAATGCCCAGC	0.647																																																0			19											93	85	88					19																	35741411		2203	4300	6503	40433251	SO:0001819	synonymous_variant	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.447C>T	19.37:g.35741411C>T			40433251	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	37	CCDS12450.1																																																																																				0.647	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35741411	C	T	35741411	2	4	102	1	0	0	0	0	0	0	0	1	9093	813	29	3		3	LSR	19	35741411	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	17363291	35741411	23387572	102	27083										
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36206338	36206338	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	agcatcctgctgatgccgccCagatatggcattcccttcta	8	14	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:36206338C>T	ENST00000392197.2	+	3	1128	c.810C>T	c.(808-810)ccC>ccT	p.P270P	ZBTB32_ENST00000262630.3_Silent_p.P270P|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000607650.1_RNA			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	270					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGATGCCGCCCAGATATGGCA	0.657																																																0			19											45	48	47					19																	36206338		2196	4293	6489	40898178	SO:0001819	synonymous_variant	27033			AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.810C>T	19.37:g.36206338C>T			40898178	Q8WVP2	Silent	SNP	ENST00000392197.2	37	CCDS12471.1																																																																																				0.657	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		T	36206338	C	T	36206338	2	4	102	1	0	0	0	0	0	0	0	1	17574	581	21	3		3	ZBTB32	19	36206338	Silent	SNP	C	TCGA-DT-5265-01A-21D-1826-10	464927	36206338	22922645	103	27084										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51169858	51169858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tccagcccctgtcaccgagaCggtggggctggtgggggtaa	17	11	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:51169858C>T	ENST00000293441.1	-	22	5377	c.5359G>A	c.(5359-5361)Gtc>Atc	p.V1787I	SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000391814.1_Missense_Mutation_p.V1795I|SHANK1_ENST00000359082.3_Missense_Mutation_p.V1778I|SHANK1_ENST00000391813.1_Missense_Mutation_p.V1174I	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1787					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GTCACCGAGACGGTGGGGCTG	0.731																																																0			19											5	7	6					19																	51169858		1697	3618	5315	55861670	SO:0001583	missense	50944			AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.5359G>A	19.37:g.51169858C>T	ENSP00000293441:p.Val1787Ile		55861670	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	C	8.485	0.860754	0.17178	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.36699	1.36;1.81;1.34;1.24	2.35	2.35	0.29111	.	1.651660	0.04151	U	0.321216	T	0.19805	0.0476	N	0.25647	0.755	0.24597	N	0.993792	B;P	0.36125	0.251;0.538	B;B	0.25506	0.008;0.061	T	0.15607	-1.0431	10	0.09338	T	0.73	.	5.0721	0.14611	0.0:0.8246:0.0:0.1754	.	1787;1174	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	I	1787;1174;1778;1795	ENSP00000293441:V1787I;ENSP00000375689:V1174I;ENSP00000351984:V1778I;ENSP00000375690:V1795I	ENSP00000293441:V1787I	V	-	1	0	SHANK1	55861670	0.740000	0.28207	0.720000	0.30636	0.719000	0.41307	0.999000	0.29757	1.334000	0.45468	0.195000	0.17529	GTC		0.731	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51169858	C	T	51169858	3	4	102	1	0	0	0	0	1	0	0	0	14301	536	19	1	1134	1	SHANK1	19	51169858	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	14963520	51169858	7959125	104	27085										
VN1R4	317703	hgsc.bcm.edu	37	chr19	53770600	53770600	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tttcctggagctgaccgtgaTcacctggaagacactcaaga	10	11	2	4			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:53770600T>C	ENST00000311170.4	-	1	372	c.319A>G	c.(319-321)Atc>Gtc	p.I107V	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	107					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		CTGACCGTGATCACCTGGAAG	0.498										HNSCC(26;0.072)																																						0			19											34	27	29					19																	53770600		2203	4299	6502	58462412	SO:0001583	missense	317703			AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.319A>G	19.37:g.53770600T>C	ENSP00000310856:p.Ile107Val		58462412	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.562777	0.27915	.	.	ENSG00000228567	ENST00000311170	T	0.12672	2.66	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.472218	0.15777	N	0.245142	T	0.20007	0.0481	L	0.46947	1.48	0.09310	N	1	P	0.51147	0.942	P	0.54270	0.747	T	0.03296	-1.1051	10	0.46703	T	0.11	.	8.5532	0.33465	0.0:0.0:0.0:1.0	.	107	Q7Z5H5	VN1R4_HUMAN	V	107	ENSP00000310856:I107V	ENSP00000310856:I107V	I	-	1	0	VN1R4	58462412	0.001000	0.12720	0.641000	0.29422	0.465000	0.32709	0.099000	0.15210	1.312000	0.45043	0.445000	0.29226	ATC		0.498	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857		C	53770600	T	C	53770600	3	2	102	1	0	0	0	0	1	0	0	0	17220	1435	50	4	589	4	VN1R4	19	53770600	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	2600742	53770600	5358383	105	27086										
KIR3DL3	115653	hgsc.bcm.edu	37	chr19	55239243	55239243	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gttggacagctccacgatgcGggttcccaggtcaactattc	11	12	1	0	rs201248696		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:55239243G>A	ENST00000291860.1	+	4	540	c.522G>A	c.(520-522)gcG>gcA	p.A174A	KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Intron	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	174	Ig-like C2-type 2. {ECO:0000305}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TCCACGATGCGGGTTCCCAGG	0.552																																																0			19											101	85	91					19																	55239243		1978	3434	5412	59931055	SO:0001819	synonymous_variant	115653			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.522G>A	19.37:g.55239243G>A			59931055	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Silent	SNP	ENST00000291860.1	37	CCDS12903.1																																																																																				0.552	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443		A	55239243	G	A	55239243	2	1	102	1	0	0	0	0	0	0	0	1	8343	1103	39	1		1	KIR3DL3	19	55239243	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10	1468643	55239243	3889740	106	27087										
USP29	57663	hgsc.bcm.edu	37	chr19	57641404	57641404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ggtagaacctaataattatcTctccatcaacctgcaccaag	5	12	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr19:57641404T>C	ENST00000254181.4	+	4	1815	c.1361T>C	c.(1360-1362)cTc>cCc	p.L454P	USP29_ENST00000598197.1_Missense_Mutation_p.L454P	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	454	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AATAATTATCTCTCCATCAAC	0.368																																																0			19											152	148	149					19																	57641404		2203	4300	6503	62333216	SO:0001583	missense	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1361T>C	19.37:g.57641404T>C	ENSP00000254181:p.Leu454Pro		62333216		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.341590	0.41498	.	.	ENSG00000131864	ENST00000254181	D	0.81739	-1.53	2.65	2.65	0.31530	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.414201	0.14115	U	0.340477	D	0.89705	0.6792	M	0.88377	2.95	0.45676	D	0.998592	D	0.89917	1.0	D	0.85130	0.997	D	0.89253	0.3592	10	0.87932	D	0	-1.2109	9.1534	0.36978	0.0:0.0:0.0:1.0	.	454	Q9HBJ7	UBP29_HUMAN	P	454	ENSP00000254181:L454P	ENSP00000254181:L454P	L	+	2	0	USP29	62333216	0.978000	0.34361	0.457000	0.27056	0.616000	0.37450	2.577000	0.46042	1.439000	0.47511	0.477000	0.44152	CTC		0.368	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			C	57641404	T	C	57641404	3	2	102	1	0	0	0	0	1	0	0	0	17099	1551	54	4	1363	4	USP29	19	57641404	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	2402161	57641404	1487579	107	27088										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32624145	32624145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gtgcaccaggaagttcttgaCggccagggcgccggccttgc	15	13	1	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr21:32624145C>T	ENST00000286827.3	-	6	1795	c.1324G>A	c.(1324-1326)Gtc>Atc	p.V442I	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Missense_Mutation_p.V442I	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	442	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AAGTTCTTGACGGCCAGGGCG	0.642																																																0			21											72	74	73					21																	32624145		2203	4300	6503	31546016	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1324G>A	21.37:g.32624145C>T	ENSP00000286827:p.Val442Ile		31546016	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822484	0.71028	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.50548	0.78;0.74	4.62	4.62	0.57501	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.064020	0.64402	D	0.000008	T	0.36331	0.0963	L	0.34521	1.04	0.80722	D	1	P;P;P;P	0.52316	0.887;0.907;0.952;0.907	B;B;B;B	0.36289	0.081;0.197;0.221;0.132	T	0.45264	-0.9273	10	0.59425	D	0.04	.	17.6527	0.88169	0.0:1.0:0.0:0.0	.	442;442;283;442	F5GZ53;B7ZLR6;E9PD83;Q13009	.;.;.;TIAM1_HUMAN	I	442;283;442	ENSP00000286827:V442I;ENSP00000441570:V442I	ENSP00000286827:V442I	V	-	1	0	TIAM1	31546016	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.494000	0.66905	2.381000	0.81170	0.655000	0.94253	GTC		0.642	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32624145	C	T	32624145	3	4	102	1	0	0	0	0	1	0	0	0	15929	536	19	1	3547	1	TIAM1	21	32624145	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10		32624145	15505750	108	27089										
GCFC1	94104	hgsc.bcm.edu	37	chr21	34117133	34117133	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttattttctgcattcactacTgaaggatatccattgattaa	5	7	2	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chr21:34117133T>C	ENST00000331923.4	-	13	2349	c.2160A>G	c.(2158-2160)tcA>tcG	p.S720S	PAXBP1-AS1_ENST00000440052.1_RNA|PAXBP1_ENST00000290178.4_Silent_p.S720S	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	720					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CATTCACTACTGAAGGATATC	0.318																																																0			21											110	122	118					21																	34117133		2203	4296	6499	33039004	SO:0001819	synonymous_variant	0			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.2160A>G	21.37:g.34117133T>C			33039004	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																				0.318	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		C	34117133	T	C	34117133	2	2	102	1	0	0	0	0	0	0	0	1	6309	1567	55	4		4	GCFC1	21	34117133	Silent	SNP	T	TCGA-DT-5265-01A-21D-1826-10	1492988	34117133	14012762	109	27090										
ARSH	347527	hgsc.bcm.edu	37	chrX	2945415	2945415	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ccagggatattccggtggccGtcagtcttggaggctgggag	17	9	2	0	rs373570475		TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:2945415G>A	ENST00000381130.2	+	7	1098	c.1098G>A	c.(1096-1098)ccG>ccA	p.P366P		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	366					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TCCGGTGGCCGTCAGTCTTGG	0.507													G|||	1	0.000264901	0	0	3775	,	,		13554	0		0.001	False		,,,				2504	0															0			X						G		0,3835		0,0,0,1632,571	182	141	155		1098	-0.2	0.2	X		155	1,6727		0,0,1,2428,1871	no	coding-synonymous	ARSH	NM_001011719.1		0,0,1,4060,2442	AA,AG,A,GG,G		0.0149,0.0,0.0095		366/563	2945415	1,10562	2203	4300	6503	2955415	SO:0001819	synonymous_variant	347527			AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"Arylsulfatase family"	32488	protein-coding gene	gene with protein product		300586	"arylsulfatase H"			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.1098G>A	X.37:g.2945415G>A			2955415		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																				0.507	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719		A	2945415	G	A	2945415	2	1	102	1	0	0	0	0	0	0	0	1	994	1132	40	1		1	ARSH	23	2945415	Silent	SNP	G	TCGA-DT-5265-01A-21D-1826-10		2945415	152325145	110	27091										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938881	12938881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ttcagaatagcaggcgtaacAcatcatctagaatttattca	6	8	4	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:12938881A>G	ENST00000218032.6	+	2	1809	c.1722A>G	c.(1720-1722)acA>acG	p.T574T	TLR8_ENST00000311912.5_Silent_p.T592T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	574					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.T592T(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGGCGTAACACATCATCTAG	0.328																																																1	Substitution - coding silent(1)	ovary(1)	X											42	43	42					X																	12938881		2203	4297	6500	12848802	SO:0001819	synonymous_variant	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1722A>G	X.37:g.12938881A>G			12848802	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																				0.328	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		G	12938881	A	G	12938881	2	3	102	1	0	0	0	0	0	0	0	1	15996	146	6	4		4	TLR8	23	12938881	Silent	SNP	A	TCGA-DT-5265-01A-21D-1826-10	9993466	12938881	142331679	111	27092										
TLR8	51311	hgsc.bcm.edu	37	chrX	12939056	12939056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	atgatgacaacaggtatatcTccattttcaaaggtctcaag	7	8	3	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:12939056T>C	ENST00000218032.6	+	2	1984	c.1897T>C	c.(1897-1899)Tcc>Ccc	p.S633P	TLR8_ENST00000311912.5_Missense_Mutation_p.S651P	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	633					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.S651T(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGGTATATCTCCATTTTCAA	0.403																																																1	Substitution - Missense(1)	ovary(1)	X											60	59	60					X																	12939056		2202	4298	6500	12848977	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1897T>C	X.37:g.12939056T>C	ENSP00000218032:p.Ser633Pro		12848977	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	T	3.559	-0.090147	0.07053	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.80214	-1.35;-1.35	5.82	-11.6	0.00059	.	1.256240	0.06147	N	0.673473	T	0.63534	0.2519	L	0.46157	1.445	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.52124	-0.8617	10	0.59425	D	0.04	.	0.3231	0.00306	0.3073:0.1443:0.206:0.3424	.	633;651	Q9NR97;D1CS70	TLR8_HUMAN;.	P	633;651	ENSP00000218032:S633P;ENSP00000312082:S651P	ENSP00000218032:S633P	S	+	1	0	TLR8	12848977	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.852000	0.04308	-1.861000	0.01153	0.486000	0.48141	TCC		0.403	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12939056	T	C	12939056	3	2	102	1	0	0	0	0	1	0	0	0	15996	1551	54	4	1903	4	TLR8	23	12939056	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	175	12939056	142331504	112	27093										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20185861	20185861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	acacatactttccatcatcaTatacctataaatttcaacat	0	11	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:20185861T>C	ENST00000379565.3	-	17	1655	c.1448A>G	c.(1447-1449)tAt>tGt	p.Y483C	RPS6KA3_ENST00000544447.1_Missense_Mutation_p.Y455C|RPS6KA3_ENST00000479809.1_5'UTR|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.Y453C|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.Y454C	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	483	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Y -> C (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Y483C(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TCCATCATCATATACCTATAA	0.284																																																1	Substitution - Missense(1)	stomach(1)	X	GRCh37	CD011196	RPS6KA3	D							108	118	115					X																	20185861		2203	4298	6501	20095782	SO:0001583	missense	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1448A>G	X.37:g.20185861T>C	ENSP00000368884:p.Tyr483Cys		20095782	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.492161	0.64074	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.61	5.61	0.85477	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.55386	0.1917	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.76494	0.999;0.995;0.997;0.998	D;D;D;D	0.72338	0.975;0.923;0.963;0.977	T	0.58498	-0.7626	10	0.87932	D	0	.	14.8128	0.70008	0.0:0.0:0.0:1.0	.	454;453;455;483	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	C	483;455;453;454	ENSP00000368884:Y483C;ENSP00000440220:Y455C;ENSP00000368865:Y453C;ENSP00000444837:Y454C	ENSP00000368865:Y453C	Y	-	2	0	RPS6KA3	20095782	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.170000	0.71920	1.880000	0.54463	0.417000	0.27973	TAT		0.284	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20185861	T	C	20185861	3	2	102	1	0	0	0	0	1	0	0	0	13689	1406	49	4	798	4	RPS6KA3	23	20185861	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	7246805	20185861	135084699	113	27094										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411677	23411677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	ctccaaggtgaagttcatcgTcttcaatccgtcctttgtat	7	11	3	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:23411677T>C	ENST00000379361.4	+	3	2902	c.2042T>C	c.(2041-2043)gTc>gCc	p.V681A		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	681					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						AAGTTCATCGTCTTCAATCCG	0.483																																																0			X											91	82	85					X																	23411677		2203	4300	6503	23321598	SO:0001583	missense	139411			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2042T>C	X.37:g.23411677T>C	ENSP00000368666:p.Val681Ala		23321598	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	37	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429925	0.43122	.	.	ENSG00000165186	ENST00000379361	D	0.88509	-2.39	5.34	5.34	0.76211	.	0.059808	0.64402	D	0.000002	D	0.84606	0.5509	L	0.34521	1.04	0.41461	D	0.988041	B	0.23937	0.094	B	0.32149	0.141	T	0.80369	-0.1411	10	0.25106	T	0.35	.	14.3778	0.66889	0.0:0.0:0.0:1.0	.	681	Q96NR3	PTHD1_HUMAN	A	681	ENSP00000368666:V681A	ENSP00000368666:V681A	V	+	2	0	PTCHD1	23321598	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.694000	0.84235	1.775000	0.52247	0.430000	0.28490	GTC		0.483	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		C	23411677	T	C	23411677	3	2	102	1	0	0	0	0	1	0	0	0	12766	1667	58	4	2052	4	PTCHD1	23	23411677	Missense_Mutation	SNP	T	TCGA-DT-5265-01A-21D-1826-10	3225816	23411677	131858883	114	27095										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29938089	29938089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcttaaggagcatcttggggAacaggaagtttccatctcat	10	8	3	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:29938089A>G	ENST00000378993.1	+	8	1608	c.935A>G	c.(934-936)gAa>gGa	p.E312G	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.E312G	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	312	Ig-like C2-type 3.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.E312A(1)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						CATCTTGGGGAACAGGAAGTT	0.383																																																1	Substitution - Missense(1)	ovary(1)	X											208	177	187					X																	29938089		2202	4300	6502	29848010	SO:0001583	missense	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.935A>G	X.37:g.29938089A>G	ENSP00000368278:p.Glu312Gly		29848010	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503756	0.85176	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.13196	2.61;2.61	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.38558	0.1045	M	0.75447	2.3	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.12863	-1.0531	9	.	.	.	.	15.3142	0.74059	1.0:0.0:0.0:0.0	.	312	Q9NZN1	IRPL1_HUMAN	G	312	ENSP00000368278:E312G;ENSP00000305200:E312G	.	E	+	2	0	IL1RAPL1	29848010	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.962000	0.93254	2.000000	0.58554	0.425000	0.28330	GAA		0.383	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		G	29938089	A	G	29938089	3	3	102	1	0	0	0	0	1	0	0	0	7682	246	9	4	961	4	IL1RAPL1	23	29938089	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	6526412	29938089	125332471	115	27096										
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71425229	71425229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	gccactgctttcctccacccCttcttctggataatcttcag	5	16	4	0			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:71425229C>T	ENST00000334463.3	-	2	3523	c.3388G>A	c.(3388-3390)Ggg>Agg	p.G1130R	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Missense_Mutation_p.G1007R	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	1130					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					TCCTCCACCCCTTCTTCTGGA	0.473																																																0			X											104	94	97					X																	71425229		2203	4300	6503	71341954	SO:0001583	missense	54821			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.3388G>A	X.37:g.71425229C>T	ENSP00000334675:p.Gly1130Arg		71341954	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.387981	0.25118	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	D;D	0.90563	-2.66;-2.69	5.22	4.33	0.51752	.	.	.	.	.	D	0.85750	0.5769	L	0.44542	1.39	0.09310	N	0.999999	B	0.29085	0.232	B	0.21360	0.034	T	0.73209	-0.4055	9	0.31617	T	0.26	-1.5171	12.2791	0.54753	0.0:0.8269:0.1731:0.0	.	1130	Q2NKX8	ERC6L_HUMAN	R	1007;1130	ENSP00000362761:G1007R;ENSP00000334675:G1130R	ENSP00000334675:G1130R	G	-	1	0	ERCC6L	71341954	0.600000	0.26899	0.004000	0.12327	0.023000	0.10783	2.486000	0.45259	0.943000	0.37553	0.594000	0.82650	GGG		0.473	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71425229	C	T	71425229	3	4	102	1	0	0	0	0	1	0	0	0	5231	681	24	3	368	3	ERCC6L	23	71425229	Missense_Mutation	SNP	C	TCGA-DT-5265-01A-21D-1826-10	41487140	71425229	83845331	116	27097										
ZDHHC15	158866	hgsc.bcm.edu	37	chrX	74742741	74742741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tacccaggcagagttcaaagAcgtaggcatagtaggaccag	12	9	1	2			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:74742741A>G	ENST00000373367.3	-	1	349	c.119T>C	c.(118-120)gTc>gCc	p.V40A	ZDHHC15_ENST00000482827.1_5'UTR|ZDHHC15_ENST00000373361.3_Missense_Mutation_p.V40A|ZDHHC15_ENST00000541184.1_Missense_Mutation_p.V40A	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	40					establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						GAGTTCAAAGACGTAGGCATA	0.562																																																0			X											102	79	87					X																	74742741		2203	4300	6503	74659466	SO:0001583	missense	158866			AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383		"Zinc fingers, DHHC-type"	20342	protein-coding gene	gene with protein product		300576					Standard	NM_144969		Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.119T>C	X.37:g.74742741A>G	ENSP00000362465:p.Val40Ala		74659466	B3KVG7|Q3SY30|Q6UWH3	Missense_Mutation	SNP	ENST00000373367.3	37	CCDS14430.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.010171	0.75046	.	.	ENSG00000102383	ENST00000373367;ENST00000541184;ENST00000373361	T;T;T	0.76839	0.7;0.98;-1.05	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.87075	0.6087	M	0.79926	2.475	0.80722	D	1	D;P;B	0.67145	0.996;0.928;0.096	D;P;B	0.75484	0.986;0.609;0.031	D	0.86510	0.1809	10	0.34782	T	0.22	-15.1225	12.4271	0.55553	1.0:0.0:0.0:0.0	.	40;40;40	Q96MV8-2;B3KVG7;Q96MV8	.;.;ZDH15_HUMAN	A	40	ENSP00000362465:V40A;ENSP00000445420:V40A;ENSP00000362459:V40A	ENSP00000362459:V40A	V	-	2	0	ZDHHC15	74659466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.618000	0.83043	1.840000	0.53500	0.430000	0.28490	GTC		0.562	ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057283.1	NM_144969		G	74742741	A	G	74742741	3	3	102	1	0	0	0	0	1	0	0	0	17644	275	10	4	1018	4	ZDHHC15	23	74742741	Missense_Mutation	SNP	A	TCGA-DT-5265-01A-21D-1826-10	3317512	74742741	80527819	117	27098										
ATRX	546	hgsc.bcm.edu	37	chrX	76888871	76888871	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	6	1	0.660949493035156	0	0.707331913599026	0.00699300699300699	0.0853146853146853	0	tcacagttgctaattcagaaAccttttgtggggaaataaag	9	6	2	1			TCGA-DT-5265-01A-21D-1826-10	TCGA-DT-5265-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	803b9cc5-41c6-4c0c-9211-dae9fb2db332	ea8c74bd-3603-4bcf-9631-b5982ed8258c	g.chrX:76888871A>G	ENST00000373344.5	-	19	5172	c.4958T>C	c.(4957-4959)gTt>gCt	p.V1653A	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Splice_Site_p.V1615A	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1653	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TAATTCAGAAACCTTTTGTGG	0.353			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)	X											152	150	150					X																	76888871		2203	4295	6498	76775527	SO:0001630	splice_region_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4957-1T>C	X.37:g.76888871A>G			76775527	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.296572	0.60086	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.94931	-3.56;-3.56	5.83	5.83	0.93111	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000003	D	0.96944	0.9002	M	0.74546	2.27	0.80722	D	1	D;D	0.89917	0.99;1.0	D;D	0.85130	0.968;0.997	D	0.97490	1.0053	10	0.87932	D	0	-4.7117	15.0984	0.72253	1.0:0.0:0.0:0.0	.	1615;1653	P46100-4;P46100	.;ATRX_HUMAN	A	1653;1615	ENSP00000362441:V1653A;ENSP00000378967:V1615A	ENSP00000362441:V1653A	V	-	2	0	ATRX	76775527	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.569000	0.90744	1.949000	0.56562	0.481000	0.45027	GTT		0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	Missense_Mutation	G	76888871	A	G	76888871	5	3	102	1	0	0	0	0	0	0	1	0	1209	57	2	4	2588	4	ATRX	23	76888871	Splice_Site	SNP	A	TCGA-DT-5265-01A-21D-1826-10	2146130	76888871	78381689	118	27099										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689289	23689289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acttttcccacactcgttacAgtcataaggcctctccccag	5	16	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:23689289A>G	ENST00000314011.4	-	4	722	c.586T>C	c.(586-588)Tgt>Cgt	p.C196R	ZNF436_ENST00000374608.3_Missense_Mutation_p.C196R	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	196			C -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C196G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CACTCGTTACAGTCATAAGGC	0.433																																																1	Substitution - Missense(1)	breast(1)	1											139	139	139					1																	23689289		2203	4300	6503	23561876	SO:0001583	missense	80818			AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.586T>C	1.37:g.23689289A>G	ENSP00000313582:p.Cys196Arg		23561876	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	37	CCDS233.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688438	0.68271	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	D;D;D	0.85258	-1.96;-1.96;-1.96	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000004	D	0.95111	0.8416	H	0.97415	4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96563	0.9417	10	0.87932	D	0	-23.981	14.0897	0.64982	1.0:0.0:0.0:0.0	.	196	Q9C0F3	ZN436_HUMAN	R	196	ENSP00000313582:C196R;ENSP00000363737:C196R;ENSP00000363736:C196R	ENSP00000313582:C196R	C	-	1	0	ZNF436	23561876	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.212000	0.71576	0.533000	0.62120	TGT		0.433	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		G	23689289	A	G	23689289	3	3	103	1	0	0	0	0	1	0	0	0	17948	188	7	4	830	4	ZNF436	1	23689289	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10		23689289	225561332	1	27100										
THRAP3	9967	hgsc.bcm.edu	37	chr1	36754874	36754874	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tataagctccgagatgacttTgagaagaagatggctgactt	11	6	0	6			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:36754874T>C	ENST00000354618.5	+	5	1478	c.1254T>C	c.(1252-1254)ttT>ttC	p.F418F	THRAP3_ENST00000469141.2_Silent_p.F418F	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	418	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.F418L(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GAGATGACTTTGAGAAGAAGA	0.418			T	USP6	aneurysmal bone cysts																																Pancreas(129;785 1795 20938 23278 32581)		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	1	Substitution - Missense(1)	ovary(1)	1											80	79	79					1																	36754874		2203	4300	6503	36527461	SO:0001819	synonymous_variant	9967			AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.1254T>C	1.37:g.36754874T>C			36527461	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	37	CCDS405.1																																																																																				0.418	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		C	36754874	T	C	36754874	2	2	103	1	0	0	0	0	0	0	0	1	15913	1809	63	4		4	THRAP3	1	36754874	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	13065585	36754874	212495747	2	27101										
USP24	23358	hgsc.bcm.edu	37	chr1	55643711	55643711	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctcgcttgtaagggatggacCaatgatcagtcaaaacacgg	11	9	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:55643711C>A	ENST00000294383.6	-	2	418	c.419G>T	c.(418-420)tGg>tTg	p.W140L	USP24_ENST00000407756.1_Intron	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	140					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AGGGATGGACCAATGATCAGT	0.423																																																0			1											191	178	182					1																	55643711		692	1591	2283	55416299	SO:0001583	missense	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.419G>T	1.37:g.55643711C>A	ENSP00000294383:p.Trp140Leu		55416299	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	C	32	5.142059	0.94560	.	.	ENSG00000162402	ENST00000294383	T	0.39056	1.1	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.62368	0.2422	M	0.66939	2.045	0.80722	D	1	.	.	.	.	.	.	T	0.63148	-0.6702	8	0.72032	D	0.01	.	19.869	0.96843	0.0:1.0:0.0:0.0	.	.	.	.	L	140	ENSP00000294383:W140L	ENSP00000294383:W140L	W	-	2	0	USP24	55416299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.463000	0.80869	2.709000	0.92574	0.591000	0.81541	TGG		0.423	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55643711	C	A	55643711	3	1	103	1	0	0	0	0	1	0	0	0	17095	595	21	2	7711	2	USP24	1	55643711	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	18888837	55643711	193606910	3	27102										
PTGFR	5737	hgsc.bcm.edu	37	chr1	78959187	78959187	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atggtaatccagctcctggcGataatgtgtgtctcctgtat	10	9	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:78959187G>A	ENST00000370757.3	+	2	996	c.759G>A	c.(757-759)gcG>gcA	p.A253A	PTGFR_ENST00000370758.1_Silent_p.A253A|PTGFR_ENST00000370756.3_Silent_p.A253A	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	253					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)	p.A253A(2)		breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	AGCTCCTGGCGATAATGTGTG	0.393																																																2	Substitution - coding silent(2)	skin(2)	1											52	49	50					1																	78959187		2203	4300	6503	78731775	SO:0001819	synonymous_variant	5737			AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.759G>A	1.37:g.78959187G>A			78731775	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	37	CCDS686.1																																																																																				0.393	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		A	78959187	G	A	78959187	2	1	103	1	0	0	0	0	0	0	0	1	12784	1045	37	1		1	PTGFR	1	78959187	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	23315476	78959187	170291434	4	27103										
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109394766	109394766	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgttttcaccatcccttttcGggttgagttggtcagtgagt	11	8	2	2	rs367879802		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:109394766G>T	ENST00000370001.3	-	2	789	c.521C>A	c.(520-522)cCg>cAg	p.P174Q	AKNAD1_ENST00000369994.1_Missense_Mutation_p.P174Q|AKNAD1_ENST00000369995.3_Missense_Mutation_p.P174Q|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	174						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						ATCCCTTTTCGGGTTGAGTTG	0.418																																																0			1											62	63	63					1																	109394766		2203	4295	6498	109196289	SO:0001583	missense	0			AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.521C>A	1.37:g.109394766G>T	ENSP00000359018:p.Pro174Gln		109196289	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	.	.	.	.	.	.	.	.	.	.	G	11.91	1.780860	0.31502	.	.	ENSG00000162641	ENST00000370001;ENST00000369994;ENST00000369995	T;T;T	0.07567	3.19;3.2;3.18	5.77	-0.0409	0.13870	.	1.091290	0.06883	N	0.802857	T	0.08582	0.0213	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.66716	0.946	T	0.25293	-1.0136	10	0.26408	T	0.33	-1.1097	4.9268	0.13898	0.2546:0.0:0.4217:0.3237	.	174	Q5T1N1	AKND1_HUMAN	Q	174	ENSP00000359018:P174Q;ENSP00000359011:P174Q;ENSP00000359012:P174Q	ENSP00000359011:P174Q	P	-	2	0	AKNAD1	109196289	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	1.891000	0.39738	0.309000	0.22966	-0.169000	0.13324	CCG		0.418	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		T	109394766	G	T	109394766	3	4	103	1	0	0	0	0	1	0	0	0	464	1116	39	2	2049	2	AKNAD1	1	109394766	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	30435579	109394766	139855855	5	27104										
RBM15	64783	hgsc.bcm.edu	37	chr1	110884866	110884866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggccaaatctgaagaagatTacctggtcatgatcattgtc	9	8	3	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:110884866T>A	ENST00000369784.3	+	1	3739	c.2839T>A	c.(2839-2841)Tac>Aac	p.Y947N	RBM15_ENST00000487146.2_Missense_Mutation_p.Y947N|RBM15_ENST00000602849.1_Missense_Mutation_p.Y947N	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	947	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			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)		TGAAGAAGATTACCTGGTCAT	0.473			T	MKL1	acute megakaryocytic leukemia																																		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	0			1											83	86	85					1																	110884866		2203	4300	6503	110686389	SO:0001583	missense	64783			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2839T>A	1.37:g.110884866T>A	ENSP00000358799:p.Tyr947Asn		110686389	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533732	0.45073	.	.	ENSG00000162775	ENST00000369784	T	0.20738	2.05	5.45	5.45	0.79879	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);	0.000000	0.41294	D	0.000907	T	0.24509	0.0594	L	0.42245	1.32	0.54753	D	0.999982	D;P	0.64830	0.994;0.678	P;B	0.57776	0.827;0.116	T	0.01791	-1.1273	10	0.72032	D	0.01	-5.7387	15.4898	0.75597	0.0:0.0:0.0:1.0	.	947;947	Q96T37-3;Q96T37	.;RBM15_HUMAN	N	947	ENSP00000358799:Y947N	ENSP00000358799:Y947N	Y	+	1	0	RBM15	110686389	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.230000	0.72301	2.066000	0.61787	0.533000	0.62120	TAC		0.473	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		A	110884866	T	A	110884866	3	1	103	1	0	0	0	0	1	0	0	0	13153	1754	61	5	2841	5	RBM15	1	110884866	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1490100	110884866	138365755	6	27105										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118570982	118570982	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaggtgggaacatccaaagtCtcttgtaaaacaggttctgg	11	7	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:118570982C>G	ENST00000336338.5	-	26	3710	c.3645G>C	c.(3643-3645)gaG>gaC	p.E1215D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1215						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CATCCAAAGTCTCTTGTAAAA	0.393																																																0			1											105	104	105					1																	118570982		2203	4300	6503	118372505	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3645G>C	1.37:g.118570982C>G	ENSP00000337804:p.Glu1215Asp		118372505	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.652551	0.29336	.	.	ENSG00000155761	ENST00000336338	T	0.32023	1.47	5.7	2.74	0.32292	.	0.908138	0.09653	N	0.773477	T	0.11410	0.0278	L	0.47716	1.5	0.23510	N	0.997527	B	0.27559	0.181	B	0.30646	0.118	T	0.37454	-0.9705	10	0.38643	T	0.18	.	6.4671	0.21987	0.0:0.6899:0.1486:0.1615	.	1215	Q6Q759	SPG17_HUMAN	D	1215	ENSP00000337804:E1215D	ENSP00000337804:E1215D	E	-	3	2	SPAG17	118372505	0.553000	0.26513	0.270000	0.24601	0.023000	0.10783	0.524000	0.22940	0.309000	0.22966	-0.126000	0.14955	GAG		0.393	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118570982	C	G	118570982	3	3	103	1	0	0	0	0	1	0	0	0	15018	912	32	5	3118	5	SPAG17	1	118570982	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	7686116	118570982	130679639	7	27106										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380806	147380806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccttgaagaggcctgtagagCagcccctgggggagattcct	14	11	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:147380806C>A	ENST00000369235.1	+	1	724	c.724C>A	c.(724-726)Cag>Aag	p.Q242K	GJA8_ENST00000240986.4_Missense_Mutation_p.Q242K			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	242					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCCTGTAGAGCAGCCCCTGGG	0.552																																					Melanoma(76;1255 1795 8195 52096)											0			1											60	59	59					1																	147380806		2203	4300	6503	145847430	SO:0001583	missense	2703			U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.724C>A	1.37:g.147380806C>A	ENSP00000358238:p.Gln242Lys		145847430	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	37	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	c	0.071	-1.202732	0.01581	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.97303	-4.33;-4.33	4.4	4.4	0.53042	.	1.571240	0.04405	N	0.364879	D	0.87313	0.6146	N	0.19112	0.55	0.34042	D	0.655108	B	0.31581	0.329	B	0.22753	0.041	T	0.66925	-0.5800	10	0.05959	T	0.93	.	14.0144	0.64515	0.0:0.8359:0.1641:0.0	.	242	P48165	CXA8_HUMAN	K	242	ENSP00000240986:Q242K;ENSP00000358238:Q242K	ENSP00000240986:Q242K	Q	+	1	0	GJA8	145847430	1.000000	0.71417	0.918000	0.36340	0.175000	0.22909	1.411000	0.34702	2.267000	0.75376	0.313000	0.20887	CAG		0.552	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		A	147380806	C	A	147380806	3	1	103	1	0	0	0	0	1	0	0	0	6425	711	25	2	726	2	GJA8	1	147380806	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	28809824	147380806	101869815	8	27107										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150529180	150529180	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cctacagggccggcgggaccGtctttcgatataaccgtcct	11	14	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:150529180G>A	ENST00000369038.2	+	8	1861	c.1660G>A	c.(1660-1662)Gtc>Atc	p.V554I	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.V554I|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.V554I|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.V577I			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	554					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	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)			CGGCGGGACCGTCTTTCGATA	0.642																																																0			1											87	102	97					1																	150529180		2203	4300	6503	148795804	SO:0001583	missense	54507			BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.1660G>A	1.37:g.150529180G>A	ENSP00000358034:p.Val554Ile		148795804	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	7.230	0.599161	0.13939	.	.	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	4.54	1.01	0.19927	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.18425	0.0442	L	0.37800	1.135	0.09310	N	1	B;B;B;B	0.28439	0.094;0.164;0.044;0.212	B;B;B;B	0.22601	0.04;0.016;0.027;0.029	T	0.15150	-1.0447	9	0.45353	T	0.12	.	6.9334	0.24453	0.4096:0.0:0.5904:0.0	.	577;577;554;554	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	I	554;554;92;577;554	ENSP00000358037:V554I;ENSP00000271643:V554I;ENSP00000358035:V577I;ENSP00000358034:V554I	ENSP00000271643:V554I	V	+	1	0	ADAMTSL4	148795804	0.037000	0.19845	0.093000	0.20910	0.077000	0.17291	1.051000	0.30417	0.022000	0.15160	0.462000	0.41574	GTC		0.642	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150529180	G	A	150529180	3	1	103	1	0	0	0	0	1	0	0	0	277	1145	40	1	1690	1	ADAMTSL4	1	150529180	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	3148374	150529180	98721441	9	27108										
RFX5	5993	hgsc.bcm.edu	37	chr1	151316903	151316903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcaaggatacttggactggcCccggccaccaagccttcgag	11	14	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:151316903C>T	ENST00000290524.4	-	7	641	c.463G>A	c.(463-465)Ggc>Agc	p.G155S	RFX5_ENST00000368870.2_Missense_Mutation_p.G155S|RP11-126K1.6_ENST00000455503.1_RNA|RFX5_ENST00000452671.2_Missense_Mutation_p.G155S|RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452513.2_Missense_Mutation_p.G115S|RFX5_ENST00000478564.1_5'Flank	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	155					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGGACTGGCCCCGGCCACCA	0.547																																																0			1											56	59	58					1																	151316903		2203	4300	6503	149583527	SO:0001583	missense	5993				CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.463G>A	1.37:g.151316903C>T	ENSP00000290524:p.Gly155Ser		149583527	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	.	.	.	.	.	.	.	.	.	.	C	34	5.405671	0.96051	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000436637;ENST00000452671;ENST00000452513;ENST00000392746;ENST00000422595;ENST00000450506;ENST00000458484	D;D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.91	5.91	0.95273	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.98507	0.9502	M	0.90705	3.14	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.97110	0.942;1.0	D	0.99170	1.0864	10	0.87932	D	0	-13.2369	18.8584	0.92262	0.0:1.0:0.0:0.0	.	115;155	B7Z848;P48382	.;RFX5_HUMAN	S	155;155;47;155;115;155;155;155;155	ENSP00000290524:G155S;ENSP00000357864:G155S;ENSP00000390769:G47S;ENSP00000389130:G155S;ENSP00000398388:G115S;ENSP00000376502:G155S;ENSP00000399095:G155S;ENSP00000398666:G155S;ENSP00000409187:G155S	ENSP00000290524:G155S	G	-	1	0	RFX5	149583527	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.105000	0.77031	2.804000	0.96469	0.462000	0.41574	GGC		0.547	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		T	151316903	C	T	151316903	3	4	103	1	0	0	0	0	1	0	0	0	13303	623	22	3	1407	3	RFX5	1	151316903	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	787723	151316903	97933718	10	27109										
HRNR	388697	hgsc.bcm.edu	37	chr1	152192382	152192382	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agagtgaccggagccagactCatatgggccacggcttgaag	14	10	1	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:152192382C>G	ENST00000368801.2	-	3	1798	c.1723G>C	c.(1723-1725)Gag>Cag	p.E575Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	575					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGCCAGACTCATATGGGCCA	0.582																																																0			1											191	194	193					1																	152192382		2203	4300	6503	150459006	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1723G>C	1.37:g.152192382C>G	ENSP00000357791:p.Glu575Gln		150459006	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.607	0.296725	0.10622	.	.	ENSG00000197915	ENST00000368801	T	0.01685	4.69	3.75	-0.304	0.12788	.	.	.	.	.	T	0.00271	0.0008	N	0.03608	-0.345	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.30238	-0.9985	9	0.13108	T	0.6	.	4.7784	0.13190	0.0:0.5501:0.1582:0.2916	.	575	Q86YZ3	HORN_HUMAN	Q	575	ENSP00000357791:E575Q	ENSP00000357791:E575Q	E	-	1	0	HRNR	150459006	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.260000	0.08708	-0.265000	0.09352	-1.140000	0.01884	GAG		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		G	152192382	C	G	152192382	3	3	103	1	0	0	0	0	1	0	0	0	7380	835	29	5	6833	5	HRNR	1	152192382	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	875479	152192382	97058239	11	27110										
ADAR	103	hgsc.bcm.edu	37	chr1	154570424	154570424	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cagaaaagaaggatgtggctGaaggggtgggggtctgggac	20	4	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:154570424G>C	ENST00000368474.4	-	4	2013	c.1814C>G	c.(1813-1815)tCa>tGa	p.S605*	ADAR_ENST00000368471.3_Nonsense_Mutation_p.S310*|ADAR_ENST00000292205.5_Nonsense_Mutation_p.S648*	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	605					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GGATGTGGCTGAAGGGGTGGG	0.478																																																0			1											42	42	42					1																	154570424		2203	4300	6503	152837048	SO:0001587	stop_gained	103			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1814C>G	1.37:g.154570424G>C	ENSP00000357459:p.Ser605*		152837048	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Nonsense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	G	37	6.072396	0.97256	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	.	.	.	5.27	5.27	0.74061	.	0.664062	0.15356	N	0.266655	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-14.7002	16.8542	0.86001	0.0:0.0:1.0:0.0	.	.	.	.	X	648;605;310;600	.	ENSP00000292205:S648X	S	-	2	0	ADAR	152837048	1.000000	0.71417	0.745000	0.31077	0.035000	0.12851	6.943000	0.75934	2.735000	0.93741	0.655000	0.94253	TCA		0.478	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		C	154570424	G	C	154570424	4	2	103	1	0	0	0	0	0	1	0	0	281	1294	45	5	1914	5	ADAR	1	154570424	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2378042	154570424	94680197	12	27111										
FAM189B	10712	hgsc.bcm.edu	37	chr1	155218028	155218028	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggcgccgtttctcggctgacCgggcacgtagcaacttgggg	16	12	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:155218028C>A	ENST00000361361.2	-	11	2155	c.1646G>T	c.(1645-1647)cGg>cTg	p.R549L	FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_Missense_Mutation_p.R531L|FAM189B_ENST00000350210.2_Missense_Mutation_p.R453L	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	549			R -> H (in dbSNP:rs2072648).			integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						CTCGGCTGACCGGGCACGTAG	0.627																																																0			1											20	27	24					1																	155218028		2202	4299	6501	153484652	SO:0001583	missense	0			AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 2"	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.1646G>T	1.37:g.155218028C>A	ENSP00000354958:p.Arg549Leu		153484652	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.328796	0.41197	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361;ENST00000323361;ENST00000491082	T;T;T;T	0.03358	3.96;3.96;3.96;3.96	4.4	-0.871	0.10642	.	0.805350	0.11448	N	0.563040	T	0.00967	0.0032	N	0.08118	0	0.28236	N	0.92591	P;B;B;B	0.41546	0.754;0.089;0.433;0.089	B;B;B;B	0.44315	0.446;0.063;0.257;0.063	T	0.48736	-0.9009	10	0.72032	D	0.01	.	7.6332	0.28251	0.0:0.5161:0.0:0.4839	.	314;531;453;549	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	L	453;531;549;232;271	ENSP00000307128:R453L;ENSP00000357352:R531L;ENSP00000354958:R549L;ENSP00000427011:R271L	ENSP00000323164:R232L	R	-	2	0	FAM189B	153484652	0.781000	0.28676	0.747000	0.31113	0.641000	0.38312	0.049000	0.14099	-0.242000	0.09667	-0.274000	0.10170	CGG		0.627	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		A	155218028	C	A	155218028	3	1	103	1	0	0	0	0	1	0	0	0	5533	652	23	2	368	2	FAM189B	1	155218028	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	647604	155218028	94032593	13	27112										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155891282	155891282	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taatgaaacagctggtggcaCtatgcttggtactccgtagg	12	8	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:155891282C>T	ENST00000368321.3	-	10	1173	c.1150G>A	c.(1150-1152)Gtg>Atg	p.V384M	KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368319.3_Missense_Mutation_p.S350N|SNORA42_ENST00000384744.1_RNA|KIAA0907_ENST00000368320.3_Missense_Mutation_p.V384M	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	384	Pro-rich.						RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			GCTGGTGGCACTATGCTTGGT	0.522																																																0			1											127	113	118					1																	155891282		2203	4300	6503	154157906	SO:0001583	missense	22889			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1150G>A	1.37:g.155891282C>T	ENSP00000357304:p.Val384Met		154157906	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	37	CCDS30885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.63|18.63	3.666324|3.666324	0.67814|0.67814	.|.	.|.	ENSG00000132680|ENSG00000132680	ENST00000368319|ENST00000368321;ENST00000368320	.|.	.|.	.|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	.|0.288814	.|0.34484	.|N	.|0.003921	T|T	0.34513|0.34513	0.0900|0.0900	N|N	0.14661|0.14661	0.345|0.345	0.27709|0.27709	N|N	0.945526|0.945526	P|D;D	0.36144|0.65815	0.539|0.995;0.985	B|D;D	0.35353|0.63877	0.201|0.919;0.919	T|T	0.29852|0.29852	-0.9998|-0.9998	8|9	0.19590|0.37606	T|T	0.45|0.19	-9.3521|-9.3521	18.9299|18.9299	0.92561|0.92561	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	350|384;384	Q7Z7F0-3|Q7Z7F0-2;Q7Z7F0	.|.;K0907_HUMAN	N|M	350|384	.|.	ENSP00000357302:S350N|ENSP00000357303:V384M	S|V	-|-	2|1	0|0	KIAA0907|KIAA0907	154157906|154157906	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.614000|2.614000	0.46359|0.46359	2.556000|2.556000	0.86216|0.86216	0.491000|0.491000	0.48974|0.48974	AGT|GTG		0.522	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		T	155891282	C	T	155891282	3	4	103	1	0	0	0	0	1	0	0	0	8220	565	20	3	714	3	KIAA0907	1	155891282	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	673254	155891282	93359339	14	27113										
ILDR2	387597	hgsc.bcm.edu	37	chr1	166890006	166890006	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gctgtggtagggcaggtcgcGgccgcggtaggacgggccgc	21	11	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:166890006G>C	ENST00000271417.3	-	9	1877	c.1822C>G	c.(1822-1824)Cgc>Ggc	p.R608G	ILDR2_ENST00000525740.1_Missense_Mutation_p.R481G|ILDR2_ENST00000469934.2_Intron|ILDR2_ENST00000529071.1_Missense_Mutation_p.R589G|ILDR2_ENST00000529387.1_Intron|ILDR2_ENST00000528703.1_Missense_Mutation_p.R549G|ILDR2_ENST00000526687.1_Missense_Mutation_p.R500G	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	608					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						GGCAGGTCGCGGCCGCGGTAG	0.682																																																0			1											6	8	8					1																	166890006		2079	4110	6189	165156630	SO:0001583	missense	387597			AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.1822C>G	1.37:g.166890006G>C	ENSP00000271417:p.Arg608Gly		165156630		Missense_Mutation	SNP	ENST00000271417.3	37	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502754	0.44558	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T	0.78816	0.42;-1.21;0.41;-1.21;-0.21	4.76	3.84	0.44239	.	1.259550	0.05306	N	0.523995	T	0.80763	0.4685	M	0.61703	1.905	0.35815	D	0.824187	D	0.71674	0.998	D	0.76071	0.987	T	0.62248	-0.6894	9	0.87932	D	0	.	8.2155	0.31509	0.0:0.131:0.4904:0.3786	.	608	Q71H61	ILDR2_HUMAN	G	608;481;589;500;549	ENSP00000271417:R608G;ENSP00000436120:R481G;ENSP00000436882:R589G;ENSP00000434273:R500G;ENSP00000432750:R549G	ENSP00000271417:R608G	R	-	1	0	ILDR2	165156630	0.901000	0.30685	0.952000	0.39060	0.625000	0.37756	1.350000	0.34010	0.959000	0.37980	-0.314000	0.08810	CGC		0.682	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		C	166890006	G	C	166890006	3	2	103	1	0	0	0	0	1	0	0	0	7731	1116	39	5	105	5	ILDR2	1	166890006	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	10998724	166890006	82360615	15	27114										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193051701	193051701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttccgaattagatcccagcaGgtggaactgattgctctctt	9	10	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:193051701G>A	ENST00000367446.3	+	8	1537	c.1327G>A	c.(1327-1329)Ggt>Agt	p.G443S	TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367445.3_Missense_Mutation_p.G443S|TROVE2_ENST00000416058.2_Missense_Mutation_p.G168S|TROVE2_ENST00000367441.1_Missense_Mutation_p.G443S|TROVE2_ENST00000400968.2_Missense_Mutation_p.G443S|TROVE2_ENST00000432079.1_Missense_Mutation_p.G168S|TROVE2_ENST00000367443.1_Missense_Mutation_p.G443S|TROVE2_ENST00000367444.3_Missense_Mutation_p.G443S	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	443	VWFA-like domain. {ECO:0000250}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						GATCCCAGCAGGTGGAACTGA	0.358																																																0			1											74	67	69					1																	193051701		1845	4083	5928	191318324	SO:0001583	missense	6738			BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.1327G>A	1.37:g.193051701G>A	ENSP00000356416:p.Gly443Ser		191318324	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	37	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848123	0.91277	.	.	ENSG00000116747	ENST00000400968;ENST00000416058;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.80071	0.4556	M	0.74389	2.26	0.80722	D	1	D;D;D;D	0.89917	0.987;0.987;0.999;1.0	D;D;D;D	0.80764	0.96;0.96;0.983;0.994	T	0.80223	-0.1471	9	0.54805	T	0.06	-27.3745	19.7303	0.96180	0.0:0.0:1.0:0.0	.	443;443;443;443	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	S	443;168;443;443;443;443;443	.	ENSP00000356411:G443S	G	+	1	0	TROVE2	191318324	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	7.836000	0.86788	2.724000	0.93272	0.557000	0.71058	GGT		0.358	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		A	193051701	G	A	193051701	3	1	103	1	0	0	0	0	1	0	0	0	16616	1000	35	3	1353	3	TROVE2	1	193051701	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	26161695	193051701	56198920	16	27115										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196448323	196448323	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acttaccttataactaagatAaccaagtaatattgtttcaa	3	7	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:196448323A>T	ENST00000294725.9	-	5	1285	c.370T>A	c.(370-372)Tat>Aat	p.Y124N	KCNT2_ENST00000609185.1_Missense_Mutation_p.Y124N|KCNT2_ENST00000451324.2_5'UTR|KCNT2_ENST00000367431.4_Missense_Mutation_p.Y124N|KCNT2_ENST00000367433.5_Missense_Mutation_p.Y124N			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	124					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TAACTAAGATAACCAAGTAAT	0.294																																																0			1											53	53	53					1																	196448323		2200	4299	6499	194714946	SO:0001583	missense	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.370T>A	1.37:g.196448323A>T	ENSP00000294725:p.Tyr124Asn		194714946	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	A	16.61	3.172016	0.57584	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.21031	2.03;2.07;2.27	5.06	5.06	0.68205	.	0.000000	0.64402	D	0.000017	T	0.47229	0.1434	M	0.86178	2.8	0.80722	D	1	P;P;P;P	0.51537	0.91;0.946;0.886;0.91	P;P;P;P	0.61800	0.616;0.894;0.726;0.616	T	0.53279	-0.8461	10	0.72032	D	0.01	-10.1573	13.0716	0.59064	1.0:0.0:0.0:0.0	.	124;124;124;124	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	N	124	ENSP00000356403:Y124N;ENSP00000356401:Y124N;ENSP00000294725:Y124N	ENSP00000294725:Y124N	Y	-	1	0	KCNT2	194714946	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.182000	0.71995	2.251000	0.74343	0.482000	0.46254	TAT		0.294	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196448323	A	T	196448323	3	4	103	1	0	0	0	0	1	0	0	0	8113	362	13	5	3133	5	KCNT2	1	196448323	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	3396622	196448323	52802298	17	27116										
ATP6V1G3	127124	hgsc.bcm.edu	37	chr1	198509734	198509734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctagcttgtccttggcccgtTtttctgcctgaagaagctgg	11	11	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:198509734T>C	ENST00000367382.1	-	1	131	c.47A>G	c.(46-48)aAa>aGa	p.K16R	ATP6V1G3_ENST00000367381.1_Missense_Mutation_p.K16R|ATP6V1G3_ENST00000281087.2_Missense_Mutation_p.K16R|ATP6V1G3_ENST00000489986.1_Missense_Mutation_p.K16R|ATP6V1G3_ENST00000309309.7_Missense_Mutation_p.K16R			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	16					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	7						CTTGGCCCGTTTTTCTGCCTG	0.493																																																0			1											219	191	201					1																	198509734		2203	4300	6503	196776357	SO:0001583	missense	127124			AY039760	CCDS1395.1, CCDS1396.1	1q32.2	2010-04-21	2006-01-13		ENSG00000151418	ENSG00000151418		"ATPases / V-type"	18265	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 13kD, V1 subunit G isoform 3", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3"			9442887	Standard	NM_133262		Approved	ATP6G3, Vma10	uc001gup.3	Q96LB4	OTTHUMG00000035661	ENST00000367382.1:c.47A>G	1.37:g.198509734T>C	ENSP00000356352:p.Lys16Arg		196776357	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049133	0.75846	.	.	ENSG00000151418	ENST00000367382;ENST00000309309;ENST00000367381;ENST00000281087;ENST00000489986	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	5.94	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	M	0.80982	2.52	0.45634	D	0.998565	D;D;P	0.89917	1.0;1.0;0.873	D;D;P	0.91635	0.998;0.999;0.49	T	0.70722	-0.4794	10	0.87932	D	0	-37.6773	10.0726	0.42341	0.0:0.0789:0.0:0.9211	.	16;16;16	Q96LB4-4;Q96LB4;Q96LB4-3	.;VATG3_HUMAN;.	R	16	ENSP00000356352:K16R;ENSP00000309574:K16R;ENSP00000356351:K16R;ENSP00000281087:K16R;ENSP00000417171:K16R	ENSP00000281087:K16R	K	-	2	0	ATP6V1G3	196776357	1.000000	0.71417	0.998000	0.56505	0.844000	0.47949	3.732000	0.55021	1.081000	0.41110	0.397000	0.26171	AAA		0.493	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326		C	198509734	T	C	198509734	3	2	103	1	0	0	0	0	1	0	0	0	1189	1841	64	4	371	4	ATP6V1G3	1	198509734	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	2061411	198509734	50740887	18	27117										
DDX59	83479	hgsc.bcm.edu	37	chr1	200619724	200619724	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggaattgtggctgaaaccaaAatggtctgacaatcattagg	11	6	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:200619724A>G	ENST00000331314.6	-	5	1356	c.1143T>C	c.(1141-1143)atT>atC	p.I381I	DDX59_ENST00000447706.2_Silent_p.I381I|DDX59_ENST00000367348.3_Silent_p.I381I	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	381	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						CTGAAACCAAAATGGTCTGAC	0.368																																																0			1											99	91	93					1																	200619724		2203	4300	6503	198886347	SO:0001819	synonymous_variant	83479			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.1143T>C	1.37:g.200619724A>G			198886347	Q6PJL2|Q8IVW3|Q9H0W3	Silent	SNP	ENST00000331314.6	37	CCDS30964.1																																																																																				0.368	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		G	200619724	A	G	200619724	2	3	103	1	0	0	0	0	0	0	0	1	4382	10	1	4		4	DDX59	1	200619724	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2109990	200619724	48630897	19	27118										
DISP1	84976	hgsc.bcm.edu	37	chr1	223179007	223179008	+	Missense_Mutation	DNP	GC	GC	AG													0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgtaaaaatagagacgtgaGcaatctggagagcagtggag							TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:223179007_223179008GC>AG	ENST00000284476.6	+	8	4432_4433	c.4268_4269GC>AG	c.(4267-4269)aGC>aAG	p.S1423K		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1423					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		AGAGACGTGAGCAATCTGGAGA	0.475																																																0			1																																								221245630|221245631	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	Exception_encountered	1.37:g.223179007_223179008delinsAG	ENSP00000284476:p.Ser1423Lys		221245630|221245631	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																				0.475	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		AG	223179008	GC	AG	223179007	3	1	103	1	0	0	0	0	1	0	0	0	4550	971	34	3	4294	3	DISP1	1	223179007	Missense_Mutation	DNP	GC	TCGA-DY-A0XA-01A-11D-A152-10	22559283	223179007	26071614	20	27119										
TLR5	7100	hgsc.bcm.edu	37	chr1	223284971	223284971	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agctgggattctctgaagggGtttgatctccactacaggag	13	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:223284971G>T	ENST00000540964.1	-	4	1864	c.1403C>A	c.(1402-1404)aCc>aAc	p.T468N	TLR5_ENST00000342210.6_Missense_Mutation_p.T468N			O60602	TLR5_HUMAN	toll-like receptor 5	468			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		CTCTGAAGGGGTTTGATCTCC	0.418																																																0			1											81	84	83					1																	223284971		2203	4300	6503	221351594	SO:0001583	missense	7100				CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1403C>A	1.37:g.223284971G>T	ENSP00000440643:p.Thr468Asn		221351594	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.533453	0.00951	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.24538	1.85;1.85;1.85	5.49	-1.32	0.09201	.	1.826510	0.02367	N	0.077472	T	0.10723	0.0262	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.14839	-1.0458	10	0.16420	T	0.52	.	1.3943	0.02257	0.1559:0.2995:0.2098:0.3348	.	468	O60602	TLR5_HUMAN	N	468	ENSP00000440643:T468N;ENSP00000355846:T468N;ENSP00000340089:T468N	ENSP00000340089:T468N	T	-	2	0	TLR5	221351594	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.109000	0.15417	0.018000	0.15052	-0.181000	0.13052	ACC		0.418	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		T	223284971	G	T	223284971	3	4	103	1	0	0	0	0	1	0	0	0	15993	1261	44	2	1177	2	TLR5	1	223284971	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	105964	223284971	25965650	21	27120										
LYST	1130	hgsc.bcm.edu	37	chr1	235938335	235938335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtatttaattaatgagagtaTaactcgcagtgctaatgctt	8	5	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:235938335T>C	ENST00000389794.3	-	18	5686	c.5512A>G	c.(5512-5514)Ata>Gta	p.I1838V	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.I1838V			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1838					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.I1838V(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AATGAGAGTATAACTCGCAGT	0.328																																																1	Substitution - Missense(1)	breast(1)	1											107	106	107					1																	235938335		2202	4296	6498	234004958	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.5512A>G	1.37:g.235938335T>C	ENSP00000374444:p.Ile1838Val		234004958	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746021	0.30955	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61859	0.07;0.07	5.21	-0.0126	0.13988	.	0.501380	0.23230	N	0.050464	T	0.40015	0.1100	L	0.31294	0.92	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.14783	-1.0460	10	0.62326	D	0.03	.	7.4996	0.27509	0.0:0.0747:0.4246:0.5007	.	1838	Q99698	LYST_HUMAN	V	1838	ENSP00000374444:I1838V;ENSP00000374443:I1838V	ENSP00000374443:I1838V	I	-	1	0	LYST	234004958	1.000000	0.71417	0.478000	0.27316	0.966000	0.64601	2.262000	0.43285	-0.020000	0.14032	0.477000	0.44152	ATA		0.328	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235938335	T	C	235938335	3	2	103	1	0	0	0	0	1	0	0	0	9158	1406	49	4	6037	4	LYST	1	235938335	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	12653364	235938335	13312286	22	27121										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	103	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-DY-A0XA-01A-11D-A152-10	4432579	240370914	8879707	23	27122										
TAF1B	9014	hgsc.bcm.edu	37	chr2	10059941	10059941	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggcttagtacacagaaattCtgcagatggtaataatgctt	9	6	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:10059941C>T	ENST00000263663.5	+	14	1745	c.1557C>T	c.(1555-1557)ttC>ttT	p.F519F	TAF1B_ENST00000396242.3_Silent_p.F264F	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	519					gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)	p.F519F(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CACAGAAATTCTGCAGATGGT	0.378																																																1	Substitution - coding silent(1)	breast(1)	2											49	47	48					2																	10059941		2203	4300	6503	9977392	SO:0001819	synonymous_variant	9014			L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.1557C>T	2.37:g.10059941C>T			9977392	B4DI42|F8WD72|Q15574|Q8WVC3	Silent	SNP	ENST00000263663.5	37	CCDS33143.1																																																																																				0.378	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		T	10059941	C	T	10059941	2	4	103	1	0	0	0	0	0	0	0	1	15559	912	32	3		3	TAF1B	2	10059941	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		10059941	233139432	24	27123										
GEN1	348654	hgsc.bcm.edu	37	chr2	17953922	17953922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcacctaaggatcatgaacGtaatggatgcagattatgta	9	6	2	2	rs202239270	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:17953922G>A	ENST00000381254.2	+	8	1038	c.824G>A	c.(823-825)cGt>cAt	p.R275H	GEN1_ENST00000317402.7_Missense_Mutation_p.R275H|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	275			R -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R275fs*37(2)|p.R275L(1)		breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GATCATGAACGTAATGGATGC	0.348								Homologous recombination					G|||	2	0.000399361	8e-04	0	5008	,	,		18094	0		0.001	False		,,,				2504	0															3	Deletion - Frameshift(2)|Substitution - Missense(1)	breast(3)	2						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	87	78	81		824,824	3.7	1	2		81	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	GEN1	NM_001130009.1,NM_182625.3	29,29	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign,benign	275/909,275/909	17953922	3,13003	2203	4300	6503	17817403	SO:0001583	missense	348654			AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"Holliday junction resolvase"	612449	"Gen endonuclease homolog 1 (Drosophila)"			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.824G>A	2.37:g.17953922G>A	ENSP00000370653:p.Arg275His		17817403	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	15.89	2.967665	0.53507	2.27E-4	2.33E-4	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000528873	T;T;T	0.45276	0.9;0.9;0.9	5.49	3.7	0.42460	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.150617	0.43579	N	0.000542	T	0.32912	0.0845	L	0.41027	1.25	0.36958	D	0.893206	B	0.25521	0.128	B	0.17098	0.017	T	0.26430	-1.0103	10	0.52906	T	0.07	-6.3158	11.0856	0.48084	0.2058:0.0:0.7942:0.0	.	275	Q17RS7	GEN_HUMAN	H	275;275;46	ENSP00000318977:R275H;ENSP00000370653:R275H;ENSP00000431542:R46H	ENSP00000318977:R275H	R	+	2	0	GEN1	17817403	0.348000	0.24861	0.996000	0.52242	0.994000	0.84299	0.648000	0.24828	0.695000	0.31675	0.655000	0.94253	CGT		0.348	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		A	17953922	G	A	17953922	3	1	103	1	0	0	0	0	1	0	0	0	6355	1145	40	1	850	1	GEN1	2	17953922	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	7893981	17953922	225245451	25	27124										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37234317	37234317	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaccagatattgctgctgcTtctgtagactctgagcacgt	9	10	2	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:37234317T>C	ENST00000233099.5	-	29	4748	c.4653A>G	c.(4651-4653)gaA>gaG	p.E1551E	HEATR5B_ENST00000354531.2_Silent_p.E1551E	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1551						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTGCTGCTGCTTCTGTAGACT	0.433																																																0			2											146	134	138					2																	37234317		2203	4300	6503	37087821	SO:0001819	synonymous_variant	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4653A>G	2.37:g.37234317T>C			37087821	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																				0.433	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37234317	T	C	37234317	2	2	103	1	0	0	0	0	0	0	0	1	7053	1606	56	4		4	HEATR5B	2	37234317	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	19280395	37234317	205965056	26	27125										
MSH2	4436	hgsc.bcm.edu	37	chr2	47657020	47657020	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caaacttacaagattgttacCgactctatcagggtataaat	6	8	2	1	rs63751108		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:47657020C>A	ENST00000233146.2	+	7	1439	c.1216C>A	c.(1216-1218)Cga>Aga	p.R406R	MSH2_ENST00000543555.1_Silent_p.R340R|MSH2_ENST00000406134.1_Silent_p.R406R	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	406					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)|p.R406*(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGATTGTTACCGACTCTATCA	0.368			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	5	Whole gene deletion(2)|Unknown(2)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)	2	GRCh37	CM930497	MSH2	M	rs63751108						85	79	81					2																	47657020		2203	4300	6503	47510524	SO:0001819	synonymous_variant	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1216C>A	2.37:g.47657020C>A			47510524	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																				0.368	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			A	47657020	C	A	47657020	2	1	103	1	0	0	0	0	0	0	0	1	9900	644	23	2		2	MSH2	2	47657020	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10422703	47657020	195542353	27	27126										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48848421	48848421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttgcaccaaacattgcaatCgtcaacaggttggataccat	7	11	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:48848421C>T	ENST00000403751.3	+	3	276	c.239C>T	c.(238-240)tCg>tTg	p.S80L	STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.S784L|GTF2A1L_ENST00000468326.1_3'UTR|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.S46L|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.S784L|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.S784L|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.S784L|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.S784L	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	80					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACATTGCAATCGTCAACAGGT	0.383																																																0			2											75	75	75					2																	48848421		2203	4300	6503	48701925	SO:0001583	missense	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.239C>T	2.37:g.48848421C>T	ENSP00000384597:p.Ser80Leu		48701925	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378136	0.24944	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000448460;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.99;0.91;0.95;0.91;0.91	3.59	3.59	0.41128	.	0.480024	0.20172	N	0.097715	T	0.41190	0.1148	L	0.56769	1.78	0.09310	N	0.99999	P;P;P;D;P	0.53462	0.625;0.659;0.919;0.96;0.816	B;B;B;P;B	0.44394	0.088;0.025;0.202;0.448;0.209	T	0.37267	-0.9713	10	0.52906	T	0.07	.	10.8977	0.47031	0.0:0.8087:0.1913:0.0	.	46;784;784;80;784	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	L	784;784;784;784;784;79;46;80;46;80	ENSP00000385499:S784L;ENSP00000385701:S784L;ENSP00000378236:S784L;ENSP00000311493:S784L;ENSP00000378234:S784L;ENSP00000412645:S46L;ENSP00000396702:S80L;ENSP00000387896:S46L;ENSP00000384597:S80L	ENSP00000384597:S80L	S	+	2	0	STON1-GTF2A1L;GTF2A1L	48701925	0.974000	0.33945	0.679000	0.29978	0.362000	0.29581	2.179000	0.42528	1.997000	0.58415	0.563000	0.77884	TCG		0.383	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		T	48848421	C	T	48848421	3	4	103	1	0	0	0	0	1	0	0	0	6874	893	31	1	249	1	GTF2A1L	2	48848421	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1191401	48848421	194350952	28	27127										
GPAT2	150763	hgsc.bcm.edu	37	chr2	96690546	96690546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatgcttgaagagcagcagcGttgccataatggccgtgctc	13	10	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:96690546G>A	ENST00000434632.1	-	15	1862	c.1403C>T	c.(1402-1404)aCg>aTg	p.T468M	GPAT2_ENST00000453542.1_Missense_Mutation_p.T397M|GPAT2_ENST00000359548.4_Missense_Mutation_p.T468M|GPAT2_ENST00000377137.3_Missense_Mutation_p.T468M|FAHD2CP_ENST00000607780.1_RNA			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	468					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						GAGCAGCAGCGTTGCCATAAT	0.652																																																0			2											119	128	125					2																	96690546		2054	4185	6239	96054273	SO:0001583	missense	0			BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"cancer/testis antigen 123"					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.1403C>T	2.37:g.96690546G>A	ENSP00000389395:p.Thr468Met		96054273	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	g	13.79	2.342914	0.41498	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542;ENST00000377137	T;T;T;T	0.77750	-1.11;-1.11;-0.11;-1.12	5.36	5.36	0.76844	.	0.261640	0.38959	N	0.001519	D	0.83538	0.5276	L	0.44542	1.39	0.09310	N	0.999994	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.81914	0.966;0.95;0.917;0.95;0.995	T	0.76782	-0.2832	10	0.72032	D	0.01	-6.0044	14.5886	0.68347	0.0:0.0:1.0:0.0	.	397;468;468;468;397	E9PE95;Q6NUI2-3;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;.;GPAT2_HUMAN;.	M	468;468;397;468	ENSP00000352547:T468M;ENSP00000389395:T468M;ENSP00000393770:T397M;ENSP00000366341:T468M	ENSP00000352547:T468M	T	-	2	0	GPAT2	96054273	0.786000	0.28738	0.464000	0.27143	0.192000	0.23643	5.405000	0.66351	2.525000	0.85131	0.637000	0.83480	ACG		0.652	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		A	96690546	G	A	96690546	3	1	103	1	0	0	0	0	1	0	0	0	6609	1145	40	1	1020	1	GPAT2	2	96690546	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	47842125	96690546	146508827	29	27128										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101883145	101883145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tctggtgtatttagctacttGgtgagttggaaaaagacccc	11	7	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:101883145G>A	ENST00000289382.3	+	5	1205	c.1042G>A	c.(1042-1044)Ggt>Agt	p.G348S		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	348					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											TTAGCTACTTGGTGAGTTGGA	0.388																																																0			2											102	104	103					2																	101883145		2203	4300	6503	101249577	SO:0001583	missense	55571			AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1042G>A	2.37:g.101883145G>A	ENSP00000289382:p.Gly348Ser		101249577	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	37	CCDS2050.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.30|12.30	1.895949|1.895949	0.33442|0.33442	.|.	.|.	ENSG00000158435|ENSG00000158435	ENST00000289382|ENST00000420107	.|.	.|.	.|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.051925|.	0.85682|.	D|.	0.000000|.	T|.	0.34832|.	0.0911|.	N|N	0.01705|0.01705	-0.755|-0.755	0.80722|0.80722	D|D	1|1	B|.	0.13145|.	0.007|.	B|.	0.08055|.	0.003|.	T|.	0.34650|.	-0.9820|.	9|.	0.09338|.	T|.	0.73|.	-17.4915|-17.4915	20.3931|20.3931	0.98965|0.98965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	348|.	Q9UKZ1|.	CB029_HUMAN|.	S|X	348|27	.|.	ENSP00000289382:G348S|.	G|W	+|+	1|2	0|0	C2orf29|C2orf29	101249577|101249577	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.992000|0.992000	0.81027|0.81027	7.930000|7.930000	0.87610|0.87610	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GGT|TGG		0.388	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		A	101883145	G	A	101883145	3	1	103	1	0	0	0	0	1	0	0	0	2167	1348	47	3	1060	3	C2orf29	2	101883145	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5192599	101883145	141316228	30	27129										
MERTK	10461	hgsc.bcm.edu	37	chr2	112687110	112687110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagttacagcaataatcgctTccttcaggtatgtgttcttt	7	8	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:112687110T>C	ENST00000295408.4	+	2	732	c.475T>C	c.(475-477)Tcc>Ccc	p.S159P	MERTK_ENST00000409780.1_Intron|MERTK_ENST00000421804.2_Missense_Mutation_p.S159P|RN7SL297P_ENST00000483161.2_RNA			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	159	Ig-like C2-type 1.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						AATAATCGCTTCCTTCAGGTA	0.343																																																0			2											107	94	98					2																	112687110		2203	4300	6503	112403581	SO:0001583	missense	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.475T>C	2.37:g.112687110T>C	ENSP00000295408:p.Ser159Pro		112403581	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	T	9.005	0.981111	0.18812	.	.	ENSG00000153208	ENST00000295408;ENST00000421804	T;T	0.69435	-0.4;-0.4	4.44	0.611	0.17586	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.665962	0.11708	U	0.537240	T	0.45558	0.1348	L	0.31752	0.955	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.43442	-0.9391	10	0.27785	T	0.31	-4.2235	0.9055	0.01283	0.3298:0.097:0.1712:0.402	.	159	Q12866	MERTK_HUMAN	P	159	ENSP00000295408:S159P;ENSP00000389152:S159P	ENSP00000295408:S159P	S	+	1	0	MERTK	112403581	0.255000	0.24002	0.988000	0.46212	0.958000	0.62258	0.391000	0.20784	0.738000	0.32606	-0.376000	0.06991	TCC		0.343	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			C	112687110	T	C	112687110	3	2	103	1	0	0	0	0	1	0	0	0	9509	1783	62	4	481	4	MERTK	2	112687110	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	10803965	112687110	130512263	31	27130										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118716002	118716002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aggaaatgactttccggcgaTgtagctgggaggttcctaat	13	7	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:118716002T>C	ENST00000376300.2	-	12	1081	c.944A>G	c.(943-945)cAt>cGt	p.H315R	CCDC93_ENST00000460781.1_5'UTR|CCDC93_ENST00000319432.5_Missense_Mutation_p.H314R	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	315			H -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.					p.H315R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						TTTCCGGCGATGTAGCTGGGA	0.398																																																1	Substitution - Missense(1)	large_intestine(1)	2											124	109	114					2																	118716002		2203	4300	6503	118432472	SO:0001583	missense	54520			BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.944A>G	2.37:g.118716002T>C	ENSP00000365477:p.His315Arg		118432472	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	37	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	T	12.41	1.930166	0.34096	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.19938	2.11;2.11	5.33	5.33	0.75918	.	0.104609	0.64402	N	0.000003	T	0.21468	0.0517	L	0.29908	0.895	0.34245	D	0.678123	P	0.43938	0.822	P	0.47941	0.562	T	0.23119	-1.0197	10	0.32370	T	0.25	-4.8735	11.6751	0.51425	0.0:0.0:0.0:1.0	.	315	Q567U6	CCD93_HUMAN	R	315;314	ENSP00000365477:H315R;ENSP00000324135:H314R	ENSP00000324135:H314R	H	-	2	0	CCDC93	118432472	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	4.776000	0.62354	2.250000	0.74265	0.456000	0.33151	CAT		0.398	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		C	118716002	T	C	118716002	3	2	103	1	0	0	0	0	1	0	0	0	2878	1464	51	4	1003	4	CCDC93	2	118716002	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	6028892	118716002	124483371	32	27131										
THSD7B	80731	hgsc.bcm.edu	37	chr2	137990530	137990530	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgtttgtgtaatgaccattcCtgtatgcagcttcactggga	10	9	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:137990530C>T	ENST00000409968.1	+	9	2155	c.1977C>T	c.(1975-1977)tcC>tcT	p.S659S	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Silent_p.S659S|THSD7B_ENST00000413152.2_Silent_p.S628S			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	659	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATGACCATTCCTGTATGCAGC	0.483																																																0			2											115	114	114					2																	137990530		1997	4163	6160	137707000	SO:0001819	synonymous_variant	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1977C>T	2.37:g.137990530C>T			137707000		Silent	SNP	ENST00000409968.1	37																																																																																					0.483	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	137990530	C	T	137990530	2	4	103	1	0	0	0	0	0	0	0	1	15919	668	24	3		3	THSD7B	2	137990530	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	19274528	137990530	105208843	33	27132										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166848031	166848031	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcacgctgaataatgacagcAgatacttcctcttgttttcg	8	10	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:166848031A>G	ENST00000303395.4	-	26	5753	c.5754T>C	c.(5752-5754)tcT>tcC	p.S1918S	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Silent_p.S1890S|SCN1A_ENST00000375405.3_Silent_p.S1907S|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000423058.2_Silent_p.S1918S			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1918	IQ.				adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAATGACAGCAGATACTTCCT	0.403																																																0			2											103	98	99					2																	166848031		2203	4300	6503	166556277	SO:0001819	synonymous_variant	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.5754T>C	2.37:g.166848031A>G			166556277	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																				0.403	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166848031	A	G	166848031	2	3	103	1	0	0	0	0	0	0	0	1	13951	175	7	4		4	SCN1A	2	166848031	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	28857501	166848031	76351342	34	27133										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171238588	171238588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgctgaaaaatactgccttgAggatgatttggtcaacctag	10	7	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:171238588A>G	ENST00000408978.4	+	10	1177	c.1034A>G	c.(1033-1035)gAg>gGg	p.E345G	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.E345G|MYO3B_ENST00000334231.6_Missense_Mutation_p.E354G	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	345	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TACTGCCTTGAGGATGATTTG	0.373																																																0			2											150	139	143					2																	171238588		1883	4101	5984	170946834	SO:0001583	missense	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1034A>G	2.37:g.171238588A>G	ENSP00000386213:p.Glu345Gly		170946834	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.86|14.86	2.661735|2.661735	0.47572|0.47572	.|.	.|.	ENSG00000071909|ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231|ENST00000442690	T;T;T;T|.	0.71698|.	-0.59;-0.59;-0.59;-0.59|.	5.97|5.97	5.97|5.97	0.96955|0.96955	Myosin head, motor domain (1);|.	0.132272|.	0.64402|.	D|.	0.000002|.	T|.	0.52191|.	0.1719|.	N|N	0.19112|0.19112	0.55|0.55	0.41035|0.41035	D|D	0.98518|0.98518	P;B;B;P|.	0.39940|.	0.696;0.244;0.351;0.542|.	B;B;B;B|.	0.38755|.	0.268;0.216;0.146;0.281|.	T|.	0.50056|.	-0.8872|.	10|.	0.48119|.	T|.	0.1|.	.|.	16.4534|16.4534	0.84003|0.84003	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	345;345;345;345|.	Q8WXR4-5;B7ZM71;Q8WXR4-4;Q8WXR4|.	.;.;.;MYO3B_HUMAN|.	G|W	345;345;344;354;354|344	ENSP00000386497:E345G;ENSP00000386213:E345G;ENSP00000446237:E354G;ENSP00000335100:E354G|.	ENSP00000314213:E344G|.	E|X	+|+	2|3	0|0	MYO3B|MYO3B	170946834|170946834	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	4.156000|4.156000	0.58138|0.58138	2.285000|2.285000	0.76669|0.76669	0.477000|0.477000	0.44152|0.44152	GAG|TGA		0.373	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			G	171238588	A	G	171238588	3	3	103	1	0	0	0	0	1	0	0	0	10107	304	11	4	1072	4	MYO3B	2	171238588	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4390557	171238588	71960785	35	27134										
TTN	7273	hgsc.bcm.edu	37	chr2	179479018	179479018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtggtgggttccatgttagaAgacatgactcattggttaca	12	6	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:179479018A>G	ENST00000591111.1	-	212	44407	c.44183T>C	c.(44182-44184)cTt>cCt	p.L14728P	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L13801P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000460472.2_Missense_Mutation_p.L7304P|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L7429P|TTN_ENST00000589042.1_Missense_Mutation_p.L16369P|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L7496P			Q8WZ42	TITIN_HUMAN	titin	14728	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		L -> V (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATGTTAGAAGACATGACTC	0.443																																																0			2											99	92	94					2																	179479018		1990	4176	6166	179187263	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44183T>C	2.37:g.179479018A>G	ENSP00000465570:p.Leu14728Pro		179187263	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.29	2.192736	0.38707	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.55	5.55	0.83447	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55641	0.1933	L	0.52266	1.64	0.58432	D	0.99999	P;P;P;P	0.41188	0.741;0.741;0.741;0.741	P;P;P;P	0.47528	0.549;0.549;0.549;0.549	T	0.59984	-0.7351	9	0.87932	D	0	.	11.716	0.51653	0.8678:0.0:0.0:0.1322	.	7304;7429;7496;14728	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	13801;7304;7496;7429;7304	ENSP00000343764:L13801P;ENSP00000434586:L7304P;ENSP00000340554:L7496P;ENSP00000352154:L7429P	ENSP00000340554:L7496P	L	-	2	0	TTN	179187263	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.077000	0.71275	2.234000	0.73211	0.533000	0.62120	CTT		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179479018	A	G	179479018	3	3	103	1	0	0	0	0	1	0	0	0	16775	72	3	4	58991	4	TTN	2	179479018	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	8240430	179479018	63720355	36	27135										
TTN	7273	hgsc.bcm.edu	37	chr2	179641476	179641476	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaggaagtgagttttttcttGaaaaatggtttctgttgttt	10	2	2	2	rs375828531		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:179641476G>C	ENST00000591111.1	-	28	5339	c.5115C>G	c.(5113-5115)ttC>ttG	p.F1705L	TTN_ENST00000342992.6_Missense_Mutation_p.F1705L|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.F1705L|TTN_ENST00000460472.2_Missense_Mutation_p.F1659L|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.F1659L|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.F1705L|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.F1659L			Q8WZ42	TITIN_HUMAN	titin	12534	Ig-like 8.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTTTTTCTTGAAAAATGGTT	0.483																																																0			2						G	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	90	82	85		4977,5115,5115,4977,4977	0.4	1	2		85	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	22,22,22,22,22	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1659/26927,1705/33424,1705/5605,1659/27052,1659/27119	179641476	1,13005	2203	4300	6503	179349721	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.5115C>G	2.37:g.179641476G>C	ENSP00000465570:p.Phe1705Leu		179349721	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	8.179	0.793367	0.16327	2.27E-4	0.0	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57	5.34	0.436	0.16549	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.85461	0.5702	M	0.92122	3.275	0.24529	N	0.994127	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.85130	0.992;0.992;0.992;0.992;0.997	T	0.74194	-0.3744	9	0.87932	D	0	.	9.5912	0.39548	0.5017:0.0:0.4983:0.0	.	1659;1659;1659;1705;1705	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	1705;1659;1659;1659;1659;1705	ENSP00000343764:F1705L;ENSP00000434586:F1659L;ENSP00000340554:F1659L;ENSP00000352154:F1659L;ENSP00000354117:F1705L	ENSP00000340554:F1659L	F	-	3	2	TTN	179349721	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.753000	0.38359	0.269000	0.21961	-0.150000	0.13652	TTC		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179641476	G	C	179641476	3	2	103	1	0	0	0	0	1	0	0	0	16775	1281	45	5	106213	5	TTN	2	179641476	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	162458	179641476	63557897	37	27136										
INPP1	3628	hgsc.bcm.edu	37	chr2	191235766	191235766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagctgcattgtcacgtgtgTgtggagatcgcatatttggg	14	6	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:191235766T>C	ENST00000322522.4	+	6	1294	c.838T>C	c.(838-840)Tgt>Cgt	p.C280R	INPP1_ENST00000541441.1_Missense_Mutation_p.C280R|INPP1_ENST00000392329.2_Missense_Mutation_p.C280R	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	280					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			GTCACGTGTGTGTGGAGATCG	0.468																																					Melanoma(130;184 1743 2185 19805 38428)											0			2											138	134	135					2																	191235766		2203	4300	6503	190944011	SO:0001583	missense	3628				CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.838T>C	2.37:g.191235766T>C	ENSP00000325423:p.Cys280Arg		190944011		Missense_Mutation	SNP	ENST00000322522.4	37	CCDS2305.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731487	0.48939	.	.	ENSG00000151689	ENST00000392329;ENST00000322522;ENST00000541441	T;T;T	0.48201	0.82;0.82;0.82	5.15	5.15	0.70609	.	0.093053	0.85682	D	0.000000	T	0.37376	0.1001	L	0.55103	1.725	0.80722	D	1	P	0.41313	0.745	B	0.30782	0.12	T	0.25606	-1.0127	10	0.23891	T	0.37	-15.4047	13.0337	0.58859	0.0:0.0:0.0:1.0	.	280	P49441	INPP_HUMAN	R	280	ENSP00000376142:C280R;ENSP00000325423:C280R;ENSP00000440650:C280R	ENSP00000325423:C280R	C	+	1	0	INPP1	190944011	1.000000	0.71417	0.903000	0.35520	0.697000	0.40408	6.676000	0.74498	2.176000	0.68965	0.369000	0.22263	TGT		0.468	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2			C	191235766	T	C	191235766	3	2	103	1	0	0	0	0	1	0	0	0	7772	1696	59	4	856	4	INPP1	2	191235766	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	11594290	191235766	51963607	38	27137										
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201281142	201281142	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaagaatggaatatgacaggAaaaaagaaggtaagattaat	10	1	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:201281142A>T	ENST00000358677.5	+	5	436	c.189A>T	c.(187-189)ggA>ggT	p.G63G	SPATS2L_ENST00000409151.1_Silent_p.G71G|SPATS2L_ENST00000409140.3_Silent_p.G63G|SPATS2L_ENST00000360760.5_Silent_p.G63G|SPATS2L_ENST00000451764.2_Silent_p.G63G|SPATS2L_ENST00000409385.1_Silent_p.G3G|SPATS2L_ENST00000409988.3_Silent_p.G63G|SPATS2L_ENST00000409755.3_Silent_p.G93G|SPATS2L_ENST00000409718.1_Silent_p.G63G	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	63						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						ATATGACAGGAAAAAAGAAGG	0.299																																																0			2											85	78	80					2																	201281142		1805	4065	5870	200989387	SO:0001819	synonymous_variant	26010			AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"DNA polymerase transactivated protein 6"	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.189A>T	2.37:g.201281142A>T			200989387	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Silent	SNP	ENST00000358677.5	37	CCDS46483.1																																																																																				0.299	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		T	201281142	A	T	201281142	2	4	103	1	0	0	0	0	0	0	0	1	15059	233	9	5		5	SPATS2L	2	201281142	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	10045376	201281142	41918231	39	27138										
ATIC	471	hgsc.bcm.edu	37	chr2	216177303	216177303	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtttgaatctggtcgcttcCggagggactgcaaaagctct	13	9	2	1	rs537063971		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:216177303C>T	ENST00000236959.9	+	2	428	c.102C>T	c.(100-102)tcC>tcT	p.S34S	ATIC_ENST00000435675.1_Silent_p.S33S|ATIC_ENST00000540518.1_5'UTR	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	34					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	TGGTCGCTTCCGGAGGGACTG	0.468			T	ALK	ALCL								C|||	1	0.000199681	0	0	5008	,	,		17656	0		0	False		,,,				2504	0.001						Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	0			2											89	88	88					2																	216177303		2203	4300	6503	215885548	SO:0001819	synonymous_variant	471				CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.102C>T	2.37:g.216177303C>T			215885548	A8K202|E9PBU3|Q13856|Q53S28	Silent	SNP	ENST00000236959.9	37	CCDS2398.1																																																																																				0.468	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044		T	216177303	C	T	216177303	2	4	103	1	0	0	0	0	0	0	0	1	1106	639	23	1		1	ATIC	2	216177303	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	14896161	216177303	27022070	40	27139										
ZFAND2B	130617	hgsc.bcm.edu	37	chr2	220072092	220072092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcctgctcaggcatcttctgCgcagaccatgtggcctacgc	11	15	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:220072092C>T	ENST00000289528.5	+	2	294	c.99C>T	c.(97-99)tgC>tgT	p.C33C	ZFAND2B_ENST00000409594.1_Silent_p.C33C|ZFAND2B_ENST00000409217.1_Silent_p.C33C|ZFAND2B_ENST00000409412.1_Silent_p.C33C|ZFAND2B_ENST00000444522.2_Silent_p.C33C|ZFAND2B_ENST00000409319.1_Silent_p.C33C|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409336.1_Silent_p.C33C|ZFAND2B_ENST00000409206.1_Silent_p.C33C|ZFAND2B_ENST00000409097.1_Silent_p.C33C	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	33						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCATCTTCTGCGCAGACCATG	0.557																																																0			2											113	103	106					2																	220072092		2203	4300	6503	219780336	SO:0001819	synonymous_variant	130617			AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"Zinc fingers, AN1-type domain containing"	25206	protein-coding gene	gene with protein product	"arsenite inducible RNA associated protein-like"	613474	"zinc finger, AN1-type 2B"			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.99C>T	2.37:g.220072092C>T			219780336	Q8NB98	Silent	SNP	ENST00000289528.5	37	CCDS2435.1																																																																																				0.557	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		T	220072092	C	T	220072092	2	4	103	1	0	0	0	0	0	0	0	1	17667	776	27	1		1	ZFAND2B	2	220072092	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	3894789	220072092	23127281	41	27140										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220164816	220164816	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcttttcttctctagcaggaCaggtgtcacagggggtctgg	14	9	4	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:220164816C>A	ENST00000295718.2	-	9	1567	c.1327G>T	c.(1327-1329)Gtc>Ttc	p.V443F	PTPRN_ENST00000409251.3_Missense_Mutation_p.V443F|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.V353F	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	443					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		TCTAGCAGGACAGGTGTCACA	0.627																																																0			2											64	73	70					2																	220164816		2203	4300	6503	219873060	SO:0001583	missense	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1327G>T	2.37:g.220164816C>A	ENSP00000295718:p.Val443Phe		219873060	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.471869	0.26423	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.03860	3.78;3.82;3.82	4.36	1.51	0.23008	.	0.307244	0.23463	N	0.047907	T	0.02888	0.0086	N	0.24115	0.695	0.21861	N	0.999502	B;P	0.35383	0.437;0.498	B;B	0.30572	0.117;0.107	T	0.42292	-0.9460	10	0.56958	D	0.05	.	4.9505	0.14011	0.0:0.577:0.1559:0.2671	.	443;443	Q6NSL1;Q16849	.;PTPRN_HUMAN	F	443;443;443;353	ENSP00000386638:V443F;ENSP00000295718:V443F;ENSP00000444244:V353F	ENSP00000295718:V443F	V	-	1	0	PTPRN	219873060	0.053000	0.20554	0.238000	0.24106	0.588000	0.36517	0.694000	0.25512	0.106000	0.17784	0.561000	0.74099	GTC		0.627	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220164816	C	A	220164816	3	1	103	1	0	0	0	0	1	0	0	0	12844	478	17	2	1672	2	PTPRN	2	220164816	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	92724	220164816	23034557	42	27141										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220421205	220421205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggagccgggcacttgtggccGtgctccctgcccgcaaagtc	14	15	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:220421205G>A	ENST00000404537.1	-	13	4363	c.4307C>T	c.(4306-4308)aCg>aTg	p.T1436M	OBSL1_ENST00000373876.1_Missense_Mutation_p.T1344M|OBSL1_ENST00000265318.4_Intron|OBSL1_ENST00000603926.1_Missense_Mutation_p.T1436M|OBSL1_ENST00000265317.5_Missense_Mutation_p.T335M|RP11-256I23.2_ENST00000597192.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1436	Ig-like 12.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACTTGTGGCCGTGCTCCCTGC	0.597																																																0			2											80	89	86					2																	220421205		2047	4175	6222	220129449	SO:0001583	missense	23363			BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4307C>T	2.37:g.220421205G>A	ENSP00000385636:p.Thr1436Met		220129449	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.897|2.897	-0.228430|-0.228430	0.06022|0.06022	.|.	.|.	ENSG00000124006|ENSG00000124006	ENST00000456147|ENST00000404537;ENST00000373876;ENST00000265317	.|T;T;T	.|0.67523	.|-0.27;-0.27;-0.27	4.51|4.51	2.6|2.6	0.31112|0.31112	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.53061|0.53061	0.1773|0.1773	L|L	0.41906|0.41906	1.305|1.305	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.34103	.|0.437;0.131;0.061;0.254	.|B;B;B;B	.|0.32677	.|0.15;0.097;0.072;0.097	T|T	0.44065|0.44065	-0.9352|-0.9352	5|9	.|0.48119	.|T	.|0.1	.|.	5.8871|5.8871	0.18888|0.18888	0.5408:0.0:0.4592:0.0|0.5408:0.0:0.4592:0.0	.|.	.|243;1437;1436;335	.|B7Z5P5;A4KVA4;O75147;E7ER99	.|.;.;OBSL1_HUMAN;.	W|M	338|1436;1344;335	.|ENSP00000385636:T1436M;ENSP00000362983:T1344M;ENSP00000265317:T335M	.|ENSP00000265317:T335M	R|T	-|-	1|2	2|0	OBSL1|OBSL1	220129449|220129449	0.003000|0.003000	0.15002|0.15002	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	1.510000|1.510000	0.35790|0.35790	0.486000|0.486000	0.27676|0.27676	0.491000|0.491000	0.48974|0.48974	CGG|ACG		0.597	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			A	220421205	G	A	220421205	3	1	103	1	0	0	0	0	1	0	0	0	10844	1145	40	1	1442	1	OBSL1	2	220421205	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	256389	220421205	22778168	43	27142										
SCLY	51540	hgsc.bcm.edu	37	chr2	238991893	238991893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caacttttccttccagttttAtggtcccaggattggcgcac	8	12	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:238991893A>G	ENST00000555827.1	+	7	846	c.782A>G	c.(781-783)tAt>tGt	p.Y261C	SCLY_ENST00000422984.2_Missense_Mutation_p.Y167C|SCLY_ENST00000409736.2_Missense_Mutation_p.Y261C|SCLY_ENST00000254663.6_Missense_Mutation_p.Y269C|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000373332.3_Missense_Mutation_p.Y179C			Q96I15	SCLY_HUMAN	selenocysteine lyase	261					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.Y261F(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		TTCCAGTTTTATGGTCCCAGG	0.443																																					Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)											1	Substitution - Missense(1)	ovary(1)	2											149	136	140					2																	238991893		2203	4300	6503	238656632	SO:0001583	missense	51540			AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.782A>G	2.37:g.238991893A>G	ENSP00000450613:p.Tyr261Cys		238656632	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.31|15.31	2.794770|2.794770	0.50102|0.50102	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000433750|ENST00000254663;ENST00000555827;ENST00000373332;ENST00000409736;ENST00000422984;ENST00000450965	.|T;T;D;D;T;D	.|0.88124	.|1.84;1.84;-2.34;-2.34;1.84;-2.34	5.79|5.79	4.64|4.64	0.57946|0.57946	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94128|0.94128	0.8117|0.8117	M|M	0.91459|0.91459	3.21|3.21	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;0.998	D|D	0.94211|0.94211	0.7459|0.7459	5|10	.|0.87932	.|D	.|0	-24.5411|-24.5411	10.9022|10.9022	0.47058|0.47058	0.9255:0.0:0.0745:0.0|0.9255:0.0:0.0745:0.0	.|.	.|167;261;261	.|E7ESG3;Q96I15;Q96I15-2	.|.;SCLY_HUMAN;.	V|C	3|269;261;179;261;167;91	.|ENSP00000254663:Y269C;ENSP00000450613:Y261C;ENSP00000362429:Y179C;ENSP00000387162:Y261C;ENSP00000416865:Y167C;ENSP00000414053:Y91C	.|ENSP00000254663:Y261C	M|Y	+|+	1|2	0|0	SCLY|SCLY	238656632|238656632	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.258000|0.258000	0.26162|0.26162	8.427000|8.427000	0.90275|0.90275	1.022000|1.022000	0.39626|0.39626	-0.256000|-0.256000	0.11100|0.11100	ATG|TAT		0.443	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		G	238991893	A	G	238991893	3	3	103	1	0	0	0	0	1	0	0	0	13944	449	16	4	808	4	SCLY	2	238991893	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	18570688	238991893	4207480	44	27143										
NEU4	129807	hgsc.bcm.edu	37	chr2	242757596	242757596	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctcaggcgagtgccagctggCggcggtggacggtgggcagg	21	10	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr2:242757596C>T	ENST00000391969.2	+	5	1388	c.677C>T	c.(676-678)gCg>gTg	p.A226V	NEU4_ENST00000325935.6_Missense_Mutation_p.A239V|NEU4_ENST00000404257.1_Missense_Mutation_p.A238V|NEU4_ENST00000405370.1_Missense_Mutation_p.A226V|NEU4_ENST00000407683.1_Missense_Mutation_p.A226V	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	226					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		TGCCAGCTGGCGGCGGTGGAC	0.697																																																0			2											26	20	22					2																	242757596		2189	4287	6476	242406269	SO:0001583	missense	129807			BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.677C>T	2.37:g.242757596C>T	ENSP00000375830:p.Ala226Val		242406269	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	37	CCDS54442.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.915|9.915	1.210709|1.210709	0.22289|0.22289	.|.	.|.	ENSG00000204099|ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000404257;ENST00000391969;ENST00000325935;ENST00000420288|ENST00000415936;ENST00000426032	D;D;D;D;D;D|T;T	0.82081|0.39787	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57|1.06;1.07	4.55|4.55	2.7|2.7	0.31948|0.31948	Neuraminidase (2);|.	0.069772|.	0.64402|.	D|.	0.000017|.	T|T	0.26448|0.26448	0.0646|0.0646	N|N	0.11560|0.11560	0.145|0.145	0.36460|0.36460	D|D	0.866642|0.866642	P;P;D|.	0.69078|.	0.821;0.557;0.997|.	B;B;P|.	0.61874|.	0.1;0.061;0.895|.	T|T	0.28267|0.28267	-1.0049|-1.0049	10|7	0.20519|0.66056	T|D	0.43|0.02	-20.1237|-20.1237	5.0162|5.0162	0.14337|0.14337	0.0:0.5991:0.0:0.4009|0.0:0.5991:0.0:0.4009	.|.	238;238;226|.	A8K211;Q8WWR8-2;Q8WWR8|.	.;.;NEUR4_HUMAN|.	V|W	226;226;236;238;226;239;226|141;153	ENSP00000385402:A226V;ENSP00000384804:A226V;ENSP00000385149:A238V;ENSP00000375830:A226V;ENSP00000320318:A239V;ENSP00000388707:A226V|ENSP00000397167:R141W;ENSP00000406678:R153W	ENSP00000320318:A239V|ENSP00000397167:R141W	A|R	+|+	2|1	0|2	NEU4|NEU4	242406269|242406269	0.868000|0.868000	0.29978|0.29978	0.885000|0.885000	0.34714|0.34714	0.160000|0.160000	0.22226|0.22226	1.345000|1.345000	0.33953|0.33953	2.076000|2.076000	0.62316|0.62316	0.443000|0.443000	0.29094|0.29094	GCG|CGG		0.697	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741		T	242757596	C	T	242757596	3	4	103	1	0	0	0	0	1	0	0	0	10375	768	27	1	730	1	NEU4	2	242757596	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	3765703	242757596	441777	45	27144										
LMCD1	29995	hgsc.bcm.edu	37	chr3	8590294	8590294	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	catccccaaggagaagcagcCagtgacaggcacagagggtg	14	11	0	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:8590294C>G	ENST00000157600.3	+	4	660	c.428C>G	c.(427-429)cCa>cGa	p.P143R	LMCD1-AS1_ENST00000439407.1_RNA|LMCD1_ENST00000397386.3_Missense_Mutation_p.P31R|LMCD1_ENST00000454244.1_Missense_Mutation_p.P70R|LMCD1_ENST00000535732.1_Missense_Mutation_p.P143R	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	143	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		GAGAAGCAGCCAGTGACAGGC	0.577																																																0			3											60	63	62					3																	8590294		2203	4300	6503	8565294	SO:0001583	missense	29995			AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"dyxin"	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.428C>G	3.37:g.8590294C>G	ENSP00000157600:p.Pro143Arg		8565294	B4DG80	Missense_Mutation	SNP	ENST00000157600.3	37	CCDS33688.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457880	0.84317	.	.	ENSG00000071282	ENST00000157600;ENST00000415597;ENST00000535732;ENST00000454244;ENST00000397386;ENST00000426878	D;D;D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96;-3.96;-3.96	5.61	5.61	0.85477	PET domain (2);	0.000000	0.64402	D	0.000001	D	0.98607	0.9534	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99577	1.0972	10	0.87932	D	0	-19.7183	18.2109	0.89869	0.0:1.0:0.0:0.0	.	143;31;143	F5GX84;B4DEY6;Q9NZU5	.;.;LMCD1_HUMAN	R	143;149;143;70;31;100	ENSP00000157600:P143R;ENSP00000400555:P149R;ENSP00000441100:P143R;ENSP00000396515:P70R;ENSP00000380542:P31R;ENSP00000411222:P100R	ENSP00000157600:P143R	P	+	2	0	LMCD1	8565294	1.000000	0.71417	0.967000	0.41034	0.885000	0.51271	7.028000	0.76470	2.629000	0.89072	0.655000	0.94253	CCA		0.577	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583		G	8590294	C	G	8590294	3	3	103	1	0	0	0	0	1	0	0	0	8868	594	21	5	442	5	LMCD1	3	8590294	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		8590294	189432136	46	27145										
VHL	7428	hgsc.bcm.edu	37	chr3	10188272	10188272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaactgaattatttgtgccaTctctcaatgttgacggacag	8	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:10188272T>C	ENST00000256474.2	+	2	1255	c.415T>C	c.(415-417)Tct>Cct	p.S139P	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	139	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.P138fs*1(2)|p.S139fs*2(2)|p.S139fs*5(1)|p.L140fs*4(1)|p.L140fs*3(1)|p.S139fs*12(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ATTTGTGCCATCTCTCAATGT	0.423		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	8	Deletion - Frameshift(6)|Complex - frameshift(1)|Insertion - Frameshift(1)	kidney(8)	3											220	203	209					3																	10188272		2203	4300	6503	10163272	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.415T>C	3.37:g.10188272T>C	ENSP00000256474:p.Ser139Pro		10163272	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.479919	0.63849	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99823	-6.95	5.07	2.18	0.27775	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.482216	0.21408	N	0.075030	D	0.98538	0.9512	N	0.08118	0	0.80722	D	1	D	0.55605	0.972	P	0.48552	0.581	D	0.97578	1.0109	10	0.44086	T	0.13	-7.2049	7.8748	0.29586	0.5151:0.0:0.0:0.4849	.	139	P40337	VHL_HUMAN	P	139;57	ENSP00000256474:S139P	ENSP00000256474:S139P	S	+	1	0	VHL	10163272	0.744000	0.28250	0.986000	0.45419	0.897000	0.52465	1.041000	0.30291	0.846000	0.35142	0.460000	0.39030	TCT		0.423	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188272	T	C	10188272	3	2	103	1	0	0	0	0	1	0	0	0	17202	1435	50	4	421	4	VHL	3	10188272	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1597978	10188272	187834158	47	27146										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15115811	15115811	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgtggcatgctgctctggggTaagcgctcctggccaacggc	15	12	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:15115811T>A	ENST00000253699.3	-	14	2446	c.1833A>T	c.(1831-1833)ttA>ttT	p.L611F	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.L611F	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	611	Necessary for the interaction with EHD1.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						TGCTCTGGGGTAAGCGCTCCT	0.602																																																0			3											54	57	56					3																	15115811		2203	4300	6503	15090815	SO:0001583	missense	64145			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.1833A>T	3.37:g.15115811T>A	ENSP00000253699:p.Leu611Phe		15090815	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	T	4.204	0.036522	0.08148	.	.	ENSG00000131381	ENST00000253699;ENST00000476527	T;T	0.53857	0.6;0.6	4.58	-4.72	0.03269	.	1.008340	0.07943	N	0.979544	T	0.35941	0.0949	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29274	-1.0017	10	0.35671	T	0.21	2.8547	1.7225	0.02915	0.2518:0.3194:0.298:0.1309	.	611	Q9H1K0	RBNS5_HUMAN	F	611	ENSP00000253699:L611F;ENSP00000422551:L611F	ENSP00000253699:L611F	L	-	3	2	ZFYVE20	15090815	0.319000	0.24607	0.000000	0.03702	0.191000	0.23601	0.493000	0.22451	-0.683000	0.05190	0.402000	0.26972	TTA		0.602	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15115811	T	A	15115811	3	1	103	1	0	0	0	0	1	0	0	0	17705	1635	57	5	525	5	ZFYVE20	3	15115811	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	4927539	15115811	182906619	48	27147										
THRB	7068	hgsc.bcm.edu	37	chr3	24188296	24188296	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggatggagatttttctgaatGgttcttctaaagaaacccta	9	6	3	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:24188296G>A	ENST00000356447.4	-	6	686	c.402C>T	c.(400-402)acC>acT	p.T134T	THRB_ENST00000396671.2_Silent_p.T134T|THRB_ENST00000280696.5_Silent_p.T149T|THRB_ENST00000416420.1_Silent_p.T134T	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	134					female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TTTTCTGAATGGTTCTTCTAA	0.348																																					Melanoma(21;896 1043 15021 37958)											0			3											96	93	94					3																	24188296		2203	4300	6503	24163300	SO:0001819	synonymous_variant	7068				CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"Nuclear hormone receptors"	11799	protein-coding gene	gene with protein product	"avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2", "oncogene ERBA2", "generalized resistance to thyroid hormone", "thyroid hormone receptor beta 1"	190160	"thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)", "pituitary resistance to thyroid hormone", "thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.402C>T	3.37:g.24188296G>A			24163300	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Silent	SNP	ENST00000356447.4	37	CCDS2641.1																																																																																				0.348	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461		A	24188296	G	A	24188296	2	1	103	1	0	0	0	0	0	0	0	1	15914	1335	47	3		3	THRB	3	24188296	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	9072485	24188296	173834134	49	27148										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41267276	41267276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaaaatggttgccttgctcaAcaaaacaaatgttaaattct	6	7	2	0	rs35288908	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:41267276A>G	ENST00000349496.5	+	6	1140	c.860A>G	c.(859-861)aAc>aGc	p.N287S	CTNNB1_ENST00000453024.1_Missense_Mutation_p.N280S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N287S|CTNNB1_ENST00000396183.3_Missense_Mutation_p.N287S|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N287S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	287					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N287S(2)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GCCTTGCTCAACAAAACAAAT	0.388		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	2	Substitution - Missense(2)	large_intestine(2)	3	GRCh37	CM043757	CTNNB1	M	rs35288908	A	SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	122	119	120		860,860,860	5.7	1	3	dbSNP_126	120	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense,missense	CTNNB1	NM_001098209.1,NM_001098210.1,NM_001904.3	46,46,46	0,13,6490	GG,GA,AA		0.1395,0.0227,0.1	benign,benign,benign	287/782,287/782,287/782	41267276	13,12993	2203	4300	6503	41242280	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.860A>G	3.37:g.41267276A>G	ENSP00000344456:p.Asn287Ser		41242280	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370081	0.24771	2.27E-4	0.001395	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.184600	0.56097	D	0.000034	T	0.37598	0.1009	N	0.02315	-0.6	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28933	-1.0028	10	0.20519	T	0.43	-1.1628	16.0129	0.80417	1.0:0.0:0.0:0.0	rs35288908	215;287	B4DSW9;P35222	.;CTNB1_HUMAN	S	287;287;287;280;287	ENSP00000385604:N287S;ENSP00000379486:N287S;ENSP00000344456:N287S;ENSP00000411226:N280S;ENSP00000379488:N287S	ENSP00000344456:N287S	N	+	2	0	CTNNB1	41242280	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.328000	0.65887	2.184000	0.69523	0.482000	0.46254	AAC		0.388	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41267276	A	G	41267276	3	3	103	1	0	0	0	0	1	0	0	0	4022	43	2	4	878	4	CTNNB1	3	41267276	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	17078980	41267276	156755154	50	27149										
KIF15	56992	hgsc.bcm.edu	37	chr3	44879835	44879835	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atgctcacagaggcctcaaaAaaacactcggggctgctgca	10	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:44879835A>T	ENST00000326047.4	+	27	3389	c.3240A>T	c.(3238-3240)aaA>aaT	p.K1080N	KIF15_ENST00000425755.1_Missense_Mutation_p.K715N	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1080					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AGGCCTCAAAAAAACACTCGG	0.502																																																0			3											52	56	55					3																	44879835		2203	4300	6503	44854839	SO:0001583	missense	56992			AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3240A>T	3.37:g.44879835A>T	ENSP00000324020:p.Lys1080Asn		44854839	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	A	9.568	1.120391	0.20877	.	.	ENSG00000163808	ENST00000326047;ENST00000396031;ENST00000425755	T;T	0.50548	0.74;0.74	5.26	-8.96	0.00761	.	0.231088	0.29868	N	0.010990	T	0.18299	0.0439	N	0.08118	0	0.23371	N	0.997814	B	0.09022	0.002	B	0.04013	0.001	T	0.16719	-1.0393	10	0.18276	T	0.48	.	11.8968	0.52661	0.3408:0.1045:0.5546:0.0	.	1080	Q9NS87	KIF15_HUMAN	N	1080;1079;715	ENSP00000324020:K1080N;ENSP00000389982:K715N	ENSP00000324020:K1080N	K	+	3	2	KIF15	44854839	0.022000	0.18835	0.027000	0.17364	0.547000	0.35210	-0.971000	0.03806	-1.471000	0.01886	0.528000	0.53228	AAA		0.502	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			T	44879835	A	T	44879835	3	4	103	1	0	0	0	0	1	0	0	0	8298	11	1	5	3346	5	KIF15	3	44879835	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	3612559	44879835	153142595	51	27150										
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50380427	50380427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gttgtgtgtgctaagcatacGgctcaaggtgctgagagaga	15	6	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:50380427G>A	ENST00000231749.3	-	7	1894	c.622C>T	c.(622-624)Cgt>Tgt	p.R208C	RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000360165.3_Intron|RASSF1_ENST00000488024.1_5'Flank|ZMYND10_ENST00000490675.1_5'Flank|RASSF1_ENST00000357043.2_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	208					inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)	p.R208C(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTAAGCATACGGCTCAAGGTG	0.637										TSP Lung(30;0.18)																																						1	Substitution - Missense(1)	lung(1)	3											146	133	137					3																	50380427		2203	4300	6503	50355431	SO:0001583	missense	51364			U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"Zinc fingers, MYND-type"	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.622C>T	3.37:g.50380427G>A	ENSP00000231749:p.Arg208Cys		50355431	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216736	0.58452	.	.	ENSG00000004838	ENST00000231749;ENST00000442887	T;T	0.32272	1.46;1.46	5.55	3.69	0.42338	.	0.047666	0.85682	N	0.000000	T	0.34687	0.0906	M	0.85462	2.755	0.80722	D	1	B	0.33212	0.402	B	0.26202	0.067	T	0.38112	-0.9676	10	0.66056	D	0.02	-17.2735	9.9703	0.41749	0.0724:0.0:0.7903:0.1374	.	208	O75800	ZMY10_HUMAN	C	208;165	ENSP00000231749:R208C;ENSP00000393687:R165C	ENSP00000231749:R208C	R	-	1	0	ZMYND10	50355431	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.792000	0.62467	1.358000	0.45922	0.561000	0.74099	CGT		0.637	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		A	50380427	G	A	50380427	3	1	103	1	0	0	0	0	1	0	0	0	17744	1116	39	1	724	1	ZMYND10	3	50380427	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5500592	50380427	147642003	52	27151										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	55021780	55021780	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aacaatgggctcctttaaaaGgtaagggttttatggtccac	10	7	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:55021780G>A	ENST00000474759.1	+	31	2738	c.2690G>A	c.(2689-2691)aGa>aAa	p.R897K	CACNA2D3_ENST00000490478.1_Splice_Site_p.R803K|CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000415676.2_Splice_Site_p.R897K|CACNA2D3_ENST00000288197.5_Splice_Site_p.R897K	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	897						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	TCCTTTAAAAGGTAAGGGTTT	0.428																																																0			3											113	109	110					3																	55021780		1813	4072	5885	54996820	SO:0001630	splice_region_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2690+1G>A	3.37:g.55021780G>A			54996820	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151969	0.57151	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44	5.79	5.79	0.91817	.	0.096936	0.64402	D	0.000002	T	0.54711	0.1875	N	0.21282	0.65	0.43782	D	0.996311	B	0.11235	0.004	B	0.12837	0.008	T	0.47005	-0.9150	10	0.21540	T	0.41	.	18.2119	0.89873	0.0:0.0:1.0:0.0	.	897	Q8IZS8	CA2D3_HUMAN	K	897;897;897;803;803	ENSP00000389506:R897K;ENSP00000419101:R897K;ENSP00000288197:R897K;ENSP00000417279:R803K	ENSP00000288197:R897K	R	+	2	0	CACNA2D3	54996820	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.214000	0.89760	2.746000	0.94184	0.655000	0.94253	AGA		0.428	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		Missense_Mutation	A	55021780	G	A	55021780	5	1	103	1	0	0	0	0	0	0	1	0	2556	1014	35	3	2812	3	CACNA2D3	3	55021780	Splice_Site	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	4641353	55021780	143000650	53	27152										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56651308	56651308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggataaaggagccagcttagAaaaagaaaacaatcggtgta	11	5	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:56651308A>G	ENST00000394672.3	+	14	2082	c.2012A>G	c.(2011-2013)gAa>gGa	p.E671G	CCDC66_ENST00000326595.7_Missense_Mutation_p.E637G|CCDC66_ENST00000436465.2_Missense_Mutation_p.E671G	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	671					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		GCCAGCTTAGAAAAAGAAAAC	0.363																																																0			3											80	76	78					3																	56651308		2203	4300	6503	56626348	SO:0001583	missense	285331			AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2012A>G	3.37:g.56651308A>G	ENSP00000378167:p.Glu671Gly		56626348	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990170	0.74589	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.28255	1.62;1.68;1.68;1.68	6.03	4.85	0.62838	.	0.302729	0.32671	N	0.005798	T	0.22513	0.0543	L	0.52364	1.645	0.80722	D	1	B	0.20671	0.047	B	0.22386	0.039	T	0.07908	-1.0748	10	0.10111	T	0.7	-7.8178	4.9059	0.13799	0.7158:0.0:0.1393:0.1449	.	671	A2RUB6	CCD66_HUMAN	G	627;671;637;671	ENSP00000401451:E627G;ENSP00000378167:E671G;ENSP00000326050:E637G;ENSP00000404320:E671G	ENSP00000326050:E637G	E	+	2	0	CCDC66	56626348	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.671000	0.54576	1.067000	0.40740	0.533000	0.62120	GAA		0.363	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		G	56651308	A	G	56651308	3	3	103	1	0	0	0	0	1	0	0	0	2844	246	9	4	2066	4	CCDC66	3	56651308	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1629528	56651308	141371122	54	27153										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706206	96706206	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	actgaaatggatgaacataaTaggcccattcacacatacca	6	10	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:96706206T>C	ENST00000389672.5	+	3	521	c.483T>C	c.(481-483)aaT>aaC	p.N161N	EPHA6_ENST00000470610.2_Silent_p.N161N|EPHA6_ENST00000542517.1_Silent_p.N67N	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	67	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						ATGAACATAATAGGCCCATTC	0.373																																																0			3											103	99	100					3																	96706206		1873	4105	5978	98188896	SO:0001819	synonymous_variant	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.483T>C	3.37:g.96706206T>C			98188896	D6RAL5	Silent	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	T	7.500	0.652483	0.14580	.	.	ENSG00000080224	ENST00000506569	.	.	.	5.74	-5.12	0.02893	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5163	0.90936	0.0:0.6431:0.0:0.3569	.	.	.	.	Q	106	.	.	X	+	1	0	EPHA6	98188896	0.987000	0.35691	0.881000	0.34555	0.955000	0.61496	0.248000	0.18198	-1.276000	0.02414	-0.250000	0.11733	TAG		0.373	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		C	96706206	T	C	96706206	2	2	103	1	0	0	0	0	0	0	0	1	5184	1403	49	4		4	EPHA6	3	96706206	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	40054898	96706206	101316224	55	27154										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112356986	112356986	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tagccatcctgttctgttttAcctccttttttcttcttgct	4	12	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:112356986A>G	ENST00000206423.3	-	2	2720	c.1767T>C	c.(1765-1767)ggT>ggC	p.G589G	CCDC80_ENST00000475181.1_5'Flank|CCDC80_ENST00000439685.2_Silent_p.G589G	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	589	Lys-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GTTCTGTTTTACCTCCTtttt	0.443																																																0			3											246	226	232					3																	112356986		2203	4300	6503	113839676	SO:0001819	synonymous_variant	151887			AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1767T>C	3.37:g.112356986A>G			113839676	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	37	CCDS2968.1																																																																																				0.443	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		G	112356986	A	G	112356986	2	3	103	1	0	0	0	0	0	0	0	1	2860	378	14	4		4	CCDC80	3	112356986	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	15650780	112356986	85665444	56	27155										
CD200R1L	344807	hgsc.bcm.edu	37	chr3	112546239	112546239	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acttggaggtgatatccacgAtggaaattcccatcaggtgt	11	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:112546239A>G	ENST00000398214.1	-	3	630	c.405T>C	c.(403-405)caT>caC	p.H135H	CD200R1L_ENST00000488794.1_Silent_p.H114H|CD200R1L_ENST00000448932.1_Silent_p.H114H	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	135	Ig-like C2-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						GATATCCACGATGGAAATTCC	0.448																																																0			3											119	115	117					3																	112546239		2203	4300	6503	114028929	SO:0001819	synonymous_variant	344807			AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"Immunoglobulin superfamily / C2-set domain containing"	24665	protein-coding gene	gene with protein product	"CD200 receptor 2"						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.405T>C	3.37:g.112546239A>G			114028929	Q6WHB7	Silent	SNP	ENST00000398214.1	37	CCDS43131.1																																																																																				0.448	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784		G	112546239	A	G	112546239	2	3	103	1	0	0	0	0	0	0	0	1	2988	330	12	4		4	CD200R1L	3	112546239	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	189253	112546239	85476191	57	27156										
BOC	91653	hgsc.bcm.edu	37	chr3	113002345	113002345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcctgaaaccatagagcggcCggtgggcactggggccatgg	16	11	0	2	rs138348732	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:113002345C>T	ENST00000495514.1	+	16	3223	c.2519C>T	c.(2518-2520)cCg>cTg	p.P840L	BOC_ENST00000273395.4_Missense_Mutation_p.P841L|BOC_ENST00000355385.3_Missense_Mutation_p.P840L			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	840					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			ATAGAGCGGCCGGTGGGCACT	0.622																																																0			3											80	90	86					3																	113002345		2203	4299	6502	114485035	SO:0001583	missense	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.2519C>T	3.37:g.113002345C>T	ENSP00000418663:p.Pro840Leu		114485035	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.46	2.243354	0.39697	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.63255	-0.03;-0.02;-0.03	5.85	5.85	0.93711	.	0.220829	0.36519	N	0.002551	T	0.72590	0.3479	L	0.51422	1.61	0.48452	D	0.999658	D;P;P	0.71674	0.998;0.933;0.89	P;P;B	0.58780	0.845;0.529;0.329	T	0.69217	-0.5203	10	0.39692	T	0.17	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	657;841;840	Q9BWV1-2;Q9BWV1-3;Q9BWV1	.;.;BOC_HUMAN	L	840;841;840	ENSP00000418663:P840L;ENSP00000273395:P841L;ENSP00000347546:P840L	ENSP00000273395:P841L	P	+	2	0	BOC	114485035	0.988000	0.35896	0.895000	0.35142	0.112000	0.19704	4.960000	0.63673	2.767000	0.95098	0.655000	0.94253	CCG		0.622	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	113002345	C	T	113002345	3	4	103	1	0	0	0	0	1	0	0	0	1482	652	23	1	2573	1	BOC	3	113002345	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	456106	113002345	85020085	58	27157										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121409535	121409535	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	actagtctgtctctgtcattTtggagtgaagacatagcttt	9	7	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:121409535T>C	ENST00000340645.5	-	14	8786	c.8661A>G	c.(8659-8661)caA>caG	p.Q2887Q	GOLGB1_ENST00000393667.3_Silent_p.Q2892Q	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2887					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CTCTGTCATTTTGGAGTGAAG	0.373																																																0			3											42	42	42					3																	121409535		2203	4300	6503	122892225	SO:0001819	synonymous_variant	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.8661A>G	3.37:g.121409535T>C			122892225	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																				0.373	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121409535	T	C	121409535	2	2	103	1	0	0	0	0	0	0	0	1	6585	1838	64	4		4	GOLGB1	3	121409535	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	8407190	121409535	76612895	59	27158										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130282099	130282099	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaattccacctgagcaccttCaaaggcaggagccccatgct	9	14	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:130282099C>T	ENST00000358511.6	+	2	283	c.252C>T	c.(250-252)ttC>ttT	p.F84F	COL6A6_ENST00000453409.2_Silent_p.F84F	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	84	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.F84L(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGAGCACCTTCAAAGGCAGGA	0.522																																																1	Substitution - Missense(1)	ovary(1)	3											69	66	67					3																	130282099		1889	4104	5993	131764789	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.252C>T	3.37:g.130282099C>T			131764789	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.522	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130282099	C	T	130282099	2	4	103	1	0	0	0	0	0	0	0	1	3709	825	29	3		3	COL6A6	3	130282099	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	8872564	130282099	67740331	60	27159										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098637	133098637	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgaccgaagcgctggcatttGccatccaggaaccatctccc	9	15	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:133098637G>C	ENST00000321871.6	+	4	292	c.82G>C	c.(82-84)Gcc>Ccc	p.A28P	TMEM108_ENST00000393130.3_Missense_Mutation_p.A28P|TMEM108_ENST00000515826.1_Missense_Mutation_p.A28P|TMEM108_ENST00000508711.1_Intron	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	28						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GCTGGCATTTGCCATCCAGGA	0.552																																																0			3											282	295	290					3																	133098637		2203	4300	6503	134581327	SO:0001583	missense	66000			AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.82G>C	3.37:g.133098637G>C	ENSP00000324651:p.Ala28Pro		134581327	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	g	17.05	3.289988	0.59976	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000512137;ENST00000511555;ENST00000515826;ENST00000510183	T;T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06;0.06	4.26	4.26	0.50523	.	0.000000	0.36374	N	0.002637	T	0.72590	0.3479	L	0.51422	1.61	0.34030	D	0.653748	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.982	T	0.80843	-0.1201	10	0.62326	D	0.03	-11.0402	13.1129	0.59283	0.0:0.0:0.8289:0.1711	.	28;28	E9PB58;Q6UXF1	.;TM108_HUMAN	P	28	ENSP00000324651:A28P;ENSP00000376838:A28P;ENSP00000426301:A28P;ENSP00000422196:A28P;ENSP00000423338:A28P;ENSP00000421486:A28P	ENSP00000324651:A28P	A	+	1	0	TMEM108	134581327	1.000000	0.71417	0.842000	0.33263	0.970000	0.65996	3.321000	0.51999	2.104000	0.64026	0.556000	0.70494	GCC		0.552	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		C	133098637	G	C	133098637	3	2	103	1	0	0	0	0	1	0	0	0	16063	1319	46	5	88	5	TMEM108	3	133098637	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2816538	133098637	64923793	61	27160										
RYK	6259	hgsc.bcm.edu	37	chr3	133921633	133921633	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaacagctaatattattgcTacgagaaatattactgcaca	5	7	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:133921633T>C	ENST00000427044.2	-	7	763	c.153A>G	c.(151-153)gtA>gtG	p.V51V	RYK_ENST00000296084.4_Silent_p.V241V			P34925	RYK_HUMAN	receptor-like tyrosine kinase	240					axon guidance (GO:0007411)|corpus callosum development (GO:0022038)|neuron differentiation (GO:0030182)|neuron projection development (GO:0031175)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of MAPK cascade (GO:0043410)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			lung(1)|ovary(3)	4						ATATTATTGCTACGAGAAATA	0.348																																																0			3											77	69	72					3																	133921633		1839	4099	5938	135404323	SO:0001819	synonymous_variant	6259			S59184	CCDS75016.1	3q22.1	2012-02-28	2012-02-28		ENSG00000163785	ENSG00000163785	2.7.10.1		10481	protein-coding gene	gene with protein product		600524	"JTK5A protein tyrosine kinase", "RYK receptor-like tyrosine kinase"	JTK5A		8386829	Standard	NM_001005861		Approved	D3S3195, RYK1, JTK5	uc003eqc.1	P34925	OTTHUMG00000159750	ENST00000427044.2:c.153A>G	3.37:g.133921633T>C			135404323	Q04696	Missense_Mutation	SNP	ENST00000427044.2	37		.	.	.	.	.	.	.	.	.	.	T	9.924	1.212979	0.22289	.	.	ENSG00000163785	ENST00000460933	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.9057	10.6396	0.45586	0.0:0.0803:0.0:0.9197	.	.	.	.	W	223	.	.	X	-	2	0	RYK	135404323	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.627000	0.24506	2.170000	0.68504	0.455000	0.32223	TAG		0.348	RYK-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001005861		C	133921633	T	C	133921633	2	2	103	1	0	0	0	0	0	0	0	1	13804	1509	53	4		4	RYK	3	133921633	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	822996	133921633	64100797	62	27161										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401870	140401870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccgcatcatcgagtactgccGcaatgacaacaaattgctct	7	13	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:140401870G>A	ENST00000286349.3	+	2	1099	c.908G>A	c.(907-909)cGc>cAc	p.R303H		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	303						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GAGTACTGCCGCAATGACAAC	0.567																																																0			3											245	209	221					3																	140401870		2203	4300	6503	141884560	SO:0001583	missense	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.908G>A	3.37:g.140401870G>A	ENSP00000286349:p.Arg303His		141884560	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033603	0.54896	.	.	ENSG00000155890	ENST00000286349	T	0.42900	0.96	5.31	4.43	0.53597	Zinc finger, B-box (2);	0.406836	0.21967	N	0.066515	T	0.29850	0.0746	N	0.19112	0.55	0.27364	N	0.95589	P	0.50710	0.938	P	0.45138	0.471	T	0.09015	-1.0694	10	0.33141	T	0.24	-30.2356	10.2685	0.43468	0.0942:0.0:0.9058:0.0	.	303	Q8IWZ5	TRI42_HUMAN	H	303	ENSP00000286349:R303H	ENSP00000286349:R303H	R	+	2	0	TRIM42	141884560	0.415000	0.25416	0.939000	0.37840	0.657000	0.38888	3.092000	0.50207	2.486000	0.83907	0.561000	0.74099	CGC		0.567	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401870	G	A	140401870	3	1	103	1	0	0	0	0	1	0	0	0	16557	1087	38	1	914	1	TRIM42	3	140401870	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	6480237	140401870	57620560	63	27162										
SUCNR1	56670	hgsc.bcm.edu	37	chr3	151599123	151599123	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcacgcctggggagttggaaGcagtatcagtgcactcaggt	14	9	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:151599123G>T	ENST00000362032.5	+	3	897	c.792G>T	c.(790-792)aaG>aaT	p.K264N	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	264						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	GGAGTTGGAAGCAGTATCAGT	0.468																																																0			3											221	194	203					3																	151599123		2203	4300	6503	153081813	SO:0001583	missense	56670			AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.792G>T	3.37:g.151599123G>T	ENSP00000355156:p.Lys264Asn		153081813	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	37	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	0.302	-0.973487	0.02215	.	.	ENSG00000198829	ENST00000362032	T	0.61158	0.13	5.46	0.0431	0.14220	GPCR, rhodopsin-like superfamily (1);	1.252330	0.05417	U	0.543447	T	0.33760	0.0874	N	0.16201	0.385	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.12477	-1.0546	10	0.16896	T	0.51	.	1.8767	0.03219	0.244:0.1853:0.444:0.1267	.	264	Q9BXA5	SUCR1_HUMAN	N	264	ENSP00000355156:K264N	ENSP00000355156:K264N	K	+	3	2	SUCNR1	153081813	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.650000	0.05378	0.058000	0.16222	0.650000	0.86243	AAG		0.468	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151599123	G	T	151599123	3	4	103	1	0	0	0	0	1	0	0	0	15405	962	34	2	798	2	SUCNR1	3	151599123	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	11197253	151599123	46423307	64	27163										
GPR149	344758	hgsc.bcm.edu	37	chr3	154055525	154055525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttcctctctttttctgtaaGctttatttaacaactggatt	4	9	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:154055525G>T	ENST00000389740.2	-	4	2258	c.2159C>A	c.(2158-2160)gCt>gAt	p.A720D		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	720					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A720V(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTTCTGTAAGCTTTATTTAA	0.433																																																1	Substitution - Missense(1)	ovary(1)	3											315	291	299					3																	154055525		1914	4119	6033	155538219	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2159C>A	3.37:g.154055525G>T	ENSP00000374390:p.Ala720Asp		155538219		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163619	0.78226	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.8	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.63651	0.2529	N	0.24115	0.695	0.58432	D	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.68834	-0.5304	9	0.87932	D	0	-11.7316	14.7238	0.69329	0.0692:0.0:0.9308:0.0	.	720	Q86SP6	GP149_HUMAN	D	720	.	ENSP00000374390:A720D	A	-	2	0	GPR149	155538219	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.433000	0.66520	1.456000	0.47831	0.650000	0.86243	GCT		0.433	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154055525	G	T	154055525	3	4	103	1	0	0	0	0	1	0	0	0	6674	971	34	2	40	2	GPR149	3	154055525	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2456402	154055525	43966905	65	27164										
PPM1L	151742	hgsc.bcm.edu	37	chr3	160786907	160786907	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acaatataacagtcatggtgGtgaagttcagaaatagcagc	10	6	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:160786907G>T	ENST00000498165.1	+	4	1146	c.1045G>T	c.(1045-1047)Gtg>Ttg	p.V349L	PPM1L_ENST00000480117.1_3'UTR|PPM1L_ENST00000295839.9_Missense_Mutation_p.V222L|PPM1L_ENST00000464260.1_Missense_Mutation_p.V170L	NM_139245.2	NP_640338.2	Q5SGD2	PPM1L_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1L	349					MAPK cascade (GO:0000165)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			AGTCATGGTGGTGAAGTTCAG	0.443																																					Pancreas(86;250 1994 13715 43211)											0			3											44	44	44					3																	160786907		2203	4300	6503	162269601	SO:0001583	missense	151742			AK055115	CCDS33886.1	3q26.1	2012-04-17	2010-03-05		ENSG00000163590	ENSG00000163590	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	16381	protein-coding gene	gene with protein product	"PP2Cepsilon", "Protein phosphatase 2C epsilon isoform"	611931	"protein phosphatase 1 (formerly 2C)-like"			12556533	Standard	XM_006713507		Approved	PP2CE	uc003fdr.3	Q5SGD2	OTTHUMG00000159048	ENST00000498165.1:c.1045G>T	3.37:g.160786907G>T	ENSP00000417659:p.Val349Leu		162269601	Q2M3J2|Q96NM7	Missense_Mutation	SNP	ENST00000498165.1	37	CCDS33886.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.802097	0.70682	.	.	ENSG00000163590	ENST00000498165;ENST00000464260;ENST00000295839	T;T;T	0.13901	2.55;2.55;2.55	5.14	5.14	0.70334	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.20047	0.0482	M	0.71871	2.18	0.80722	D	1	P;P	0.43750	0.811;0.816	B;B	0.38264	0.269;0.194	T	0.04900	-1.0919	10	0.87932	D	0	.	17.5985	0.88018	0.0:0.0:1.0:0.0	.	222;349	Q5SGD2-3;Q5SGD2	.;PPM1L_HUMAN	L	349;170;222	ENSP00000417659:V349L;ENSP00000420746:V170L;ENSP00000295839:V222L	ENSP00000295839:V222L	V	+	1	0	PPM1L	162269601	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.447000	0.97595	2.395000	0.81488	0.655000	0.94253	GTG		0.443	PPM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353019.1	NM_139245		T	160786907	G	T	160786907	3	4	103	1	0	0	0	0	1	0	0	0	12378	1261	44	2	1059	2	PPM1L	3	160786907	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	6731382	160786907	37235523	66	27165										
SKIL	6498	hgsc.bcm.edu	37	chr3	170110052	170110052	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttttaaatcacatagttggcAgaactgaggcagagattgga	11	5	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:170110052A>G	ENST00000458537.3	+	6	2611	c.1902A>G	c.(1900-1902)gcA>gcG	p.A634A	SKIL_ENST00000426052.2_Silent_p.A614A|SKIL_ENST00000413427.2_Silent_p.A588A|SKIL_ENST00000259119.4_Silent_p.A634A	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	634					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CATAGTTGGCAGAACTGAGGC	0.363																																																0			3											86	90	89					3																	170110052		2203	4300	6503	171592746	SO:0001819	synonymous_variant	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.1902A>G	3.37:g.170110052A>G			171592746	A6NGT1|B4DT50|O00464|P12756|Q07501	Silent	SNP	ENST00000458537.3	37	CCDS33890.1																																																																																				0.363	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		G	170110052	A	G	170110052	2	3	103	1	0	0	0	0	0	0	0	1	14395	175	7	4		4	SKIL	3	170110052	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	9323145	170110052	27912378	67	27166										
KCNMB2	10242	hgsc.bcm.edu	37	chr3	178560615	178560615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccaacgtgctgttccattcaCtcttctggccaacctgtatg	7	14	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:178560615C>T	ENST00000432997.1	+	5	950	c.598C>T	c.(598-600)Ctc>Ttc	p.L200F	RP11-385J1.2_ENST00000437488.1_RNA|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA|KCNMB2_ENST00000452583.1_Missense_Mutation_p.L200F|KCNMB2_ENST00000420517.2_Missense_Mutation_p.L200F|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000358316.3_Missense_Mutation_p.L200F	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	214					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)	p.L200V(1)		NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	GTTCCATTCACTCTTCTGGCC	0.468																																																1	Substitution - Missense(1)	ovary(1)	3											91	87	88					3																	178560615		2203	4300	6503	180043309	SO:0001583	missense	27094			AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"Potassium channels"	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.598C>T	3.37:g.178560615C>T	ENSP00000407592:p.Leu200Phe		180043309	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	37	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980876	0.53827	.	.	ENSG00000197584	ENST00000420517;ENST00000452583;ENST00000432997;ENST00000358316;ENST00000457763	T;T;T;T	0.15256	2.44;2.44;2.44;2.44	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.29817	0.0745	L	0.36672	1.1	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.02064	-1.1220	10	0.34782	T	0.22	-15.6833	11.7155	0.51650	0.0:0.8656:0.0:0.1344	.	200	Q9Y691	KCMB2_HUMAN	F	200;200;200;200;181	ENSP00000408252:L200F;ENSP00000397483:L200F;ENSP00000407592:L200F;ENSP00000351068:L200F	ENSP00000351068:L200F	L	+	1	0	KCNMB2	180043309	0.992000	0.36948	0.997000	0.53966	0.981000	0.71138	2.928000	0.48908	1.627000	0.50400	0.655000	0.94253	CTC		0.468	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361		T	178560615	C	T	178560615	3	4	103	1	0	0	0	0	1	0	0	0	8096	565	20	3	612	3	KCNMB2	3	178560615	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	8450563	178560615	19461815	68	27167										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916836	178916836	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acattttcgtaagtgttactCaagaagcagaaagggaagaa	10	5	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:178916836C>A	ENST00000263967.3	+	2	380	c.223C>A	c.(223-225)Caa>Aaa	p.Q75K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	75	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q75E(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAGTGTTACTCAAGAAGCAGA	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	central_nervous_system(1)	3											101	96	97					3																	178916836		1816	4084	5900	180399530	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.223C>A	3.37:g.178916836C>A	ENSP00000263967:p.Gln75Lys		180399530	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.197211	0.58126	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.72942	-0.7;-0.7	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	L	0.39898	1.24	0.80722	D	1	P	0.36086	0.536	B	0.31686	0.134	T	0.60850	-0.7181	9	.	.	.	-0.0534	19.2635	0.93977	0.0:1.0:0.0:0.0	.	75	P42336	PK3CA_HUMAN	K	75	ENSP00000263967:Q75K;ENSP00000417479:Q75K	.	Q	+	1	0	PIK3CA	180399530	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.436000	0.80404	2.547000	0.85894	0.555000	0.69702	CAA		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178916836	C	A	178916836	3	1	103	1	0	0	0	0	1	0	0	0	11944	827	29	2	225	2	PIK3CA	3	178916836	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	356221	178916836	19105594	69	27168										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916957	178916957	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgaagaaaagatcctcaatcGagaaattggtatgatacaat	8	5	1	5	rs200018596		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:178916957G>C	ENST00000263967.3	+	2	501	c.344G>C	c.(343-345)cGa>cCa	p.R115P		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	115					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R115L(3)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATCCTCAATCGAGAAATTGGT	0.333		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Substitution - Missense(3)	endometrium(2)|upper_aerodigestive_tract(1)	3											71	67	69					3																	178916957		1815	4070	5885	180399651	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.344G>C	3.37:g.178916957G>C	ENSP00000263967:p.Arg115Pro		180399651	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.428354	0.62844	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.72725	0.92;-0.68	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.65217	0.2670	L	0.44542	1.39	0.80722	D	1	P	0.47841	0.901	B	0.39876	0.312	T	0.65442	-0.6167	9	.	.	.	-14.1086	19.4271	0.94746	0.0:0.0:1.0:0.0	.	115	P42336	PK3CA_HUMAN	P	115	ENSP00000263967:R115P;ENSP00000417479:R115P	.	R	+	2	0	PIK3CA	180399651	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.289000	0.96061	2.584000	0.87258	0.555000	0.69702	CGA		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178916957	G	C	178916957	3	2	103	1	0	0	0	0	1	0	0	0	11944	1058	37	5	346	5	PIK3CA	3	178916957	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	121	178916957	19105473	70	27169										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178928081	178928081	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccagtacctcatggattagaAgatttgctgaaccctattgg	9	9	1	3	rs397517200		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:178928081A>G	ENST00000263967.3	+	8	1516	c.1359A>G	c.(1357-1359)gaA>gaG	p.E453E		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	453	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		E -> Q (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity; may disrupt the interaction of the C2 PI3K-type domain with the iSH2 region of the p85 regulatory subunit).|Missing (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H450fs*9(1)|p.G451_L456>V(1)|p.P449_L455del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGGATTAGAAGATTTGCTGA	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	3	Complex - frameshift(1)|Complex - deletion inframe(1)|Deletion - In frame(1)	endometrium(2)|breast(1)	3											136	129	131					3																	178928081		1828	4091	5919	180410775	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1359A>G	3.37:g.178928081A>G			180410775	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178928081	A	G	178928081	2	3	103	1	0	0	0	0	0	0	0	1	11944	69	3	4		4	PIK3CA	3	178928081	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	11124	178928081	19094349	71	27170										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182755018	182755018	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttccataccatgtgcctgaaGagtgaaagtgtcggtcatgg	12	8	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:182755018G>A	ENST00000265594.4	-	13	1728	c.1582C>T	c.(1582-1584)Ctt>Ttt	p.L528F	MCCC1_ENST00000492597.1_Missense_Mutation_p.L419F|MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000539926.1_Missense_Mutation_p.L393F	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	528					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	TGTGCCTGAAGAGTGAAAGTG	0.473																																																0			3											107	90	96					3																	182755018		2203	4300	6503	184237712	SO:0001583	missense	56922			AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1582C>T	3.37:g.182755018G>A	ENSP00000265594:p.Leu528Phe		184237712	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	G	0.433	-0.902620	0.02453	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176	D;D;D;D	0.95724	-3.79;-3.72;-3.57;-3.53	5.93	1.42	0.22433	.	0.514577	0.15064	U	0.282612	D	0.87309	0.6145	L	0.29908	0.895	0.09310	N	1	P;P;B	0.40266	0.71;0.71;0.002	B;B;B	0.30029	0.11;0.11;0.009	T	0.80656	-0.1285	10	0.45353	T	0.12	.	3.4677	0.07555	0.0868:0.1469:0.4103:0.356	.	481;419;528	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	F	528;419;378;393;481	ENSP00000265594:L528F;ENSP00000419898:L419F;ENSP00000441253:L393F;ENSP00000420433:L481F	ENSP00000265594:L528F	L	-	1	0	MCCC1	184237712	0.006000	0.16342	0.003000	0.11579	0.003000	0.03518	1.209000	0.32357	0.729000	0.32403	0.561000	0.74099	CTT		0.473	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		A	182755018	G	A	182755018	3	1	103	1	0	0	0	0	1	0	0	0	9404	942	33	3	623	3	MCCC1	3	182755018	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	3826937	182755018	15267412	72	27171										
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183860605	183860605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagaagagagtgaaagtgaaAgtgagcaaagtatggattct	13	2	1	5			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:183860605A>G	ENST00000273783.3	+	11	1707	c.1585A>G	c.(1585-1587)Agt>Ggt	p.S529G	EIF2B5_ENST00000444495.1_Missense_Mutation_p.S529G	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	529					astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			TGAAAGTGAAAGTGAGCAAAG	0.483																																																0			3											38	42	41					3																	183860605		2203	4300	6503	185343299	SO:0001583	missense	8893			U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.1585A>G	3.37:g.183860605A>G	ENSP00000273783:p.Ser529Gly		185343299	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	a	15.21	2.767130	0.49574	.	.	ENSG00000145191	ENST00000273783;ENST00000444495;ENST00000544027	D;D	0.98164	-4.76;-4.73	5.89	4.72	0.59763	.	0.080417	0.85682	D	0.000000	D	0.97983	0.9336	M	0.65498	2.005	0.80722	D	1	P;D	0.60575	0.935;0.988	P;P	0.54759	0.559;0.76	D	0.97028	0.9748	10	0.39692	T	0.17	.	13.3526	0.60611	0.8684:0.1316:0.0:0.0	.	529;529	E9PC74;Q13144	.;EI2BE_HUMAN	G	529;529;285	ENSP00000273783:S529G;ENSP00000409142:S529G	ENSP00000273783:S529G	S	+	1	0	EIF2B5	185343299	1.000000	0.71417	0.996000	0.52242	0.923000	0.55619	8.691000	0.91279	1.038000	0.40049	0.459000	0.35465	AGT		0.483	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1			G	183860605	A	G	183860605	3	3	103	1	0	0	0	0	1	0	0	0	5015	72	3	4	1627	4	EIF2B5	3	183860605	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1105587	183860605	14161825	73	27172										
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184428939	184428939	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaggcacccgcctgtaactgAgatatcgctgctgcacaaaa	10	12	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:184428939A>C	ENST00000317897.3	-	1	897	c.671T>G	c.(670-672)cTc>cGc	p.L224R		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	224	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(143;4.61e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;5.64e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.56e-22)			CCTGTAACTGAGATATCGCTG	0.502																																																0			3											62	70	67					3																	184428939		2203	4300	6503	185911633	SO:0001583	missense	64110			AF295378	CCDS3269.1	3q13	2008-02-05			ENSG00000177383	ENSG00000177383			29639	protein-coding gene	gene with protein product		609267				11313144	Standard	NM_022149		Approved		uc003fpa.3	Q9HAY2	OTTHUMG00000156712	ENST00000317897.3:c.671T>G	3.37:g.184428939A>C	ENSP00000315064:p.Leu224Arg		185911633	Q9H215	Missense_Mutation	SNP	ENST00000317897.3	37	CCDS3269.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.968533	0.53614	.	.	ENSG00000177383	ENST00000317897	T	0.19806	2.12	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000003	T	0.55081	0.1898	H	0.94698	3.57	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57568	-0.7789	10	0.87932	D	0	.	10.6447	0.45613	1.0:0.0:0.0:0.0	.	224	Q9HAY2	MAGF1_HUMAN	R	224	ENSP00000315064:L224R	ENSP00000315064:L224R	L	-	2	0	MAGEF1	185911633	0.284000	0.24287	0.025000	0.17156	0.661000	0.39034	2.276000	0.43408	2.087000	0.62958	0.528000	0.53228	CTC		0.502	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		C	184428939	A	C	184428939	3	2	103	1	0	0	0	0	1	0	0	0	9217	304	11	4	256	4	MAGEF1	3	184428939	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	568334	184428939	13593491	74	27173										
HRG	3273	hgsc.bcm.edu	37	chr3	186389431	186389431	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtctcttcagcactggccaaTaccaaagatagtccggtcct	8	13	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:186389431T>C	ENST00000232003.4	+	4	491	c.411T>C	c.(409-411)aaT>aaC	p.N137N		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	137	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.N137K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		CACTGGCCAATACCAAAGATA	0.433																																																1	Substitution - Missense(1)	ovary(1)	3											94	93	93					3																	186389431		2203	4300	6503	187872125	SO:0001819	synonymous_variant	3273				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.411T>C	3.37:g.186389431T>C			187872125	B9EK35|D3DNU7	Silent	SNP	ENST00000232003.4	37	CCDS3280.1																																																																																				0.433	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		C	186389431	T	C	186389431	2	2	103	1	0	0	0	0	0	0	0	1	7375	1403	49	4		4	HRG	3	186389431	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1960492	186389431	11632999	75	27174										
RTP1	132112	hgsc.bcm.edu	37	chr3	186917742	186917742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggcgcccagccccaccaagTcgcaggaccagacgggctca	13	17	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:186917742T>C	ENST00000312295.4	+	2	706	c.676T>C	c.(676-678)Tcg>Ccg	p.S226P	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	226					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		CCCCACCAAGTCGCAGGACCA	0.627																																																0			3											58	55	56					3																	186917742		2203	4300	6503	188400436	SO:0001583	missense	132112			BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.676T>C	3.37:g.186917742T>C	ENSP00000311712:p.Ser226Pro		188400436		Missense_Mutation	SNP	ENST00000312295.4	37	CCDS3287.2	.	.	.	.	.	.	.	.	.	.	T	8.903	0.956859	0.18507	.	.	ENSG00000175077	ENST00000312295	T	0.13778	2.56	5.74	2.88	0.33553	.	0.266250	0.32028	N	0.006696	T	0.03011	0.0089	N	0.01576	-0.805	0.22156	N	0.999324	B	0.02656	0.0	B	0.01281	0.0	T	0.44360	-0.9333	10	0.02654	T	1	.	3.4376	0.07452	0.1637:0.5635:0.1789:0.094	.	226	P59025	RTP1_HUMAN	P	226	ENSP00000311712:S226P	ENSP00000311712:S226P	S	+	1	0	RTP1	188400436	0.803000	0.28956	0.993000	0.49108	0.274000	0.26718	0.581000	0.23819	1.449000	0.47699	-0.132000	0.14878	TCG		0.627	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		C	186917742	T	C	186917742	3	2	103	1	0	0	0	0	1	0	0	0	13770	1667	58	4	682	4	RTP1	3	186917742	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	528311	186917742	11104688	76	27175										
TP63	8626	hgsc.bcm.edu	37	chr3	189585724	189585724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taatcattgttactctggaaAccagagagtaagtggcgtat	10	6	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr3:189585724A>G	ENST00000264731.3	+	7	1074	c.985A>G	c.(985-987)Acc>Gcc	p.T329A	TP63_ENST00000392461.3_Missense_Mutation_p.T235A|TP63_ENST00000392460.3_Missense_Mutation_p.T329A|TP63_ENST00000456148.1_Missense_Mutation_p.T235A|TP63_ENST00000382063.4_Missense_Mutation_p.T244A|TP63_ENST00000418709.2_Missense_Mutation_p.T329A|TP63_ENST00000320472.5_Missense_Mutation_p.T329A|TP63_ENST00000440651.2_Missense_Mutation_p.T329A|TP63_ENST00000392463.2_Missense_Mutation_p.T235A|TP63_ENST00000354600.5_Missense_Mutation_p.T235A|TP63_ENST00000437221.1_Missense_Mutation_p.T235A|TP63_ENST00000449992.1_Missense_Mutation_p.T150A	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	329					apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)	p.T329P(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TACTCTGGAAACCAGAGAGTA	0.403										HNSCC(45;0.13)																																						1	Substitution - Missense(1)	ovary(1)	3											76	70	72					3																	189585724		2203	4300	6503	191068418	SO:0001583	missense	8626			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.985A>G	3.37:g.189585724A>G	ENSP00000264731:p.Thr329Ala		191068418	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.953910	0.53293	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000449992;ENST00000456148	D;D;D;D;D;D;D;D;D;D;D;D	0.99755	-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64	5.61	4.44	0.53790	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99354	0.9773	M	0.75615	2.305	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.28055	0.033;0.033;0.166;0.016;0.033;0.044;0.019;0.089;0.199;0.044	B;B;B;B;B;B;B;B;B;B	0.40165	0.128;0.077;0.215;0.096;0.128;0.059;0.098;0.128;0.321;0.059	D	0.99947	1.1483	9	.	.	.	-3.4352	11.1089	0.48221	0.9262:0.0:0.0738:0.0	.	150;329;329;235;235;235;235;329;329;329	Q9H3D4-10;Q9H3D4-7;Q9H3D4-11;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;.;.;.;.;.;.;P63_HUMAN;.	A	329;329;329;329;329;244;235;235;235;235;150;235	ENSP00000264731:T329A;ENSP00000407144:T329A;ENSP00000317510:T329A;ENSP00000376253:T329A;ENSP00000394337:T329A;ENSP00000371495:T244A;ENSP00000346614:T235A;ENSP00000392488:T235A;ENSP00000376256:T235A;ENSP00000376254:T235A;ENSP00000387839:T150A;ENSP00000389485:T235A	.	T	+	1	0	TP63	191068418	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.014000	0.64029	2.143000	0.66587	0.533000	0.62120	ACC		0.403	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		G	189585724	A	G	189585724	3	3	103	1	0	0	0	0	1	0	0	0	16432	43	2	4	1057	4	TP63	3	189585724	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2667982	189585724	8436706	77	27176										
KIT	3815	hgsc.bcm.edu	37	chr4	55592081	55592081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taaactcatctgggccaccgTttggaaagctagtggttcag	11	9	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:55592081T>C	ENST00000288135.5	+	9	1502	c.1405T>C	c.(1405-1407)Ttt>Ctt	p.F469L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	469	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.F469L(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGGCCACCGTTTGGAAAGCT	0.458		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - Missense(1)	bone(1)	4											112	101	105					4																	55592081		2203	4300	6503	55286838	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1405T>C	4.37:g.55592081T>C	ENSP00000288135:p.Phe469Leu		55286838	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.412154	0.42817	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.02837	4.14;4.14	5.9	4.72	0.59763	Immunoglobulin-like fold (1);	0.281938	0.30890	N	0.008661	T	0.04543	0.0124	M	0.62209	1.925	0.36234	D	0.852837	B;B	0.09022	0.002;0.0	B;B	0.09377	0.003;0.004	T	0.19289	-1.0310	10	0.35671	T	0.21	.	10.5319	0.44981	0.0:0.073:0.0:0.927	.	469;469	P10721-2;P10721	.;KIT_HUMAN	L	469	ENSP00000288135:F469L;ENSP00000390987:F469L	ENSP00000288135:F469L	F	+	1	0	KIT	55286838	0.998000	0.40836	0.008000	0.14137	0.016000	0.09150	3.562000	0.53777	1.062000	0.40625	0.533000	0.62120	TTT		0.458	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55592081	T	C	55592081	3	2	103	1	0	0	0	0	1	0	0	0	8350	1725	60	4	1439	4	KIT	4	55592081	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10		55592081	135562195	78	27177										
KIT	3815	hgsc.bcm.edu	37	chr4	55593694	55593694	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caaatgggagtttcccagaaAcaggctgagttttggtcagt	12	7	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:55593694A>G	ENST00000288135.5	+	11	1857	c.1760A>G	c.(1759-1761)aAc>aGc	p.N587S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	587					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.I571_N587del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTTCCCAGAAACAGGCTGAGT	0.408		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Deletion - In frame(1)	soft_tissue(1)	4											69	67	68					4																	55593694		2203	4300	6503	55288451	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1760A>G	4.37:g.55593694A>G	ENSP00000288135:p.Asn587Ser		55288451	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066869	0.55539	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.89050	-2.46;-2.46	6.06	4.89	0.63831	Protein kinase-like domain (1);	0.080023	0.53938	N	0.000060	D	0.87273	0.6136	M	0.75777	2.31	0.42796	D	0.993915	B;P;B	0.35208	0.08;0.49;0.388	B;B;B	0.31016	0.016;0.096;0.123	D	0.86440	0.1766	10	0.72032	D	0.01	.	11.8041	0.52143	0.9322:0.0:0.0678:0.0	.	94;583;587	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	S	587;583	ENSP00000288135:N587S;ENSP00000390987:N583S	ENSP00000288135:N587S	N	+	2	0	KIT	55288451	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	9.150000	0.94667	1.128000	0.42052	0.533000	0.62120	AAC		0.408	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55593694	A	G	55593694	3	3	103	1	0	0	0	0	1	0	0	0	8350	43	2	4	1802	4	KIT	4	55593694	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1613	55593694	135560582	79	27178										
KIT	3815	hgsc.bcm.edu	37	chr4	55595599	55595599	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttgttcaaagcaggaagatCatgcagaagctgcactttat	9	7	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:55595599C>T	ENST00000288135.5	+	14	2186	c.2089C>T	c.(2089-2091)Cat>Tat	p.H697Y		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	697	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.H697Y(1)|p.H697fs*28(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCAGGAAGATCATGCAGAAGC	0.378		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	2	Substitution - Missense(1)|Deletion - Frameshift(1)	thymus(1)|soft_tissue(1)	4											108	112	111					4																	55595599		2203	4300	6503	55290356	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2089C>T	4.37:g.55595599C>T	ENSP00000288135:p.His697Tyr		55290356	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523887	0.27299	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.77098	-1.07;-1.06	6.06	6.06	0.98353	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.379912	0.25310	N	0.031594	T	0.69378	0.3104	N	0.19112	0.55	0.37226	D	0.905454	B;B;B	0.33238	0.301;0.006;0.403	B;B;P	0.44860	0.089;0.012;0.462	T	0.64054	-0.6497	10	0.02654	T	1	.	14.4463	0.67352	0.147:0.853:0.0:0.0	.	204;693;697	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	Y	697;693	ENSP00000288135:H697Y;ENSP00000390987:H693Y	ENSP00000288135:H697Y	H	+	1	0	KIT	55290356	1.000000	0.71417	0.634000	0.29324	0.686000	0.39977	2.782000	0.47758	2.882000	0.98803	0.655000	0.94253	CAT		0.378	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55595599	C	T	55595599	3	4	103	1	0	0	0	0	1	0	0	0	8350	826	29	3	2143	3	KIT	4	55595599	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1905	55595599	135558677	80	27179										
KDR	3791	hgsc.bcm.edu	37	chr4	55946257	55946257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgtgtcatcggagtgatatcCggactggtagccgcttgtct	13	9	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:55946257C>T	ENST00000263923.4	-	30	4217	c.3922G>A	c.(3922-3924)Gga>Aga	p.G1308R	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1308					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.G1308*(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAGTGATATCCGGACTGGTAG	0.512			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - Nonsense(1)	lung(1)	4											180	172	175					4																	55946257		2203	4300	6503	55641014	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3922G>A	4.37:g.55946257C>T	ENSP00000263923:p.Gly1308Arg		55641014	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487782	0.84854	.	.	ENSG00000128052	ENST00000263923	T	0.75821	-0.97	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.85974	0.5822	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82587	-0.0383	10	0.25751	T	0.34	.	19.6607	0.95868	0.0:1.0:0.0:0.0	.	1308	P35968	VGFR2_HUMAN	R	1308	ENSP00000263923:G1308R	ENSP00000263923:G1308R	G	-	1	0	KDR	55641014	1.000000	0.71417	0.925000	0.36789	0.894000	0.52154	7.487000	0.81328	2.660000	0.90430	0.650000	0.86243	GGA		0.512	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			T	55946257	C	T	55946257	3	4	103	1	0	0	0	0	1	0	0	0	8160	661	23	1	152	1	KDR	4	55946257	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	350658	55946257	135208019	81	27180										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79238639	79238639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccgctgtggagagggtttctActctgaccatggagtctgca	13	10	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:79238639A>G	ENST00000325942.6	+	17	2377	c.1937A>G	c.(1936-1938)tAc>tGc	p.Y646C	FRAS1_ENST00000264895.6_Missense_Mutation_p.Y646C|FRAS1_ENST00000264899.6_Missense_Mutation_p.Y646C	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	646					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAGGGTTTCTACTCTGACCAT	0.522																																																0			4											72	76	75					4																	79238639		2026	4198	6224	79457663	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1937A>G	4.37:g.79238639A>G	ENSP00000326330:p.Tyr646Cys		79457663	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.09|13.09	2.133104|2.133104	0.37630|0.37630	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000325942;ENST00000264895;ENST00000264899	.|D;D;D	.|0.90004	.|-2.6;-2.6;-2.6	5.71|5.71	5.71|5.71	0.89125|0.89125	.|Growth factor, receptor (1);	.|0.071118	.|0.64402	.|D	.|0.000018	D|D	0.95655|0.95655	0.8587|0.8587	H|H	0.95679|0.95679	3.705|3.705	0.42869|0.42869	D|D	0.994136|0.994136	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.79784	.|0.971;0.982;0.979;0.993	D|D	0.96391|0.96391	0.9289|0.9289	5|10	.|0.87932	.|D	.|0	.|.	10.25|10.25	0.43364|0.43364	0.8521:0.0:0.0:0.1479|0.8521:0.0:0.0:0.1479	.|.	.|646;646;646;646	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	A|C	575|646	.|ENSP00000326330:Y646C;ENSP00000264895:Y646C;ENSP00000264899:Y646C	.|ENSP00000264895:Y646C	T|Y	+|+	1|2	0|0	FRAS1|FRAS1	79457663|79457663	0.998000|0.998000	0.40836|0.40836	0.991000|0.991000	0.47740|0.47740	0.056000|0.056000	0.15407|0.15407	4.162000|4.162000	0.58177|0.58177	2.184000|2.184000	0.69523|0.69523	0.459000|0.459000	0.35465|0.35465	ACT|TAC		0.522	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			G	79238639	A	G	79238639	3	3	103	1	0	0	0	0	1	0	0	0	6061	391	14	4	2003	4	FRAS1	4	79238639	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	23292382	79238639	111915637	82	27181										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79786719	79786719	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttctgttgtagaataacagAtaccattggaccaacagaaa	7	8	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:79786719A>G	ENST00000335016.5	+	10	1242	c.1076A>G	c.(1075-1077)gAt>gGt	p.D359G	BMP2K_ENST00000502871.1_Missense_Mutation_p.D359G	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	359					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AGAATAACAGATACCATTGGA	0.358																																																0			4											95	89	91					4																	79786719		2203	4300	6503	80005743	SO:0001583	missense	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1076A>G	4.37:g.79786719A>G	ENSP00000334836:p.Asp359Gly		80005743	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109071	0.77096	.	.	ENSG00000138756	ENST00000502871;ENST00000335016;ENST00000264889	T;T	0.73897	1.98;-0.79	5.26	5.26	0.73747	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.77811	0.4186	M	0.72353	2.195	0.80722	D	1	P;P	0.49185	0.92;0.79	P;B	0.48304	0.573;0.306	T	0.76653	-0.2880	10	0.27082	T	0.32	-15.5031	15.4859	0.75569	1.0:0.0:0.0:0.0	.	359;359	Q9NSY1;Q4W5H2	BMP2K_HUMAN;.	G	359;359;373	ENSP00000421768:D359G;ENSP00000334836:D359G	ENSP00000264889:D373G	D	+	2	0	BMP2K	80005743	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.378000	0.90144	2.125000	0.65367	0.533000	0.62120	GAT		0.358	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		G	79786719	A	G	79786719	3	3	103	1	0	0	0	0	1	0	0	0	1461	333	12	4	1114	4	BMP2K	4	79786719	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	548080	79786719	111367557	83	27182										
ATOH1	474	hgsc.bcm.edu	37	chr4	94750181	94750181	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cccgcaaccgccgccgccgcCgcagccacctgcaactttgc	9	22	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:94750181C>A	ENST00000306011.3	+	1	140	c.104C>A	c.(103-105)cCg>cAg	p.P35Q		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	35	Poly-Pro.				auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CCGCCGCCGCCGCAGCCACCT	0.672																																																0			4											23	26	25					4																	94750181		2197	4289	6486	94969204	SO:0001583	missense	474			U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"Basic helix-loop-helix proteins"	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.104C>A	4.37:g.94750181C>A	ENSP00000302216:p.Pro35Gln		94969204	Q14CT9	Missense_Mutation	SNP	ENST00000306011.3	37	CCDS3638.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006290	0.19199	.	.	ENSG00000172238	ENST00000306011	D	0.99089	-5.41	4.2	4.2	0.49525	.	.	.	.	.	D	0.95733	0.8612	N	0.08118	0	0.27740	N	0.944506	P	0.42039	0.769	B	0.39738	0.308	D	0.92211	0.5776	9	0.35671	T	0.21	-8.1124	14.1101	0.65115	0.0:1.0:0.0:0.0	.	35	Q92858	ATOH1_HUMAN	Q	35	ENSP00000302216:P35Q	ENSP00000302216:P35Q	P	+	2	0	ATOH1	94969204	0.036000	0.19791	0.408000	0.26446	0.011000	0.07611	0.804000	0.27098	2.173000	0.68751	0.573000	0.79308	CCG		0.672	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		A	94750181	C	A	94750181	3	1	103	1	0	0	0	0	1	0	0	0	1113	652	23	2	106	2	ATOH1	4	94750181	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	14963462	94750181	96404095	84	27183										
UNC5C	8633	hgsc.bcm.edu	37	chr4	96199474	96199474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttcctgttccaaagacactTcctttcctaggggttcctgc	7	14	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:96199474T>C	ENST00000453304.1	-	4	878	c.530A>G	c.(529-531)gAa>gGa	p.E177G	UNC5C_ENST00000504962.1_Missense_Mutation_p.E177G|UNC5C_ENST00000506749.1_Missense_Mutation_p.E177G	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	177	Ig-like C2-type.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CAAAGACACTTCCTTTCCTAG	0.413																																																0			4											153	136	142					4																	96199474		2203	4300	6503	96418497	SO:0001583	missense	8633			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.530A>G	4.37:g.96199474T>C	ENSP00000406022:p.Glu177Gly		96418497	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.702447	0.88924	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796;ENST00000506749;ENST00000504962	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.64	5.64	0.86602	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	M	0.73372	2.23	0.80722	D	1	B;P;P	0.47191	0.02;0.891;0.761	B;P;P	0.51487	0.049;0.671;0.58	T	0.77395	-0.2604	10	0.52906	T	0.07	.	15.862	0.79032	0.0:0.0:0.0:1.0	.	177;177;177	A8K385;E0CX15;O95185	.;.;UNC5C_HUMAN	G	177;136;177;177;177	ENSP00000406022:E177G;ENSP00000426924:E177G;ENSP00000426153:E177G;ENSP00000425117:E177G	ENSP00000328673:E136G	E	-	2	0	UNC5C	96418497	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.984000	0.88150	2.145000	0.66743	0.460000	0.39030	GAA		0.413	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		C	96199474	T	C	96199474	3	2	103	1	0	0	0	0	1	0	0	0	17033	1783	62	4	2317	4	UNC5C	4	96199474	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1449293	96199474	94954802	85	27184										
GAB1	2549	hgsc.bcm.edu	37	chr4	144359719	144359719	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcgccttcacgtagtaatacCatttccactgtggatttaaa	6	10	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:144359719C>T	ENST00000262994.4	+	4	1463	c.1161C>T	c.(1159-1161)acC>acT	p.T387T	GAB1_ENST00000262995.4_Silent_p.T387T|GAB1_ENST00000505913.1_Silent_p.T284T	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	387			T -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					GTAGTAATACCATTTCCACTG	0.413																																																0			4											110	99	103					4																	144359719		2203	4300	6503	144579169	SO:0001819	synonymous_variant	128869			U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1161C>T	4.37:g.144359719C>T			144579169	A8K152|Q4W5G2|Q6P1W2	Silent	SNP	ENST00000262994.4	37	CCDS3759.1																																																																																				0.413	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		T	144359719	C	T	144359719	2	4	103	1	0	0	0	0	0	0	0	1	6167	581	21	3		3	GAB1	4	144359719	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	48160245	144359719	46794557	86	27185										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249383	153249383	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttttcatgaagatgcatacaAcgcacagtggaagtatgccc	9	9	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:153249383A>G	ENST00000281708.4	-	9	2624	c.1395T>C	c.(1393-1395)cgT>cgC	p.R465R	FBXW7_ENST00000393956.3_Silent_p.R289R|FBXW7_ENST00000296555.5_Silent_p.R347R|FBXW7_ENST00000263981.5_Silent_p.R385R|FBXW7_ENST00000603841.1_Silent_p.R465R|FBXW7_ENST00000603548.1_Silent_p.R465R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GATGCATACAACGCACAGTGG	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											253	218	230					4																	153249383		2203	4300	6503	153468833	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1395T>C	4.37:g.153249383A>G			153468833	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153249383	A	G	153249383	2	3	103	1	0	0	0	0	0	0	0	1	5788	30	2	4		4	FBXW7	4	153249383	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	8889664	153249383	37904893	87	27186										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153253790	153253790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccagagaaggttgtcttcagCcaaaattctccagtagcgac	9	11	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:153253790C>T	ENST00000281708.4	-	6	2172	c.943G>A	c.(943-945)Gct>Act	p.A315T	FBXW7_ENST00000393956.3_Missense_Mutation_p.A139T|FBXW7_ENST00000296555.5_Missense_Mutation_p.A197T|FBXW7_ENST00000263981.5_Missense_Mutation_p.A235T|FBXW7_ENST00000603841.1_Missense_Mutation_p.A315T|FBXW7_ENST00000603548.1_Missense_Mutation_p.A315T	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	315	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.A315T(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TTGTCTTCAGCCAAAATTCTC	0.403			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	2	Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	4											76	78	77					4																	153253790		2203	4300	6503	153473240	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.943G>A	4.37:g.153253790C>T	ENSP00000281708:p.Ala315Thr		153473240	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.117157	0.94385	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.05	6.05	0.98169	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.52789	0.1756	L	0.56199	1.76	0.80722	D	1	P;P;P;P	0.43542	0.727;0.81;0.68;0.68	B;B;B;B	0.40659	0.224;0.336;0.143;0.143	T	0.44452	-0.9327	10	0.23302	T	0.38	-19.4569	20.6013	0.99457	0.0:1.0:0.0:0.0	.	139;315;197;235	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	T	315;197;235;139	ENSP00000281708:A315T;ENSP00000296555:A197T;ENSP00000263981:A235T;ENSP00000377528:A139T	ENSP00000263981:A235T	A	-	1	0	FBXW7	153473240	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.760000	0.85248	2.878000	0.98634	0.650000	0.86243	GCT		0.403	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153253790	C	T	153253790	3	4	103	1	0	0	0	0	1	0	0	0	5788	739	26	3	1208	3	FBXW7	4	153253790	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	4407	153253790	37900486	88	27187										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158257749	158257749	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgtagttttattcctggtcaGcagatttagcccctacgagt	9	9	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:158257749G>T	ENST00000264426.9	+	11	1973	c.1694G>T	c.(1693-1695)aGc>aTc	p.S565I	GRIA2_ENST00000393815.2_Missense_Mutation_p.S518I|GRIA2_ENST00000507898.1_Missense_Mutation_p.S518I|GRIA2_ENST00000296526.7_Missense_Mutation_p.S565I|GRIA2_ENST00000449365.1_Missense_Mutation_p.S518I	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	565					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTCCTGGTCAGCAGATTTAGC	0.403																																																0			4											175	164	168					4																	158257749		2203	4300	6503	158477199	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1694G>T	4.37:g.158257749G>T	ENSP00000264426:p.Ser565Ile		158477199	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371626	0.82573	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91	5.46	5.46	0.80206	Ionotropic glutamate receptor (2);	0.082206	0.85682	D	0.000000	T	0.56673	0.2001	M	0.81497	2.545	0.80722	D	1	P;D;D	0.89917	0.529;1.0;0.998	B;D;D	0.91635	0.194;0.999;0.993	T	0.60454	-0.7260	10	0.87932	D	0	.	19.6634	0.95882	0.0:0.0:1.0:0.0	.	565;565;518	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	I	518;518;565;565;518	ENSP00000426845:S518I;ENSP00000377403:S518I;ENSP00000296526:S565I;ENSP00000264426:S565I;ENSP00000389837:S518I	ENSP00000264426:S565I	S	+	2	0	GRIA2	158477199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.720000	0.93068	0.655000	0.94253	AGC		0.403	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			T	158257749	G	T	158257749	3	4	103	1	0	0	0	0	1	0	0	0	6789	971	34	2	1736	2	GRIA2	4	158257749	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5003959	158257749	32896527	89	27188										
WDR17	116966	hgsc.bcm.edu	37	chr4	177049909	177049909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	attctcaagtgggtgttttaCgcatttggaatgtttcaaga	10	5	2	1	rs146789582	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr4:177049909C>T	ENST00000280190.4	+	7	1039	c.883C>T	c.(883-885)Cgc>Tgc	p.R295C	WDR17_ENST00000393643.2_Missense_Mutation_p.R271C|WDR17_ENST00000508596.1_Missense_Mutation_p.R271C|WDR17_ENST00000507824.2_Missense_Mutation_p.R278C			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	295								p.R295C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GGGTGTTTTACGCATTTGGAA	0.303													C|||	2	0.000399361	8e-04	0	5008	,	,		14386	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	4						C	CYS/ARG,CYS/ARG	0,4404		0,0,2202	55	53	54		883,811	4.5	1	4	dbSNP_134	54	1,8579	1.2+/-3.3	0,1,4289	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	180,180	0,1,6491	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	295/1323,271/1284	177049909	1,12983	2202	4290	6492	177286903	SO:0001583	missense	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.883C>T	4.37:g.177049909C>T	ENSP00000280190:p.Arg295Cys		177286903	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	19.75	3.885671	0.72410	0.0	1.17E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.64260	-0.09;-0.09;-0.09	5.45	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.77857	0.4193	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80531	-0.1341	10	0.87932	D	0	-16.6086	14.1509	0.65384	0.2327:0.7673:0.0:0.0	.	271;295	E7EQX0;Q8IZU2	.;WDR17_HUMAN	C	271;271;295;278	ENSP00000422763:R271C;ENSP00000377258:R271C;ENSP00000280190:R295C	ENSP00000280190:R295C	R	+	1	0	WDR17	177286903	0.995000	0.38212	0.962000	0.40283	0.959000	0.62525	2.620000	0.46410	2.555000	0.86185	0.650000	0.86243	CGC		0.303	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177049909	C	T	177049909	3	4	103	1	0	0	0	0	1	0	0	0	17317	536	19	1	905	1	WDR17	4	177049909	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	18792160	177049909	14104367	90	27189										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527676	23527676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcagacaccagaggacacacAcaggggagaagccctatgtc	11	12	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:23527676A>G	ENST00000296682.3	+	11	2661	c.2479A>G	c.(2479-2481)Aca>Gca	p.T827A		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	827					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GAGGACACACACAGGGGAGAA	0.577										HNSCC(3;0.000094)																																						0			5											40	53	49					5																	23527676		2148	4271	6419	23563433	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2479A>G	5.37:g.23527676A>G	ENSP00000296682:p.Thr827Ala		23563433	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	7.170	0.587362	0.13812	.	.	ENSG00000164256	ENST00000296682	T	0.26518	1.73	3.02	0.0225	0.14133	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23054	0.0557	L	0.59912	1.85	0.36169	D	0.848652	B	0.10296	0.003	B	0.17979	0.02	T	0.12167	-1.0558	9	0.66056	D	0.02	-0.0365	6.8079	0.23788	0.5591:0.0:0.0:0.4409	.	827	Q9NQV7	PRDM9_HUMAN	A	827	ENSP00000296682:T827A	ENSP00000296682:T827A	T	+	1	0	PRDM9	23563433	0.998000	0.40836	0.999000	0.59377	0.178000	0.23041	1.473000	0.35387	0.028000	0.15324	0.386000	0.25728	ACA		0.577	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		G	23527676	A	G	23527676	3	3	103	1	0	0	0	0	1	0	0	0	12497	159	6	4	2517	4	PRDM9	5	23527676	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10		23527676	157387584	91	27190										
TBCA	6902	hgsc.bcm.edu	37	chr5	76989142	76989142	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tccaacctgcgctggcaatcTgggatcatcatcctggattc	9	13	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:76989142T>C	ENST00000380377.4	-	3	298	c.195A>G	c.(193-195)ccA>ccG	p.P65P	TBCA_ENST00000522370.1_Silent_p.P41P|TBCA_ENST00000520361.1_Intron|TBCA_ENST00000518338.2_Silent_p.P88P|TBCA_ENST00000517679.1_Silent_p.P76P|TBCA_ENST00000517881.1_5'UTR|TBCA_ENST00000306388.6_Silent_p.P65P|TBCA_ENST00000520039.1_3'UTR	NM_004607.2	NP_004598.1	O75347	TBCA_HUMAN	tubulin folding cofactor A	65					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_lung(232;0.000511)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.02e-49)|Epithelial(54;1.05e-44)|all cancers(79;4.08e-40)		GCTGGCAATCTGGGATCATCA	0.403																																																0			5											74	71	72					5																	76989142		2203	4300	6503	77024898	SO:0001819	synonymous_variant	6902			AF038952	CCDS4040.1, CCDS75263.1	5q14.1	2008-02-05	2006-11-21		ENSG00000171530	ENSG00000171530			11579	protein-coding gene	gene with protein product		610058	"tubulin-specific chaperone a"			9653160, 8706133	Standard	XM_005248586		Approved		uc003kfh.1	O75347	OTTHUMG00000102173	ENST00000380377.4:c.195A>G	5.37:g.76989142T>C			77024898	B4DT30	Silent	SNP	ENST00000380377.4	37	CCDS4040.1																																																																																				0.403	TBCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220021.3	NM_004607		C	76989142	T	C	76989142	2	2	103	1	0	0	0	0	0	0	0	1	15668	1567	55	4		4	TBCA	5	76989142	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	53461466	76989142	103926118	92	27191										
GPR98	84059	hgsc.bcm.edu	37	chr5	89989843	89989843	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggtgcctgacccactttggAgaacttggatgaatgtctct	12	9	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:89989843A>G	ENST00000405460.2	+	33	7366	c.7270A>G	c.(7270-7272)Aga>Gga	p.R2424G		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2424					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCCACTTTGGAGAACTTGGAT	0.483																																																0			5											80	78	78					5																	89989843		1911	4115	6026	90025599	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7270A>G	5.37:g.89989843A>G	ENSP00000384582:p.Arg2424Gly		90025599	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	5.408	0.260433	0.10239	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27557	1.66	5.92	5.92	0.95590	.	0.251771	0.44285	D	0.000467	T	0.32496	0.0831	L	0.60455	1.87	0.58432	D	0.999999	B;B	0.23490	0.086;0.041	B;B	0.24394	0.053;0.022	T	0.11060	-1.0603	10	0.66056	D	0.02	.	12.2322	0.54495	0.8582:0.1418:0.0:0.0	.	2424;2424	E7ETI5;Q8WXG9	.;GPR98_HUMAN	G	2424	ENSP00000384582:R2424G	ENSP00000296619:R2424G	R	+	1	2	GPR98	90025599	1.000000	0.71417	0.992000	0.48379	0.015000	0.08874	3.727000	0.54984	2.255000	0.74692	0.533000	0.62120	AGA		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89989843	A	G	89989843	3	3	103	1	0	0	0	0	1	0	0	0	6742	296	11	4	7400	4	GPR98	5	89989843	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	13000701	89989843	90925417	93	27192										
APC	324	hgsc.bcm.edu	37	chr5	112173801	112173801	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gttacccagctcctcttcatCaagaggaagcttagatagtt	8	10	3	2	rs79512956		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:112173801C>A	ENST00000457016.1	+	16	2890	c.2510C>A	c.(2509-2511)tCa>tAa	p.S837*	APC_ENST00000508376.2_Nonsense_Mutation_p.S837*|APC_ENST00000257430.4_Nonsense_Mutation_p.S837*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	837	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCCTCTTCATCAAGAGGAAGC	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5	GRCh37	CD011083|CD084036|CM014886	APC	D|M	rs79512956						57	59	59					5																	112173801		2202	4300	6502	112201700	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2510C>A	5.37:g.112173801C>A	ENSP00000413133:p.Ser837*		112201700	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.871363	0.97049	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.41	5.41	0.78517	.	0.376434	0.25464	N	0.030484	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7031	19.2326	0.93846	0.0:1.0:0.0:0.0	.	.	.	.	X	837;819;837;837;837	.	ENSP00000257430:S837X	S	+	2	0	APC	112201700	0.594000	0.26849	1.000000	0.80357	0.989000	0.77384	2.664000	0.46783	2.538000	0.85594	0.650000	0.86243	TCA		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112173801	C	A	112173801	4	1	103	1	0	0	0	0	0	1	0	0	763	838	29	2	2568	2	APC	5	112173801	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	22183958	112173801	68741459	94	27193			1	26		4	4	1680	N	T_G_C_A	9.41201e-07
APC	324	hgsc.bcm.edu	37	chr5	112175213	112175213	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccctgcaaatagcagaaataAaagaaaagattggaactagg	9	6	0	3	rs121913224		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:112175213A>T	ENST00000457016.1	+	16	4302	c.3922A>T	c.(3922-3924)Aaa>Taa	p.K1308*	APC_ENST00000508376.2_Nonsense_Mutation_p.K1308*|APC_ENST00000257430.4_Nonsense_Mutation_p.K1308*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1308	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*4(37)|p.I1307fs*6(12)|p.K1308*(6)|p.?(1)|p.K1192fs*3(1)|p.K1308E(1)|p.K1308fs*4(1)|p.K1308fs*6(1)|p.I1307fs*13(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGCAGAAATAAAAGAAAAGAT	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	61	Deletion - Frameshift(53)|Substitution - Nonsense(6)|Unknown(1)|Substitution - Missense(1)	large_intestine(57)|stomach(2)|soft_tissue(1)|skin(1)	5											53	55	54					5																	112175213		2202	4300	6502	112203112	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3922A>T	5.37:g.112175213A>T	ENSP00000413133:p.Lys1308*		112203112	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	37	6.614051	0.97705	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	5.73	5.73	0.89815	.	0.144296	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.286	15.9856	0.80151	1.0:0.0:0.0:0.0	.	.	.	.	X	1308	.	.	K	+	1	0	APC	112203112	1.000000	0.71417	0.992000	0.48379	0.721000	0.41392	4.589000	0.61006	2.308000	0.77769	0.533000	0.62120	AAA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175213	A	T	112175213	4	4	103	1	0	0	0	0	0	1	0	0	763	15	1	5	3980	5	APC	5	112175213	Nonsense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1412	112175213	68740047	95	27194			1	26		4	4	1680	N	T_G_C_A	9.41201e-07
APC	324	hgsc.bcm.edu	37	chr5	112175308	112175308	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaatccagcagactgcagggTtctagtttatcttcagaatc	8	9	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:112175308T>C	ENST00000457016.1	+	16	4397	c.4017T>C	c.(4015-4017)ggT>ggC	p.G1339G	APC_ENST00000508376.2_Silent_p.G1339G|APC_ENST00000257430.4_Silent_p.G1339G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1339	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1335fs*70(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GACTGCAGGGTTCTAGTTTAT	0.458		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											56	60	59					5																	112175308		2202	4300	6502	112203207	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4017T>C	5.37:g.112175308T>C			112203207	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175308	T	C	112175308	2	2	103	1	0	0	0	0	0	0	0	1	763	1712	60	4		4	APC	5	112175308	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	95	112175308	68739952	96	27195			1	26		4	4	1680	N	T_G_C_A	9.41201e-07
APC	324	hgsc.bcm.edu	37	chr5	112175480	112175480	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcagttcacttgatagttttGagagtcgttcgattgccagc	10	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:112175480G>T	ENST00000457016.1	+	16	4569	c.4189G>T	c.(4189-4191)Gag>Tag	p.E1397*	APC_ENST00000508376.2_Nonsense_Mutation_p.E1397*|APC_ENST00000257430.4_Nonsense_Mutation_p.E1397*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1397	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1399fs*9(18)|p.E1397*(8)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.E1397fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGATAGTTTTGAGAGTCGTTC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Deletion - Frameshift(20)|Substitution - Nonsense(8)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(28)|soft_tissue(1)|skin(1)	5	GRCh37	CM992136	APC	M							104	98	100					5																	112175480		2202	4300	6502	112203379	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4189G>T	5.37:g.112175480G>T	ENSP00000413133:p.Glu1397*		112203379	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	41	8.742411	0.98937	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.111909	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.9405	20.4898	0.99202	0.0:0.0:1.0:0.0	.	.	.	.	X	1397	.	.	E	+	1	0	APC	112203379	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.281000	0.78621	2.941000	0.99782	0.655000	0.94253	GAG		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175480	G	T	112175480	4	4	103	1	0	0	0	0	0	1	0	0	763	1291	45	2	4247	2	APC	5	112175480	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	172	112175480	68739780	97	27196			1	26		4	4	1680	N	T_G_C_A	9.41201e-07
TSSK1B	83942	hgsc.bcm.edu	37	chr5	112770459	112770459	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgctcagagtaagcagatttTacttttgcataggagccctc	9	10	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:112770459T>C	ENST00000390666.3	-	1	269	c.78A>G	c.(76-78)gtA>gtG	p.V26V	CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA|MCC_ENST00000408903.3_Intron	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	26	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		AAGCAGATTTTACTTTTGCAT	0.537																																																0			5											47	52	51					5																	112770459		2171	4287	6458	112798358	SO:0001819	synonymous_variant	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"serine/threonine kinase 22D (spermiogenesis associated)", "testis-specific serine kinase 1"	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.78A>G	5.37:g.112770459T>C			112798358	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																				0.537	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		C	112770459	T	C	112770459	2	2	103	1	0	0	0	0	0	0	0	1	16708	1741	61	4		4	TSSK1B	5	112770459	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	594979	112770459	68144801	98	27197										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139892480	139892480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cccttctgatatagaatgcaTgagatacatagcaacaatta	6	8	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:139892480T>C	ENST00000360839.2	+	23	4326	c.4172T>C	c.(4171-4173)aTg>aCg	p.M1391T	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.M1391T|ANKHD1_ENST00000297183.6_Missense_Mutation_p.M1391T	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1391						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATAGAATGCATGAGATACATA	0.333																																																0			5											123	128	126					5																	139892480		2202	4299	6501	139872664	SO:0001583	missense	54882			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4172T>C	5.37:g.139892480T>C	ENSP00000354085:p.Met1391Thr		139872664	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.03|14.03	2.413844|2.413844	0.42817|0.42817	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000235510;ENST00000421134;ENST00000412116;ENST00000431508;ENST00000532219|ENST00000246149	T;T;T;T;T;T|.	0.65732|.	-0.14;-0.17;-0.06;-0.14;1.86;-0.17|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.56863|.	0.2014|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	B;B;B;B;D;P|.	0.55800|.	0.022;0.012;0.038;0.011;0.973;0.932|.	B;B;B;B;P;P|.	0.61201|.	0.094;0.008;0.245;0.035;0.885;0.838|.	T|.	0.53823|.	-0.8384|.	10|.	0.23302|.	T|.	0.38|.	.|.	15.4127|15.4127	0.74941|0.74941	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1391;602;1391;1410;1391;1391|.	E9PF56;E7ET58;Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3|.	.;.;.;.;.;ANKH1_HUMAN|.	T|R	1391;1424;1391;1391;925;602;1410;544;47;1391|617	ENSP00000354085:M1391T;ENSP00000297183:M1391T;ENSP00000394489:M1410T;ENSP00000405602:M544T;ENSP00000393204:M47T;ENSP00000432016:M1391T|.	ENSP00000432016:M1391T|.	M|X	+|+	2|1	0|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139872664|139872664	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	7.997000|7.997000	0.88414|0.88414	2.106000|2.106000	0.64143|0.64143	0.456000|0.456000	0.33151|0.33151	ATG|TGA		0.333	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139892480	T	C	139892480	3	2	103	1	0	0	0	0	1	0	0	0	628	1464	51	4	4368	4	ANKHD1	5	139892480	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	27122021	139892480	41022780	99	27198										
WDR55	54853	hgsc.bcm.edu	37	chr5	140047905	140047905	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgccgagctgtggccttctCtgaagatgggcagagtgagt	15	9	1	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:140047905C>G	ENST00000358337.5	+	2	515	c.278C>G	c.(277-279)tCt>tGt	p.S93C		NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	93					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGCCTTCTCTGAAGATGGG	0.567																																																0			5											117	105	109					5																	140047905		2203	4300	6503	140028089	SO:0001583	missense	54853			AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.278C>G	5.37:g.140047905C>G	ENSP00000351100:p.Ser93Cys		140028089	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927349	0.73327	.	.	ENSG00000120314	ENST00000358337	T	0.66280	-0.2	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.81370	0.4808	M	0.90542	3.125	0.80722	D	1	D	0.64830	0.994	P	0.60682	0.878	D	0.85394	0.1127	10	0.72032	D	0.01	-8.5453	17.4665	0.87634	0.0:1.0:0.0:0.0	.	93	Q9H6Y2	WDR55_HUMAN	C	93	ENSP00000351100:S93C	ENSP00000351100:S93C	S	+	2	0	WDR55	140028089	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.453000	0.80700	2.644000	0.89710	0.563000	0.77884	TCT		0.567	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		G	140047905	C	G	140047905	3	3	103	1	0	0	0	0	1	0	0	0	17347	913	32	5	284	5	WDR55	5	140047905	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	155425	140047905	40867355	100	27199										
UBLCP1	134510	hgsc.bcm.edu	37	chr5	158696934	158696934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aggcaaacctgcagaaaatgAtgttaagcttggagctctca	10	8	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:158696934A>G	ENST00000296786.6	+	3	499	c.173A>G	c.(172-174)gAt>gGt	p.D58G		NM_145049.3	NP_659486.2	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase 1	58	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|kidney(3)|large_intestine(4)|ovary(1)	9	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCAGAAAATGATGTTAAGCTT	0.353																																																0			5											93	88	90					5																	158696934		2203	4300	6503	158629512	SO:0001583	missense	134510			AK057996	CCDS4345.1	5q33.3	2010-06-21			ENSG00000164332	ENSG00000164332	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	28110	protein-coding gene	gene with protein product	"CTD phosphatase-like with ubiquitin domain 1"	609867				15883030	Standard	NM_145049		Approved	MGC10067, CPUB1	uc003lxq.2	Q8WVY7	OTTHUMG00000130305	ENST00000296786.6:c.173A>G	5.37:g.158696934A>G	ENSP00000296786:p.Asp58Gly		158629512	D3DQJ7|Q96DK5	Missense_Mutation	SNP	ENST00000296786.6	37	CCDS4345.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028952	0.35797	.	.	ENSG00000164332	ENST00000296786	T	0.74209	-0.82	6.06	6.06	0.98353	Ubiquitin supergroup (1);Ubiquitin (2);	0.137789	0.64402	D	0.000003	T	0.69504	0.3118	L	0.42008	1.315	0.49687	D	0.999813	B	0.09022	0.002	B	0.10450	0.005	T	0.64067	-0.6494	10	0.44086	T	0.13	-11.52	16.6245	0.84952	1.0:0.0:0.0:0.0	.	58	Q8WVY7	UBCP1_HUMAN	G	58	ENSP00000296786:D58G	ENSP00000296786:D58G	D	+	2	0	UBLCP1	158629512	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.779000	0.68948	2.323000	0.78572	0.528000	0.53228	GAT		0.353	UBLCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252650.2	NM_145049		G	158696934	A	G	158696934	3	3	103	1	0	0	0	0	1	0	0	0	16931	333	12	4	179	4	UBLCP1	5	158696934	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	18649029	158696934	22218326	101	27200										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161580118	161580118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggcccctaccattgatatccGcccaagatcagcaaccattc	6	16	1	2	rs528036202	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:161580118G>A	ENST00000361925.4	+	9	1368	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	GABRG2_ENST00000356592.3_Missense_Mutation_p.R391H|GABRG2_ENST00000393933.4_Missense_Mutation_p.R288H|GABRG2_ENST00000414552.2_Missense_Mutation_p.R431H			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	383					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	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)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATTGATATCCGCCCAAGATCA	0.488													G|||	2	0.000399361	0	0	5008	,	,		19874	0		0	False		,,,				2504	0.002															0			5											118	107	111					5																	161580118		2203	4300	6503	161512696	SO:0001583	missense	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1148G>A	5.37:g.161580118G>A	ENSP00000354651:p.Arg383His		161512696	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321214	0.41096	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.85702	-2.0;-2.0;-2.02;-2.02	5.95	5.08	0.68730	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.176085	0.51477	D	0.000096	T	0.76751	0.4031	N	0.24115	0.695	0.80722	D	1	B;B;B	0.23442	0.085;0.014;0.043	B;B;B	0.20577	0.02;0.022;0.03	T	0.71636	-0.4533	10	0.32370	T	0.25	.	15.3601	0.74464	0.0668:0.0:0.9332:0.0	.	431;383;391	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	H	391;431;383;288	ENSP00000349000:R391H;ENSP00000410732:R431H;ENSP00000354651:R383H;ENSP00000377510:R288H	ENSP00000349000:R391H	R	+	2	0	GABRG2	161512696	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.671000	0.74472	1.526000	0.49068	0.655000	0.94253	CGC		0.488	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161580118	G	A	161580118	3	1	103	1	0	0	0	0	1	0	0	0	6191	1087	38	1	1334	1	GABRG2	5	161580118	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2883184	161580118	19335142	102	27201										
GRM6	2916	hgsc.bcm.edu	37	chr5	178413622	178413622	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtccacctggaagcggtaccCgtcacaggcctcgcagtgcc	12	16	1	0	rs554079886		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr5:178413622C>T	ENST00000517717.1	-	9	1671	c.1633G>A	c.(1633-1635)Ggg>Agg	p.G545R	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Missense_Mutation_p.G545R			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	545					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		AAGCGGTACCCGTCACAGGCC	0.687																																																0			5											44	39	41					5																	178413622		2203	4298	6501	178346228	SO:0001583	missense	2916			U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1633G>A	5.37:g.178413622C>T	ENSP00000430767:p.Gly545Arg		178346228		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550129	0.86127	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.89343	-2.5;-2.5	4.97	4.97	0.65823	GPCR, family 3, conserved site (1);GPCR, family 3, nine cysteines domain (1);	.	.	.	.	D	0.93588	0.7953	M	0.75615	2.305	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;P	0.97110	1.0;0.892	D	0.92087	0.5677	9	0.27785	T	0.31	.	16.0945	0.81110	0.0:1.0:0.0:0.0	.	701;545	E7EX65;O15303	.;GRM6_HUMAN	R	701;545;545	ENSP00000231188:G545R;ENSP00000430767:G545R	ENSP00000231188:G545R	G	-	1	0	GRM6	178346228	1.000000	0.71417	0.829000	0.32907	0.973000	0.67179	7.658000	0.83755	2.461000	0.83175	0.462000	0.41574	GGG		0.687	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			T	178413622	C	T	178413622	3	4	103	1	0	0	0	0	1	0	0	0	6822	652	23	1	1012	1	GRM6	5	178413622	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	16833504	178413622	2501638	103	27202										
BTN1A1	696	hgsc.bcm.edu	37	chr6	26509025	26509025	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgtagagttgtatggaaatGggtactgggccctcactcct	12	9	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:26509025G>T	ENST00000244513.6	+	7	1270	c.1204G>T	c.(1204-1206)Ggg>Tgg	p.G402W		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	402	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						GTATGGAAATGGGTACTGGGC	0.542																																																0			6											109	104	106					6																	26509025		2203	4300	6503	26617004	SO:0001583	missense	696			U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1204G>T	6.37:g.26509025G>T	ENSP00000244513:p.Gly402Trp		26617004	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498137	0.64186	.	.	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.70986	-0.53	5.91	5.04	0.67666	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.200439	0.35970	N	0.002876	T	0.69061	0.3069	L	0.45352	1.415	0.36627	D	0.876102	D	0.71674	0.998	D	0.72075	0.976	T	0.75448	-0.3314	10	0.72032	D	0.01	.	8.9869	0.35999	0.1665:0.0:0.8335:0.0	.	402	Q13410	BT1A1_HUMAN	W	402	ENSP00000244513:G402W	ENSP00000244513:G402W	G	+	1	0	BTN1A1	26617004	0.000000	0.05858	0.976000	0.42696	0.992000	0.81027	-0.022000	0.12480	1.500000	0.48636	0.655000	0.94253	GGG		0.542	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732		T	26509025	G	T	26509025	3	4	103	1	0	0	0	0	1	0	0	0	1562	1348	47	2	1230	2	BTN1A1	6	26509025	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		26509025	144606042	104	27203										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28327608	28327608	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcagcctgagatgcacagcaAggagcagatcctggagctgc	14	11	0	2	rs537641620	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:28327608A>C	ENST00000377255.3	+	3	542	c.245A>C	c.(244-246)aAg>aCg	p.K82T	ZKSCAN3_ENST00000341464.5_Intron|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K82T	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	82	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						ATGCACAGCAAGGAGCAGATC	0.667																																																0			6											35	39	37					6																	28327608		2203	4295	6498	28435587	SO:0001583	missense	80317			U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.245A>C	6.37:g.28327608A>C	ENSP00000366465:p.Lys82Thr		28435587	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	.	.	.	.	.	.	.	.	.	.	.	17.98	3.520085	0.64747	.	.	ENSG00000189298	ENST00000252211;ENST00000454413;ENST00000377255	T;T	0.08458	3.09;3.09	3.71	3.71	0.42584	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.28333	0.0700	H	0.95816	3.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.31641	-0.9936	9	0.66056	D	0.02	.	10.276	0.43510	1.0:0.0:0.0:0.0	.	82	Q9BRR0	ZKSC3_HUMAN	T	82	ENSP00000252211:K82T;ENSP00000366465:K82T	ENSP00000252211:K82T	K	+	2	0	ZKSCAN3	28435587	0.985000	0.35326	1.000000	0.80357	0.988000	0.76386	2.942000	0.49018	1.684000	0.51022	0.377000	0.23210	AAG		0.667	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		C	28327608	A	C	28327608	3	2	103	1	0	0	0	0	1	0	0	0	17727	72	3	4	247	4	ZKSCAN3	6	28327608	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1818583	28327608	142787459	105	27204										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29589555	29589555	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaaactttccgggcttcagTctcatagaaaagtcccacga	7	11	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:29589555T>C	ENST00000377034.4	-	10	1440	c.1105A>G	c.(1105-1107)Act>Gct	p.T369A	GABBR1_ENST00000376977.3_Missense_Mutation_p.T369A|GABBR1_ENST00000355973.3_Missense_Mutation_p.T252A|GABBR1_ENST00000377016.4_Missense_Mutation_p.T307A|GABBR1_ENST00000377012.4_Missense_Mutation_p.T252A	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	369					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CGGGCTTCAGTCTCATAGAAA	0.547																																																0			6											62	66	64					6																	29589555		2203	4300	6503	29697534	SO:0001583	missense	10537			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1105A>G	6.37:g.29589555T>C	ENSP00000366233:p.Thr369Ala		29697534	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360990	0.61403	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75	4.55	4.55	0.56014	Extracellular ligand-binding receptor (1);	0.105878	0.64402	D	0.000006	T	0.56426	0.1984	N	0.14661	0.345	0.53005	D	0.999969	B;D;D;D	0.56035	0.113;0.974;0.973;0.973	B;P;P;P	0.57101	0.07;0.778;0.813;0.813	T	0.57242	-0.7845	10	0.16896	T	0.51	-22.946	11.8871	0.52608	0.0:0.0:0.0:1.0	.	369;307;369;252	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	A	252;369;307;252;369	ENSP00000348248:T252A;ENSP00000366176:T369A;ENSP00000366215:T307A;ENSP00000366211:T252A;ENSP00000366233:T369A	ENSP00000348248:T252A	T	-	1	0	GABBR1	29697534	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.983000	0.76180	1.928000	0.55862	0.519000	0.50382	ACT		0.547	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			C	29589555	T	C	29589555	3	2	103	1	0	0	0	0	1	0	0	0	6174	1667	58	4	1836	4	GABBR1	6	29589555	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1261947	29589555	141525512	106	27205										
DEFB112	245915	hgsc.bcm.edu	37	chr6	50016275	50016275	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgattttctctgtcccatgTcgggccttttcaaatattgt	7	10	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:50016275T>C	ENST00000322246.4	-	1	89	c.90A>G	c.(88-90)cgA>cgG	p.R30R		NM_001037498.1	NP_001032587.1	Q30KQ8	DB112_HUMAN	defensin, beta 112	30					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.042)					CTGTCCCATGTCGGGCCTTTT	0.308																																																0			6											135	129	131					6																	50016275		2203	4298	6501	50124234	SO:0001819	synonymous_variant	245915			DQ012016	CCDS34476.1	6p12.3	2010-03-30			ENSG00000180872	ENSG00000180872		"Defensins, beta"	18093	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037498		Approved	DEFB-12	uc011dws.2	Q30KQ8	OTTHUMG00000160215	ENST00000322246.4:c.90A>G	6.37:g.50016275T>C			50124234	Q8NET0	Silent	SNP	ENST00000322246.4	37	CCDS34476.1																																																																																				0.308	DEFB112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359672.1	NM_001037498		C	50016275	T	C	50016275	2	2	103	1	0	0	0	0	0	0	0	1	4411	1654	58	4		4	DEFB112	6	50016275	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	20426720	50016275	121098792	107	27206										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51523858	51523858	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cagtgatgactcgatgagccAaattctgtaatttgttactt	8	7	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:51523858A>T	ENST00000371117.3	-	61	11341	c.11066T>A	c.(11065-11067)tTg>tAg	p.L3689*		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3689					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCGATGAGCCAAATTCTGTAA	0.398																																																0			6											162	153	156					6																	51523858		2203	4300	6503	51631817	SO:0001587	stop_gained	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11066T>A	6.37:g.51523858A>T	ENSP00000360158:p.Leu3689*		51631817	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Nonsense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	53	21.024046	0.99936	.	.	ENSG00000170927	ENST00000371117	.	.	.	5.91	5.91	0.95273	.	0.487586	0.19483	N	0.113162	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5264	0.75910	1.0:0.0:0.0:0.0	.	.	.	.	X	3689	.	ENSP00000360158:L3689X	L	-	2	0	PKHD1	51631817	0.998000	0.40836	0.972000	0.41901	0.659000	0.38960	6.186000	0.72026	2.261000	0.74972	0.533000	0.62120	TTG		0.398	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51523858	A	T	51523858	4	4	103	1	0	0	0	0	0	1	0	0	12002	131	5	5	1186	5	PKHD1	6	51523858	Nonsense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1507583	51523858	119591209	108	27207										
TINAG	27283	hgsc.bcm.edu	37	chr6	54212312	54212312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttggtggtacctgagaaaacGtgggtaaatagctgctcaac	12	7	1	1	rs201629982		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:54212312G>A	ENST00000259782.4	+	6	992	c.896G>A	c.(895-897)cGt>cAt	p.R299H		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	299					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			CTGAGAAAACGTGGGTAAATA	0.398													G|||	1	0.000199681	0	0	5008	,	,		15424	0		0.001	False		,,,				2504	0															0			6											85	75	79					6																	54212312		2203	4300	6503	54320271	SO:0001583	missense	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.896G>A	6.37:g.54212312G>A	ENSP00000259782:p.Arg299His		54320271	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.78	2.933656	0.52866	.	.	ENSG00000137251	ENST00000259782	D	0.83591	-1.74	5.77	5.77	0.91146	Peptidase C1A, papain C-terminal (2);	0.168599	0.43919	D	0.000514	T	0.54759	0.1878	N	0.11698	0.16	0.80722	D	1	B	0.26081	0.141	B	0.26517	0.07	T	0.55866	-0.8073	10	0.17369	T	0.5	.	12.8911	0.58071	0.0784:0.0:0.9216:0.0	.	299	Q9UJW2	TINAG_HUMAN	H	299	ENSP00000259782:R299H	ENSP00000259782:R299H	R	+	2	0	TINAG	54320271	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.670000	0.54569	2.728000	0.93425	0.591000	0.81541	CGT		0.398	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		A	54212312	G	A	54212312	3	1	103	1	0	0	0	0	1	0	0	0	15960	1145	40	1	918	1	TINAG	6	54212312	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2688454	54212312	116902755	109	27208										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75884983	75884983	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caagataatttcatagtagaCgtcgtagggtcagaaactct	9	7	3	3	rs35170847	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:75884983C>T	ENST00000322507.8	-	13	2790	c.2481G>A	c.(2479-2481)acG>acA	p.T827T	COL12A1_ENST00000416123.2_Silent_p.T827T|COL12A1_ENST00000483888.2_Silent_p.T827T|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	827	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCATAGTAGACGTCGTAGGGT	0.398													C|||	38	0.00758786	0.028	0.0014	5008	,	,		19448	0		0	False		,,,				2504	0															0			6						C	,	56,3664		0,56,1804	115	109	111		2481,	3.3	1	6	dbSNP_126	111	2,8168		0,2,4083	no	coding-synonymous,intron	COL12A1	NM_004370.5,NM_080645.2	,	0,58,5887	TT,TC,CC		0.0245,1.5054,0.4878	,	827/3064,	75884983	58,11832	1860	4085	5945	75941703	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2481G>A	6.37:g.75884983C>T			75941703	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.398	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75884983	C	T	75884983	2	4	103	1	0	0	0	0	0	0	0	1	3675	523	19	1		1	COL12A1	6	75884983	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	21672671	75884983	95230084	110	27209										
HTR1E	3354	hgsc.bcm.edu	37	chr6	87725685	87725685	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atttaccacgcggccaagagCctttaccagaaaaggggatc	10	11	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:87725685C>G	ENST00000305344.5	+	2	1336	c.633C>G	c.(631-633)agC>agG	p.S211R		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	211					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CGGCCAAGAGCCTTTACCAGA	0.433																																																0			6											94	94	94					6																	87725685		2203	4300	6503	87782404	SO:0001583	missense	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.633C>G	6.37:g.87725685C>G	ENSP00000307766:p.Ser211Arg		87782404	E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	37	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	C	7.524	0.657275	0.14580	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.32753	1.44;1.44	4.38	0.4	0.16331	GPCR, rhodopsin-like superfamily (1);	0.164580	0.37437	U	0.002088	T	0.03434	0.0099	N	0.01809	-0.71	0.34168	D	0.669489	B	0.30361	0.277	B	0.37943	0.261	T	0.33111	-0.9881	10	0.05620	T	0.96	.	10.1514	0.42796	0.0:0.4626:0.0:0.5374	.	211	P28566	5HT1E_HUMAN	R	211	ENSP00000307766:S211R;ENSP00000358597:S211R	ENSP00000307766:S211R	S	+	3	2	HTR1E	87782404	0.210000	0.23517	0.999000	0.59377	0.743000	0.42351	-0.544000	0.06077	0.016000	0.14998	0.195000	0.17529	AGC		0.433	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		G	87725685	C	G	87725685	3	3	103	1	0	0	0	0	1	0	0	0	7460	738	26	5	635	5	HTR1E	6	87725685	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	11840702	87725685	83389382	111	27210										
MDN1	23195	hgsc.bcm.edu	37	chr6	90484418	90484418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aatctagctcattgatcacaAtttctggtttataaagttga	6	6	4	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:90484418A>G	ENST00000369393.3	-	13	1971	c.1856T>C	c.(1855-1857)aTt>aCt	p.I619T	MDN1_ENST00000428876.1_Missense_Mutation_p.I619T			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	619					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATTGATCACAATTTCTGGTTT	0.408																																																0			6											138	127	131					6																	90484418		2203	4300	6503	90541139	SO:0001583	missense	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1856T>C	6.37:g.90484418A>G	ENSP00000358400:p.Ile619Thr		90541139	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.357154	0.41801	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.18960	3.87;3.87;2.18	5.32	5.32	0.75619	ATPase, AAA+ type, core (1);	0.062472	0.64402	D	0.000006	T	0.35595	0.0937	M	0.81942	2.565	0.49051	D	0.999744	D;B	0.63046	0.992;0.428	P;B	0.61477	0.889;0.191	T	0.21075	-1.0256	10	0.45353	T	0.12	.	14.9554	0.71110	1.0:0.0:0.0:0.0	.	546;619	Q5T795;Q9NU22	.;MDN1_HUMAN	T	619;619;546	ENSP00000358400:I619T;ENSP00000413970:I619T;ENSP00000409664:I546T	ENSP00000358400:I619T	I	-	2	0	MDN1	90541139	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.971000	0.76105	2.018000	0.59344	0.533000	0.62120	ATT		0.408	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90484418	A	G	90484418	3	3	103	1	0	0	0	0	1	0	0	0	9445	101	4	4	15294	4	MDN1	6	90484418	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2758733	90484418	80630649	112	27211										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99323420	99323420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctggtgtgccagtctggtgaAgcacccggtgctgctctgca	14	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:99323420A>G	ENST00000369244.2	-	9	2001	c.1573T>C	c.(1573-1575)Ttc>Ctc	p.F525L	FBXL4_ENST00000229971.1_Missense_Mutation_p.F525L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	525					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		AGTCTGGTGAAGCACCCGGTG	0.483																																																0			6											91	87	88					6																	99323420		2203	4300	6503	99430141	SO:0001583	missense	26235			AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1573T>C	6.37:g.99323420A>G	ENSP00000358247:p.Phe525Leu		99430141	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	37	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192762	0.38707	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.00745	5.75;5.75	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.00724	0.0024	N	0.21097	0.63	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.97	T	0.66492	-0.5910	10	0.02654	T	1	.	16.2898	0.82742	1.0:0.0:0.0:0.0	.	525;525	B2R7Q5;Q9UKA2	.;FBXL4_HUMAN	L	525	ENSP00000358247:F525L;ENSP00000229971:F525L	ENSP00000229971:F525L	F	-	1	0	FBXL4	99430141	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.000000	0.76290	2.250000	0.74265	0.482000	0.46254	TTC		0.483	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			G	99323420	A	G	99323420	3	3	103	1	0	0	0	0	1	0	0	0	5740	72	3	4	300	4	FBXL4	6	99323420	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	8839002	99323420	71791647	113	27212										
PDSS2	57107	hgsc.bcm.edu	37	chr6	107566786	107566786	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttcatgatatactccttgtAccaagtccataagagcactt	5	10	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:107566786A>G	ENST00000369037.4	-	4	945	c.668T>C	c.(667-669)gTa>gCa	p.V223A	PDSS2_ENST00000453874.2_Missense_Mutation_p.V223A	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	223					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		TACTCCTTGTACCAAGTCCAT	0.294																																																0			6											43	41	42					6																	107566786		2202	4295	6497	107673479	SO:0001583	missense	57107			AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"chromosome 6 open reading frame 210"	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.668T>C	6.37:g.107566786A>G	ENSP00000358033:p.Val223Ala		107673479	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Missense_Mutation	SNP	ENST00000369037.4	37	CCDS5059.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.716064	0.30413	.	.	ENSG00000164494	ENST00000369037;ENST00000453874	T;T	0.63096	-0.02;-0.02	5.6	5.6	0.85130	Terpenoid synthase (2);	0.056183	0.64402	D	0.000001	T	0.56848	0.2013	L	0.54908	1.71	0.58432	D	0.999996	P;D;D	0.53885	0.924;0.963;0.963	P;P;P	0.54889	0.763;0.74;0.74	T	0.56220	-0.8015	10	0.12766	T	0.61	.	15.7873	0.78315	1.0:0.0:0.0:0.0	.	223;223;223	B4DKU5;B2RE48;Q86YH6	.;.;DLP1_HUMAN	A	223	ENSP00000358033:V223A;ENSP00000399691:V223A	ENSP00000358033:V223A	V	-	2	0	PDSS2	107673479	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.082000	0.76851	2.127000	0.65507	0.477000	0.44152	GTA		0.294	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381		G	107566786	A	G	107566786	3	3	103	1	0	0	0	0	1	0	0	0	11725	391	14	4	551	4	PDSS2	6	107566786	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	8243366	107566786	63548281	114	27213										
PDSS2	57107	hgsc.bcm.edu	37	chr6	107595389	107595389	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atcccacgatgtacaaggagAgcaatatgaattagctccgt	9	9	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:107595389A>G	ENST00000369037.4	-	3	751	c.474T>C	c.(472-474)gcT>gcC	p.A158A	PDSS2_ENST00000369031.4_Silent_p.A158A|PDSS2_ENST00000453874.2_Silent_p.A158A	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	158					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.A158A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		GTACAAGGAGAGCAATATGAA	0.343																																																1	Substitution - coding silent(1)	ovary(1)	6											77	72	74					6																	107595389		2203	4300	6503	107702082	SO:0001819	synonymous_variant	57107			AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"chromosome 6 open reading frame 210"	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.474T>C	6.37:g.107595389A>G			107702082	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Silent	SNP	ENST00000369037.4	37	CCDS5059.1																																																																																				0.343	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381		G	107595389	A	G	107595389	2	3	103	1	0	0	0	0	0	0	0	1	11725	291	11	4		4	PDSS2	6	107595389	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	28603	107595389	63519678	115	27214										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117121829	117121829	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtcatattctgccatcttaGtgacagtcatgtgtccattg	9	9	4	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:117121829G>A	ENST00000310357.3	-	4	1487	c.1466C>T	c.(1465-1467)aCt>aTt	p.T489I	GPRC6A_ENST00000368549.3_Intron|GPRC6A_ENST00000530250.1_Missense_Mutation_p.T314I	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	489					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGCCATCTTAGTGACAGTCAT	0.398																																																0			6											215	187	197					6																	117121829		2203	4300	6503	117228522	SO:0001583	missense	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1466C>T	6.37:g.117121829G>A	ENSP00000309493:p.Thr489Ile		117228522	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.683956	0.29872	.	.	ENSG00000173612	ENST00000310357;ENST00000530250	D;D	0.85861	-2.04;-2.04	5.35	3.42	0.39159	.	0.378211	0.22334	N	0.061425	T	0.50769	0.1635	N	0.08118	0	0.30015	N	0.8148	P;B	0.34864	0.473;0.005	B;B	0.24541	0.054;0.004	T	0.49532	-0.8930	10	0.35671	T	0.21	.	12.4156	0.55492	0.1575:0.0:0.8425:0.0	.	314;489	Q5T6X5-2;Q5T6X5	.;GPC6A_HUMAN	I	489;314	ENSP00000309493:T489I;ENSP00000433465:T314I	ENSP00000309493:T489I	T	-	2	0	GPRC6A	117228522	1.000000	0.71417	0.339000	0.25562	0.986000	0.74619	2.717000	0.47227	1.483000	0.48342	0.585000	0.79938	ACT		0.398	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			A	117121829	G	A	117121829	3	1	103	1	0	0	0	0	1	0	0	0	6749	1029	36	3	1326	3	GPRC6A	6	117121829	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	9526440	117121829	53993238	116	27215										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143090797	143090797	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	attttttgcttggacctcagAagagccagcgtggtcttggt	12	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:143090797A>G	ENST00000367604.1	-	4	5718	c.5079T>C	c.(5077-5079)ctT>ctC	p.L1693L	HIVEP2_ENST00000367603.2_Silent_p.L1693L|HIVEP2_ENST00000012134.2_Silent_p.L1693L			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1693					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TGGACCTCAGAAGAGCCAGCG	0.468																																					Esophageal Squamous(107;843 1510 13293 16805 42198)											0			6											147	137	140					6																	143090797		1890	4125	6015	143132490	SO:0001819	synonymous_variant	3097			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5079T>C	6.37:g.143090797A>G			143132490	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																				0.468	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			G	143090797	A	G	143090797	2	3	103	1	0	0	0	0	0	0	0	1	7208	233	9	4		4	HIVEP2	6	143090797	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	25968968	143090797	28024270	117	27216										
FUCA2	2519	hgsc.bcm.edu	37	chr6	143825327	143825327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagttccttgacaatgtcccTcttgggcccctcatctatgg	8	13	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:143825327T>C	ENST00000002165.6	-	3	530	c.475A>G	c.(475-477)Agg>Ggg	p.R159G	RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|FUCA2_ENST00000438118.2_Intron|FUCA2_ENST00000367585.1_Intron	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	159					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		ACAATGTCCCTCTTGGGCCCC	0.443																																																0			6											110	113	112					6																	143825327		2203	4300	6503	143867020	SO:0001583	missense	2519			BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.475A>G	6.37:g.143825327T>C	ENSP00000002165:p.Arg159Gly		143867020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.681128	0.68042	.	.	ENSG00000001036	ENST00000002165	T	0.60548	0.18	5.61	4.43	0.53597	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.74898	0.3777	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.81499	-0.0905	10	0.87932	D	0	-19.406	12.3612	0.55205	0.0:0.0:0.334:0.666	.	159	Q9BTY2	FUCO2_HUMAN	G	159	ENSP00000002165:R159G	ENSP00000002165:R159G	R	-	1	2	FUCA2	143867020	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.105000	0.31086	0.926000	0.37118	0.528000	0.53228	AGG		0.443	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020		C	143825327	T	C	143825327	3	2	103	1	0	0	0	0	1	0	0	0	6114	1550	54	4	948	4	FUCA2	6	143825327	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	734530	143825327	27289740	118	27217										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161533758	161533758	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gagggccatgggcgtgcggcCgacatctggagtctggggtg	20	9	2	0	rs201719431		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:161533758C>T	ENST00000392142.4	+	25	4726	c.4578C>T	c.(4576-4578)gcC>gcT	p.A1526A	MAP3K4_ENST00000366919.2_Silent_p.A1476A|MAP3K4_ENST00000366920.2_Silent_p.A1522A|MAP3K4_ENST00000348824.7_Silent_p.A1472A	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1526	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.A1525A(1)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GGCGTGCGGCCGACATCTGGA	0.527													C|||	1	0.000199681	0	0	5008	,	,		17042	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	stomach(1)	6											133	130	131					6																	161533758		2203	4300	6503	161453748	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.4578C>T	6.37:g.161533758C>T			161453748	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.527	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161533758	C	T	161533758	2	4	103	1	0	0	0	0	0	0	0	1	9282	639	23	1		1	MAP3K4	6	161533758	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	17708431	161533758	9581309	119	27218										
TCP10	6953	hgsc.bcm.edu	37	chr6	167796306	167796306	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaggtcagctcaccggcatcTccccggcattgctgtcctcc	10	17	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:167796306T>C	ENST00000397829.4	-	2	223	c.56A>G	c.(55-57)gAg>gGg	p.E19G	TCP10_ENST00000476779.2_Missense_Mutation_p.E19G|TCP10_ENST00000366827.2_Missense_Mutation_p.E19G	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	46						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CACCGGCATCTCCCCGGCATT	0.642																																																0			6											29	38	35					6																	167796306		2167	4280	6447	167716296	SO:0001583	missense	6953			U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"t-complex 10 (a murine tcp homolog)", "t-complex 10 (mouse)", "t-complex 10 homolog (mouse)"			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.56A>G	6.37:g.167796306T>C	ENSP00000380929:p.Glu19Gly		167716296	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.643542	0.47258	.	.	ENSG00000203690	ENST00000366827;ENST00000397829;ENST00000476779;ENST00000485157	T;T;T;T	0.35236	2.03;2.03;1.32;1.32	2.02	2.02	0.26589	.	.	.	.	.	T	0.38161	0.1030	M	0.66939	2.045	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.986	T	0.07102	-1.0790	9	0.62326	D	0.03	.	5.978	0.19391	0.0:0.0:0.0:1.0	.	46;46	Q12799;Q12799-2	TCP10_HUMAN;.	G	19	ENSP00000355792:E19G;ENSP00000380929:E19G;ENSP00000427675:E19G;ENSP00000423829:E19G	ENSP00000355792:E19G	E	-	2	0	TCP10	167716296	0.000000	0.05858	0.003000	0.11579	0.141000	0.21300	0.392000	0.20801	0.937000	0.37394	0.254000	0.18369	GAG		0.642	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610		C	167796306	T	C	167796306	3	2	103	1	0	0	0	0	1	0	0	0	15749	1551	54	4	952	4	TCP10	6	167796306	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	6262548	167796306	3318761	120	27219										
THBS2	7058	hgsc.bcm.edu	37	chr6	169640603	169640603	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgtttcattttccgcaaagaAccggccatcctgccagcaag	8	14	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr6:169640603A>C	ENST00000366787.3	-	7	1225	c.976T>G	c.(976-978)Ttc>Gtc	p.F326V	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	326	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		TCCGCAAAGAACCGGCCATCC	0.547																																					Esophageal Squamous(91;219 1934 18562 44706)											0			6											97	91	93					6																	169640603		2203	4300	6503	169382528	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.976T>G	6.37:g.169640603A>C	ENSP00000355751:p.Phe326Val		169382528	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	A	7.384	0.629490	0.14257	.	.	ENSG00000186340	ENST00000366787	T	0.69806	-0.43	5.29	-0.683	0.11335	von Willebrand factor, type C (3);	0.381307	0.18947	U	0.126789	T	0.14098	0.0341	N	0.05383	-0.06	0.22745	N	0.998783	B	0.02656	0.0	B	0.06405	0.002	T	0.24368	-1.0162	10	0.15952	T	0.53	-21.764	2.1515	0.03801	0.2858:0.3997:0.0816:0.2329	.	326	P35442	TSP2_HUMAN	V	326	ENSP00000355751:F326V	ENSP00000355751:F326V	F	-	1	0	THBS2	169382528	0.761000	0.28439	0.975000	0.42487	0.593000	0.36681	1.141000	0.31528	-0.029000	0.13827	0.459000	0.35465	TTC		0.547	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		C	169640603	A	C	169640603	3	2	103	1	0	0	0	0	1	0	0	0	15893	43	2	4	2610	4	THBS2	6	169640603	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1844297	169640603	1474464	121	27220										
DGKB	1607	hgsc.bcm.edu	37	chr7	14652999	14652999	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tccaccacttttggggttcaCaaaaactaaaagtgggtgag	10	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:14652999C>G	ENST00000403951.2	-	16	1746	c.1327G>C	c.(1327-1329)Gtg>Ctg	p.V443L	DGKB_ENST00000402815.1_Missense_Mutation_p.V442L|DGKB_ENST00000406247.3_Missense_Mutation_p.V443L|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000258767.5_Missense_Mutation_p.V443L|DGKB_ENST00000444700.2_Missense_Mutation_p.V424L|DGKB_ENST00000399322.3_Missense_Mutation_p.V443L|DGKB_ENST00000407950.1_Missense_Mutation_p.V435L			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	443	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TTGGGGTTCACAAAAACTAAA	0.333																																																0			7											41	39	40					7																	14652999		1815	4062	5877	14619524	SO:0001583	missense	1607			AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"EF-hand domain containing"	2850	protein-coding gene	gene with protein product		604070	"diacylglycerol kinase, beta (90kD)"	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1327G>C	7.37:g.14652999C>G	ENSP00000385780:p.Val443Leu		14619524	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665393	0.88251	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85;1.85	5.36	5.36	0.76844	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.64402	D	0.000001	T	0.48187	0.1486	M	0.71206	2.165	0.58432	D	0.999995	D;P;P;P	0.56521	0.976;0.939;0.939;0.92	P;P;P;P	0.57283	0.817;0.612;0.684;0.597	T	0.47898	-0.9081	10	0.66056	D	0.02	.	19.457	0.94897	0.0:1.0:0.0:0.0	.	442;424;443;443	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	L	443;443;443;442;435;424;443	ENSP00000385780:V443L;ENSP00000382260:V443L;ENSP00000258767:V443L;ENSP00000384909:V442L;ENSP00000385031:V435L;ENSP00000388451:V424L;ENSP00000386066:V443L	ENSP00000258767:V443L	V	-	1	0	DGKB	14619524	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.651000	0.74372	2.676000	0.91093	0.655000	0.94253	GTG		0.333	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		G	14652999	C	G	14652999	3	3	103	1	0	0	0	0	1	0	0	0	4477	478	17	5	1146	5	DGKB	7	14652999	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		14652999	144485664	122	27221										
SP4	6671	hgsc.bcm.edu	37	chr7	21469947	21469947	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggaatgcagaatgcacaggaTcaatcaaattctcttcagca	8	9	4	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:21469947T>C	ENST00000222584.3	+	3	1382	c.1164T>C	c.(1162-1164)gaT>gaC	p.D388D		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	388					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.D388E(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						ATGCACAGGATCAATCAAATT	0.473																																																1	Substitution - Missense(1)	ovary(1)	7											90	87	88					7																	21469947		2203	4300	6503	21436472	SO:0001819	synonymous_variant	6671				CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1164T>C	7.37:g.21469947T>C			21436472	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																				0.473	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		C	21469947	T	C	21469947	2	2	103	1	0	0	0	0	0	0	0	1	15003	1432	50	4		4	SP4	7	21469947	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	6816948	21469947	137668716	123	27222										
NUPL2	11097	hgsc.bcm.edu	37	chr7	23239115	23239115	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggagtaaatcaagcagcaccTgcatttggatttggcagcag	12	8	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:23239115T>C	ENST00000258742.5	+	6	907	c.648T>C	c.(646-648)ccT>ccC	p.P216P		NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN	nucleoporin like 2	216					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AAGCAGCACCTGCATTTGGAT	0.358																																																0			7											162	159	160					7																	23239115		2203	4300	6503	23205640	SO:0001819	synonymous_variant	11097			U97198	CCDS5379.1	7p15	2003-08-07			ENSG00000136243	ENSG00000136243			17010	protein-coding gene	gene with protein product	"nucleoporin-like protein 1"					10358091, 9450185	Standard	NM_007342		Approved	NLP_1, CG1, hCG1, H_RG271G13.9	uc003svu.3	O15504	OTTHUMG00000096955	ENST00000258742.5:c.648T>C	7.37:g.23239115T>C			23205640	A4D143|B4DP42|Q49AE7|Q9BS49	Silent	SNP	ENST00000258742.5	37	CCDS5379.1																																																																																				0.358	NUPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214017.2	NM_007342		C	23239115	T	C	23239115	2	2	103	1	0	0	0	0	0	0	0	1	10806	1567	55	4		4	NUPL2	7	23239115	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1769168	23239115	135899548	124	27223										
GLI3	2737	hgsc.bcm.edu	37	chr7	42064965	42064965	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgctcactgcagactcactCgtgggcttgttctgctggtc	11	13	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:42064965C>A	ENST00000395925.3	-	9	1338	c.1254G>T	c.(1252-1254)acG>acT	p.T418T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	418					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CAGACTCACTCGTGGGCTTGT	0.527									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											131	109	116					7																	42064965		2203	4300	6503	42031490	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1254G>T	7.37:g.42064965C>A			42031490	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.527	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42064965	C	A	42064965	2	1	103	1	0	0	0	0	0	0	0	1	6459	871	31	2		2	GLI3	7	42064965	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	18825850	42064965	117073698	125	27224										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318316	48318316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggtcatgctgttgaatgacAgtgctgacctgagagatctt	12	7	2	5	rs36117801		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:48318316A>G	ENST00000435803.1	+	18	7549	c.7525A>G	c.(7525-7527)Agt>Ggt	p.S2509G		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2509					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GTTGAATGACAGTGCTGACCT	0.428																																																0			7											193	193	193					7																	48318316		1868	4101	5969	48288862	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7525A>G	7.37:g.48318316A>G	ENSP00000411096:p.Ser2509Gly		48288862	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560224	0.45590	.	.	ENSG00000179869	ENST00000435803	T	0.54866	0.55	4.87	2.39	0.29439	.	0.554792	0.16119	N	0.228747	T	0.31949	0.0813	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16630	-1.0396	10	0.25106	T	0.35	.	6.1155	0.20124	0.7732:0.0:0.2268:0.0	.	2509	Q86UQ4	ABCAD_HUMAN	G	2509	ENSP00000411096:S2509G	ENSP00000411096:S2509G	S	+	1	0	ABCA13	48288862	0.000000	0.05858	0.001000	0.08648	0.889000	0.51656	0.894000	0.28350	0.202000	0.20498	0.533000	0.62120	AGT		0.428	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48318316	A	G	48318316	3	3	103	1	0	0	0	0	1	0	0	0	31	188	7	4	7424	4	ABCA13	7	48318316	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	6253351	48318316	110820347	126	27225										
EGFR	1956	hgsc.bcm.edu	37	chr7	55241650	55241650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cacccagtggagaagctcccAaccaagctctcttgaggatc	9	14	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:55241650A>G	ENST00000275493.2	+	18	2275	c.2098A>G	c.(2098-2100)Aac>Gac	p.N700D	EGFR_ENST00000454757.2_Missense_Mutation_p.N647D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.N655D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	700	Important for dimerization, phosphorylation and activation.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.N700D(1)|p.N700Y(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGAAGCTCCCAACCAAGCTCT	0.542		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	2	Substitution - Missense(2)	lung(2)	7											95	99	98					7																	55241650		2203	4300	6503	55209144	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2098A>G	7.37:g.55241650A>G	ENSP00000275493:p.Asn700Asp		55209144	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.896315	0.91962	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.74947	-0.88;-0.89;-0.89	5.83	5.83	0.93111	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.80210	0.4581	M	0.72894	2.215	0.58432	D	0.999991	P;P	0.51791	0.868;0.948	P;P	0.50570	0.529;0.644	T	0.83025	-0.0165	10	0.87932	D	0	.	15.0123	0.71557	1.0:0.0:0.0:0.0	.	655;700	Q504U8;P00533	.;EGFR_HUMAN	D	655;570;700;647	ENSP00000415559:N655D;ENSP00000275493:N700D;ENSP00000395243:N647D	ENSP00000275493:N700D	N	+	1	0	EGFR	55209144	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.306000	0.96204	2.215000	0.71742	0.460000	0.39030	AAC		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55241650	A	G	55241650	3	3	103	1	0	0	0	0	1	0	0	0	4978	130	5	4	2432	4	EGFR	7	55241650	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	6923334	55241650	103897013	127	27226										
EGFR	1956	hgsc.bcm.edu	37	chr7	55241713	55241713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agatcaaagtgctgggctccGgtgcgttcggcacggtgtat	15	9	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:55241713G>A	ENST00000275493.2	+	18	2338	c.2161G>A	c.(2161-2163)Ggt>Agt	p.G721S	EGFR_ENST00000454757.2_Missense_Mutation_p.G668S|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.G676S	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	721	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.G721S(3)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCTGGGCTCCGGTGCGTTCGG	0.572		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	3	Substitution - Missense(3)	lung(2)|ovary(1)	7											63	65	65					7																	55241713		2203	4300	6503	55209207	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2161G>A	7.37:g.55241713G>A	ENSP00000275493:p.Gly721Ser		55209207	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.845199	0.71603	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	D;D;D	0.94793	-3.52;-3.52;-3.52	5.5	5.5	0.81552	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98409	0.9471	H	0.97390	3.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.985;0.999	D	0.99683	1.0999	10	0.87932	D	0	.	17.9478	0.89044	0.0:0.0:1.0:0.0	.	676;721	Q504U8;P00533	.;EGFR_HUMAN	S	676;591;721;668	ENSP00000415559:G676S;ENSP00000275493:G721S;ENSP00000395243:G668S	ENSP00000275493:G721S	G	+	1	0	EGFR	55209207	1.000000	0.71417	0.304000	0.25085	0.005000	0.04900	9.772000	0.98984	2.562000	0.86427	0.563000	0.77884	GGT		0.572	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55241713	G	A	55241713	3	1	103	1	0	0	0	0	1	0	0	0	4978	1116	39	1	2495	1	EGFR	7	55241713	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	63	55241713	103896950	128	27227										
EGFR	1956	hgsc.bcm.edu	37	chr7	55269457	55269457	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agcaacaattccaccgtggcTtgcattgatagaaatggggt	11	8	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:55269457T>G	ENST00000275493.2	+	26	3321	c.3144T>G	c.(3142-3144)gcT>gcG	p.A1048A	EGFR_ENST00000454757.2_Silent_p.A995A|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.A1003A	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1048					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCACCGTGGCTTGCATTGATA	0.413		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											162	149	154					7																	55269457		2203	4300	6503	55236951	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3144T>G	7.37:g.55269457T>G			55236951	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.413	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55269457	T	G	55269457	2	3	103	1	0	0	0	0	0	0	0	1	4978	1596	56	4		4	EGFR	7	55269457	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	27744	55269457	103869206	129	27228										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77230117	77230117	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agatgttcctatttgtattcAttgcaggtacaaaagaattt	7	5	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:77230117A>G	ENST00000248594.6	+	8	961	c.689A>G	c.(688-690)cAt>cGt	p.H230R	PTPN12_ENST00000435495.2_Missense_Mutation_p.H100R|PTPN12_ENST00000415482.2_Missense_Mutation_p.H111R	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	230	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						ATTTGTATTCATTGCAGGTAC	0.299																																																0			7											71	66	68					7																	77230117		2203	4300	6503	77068053	SO:0001583	missense	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.689A>G	7.37:g.77230117A>G	ENSP00000248594:p.His230Arg		77068053	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.5|23.5	4.424051|4.424051	0.83667|0.83667	.|.	.|.	ENSG00000127947|ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495|ENST00000522115	T;D;D|.	0.87571|.	1.62;-2.27;-2.27|.	5.17|5.17	5.17|5.17	0.71159|0.71159	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.91415|0.91415	0.7291|0.7291	H|H	0.99719|0.99719	4.725|4.725	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.95131|0.95131	0.8255|0.8255	10|5	0.87932|.	D|.	0|.	.|.	15.0121|15.0121	0.71557|0.71557	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	230|.	Q05209|.	PTN12_HUMAN|.	R|V	230;111;111;100|169	ENSP00000248594:H230R;ENSP00000392429:H111R;ENSP00000397991:H100R|.	ENSP00000248594:H230R|.	H|I	+|+	2|1	0|0	PTPN12|PTPN12	77068053|77068053	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	9.281000|9.281000	0.95811|0.95811	1.960000|1.960000	0.56953|0.56953	0.455000|0.455000	0.32223|0.32223	CAT|ATT		0.299	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			G	77230117	A	G	77230117	3	3	103	1	0	0	0	0	1	0	0	0	12816	217	8	4	719	4	PTPN12	7	77230117	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	21960660	77230117	81908546	130	27229										
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95799433	95799433	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atttatccctcacaaaatcgTtcaccttgaagaaaaatatt	3	9	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:95799433T>C	ENST00000265631.5	-	13	1371	c.1235A>G	c.(1234-1236)aAc>aGc	p.N412S	SLC25A13_ENST00000416240.2_Missense_Mutation_p.N413S|SLC25A13_ENST00000542654.1_Missense_Mutation_p.N304S			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	412					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	CACAAAATCGTTCACCTTGAA	0.333																																																0			7											77	80	79					7																	95799433		2203	4300	6503	95637369	SO:0001583	missense	10165			AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1235A>G	7.37:g.95799433T>C	ENSP00000265631:p.Asn412Ser		95637369	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990117	0.74589	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.78924	-1.22;-1.22;-1.22	5.06	5.06	0.68205	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.88894	0.6561	M	0.86028	2.79	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90638	0.4572	10	0.72032	D	0.01	-19.6936	15.2988	0.73931	0.0:0.0:0.0:1.0	.	304;413;412	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	S	412;413;304	ENSP00000265631:N412S;ENSP00000400101:N413S;ENSP00000440484:N304S	ENSP00000265631:N412S	N	-	2	0	SLC25A13	95637369	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.702000	0.74628	2.267000	0.75376	0.383000	0.25322	AAC		0.333	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		C	95799433	T	C	95799433	3	2	103	1	0	0	0	0	1	0	0	0	14512	1725	60	4	816	4	SLC25A13	7	95799433	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	18569316	95799433	63339230	131	27230										
RELN	5649	hgsc.bcm.edu	37	chr7	103113286	103113286	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tatcgcctaagtgaccttcgTcttctgttgtagaaatgtct	8	9	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:103113286T>C	ENST00000428762.1	-	65	10515	c.10356A>G	c.(10354-10356)agA>agG	p.R3452R	RELN_ENST00000424685.2_Silent_p.R3452R|RELN_ENST00000343529.5_Silent_p.R3450R|CTB-107G13.1_ENST00000422488.1_RNA	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3452	Arg-rich (basic).				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GTGACCTTCGTCTTCTGTTGT	0.378																																					NSCLC(146;835 1944 15585 22231 52158)											0			7											172	161	165					7																	103113286		2203	4300	6503	102900522	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.10356A>G	7.37:g.103113286T>C			102900522	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.378	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103113286	T	C	103113286	2	2	103	1	0	0	0	0	0	0	0	1	13257	1664	58	4		4	RELN	7	103113286	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	7313853	103113286	56025377	132	27231										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107818499	107818499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggctcggtggatcccattcCaaagtgagagagtccagtgt	13	9	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:107818499C>A	ENST00000425651.2	-	23	2909	c.2910G>T	c.(2908-2910)ttG>ttT	p.L970F	NRCAM_ENST00000413765.2_Missense_Mutation_p.L951F|NRCAM_ENST00000379028.3_Missense_Mutation_p.L970F|NRCAM_ENST00000379024.4_Missense_Mutation_p.L951F|NRCAM_ENST00000379022.4_Missense_Mutation_p.L970F|NRCAM_ENST00000351718.4_Missense_Mutation_p.L954F	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	970	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)	p.L954L(1)		breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GATCCCATTCCAAAGTGAGAG	0.453																																																1	Substitution - coding silent(1)	ovary(1)	7											85	74	78					7																	107818499		2203	4300	6503	107605735	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2910G>T	7.37:g.107818499C>A	ENSP00000401244:p.Leu970Phe		107605735	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.223364	0.79464	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	6.05	6.05	0.98169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.065294	0.64402	D	0.000007	T	0.81823	0.4904	M	0.87038	2.855	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;1.0	D;D;D;D;D	0.91635	0.998;0.994;0.998;0.949;0.999	D	0.84078	0.0383	10	0.87932	D	0	.	15.3397	0.74287	0.1396:0.8604:0.0:0.0	.	970;951;951;954;970	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	F	970;970;951;970;954;951;970;970	ENSP00000368314:L970F;ENSP00000407858:L951F;ENSP00000325269:L954F;ENSP00000368310:L951F;ENSP00000401244:L970F;ENSP00000368308:L970F	ENSP00000325269:L954F	L	-	3	2	NRCAM	107605735	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.286000	0.33273	2.866000	0.98385	0.650000	0.86243	TTG		0.453	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107818499	C	A	107818499	3	1	103	1	0	0	0	0	1	0	0	0	10675	593	21	2	1066	2	NRCAM	7	107818499	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	4705213	107818499	51320164	133	27232										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112424370	112424370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agacttctccaccaacatagTtgtgctggcaatggcaaatc	8	11	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:112424370T>C	ENST00000312814.6	-	2	1071	c.511A>G	c.(511-513)Act>Gct	p.T171A	TMEM168_ENST00000454074.1_Missense_Mutation_p.T171A	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	171						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						ACCAACATAGTTGTGCTGGCA	0.423																																																0			7											64	64	64					7																	112424370		2203	4300	6503	112211606	SO:0001583	missense	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.511A>G	7.37:g.112424370T>C	ENSP00000323068:p.Thr171Ala		112211606	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	T	6.978	0.550437	0.13374	.	.	ENSG00000146802	ENST00000312814;ENST00000454074	.	.	.	5.93	5.93	0.95920	.	0.302747	0.41500	D	0.000870	T	0.40645	0.1125	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30966	-0.9960	9	0.13108	T	0.6	-31.3682	16.3786	0.83431	0.0:0.0:0.0:1.0	.	171	Q9H0V1	TM168_HUMAN	A	171	.	ENSP00000323068:T171A	T	-	1	0	TMEM168	112211606	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.749000	0.55150	2.269000	0.75478	0.454000	0.30748	ACT		0.423	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		C	112424370	T	C	112424370	3	2	103	1	0	0	0	0	1	0	0	0	16122	1725	60	4	1598	4	TMEM168	7	112424370	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	4605871	112424370	46714293	134	27233										
GPR85	54329	hgsc.bcm.edu	37	chr7	112723723	112723723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tctgcagtaaagaagggttgTgctgaaacagcgcctcagct	12	9	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:112723723T>C	ENST00000297146.3	-	3	1657	c.1054A>G	c.(1054-1056)Aca>Gca	p.T352A	GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000501255.2_Missense_Mutation_p.T352A|GPR85_ENST00000424100.1_Missense_Mutation_p.T352A|GPR85_ENST00000449591.1_Missense_Mutation_p.T352A	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	352					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T352P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						AGAAGGGTTGTGCTGAAACAG	0.438																																																1	Substitution - Missense(1)	central_nervous_system(1)	7											75	76	75					7																	112723723		2203	4300	6503	112510959	SO:0001583	missense	54329			AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"GPCR / Class A : Orphans"	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.1054A>G	7.37:g.112723723T>C	ENSP00000297146:p.Thr352Ala		112510959	Q9JHI6|Q9NPD1	Missense_Mutation	SNP	ENST00000297146.3	37	CCDS5758.1	.	.	.	.	.	.	.	.	.	.	T	3.511	-0.099863	0.07010	.	.	ENSG00000164604	ENST00000501255;ENST00000297146;ENST00000424100;ENST00000449591	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.21103	0.0508	N	0.08118	0	0.80722	D	1	B	0.15141	0.012	B	0.10450	0.005	T	0.05115	-1.0905	10	0.29301	T	0.29	.	14.9933	0.71406	0.0:0.0:0.0:1.0	.	352	P60893	GPR85_HUMAN	A	352	ENSP00000445808:T352A;ENSP00000297146:T352A;ENSP00000396763:T352A;ENSP00000401178:T352A	ENSP00000297146:T352A	T	-	1	0	GPR85	112510959	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	2.195000	0.70347	0.477000	0.44152	ACA		0.438	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			C	112723723	T	C	112723723	3	2	103	1	0	0	0	0	1	0	0	0	6735	1696	59	4	62	4	GPR85	7	112723723	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	299353	112723723	46414940	135	27234										
MET	4233	hgsc.bcm.edu	37	chr7	116380997	116380997	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	accctttgttcagtgtggctGgtgccacgacaaatgtgtgc	12	10	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:116380997G>A	ENST00000318493.6	+	5	1806	c.1619G>A	c.(1618-1620)tGg>tAg	p.W540*	MET_ENST00000436117.2_Nonsense_Mutation_p.W540*|MET_ENST00000397752.3_Nonsense_Mutation_p.W540*|MET_ENST00000495962.1_3'UTR			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CAGTGTGGCTGGTGCCACGAC	0.522			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											114	117	116					7																	116380997		1967	4140	6107	116168233	SO:0001587	stop_gained	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1619G>A	7.37:g.116380997G>A	ENSP00000317272:p.Trp540*		116168233	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Nonsense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	40	8.332855	0.98764	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.3167	0.98654	0.0:0.0:1.0:0.0	.	.	.	.	X	540	.	ENSP00000317272:W540X	W	+	2	0	MET	116168233	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.126000	0.77201	2.809000	0.96659	0.557000	0.71058	TGG		0.522	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116380997	G	A	116380997	4	1	103	1	0	0	0	0	0	1	0	0	9515	1357	47	3	1633	3	MET	7	116380997	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	3657274	116380997	42757666	136	27235										
GRM8	2918	hgsc.bcm.edu	37	chr7	126746620	126746620	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcccctcagaagccagtgtCgaaacataattccatcccag	6	14	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:126746620C>T	ENST00000339582.2	-	3	1465	c.657G>A	c.(655-657)tcG>tcA	p.S219S	GRM8_ENST00000405249.1_Silent_p.S219S|GRM8_ENST00000358373.3_Silent_p.S219S|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000444921.2_Silent_p.S219S			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	219					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.S219S(4)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				AAGCCAGTGTCGAAACATAAT	0.493										HNSCC(24;0.065)																																						4	Substitution - coding silent(4)	large_intestine(3)|ovary(1)	7											137	119	125					7																	126746620		2203	4300	6503	126533856	SO:0001819	synonymous_variant	2918				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.657G>A	7.37:g.126746620C>T			126533856	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	37	CCDS5794.1																																																																																				0.493	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			T	126746620	C	T	126746620	2	4	103	1	0	0	0	0	0	0	0	1	6824	871	31	1		1	GRM8	7	126746620	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10365623	126746620	32392043	137	27236										
EZH2	2146	hgsc.bcm.edu	37	chr7	148523589	148523589	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagcagtcatatttaaaacaTcgcctacagaaaagcgtatg	7	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr7:148523589T>C	ENST00000460911.1	-	8	952	c.864A>G	c.(862-864)cgA>cgG	p.R288R	EZH2_ENST00000476773.1_Silent_p.R279R|EZH2_ENST00000320356.2_Silent_p.R288R|EZH2_ENST00000541220.1_Silent_p.R279R|EZH2_ENST00000350995.2_Silent_p.R249R|EZH2_ENST00000483967.1_Silent_p.R279R|EZH2_ENST00000478654.1_Silent_p.R279R|EZH2_ENST00000536783.1_Silent_p.R179R			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	288	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			ATTTAAAACATCGCCTACAGA	0.383			Mis		DLBCL																																		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	0			7											150	125	134					7																	148523589		2203	4300	6503	148154522	SO:0001819	synonymous_variant	2146				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.864A>G	7.37:g.148523589T>C			148154522	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	37	CCDS56516.1																																																																																				0.383	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		C	148523589	T	C	148523589	2	2	103	1	0	0	0	0	0	0	0	1	5347	1422	50	4		4	EZH2	7	148523589	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	21776969	148523589	10615074	138	27237										
NKX3-1	4824	hgsc.bcm.edu	37	chr8	23538889	23538889	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtctcccagctccgaggagaGctgctttcgcttagtcttat	10	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:23538889G>T	ENST00000380871.4	-	2	587	c.550C>A	c.(550-552)Ctc>Atc	p.L184I	NKX3-1_ENST00000523261.1_Missense_Mutation_p.L109I	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	184					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|androgen receptor signaling pathway (GO:0030521)|branching involved in prostate gland morphogenesis (GO:0060442)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to steroid hormone stimulus (GO:0071383)|cellular response to tumor necrosis factor (GO:0071356)|dorsal aorta development (GO:0035907)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|heart development (GO:0007507)|male gonad development (GO:0008584)|metanephros development (GO:0001656)|mitotic cell cycle arrest (GO:0071850)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of transcription, DNA-templated (GO:0045892)|pharyngeal system development (GO:0060037)|positive regulation of androgen secretion (GO:2000836)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell death (GO:0010942)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein kinase B signaling (GO:0043491)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|salivary gland development (GO:0007431)|somitogenesis (GO:0001756)|steroid hormone mediated signaling pathway (GO:0043401)	intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|core promoter binding (GO:0001047)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|histone deacetylase binding (GO:0042826)|protein kinase activator activity (GO:0030295)|protein self-association (GO:0043621)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		TCCGAGGAGAGCTGCTTTCGC	0.577																																																0			8											146	144	145					8																	23538889		2203	4300	6503	23594834	SO:0001583	missense	4824				CCDS6042.1, CCDS59095.1	8p21.2	2012-03-09	2007-07-09	2002-10-04	ENSG00000167034	ENSG00000167034		"Homeoboxes / ANTP class : NKL subclass"	7838	protein-coding gene	gene with protein product		602041	"NK homeobox (Drosophila), family 3, A", "NK3 transcription factor related, locus 1 (Drosophila)"	NKX3A		9226374	Standard	NM_006167		Approved	NKX3.1, BAPX2	uc011kzx.2	Q99801	OTTHUMG00000097851	ENST00000380871.4:c.550C>A	8.37:g.23538889G>T	ENSP00000370253:p.Leu184Ile		23594834	O15465|Q9H2P4|Q9H2P5|Q9H2P6|Q9H2P7|Q9HBG0	Missense_Mutation	SNP	ENST00000380871.4	37	CCDS6042.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989593	0.53934	.	.	ENSG00000167034	ENST00000380871;ENST00000300332;ENST00000523261	D;D	0.92249	-2.88;-3.0	5.87	5.87	0.94306	Homeobox (1);Homeodomain-like (1);	0.000000	0.44285	D	0.000467	D	0.92338	0.7569	M	0.64404	1.975	0.53005	D	0.99996	B	0.33212	0.402	B	0.40825	0.341	D	0.89561	0.3806	10	0.30078	T	0.28	.	18.0718	0.89410	0.0:0.0:1.0:0.0	.	184	Q99801	NKX31_HUMAN	I	184;140;109	ENSP00000370253:L184I;ENSP00000429729:L109I	ENSP00000300332:L140I	L	-	1	0	NKX3-1	23594834	0.993000	0.37304	0.998000	0.56505	0.393000	0.30537	1.201000	0.32259	2.941000	0.99782	0.655000	0.94253	CTC		0.577	NKX3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215141.2			T	23538889	G	T	23538889	3	4	103	1	0	0	0	0	1	0	0	0	10486	971	34	2	158	2	NKX3-1	8	23538889	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		23538889	122825133	139	27238										
FGFR1	2260	hgsc.bcm.edu	37	chr8	38285891	38285891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtttggtttggtgttatctgTttctttctcctctgaagagg	11	6	4	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:38285891T>C	ENST00000447712.2	-	4	1362	c.421A>G	c.(421-423)Aca>Gca	p.T141A	FGFR1_ENST00000326324.6_Missense_Mutation_p.T52A|FGFR1_ENST00000532791.1_Missense_Mutation_p.T141A|FGFR1_ENST00000397113.2_Missense_Mutation_p.T141A|RP11-350N15.4_ENST00000528407.1_RNA|FGFR1_ENST00000425967.3_Missense_Mutation_p.T174A|FGFR1_ENST00000397108.4_Missense_Mutation_p.T141A|FGFR1_ENST00000397103.1_Missense_Mutation_p.T52A|FGFR1_ENST00000397091.5_Missense_Mutation_p.T141A|FGFR1_ENST00000356207.5_Missense_Mutation_p.T52A|FGFR1_ENST00000341462.5_Missense_Mutation_p.T144A|FGFR1_ENST00000335922.5_Missense_Mutation_p.T133A	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	141					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GTGTTATCTGTTTCTTTCTCC	0.502		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	0			8											228	234	232					8																	38285891		1985	4162	6147	38405048	SO:0001583	missense	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.421A>G	8.37:g.38285891T>C	ENSP00000400162:p.Thr141Ala		38405048	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	37	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	T	8.797	0.932054	0.18131	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108;ENST00000326296;ENST00000525001;ENST00000526742;ENST00000529552;ENST00000530568;ENST00000434187	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78003	-1.11;-1.12;-1.12;-1.11;-1.12;-1.11;-1.12;-1.14;-1.04;-1.05;-1.11;-0.93;-0.87;-0.91;-0.69;-0.05	5.69	4.42	0.53409	.	0.239911	0.43919	D	0.000510	T	0.47637	0.1456	N	0.03608	-0.345	0.32327	N	0.561608	B;B;B;B;B;B;B;B;B;B;B;B	0.13145	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.003;0.007;0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.15484	0.002;0.001;0.001;0.001;0.0;0.001;0.002;0.0;0.001;0.006;0.013;0.001	T	0.49908	-0.8889	10	0.07813	T	0.8	.	4.9835	0.14178	0.2619:0.0909:0.0:0.6472	.	52;52;141;174;52;52;52;141;133;52;52;141	B5A959;P11362-3;P11362-7;P11362-21;B5A958;P11362-14;P11362-4;P11362;P11362-20;P11362-16;P11362-18;P11362-2	.;.;.;.;.;.;.;FGFR1_HUMAN;.;.;.;.	A	141;174;141;144;141;141;141;52;133;52;52;141;144;141;52;52;52;52	ENSP00000380280:T141A;ENSP00000393312:T174A;ENSP00000400162:T141A;ENSP00000340636:T144A;ENSP00000432972:T141A;ENSP00000380302:T141A;ENSP00000348537:T52A;ENSP00000337247:T133A;ENSP00000327229:T52A;ENSP00000380292:T52A;ENSP00000380297:T141A;ENSP00000434712:T141A;ENSP00000433569:T52A;ENSP00000435283:T52A;ENSP00000434473:T52A;ENSP00000392645:T52A	ENSP00000311337:T141A	T	-	1	0	FGFR1	38405048	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.128000	0.31369	2.174000	0.68829	0.460000	0.39030	ACA		0.502	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	38285891	T	C	38285891	3	2	103	1	0	0	0	0	1	0	0	0	5882	1725	60	4	2347	4	FGFR1	8	38285891	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	14747002	38285891	108078131	140	27239										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39581383	39581383	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgtgatctttaaaagaaatGaaataagtaaatcatgtaac	6	4	2	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:39581383G>T	ENST00000265707.5	+	19	2179	c.2134G>T	c.(2134-2136)Gaa>Taa	p.E712*	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Nonsense_Mutation_p.E688*|ADAM18_ENST00000541111.1_Nonsense_Mutation_p.E126*	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	712					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E712K(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		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)			TAAAAGAAATGAAATAAGTAA	0.313																																																1	Substitution - Missense(1)	skin(1)	8											101	107	105					8																	39581383		2202	4296	6498	39700540	SO:0001587	stop_gained	8749			AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.2134G>T	8.37:g.39581383G>T	ENSP00000265707:p.Glu712*		39700540	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Nonsense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	g	44	11.243873	0.99536	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	.	.	.	4.77	4.77	0.60923	.	0.000000	0.46758	D	0.000276	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0349	0.64638	0.0:0.0:1.0:0.0	.	.	.	.	X	712;688;126	.	ENSP00000265707:E712X	E	+	1	0	ADAM18	39700540	1.000000	0.71417	0.883000	0.34634	0.146000	0.21551	2.239000	0.43079	2.590000	0.87494	0.552000	0.68991	GAA		0.313	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39581383	G	T	39581383	4	4	103	1	0	0	0	0	0	1	0	0	239	1291	45	2	2208	2	ADAM18	8	39581383	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1295492	39581383	106782639	141	27240										
C8orf34	116328	hgsc.bcm.edu	37	chr8	69358569	69358569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	attttgttttaacagaatccAaaggaacaagaagggatttc	8	5	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:69358569A>G	ENST00000539993.1	+	3	772	c.223A>G	c.(223-225)Aaa>Gaa	p.K75E	C8orf34_ENST00000348340.2_Missense_Mutation_p.K75E|C8orf34_ENST00000518698.1_Missense_Mutation_p.K161E|C8orf34_ENST00000337103.4_Missense_Mutation_p.K50E|C8orf34_ENST00000349492.3_3'UTR|C8orf34_ENST00000523686.1_Missense_Mutation_p.K75E			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	75			K -> N (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.							NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			AACAGAATCCAAAGGAACAAG	0.313																																																0			8											75	80	79					8																	69358569		2203	4300	6503	69521123	SO:0001583	missense	116328			AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"vestibule 1"						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.223A>G	8.37:g.69358569A>G	ENSP00000438159:p.Lys75Glu		69521123	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	37		.	.	.	.	.	.	.	.	.	.	A	21.1	4.097843	0.76870	.	.	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000523686;ENST00000348340;ENST00000337103	T;T;T	0.54866	0.55;0.59;0.74	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.67373	0.2886	L	0.50919	1.6	0.44373	D	0.997272	P;D;D	0.71674	0.925;0.998;0.99	P;D;P	0.78314	0.54;0.991;0.819	T	0.65467	-0.6161	9	.	.	.	-25.6337	16.3631	0.83280	1.0:0.0:0.0:0.0	.	75;75;75	Q49A92;Q49A92-3;Q49A92-5	CH034_HUMAN;.;.	E	161;75;75;75;50	ENSP00000427820:K161E;ENSP00000438159:K75E;ENSP00000337174:K50E	.	K	+	1	0	C8orf34	69521123	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.839000	0.92120	2.266000	0.75297	0.533000	0.62120	AAA		0.313	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958		G	69358569	A	G	69358569	3	3	103	1	0	0	0	0	1	0	0	0	2428	131	5	4	154	4	C8orf34	8	69358569	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	29777186	69358569	77005453	142	27241										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885187	88885187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gacggaggctccagattctcGtgtagcagtcctggcccacg	13	13	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:88885187G>A	ENST00000319675.3	-	1	1109	c.1013C>T	c.(1012-1014)aCg>aTg	p.T338M		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	338								p.T338M(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CCAGATTCTCGTGTAGCAGTC	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	8											78	86	84					8																	88885187		2203	4300	6503	88954303	SO:0001583	missense	0			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.1013C>T	8.37:g.88885187G>A	ENSP00000316496:p.Thr338Met		88954303		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.862744	0.71949	.	.	ENSG00000176566	ENST00000319675	T	0.70282	-0.47	1.49	-0.835	0.10775	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74207	0.3686	M	0.78916	2.43	0.35500	D	0.799753	D	0.56521	0.976	P	0.55508	0.777	T	0.74156	-0.3756	10	0.59425	D	0.04	.	5.5945	0.17319	0.3411:0.0:0.6589:0.0	.	338	Q8NA75	DC4L2_HUMAN	M	338	ENSP00000316496:T338M	ENSP00000316496:T338M	T	-	2	0	DCAF4L2	88954303	1.000000	0.71417	0.101000	0.21167	0.888000	0.51559	6.093000	0.71422	-0.533000	0.06323	0.467000	0.42956	ACG		0.577	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885187	G	A	88885187	3	1	103	1	0	0	0	0	1	0	0	0	4278	1145	40	1	178	1	DCAF4L2	8	88885187	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	19526618	88885187	57478835	143	27242										
DPY19L4	286148	hgsc.bcm.edu	37	chr8	95746967	95746967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taccatgaacggaaattctgGttttccaacaggcaggtaag	10	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:95746967G>T	ENST00000414645.2	+	3	336	c.237G>T	c.(235-237)tgG>tgT	p.W79C		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	79						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					GGAAATTCTGGTTTTCCAACA	0.388																																																0			8											74	69	71					8																	95746967		2203	4300	6503	95816143	SO:0001583	missense	286148				CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.237G>T	8.37:g.95746967G>T	ENSP00000389630:p.Trp79Cys		95816143	Q6ZW32|Q6ZW42|Q7Z329	Missense_Mutation	SNP	ENST00000414645.2	37	CCDS34924.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.902307	0.72754	.	.	ENSG00000156162	ENST00000414645;ENST00000519176	T;T	0.56611	0.45;0.45	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.73313	0.3571	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74833	-0.3530	10	0.59425	D	0.04	-4.9868	19.2974	0.94128	0.0:0.0:1.0:0.0	.	79	Q7Z388	D19L4_HUMAN	C	79;50	ENSP00000389630:W79C;ENSP00000430417:W50C	ENSP00000389630:W79C	W	+	3	0	DPY19L4	95816143	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.392000	0.90180	2.537000	0.85549	0.591000	0.81541	TGG		0.388	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787		T	95746967	G	T	95746967	3	4	103	1	0	0	0	0	1	0	0	0	4754	1270	44	2	247	2	DPY19L4	8	95746967	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	6861780	95746967	50617055	144	27243										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100847793	100847793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caaagtttgaggtttattgcAaaaaaattccctccgagtgc	8	8	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:100847793A>G	ENST00000358544.2	+	54	9955	c.9844A>G	c.(9844-9846)Aaa>Gaa	p.K3282E	VPS13B_ENST00000357162.2_Missense_Mutation_p.K3257E|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3282					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGTTTATTGCAAAAAAATTCC	0.388																																					Colon(161;2205 2542 7338 31318)											0			8											57	61	60					8																	100847793		2203	4300	6503	100916969	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.9844A>G	8.37:g.100847793A>G	ENSP00000351346:p.Lys3282Glu		100916969	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618935	0.46736	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69561	-0.41;-0.41	5.91	2.09	0.27110	.	0.392249	0.27730	N	0.018093	T	0.53302	0.1788	L	0.29908	0.895	0.80722	D	1	B;B	0.20368	0.003;0.044	B;B	0.15870	0.004;0.014	T	0.41538	-0.9503	10	0.36615	T	0.2	.	14.3265	0.66523	0.501:0.499:0.0:0.0	.	3257;3282	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	E	3257;3282	ENSP00000349685:K3257E;ENSP00000351346:K3282E	ENSP00000349685:K3257E	K	+	1	0	VPS13B	100916969	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	1.644000	0.37228	0.112000	0.17975	0.533000	0.62120	AAA		0.388	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100847793	A	G	100847793	3	3	103	1	0	0	0	0	1	0	0	0	17230	131	5	4	10248	4	VPS13B	8	100847793	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	5100826	100847793	45516229	145	27244										
TMEM74	157753	hgsc.bcm.edu	37	chr8	109796472	109796472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttccagagtgttttcattcgTgctggttttcatcctgaagt	9	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:109796472T>C	ENST00000297459.3	-	2	1034	c.856A>G	c.(856-858)Acg>Gcg	p.T286A	TMEM74_ENST00000518838.1_Intron	NM_153015.1	NP_694560.1	Q96NL1	TMM74_HUMAN	transmembrane protein 74	286					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			TTTTCATTCGTGCTGGTTTTC	0.448																																																0			8											87	84	85					8																	109796472		2203	4300	6503	109865648	SO:0001583	missense	157753			AK055230	CCDS6310.1	8q23.1	2009-11-06				ENSG00000164841			26409	protein-coding gene	gene with protein product		613935				12477932	Standard	NM_153015		Approved	FLJ30668, NET36	uc003ymy.1	Q96NL1		ENST00000297459.3:c.856A>G	8.37:g.109796472T>C	ENSP00000297459:p.Thr286Ala		109865648		Missense_Mutation	SNP	ENST00000297459.3	37	CCDS6310.1	.	.	.	.	.	.	.	.	.	.	T	2.432	-0.330578	0.05314	.	.	ENSG00000164841	ENST00000297459	.	.	.	5.96	-4.89	0.03103	.	1.099310	0.06758	N	0.781274	T	0.23330	0.0564	N	0.10874	0.06	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24440	-1.0160	9	0.32370	T	0.25	1.172	13.2251	0.59911	0.0:0.6257:0.1989:0.1753	.	286	Q96NL1	TMM74_HUMAN	A	286	.	ENSP00000297459:T286A	T	-	1	0	TMEM74	109865648	0.000000	0.05858	0.000000	0.03702	0.295000	0.27426	-0.976000	0.03786	-0.742000	0.04790	-0.408000	0.06270	ACG		0.448	TMEM74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380755.1	NM_153015		C	109796472	T	C	109796472	3	2	103	1	0	0	0	0	1	0	0	0	16241	1696	59	4	65	4	TMEM74	8	109796472	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	8948679	109796472	36567550	146	27245										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113267536	113267536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	catctgcttgacatattctgGtgcttgatcccactaatatg	7	10	2	2	rs536934063		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:113267536G>A	ENST00000297405.5	-	62	10227	c.9983C>T	c.(9982-9984)aCc>aTc	p.T3328I	CSMD3_ENST00000343508.3_Missense_Mutation_p.T3288I|CSMD3_ENST00000352409.3_Missense_Mutation_p.T3258I|CSMD3_ENST00000455883.2_Missense_Mutation_p.T3159I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3328	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACATATTCTGGTGCTTGATCC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			G|||	1	0.000199681	0	0	5008	,	,		15874	0.001		0	False		,,,				2504	0															0			8											134	121	125					8																	113267536		2203	4300	6503	113336712	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9983C>T	8.37:g.113267536G>A	ENSP00000297405:p.Thr3328Ile		113336712	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805355	0.70682	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.19	4.31	0.51392	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.76212	0.3956	L	0.53561	1.675	0.43982	D	0.996674	D;D;B	0.89917	1.0;1.0;0.113	D;D;B	0.80764	0.994;0.993;0.07	T	0.72874	-0.4160	10	0.21014	T	0.42	.	15.3451	0.74330	0.0:0.0:0.8595:0.1405	.	3159;3328;3288	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	3288;3328;2598;3159;3258	ENSP00000345799:T3288I;ENSP00000297405:T3328I;ENSP00000341558:T2598I;ENSP00000412263:T3159I;ENSP00000343124:T3258I	ENSP00000297405:T3328I	T	-	2	0	CSMD3	113336712	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	5.346000	0.65992	1.415000	0.47037	0.650000	0.86243	ACC		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113267536	G	A	113267536	3	1	103	1	0	0	0	0	1	0	0	0	3952	1261	44	3	1180	3	CSMD3	8	113267536	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	3471064	113267536	33096486	147	27246										
NOV	4856	hgsc.bcm.edu	37	chr8	120435161	120435161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caccagcctgcacacctacaAgcccaggttctgtggggtct	10	15	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:120435161A>G	ENST00000259526.3	+	5	1090	c.863A>G	c.(862-864)aAg>aGg	p.K288R	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			CACACCTACAAGCCCAGGTTC	0.512																																																0			8											88	87	87					8																	120435161		2203	4300	6503	120504342	SO:0001583	missense	6134			X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.863A>G	8.37:g.120435161A>G	ENSP00000259526:p.Lys288Arg		120504342		Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	A	1.415	-0.574389	0.03882	.	.	ENSG00000136999	ENST00000259526	T	0.03717	3.83	5.85	4.7	0.59300	Cystine knot (1);Cystine knot, C-terminal (2);	0.045665	0.85682	D	0.000000	T	0.02193	0.0068	N	0.11845	0.185	0.33155	D	0.546207	B	0.24258	0.1	B	0.26094	0.066	T	0.26467	-1.0102	10	0.02654	T	1	-25.3212	10.3981	0.44214	0.8647:0.0:0.1353:0.0	.	288	P48745	NOV_HUMAN	R	288	ENSP00000259526:K288R	ENSP00000259526:K288R	K	+	2	0	NOV	120504342	1.000000	0.71417	1.000000	0.80357	0.447000	0.32167	1.511000	0.35801	1.048000	0.40298	-0.256000	0.11100	AAG		0.512	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		G	120435161	A	G	120435161	3	3	103	1	0	0	0	0	1	0	0	0	10584	72	3	4	881	4	NOV	8	120435161	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	7167625	120435161	25928861	148	27247										
DSCC1	79075	hgsc.bcm.edu	37	chr8	120865287	120865287	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cagagtacagaaaagagcacCtcagtgtgaataatgttaca	9	7	1	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:120865287C>T	ENST00000313655.4	-	2	565	c.351G>A	c.(349-351)gaG>gaA	p.E117E		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	117					DNA replication (GO:0006260)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AAAAGAGCACCTCAGTGTGAA	0.333																																																0			8											121	111	114					8																	120865287		2203	4300	6503	120934468	SO:0001630	splice_region_variant	79075				CCDS6330.1	8q24.12	2013-05-24	2013-05-24		ENSG00000136982	ENSG00000136982			24453	protein-coding gene	gene with protein product	"defective in sister chromatid cohesion homolog 1 (S. cerevisiae)"	613203	"defective in sister chromatid cohesion 1 homolog (S. cerevisiae)"			12766176, 20826785	Standard	NM_024094		Approved	DCC1, hDCC1, MGC5528	uc003yov.3	Q9BVC3	OTTHUMG00000165010	ENST00000313655.4:c.351+1G>A	8.37:g.120865287C>T			120934468	Q969N5	Silent	SNP	ENST00000313655.4	37	CCDS6330.1																																																																																				0.333	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094	Silent	T	120865287	C	T	120865287	5	4	103	1	0	0	0	0	0	0	1	0	4781	695	24	3	862	3	DSCC1	8	120865287	Splice_Site	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	430126	120865287	25498735	149	27248										
FER1L6	654463	hgsc.bcm.edu	37	chr8	124968258	124968258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatgtttgggctgaaggtgaAgaagaagagaaataaggcag	16	2	0	5			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:124968258A>G	ENST00000522917.1	+	2	226	c.20A>G	c.(19-21)aAg>aGg	p.K7R	FER1L6_ENST00000399018.1_Missense_Mutation_p.K7R	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	7						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CTGAAGGTGAAGAAGAAGAGA	0.443																																																0			8											53	52	52					8																	124968258		1889	4113	6002	125037439	SO:0001583	missense	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.20A>G	8.37:g.124968258A>G	ENSP00000428280:p.Lys7Arg		125037439		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.186230	0.78789	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.82711	-1.64;-1.64	5.55	5.55	0.83447	.	0.517672	0.11857	U	0.522712	D	0.85225	0.5648	L	0.29908	0.895	0.51233	D	0.999913	D	0.63880	0.993	D	0.70935	0.971	T	0.78610	-0.2137	10	0.21014	T	0.42	.	13.3499	0.60595	1.0:0.0:0.0:0.0	.	7	Q2WGJ9	FR1L6_HUMAN	R	7	ENSP00000428280:K7R;ENSP00000381982:K7R	ENSP00000381982:K7R	K	+	2	0	FER1L6	125037439	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.163000	0.50763	2.233000	0.73108	0.533000	0.62120	AAG		0.443	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	124968258	A	G	124968258	3	3	103	1	0	0	0	0	1	0	0	0	5834	72	3	4	22	4	FER1L6	8	124968258	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4102971	124968258	21395764	150	27249										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139153456	139153456	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttacctgtactaaccagggTgctgttgttgtacagggttc	11	9	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:139153456T>C	ENST00000395297.1	-	17	3945	c.3775A>G	c.(3775-3777)Acc>Gcc	p.T1259A		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1259										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CTAACCAGGGTGCTGTTGTTG	0.542										HNSCC(54;0.14)																																						0			8											118	124	122					8																	139153456		1941	4126	6067	139222638	SO:0001583	missense	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3775A>G	8.37:g.139153456T>C	ENSP00000378710:p.Thr1259Ala		139222638	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	2.364	-0.345923	0.05208	.	.	ENSG00000147724	ENST00000395297	T	0.39997	1.05	5.83	-0.834	0.10779	Domain of unknown function DUF676, lipase-like (1);	0.315094	0.34223	N	0.004148	T	0.21468	0.0517	N	0.25144	0.715	0.34459	D	0.701567	B	0.15719	0.014	B	0.17722	0.019	T	0.44065	-0.9352	10	0.02654	T	1	-6.9754	10.8411	0.46715	0.0:0.4948:0.0:0.5052	.	1259	Q49AJ0	F135B_HUMAN	A	1259	ENSP00000378710:T1259A	ENSP00000378710:T1259A	T	-	1	0	FAM135B	139222638	0.814000	0.29104	0.934000	0.37439	0.893000	0.52053	0.144000	0.16135	-0.368000	0.08040	-0.408000	0.06270	ACC		0.542	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139153456	T	C	139153456	3	2	103	1	0	0	0	0	1	0	0	0	5465	1696	59	4	461	4	FAM135B	8	139153456	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	14185198	139153456	7210566	151	27250										
RHPN1	114822	hgsc.bcm.edu	37	chr8	144461593	144461593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatggcccaggcccaggaatGtgtgtttgagggcctctcac	14	11	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:144461593G>A	ENST00000289013.6	+	8	961	c.860G>A	c.(859-861)tGt>tAt	p.C287Y		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	287	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GCCCAGGAATGTGTGTTTGAG	0.677																																																0			8											20	23	22					8																	144461593		2021	4176	6197	144532736	SO:0001583	missense	114822			AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.860G>A	8.37:g.144461593G>A	ENSP00000289013:p.Cys287Tyr		144532736	Q8TAV1|Q96PV9	Missense_Mutation	SNP	ENST00000289013.6	37	CCDS47927.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.762631	0.49574	.	.	ENSG00000158106	ENST00000289013	T	0.21734	1.99	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.52565	0.1742	M	0.91354	3.2	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.62909	-0.6754	10	0.87932	D	0	-20.9379	11.7765	0.51989	0.0922:0.0:0.9078:0.0	.	287	Q8TCX5-2	.	Y	287	ENSP00000289013:C287Y	ENSP00000289013:C287Y	C	+	2	0	RHPN1	144532736	1.000000	0.71417	0.965000	0.40720	0.124000	0.20399	6.157000	0.71846	2.099000	0.63709	0.436000	0.28706	TGT		0.677	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1			A	144461593	G	A	144461593	3	1	103	1	0	0	0	0	1	0	0	0	13387	1377	48	3	890	3	RHPN1	8	144461593	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5308137	144461593	1902429	152	27251										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145667648	145667648	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcaataaccacgcagcactcGctctccatgaaccgcttcct	6	17	1	1	rs112264814	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr8:145667648G>A	ENST00000409379.3	-	6	755	c.726C>T	c.(724-726)agC>agT	p.S242S	AC084125.4_ENST00000442850.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	242					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CGCAGCACTCGCTCTCCATGA	0.627													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		20247	0		0	False		,,,				2504	0															0			8						G		24,4382	30.8+/-60.4	0,24,2179	80	73	75		726	1.4	1	8	dbSNP_132	75	0,8598		0,0,4299	no	coding-synonymous	TONSL	NM_013432.4		0,24,6478	AA,AG,GG		0.0,0.5447,0.1846		242/1379	145667648	24,12980	2203	4299	6502	145638456	SO:0001819	synonymous_variant	0				CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.726C>T	8.37:g.145667648G>A			145638456	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	37	CCDS34968.2																																																																																				0.627	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		A	145667648	G	A	145667648	2	1	103	1	0	0	0	0	0	0	0	1	10413	1078	38	1		1	NFKBIL2	8	145667648	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1206055	145667648	696374	153	27252										
DMRT3	58524	hgsc.bcm.edu	37	chr9	990868	990868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gctcgcccgtccttcctgccCgcgccacggaagaccctcgg	11	20	0	1	rs141821476	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:990868C>T	ENST00000190165.2	+	2	1320	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	428					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R428C(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CCTTCCTGCCCGCGCCACGGA	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	9						C	CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	85	72	76		1282	5.2	0.1	9	dbSNP_134	76	0,8600		0,0,4300	yes	missense	DMRT3	NM_021240.2	180	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	428/473	990868	5,13001	2203	4300	6503	980868	SO:0001583	missense	58524			AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"testis-specific protein"	614754	"DMRT-like family A3"	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1282C>T	9.37:g.990868C>T	ENSP00000190165:p.Arg428Cys		980868	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518218	0.44763	0.001135	0.0	ENSG00000064218	ENST00000190165	T	0.39592	1.07	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.53222	0.1783	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.56044	-0.8044	10	0.87932	D	0	-34.3542	13.7296	0.62779	0.1538:0.8462:0.0:0.0	.	428	Q9NQL9	DMRT3_HUMAN	C	428	ENSP00000190165:R428C	ENSP00000190165:R428C	R	+	1	0	DMRT3	980868	0.998000	0.40836	0.096000	0.21009	0.357000	0.29423	4.120000	0.57897	2.424000	0.82194	0.655000	0.94253	CGC		0.552	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		T	990868	C	T	990868	3	4	103	1	0	0	0	0	1	0	0	0	4598	652	23	1	1288	1	DMRT3	9	990868	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		990868	140222563	154	27253										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18474257	18474257	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgctgccgtcgggcaactccTggcacactgctcctctttct	9	16	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:18474257T>A	ENST00000380548.4	+	1	366	c.27T>A	c.(25-27)ccT>ccA	p.P9P	ADAMTSL1_ENST00000431052.2_Silent_p.P9P|ADAMTSL1_ENST00000276935.6_Silent_p.P9P|ADAMTSL1_ENST00000380566.4_Silent_p.P9P|ADAMTSL1_ENST00000380570.4_Silent_p.P9P|ADAMTSL1_ENST00000327883.7_Silent_p.P9P	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	9						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GGGCAACTCCTGGCACACTGC	0.522																																																0			9											203	171	182					9																	18474257		2203	4300	6503	18464257	SO:0001819	synonymous_variant	92949			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.27T>A	9.37:g.18474257T>A			18464257	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																				0.522	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			A	18474257	T	A	18474257	2	1	103	1	0	0	0	0	0	0	0	1	274	1567	55	5		5	ADAMTSL1	9	18474257	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	17483389	18474257	122739174	155	27254										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32633292	32633292	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcacgaaaaaggttgttctcAagtgcctgcagtaattggcc	11	9	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:32633292A>G	ENST00000242310.4	-	1	2375	c.2286T>C	c.(2284-2286)ctT>ctC	p.L762L	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	762			L -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGTTGTTCTCAAGTGCCTGCA	0.433																																																0			9											188	184	185					9																	32633292		2203	4300	6503	32623292	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2286T>C	9.37:g.32633292A>G			32623292	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.433	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32633292	A	G	32633292	2	3	103	1	0	0	0	0	0	0	0	1	15562	117	5	4		4	TAF1L	9	32633292	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	14159035	32633292	108580139	156	27255										
KIAA1161	57462	hgsc.bcm.edu	37	chr9	34371167	34371167	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccgcgtcgtagcgccagggcGggatagagaactgcatggcc	16	12	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:34371167G>T	ENST00000297625.7	-	2	1898	c.1673C>A	c.(1672-1674)cCg>cAg	p.P558Q		NM_020702.3	NP_065753.2	Q6NSJ0	K1161_HUMAN	KIAA1161	592					carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		GCGCCAGGGCGGGATAGAGAA	0.687																																																0			9											15	19	18					9																	34371167		1996	4141	6137	34361167	SO:0001583	missense	57462			AB032987		9p11.2	2009-11-06			ENSG00000164976	ENSG00000164976			19918	protein-coding gene	gene with protein product						10574461	Standard	XM_006716808		Approved	NET37	uc003zue.4	Q6NSJ0	OTTHUMG00000019816	ENST00000297625.7:c.1673C>A	9.37:g.34371167G>T	ENSP00000297625:p.Pro558Gln		34361167	Q5T587|Q5T588|Q9ULQ9	Missense_Mutation	SNP	ENST00000297625.7	37		.	.	.	.	.	.	.	.	.	.	G	20.5	3.995744	0.74703	.	.	ENSG00000164976	ENST00000297625	D	0.90563	-2.69	5.56	5.56	0.83823	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.94112	0.8112	L	0.55481	1.735	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.94094	0.7356	10	0.59425	D	0.04	-30.666	18.5218	0.90956	0.0:0.0:1.0:0.0	.	592	Q6NSJ0	K1161_HUMAN	Q	558	ENSP00000297625:P558Q	ENSP00000297625:P558Q	P	-	2	0	KIAA1161	34361167	1.000000	0.71417	0.743000	0.31040	0.989000	0.77384	9.869000	0.99810	2.637000	0.89404	0.455000	0.32223	CCG		0.687	KIAA1161-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000052158.1	XM_351807		T	34371167	G	T	34371167	3	4	103	1	0	0	0	0	1	0	0	0	8232	1116	39	2	373	2	KIAA1161	9	34371167	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1737875	34371167	106842264	157	27256										
SMC5	23137	hgsc.bcm.edu	37	chr9	72929699	72929699	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agagtaaatgctgttattgcTcccaagagttcatatgcaga	9	7	1	3	rs150292183		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:72929699T>C	ENST00000361138.5	+	12	1678	c.1620T>C	c.(1618-1620)gcT>gcC	p.A540A		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	540	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						CTGTTATTGCTCCCAAGAGTT	0.264																																																0			9						T		1,4397	2.1+/-5.4	0,1,2198	49	51	50		1620	1	1	9	dbSNP_134	50	2,8586	2.2+/-6.3	0,2,4292	no	coding-synonymous	SMC5	NM_015110.3		0,3,6490	CC,CT,TT		0.0233,0.0227,0.0231		540/1102	72929699	3,12983	2199	4294	6493	72119519	SO:0001819	synonymous_variant	23137			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.1620T>C	9.37:g.72929699T>C			72119519	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	37	CCDS6632.1																																																																																				0.264	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		C	72929699	T	C	72929699	2	2	103	1	0	0	0	0	0	0	0	1	14823	1538	54	4		4	SMC5	9	72929699	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	38558532	72929699	68283732	158	27257										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88937965	88937965	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcttcatacttagcagcttcGcctaactcatcatcctcttc	3	15	5	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:88937965G>A	ENST00000375963.3	-	13	2872	c.2700C>T	c.(2698-2700)ggC>ggT	p.G900G	ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000277141.6_Silent_p.G189G|ZCCHC6_ENST00000375960.2_Silent_p.G777G|ZCCHC6_ENST00000375961.2_Silent_p.G900G	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	900	Glu-rich.			G -> V (in Ref. 1; CAI45944). {ECO:0000305}.	RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.G900G(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						TAGCAGCTTCGCCTAACTCAT	0.423																																																2	Substitution - coding silent(2)	ovary(1)|endometrium(1)	9											173	147	156					9																	88937965		2203	4300	6503	88127785	SO:0001819	synonymous_variant	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2700C>T	9.37:g.88937965G>A			88127785	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Silent	SNP	ENST00000375963.3	37	CCDS35057.1																																																																																				0.423	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88937965	G	A	88937965	2	1	103	1	0	0	0	0	0	0	0	1	17631	1074	38	1		1	ZCCHC6	9	88937965	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	16008266	88937965	52275466	159	27258										
FAM22G	441457	hgsc.bcm.edu	37	chr9	99694095	99694095	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttgccacaccctctcccggCccaacacacaggccgcccct	6	22	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:99694095C>T	ENST00000372322.3	+	2	129	c.108C>T	c.(106-108)ggC>ggT	p.G36G	NUTM2G_ENST00000354649.3_Silent_p.G36G|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	36																	CCTCTCCCGGCCCAACACACA	0.657																																																0			9											31	41	38					9																	99694095		1964	4161	6125	98733916	SO:0001819	synonymous_variant	441457				CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"family with sequence similarity 22, member G"	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.108C>T	9.37:g.99694095C>T			98733916	A6NNI5|Q5VZR3	Silent	SNP	ENST00000372322.3	37	CCDS55329.1																																																																																				0.657	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741		T	99694095	C	T	99694095	2	4	103	1	0	0	0	0	0	0	0	1	5562	726	26	3		3	FAM22G	9	99694095	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10756130	99694095	41519336	160	27259										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101340282	101340282	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gacggatggacagacgcctcCaaacaccatcaagtggttag	11	11	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:101340282C>A	ENST00000259455.2	-	2	853	c.394G>T	c.(394-396)Gga>Tga	p.G132*		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	132					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CAGACGCCTCCAAACACCATC	0.498																																																0			9											207	189	195					9																	101340282		2203	4300	6503	100380103	SO:0001587	stop_gained	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.394G>T	9.37:g.101340282C>A	ENSP00000259455:p.Gly132*		100380103	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Nonsense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	c	42	9.588533	0.99213	.	.	ENSG00000136928	ENST00000259455	.	.	.	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.9707	0.71232	0.0:1.0:0.0:0.0	.	.	.	.	X	132	.	ENSP00000259455:G132X	G	-	1	0	GABBR2	100380103	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.724000	0.84798	2.113000	0.64589	0.550000	0.68814	GGA		0.498	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101340282	C	A	101340282	4	1	103	1	0	0	0	0	0	1	0	0	6175	603	21	2	2503	2	GABBR2	9	101340282	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1646187	101340282	39873149	161	27260										
RNF20	56254	hgsc.bcm.edu	37	chr9	104309422	104309422	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctttgtgttctctgtaggtgAattccaaaggttataaggtg	11	5	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:104309422A>G	ENST00000389120.3	+	8	988	c.898A>G	c.(898-900)Aat>Gat	p.N300D	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	300					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		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)		TCTGTAGGTGAATTCCAAAGG	0.403																																																0			9											107	103	104					9																	104309422		2203	4300	6503	103349243	SO:0001583	missense	56254			AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.898A>G	9.37:g.104309422A>G	ENSP00000373772:p.Asn300Asp		103349243	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.809203	0.31961	.	.	ENSG00000155827	ENST00000389120	T	0.31769	1.48	5.84	5.84	0.93424	.	0.087718	0.85682	D	0.000000	T	0.47192	0.1432	L	0.49126	1.545	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.26538	-1.0100	10	0.14656	T	0.56	-28.4988	15.8917	0.79303	1.0:0.0:0.0:0.0	.	300	Q5VTR2	BRE1A_HUMAN	D	300	ENSP00000373772:N300D	ENSP00000373772:N300D	N	+	1	0	RNF20	103349243	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	8.927000	0.92846	2.228000	0.72767	0.533000	0.62120	AAT		0.403	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		G	104309422	A	G	104309422	3	3	103	1	0	0	0	0	1	0	0	0	13510	246	9	4	924	4	RNF20	9	104309422	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2969140	104309422	36904009	162	27261										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123210314	123210314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatctggctctgcagctgcgTcaccacctcctgggtggcag	13	14	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:123210314T>C	ENST00000349780.4	-	22	3063	c.2884A>G	c.(2884-2886)Acg>Gcg	p.T962A	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.T962A|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.T962A|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.T930A	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	962	Interaction with MAPRE1.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.T962S(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TGCAGCTGCGTCACCACCTCC	0.483																																																1	Substitution - Missense(1)	lung(1)	9											103	105	104					9																	123210314		2203	4300	6503	122250135	SO:0001583	missense	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2884A>G	9.37:g.123210314T>C	ENSP00000343818:p.Thr962Ala		122250135	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.024559	0.00414	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.20598	4.06;3.89;4.03;3.93;2.38;2.06	4.83	1.42	0.22433	.	0.644384	0.13550	N	0.379597	T	0.05364	0.0142	N	0.01168	-0.975	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.0;0.001	T	0.40572	-0.9556	10	0.14252	T	0.57	.	3.6032	0.08032	0.1467:0.5128:0.2432:0.0973	.	13;731;930;962;962;356	Q5JTU8;Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;.;CK5P2_HUMAN;.	A	930;962;962;962;356;13;734	ENSP00000354065:T930A;ENSP00000352258:T962A;ENSP00000343818:T962A;ENSP00000353317:T962A;ENSP00000400395:T356A;ENSP00000409941:T13A	ENSP00000341695:T734A	T	-	1	0	CDK5RAP2	122250135	0.000000	0.05858	0.903000	0.35520	0.209000	0.24338	-0.676000	0.05221	1.004000	0.39156	-0.621000	0.04028	ACG		0.483	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		C	123210314	T	C	123210314	3	2	103	1	0	0	0	0	1	0	0	0	3152	1667	58	4	2865	4	CDK5RAP2	9	123210314	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	18900892	123210314	18003117	163	27262										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123222897	123222897	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	actcaggaaattaatctcgtCatcctccccaattttgatcg	5	12	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:123222897C>T	ENST00000349780.4	-	19	2334	c.2155G>A	c.(2155-2157)Gac>Aac	p.D719N	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.D719N|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.D719N|CDK5RAP2_ENST00000360822.3_Intron	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	719					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TTAATCTCGTCATCCTCCCCA	0.443																																																0			9											221	185	197					9																	123222897		2203	4300	6503	122262718	SO:0001583	missense	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2155G>A	9.37:g.123222897C>T	ENSP00000343818:p.Asp719Asn		122262718	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.316207	0.60524	.	.	ENSG00000136861	ENST00000359309;ENST00000349780;ENST00000360190	T;T;T	0.03717	3.83;3.96;3.86	5.66	5.66	0.87406	.	0.316532	0.27076	N	0.021043	T	0.09335	0.0230	L	0.29908	0.895	0.26274	N	0.978388	D;P	0.76494	0.999;0.906	D;P	0.64321	0.924;0.521	T	0.34650	-0.9820	10	0.25751	T	0.34	.	16.4703	0.84109	0.0:1.0:0.0:0.0	.	719;719	Q96SN8-4;Q96SN8	.;CK5P2_HUMAN	N	719	ENSP00000352258:D719N;ENSP00000343818:D719N;ENSP00000353317:D719N	ENSP00000343818:D719N	D	-	1	0	CDK5RAP2	122262718	0.022000	0.18835	0.534000	0.28014	0.500000	0.33767	1.865000	0.39479	2.693000	0.91896	0.650000	0.86243	GAC		0.443	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123222897	C	T	123222897	3	4	103	1	0	0	0	0	1	0	0	0	3152	826	29	3	3606	3	CDK5RAP2	9	123222897	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	12583	123222897	17990534	164	27263										
RC3H2	54542	hgsc.bcm.edu	37	chr9	125622278	125622278	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atgttttcagaatgcggaggAtatactggtactctagttag	11	5	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:125622278A>G	ENST00000373670.1	-	10	2367	c.1767T>C	c.(1765-1767)taT>taC	p.Y589Y	RC3H2_ENST00000357244.2_Silent_p.Y589Y|RC3H2_ENST00000423239.2_Silent_p.Y589Y			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	589	Pro-rich.				B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						AATGCGGAGGATATACTGGTA	0.433																																																0			9											213	211	211					9																	125622278		1843	4097	5940	124662099	SO:0001819	synonymous_variant	54542			AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.1767T>C	9.37:g.125622278A>G			124662099	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	37	CCDS43874.1																																																																																				0.433	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		G	125622278	A	G	125622278	2	3	103	1	0	0	0	0	0	0	0	1	13204	340	12	4		4	RC3H2	9	125622278	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2399381	125622278	15591153	165	27264										
ABL1	25	hgsc.bcm.edu	37	chr9	133730245	133730245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggaatggtgtgaagcccaaaCcaaaaatggccaaggctggg	14	8	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:133730245C>T	ENST00000318560.5	+	3	692	c.311C>T	c.(310-312)aCc>aTc	p.T104I		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	104	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GAAGCCCAAACCAAAAATGGC	0.502			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	0			9											101	88	93					9																	133730245		2203	4300	6503	132720066	SO:0001583	missense	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.311C>T	9.37:g.133730245C>T	ENSP00000323315:p.Thr104Ile		132720066	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.437058	0.83885	.	.	ENSG00000097007	ENST00000372348;ENST00000438426;ENST00000318560	T;T	0.47528	0.84;0.84	5.67	5.67	0.87782	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.40040	0.1101	N	0.16201	0.385	0.80722	D	1	B;B	0.31413	0.322;0.322	B;B	0.37239	0.244;0.244	T	0.42155	-0.9468	10	0.87932	D	0	.	18.8246	0.92111	0.0:1.0:0.0:0.0	.	104;141	P00519;Q59FK4	ABL1_HUMAN;.	I	123;150;104	ENSP00000361423:T123I;ENSP00000323315:T104I	ENSP00000323315:T104I	T	+	2	0	ABL1	132720066	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.775000	0.85489	2.677000	0.91161	0.638000	0.83543	ACC		0.502	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133730245	C	T	133730245	3	4	103	1	0	0	0	0	1	0	0	0	92	507	18	3	461	3	ABL1	9	133730245	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	8107967	133730245	7483186	166	27265										
FAM163B	642968	hgsc.bcm.edu	37	chr9	136444471	136444471	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	accaggttgcggttggagtgCagcgggggcaggtgcgagtg	21	7	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr9:136444471C>T	ENST00000496132.1	-	3	418	c.174G>A	c.(172-174)ctG>ctA	p.L58L	FAM163B_ENST00000356873.3_Silent_p.L58L			P0C2L3	F163B_HUMAN	family with sequence similarity 163, member B	58						integral component of membrane (GO:0016021)				large_intestine(1)	1						GGTTGGAGTGCAGCGGGGGCA	0.677																																																0			9											1	1	1					9																	136444471		453	1263	1716	135434292	SO:0001819	synonymous_variant	642968			BX629352	CCDS35171.1	9q34.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000196990	ENSG00000196990			33277	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 166"	C9orf166			Standard	NM_001080515		Approved		uc011mdm.2	P0C2L3	OTTHUMG00000159557	ENST00000496132.1:c.174G>A	9.37:g.136444471C>T			135434292	B2RUZ5	Silent	SNP	ENST00000496132.1	37	CCDS35171.1																																																																																				0.677	FAM163B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356190.1	NM_001080515		T	136444471	C	T	136444471	2	4	103	1	0	0	0	0	0	0	0	1	5493	697	25	3		3	FAM163B	9	136444471	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2714226	136444471	4768960	167	27266										
UPF2	26019	hgsc.bcm.edu	37	chr10	12039754	12039754	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcatgcaaaaatccattgcTgcctattgggaaaaagtaaa	7	7	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:12039754T>C	ENST00000356352.2	-	7	2234	c.1761A>G	c.(1759-1761)gcA>gcG	p.A587A	UPF2_ENST00000397053.2_Silent_p.A587A|UPF2_ENST00000357604.5_Silent_p.A587A			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	587	MIF4G 2.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				AATCCATTGCTGCCTATTGGG	0.343																																																0			10											155	143	147					10																	12039754		2203	4300	6503	12079760	SO:0001819	synonymous_variant	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1761A>G	10.37:g.12039754T>C			12079760	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Silent	SNP	ENST00000356352.2	37	CCDS7086.1																																																																																				0.343	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			C	12039754	T	C	12039754	2	2	103	1	0	0	0	0	0	0	0	1	17044	1567	55	4		4	UPF2	10	12039754	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10		12039754	123494993	168	27267										
DCLRE1C	64421	hgsc.bcm.edu	37	chr10	14976408	14976408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taattcttcactaaggttggTgaacagatattcatagccat	7	7	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:14976408T>C	ENST00000378278.2	-	8	686	c.649A>G	c.(649-651)Acc>Gcc	p.T217A	DCLRE1C_ENST00000378289.4_Missense_Mutation_p.T217A|DCLRE1C_ENST00000453695.2_Missense_Mutation_p.T97A|DCLRE1C_ENST00000378255.1_Missense_Mutation_p.T97A|DCLRE1C_ENST00000378249.1_Missense_Mutation_p.T102A|DCLRE1C_ENST00000357717.2_Missense_Mutation_p.T102A|DCLRE1C_ENST00000378246.2_Missense_Mutation_p.T102A|DCLRE1C_ENST00000378258.1_Missense_Mutation_p.T97A|DCLRE1C_ENST00000396817.2_Missense_Mutation_p.T97A|DCLRE1C_ENST00000378254.1_Missense_Mutation_p.T97A			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	217					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						CTAAGGTTGGTGAACAGATAT	0.423								Non-homologous end-joining																																								0			10											118	137	131					10																	14976408		2203	4300	6503	15016414	SO:0001583	missense	64421			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.649A>G	10.37:g.14976408T>C	ENSP00000367527:p.Thr217Ala		15016414	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722578	0.68959	.	.	ENSG00000152457	ENST00000378289;ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000418843	T;T;T;T;T;T;T;T;T;T;T	0.79247	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-1.25	5.36	5.36	0.76844	.	0.045033	0.85682	D	0.000000	T	0.81513	0.4838	L	0.44542	1.39	0.49582	D	0.999804	B;D;B	0.61697	0.012;0.99;0.136	B;P;B	0.59643	0.037;0.861;0.075	T	0.80788	-0.1226	10	0.37606	T	0.19	.	15.3355	0.74250	0.0:0.0:0.0:1.0	.	217;102;217	Q96SD1-4;Q96SD1-3;Q96SD1	.;.;DCR1C_HUMAN	A	217;97;102;102;102;97;97;97;217;97;71	ENSP00000367538:T217A;ENSP00000400529:T97A;ENSP00000367492:T102A;ENSP00000350349:T102A;ENSP00000367496:T102A;ENSP00000380030:T97A;ENSP00000367503:T97A;ENSP00000367502:T97A;ENSP00000367527:T217A;ENSP00000367506:T97A;ENSP00000391428:T71A	ENSP00000350349:T102A	T	-	1	0	DCLRE1C	15016414	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.168000	0.64978	2.030000	0.59900	0.528000	0.53228	ACC		0.423	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		C	14976408	T	C	14976408	3	2	103	1	0	0	0	0	1	0	0	0	4302	1696	59	4	1457	4	DCLRE1C	10	14976408	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	2936654	14976408	120558339	169	27268										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15296824	15296824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtcactgtagctggtgttcTcaggcaacctcagagccctt	11	12	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:15296824T>C	ENST00000378116.4	-	4	479	c.473A>G	c.(472-474)gAg>gGg	p.E158G		NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	158						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						GCTGGTGTTCTCAGGCAACCT	0.562																																																0			10											62	58	60					10																	15296824		2203	4300	6503	15336830	SO:0001583	missense	221061			AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.473A>G	10.37:g.15296824T>C	ENSP00000367356:p.Glu158Gly		15336830	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	T	10.45	1.353190	0.24512	.	.	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.31510	1.49	5.11	3.95	0.45737	.	0.364462	0.29616	N	0.011647	T	0.17831	0.0428	N	0.22421	0.69	0.35449	D	0.795491	B	0.09022	0.002	B	0.14578	0.011	T	0.15636	-1.0430	10	0.21540	T	0.41	-25.5114	6.9177	0.24369	0.0:0.0755:0.152:0.7725	.	158	Q5VUB5	F1711_HUMAN	G	158;159	ENSP00000367356:E158G	ENSP00000367356:E158G	E	-	2	0	FAM171A1	15336830	1.000000	0.71417	0.985000	0.45067	0.931000	0.56810	2.554000	0.45845	0.874000	0.35823	0.528000	0.53228	GAG		0.562	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		C	15296824	T	C	15296824	3	2	103	1	0	0	0	0	1	0	0	0	5506	1551	54	4	2219	4	FAM171A1	10	15296824	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	320416	15296824	120237923	170	27269										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18937511	18937511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgtaaatgatggaggatgtgAcaggtgctttaacaaagttt	12	3	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:18937511A>G	ENST00000377304.4	-	2	557	c.139T>C	c.(139-141)Tca>Cca	p.S47P	RP11-139J15.7_ENST00000606425.1_Missense_Mutation_p.S35P	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	47							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)	p.S47T(1)		endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						GGAGGATGTGACAGGTGCTTT	0.348																																																1	Substitution - Missense(1)	ovary(1)	10											216	204	208					10																	18937511		2203	4300	6503	18977517	SO:0001583	missense	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.139T>C	10.37:g.18937511A>G	ENSP00000366519:p.Ser47Pro		18977517	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	37	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.283355	0.59867	.	.	ENSG00000241058	ENST00000377304	T	0.32272	1.46	4.95	4.95	0.65309	.	0.060303	0.64402	D	0.000002	T	0.42562	0.1208	M	0.78637	2.42	0.53005	D	0.999966	P	0.48998	0.918	P	0.48425	0.577	T	0.45934	-0.9227	10	0.59425	D	0.04	.	10.7457	0.46179	0.8407:0.1593:0.0:0.0	.	47	Q8TEA1	NSUN6_HUMAN	P	47	ENSP00000366519:S47P	ENSP00000366519:S47P	S	-	1	0	NSUN6	18977517	0.983000	0.35010	0.795000	0.32087	0.822000	0.46500	2.066000	0.41452	1.864000	0.54056	0.383000	0.25322	TCA		0.348	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		G	18937511	A	G	18937511	3	3	103	1	0	0	0	0	1	0	0	0	10713	275	10	4	1310	4	NSUN6	10	18937511	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	3640687	18937511	116597236	171	27270										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887718	25887718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctcaccacaagcctaaggcaGctgaggtttgtcagcaatcc	9	13	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:25887718G>A	ENST00000376351.3	+	11	3522	c.3163G>A	c.(3163-3165)Gct>Act	p.A1055T	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1055					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GCCTAAGGCAGCTGAGGTTTG	0.428																																																0			10											90	89	90					10																	25887718		2203	4300	6503	25927724	SO:0001583	missense	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3163G>A	10.37:g.25887718G>A	ENSP00000365529:p.Ala1055Thr		25927724	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	6.688	0.495571	0.12762	.	.	ENSG00000151025	ENST00000376351	T	0.29655	1.56	4.33	-0.301	0.12800	.	0.539313	0.16516	N	0.211010	T	0.17916	0.0430	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22034	-1.0228	10	0.13853	T	0.58	.	1.5941	0.02660	0.1675:0.2462:0.3594:0.2269	.	1055	Q5T848	GP158_HUMAN	T	1055	ENSP00000365529:A1055T	ENSP00000365529:A1055T	A	+	1	0	GPR158	25927724	0.996000	0.38824	0.918000	0.36340	0.801000	0.45260	0.968000	0.29357	0.064000	0.16427	0.655000	0.94253	GCT		0.428	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25887718	G	A	25887718	3	1	103	1	0	0	0	0	1	0	0	0	6683	971	34	3	3205	3	GPR158	10	25887718	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	6950207	25887718	109647029	172	27271										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26442855	26442855	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaaaaattaatcaacctggcAaaggtaagaaaatgcttttt	7	5	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:26442855A>G	ENST00000265944.5	+	24	2878	c.2712A>G	c.(2710-2712)gcA>gcG	p.A904A	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	904	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCAACCTGGCAAAGGTAAGAA	0.308																																																0			10											30	31	31					10																	26442855		2201	4291	6492	26482861	SO:0001819	synonymous_variant	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2712A>G	10.37:g.26442855A>G			26482861	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																				0.308	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26442855	A	G	26442855	2	3	103	1	0	0	0	0	0	0	0	1	10106	117	5	4		4	MYO3A	10	26442855	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	555137	26442855	109091892	173	27272										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26443698	26443698	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gacactggagaagccacacgTcatgccagagagacaaccaa	10	12	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:26443698T>C	ENST00000265944.5	+	25	2905	c.2739T>C	c.(2737-2739)cgT>cgC	p.R913R	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	913	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAGCCACACGTCATGCCAGAG	0.408																																																0			10											120	118	119					10																	26443698		2203	4300	6503	26483704	SO:0001819	synonymous_variant	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2739T>C	10.37:g.26443698T>C			26483704	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																				0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26443698	T	C	26443698	2	2	103	1	0	0	0	0	0	0	0	1	10106	1654	58	4		4	MYO3A	10	26443698	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	843	26443698	109091049	174	27273										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49654531	49654531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcaacagctggttcctcctcTccgcatcctcccgcgcccgt	8	20	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:49654531T>C	ENST00000249601.4	-	10	2296	c.2000A>G	c.(1999-2001)gAg>gGg	p.E667G	ARHGAP22_ENST00000435790.2_Missense_Mutation_p.E673G|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.E683G|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.E558G|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.E500G|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.E577G|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.E508G	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	667					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTTCCTCCTCTCCGCATCCTC	0.507																																																0			10											150	142	144					10																	49654531		2203	4300	6503	49324537	SO:0001583	missense	58504			AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.2000A>G	10.37:g.49654531T>C	ENSP00000249601:p.Glu667Gly		49324537	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.590715	0.66219	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04;0.04	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.79787	0.4506	M	0.85859	2.78	0.58432	D	0.999995	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.85130	0.994;0.994;0.994;0.994;0.997;0.997	T	0.83134	-0.0112	10	0.87932	D	0	.	12.3683	0.55240	0.0:0.0:0.0:1.0	.	673;667;683;667;577;500	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	G	667;558;508;500;577;673;683	ENSP00000249601:E667G;ENSP00000363287:E558G;ENSP00000363285:E508G;ENSP00000422868:E500G;ENSP00000410054:E577G;ENSP00000416701:E673G;ENSP00000412461:E683G	ENSP00000249601:E667G	E	-	2	0	ARHGAP22	49324537	1.000000	0.71417	0.863000	0.33907	0.427000	0.31564	7.849000	0.86908	1.523000	0.49018	0.402000	0.26972	GAG		0.507	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		C	49654531	T	C	49654531	3	2	103	1	0	0	0	0	1	0	0	0	872	1551	54	4	100	4	ARHGAP22	10	49654531	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	23210833	49654531	85880216	175	27274										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50678894	50678894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaggctggttgaatccttcTttttagatggcatttgggtg	12	5	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:50678894T>C	ENST00000355832.5	-	18	3190	c.3112A>G	c.(3112-3114)Aga>Gga	p.R1038G	ERCC6_ENST00000542458.1_Missense_Mutation_p.R408G|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1038			R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGAATCCTTCTTTTTAGATGG	0.388								Direct reversal of damage;Nucleotide excision repair (NER)																																								0			10											126	127	127					10																	50678894		2203	4300	6503	50348900	SO:0001583	missense	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3112A>G	10.37:g.50678894T>C	ENSP00000348089:p.Arg1038Gly		50348900	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	9.409	1.080124	0.20309	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83419	-1.72;-1.46	5.95	4.8	0.61643	.	.	.	.	.	T	0.79695	0.4490	M	0.64404	1.975	0.23809	N	0.996785	B;B	0.13145	0.002;0.007	B;B	0.08055	0.001;0.003	T	0.65146	-0.6239	9	0.25106	T	0.35	-18.2246	11.3011	0.49306	0.0:0.0:0.3622:0.6378	.	1038;415	Q03468;Q59FF6	ERCC6_HUMAN;.	G	1038;415;408	ENSP00000348089:R1038G;ENSP00000445134:R408G	ENSP00000348089:R1038G	R	-	1	2	ERCC6	50348900	0.994000	0.37717	0.351000	0.25721	0.072000	0.16883	1.898000	0.39809	1.039000	0.40074	0.533000	0.62120	AGA		0.388	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50678894	T	C	50678894	3	2	103	1	0	0	0	0	1	0	0	0	5230	1617	56	4	1385	4	ERCC6	10	50678894	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1024363	50678894	84855853	176	27275										
ANK3	288	hgsc.bcm.edu	37	chr10	61967870	61967870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aatggccacagtgggcagccAcgtgtagggcagtcaggtag	16	9	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:61967870A>G	ENST00000280772.2	-	10	1309	c.1118T>C	c.(1117-1119)gTg>gCg	p.V373A	ANK3_ENST00000373827.2_Missense_Mutation_p.V367A|ANK3_ENST00000503366.1_Missense_Mutation_p.V356A	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	373					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTGGGCAGCCACGTGTAGGGC	0.522																																																0			10											171	140	150					10																	61967870		2203	4300	6503	61637876	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.1118T>C	10.37:g.61967870A>G	ENSP00000280772:p.Val373Ala		61637876	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459153	0.84317	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000503366;ENST00000395299;ENST00000395293;ENST00000395304	T;T;T	0.64438	-0.1;-0.1;-0.1	4.78	4.78	0.61160	Ankyrin repeat-containing domain (4);	0.000000	0.38058	N	0.001836	T	0.68183	0.2973	L	0.28054	0.825	0.80722	D	1	P;D;P;D	0.76494	0.873;0.989;0.844;0.999	B;D;P;D	0.80764	0.1;0.946;0.679;0.994	T	0.72877	-0.4159	10	0.87932	D	0	.	14.4831	0.67597	1.0:0.0:0.0:0.0	.	356;34;367;373	E9PE32;E7EMJ1;Q5CZH9;Q12955	.;.;.;ANK3_HUMAN	A	373;367;356;335;34;34	ENSP00000280772:V373A;ENSP00000362933:V367A;ENSP00000425236:V356A	ENSP00000280772:V373A	V	-	2	0	ANK3	61637876	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.088000	0.94132	2.014000	0.59158	0.460000	0.39030	GTG		0.522	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61967870	A	G	61967870	3	3	103	1	0	0	0	0	1	0	0	0	622	159	6	4	12484	4	ANK3	10	61967870	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	11288976	61967870	73566877	177	27276										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624277	89624277	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agaaacaaaaggagatatcaAgaggatggattcgacttaga	11	4	1	4	rs587781912		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:89624277A>G	ENST00000371953.3	+	1	1408	c.51A>G	c.(49-51)caA>caG	p.Q17Q	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	17	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Q17del(2)|p.R15fs*23(1)|p.R14fs*26(1)|p.Y16fs*21(1)|p.N12fs*6(1)|p.R14_D22del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGAGATATCAAGAGGATGGAT	0.473		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	57	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(4)|Deletion - In frame(3)	prostate(14)|central_nervous_system(13)|skin(7)|lung(6)|endometrium(3)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											181	173	176					10																	89624277		2203	4300	6503	89614257	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.51A>G	10.37:g.89624277A>G			89614257	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.473	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89624277	A	G	89624277	2	3	103	1	0	0	0	0	0	0	0	1	12772	69	3	4		4	PTEN	10	89624277	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	27656407	89624277	45910470	178	27277										
PTEN	5728	hgsc.bcm.edu	37	chr10	89653842	89653842	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagacttgaaggcgtatacaGgaacaatattgatgatgtag	11	4	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:89653842G>T	ENST00000371953.3	+	2	1497	c.140G>T	c.(139-141)aGg>aTg	p.R47M		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	47	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		R -> G (in CWS1). {ECO:0000269|PubMed:11494117}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(2)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGCGTATACAGGAACAATATT	0.289		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	47	Whole gene deletion(37)|Unknown(8)|Deletion - Frameshift(2)	prostate(14)|central_nervous_system(8)|skin(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|ovary(3)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	10											112	112	112					10																	89653842		2203	4296	6499	89643822	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.140G>T	10.37:g.89653842G>T	ENSP00000361021:p.Arg47Met		89643822	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.910633	0.92107	.	.	ENSG00000171862	ENST00000371953	D	0.98822	-5.16	5.08	5.08	0.68730	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99510	0.9825	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97960	1.0337	9	.	.	.	-7.4116	17.2284	0.86978	0.0:0.0:1.0:0.0	.	47	P60484	PTEN_HUMAN	M	47	ENSP00000361021:R47M	.	R	+	2	0	PTEN	89643822	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.977000	0.93446	2.364000	0.80123	0.655000	0.94253	AGG		0.289	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89653842	G	T	89653842	3	4	103	1	0	0	0	0	1	0	0	0	12772	1000	35	2	146	2	PTEN	10	89653842	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	29565	89653842	45880905	179	27278										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105178280	105178280	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aacatccgtgctttcctcccCacatctcatctgtcggacca	5	17	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:105178280C>T	ENST00000369797.3	+	15	2089	c.1995C>T	c.(1993-1995)ccC>ccT	p.P665P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	665	S1 motif 7. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CTTTCCTCCCCACATCTCATC	0.547																																																0			10											185	137	153					10																	105178280		2203	4300	6503	105168270	SO:0001819	synonymous_variant	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1995C>T	10.37:g.105178280C>T			105168270	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																				0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105178280	C	T	105178280	2	4	103	1	0	0	0	0	0	0	0	1	11648	581	21	3		3	PDCD11	10	105178280	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	15524438	105178280	30356467	180	27279										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123279563	123279563	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcttttccacgtgcttgatcCactggatgtggggctgggca	13	10	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr10:123279563C>T	ENST00000358487.5	-	7	1141	c.869G>A	c.(868-870)tGg>tAg	p.W290*	FGFR2_ENST00000369056.1_Nonsense_Mutation_p.W290*|FGFR2_ENST00000369060.4_Nonsense_Mutation_p.W290*|FGFR2_ENST00000351936.6_Nonsense_Mutation_p.W290*|FGFR2_ENST00000357555.5_Nonsense_Mutation_p.W201*|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000346997.2_Nonsense_Mutation_p.W290*|FGFR2_ENST00000356226.4_Nonsense_Mutation_p.W175*|FGFR2_ENST00000478859.1_Nonsense_Mutation_p.W62*|FGFR2_ENST00000457416.2_Nonsense_Mutation_p.W290*|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000360144.3_Nonsense_Mutation_p.W201*|FGFR2_ENST00000369059.1_Nonsense_Mutation_p.W175*	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	290	Ig-like C2-type 3.		W -> C (in PS; severe; also in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:11781872, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9150725}.|W -> G (in CS). {ECO:0000269|PubMed:8528214}.|W -> R (in CS).		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GTGCTTGATCCACTGGATGTG	0.547		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											130	119	123					10																	123279563		2203	4300	6503	123269553	SO:0001587	stop_gained	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.869G>A	10.37:g.123279563C>T	ENSP00000351276:p.Trp290*		123269553	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Nonsense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	43	10.401376	0.99398	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0368	0.97565	0.0:1.0:0.0:0.0	.	.	.	.	X	201;290;290;175;290;175;290;290;290;201;290;290;201	.	ENSP00000337665:W201X	W	-	2	0	FGFR2	123269553	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.811000	0.86092	2.735000	0.93741	0.563000	0.77884	TGG		0.547	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123279563	C	T	123279563	4	4	103	1	0	0	0	0	0	1	0	0	5885	595	21	3	1900	3	FGFR2	10	123279563	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	18101283	123279563	12255184	181	27280										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	720175	720175	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atctggacccaggagatgctGctgcaggtgaacgaccagtc	13	11	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:720175G>C	ENST00000533256.1	+	6	654	c.279G>C	c.(277-279)ctG>ctC	p.L93L	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Silent_p.L93L|EPS8L2_ENST00000530636.1_Silent_p.L93L|EPS8L2_ENST00000526198.1_Silent_p.L93L			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	93	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGGAGATGCTGCTGCAGGTGA	0.632																																																0			11											73	58	63					11																	720175		2203	4300	6503	710175	SO:0001819	synonymous_variant	64787			AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.279G>C	11.37:g.720175G>C			710175	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																				0.632	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		C	720175	G	C	720175	2	2	103	1	0	0	0	0	0	0	0	1	5209	1306	46	5		5	EPS8L2	11	720175	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		720175	134286341	182	27281										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17135987	17135987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tctgaaaaaaggactgtactCgttccatacttctttggaga	8	8	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:17135987C>T	ENST00000265970.7	-	19	3241	c.3242G>A	c.(3241-3243)cGa>cAa	p.R1081Q	RNU6-593P_ENST00000364716.1_RNA|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.R701Q|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1081					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						GGACTGTACTCGTTCCATACT	0.333																																																0			11											113	111	112					11																	17135987		2200	4293	6493	17092563	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3242G>A	11.37:g.17135987C>T	ENSP00000265970:p.Arg1081Gln		17092563	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065366	0.76187	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80566	-1.39;-1.39	4.97	4.97	0.65823	Protein kinase-like domain (1);	0.130066	0.53938	D	0.000055	T	0.82056	0.4954	L	0.47190	1.495	0.53005	D	0.999964	D	0.71674	0.998	P	0.52066	0.689	T	0.80630	-0.1297	10	0.30854	T	0.27	-7.6658	18.2258	0.89916	0.0:1.0:0.0:0.0	.	1081	O00443	P3C2A_HUMAN	Q	1081;701	ENSP00000265970:R1081Q;ENSP00000438687:R701Q	ENSP00000265970:R1081Q	R	-	2	0	PIK3C2A	17092563	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.188000	0.50958	2.309000	0.77851	0.460000	0.39030	CGA		0.333	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		T	17135987	C	T	17135987	3	4	103	1	0	0	0	0	1	0	0	0	11940	884	31	1	1874	1	PIK3C2A	11	17135987	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	16415812	17135987	117870529	183	27282										
DCDC1	341019	hgsc.bcm.edu	37	chr11	31349698	31349698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caaaatatatttgtaaattgGgtttacagtattcccatcca	5	7	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:31349698G>A	ENST00000452803.1	-	3	331	c.130C>T	c.(130-132)Cca>Tca	p.P44S	DCDC1_ENST00000597505.1_Missense_Mutation_p.P44S	NM_181807.3	NP_861523.2	P59894	DCDC1_HUMAN	doublecortin domain containing 1	44					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TTGTAAATTGGGTTTACAGTA	0.353																																																0			11											75	74	74					11																	31349698		2202	4299	6501	31306274	SO:0001583	missense	341019			AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000452803.1:c.130C>T	11.37:g.31349698G>A	ENSP00000389792:p.Pro44Ser		31306274	A6PVL6|B7WNX6|Q6ZU04	Missense_Mutation	SNP	ENST00000452803.1	37	CCDS7872.1	.	.	.	.	.	.	.	.	.	.	G	9.935	1.215779	0.22373	.	.	ENSG00000188682	ENST00000452803	T	0.27890	1.64	4.93	-0.691	0.11305	.	0.899079	0.09338	N	0.815946	T	0.13030	0.0316	N	0.12182	0.205	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.28713	-1.0035	10	0.28530	T	0.3	.	0.8829	0.01238	0.2783:0.16:0.3975:0.1642	.	44	P59894	DCDC1_HUMAN	S	44	ENSP00000389792:P44S	ENSP00000343496:P44S	P	-	1	0	DCDC1	31306274	0.001000	0.12720	0.000000	0.03702	0.256000	0.26092	0.118000	0.15605	0.059000	0.16252	-0.266000	0.10368	CCA		0.353	DCDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316531.1	NM_181807		A	31349698	G	A	31349698	3	1	103	1	0	0	0	0	1	0	0	0	4290	1232	43	3	962	3	DCDC1	11	31349698	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	14213711	31349698	103656818	184	27283										
MADD	8567	hgsc.bcm.edu	37	chr11	47306652	47306652	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aatctatgacaatccatactTcgagccccaatatggctttc	5	12	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:47306652T>G	ENST00000311027.5	+	13	2483	c.2318T>G	c.(2317-2319)tTc>tGc	p.F773C	MADD_ENST00000395336.3_Missense_Mutation_p.F773C|MADD_ENST00000402799.1_Intron|MADD_ENST00000402192.2_Missense_Mutation_p.F773C|MADD_ENST00000406482.1_Intron|MADD_ENST00000342922.4_Missense_Mutation_p.F773C|MADD_ENST00000407859.3_Intron|MADD_ENST00000349238.3_Missense_Mutation_p.F773C|MADD_ENST00000395344.3_Intron	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		AATCCATACTTCGAGCCCCAA	0.547																																																0			11											86	82	84					11																	47306652		2201	4298	6499	47263228	SO:0001583	missense	8567			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.2318T>G	11.37:g.47306652T>G	ENSP00000310933:p.Phe773Cys		47263228		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211788	0.79240	.	.	ENSG00000110514	ENST00000342922;ENST00000349238;ENST00000311027;ENST00000395336;ENST00000402192	T;T;T;T;T	0.08634	3.07;3.08;3.1;3.1;3.08	6.17	3.9	0.45041	.	0.149324	0.64402	D	0.000008	T	0.12732	0.0309	L	0.32530	0.975	0.80722	D	1	P;P;P;P	0.51351	0.708;0.816;0.584;0.944	P;P;P;P	0.54210	0.736;0.678;0.479;0.745	T	0.01405	-1.1363	10	0.66056	D	0.02	-4.3537	10.2789	0.43528	0.0:0.1312:0.0:0.8688	.	773;773;773;773	Q8WXG6-7;Q8WXG6-2;Q8WXG6;Q8WXG6-3	.;.;MADD_HUMAN;.	C	773	ENSP00000343902:F773C;ENSP00000304505:F773C;ENSP00000310933:F773C;ENSP00000378745:F773C;ENSP00000384287:F773C	ENSP00000310933:F773C	F	+	2	0	MADD	47263228	1.000000	0.71417	0.976000	0.42696	0.997000	0.91878	3.251000	0.51453	0.586000	0.29626	0.533000	0.62120	TTC		0.547	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			G	47306652	T	G	47306652	3	3	103	1	0	0	0	0	1	0	0	0	9182	1783	62	4	2364	4	MADD	11	47306652	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	15956954	47306652	87699864	185	27284										
OR5A1	219982	hgsc.bcm.edu	37	chr11	59211352	59211352	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atcccttcagcagagggccgAtggaaagcctgcaacacgtg	12	12	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:59211352A>G	ENST00000302030.2	+	1	736	c.711A>G	c.(709-711)cgA>cgG	p.R237R		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						CAGAGGGCCGATGGAAAGCCT	0.547																																																0			11											266	220	236					11																	59211352		2201	4295	6496	58967928	SO:0001819	synonymous_variant	219982			AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"GPCR / Class A : Olfactory receptors"	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.711A>G	11.37:g.59211352A>G			58967928	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																				0.547	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728		G	59211352	A	G	59211352	2	3	103	1	0	0	0	0	0	0	0	1	11170	320	12	4		4	OR5A1	11	59211352	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	11904700	59211352	75795164	186	27285										
OR4D10	390197	hgsc.bcm.edu	37	chr11	59245207	59245207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcattgcttcactcagatgtTtctattccaccttattggag	6	10	4	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:59245207T>C	ENST00000530162.1	+	1	362	c.305T>C	c.(304-306)tTt>tCt	p.F102S		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACTCAGATGTTTCTATTCCAC	0.473																																																0			11											94	95	95					11																	59245207		2103	4240	6343	59001783	SO:0001583	missense	390197			AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"GPCR / Class A : Olfactory receptors"	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.305T>C	11.37:g.59245207T>C	ENSP00000436424:p.Phe102Ser		59001783	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451676	0.43531	.	.	ENSG00000254466	ENST00000530162	T	0.00397	7.57	4.4	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00875	0.0029	M	0.79805	2.47	0.38104	D	0.937369	D	0.89917	1.0	D	0.97110	1.0	T	0.64892	-0.6300	9	0.87932	D	0	.	8.3873	0.32508	0.1751:0.0:0.0:0.8249	.	102	Q8NGI6	OR4DA_HUMAN	S	102	ENSP00000436424:F102S	ENSP00000436424:F102S	F	+	2	0	OR4D10	59001783	0.622000	0.27085	0.997000	0.53966	0.153000	0.21895	0.973000	0.29422	1.733000	0.51620	0.533000	0.62120	TTT		0.473	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705		C	59245207	T	C	59245207	3	2	103	1	0	0	0	0	1	0	0	0	11085	1841	64	4	307	4	OR4D10	11	59245207	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	33855	59245207	75761309	187	27286										
MEN1	4221	hgsc.bcm.edu	37	chr11	64571983	64571983	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcatcttctcactctggaaAgtgagcactggaccctccgg	9	13	4	1	rs143423552		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:64571983A>G	ENST00000337652.1	-	10	2174	c.1671T>C	c.(1669-1671)acT>acC	p.T557T	MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000377313.1_Silent_p.T557T|MEN1_ENST00000394374.2_Silent_p.T557T|MEN1_ENST00000394376.1_Silent_p.T557T|MEN1_ENST00000478548.1_5'UTR|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000377321.1_Silent_p.T517T|MEN1_ENST00000377316.2_Silent_p.T497T|MEN1_ENST00000377326.3_Silent_p.T552T|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000443283.1_Silent_p.T557T|MEN1_ENST00000315422.4_Silent_p.T552T|MEN1_ENST00000312049.6_Silent_p.T552T	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	557			T -> S (in adrenal adenoma; somatic). {ECO:0000269|PubMed:10647896}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CACTCTGGAAAGTGAGCACTG	0.622			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated				A|||	1	0.000199681	0	0	5008	,	,		15155	0		0.001	False		,,,				2504	0				Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	0			11						A	,,,,,,	0,4402		0,0,2201	133	114	120		1671,1656,1671,1671,1671,1671,1671	-1.6	1	11	dbSNP_134	120	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEN1	NM_000244.3,NM_130799.2,NM_130800.2,NM_130801.2,NM_130802.2,NM_130803.2,NM_130804.2	,,,,,,	0,1,6497	GG,GA,AA		0.0116,0.0,0.0077	,,,,,,	557/616,552/611,557/616,557/616,557/616,557/616,557/616	64571983	1,12995	2201	4297	6498	64328559	SO:0001819	synonymous_variant	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1671T>C	11.37:g.64571983A>G			64328559	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000337652.1	37	CCDS8083.1																																																																																				0.622	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			G	64571983	A	G	64571983	2	3	103	1	0	0	0	0	0	0	0	1	9502	59	3	4		4	MEN1	11	64571983	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	5326776	64571983	70434533	188	27287										
ADRBK1	156	hgsc.bcm.edu	37	chr11	67052395	67052395	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccttcctgacccagtggcagCggcggtacttctacctgttc	10	15	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:67052395C>A	ENST00000308595.5	+	19	2022	c.1732C>A	c.(1732-1734)Cgg>Agg	p.R578R	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	578	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		R -> Q (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCAGTGGCAGCGGCGGTACTT	0.672																																																0			11											74	54	61					11																	67052395		2198	4295	6493	66808971	SO:0001819	synonymous_variant	156			X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1732C>A	11.37:g.67052395C>A			66808971	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																				0.672	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		A	67052395	C	A	67052395	2	1	103	1	0	0	0	0	0	0	0	1	343	759	27	2		2	ADRBK1	11	67052395	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2480412	67052395	67954121	189	27288										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99944920	99944920	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atcaactgaagaaaacaataAttgttaccaaagaccaagaa	5	7	1	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:99944920A>T	ENST00000524871.1	+	13	1764	c.1474A>T	c.(1474-1476)Att>Ttt	p.I492F	CNTN5_ENST00000418526.2_Missense_Mutation_p.I418F|CNTN5_ENST00000527185.1_Missense_Mutation_p.I492F|CNTN5_ENST00000528682.1_Missense_Mutation_p.I492F|CNTN5_ENST00000279463.3_Missense_Mutation_p.I492F	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	492	Ig-like C2-type 5.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		GAAAACAATAATTGTTACCAA	0.378																																																0			11											60	59	59					11																	99944920		1845	4093	5938	99450130	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1474A>T	11.37:g.99944920A>T	ENSP00000435637:p.Ile492Phe		99450130	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.564701	0.65651	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.51	3.23	0.37069	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.149457	0.64402	D	0.000017	T	0.68302	0.2986	L	0.46885	1.475	0.51012	D	0.999904	P;P;P	0.50272	0.933;0.745;0.933	P;P;P	0.58077	0.832;0.558;0.832	T	0.66563	-0.5892	10	0.41790	T	0.15	.	7.8353	0.29365	0.7926:0.0:0.2074:0.0	.	492;418;492	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	F	492;492;492;418;492	ENSP00000433575:I492F;ENSP00000436185:I492F;ENSP00000435637:I492F;ENSP00000393229:I418F;ENSP00000279463:I492F	ENSP00000279463:I492F	I	+	1	0	CNTN5	99450130	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.838000	0.62803	2.095000	0.63458	0.456000	0.33151	ATT		0.378	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99944920	A	T	99944920	3	4	103	1	0	0	0	0	1	0	0	0	3650	101	4	5	1516	5	CNTN5	11	99944920	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	32892525	99944920	35061596	190	27289										
MMP8	4317	hgsc.bcm.edu	37	chr11	102593394	102593394	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttggtaattggtagaactttTccaggtagtcctggacaaag	11	6	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:102593394T>C	ENST00000236826.3	-	2	211	c.113A>G	c.(112-114)gAa>gGa	p.E38G		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	38					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	GTAGAACTTTTCCAGGTAGTC	0.428																																																0			11											86	84	85					11																	102593394		2203	4298	6501	102098604	SO:0001583	missense	4317			J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.113A>G	11.37:g.102593394T>C	ENSP00000236826:p.Glu38Gly		102098604	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.562778	0.45694	.	.	ENSG00000118113	ENST00000236826;ENST00000544383	T	0.37058	1.22	5.99	4.87	0.63330	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.547984	0.17776	N	0.162437	T	0.42177	0.1191	M	0.66378	2.025	0.09310	N	1	B;B	0.21309	0.054;0.022	B;B	0.32762	0.152;0.104	T	0.42865	-0.9426	10	0.62326	D	0.03	.	11.3	0.49300	0.0:0.0715:0.0:0.9285	.	38;38	A8K9E4;P22894	.;MMP8_HUMAN	G	38;15	ENSP00000236826:E38G	ENSP00000236826:E38G	E	-	2	0	MMP8	102098604	0.088000	0.21588	0.079000	0.20413	0.986000	0.74619	2.837000	0.48191	1.102000	0.41551	0.533000	0.62120	GAA		0.428	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		C	102593394	T	C	102593394	3	2	103	1	0	0	0	0	1	0	0	0	9698	1783	62	4	1326	4	MMP8	11	102593394	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	2648474	102593394	32413122	191	27290										
MMP13	4322	hgsc.bcm.edu	37	chr11	102826346	102826346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggaggtcttcctcagacaaaTcatcttcatcaccaccactg	6	14	6	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:102826346T>C	ENST00000260302.3	-	1	117	c.89A>G	c.(88-90)gAt>gGt	p.D30G	MMP13_ENST00000340273.4_Missense_Mutation_p.D30G	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	30					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CTCAGACAAATCATCTTCATC	0.502																																																0			11											113	101	105					11																	102826346		2202	4299	6501	102331556	SO:0001583	missense	4322			X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.89A>G	11.37:g.102826346T>C	ENSP00000260302:p.Asp30Gly		102331556	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	T	8.414	0.844909	0.16963	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.36520	1.25;1.25	5.62	4.49	0.54785	Metallopeptidase, catalytic domain (1);	0.422167	0.28742	N	0.014293	T	0.18759	0.0450	N	0.08118	0	0.24237	N	0.995371	B	0.31026	0.304	B	0.26693	0.072	T	0.11817	-1.0572	10	0.33141	T	0.24	.	11.8916	0.52633	0.0:0.0686:0.0:0.9314	.	30	P45452	MMP13_HUMAN	G	30	ENSP00000260302:D30G;ENSP00000339672:D30G	ENSP00000260302:D30G	D	-	2	0	MMP13	102331556	0.671000	0.27521	0.040000	0.18447	0.120000	0.20174	3.454000	0.52986	1.052000	0.40392	0.533000	0.62120	GAT		0.502	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		C	102826346	T	C	102826346	3	2	103	1	0	0	0	0	1	0	0	0	9682	1435	50	4	1366	4	MMP13	11	102826346	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	232952	102826346	32180170	192	27291										
CASP5	838	hgsc.bcm.edu	37	chr11	104871023	104871023	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggacaatgatgaccttgggtTtgtcctttagactgaggcag	13	7	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:104871023T>A	ENST00000260315.3	-	6	916	c.917A>T	c.(916-918)aAa>aTa	p.K306I	CASP5_ENST00000531367.1_Missense_Mutation_p.K164I|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000393141.2_Missense_Mutation_p.K319I|CASP5_ENST00000526056.1_Missense_Mutation_p.K319I|CASP5_ENST00000444749.2_Missense_Mutation_p.K248I|CASP5_ENST00000418434.1_Missense_Mutation_p.K164I			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	306					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GACCTTGGGTTTGTCCTTTAG	0.458																																																0			11											200	173	182					11																	104871023		2202	4299	6501	104376233	SO:0001583	missense	838				CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"Caspases"	1506	protein-coding gene	gene with protein product		602665	"caspase 5, apoptosis-related cysteine protease"			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.917A>T	11.37:g.104871023T>A	ENSP00000260315:p.Lys306Ile		104376233	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	.	20.6	4.016701	0.75161	.	.	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75	4.34	4.34	0.51931	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (2);Peptidase C14, ICE, catalytic subunit p20 (1);	0.000000	0.85682	D	0.000000	T	0.47488	0.1448	H	0.97896	4.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.65207	-0.6224	10	0.87932	D	0	.	11.772	0.51965	0.0:0.0:0.0:1.0	.	164;248;306;319	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	I	319;164;306;248;319;164	ENSP00000376849:K319I;ENSP00000398130:K164I;ENSP00000260315:K306I;ENSP00000388365:K248I;ENSP00000436877:K319I;ENSP00000434471:K164I	ENSP00000260315:K306I	K	-	2	0	CASP5	104376233	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.378000	0.73150	1.736000	0.51660	0.334000	0.21626	AAA		0.458	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347		A	104871023	T	A	104871023	3	1	103	1	0	0	0	0	1	0	0	0	2680	1841	64	5	403	5	CASP5	11	104871023	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	2044677	104871023	30135493	193	27292										
CBL	867	hgsc.bcm.edu	37	chr11	119144733	119144733	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	catctttacccgactctttcAggtaggacactaaaaaagtt	6	10	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:119144733A>G	ENST00000264033.4	+	4	1122	c.746A>G	c.(745-747)cAg>cGg	p.Q249R		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	249	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.|Sufficient for interaction with EPHB1.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CGACTCTTTCAGGTAGGACAC	0.368			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	0			11											84	86	86					11																	119144733		2199	4295	6494	118649943	SO:0001630	splice_region_variant	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.747+1A>G	11.37:g.119144733A>G			118649943	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.712679	0.68730	.	.	ENSG00000110395	ENST00000264033	T	0.80566	-1.39	5.48	5.48	0.80851	Adaptor protein Cbl, PTB domain (1);EF-hand-like domain (1);Adaptor protein Cbl, EF hand-like (1);	0.000000	0.85682	D	0.000000	D	0.89546	0.6746	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90701	0.4620	10	0.66056	D	0.02	-32.8161	15.5788	0.76414	1.0:0.0:0.0:0.0	.	249	P22681	CBL_HUMAN	R	249	ENSP00000264033:Q249R	ENSP00000264033:Q249R	Q	+	2	0	CBL	118649943	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.324000	0.96373	2.096000	0.63516	0.402000	0.26972	CAG		0.368	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	Missense_Mutation	G	119144733	A	G	119144733	5	3	103	1	0	0	0	0	0	0	1	0	2706	202	7	4	760	4	CBL	11	119144733	Splice_Site	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	14273710	119144733	15861783	194	27293										
CBL	867	hgsc.bcm.edu	37	chr11	119148923	119148923	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggctccacattccaactatgTaaaatatgtgctgaaaatga	7	8	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:119148923T>C	ENST00000264033.4	+	8	1519	c.1143T>C	c.(1141-1143)tgT>tgC	p.C381C		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	381	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E366_Q409del(13)|p.E369_Q409del(1)|p.E369_D390del(1)|p.?(1)|p.E366_K477del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCCAACTATGTAAAATATGTG	0.348			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	17	Deletion - In frame(16)|Unknown(1)	haematopoietic_and_lymphoid_tissue(17)	11											88	83	84					11																	119148923		2199	4295	6494	118654133	SO:0001819	synonymous_variant	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1143T>C	11.37:g.119148923T>C			118654133	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																				0.348	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119148923	T	C	119148923	2	2	103	1	0	0	0	0	0	0	0	1	2706	1644	57	4		4	CBL	11	119148923	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	4190	119148923	15857593	195	27294										
TECTA	7007	hgsc.bcm.edu	37	chr11	120989281	120989281	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acttgctggcccgacagtgtTtgcagacttccagcctccct	9	15	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:120989281T>G	ENST00000392793.1	+	7	1328	c.1057T>G	c.(1057-1059)Ttg>Gtg	p.L353V	TECTA_ENST00000264037.2_Missense_Mutation_p.L353V			O75443	TECTA_HUMAN	tectorin alpha	353	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CCGACAGTGTTTGCAGACTTC	0.562																																																0			11											133	120	124					11																	120989281		2203	4299	6502	120494491	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1057T>G	11.37:g.120989281T>G	ENSP00000376543:p.Leu353Val		120494491		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	T	9.313	1.056109	0.19907	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.60040	0.22;0.22	5.72	-4.79	0.03200	von Willebrand factor, type D domain (3);	0.151991	0.45361	N	0.000370	T	0.30070	0.0753	N	0.17564	0.495	0.24446	N	0.994505	B	0.06786	0.001	B	0.06405	0.002	T	0.26985	-1.0087	10	0.13853	T	0.58	.	9.3696	0.38246	0.0:0.4444:0.1076:0.448	.	353	O75443	TECTA_HUMAN	V	353	ENSP00000376543:L353V;ENSP00000264037:L353V	ENSP00000264037:L353V	L	+	1	2	TECTA	120494491	1.000000	0.71417	0.518000	0.27811	0.991000	0.79684	0.860000	0.27871	-0.678000	0.05224	-0.376000	0.06991	TTG		0.562	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	120989281	T	G	120989281	3	3	103	1	0	0	0	0	1	0	0	0	15786	1838	64	4	1079	4	TECTA	11	120989281	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	1840358	120989281	14017235	196	27295										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676949	123676949	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatggtgatgtttcctgttgCtgttaatgtgtaagttacca	11	5	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:123676949C>G	ENST00000309154.2	-	1	146	c.109G>C	c.(109-111)Gca>Cca	p.A37P		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		TTTCCTGTTGCTGTTAATGTG	0.433																																																0			11											142	122	129					11																	123676949		2202	4299	6501	123182159	SO:0001583	missense	390261			AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.109G>C	11.37:g.123676949C>G	ENSP00000311038:p.Ala37Pro		123182159	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	C	2.300	-0.360355	0.05103	.	.	ENSG00000196099	ENST00000309154	T	0.00441	7.41	3.69	0.407	0.16371	.	1.143100	0.06913	U	0.808030	T	0.00271	0.0008	N	0.19112	0.55	0.09310	N	1	B	0.26744	0.158	B	0.26094	0.066	T	0.38023	-0.9680	10	0.87932	D	0	.	3.9925	0.09543	0.0:0.364:0.3893:0.2467	.	37	Q8NGM8	OR6M1_HUMAN	P	37	ENSP00000311038:A37P	ENSP00000311038:A37P	A	-	1	0	OR6M1	123182159	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-6.558000	0.00061	0.236000	0.21180	-0.953000	0.02652	GCA		0.433	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		G	123676949	C	G	123676949	3	3	103	1	0	0	0	0	1	0	0	0	11236	797	28	5	835	5	OR6M1	11	123676949	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2687668	123676949	11329567	197	27296										
ETS1	2113	hgsc.bcm.edu	37	chr11	128360420	128360420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tagcttttaatgcttgagacAtcatttctttgctgcttgga	8	7	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:128360420A>G	ENST00000319397.6	-	2	443	c.134T>C	c.(133-135)aTg>aCg	p.M45T	ETS1_ENST00000345075.4_Missense_Mutation_p.M45T|ETS1_ENST00000535549.1_Intron|ETS1_ENST00000526145.2_Missense_Mutation_p.M45T|ETS1_ENST00000392668.4_Missense_Mutation_p.M89T|ETS1_ENST00000531611.1_Missense_Mutation_p.M45T	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	45					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		TGCTTGAGACATCATTTCTTT	0.363																																																0			11											135	127	130					11																	128360420		2201	4297	6498	127865630	SO:0001583	missense	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.134T>C	11.37:g.128360420A>G	ENSP00000324578:p.Met45Thr		127865630	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.086712	0.76642	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.65	5.65	0.86999	Sterile alpha motif/pointed domain (1);	0.000000	0.85682	D	0.000000	T	0.54711	0.1875	M	0.67397	2.05	0.80722	D	1	P;P;D	0.57257	0.867;0.915;0.979	D;D;D	0.74348	0.982;0.935;0.983	T	0.57877	-0.7735	10	0.87932	D	0	.	15.8653	0.79060	1.0:0.0:0.0:0.0	.	45;45;89	P14921;Q96AC5;Q6N087	ETS1_HUMAN;.;.	T	45;89;45;45;45	ENSP00000340485:M45T;ENSP00000376436:M89T;ENSP00000435666:M45T;ENSP00000324578:M45T;ENSP00000433500:M45T	ENSP00000324578:M45T	M	-	2	0	ETS1	127865630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.149000	0.67028	0.460000	0.39030	ATG		0.363	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		G	128360420	A	G	128360420	3	3	103	1	0	0	0	0	1	0	0	0	5288	217	8	4	1219	4	ETS1	11	128360420	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4683471	128360420	6646096	198	27297										
NTM	50863	hgsc.bcm.edu	37	chr11	132016193	132016193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caggtgcactattgacaaccGggtcacccgggtggcctggc	14	13	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr11:132016193G>A	ENST00000374786.1	+	2	664	c.185G>A	c.(184-186)cGg>cAg	p.R62Q	NTM_ENST00000374784.1_Missense_Mutation_p.R62Q|NTM_ENST00000374791.3_Missense_Mutation_p.R62Q|NTM_ENST00000425719.2_Missense_Mutation_p.R62Q|NTM_ENST00000539799.1_Missense_Mutation_p.R62Q|NTM_ENST00000427481.2_Missense_Mutation_p.R53Q	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	62	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ATTGACAACCGGGTCACCCGG	0.577																																																0			11											115	93	100					11																	132016193		2201	4297	6498	131521403	SO:0001583	missense	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.185G>A	11.37:g.132016193G>A	ENSP00000363918:p.Arg62Gln		131521403	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245003	0.59103	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.69	5.69	0.88448	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054148	0.64402	D	0.000001	T	0.63988	0.2558	L	0.34521	1.04	0.44890	D	0.9979	P;P;P;B;B;B	0.47253	0.892;0.504;0.763;0.335;0.287;0.357	P;B;B;B;B;B	0.45610	0.487;0.283;0.355;0.174;0.067;0.186	T	0.62081	-0.6929	10	0.35671	T	0.21	-18.7026	19.819	0.96583	0.0:0.0:1.0:0.0	.	62;53;62;62;62;62	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	Q	62;62;53;53;62;62;62	ENSP00000363923:R62Q;ENSP00000437668:R62Q;ENSP00000448104:R53Q;ENSP00000416320:R53Q;ENSP00000363918:R62Q;ENSP00000396722:R62Q;ENSP00000363916:R62Q	ENSP00000363916:R62Q	R	+	2	0	NTM	131521403	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.266000	0.72540	2.691000	0.91804	0.655000	0.94253	CGG		0.577	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		A	132016193	G	A	132016193	3	1	103	1	0	0	0	0	1	0	0	0	10730	1116	39	1	277	1	NTM	11	132016193	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	3655773	132016193	2990323	199	27298										
FOXM1	2305	hgsc.bcm.edu	37	chr12	2968475	2968475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttttctccgagaccggctccTctccctcctctccctgtgtt	6	18	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:2968475T>C	ENST00000359843.3	-	9	1689	c.1621A>G	c.(1621-1623)Agg>Ggg	p.R541G	Y_RNA_ENST00000410561.1_RNA|FOXM1_ENST00000342628.2_Missense_Mutation_p.R579G|FOXM1_ENST00000361953.3_Missense_Mutation_p.R526G|ITFG2_ENST00000545509.1_Intron|AC005841.1_ENST00000382678.3_5'Flank	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	541					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GACCGGCTCCTCTCCCTCCTC	0.592																																																0			12											62	62	62					12																	2968475		2203	4300	6503	2838736	SO:0001583	missense	2305			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"Forkhead boxes"	3818	protein-coding gene	gene with protein product	"M-phase phosphoprotein 2"	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1621A>G	12.37:g.2968475T>C	ENSP00000352901:p.Arg541Gly		2838736	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Missense_Mutation	SNP	ENST00000359843.3	37	CCDS8515.1	.	.	.	.	.	.	.	.	.	.	T	6.313	0.425871	0.11987	.	.	ENSG00000111206	ENST00000342628;ENST00000361953;ENST00000359843	D;D;D	0.92545	-2.98;-3.06;-2.98	4.45	0.505	0.16953	.	1.175620	0.05901	N	0.629976	D	0.82609	0.5074	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.29571	0.036;0.0;0.0;0.0;0.249	B;B;B;B;B	0.31869	0.04;0.001;0.002;0.001;0.137	T	0.73190	-0.4061	10	0.54805	T	0.06	.	4.4804	0.11764	0.0:0.1866:0.3235:0.4899	.	525;541;526;541;579	A8K591;Q53Y49;Q08050-2;Q08050;Q08050-3	.;.;.;FOXM1_HUMAN;.	G	579;526;541	ENSP00000342307:R579G;ENSP00000354492:R526G;ENSP00000352901:R541G	ENSP00000342307:R579G	R	-	1	2	FOXM1	2838736	0.002000	0.14202	0.893000	0.35052	0.924000	0.55760	0.333000	0.19768	0.005000	0.14708	0.459000	0.35465	AGG		0.592	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		C	2968475	T	C	2968475	3	2	103	1	0	0	0	0	1	0	0	0	6037	1550	54	4	674	4	FOXM1	12	2968475	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10		2968475	130883420	200	27299										
TSPAN9	10867	hgsc.bcm.edu	37	chr12	3310386	3310386	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aggggctgcctctgctgcttGaagtacatgatgttcctctt	11	10	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:3310386G>C	ENST00000011898.5	+	3	188	c.27G>C	c.(25-27)ttG>ttC	p.L9F	TSPAN9_ENST00000537971.1_Missense_Mutation_p.L9F|TSPAN9_ENST00000407263.1_Missense_Mutation_p.L9F	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	9						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)				endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			TCTGCTGCTTGAAGTACATGA	0.488																																																0			12											356	269	298					12																	3310386		2203	4300	6503	3180647	SO:0001583	missense	10867			AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"Tetraspanins"	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.27G>C	12.37:g.3310386G>C	ENSP00000011898:p.Leu9Phe		3180647	D3DUQ7|Q53FV2|Q6FGJ8	Missense_Mutation	SNP	ENST00000011898.5	37	CCDS8520.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.543715	0.65198	.	.	ENSG00000011105	ENST00000537971;ENST00000011898;ENST00000407263	D;D;D	0.81996	-1.56;-1.56;-1.56	5.08	3.1	0.35709	.	0.808779	0.10941	N	0.617264	D	0.83138	0.5189	L	0.45581	1.43	0.41594	D	0.988813	B	0.23185	0.081	B	0.38655	0.278	T	0.79780	-0.1659	10	0.72032	D	0.01	.	12.8103	0.57635	0.0:0.3144:0.6856:0.0	.	9	O75954	TSN9_HUMAN	F	9	ENSP00000444799:L9F;ENSP00000011898:L9F;ENSP00000384488:L9F	ENSP00000011898:L9F	L	+	3	2	TSPAN9	3180647	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.277000	0.51654	1.114000	0.41781	0.561000	0.74099	TTG		0.488	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675		C	3310386	G	C	3310386	3	2	103	1	0	0	0	0	1	0	0	0	16694	1281	45	5	29	5	TSPAN9	12	3310386	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	341911	3310386	130541509	201	27300										
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13722836	13722836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atctttttggatggcaatgcCatagccagtggaagcaaaga	11	7	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:13722836C>T	ENST00000609686.1	-	11	2496	c.2287G>A	c.(2287-2289)Ggc>Agc	p.G763S		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	763					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ATGGCAATGCCATAGCCAGTG	0.512																																																0			12											80	65	70					12																	13722836		2203	4300	6503	13614103	SO:0001583	missense	2904				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2287G>A	12.37:g.13722836C>T	ENSP00000477455:p.Gly763Ser		13614103	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	C	36	5.640786	0.96693	.	.	ENSG00000150086	ENST00000279593	T	0.59638	0.25	5.55	5.55	0.83447	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.056868	0.64402	D	0.000001	T	0.81894	0.4919	M	0.92268	3.29	0.80722	D	1	D	0.60160	0.987	D	0.66196	0.942	D	0.86128	0.1573	10	0.87932	D	0	.	19.5042	0.95108	0.0:1.0:0.0:0.0	.	763	Q13224	NMDE2_HUMAN	S	763	ENSP00000279593:G763S	ENSP00000279593:G763S	G	-	1	0	GRIN2B	13614103	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.771000	0.85420	2.590000	0.87494	0.655000	0.94253	GGC		0.512	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			T	13722836	C	T	13722836	3	4	103	1	0	0	0	0	1	0	0	0	6801	594	21	3	2179	3	GRIN2B	12	13722836	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10412450	13722836	120129059	202	27301										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21353504	21353504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atgttatgtttgtgcttttgAcgttgttacaagtaagcagc	10	5	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:21353504A>G	ENST00000256958.2	+	9	1129	c.1033A>G	c.(1033-1035)Acg>Gcg	p.T345A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	345					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TGTGCTTTTGACGTTGTTACA	0.323																																																0			12											116	105	109					12																	21353504		2203	4299	6502	21244771	SO:0001583	missense	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1033A>G	12.37:g.21353504A>G	ENSP00000256958:p.Thr345Ala		21244771	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	A	8.881	0.951601	0.18431	.	.	ENSG00000134538	ENST00000256958	T	0.57907	0.37	3.34	-1.18	0.09617	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.896444	0.09749	N	0.760806	T	0.36908	0.0984	L	0.42581	1.335	0.09310	N	1	B	0.21071	0.051	B	0.28305	0.088	T	0.33189	-0.9878	10	0.24483	T	0.36	.	0.5125	0.00597	0.3332:0.187:0.1156:0.3643	.	345	Q9Y6L6	SO1B1_HUMAN	A	345	ENSP00000256958:T345A	ENSP00000256958:T345A	T	+	1	0	SLCO1B1	21244771	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.255000	0.08769	0.021000	0.15133	0.402000	0.26972	ACG		0.323	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21353504	A	G	21353504	3	3	103	1	0	0	0	0	1	0	0	0	14760	275	10	4	1063	4	SLCO1B1	12	21353504	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	7630668	21353504	112498391	203	27302										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380236	25380236	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acacaaagaaagccctccccAgtcctcatgtactggtccct	6	16	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:25380236A>T	ENST00000256078.4	-	3	285	c.222T>A	c.(220-222)acT>acA	p.T74T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Silent_p.T74T	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	74					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			AGCCCTCCCCAGTCCTCATGT	0.388		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											112	104	107					12																	25380236		2203	4300	6503	25271503	SO:0001819	synonymous_variant	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.222T>A	12.37:g.25380236A>T			25271503	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.388	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25380236	A	T	25380236	2	4	103	1	0	0	0	0	0	0	0	1	8459	175	7	5		5	KRAS	12	25380236	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4026732	25380236	108471659	204	27303										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29648367	29648367	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggctgtactccccagaagtcAcagttatattcttcagctgc	8	12	3	1	rs111993736	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:29648367A>G	ENST00000318184.5	-	4	304	c.305T>C	c.(304-306)gTg>gCg	p.V102A		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	102	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V102A(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CCCAGAAGTCACAGTTATATT	0.363													A|||	24	0.00479233	0.0174	0.0014	5008	,	,		17837	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	12						A	ALA/VAL	47,3599		0,47,1776	77	71	73		305	2.9	0.5	12	dbSNP_132	73	0,8170		0,0,4085	yes	missense	OVCH1	NM_183378.2	64	0,47,5861	GG,GA,AA		0.0,1.2891,0.3978	possibly-damaging	102/1135	29648367	47,11769	1823	4085	5908	29539634	SO:0001583	missense	341350			BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.305T>C	12.37:g.29648367A>G	ENSP00000326708:p.Val102Ala		29539634		Missense_Mutation	SNP	ENST00000318184.5	37		9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	9.768	1.172009	0.21704	0.012891	0.0	ENSG00000187950	ENST00000318184	D	0.96136	-3.92	2.89	2.89	0.33648	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.84938	0.5583	L	0.41124	1.26	0.09310	N	1	P	0.40731	0.728	B	0.41619	0.361	T	0.79487	-0.1783	9	0.20519	T	0.43	.	4.74	0.13008	0.8579:0.0:0.1421:0.0	.	102	Q7RTY7	OVCH1_HUMAN	A	102	ENSP00000326708:V102A	ENSP00000326708:V102A	V	-	2	0	OVCH1	29539634	0.972000	0.33761	0.481000	0.27354	0.053000	0.15095	3.778000	0.55371	1.569000	0.49696	0.533000	0.62120	GTG		0.363	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		G	29648367	A	G	29648367	3	3	103	1	0	0	0	0	1	0	0	0	11354	159	6	4	3199	4	OVCH1	12	29648367	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4268131	29648367	104203528	205	27304										
ALG10B	144245	hgsc.bcm.edu	37	chr12	38714221	38714221	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaagttaactgaggcttggAaaactgagctacaaaagaag	10	5	0	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:38714221A>C	ENST00000308742.4	+	3	944	c.628A>C	c.(628-630)Aaa>Caa	p.K210Q	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	210					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TGAGGCTTGGAAAACTGAGCT	0.398																																																0			12											135	138	137					12																	38714221		2203	4299	6502	37000488	SO:0001583	missense	144245			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.628A>C	12.37:g.38714221A>C	ENSP00000310120:p.Lys210Gln		37000488	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	N	15.13	2.740948	0.49151	.	.	ENSG00000175548	ENST00000308742	T	0.55234	0.53	3.24	3.24	0.37175	.	0.139110	0.64402	D	0.000005	T	0.56659	0.2000	M	0.64567	1.98	0.80722	D	1	P	0.51537	0.946	P	0.53062	0.717	T	0.53669	-0.8406	10	0.24483	T	0.36	.	10.1623	0.42860	1.0:0.0:0.0:0.0	.	210	Q5I7T1	AG10B_HUMAN	Q	210	ENSP00000310120:K210Q	ENSP00000310120:K210Q	K	+	1	0	ALG10B	37000488	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	5.419000	0.66435	1.719000	0.51432	0.448000	0.29417	AAA		0.398	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		C	38714221	A	C	38714221	3	2	103	1	0	0	0	0	1	0	0	0	512	247	9	4	638	4	ALG10B	12	38714221	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	9065854	38714221	95137674	206	27305										
MLL2	8085	hgsc.bcm.edu	37	chr12	49433711	49433711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtgcaggtggtggcagaacCgacggagggcgtagtgggga	22	6	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:49433711C>T	ENST00000301067.7	-	31	7841	c.7842G>A	c.(7840-7842)tcG>tcA	p.S2614S	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2614	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GTGGCAGAACCGACGGAGGGC	0.652																																																0			12											42	46	45					12																	49433711		2012	4175	6187	47719978	SO:0001819	synonymous_variant	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7842G>A	12.37:g.49433711C>T			47719978	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																				0.652	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49433711	C	T	49433711	2	4	103	1	0	0	0	0	0	0	0	1	9651	639	23	1		1	MLL2	12	49433711	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10719490	49433711	84418184	207	27306										
OR6C6	283365	hgsc.bcm.edu	37	chr12	55688511	55688511	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taaagtggtcaatagttttgGaagcacaaaaatccagcttg	9	6	1	0	rs192785175	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:55688511G>C	ENST00000358433.2	-	1	505	c.506C>G	c.(505-507)tCc>tGc	p.S169C		NM_001005493.1	NP_001005493.1	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C, member 6	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						AATAGTTTTGGAAGCACAAAA	0.413																																																0			12											92	88	89					12																	55688511		2203	4300	6503	53974778	SO:0001583	missense	283365				CCDS31817.1	12q13.13	2012-08-09			ENSG00000188324	ENSG00000188324		"GPCR / Class A : Olfactory receptors"	31293	protein-coding gene	gene with protein product							Standard	NM_001005493		Approved		uc010sph.2	A6NF89	OTTHUMG00000168101	ENST00000358433.2:c.506C>G	12.37:g.55688511G>C	ENSP00000351211:p.Ser169Cys		53974778		Missense_Mutation	SNP	ENST00000358433.2	37	CCDS31817.1	.	.	.	.	.	.	.	.	.	.	-	12.92	2.081605	0.36758	.	.	ENSG00000188324	ENST00000358433	T	0.00421	7.46	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000096	T	0.01558	0.0050	M	0.91300	3.195	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.12116	-1.0560	10	0.87932	D	0	.	13.0818	0.59117	0.0:0.2106:0.7894:0.0	.	169	A6NF89	OR6C6_HUMAN	C	169	ENSP00000351211:S169C	ENSP00000351211:S169C	S	-	2	0	OR6C6	53974778	0.012000	0.17670	0.926000	0.36857	0.751000	0.42716	1.446000	0.35090	2.359000	0.80004	0.580000	0.79431	TCC		0.413	OR6C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398151.1			C	55688511	G	C	55688511	3	2	103	1	0	0	0	0	1	0	0	0	11225	1174	41	5	440	5	OR6C6	12	55688511	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	6254800	55688511	78163384	208	27307										
OR6C3	254786	hgsc.bcm.edu	37	chr12	55725539	55725539	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgggcctttctgatgatcctGaccttcagattgtgattttt	9	8	2	5			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:55725539G>T	ENST00000379667.1	+	1	55	c.55G>T	c.(55-57)Gac>Tac	p.D19Y		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	19					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TGATGATCCTGACCTTCAGAT	0.413																																																0			12											142	148	146					12																	55725539		2203	4300	6503	54011806	SO:0001583	missense	254786			AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"GPCR / Class A : Olfactory receptors"	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.55G>T	12.37:g.55725539G>T	ENSP00000368989:p.Asp19Tyr		54011806		Missense_Mutation	SNP	ENST00000379667.1	37	CCDS31819.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.380195	0.42207	.	.	ENSG00000205329	ENST00000379667	T	0.00448	7.38	4.98	-4.93	0.03066	.	0.843533	0.10066	N	0.720291	T	0.00356	0.0011	L	0.46947	1.48	0.09310	N	1	B	0.22346	0.068	B	0.28385	0.089	T	0.30534	-0.9975	10	0.87932	D	0	.	11.3174	0.49401	0.2004:0.54:0.2595:0.0	.	19	Q9NZP0	OR6C3_HUMAN	Y	19	ENSP00000368989:D19Y	ENSP00000368989:D19Y	D	+	1	0	OR6C3	54011806	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-1.090000	0.03372	-0.730000	0.04869	0.586000	0.80456	GAC		0.413	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1			T	55725539	G	T	55725539	3	4	103	1	0	0	0	0	1	0	0	0	11223	1290	45	2	57	2	OR6C3	12	55725539	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	37028	55725539	78126356	209	27308										
MARS	4141	hgsc.bcm.edu	37	chr12	57898052	57898052	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcatgccctgtggtgcagtcGagccagcacctgtttctgga	12	12	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:57898052G>A	ENST00000262027.5	+	11	1472	c.1338G>A	c.(1336-1338)tcG>tcA	p.S446S	MARS_ENST00000315473.5_Silent_p.S212S|MARS_ENST00000447721.2_3'UTR	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	446					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	TGGTGCAGTCGAGCCAGCACC	0.542																																																0			12											134	125	128					12																	57898052		2203	4300	6503	56184319	SO:0001819	synonymous_variant	4141			X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1338G>A	12.37:g.57898052G>A			56184319	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	37	CCDS8942.1																																																																																				0.542	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		A	57898052	G	A	57898052	2	1	103	1	0	0	0	0	0	0	0	1	9346	1045	37	1		1	MARS	12	57898052	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2172513	57898052	75953843	210	27309										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81799574	81799574	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtgtgtcataccttctcatGgactttctgtccaggttcca	9	11	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:81799574G>T	ENST00000549396.1	-	8	914	c.754C>A	c.(754-756)Cat>Aat	p.H252N	PPFIA2_ENST00000549325.1_Missense_Mutation_p.H234N|PPFIA2_ENST00000333447.7_Missense_Mutation_p.H234N|PPFIA2_ENST00000443686.3_Missense_Mutation_p.H153N|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000407050.4_Missense_Mutation_p.H178N|PPFIA2_ENST00000550359.2_Missense_Mutation_p.H99N|PPFIA2_ENST00000552948.1_Missense_Mutation_p.H252N|PPFIA2_ENST00000550584.2_Missense_Mutation_p.H252N|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000548586.1_Missense_Mutation_p.H252N	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	252	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.H252N(3)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						ACCTTCTCATGGACTTTCTGT	0.373																																																3	Substitution - Missense(3)	lung(3)	12											100	93	95					12																	81799574		1917	4119	6036	80323705	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.754C>A	12.37:g.81799574G>T	ENSP00000450337:p.His252Asn		80323705	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	8.852	0.944745	0.18356	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948	T;T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.62;1.3	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.25975	0.0633	N	0.19112	0.55	0.80722	D	1	B;B	0.24721	0.11;0.016	B;B	0.24848	0.056;0.011	T	0.06058	-1.0848	10	0.14656	T	0.56	-16.3209	17.7666	0.88480	0.0:0.0:1.0:0.0	.	152;252	B7Z4H8;O75334	.;LIPA2_HUMAN	N	252;234;178;263;234;252;153;252	ENSP00000450337:H252N;ENSP00000450298:H234N;ENSP00000385093:H178N;ENSP00000327416:H234N;ENSP00000449338:H252N;ENSP00000388373:H153N;ENSP00000447868:H252N	ENSP00000327416:H234N	H	-	1	0	PPFIA2	80323705	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.731000	0.84895	2.565000	0.86533	0.557000	0.71058	CAT		0.373	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81799574	G	T	81799574	3	4	103	1	0	0	0	0	1	0	0	0	12341	1348	47	2	3119	2	PPFIA2	12	81799574	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	23901522	81799574	52052321	211	27310										
CEP290	80184	hgsc.bcm.edu	37	chr12	88474162	88474162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttcacttcatcttcatggtTttcttgaagcctgatgtaaa	6	8	5	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:88474162T>C	ENST00000552810.1	-	38	5366	c.5023A>G	c.(5023-5025)Aac>Gac	p.N1675D	CEP290_ENST00000309041.7_Missense_Mutation_p.N1677D|CEP290_ENST00000397838.3_Missense_Mutation_p.N735D|CEP290_ENST00000547691.2_Missense_Mutation_p.N735D	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TCTTCATGGTTTTCTTGAAGC	0.363																																																0			12											108	97	100					12																	88474162		1818	4077	5895	86998293	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5023A>G	12.37:g.88474162T>C	ENSP00000448012:p.Asn1675Asp		86998293	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	6.754	0.507937	0.12883	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92	4.35	4.35	0.52113	.	0.424145	0.27420	N	0.019448	D	0.84669	0.5523	N	0.24115	0.695	0.26288	N	0.978165	B	0.21309	0.054	B	0.20384	0.029	T	0.67879	-0.5556	10	0.11485	T	0.65	.	13.8052	0.63225	0.0:0.0:0.0:1.0	.	1675	O15078	CE290_HUMAN	D	735;1675;1677;735	ENSP00000446905:N735D;ENSP00000448012:N1675D;ENSP00000308021:N1677D;ENSP00000380938:N735D	ENSP00000308021:N1677D	N	-	1	0	CEP290	86998293	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	2.451000	0.44952	1.731000	0.51592	0.377000	0.23210	AAC		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88474162	T	C	88474162	3	2	103	1	0	0	0	0	1	0	0	0	3259	1841	64	4	2484	4	CEP290	12	88474162	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	6674588	88474162	45377733	212	27311										
APAF1	317	hgsc.bcm.edu	37	chr12	99043328	99043328	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgtttttgtcacaaggaagaAgctggtgaatgcaattcagc	11	6	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:99043328A>G	ENST00000551964.1	+	4	1128	c.392A>G	c.(391-393)aAg>aGg	p.K131R	APAF1_ENST00000552268.1_Missense_Mutation_p.K131R|APAF1_ENST00000333991.1_Missense_Mutation_p.K131R|APAF1_ENST00000547045.1_Missense_Mutation_p.K131R|APAF1_ENST00000359972.2_Missense_Mutation_p.K120R|APAF1_ENST00000357310.1_Missense_Mutation_p.K131R|APAF1_ENST00000549007.1_Missense_Mutation_p.K131R|APAF1_ENST00000339433.3_Missense_Mutation_p.K131R|APAF1_ENST00000550527.1_Missense_Mutation_p.K120R	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	131	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)	p.K131M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	ACAAGGAAGAAGCTGGTGAAT	0.438																																																1	Substitution - Missense(1)	lung(1)	12											128	120	122					12																	99043328		2203	4300	6503	97567459	SO:0001583	missense	317			AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.392A>G	12.37:g.99043328A>G	ENSP00000448165:p.Lys131Arg		97567459	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	37	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.634508	0.29068	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.55	5.55	0.83447	NB-ARC (1);	0.183845	0.64402	D	0.000019	T	0.72120	0.3421	L	0.36672	1.1	0.42714	D	0.993655	B;B;B;B;B	0.24317	0.017;0.09;0.007;0.096;0.101	B;B;B;B;B	0.32022	0.022;0.139;0.012;0.061;0.018	T	0.67821	-0.5571	10	0.27785	T	0.31	-13.726	15.676	0.77321	1.0:0.0:0.0:0.0	.	131;131;120;131;120	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	131;120;131;131;131;131;120;131;131	ENSP00000448165:K131R;ENSP00000353059:K120R;ENSP00000349862:K131R;ENSP00000341830:K131R;ENSP00000334558:K131R;ENSP00000448826:K131R;ENSP00000448449:K120R;ENSP00000449791:K131R;ENSP00000448161:K131R	ENSP00000334558:K131R	K	+	2	0	APAF1	97567459	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	5.715000	0.68430	2.109000	0.64355	0.533000	0.62120	AAG		0.438	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99043328	A	G	99043328	3	3	103	1	0	0	0	0	1	0	0	0	755	72	3	4	402	4	APAF1	12	99043328	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	10569166	99043328	34808567	213	27312										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100732736	100732736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	catgaaccagttatcacaacAgaaaccaaatcagtggctta	6	10	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:100732736A>G	ENST00000360820.2	+	18	3013	c.2576A>G	c.(2575-2577)cAg>cGg	p.Q859R		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	859	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						TTATCACAACAGAAACCAAAT	0.443																																																0			12											167	167	167					12																	100732736		2203	4300	6503	99256867	SO:0001583	missense	55681			AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2576A>G	12.37:g.100732736A>G	ENSP00000354061:p.Gln859Arg		99256867	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.003637	0.35320	.	.	ENSG00000136021	ENST00000360820	T	0.29655	1.56	5.86	5.86	0.93980	.	0.385285	0.32459	N	0.006074	T	0.24122	0.0584	L	0.29908	0.895	0.38648	D	0.951784	B	0.30406	0.278	B	0.27887	0.084	T	0.08827	-1.0703	10	0.21540	T	0.41	-7.3003	16.5602	0.84551	1.0:0.0:0.0:0.0	.	859	Q6P3W7	SCYL2_HUMAN	R	859	ENSP00000354061:Q859R	ENSP00000354061:Q859R	Q	+	2	0	SCYL2	99256867	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.664000	0.54525	2.367000	0.80283	0.528000	0.53228	CAG		0.443	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		G	100732736	A	G	100732736	3	3	103	1	0	0	0	0	1	0	0	0	13985	188	7	4	2642	4	SCYL2	12	100732736	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1689408	100732736	33119159	214	27313										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112888211	112888211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaaatttgccactttggctgAgttggtccagtattacatgg	11	7	0	1	rs121918465		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:112888211A>G	ENST00000351677.2	+	3	425	c.227A>G	c.(226-228)gAg>gGg	p.E76G	PTPN11_ENST00000392597.1_Missense_Mutation_p.E76G	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	76	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		E -> A (in JMML; also in myelodysplastic syndrome). {ECO:0000269|PubMed:12717436}.|E -> D (in NS1). {ECO:0000269|PubMed:11704759, ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12634870}.|E -> G (in JMML). {ECO:0000269|PubMed:12717436}.|E -> K (in JMML; dbSNP:rs28933388). {ECO:0000269|PubMed:12717436}.|E -> V (in JMML). {ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.E76G(29)|p.E76V(7)|p.E76A(7)|p.E76M(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ACTTTGGCTGAGTTGGTCCAG	0.418			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	44	Substitution - Missense(44)	haematopoietic_and_lymphoid_tissue(44)	12											149	137	141					12																	112888211		2203	4300	6503	111372594	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.227A>G	12.37:g.112888211A>G	ENSP00000340944:p.Glu76Gly		111372594	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	33	5.200620	0.94997	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.97256	-4.31;-4.31	5.9	5.9	0.94986	.	0.047680	0.85682	D	0.000000	D	0.98460	0.9487	H	0.94734	3.575	0.80722	D	1	D;P	0.61697	0.99;0.941	P;P	0.53760	0.734;0.734	D	0.99346	1.0913	10	0.87932	D	0	.	16.3291	0.83001	1.0:0.0:0.0:0.0	.	76;76	Q06124-2;Q06124-3	.;.	G	76	ENSP00000376376:E76G;ENSP00000340944:E76G	ENSP00000340944:E76G	E	+	2	0	PTPN11	111372594	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.332000	0.96446	2.257000	0.74773	0.528000	0.53228	GAG		0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112888211	A	G	112888211	3	3	103	1	0	0	0	0	1	0	0	0	12815	304	11	4	237	4	PTPN11	12	112888211	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	12155475	112888211	20963684	215	27314										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120599361	120599361	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgttctctcgcttcatgttgGccttttttatgctgtcctgc	8	11	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:120599361G>C	ENST00000300648.6	-	22	2381	c.2369C>G	c.(2368-2370)gCc>gGc	p.A790G		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	790					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTCATGTTGGCCTTTTTTAT	0.532																																																0			12											222	216	218					12																	120599361		2101	4235	6336	119083744	SO:0001583	missense	10985			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.2369C>G	12.37:g.120599361G>C	ENSP00000300648:p.Ala790Gly		119083744	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670602	0.47781	.	.	ENSG00000089154	ENST00000300648	T	0.45276	0.9	5.82	4.93	0.64822	Armadillo-type fold (1);	0.166550	0.52532	D	0.000064	T	0.31734	0.0806	L	0.31752	0.955	0.58432	D	0.999997	B	0.06786	0.001	B	0.04013	0.001	T	0.06516	-1.0822	10	0.21540	T	0.41	.	14.7521	0.69533	0.0689:0.0:0.9311:0.0	.	790	Q92616	GCN1L_HUMAN	G	790	ENSP00000300648:A790G	ENSP00000300648:A790G	A	-	2	0	GCN1L1	119083744	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.210000	0.58500	1.484000	0.48361	0.655000	0.94253	GCC		0.532	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120599361	G	C	120599361	3	2	103	1	0	0	0	0	1	0	0	0	6319	1203	42	5	5794	5	GCN1L1	12	120599361	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	7711150	120599361	13252534	216	27315										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124297818	124297818	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aatgatatctctctgaacccTcagataattgaacaagctgt	6	9	3	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:124297818T>C	ENST00000409039.3	+	19	2923	c.2898T>C	c.(2896-2898)ccT>ccC	p.P966P		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	966	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P784P(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTCTGAACCCTCAGATAATTG	0.408																																																1	Substitution - coding silent(1)	ovary(1)	12											95	96	95					12																	124297818		2203	4300	6503	122863771	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2898T>C	12.37:g.124297818T>C			122863771	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.408	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124297818	T	C	124297818	2	2	103	1	0	0	0	0	0	0	0	1	4609	1538	54	4		4	DNAH10	12	124297818	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	3698457	124297818	9554077	217	27316										
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133384883	133384883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgggacatttcccccagaatTccccgcatttgaatcttcag	7	14	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr12:133384883T>C	ENST00000450791.2	-	4	955	c.772A>G	c.(772-774)Aat>Gat	p.N258D	GOLGA3_ENST00000537452.1_Missense_Mutation_p.N258D|GOLGA3_ENST00000545875.1_Missense_Mutation_p.N258D|GOLGA3_ENST00000204726.3_Missense_Mutation_p.N258D|GOLGA3_ENST00000456883.2_Missense_Mutation_p.N258D			Q08378	GOGA3_HUMAN	golgin A3	258					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CCCCCAGAATTCCCCGCATTT	0.537																																																0			12											139	153	148					12																	133384883		2203	4300	6503	131894956	SO:0001583	missense	2802			AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"SY2/SY10 protein", "Golgi complex-associated protein of 170 kD"	602581	"golgi autoantigen, golgin subfamily a, 3"			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.772A>G	12.37:g.133384883T>C	ENSP00000410378:p.Asn258Asp		131894956	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	T	2.027	-0.423245	0.04734	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56	3.9	1.24	0.21308	.	1.017860	0.07810	N	0.957950	T	0.16938	0.0407	N	0.22421	0.69	0.09310	N	0.999997	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.08055	0.003;0.003;0.001	T	0.33214	-0.9877	10	0.10377	T	0.69	.	5.0597	0.14551	0.0:0.1093:0.1805:0.7102	.	258;258;258	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	D	258	ENSP00000204726:N258D;ENSP00000410378:N258D;ENSP00000409303:N258D;ENSP00000442143:N258D;ENSP00000442603:N258D	ENSP00000204726:N258D	N	-	1	0	GOLGA3	131894956	0.005000	0.15991	0.015000	0.15790	0.291000	0.27294	1.349000	0.33998	0.501000	0.28013	0.477000	0.44152	AAT		0.537	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		C	133384883	T	C	133384883	3	2	103	1	0	0	0	0	1	0	0	0	6574	1783	62	4	3942	4	GOLGA3	12	133384883	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	9087065	133384883	467012	218	27317										
SACS	26278	hgsc.bcm.edu	37	chr13	23932592	23932592	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cagtcctctggggtgaaaacCgcgttgttgtacacatagag	12	9	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:23932592C>T	ENST00000382292.3	-	6	759	c.486G>A	c.(484-486)gcG>gcA	p.A162A	SACS_ENST00000382298.3_Silent_p.A162A|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	162					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GGGTGAAAACCGCGTTGTTGT	0.453																																																0			13											130	128	129					13																	23932592		2203	4300	6503	22830592	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.486G>A	13.37:g.23932592C>T			22830592	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	8.459	0.854964	0.17106	.	.	ENSG00000151835	ENST00000455470	.	.	.	5.64	-11.3	0.00108	.	.	.	.	.	T	0.30916	0.0780	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41324	-0.9515	4	.	.	.	.	1.4762	0.02426	0.2045:0.169:0.1509:0.4755	.	.	.	.	S	62	.	.	G	-	1	0	SACS	22830592	0.000000	0.05858	0.000000	0.03702	0.825000	0.46686	-2.814000	0.00753	-2.871000	0.00323	-0.140000	0.14226	GGT		0.453	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23932592	C	T	23932592	2	4	103	1	0	0	0	0	0	0	0	1	13841	639	23	1		1	SACS	13	23932592	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		23932592	91237286	219	27318										
LNX2	222484	hgsc.bcm.edu	37	chr13	28127354	28127354	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcgctcagtacctgggaagcCcaagccacatgacccatgat	10	14	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:28127354C>G	ENST00000316334.3	-	8	1898	c.1769G>C	c.(1768-1770)gGg>gCg	p.G590A		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	590					protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CCTGGGAAGCCCAAGCCACAT	0.478																																																0			13											88	79	82					13																	28127354		2203	4300	6503	27025354	SO:0001583	missense	222484			AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1769G>C	13.37:g.28127354C>G	ENSP00000325929:p.Gly590Ala		27025354	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112029	0.77210	.	.	ENSG00000139517	ENST00000316334	T	0.05855	3.38	5.96	5.1	0.69264	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.10637	0.0260	M	0.67953	2.075	0.80722	D	1	B	0.20671	0.047	B	0.24006	0.05	T	0.08659	-1.0711	10	0.17369	T	0.5	.	17.0675	0.86563	0.0:0.873:0.127:0.0	.	590	Q8N448	LNX2_HUMAN	A	590	ENSP00000325929:G590A	ENSP00000325929:G590A	G	-	2	0	LNX2	27025354	1.000000	0.71417	0.813000	0.32504	0.993000	0.82548	7.484000	0.81180	1.481000	0.48307	0.585000	0.79938	GGG		0.478	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			G	28127354	C	G	28127354	3	3	103	1	0	0	0	0	1	0	0	0	8890	623	22	5	315	5	LNX2	13	28127354	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	4194762	28127354	87042524	220	27319										
FLT3	2322	hgsc.bcm.edu	37	chr13	28592622	28592622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acattgcccctgacaacataGttggaatcactcatgatatc	6	11	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:28592622G>T	ENST00000241453.7	-	20	2604	c.2523C>A	c.(2521-2523)aaC>aaA	p.N841K	FLT3_ENST00000380982.4_Missense_Mutation_p.N841K|FLT3_ENST00000537084.1_Intron	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	841	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.N841K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGACAACATAGTTGGAATCAC	0.453			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	13											182	140	154					13																	28592622		2203	4300	6503	27490622	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2523C>A	13.37:g.28592622G>T	ENSP00000241453:p.Asn841Lys		27490622	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117472	0.77323	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.82344	-1.6;-1.6	5.84	5.0	0.66597	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.069113	0.64402	D	0.000009	T	0.81278	0.4789	L	0.33293	1	0.80722	D	1	P	0.44986	0.847	P	0.48270	0.572	D	0.83526	0.0088	10	0.87932	D	0	.	14.8829	0.70547	0.0687:0.0:0.9313:0.0	.	841	P36888	FLT3_HUMAN	K	841	ENSP00000241453:N841K;ENSP00000370369:N841K	ENSP00000241453:N841K	N	-	3	2	FLT3	27490622	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.788000	0.62439	1.488000	0.48433	0.556000	0.70494	AAC		0.453	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			T	28592622	G	T	28592622	3	4	103	1	0	0	0	0	1	0	0	0	5961	1020	36	2	478	2	FLT3	13	28592622	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	465268	28592622	86577256	221	27320										
FLT1	2321	hgsc.bcm.edu	37	chr13	29001453	29001453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttttcgtaaatctggggttTcactggaaaggagatgaaga	12	5	2	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:29001453T>C	ENST00000282397.4	-	10	1530	c.1279A>G	c.(1279-1281)Aaa>Gaa	p.K427E	FLT1_ENST00000541932.1_Missense_Mutation_p.K427E|FLT1_ENST00000539099.1_Missense_Mutation_p.K427E	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	427					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATCTGGGGTTTCACTGGAAAG	0.502																																																0			13											66	60	62					13																	29001453		2203	4300	6503	27899453	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1279A>G	13.37:g.29001453T>C	ENSP00000282397:p.Lys427Glu		27899453	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.665237	0.88251	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	T;T;T	0.36157	1.27;1.27;1.52	5.9	5.9	0.94986	Immunoglobulin-like fold (1);	0.104175	0.64402	D	0.000005	T	0.56645	0.1999	M	0.70595	2.14	0.53688	D	0.999975	D;D;D;D	0.67145	0.996;0.996;0.996;0.992	D;D;D;P	0.65987	0.94;0.94;0.919;0.872	T	0.52358	-0.8586	10	0.20519	T	0.43	.	16.3291	0.83001	0.0:0.0:0.0:1.0	.	427;427;427;427	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	E	427	ENSP00000282397:K427E;ENSP00000437631:K427E;ENSP00000442630:K427E	ENSP00000282397:K427E	K	-	1	0	FLT1	27899453	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.294000	0.59043	2.257000	0.74773	0.528000	0.53228	AAA		0.502	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	29001453	T	C	29001453	3	2	103	1	0	0	0	0	1	0	0	0	5960	1792	62	4	3084	4	FLT1	13	29001453	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	408831	29001453	86168425	222	27321										
RB1	5925	hgsc.bcm.edu	37	chr13	48936996	48936996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcacctcgaacacccaggcGaggtcagaacaggagtgcac	11	13	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:48936996G>A	ENST00000267163.4	+	8	902	c.764G>A	c.(763-765)cGa>cAa	p.R255Q		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	255					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACACCCAGGCGAGGTCAGAAC	0.343		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	21	Whole gene deletion(15)|Unknown(6)	bone(11)|breast(5)|eye(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											109	112	111					13																	48936996		2203	4300	6503	47834997	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.764G>A	13.37:g.48936996G>A	ENSP00000267163:p.Arg255Gln		47834997	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.429997	0.83776	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92099	-2.97	6.03	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.94771	0.8312	M	0.65975	2.015	0.48087	D	0.999589	D	0.89917	1.0	D	0.69307	0.963	D	0.93882	0.7172	10	0.35671	T	0.21	.	14.1218	0.65192	0.0729:0.0:0.9271:0.0	.	255	P06400	RB_HUMAN	Q	234;255	ENSP00000267163:R255Q	ENSP00000267163:R255Q	R	+	2	0	RB1	47834997	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	6.281000	0.72632	1.541000	0.49316	0.655000	0.94253	CGA		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48936996	G	A	48936996	3	1	103	1	0	0	0	0	1	0	0	0	13135	1058	37	1	794	1	RB1	13	48936996	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	19935543	48936996	66232882	223	27322										
DACH1	1602	hgsc.bcm.edu	37	chr13	72063261	72063261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aggctgtctcttgcggttggTgtagaaagcggggtctcatc	15	8	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:72063261T>C	ENST00000359684.2	-	8	1751	c.1752A>G	c.(1750-1752)acA>acG	p.T584T	DACH1_ENST00000354591.4_Silent_p.T330T|DACH1_ENST00000305425.4_Silent_p.T532T|DACH1_ENST00000313174.7_Silent_p.T384T			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	584					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TTGCGGTTGGTGTAGAAAGCG	0.448																																																0			13											205	204	204					13																	72063261		1902	4128	6030	70961262	SO:0001819	synonymous_variant	1602			AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.1752A>G	13.37:g.72063261T>C			70961262	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Silent	SNP	ENST00000359684.2	37																																																																																					0.448	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		C	72063261	T	C	72063261	2	2	103	1	0	0	0	0	0	0	0	1	4226	1683	59	4		4	DACH1	13	72063261	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	23126265	72063261	43106617	224	27323										
KCTD12	115207	hgsc.bcm.edu	37	chr13	77459362	77459362	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccagatcttgtcctcgctctGgtcggtgctgctggcaaagg	13	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:77459362G>T	ENST00000377474.2	-	1	1163	c.922C>A	c.(922-924)Cag>Aag	p.Q308K	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Missense_Mutation_p.Q308K	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	308					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		TCCTCGCTCTGGTCGGTGCTG	0.637											OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			13											69	56	60					13																	77459362		2203	4300	6503	76357363	SO:0001583	missense	115207			AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"predominantly fetal expressed T1 domain"	610521	"chromosome 13 open reading frame 2", "potassium channel tetramerisation domain containing 12"	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.922C>A	13.37:g.77459362G>T	ENSP00000366694:p.Gln308Lys	1175	76357363		Missense_Mutation	SNP	ENST00000377474.2	37	CCDS9455.1	.	.	.	.	.	.	.	.	.	.	G	9.842	1.191365	0.21954	.	.	ENSG00000178695	ENST00000377474;ENST00000317765	T;T	0.41400	1.0;1.0	4.84	4.84	0.62591	.	0.055104	0.85682	D	0.000000	T	0.36054	0.0953	L	0.50333	1.59	0.52099	D	0.999949	P	0.50156	0.932	B	0.36959	0.237	T	0.24404	-1.0161	10	0.23891	T	0.37	.	17.9207	0.88965	0.0:0.0:1.0:0.0	.	308	Q96CX2	KCD12_HUMAN	K	308	ENSP00000366694:Q308K;ENSP00000317141:Q308K	ENSP00000317141:Q308K	Q	-	1	0	KCTD12	76357363	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.323000	0.96364	2.399000	0.81585	0.462000	0.41574	CAG		0.637	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444		T	77459362	G	T	77459362	3	4	103	1	0	0	0	0	1	0	0	0	8120	1357	47	2	59	2	KCTD12	13	77459362	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5396101	77459362	37710516	225	27324										
DCT	1638	hgsc.bcm.edu	37	chr13	95114392	95114392	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atttgatttcttctcagcaaAccttcataggttccattgca	5	10	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:95114392A>G	ENST00000377028.5	-	5	1328	c.915T>C	c.(913-915)ggT>ggC	p.G305G	DCT_ENST00000446125.1_Silent_p.G305G|DCT_ENST00000490854.1_5'UTR	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	305					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		TTCTCAGCAAACCTTCATAGG	0.398																																																0			13											130	111	117					13																	95114392		2203	4300	6503	93912393	SO:0001819	synonymous_variant	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.915T>C	13.37:g.95114392A>G			93912393	Q09GT4	Silent	SNP	ENST00000377028.5	37	CCDS9470.1																																																																																				0.398	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			G	95114392	A	G	95114392	2	3	103	1	0	0	0	0	0	0	0	1	4310	30	2	4		4	DCT	13	95114392	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	17655030	95114392	20055486	226	27325										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96277051	96277051	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgctgaattcttcgaagttaAttctttaaattccttcataa	4	7	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:96277051A>G	ENST00000376829.2	-	8	1794	c.943T>C	c.(943-945)Tta>Cta	p.L315L	DZIP1_ENST00000361156.3_Silent_p.L315L|DZIP1_ENST00000347108.3_Silent_p.L315L|DZIP1_ENST00000361396.2_Silent_p.L315L	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	315					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TTCGAAGTTAATTCTTTAAAT	0.333																																																0			13											102	95	97					13																	96277051		2196	4300	6496	95075052	SO:0001819	synonymous_variant	22873			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.943T>C	13.37:g.96277051A>G			95075052	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																				0.333	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		G	96277051	A	G	96277051	2	3	103	1	0	0	0	0	0	0	0	1	4874	98	4	4		4	DZIP1	13	96277051	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1162659	96277051	18892827	227	27326										
MBNL2	10150	hgsc.bcm.edu	37	chr13	98009771	98009771	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gctcttcatcctttaccaaaGagacaagcacttgaaaaaag	6	10	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:98009771G>T	ENST00000376673.3	+	6	1621	c.840G>T	c.(838-840)aaG>aaT	p.K280N	MBNL2_ENST00000445661.2_Missense_Mutation_p.K125N|MBNL2_ENST00000397601.1_Missense_Mutation_p.K280N|MBNL2_ENST00000343600.4_Missense_Mutation_p.K280N|MBNL2_ENST00000345429.6_Missense_Mutation_p.K280N			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	280					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			CTTTACCAAAGAGACAAGCAC	0.473																																																0			13											136	121	126					13																	98009771		2203	4300	6503	96807772	SO:0001583	missense	10150			AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"Zinc fingers, CCCH-type domain containing"	16746	protein-coding gene	gene with protein product		607327	"muscleblind-like 2 (Drosophila)"			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.840G>T	13.37:g.98009771G>T	ENSP00000365861:p.Lys280Asn		96807772	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Missense_Mutation	SNP	ENST00000376673.3	37		.	.	.	.	.	.	.	.	.	.	G	18.97	3.735273	0.69189	.	.	ENSG00000139793	ENST00000397601;ENST00000343600;ENST00000376679;ENST00000345429;ENST00000376673;ENST00000445661;ENST00000449284	T;T;T;T;T	0.55760	0.62;0.62;0.5;1.06;0.61	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.76765	0.4033	M	0.82823	2.61	0.52501	D	0.99995	P;D;D;D;D	0.89917	0.927;1.0;1.0;1.0;0.999	P;D;D;D;D	0.91635	0.628;0.999;0.999;0.999;0.999	T	0.77313	-0.2634	10	0.54805	T	0.06	.	20.1858	0.98214	0.0:0.0:1.0:0.0	.	125;280;280;280;280	B4E3F7;Q5VZF2;Q5VZF2-3;A2A3S3;Q5VZF2-2	.;MBNL2_HUMAN;.;.;.	N	280;280;31;280;280;125;30	ENSP00000380726:K280N;ENSP00000344214:K280N;ENSP00000267287:K280N;ENSP00000365861:K280N;ENSP00000406842:K125N	ENSP00000344214:K280N	K	+	3	2	MBNL2	96807772	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.954000	0.87848	2.777000	0.95525	0.591000	0.81541	AAG		0.473	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778		T	98009771	G	T	98009771	3	4	103	1	0	0	0	0	1	0	0	0	9384	933	33	2	858	2	MBNL2	13	98009771	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1732720	98009771	17160107	228	27327										
CDC16	8881	hgsc.bcm.edu	37	chr13	115008808	115008808	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttgctgcgttttctatttgaGaacaaattgaaaaaagtaag	8	4	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr13:115008808G>A	ENST00000356221.3	+	7	726	c.618G>A	c.(616-618)gaG>gaA	p.E206E	CDC16_ENST00000375312.3_Silent_p.E112E|CDC16_ENST00000375308.1_Silent_p.E112E|CDC16_ENST00000252458.6_Silent_p.E112E|CDC16_ENST00000375310.1_Silent_p.E112E|CDC16_ENST00000360383.3_Silent_p.E206E|CDC16_ENST00000252457.5_Silent_p.E205E|MIR548AR_ENST00000582191.1_RNA			Q13042	CDC16_HUMAN	cell division cycle 16	206					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TTCTATTTGAGAACAAATTGA	0.299																																																0			13											63	68	66					13																	115008808		2203	4296	6499	114026910	SO:0001819	synonymous_variant	8881			U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.618G>A	13.37:g.115008808G>A			114026910	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																				0.299	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		A	115008808	G	A	115008808	2	1	103	1	0	0	0	0	0	0	0	1	3064	933	33	3		3	CDC16	13	115008808	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	16999037	115008808	161070	229	27328										
OR4L1	122742	hgsc.bcm.edu	37	chr14	20529108	20529108	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agaggccataagaaaattacGgttccaatatgttagttctg	9	6	1	2	rs144249994	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:20529108G>T	ENST00000315683.1	+	1	905	c.905G>T	c.(904-906)cGg>cTg	p.R302L		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R302L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AGAAAATTACGGTTCCAATAT	0.303																																																1	Substitution - Missense(1)	ovary(1)	14											51	57	55					14																	20529108		2203	4298	6501	19598948	SO:0001583	missense	122742				CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"GPCR / Class A : Olfactory receptors"	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.905G>T	14.37:g.20529108G>T	ENSP00000319217:p.Arg302Leu		19598948	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	.	.	.	.	.	.	.	.	.	.	.	0.958	-0.704240	0.03255	.	.	ENSG00000176246	ENST00000315683	T	0.26660	1.72	4.37	-8.75	0.00834	.	2.575630	0.01495	N	0.017262	T	0.05640	0.0148	N	0.00427	-1.505	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.26155	-1.0111	10	0.11485	T	0.65	.	7.2034	0.25893	0.5851:0.0:0.1268:0.2881	.	302	Q8NH43	OR4L1_HUMAN	L	302	ENSP00000319217:R302L	ENSP00000319217:R302L	R	+	2	0	OR4L1	19598948	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.435000	0.02423	-2.238000	0.00712	-2.498000	0.00192	CGG		0.303	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1			T	20529108	G	T	20529108	3	4	103	1	0	0	0	0	1	0	0	0	11105	1116	39	2	907	2	OR4L1	14	20529108	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		20529108	86820432	230	27329										
OR11H4	390442	hgsc.bcm.edu	37	chr14	20711205	20711205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttgagatctggtatgtgtcCtccactattcctaacatgct	7	11	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:20711205C>T	ENST00000315409.2	+	1	308	c.255C>T	c.(253-255)tcC>tcT	p.S85S		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S85S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		GGTATGTGTCCTCCACTATTC	0.453																																																1	Substitution - coding silent(1)	ovary(1)	14											168	162	164					14																	20711205		2203	4300	6503	19781045	SO:0001819	synonymous_variant	390442				CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"GPCR / Class A : Olfactory receptors"	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.255C>T	14.37:g.20711205C>T			19781045	B2RNQ4|Q6IF07	Silent	SNP	ENST00000315409.2	37	CCDS32034.1																																																																																				0.453	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1			T	20711205	C	T	20711205	2	4	103	1	0	0	0	0	0	0	0	1	10959	668	24	3		3	OR11H4	14	20711205	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	182097	20711205	86638335	231	27330										
SLC39A2	29986	hgsc.bcm.edu	37	chr14	21467685	21467685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggctgtggccttactcccaTctgcttcaaatggttccaga	10	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:21467685T>C	ENST00000298681.4	+	1	237	c.80T>C	c.(79-81)aTc>aCc	p.I27T	SLC39A2_ENST00000554422.1_Missense_Mutation_p.I27T|RP11-84C10.4_ENST00000557335.1_RNA	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	27					transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		CTTACTCCCATCTGCTTCAAA	0.517																																																0			14											178	137	151					14																	21467685		2203	4300	6503	20537525	SO:0001583	missense	29986			AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"Solute carriers"	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.80T>C	14.37:g.21467685T>C	ENSP00000298681:p.Ile27Thr		20537525	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234179	0.58886	.	.	ENSG00000165794	ENST00000554422;ENST00000298681	T;T	0.52057	0.68;0.68	5.43	5.43	0.79202	.	0.187131	0.46758	D	0.000276	T	0.49474	0.1559	M	0.74881	2.28	0.35272	D	0.780523	P	0.43231	0.801	B	0.43990	0.438	T	0.62849	-0.6767	10	0.36615	T	0.2	-12.7817	7.9388	0.29946	0.0:0.0885:0.0:0.9115	.	27	Q9NP94	S39A2_HUMAN	T	27	ENSP00000452568:I27T;ENSP00000298681:I27T	ENSP00000298681:I27T	I	+	2	0	SLC39A2	20537525	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	3.101000	0.50283	2.279000	0.76181	0.533000	0.62120	ATC		0.517	SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579		C	21467685	T	C	21467685	3	2	103	1	0	0	0	0	1	0	0	0	14655	1435	50	4	82	4	SLC39A2	14	21467685	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	756480	21467685	85881855	232	27331										
MYH6	4624	hgsc.bcm.edu	37	chr14	23856751	23856751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccctcacctctgcctcctccAgggctgactgcagctccagc	8	20	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:23856751A>G	ENST00000356287.3	-	31	4666	c.4637T>C	c.(4636-4638)cTg>cCg	p.L1546P	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Missense_Mutation_p.L1546P			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1546					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGCCTCCTCCAGGGCTGACTG	0.612																																																0			14											89	69	76					14																	23856751		2203	4300	6503	22926591	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.4637T>C	14.37:g.23856751A>G	ENSP00000348634:p.Leu1546Pro		22926591	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	a	19.73	3.882334	0.72294	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.82167	-1.58;-1.58	4.64	4.64	0.57946	Myosin tail (1);	.	.	.	.	D	0.94112	0.8112	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96016	0.9005	9	0.87932	D	0	.	14.3782	0.66892	1.0:0.0:0.0:0.0	.	1546	P13533	MYH6_HUMAN	P	1546	ENSP00000386041:L1546P;ENSP00000348634:L1546P	ENSP00000348634:L1546P	L	-	2	0	MYH6	22926591	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	9.111000	0.94308	1.860000	0.53959	0.459000	0.35465	CTG		0.612	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			G	23856751	A	G	23856751	3	3	103	1	0	0	0	0	1	0	0	0	10068	188	7	4	1214	4	MYH6	14	23856751	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2389066	23856751	83492789	233	27332										
SRP54	6729	hgsc.bcm.edu	37	chr14	35492183	35492183	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agaatccaaagagtagcaagAggatcgggtgtatcaacaag	12	6	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:35492183A>G	ENST00000556994.1	+	15	1621	c.1224A>G	c.(1222-1224)agA>agG	p.R408R	SRP54_ENST00000546080.1_Silent_p.R359R|SRP54_ENST00000555557.1_Silent_p.R344R|SRP54_ENST00000216774.6_Silent_p.R408R			P61011	SRP54_HUMAN	signal recognition particle 54kDa	408	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)	p.R408R(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		GAGTAGCAAGAGGATCGGGTG	0.393																																																1	Substitution - coding silent(1)	ovary(1)	14											107	99	102					14																	35492183		2203	4300	6503	34561934	SO:0001819	synonymous_variant	6729			X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1224A>G	14.37:g.35492183A>G			34561934	B2R759|B4DUW6|P13624	Silent	SNP	ENST00000556994.1	37	CCDS9652.1																																																																																				0.393	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		G	35492183	A	G	35492183	2	3	103	1	0	0	0	0	0	0	0	1	15194	301	11	4		4	SRP54	14	35492183	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	11635432	35492183	71857357	234	27333										
SEC23A	10484	hgsc.bcm.edu	37	chr14	39565310	39565310	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	attttgttgaatgaattccaAataggttgtcattgtggagt	10	3	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:39565310A>G	ENST00000307712.6	-	2	530	c.13T>C	c.(13-15)Ttg>Ctg	p.L5L	SEC23A_ENST00000548032.2_Silent_p.L5L|SEC23A_ENST00000536508.1_Intron|SEC23A_ENST00000545328.2_Silent_p.L5L|SEC23A_ENST00000553970.1_Silent_p.L5L|SEC23A_ENST00000557280.1_Silent_p.L5L	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	5					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ATGAATTCCAAATAGGTTGTC	0.333																																																0			14											105	99	101					14																	39565310		2203	4300	6503	38635061	SO:0001819	synonymous_variant	10484			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.13T>C	14.37:g.39565310A>G			38635061	B2R5P4|B3KXI2|Q8NE16	Silent	SNP	ENST00000307712.6	37	CCDS9668.1																																																																																				0.333	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			G	39565310	A	G	39565310	2	3	103	1	0	0	0	0	0	0	0	1	14028	11	1	4		4	SEC23A	14	39565310	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4073127	39565310	67784230	235	27334										
NIN	51199	hgsc.bcm.edu	37	chr14	51288636	51288636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taatgtctgctgcagcactgGggccacctcctccaagctca	9	15	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:51288636G>A	ENST00000382041.3	-	3	329	c.139C>T	c.(139-141)Cca>Tca	p.P47S	NIN_ENST00000245441.5_Missense_Mutation_p.P47S|RP11-286O18.1_ENST00000555966.1_RNA|NIN_ENST00000382043.4_Missense_Mutation_p.P47S|NIN_ENST00000453196.1_Missense_Mutation_p.P47S|NIN_ENST00000389868.3_Missense_Mutation_p.P47S|NIN_ENST00000530997.2_Missense_Mutation_p.P47S|NIN_ENST00000324330.9_Missense_Mutation_p.P47S	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	47	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TGCAGCACTGGGGCCACCTCC	0.587			T	PDGFRB	MPD																																		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	0			14											242	231	235					14																	51288636		2203	4300	6503	50358386	SO:0001583	missense	51199			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.139C>T	14.37:g.51288636G>A	ENSP00000371472:p.Pro47Ser		50358386	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	G	32	5.108196	0.94292	.	.	ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196;ENST00000453401;ENST00000496749	T;T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21;1.95;1.75	5.5	5.5	0.81552	EF-hand-like domain (1);	0.103077	0.64402	D	0.000002	T	0.48314	0.1493	N	0.24115	0.695	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.998;0.999;0.998	T	0.49303	-0.8954	10	0.54805	T	0.06	-15.6279	17.9665	0.89100	0.0:0.0:1.0:0.0	.	53;47;47;47;47	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7	.;.;NIN_HUMAN;.;.	S	47;47;47;47;53;47;47;47;9;47	ENSP00000245441:P47S;ENSP00000374518:P47S;ENSP00000371474:P47S;ENSP00000371472:P47S;ENSP00000324210:P47S;ENSP00000412391:P47S;ENSP00000398641:P9S;ENSP00000431826:P47S	ENSP00000245441:P47S	P	-	1	0	NIN	50358386	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.986000	0.70563	2.576000	0.86940	0.655000	0.94253	CCA		0.587	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51288636	G	A	51288636	3	1	103	1	0	0	0	0	1	0	0	0	10448	1232	43	3	6526	3	NIN	14	51288636	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	11723326	51288636	56060904	236	27335										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60903645	60903645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaggtattgaattttgacccTgtccaaatgaaaatggaaaa	8	5	0	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:60903645T>C	ENST00000321731.3	-	18	1841	c.1682A>G	c.(1681-1683)cAg>cGg	p.Q561R		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	561					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		ATTTTGACCCTGTCCAAATGA	0.323																																																0			14											148	168	162					14																	60903645		2203	4295	6498	59973398	SO:0001583	missense	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1682A>G	14.37:g.60903645T>C	ENSP00000324920:p.Gln561Arg		59973398	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	T	13.00	2.106462	0.37145	.	.	ENSG00000179008	ENST00000321731	T	0.28454	1.61	5.39	2.9	0.33743	.	0.393532	0.21928	N	0.067061	T	0.22704	0.0548	L	0.40543	1.245	0.29979	N	0.817863	B	0.16802	0.019	B	0.14023	0.01	T	0.12656	-1.0539	10	0.49607	T	0.09	-0.1639	7.2177	0.25969	0.0:0.0767:0.146:0.7773	.	561	Q8N1H7	S6OS1_HUMAN	R	561	ENSP00000324920:Q561R	ENSP00000324920:Q561R	Q	-	2	0	C14orf39	59973398	1.000000	0.71417	0.998000	0.56505	0.824000	0.46624	2.532000	0.45659	0.892000	0.36259	0.455000	0.32223	CAG		0.323	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		C	60903645	T	C	60903645	3	2	103	1	0	0	0	0	1	0	0	0	1776	1580	55	4	85	4	C14orf39	14	60903645	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	9615009	60903645	46445895	237	27336										
MLH3	27030	hgsc.bcm.edu	37	chr14	75514888	75514888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	taaagagctatgttccaggaAagattttttatgtttctcat	7	5	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:75514888A>G	ENST00000556740.1	-	1	1506	c.1471T>C	c.(1471-1473)Ttc>Ctc	p.F491L	MLH3_ENST00000238662.7_Missense_Mutation_p.F491L|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000355774.2_Missense_Mutation_p.F491L|MLH3_ENST00000556257.1_Missense_Mutation_p.F491L|MLH3_ENST00000544985.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	491					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TGTTCCAGGAAAGATTTTTTA	0.378								Mismatch excision repair (MMR)																																								0			14											90	97	94					14																	75514888		2203	4299	6502	74584641	SO:0001583	missense	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1471T>C	14.37:g.75514888A>G	ENSP00000452316:p.Phe491Leu		74584641	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.305360	0.00240	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	T;T;T;T	0.79554	-1.23;-1.23;-1.28;-1.23	5.34	3.02	0.34903	.	0.909482	0.09557	N	0.786102	T	0.59797	0.2220	N	0.08118	0	0.09310	N	0.999993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46582	-0.9181	10	0.21014	T	0.42	7.7872	5.4098	0.16342	0.6728:0.1623:0.1649:0.0	.	491;491	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	L	491	ENSP00000348020:F491L;ENSP00000238662:F491L;ENSP00000451540:F491L;ENSP00000452316:F491L	ENSP00000238662:F491L	F	-	1	0	MLH3	74584641	0.001000	0.12720	0.137000	0.22149	0.389000	0.30415	0.662000	0.25038	0.873000	0.35799	0.477000	0.44152	TTC		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		G	75514888	A	G	75514888	3	3	103	1	0	0	0	0	1	0	0	0	9648	14	1	4	2938	4	MLH3	14	75514888	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	14611243	75514888	31834652	238	27337										
SERPINA11	256394	hgsc.bcm.edu	37	chr14	94912753	94912753	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cattttccccgggtcagggaGgaccagcagcgccaaggcat	13	13	1	0	rs576980680		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr14:94912753G>C	ENST00000334708.3	-	3	896	c.832C>G	c.(832-834)Ctc>Gtc	p.L278V	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	278					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		GGGTCAGGGAGGACCAGCAGC	0.542																																																0			14											109	101	104					14																	94912753		2203	4300	6503	93982506	SO:0001583	missense	327657			BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"Serine (or cysteine) peptidase inhibitors"	19193	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.832C>G	14.37:g.94912753G>C	ENSP00000335024:p.Leu278Val		93982506	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	37	CCDS32149.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.341333	0.41498	.	.	ENSG00000186910	ENST00000334708	D	0.90444	-2.67	5.53	5.53	0.82687	Serpin domain (3);	0.000000	0.52532	D	0.000076	D	0.94938	0.8363	M	0.83012	2.62	0.39507	D	0.968291	D	0.89917	1.0	D	0.97110	1.0	D	0.95450	0.8533	10	0.87932	D	0	.	10.9211	0.47165	0.1448:0.0:0.8552:0.0	.	278	Q86U17	SPA11_HUMAN	V	278	ENSP00000335024:L278V	ENSP00000335024:L278V	L	-	1	0	SERPINA11	93982506	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	1.499000	0.35671	2.591000	0.87537	0.555000	0.69702	CTC		0.542	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451		C	94912753	G	C	94912753	3	2	103	1	0	0	0	0	1	0	0	0	14125	1000	35	5	448	5	SERPINA11	14	94912753	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	19397865	94912753	12436787	239	27338										
CYFIP1	23191	hgsc.bcm.edu	37	chr15	22963842	22963842	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccctagaactggcgattggaCgatttgaaagtgaagatttg	12	6	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:22963842C>A	ENST00000313077.7	+	21	2481	c.2356C>A	c.(2356-2358)Cga>Aga	p.R786R	CYFIP1_ENST00000435939.2_Silent_p.R355R|CYFIP1_ENST00000560848.1_Silent_p.R786R	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		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)		GGCGATTGGACGATTTGAAAG	0.448																																																0			15											139	128	132					15																	22963842		2203	4300	6503	20515283	SO:0001819	synonymous_variant	23191			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2356C>A	15.37:g.22963842C>A			20515283		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																				0.448	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		A	22963842	C	A	22963842	2	1	103	1	0	0	0	0	0	0	0	1	4143	528	19	2		2	CYFIP1	15	22963842	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		22963842	79567550	240	27339										
MGA	23269	hgsc.bcm.edu	37	chr15	42041565	42041565	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agtaaaacaggctctgaaacCaaaataacttatagctcagg	7	8	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:42041565C>A	ENST00000570161.1	+	16	5760	c.5760C>A	c.(5758-5760)acC>acA	p.T1920T	MGA_ENST00000219905.7_Silent_p.T1920T|MGA_ENST00000566586.1_Silent_p.T1711T|MGA_ENST00000389936.4_Silent_p.T1881T|MGA_ENST00000545763.1_Silent_p.T1711T			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCTCTGAAACCAAAATAACTT	0.463																																																0			15											58	53	55					15																	42041565		1872	4103	5975	39828857	SO:0001819	synonymous_variant	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5760C>A	15.37:g.42041565C>A			39828857	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																				0.463	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42041565	C	A	42041565	2	1	103	1	0	0	0	0	0	0	0	1	9570	581	21	2		2	MGA	15	42041565	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	19077723	42041565	60489827	241	27340										
SLC28A2	9153	hgsc.bcm.edu	37	chr15	45555370	45555370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggttcactcgtttttgaaaaAgctcctgggcaaaaaattaa	8	7	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:45555370A>G	ENST00000347644.3	+	5	439	c.374A>G	c.(373-375)aAg>aGg	p.K125R	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	125					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		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)	Mercaptopurine(DB01033)	TTTTTGAAAAAGCTCCTGGGC	0.453																																					NSCLC(92;493 1501 26361 28917 47116)											0			15											92	89	90					15																	45555370		2198	4298	6496	43342662	SO:0001583	missense	9153			U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"Solute carriers"	11002	protein-coding gene	gene with protein product		606208	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.374A>G	15.37:g.45555370A>G	ENSP00000315006:p.Lys125Arg		43342662	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.481039	0.01027	.	.	ENSG00000137860	ENST00000347644	T	0.79845	-1.31	5.92	-0.316	0.12743	.	0.603852	0.19398	N	0.115249	T	0.61350	0.2340	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41840	-0.9486	10	0.11794	T	0.64	-3.0678	11.3572	0.49623	0.852:0.0:0.148:0.0	.	125	O43868	S28A2_HUMAN	R	125	ENSP00000315006:K125R	ENSP00000315006:K125R	K	+	2	0	SLC28A2	43342662	0.902000	0.30710	0.059000	0.19551	0.009000	0.06853	1.165000	0.31822	-0.103000	0.12175	0.528000	0.53228	AAG		0.453	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212		G	45555370	A	G	45555370	3	3	103	1	0	0	0	0	1	0	0	0	14569	72	3	4	388	4	SLC28A2	15	45555370	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	3513805	45555370	56976022	242	27341										
PDCD7	10081	hgsc.bcm.edu	37	chr15	65412078	65412078	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggatccccaaacaacttggaCtcaatttcacgtttctgaag	7	11	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:65412078C>G	ENST00000204549.4	-	3	1278	c.1224G>C	c.(1222-1224)gaG>gaC	p.E408D		NM_005707.1	NP_005698.1	Q8N8D1	PDCD7_HUMAN	programmed cell death 7	408					apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of T cell apoptotic process (GO:0070234)|response to glucocorticoid (GO:0051384)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)				endometrium(4)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7						ACAACTTGGACTCAATTTCAC	0.363																																																0			15											73	74	74					15																	65412078		2202	4299	6501	63199131	SO:0001583	missense	10081			AF083930	CCDS10201.1	15q22.2	2012-06-07			ENSG00000090470	ENSG00000090470			8767	protein-coding gene	gene with protein product	"U11/U12 snRNP 59K"	608138				10037816	Standard	NM_005707		Approved	HES18, ES18	uc002aol.3	Q8N8D1	OTTHUMG00000133117	ENST00000204549.4:c.1224G>C	15.37:g.65412078C>G	ENSP00000204549:p.Glu408Asp		63199131	Q96AK8|Q9Y6D7	Missense_Mutation	SNP	ENST00000204549.4	37	CCDS10201.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723991	0.30593	.	.	ENSG00000090470	ENST00000204549;ENST00000431964;ENST00000380204	.	.	.	5.31	1.12	0.20585	.	0.580151	0.16698	N	0.203242	T	0.24586	0.0596	L	0.41236	1.265	0.26537	N	0.974157	B	0.16603	0.018	B	0.10450	0.005	T	0.09335	-1.0679	9	0.20046	T	0.44	-12.4634	0.8947	0.01261	0.2232:0.3982:0.1165:0.2621	.	408	Q8N8D1	PDCD7_HUMAN	D	408;193;202	.	ENSP00000204549:E408D	E	-	3	2	PDCD7	63199131	0.937000	0.31787	1.000000	0.80357	0.996000	0.88848	-0.075000	0.11431	0.715000	0.32103	0.655000	0.94253	GAG		0.363	PDCD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256784.2	NM_005707		G	65412078	C	G	65412078	3	3	103	1	0	0	0	0	1	0	0	0	11656	564	20	5	245	5	PDCD7	15	65412078	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	19856708	65412078	37119314	243	27342										
SMAD3	4088	hgsc.bcm.edu	37	chr15	67482774	67482774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acagactgtgaccagtacccCctgctggattgagctgcacc	10	14	0	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:67482774C>T	ENST00000327367.4	+	9	1488	c.1178C>T	c.(1177-1179)cCc>cTc	p.P393L	SMAD3_ENST00000439724.3_Missense_Mutation_p.P349L|SMAD3_ENST00000537194.2_Missense_Mutation_p.P198L|SMAD3_ENST00000540846.2_Missense_Mutation_p.P288L	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	393	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		P -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P393L(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		ACCAGTACCCCCTGCTGGATT	0.527																																																1	Substitution - Missense(1)	large_intestine(1)	15											61	59	59					15																	67482774		2201	4299	6500	65269828	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.1178C>T	15.37:g.67482774C>T	ENSP00000332973:p.Pro393Leu		65269828	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088291	0.94100	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.99722	-6.53;-6.53;-6.53;-6.53	5.14	5.14	0.70334	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96529	0.9391	10	0.87932	D	0	.	18.6193	0.91316	0.0:1.0:0.0:0.0	.	349;393	B7Z4Z5;P84022	.;SMAD3_HUMAN	L	393;393;288;349;198	ENSP00000332973:P393L;ENSP00000437757:P288L;ENSP00000401133:P349L;ENSP00000445348:P198L	ENSP00000332973:P393L	P	+	2	0	SMAD3	65269828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.723000	0.84788	2.401000	0.81631	0.561000	0.74099	CCC		0.527	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		T	67482774	C	T	67482774	3	4	103	1	0	0	0	0	1	0	0	0	14796	623	22	3	1290	3	SMAD3	15	67482774	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2070696	67482774	35048618	244	27343										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86813248	86813248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tatgcaggcggccatcccttAccacttcaacatcatcaact	5	15	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:86813248A>T	ENST00000441037.2	+	13	1894	c.1799A>T	c.(1798-1800)tAc>tTc	p.Y600F	AGBL1_ENST00000389298.3_Missense_Mutation_p.Y331F|AGBL1_ENST00000421325.2_Missense_Mutation_p.Y600F	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	600					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GCCATCCCTTACCACTTCAAC	0.498																																																0			15											55	54	54					15																	86813248		1946	4160	6106	84614252	SO:0001583	missense	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1799A>T	15.37:g.86813248A>T	ENSP00000413001:p.Tyr600Phe		84614252	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743810	0.69418	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.36520	1.25;1.25	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.68723	0.3032	M	0.93106	3.38	0.47276	D	0.99937	D;D;D	0.76494	0.982;0.994;0.999	P;P;D	0.80764	0.868;0.828;0.994	T	0.77487	-0.2569	10	0.87932	D	0	-26.9199	15.0613	0.71955	1.0:0.0:0.0:0.0	.	299;331;600	Q96MI9-2;Q96MI9-3;Q96MI9	.;.;CBPC4_HUMAN	F	629;600;331	ENSP00000397173:Y600F;ENSP00000373949:Y331F	ENSP00000373949:Y331F	Y	+	2	0	AGBL1	84614252	1.000000	0.71417	0.937000	0.37676	0.282000	0.26991	9.146000	0.94640	2.152000	0.67230	0.459000	0.35465	TAC		0.498	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	86813248	A	T	86813248	3	4	103	1	0	0	0	0	1	0	0	0	375	391	14	5	1845	5	AGBL1	15	86813248	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	19330474	86813248	15718144	245	27344										
HAPLN3	145864	hgsc.bcm.edu	37	chr15	89422386	89422386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccaggccctcctcccaggccCggaagagctgctcaaaggag	12	16	1	1	rs75200279	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:89422386C>T	ENST00000359595.3	-	4	822	c.608G>A	c.(607-609)cGg>cAg	p.R203Q	HAPLN3_ENST00000562889.1_Missense_Mutation_p.R265Q	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	203	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	CTCCCAGGCCCGGAAGAGCTG	0.677											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	67	0.0133786	0.0484	0.0043	5008	,	,		15581	0		0	False		,,,				2504	0															0			15						C	GLN/ARG	157,4243	97.6+/-136.3	1,155,2044	33	37	36		608	3.4	1	15	dbSNP_131	36	1,8597	1.2+/-3.3	0,1,4298	yes	missense	HAPLN3	NM_178232.2	43	1,156,6342	TT,TC,CC		0.0116,3.5682,1.2156	benign	203/361	89422386	158,12840	2200	4299	6499	87223390	SO:0001583	missense	145864			AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"Immunoglobulin superfamily / V-set domain containing"	21446	protein-coding gene	gene with protein product			"extracellular link domain containing, 1"	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.608G>A	15.37:g.89422386C>T	ENSP00000352606:p.Arg203Gln	1267	87223390	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	C	15.97	2.989436	0.53934	0.035682	1.16E-4	ENSG00000140511	ENST00000359595	T	0.09538	2.97	4.36	3.44	0.39384	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.597953	0.16984	N	0.191571	T	0.00440	0.0014	N	0.20445	0.575	0.29557	N	0.850945	B;B	0.27316	0.175;0.175	B;B	0.20955	0.032;0.032	T	0.34477	-0.9827	10	0.22706	T	0.39	-23.1519	6.4344	0.21815	0.0:0.7031:0.0:0.2969	.	203;203	A8K7T8;Q96S86	.;HPLN3_HUMAN	Q	203	ENSP00000352606:R203Q	ENSP00000352606:R203Q	R	-	2	0	HAPLN3	87223390	0.997000	0.39634	1.000000	0.80357	1.000000	0.99986	3.226000	0.51254	0.944000	0.37579	0.655000	0.94253	CGG		0.677	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232		T	89422386	C	T	89422386	3	4	103	1	0	0	0	0	1	0	0	0	6977	652	23	1	482	1	HAPLN3	15	89422386	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2609138	89422386	13109006	246	27345										
TTC23	64927	hgsc.bcm.edu	37	chr15	99679553	99679553	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcccatggcctgctgggtggCcagagtccttttgtcctgcg	14	13	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr15:99679553C>A	ENST00000394132.2	-	13	2012	c.1195G>T	c.(1195-1197)Gcc>Tcc	p.A399S	TTC23_ENST00000262074.4_Missense_Mutation_p.A399S|TTC23_ENST00000394136.1_Missense_Mutation_p.A399S|TTC23_ENST00000558613.1_Missense_Mutation_p.A399S|RP11-6O2.3_ENST00000564527.1_RNA|TTC23_ENST00000558663.1_Missense_Mutation_p.A399S|TTC23_ENST00000394135.3_Missense_Mutation_p.A399S			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	399										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TGCTGGGTGGCCAGAGTCCTT	0.517																																																0			15											74	70	71					15																	99679553		2197	4297	6494	97497076	SO:0001583	missense	64927				CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"Tetratricopeptide (TTC) repeat domain containing"	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.1195G>T	15.37:g.99679553C>A	ENSP00000377690:p.Ala399Ser		97497076	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Missense_Mutation	SNP	ENST00000394132.2	37	CCDS10379.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.76|17.76	3.467620|3.467620	0.63625|0.63625	.|.	.|.	ENSG00000103852|ENSG00000103852	ENST00000394132;ENST00000394136;ENST00000262074;ENST00000394135|ENST00000434594	T;T;T;T|.	0.16897|.	2.31;2.31;2.31;2.31|.	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	0.000000|.	0.64402|.	U|.	0.000010|.	T|T	0.57873|0.57873	0.2083|0.2083	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.78314|.	0.991|.	T|T	0.52689|0.52689	-0.8542|-0.8542	10|5	0.15066|.	T|.	0.55|.	-11.4527|-11.4527	14.9033|14.9033	0.70696|0.70696	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	399|.	Q5W5X9|.	TTC23_HUMAN|.	S|C	399|209	ENSP00000377690:A399S;ENSP00000377693:A399S;ENSP00000262074:A399S;ENSP00000377692:A399S|.	ENSP00000262074:A399S|.	A|W	-|-	1|3	0|0	TTC23|TTC23	97497076|97497076	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.146000|0.146000	0.21551|0.21551	4.676000|4.676000	0.61627|0.61627	2.652000|2.652000	0.90054|0.90054	0.655000|0.655000	0.94253|0.94253	GCC|TGG		0.517	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905		A	99679553	C	A	99679553	3	1	103	1	0	0	0	0	1	0	0	0	16730	739	26	2	156	2	TTC23	15	99679553	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	10257167	99679553	2851839	247	27346										
MRPS34	65993	hgsc.bcm.edu	37	chr16	1822399	1822399	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggtacggcacggaggccagGctgtcttccggcgccggcgt	18	13	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:1822399G>A	ENST00000397375.2	-	3	515	c.480C>T	c.(478-480)agC>agT	p.S160S	NME3_ENST00000219302.3_5'Flank|EME2_ENST00000307394.7_5'Flank|NME3_ENST00000563498.1_5'Flank|MRPS34_ENST00000177742.3_Silent_p.S167S|EME2_ENST00000568449.1_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	160						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						CGGAGGCCAGGCTGTCTTCCG	0.627																																																0			16											69	64	65					16																	1822399		2195	4300	6495	1762400	SO:0001819	synonymous_variant	65993			BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"Mitochondrial ribosomal proteins / small subunits"	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.480C>T	16.37:g.1822399G>A			1762400	Q9BVI7	Silent	SNP	ENST00000397375.2	37	CCDS10444.1																																																																																				0.627	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936		A	1822399	G	A	1822399	2	1	103	1	0	0	0	0	0	0	0	1	9873	1194	42	3		3	MRPS34	16	1822399	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		1822399	88532354	248	27347										
TSC2	7249	hgsc.bcm.edu	37	chr16	2121553	2121553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgcgggccgactcactgcacCgcctgggcctgcccaacaag	12	17	1	0	rs45437797		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:2121553C>T	ENST00000219476.3	+	18	2512	c.1882C>T	c.(1882-1884)Cgc>Tgc	p.R628C	TSC2_ENST00000382538.6_Missense_Mutation_p.R579C|TSC2_ENST00000439673.2_Missense_Mutation_p.R591C|TSC2_ENST00000401874.2_Missense_Mutation_p.R628C|TSC2_ENST00000353929.4_Missense_Mutation_p.R628C|TSC2_ENST00000350773.4_Missense_Mutation_p.R628C|TSC2_ENST00000568454.1_Missense_Mutation_p.R639C	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	628					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CTCACTGCACCGCCTGGGCCT	0.642			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																													yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	0			16						C	CYS/ARG,CYS/ARG,CYS/ARG	2,4394	4.2+/-10.8	0,2,2196	79	55	63	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1882,1882,1882	5.4	1	16	dbSNP_127	63	0,8598		0,0,4299	no	missense,missense,missense	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	180,180,180	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging,probably-damaging,probably-damaging	628/1808,628/1741,628/1785	2121553	2,12992	2198	4299	6497	2061554	SO:0001583	missense	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.1882C>T	16.37:g.2121553C>T	ENSP00000219476:p.Arg628Cys		2061554	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	34	5.352462	0.95830	4.55E-4	0.0	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	5.45	5.45	0.79879	Tuberin-type domain (1);	0.000000	0.85682	D	0.000000	D	0.92315	0.7562	L	0.54323	1.7	0.80722	D	1	D;D;P;D;P;D	0.89917	0.975;1.0;0.89;1.0;0.882;1.0	P;D;B;D;B;D	0.91635	0.833;0.996;0.422;0.999;0.439;0.997	D	0.92716	0.6187	10	0.72032	D	0.01	-29.7962	19.2777	0.94039	0.0:1.0:0.0:0.0	.	579;591;628;628;628;628	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	C	628;628;628;591;579;628	ENSP00000219476:R628C;ENSP00000384468:R628C;ENSP00000248099:R628C;ENSP00000399232:R591C;ENSP00000371978:R579C;ENSP00000344383:R628C	ENSP00000219476:R628C	R	+	1	0	TSC2	2061554	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.422000	0.80217	2.551000	0.86045	0.462000	0.41574	CGC		0.642	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2121553	C	T	2121553	3	4	103	1	0	0	0	0	1	0	0	0	16646	652	23	1	1948	1	TSC2	16	2121553	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	299154	2121553	88233200	249	27348										
TSC2	7249	hgsc.bcm.edu	37	chr16	2136355	2136355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gaggacggccagttcacctaCtgctggcacgatgacatcat	11	12	2	1	rs137854134		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:2136355C>T	ENST00000219476.3	+	37	5454	c.4824C>T	c.(4822-4824)taC>taT	p.Y1608Y	TSC2_ENST00000382538.6_Silent_p.Y1493Y|TSC2_ENST00000439673.2_Silent_p.Y1505Y|TSC2_ENST00000401874.2_Silent_p.Y1541Y|TSC2_ENST00000353929.4_Silent_p.Y1565Y|TSC2_ENST00000350773.4_Silent_p.Y1585Y|TSC2_ENST00000568454.1_Silent_p.Y1552Y	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1608	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AGTTCACCTACTGCTGGCACG	0.662			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																													yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	0			16											135	104	114					16																	2136355		2196	4299	6495	2076356	SO:0001819	synonymous_variant	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4824C>T	16.37:g.2136355C>T			2076356	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																				0.662	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2136355	C	T	2136355	2	4	103	1	0	0	0	0	0	0	0	1	16646	576	20	3		3	TSC2	16	2136355	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	14802	2136355	88218398	250	27349										
CORO7	79585	hgsc.bcm.edu	37	chr16	4455502	4455502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcctgctcaccttgcacgccGtgcccaccagggctccatct	9	19	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:4455502G>A	ENST00000251166.4	-	6	699	c.554C>T	c.(553-555)aCg>aTg	p.T185M	CORO7_ENST00000423908.2_Intron|CORO7_ENST00000539968.1_De_novo_Start_InFrame|CORO7_ENST00000577144.1_5'Flank|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.T185M|CORO7_ENST00000574025.1_Missense_Mutation_p.T100M|CORO7_ENST00000537233.2_Missense_Mutation_p.T167M	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	185					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						CTTGCACGCCGTGCCCACCAG	0.677																																																0			16											44	42	43					16																	4455502		2197	4299	6496	4395503	SO:0001583	missense	79585			AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.554C>T	16.37:g.4455502G>A	ENSP00000251166:p.Thr185Met		4395503	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.850999	0.51270	.	.	ENSG00000103426	ENST00000251166;ENST00000537233	T	0.68181	-0.31	4.4	4.4	0.53042	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.679936	0.12147	U	0.495271	D	0.87144	0.6104	H	0.95365	3.66	0.80722	D	1	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	P;D;D;D	0.91635	0.752;0.999;0.984;0.963	D	0.88671	0.3195	10	0.87932	D	0	-12.9482	14.1838	0.65592	0.0:0.0:1.0:0.0	.	100;167;185;166	P57737-2;B4DFD6;P57737;B4DKU9	.;.;CORO7_HUMAN;.	M	185;100	ENSP00000251166:T185M	ENSP00000251166:T185M	T	-	2	0	CORO7	4395503	1.000000	0.71417	0.892000	0.35008	0.014000	0.08584	6.441000	0.73439	2.432000	0.82394	0.655000	0.94253	ACG		0.677	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535		A	4455502	G	A	4455502	3	1	103	1	0	0	0	0	1	0	0	0	3765	1145	40	1	2315	1	CORO7	16	4455502	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2319147	4455502	85899251	251	27350										
USP7	7874	hgsc.bcm.edu	37	chr16	9014257	9014257	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcctgtacaaagacttcaaaGgtaactttgtcatcatctat	6	9	4	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:9014257G>T	ENST00000344836.4	-	5	768	c.570C>A	c.(568-570)acC>acA	p.T190T	USP7_ENST00000381886.4_Silent_p.T174T|USP7_ENST00000535863.1_Silent_p.T91T|USP7_ENST00000566224.1_5'Flank	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	190	Interaction with TSPYL5.|Interaction with p53/TP53, MDM2 and EBNA1.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Necessary for nuclear localization.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						AGACTTCAAAGGTAACTTTGT	0.363																																																0			16											101	97	98					16																	9014257		2197	4300	6497	8921758	SO:0001819	synonymous_variant	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.570C>A	16.37:g.9014257G>T			8921758	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																				0.363	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			T	9014257	G	T	9014257	2	4	103	1	0	0	0	0	0	0	0	1	17128	987	35	2		2	USP7	16	9014257	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	4558755	9014257	81340496	252	27351										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21136639	21136639	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gttgctcttgggagcaaaatGaatccagtgctccttccgtg	11	10	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:21136639G>A	ENST00000261383.3	-	9	1260	c.1261C>T	c.(1261-1263)Cat>Tat	p.H421Y	DNAH3_ENST00000415178.1_Missense_Mutation_p.H421Y|CTC-508F8.1_ENST00000575612.1_RNA	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	421	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGAGCAAAATGAATCCAGTGC	0.498																																																0			16											100	101	101					16																	21136639		2201	4300	6501	21044140	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1261C>T	16.37:g.21136639G>A	ENSP00000261383:p.His421Tyr		21044140	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.872062	0.00542	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.22945	1.93;2.09	5.75	3.8	0.43715	.	0.811324	0.11533	N	0.554539	T	0.19765	0.0475	L	0.36672	1.1	0.09310	N	1	B;B	0.17038	0.0;0.02	B;B	0.13407	0.001;0.009	T	0.21793	-1.0235	10	0.14252	T	0.57	.	11.0236	0.47732	0.1519:0.0:0.8481:0.0	.	421;392	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	Y	421;421;392	ENSP00000261383:H421Y;ENSP00000394245:H421Y	ENSP00000261383:H421Y	H	-	1	0	DNAH3	21044140	0.998000	0.40836	0.104000	0.21259	0.014000	0.08584	4.779000	0.62375	1.451000	0.47736	0.655000	0.94253	CAT		0.498	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21136639	G	A	21136639	3	1	103	1	0	0	0	0	1	0	0	0	4614	1290	45	3	11304	3	DNAH3	16	21136639	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	12122382	21136639	69218114	253	27352										
SH2B1	25970	hgsc.bcm.edu	37	chr16	28880332	28880332	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtctcatctctgtaggtggaAggtccatccgagtatatcat	10	9	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:28880332A>G	ENST00000322610.8	+	6	1486	c.1047A>G	c.(1045-1047)gaA>gaG	p.E349E	SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000395532.4_Silent_p.E349E|SH2B1_ENST00000359285.5_Silent_p.E349E|SH2B1_ENST00000538342.1_Silent_p.E13E|SH2B1_ENST00000337120.5_Silent_p.E349E|SH2B1_ENST00000545570.1_Silent_p.E39E			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	349	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.|PH.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						TGTAGGTGGAAGGTCCATCCG	0.547																																																0			16											126	114	118					16																	28880332		2197	4300	6497	28787833	SO:0001819	synonymous_variant	25970			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1047A>G	16.37:g.28880332A>G			28787833	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Silent	SNP	ENST00000322610.8	37	CCDS53996.1																																																																																				0.547	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		G	28880332	A	G	28880332	2	3	103	1	0	0	0	0	0	0	0	1	14264	69	3	4		4	SH2B1	16	28880332	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	7743693	28880332	61474421	254	27353										
RABEP2	79874	hgsc.bcm.edu	37	chr16	28925786	28925786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgcagttgtgagcgaaggccTcagcggctggacccccatct	13	14	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:28925786T>C	ENST00000358201.4	-	5	1253	c.665A>G	c.(664-666)gAg>gGg	p.E222G	RABEP2_ENST00000357573.6_Missense_Mutation_p.E222G|RABEP2_ENST00000544477.1_Missense_Mutation_p.E151G|RABEP2_ENST00000561803.1_5'Flank	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	222					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						AGCGAAGGCCTCAGCGGCTGG	0.692																																					Pancreas(66;639 1284 10093 31061 49099)											0			16											22	28	26					16																	28925786		2020	4179	6199	28833287	SO:0001583	missense	79874			AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.665A>G	16.37:g.28925786T>C	ENSP00000350934:p.Glu222Gly		28833287		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.501972	0.64298	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.52754	0.65;0.65;0.69	5.13	5.13	0.70059	.	0.179276	0.47852	D	0.000207	T	0.55673	0.1935	L	0.27053	0.805	0.35465	D	0.796886	D;D;D;D	0.89917	0.999;1.0;0.979;0.999	D;D;P;D	0.80764	0.986;0.994;0.747;0.986	T	0.68217	-0.5467	10	0.87932	D	0	-23.5048	13.9151	0.63893	0.0:0.0:0.0:1.0	.	151;222;222;222	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	G	222;222;151	ENSP00000350934:E222G;ENSP00000350186:E222G;ENSP00000442798:E151G	ENSP00000350186:E222G	E	-	2	0	RABEP2	28833287	0.995000	0.38212	0.995000	0.50966	0.449000	0.32228	1.771000	0.38542	1.933000	0.56026	0.379000	0.24179	GAG		0.692	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		C	28925786	T	C	28925786	3	2	103	1	0	0	0	0	1	0	0	0	12999	1551	54	4	1080	4	RABEP2	16	28925786	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	45454	28925786	61428967	255	27354										
ABCC11	85320	hgsc.bcm.edu	37	chr16	48234337	48234337	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcggaatagacggcgcgggcCaggctgatcctctgtttctg	14	11	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:48234337C>A	ENST00000394747.1	-	14	2281	c.1932G>T	c.(1930-1932)ctG>ctT	p.L644L	ABCC11_ENST00000356608.2_Silent_p.L644L|ABCC11_ENST00000394748.1_Silent_p.L644L|ABCC11_ENST00000353782.5_Silent_p.L644L|ABCC11_ENST00000537808.1_Silent_p.L644L	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	644	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CGGCGCGGGCCAGGCTGATCC	0.592																																																0			16											71	58	62					16																	48234337		2201	4300	6501	46791838	SO:0001819	synonymous_variant	85320			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1932G>T	16.37:g.48234337C>A			46791838	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																				0.592	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48234337	C	A	48234337	2	1	103	1	0	0	0	0	0	0	0	1	51	581	21	2		2	ABCC11	16	48234337	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	19308551	48234337	42120416	256	27355										
CES7	221223	hgsc.bcm.edu	37	chr16	55880570	55880570	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agattataagctggccacagAgacaggtcgttcccattagg	11	9	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:55880570A>G	ENST00000290567.9	-	13	1642	c.1521T>C	c.(1519-1521)tcT>tcC	p.S507S	CES5A_ENST00000521992.1_Silent_p.S536S|CES5A_ENST00000518005.1_Silent_p.S401S|CES5A_ENST00000520435.1_Silent_p.S477S|CES5A_ENST00000319165.9_Silent_p.S457S|CES5A_ENST00000541580.1_5'UTR	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	507						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						CTGGCCACAGAGACAGGTCGT	0.547																																																0			16											172	174	173					16																	55880570		2198	4300	6498	54438071	SO:0001819	synonymous_variant	0			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1521T>C	16.37:g.55880570A>G			54438071	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Silent	SNP	ENST00000290567.9	37	CCDS45490.1																																																																																				0.547	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		G	55880570	A	G	55880570	2	3	103	1	0	0	0	0	0	0	0	1	3278	291	11	4		4	CES7	16	55880570	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	7646233	55880570	34474183	257	27356										
KATNB1	10300	hgsc.bcm.edu	37	chr16	57787863	57787863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tctttcctctgcaggtcggaCgccaccccggagaagtgagc	12	14	2	2	rs143811277		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:57787863C>T	ENST00000379661.3	+	13	1576	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M		NM_005886.2	NP_005877.2			katanin p80 (WD repeat containing) subunit B 1											cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_neural(199;0.223)				GCAGGTCGGACGCCACCCCGG	0.677																																																0			16						C	MET/THR	2,4394	4.2+/-10.8	0,2,2196	62	55	57		1184	4.8	1	16	dbSNP_134	57	0,8600		0,0,4300	yes	missense	KATNB1	NM_005886.2	81	0,2,6496	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	395/656	57787863	2,12994	2198	4300	6498	56345364	SO:0001583	missense	10300			AF052432	CCDS10788.1	16q12.2	2013-01-09	2003-03-13		ENSG00000140854	ENSG00000140854		"WD repeat domain containing"	6217	protein-coding gene	gene with protein product		602703	"katanin p80 (WD40-containing) subunit B 1"			9568719	Standard	XM_006721121		Approved		uc002eml.1	Q9BVA0	OTTHUMG00000133467	ENST00000379661.3:c.1184C>T	16.37:g.57787863C>T	ENSP00000368982:p.Thr395Met		56345364		Missense_Mutation	SNP	ENST00000379661.3	37	CCDS10788.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417642	0.83449	4.55E-4	0.0	ENSG00000140854	ENST00000379661	T	0.56275	0.47	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.71821	0.3385	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.76102	-0.3082	10	0.87932	D	0	5.7195	16.4232	0.83773	0.0:1.0:0.0:0.0	.	395	Q9BVA0	KTNB1_HUMAN	M	395	ENSP00000368982:T395M	ENSP00000368982:T395M	T	+	2	0	KATNB1	56345364	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	5.634000	0.67833	2.216000	0.71823	0.313000	0.20887	ACG		0.677	KATNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257343.3			T	57787863	C	T	57787863	3	4	103	1	0	0	0	0	1	0	0	0	8008	536	19	1	1230	1	KATNB1	16	57787863	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1907293	57787863	32566890	258	27357										
CDH11	1009	hgsc.bcm.edu	37	chr16	64981767	64981767	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acatccacgctgttgggcgcTggccggagcccaggtctagg	15	13	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:64981767T>C	ENST00000268603.4	-	13	2745	c.2130A>G	c.(2128-2130)ccA>ccG	p.P710P	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Silent_p.P584P	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	710					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGTTGGGCGCTGGCCGGAGCC	0.507			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																													Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	0			16											119	111	114					16																	64981767		2203	4300	6503	63539268	SO:0001819	synonymous_variant	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2130A>G	16.37:g.64981767T>C			63539268	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.507	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		C	64981767	T	C	64981767	2	2	103	1	0	0	0	0	0	0	0	1	3103	1567	55	4		4	CDH11	16	64981767	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	7193904	64981767	25372986	259	27358										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72184567	72184567	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acttggcattctagtaactcGatgttgctcagggaagactg	11	8	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr16:72184567G>C	ENST00000237353.10	-	5	837	c.576C>G	c.(574-576)atC>atG	p.I192M	PMFBP1_ENST00000355636.6_Missense_Mutation_p.I47M|PMFBP1_ENST00000537465.1_Missense_Mutation_p.I192M	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	192						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				CTAGTAACTCGATGTTGCTCA	0.527																																																0			16											166	152	157					16																	72184567		2198	4300	6498	70742068	SO:0001583	missense	83449			AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.576C>G	16.37:g.72184567G>C	ENSP00000237353:p.Ile192Met		70742068	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709510	0.68730	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.77620	-1.11;-1.11;2.53	6.17	-8.37	0.00976	.	0.000000	0.52532	D	0.000061	T	0.69324	0.3098	N	0.24115	0.695	0.24619	N	0.99368	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70487	0.969;0.969;0.969	T	0.66002	-0.6031	10	0.33141	T	0.24	-18.89	7.5191	0.27618	0.5896:0.0:0.2119:0.1985	.	192;192;192	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	M	192;192;47	ENSP00000443817:I192M;ENSP00000237353:I192M;ENSP00000347854:I47M	ENSP00000237353:I192M	I	-	3	3	PMFBP1	70742068	0.040000	0.19996	0.835000	0.33067	0.925000	0.55904	-1.676000	0.01946	-1.103000	0.03019	-0.140000	0.14226	ATC		0.527	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		C	72184567	G	C	72184567	3	2	103	1	0	0	0	0	1	0	0	0	12165	1048	37	5	2575	5	PMFBP1	16	72184567	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	7202800	72184567	18170186	260	27359										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5463207	5463207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttggttaaaatcctcatttTtccagggccatgtggaacag	9	8	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:5463207T>C	ENST00000572272.1	-	4	808	c.809A>G	c.(808-810)aAa>aGa	p.K270R	NLRP1_ENST00000577119.1_Missense_Mutation_p.K270R|NLRP1_ENST00000262467.5_Missense_Mutation_p.K270R|NLRP1_ENST00000354411.3_Missense_Mutation_p.K270R|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000269280.4_Missense_Mutation_p.K270R|NLRP1_ENST00000345221.3_Missense_Mutation_p.K270R			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	270					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				ATCCTCATTTTTCCAGGGCCA	0.537																																																0			17											190	196	194					17																	5463207		2203	4300	6503	5403931	SO:0001583	missense	22861			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.809A>G	17.37:g.5463207T>C	ENSP00000460475:p.Lys270Arg		5403931	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.239557	0.39598	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.71934	-0.61;-0.61;-0.59;-0.56;-0.59	4.49	3.41	0.39046	.	0.532184	0.15814	N	0.243319	T	0.56093	0.1962	L	0.41824	1.3	0.09310	N	1	B;B;B;B;B	0.33748	0.423;0.423;0.101;0.292;0.193	B;B;B;B;B	0.27380	0.079;0.079;0.036;0.079;0.036	T	0.50056	-0.8872	10	0.51188	T	0.08	.	6.7617	0.23544	0.0:0.1068:0.0:0.8932	.	270;270;270;270;270	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	R	270	ENSP00000442029:K270R;ENSP00000262467:K270R;ENSP00000269280:K270R;ENSP00000346390:K270R;ENSP00000324366:K270R	ENSP00000262467:K270R	K	-	2	0	NLRP1	5403931	0.000000	0.05858	0.005000	0.12908	0.467000	0.32768	0.089000	0.15002	0.873000	0.35799	0.529000	0.55759	AAA		0.537	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		C	5463207	T	C	5463207	3	2	103	1	0	0	0	0	1	0	0	0	10502	1841	64	4	3743	4	NLRP1	17	5463207	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10		5463207	75732003	261	27360										
TP53	7157	hgsc.bcm.edu	37	chr17	7578524	7578524	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agggcaggtcttggccagttGgcaaaacatcttgttgaggg	15	7	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:7578524G>A	ENST00000269305.4	-	5	595	c.406C>T	c.(406-408)Caa>Taa	p.Q136*	TP53_ENST00000420246.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q136*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q136*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	136	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> E (in sporadic cancers; somatic mutation).|Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q136*(34)|p.0?(8)|p.C135fs*9(3)|p.Q136E(3)|p.N131fs*27(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.Q136K(1)|p.S127_Q136del10(1)|p.V73fs*9(1)|p.Q43*(1)|p.Y126fs*11(1)|p.Q4*(1)|p.C3fs*9(1)|p.C42fs*9(1)|p.C135_A138delCQLA(1)|p.Q136_K139delQLAK(1)|p.Q136fs*34(1)|p.C135_T140delCQLAKT(1)|p.Q136fs*13(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTGGCCAGTTGGCAAAACATC	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	67	Substitution - Nonsense(36)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(5)|Substitution - Missense(4)|Insertion - In frame(2)|Insertion - Frameshift(1)|Complex - deletion inframe(1)	upper_aerodigestive_tract(9)|ovary(9)|urinary_tract(8)|central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(6)|stomach(5)|breast(4)|bone(4)|large_intestine(3)|oesophagus(3)|skin(3)|lung(3)|soft_tissue(1)|endometrium(1)|pancreas(1)	17	GRCh37	CM971503	TP53	M							52	52	52					17																	7578524		2203	4300	6503	7519249	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.406C>T	17.37:g.7578524G>A	ENSP00000269305:p.Gln136*		7519249	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349260	0.95830	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.5387	17.2272	0.86973	0.0:0.0:1.0:0.0	.	.	.	.	X	136;136;136;136;136;136;125;43;4;43;4;136	.	ENSP00000269305:Q136X	Q	-	1	0	TP53	7519249	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.809000	0.99208	2.733000	0.93635	0.655000	0.94253	CAA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578524	G	A	7578524	4	1	103	1	0	0	0	0	0	1	0	0	16421	1357	47	3	892	3	TP53	17	7578524	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2115317	7578524	73616686	262	27361										
MYH3	4621	hgsc.bcm.edu	37	chr17	10538195	10538195	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttcttgtccagagcggcggCcaaggaattggctctttcaa	11	11	3	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:10538195C>A	ENST00000583535.1	-	31	4405	c.4318G>T	c.(4318-4320)Gcc>Tcc	p.A1440S	MYH3_ENST00000226209.7_Missense_Mutation_p.A1440S	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1440					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AGAGCGGCGGCCAAGGAATTG	0.532																																																0			17											117	102	107					17																	10538195		2203	4300	6503	10478920	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4318G>T	17.37:g.10538195C>A	ENSP00000464317:p.Ala1440Ser		10478920	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.926427	0.73327	.	.	ENSG00000109063	ENST00000226209	D	0.82984	-1.67	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.85881	0.5800	M	0.80508	2.5	0.39781	D	0.972296	B	0.26363	0.147	B	0.35353	0.201	D	0.86047	0.1523	9	0.66056	D	0.02	.	15.0101	0.71545	0.1513:0.8487:0.0:0.0	.	1440	P11055	MYH3_HUMAN	S	1440	ENSP00000226209:A1440S	ENSP00000226209:A1440S	A	-	1	0	MYH3	10478920	0.999000	0.42202	0.998000	0.56505	0.902000	0.53008	4.047000	0.57383	2.604000	0.88044	0.655000	0.94253	GCC		0.532	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10538195	C	A	10538195	3	1	103	1	0	0	0	0	1	0	0	0	10066	739	26	2	1548	2	MYH3	17	10538195	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2959671	10538195	70657015	263	27362										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305784	39305785	+	In_Frame_Ins	INS	-	-	TGGGGCGGCAGCAGC													0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcaggtggtctggcagcagcINSaggggcggcagcagctggat					rs411367		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:39305784_39305785insTGGGGCGGCAGCAGC	ENST00000343246.4	-	1	269_270	c.235_236insGCTGCTGCCGCCCCA	c.(235-237)tgc>tGCTGCTGCCGCCCCAgc	p.79_80insCCRPS		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	79	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> CCCRPS.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ctggcagcagcaggggcggcag	0.658																																																0			17																																								36559311	SO:0001652	inframe_insertion	85289			AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.235_236insGCTGCTGCCGCCCCA	17.37:g.39305784_39305785insTGGGGCGGCAGCAGC	ENSP00000340546:p.Cys79_Cys80insCysCysArgProSer		36559310		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																				0.658	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			TGGGGCGGCAGCAGC	39305785	-	TGGGGCGGCAGCAGC	39305784	7	5	103	1	0	1	1	0	0	0	0	0	8576	710	25	0	313	0	KRTAP4-5	17	39305784	In_Frame_Ins	INS	-	TCGA-DY-A0XA-01A-11D-A152-10	28767589	39305784	41889426	264	27363										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48155479	48155479	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggaccttcaggtgcagctgCagctctccacgtgagtgacc	13	13	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:48155479C>T	ENST00000320031.8	+	17	2539	c.2209C>T	c.(2209-2211)Cag>Tag	p.Q737*	ITGA3_ENST00000007722.7_Nonsense_Mutation_p.Q737*	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	737					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GGTGCAGCTGCAGCTCTCCAC	0.582																																																0			17											130	113	119					17																	48155479		2203	4300	6503	45510478	SO:0001587	stop_gained	3675			M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2209C>T	17.37:g.48155479C>T	ENSP00000315190:p.Gln737*		45510478	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Nonsense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.316091|10.316091	0.99381|0.99381	.|.	.|.	ENSG00000005884|ENSG00000005884	ENST00000506827|ENST00000007722;ENST00000538917;ENST00000320031	.|.	.|.	.|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.174366	.|0.51477	.|D	.|0.000095	T|.	0.58366|.	0.2117|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.51068|.	-0.8752|.	4|.	.|0.19590	.|T	.|0.45	.|.	14.3399|14.3399	0.66619|0.66619	0.0:0.8506:0.1493:0.0|0.0:0.8506:0.1493:0.0	.|.	.|.	.|.	.|.	V|X	115|737;723;737	.|.	.|ENSP00000007722:Q737X	A|Q	+|+	2|1	0|0	ITGA3|ITGA3	45510478|45510478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.659000|1.659000	0.37387|0.37387	2.569000|2.569000	0.86673|0.86673	0.655000|0.655000	0.94253|0.94253	GCA|CAG		0.582	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		T	48155479	C	T	48155479	4	4	103	1	0	0	0	0	0	1	0	0	7898	711	25	3	2275	3	ITGA3	17	48155479	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	8849695	48155479	33039731	265	27364										
MBTD1	54799	hgsc.bcm.edu	37	chr17	49272710	49272710	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gatcccaatcatcaggaatcCgtcagctagcaccttttcaa	6	13	4	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:49272710C>A	ENST00000586178.1	-	13	1580	c.1237G>T	c.(1237-1239)Gga>Tga	p.G413*	MBTD1_ENST00000415868.1_Nonsense_Mutation_p.G413*|MBTD1_ENST00000376381.2_Intron	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	413					chromatin modification (GO:0016568)|embryonic skeletal system development (GO:0048706)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			ATCAGGAATCCGTCAGCTAGC	0.388																																																0			17											99	85	90					17																	49272710		2203	4300	6503	46627709	SO:0001587	stop_gained	54799			AK000062	CCDS11581.2	17q24.1	2003-01-15			ENSG00000011258	ENSG00000011258			19866	protein-coding gene	gene with protein product							Standard	NM_017643		Approved	SA49P01, FLJ20055	uc002itr.4	Q05BQ5	OTTHUMG00000150442	ENST00000586178.1:c.1237G>T	17.37:g.49272710C>A	ENSP00000468304:p.Gly413*		46627709	Q6ZVU7|Q9NXU1	Nonsense_Mutation	SNP	ENST00000586178.1	37	CCDS11581.2	.	.	.	.	.	.	.	.	.	.	C	37	6.384318	0.97524	.	.	ENSG00000011258	ENST00000405860;ENST00000415868	.	.	.	5.51	5.51	0.81932	.	0.053226	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.756	0.96291	0.0:1.0:0.0:0.0	.	.	.	.	X	413	.	ENSP00000386072:G413X	G	-	1	0	MBTD1	46627709	1.000000	0.71417	0.967000	0.41034	0.792000	0.44763	7.769000	0.85360	2.735000	0.93741	0.643000	0.83706	GGA		0.388	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			A	49272710	C	A	49272710	4	1	103	1	0	0	0	0	0	1	0	0	9390	661	23	2	669	2	MBTD1	17	49272710	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1117231	49272710	31922500	266	27365										
METTL2A	339175	hgsc.bcm.edu	37	chr17	60503802	60503802	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	caaaatcatttgaaggactgGttcttggagaacaagagtga	11	5	2	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:60503802G>A	ENST00000311506.5	+	3	381	c.345G>A	c.(343-345)tgG>tgA	p.W115*		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	115					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			TGAAGGACTGGTTCTTGGAGA	0.403																																																0			17											97	77	83					17																	60503802		692	1591	2283	57857534	SO:0001587	stop_gained	339175			AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.345G>A	17.37:g.60503802G>A	ENSP00000309610:p.Trp115*		57857534	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Nonsense_Mutation	SNP	ENST00000311506.5	37	CCDS45752.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325194	0.60634	.	.	ENSG00000087995	ENST00000311506;ENST00000333483	.	.	.	5.02	2.97	0.34412	.	1.189680	0.05794	N	0.610975	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-1.6675	6.864	0.24082	0.1511:0.0:0.7074:0.1415	.	.	.	.	X	115	.	ENSP00000309610:W115X	W	+	3	0	METTL2A	57857534	0.000000	0.05858	0.001000	0.08648	0.084000	0.17831	0.648000	0.24828	0.494000	0.27859	0.555000	0.69702	TGG		0.403	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725		A	60503802	G	A	60503802	4	1	103	1	0	0	0	0	0	1	0	0	9529	1270	44	3	355	3	METTL2A	17	60503802	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	11231092	60503802	20691408	267	27366										
TTYH2	94015	hgsc.bcm.edu	37	chr17	72248451	72248451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttggcctcttctccttcctgGccgccctcgccttctccacc	6	21	3	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:72248451G>A	ENST00000269346.4	+	11	1269	c.1195G>A	c.(1195-1197)Gcc>Acc	p.A399T	TTYH2_ENST00000529107.1_Missense_Mutation_p.A378T|TTYH2_ENST00000441391.2_Missense_Mutation_p.A78T	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	399						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CTCCTTCCTGGCCGCCCTCGC	0.617																																																0			17											107	87	94					17																	72248451		2203	4300	6503	69760046	SO:0001583	missense	94015				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1195G>A	17.37:g.72248451G>A	ENSP00000269346:p.Ala399Thr		69760046	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122335	0.77436	.	.	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.12255	2.7;2.7;2.7	5.79	5.79	0.91817	.	0.050277	0.85682	D	0.000000	T	0.29321	0.0730	L	0.47016	1.485	0.80722	D	1	D;D	0.89917	1.0;0.993	D;D	0.97110	1.0;0.95	T	0.02059	-1.1221	10	0.07990	T	0.79	-14.0653	18.8188	0.92088	0.0:0.0:1.0:0.0	.	378;399	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	T	399;378;78	ENSP00000269346:A399T;ENSP00000433089:A378T;ENSP00000394576:A78T	ENSP00000269346:A399T	A	+	1	0	TTYH2	69760046	1.000000	0.71417	0.996000	0.52242	0.731000	0.41821	6.139000	0.71728	2.722000	0.93159	0.655000	0.94253	GCC		0.617	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			A	72248451	G	A	72248451	3	1	103	1	0	0	0	0	1	0	0	0	16780	1203	42	3	1237	3	TTYH2	17	72248451	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	11744649	72248451	8946759	268	27367										
BAHCC1	57597	hgsc.bcm.edu	37	chr17	79409528	79409528	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cgctgcaggacaaagcccccCgggacctaaaggccagcggg	14	15	0	0	rs370294799	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:79409528C>T	ENST00000307745.7	+	9	1153	c.1153C>T	c.(1153-1155)Cgg>Tgg	p.R385W																								CAAAGCCCCCCGGGACCTAAA	0.746																																																0			17											5	6	6					17																	79409528		1716	3796	5512	77024123	SO:0001583	missense	57597																														ENST00000307745.7:c.1153C>T	17.37:g.79409528C>T	ENSP00000303486:p.Arg385Trp		77024123		Missense_Mutation	SNP	ENST00000307745.7	37		.	.	.	.	.	.	.	.	.	.	c	17.83	3.485965	0.63962	.	.	ENSG00000171282	ENST00000307745	T	0.23754	1.89	4.01	4.01	0.46588	.	.	.	.	.	T	0.45054	0.1323	M	0.64997	1.995	0.40585	D	0.981435	D	0.89917	1.0	D	0.77004	0.989	T	0.45977	-0.9224	9	0.87932	D	0	.	10.5039	0.44821	0.1943:0.8057:0.0:0.0	.	385	Q9P281	BAHC1_HUMAN	W	385	ENSP00000303486:R385W	ENSP00000303486:R385W	R	+	1	2	AC110285.1	77024123	0.120000	0.22244	1.000000	0.80357	0.794000	0.44872	0.148000	0.16224	2.101000	0.63845	0.282000	0.19409	CGG		0.746	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	79409528	C	T	79409528	3	4	103	1	0	0	0	0	1	0	0	0	1297	643	23	1	1002	1	BAHCC1	17	79409528	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	7161077	79409528	1785682	269	27368										
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79967066	79967066	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggcccagctcaagagtgagCggtgggtgccccctcagtgc	15	13	2	2	rs558896726		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr17:79967066C>T	ENST00000306739.4	+	8	1184	c.1087C>T	c.(1087-1089)Cgg>Tgg	p.R363W	ASPSCR1_ENST00000306729.7_Splice_Site_p.R363W|ASPSCR1_ENST00000580534.1_Splice_Site_p.R286W	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	363	Interaction with GLUT4. {ECO:0000250}.				glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CAAGAGTGAGCGGTGGGTGCC	0.672			T	TFE3	alveolar soft part sarcoma								C|||	1	0.000199681	0	0	5008	,	,		15399	0		0	False		,,,				2504	0.001						Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	0			17											48	40	43					17																	79967066		2196	4297	6493	77560355	SO:0001630	splice_region_variant	79058			AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"UBX domain containing"	13825	protein-coding gene	gene with protein product	"UBX domain protein 9"	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.1088+1C>T	17.37:g.79967066C>T			77560355	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	37	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789400	0.90367	.	.	ENSG00000169696	ENST00000306739;ENST00000306729;ENST00000344865	T;T	0.10960	2.82;2.82	5.48	4.45	0.53987	.	0.054169	0.64402	D	0.000001	T	0.29783	0.0744	M	0.72118	2.19	0.47245	D	0.999367	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.995;0.995;0.991;0.999	T	0.01007	-1.1483	10	0.87932	D	0	-30.4621	11.0906	0.48113	0.2816:0.7183:0.0:0.0	.	286;286;363;363;286	Q9BZE9-3;Q9BZE9-4;Q9BZE9-2;Q9BZE9;C9JAL9	.;.;.;ASPC1_HUMAN;.	W	363;363;286	ENSP00000302176:R363W;ENSP00000306625:R363W	ENSP00000306625:R363W	R	+	1	2	ASPSCR1	77560355	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.650000	0.46665	2.563000	0.86464	0.655000	0.94253	CGG		0.672	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	Missense_Mutation	T	79967066	C	T	79967066	5	4	103	1	0	0	0	0	0	0	1	0	1060	782	27	1	1117	1	ASPSCR1	17	79967066	Splice_Site	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	557538	79967066	1228144	270	27369										
ESCO1	114799	hgsc.bcm.edu	37	chr18	19153967	19153967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcaggcactgatggctgtgGactttttgggagtgttgtgt	15	5	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr18:19153967G>T	ENST00000269214.5	-	4	1775	c.838C>A	c.(838-840)Cca>Aca	p.P280T		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	280					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						GATGGCTGTGGACTTTTTGGG	0.428																																																0			18											136	137	137					18																	19153967		2203	4300	6503	17407965	SO:0001583	missense	114799			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.838C>A	18.37:g.19153967G>T	ENSP00000269214:p.Pro280Thr		17407965	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	37	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606392	0.28623	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.58358	0.34;1.88	5.5	1.19	0.21007	.	0.457002	0.20803	N	0.085387	T	0.43299	0.1241	L	0.57536	1.79	0.28106	N	0.931206	B	0.20887	0.049	B	0.22386	0.039	T	0.34129	-0.9841	10	0.38643	T	0.18	-22.9051	6.1635	0.20378	0.6007:0.0:0.3993:0.0	.	280	Q5FWF5	ESCO1_HUMAN	T	280	ENSP00000269214:P280T;ENSP00000372763:P280T	ENSP00000269214:P280T	P	-	1	0	ESCO1	17407965	0.998000	0.40836	0.986000	0.45419	0.986000	0.74619	1.178000	0.31981	0.311000	0.23014	0.655000	0.94253	CCA		0.428	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		T	19153967	G	T	19153967	3	4	103	1	0	0	0	0	1	0	0	0	5261	1174	41	2	1720	2	ESCO1	18	19153967	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		19153967	58923281	271	27370										
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39567805	39567805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gctcatcgacaaggacacatGgtgaaagtagattggctgga	13	7	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr18:39567805G>A	ENST00000262039.4	+	5	647	c.561G>A	c.(559-561)atG>atA	p.M187I	PIK3C3_ENST00000398870.3_Missense_Mutation_p.M124I	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	187					autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						AAGGACACATGGTGAAAGTAG	0.308										TSP Lung(28;0.18)																											NSCLC(37;552 1060 2683 16430 37914)											0			18											103	105	104					18																	39567805		2203	4300	6503	37821803	SO:0001583	missense	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.561G>A	18.37:g.39567805G>A	ENSP00000262039:p.Met187Ile		37821803	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.078133	0.55753	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.75154	-0.91;-0.91	5.66	5.66	0.87406	Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.59266	0.2181	N	0.11000	0.08	0.80722	D	1	B;B	0.14012	0.005;0.009	B;B	0.17098	0.017;0.017	T	0.53795	-0.8388	9	.	.	.	.	20.1041	0.97884	0.0:0.0:1.0:0.0	.	124;187	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	I	187;124	ENSP00000262039:M187I;ENSP00000381845:M124I	.	M	+	3	0	PIK3C3	37821803	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.781000	0.99029	2.826000	0.97356	0.655000	0.94253	ATG		0.308	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		A	39567805	G	A	39567805	3	1	103	1	0	0	0	0	1	0	0	0	11943	1348	47	3	579	3	PIK3C3	18	39567805	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	20413838	39567805	38509443	272	27371										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575189	48575189	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaatgtgatagtgtctgtgTgaatccatatcactacgaac	8	7	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr18:48575189T>C	ENST00000342988.3	+	3	921	c.383T>C	c.(382-384)gTg>gCg	p.V128A	SMAD4_ENST00000452201.2_Missense_Mutation_p.V128A|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.V128A|SMAD4_ENST00000398417.2_Missense_Mutation_p.V128A	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	128	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGTGTCTGTGTGAATCCATAT	0.373																																																40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	18											152	136	141					18																	48575189		2203	4300	6503	46829187	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.383T>C	18.37:g.48575189T>C	ENSP00000341551:p.Val128Ala		46829187	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855079	0.91355	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	T;T;T	0.80566	-1.39;-1.39;-1.39	5.48	5.48	0.80851	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.90410	0.6998	M	0.88377	2.95	0.58432	D	0.999999	D	0.63046	0.992	D	0.66196	0.942	D	0.92229	0.5791	10	0.87932	D	0	.	14.5339	0.67947	0.0:0.0:0.0:1.0	.	128	Q13485	SMAD4_HUMAN	A	128	ENSP00000409551:V128A;ENSP00000341551:V128A;ENSP00000381452:V128A	ENSP00000341551:V128A	V	+	2	0	SMAD4	46829187	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.014000	0.88676	2.053000	0.61076	0.477000	0.44152	GTG		0.373	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48575189	T	C	48575189	3	2	103	1	0	0	0	0	1	0	0	0	14797	1696	59	4	389	4	SMAD4	18	48575189	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	9007384	48575189	29502059	273	27372										
SERPINB5	5268	hgsc.bcm.edu	37	chr18	61170747	61170747	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cacatctgatttctctggaaTgtcagagaccaagggagtgg	12	8	3	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr18:61170747T>C	ENST00000382771.4	+	7	1212	c.920T>C	c.(919-921)aTg>aCg	p.M307T		NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	307					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						TTCTCTGGAATGTCAGAGACC	0.438																																																0			18											97	83	87					18																	61170747		2203	4300	6503	59321727	SO:0001583	missense	5268			U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"Serine (or cysteine) peptidase inhibitors"	8949	protein-coding gene	gene with protein product	"protease inhibitor 5 (maspin)"	154790	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.920T>C	18.37:g.61170747T>C	ENSP00000372221:p.Met307Thr		59321727	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742847	0.69418	.	.	ENSG00000206075	ENST00000382771	D	0.85411	-1.98	5.95	4.78	0.61160	Serpin domain (3);	0.211041	0.49305	D	0.000145	D	0.88474	0.6446	M	0.88704	2.975	0.80722	D	1	B	0.31680	0.335	B	0.36608	0.229	D	0.87803	0.2626	10	0.87932	D	0	.	13.4366	0.61088	0.0:0.0:0.1309:0.8691	.	307	P36952	SPB5_HUMAN	T	307	ENSP00000372221:M307T	ENSP00000372221:M307T	M	+	2	0	SERPINB5	59321727	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.052000	0.76634	1.061000	0.40601	0.533000	0.62120	ATG		0.438	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639		C	61170747	T	C	61170747	3	2	103	1	0	0	0	0	1	0	0	0	14141	1464	51	4	942	4	SERPINB5	18	61170747	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	12595558	61170747	16906501	274	27373										
KCNG2	26251	hgsc.bcm.edu	37	chr18	77659494	77659494	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctccagcgtgcccgccagctAttggtgggccgtcatctcca	11	16	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr18:77659494A>C	ENST00000316249.3	+	2	1079	c.1079A>C	c.(1078-1080)tAt>tCt	p.Y360S	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	360					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		CCCGCCAGCTATTGGTGGGCC	0.711																																																0			18											29	29	29					18																	77659494		2202	4298	6500	75760482	SO:0001583	missense	26251			AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.1079A>C	18.37:g.77659494A>C	ENSP00000315654:p.Tyr360Ser		75760482		Missense_Mutation	SNP	ENST00000316249.3	37	CCDS12019.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060287	0.76074	.	.	ENSG00000178342	ENST00000316249	D	0.98474	-4.95	3.31	3.31	0.37934	Ion transport (1);	0.000000	0.64402	U	0.000003	D	0.98292	0.9434	L	0.59912	1.85	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98681	1.0692	10	0.87932	D	0	.	11.8902	0.52624	1.0:0.0:0.0:0.0	.	360	Q9UJ96	KCNG2_HUMAN	S	360	ENSP00000315654:Y360S	ENSP00000315654:Y360S	Y	+	2	0	KCNG2	75760482	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.977000	0.88081	1.391000	0.46566	0.333000	0.21579	TAT		0.711	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283		C	77659494	A	C	77659494	3	2	103	1	0	0	0	0	1	0	0	0	8049	449	16	4	1085	4	KCNG2	18	77659494	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	16488747	77659494	417754	275	27374										
C19orf36	113177	hgsc.bcm.edu	37	chr19	2099265	2099265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tccccgcagcctggtatcgcCagccttaaggtgtctggagc	12	14	1	0	rs529446582	byFrequency	TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:2099265C>T	ENST00000395301.3	+	10	684	c.620C>T	c.(619-621)cCa>cTa	p.P207L	MOB3A_ENST00000357066.3_5'Flank|IZUMO4_ENST00000395307.2_Missense_Mutation_p.P189L	NM_001039846.1	NP_001034935.1	Q1ZYL8	IZUM4_HUMAN	IZUMO family member 4	207						extracellular region (GO:0005576)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	6						CTGGTATCGCCAGCCTTAAGG	0.667																																																0			19											85	54	65					19																	2099265		2203	4300	6503	2050265	SO:0001583	missense	0			BC014609	CCDS35499.1, CCDS42458.1	19p13.3	2014-02-17	2010-07-29	2010-07-29	ENSG00000099840	ENSG00000099840		"-"	26950	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 36"	C19orf36		12975309, 19658160, 22957301	Standard	XM_005259480		Approved		uc002luw.1	Q1ZYL8	OTTHUMG00000141290	ENST00000395301.3:c.620C>T	19.37:g.2099265C>T	ENSP00000378712:p.Pro207Leu		2050265	A7RA93|A7RA94|Q6UXA2|Q96FT6|Q96L02	Missense_Mutation	SNP	ENST00000395301.3	37	CCDS42458.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.752625	0.49362	.	.	ENSG00000099840	ENST00000395307;ENST00000300960;ENST00000395301	T;T;T	0.24151	1.89;1.92;1.87	4.22	3.15	0.36227	.	0.491076	0.15303	N	0.269539	T	0.16557	0.0398	N	0.24115	0.695	0.30830	N	0.736812	B;P	0.36535	0.403;0.557	B;B	0.33750	0.121;0.169	T	0.10636	-1.0621	10	0.72032	D	0.01	-4.0013	9.542	0.39257	0.2205:0.7795:0.0:0.0	.	189;207	A7RA93;Q1ZYL8	.;IZUM4_HUMAN	L	236;189;207	ENSP00000378718:P236L;ENSP00000300960:P189L;ENSP00000378712:P207L	ENSP00000300960:P189L	P	+	2	0	IZUMO4	2050265	0.004000	0.15560	0.005000	0.12908	0.009000	0.06853	1.059000	0.30517	1.011000	0.39340	0.462000	0.41574	CCA		0.667	IZUMO4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280536.3	NM_052878		T	2099265	C	T	2099265	3	4	103	1	0	0	0	0	1	0	0	0	1927	594	21	3	658	3	C19orf36	19	2099265	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10		2099265	57029718	276	27375										
TNFSF14	8740	hgsc.bcm.edu	37	chr19	6669933	6669933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccagccttggacggccagccCggcccccatcagcaacagca	10	19	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:6669933C>T	ENST00000599359.1	-	2	529	c.148G>A	c.(148-150)Ggg>Agg	p.G50R	TNFSF14_ENST00000326176.9_Intron|TNFSF14_ENST00000245912.3_Intron			O43557	TNF14_HUMAN	tumor necrosis factor (ligand) superfamily, member 14	50					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of T cell chemotaxis (GO:0010820)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|receptor binding (GO:0005102)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18						ACGGCCAGCCCGGCCCCCATC	0.667																																																0			19											88	83	85					19																	6669933		2203	4300	6503	6620933	SO:0001583	missense	8740			AF036581	CCDS12171.1, CCDS45939.1	19p13.3	2008-02-05				ENSG00000125735		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11930	protein-coding gene	gene with protein product		604520				9462508	Standard	NM_172014		Approved	LIGHT, LTg, HVEM-L, CD258	uc002mfk.2	O43557		ENST00000599359.1:c.148G>A	19.37:g.6669933C>T	ENSP00000469049:p.Gly50Arg		6620933	A8K7M2|C9J5H4|O75476|Q6FHA1|Q8WVF8|Q96LD2	Missense_Mutation	SNP	ENST00000599359.1	37	CCDS12171.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096431	0.56075	.	.	ENSG00000125735	ENST00000245912	.	.	.	4.89	4.89	0.63831	.	0.782790	0.11148	N	0.594488	T	0.67896	0.2942	M	0.71581	2.175	0.80722	D	1	D	0.57257	0.979	P	0.51016	0.656	T	0.69862	-0.5030	9	0.87932	D	0	-21.115	13.902	0.63809	0.0:1.0:0.0:0.0	.	50	O43557	TNF14_HUMAN	R	50	.	ENSP00000245912:G50R	G	-	1	0	TNFSF14	6620933	0.004000	0.15560	0.876000	0.34364	0.011000	0.07611	1.540000	0.36115	2.409000	0.81822	0.563000	0.77884	GGG		0.667	TNFSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457863.1			T	6669933	C	T	6669933	3	4	103	1	0	0	0	0	1	0	0	0	16346	652	23	1	590	1	TNFSF14	19	6669933	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	4570668	6669933	52459050	277	27376										
GPR108	56927	hgsc.bcm.edu	37	chr19	6734042	6734042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cactgcgggtgttgacttggGcttgctggctgcagaggtcc	16	10	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:6734042G>T	ENST00000264080.7	-	6	549	c.523C>A	c.(523-525)Ccc>Acc	p.P175T	GPR108_ENST00000430424.4_5'UTR|GPR108_ENST00000598626.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	175						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						GTTGACTTGGGCTTGCTGGCT	0.607											OREG0025092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			19											94	94	94					19																	6734042		1970	4153	6123	6685042	SO:0001583	missense	56927				CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"GPCR / Unclassified : 7TM orphan receptors"	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.523C>A	19.37:g.6734042G>T	ENSP00000264080:p.Pro175Thr	636	6685042	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.601|8.601	0.886912|0.886912	0.17540|0.17540	.|.	.|.	ENSG00000125734|ENSG00000125734	ENST00000549846|ENST00000264080	.|T	.|0.21361	.|2.01	3.87|3.87	-1.78|-1.78	0.07957|0.07957	.|.	.|13.593400	.|0.00628	.|U	.|0.000479	T|T	0.13756|0.13756	0.0333|0.0333	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.20405|0.20405	-1.0276|-1.0276	5|10	.|0.14252	.|T	.|0.57	0.1214|0.1214	7.5794|7.5794	0.27955|0.27955	0.0:0.3804:0.5139:0.1056|0.0:0.3804:0.5139:0.1056	.|.	.|175	.|Q9NPR9	.|GP108_HUMAN	D|T	157|175	.|ENSP00000264080:P175T	.|ENSP00000264080:P175T	A|P	-|-	2|1	0|0	GPR108|GPR108	6685042|6685042	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.034000|0.034000	0.12701|0.12701	0.222000|0.222000	0.17699|0.17699	-0.245000|-0.245000	0.09625|0.09625	-0.311000|-0.311000	0.09066|0.09066	GCC|CCC		0.607	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2			T	6734042	G	T	6734042	3	4	103	1	0	0	0	0	1	0	0	0	6644	1203	42	2	1160	2	GPR108	19	6734042	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	64109	6734042	52394941	278	27377										
BEST2	54831	hgsc.bcm.edu	37	chr19	12866268	12866268	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcgtacccctcgtgtacacgCaggtaaccccatcatgcctc	8	17	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:12866268C>T	ENST00000549706.1	+	6	1036	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	BEST2_ENST00000042931.1_Nonsense_Mutation_p.Q238*|BEST2_ENST00000553030.1_Nonsense_Mutation_p.Q238*			Q8NFU1	BEST2_HUMAN	bestrophin 2	238					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.Q238*(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						CGTGTACACGCAGGTAACCCC	0.498																																																1	Substitution - Nonsense(1)	ovary(1)	19											135	131	132					19																	12866268		1994	4176	6170	12727268	SO:0001587	stop_gained	54831			AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17107	protein-coding gene	gene with protein product		607335	"vitelliform macular dystrophy 2-like 1"	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.712C>T	19.37:g.12866268C>T	ENSP00000448310:p.Gln238*		12727268	Q53YQ8|Q9NXP0	Nonsense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	39	7.302286	0.98196	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	.	.	.	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.5097	15.6627	0.77199	0.0:1.0:0.0:0.0	.	.	.	.	X	238	.	ENSP00000042931:Q238X	Q	+	1	0	BEST2	12727268	1.000000	0.71417	0.998000	0.56505	0.712000	0.41017	7.458000	0.80787	2.283000	0.76528	0.544000	0.68410	CAG		0.498	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682		T	12866268	C	T	12866268	4	4	103	1	0	0	0	0	0	1	0	0	1406	711	25	3	730	3	BEST2	19	12866268	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	6132226	12866268	46262715	279	27378										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935438	30935438	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agccacgtggagaaggcacaCatcacggccgagtcggccca	13	14	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:30935438C>T	ENST00000355537.3	+	2	1116	c.969C>T	c.(967-969)caC>caT	p.H323H		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	323					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					AGAAGGCACACATCACGGCCG	0.657																																																0			19											90	101	97					19																	30935438		2203	4300	6503	35627278	SO:0001819	synonymous_variant	9745				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.969C>T	19.37:g.30935438C>T			35627278	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																				0.657	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935438	C	T	30935438	2	4	103	1	0	0	0	0	0	0	0	1	18013	477	17	3		3	ZNF536	19	30935438	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	18069170	30935438	28193545	280	27379										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440553	37440553	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaatatttcctctgagttcAgacattgttacttcaagaca	5	8	3	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:37440553A>G	ENST00000333987.7	+	7	1004	c.498A>G	c.(496-498)tcA>tcG	p.S166S	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Silent_p.S102S	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	166					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTCTGAGTTCAGACATTGTTA	0.338																																																0			19											90	83	85					19																	37440553		1839	4084	5923	42132393	SO:0001819	synonymous_variant	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.498A>G	19.37:g.37440553A>G			42132393	B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	ENST00000333987.7	37	CCDS42558.1																																																																																				0.338	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		G	37440553	A	G	37440553	2	3	103	1	0	0	0	0	0	0	0	1	18038	175	7	4		4	ZNF568	19	37440553	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	6505115	37440553	21688430	281	27380										
ACTN4	81	hgsc.bcm.edu	37	chr19	39198787	39198787	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtcttgccttcaatgccctGatccaccggcacagaccaga	9	15	2	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:39198787G>C	ENST00000252699.2	+	6	679	c.603G>C	c.(601-603)ctG>ctC	p.L201L	ACTN4_ENST00000390009.3_Intron|ACTN4_ENST00000424234.2_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	201	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCAATGCCCTGATCCACCGGC	0.577																																					Colon(168;199 1940 10254 46213 46384)											0			19											228	150	177					19																	39198787		2203	4300	6503	43890627	SO:0001819	synonymous_variant	81			D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.603G>C	19.37:g.39198787G>C			43890627	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																				0.577	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			C	39198787	G	C	39198787	2	2	103	1	0	0	0	0	0	0	0	1	207	1277	45	5		5	ACTN4	19	39198787	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1758234	39198787	19930196	282	27381										
ZNF285	26974	hgsc.bcm.edu	37	chr19	44890675	44890675	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atgtagtctttgatgagtcaGaaggtcctttccacgctcac	9	10	3	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:44890675G>C	ENST00000330997.4	-	4	1796	c.1732C>G	c.(1732-1734)Ctg>Gtg	p.L578V	ZNF285_ENST00000544719.2_Missense_Mutation_p.L578V|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.L585V	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	578					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TGATGAGTCAGAAGGTCCTTT	0.413																																																0			19											152	124	134					19																	44890675		2203	4300	6503	49582515	SO:0001583	missense	26974			AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1732C>G	19.37:g.44890675G>C	ENSP00000333595:p.Leu578Val		49582515	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.560447	0.00910	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.05925	3.37	3.13	0.867	0.19085	.	.	.	.	.	T	0.02807	0.0084	N	0.16656	0.425	0.09310	N	1	B;B	0.21905	0.062;0.062	B;B	0.14578	0.011;0.011	T	0.46498	-0.9187	9	0.07990	T	0.79	.	1.9762	0.03416	0.1221:0.3441:0.3472:0.1865	.	602;578	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	V	601;578	ENSP00000333595:L578V	ENSP00000333595:L578V	L	-	1	2	ZNF285	49582515	0.002000	0.14202	0.005000	0.12908	0.359000	0.29487	0.684000	0.25364	0.612000	0.30071	0.454000	0.30748	CTG		0.413	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44890675	G	C	44890675	3	2	103	1	0	0	0	0	1	0	0	0	17861	933	33	5	44	5	ZNF285	19	44890675	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	5691888	44890675	14238308	283	27382										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52031044	52031044	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggttcacatcatccgtgtttTgcactggctgggctgctttc	11	11	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:52031044T>C	ENST00000425629.3	-	7	1299	c.1145A>G	c.(1144-1146)cAa>cGa	p.Q382R	SIGLEC6_ENST00000346477.3_Missense_Mutation_p.Q366R|SIGLEC6_ENST00000343300.4_Intron|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.Q330R|SIGLEC6_ENST00000391797.3_Intron|SIGLEC6_ENST00000359982.4_Intron|SIGLEC6_ENST00000474054.1_5'UTR	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	382					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		ATCCGTGTTTTGCACTGGCTG	0.488																																																0			19											182	179	180					19																	52031044		1941	4154	6095	56722856	SO:0001583	missense	946			D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1145A>G	19.37:g.52031044T>C	ENSP00000401502:p.Gln382Arg		56722856	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	.	.	.	.	.	.	.	.	.	.	.	5.390	0.257190	0.10239	.	.	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000436458	T;T	0.48201	1.26;0.82	3.02	-3.81	0.04294	.	.	.	.	.	T	0.32285	0.0824	L	0.40543	1.245	0.09310	N	1	B;B;B	0.19200	0.001;0.034;0.007	B;B;B	0.20577	0.003;0.03;0.006	T	0.22591	-1.0212	9	0.29301	T	0.29	.	6.4581	0.21940	0.0:0.5627:0.1803:0.257	.	330;366;382	C9JBE5;O43699-3;O43699	.;.;SIGL6_HUMAN	R	355;366;382;330	ENSP00000401502:Q382R;ENSP00000410679:Q330R	ENSP00000344064:Q355R	Q	-	2	0	SIGLEC6	56722856	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-0.429000	0.06982	-1.031000	0.03308	0.338000	0.21704	CAA		0.488	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		C	52031044	T	C	52031044	3	2	103	1	0	0	0	0	1	0	0	0	14349	1812	63	4	224	4	SIGLEC6	19	52031044	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	7140369	52031044	7097939	284	27383										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54395020	54395020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcccagaccctcggaacctgAcgaaacagaagacccgaacg	9	15	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr19:54395020A>G	ENST00000263431.3	+	6	904	c.622A>G	c.(622-624)Acg>Gcg	p.T208A	PRKCG_ENST00000542049.1_Missense_Mutation_p.T95A|PRKCG_ENST00000536044.1_Missense_Mutation_p.T208A|PRKCG_ENST00000540413.1_Missense_Mutation_p.T208A	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	208	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TCGGAACCTGACGAAACAGAA	0.527																																																0			19											142	116	125					19																	54395020		2203	4300	6503	59086832	SO:0001583	missense	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.622A>G	19.37:g.54395020A>G	ENSP00000263431:p.Thr208Ala		59086832	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392993	0.62066	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.25	5.25	0.73442	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.56187	0.1968	L	0.38838	1.175	0.45035	D	0.998055	B;B;B;B;B	0.18013	0.025;0.004;0.003;0.002;0.0	B;B;B;B;B	0.24701	0.055;0.027;0.014;0.007;0.006	T	0.51172	-0.8739	9	0.16420	T	0.52	.	13.4075	0.60922	1.0:0.0:0.0:0.0	.	95;208;208;208;208	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	A	208;208;208;95	ENSP00000440541:T208A;ENSP00000443493:T208A;ENSP00000263431:T208A;ENSP00000438090:T95A	ENSP00000263431:T208A	T	+	1	0	PRKCG	59086832	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.608000	0.67654	2.124000	0.65301	0.459000	0.35465	ACG		0.527	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		G	54395020	A	G	54395020	3	3	103	1	0	0	0	0	1	0	0	0	12546	275	10	4	644	4	PRKCG	19	54395020	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	2363976	54395020	4733963	285	27384										
PAK7	57144	hgsc.bcm.edu	37	chr20	9525073	9525073	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gccatccagtagggagtgccAaccaatgatttcctcttcgg	10	12	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:9525073A>G	ENST00000378429.3	-	9	2358	c.1812T>C	c.(1810-1812)gtT>gtC	p.V604V	PAK7_ENST00000378423.1_Silent_p.V604V|PAK7_ENST00000353224.5_Silent_p.V604V	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			AGGGAGTGCCAACCAATGATT	0.488																																																0			20											121	112	115					20																	9525073		2203	4300	6503	9473073	SO:0001819	synonymous_variant	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1812T>C	20.37:g.9525073A>G			9473073	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	37	CCDS13107.1																																																																																				0.488	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9525073	A	G	9525073	2	3	103	1	0	0	0	0	0	0	0	1	11436	117	5	4		4	PAK7	20	9525073	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10		9525073	53500447	286	27385										
RBL1	5933	hgsc.bcm.edu	37	chr20	35635839	35635839	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ggtcctgattcgccaagtcgTatttcagtgcaaatgacttc	9	10	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:35635839T>C	ENST00000373664.3	-	20	2912	c.2846A>G	c.(2845-2847)tAc>tGc	p.Y949C	RBL1_ENST00000344359.3_Missense_Mutation_p.Y949C	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	949	Domain B.|Pocket; binds T and E1A.				chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				CGCCAAGTCGTATTTCAGTGC	0.333																																																0			20											141	136	138					20																	35635839		2203	4300	6503	35069253	SO:0001583	missense	5933			L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.2846A>G	20.37:g.35635839T>C	ENSP00000362768:p.Tyr949Cys		35069253	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	37	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861774	0.71949	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	T;T	0.59083	0.29;0.29	5.29	5.29	0.74685	Cyclin-like (2);	0.128199	0.53938	D	0.000042	T	0.75759	0.3893	M	0.81341	2.54	0.58432	D	0.999997	D;D	0.89917	1.0;0.998	D;D	0.70935	0.971;0.91	T	0.79082	-0.1949	10	0.62326	D	0.03	-11.5325	13.9334	0.64010	0.0:0.0:0.0:1.0	.	949;949	P28749-2;P28749	.;RBL1_HUMAN	C	949	ENSP00000362768:Y949C;ENSP00000343646:Y949C	ENSP00000343646:Y949C	Y	-	2	0	RBL1	35069253	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.111000	0.71541	2.220000	0.72140	0.477000	0.44152	TAC		0.333	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		C	35635839	T	C	35635839	3	2	103	1	0	0	0	0	1	0	0	0	13146	1638	57	4	381	4	RBL1	20	35635839	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	26110766	35635839	27389681	287	27386										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41100965	41100965	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ttcggccctcggggttagacAgcaagagtcgcagccggatg	15	11	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:41100965A>T	ENST00000373187.1	-	8	1390	c.1391T>A	c.(1390-1392)cTg>cAg	p.L464Q	PTPRT_ENST00000373201.1_Missense_Mutation_p.L464Q|PTPRT_ENST00000356100.2_Missense_Mutation_p.L464Q|PTPRT_ENST00000373198.4_Missense_Mutation_p.L464Q|PTPRT_ENST00000373193.3_Missense_Mutation_p.L464Q|PTPRT_ENST00000373190.1_Missense_Mutation_p.L464Q|PTPRT_ENST00000373184.1_Missense_Mutation_p.L464Q			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	464	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GGGGTTAGACAGCAAGAGTCG	0.607																																																0			20											56	61	59					20																	41100965		2130	4239	6369	40534379	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1391T>A	20.37:g.41100965A>T	ENSP00000362283:p.Leu464Gln		40534379	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.584525	0.86748	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.28	5.28	0.74379	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.73133	0.3548	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.77482	-0.2571	10	0.87932	D	0	.	15.1951	0.73081	1.0:0.0:0.0:0.0	.	464;464	O14522-1;O14522	.;PTPRT_HUMAN	Q	464	ENSP00000362286:L464Q;ENSP00000362283:L464Q;ENSP00000362289:L464Q;ENSP00000348408:L464Q;ENSP00000362294:L464Q;ENSP00000362280:L464Q;ENSP00000362297:L464Q	ENSP00000348408:L464Q	L	-	2	0	PTPRT	40534379	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.136000	0.94489	2.005000	0.58758	0.374000	0.22700	CTG		0.607	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	41100965	A	T	41100965	3	4	103	1	0	0	0	0	1	0	0	0	12849	188	7	5	3091	5	PTPRT	20	41100965	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	5465126	41100965	21924555	288	27387										
GDAP1L1	78997	hgsc.bcm.edu	37	chr20	42887122	42887122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gggcagcctgcagcacgcacGggtgctgcagtaccgggagc	17	13	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:42887122G>A	ENST00000342560.5	+	3	510	c.422G>A	c.(421-423)cGg>cAg	p.R141Q	GDAP1L1_ENST00000537864.1_Intron|GDAP1L1_ENST00000372952.3_3'UTR	NM_001256737.1|NM_024034.4	NP_001243666.1|NP_076939.3	Q96MZ0	GD1L1_HUMAN	ganglioside induced differentiation associated protein 1-like 1	141			R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.							endometrium(1)|large_intestine(5)|lung(10)|pancreas(1)|prostate(1)	18		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CAGCACGCACGGGTGCTGCAG	0.692																																																0			20											24	18	20					20																	42887122		2172	4257	6429	42320536	SO:0001583	missense	78997				CCDS13328.1, CCDS74725.1, CCDS74726.1, CCDS74727.1	20q12	2012-02-09	2012-02-09		ENSG00000124194	ENSG00000124194			4213	protein-coding gene	gene with protein product							Standard	NM_024034		Approved		uc010zwl.3	Q96MZ0	OTTHUMG00000032530	ENST00000342560.5:c.422G>A	20.37:g.42887122G>A	ENSP00000341782:p.Arg141Gln		42320536	B7Z621|Q5TE60|Q68CW7|Q9BQJ7|Q9BQV4|Q9BWJ4|Q9H3Y2|Q9H4G5	Missense_Mutation	SNP	ENST00000342560.5	37	CCDS13328.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.669397	0.88348	.	.	ENSG00000124194	ENST00000342560	D	0.99113	-5.44	5.41	5.41	0.78517	.	0.056581	0.64402	D	0.000002	D	0.99118	0.9696	M	0.70275	2.135	0.80722	D	1	D;P;D	0.76494	0.997;0.929;0.999	P;B;D	0.72625	0.784;0.398;0.978	D	0.99863	1.1085	10	0.30078	T	0.28	.	19.1922	0.93671	0.0:0.0:1.0:0.0	.	160;141;87	B7Z621;Q96MZ0;Q5JY50	.;GD1L1_HUMAN;.	Q	141	ENSP00000341782:R141Q	ENSP00000341782:R141Q	R	+	2	0	GDAP1L1	42320536	1.000000	0.71417	0.993000	0.49108	0.376000	0.30014	9.385000	0.97223	2.542000	0.85734	0.505000	0.49811	CGG		0.692	GDAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079356.1	NM_024034		A	42887122	G	A	42887122	3	1	103	1	0	0	0	0	1	0	0	0	6328	1116	39	1	432	1	GDAP1L1	20	42887122	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1786157	42887122	20138398	289	27388										
SPINT4	391253	hgsc.bcm.edu	37	chr20	44351098	44351098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggtgttaataaaattgcggAgaagatatgtggagacctca	12	4	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:44351098A>G	ENST00000279058.3	+	1	109	c.92A>G	c.(91-93)gAg>gGg	p.E31G		NM_178455.1	NP_848550.1	Q6UDR6	SPIT4_HUMAN	serine peptidase inhibitor, Kunitz type 4	31						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(6)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.028)				AAAATTGCGGAGAAGATATGT	0.393																																																0			20											143	135	137					20																	44351098		2203	4300	6503	43784512	SO:0001583	missense	391253			AY372174	CCDS33477.1	20q13.12	2012-08-20	2005-10-18	2005-10-25	ENSG00000149651	ENSG00000149651			16130	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 137", "serine peptidase inhibitor, Kunitz type 4"	C20orf137		21988899	Standard	NM_178455		Approved	dJ601O1.1	uc002xpe.1	Q6UDR6	OTTHUMG00000130153	ENST00000279058.3:c.92A>G	20.37:g.44351098A>G	ENSP00000279058:p.Glu31Gly		43784512	Q9BQN3	Missense_Mutation	SNP	ENST00000279058.3	37	CCDS33477.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.390010	0.25118	.	.	ENSG00000149651	ENST00000279058	T	0.57107	0.42	3.97	2.85	0.33270	.	1.069190	0.07336	N	0.879966	T	0.38214	0.1032	.	.	.	0.09310	N	1	P	0.35011	0.48	B	0.22386	0.039	T	0.28744	-1.0034	9	0.66056	D	0.02	-0.2417	7.6938	0.28583	0.7865:0.2135:0.0:0.0	.	31	Q6UDR6	SPIT4_HUMAN	G	31	ENSP00000279058:E31G	ENSP00000279058:E31G	E	+	2	0	SPINT4	43784512	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	0.955000	0.29188	0.836000	0.34901	0.528000	0.53228	GAG		0.393	SPINT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252463.2	XM_372869		G	44351098	A	G	44351098	3	3	103	1	0	0	0	0	1	0	0	0	15109	304	11	4	94	4	SPINT4	20	44351098	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1463976	44351098	18674422	290	27389										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44664478	44664478	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctgcagaacatctttggcgtCatcctcttcctgcggctcac	8	15	4	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:44664478C>T	ENST00000454036.2	+	4	460	c.411C>T	c.(409-411)gtC>gtT	p.V137V	SLC12A5_ENST00000372315.1_Silent_p.V114V|SLC12A5_ENST00000243964.3_Silent_p.V114V|SLC12A5_ENST00000608944.1_Silent_p.V63V	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	137					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCTTTGGCGTCATCCTCTTCC	0.602																																																0			20											186	129	148					20																	44664478		2203	4300	6503	44097885	SO:0001819	synonymous_variant	57468			AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.411C>T	20.37:g.44664478C>T			44097885	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																				0.602	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			T	44664478	C	T	44664478	2	4	103	1	0	0	0	0	0	0	0	1	14423	813	29	3		3	SLC12A5	20	44664478	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	313380	44664478	18361042	291	27390										
PREX1	57580	hgsc.bcm.edu	37	chr20	47305235	47305235	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gacagtgctcagctttctccGgcggtccttgatgaggttca	12	11	3	2	rs568035687		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:47305235G>T	ENST00000371941.3	-	10	1316	c.1294C>A	c.(1294-1296)Cgg>Agg	p.R432R	PREX1_ENST00000396220.1_Silent_p.R432R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	432	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGCTTTCTCCGGCGGTCCTTG	0.567																																																0			20											169	120	137					20																	47305235		2203	4300	6503	46738642	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1294C>A	20.37:g.47305235G>T			46738642	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																				0.567	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47305235	G	T	47305235	2	4	103	1	0	0	0	0	0	0	0	1	12510	1115	39	2		2	PREX1	20	47305235	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2640757	47305235	15720285	292	27391										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49225051	49225051	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcacccacagccagcgagccCaggccccgcaactccgtcac	9	21	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:49225051C>T	ENST00000327979.2	-	11	1230	c.819G>A	c.(817-819)ctG>ctA	p.L273L	FAM65C_ENST00000535356.1_Silent_p.L277L|FAM65C_ENST00000045083.2_Silent_p.L273L			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	273										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCAGCGAGCCCAGGCCCCGCA	0.682																																																0			20											77	77	77					20																	49225051		2203	4300	6503	48658458	SO:0001819	synonymous_variant	140876			AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.819G>A	20.37:g.49225051C>T			48658458	Q5QPB6|Q9NQQ2	Silent	SNP	ENST00000327979.2	37	CCDS13431.2																																																																																				0.682	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			T	49225051	C	T	49225051	2	4	103	1	0	0	0	0	0	0	0	1	5620	581	21	3		3	FAM65C	20	49225051	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1919816	49225051	13800469	293	27392										
SS18L1	26039	hgsc.bcm.edu	37	chr20	60740531	60740531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	acacggagcagagctacgacCggtccttcgaggagtccacg	13	13	0	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:60740531C>T	ENST00000331758.3	+	8	903	c.877C>T	c.(877-879)Cgg>Tgg	p.R293W	SS18L1_ENST00000370848.4_Missense_Mutation_p.R296W|SS18L1_ENST00000421564.1_Missense_Mutation_p.R293W	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	293	Gln-rich.|MFD domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)		p.R293W(1)	SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GAGCTACGACCGGTCCTTCGA	0.617			T	SSX1	synovial sarcoma																																		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	1	Substitution - Missense(1)	ovary(1)	20											78	58	64					20																	60740531		2203	4300	6503	60173926	SO:0001583	missense	26039			AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.877C>T	20.37:g.60740531C>T	ENSP00000333012:p.Arg293Trp		60173926	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Missense_Mutation	SNP	ENST00000331758.3	37	CCDS13491.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653949	0.47362	.	.	ENSG00000184402	ENST00000421564;ENST00000331758;ENST00000370848	T;T;T	0.37915	1.17;1.17;1.2	5.09	1.56	0.23342	.	0.053577	0.64402	D	0.000002	T	0.55386	0.1917	L	0.59436	1.845	0.35417	D	0.792929	D;D	0.89917	1.0;1.0	D;D	0.87578	0.965;0.998	T	0.70029	-0.4984	10	0.87932	D	0	-51.9805	16.4383	0.83889	0.4049:0.5951:0.0:0.0	.	293;293	B4DSR7;O75177	.;CREST_HUMAN	W	293;293;296	ENSP00000393999:R293W;ENSP00000333012:R293W;ENSP00000359885:R296W	ENSP00000333012:R293W	R	+	1	2	SS18L1	60173926	0.992000	0.36948	0.932000	0.37286	0.186000	0.23388	1.432000	0.34936	0.514000	0.28300	0.313000	0.20887	CGG		0.617	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			T	60740531	C	T	60740531	3	4	103	1	0	0	0	0	1	0	0	0	15215	643	23	1	907	1	SS18L1	20	60740531	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	11515480	60740531	2284989	294	27393										
OSBPL2	9885	hgsc.bcm.edu	37	chr20	60859123	60859123	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaaagaagctctttatgatCtatggcaaatggacggaatg	10	5	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:60859123C>T	ENST00000313733.3	+	10	1096	c.894C>T	c.(892-894)atC>atT	p.I298I	OSBPL2_ENST00000358053.2_Silent_p.I286I|OSBPL2_ENST00000439951.2_Silent_p.I206I	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2	298					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.I298I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			TCTTTATGATCTATGGCAAAT	0.408																																																1	Substitution - coding silent(1)	central_nervous_system(1)	20											96	90	92					20																	60859123		2203	4300	6503	60292518	SO:0001819	synonymous_variant	9885			AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"Oxysterol binding proteins"	15761	protein-coding gene	gene with protein product		606731	"oxysterol-binding protein-like 2"			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.894C>T	20.37:g.60859123C>T			60292518	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Silent	SNP	ENST00000313733.3	37	CCDS13495.1																																																																																				0.408	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835		T	60859123	C	T	60859123	2	4	103	1	0	0	0	0	0	0	0	1	11309	903	32	3		3	OSBPL2	20	60859123	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	118592	60859123	2166397	295	27394										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61527957	61527957	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttggctgcgatggtgcagcActcatagccccaaggcgtcc	12	13	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:61527957A>G	ENST00000266070.4	-	7	2305	c.1980T>C	c.(1978-1980)agT>agC	p.S660S	DIDO1_ENST00000395343.1_Silent_p.S660S|DIDO1_ENST00000395340.1_Silent_p.S660S|DIDO1_ENST00000395335.2_Silent_p.S660S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	660					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ATGGTGCAGCACTCATAGCCC	0.522																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0			20											91	104	99					20																	61527957		2203	4300	6503	60998402	SO:0001819	synonymous_variant	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1980T>C	20.37:g.61527957A>G			60998402	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																				0.522	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		G	61527957	A	G	61527957	2	3	103	1	0	0	0	0	0	0	0	1	4533	156	6	4		4	DIDO1	20	61527957	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	668834	61527957	1497563	296	27395										
C20orf195	79025	hgsc.bcm.edu	37	chr20	62187859	62187859	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cccaaccgatcctataagttCaccatcaagagggccgagac	8	14	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr20:62187859C>A	ENST00000370098.3	+	2	935	c.843C>A	c.(841-843)ttC>ttA	p.F281L	C20orf195_ENST00000370097.1_Missense_Mutation_p.F281L	NM_024059.2	NP_076964.1	Q9BVV2	CT195_HUMAN	chromosome 20 open reading frame 195	281	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular vesicular exosome (GO:0070062)				large_intestine(3)|lung(4)	7	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CCTATAAGTTCACCATCAAGA	0.662																																																0			20											98	103	101					20																	62187859		2203	4299	6502	61658303	SO:0001583	missense	79025				CCDS13526.1	20q13.33	2014-02-12			ENSG00000125531	ENSG00000125531			28764	protein-coding gene	gene with protein product						12477932	Standard	NM_024059		Approved	MGC5356	uc002yfj.3	Q9BVV2	OTTHUMG00000032980	ENST00000370098.3:c.843C>A	20.37:g.62187859C>A	ENSP00000359116:p.Phe281Leu		61658303		Missense_Mutation	SNP	ENST00000370098.3	37	CCDS13526.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368487	0.82463	.	.	ENSG00000125531	ENST00000370098;ENST00000370097	.	.	.	5.53	4.6	0.57074	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000028	T	0.65575	0.2704	L	0.29908	0.895	0.37785	D	0.927165	D	0.76494	0.999	D	0.83275	0.996	T	0.72659	-0.4226	9	0.87932	D	0	-26.5899	14.328	0.66532	0.0:0.9283:0.0:0.0717	.	281	Q9BVV2	CT195_HUMAN	L	281	.	ENSP00000359115:F281L	F	+	3	2	C20orf195	61658303	0.999000	0.42202	1.000000	0.80357	0.950000	0.60333	2.025000	0.41059	1.355000	0.45865	-0.136000	0.14681	TTC		0.662	C20orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080155.1	NM_024059		A	62187859	C	A	62187859	3	1	103	1	0	0	0	0	1	0	0	0	2106	825	29	2	845	2	C20orf195	20	62187859	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	659902	62187859	837661	297	27396										
USP25	29761	hgsc.bcm.edu	37	chr21	17250151	17250151	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccgcagaactcttcgaatctGgagaggatcgagaagtaaac	11	9	2	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr21:17250151G>T	ENST00000285679.6	+	23	3205	c.2836G>T	c.(2836-2838)Gga>Tga	p.G946*	USP25_ENST00000285681.2_Nonsense_Mutation_p.G978*|USP25_ENST00000400183.2_Nonsense_Mutation_p.G1016*|USP25_ENST00000351097.5_Nonsense_Mutation_p.G341*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	946					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.G946R(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				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)		CTTCGAATCTGGAGAGGATCG	0.328																																																1	Substitution - Missense(1)	ovary(1)	21											91	93	92					21																	17250151		2203	4300	6503	16172022	SO:0001587	stop_gained	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2836G>T	21.37:g.17250151G>T	ENSP00000285679:p.Gly946*		16172022	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	G	44	10.614539	0.99438	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.1605	0.93529	0.0:0.0:1.0:0.0	.	.	.	.	X	978;946;341;1016	.	ENSP00000285679:G946X	G	+	1	0	USP25	16172022	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.412000	0.97347	2.641000	0.89580	0.585000	0.79938	GGA		0.328	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17250151	G	T	17250151	4	4	103	1	0	0	0	0	0	1	0	0	17096	1349	47	2	2926	2	USP25	21	17250151	Nonsense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		17250151	30879744	298	27397										
SON	6651	hgsc.bcm.edu	37	chr21	34925259	34925259	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atcagatccctcagttttagTatcagaggctgctgtgactg	10	9	3	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr21:34925259T>C	ENST00000356577.4	+	3	4197	c.3722T>C	c.(3721-3723)gTa>gCa	p.V1241A	SON_ENST00000381679.4_Missense_Mutation_p.V1241A|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Missense_Mutation_p.V1241A|SON_ENST00000300278.4_Missense_Mutation_p.V1241A	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1241					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TCAGTTTTAGTATCAGAGGCT	0.473																																																0			21											141	148	145					21																	34925259		2203	4300	6503	33847129	SO:0001583	missense	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.3722T>C	21.37:g.34925259T>C	ENSP00000348984:p.Val1241Ala		33847129	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.368|0.368	-0.935563|-0.935563	0.02340|0.02340	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679|ENST00000436227	T;T;T;T|.	0.10860|.	3.03;3.02;3.01;2.83|.	5.54|5.54	1.46|1.46	0.22682|0.22682	.|.	0.729009|.	0.12327|.	N|.	0.478733|.	T|T	0.18299|0.18299	0.0439|0.0439	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.06786|.	0.001;0.001;0.0;0.001;0.001|.	B;B;B;B;B|.	0.06405|.	0.002;0.001;0.001;0.002;0.002|.	T|T	0.24476|0.24476	-1.0159|-1.0159	10|5	0.02654|.	T|.	1|.	.|.	4.1841|4.1841	0.10390|0.10390	0.1549:0.4071:0.0:0.438|0.1549:0.4071:0.0:0.438	.|.	1241;1241;922;1241;1241|.	P18583-10;P18583;P18583-2;P18583-3;P18583-6|.	.;SON_HUMAN;.;.;.|.	A|H	1241|236	ENSP00000348984:V1241A;ENSP00000290239:V1241A;ENSP00000300278:V1241A;ENSP00000371095:V1241A|.	ENSP00000290239:V1241A|.	V|Y	+|+	2|1	0|0	SON|SON	33847129|33847129	0.154000|0.154000	0.22792|0.22792	0.758000|0.758000	0.31321|0.31321	0.740000|0.740000	0.42216|0.42216	-0.428000|-0.428000	0.06991|0.06991	-0.013000|-0.013000	0.14199|0.14199	-0.468000|-0.468000	0.05107|0.05107	GTA|TAT		0.473	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34925259	T	C	34925259	3	2	103	1	0	0	0	0	1	0	0	0	14963	1638	57	4	3732	4	SON	21	34925259	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	17675108	34925259	13204636	299	27398										
KLHL22	84861	hgsc.bcm.edu	37	chr22	20843447	20843447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gttcacgcagtgtgggtgtgAgggctgtgcaggcaacttgc	17	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:20843447A>G	ENST00000328879.4	-	2	208	c.52T>C	c.(52-54)Tca>Cca	p.S18P	KLHL22_ENST00000470335.1_5'UTR|KLHL22_ENST00000440659.2_5'UTR	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	18					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	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)			TGTGGGTGTGAGGGCTGTGCA	0.597																																																0			22											146	117	127					22																	20843447		2203	4300	6503	19173447	SO:0001583	missense	84861				CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.52T>C	22.37:g.20843447A>G	ENSP00000331682:p.Ser18Pro		19173447	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Missense_Mutation	SNP	ENST00000328879.4	37	CCDS13780.1	.	.	.	.	.	.	.	.	.	.	a	11.57	1.677315	0.29783	.	.	ENSG00000099910	ENST00000328879;ENST00000444967;ENST00000458248;ENST00000443285;ENST00000431430;ENST00000423364	T;T;T;T;D	0.85258	-0.9;-0.59;-0.51;-0.56;-1.96	4.88	-0.477	0.12097	.	0.804957	0.11543	N	0.553590	T	0.63248	0.2495	N	0.08118	0	0.19575	N	0.999969	B	0.02656	0.0	B	0.01281	0.0	T	0.48625	-0.9019	10	0.22109	T	0.4	.	1.9928	0.03450	0.4783:0.276:0.0929:0.1529	.	18	Q53GT1	KLH22_HUMAN	P	18;50;18;52;18;50	ENSP00000331682:S18P;ENSP00000403999:S50P;ENSP00000398616:S18P;ENSP00000397882:S52P;ENSP00000409092:S18P	ENSP00000331682:S18P	S	-	1	0	KLHL22	19173447	0.918000	0.31147	0.917000	0.36280	0.887000	0.51463	0.241000	0.18065	0.180000	0.19960	0.449000	0.29647	TCA		0.597	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		G	20843447	A	G	20843447	3	3	103	1	0	0	0	0	1	0	0	0	8398	304	11	4	1876	4	KLHL22	22	20843447	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10		20843447	30461119	300	27399										
YWHAH	7533	hgsc.bcm.edu	37	chr22	32352207	32352207	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agaatgtggttggtgccaggCgatcttcctggagggtcatt	15	7	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:32352207C>T	ENST00000248975.5	+	2	442	c.169C>T	c.(169-171)Cga>Tga	p.R57*	snoU13_ENST00000459049.1_RNA|YWHAH_ENST00000397492.1_3'UTR|YWHAH_ENST00000471374.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	57		Interaction with phosphoserine on interacting protein.			apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)	p.R57*(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						TGGTGCCAGGCGATCTTCCTG	0.458																																					Ovarian(98;460 2060 9263 44007)											1	Substitution - Nonsense(1)	central_nervous_system(1)	22											94	86	89					22																	32352207		2203	4300	6503	30682207	SO:0001587	stop_gained	7533			X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.169C>T	22.37:g.32352207C>T	ENSP00000248975:p.Arg57*		30682207		Nonsense_Mutation	SNP	ENST00000248975.5	37	CCDS13901.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422997	0.62733	.	.	ENSG00000128245	ENST00000248975;ENST00000420430	.	.	.	5.95	4.94	0.65067	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4622	13.8121	0.63270	0.0:0.9277:0.0:0.0723	.	.	.	.	X	57;44	.	ENSP00000248975:R57X	R	+	1	2	YWHAH	30682207	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.630000	0.83225	1.527000	0.49086	0.655000	0.94253	CGA		0.458	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		T	32352207	C	T	32352207	4	4	103	1	0	0	0	0	0	1	0	0	17544	760	27	1	175	1	YWHAH	22	32352207	Nonsense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	11508760	32352207	18952359	301	27400										
APOBEC3H	164668	hgsc.bcm.edu	37	chr22	39497388	39497388	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gttgacttcatcaaggctcaCgaccatctgaacctgggcat	9	12	4	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:39497388C>T	ENST00000401756.1	+	3	373	c.297C>T	c.(295-297)caC>caT	p.H99H	APOBEC3H_ENST00000348946.4_Silent_p.H99H|APOBEC3H_ENST00000442487.3_Silent_p.H99H|APOBEC3H_ENST00000421988.2_Silent_p.H99H	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	99					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)	p.H99H(1)		central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					TCAAGGCTCACGACCATCTGA	0.612																																																1	Substitution - coding silent(1)	ovary(1)	22											115	81	93					22																	39497388		2203	4300	6503	37827334	SO:0001819	synonymous_variant	164668			BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"Apolipoprotein B mRNA editing enzymes"	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.297C>T	22.37:g.39497388C>T			37827334	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Silent	SNP	ENST00000401756.1	37	CCDS54530.1																																																																																				0.612	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773		T	39497388	C	T	39497388	2	4	103	1	0	0	0	0	0	0	0	1	795	535	19	1		1	APOBEC3H	22	39497388	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	7145181	39497388	11807178	302	27401										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	39966975	39966975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cagcccccggaactggtgcaTcaagatggtgtgcaacccat	11	13	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:39966975T>C	ENST00000402142.3	+	1	218	c.218T>C	c.(217-219)aTc>aCc	p.I73T	CACNA1I_ENST00000407673.1_Missense_Mutation_p.I73T|CACNA1I_ENST00000401624.1_Missense_Mutation_p.I73T|CACNA1I_ENST00000400164.3_Missense_Mutation_p.I73T|CACNA1I_ENST00000404898.1_Missense_Mutation_p.I73T|CACNA1I_ENST00000336649.4_Missense_Mutation_p.I73T	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	73					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	AACTGGTGCATCAAGATGGTG	0.627																																																0			22											73	79	77					22																	39966975		2096	4205	6301	38296921	SO:0001583	missense	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.218T>C	22.37:g.39966975T>C	ENSP00000385019:p.Ile73Thr		38296921	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.052127	0.55218	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97404	-4.37;-4.33;-4.36;-4.33;-4.31;-4.22	5.27	5.27	0.74061	.	4.175510	0.01876	N	0.037522	D	0.96037	0.8709	N	0.19112	0.55	0.52501	D	0.999956	P;P	0.51933	0.949;0.915	P;B	0.49085	0.6;0.395	D	0.86292	0.1674	10	0.39692	T	0.17	.	15.4677	0.75416	0.0:0.0:0.0:1.0	.	73;73	Q9P0X4-4;Q9P0X4	.;CAC1I_HUMAN	T	73	ENSP00000385019:I73T;ENSP00000384093:I73T;ENSP00000383887:I73T;ENSP00000385680:I73T;ENSP00000337829:I73T;ENSP00000383028:I73T	ENSP00000337829:I73T	I	+	2	0	CACNA1I	38296921	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.436000	0.80404	2.127000	0.65507	0.459000	0.35465	ATC		0.627	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		C	39966975	T	C	39966975	3	2	103	1	0	0	0	0	1	0	0	0	2552	1435	50	4	220	4	CACNA1I	22	39966975	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	469587	39966975	11337591	303	27402										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40054286	40054286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gtaacccctacaacatcttcGacagcatcattgtcatcatc	4	14	4	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:40054286G>A	ENST00000402142.3	+	11	2122	c.2122G>A	c.(2122-2124)Gac>Aac	p.D708N	CACNA1I_ENST00000407673.1_Missense_Mutation_p.D673N|CACNA1I_ENST00000401624.1_Missense_Mutation_p.D708N|CACNA1I_ENST00000400164.3_Missense_Mutation_p.D673N|CACNA1I_ENST00000404898.1_Missense_Mutation_p.D673N|CACNA1I_ENST00000336649.4_Missense_Mutation_p.D714N	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	708					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CAACATCTTCGACAGCATCAT	0.542																																																0			22											118	117	117					22																	40054286		2059	4206	6265	38384232	SO:0001583	missense	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2122G>A	22.37:g.40054286G>A	ENSP00000385019:p.Asp708Asn		38384232	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	G	32	5.162891	0.94727	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.99376	-5.79;-5.79;-5.79;-5.79;-5.79;-5.79	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99718	0.9891	H	0.98901	4.365	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.97108	0.9802	10	0.87932	D	0	.	18.1056	0.89519	0.0:0.0:1.0:0.0	.	673;708;673;708	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	N	708;673;708;673;714;673	ENSP00000385019:D708N;ENSP00000384093:D673N;ENSP00000383887:D708N;ENSP00000385680:D673N;ENSP00000337829:D714N;ENSP00000383028:D673N	ENSP00000337829:D714N	D	+	1	0	CACNA1I	38384232	1.000000	0.71417	0.966000	0.40874	0.721000	0.41392	9.754000	0.98908	2.579000	0.87056	0.655000	0.94253	GAC		0.542	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40054286	G	A	40054286	3	1	103	1	0	0	0	0	1	0	0	0	2552	1058	37	1	2164	1	CACNA1I	22	40054286	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	87311	40054286	11250280	304	27403										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46772969	46772969	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tggccataccgggttttccgTctggttgatcccaatcacga	10	12	2	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:46772969T>A	ENST00000262738.3	-	24	7572	c.7573A>T	c.(7573-7575)Acg>Tcg	p.T2525S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2525					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GGGTTTTCCGTCTGGTTGATC	0.617																																																0			22											57	46	49					22																	46772969		2203	4300	6503	45151633	SO:0001583	missense	9620			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7573A>T	22.37:g.46772969T>A	ENSP00000262738:p.Thr2525Ser		45151633	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.326221	0.60743	.	.	ENSG00000075275	ENST00000262738	T	0.46451	0.87	4.67	4.67	0.58626	GPCR, family 2-like (1);	0.000000	0.64402	U	0.000002	T	0.65502	0.2697	M	0.86573	2.825	0.80722	D	1	D;D	0.60575	0.988;0.962	D;P	0.64506	0.926;0.842	T	0.69851	-0.5033	10	0.42905	T	0.14	.	13.1435	0.59448	0.0:0.0:0.0:1.0	.	846;2525	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	S	2525	ENSP00000262738:T2525S	ENSP00000262738:T2525S	T	-	1	0	CELSR1	45151633	1.000000	0.71417	0.928000	0.36995	0.193000	0.23685	3.647000	0.54403	1.752000	0.51891	0.397000	0.26171	ACG		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46772969	T	A	46772969	3	1	103	1	0	0	0	0	1	0	0	0	3227	1667	58	5	1519	5	CELSR1	22	46772969	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	6718683	46772969	4531597	305	27404										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50656444	50656444	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccccgcgggcccccagggggCccccaggcctgggagatgag	17	17	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:50656444C>A	ENST00000248846.5	-	24	5375	c.5271G>T	c.(5269-5271)ggG>ggT	p.G1757G	TUBGCP6_ENST00000439308.2_3'UTR|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1757					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		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)		CCCCAGGGGGCCCCCAGGCCT	0.612																																																0			22											27	38	34					22																	50656444		2164	4220	6384	48998571	SO:0001819	synonymous_variant	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.5271G>T	22.37:g.50656444C>A			48998571	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																				0.612	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		A	50656444	C	A	50656444	2	1	103	1	0	0	0	0	0	0	0	1	16810	726	26	2		2	TUBGCP6	22	50656444	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	3883475	50656444	648122	306	27405										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50714223	50714223	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgggcggcaggatcctcctcCaaggcattgatgatctgagg	14	10	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chr22:50714223C>G	ENST00000449103.1	-	37	5567	c.5427G>C	c.(5425-5427)ttG>ttC	p.L1809F	PLXNB2_ENST00000359337.4_Missense_Mutation_p.L1809F|AL022328.1_ENST00000595015.1_Missense_Mutation_p.Q41E			O15031	PLXB2_HUMAN	plexin B2	1809					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-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)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GATCCTCCTCCAAGGCATTGA	0.647											OREG0026679	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			22											43	49	47					22																	50714223		2125	4263	6388	49056350	SO:0001583	missense	23654				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.5427G>C	22.37:g.50714223C>G	ENSP00000409171:p.Leu1809Phe	971	49056350	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.445964	0.63178	.	.	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.16073	2.37;2.37	4.17	0.834	0.18880	.	0.000000	0.52532	D	0.000066	T	0.39279	0.1072	M	0.89478	3.035	0.50313	D	0.999869	D	0.89917	1.0	D	0.74348	0.983	T	0.19321	-1.0309	10	0.87932	D	0	.	4.928	0.13903	0.1506:0.5157:0.0:0.3337	.	1809	O15031	PLXB2_HUMAN	F	1809	ENSP00000409171:L1809F;ENSP00000352288:L1809F	ENSP00000352288:L1809F	L	-	3	2	PLXNB2	49056350	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	1.174000	0.31932	0.423000	0.26033	0.462000	0.41574	TTG		0.647	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		G	50714223	C	G	50714223	3	3	103	1	0	0	0	0	1	0	0	0	12155	593	21	5	93	5	PLXNB2	22	50714223	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	57779	50714223	590343	307	27406										
TLR8	51311	hgsc.bcm.edu	37	chrX	12940021	12940021	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaaaatatgcaaaaagctgGaactttaaaacagcttttta	5	5	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:12940021G>C	ENST00000218032.6	+	2	2949	c.2862G>C	c.(2860-2862)tgG>tgC	p.W954C	TLR8_ENST00000311912.5_Missense_Mutation_p.W972C	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	954	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAAAAAGCTGGAACTTTAAAA	0.398																																																0			X											65	63	64					X																	12940021		2203	4299	6502	12849942	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2862G>C	X.37:g.12940021G>C	ENSP00000218032:p.Trp954Cys		12849942	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858209	0.32791	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.07800	3.16;3.16	5.7	5.7	0.88788	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.000000	0.38326	N	0.001729	T	0.16428	0.0395	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.01566	-1.1323	10	0.48119	T	0.1	.	8.1073	0.30894	0.0881:0.2202:0.6918:0.0	.	954;972	Q9NR97;D1CS70	TLR8_HUMAN;.	C	954;972	ENSP00000218032:W954C;ENSP00000312082:W972C	ENSP00000218032:W954C	W	+	3	0	TLR8	12849942	0.994000	0.37717	1.000000	0.80357	0.977000	0.68977	1.342000	0.33919	2.406000	0.81754	0.600000	0.82982	TGG		0.398	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12940021	G	C	12940021	3	2	103	1	0	0	0	0	1	0	0	0	15996	1183	41	5	2868	5	TLR8	23	12940021	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10		12940021	142330539	308	27407										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29938090	29938090	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cttaaggagcatcttggggaAcaggaagtttccatctcatt	10	8	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:29938090A>G	ENST00000378993.1	+	8	1609	c.936A>G	c.(934-936)gaA>gaG	p.E312E	IL1RAPL1_ENST00000302196.4_Silent_p.E312E	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	312	Ig-like C2-type 3.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						ATCTTGGGGAACAGGAAGTTT	0.378																																																0			X											211	179	190					X																	29938090		2202	4300	6502	29848011	SO:0001819	synonymous_variant	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.936A>G	X.37:g.29938090A>G			29848011	A0AVG4|Q9UJ53	Silent	SNP	ENST00000378993.1	37	CCDS14218.1																																																																																				0.378	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		G	29938090	A	G	29938090	2	3	103	1	0	0	0	0	0	0	0	1	7682	40	2	4		4	IL1RAPL1	23	29938090	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	16998069	29938090	125332470	309	27408										
DMD	1756	hgsc.bcm.edu	37	chrX	31165491	31165491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tccaggcggcctttgtgttgAcgcagtagcttggcctcagc	13	12	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:31165491A>G	ENST00000357033.4	-	75	10904	c.10698T>C	c.(10696-10698)cgT>cgC	p.R3566R	DMD_ENST00000378707.3_Silent_p.R1106R|DMD_ENST00000541735.1_Silent_p.R996R|DMD_ENST00000378677.2_Silent_p.R3562R|DMD_ENST00000378723.3_Silent_p.R498R|DMD_ENST00000343523.2_Silent_p.R996R|DMD_ENST00000361471.4_Silent_p.R485R|DMD_ENST00000378702.4_Silent_p.R498R|DMD_ENST00000359836.1_Silent_p.R1093R|DMD_ENST00000474231.1_Silent_p.R1106R|DMD_ENST00000378680.2_Silent_p.R388R	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3566					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				CTTTGTGTTGACGCAGTAGCT	0.567																																																0			X											82	68	73					X																	31165491		2202	4300	6502	31075412	SO:0001819	synonymous_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10698T>C	X.37:g.31165491A>G			31075412	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.274694	0.23307	.	.	ENSG00000198947	ENST00000465285	.	.	.	4.62	0.97	0.19692	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44817	-0.9303	4	.	.	.	.	7.5977	0.28058	0.4611:0.0:0.5388:0.0	.	.	.	.	P	1295	.	.	S	-	1	0	DMD	31075412	0.988000	0.35896	1.000000	0.80357	0.987000	0.75469	0.321000	0.19558	0.177000	0.19895	0.417000	0.27973	TCA		0.567	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31165491	A	G	31165491	2	3	103	1	0	0	0	0	0	0	0	1	4591	262	10	4		4	DMD	23	31165491	Silent	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	1227401	31165491	124105069	310	27409										
SLC35A2	7355	hgsc.bcm.edu	37	chrX	48762432	48762432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cacggcggtaccctcagcccAccagagccccaccaggccca	9	21	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:48762432A>G	ENST00000247138.5	-	4	757	c.754T>C	c.(754-756)Tgg>Cgg	p.W252R	SLC35A2_ENST00000376521.1_Missense_Mutation_p.W252R|SLC35A2_ENST00000445167.2_Intron|SLC35A2_ENST00000376529.3_Intron|SLC35A2_ENST00000452555.2_Missense_Mutation_p.W280R|SLC35A2_ENST00000413561.2_Missense_Mutation_p.W191R|SLC35A2_ENST00000376515.3_Intron	NM_005660.1	NP_005651.1	P78381	S35A2_HUMAN	solute carrier family 35 (UDP-galactose transporter), member A2	252			W -> C (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		galactose metabolic process (GO:0006012)|transmembrane transport (GO:0055085)|UDP-galactose transport (GO:0015785)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	sugar:proton symporter activity (GO:0005351)|UDP-galactose transmembrane transporter activity (GO:0005459)			breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(2)	15						CCCTCAGCCCACCAGAGCCCC	0.627																																																0			X											30	21	24					X																	48762432		2201	4297	6498	48647376	SO:0001583	missense	7355			D88146	CCDS14311.1, CCDS35247.1, CCDS43937.1, CCDS65253.1, CCDS65254.1, CCDS75973.1, CCDS75974.1, CCDS75975.1	Xp11.23-p11.22	2013-05-22			ENSG00000102100	ENSG00000102100		"Solute carriers"	11022	protein-coding gene	gene with protein product		314375	"solute carrier family 35 (UDP-galactose transporter), member 2"	UGALT		8128316	Standard	NM_001042498		Approved	UGAT, UGT, UGT1, UGT2, UGTL	uc004dlo.1	P78381	OTTHUMG00000024129	ENST00000247138.5:c.754T>C	X.37:g.48762432A>G	ENSP00000247138:p.Trp252Arg		48647376	A8K2L9|A8K9V1|B4DE11|B4DPT2|E7EW45|Q8IV21|Q92553	Missense_Mutation	SNP	ENST00000247138.5	37	CCDS14311.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.626072	0.28978	.	.	ENSG00000102100	ENST00000247138;ENST00000376521;ENST00000413561;ENST00000452555	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.86	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.34919	0.0914	L	0.41824	1.3	0.53005	D	0.999961	P;B;P;B;B	0.47302	0.691;0.331;0.893;0.165;0.349	B;B;B;B;B	0.43623	0.326;0.326;0.268;0.219;0.425	T	0.04053	-1.0981	10	0.28530	T	0.3	-5.0746	10.0341	0.42118	0.8328:0.1672:0.0:0.0	.	191;280;265;252;252	B4DE11;E7EW45;B4DE15;P78381-2;P78381	.;.;.;.;S35A2_HUMAN	R	252;252;191;280	ENSP00000247138:W252R;ENSP00000365704:W252R;ENSP00000393233:W191R;ENSP00000416002:W280R	ENSP00000247138:W252R	W	-	1	0	SLC35A2	48647376	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.114000	0.50383	0.796000	0.33947	0.486000	0.48141	TGG		0.627	SLC35A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060790.1	NM_005660		G	48762432	A	G	48762432	3	3	103	1	0	0	0	0	1	0	0	0	14608	159	6	4	600	4	SLC35A2	23	48762432	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	17596941	48762432	106508128	311	27410										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50037950	50037950	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	agaagataaacaggaacacaCatgctcttggactggccaaa	9	9	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:50037950C>A	ENST00000376042.1	+	5	590	c.292C>A	c.(292-294)Cat>Aat	p.H98N	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.H98N			Q8WWL7	CCNB3_HUMAN	cyclin B3	98					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CAGGAACACACATGCTCTTGG	0.393																																																0			X											122	104	110					X																	50037950		2203	4300	6503	50054690	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.292C>A	X.37:g.50037950C>A	ENSP00000365210:p.His98Asn		50054690	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	3.924	-0.017509	0.07681	.	.	ENSG00000147082	ENST00000376042;ENST00000396540;ENST00000276014	T;T	0.11712	2.75;2.75	2.97	-4.44	0.03557	.	10.623200	0.00166	N	0.000005	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.27606	-1.0069	9	.	.	.	.	0.3668	0.00373	0.2912:0.1988:0.2862:0.2237	.	98	Q8WWL7	CCNB3_HUMAN	N	98	ENSP00000365210:H98N;ENSP00000276014:H98N	.	H	+	1	0	CCNB3	50054690	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.198000	0.01239	-1.113000	0.02981	-1.026000	0.02426	CAT		0.393	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			A	50037950	C	A	50037950	3	1	103	1	0	0	0	0	1	0	0	0	2920	478	17	2	302	2	CCNB3	23	50037950	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	1275518	50037950	105232610	312	27411										
MAGED2	10916	hgsc.bcm.edu	37	chrX	54841194	54841194	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccagcaagatgaaagtcctcAagtttgcctgcaaggtaatt	9	9	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:54841194A>G	ENST00000375068.1	+	11	1605	c.1372A>G	c.(1372-1374)Aag>Gag	p.K458E	MAGED2_ENST00000347546.4_Missense_Mutation_p.K440E|MAGED2_ENST00000375060.1_Missense_Mutation_p.K373E|MAGED2_ENST00000218439.4_Missense_Mutation_p.K458E|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375058.1_Missense_Mutation_p.K458E|MAGED2_ENST00000375062.4_Missense_Mutation_p.K373E|MAGED2_ENST00000396224.1_Missense_Mutation_p.K458E|MAGED2_ENST00000375053.2_Missense_Mutation_p.K458E			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	458	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		K -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			membrane (GO:0016020)		p.K458Q(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						GAAAGTCCTCAAGTTTGCCTG	0.547																																																1	Substitution - Missense(1)	breast(1)	X											62	53	56					X																	54841194		2203	4300	6503	54857919	SO:0001583	missense	10916			AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated protein", "breast cancer associated gene 1", "melanoma-associated antigen D2", "hepatocellular carcinoma-associated protein HCA10"	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1372A>G	X.37:g.54841194A>G	ENSP00000364209:p.Lys458Glu		54857919	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	A	12.53	1.966120	0.34659	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.02763	4.2;4.2;4.28;4.21;4.17;4.2;4.2;4.17;4.2	4.32	4.32	0.51571	.	0.000000	0.45606	D	0.000346	T	0.01029	0.0034	N	0.02830	-0.485	0.30487	N	0.771783	P;B	0.36909	0.573;0.02	B;B	0.30716	0.119;0.056	T	0.34700	-0.9818	10	0.12766	T	0.61	.	4.3394	0.11103	0.6869:0.2024:0.1107:0.0	.	373;458	Q5H907;Q9UNF1	.;MAGD2_HUMAN	E	458;458;402;440;373;458;458;373;458	ENSP00000364209:K458E;ENSP00000364193:K458E;ENSP00000336962:K402E;ENSP00000340290:K440E;ENSP00000364202:K373E;ENSP00000218439:K458E;ENSP00000364198:K458E;ENSP00000364200:K373E;ENSP00000379526:K458E	ENSP00000218439:K458E	K	+	1	0	MAGED2	54857919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.733000	0.38156	1.676000	0.50930	0.417000	0.27973	AAG		0.547	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		G	54841194	A	G	54841194	3	3	103	1	0	0	0	0	1	0	0	0	9214	131	5	4	1410	4	MAGED2	23	54841194	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	4803244	54841194	100429366	313	27412										
FAAH2	158584	hgsc.bcm.edu	37	chrX	57358060	57358060	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	attcttctggactcatgaacCgtcgtgatgccattgccaaa	8	11	3	2	rs141132166		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:57358060C>A	ENST00000374900.4	+	4	562	c.442C>A	c.(442-444)Cgt>Agt	p.R148S		NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	148						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)	p.R148C(1)		endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						ACTCATGAACCGTCGTGATGC	0.413										HNSCC(52;0.14)																																						1	Substitution - Missense(1)	ovary(1)	X											101	83	89					X																	57358060		2203	4300	6503	57374785	SO:0001583	missense	158584			AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"amidase domain containing"	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.442C>A	X.37:g.57358060C>A	ENSP00000364035:p.Arg148Ser		57374785	Q86VT2|Q96N98	Missense_Mutation	SNP	ENST00000374900.4	37	CCDS14375.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.551159	0.27739	.	.	ENSG00000165591	ENST00000374900	T	0.63744	-0.06	2.38	1.49	0.22878	Amidase signature domain (2);	0.000000	0.64402	U	0.000001	T	0.75831	0.3903	M	0.85630	2.765	0.45995	D	0.998801	D	0.67145	0.996	D	0.74023	0.982	T	0.72503	-0.4273	10	0.56958	D	0.05	.	6.7878	0.23683	0.0:0.8359:0.0:0.1641	.	148	Q6GMR7	FAAH2_HUMAN	S	148	ENSP00000364035:R148S	ENSP00000364035:R148S	R	+	1	0	FAAH2	57374785	0.995000	0.38212	0.534000	0.28014	0.381000	0.30169	3.093000	0.50217	0.052000	0.16007	-0.322000	0.08575	CGT		0.413	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		A	57358060	C	A	57358060	3	1	103	1	0	0	0	0	1	0	0	0	5370	652	23	2	456	2	FAAH2	23	57358060	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	2516866	57358060	97912500	314	27413										
HEPH	9843	hgsc.bcm.edu	37	chrX	65427042	65427042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttggattcctctagttatgGttacattttcctgagcaaca	7	8	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:65427042G>T	ENST00000343002.2	+	13	2961	c.2297G>T	c.(2296-2298)gGt>gTt	p.G766V	HEPH_ENST00000374727.3_Missense_Mutation_p.G769V|HEPH_ENST00000519389.1_Missense_Mutation_p.G820V|HEPH_ENST00000419594.1_Missense_Mutation_p.G577V|HEPH_ENST00000336279.5_Missense_Mutation_p.G499V|HEPH_ENST00000441993.2_Missense_Mutation_p.G769V			Q9BQS7	HEPH_HUMAN	hephaestin	766	Plastocyanin-like 5.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						TCTAGTTATGGTTACATTTTC	0.448																																																0			X											117	99	105					X																	65427042		2203	4300	6503	65343767	SO:0001583	missense	9843			AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.2297G>T	X.37:g.65427042G>T	ENSP00000343939:p.Gly766Val		65343767	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	G	14.80	2.643385	0.47258	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002;ENST00000425114	D;D;D;D;D;D;D	0.98978	-5.29;-5.29;-5.29;-5.29;-5.29;-5.29;-5.29	4.95	4.95	0.65309	Cupredoxin (2);	0.314636	0.33496	N	0.004845	D	0.98960	0.9646	M	0.73430	2.235	0.58432	D	0.999993	D;D;D;D	0.71674	0.968;0.985;0.977;0.998	P;P;P;D	0.65010	0.807;0.689;0.691;0.931	D	0.98939	1.0790	10	0.54805	T	0.06	.	12.3718	0.55260	0.0:0.1667:0.8333:0.0	.	820;166;577;766	E9PHN8;B4DFV3;E7ES21;Q9BQS7	.;.;.;HEPH_HUMAN	V	820;769;499;769;577;766;723	ENSP00000430620:G820V;ENSP00000363859:G769V;ENSP00000337418:G499V;ENSP00000411687:G769V;ENSP00000413211:G577V;ENSP00000343939:G766V;ENSP00000398078:G723V	ENSP00000337418:G499V	G	+	2	0	HEPH	65343767	1.000000	0.71417	0.983000	0.44433	0.502000	0.33828	4.624000	0.61254	2.302000	0.77476	0.544000	0.68410	GGT		0.448	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65427042	G	T	65427042	3	4	103	1	0	0	0	0	1	0	0	0	7075	1261	44	2	2513	2	HEPH	23	65427042	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	8068982	65427042	89843518	315	27414										
STARD8	9754	hgsc.bcm.edu	37	chrX	67937560	67937560	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tgggccgccacctcagccggTggcagtggtgccaatactcg	14	14	1	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:67937560T>C	ENST00000252336.6	+	5	936	c.564T>C	c.(562-564)ggT>ggC	p.G188G	STARD8_ENST00000374599.3_Silent_p.G268G|STARD8_ENST00000374597.3_Silent_p.G188G	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	188			G -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						CCTCAGCCGGTGGCAGTGGTG	0.612																																																0			X											41	37	39					X																	67937560		2203	4300	6503	67854285	SO:0001819	synonymous_variant	9754			D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.564T>C	X.37:g.67937560T>C			67854285	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Silent	SNP	ENST00000252336.6	37	CCDS14390.1																																																																																				0.612	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		C	67937560	T	C	67937560	2	2	103	1	0	0	0	0	0	0	0	1	15302	1683	59	4		4	STARD8	23	67937560	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	2510518	67937560	87333000	316	27415										
TAF1	6872	hgsc.bcm.edu	37	chrX	70595105	70595105	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ccacccccgggaccaatgaaGaaggataaggaccaggattc	11	12	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:70595105G>A	ENST00000373790.4	+	4	552	c.501G>A	c.(499-501)aaG>aaA	p.K167K	TAF1_ENST00000423759.1_Silent_p.K167K|TAF1_ENST00000276072.3_Silent_p.K167K|TAF1_ENST00000449580.1_Silent_p.K167K	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	167	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GACCAATGAAGAAGGATAAGG	0.433																																																0			X											117	99	105					X																	70595105		2203	4300	6503	70511830	SO:0001819	synonymous_variant	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.501G>A	X.37:g.70595105G>A			70511830	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																				0.433	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70595105	G	A	70595105	2	1	103	1	0	0	0	0	0	0	0	1	15552	933	33	3		3	TAF1	23	70595105	Silent	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	2657545	70595105	84675455	317	27416										
SLC16A2	6567	hgsc.bcm.edu	37	chrX	73751291	73751291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tcaaaggatgttcaagaaagAgcagagagattccagcaagg	12	6	2	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:73751291A>G	ENST00000587091.1	+	6	1700	c.1523A>G	c.(1522-1524)gAg>gGg	p.E508G	SLC16A2_ENST00000276033.5_Missense_Mutation_p.E582G	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	508					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	TTCAAGAAAGAGCAGAGAGAT	0.547																																																0			X											106	92	97					X																	73751291		2203	4300	6503	73668016	SO:0001583	missense	6567				CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"Solute carriers"	10923	protein-coding gene	gene with protein product		300095	"solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)", "Allan-Herndon-Dudley syndrome", "solute carrier family 16 (monocarboxylic acid transporters), member 2", "mental retardation, X-linked 22", "solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.1523A>G	X.37:g.73751291A>G	ENSP00000465734:p.Glu508Gly		73668016	Q7Z797	Missense_Mutation	SNP	ENST00000587091.1	37	CCDS14426.2	.	.	.	.	.	.	.	.	.	.	A	12.67	2.008991	0.35415	.	.	ENSG00000147100	ENST00000276033	T	0.11712	2.75	5.3	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.775103	0.12099	N	0.499630	T	0.07728	0.0194	N	0.17082	0.46	0.30984	N	0.722118	B	0.12013	0.005	B	0.15052	0.012	T	0.05903	-1.0857	10	0.45353	T	0.12	.	9.7488	0.40464	0.9179:0.0:0.0821:0.0	.	508	P36021	MOT8_HUMAN	G	582	ENSP00000276033:E582G	ENSP00000276033:E582G	E	+	2	0	SLC16A2	73668016	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.510000	0.60455	1.770000	0.52166	0.430000	0.28490	GAG		0.547	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3			G	73751291	A	G	73751291	3	3	103	1	0	0	0	0	1	0	0	0	14445	304	11	4	1767	4	SLC16A2	23	73751291	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	3156186	73751291	81519269	318	27417										
RLIM	51132	hgsc.bcm.edu	37	chrX	73811648	73811648	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cacctgatgagcctgatgatGagcttccttcattactgcct	8	12	1	5	rs200629905		TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:73811648G>A	ENST00000332687.6	-	4	1720	c.1502C>T	c.(1501-1503)tCa>tTa	p.S501L	RLIM_ENST00000349225.2_Missense_Mutation_p.S501L	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	501	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S501L(3)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTGATGATGAGCTTCCTTC	0.488																																					Esophageal Squamous(169;1899 1923 14997 18818 32118)											3	Substitution - Missense(3)	prostate(2)|ovary(1)	X											45	38	40					X																	73811648		2203	4300	6503	73728373	SO:0001583	missense	51132			AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1502C>T	X.37:g.73811648G>A	ENSP00000328059:p.Ser501Leu		73728373	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	7.117	0.577275	0.13686	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.08984	3.03;3.03	5.41	4.55	0.56014	.	0.666655	0.15400	N	0.264373	T	0.10121	0.0248	L	0.49126	1.545	0.38573	D	0.949983	B	0.02656	0.0	B	0.01281	0.0	T	0.08764	-1.0706	10	0.23891	T	0.37	-0.2985	13.4694	0.61273	0.0772:0.0:0.9228:0.0	.	501	Q9NVW2	RNF12_HUMAN	L	501	ENSP00000328059:S501L;ENSP00000253571:S501L	ENSP00000328059:S501L	S	-	2	0	RLIM	73728373	0.997000	0.39634	0.969000	0.41365	0.831000	0.47069	2.664000	0.46783	1.072000	0.40860	-0.192000	0.12808	TCA		0.488	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811648	G	A	73811648	3	1	103	1	0	0	0	0	1	0	0	0	13427	1294	45	3	376	3	RLIM	23	73811648	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	60357	73811648	81458912	319	27418										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963106	73963106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	atgtctccagggaattagcaAgatggccctgctttggattc	11	9	1	1			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:73963106A>G	ENST00000055682.6	-	3	1897	c.1286T>C	c.(1285-1287)cTt>cCt	p.L429P		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	429					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GGAATTAGCAAGATGGCCCTG	0.428																																																0			X											175	143	154					X																	73963106		2203	4300	6503	73879831	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.1286T>C	X.37:g.73963106A>G	ENSP00000055682:p.Leu429Pro		73879831	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	A	8.003	0.755836	0.15846	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.40225	1.04;1.04	6.03	3.33	0.38152	.	0.355912	0.20754	N	0.086294	T	0.28995	0.0720	L	0.31578	0.945	0.20489	N	0.999894	B	0.06786	0.001	B	0.09377	0.004	T	0.23726	-1.0180	10	0.72032	D	0.01	-2.1432	7.4999	0.27511	0.6777:0.0:0.3223:0.0	.	429	Q5QGS0	K2022_HUMAN	P	429	ENSP00000362567:L429P;ENSP00000055682:L429P	ENSP00000055682:L429P	L	-	2	0	KIAA2022	73879831	1.000000	0.71417	0.307000	0.25127	0.537000	0.34900	4.032000	0.57274	0.885000	0.36088	0.486000	0.48141	CTT		0.428	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		G	73963106	A	G	73963106	3	3	103	1	0	0	0	0	1	0	0	0	8290	72	3	4	3272	4	KIAA2022	23	73963106	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	151458	73963106	81307454	320	27419										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216071	78216071	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aagatgggtagcaacagtacCagcactgctgagatttactg	11	8	0	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:78216071C>A	ENST00000171757.2	+	4	334	c.54C>A	c.(52-54)acC>acA	p.T18T	P2RY10_ENST00000544091.1_Silent_p.T18T|P2RY10_ENST00000475374.1_3'UTR	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						GCAACAGTACCAGCACTGCTG	0.378																																																0			X											142	110	121					X																	78216071		2203	4300	6503	78102727	SO:0001819	synonymous_variant	27334			AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.54C>A	X.37:g.78216071C>A			78102727	D3DTE5|Q4VBN7|Q86V16	Silent	SNP	ENST00000171757.2	37	CCDS14442.1																																																																																				0.378	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			A	78216071	C	A	78216071	2	1	103	1	0	0	0	0	0	0	0	1	11378	581	21	2		2	P2RY10	23	78216071	Silent	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	4252965	78216071	77054489	321	27420										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698872	79698872	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	catatagaagaacagcaaaaGaaaattgaatcatacctcca	5	8	1	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:79698872G>T	ENST00000308293.5	+	3	1073	c.834G>T	c.(832-834)aaG>aaT	p.K278N	FAM46D_ENST00000538312.1_Missense_Mutation_p.K278N	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	278										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						AACAGCAAAAGAAAATTGAAT	0.368													G|||	1	0.000264901	0	0	3775	,	,		15735	0.001		0	False		,,,				2504	0															0			X											76	67	70					X																	79698872		2202	4296	6498	79585528	SO:0001583	missense	169966			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.834G>T	X.37:g.79698872G>T	ENSP00000308575:p.Lys278Asn		79585528	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.662616	0.29515	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.23348	1.91;1.91	4.46	1.63	0.23807	Domain of unknown function DUF1693 (1);	0.114669	0.56097	D	0.000038	T	0.19604	0.0471	N	0.24115	0.695	0.33469	D	0.58591	P	0.39717	0.684	P	0.46049	0.502	T	0.22941	-1.0202	10	0.36615	T	0.2	-3.0277	7.3187	0.26515	0.3963:0.0:0.6037:0.0	.	278	Q8NEK8	FA46D_HUMAN	N	278	ENSP00000443410:K278N;ENSP00000308575:K278N	ENSP00000308575:K278N	K	+	3	2	FAM46D	79585528	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	1.341000	0.33907	0.358000	0.24211	0.583000	0.79449	AAG		0.368	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		T	79698872	G	T	79698872	3	4	103	1	0	0	0	0	1	0	0	0	5587	933	33	2	836	2	FAM46D	23	79698872	Missense_Mutation	SNP	G	TCGA-DY-A0XA-01A-11D-A152-10	1482801	79698872	75571688	322	27421										
MUM1L1	139221	hgsc.bcm.edu	37	chrX	105450659	105450659	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttggccagcagtgataaaaAgtatcagacgaaaagagagg	12	5	1	3			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:105450659A>G	ENST00000357175.2	+	4	1883	c.1234A>G	c.(1234-1236)Agt>Ggt	p.S412G	MUM1L1_ENST00000337685.2_Missense_Mutation_p.S412G|MUM1L1_ENST00000372552.1_Missense_Mutation_p.S412G	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	412	PWWP.					extracellular vesicular exosome (GO:0070062)		p.S412C(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						AGTGATAAAAAGTATCAGACG	0.343																																																1	Substitution - Missense(1)	ovary(1)	X											37	33	34					X																	105450659		1836	4072	5908	105337315	SO:0001583	missense	139221			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1234A>G	X.37:g.105450659A>G	ENSP00000349699:p.Ser412Gly		105337315	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	A	11.07	1.531289	0.27387	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.71461	-0.57;-0.57;-0.57	4.31	4.31	0.51392	.	0.000000	0.64402	D	0.000012	T	0.62233	0.2411	M	0.68317	2.08	0.29455	N	0.85816	P	0.47484	0.896	B	0.35182	0.197	T	0.69068	-0.5243	10	0.87932	D	0	-33.04	8.8406	0.35140	1.0:0.0:0.0:0.0	.	412	Q5H9M0	MUML1_HUMAN	G	412	ENSP00000349699:S412G;ENSP00000338641:S412G;ENSP00000361632:S412G	ENSP00000338641:S412G	S	+	1	0	MUM1L1	105337315	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	4.085000	0.57657	1.908000	0.55244	0.430000	0.28490	AGT		0.343	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		G	105450659	A	G	105450659	3	3	103	1	0	0	0	0	1	0	0	0	10016	72	3	4	1236	4	MUM1L1	23	105450659	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	25751787	105450659	49819901	323	27422										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123631097	123631097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaatgaacatattttctccaTtccctttatgtatgattcct	3	9	1	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:123631097T>C	ENST00000371130.3	-	20	3527	c.3464A>G	c.(3463-3465)aAt>aGt	p.N1155S	TENM1_ENST00000461429.1_5'Flank|TENM1_ENST00000422452.2_Missense_Mutation_p.N1155S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1155					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ATTTTCTCCATTCCCTTTATG	0.368																																																0			X											89	76	80					X																	123631097		2202	4300	6502	123458778	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.3464A>G	X.37:g.123631097T>C	ENSP00000360171:p.Asn1155Ser		123458778	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904643	0.33628	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87029	-2.2;-2.13	5.55	5.55	0.83447	.	0.106321	0.64402	N	0.000006	T	0.74839	0.3769	N	0.16862	0.45	0.52501	D	0.99995	P;P;B	0.43094	0.651;0.799;0.102	B;B;B	0.30179	0.112;0.112;0.018	T	0.78160	-0.2312	10	0.46703	T	0.11	.	14.705	0.69183	0.0:0.0:0.0:1.0	.	1154;1155;1155	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	1155	ENSP00000360171:N1155S;ENSP00000403954:N1155S	ENSP00000360171:N1155S	N	-	2	0	ODZ1	123458778	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	6.245000	0.72398	1.853000	0.53794	0.486000	0.48141	AAT		0.368	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123631097	T	C	123631097	3	2	103	1	0	0	0	0	1	0	0	0	10865	1493	52	4	4786	4	ODZ1	23	123631097	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	18180438	123631097	31639463	324	27423										
SASH3	54440	hgsc.bcm.edu	37	chrX	128926971	128926971	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcctctgcctacaggagcacAcatccaccctcctgctcaat	6	18	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:128926971A>T	ENST00000356892.3	+	7	922	c.808A>T	c.(808-810)Aca>Tca	p.T270S	RP4-753P9.3_ENST00000432513.1_RNA	NM_018990.3	NP_061863.1	O75995	SASH3_HUMAN	SAM and SH3 domain containing 3	270	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				homeostasis of number of cells within a tissue (GO:0048873)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tumor necrosis factor production (GO:0032760)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	12						ACAGGAGCACACATCCACCCT	0.567																																																0			X											100	75	84					X																	128926971		2203	4300	6503	128754652	SO:0001583	missense	54440			BC051881	CCDS14614.1	Xq26	2013-01-10	2008-02-18	2008-02-18	ENSG00000122122	ENSG00000122122		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	15975	protein-coding gene	gene with protein product		300441	"chromosome X open reading frame 9"	CXorf9		11470164	Standard	NM_018990		Approved	SLY, 753P9, SH3D6C, HACS2	uc004euu.3	O75995	OTTHUMG00000022372	ENST00000356892.3:c.808A>T	X.37:g.128926971A>T	ENSP00000349359:p.Thr270Ser		128754652	A6NCH1|A8K7K8|Q5JZ38	Missense_Mutation	SNP	ENST00000356892.3	37	CCDS14614.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324839	0.41197	.	.	ENSG00000122122	ENST00000443760;ENST00000356892	D	0.85955	-2.05	5.66	4.48	0.54585	Src homology-3 domain (1);Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.246302	0.48767	D	0.000169	T	0.80380	0.4612	L	0.51422	1.61	0.41515	D	0.988366	B;B	0.22983	0.078;0.003	B;B	0.24848	0.056;0.006	T	0.76493	-0.2939	10	0.33141	T	0.24	-23.3621	10.7881	0.46417	0.9223:0.0:0.0777:0.0	.	288;270	B4DKQ0;O75995	.;SASH3_HUMAN	S	288;270	ENSP00000349359:T270S	ENSP00000349359:T270S	T	+	1	0	SASH3	128754652	0.888000	0.30383	0.987000	0.45799	0.739000	0.42172	1.577000	0.36515	1.914000	0.55421	0.430000	0.28490	ACA		0.567	SASH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058208.1	NM_018990		T	128926971	A	T	128926971	3	4	103	1	0	0	0	0	1	0	0	0	13886	159	6	5	834	5	SASH3	23	128926971	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	5295874	128926971	26343589	325	27424										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129283521	129283521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	tttcattgtatcttttttcaTcctctttcatagtcttgtag	4	8	6	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:129283521T>C	ENST00000287295.3	-	3	502	c.272A>G	c.(271-273)gAt>gGt	p.D91G	AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000319908.3_Missense_Mutation_p.D87G|AIFM1_ENST00000535724.1_Missense_Mutation_p.D4G	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	TCTTTTTTCATCCTCTTTCAT	0.383																																																0			X											206	182	190					X																	129283521		2202	4300	6502	129111202	SO:0001583	missense	9131			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.272A>G	X.37:g.129283521T>C	ENSP00000287295:p.Asp91Gly		129111202	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	37	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.745892	0.30955	.	.	ENSG00000156709	ENST00000319908;ENST00000535724;ENST00000287295	T;D;T	0.83992	0.71;-1.79;0.71	5.5	5.5	0.81552	.	0.230096	0.51477	D	0.000097	T	0.81555	0.4847	M	0.64404	1.975	0.33277	D	0.561823	B;B;B	0.30146	0.27;0.043;0.031	B;B;B	0.33890	0.113;0.172;0.034	D	0.85624	0.1266	10	0.51188	T	0.08	-3.0781	12.1135	0.53852	0.0:0.0:0.0:1.0	.	91;87;91	Q1L6K6;O95831-3;O95831	.;.;AIFM1_HUMAN	G	87;4;91	ENSP00000315122:D87G;ENSP00000446113:D4G;ENSP00000287295:D91G	ENSP00000287295:D91G	D	-	2	0	AIFM1	129111202	0.974000	0.33945	0.125000	0.21846	0.318000	0.28184	2.777000	0.47717	1.846000	0.53633	0.472000	0.43445	GAT		0.383	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129283521	T	C	129283521	3	2	103	1	0	0	0	0	1	0	0	0	426	1435	50	4	1637	4	AIFM1	23	129283521	Missense_Mutation	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	356550	129283521	25987039	326	27425										
RBMX2	51634	hgsc.bcm.edu	37	chrX	129546359	129546359	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	aaaggaaaaaaagaaaaaaaAgaaagaaaaagagaaagccg	9	2	0	4			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:129546359A>G	ENST00000305536.6	+	6	570	c.506A>G	c.(505-507)aAg>aGg	p.K169R		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	169	Lys-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						aagaaaaaaaagaaagaaaaa	0.383																																																0			X											33	34	34					X																	129546359		1801	4066	5867	129374040	SO:0001583	missense	51634			AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"RNA binding motif (RRM) containing"	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.506A>G	X.37:g.129546359A>G	ENSP00000339090:p.Lys169Arg		129374040	A8K9Z0|Q5JY82|Q9Y3I8	Missense_Mutation	SNP	ENST00000305536.6	37	CCDS43993.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.543688	0.27563	.	.	ENSG00000134597	ENST00000305536;ENST00000538614	T	0.13420	2.59	3.72	1.27	0.21489	.	0.126159	0.51477	N	0.000085	T	0.08179	0.0204	L	0.29908	0.895	0.42095	D	0.991319	B	0.09022	0.002	B	0.08055	0.003	T	0.21143	-1.0254	10	0.38643	T	0.18	.	4.654	0.12608	0.7113:0.0:0.2887:0.0	.	169	Q9Y388	RBMX2_HUMAN	R	169	ENSP00000339090:K169R	ENSP00000339090:K169R	K	+	2	0	RBMX2	129374040	1.000000	0.71417	0.829000	0.32907	0.951000	0.60555	2.256000	0.43231	0.432000	0.26286	0.486000	0.48141	AAG		0.383	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		G	129546359	A	G	129546359	3	3	103	1	0	0	0	0	1	0	0	0	13189	72	3	4	528	4	RBMX2	23	129546359	Missense_Mutation	SNP	A	TCGA-DY-A0XA-01A-11D-A152-10	262838	129546359	25724201	327	27426										
AFF2	2334	hgsc.bcm.edu	37	chrX	148037366	148037366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	ctcattagggagaaagcccgTccacggcccactcagaaaat	9	13	2	2			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:148037366T>C	ENST00000370460.2	+	11	2270	c.1791T>C	c.(1789-1791)cgT>cgC	p.R597R	AFF2_ENST00000342251.3_Silent_p.R564R|AFF2_ENST00000370457.5_Silent_p.R564R|AFF2_ENST00000286437.5_Silent_p.R238R	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	597					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AGAAAGCCCGTCCACGGCCCA	0.468																																																0			X											96	100	99					X																	148037366		2203	4300	6503	147845066	SO:0001819	synonymous_variant	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1791T>C	X.37:g.148037366T>C			147845066	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																				0.468	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		C	148037366	T	C	148037366	2	2	103	1	0	0	0	0	0	0	0	1	357	1654	58	4		4	AFF2	23	148037366	Silent	SNP	T	TCGA-DY-A0XA-01A-11D-A152-10	18491007	148037366	7233194	328	27427										
AFF2	2334	hgsc.bcm.edu	37	chrX	148068985	148068985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	gcccagtcaccattccccagCgcattcaccacatggctgcc	7	19	2	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:148068985C>T	ENST00000370460.2	+	20	4191	c.3712C>T	c.(3712-3714)Cgc>Tgc	p.R1238C	AFF2_ENST00000342251.3_Missense_Mutation_p.R1205C|AFF2_ENST00000370457.5_Missense_Mutation_p.R1203C|AFF2_ENST00000286437.5_Missense_Mutation_p.R879C	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1238					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CATTCCCCAGCGCATTCACCA	0.517																																																0			X											212	161	178					X																	148068985		2203	4300	6503	147876691	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3712C>T	X.37:g.148068985C>T	ENSP00000359489:p.Arg1238Cys		147876691	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593941	0.86953	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.74	4.83	0.62350	.	0.062858	0.64402	D	0.000008	T	0.81297	0.4793	M	0.81497	2.545	0.80722	D	1	D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.992;0.996;0.999;0.999;0.999;0.999	D	0.83552	0.0102	10	0.72032	D	0.01	.	12.6336	0.56671	0.2874:0.7126:0.0:0.0	.	879;1203;1203;1199;1228;1238	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	C	1238;1203;1205;879	ENSP00000359489:R1238C;ENSP00000359486:R1203C;ENSP00000345459:R1205C;ENSP00000286437:R879C	ENSP00000286437:R879C	R	+	1	0	AFF2	147876691	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.838000	0.55828	2.423000	0.82170	0.600000	0.82982	CGC		0.517	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	148068985	C	T	148068985	3	4	103	1	0	0	0	0	1	0	0	0	357	768	27	1	3845	1	AFF2	23	148068985	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	31619	148068985	7201575	329	27428										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153695461	153695461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0575757575757576	19	1	1.10163106146628	2.261242705115	0.802376443750484	0.569404760261442	1	0	cggtccaggagccccgggtcCgtgccaagtaccgcggcatt	14	15	0	0			TCGA-DY-A0XA-01A-11D-A152-10	TCGA-DY-A0XA-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	eeee1bff-73f7-4ae7-a9de-a1aa3d4d6004	d3a7343f-ec42-43ca-8539-58d8475a84ed	g.chrX:153695461C>T	ENST00000369682.3	+	18	3344	c.3169C>T	c.(3169-3171)Cgt>Tgt	p.R1057C		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1057	IPT/TIG 3.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCCCCGGGTCCGTGCCAAGTA	0.667																																																0			X											79	72	74					X																	153695461		2203	4300	6503	153348655	SO:0001583	missense	55558			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.3169C>T	X.37:g.153695461C>T	ENSP00000358696:p.Arg1057Cys		153348655	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.641453	0.87859	.	.	ENSG00000130827	ENST00000369682	T	0.78364	-1.17	5.8	5.8	0.92144	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89079	0.6613	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89436	0.3720	10	0.51188	T	0.08	.	17.6415	0.88138	0.0:1.0:0.0:0.0	.	1057	P51805	PLXA3_HUMAN	C	1057	ENSP00000358696:R1057C	ENSP00000358696:R1057C	R	+	1	0	PLXNA3	153348655	0.940000	0.31905	0.999000	0.59377	0.801000	0.45260	1.677000	0.37576	2.438000	0.82558	0.600000	0.82982	CGT		0.667	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153695461	C	T	153695461	3	4	103	1	0	0	0	0	1	0	0	0	12152	652	23	1	3235	1	PLXNA3	23	153695461	Missense_Mutation	SNP	C	TCGA-DY-A0XA-01A-11D-A152-10	5626476	153695461	1575099	330	27429										
CROCC	9696	hgsc.bcm.edu	37	chr1	17263152	17263152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggacctgctgcagctgggagGggagctggcccggacatcac	17	12	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:17263152G>T	ENST00000375541.5	+	9	1046	c.977G>T	c.(976-978)gGg>gTg	p.G326V	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCTGGGAGGGGAGCTGGCC	0.652																																																0			1											7	8	8					1																	17263152		2058	4053	6111	17135739	SO:0001583	missense	9696			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.977G>T	1.37:g.17263152G>T	ENSP00000364691:p.Gly326Val		17135739		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.892579	0.33442	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09630	2.96	3.91	2.91	0.33838	.	.	.	.	.	T	0.11452	0.0279	L	0.41236	1.265	0.48901	D	0.999728	B;B;P	0.50819	0.291;0.291;0.939	B;B;P	0.51101	0.091;0.204;0.659	T	0.09618	-1.0666	9	0.33141	T	0.24	.	2.999	0.06008	0.2044:0.0:0.5628:0.2329	.	189;189;326	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	V	326;207	ENSP00000364691:G326V	ENSP00000364691:G326V	G	+	2	0	CROCC	17135739	0.605000	0.26941	1.000000	0.80357	0.708000	0.40852	0.395000	0.20850	2.188000	0.69820	0.462000	0.41574	GGG		0.652	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17263152	G	T	17263152	3	4	104	1	0	0	0	0	1	0	0	0	3899	1232	43	2	1011	2	CROCC	1	17263152	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		17263152	231987469	1	27430										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32262199	32262199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctccaacttaaccaccagatCctccagggtcagtgtctggt	8	14	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:32262199C>T	ENST00000360482.2	-	10	2392	c.2263G>A	c.(2263-2265)Gat>Aat	p.D755N	SPOCD1_ENST00000533231.1_Missense_Mutation_p.D755N|SPOCD1_ENST00000373648.2_3'UTR|SPOCD1_ENST00000257100.3_Missense_Mutation_p.D248N	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	755					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		accaccaGATCCTCCAGGGTC	0.607																																																0			1											161	126	138					1																	32262199		2203	4300	6503	32034786	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2263G>A	1.37:g.32262199C>T	ENSP00000353670:p.Asp755Asn		32034786	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432521	0.43224	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231	T;T;T;T	0.47869	0.83;1.84;0.88;1.84	4.34	3.34	0.38264	.	.	.	.	.	T	0.57607	0.2065	L	0.58101	1.795	0.80722	D	1	D;P;P;P	0.64830	0.994;0.811;0.713;0.713	D;B;B;B	0.63703	0.917;0.284;0.209;0.224	T	0.54357	-0.8306	9	0.35671	T	0.21	-10.6938	9.6546	0.39919	0.0:0.787:0.213:0.0	.	99;755;192;755	Q6ZMY3-4;Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;.;SPOC1_HUMAN	N	248;755;153;192;755	ENSP00000257100:D248N;ENSP00000353670:D755N;ENSP00000399778:D192N;ENSP00000435851:D755N	ENSP00000257100:D248N	D	-	1	0	SPOCD1	32034786	1.000000	0.71417	0.998000	0.56505	0.463000	0.32649	1.556000	0.36288	2.140000	0.66376	0.462000	0.41574	GAT		0.607	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32262199	C	T	32262199	3	4	104	1	0	0	0	0	1	0	0	0	15117	855	30	3	1415	3	SPOCD1	1	32262199	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	14999047	32262199	216988422	2	27431										
GJB4	127534	hgsc.bcm.edu	37	chr1	35227018	35227018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agaaggactttgtctgcaacAccaagcagcccggctgcccc	10	15	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:35227018A>T	ENST00000339480.1	+	2	533	c.163A>T	c.(163-165)Acc>Tcc	p.T55S	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	55					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGTCTGCAACACCAAGCAGCC	0.612																																																0			1											227	155	179					1																	35227018		2203	4300	6503	34999605	SO:0001583	missense	127534				CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"Ion channels / Gap junction proteins (connexins)"	4286	protein-coding gene	gene with protein product	"connexin 30.3"	605425	"gap junction protein, beta 4 (connexin 30.3)", "gap junction protein, beta 4"				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.163A>T	1.37:g.35227018A>T	ENSP00000345868:p.Thr55Ser		34999605	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.972821	0.92919	.	.	ENSG00000189433	ENST00000339480	D	0.99338	-5.76	5.56	4.42	0.53409	Connexin, conserved site (1);Connexin, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.99263	0.9743	M	0.90082	3.085	0.36543	D	0.871404	D	0.53745	0.962	P	0.55545	0.778	D	0.99919	1.1240	10	0.66056	D	0.02	.	12.4477	0.55659	0.8597:0.1403:0.0:0.0	.	55	Q9NTQ9	CXB4_HUMAN	S	55	ENSP00000345868:T55S	ENSP00000345868:T55S	T	+	1	0	GJB4	34999605	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.281000	0.95811	0.930000	0.37217	0.533000	0.62120	ACC		0.612	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		T	35227018	A	T	35227018	3	4	104	1	0	0	0	0	1	0	0	0	6430	159	6	5	165	5	GJB4	1	35227018	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	2964819	35227018	214023603	3	27432										
PIK3R3	8503	hgsc.bcm.edu	37	chr1	46509456	46509456	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	taatggagcactagctccttCagagagctgtacaggttgta	11	8	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:46509456C>T	ENST00000262741.5	-	10	1964	c.1275G>A	c.(1273-1275)ctG>ctA	p.L425L	PIK3R3_ENST00000340332.6_Silent_p.L330L|PIK3R3_ENST00000354242.4_Silent_p.L366L|PIK3R3_ENST00000540385.1_Silent_p.L471L|PIK3R3_ENST00000372006.1_Silent_p.L425L|PIK3R3_ENST00000423209.1_Silent_p.L366L|PIK3R3_ENST00000420542.1_Silent_p.L425L|PIK3R3_ENST00000488808.1_5'UTR	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	425	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CTAGCTCCTTCAGAGAGCTGT	0.547																																																0			1											146	123	131					1																	46509456		2203	4300	6503	46282043	SO:0001819	synonymous_variant	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.1275G>A	1.37:g.46509456C>T			46282043	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Silent	SNP	ENST00000262741.5	37	CCDS529.1																																																																																				0.547	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		T	46509456	C	T	46509456	2	4	104	1	0	0	0	0	0	0	0	1	11951	813	29	3		3	PIK3R3	1	46509456	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	11282438	46509456	202741165	4	27433										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65130218	65130218	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agtaatggctaccagccacgTcacagatgaatggatgacac	10	10	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:65130218T>C	ENST00000371073.2	+	15	2132	c.2132T>C	c.(2131-2133)gTc>gCc	p.V711A	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.V660A			Q5VU97	CAHD1_HUMAN	cache domain containing 1	711					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ACCAGCCACGTCACAGATGAA	0.443																																																0			1											128	113	118					1																	65130218		2203	4300	6503	64902806	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2132T>C	1.37:g.65130218T>C	ENSP00000360113:p.Val711Ala		64902806	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	T	15.45	2.836663	0.50951	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.24151	1.87;1.88	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.07999	0.0200	N	0.16478	0.41	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.18085	-1.0348	10	0.25106	T	0.35	-33.1974	13.7672	0.63002	0.0:0.0:0.1275:0.8725	.	711	Q5VU97	CAHD1_HUMAN	A	711;660	ENSP00000360113:V711A;ENSP00000290039:V660A	ENSP00000290039:V660A	V	+	2	0	CACHD1	64902806	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.001000	0.70685	2.371000	0.80710	0.533000	0.62120	GTC		0.443	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		C	65130218	T	C	65130218	3	2	104	1	0	0	0	0	1	0	0	0	2543	1667	58	4	2037	4	CACHD1	1	65130218	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	18620762	65130218	184120403	5	27434										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67787504	67787504	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tccccttggtacaaccttgtTtgtctgcaaactggcctgta	8	12	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:67787504T>C	ENST00000262345.1	+	3	936	c.296T>C	c.(295-297)tTt>tCt	p.F99S	IL12RB2_ENST00000371000.1_Missense_Mutation_p.F99S|IL12RB2_ENST00000541374.1_Missense_Mutation_p.F99S|IL12RB2_ENST00000544434.1_Missense_Mutation_p.F99S	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	99					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.F99C(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ACAACCTTGTTTGTCTGCAAA	0.393																																																1	Substitution - Missense(1)	ovary(1)	1											168	161	163					1																	67787504		2203	4300	6503	67560092	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.296T>C	1.37:g.67787504T>C	ENSP00000262345:p.Phe99Ser		67560092	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.699980	0.48307	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.95	5.95	0.96441	Immunoglobulin C2-set-like, ligand-binding (1);	0.144837	0.64402	D	0.000005	T	0.77765	0.4179	L	0.36672	1.1	0.45139	D	0.998156	B;D;D;D	0.89917	0.163;1.0;0.993;0.997	B;D;P;D	0.74674	0.076;0.984;0.854;0.955	T	0.80975	-0.1142	10	0.56958	D	0.05	-28.3087	12.8126	0.57647	0.0:0.0:0.0:1.0	.	99;99;99;99	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	S	99	ENSP00000262345:F99S;ENSP00000360039:F99S;ENSP00000445276:F99S;ENSP00000442443:F99S	ENSP00000262345:F99S	F	+	2	0	IL12RB2	67560092	0.996000	0.38824	0.961000	0.40146	0.005000	0.04900	3.848000	0.55903	2.274000	0.75844	0.528000	0.53228	TTT		0.393	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67787504	T	C	67787504	3	2	104	1	0	0	0	0	1	0	0	0	7648	1841	64	4	302	4	IL12RB2	1	67787504	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	2657286	67787504	181463117	6	27435										
VCAM1	7412	hgsc.bcm.edu	37	chr1	101198073	101198073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagccagggctttcctgctcCgaaaatcctgtggagcaggc	13	12	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:101198073C>T	ENST00000294728.2	+	7	1726	c.1625C>T	c.(1624-1626)cCg>cTg	p.P542L	VCAM1_ENST00000370119.4_Missense_Mutation_p.P480L|VCAM1_ENST00000347652.2_Missense_Mutation_p.P450L|VCAM1_ENST00000370115.1_Missense_Mutation_p.P343L	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	542	Ig-like C2-type 6.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTTCCTGCTCCGAAAATCCTG	0.512																																																0			1											51	54	53					1																	101198073		2203	4300	6503	100970661	SO:0001583	missense	7412			M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1625C>T	1.37:g.101198073C>T	ENSP00000294728:p.Pro542Leu		100970661	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.956312	0.53293	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.57	5.57	0.84162	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.386787	0.30446	N	0.009613	T	0.64821	0.2633	M	0.92077	3.27	0.44188	D	0.997003	D;P;D	0.56287	0.968;0.956;0.975	P;P;P	0.58820	0.846;0.633;0.771	T	0.72766	-0.4194	10	0.66056	D	0.02	-13.211	17.0763	0.86587	0.0:1.0:0.0:0.0	.	480;450;542	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	L	480;450;542;343	ENSP00000359137:P480L;ENSP00000304611:P450L;ENSP00000294728:P542L;ENSP00000359133:P343L	ENSP00000294728:P542L	P	+	2	0	VCAM1	100970661	0.108000	0.22018	0.631000	0.29282	0.319000	0.28217	2.897000	0.48664	2.785000	0.95823	0.655000	0.94253	CCG		0.512	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		T	101198073	C	T	101198073	3	4	104	1	0	0	0	0	1	0	0	0	17177	652	23	1	1651	1	VCAM1	1	101198073	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	33410569	101198073	148052548	7	27436										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102270066	102270066	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccctgcacttctcttggggtAgccagtgctccagctcttca	9	15	3	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:102270066A>G	ENST00000338858.5	-	6	1164	c.1165T>C	c.(1165-1167)Tac>Cac	p.Y389H	OLFM3_ENST00000370103.4_Missense_Mutation_p.Y369H|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_3'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	389	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CTCTTGGGGTAGCCAGTGCTC	0.478																																																0			1											127	107	114					1																	102270066		2203	4300	6503	102042654	SO:0001583	missense	118427			AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.1165T>C	1.37:g.102270066A>G	ENSP00000345192:p.Tyr389His		102042654	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	37		.	.	.	.	.	.	.	.	.	.	A	17.35	3.367022	0.61513	.	.	ENSG00000118733	ENST00000370103;ENST00000338858	D;D	0.89196	-2.48;-2.48	5.67	5.67	0.87782	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.89399	0.6704	L	0.33245	0.995	0.80722	D	1	B;D	0.76494	0.118;0.999	B;D	0.85130	0.12;0.997	D	0.90279	0.4313	10	0.46703	T	0.11	.	15.8913	0.79299	1.0:0.0:0.0:0.0	.	369;389	Q5T3V6;Q96PB7	.;NOE3_HUMAN	H	369;389	ENSP00000359121:Y369H;ENSP00000345192:Y389H	ENSP00000345192:Y389H	Y	-	1	0	OLFM3	102042654	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.339000	0.96797	2.157000	0.67596	0.528000	0.53228	TAC		0.478	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			G	102270066	A	G	102270066	3	3	104	1	0	0	0	0	1	0	0	0	10885	420	15	4	275	4	OLFM3	1	102270066	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	1071993	102270066	146980555	8	27437										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103540200	103540200	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aacttcttcatccaaaatccTtgttccaaaaaccgtgattc	3	12	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:103540200T>A	ENST00000370096.3	-	4	937	c.625A>T	c.(625-627)Agg>Tgg	p.R209W	COL11A1_ENST00000512756.1_Missense_Mutation_p.R209W|COL11A1_ENST00000353414.4_Missense_Mutation_p.R209W|COL11A1_ENST00000358392.2_Missense_Mutation_p.R209W	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	209	Laminin G-like.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		TCCAAAATCCTTGTTCCAAAA	0.343																																																0			1											135	124	128					1																	103540200		2202	4300	6502	103312788	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.625A>T	1.37:g.103540200T>A	ENSP00000359114:p.Arg209Trp		103312788	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.996035	0.54147	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.73	4.6	0.57074	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.87289	0.6140	M	0.92649	3.33	0.58432	D	0.999998	D;D;D;D	0.71674	0.995;0.997;0.998;0.997	D;D;D;D	0.67900	0.954;0.924;0.924;0.954	D	0.90034	0.4137	10	0.87932	D	0	.	13.0354	0.58867	0.0:0.0:0.1347:0.8653	.	209;209;209;209	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	W	209;209;209;209;209;136	ENSP00000359114:R209W;ENSP00000351163:R209W;ENSP00000302551:R209W;ENSP00000426533:R209W;ENSP00000408640:R209W;ENSP00000410177:R136W	ENSP00000302551:R209W	R	-	1	2	COL11A1	103312788	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.091000	0.57700	0.975000	0.38392	0.528000	0.53228	AGG		0.343	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103540200	T	A	103540200	3	1	104	1	0	0	0	0	1	0	0	0	3673	1608	56	5	5208	5	COL11A1	1	103540200	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	1270134	103540200	145710421	9	27438										
PI4KB	5298	hgsc.bcm.edu	37	chr1	151274711	151274711	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctttgagagcaactgcagaAggatcttctgggtctcgttt	11	8	4	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:151274711A>G	ENST00000368873.1	-	7	1752	c.1584T>C	c.(1582-1584)ccT>ccC	p.P528P	PI4KB_ENST00000368872.1_Silent_p.P513P|PI4KB_ENST00000271657.5_Silent_p.P540P|PI4KB_ENST00000368874.4_Silent_p.P513P|RN7SL444P_ENST00000578948.1_RNA|PI4KB_ENST00000368875.2_Silent_p.P540P|PI4KB_ENST00000529142.1_Silent_p.P196P			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	528					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAACTGCAGAAGGATCTTCTG	0.537																																					Colon(154;765 1838 9854 28443 37492)											0			1											149	145	146					1																	151274711		2203	4300	6503	149541335	SO:0001819	synonymous_variant	5298			AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368873.1:c.1584T>C	1.37:g.151274711A>G			149541335	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Silent	SNP	ENST00000368873.1	37																																																																																					0.537	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		G	151274711	A	G	151274711	2	3	104	1	0	0	0	0	0	0	0	1	11905	59	3	4		4	PI4KB	1	151274711	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	47734511	151274711	97975910	10	27439										
TCHH	7062	hgsc.bcm.edu	37	chr1	152085111	152085111	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtttcgtgacctttgcaactCtgcagctgctcttcctctgc	8	14	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:152085111C>G	ENST00000368804.1	-	2	581	c.582G>C	c.(580-582)caG>caC	p.Q194H		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	194					keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTTGCAACTCTGCAGCTGCT	0.607																																																0			1											91	98	96					1																	152085111		2060	4188	6248	150351735	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.582G>C	1.37:g.152085111C>G	ENSP00000357794:p.Gln194His		150351735	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	8.948	0.967395	0.18659	.	.	ENSG00000159450	ENST00000368804	T	0.05649	3.41	4.51	-0.047	0.13845	.	.	.	.	.	T	0.02047	0.0064	N	0.08118	0	0.09310	N	1	D	0.61080	0.989	P	0.55965	0.788	T	0.42766	-0.9432	9	0.48119	T	0.1	-1.4809	5.2514	0.15524	0.0:0.5292:0.1628:0.308	.	194	Q07283	TRHY_HUMAN	H	194	ENSP00000357794:Q194H	ENSP00000357794:Q194H	Q	-	3	2	TCHH	150351735	0.000000	0.05858	0.000000	0.03702	0.192000	0.23643	-1.143000	0.03200	0.127000	0.18452	0.502000	0.49764	CAG		0.607	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		G	152085111	C	G	152085111	3	3	104	1	0	0	0	0	1	0	0	0	15739	912	32	5	5253	5	TCHH	1	152085111	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	810400	152085111	97165510	11	27440										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153910230	153910230	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagtggattcactgccctctGgtaaggcaggctcctcggga	14	11	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:153910230G>C	ENST00000361217.4	-	14	2493	c.2075C>G	c.(2074-2076)cCa>cGa	p.P692R		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	692					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACTGCCCTCTGGTAAGGCAGG	0.567																																																0			1											155	155	155					1																	153910230		1985	4176	6161	152176854	SO:0001583	missense	9909			AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2075C>G	1.37:g.153910230G>C	ENSP00000354597:p.Pro692Arg		152176854	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629272	0.28978	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.08008	3.14;3.14	5.18	4.25	0.50352	.	0.499546	0.21946	N	0.066801	T	0.03695	0.0105	L	0.58810	1.83	0.09310	N	1	B	0.14438	0.01	B	0.22386	0.039	T	0.33445	-0.9868	10	0.25106	T	0.35	-0.1149	11.8729	0.52531	0.0869:0.0:0.9131:0.0	.	692	O75064	DEN4B_HUMAN	R	692;703	ENSP00000354597:P692R;ENSP00000357635:P703R	ENSP00000354597:P692R	P	-	2	0	DENND4B	152176854	1.000000	0.71417	0.067000	0.19924	0.670000	0.39368	7.473000	0.81007	1.374000	0.46228	0.655000	0.94253	CCA		0.567	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153910230	G	C	153910230	3	2	104	1	0	0	0	0	1	0	0	0	4445	1348	47	5	2475	5	DENND4B	1	153910230	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	1825119	153910230	95340391	12	27441										
TNFSF4	7292	hgsc.bcm.edu	37	chr1	173155919	173155919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atgagataaaacccatcacaGttgatgatgactgagttgtt	9	6	1	5			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:173155919G>T	ENST00000281834.3	-	3	424	c.288C>A	c.(286-288)aaC>aaA	p.N96K	TNFSF4_ENST00000488053.1_5'Flank|TNFSF4_ENST00000367718.1_Missense_Mutation_p.N46K	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	96					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						ACCCATCACAGTTGATGATGA	0.453																																																0			1											115	118	117					1																	173155919		2203	4300	6503	171422542	SO:0001583	missense	7292			D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11934	protein-coding gene	gene with protein product		603594	"tax-transcriptionally activated glycoprotein 1, 34kD"	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.288C>A	1.37:g.173155919G>T	ENSP00000281834:p.Asn96Lys		171422542	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	G	5.729	0.318930	0.10845	.	.	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94417	-3.42;-3.42	5.76	-8.17	0.01057	Tumour necrosis factor (2);Tumour necrosis factor-like (1);Tumour necrosis factor, conserved site (1);	1.693150	0.02418	N	0.082257	T	0.76162	0.3949	L	0.43152	1.355	0.09310	N	0.999996	B;B	0.22800	0.075;0.026	B;B	0.14578	0.011;0.011	T	0.73116	-0.4084	10	0.02654	T	1	0.119	7.7885	0.29106	0.0708:0.5744:0.1566:0.1982	.	96;46	P23510;Q8IV74	TNFL4_HUMAN;.	K	46;96;46	ENSP00000356691:N46K;ENSP00000281834:N96K	ENSP00000281834:N96K	N	-	3	2	TNFSF4	171422542	0.018000	0.18449	0.004000	0.12327	0.455000	0.32408	-0.146000	0.10250	-0.875000	0.04022	0.655000	0.94253	AAC		0.453	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1			T	173155919	G	T	173155919	3	4	104	1	0	0	0	0	1	0	0	0	16349	1020	36	2	267	2	TNFSF4	1	173155919	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	19245689	173155919	76094702	13	27442										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564652	176564652	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agtgtaacaacatgctgaacGactttgacgacggagactgc	11	9	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:176564652G>A	ENST00000367662.3	+	3	3076	c.1912G>A	c.(1912-1914)Gac>Aac	p.D638N	PAPPA2_ENST00000367661.3_Missense_Mutation_p.D638N	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	638	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CATGCTGAACGACTTTGACGA	0.602																																																0			1											70	76	74					1																	176564652		2168	4268	6436	174831275	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1912G>A	1.37:g.176564652G>A	ENSP00000356634:p.Asp638Asn		174831275	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.017218	0.54576	.	.	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.30182	4.78;1.54	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.26593	0.0650	L	0.28400	0.85	0.43195	D	0.99503	B;D	0.56968	0.354;0.978	B;P	0.46479	0.044;0.518	T	0.01476	-1.1345	10	0.21014	T	0.42	-25.7887	13.1942	0.59728	0.0769:0.0:0.9231:0.0	.	638;638	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	N	638	ENSP00000356634:D638N;ENSP00000356633:D638N	ENSP00000356633:D638N	D	+	1	0	PAPPA2	174831275	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	3.863000	0.56016	2.542000	0.85734	0.650000	0.86243	GAC		0.602	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176564652	G	A	176564652	3	1	104	1	0	0	0	0	1	0	0	0	11464	1058	37	1	1918	1	PAPPA2	1	176564652	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	3408733	176564652	72685969	14	27443										
USH2A	7399	hgsc.bcm.edu	37	chr1	216256829	216256829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	caggtccatctttgttataaAcgaaaagaagcaatccattt	6	8	1	1	rs368520422		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:216256829A>G	ENST00000307340.3	-	26	5653	c.5267T>C	c.(5266-5268)gTt>gCt	p.V1756A	RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.V1756A|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1756	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTTGTTATAAACGAAAAGAAG	0.303										HNSCC(13;0.011)																																						0			1						A	ALA/VAL	0,4404		0,0,2202	96	100	98		5267	3.2	0.7	1		98	1,8597	1.2+/-3.3	0,1,4298	no	missense	USH2A	NM_206933.2	64	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	benign	1756/5203	216256829	1,13001	2202	4299	6501	214323452	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5267T>C	1.37:g.216256829A>G	ENSP00000305941:p.Val1756Ala		214323452	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	10.38	1.333660	0.24167	0.0	1.16E-4	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.76839	-1.05;-1.05	4.38	3.25	0.37280	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.783880	0.10646	N	0.650406	T	0.62998	0.2474	L	0.27053	0.805	0.20074	N	0.999939	B	0.20459	0.045	B	0.21360	0.034	T	0.43081	-0.9413	10	0.08179	T	0.78	.	9.8214	0.40885	0.9176:0.0:0.0824:0.0	.	1756	O75445	USH2A_HUMAN	A	1756	ENSP00000305941:V1756A;ENSP00000355910:V1756A	ENSP00000305941:V1756A	V	-	2	0	USH2A	214323452	0.879000	0.30193	0.685000	0.30070	0.941000	0.58515	3.282000	0.51693	0.656000	0.30886	0.533000	0.62120	GTT		0.303	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216256829	A	G	216256829	3	3	104	1	0	0	0	0	1	0	0	0	17076	43	2	4	10529	4	USH2A	1	216256829	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	39692177	216256829	32993792	15	27444										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371443	240371475	+	In_Frame_Del	DEL	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	-													0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagtgggcatacctcctccgCcccctctacccggagcgggc					rs200800873|rs199920451|rs112021213|rs367816204|rs199702261|rs200682272|rs201396397|rs181634878	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENST00000319653.9	+	5	3561_3593	c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	c.(3331-3363)ccccctctacccggagcgggcataccccctcctdel	p.PPLPGAGIPPP1133del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1133	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.A1259A(1)|p.G1260C(1)|p.P1262P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCTCCTCCGCCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCTCTAC	0.721																																																3	Substitution - coding silent(2)|Substitution - Missense(1)	lung(2)|prostate(1)	1								366,2650		115,136,1257						-4.9	0			10	861,5641		256,349,2646	no	coding	FMN2	NM_020066.4		371,485,3903	A1A1,A1R,RR		13.2421,12.1353,12.8914				1227,8291				238438098	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	1.37:g.240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENSP00000318884:p.Pro1133_Pro1143del		238438066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.721	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240371475	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	-	240371443	7	5	104	1	0	1	0	1	0	0	0	0	5969	739	26	0	3349	0	FMN2	1	240371443	In_Frame_Del	DEL	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	TCGA-DY-A1DC-01A-31D-A152-10	24114614	240371443	8879178	16	27445										
OR2C3	81472	hgsc.bcm.edu	37	chr1	247695310	247695310	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atgcaattgttcccacacagCggtaggagcatggtgagcgt	13	9	0	1	rs544163828		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:247695310C>T	ENST00000366487.3	-	2	865	c.504G>A	c.(502-504)ccG>ccA	p.P168P	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-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)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			TCCCACACAGCGGTAGGAGCA	0.547													C|||	1	0.000199681	8e-04	0	5008	,	,		22838	0		0	False		,,,				2504	0															0			1											67	61	63					1																	247695310		2203	4300	6503	245761933	SO:0001819	synonymous_variant	81472			BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.504G>A	1.37:g.247695310C>T			245761933	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	37	CCDS1634.2																																																																																				0.547	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		T	247695310	C	T	247695310	2	4	104	1	0	0	0	0	0	0	0	1	11024	755	27	1		1	OR2C3	1	247695310	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	7323867	247695310	1555311	17	27446										
ALLC	55821	hgsc.bcm.edu	37	chr2	3750040	3750040	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccaggctcaccatcgtccccGacgggggagtgagccgcctt	13	16	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:3750040G>A	ENST00000252505.3	+	12	1225	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N	AC010907.5_ENST00000441632.1_RNA	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	374					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		CATCGTCCCCGACGGGGGAGT	0.592										HNSCC(21;0.051)																																						0			2											30	33	32					2																	3750040		1922	4120	6042	3727915	SO:0001583	missense	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.1063G>A	2.37:g.3750040G>A	ENSP00000252505:p.Asp355Asn		3727915	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162708	0.78226	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.04	5.04	0.67666	Allantoicase domain (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.87233	0.6126	H	0.96015	3.755	0.50039	D	0.999845	D	0.89917	1.0	D	0.74348	0.983	D	0.91263	0.5038	9	0.87932	D	0	-6.7836	16.2404	0.82405	0.0:0.0:1.0:0.0	.	374	Q8N6M5	ALLC_HUMAN	N	355	.	ENSP00000252505:D355N	D	+	1	0	ALLC	3727915	1.000000	0.71417	0.373000	0.26003	0.561000	0.35649	6.194000	0.72082	2.494000	0.84150	0.591000	0.81541	GAC		0.592	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			A	3750040	G	A	3750040	3	1	104	1	0	0	0	0	1	0	0	0	534	1058	37	1	1105	1	ALLC	2	3750040	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		3750040	239449333	18	27447										
NBAS	51594	hgsc.bcm.edu	37	chr2	15608582	15608582	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	taatccatactgaagcagttCttttgcagcatccacatttt	5	10	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:15608582C>G	ENST00000281513.5	-	17	1826	c.1801G>C	c.(1801-1803)Gaa>Caa	p.E601Q	NBAS_ENST00000441750.1_Missense_Mutation_p.E601Q	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	601					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TGAAGCAGTTCTTTTGCAGCA	0.418																																																0			2											133	131	131					2																	15608582		2203	4300	6503	15526033	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1801G>C	2.37:g.15608582C>G	ENSP00000281513:p.Glu601Gln		15526033	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.338150	0.60963	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.12465	2.68;2.83	5.93	5.05	0.67936	.	0.050150	0.85682	D	0.000000	T	0.25269	0.0614	M	0.70275	2.135	0.27979	N	0.936114	D	0.59767	0.986	P	0.50659	0.647	T	0.15009	-1.0452	10	0.87932	D	0	.	11.6926	0.51525	0.0:0.8482:0.0:0.1518	.	601	A2RRP1	NBAS_HUMAN	Q	601	ENSP00000413201:E601Q;ENSP00000281513:E601Q	ENSP00000281513:E601Q	E	-	1	0	NBAS	15526033	1.000000	0.71417	0.898000	0.35279	0.986000	0.74619	4.989000	0.63870	1.515000	0.48885	0.650000	0.86243	GAA		0.418	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15608582	C	G	15608582	3	3	104	1	0	0	0	0	1	0	0	0	10216	922	32	5	5458	5	NBAS	2	15608582	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	11858542	15608582	227590791	19	27448										
LCLAT1	253558	hgsc.bcm.edu	37	chr2	30863099	30863099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aaatccactttcacgtccacCggtatccaatagacaccctc	4	16	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:30863099C>T	ENST00000309052.4	+	7	1068	c.859C>T	c.(859-861)Cgg>Tgg	p.R287W	LCLAT1_ENST00000540623.1_Missense_Mutation_p.R249W|LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000379509.3_Missense_Mutation_p.R249W	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	287					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R287W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCACGTCCACCGGTATCCAAT	0.507																																																1	Substitution - Missense(1)	ovary(1)	2											96	92	93					2																	30863099		2203	4300	6503	30716603	SO:0001583	missense	253558			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.859C>T	2.37:g.30863099C>T	ENSP00000310551:p.Arg287Trp		30716603	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192263	0.38707	.	.	ENSG00000172954	ENST00000379509;ENST00000444270;ENST00000309052;ENST00000540623	T;T;T	0.41758	0.99;0.99;0.99	5.77	2.63	0.31362	.	0.098864	0.64402	D	0.000002	T	0.68430	0.3000	M	0.88241	2.94	0.53688	D	0.999974	D	0.89917	1.0	D	0.85130	0.997	T	0.76187	-0.3051	10	0.72032	D	0.01	-18.7519	14.6333	0.68671	0.5279:0.4721:0.0:0.0	.	287	Q6UWP7	LCLT1_HUMAN	W	249;249;287;249	ENSP00000368823:R249W;ENSP00000310551:R287W;ENSP00000442857:R249W	ENSP00000310551:R287W	R	+	1	2	LCLAT1	30716603	0.803000	0.28956	0.233000	0.24025	0.059000	0.15707	1.579000	0.36536	0.750000	0.32877	0.557000	0.71058	CGG		0.507	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		T	30863099	C	T	30863099	3	4	104	1	0	0	0	0	1	0	0	0	8699	643	23	1	881	1	LCLAT1	2	30863099	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	15254517	30863099	212336274	20	27449										
ANTXR1	84168	hgsc.bcm.edu	37	chr2	69297841	69297841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gccaggaggagacacttacaTgcatgaaggatttgaaaggg	14	6	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:69297841T>C	ENST00000303714.4	+	4	681	c.359T>C	c.(358-360)aTg>aCg	p.M120T	ANTXR1_ENST00000409349.3_Missense_Mutation_p.M120T|ANTXR1_ENST00000409829.3_Missense_Mutation_p.M120T	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	120	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						GACACTTACATGCATGAAGGA	0.373									Familial Infantile Hemangioma																																							0			2											78	78	78					2																	69297841		2203	4300	6503	69151345	SO:0001583	missense	84168	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.359T>C	2.37:g.69297841T>C	ENSP00000301945:p.Met120Thr		69151345	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Missense_Mutation	SNP	ENST00000303714.4	37	CCDS1892.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.168585	0.57584	.	.	ENSG00000169604	ENST00000303714;ENST00000409829;ENST00000409349	T;T;T	0.78816	-1.21;-1.21;-1.21	6.03	4.86	0.63082	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.83575	0.5284	L	0.51853	1.615	0.49687	D	0.999813	D;P;P;D	0.89917	1.0;0.931;0.953;1.0	D;P;P;D	0.87578	0.99;0.743;0.831;0.998	T	0.82561	-0.0396	10	0.44086	T	0.13	-25.7359	11.7363	0.51767	0.0:0.0:0.1477:0.8523	.	120;120;120;120	Q9H6X2;Q9H6X2-2;Q9H6X2-4;Q9H6X2-3	ANTR1_HUMAN;.;.;.	T	120	ENSP00000301945:M120T;ENSP00000387058:M120T;ENSP00000386494:M120T	ENSP00000301945:M120T	M	+	2	0	ANTXR1	69151345	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.719000	0.74718	1.081000	0.41110	0.533000	0.62120	ATG		0.373	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		C	69297841	T	C	69297841	3	2	104	1	0	0	0	0	1	0	0	0	711	1464	51	4	373	4	ANTXR1	2	69297841	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	38434742	69297841	173901532	21	27450										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98409024	98409024	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaagggtgtgcgaggggggcGggagacagcctttcaggctg	21	7	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:98409024G>A	ENST00000186436.5	-	31	4197	c.3969C>T	c.(3967-3969)ccC>ccT	p.P1323P		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1323	Pro-rich.					integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CGAGGGGGGCGGGAGACAGCC	0.662																																																0			2											23	26	25					2																	98409024		2090	4210	6300	97775456	SO:0001819	synonymous_variant	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.3969C>T	2.37:g.98409024G>A			97775456		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																				0.662	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		A	98409024	G	A	98409024	2	1	104	1	0	0	0	0	0	0	0	1	16083	1103	39	1		1	TMEM131	2	98409024	Silent	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	29111183	98409024	144790349	22	27451										
UXS1	80146	hgsc.bcm.edu	37	chr2	106713247	106713247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctgtgggtcatcctgggctTcggagagaaactgaatttca	12	8	3	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:106713247T>C	ENST00000409501.3	-	14	1115	c.1058A>G	c.(1057-1059)gAa>gGa	p.E353G	UXS1_ENST00000283148.7_Missense_Mutation_p.E358G|UXS1_ENST00000540130.1_Missense_Mutation_p.E296G|UXS1_ENST00000409032.1_Missense_Mutation_p.E185G			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	353					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						ATCCTGGGCTTCGGAGAGAAA	0.463																																																0			2											107	96	100					2																	106713247		1866	4109	5975	106079679	SO:0001583	missense	80146			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	17729	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 6E, member 12"	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.1058A>G	2.37:g.106713247T>C	ENSP00000387019:p.Glu353Gly		106079679	Q8NBX3|Q9H5C2	Missense_Mutation	SNP	ENST00000409501.3	37	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976254	0.53720	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.46444	0.1393	L	0.42632	1.34	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.32613	-0.9900	10	0.27785	T	0.31	-9.4366	15.8945	0.79325	0.0:0.0:0.0:1.0	.	358;353;358	Q8NBZ7-2;Q8NBZ7;A8K3Q3	.;UXS1_HUMAN;.	G	358;296;353;185	ENSP00000283148:E358G;ENSP00000438265:E296G;ENSP00000387019:E353G;ENSP00000387096:E185G	ENSP00000283148:E358G	E	-	2	0	UXS1	106079679	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.632000	0.83247	2.152000	0.67230	0.455000	0.32223	GAA		0.463	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3		C	106713247	T	C	106713247	3	2	104	1	0	0	0	0	1	0	0	0	17149	1783	62	4	212	4	UXS1	2	106713247	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	8304223	106713247	136486126	23	27452										
LCT	3938	hgsc.bcm.edu	37	chr2	136564712	136564712	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cctcacctgatatgcagcagAagctgcactccagatgaagc	9	13	1	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:136564712A>G	ENST00000264162.2	-	9	4169	c.4159T>C	c.(4159-4161)Tct>Cct	p.S1387P		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1387	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TATGCAGCAGAAGCTGCACTC	0.572																																																0			2											128	102	111					2																	136564712		2203	4300	6503	136281182	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4159T>C	2.37:g.136564712A>G	ENSP00000264162:p.Ser1387Pro		136281182	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.384799	0.61956	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.35605	1.3	5.87	-1.37	0.09056	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.345527	0.33346	N	0.005004	T	0.61223	0.2330	M	0.91612	3.225	0.23076	N	0.998335	D	0.56035	0.974	P	0.61874	0.895	T	0.62186	-0.6907	10	0.62326	D	0.03	-17.9564	14.3548	0.66730	0.3265:0.0:0.0:0.6735	.	1387	P09848	LPH_HUMAN	P	1387;819	ENSP00000264162:S1387P	ENSP00000264162:S1387P	S	-	1	0	LCT	136281182	0.079000	0.21365	0.114000	0.21550	0.965000	0.64279	0.372000	0.20467	-0.470000	0.06901	0.533000	0.62120	TCT		0.572	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136564712	A	G	136564712	3	3	104	1	0	0	0	0	1	0	0	0	8715	246	9	4	1660	4	LCT	2	136564712	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	29851465	136564712	106634661	24	27453										
ACVR1	90	hgsc.bcm.edu	37	chr2	158594089	158594089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gggaattatcaattttggtcAaagtctttttgatacgcagt	9	5	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:158594089A>G	ENST00000263640.3	-	11	1913	c.1484T>C	c.(1483-1485)tTg>tCg	p.L495S	ACVR1_ENST00000409283.2_Missense_Mutation_p.L495S|ACVR1_ENST00000434821.1_Missense_Mutation_p.L495S|AC019186.1_ENST00000447019.1_lincRNA|ACVR1_ENST00000410057.2_Missense_Mutation_p.L495S	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	495	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AATTTTGGTCAAAGTCTTTTT	0.403																																																0			2											141	128	133					2																	158594089		2203	4300	6503	158302335	SO:0001583	missense	90				CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.1484T>C	2.37:g.158594089A>G	ENSP00000263640:p.Leu495Ser		158302335		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.852255	0.71719	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	6.16	6.16	0.99307	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.060701	0.64402	D	0.000002	D	0.98112	0.9377	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99153	1.0859	10	0.87932	D	0	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	495	Q04771	ACVR1_HUMAN	S	495	ENSP00000263640:L495S;ENSP00000387273:L495S;ENSP00000405004:L495S;ENSP00000387127:L495S	ENSP00000263640:L495S	L	-	2	0	ACVR1	158302335	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TTG		0.403	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		G	158594089	A	G	158594089	3	3	104	1	0	0	0	0	1	0	0	0	220	131	5	4	49	4	ACVR1	2	158594089	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	22029377	158594089	84605284	25	27454										
TTN	7273	hgsc.bcm.edu	37	chr2	179410403	179410403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cccaacttcttcaggtatgcCgggtggtgatggaatagctg	13	9	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:179410403C>T	ENST00000591111.1	-	294	90735	c.90511G>A	c.(90511-90513)Ggc>Agc	p.G30171S	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G22872S|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G22747S|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G31812S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G29244S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G22939S|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30171	Fibronectin type-III 120. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGGTATGCCGGGTGGTGAT	0.418																																																0			2											156	148	151					2																	179410403		1920	4139	6059	179118649	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.90511G>A	2.37:g.179410403C>T	ENSP00000465570:p.Gly30171Ser		179118649	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.280670	0.80692	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.82	5.82	0.92795	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66877	0.2834	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67945	-0.5539	9	0.87932	D	0	.	20.1086	0.97902	0.0:1.0:0.0:0.0	.	22747;22872;22939;30171	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	29244;22747;22939;22872;22744	ENSP00000343764:G29244S;ENSP00000434586:G22747S;ENSP00000340554:G22939S;ENSP00000352154:G22872S	ENSP00000340554:G22939S	G	-	1	0	TTN	179118649	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.818000	0.86416	2.756000	0.94617	0.563000	0.77884	GGC		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179410403	C	T	179410403	3	4	104	1	0	0	0	0	1	0	0	0	16775	652	23	1	12621	1	TTN	2	179410403	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	20816314	179410403	63788970	26	27455										
TTN	7273	hgsc.bcm.edu	37	chr2	179591845	179591845	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ataaccttggtactgcagctTgtgctgccagcgggattctg	12	10	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:179591845T>A	ENST00000591111.1	-	67	19520	c.19296A>T	c.(19294-19296)acA>acT	p.T6432T	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T6749T|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342992.6_Silent_p.T5505T|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	13199	Ig-like 45.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACTGCAGCTTGTGCTGCCAG	0.423																																																0			2											120	117	118					2																	179591845		1902	4119	6021	179300090	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19296A>T	2.37:g.179591845T>A			179300090	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179591845	T	A	179591845	2	1	104	1	0	0	0	0	0	0	0	1	16775	1799	63	5		5	TTN	2	179591845	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	181442	179591845	63607528	27	27456										
MSTN	2660	hgsc.bcm.edu	37	chr2	190927004	190927004	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcgtgataatcgtcatcttCcaaagagccatcgctgctgt	9	11	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:190927004C>G	ENST00000260950.4	-	1	451	c.319G>C	c.(319-321)Gaa>Caa	p.E107Q	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	107					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			TCGTCATCTTCCAAAGAGCCA	0.428																																																0			2											145	131	136					2																	190927004		2203	4300	6503	190635249	SO:0001583	missense	2660			AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.319G>C	2.37:g.190927004C>G	ENSP00000260950:p.Glu107Gln		190635249	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	37	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424863	0.83667	.	.	ENSG00000138379	ENST00000260950	T	0.64991	-0.13	5.35	5.35	0.76521	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79522	0.4460	M	0.75085	2.285	0.80722	D	1	D	0.63880	0.993	D	0.68621	0.959	T	0.80867	-0.1190	10	0.72032	D	0.01	-21.5226	19.2576	0.93952	0.0:1.0:0.0:0.0	.	107	O14793	GDF8_HUMAN	Q	107	ENSP00000260950:E107Q	ENSP00000260950:E107Q	E	-	1	0	MSTN	190635249	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.932000	0.70121	2.789000	0.95967	0.655000	0.94253	GAA		0.428	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		G	190927004	C	G	190927004	3	3	104	1	0	0	0	0	1	0	0	0	9923	864	30	5	820	5	MSTN	2	190927004	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	11335159	190927004	52272369	28	27457										
ALS2CR11	151254	hgsc.bcm.edu	37	chr2	202483686	202483686	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggcagggccgtcgtgccctgGttcagggcgtaagggaccga	18	11	1	0	rs142023452	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:202483686G>C	ENST00000286195.3	-	1	212	c.168C>G	c.(166-168)aaC>aaG	p.N56K	ALS2CR11_ENST00000450242.1_Missense_Mutation_p.N56K|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.N56K|ALS2CR11_ENST00000439140.1_Missense_Mutation_p.N56K	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	56										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TCGTGCCCTGGTTCAGGGCGT	0.637																																																0			2											60	59	59					2																	202483686		2203	4300	6503	202191931	SO:0001583	missense	151254			AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.168C>G	2.37:g.202483686G>C	ENSP00000286195:p.Asn56Lys		202191931	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	G	0.526	-0.860182	0.02610	.	.	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.44881	0.92;0.92;0.91;0.91	3.26	-1.04	0.10068	.	4.384240	0.00738	N	0.000993	T	0.18551	0.0445	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.13255	-1.0516	10	0.06365	T	0.9	.	2.3281	0.04228	0.1423:0.4475:0.2619:0.1483	.	56;56;56	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	K	56	ENSP00000286195:N56K;ENSP00000400672:N56K;ENSP00000409937:N56K;ENSP00000399016:N56K	ENSP00000286195:N56K	N	-	3	2	ALS2CR11	202191931	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.057000	0.03486	-0.225000	0.09913	0.557000	0.71058	AAC		0.637	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		C	202483686	G	C	202483686	3	2	104	1	0	0	0	0	1	0	0	0	552	1252	44	5	5505	5	ALS2CR11	2	202483686	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	11556682	202483686	40715687	29	27458										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234873393	234873393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggctaatgagtacgagacccGggctgttggtgagtccacag	15	9	0	3	rs201008719		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:234873393G>A	ENST00000324695.4	+	14	1911	c.1871G>A	c.(1870-1872)cGg>cAg	p.R624Q	TRPM8_ENST00000433712.2_Missense_Mutation_p.R312Q	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	624					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TACGAGACCCGGGCTGTTGGT	0.582																																																0			2											79	62	68					2																	234873393		2203	4300	6503	234538132	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1871G>A	2.37:g.234873393G>A	ENSP00000323926:p.Arg624Gln		234538132	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419346	0.25552	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.62788	-0.0;-0.0	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000004	T	0.54287	0.1849	L	0.58428	1.81	0.33618	D	0.604483	P;B	0.38800	0.648;0.123	B;B	0.23852	0.049;0.008	T	0.66980	-0.5786	10	0.29301	T	0.29	-17.911	17.9113	0.88934	0.0:0.0:1.0:0.0	.	312;624	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	Q	624;312	ENSP00000323926:R624Q;ENSP00000404423:R312Q	ENSP00000323926:R624Q	R	+	2	0	TRPM8	234538132	0.730000	0.28100	0.607000	0.28956	0.039000	0.13416	3.958000	0.56737	2.563000	0.86464	0.655000	0.94253	CGG		0.582	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234873393	G	A	234873393	3	1	104	1	0	0	0	0	1	0	0	0	16632	1116	39	1	1921	1	TRPM8	2	234873393	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	32389707	234873393	8325980	30	27459										
TGFBR2	7048	hgsc.bcm.edu	37	chr3	30729947	30729947	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtgtcgaaagcatgaaggacAacgtgttgagagatcgaggg	16	5	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:30729947A>G	ENST00000295754.5	+	6	1850	c.1468A>G	c.(1468-1470)Aac>Gac	p.N490D	TGFBR2_ENST00000359013.4_Missense_Mutation_p.N515D	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	490	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> S (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CATGAAGGACAACGTGTTGAG	0.488																																																0			3											127	118	121					3																	30729947		2203	4300	6503	30704951	SO:0001583	missense	7048				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"transforming growth factor, beta receptor II (70-80kD)"	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1468A>G	3.37:g.30729947A>G	ENSP00000295754:p.Asn490Asp		30704951	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047392	0.75846	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	T;T	0.65178	-0.14;-0.14	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.239102	0.48767	D	0.000176	T	0.47967	0.1474	N	0.16201	0.385	0.58432	D	0.999997	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.45220	-0.9276	10	0.62326	D	0.03	.	15.6821	0.77376	1.0:0.0:0.0:0.0	.	490;515	P37173;D2JYI1	TGFR2_HUMAN;.	D	490;515;320	ENSP00000295754:N490D;ENSP00000351905:N515D	ENSP00000295754:N490D	N	+	1	0	TGFBR2	30704951	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	9.065000	0.93941	2.165000	0.68154	0.482000	0.46254	AAC		0.488	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2			G	30729947	A	G	30729947	3	3	104	1	0	0	0	0	1	0	0	0	15861	130	5	4	1569	4	TGFBR2	3	30729947	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10		30729947	167292483	31	27460										
USP4	7375	hgsc.bcm.edu	37	chr3	49337909	49337909	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gattctgtcacctgagtaggTctgcagtgagggtcagcagg	15	8	4	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:49337909T>C	ENST00000265560.4	-	11	1549	c.1503A>G	c.(1501-1503)agA>agG	p.R501R	USP4_ENST00000351842.4_Silent_p.R454R|USP4_ENST00000488520.1_5'Flank	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	501	USP.|Ubiquitin-like 2.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		CCTGAGTAGGTCTGCAGTGAG	0.532																																																0			3											116	114	114					3																	49337909		2203	4300	6503	49312913	SO:0001819	synonymous_variant	7375			U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1503A>G	3.37:g.49337909T>C			49312913	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.280966	0.23392	.	.	ENSG00000114316	ENST00000431357	.	.	.	5.83	0.917	0.19380	.	.	.	.	.	T	0.55800	0.1943	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47394	-0.9121	4	.	.	.	-18.5278	8.833	0.35096	0.0:0.2953:0.0:0.7047	.	.	.	.	A	240	.	.	T	-	1	0	USP4	49312913	0.996000	0.38824	0.997000	0.53966	0.991000	0.79684	0.344000	0.19962	0.141000	0.18875	0.459000	0.35465	ACC		0.532	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49337909	T	C	49337909	2	2	104	1	0	0	0	0	0	0	0	1	17111	1664	58	4		4	USP4	3	49337909	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	18607962	49337909	148684521	32	27461										
NEK4	6787	hgsc.bcm.edu	37	chr3	52800367	52800367	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttgagttttcagatctcgatGaaggatgtgtttttcatgta	10	4	3	3	rs141525620		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:52800367G>T	ENST00000233027.5	-	3	587	c.385C>A	c.(385-387)Cat>Aat	p.H129N	NEK4_ENST00000535191.1_Missense_Mutation_p.H40N|NEK4_ENST00000383721.4_Missense_Mutation_p.H129N	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	129	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		AGATCTCGATGAAGGATGTGT	0.328																																																0			3											171	152	158					3																	52800367		2203	4300	6503	52775407	SO:0001583	missense	6787			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.385C>A	3.37:g.52800367G>T	ENSP00000233027:p.His129Asn		52775407	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	G	31	5.071423	0.93950	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.66099	-0.19;-0.07;-0.19;-0.07	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89822	0.6826	H	0.99719	4.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93794	0.7095	10	0.87932	D	0	.	20.3697	0.98890	0.0:0.0:1.0:0.0	.	40;129;129	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	N	129;40;129;40	ENSP00000233027:H129N;ENSP00000437703:H40N;ENSP00000373227:H129N;ENSP00000419666:H40N	ENSP00000233027:H129N	H	-	1	0	NEK4	52775407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.811000	0.96726	0.655000	0.94253	CAT		0.328	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		T	52800367	G	T	52800367	3	4	104	1	0	0	0	0	1	0	0	0	10357	1290	45	2	2196	2	NEK4	3	52800367	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	3462458	52800367	145222063	33	27462										
ACOX2	8309	hgsc.bcm.edu	37	chr3	58519219	58519219	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcagcgtggggctgtgtatcAcaaactcctgggtggctgcg	15	10	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:58519219A>T	ENST00000302819.5	-	5	827	c.536T>A	c.(535-537)gTg>gAg	p.V179E	ACOX2_ENST00000459701.2_Missense_Mutation_p.V179E	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	179					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GCTGTGTATCACAAACTCCTG	0.532											OREG0015638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			3											171	170	170					3																	58519219		2203	4300	6503	58494259	SO:0001583	missense	8309			X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"trihydroxycoprostanoyl-CoA oxidase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"	601641	"acyl-Coenzyme A oxidase 2, branched chain"			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.536T>A	3.37:g.58519219A>T	ENSP00000307697:p.Val179Glu	1031	58494259	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	37	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133429	0.77662	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	D;D	0.96232	-3.95;-3.95	4.85	3.66	0.41972	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.210963	0.31859	N	0.006947	D	0.96433	0.8836	L	0.55743	1.74	0.48762	D	0.999708	D	0.61697	0.99	P	0.60286	0.872	D	0.95496	0.8573	10	0.59425	D	0.04	-0.2733	10.7347	0.46117	0.857:0.0:0.0:0.143	.	179	Q99424	ACOX2_HUMAN	E	179	ENSP00000418562:V179E;ENSP00000307697:V179E	ENSP00000307697:V179E	V	-	2	0	ACOX2	58494259	0.999000	0.42202	0.947000	0.38551	0.991000	0.79684	4.219000	0.58561	0.782000	0.33613	0.459000	0.35465	GTG		0.532	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			T	58519219	A	T	58519219	3	4	104	1	0	0	0	0	1	0	0	0	159	159	6	5	1553	5	ACOX2	3	58519219	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	5718852	58519219	139503211	34	27463										
MAGI1	9223	hgsc.bcm.edu	37	chr3	65607705	65607705	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgctggagctcatgatcaggAgaccccttctggaatcgctg	12	11	3	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:65607705A>G	ENST00000497477.2	-	2	371	c.372T>C	c.(370-372)tcT>tcC	p.S124S	MAGI1_ENST00000402939.2_Silent_p.S124S|MAGI1_ENST00000330909.8_Silent_p.S124S|MAGI1_ENST00000483466.1_Silent_p.S124S|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	124	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.			S -> F (in Ref. 1; BAA32002 and 2; AAK94064/AAK94065/AAK94066/AAC51326). {ECO:0000305}.	cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CATGATCAGGAGACCCCTTCT	0.478																																																0			3											152	133	139					3																	65607705		2203	4300	6503	65582745	SO:0001819	synonymous_variant	154043			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.372T>C	3.37:g.65607705A>G			65582745	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37																																																																																					0.478	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		G	65607705	A	G	65607705	2	3	104	1	0	0	0	0	0	0	0	1	9220	291	11	4		4	MAGI1	3	65607705	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7088486	65607705	132414725	35	27464										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89391111	89391111	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agtttggactcaccaacaccAcggtgacagtgacagacctt	9	12	1	3	rs533112669		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:89391111A>G	ENST00000336596.2	+	5	1402	c.1177A>G	c.(1177-1179)Acg>Gcg	p.T393A	EPHA3_ENST00000494014.1_Missense_Mutation_p.T393A|EPHA3_ENST00000452448.2_Missense_Mutation_p.T393A	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	393	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CACCAACACCACGGTGACAGT	0.483										TSP Lung(6;0.00050)																																						0			3											104	89	94					3																	89391111		2203	4300	6503	89473801	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1177A>G	3.37:g.89391111A>G	ENSP00000337451:p.Thr393Ala		89473801	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.840910	0.32513	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.58506	0.33;0.33;0.33	5.66	5.66	0.87406	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	L	0.36672	1.1	0.58432	D	0.999999	B;B	0.30211	0.273;0.059	B;B	0.34590	0.186;0.06	T	0.43956	-0.9359	9	.	.	.	.	12.4245	0.55538	0.8745:0.0:0.0:0.1255	.	393;393	P29320;P29320-2	EPHA3_HUMAN;.	A	393	ENSP00000337451:T393A;ENSP00000399926:T393A;ENSP00000419190:T393A	.	T	+	1	0	EPHA3	89473801	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	6.082000	0.71318	2.285000	0.76669	0.533000	0.62120	ACG		0.483	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89391111	A	G	89391111	3	3	104	1	0	0	0	0	1	0	0	0	5181	159	6	4	1195	4	EPHA3	3	89391111	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	23783406	89391111	108631319	36	27465										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96963114	96963114	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gccattcacagctattacagTgaccacggatcaagatggta	9	10	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:96963114T>G	ENST00000389672.5	+	5	1627	c.1589T>G	c.(1588-1590)gTg>gGg	p.V530G	EPHA6_ENST00000470610.2_Missense_Mutation_p.V530G	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	436	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						GCTATTACAGTGACCACGGAT	0.393																																																0			3											105	99	101					3																	96963114		1881	4121	6002	98445804	SO:0001583	missense	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.1589T>G	3.37:g.96963114T>G	ENSP00000374323:p.Val530Gly		98445804	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006414	0.74932	.	.	ENSG00000080224	ENST00000470610;ENST00000389672	T;T	0.57107	4.45;0.42	5.49	5.49	0.81192	.	.	.	.	.	T	0.72407	0.3456	M	0.83774	2.66	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61477	0.889;0.889	T	0.77854	-0.2433	9	0.87932	D	0	.	15.6046	0.76652	0.0:0.0:0.0:1.0	.	530;530	B3KS12;E7EU71	.;.	G	530	ENSP00000420598:V530G;ENSP00000374323:V530G	ENSP00000374323:V530G	V	+	2	0	EPHA6	98445804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.685000	0.84117	2.089000	0.63090	0.528000	0.53228	GTG		0.393	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		G	96963114	T	G	96963114	3	3	104	1	0	0	0	0	1	0	0	0	5184	1696	59	4	1607	4	EPHA6	3	96963114	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	7572003	96963114	101059316	37	27466										
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125826045	125826045	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctcctccttggctatgaacaTgtggtcttccacgtctgtga	9	12	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:125826045T>C	ENST00000393434.2	-	21	2741	c.2392A>G	c.(2392-2394)Atg>Gtg	p.M798V	ALDH1L1_ENST00000452905.2_Missense_Mutation_p.M697V|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.M808V|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.M798V	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	798	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	GCTATGAACATGTGGTCTTCC	0.532																																																0			3											181	155	164					3																	125826045		2203	4300	6503	127308735	SO:0001583	missense	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2392A>G	3.37:g.125826045T>C	ENSP00000377083:p.Met798Val		127308735	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209220	0.58343	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	3.98	3.98	0.46160	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.88640	0.6491	H	0.94542	3.55	0.80722	D	1	D;D;D	0.60160	0.987;0.984;0.975	P;P;P	0.59221	0.822;0.854;0.73	D	0.90851	0.4731	10	0.87932	D	0	.	10.8723	0.46891	0.0:0.0:0.0:1.0	.	697;333;798	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	808;798;697;798	ENSP00000273450:M808V;ENSP00000420293:M798V;ENSP00000395881:M697V;ENSP00000377083:M798V	ENSP00000273450:M808V	M	-	1	0	ALDH1L1	127308735	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	7.527000	0.81931	1.677000	0.50941	0.260000	0.18958	ATG		0.532	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		C	125826045	T	C	125826045	3	2	104	1	0	0	0	0	1	0	0	0	494	1464	51	4	328	4	ALDH1L1	3	125826045	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	28862931	125826045	72196385	38	27467										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130287019	130287019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agtctcagattggaccagatCgggtgcaaattggtgtagtc	13	7	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:130287019C>T	ENST00000358511.6	+	5	2003	c.1972C>T	c.(1972-1974)Cgg>Tgg	p.R658W	COL6A6_ENST00000453409.2_Missense_Mutation_p.R658W	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	658	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGGACCAGATCGGGTGCAAAT	0.418																																																0			3											166	160	162					3																	130287019		1887	4109	5996	131769709	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1972C>T	3.37:g.130287019C>T	ENSP00000351310:p.Arg658Trp		131769709	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	3.726	-0.056643	0.07362	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79141	-1.24;-1.24	5.53	0.305	0.15801	von Willebrand factor, type A (3);	0.395727	0.21379	N	0.075504	T	0.74596	0.3737	M	0.82517	2.595	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.66842	-0.5821	10	0.72032	D	0.01	.	6.5339	0.22341	0.5293:0.3035:0.1039:0.0634	.	658	A6NMZ7	CO6A6_HUMAN	W	658	ENSP00000351310:R658W;ENSP00000399236:R658W	ENSP00000351310:R658W	R	+	1	2	COL6A6	131769709	0.000000	0.05858	0.018000	0.16275	0.030000	0.12068	-0.547000	0.06055	-0.237000	0.09739	-0.182000	0.12963	CGG		0.418	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130287019	C	T	130287019	3	4	104	1	0	0	0	0	1	0	0	0	3709	875	31	1	1990	1	COL6A6	3	130287019	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4460974	130287019	67735411	39	27468										
NEK11	79858	hgsc.bcm.edu	37	chr3	130947448	130947448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tattgtgaagagagtgatgaGgaggaagaagaaatagcgtt	15	1	0	6	rs145914506		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:130947448G>T	ENST00000510769.1	+	11	1414	c.1161G>T	c.(1159-1161)gaG>gaT	p.E387D	NEK11_ENST00000508196.1_Missense_Mutation_p.E492D|NEK11_ENST00000383366.4_Missense_Mutation_p.E492D|NEK11_ENST00000510688.1_Missense_Mutation_p.E492D|NEK11_ENST00000412440.2_Missense_Mutation_p.E308D|NEK11_ENST00000429253.2_Missense_Mutation_p.E492D					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						AGAGTGATGAGGAGGAAGAAG	0.433																																																0			3						G	ASP/GLU,ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	130	120	124		1476,1476	0.3	1	3	dbSNP_134	124	0,8600		0,0,4300	no	missense,missense	NEK11	NM_001146003.1,NM_024800.4	45,45	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	benign,benign	492/600,492/646	130947448	1,13005	2203	4300	6503	132430138	SO:0001583	missense	79858			AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"NIMA (never in mitosis gene a)- related kinase 11"				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1161G>T	3.37:g.130947448G>T	ENSP00000421549:p.Glu387Asp		132430138		Missense_Mutation	SNP	ENST00000510769.1	37		.	.	.	.	.	.	.	.	.	.	G	8.229	0.804269	0.16467	2.27E-4	0.0	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000510688;ENST00000383366;ENST00000412440;ENST00000508196	T;T;T;T;T;T	0.73469	-0.7;-0.52;-0.65;-0.52;-0.75;-0.52	5.53	0.33	0.15929	.	0.502608	0.16645	N	0.205469	T	0.46405	0.1391	N	0.12746	0.255	0.27115	N	0.962279	B;B;B;B	0.13145	0.004;0.004;0.003;0.007	B;B;B;B	0.14578	0.011;0.005;0.011;0.007	T	0.18023	-1.0350	10	0.15499	T	0.54	.	2.1536	0.03806	0.1468:0.1211:0.3602:0.3719	.	387;308;492;492	E9PHI8;B4DDN2;Q8NG66-4;Q8NG66	.;.;.;NEK11_HUMAN	D	387;492;492;492;308;492	ENSP00000421549:E387D;ENSP00000397180:E492D;ENSP00000423458:E492D;ENSP00000372857:E492D;ENSP00000411888:E308D;ENSP00000421851:E492D	ENSP00000372857:E492D	E	+	3	2	NEK11	132430138	0.777000	0.28628	0.990000	0.47175	0.449000	0.32228	-0.157000	0.10085	-0.002000	0.14469	0.561000	0.74099	GAG		0.433	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		T	130947448	G	T	130947448	3	4	104	1	0	0	0	0	1	0	0	0	10354	991	35	2	1544	2	NEK11	3	130947448	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	660429	130947448	67074982	40	27469										
XRN1	54464	hgsc.bcm.edu	37	chr3	142102234	142102234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgttttgatattggagaaacGggagtcgaaagctcggatgt	14	4	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:142102234G>A	ENST00000264951.4	-	22	2641	c.2524C>T	c.(2524-2526)Cgt>Tgt	p.R842C	XRN1_ENST00000392981.2_Missense_Mutation_p.R842C	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	842					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R842S(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TTGGAGAAACGGGAGTCGAAA	0.353																																																1	Substitution - Missense(1)	large_intestine(1)	3											72	71	71					3																	142102234		2203	4300	6503	143584924	SO:0001583	missense	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.2524C>T	3.37:g.142102234G>A	ENSP00000264951:p.Arg842Cys		143584924	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499535	0.85176	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.37058	1.22;1.23	5.97	5.97	0.96955	.	0.169118	0.56097	D	0.000032	T	0.54240	0.1846	M	0.73430	2.235	0.80722	D	1	P;D;D	0.69078	0.877;0.997;0.995	B;P;P	0.54924	0.093;0.764;0.586	T	0.57470	-0.7806	10	0.87932	D	0	-16.1482	15.8636	0.79043	0.0:0.1348:0.8652:0.0	.	703;842;842	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	C	842	ENSP00000264951:R842C;ENSP00000376707:R842C	ENSP00000264951:R842C	R	-	1	0	XRN1	143584924	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.659000	0.61504	2.833000	0.97629	0.585000	0.79938	CGT		0.353	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		A	142102234	G	A	142102234	3	1	104	1	0	0	0	0	1	0	0	0	17499	1116	39	1	2680	1	XRN1	3	142102234	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	11154786	142102234	55920196	41	27470										
PLSCR1	5359	hgsc.bcm.edu	37	chr3	146239397	146239397	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttatttttagtacatcctcTcttttctcattttgaattgt	3	8	2	1	rs201312426		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:146239397T>C	ENST00000342435.4	-	7	1082	c.672A>G	c.(670-672)agA>agG	p.R224R	PLSCR1_ENST00000448787.2_Silent_p.R143R|PLSCR1_ENST00000448205.1_Intron|PLSCR1_ENST00000487389.1_Silent_p.R217R	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	224					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						GTACATCCTCTCTTTTCTCAT	0.368																																																0			3											194	186	189					3																	146239397		2203	4300	6503	147722087	SO:0001819	synonymous_variant	5359			AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.672A>G	3.37:g.146239397T>C			147722087	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	37	CCDS3135.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	8.294	0.818427	0.16607	.	.	ENSG00000188313	ENST00000483300	.	.	.	5.17	2.46	0.29980	.	.	.	.	.	T	0.27313	0.0670	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.18999	-1.0319	4	.	.	.	.	5.6164	0.17434	0.1324:0.1702:0.0:0.6974	.	.	.	.	G	91	.	.	E	-	2	0	PLSCR1	147722087	0.000000	0.05858	0.894000	0.35097	0.934000	0.57294	0.005000	0.13129	0.828000	0.34709	0.528000	0.53228	GAG		0.368	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105		C	146239397	T	C	146239397	2	2	104	1	0	0	0	0	0	0	0	1	12140	1548	54	4		4	PLSCR1	3	146239397	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	4137163	146239397	51783033	42	27471										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147130434	147130434	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	caagatgtgcgacaagtcctAcacgcatcccagttcgctgc	9	14	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:147130434A>G	ENST00000282928.4	+	2	1841	c.1112A>G	c.(1111-1113)tAc>tGc	p.Y371C		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	371					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GACAAGTCCTACACGCATCCC	0.597																																																0			3											155	120	132					3																	147130434		2203	4300	6503	148613124	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.1112A>G	3.37:g.147130434A>G	ENSP00000282928:p.Tyr371Cys		148613124	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.288029|4.288029	0.80803|0.80803	.|.	.|.	ENSG00000152977|ENSG00000152977	ENST00000488404|ENST00000282928	.|T	.|0.53423	.|0.62	4.12|4.12	4.12|4.12	0.48240|0.48240	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.64402	.|U	.|0.000001	T|T	0.59891|0.59891	0.2227|0.2227	L|L	0.42686|0.42686	1.345|1.345	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.63633|0.63633	-0.6593|-0.6593	5|10	.|0.87932	.|D	.|0	.|.	13.1397|13.1397	0.59428|0.59428	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|371	.|Q15915	.|ZIC1_HUMAN	A|C	60|371	.|ENSP00000282928:Y371C	.|ENSP00000282928:Y371C	T|Y	+|+	1|2	0|0	ZIC1|ZIC1	148613124|148613124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	8.833000|8.833000	0.92089|0.92089	1.506000|1.506000	0.48736|0.48736	0.379000|0.379000	0.24179|0.24179	ACA|TAC		0.597	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		G	147130434	A	G	147130434	3	3	104	1	0	0	0	0	1	0	0	0	17717	391	14	4	1118	4	ZIC1	3	147130434	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	891037	147130434	50891996	43	27472										
AADAC	13	hgsc.bcm.edu	37	chr3	151545933	151545933	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cacagacttataaatcagtaTattgagtggctaaaggaaaa	8	5	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:151545933T>G	ENST00000232892.7	+	5	1299	c.1173T>G	c.(1171-1173)taT>taG	p.Y391*	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	391					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TAAATCAGTATATTGAGTGGC	0.323																																					Ovarian(30;839 841 2699 32801 46334)											0			3											35	38	37					3																	151545933		2185	4293	6478	153028623	SO:0001587	stop_gained	13			L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.1173T>G	3.37:g.151545933T>G	ENSP00000232892:p.Tyr391*		153028623	A8K3L3|D3DNJ6|Q8N1A9	Nonsense_Mutation	SNP	ENST00000232892.7	37	CCDS33877.1	.	.	.	.	.	.	.	.	.	.	T	33	5.220925	0.95139	.	.	ENSG00000114771	ENST00000232892	.	.	.	4.79	2.43	0.29744	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.3419	6.3466	0.21353	0.0:0.6027:0.0:0.3973	.	.	.	.	X	391	.	ENSP00000232892:Y391X	Y	+	3	2	AADAC	153028623	0.017000	0.18338	0.306000	0.25113	0.451000	0.32288	-0.171000	0.09883	0.677000	0.31305	0.482000	0.46254	TAT		0.323	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		G	151545933	T	G	151545933	4	3	104	1	0	0	0	0	0	1	0	0	10	1413	49	4	1191	4	AADAC	3	151545933	Nonsense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	4415499	151545933	46476497	44	27473										
ZMAT3	64393	hgsc.bcm.edu	37	chr3	178742984	178742984	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggccagatcacgtggaattcTctgccgagagcggggattga	15	9	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178742984T>A	ENST00000311417.2	-	6	1432	c.691A>T	c.(691-693)Aga>Tga	p.R231*	ZMAT3_ENST00000432729.1_Nonsense_Mutation_p.R230*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			CGTGGAATTCTCTGCCGAGAG	0.423																																																0			3											68	61	63					3																	178742984		2203	4300	6503	180225678	SO:0001587	stop_gained	64393			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.691A>T	3.37:g.178742984T>A	ENSP00000311221:p.Arg231*		180225678		Nonsense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	T	43	10.207832	0.99359	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	.	.	.	5.6	3.14	0.36123	.	0.048656	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-13.1297	8.6177	0.33842	0.1165:0.0:0.1938:0.6896	.	.	.	.	X	231;230	.	ENSP00000311221:R231X	R	-	1	2	ZMAT3	180225678	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.689000	0.54706	2.123000	0.65237	0.528000	0.53228	AGA		0.423	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		A	178742984	T	A	178742984	4	1	104	1	0	0	0	0	0	1	0	0	17732	1559	54	5	182	5	ZMAT3	3	178742984	Nonsense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	27197051	178742984	19279446	45	27474										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916663	178916663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtggggcatccacttgatgcCcccaagaatcctagtagaat	10	11	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178916663C>T	ENST00000263967.3	+	2	207	c.50C>T	c.(49-51)cCc>cTc	p.P17L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	17	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.I13_R19del(1)|p.L15_V22>PM(1)|p.P17del(1)|p.E9_R19del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CACTTGATGCCCCCAAGAATC	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	4	Deletion - In frame(3)|Complex - deletion inframe(1)	endometrium(2)|central_nervous_system(2)	3											56	56	56					3																	178916663		1854	4093	5947	180399357	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.50C>T	3.37:g.178916663C>T	ENSP00000263967:p.Pro17Leu		180399357	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569902	0.86542	.	.	ENSG00000121879	ENST00000477735;ENST00000263967;ENST00000468036	T;T	0.73047	-0.67;-0.71	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.82259	0.4998	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.83082	-0.0137	10	0.54805	T	0.06	-23.0055	18.8096	0.92053	0.0:1.0:0.0:0.0	.	17	P42336	PK3CA_HUMAN	L	17	ENSP00000263967:P17L;ENSP00000417479:P17L	ENSP00000263967:P17L	P	+	2	0	PIK3CA	180399357	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.394000	0.79862	2.506000	0.84524	0.650000	0.86243	CCC		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916663	C	T	178916663	3	4	104	1	0	0	0	0	1	0	0	0	11944	623	22	3	52	3	PIK3CA	3	178916663	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	173679	178916663	19105767	46	27475										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178927975	178927975	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tttttctttgttttttaaggAacactgtccattggcatggg	9	6	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178927975A>G	ENST00000263967.3	+	8	1410	c.1253A>G	c.(1252-1254)gAa>gGa	p.E418G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	418	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTTTTTAAGGAACACTGTCCA	0.323		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											77	73	74					3																	178927975		1816	4075	5891	180410669	SO:0001630	splice_region_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1252-1A>G	3.37:g.178927975A>G			180410669	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.005342	0.54254	.	.	ENSG00000121879	ENST00000263967	T	0.76578	-1.03	5.29	5.29	0.74685	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.057452	0.64402	D	0.000002	T	0.74329	0.3702	L	0.45698	1.435	0.80722	D	1	P	0.39737	0.685	B	0.41412	0.356	T	0.73691	-0.3903	10	0.33940	T	0.23	-10.6747	15.2222	0.73320	1.0:0.0:0.0:0.0	.	418	P42336	PK3CA_HUMAN	G	418	ENSP00000263967:E418G	ENSP00000263967:E418G	E	+	2	0	PIK3CA	180410669	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.962000	0.93254	2.012000	0.59069	0.460000	0.39030	GAA		0.323	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		Missense_Mutation	G	178927975	A	G	178927975	5	3	104	1	0	0	0	0	0	0	1	0	11944	260	9	4	1279	4	PIK3CA	3	178927975	Splice_Site	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	11312	178927975	19094455	47	27476										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952076	178952076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtatttcatgaaacaaatgaAtgatgcacatcatggtggct	9	6	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178952076A>G	ENST00000263967.3	+	21	3288	c.3131A>G	c.(3130-3132)aAt>aGt	p.N1044S	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1044	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N1044S(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAACAAATGAATGATGCACAT	0.373		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	3											99	89	92					3																	178952076		1910	4124	6034	180434770	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3131A>G	3.37:g.178952076A>G	ENSP00000263967:p.Asn1044Ser		180434770	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813104	0.50527	.	.	ENSG00000121879	ENST00000263967	T	0.81078	-1.45	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.39566	1.225	0.80722	D	1	P	0.45078	0.85	B	0.39339	0.297	T	0.71708	-0.4511	10	0.19590	T	0.45	-24.648	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1044	P42336	PK3CA_HUMAN	S	1044	ENSP00000263967:N1044S	ENSP00000263967:N1044S	N	+	2	0	PIK3CA	180434770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	AAT		0.373	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952076	A	G	178952076	3	3	104	1	0	0	0	0	1	0	0	0	11944	101	4	4	3209	4	PIK3CA	3	178952076	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	24101	178952076	19070354	48	27477										
APOD	347	hgsc.bcm.edu	37	chr3	195295922	195295922	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aagcaaaatccacgtgaaaaAgttggatgatgcaggtacag	11	6	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:195295922A>G	ENST00000343267.3	-	5	780	c.419T>C	c.(418-420)cTt>cCt	p.L140P		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	140					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CACGTGAAAAAGTTGGATGAT	0.448																																																0			3											151	152	151					3																	195295922		2203	4300	6503	196777211	SO:0001583	missense	347				CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"Lipocalins", "Apolipoproteins"	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.419T>C	3.37:g.195295922A>G	ENSP00000345179:p.Leu140Pro		196777211	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.933118	0.52866	.	.	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.29397	1.57;1.57;1.96	6.06	6.06	0.98353	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.33381	0.0861	L	0.59436	1.845	0.80722	D	1	B	0.29552	0.248	B	0.31245	0.126	T	0.11179	-1.0598	10	0.54805	T	0.06	-19.8325	13.0011	0.58676	1.0:0.0:0.0:0.0	.	140	P05090	APOD_HUMAN	P	140;168;140	ENSP00000345179:L140P;ENSP00000415235:L168P;ENSP00000393076:L140P	ENSP00000345179:L140P	L	-	2	0	APOD	196777211	1.000000	0.71417	0.982000	0.44146	0.009000	0.06853	8.321000	0.89997	2.324000	0.78689	0.533000	0.62120	CTT		0.448	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		G	195295922	A	G	195295922	3	3	104	1	0	0	0	0	1	0	0	0	801	72	3	4	154	4	APOD	3	195295922	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	16343846	195295922	2726508	49	27478										
EVC2	132884	hgsc.bcm.edu	37	chr4	5664855	5664855	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttctaaggcttgaagcatgCtcccagggtcctcggaagac	11	12	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:5664855C>G	ENST00000344408.5	-	9	1177	c.1124G>C	c.(1123-1125)aGc>aCc	p.S375T	EVC2_ENST00000344938.1_Missense_Mutation_p.S375T|EVC2_ENST00000310917.2_Missense_Mutation_p.S295T	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	375					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TTGAAGCATGCTCCCAGGGTC	0.448																																																0			4											117	110	113					4																	5664855		2203	4300	6503	5715756	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1124G>C	4.37:g.5664855C>G	ENSP00000342144:p.Ser375Thr		5715756	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	14.51	2.555583	0.45487	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.77877	-1.13;-1.13;-1.13	5.07	3.31	0.37934	.	0.276138	0.30890	N	0.008670	T	0.80502	0.4635	M	0.65975	2.015	0.25250	N	0.989681	D	0.57571	0.98	P	0.55713	0.782	T	0.71427	-0.4596	10	0.59425	D	0.04	-8.5276	7.0728	0.25187	0.0:0.7964:0.0:0.2035	.	375	Q86UK5	LBN_HUMAN	T	375;295;375	ENSP00000339954:S375T;ENSP00000311683:S295T;ENSP00000342144:S375T	ENSP00000311683:S295T	S	-	2	0	EVC2	5715756	0.570000	0.26651	0.997000	0.53966	0.367000	0.29736	0.414000	0.21164	1.247000	0.43917	0.655000	0.94253	AGC		0.448	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		G	5664855	C	G	5664855	3	3	104	1	0	0	0	0	1	0	0	0	5299	797	28	5	2858	5	EVC2	4	5664855	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		5664855	185489421	50	27479										
PROM1	8842	hgsc.bcm.edu	37	chr4	15985929	15985929	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	acagaaagacatcaacagcaGtatctagagcggtggccaca	10	10	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:15985929G>T	ENST00000510224.1	-	23	2578	c.2330C>A	c.(2329-2331)aCt>aAt	p.T777N	PROM1_ENST00000543373.1_Missense_Mutation_p.T768N|PROM1_ENST00000540805.1_Missense_Mutation_p.T777N|PROM1_ENST00000508167.1_Missense_Mutation_p.T768N|PROM1_ENST00000539194.1_Missense_Mutation_p.T777N|PROM1_ENST00000505450.1_Missense_Mutation_p.T768N|PROM1_ENST00000447510.2_Missense_Mutation_p.T777N			O43490	PROM1_HUMAN	prominin 1	777					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ATCAACAGCAGTATCTAGAGC	0.438																																																0			4											82	81	81					4																	15985929		1938	4138	6076	15595027	SO:0001583	missense	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.2330C>A	4.37:g.15985929G>T	ENSP00000426809:p.Thr777Asn		15595027	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.326084|4.326084	0.81580|0.81580	.|.	.|.	ENSG00000007062|ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373|ENST00000513946	T;T;T;T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.156381|.	0.53938|.	D|.	0.000058|.	T|.	0.54334|.	0.1852|.	N|N	0.17474|0.17474	0.49|0.49	0.41425|0.41425	D|D	0.987821|0.987821	D;D;D;D;P;P|.	0.54964|.	0.969;0.969;0.969;0.969;0.628;0.949|.	P;P;P;P;B;P|.	0.58780|.	0.845;0.845;0.813;0.845;0.184;0.845|.	T|.	0.47736|.	-0.9094|.	9|.	.|.	.|.	.|.	-2.4275|-2.4275	20.2985|20.2985	0.98592|0.98592	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	768;777;768;777;768;777|.	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490|.	.;.;.;.;.;PROM1_HUMAN|.	N|X	777;777;777;768;768;777;768|27	ENSP00000415481:T777N;ENSP00000438045:T777N;ENSP00000443620:T777N;ENSP00000426090:T768N;ENSP00000427346:T768N;ENSP00000426809:T777N;ENSP00000445526:T768N|.	.|.	T|Y	-|-	2|3	0|2	PROM1|PROM1	15595027|15595027	1.000000|1.000000	0.71417|0.71417	0.137000|0.137000	0.22149|0.22149	0.045000|0.045000	0.14185|0.14185	6.141000|6.141000	0.71744|0.71744	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	ACT|TAC		0.438	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		T	15985929	G	T	15985929	3	4	104	1	0	0	0	0	1	0	0	0	12589	1029	36	2	287	2	PROM1	4	15985929	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	10321074	15985929	175168347	51	27480										
KIT	3815	hgsc.bcm.edu	37	chr4	55592166	55592166	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atgtaaggcttacaacgatgTgggcaagacttctgcctatt	10	8	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:55592166T>C	ENST00000288135.5	+	9	1587	c.1490T>C	c.(1489-1491)gTg>gCg	p.V497A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	497	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E490_F504>DHIVVSLTF(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACAACGATGTGGGCAAGACT	0.398		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Complex - deletion inframe(1)	soft_tissue(1)	4											132	118	123					4																	55592166		2203	4300	6503	55286923	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1490T>C	4.37:g.55592166T>C	ENSP00000288135:p.Val497Ala		55286923	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	12.42	1.931574	0.34096	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.76839	-1.05;2.5	6.02	4.81	0.61882	Immunoglobulin-like fold (1);	0.111084	0.39759	N	0.001269	T	0.75583	0.3869	M	0.77406	2.37	0.44603	D	0.997579	B;B	0.10296	0.002;0.003	B;B	0.14023	0.01;0.007	T	0.71603	-0.4543	10	0.51188	T	0.08	.	7.909	0.29778	0.0:0.0728:0.1468:0.7804	.	497;497	P10721-2;P10721	.;KIT_HUMAN	A	497	ENSP00000288135:V497A;ENSP00000390987:V497A	ENSP00000288135:V497A	V	+	2	0	KIT	55286923	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.073000	0.50057	1.069000	0.40788	0.533000	0.62120	GTG		0.398	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55592166	T	C	55592166	3	2	104	1	0	0	0	0	1	0	0	0	8350	1696	59	4	1524	4	KIT	4	55592166	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	39606237	55592166	135562110	52	27481										
KIT	3815	hgsc.bcm.edu	37	chr4	55593994	55593994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcttccttcctacagggaaaAccctgggtgctggagctttc	10	12	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:55593994A>G	ENST00000288135.5	+	12	1877	c.1780A>G	c.(1780-1782)Acc>Gcc	p.T594A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACAGGGAAAACCCTGGGTGC	0.458		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4											68	61	64					4																	55593994		2203	4300	6503	55288751	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1780A>G	4.37:g.55593994A>G	ENSP00000288135:p.Thr594Ala		55288751	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610837	0.66558	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.89196	-2.48;-2.48	6.04	4.85	0.62838	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000007	D	0.87458	0.6182	N	0.25201	0.72	0.58432	D	0.999999	B;D;D	0.55800	0.246;0.973;0.961	B;P;P	0.54499	0.27;0.754;0.658	D	0.88026	0.2772	10	0.59425	D	0.04	.	13.5393	0.61664	0.8699:0.1301:0.0:0.0	.	101;590;594	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	A	594;590	ENSP00000288135:T594A;ENSP00000390987:T590A	ENSP00000288135:T594A	T	+	1	0	KIT	55288751	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	9.248000	0.95456	1.092000	0.41356	0.460000	0.39030	ACC		0.458	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55593994	A	G	55593994	3	3	104	1	0	0	0	0	1	0	0	0	8350	43	2	4	1826	4	KIT	4	55593994	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	1828	55593994	135560282	53	27482										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79786721	79786721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctgttgtagaataacagatAccattggaccaacagaaacc	7	9	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:79786721A>G	ENST00000335016.5	+	10	1244	c.1078A>G	c.(1078-1080)Acc>Gcc	p.T360A	BMP2K_ENST00000502871.1_Missense_Mutation_p.T360A	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	360					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AATAACAGATACCATTGGACC	0.368																																																0			4											98	91	93					4																	79786721		2203	4300	6503	80005745	SO:0001583	missense	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1078A>G	4.37:g.79786721A>G	ENSP00000334836:p.Thr360Ala		80005745	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.41|11.41	1.630669|1.630669	0.28978|0.28978	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502871;ENST00000335016;ENST00000264889|ENST00000502613	T;T|.	0.71698|.	1.92;-0.59|.	5.26|5.26	2.76|2.76	0.32466|0.32466	Protein kinase-like domain (1);|.	0.378699|.	0.27437|.	N|.	0.019370|.	T|T	0.31949|0.31949	0.0813|0.0813	L|L	0.44542|0.44542	1.39|1.39	0.30104|0.30104	N|N	0.807177|0.807177	B;B|.	0.28998|.	0.112;0.23|.	B;B|.	0.27076|.	0.076;0.05|.	T|T	0.33954|0.33954	-0.9848|-0.9848	10|5	0.51188|.	T|.	0.08|.	-12.5546|-12.5546	0.3559|0.3559	0.00356|0.00356	0.4006:0.1333:0.2091:0.2569|0.4006:0.1333:0.2091:0.2569	.|.	360;360|.	Q9NSY1;Q4W5H2|.	BMP2K_HUMAN;.|.	A|C	360;360;374|52	ENSP00000421768:T360A;ENSP00000334836:T360A|.	ENSP00000264889:T374A|.	T|Y	+|+	1|2	0|0	BMP2K|BMP2K	80005745|80005745	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	0.468000|0.468000	0.22051|0.22051	0.378000|0.378000	0.24764|0.24764	-0.290000|-0.290000	0.09829|0.09829	ACC|TAC		0.368	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		G	79786721	A	G	79786721	3	3	104	1	0	0	0	0	1	0	0	0	1461	391	14	4	1116	4	BMP2K	4	79786721	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	24192727	79786721	111367555	54	27483										
HERC3	8916	hgsc.bcm.edu	37	chr4	89591099	89591099	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctttatctactgaggggaagAaagacattcttaattcccgt	8	8	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:89591099A>G	ENST00000402738.1	+	15	1961	c.1722A>G	c.(1720-1722)agA>agG	p.R574R	HERC3_ENST00000264345.3_Silent_p.R574R|HERC3_ENST00000543130.1_Silent_p.R18R	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	574					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TGAGGGGAAGAAAGACATTCT	0.403																																																0			4											115	116	116					4																	89591099		2203	4300	6503	89810122	SO:0001819	synonymous_variant	8916			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1722A>G	4.37:g.89591099A>G			89810122	A8K1S5|Q8IXX3	Silent	SNP	ENST00000402738.1	37	CCDS34028.1																																																																																				0.403	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		G	89591099	A	G	89591099	2	3	104	1	0	0	0	0	0	0	0	1	7080	243	9	4		4	HERC3	4	89591099	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	9804378	89591099	101563177	55	27484										
MTTP	4547	hgsc.bcm.edu	37	chr4	100543934	100543934	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gatgtgaattcccgctccatCaagagaactcagagatgtgc	10	10	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:100543934C>A	ENST00000265517.5	+	18	2817	c.2614C>A	c.(2614-2616)Caa>Aaa	p.Q872K	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.Q872K|MTTP_ENST00000511045.1_Missense_Mutation_p.Q899K			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	872					cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	CCCGCTCCATCAAGAGAACTC	0.433																																																0			4											161	159	160					4																	100543934		2203	4300	6503	100762957	SO:0001583	missense	4571				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.2614C>A	4.37:g.100543934C>A	ENSP00000265517:p.Gln872Lys		100762957	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222799	0.95139	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.65364	-0.15;-0.13;-0.13	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.79868	0.4520	M	0.71581	2.175	0.80722	D	1	D;D	0.69078	0.995;0.997	P;D	0.73380	0.777;0.98	T	0.78414	-0.2213	10	0.56958	D	0.05	-19.5906	20.4702	0.99162	0.0:1.0:0.0:0.0	.	899;872	E9PBP6;P55157	.;MTP_HUMAN	K	899;872;872	ENSP00000427679:Q899K;ENSP00000400821:Q872K;ENSP00000265517:Q872K	ENSP00000265517:Q872K	Q	+	1	0	MTTP	100762957	1.000000	0.71417	0.999000	0.59377	0.856000	0.48823	7.142000	0.77339	2.937000	0.99478	0.650000	0.86243	CAA		0.433	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100543934	C	A	100543934	3	1	104	1	0	0	0	0	1	0	0	0	9994	827	29	2	2684	2	MTTP	4	100543934	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	10952835	100543934	90610342	56	27485										
ELOVL6	79071	hgsc.bcm.edu	37	chr4	110980783	110980783	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttcgggtgctttgcttagcaCaaatgcataagcccagaatt	9	9	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:110980783C>G	ENST00000394607.3	-	4	512	c.349G>C	c.(349-351)Gtg>Ctg	p.V117L	ELOVL6_ENST00000506461.1_5'Flank|ELOVL6_ENST00000302274.3_Missense_Mutation_p.V117L			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	117					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		TTGCTTAGCACAAATGCATAA	0.408																																																0			4											92	80	84					4																	110980783		2203	4300	6503	111200232	SO:0001583	missense	79071			AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.349G>C	4.37:g.110980783C>G	ENSP00000378105:p.Val117Leu		111200232	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	37	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519622	0.85495	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625	T;T;T	0.22945	1.93;1.93;1.93	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	L	0.28400	0.85	0.80722	D	1	B	0.20988	0.05	B	0.28011	0.085	T	0.04128	-1.0975	10	0.23302	T	0.38	-5.5054	19.8016	0.96509	0.0:1.0:0.0:0.0	.	117	Q9H5J4	ELOV6_HUMAN	L	117	ENSP00000378105:V117L;ENSP00000304736:V117L;ENSP00000425488:V117L	ENSP00000304736:V117L	V	-	1	0	ELOVL6	111200232	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.718000	0.84743	2.770000	0.95276	0.655000	0.94253	GTG		0.408	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		G	110980783	C	G	110980783	3	3	104	1	0	0	0	0	1	0	0	0	5091	478	17	5	456	5	ELOVL6	4	110980783	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	10436849	110980783	80173493	57	27486										
PDE5A	8654	hgsc.bcm.edu	37	chr4	120486475	120486475	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttctttagtaatcagactgaCctgatttctcttgttctcca	5	10	4	3	rs201028578		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:120486475C>T	ENST00000354960.3	-	5	1313		c.e5+1		PDE5A_ENST00000264805.5_Splice_Site|PDE5A_ENST00000394439.1_Splice_Site	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific						blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	ATCAGACTGACCTGATTTCTC	0.313																																																0			4											67	62	63					4																	120486475		2203	4299	6502	120705923	SO:0001630	splice_region_variant	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.993+1G>A	4.37:g.120486475C>T			120705923	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Splice_Site	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791214	0.90367	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7068	0.96076	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE5A	120705923	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.083000	0.76859	2.824000	0.97209	0.655000	0.94253	.		0.313	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	Intron	T	120486475	C	T	120486475	5	4	104	1	0	0	0	0	0	0	1	0	11675	521	18	3	1701	3	PDE5A	4	120486475	Splice_Site	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	9505692	120486475	70667801	58	27487										
TDO2	6999	hgsc.bcm.edu	37	chr4	156831349	156831349	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctgagcaggaaaagacacttCtggaattagtggaggtatgg	14	5	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:156831349C>A	ENST00000536354.2	+	6	668	c.604C>A	c.(604-606)Ctg>Atg	p.L202M		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		AAAGACACTTCTGGAATTAGT	0.308																																					Colon(57;928 1036 2595 6946 26094)											0			4											55	59	57					4																	156831349		2202	4299	6501	157050799	SO:0001583	missense	6999				CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.604C>A	4.37:g.156831349C>A	ENSP00000444788:p.Leu202Met		157050799		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.528840	0.44969	.	.	ENSG00000151790	ENST00000536354	.	.	.	4.92	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.74230	0.3689	M	0.85710	2.77	0.80722	D	1	P	0.44006	0.824	P	0.51866	0.682	T	0.76537	-0.2923	9	0.46703	T	0.11	-14.8693	12.6982	0.57016	0.0:0.9177:0.0:0.0823	.	202	P48775	T23O_HUMAN	M	202	.	ENSP00000281525:L202M	L	+	1	2	TDO2	157050799	0.984000	0.35163	0.799000	0.32177	0.126000	0.20510	2.684000	0.46951	1.175000	0.42826	0.644000	0.83932	CTG		0.308	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		A	156831349	C	A	156831349	3	1	104	1	0	0	0	0	1	0	0	0	15766	912	32	2	626	2	TDO2	4	156831349	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	36344874	156831349	34322927	59	27488										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167656131	167656131	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atccccttcatcttcatcatCatcttcaatttcatcttcat	0	14	10	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:167656131C>T	ENST00000357154.3	-	12	1389	c.1252G>A	c.(1252-1254)Gat>Aat	p.D418N	SPOCK3_ENST00000502330.1_Missense_Mutation_p.D418N|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000421836.2_Missense_Mutation_p.D367N|SPOCK3_ENST00000357545.4_Missense_Mutation_p.D415N|SPOCK3_ENST00000534949.1_Missense_Mutation_p.D322N|SPOCK3_ENST00000504953.1_Missense_Mutation_p.D415N|SPOCK3_ENST00000506886.1_Missense_Mutation_p.D418N|SPOCK3_ENST00000541354.1_Missense_Mutation_p.D298N|SPOCK3_ENST00000510741.1_Missense_Mutation_p.D375N|SPOCK3_ENST00000535728.1_Missense_Mutation_p.D286N|SPOCK3_ENST00000541637.1_Missense_Mutation_p.D320N|SPOCK3_ENST00000511269.1_Missense_Mutation_p.D415N|SPOCK3_ENST00000512681.1_Missense_Mutation_p.D320N|SPOCK3_ENST00000511531.1_Missense_Mutation_p.D418N	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	418	Asp-rich.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		tcttcatcatcatcttcaatt	0.348																																																0			4											180	172	174					4																	167656131		2203	4299	6502	167892706	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1252G>A	4.37:g.167656131C>T	ENSP00000349677:p.Asp418Asn		167892706	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	C	7.525	0.657401	0.14645	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.14	5.14	0.70334	.	0.141330	0.44902	U	0.000408	D	0.82926	0.5143	L	0.32530	0.975	0.52501	D	0.999954	D;D;D;D;D;D;D	0.89917	0.993;0.996;1.0;1.0;1.0;0.996;0.993	D;D;D;D;D;D;D	0.80764	0.984;0.993;0.994;0.994;0.994;0.993;0.984	T	0.83062	-0.0147	10	0.45353	T	0.12	-22.9046	18.5789	0.91164	0.0:1.0:0.0:0.0	.	320;322;367;427;375;415;418	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	N	418;415;415;418;418;418;375;298;320;415;286;367;320;322	ENSP00000349677:D418N;ENSP00000350153:D415N;ENSP00000425570:D415N;ENSP00000420920:D418N;ENSP00000423421:D418N;ENSP00000423606:D418N;ENSP00000426716:D375N;ENSP00000444789:D298N;ENSP00000426318:D320N;ENSP00000425502:D415N;ENSP00000441396:D286N;ENSP00000411344:D367N;ENSP00000445430:D320N;ENSP00000438142:D322N	ENSP00000349677:D418N	D	-	1	0	SPOCK3	167892706	1.000000	0.71417	0.990000	0.47175	0.063000	0.16089	5.206000	0.65192	2.552000	0.86080	0.637000	0.83480	GAT		0.348	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			T	167656131	C	T	167656131	3	4	104	1	0	0	0	0	1	0	0	0	15120	826	29	3	62	3	SPOCK3	4	167656131	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	10824782	167656131	23498145	60	27489										
CDH9	1007	hgsc.bcm.edu	37	chr5	26885951	26885951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gcgactgtagccatctttccGagtcatgattcctgctgtat	9	11	2	1	rs370038496		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:26885951G>A	ENST00000231021.4	-	11	1826	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCATCTTTCCGAGTCATGATT	0.343																																					Melanoma(8;187 585 15745 40864 52829)											0			5											59	60	60					5																	26885951		2203	4300	6503	26921708	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1654C>T	5.37:g.26885951G>A	ENSP00000231021:p.Arg552Trp		26921708	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791338	0.70452	.	.	ENSG00000113100	ENST00000231021	T	0.20332	2.08	5.79	4.9	0.64082	Cadherin (4);Cadherin-like (1);	0.056327	0.64402	D	0.000002	T	0.54515	0.1863	M	0.92077	3.27	0.41099	D	0.985659	D;D	0.89917	0.999;1.0	D;D	0.83275	0.978;0.996	T	0.64558	-0.6379	9	.	.	.	.	12.9437	0.58362	0.0:0.0:0.6774:0.3226	.	145;552	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	552	ENSP00000231021:R552W	.	R	-	1	2	CDH9	26921708	0.862000	0.29867	1.000000	0.80357	0.978000	0.69477	1.654000	0.37334	2.740000	0.93945	0.563000	0.77884	CGG		0.343	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26885951	G	A	26885951	3	1	104	1	0	0	0	0	1	0	0	0	3123	1057	37	1	723	1	CDH9	5	26885951	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		26885951	154029309	61	27490										
AGXT2	64902	hgsc.bcm.edu	37	chr5	35047957	35047957	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcctgggagcggaagtgaccAggcacaagggtctcagcaaa	14	10	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:35047957A>G	ENST00000231420.6	-	1	241	c.41T>C	c.(40-42)cTg>cCg	p.L14P		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	14					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	GGAAGTGACCAGGCACAAGGG	0.547																																																0			5											72	64	67					5																	35047957		2203	4300	6503	35083714	SO:0001583	missense	64902			AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"beta-alanine-pyruvate aminotransferase", "beta-ALAAT II"	612471	"alanine-glyoxylate aminotransferase 2"			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.41T>C	5.37:g.35047957A>G	ENSP00000231420:p.Leu14Pro		35083714	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.952327	0.34471	.	.	ENSG00000113492	ENST00000231420	D	0.83914	-1.78	3.42	0.846	0.18955	.	21.161200	0.00166	N	0.000000	T	0.80834	0.4699	L	0.51422	1.61	0.09310	N	0.999991	D;P	0.56968	0.978;0.61	P;B	0.45913	0.497;0.136	T	0.64952	-0.6286	10	0.30854	T	0.27	-10.1234	5.9647	0.19318	0.5737:0.0:0.0:0.4263	.	14;14	E9PDL7;Q9BYV1	.;AGT2_HUMAN	P	14	ENSP00000231420:L14P	ENSP00000231420:L14P	L	-	2	0	AGXT2	35083714	0.107000	0.21998	0.023000	0.16930	0.515000	0.34225	1.300000	0.33436	0.167000	0.19631	0.454000	0.30748	CTG		0.547	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900		G	35047957	A	G	35047957	3	3	104	1	0	0	0	0	1	0	0	0	405	188	7	4	1559	4	AGXT2	5	35047957	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	8162006	35047957	145867303	62	27491										
GPR98	84059	hgsc.bcm.edu	37	chr5	90049411	90049411	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	attttatttactgaaggccaGgtactgtcaacaatcactct	6	9	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:90049411G>C	ENST00000405460.2	+	54	11238	c.11142G>C	c.(11140-11142)caG>caC	p.Q3714H		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3714	Calx-beta 24. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTGAAGGCCAGGTACTGTCAA	0.318																																																0			5											95	94	94					5																	90049411		1819	4076	5895	90085167	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11142G>C	5.37:g.90049411G>C	ENSP00000384582:p.Gln3714His		90085167	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.66|15.66	2.899392|2.899392	0.52227|0.52227	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.33216|.	1.42|.	5.53|5.53	2.83|2.83	0.33086|0.33086	.|.	0.132302|.	0.52532|.	D|.	0.000062|.	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.996|.	D;P|.	0.69142|.	0.962;0.846|.	T|T	0.56214|0.56214	-0.8016|-0.8016	10|5	0.62326|.	D|.	0.03|.	.|.	8.3567|8.3567	0.32335|0.32335	0.3103:0.0:0.6897:0.0|0.3103:0.0:0.6897:0.0	.|.	3714;3714|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	H|T	3714|1280	ENSP00000384582:Q3714H|.	ENSP00000296619:Q3714H|.	Q|R	+|+	3|2	2|0	GPR98|GPR98	90085167|90085167	1.000000|1.000000	0.71417|0.71417	0.833000|0.833000	0.33012|0.33012	0.746000|0.746000	0.42486|0.42486	1.918000|1.918000	0.40006|0.40006	0.314000|0.314000	0.23086|0.23086	-0.262000|-0.262000	0.10625|0.10625	CAG|AGG		0.318	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90049411	G	C	90049411	3	2	104	1	0	0	0	0	1	0	0	0	6742	991	35	5	11356	5	GPR98	5	90049411	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	55001454	90049411	90865849	63	27492										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101834371	101834371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttttcggaaaccgccgaaccTtatcaaggcctctggaagta	9	11	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:101834371T>C	ENST00000506729.1	-	1	349	c.178A>G	c.(178-180)Agg>Ggg	p.R60G	SLCO6A1_ENST00000514551.1_5'Flank|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.R60G|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.R60G|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.R60G|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.R60G			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CCGCCGAACCTTATCAAGGCC	0.552																																																0			5											153	169	164					5																	101834371		2203	4300	6503	101862270	SO:0001583	missense	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.178A>G	5.37:g.101834371T>C	ENSP00000421339:p.Arg60Gly		101862270	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.313220	0.23908	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.48836	0.87;0.87;0.88;0.8;0.8	3.41	0.995	0.19838	.	11.615200	0.00166	N	0.000000	T	0.34048	0.0884	N	0.19112	0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.21177	-1.0253	10	0.48119	T	0.1	.	5.0536	0.14522	0.0:0.2566:0.0:0.7434	.	60;60;60	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	G	60	ENSP00000421339:R60G;ENSP00000369135:R60G;ENSP00000373671:R60G;ENSP00000421990:R60G;ENSP00000369138:R60G	ENSP00000369135:R60G	R	-	1	2	SLCO6A1	101862270	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.710000	0.25748	0.210000	0.20664	0.397000	0.26171	AGG		0.552	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		C	101834371	T	C	101834371	3	2	104	1	0	0	0	0	1	0	0	0	14769	1608	56	4	2033	4	SLCO6A1	5	101834371	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	11784960	101834371	79080889	64	27493										
APC	324	hgsc.bcm.edu	37	chr5	112175118	112175118	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atgtttttcaagatgtagttCattatcatctttgtcatcag	6	6	6	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175118C>T	ENST00000457016.1	+	16	4207	c.3827C>T	c.(3826-3828)tCa>tTa	p.S1276L	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.S1276L|APC_ENST00000257430.4_Missense_Mutation_p.S1276L			P25054	APC_HUMAN	adenomatous polyposis coli	1276	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1276*(5)|p.S1276L(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGATGTAGTTCATTATCATCT	0.353		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	8	Substitution - Nonsense(5)|Substitution - Missense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(5)|soft_tissue(1)|breast(1)|skin(1)	5	GRCh37	CD086479|CM086472|CM990161	APC	D|M							53	56	55					5																	112175118		2202	4300	6502	112203017	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3827C>T	5.37:g.112175118C>T	ENSP00000413133:p.Ser1276Leu		112203017	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.809899	0.70797	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.97424	0.9157	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.96781	0.9575	9	.	.	.	-13.3116	20.1672	0.98154	0.0:1.0:0.0:0.0	.	1278;1276	Q4LE70;P25054	.;APC_HUMAN	L	1276	ENSP00000413133:S1276L;ENSP00000257430:S1276L;ENSP00000427089:S1276L;ENSP00000423828:S1276L	.	S	+	2	0	APC	112203017	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.861000	0.98227	0.655000	0.94253	TCA		0.353	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175118	C	T	112175118	3	4	104	1	0	0	0	0	1	0	0	0	763	838	29	3	3885	3	APC	5	112175118	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	10340747	112175118	68740142	65	27494			1	27		3	3	825	N	C_A	1.55457e-05
APC	324	hgsc.bcm.edu	37	chr5	112175576	112175576	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atcttccagatagccctggaCaaaccatgccaccaagcaga	7	14	1	2	rs74535574		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175576C>T	ENST00000457016.1	+	16	4665	c.4285C>T	c.(4285-4287)Caa>Taa	p.Q1429*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1429*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1429*			P25054	APC_HUMAN	adenomatous polyposis coli	1429	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1429*(35)|p.Q1429fs*8(4)|p.Y1376fs*41(1)|p.?(1)|p.P1424fs*19(1)|p.S1411fs*41(1)|p.K1192fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGCCCTGGACAAACCATGCC	0.468	Q1429*(NCIH747_LARGE_INTESTINE)|Q1429*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	44	Substitution - Nonsense(35)|Deletion - Frameshift(8)|Unknown(1)	large_intestine(42)|soft_tissue(1)|skin(1)	5	GRCh37	HM050024	APC	M	rs74535574						109	98	102					5																	112175576		2202	4300	6502	112203475	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4285C>T	5.37:g.112175576C>T	ENSP00000413133:p.Gln1429*		112203475	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.799924	0.98958	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8813	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	1429	.	.	Q	+	1	0	APC	112203475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.884000	0.98904	0.655000	0.94253	CAA		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175576	C	T	112175576	4	4	104	1	0	0	0	0	0	1	0	0	763	479	17	3	4343	3	APC	5	112175576	Nonsense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	458	112175576	68739684	66	27495			1	27		3	3	825	N	C_A	1.55457e-05
APC	324	hgsc.bcm.edu	37	chr5	112175942	112175942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aatcaaatgaaaaccaagagAaagaggcagaaaaaactatt	7	5	1	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175942A>G	ENST00000457016.1	+	16	5031	c.4651A>G	c.(4651-4653)Aaa>Gaa	p.K1551E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.K1551E|APC_ENST00000257430.4_Missense_Mutation_p.K1551E			P25054	APC_HUMAN	adenomatous polyposis coli	1551	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)|p.K1551*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAACCAAGAGAAAGAGGCAGA	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											79	86	83					5																	112175942		2202	4300	6502	112203841	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4651A>G	5.37:g.112175942A>G	ENSP00000413133:p.Lys1551Glu		112203841	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	8.039	0.763515	0.15914	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88664	-2.41;-2.41;-2.41	6.16	5.01	0.66863	.	0.240065	0.49916	N	0.000138	T	0.82195	0.4984	L	0.35414	1.06	0.42707	D	0.993632	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.75280	-0.3373	9	.	.	.	-18.9638	12.1206	0.53889	0.9339:0.0:0.0661:0.0	.	1553;1551	Q4LE70;P25054	.;APC_HUMAN	E	1551	ENSP00000413133:K1551E;ENSP00000257430:K1551E;ENSP00000427089:K1551E	.	K	+	1	0	APC	112203841	1.000000	0.71417	0.987000	0.45799	0.956000	0.61745	3.319000	0.51983	1.163000	0.42636	0.528000	0.53228	AAA		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175942	A	G	112175942	3	3	104	1	0	0	0	0	1	0	0	0	763	247	9	4	4709	4	APC	5	112175942	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	366	112175942	68739318	67	27496			1	27		3	3	825	N	C_A	1.55457e-05
TSSK1B	83942	hgsc.bcm.edu	37	chr5	112769828	112769828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gcctgtcaggtgcttggagcGtgggaagttgacgcggtgct	18	8	1	1	rs55738530	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112769828G>A	ENST00000390666.3	-	1	900	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> C (in dbSNP:rs55738530). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		TGCTTGGAGCGTGGGAAGTTG	0.587													G|||	4	0.000798722	0	0.0029	5008	,	,		21207	0		0	False		,,,				2504	0.002															0			5						G	,CYS/ARG	0,4404		0,0,2202	80	73	76		,709	0.9	0.3	5	dbSNP_129	76	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,180	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,possibly-damaging	,237/368	112769828	1,13003	2202	4300	6502	112797727	SO:0001583	missense	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"serine/threonine kinase 22D (spermiogenesis associated)", "testis-specific serine kinase 1"	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.709C>T	5.37:g.112769828G>A	ENSP00000375081:p.Arg237Cys		112797727	B2R8D9	Missense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	7.873	0.728635	0.15507	0.0	1.16E-4	ENSG00000212122	ENST00000390666	T	0.24723	1.84	0.9	0.9	0.19278	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.236472	0.21381	U	0.075478	T	0.24928	0.0605	L	0.50993	1.605	0.09310	N	0.999999	D	0.65815	0.995	P	0.58970	0.849	T	0.05451	-1.0884	10	0.72032	D	0.01	.	4.9573	0.14048	0.0:0.0:1.0:0.0	rs55738530	237	Q9BXA7	TSSK1_HUMAN	C	237	ENSP00000375081:R237C	ENSP00000375081:R237C	R	-	1	0	TSSK1B	112797727	0.004000	0.15560	0.313000	0.25210	0.177000	0.22998	0.069000	0.14552	0.308000	0.22923	0.313000	0.20887	CGC		0.587	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		A	112769828	G	A	112769828	3	1	104	1	0	0	0	0	1	0	0	0	16708	1145	40	1	398	1	TSSK1B	5	112769828	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	593886	112769828	68145432	68	27497										
GFRA3	2676	hgsc.bcm.edu	37	chr5	137589745	137589745	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tacacatgcccccagcctcaCcaatcagccccaggtatgct	6	18	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:137589745C>T	ENST00000274721.3	-	5	1136		c.e5+1		GFRA3_ENST00000378362.3_Splice_Site	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3						nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCAGCCTCACCAATCAGCCC	0.547																																																0			5											148	130	136					5																	137589745		2203	4300	6503	137617644	SO:0001630	splice_region_variant	2676			AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.889+1G>A	5.37:g.137589745C>T			137617644	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Splice_Site	SNP	ENST00000274721.3	37	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049834	0.75846	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2504	0.54595	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GFRA3	137617644	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.689000	0.61723	2.245000	0.73994	0.650000	0.86243	.		0.547	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496	Intron	T	137589745	C	T	137589745	5	4	104	1	0	0	0	0	0	0	1	0	6369	521	18	3	328	3	GFRA3	5	137589745	Splice_Site	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	24819917	137589745	43325515	69	27498										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203403	140203403	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccgaaggcctcatcgcgggcGtcggcgggcgctgtgggtcc	18	14	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:140203403G>A	ENST00000529859.1	+	1	2043	c.2043G>A	c.(2041-2043)gcG>gcA	p.A681A	PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Silent_p.A681A|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000378126.3_Silent_p.A681A|PCDHA4_ENST00000530339.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	681					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATCGCGGGCGTCGGCGGGCG	0.667																																																0			5											42	49	46					5																	140203403		2203	4296	6499	140183587	SO:0001819	synonymous_variant	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2043G>A	5.37:g.140203403G>A			140183587	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																				0.667	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140203403	G	A	140203403	2	1	104	1	0	0	0	0	0	0	0	1	11558	1132	40	1		1	PCDHA5	5	140203403	Silent	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	2613658	140203403	40711857	70	27499										
CSF1R	1436	hgsc.bcm.edu	37	chr5	149453042	149453042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gttctgctcagagctcaagtTcaagtaggcactctctggaa	10	10	5	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:149453042T>C	ENST00000286301.3	-	7	1195	c.904A>G	c.(904-906)Aac>Gac	p.N302D	CSF1R_ENST00000543093.1_Intron	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	302	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GAGCTCAAGTTCAAGTAGGCA	0.502																																																0			5											104	95	98					5																	149453042		2203	4300	6503	149433235	SO:0001583	missense	1436			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.904A>G	5.37:g.149453042T>C	ENSP00000286301:p.Asn302Asp		149433235	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	T	1.645	-0.515408	0.04200	.	.	ENSG00000182578	ENST00000286301;ENST00000394307	T	0.78003	-1.14	4.81	3.64	0.41730	Immunoglobulin-like fold (1);	0.239562	0.29100	N	0.013148	T	0.65883	0.2734	L	0.51422	1.61	0.80722	D	1	B;P	0.44627	0.007;0.839	B;B	0.35550	0.016;0.205	T	0.57774	-0.7753	10	0.22706	T	0.39	.	9.5487	0.39297	0.0:0.0926:0.0:0.9074	.	154;302	B4E2Y8;P07333	.;CSF1R_HUMAN	D	302;154	ENSP00000286301:N302D	ENSP00000286301:N302D	N	-	1	0	CSF1R	149433235	1.000000	0.71417	0.998000	0.56505	0.056000	0.15407	2.195000	0.42677	0.210000	0.20664	-1.139000	0.01908	AAC		0.502	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		C	149453042	T	C	149453042	3	2	104	1	0	0	0	0	1	0	0	0	3938	1783	62	4	2078	4	CSF1R	5	149453042	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	9249639	149453042	31462218	71	27500										
UIMC1	51720	hgsc.bcm.edu	37	chr5	176396701	176396701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcggaagcatcagaaggccGgcaactctgaaacaagtgat	12	9	2	3	rs369146532		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:176396701G>A	ENST00000377227.4	-	5	496	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	UIMC1_ENST00000511320.1_Missense_Mutation_p.R122W|UIMC1_ENST00000503273.1_5'Flank|UIMC1_ENST00000506128.1_Missense_Mutation_p.R122W|UIMC1_ENST00000377219.2_Missense_Mutation_p.R122W			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	122	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGAAGGCCGGCAACTCTGA	0.493																																																0			5											96	93	94					5																	176396701		2203	4300	6503	176329307	SO:0001583	missense	51720			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.364C>T	5.37:g.176396701G>A	ENSP00000366434:p.Arg122Trp		176329307	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109611	0.56398	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000509236	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	5.64	3.82	0.43975	Ubiquitin interacting motif (1);	0.486110	0.19314	N	0.117319	T	0.15349	0.0370	N	0.08118	0	0.51012	D	0.999902	B	0.22211	0.066	B	0.14578	0.011	T	0.05419	-1.0886	10	0.39692	T	0.17	0.0817	9.1461	0.36933	0.0783:0.1467:0.775:0.0	.	122	Q96RL1	UIMC1_HUMAN	W	122;122;122;122;44;122	ENSP00000366434:R122W;ENSP00000366425:R122W;ENSP00000421926:R122W;ENSP00000427480:R122W;ENSP00000423885:R122W	ENSP00000366425:R122W	R	-	1	2	UIMC1	176329307	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.227000	0.58612	0.701000	0.31803	0.561000	0.74099	CGG		0.493	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		A	176396701	G	A	176396701	3	1	104	1	0	0	0	0	1	0	0	0	17011	1115	39	1	1839	1	UIMC1	5	176396701	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	26943659	176396701	4518559	72	27501										
ERVFRDE1	405754	hgsc.bcm.edu	37	chr6	11105007	11105007	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcaaagttccctgaggaaaAgtaatatttggaggtttggg	13	4	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:11105007A>G	ENST00000472091.1	-	2	912	c.537T>C	c.(535-537)acT>acC	p.T179T	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Silent_p.T179T	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	179					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						CCTGAGGAAAAGTAATATTTG	0.448																																																0			6											138	152	147					6																	11105007		2203	4299	6502	11212993	SO:0001819	synonymous_variant	0			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.537T>C	6.37:g.11105007A>G			11212993		Silent	SNP	ENST00000472091.1	37	CCDS4519.1																																																																																				0.448	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		G	11105007	A	G	11105007	2	3	104	1	0	0	0	0	0	0	0	1	5259	59	3	4		4	ERVFRDE1	6	11105007	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10		11105007	160010060	73	27502										
UBR2	23304	hgsc.bcm.edu	37	chr6	42612253	42612253	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctctaatagaagaaatgctaTacctcattataatgcttgtt	5	7	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:42612253T>C	ENST00000372899.1	+	20	2521	c.2263T>C	c.(2263-2265)Tac>Cac	p.Y755H	UBR2_ENST00000372883.3_Missense_Mutation_p.Y259H|UBR2_ENST00000372901.1_Missense_Mutation_p.Y755H	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	755					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AGAAATGCTATACCTCATTAT	0.313																																																0			6											96	97	97					6																	42612253		2203	4299	6502	42720231	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2263T>C	6.37:g.42612253T>C	ENSP00000361990:p.Tyr755His		42720231	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.637932	0.29157	.	.	ENSG00000024048	ENST00000372899;ENST00000372901;ENST00000372883	T;T;T	0.48201	0.82;0.82;0.82	5.86	5.86	0.93980	.	0.055638	0.85682	D	0.000000	T	0.06462	0.0166	N	0.00599	-1.345	0.49582	D	0.999801	B;B	0.12630	0.006;0.0	B;B	0.13407	0.009;0.001	T	0.33574	-0.9863	10	0.13108	T	0.6	0.0073	10.8408	0.46715	0.0:0.0702:0.0:0.9298	.	755;755	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	H	755;755;259	ENSP00000361990:Y755H;ENSP00000361992:Y755H;ENSP00000361974:Y259H	ENSP00000361974:Y259H	Y	+	1	0	UBR2	42720231	1.000000	0.71417	0.979000	0.43373	0.974000	0.67602	3.792000	0.55476	2.367000	0.80283	0.528000	0.53228	TAC		0.313	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		C	42612253	T	C	42612253	3	2	104	1	0	0	0	0	1	0	0	0	16942	1406	49	4	2487	4	UBR2	6	42612253	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	31507246	42612253	128502814	74	27503										
CDC5L	988	hgsc.bcm.edu	37	chr6	44387290	44387290	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcaggtgtaactccacagcgAcaagttgtacagactccaaa	8	11	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:44387290A>G	ENST00000371477.3	+	9	1496	c.1197A>G	c.(1195-1197)cgA>cgG	p.R399R		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	399	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCCACAGCGACAAGTTGTAC	0.428																																																0			6											160	142	148					6																	44387290		2203	4300	6503	44495268	SO:0001819	synonymous_variant	988			D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1197A>G	6.37:g.44387290A>G			44495268	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																				0.428	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			G	44387290	A	G	44387290	2	3	104	1	0	0	0	0	0	0	0	1	3088	262	10	4		4	CDC5L	6	44387290	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	1775037	44387290	126727777	75	27504										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51889913	51889913	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ataatgtagaagtgtctggaAacattaccagaacaagcata	8	6	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:51889913A>G	ENST00000371117.3	-	32	4970	c.4695T>C	c.(4693-4695)gtT>gtC	p.V1565V	PKHD1_ENST00000340994.4_Silent_p.V1565V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1565	IPT/TIG 10.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGTGTCTGGAAACATTACCAG	0.453																																																0			6											66	66	66					6																	51889913		2203	4300	6503	51997872	SO:0001819	synonymous_variant	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.4695T>C	6.37:g.51889913A>G			51997872	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																				0.453	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51889913	A	G	51889913	2	3	104	1	0	0	0	0	0	0	0	1	12002	1	1	4		4	PKHD1	6	51889913	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7502623	51889913	119225154	76	27505										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83843971	83843971	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctaacgagagatctccatatAaataaatcttcatcttttgt	4	8	4	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:83843971A>T	ENST00000349129.2	+	19	3095	c.2835A>T	c.(2833-2835)atA>atT	p.I945I	DOPEY1_ENST00000369739.3_Silent_p.I936I|DOPEY1_ENST00000237163.5_Silent_p.I926I	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	945					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		ATCTCCATATAAATAAATCTT	0.343																																																0			6											121	117	119					6																	83843971		2203	4300	6503	83900690	SO:0001819	synonymous_variant	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2835A>T	6.37:g.83843971A>T			83900690	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																				0.343	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83843971	A	T	83843971	2	4	104	1	0	0	0	0	0	0	0	1	4718	352	13	5		5	DOPEY1	6	83843971	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	31954058	83843971	87271096	77	27506										
SNX14	57231	hgsc.bcm.edu	37	chr6	86223808	86223808	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctctgagaagtgttatgagtGagaccaaacggtgctcctga	12	8	1	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:86223808G>T	ENST00000314673.3	-	25	2713	c.2537C>A	c.(2536-2538)tCa>tAa	p.S846*	SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000369627.2_Nonsense_Mutation_p.S837*|SNX14_ENST00000513865.1_Nonsense_Mutation_p.S565*|SNX14_ENST00000346348.3_Nonsense_Mutation_p.S793*|SNX14_ENST00000505648.1_Nonsense_Mutation_p.S794*	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	846					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TGTTATGAGTGAGACCAAACG	0.338																																																0			6											102	106	104					6																	86223808		2203	4300	6503	86280527	SO:0001587	stop_gained	57231			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.2537C>A	6.37:g.86223808G>T	ENSP00000313121:p.Ser846*		86280527	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Nonsense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	42|42	9.721242|9.721242	0.99247|0.99247	.|.	.|.	ENSG00000135317|ENSG00000135317	ENST00000508658|ENST00000346348;ENST00000314673;ENST00000513865;ENST00000505648;ENST00000369627;ENST00000515216	.|.	.|.	.|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.47783|.	0.1464|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.45731|.	-0.9241|.	3|.	.|0.08179	.|T	.|0.78	-11.9075|-11.9075	20.221|20.221	0.98325|0.98325	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	N|X	85|793;846;565;794;837;764	.|.	.|ENSP00000313121:S846X	H|S	-|-	1|2	0|0	SNX14|SNX14	86280527|86280527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.476000|9.476000	0.97823|0.97823	2.792000|2.792000	0.96026|0.96026	0.555000|0.555000	0.69702|0.69702	CAC|TCA		0.338	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		T	86223808	G	T	86223808	4	4	104	1	0	0	0	0	0	1	0	0	14922	1294	45	2	323	2	SNX14	6	86223808	Nonsense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	2379837	86223808	84891259	78	27507										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246935	97246935	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aaacacacactggggagctcGggaaggtatctgcaggtcgg	15	9	1	0	rs146501968		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:97246935G>A	ENST00000229955.3	-	2	1018	c.673C>T	c.(673-675)Cga>Tga	p.R225*	GPR63_ENST00000417980.1_Nonsense_Mutation_p.R225*	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TGGGGAGCTCGGGAAGGTATC	0.458																																																0			6						G	stop/ARG,stop/ARG	0,4406		0,0,2203	73	77	76		673,673	1.8	1	6	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	GPR63	NM_001143957.1,NM_030784.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	225/420,225/420	97246935	1,13005	2203	4300	6503	97353656	SO:0001587	stop_gained	81491			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.673C>T	6.37:g.97246935G>A	ENSP00000229955:p.Arg225*		97353656	Q9UJH3	Nonsense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	G	40	8.086701	0.98646	0.0	1.16E-4	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	.	.	.	5.2	1.76	0.24704	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2961	13.2464	0.60026	0.0:0.0:0.2866:0.7134	.	.	.	.	X	249;225;225;225	.	ENSP00000229955:R225X	R	-	1	2	GPR63	97353656	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.371000	0.44248	0.638000	0.30545	0.650000	0.86243	CGA		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			A	97246935	G	A	97246935	4	1	104	1	0	0	0	0	0	1	0	0	6724	1124	39	1	590	1	GPR63	6	97246935	Nonsense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	11023127	97246935	73868132	79	27508										
ROS1	6098	hgsc.bcm.edu	37	chr6	117645542	117645542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaaatattccaactataataGtaagtatgaaacttgtttct	5	5	1	1	rs373534757		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:117645542G>A	ENST00000368508.3	-	34	5792	c.5594C>T	c.(5593-5595)aCt>aTt	p.T1865I	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.T1859I	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1865					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AACTATAATAGTAAGTATGAA	0.284			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	0			6											45	48	47					6																	117645542		2201	4289	6490	117752235	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.5594C>T	6.37:g.117645542G>A	ENSP00000357494:p.Thr1865Ile		117752235	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	6.522	0.464621	0.12402	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70516	-0.49;-0.49	5.41	0.353	0.16058	.	0.877075	0.09899	N	0.741325	T	0.29093	0.0723	N	0.19112	0.55	0.09310	N	1	B	0.20887	0.049	B	0.19148	0.024	T	0.19353	-1.0308	10	0.32370	T	0.25	.	6.1554	0.20334	0.3365:0.131:0.5326:0.0	.	1865	P08922	ROS1_HUMAN	I	1865;1859	ENSP00000357494:T1865I;ENSP00000357493:T1859I	ENSP00000357493:T1859I	T	-	2	0	ROS1	117752235	0.003000	0.15002	0.043000	0.18650	0.564000	0.35744	-0.080000	0.11339	-0.150000	0.11195	-0.810000	0.03169	ACT		0.284	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117645542	G	A	117645542	3	1	104	1	0	0	0	0	1	0	0	0	13568	1029	36	3	1489	3	ROS1	6	117645542	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	20398607	117645542	53469525	80	27509										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129712777	129712777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aaatctagagacacaaaaggAaattgctgaagatgagttgg	11	4	1	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:129712777A>G	ENST00000421865.2	+	36	5262	c.5213A>G	c.(5212-5214)gAa>gGa	p.E1738G		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1738	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACACAAAAGGAAATTGCTGAA	0.348																																																0			6											111	124	120					6																	129712777		2203	4300	6503	129754470	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5213A>G	6.37:g.129712777A>G	ENSP00000400365:p.Glu1738Gly		129754470	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533615	0.27387	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.21031	2.03	6.06	6.06	0.98353	Laminin I (1);	0.238690	0.44688	D	0.000428	T	0.08758	0.0217	L	0.29908	0.895	0.29874	N	0.826613	P;P	0.39576	0.679;0.485	B;B	0.40066	0.318;0.248	T	0.10268	-1.0637	10	0.42905	T	0.14	.	12.4313	0.55575	0.9333:0.0:0.0667:0.0	.	1738;1738	A6NF00;P24043	.;LAMA2_HUMAN	G	1738	ENSP00000400365:E1738G	ENSP00000346769:E1738G	E	+	2	0	LAMA2	129754470	1.000000	0.71417	1.000000	0.80357	0.175000	0.22909	3.080000	0.50112	2.323000	0.78572	0.528000	0.53228	GAA		0.348	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129712777	A	G	129712777	3	3	104	1	0	0	0	0	1	0	0	0	8628	246	9	4	5355	4	LAMA2	6	129712777	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	12067235	129712777	41402290	81	27510										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138199578	138199578	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttggtcttcaggttggatgaAgctaacttaccaaaagaaat	9	6	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:138199578A>G	ENST00000237289.4	+	7	1062	c.996A>G	c.(994-996)gaA>gaG	p.E332E	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	332	2 X approximate repeats.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.?(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GGTTGGATGAAGCTAACTTAC	0.358			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	26	Whole gene deletion(25)|Unknown(1)	haematopoietic_and_lymphoid_tissue(26)	6											37	38	37					6																	138199578		2203	4300	6503	138241271	SO:0001819	synonymous_variant	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.996A>G	6.37:g.138199578A>G			138241271	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																				0.358	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138199578	A	G	138199578	2	3	104	1	0	0	0	0	0	0	0	1	16313	69	3	4		4	TNFAIP3	6	138199578	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	8486801	138199578	32915489	82	27511										
CCM2	83605	hgsc.bcm.edu	37	chr7	45108041	45108041	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagatggtgttgacttctcaGcccaggacccagggatctcc	12	12	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:45108041G>A	ENST00000258781.6	+	5	621		c.e5-1		CCM2_ENST00000461377.1_Splice_Site|CCM2_ENST00000475551.1_Splice_Site|CCM2_ENST00000474617.1_Intron|CCM2_ENST00000544363.1_Intron|CCM2_ENST00000541586.1_Splice_Site|CCM2_ENST00000381112.3_Splice_Site	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2						blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TGACTTCTCAGCCCAGGACCC	0.607																																																0			7											96	88	90					7																	45108041		2203	4300	6503	45074566	SO:0001630	splice_region_variant	83605			BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.473-1G>A	7.37:g.45108041G>A			45074566	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Splice_Site	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.111386	0.56398	.	.	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000475551;ENST00000381112	.	.	.	4.2	4.2	0.49525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.476	0.75481	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCM2	45074566	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	8.956000	0.93066	2.049000	0.60858	0.561000	0.74099	.		0.607	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Intron	A	45108041	G	A	45108041	5	1	104	1	0	0	0	0	0	0	1	0	2914	985	34	3	587	3	CCM2	7	45108041	Splice_Site	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		45108041	114030622	83	27512										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48428801	48428801	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgctggggacaaacggtgccGggaaaaccactatcatgtgg	14	9	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:48428801G>A	ENST00000435803.1	+	37	11662	c.11638G>A	c.(11638-11640)Ggg>Agg	p.G3880R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3880	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAACGGTGCCGGGAAAACCAC	0.483																																																0			7											45	47	46					7																	48428801		1873	4120	5993	48399347	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11638G>A	7.37:g.48428801G>A	ENSP00000411096:p.Gly3880Arg		48399347	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.473386	0.63737	.	.	ENSG00000179869	ENST00000435803	D	0.99878	-7.42	4.59	4.59	0.56863	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.43747	D	0.000537	D	0.99928	0.9967	H	0.99830	4.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95889	0.8905	10	0.87932	D	0	.	14.4612	0.67450	0.0:0.0:1.0:0.0	.	1582;3880	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	R	3880	ENSP00000411096:G3880R	ENSP00000411096:G3880R	G	+	1	0	ABCA13	48399347	1.000000	0.71417	0.918000	0.36340	0.464000	0.32679	8.057000	0.89457	2.254000	0.74563	0.655000	0.94253	GGG		0.483	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48428801	G	A	48428801	3	1	104	1	0	0	0	0	1	0	0	0	31	1116	39	1	11613	1	ABCA13	7	48428801	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	3320760	48428801	110709862	84	27513										
CASD1	64921	hgsc.bcm.edu	37	chr7	94168340	94168340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctggatgcaacttgtgatttTgatttatcacatttctggag	9	6	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:94168340T>C	ENST00000297273.4	+	10	1615	c.1328T>C	c.(1327-1329)tTg>tCg	p.L443S		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	443						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	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)			CTTGTGATTTTGATTTATCAC	0.318																																																0			7											119	115	117					7																	94168340		2203	4298	6501	94006276	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1328T>C	7.37:g.94168340T>C	ENSP00000297273:p.Leu443Ser		94006276	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.330568	0.81690	.	.	ENSG00000127995	ENST00000297273	T	0.63255	-0.03	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000001	T	0.81819	0.4903	M	0.88775	2.98	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	D	0.85886	0.1425	10	0.87932	D	0	.	14.6718	0.68951	0.0:0.0:0.0:1.0	.	443;443	Q8WZ77;Q96PB1	.;CASD1_HUMAN	S	443	ENSP00000297273:L443S	ENSP00000297273:L443S	L	+	2	0	CASD1	94006276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.928000	0.87587	1.938000	0.56188	0.482000	0.46254	TTG		0.318	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		C	94168340	T	C	94168340	3	2	104	1	0	0	0	0	1	0	0	0	2670	1821	63	4	1366	4	CASD1	7	94168340	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	45739539	94168340	64970323	85	27514										
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99434084	99434084	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tttattttatagttatgggaCccattcacataaacttttta	4	6	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:99434084C>G	ENST00000354829.2	+	2	183	c.80C>G	c.(79-81)aCc>aGc	p.T27S	CYP3A43_ENST00000421837.2_Missense_Mutation_p.T27S|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000417625.1_Missense_Mutation_p.T27S|CYP3A43_ENST00000415413.1_Missense_Mutation_p.T27S|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000312017.5_Missense_Mutation_p.T27S|CYP3A43_ENST00000222382.5_Missense_Mutation_p.T27S	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	27			T -> A (in dbSNP:rs45558032).|YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	AGTTATGGGACCCATTCACAT	0.388																																																0			7											80	80	80					7																	99434084		2203	4300	6503	99272020	SO:0001583	missense	64816			AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.80C>G	7.37:g.99434084C>G	ENSP00000346887:p.Thr27Ser		99272020	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.515296	0.27123	.	.	ENSG00000021461	ENST00000354829;ENST00000421837;ENST00000417625;ENST00000415413;ENST00000312017;ENST00000222382;ENST00000379654	T;T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0;3.0	2.44	2.44	0.29823	.	0.404335	0.24859	N	0.035040	T	0.21718	0.0523	M	0.61703	1.905	0.37616	D	0.92111	P;B;B;B	0.52170	0.951;0.007;0.004;0.02	P;B;B;B	0.60012	0.867;0.005;0.002;0.005	T	0.03887	-1.0995	10	0.42905	T	0.14	.	8.4505	0.32869	0.0:1.0:0.0:0.0	.	27;27;27;27	Q495Y1;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;CP343_HUMAN	S	27	ENSP00000346887:T27S;ENSP00000397332:T27S;ENSP00000416581:T27S;ENSP00000401521:T27S;ENSP00000312110:T27S;ENSP00000222382:T27S	ENSP00000222382:T27S	T	+	2	0	CYP3A43	99272020	0.554000	0.26522	0.252000	0.24328	0.474000	0.32979	1.065000	0.30592	1.658000	0.50742	0.205000	0.17691	ACC		0.388	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			G	99434084	C	G	99434084	3	3	104	1	0	0	0	0	1	0	0	0	4185	507	18	5	86	5	CYP3A43	7	99434084	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	5265744	99434084	59704579	86	27515										
RELN	5649	hgsc.bcm.edu	37	chr7	103276881	103276881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgggaatgtctgggatgccaTctcacaagctgggccagaaa	13	9	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:103276881T>C	ENST00000428762.1	-	18	2263	c.2104A>G	c.(2104-2106)Atg>Gtg	p.M702V	RELN_ENST00000424685.2_Missense_Mutation_p.M702V|RELN_ENST00000343529.5_Missense_Mutation_p.M702V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	702					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TGGGATGCCATCTCACAAGCT	0.428																																					NSCLC(146;835 1944 15585 22231 52158)											0			7											43	47	46					7																	103276881		2203	4300	6503	103064117	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2104A>G	7.37:g.103276881T>C	ENSP00000392423:p.Met702Val		103064117	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	7.599	0.672404	0.14776	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.06849	3.25;3.25;3.25	5.76	5.76	0.90799	.	0.102069	0.64402	D	0.000001	T	0.05410	0.0143	N	0.14661	0.345	0.35253	D	0.778912	B;B	0.13594	0.008;0.004	B;B	0.18263	0.021;0.007	T	0.11372	-1.0590	10	0.02654	T	1	.	16.0711	0.80936	0.0:0.0:0.0:1.0	.	702;702	P78509-2;P78509	.;RELN_HUMAN	V	702	ENSP00000392423:M702V;ENSP00000345694:M702V;ENSP00000388446:M702V	ENSP00000345694:M702V	M	-	1	0	RELN	103064117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.912000	0.63335	2.197000	0.70478	0.482000	0.46254	ATG		0.428	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103276881	T	C	103276881	3	2	104	1	0	0	0	0	1	0	0	0	13257	1435	50	4	8470	4	RELN	7	103276881	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	3842797	103276881	55861782	87	27516										
TRIM24	8805	hgsc.bcm.edu	37	chr7	138262232	138262232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcccagtggtcatgctggagCcaattcgaataaaacaagaa	9	9	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:138262232C>T	ENST00000343526.4	+	14	2370	c.2155C>T	c.(2155-2157)Cca>Tca	p.P719S	TRIM24_ENST00000415680.2_Missense_Mutation_p.P685S			O15164	TIF1A_HUMAN	tripartite motif containing 24	719					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						CATGCTGGAGCCAATTCGAAT	0.423																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)											0			7											85	84	84					7																	138262232		2203	4300	6503	137912772	SO:0001583	missense	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.2155C>T	7.37:g.138262232C>T	ENSP00000340507:p.Pro719Ser		137912772	A4D1R7|A4D1R8|O95854	Missense_Mutation	SNP	ENST00000343526.4	37	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163749	0.57476	.	.	ENSG00000122779	ENST00000343526;ENST00000536822;ENST00000415680	T;T	0.75704	-0.95;-0.96	5.67	5.67	0.87782	.	0.104158	0.64402	D	0.000002	T	0.62036	0.2395	L	0.29908	0.895	0.58432	D	0.999997	P;B	0.38420	0.63;0.383	B;B	0.32928	0.113;0.155	T	0.60627	-0.7226	10	0.12766	T	0.61	-14.7886	19.3578	0.94422	0.0:1.0:0.0:0.0	.	719;685	O15164;O15164-2	TIF1A_HUMAN;.	S	719;630;685	ENSP00000340507:P719S;ENSP00000390829:P685S	ENSP00000340507:P719S	P	+	1	0	TRIM24	137912772	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.266000	0.65525	2.661000	0.90470	0.460000	0.39030	CCA		0.423	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		T	138262232	C	T	138262232	3	4	104	1	0	0	0	0	1	0	0	0	16538	739	26	3	2209	3	TRIM24	7	138262232	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	34985351	138262232	20876431	88	27517										
WEE2	494551	hgsc.bcm.edu	37	chr7	141423048	141423048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tggccttaattacatccacaActctagcatggtacacctgg	7	12	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:141423048A>G	ENST00000397541.2	+	6	1401	c.995A>G	c.(994-996)aAc>aGc	p.N332S	WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000486906.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	332	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> K (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					TACATCCACAACTCTAGCATG	0.408																																																0			7											283	265	271					7																	141423048		1917	4131	6048	141069517	SO:0001583	missense	494551			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.995A>G	7.37:g.141423048A>G	ENSP00000380675:p.Asn332Ser		141069517		Missense_Mutation	SNP	ENST00000397541.2	37	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	A	2.325	-0.354835	0.05138	.	.	ENSG00000214102	ENST00000397541;ENST00000493845	T;T	0.61980	1.31;0.06	5.65	-2.26	0.06867	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.409615	0.25427	N	0.030743	T	0.18002	0.0432	N	0.00358	-1.6	0.23896	N	0.996531	B	0.06786	0.001	B	0.08055	0.003	T	0.41106	-0.9527	10	0.02654	T	1	.	9.2863	0.37760	0.3638:0.1243:0.5119:0.0	.	332	P0C1S8	WEE2_HUMAN	S	332;107	ENSP00000380675:N332S;ENSP00000420388:N107S	ENSP00000380675:N332S	N	+	2	0	WEE2	141069517	0.833000	0.29383	0.436000	0.26797	0.871000	0.50021	0.121000	0.15667	-0.674000	0.05253	0.528000	0.53228	AAC		0.408	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		G	141423048	A	G	141423048	3	3	104	1	0	0	0	0	1	0	0	0	17385	43	2	4	1017	4	WEE2	7	141423048	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	3160816	141423048	17715615	89	27518										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157874041	157874041	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gttttggacattggcgctcaCtttgaaggtcactgctggtc	12	9	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:157874041C>T	ENST00000389418.4	-	11	1681	c.1672G>A	c.(1672-1674)Gtg>Atg	p.V558M	PTPRN2_ENST00000389416.4_Missense_Mutation_p.V541M|PTPRN2_ENST00000389413.3_Missense_Mutation_p.V529M|PTPRN2_ENST00000404321.2_Missense_Mutation_p.V581M|PTPRN2_ENST00000409483.1_Missense_Mutation_p.V520M	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	558					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V558M(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	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)		TTGGCGCTCACTTTGAAGGTC	0.502																																																1	Substitution - Missense(1)	ovary(1)	7											301	212	242					7																	157874041		2203	4300	6503	157566802	SO:0001583	missense	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1672G>A	7.37:g.157874041C>T	ENSP00000374069:p.Val558Met		157566802	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132425	0.37630	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.05786	3.42;3.67;3.4;3.42;3.39	5.06	4.17	0.49024	.	0.464362	0.14485	U	0.316708	T	0.20292	0.0488	L	0.52573	1.65	0.32210	N	0.576637	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.80764	0.99;0.994;0.99;0.986;0.994	T	0.08700	-1.0709	10	0.87932	D	0	.	14.3595	0.66761	0.0:0.851:0.149:0.0	.	581;520;529;541;558	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	M	520;529;541;558;581	ENSP00000387114:V520M;ENSP00000374064:V529M;ENSP00000374067:V541M;ENSP00000374069:V558M;ENSP00000385464:V581M	ENSP00000374064:V529M	V	-	1	0	PTPRN2	157566802	1.000000	0.71417	0.319000	0.25293	0.044000	0.14063	1.771000	0.38542	1.131000	0.42111	0.650000	0.86243	GTG		0.502	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	157874041	C	T	157874041	3	4	104	1	0	0	0	0	1	0	0	0	12845	565	20	3	1427	3	PTPRN2	7	157874041	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	16450993	157874041	1264622	90	27519										
DUSP26	78986	hgsc.bcm.edu	37	chr8	33451072	33451072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcctggctggctcagcgcccGgtggatgaagtcggcagccg	16	13	1	1	rs376826832		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:33451072G>A	ENST00000256261.4	-	3	932	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W	DUSP26_ENST00000523956.1_Missense_Mutation_p.R139W	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	139	Tyrosine-protein phosphatase.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		CTCAGCGCCCGGTGGATGAAG	0.607																																																0			8											47	43	44					8																	33451072		2203	4300	6503	33570614	SO:0001583	missense	285193			AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.415C>T	8.37:g.33451072G>A	ENSP00000256261:p.Arg139Trp		33570614	D3DSV8|Q9BTW0	Missense_Mutation	SNP	ENST00000256261.4	37	CCDS6092.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365295	0.41902	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	D;D;D	0.86097	-2.07;-2.07;-2.07	4.77	3.86	0.44501	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.326541	0.29473	N	0.012052	D	0.86936	0.6053	M	0.88570	2.965	0.39036	D	0.960046	B	0.22146	0.065	B	0.23419	0.046	D	0.86329	0.1697	10	0.87932	D	0	-13.375	11.8524	0.52419	0.0:0.0:0.5538:0.4462	.	139	Q9BV47	DUS26_HUMAN	W	139	ENSP00000256261:R139W;ENSP00000429176:R139W;ENSP00000430922:R139W	ENSP00000256261:R139W	R	-	1	2	DUSP26	33570614	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.712000	0.47186	1.073000	0.40885	0.563000	0.77884	CGG		0.607	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025		A	33451072	G	A	33451072	3	1	104	1	0	0	0	0	1	0	0	0	4834	1115	39	1	228	1	DUSP26	8	33451072	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		33451072	112912950	91	27520										
LETM2	137994	hgsc.bcm.edu	37	chr8	38250441	38250441	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttctacttactttggattgaCgccaaagttgctgccagaat	8	9	1	2	rs369104625		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:38250441C>T	ENST00000379957.4	+	3	556	c.429C>T	c.(427-429)gaC>gaT	p.D143D	LETM2_ENST00000519476.2_Silent_p.D143D|LETM2_ENST00000523983.2_Silent_p.D96D|LETM2_ENST00000524874.1_Silent_p.D143D|LETM2_ENST00000297720.5_Silent_p.D96D	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	143	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			TTTGGATTGACGCCAAAGTTG	0.393																																																0			8						C	,,	0,4406		0,0,2203	61	62	62		288,,288	3.9	1	8		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-5,coding-synonymous	LETM2	NM_001199659.1,NM_001199660.1,NM_144652.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	96/445,,96/397	38250441	1,13005	2203	4300	6503	38369598	SO:0001819	synonymous_variant	137994			AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"EF-hand domain containing"	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.429C>T	8.37:g.38250441C>T			38369598	A6NMG3|Q8NCR2|Q96LL1	Silent	SNP	ENST00000379957.4	37																																																																																					0.393	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652		T	38250441	C	T	38250441	2	4	104	1	0	0	0	0	0	0	0	1	8757	535	19	1		1	LETM2	8	38250441	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4799369	38250441	108113581	92	27521										
RP1	6101	hgsc.bcm.edu	37	chr8	55534038	55534038	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaagacgaggcgtgcggttcTtctgagcaggagggtcaccc	16	10	3	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:55534038T>G	ENST00000220676.1	+	2	660	c.512T>G	c.(511-513)cTt>cGt	p.L171R		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	171	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		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)			CGTGCGGTTCTTCTGAGCAGG	0.652																																					Colon(91;1014 1389 7634 14542 40420)											0			8											101	102	102					8																	55534038		2203	4300	6503	55696591	SO:0001583	missense	10982			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.512T>G	8.37:g.55534038T>G	ENSP00000220676:p.Leu171Arg		55696591		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.401866	0.42613	.	.	ENSG00000104237	ENST00000220676	D	0.93076	-3.16	5.14	3.97	0.46021	Doublecortin domain (5);	0.836191	0.10222	N	0.700757	D	0.94251	0.8154	L	0.46157	1.445	0.09310	N	1	D	0.54397	0.966	P	0.58331	0.837	D	0.85918	0.1444	10	0.87932	D	0	0.0111	10.9459	0.47299	0.0:0.0742:0.0:0.9258	.	171	P56715	RP1_HUMAN	R	171	ENSP00000220676:L171R	ENSP00000220676:L171R	L	+	2	0	RP1	55696591	0.811000	0.29063	0.001000	0.08648	0.154000	0.21943	5.012000	0.64017	0.790000	0.33803	0.528000	0.53228	CTT		0.652	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55534038	T	G	55534038	3	3	104	1	0	0	0	0	1	0	0	0	13569	1609	56	4	514	4	RP1	8	55534038	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	17283597	55534038	90829984	93	27522										
TRAM1	23471	hgsc.bcm.edu	37	chr8	71487172	71487172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttagtttataattcattatgAagatttctcttttttattcc	3	5	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:71487172A>G	ENST00000262213.2	-	11	1289	c.1120T>C	c.(1120-1122)Tca>Cca	p.S374P	TRAM1_ENST00000536748.1_Missense_Mutation_p.S343P|TRAM1_ENST00000521425.1_Missense_Mutation_p.S288P	NM_014294.5	NP_055109.1	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	374					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	17			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			ATTCATTATGAAGATTTCTCT	0.313																																					Ovarian(85;984 1334 5116 12432 40638)											0			8											44	44	44					8																	71487172		2201	4290	6491	71649726	SO:0001583	missense	23471			X63679	CCDS6207.1	8q13.1	2004-01-22			ENSG00000067167	ENSG00000067167			20568	protein-coding gene	gene with protein product		605190				1315422	Standard	NM_014294		Approved	TRAM, TRAMP	uc003xyo.2	Q15629	OTTHUMG00000164428	ENST00000262213.2:c.1120T>C	8.37:g.71487172A>G	ENSP00000262213:p.Ser374Pro		71649726	B4E0K2	Missense_Mutation	SNP	ENST00000262213.2	37	CCDS6207.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554624	0.65425	.	.	ENSG00000067167	ENST00000521425;ENST00000262213;ENST00000536748	T;T;T	0.54479	0.57;1.19;1.19	5.94	5.94	0.96194	.	0.065801	0.64402	D	0.000005	T	0.60625	0.2283	L	0.39566	1.225	0.58432	D	0.999997	D	0.63046	0.992	D	0.63488	0.915	T	0.53844	-0.8381	10	0.13470	T	0.59	.	16.3998	0.83635	1.0:0.0:0.0:0.0	.	374	Q15629	TRAM1_HUMAN	P	288;374;343	ENSP00000428052:S288P;ENSP00000262213:S374P;ENSP00000439359:S343P	ENSP00000262213:S374P	S	-	1	0	TRAM1	71649726	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.404000	0.73268	2.275000	0.75901	0.528000	0.53228	TCA		0.313	TRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378738.1	NM_014294		G	71487172	A	G	71487172	3	3	104	1	0	0	0	0	1	0	0	0	16491	246	9	4	8	4	TRAM1	8	71487172	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	15953134	71487172	74876850	94	27523										
PI15	51050	hgsc.bcm.edu	37	chr8	75756320	75756320	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tttttgggccaaaatctatcTgtacgcactggaaggtagga	11	7	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:75756320T>A	ENST00000260113.2	+	3	557	c.378T>A	c.(376-378)tcT>tcA	p.S126S	RP11-758M4.4_ENST00000518128.1_RNA|RP11-758M4.4_ENST00000523860.1_RNA|PI15_ENST00000523773.1_Silent_p.S126S|RP11-758M4.4_ENST00000522914.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	126	SCP.					extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			AAAATCTATCTGTACGCACTG	0.418																																																0			8											167	164	165					8																	75756320		2203	4300	6503	75918875	SO:0001819	synonymous_variant	51050			D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"protease inhibitor 15"			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.378T>A	8.37:g.75756320T>A			75918875	Q68CY1	Silent	SNP	ENST00000260113.2	37	CCDS6218.1																																																																																				0.418	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		A	75756320	T	A	75756320	2	1	104	1	0	0	0	0	0	0	0	1	11899	1567	55	5		5	PI15	8	75756320	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	4269148	75756320	70607702	95	27524										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77765695	77765695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcaaacactggtttagaaatAcgctttttaaggaacgacag	8	7	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:77765695A>G	ENST00000521891.2	+	10	6986	c.6538A>G	c.(6538-6540)Acg>Gcg	p.T2180A	ZFHX4_ENST00000518282.1_Missense_Mutation_p.T2154A|ZFHX4_ENST00000455469.2_Missense_Mutation_p.T2135A|ZFHX4_ENST00000050961.6_Missense_Mutation_p.T2135A	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTTTAGAAATACGCTTTTTAA	0.368										HNSCC(33;0.089)																																						0			8											112	109	110					8																	77765695		1835	4088	5923	77928250	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6538A>G	8.37:g.77765695A>G	ENSP00000430497:p.Thr2180Ala		77928250	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779563	0.49891	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.95949	-3.86;-3.86;-3.86;-3.86	3.92	3.92	0.45320	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.45867	U	0.000339	D	0.95404	0.8508	L	0.34521	1.04	0.80722	D	1	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.80764	0.994;0.99;0.99	D	0.94233	0.7478	10	0.33141	T	0.24	.	13.2107	0.59822	1.0:0.0:0.0:0.0	.	2135;2135;2180	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	A	2180;2164;2135;2135;2154	ENSP00000430497:T2180A;ENSP00000399605:T2135A;ENSP00000050961:T2135A;ENSP00000430848:T2154A	ENSP00000050961:T2135A	T	+	1	0	ZFHX4	77928250	1.000000	0.71417	0.787000	0.31911	0.733000	0.41908	9.013000	0.93629	1.784000	0.52394	0.374000	0.22700	ACG		0.368	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77765695	A	G	77765695	3	3	104	1	0	0	0	0	1	0	0	0	17674	391	14	4	6572	4	ZFHX4	8	77765695	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	2009375	77765695	68598327	96	27525										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100711856	100711856	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aagataaaaaatgcacacagTttggcacatagtgaagagac	9	6	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:100711856T>C	ENST00000358544.2	+	36	6336	c.6225T>C	c.(6223-6225)agT>agC	p.S2075S	VPS13B_ENST00000357162.2_Silent_p.S2050S|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2075					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ATGCACACAGTTTGGCACATA	0.373																																					Colon(161;2205 2542 7338 31318)											0			8											79	81	80					8																	100711856		2203	4300	6503	100781032	SO:0001819	synonymous_variant	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6225T>C	8.37:g.100711856T>C			100781032	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.373	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100711856	T	C	100711856	2	2	104	1	0	0	0	0	0	0	0	1	17230	1722	60	4		4	VPS13B	8	100711856	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	22946161	100711856	45652166	97	27526										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104943609	104943609	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttatgttaaaatttactttcTtccagacagaaggtaaggat	7	5	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:104943609T>C	ENST00000436393.2	+	10	1938	c.1697T>C	c.(1696-1698)cTt>cCt	p.L566P	RIMS2_ENST00000262231.10_Missense_Mutation_p.L627P|RIMS2_ENST00000507740.1_Missense_Mutation_p.L580P|RIMS2_ENST00000406091.3_Missense_Mutation_p.L788P			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	850					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.L580P(1)|p.L566P(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			ATTTACTTTCTTCCAGACAGA	0.333										HNSCC(12;0.0054)																																						2	Substitution - Missense(2)	ovary(2)	8											50	49	50					8																	104943609		1800	4058	5858	105012785	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1697T>C	8.37:g.104943609T>C	ENSP00000390665:p.Leu566Pro		105012785	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	T	23.2	4.391061	0.82902	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	6.07	6.07	0.98685	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	D	0.93187	0.7830	H	0.96460	3.825	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.998;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;0.999;1.0	D	0.95085	0.8217	9	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	850;850;566;627;580;788	Q9UQ26;Q9UQ26-2;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.;.	P	788;803;788;850;580;627;580;580;566	ENSP00000427018:L788P;ENSP00000384892:L788P;ENSP00000425205:L580P;ENSP00000262231:L627P;ENSP00000423559:L580P;ENSP00000386228:L580P;ENSP00000390665:L566P	ENSP00000262231:L627P	L	+	2	0	RIMS2	105012785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.991000	0.88244	2.326000	0.78906	0.533000	0.62120	CTT		0.333	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		C	104943609	T	C	104943609	3	2	104	1	0	0	0	0	1	0	0	0	13405	1609	56	4	2535	4	RIMS2	8	104943609	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	4231753	104943609	41420413	98	27527										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108315592	108315592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctctttttcctccctttagtAaaactgcaaaaaaaaaaaaa	2	9	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:108315592A>G	ENST00000520734.1	-	4	497	c.212T>C	c.(211-213)tTa>tCa	p.L71S	ANGPT1_ENST00000518386.1_Intron|ANGPT1_ENST00000520052.1_Missense_Mutation_p.L70S			Q15389	ANGP1_HUMAN	angiopoietin 1	271					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TCCCTTTAGTAAAACTGCAAA	0.323																																																0			8											67	78	74					8																	108315592		2201	4300	6501	108384768	SO:0001583	missense	284			D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.212T>C	8.37:g.108315592A>G	ENSP00000430750:p.Leu71Ser		108384768	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	37		.	.	.	.	.	.	.	.	.	.	A	3.169	-0.170398	0.06461	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000395820;ENST00000520734;ENST00000520052	T;T;T;T	0.53857	0.99;0.92;0.6;0.6	4.45	4.45	0.53987	.	0.564434	0.18578	N	0.137133	T	0.36303	0.0962	L	0.36672	1.1	0.39285	D	0.964633	B;B;B	0.09022	0.0;0.002;0.002	B;B;B	0.09377	0.0;0.004;0.004	T	0.15464	-1.0436	10	0.07325	T	0.83	.	8.5917	0.33690	0.914:0.0:0.086:0.0	.	70;271;271	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	S	271;270;83;71;70	ENSP00000428340:L271S;ENSP00000297450:L270S;ENSP00000430750:L71S;ENSP00000429349:L70S	ENSP00000297450:L270S	L	-	2	0	ANGPT1	108384768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.623000	0.61247	1.862000	0.54008	0.528000	0.53228	TTA		0.323	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		G	108315592	A	G	108315592	3	3	104	1	0	0	0	0	1	0	0	0	610	372	13	4	704	4	ANGPT1	8	108315592	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	3371983	108315592	38048430	99	27528										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113266531	113266531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	catgccgaggcacacctgggTtttcacaagaggtttgggta	13	9	1	1	rs376050476		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:113266531T>C	ENST00000297405.5	-	63	10305	c.10061A>G	c.(10060-10062)aAc>aGc	p.N3354S	CSMD3_ENST00000352409.3_Missense_Mutation_p.N3284S|CSMD3_ENST00000343508.3_Missense_Mutation_p.N3314S|CSMD3_ENST00000455883.2_Missense_Mutation_p.N3185S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3354	Sushi 27. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N3354T(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CACACCTGGGTTTTCACAAGA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	ovary(1)	8											189	189	189					8																	113266531		2203	4300	6503	113335707	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10061A>G	8.37:g.113266531T>C	ENSP00000297405:p.Asn3354Ser		113335707	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.214579	0.58452	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	5.22	5.22	0.72569	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	L	0.35723	1.085	0.49582	D	0.999805	D;D;B	0.76494	0.996;0.999;0.178	D;D;B	0.83275	0.957;0.996;0.108	T	0.62300	-0.6883	10	0.11794	T	0.64	.	15.284	0.73814	0.0:0.0:0.0:1.0	.	3185;3354;3314	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	3314;3354;2624;3185;3284	ENSP00000345799:N3314S;ENSP00000297405:N3354S;ENSP00000341558:N2624S;ENSP00000412263:N3185S;ENSP00000343124:N3284S	ENSP00000297405:N3354S	N	-	2	0	CSMD3	113335707	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	5.683000	0.68189	2.201000	0.70794	0.533000	0.62120	AAC		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113266531	T	C	113266531	3	2	104	1	0	0	0	0	1	0	0	0	3952	1725	60	4	1098	4	CSMD3	8	113266531	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	4950939	113266531	33097491	100	27529										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113871405	113871405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcactgctgtgatgacccagAcacattgtgcattgctgtca	9	11	2	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:113871405A>G	ENST00000297405.5	-	11	1968	c.1724T>C	c.(1723-1725)gTc>gCc	p.V575A	CSMD3_ENST00000352409.3_Missense_Mutation_p.V575A|CSMD3_ENST00000343508.3_Missense_Mutation_p.V535A|CSMD3_ENST00000455883.2_Missense_Mutation_p.V471A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	575	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GATGACCCAGACACATTGTGC	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											148	133	138					8																	113871405		2203	4299	6502	113940581	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1724T>C	8.37:g.113871405A>G	ENSP00000297405:p.Val575Ala		113940581	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322555	0.81580	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.67	5.67	0.87782	CUB (5);	0.000000	0.64402	D	0.000007	T	0.50360	0.1611	M	0.70595	2.14	0.42474	D	0.992835	D;D;P	0.69078	0.997;0.996;0.814	D;D;P	0.85130	0.967;0.997;0.9	T	0.51694	-0.8673	10	0.05620	T	0.96	.	15.9132	0.79488	1.0:0.0:0.0:0.0	.	471;575;535	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	535;575;471;575	ENSP00000345799:V535A;ENSP00000297405:V575A;ENSP00000412263:V471A;ENSP00000343124:V575A	ENSP00000297405:V575A	V	-	2	0	CSMD3	113940581	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	9.251000	0.95483	2.154000	0.67381	0.482000	0.46254	GTC		0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113871405	A	G	113871405	3	3	104	1	0	0	0	0	1	0	0	0	3952	275	10	4	9643	4	CSMD3	8	113871405	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	604874	113871405	32492617	101	27530										
JRK	8629	hgsc.bcm.edu	37	chr8	143747023	143747023	+	RNA	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggtcggctgactgcttttcaCtggatgcatctagcttttta	10	9	2	1	rs201592742	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:143747023C>A	ENST00000507178.2	-	0	787							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ctgcttttcactggatgcatc	0.572																																																0			8											40	46	44					8																	143747023		1759	3576	5335	143744025			8629			AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143747023C>A			143744025	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																					0.572	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		A	143747023	C	A	143747023	1	1	104	0	1	0	0	0	0	0	0	0	7985	565	20	2		2	JRK	8	143747023	RNA	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	29875618	143747023	2616999	102	27531										
IFNK	56832	hgsc.bcm.edu	37	chr9	27524677	27524677	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agagacacctcaaacaaatcCaaataggacttgatcagcaa	6	10	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:27524677C>A	ENST00000276943.2	+	1	366	c.343C>A	c.(343-345)Caa>Aaa	p.Q115K	MOB3B_ENST00000262244.5_Intron	NM_020124.2	NP_064509.2	Q9P0W0	IFNK_HUMAN	interferon, kappa	115					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of cell proliferation (GO:0008285)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of transcription, DNA-templated (GO:0006355)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(1)	1		all_neural(11;7.9e-11)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.000158)		CAAACAAATCCAAATAGGACT	0.403																																																0			9											139	146	143					9																	27524677		2203	4300	6503	27514677	SO:0001583	missense	56832			AF384048	CCDS6521.1	9p21.2	2008-02-05			ENSG00000147896	ENSG00000147896		"Interferons"	21714	protein-coding gene	gene with protein product		615326				12391192, 11514542	Standard	NM_020124		Approved		uc003zqp.3	Q9P0W0	OTTHUMG00000019715	ENST00000276943.2:c.343C>A	9.37:g.27524677C>A	ENSP00000276943:p.Gln115Lys		27514677	Q5T166	Missense_Mutation	SNP	ENST00000276943.2	37	CCDS6521.1	.	.	.	.	.	.	.	.	.	.	C	1.305	-0.603909	0.03717	.	.	ENSG00000147896	ENST00000276943	T	0.17054	2.3	6.16	4.24	0.50183	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.503507	0.18947	N	0.126783	T	0.20536	0.0494	M	0.70595	2.14	0.09310	N	1	B	0.30068	0.267	B	0.35039	0.194	T	0.17961	-1.0352	10	0.30078	T	0.28	-16.7209	7.3012	0.26422	0.2098:0.705:0.0:0.0851	.	115	Q9P0W0	IFNK_HUMAN	K	115	ENSP00000276943:Q115K	ENSP00000276943:Q115K	Q	+	1	0	IFNK	27514677	0.011000	0.17503	0.002000	0.10522	0.001000	0.01503	0.464000	0.21988	0.802000	0.34089	-0.142000	0.14014	CAA		0.403	IFNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051968.1	NM_020124		A	27524677	C	A	27524677	3	1	104	1	0	0	0	0	1	0	0	0	7572	595	21	2	345	2	IFNK	9	27524677	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		27524677	113688754	103	27532										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98212180	98212180	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcaaaaccagcccattgagAacgccgaggatggtgaggat	13	9	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:98212180A>G	ENST00000331920.6	-	21	3791	c.3492T>C	c.(3490-3492)gtT>gtC	p.V1164V	PTCH1_ENST00000421141.1_Silent_p.V1013V|PTCH1_ENST00000437951.1_Silent_p.V1098V|PTCH1_ENST00000418258.1_Silent_p.V1013V|PTCH1_ENST00000429896.2_Silent_p.V1013V|PTCH1_ENST00000375274.2_Silent_p.V1163V|PTCH1_ENST00000430669.2_Silent_p.V1098V	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1164					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GCCCATTGAGAACGCCGAGGA	0.557																																																0			9											125	107	113					9																	98212180		2203	4300	6503	97252001	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.3492T>C	9.37:g.98212180A>G			97252001	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.557	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		G	98212180	A	G	98212180	2	3	104	1	0	0	0	0	0	0	0	1	12764	233	9	4		4	PTCH1	9	98212180	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	70687503	98212180	43001251	104	27533										
INVS	27130	hgsc.bcm.edu	37	chr9	103015295	103015295	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atattaatagaaaataagatCaatccaaatgtccaggatta	5	5	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:103015295C>T	ENST00000262457.2	+	10	1526	c.1341C>T	c.(1339-1341)atC>atT	p.I447I	INVS_ENST00000262456.2_Silent_p.I447I|INVS_ENST00000541287.1_Silent_p.I351I	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	447					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.I447M(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				AAAATAAGATCAATCCAAATG	0.428																																																1	Substitution - Missense(1)	ovary(1)	9											100	100	100					9																	103015295		2203	4300	6503	102055116	SO:0001819	synonymous_variant	27130			AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"Ankyrin repeat domain containing"	17870	protein-coding gene	gene with protein product	"nephrocystin 2"	243305	"nephronophthisis 2 (infantile)"	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.1341C>T	9.37:g.103015295C>T			102055116	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Silent	SNP	ENST00000262457.2	37	CCDS6746.1																																																																																				0.428	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425		T	103015295	C	T	103015295	2	4	104	1	0	0	0	0	0	0	0	1	7808	816	29	3		3	INVS	9	103015295	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4803115	103015295	38198136	105	27534										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131370209	131370209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gacagcagctgttggctcacGgacactatgccagccctgag	12	13	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:131370209G>A	ENST00000372731.4	+	33	4335	c.4225G>A	c.(4225-4227)Gga>Aga	p.G1409R	SPTAN1_ENST00000372739.3_Missense_Mutation_p.G1409R|SPTAN1_ENST00000358161.5_Missense_Mutation_p.G1409R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1409					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.G1409R(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GTTGGCTCACGGACACTATGC	0.547																																					NSCLC(120;833 1744 2558 35612 37579)											1	Substitution - Missense(1)	large_intestine(1)	9											78	74	75					9																	131370209		2203	4300	6503	130410030	SO:0001583	missense	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4225G>A	9.37:g.131370209G>A	ENSP00000361816:p.Gly1409Arg		130410030	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145205	0.57044	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.54675	0.56;0.56;0.56	5.54	4.65	0.58169	.	0.048617	0.85682	N	0.000000	T	0.68348	0.2991	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	B;D;D	0.75484	0.411;0.976;0.986	T	0.71702	-0.4513	10	0.66056	D	0.02	.	14.7251	0.69339	0.0699:0.0:0.9301:0.0	.	1389;1409;1409	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	R	1409;1409;1409;1389	ENSP00000350882:G1409R;ENSP00000361816:G1409R;ENSP00000361824:G1409R	ENSP00000350882:G1409R	G	+	1	0	SPTAN1	130410030	1.000000	0.71417	0.996000	0.52242	0.938000	0.57974	6.594000	0.74104	1.488000	0.48433	0.591000	0.81541	GGA		0.547	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131370209	G	A	131370209	3	1	104	1	0	0	0	0	1	0	0	0	15156	1117	39	1	4351	1	SPTAN1	9	131370209	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	28354914	131370209	9843222	106	27535										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137591756	137591756	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cctctgtgctctgttccagcGtctgcatttcccgaggactt	9	14	3	0	rs145090868		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:137591756G>A	ENST00000371817.3	+	3	693	c.279G>A	c.(277-279)gcG>gcA	p.A93A	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	93	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CTGTTCCAGCGTCTGCATTTC	0.587													g|||	1	0.000199681	0	0	5008	,	,		16872	0.001		0	False		,,,				2504	0															0			9						A		0,4406		0,0,2203	81	76	78		279	-9.6	0	9	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		93/1839	137591756	1,13005	2203	4300	6503	136731577	SO:0001630	splice_region_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.278-1G>A	9.37:g.137591756G>A			136731577	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.587	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent	A	137591756	G	A	137591756	5	1	104	1	0	0	0	0	0	0	1	0	3702	1159	40	1	289	1	COL5A1	9	137591756	Splice_Site	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	6221547	137591756	3621675	107	27536										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137727033	137727033	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	acaacccctacatccgcgccCtggtggacggctgtgctgtg	12	15	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:137727033C>A	ENST00000371817.3	+	65	5767	c.5353C>A	c.(5353-5355)Ctg>Atg	p.L1785M		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1785	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CATCCGCGCCCTGGTGGACGG	0.667																																																0			9											71	61	64					9																	137727033		2203	4300	6503	136866854	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5353C>A	9.37:g.137727033C>A	ENSP00000360882:p.Leu1785Met		136866854	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.78|14.78	2.638097|2.638097	0.47153|0.47153	.|.	.|.	ENSG00000130635|ENSG00000130635	ENST00000371817;ENST00000355306|ENST00000371820	T|.	0.75589|.	-0.95|.	5.03|5.03	4.07|4.07	0.47477|0.47477	Fibrillar collagen, C-terminal (4);|.	0.521506|.	0.15238|.	U|.	0.273058|.	T|T	0.65647|0.65647	0.2711|0.2711	M|M	0.89715|0.89715	3.055|3.055	0.28690|0.28690	N|N	0.904647|0.904647	P|.	0.42518|.	0.782|.	P|.	0.51742|.	0.678|.	T|T	0.64262|0.64262	-0.6449|-0.6449	10|5	0.66056|.	D|.	0.02|.	.|.	8.3524|8.3524	0.32310|0.32310	0.1353:0.5862:0.2784:0.0|0.1353:0.5862:0.2784:0.0	.|.	1785|.	P20908|.	CO5A1_HUMAN|.	M|H	1785;322|204	ENSP00000360882:L1785M|.	ENSP00000347458:L322M|.	L|P	+|+	1|2	2|0	COL5A1|COL5A1	136866854|136866854	0.678000|0.678000	0.27586|0.27586	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	0.784000|0.784000	0.26816|0.26816	2.340000|2.340000	0.79590|0.79590	0.561000|0.561000	0.74099|0.74099	CTG|CCT		0.667	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137727033	C	A	137727033	3	1	104	1	0	0	0	0	1	0	0	0	3702	680	24	2	5611	2	COL5A1	9	137727033	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	135277	137727033	3486398	108	27537										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363274	17363274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgaaggaaaatgctggcagaAgaaaaaatgcatctccatag	10	6	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:17363274A>G	ENST00000377602.4	-	8	874	c.800T>C	c.(799-801)cTt>cCt	p.L267P		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	267					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)	p.L267R(1)		endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TGCTGGCAGAAGAAAAAATGC	0.368																																																1	Substitution - Missense(1)	ovary(1)	10											73	81	78					10																	17363274		2203	4300	6503	17403280	SO:0001583	missense	338596				CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.800T>C	10.37:g.17363274A>G	ENSP00000366827:p.Leu267Pro		17403280	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.237079	0.79800	.	.	ENSG00000148488	ENST00000377610;ENST00000377602	T	0.33865	1.39	5.18	5.18	0.71444	.	0.061476	0.64402	D	0.000005	T	0.65873	0.2733	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.72316	-0.4330	10	0.56958	D	0.05	-5.111	15.4962	0.75653	1.0:0.0:0.0:0.0	.	267	P61647	SIA8F_HUMAN	P	97;267	ENSP00000366827:L267P	ENSP00000366827:L267P	L	-	2	0	ST8SIA6	17403280	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	6.974000	0.76122	2.307000	0.77673	0.528000	0.53228	CTT		0.368	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		G	17363274	A	G	17363274	3	3	104	1	0	0	0	0	1	0	0	0	15275	72	3	4	400	4	ST8SIA6	10	17363274	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10		17363274	118171473	109	27538										
STAM	8027	hgsc.bcm.edu	37	chr10	17730082	17730082	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atggttgaatggacagatgaAtttaagaatgatccacagct	10	5	0	5			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:17730082A>G	ENST00000377524.3	+	5	569	c.354A>G	c.(352-354)gaA>gaG	p.E118E	STAM_ENST00000540523.1_Silent_p.E7E	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	118	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						GGACAGATGAATTTAAGAATG	0.363																																																0			10											131	134	133					10																	17730082		2203	4300	6503	17770088	SO:0001819	synonymous_variant	8027			U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.354A>G	10.37:g.17730082A>G			17770088	B0YJ99|D3DRU5|Q8N6D9	Silent	SNP	ENST00000377524.3	37	CCDS7122.1																																																																																				0.363	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		G	17730082	A	G	17730082	2	3	104	1	0	0	0	0	0	0	0	1	15287	98	4	4		4	STAM	10	17730082	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	366808	17730082	117804665	110	27539										
ZNF22	7570	hgsc.bcm.edu	37	chr10	45498857	45498857	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcgggtatttctcggagctCaagccaaggaaaggcctatg	13	9	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:45498857C>G	ENST00000298299.3	+	2	634	c.41C>G	c.(40-42)tCa>tGa	p.S14*	C10orf25_ENST00000298298.1_5'Flank|CEP164P1_ENST00000456938.2_RNA	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	14					odontogenesis (GO:0042476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				TCTCGGAGCTCAAGCCAAGGA	0.458																																																0			10											60	64	63					10																	45498857		2203	4300	6503	44818863	SO:0001587	stop_gained	7570			BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"Zinc fingers, C2H2-type"	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.41C>G	10.37:g.45498857C>G	ENSP00000298299:p.Ser14*		44818863	Q5T741|Q96FM4	Nonsense_Mutation	SNP	ENST00000298299.3	37	CCDS7211.1	.	.	.	.	.	.	.	.	.	.	C	40	8.453381	0.98817	.	.	ENSG00000165512	ENST00000298299	.	.	.	4.94	4.94	0.65067	.	0.385029	0.19198	N	0.120243	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-1.3829	16.0476	0.80731	0.0:1.0:0.0:0.0	.	.	.	.	X	14	.	ENSP00000298299:S14X	S	+	2	0	ZNF22	44818863	0.000000	0.05858	1.000000	0.80357	0.961000	0.63080	0.503000	0.22610	2.706000	0.92434	0.655000	0.94253	TCA		0.458	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963		G	45498857	C	G	45498857	4	3	104	1	0	0	0	0	0	1	0	0	17813	838	29	5	43	5	ZNF22	10	45498857	Nonsense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	27768775	45498857	90035890	111	27540										
ANUBL1	93550	hgsc.bcm.edu	37	chr10	46148454	46148454	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtaatcattcaagcaataatCattttcaagttccatgttat	4	7	4	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:46148454C>A	ENST00000344646.5	-	3	453	c.238G>T	c.(238-240)Gat>Tat	p.D80Y	ZFAND4_ENST00000374371.2_Missense_Mutation_p.D80Y|ZFAND4_ENST00000335258.7_Missense_Mutation_p.D80Y|ZFAND4_ENST00000374366.3_Missense_Mutation_p.D6Y	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	80	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.						zinc ion binding (GO:0008270)										AAGCAATAATCATTTTCAAGT	0.303																																																0			10											170	136	148					10																	46148454		2202	4299	6501	45468460	SO:0001583	missense	93550			AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.238G>T	10.37:g.46148454C>A	ENSP00000339484:p.Asp80Tyr		45468460	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827608	0.71143	.	.	ENSG00000172671	ENST00000344646;ENST00000374371;ENST00000374366;ENST00000374376;ENST00000335258	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	6.07	4.25	0.50352	Ubiquitin supergroup (1);Ubiquitin (2);	0.189606	0.46758	D	0.000279	T	0.57621	0.2066	M	0.80982	2.52	0.47621	D	0.999475	D;D;D	0.65815	0.981;0.983;0.995	P;P;D	0.64237	0.882;0.905;0.923	T	0.61667	-0.7016	10	0.87932	D	0	-5.3188	10.952	0.47334	0.0:0.8491:0.0:0.1509	.	80;80;80	Q5VVY2;Q5VVY4;Q86XD8	.;.;ANUB1_HUMAN	Y	80;80;6;80;80	ENSP00000339484:D80Y;ENSP00000363491:D80Y;ENSP00000363486:D6Y;ENSP00000335586:D80Y	ENSP00000335586:D80Y	D	-	1	0	ANUBL1	45468460	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.946000	0.75953	0.914000	0.36822	-0.136000	0.14681	GAT		0.303	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		A	46148454	C	A	46148454	3	1	104	1	0	0	0	0	1	0	0	0	713	826	29	2	1977	2	ANUBL1	10	46148454	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	649597	46148454	89386293	112	27541										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64936164	64936164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cctttgacggagctttttgtTcacataccaactttggtcac	7	11	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:64936164T>C	ENST00000399262.2	-	24	7512	c.7294A>G	c.(7294-7296)Aac>Gac	p.N2432D	JMJD1C_ENST00000542921.1_Missense_Mutation_p.N2250D|JMJD1C_ENST00000402544.1_Missense_Mutation_p.N2195D|JMJD1C_ENST00000399251.1_3'UTR	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2432	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGCTTTTTGTTCACATACCAA	0.398																																																0			10											127	117	120					10																	64936164		1866	4086	5952	64606170	SO:0001583	missense	221037			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7294A>G	10.37:g.64936164T>C	ENSP00000382204:p.Asn2432Asp		64606170	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827337	0.32329	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.71341	-0.56;-0.56;-0.56	5.75	5.75	0.90469	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.046736	0.85682	D	0.000000	T	0.43656	0.1257	N	0.01817	-0.705	0.80722	D	1	P;B	0.40360	0.714;0.025	B;B	0.40134	0.32;0.021	T	0.57213	-0.7850	10	0.02654	T	1	-15.2545	15.7237	0.77736	0.0:0.0:0.0:1.0	.	2432;2250	Q15652;A0T124	JHD2C_HUMAN;.	D	2432;2195;2250	ENSP00000382204:N2432D;ENSP00000384990:N2195D;ENSP00000444682:N2250D	ENSP00000382204:N2432D	N	-	1	0	JMJD1C	64606170	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.204000	0.58460	2.195000	0.70347	0.533000	0.62120	AAC		0.398	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64936164	T	C	64936164	3	2	104	1	0	0	0	0	1	0	0	0	7971	1783	62	4	340	4	JMJD1C	10	64936164	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	18787710	64936164	70598583	113	27542										
MYST4	23522	hgsc.bcm.edu	37	chr10	76737194	76737194	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggcccaggaactttcttgggAggtaaggcgaggatcccaca	14	10	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:76737194A>G	ENST00000287239.4	+	9	2603	c.2114A>G	c.(2113-2115)gAg>gGg	p.E705G	KAT6B_ENST00000372714.1_Splice_Site_p.E413G|KAT6B_ENST00000372711.1_Splice_Site_p.E522G|KAT6B_ENST00000372725.1_Splice_Site_p.E413G|KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372724.1_Splice_Site_p.E413G	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	705	Negatively regulates HAT activity.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTTTCTTGGGAGGTAAGGCGA	0.378																																																0			10											207	188	194					10																	76737194		2203	4300	6503	76407200	SO:0001630	splice_region_variant	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2115+1A>G	10.37:g.76737194A>G			76407200	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.642470	0.67244	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	5.63	5.63	0.86233	.	0.000000	0.46145	D	0.000317	T	0.81640	0.4865	L	0.41415	1.275	0.47994	D	0.99956	D;P;D	0.63880	0.983;0.939;0.993	P;P;P	0.60886	0.85;0.586;0.88	D	0.83554	0.0103	10	0.72032	D	0.01	-13.1071	14.386	0.66945	1.0:0.0:0.0:0.0	.	522;413;705	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	G	413;413;705;413;522	ENSP00000361810:E413G;ENSP00000361809:E413G;ENSP00000287239:E705G;ENSP00000361799:E413G;ENSP00000361796:E522G	ENSP00000287239:E705G	E	+	2	0	KAT6B	76407200	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.201000	0.72124	2.151000	0.67156	0.477000	0.44152	GAG		0.378	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	Missense_Mutation	G	76737194	A	G	76737194	5	3	104	1	0	0	0	0	0	0	1	0	10135	318	11	4	2140	4	MYST4	10	76737194	Splice_Site	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	11801030	76737194	58797553	114	27543										
HPSE2	60495	hgsc.bcm.edu	37	chr10	100242479	100242479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtcccagccagcttgattttCtttcttgatcgatgcaagtt	8	10	2	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:100242479C>A	ENST00000370552.3	-	11	1586	c.1527G>T	c.(1525-1527)aaG>aaT	p.K509N	HPSE2_ENST00000404542.1_Missense_Mutation_p.K397N|HPSE2_ENST00000370549.1_Missense_Mutation_p.K451N|HPSE2_ENST00000370546.1_Missense_Mutation_p.K509N	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	509					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		GCTTGATTTTCTTTCTTGATC	0.478																																																0			10											139	123	129					10																	100242479		2203	4300	6503	100232469	SO:0001583	missense	60495			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1527G>T	10.37:g.100242479C>A	ENSP00000359583:p.Lys509Asn		100232469	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.207196	0.79127	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.49139	0.79;0.81;1.42;0.82	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.59742	0.2216	L	0.52126	1.63	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.998	D;D;D;D	0.83275	0.994;0.982;0.996;0.987	T	0.51803	-0.8659	10	0.22109	T	0.4	-9.9925	12.7436	0.57268	0.0:0.925:0.0:0.075	.	397;509;451;509	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	N	509;451;509;397	ENSP00000359583:K509N;ENSP00000359580:K451N;ENSP00000359577:K509N;ENSP00000384384:K397N	ENSP00000359577:K509N	K	-	3	2	HPSE2	100232469	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.677000	0.91161	0.655000	0.94253	AAG		0.478	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		A	100242479	C	A	100242479	3	1	104	1	0	0	0	0	1	0	0	0	7366	912	32	2	297	2	HPSE2	10	100242479	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	23505285	100242479	35292268	115	27544										
FGF8	2253	hgsc.bcm.edu	37	chr10	103534937	103534937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcccggaacagggaagcgaGctccctgcccagcgcagggc	15	15	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:103534937G>T	ENST00000344255.3	-	3	105	c.106C>A	c.(106-108)Ctc>Atc	p.L36I	FGF8_ENST00000320185.2_Missense_Mutation_p.L36I|FGF8_ENST00000346714.3_Intron|FGF8_ENST00000347978.2_Intron|FGF8_ENST00000485728.1_Intron			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	36					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		AGGGAAGCGAGCTCCCTGCCC	0.667																																																0			10											5	7	6					10																	103534937		1973	3917	5890	103524927	SO:0001583	missense	2253			D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"Endogenous ligands"	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.106C>A	10.37:g.103534937G>T	ENSP00000340039:p.Leu36Ile		103524927	A1A514|Q14915|Q15766	Missense_Mutation	SNP	ENST00000344255.3	37	CCDS7517.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779244	0.31502	.	.	ENSG00000107831	ENST00000344255;ENST00000320185	T;T	0.81415	-1.49;-1.33	2.84	1.94	0.25998	.	1.124660	0.07297	U	0.873380	T	0.63224	0.2493	N	0.22421	0.69	0.49687	D	0.999816	P;B	0.36354	0.549;0.198	B;B	0.25140	0.058;0.026	T	0.52837	-0.8522	10	0.21014	T	0.42	.	7.8466	0.29428	0.1254:0.0:0.8746:0.0	.	36;36	P55075-4;P55075	.;FGF8_HUMAN	I	36	ENSP00000340039:L36I;ENSP00000321797:L36I	ENSP00000321797:L36I	L	-	1	0	FGF8	103524927	0.034000	0.19679	0.119000	0.21687	0.924000	0.55760	0.669000	0.25142	0.791000	0.33826	-0.381000	0.06696	CTC		0.667	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165		T	103534937	G	T	103534937	3	4	104	1	0	0	0	0	1	0	0	0	5877	971	34	2	644	2	FGF8	10	103534937	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	3292458	103534937	31999810	116	27545										
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679546	104679546	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aggagctgaacatcatccaaGgggcgctggagctccgcacc	13	13	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:104679546G>T	ENST00000369878.4	+	1	1497	c.1309G>T	c.(1309-1311)Ggg>Tgg	p.G437W	CNNM2_ENST00000433628.2_Missense_Mutation_p.G437W|CNNM2_ENST00000369875.3_Missense_Mutation_p.G437W	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	437					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CATCATCCAAGGGGCGCTGGA	0.577																																																0			10											69	66	67					10																	104679546		2203	4300	6503	104669536	SO:0001583	missense	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1309G>T	10.37:g.104679546G>T	ENSP00000358894:p.Gly437Trp		104669536	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640439	0.67244	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	T;T;T	0.76968	-1.06;-1.06;-1.06	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	D	0.92922	0.7748	H	0.98333	4.205	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.96052	0.9032	10	0.87932	D	0	.	17.2856	0.87140	0.0:0.0:1.0:0.0	.	437;437;437	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	W	437	ENSP00000392875:G437W;ENSP00000358891:G437W;ENSP00000358894:G437W	ENSP00000286899:G437W	G	+	1	0	CNNM2	104669536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.852000	0.99516	2.043000	0.60533	0.555000	0.69702	GGG		0.577	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104679546	G	T	104679546	3	4	104	1	0	0	0	0	1	0	0	0	3619	1000	35	2	1311	2	CNNM2	10	104679546	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	1144609	104679546	30855201	117	27546										
PDCD4	27250	hgsc.bcm.edu	37	chr10	112653929	112653929	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttaaggaactggaagtaccTcattttcaccatgagcttgt	8	9	2	1	rs185605824	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:112653929T>G	ENST00000280154.7	+	9	1345	c.1071T>G	c.(1069-1071)ccT>ccG	p.P357P	PDCD4_ENST00000393104.2_Silent_p.P346P|PDCD4_ENST00000481353.1_3'UTR	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	357	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.P357P(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		TGGAAGTACCTCATTTTCACC	0.333													T|||	2	0.000399361	0	0	5008	,	,		19438	0.002		0	False		,,,				2504	0				Ovarian(115;1498 1603 9363 40056 40885)											1	Substitution - coding silent(1)	lung(1)	10											130	136	134					10																	112653929		2203	4298	6501	112643919	SO:0001819	synonymous_variant	27250			U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"nuclear antigen H731"	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1071T>G	10.37:g.112653929T>G			112643919	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																				0.333	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		G	112653929	T	G	112653929	2	3	104	1	0	0	0	0	0	0	0	1	11652	1538	54	4		4	PDCD4	10	112653929	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	7974383	112653929	22880818	118	27547										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118220538	118220538	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggaagtcaggctagacccctCggatgccaactttgttgacg	12	11	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:118220538C>A	ENST00000369230.3	+	6	772	c.626C>A	c.(625-627)tCg>tAg	p.S209*		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	209					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CTAGACCCCTCGGATGCCAAC	0.448																																																0			10											130	116	121					10																	118220538		2203	4300	6503	118210528	SO:0001587	stop_gained	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.626C>A	10.37:g.118220538C>A	ENSP00000358232:p.Ser209*		118210528		Nonsense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	C	35	5.516483	0.96402	.	.	ENSG00000203837	ENST00000369230	.	.	.	4.78	0.443	0.16587	.	0.299402	0.23400	N	0.048589	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2145	0.54398	0.1167:0.5483:0.335:0.0	.	.	.	.	X	209	.	ENSP00000358232:S209X	S	+	2	0	PNLIPRP3	118210528	0.012000	0.17670	0.271000	0.24616	0.530000	0.34684	1.098000	0.31000	0.559000	0.29153	0.591000	0.81541	TCG		0.448	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		A	118220538	C	A	118220538	4	1	104	1	0	0	0	0	0	1	0	0	12183	893	31	2	648	2	PNLIPRP3	10	118220538	Nonsense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	5566609	118220538	17314209	119	27548										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128193073	128193073	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggggtgtctggagaaaaactGgtctctttgtcgtctgcatg	14	7	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:128193073G>T	ENST00000284694.7	-	3	816	c.696C>A	c.(694-696)acC>acA	p.T232T	C10orf90_ENST00000392694.1_Silent_p.T185T|C10orf90_ENST00000544758.1_Silent_p.T329T|C10orf90_ENST00000454341.1_Silent_p.T232T|C10orf90_ENST00000356858.3_Silent_p.T185T|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	232					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GAGAAAAACTGGTCTCTTTGT	0.552											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			10											72	77	75					10																	128193073		2203	4300	6503	128183063	SO:0001819	synonymous_variant	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.696C>A	10.37:g.128193073G>T		1563	128183063	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																				0.552	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128193073	G	T	128193073	2	4	104	1	0	0	0	0	0	0	0	1	1627	1335	47	2		2	C10orf90	10	128193073	Silent	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	9972535	128193073	7341674	120	27549										
RRP8	23378	hgsc.bcm.edu	37	chr11	6622505	6622505	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggaagagacgctgtgcagcaCtgctgggccctgagtacaac	14	11	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:6622505C>T	ENST00000254605.6	-	3	908	c.791G>A	c.(790-792)aGt>aAt	p.S264N	ILK_ENST00000396751.2_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000299421.4_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000537806.1_5'Flank|RRP8_ENST00000534343.1_Intron	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	264					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						CTGTGCAGCACTGCTGGGCCC	0.607																																																0			11											30	29	29					11																	6622505		2201	4296	6497	6579081	SO:0001583	missense	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.791G>A	11.37:g.6622505C>T	ENSP00000254605:p.Ser264Asn		6579081	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927745	0.52759	.	.	ENSG00000132275	ENST00000254605;ENST00000533907	T;T	0.46819	0.86;0.86	5.85	4.88	0.63580	.	0.268520	0.43579	D	0.000557	T	0.35480	0.0933	N	0.21282	0.65	0.80722	D	1	B	0.13594	0.008	B	0.16289	0.015	T	0.09422	-1.0675	10	0.38643	T	0.18	-16.0634	15.2066	0.73183	0.0:0.8588:0.1412:0.0	.	264	O43159	RRP8_HUMAN	N	264	ENSP00000254605:S264N;ENSP00000436246:S264N	ENSP00000254605:S264N	S	-	2	0	RRP8	6579081	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.505000	0.45424	2.773000	0.95371	0.650000	0.86243	AGT		0.607	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6622505	C	T	6622505	3	4	104	1	0	0	0	0	1	0	0	0	13727	565	20	3	599	3	RRP8	11	6622505	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		6622505	128384011	121	27550										
SYT9	143425	hgsc.bcm.edu	37	chr11	7441835	7441835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aatgttgtcatatcctcggaAgcccattgcacactggcatt	8	11	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:7441835A>G	ENST00000318881.6	+	6	1673	c.1436A>G	c.(1435-1437)aAg>aGg	p.K479R		NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	479					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TATCCTCGGAAGCCCATTGCA	0.498																																																0			11											166	135	146					11																	7441835		2201	4296	6497	7398411	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1436A>G	11.37:g.7441835A>G	ENSP00000324419:p.Lys479Arg		7398411		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.821745	0.71028	.	.	ENSG00000170743	ENST00000318881	T	0.72282	-0.64	5.64	5.64	0.86602	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000012	T	0.76198	0.3954	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70963	-0.4729	10	0.10636	T	0.68	.	13.8014	0.63202	1.0:0.0:0.0:0.0	.	479	Q86SS6	SYT9_HUMAN	R	479	ENSP00000324419:K479R	ENSP00000324419:K479R	K	+	2	0	SYT9	7398411	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.148000	0.66965	0.533000	0.62120	AAG		0.498	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		G	7441835	A	G	7441835	3	3	104	1	0	0	0	0	1	0	0	0	15520	72	3	4	1458	4	SYT9	11	7441835	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	819330	7441835	127564681	122	27551										
RAG1	5896	hgsc.bcm.edu	37	chr11	36596672	36596672	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagtcttgtgatggaatgggAgacgtgagtgagaagcatgg	18	3	1	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:36596672A>G	ENST00000299440.5	+	2	1930	c.1818A>G	c.(1816-1818)ggA>ggG	p.G606G		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	606					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G606G(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				ATGGAATGGGAGACGTGAGTG	0.473									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											1	Substitution - coding silent(1)	kidney(1)	11											108	90	96					11																	36596672		2202	4298	6500	36553248	SO:0001819	synonymous_variant	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1818A>G	11.37:g.36596672A>G			36553248	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	37	CCDS7902.1																																																																																				0.473	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		G	36596672	A	G	36596672	2	3	104	1	0	0	0	0	0	0	0	1	13040	291	11	4		4	RAG1	11	36596672	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	29154837	36596672	98409844	123	27552										
CARNS1	57571	hgsc.bcm.edu	37	chr11	67191083	67191083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gcagctccccagctgccatgCgcctggctaagcagaagagc	12	15	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:67191083C>T	ENST00000307823.3	+	9	1947	c.1495C>T	c.(1495-1497)Cgc>Tgc	p.R499C	CARNS1_ENST00000445895.2_Missense_Mutation_p.R622C|CARNS1_ENST00000423745.2_Missense_Mutation_p.R499C|CARNS1_ENST00000531040.1_Missense_Mutation_p.R596C|CARNS1_ENST00000524740.1_3'UTR	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	499					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						AGCTGCCATGCGCCTGGCTAA	0.647																																																0			11											25	31	29					11																	67191083		2163	4248	6411	66947659	SO:0001583	missense	0				CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1495C>T	11.37:g.67191083C>T	ENSP00000308268:p.Arg499Cys		66947659	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	C	9.869	1.198358	0.22037	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.37	-1.85	0.07784	.	0.817364	0.10808	N	0.631986	T	0.15652	0.0377	N	0.14661	0.345	0.40671	D	0.982218	B;B	0.13145	0.004;0.007	B;B	0.12156	0.003;0.007	T	0.07770	-1.0755	10	0.44086	T	0.13	-8.0023	6.8584	0.24054	0.2303:0.5722:0.0:0.1974	.	499;638	A5YM72;A5YM72-3	CRNS1_HUMAN;.	C	596;499;596;499;622	ENSP00000431670:R596C;ENSP00000308268:R499C;ENSP00000401519:R499C;ENSP00000389009:R622C	ENSP00000308268:R499C	R	+	1	0	CARNS1	66947659	1.000000	0.71417	0.996000	0.52242	0.581000	0.36288	0.973000	0.29422	-0.149000	0.11215	0.549000	0.68633	CGC		0.647	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		T	67191083	C	T	67191083	3	4	104	1	0	0	0	0	1	0	0	0	2662	768	27	1	1898	1	CARNS1	11	67191083	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	30594411	67191083	67815433	124	27553										
ATM	472	hgsc.bcm.edu	37	chr11	108188129	108188129	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aatttgggactctgccatatTctttccgtctatttaaaagg	7	8	3	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108188129T>C	ENST00000452508.2	+	44	6417	c.6228T>C	c.(6226-6228)atT>atC	p.I2076I	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.I2076I			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2076	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCTGCCATATTCTTTCCGTCT	0.358			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11	GRCh37	CD000915	ATM	D							86	87	87					11																	108188129		2201	4298	6499	107693339	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.6228T>C	11.37:g.108188129T>C			107693339	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108188129	T	C	108188129	2	2	104	1	0	0	0	0	0	0	0	1	1110	1771	62	4		4	ATM	11	108188129	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	40997046	108188129	26818387	125	27554										
ATM	472	hgsc.bcm.edu	37	chr11	108199781	108199781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctggaaattatgatggagaaAgtagtgatgagctaagaaat	12	2	0	5			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108199781A>G	ENST00000452508.2	+	50	7312	c.7123A>G	c.(7123-7125)Agt>Ggt	p.S2375G	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.S2375G			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2375	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGATGGAGAAAGTAGTGATGA	0.313			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											65	69	68					11																	108199781		2201	4298	6499	107704991	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7123A>G	11.37:g.108199781A>G	ENSP00000388058:p.Ser2375Gly		107704991	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131768	0.37630	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.68624	-0.34;-0.34	5.7	3.3	0.37823	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.464389	0.28268	N	0.015971	T	0.55497	0.1924	L	0.46157	1.445	0.80722	D	1	B	0.22276	0.067	B	0.27380	0.079	T	0.48758	-0.9007	10	0.30078	T	0.28	.	6.6774	0.23102	0.7925:0.0:0.0725:0.135	.	2375	Q13315	ATM_HUMAN	G	2375	ENSP00000278616:S2375G;ENSP00000388058:S2375G	ENSP00000278616:S2375G	S	+	1	0	ATM	107704991	0.999000	0.42202	0.967000	0.41034	0.832000	0.47134	2.544000	0.45761	0.993000	0.38866	-0.256000	0.11100	AGT		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108199781	A	G	108199781	3	3	104	1	0	0	0	0	1	0	0	0	1110	72	3	4	7313	4	ATM	11	108199781	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	11652	108199781	26806735	126	27555										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108381959	108381959	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctgaaagagctggaagactAgagggaccactgttacttga	12	7	1	5			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108381959A>G	ENST00000265843.4	-	6	4385	c.4275T>C	c.(4273-4275)tcT>tcC	p.S1425S	EXPH5_ENST00000428840.1_Silent_p.S1349S|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Silent_p.S1418S|EXPH5_ENST00000443411.1_Silent_p.S1237S	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1425					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTGGAAGACTAGAGGGACCAC	0.378																																																0			11											107	107	107					11																	108381959		2201	4298	6499	107887169	SO:0001819	synonymous_variant	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4275T>C	11.37:g.108381959A>G			107887169	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																				0.378	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108381959	A	G	108381959	2	3	104	1	0	0	0	0	0	0	0	1	5335	407	15	4		4	EXPH5	11	108381959	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	182178	108381959	26624557	127	27556										
ANKK1	255239	hgsc.bcm.edu	37	chr11	113269881	113269881	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccagacggcctctggatacaCgcccctcctgatcgccgccc	9	20	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:113269881C>A	ENST00000303941.3	+	8	1284	c.1190C>A	c.(1189-1191)aCg>aAg	p.T397K		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	397							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TCTGGATACACGCCCCTCCTG	0.652																																																0			11											31	34	33					11																	113269881		2095	4200	6295	112775091	SO:0001583	missense	255239			AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1190C>A	11.37:g.113269881C>A	ENSP00000306678:p.Thr397Lys		112775091		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.614236	0.28712	.	.	ENSG00000170209	ENST00000303941	T	0.30182	1.54	4.69	1.71	0.24356	Ankyrin repeat-containing domain (4);	0.213462	0.31747	N	0.007128	T	0.57917	0.2086	M	0.91140	3.18	0.41295	D	0.987002	D	0.89917	1.0	D	0.80764	0.994	T	0.60224	-0.7305	10	0.87932	D	0	-6.4367	8.4287	0.32744	0.0:0.7306:0.0:0.2694	.	397	Q8NFD2	ANKK1_HUMAN	K	397	ENSP00000306678:T397K	ENSP00000306678:T397K	T	+	2	0	ANKK1	112775091	0.978000	0.34361	0.129000	0.21949	0.023000	0.10783	2.518000	0.45537	0.178000	0.19917	-0.384000	0.06662	ACG		0.652	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		A	113269881	C	A	113269881	3	1	104	1	0	0	0	0	1	0	0	0	631	536	19	2	1220	2	ANKK1	11	113269881	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4887922	113269881	21736635	128	27557										
USP28	57646	hgsc.bcm.edu	37	chr11	113704982	113704982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccaacttactgtatgacttcGacaattttcaagtacatttt	4	9	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:113704982G>C	ENST00000003302.4	-	6	678	c.610C>G	c.(610-612)Cga>Gga	p.R204G	USP28_ENST00000537706.1_Missense_Mutation_p.R204G|USP28_ENST00000545540.1_Missense_Mutation_p.R79G|USP28_ENST00000260188.5_Missense_Mutation_p.R204G|USP28_ENST00000542033.1_5'UTR	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	204	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		GTATGACTTCGACAATTTTCA	0.373																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											0			11											135	120	125					11																	113704982		2201	4296	6497	113210192	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.610C>G	11.37:g.113704982G>C	ENSP00000003302:p.Arg204Gly		113210192	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307198	0.40795	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000545540;ENST00000537706	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.08	4.17	0.49024	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.191511	0.45867	D	0.000325	T	0.40448	0.1117	L	0.56199	1.76	0.35679	D	0.813928	B;B;B;P	0.34699	0.142;0.42;0.09;0.464	B;B;B;P	0.46796	0.111;0.18;0.152;0.527	T	0.51834	-0.8655	10	0.41790	T	0.15	-0.2028	12.5263	0.56087	0.0808:0.0:0.9192:0.0	.	204;79;204;204	B4E2Q2;B4E3L3;Q6NZX9;Q96RU2	.;.;.;UBP28_HUMAN	G	204;204;79;204	ENSP00000003302:R204G;ENSP00000260188:R204G;ENSP00000444991:R79G;ENSP00000445743:R204G	ENSP00000003302:R204G	R	-	1	2	USP28	113210192	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	3.845000	0.55880	1.139000	0.42245	0.460000	0.39030	CGA		0.373	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			C	113704982	G	C	113704982	3	2	104	1	0	0	0	0	1	0	0	0	17098	1066	37	5	2703	5	USP28	11	113704982	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	435101	113704982	21301534	129	27558										
HSPA8	3312	hgsc.bcm.edu	37	chr11	122931831	122931831	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	taaaattaggaactcaccaaAaactgtgttggtggggttca	10	6	2	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:122931831A>T	ENST00000532636.1	-	2	321	c.202T>A	c.(202-204)Ttt>Att	p.F68I	HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000533540.1_Missense_Mutation_p.F68I|HSPA8_ENST00000534624.1_Missense_Mutation_p.F68I|SNORD14D_ENST00000384390.1_RNA|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000453788.2_Missense_Mutation_p.F68I|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000227378.3_Missense_Mutation_p.F68I|HSPA8_ENST00000526110.1_Missense_Mutation_p.F68I			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	68					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AACTCACCAAAAACTGTGTTG	0.408																																					Colon(21;486 594 5900 6733 14272)											0			11											51	47	48					11																	122931831		2202	4299	6501	122437041	SO:0001583	missense	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.202T>A	11.37:g.122931831A>T	ENSP00000437125:p.Phe68Ile		122437041	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	32	5.119719	0.94385	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000528292;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.03889	3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.30823	0.0777	H	0.95365	3.66	0.80722	D	1	P;D;D;D;D	0.76494	0.869;0.999;0.995;0.994;0.986	B;D;D;D;D	0.72982	0.397;0.979;0.971;0.951;0.979	T	0.48536	-0.9027	10	0.87932	D	0	.	13.9807	0.64304	1.0:0.0:0.0:0.0	.	68;68;68;68;68	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	I	68;68;68;68;68;68;8;68;68;68;68;68;68;68	ENSP00000437125:F68I;ENSP00000437189:F68I;ENSP00000432083:F68I;ENSP00000404372:F68I;ENSP00000227378:F68I;ENSP00000433584:F68I;ENSP00000432884:F8I;ENSP00000436762:F68I;ENSP00000435154:F68I;ENSP00000431641:F68I;ENSP00000436183:F68I;ENSP00000434415:F68I;ENSP00000434565:F68I;ENSP00000434851:F68I	ENSP00000227378:F68I	F	-	1	0	HSPA8	122437041	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.337000	0.96545	1.748000	0.51833	0.397000	0.26171	TTT		0.408	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			T	122931831	A	T	122931831	3	4	104	1	0	0	0	0	1	0	0	0	7437	14	1	5	1770	5	HSPA8	11	122931831	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	9226849	122931831	12074685	130	27559										
KDM5A	5927	hgsc.bcm.edu	37	chr12	406230	406230	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gagaacaactcttagaagcaGaagaataagcatgctctgca	9	8	2	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:406230G>T	ENST00000399788.2	-	25	4573	c.4211C>A	c.(4210-4212)tCt>tAt	p.S1404Y	KDM5A_ENST00000382815.4_Missense_Mutation_p.S1404Y	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1404					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CTTAGAAGCAGAAGAATAAGC	0.398			T	NUP98	AML																																		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	0			12											58	57	57					12																	406230		1863	4106	5969	276491	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4211C>A	12.37:g.406230G>T	ENSP00000382688:p.Ser1404Tyr		276491	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933069	0.34096	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.86956	-2.19;-2.01	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.88760	0.6524	N	0.22421	0.69	0.58432	D	0.999999	D;D	0.69078	0.995;0.997	D;D	0.80764	0.986;0.994	D	0.85178	0.1002	10	0.16896	T	0.51	-14.8326	19.7243	0.96157	0.0:0.0:1.0:0.0	.	1404;1404	P29375;P29375-2	KDM5A_HUMAN;.	Y	1404	ENSP00000382688:S1404Y;ENSP00000372265:S1404Y	ENSP00000372265:S1404Y	S	-	2	0	KDM5A	276491	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.836000	0.99456	2.647000	0.89833	0.655000	0.94253	TCT		0.398	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		T	406230	G	T	406230	3	4	104	1	0	0	0	0	1	0	0	0	8154	942	33	2	877	2	KDM5A	12	406230	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		406230	133445665	131	27560										
VWF	7450	hgsc.bcm.edu	37	chr12	6219731	6219731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctagatacagccctttggagGcatagggcatggagactctg	13	9	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:6219731G>A	ENST00000261405.5	-	5	595	c.341C>T	c.(340-342)gCc>gTc	p.A114V	VWF_ENST00000572068.1_Missense_Mutation_p.A151V	NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	114	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCTTTGGAGGCATAGGGCAT	0.532																																																0			12											77	81	80					12																	6219731		2203	4300	6503	6089992	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.341C>T	12.37:g.6219731G>A	ENSP00000261405:p.Ala114Val		6089992	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	24.2	4.509418	0.85282	.	.	ENSG00000110799	ENST00000261405	T	0.59083	0.29	5.9	5.9	0.94986	von Willebrand factor, type D domain (3);	0.000000	0.42821	D	0.000648	T	0.73202	0.3557	L	0.48986	1.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.994	T	0.73436	-0.3983	10	0.72032	D	0.01	.	19.2581	0.93955	0.0:0.0:1.0:0.0	.	114;151;114	B4DNX0;Q8TCE8;P04275	.;.;VWF_HUMAN	V	114	ENSP00000261405:A114V	ENSP00000261405:A114V	A	-	2	0	VWF	6089992	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.269000	0.72558	2.804000	0.96469	0.655000	0.94253	GCC		0.532	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6219731	G	A	6219731	3	1	104	1	0	0	0	0	1	0	0	0	17286	1203	42	3	8292	3	VWF	12	6219731	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	5813501	6219731	127632164	132	27561										
CD163	9332	hgsc.bcm.edu	37	chr12	7640085	7640085	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctccagatctgaccatttccTtttccaaaacgtgctcctcc	4	16	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:7640085T>C	ENST00000359156.4	-	8	2122	c.1920A>G	c.(1918-1920)aaA>aaG	p.K640K	CD163_ENST00000541972.1_Silent_p.K628K|CD163_ENST00000396620.3_Silent_p.K673K|CD163_ENST00000432237.2_Silent_p.K640K|CD163_ENST00000539632.1_5'Flank	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	640	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GACCATTTCCTTTTCCAAAAC	0.478																																																0			12											154	140	145					12																	7640085		2203	4300	6503	7531352	SO:0001819	synonymous_variant	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1920A>G	12.37:g.7640085T>C			7531352	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																				0.478	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		C	7640085	T	C	7640085	2	2	104	1	0	0	0	0	0	0	0	1	2973	1606	56	4		4	CD163	12	7640085	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	1420354	7640085	126211810	133	27562										
STK38L	23012	hgsc.bcm.edu	37	chr12	27461382	27461382	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctgaaagttataggaagaggAgcttttggagaggtgtgctt	15	3	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:27461382A>G	ENST00000389032.3	+	4	466	c.297A>G	c.(295-297)ggA>ggG	p.G99G	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TAGGAAGAGGAGCTTTTGGAG	0.383																																																0			12											107	112	110					12																	27461382		2203	4300	6503	27352649	SO:0001819	synonymous_variant	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.297A>G	12.37:g.27461382A>G			27352649		Silent	SNP	ENST00000389032.3	37	CCDS31761.1																																																																																				0.383	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		G	27461382	A	G	27461382	2	3	104	1	0	0	0	0	0	0	0	1	15343	291	11	4		4	STK38L	12	27461382	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	19821297	27461382	106390513	134	27563										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40692172	40692172	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgacattggaccctcagtggTtttagatcctacagtgaaat	9	8	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:40692172T>G	ENST00000298910.7	+	24	3282	c.3224T>G	c.(3223-3225)gTt>gGt	p.V1075G	LRRK2_ENST00000343742.2_Missense_Mutation_p.V1075G	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1075					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CCCTCAGTGGTTTTAGATCCT	0.363																																																0			12											143	135	138					12																	40692172		2203	4300	6503	38978439	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.3224T>G	12.37:g.40692172T>G	ENSP00000298910:p.Val1075Gly		38978439	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	9.683	1.149822	0.21288	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.71934	2.23;-0.61	5.85	0.629	0.17687	.	0.418063	0.26112	N	0.026269	T	0.48572	0.1507	N	0.22421	0.69	0.19300	N	0.999979	B;B	0.20887	0.049;0.014	B;B	0.16722	0.016;0.013	T	0.22906	-1.0203	10	0.23891	T	0.37	.	5.8643	0.18767	0.1339:0.4187:0.0:0.4474	.	1075;1075	E9PC85;Q5S007	.;LRRK2_HUMAN	G	1075	ENSP00000341930:V1075G;ENSP00000298910:V1075G	ENSP00000298910:V1075G	V	+	2	0	LRRK2	38978439	0.014000	0.17966	0.003000	0.11579	0.974000	0.67602	0.391000	0.20784	0.072000	0.16694	-0.250000	0.11733	GTT		0.363	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		G	40692172	T	G	40692172	3	3	104	1	0	0	0	0	1	0	0	0	9062	1725	60	4	3318	4	LRRK2	12	40692172	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	13230790	40692172	93159723	135	27564										
SENP1	29843	hgsc.bcm.edu	37	chr12	48457593	48457593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttcatcctgattcccattaCgaaatacattctttatttct	2	11	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:48457593C>T	ENST00000004980.5	-	13	1785	c.1307G>A	c.(1306-1308)cGt>cAt	p.R436H	SENP1_ENST00000549595.1_Missense_Mutation_p.R436H|SENP1_ENST00000339976.6_3'UTR|SENP1_ENST00000448372.1_Missense_Mutation_p.R436H|SENP1_ENST00000549518.1_Missense_Mutation_p.R436H|SENP1_ENST00000551330.1_Missense_Mutation_p.R436H			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	436					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				ATTCCCATTACGAAATACATT	0.383																																																0			12											122	113	116					12																	48457593		1868	4109	5977	46743860	SO:0001583	missense	29843			AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.1307G>A	12.37:g.48457593C>T	ENSP00000004980:p.Arg436His		46743860	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	37	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	C	15.56	2.871056	0.51695	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.42900	0.96;1.53;0.96;1.53;0.96	5.24	5.24	0.73138	.	0.222255	0.41605	D	0.000860	T	0.24624	0.0597	L	0.28054	0.825	0.80722	D	1	P;P	0.37423	0.594;0.59	B;B	0.25614	0.016;0.062	T	0.07809	-1.0753	10	0.15066	T	0.55	-11.017	13.7327	0.62799	0.154:0.846:0.0:0.0	.	436;436	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	H	436	ENSP00000004980:R436H;ENSP00000394791:R436H;ENSP00000446681:R436H;ENSP00000450076:R436H;ENSP00000447328:R436H	ENSP00000004980:R436H	R	-	2	0	SENP1	46743860	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.912000	0.48782	2.615000	0.88500	0.655000	0.94253	CGT		0.383	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		T	48457593	C	T	48457593	3	4	104	1	0	0	0	0	1	0	0	0	14083	536	19	1	648	1	SENP1	12	48457593	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	7765421	48457593	85394302	136	27565										
DDX23	9416	hgsc.bcm.edu	37	chr12	49230468	49230468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggtgatgctgtagtcctcacGgaagatccgccagtccctgt	12	12	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:49230468G>A	ENST00000308025.3	-	10	1199	c.1120C>T	c.(1120-1122)Cgt>Tgt	p.R374C	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	374					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.R374C(1)		NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TAGTCCTCACGGAAGATCCGC	0.522																																																1	Substitution - Missense(1)	kidney(1)	12											159	139	146					12																	49230468		2203	4300	6503	47516735	SO:0001583	missense	9416			AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1120C>T	12.37:g.49230468G>A	ENSP00000310723:p.Arg374Cys		47516735	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905236	0.52333	.	.	ENSG00000174243	ENST00000308025	T	0.25414	1.8	5.82	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	H	0.95645	3.7	0.80722	D	1	P	0.47191	0.891	B	0.32677	0.15	T	0.60182	-0.7313	10	0.87932	D	0	-1.5578	13.0504	0.58952	0.0:0.0:0.7076:0.2924	.	374	Q9BUQ8	DDX23_HUMAN	C	374	ENSP00000310723:R374C	ENSP00000310723:R374C	R	-	1	0	DDX23	47516735	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.381000	0.52455	1.450000	0.47717	0.561000	0.74099	CGT		0.522	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		A	49230468	G	A	49230468	3	1	104	1	0	0	0	0	1	0	0	0	4356	1116	39	1	1374	1	DDX23	12	49230468	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	772875	49230468	84621427	137	27566										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56477659	56477659	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttgagattgtgctcacgggAcacaatgccgacctctcctt	9	13	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:56477659A>G	ENST00000267101.3	+	2	647	c.207A>G	c.(205-207)ggA>ggG	p.G69G	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Silent_p.G10G|ERBB3_ENST00000411731.2_Silent_p.G69G	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	69					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TGCTCACGGGACACAATGCCG	0.542																																																0			12											277	221	240					12																	56477659		2203	4300	6503	54763926	SO:0001819	synonymous_variant	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.207A>G	12.37:g.56477659A>G			54763926	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																				0.542	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			G	56477659	A	G	56477659	2	3	104	1	0	0	0	0	0	0	0	1	5221	262	10	4		4	ERBB3	12	56477659	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7247191	56477659	77374236	138	27567										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57970146	57970146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	caacgagaagcagaagaccaTtgatgagctcaaagagtaag	11	7	1	6			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:57970146T>C	ENST00000455537.2	+	19	2457	c.2183T>C	c.(2182-2184)aTt>aCt	p.I728T	KIF5A_ENST00000286452.5_Missense_Mutation_p.I639T	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	728					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAGAAGACCATTGATGAGCTC	0.592																																																0			12											37	43	41					12																	57970146		2203	4300	6503	56256413	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2183T>C	12.37:g.57970146T>C	ENSP00000408979:p.Ile728Thr		56256413	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699072	0.68501	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.74737	-0.87;-0.87	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.85710	2.77	0.58432	D	0.999991	P;P	0.50443	0.935;0.914	P;P	0.54590	0.756;0.71	D	0.85496	0.1188	10	0.52906	T	0.07	.	13.0026	0.58685	0.0:0.0:0.0:1.0	.	639;728	B7Z2M7;Q12840	.;KIF5A_HUMAN	T	728;639	ENSP00000408979:I728T;ENSP00000286452:I639T	ENSP00000286452:I639T	I	+	2	0	KIF5A	56256413	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.640000	0.83355	2.082000	0.62665	0.459000	0.35465	ATT		0.592	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		C	57970146	T	C	57970146	3	2	104	1	0	0	0	0	1	0	0	0	8326	1493	52	4	2257	4	KIF5A	12	57970146	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	1492487	57970146	75881749	139	27568										
PTPRB	5801	hgsc.bcm.edu	37	chr12	71029607	71029607	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttccacctcaaggaagccttCctgatcatagcaggtccatc	7	14	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:71029607C>T	ENST00000283228.2	-	0	3529				PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Missense_Mutation_p.E99K|PTPRB_ENST00000551525.1_Missense_Mutation_p.E98K|PTPRR_ENST00000537619.2_5'Flank|PTPRB_ENST00000334414.6_Missense_Mutation_p.E99K	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AGGAAGCCTTCCTGATCATAG	0.557																																																0			12											51	50	50					12																	71029607		1926	4131	6057	69315874	SO:0001628	intergenic_variant	5787			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502		12.37:g.71029607C>T			69315874	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652964	0.47362	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.05258	4.01;3.97;3.47	6.04	2.12	0.27331	.	.	.	.	.	T	0.04907	0.0132	L	0.27053	0.805	0.09310	N	0.999994	B;B;B;B	0.26195	0.144;0.006;0.006;0.006	B;B;B;B	0.15870	0.014;0.007;0.003;0.003	T	0.37220	-0.9715	9	0.87932	D	0	.	7.4804	0.27402	0.0:0.6049:0.2566:0.1384	.	99;98;99;99	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	K	99;99;99;98	ENSP00000334928:E99K;ENSP00000448058:E99K;ENSP00000448349:E98K	ENSP00000334928:E99K	E	-	1	0	PTPRB	69315874	0.999000	0.42202	0.004000	0.12327	0.841000	0.47740	1.967000	0.40491	0.122000	0.18314	0.563000	0.77884	GAA		0.557	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		T	71029607	C	T	71029607	1	4	104	0	1	0	0	0	0	0	0	0	12833	864	30	3		3	PTPRB	12	71029607	IGR	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	13059461	71029607	62822288	140	27569										
PAH	5053	hgsc.bcm.edu	37	chr12	103288665	103288665	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctttaaacgagaaggtctaGattcaatgtgggtcaggttt	11	5	4	2	rs199475570		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:103288665G>C	ENST00000553106.1	-	3	672	c.200C>G	c.(199-201)tCt>tGt	p.S67C	PAH_ENST00000307000.2_Missense_Mutation_p.S62C|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	67	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.		S -> P (in PKU; haplotype 4).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	AGAAGGTCTAGATTCAATGTG	0.438																																																0			12											127	119	122					12																	103288665		2203	4300	6503	101812795	SO:0001583	missense	5053			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.200C>G	12.37:g.103288665G>C	ENSP00000448059:p.Ser67Cys		101812795	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994030	0.93167	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337;ENST00000546844	D;D;D;D	0.99207	-5.56;-5.56;-5.56;-5.56	6.17	6.17	0.99709	Amino acid-binding ACT (1);	0.000000	0.85682	D	0.000000	D	0.99771	0.9906	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97122	0.9812	10	0.87932	D	0	-29.0654	20.8794	0.99867	0.0:0.0:1.0:0.0	.	67;67	B4DPN2;P00439	.;PH4H_HUMAN	C	67;62;67;67	ENSP00000448059:S67C;ENSP00000303500:S62C;ENSP00000447620:S67C;ENSP00000446658:S67C	ENSP00000303500:S62C	S	-	2	0	PAH	101812795	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.877000	0.92386	2.941000	0.99782	0.655000	0.94253	TCT		0.438	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			C	103288665	G	C	103288665	3	2	104	1	0	0	0	0	1	0	0	0	11425	942	33	5	1202	5	PAH	12	103288665	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	32259058	103288665	30563230	141	27570										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926888	112926888	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggtgcggtctcagaggtcagGgatggtccagacagaagcac	16	9	2	3	rs397507546		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:112926888G>T	ENST00000351677.2	+	13	1706	c.1508G>T	c.(1507-1509)gGg>gTg	p.G503V		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	507	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.G503A(12)|p.G503V(8)|p.G503E(2)|p.G503L(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CAGAGGTCAGGGATGGTCCAG	0.468			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	23	Substitution - Missense(23)	haematopoietic_and_lymphoid_tissue(21)|lung(2)	12	GRCh37	CM086897	PTPN11	M							181	169	173					12																	112926888		2203	4300	6503	111411271	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1508G>T	12.37:g.112926888G>T	ENSP00000340944:p.Gly503Val		111411271	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172790	0.94807	.	.	ENSG00000179295	ENST00000351677	D	0.99399	-5.83	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97291	0.9924	10	0.66056	D	0.02	.	18.9358	0.92584	0.0:0.0:1.0:0.0	.	503	Q06124-2	.	V	503	ENSP00000340944:G503V	ENSP00000340944:G503V	G	+	2	0	PTPN11	111411271	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.420000	0.97426	2.553000	0.86117	0.650000	0.86243	GGG		0.468	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112926888	G	T	112926888	3	4	104	1	0	0	0	0	1	0	0	0	12815	1232	43	2	1558	2	PTPN11	12	112926888	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	9638223	112926888	20925007	142	27571										
P2RX7	5027	hgsc.bcm.edu	37	chr12	121570848	121570848	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	actcggatccagagcatgaaTtatggcaccattaagtggtt	10	8	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:121570848T>C	ENST00000546057.1	+	1	218	c.75T>C	c.(73-75)aaT>aaC	p.N25N	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000541446.1_5'UTR|P2RX7_ENST00000328963.5_5'UTR|P2RX7_ENST00000377162.2_Silent_p.N25N|P2RX7_ENST00000535250.1_5'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	25			N -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AGAGCATGAATTATGGCACCA	0.537																																																0			12											196	156	170					12																	121570848		2203	4300	6503	120055231	SO:0001819	synonymous_variant	5027			Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.75T>C	12.37:g.121570848T>C			120055231	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Silent	SNP	ENST00000546057.1	37	CCDS9213.1																																																																																				0.537	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		C	121570848	T	C	121570848	2	2	104	1	0	0	0	0	0	0	0	1	11376	1490	52	4		4	P2RX7	12	121570848	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	8643960	121570848	12281047	143	27572										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36700001	36700001	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gttatccgacagagttcgggTcaaatcagccagcagggcct	12	11	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:36700001T>G	ENST00000360631.3	-	2	485	c.274A>C	c.(274-276)Acc>Ccc	p.T92P	DCLK1_ENST00000255448.4_Missense_Mutation_p.T92P|DCLK1_ENST00000379892.4_Missense_Mutation_p.T92P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	92	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		AGAGTTCGGGTCAAATCAGCC	0.498																																																0			13											105	96	99					13																	36700001		2203	4300	6503	35598001	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.274A>C	13.37:g.36700001T>G	ENSP00000353846:p.Thr92Pro		35598001	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	T	26.4	4.732617	0.89482	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	D;D;D	0.96427	-4.01;-4.01;-4.01	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.98611	0.9535	M	0.94021	3.485	0.80722	D	1	D	0.71674	0.998	D	0.85130	0.997	D	0.99727	1.1011	10	0.87932	D	0	.	16.1875	0.81962	0.0:0.0:0.0:1.0	.	92	O15075-2	.	P	92	ENSP00000255448:T92P;ENSP00000353846:T92P;ENSP00000369222:T92P	ENSP00000255448:T92P	T	-	1	0	DCLK1	35598001	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.860000	0.86993	2.225000	0.72522	0.533000	0.62120	ACC		0.498	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36700001	T	G	36700001	3	3	104	1	0	0	0	0	1	0	0	0	4297	1667	58	4	1983	4	DCLK1	13	36700001	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10		36700001	78469877	144	27573										
FREM2	341640	hgsc.bcm.edu	37	chr13	39425853	39425853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	taaatttggagaaaccaaatTtagtgtcactgaacccaaag	7	7	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:39425853T>C	ENST00000280481.7	+	11	6989	c.6773T>C	c.(6772-6774)tTt>tCt	p.F2258S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2258	Calx-beta 5.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAAACCAAATTTAGTGTCACT	0.383																																																0			13											48	49	49					13																	39425853		2203	4300	6503	38323853	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6773T>C	13.37:g.39425853T>C	ENSP00000280481:p.Phe2258Ser		38323853	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.646110	0.67358	.	.	ENSG00000150893	ENST00000280481	T	0.30981	1.51	5.62	5.62	0.85841	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.48696	0.1514	M	0.67700	2.07	0.50171	D	0.999855	D;D	0.60160	0.987;0.978	P;D	0.63033	0.854;0.91	T	0.51474	-0.8701	10	0.72032	D	0.01	.	9.7721	0.40595	0.2657:0.0:0.0:0.7343	.	2258;2258	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	S	2258	ENSP00000280481:F2258S	ENSP00000280481:F2258S	F	+	2	0	FREM2	38323853	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	1.487000	0.35540	2.141000	0.66446	0.528000	0.53228	TTT		0.383	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39425853	T	C	39425853	3	2	104	1	0	0	0	0	1	0	0	0	6064	1841	64	4	6815	4	FREM2	13	39425853	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	2725852	39425853	75744025	145	27574										
NHLRC3	387921	hgsc.bcm.edu	37	chr13	39613309	39613309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cttttgcagtttcctggagaActgagaaaattctttaccgg	9	8	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:39613309A>G	ENST00000379600.3	+	2	443	c.121A>G	c.(121-123)Act>Gct	p.T41A	NHLRC3_ENST00000470258.1_5'UTR|PROSER1_ENST00000352251.3_5'Flank|PROSER1_ENST00000350125.3_5'Flank|NHLRC3_ENST00000379599.2_Missense_Mutation_p.T41A	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	41						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		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;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		TTCCTGGAGAACTGAGAAAAT	0.403																																																0			13											79	84	82					13																	39613309		2203	4300	6503	38511309	SO:0001583	missense	387921				CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.121A>G	13.37:g.39613309A>G	ENSP00000368920:p.Thr41Ala		38511309	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	37	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.891193	0.33442	.	.	ENSG00000188811	ENST00000379600;ENST00000379599;ENST00000537150	T;D	0.89939	0.98;-2.59	5.11	-9.17	0.00691	.	0.627020	0.15128	N	0.278998	T	0.67468	0.2896	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.59747	-0.7396	9	.	.	.	0.0547	0.3746	0.00385	0.2325:0.2202:0.2658:0.2815	.	41;41;41;41	B4DTL0;Q5JS37;B4DRC8;F5GZB5	.;NHLC3_HUMAN;.;.	A	41	ENSP00000368920:T41A;ENSP00000368919:T41A	.	T	+	1	0	NHLRC3	38511309	0.000000	0.05858	0.000000	0.03702	0.718000	0.41266	0.267000	0.18552	-2.193000	0.00754	-0.609000	0.04063	ACT		0.403	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754		G	39613309	A	G	39613309	3	3	104	1	0	0	0	0	1	0	0	0	10438	43	2	4	127	4	NHLRC3	13	39613309	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	187456	39613309	75556569	146	27575										
DCT	1638	hgsc.bcm.edu	37	chr13	95121161	95121161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctctcttcttcgcgagatctAaggcgcccaagaactgctct	8	14	4	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:95121161A>G	ENST00000377028.5	-	2	847	c.434T>C	c.(433-435)tTa>tCa	p.L145S	DCT_ENST00000490854.1_5'Flank|DCT_ENST00000446125.1_Missense_Mutation_p.L145S	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	145					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CGCGAGATCTAAGGCGCCCAA	0.572																																																0			13											224	223	223					13																	95121161		2203	4300	6503	93919162	SO:0001583	missense	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.434T>C	13.37:g.95121161A>G	ENSP00000366227:p.Leu145Ser		93919162	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240173	0.58995	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.99167	-5.51;-5.51	5.79	5.79	0.91817	Uncharacterised domain, di-copper centre (2);	0.067025	0.64402	D	0.000011	D	0.99444	0.9803	H	0.95402	3.665	0.80722	D	1	D;D	0.65815	0.995;0.985	P;P	0.61800	0.894;0.691	D	0.98364	1.0550	9	.	.	.	-7.3318	16.1354	0.81481	1.0:0.0:0.0:0.0	.	145;145	Q09GT4;P40126	.;TYRP2_HUMAN	S	145	ENSP00000366227:L145S;ENSP00000392762:L145S	.	L	-	2	0	DCT	93919162	1.000000	0.71417	0.611000	0.29010	0.029000	0.11900	8.962000	0.93254	2.207000	0.71202	0.533000	0.62120	TTA		0.572	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			G	95121161	A	G	95121161	3	3	104	1	0	0	0	0	1	0	0	0	4310	372	13	4	1260	4	DCT	13	95121161	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	55507852	95121161	20048717	147	27576										
OR4K5	79317	hgsc.bcm.edu	37	chr14	20389325	20389325	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcttcctcgagtcaccaaacTtgcctgcctggactcttaca	6	15	3	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:20389325T>G	ENST00000315915.4	+	1	585	c.560T>G	c.(559-561)cTt>cGt	p.L187R		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GTCACCAAACTTGCCTGCCTG	0.408																																																0			14											248	262	257					14																	20389325		2203	4300	6503	19459165	SO:0001583	missense	79317			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"GPCR / Class A : Olfactory receptors"	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.560T>G	14.37:g.20389325T>G	ENSP00000319511:p.Leu187Arg		19459165	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	11.89	1.773765	0.31411	.	.	ENSG00000176281	ENST00000315915	T	0.00411	7.53	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000430	T	0.02418	0.0074	H	0.99675	4.695	0.22266	N	0.999246	D	0.89917	1.0	D	0.97110	1.0	T	0.40572	-0.9556	10	0.87932	D	0	.	6.648	0.22947	0.0:0.106:0.0:0.894	.	187	Q8NGD3	OR4K5_HUMAN	R	187	ENSP00000319511:L187R	ENSP00000319511:L187R	L	+	2	0	OR4K5	19459165	0.429000	0.25530	0.919000	0.36401	0.073000	0.16967	4.076000	0.57591	1.886000	0.54624	0.533000	0.62120	CTT		0.408	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483		G	20389325	T	G	20389325	3	3	104	1	0	0	0	0	1	0	0	0	11104	1609	56	4	562	4	OR4K5	14	20389325	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10		20389325	86960215	148	27577										
OR6S1	341799	hgsc.bcm.edu	37	chr14	21109839	21109839	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggatcactactgtggttcccAtcaggactcattgtcttttt	8	10	4	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:21109839A>T	ENST00000320704.3	-	1	11	c.12T>A	c.(10-12)gaT>gaA	p.D4E		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TGTGGTTCCCATCAGGACTCA	0.438																																																0			14											98	104	102					14																	21109839		2202	4300	6502	20179679	SO:0001583	missense	341799			AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"GPCR / Class A : Olfactory receptors"	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.12T>A	14.37:g.21109839A>T	ENSP00000313110:p.Asp4Glu		20179679	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	A	7.681	0.688936	0.14973	.	.	ENSG00000181803	ENST00000320704	T	0.00000	9.95	5.31	-10.6	0.00265	.	1.090690	0.07137	N	0.846613	T	0.00039	0.0001	N	0.04132	-0.27	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.40098	-0.9581	10	0.02654	T	1	0.0949	7.4898	0.27456	0.1439:0.2078:0.5458:0.1025	.	4	Q8NH40	OR6S1_HUMAN	E	4	ENSP00000313110:D4E	ENSP00000313110:D4E	D	-	3	2	OR6S1	20179679	0.000000	0.05858	0.000000	0.03702	0.832000	0.47134	-2.869000	0.00721	-2.264000	0.00689	0.533000	0.62120	GAT		0.438	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1			T	21109839	A	T	21109839	3	4	104	1	0	0	0	0	1	0	0	0	11240	214	8	5	987	5	OR6S1	14	21109839	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	720514	21109839	86239701	149	27578										
CHD8	57680	hgsc.bcm.edu	37	chr14	21876941	21876941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggtttctgtttttatattcaTgtgatagctccaatttcttc	6	7	3	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:21876941T>C	ENST00000557364.1	-	12	2671	c.2408A>G	c.(2407-2409)cAt>cGt	p.H803R	CHD8_ENST00000399982.2_Missense_Mutation_p.H803R|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Missense_Mutation_p.H524R			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	803					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.H803R(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TTTATATTCATGTGATAGCTC	0.388																																																1	Substitution - Missense(1)	ovary(1)	14											89	76	80					14																	21876941		1810	4080	5890	20946781	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2408A>G	14.37:g.21876941T>C	ENSP00000451601:p.His803Arg		20946781	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	T	3.139	-0.176663	0.06380	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.93189	-3.18;-3.18;-3.18	5.31	5.31	0.75309	.	0.061993	0.64402	D	0.000007	T	0.71350	0.3329	N	0.00254	-1.765	0.34308	D	0.685128	B	0.02656	0.0	B	0.01281	0.0	T	0.73199	-0.4058	10	0.02654	T	1	-21.6595	8.9353	0.35695	0.0:0.0833:0.0:0.9167	.	524	Q9HCK8-2	.	R	524;803;523;803	ENSP00000406288:H524R;ENSP00000382863:H803R;ENSP00000451601:H803R	ENSP00000262707:H523R	H	-	2	0	CHD8	20946781	0.992000	0.36948	1.000000	0.80357	0.993000	0.82548	1.457000	0.35212	2.219000	0.72066	0.528000	0.53228	CAT		0.388	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		C	21876941	T	C	21876941	3	2	104	1	0	0	0	0	1	0	0	0	3337	1464	51	4	5445	4	CHD8	14	21876941	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	767102	21876941	85472599	150	27579										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174536	63174536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cagcctggatgggactgtgcTctagcggacttcgggcctcc	14	13	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:63174536T>C	ENST00000322893.7	-	11	2925	c.2657A>G	c.(2656-2658)gAg>gGg	p.E886G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	886					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGGACTGTGCTCTAGCGGACT	0.502																																																0			14											128	115	119					14																	63174536		2203	4300	6503	62244289	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2657A>G	14.37:g.63174536T>C	ENSP00000321427:p.Glu886Gly		62244289	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.522810	0.27211	.	.	ENSG00000140015	ENST00000322893	D	0.99060	-5.38	5.44	5.44	0.79542	.	0.278712	0.35772	N	0.002984	D	0.96275	0.8785	N	0.14661	0.345	0.80722	D	1	B	0.22683	0.073	B	0.24701	0.055	D	0.94546	0.7749	10	0.30854	T	0.27	.	15.6661	0.77230	0.0:0.0:0.0:1.0	.	886	Q8NCM2	KCNH5_HUMAN	G	886	ENSP00000321427:E886G	ENSP00000321427:E886G	E	-	2	0	KCNH5	62244289	1.000000	0.71417	0.998000	0.56505	0.529000	0.34654	4.510000	0.60455	2.285000	0.76669	0.533000	0.62120	GAG		0.502	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		C	63174536	T	C	63174536	3	2	104	1	0	0	0	0	1	0	0	0	8056	1551	54	4	313	4	KCNH5	14	63174536	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	41297595	63174536	44175004	151	27580										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72200383	72200383	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttcctcctcccttcccgcagGagagttctcagcctcggaca	8	17	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:72200383G>C	ENST00000555818.1	+	19	5273	c.4925G>C	c.(4924-4926)gGa>gCa	p.G1642A	SIPA1L1_ENST00000537413.1_Splice_Site_p.G1096A|SIPA1L1_ENST00000358550.2_Splice_Site_p.G1621A|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_Splice_Site_p.G1621A	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1642					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.G1642A(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CTTCCCGCAGGAGAGTTCTCA	0.557																																																1	Substitution - Missense(1)	lung(1)	14											85	87	86					14																	72200383		2203	4300	6503	71270136	SO:0001630	splice_region_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4925-1G>C	14.37:g.72200383G>C			71270136	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.412373	0.25465	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.09	5.09	0.68999	.	0.048793	0.85682	D	0.000000	T	0.29945	0.0749	L	0.36672	1.1	0.80722	D	1	P;P;B;P;B	0.45531	0.86;0.816;0.118;0.577;0.09	B;B;B;B;B	0.42422	0.359;0.387;0.129;0.269;0.114	T	0.02251	-1.1188	9	.	.	.	.	18.8772	0.92343	0.0:0.0:1.0:0.0	.	1096;1642;1096;1621;1642	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	A	1621;1642;1621;1096	ENSP00000370630:G1621A;ENSP00000450832:G1642A;ENSP00000351352:G1621A;ENSP00000440682:G1096A	.	G	+	2	0	SIPA1L1	71270136	1.000000	0.71417	0.998000	0.56505	0.084000	0.17831	5.629000	0.67798	2.526000	0.85167	0.561000	0.74099	GGA		0.557	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	Missense_Mutation	C	72200383	G	C	72200383	5	2	104	1	0	0	0	0	0	0	1	0	14366	1188	41	5	4995	5	SIPA1L1	14	72200383	Splice_Site	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	9025847	72200383	35149157	152	27581										
RBM25	58517	hgsc.bcm.edu	37	chr14	73576088	73576088	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aaggttgcgtgatagagaaaAggaaatggaagcagatgaac	14	3	0	4			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:73576088A>G	ENST00000261973.7	+	14	1865	c.1580A>G	c.(1579-1581)aAg>aGg	p.K527R	RBM25_ENST00000532483.1_3'UTR|RBM25_ENST00000527432.1_Missense_Mutation_p.K527R	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	527	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K527R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		GATAGAGAAAAGGAAATGGAA	0.438																																																1	Substitution - Missense(1)	ovary(1)	14											120	124	123					14																	73576088		2203	4300	6503	72645841	SO:0001583	missense	58517			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1580A>G	14.37:g.73576088A>G	ENSP00000261973:p.Lys527Arg		72645841	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449694	0.63290	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.10860	2.83;2.83	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.15349	0.0370	N	0.17379	0.485	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.16837	-1.0389	10	0.08599	T	0.76	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	527	P49756	RBM25_HUMAN	R	527	ENSP00000261973:K527R;ENSP00000431150:K527R	ENSP00000261973:K527R	K	+	2	0	RBM25	72645841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.141000	0.94612	2.288000	0.76882	0.533000	0.62120	AAG		0.438	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		G	73576088	A	G	73576088	3	3	104	1	0	0	0	0	1	0	0	0	13162	72	3	4	1630	4	RBM25	14	73576088	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	1375705	73576088	33773452	153	27582										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75150178	75150178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctagctcgacatgagagatgTgaactcttagtcccacaggc	10	11	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:75150178T>C	ENST00000356357.4	-	5	817	c.302A>G	c.(301-303)cAc>cGc	p.H101R	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	101					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										ATGAGAGATGTGAACTCTTAG	0.512																																																0			14											109	102	104					14																	75150178		1942	4140	6082	74219931	SO:0001583	missense	9870			AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.302A>G	14.37:g.75150178T>C	ENSP00000348714:p.His101Arg		74219931	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	37	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.600712	0.46423	.	.	ENSG00000119682	ENST00000356357;ENST00000555249	T;T	0.49720	0.77;0.77	5.68	5.68	0.88126	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.090386	0.85682	D	0.000000	T	0.28034	0.0691	N	0.08118	0	0.45852	D	0.998713	B;B	0.10296	0.003;0.001	B;B	0.10450	0.005;0.003	T	0.09487	-1.0672	10	0.45353	T	0.12	.	10.2988	0.43639	0.0:0.0733:0.0:0.9267	.	101;101	O15033-2;O15033	.;K0317_HUMAN	R	101	ENSP00000348714:H101R;ENSP00000450458:H101R	ENSP00000348714:H101R	H	-	2	0	KIAA0317	74219931	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.938000	0.70170	2.158000	0.67659	0.533000	0.62120	CAC		0.512	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		C	75150178	T	C	75150178	3	2	104	1	0	0	0	0	1	0	0	0	8188	1696	59	4	2233	4	KIAA0317	14	75150178	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	1574090	75150178	32199362	154	27583										
PSMC1	5700	hgsc.bcm.edu	37	chr14	90734705	90734705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgttccgagttgctgaagaaCatgcaccgtccatcgtgttt	10	10	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:90734705C>T	ENST00000261303.8	+	8	932	c.829C>T	c.(829-831)Cat>Tat	p.H277Y	PSMC1_ENST00000543772.2_Missense_Mutation_p.H204Y	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	277					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		TGCTGAAGAACATGCACCGTC	0.448																																																0			14											103	97	99					14																	90734705		2203	4297	6500	89804458	SO:0001583	missense	5700			L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.829C>T	14.37:g.90734705C>T	ENSP00000261303:p.His277Tyr		89804458	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	Missense_Mutation	SNP	ENST00000261303.8	37	CCDS32139.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998544	0.54147	.	.	ENSG00000100764	ENST00000261303;ENST00000543772	D;D	0.92911	-3.13;-3.13	5.04	5.04	0.67666	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.86703	0.5996	N	0.16368	0.405	0.80722	D	1	B	0.11235	0.004	B	0.12156	0.007	T	0.81865	-0.0736	10	0.48119	T	0.1	-14.4757	18.7511	0.91816	0.0:1.0:0.0:0.0	.	277	P62191	PRS4_HUMAN	Y	277;204	ENSP00000261303:H277Y;ENSP00000445147:H204Y	ENSP00000261303:H277Y	H	+	1	0	PSMC1	89804458	1.000000	0.71417	0.959000	0.39883	0.995000	0.86356	7.818000	0.86416	2.502000	0.84385	0.563000	0.77884	CAT		0.448	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802		T	90734705	C	T	90734705	3	4	104	1	0	0	0	0	1	0	0	0	12719	478	17	3	859	3	PSMC1	14	90734705	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	15584527	90734705	16614835	155	27584										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92465662	92465662	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctttcttagtttagcctctCtatcttctgcagccaaagct	5	12	5	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:92465662C>G	ENST00000267622.4	-	13	5187	c.4814G>C	c.(4813-4815)aGa>aCa	p.R1605T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1605					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTTAGCCTCTCTATCTTCTGC	0.358			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											113	104	107					14																	92465662		2203	4300	6503	91535415	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4814G>C	14.37:g.92465662C>G	ENSP00000267622:p.Arg1605Thr		91535415	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.106400|4.106400	0.77096|0.77096	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.06528|.	3.29|.	5.38|5.38	4.5|4.5	0.54988|0.54988	.|.	0.046152|.	0.85682|.	D|.	0.000000|.	T|.	0.73450|.	0.3588|.	M|M	0.76574|0.76574	2.34|2.34	0.45867|0.45867	D|D	0.998721|0.998721	D;D|.	0.89917|.	0.992;1.0|.	P;D|.	0.74348|.	0.891;0.983|.	T|.	0.74275|.	-0.3718|.	10|.	0.51188|.	T|.	0.08|.	.|.	14.0449|14.0449	0.64700|0.64700	0.0:0.9275:0.0:0.0725|0.0:0.9275:0.0:0.0725	.|.	1341;1605|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	T|Y	1605;1341|1320	ENSP00000267622:R1605T|.	ENSP00000267622:R1605T|.	R|X	-|-	2|3	0|2	TRIP11|TRIP11	91535415|91535415	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.415000|5.415000	0.66411|0.66411	1.290000|1.290000	0.44636|0.44636	0.655000|0.655000	0.94253|0.94253	AGA|TAG		0.358	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			G	92465662	C	G	92465662	3	3	104	1	0	0	0	0	1	0	0	0	16595	913	32	5	1161	5	TRIP11	14	92465662	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	1730957	92465662	14883878	156	27585										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408336	105408336	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggcgcagacacatccaccgaGacctcgatggacttgcctgg	12	14	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:105408336G>A	ENST00000333244.5	-	7	13571	c.13452C>T	c.(13450-13452)gtC>gtT	p.V4484V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4484						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CATCCACCGAGACCTCGATGG	0.562																																																0			14											186	193	191					14																	105408336		2036	4179	6215	104479381	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13452C>T	14.37:g.105408336G>A			104479381	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.562	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105408336	G	A	105408336	2	1	104	1	0	0	0	0	0	0	0	1	415	929	33	3		3	AHNAK2	14	105408336	Silent	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	12942674	105408336	1941204	157	27586										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32908529	32908529	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aggagacatgaaacagcagcCacggaaataggggtaagttc	13	7	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:32908529C>T	ENST00000361627.3	+	1	839	c.117C>T	c.(115-117)gcC>gcT	p.A39A	ARHGAP11A_ENST00000543522.1_Intron|ARHGAP11A_ENST00000565905.1_Intron|ARHGAP11A_ENST00000567348.1_Silent_p.A39A|RP11-1000B6.5_ENST00000500941.2_lincRNA|AC123768.4_ENST00000576873.1_lincRNA|ARHGAP11A_ENST00000563864.1_Silent_p.A39A	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	39					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AAACAGCAGCCACGGAAATAG	0.483																																					Colon(45;757 1134 30003 36652)											0			15											50	47	48					15																	32908529		2201	4292	6493	30695821	SO:0001819	synonymous_variant	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.117C>T	15.37:g.32908529C>T			30695821	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																				0.483	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32908529	C	T	32908529	2	4	104	1	0	0	0	0	0	0	0	1	863	581	21	3		3	ARHGAP11A	15	32908529	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		32908529	69622863	158	27587										
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42438057	42438057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctcggtgggaacataagcccCgtacttggggaagccaacct	12	12	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:42438057C>T	ENST00000382396.4	-	15	1665	c.1579G>A	c.(1579-1581)Ggg>Agg	p.G527R	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.G529R			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	527	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACATAAGCCCCGTACTTGGGG	0.592																																																0			15																																								40225349	SO:0001583	missense	255189				CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1579G>A	15.37:g.42438057C>T	ENSP00000371833:p.Gly527Arg		40225349	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731369	0.69189	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.05717	3.4;3.4	5.52	5.52	0.82312	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.211792	0.33938	N	0.004401	T	0.29882	0.0747	M	0.81614	2.55	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.01925	-1.1246	10	0.87932	D	0	-35.3945	19.4533	0.94876	0.0:1.0:0.0:0.0	.	314;527	A2RRC4;Q68DD2	.;PA24F_HUMAN	R	523;529;527;527	ENSP00000380442:G529R;ENSP00000371833:G527R	ENSP00000290497:G523R	G	-	1	0	PLA2G4F	40225349	1.000000	0.71417	0.898000	0.35279	0.111000	0.19643	6.096000	0.71446	2.604000	0.88044	0.555000	0.69702	GGG		0.592	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		T	42438057	C	T	42438057	3	4	104	1	0	0	0	0	1	0	0	0	12037	652	23	1	994	1	PLA2G4F	15	42438057	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	9529528	42438057	60093335	159	27588										
SMAD3	4088	hgsc.bcm.edu	37	chr15	67473777	67473777	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaatgcagcagtggagctgaCacggagacacatcggtatgg	15	8	0	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:67473777C>G	ENST00000327367.4	+	6	1167	c.857C>G	c.(856-858)aCa>aGa	p.T286R	SMAD3_ENST00000537194.2_Missense_Mutation_p.T91R|SMAD3_ENST00000439724.3_Missense_Mutation_p.T242R|SMAD3_ENST00000540846.2_Missense_Mutation_p.T181R	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	286	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.|Sufficient for interaction with XPO4.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GTGGAGCTGACACGGAGACAC	0.627																																																0			15											54	51	52					15																	67473777		2201	4299	6500	65260831	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.857C>G	15.37:g.67473777C>G	ENSP00000332973:p.Thr286Arg		65260831	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429109	0.62844	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47	5.1	5.1	0.69264	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.99690	1.1001	10	0.87932	D	0	.	18.8753	0.92332	0.0:1.0:0.0:0.0	.	242;286	B7Z4Z5;P84022	.;SMAD3_HUMAN	R	286;286;181;242;91	ENSP00000332973:T286R;ENSP00000437757:T181R;ENSP00000401133:T242R;ENSP00000445348:T91R	ENSP00000332973:T286R	T	+	2	0	SMAD3	65260831	1.000000	0.71417	0.648000	0.29521	0.202000	0.24057	7.675000	0.84002	2.515000	0.84797	0.555000	0.69702	ACA		0.627	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		G	67473777	C	G	67473777	3	3	104	1	0	0	0	0	1	0	0	0	14796	478	17	5	957	5	SMAD3	15	67473777	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	25035720	67473777	35057615	160	27589										
FEM1B	10116	hgsc.bcm.edu	37	chr15	68583063	68583063	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tttagtgtgcatctctaccaAaacacagtgcagcgaagaag	9	9	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:68583063A>C	ENST00000306917.4	+	2	1982	c.1367A>C	c.(1366-1368)aAa>aCa	p.K456T		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	456					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						ATCTCTACCAAAACACAGTGC	0.388																																																0			15											128	118	122					15																	68583063		2200	4298	6498	66370117	SO:0001583	missense	10116				CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"Ankyrin repeat domain containing"	3649	protein-coding gene	gene with protein product		613539	"FEM-1 (C. elegans) homolog b"			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1367A>C	15.37:g.68583063A>C	ENSP00000307298:p.Lys456Thr		66370117	O43146	Missense_Mutation	SNP	ENST00000306917.4	37	CCDS10228.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670629	0.29693	.	.	ENSG00000169018	ENST00000306917	T	0.47869	0.83	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.61426	0.2346	M	0.64404	1.975	0.80722	D	1	D	0.67145	0.996	P	0.58970	0.849	T	0.58842	-0.7565	10	0.32370	T	0.25	2.3198	15.5864	0.76485	1.0:0.0:0.0:0.0	.	456	Q9UK73	FEM1B_HUMAN	T	456	ENSP00000307298:K456T	ENSP00000307298:K456T	K	+	2	0	FEM1B	66370117	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.268000	0.95675	2.279000	0.76181	0.402000	0.26972	AAA		0.388	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1			C	68583063	A	C	68583063	3	2	104	1	0	0	0	0	1	0	0	0	5829	14	1	4	1373	4	FEM1B	15	68583063	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	1109286	68583063	33948329	161	27590										
HCN4	10021	hgsc.bcm.edu	37	chr15	73617474	73617474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atggacgtcacgaagttgggGtccgcattggcaaacagtgg	15	8	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:73617474G>T	ENST00000261917.3	-	6	2793	c.1800C>A	c.(1798-1800)gaC>gaA	p.D600E		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	600					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		CGAAGTTGGGGTCCGCATTGG	0.562																																																0			15											141	124	129					15																	73617474		2198	4297	6495	71404527	SO:0001583	missense	10021			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1800C>A	15.37:g.73617474G>T	ENSP00000261917:p.Asp600Glu		71404527	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534257	0.45073	.	.	ENSG00000138622	ENST00000261917	D	0.96940	-4.18	3.65	0.593	0.17478	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	.	.	.	.	D	0.96741	0.8936	M	0.77486	2.375	0.49798	D	0.999825	D	0.57571	0.98	P	0.60236	0.871	D	0.93983	0.7260	9	0.33940	T	0.23	.	9.1471	0.36939	0.3284:0.0:0.6716:0.0	.	600	Q9Y3Q4	HCN4_HUMAN	E	600	ENSP00000261917:D600E	ENSP00000261917:D600E	D	-	3	2	HCN4	71404527	0.998000	0.40836	0.992000	0.48379	0.954000	0.61252	0.419000	0.21247	-0.055000	0.13244	0.561000	0.74099	GAC		0.562	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73617474	G	T	73617474	3	4	104	1	0	0	0	0	1	0	0	0	7020	1252	44	2	1823	2	HCN4	15	73617474	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	5034411	73617474	28913918	162	27591										
ARNT2	9915	hgsc.bcm.edu	37	chr15	80762677	80762677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggaagccagacaagctcaccAtcctccgcatggccgtctcg	10	16	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:80762677A>G	ENST00000303329.4	+	4	478	c.313A>G	c.(313-315)Atc>Gtc	p.I105V	ARNT2_ENST00000527771.1_Missense_Mutation_p.I94V|ARNT2_ENST00000531595.3_3'UTR|ARNT2_ENST00000533983.1_Missense_Mutation_p.I94V	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	105	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.I105V(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			CAAGCTCACCATCCTCCGCAT	0.587																																																1	Substitution - Missense(1)	central_nervous_system(1)	15											98	75	83					15																	80762677		2203	4300	6503	78549732	SO:0001583	missense	9915			AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"Basic helix-loop-helix proteins"	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.313A>G	15.37:g.80762677A>G	ENSP00000307479:p.Ile105Val		78549732	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492889	0.84962	.	.	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	D	0.98958	-5.27	5.0	5.0	0.66597	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.96445	0.8840	N	0.10782	0.045	0.80722	D	1	P;P	0.41546	0.677;0.754	P;P	0.51415	0.584;0.669	D	0.95502	0.8578	10	0.12103	T	0.63	.	14.8575	0.70351	1.0:0.0:0.0:0.0	.	105;105	Q9HBZ2;Q86TN1	ARNT2_HUMAN;.	V	94;105;105	ENSP00000307479:I105V	ENSP00000307479:I105V	I	+	1	0	ARNT2	78549732	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.697000	0.91307	2.099000	0.63709	0.528000	0.53228	ATC		0.587	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			G	80762677	A	G	80762677	3	3	104	1	0	0	0	0	1	0	0	0	967	217	8	4	327	4	ARNT2	15	80762677	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7145203	80762677	21768715	163	27592										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85431000	85431000	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aaggtctgggacatggagaaCgacccctcgagacgaagaga	14	9	1	3	rs8187737	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:85431000C>G	ENST00000286749.3	+	2	99	c.9C>G	c.(7-9)aaC>aaG	p.N3K	SLC28A1_ENST00000537216.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000537703.1_5'UTR|SLC28A1_ENST00000394573.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000538177.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000537624.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000338602.2_Missense_Mutation_p.N3K			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	3					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	ACATGGAGAACGACCCCTCGA	0.592																																																0			15											137	115	123					15																	85431000		2203	4299	6502	83232004	SO:0001583	missense	9154			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.9C>G	15.37:g.85431000C>G	ENSP00000286749:p.Asn3Lys		83232004	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358397	0.24598	.	.	ENSG00000156222	ENST00000338602;ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T;T;T	0.12361	2.69;4.56;4.31;4.74;4.75;4.75	4.21	-1.74	0.08056	.	1.284090	0.05783	N	0.609075	T	0.05823	0.0152	N	0.22421	0.69	0.21878	N	0.999492	B;B;B;B;P	0.38978	0.057;0.002;0.11;0.033;0.652	B;B;B;B;B	0.29353	0.019;0.004;0.032;0.019;0.101	T	0.29058	-1.0024	10	0.22109	T	0.4	-10.9961	0.632	0.00796	0.3904:0.2592:0.1411:0.2093	.	3;3;3;3;3	B7Z533;F5H560;B7Z3L6;O00337;O00337-2	.;.;.;S28A1_HUMAN;.	K	3	ENSP00000341629:N3K;ENSP00000440546:N3K;ENSP00000443752:N3K;ENSP00000444700:N3K;ENSP00000286749:N3K;ENSP00000378074:N3K	ENSP00000286749:N3K	N	+	3	2	SLC28A1	83232004	0.002000	0.14202	0.029000	0.17559	0.079000	0.17450	-0.482000	0.06544	-0.127000	0.11661	0.563000	0.77884	AAC		0.592	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			G	85431000	C	G	85431000	3	3	104	1	0	0	0	0	1	0	0	0	14568	535	19	5	11	5	SLC28A1	15	85431000	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4668323	85431000	17100392	164	27593										
ACAN	176	hgsc.bcm.edu	37	chr15	89381985	89381985	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	accatcccctgctatttcatCgaccccatgcaccctgtgac	5	18	1	1	rs377037099	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:89381985C>T	ENST00000561243.1	+	2	162	c.162C>T	c.(160-162)atC>atT	p.I54I	ACAN_ENST00000559004.1_Silent_p.I54I|ACAN_ENST00000439576.2_Silent_p.I54I|ACAN_ENST00000352105.7_Silent_p.I54I|ACAN_ENST00000558207.1_Silent_p.I54I			P16112	PGCA_HUMAN	aggrecan	54	G1-A.|Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCTATTTCATCGACCCCATGC	0.622													C|||	2	0.000399361	0	0	5008	,	,		17737	0.002		0	False		,,,				2504	0															0			15						C	,	1,4013		0,1,2006	100	111	108		162,162	2.2	1	15		108	0,8312		0,0,4156	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	0,1,6162	TT,TC,CC		0.0,0.0249,0.0081	,	54/2432,54/2531	89381985	1,12325	2007	4156	6163	87182989	SO:0001819	synonymous_variant	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.162C>T	15.37:g.89381985C>T			87182989	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																				0.622	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89381985	C	T	89381985	2	4	104	1	0	0	0	0	0	0	0	1	117	874	31	1		1	ACAN	15	89381985	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	3950985	89381985	13149407	165	27594										
IFT140	9742	hgsc.bcm.edu	37	chr16	1636257	1636257	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atggctactcgccctctgtcGgtaccagcggccagaagacc	11	15	1	2	rs556379159		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:1636257G>A	ENST00000426508.2	-	10	1392	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	343					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.T343T(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				GCCCTCTGTCGGTACCAGCGG	0.552													G|||	1	0.000199681	0	0	5008	,	,		17974	0		0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	endometrium(1)	16											82	76	78					16																	1636257		2199	4300	6499	1576258	SO:0001819	synonymous_variant	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1029C>T	16.37:g.1636257G>A			1576258	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				0.552	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1636257	G	A	1636257	2	1	104	1	0	0	0	0	0	0	0	1	7577	1103	39	1		1	IFT140	16	1636257	Silent	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		1636257	88718496	166	27595										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20975977	20975977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtcaatcattaaggcccagcGtctggaattggatacaatga	10	8	3	1	rs372316224		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:20975977G>A	ENST00000261383.3	-	53	9228	c.9229C>T	c.(9229-9231)Cgc>Tgc	p.R3077C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3077	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R3077C(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AAGGCCCAGCGTCTGGAATTG	0.483																																																2	Substitution - Missense(2)	large_intestine(2)	16						G	CYS/ARG	0,4402		0,0,2201	80	74	76		9229	4.9	1	16		76	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH3	NM_017539.1	180	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3077/4117	20975977	1,13001	2201	4300	6501	20883478	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.9229C>T	16.37:g.20975977G>A	ENSP00000261383:p.Arg3077Cys		20883478	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112425	0.56398	0.0	1.16E-4	ENSG00000158486	ENST00000261383	T	0.34072	1.38	5.88	4.88	0.63580	.	0.062427	0.64402	D	0.000010	T	0.76343	0.3974	H	0.99525	4.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85743	0.1338	10	0.87932	D	0	.	14.1248	0.65213	0.0:0.0:0.7441:0.2559	.	3077	Q8TD57	DYH3_HUMAN	C	3077	ENSP00000261383:R3077C	ENSP00000261383:R3077C	R	-	1	0	DNAH3	20883478	1.000000	0.71417	0.983000	0.44433	0.939000	0.58152	3.322000	0.52007	2.797000	0.96272	0.561000	0.74099	CGC		0.483	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	20975977	G	A	20975977	3	1	104	1	0	0	0	0	1	0	0	0	4614	1145	40	1	3160	1	DNAH3	16	20975977	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	19339720	20975977	69378776	167	27596										
ARMC5	79798	hgsc.bcm.edu	37	chr16	31477995	31477995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tccacctgggaccccagggtGgcccggagtcagtgggtgag	17	12	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:31477995G>A	ENST00000563544.1	+	7	3139	c.2593G>A	c.(2593-2595)Ggc>Agc	p.G865S	ARMC5_ENST00000412665.2_Missense_Mutation_p.G509S|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000408912.3_Missense_Mutation_p.G960S|ARMC5_ENST00000538189.1_Missense_Mutation_p.G897S|ARMC5_ENST00000268314.4_Missense_Mutation_p.G865S			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	865										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						ACCCCAGGGTGGCCCGGAGTC	0.716																																																0			16											18	28	24					16																	31477995		2166	4263	6429	31385496	SO:0001583	missense	79798			AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2593G>A	16.37:g.31477995G>A	ENSP00000456877:p.Gly865Ser		31385496	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	G	7.329	0.618629	0.14129	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.40756	2.3;2.33;2.34;1.02	5.07	-0.357	0.12579	.	0.877779	0.09945	N	0.735429	T	0.18383	0.0441	N	0.08118	0	0.09310	N	1	B;B;B;B	0.14805	0.0;0.0;0.011;0.0	B;B;B;B	0.14023	0.005;0.005;0.01;0.005	T	0.21827	-1.0234	10	0.59425	D	0.04	-16.304	0.5668	0.00688	0.2925:0.193:0.3411:0.1735	.	897;897;960;865	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	S	960;897;865;509	ENSP00000386125:G960S;ENSP00000443995:G897S;ENSP00000268314:G865S;ENSP00000400183:G509S	ENSP00000268314:G865S	G	+	1	0	ARMC5	31385496	0.008000	0.16893	0.098000	0.21074	0.740000	0.42216	0.475000	0.22164	0.095000	0.17434	0.448000	0.29417	GGC		0.716	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		A	31477995	G	A	31477995	3	1	104	1	0	0	0	0	1	0	0	0	955	1348	47	3	2929	3	ARMC5	16	31477995	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	10502018	31477995	58876758	168	27597										
CYLD	1540	hgsc.bcm.edu	37	chr16	50810186	50810186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcataataaaccaaaggctaCaggtatggattaatagcata	7	6	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:50810186C>T	ENST00000427738.3	+	6	1224	c.1019C>T	c.(1018-1020)aCa>aTa	p.T340I	CYLD_ENST00000566206.1_Missense_Mutation_p.T337I|CYLD_ENST00000569418.1_Missense_Mutation_p.T337I|CYLD_ENST00000540145.1_Missense_Mutation_p.T340I|CYLD_ENST00000568704.2_Missense_Mutation_p.T337I|CYLD_ENST00000564326.1_Missense_Mutation_p.T337I|CYLD_ENST00000311559.9_Missense_Mutation_p.T340I|CYLD_ENST00000398568.2_Missense_Mutation_p.T337I			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	340	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CCAAAGGCTACAGGTATGGAT	0.383			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											83	83	83					16																	50810186		1862	4092	5954	49367687	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1019C>T	16.37:g.50810186C>T	ENSP00000392025:p.Thr340Ile		49367687	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.019298	0.54576	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D	0.93712	-3.27;-3.27;-3.27	6.17	6.17	0.99709	.	0.095441	0.64402	D	0.000001	D	0.88001	0.6320	N	0.24115	0.695	0.41967	D	0.990738	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.08055	0.001;0.003;0.003;0.001	T	0.82204	-0.0573	10	0.27785	T	0.31	-16.9065	14.9696	0.71223	0.0:0.9306:0.0:0.0694	.	337;340;337;340	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	I	340;340;337;337	ENSP00000445447:T340I;ENSP00000308928:T340I;ENSP00000381574:T337I	ENSP00000308928:T340I	T	+	2	0	CYLD	49367687	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.879000	0.39618	2.941000	0.99782	0.655000	0.94253	ACA		0.383	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			T	50810186	C	T	50810186	3	4	104	1	0	0	0	0	1	0	0	0	4149	478	17	3	1037	3	CYLD	16	50810186	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	19332191	50810186	39544567	169	27598										
NAE1	8883	hgsc.bcm.edu	37	chr16	66842914	66842914	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	atttcatccttgttaattgtAtccaaaccatattcttcagc	3	10	3	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:66842914A>G	ENST00000290810.3	-	16	1312	c.1215T>C	c.(1213-1215)gaT>gaC	p.D405D	NAE1_ENST00000359087.4_Silent_p.D408D|NAE1_ENST00000379463.2_Silent_p.D399D|NAE1_ENST00000394074.2_Silent_p.D316D			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	405					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	TGTTAATTGTATCCAAACCAT	0.308																																																0			16											89	84	86					16																	66842914		2200	4300	6500	65400415	SO:0001819	synonymous_variant	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.1215T>C	16.37:g.66842914A>G			65400415	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Silent	SNP	ENST00000290810.3	37	CCDS10820.1																																																																																				0.308	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905		G	66842914	A	G	66842914	2	3	104	1	0	0	0	0	0	0	0	1	10169	446	16	4		4	NAE1	16	66842914	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	16032728	66842914	23511839	170	27599										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70867911	70867911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctccagggcctggcagcagcCgctaaggaggaagagggggc	18	11	0	1	rs200437208		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:70867911C>T	ENST00000393567.2	-	79	13708	c.13558G>A	c.(13558-13560)Ggc>Agc	p.G4520S		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4520			G -> S (in dbSNP:rs2292127).		cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGCAGCAGCCGCTAAGGAGG	0.567																																																0			16											7	7	7					16																	70867911		1591	3556	5147	69425412	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13558G>A	16.37:g.70867911C>T	ENSP00000377197:p.Gly4520Ser		69425412	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443704	0.83993	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.03860	3.78	4.87	4.87	0.63330	.	0.000000	0.33631	U	0.004719	T	0.24967	0.0606	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02214	-1.1194	10	0.54805	T	0.06	.	17.6354	0.88120	0.0:1.0:0.0:0.0	rs2292127	4519	F8WD23	.	S	4520;4519	ENSP00000377197:G4520S	ENSP00000313052:G4519S	G	-	1	0	HYDIN	69425412	1.000000	0.71417	0.945000	0.38365	0.470000	0.32858	7.043000	0.76572	2.257000	0.74773	0.511000	0.50034	GGC		0.567	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70867911	C	T	70867911	3	4	104	1	0	0	0	0	1	0	0	0	7488	652	23	1	1839	1	HYDIN	16	70867911	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	4024997	70867911	19486842	171	27600										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70917831	70917831	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agtggtcagtacctggtagaCaggcttcagctagcaaagtg	13	8	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:70917831C>G	ENST00000393567.2	-	59	10121	c.9971G>C	c.(9970-9972)tGt>tCt	p.C3324S		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3324					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ACCTGGTAGACAGGCTTCAGC	0.532																																																0			16											44	48	47					16																	70917831		1915	4142	6057	69475332	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.9971G>C	16.37:g.70917831C>G	ENSP00000377197:p.Cys3324Ser		69475332	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724868	0.48833	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01139	5.28	5.01	5.01	0.66863	.	0.000000	0.36134	U	0.002768	T	0.02727	0.0082	M	0.72118	2.19	0.80722	D	1	B	0.31680	0.335	B	0.34722	0.188	T	0.57130	-0.7864	10	0.32370	T	0.25	.	17.9159	0.88950	0.0:1.0:0.0:0.0	.	3323	F8WD23	.	S	3324;3323	ENSP00000377197:C3324S	ENSP00000313052:C3323S	C	-	2	0	HYDIN	69475332	1.000000	0.71417	0.979000	0.43373	0.573000	0.36030	5.337000	0.65941	2.325000	0.78763	0.511000	0.50034	TGT		0.532	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	70917831	C	G	70917831	3	3	104	1	0	0	0	0	1	0	0	0	7488	478	17	5	5506	5	HYDIN	16	70917831	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	49920	70917831	19436922	172	27601										
DPEP1	1800	hgsc.bcm.edu	37	chr16	89702769	89702770	+	Frame_Shift_Ins	INS	-	-	C													0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	caccgcatgtgccggatgtaINScccggagaccttcctgtatg							TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:89702769_89702770insC	ENST00000393092.3	+	4	626_627	c.335_336insC	c.(334-339)tacccgfs	p.YP112fs	DPEP1_ENST00000421184.1_Frame_Shift_Ins_p.YP112fs|DPEP1_ENST00000261615.4_Frame_Shift_Ins_p.YP112fs	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	112					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	TGCCGGATGTACCCGGAGACCT	0.629																																																0			16																																								88230271	SO:0001589	frameshift_variant	1800				CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.338dupC	16.37:g.89702772_89702772dupC	ENSP00000376807:p.Tyr112fs		88230270	D3DX80|Q96AK2	Frame_Shift_Ins	INS	ENST00000393092.3	37	CCDS10982.1																																																																																				0.629	DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141		C	89702770	-	C	89702769	7	5	104	1	0	1	1	0	0	0	0	0	4724	391	14	0	345	0	DPEP1	16	89702769	Frame_Shift_Ins	INS	-	TCGA-DY-A1DC-01A-31D-A152-10	18784938	89702769	651984	173	27602										
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085266	5085266	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtcctactacactgattacaCcaataaactttcttttcctg	3	12	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:5085266C>A	ENST00000399604.4	-	1	2426	c.2286G>T	c.(2284-2286)tgG>tgT	p.W762C	ZNF594_ENST00000575779.1_Missense_Mutation_p.W762C			Q96JF6	ZN594_HUMAN	zinc finger protein 594	762					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ACTGATTACACCAATAAACTT	0.418																																																0			17											208	210	209					17																	5085266		1984	4167	6151	5025990	SO:0001583	missense	84622			AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2286G>T	17.37:g.5085266C>A	ENSP00000382513:p.Trp762Cys		5025990	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	2.538	-0.307054	0.05458	.	.	ENSG00000180626	ENST00000399604	T	0.14766	2.48	1.04	-0.0977	0.13631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06600	0.0169	N	0.11201	0.11	0.20975	N	0.999816	B	0.02656	0.0	B	0.01281	0.0	T	0.34304	-0.9834	9	0.72032	D	0.01	.	4.8952	0.13746	0.0:0.7309:0.0:0.2691	.	762	Q96JF6	ZN594_HUMAN	C	762	ENSP00000382513:W762C	ENSP00000382513:W762C	W	-	3	0	ZNF594	5025990	.	.	0.012000	0.15200	0.113000	0.19764	.	.	0.496000	0.27904	0.298000	0.19748	TGG		0.418	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		A	5085266	C	A	5085266	3	1	104	1	0	0	0	0	1	0	0	0	18063	508	18	2	141	2	ZNF594	17	5085266	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		5085266	76109944	174	27603										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	104	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	2493140	7578406	73616804	175	27604										
MYH13	8735	hgsc.bcm.edu	37	chr17	10219217	10219218	+	Splice_Site	INS	-	-	G													0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agccctgcccattctcaccaINSttttgggtctgcagtcttgc							TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:10219217_10219218insG	ENST00000418404.3	-	27	4026_4027	c.3863_3864insC	c.(3862-3864)aat>aaCt	p.N1288fs	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Splice_Site_p.N1288fs			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1288					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CATTCTCACCATTTTGGGTCTG	0.53																																																0			17																																								10159943	SO:0001630	splice_region_variant	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3865+1->C	17.37:g.10219217_10219218insG			10159942	O95252|Q9P0U8	Frame_Shift_Ins	INS	ENST00000418404.3	37	CCDS45613.1																																																																																				0.53	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	Frame_Shift_Ins	G	10219218	-	G	10219217	8	5	104	1	0	1	1	0	0	0	1	0	10062	231	8	0	2008	0	MYH13	17	10219217	Splice_Site	INS	-	TCGA-DY-A1DC-01A-31D-A152-10	2640811	10219217	70975993	176	27605	47	2								
MYH13	8735	hgsc.bcm.edu	37	chr17	10219218	10219218	+	Missense_Mutation	SNP	T	T	G													0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agccctgcccattctcaccaTtttgggtctgcagtcttgct							TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:10219218T>G	ENST00000418404.3	-	27	4026	c.3863A>C	c.(3862-3864)aAt>aCt	p.N1288T	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.N1288T			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1288					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						ATTCTCACCATTTTGGGTCTG	0.527																																																0			17											226	223	224					17																	10219218		1992	4155	6147	10159943	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3863A>C	17.37:g.10219218T>G	ENSP00000404570:p.Asn1288Thr		10159943	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	T	9.042	0.989839	0.18966	.	.	ENSG00000006788	ENST00000252172	T	0.80738	-1.41	4.39	4.39	0.52855	Myosin tail (1);	.	.	.	.	T	0.79375	0.4435	M	0.68317	2.08	0.34672	D	0.723824	B	0.02656	0.0	B	0.17979	0.02	T	0.82319	-0.0516	9	0.54805	T	0.06	.	13.8848	0.63702	0.0:0.0:0.0:1.0	.	1288	Q9UKX3	MYH13_HUMAN	T	1288	ENSP00000252172:N1288T	ENSP00000252172:N1288T	N	-	2	0	MYH13	10159943	0.189000	0.23263	1.000000	0.80357	0.157000	0.22087	1.372000	0.34261	1.734000	0.51633	0.450000	0.29827	AAT		0.527	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		G	10219218	T	G	10219218	3	3	104	1	0	0	0	0	1	0	0	0	10062	1493	52	4	2009	4	MYH13	17	10219218	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	1	10219218	70975992	177	27606	47	2								
TNS4	84951	hgsc.bcm.edu	37	chr17	38633853	38633853	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctctcccctacatcctttctGcgtcctgcagcagagcagtc	7	17	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:38633853G>T	ENST00000254051.6	-	13	2293	c.2135C>A	c.(2134-2136)gCa>gAa	p.A712E		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	712	Phosphatase tensin-type.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CATCCTTTCTGCGTCCTGCAG	0.607																																																0			17											116	94	101					17																	38633853		2203	4300	6503	35887379	SO:0001583	missense	84951			AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"SH2 domain containing"	24352	protein-coding gene	gene with protein product	"C terminal tensin like"	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.2135C>A	17.37:g.38633853G>T	ENSP00000254051:p.Ala712Glu		35887379	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	37	CCDS11368.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978985	0.34942	.	.	ENSG00000131746	ENST00000377816;ENST00000394072;ENST00000254051	T	0.17691	2.26	5.27	2.19	0.27852	.	1.178600	0.06142	N	0.672496	T	0.14013	0.0339	L	0.34521	1.04	0.19945	N	0.999948	B;P	0.39576	0.183;0.679	B;B	0.36030	0.131;0.216	T	0.27806	-1.0063	10	0.72032	D	0.01	2.3817	7.2818	0.26316	0.2598:0.0:0.7402:0.0	.	712;125	Q8IZW8;F2Z318	TENS4_HUMAN;.	E	712;125;712	ENSP00000254051:A712E	ENSP00000254051:A712E	A	-	2	0	TNS4	35887379	0.216000	0.23585	0.862000	0.33874	0.367000	0.29736	2.498000	0.45363	1.250000	0.43966	-0.219000	0.12488	GCA		0.607	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865		T	38633853	G	T	38633853	3	4	104	1	0	0	0	0	1	0	0	0	16384	1319	46	2	16	2	TNS4	17	38633853	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	28414635	38633853	42561357	178	27607										
TEX14	56155	hgsc.bcm.edu	37	chr17	56676529	56676529	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccagcacacacttactgatgAgatactcctcagtcgtggac	8	13	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:56676529A>T	ENST00000240361.8	-	14	2280	c.2195T>A	c.(2194-2196)cTc>cAc	p.L732H	TEX14_ENST00000389934.3_Missense_Mutation_p.L726H|TEX14_ENST00000349033.5_Missense_Mutation_p.L726H			Q8IWB6	TEX14_HUMAN	testis expressed 14	732					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTACTGATGAGATACTCCTC	0.443																																																0			17											282	267	272					17																	56676529		2203	4300	6503	54031528	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2195T>A	17.37:g.56676529A>T	ENSP00000240361:p.Leu732His		54031528	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	A	6.273	0.418536	0.11870	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78481	-1.18;-1.18;-1.14	0.235	-0.47	0.12131	.	.	.	.	.	T	0.45776	0.1359	N	0.08118	0	0.20307	N	0.999917	B;B;B	0.34264	0.318;0.446;0.446	B;B;B	0.22753	0.019;0.041;0.041	T	0.34502	-0.9826	8	0.12430	T	0.62	.	.	.	.	.	732;726;726	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	H	732;726;726	ENSP00000240361:L732H;ENSP00000374584:L726H;ENSP00000268910:L726H	ENSP00000240361:L732H	L	-	2	0	TEX14	54031528	0.996000	0.38824	0.947000	0.38551	0.438000	0.31896	-0.499000	0.06413	-0.931000	0.03746	-0.991000	0.02546	CTC		0.443	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56676529	A	T	56676529	3	4	104	1	0	0	0	0	1	0	0	0	15817	304	11	5	2378	5	TEX14	17	56676529	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	18042676	56676529	24518681	179	27608										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67133464	67133464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aagaggagcaagtgctgtttTattcattatctgctgggtta	11	5	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:67133464T>C	ENST00000284425.2	-	3	448	c.274A>G	c.(274-276)Aaa>Gaa	p.K92E	ABCA6_ENST00000590645.1_Missense_Mutation_p.K92E	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	92					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AGTGCTGTTTTATTCATTATC	0.343																																																0			17											110	115	113					17																	67133464		2203	4300	6503	64645059	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.274A>G	17.37:g.67133464T>C	ENSP00000284425:p.Lys92Glu		64645059	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	t	15.77	2.931129	0.52866	.	.	ENSG00000154262	ENST00000284425	D	0.86865	-2.18	4.79	2.41	0.29592	.	0.398453	0.21064	N	0.080766	D	0.90570	0.7044	M	0.69358	2.11	0.23501	N	0.997541	D;P	0.89917	1.0;0.795	D;P	0.87578	0.998;0.649	T	0.81269	-0.1009	10	0.32370	T	0.25	.	8.7968	0.34885	0.0:0.0:0.375:0.625	.	92;92	Q8N139-3;Q8N139	.;ABCA6_HUMAN	E	92	ENSP00000284425:K92E	ENSP00000284425:K92E	K	-	1	0	ABCA6	64645059	0.605000	0.26941	0.996000	0.52242	0.675000	0.39556	0.495000	0.22483	0.360000	0.24265	0.524000	0.50904	AAA		0.343	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		C	67133464	T	C	67133464	3	2	104	1	0	0	0	0	1	0	0	0	36	1763	61	4	4727	4	ABCA6	17	67133464	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	10456935	67133464	14061746	180	27609										
FASN	2194	hgsc.bcm.edu	37	chr17	80039654	80039654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cgtgccactgacgatcgtgtCgttggtgctcatcgtctcca	11	13	2	1	rs141935205	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:80039654C>T	ENST00000306749.2	-	37	6447	c.6229G>A	c.(6229-6231)Gac>Aac	p.D2077N	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2077	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	ACGATCGTGTCGTTGGTGCTC	0.667													.|||	3	0.000599042	0.0015	0	5008	,	,		13005	0		0.001	False		,,,				2504	0				Colon(59;314 1043 11189 28578 32273)											0			17						C	ASN/ASP	3,4401	6.2+/-15.9	0,3,2199	65	54	58		6229	3.7	0.1	17	dbSNP_134	58	0,8596		0,0,4298	yes	missense	FASN	NM_004104.4	23	0,3,6497	TT,TC,CC		0.0,0.0681,0.0231	benign	2077/2512	80039654	3,12997	2202	4298	6500	77632943	SO:0001583	missense	2194			U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6229G>A	17.37:g.80039654C>T	ENSP00000304592:p.Asp2077Asn		77632943	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	8.242	0.806964	0.16467	6.81E-4	0.0	ENSG00000169710	ENST00000306749	T	0.28069	1.63	4.68	3.71	0.42584	NAD(P)-binding domain (1);	0.236860	0.40728	N	0.001031	T	0.33990	0.0882	M	0.73962	2.25	0.45216	D	0.998224	B	0.11235	0.004	B	0.09377	0.004	T	0.13764	-1.0497	10	0.33940	T	0.23	-34.348	13.0177	0.58768	0.0:0.9201:0.0:0.0799	.	2077	P49327	FAS_HUMAN	N	2077	ENSP00000304592:D2077N	ENSP00000304592:D2077N	D	-	1	0	FASN	77632943	1.000000	0.71417	0.060000	0.19600	0.001000	0.01503	4.340000	0.59328	0.946000	0.37632	-0.671000	0.03813	GAC		0.667	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80039654	C	T	80039654	3	4	104	1	0	0	0	0	1	0	0	0	5702	884	31	1	1334	1	FASN	17	80039654	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	12906190	80039654	1155556	181	27610										
WDR45L	56270	hgsc.bcm.edu	37	chr17	80579568	80579568	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctcgtgtgcaggaatgtccaCgggtggcttctccgtgctgg	15	11	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:80579568C>A	ENST00000392325.4	-	6	729	c.535G>T	c.(535-537)Gtg>Ttg	p.V179L	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	179																	GGAATGTCCACGGGTGGCTTC	0.567																																																0			17											102	78	86					17																	80579568		2203	4300	6503	78172857	SO:0001583	missense	56270			AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.535G>T	17.37:g.80579568C>A	ENSP00000376139:p.Val179Leu		78172857	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	C	3.430	-0.116287	0.06881	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.76968	-1.06	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.54062	0.1835	N	0.01779	-0.725	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.54070	-0.8348	10	0.11485	T	0.65	-14.3782	18.2586	0.90026	0.0:1.0:0.0:0.0	.	179	Q5MNZ6	WIPI3_HUMAN	L	179;151	ENSP00000376139:V179L	ENSP00000376139:V179L	V	-	1	0	WDR45L	78172857	1.000000	0.71417	0.941000	0.38009	0.150000	0.21749	5.604000	0.67626	2.389000	0.81357	0.563000	0.77884	GTG		0.567	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		A	80579568	C	A	80579568	3	1	104	1	0	0	0	0	1	0	0	0	17338	536	19	2	519	2	WDR45L	17	80579568	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	539914	80579568	615642	182	27611										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6983192	6983192	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tgtaatggacataggctgcaCtggtggcattcagggacaca	13	8	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr18:6983192C>A	ENST00000389658.3	-	40	5795	c.5702G>T	c.(5701-5703)aGt>aTt	p.S1901I		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1901	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATAGGCTGCACTGGTGGCATT	0.448																																																0			18											114	100	105					18																	6983192		2203	4300	6503	6973192	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5702G>T	18.37:g.6983192C>A	ENSP00000374309:p.Ser1901Ile		6973192		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613846	0.28712	.	.	ENSG00000101680	ENST00000389658	T	0.18502	2.21	5.87	4.0	0.46444	.	0.491230	0.22779	N	0.055742	T	0.12817	0.0311	L	0.46157	1.445	0.25284	N	0.989412	B	0.12630	0.006	B	0.13407	0.009	T	0.09796	-1.0658	10	0.42905	T	0.14	.	3.0858	0.06277	0.1347:0.4535:0.2758:0.136	.	1901	P25391	LAMA1_HUMAN	I	1901	ENSP00000374309:S1901I	ENSP00000374309:S1901I	S	-	2	0	LAMA1	6973192	0.050000	0.20438	0.964000	0.40570	0.722000	0.41435	-0.012000	0.12699	2.774000	0.95407	0.650000	0.86243	AGT		0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	6983192	C	A	6983192	3	1	104	1	0	0	0	0	1	0	0	0	8627	565	20	2	3621	2	LAMA1	18	6983192	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		6983192	71094056	183	27612										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7013845	7013845	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	aggccccggtttcctccacaCagccgcagagaccctgctcc	9	19	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr18:7013845C>G	ENST00000389658.3	-	23	3425	c.3332G>C	c.(3331-3333)tGt>tCt	p.C1111S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1111	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCCTCCACACAGCCGCAGAG	0.577																																																0			18											61	61	61					18																	7013845		2203	4300	6503	7003845	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3332G>C	18.37:g.7013845C>G	ENSP00000374309:p.Cys1111Ser		7003845		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452256	0.63290	.	.	ENSG00000101680	ENST00000389658	T	0.23552	1.9	5.36	5.36	0.76844	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	T	0.58708	0.2141	M	0.87381	2.88	0.52501	D	0.999953	D	0.89917	1.0	D	0.79784	0.993	T	0.62905	-0.6755	10	0.51188	T	0.08	.	19.4486	0.94859	0.0:1.0:0.0:0.0	.	1111	P25391	LAMA1_HUMAN	S	1111	ENSP00000374309:C1111S	ENSP00000374309:C1111S	C	-	2	0	LAMA1	7003845	1.000000	0.71417	0.996000	0.52242	0.565000	0.35776	5.343000	0.65976	2.668000	0.90789	0.637000	0.83480	TGT		0.577	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7013845	C	G	7013845	3	3	104	1	0	0	0	0	1	0	0	0	8627	478	17	5	6059	5	LAMA1	18	7013845	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	30653	7013845	71063403	184	27613										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5131093	5131093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tcctcttcccacagaggacgGgaggggcaagctgcggccaa	14	13	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:5131093G>A	ENST00000159111.4	+	12	1540	c.1322G>A	c.(1321-1323)gGg>gAg	p.G441E	KDM4B_ENST00000536461.1_Missense_Mutation_p.G475E	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	441					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						ACAGAGGACGGGAGGGGCAAG	0.657																																																0			19											16	21	19					19																	5131093		2174	4284	6458	5082093	SO:0001583	missense	23030			AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1322G>A	19.37:g.5131093G>A	ENSP00000159111:p.Gly441Glu		5082093	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	37	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.129239	0.37533	.	.	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.18502	2.21;2.28	4.09	4.09	0.47781	.	1.406310	0.04489	N	0.379144	T	0.13543	0.0328	N	0.25286	0.73	0.09310	N	1	P;P	0.44429	0.835;0.745	B;B	0.40066	0.318;0.169	T	0.04976	-1.0914	10	0.02654	T	1	-24.7636	14.6691	0.68932	0.0:0.0:1.0:0.0	.	475;441	F5GX28;O94953	.;KDM4B_HUMAN	E	441;475	ENSP00000159111:G441E;ENSP00000440495:G475E	ENSP00000159111:G441E	G	+	2	0	KDM4B	5082093	0.953000	0.32496	0.322000	0.25334	0.647000	0.38526	5.860000	0.69546	2.114000	0.64651	0.561000	0.74099	GGG		0.657	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		A	5131093	G	A	5131093	3	1	104	1	0	0	0	0	1	0	0	0	8150	1232	43	3	1360	3	KDM4B	19	5131093	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10		5131093	53997890	185	27614										
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7623912	7623912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	acatggctgaaatccagtccCgcctggcctacgtgtcctgt	10	14	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:7623912C>T	ENST00000221249.6	+	31	3891	c.3460C>T	c.(3460-3462)Cgc>Tgc	p.R1154C	PNPLA6_ENST00000600737.1_Missense_Mutation_p.R1192C|PNPLA6_ENST00000450331.3_Missense_Mutation_p.R1154C|PNPLA6_ENST00000414982.3_Missense_Mutation_p.R1202C|PNPLA6_ENST00000545201.2_Missense_Mutation_p.R1127C	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	1193					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						AATCCAGTCCCGCCTGGCCTA	0.607																																																0			19											84	64	71					19																	7623912		2203	4300	6503	7529912	SO:0001583	missense	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.3460C>T	19.37:g.7623912C>T	ENSP00000221249:p.Arg1154Cys		7529912	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.550757	0.86127	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	4.78	4.78	0.61160	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.058982	0.64402	N	0.000001	T	0.65954	0.2741	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.76494	0.976;0.986;0.986;0.999	P;P;P;D	0.64776	0.624;0.616;0.792;0.929	T	0.75717	-0.3220	10	0.87932	D	0	-26.932	15.3194	0.74109	0.0:1.0:0.0:0.0	.	1193;1127;1192;1154	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	C	1154;1127;1202;1154	ENSP00000221249:R1154C;ENSP00000443323:R1127C;ENSP00000407509:R1202C;ENSP00000394348:R1154C	ENSP00000221249:R1154C	R	+	1	0	PNPLA6	7529912	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.858000	0.62947	2.209000	0.71365	0.561000	0.74099	CGC		0.607	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		T	7623912	C	T	7623912	3	4	104	1	0	0	0	0	1	0	0	0	12200	652	23	1	3718	1	PNPLA6	19	7623912	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	2492819	7623912	51505071	186	27615										
RNASEH2A	10535	hgsc.bcm.edu	37	chr19	12918232	12918232	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gggctctgttccccaccacaGggtcaaatacaacctgaact	8	14	2	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:12918232G>A	ENST00000221486.4	+	4	417		c.e4-1			NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A						DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						CCCCACCACAGGGTCAAATAC	0.552																																																0			19											146	125	132					19																	12918232		2203	4300	6503	12779232	SO:0001630	splice_region_variant	10535			Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"ribonuclease H2, large subunit", "Aicardi-Goutieres syndrome 4"			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.324-1G>A	19.37:g.12918232G>A			12779232	B2RCY1|Q96F11	Splice_Site	SNP	ENST00000221486.4	37	CCDS12282.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454974	0.63290	.	.	ENSG00000104889	ENST00000221486	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4625	0.75369	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNASEH2A	12779232	1.000000	0.71417	0.997000	0.53966	0.728000	0.41692	8.858000	0.92256	1.926000	0.55796	0.400000	0.26472	.		0.552	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397	Intron	A	12918232	G	A	12918232	5	1	104	1	0	0	0	0	0	0	1	0	13449	1014	35	3	337	3	RNASEH2A	19	12918232	Splice_Site	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	5294320	12918232	46210751	187	27616										
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938830	14938830	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gcatttttggaatggtggtgGaagtaacacaaatgtcagca	12	5	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:14938830G>C	ENST00000322301.3	-	2	311	c.224C>G	c.(223-225)tCc>tGc	p.S75C	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Missense_Mutation_p.S75C			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	75					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						AATGGTGGTGGAAGTAACACA	0.458																																																0			19											189	168	175					19																	14938830		2203	4300	6503	14799830	SO:0001583	missense	26659			X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.224C>G	19.37:g.14938830G>C	ENSP00000316955:p.Ser75Cys		14799830	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	37	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	g	11.39	1.623268	0.28889	.	.	ENSG00000188269	ENST00000322301	T	0.12039	2.72	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31507	U	0.007530	T	0.31009	0.0783	M	0.90145	3.09	0.09310	N	1	P	0.52842	0.956	P	0.49829	0.623	T	0.31052	-0.9957	10	0.87932	D	0	.	12.25	0.54593	0.0:0.0:1.0:0.0	.	75	Q15622	OR7A5_HUMAN	C	75	ENSP00000316955:S75C	ENSP00000316955:S75C	S	-	2	0	OR7A5	14799830	0.025000	0.19082	0.347000	0.25668	0.452000	0.32318	2.004000	0.40854	1.807000	0.52817	0.134000	0.15878	TCC		0.458	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		C	14938830	G	C	14938830	3	2	104	1	0	0	0	0	1	0	0	0	11247	1174	41	5	739	5	OR7A5	19	14938830	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	2020598	14938830	44190153	188	27617										
OR7C2	26658	hgsc.bcm.edu	37	chr19	15052697	15052697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctgttaccccctgcactacAcggtcatcatgaacccccgg	7	17	3	1	rs202241920		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:15052697A>G	ENST00000248072.3	+	1	397	c.397A>G	c.(397-399)Acg>Gcg	p.T133A		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					CCTGCACTACACGGTCATCAT	0.517																																																0			19											128	121	123					19																	15052697		2203	4300	6503	14913697	SO:0001583	missense	26658			U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.397A>G	19.37:g.15052697A>G	ENSP00000248072:p.Thr133Ala		14913697	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	37	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	a	9.120	1.008835	0.19199	.	.	ENSG00000127529	ENST00000248072	T	0.19250	2.16	4.19	-4.43	0.03568	GPCR, rhodopsin-like superfamily (1);	1.912540	0.03002	U	0.148334	T	0.18341	0.0440	L	0.48877	1.53	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.32402	-0.9908	10	0.51188	T	0.08	.	6.5883	0.22632	0.3482:0.2509:0.4009:0.0	.	133	O60412	OR7C2_HUMAN	A	133	ENSP00000248072:T133A	ENSP00000248072:T133A	T	+	1	0	OR7C2	14913697	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.478000	0.00457	-0.947000	0.03673	-1.955000	0.00483	ACG		0.517	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			G	15052697	A	G	15052697	3	3	104	1	0	0	0	0	1	0	0	0	11249	159	6	4	399	4	OR7C2	19	15052697	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	113867	15052697	44076286	189	27618										
ILVBL	10994	hgsc.bcm.edu	37	chr19	15234379	15234379	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccgccatgccggacgcttgcCttgtccacctgggcccaagg	12	17	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:15234379C>G	ENST00000263383.3	-	3	283	c.144G>C	c.(142-144)aaG>aaC	p.K48N	ILVBL_ENST00000531635.1_5'UTR|AC003956.1_ENST00000598450.1_RNA|ILVBL_ENST00000534378.1_5'UTR	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	48						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						GGACGCTTGCCTTGTCCACCT	0.642																																																0			19											52	47	49					19																	15234379		2203	4300	6503	15095379	SO:0001583	missense	10994			U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.144G>C	19.37:g.15234379C>G	ENSP00000263383:p.Lys48Asn		15095379	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	37	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	C	2.003	-0.429003	0.04701	.	.	ENSG00000105135	ENST00000263383;ENST00000269733;ENST00000527093;ENST00000533747	T	0.30981	1.51	4.19	2.88	0.33553	.	0.809573	0.11365	N	0.571476	T	0.25082	0.0609	L	0.50333	1.59	0.09310	N	1	B	0.25772	0.134	B	0.24155	0.051	T	0.12477	-1.0546	10	0.36615	T	0.2	-4.269	5.2754	0.15647	0.2057:0.6668:0.0:0.1275	.	48	A1L0T0	ILVBL_HUMAN	N	48	ENSP00000263383:K48N	ENSP00000263383:K48N	K	-	3	2	ILVBL	15095379	0.000000	0.05858	0.362000	0.25862	0.084000	0.17831	-0.783000	0.04638	1.890000	0.54733	0.462000	0.41574	AAG		0.642	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		G	15234379	C	G	15234379	3	3	104	1	0	0	0	0	1	0	0	0	7736	680	24	5	1810	5	ILVBL	19	15234379	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	181682	15234379	43894604	190	27619										
HIPK4	147746	hgsc.bcm.edu	37	chr19	40886845	40886845	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gtctcgtgggcactgcgcagCtgctgcatggacacgaaggg	16	11	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:40886845C>T	ENST00000291823.2	-	3	1337	c.1053G>A	c.(1051-1053)caG>caA	p.Q351Q		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	351					histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			CACTGCGCAGCTGCTGCATGG	0.657																																																0			19											70	69	69					19																	40886845		2203	4300	6503	45578685	SO:0001819	synonymous_variant	147746			BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.1053G>A	19.37:g.40886845C>T			45578685	A8K863|Q96M54	Silent	SNP	ENST00000291823.2	37	CCDS12555.1																																																																																				0.657	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		T	40886845	C	T	40886845	2	4	104	1	0	0	0	0	0	0	0	1	7140	796	28	3		3	HIPK4	19	40886845	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	25652466	40886845	18242138	191	27620										
PPP1R15A	23645	hgsc.bcm.edu	37	chr19	49378015	49378015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctgagccctgccccttccgaGtggccatctatgtacctgga	10	15	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:49378015G>A	ENST00000200453.5	+	2	1794	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	509	4 X 34 AA approximate repeats.|Interaction with KMT2A/MLL1.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CCCCTTCCGAGTGGCCATCTA	0.627																																																0			19											59	56	57					19																	49378015		2203	4300	6503	54069827	SO:0001583	missense	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1525G>A	19.37:g.49378015G>A	ENSP00000200453:p.Val509Met		54069827	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248583	0.80024	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.11169	2.8	4.43	4.43	0.53597	.	0.224693	0.29145	N	0.013007	T	0.27419	0.0673	L	0.54323	1.7	0.44006	D	0.996719	D	0.89917	1.0	D	0.87578	0.998	T	0.00684	-1.1611	10	0.72032	D	0.01	-19.8211	13.3017	0.60328	0.0:0.0:1.0:0.0	.	509	O75807	PR15A_HUMAN	M	509;349;467	ENSP00000200453:V509M	ENSP00000200453:V509M	V	+	1	0	PPP1R15A	54069827	0.990000	0.36364	0.974000	0.42286	0.983000	0.72400	2.314000	0.43743	2.414000	0.81942	0.650000	0.86243	GTG		0.627	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49378015	G	A	49378015	3	1	104	1	0	0	0	0	1	0	0	0	12397	1029	36	3	1527	3	PPP1R15A	19	49378015	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	8491170	49378015	9750968	192	27621										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51983772	51983772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ttatcagccacaaaccgcccAgtgcccagcagcctgggccc	9	18	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:51983772A>G	ENST00000396477.4	+	2	259	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	CEACAM18_ENST00000451626.1_Missense_Mutation_p.S141G	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	80										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAAACCGCCCAGTGCCCAGCA	0.552																																																0			19											56	58	58					19																	51983772		2022	4178	6200	56675584	SO:0001583	missense	729767					19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.238A>G	19.37:g.51983772A>G	ENSP00000379738:p.Ser80Gly		56675584	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		.	.	.	.	.	.	.	.	.	.	.	4.038	0.004689	0.07866	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.01474	4.85	2.79	-4.06	0.03986	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01523	0.0049	L	0.35854	1.095	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.44050	-0.9353	9	0.31617	T	0.26	0.3836	5.4071	0.16328	0.3578:0.1778:0.4643:0.0	.	141	A8MTB9	CEA18_HUMAN	G	141;80;80	ENSP00000402203:S141G	ENSP00000379738:S80G	S	+	1	0	CEACAM18	56675584	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.347000	0.02632	-1.116000	0.02969	0.529000	0.55759	AGT		0.552	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2			G	51983772	A	G	51983772	3	3	104	1	0	0	0	0	1	0	0	0	3195	188	7	4	431	4	CEACAM18	19	51983772	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	2605757	51983772	7145211	193	27622										
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941770	52941770	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cagttcatactggagagagaCcatacaaatgtaatgaatgt	9	6	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:52941770C>A	ENST00000332323.6	+	4	1157	c.1096C>A	c.(1096-1098)Cca>Aca	p.P366T	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.P353T|ZNF534_ENST00000432303.2_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						TGGAGAGAGACCATACAAATG	0.418																																																0			19											103	99	100					19																	52941770		692	1591	2283	57633582	SO:0001583	missense	147658			AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.1096C>A	19.37:g.52941770C>A	ENSP00000327538:p.Pro366Thr		57633582	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	37	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.190978	0.38707	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.28895	1.59;1.59	1.82	1.82	0.25136	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49729	0.1574	M	0.66560	2.04	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.87578	0.864;0.998	T	0.52866	-0.8518	9	0.87932	D	0	.	10.6089	0.45410	0.0:1.0:0.0:0.0	.	353;366	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	T	366;353;365	ENSP00000327538:P366T;ENSP00000391358:P353T	ENSP00000327538:P366T	P	+	1	0	ZNF534	57633582	0.001000	0.12720	0.029000	0.17559	0.004000	0.04260	1.477000	0.35431	0.983000	0.38602	0.467000	0.42956	CCA		0.418	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		A	52941770	C	A	52941770	3	1	104	1	0	0	0	0	1	0	0	0	18012	507	18	2	1110	2	ZNF534	19	52941770	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	957998	52941770	6187213	194	27623										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56303710	56303710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tggaaacagcaagggaaacgTcacatgcaacactccgtaat	9	10	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:56303710T>C	ENST00000589093.1	-	7	2563	c.2470A>G	c.(2470-2472)Acg>Gcg	p.T824A	NLRP11_ENST00000443188.1_Missense_Mutation_p.T824A|NLRP11_ENST00000592953.1_Missense_Mutation_p.T725A|NLRP11_ENST00000360133.3_Missense_Mutation_p.T770A|NLRP11_ENST00000589824.2_Missense_Mutation_p.T770A			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	824							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AAGGGAAACGTCACATGCAAC	0.483																																																0			19											201	176	185					19																	56303710		2203	4300	6503	60995522	SO:0001583	missense	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2470A>G	19.37:g.56303710T>C	ENSP00000466285:p.Thr824Ala		60995522	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	T	6.420	0.445561	0.12164	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.48836	0.8;0.8	2.18	-4.36	0.03645	.	.	.	.	.	T	0.26955	0.0660	N	0.14661	0.345	0.09310	N	1	B;P	0.36378	0.09;0.55	B;B	0.41691	0.046;0.364	T	0.22487	-1.0215	9	0.66056	D	0.02	.	1.0411	0.01559	0.4876:0.1279:0.1643:0.2202	.	824;770	P59045;P59045-2	NAL11_HUMAN;.	A	824;770	ENSP00000409898:T824A;ENSP00000353251:T770A	ENSP00000353251:T770A	T	-	1	0	NLRP11	60995522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.012000	0.03649	-2.085000	0.00864	-1.221000	0.01599	ACG		0.483	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56303710	T	C	56303710	3	2	104	1	0	0	0	0	1	0	0	0	10504	1667	58	4	647	4	NLRP11	19	56303710	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	3361940	56303710	2825273	195	27624										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58564801	58564801	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ccctcgccctccacagggtcCcgggcccgcttgcctctgaa	10	20	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:58564801C>A	ENST00000282326.1	+	6	856	c.609C>A	c.(607-609)tcC>tcA	p.S203S		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	203					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		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)		CCACAGGGTCCCGGGCCCGCT	0.652																																																0			19											44	47	46					19																	58564801		2203	4296	6499	63256613	SO:0001819	synonymous_variant	284312			AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.609C>A	19.37:g.58564801C>A			63256613	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	37	CCDS12969.1																																																																																				0.652	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58564801	C	A	58564801	2	1	104	1	0	0	0	0	0	0	0	1	18265	610	22	2		2	ZSCAN1	19	58564801	Silent	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	2261091	58564801	564182	196	27625										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33568496	33568496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctcagattccccgccccataTatatgcggtggcggacaacg	10	14	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:33568496T>C	ENST00000262873.7	+	6	676	c.584T>C	c.(583-585)aTa>aCa	p.I195T	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	153	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CCGCCCCATATATATGCGGTG	0.612																																																0			20											70	79	76					20																	33568496		2115	4242	6357	33032157	SO:0001583	missense	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.584T>C	20.37:g.33568496T>C	ENSP00000262873:p.Ile195Thr		33032157	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102722	0.56183	.	.	ENSG00000078814	ENST00000262873	D	0.90620	-2.7	4.46	4.46	0.54185	Myosin head, motor domain (2);	0.000000	0.41823	D	0.000806	D	0.97284	0.9112	H	0.98951	4.38	0.58432	D	0.999996	D	0.65815	0.995	D	0.91635	0.999	D	0.98595	1.0656	10	0.87932	D	0	.	14.1848	0.65598	0.0:0.0:0.0:1.0	.	153	A7E2Y1	MYH7B_HUMAN	T	195	ENSP00000262873:I195T	ENSP00000262873:I195T	I	+	2	0	MYH7B	33032157	1.000000	0.71417	0.738000	0.30950	0.022000	0.10575	7.868000	0.87116	2.001000	0.58596	0.533000	0.62120	ATA		0.612	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		C	33568496	T	C	33568496	3	2	104	1	0	0	0	0	1	0	0	0	10070	1406	49	4	606	4	MYH7B	20	33568496	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10		33568496	29457024	197	27626										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872956	51872956	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctccagaaacaatagctgccGaagaggacacagactctaaa	8	11	1	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:51872956G>A	ENST00000371497.5	+	2	3846	c.2959G>A	c.(2959-2961)Gaa>Aaa	p.E987K	TSHZ2_ENST00000603338.2_Missense_Mutation_p.E984K|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.E984K	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	987					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			AATAGCTGCCGAAGAGGACAC	0.502																																																0			20											84	68	73					20																	51872956		2203	4300	6503	51306363	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2959G>A	20.37:g.51872956G>A	ENSP00000360552:p.Glu987Lys		51306363	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.972459	0.92919	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.20598	2.07;2.06	5.69	5.69	0.88448	.	0.103320	0.64402	D	0.000002	T	0.44159	0.1280	M	0.78223	2.4	0.80722	D	1	D	0.61080	0.989	P	0.54270	0.747	T	0.43393	-0.9394	10	0.87932	D	0	-3.8792	19.8075	0.96536	0.0:0.0:1.0:0.0	.	987	Q9NRE2	TSH2_HUMAN	K	987;984;513	ENSP00000360552:E987K;ENSP00000333114:E984K	ENSP00000333114:E984K	E	+	1	0	TSHZ2	51306363	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.470000	0.97683	2.681000	0.91329	0.637000	0.83480	GAA		0.502	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51872956	G	A	51872956	3	1	104	1	0	0	0	0	1	0	0	0	16664	1059	37	1	2965	1	TSHZ2	20	51872956	Missense_Mutation	SNP	G	TCGA-DY-A1DC-01A-31D-A152-10	18304460	51872956	11152564	198	27627										
MC3R	4159	hgsc.bcm.edu	37	chr20	54824096	54824096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tatcctggccgtggtcaggaAcggcaacctgcactccccga	11	15	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:54824096A>G	ENST00000243911.2	+	1	309	c.197A>G	c.(196-198)aAc>aGc	p.N66S		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	66					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			GTGGTCAGGAACGGCAACCTG	0.567																																																0			20											91	73	79					20																	54824096		2203	4300	6503	54257503	SO:0001583	missense	4159				CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"GPCR / Class A : Melanocortin receptors"	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.197A>G	20.37:g.54824096A>G	ENSP00000243911:p.Asn66Ser		54257503	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	37	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	A	19.84	3.901786	0.72754	.	.	ENSG00000124089	ENST00000243911	T	0.03772	3.81	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.17323	0.0416	L	0.55990	1.75	0.50313	D	0.999861	D	0.76494	0.999	D	0.83275	0.996	T	0.00276	-1.1855	10	0.87932	D	0	.	14.4027	0.67060	1.0:0.0:0.0:0.0	.	103	P41968	MC3R_HUMAN	S	66	ENSP00000243911:N66S	ENSP00000243911:N66S	N	+	2	0	MC3R	54257503	1.000000	0.71417	0.033000	0.17914	0.896000	0.52359	9.103000	0.94232	1.878000	0.54408	0.528000	0.53228	AAC		0.567	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2			G	54824096	A	G	54824096	3	3	104	1	0	0	0	0	1	0	0	0	9395	43	2	4	199	4	MC3R	20	54824096	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	2951140	54824096	8201424	199	27628										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62324588	62324588	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gctgtggctatcggcctgagCacagcattccccgaaggcag	13	13	0	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:62324588C>G	ENST00000360203.5	+	30	3269	c.2944C>G	c.(2944-2946)Cac>Gac	p.H982D	RTEL1_ENST00000370018.3_Missense_Mutation_p.H982D|RTEL1_ENST00000370003.1_Missense_Mutation_p.H227D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.H982D|RTEL1_ENST00000318100.4_Missense_Mutation_p.H982D|RTEL1_ENST00000508582.2_Missense_Mutation_p.H1006D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			TCGGCCTGAGCACAGCATTCC	0.617																																																0			20											90	93	92					20																	62324588		2198	4289	6487	61795032	SO:0001583	missense	51750			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2944C>G	20.37:g.62324588C>G	ENSP00000353332:p.His982Asp		61795032		Missense_Mutation	SNP	ENST00000360203.5	37		.	.	.	.	.	.	.	.	.	.	C	15.94	2.981294	0.53827	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94	4.52	2.42	0.29668	.	0.549660	0.19745	N	0.107026	T	0.19005	0.0456	L	0.58101	1.795	0.27457	N	0.953256	P;P;P;D	0.55385	0.716;0.672;0.594;0.971	P;B;B;P	0.51999	0.49;0.268;0.215;0.687	T	0.03641	-1.1017	10	0.62326	D	0.03	-6.1252	11.5019	0.50444	0.3378:0.6622:0.0:0.0	.	1006;227;982;982	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	982;982;1006;982;227	ENSP00000359035:H982D;ENSP00000322287:H982D;ENSP00000424307:H1006D;ENSP00000353332:H982D;ENSP00000359020:H227D	ENSP00000353332:H982D	H	+	1	0	AL353715.1	61795032	0.998000	0.40836	0.001000	0.08648	0.020000	0.10135	2.364000	0.44187	0.270000	0.21984	0.289000	0.19496	CAC		0.617	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		G	62324588	C	G	62324588	3	3	104	1	0	0	0	0	1	0	0	0	13757	710	25	5	3058	5	RTEL1	20	62324588	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	7500492	62324588	700932	200	27629										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19725329	19725329	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tttagatcctggacccagaaAcaaaagccatcctcaaagtt	6	11	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:19725329A>G	ENST00000284885.3	-	10	1095	c.1062T>C	c.(1060-1062)tgT>tgC	p.C354C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	354	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GGACCCAGAAACAAAAGCCAT	0.333																																																0			21											80	85	83					21																	19725329		2203	4300	6503	18647200	SO:0001819	synonymous_variant	0				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1062T>C	21.37:g.19725329A>G			18647200	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																				0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19725329	A	G	19725329	2	3	104	1	0	0	0	0	0	0	0	1	16285	41	2	4		4	TMPRSS15	21	19725329	Silent	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10		19725329	28404566	201	27630										
TTC3	7267	hgsc.bcm.edu	37	chr21	38525452	38525452	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tctaaatgaagcagtggactAtgttattcgccacttgattc	8	8	1	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:38525452A>T	ENST00000399017.2	+	27	5362	c.2615A>T	c.(2614-2616)tAt>tTt	p.Y872F	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.Y872F|TTC3_ENST00000540756.1_Missense_Mutation_p.Y562F|TTC3_ENST00000354749.2_Missense_Mutation_p.Y872F	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	872					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCAGTGGACTATGTTATTCGC	0.373																																					Ovarian(38;194 1649 35661)											0			21											91	99	97					21																	38525452		2203	4299	6502	37447322	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2615A>T	21.37:g.38525452A>T	ENSP00000381981:p.Tyr872Phe		37447322	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.95|12.95	2.091181|2.091181	0.36855|0.36855	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000414818;ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	.|T;T;T;T;T;T	.|0.43294	.|2.75;2.75;3.09;0.95;3.09;3.09	5.31|5.31	0.825|0.825	0.18824|0.18824	.|.	.|0.743599	.|0.12354	.|N	.|0.476242	T|T	0.34337|0.34337	0.0894|0.0894	L|L	0.57536|0.57536	1.79|1.79	0.25122|0.25122	N|N	0.990631|0.990631	.|B;B	.|0.16166	.|0.0;0.016	.|B;B	.|0.14023	.|0.001;0.01	T|T	0.32877|0.32877	-0.9890|-0.9890	5|10	.|0.52906	.|T	.|0.07	-4.6424|-4.6424	4.3559|4.3559	0.11178|0.11178	0.6612:0.0:0.1601:0.1787|0.6612:0.0:0.1601:0.1787	.|.	.|562;872	.|B4DSZ9;P53804	.|.;TTC3_HUMAN	L|F	236;10|872;854;872;562;872;872	.|ENSP00000403943:Y872F;ENSP00000391891:Y854F;ENSP00000347889:Y872F;ENSP00000442875:Y562F;ENSP00000381981:Y872F;ENSP00000346791:Y872F	.|ENSP00000346791:Y872F	M|Y	+|+	1|2	0|0	TTC3|TTC3	37447322|37447322	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.986000|0.986000	0.74619|0.74619	2.417000|2.417000	0.44653|0.44653	0.338000|0.338000	0.23692|0.23692	0.528000|0.528000	0.53228|0.53228	ATG|TAT		0.373	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38525452	A	T	38525452	3	4	104	1	0	0	0	0	1	0	0	0	16737	449	16	5	2717	5	TTC3	21	38525452	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	18800123	38525452	9604443	202	27631										
KRTAP10-1	386677	hgsc.bcm.edu	37	chr21	45959553	45959553	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	agactgctggcagcatgaagAggaatcctcagagcaggtgg	15	8	1	4	rs9980010		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:45959553A>C	ENST00000400375.1	-	1	525	c.481T>G	c.(481-483)Tct>Gct	p.S161A	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	161	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						CAGCATGAAGAGGAATCCTCA	0.617																																																0			21											105	111	109					21																	45959553		2203	4300	6503	44783981	SO:0001583	missense	386677			AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"Keratin associated proteins"	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.481T>G	21.37:g.45959553A>C	ENSP00000383226:p.Ser161Ala		44783981	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	.	.	.	.	.	.	.	.	.	.	a	0.029	-1.345627	0.01266	.	.	ENSG00000215455	ENST00000400375;ENST00000545982	T	0.01106	5.33	2.39	-0.157	0.13387	.	.	.	.	.	T	0.01695	0.0054	M	0.78049	2.395	0.09310	N	1	B	0.29253	0.239	B	0.29524	0.103	T	0.42649	-0.9439	9	0.33940	T	0.23	.	2.0673	0.03605	0.4619:0.0:0.2957:0.2423	.	161	P60331	KR101_HUMAN	A	161	ENSP00000383226:S161A	ENSP00000383226:S161A	S	-	1	0	KRTAP10-1	44783981	0.012000	0.17670	0.008000	0.14137	0.022000	0.10575	1.191000	0.32138	-0.040000	0.13580	0.358000	0.22013	TCT		0.617	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1			C	45959553	A	C	45959553	3	2	104	1	0	0	0	0	1	0	0	0	8526	304	11	4	371	4	KRTAP10-1	21	45959553	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7434101	45959553	2170342	203	27632										
ISX	91464	hgsc.bcm.edu	37	chr22	35481587	35481587	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	cacccatgggaaacacagccTgtcccaggtcttcccatcca	7	17	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr22:35481587T>C	ENST00000308700.6	+	4	1591	c.639T>C	c.(637-639)ccT>ccC	p.P213P	ISX_ENST00000404699.2_Silent_p.P213P	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	213					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						AAACACAGCCTGTCCCAGGTC	0.572																																																0			22											222	151	175					22																	35481587		2203	4300	6503	33811587	SO:0001819	synonymous_variant	91464			AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"Homeoboxes / PRD class"	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.639T>C	22.37:g.35481587T>C			33811587	Q68DJ5	Silent	SNP	ENST00000308700.6	37	CCDS33640.1																																																																																				0.572	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494		C	35481587	T	C	35481587	2	2	104	1	0	0	0	0	0	0	0	1	7886	1567	55	4		4	ISX	22	35481587	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10		35481587	15822979	204	27633										
NAGA	4668	hgsc.bcm.edu	37	chr22	42456978	42456978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ctggccaagggaggagtggtAgcgataaggcatatcggtcc	16	8	0	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr22:42456978A>G	ENST00000396398.3	-	8	1583	c.1051T>C	c.(1051-1053)Tac>Cac	p.Y351H	NAGA_ENST00000402937.1_Missense_Mutation_p.Y351H|NAGA_ENST00000403363.1_Missense_Mutation_p.Y351H	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	351					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GAGGAGTGGTAGCGATAAGGC	0.557																																																0			22											121	105	110					22																	42456978		2203	4300	6503	40786924	SO:0001583	missense	4668				CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.1051T>C	22.37:g.42456978A>G	ENSP00000379680:p.Tyr351His		40786924		Missense_Mutation	SNP	ENST00000396398.3	37	CCDS14030.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.732489	0.89482	.	.	ENSG00000198951	ENST00000396398;ENST00000403363;ENST00000402937	D;D;D	0.88741	-2.42;-2.42;-2.42	5.68	5.68	0.88126	Glycosyl hydrolase, family 13, all-beta (1);	0.113006	0.64402	D	0.000007	D	0.89441	0.6716	M	0.76328	2.33	0.58432	D	0.999999	B	0.21688	0.059	B	0.29267	0.1	D	0.87182	0.2228	10	0.56958	D	0.05	-22.3075	14.5003	0.67716	1.0:0.0:0.0:0.0	.	351	P17050	NAGAB_HUMAN	H	351	ENSP00000379680:Y351H;ENSP00000385283:Y351H;ENSP00000384603:Y351H	ENSP00000379680:Y351H	Y	-	1	0	NAGA	40786924	1.000000	0.71417	0.591000	0.28745	0.393000	0.30537	7.948000	0.87774	2.163000	0.67991	0.496000	0.49642	TAC		0.557	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1			G	42456978	A	G	42456978	3	3	104	1	0	0	0	0	1	0	0	0	10171	420	15	4	192	4	NAGA	22	42456978	Missense_Mutation	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	6975391	42456978	8847588	205	27634										
ZNF645	158506	hgsc.bcm.edu	37	chrX	22292291	22292291	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaaggtggcctgcatggaaaCgactgtcaccttgtccacca	11	12	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:22292291C>T	ENST00000323684.1	+	1	1227	c.1183C>T	c.(1183-1185)Cga>Tga	p.R395*		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	395					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						TGCATGGAAACGACTGTCACC	0.463																																																0			X											138	103	115					X																	22292291		2203	4300	6503	22202212	SO:0001587	stop_gained	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.1183C>T	X.37:g.22292291C>T	ENSP00000323348:p.Arg395*		22202212	A0AV29|A0AV31|E3SBK4|Q6DJY9	Nonsense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.632824	0.47049	.	.	ENSG00000175809	ENST00000323684	.	.	.	3.05	-0.943	0.10395	.	0.275715	0.34531	U	0.003885	.	.	.	.	.	.	0.47476	D	0.999431	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	1.4962	0.02467	0.22:0.1614:0.4528:0.1658	.	.	.	.	X	395	.	ENSP00000323348:R395X	R	+	1	2	ZNF645	22202212	0.998000	0.40836	0.000000	0.03702	0.000000	0.00434	1.600000	0.36762	-0.392000	0.07751	-0.866000	0.03004	CGA		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		T	22292291	C	T	22292291	4	4	104	1	0	0	0	0	0	1	0	0	18100	528	19	1	1185	1	ZNF645	23	22292291	Nonsense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10		22292291	132978269	206	27635										
POLA1	5422	hgsc.bcm.edu	37	chrX	24732734	24732734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	gaagctcgcagtgacaaaacCgaacaacattaagtcaatgt	8	9	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:24732734C>T	ENST00000379059.3	+	5	407	c.392C>T	c.(391-393)cCg>cTg	p.P131L	POLA1_ENST00000379068.3_Missense_Mutation_p.P137L	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	131					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.P131L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GTGACAAAACCGAACAACATT	0.358																																																1	Substitution - Missense(1)	ovary(1)	X											104	93	97					X																	24732734		2202	4298	6500	24642655	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.392C>T	X.37:g.24732734C>T	ENSP00000368349:p.Pro131Leu		24642655	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.391039	0.62066	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.18174	2.23;2.23	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.45115	0.1326	M	0.78637	2.42	0.80722	D	1	P;D	0.89917	0.617;1.0	B;D	0.74023	0.14;0.982	T	0.20240	-1.0281	10	0.34782	T	0.22	-7.8106	19.2516	0.93926	0.0:1.0:0.0:0.0	.	137;131	A6NMQ1;P09884	.;DPOLA_HUMAN	L	137;131	ENSP00000368358:P137L;ENSP00000368349:P131L	ENSP00000368349:P131L	P	+	2	0	POLA1	24642655	1.000000	0.71417	0.997000	0.53966	0.634000	0.38068	6.872000	0.75536	2.498000	0.84270	0.600000	0.82982	CCG		0.358	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24732734	C	T	24732734	3	4	104	1	0	0	0	0	1	0	0	0	12218	652	23	1	410	1	POLA1	23	24732734	Missense_Mutation	SNP	C	TCGA-DY-A1DC-01A-31D-A152-10	2440443	24732734	130537826	207	27636										
KDM6A	7403	hgsc.bcm.edu	37	chrX	44929213	44929213	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggagattctaagtcaccaggTttactaagttcagacaatcc	8	9	3	2			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:44929213T>C	ENST00000377967.4	+	17	2354	c.2313T>C	c.(2311-2313)ggT>ggC	p.G771G	KDM6A_ENST00000382899.4_Silent_p.G778G|KDM6A_ENST00000536777.1_Silent_p.G726G|KDM6A_ENST00000543216.1_Silent_p.G692G	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	771	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AGTCACCAGGTTTACTAAGTT	0.468			"D, N, F, S"		"renal, oesophageal SCC, MM"																																Colon(129;1273 1667 15230 27352 52914)		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	X											136	101	113					X																	44929213		2203	4300	6503	44814157	SO:0001819	synonymous_variant	7403			AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.2313T>C	X.37:g.44929213T>C			44814157	Q52LL9|Q5JVQ7	Silent	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	T	6.037	0.375209	0.11409	.	.	ENSG00000147050	ENST00000414389;ENST00000433797	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	T	0.70360	0.3215	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70008	-0.4990	4	.	.	.	-0.1176	14.2214	0.65830	0.0:0.0:0.0:1.0	.	.	.	.	L	369;414	.	.	F	+	1	0	KDM6A	44814157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.549000	0.60726	1.805000	0.52779	0.486000	0.48141	TTT		0.468	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		C	44929213	T	C	44929213	2	2	104	1	0	0	0	0	0	0	0	1	8158	1712	60	4		4	KDM6A	23	44929213	Silent	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	20196479	44929213	110341347	208	27637										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50053208	50053208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggaactattttcattgcatgTtaagcataccaacaaaagtg	7	7	1	0			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:50053208T>C	ENST00000376042.1	+	6	2337	c.2039T>C	c.(2038-2040)gTt>gCt	p.V680A	CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.V680A|CCNB3_ENST00000376038.1_Intron			Q8WWL7	CCNB3_HUMAN	cyclin B3	680					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TCATTGCATGTTAAGCATACC	0.468																																																0			X											35	29	31					X																	50053208		2203	4300	6503	50069948	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2039T>C	X.37:g.50053208T>C	ENSP00000365210:p.Val680Ala		50069948	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953633	0.34471	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.37058	1.22;1.22	4.19	-1.46	0.08800	.	.	.	.	.	T	0.16514	0.0397	N	0.16478	0.41	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.24225	-1.0166	8	.	.	.	.	2.7077	0.05166	0.4249:0.2538:0.0:0.3213	.	680	Q8WWL7	CCNB3_HUMAN	A	680	ENSP00000365210:V680A;ENSP00000276014:V680A	.	V	+	2	0	CCNB3	50069948	0.000000	0.05858	0.000000	0.03702	0.545000	0.35147	-0.905000	0.04075	-0.374000	0.07967	0.486000	0.48141	GTT		0.468	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			C	50053208	T	C	50053208	3	2	104	1	0	0	0	0	1	0	0	0	2920	1725	60	4	2053	4	CCNB3	23	50053208	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	5123995	50053208	105217352	209	27638										
OPHN1	4983	hgsc.bcm.edu	37	chrX	67283810	67283810	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	ggcctttggggtgatcttggTccctccatcctgcagcctag	12	13	1	1			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:67283810T>C	ENST00000355520.5	-	21	2685	c.2044A>G	c.(2044-2046)Acc>Gcc	p.T682A	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Intron	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	682	Pro-rich.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						GTGATCTTGGTCCCTCCATCC	0.612																																																0			X											78	59	66					X																	67283810		2203	4300	6503	67200535	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.2044A>G	X.37:g.67283810T>C	ENSP00000347710:p.Thr682Ala		67200535	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	T	1.656	-0.512610	0.04200	.	.	ENSG00000079482	ENST00000355520	T	0.43294	0.95	4.9	2.48	0.30137	.	0.909070	0.09418	N	0.804851	T	0.18964	0.0455	N	0.08118	0	0.54753	D	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	10	0.12766	T	0.61	.	3.8876	0.09105	0.0:0.1187:0.2398:0.6415	.	682	O60890	OPHN1_HUMAN	A	682	ENSP00000347710:T682A	ENSP00000347710:T682A	T	-	1	0	OPHN1	67200535	0.994000	0.37717	0.856000	0.33681	0.348000	0.29142	0.755000	0.26405	0.705000	0.31890	-0.472000	0.04984	ACC		0.612	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		C	67283810	T	C	67283810	3	2	104	1	0	0	0	0	1	0	0	0	10906	1667	58	4	380	4	OPHN1	23	67283810	Missense_Mutation	SNP	T	TCGA-DY-A1DC-01A-31D-A152-10	17230602	67283810	87986750	210	27639										
ZDHHC15	158866	hgsc.bcm.edu	37	chrX	74698819	74698819	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	10	1	0.855295566502463	1.62913441238564	0.579861401018619	1	1	0	tggtagagtatgaggtaaatAactgaaataaaaaaaaaatc	8	2	0	3			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:74698819A>G	ENST00000373367.3	-	3	395	c.165T>C	c.(163-165)gtT>gtC	p.V55V	ZDHHC15_ENST00000373361.3_Splice_Site_p.V55V|ZDHHC15_ENST00000541184.1_Splice_Site_p.V46V	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	55					establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						TGAGGTAAATAACTGAAATAA	0.323																																																0			X											49	42	44					X																	74698819		2203	4300	6503	74615544	SO:0001630	splice_region_variant	158866			AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383		"Zinc fingers, DHHC-type"	20342	protein-coding gene	gene with protein product		300576					Standard	NM_144969		Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.164-1T>C	X.37:g.74698819A>G			74615544	B3KVG7|Q3SY30|Q6UWH3	Silent	SNP	ENST00000373367.3	37	CCDS14430.1																																																																																				0.323	ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057283.1	NM_144969	Silent	G	74698819	A	G	74698819	5	3	104	1	0	0	0	0	0	0	1	0	17644	376	13	4	964	4	ZDHHC15	23	74698819	Splice_Site	SNP	A	TCGA-DY-A1DC-01A-31D-A152-10	7415009	74698819	80571741	211	27640										
C1orf201	90529	hgsc.bcm.edu	37	chr1	24687367	24687367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caggcaggcctggctgaggcGgcgccgctgtccaccggctg	17	15	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:24687367G>A	ENST00000374409.1	-	8	1156	c.902C>T	c.(901-903)cCg>cTg	p.P301L	STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000337248.4_Missense_Mutation_p.P301L|GRHL3_ENST00000350501.5_Intron|STPG1_ENST00000440416.1_Missense_Mutation_p.P254L|STPG1_ENST00000003583.8_Missense_Mutation_p.P254L	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	301					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TGGCTGAGGCGGCGCCGCTGT	0.507																																																0			1											54	62	59					1																	24687367		2201	4297	6498	24559954	SO:0001583	missense	90529			BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 2"	615826	"chromosome 1 open reading frame 201"	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.902C>T	1.37:g.24687367G>A	ENSP00000363530:p.Pro301Leu		24559954	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	.	.	.	.	.	.	.	.	.	.	G	5.021	0.189609	0.09547	.	.	ENSG00000001460	ENST00000374409;ENST00000440416;ENST00000003583;ENST00000337248	.	.	.	5.9	3.94	0.45596	.	0.631432	0.16046	N	0.232185	T	0.16981	0.0408	L	0.38531	1.155	0.09310	N	1	P;P	0.44006	0.824;0.792	B;B	0.34385	0.157;0.181	T	0.08534	-1.0717	9	0.07482	T	0.82	.	8.163	0.31209	0.08:0.3066:0.6134:0.0	.	301;254	Q5TH74;Q5TH74-3	CA201_HUMAN;.	L	301;254;254;301	.	ENSP00000003583:P254L	P	-	2	0	C1orf201	24559954	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.906000	0.28517	0.755000	0.32990	0.563000	0.77884	CCG		0.507	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122		A	24687367	G	A	24687367	3	1	105	1	0	0	0	0	1	0	0	0	2033	1116	39	1	110	1	C1orf201	1	24687367	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		24687367	224563254	1	27641										
KLF17	128209	hgsc.bcm.edu	37	chr1	44595667	44595667	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcaggactctcttgtcagtCagccagactctcaagaaggc	9	13	5	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:44595667C>T	ENST00000372299.3	+	2	782	c.724C>T	c.(724-726)Cag>Tag	p.Q242*	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	242					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TCTTGTCAGTCAGCCAGACTC	0.562																																																0			1											68	67	68					1																	44595667		2203	4300	6503	44368254	SO:0001587	stop_gained	128209			BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	18830	protein-coding gene	gene with protein product		609602	"zinc finger protein 393"	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.724C>T	1.37:g.44595667C>T	ENSP00000361373:p.Gln242*		44368254	Q86VQ7|Q8N805	Nonsense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.310653	0.40895	.	.	ENSG00000171872	ENST00000372299	.	.	.	4.78	0.696	0.18075	.	0.748949	0.11934	N	0.515403	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	3.9482	0.09358	0.1546:0.4608:0.2997:0.0849	.	.	.	.	X	242	.	ENSP00000361373:Q242X	Q	+	1	0	KLF17	44368254	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.372000	0.20467	0.146000	0.19002	-0.182000	0.12963	CAG		0.562	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484		T	44595667	C	T	44595667	4	4	105	1	0	0	0	0	0	1	0	0	8366	827	29	3	730	3	KLF17	1	44595667	Nonsense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	19908300	44595667	204654954	2	27642										
KIF2C	11004	hgsc.bcm.edu	37	chr1	45213057	45213057	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttttacttgctccttgcagaTtgattttgatgatgtggctg	10	6	0	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:45213057T>C	ENST00000372224.4	+	3	280	c.167T>C	c.(166-168)aTt>aCt	p.I56T	KIF2C_ENST00000372218.4_Splice_Site_p.I56T|KIF2C_ENST00000372217.1_Splice_Site_p.I2T|KIF2C_ENST00000372222.3_5'UTR|KIF2C_ENST00000493027.1_3'UTR	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	56	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					TCCTTGCAGATTGATTTTGAT	0.373																																																0			1											120	117	118					1																	45213057		2203	4300	6503	44985644	SO:0001630	splice_region_variant	11004			U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.166-1T>C	1.37:g.45213057T>C			44985644	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	.	.	.	.	.	.	.	.	.	.	t	17.52	3.409031	0.62399	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000455186;ENST00000372217	T;T;T;T;T	0.80994	0.54;-1.44;-1.25;0.15;-1.15	6.07	6.07	0.98685	.	0.224883	0.43260	D	0.000599	D	0.85805	0.5782	M	0.75085	2.285	0.80722	D	1	B;B;P	0.41643	0.244;0.421;0.758	B;B;P	0.49451	0.089;0.221;0.611	D	0.87220	0.2253	10	0.87932	D	0	.	15.1999	0.73126	0.0:0.0:0.0:1.0	.	56;2;56	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	T	56;56;56;47;2	ENSP00000410346:I56T;ENSP00000361298:I56T;ENSP00000361292:I56T;ENSP00000395050:I47T;ENSP00000361291:I2T	ENSP00000361291:I2T	I	+	2	0	KIF2C	44985644	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.841000	0.62824	2.326000	0.78906	0.533000	0.62120	ATT		0.373	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	Missense_Mutation	C	45213057	T	C	45213057	5	2	105	1	0	0	0	0	0	0	1	0	8320	1507	52	4	177	4	KIF2C	1	45213057	Splice_Site	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	617390	45213057	204037564	3	27643										
AGBL4	84871	hgsc.bcm.edu	37	chr1	49100247	49100247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gagagggatccagccagtgaCgattcagatcaaatcccatc	10	11	2	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:49100247C>T	ENST00000371839.1	-	9	985	c.869G>A	c.(868-870)cGt>cAt	p.R290H	AGBL4_ENST00000371838.1_Missense_Mutation_p.R290H|AGBL4_ENST00000334103.7_Missense_Mutation_p.R23H	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	290					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		CAGCCAGTGACGATTCAGATC	0.468																																																0			1											85	87	86					1																	49100247		1975	4155	6130	48872834	SO:0001583	missense	84871			AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 6"					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.869G>A	1.37:g.49100247C>T	ENSP00000360905:p.Arg290His		48872834	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.194569|5.194569	0.94960|0.94960	.|.	.|.	ENSG00000186094|ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000334103;ENST00000371838|ENST00000416121	T;T;T|.	0.24151|.	1.87;1.87;1.87|.	5.6|5.6	5.6|5.6	0.85130|0.85130	Peptidase M14, carboxypeptidase A (1);|.	0.193068|.	0.56097|.	D|.	0.000029|.	D|D	0.86062|0.86062	0.5843|0.5843	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.91635|.	0.978;0.953;0.988;0.998;0.999|.	D|D	0.89102|0.89102	0.3490|0.3490	9|5	.|.	.|.	.|.	-18.2076|-18.2076	17.0797|17.0797	0.86595|0.86595	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	105;302;23;135;290|.	A0AVJ2;Q5VU57-2;B4DGK1;B1AMW2;Q5VU57|.	.;.;.;.;CBPC6_HUMAN|.	H|I	290;284;23;290|136	ENSP00000360905:R290H;ENSP00000335516:R23H;ENSP00000360904:R290H|.	.|.	R|V	-|-	2|1	0|0	AGBL4|AGBL4	48872834|48872834	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.994000|0.994000	0.84299|0.84299	6.832000|6.832000	0.75329|0.75329	2.636000|2.636000	0.89361|0.89361	0.462000|0.462000	0.41574|0.41574	CGT|GTC		0.468	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		T	49100247	C	T	49100247	3	4	105	1	0	0	0	0	1	0	0	0	377	536	19	1	666	1	AGBL4	1	49100247	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	3887190	49100247	200150374	4	27644										
SNX7	51375	hgsc.bcm.edu	37	chr1	99203797	99203797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttgtgacttaattcagcttcCagaggagattggaaaacttg	10	6	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:99203797C>T	ENST00000306121.3	+	8	1139	c.1130C>T	c.(1129-1131)cCa>cTa	p.P377L	SNX7_ENST00000529992.1_Missense_Mutation_p.P322L|SNX7_ENST00000370189.5_Intron	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	313					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		ATTCAGCTTCCAGAGGAGATT	0.343																																																0			1											81	84	83					1																	99203797		2203	4300	6503	98976385	SO:0001583	missense	51375			AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"Sorting nexins"	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.1130C>T	1.37:g.99203797C>T	ENSP00000304429:p.Pro377Leu		98976385	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	C	10.93	1.491015	0.26774	.	.	ENSG00000162627	ENST00000529992;ENST00000306121	T;T	0.20738	2.05;2.05	5.76	4.84	0.62591	.	0.621133	0.17781	N	0.162239	T	0.07503	0.0189	L	0.29908	0.895	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.003	T	0.09058	-1.0692	10	0.33141	T	0.24	-9.8813	13.0876	0.59151	0.2917:0.7083:0.0:0.0	.	322;377	E9PNL2;Q9UNH6-3	.;.	L	322;377	ENSP00000434731:P322L;ENSP00000304429:P377L	ENSP00000304429:P377L	P	+	2	0	SNX7	98976385	1.000000	0.71417	0.999000	0.59377	0.539000	0.34962	1.733000	0.38156	1.408000	0.46895	0.591000	0.81541	CCA		0.343	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			T	99203797	C	T	99203797	3	4	105	1	0	0	0	0	1	0	0	0	14944	594	21	3	1160	3	SNX7	1	99203797	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	50103550	99203797	150046824	5	27645										
FAM63A	55793	hgsc.bcm.edu	37	chr1	150972986	150972986	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tatgcctagcaggtcaaagaCactgcactcgggtgtatact	10	10	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:150972986C>A	ENST00000361936.5	-	6	1636	c.682G>T	c.(682-684)Gtc>Ttc	p.V228F	FAM63A_ENST00000312210.5_Missense_Mutation_p.V86F|FAM63A_ENST00000361738.6_Missense_Mutation_p.V276F|FAM63A_ENST00000470877.1_Intron|FAM63A_ENST00000493834.2_Missense_Mutation_p.V133F	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	228						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	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)			AGGTCAAAGACACTGCACTCG	0.532																																																0			1											105	98	100					1																	150972986		2203	4300	6503	149239610	SO:0001583	missense	55793			BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.682G>T	1.37:g.150972986C>A	ENSP00000354814:p.Val228Phe		149239610	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Missense_Mutation	SNP	ENST00000361936.5	37	CCDS976.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968842	0.53614	.	.	ENSG00000143409	ENST00000312210;ENST00000361936;ENST00000361738;ENST00000493834	T;T;T;T	0.48836	0.8;0.82;0.8;0.83	4.82	-2.37	0.06643	.	0.262290	0.36628	N	0.002487	T	0.44265	0.1285	M	0.65498	2.005	0.46774	D	0.99919	B;D	0.53885	0.2;0.963	B;P	0.59171	0.087;0.853	T	0.52003	-0.8633	10	0.59425	D	0.04	-4.9573	10.7418	0.46158	0.0:0.6334:0.0:0.3666	.	276;228	Q8N5J2-3;Q8N5J2	.;FA63A_HUMAN	F	86;228;276;133	ENSP00000310923:V86F;ENSP00000354814:V228F;ENSP00000354669:V276F;ENSP00000437174:V133F	ENSP00000310923:V86F	V	-	1	0	FAM63A	149239610	0.312000	0.24545	0.113000	0.21522	0.472000	0.32918	0.933000	0.28897	-0.723000	0.04915	0.563000	0.77884	GTC		0.532	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379		A	150972986	C	A	150972986	3	1	105	1	0	0	0	0	1	0	0	0	5615	478	17	2	751	2	FAM63A	1	150972986	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	51769189	150972986	98277635	6	27646										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155451193	155451193	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attaaacatttctttctccaAattaatgatttcttttcgta	2	7	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:155451193A>C	ENST00000368346.3	-	3	2107	c.1468T>G	c.(1468-1470)Ttg>Gtg	p.L490V	ASH1L_ENST00000392403.3_Missense_Mutation_p.L490V			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	490					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTTTCTCCAAATTAATGATT	0.358																																																0			1											71	67	68					1																	155451193		2203	4300	6503	153717817	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1468T>G	1.37:g.155451193A>C	ENSP00000357330:p.Leu490Val		153717817	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	A	11.01	1.513156	0.27123	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88201	-2.35;-2.35	5.08	5.08	0.68730	.	0.209267	0.32703	N	0.005752	T	0.67618	0.2912	N	0.14661	0.345	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.66316	-0.5954	10	0.31617	T	0.26	.	9.7392	0.40406	0.777:0.223:0.0:0.0	.	490;490	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	V	490	ENSP00000357330:L490V;ENSP00000376204:L490V	ENSP00000357330:L490V	L	-	1	2	ASH1L	153717817	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.526000	0.35964	2.261000	0.74972	0.533000	0.62120	TTG		0.358	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155451193	A	C	155451193	3	2	105	1	0	0	0	0	1	0	0	0	1042	11	1	4	7530	4	ASH1L	1	155451193	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4478207	155451193	93799428	7	27647										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157771888	157771888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccagtacaggatcggaggagAgcctctcagggcctcacagt	13	12	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:157771888A>G	ENST00000368176.3	-	5	770	c.703T>C	c.(703-705)Tct>Cct	p.S235P	FCRL1_ENST00000491942.1_Missense_Mutation_p.S235P|FCRL1_ENST00000358292.3_Missense_Mutation_p.S235P|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	235	Ig-like C2-type 3.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			ATCGGAGGAGAGCCTCTCAGG	0.612																																					GBM(54;482 1003 11223 30131 35730)											0			1											42	43	43					1																	157771888		2203	4300	6503	156038512	SO:0001583	missense	115350			BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.703T>C	1.37:g.157771888A>G	ENSP00000357158:p.Ser235Pro		156038512	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	37	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562149	0.45590	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.02177	4.41;4.41;4.41	4.96	4.96	0.65561	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.205916	0.35466	N	0.003189	T	0.07773	0.0195	M	0.86097	2.795	0.35420	D	0.793136	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.994;0.985	T	0.01108	-1.1449	9	.	.	.	.	11.2038	0.48758	1.0:0.0:0.0:0.0	.	235;235;235	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	P	235	ENSP00000351039:S235P;ENSP00000357158:S235P;ENSP00000418130:S235P	.	S	-	1	0	FCRL1	156038512	1.000000	0.71417	0.984000	0.44739	0.035000	0.12851	2.746000	0.47467	2.193000	0.70182	0.533000	0.62120	TCT		0.612	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		G	157771888	A	G	157771888	3	3	105	1	0	0	0	0	1	0	0	0	5813	304	11	4	680	4	FCRL1	1	157771888	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	2320695	157771888	91478733	8	27648										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160128841	160128841	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gatgcaaattaatgtacaagAggtggtgttgggagacctgg	15	4	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:160128841A>G	ENST00000368081.4	+	5	1046	c.575A>G	c.(574-576)gAg>gGg	p.E192G		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	192					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AATGTACAAGAGGTGGTGTTG	0.493																																																0			1											131	116	121					1																	160128841		2203	4300	6503	158395465	SO:0001583	missense	480			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.575A>G	1.37:g.160128841A>G	ENSP00000357060:p.Glu192Gly		158395465	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585415	0.28268	.	.	ENSG00000132681	ENST00000368081	D	0.92299	-3.01	4.86	4.86	0.63082	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	1.102020	0.06700	N	0.771276	D	0.90689	0.7079	M	0.87456	2.885	0.80722	D	1	B	0.02656	0.0	B	0.12156	0.007	D	0.85585	0.1242	10	0.56958	D	0.05	.	12.7189	0.57131	1.0:0.0:0.0:0.0	.	192	Q13733	AT1A4_HUMAN	G	192	ENSP00000357060:E192G	ENSP00000357060:E192G	E	+	2	0	ATP1A4	158395465	0.070000	0.21116	0.004000	0.12327	0.009000	0.06853	3.661000	0.54503	1.948000	0.56530	0.459000	0.35465	GAG		0.493	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		G	160128841	A	G	160128841	3	3	105	1	0	0	0	0	1	0	0	0	1132	304	11	4	593	4	ATP1A4	1	160128841	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	2356953	160128841	89121780	9	27649										
TNR	7143	hgsc.bcm.edu	37	chr1	175372552	175372552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gctgcagtctgttgggcaccGgagttcggaacagtcatccc	13	12	2	0	rs371035988		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:175372552G>A	ENST00000367674.2	-	4	1408	c.700C>T	c.(700-702)Cgg>Tgg	p.R234W	TNR_ENST00000263525.2_Missense_Mutation_p.R234W			Q92752	TENR_HUMAN	tenascin R	234	Cys-rich.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GTTGGGCACCGGAGTTCGGAA	0.652																																																0			1						G	TRP/ARG	0,4406		0,0,2203	99	92	94		700	6.2	1	1		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	TNR	NM_003285.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	234/1359	175372552	2,13004	2203	4300	6503	173639175	SO:0001583	missense	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.700C>T	1.37:g.175372552G>A	ENSP00000356646:p.Arg234Trp		173639175	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.584818	0.86748	0.0	2.33E-4	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.03330	3.97;3.97	6.17	6.17	0.99709	.	0.063688	0.64402	D	0.000003	T	0.11410	0.0278	L	0.37697	1.125	0.52501	D	0.999955	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.935	T	0.00540	-1.1681	10	0.66056	D	0.02	.	13.6552	0.62333	0.0706:0.0:0.9294:0.0	.	234;234	B4DIX8;Q92752	.;TENR_HUMAN	W	234	ENSP00000356646:R234W;ENSP00000263525:R234W	ENSP00000263525:R234W	R	-	1	2	TNR	173639175	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.527000	0.67123	2.941000	0.99782	0.655000	0.94253	CGG		0.652	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175372552	G	A	175372552	3	1	105	1	0	0	0	0	1	0	0	0	16377	1115	39	1	3456	1	TNR	1	175372552	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	15243711	175372552	73878069	10	27650										
ASPM	259266	hgsc.bcm.edu	37	chr1	197072050	197072050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtgcatgtgttgaatatgtcTtctaactctaatacctctat	6	8	4	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:197072050T>C	ENST00000367409.4	-	18	6587	c.6331A>G	c.(6331-6333)Aga>Gga	p.R2111G	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2111	IQ 16. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TGAATATGTCTTCTAACTCTA	0.328																																																0			1											110	117	114					1																	197072050		2203	4297	6500	195338673	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.6331A>G	1.37:g.197072050T>C	ENSP00000356379:p.Arg2111Gly		195338673	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	t	12.01	1.810845	0.32053	.	.	ENSG00000066279	ENST00000367409	T	0.72942	-0.7	5.59	4.44	0.53790	.	0.134493	0.51477	D	0.000099	D	0.86871	0.6037	H	0.94582	3.555	0.09310	N	0.999993	D	0.60160	0.987	D	0.67231	0.95	T	0.81165	-0.1057	10	0.87932	D	0	.	12.0466	0.53483	0.0:0.0:0.3364:0.6636	.	2111	Q8IZT6	ASPM_HUMAN	G	2111	ENSP00000356379:R2111G	ENSP00000356379:R2111G	R	-	1	2	ASPM	195338673	0.017000	0.18338	0.362000	0.25862	0.421000	0.31385	0.304000	0.19228	0.916000	0.36871	0.520000	0.50463	AGA		0.328	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		C	197072050	T	C	197072050	3	2	105	1	0	0	0	0	1	0	0	0	1057	1617	56	4	4146	4	ASPM	1	197072050	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	21699498	197072050	52178571	11	27651										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202699028	202699028	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggctcagtttgattttcttcTttttgggggtccgcattttc	10	8	3	1	rs34591577		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:202699028T>C	ENST00000367265.3	-	26	5468	c.4304A>G	c.(4303-4305)aAg>aGg	p.K1435R	KDM5B_ENST00000367264.2_Missense_Mutation_p.K1471R	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1435	Poly-Lys.				histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.K1572R(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GATTTTCTTCTTTTTGGGGGT	0.458																																																1	Substitution - Missense(1)	breast(1)	1											199	190	193					1																	202699028		2203	4300	6503	200965651	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.4304A>G	1.37:g.202699028T>C	ENSP00000356234:p.Lys1435Arg		200965651	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756501	0.31137	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264	D;D	0.87809	-2.3;-2.12	5.23	4.1	0.47936	.	0.239296	0.43416	N	0.000579	T	0.81959	0.4933	L	0.55481	1.735	0.42331	D	0.992295	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.002	T	0.73135	-0.4078	10	0.14656	T	0.56	-18.6395	10.7594	0.46256	0.0:0.0748:0.0:0.9252	.	1471;1435	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	R	1435;1277;1471	ENSP00000356234:K1435R;ENSP00000356233:K1471R	ENSP00000356233:K1471R	K	-	2	0	KDM5B	200965651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.003000	0.57061	0.835000	0.34877	0.528000	0.53228	AAG		0.458	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		C	202699028	T	C	202699028	3	2	105	1	0	0	0	0	1	0	0	0	8155	1609	56	4	338	4	KDM5B	1	202699028	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	5626978	202699028	46551593	12	27652										
MARK1	4139	hgsc.bcm.edu	37	chr1	220809239	220809239	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caggctaacagtgtggaaagTgaacagaaagaggagtggga	16	4	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:220809239T>C	ENST00000366917.4	+	13	1607	c.1341T>C	c.(1339-1341)agT>agC	p.S447S	MARK1_ENST00000402574.1_Silent_p.S312S|MARK1_ENST00000366918.4_Silent_p.S425S					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		GTGTGGAAAGTGAACAGAAAG	0.433																																																0			1											102	99	100					1																	220809239		2203	4300	6503	218875862	SO:0001819	synonymous_variant	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1341T>C	1.37:g.220809239T>C			218875862		Silent	SNP	ENST00000366917.4	37	CCDS31029.2																																																																																				0.433	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			C	220809239	T	C	220809239	2	2	105	1	0	0	0	0	0	0	0	1	9342	1693	59	4		4	MARK1	1	220809239	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	18110211	220809239	28441382	13	27653										
TRIM11	81559	hgsc.bcm.edu	37	chr1	228589824	228589824	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aacagcaacgcatcctgcatCtgcttccggagatgctccag	9	14	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:228589824C>T	ENST00000284551.6	-	2	725	c.447G>A	c.(445-447)caG>caA	p.Q149Q	TRIM11_ENST00000460651.1_5'Flank|TRIM11_ENST00000366699.3_Silent_p.Q149Q|TRIM11_ENST00000493030.2_Silent_p.Q24Q	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	149					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				CATCCTGCATCTGCTTCCGGA	0.627																																																0			1											86	73	78					1																	228589824		2203	4300	6503	226656447	SO:0001819	synonymous_variant	81559			AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16281	protein-coding gene	gene with protein product		607868	"tripartite motif-containing 11"			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.447G>A	1.37:g.228589824C>T			226656447	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Silent	SNP	ENST00000284551.6	37	CCDS31048.1																																																																																				0.627	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		T	228589824	C	T	228589824	2	4	105	1	0	0	0	0	0	0	0	1	16527	912	32	3		3	TRIM11	1	228589824	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	7780585	228589824	20660797	14	27654										
GNPAT	8443	hgsc.bcm.edu	37	chr1	231408063	231408063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgcatttatttccagaggatGtctacagttgctttcgcttc	8	9	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:231408063G>A	ENST00000366647.4	+	11	1697	c.1528G>A	c.(1528-1530)Gtc>Atc	p.V510I	GNPAT_ENST00000366646.3_Missense_Mutation_p.V449I	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	510					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)	p.V510F(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TCCAGAGGATGTCTACAGTTG	0.373																																																1	Substitution - Missense(1)	ovary(1)	1											304	290	294					1																	231408063		2203	4300	6503	229474686	SO:0001583	missense	8443			AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1528G>A	1.37:g.231408063G>A	ENSP00000355607:p.Val510Ile		229474686	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.477077	0.26511	.	.	ENSG00000116906	ENST00000366647;ENST00000366646;ENST00000416000	T;T;T	0.63417	-0.02;-0.02;-0.04	4.71	2.83	0.33086	.	0.205916	0.42964	D	0.000640	T	0.38480	0.1042	N	0.16743	0.435	0.46678	D	0.999151	B;B	0.11235	0.004;0.002	B;B	0.16289	0.015;0.004	T	0.11991	-1.0565	10	0.10636	T	0.68	.	7.9026	0.29744	0.3087:0.0:0.6913:0.0	.	449;510	B4DNM9;O15228	.;GNPAT_HUMAN	I	510;449;500	ENSP00000355607:V510I;ENSP00000355606:V449I;ENSP00000411640:V500I	ENSP00000355606:V449I	V	+	1	0	GNPAT	229474686	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	1.325000	0.33724	1.339000	0.45563	0.563000	0.77884	GTC		0.373	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			A	231408063	G	A	231408063	3	1	105	1	0	0	0	0	1	0	0	0	6561	1377	48	3	1570	3	GNPAT	1	231408063	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2818239	231408063	17842558	15	27655										
ADSS	159	hgsc.bcm.edu	37	chr1	244587341	244587341	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gacgaataaactgggccaatGcccttttttgttgtacccaa	8	10	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:244587341G>A	ENST00000366535.3	-	6	811	c.495C>T	c.(493-495)ggC>ggT	p.G165G	ADSS_ENST00000462358.1_5'UTR	NM_001126.3	NP_001117.2			adenylosuccinate synthase									p.G165G(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			CTGGGCCAATGCCCTTTTTTG	0.423																																																1	Substitution - coding silent(1)	ovary(1)	1											59	56	57					1																	244587341		2203	4300	6503	242653964	SO:0001819	synonymous_variant	159			BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.495C>T	1.37:g.244587341G>A			242653964		Silent	SNP	ENST00000366535.3	37	CCDS1624.1																																																																																				0.423	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		A	244587341	G	A	244587341	2	1	105	1	0	0	0	0	0	0	0	1	347	1306	46	3		3	ADSS	1	244587341	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	13179278	244587341	4663280	16	27656										
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343304	248343304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	catcatggcatgggagaatcAgaccttcaactccgacttca	8	12	4	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr1:248343304A>G	ENST00000359682.2	+	1	17	c.17A>G	c.(16-18)cAg>cGg	p.Q6R		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q6R(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TGGGAGAATCAGACCTTCAAC	0.423																																																1	Substitution - Missense(1)	ovary(1)	1											198	195	196					1																	248343304		2203	4300	6503	246409927	SO:0001583	missense	391194			AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.17A>G	1.37:g.248343304A>G	ENSP00000352710:p.Gln6Arg		246409927	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	a	12.92	2.082954	0.36758	.	.	ENSG00000198601	ENST00000359682	T	0.00262	8.4	1.44	1.44	0.22558	.	0.306691	0.17821	U	0.160853	T	0.00144	0.0004	L	0.41906	1.305	0.21290	N	0.999737	B	0.34264	0.446	B	0.35182	0.197	T	0.26573	-1.0099	10	0.52906	T	0.07	.	7.7689	0.28997	1.0:0.0:0.0:0.0	.	6	Q96R28	OR2M2_HUMAN	R	6	ENSP00000352710:Q6R	ENSP00000352710:Q6R	Q	+	2	0	OR2M2	246409927	0.000000	0.05858	0.062000	0.19696	0.564000	0.35744	0.030000	0.13688	0.651000	0.30788	0.248000	0.18094	CAG		0.423	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		G	248343304	A	G	248343304	3	3	105	1	0	0	0	0	1	0	0	0	11041	188	7	4	19	4	OR2M2	1	248343304	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	3755963	248343304	907317	17	27657										
ALLC	55821	hgsc.bcm.edu	37	chr2	3745027	3745027	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtaataactcgaattgaaatTgacacaaaatattttgaagg	7	4	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:3745027T>C	ENST00000252505.3	+	10	993	c.831T>C	c.(829-831)atT>atC	p.I277I	ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	296					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GAATTGAAATTGACACAAAAT	0.388										HNSCC(21;0.051)																																						0			2											127	122	124					2																	3745027		1836	4088	5924	3722902	SO:0001819	synonymous_variant	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.831T>C	2.37:g.3745027T>C			3722902	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Silent	SNP	ENST00000252505.3	37	CCDS46223.1																																																																																				0.388	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			C	3745027	T	C	3745027	2	2	105	1	0	0	0	0	0	0	0	1	534	1800	63	4		4	ALLC	2	3745027	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10		3745027	239454346	18	27658										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43939418	43939418	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cagattctcccaatatattgGaagagtggattaaagtgtta	9	5	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:43939418G>C	ENST00000282406.4	+	15	2466	c.2356G>C	c.(2356-2358)Gaa>Caa	p.E786Q		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	786	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAATATATTGGAAGAGTGGAT	0.428																																																0			2											143	132	135					2																	43939418		2203	4300	6503	43792922	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2356G>C	2.37:g.43939418G>C	ENSP00000282406:p.Glu786Gln		43792922	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.656763	0.88154	.	.	ENSG00000152527	ENST00000282406	T	0.76186	-1.0	4.93	4.93	0.64822	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.106321	0.64402	D	0.000007	T	0.78071	0.4226	L	0.48174	1.505	0.58432	D	0.999997	P;D	0.53619	0.504;0.961	B;P	0.52159	0.401;0.691	T	0.81152	-0.1063	10	0.72032	D	0.01	-7.8798	18.1513	0.89675	0.0:0.0:1.0:0.0	.	786;223	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	Q	786	ENSP00000282406:E786Q	ENSP00000282406:E786Q	E	+	1	0	PLEKHH2	43792922	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	9.340000	0.97038	2.275000	0.75901	0.460000	0.39030	GAA		0.428	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		C	43939418	G	C	43939418	3	2	105	1	0	0	0	0	1	0	0	0	12108	1175	41	5	2410	5	PLEKHH2	2	43939418	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	40194391	43939418	199259955	19	27659										
PSME4	23198	hgsc.bcm.edu	37	chr2	54128521	54128521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caattgtttcatactgcctaTgaatcttttctgcaagatca	5	9	4	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:54128521T>C	ENST00000404125.1	-	28	3306	c.3251A>G	c.(3250-3252)cAt>cGt	p.H1084R	PSME4_ENST00000421748.2_Missense_Mutation_p.H228R	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1084					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ATACTGCCTATGAATCTTTTC	0.388																																																0			2											107	97	101					2																	54128521		2203	4300	6503	53982025	SO:0001583	missense	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3251A>G	2.37:g.54128521T>C	ENSP00000384211:p.His1084Arg		53982025	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781043	0.70222	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.23147	1.92;1.93	5.6	5.6	0.85130	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35885	0.0947	M	0.62723	1.935	0.80722	D	1	P;P;P	0.49090	0.919;0.804;0.794	P;B;B	0.48677	0.586;0.288;0.102	T	0.06607	-1.0817	10	0.25106	T	0.35	.	15.7852	0.78297	0.0:0.0:0.0:1.0	.	459;228;1084	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	R	228;1084	ENSP00000410830:H228R;ENSP00000384211:H1084R	ENSP00000384211:H1084R	H	-	2	0	PSME4	53982025	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.128000	0.65567	0.455000	0.32223	CAT		0.388	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54128521	T	C	54128521	3	2	105	1	0	0	0	0	1	0	0	0	12743	1464	51	4	2356	4	PSME4	2	54128521	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	10189103	54128521	189070852	20	27660										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54839316	54839316	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agcctaaacccaccaagggaCgaatgcgcatccactgctta	8	14	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:54839316C>T	ENST00000356805.4	+	4	600	c.319C>T	c.(319-321)Cga>Tga	p.R107*	SPTBN1_ENST00000333896.5_Nonsense_Mutation_p.R94*	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	107	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.R107*(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CACCAAGGGACGAATGCGCAT	0.517																																																1	Substitution - Nonsense(1)	breast(1)	2											111	103	106					2																	54839316		2203	4300	6503	54692820	SO:0001587	stop_gained	6711				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.319C>T	2.37:g.54839316C>T	ENSP00000349259:p.Arg107*		54692820	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Nonsense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	39	7.426318	0.98275	.	.	ENSG00000115306	ENST00000356805;ENST00000389980;ENST00000333896	.	.	.	5.33	3.19	0.36642	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8598	0.52459	0.5838:0.4162:0.0:0.0	.	.	.	.	X	107;107;94	.	ENSP00000334156:R94X	R	+	1	2	SPTBN1	54692820	0.996000	0.38824	0.428000	0.26697	0.962000	0.63368	3.440000	0.52886	1.324000	0.45282	0.561000	0.74099	CGA		0.517	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54839316	C	T	54839316	4	4	105	1	0	0	0	0	0	1	0	0	15158	528	19	1	442	1	SPTBN1	2	54839316	Nonsense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	710795	54839316	188360057	21	27661										
TET3	200424	hgsc.bcm.edu	37	chr2	74275179	74275179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caagctggaagagctcatccGgcagtttgaggctgaatttg	13	8	1	3	rs57955681	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:74275179G>A	ENST00000409262.3	+	1	1730	c.1730G>A	c.(1729-1731)cGg>cAg	p.R577Q		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	577			R -> Q (in dbSNP:rs57955681).		DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAGCTCATCCGGCAGTTTGAG	0.602													G|||	14	0.00279553	0.0106	0	5008	,	,		17424	0		0	False		,,,				2504	0															0			2						G	GLN/ARG	21,3813		0,21,1896	41	46	44		1730	3.4	1	2	dbSNP_129	44	0,8238		0,0,4119	yes	missense	TET3	NM_144993.1	43	0,21,6015	AA,AG,GG		0.0,0.5477,0.174	probably-damaging	577/1661	74275179	21,12051	1917	4119	6036	74128687	SO:0001583	missense	200424				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1730G>A	2.37:g.74275179G>A	ENSP00000386869:p.Arg577Gln		74128687	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	11.50	1.656276	0.29425	0.005477	0.0	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.26810	1.71;2.65	5.38	3.44	0.39384	.	.	.	.	.	T	0.09024	0.0223	N	0.17082	0.46	0.33426	D	0.580472	B	0.25312	0.123	B	0.10450	0.005	T	0.18209	-1.0344	9	0.13470	T	0.59	.	8.3192	0.32119	0.2359:0.0:0.7641:0.0	rs57955681	577	O43151	TET3_HUMAN	Q	619;577;577	ENSP00000307803:R619Q;ENSP00000386869:R577Q	ENSP00000233310:R577Q	R	+	2	0	TET3	74128687	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.773000	0.62331	1.500000	0.48636	0.655000	0.94253	CGG		0.602	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			A	74275179	G	A	74275179	3	1	105	1	0	0	0	0	1	0	0	0	15810	1116	39	1	1732	1	TET3	2	74275179	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	19435863	74275179	168924194	22	27662										
CHST10	9486	hgsc.bcm.edu	37	chr2	101014521	101014521	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttcttcagggcatcatccctGcagacgtttctgatgagttc	9	11	4	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:101014521G>T	ENST00000264249.3	-	5	661	c.276C>A	c.(274-276)tgC>tgA	p.C92*	CHST10_ENST00000409701.1_Nonsense_Mutation_p.C92*|CHST10_ENST00000542617.1_Nonsense_Mutation_p.C140*	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	92					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)	p.C92*(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						CATCATCCCTGCAGACGTTTC	0.527																																																1	Substitution - Nonsense(1)	ovary(1)	2											138	140	139					2																	101014521		2203	4300	6503	100380953	SO:0001587	stop_gained	9486			BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.276C>A	2.37:g.101014521G>T	ENSP00000264249:p.Cys92*		100380953	Q53T18	Nonsense_Mutation	SNP	ENST00000264249.3	37	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.861171	0.91433	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701;ENST00000409046;ENST00000420858;ENST00000448989	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-34.8109	19.5919	0.95518	0.0:0.0:1.0:0.0	.	.	.	.	X	92;140;92;92;92;140	.	ENSP00000264249:C92X	C	-	3	2	CHST10	100380953	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.343000	0.72986	2.628000	0.89032	0.655000	0.94253	TGC		0.527	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		T	101014521	G	T	101014521	4	4	105	1	0	0	0	0	0	1	0	0	3404	1311	46	2	806	2	CHST10	2	101014521	Nonsense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	26739342	101014521	142184852	23	27663										
IMP4	92856	hgsc.bcm.edu	37	chr2	131103401	131103401	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggtcctactgcctacttcacGctgtgcaatgtggtcatgcg	11	12	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:131103401G>A	ENST00000259239.3	+	6	1197	c.489G>A	c.(487-489)acG>acA	p.T163T	IMP4_ENST00000409935.1_Silent_p.T163T	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	163	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)				central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					CCTACTTCACGCTGTGCAATG	0.637																																																0			2											101	93	95					2																	131103401		2203	4300	6503	130819871	SO:0001819	synonymous_variant	92856			BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.489G>A	2.37:g.131103401G>A			130819871	Q3ZTT3	Silent	SNP	ENST00000259239.3	37	CCDS2160.1	.	.	.	.	.	.	.	.	.	.	G	6.563	0.472158	0.12461	.	.	ENSG00000136718	ENST00000452955	.	.	.	5.18	-10.4	0.00318	.	.	.	.	.	T	0.40743	0.1129	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52419	-0.8578	4	.	.	.	-26.3252	4.5027	0.11872	0.2533:0.3327:0.3318:0.0822	.	.	.	.	H	152	.	.	R	+	2	0	IMP4	130819871	0.000000	0.05858	0.063000	0.19743	0.904000	0.53231	-3.140000	0.00586	-3.647000	0.00127	-1.785000	0.00643	CGC		0.637	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416		A	131103401	G	A	131103401	2	1	105	1	0	0	0	0	0	0	0	1	7741	1074	38	1		1	IMP4	2	131103401	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	30088880	131103401	112095972	24	27664										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186268	157186268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgtggagagatcccgggtcgTcccacatggggctgtgctgc	16	11	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:157186268T>C	ENST00000339562.4	-	3	793	c.431A>G	c.(430-432)gAc>gGc	p.D144G	NR4A2_ENST00000429376.1_Missense_Mutation_p.D81G|NR4A2_ENST00000426264.1_Missense_Mutation_p.D81G|NR4A2_ENST00000409572.1_Missense_Mutation_p.D144G|NR4A2_ENST00000539077.1_Missense_Mutation_p.D155G|NR4A2_ENST00000409108.2_Missense_Mutation_p.D144G	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	144	Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TCCCGGGTCGTCCCACATGGG	0.632																																																0			2											74	87	82					2																	157186268		2203	4300	6503	156894514	SO:0001583	missense	4929			X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.431A>G	2.37:g.157186268T>C	ENSP00000344479:p.Asp144Gly		156894514	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813424	0.70912	.	.	ENSG00000153234	ENST00000339562;ENST00000426264;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000429376;ENST00000424077;ENST00000421709	D;D;D;D;D;D;D;D	0.94046	-2.98;-3.17;-2.98;-2.99;-3.23;-3.34;-1.87;-2.59	6.07	6.07	0.98685	.	2.065020	0.01923	N	0.040623	D	0.94788	0.8317	L	0.34521	1.04	0.80722	D	1	P	0.49862	0.929	P	0.54431	0.752	T	0.82621	-0.0367	10	0.48119	T	0.1	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	144	P43354	NR4A2_HUMAN	G	144;81;144;155;144;81;144;81	ENSP00000344479:D144G;ENSP00000389986:D81G;ENSP00000386747:D144G;ENSP00000444925:D155G;ENSP00000386993:D144G;ENSP00000410952:D81G;ENSP00000406808:D144G;ENSP00000388120:D81G	ENSP00000344479:D144G	D	-	2	0	NR4A2	156894514	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	GAC		0.632	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			C	157186268	T	C	157186268	3	2	105	1	0	0	0	0	1	0	0	0	10664	1667	58	4	1389	4	NR4A2	2	157186268	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	26082867	157186268	86013105	25	27665										
CIR1	9541	hgsc.bcm.edu	37	chr2	175213554	175213554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gctgtcctccctagaactctCgtgttttaagaacctgggct	9	12	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:175213554C>T	ENST00000342016.3	-	10	1116	c.1024G>A	c.(1024-1026)Gag>Aag	p.E342K	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	342	Lys/Ser-rich.				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E342*(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						CTAGAACTCTCGTGTTTTAAG	0.438																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											160	160	160					2																	175213554		2203	4300	6503	174921800	SO:0001583	missense	7335			AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"recepin", "CBF1 interacting corepressor"	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.1024G>A	2.37:g.175213554C>T	ENSP00000339723:p.Glu342Lys		174921800	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Missense_Mutation	SNP	ENST00000342016.3	37	CCDS2256.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.855513	0.51376	.	.	ENSG00000138433	ENST00000342016	.	.	.	6.16	6.16	0.99307	.	0.277370	0.34531	N	0.003885	T	0.61949	0.2388	L	0.56769	1.78	0.37544	D	0.918435	D;D	0.56521	0.976;0.957	P;B	0.46275	0.51;0.198	T	0.66272	-0.5965	9	0.48119	T	0.1	.	18.648	0.91418	0.0:1.0:0.0:0.0	.	342;342	A0PJI7;Q86X95	.;CIR1_HUMAN	K	342	.	ENSP00000339723:E342K	E	-	1	0	CIR1	174921800	1.000000	0.71417	0.428000	0.26697	0.024000	0.10985	3.879000	0.56138	2.937000	0.99478	0.650000	0.86243	GAG		0.438	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882		T	175213554	C	T	175213554	3	4	105	1	0	0	0	0	1	0	0	0	3438	893	31	1	332	1	CIR1	2	175213554	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	18027286	175213554	67985819	26	27666										
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175618347	175618347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcatgacgaagtggtaggtgAtgtccaggtagggggtgtcg	19	5	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:175618347A>G	ENST00000261007.5	-	7	803	c.737T>C	c.(736-738)aTc>aCc	p.I246T	CHRNA1_ENST00000348749.5_Missense_Mutation_p.I221T|CHRNA1_ENST00000409323.1_Missense_Mutation_p.I221T|CHRNA1_ENST00000409542.1_Missense_Mutation_p.I139T|CHRNA1_ENST00000409219.1_Missense_Mutation_p.I221T|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	246					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GTGGTAGGTGATGTCCAGGTA	0.577																																																0			2											177	163	168					2																	175618347		2203	4300	6503	175326593	SO:0001583	missense	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.737T>C	2.37:g.175618347A>G	ENSP00000261007:p.Ile246Thr		175326593	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.752979	0.69648	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	5.17	5.17	0.71159	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.91126	0.7206	M	0.84433	2.695	0.80722	D	1	D;P;D	0.64830	0.994;0.818;0.961	D;P;P	0.65140	0.932;0.555;0.864	D	0.92681	0.6158	10	0.87932	D	0	.	15.3121	0.74042	1.0:0.0:0.0:0.0	.	221;221;246	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	T	221;246;139;221;221	ENSP00000261008:I221T;ENSP00000261007:I246T;ENSP00000387026:I139T;ENSP00000386611:I221T;ENSP00000386684:I221T	ENSP00000261007:I246T	I	-	2	0	CHRNA1	175326593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.231000	0.95317	2.075000	0.62263	0.528000	0.53228	ATC		0.577	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			G	175618347	A	G	175618347	3	3	105	1	0	0	0	0	1	0	0	0	3387	333	12	4	727	4	CHRNA1	2	175618347	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	404793	175618347	67581026	27	27667										
TTN	7273	hgsc.bcm.edu	37	chr2	179604887	179604887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccacgggctctcttttagacTcaatgatttggtctgggggc	12	10	3	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:179604887T>C	ENST00000591111.1	-	46	12346	c.12122A>G	c.(12121-12123)gAg>gGg	p.E4041G	TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E4187G|TTN_ENST00000460472.2_Missense_Mutation_p.E3995G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E4120G|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E4358G			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTTTAGACTCAATGATTTG	0.463																																																0			2											79	78	78					2																	179604887		1859	4097	5956	179313132	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12122A>G	2.37:g.179604887T>C	ENSP00000465570:p.Glu4041Gly		179313132	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	4.147	0.025761	0.08054	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.61274	0.17;0.13;0.12	5.92	4.75	0.60458	.	.	.	.	.	T	0.45458	0.1343	N	0.24115	0.695	0.09310	N	1	B;B;B	0.19817	0.011;0.011;0.039	B;B;B	0.14023	0.01;0.01;0.01	T	0.42716	-0.9435	9	0.87932	D	0	.	12.4646	0.55751	0.1257:0.0:0.0:0.8743	.	3995;4120;4187	D3DPF9;E7EQE6;E7ET18	.;.;.	G	3995;4187;4120;3995	ENSP00000434586:E3995G;ENSP00000340554:E4187G;ENSP00000352154:E4120G	ENSP00000340554:E4187G	E	-	2	0	TTN	179313132	0.000000	0.05858	0.021000	0.16686	0.049000	0.14656	0.292000	0.19011	1.044000	0.40200	-0.333000	0.08304	GAG		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179604887	T	C	179604887	3	2	105	1	0	0	0	0	1	0	0	0	16775	1551	54	4	91716	4	TTN	2	179604887	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	3986540	179604887	63594486	28	27668										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180634397	180634397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agaaggagaaaagaattttcTttttctctttgctcaactgg	8	6	3	3	rs373649075		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:180634397T>C	ENST00000410066.1	-	3	689	c.86A>G	c.(85-87)aAg>aGg	p.K29R		NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	29	Required for induction of apoptosis.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			AAGAATTTTCTTTTTCTCTTT	0.468																																					Colon(155;204 2491 32774 51842)											0			2						T	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	84	82	83		86	4.8	1	2		83	0,8600		0,0,4300	no	missense	ZNF385B	NM_152520.4	26	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging	29/472	180634397	1,13005	2203	4300	6503	180342642	SO:0001583	missense	151126			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.86A>G	2.37:g.180634397T>C	ENSP00000386845:p.Lys29Arg		180342642	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.088850	0.36855	2.27E-4	0.0	ENSG00000144331	ENST00000410066;ENST00000451732;ENST00000438871	T;T	0.45668	0.89;0.89	5.92	4.76	0.60689	.	0.206931	0.41823	N	0.000802	T	0.31670	0.0804	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.07102	-1.0790	10	0.56958	D	0.05	-3.3751	11.0983	0.48160	0.0:0.072:0.0:0.928	.	29	Q569K4	Z385B_HUMAN	R	29	ENSP00000386845:K29R;ENSP00000409978:K29R	ENSP00000386845:K29R	K	-	2	0	ZNF385B	180342642	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.787000	0.47798	1.065000	0.40693	0.459000	0.35465	AAG		0.468	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		C	180634397	T	C	180634397	3	2	105	1	0	0	0	0	1	0	0	0	17916	1609	56	4	1390	4	ZNF385B	2	180634397	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	1029510	180634397	62564976	29	27669										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182322413	182322413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agcgaggcgcgaacccggccCccgaagggccgccgtccggg	17	17	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:182322413C>T	ENST00000397033.2	+	1	462	c.32C>T	c.(31-33)cCc>cTc	p.P11L	ITGA4_ENST00000339307.4_Missense_Mutation_p.P11L	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	11					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.P11L(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GAACCCGGCCCCCGAAGGGCC	0.657																																																1	Substitution - Missense(1)	lung(1)	2											13	17	16					2																	182322413		1888	4102	5990	182030658	SO:0001583	missense	3676				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.32C>T	2.37:g.182322413C>T	ENSP00000380227:p.Pro11Leu		182030658	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114921	0.37339	.	.	ENSG00000115232	ENST00000425522;ENST00000339307;ENST00000397033;ENST00000233573	D;D;D	0.92299	-3.01;-3.01;-3.01	4.5	4.5	0.54988	.	7739.210000	0.00166	N	0.000002	D	0.90352	0.6981	N	0.16478	0.41	0.09310	N	1	P;P;D	0.54047	0.535;0.535;0.964	B;B;P	0.50314	0.084;0.133;0.637	T	0.81750	-0.0790	10	0.49607	T	0.09	.	10.5807	0.45255	0.0:0.8045:0.1954:0.0	.	11;11;11	E7EP60;P13612;E7ESG7	.;ITA4_HUMAN;.	L	11	ENSP00000340149:P11L;ENSP00000380227:P11L;ENSP00000233573:P11L	ENSP00000233573:P11L	P	+	2	0	ITGA4	182030658	0.005000	0.15991	0.237000	0.24090	0.004000	0.04260	0.525000	0.22956	2.327000	0.79052	0.561000	0.74099	CCC		0.657	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182322413	C	T	182322413	3	4	105	1	0	0	0	0	1	0	0	0	7899	623	22	3	34	3	ITGA4	2	182322413	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	1688016	182322413	60876960	30	27670										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198511328	198511328	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atatcctttaagataatagtTttccacttttgttactatat	3	6	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:198511328T>A	ENST00000295049.4	-	2	738	c.202A>T	c.(202-204)Aac>Tac	p.N68Y		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	68					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						AGATAATAGTTTTCCACTTTT	0.358																																																0			2											78	79	78					2																	198511328		2203	4300	6503	198219573	SO:0001583	missense	130132			AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.202A>T	2.37:g.198511328T>A	ENSP00000295049:p.Asn68Tyr		198219573	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	37	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.943245	0.53079	.	.	ENSG00000162944	ENST00000295049;ENST00000429081	T;T	0.31510	1.49;1.49	5.39	4.52	0.55395	.	0.723544	0.14688	N	0.304357	T	0.19087	0.0458	N	0.08118	0	0.23227	N	0.998081	B	0.32717	0.381	B	0.33392	0.163	T	0.19614	-1.0300	10	0.72032	D	0.01	-8.7828	13.0908	0.59166	0.0:0.9247:0.0:0.0753	.	68	Q52LD8	RFTN2_HUMAN	Y	68	ENSP00000295049:N68Y;ENSP00000398128:N68Y	ENSP00000295049:N68Y	N	-	1	0	RFTN2	198219573	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.149000	0.50655	1.412000	0.46977	-0.221000	0.12465	AAC		0.358	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		A	198511328	T	A	198511328	3	1	105	1	0	0	0	0	1	0	0	0	13296	1841	64	5	1335	5	RFTN2	2	198511328	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	16188915	198511328	44688045	31	27671										
CPO	130749	hgsc.bcm.edu	37	chr2	207827152	207827152	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctaggtattggtgcctctagAaactgccaagatcaaacatt	8	9	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:207827152A>G	ENST00000272852.3	+	7	637	c.591A>G	c.(589-591)agA>agG	p.R197R		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	197						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		GTGCCTCTAGAAACTGCCAAG	0.448																																																0			2											166	164	164					2																	207827152		2203	4300	6503	207535397	SO:0001819	synonymous_variant	130749				CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"metallocarboxypeptidase O", "metallocarboxypeptidase C"	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.591A>G	2.37:g.207827152A>G			207535397	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																				0.448	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		G	207827152	A	G	207827152	2	3	105	1	0	0	0	0	0	0	0	1	3826	243	9	4		4	CPO	2	207827152	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	9315824	207827152	35372221	32	27672										
PTH2R	5746	hgsc.bcm.edu	37	chr2	209302575	209302575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caattattcagactgccttcGctttctgcagccagatatca	6	12	3	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:209302575G>A	ENST00000272847.2	+	4	593	c.380G>A	c.(379-381)cGc>cAc	p.R127H	PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	127					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	GACTGCCTTCGCTTTCTGCAG	0.378																																																0			2											95	92	93					2																	209302575		2203	4300	6503	209010820	SO:0001583	missense	5746			BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.380G>A	2.37:g.209302575G>A	ENSP00000272847:p.Arg127His		209010820	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	G	8.632	0.893975	0.17613	.	.	ENSG00000144407	ENST00000272847	T	0.37235	1.21	4.09	3.19	0.36642	GPCR, family 2, extracellular hormone receptor domain (2);	0.331033	0.20641	U	0.088402	T	0.14013	0.0339	N	0.02973	-0.45	0.25032	N	0.991268	B;B	0.18610	0.014;0.029	B;B	0.15484	0.002;0.013	T	0.07947	-1.0746	10	0.44086	T	0.13	.	5.7434	0.18106	0.2305:0.0:0.7695:0.0	.	16;127	B4DFN8;P49190	.;PTH2R_HUMAN	H	127	ENSP00000272847:R127H	ENSP00000272847:R127H	R	+	2	0	PTH2R	209010820	0.790000	0.28787	1.000000	0.80357	0.933000	0.57130	0.120000	0.15647	1.992000	0.58205	0.467000	0.42956	CGC		0.378	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		A	209302575	G	A	209302575	3	1	105	1	0	0	0	0	1	0	0	0	12795	1087	38	1	394	1	PTH2R	2	209302575	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	1475423	209302575	33896798	33	27673										
MAP2	4133	hgsc.bcm.edu	37	chr2	210561666	210561667	+	Frame_Shift_Ins	INS	-	-	A													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ataagaaggctgaacttgctINSaaaaaaacagaagttcaggc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:210561666_210561667insA	ENST00000360351.4	+	9	4919_4920	c.4413_4414insA	c.(4414-4416)aaafs	p.K1472fs	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Frame_Shift_Ins_p.K1468fs|MAP2_ENST00000475600.1_Intron|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1472					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.T1474fs*14(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTGAACTTGCTAAAAAAACAGA	0.366																																					Pancreas(27;423 979 28787 29963)											1	Deletion - Frameshift(1)	large_intestine(1)	2																																								210269912	SO:0001589	frameshift_variant	10988				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4420dupA	2.37:g.210561673_210561673dupA	ENSP00000353508:p.Lys1472fs		210269911	Q17S04|Q8IUX2|Q99975|Q99976	Frame_Shift_Ins	INS	ENST00000360351.4	37	CCDS2384.1																																																																																				0.366	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210561667	-	A	210561666	7	5	105	1	0	1	1	0	0	0	0	0	9265	1509	53	0	4435	0	MAP2	2	210561666	Frame_Shift_Ins	INS	-	TCGA-DY-A1DD-01A-21D-A152-10	1259091	210561666	32637707	34	27674										
DES	1674	hgsc.bcm.edu	37	chr2	220285595	220285595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acaagaacaacgacgccctgCgccaggccaagcaggagatg	12	13	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:220285595C>T	ENST00000373960.3	+	5	1029	c.943C>T	c.(943-945)Cgc>Tgc	p.R315C		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	315	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CGACGCCCTGCGCCAGGCCAA	0.592																																																0			2											87	81	83					2																	220285595		2203	4300	6503	219993839	SO:0001583	missense	1674			AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"Intermediate filaments type III"	2770	protein-coding gene	gene with protein product	"intermediate filament protein"	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.943C>T	2.37:g.220285595C>T	ENSP00000363071:p.Arg315Cys		219993839	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	.	.	.	.	.	.	.	.	.	.	C	19.01	3.743583	0.69418	.	.	ENSG00000175084	ENST00000373960	D	0.95724	-3.79	4.91	3.96	0.45880	Filament (1);	0.000000	0.45606	D	0.000350	D	0.97879	0.9303	M	0.90198	3.095	0.48632	D	0.999681	D	0.89917	1.0	D	0.79108	0.992	D	0.98356	1.0546	10	0.87932	D	0	.	14.8167	0.70039	0.1823:0.8177:0.0:0.0	.	315	P17661	DESM_HUMAN	C	315	ENSP00000363071:R315C	ENSP00000363071:R315C	R	+	1	0	DES	219993839	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.350000	0.44063	2.533000	0.85409	0.561000	0.74099	CGC		0.592	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		T	220285595	C	T	220285595	3	4	105	1	0	0	0	0	1	0	0	0	4460	768	27	1	961	1	DES	2	220285595	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	9723929	220285595	22913778	35	27675										
PAX3	5077	hgsc.bcm.edu	37	chr2	223096882	223096882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aatgagttctctcaaaagcaCgctccagttcctccagctgt	7	13	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:223096882C>T	ENST00000350526.4	-	5	843	c.707G>A	c.(706-708)cGt>cAt	p.R236H	PAX3_ENST00000392069.2_Missense_Mutation_p.R236H|PAX3_ENST00000344493.4_Missense_Mutation_p.R236H|PAX3_ENST00000392070.2_Missense_Mutation_p.R236H|PAX3_ENST00000336840.6_Missense_Mutation_p.R236H|PAX3_ENST00000409551.3_Missense_Mutation_p.R235H	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	236					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R236H(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTCAAAAGCACGCTCCAGTTC	0.512			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																Dom	yes		2	2q35	5077	paired box gene 3	yes	M	1	Substitution - Missense(1)	ovary(1)	2											159	156	157					2																	223096882		2203	4300	6503	222805126	SO:0001583	missense	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.707G>A	2.37:g.223096882C>T	ENSP00000343052:p.Arg236His		222805126	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	37	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766099	0.90020	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551	D;D;D;D;D;D	0.96459	-4.02;-4.02;-4.02;-4.02;-4.02;-4.02	5.37	5.37	0.77165	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98311	0.9440	M	0.84773	2.715	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.932;0.999;0.987;0.969;0.982	D	0.99267	1.0892	10	0.87932	D	0	.	19.1177	0.93348	0.0:1.0:0.0:0.0	.	236;235;236;236;236	P23760;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.	H	236;236;236;236;236;235	ENSP00000375921:R236H;ENSP00000342092:R236H;ENSP00000343052:R236H;ENSP00000375922:R236H;ENSP00000338767:R236H;ENSP00000386750:R235H	ENSP00000338767:R236H	R	-	2	0	PAX3	222805126	1.000000	0.71417	0.760000	0.31359	0.961000	0.63080	6.089000	0.71384	2.510000	0.84645	0.557000	0.71058	CGT		0.512	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223096882	C	T	223096882	3	4	105	1	0	0	0	0	1	0	0	0	11511	536	19	1	862	1	PAX3	2	223096882	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	2811287	223096882	20102491	36	27676										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242277167	242277167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgtcattgcaaaagctgacActctcaccctgaaggaacgg	9	12	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr2:242277167A>G	ENST00000391973.2	+	7	1084	c.556A>G	c.(556-558)Act>Gct	p.T186A	SEPT2_ENST00000391971.2_Missense_Mutation_p.T186A|SEPT2_ENST00000402092.2_Missense_Mutation_p.T186A|SEPT2_ENST00000401990.1_Missense_Mutation_p.T196A|SEPT2_ENST00000360051.3_Missense_Mutation_p.T186A|SEPT2_ENST00000407971.1_Missense_Mutation_p.T146A	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	186	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		AAAAGCTGACACTCTCACCCT	0.493																																																0			2											81	76	78					2																	242277167		2203	4300	6503	241925840	SO:0001583	missense	23157			D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.556A>G	2.37:g.242277167A>G	ENSP00000375834:p.Thr186Ala		241925840	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Missense_Mutation	SNP	ENST00000391973.2	37	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121609	0.77436	.	.	ENSG00000168385	ENST00000391973;ENST00000428282;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717	T;T;T;T;T;T;T;T	0.79554	1.4;1.4;1.4;1.4;1.4;-1.28;1.4;-1.28	5.23	4.09	0.47781	.	0.098605	0.64402	D	0.000002	T	0.76821	0.4041	L	0.56280	1.765	0.80722	D	1	P;P;B	0.42620	0.561;0.785;0.008	B;B;B	0.42995	0.138;0.404;0.026	T	0.77715	-0.2484	10	0.48119	T	0.1	.	10.4026	0.44239	0.9236:0.0:0.0764:0.0	.	221;146;186	Q15019-2;B5MCX3;Q15019	.;.;SEPT2_HUMAN	A	186;146;186;186;196;146;186;221;41	ENSP00000375834:T186A;ENSP00000397195:T146A;ENSP00000353157:T186A;ENSP00000375832:T186A;ENSP00000385109:T196A;ENSP00000384525:T146A;ENSP00000385172:T186A;ENSP00000408296:T41A	ENSP00000353157:T186A	T	+	1	0	SEPT2	241925840	1.000000	0.71417	0.911000	0.35937	0.982000	0.71751	7.253000	0.78320	1.982000	0.57802	0.533000	0.62120	ACT		0.493	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		G	242277167	A	G	242277167	3	3	105	1	0	0	0	0	1	0	0	0	14101	159	6	4	578	4	SEPT2	2	242277167	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	19180285	242277167	922206	37	27677										
VHL	7428	hgsc.bcm.edu	37	chr3	10188315	10188315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tatttttgccaatatcacacTgccaggtactgacgttttac	6	10	1	1	rs193922611		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:10188315T>C	ENST00000256474.2	+	2	1298	c.458T>C	c.(457-459)cTg>cCg	p.L153P	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	153	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L153P(5)|p.?(2)|p.L153fs*4(1)|p.?fs(1)|p.P154fs*2(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AATATCACACTGCCAGGTACT	0.403		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	11	Substitution - Missense(5)|Deletion - Frameshift(2)|Insertion - Frameshift(2)|Unknown(2)	kidney(11)	3											182	172	175					3																	10188315		2203	4300	6503	10163315	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.458T>C	3.37:g.10188315T>C	ENSP00000256474:p.Leu153Pro		10163315	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.930995	0.73327	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	4.79	4.79	0.61399	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.64402	D	0.000001	D	0.99715	0.9890	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97136	0.9821	10	0.72032	D	0.01	0.5194	12.5822	0.56397	0.0:0.0:0.0:1.0	.	153	P40337	VHL_HUMAN	P	153;71	ENSP00000256474:L153P	ENSP00000256474:L153P	L	+	2	0	VHL	10163315	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.968000	0.70413	1.928000	0.55862	0.460000	0.39030	CTG		0.403	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188315	T	C	10188315	3	2	105	1	0	0	0	0	1	0	0	0	17202	1580	55	4	464	4	VHL	3	10188315	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10		10188315	187834115	38	27678										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19436627	19436627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcatcttctaaagacagtgcGcctcttgcgtcttttgcgtc	9	12	4	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:19436627G>A	ENST00000328405.2	+	7	1267	c.1001G>A	c.(1000-1002)cGc>cAc	p.R334H	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_5'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	334					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAGACAGTGCGCCTCTTGCGT	0.473																																					NSCLC(124;1625 1765 8018 24930 42026)											0			3											179	152	161					3																	19436627		2203	4300	6503	19411631	SO:0001583	missense	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1001G>A	3.37:g.19436627G>A	ENSP00000328813:p.Arg334His		19411631	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397805	0.83120	.	.	ENSG00000183960	ENST00000328405	D	0.99353	-5.77	5.78	5.78	0.91487	Ion transport (1);	0.000000	0.27725	U	0.018106	D	0.99569	0.9845	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.98501	1.0614	9	.	.	.	.	20.0118	0.97458	0.0:0.0:1.0:0.0	.	334;334	B7Z398;Q96L42	.;KCNH8_HUMAN	H	334	ENSP00000328813:R334H	.	R	+	2	0	KCNH8	19411631	1.000000	0.71417	0.545000	0.28153	0.170000	0.22686	9.869000	0.99810	2.742000	0.94016	0.650000	0.86243	CGC		0.473	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		A	19436627	G	A	19436627	3	1	105	1	0	0	0	0	1	0	0	0	8059	1087	38	1	1027	1	KCNH8	3	19436627	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	9248312	19436627	178585803	39	27679										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37514868	37514868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agaatcggggcacgtcctgcGgaaagacctgccgggaagac	15	11	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:37514868G>A	ENST00000264741.5	+	3	593	c.337G>A	c.(337-339)Gga>Aga	p.G113R	ITGA9_ENST00000422441.1_Missense_Mutation_p.G113R	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	113					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CACGTCCTGCGGAAAGACCTG	0.602																																																0			3											58	58	58					3																	37514868		2203	4300	6503	37489872	SO:0001583	missense	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.337G>A	3.37:g.37514868G>A	ENSP00000264741:p.Gly113Arg		37489872	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.024881	0.93518	.	.	ENSG00000144668	ENST00000422441;ENST00000264741	T;T	0.59638	0.25;0.25	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.78528	0.4297	M	0.80422	2.495	0.80722	D	1	P;D	0.89917	0.953;1.0	P;D	0.83275	0.556;0.996	T	0.80668	-0.1280	10	0.72032	D	0.01	.	18.4791	0.90804	0.0:0.0:1.0:0.0	.	113;113	Q13797;E9PDS3	ITA9_HUMAN;.	R	113	ENSP00000397258:G113R;ENSP00000264741:G113R	ENSP00000264741:G113R	G	+	1	0	ITGA9	37489872	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.636000	0.91010	2.642000	0.89623	0.650000	0.86243	GGA		0.602	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		A	37514868	G	A	37514868	3	1	105	1	0	0	0	0	1	0	0	0	7904	1117	39	1	347	1	ITGA9	3	37514868	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	18078241	37514868	160507562	40	27680										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38354566	38354566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agcaggtgctgtgctacgccGcaagtgtgaacaagaagacc	13	10	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:38354566G>A	ENST00000273173.4	+	5	1112	c.1021G>A	c.(1021-1023)Gca>Aca	p.A341T	SLC22A14_ENST00000448498.1_Missense_Mutation_p.A341T	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	341					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		GTGCTACGCCGCAAGTGTGAA	0.602																																																0			3											67	63	64					3																	38354566		2203	4300	6503	38329570	SO:0001583	missense	9389			AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1021G>A	3.37:g.38354566G>A	ENSP00000273173:p.Ala341Thr		38329570	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.391129	0.82902	.	.	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.59364	0.27;0.27	4.14	4.14	0.48551	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.113352	0.64402	D	0.000016	T	0.78691	0.4323	M	0.89353	3.025	0.49798	D	0.999821	D	0.89917	1.0	D	0.87578	0.998	D	0.83462	0.0054	10	0.87932	D	0	.	13.9454	0.64082	0.0:0.0:1.0:0.0	.	341	Q9Y267	S22AE_HUMAN	T	341	ENSP00000396283:A341T;ENSP00000273173:A341T	ENSP00000273173:A341T	A	+	1	0	SLC22A14	38329570	1.000000	0.71417	0.040000	0.18447	0.001000	0.01503	5.784000	0.68990	2.211000	0.71520	0.591000	0.81541	GCA		0.602	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		A	38354566	G	A	38354566	3	1	105	1	0	0	0	0	1	0	0	0	14482	1087	38	1	1039	1	SLC22A14	3	38354566	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	839698	38354566	159667864	41	27681										
SEC22C	9117	hgsc.bcm.edu	37	chr3	42605030	42605030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caaaccaaactcaagaaaagCgtatggcctggaggctaggc	11	10	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:42605030C>T	ENST00000264454.3	-	3	474	c.331G>A	c.(331-333)Gct>Act	p.A111T	SEC22C_ENST00000417572.1_Missense_Mutation_p.A111T|SEC22C_ENST00000423701.2_Missense_Mutation_p.A111T|SEC22C_ENST00000273156.7_Missense_Mutation_p.A111T|SEC22C_ENST00000536332.1_Missense_Mutation_p.A41T|SEC22C_ENST00000493107.1_5'UTR			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	111	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TCAAGAAAAGCGTATGGCCTG	0.453																																																0			3											82	83	83					3																	42605030		2203	4300	6503	42580034	SO:0001583	missense	9117			AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.331G>A	3.37:g.42605030C>T	ENSP00000264454:p.Ala111Thr		42580034	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	37	CCDS2700.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.550359|4.550359	0.86127|0.86127	.|.	.|.	ENSG00000093183|ENSG00000093183	ENST00000423701;ENST00000273156;ENST00000417572;ENST00000536332;ENST00000264454;ENST00000456515;ENST00000450981|ENST00000451653	T;T;T;T;T;T;T|.	0.26373|.	1.74;1.74;1.74;1.74;1.74;1.74;1.74|.	5.58|5.58	4.71|4.71	0.59529|0.59529	Longin (2);Longin-like (1);|.	0.164768|.	0.53938|.	D|.	0.000049|.	T|T	0.66867|0.66867	0.2833|0.2833	M|M	0.76574|0.76574	2.34|2.34	0.41643|0.41643	D|D	0.989085|0.989085	D;D;D;D|.	0.69078|.	0.997;0.996;0.996;0.997|.	P;P;P;P|.	0.55011|.	0.766;0.606;0.726;0.681|.	T|T	0.67654|0.67654	-0.5615|-0.5615	10|5	0.62326|.	D|.	0.03|.	-14.4634|-14.4634	9.356|9.356	0.38166|0.38166	0.1431:0.7842:0.0:0.0727|0.1431:0.7842:0.0:0.0727	.|.	41;111;111;111|.	F5H0H7;Q9BRL7-3;Q9BRL7;Q9BRL7-2|.	.;.;SC22C_HUMAN;.|.	T|H	111;111;111;41;111;111;111|32	ENSP00000414576:A111T;ENSP00000273156:A111T;ENSP00000407564:A111T;ENSP00000439845:A41T;ENSP00000264454:A111T;ENSP00000391170:A111T;ENSP00000397170:A111T|.	ENSP00000264454:A111T|.	A|R	-|-	1|2	0|0	SEC22C|SEC22C	42580034|42580034	0.977000|0.977000	0.34250|0.34250	0.667000|0.667000	0.29798|0.29798	0.993000|0.993000	0.82548|0.82548	2.136000|2.136000	0.42121|0.42121	1.357000|1.357000	0.45904|0.45904	0.585000|0.585000	0.79938|0.79938	GCT|CGC		0.453	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206		T	42605030	C	T	42605030	3	4	105	1	0	0	0	0	1	0	0	0	14027	768	27	1	646	1	SEC22C	3	42605030	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	4250464	42605030	155417400	42	27682										
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50380426	50380426	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggttgtgtgtgctaagcataCggctcaaggtgctgagagag	16	6	1	2	rs368114874		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:50380426C>G	ENST00000231749.3	-	7	1895	c.623G>C	c.(622-624)cGt>cCt	p.R208P	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000488024.1_5'Flank|RASSF1_ENST00000357043.2_5'Flank|ZMYND10_ENST00000490675.1_5'Flank|ZMYND10_ENST00000360165.3_Intron|RASSF1_ENST00000359365.4_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	208					inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCTAAGCATACGGCTCAAGGT	0.632										TSP Lung(30;0.18)																																						0			3											146	133	137					3																	50380426		2203	4300	6503	50355430	SO:0001583	missense	51364			U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"Zinc fingers, MYND-type"	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.623G>C	3.37:g.50380426C>G	ENSP00000231749:p.Arg208Pro		50355430	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732575	0.89482	.	.	ENSG00000004838	ENST00000231749;ENST00000442887	T;T	0.32023	1.47;1.47	5.55	5.55	0.83447	.	0.047666	0.85682	D	0.000000	T	0.62588	0.2440	M	0.90309	3.105	0.80722	D	1	D	0.58268	0.982	P	0.61874	0.895	T	0.70630	-0.4819	10	0.87932	D	0	-17.2735	18.4981	0.90872	0.0:1.0:0.0:0.0	.	208	O75800	ZMY10_HUMAN	P	208;165	ENSP00000231749:R208P;ENSP00000393687:R165P	ENSP00000231749:R208P	R	-	2	0	ZMYND10	50355430	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.289000	0.59013	2.627000	0.88993	0.561000	0.74099	CGT		0.632	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		G	50380426	C	G	50380426	3	3	105	1	0	0	0	0	1	0	0	0	17744	536	19	5	723	5	ZMYND10	3	50380426	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	7775396	50380426	147642004	43	27683										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74419065	74419065	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aagggcaaaacattccaattTcacagtcgaacctttagctg	7	10	1	0	rs62620465	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:74419065T>C	ENST00000263665.6	-	6	763	c.736A>G	c.(736-738)Aaa>Gaa	p.K246E		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	246	Ig-like C2-type 3.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.K246E(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CATTCCAATTTCACAGTCGAA	0.343													T|||	336	0.0670927	0.2428	0.0173	5008	,	,		14582	0		0.003	False		,,,				2504	0															1	Substitution - Missense(1)	breast(1)	3						T	GLU/LYS	871,3535	335.5+/-303.9	94,683,1426	93	95	94		736	2.7	0.9	3	dbSNP_129	94	20,8578	14.6+/-50.1	0,20,4279	yes	missense	CNTN3	NM_020872.1	56	94,703,5705	CC,CT,TT		0.2326,19.7685,6.8517	benign	246/1029	74419065	891,12113	2203	4299	6502	74501755	SO:0001583	missense	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.736A>G	3.37:g.74419065T>C	ENSP00000263665:p.Lys246Glu		74501755	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	122	0.055860805860805864	116	0.23577235772357724	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	17.63	3.438101	0.62955	0.197685	0.002326	ENSG00000113805	ENST00000263665	T	0.65364	-0.15	5.32	2.67	0.31697	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.215941	0.47455	D	0.000232	T	0.00012	0.0000	N	0.10874	0.06	0.31940	P	0.611094	B	0.18610	0.029	B	0.22601	0.04	T	0.08785	-1.0705	9	0.15952	T	0.53	.	11.8081	0.52167	0.0:0.0:0.2777:0.7223	rs62620465	246	Q9P232	CNTN3_HUMAN	E	246	ENSP00000263665:K246E	ENSP00000263665:K246E	K	-	1	0	CNTN3	74501755	1.000000	0.71417	0.878000	0.34440	0.993000	0.82548	5.926000	0.70070	0.917000	0.36895	0.482000	0.46254	AAA		0.343	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		C	74419065	T	C	74419065	3	2	105	1	0	0	0	0	1	0	0	0	3648	1792	62	4	2418	4	CNTN3	3	74419065	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	24038639	74419065	123603365	44	27684										
CGGBP1	8545	hgsc.bcm.edu	37	chr3	88104676	88104676	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attctcatatccatcaggaaGatatgccctccgtagctggt	8	11	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:88104676G>A	ENST00000398392.2	-	1	1783	c.451C>T	c.(451-453)Ctt>Ttt	p.L151F	CGGBP1_ENST00000474441.1_5'Flank|CGGBP1_ENST00000482016.1_Missense_Mutation_p.L151F|CGGBP1_ENST00000309534.6_Missense_Mutation_p.L151F|CGGBP1_ENST00000462901.1_Missense_Mutation_p.L151F			Q9UFW8	CGBP1_HUMAN	CGG triplet repeat binding protein 1	151					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			kidney(1)|large_intestine(2)|lung(2)	5		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)		CCATCAGGAAGATATGCCCTC	0.448																																																0			3											134	126	128					3																	88104676		1948	4161	6109	88187366	SO:0001583	missense	8545			AJ000258	CCDS43111.1	3p12-p11.1	2008-07-18			ENSG00000163320	ENSG00000163320			1888	protein-coding gene	gene with protein product	"p20-CGG binding protein"	603363				9201980, 14667814	Standard	NM_001195308		Approved	p20-CGGBP, CGGBP	uc003dqt.3	Q9UFW8	OTTHUMG00000159009	ENST00000398392.2:c.451C>T	3.37:g.88104676G>A	ENSP00000381429:p.Leu151Phe		88187366	D3DU38|O15183	Missense_Mutation	SNP	ENST00000398392.2	37	CCDS43111.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.568355	0.65651	.	.	ENSG00000163320	ENST00000309534;ENST00000398392;ENST00000482016;ENST00000462901	.	.	.	5.7	5.7	0.88788	.	0.000000	0.31859	U	0.006951	T	0.65481	0.2695	L	0.29908	0.895	0.44221	D	0.997051	D	0.62365	0.991	D	0.65323	0.934	T	0.67440	-0.5670	9	0.66056	D	0.02	-10.8687	17.0533	0.86525	0.0:0.0:1.0:0.0	.	151	Q9UFW8	CGBP1_HUMAN	F	151	.	ENSP00000381428:L151F	L	-	1	0	CGGBP1	88187366	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	3.598000	0.54038	2.711000	0.92665	0.650000	0.86243	CTT		0.448	CGGBP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352955.1	NM_001008390		A	88104676	G	A	88104676	3	1	105	1	0	0	0	0	1	0	0	0	3308	942	33	3	56	3	CGGBP1	3	88104676	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	13685611	88104676	109917754	45	27685										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113187692	113187692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctagagtctcagtagattctTcaggctgaagcctggtttgg	12	8	3	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:113187692T>C	ENST00000295872.4	-	9	1065	c.806A>G	c.(805-807)gAa>gGa	p.E269G		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	269					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						AGTAGATTCTTCAGGCTGAAG	0.418																																																0			3											97	87	90					3																	113187692		2203	4300	6503	114670382	SO:0001583	missense	0			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.806A>G	3.37:g.113187692T>C	ENSP00000295872:p.Glu269Gly		114670382	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.189|9.189	1.025554|1.025554	0.19512|0.19512	.|.	.|.	ENSG00000163611|ENSG00000163611	ENST00000295872|ENST00000467618	T|.	0.36520|.	1.25|.	5.05|5.05	2.6|2.6	0.31112|0.31112	.|.	0.683462|.	0.15173|.	N|.	0.276533|.	T|T	0.59211|0.59211	0.2177|0.2177	M|M	0.64997|0.64997	1.995|1.995	0.35543|0.35543	D|D	0.803208|0.803208	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.11329|.	0.006;0.006|.	T|T	0.61888|0.61888	-0.6970|-0.6970	10|5	0.87932|.	D|.	0|.	-8.2372|-8.2372	6.6621|6.6621	0.23020|0.23020	0.0:0.0789:0.1541:0.767|0.0:0.0789:0.1541:0.767	.|.	165;269|.	B3KX77;Q8N0Z3|.	.;SPICE_HUMAN|.	G|E	269|81	ENSP00000295872:E269G|.	ENSP00000295872:E269G|.	E|K	-|-	2|1	0|0	SPICE1|SPICE1	114670382|114670382	1.000000|1.000000	0.71417|0.71417	0.200000|0.200000	0.23457|0.23457	0.034000|0.034000	0.12701|0.12701	1.748000|1.748000	0.38308|0.38308	0.329000|0.329000	0.23460|0.23460	-0.326000|-0.326000	0.08463|0.08463	GAA|AAG		0.418	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		C	113187692	T	C	113187692	3	2	105	1	0	0	0	0	1	0	0	0	2828	1783	62	4	1801	4	CCDC52	3	113187692	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	25083016	113187692	84834738	46	27686										
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955429	113955429	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtaaaaggtttttccacattCtttgcacccaaagagttttt	6	8	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:113955429C>A	ENST00000482457.2	-	1	996	c.493G>T	c.(493-495)Gaa>Taa	p.E165*	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TTTCCACATTCTTTGCACCCA	0.488																																					GBM(23;986 1114 21716)											0			3											105	109	107					3																	113955429		2203	4300	6503	115438119	SO:0001587	stop_gained	7634			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.493G>T	3.37:g.113955429C>A	ENSP00000417192:p.Glu165*		115438119	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	.	.	.	.	.	.	.	.	.	.	C	37	6.275819	0.97435	.	.	ENSG00000174255	ENST00000482457	.	.	.	3.0	1.14	0.20703	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	5.4355	0.16478	0.1987:0.6838:0.0:0.1175	.	.	.	.	X	165	.	ENSP00000309812:E165X	E	-	1	0	ZNF80	115438119	0.000000	0.05858	0.005000	0.12908	0.342000	0.28953	-1.005000	0.03674	0.289000	0.22422	0.491000	0.48974	GAA		0.488	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		A	113955429	C	A	113955429	4	1	105	1	0	0	0	0	0	1	0	0	18207	922	32	2	332	2	ZNF80	3	113955429	Nonsense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	767737	113955429	84067001	47	27687										
FAIM	55179	hgsc.bcm.edu	37	chr3	138341076	138341076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caaattagtgggcaaagaaaCattctatgttggagctgcaa	10	6	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:138341076C>T	ENST00000393035.2	+	3	267	c.158C>T	c.(157-159)aCa>aTa	p.T53I	FAIM_ENST00000338446.4_Missense_Mutation_p.T87I|FAIM_ENST00000393034.2_Missense_Mutation_p.T53I|FAIM_ENST00000464668.1_Missense_Mutation_p.T53I|FAIM_ENST00000360570.3_Missense_Mutation_p.T75I	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	53					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						GGCAAAGAAACATTCTATGTT	0.318																																																0			3											70	73	72					3																	138341076		2203	4300	6503	139823766	SO:0001583	missense	55179			AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.158C>T	3.37:g.138341076C>T	ENSP00000376755:p.Thr53Ile		139823766	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485329	0.63962	.	.	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15;1.15	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	M	0.73217	2.22	0.80722	D	1	B;P;P;B	0.36683	0.164;0.565;0.565;0.02	B;B;B;B	0.36335	0.22;0.222;0.222;0.055	T	0.29027	-1.0025	10	0.41790	T	0.15	-3.3881	18.0409	0.89318	0.0:1.0:0.0:0.0	.	53;75;87;53	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	I	87;75;53;53;53;53	ENSP00000342805:T87I;ENSP00000353775:T75I;ENSP00000376755:T53I;ENSP00000376754:T53I;ENSP00000417642:T53I;ENSP00000420543:T53I	ENSP00000342805:T87I	T	+	2	0	FAIM	139823766	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	6.056000	0.71111	2.850000	0.98022	0.650000	0.86243	ACA		0.318	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032		T	138341076	C	T	138341076	3	4	105	1	0	0	0	0	1	0	0	0	5391	478	17	3	318	3	FAIM	3	138341076	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	24385647	138341076	59681354	48	27688										
C3orf72	401089	hgsc.bcm.edu	37	chr3	138668423	138668423	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	accctgggaagggctggaatCggtctccccaagatgtgcct	13	12	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:138668423C>T	ENST00000383165.3	+	2	293	c.162C>T	c.(160-162)atC>atT	p.I54I	FOXL2_ENST00000330315.3_5'Flank	NM_001040061.2	NP_001035150.1	Q6ZUU3	FOXNB_HUMAN		54										large_intestine(1)|lung(3)	4						GGGCTGGAATCGGTCTCCCCA	0.527																																																0			3											76	81	80					3																	138668423		1949	4154	6103	140151113	SO:0001819	synonymous_variant	401089																														ENST00000383165.3:c.162C>T	3.37:g.138668423C>T			140151113	A6NGX0	Silent	SNP	ENST00000383165.3	37	CCDS43155.1																																																																																				0.527	C3orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357986.1			T	138668423	C	T	138668423	2	4	105	1	0	0	0	0	0	0	0	1	2250	874	31	1		1	C3orf72	3	138668423	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	327347	138668423	59354007	49	27689										
PAQR9	344838	hgsc.bcm.edu	37	chr3	142681549	142681549	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gccacaggcagcaccagggcGcggtaggcggcgataaggcg	18	12	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:142681549G>A	ENST00000340634.3	-	1	629	c.630C>T	c.(628-630)cgC>cgT	p.R210R	RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	210						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						GCACCAGGGCGCGGTAGGCGG	0.657																																																0			3											38	36	37					3																	142681549		2203	4299	6502	144164239	SO:0001819	synonymous_variant	344838			AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.630C>T	3.37:g.142681549G>A			144164239	Q147T6	Silent	SNP	ENST00000340634.3	37	CCDS3128.1																																																																																				0.657	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		A	142681549	G	A	142681549	2	1	105	1	0	0	0	0	0	0	0	1	11473	1074	38	1		1	PAQR9	3	142681549	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	4013126	142681549	55340881	50	27690										
CP	1356	hgsc.bcm.edu	37	chr3	148930325	148930325	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	taagtgtacataaactttatCtccagtttcagctttgataa	5	7	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:148930325C>A	ENST00000264613.6	-	2	569	c.307G>T	c.(307-309)Gat>Tat	p.D103Y		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	103	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TAAACTTTATCTCCAGTTTCA	0.398																																																0			3											119	120	119					3																	148930325		2203	4300	6503	150413015	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.307G>T	3.37:g.148930325C>A	ENSP00000264613:p.Asp103Tyr		150413015	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860375	0.71834	.	.	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99454	-5.92;-5.92	5.42	4.54	0.55810	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.099520	0.64402	D	0.000002	D	0.99753	0.9901	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96833	0.9612	10	0.87932	D	0	-26.4056	16.315	0.82915	0.0:0.8676:0.1324:0.0	.	103;103	A8K5A4;P00450	.;CERU_HUMAN	Y	103;143	ENSP00000264613:D103Y;ENSP00000426888:D143Y	ENSP00000264613:D103Y	D	-	1	0	CP	150413015	1.000000	0.71417	0.990000	0.47175	0.982000	0.71751	7.320000	0.79064	1.513000	0.48852	-0.300000	0.09419	GAT		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148930325	C	A	148930325	3	1	105	1	0	0	0	0	1	0	0	0	3793	913	32	2	2962	2	CP	3	148930325	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	6248776	148930325	49092105	51	27691										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157004361	157004361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcaccagttgctttctcagGattgttgcacatgaagcatt	8	10	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:157004361G>T	ENST00000362010.2	-	12	2420	c.2113C>A	c.(2113-2115)Cct>Act	p.P705T	RP11-550I24.2_ENST00000487238.1_RNA|RP11-550I24.2_ENST00000488040.1_RNA|VEPH1_ENST00000392832.2_Missense_Mutation_p.P705T|RP11-550I24.2_ENST00000494885.1_RNA|VEPH1_ENST00000543418.1_Missense_Mutation_p.P660T|RP11-550I24.2_ENST00000475102.1_RNA|VEPH1_ENST00000392833.2_Missense_Mutation_p.P660T	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	705						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GCTTTCTCAGGATTGTTGCAC	0.488																																																0			3											225	209	214					3																	157004361		2203	4300	6503	158487055	SO:0001583	missense	79674			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.2113C>A	3.37:g.157004361G>T	ENSP00000354919:p.Pro705Thr		158487055	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454115	0.84209	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.56941	2.4;0.43;2.4;0.43	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.73401	0.3582	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.74965	-0.3484	10	0.87932	D	0	-11.9826	18.8102	0.92054	0.0:0.0:1.0:0.0	.	660;705	Q14D04-2;Q14D04	.;MELT_HUMAN	T	660;705;660;705	ENSP00000376578:P660T;ENSP00000354919:P705T;ENSP00000446258:P660T;ENSP00000376577:P705T	ENSP00000354919:P705T	P	-	1	0	VEPH1	158487055	1.000000	0.71417	0.995000	0.50966	0.925000	0.55904	8.811000	0.91954	2.738000	0.93877	0.637000	0.83480	CCT		0.488	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		T	157004361	G	T	157004361	3	4	105	1	0	0	0	0	1	0	0	0	17194	1174	41	2	400	2	VEPH1	3	157004361	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	8074036	157004361	41018069	52	27692										
PRKCI	5584	hgsc.bcm.edu	37	chr3	170009728	170009728	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attttaagaggagaagattaTggtaataaataaattggtgg	11	0	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:170009728T>C	ENST00000295797.4	+	13	1595	c.1290T>C	c.(1288-1290)taT>taC	p.Y430Y		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	430	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	GAGAAGATTATGGTAATAAAT	0.348																																																0			3											42	43	42					3																	170009728		2203	4298	6501	171492422	SO:0001630	splice_region_variant	5584				CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1291+1T>C	3.37:g.170009728T>C			171492422	D3DNQ4|Q8WW06	Silent	SNP	ENST00000295797.4	37	CCDS3212.2																																																																																				0.348	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740	Silent	C	170009728	T	C	170009728	5	2	105	1	0	0	0	0	0	0	1	0	12548	1478	51	4	1340	4	PRKCI	3	170009728	Splice_Site	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	13005367	170009728	28012702	53	27693										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936072	178936072	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aaagcaatttctacacgagaTcctctctctgaaatcactga	5	11	4	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:178936072T>C	ENST00000263967.3	+	10	1771	c.1614T>C	c.(1612-1614)gaT>gaC	p.D538D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	538	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTACACGAGATCCTCTCTCTG	0.328		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											52	52	52					3																	178936072		1806	4068	5874	180418766	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1614T>C	3.37:g.178936072T>C			180418766	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.328	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178936072	T	C	178936072	2	2	105	1	0	0	0	0	0	0	0	1	11944	1432	50	4		4	PIK3CA	3	178936072	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	8926344	178936072	19086358	54	27694										
HRG	3273	hgsc.bcm.edu	37	chr3	186395001	186395001	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gacccccacctcctccagatGaaagagatcactcacatgga	7	15	2	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr3:186395001G>A	ENST00000232003.4	+	7	987	c.907G>A	c.(907-909)Gaa>Aaa	p.E303K		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	303	Pro-rich.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TCCTCCAGATGAAAGAGATCA	0.527																																																0			3											209	170	184					3																	186395001		2203	4300	6503	187877695	SO:0001583	missense	3273				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.907G>A	3.37:g.186395001G>A	ENSP00000232003:p.Glu303Lys		187877695	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	G	0.652	-0.808978	0.02819	.	.	ENSG00000113905	ENST00000232003	T	0.20332	2.08	3.76	1.92	0.25849	.	1.401000	0.04631	N	0.403727	T	0.11410	0.0278	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29366	-1.0014	10	0.08381	T	0.77	2.1006	5.4632	0.16627	0.1138:0.203:0.6831:0.0	.	303	P04196	HRG_HUMAN	K	303	ENSP00000232003:E303K	ENSP00000232003:E303K	E	+	1	0	HRG	187877695	0.007000	0.16637	0.004000	0.12327	0.001000	0.01503	1.745000	0.38278	0.401000	0.25424	-0.226000	0.12346	GAA		0.527	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		A	186395001	G	A	186395001	3	1	105	1	0	0	0	0	1	0	0	0	7375	1291	45	3	933	3	HRG	3	186395001	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	7458929	186395001	11627429	55	27695										
FGFRL1	53834	hgsc.bcm.edu	37	chr4	1018763	1018763	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgccgtggcccgtggtcatCggcatcccagccggcgctgt	14	16	1	0	rs146112374		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:1018763C>T	ENST00000398484.2	+	8	1723	c.1143C>T	c.(1141-1143)atC>atT	p.I381I	FGFRL1_ENST00000264748.6_Silent_p.I381I|FGFRL1_ENST00000504138.1_Silent_p.I381I|RP11-460I19.2_ENST00000503095.1_lincRNA|FGFRL1_ENST00000510644.1_Silent_p.I381I			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	381					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCGTGGTCATCGGCATCCCAG	0.682																																																0			4							,,	0,4398		0,0,2199	24	28	27		1143,1143,1143	-6.7	0.7	4	dbSNP_134	27	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	,,	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	,,	381/505,381/505,381/505	1018763	1,12991	2199	4297	6496	1008763	SO:0001819	synonymous_variant	53834				CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"Immunoglobulin superfamily / I-set domain containing"	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.1143C>T	4.37:g.1018763C>T			1008763	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Silent	SNP	ENST00000398484.2	37	CCDS3344.1																																																																																				0.682	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923		T	1018763	C	T	1018763	2	4	105	1	0	0	0	0	0	0	0	1	5888	874	31	1		1	FGFRL1	4	1018763	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		1018763	190135513	56	27696										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389220	1389248	+	Frame_Shift_Del	DEL	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cctgctcacacgtgccgacgTggagtgcccgcctgctcacg					rs1140009|rs200438890|rs141376932|rs550271289|rs150174653|rs145563943|rs547759244	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TGGAGTGCCCGCCTGCTCACGTGCCCATA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENST00000324803.4	+	1	3881_3909	c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	c.(919-951)cgtggagtgcccgcctgctcacgtgcccatatgfs	p.GVPACSRAHM308fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	308					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P310fs*95(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCGACGTGGAGTGCCCGCCTGCTCACGTGCCCATATGGAGTGCCC	0.668																																																1	Deletion - Frameshift(1)	prostate(1)	4								1378,2876		542,294,1291						0.8	0			153	3662,4580		1557,548,2016	no	frameshift	CRIPAK	NM_175918.3		2099,842,3307	A1A1,A1R,RR		44.431,32.393,40.3329				5040,7456				1379248	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.921_949delTGGAGTGCCCGCCTGCTCACGTGCCCATA	4.37:g.1389220_1389248delTGGAGTGCCCGCCTGCTCACGTGCCCATA	ENSP00000323978:p.Gly308fs		1379220	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.668	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1389248	TGGAGTGCCCGCCTGCTCACGTGCCCATA	-	1389220	7	5	105	1	0	1	0	1	0	0	0	0	3883	1683	59	0	923	0	CRIPAK	4	1389220	Frame_Shift_Del	DEL	TGGAGTGCCCGCCTGCTCACGTGCCCATA	TCGA-DY-A1DD-01A-21D-A152-10	370457	1389220	189765056	57	27697										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1902850	1902850	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atgtgtctcagtcagaagaaAatggacaaaaaccagaaaac	8	7	2	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:1902850A>T	ENST00000382895.3	+	4	900	c.469A>T	c.(469-471)Aat>Tat	p.N157Y	WHSC1_ENST00000514045.1_Missense_Mutation_p.N157Y|WHSC1_ENST00000436793.1_Missense_Mutation_p.N157Y|WHSC1_ENST00000503128.1_Missense_Mutation_p.N157Y|WHSC1_ENST00000398261.1_Missense_Mutation_p.N157Y|WHSC1_ENST00000508803.1_Missense_Mutation_p.N157Y|WHSC1_ENST00000382892.2_Missense_Mutation_p.N157Y|WHSC1_ENST00000420906.2_Missense_Mutation_p.N157Y|WHSC1_ENST00000382891.5_Missense_Mutation_p.N157Y	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	157					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GTCAGAAGAAAATGGACAAAA	0.438			T	IGH@	MM																																		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	0			4											67	64	65					4																	1902850		2203	4300	6503	1872648	SO:0001583	missense	7468			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.469A>T	4.37:g.1902850A>T	ENSP00000372351:p.Asn157Tyr		1872648	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187421	0.38609	.	.	ENSG00000109685	ENST00000508803;ENST00000514045;ENST00000515806;ENST00000382891;ENST00000382892;ENST00000436793;ENST00000420906;ENST00000382895;ENST00000503128;ENST00000509115;ENST00000398261	D;T;T;D;D;T;T;D;T;T;T	0.95103	-3.61;1.2;0.87;-3.61;-3.61;0.88;1.2;-3.61;1.19;1.2;1.19	4.94	-0.492	0.12041	.	0.543896	0.17644	N	0.166911	D	0.92672	0.7671	L	0.40543	1.245	0.24426	N	0.994594	D;P;P;D;D	0.54047	0.964;0.923;0.874;0.964;0.964	P;P;B;P;P	0.56751	0.805;0.521;0.176;0.805;0.805	D	0.85832	0.1392	10	0.66056	D	0.02	.	5.5807	0.17248	0.639:0.1331:0.2279:0.0	.	157;157;157;157;157	O96028-3;O96028-7;O96028;O96028-5;O96028-6	.;.;NSD2_HUMAN;.;.	Y	157	ENSP00000423972:N157Y;ENSP00000421681:N157Y;ENSP00000427434:N157Y;ENSP00000372347:N157Y;ENSP00000372348:N157Y;ENSP00000416725:N157Y;ENSP00000399251:N157Y;ENSP00000372351:N157Y;ENSP00000425761:N157Y;ENSP00000422878:N157Y;ENSP00000381311:N157Y	ENSP00000308780:N157Y	N	+	1	0	WHSC1	1872648	0.997000	0.39634	0.021000	0.16686	0.991000	0.79684	2.031000	0.41117	-0.208000	0.10171	0.533000	0.62120	AAT		0.438	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		T	1902850	A	T	1902850	3	4	105	1	0	0	0	0	1	0	0	0	17402	14	1	5	471	5	WHSC1	4	1902850	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	513630	1902850	189251426	58	27698										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10446086	10446086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atcattagtgttgttagtccTttcagaattctttaattcca	5	7	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:10446086T>C	ENST00000326756.3	-	3	2305	c.1867A>G	c.(1867-1869)Agg>Ggg	p.R623G		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	623					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						TTGTTAGTCCTTTCAGAATTC	0.398																																																0			4											137	138	137					4																	10446086		2203	4300	6503	10055184	SO:0001583	missense	85460			AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1867A>G	4.37:g.10446086T>C	ENSP00000317614:p.Arg623Gly		10055184	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.198735	0.38806	.	.	ENSG00000178163	ENST00000326756	T	0.01527	4.8	6.06	3.64	0.41730	.	0.964866	0.08541	N	0.930553	T	0.01387	0.0045	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47341	-0.9125	10	0.11485	T	0.65	-8.0171	8.022	0.30415	0.0:0.0699:0.1379:0.7922	.	623	Q9C0D4	Z518B_HUMAN	G	623	ENSP00000317614:R623G	ENSP00000317614:R623G	R	-	1	2	ZNF518B	10055184	0.934000	0.31675	0.002000	0.10522	0.324000	0.28378	2.493000	0.45320	1.096000	0.41439	0.533000	0.62120	AGG		0.398	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		C	10446086	T	C	10446086	3	2	105	1	0	0	0	0	1	0	0	0	18002	1608	56	4	1361	4	ZNF518B	4	10446086	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	8543236	10446086	180708190	59	27699										
RFC1	5981	hgsc.bcm.edu	37	chr4	39291552	39291552	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tttaattcttcattgtattcCgaatccagggatgggcttgt	9	7	2	0	rs201096166		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:39291552C>T	ENST00000381897.1	-	24	3412	c.3279G>A	c.(3277-3279)tcG>tcA	p.S1093S	RFC1_ENST00000349703.2_Silent_p.S1092S	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	1093					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.S1093S(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CATTGTATTCCGAATCCAGGG	0.408													C|||	1	0.000199681	0	0.0014	5008	,	,		18411	0		0	False		,,,				2504	0				Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											1	Substitution - coding silent(1)	lung(1)	4											232	227	229					4																	39291552		2203	4300	6503	38967947	SO:0001819	synonymous_variant	6573			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.3279G>A	4.37:g.39291552C>T			38967947	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	0.137	-1.106385	0.01828	.	.	ENSG00000035928	ENST00000514572	.	.	.	5.83	-1.19	0.09585	.	.	.	.	.	T	0.40067	0.1102	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29518	-1.0009	4	.	.	.	-2.8882	1.5395	0.02552	0.3434:0.2867:0.0819:0.2879	.	.	.	.	R	70	.	.	G	-	1	0	RFC1	38967947	0.369000	0.25039	0.905000	0.35620	0.002000	0.02628	-0.254000	0.08781	0.104000	0.17725	-0.397000	0.06425	GGA		0.408	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39291552	C	T	39291552	2	4	105	1	0	0	0	0	0	0	0	1	13281	639	23	1		1	RFC1	4	39291552	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	28845466	39291552	151862724	60	27700										
KIT	3815	hgsc.bcm.edu	37	chr4	55569914	55569915	+	Frame_Shift_Ins	INS	-	-	G													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	actacaggagaaatataataINSgctggcatcacggtgacttc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:55569914_55569915insG	ENST00000288135.5	+	5	878_879	c.781_782insG	c.(781-783)agcfs	p.S261fs		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	261	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAAATATAATAGCTGGCATCAC	0.342		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4																																								55264672	SO:0001589	frameshift_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.782dupG	4.37:g.55569915_55569915dupG	ENSP00000288135:p.Ser261fs		55264671	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Frame_Shift_Ins	INS	ENST00000288135.5	37	CCDS3496.1																																																																																				0.342	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55569915	-	G	55569914	7	5	105	1	0	1	1	0	0	0	0	0	8350	420	15	0	799	0	KIT	4	55569914	Frame_Shift_Ins	INS	-	TCGA-DY-A1DD-01A-21D-A152-10	16278362	55569914	135584362	61	27701										
AASDH	132949	hgsc.bcm.edu	37	chr4	57217540	57217540	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgtaatttttcccaaaggtCctctttcccactgagcttat	5	12	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:57217540C>T	ENST00000205214.6	-	10	1840	c.1660G>A	c.(1660-1662)Gac>Aac	p.D554N	AASDH_ENST00000513376.1_Missense_Mutation_p.D454N|AASDH_ENST00000434343.2_Missense_Mutation_p.D69N|AASDH_ENST00000451613.1_Missense_Mutation_p.D554N|AASDH_ENST00000602986.1_Missense_Mutation_p.D401N|AASDH_ENST00000502617.1_Missense_Mutation_p.D554N	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	554					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TCCCAAAGGTCCTCTTTCCCA	0.279																																																0			4											53	59	57					4																	57217540		2199	4273	6472	56912297	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1660G>A	4.37:g.57217540C>T	ENSP00000205214:p.Asp554Asn		56912297	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049041	0.55110	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.65549	-0.16;-0.02;2.11;0.43;0.43	5.35	3.49	0.39957	Acyl carrier protein-like (1);	0.557597	0.21936	N	0.066942	T	0.46737	0.1408	N	0.14661	0.345	0.31572	N	0.656161	B;B;B;B	0.21821	0.061;0.045;0.045;0.012	B;B;B;B	0.20767	0.027;0.031;0.019;0.004	T	0.55198	-0.8178	10	0.54805	T	0.06	-9.1322	15.6361	0.76953	0.0:0.7409:0.2591:0.0	.	401;554;554;554	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	N	554;454;69;554;401;554	ENSP00000205214:D554N;ENSP00000423760:D454N;ENSP00000392158:D69N;ENSP00000409656:D554N;ENSP00000421171:D554N	ENSP00000205214:D554N	D	-	1	0	AASDH	56912297	0.995000	0.38212	1.000000	0.80357	0.977000	0.68977	2.959000	0.49153	1.385000	0.46445	0.591000	0.81541	GAC		0.279	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57217540	C	T	57217540	3	4	105	1	0	0	0	0	1	0	0	0	22	855	30	3	1660	3	AASDH	4	57217540	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	1647626	57217540	133936736	62	27702										
NAAA	27163	hgsc.bcm.edu	37	chr4	76841113	76841113	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgtcctgtagcattaagggcCttgatggcagatgttctgta	12	7	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:76841113C>A	ENST00000286733.4	-	8	1019	c.918G>T	c.(916-918)aaG>aaT	p.K306N	NAAA_ENST00000505594.1_Missense_Mutation_p.K205N|NAAA_ENST00000511606.1_5'UTR|NAAA_ENST00000507956.1_Missense_Mutation_p.K306N|NAAA_ENST00000399497.3_Missense_Mutation_p.K306N	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	306					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						CATTAAGGGCCTTGATGGCAG	0.473																																																0			4											170	175	173					4																	76841113		2007	4168	6175	77060137	SO:0001583	missense	27163			M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.918G>T	4.37:g.76841113C>A	ENSP00000286733:p.Lys306Asn		77060137	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	37	CCDS43239.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.41|16.41	3.115620|3.115620	0.56505|0.56505	.|.	.|.	ENSG00000138744|ENSG00000138744	ENST00000513045|ENST00000399497;ENST00000286733;ENST00000507956;ENST00000505594	.|T;T;T;T	.|0.80123	.|-0.47;-0.32;-0.47;-1.34	5.59|5.59	3.27|3.27	0.37495|0.37495	.|.	.|0.264908	.|0.41938	.|D	.|0.000796	T|T	0.79341|0.79341	0.4429|0.4429	L|L	0.60957|0.60957	1.885|1.885	0.43417|0.43417	D|D	0.995563|0.995563	.|P;P	.|0.49635	.|0.875;0.926	.|P;P	.|0.52646	.|0.46;0.705	T|T	0.74794|0.74794	-0.3544|-0.3544	5|10	.|0.30854	.|T	.|0.27	-18.4115|-18.4115	4.8694|4.8694	0.13625|0.13625	0.0:0.3866:0.0:0.6133|0.0:0.3866:0.0:0.6133	.|.	.|205;306	.|B4DVL2;Q02083	.|.;NAAA_HUMAN	C|N	111|306;306;306;205	.|ENSP00000382420:K306N;ENSP00000286733:K306N;ENSP00000427641:K306N;ENSP00000426977:K205N	.|ENSP00000286733:K306N	G|K	-|-	1|3	0|2	NAAA|NAAA	77060137|77060137	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.618000|0.618000	0.37518|0.37518	1.656000|1.656000	0.37355|0.37355	0.967000|0.967000	0.38186|0.38186	-0.302000|-0.302000	0.09304|0.09304	GGC|AAG		0.473	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4			A	76841113	C	A	76841113	3	1	105	1	0	0	0	0	1	0	0	0	10157	680	24	2	180	2	NAAA	4	76841113	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	19623573	76841113	114313163	63	27703										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85626556	85626556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aagttccttaccattaggatCctcccagtctttataccgct	5	13	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:85626556C>T	ENST00000295888.4	-	54	8733	c.8326G>A	c.(8326-8328)Gat>Aat	p.D2776N	WDFY3_ENST00000322366.6_Missense_Mutation_p.D2759N	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2776	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CCATTAGGATCCTCCCAGTCT	0.408																																																0			4											224	198	207					4																	85626556		2203	4300	6503	85845580	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.8326G>A	4.37:g.85626556C>T	ENSP00000295888:p.Asp2776Asn		85845580	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118524	0.94385	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.64438	-0.1;-0.1;-0.1	5.64	5.64	0.86602	BEACH domain (4);	0.000000	0.85682	D	0.000000	T	0.79770	0.4503	M	0.72353	2.195	0.80722	D	1	D	0.69078	0.997	D	0.76575	0.988	T	0.80209	-0.1477	10	0.87932	D	0	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2776	Q8IZQ1	WDFY3_HUMAN	N	2759;2776;379	ENSP00000318466:D2759N;ENSP00000295888:D2776N;ENSP00000424987:D379N	ENSP00000295888:D2776N	D	-	1	0	WDFY3	85845580	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.564000	0.82326	2.937000	0.99478	0.650000	0.86243	GAT		0.408	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85626556	C	T	85626556	3	4	105	1	0	0	0	0	1	0	0	0	17310	855	30	3	2314	3	WDFY3	4	85626556	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8785443	85626556	105527720	64	27704										
CENPE	1062	hgsc.bcm.edu	37	chr4	104065688	104065688	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggtctcaaattgctccttcaAgtgttctatttcacacattt	5	10	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:104065688A>G	ENST00000265148.3	-	33	5034	c.4945T>C	c.(4945-4947)Ttg>Ctg	p.L1649L	CENPE_ENST00000380026.3_Silent_p.L1624L	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1649					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.L1649L(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGCTCCTTCAAGTGTTCTATT	0.343																																																1	Substitution - coding silent(1)	ovary(1)	4											118	113	115					4																	104065688		2203	4299	6502	104285137	SO:0001819	synonymous_variant	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4945T>C	4.37:g.104065688A>G			104285137	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																				0.343	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	104065688	A	G	104065688	2	3	105	1	0	0	0	0	0	0	0	1	3236	69	3	4		4	CENPE	4	104065688	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	18439132	104065688	87088588	65	27705										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005715	118005715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atcaggattccgattctgcgAtccagccaggtgaaacccaa	9	12	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:118005715A>G	ENST00000310754.4	-	1	1021	c.835T>C	c.(835-837)Tcg>Ccg	p.S279P		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	279	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						CGATTCTGCGATCCAGCCAGG	0.458																																																0			4											82	74	77					4																	118005715		2203	4300	6503	118225163	SO:0001583	missense	133022			AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.835T>C	4.37:g.118005715A>G	ENSP00000309402:p.Ser279Pro		118225163	Q8N2L7	Missense_Mutation	SNP	ENST00000310754.4	37	CCDS3707.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314349	0.23908	.	.	ENSG00000174599	ENST00000310754	D	0.84873	-1.91	3.37	1.29	0.21616	TRAM/LAG1/CLN8 homology domain (3);	0.875430	0.09906	N	0.740465	T	0.80844	0.4701	N	0.24115	0.695	0.09310	N	1	B	0.32071	0.355	B	0.43838	0.433	T	0.71213	-0.4659	10	0.46703	T	0.11	-20.573	9.2283	0.37421	0.4738:0.5262:0.0:0.0	.	279	Q8N609	TR1L1_HUMAN	P	279	ENSP00000309402:S279P	ENSP00000309402:S279P	S	-	1	0	TRAM1L1	118225163	0.003000	0.15002	0.000000	0.03702	0.430000	0.31655	0.534000	0.23098	0.301000	0.22738	0.528000	0.53228	TCG		0.458	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		G	118005715	A	G	118005715	3	3	105	1	0	0	0	0	1	0	0	0	16492	333	12	4	278	4	TRAM1L1	4	118005715	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	13940027	118005715	73148561	66	27706										
FAT4	79633	hgsc.bcm.edu	37	chr4	126238184	126238184	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgcatctggtgtccaagggCggactggaccgtgaggtcac	15	11	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:126238184C>A	ENST00000394329.3	+	1	631	c.618C>A	c.(616-618)ggC>ggA	p.G206G		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	206	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGTCCAAGGGCGGACTGGACC	0.637											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4											43	50	48					4																	126238184		2100	4225	6325	126457634	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.618C>A	4.37:g.126238184C>A		1548	126457634	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.637	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126238184	C	A	126238184	2	1	105	1	0	0	0	0	0	0	0	1	5711	755	27	2		2	FAT4	4	126238184	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8232469	126238184	64916092	67	27707										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148800446	148800446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtatcgaaaagcagcaaagaAgttcaacatgatcccatttg	8	8	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:148800446A>G	ENST00000336498.3	+	9	1135	c.896A>G	c.(895-897)aAg>aGg	p.K299R	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GCAGCAAAGAAGTTCAACATG	0.393																																																0			4											154	146	149					4																	148800446		2203	4300	6503	149019896	SO:0001583	missense	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.896A>G	4.37:g.148800446A>G	ENSP00000336923:p.Lys299Arg		149019896	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	37	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	A	8.749	0.920871	0.17982	.	.	ENSG00000071205	ENST00000336498	T	0.42513	0.97	5.1	3.86	0.44501	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.228786	0.47455	N	0.000240	T	0.25680	0.0625	L	0.31065	0.9	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06698	-1.0812	10	0.18710	T	0.47	.	5.7181	0.17972	0.7384:0.1637:0.0979:0.0	.	299	A1A4S6	RHG10_HUMAN	R	299	ENSP00000336923:K299R	ENSP00000336923:K299R	K	+	2	0	ARHGAP10	149019896	0.995000	0.38212	0.999000	0.59377	0.990000	0.78478	1.641000	0.37197	0.716000	0.32124	0.459000	0.35465	AAG		0.393	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		G	148800446	A	G	148800446	3	3	105	1	0	0	0	0	1	0	0	0	862	72	3	4	930	4	ARHGAP10	4	148800446	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	22562262	148800446	42353830	68	27708										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153244078	153244078	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agcaccagcagcttggtttcTtcagtcccattccgactccc	7	16	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:153244078T>C	ENST00000281708.4	-	12	3308	c.2079A>G	c.(2077-2079)gaA>gaG	p.E693E	FBXW7_ENST00000603548.1_Silent_p.E693E|FBXW7_ENST00000263981.5_Silent_p.E613E|FBXW7_ENST00000603841.1_Silent_p.E693E|FBXW7_ENST00000296555.5_Silent_p.E575E|RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000393956.3_Silent_p.E517E	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	693					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GCTTGGTTTCTTCAGTCCCAT	0.502			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											163	159	160					4																	153244078		2203	4300	6503	153463528	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.2079A>G	4.37:g.153244078T>C			153463528	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.502	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153244078	T	C	153244078	2	2	105	1	0	0	0	0	0	0	0	1	5788	1606	56	4		4	FBXW7	4	153244078	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	4443632	153244078	37910198	69	27709										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156638344	156638344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcgatgcctattgtgtagctGggggattacacaaagagagt	14	6	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr4:156638344G>T	ENST00000296518.7	+	8	1815	c.1606G>T	c.(1606-1608)Ggg>Tgg	p.G536W	GUCY1A3_ENST00000455639.2_Missense_Mutation_p.G536W|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.G536W|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.G278W|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.G536W|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.G536W|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.G536W			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	536	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TTGTGTAGCTGGGGGATTACA	0.438																																																0			4											157	148	151					4																	156638344		2203	4300	6503	156857794	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1606G>T	4.37:g.156638344G>T	ENSP00000296518:p.Gly536Trp		156857794	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015415	0.93404	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81	5.64	5.64	0.86602	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.64402	D	0.000006	D	0.95322	0.8482	H	0.96175	3.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96360	0.9265	10	0.87932	D	0	.	19.6996	0.96048	0.0:0.0:1.0:0.0	.	536;536	B3KU69;Q02108	.;GCYA3_HUMAN	W	536;536;536;536;278;536;536	ENSP00000424361:G536W;ENSP00000421493:G536W;ENSP00000426968:G536W;ENSP00000412201:G536W;ENSP00000377418:G278W;ENSP00000296518:G536W;ENSP00000426040:G536W	ENSP00000296518:G536W	G	+	1	0	GUCY1A3	156857794	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	9.835000	0.99442	2.646000	0.89796	0.655000	0.94253	GGG		0.438	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156638344	G	T	156638344	3	4	105	1	0	0	0	0	1	0	0	0	6915	1348	47	2	1643	2	GUCY1A3	4	156638344	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	3394266	156638344	34515932	70	27710										
TAS2R1	50834	hgsc.bcm.edu	37	chr5	9629599	9629599	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ataagcaatggcactgagaaCtcagcaacaaaagagaaaat	8	7	1	2	rs371368242		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:9629599C>T	ENST00000382492.2	-	1	864	c.546G>A	c.(544-546)gaG>gaA	p.E182E	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	182					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						GCACTGAGAACTCAGCAACAA	0.428																																																0			5						C		0,4406		0,0,2203	74	82	79		546	-2.1	0	5		79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TAS2R1	NM_019599.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		182/300	9629599	1,13005	2203	4300	6503	9682599	SO:0001819	synonymous_variant	50834			AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.546G>A	5.37:g.9629599C>T			9682599	Q646G8	Silent	SNP	ENST00000382492.2	37	CCDS3876.1																																																																																				0.428	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			T	9629599	C	T	9629599	2	4	105	1	0	0	0	0	0	0	0	1	15604	564	20	3		3	TAS2R1	5	9629599	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		9629599	171285661	71	27711										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33577194	33577194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttgggtttccttgtcacatcGcaaggttcatcatggttctt	9	9	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:33577194G>A	ENST00000504830.1	-	19	3272	c.2937C>T	c.(2935-2937)tgC>tgT	p.C979C	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Silent_p.C894C	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	979	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.C979C(2)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TTGTCACATCGCAAGGTTCAT	0.507										HNSCC(64;0.19)																																						2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	5											129	123	125					5																	33577194		2203	4300	6503	33612951	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2937C>T	5.37:g.33577194G>A			33612951	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33577194	G	A	33577194	2	1	105	1	0	0	0	0	0	0	0	1	257	1079	38	1		1	ADAMTS12	5	33577194	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	23947595	33577194	147338066	72	27712										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33643573	33643573	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caccacagtgtctggcagacGttctagaaaacaaattgcac	8	11	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:33643573G>A	ENST00000504830.1	-	10	1817	c.1482C>T	c.(1480-1482)aaC>aaT	p.N494N	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Silent_p.N494N	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	494	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.N494K(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCTGGCAGACGTTCTAGAAAA	0.443										HNSCC(64;0.19)																																						1	Substitution - Missense(1)	ovary(1)	5											111	114	113					5																	33643573		2203	4300	6503	33679330	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1482C>T	5.37:g.33643573G>A			33679330	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.443	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33643573	G	A	33643573	2	1	105	1	0	0	0	0	0	0	0	1	257	1136	40	1		1	ADAMTS12	5	33643573	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	66379	33643573	147271687	73	27713										
AGGF1	55109	hgsc.bcm.edu	37	chr5	76355533	76355533	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caggttggaagtgaaggaacTttccaaagagatgatgctcc	12	7	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:76355533T>A	ENST00000312916.7	+	12	2191	c.1809T>A	c.(1807-1809)acT>acA	p.T603T		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	603					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		GTGAAGGAACTTTCCAAAGAG	0.368																																																0			5											97	96	97					5																	76355533		2203	4300	6503	76391289	SO:0001819	synonymous_variant	55109			AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.1809T>A	5.37:g.76355533T>A			76391289	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																				0.368	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76355533	T	A	76355533	2	1	105	1	0	0	0	0	0	0	0	1	382	1596	56	5		5	AGGF1	5	76355533	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	42711960	76355533	104559727	74	27714										
DMGDH	29958	hgsc.bcm.edu	37	chr5	78322314	78322314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tggcataggttccaaaattgTcgattccctcctcctggcct	8	13	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:78322314T>C	ENST00000255189.3	-	13	2151	c.2123A>G	c.(2122-2124)gAc>gGc	p.D708G	DMGDH_ENST00000540686.1_Missense_Mutation_p.D328G|DMGDH_ENST00000380311.4_Missense_Mutation_p.D507G	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	708					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TCCAAAATTGTCGATTCCCTC	0.458																																																0			5											118	107	111					5																	78322314		2203	4300	6503	78358070	SO:0001583	missense	29958			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2123A>G	5.37:g.78322314T>C	ENSP00000255189:p.Asp708Gly		78358070	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	T	8.025	0.760553	0.15914	.	.	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.32	-0.162	0.13367	Glycine cleavage T-protein, N-terminal (1);	0.186054	0.56097	N	0.000033	T	0.38295	0.1035	N	0.01277	-0.915	0.45995	D	0.998804	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.12156	0.007;0.001;0.0;0.0	T	0.02661	-1.1127	10	0.18710	T	0.47	.	6.0936	0.20008	0.0:0.2046:0.1256:0.6698	.	328;507;558;708	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	G	708;547;507;328;558	ENSP00000255189:D708G;ENSP00000430972:D547G;ENSP00000369667:D507G;ENSP00000439478:D328G	ENSP00000255189:D708G	D	-	2	0	DMGDH	78358070	1.000000	0.71417	0.964000	0.40570	0.907000	0.53573	2.648000	0.46647	-0.242000	0.09667	0.459000	0.35465	GAC		0.458	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		C	78322314	T	C	78322314	3	2	105	1	0	0	0	0	1	0	0	0	4592	1667	58	4	493	4	DMGDH	5	78322314	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	1966781	78322314	102592946	75	27715										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79027026	79027026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgcaacacaggaatctcaaaAgaaaataatcaatgaggcat	7	7	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:79027026A>G	ENST00000446378.2	+	2	2469	c.2438A>G	c.(2437-2439)aAg>aGg	p.K813R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	813					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.K813R(3)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAATCTCAAAAGAAAATAATC	0.448																																																3	Substitution - Missense(3)	lung(3)	5											85	80	82					5																	79027026		1923	4134	6057	79062782	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.2438A>G	5.37:g.79027026A>G	ENSP00000394770:p.Lys813Arg		79062782	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502453	0.44455	.	.	ENSG00000164309	ENST00000446378	T	0.39592	1.07	5.41	1.63	0.23807	.	0.766243	0.11893	N	0.519392	T	0.41604	0.1166	L	0.58428	1.81	0.09310	N	1	P	0.52842	0.956	P	0.47299	0.543	T	0.28202	-1.0051	10	0.66056	D	0.02	.	5.3538	0.16050	0.6938:0.1484:0.1578:0.0	.	813	Q8N3K9	CMYA5_HUMAN	R	813	ENSP00000394770:K813R	ENSP00000394770:K813R	K	+	2	0	CMYA5	79062782	0.006000	0.16342	0.001000	0.08648	0.005000	0.04900	0.367000	0.20382	0.103000	0.17682	0.528000	0.53228	AAG		0.448	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79027026	A	G	79027026	3	3	105	1	0	0	0	0	1	0	0	0	3596	72	3	4	2444	4	CMYA5	5	79027026	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	704712	79027026	101888234	76	27716										
GPR98	84059	hgsc.bcm.edu	37	chr5	90052963	90052963	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccatctcatgggattcttgaAtttgcagataaacaggtatg	9	7	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:90052963A>G	ENST00000405460.2	+	57	12021	c.11925A>G	c.(11923-11925)gaA>gaG	p.E3975E		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3975	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGATTCTTGAATTTGCAGATA	0.418																																																0			5											77	79	79					5																	90052963		1871	4116	5987	90088719	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11925A>G	5.37:g.90052963A>G			90088719	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	6.698	0.497523	0.12762	.	.	ENSG00000164199	ENST00000509621	.	.	.	5.08	-0.254	0.12992	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39272	-0.9622	4	.	.	.	.	5.9256	0.19110	0.4594:0.3165:0.2241:0.0	.	.	.	.	S	1541	.	.	N	+	2	0	GPR98	90088719	0.985000	0.35326	0.996000	0.52242	0.754000	0.42855	0.244000	0.18124	0.077000	0.16863	0.383000	0.25322	AAT		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90052963	A	G	90052963	2	3	105	1	0	0	0	0	0	0	0	1	6742	98	4	4		4	GPR98	5	90052963	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	11025937	90052963	90862297	77	27717										
APC	324	hgsc.bcm.edu	37	chr5	112154955	112154955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgaaatccgagtccttcatcTtttggaacagatacgcgctt	8	10	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:112154955T>C	ENST00000457016.1	+	10	1606	c.1226T>C	c.(1225-1227)cTt>cCt	p.L409P	APC_ENST00000508376.2_Missense_Mutation_p.L409P|APC_ENST00000257430.4_Missense_Mutation_p.L409P			P25054	APC_HUMAN	adenomatous polyposis coli	409	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTCCTTCATCTTTTGGAACAG	0.502		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	0			5											52	51	51					5																	112154955		2202	4300	6502	112182854	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1226T>C	5.37:g.112154955T>C	ENSP00000413133:p.Leu409Pro		112182854	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440011	0.83993	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.94	5.94	0.96194	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76695	0.4023	L	0.59436	1.845	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.78723	-0.2093	10	0.87932	D	0	-14.1993	16.4445	0.83913	0.0:0.0:0.0:1.0	.	411;409	Q4LE70;P25054	.;APC_HUMAN	P	409;391;409;409;409	ENSP00000413133:L409P;ENSP00000423224:L391P;ENSP00000257430:L409P;ENSP00000427089:L409P;ENSP00000423828:L409P	ENSP00000257430:L409P	L	+	2	0	APC	112182854	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.284000	0.76573	0.529000	0.55759	CTT		0.502	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112154955	T	C	112154955	3	2	105	1	0	0	0	0	1	0	0	0	763	1609	56	4	1260	4	APC	5	112154955	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	22101992	112154955	68760305	78	27718										
APC	324	hgsc.bcm.edu	37	chr5	112175322	112175322	+	Frame_Shift_Del	DEL	C	C	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcagggttctagtttatcttCagaatcagccaggcacaaag							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:112175322delC	ENST00000457016.1	+	16	4411	c.4031delC	c.(4030-4032)tcafs	p.S1344fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Del_p.S1344fs|APC_ENST00000257430.4_Frame_Shift_Del_p.S1344fs			P25054	APC_HUMAN	adenomatous polyposis coli	1344	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1344*(2)|p.S1335fs*70(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGTTTATCTTCAGAATCAGCC	0.473		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Substitution - Nonsense(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5											57	61	59					5																	112175322		2202	4300	6502	112203221	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4031delC	5.37:g.112175322delC	ENSP00000413133:p.Ser1344fs		112203221	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175322	C	-	112175322	7	5	105	1	0	1	0	1	0	0	0	0	763	838	29	0	4089	0	APC	5	112175322	Frame_Shift_Del	DEL	C	TCGA-DY-A1DD-01A-21D-A152-10	20367	112175322	68739938	79	27719										
FBN2	2201	hgsc.bcm.edu	37	chr5	127685090	127685090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aaggccttcagggcactcgcAatgaaaagatcccttactgt	9	11	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:127685090A>T	ENST00000508053.1	-	29	3912	c.2938T>A	c.(2938-2940)Tgc>Agc	p.C980S	FBN2_ENST00000508989.1_Missense_Mutation_p.C947S|FBN2_ENST00000262464.4_Missense_Mutation_p.C980S			P35556	FBN2_HUMAN	fibrillin 2	980	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGGCACTCGCAATGAAAAGAT	0.468																																																0			5											120	99	106					5																	127685090		2203	4300	6503	127712989	SO:0001583	missense	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2938T>A	5.37:g.127685090A>T	ENSP00000424571:p.Cys980Ser		127712989	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596649	0.86953	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.99429	-5.89;-5.89;-5.89	4.04	4.04	0.47022	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000005	D	0.99725	0.9893	H	0.98818	4.34	0.80722	D	1	D;B	0.67145	0.996;0.007	D;B	0.70016	0.967;0.008	D	0.97003	0.9730	10	0.87932	D	0	.	14.0381	0.64658	1.0:0.0:0.0:0.0	.	947;980	D6RJI3;P35556	.;FBN2_HUMAN	S	980;980;947	ENSP00000262464:C980S;ENSP00000424571:C980S;ENSP00000425596:C947S	ENSP00000262464:C980S	C	-	1	0	FBN2	127712989	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	9.013000	0.93629	2.070000	0.61991	0.533000	0.62120	TGC		0.468	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127685090	A	T	127685090	3	4	105	1	0	0	0	0	1	0	0	0	5722	130	5	5	5972	5	FBN2	5	127685090	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	15509768	127685090	53230170	80	27720										
AFF4	27125	hgsc.bcm.edu	37	chr5	132270223	132270223	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tggggttttccagggctggaAgaacgtgatttggagtgttc	16	5	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:132270223A>G	ENST00000265343.5	-	3	913	c.534T>C	c.(532-534)tcT>tcC	p.S178S	AFF4_ENST00000491831.1_5'UTR|AFF4_ENST00000378595.3_Silent_p.S178S	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	178	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGGGCTGGAAGAACGTGATT	0.473																																					Ovarian(126;889 1733 2942 10745 11605)											0			5											142	141	141					5																	132270223		2203	4300	6503	132298122	SO:0001819	synonymous_variant	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.534T>C	5.37:g.132270223A>G			132298122	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Silent	SNP	ENST00000265343.5	37	CCDS4164.1																																																																																				0.473	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		G	132270223	A	G	132270223	2	3	105	1	0	0	0	0	0	0	0	1	359	59	3	4		4	AFF4	5	132270223	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4585133	132270223	48645037	81	27721										
PPP2R2B	5521	hgsc.bcm.edu	37	chr5	146257573	146257573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggctggcgttaccttcggtcGcatagctgtggtcgcgcagg	16	11	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:146257573G>A	ENST00000394413.3	-	1	632	c.62C>T	c.(61-63)gCg>gTg	p.A21V	PPP2R2B_ENST00000336640.6_Intron|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000508545.2_Intron|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.A21V|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.A21V|PPP2R2B_ENST00000504198.1_Intron|PPP2R2B_ENST00000394410.2_Intron|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.A79V|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.A87V|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.A21V			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	21					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACCTTCGGTCGCATAGCTGTG	0.617																																																0			5											113	95	101					5																	146257573		2203	4300	6503	146237766	SO:0001583	missense	5521			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9305	protein-coding gene	gene with protein product	"PP2A subunit B isoform beta"	604325	"spinocerebellar ataxia 12", "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.62C>T	5.37:g.146257573G>A	ENSP00000377935:p.Ala21Val		146237766	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.144766	0.37825	.	.	ENSG00000156475	ENST00000394413;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394409	T;T;T;T;T;T	0.72167	-0.63;1.66;-0.63;-0.63;-0.63;1.66	4.56	3.69	0.42338	WD40 repeat-like-containing domain (1);	0.265667	0.22617	U	0.057757	T	0.28632	0.0709	N	0.00226	-1.805	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.46624	-0.9178	10	0.02654	T	1	-0.6041	11.6292	0.51164	0.0886:0.0:0.9114:0.0	.	79;21	Q00005-4;Q00005	.;2ABB_HUMAN	V	21;87;21;21;21;79	ENSP00000377935:A21V;ENSP00000377936:A87V;ENSP00000377933:A21V;ENSP00000349283:A21V;ENSP00000398779:A21V;ENSP00000377931:A79V	ENSP00000349283:A21V	A	-	2	0	AC011357.1	146237766	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	5.580000	0.67464	1.159000	0.42565	-0.258000	0.10820	GCG		0.617	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678		A	146257573	G	A	146257573	3	1	105	1	0	0	0	0	1	0	0	0	12419	1087	38	1	1346	1	PPP2R2B	5	146257573	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	13987350	146257573	34657687	82	27722										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154287314	154287314	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gttctcaaggtgggctttttCttctttttgggctttgcctt	10	8	3	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:154287314C>T	ENST00000285873.7	-	16	2307	c.2232G>A	c.(2230-2232)aaG>aaA	p.K744K		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	744	Poly-Lys.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGGGCTTTTTCTTCTTTTTGG	0.393																																																0			5											187	189	188					5																	154287314		2203	4300	6503	154267507	SO:0001819	synonymous_variant	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2232G>A	5.37:g.154287314C>T			154267507	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																				0.393	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			T	154287314	C	T	154287314	2	4	105	1	0	0	0	0	0	0	0	1	6351	912	32	3		3	GEMIN5	5	154287314	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8029741	154287314	26627946	83	27723										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176005458	176005458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gagccaggccgtgtactaccTgacgctgcaggccacagacg	13	14	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr5:176005458T>A	ENST00000510636.1	+	16	1941	c.1667T>A	c.(1666-1668)cTg>cAg	p.L556Q	CDHR2_ENST00000506348.1_Missense_Mutation_p.L556Q|CDHR2_ENST00000261944.5_Missense_Mutation_p.L556Q	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	556	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GTGTACTACCTGACGCTGCAG	0.632																																																0			5											73	57	62					5																	176005458		2203	4300	6503	175938064	SO:0001583	missense	0			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.1667T>A	5.37:g.176005458T>A	ENSP00000424565:p.Leu556Gln		175938064	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882220	0.51908	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.74421	-0.84;-0.84;-0.84	5.33	5.33	0.75918	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.88051	0.6333	H	0.95574	3.69	0.37403	D	0.912935	D	0.89917	1.0	D	0.81914	0.995	D	0.90562	0.4516	9	0.87932	D	0	-13.9385	5.7398	0.18087	0.0:0.2133:0.0:0.7867	.	556	Q9BYE9	CDHR2_HUMAN	Q	556	ENSP00000424565:L556Q;ENSP00000261944:L556Q;ENSP00000421078:L556Q	ENSP00000261944:L556Q	L	+	2	0	CDHR2	175938064	1.000000	0.71417	0.981000	0.43875	0.300000	0.27592	2.105000	0.41825	2.026000	0.59711	0.443000	0.29094	CTG		0.632	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176005458	T	A	176005458	3	1	105	1	0	0	0	0	1	0	0	0	3125	1580	55	5	1725	5	CDHR2	5	176005458	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	21718144	176005458	4909802	84	27724										
SERPINB6	5269	hgsc.bcm.edu	37	chr6	2948717	2948717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctccacaaaagacttgtgcaCgaccttggacagagacaggt	10	11	0	2	rs550855004		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:2948717C>T	ENST00000380520.1	-	6	2940	c.946G>A	c.(946-948)Gtg>Atg	p.V316M	SERPINB6_ENST00000380524.1_Missense_Mutation_p.V316M|SERPINB6_ENST00000335686.5_Missense_Mutation_p.V316M|SERPINB6_ENST00000380539.1_Missense_Mutation_p.V316M|SERPINB6_ENST00000380529.1_Missense_Mutation_p.V316M|SERPINB6_ENST00000380546.3_Missense_Mutation_p.V316M			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	316					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	GACTTGTGCACGACCTTGGAC	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		17561	0		0	False		,,,				2504	0															0			6											79	73	75					6																	2948717		2203	4300	6503	2893716	SO:0001583	missense	5269			Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.946G>A	6.37:g.2948717C>T	ENSP00000369891:p.Val316Met		2893716	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Missense_Mutation	SNP	ENST00000380520.1	37	CCDS4479.1	.	.	.	.	.	.	.	.	.	.	C	9.909	1.209122	0.22205	.	.	ENSG00000124570	ENST00000380524;ENST00000380520;ENST00000335686;ENST00000380529;ENST00000380539;ENST00000380546;ENST00000440670	D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	5.01	1.08	0.20341	Serpin domain (3);	0.672017	0.15620	N	0.252927	T	0.62392	0.2424	L	0.49778	1.585	0.09310	N	1	P	0.37864	0.61	B	0.35859	0.212	T	0.54470	-0.8289	10	0.44086	T	0.13	.	4.4014	0.11388	0.3432:0.4258:0.0:0.231	.	316	P35237	SPB6_HUMAN	M	316;316;316;316;316;316;132	ENSP00000369896:V316M;ENSP00000369891:V316M;ENSP00000338358:V316M;ENSP00000369901:V316M;ENSP00000369912:V316M;ENSP00000369919:V316M	ENSP00000338358:V316M	V	-	1	0	SERPINB6	2893716	0.000000	0.05858	0.027000	0.17364	0.018000	0.09664	-1.020000	0.03618	0.063000	0.16370	0.551000	0.68910	GTG		0.582	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1			T	2948717	C	T	2948717	3	4	105	1	0	0	0	0	1	0	0	0	14142	536	19	1	188	1	SERPINB6	6	2948717	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		2948717	168166350	85	27725										
RREB1	6239	hgsc.bcm.edu	37	chr6	7226816	7226816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acctttcatacagaacaaccCttcaattcctgctggcttcc	4	15	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:7226816C>T	ENST00000349384.6	+	9	1138	c.824C>T	c.(823-825)cCt>cTt	p.P275L	RREB1_ENST00000379938.2_Missense_Mutation_p.P275L|RREB1_ENST00000379933.3_Missense_Mutation_p.P275L|RREB1_ENST00000334984.6_Missense_Mutation_p.P275L	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	275					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P275H(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CAGAACAACCCTTCAATTCCT	0.502																																																1	Substitution - Missense(1)	ovary(1)	6											212	186	195					6																	7226816		2203	4300	6503	7171815	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.824C>T	6.37:g.7226816C>T	ENSP00000305560:p.Pro275Leu		7171815	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891321	0.91889	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.12569	2.85;2.77;2.85;2.67;2.85	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000016	T	0.16557	0.0398	L	0.39397	1.21	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.996;0.99;1.0	T	0.05225	-1.0898	10	0.09843	T	0.71	-17.4617	18.2888	0.90122	0.0:1.0:0.0:0.0	.	275;275;275	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	L	275	ENSP00000369265:P275L;ENSP00000369270:P275L;ENSP00000305560:P275L;ENSP00000335574:P275L;ENSP00000419511:P275L	ENSP00000335574:P275L	P	+	2	0	RREB1	7171815	1.000000	0.71417	0.975000	0.42487	0.967000	0.64934	5.350000	0.66016	2.311000	0.77944	0.655000	0.94253	CCT		0.502	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7226816	C	T	7226816	3	4	105	1	0	0	0	0	1	0	0	0	13716	681	24	3	846	3	RREB1	6	7226816	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	4278099	7226816	163888251	86	27726										
MDC1	9656	hgsc.bcm.edu	37	chr6	30676047	30676047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtccataggcctcaaggtgcGtgtcaaaaggctgggtctca	13	10	3	0	rs529970009		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:30676047G>A	ENST00000376406.3	-	8	2956	c.2309C>T	c.(2308-2310)aCg>aTg	p.T770M	MDC1_ENST00000376405.2_Intron|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	770				Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CTCAAGGTGCGTGTCAAAAGG	0.552								Other conserved DNA damage response genes					g|||	1	0.000199681	0	0	5008	,	,		18793	0.001		0	False		,,,				2504	0															0			6											103	99	100					6																	30676047		1509	2709	4218	30784026	SO:0001583	missense	9656			D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.2309C>T	6.37:g.30676047G>A	ENSP00000365588:p.Thr770Met		30784026	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	g	12.08	1.831805	0.32421	.	.	ENSG00000137337	ENST00000376406;ENST00000429610	T	0.02944	4.1	4.22	3.33	0.38152	.	.	.	.	.	T	0.02848	0.0085	L	0.47716	1.5	0.21933	N	0.999461	D	0.89917	1.0	P	0.54856	0.762	T	0.45071	-0.9286	9	0.54805	T	0.06	0.6594	9.3475	0.38118	0.1088:0.0:0.8912:0.0	.	770	Q14676	MDC1_HUMAN	M	770	ENSP00000365588:T770M	ENSP00000365588:T770M	T	-	2	0	MDC1	30784026	0.000000	0.05858	0.005000	0.12908	0.112000	0.19704	0.576000	0.23744	2.048000	0.60808	0.457000	0.33378	ACG		0.552	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30676047	G	A	30676047	3	1	105	1	0	0	0	0	1	0	0	0	9433	1145	40	1	3992	1	MDC1	6	30676047	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	23449231	30676047	140439020	87	27727										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31734091	31734091	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggtcaagatcctgagggcccGagaagctggcgatgcggaga	17	9	1	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:31734091G>T	ENST00000375688.4	-	15	2455	c.2255C>A	c.(2254-2256)tCg>tAg	p.S752*	SAPCD1-AS1_ENST00000419679.1_RNA|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Nonsense_Mutation_p.S752*			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	752						extracellular region (GO:0005576)											CTGAGGGCCCGAGAAGCTGGC	0.612																																																0			6											35	30	32					6																	31734091		1509	2709	4218	31842070	SO:0001587	stop_gained	80737				CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.2255C>A	6.37:g.31734091G>T	ENSP00000364840:p.Ser752*		31842070	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Nonsense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	G	38	6.935249	0.97948	.	.	ENSG00000204396	ENST00000375688;ENST00000375686	.	.	.	4.87	0.628	0.17681	.	0.744443	0.12094	N	0.500126	.	.	.	.	.	.	0.22253	N	0.999257	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.951	5.2751	0.15645	0.1941:0.3044:0.5015:0.0	.	.	.	.	X	752	.	ENSP00000364838:S752X	S	-	2	0	C6orf27	31842070	0.212000	0.23540	0.067000	0.19924	0.796000	0.44982	0.262000	0.18460	-0.070000	0.12908	-1.253000	0.01494	TCG		0.612	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		T	31734091	G	T	31734091	4	4	105	1	0	0	0	0	0	1	0	0	2368	1059	37	2	431	2	C6orf27	6	31734091	Nonsense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	1058044	31734091	139380976	88	27728										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73904984	73904984	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtgggtcccgaagagacagaGacagacacttttgatgccgc	13	10	0	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:73904984G>T	ENST00000370398.1	+	14	2755	c.2646G>T	c.(2644-2646)gaG>gaT	p.E882D	KCNQ5_ENST00000355635.3_Missense_Mutation_p.E883D|KCNQ5_ENST00000355194.4_Missense_Mutation_p.E882D|KCNQ5_ENST00000402622.2_Missense_Mutation_p.E892D|KCNQ5_ENST00000414165.2_Missense_Mutation_p.E772D|KCNQ5_ENST00000342056.2_Missense_Mutation_p.E901D|KCNQ5_ENST00000403813.2_Missense_Mutation_p.E873D	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	882					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	AAGAGACAGAGACAGACACTT	0.498																																					GBM(142;1375 1859 14391 23261 44706)											0			6											92	97	95					6																	73904984		2203	4300	6503	73961705	SO:0001583	missense	56479			AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2646G>T	6.37:g.73904984G>T	ENSP00000359425:p.Glu882Asp		73961705	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569168	0.28003	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99394	-5.61;-5.61;-5.61;-5.61;-5.62;-5.64;-5.82	5.97	2.82	0.32997	.	0.197406	0.44688	D	0.000440	D	0.95277	0.8468	N	0.19112	0.55	0.18873	N	0.999985	D;P;B;B;B	0.57257	0.979;0.571;0.001;0.001;0.001	P;B;B;B;B	0.55999	0.789;0.153;0.002;0.003;0.001	D	0.92540	0.6041	10	0.09590	T	0.72	.	4.7959	0.13272	0.3792:0.1592:0.4616:0.0	.	772;892;901;873;882	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	D	901;901;882;882;892;883;873;772	ENSP00000345055:E901D;ENSP00000347326:E882D;ENSP00000359425:E882D;ENSP00000385501:E892D;ENSP00000347853:E883D;ENSP00000384453:E873D;ENSP00000409861:E772D	ENSP00000345055:E901D	E	+	3	2	KCNQ5	73961705	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.618000	0.46393	0.837000	0.34925	0.650000	0.86243	GAG		0.498	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		T	73904984	G	T	73904984	3	4	105	1	0	0	0	0	1	0	0	0	8107	933	33	2	2761	2	KCNQ5	6	73904984	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	42170893	73904984	97210083	89	27729										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88119576	88119576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gaatgcctccaactcaggccGaaagtgttataaggagtatt	10	8	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:88119576G>A	ENST00000507897.1	+	2	102	c.19G>A	c.(19-21)Gaa>Aaa	p.E7K	C6ORF165_ENST00000369562.4_Missense_Mutation_p.E7K			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	7										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		AACTCAGGCCGAAAGTGTTAT	0.333																																																0			6											116	119	118					6																	88119576		2203	4300	6503	88176295	SO:0001583	missense	154313			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.19G>A	6.37:g.88119576G>A	ENSP00000426769:p.Glu7Lys		88176295	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408718	0.96072	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.40225	1.04;1.04	5.39	5.39	0.77823	.	0.096875	0.64402	D	0.000002	T	0.57989	0.2091	M	0.81239	2.535	0.58432	D	0.999997	D;D	0.71674	0.995;0.998	P;P	0.58660	0.743;0.843	T	0.63695	-0.6579	10	0.72032	D	0.01	.	19.1063	0.93296	0.0:0.0:1.0:0.0	.	7;7	Q8IYR0;E1P509	CF165_HUMAN;.	K	7	ENSP00000358575:E7K;ENSP00000422494:E7K	ENSP00000358575:E7K	E	+	1	0	C6orf165	88176295	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	4.814000	0.62627	2.671000	0.90904	0.655000	0.94253	GAA		0.333	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		A	88119576	G	A	88119576	3	1	105	1	0	0	0	0	1	0	0	0	2347	1059	37	1	21	1	C6orf165	6	88119576	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	14214592	88119576	82995491	90	27730										
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96988489	96988489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctttagaaagcgttagtacaAgtaaaaaggataaaaaagat	8	3	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:96988489A>G	ENST00000369278.4	+	11	1303	c.1237A>G	c.(1237-1239)Agt>Ggt	p.S413G		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	413					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										CGTTAGTACAAGTAAAAAGGA	0.299																																																0			6											65	66	66					6																	96988489		2203	4295	6498	97095210	SO:0001583	missense	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1237A>G	6.37:g.96988489A>G	ENSP00000358283:p.Ser413Gly		97095210	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.813080	0.32053	.	.	ENSG00000014123	ENST00000369278	T	0.43688	0.94	6.16	5.01	0.66863	.	0.449979	0.29924	N	0.010844	T	0.18257	0.0438	L	0.50333	1.59	0.32830	D	0.503862	B	0.02656	0.0	B	0.04013	0.001	T	0.09357	-1.0678	10	0.21540	T	0.41	-3.722	11.3719	0.49704	0.9303:0.0:0.0697:0.0	.	413	O94874	UFL1_HUMAN	G	413	ENSP00000358283:S413G	ENSP00000358283:S413G	S	+	1	0	KIAA0776	97095210	1.000000	0.71417	0.999000	0.59377	0.639000	0.38242	2.955000	0.49121	1.162000	0.42619	0.528000	0.53228	AGT		0.299	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		G	96988489	A	G	96988489	3	3	105	1	0	0	0	0	1	0	0	0	8214	72	3	4	1279	4	KIAA0776	6	96988489	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	8868913	96988489	74126578	91	27731										
ROS1	6098	hgsc.bcm.edu	37	chr6	117665427	117665427	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agagacagaaacgctttatcTaaaataagaagaaaccaaaa	6	6	1	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:117665427T>A	ENST00000368508.3	-	27	4520		c.e27-2		ROS1_ENST00000368507.3_Splice_Site|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase						cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.?(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ACGCTTTATCTAAAATAAGAA	0.323			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	1	Unknown(1)	central_nervous_system(1)	6											109	108	108					6																	117665427		2203	4300	6503	117772120	SO:0001630	splice_region_variant	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4322-2A>T	6.37:g.117665427T>A			117772120	Q15368|Q5TDB5	Splice_Site	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.135550	0.37728	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	.	.	.	5.16	3.91	0.45181	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6017	0.33749	0.1712:0.0:0.0:0.8288	.	.	.	.	.	-1	.	.	.	-	.	.	ROS1	117772120	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	3.397000	0.52572	2.077000	0.62373	0.459000	0.35465	.		0.323	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		Intron	A	117665427	T	A	117665427	5	1	105	1	0	0	0	0	0	0	1	0	13568	1536	53	5	2791	5	ROS1	6	117665427	Splice_Site	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	20676938	117665427	53449640	92	27732										
THBS2	7058	hgsc.bcm.edu	37	chr6	169650827	169650827	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acaggctctgaggacactcaCcttgcgtgctgggccacacc	11	15	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr6:169650827C>T	ENST00000366787.3	-	3	302		c.e3+1			NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2						cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.?(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		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)		AGGACACTCACCTTGCGTGCT	0.542																																					Esophageal Squamous(91;219 1934 18562 44706)											1	Unknown(1)	ovary(1)	6											58	49	52					6																	169650827		2203	4300	6503	169392752	SO:0001630	splice_region_variant	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.52+1G>A	6.37:g.169650827C>T			169392752	A6H8N1|A7E232|Q5RI52	Splice_Site	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.879802	0.33162	.	.	ENSG00000186340	ENST00000366787;ENST00000435791	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3763	0.60741	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	THBS2	169392752	1.000000	0.71417	0.997000	0.53966	0.313000	0.28021	3.140000	0.50585	2.515000	0.84797	0.655000	0.94253	.		0.542	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	Intron	T	169650827	C	T	169650827	5	4	105	1	0	0	0	0	0	0	1	0	15893	521	18	3	3549	3	THBS2	6	169650827	Splice_Site	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	51985400	169650827	1464240	93	27733										
CHST12	55501	hgsc.bcm.edu	37	chr7	2472417	2472417	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	taggccgcacacggggccgcCgctgcccacgcccgggccgg	16	19	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:2472417C>T	ENST00000258711.6	+	2	278	c.143C>T	c.(142-144)cCg>cTg	p.P48L		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	48					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		ACGGGGCCGCCGCTGCCCACG	0.637																																																0			7											45	52	50					7																	2472417		2203	4299	6502	2438943	SO:0001583	missense	55501			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.143C>T	7.37:g.2472417C>T	ENSP00000258711:p.Pro48Leu		2438943	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	C	5.912	0.352372	0.11182	.	.	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.62232	0.04;0.87	4.76	2.9	0.33743	.	2.919880	0.01280	N	0.009707	T	0.56046	0.1959	L	0.41236	1.265	0.09310	N	0.999999	B	0.10296	0.003	B	0.04013	0.001	T	0.35798	-0.9774	10	0.36615	T	0.2	-11.1575	8.078	0.30729	0.0:0.753:0.1608:0.0862	.	48	Q9NRB3	CHSTC_HUMAN	L	48	ENSP00000258711:P48L;ENSP00000411207:P48L	ENSP00000258711:P48L	P	+	2	0	CHST12	2438943	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	1.289000	0.33307	0.984000	0.38629	0.485000	0.47835	CCG		0.637	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		T	2472417	C	T	2472417	3	4	105	1	0	0	0	0	1	0	0	0	3406	652	23	1	145	1	CHST12	7	2472417	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		2472417	156666246	94	27734										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23391065	23391065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cggatcctggagacccctgcCttgaggagcccctctgccca	11	17	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:23391065C>T	ENST00000258729.3	-	6	898	c.542G>A	c.(541-543)aGg>aAg	p.R181K	IGF2BP3_ENST00000491719.1_5'UTR	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	181					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)	p.R181M(1)|p.R181K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						AGACCCCTGCCTTGAGGAGCC	0.567																																																2	Substitution - Missense(2)	ovary(1)|skin(1)	7											54	53	53					7																	23391065		2203	4300	6503	23357590	SO:0001583	missense	10643			AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.542G>A	7.37:g.23391065C>T	ENSP00000258729:p.Arg181Lys		23357590	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Missense_Mutation	SNP	ENST00000258729.3	37	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120209	0.94385	.	.	ENSG00000136231	ENST00000258729	T	0.15372	2.43	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	M	0.61703	1.905	0.80722	D	1	B	0.34161	0.439	B	0.29353	0.101	T	0.06232	-1.0838	10	0.13470	T	0.59	-10.6987	20.2405	0.98372	0.0:1.0:0.0:0.0	.	181	O00425	IF2B3_HUMAN	K	181	ENSP00000258729:R181K	ENSP00000258729:R181K	R	-	2	0	IGF2BP3	23357590	0.993000	0.37304	0.944000	0.38274	0.961000	0.63080	7.770000	0.85390	2.797000	0.96272	0.561000	0.74099	AGG		0.567	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		T	23391065	C	T	23391065	3	4	105	1	0	0	0	0	1	0	0	0	7596	681	24	3	1237	3	IGF2BP3	7	23391065	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	20918648	23391065	135747598	95	27735										
STK31	56164	hgsc.bcm.edu	37	chr7	23775222	23775222	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atgagaattaaagcaacctcTgaagatggaacagttattgc	9	6	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:23775222T>C	ENST00000355870.3	+	7	668	c.549T>C	c.(547-549)tcT>tcC	p.S183S	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000433467.2_Silent_p.S183S|STK31_ENST00000354639.3_Silent_p.S160S|STK31_ENST00000428484.1_Silent_p.S160S	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	183						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						AAGCAACCTCTGAAGATGGAA	0.398																																																0			7											123	119	120					7																	23775222		2203	4300	6503	23741747	SO:0001819	synonymous_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.549T>C	7.37:g.23775222T>C			23741747	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				0.398	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		C	23775222	T	C	23775222	2	2	105	1	0	0	0	0	0	0	0	1	15335	1567	55	4		4	STK31	7	23775222	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	384157	23775222	135363441	96	27736										
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35674832	35674832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgctaaggagaatcgcagctCgtgagaacgtgtacatccag	12	9	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:35674832C>T	ENST00000396081.1	-	6	1658	c.854G>A	c.(853-855)cGa>cAa	p.R285Q	HERPUD2_ENST00000426180.1_5'UTR|HERPUD2_ENST00000311350.3_Missense_Mutation_p.R285Q	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	285					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.R285Q(1)		kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						AATCGCAGCTCGTGAGAACGT	0.418																																																1	Substitution - Missense(1)	ovary(1)	7											184	165	172					7																	35674832		2203	4300	6503	35641357	SO:0001583	missense	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.854G>A	7.37:g.35674832C>T	ENSP00000379390:p.Arg285Gln		35641357	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	C	36	5.743175	0.96873	.	.	ENSG00000122557	ENST00000396081;ENST00000311350	T;T	0.20738	2.05;2.05	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.46983	0.1421	L	0.58510	1.815	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.24905	-1.0147	10	0.66056	D	0.02	-32.1447	20.422	0.99049	0.0:1.0:0.0:0.0	.	285	Q9BSE4	HERP2_HUMAN	Q	285	ENSP00000379390:R285Q;ENSP00000310729:R285Q	ENSP00000310729:R285Q	R	-	2	0	HERPUD2	35641357	1.000000	0.71417	0.566000	0.28421	0.991000	0.79684	7.818000	0.86416	2.832000	0.97577	0.655000	0.94253	CGA		0.418	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35674832	C	T	35674832	3	4	105	1	0	0	0	0	1	0	0	0	7085	884	31	1	378	1	HERPUD2	7	35674832	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	11899610	35674832	123463831	97	27737										
URGCP	55665	hgsc.bcm.edu	37	chr7	43917510	43917510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtgcttctcaggggggtccaCggcccactggagctggcaga	16	12	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:43917510C>T	ENST00000453200.1	-	6	2045	c.1552G>A	c.(1552-1554)Gtg>Atg	p.V518M	URGCP_ENST00000443736.1_Missense_Mutation_p.V475M|URGCP_ENST00000402306.3_Missense_Mutation_p.V509M|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Missense_Mutation_p.V475M|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000223341.7_Missense_Mutation_p.V475M|URGCP_ENST00000336086.6_Missense_Mutation_p.V475M			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	518					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGGGGGTCCACGGCCCACTGG	0.632																																																0			7											56	60	59					7																	43917510		1982	4164	6146	43884035	SO:0001583	missense	0				CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1552G>A	7.37:g.43917510C>T	ENSP00000396918:p.Val518Met		43884035	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	C	6.406	0.443065	0.12164	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.79	-0.69	0.11309	.	0.724608	0.12948	N	0.426046	T	0.04137	0.0115	N	0.08118	0	0.09310	N	1	P;P	0.38922	0.651;0.651	B;B	0.34722	0.188;0.188	T	0.32824	-0.9892	10	0.72032	D	0.01	-5.7877	3.0448	0.06149	0.1003:0.4649:0.1445:0.2903	.	509;518	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	M	475;475;509;475;518;475	ENSP00000223341:V475M;ENSP00000336872:V475M;ENSP00000384955:V509M;ENSP00000392136:V475M;ENSP00000396918:V518M;ENSP00000402803:V475M	ENSP00000223341:V475M	V	-	1	0	URGCP	43884035	0.000000	0.05858	0.000000	0.03702	0.460000	0.32559	0.086000	0.14935	-0.467000	0.06932	-0.302000	0.09304	GTG		0.632	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		T	43917510	C	T	43917510	3	4	105	1	0	0	0	0	1	0	0	0	17066	536	19	1	1247	1	URGCP	7	43917510	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8242678	43917510	115221153	98	27738										
URGCP	55665	hgsc.bcm.edu	37	chr7	43917673	43917673	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgacactcctcacagtcctcGtcgacctttaggcccagttt	7	15	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:43917673G>A	ENST00000453200.1	-	6	1882	c.1389C>T	c.(1387-1389)gaC>gaT	p.D463D	URGCP_ENST00000443736.1_Silent_p.D420D|URGCP_ENST00000402306.3_Silent_p.D454D|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Silent_p.D420D|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000223341.7_Silent_p.D420D|URGCP_ENST00000336086.6_Silent_p.D420D			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	463					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CACAGTCCTCGTCGACCTTTA	0.592																																																0			7											125	132	130					7																	43917673		2044	4188	6232	43884198	SO:0001819	synonymous_variant	0				CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1389C>T	7.37:g.43917673G>A			43884198	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																				0.592	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		A	43917673	G	A	43917673	2	1	105	1	0	0	0	0	0	0	0	1	17066	1136	40	1		1	URGCP	7	43917673	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	163	43917673	115220990	99	27739										
HUS1	3364	hgsc.bcm.edu	37	chr7	48007445	48007445	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tacttgttgtccagcaagaaActgtaggagcttcctaatat	8	8	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:48007445A>G	ENST00000258774.5	-	7	741	c.718T>C	c.(718-720)Ttt>Ctt	p.F240L	HUS1_ENST00000432325.1_Missense_Mutation_p.F219L	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	240					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				CCAGCAAGAAACTGTAGGAGC	0.398								Direct reversal of damage;Other conserved DNA damage response genes																													Ovarian(103;466 1517 21788 34610 43890)											0			7											178	158	165					7																	48007445		2203	4300	6503	47973970	SO:0001583	missense	3364			Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"hus1+-like protein"	603760	"HUS1 (S. pombe) checkpoint homolog"			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.718T>C	7.37:g.48007445A>G	ENSP00000258774:p.Phe240Leu		47973970	B4DFI9	Missense_Mutation	SNP	ENST00000258774.5	37	CCDS34635.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481827	0.44147	.	.	ENSG00000136273	ENST00000258774;ENST00000432325	T;T	0.10960	2.82;2.82	5.34	4.18	0.49190	.	0.099013	0.64402	N	0.000001	T	0.08088	0.0202	L	0.33189	0.99	0.58432	D	0.999998	B	0.24317	0.101	B	0.27262	0.078	T	0.22695	-1.0209	10	0.13108	T	0.6	-2.9456	8.5092	0.33206	0.9006:0.0:0.0994:0.0	.	240	O60921	HUS1_HUMAN	L	240;219	ENSP00000258774:F240L;ENSP00000416588:F219L	ENSP00000258774:F240L	F	-	1	0	HUS1	47973970	1.000000	0.71417	0.881000	0.34555	0.995000	0.86356	2.083000	0.41615	0.954000	0.37851	0.528000	0.53228	TTT		0.398	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507		G	48007445	A	G	48007445	3	3	105	1	0	0	0	0	1	0	0	0	7480	43	2	4	132	4	HUS1	7	48007445	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4089772	48007445	111131218	100	27740										
SUN3	256979	hgsc.bcm.edu	37	chr7	48046831	48046831	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgattattgtccataccatcCttcatatctcttagcaatgc	4	11	2	1	rs556391462		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:48046831C>A	ENST00000297325.4	-	5	582	c.423G>T	c.(421-423)aaG>aaT	p.K141N	SUN3_ENST00000453192.2_Missense_Mutation_p.K129N|SUN3_ENST00000412142.1_Missense_Mutation_p.K41N|SUN3_ENST00000395572.2_Missense_Mutation_p.K141N	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	141						integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCATACCATCCTTCATATCTC	0.463																																																0			7											154	147	149					7																	48046831		2203	4300	6503	48013356	SO:0001583	missense	0			AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.423G>T	7.37:g.48046831C>A	ENSP00000297325:p.Lys141Asn		48013356	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	37	CCDS34636.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.93|11.93	1.786171|1.786171	0.31593|0.31593	.|.	.|.	ENSG00000164744|ENSG00000164744	ENST00000297325;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771|ENST00000453071	T;T;T;T;T|.	0.25414|.	1.8;1.87;1.8;2.45;1.87|.	5.56|5.56	3.42|3.42	0.39159|0.39159	.|.	0.507802|.	0.19235|.	N|.	0.119311|.	T|T	0.32102|0.32102	0.0818|0.0818	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	P;P;P|.	0.38504|.	0.454;0.634;0.454|.	B;B;B|.	0.39465|.	0.079;0.3;0.115|.	T|T	0.17930|0.17930	-1.0353|-1.0353	10|5	0.54805|.	T|.	0.06|.	.|.	8.7571|8.7571	0.34652|0.34652	0.0:0.8002:0.0:0.1998|0.0:0.8002:0.0:0.1998	.|.	129;41;141|.	E7EWC8;Q8TAQ9-2;Q8TAQ9|.	.;.;SUN3_HUMAN|.	N|M	141;41;141;129;41|61	ENSP00000297325:K141N;ENSP00000410204:K41N;ENSP00000378939:K141N;ENSP00000387525:K129N;ENSP00000409077:K41N|.	ENSP00000297325:K141N|.	K|R	-|-	3|2	2|0	SUN3|SUN3	48013356|48013356	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.023000|0.023000	0.10783|0.10783	1.255000|1.255000	0.32909|0.32909	1.346000|1.346000	0.45694|0.45694	0.655000|0.655000	0.94253|0.94253	AAG|AGG		0.463	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		A	48046831	C	A	48046831	3	1	105	1	0	0	0	0	1	0	0	0	15432	680	24	2	674	2	SUN3	7	48046831	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	39386	48046831	111091832	101	27741										
EGFR	1956	hgsc.bcm.edu	37	chr7	55248992	55248992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctccctccctccaggaagccTacgtgatggccagcgtggac	11	16	0	1	rs397517105		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:55248992T>C	ENST00000275493.2	+	20	2467	c.2290T>C	c.(2290-2292)Tac>Cac	p.Y764H	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Missense_Mutation_p.Y711H|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Missense_Mutation_p.Y719H	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	764	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.A763_Y764insFQEA(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCAGGAAGCCTACGTGATGGC	0.637		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	1	Insertion - In frame(1)	lung(1)	7											100	93	96					7																	55248992		2203	4300	6503	55216486	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2290T>C	7.37:g.55248992T>C	ENSP00000275493:p.Tyr764His		55216486	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.507936	0.85282	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	D;D;D	0.82255	-1.59;-1.59;-1.59	5.85	5.85	0.93711	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79902	0.4526	N	0.02403	-0.565	0.80722	D	1	P;D	0.76494	0.546;0.999	B;D	0.81914	0.248;0.995	D	0.86441	0.1767	10	0.87932	D	0	.	15.0565	0.71917	0.0:0.0:0.0:1.0	.	719;764	Q504U8;P00533	.;EGFR_HUMAN	H	719;634;764;711	ENSP00000415559:Y719H;ENSP00000275493:Y764H;ENSP00000395243:Y711H	ENSP00000275493:Y764H	Y	+	1	0	EGFR	55216486	1.000000	0.71417	0.996000	0.52242	0.870000	0.49936	8.009000	0.88606	2.228000	0.72767	0.533000	0.62120	TAC		0.637	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		C	55248992	T	C	55248992	3	2	105	1	0	0	0	0	1	0	0	0	4978	1522	53	4	2632	4	EGFR	7	55248992	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	7202161	55248992	103889671	102	27742										
PCLO	27445	hgsc.bcm.edu	37	chr7	82785222	82785222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggaggttgtgatttaattttTtctggttgttgagaagatat	12	1	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:82785222T>A	ENST00000333891.9	-	2	1072	c.735A>T	c.(733-735)gaA>gaT	p.E245D	PCLO_ENST00000423517.2_Missense_Mutation_p.E245D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATTTAATTTTTTCTGGTTGTT	0.478																																																0			7											94	84	87					7																	82785222		1928	4149	6077	82623158	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.735A>T	7.37:g.82785222T>A	ENSP00000334319:p.Glu245Asp		82623158		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476807	0.44044	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.18174	2.23;2.24	5.57	3.21	0.36854	.	.	.	.	.	T	0.14657	0.0354	L	0.42245	1.32	0.80722	D	1	P;P	0.36249	0.545;0.545	B;B	0.35770	0.21;0.21	T	0.03212	-1.1060	9	0.87932	D	0	.	7.962	0.30076	0.0:0.1642:0.0:0.8358	.	245;245	Q9Y6V0-5;Q9Y6V0-6	.;.	D	245	ENSP00000334319:E245D;ENSP00000388393:E245D	ENSP00000334319:E245D	E	-	3	2	PCLO	82623158	0.005000	0.15991	0.859000	0.33776	0.958000	0.62258	0.132000	0.15891	0.413000	0.25759	0.533000	0.62120	GAA		0.478	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82785222	T	A	82785222	3	1	105	1	0	0	0	0	1	0	0	0	11614	1838	64	5	14806	5	PCLO	7	82785222	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	27536230	82785222	76353441	103	27743										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87032470	87032470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccttttcactttcagtatccAgagctgatgtagcttcatcc	6	12	3	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:87032470A>G	ENST00000265723.4	-	27	3746	c.3635T>C	c.(3634-3636)cTg>cCg	p.L1212P	ABCB4_ENST00000359206.3_Missense_Mutation_p.L1205P|ABCB4_ENST00000545634.1_Missense_Mutation_p.L1205P|ABCB4_ENST00000358400.3_Missense_Mutation_p.L1158P|ABCB4_ENST00000453593.1_Missense_Mutation_p.L1158P	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	1212	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TTCAGTATCCAGAGCTGATGT	0.433																																																0			7											167	149	155					7																	87032470		2203	4300	6503	86870406	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.3635T>C	7.37:g.87032470A>G	ENSP00000265723:p.Leu1212Pro		86870406	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.340766	0.60963	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.25	5.25	0.73442	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.64402	D	0.000001	D	0.97532	0.9192	H	0.98664	4.295	0.80722	D	1	D;P;B	0.58970	0.984;0.474;0.343	D;B;B	0.64237	0.923;0.386;0.216	D	0.99019	1.0817	10	0.72032	D	0.01	-8.5153	15.4608	0.75356	1.0:0.0:0.0:0.0	.	1158;1205;1212	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	P	1205;1158;1212;1158;1205	ENSP00000352135:L1205P;ENSP00000351172:L1158P;ENSP00000265723:L1212P;ENSP00000392983:L1158P;ENSP00000437465:L1205P	ENSP00000265723:L1212P	L	-	2	0	ABCB4	86870406	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	9.287000	0.95975	2.113000	0.64589	0.459000	0.35465	CTG		0.433	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		G	87032470	A	G	87032470	3	3	105	1	0	0	0	0	1	0	0	0	43	188	7	4	233	4	ABCB4	7	87032470	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4247248	87032470	72106193	104	27744										
C7orf63	79846	hgsc.bcm.edu	37	chr7	89897634	89897634	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ataccaagttctgaattgagGatacaaatttgtaagtgtat	8	4	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:89897634G>C	ENST00000389297.4	+	6	719	c.468G>C	c.(466-468)agG>agC	p.R156S	AC002064.4_ENST00000420245.1_RNA|C7orf63_ENST00000316089.8_Missense_Mutation_p.R156S|C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000497910.1_Missense_Mutation_p.R156S	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		156										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CTGAATTGAGGATACAAATTT	0.338																																																0			7											120	110	113					7																	89897634		1834	4089	5923	89735570	SO:0001583	missense	79846																														ENST00000389297.4:c.468G>C	7.37:g.89897634G>C	ENSP00000373948:p.Arg156Ser		89735570	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996822	0.74818	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000457170	T;T;T;T	0.57107	0.42;0.42;0.77;0.42	5.71	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.69851	0.3157	M	0.77103	2.36	0.36312	D	0.857694	D;D;D	0.89917	0.968;0.975;1.0	P;P;D	0.72338	0.818;0.83;0.977	T	0.76892	-0.2791	10	0.87932	D	0	-13.6775	10.4461	0.44495	0.2156:0.0:0.7844:0.0	.	156;156;154	A5D8W1-5;A5D8W1;A5D8W1-4	.;CG063_HUMAN;.	S	156;156;156;96	ENSP00000373948:R156S;ENSP00000321753:R156S;ENSP00000419549:R156S;ENSP00000392365:R96S	ENSP00000321753:R156S	R	+	3	2	C7orf63	89735570	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.792000	0.38754	0.776000	0.33473	0.655000	0.94253	AGG		0.338	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			C	89897634	G	C	89897634	3	2	105	1	0	0	0	0	1	0	0	0	2415	1165	41	5	490	5	C7orf63	7	89897634	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2865164	89897634	69241029	105	27745										
PDK4	5166	hgsc.bcm.edu	37	chr7	95221867	95221867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agttaggatcaatgcttccaAtgtggcttgggtttcctgtc	11	8	1	0	rs138077797		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:95221867A>G	ENST00000005178.5	-	5	769	c.572T>C	c.(571-573)aTt>aCt	p.I191T		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	191	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			AATGCTTCCAATGTGGCTTGG	0.328																																																0			7						A	THR/ILE	0,4406		0,0,2203	171	164	166		572	5.6	1	7	dbSNP_134	166	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDK4	NM_002612.3	89	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	191/412	95221867	1,13005	2203	4300	6503	95059803	SO:0001583	missense	5166			U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.572T>C	7.37:g.95221867A>G	ENSP00000005178:p.Ile191Thr		95059803		Missense_Mutation	SNP	ENST00000005178.5	37	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.619477	0.87460	0.0	1.16E-4	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.38401	1.14	5.6	5.6	0.85130	ATPase-like, ATP-binding domain (1);Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.69967	0.3170	M	0.93978	3.48	0.80722	D	1	D	0.54047	0.964	D	0.74023	0.982	T	0.78074	-0.2346	10	0.62326	D	0.03	.	16.0934	0.81106	1.0:0.0:0.0:0.0	.	191	Q16654	PDK4_HUMAN	T	191;155	ENSP00000005178:I191T	ENSP00000005178:I191T	I	-	2	0	PDK4	95059803	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.109000	0.94291	2.254000	0.74563	0.528000	0.53228	ATT		0.328	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		G	95221867	A	G	95221867	3	3	105	1	0	0	0	0	1	0	0	0	11709	101	4	4	691	4	PDK4	7	95221867	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	5324233	95221867	63916796	106	27746										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107323968	107323968	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tacaatgctggcattgttaaAtccatcccaagggggtgagt	11	8	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:107323968A>G	ENST00000265715.3	+	8	1211	c.987A>G	c.(985-987)aaA>aaG	p.K329K		NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	329					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GCATTGTTAAATCCATCCCAA	0.333									Pendred syndrome																																							0			7											67	68	68					7																	107323968		2203	4300	6503	107111204	SO:0001819	synonymous_variant	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.987A>G	7.37:g.107323968A>G			107111204	B7Z266|O43170	Silent	SNP	ENST00000265715.3	37	CCDS5746.1																																																																																				0.333	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		G	107323968	A	G	107323968	2	3	105	1	0	0	0	0	0	0	0	1	14556	98	4	4		4	SLC26A4	7	107323968	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	12102101	107323968	51814695	107	27747										
LRRC4	64101	hgsc.bcm.edu	37	chr7	127668959	127668959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgctgttgctgctgcggatgTtgctgctgggatgtcttcgt	15	8	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:127668959T>C	ENST00000249363.3	-	2	1992	c.1735A>G	c.(1735-1737)Aca>Gca	p.T579A	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	579			T -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.T579A(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		gctgcggatgttgctgctgGG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	7											103	84	90					7																	127668959		2203	4300	6503	127456195	SO:0001583	missense	64101			AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"Immunoglobulin superfamily / I-set domain containing"	15586	protein-coding gene	gene with protein product		610486	"leucine-rich repeat-containing 4"			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1735A>G	7.37:g.127668959T>C	ENSP00000249363:p.Thr579Ala		127456195	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	37	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.455999	0.01071	.	.	ENSG00000128594	ENST00000249363	T	0.26223	1.75	4.24	2.39	0.29439	.	0.612104	0.15196	N	0.275281	T	0.08980	0.0222	N	0.08118	0	0.29210	N	0.874632	B	0.22346	0.068	B	0.15870	0.014	T	0.34104	-0.9842	10	0.02654	T	1	.	5.4652	0.16639	0.0:0.7427:0.0:0.2573	.	579	Q9HBW1	LRRC4_HUMAN	A	579	ENSP00000249363:T579A	ENSP00000249363:T579A	T	-	1	0	LRRC4	127456195	0.001000	0.12720	0.631000	0.29282	0.926000	0.56050	-0.172000	0.09868	1.100000	0.41517	-0.366000	0.07423	ACA		0.532	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		C	127668959	T	C	127668959	3	2	105	1	0	0	0	0	1	0	0	0	9026	1725	60	4	230	4	LRRC4	7	127668959	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	20344991	127668959	31469704	108	27748										
BRAF	673	hgsc.bcm.edu	37	chr7	140453155	140453155	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cactgtagctagaccaaaatCacctatttttactgtgaggt	7	9	1	2	rs397516896		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:140453155C>T	ENST00000288602.6	-	15	1840	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in NHL). {ECO:0000269|PubMed:14612909}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D594N(9)|p.D594H(2)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AGACCAAAATCACCTATTTTT	0.378		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	11	Substitution - Missense(11)	skin(6)|large_intestine(2)|lung(2)|haematopoietic_and_lymphoid_tissue(1)	7											106	100	102					7																	140453155		2203	4300	6503	140099624	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1780G>A	7.37:g.140453155C>T	ENSP00000288602:p.Asp594Asn		140099624	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	C	36	5.616687	0.96649	.	.	ENSG00000157764	ENST00000288602	D	0.99849	-7.15	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96728	0.9537	10	0.87932	D	0	.	19.7917	0.96461	0.0:1.0:0.0:0.0	.	594	P15056	BRAF_HUMAN	N	594	ENSP00000288602:D594N	ENSP00000288602:D594N	D	-	1	0	BRAF	140099624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.686000	0.91538	0.650000	0.86243	GAT		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453155	C	T	140453155	3	4	105	1	0	0	0	0	1	0	0	0	1499	826	29	3	536	3	BRAF	7	140453155	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	12784196	140453155	18685508	109	27749										
AGK	55750	hgsc.bcm.edu	37	chr7	141321598	141321598	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccacttgatgtcttgcagatCaaggtaaatcttttcatcac	6	10	5	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:141321598C>A	ENST00000355413.4	+	9	845	c.585C>A	c.(583-585)atC>atA	p.I195I	AGK_ENST00000535825.1_Silent_p.I192I|AGK_ENST00000473247.1_Silent_p.I167I	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	195	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					TCTTGCAGATCAAGGTAAATC	0.318																																																0			7											125	115	119					7																	141321598		2203	4300	6503	140968067	SO:0001819	synonymous_variant	55750			BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.585C>A	7.37:g.141321598C>A			140968067	Q75KN1|Q96GC3|Q9NP48	Silent	SNP	ENST00000355413.4	37	CCDS5865.1																																																																																				0.318	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		A	141321598	C	A	141321598	2	1	105	1	0	0	0	0	0	0	0	1	383	816	29	2		2	AGK	7	141321598	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	868443	141321598	17817065	110	27750										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142569702	142569702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtggaaggcctgtgcgtagcGttggatccgctgccggttga	17	9	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:142569702G>A	ENST00000359396.3	-	15	2181	c.1936C>T	c.(1936-1938)Cgc>Tgc	p.R646C		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	646					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					TGTGCGTAGCGTTGGATCCGC	0.567																																																0			7											123	114	117					7																	142569702		2203	4300	6503	142279824	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1936C>T	7.37:g.142569702G>A	ENSP00000352358:p.Arg646Cys		142279824	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540202	0.85917	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.47869	0.83	5.55	5.55	0.83447	.	0.125201	0.56097	D	0.000028	T	0.71913	0.3396	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75983	-0.3125	10	0.87932	D	0	-24.1221	16.6621	0.85243	0.0:0.0:1.0:0.0	.	646	Q9H1D0	TRPV6_HUMAN	C	646;478	ENSP00000352358:R646C	ENSP00000310825:R478C	R	-	1	0	TRPV6	142279824	1.000000	0.71417	0.959000	0.39883	0.742000	0.42306	3.877000	0.56123	2.622000	0.88805	0.561000	0.74099	CGC		0.567	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		A	142569702	G	A	142569702	3	1	105	1	0	0	0	0	1	0	0	0	16640	1145	40	1	245	1	TRPV6	7	142569702	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	1248104	142569702	16568961	111	27751										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142622681	142622681	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gaatgagtgcggttgccaccAcgaaacttaagggggcggta	15	8	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:142622681A>G	ENST00000265310.1	-	8	1413	c.1065T>C	c.(1063-1065)cgT>cgC	p.R355R	TRPV5_ENST00000442623.1_Silent_p.R355R	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	355					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					GGTTGCCACCACGAAACTTAA	0.522																																																0			7											122	107	112					7																	142622681		2203	4300	6503	142332803	SO:0001819	synonymous_variant	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1065T>C	7.37:g.142622681A>G			142332803	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	37	CCDS5875.1																																																																																				0.522	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		G	142622681	A	G	142622681	2	3	105	1	0	0	0	0	0	0	0	1	16639	146	6	4		4	TRPV5	7	142622681	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	52979	142622681	16515982	112	27752										
ABCB8	11194	hgsc.bcm.edu	37	chr7	150730984	150730984	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttctgcacccccacctgctgGtcctgggggtagccgtcgtg	13	15	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr7:150730984G>T	ENST00000297504.6	+	3	505	c.439G>T	c.(439-441)Gtc>Ttc	p.V147F	ABCB8_ENST00000477092.1_Missense_Mutation_p.V130F|ABCB8_ENST00000542328.1_Intron|ABCB8_ENST00000356058.4_Missense_Mutation_p.V167F|ABCB8_ENST00000493338.1_3'UTR|ABCB8_ENST00000477719.1_Missense_Mutation_p.V130F|ABCB8_ENST00000498578.1_Missense_Mutation_p.V130F|ABCB8_ENST00000358849.4_Missense_Mutation_p.V130F			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	147					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CCACCTGCTGGTCCTGGGGGT	0.627																																																0			7											47	45	46					7																	150730984		2203	4300	6503	150361917	SO:0001583	missense	11194			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.439G>T	7.37:g.150730984G>T	ENSP00000297504:p.Val147Phe		150361917	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		.	.	.	.	.	.	.	.	.	.	G	8.037	0.763075	0.15914	.	.	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;T;T;T	0.94457	-3.43;-3.43;-3.43;-1.37;-1.37;-1.37	4.18	-1.33	0.09172	ABC transporter, transmembrane domain, type 1 (1);	0.546488	0.19176	N	0.120801	D	0.83105	0.5182	N	0.08118	0	0.21697	N	0.999584	B;B;B;B;B	0.14438	0.003;0.003;0.002;0.01;0.01	B;B;B;B;B	0.29440	0.063;0.063;0.038;0.102;0.063	T	0.71708	-0.4511	10	0.09843	T	0.71	-0.8968	5.4438	0.16523	0.2704:0.4416:0.288:0.0	.	130;147;130;130;167	A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;ABCB8_HUMAN;.;.;.	F	130;113;147;130;167;130;130	ENSP00000351717:V130F;ENSP00000297504:V147F;ENSP00000418271:V130F;ENSP00000348353:V167F;ENSP00000419891:V130F;ENSP00000419558:V130F	ENSP00000297504:V147F	V	+	1	0	ABCB8	150361917	0.996000	0.38824	0.614000	0.29051	0.865000	0.49528	0.224000	0.17738	-0.386000	0.07821	0.561000	0.74099	GTC		0.627	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		T	150730984	G	T	150730984	3	4	105	1	0	0	0	0	1	0	0	0	47	1261	44	2	394	2	ABCB8	7	150730984	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	8108303	150730984	8407679	113	27753										
XKR6	286046	hgsc.bcm.edu	37	chr8	10756077	10756077	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcaaacattcgatatcgagtCcgcccttccttgacgttaaa	7	12	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:10756077C>T	ENST00000416569.2	-	3	1337	c.1311G>A	c.(1309-1311)cgG>cgA	p.R437R	XKR6_ENST00000304437.2_Silent_p.R158R	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	437						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GATATCGAGTCCGCCCTTCCT	0.473																																																0			8											138	119	125					8																	10756077		2203	4300	6503	10793487	SO:0001819	synonymous_variant	286046			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.1311G>A	8.37:g.10756077C>T			10793487	Q8TBA0	Silent	SNP	ENST00000416569.2	37	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	C	5.078	0.199971	0.09652	.	.	ENSG00000171044	ENST00000382461	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	T	0.74183	0.3683	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73300	-0.4026	4	.	.	.	-27.6178	17.8783	0.88831	0.0:1.0:0.0:0.0	.	.	.	.	E	214	.	.	G	-	2	0	XKR6	10793487	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.457000	0.83068	0.561000	0.74099	GGA		0.473	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		T	10756077	C	T	10756077	2	4	105	1	0	0	0	0	0	0	0	1	17475	842	30	3		3	XKR6	8	10756077	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		10756077	135607945	114	27754										
BMP1	649	hgsc.bcm.edu	37	chr8	22049654	22049654	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gatggcttctggaggaaggcGcccctccgaggtaacggcac	15	12	1	0	rs76021885	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:22049654G>T	ENST00000306385.5	+	9	1840	c.1170G>T	c.(1168-1170)gcG>gcT	p.A390A	BMP1_ENST00000397816.3_Silent_p.A390A|BMP1_ENST00000306349.8_Silent_p.A390A|BMP1_ENST00000397814.3_Silent_p.A390A|BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	390	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.A390A(2)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GGAGGAAGGCGCCCCTCCGAG	0.622													G|||	8	0.00159744	0.0061	0	5008	,	,		16647	0		0	False		,,,				2504	0															2	Substitution - coding silent(2)	lung(2)	8						G	,	20,4386	27.2+/-55.0	0,20,2183	138	116	123		1170,1170	-6	0.9	8	dbSNP_131	123	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BMP1	NM_001199.3,NM_006129.4	,	0,20,6483	TT,TG,GG		0.0,0.4539,0.1538	,	390/731,390/987	22049654	20,12986	2203	4300	6503	22105599	SO:0001819	synonymous_variant	649				CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1170G>T	8.37:g.22049654G>T			22105599	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																				0.622	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		T	22049654	G	T	22049654	2	4	105	1	0	0	0	0	0	0	0	1	1457	1074	38	2		2	BMP1	8	22049654	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	11293577	22049654	124314368	115	27755										
CHMP7	91782	hgsc.bcm.edu	37	chr8	23112920	23112920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcagaaggagaagagggtcaCagtcctcgagcagaacgggg	17	8	1	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:23112920C>T	ENST00000397677.1	+	4	1280	c.632C>T	c.(631-633)aCa>aTa	p.T211I	CHMP7_ENST00000313219.7_Missense_Mutation_p.T211I	NM_152272.3	NP_689485.1	Q8WUX9	CHMP7_HUMAN	charged multivesicular body protein 7	211					endosomal transport (GO:0016197)|late endosome to vacuole transport (GO:0045324)|membrane organization (GO:0061024)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|ESCRT III complex (GO:0000815)	protein transporter activity (GO:0008565)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		AAGAGGGTCACAGTCCTCGAG	0.522																																																0			8											116	103	108					8																	23112920		2203	4300	6503	23168865	SO:0001583	missense	91782			BC019110	CCDS6040.1	8p21.2	2011-09-21	2011-09-21		ENSG00000147457	ENSG00000147457		"Charged multivesicular body proteins"	28439	protein-coding gene	gene with protein product		611130	"CHMP family, member 7"			16856878	Standard	NM_152272		Approved	MGC29816	uc003xdc.2	Q8WUX9	OTTHUMG00000131785	ENST00000397677.1:c.632C>T	8.37:g.23112920C>T	ENSP00000380794:p.Thr211Ile		23168865	B2RDT3|B4DKJ6|D3DSS1|Q8NDM1|Q9BT50	Missense_Mutation	SNP	ENST00000397677.1	37	CCDS6040.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616627	0.87359	.	.	ENSG00000147457	ENST00000397677;ENST00000313219	T;T	0.58940	0.3;0.3	5.97	5.97	0.96955	.	0.139826	0.64402	D	0.000004	T	0.39545	0.1082	L	0.32530	0.975	0.48511	D	0.999664	P;P	0.40197	0.675;0.706	B;B	0.33121	0.158;0.115	T	0.42050	-0.9474	10	0.02654	T	1	-8.9085	14.5816	0.68295	0.0:0.8541:0.1459:0.0	.	101;211	B3KRZ9;Q8WUX9	.;CHMP7_HUMAN	I	211	ENSP00000380794:T211I;ENSP00000324491:T211I	ENSP00000324491:T211I	T	+	2	0	CHMP7	23168865	0.982000	0.34865	0.972000	0.41901	0.995000	0.86356	2.551000	0.45820	2.828000	0.97474	0.655000	0.94253	ACA		0.522	CHMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254717.1	NM_152272		T	23112920	C	T	23112920	3	4	105	1	0	0	0	0	1	0	0	0	3367	478	17	3	642	3	CHMP7	8	23112920	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	1063266	23112920	123251102	116	27756										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68102916	68102916	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gagacatatcctgccattgaAgatgacgtcctccctccacc	7	15	0	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:68102916A>G	ENST00000262210.5	+	27	3268	c.3237A>G	c.(3235-3237)gaA>gaG	p.E1079E	CSPP1_ENST00000521168.1_3'UTR|ARFGEF1_ENST00000520381.1_Intron|CSPP1_ENST00000412460.1_Silent_p.E734E	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1114					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CTGCCATTGAAGATGACGTCC	0.488																																																0			8											119	115	116					8																	68102916		1948	4138	6086	68265470	SO:0001819	synonymous_variant	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3237A>G	8.37:g.68102916A>G			68265470	A6ND63|Q70F00|Q8TBC1	Silent	SNP	ENST00000262210.5	37	CCDS43744.1																																																																																				0.488	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68102916	A	G	68102916	2	3	105	1	0	0	0	0	0	0	0	1	3968	69	3	4		4	CSPP1	8	68102916	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	44989996	68102916	78261106	117	27757										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70971028	70971028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgcttatctctgtaatatttGtaggtaaataccttcccaca	5	9	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:70971028G>A	ENST00000276594.2	-	6	1434	c.1233C>T	c.(1231-1233)taC>taT	p.Y411Y		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	411					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TGTAATATTTGTAGGTAAATA	0.453																																					NSCLC(129;99 1813 5906 40656 46114)											0			8											109	97	101					8																	70971028		2203	4300	6503	71133582	SO:0001819	synonymous_variant	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1233C>T	8.37:g.70971028G>A			71133582	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																				0.453	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			A	70971028	G	A	70971028	2	1	105	1	0	0	0	0	0	0	0	1	12489	1372	48	3		3	PRDM14	8	70971028	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2868112	70971028	75392994	118	27758										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848535	73848535	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcaggatcctgaaactcgcCaggcattcgacaggcctgca	10	14	1	1	rs556315875		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:73848535C>A	ENST00000523207.1	+	3	1533	c.945C>A	c.(943-945)gcC>gcA	p.A315A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	315					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TGAAACTCGCCAGGCATTCGA	0.512																																																0			8											77	76	76					8																	73848535		2203	4300	6503	74011089	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.945C>A	8.37:g.73848535C>A			74011089	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.512	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73848535	C	A	73848535	2	1	105	1	0	0	0	0	0	0	0	1	8034	581	21	2		2	KCNB2	8	73848535	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	2877507	73848535	72515487	119	27759										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95531470	95531470	+	Frame_Shift_Del	DEL	A	A	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aaggcaaatgcatcatcaatAacaccatcagattggagacc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:95531470delA	ENST00000297591.5	-	9	2331	c.2256delT	c.(2254-2256)gttfs	p.V752fs	KIAA1429_ENST00000421249.2_Frame_Shift_Del_p.V752fs|KIAA1429_ENST00000437199.1_Frame_Shift_Del_p.V752fs	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	752					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CATCATCAATAACACCATCAG	0.398																																																0			8											110	92	98					8																	95531470		2203	4300	6503	95600646	SO:0001589	frameshift_variant	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2256delT	8.37:g.95531470delA	ENSP00000297591:p.Val752fs		95600646	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Frame_Shift_Del	DEL	ENST00000297591.5	37	CCDS34923.1																																																																																				0.398	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		-	95531470	A	-	95531470	7	5	105	1	0	1	0	1	0	0	0	0	8252	349	13	0	3300	0	KIAA1429	8	95531470	Frame_Shift_Del	DEL	A	TCGA-DY-A1DD-01A-21D-A152-10	21682935	95531470	50832552	120	27760										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100128073	100128073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aatagaggaccttacttgtcAtaataaagatatgctaggaa	8	5	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:100128073A>G	ENST00000358544.2	+	7	1019	c.908A>G	c.(907-909)cAt>cGt	p.H303R	VPS13B_ENST00000395996.1_Missense_Mutation_p.H303R|VPS13B_ENST00000441350.2_Missense_Mutation_p.H303R|VPS13B_ENST00000357162.2_Missense_Mutation_p.H303R|VPS13B_ENST00000355155.1_Missense_Mutation_p.H303R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	303					protein transport (GO:0015031)			p.H303R(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTTACTTGTCATAATAAAGAT	0.299																																					Colon(161;2205 2542 7338 31318)											1	Substitution - Missense(1)	ovary(1)	8											67	69	68					8																	100128073		2203	4296	6499	100197249	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.908A>G	8.37:g.100128073A>G	ENSP00000351346:p.His303Arg		100197249	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.299077	0.23650	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	T;T;T;T;D	0.82433	-1.03;-0.32;-0.32;-0.03;-1.61	5.65	3.25	0.37280	.	0.339565	0.27451	N	0.019317	T	0.64114	0.2569	N	0.22421	0.69	0.29101	N	0.881461	P;B;B;B;B	0.34757	0.467;0.112;0.256;0.095;0.078	B;B;B;B;B	0.31547	0.132;0.015;0.086;0.023;0.033	T	0.54323	-0.8311	10	0.18710	T	0.47	.	3.2179	0.06705	0.6424:0.1406:0.0737:0.1433	.	303;303;303;303;303	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	R	303	ENSP00000347281:H303R;ENSP00000349685:H303R;ENSP00000351346:H303R;ENSP00000379318:H303R;ENSP00000398472:H303R	ENSP00000347281:H303R	H	+	2	0	VPS13B	100197249	0.980000	0.34600	0.997000	0.53966	0.775000	0.43874	2.275000	0.43399	0.940000	0.37473	0.533000	0.62120	CAT		0.299	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100128073	A	G	100128073	3	3	105	1	0	0	0	0	1	0	0	0	17230	217	8	4	930	4	VPS13B	8	100128073	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4596603	100128073	46235949	121	27761										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124381300	124381300	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	actatatcagaaccaaacctGttcattcgtttacagtaagg	6	9	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:124381300G>C	ENST00000287394.5	-	8	1154	c.1047C>G	c.(1045-1047)aaC>aaG	p.N349K	ATAD2_ENST00000534257.1_5'UTR|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	349					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AACCAAACCTGTTCATTCGTT	0.388																																																0			8											105	93	97					8																	124381300		2203	4300	6503	124450481	SO:0001583	missense	29028			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1047C>G	8.37:g.124381300G>C	ENSP00000287394:p.Asn349Lys		124450481	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.634813	0.29068	.	.	ENSG00000156802	ENST00000287394	D	0.91631	-2.88	5.34	5.34	0.76211	.	0.360715	0.20098	U	0.099297	D	0.85314	0.5668	N	0.22421	0.69	0.80722	D	1	B;B	0.14805	0.011;0.002	B;B	0.16289	0.015;0.004	T	0.79230	-0.1889	10	0.05436	T	0.98	-10.2378	18.183	0.89785	0.0:0.0:1.0:0.0	.	179;349	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	K	349	ENSP00000287394:N349K	ENSP00000287394:N349K	N	-	3	2	ATAD2	124450481	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.379000	0.44318	2.645000	0.89757	0.650000	0.86243	AAC		0.388	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		C	124381300	G	C	124381300	3	2	105	1	0	0	0	0	1	0	0	0	1072	1368	48	5	3209	5	ATAD2	8	124381300	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	24253227	124381300	21982722	122	27762										
ADCY8	114	hgsc.bcm.edu	37	chr8	131826350	131826350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cttctctaggaaatggcgggCcacatggctgggtaagatat	13	8	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:131826350C>T	ENST00000286355.5	-	14	4970	c.2878G>A	c.(2878-2880)Gcc>Acc	p.A960T	ADCY8_ENST00000377928.3_Missense_Mutation_p.A829T	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	960					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AAATGGCGGGCCACATGGCTG	0.527										HNSCC(32;0.087)																																						0			8											179	139	153					8																	131826350		2203	4300	6503	131895532	SO:0001583	missense	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2878G>A	8.37:g.131826350C>T	ENSP00000286355:p.Ala960Thr		131895532		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	36	5.803609	0.96960	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	D;D	0.84873	-1.91;-1.8	5.87	5.87	0.94306	Adenylyl cyclase class-3/4/guanylyl cyclase (1);	0.000000	0.85682	D	0.000000	D	0.93471	0.7917	M	0.86953	2.85	0.47659	D	0.999485	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93793	0.7094	10	0.87932	D	0	.	17.7375	0.88397	0.0:1.0:0.0:0.0	.	829;960	E7EVL1;P40145	.;ADCY8_HUMAN	T	960;829	ENSP00000286355:A960T;ENSP00000367161:A829T	ENSP00000286355:A960T	A	-	1	0	ADCY8	131895532	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.432000	0.80349	2.941000	0.99782	0.655000	0.94253	GCC		0.527	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131826350	C	T	131826350	3	4	105	1	0	0	0	0	1	0	0	0	300	739	26	3	897	3	ADCY8	8	131826350	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	7445050	131826350	14537672	123	27763										
KCNK9	51305	hgsc.bcm.edu	37	chr8	140630763	140630763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	actgcaggtccgggacgtccGccttgtacctgggccggctg	15	14	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr8:140630763G>A	ENST00000520439.1	-	2	926	c.863C>T	c.(862-864)gCg>gTg	p.A288V	KCNK9_ENST00000303015.1_Missense_Mutation_p.A288V|KCNK9_ENST00000523477.1_5'Flank	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	288					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A288V(1)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGGGACGTCCGCCTTGTACCT	0.667																																																1	Substitution - Missense(1)	ovary(1)	8											48	53	51					8																	140630763		2203	4300	6503	140699945	SO:0001583	missense	51305			AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.863C>T	8.37:g.140630763G>A	ENSP00000430676:p.Ala288Val		140699945	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	37	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676779	0.47886	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.17528	2.27;2.27;2.27	5.53	3.67	0.42095	.	1.078660	0.07116	N	0.843000	T	0.22282	0.0537	M	0.63843	1.955	0.26385	N	0.976664	B	0.26876	0.162	B	0.25759	0.063	T	0.42258	-0.9462	10	0.15066	T	0.55	.	14.9469	0.71039	0.0:0.2816:0.7184:0.0	.	288	Q9NPC2	KCNK9_HUMAN	V	288	ENSP00000429847:A288V;ENSP00000302166:A288V;ENSP00000430676:A288V	ENSP00000302166:A288V	A	-	2	0	KCNK9	140699945	0.997000	0.39634	0.905000	0.35620	0.886000	0.51366	3.277000	0.51654	0.624000	0.30286	0.591000	0.81541	GCG		0.667	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		A	140630763	G	A	140630763	3	1	105	1	0	0	0	0	1	0	0	0	8093	1087	38	1	265	1	KCNK9	8	140630763	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	8804413	140630763	5733259	124	27764										
RPS6	6194	hgsc.bcm.edu	37	chr9	19378482	19378482	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccaggcggcgaggcactgtaGtatcagtcagtccaggaata	13	10	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:19378482G>T	ENST00000380394.4	-	4	438	c.380C>A	c.(379-381)aCt>aAt	p.T127N	RPS6_ENST00000498815.1_5'Flank|RPS6_ENST00000380384.1_Missense_Mutation_p.T96N|RP11-513M16.8_ENST00000609982.1_RNA|RPS6_ENST00000315377.4_Missense_Mutation_p.T96N	NM_001010.2	NP_001001.2	P62753	RS6_HUMAN	ribosomal protein S6	127					activation-induced cell death of T cells (GO:0006924)|cellular protein metabolic process (GO:0044267)|erythrocyte development (GO:0048821)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|oogenesis stage (GO:0022605)|placenta development (GO:0001890)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit assembly (GO:0000028)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell differentiation in thymus (GO:0033077)|T cell proliferation involved in immune response (GO:0002309)|TOR signaling (GO:0031929)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|dendrite (GO:0030425)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|urinary_tract(1)	7		Colorectal(97;3.46e-05)|Myeloproliferative disorder(762;0.0255)		Lung(42;0.161)|LUSC - Lung squamous cell carcinoma(42;0.234)		AGGCACTGTAGTATCAGTCAG	0.403																																																0			9											64	65	64					9																	19378482		2203	4300	6503	19368482	SO:0001583	missense	6194				CCDS6492.1	9p21	2011-04-05			ENSG00000137154	ENSG00000137154		"S ribosomal proteins"	10429	protein-coding gene	gene with protein product	"40S ribosomal protein S6", "phosphoprotein NP33"	180460				1577483	Standard	NM_001010		Approved	S6	uc003znv.1	P62753	OTTHUMG00000019642	ENST00000380394.4:c.380C>A	9.37:g.19378482G>T	ENSP00000369757:p.Thr127Asn		19368482	P08227|P10660|Q4VBY7|Q8N6Z7	Missense_Mutation	SNP	ENST00000380394.4	37	CCDS6492.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312049	0.23821	.	.	ENSG00000137154	ENST00000380394;ENST00000380384;ENST00000315377	T;T;T	0.47177	0.85;0.86;0.86	5.32	5.32	0.75619	.	0.154832	0.56097	D	0.000036	T	0.44644	0.1303	L	0.60012	1.86	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.15484	0.013;0.013	T	0.27606	-1.0069	9	.	.	.	-14.3693	14.227	0.65866	0.0:0.0:0.8508:0.1492	.	96;127	A2A3R5;P62753	.;RS6_HUMAN	N	127;96;96	ENSP00000369757:T127N;ENSP00000369745:T96N;ENSP00000369743:T96N	.	T	-	2	0	RPS6	19368482	1.000000	0.71417	0.959000	0.39883	0.110000	0.19582	3.653000	0.54446	2.646000	0.89796	0.655000	0.94253	ACT		0.403	RPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051858.1	NM_001010		T	19378482	G	T	19378482	3	4	105	1	0	0	0	0	1	0	0	0	13686	1029	36	2	381	2	RPS6	9	19378482	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		19378482	121834949	125	27765										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632174	32632174	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cctcccattcacgtgacagcTgagagctggttttcttgttc	9	12	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:32632174T>C	ENST00000242310.4	-	1	3493	c.3404A>G	c.(3403-3405)cAg>cGg	p.Q1135R	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1135					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ACGTGACAGCTGAGAGCTGGT	0.468																																																0			9											216	171	186					9																	32632174		2203	4300	6503	32622174	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3404A>G	9.37:g.32632174T>C	ENSP00000418379:p.Gln1135Arg		32622174	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.489789	0.44249	.	.	ENSG00000122728	ENST00000242310	T	0.08282	3.11	0.479	0.479	0.16796	.	0.000000	0.85682	D	0.000000	T	0.08179	0.0204	L	0.56769	1.78	0.49389	D	0.999782	B	0.22800	0.075	B	0.22753	0.041	T	0.13818	-1.0495	10	0.56958	D	0.05	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1135	Q8IZX4	TAF1L_HUMAN	R	1135	ENSP00000418379:Q1135R	ENSP00000418379:Q1135R	Q	-	2	0	TAF1L	32622174	1.000000	0.71417	0.995000	0.50966	0.677000	0.39632	5.066000	0.64351	0.426000	0.26116	0.164000	0.16699	CAG		0.468	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			C	32632174	T	C	32632174	3	2	105	1	0	0	0	0	1	0	0	0	15562	1580	55	4	2080	4	TAF1L	9	32632174	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	13253692	32632174	108581257	126	27766										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77386705	77386705	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tatttttccacgcactgctcCtcaaaatcatgaagtttttt	4	10	2	1	rs138880537	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:77386705C>T	ENST00000360774.1	-	25	3687	c.3450G>A	c.(3448-3450)gaG>gaA	p.E1150E	TRPM6_ENST00000451710.3_Silent_p.E1150E|TRPM6_ENST00000361255.3_Silent_p.E1145E|TRPM6_ENST00000376864.4_Silent_p.E1150E|TRPM6_ENST00000449912.2_Silent_p.E1145E|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376872.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1150					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.E1150E(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CGCACTGCTCCTCAAAATCAT	0.368													C|||	2	0.000399361	0	0	5008	,	,		18292	0		0.002	False		,,,				2504	0															1	Substitution - coding silent(1)	lung(1)	9						C	,,	0,4406		0,0,2203	111	101	104		3435,3435,3450	-0.8	1	9	dbSNP_134	104	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,	1145/2018,1145/2018,1150/2023	77386705	2,13004	2203	4300	6503	76576525	SO:0001819	synonymous_variant	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3450G>A	9.37:g.77386705C>T			76576525	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																				0.368	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77386705	C	T	77386705	2	4	105	1	0	0	0	0	0	0	0	1	16630	680	24	3		3	TRPM6	9	77386705	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	44754531	77386705	63826726	127	27767										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98231075	98231075	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aaaggagcatagtgcttctcAgcaaaagatgagagtgtcca	11	7	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:98231075A>G	ENST00000331920.6	-	14	2507	c.2208T>C	c.(2206-2208)gcT>gcC	p.A736A	PTCH1_ENST00000437951.1_Silent_p.A670A|PTCH1_ENST00000430669.2_Silent_p.A670A|PTCH1_ENST00000375274.2_Silent_p.A735A|PTCH1_ENST00000429896.2_Silent_p.A585A|PTCH1_ENST00000421141.1_Silent_p.A585A|PTCH1_ENST00000418258.1_Silent_p.A585A	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	736					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGTGCTTCTCAGCAAAAGATG	0.502																																																0			9											134	148	143					9																	98231075		2203	4300	6503	97270896	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2208T>C	9.37:g.98231075A>G			97270896	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.502	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		G	98231075	A	G	98231075	2	3	105	1	0	0	0	0	0	0	0	1	12764	175	7	4		4	PTCH1	9	98231075	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	20844370	98231075	42982356	128	27768										
TNC	3371	hgsc.bcm.edu	37	chr9	117808873	117808873	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attttgagaacaaaattgtcGaagaccccttcatcagctgt	7	9	2	2	rs201689087		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:117808873G>A	ENST00000350763.4	-	17	5352	c.4941C>T	c.(4939-4941)ttC>ttT	p.F1647F	TNC_ENST00000542877.1_Silent_p.F1284F|TNC_ENST00000481475.1_5'Flank|TNC_ENST00000340094.3_Silent_p.F1283F|TNC_ENST00000423613.2_Intron|TNC_ENST00000341037.4_Silent_p.F1465F|TNC_ENST00000535648.1_Silent_p.F1192F|TNC_ENST00000345230.3_Intron|TNC_ENST00000537320.1_Intron|TNC_ENST00000346706.3_Silent_p.F1101F	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1647	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CAAAATTGTCGAAGACCCCTT	0.502													G|||	1	0.000199681	0	0	5008	,	,		19157	0		0.001	False		,,,				2504	0															0			9											76	80	79					9																	117808873		2203	4300	6503	116848694	SO:0001819	synonymous_variant	7134				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.4941C>T	9.37:g.117808873G>A			116848694	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.262	0.416385	0.11870	.	.	ENSG00000041982	ENST00000544972	.	.	.	5.94	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9139	0.35570	0.2315:0.0:0.7685:0.0	.	.	.	.	X	210	.	.	R	-	1	2	TNC	116848694	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.394000	0.44450	0.779000	0.33543	0.655000	0.94253	CGA		0.502	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		A	117808873	G	A	117808873	2	1	105	1	0	0	0	0	0	0	0	1	16309	1049	37	1		1	TNC	9	117808873	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	19577798	117808873	23404558	129	27769										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119737511	119737511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	catctgcagggtcttccgtgAcgagcacatcggtcttgcag	12	12	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:119737511A>G	ENST00000313400.4	-	10	1965	c.1865T>C	c.(1864-1866)gTc>gCc	p.V622A	ASTN2_ENST00000373996.3_Missense_Mutation_p.V618A|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.V571A			O75129	ASTN2_HUMAN	astrotactin 2	622					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GTCTTCCGTGACGAGCACATC	0.547																																																0			9											88	88	88					9																	119737511		2203	4300	6503	118777332	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1865T>C	9.37:g.119737511A>G	ENSP00000314038:p.Val622Ala		118777332	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	A	20.3	3.968187	0.74131	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.15256	2.6;2.6;2.44;2.64	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.71674	0.998;0.991;0.995	D;P;D	0.77557	0.99;0.82;0.91	T	0.02179	-1.1200	9	.	.	.	-37.0355	16.1282	0.81408	1.0:0.0:0.0:0.0	.	571;622;618	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	A	622;618;345;571	ENSP00000314038:V622A;ENSP00000363108:V618A;ENSP00000363098:V345A;ENSP00000354504:V571A	.	V	-	2	0	ASTN2	118777332	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.209000	0.71365	0.459000	0.35465	GTC		0.547	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		G	119737511	A	G	119737511	3	3	105	1	0	0	0	0	1	0	0	0	1066	275	10	4	2442	4	ASTN2	9	119737511	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	1928638	119737511	21475920	130	27770										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140082199	140082199	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtgctaaagaacaagactccGcgcaacatagtgtggacttc	10	10	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr9:140082199G>A	ENST00000323927.2	-	2	478	c.474C>T	c.(472-474)cgC>cgT	p.R158R	SSNA1_ENST00000322310.5_5'Flank	NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	158					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		ACAAGACTCCGCGCAACATAG	0.547																																																0			9											81	83	83					9																	140082199		2203	4300	6503	139202020	SO:0001819	synonymous_variant	29882			AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.474C>T	9.37:g.140082199G>A			139202020	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Silent	SNP	ENST00000323927.2	37	CCDS7033.1																																																																																				0.547	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		A	140082199	G	A	140082199	2	1	105	1	0	0	0	0	0	0	0	1	603	1074	38	1		1	ANAPC2	9	140082199	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	20344688	140082199	1131232	131	27771										
C10orf111	221060	hgsc.bcm.edu	37	chr10	15138522	15138522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtcttctaagttctggccaaGggtagatcaacagatccaga	10	9	4	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr10:15138522G>T	ENST00000378207.3	-	2	575	c.302C>A	c.(301-303)cCt>cAt	p.P101H	RPP38_ENST00000378202.5_5'Flank|RPP38_ENST00000378197.4_5'Flank	NM_153244.1	NP_694976.1	Q8N326	CJ111_HUMAN	chromosome 10 open reading frame 111	101						integral component of membrane (GO:0016021)				lung(5)|upper_aerodigestive_tract(1)	6						TTCTGGCCAAGGGTAGATCAA	0.522																																																0			10											113	116	115					10																	15138522		2203	4300	6503	15178528	SO:0001583	missense	221060			BC029034	CCDS7107.1	10p13	2004-04-20			ENSG00000176236	ENSG00000176236			28582	protein-coding gene	gene with protein product						12477932	Standard	NM_153244		Approved	MGC35468, bA455B2.4	uc001inw.3	Q8N326	OTTHUMG00000017727	ENST00000378207.3:c.302C>A	10.37:g.15138522G>T	ENSP00000367449:p.Pro101His		15178528	B2RAC4	Missense_Mutation	SNP	ENST00000378207.3	37	CCDS7107.1	.	.	.	.	.	.	.	.	.	.	G	5.354	0.250640	0.10130	.	.	ENSG00000176236	ENST00000378207	T	0.57907	0.37	3.08	2.17	0.27698	.	.	.	.	.	T	0.44138	0.1279	N	0.08118	0	0.09310	N	1	D	0.71674	0.998	P	0.59012	0.85	T	0.22765	-1.0207	9	0.87932	D	0	.	6.3151	0.21186	0.1397:0.0:0.8603:0.0	.	101	Q8N326	CJ111_HUMAN	H	101	ENSP00000367449:P101H	ENSP00000367449:P101H	P	-	2	0	C10orf111	15178528	0.000000	0.05858	0.003000	0.11579	0.064000	0.16182	0.408000	0.21065	0.853000	0.35312	0.407000	0.27541	CCT		0.522	C10orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046975.1	NM_153244		T	15138522	G	T	15138522	3	4	105	1	0	0	0	0	1	0	0	0	1587	1000	35	2	169	2	C10orf111	10	15138522	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		15138522	120396225	132	27772										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78944639	78944639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccatgtcgatctgtaatgtgAaatctttgtagaaattctgg	9	6	3	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr10:78944639A>G	ENST00000286628.8	-	4	637	c.638T>C	c.(637-639)tTc>tCc	p.F213S	KCNMA1_ENST00000404771.3_Missense_Mutation_p.F213S|KCNMA1_ENST00000406533.3_Missense_Mutation_p.F213S|KCNMA1_ENST00000286627.5_Missense_Mutation_p.F213S|KCNMA1_ENST00000372440.1_Missense_Mutation_p.F213S|KCNMA1_ENST00000354353.5_Missense_Mutation_p.F213S|KCNMA1_ENST00000372443.1_Missense_Mutation_p.F213S|KCNMA1_ENST00000404857.1_Missense_Mutation_p.F213S	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	213					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.F213C(1)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CTGTAATGTGAAATCTTTGTA	0.418																																																1	Substitution - Missense(1)	ovary(1)	10											171	154	160					10																	78944639		2203	4300	6503	78614645	SO:0001583	missense	3778			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.638T>C	10.37:g.78944639A>G	ENSP00000286628:p.Phe213Ser		78614645	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.86|12.86	2.065482|2.065482	0.36470|0.36470	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857|ENST00000372403	T;T;T;T;T;T;T;T;T|.	0.39997|.	1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.053287|.	0.85682|.	D|.	0.000000|.	T|T	0.39708|0.39708	0.1088|0.1088	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B|.	0.28208|.	0.203;0.008;0.026;0.008;0.03;0.002|.	B;B;B;B;B;B|.	0.29077|.	0.098;0.019;0.043;0.028;0.043;0.005|.	T|T	0.32719|0.32719	-0.9896|-0.9896	10|5	0.22706|.	T|.	0.39|.	-20.8216|-20.8216	15.9692|15.9692	0.79998|0.79998	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	213;213;213;213;213;213|.	Q12791-4;B7ZMF5;Q12791-2;Q12791;Q12791-5;Q5SVJ7|.	.;.;.;KCMA1_HUMAN;.;.|.	S|P	213;150;148;187;150;213;213;187;213;213;213|164	ENSP00000361517:F213S;ENSP00000361485:F150S;ENSP00000361514:F148S;ENSP00000396608:F187S;ENSP00000361520:F213S;ENSP00000286627:F213S;ENSP00000385552:F213S;ENSP00000346321:F213S;ENSP00000385806:F213S|.	ENSP00000286627:F213S|.	F|S	-|-	2|1	0|0	KCNMA1|KCNMA1	78614645|78614645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.216000|9.216000	0.95154|0.95154	2.302000|2.302000	0.77476|0.77476	0.533000|0.533000	0.62120|0.62120	TTC|TCA		0.418	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		G	78944639	A	G	78944639	3	3	105	1	0	0	0	0	1	0	0	0	8094	246	9	4	3344	4	KCNMA1	10	78944639	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	63806117	78944639	56590108	133	27773										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692999	89692999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tatggggaagtaaggaccagAgacaaaaaggtaagttattt	12	3	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr10:89692999A>G	ENST00000371953.3	+	5	1840	c.483A>G	c.(481-483)agA>agG	p.R161R		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	161	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(5)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TAAGGACCAGAGACAAAAAGG	0.363		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											50	52	51					10																	89692999		2203	4300	6503	89682979	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.483A>G	10.37:g.89692999A>G			89682979	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.363	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692999	A	G	89692999	2	3	105	1	0	0	0	0	0	0	0	1	12772	301	11	4		4	PTEN	10	89692999	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	10748360	89692999	45841748	134	27774										
PSMD13	5719	hgsc.bcm.edu	37	chr11	247370	247370	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atctctccagtaaatactatCaaacaatcggaaaccacgcg	5	12	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:247370C>A	ENST00000532097.1	+	7	994	c.490C>A	c.(490-492)Caa>Aaa	p.Q164K	PSMD13_ENST00000352303.5_Missense_Mutation_p.Q164K|PSMD13_ENST00000431206.2_Missense_Mutation_p.Q166K	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	164					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.Q164E(1)|p.Q166E(1)		NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TAAATACTATCAAACAATCGG	0.423																																																2	Substitution - Missense(2)	ovary(2)	11											113	97	103					11																	247370		2203	4300	6503	237370	SO:0001583	missense	5719			AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.490C>A	11.37:g.247370C>A	ENSP00000436186:p.Gln164Lys		237370	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.119120	0.56505	.	.	ENSG00000185627	ENST00000532097;ENST00000538343;ENST00000431206;ENST00000528906;ENST00000352303	T;T;T;T	0.12569	2.67;2.68;2.69;2.7	5.71	5.71	0.89125	.	0.275074	0.42294	D	0.000734	T	0.09512	0.0234	N	0.17901	0.54	0.52099	D	0.999944	B;B;B;B	0.22003	0.063;0.001;0.004;0.004	B;B;B;B	0.18871	0.023;0.004;0.003;0.003	T	0.07693	-1.0759	10	0.02654	T	1	.	18.8888	0.92389	0.0:1.0:0.0:0.0	.	166;99;164;164	Q9UNM6-2;B4DJ66;B2RBM7;Q9UNM6	.;.;.;PSD13_HUMAN	K	164;99;166;126;164	ENSP00000436186:Q164K;ENSP00000396937:Q166K;ENSP00000433364:Q126K;ENSP00000333811:Q164K	ENSP00000333811:Q164K	Q	+	1	0	PSMD13	237370	1.000000	0.71417	0.986000	0.45419	0.898000	0.52572	6.076000	0.71267	2.890000	0.99128	0.650000	0.86243	CAA		0.423	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		A	247370	C	A	247370	3	1	105	1	0	0	0	0	1	0	0	0	12730	827	29	2	597	2	PSMD13	11	247370	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		247370	134759146	135	27775										
OR56B4	196335	hgsc.bcm.edu	37	chr11	6129813	6129813	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgctgtctgtcacacaccttGcagagaaaaagattcccctt	7	12	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:6129813G>T	ENST00000316529.3	+	1	900	c.805G>T	c.(805-807)Gca>Tca	p.A269S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A269T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACACACCTTGCAGAGAAAAA	0.512																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											115	114	114					11																	6129813		2201	4296	6497	6086389	SO:0001583	missense	196335			AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"GPCR / Class A : Olfactory receptors"	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.805G>T	11.37:g.6129813G>T	ENSP00000321196:p.Ala269Ser		6086389	Q6IFD7	Missense_Mutation	SNP	ENST00000316529.3	37	CCDS31406.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420475	0.25639	.	.	ENSG00000180919	ENST00000316529	T	0.00019	9.06	4.01	4.01	0.46588	.	0.209872	0.23569	U	0.046772	T	0.00178	0.0005	L	0.53617	1.68	0.09310	N	1	B	0.33919	0.432	B	0.39531	0.302	T	0.32481	-0.9905	10	0.72032	D	0.01	.	12.0357	0.53423	0.0:0.0:0.815:0.185	.	269	Q8NH76	O56B4_HUMAN	S	269	ENSP00000321196:A269S	ENSP00000321196:A269S	A	+	1	0	OR56B4	6086389	0.007000	0.16637	0.137000	0.22149	0.773000	0.43773	1.281000	0.33214	2.220000	0.72140	0.549000	0.68633	GCA		0.512	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181		T	6129813	G	T	6129813	3	4	105	1	0	0	0	0	1	0	0	0	11169	1319	46	2	807	2	OR56B4	11	6129813	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	5882443	6129813	128876703	136	27776										
MADD	8567	hgsc.bcm.edu	37	chr11	47310525	47310525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attttgtgtcccagtatttgGgctaaatactctaatggaga	9	6	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:47310525G>A	ENST00000311027.5	+	16	2825	c.2660G>A	c.(2659-2661)gGg>gAg	p.G887E	MADD_ENST00000402799.1_Intron|MADD_ENST00000406482.1_Intron|MADD_ENST00000402192.2_Intron|MADD_ENST00000407859.3_Missense_Mutation_p.G844E|MADD_ENST00000349238.3_Missense_Mutation_p.G887E|MADD_ENST00000342922.4_Intron|MADD_ENST00000395336.3_Missense_Mutation_p.G887E|MADD_ENST00000395344.3_Intron	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		CCAGTATTTGGGCTAAATACT	0.473																																																0			11											166	173	171					11																	47310525		2201	4298	6499	47267101	SO:0001583	missense	8567			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.2660G>A	11.37:g.47310525G>A	ENSP00000310933:p.Gly887Glu		47267101		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	33	5.199168	0.94997	.	.	ENSG00000110514	ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395336	T;T;T;T	0.07021	3.46;3.48;3.23;3.47	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	T	0.00651	-1.1626	10	0.59425	D	0.04	-21.928	20.422	0.99049	0.0:0.0:1.0:0.0	.	887;887;844;887	Q8WXG6-7;Q8WXG6-2;Q8WXG6-4;Q8WXG6	.;.;.;MADD_HUMAN	E	887;887;844;887	ENSP00000304505:G887E;ENSP00000310933:G887E;ENSP00000384204:G844E;ENSP00000378745:G887E	ENSP00000310933:G887E	G	+	2	0	MADD	47267101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.832000	0.97577	0.655000	0.94253	GGG		0.473	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			A	47310525	G	A	47310525	3	1	105	1	0	0	0	0	1	0	0	0	9182	1232	43	3	2718	3	MADD	11	47310525	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	41180712	47310525	87695991	137	27777										
SYT7	9066	hgsc.bcm.edu	37	chr11	61295556	61295556	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttcatgatcttcacggtgagCgtggactcctggaagttgta	12	8	3	2	rs372903756		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:61295556C>T	ENST00000263846.4	-	5	780	c.453G>A	c.(451-453)acG>acA	p.T151T	SYT7_ENST00000535826.1_Silent_p.T270T|SYT7_ENST00000542836.1_Silent_p.T195T|SYT7_ENST00000539008.1_Silent_p.T434T|SYT7_ENST00000542670.1_Silent_p.T359T|SYT7_ENST00000540677.1_Silent_p.T226T|SYT7_ENST00000540831.1_5'UTR	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	151	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TCACGGTGAGCGTGGACTCCT	0.622																																																0			11						C		0,4404		0,0,2202	73	77	75		453	-4.3	1	11		75	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	SYT7	NM_004200.2		0,1,6500	TT,TC,CC		0.0116,0.0,0.0077		151/404	61295556	1,13001	2202	4299	6501	61052132	SO:0001819	synonymous_variant	9066			AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"Synaptotagmins"	11514	protein-coding gene	gene with protein product		604146	"prostate cancer associated protein 7"	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.453G>A	11.37:g.61295556C>T			61052132	F5GZU9|Q08AH6	Silent	SNP	ENST00000263846.4	37	CCDS31577.1																																																																																				0.622	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		T	61295556	C	T	61295556	2	4	105	1	0	0	0	0	0	0	0	1	15518	755	27	1		1	SYT7	11	61295556	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	13985031	61295556	73710960	138	27778										
SF1	7536	hgsc.bcm.edu	37	chr11	64544047	64544047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctggaatcactgtcttctgtTccattgtgtcttggttccag	9	10	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:64544047T>C	ENST00000377390.3	-	2	420	c.83A>G	c.(82-84)gAa>gGa	p.E28G	SF1_ENST00000334944.5_Missense_Mutation_p.E28G|SF1_ENST00000377387.1_Missense_Mutation_p.E153G|AP001462.6_ENST00000594089.1_lincRNA|SF1_ENST00000377394.3_Missense_Mutation_p.E28G|SF1_ENST00000433274.2_Missense_Mutation_p.E2G|SF1_ENST00000422298.2_5'UTR|SF1_ENST00000227503.9_Missense_Mutation_p.E28G	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	28					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						TGTCTTCTGTTCCATTGTGTC	0.423																																																0			11											156	146	150					11																	64544047		2201	4297	6498	64300623	SO:0001583	missense	7536			D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.83A>G	11.37:g.64544047T>C	ENSP00000366607:p.Glu28Gly		64300623	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	37	CCDS31599.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.676175	0.67928	.	.	ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000377394;ENST00000334944;ENST00000433274;ENST00000432725;ENST00000416674	T;T;T;T;T;T	0.49432	0.8;0.82;0.83;0.82;0.82;0.78	5.32	5.32	0.75619	.	0.056472	0.64402	D	0.000002	T	0.46014	0.1371	L	0.38175	1.15	0.80722	D	1	P;B;B;B;B;B	0.40660	0.726;0.013;0.013;0.016;0.027;0.074	P;B;B;B;B;B	0.46026	0.501;0.008;0.008;0.011;0.026;0.026	T	0.42716	-0.9435	10	0.45353	T	0.12	.	13.2284	0.59927	0.0:0.0:0.0:1.0	.	28;28;28;28;28;153	Q14820;Q15637-6;Q15637-4;Q15637;Q15637-2;Q15637-5	.;.;.;SF01_HUMAN;.;.	G	153;28;28;28;28;2;2;28	ENSP00000366604:E153G;ENSP00000366607:E28G;ENSP00000227503:E28G;ENSP00000366611:E28G;ENSP00000334414:E28G;ENSP00000396793:E2G	ENSP00000227503:E28G	E	-	2	0	SF1	64300623	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.633000	0.67825	2.017000	0.59298	0.460000	0.39030	GAA		0.423	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		C	64544047	T	C	64544047	3	2	105	1	0	0	0	0	1	0	0	0	14182	1783	62	4	2022	4	SF1	11	64544047	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	3248491	64544047	70462469	139	27779										
MEN1	4221	hgsc.bcm.edu	37	chr11	64575485	64575485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tacccaggcatgatcctcagAcagggcgaggtggacatccc	12	13	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:64575485A>G	ENST00000337652.1	-	3	1050	c.547T>C	c.(547-549)Tct>Cct	p.S183P	MEN1_ENST00000443283.1_Missense_Mutation_p.S183P|MEN1_ENST00000312049.6_Missense_Mutation_p.S178P|MEN1_ENST00000394376.1_Missense_Mutation_p.S183P|MEN1_ENST00000478548.1_5'Flank|MEN1_ENST00000377326.3_Missense_Mutation_p.S178P|MEN1_ENST00000377313.1_Missense_Mutation_p.S183P|MEN1_ENST00000394374.2_Missense_Mutation_p.S183P|MEN1_ENST00000315422.4_Missense_Mutation_p.S178P|MEN1_ENST00000377316.2_Missense_Mutation_p.S178P|MEN1_ENST00000377321.1_Missense_Mutation_p.S178P	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	183					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TGATCCTCAGACAGGGCGAGG	0.642			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	0			11											64	55	58					11																	64575485		2201	4297	6498	64332061	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.547T>C	11.37:g.64575485A>G	ENSP00000337088:p.Ser183Pro		64332061	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.606268	0.87157	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626	D;D;D;D;D;D;D;D;D;D;D;D;D	0.99656	-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31	4.76	4.76	0.60689	.	0.134605	0.51477	D	0.000091	D	0.99438	0.9801	M	0.69358	2.11	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.83275	0.989;0.986;0.996	D	0.98479	1.0604	10	0.87932	D	0	-7.9992	12.6037	0.56511	1.0:0.0:0.0:0.0	.	178;178;183	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	P	178;178;178;178;178;183;183;183;183;183;178;178;178	ENSP00000366533:S178P;ENSP00000366538:S178P;ENSP00000366543:S178P;ENSP00000308975:S178P;ENSP00000323747:S178P;ENSP00000337088:S183P;ENSP00000377901:S183P;ENSP00000377899:S183P;ENSP00000396940:S183P;ENSP00000366530:S183P;ENSP00000413944:S178P;ENSP00000394933:S178P;ENSP00000411218:S178P	ENSP00000308975:S178P	S	-	1	0	MEN1	64332061	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.395000	0.73228	1.930000	0.55929	0.374000	0.22700	TCT		0.642	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			G	64575485	A	G	64575485	3	3	105	1	0	0	0	0	1	0	0	0	9502	275	10	4	1332	4	MEN1	11	64575485	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	31438	64575485	70431031	140	27780										
DLG2	1740	hgsc.bcm.edu	37	chr11	83770480	83770480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccaccgctttactgtgggaaAcctctgacacatcaacctca	6	15	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:83770480A>G	ENST00000532653.1	-	6	784	c.482T>C	c.(481-483)gTt>gCt	p.V161A	DLG2_ENST00000398309.2_Missense_Mutation_p.V161A|DLG2_ENST00000418306.2_Missense_Mutation_p.V110A|DLG2_ENST00000524982.1_Missense_Mutation_p.V161A|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000330014.6_Missense_Mutation_p.V100A|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000531015.1_Missense_Mutation_p.V128A|DLG2_ENST00000398301.2_Missense_Mutation_p.V200A|DLG2_ENST00000376104.2_Missense_Mutation_p.V266A|DLG2_ENST00000543673.1_Missense_Mutation_p.V266A|DLG2_ENST00000280241.8_Missense_Mutation_p.V200A			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ACTGTGGGAAACCTCTGACAC	0.473																																																0			11											90	82	84					11																	83770480		1916	4153	6069	83448128	SO:0001583	missense	4355			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.482T>C	11.37:g.83770480A>G	ENSP00000435849:p.Val161Ala		83448128	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	A	24.7	4.560384	0.86335	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301;ENST00000398299	T;T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.17	5.17	0.71159	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000019	T	0.47248	0.1435	L	0.45352	1.415	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;0.993;0.998;0.996;0.999	D;D;D;D;D;D;D;D	0.97110	0.999;0.999;0.993;1.0;0.984;0.998;0.987;0.999	T	0.34650	-0.9820	9	.	.	.	.	15.0062	0.71513	1.0:0.0:0.0:0.0	.	128;161;161;100;200;266;161;110	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	A	161;266;110;266;200;100;161;161;266;128;200;78	ENSP00000381355:V161A;ENSP00000365272:V266A;ENSP00000402275:V110A;ENSP00000441994:V266A;ENSP00000280241:V200A;ENSP00000381353:V100A;ENSP00000432894:V161A;ENSP00000435849:V161A;ENSP00000433848:V128A;ENSP00000381346:V200A;ENSP00000381344:V78A	.	V	-	2	0	DLG2	83448128	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	1.959000	0.56917	0.377000	0.23210	GTT		0.473	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		G	83770480	A	G	83770480	3	3	105	1	0	0	0	0	1	0	0	0	4566	43	2	4	2252	4	DLG2	11	83770480	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	19194995	83770480	51236036	141	27781										
ATM	472	hgsc.bcm.edu	37	chr11	108142044	108142044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attttaaaccatgtccttcaTgtagtgaaaaacctaggtca	6	8	2	1	rs559676197		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:108142044T>C	ENST00000452508.2	+	21	3177	c.2988T>C	c.(2986-2988)caT>caC	p.H996H	ATM_ENST00000278616.4_Silent_p.H996H			Q13315	ATM_HUMAN	ATM serine/threonine kinase	996					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.H996Q(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATGTCCTTCATGTAGTGAAAA	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											180	172	175					11																	108142044		2201	4298	6499	107647254	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2988T>C	11.37:g.108142044T>C			107647254	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108142044	T	C	108142044	2	2	105	1	0	0	0	0	0	0	0	1	1110	1461	51	4		4	ATM	11	108142044	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	24371564	108142044	26864472	142	27782										
RDX	5962	hgsc.bcm.edu	37	chr11	110124812	110124812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tccgcttattgattctcagaCgaggtgcataaaacacaaaa	7	9	1	2	rs142346566		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:110124812C>T	ENST00000343115.4	-	9	1137	c.818G>A	c.(817-819)cGt>cAt	p.R273H	RDX_ENST00000405097.1_Missense_Mutation_p.R273H|RDX_ENST00000528498.1_Missense_Mutation_p.R273H|RDX_ENST00000528900.1_Intron|RDX_ENST00000544551.1_Missense_Mutation_p.R137H|RDX_ENST00000530301.1_Intron	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	273	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GATTCTCAGACGAGGTGCATA	0.343													C|||	0	0	0	0	5008	,	,		17407	0		0	False		,,,				2504	0				Esophageal Squamous(55;25 1062 11040 28755 44273)											0			11											85	76	79					11																	110124812		2201	4298	6499	109630022	SO:0001583	missense	5962			BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.818G>A	11.37:g.110124812C>T	ENSP00000342830:p.Arg273His		109630022	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	37	CCDS8343.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	26.4	4.733416	0.89482	.	.	ENSG00000137710	ENST00000528498;ENST00000429481;ENST00000405097;ENST00000343115;ENST00000544551	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	5.72	5.72	0.89469	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.91935	0.7446	M	0.85373	2.75	0.80722	D	1	P;D;B	0.76494	0.719;0.999;0.24	B;D;B	0.64506	0.198;0.926;0.085	D	0.92571	0.6066	10	0.87932	D	0	.	19.8831	0.96905	0.0:1.0:0.0:0.0	.	137;273;273	F5H1A7;A7YIJ8;P35241	.;.;RADI_HUMAN	H	273;273;273;273;137	ENSP00000432112:R273H;ENSP00000384136:R273H;ENSP00000342830:R273H;ENSP00000445826:R137H	ENSP00000342830:R273H	R	-	2	0	RDX	109630022	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.765000	0.85310	2.705000	0.92388	0.655000	0.94253	CGT		0.343	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		T	110124812	C	T	110124812	3	4	105	1	0	0	0	0	1	0	0	0	13235	536	19	1	957	1	RDX	11	110124812	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	1982768	110124812	24881704	143	27783										
USP28	57646	hgsc.bcm.edu	37	chr11	113670059	113670059	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aattgggtcgaattgttggaGgctctttcaagacgatgatt	12	5	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:113670059G>T	ENST00000003302.4	-	25	3205	c.3137C>A	c.(3136-3138)cCt>cAt	p.P1046H	USP28_ENST00000545540.1_Missense_Mutation_p.P889H|USP28_ENST00000544967.1_Missense_Mutation_p.P722H|USP28_ENST00000260188.5_Missense_Mutation_p.P1014H	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	1046					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.P1046H(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		AATTGTTGGAGGCTCTTTCAA	0.458																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											1	Substitution - Missense(1)	large_intestine(1)	11											122	124	123					11																	113670059		2201	4296	6497	113175269	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.3137C>A	11.37:g.113670059G>T	ENSP00000003302:p.Pro1046His		113175269	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916822	0.92249	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	T;T;T;T	0.60171	0.69;0.75;0.21;0.78	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.76428	0.3986	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.993;0.999	T	0.77501	-0.2564	10	0.87932	D	0	-21.4559	19.8677	0.96824	0.0:0.0:1.0:0.0	.	889;1046;722	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	H	1046;1014;722;889	ENSP00000003302:P1046H;ENSP00000260188:P1014H;ENSP00000442431:P722H;ENSP00000444991:P889H	ENSP00000003302:P1046H	P	-	2	0	USP28	113175269	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.361000	0.97122	2.709000	0.92574	0.655000	0.94253	CCT		0.458	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113670059	G	T	113670059	3	4	105	1	0	0	0	0	1	0	0	0	17098	1000	35	2	100	2	USP28	11	113670059	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	3545247	113670059	21336457	144	27784										
USP28	57646	hgsc.bcm.edu	37	chr11	113701632	113701632	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aaagtaccatagaacagctgCaccattggattttcagattt	7	8	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:113701632C>T	ENST00000003302.4	-	9	935	c.867G>A	c.(865-867)gtG>gtA	p.V289V	USP28_ENST00000537706.1_Silent_p.V289V|USP28_ENST00000545540.1_Silent_p.V164V|USP28_ENST00000544967.1_5'Flank|USP28_ENST00000542033.1_5'UTR|USP28_ENST00000260188.5_Silent_p.V289V	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	289	USP.			VQLFYGTFLTEGVRE -> IVIVMSFLKSLSLCL (in Ref. 4; BAA96039). {ECO:0000305}.	cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.V289V(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		AGAACAGCTGCACCATTGGAT	0.373																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											1	Substitution - coding silent(1)	kidney(1)	11											171	162	165					11																	113701632		2201	4296	6497	113206842	SO:0001819	synonymous_variant	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.867G>A	11.37:g.113701632C>T			113206842	B0YJC0|B0YJC1|Q9P213	Silent	SNP	ENST00000003302.4	37	CCDS31680.1																																																																																				0.373	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113701632	C	T	113701632	2	4	105	1	0	0	0	0	0	0	0	1	17098	697	25	3		3	USP28	11	113701632	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	31573	113701632	21304884	145	27785										
RNF26	79102	hgsc.bcm.edu	37	chr11	119205979	119205979	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtctacaacctgccgcacacGgtactgactagtcttctgca	8	14	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:119205979G>A	ENST00000311413.4	+	1	743	c.147G>A	c.(145-147)acG>acA	p.T49T	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	49						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		TGCCGCACACGGTACTGACTA	0.602																																																0			11											185	155	165					11																	119205979		2199	4295	6494	118711189	SO:0001819	synonymous_variant	79102			AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"RING-type (C3HC4) zinc fingers"	14646	protein-coding gene	gene with protein product	"ring finger protein with leucine zipper"	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.147G>A	11.37:g.119205979G>A			118711189	Q542Y8	Silent	SNP	ENST00000311413.4	37	CCDS8419.1																																																																																				0.602	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		A	119205979	G	A	119205979	2	1	105	1	0	0	0	0	0	0	0	1	13523	1103	39	1		1	RNF26	11	119205979	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	5504347	119205979	15800537	146	27786										
CCDC15	80071	hgsc.bcm.edu	37	chr11	124847418	124847418	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tccactgggataaatacaggAataagaggagagttgcccat	11	7	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr11:124847418A>G	ENST00000344762.5	+	6	934	c.675A>G	c.(673-675)ggA>ggG	p.G225G	CCDC15_ENST00000529051.1_Silent_p.G225G	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	225						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		TAAATACAGGAATAAGAGGAG	0.368																																																0			11											66	64	65					11																	124847418		1828	4077	5905	124352628	SO:0001819	synonymous_variant	80071			BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.675A>G	11.37:g.124847418A>G			124352628	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																				0.368	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004		G	124847418	A	G	124847418	2	3	105	1	0	0	0	0	0	0	0	1	2790	233	9	4		4	CCDC15	11	124847418	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	5641439	124847418	10159098	147	27787										
WNK1	65125	hgsc.bcm.edu	37	chr12	988973	988973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tcacaatggcagctggcattActcagcctctgctcacgttg	9	13	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:988973A>T	ENST00000315939.6	+	11	3251	c.2608A>T	c.(2608-2610)Act>Tct	p.T870S	WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Missense_Mutation_p.T1368S|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000340908.4_Missense_Mutation_p.T463S	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	870					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AGCTGGCATTACTCAGCCTCT	0.532																																					Colon(19;451 567 6672 12618 28860)											0			12											164	137	146					12																	988973		2203	4300	6503	859234	SO:0001583	missense	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2608A>T	12.37:g.988973A>T	ENSP00000313059:p.Thr870Ser		859234	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	4.645	0.119958	0.08881	.	.	ENSG00000060237	ENST00000315939;ENST00000530271;ENST00000340908;ENST00000535698	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.75	1.92	0.25849	.	0.377586	0.25114	N	0.033031	T	0.05318	0.0141	N	0.03608	-0.345	0.21416	N	0.999692	B	0.02656	0.0	B	0.01281	0.0	T	0.41378	-0.9512	10	0.08837	T	0.75	-3.875	5.3693	0.16131	0.6529:0.1368:0.2103:0.0	.	870	Q9H4A3	WNK1_HUMAN	S	870;1368;463;140	ENSP00000313059:T870S;ENSP00000433548:T1368S;ENSP00000341292:T463S;ENSP00000439552:T140S	ENSP00000313059:T870S	T	+	1	0	WNK1	859234	1.000000	0.71417	0.982000	0.44146	0.912000	0.54170	2.690000	0.47001	0.446000	0.26666	0.455000	0.32223	ACT		0.532	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	988973	A	T	988973	3	4	105	1	0	0	0	0	1	0	0	0	17417	391	14	5	4152	5	WNK1	12	988973	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10		988973	132862922	148	27788										
C12orf59	120939	hgsc.bcm.edu	37	chr12	10339027	10339028	+	Frame_Shift_Ins	INS	-	-	G													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggcttttgcaggttgctagtINSggtaattggcgcgctgcttc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:10339027_10339028insG	ENST00000381923.2	+	5	550_551	c.146_147insG	c.(145-150)gtggtafs	p.V50fs	TMEM52B_ENST00000298530.3_Frame_Shift_Ins_p.V30fs|TMEM52B_ENST00000536952.1_Frame_Shift_Ins_p.V50fs			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	50						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AGGTTGCTAGTGGTAATTGGCG	0.569																																																0			12																																								10230295	SO:0001589	frameshift_variant	120939			AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 59"	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.148dupG	12.37:g.10339029_10339029dupG	ENSP00000371348:p.Val50fs		10230294	Q96NA7	Frame_Shift_Ins	INS	ENST00000381923.2	37																																																																																					0.569	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		G	10339028	-	G	10339027	7	5	105	1	0	1	1	0	0	0	0	0	1706	1696	59	0	96	0	C12orf59	12	10339027	Frame_Shift_Ins	INS	-	TCGA-DY-A1DD-01A-21D-A152-10	9350054	10339027	123512868	149	27789										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40668477	40668477	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttagagatgttatccctggaAggtgctatggattcagtgct	12	6	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:40668477A>G	ENST00000298910.7	+	15	1807	c.1749A>G	c.(1747-1749)gaA>gaG	p.E583E	LRRK2_ENST00000343742.2_Silent_p.E583E	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	583					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.E583D(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TATCCCTGGAAGGTGCTATGG	0.363																																																2	Substitution - Missense(2)	ovary(2)	12											151	149	150					12																	40668477		2203	4300	6503	38954744	SO:0001819	synonymous_variant	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1749A>G	12.37:g.40668477A>G			38954744	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																				0.363	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		G	40668477	A	G	40668477	2	3	105	1	0	0	0	0	0	0	0	1	9062	69	3	4		4	LRRK2	12	40668477	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	30329450	40668477	93183418	150	27790										
PRKAG1	5571	hgsc.bcm.edu	37	chr12	49396782	49396782	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tttcatccaccactacaagtCggtgaacctggcacagagca	8	13	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:49396782C>T	ENST00000548065.1	-	12	1352	c.896G>A	c.(895-897)cGa>cAa	p.R299Q	PRKAG1_ENST00000316299.5_Missense_Mutation_p.R308Q|PRKAG1_ENST00000552212.1_Missense_Mutation_p.R267Q|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|PRKAG1_ENST00000395170.3_Missense_Mutation_p.R215Q|RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000547306.1_Missense_Mutation_p.R248Q|RP11-386G11.5_ENST00000547866.1_RNA			P54619	AAKG1_HUMAN	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	299	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of glycolytic process (GO:0006110)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.R299Q(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	9					Acetylsalicylic acid(DB00945)	CACTACAAGTCGGTGAACCTG	0.542																																																1	Substitution - Missense(1)	large_intestine(1)	12											146	119	128					12																	49396782		2203	4300	6503	47683049	SO:0001583	missense	5571			U42412	CCDS8777.1, CCDS55824.1, CCDS55825.1	12q12-q14	1998-07-16				ENSG00000181929			9385	protein-coding gene	gene with protein product		602742				8557660, 8621499	Standard	NM_002733		Approved		uc001rsz.3	P54619	OTTHUMG00000170406	ENST00000548065.1:c.896G>A	12.37:g.49396782C>T	ENSP00000447433:p.Arg299Gln		47683049	B4DDT7|Q8N7V9	Missense_Mutation	SNP	ENST00000548065.1	37	CCDS8777.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.526842	0.64860	.	.	ENSG00000181929	ENST00000548362;ENST00000395170;ENST00000547306;ENST00000316299;ENST00000548065;ENST00000552212;ENST00000551770;ENST00000551696	D;D;D;D;D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49;-3.49;-3.49;-3.49;-3.49	5.18	4.28	0.50868	Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (3);	0.056121	0.64402	D	0.000001	D	0.97620	0.9220	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98472	1.0601	10	0.87932	D	0	-4.9987	14.178	0.65555	0.151:0.849:0.0:0.0	.	308;299	Q8N7V9;P54619	.;AAKG1_HUMAN	Q	64;215;248;308;299;267;219;193	ENSP00000446987:R64Q;ENSP00000378599:R215Q;ENSP00000448873:R248Q;ENSP00000323867:R308Q;ENSP00000447433:R299Q;ENSP00000448972:R267Q;ENSP00000449121:R219Q;ENSP00000447671:R193Q	ENSP00000323867:R308Q	R	-	2	0	PRKAG1	47683049	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.574000	0.82434	1.402000	0.46780	0.655000	0.94253	CGA		0.542	PRKAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408946.1	NM_002733		T	49396782	C	T	49396782	3	4	105	1	0	0	0	0	1	0	0	0	12534	884	31	1	103	1	PRKAG1	12	49396782	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8728305	49396782	84455113	151	27791										
POU6F1	5463	hgsc.bcm.edu	37	chr12	51584192	51584192	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttctcaaaataggcattgagAgcctctatggcctggggggt	13	8	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:51584192A>G	ENST00000389243.4	-	11	1683	c.744T>C	c.(742-744)gcT>gcC	p.A248A	POU6F1_ENST00000550824.1_Silent_p.A248A|POU6F1_ENST00000333640.10_Silent_p.A248A			Q14863	PO6F1_HUMAN	POU class 6 homeobox 1	248					brain development (GO:0007420)|heart development (GO:0007507)|muscle organ development (GO:0007517)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	11						AGGCATTGAGAGCCTCTATGG	0.567																																																0			12											117	116	116					12																	51584192		2203	4300	6503	49870459	SO:0001819	synonymous_variant	5463			AL832881	CCDS31803.1	12q13.13	2011-06-20	2007-07-13			ENSG00000184271		"Homeoboxes / POU class"	9224	protein-coding gene	gene with protein product			"POU domain, class 6, transcription factor 1"			7908264	Standard	NM_002702		Approved	BRN5, MPOU, TCFB1	uc001rxz.3	Q14863		ENST00000389243.4:c.744T>C	12.37:g.51584192A>G			49870459	Q15944|Q6DK47|Q7Z7P6	Silent	SNP	ENST00000389243.4	37	CCDS31803.1																																																																																				0.567	POU6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405126.1	NM_002702		G	51584192	A	G	51584192	2	3	105	1	0	0	0	0	0	0	0	1	12315	291	11	4		4	POU6F1	12	51584192	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	2187410	51584192	82267703	152	27792										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52886880	52886880	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acggagacgctgctgaagccAgagcggctgaccccagggag	16	12	0	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:52886880A>C	ENST00000330722.6	-	1	161	c.93T>G	c.(91-93)tcT>tcG	p.S31S		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	31	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCTGAAGCCAGAGCGGCTGA	0.662																																																0			12											39	48	45					12																	52886880		2202	4300	6502	51173147	SO:0001819	synonymous_variant	3853			BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.93T>G	12.37:g.52886880A>C			51173147	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																				0.662	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		C	52886880	A	C	52886880	2	2	105	1	0	0	0	0	0	0	0	1	8501	175	7	4		4	KRT6A	12	52886880	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	1302688	52886880	80965015	153	27793										
ITGB7	3695	hgsc.bcm.edu	37	chr12	53590473	53590473	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gaaggcttgtgcgtcccccgTcagggacagcacatggtgaa	14	11	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:53590473T>C	ENST00000267082.5	-	6	937	c.706A>G	c.(706-708)Acg>Gcg	p.T236A	ITGB7_ENST00000550743.2_Missense_Mutation_p.T236A|ITGB7_ENST00000422257.3_Missense_Mutation_p.T236A|ITGB7_ENST00000338737.4_Missense_Mutation_p.T236A	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	236	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCGTCCCCCGTCAGGGACAGC	0.642																																																0			12											48	43	45					12																	53590473		2203	4300	6503	51876740	SO:0001583	missense	3695				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.706A>G	12.37:g.53590473T>C	ENSP00000267082:p.Thr236Ala		51876740	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	T	18.92	3.725548	0.68959	.	.	ENSG00000139626	ENST00000422257;ENST00000267082;ENST00000338737;ENST00000542497	D;D;D;D	0.98329	-4.87;-4.87;-4.87;-4.87	4.65	4.65	0.58169	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.225469	0.22853	N	0.054824	D	0.98940	0.9640	M	0.86420	2.815	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.99723	1.1010	10	0.87932	D	0	.	13.7943	0.63162	0.0:0.0:0.0:1.0	.	236	P26010	ITB7_HUMAN	A	236	ENSP00000408741:T236A;ENSP00000267082:T236A;ENSP00000345501:T236A;ENSP00000437375:T236A	ENSP00000267082:T236A	T	-	1	0	ITGB7	51876740	1.000000	0.71417	0.685000	0.30070	0.277000	0.26821	7.997000	0.88414	2.041000	0.60428	0.454000	0.30748	ACG		0.642	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			C	53590473	T	C	53590473	3	2	105	1	0	0	0	0	1	0	0	0	7921	1667	58	4	1734	4	ITGB7	12	53590473	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	703593	53590473	80261422	154	27794										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66849242	66849242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tcctcatcatggttccacgtGggctggtggagtagaggctt	14	9	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:66849242G>A	ENST00000398016.3	-	10	1213	c.1145C>T	c.(1144-1146)cCa>cTa	p.P382L	GRIP1_ENST00000286445.7_Missense_Mutation_p.P434L|GRIP1_ENST00000359742.4_Missense_Mutation_p.P434L	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GGTTCCACGTGGGCTGGTGGA	0.488																																																0			12											159	157	157					12																	66849242		1954	4158	6112	65135509	SO:0001583	missense	85329			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1145C>T	12.37:g.66849242G>A	ENSP00000381098:p.Pro382Leu		65135509	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.3|22.3	4.275483|4.275483	0.80580|0.80580	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433	.|T;T;T;T;T	.|0.23147	.|1.92;1.99;1.99;1.93;2.04	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.106321	.|0.64402	.|D	.|0.000003	T|T	0.50939|0.50939	0.1645|0.1645	M|M	0.71036|0.71036	2.16|2.16	0.80722|0.80722	D|D	1|1	.|D;B;D	.|0.61080	.|0.972;0.317;0.989	.|P;B;D	.|0.65140	.|0.844;0.177;0.932	T|T	0.41124|0.41124	-0.9526|-0.9526	5|9	.|.	.|.	.|.	-11.5531|-11.5531	19.8063|19.8063	0.96533|0.96533	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|382;382;434	.|F5H4N6;Q9Y3R0-3;Q9Y3R0-2	.|.;.;.	Y|L	249|382;434;434;382;326	.|ENSP00000381098:P382L;ENSP00000352780:P434L;ENSP00000286445:P434L;ENSP00000446047:P382L;ENSP00000446024:P326L	.|.	H|P	-|-	1|2	0|0	GRIP1|GRIP1	65135509|65135509	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	9.869000|9.869000	0.99810|0.99810	2.767000|2.767000	0.95098|0.95098	0.561000|0.561000	0.74099|0.74099	CAC|CCA		0.488	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66849242	G	A	66849242	3	1	105	1	0	0	0	0	1	0	0	0	6808	1348	47	3	2145	3	GRIP1	12	66849242	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	13258769	66849242	67002653	155	27795										
LGR5	8549	hgsc.bcm.edu	37	chr12	71965354	71965354	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tcagtctgccaaaagcttcaGaaaatgtaagtctagaagtc	8	8	4	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:71965354G>A	ENST00000266674.5	+	12	1442	c.1131G>A	c.(1129-1131)caG>caA	p.Q377Q	LGR5_ENST00000540815.2_Silent_p.Q353Q|LGR5_ENST00000536515.1_Silent_p.Q305Q			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	377					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						AAAAGCTTCAGAAAATGTAAG	0.378																																																0			12											84	81	82					12																	71965354		2203	4299	6502	70251621	SO:0001819	synonymous_variant	8549			AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1131G>A	12.37:g.71965354G>A			70251621	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Silent	SNP	ENST00000266674.5	37	CCDS9000.1																																																																																				0.378	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		A	71965354	G	A	71965354	2	1	105	1	0	0	0	0	0	0	0	1	8780	933	33	3		3	LGR5	12	71965354	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	5116112	71965354	61886541	156	27796										
KCNC2	3747	hgsc.bcm.edu	37	chr12	75444893	75444893	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgaaaaaacaatacggactaAaaattcaaaagtaaaccaca	4	7	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:75444893A>G	ENST00000549446.1	-	3	1572	c.892T>C	c.(892-894)Tta>Cta	p.L298L	KCNC2_ENST00000550433.1_Silent_p.L298L|KCNC2_ENST00000298972.1_Silent_p.L298L|KCNC2_ENST00000548513.1_Silent_p.L298L|KCNC2_ENST00000350228.2_Silent_p.L298L|KCNC2_ENST00000548243.1_5'Flank|KCNC2_ENST00000540018.1_Silent_p.L298L|KCNC2_ENST00000341669.3_Silent_p.L298L|KCNC2_ENST00000393288.2_Silent_p.L298L	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	298					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	ATACGGACTAAAAATTCAAAA	0.378																																																0			12											129	118	122					12																	75444893		2203	4300	6503	73731160	SO:0001819	synonymous_variant	3747			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.892T>C	12.37:g.75444893A>G			73731160	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	37	CCDS9007.1																																																																																				0.378	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		G	75444893	A	G	75444893	2	3	105	1	0	0	0	0	0	0	0	1	8036	11	1	4		4	KCNC2	12	75444893	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	3479539	75444893	58407002	157	27797										
KRR1	11103	hgsc.bcm.edu	37	chr12	75897753	75897753	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtttttttctttggttccttGcgtttattcacatttttgtg	7	6	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:75897753G>A	ENST00000229214.4	-	7	785	c.762C>T	c.(760-762)cgC>cgT	p.R254R	KRR1_ENST00000438169.2_Intron	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	254	Lys-rich.				rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						TTGGTTCCTTGCGTTTATTCA	0.358																																																0			12											217	201	207					12																	75897753		2203	4300	6503	74184020	SO:0001819	synonymous_variant	11103			U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.762C>T	12.37:g.75897753G>A			74184020	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																				0.358	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043		A	75897753	G	A	75897753	2	1	105	1	0	0	0	0	0	0	0	1	8467	1306	46	3		3	KRR1	12	75897753	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	452860	75897753	57954142	158	27798										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101012348	101012349	+	Nonsense_Mutation	DNP	GA	GA	TG													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caaaatcatgctgtcggcatGaagagctacatgaagctgta							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G|A	G|A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:101012348_101012349GA>TG	ENST00000539410.1	+	7	1017_1018	c.631_632GA>TG	c.(631-633)GAa>TGa	p.E211*	GAS2L3_ENST00000266754.5_Nonsense_Mutation_p.E211*|GAS2L3_ENST00000547754.1_Nonsense_Mutation_p.E211*|GAS2L3_ENST00000537247.1_Nonsense_Mutation_p.E107*			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	211	GAR. {ECO:0000255|PROSITE- ProRule:PRU00792}.				actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						CTGTCGGCATGAAGAGCTACAT	0.396																																																0			12																																								99536479|99536480	SO:0001587	stop_gained	283431			AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	Exception_encountered	12.37:g.101012348_101012349delinsTG	ENSP00000439672:p.Glu211*		99536479|99536480	B2RCN2	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1																																																																																				0.396	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		TG	101012349	GA	TG	101012348	4	4	105	1	0	0	0	0	0	1	0	0	6268	1291	45	2	653	2	GAS2L3	12	101012348	Nonsense_Mutation	DNP	GA	TCGA-DY-A1DD-01A-21D-A152-10	25114595	101012348	32839547	159	27799										
PRDM4	11108	hgsc.bcm.edu	37	chr12	108128244	108128244	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agaattgagatgcttctttaAgtgatttgttctcaagaaca	8	5	2	4			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:108128244A>T	ENST00000228437.5	-	12	2608	c.2149T>A	c.(2149-2151)Tta>Ata	p.L717I	RP11-864J10.4_ENST00000546714.1_RNA|RP11-864J10.4_ENST00000546829.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	717					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						TGCTTCTTTAAGTGATTTGTT	0.383																																																0			12											187	189	188					12																	108128244		2203	4300	6503	106652374	SO:0001583	missense	11108			AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"Zinc fingers, C2H2-type"	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.2149T>A	12.37:g.108128244A>T	ENSP00000228437:p.Leu717Ile		106652374	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	37	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.415140	0.83449	.	.	ENSG00000110851	ENST00000228437	T	0.14640	2.49	6.03	3.68	0.42216	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.43765	0.1262	H	0.94847	3.59	0.50467	D	0.999871	D	0.63880	0.993	D	0.76071	0.987	T	0.48007	-0.9072	10	0.87932	D	0	-0.7729	7.3147	0.26493	0.6665:0.0:0.3335:0.0	.	717	Q9UKN5	PRDM4_HUMAN	I	717	ENSP00000228437:L717I	ENSP00000228437:L717I	L	-	1	2	PRDM4	106652374	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.060000	0.41394	1.118000	0.41863	0.454000	0.30748	TTA		0.383	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		T	108128244	A	T	108128244	3	4	105	1	0	0	0	0	1	0	0	0	12493	69	3	5	260	5	PRDM4	12	108128244	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	7115896	108128244	25723651	160	27800										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112915743	112915743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgcctgcaaaacacggtgaAtgacttttggcggatggtgt	13	8	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:112915743A>G	ENST00000351677.2	+	9	1214	c.1016A>G	c.(1015-1017)aAt>aGt	p.N339S	PTPN11_ENST00000392597.1_Missense_Mutation_p.N339S	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	339	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.N339S(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						AACACGGTGAATGACTTTTGG	0.413			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	1	Substitution - Missense(1)	ovary(1)	12											70	63	66					12																	112915743		2203	4300	6503	111400126	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1016A>G	12.37:g.112915743A>G	ENSP00000340944:p.Asn339Ser		111400126	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.512834	0.27123	.	.	ENSG00000179295	ENST00000392597;ENST00000351677	D;D	0.83075	-1.68;-1.68	6.03	6.03	0.97812	.	0.124428	0.64402	D	0.000001	T	0.76608	0.4011	L	0.33093	0.98	0.44000	D	0.996707	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.70223	-0.4931	10	0.31617	T	0.26	.	16.6115	0.84884	1.0:0.0:0.0:0.0	.	339;339	Q06124-2;Q06124-3	.;.	S	339	ENSP00000376376:N339S;ENSP00000340944:N339S	ENSP00000340944:N339S	N	+	2	0	PTPN11	111400126	1.000000	0.71417	0.945000	0.38365	0.921000	0.55340	4.731000	0.62022	2.327000	0.79052	0.524000	0.50904	AAT		0.413	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112915743	A	G	112915743	3	3	105	1	0	0	0	0	1	0	0	0	12815	101	4	4	1050	4	PTPN11	12	112915743	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	4787499	112915743	20936152	161	27801										
NOS1	4842	hgsc.bcm.edu	37	chr12	117718606	117718606	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agccagcgtagcggatgagcTgggagttccagactcggaag	16	9	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr12:117718606T>G	ENST00000338101.4	-	7	1452	c.1448A>C	c.(1447-1449)cAg>cCg	p.Q483P	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.Q483P			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCGGATGAGCTGGGAGTTCCA	0.627																																					Esophageal Squamous(162;1748 2599 51982 52956)											0			12											60	70	67					12																	117718606		2108	4248	6356	116202989	SO:0001583	missense	340719				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1448A>C	12.37:g.117718606T>G	ENSP00000337459:p.Gln483Pro		116202989		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.744164	0.89663	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.31247	1.5;1.5	5.14	5.14	0.70334	Nitric oxide synthase, oxygenase domain (3);	0.000000	0.85682	D	0.000000	T	0.68302	0.2986	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79864	-0.1623	10	0.87932	D	0	-33.6262	15.1255	0.72481	0.0:0.0:0.0:1.0	.	483	P29475	NOS1_HUMAN	P	483	ENSP00000320758:Q483P;ENSP00000337459:Q483P	ENSP00000320758:Q483P	Q	-	2	0	NOS1	116202989	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.818000	0.86416	2.144000	0.66660	0.460000	0.39030	CAG		0.627	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			G	117718606	T	G	117718606	3	3	105	1	0	0	0	0	1	0	0	0	10572	1580	55	4	2944	4	NOS1	12	117718606	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	4802863	117718606	16133289	162	27802										
FLT1	2321	hgsc.bcm.edu	37	chr13	29001900	29001900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caaacttaccattgacaattAgagtggcagtgaggttttta	9	6	0	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:29001900A>G	ENST00000282397.4	-	9	1516	c.1265T>C	c.(1264-1266)cTa>cCa	p.L422P	FLT1_ENST00000539099.1_Missense_Mutation_p.L422P|FLT1_ENST00000541932.1_Missense_Mutation_p.L422P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	422			L -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTGACAATTAGAGTGGCAGT	0.353																																																0			13											140	127	131					13																	29001900		2203	4300	6503	27899900	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1265T>C	13.37:g.29001900A>G	ENSP00000282397:p.Leu422Pro		27899900	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740481	0.69304	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	D;D;D	0.87571	-2.27;-2.27;-2.27	5.73	5.73	0.89815	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.96178	0.8754	H	0.97852	4.09	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97789	1.0237	10	0.87932	D	0	.	16.026	0.80545	1.0:0.0:0.0:0.0	.	422;422;422;422	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	P	422	ENSP00000282397:L422P;ENSP00000437631:L422P;ENSP00000442630:L422P	ENSP00000282397:L422P	L	-	2	0	FLT1	27899900	1.000000	0.71417	0.794000	0.32065	0.746000	0.42486	8.219000	0.89770	2.189000	0.69895	0.528000	0.53228	CTA		0.353	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			G	29001900	A	G	29001900	3	3	105	1	0	0	0	0	1	0	0	0	5960	420	15	4	3102	4	FLT1	13	29001900	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10		29001900	86167978	163	27803										
BRCA2	675	hgsc.bcm.edu	37	chr13	32914504	32914504	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caagtgttttctgaaatagaAgatagtaccaagcaagtctt	8	6	2	3	rs397507362|rs572976024		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:32914504A>G	ENST00000380152.3	+	11	6245	c.6012A>G	c.(6010-6012)gaA>gaG	p.E2004E	BRCA2_ENST00000544455.1_Silent_p.E2004E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2004					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CTGAAATAGAAGATAGTACCA	0.373			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1	0.000199681	0	0	5008	,	,		19926	0		0	False		,,,				2504	0.001				Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											59	63	62					13																	32914504		2203	4298	6501	31812504	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6012A>G	13.37:g.32914504A>G			31812504	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32914504	A	G	32914504	2	3	105	1	0	0	0	0	0	0	0	1	1502	69	3	4		4	BRCA2	13	32914504	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	3912604	32914504	82255374	164	27804										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37598536	37598536	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtgggggtcgatgttttacaCccttccccaataccgaagac	10	12	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:37598536C>A	ENST00000350612.6	-	18	1593	c.1373G>T	c.(1372-1374)gGt>gTt	p.G458V	SUPT20H_ENST00000356185.3_Missense_Mutation_p.G459V|SUPT20H_ENST00000542180.1_Missense_Mutation_p.G422V|SUPT20H_ENST00000464744.1_Missense_Mutation_p.G459V|SUPT20H_ENST00000475892.1_Missense_Mutation_p.G458V|SUPT20H_ENST00000360252.4_Missense_Mutation_p.G459V	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	458					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										ATGTTTTACACCCTTCCCCAA	0.378																																																0			13											78	73	75					13																	37598536		2203	4300	6503	36496536	SO:0001583	missense	55578			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1373G>T	13.37:g.37598536C>A	ENSP00000218894:p.Gly458Val		36496536	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.9|20.9	4.070374|4.070374	0.76301|0.76301	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180|ENST00000469488	T;T;T;T;T;T|.	0.57752|.	0.6;0.51;1.14;0.6;0.6;0.38|.	5.87|5.87	5.03|5.03	0.67393|0.67393	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77870|0.77870	0.4195|0.4195	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.71674|.	0.983;0.983;0.996;0.991;0.995;0.998;0.995|.	D;D;D;D;D;D;D|.	0.70487|.	0.917;0.917;0.969;0.92;0.951;0.937;0.951|.	T|T	0.79676|0.79676	-0.1704|-0.1704	10|5	0.45353|.	T|.	0.12|.	-10.1248|-10.1248	17.1383|17.1383	0.86745|0.86745	0.0:0.8736:0.1264:0.0|0.0:0.8736:0.1264:0.0	.|.	422;458;458;459;459;458;458|.	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7;F5GX46|.	.;.;.;.;.;FA48A_HUMAN;.|.	V|L	459;458;458;459;458;459;422|66	ENSP00000353388:G459V;ENSP00000417510:G458V;ENSP00000218894:G458V;ENSP00000348512:G459V;ENSP00000419754:G459V;ENSP00000439000:G422V|.	ENSP00000218894:G458V|.	G|V	-|-	2|1	0|0	FAM48A|FAM48A	36496536|36496536	1.000000|1.000000	0.71417|0.71417	0.556000|0.556000	0.28293|0.28293	0.750000|0.750000	0.42670|0.42670	7.056000|7.056000	0.76662|0.76662	1.476000|1.476000	0.48215|0.48215	0.585000|0.585000	0.79938|0.79938	GGT|GTG		0.378	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		A	37598536	C	A	37598536	3	1	105	1	0	0	0	0	1	0	0	0	5591	507	18	2	1002	2	FAM48A	13	37598536	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	4684032	37598536	77571342	165	27805										
KDELC1	79070	hgsc.bcm.edu	37	chr13	103450845	103450845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtttctcgacttacttattcCctgatgtatccactgcctga	6	12	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:103450845C>T	ENST00000376004.4	-	1	512	c.176G>A	c.(175-177)gGg>gAg	p.G59E	BIVM_ENST00000419638.1_5'Flank|BIVM_ENST00000448849.2_5'Flank|BIVM_ENST00000257336.1_5'Flank|KDELC1_ENST00000460338.1_5'UTR	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	59						endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTACTTATTCCCTGATGTATC	0.473																																																0			13											63	64	64					13																	103450845		2203	4300	6503	102248846	SO:0001583	missense	79070			BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.176G>A	13.37:g.103450845C>T	ENSP00000365172:p.Gly59Glu		102248846	Q53HL3|Q9BVD2	Missense_Mutation	SNP	ENST00000376004.4	37	CCDS9504.1	.	.	.	.	.	.	.	.	.	.	C	35	5.469689	0.96274	.	.	ENSG00000134901	ENST00000376004	D	0.88277	-2.36	5.32	5.32	0.75619	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94198	0.8138	M	0.79011	2.435	0.80722	D	1	D	0.61080	0.989	D	0.64877	0.93	D	0.94505	0.7713	10	0.72032	D	0.01	.	18.9883	0.92780	0.0:1.0:0.0:0.0	.	59	Q6UW63	KDEL1_HUMAN	E	59	ENSP00000365172:G59E	ENSP00000365172:G59E	G	-	2	0	KDELC1	102248846	1.000000	0.71417	0.570000	0.28473	0.995000	0.86356	7.250000	0.78287	2.648000	0.89879	0.650000	0.86243	GGG		0.473	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1			T	103450845	C	T	103450845	3	4	105	1	0	0	0	0	1	0	0	0	8138	623	22	3	1372	3	KDELC1	13	103450845	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	65852309	103450845	11719033	166	27806										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111143590	111143590	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtggttgcaggtctgaagggAttctttggagagaagggaac	17	4	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:111143590A>G	ENST00000360467.5	+	37	3663	c.3357A>G	c.(3355-3357)ggA>ggG	p.G1119G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1119	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GTCTGAAGGGATTCTTTGGAG	0.552																																																0			13											70	73	72					13																	111143590		2022	4171	6193	109941591	SO:0001819	synonymous_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3357A>G	13.37:g.111143590A>G			109941591	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																				0.552	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		G	111143590	A	G	111143590	2	3	105	1	0	0	0	0	0	0	0	1	3696	320	12	4		4	COL4A2	13	111143590	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	7692745	111143590	4026288	167	27807										
ING1	3621	hgsc.bcm.edu	37	chr13	111372142	111372142	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acgacgagtgccccatcgagTggttccacttctcgtgcgtg	12	13	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:111372142T>C	ENST00000375774.3	+	2	1594	c.1132T>C	c.(1132-1134)Tgg>Cgg	p.W378R	ING1_ENST00000375775.3_Missense_Mutation_p.W166R|ING1_ENST00000333219.7_Missense_Mutation_p.W235R|ING1_ENST00000338450.7_Missense_Mutation_p.W191R	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	378					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.W235R(1)		endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCCCATCGAGTGGTTCCACTT	0.587																																																1	Substitution - Missense(1)	large_intestine(1)	13											81	71	74					13																	111372142		2203	4300	6503	110170143	SO:0001583	missense	3621				CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.1132T>C	13.37:g.111372142T>C	ENSP00000364929:p.Trp378Arg		110170143	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243556	0.79912	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.5	5.5	0.81552	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	H	0.99609	4.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.994	D	0.92873	0.6316	10	0.72032	D	0.01	-40.1282	15.5913	0.76530	0.0:0.0:0.0:1.0	.	378;235;191	Q9UK53;Q5T9H0;Q9UK53-4	ING1_HUMAN;.;.	R	191;235;166;378	ENSP00000345202:W191R;ENSP00000328436:W235R;ENSP00000364930:W166R;ENSP00000364929:W378R	ENSP00000328436:W235R	W	+	1	0	ING1	110170143	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.529000	0.81952	2.089000	0.63090	0.402000	0.26972	TGG		0.587	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		C	111372142	T	C	111372142	3	2	105	1	0	0	0	0	1	0	0	0	7756	1696	59	4	1286	4	ING1	13	111372142	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	228552	111372142	3797736	168	27808										
GRK1	6011	hgsc.bcm.edu	37	chr13	114324053	114324053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aagtacacagcaggttcatcGtgtctctggcctatgcgttt	10	10	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr13:114324053G>A	ENST00000335678.6	+	2	983	c.751G>A	c.(751-753)Gtg>Atg	p.V251M		NM_002929.2	NP_002920.1	Q15835	RK_HUMAN	G protein-coupled receptor kinase 1	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of apoptotic process (GO:0043066)|photoreceptor cell morphogenesis (GO:0008594)|phototransduction, visible light (GO:0007603)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)|rhodopsin kinase activity (GO:0050254)			ovary(2)	2	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.234)			CAGGTTCATCGTGTCTCTGGC	0.517																																																0			13											210	216	214					13																	114324053		2098	4215	6313	113372054	SO:0001583	missense	6011					13q34	2013-09-02	2004-03-23	2004-03-24	ENSG00000185974	ENSG00000185974	2.7.11.14		10013	protein-coding gene	gene with protein product		180381	"rhodopsin kinase"	RHOK		8812493, 15057823	Standard	NM_002929		Approved	GPRK1, RK	uc010tkf.2	Q15835	OTTHUMG00000185528	ENST00000335678.6:c.751G>A	13.37:g.114324053G>A	ENSP00000334876:p.Val251Met		113372054	Q53X14	Missense_Mutation	SNP	ENST00000335678.6	37		.	.	.	.	.	.	.	.	.	.	g	17.97	3.517523	0.64634	.	.	ENSG00000185974	ENST00000335678	T	0.39592	1.07	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.128785	0.51477	D	0.000088	T	0.65048	0.2654	.	.	.	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	T	0.70941	-0.4735	9	0.87932	D	0	-44.2014	14.7555	0.69560	0.0:0.0:1.0:0.0	.	251	Q15835	RK_HUMAN	M	251	ENSP00000334876:V251M	ENSP00000334876:V251M	V	+	1	0	GRK1	113372054	1.000000	0.71417	0.960000	0.40013	0.449000	0.32228	8.653000	0.91088	2.131000	0.65755	0.511000	0.50034	GTG		0.517	GRK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470655.1	NM_002929		A	114324053	G	A	114324053	3	1	105	1	0	0	0	0	1	0	0	0	6811	1145	40	1	757	1	GRK1	13	114324053	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2951911	114324053	845825	169	27809										
RNASE3	6037	hgsc.bcm.edu	37	chr14	21360033	21360033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aattaacaattatcgatggcGttgcaaaaaccaaaatactt	5	7	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:21360033G>A	ENST00000304639.3	+	2	246	c.188G>A	c.(187-189)cGt>cAt	p.R63H		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	63	Required for nearly all of the bactericidal activity; partially involved in LPS-binding and bacterial membrane depolarization.				antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TATCGATGGCGTTGCAAAAAC	0.438																																																0			14											124	126	125					14																	21360033		2191	4300	6491	20429873	SO:0001583	missense	6037			X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"Ribonucleases, RNase A"	10046	protein-coding gene	gene with protein product	"eosinophil cationic protein"	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.188G>A	14.37:g.21360033G>A	ENSP00000302324:p.Arg63His		20429873	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	.	.	.	.	.	.	.	.	.	.	g	0.431	-0.903137	0.02453	.	.	ENSG00000169397	ENST00000304639	T	0.74002	-0.8	2.44	-4.89	0.03103	Ribonuclease A, domain (4);	3.170440	0.02219	U	0.063891	T	0.61986	0.2391	L	0.48174	1.505	0.09310	N	1	B	0.24258	0.1	B	0.23419	0.046	T	0.42137	-0.9469	10	0.26408	T	0.33	.	1.418	0.02306	0.1887:0.1296:0.3979:0.2838	.	63	P12724	ECP_HUMAN	H	63	ENSP00000302324:R63H	ENSP00000302324:R63H	R	+	2	0	RNASE3	20429873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.754000	0.01816	-2.841000	0.00335	-0.311000	0.09066	CGT		0.438	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935		A	21360033	G	A	21360033	3	1	105	1	0	0	0	0	1	0	0	0	13442	1145	40	1	190	1	RNASE3	14	21360033	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		21360033	85989507	170	27810										
MIA2	117153	hgsc.bcm.edu	37	chr14	39703358	39703358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acagaatccttcttctggctAtttctctgacaaagtgtctg	7	10	4	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:39703358A>G	ENST00000280082.3	+	1	239	c.40A>G	c.(40-42)Att>Gtt	p.I14V	MIA2_ENST00000556784.1_Missense_Mutation_p.I14V|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I14V	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	14					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		TCTTCTGGCTATTTCTCTGAC	0.433																																																0			14											107	102	104					14																	39703358		2203	4300	6503	38773109	SO:0001583	missense	117153			BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.40A>G	14.37:g.39703358A>G	ENSP00000280082:p.Ile14Val		38773109	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	A	7.586	0.669850	0.14776	.	.	ENSG00000150526;ENSG00000150526;ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000557148;ENST00000555143;ENST00000280082;ENST00000556784;ENST00000553728	T;T;T;T;T	0.45276	1.05;1.01;0.9;0.92;3.28	5.5	-0.0931	0.13652	.	0.389260	0.18870	N	0.128871	T	0.31040	0.0784	M	0.67953	2.075	0.18873	N	0.999982	B	0.23377	0.084	B	0.20184	0.028	T	0.22103	-1.0226	9	.	.	.	-14.7284	0.5314	0.00629	0.3895:0.2387:0.1576:0.2142	.	14	Q96PC5-2	.	V	14	ENSP00000451883:I14V;ENSP00000451217:I14V;ENSP00000280082:I14V;ENSP00000451934:I14V;ENSP00000452252:I14V	.	I	+	1	0	MIA2;RP11-407N17.3	38773109	0.905000	0.30787	0.891000	0.34965	0.314000	0.28054	0.214000	0.17541	-0.175000	0.10725	-0.341000	0.08007	ATT		0.433	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39703358	A	G	39703358	3	3	105	1	0	0	0	0	1	0	0	0	9594	449	16	4	42	4	MIA2	14	39703358	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	18343325	39703358	67646182	171	27811										
NID2	22795	hgsc.bcm.edu	37	chr14	52481904	52481904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	caggtcatcgcactggggcaCgtactggtcatcccgggggg	16	12	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:52481904C>T	ENST00000216286.5	-	15	3117	c.3118G>A	c.(3118-3120)Gtg>Atg	p.V1040M	NID2_ENST00000541773.1_Missense_Mutation_p.V939M	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1040	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					CACTGGGGCACGTACTGGTCA	0.632																																																0			14											57	51	53					14																	52481904		2203	4300	6503	51551654	SO:0001583	missense	22795			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3118G>A	14.37:g.52481904C>T	ENSP00000216286:p.Val1040Met		51551654	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.04|18.04	3.534523|3.534523	0.64972|0.64972	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.|T;T	.|0.66460	.|-0.21;-0.21	5.67|5.67	4.76|4.76	0.60689|0.60689	.|Thyroglobulin type-1 (6);	.|0.307436	.|0.35870	.|N	.|0.002936	T|T	0.80747|0.80747	0.4682|0.4682	M|M	0.74389|0.74389	2.26|2.26	0.32173|0.32173	N|N	0.581438|0.581438	.|D;D;D;D	.|0.89917	.|0.977;1.0;1.0;0.997	.|P;D;D;P	.|0.91635	.|0.73;0.999;0.993;0.876	D|D	0.83392|0.83392	0.0018|0.0018	5|10	.|0.31617	.|T	.|0.26	.|.	16.0582|16.0582	0.80820|0.80820	0.0:0.8654:0.1346:0.0|0.0:0.8654:0.1346:0.0	.|.	.|634;939;1042;1040	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	H|M	308|1040;634;939;1042	.|ENSP00000216286:V1040M;ENSP00000443730:V939M	.|ENSP00000216286:V1040M	R|V	-|-	2|1	0|0	NID2|NID2	51551654|51551654	0.263000|0.263000	0.24083|0.24083	0.986000|0.986000	0.45419|0.45419	0.978000|0.978000	0.69477|0.69477	0.791000|0.791000	0.26915|0.26915	1.342000|1.342000	0.45619|0.45619	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.632	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52481904	C	T	52481904	3	4	105	1	0	0	0	0	1	0	0	0	10446	536	19	1	1041	1	NID2	14	52481904	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	12778546	52481904	54867636	172	27812										
KTN1	3895	hgsc.bcm.edu	37	chr14	56119764	56119764	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gaagaaaatgaatctttaaaAgcacatgttcaggaagtagc	9	5	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:56119764A>G	ENST00000395314.3	+	27	2792	c.2724A>G	c.(2722-2724)aaA>aaG	p.K908K	KTN1_ENST00000554507.1_Silent_p.K203K|KTN1_ENST00000395311.1_Silent_p.K885K|KTN1_ENST00000413890.2_Silent_p.K885K|KTN1_ENST00000395308.1_Silent_p.K885K|KTN1_ENST00000416613.1_Silent_p.K908K|KTN1_ENST00000395309.3_Silent_p.K908K|Y_RNA_ENST00000363872.1_RNA|KTN1_ENST00000438792.2_Silent_p.K908K	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	908					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AATCTTTAAAAGCACATGTTC	0.259			T	RET	papillary thryoid																																		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	0			14											338	363	355					14																	56119764		2201	4293	6494	55189517	SO:0001819	synonymous_variant	3895				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2724A>G	14.37:g.56119764A>G			55189517	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																				0.259	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56119764	A	G	56119764	2	3	105	1	0	0	0	0	0	0	0	1	8607	69	3	4		4	KTN1	14	56119764	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	3637860	56119764	51229776	173	27813										
PSEN1	5663	hgsc.bcm.edu	37	chr14	73637706	73637706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctctctgcatggtggtggtcGtggctaccattaagtcagtc	12	10	2	0	rs63750852		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:73637706G>A	ENST00000324501.5	+	4	561	c.289G>A	c.(289-291)Gtg>Atg	p.V97M	PSEN1_ENST00000406768.1_Missense_Mutation_p.V5M|PSEN1_ENST00000357710.4_Missense_Mutation_p.V93M|PSEN1_ENST00000394164.1_Missense_Mutation_p.V93M|PSEN1_ENST00000261970.3_Missense_Mutation_p.V97M|PSEN1_ENST00000344094.3_Missense_Mutation_p.V97M|PSEN1_ENST00000557511.1_Missense_Mutation_p.V97M|PSEN1_ENST00000394157.3_Missense_Mutation_p.V97M	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	97	Poly-Val.				activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		GGTGGTGGTCGTGGCTACCAT	0.458																																																0			14	GRCh37	CM056038	PSEN1	M	rs63750852						134	113	120					14																	73637706		2203	4300	6503	72707459	SO:0001583	missense	5663			AJ008005	CCDS9812.1, CCDS9813.1	14q24.3	2014-09-17	2008-07-28		ENSG00000080815	ENSG00000080815			9508	protein-coding gene	gene with protein product		104311	"Alzheimer disease 3"	AD3		1411576	Standard	NM_007318		Approved	FAD, S182, PS1	uc001xnr.3	P49768	OTTHUMG00000141279	ENST00000324501.5:c.289G>A	14.37:g.73637706G>A	ENSP00000326366:p.Val97Met		72707459	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Missense_Mutation	SNP	ENST00000324501.5	37	CCDS9812.1	.	.	.	.	.	.	.	.	.	.	G	32	5.181027	0.94846	.	.	ENSG00000080815	ENST00000557356;ENST00000557293;ENST00000553719;ENST00000394157;ENST00000324501;ENST00000357710;ENST00000555254;ENST00000261970;ENST00000344094;ENST00000554131;ENST00000394164;ENST00000557511;ENST00000406768	D;D;D;D;D;D;D;D;D;D;D;D;D	0.99698	-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44;-6.44	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.999;1.0	D	0.97037	0.9754	10	0.87932	D	0	-16.732	18.8208	0.92096	0.0:0.0:1.0:0.0	.	93;97;97	P49768-2;P49768;P49768-4	.;PSN1_HUMAN;.	M	93;97;93;97;97;93;97;97;97;97;93;97;5	ENSP00000451498:V93M;ENSP00000451880:V97M;ENSP00000451674:V93M;ENSP00000377712:V97M;ENSP00000326366:V97M;ENSP00000350342:V93M;ENSP00000450652:V97M;ENSP00000261970:V97M;ENSP00000339523:V97M;ENSP00000451915:V97M;ENSP00000377719:V93M;ENSP00000451429:V97M;ENSP00000385948:V5M	ENSP00000261970:V97M	V	+	1	0	PSEN1	72707459	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	9.657000	0.98554	2.676000	0.91093	0.563000	0.77884	GTG		0.458	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			A	73637706	G	A	73637706	3	1	105	1	0	0	0	0	1	0	0	0	12684	1145	40	1	295	1	PSEN1	14	73637706	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	17517942	73637706	33711834	174	27814										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92472683	92472683	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgtccattttatcatcttcaAgttgatgaactctctttttt	4	8	4	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:92472683A>G	ENST00000267622.4	-	11	2010	c.1637T>C	c.(1636-1638)cTt>cCt	p.L546P		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	546					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		ATCATCTTCAAGTTGATGAAC	0.308			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											82	78	79					14																	92472683		2202	4296	6498	91542436	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.1637T>C	14.37:g.92472683A>G	ENSP00000267622:p.Leu546Pro		91542436	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506183	0.44558	.	.	ENSG00000100815	ENST00000267622;ENST00000542257	T	0.09073	3.02	6.16	6.16	0.99307	.	0.219434	0.37437	N	0.002088	T	0.27798	0.0684	M	0.74881	2.28	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.976;0.998	T	0.01084	-1.1457	10	0.72032	D	0.01	.	11.0377	0.47811	0.9314:0.0:0.0686:0.0	.	282;546	F5H1Z0;Q15643	.;TRIPB_HUMAN	P	546;282	ENSP00000267622:L546P	ENSP00000267622:L546P	L	-	2	0	TRIP11	91542436	0.829000	0.29322	0.634000	0.29324	0.273000	0.26683	2.406000	0.44557	2.367000	0.80283	0.528000	0.53228	CTT		0.308	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			G	92472683	A	G	92472683	3	3	105	1	0	0	0	0	1	0	0	0	16595	72	3	4	4346	4	TRIP11	14	92472683	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	18834977	92472683	14876857	175	27815										
RIN3	79890	hgsc.bcm.edu	37	chr14	93118468	93118468	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggccccctcagggaggaagcGatgaagccaggggcagcctc	16	13	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:93118468G>A	ENST00000216487.7	+	6	1233	c.1074G>A	c.(1072-1074)gcG>gcA	p.A358A	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	358	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				GGGAGGAAGCGATGAAGCCAG	0.677																																																0			14											27	28	28					14																	93118468		2168	4257	6425	92188221	SO:0001819	synonymous_variant	79890			BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1074G>A	14.37:g.93118468G>A			92188221	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																				0.677	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			A	93118468	G	A	93118468	2	1	105	1	0	0	0	0	0	0	0	1	13410	1045	37	1		1	RIN3	14	93118468	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	645785	93118468	14231072	176	27816										
BDKRB1	623	hgsc.bcm.edu	37	chr14	96730615	96730615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cctcccccatgaggcctggcActttgcaaggattgtggagt	12	12	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr14:96730615A>G	ENST00000216629.6	+	3	1202	c.596A>G	c.(595-597)cAc>cGc	p.H199R	RP11-404P21.3_ENST00000553638.1_RNA|BDKRB1_ENST00000553356.1_Missense_Mutation_p.H199R	NM_000710.3	NP_000701.2	P46663	BKRB1_HUMAN	bradykinin receptor B1	199					cell migration (GO:0016477)|inflammatory response (GO:0006954)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell growth (GO:0030308)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|peptide binding (GO:0042277)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(4)|skin(1)|urinary_tract(1)	16		all_cancers(154;0.0677)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.208)|Epithelial(152;0.226)		GAGGCCTGGCACTTTGCAAGG	0.567																																																0			14											86	78	81					14																	96730615		2203	4300	6503	95800368	SO:0001583	missense	623			L42383	CCDS9943.1	14q32.1-q32.2	2012-08-08				ENSG00000100739		"GPCR / Class A : Bradykinin receptors"	1029	protein-coding gene	gene with protein product		600337				8808279	Standard	NM_000710		Approved	BKR1, B1BKR, bradyb1	uc001yfh.3	P46663		ENST00000216629.6:c.596A>G	14.37:g.96730615A>G	ENSP00000216629:p.His199Arg		95800368	A8K7F5|Q546S7|Q8N0Y8	Missense_Mutation	SNP	ENST00000216629.6	37	CCDS9943.1	.	.	.	.	.	.	.	.	.	.	A	0.137	-1.107085	0.01813	.	.	ENSG00000100739	ENST00000216629;ENST00000553356	T;T	0.36520	1.25;1.25	4.95	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.852869	0.10393	U	0.680207	T	0.12646	0.0307	N	0.02412	-0.56	0.09310	N	0.999994	B;B	0.17465	0.022;0.005	B;B	0.15052	0.01;0.012	T	0.31194	-0.9952	10	0.16420	T	0.52	-5.8753	3.4635	0.07541	0.6454:0.1481:0.0788:0.1277	.	199;199	G3V4Y2;P46663	.;BKRB1_HUMAN	R	199	ENSP00000216629:H199R;ENSP00000452064:H199R	ENSP00000216629:H199R	H	+	2	0	BDKRB1	95800368	0.000000	0.05858	0.955000	0.39395	0.303000	0.27691	-0.156000	0.10100	0.754000	0.32968	0.379000	0.24179	CAC		0.567	BDKRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413300.1			G	96730615	A	G	96730615	3	3	105	1	0	0	0	0	1	0	0	0	1393	159	6	4	598	4	BDKRB1	14	96730615	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	3612147	96730615	10618925	177	27817										
ATP10A	57194	hgsc.bcm.edu	37	chr15	26026234	26026234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tccatccaggttggcggtctCgatgtggcatagcccgtcgg	14	12	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr15:26026234C>T	ENST00000356865.6	-	2	697	c.586G>A	c.(586-588)Gag>Aag	p.E196K		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	196					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTGGCGGTCTCGATGTGGCAT	0.602																																																0			15											90	88	89					15																	26026234		2203	4300	6503	23577327	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.586G>A	15.37:g.26026234C>T	ENSP00000349325:p.Glu196Lys		23577327	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	35	5.482963	0.96307	.	.	ENSG00000206190	ENST00000356865	D	0.90385	-2.66	4.67	4.67	0.58626	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.97077	0.9045	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.98452	1.0592	10	0.72032	D	0.01	-31.4504	16.7413	0.85460	0.0:1.0:0.0:0.0	.	196	O60312	AT10A_HUMAN	K	196	ENSP00000349325:E196K	ENSP00000349325:E196K	E	-	1	0	ATP10A	23577327	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.356000	0.79445	2.428000	0.82296	0.561000	0.74099	GAG		0.602	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	26026234	C	T	26026234	3	4	105	1	0	0	0	0	1	0	0	0	1117	893	31	1	3993	1	ATP10A	15	26026234	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		26026234	76505158	178	27818										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86269655	86269655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttccagaggttcaagcagttCttctcactgacattttagtt	7	9	3	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr15:86269655C>A	ENST00000394518.2	+	27	6855	c.6760C>A	c.(6760-6762)Ctt>Att	p.L2254I	AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Missense_Mutation_p.L499I|AKAP13_ENST00000361243.2_Missense_Mutation_p.L2258I|RP11-158M2.2_ENST00000561417.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2254	Interaction with ESR1.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TCAAGCAGTTCTTCTCACTGA	0.348																																					Melanoma(94;603 1453 3280 32295 32951)											0			15											187	189	188					15																	86269655		2202	4298	6500	84070659	SO:0001583	missense	11214			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.6760C>A	15.37:g.86269655C>A	ENSP00000378026:p.Leu2254Ile		84070659	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766626	0.90020	.	.	ENSG00000170776	ENST00000426424;ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	D;D;D	0.91792	-1.61;-1.61;-2.91	5.31	4.39	0.52855	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.95887	0.8661	M	0.87038	2.855	0.49389	D	0.999786	P;P;P	0.41420	0.705;0.749;0.705	P;P;P	0.60012	0.791;0.867;0.791	D	0.96165	0.9118	9	0.87932	D	0	.	12.4559	0.55704	0.0:0.9192:0.0:0.0808	.	2234;2254;2258	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	I	334;2258;2254;2257;2233;499	ENSP00000354718:L2258I;ENSP00000378026:L2254I;ENSP00000378018:L499I	ENSP00000354718:L2258I	L	+	1	0	AKAP13	84070659	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	4.434000	0.59935	2.484000	0.83849	0.484000	0.47621	CTT		0.348	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		A	86269655	C	A	86269655	3	1	105	1	0	0	0	0	1	0	0	0	449	913	32	2	6932	2	AKAP13	15	86269655	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	60243421	86269655	16261737	179	27819										
ROGDI	79641	hgsc.bcm.edu	37	chr16	4850570	4850570	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gttgttccggggcatcttcaGgttcacatcctgacaggcaa	11	11	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr16:4850570G>A	ENST00000322048.7	-	5	643	c.265C>T	c.(265-267)Ctg>Ttg	p.L89L	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	89					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GGCATCTTCAGGTTCACATCC	0.632																																																0			16											36	31	32					16																	4850570		2194	4285	6479	4790571	SO:0001819	synonymous_variant	79641			AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.265C>T	16.37:g.4850570G>A			4790571	Q6IA00	Silent	SNP	ENST00000322048.7	37	CCDS10523.1																																																																																				0.632	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		A	4850570	G	A	4850570	2	1	105	1	0	0	0	0	0	0	0	1	13557	991	35	3		3	ROGDI	16	4850570	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		4850570	85504183	180	27820										
SMG1	23049	hgsc.bcm.edu	37	chr16	18861443	18861443	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctagggtcatcctcatctaaAggaatctaagagtgaaagat	9	7	4	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr16:18861443A>G	ENST00000446231.2	-	35	5701	c.5289T>C	c.(5287-5289)ccT>ccC	p.P1763P	SMG1_ENST00000389467.3_Silent_p.P1763P			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1763	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CCTCATCTAAAGGAATCTAAG	0.383																																																0			16											61	58	59					16																	18861443		1939	4148	6087	18768944	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5289T>C	16.37:g.18861443A>G			18768944	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.383	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18861443	A	G	18861443	2	3	105	1	0	0	0	0	0	0	0	1	14832	59	3	4		4	SMG1	16	18861443	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	14010873	18861443	71493310	181	27821										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	105	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10		7577094	73618116	182	27822										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33477186	33477186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gttgtgccaccctcgagccaCggaaccagaacttccaggag	11	14	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:33477186C>T	ENST00000268876.5	+	4	422	c.325C>T	c.(325-327)Cgg>Tgg	p.R109W	UNC45B_ENST00000394570.2_Missense_Mutation_p.R109W|UNC45B_ENST00000378449.1_Missense_Mutation_p.R109W|UNC45B_ENST00000591048.1_Missense_Mutation_p.R109W|UNC45B_ENST00000433649.1_Missense_Mutation_p.R109W	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	109					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CCTCGAGCCACGGAACCAGAA	0.607																																																0			17											100	84	90					17																	33477186		2203	4300	6503	30501299	SO:0001583	missense	146862			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.325C>T	17.37:g.33477186C>T	ENSP00000268876:p.Arg109Trp		30501299	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502579	0.64298	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.55	-1.54	0.08584	Armadillo-like helical (1);Armadillo-type fold (1);Tetratricopeptide repeat-containing (1);	0.485095	0.21974	N	0.066416	T	0.61286	0.2335	L	0.27053	0.805	0.09310	N	0.999998	D;P;P	0.89917	1.0;0.949;0.931	D;B;P	0.72338	0.977;0.426;0.905	T	0.56019	-0.8048	10	0.72032	D	0.01	-8.3887	8.9045	0.35515	0.5919:0.3296:0.0:0.0785	.	109;109;109	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	W	109	ENSP00000378071:R109W;ENSP00000268876:R109W;ENSP00000412840:R109W;ENSP00000367710:R109W	ENSP00000268876:R109W	R	+	1	2	UNC45B	30501299	0.955000	0.32602	0.869000	0.34112	0.990000	0.78478	1.689000	0.37700	-0.060000	0.13132	0.650000	0.86243	CGG		0.607	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		T	33477186	C	T	33477186	3	4	105	1	0	0	0	0	1	0	0	0	17029	527	19	1	335	1	UNC45B	17	33477186	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	25900092	33477186	47718024	183	27823										
MYO19	80179	hgsc.bcm.edu	37	chr17	34863737	34863737	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cagactgttgtcaggaaatgAttcaaatccatacacatcca	6	10	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:34863737A>G	ENST00000431794.3	-	15	1780	c.1258T>C	c.(1258-1260)Tca>Cca	p.S420P	MYO19_ENST00000268852.9_Missense_Mutation_p.S420P	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	420	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TCAGGAAATGATTCAAATCCA	0.542																																																0			17											77	78	77					17																	34863737		2141	4267	6408	31937850	SO:0001583	missense	80179			BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.1258T>C	17.37:g.34863737A>G	ENSP00000409936:p.Ser420Pro		31937850	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	A	19.20	3.780697	0.70222	.	.	ENSG00000141140	ENST00000415126;ENST00000431794;ENST00000268852	D;D	0.87412	-2.25;-2.25	5.79	5.79	0.91817	Myosin head, motor domain (3);	0.230079	0.22185	N	0.063459	D	0.93916	0.8053	M	0.90145	3.09	0.49389	D	0.999787	D;D	0.69078	0.997;0.967	D;P	0.69824	0.966;0.806	D	0.94414	0.7634	10	0.62326	D	0.03	.	11.6091	0.51049	0.8514:0.1486:0.0:0.0	.	420;420	Q96H55;Q96H55-4	MYO19_HUMAN;.	P	155;420;420	ENSP00000409936:S420P;ENSP00000268852:S420P	ENSP00000268852:S420P	S	-	1	0	MYO19	31937850	1.000000	0.71417	0.685000	0.30070	0.991000	0.79684	4.481000	0.60250	2.208000	0.71279	0.533000	0.62120	TCA		0.542	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		G	34863737	A	G	34863737	3	3	105	1	0	0	0	0	1	0	0	0	10097	333	12	4	1702	4	MYO19	17	34863737	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	1386551	34863737	46331473	184	27824										
HSF5	124535	hgsc.bcm.edu	37	chr17	56557479	56557479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tccaggatgcattccaagggAgttctgccatattctatgag	10	9	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:56557479A>G	ENST00000323777.3	-	2	809	c.700T>C	c.(700-702)Tcc>Ccc	p.S234P		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	234					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATTCCAAGGGAGTTCTGCCAT	0.478																																																0			17											145	135	138					17																	56557479		2203	4300	6503	53912478	SO:0001583	missense	124535			BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.700T>C	17.37:g.56557479A>G	ENSP00000313243:p.Ser234Pro		53912478	Q08EH7|Q8N7V2	Missense_Mutation	SNP	ENST00000323777.3	37	CCDS32690.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049079	0.75846	.	.	ENSG00000176160	ENST00000412540;ENST00000323777	T	0.73258	-0.73	5.5	5.5	0.81552	.	0.000000	0.56097	D	0.000038	T	0.73528	0.3598	N	0.24115	0.695	0.37669	D	0.923042	D	0.71674	0.998	D	0.75484	0.986	T	0.77308	-0.2636	10	0.44086	T	0.13	.	12.9827	0.58572	1.0:0.0:0.0:0.0	.	234	Q4G112	HSF5_HUMAN	P	134;234	ENSP00000313243:S234P	ENSP00000313243:S234P	S	-	1	0	HSF5	53912478	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.346000	0.59367	2.091000	0.63221	0.533000	0.62120	TCC		0.478	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190		G	56557479	A	G	56557479	3	3	105	1	0	0	0	0	1	0	0	0	7420	304	11	4	1110	4	HSF5	17	56557479	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	21693742	56557479	24637731	185	27825										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73831795	73831795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtagagctggaacagactctCgcccatctctggggacacta	11	12	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:73831795C>T	ENST00000207549.4	-	19	2039	c.1660G>A	c.(1660-1662)Gag>Aag	p.E554K	UNC13D_ENST00000412096.2_Missense_Mutation_p.E554K	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	554					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			AACAGACTCTCGCCCATCTCT	0.627									Familial Hemophagocytic Lymphohistiocytosis																																							0			17											54	51	52					17																	73831795		2203	4300	6503	71343390	SO:0001583	missense	201294	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.1660G>A	17.37:g.73831795C>T	ENSP00000207549:p.Glu554Lys		71343390	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.245060	0.59103	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.69561	-0.39;-0.41	4.72	4.72	0.59763	.	0.138185	0.49305	D	0.000147	T	0.61800	0.2376	M	0.61703	1.905	0.50467	D	0.999879	P;P	0.49696	0.927;0.607	B;B	0.40901	0.343;0.036	T	0.63580	-0.6605	10	0.08179	T	0.78	-19.5763	17.6528	0.88169	0.0:1.0:0.0:0.0	.	554;554	Q70J99-3;Q70J99	.;UN13D_HUMAN	K	554	ENSP00000207549:E554K;ENSP00000388093:E554K	ENSP00000207549:E554K	E	-	1	0	UNC13D	71343390	0.993000	0.37304	0.996000	0.52242	0.950000	0.60333	4.017000	0.57167	2.154000	0.67381	0.491000	0.48974	GAG		0.627	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73831795	C	T	73831795	3	4	105	1	0	0	0	0	1	0	0	0	17027	893	31	1	1668	1	UNC13D	17	73831795	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	17274316	73831795	7363415	186	27826										
CCDC40	55036	hgsc.bcm.edu	37	chr17	78063611	78063611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atccaactggcaaaagagatGcgttcctcagtggattccga	10	10	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr17:78063611G>A	ENST00000397545.4	+	17	2787	c.2760G>A	c.(2758-2760)atG>atA	p.M920I	CCDC40_ENST00000374877.3_Missense_Mutation_p.M920I|CCDC40_ENST00000573903.1_3'UTR	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	920					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)		p.M920I(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CAAAAGAGATGCGTTCCTCAG	0.517																																																1	Substitution - Missense(1)	ovary(1)	17											63	63	63					17																	78063611		1929	4131	6060	75678206	SO:0001583	missense	55036			AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.2760G>A	17.37:g.78063611G>A	ENSP00000380679:p.Met920Ile		75678206	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702960	0.48412	.	.	ENSG00000141519	ENST00000374877;ENST00000397545	T;T	0.51574	0.7;0.72	4.63	4.63	0.57726	.	.	.	.	.	T	0.57961	0.2089	M	0.82323	2.585	0.39013	D	0.959599	P;P	0.48640	0.553;0.913	B;P	0.45099	0.218;0.469	T	0.67821	-0.5571	9	0.41790	T	0.15	-41.6276	17.808	0.88607	0.0:0.0:1.0:0.0	.	920;703	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	I	920	ENSP00000364011:M920I;ENSP00000380679:M920I	ENSP00000364011:M920I	M	+	3	0	CCDC40	75678206	1.000000	0.71417	1.000000	0.80357	0.453000	0.32348	3.269000	0.51592	2.294000	0.77228	0.563000	0.77884	ATG		0.517	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		A	78063611	G	A	78063611	3	1	105	1	0	0	0	0	1	0	0	0	2818	1319	46	3	2826	3	CCDC40	17	78063611	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	4231816	78063611	3131599	187	27827										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48593532	48593532	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acctggagatgctgttcataAgatctacccaagtgcatata	8	9	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr18:48593532A>T	ENST00000342988.3	+	10	1821	c.1283A>T	c.(1282-1284)aAg>aTg	p.K428M	SMAD4_ENST00000588745.1_Missense_Mutation_p.K332M|SMAD4_ENST00000398417.2_Missense_Mutation_p.K428M	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	428	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.K428R(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GCTGTTCATAAGATCTACCCA	0.398																																																39	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|biliary_tract(1)|oesophagus(1)	18											114	98	104					18																	48593532		2203	4300	6503	46847530	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1283A>T	18.37:g.48593532A>T	ENSP00000341551:p.Lys428Met		46847530	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.645628	0.87958	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99376	-5.79;-5.79	5.17	5.17	0.71159	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.094910	0.64402	D	0.000001	D	0.99542	0.9836	H	0.95402	3.665	0.80722	D	1	D	0.65815	0.995	D	0.66196	0.942	D	0.98023	1.0372	10	0.87932	D	0	.	14.3127	0.66426	1.0:0.0:0.0:0.0	.	428	Q13485	SMAD4_HUMAN	M	428	ENSP00000341551:K428M;ENSP00000381452:K428M	ENSP00000341551:K428M	K	+	2	0	SMAD4	46847530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.171000	0.94802	2.083000	0.62718	0.455000	0.32223	AAG		0.398	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48593532	A	T	48593532	3	4	105	1	0	0	0	0	1	0	0	0	14797	72	3	5	1317	5	SMAD4	18	48593532	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10		48593532	29483716	188	27828										
TRIP10	9322	hgsc.bcm.edu	37	chr19	6744988	6744988	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gccgcaccaagcgctggcctTttggcaagaagaacaaggtg	13	11	0	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:6744988T>A	ENST00000313244.9	+	9	1002	c.967T>A	c.(967-969)Ttt>Att	p.F323I	TRIP10_ENST00000596758.1_Missense_Mutation_p.F323I|TRIP10_ENST00000313285.8_Missense_Mutation_p.F323I|TRIP10_ENST00000600428.1_Missense_Mutation_p.F215I			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	323	Interaction with CDC42.|Interaction with PDE6G. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GCGCTGGCCTTTTGGCAAGAA	0.667																																																0			19											18	21	20					19																	6744988		2195	4286	6481	6695988	SO:0001583	missense	9322			AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.967T>A	19.37:g.6744988T>A	ENSP00000320117:p.Phe323Ile		6695988	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.853952	0.91355	.	.	ENSG00000125733	ENST00000313285;ENST00000313244;ENST00000420690	D;D	0.91295	-2.82;-2.82	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.93122	0.7810	L	0.47016	1.485	0.58432	D	0.999999	D;P;D	0.89917	1.0;0.817;1.0	D;B;D	0.91635	0.999;0.23;0.997	D	0.93742	0.7051	10	0.87932	D	0	-20.3656	13.1857	0.59680	0.0:0.0:0.0:1.0	.	323;323;323	G5E9U1;Q15642;Q15642-2	.;CIP4_HUMAN;.	I	323	ENSP00000320493:F323I;ENSP00000320117:F323I	ENSP00000320117:F323I	F	+	1	0	TRIP10	6695988	1.000000	0.71417	0.946000	0.38457	0.713000	0.41058	7.180000	0.77674	2.010000	0.58986	0.402000	0.26972	TTT		0.667	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			A	6744988	T	A	6744988	3	1	105	1	0	0	0	0	1	0	0	0	16594	1841	64	5	1001	5	TRIP10	19	6744988	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10		6744988	52383995	189	27829										
FBN3	84467	hgsc.bcm.edu	37	chr19	8203386	8203386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgcctgcgagtgtagtggcCggcgaggtctccagcacagc	15	13	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:8203386C>T	ENST00000600128.1	-	9	1342	c.928G>A	c.(928-930)Ggc>Agc	p.G310S	FBN3_ENST00000601739.1_Missense_Mutation_p.G310S|FBN3_ENST00000270509.2_Missense_Mutation_p.G310S			Q75N90	FBN3_HUMAN	fibrillin 3	310	TB 2.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GTGTAGTGGCCGGCGAGGTCT	0.652																																																0			19											23	25	25					19																	8203386		2201	4299	6500	8109386	SO:0001583	missense	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.928G>A	19.37:g.8203386C>T	ENSP00000470498:p.Gly310Ser		8109386	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	c	13.90	2.374613	0.42105	.	.	ENSG00000142449	ENST00000270509	D	0.93953	-3.32	4.06	4.06	0.47325	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	U	0.000000	D	0.96654	0.8908	M	0.88031	2.925	0.43885	D	0.996502	D	0.89917	1.0	D	0.78314	0.991	D	0.96021	0.9009	10	0.18276	T	0.48	.	16.1794	0.81889	0.0:1.0:0.0:0.0	.	310	Q75N90	FBN3_HUMAN	S	310	ENSP00000270509:G310S	ENSP00000270509:G310S	G	-	1	0	FBN3	8109386	0.948000	0.32251	0.032000	0.17829	0.008000	0.06430	2.859000	0.48364	1.974000	0.57490	0.556000	0.70494	GGC		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8203386	C	T	8203386	3	4	105	1	0	0	0	0	1	0	0	0	5723	652	23	1	7725	1	FBN3	19	8203386	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	1458398	8203386	50925597	190	27830										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13941113	13941113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cacacacgccactctgctgcGactgcagctggacacatcgc	9	17	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:13941113G>A	ENST00000254323.2	+	13	2408	c.2219G>A	c.(2218-2220)cGa>cAa	p.R740Q	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.R574Q	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	740							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			ACTCTGCTGCGACTGCAGCTG	0.617																																																0			19											62	60	61					19																	13941113		2203	4300	6503	13802113	SO:0001583	missense	65249			AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.2219G>A	19.37:g.13941113G>A	ENSP00000254323:p.Arg740Gln		13802113		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.913703	0.72983	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.53206	0.63;0.64	4.15	4.15	0.48705	.	0.000000	0.53938	D	0.000045	T	0.63034	0.2477	L	0.59436	1.845	0.42845	D	0.994067	D;P	0.76494	0.999;0.941	D;P	0.77557	0.99;0.541	T	0.64474	-0.6399	10	0.44086	T	0.13	-32.9217	13.9159	0.63897	0.0:0.0:1.0:0.0	.	574;740	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	Q	740;574	ENSP00000254323:R740Q;ENSP00000405278:R574Q	ENSP00000254323:R740Q	R	+	2	0	ZSWIM4	13802113	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	9.384000	0.97219	1.853000	0.53794	0.491000	0.48974	CGA		0.617	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		A	13941113	G	A	13941113	3	1	105	1	0	0	0	0	1	0	0	0	18282	1058	37	1	2269	1	ZSWIM4	19	13941113	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	5737727	13941113	45187870	191	27831										
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15789139	15789139	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acctattcccagggctttacGatatggctgggtcccatcat	9	12	1	0	rs568094588		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:15789139G>T	ENST00000550308.1	+	3	647	c.267G>T	c.(265-267)acG>acT	p.T89T	CYP4F12_ENST00000324632.10_Silent_p.T89T	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	89					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	AGGGCTTTACGATATGGCTGG	0.537																																																0			19											138	138	138					19																	15789139		2178	4288	6466	15650139	SO:0001819	synonymous_variant	66002			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"Cytochrome P450s"	18857	protein-coding gene	gene with protein product		611485	"cytochrome P450, subfamily IVF, polypeptide 12"			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.267G>T	19.37:g.15789139G>T			15650139	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																				0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15789139	G	T	15789139	2	4	105	1	0	0	0	0	0	0	0	1	4193	1045	37	2		2	CYP4F12	19	15789139	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	1848026	15789139	43339844	192	27832										
HAMP	57817	hgsc.bcm.edu	37	chr19	35775901	35775901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccatctgcattttctgctgcGgctgctgtcatcgatcaaag	9	12	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:35775901G>T	ENST00000598398.1	+	4	507	c.211G>T	c.(211-213)Ggc>Tgc	p.G71C	HAMP_ENST00000222304.3_Missense_Mutation_p.G71C	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	71			G -> D (in HFE2B; dbSNP:rs104894696). {ECO:0000269|PubMed:12915468, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:14670915}.		cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TTTCTGCTGCGGCTGCTGTCA	0.577																																																0			19											141	127	132					19																	35775901		2203	4300	6503	40467741	SO:0001583	missense	57817			AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.211G>T	19.37:g.35775901G>T	ENSP00000471894:p.Gly71Cys		40467741	Q1HE14|Q9BY68	Missense_Mutation	SNP	ENST00000598398.1	37	CCDS12454.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.793758	0.50102	.	.	ENSG00000105697	ENST00000222304	D	0.89123	-2.47	4.51	-3.16	0.05217	.	2.232930	0.01537	N	0.019048	D	0.92496	0.7617	.	.	.	0.09310	N	1	D	0.69078	0.997	P	0.61874	0.895	T	0.82900	-0.0228	9	0.87932	D	0	-0.9416	9.888	0.41272	0.749:0.0:0.251:0.0	.	71	P81172	HEPC_HUMAN	C	71	ENSP00000222304:G71C	ENSP00000222304:G71C	G	+	1	0	HAMP	40467741	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	-0.288000	0.08377	-0.445000	0.07159	-0.258000	0.10820	GGC		0.577	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		T	35775901	G	T	35775901	3	4	105	1	0	0	0	0	1	0	0	0	6969	1116	39	2	221	2	HAMP	19	35775901	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	19986762	35775901	23353082	193	27833										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44536594	44536594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aattcatactggggagaagcCattcaaatgtgaaatatgtg	10	5	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:44536594C>T	ENST00000187879.8	+	4	929	c.767C>T	c.(766-768)cCa>cTa	p.P256L	ZNF222_ENST00000391960.3_Missense_Mutation_p.P296L|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GGGGAGAAGCCATTCAAATGT	0.398																																																0			19											131	137	135					19																	44536594		2203	4300	6503	49228434	SO:0001583	missense	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.767C>T	19.37:g.44536594C>T	ENSP00000187879:p.Pro256Leu		49228434	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	37	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.956137	0.73902	.	.	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	T;T	0.17054	2.3;2.3	2.79	2.79	0.32731	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29061	0.0722	M	0.81239	2.535	0.46078	D	0.998856	P;P	0.49253	0.92;0.921	P;P	0.47346	0.507;0.544	T	0.35351	-0.9792	9	0.66056	D	0.02	.	12.7225	0.57149	0.0:1.0:0.0:0.0	.	296;256	G5E9B9;Q9UK12	.;ZN222_HUMAN	L	296;256;202	ENSP00000375822:P296L;ENSP00000187879:P256L	ENSP00000187879:P256L	P	+	2	0	ZNF222	49228434	0.912000	0.30974	0.010000	0.14722	0.453000	0.32348	2.735000	0.47377	1.531000	0.49152	0.205000	0.17691	CCA		0.398	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			T	44536594	C	T	44536594	3	4	105	1	0	0	0	0	1	0	0	0	17815	594	21	3	920	3	ZNF222	19	44536594	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	8760693	44536594	14592389	194	27834										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47177807	47177807	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acactgatgcgctccgccagCccctgcatgtcgtggtcctg	11	16	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:47177807C>A	ENST00000291281.4	-	18	2835	c.2610G>T	c.(2608-2610)ggG>ggT	p.G870G	PRKD2_ENST00000601806.1_Silent_p.G713G|DACT3-AS1_ENST00000525008.1_RNA|PRKD2_ENST00000433867.1_Silent_p.G870G|PRKD2_ENST00000595515.1_Silent_p.G880G|DACT3-AS1_ENST00000525352.1_RNA|PRKD2_ENST00000600194.1_Silent_p.G713G			Q9BZL6	KPCD2_HUMAN	protein kinase D2	870			G -> E (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCTCCGCCAGCCCCTGCATGT	0.632																																																0			19											44	33	37					19																	47177807		2203	4300	6503	51869647	SO:0001819	synonymous_variant	25865			AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.2610G>T	19.37:g.47177807C>A			51869647	Q8TB08|Q9P0T6|Q9Y3X8	Silent	SNP	ENST00000291281.4	37	CCDS12689.1																																																																																				0.632	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		A	47177807	C	A	47177807	2	1	105	1	0	0	0	0	0	0	0	1	12553	726	26	2		2	PRKD2	19	47177807	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	2641213	47177807	11951176	195	27835										
PRR12	57479	hgsc.bcm.edu	37	chr19	50098694	50098694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gggccacgggccctgaggcaGcagggggcggtggggctggg	24	10	0	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:50098694G>T	ENST00000418929.2	+	4	1114	c.1102G>T	c.(1102-1104)Gca>Tca	p.A368S		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		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)		CCCTGAGGCAGCAGGGGGCGG	0.711																																																0			19											2	3	2					19																	50098694		1346	3171	4517	54790506	SO:0001583	missense	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.1102G>T	19.37:g.50098694G>T	ENSP00000394510:p.Ala368Ser		54790506	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	1.226	-0.625452	0.03610	.	.	ENSG00000126464	ENST00000418929	.	.	.	3.83	-2.59	0.06209	.	.	.	.	.	T	0.12008	0.0292	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29150	-1.0021	7	0.08837	T	0.75	.	1.0517	0.01581	0.3805:0.1492:0.3181:0.1522	.	368	Q9ULL5-3	.	S	368	.	ENSP00000394510:A368S	A	+	1	0	PRR12	54790506	0.003000	0.15002	0.000000	0.03702	0.053000	0.15095	-0.579000	0.05834	-0.452000	0.07087	-0.379000	0.06801	GCA		0.711	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50098694	G	T	50098694	3	4	105	1	0	0	0	0	1	0	0	0	12618	971	34	2	1116	2	PRR12	19	50098694	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2920887	50098694	9030289	196	27836										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51955690	51955690	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcaaacaggcctgagtctcTgcagtttctcgcttgtggat	10	11	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:51955690T>C	ENST00000321424.3	-	7	1509	c.1443A>G	c.(1441-1443)gcA>gcG	p.A481A	SIGLEC8_ENST00000340550.5_Silent_p.A388A|SIGLEC8_ENST00000430817.1_Silent_p.A372A	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	481					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CCTGAGTCTCTGCAGTTTCTC	0.517																																																0			19											131	119	123					19																	51955690		2203	4300	6503	56647502	SO:0001819	synonymous_variant	27181			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.1443A>G	19.37:g.51955690T>C			56647502	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																				0.517	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		C	51955690	T	C	51955690	2	2	105	1	0	0	0	0	0	0	0	1	14351	1567	55	4		4	SIGLEC8	19	51955690	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	1856996	51955690	7173293	197	27837										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56320620	56320620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gctgtacaaaactcctggacGttcaagtgtatgaacttgta	9	8	1	1	rs147156673	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:56320620G>A	ENST00000589093.1	-	3	1449	c.1356C>T	c.(1354-1356)aaC>aaT	p.N452N	NLRP11_ENST00000443188.1_Silent_p.N452N|NLRP11_ENST00000589824.2_Silent_p.N452N|NLRP11_ENST00000592953.1_Silent_p.N353N|NLRP11_ENST00000360133.3_Silent_p.N452N			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	452	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ACTCCTGGACGTTCAAGTGTA	0.453																																																0			19						G		0,4406		0,0,2203	69	68	69		1356	-3.5	0	19	dbSNP_134	69	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	NLRP11	NM_145007.3		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		452/1034	56320620	3,13003	2203	4300	6503	61012432	SO:0001819	synonymous_variant	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.1356C>T	19.37:g.56320620G>A			61012432	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																				0.453	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		A	56320620	G	A	56320620	2	1	105	1	0	0	0	0	0	0	0	1	10504	1136	40	1		1	NLRP11	19	56320620	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	4364930	56320620	2808363	198	27838										
ZNF586	54807	hgsc.bcm.edu	37	chr19	58290195	58290195	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	catatatacaaagaccagggAggtcatagtggagaaaggcc	12	7	1	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr19:58290195A>G	ENST00000396154.2	+	3	413	c.240A>G	c.(238-240)ggA>ggG	p.G80G	ZNF586_ENST00000598183.1_Intron|ZNF586_ENST00000599802.1_Intron|ZNF586_ENST00000396150.4_Missense_Mutation_p.E38G|ZNF586_ENST00000391702.3_Silent_p.G37G|ZNF586_ENST00000598885.1_Intron	NM_017652.3	NP_060122.2	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	80	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G80G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)	15		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;0.026)		AAGACCAGGGAGGTCATAGTG	0.443																																																1	Substitution - coding silent(1)	ovary(1)	19											73	71	71					19																	58290195		2008	4198	6206	62982007	SO:0001819	synonymous_variant	54807			AK095993	CCDS42640.1, CCDS56107.1, CCDS56108.1	19q13.43	2013-01-08				ENSG00000083828		"Zinc fingers, C2H2-type", "-"	25949	protein-coding gene	gene with protein product						12477932	Standard	NM_017652		Approved	FLJ20070	uc002qqd.3	Q9NXT0		ENST00000396154.2:c.240A>G	19.37:g.58290195A>G			62982007	A0JLV8|A8MY63|B3KTS9|E7ERT1|G3XAH3	Silent	SNP	ENST00000396154.2	37	CCDS42640.1	.	.	.	.	.	.	.	.	.	.	A	9.449	1.090181	0.20390	.	.	ENSG00000083828	ENST00000396150	T	0.50813	0.73	1.75	1.75	0.24633	.	.	.	.	.	T	0.39306	0.1073	.	.	.	0.20873	N	0.999837	P	0.34587	0.458	B	0.40410	0.328	T	0.26883	-1.0090	7	.	.	.	.	8.2724	0.31853	1.0:0.0:0.0:0.0	.	38	A0JLV8	.	G	38	ENSP00000379454:E38G	.	E	+	2	0	ZNF586	62982007	0.001000	0.12720	0.011000	0.14972	0.068000	0.16541	1.118000	0.31246	0.776000	0.33473	0.459000	0.35465	GAG		0.443	ZNF586-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466825.2	NM_017652		G	58290195	A	G	58290195	2	3	105	1	0	0	0	0	0	0	0	1	18058	291	11	4		4	ZNF586	19	58290195	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	1969575	58290195	838788	199	27839										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16360331	16360331	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aggagctggatcatctcctgCttctctcggagctgctcttc	10	13	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:16360331C>A	ENST00000354981.2	-	19	2473	c.2316G>T	c.(2314-2316)aaG>aaT	p.K772N	KIF16B_ENST00000408042.1_Missense_Mutation_p.K772N|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.K772N	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	772	Glu-rich.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.K772K(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TCATCTCCTGCTTCTCTCGGA	0.567																																																1	Substitution - coding silent(1)	prostate(1)	20											111	105	107					20																	16360331		2203	4300	6503	16308331	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2316G>T	20.37:g.16360331C>A	ENSP00000347076:p.Lys772Asn		16308331	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.185218	0.57909	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000408042	T;T;T	0.18502	2.21;2.21;2.21	5.51	3.36	0.38483	.	0.275521	0.40064	N	0.001182	T	0.23014	0.0556	L	0.60455	1.87	0.80722	D	1	P;P;P;P	0.51240	0.943;0.897;0.903;0.843	P;P;B;B	0.50590	0.629;0.645;0.407;0.231	T	0.01319	-1.1386	10	0.54805	T	0.06	.	6.7787	0.23634	0.0:0.6293:0.0:0.3707	.	772;772;772;772	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	N	772	ENSP00000347076:K772N;ENSP00000347995:K772N;ENSP00000384164:K772N	ENSP00000347076:K772N	K	-	3	2	KIF16B	16308331	0.999000	0.42202	0.967000	0.41034	0.893000	0.52053	0.649000	0.24843	1.334000	0.45468	0.585000	0.79938	AAG		0.567	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16360331	C	A	16360331	3	1	105	1	0	0	0	0	1	0	0	0	8299	796	28	2	1669	2	KIF16B	20	16360331	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		16360331	46665189	200	27840										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18393296	18393300	+	Frame_Shift_Del	DEL	CTGGG	CTGGG	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atcctcccccttacctcttcCtgggctgatggctgtcagga							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	CTGGG	CTGGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:18393296_18393300delCTGGG	ENST00000358866.6	-	12	1444_1448	c.1422_1426delCCCAG	c.(1420-1428)agcccaggafs	p.SPG474fs	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000262547.5_Frame_Shift_Del_p.SPG474fs|DZANK1_ENST00000357236.4_Frame_Shift_Del_p.SPG360fs|DZANK1_ENST00000329494.5_Frame_Shift_Del_p.SPG476fs			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	474							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						TTACCTCTTCCTGGGCTGATGGCTG	0.459																																																0			20																																								18341300	SO:0001589	frameshift_variant	55184			AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1422_1426delCCCAG	20.37:g.18393296_18393300delCTGGG	ENSP00000351734:p.Ser474fs		18341296	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Frame_Shift_Del	DEL	ENST00000358866.6	37	CCDS46582.1																																																																																				0.459	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		-	18393300	CTGGG	-	18393296	7	5	105	1	0	1	0	1	0	0	0	0	2091	690	24	0	868	0	C20orf12	20	18393296	Frame_Shift_Del	DEL	CTGGG	TCGA-DY-A1DD-01A-21D-A152-10	2032965	18393296	44632224	201	27841										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023895	31023895	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggttcttccaccagcccacgAtgacagcatgtcagaatccc	8	15	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:31023895A>G	ENST00000375687.4	+	13	3804	c.3380A>G	c.(3379-3381)gAt>gGt	p.D1127G	ASXL1_ENST00000306058.5_Missense_Mutation_p.D1122G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1127					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CCAGCCCACGATGACAGCATG	0.532			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20											83	75	78					20																	31023895		2203	4300	6503	30487556	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3380A>G	20.37:g.31023895A>G	ENSP00000364839:p.Asp1127Gly		30487556	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	A	1.132	-0.652229	0.03480	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.14022	2.54;2.54	4.56	0.149	0.14863	.	1.245900	0.05131	N	0.492596	T	0.04452	0.0122	N	0.01267	-0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39583	-0.9607	10	0.12766	T	0.61	0.5888	6.7275	0.23365	0.076:0.4694:0.335:0.1196	.	1122;1127	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	G	1127;1127;1127;1048;1122	ENSP00000364839:D1127G;ENSP00000305119:D1122G	ENSP00000305119:D1122G	D	+	2	0	ASXL1	30487556	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.322000	0.19576	0.071000	0.16664	-1.251000	0.01509	GAT		0.532	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31023895	A	G	31023895	3	3	105	1	0	0	0	0	1	0	0	0	1067	333	12	4	3436	4	ASXL1	20	31023895	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	12630599	31023895	32001625	202	27842										
CDH22	64405	hgsc.bcm.edu	37	chr20	44869782	44869782	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tttctgctcgcggtccaggcGctccatggcatgaatgtcgc	12	13	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:44869782G>T	ENST00000372262.3	-	2	770	c.370C>A	c.(370-372)Cgc>Agc	p.R124S	CDH22_ENST00000537909.1_Missense_Mutation_p.R124S	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	124	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CGGTCCAGGCGCTCCATGGCA	0.617																																																0			20											79	67	71					20																	44869782		2203	4300	6503	44303189	SO:0001583	missense	64405			AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.370C>A	20.37:g.44869782G>T	ENSP00000361336:p.Arg124Ser		44303189	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.065581	0.55539	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.52057	0.68;0.68	4.21	4.21	0.49690	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.49338	0.1551	N	0.12887	0.27	0.48632	D	0.999687	D	0.89917	1.0	D	0.87578	0.998	T	0.48281	-0.9049	10	0.24483	T	0.36	.	16.127	0.81402	0.0:0.0:1.0:0.0	.	124	Q9UJ99	CAD22_HUMAN	S	124	ENSP00000361336:R124S;ENSP00000437790:R124S	ENSP00000361336:R124S	R	-	1	0	CDH22	44303189	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.917000	0.48821	2.364000	0.80123	0.455000	0.32223	CGC		0.617	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		T	44869782	G	T	44869782	3	4	105	1	0	0	0	0	1	0	0	0	3113	1087	38	2	2156	2	CDH22	20	44869782	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	13845887	44869782	18155738	203	27843										
EYA2	2139	hgsc.bcm.edu	37	chr20	45725728	45725728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctctctttcatcacagcgtgTgttcgtgtgggacttggatg	12	9	3	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:45725728T>C	ENST00000327619.5	+	9	1183	c.809T>C	c.(808-810)gTg>gCg	p.V270A	EYA2_ENST00000357410.3_Missense_Mutation_p.V270A|EYA2_ENST00000317304.6_Missense_Mutation_p.V270A	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	270					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				TCACAGCGTGTGTTCGTGTGG	0.423																																					Pancreas(120;56 1725 18501 25218 43520)											0			20											244	221	229					20																	45725728		2203	4300	6503	45159135	SO:0001583	missense	2139				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.809T>C	20.37:g.45725728T>C	ENSP00000333640:p.Val270Ala		45159135	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Missense_Mutation	SNP	ENST00000327619.5	37	CCDS13403.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.346896	0.41599	.	.	ENSG00000064655	ENST00000327619;ENST00000357410;ENST00000484200;ENST00000317304;ENST00000458636	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	5.67	5.67	0.87782	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.000000	0.85682	D	0.000000	D	0.92014	0.7470	M	0.76727	2.345	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.994;0.999;0.999	D	0.92920	0.6354	10	0.87932	D	0	-1.2596	15.9204	0.79562	0.0:0.0:0.0:1.0	.	270;270;270;270	O00167-3;E7ETN2;A8KAG7;O00167	.;.;.;EYA2_HUMAN	A	270;270;270;270;141	ENSP00000333640:V270A;ENSP00000349986:V270A;ENSP00000321590:V270A;ENSP00000395427:V141A	ENSP00000321590:V270A	V	+	2	0	EYA2	45159135	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.244000	0.78228	2.164000	0.68074	0.533000	0.62120	GTG		0.423	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244		C	45725728	T	C	45725728	3	2	105	1	0	0	0	0	1	0	0	0	5342	1696	59	4	839	4	EYA2	20	45725728	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	855946	45725728	17299792	204	27844										
B4GALT5	9334	hgsc.bcm.edu	37	chr20	48263529	48263529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agggagtctttcagggcaggTatggtttgcaaagtaggtga	16	4	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:48263529T>C	ENST00000371711.4	-	3	524	c.337A>G	c.(337-339)Acc>Gcc	p.T113A		NM_004776.3	NP_004767.1	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5	113					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			TCAGGGCAGGTATGGTTTGCA	0.453																																																0			20											203	186	192					20																	48263529		2203	4300	6503	47696936	SO:0001583	missense	9334			AB004550	CCDS13420.1	20q13.1-q13.2	2013-02-19			ENSG00000158470	ENSG00000158470		"Beta 4-glycosyltransferases"	928	protein-coding gene	gene with protein product	"beta4-GalT IV"	604016				9597550, 9435216	Standard	NM_004776		Approved	beta4GalT-V	uc002xuu.4	O43286	OTTHUMG00000033086	ENST00000371711.4:c.337A>G	20.37:g.48263529T>C	ENSP00000360776:p.Thr113Ala		47696936	E1P625|Q2M394|Q9UJQ8	Missense_Mutation	SNP	ENST00000371711.4	37	CCDS13420.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.498439	0.26861	.	.	ENSG00000158470	ENST00000371711	T	0.34072	1.38	5.45	4.36	0.52297	.	0.152267	0.64402	D	0.000012	T	0.21145	0.0509	N	0.25647	0.755	0.26405	N	0.976358	B	0.02656	0.0	B	0.04013	0.001	T	0.22382	-1.0218	10	0.11794	T	0.64	-11.0264	7.5831	0.27976	0.1268:0.0:0.1716:0.7015	.	113	O43286	B4GT5_HUMAN	A	113	ENSP00000360776:T113A	ENSP00000360776:T113A	T	-	1	0	B4GALT5	47696936	0.838000	0.29461	0.993000	0.49108	0.988000	0.76386	1.029000	0.30140	1.055000	0.40461	0.528000	0.53228	ACC		0.453	B4GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080543.3	NM_004776		C	48263529	T	C	48263529	3	2	105	1	0	0	0	0	1	0	0	0	1275	1638	57	4	857	4	B4GALT5	20	48263529	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	2537801	48263529	14761991	205	27845										
C20orf43	51507	hgsc.bcm.edu	37	chr20	55088412	55088412	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gatgatgtcatcatgctcaaTggcaccaaggaggatgtgga	13	7	3	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr20:55088412T>C	ENST00000023939.4	+	6	626	c.519T>C	c.(517-519)aaT>aaC	p.N173N	GCNT7_ENST00000243913.4_Intron|RTFDC1_ENST00000357348.5_Silent_p.N203N|RTFDC1_ENST00000395881.3_Silent_p.N173N	NM_001283035.1|NM_001283036.1|NM_016407.3	NP_001269964.1|NP_001269965.1|NP_057491.2	Q9BY42	RTF2_HUMAN	replication termination factor 2 domain containing 1	173																	TCATGCTCAATGGCACCAAGG	0.557																																																0			20											146	88	108					20																	55088412		2203	4300	6503	54521819	SO:0001819	synonymous_variant	51507			AF161513	CCDS13453.1, CCDS63316.1, CCDS63317.1	20q13	2012-10-29	2012-10-29	2012-10-29	ENSG00000022277	ENSG00000022277			15890	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 43"	C20orf43			Standard	NM_001283035		Approved	HSPC164, CDAO5	uc002xxt.2	Q9BY42	OTTHUMG00000032801	ENST00000023939.4:c.519T>C	20.37:g.55088412T>C			54521819	E1P5Z9|Q9BYL7|Q9HCV9|Q9NX29|Q9NZZ8|Q9P002|Q9UHW3	Silent	SNP	ENST00000023939.4	37	CCDS13453.1																																																																																				0.557	RTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079817.2	NM_016407		C	55088412	T	C	55088412	2	2	105	1	0	0	0	0	0	0	0	1	2118	1461	51	4		4	C20orf43	20	55088412	Silent	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	6824883	55088412	7937108	206	27846										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28214928	28214928	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgccgtggaattctgccatCgactggtctgccacaagcat	10	13	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr21:28214928C>T	ENST00000284984.3	-	2	1261	c.807G>A	c.(805-807)tcG>tcA	p.S269S		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	269	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		ATTCTGCCATCGACTGGTCTG	0.448																																																0			21											75	69	71					21																	28214928		2203	4300	6503	27136799	SO:0001819	synonymous_variant	9510			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.807G>A	21.37:g.28214928C>T			27136799	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	C	9.483	1.098708	0.20552	.	.	ENSG00000154734	ENST00000451462	.	.	.	5.38	-10.8	0.00216	.	.	.	.	.	T	0.41903	0.1179	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49790	-0.8902	4	.	.	.	.	5.4493	0.16554	0.1931:0.355:0.3644:0.0875	.	.	.	.	Q	51	.	.	R	-	2	0	ADAMTS1	27136799	0.016000	0.18221	0.473000	0.27253	0.995000	0.86356	-0.917000	0.04025	-2.238000	0.00712	-0.345000	0.07892	CGA		0.448	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28214928	C	T	28214928	2	4	105	1	0	0	0	0	0	0	0	1	255	871	31	1		1	ADAMTS1	21	28214928	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10		28214928	19914967	207	27847										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43547822	43547822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	acaccaacgtgattgagaacGgcaactccaataaggcccag	9	12	0	2	rs201879010		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr21:43547822G>A	ENST00000408910.2	+	20	3571	c.3571G>A	c.(3571-3573)Ggc>Agc	p.G1191S	UMODL1_ENST00000408989.2_Missense_Mutation_p.G1319S|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Missense_Mutation_p.G1119S|UMODL1_ENST00000400427.1_Missense_Mutation_p.G1247S	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1191	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GATTGAGAACGGCAACTCCAA	0.527													G|||	1	0.000199681	0	0	5008	,	,		19907	0.001		0	False		,,,				2504	0				Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)											0			21											103	101	101					21																	43547822		2025	4199	6224	42420891	SO:0001583	missense	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3571G>A	21.37:g.43547822G>A	ENSP00000386147:p.Gly1191Ser		42420891	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.59	2.877423	0.51801	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	3.67	3.67	0.42095	Zona pellucida sperm-binding protein (3);	0.000000	0.44902	D	0.000404	D	0.88757	0.6523	M	0.79475	2.455	0.49130	D	0.999755	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89256	0.3594	9	.	.	.	-34.8229	14.8451	0.70254	0.0:0.0:1.0:0.0	.	1319;1191	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	S	1247;1119;1319;1191;76	ENSP00000383279:G1247S;ENSP00000383276:G1119S;ENSP00000386126:G1319S;ENSP00000386147:G1191S	.	G	+	1	0	UMODL1	42420891	1.000000	0.71417	0.961000	0.40146	0.124000	0.20399	5.473000	0.66774	2.350000	0.79820	0.561000	0.74099	GGC		0.527	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43547822	G	A	43547822	3	1	105	1	0	0	0	0	1	0	0	0	17020	1116	39	1	4029	1	UMODL1	21	43547822	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	15332894	43547822	4582073	208	27848										
PCNT	5116	hgsc.bcm.edu	37	chr21	47817955	47817955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cagccgagcgggagcacgagCgcgaggagttccagcaggag	18	11	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr21:47817955C>T	ENST00000359568.5	+	23	4581	c.4474C>T	c.(4474-4476)Cgc>Tgc	p.R1492C	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1492					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGAGCACGAGCGCGAGGAGTT	0.706																																																0			21											18	18	18					21																	47817955		2188	4293	6481	46642383	SO:0001583	missense	5116			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4474C>T	21.37:g.47817955C>T	ENSP00000352572:p.Arg1492Cys		46642383	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098812	0.56183	.	.	ENSG00000160299	ENST00000359568	T	0.74315	-0.83	4.96	4.96	0.65561	.	0.000000	0.33005	N	0.005383	D	0.85544	0.5721	M	0.83953	2.67	0.46185	D	0.998918	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.86913	0.2062	10	0.87932	D	0	.	10.7392	0.46143	0.1895:0.8104:0.0:0.0	.	1374;1492	O95613-2;O95613	.;PCNT_HUMAN	C	1492	ENSP00000352572:R1492C	ENSP00000352572:R1492C	R	+	1	0	PCNT	46642383	1.000000	0.71417	0.914000	0.36105	0.205000	0.24178	1.539000	0.36104	2.564000	0.86499	0.561000	0.74099	CGC		0.706	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47817955	C	T	47817955	3	4	105	1	0	0	0	0	1	0	0	0	11621	768	27	1	4564	1	PCNT	21	47817955	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	4270133	47817955	311940	209	27849										
GGT1	2678	hgsc.bcm.edu	37	chr22	25023869	25023869	+	Frame_Shift_Del	DEL	A	A	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cgggatcctgttcaataatgAaatggacgacttcagctctc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr22:25023869delA	ENST00000400382.1	+	13	2014	c.1259delA	c.(1258-1260)gaafs	p.E420fs	GGT1_ENST00000404223.1_Frame_Shift_Del_p.E76fs|GGT1_ENST00000403838.1_Frame_Shift_Del_p.E76fs|GGT1_ENST00000406383.2_Frame_Shift_Del_p.E420fs|GGT1_ENST00000400380.1_Frame_Shift_Del_p.E420fs|GGT1_ENST00000404920.1_Frame_Shift_Del_p.E76fs|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Frame_Shift_Del_p.E420fs|GGT1_ENST00000248923.4_Frame_Shift_Del_p.E420fs|GGT1_ENST00000401885.1_Frame_Shift_Del_p.E76fs|GGT1_ENST00000404532.1_Frame_Shift_Del_p.E76fs			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	420					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TTCAATAATGAAATGGACGAC	0.612																																																0			22											67	74	72					22																	25023869		2203	4300	6503	23353869	SO:0001589	frameshift_variant	2678			M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"CD molecules", "Gamma-glutamyltransferases"	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1259delA	22.37:g.25023869delA	ENSP00000383232:p.Glu420fs		23353869	Q08247|Q14404|Q8TBS1|Q9UMK1	Frame_Shift_Del	DEL	ENST00000400382.1	37	CCDS42992.1																																																																																				0.612	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		-	25023869	A	-	25023869	7	5	105	1	0	1	0	1	0	0	0	0	6381	246	9	0	1293	0	GGT1	22	25023869	Frame_Shift_Del	DEL	A	TCGA-DY-A1DD-01A-21D-A152-10		25023869	26280697	210	27850										
YWHAH	7533	hgsc.bcm.edu	37	chr22	32352209	32352209	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	aatgtggttggtgccaggcgAtcttcctggagggtcattag	15	7	2	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr22:32352209A>G	ENST00000248975.5	+	2	444	c.171A>G	c.(169-171)cgA>cgG	p.R57R	YWHAH_ENST00000471374.1_3'UTR|snoU13_ENST00000459049.1_RNA|YWHAH_ENST00000397492.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	57		Interaction with phosphoserine on interacting protein.			apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						GTGCCAGGCGATCTTCCTGGA	0.458																																					Ovarian(98;460 2060 9263 44007)											0			22											96	88	90					22																	32352209		2203	4300	6503	30682209	SO:0001819	synonymous_variant	7533			X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.171A>G	22.37:g.32352209A>G			30682209		Silent	SNP	ENST00000248975.5	37	CCDS13901.1																																																																																				0.458	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		G	32352209	A	G	32352209	2	3	105	1	0	0	0	0	0	0	0	1	17544	320	12	4		4	YWHAH	22	32352209	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	7328340	32352209	18952357	211	27851										
EP300	2033	hgsc.bcm.edu	37	chr22	41523526	41523526	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccgcaggtccagcagccaggCctggtgactccagttgccca	12	16	0	1	rs20553	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr22:41523526C>T	ENST00000263253.7	+	4	2161	c.942C>T	c.(940-942)ggC>ggT	p.G314G		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	314					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGCAGCCAGGCCTGGTGACTC	0.483			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome				C|||	109	0.0217652	0.0794	0.0058	5008	,	,		19349	0		0	False		,,,				2504	0						Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22						C		265,4141	148.4+/-182.8	11,243,1949	73	78	77		942	3.8	1	22	dbSNP_67	77	1,8599		0,1,4299	no	coding-synonymous	EP300	NM_001429.3		11,244,6248	TT,TC,CC		0.0116,6.0145,2.0452		314/2415	41523526	266,12740	2203	4300	6503	39853472	SO:0001819	synonymous_variant	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.942C>T	22.37:g.41523526C>T			39853472	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																				0.483	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41523526	C	T	41523526	2	4	105	1	0	0	0	0	0	0	0	1	5161	726	26	3		3	EP300	22	41523526	Silent	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	9171317	41523526	9781040	212	27852										
BRD1	23774	hgsc.bcm.edu	37	chr22	50169244	50169244	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggcctctcaactcaccaactTctcttattatcaaaaaagag	4	12	4	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chr22:50169244T>A	ENST00000216267.8	-	11	3474	c.2988A>T	c.(2986-2988)agA>agT	p.R996S	BRD1_ENST00000404760.1_Missense_Mutation_p.R1127S|BRD1_ENST00000457780.2_3'UTR|BRD1_ENST00000342989.5_Missense_Mutation_p.R722S|BRD1_ENST00000404034.1_Missense_Mutation_p.R996S|BRD1_ENST00000542442.1_Missense_Mutation_p.R684S	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	996	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		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)		CTCACCAACTTCTCTTATTAT	0.577																																																0			22											103	120	114					22																	50169244		2203	4300	6503	48555248	SO:0001583	missense	23774			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"BR140-like"	604589	"bromodomain-containing 1"			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2988A>T	22.37:g.50169244T>A	ENSP00000216267:p.Arg996Ser		48555248	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.574718	0.65878	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	4.84	-9.36	0.00629	PWWP (3);	0.000000	0.85682	D	0.000000	T	0.44623	0.1302	M	0.80982	2.52	0.80722	D	1	D;D;D;D	0.76494	0.993;0.998;0.999;0.992	D;D;D;P	0.80764	0.909;0.909;0.994;0.853	T	0.72459	-0.4287	10	0.40728	T	0.16	.	17.6335	0.88115	0.0:0.6377:0.0:0.3623	.	1127;722;996;1127	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	S	996;996;1127;684;722;587	ENSP00000216267:R996S;ENSP00000384076:R996S;ENSP00000385858:R1127S;ENSP00000437514:R684S;ENSP00000345886:R722S	ENSP00000216267:R996S	R	-	3	2	BRD1	48555248	0.882000	0.30256	0.659000	0.29680	0.963000	0.63663	-0.111000	0.10807	-2.028000	0.00931	0.482000	0.46254	AGA		0.577	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50169244	T	A	50169244	3	1	105	1	0	0	0	0	1	0	0	0	1504	1780	62	5	196	5	BRD1	22	50169244	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	8645718	50169244	1135322	213	27853										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3229192	3229192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	cctgaaccgccaagtaagtcTtgttccggatggtggcgggc	14	11	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:3229192T>C	ENST00000217939.6	-	7	7206	c.7052A>G	c.(7051-7053)aAg>aGg	p.K2351R		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2351	Ig-like C2-type 8.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CAAGTAAGTCTTGTTCCGGAT	0.562																																																0			X											152	124	133					X																	3229192		2203	4300	6503	3239192	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.7052A>G	X.37:g.3229192T>C	ENSP00000217939:p.Lys2351Arg		3239192	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.070727	0.36566	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64085	-0.08	4.29	4.29	0.51040	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.39687	U	0.001284	T	0.53706	0.1813	L	0.31157	0.91	0.44221	D	0.997057	B	0.31625	0.332	B	0.38954	0.286	T	0.51100	-0.8748	10	0.29301	T	0.29	.	12.9595	0.58449	0.0:0.0:0.0:1.0	.	2351	Q9NR99	MXRA5_HUMAN	R	2351	ENSP00000217939:K2351R	ENSP00000217939:K2351R	K	-	2	0	MXRA5	3239192	1.000000	0.71417	0.852000	0.33557	0.258000	0.26162	3.758000	0.55220	1.425000	0.47237	0.483000	0.47432	AAG		0.562	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3229192	T	C	3229192	3	2	105	1	0	0	0	0	1	0	0	0	10033	1609	56	4	1438	4	MXRA5	23	3229192	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10		3229192	152041368	214	27854										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctgactcagtggttcttccaCctcgctctcctgactcaggg					rs1058237|rs144469326	byFrequency	TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs		8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				0.642	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138168	CCTC	-	8138165	7	5	105	1	0	1	0	1	0	0	0	0	17183	507	18	0	95	0	VCX2	23	8138165	Frame_Shift_Del	DEL	CCTC	TCGA-DY-A1DD-01A-21D-A152-10	4908973	8138165	147132395	215	27855										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18664127	18664127	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tgtttctccccactaactagAcggtggatgtgatggcagaa	11	9	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:18664127A>G	ENST00000379989.3	+	20	2999	c.2714A>G	c.(2713-2715)gAc>gGc	p.D905G	CDKL5_ENST00000379996.3_Splice_Site_p.D905G|RS1_ENST00000379984.3_Intron|RS1_ENST00000476595.1_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					cactaactagacggtggatgt	0.488																																																0			X											140	112	122					X																	18664127		2203	4300	6503	18574048	SO:0001630	splice_region_variant	6792			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2714-1A>G	X.37:g.18664127A>G			18574048	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752565	0.15778	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.68624	-0.34;-0.34	1.89	0.648	0.17801	.	0.326495	0.27577	N	0.018744	T	0.28167	0.0695	N	0.01168	-0.975	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.21008	-1.0258	9	.	.	.	.	4.4178	0.11465	0.6504:0.3496:0.0:0.0	.	905	O76039	CDKL5_HUMAN	G	905	ENSP00000369332:D905G;ENSP00000369325:D905G	.	D	+	2	0	CDKL5	18574048	0.389000	0.25205	0.165000	0.22776	0.063000	0.16089	0.479000	0.22228	0.105000	0.17753	0.340000	0.21749	GAC		0.488	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Missense_Mutation	G	18664127	A	G	18664127	5	3	105	1	0	0	0	0	0	0	1	0	3163	289	10	4	2784	4	CDKL5	23	18664127	Splice_Site	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	10525962	18664127	136606433	216	27856										
MAOB	4129	hgsc.bcm.edu	37	chrX	43628574	43628574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctctcgggctgctctctcccCggcctctacagccccctcca	7	22	3	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:43628574C>T	ENST00000378069.4	-	13	1474	c.1327G>A	c.(1327-1329)Ggg>Agg	p.G443R	MAOB_ENST00000536181.1_Missense_Mutation_p.G427R|MAOB_ENST00000538942.1_Missense_Mutation_p.R394Q	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	443					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	GCTCTCTCCCCGGCCTCTACA	0.567																																																0			X											74	55	62					X																	43628574		2203	4300	6503	43513518	SO:0001583	missense	4129				CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.1327G>A	X.37:g.43628574C>T	ENSP00000367309:p.Gly443Arg		43513518	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	37	CCDS14261.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.602297|4.602297	0.87055|0.87055	.|.	.|.	ENSG00000069535|ENSG00000069535	ENST00000378069;ENST00000536181|ENST00000538942	D;D|T	0.98585|0.35605	-5.01;-5.01|1.3	6.03|6.03	6.03|6.03	0.97812|0.97812	Amine oxidase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56659|0.56659	0.2000|0.2000	H|H	0.96833|0.96833	3.89|3.89	0.42021|0.42021	D|D	0.990988|0.990988	D|B	0.89917|0.29212	1.0|0.237	D|B	0.97110|0.24848	1.0|0.056	T|T	0.64875|0.64875	-0.6304|-0.6304	10|8	0.87932|.	D|.	0|.	-23.4429|-23.4429	18.0899|18.0899	0.89471|0.89471	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	443|394	P27338|B7Z5H3	AOFB_HUMAN|.	R|Q	443;427|394	ENSP00000367309:G443R;ENSP00000441613:G427R|ENSP00000442240:R394Q	ENSP00000367309:G443R|.	G|R	-|-	1|2	0|0	MAOB|MAOB	43513518|43513518	1.000000|1.000000	0.71417|0.71417	0.928000|0.928000	0.36995|0.36995	0.894000|0.894000	0.52154|0.52154	7.008000|7.008000	0.76341|0.76341	2.549000|2.549000	0.85964|0.85964	0.583000|0.583000	0.79449|0.79449	GGG|CGG		0.567	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43628574	C	T	43628574	3	4	105	1	0	0	0	0	1	0	0	0	9256	652	23	1	247	1	MAOB	23	43628574	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	24964447	43628574	111641986	217	27857										
SLC9A7	84679	hgsc.bcm.edu	37	chrX	46521556	46521556	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcagcagcatcaaaggcgtgAgtgttcagtcccgctggctg	14	11	2	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:46521556A>G	ENST00000328306.4	-	7	961	c.936T>C	c.(934-936)acT>acC	p.T312T		NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	312					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						CAAAGGCGTGAGTGTTCAGTC	0.418																																					Pancreas(118;454 1696 1930 13865 39976)											0			X											59	49	52					X																	46521556		2203	4300	6503	46406500	SO:0001819	synonymous_variant	84679			AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"Solute carriers"	17123	protein-coding gene	gene with protein product		300368	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 7", "solute carrier family 9 (sodium/hydrogen exchanger), member 7"			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.936T>C	X.37:g.46521556A>G			46406500	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	37	CCDS14269.1																																																																																				0.418	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		G	46521556	A	G	46521556	2	3	105	1	0	0	0	0	0	0	0	1	14756	291	11	4		4	SLC9A7	23	46521556	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	2892982	46521556	108749004	218	27858										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50053621	50053621	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agaaggaagctgtcctcaagGagcccactattgacacagaa	10	10	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:50053621G>C	ENST00000376042.1	+	6	2750	c.2452G>C	c.(2452-2454)Gag>Cag	p.E818Q	CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.E818Q|CCNB3_ENST00000376038.1_Intron			Q8WWL7	CCNB3_HUMAN	cyclin B3	818					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TGTCCTCAAGGAGCCCACTAT	0.557																																																0			X											40	36	37					X																	50053621		2203	4300	6503	50070361	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2452G>C	X.37:g.50053621G>C	ENSP00000365210:p.Glu818Gln		50070361	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	G	9.183	1.024109	0.19433	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.34859	1.34;1.34	2.43	1.51	0.23008	.	2.524280	0.01497	N	0.017349	T	0.35799	0.0944	L	0.27053	0.805	0.09310	N	1	D	0.59357	0.985	P	0.50270	0.636	T	0.20371	-1.0277	9	.	.	.	.	6.2881	0.21045	0.0:0.309:0.691:0.0	.	818	Q8WWL7	CCNB3_HUMAN	Q	818	ENSP00000365210:E818Q;ENSP00000276014:E818Q	.	E	+	1	0	CCNB3	50070361	0.049000	0.20398	0.002000	0.10522	0.275000	0.26752	0.155000	0.16362	0.431000	0.26258	0.483000	0.47432	GAG		0.557	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			C	50053621	G	C	50053621	3	2	105	1	0	0	0	0	1	0	0	0	2920	1175	41	5	2466	5	CCNB3	23	50053621	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	3532065	50053621	105216939	219	27859										
FGD1	2245	hgsc.bcm.edu	37	chrX	54496631	54496632	+	Frame_Shift_Ins	INS	-	-	G													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ccagggcagaggctgtggctINSggggggcccgtcatcactga							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:54496631_54496632insG	ENST00000375135.3	-	4	1651_1652	c.918_919insC	c.(916-921)cccagcfs	p.S307fs		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	307	Pro-rich.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AGGCTGTGGCTGGGGGGCCCGT	0.658																																																0			X																																								54513357	SO:0001589	frameshift_variant	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.919dupC	X.37:g.54496637_54496637dupG	ENSP00000364277:p.Ser307fs		54513356	Q5H999|Q8N4D9	Frame_Shift_Ins	INS	ENST00000375135.3	37	CCDS14359.1																																																																																				0.658	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		G	54496632	-	G	54496631	7	5	105	1	0	1	1	0	0	0	0	0	5851	1580	55	0	2026	0	FGD1	23	54496631	Frame_Shift_Ins	INS	-	TCGA-DY-A1DD-01A-21D-A152-10	4443010	54496631	100773929	220	27860										
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56590491	56590491	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gcagtttaaggaagcgatttCgaaacgcttcaaatcccaaa	8	9	1	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:56590491C>T	ENST00000338222.5	+	1	466	c.185C>T	c.(184-186)tCg>tTg	p.S62L		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	62	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						GAAGCGATTTCGAAACGCTTC	0.463																																					Esophageal Squamous(104;218 1492 6022 10838 28884)											0			X											21	20	20					X																	56590491		2203	4298	6501	56607216	SO:0001583	missense	29978			AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"Ubiquilin family"	12509	protein-coding gene	gene with protein product	"NEDD4 binding protein 4"	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.185C>T	X.37:g.56590491C>T	ENSP00000345195:p.Ser62Leu		56607216	O94798|Q5D027|Q9H3W6|Q9HAZ4	Missense_Mutation	SNP	ENST00000338222.5	37	CCDS14374.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967507	0.74131	.	.	ENSG00000188021	ENST00000338222;ENST00000535171	T	0.73575	-0.76	4.64	4.64	0.57946	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.64402	D	0.000004	D	0.82527	0.5056	L	0.55481	1.735	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.83422	0.0033	10	0.54805	T	0.06	-6.4625	14.1984	0.65686	0.0:1.0:0.0:0.0	.	62;62	B4DZF1;Q9UHD9	.;UBQL2_HUMAN	L	62	ENSP00000345195:S62L	ENSP00000345195:S62L	S	+	2	0	UBQLN2	56607216	1.000000	0.71417	0.840000	0.33206	0.987000	0.75469	7.604000	0.82830	2.317000	0.78254	0.544000	0.68410	TCG		0.463	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		T	56590491	C	T	56590491	3	4	105	1	0	0	0	0	1	0	0	0	16937	893	31	1	187	1	UBQLN2	23	56590491	Missense_Mutation	SNP	C	TCGA-DY-A1DD-01A-21D-A152-10	2093860	56590491	98680069	221	27861										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412871	63412871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ggccatgggctgcttcactcAggccatcgtgggtcttgctc	13	13	3	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:63412871A>G	ENST00000330258.3	-	2	568	c.296T>C	c.(295-297)cTg>cCg	p.L99P	AMER1_ENST00000403336.1_Missense_Mutation_p.L99P|AMER1_ENST00000374869.3_Missense_Mutation_p.L99P	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	99					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TGCTTCACTCAGGCCATCGTG	0.537																																																67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	X											115	84	94					X																	63412871		2203	4300	6503	63329596	SO:0001583	missense	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.296T>C	X.37:g.63412871A>G	ENSP00000329117:p.Leu99Pro		63329596	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154119	0.57259	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.35789	1.29;1.29;1.29	4.59	3.42	0.39159	.	0.191518	0.34750	N	0.003720	T	0.37652	0.1011	M	0.71036	2.16	0.54753	D	0.99998	B	0.25390	0.125	B	0.29598	0.104	T	0.32079	-0.9920	10	0.87932	D	0	-0.8303	8.6403	0.33972	0.9054:0.0:0.0946:0.0	.	99	Q5JTC6	F123B_HUMAN	P	99	ENSP00000364003:L99P;ENSP00000329117:L99P;ENSP00000384722:L99P	ENSP00000329117:L99P	L	-	2	0	FAM123B	63329596	1.000000	0.71417	0.743000	0.31040	0.940000	0.58332	6.859000	0.75467	0.868000	0.35678	0.486000	0.48141	CTG		0.537	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63412871	A	G	63412871	3	3	105	1	0	0	0	0	1	0	0	0	5439	188	7	4	3115	4	FAM123B	23	63412871	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	6822380	63412871	91857689	222	27862										
NHSL2	340526	hgsc.bcm.edu	37	chrX	71351947	71351947	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	agctgcagctaactcgggtcGggaaaatgcgacagcgactg	14	10	0	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:71351947G>A	ENST00000545866.1	-	0	0				NHSL2_ENST00000535692.1_5'Flank|RGAG4_ENST00000609883.1_5'Flank|NHSL2_ENST00000373677.1_5'Flank|NHSL2_ENST00000540800.1_Missense_Mutation_p.R100Q|NHSL2_ENST00000510661.1_5'Flank	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4											cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					AACTCGGGTCGGGAAAATGCG	0.672																																																0			X											47	45	46					X																	71351947		692	1591	2283	71268672	SO:0001631	upstream_gene_variant	340527			AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808		X.37:g.71351947G>A	Exception_encountered		71268672	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	g	19.46	3.830839	0.71258	.	.	ENSG00000204131	ENST00000540800	T	0.29397	1.57	5.38	2.32	0.28847	.	.	.	.	.	T	0.12603	0.0306	N	0.08118	0	0.80722	D	1	B	0.15473	0.013	B	0.08055	0.003	T	0.10405	-1.0631	9	0.24483	T	0.36	.	4.1963	0.10445	0.168:0.0:0.5915:0.2406	.	100	F5H593	.	Q	100	ENSP00000444617:R100Q	ENSP00000444617:R100Q	R	+	2	0	NHSL2	71268672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.369000	0.34227	0.470000	0.27294	0.472000	0.43445	CGG		0.672	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		A	71351947	G	A	71351947	1	1	105	0	1	0	0	0	0	0	0	0	10443	1116	39	1		1	NHSL2	23	71351947	5'Flank	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	7939076	71351947	83918613	223	27863										
IRS4	8471	hgsc.bcm.edu	37	chrX	107976663	107976663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gatctgagaggtcgtttgctGgatttggaaatggcactcca	13	7	1	1			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:107976663G>A	ENST00000372129.2	-	1	2988	c.2912C>T	c.(2911-2913)cCa>cTa	p.P971L	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	971					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.P971L(2)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GTCGTTTGCTGGATTTGGAAA	0.483																																																2	Substitution - Missense(2)	ovary(1)|lung(1)	X											152	139	143					X																	107976663		2203	4300	6503	107863319	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2912C>T	X.37:g.107976663G>A	ENSP00000361202:p.Pro971Leu		107863319		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.473876	0.26423	.	.	ENSG00000133124	ENST00000372129	T	0.35973	1.28	5.16	4.27	0.50696	.	0.367155	0.25683	N	0.028995	T	0.24586	0.0596	L	0.29908	0.895	0.09310	N	0.999999	B	0.28128	0.201	B	0.22386	0.039	T	0.14448	-1.0472	10	0.42905	T	0.14	-1.6166	9.2734	0.37686	0.0791:0.0:0.7755:0.1454	.	971	O14654	IRS4_HUMAN	L	971	ENSP00000361202:P971L	ENSP00000361202:P971L	P	-	2	0	IRS4	107863319	0.008000	0.16893	0.006000	0.13384	0.194000	0.23727	0.472000	0.22116	1.084000	0.41184	0.600000	0.82982	CCA		0.483	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107976663	G	A	107976663	3	1	105	1	0	0	0	0	1	0	0	0	7863	1348	47	3	865	3	IRS4	23	107976663	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	36624716	107976663	47293897	224	27864										
ZCCHC12	170261	hgsc.bcm.edu	37	chrX	117959861	117959861	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ttaatcagaatggtaagggaGgaagaggattgggatgatgc	16	2	1	3	rs374504390		TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:117959861G>A	ENST00000310164.2	+	4	1161	c.654G>A	c.(652-654)gaG>gaA	p.E218E		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	218					BMP signaling pathway (GO:0030509)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	22						TGGTAAGGGAGGAAGAGGATT	0.493																																																0			X						G		0,3835		0,0,0,1632,571	55	51	52		654	2.4	1	X		52	2,6726		0,1,1,2427,1871	no	coding-synonymous	ZCCHC12	NM_173798.2		0,1,1,4059,2442	AA,AG,A,GG,G		0.0297,0.0,0.0189		218/403	117959861	2,10561	2203	4300	6503	117843889	SO:0001819	synonymous_variant	170261			AK122676	CCDS14574.1	Xq24	2013-10-11			ENSG00000174460	ENSG00000174460		"Zinc fingers, CCHC domain containing", "Paraneoplastic Ma antigens"	27273	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 7A"	300701				21739307, 19578717	Standard	NM_173798		Approved	FLJ16123, SIZN, SIZN1, PNMA7A	uc004equ.3	Q6PEW1	OTTHUMG00000022261	ENST00000310164.2:c.654G>A	X.37:g.117959861G>A			117843889	B3KV48|Q6PID5|Q8N1C1	Silent	SNP	ENST00000310164.2	37	CCDS14574.1																																																																																				0.493	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058014.1	NM_173798		A	117959861	G	A	117959861	2	1	105	1	0	0	0	0	0	0	0	1	17620	991	35	3		3	ZCCHC12	23	117959861	Silent	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	9983198	117959861	37310699	225	27865										
STAG2	10735	hgsc.bcm.edu	37	chrX	123200091	123200091	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcttgaaaactggaatcgaAaatggagacatgcctgagca	10	8	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:123200091A>G	ENST00000371160.1	+	22	2453	c.2163A>G	c.(2161-2163)gaA>gaG	p.E721E	STAG2_ENST00000371145.3_Silent_p.E721E|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Silent_p.E652E|STAG2_ENST00000218089.9_Silent_p.E721E|STAG2_ENST00000371144.3_Silent_p.E721E|STAG2_ENST00000371157.3_Silent_p.E721E	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	721					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CTGGAATCGAAAATGGAGACA	0.279																																																0			X											95	101	99					X																	123200091		2202	4298	6500	123027772	SO:0001819	synonymous_variant	10735			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2163A>G	X.37:g.123200091A>G			123027772	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	37	CCDS14607.1																																																																																				0.279	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123200091	A	G	123200091	2	3	105	1	0	0	0	0	0	0	0	1	15282	11	1	4		4	STAG2	23	123200091	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	5240230	123200091	32070469	226	27866										
ZNF449	203523	hgsc.bcm.edu	37	chrX	134493889	134493889	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gccatgggtgaaggaattacAggattctaaagaaatgaaac	11	5	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:134493889A>G	ENST00000339249.4	+	4	772	c.632A>G	c.(631-633)cAg>cGg	p.Q211R		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	211					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					AAGGAATTACAGGATTCTAAA	0.328																																																0			X											100	97	98					X																	134493889		2203	4299	6502	134321555	SO:0001583	missense	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.632A>G	X.37:g.134493889A>G	ENSP00000339585:p.Gln211Arg		134321555	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	37	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096944	0.37048	.	.	ENSG00000173275	ENST00000339249	T	0.05925	3.37	4.85	4.85	0.62838	.	0.161421	0.29572	N	0.011763	T	0.04770	0.0129	N	0.24115	0.695	0.80722	D	1	B	0.26635	0.155	B	0.25759	0.063	T	0.45556	-0.9253	10	0.14252	T	0.57	.	11.5598	0.50769	1.0:0.0:0.0:0.0	.	211	Q6P9G9	ZN449_HUMAN	R	211	ENSP00000339585:Q211R	ENSP00000339585:Q211R	Q	+	2	0	ZNF449	134321555	0.020000	0.18652	0.963000	0.40424	0.973000	0.67179	1.028000	0.30128	1.932000	0.55993	0.425000	0.28330	CAG		0.328	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		G	134493889	A	G	134493889	3	3	105	1	0	0	0	0	1	0	0	0	17959	188	7	4	642	4	ZNF449	23	134493889	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	11293798	134493889	20776671	227	27867										
SPANXN3	139067	hgsc.bcm.edu	37	chrX	142596797	142596797	+	Missense_Mutation	SNP	T	T	A													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tcatttgaagatccttcagaTaagtctacgccttcgtcctc							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:142596797T>A	ENST00000370503.2	-	2	356	c.273A>T	c.(271-273)ttA>ttT	p.L91F	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	91										endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					ATCCTTCAGATAAGTCTACGC	0.443																																																0			X											216	178	191					X																	142596797		2203	4300	6503	142424463	SO:0001583	missense	139067				CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 8"	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.273A>T	X.37:g.142596797T>A	ENSP00000359534:p.Leu91Phe		142424463	Q0ZNK4	Missense_Mutation	SNP	ENST00000370503.2	37	CCDS35418.1	.	.	.	.	.	.	.	.	.	.	t	5.648	0.304206	0.10678	.	.	ENSG00000189252	ENST00000370503	T	0.07021	3.23	0.73	-1.46	0.08800	.	.	.	.	.	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	P	0.37176	0.586	B	0.38378	0.272	T	0.26326	-1.0106	8	0.44086	T	0.13	.	.	.	.	.	91	Q5MJ09	SPXN3_HUMAN	F	91	ENSP00000359534:L91F	ENSP00000359534:L91F	L	-	3	2	SPANXN3	142424463	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.853000	0.01666	-1.895000	0.01104	0.227000	0.17789	TTA		0.443	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609		A	142596797	T	A	142596797	3	1	105	1	0	0	0	0	1	0	0	0	15031	1403	49	5	156	5	SPANXN3	23	142596797	Missense_Mutation	SNP	T	TCGA-DY-A1DD-01A-21D-A152-10	8102908	142596797	12673763	228	27868	48	2								
SPANXN3	139067	hgsc.bcm.edu	37	chrX	142596799	142596799	+	Missense_Mutation	SNP	A	A	T													0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	atttgaagatccttcagataAgtctacgccttcgtcctcct							TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:142596799A>T	ENST00000370503.2	-	2	354	c.271T>A	c.(271-273)Tta>Ata	p.L91I	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	91								p.L91I(1)		endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					CCTTCAGATAAGTCTACGCCT	0.438																																																1	Substitution - Missense(1)	ovary(1)	X											218	180	193					X																	142596799		2203	4300	6503	142424465	SO:0001583	missense	139067				CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 8"	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.271T>A	X.37:g.142596799A>T	ENSP00000359534:p.Leu91Ile		142424465	Q0ZNK4	Missense_Mutation	SNP	ENST00000370503.2	37	CCDS35418.1	.	.	.	.	.	.	.	.	.	.	a	0.016	-1.512278	0.00984	.	.	ENSG00000189252	ENST00000370503	T	0.05925	3.37	0.73	-1.46	0.08800	.	.	.	.	.	T	0.01353	0.0044	N	0.00926	-1.1	0.09310	N	1	B	0.32396	0.369	B	0.30251	0.113	T	0.27191	-1.0081	8	0.08179	T	0.78	.	.	.	.	.	91	Q5MJ09	SPXN3_HUMAN	I	91	ENSP00000359534:L91I	ENSP00000359534:L91I	L	-	1	2	SPANXN3	142424465	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.189000	0.03061	-2.164000	0.00782	-0.853000	0.03031	TTA		0.438	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609		T	142596799	A	T	142596799	3	4	105	1	0	0	0	0	1	0	0	0	15031	69	3	5	158	5	SPANXN3	23	142596799	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	2	142596799	12673761	229	27869	48	2								
PASD1	139135	hgsc.bcm.edu	37	chrX	150842517	150842517	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	tttcccataacttcagactcAaccataagcaccctggagac	5	14	2	2			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:150842517A>G	ENST00000370357.4	+	15	2279	c.2034A>G	c.(2032-2034)tcA>tcG	p.S678S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	678						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.S678S(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CTTCAGACTCAACCATAAGCA	0.498																																																1	Substitution - coding silent(1)	ovary(1)	X											128	115	119					X																	150842517		2203	4300	6503	150593173	SO:0001819	synonymous_variant	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2034A>G	X.37:g.150842517A>G			150593173	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																				0.498	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		G	150842517	A	G	150842517	2	3	105	1	0	0	0	0	0	0	0	1	11502	117	5	4		4	PASD1	23	150842517	Silent	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	8245718	150842517	4428043	230	27870										
SLC10A3	8273	hgsc.bcm.edu	37	chrX	153716358	153716358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	ctcatggatgctgagcaggcGgctgtagatggccgaagaca	15	9	1	3			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:153716358G>A	ENST00000393587.4	-	3	1185	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C	SLC10A3_ENST00000369649.4_Missense_Mutation_p.R279C|UBL4A_ENST00000369653.4_5'Flank|SLC10A3_ENST00000263512.4_Missense_Mutation_p.R308C|UBL4A_ENST00000477777.1_5'Flank|SLC10A3_ENST00000393586.1_Missense_Mutation_p.R363C|UBL4A_ENST00000369660.4_5'Flank	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	308					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGAGCAGGCGGCTGTAGATG	0.597																																																0			X											63	63	63					X																	153716358		2202	4300	6502	153369552	SO:0001583	missense	8273			X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"Solute carriers"	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.922C>T	X.37:g.153716358G>A	ENSP00000377212:p.Arg308Cys		153369552	Q5HY79|Q9BSL2	Missense_Mutation	SNP	ENST00000393587.4	37	CCDS14755.1	.	.	.	.	.	.	.	.	.	.	G	9.434	1.086212	0.20390	.	.	ENSG00000126903	ENST00000369649;ENST00000393586;ENST00000263512;ENST00000393587	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.09	3.29	0.37713	.	0.233463	0.36101	U	0.002782	T	0.34571	0.0902	M	0.89287	3.02	0.32258	N	0.570573	D;D	0.69078	0.997;0.988	P;P	0.59761	0.863;0.863	T	0.50457	-0.8826	10	0.59425	D	0.04	-13.2509	8.0014	0.30299	0.2772:0.0:0.7228:0.0	.	279;308	Q9BSL2;P09131	.;P3_HUMAN	C	279;363;308;308	ENSP00000358663:R279C;ENSP00000377211:R363C;ENSP00000263512:R308C;ENSP00000377212:R308C	ENSP00000263512:R308C	R	-	1	0	SLC10A3	153369552	0.407000	0.25352	0.493000	0.27502	0.145000	0.21501	1.312000	0.33574	0.360000	0.24265	0.600000	0.82982	CGC		0.597	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3	NM_019848		A	153716358	G	A	153716358	3	1	105	1	0	0	0	0	1	0	0	0	14412	1116	39	1	515	1	SLC10A3	23	153716358	Missense_Mutation	SNP	G	TCGA-DY-A1DD-01A-21D-A152-10	2873841	153716358	1554202	231	27871										
G6PD	2539	hgsc.bcm.edu	37	chrX	153760262	153760262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	7	1	0.514400825758332	0	0.543299748553744	0.00521739130434783	0.0785829307568439	0	gtaggtgccctcatactggaAacccactctcttcatcagct	7	14	4	0			TCGA-DY-A1DD-01A-21D-A152-10	TCGA-DY-A1DD-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f55580c3-a0a4-49b5-af2e-ceebd2d81a18	7bf87d5b-d789-4e0e-8f98-ef00836053a3	g.chrX:153760262A>G	ENST00000393564.2	-	13	1613	c.1501T>C	c.(1501-1503)Ttc>Ctc	p.F501L	G6PD_ENST00000369620.2_Missense_Mutation_p.F547L|G6PD_ENST00000393562.2_Missense_Mutation_p.F531L	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	501					carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCATACTGGAAACCCACTCTC	0.672																																																0			X											64	41	48					X																	153760262		2203	4299	6502	153413456	SO:0001583	missense	8266			X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.1501T>C	X.37:g.153760262A>G	ENSP00000377194:p.Phe501Leu		153413456	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	37	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.450346	0.84101	.	.	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620	D;D;D	0.98178	-4.77;-4.77;-4.77	5.33	5.33	0.75918	Glucose-6-phosphate dehydrogenase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98620	0.9538	M	0.76433	2.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.976	D	0.99387	1.0924	10	0.62326	D	0.03	.	12.1233	0.53903	1.0:0.0:0.0:0.0	.	501;531	P11413;P11413-3	G6PD_HUMAN;.	L	531;501;501;547	ENSP00000377192:F531L;ENSP00000377194:F501L;ENSP00000358633:F547L	ENSP00000291567:F501L	F	-	1	0	G6PD	153413456	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	8.253000	0.89842	1.766000	0.52107	0.483000	0.47432	TTC		0.672	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402		G	153760262	A	G	153760262	3	3	105	1	0	0	0	0	1	0	0	0	6165	14	1	4	50	4	G6PD	23	153760262	Missense_Mutation	SNP	A	TCGA-DY-A1DD-01A-21D-A152-10	43904	153760262	1510298	232	27872										
C1orf187	374946	hgsc.bcm.edu	37	chr1	11766487	11766487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cgcctcaggccagccaccacCgccggcggggcccgggcaag	15	19	1	0	rs533314493		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:11766487C>T	ENST00000294485.5	+	2	307	c.172C>T	c.(172-174)Cgc>Tgc	p.R58C		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		CAGCCACCACCGCCGGCGGGG	0.731													C|||	1	0.000199681	0	0	5008	,	,		13661	0		0	False		,,,				2504	0.001															0			1											11	14	13					1																	11766487		2178	4269	6447	11689074	SO:0001583	missense	374946			AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"dorsal repulsive axon guidance protein", "neural tissue-specific cysteine-rich protein"	612682	"chromosome 1 open reading frame 187"	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.172C>T	1.37:g.11766487C>T	ENSP00000294485:p.Arg58Cys		11689074		Missense_Mutation	SNP	ENST00000294485.5	37	CCDS135.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348810	0.41599	.	.	ENSG00000162490	ENST00000294485	T	0.49720	0.77	4.75	2.73	0.32206	.	0.685000	0.13322	N	0.396596	T	0.52224	0.1721	M	0.62723	1.935	0.38910	D	0.957501	D	0.60160	0.987	P	0.50896	0.653	T	0.56992	-0.7887	10	0.72032	D	0.01	-14.9831	8.7219	0.34445	0.1651:0.6635:0.1714:0.0	.	58	Q8NBI3	DRAXI_HUMAN	C	58	ENSP00000294485:R58C	ENSP00000294485:R58C	R	+	1	0	C1orf187	11689074	0.419000	0.25449	0.999000	0.59377	0.080000	0.17528	1.006000	0.29847	0.942000	0.37525	0.313000	0.20887	CGC		0.731	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545		T	11766487	C	T	11766487	3	4	106	1	0	0	0	0	1	0	0	0	2027	652	23	1	174	1	C1orf187	1	11766487	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		11766487	237484134	1	27873										
CELA3B	23436	hgsc.bcm.edu	37	chr1	22313136	22313136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cacccgcaggaagcccacggTgttcactcgagtctccgcct	10	17	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:22313136T>C	ENST00000337107.6	+	7	774	c.755T>C	c.(754-756)gTg>gCg	p.V252A	RN7SL386P_ENST00000485776.2_RNA|CELA3B_ENST00000473526.1_3'UTR|RNU6-1022P_ENST00000365049.1_RNA	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	252	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						AAGCCCACGGTGTTCACTCGA	0.617																																																0			1											64	56	59					1																	22313136		2203	4300	6503	22185723	SO:0001583	missense	23436			M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"proteinase E", "elastase 1", "cholesterol-binding pancreatic protease", "pancreatic endopeptidase E"		"elastase 3B, pancreatic"	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.755T>C	1.37:g.22313136T>C	ENSP00000338369:p.Val252Ala		22185723	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	37	CCDS219.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.908528	0.52333	.	.	ENSG00000219073	ENST00000337107;ENST00000400277	D;D	0.91407	-2.84;-2.84	4.05	4.05	0.47172	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000001	D	0.94761	0.8309	M	0.82716	2.605	0.51482	D	0.999928	D	0.76494	0.999	D	0.76575	0.988	D	0.95057	0.8192	10	0.87932	D	0	-23.3612	11.3087	0.49351	0.0:0.0:0.0:1.0	.	252	P08861	CEL3B_HUMAN	A	252;155	ENSP00000338369:V252A;ENSP00000383135:V155A	ENSP00000338369:V252A	V	+	2	0	CELA3B	22185723	1.000000	0.71417	0.986000	0.45419	0.090000	0.18270	7.579000	0.82511	1.838000	0.53458	0.409000	0.27619	GTG		0.617	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		C	22313136	T	C	22313136	3	2	106	1	0	0	0	0	1	0	0	0	3220	1696	59	4	781	4	CELA3B	1	22313136	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	10546649	22313136	226937485	2	27874										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27088787	27088788	+	Frame_Shift_Ins	INS	-	-	G													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atggggagctatggtccccaINSggggggtcagtatggcccac							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:27088787_27088788insG	ENST00000324856.7	+	7	2767_2768	c.2396_2397insG	c.(2395-2400)caggggfs	p.QG799fs	RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.QG416fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.QG799fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	799					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		TATGGTCCCCAGGGGGGTCAGT	0.554			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1																																								26961375	SO:0001589	frameshift_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2402dupG	1.37:g.27088793_27088793dupG	ENSP00000320485:p.Gln799fs		26961374	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	37	CCDS285.1																																																																																				0.554	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27088788	-	G	27088787	7	5	106	1	0	1	1	0	0	0	0	0	913	188	7	0	2422	0	ARID1A	1	27088787	Frame_Shift_Ins	INS	-	TCGA-DY-A1DF-01A-11D-A152-10	4775651	27088787	222161834	3	27875										
WASF2	10163	hgsc.bcm.edu	37	chr1	27744828	27744828	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acaggtattgtatgtttctaAgacaggcactgggagagagt	13	5	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:27744828A>G	ENST00000430629.2	-	4	576	c.361T>C	c.(361-363)Tta>Cta	p.L121L	WASF2_ENST00000536657.1_Silent_p.L121L	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	121					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		TATGTTTCTAAGACAGGCACT	0.453																																																0			1											119	120	120					1																	27744828		2203	4297	6500	27617415	SO:0001819	synonymous_variant	10163			AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.361T>C	1.37:g.27744828A>G			27617415	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	37	CCDS304.1																																																																																				0.453	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27744828	A	G	27744828	2	3	106	1	0	0	0	0	0	0	0	1	17293	69	3	4		4	WASF2	1	27744828	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	656041	27744828	221505793	4	27876										
PTPRF	5792	hgsc.bcm.edu	37	chr1	44070989	44070989	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agcagcgcagggggcctgcaGcacctggtgtccatccgcac	14	15	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:44070989G>A	ENST00000359947.4	+	18	3604	c.3264G>A	c.(3262-3264)caG>caA	p.Q1088Q	PTPRF_ENST00000438120.1_Silent_p.Q1079Q|PTPRF_ENST00000372413.3_Silent_p.Q1079Q|PTPRF_ENST00000422171.2_Silent_p.Q436Q|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372414.3_Silent_p.Q1088Q	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1088	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGCCTGCAGCACCTGGTGT	0.642																																																0			1											57	60	59					1																	44070989		2203	4300	6503	43843576	SO:0001819	synonymous_variant	5792			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3264G>A	1.37:g.44070989G>A			43843576	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.975|8.975	0.973913|0.973913	0.18736|0.18736	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.31|5.31	4.4|4.4	0.53042|0.53042	.|.	.|.	.|.	.|.	.|.	T|T	0.70020|0.70020	0.3176|0.3176	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.69495|0.69495	-0.5130|-0.5130	4|4	.|.	.|.	.|.	.|.	14.3391|14.3391	0.66614|0.66614	0.0718:0.0:0.9282:0.0|0.0718:0.0:0.9282:0.0	.|.	.|.	.|.	.|.	T|N	461;502|734	.|.	.|.	A|S	+|+	1|2	0|0	PTPRF|PTPRF	43843576|43843576	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.884000|0.884000	0.51177|0.51177	6.788000|6.788000	0.75105|0.75105	1.402000|1.402000	0.46780|0.46780	0.591000|0.591000	0.81541|0.81541	GCA|AGC		0.642	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			A	44070989	G	A	44070989	2	1	106	1	0	0	0	0	0	0	0	1	12838	962	34	3		3	PTPRF	1	44070989	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	16326161	44070989	205179632	5	27877										
MKNK1	8569	hgsc.bcm.edu	37	chr1	47030721	47030721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aagcatacgtactggggtggTcagctctggtgtggttatgg	16	6	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:47030721T>C	ENST00000371946.4	-	10	923	c.760A>G	c.(760-762)Acc>Gcc	p.T254A	MKNK1_ENST00000428112.2_Missense_Mutation_p.T213A|MKNK1_ENST00000371945.4_Missense_Mutation_p.T213A|MKNK1_ENST00000341183.5_Missense_Mutation_p.T213A|MKNK1-AS1_ENST00000602433.1_RNA|MKNK1_ENST00000371944.4_Missense_Mutation_p.T118A	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T254S(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					ACTGGGGTGGTCAGCTCTGGT	0.493																																																1	Substitution - Missense(1)	lung(1)	1											230	210	216					1																	47030721		2203	4300	6503	46803308	SO:0001583	missense	8569			AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.760A>G	1.37:g.47030721T>C	ENSP00000361014:p.Thr254Ala		46803308	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	37	CCDS538.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.18|12.18	1.859920|1.859920	0.32884|0.32884	.|.	.|.	ENSG00000079277|ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112|ENST00000524749	T;T;T;T;T|.	0.66995|.	-0.24;-0.24;-0.24;-0.24;-0.24|.	5.8|5.8	4.61|4.61	0.57282|0.57282	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.40546|.	0.1121|.	N|N	0.13003|0.13003	0.285|0.285	0.80722|0.80722	D|D	1|1	B;B;B;B;B;P|.	0.42161|.	0.004;0.025;0.009;0.008;0.336;0.772|.	B;B;B;B;B;P|.	0.52343|.	0.017;0.03;0.017;0.01;0.431;0.696|.	T|.	0.24621|.	-1.0155|.	10|.	0.10902|.	T|.	0.67|.	-17.4372|-17.4372	11.9732|11.9732	0.53075|0.53075	0.0:0.0:0.1446:0.8554|0.0:0.0:0.1446:0.8554	.|.	118;118;213;213;213;254|.	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5|.	.;.;.;.;.;MKNK1_HUMAN|.	A|W	254;213;118;213;213|5	ENSP00000361014:T254A;ENSP00000361013:T213A;ENSP00000361012:T118A;ENSP00000339573:T213A;ENSP00000411135:T213A|.	ENSP00000339573:T213A|.	T|X	-|-	1|3	0|0	MKNK1|MKNK1	46803308|46803308	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.716000|0.716000	0.41182|0.41182	4.091000|4.091000	0.57700|0.57700	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	ACC|TGA		0.493	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684		C	47030721	T	C	47030721	3	2	106	1	0	0	0	0	1	0	0	0	9634	1667	58	4	657	4	MKNK1	1	47030721	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	2959732	47030721	202219900	6	27878										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52704525	52704525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttatctatctaatggttgtgAttcctatggaatgcaagacc	8	7	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:52704525A>G	ENST00000371591.1	+	3	1567	c.1436A>G	c.(1435-1437)gAt>gGt	p.D479G	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.D479G|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.D479G	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	479					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						AATGGTTGTGATTCCTATGGA	0.368																																																0			1											94	100	98					1																	52704525		2203	4299	6502	52477113	SO:0001583	missense	9372			AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1436A>G	1.37:g.52704525A>G	ENSP00000360647:p.Asp479Gly		52477113	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.095149	0.56075	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.70516	-0.06;-0.49;0.22;0.22	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000012	T	0.76183	0.3952	L	0.27053	0.805	0.45690	D	0.998601	D;D;D	0.71674	0.998;0.997;0.989	D;D;P	0.81914	0.995;0.989;0.783	T	0.79009	-0.1978	10	0.62326	D	0.03	.	15.9487	0.79813	1.0:0.0:0.0:0.0	.	479;479;479	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	G	479	ENSP00000349737:D479G;ENSP00000355358:D479G;ENSP00000287727:D479G;ENSP00000360647:D479G	ENSP00000287727:D479G	D	+	2	0	ZFYVE9	52477113	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.527000	0.67123	2.173000	0.68751	0.533000	0.62120	GAT		0.368	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		G	52704525	A	G	52704525	3	3	106	1	0	0	0	0	1	0	0	0	17710	333	12	4	1442	4	ZFYVE9	1	52704525	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	5673804	52704525	196546096	7	27879										
ORC1L	4998	hgsc.bcm.edu	37	chr1	52850337	52850337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cctgctgcaggcagcgtatcActtcatgaacagtggcagtc	11	12	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:52850337A>G	ENST00000371568.3	-	11	1858	c.1640T>C	c.(1639-1641)gTg>gCg	p.V547A	ORC1_ENST00000371566.1_Missense_Mutation_p.V547A	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	547	Necessary and sufficient for ORC complex assembly.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCAGCGTATCACTTCATGAAC	0.547																																																0			1											97	77	84					1																	52850337		2203	4300	6503	52622925	SO:0001583	missense	10166				CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1640T>C	1.37:g.52850337A>G	ENSP00000360623:p.Val547Ala		52622925	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.258348	0.80246	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	D;D	0.95035	-3.59;-3.59	5.81	5.81	0.92471	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.053822	0.85682	D	0.000000	D	0.97052	0.9037	M	0.79475	2.455	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.73380	0.98;0.98	D	0.97634	1.0144	10	0.87932	D	0	-19.4153	16.158	0.81680	1.0:0.0:0.0:0.0	.	542;547	B7Z8H0;Q13415	.;ORC1_HUMAN	A	547	ENSP00000360623:V547A;ENSP00000360621:V547A	ENSP00000360621:V547A	V	-	2	0	ORC1	52622925	1.000000	0.71417	0.990000	0.47175	0.550000	0.35303	8.523000	0.90576	2.206000	0.71126	0.533000	0.62120	GTG		0.547	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		G	52850337	A	G	52850337	3	3	106	1	0	0	0	0	1	0	0	0	11292	159	6	4	973	4	ORC1L	1	52850337	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	145812	52850337	196400284	8	27880										
PRKAA2	5563	hgsc.bcm.edu	37	chr1	57173294	57173294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcactggctctttgaccggaAgcacattgtcttcagtttca	8	11	5	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:57173294A>G	ENST00000371244.4	+	9	1633	c.1567A>G	c.(1567-1569)Agc>Ggc	p.S523G		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	523			S -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.S523G(2)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TTTGACCGGAAGCACATTGTC	0.473																																																2	Substitution - Missense(2)	breast(2)	1											176	158	164					1																	57173294		2203	4300	6503	56945882	SO:0001583	missense	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.1567A>G	1.37:g.57173294A>G	ENSP00000360290:p.Ser523Gly		56945882	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.861126	0.51482	.	.	ENSG00000162409	ENST00000371244	T	0.72835	-0.69	5.46	5.46	0.80206	.	0.105227	0.64402	D	0.000009	T	0.66458	0.2791	L	0.50333	1.59	0.80722	D	1	B	0.09022	0.002	B	0.12837	0.008	T	0.62253	-0.6893	10	0.39692	T	0.17	-12.4265	15.7119	0.77635	1.0:0.0:0.0:0.0	.	523	P54646	AAPK2_HUMAN	G	523	ENSP00000360290:S523G	ENSP00000360290:S523G	S	+	1	0	PRKAA2	56945882	1.000000	0.71417	0.972000	0.41901	0.636000	0.38137	8.761000	0.91691	2.291000	0.77112	0.533000	0.62120	AGC		0.473	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		G	57173294	A	G	57173294	3	3	106	1	0	0	0	0	1	0	0	0	12528	72	3	4	1601	4	PRKAA2	1	57173294	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	4322957	57173294	192077327	9	27881										
GTF2B	2959	hgsc.bcm.edu	37	chr1	89325690	89325690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcttgaataaattatttgttCgatccttcaaagcagagaaa	7	6	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:89325690C>T	ENST00000370500.5	-	5	528	c.410G>A	c.(409-411)cGa>cAa	p.R137Q	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	137					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		ATTATTTGTTCGATCCTTCAA	0.338																																																0			1											133	135	134					1																	89325690		2203	4300	6503	89098278	SO:0001583	missense	2959			M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.410G>A	1.37:g.89325690C>T	ENSP00000359531:p.Arg137Gln		89098278	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	37	CCDS715.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003996	0.74932	.	.	ENSG00000137947	ENST00000370500;ENST00000448623;ENST00000418217	T;T;T	0.47869	0.86;0.83;0.86	5.49	4.59	0.56863	Transcription factor TFIIB, cyclin-related (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.22126	0.0533	L	0.56769	1.78	0.80722	D	1	P	0.48350	0.909	B	0.33295	0.161	T	0.09465	-1.0673	10	0.15499	T	0.54	15.9647	14.5673	0.68185	0.0:0.9295:0.0:0.0705	.	137	Q00403	TF2B_HUMAN	Q	137;136;132	ENSP00000359531:R137Q;ENSP00000415741:R136Q;ENSP00000402345:R132Q	ENSP00000359531:R137Q	R	-	2	0	GTF2B	89098278	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.442000	0.80503	1.442000	0.47568	0.591000	0.81541	CGA		0.338	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		T	89325690	C	T	89325690	3	4	106	1	0	0	0	0	1	0	0	0	6876	884	31	1	552	1	GTF2B	1	89325690	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	32152396	89325690	159924931	10	27882										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103388942	103388942	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttcaccaggtgggcctggcaGaccctaagaaaatataatag	10	9	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:103388942G>T	ENST00000370096.3	-	47	3916	c.3604C>A	c.(3604-3606)Ctg>Atg	p.L1202M	COL11A1_ENST00000512756.1_Missense_Mutation_p.L1086M|COL11A1_ENST00000358392.2_Missense_Mutation_p.L1214M|COL11A1_ENST00000353414.4_Missense_Mutation_p.L1163M	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1202	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		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)		GGGCCTGGCAGACCCTAAGAA	0.328																																																0			1											40	38	39					1																	103388942		2202	4300	6502	103161530	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3604C>A	1.37:g.103388942G>T	ENSP00000359114:p.Leu1202Met		103161530	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845859	0.32606	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53	5.15	3.26	0.37387	.	0.000000	0.64402	D	0.000006	D	0.92378	0.7581	L	0.35644	1.08	0.54753	D	0.999982	D;D;D;D;D	0.76494	0.995;0.998;0.999;0.998;0.997	D;D;D;D;D	0.85130	0.979;0.997;0.997;0.994;0.986	D	0.90207	0.4261	10	0.32370	T	0.25	.	9.3932	0.38386	0.2395:0.0:0.7605:0.0	.	1086;1163;1214;1202;422	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	M	1202;1214;1163;422;1086	ENSP00000359114:L1202M;ENSP00000351163:L1214M;ENSP00000302551:L1163M;ENSP00000426533:L1086M	ENSP00000302551:L1163M	L	-	1	2	COL11A1	103161530	0.980000	0.34600	0.998000	0.56505	0.916000	0.54674	1.508000	0.35769	0.546000	0.28920	0.460000	0.39030	CTG		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103388942	G	T	103388942	3	4	106	1	0	0	0	0	1	0	0	0	3673	933	33	2	1900	2	COL11A1	1	103388942	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	14063252	103388942	145861679	11	27883										
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110527681	110527681	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gggccggccggggaatgtcgAtgcctgacgcgatgccgctg	18	12	0	1	rs538673946		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:110527681A>C	ENST00000369799.5	+	1	374	c.7A>C	c.(7-9)Atg>Ctg	p.M3L	AHCYL1_ENST00000475081.1_3'UTR	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	3					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		gGGAATGTCGATGCCTGACGC	0.736													A|||	1	0.000199681	0	0.0014	5008	,	,		9838	0		0	False		,,,				2504	0															0			1											13	13	13					1																	110527681		2160	4272	6432	110329204	SO:0001583	missense	10768			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.7A>C	1.37:g.110527681A>C	ENSP00000358814:p.Met3Leu		110329204	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	A	8.873	0.949654	0.18431	.	.	ENSG00000168710	ENST00000369799	T	0.74632	-0.86	4.96	2.25	0.28309	.	0.440186	0.23217	N	0.050605	T	0.26593	0.0650	N	0.03608	-0.345	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.07366	-1.0776	10	0.23891	T	0.37	-12.6886	6.2953	0.21083	0.7049:0.0:0.2951:0.0	.	3	O43865	SAHH2_HUMAN	L	3	ENSP00000358814:M3L	ENSP00000358814:M3L	M	+	1	0	AHCYL1	110329204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.301000	0.33447	0.722000	0.32252	0.533000	0.62120	ATG		0.736	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			C	110527681	A	C	110527681	3	2	106	1	0	0	0	0	1	0	0	0	410	333	12	4	9	4	AHCYL1	1	110527681	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	7138739	110527681	138722940	12	27884										
RPTN	126638	hgsc.bcm.edu	37	chr1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cttgtctctcaggctgactgTggtgggaatctctgtcttgt					rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152129101	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	152129066	7	5	106	1	0	1	0	1	0	0	0	0	13701	1696	59	0	1849	0	RPTN	1	152129066	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TCGA-DY-A1DF-01A-11D-A152-10	41601385	152129066	97121555	13	27885										
TNR	7143	hgsc.bcm.edu	37	chr1	175355223	175355223	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttggtccctcggacggcactGactgacacctcgtatcggga	12	13	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:175355223G>A	ENST00000367674.2	-	8	2430	c.1722C>T	c.(1720-1722)gtC>gtT	p.V574V	TNR_ENST00000263525.2_Silent_p.V574V			Q92752	TENR_HUMAN	tenascin R	574	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GGACGGCACTGACTGACACCT	0.642																																																0			1											85	78	80					1																	175355223		2203	4300	6503	173621846	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1722C>T	1.37:g.175355223G>A			173621846	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.642	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175355223	G	A	175355223	2	1	106	1	0	0	0	0	0	0	0	1	16377	1277	45	3		3	TNR	1	175355223	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	23226157	175355223	73895398	14	27886										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564383	176564383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgtgagtgaggagcagattcGtctgcagcacgaggcactga	15	8	1	4	rs555801320		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:176564383G>A	ENST00000367662.3	+	3	2807	c.1643G>A	c.(1642-1644)cGt>cAt	p.R548H	PAPPA2_ENST00000367661.3_Missense_Mutation_p.R548H	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	548	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GAGCAGATTCGTCTGCAGCAC	0.572													G|||	1	0.000199681	0	0	5008	,	,		20994	0.001		0	False		,,,				2504	0															0			1											66	68	67					1																	176564383		2147	4247	6394	174831006	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1643G>A	1.37:g.176564383G>A	ENSP00000356634:p.Arg548His		174831006	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	5.186	0.219816	0.09863	.	.	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.42131	0.98;0.98	5.11	-4.39	0.03611	.	2.209890	0.01334	N	0.011321	T	0.25531	0.0621	L	0.38531	1.155	0.09310	N	1	B;D	0.53619	0.015;0.961	B;B	0.35240	0.007;0.198	T	0.41106	-0.9527	10	0.41790	T	0.15	1.5103	4.4333	0.11538	0.3447:0.1306:0.441:0.0837	.	548;548	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	H	548	ENSP00000356634:R548H;ENSP00000356633:R548H	ENSP00000356633:R548H	R	+	2	0	PAPPA2	174831006	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.552000	0.06020	-0.714000	0.04975	-0.259000	0.10710	CGT		0.572	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176564383	G	A	176564383	3	1	106	1	0	0	0	0	1	0	0	0	11464	1145	40	1	1649	1	PAPPA2	1	176564383	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	1209160	176564383	72686238	15	27887										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181764027	181764027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cagaccctagctccatgagaCgttcattttccactattcgg	7	13	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:181764027C>T	ENST00000367573.2	+	46	6055	c.6055C>T	c.(6055-6057)Cgt>Tgt	p.R2019C	CACNA1E_ENST00000360108.3_Missense_Mutation_p.R2000C|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1957C|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1908C|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R1976C|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1583C|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R1970C	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2019					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTCCATGAGACGTTCATTTTC	0.468																																																0			1											78	74	75					1																	181764027		1910	4137	6047	180030650	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6055C>T	1.37:g.181764027C>T	ENSP00000356545:p.Arg2019Cys		180030650	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	33	5.211492	0.95069	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.99259	-5.22;-5.2;-5.64;-5.19;-5.37;-5.63;-5.64	5.91	5.91	0.95273	.	0.411995	0.25848	N	0.027919	D	0.99177	0.9715	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.99920	1.1248	10	0.87932	D	0	.	19.8936	0.96942	0.0:1.0:0.0:0.0	.	1957;1976	Q15878-2;Q15878-3	.;.	C	1976;1957;1970;1908;1583;2000;2019	ENSP00000356542:R1976C;ENSP00000434814:R1957C;ENSP00000350183:R1970C;ENSP00000351101:R1908C;ENSP00000356539:R1583C;ENSP00000353222:R2000C;ENSP00000356545:R2019C	ENSP00000350183:R1970C	R	+	1	0	CACNA1E	180030650	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.145000	0.64839	2.793000	0.96121	0.655000	0.94253	CGT		0.468	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181764027	C	T	181764027	3	4	106	1	0	0	0	0	1	0	0	0	2548	536	19	1	6104	1	CACNA1E	1	181764027	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5199644	181764027	67486594	16	27888										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185984511	185984511	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tctgattcagcaacatatacGtgtcatgtagccaatgttgc	8	9	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:185984511G>A	ENST00000271588.4	+	31	5080	c.4851G>A	c.(4849-4851)acG>acA	p.T1617T	HMCN1_ENST00000367492.2_Silent_p.T1617T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1617	Ig-like C2-type 13.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CAACATATACGTGTCATGTAG	0.398																																																0			1											102	101	102					1																	185984511		2203	4299	6502	184251134	SO:0001819	synonymous_variant	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4851G>A	1.37:g.185984511G>A			184251134	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185984511	G	A	185984511	2	1	106	1	0	0	0	0	0	0	0	1	7241	1132	40	1		1	HMCN1	1	185984511	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	4220484	185984511	63266110	17	27889										
CFHR3	10878	hgsc.bcm.edu	37	chr1	196757505	196757505	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tacatgtttgcaaaatggatGgtcagcacaaccaatttgca	8	8	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:196757505G>C	ENST00000367425.4	+	4	682	c.590G>C	c.(589-591)tGg>tCg	p.W197S	CFHR3_ENST00000391985.3_Intron|CFHR3_ENST00000471440.2_Missense_Mutation_p.W197S	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	197	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						CAAAATGGATGGTCAGCACAA	0.303																																																0			1											70	89	83					1																	196757505		1980	4164	6144	195024128	SO:0001583	missense	10878			X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"Complement system"	16980	protein-coding gene	gene with protein product	"complement factor H related 3"	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.590G>C	1.37:g.196757505G>C	ENSP00000356395:p.Trp197Ser		195024128	B4DPR0|Q9UJ16	Missense_Mutation	SNP	ENST00000367425.4	37	CCDS30958.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.376062	0.42105	.	.	ENSG00000116785	ENST00000367425;ENST00000471440	D;D	0.88431	-2.38;-2.38	2.94	2.94	0.34122	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.95698	0.8601	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95471	0.8551	9	0.87932	D	0	.	9.7198	0.40295	0.0:0.0:1.0:0.0	.	197;197	Q02985;Q6NSD3	FHR3_HUMAN;.	S	197	ENSP00000356395:W197S;ENSP00000436258:W197S	ENSP00000356395:W197S	W	+	2	0	CFHR3	195024128	1.000000	0.71417	0.835000	0.33067	0.057000	0.15508	3.582000	0.53921	1.386000	0.46466	0.392000	0.25879	TGG		0.303	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023		C	196757505	G	C	196757505	3	2	106	1	0	0	0	0	1	0	0	0	3292	1357	47	5	604	5	CFHR3	1	196757505	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	10772994	196757505	52493116	18	27890										
CAPN2	824	hgsc.bcm.edu	37	chr1	223940648	223940648	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tccaccgcgggaggttgcagGaactacccgagtaagggctg	15	11	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:223940648G>T	ENST00000295006.5	+	9	1434	c.1125G>T	c.(1123-1125)agG>agT	p.R375S	CAPN2_ENST00000433674.2_Missense_Mutation_p.R297S	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	375	Domain III.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		GAGGTTGCAGGAACTACCCGA	0.582																																																0			1											84	94	90					1																	223940648		2203	4300	6503	222007271	SO:0001583	missense	824			J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1125G>T	1.37:g.223940648G>T	ENSP00000295006:p.Arg375Ser		222007271	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.042287	0.75732	.	.	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	D;D	0.88664	-2.41;-2.41	5.3	4.38	0.52667	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.000000	0.85682	D	0.000000	D	0.93756	0.8004	M	0.83953	2.67	0.80722	D	1	P;D	0.67145	0.748;0.996	P;D	0.78314	0.786;0.991	D	0.93592	0.6922	10	0.62326	D	0.03	.	11.1248	0.48310	0.1423:0.0:0.8577:0.0	.	297;375	B7ZA96;P17655	.;CAN2_HUMAN	S	297;375;404	ENSP00000413158:R297S;ENSP00000295006:R375S	ENSP00000295006:R375S	R	+	3	2	CAPN2	222007271	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	0.752000	0.26362	2.640000	0.89533	0.561000	0.74099	AGG		0.582	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		T	223940648	G	T	223940648	3	4	106	1	0	0	0	0	1	0	0	0	2633	1165	41	2	1166	2	CAPN2	1	223940648	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	27183143	223940648	25309973	19	27891										
ZNF124	7678	hgsc.bcm.edu	37	chr1	247320093	247320093	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgagttttctcgtgtttctgAagggaactggcgtatctgaa	12	6	3	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr1:247320093A>G	ENST00000543802.2	-	4	920	c.831T>C	c.(829-831)ctT>ctC	p.L277L	ZNF124_ENST00000491356.1_Intron|ZNF124_ENST00000472531.1_Intron|ZNF124_ENST00000491848.1_5'Flank|ZNF124_ENST00000340684.6_Silent_p.L215L			Q15973	ZN124_HUMAN	zinc finger protein 124	277					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			CGTGTTTCTGAAGGGAACTGG	0.438																																																0			1											145	135	139					1																	247320093		2203	4300	6503	245386716	SO:0001819	synonymous_variant	7678			S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418		"Zinc fingers, C2H2-type", "-"	12907	protein-coding gene	gene with protein product		194631	"zinc finger protein 124 (HZF-16)"			7916577	Standard	XM_005273256		Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000543802.2:c.831T>C	1.37:g.247320093A>G			245386716	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	Silent	SNP	ENST00000543802.2	37																																																																																					0.438	ZNF124-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000447393.1	NM_003431		G	247320093	A	G	247320093	2	3	106	1	0	0	0	0	0	0	0	1	17759	233	9	4		4	ZNF124	1	247320093	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	23379445	247320093	1930528	20	27892										
PNO1	56902	hgsc.bcm.edu	37	chr2	68385614	68385614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctcctattgtggaacatttgGgacttcagatacgctttaac	8	9	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:68385614G>A	ENST00000263657.2	+	2	401	c.310G>A	c.(310-312)Gga>Aga	p.G104R	RP11-474G23.1_ENST00000406334.3_Intron|WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000295121.6_5'Flank|WDR92_ENST00000406245.2_5'Flank|WDR92_ENST00000492039.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	104						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						GGAACATTTGGGACTTCAGAT	0.383																																					NSCLC(83;642 1410 13044 32832 40058)											0			2											104	104	104					2																	68385614		2203	4300	6503	68239118	SO:0001583	missense	56902			AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"RNA binding protein"		"KH-type RNA binding protein 1", "KH-type RNA-binding protein 1"	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.310G>A	2.37:g.68385614G>A	ENSP00000263657:p.Gly104Arg		68239118	A8K6Q0|Q53G13|Q8WVB8	Missense_Mutation	SNP	ENST00000263657.2	37	CCDS1885.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919197	0.33908	.	.	ENSG00000115946	ENST00000263657	T	0.39406	1.08	6.03	6.03	0.97812	.	0.100288	0.64402	D	0.000001	T	0.34919	0.0914	L	0.34521	1.04	0.49798	D	0.999827	B	0.09022	0.002	B	0.08055	0.003	T	0.05402	-1.0887	10	0.48119	T	0.1	-10.5022	14.8676	0.70427	0.0:0.2506:0.7494:0.0	.	104	Q9NRX1	PNO1_HUMAN	R	104	ENSP00000263657:G104R	ENSP00000263657:G104R	G	+	1	0	PNO1	68239118	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.735000	0.74806	2.861000	0.98227	0.655000	0.94253	GGA		0.383	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143		A	68385614	G	A	68385614	3	1	106	1	0	0	0	0	1	0	0	0	12192	1233	43	3	316	3	PNO1	2	68385614	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		68385614	174813759	21	27893										
TLX2	3196	hgsc.bcm.edu	37	chr2	74742120	74742120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gagcctcgggctacggtcccGccggctcacttgccccgctg	13	18	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:74742120G>A	ENST00000233638.7	+	1	510	c.187G>A	c.(187-189)Gcc>Acc	p.A63T	TLX2_ENST00000497238.1_Intron	NM_016170.4	NP_057254.1	O43763	TLX2_HUMAN	T-cell leukemia homeobox 2	63	Gly-rich.				enteric nervous system development (GO:0048484)|mesoderm formation (GO:0001707)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|ovary(1)	2						CTACGGTCCCGCCGGCTCACT	0.756																																					Esophageal Squamous(7;240 533 18610 24312)											0			2											9	6	7					2																	74742120		2093	4138	6231	74595628	SO:0001583	missense	3196			AJ002607	CCDS1947.1	2p13.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000115297	ENSG00000115297		"Homeoboxes / ANTP class : NKL subclass"	5057	protein-coding gene	gene with protein product		604240	"homeo box 11-like 1", "T-cell leukemia, homeobox 2"	HOX11L1		10343123	Standard	NM_016170		Approved	Enx, Tlx2, NCX	uc002sma.2	O43763	OTTHUMG00000129960	ENST00000233638.7:c.187G>A	2.37:g.74742120G>A	ENSP00000233638:p.Ala63Thr		74595628	Q9UD56|Q9UQ48	Missense_Mutation	SNP	ENST00000233638.7	37	CCDS1947.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381065	0.24944	.	.	ENSG00000115297	ENST00000233638	D	0.89810	-2.57	4.22	1.03	0.20045	.	0.389995	0.18936	N	0.127079	D	0.82472	0.5044	L	0.58101	1.795	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.66106	-0.6006	10	0.23891	T	0.37	.	5.2923	0.15733	0.2033:0.0:0.6238:0.1729	.	63	O43763	TLX2_HUMAN	T	63	ENSP00000233638:A63T	ENSP00000233638:A63T	A	+	1	0	TLX2	74595628	0.017000	0.18338	0.026000	0.17262	0.523000	0.34469	0.577000	0.23758	0.417000	0.25871	0.561000	0.74099	GCC		0.756	TLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252224.3			A	74742120	G	A	74742120	3	1	106	1	0	0	0	0	1	0	0	0	16000	1087	38	1	189	1	TLX2	2	74742120	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	6356506	74742120	168457253	22	27894										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74900583	74900583	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctcctccctgtcgccctgcaGggggggtcctctatgctgcc	12	17	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:74900583G>T	ENST00000357877.2	+	6	699		c.e6-1		SEMA4F_ENST00000339773.5_Intron	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F						axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TCGCCCTGCAGGGGGGGTCCT	0.587																																																0			2											56	58	58					2																	74900583		2203	4300	6503	74754091	SO:0001630	splice_region_variant	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.551-1G>T	2.37:g.74900583G>T			74754091	Q542Y7|Q9NS35	Splice_Site	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440376	0.63067	.	.	ENSG00000135622	ENST00000357877;ENST00000434486	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.999	0.58664	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEMA4F	74754091	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	7.635000	0.83286	2.436000	0.82500	0.456000	0.33151	.		0.587	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263	Intron	T	74900583	G	T	74900583	5	4	106	1	0	0	0	0	0	0	1	0	14072	1014	35	2	572	2	SEMA4F	2	74900583	Splice_Site	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	158463	74900583	168298790	23	27895										
GLI2	2736	hgsc.bcm.edu	37	chr2	121740365	121740365	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcggtcccacaccggggagaAgccatatgtgtgtgagcacg	15	11	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:121740365A>C	ENST00000452319.1	+	11	1652	c.1592A>C	c.(1591-1593)aAg>aCg	p.K531T	GLI2_ENST00000314490.11_Missense_Mutation_p.K203T|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.K531T					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				ACCGGGGAGAAGCCATATGTG	0.602																																																0			2											65	60	62					2																	121740365		2203	4300	6503	121456835	SO:0001583	missense	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1592A>C	2.37:g.121740365A>C	ENSP00000390436:p.Lys531Thr		121456835		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813793	0.90790	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	T;T;T	0.42131	0.98;0.98;0.98	4.39	4.39	0.52855	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.046780	0.85682	D	0.000000	T	0.65595	0.2706	M	0.81112	2.525	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.992	T	0.71758	-0.4496	10	0.87932	D	0	.	14.0429	0.64687	1.0:0.0:0.0:0.0	.	531;514;186;186;203	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	T	531;531;203	ENSP00000390436:K531T;ENSP00000354586:K531T;ENSP00000312694:K203T	ENSP00000312694:K203T	K	+	2	0	GLI2	121456835	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.075000	0.94004	1.966000	0.57179	0.397000	0.26171	AAG		0.602	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		C	121740365	A	C	121740365	3	2	106	1	0	0	0	0	1	0	0	0	6458	72	3	4	1630	4	GLI2	2	121740365	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	46839782	121740365	121459008	24	27896										
TNFAIP6	7130	hgsc.bcm.edu	37	chr2	152235986	152235986	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caaatccagtcaaggaaaaaAtacaagtactacttctactg	5	9	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:152235986A>C	ENST00000243347.3	+	6	848	c.773A>C	c.(772-774)aAt>aCt	p.N258T		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	258					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	CAAGGAAAAAATACAAGTACT	0.333																																																0			2											87	94	92					2																	152235986		2203	4300	6503	151944232	SO:0001583	missense	7130				CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.773A>C	2.37:g.152235986A>C	ENSP00000243347:p.Asn258Thr		151944232	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178532	0.57692	.	.	ENSG00000123610	ENST00000243347	T	0.18502	2.21	5.56	5.56	0.83823	.	0.055949	0.64402	D	0.000002	T	0.27524	0.0676	L	0.29908	0.895	0.46564	D	0.999103	D	0.63880	0.993	D	0.70935	0.971	T	0.04165	-1.0972	10	0.15066	T	0.55	.	15.3597	0.74460	1.0:0.0:0.0:0.0	.	258	P98066	TSG6_HUMAN	T	258	ENSP00000243347:N258T	ENSP00000243347:N258T	N	+	2	0	TNFAIP6	151944232	1.000000	0.71417	0.998000	0.56505	0.746000	0.42486	4.606000	0.61126	2.099000	0.63709	0.533000	0.62120	AAT		0.333	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		C	152235986	A	C	152235986	3	2	106	1	0	0	0	0	1	0	0	0	16314	101	4	4	795	4	TNFAIP6	2	152235986	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	30495621	152235986	90963387	25	27897										
NEB	4703	hgsc.bcm.edu	37	chr2	152484275	152484275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	catgcatggaccacatcatcTtggggtcatcttcaatgttc	8	11	5	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:152484275T>C	ENST00000172853.10	-	65	9323	c.9176A>G	c.(9175-9177)aAg>aGg	p.K3059R	NEB_ENST00000397345.3_Missense_Mutation_p.K3302R|NEB_ENST00000603639.1_Missense_Mutation_p.K3302R|NEB_ENST00000604864.1_Missense_Mutation_p.K3302R|NEB_ENST00000409198.1_Missense_Mutation_p.K3059R|NEB_ENST00000427231.2_Missense_Mutation_p.K3302R			P20929	NEBU_HUMAN	nebulin	3059					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CCACATCATCTTGGGGTCATC	0.473																																																0			2											285	267	273					2																	152484275		1919	4131	6050	152192521	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.9176A>G	2.37:g.152484275T>C	ENSP00000172853:p.Lys3059Arg		152192521	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	20.9	4.073850	0.76415	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.58	5.58	0.84498	.	0.122957	0.56097	D	0.000026	T	0.64023	0.2561	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.62020	-0.6942	10	0.35671	T	0.21	.	15.759	0.78063	0.0:0.0:0.0:1.0	.	3059	P20929	NEBU_HUMAN	R	3059;3302;3302;3059	ENSP00000386259:K3059R;ENSP00000380505:K3302R;ENSP00000416578:K3302R;ENSP00000172853:K3059R	ENSP00000172853:K3059R	K	-	2	0	NEB	152192521	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.033000	0.70925	2.121000	0.65114	0.533000	0.62120	AAG		0.473	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152484275	T	C	152484275	3	2	106	1	0	0	0	0	1	0	0	0	10333	1609	56	4	16237	4	NEB	2	152484275	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	248289	152484275	90715098	26	27898										
CACNB4	785	hgsc.bcm.edu	37	chr2	152830189	152830189	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atgaaaatacttacagcctcCgagtcttcaattccatgcag	6	11	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:152830189C>T	ENST00000539935.1	-	3	215				CACNB4_ENST00000475848.1_5'UTR|CACNB4_ENST00000427385.1_Intron|CACNB4_ENST00000201943.5_Intron|CACNB4_ENST00000397327.2_5'UTR|CACNB4_ENST00000360283.6_Silent_p.S13S|CACNB4_ENST00000534999.1_Silent_p.S13S	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit						adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TTACAGCCTCCGAGTCTTCAA	0.463																																																0			2											72	71	71					2																	152830189		1864	4106	5970	152538435	SO:0001627	intron_variant	785			AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.148-90305G>A	2.37:g.152830189C>T			152538435	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Silent	SNP	ENST00000539935.1	37	CCDS46426.1																																																																																				0.463	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		T	152830189	C	T	152830189	1	4	106	0	1	0	0	0	0	0	0	0	2561	639	23	1		1	CACNB4	2	152830189	Intron	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	345914	152830189	90369184	27	27899										
PKP4	8502	hgsc.bcm.edu	37	chr2	159481794	159481794	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caaggccaggtggggtcgtcGtcccccaaacgctcagggat	14	13	1	0	rs200934987		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:159481794G>A	ENST00000389759.3	+	7	1120	c.1008G>A	c.(1006-1008)tcG>tcA	p.S336S	PKP4_ENST00000389757.3_Silent_p.S336S	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	336				S -> V (in Ref. 1; CAA57478). {ECO:0000305}.	cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)		p.S336S(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TGGGGTCGTCGTCCCCCAAAC	0.592										HNSCC(62;0.18)																																						1	Substitution - coding silent(1)	ovary(1)	2											70	63	66					2																	159481794		2203	4300	6503	159190040	SO:0001819	synonymous_variant	8502			X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1008G>A	2.37:g.159481794G>A			159190040	Q86W91	Silent	SNP	ENST00000389759.3	37	CCDS33305.1																																																																																				0.592	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159481794	G	A	159481794	2	1	106	1	0	0	0	0	0	0	0	1	12018	1132	40	1		1	PKP4	2	159481794	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	6651605	159481794	83717579	28	27900										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165986535	165986535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccatacagtcccacatggtcTctatccactctccacacagc	4	18	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:165986535T>C	ENST00000360093.3	-	17	3328	c.2837A>G	c.(2836-2838)gAg>gGg	p.E946G	SCN3A_ENST00000409101.3_Missense_Mutation_p.E897G|SCN3A_ENST00000283254.7_Missense_Mutation_p.E946G	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	946					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E946G(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCACATGGTCTCTATCCACTC	0.488																																																1	Substitution - Missense(1)	breast(1)	2											163	158	160					2																	165986535		2203	4298	6501	165694781	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2837A>G	2.37:g.165986535T>C	ENSP00000353206:p.Glu946Gly		165694781	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	T	32	5.150303	0.94645	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	5.63	5.63	0.86233	Ion transport (1);	0.000000	0.64402	D	0.000011	D	0.98071	0.9364	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;0.999;1.0	D;D;D;D;D	0.97110	1.0;0.995;0.991;0.991;1.0	D	0.99236	1.0883	10	0.87932	D	0	.	15.8326	0.78769	0.0:0.0:0.0:1.0	.	946;897;897;897;946	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	G	946;946;897;897	ENSP00000353206:E946G;ENSP00000283254:E946G;ENSP00000386726:E897G;ENSP00000403348:E897G	ENSP00000283254:E946G	E	-	2	0	SCN3A	165694781	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.142000	0.66516	0.460000	0.39030	GAG		0.488	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165986535	T	C	165986535	3	2	106	1	0	0	0	0	1	0	0	0	13955	1551	54	4	3213	4	SCN3A	2	165986535	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	6504741	165986535	77212838	29	27901										
TTN	7273	hgsc.bcm.edu	37	chr2	179447066	179447066	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggttcagtgaagactggatcGcctactccatatttattttc	8	9	1	2	rs369516025		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:179447066G>A	ENST00000591111.1	-	264	61418	c.61194C>T	c.(61192-61194)ggC>ggT	p.G20398G	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Silent_p.G13099G|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.G12974G|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Silent_p.G19471G|TTN_ENST00000589042.1_Silent_p.G22039G|TTN_ENST00000342175.6_Silent_p.G13166G|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20398	Fibronectin type-III 47. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGACTGGATCGCCTACTCCAT	0.408																																																0			2						G	,,,	0,3750		0,0,1875	47	45	46		38922,58413,39297,39498	-11.7	0	2		46	1,8197		0,1,4098	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,5973	AA,AG,GG		0.0122,0.0,0.0084	,,,	12974/26927,19471/33424,13099/27052,13166/27119	179447066	1,11947	1875	4099	5974	179155312	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.61194C>T	2.37:g.179447066G>A			179155312	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179447066	G	A	179447066	2	1	106	1	0	0	0	0	0	0	0	1	16775	1074	38	1		1	TTN	2	179447066	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	13460531	179447066	63752307	30	27902										
TTN	7273	hgsc.bcm.edu	37	chr2	179452059	179452059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgtgtcacttggctcccaccGtcgttttcaggaggggccca	12	13	2	0	rs200463088		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:179452059G>A	ENST00000591111.1	-	257	59180	c.58956C>T	c.(58954-58956)gaC>gaT	p.D19652D	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Silent_p.D12353D|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.D12228D|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Silent_p.D18725D|TTN_ENST00000589042.1_Silent_p.D21293D|TTN_ENST00000342175.6_Silent_p.D12420D|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19652	Fibronectin type-III 42. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGCTCCCACCGTCGTTTTCAG	0.463																																																0			2						G	,,,	10,3802		0,10,1896	63	59	60		36684,56175,37059,37260	-3.3	1	2		60	1,8255		0,1,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,11,6023	AA,AG,GG		0.0121,0.2623,0.0912	,,,	12228/26927,18725/33424,12353/27052,12420/27119	179452059	11,12057	1906	4128	6034	179160305	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58956C>T	2.37:g.179452059G>A			179160305	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179452059	G	A	179452059	2	1	106	1	0	0	0	0	0	0	0	1	16775	1136	40	1		1	TTN	2	179452059	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	4993	179452059	63747314	31	27903										
TTN	7273	hgsc.bcm.edu	37	chr2	179459278	179459278	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	taggacatagttaataatttCtgacccaccatcatacttag	5	9	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:179459278C>A	ENST00000591111.1	-	246	53244	c.53020G>T	c.(53020-53022)Gaa>Taa	p.E17674*	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.E10375*|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.E10250*|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.E16747*|TTN_ENST00000589042.1_Nonsense_Mutation_p.E19315*|TTN_ENST00000342175.6_Nonsense_Mutation_p.E10442*|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17674	Fibronectin type-III 28. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAATAATTTCTGACCCACCA	0.403																																																0			2											129	123	125					2																	179459278		1827	4091	5918	179167524	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53020G>T	2.37:g.179459278C>A	ENSP00000465570:p.Glu17674*		179167524	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	60	50.033692	0.99988	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	.	.	.	X	16747;10250;10442;10375;10248	.	ENSP00000340554:E10442X	E	-	1	0	TTN	179167524	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.832000	0.62759	2.854000	0.98071	0.655000	0.94253	GAA		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179459278	C	A	179459278	4	1	106	1	0	0	0	0	0	1	0	0	16775	922	32	2	50304	2	TTN	2	179459278	Nonsense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	7219	179459278	63740095	32	27904										
TTN	7273	hgsc.bcm.edu	37	chr2	179500354	179500354	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cacttaatgtttggagtatcTtttgctatatcacaggcaaa	7	7	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:179500354T>G	ENST00000591111.1	-	177	36998	c.36774A>C	c.(36772-36774)aaA>aaC	p.K12258N	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K4959N|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K4834N|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K11331N|TTN_ENST00000589042.1_Missense_Mutation_p.K13899N|TTN_ENST00000342175.6_Missense_Mutation_p.K5026N|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12258	Ig-like 82.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K11331K(2)|p.K4834K(1)|p.K5026K(1)|p.K4959K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGAGTATCTTTTGCTATAT	0.388																																																5	Substitution - coding silent(5)	kidney(5)	2											101	87	91					2																	179500354		1826	4095	5921	179208599	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36774A>C	2.37:g.179500354T>G	ENSP00000465570:p.Lys12258Asn		179208599	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.83	2.055696	0.36277	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	6.05	1.55	0.23275	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.44095	0.1277	M	0.69823	2.125	0.46416	D	0.999034	P;P;P;P	0.47191	0.891;0.891;0.891;0.891	B;B;B;B	0.44044	0.318;0.318;0.318;0.439	T	0.48917	-0.8992	9	0.87932	D	0	.	10.3512	0.43937	0.0:0.6298:0.0:0.3702	.	4834;4959;5026;12258	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	11331;4834;5026;4959;4834	ENSP00000343764:K11331N;ENSP00000434586:K4834N;ENSP00000340554:K5026N;ENSP00000352154:K4959N	ENSP00000340554:K5026N	K	-	3	2	TTN	179208599	0.997000	0.39634	0.998000	0.56505	0.993000	0.82548	0.580000	0.23803	0.387000	0.25024	0.528000	0.53228	AAA		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179500354	T	G	179500354	3	3	106	1	0	0	0	0	1	0	0	0	16775	1606	56	4	66540	4	TTN	2	179500354	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	41076	179500354	63699019	33	27905										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207425853	207425853	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agcactgctttttcttaaggCgggtgacatttcactataag	9	8	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:207425853C>T	ENST00000264377.3	+	12	1499	c.1171C>T	c.(1171-1173)Cgg>Tgg	p.R391W	ADAM23_ENST00000374416.1_Splice_Site_p.R391W|ADAM23_ENST00000374415.3_Splice_Site_p.R391W	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	391	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TTTCTTAAGGCGGGTGACATT	0.428																																					Melanoma(194;1127 2130 19620 24042 27855)											0			2											118	117	118					2																	207425853		2203	4300	6503	207134098	SO:0001630	splice_region_variant	10863			AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1170-1C>T	2.37:g.207425853C>T			207134098	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	37	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600467	0.87055	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.10860	2.83;2.83;2.83	5.92	4.99	0.66335	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.222801	0.31784	N	0.007071	T	0.12518	0.0304	N	0.08118	0	0.39104	D	0.961349	D	0.55172	0.97	P	0.58928	0.848	T	0.10291	-1.0636	10	0.87932	D	0	.	11.9977	0.53212	0.2641:0.7359:0.0:0.0	.	391	O75077	ADA23_HUMAN	W	391;391;285;391	ENSP00000264377:R391W;ENSP00000363537:R391W;ENSP00000363536:R391W	ENSP00000264377:R391W	R	+	1	2	ADAM23	207134098	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.137000	0.58010	2.804000	0.96469	0.655000	0.94253	CGG		0.428	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	Missense_Mutation	T	207425853	C	T	207425853	5	4	106	1	0	0	0	0	0	0	1	0	245	782	27	1	1217	1	ADAM23	2	207425853	Splice_Site	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	27925499	207425853	35773520	34	27906										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220396733	220396733	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgctgtgcagatgagacgtcGtttgaggcaggtattcgggt	16	6	0	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:220396733G>A	ENST00000347842.3	+	3	1133	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	ASIC4_ENST00000473709.1_3'UTR|ASIC4_ENST00000358078.4_Silent_p.S373S	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	373					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										ATGAGACGTCGTTTGAGGCAG	0.627																																																0			2											117	125	122					2																	220396733		2203	4300	6503	220104977	SO:0001819	synonymous_variant	55515			AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1119G>A	2.37:g.220396733G>A			220104977	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Silent	SNP	ENST00000347842.3	37	CCDS2442.1																																																																																				0.627	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		A	220396733	G	A	220396733	2	1	106	1	0	0	0	0	0	0	0	1	131	1132	40	1		1	ACCN4	2	220396733	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	12970880	220396733	22802640	35	27907										
ESPNL	339768	hgsc.bcm.edu	37	chr2	239040031	239040031	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttcgagcacctgggcacccaCggctgggaggctgtgcgcgc	16	14	0	0	rs557336771		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr2:239040031C>T	ENST00000343063.3	+	9	2939	c.2676C>T	c.(2674-2676)caC>caT	p.H892H	ESPNL_ENST00000409506.1_Silent_p.H524H|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409169.1_Silent_p.H848H	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	892										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		TGGGCACCCACGGCTGGGAGG	0.697													C|||	1	0.000199681	0	0	5008	,	,		14782	0		0.001	False		,,,				2504	0															0			2											12	12	12					2																	239040031		2178	4271	6449	238704770	SO:0001819	synonymous_variant	339768			AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"Ankyrin repeat domain containing"	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2676C>T	2.37:g.239040031C>T			238704770	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																				0.697	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		T	239040031	C	T	239040031	2	4	106	1	0	0	0	0	0	0	0	1	5268	535	19	1		1	ESPNL	2	239040031	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	18643298	239040031	4159342	36	27908										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266125	41266125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aatccattctggtgccactaCcacagctccttctctgagtg	7	14	2	1	rs121913413		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:41266125C>T	ENST00000349496.5	+	3	402	c.122C>T	c.(121-123)aCc>aTc	p.T41I	CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41I(74)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41N(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A39_T42del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGTGCCACTACCACAGCTCCT	0.507		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	204	Deletion - In frame(95)|Substitution - Missense(83)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	liver(105)|large_intestine(24)|pituitary(20)|endometrium(14)|stomach(8)|skin(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|pancreas(3)|thyroid(2)|small_intestine(2)|prostate(2)|ovary(2)|bone(2)|adrenal_gland(1)|cervix(1)	3											90	77	81					3																	41266125		2203	4300	6503	41241129	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.122C>T	3.37:g.41266125C>T	ENSP00000344456:p.Thr41Ile		41241129	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568904	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.79258	2.445	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	T	0.72893	-0.4154	10	0.87932	D	0	-8.9189	20.2983	0.98569	0.0:1.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	I	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34I;ENSP00000385604:T41I;ENSP00000412219:T41I;ENSP00000379486:T41I;ENSP00000344456:T41I;ENSP00000411226:T34I;ENSP00000379488:T41I;ENSP00000409302:T41I;ENSP00000401599:T41I	ENSP00000344456:T41I	T	+	2	0	CTNNB1	41241129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	ACC		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266125	C	T	41266125	3	4	106	1	0	0	0	0	1	0	0	0	4022	507	18	3	128	3	CTNNB1	3	41266125	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		41266125	156756305	37	27909										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54661843	54661843	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gagcatctggacaaacttttCgccaaaggaattggaatgtt	10	7	1	0	rs375011891		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:54661843C>T	ENST00000474759.1	+	10	1041	c.993C>T	c.(991-993)ttC>ttT	p.F331F	CACNA2D3_ENST00000490478.1_Silent_p.F237F|CACNA2D3_ENST00000415676.2_Silent_p.F331F|CACNA2D3_ENST00000288197.5_Silent_p.F331F	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	331	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.F331F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	ACAAACTTTTCGCCAAAGGAA	0.413																																																1	Substitution - coding silent(1)	large_intestine(1)	3						C		0,3872		0,0,1936	103	95	98		993	2.9	1	3		98	2,8250		0,2,4124	no	coding-synonymous	CACNA2D3	NM_018398.2		0,2,6060	TT,TC,CC		0.0242,0.0,0.0165		331/1092	54661843	2,12122	1936	4126	6062	54636883	SO:0001819	synonymous_variant	55799			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.993C>T	3.37:g.54661843C>T			54636883	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																				0.413	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54661843	C	T	54661843	2	4	106	1	0	0	0	0	0	0	0	1	2556	883	31	1		1	CACNA2D3	3	54661843	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	13395718	54661843	143360587	38	27910										
RABL3	285282	hgsc.bcm.edu	37	chr3	120417419	120417419	+	Splice_Site	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaactgttcttgatcataatCcctgtgataaataataatga	5	6	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:120417419C>G	ENST00000273375.3	-	5	414	c.385G>C	c.(385-387)Gat>Cat	p.D129H	RABL3_ENST00000491398.1_5'UTR|RABL3_ENST00000483733.1_Splice_Site_p.D129H	NM_173825.3	NP_776186.2	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3	129	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)	17				GBM - Glioblastoma multiforme(114;0.151)		TGATCATAATCCCTGTGATAA	0.328																																																0			3											184	202	196					3																	120417419		2203	4296	6499	121900109	SO:0001630	splice_region_variant	285282			BC020832	CCDS3001.1	3q13.33	2008-02-05			ENSG00000144840	ENSG00000144840			18072	protein-coding gene	gene with protein product						12477932	Standard	NM_173825		Approved	MGC23920	uc003edx.3	Q5HYI8	OTTHUMG00000159668	ENST00000273375.3:c.384-1G>C	3.37:g.120417419C>G			121900109	Q8WUD3	Missense_Mutation	SNP	ENST00000273375.3	37	CCDS3001.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273984	0.80580	.	.	ENSG00000144840	ENST00000273375;ENST00000483733	T;T	0.72394	-0.65;-0.62	5.72	5.72	0.89469	.	0.044427	0.85682	D	0.000000	T	0.80773	0.4687	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.67382	0.951	T	0.80118	-0.1516	10	0.51188	T	0.08	-16.9736	18.8571	0.92257	0.0:1.0:0.0:0.0	.	129	Q5HYI8	RABL3_HUMAN	H	129	ENSP00000273375:D129H;ENSP00000419986:D129H	ENSP00000273375:D129H	D	-	1	0	RABL3	121900109	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.364000	0.79526	2.695000	0.91970	0.557000	0.71058	GAT		0.328	RABL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356776.1	NM_173825	Missense_Mutation	G	120417419	C	G	120417419	5	3	106	1	0	0	0	0	0	0	1	0	13009	869	30	5	341	5	RABL3	3	120417419	Splice_Site	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	65755576	120417419	77605011	39	27911										
IFT122	55764	hgsc.bcm.edu	37	chr3	129185862	129185862	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agtcagggtagtgaggcagaGgaggaagaaccagaggaaga	18	4	1	5			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:129185862G>T	ENST00000348417.2	+	8	770	c.693G>T	c.(691-693)gaG>gaT	p.E231D	IFT122_ENST00000347300.2_Intron|IFT122_ENST00000504021.1_Intron|IFT122_ENST00000431818.2_Missense_Mutation_p.E81D|IFT122_ENST00000296266.3_Missense_Mutation_p.E282D|IFT122_ENST00000349441.2_Intron|IFT122_ENST00000440957.2_Intron|IFT122_ENST00000507564.1_Intron	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	231					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GTGAGGCAGAGGAGGAAGAAC	0.527																																																0			3											151	156	154					3																	129185862		2203	4300	6503	130668552	SO:0001583	missense	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.693G>T	3.37:g.129185862G>T	ENSP00000324005:p.Glu231Asp		130668552	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.391906	0.62066	.	.	ENSG00000163913	ENST00000296266;ENST00000431818;ENST00000348417	T;T;T	0.60797	0.16;0.35;0.82	4.64	4.64	0.57946	WD40 repeat-like-containing domain (1);	0.373706	0.24851	N	0.035095	T	0.53899	0.1825	N	0.08118	0	0.80722	D	1	P;D	0.56035	0.956;0.974	D;D	0.70487	0.931;0.969	T	0.49862	-0.8894	10	0.14656	T	0.56	-26.0989	14.5398	0.67984	0.0:0.0:1.0:0.0	.	231;282	Q9HBG6;G3XAB1	IF122_HUMAN;.	D	282;81;231	ENSP00000296266:E282D;ENSP00000410946:E81D;ENSP00000324005:E231D	ENSP00000296266:E282D	E	+	3	2	IFT122	130668552	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.153000	0.42282	2.421000	0.82119	0.462000	0.41574	GAG		0.527	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		T	129185862	G	T	129185862	3	4	106	1	0	0	0	0	1	0	0	0	7576	991	35	2	880	2	IFT122	3	129185862	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	8768443	129185862	68836568	40	27912										
ESYT3	83850	hgsc.bcm.edu	37	chr3	138187694	138187694	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	actacctgaatggtgaatatCgagccaaaaaactctccagg	8	10	1	2	rs184387509		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:138187694C>T	ENST00000389567.4	+	14	1591	c.1405C>T	c.(1405-1407)Cga>Tga	p.R469*		NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	469	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						TGGTGAATATCGAGCCAAAAA	0.468													C|||	1	0.000199681	0	0	5008	,	,		22603	0		0	False		,,,				2504	0.001															0			3											219	242	234					3																	138187694		2203	4300	6503	139670384	SO:0001587	stop_gained	83850			AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"Synaptotagmins"	24295	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member C"	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.1405C>T	3.37:g.138187694C>T	ENSP00000374218:p.Arg469*		139670384	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Nonsense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	38	6.730251	0.97796	.	.	ENSG00000158220	ENST00000389567	.	.	.	4.29	2.26	0.28386	.	0.531681	0.16193	N	0.225282	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-6.0E-4	8.5551	0.33476	0.4513:0.5487:0.0:0.0	.	.	.	.	X	469	.	ENSP00000374218:R469X	R	+	1	2	ESYT3	139670384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.419000	0.34793	0.998000	0.38996	0.462000	0.41574	CGA		0.468	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		T	138187694	C	T	138187694	4	4	106	1	0	0	0	0	0	1	0	0	5279	876	31	1	1459	1	ESYT3	3	138187694	Nonsense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	9001832	138187694	59834736	41	27913										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138478049	138478049	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaatggtagcttcccgaggtAcctccaactggatataaatc	8	10	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:138478049A>T	ENST00000477593.1	-	2	210	c.137T>A	c.(136-138)gTa>gAa	p.V46E	PIK3CB_ENST00000289153.2_Missense_Mutation_p.V46E			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	46	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	TTCCCGAGGTACCTCCAACTG	0.418																																																0			3											67	65	66					3																	138478049		2203	4300	6503	139960739	SO:0001583	missense	5291				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.137T>A	3.37:g.138478049A>T	ENSP00000418143:p.Val46Glu		139960739	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.656313	0.88056	.	.	ENSG00000051382	ENST00000477593;ENST00000289153;ENST00000483968;ENST00000461451;ENST00000465581	T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96	5.84	5.84	0.93424	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.84750	0.5541	M	0.67397	2.05	0.80722	D	1	D	0.67145	0.996	D	0.70487	0.969	D	0.86197	0.1616	10	0.72032	D	0.01	-18.386	16.2302	0.82332	1.0:0.0:0.0:0.0	.	46	P42338	PK3CB_HUMAN	E	46	ENSP00000418143:V46E;ENSP00000289153:V46E;ENSP00000419857:V46E;ENSP00000420399:V46E	ENSP00000289153:V46E	V	-	2	0	PIK3CB	139960739	1.000000	0.71417	0.997000	0.53966	0.813000	0.45954	8.851000	0.92205	2.228000	0.72767	0.533000	0.62120	GTA		0.418	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			T	138478049	A	T	138478049	3	4	106	1	0	0	0	0	1	0	0	0	11945	391	14	5	3161	5	PIK3CB	3	138478049	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	290355	138478049	59544381	42	27914										
RBP2	5948	hgsc.bcm.edu	37	chr3	139171980	139171980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atttctttttgaacacttgaCggcacacctggtcaccacag	7	12	2	2	rs117646086		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:139171980C>T	ENST00000232217.2	-	4	439	c.383G>A	c.(382-384)cGt>cAt	p.R128H	RP11-319G6.1_ENST00000515247.1_RNA|RP11-319G6.1_ENST00000510068.1_RNA	NM_004164.2	NP_004155.2	P50120	RET2_HUMAN	retinol binding protein 2, cellular	128					epidermis development (GO:0008544)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12					Vitamin A(DB00162)	GAACACTTGACGGCACACCTG	0.572													C|||	1	0.000199681	0	0	5008	,	,		16087	0.001		0	False		,,,				2504	0															0			3											84	71	75					3																	139171980		2203	4300	6503	140654670	SO:0001583	missense	23504			U13831	CCDS3109.1	3q23	2013-03-01	2001-11-28		ENSG00000114113	ENSG00000114113		"Fatty acid binding protein family"	9920	protein-coding gene	gene with protein product		180280	"retinol-binding protein 2, cellular"			7657783, 10072590	Standard	NM_004164		Approved	CRBP2, RBPC2, CRBPII, CRABP-II	uc003eth.3	P50120	OTTHUMG00000159956	ENST00000232217.2:c.383G>A	3.37:g.139171980C>T	ENSP00000232217:p.Arg128His		140654670	A8K7G3|Q6ISQ9|Q6ISS7	Missense_Mutation	SNP	ENST00000232217.2	37	CCDS3109.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	14.47	2.545427	0.45280	.	.	ENSG00000114113	ENST00000232217	T	0.07908	3.15	6.04	-10.1	0.00402	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.698788	0.15320	N	0.268609	T	0.03434	0.0099	N	0.08118	0	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.35599	-0.9782	10	0.38643	T	0.18	.	15.2104	0.73219	0.079:0.0931:0.0:0.8279	.	128	P50120	RET2_HUMAN	H	128	ENSP00000232217:R128H	ENSP00000232217:R128H	R	-	2	0	RBP2	140654670	0.002000	0.14202	0.001000	0.08648	0.993000	0.82548	-0.442000	0.06871	-1.698000	0.01418	-0.215000	0.12644	CGT		0.572	RBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358490.1	NM_004164		T	139171980	C	T	139171980	3	4	106	1	0	0	0	0	1	0	0	0	13193	536	19	1	25	1	RBP2	3	139171980	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	693931	139171980	58850450	43	27915										
CP	1356	hgsc.bcm.edu	37	chr3	148916279	148916279	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agctagacacacaggatctgCattagtgggtcctacttctt	9	10	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:148916279C>A	ENST00000264613.6	-	9	1850	c.1588G>T	c.(1588-1590)Gca>Tca	p.A530S	CP_ENST00000462336.1_5'Flank	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	530	F5/8 type A 2.|Plastocyanin-like 3.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	ACAGGATCTGCATTAGTGGGT	0.458																																																0			3											67	61	63					3																	148916279		2203	4300	6503	150398969	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1588G>T	3.37:g.148916279C>A	ENSP00000264613:p.Ala530Ser		150398969	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	3.831	-0.035778	0.07497	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98178	-4.77;-4.77	5.62	1.09	0.20402	Cupredoxin (2);	0.553554	0.20678	N	0.087705	D	0.88529	0.6461	N	0.03050	-0.425	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.002;0.002;0.002;0.003	T	0.81309	-0.0991	10	0.02654	T	1	-6.4354	1.5087	0.02492	0.1336:0.4089:0.15:0.3074	.	530;530;530;530	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	S	530;313	ENSP00000264613:A530S;ENSP00000420545:A313S	ENSP00000264613:A530S	A	-	1	0	CP	150398969	0.000000	0.05858	0.390000	0.26220	0.978000	0.69477	-0.281000	0.08456	0.590000	0.29694	0.650000	0.86243	GCA		0.458	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148916279	C	A	148916279	3	1	106	1	0	0	0	0	1	0	0	0	3793	710	25	2	1653	2	CP	3	148916279	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	9744299	148916279	49106151	44	27916										
FBXO45	200933	hgsc.bcm.edu	37	chr3	196311032	196311032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aagaattcgagtcatcttggAcatggaagataagactttag	10	5	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr3:196311032A>G	ENST00000311630.6	+	3	1001	c.704A>G	c.(703-705)gAc>gGc	p.D235G	FBXO45_ENST00000440469.1_Missense_Mutation_p.D56G	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GTCATCTTGGACATGGAAGAT	0.408																																																0			3											135	129	131					3																	196311032		1838	4087	5925	197795429	SO:0001583	missense	200933			AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.704A>G	3.37:g.196311032A>G	ENSP00000310332:p.Asp235Gly		197795429	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918358	0.73098	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	D;D	0.82526	-1.62;-1.62	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95098	0.8228	10	0.87932	D	0	-16.4144	15.0971	0.72244	1.0:0.0:0.0:0.0	.	235	P0C2W1	FBSP1_HUMAN	G	56;235	ENSP00000389868:D56G;ENSP00000310332:D235G	ENSP00000310332:D235G	D	+	2	0	FBXO45	197795429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.500000	0.90498	2.212000	0.71576	0.460000	0.39030	GAC		0.408	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			G	196311032	A	G	196311032	3	3	106	1	0	0	0	0	1	0	0	0	5773	275	10	4	714	4	FBXO45	3	196311032	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	47394753	196311032	1711398	45	27917										
PGM2	55276	hgsc.bcm.edu	37	chr4	37851852	37851852	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctattttatctgccatgatcAagaaaccattaagaaattat	4	7	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:37851852A>G	ENST00000381967.4	+	12	1560	c.1460A>G	c.(1459-1461)cAa>cGa	p.Q487R	PGM2_ENST00000537241.1_Missense_Mutation_p.Q327R	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	487					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TGCCATGATCAAGAAACCATT	0.318																																																0			4											50	54	53					4																	37851852		2203	4299	6502	37528247	SO:0001583	missense	55276			BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.1460A>G	4.37:g.37851852A>G	ENSP00000371393:p.Gln487Arg		37528247	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Missense_Mutation	SNP	ENST00000381967.4	37	CCDS3443.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790828	0.31685	.	.	ENSG00000169299	ENST00000381967;ENST00000537241	T;T	0.29142	1.58;1.58	5.53	2.97	0.34412	.	0.164709	0.56097	D	0.000033	T	0.33235	0.0856	M	0.71296	2.17	0.48341	D	0.999637	B	0.25048	0.117	B	0.21546	0.035	T	0.11446	-1.0587	10	0.46703	T	0.11	-11.5949	12.9966	0.58650	0.5896:0.4104:0.0:0.0	.	487	Q96G03	PGM2_HUMAN	R	487;327	ENSP00000371393:Q487R;ENSP00000437342:Q327R	ENSP00000371393:Q487R	Q	+	2	0	PGM2	37528247	0.997000	0.39634	0.898000	0.35279	0.724000	0.41520	1.050000	0.30404	0.345000	0.23873	0.528000	0.53228	CAA		0.318	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		G	37851852	A	G	37851852	3	3	106	1	0	0	0	0	1	0	0	0	11829	130	5	4	1506	4	PGM2	4	37851852	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10		37851852	153302424	46	27918										
H2AFZ	3015	hgsc.bcm.edu	37	chr4	100870498	100870499	+	Missense_Mutation	DNP	TG	TG	AT													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cgcgcccacacgtccatgacTggtcgtcctagattttaggt							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T|G	T|G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:100870498_100870499TG>AT	ENST00000296417.5	-	3	343_344	c.126_127CA>AT	c.(124-129)acCAgt>acATgt	p.S43C	DNAJB14_ENST00000442697.2_5'Flank|RP11-15B17.1_ENST00000501976.2_RNA|H2AFZ_ENST00000529158.1_5'UTR|RP11-15B17.1_ENST00000507494.1_RNA|DNAJB14_ENST00000471738.1_5'Flank|RP11-15B17.1_ENST00000514624.1_RNA	NM_002106.3	NP_002097.1	P0C0S5	H2AZ_HUMAN	H2A histone family, member Z	43					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular vesicular exosome (GO:0070062)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|endometrium(3)|lung(1)	5				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)		CGTCCATGACTGGTCGTCCTAG	0.49											OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4																																								101089521|101089522	SO:0001583	missense	3015			X52317	CCDS3654.1	4q23	2011-01-27			ENSG00000164032	ENSG00000164032		"Histones / Replication-independent"	4741	protein-coding gene	gene with protein product		142763		H2AZ		1697587	Standard	XM_005262971		Approved	H2A.Z	uc003hvo.1	P0C0S5	OTTHUMG00000131048	ENST00000296417.5:c.126_127delinsAT	4.37:g.100870498_100870499delinsAT	ENSP00000296417:p.Ser43Cys	1354	101089521|101089522	B2RD56|P17317|Q6I9U0	Missense_Mutation|Silent	SNP	ENST00000296417.5	37	CCDS3654.1																																																																																				0.49	H2AFZ-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000253695.1	NM_002106		AT	100870499	TG	AT	100870498	3	1	106	1	0	0	0	0	1	0	0	0	6952	1580	55	5	271	5	H2AFZ	4	100870498	Missense_Mutation	DNP	TG	TCGA-DY-A1DF-01A-11D-A152-10	63018646	100870498	90283778	47	27919										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005715	118005715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atcaggattccgattctgcgAtccagccaggtgaaacccaa	9	12	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:118005715A>G	ENST00000310754.4	-	1	1021	c.835T>C	c.(835-837)Tcg>Ccg	p.S279P		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	279	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						CGATTCTGCGATCCAGCCAGG	0.458																																																0			4											82	74	77					4																	118005715		2203	4300	6503	118225163	SO:0001583	missense	133022			AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.835T>C	4.37:g.118005715A>G	ENSP00000309402:p.Ser279Pro		118225163	Q8N2L7	Missense_Mutation	SNP	ENST00000310754.4	37	CCDS3707.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314349	0.23908	.	.	ENSG00000174599	ENST00000310754	D	0.84873	-1.91	3.37	1.29	0.21616	TRAM/LAG1/CLN8 homology domain (3);	0.875430	0.09906	N	0.740465	T	0.80844	0.4701	N	0.24115	0.695	0.09310	N	1	B	0.32071	0.355	B	0.43838	0.433	T	0.71213	-0.4659	10	0.46703	T	0.11	-20.573	9.2283	0.37421	0.4738:0.5262:0.0:0.0	.	279	Q8N609	TR1L1_HUMAN	P	279	ENSP00000309402:S279P	ENSP00000309402:S279P	S	-	1	0	TRAM1L1	118225163	0.003000	0.15002	0.000000	0.03702	0.430000	0.31655	0.534000	0.23098	0.301000	0.22738	0.528000	0.53228	TCG		0.458	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		G	118005715	A	G	118005715	3	3	106	1	0	0	0	0	1	0	0	0	16492	333	12	4	278	4	TRAM1L1	4	118005715	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	17135217	118005715	73148561	48	27920										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122250833	122250833	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcacgatagcaaaaatcatcTtgattgtgacatcatcatat	6	8	4	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:122250833T>G	ENST00000394427.2	-	6	1343	c.932A>C	c.(931-933)aAg>aCg	p.K311T	QRFPR_ENST00000334383.5_3'UTR|Y_RNA_ENST00000384419.1_RNA	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	311					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						AAAAATCATCTTGATTGTGAC	0.264																																																0			4											31	31	31					4																	122250833		2201	4297	6498	122470283	SO:0001583	missense	84109			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.932A>C	4.37:g.122250833T>G	ENSP00000377948:p.Lys311Thr		122470283		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.541034	0.45280	.	.	ENSG00000186867	ENST00000394427	T	0.72282	-0.64	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.046090	0.85682	D	0.000000	T	0.70107	0.3186	N	0.21324	0.655	0.80722	D	1	D	0.63046	0.992	P	0.58013	0.831	T	0.68277	-0.5451	10	0.26408	T	0.33	.	15.5292	0.75942	0.0:0.0:0.0:1.0	.	311	Q96P65	QRFPR_HUMAN	T	311	ENSP00000377948:K311T	ENSP00000377948:K311T	K	-	2	0	QRFPR	122470283	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.763000	0.68818	2.076000	0.62316	0.402000	0.26972	AAG		0.264	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		G	122250833	T	G	122250833	3	3	106	1	0	0	0	0	1	0	0	0	12915	1609	56	4	367	4	QRFPR	4	122250833	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	4245118	122250833	68903443	49	27921										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125590230	125590230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtttaaggcttaattctgtcTctgaggaagggtatccctcc	10	9	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:125590230T>C	ENST00000504087.1	-	4	5239	c.4202A>G	c.(4201-4203)gAg>gGg	p.E1401G	ANKRD50_ENST00000515641.1_Missense_Mutation_p.E1222G	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1401								p.E1401V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TAATTCTGTCTCTGAGGAAGG	0.413																																																1	Substitution - Missense(1)	central_nervous_system(1)	4											127	116	120					4																	125590230		2203	4300	6503	125809680	SO:0001583	missense	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.4202A>G	4.37:g.125590230T>C	ENSP00000425658:p.Glu1401Gly		125809680	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.774898	0.49786	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.69806	-0.43;-0.39	5.35	5.35	0.76521	.	0.116058	0.64402	D	0.000020	T	0.53610	0.1807	N	0.19112	0.55	0.39158	D	0.962351	B	0.20261	0.043	B	0.14578	0.011	T	0.55309	-0.8161	10	0.59425	D	0.04	.	15.5138	0.75806	0.0:0.0:0.0:1.0	.	1401	Q9ULJ7	ANR50_HUMAN	G	1401;1222	ENSP00000425658:E1401G;ENSP00000425355:E1222G	ENSP00000425658:E1401G	E	-	2	0	ANKRD50	125809680	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	5.544000	0.67231	2.250000	0.74265	0.454000	0.30748	GAG		0.413	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		C	125590230	T	C	125590230	3	2	106	1	0	0	0	0	1	0	0	0	677	1551	54	4	91	4	ANKRD50	4	125590230	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	3339397	125590230	65564046	50	27922										
HSPA4L	22824	hgsc.bcm.edu	37	chr4	128717033	128717033	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aggcttccctatgaactgcaGaaaatgcctaatggaagtgc	10	9	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:128717033G>T	ENST00000296464.4	+	3	687	c.276G>T	c.(274-276)caG>caT	p.Q92H	HSPA4L_ENST00000439123.2_Missense_Mutation_p.Q123H|HSPA4L_ENST00000505726.1_Missense_Mutation_p.Q66H|HSPA4L_ENST00000508776.1_Missense_Mutation_p.Q92H	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	92					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						ATGAACTGCAGAAAATGCCTA	0.373																																																0			4											100	98	99					4																	128717033		2203	4300	6503	128936483	SO:0001583	missense	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.276G>T	4.37:g.128717033G>T	ENSP00000296464:p.Gln92His		128936483	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671893	0.29693	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000508549;ENST00000505726	T;T;T;T;T	0.01527	5.44;5.44;5.44;4.8;5.44	4.75	2.11	0.27256	.	0.066901	0.64402	D	0.000010	T	0.01558	0.0050	N	0.22421	0.69	0.36158	D	0.84793	B;B;B	0.13145	0.003;0.002;0.007	B;B;B	0.14023	0.01;0.008;0.005	T	0.51340	-0.8718	10	0.59425	D	0.04	.	8.2102	0.31479	0.3076:0.0:0.6924:0.0	.	66;92;92	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	H	92;123;92;92;66	ENSP00000422482:Q92H;ENSP00000393926:Q123H;ENSP00000296464:Q92H;ENSP00000427305:Q92H;ENSP00000425645:Q66H	ENSP00000296464:Q92H	Q	+	3	2	HSPA4L	128936483	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	0.652000	0.24888	0.241000	0.21283	-0.373000	0.07131	CAG		0.373	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		T	128717033	G	T	128717033	3	4	106	1	0	0	0	0	1	0	0	0	7434	933	33	2	286	2	HSPA4L	4	128717033	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	3126803	128717033	62437243	51	27923										
FRG1	2483	hgsc.bcm.edu	37	chr4	190883032	190883032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaataagtaaagaagacagtAaaattcttaaaaaggctcgg	8	4	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr4:190883032A>G	ENST00000226798.4	+	8	907	c.685A>G	c.(685-687)Aaa>Gaa	p.K229E		NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	229					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		AGAAGACAGTAAAATTCTTAA	0.323																																																0			4											78	96	90					4																	190883032		2159	4225	6384	191120026	SO:0001583	missense	2483			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.685A>G	4.37:g.190883032A>G	ENSP00000226798:p.Lys229Glu		191120026	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.337633	0.24253	.	.	ENSG00000109536	ENST00000226798;ENST00000524583	T	0.35236	1.32	3.89	3.89	0.44902	.	0.311639	0.35970	N	0.002862	T	0.32912	0.0845	L	0.54323	1.7	0.36681	D	0.879026	B	0.18741	0.03	B	0.20767	0.031	T	0.32375	-0.9909	10	0.36615	T	0.2	0.2056	11.0282	0.47757	1.0:0.0:0.0:0.0	.	229	Q14331	FRG1_HUMAN	E	229;101	ENSP00000226798:K229E	ENSP00000226798:K229E	K	+	1	0	FRG1	191120026	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.303000	0.51858	1.541000	0.49316	0.392000	0.25879	AAA		0.323	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477		G	190883032	A	G	190883032	3	3	106	1	0	0	0	0	1	0	0	0	6065	363	13	4	715	4	FRG1	4	190883032	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	62165999	190883032	271244	52	27924										
APC	324	hgsc.bcm.edu	37	chr5	112170652	112170652	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttctgtttcttactaggaatCaaccctcaaaagcgtattga	6	9	4	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:112170652C>A	ENST00000457016.1	+	15	2128	c.1748C>A	c.(1747-1749)tCa>tAa	p.S583*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S583*|APC_ENST00000508376.2_Nonsense_Mutation_p.S583*			P25054	APC_HUMAN	adenomatous polyposis coli	583	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TACTAGGAATCAACCCTCAAA	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											131	114	120					5																	112170652		2202	4300	6502	112198551	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1748C>A	5.37:g.112170652C>A	ENSP00000413133:p.Ser583*		112198551	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	7.115723	0.98074	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5639	20.3409	0.98764	0.0:1.0:0.0:0.0	.	.	.	.	X	583;565;583;583;583	.	ENSP00000257430:S583X	S	+	2	0	APC	112198551	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.487000	0.81328	2.814000	0.96858	0.655000	0.94253	TCA		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112170652	C	A	112170652	4	1	106	1	0	0	0	0	0	1	0	0	763	838	29	2	1802	2	APC	5	112170652	Nonsense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		112170652	68744608	53	27925										
APC	324	hgsc.bcm.edu	37	chr5	112175931	112175931	+	Frame_Shift_Del	DEL	A	A	-													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcagcctaaagaatcaaatgAaaaccaagagaaagaggcag							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:112175931delA	ENST00000457016.1	+	16	5020	c.4640delA	c.(4639-4641)gaafs	p.E1547fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.E1547fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1547fs			P25054	APC_HUMAN	adenomatous polyposis coli	1547	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)|p.E1547fs*13(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATCAAATGAAAACCAAGAG	0.323		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Unknown(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											77	84	81					5																	112175931		2202	4300	6502	112203830	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4640delA	5.37:g.112175931delA	ENSP00000413133:p.Glu1547fs		112203830	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175931	A	-	112175931	7	5	106	1	0	1	0	1	0	0	0	0	763	246	9	0	4698	0	APC	5	112175931	Frame_Shift_Del	DEL	A	TCGA-DY-A1DF-01A-11D-A152-10	5279	112175931	68739329	54	27926	49	2								
APC	324	hgsc.bcm.edu	37	chr5	112175936	112175936	+	Missense_Mutation	SNP	C	C	A													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctaaagaatcaaatgaaaacCaagagaaagaggcagaaaaa							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:112175936C>A	ENST00000457016.1	+	16	5025	c.4645C>A	c.(4645-4647)Caa>Aaa	p.Q1549K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1549K|APC_ENST00000508376.2_Missense_Mutation_p.Q1549K			P25054	APC_HUMAN	adenomatous polyposis coli	1549	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1549*(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAATGAAAACCAAGAGAAAGA	0.328		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Substitution - Nonsense(1)|Unknown(1)|Deletion - Frameshift(1)	stomach(1)|soft_tissue(1)|skin(1)	5											77	84	82					5																	112175936		2202	4300	6502	112203835	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4645C>A	5.37:g.112175936C>A	ENSP00000413133:p.Gln1549Lys		112203835	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	1.094	-0.663105	0.03428	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88664	-2.41;-2.41;-2.41	6.16	4.2	0.49525	.	0.408875	0.29737	N	0.011337	T	0.80763	0.4685	N	0.17474	0.49	0.28631	N	0.907666	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.65907	-0.6054	9	.	.	.	-1.4961	17.2532	0.87048	0.2393:0.7607:0.0:0.0	.	1551;1549	Q4LE70;P25054	.;APC_HUMAN	K	1549	ENSP00000413133:Q1549K;ENSP00000257430:Q1549K;ENSP00000427089:Q1549K	.	Q	+	1	0	APC	112203835	0.123000	0.22298	1.000000	0.80357	0.981000	0.71138	1.683000	0.37638	1.591000	0.50007	0.650000	0.86243	CAA		0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175936	C	A	112175936	3	1	106	1	0	0	0	0	1	0	0	0	763	595	21	2	4703	2	APC	5	112175936	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5	112175936	68739324	55	27927	49	2								
IK	3550	hgsc.bcm.edu	37	chr5	140038633	140038633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atcgggaaagagacagagacCgtgaccgagagcgagagcga	16	8	0	5			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:140038633C>T	ENST00000417647.2	+	12	1199	c.1060C>T	c.(1060-1062)Cgt>Tgt	p.R354C		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	354	17 X 2 AA tandem repeats of R-[ED].				cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			agacagagaccgtgaccgaga	0.562																																																0			5											81	94	90					5																	140038633		2156	4282	6438	140018817	SO:0001583	missense	3550			BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.1060C>T	5.37:g.140038633C>T	ENSP00000396301:p.Arg354Cys		140018817	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	37	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593589	0.86953	.	.	ENSG00000113141	ENST00000417647	T	0.19669	2.13	4.66	3.75	0.43078	.	0.285757	0.30565	N	0.009347	T	0.35970	0.0950	L	0.45352	1.415	0.58432	D	0.999994	D	0.89917	1.0	D	0.71414	0.973	T	0.07028	-1.0794	10	0.56958	D	0.05	.	12.8058	0.57612	0.1709:0.8291:0.0:0.0	.	354	Q13123	RED_HUMAN	C	354	ENSP00000396301:R354C	ENSP00000396301:R354C	R	+	1	0	IK	140018817	0.993000	0.37304	1.000000	0.80357	0.993000	0.82548	1.206000	0.32321	1.007000	0.39238	0.655000	0.94253	CGT		0.562	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		T	140038633	C	T	140038633	3	4	106	1	0	0	0	0	1	0	0	0	7629	652	23	1	1106	1	IK	5	140038633	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	27862697	140038633	40876627	56	27928										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140249498	140249498	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctaaacgccacagaccgagaCgaaggagtcaatggagaggt	13	9	1	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:140249498C>T	ENST00000398640.2	+	1	810	c.810C>T	c.(808-810)gaC>gaT	p.D270D	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	270	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGACCGAGACGAAGGAGTCA	0.388																																																0			5											34	34	34					5																	140249498		1925	4142	6067	140229682	SO:0001819	synonymous_variant	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.810C>T	5.37:g.140249498C>T			140229682	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																				0.388	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140249498	C	T	140249498	2	4	106	1	0	0	0	0	0	0	0	1	11552	535	19	1		1	PCDHA11	5	140249498	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	210865	140249498	40665762	57	27929										
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140788328	140788328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	taatggttagagttaattccGatggtggcaaatacccagag	11	6	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:140788328G>A	ENST00000520790.1	+	1	559	c.559G>A	c.(559-561)Gat>Aat	p.D187N	PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTTAATTCCGATGGTGGCAA	0.408																																																0			5											23	23	23					5																	140788328		1827	4085	5912	140768512	SO:0001583	missense	56100			AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.559G>A	5.37:g.140788328G>A	ENSP00000428603:p.Asp187Asn		140768512	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	g	16.37	3.103141	0.56183	.	.	ENSG00000253305	ENST00000520790	T	0.19938	2.11	5.34	5.34	0.76211	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.37237	0.0996	M	0.78916	2.43	0.24988	N	0.991551	D;P	0.54047	0.964;0.935	P;B	0.51385	0.668;0.329	T	0.30387	-0.9980	9	0.48119	T	0.1	.	12.0862	0.53698	0.0797:0.0:0.9203:0.0	.	187;187	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	N	187	ENSP00000428603:D187N	ENSP00000428603:D187N	D	+	1	0	PCDHGB6	140768512	1.000000	0.71417	0.784000	0.31847	0.925000	0.55904	4.867000	0.63013	2.502000	0.84385	0.467000	0.42956	GAT		0.408	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		A	140788328	G	A	140788328	3	1	106	1	0	0	0	0	1	0	0	0	11598	1058	37	1	561	1	PCDHGB6	5	140788328	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	538830	140788328	40126932	58	27930										
SLC26A2	1836	hgsc.bcm.edu	37	chr5	149360763	149360763	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aggcctacttgttggggtttGtttttctatattttgtgtca	10	5	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr5:149360763G>T	ENST00000286298.4	+	3	1875	c.1607G>T	c.(1606-1608)tGt>tTt	p.C536F		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	536					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GTTGGGGTTTGTTTTTCTATA	0.418																																																0			5											123	131	129					5																	149360763		2203	4299	6502	149340956	SO:0001583	missense	1836			U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.1607G>T	5.37:g.149360763G>T	ENSP00000286298:p.Cys536Phe		149340956	A8K2U3|B2R6J1|Q6N051	Missense_Mutation	SNP	ENST00000286298.4	37	CCDS4300.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.273704	0.23221	.	.	ENSG00000155850	ENST00000286298	D	0.93307	-3.2	6.17	6.17	0.99709	.	0.370432	0.33075	N	0.005312	D	0.90198	0.6936	L	0.43152	1.355	0.35952	D	0.834009	B	0.12013	0.005	B	0.09377	0.004	D	0.87307	0.2309	10	0.31617	T	0.26	.	15.581	0.76439	0.0:0.0:0.8623:0.1377	.	536	P50443	S26A2_HUMAN	F	536	ENSP00000286298:C536F	ENSP00000286298:C536F	C	+	2	0	SLC26A2	149340956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.653000	0.67967	2.941000	0.99782	0.655000	0.94253	TGT		0.418	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		T	149360763	G	T	149360763	3	4	106	1	0	0	0	0	1	0	0	0	14554	1377	48	2	1613	2	SLC26A2	5	149360763	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	8572435	149360763	31554497	59	27931										
TNF	7124	hgsc.bcm.edu	37	chr6	31545064	31545064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctgcccctccacccatgtgcTcctcacccacaccatcagcc	4	23	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:31545064T>C	ENST00000449264.2	+	4	627	c.452T>C	c.(451-453)cTc>cCc	p.L151P		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	151					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	ACCCATGTGCTCCTCACCCAC	0.617									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																																							0			6											144	100	116					6																	31545064		1511	2709	4220	31653043	SO:0001583	missense	7124	Familial Cancer Database	incl.: Familial Head and Neck Cancer	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.452T>C	6.37:g.31545064T>C	ENSP00000398698:p.Leu151Pro		31653043	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	37	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.404968	0.42613	.	.	ENSG00000232810	ENST00000449264	D	0.93763	-3.28	5.4	5.4	0.78164	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.428589	0.26411	N	0.024521	D	0.91865	0.7425	L	0.46567	1.45	0.58432	D	0.999999	D	0.62365	0.991	D	0.63192	0.912	D	0.90746	0.4653	10	0.32370	T	0.25	.	8.8056	0.34936	0.1678:0.0:0.0:0.8322	.	151	P01375	TNFA_HUMAN	P	151	ENSP00000398698:L151P	ENSP00000398698:L151P	L	+	2	0	TNF	31653043	0.115000	0.22152	0.844000	0.33320	0.647000	0.38526	0.884000	0.28214	2.052000	0.61016	0.459000	0.35465	CTC		0.617	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			C	31545064	T	C	31545064	3	2	106	1	0	0	0	0	1	0	0	0	16310	1551	54	4	466	4	TNF	6	31545064	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10		31545064	139570003	60	27932										
PRPH2	5961	hgsc.bcm.edu	37	chr6	42672305	42672305	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gattgcagcagctgaaagggAcgccgtccaccaggtaccgc	13	13	0	1	rs62645934|rs281865372		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:42672305A>G	ENST00000230381.5	-	2	865	c.626T>C	c.(625-627)gTc>gCc	p.V209A		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	209					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			GCTGAAAGGGACGCCGTCCAC	0.572																																																0			6											157	119	132					6																	42672305		2203	4300	6503	42780283	SO:0001583	missense	5961				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.626T>C	6.37:g.42672305A>G	ENSP00000230381:p.Val209Ala		42780283	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069831	0.76301	.	.	ENSG00000112619	ENST00000230381	D	0.88201	-2.35	5.1	5.1	0.69264	Tetraspanin, EC2 domain (1);Peripherin/rom-1, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94118	0.8114	M	0.88775	2.98	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	D	0.94988	0.8132	10	0.62326	D	0.03	.	14.8867	0.70575	1.0:0.0:0.0:0.0	.	209	P23942	PRPH2_HUMAN	A	209	ENSP00000230381:V209A	ENSP00000230381:V209A	V	-	2	0	PRPH2	42780283	1.000000	0.71417	0.928000	0.36995	0.718000	0.41266	9.273000	0.95719	1.931000	0.55961	0.533000	0.62120	GTC		0.572	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		G	42672305	A	G	42672305	3	3	106	1	0	0	0	0	1	0	0	0	12611	275	10	4	422	4	PRPH2	6	42672305	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	11127241	42672305	128442762	61	27933										
BAI3	577	hgsc.bcm.edu	37	chr6	70048830	70048830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agatgagtgagcctcatagcGgtttgacgctcaaatgtgcc	12	9	2	4	rs74732221		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:70048830G>A	ENST00000370598.1	+	25	4032	c.3211G>A	c.(3211-3213)Ggt>Agt	p.G1071S	BAI3_ENST00000546190.1_Missense_Mutation_p.G35S|BAI3_ENST00000238918.8_Missense_Mutation_p.G277S	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1071					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GCCTCATAGCGGTTTGACGCT	0.418													G|||	1	0.000199681	0	0	5008	,	,		15621	0.001		0	False		,,,				2504	0															0			6											227	223	224					6																	70048830		2203	4300	6503	70105551	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3211G>A	6.37:g.70048830G>A	ENSP00000359630:p.Gly1071Ser		70105551	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.79	3.892886	0.72524	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.41400	2.04;2.66;1.0	6.16	6.16	0.99307	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.32585	0.0834	N	0.10874	0.06	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.05733	-1.0867	10	0.06757	T	0.87	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	277;1071;1071	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	S	1071;277;35	ENSP00000359630:G1071S;ENSP00000238918:G277S;ENSP00000441821:G35S	ENSP00000238918:G277S	G	+	1	0	BAI3	70105551	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.659000	0.68010	2.937000	0.99478	0.650000	0.86243	GGT		0.418	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	70048830	G	A	70048830	3	1	106	1	0	0	0	0	1	0	0	0	1301	1116	39	1	3301	1	BAI3	6	70048830	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	27376525	70048830	101066237	62	27934										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75833803	75833803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cgcactgtaatttcttgtccCcttgttcctgattatgacaa	6	11	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:75833803C>A	ENST00000322507.8	-	42	7041	c.6732G>T	c.(6730-6732)agG>agT	p.R2244S	COL12A1_ENST00000483888.2_Missense_Mutation_p.R2244S|COL12A1_ENST00000345356.6_Missense_Mutation_p.R1080S|COL12A1_ENST00000416123.2_Missense_Mutation_p.R2244S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2244	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTTCTTGTCCCCTTGTTCCTG	0.383																																																0			6											113	106	108					6																	75833803		1905	4118	6023	75890523	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.6732G>T	6.37:g.75833803C>A	ENSP00000325146:p.Arg2244Ser		75890523	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.012670	0.54468	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.34	1.44	0.22558	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.054039	0.64402	D	0.000001	T	0.22820	0.0551	L	0.44542	1.39	0.40950	D	0.984538	B;B	0.33448	0.2;0.412	B;B	0.30316	0.069;0.114	T	0.04360	-1.0957	10	0.44086	T	0.13	.	8.833	0.35096	0.0:0.2227:0.0:0.7773	.	1080;2244	Q99715-2;Q99715	.;COCA1_HUMAN	S	2244;2244;1080;2244;2244	ENSP00000325146:R2244S;ENSP00000305147:R1080S;ENSP00000412864:R2244S;ENSP00000421216:R2244S	ENSP00000325146:R2244S	R	-	3	2	COL12A1	75890523	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	1.599000	0.36751	0.110000	0.17919	-0.423000	0.05987	AGG		0.383	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75833803	C	A	75833803	3	1	106	1	0	0	0	0	1	0	0	0	3675	622	22	2	2559	2	COL12A1	6	75833803	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5784973	75833803	95281264	63	27935										
SENP6	26054	hgsc.bcm.edu	37	chr6	76373082	76373082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gttttatggcaacaatgtggAaaaggttccaattgatatta	9	4	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:76373082A>G	ENST00000447266.2	+	9	1320	c.842A>G	c.(841-843)gAa>gGa	p.E281G	SENP6_ENST00000327284.8_Missense_Mutation_p.E274G|SENP6_ENST00000370010.2_Missense_Mutation_p.E274G|SENP6_ENST00000370014.3_Missense_Mutation_p.E281G	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	281					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				AACAATGTGGAAAAGGTTCCA	0.348																																																0			6											117	113	114					6																	76373082		1851	4097	5948	76429802	SO:0001583	missense	26054				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.842A>G	6.37:g.76373082A>G	ENSP00000402527:p.Glu281Gly		76429802	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.680065	0.00751	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.43688	2.75;2.75;1.52;2.76;0.94;1.52	5.77	1.48	0.22813	.	0.250024	0.40385	N	0.001115	T	0.02230	0.0069	N	0.00237	-1.79	0.58432	D	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39251	-0.9623	10	0.07030	T	0.85	-3.3924	4.5623	0.12166	0.4401:0.0:0.411:0.1489	.	274;281;274	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	G	274;281;274;281;171;171	ENSP00000359027:E274G;ENSP00000359031:E281G;ENSP00000321820:E274G;ENSP00000402527:E281G;ENSP00000426480:E171G;ENSP00000391426:E171G	ENSP00000321820:E274G	E	+	2	0	SENP6	76429802	1.000000	0.71417	0.976000	0.42696	0.125000	0.20455	1.876000	0.39588	0.036000	0.15547	-0.256000	0.11100	GAA		0.348	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76373082	A	G	76373082	3	3	106	1	0	0	0	0	1	0	0	0	14087	246	9	4	876	4	SENP6	6	76373082	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	539279	76373082	94741985	64	27936										
FRK	2444	hgsc.bcm.edu	37	chr6	116264271	116264271	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttaatgctgaatttattactAcgaatggcttcgggcgcagt	10	7	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:116264271A>G	ENST00000606080.1	-	7	1664	c.1218T>C	c.(1216-1218)cgT>cgC	p.R406R	FRK_ENST00000538210.1_Silent_p.R264R	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	406	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	ATTTATTACTACGAATGGCTT	0.378																																																0			6											82	77	79					6																	116264271		2203	4300	6503	116370964	SO:0001819	synonymous_variant	2444			U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.1218T>C	6.37:g.116264271A>G			116370964	B4DY49|Q13128|Q9NTR5	Silent	SNP	ENST00000606080.1	37	CCDS5103.1																																																																																				0.378	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		G	116264271	A	G	116264271	2	3	106	1	0	0	0	0	0	0	0	1	6067	378	14	4		4	FRK	6	116264271	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	39891189	116264271	54850796	65	27937										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152473216	152473216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gttctccctggccaggcggcGgtactgcttgttgatcagtt	13	11	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:152473216G>A	ENST00000367255.5	-	134	24791	c.24190C>T	c.(24190-24192)Cgc>Tgc	p.R8064C	SYNE1_ENST00000354674.4_Missense_Mutation_p.R219C|SYNE1_ENST00000448038.1_Missense_Mutation_p.R7993C|SYNE1_ENST00000341594.5_Missense_Mutation_p.R7676C|SYNE1_ENST00000265368.4_Missense_Mutation_p.R8064C|SYNE1_ENST00000423061.1_Missense_Mutation_p.R7993C|SYNE1_ENST00000356820.4_Missense_Mutation_p.R2588C|SYNE1_ENST00000539504.1_Missense_Mutation_p.R219C|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8064					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCCAGGCGGCGGTACTGCTTG	0.547										HNSCC(10;0.0054)																																						0			6											110	86	94					6																	152473216		2203	4300	6503	152514909	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.24190C>T	6.37:g.152473216G>A	ENSP00000356224:p.Arg8064Cys		152514909	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795575	0.90453	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26	5.72	4.78	0.61160	.	0.000000	0.51477	D	0.000085	T	0.57213	0.2038	M	0.80028	2.48	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.986	D;D;D;D;P	0.81914	0.988;0.988;0.995;0.988;0.858	T	0.62435	-0.6855	10	0.87932	D	0	.	17.4496	0.87588	0.0:0.0:0.8673:0.1327	.	8064;8064;7993;7993;266	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	C	8064;219;710;7993;8064;7993;7676;2588;226;221;986;219	ENSP00000356224:R8064C;ENSP00000441052:R219C;ENSP00000356226:R710C;ENSP00000396024:R7993C;ENSP00000265368:R8064C;ENSP00000390975:R7993C;ENSP00000341887:R7676C;ENSP00000349276:R2588C;ENSP00000356220:R986C;ENSP00000346701:R219C	ENSP00000265368:R8064C	R	-	1	0	SYNE1	152514909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.704000	0.54815	2.716000	0.92895	0.650000	0.86243	CGC		0.547	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152473216	G	A	152473216	3	1	106	1	0	0	0	0	1	0	0	0	15484	1116	39	1	2328	1	SYNE1	6	152473216	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	36208945	152473216	18641851	66	27938										
MRPL18	29074	hgsc.bcm.edu	37	chr6	160218385	160218385	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	catcagaatggcaaggttgtGgtttcggcctccactcgtga	12	10	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr6:160218385G>A	ENST00000367034.4	+	3	428	c.306G>A	c.(304-306)gtG>gtA	p.V102V	MRPL18_ENST00000480842.1_3'UTR|PNLDC1_ENST00000392167.3_5'Flank|PNLDC1_ENST00000610273.1_5'Flank	NM_014161.3	NP_054880.2	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18	102					rRNA import into mitochondrion (GO:0035928)|translation (GO:0006412)	extracellular space (GO:0005615)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	11		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		GCAAGGTTGTGGTTTCGGCCT	0.448																																																0			6											133	117	122					6																	160218385		2203	4300	6503	160138375	SO:0001819	synonymous_variant	29074			AF161556	CCDS5270.1	6q25.3	2012-09-13			ENSG00000112110	ENSG00000112110		"Mitochondrial ribosomal proteins / large subunits"	14477	protein-coding gene	gene with protein product		611831				11042152, 11551941	Standard	NM_014161		Approved	HSPC071	uc003qsw.4	Q9H0U6	OTTHUMG00000015942	ENST00000367034.4:c.306G>A	6.37:g.160218385G>A			160138375	Q5TAP9|Q9NZW8	Silent	SNP	ENST00000367034.4	37	CCDS5270.1																																																																																				0.448	MRPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042925.1			A	160218385	G	A	160218385	2	1	106	1	0	0	0	0	0	0	0	1	9813	1335	47	3		3	MRPL18	6	160218385	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	7745169	160218385	10896682	67	27939										
PAPOLB	56903	hgsc.bcm.edu	37	chr7	4900243	4900243	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccaagctcccaaccaggattCggatctttgattccaccaag	7	14	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:4900243C>T	ENST00000404991.1	-	1	1382	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	399		Interaction with RNA. {ECO:0000250}.			mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		AACCAGGATTCGGATCTTTGA	0.398																																																0			7											194	208	203					7																	4900243		2202	4300	6502	4866769	SO:0001583	missense	56903			AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1196G>A	7.37:g.4900243C>T	ENSP00000384700:p.Arg399Gln		4866769	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	37		.	.	.	.	.	.	.	.	.	.	C	20.5	3.996640	0.74818	.	.	ENSG00000218823	ENST00000404991	.	.	.	4.7	3.78	0.43462	.	.	.	.	.	T	0.69079	0.3071	M	0.82630	2.6	0.80722	D	1	D	0.60160	0.987	P	0.54210	0.745	T	0.74575	-0.3620	8	0.87932	D	0	.	10.5264	0.44952	0.0:0.9:0.0:0.1	.	400	A4D1Z6	.	Q	399	.	ENSP00000384700:R399Q	R	-	2	0	PAPOLB	4866769	1.000000	0.71417	0.999000	0.59377	0.813000	0.45954	7.609000	0.82925	1.520000	0.48965	0.591000	0.81541	CGA		0.398	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		T	4900243	C	T	4900243	3	4	106	1	0	0	0	0	1	0	0	0	11461	884	31	1	718	1	PAPOLB	7	4900243	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		4900243	154238420	68	27940										
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35674831	35674831	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atgctaaggagaatcgcagcTcgtgagaacgtgtacatcca	11	9	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:35674831T>C	ENST00000396081.1	-	6	1659	c.855A>G	c.(853-855)cgA>cgG	p.R285R	HERPUD2_ENST00000426180.1_5'UTR|HERPUD2_ENST00000311350.3_Silent_p.R285R	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	285					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						GAATCGCAGCTCGTGAGAACG	0.413																																																0			7											184	165	171					7																	35674831		2203	4300	6503	35641356	SO:0001819	synonymous_variant	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.855A>G	7.37:g.35674831T>C			35641356	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	37	CCDS5446.1																																																																																				0.413	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		C	35674831	T	C	35674831	2	2	106	1	0	0	0	0	0	0	0	1	7085	1538	54	4		4	HERPUD2	7	35674831	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	30774588	35674831	123463832	69	27941										
AMPH	273	hgsc.bcm.edu	37	chr7	38516554	38516554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtccactagcttcctgctgcGcttggcgatgcgattctgtc	11	13	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:38516554G>A	ENST00000356264.2	-	6	627	c.412C>T	c.(412-414)Cgc>Tgc	p.R138C	AMPH_ENST00000325590.5_Missense_Mutation_p.R138C|AMPH_ENST00000428293.2_Missense_Mutation_p.R138C	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	138	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						TTCCTGCTGCGCTTGGCGATG	0.502																																																0			7											115	100	105					7																	38516554		2203	4300	6503	38483079	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.412C>T	7.37:g.38516554G>A	ENSP00000348602:p.Arg138Cys		38483079	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.756726	0.69648	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000544070	T;T;T	0.71222	-0.55;-0.55;-0.55	5.52	3.38	0.38709	BAR (3);	0.000000	0.85682	D	0.000000	D	0.85566	0.5726	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88450	0.3048	10	0.87932	D	0	-12.9834	12.8186	0.57679	0.0:0.0:0.5903:0.4096	.	138;138	P49418-2;P49418	.;AMPH_HUMAN	C	138	ENSP00000317441:R138C;ENSP00000348602:R138C;ENSP00000390734:R138C	ENSP00000317441:R138C	R	-	1	0	AMPH	38483079	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.303000	0.33470	1.423000	0.47198	0.585000	0.79938	CGC		0.502	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38516554	G	A	38516554	3	1	106	1	0	0	0	0	1	0	0	0	588	1087	38	1	1739	1	AMPH	7	38516554	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	2841723	38516554	120622109	70	27942										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729765	41729765	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcttcttcttgcccaggagaAccaagctggcgccactctcc	8	16	4	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:41729765A>C	ENST00000242208.4	-	3	1010	c.764T>G	c.(763-765)gTt>gGt	p.V255G	INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_Missense_Mutation_p.V255G	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	255					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GCCCAGGAGAACCAAGCTGGC	0.592										TSP Lung(11;0.080)																																						0			7											37	38	38					7																	41729765		2203	4300	6503	41696290	SO:0001583	missense	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.764T>G	7.37:g.41729765A>C	ENSP00000242208:p.Val255Gly		41696290	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	27.4	4.824437	0.90955	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.62498	0.02;0.02	6.06	6.06	0.98353	Transforming growth factor-beta, N-terminal (1);	0.295439	0.34133	N	0.004224	T	0.73410	0.3583	M	0.61703	1.905	0.80722	D	1	D	0.57571	0.98	P	0.62740	0.906	T	0.68538	-0.5382	10	0.14252	T	0.57	-24.5592	16.6093	0.84858	1.0:0.0:0.0:0.0	.	255	P08476	INHBA_HUMAN	G	255	ENSP00000242208:V255G;ENSP00000397197:V255G	ENSP00000242208:V255G	V	-	2	0	INHBA	41696290	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.364000	0.90105	2.324000	0.78689	0.533000	0.62120	GTT		0.592	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			C	41729765	A	C	41729765	3	2	106	1	0	0	0	0	1	0	0	0	7762	43	2	4	520	4	INHBA	7	41729765	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	3213211	41729765	117408898	71	27943										
IGFBP3	3486	hgsc.bcm.edu	37	chr7	45956872	45956872	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtatctgtgctctgagactcGtagtcaactttgtagcgctg	11	9	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:45956872G>A	ENST00000275521.6	-	2	703	c.570C>T	c.(568-570)taC>taT	p.Y190Y	IGFBP3_ENST00000465642.1_5'UTR|IGFBP3_ENST00000381083.4_Silent_p.Y196Y|IGFBP3_ENST00000381086.5_Silent_p.Y93Y	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	190					apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)			large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	TCTGAGACTCGTAGTCAACTT	0.502											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			7											181	160	167					7																	45956872		2203	4300	6503	45923397	SO:0001819	synonymous_variant	3486				CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"growth hormone-dependent binding protein", "acid stable subunit of the 140 K IGF complex", "binding protein 53", "binding protein 29", "IGF-binding protein 3"	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.570C>T	7.37:g.45956872G>A		935	45923397	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Silent	SNP	ENST00000275521.6	37	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.718|7.718	0.696573|0.696573	0.15106|0.15106	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000417621|ENST00000428530	.|.	.|.	.|.	5.29|5.29	-6.09|-6.09	0.02145|0.02145	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34077	.|0.0885	.|.	.|.	.|.	0.22266|0.22266	N|N	0.999242|0.999242	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.38373	.|-0.9664	.|4	.|.	.|.	.|.	-31.9254|-31.9254	13.262|13.262	0.60111|0.60111	0.7501:0.0:0.2499:0.0|0.7501:0.0:0.2499:0.0	.|.	.|.	.|.	.|.	X|M	52|42	.|.	.|.	R|T	-|-	1|2	2|0	IGFBP3|IGFBP3	45923397|45923397	0.003000|0.003000	0.15002|0.15002	0.678000|0.678000	0.29963|0.29963	0.926000|0.926000	0.56050|0.56050	-1.417000|-1.417000	0.02464|0.02464	-1.084000|-1.084000	0.03092|0.03092	-0.940000|-0.940000	0.02684|0.02684	CGA|ACG		0.502	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398		A	45956872	G	A	45956872	2	1	106	1	0	0	0	0	0	0	0	1	7601	1140	40	1		1	IGFBP3	7	45956872	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	4227107	45956872	113181791	72	27944										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312293	48312293	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttccaaaacatcagtaaagcAtttgcatttttatttaagac	4	7	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:48312293A>T	ENST00000435803.1	+	17	3054	c.3030A>T	c.(3028-3030)gcA>gcT	p.A1010A		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1010					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCAGTAAAGCATTTGCATTTT	0.323																																																0			7											24	23	23					7																	48312293		1804	4056	5860	48282839	SO:0001819	synonymous_variant	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.3030A>T	7.37:g.48312293A>T			48282839	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																				0.323	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48312293	A	T	48312293	2	4	106	1	0	0	0	0	0	0	0	1	31	204	8	5		5	ABCA13	7	48312293	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	2355421	48312293	110826370	73	27945										
EGFR	1956	hgsc.bcm.edu	37	chr7	55242488	55242488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	attaagagaagcaacatctcCgaaagccaacaaggaaatcc	7	10	1	1	rs559717059|rs121913463|rs397517100|rs397517099|rs121913437		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:55242488C>T	ENST00000275493.2	+	19	2435	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.P708L|EGFR_ENST00000454757.2_Missense_Mutation_p.P700L	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	753	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Missing (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.S752_I759del(13)|p.T751_I759>N(8)|p.L747_P753>Q(7)|p.T751_I759>S(3)|p.T751_I759del(2)|p.A750_E758>P(2)|p.L747_K754del(2)|p.E746_P753>IS(1)|p.L747_K754>ST(1)|p.L747_P753del(1)|p.A750_E758del(1)|p.T751_I759>REA(1)|p.A750_K754del(1)|p.T751_E758del(1)|p.L747_K754>N(1)|p.P753_I759del(1)|p.E746_P753>VQ(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCAACATCTCCGAAAGCCAAC	0.488	L747_P753>Q(HCC4006_LUNG)	8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	47	Complex - deletion inframe(25)|Deletion - In frame(22)	lung(45)|breast(2)	7											104	99	101					7																	55242488		2203	4300	6503	55209982	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2258C>T	7.37:g.55242488C>T	ENSP00000275493:p.Pro753Leu		55209982	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.649807	0.67358	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	D;D;D	0.82344	-1.6;-1.6;-1.6	5.45	5.45	0.79879	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84442	0.5473	L	0.31752	0.955	0.80722	D	1	D;D	0.65815	0.987;0.995	B;P	0.57679	0.115;0.825	D	0.85897	0.1432	10	0.59425	D	0.04	.	17.8402	0.88713	0.0:1.0:0.0:0.0	.	708;753	Q504U8;P00533	.;EGFR_HUMAN	L	708;623;753;700	ENSP00000415559:P708L;ENSP00000275493:P753L;ENSP00000395243:P700L	ENSP00000275493:P753L	P	+	2	0	EGFR	55209982	1.000000	0.71417	0.950000	0.38849	0.655000	0.38815	5.896000	0.69822	2.558000	0.86282	0.561000	0.74099	CCG		0.488	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55242488	C	T	55242488	3	4	106	1	0	0	0	0	1	0	0	0	4978	652	23	1	2596	1	EGFR	7	55242488	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	6930195	55242488	103896175	74	27946										
GTF2IRD1	9569	hgsc.bcm.edu	37	chr7	73944105	73944105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acatggtccccgtgccctacCggaagattgcctgtgacccg	11	15	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:73944105C>T	ENST00000265755.3	+	9	1525	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.R410W|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.R378W	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	378				R -> Q (in Ref. 5; AAF21796). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R378W(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGTGCCCTACCGGAAGATTGC	0.607																																																1	Substitution - Missense(1)	ovary(1)	7											69	59	62					7																	73944105		2203	4300	6503	73582041	SO:0001583	missense	9569			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1132C>T	7.37:g.73944105C>T	ENSP00000265755:p.Arg378Trp		73582041	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	c	19.69	3.873889	0.72180	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.46	-2.05	0.07321	.	0.000000	0.85682	D	0.000000	T	0.46927	0.1418	N	0.19112	0.55	0.52501	D	0.999952	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.993;0.957;0.996;0.974	T	0.52245	-0.8601	10	0.87932	D	0	-25.9307	17.2233	0.86963	0.259:0.7409:0.0:0.0	.	410;378;378;378	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	W	378;410;378;378	ENSP00000265755:R378W;ENSP00000397566:R410W;ENSP00000408477:R378W;ENSP00000418383:R378W	ENSP00000265755:R378W	R	+	1	2	GTF2IRD1	73582041	1.000000	0.71417	0.996000	0.52242	0.862000	0.49288	2.453000	0.44970	-0.142000	0.11354	-0.535000	0.04281	CGG		0.607	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		T	73944105	C	T	73944105	3	4	106	1	0	0	0	0	1	0	0	0	6889	643	23	1	1162	1	GTF2IRD1	7	73944105	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	18701617	73944105	85194558	75	27947										
ATP5J2	9551	hgsc.bcm.edu	37	chr7	99057763	99057763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gaagtcccgcatcaagatccAgcttggcagctcccccagtt	9	15	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:99057763A>G	ENST00000292475.3	-	2	274	c.85T>C	c.(85-87)Tgg>Cgg	p.W29R	PTCD1_ENST00000555673.1_Missense_Mutation_p.W23R|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.W23R|ATP5J2_ENST00000544611.1_Missense_Mutation_p.W23R|ATP5J2_ENST00000488775.1_Missense_Mutation_p.W23R|ATP5J2_ENST00000359832.4_Missense_Mutation_p.W29R|ATP5J2_ENST00000466753.1_Intron|ATP5J2_ENST00000449683.1_Missense_Mutation_p.W33R|ATP5J2-PTCD1_ENST00000437572.1_Intron|ATP5J2_ENST00000394186.3_Missense_Mutation_p.W23R	NM_004889.3	NP_004880.1	P56134	ATPK_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2	29					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|nucleus (GO:0005634)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	transmembrane transporter activity (GO:0022857)			large_intestine(1)|ovary(1)	2	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ATCAAGATCCAGCTTGGCAGC	0.473																																																0			7											171	186	181					7																	99057763		2203	4300	6503	98895699	SO:0001583	missense	0			AF047436	CCDS5665.1, CCDS34692.1, CCDS47653.1, CCDS47654.1	7q22.1	2012-10-12	2010-06-11		ENSG00000241468	ENSG00000241468		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	848	protein-coding gene	gene with protein product	"F1Fo-ATPase synthase f subunit", "ATP synthase f chain, mitochondrial", "F1Fo-ATP synthase complex Fo membrane domain f subunit"		"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, isoform 2", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2"			9653160	Standard	NM_004889		Approved	F1Fo-ATPase, ATP5JL		P56134	OTTHUMG00000154609	ENST00000292475.3:c.85T>C	7.37:g.99057763A>G	ENSP00000292475:p.Trp29Arg		98895699	C9J8H9|F8W7V3|O76079|Q6IBB3|Q96L83|Q9BTI8	Missense_Mutation	SNP	ENST00000292475.3	37	CCDS5665.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577641	0.86645	.	.	ENSG00000106246;ENSG00000248919;ENSG00000241468;ENSG00000241468;ENSG00000241468;ENSG00000241468;ENSG00000241468;ENSG00000241468	ENST00000555673;ENST00000413834;ENST00000449683;ENST00000359832;ENST00000292475;ENST00000544611;ENST00000488775;ENST00000394186	D;D;T;T	0.93366	-3.21;-3.21;2.74;2.74	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.95774	0.8625	M	0.62088	1.915	0.38185	D	0.939747	D;D;P;D;P	0.89917	1.0;1.0;0.928;0.958;0.91	D;D;P;D;P	0.91635	0.999;0.999;0.851;0.934;0.807	D	0.97011	0.9736	10	0.62326	D	0.03	.	14.5027	0.67732	1.0:0.0:0.0:0.0	.	23;29;23;29;23	G3V325;F8W7V3;C9J8H9;P56134;P56134-2	.;.;.;ATPK_HUMAN;.	R	23;23;33;29;29;23;23;23	ENSP00000450995:W23R;ENSP00000400168:W23R;ENSP00000407540:W33R;ENSP00000377740:W23R	ENSP00000292475:W29R	W	-	1	0	ATP5J2;ATP5J2-PTCD1;PTCD1	98895699	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.182000	0.89698	1.924000	0.55735	0.379000	0.24179	TGG		0.473	ATP5J2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336263.1	NM_004889		G	99057763	A	G	99057763	3	3	106	1	0	0	0	0	1	0	0	0	1160	188	7	4	240	4	ATP5J2	7	99057763	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	25113658	99057763	60080900	76	27948										
RINT1	60561	hgsc.bcm.edu	37	chr7	105207742	105207742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	taatttgaggacaaattggcCtaatactggaaaataatgtc	8	5	0	1	rs199604799		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:105207742C>T	ENST00000257700.2	+	15	2594	c.2363C>T	c.(2362-2364)cCt>cTt	p.P788L	EFCAB10_ENST00000460135.1_3'UTR|EFCAB10_ENST00000485614.1_Intron|EFCAB10_ENST00000490493.1_5'UTR|EFCAB10_ENST00000480514.1_Intron|EFCAB10_ENST00000486180.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	788	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.P788L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						ACAAATTGGCCTAATACTGGA	0.353													C|||	1	0.000199681	0	0.0014	5008	,	,		18357	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	central_nervous_system(1)	7											61	60	60					7																	105207742		2203	4300	6503	104994978	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.2363C>T	7.37:g.105207742C>T	ENSP00000257700:p.Pro788Leu		104994978	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	16.12	3.032742	0.54790	.	.	ENSG00000135249	ENST00000257700	T	0.24723	1.84	5.98	5.98	0.97165	.	0.047434	0.85682	D	0.000000	T	0.26340	0.0643	L	0.43152	1.355	0.80722	D	1	P	0.36199	0.543	B	0.34873	0.191	T	0.01532	-1.1331	10	0.23891	T	0.37	-25.759	20.452	0.99131	0.0:1.0:0.0:0.0	.	788	Q6NUQ1	RINT1_HUMAN	L	788	ENSP00000257700:P788L	ENSP00000257700:P788L	P	+	2	0	RINT1	104994978	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.891000	0.63185	2.838000	0.97847	0.591000	0.81541	CCT		0.353	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		T	105207742	C	T	105207742	3	4	106	1	0	0	0	0	1	0	0	0	13413	681	24	3	2421	3	RINT1	7	105207742	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	6149979	105207742	53930921	77	27949										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518303	113518303	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttacaaatattttctgatttCgtagaaataggttggctagc	8	5	1	2	rs150965727		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:113518303C>T	ENST00000284601.3	-	4	2912	c.2844G>A	c.(2842-2844)acG>acA	p.T948T		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	948					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.T948T(3)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTTCTGATTTCGTAGAAATAG	0.378																																																3	Substitution - coding silent(3)	skin(3)	7						C		0,4406		0,0,2203	86	86	86	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2844	-8.2	0	7	dbSNP_134	86	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PPP1R3A	NM_002711.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		948/1123	113518303	1,13003	2203	4299	6502	113305539	SO:0001819	synonymous_variant	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2844G>A	7.37:g.113518303C>T			113305539	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	37	CCDS5759.1																																																																																				0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113518303	C	T	113518303	2	4	106	1	0	0	0	0	0	0	0	1	12405	871	31	1		1	PPP1R3A	7	113518303	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	8310561	113518303	45620360	78	27950										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117375142	117375142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	catgaaagtaataacattcgGacagtccatttcctgaaaca	6	9	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:117375142G>A	ENST00000160373.3	-	16	3792	c.3701C>T	c.(3700-3702)tCc>tTc	p.S1234F		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1234					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ATAACATTCGGACAGTCCATT	0.448																																																0			7											48	52	50					7																	117375142		2203	4300	6503	117162378	SO:0001583	missense	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3701C>T	7.37:g.117375142G>A	ENSP00000160373:p.Ser1234Phe		117162378	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.235701	0.22626	.	.	ENSG00000077063	ENST00000160373	T	0.53206	0.63	5.52	5.52	0.82312	.	0.439524	0.27008	N	0.021393	T	0.56426	0.1984	M	0.82630	2.6	0.22240	N	0.999265	B	0.11235	0.004	B	0.12156	0.007	T	0.50533	-0.8817	10	0.45353	T	0.12	4.5035	19.8125	0.96553	0.0:0.0:1.0:0.0	.	1234	Q8WZ74	CTTB2_HUMAN	F	1234	ENSP00000160373:S1234F	ENSP00000160373:S1234F	S	-	2	0	CTTNBP2	117162378	0.965000	0.33210	0.015000	0.15790	0.056000	0.15407	5.058000	0.64300	2.745000	0.94114	0.655000	0.94253	TCC		0.448	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117375142	G	A	117375142	3	1	106	1	0	0	0	0	1	0	0	0	4051	1174	41	3	1322	3	CTTNBP2	7	117375142	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	3856839	117375142	41763521	79	27951										
AKR1B1	231	hgsc.bcm.edu	37	chr7	134127504	134127504	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aactcttcatggaaggggtaAtccttgtgggaggtacagct	13	7	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:134127504A>C	ENST00000285930.4	-	10	1006	c.927T>G	c.(925-927)gaT>gaG	p.D309E		NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	309					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	GGAAGGGGTAATCCTTGTGGG	0.438																																																0			7											114	112	113					7																	134127504		2203	4300	6503	133778044	SO:0001583	missense	231			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.927T>G	7.37:g.134127504A>C	ENSP00000285930:p.Asp309Glu		133778044	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Missense_Mutation	SNP	ENST00000285930.4	37	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	A	8.326	0.825328	0.16749	.	.	ENSG00000085662	ENST00000285930	T	0.10960	2.82	4.97	1.27	0.21489	NADP-dependent oxidoreductase domain (2);	0.180017	0.64402	D	0.000018	T	0.05456	0.0144	L	0.32530	0.975	0.44745	D	0.997745	B	0.13145	0.007	B	0.14578	0.011	T	0.37709	-0.9694	10	0.10636	T	0.68	.	1.082	0.01644	0.4328:0.1498:0.272:0.1454	.	309	P15121	ALDR_HUMAN	E	309	ENSP00000285930:D309E	ENSP00000285930:D309E	D	-	3	2	AKR1B1	133778044	0.677000	0.27577	0.998000	0.56505	0.755000	0.42902	-0.320000	0.08028	0.042000	0.15717	0.459000	0.35465	GAT		0.438	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		C	134127504	A	C	134127504	3	2	106	1	0	0	0	0	1	0	0	0	466	98	4	4	27	4	AKR1B1	7	134127504	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	16752362	134127504	25011159	80	27952										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135406185	135406185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aagaacgggtaaaggaaggcCggcaccagggctgcagctcc	15	11	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:135406185C>T	ENST00000354042.4	-	2	875	c.186G>A	c.(184-186)ccG>ccA	p.P62P		NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	62					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AAAGGAAGGCCGGCACCAGGG	0.617																																																0			7											52	44	46					7																	135406185		2203	4300	6503	135056725	SO:0001819	synonymous_variant	26266			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.186G>A	7.37:g.135406185C>T			135056725	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																				0.617	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		T	135406185	C	T	135406185	2	4	106	1	0	0	0	0	0	0	0	1	14431	639	23	1		1	SLC13A4	7	135406185	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	1278681	135406185	23732478	81	27953										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138768735	138768735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttgaacacggtggctgctggTtacaaatctgctgccgaccc	11	12	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:138768735T>C	ENST00000242351.5	-	3	804	c.488A>G	c.(487-489)aAc>aGc	p.N163S	ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.N163S|ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.N163S	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	163	N-terminal domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TGGCTGCTGGTTACAAATCTG	0.488																																																0			7											111	105	107					7																	138768735		2203	4300	6503	138419275	SO:0001583	missense	56829			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.488A>G	7.37:g.138768735T>C	ENSP00000242351:p.Asn163Ser		138419275	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.827354	0.00584	.	.	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652	T;T;T	0.37235	1.21;1.21;1.21	4.5	-7.66	0.01277	.	1.249470	0.05360	N	0.533559	T	0.18841	0.0452	N	0.05280	-0.08	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.25779	-1.0122	10	0.23302	T	0.38	.	17.3856	0.87415	0.0:0.7664:0.0:0.2336	.	163;163	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	S	163	ENSP00000242351:N163S;ENSP00000418385:N163S;ENSP00000419855:N163S	ENSP00000242351:N163S	N	-	2	0	ZC3HAV1	138419275	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.470000	0.00991	-1.689000	0.01434	-1.064000	0.02280	AAC		0.488	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		C	138768735	T	C	138768735	3	2	106	1	0	0	0	0	1	0	0	0	17614	1725	60	4	2268	4	ZC3HAV1	7	138768735	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	3362550	138768735	20369928	82	27954										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142575018	142575018	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctggttcacaacagcgatgtGcagtgcagtctgacctggcc	12	12	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:142575018G>C	ENST00000359396.3	-	4	609	c.364C>G	c.(364-366)Cac>Gac	p.H122D	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	122					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					ACAGCGATGTGCAGTGCAGTC	0.622																																																0			7											81	76	78					7																	142575018		2203	4300	6503	142285140	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.364C>G	7.37:g.142575018G>C	ENSP00000352358:p.His122Asp		142285140	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.216006	0.79352	.	.	ENSG00000165125	ENST00000359396;ENST00000431833	T;T	0.71222	-0.55;0.08	3.86	3.86	0.44501	Ankyrin repeat-containing domain (4);	0.122556	0.64402	D	0.000008	D	0.83931	0.5361	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87000	0.2116	10	0.87932	D	0	-27.9378	14.9814	0.71313	0.0:0.0:1.0:0.0	.	122	Q9H1D0	TRPV6_HUMAN	D	122;49	ENSP00000352358:H122D;ENSP00000415917:H49D	ENSP00000352358:H122D	H	-	1	0	TRPV6	142285140	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	9.084000	0.94076	1.995000	0.58328	0.655000	0.94253	CAC		0.622	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		C	142575018	G	C	142575018	3	2	106	1	0	0	0	0	1	0	0	0	16640	1319	46	5	1861	5	TRPV6	7	142575018	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	3806283	142575018	16563645	83	27955										
KRBA1	84626	hgsc.bcm.edu	37	chr7	149430494	149430494	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcggagaagctggatcggctCgccacagcgctggcaggcct	16	13	0	1	rs200788949		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:149430494C>T	ENST00000485033.2	+	15	2268	c.2268C>T	c.(2266-2268)ctC>ctT	p.L756L	KRBA1_ENST00000319551.8_Silent_p.L756L|KRBA1_ENST00000255992.10_Silent_p.L816L|KRBA1_ENST00000479560.1_3'UTR			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	817	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGGATCGGCTCGCCACAGCGC	0.692																																																0			7						C		2,4046		0,2,2022	8	11	10		2450	-9.8	0	7		10	3,8277		0,3,4137	yes	coding-synonymous	KRBA1	NM_032534.2		0,5,6159	TT,TC,CC		0.0362,0.0494,0.0406		817/1031	149430494	5,12323	2024	4140	6164	149061427	SO:0001819	synonymous_variant	84626			AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.2268C>T	7.37:g.149430494C>T			149061427	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37																																																																																					0.692	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534		T	149430494	C	T	149430494	2	4	106	1	0	0	0	0	0	0	0	1	8460	871	31	1		1	KRBA1	7	149430494	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	6855476	149430494	9708169	84	27956										
ABCB8	11194	hgsc.bcm.edu	37	chr7	150742298	150742298	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttccctcccatcttccaggcTgggacacatgaagagctcct	8	15	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:150742298T>C	ENST00000297504.6	+	17	2136	c.2070T>C	c.(2068-2070)gcT>gcC	p.A690A	ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000498578.1_Silent_p.A648A|ABCB8_ENST00000358849.4_Silent_p.A673A|ABCB8_ENST00000542328.1_Silent_p.A585A			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	690	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		A -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	TCTTCCAGGCTGGGACACATG	0.622																																																0			7											74	70	72					7																	150742298		2203	4300	6503	150373231	SO:0001819	synonymous_variant	11194			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.2070T>C	7.37:g.150742298T>C			150373231	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Silent	SNP	ENST00000297504.6	37																																																																																					0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		C	150742298	T	C	150742298	2	2	106	1	0	0	0	0	0	0	0	1	47	1567	55	4		4	ABCB8	7	150742298	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	1311804	150742298	8396365	85	27957										
MLL3	58508	hgsc.bcm.edu	37	chr7	151960154	151960155	+	Frame_Shift_Ins	INS	-	-	C													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ataactggttgaagacaaaaINSagtatgataccctttgtcac							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr7:151960154_151960155insC	ENST00000262189.6	-	9	1463_1464	c.1245_1246insG	c.(1243-1248)acttttfs	p.F416fs	KMT2C_ENST00000355193.2_Frame_Shift_Ins_p.F416fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	416					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGAAGACAAAAAGTATGATACC	0.312																																																0			7																																								151591088	SO:0001589	frameshift_variant	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1245_1246insG	7.37:g.151960154_151960155insC	ENSP00000262189:p.Phe416fs		151591087	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Ins	INS	ENST00000262189.6	37	CCDS5931.1																																																																																				0.312	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151960155	-	C	151960154	7	5	106	1	0	1	1	0	0	0	0	0	9652	14	1	0	13693	0	MLL3	7	151960154	Frame_Shift_Ins	INS	-	TCGA-DY-A1DF-01A-11D-A152-10	1217856	151960154	7178509	86	27958										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2091341	2091341	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcagatcgtggcaggttgatCggcggcttgcctgacgtggt	17	9	0	3	rs2280908	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:2091341C>T	ENST00000262113.4	+	36	4182	c.4041C>T	c.(4039-4041)atC>atT	p.I1347I	MYOM2_ENST00000520298.1_3'UTR|MYOM2_ENST00000523438.1_Silent_p.I772I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1347	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GCAGGTTGATCGGCGGCTTGC	0.597													T|||	56	0.0111821	0	0.0245	5008	,	,		16697	0.0357		0.003	False		,,,				2504	0															0			8						T		3,4403	825.9+/-416.6	0,3,2200	120	87	98		4041	-6.5	0	8	dbSNP_100	98	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	MYOM2	NM_003970.2		0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384		1347/1466	2091341	5,13001	2203	4300	6503	2078748	SO:0001819	synonymous_variant	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.4041C>T	8.37:g.2091341C>T			2078748	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																				0.597	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2091341	C	T	2091341	2	4	106	1	0	0	0	0	0	0	0	1	10122	874	31	1		1	MYOM2	8	2091341	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		2091341	144272681	87	27959										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3245155	3245155	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tctccaccgtggcgatggccGttcacagggatgcccgggtc	14	14	2	0	rs370427726		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:3245155G>A	ENST00000520002.1	-	19	3201	c.2646C>T	c.(2644-2646)aaC>aaT	p.N882N	CSMD1_ENST00000539096.1_Silent_p.N881N|CSMD1_ENST00000537824.1_Silent_p.N881N|CSMD1_ENST00000602723.1_Silent_p.N882N|CSMD1_ENST00000400186.3_Silent_p.N882N|CSMD1_ENST00000542608.1_Silent_p.N881N|CSMD1_ENST00000602557.1_Silent_p.N882N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	882	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				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)		GGCGATGGCCGTTCACAGGGA	0.562																																																0			8						G		0,4230		0,0,2115	36	43	41		2643	-9.7	0.1	8		41	1,8445		0,1,4222	no	coding-synonymous	CSMD1	NM_033225.5		0,1,6337	AA,AG,GG		0.0118,0.0,0.0079		881/3565	3245155	1,12675	2115	4223	6338	3232562	SO:0001819	synonymous_variant	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2646C>T	8.37:g.3245155G>A			3232562	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	7.732	0.699443	0.15106	0.0	1.18E-4	ENSG00000183117	ENST00000335551	.	.	.	5.11	-9.68	0.00528	.	.	.	.	.	T	0.58864	0.2152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69412	-0.5152	4	.	.	.	.	14.5795	0.68278	0.5168:0.0:0.4832:0.0	.	.	.	.	W	362	.	.	R	-	1	2	CSMD1	3232562	0.997000	0.39634	0.064000	0.19789	0.657000	0.38888	0.675000	0.25232	-2.273000	0.00681	-0.781000	0.03364	CGG		0.562	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3245155	G	A	3245155	2	1	106	1	0	0	0	0	0	0	0	1	3950	1136	40	1		1	CSMD1	8	3245155	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	1153814	3245155	143118867	88	27960										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67511374	67511374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctggcactgaaaatcagagcGattctgaaaaaatttagaag	9	6	2	4			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:67511374G>A	ENST00000522677.3	-	4	612	c.202C>T	c.(202-204)Cgc>Tgc	p.R68C	MYBL1_ENST00000517885.1_Missense_Mutation_p.R68C|MYBL1_ENST00000524176.2_Missense_Mutation_p.R68C	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	68	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			AAATCAGAGCGATTCTGAAAA	0.368																																																0			8											42	39	40					8																	67511374		1849	4128	5977	67673928	SO:0001583	missense	4603			X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.202C>T	8.37:g.67511374G>A	ENSP00000429633:p.Arg68Cys		67673928	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185098	0.78677	.	.	ENSG00000185697	ENST00000522677;ENST00000517885;ENST00000524176	T;T;T	0.44482	2.08;0.92;1.62	5.54	5.54	0.83059	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.80491	0.4633	H	0.98996	4.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.998	D	0.88507	0.3086	10	0.87932	D	0	-9.6936	19.4831	0.95018	0.0:0.0:1.0:0.0	.	68;68;68	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	C	68	ENSP00000429633:R68C;ENSP00000428265:R68C;ENSP00000428011:R68C	ENSP00000428265:R68C	R	-	1	0	MYBL1	67673928	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	3.314000	0.51943	2.606000	0.88127	0.650000	0.86243	CGC		0.368	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67511374	G	A	67511374	3	1	106	1	0	0	0	0	1	0	0	0	10039	1058	37	1	2108	1	MYBL1	8	67511374	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	64266219	67511374	78852648	89	27961										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848485	73848485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agttccaaaacgtgaggcgcGtggtccagatcttccgaatc	11	11	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:73848485G>A	ENST00000523207.1	+	3	1483	c.895G>A	c.(895-897)Gtg>Atg	p.V299M		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	299					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CGTGAGGCGCGTGGTCCAGAT	0.522																																																0			8											88	85	86					8																	73848485		2203	4300	6503	74011039	SO:0001583	missense	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.895G>A	8.37:g.73848485G>A	ENSP00000430846:p.Val299Met		74011039	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	G	34	5.296524	0.95574	.	.	ENSG00000182674	ENST00000523207	D	0.98807	-5.15	5.74	5.74	0.90152	Ion transport (1);	0.000000	0.41097	D	0.000947	D	0.98969	0.9649	M	0.62088	1.915	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99906	1.1180	10	0.87932	D	0	.	19.91	0.97023	0.0:0.0:1.0:0.0	.	299	Q92953	KCNB2_HUMAN	M	299	ENSP00000430846:V299M	ENSP00000430846:V299M	V	+	1	0	KCNB2	74011039	1.000000	0.71417	0.959000	0.39883	0.987000	0.75469	9.869000	0.99810	2.702000	0.92279	0.655000	0.94253	GTG		0.522	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73848485	G	A	73848485	3	1	106	1	0	0	0	0	1	0	0	0	8034	1145	40	1	901	1	KCNB2	8	73848485	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	6337111	73848485	72515537	90	27962										
RALYL	138046	hgsc.bcm.edu	37	chr8	85717027	85717027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttgaatcaaaggaacctttcCtgtctgttgggtaagtatat	9	6	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:85717027C>T	ENST00000521268.1	+	4	1460	c.355C>T	c.(355-357)Ctg>Ttg	p.L119L	RALYL_ENST00000517638.1_Silent_p.L132L|RALYL_ENST00000518566.1_Intron|RALYL_ENST00000521376.1_Silent_p.L46L|RALYL_ENST00000523850.1_Silent_p.L46L|RALYL_ENST00000521695.1_Silent_p.L119L|RALYL_ENST00000522455.1_Silent_p.L119L	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	119							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						GGAACCTTTCCTGTCTGTTGG	0.244																																																0			8											9	8	9					8																	85717027		872	1963	2835	85879582	SO:0001819	synonymous_variant	138046				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.355C>T	8.37:g.85717027C>T			85879582	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Silent	SNP	ENST00000521268.1	37	CCDS55253.1																																																																																				0.244	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			T	85717027	C	T	85717027	2	4	106	1	0	0	0	0	0	0	0	1	13057	680	24	3		3	RALYL	8	85717027	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	11868542	85717027	60646995	91	27963										
MMP16	4325	hgsc.bcm.edu	37	chr8	89053801	89053801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggaggcataaggccaagatgCagggaatgacaatagctatg	14	6	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:89053801C>T	ENST00000286614.6	-	10	1993	c.1712G>A	c.(1711-1713)tGc>tAc	p.C571Y		NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	571					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGCCAAGATGCAGGGAATGAC	0.458																																																0			8											290	227	249					8																	89053801		2203	4300	6503	89122917	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.1712G>A	8.37:g.89053801C>T	ENSP00000286614:p.Cys571Tyr		89122917	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.369521	0.82463	.	.	ENSG00000156103	ENST00000286614	T	0.36157	1.27	5.62	5.62	0.85841	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.59810	0.2221	M	0.68593	2.085	0.80722	D	1	D	0.60575	0.988	D	0.66196	0.942	T	0.59915	-0.7364	10	0.59425	D	0.04	.	19.6577	0.95849	0.0:1.0:0.0:0.0	.	571	P51512	MMP16_HUMAN	Y	571	ENSP00000286614:C571Y	ENSP00000286614:C571Y	C	-	2	0	MMP16	89122917	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.814000	0.86154	2.638000	0.89438	0.591000	0.81541	TGC		0.458	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		T	89053801	C	T	89053801	3	4	106	1	0	0	0	0	1	0	0	0	9685	710	25	3	115	3	MMP16	8	89053801	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	3336774	89053801	57310221	92	27964										
NBN	4683	hgsc.bcm.edu	37	chr8	90976653	90976653	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	attacctgtactgggatggcCctgaggatcacagtaattct	10	9	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:90976653C>A	ENST00000265433.3	-	8	1133	c.979G>T	c.(979-981)Ggc>Tgc	p.G327C	NBN_ENST00000409330.1_Missense_Mutation_p.G245C	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	327	Interaction with MTOR, MAPKAP1 and RICTOR.|Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			CTGGGATGGCCCTGAGGATCA	0.343								Homologous recombination																																								0			8											112	110	111					8																	90976653		2203	4300	6503	91045829	SO:0001583	missense	9048			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.979G>T	8.37:g.90976653C>A	ENSP00000265433:p.Gly327Cys		91045829	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.272615	0.23221	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387	T;T	0.58358	0.34;0.34	5.12	3.27	0.37495	.	0.899561	0.09902	N	0.740933	T	0.46870	0.1415	L	0.51422	1.61	0.09310	N	1	B;B	0.14805	0.011;0.011	B;B	0.17098	0.017;0.017	T	0.42413	-0.9453	10	0.59425	D	0.04	7.0E-4	8.0504	0.30575	0.0:0.747:0.1646:0.0884	.	327;327	A6H8Y5;O60934	.;NBN_HUMAN	C	327;245;327	ENSP00000265433:G327C;ENSP00000386924:G245C	ENSP00000265433:G327C	G	-	1	0	NBN	91045829	0.012000	0.17670	0.700000	0.30305	0.619000	0.37552	1.334000	0.33827	1.436000	0.47453	0.643000	0.83706	GGC		0.343	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		A	90976653	C	A	90976653	3	1	106	1	0	0	0	0	1	0	0	0	10221	623	22	2	1321	2	NBN	8	90976653	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	1922852	90976653	55387369	93	27965										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124267210	124267210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaaaccatatcttgatctgtTcctctgtatattttgcttga	5	8	3	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:124267210T>C	ENST00000522655.1	-	3	1517	c.977A>G	c.(976-978)gAa>gGa	p.E326G	ZHX1_ENST00000395571.3_Missense_Mutation_p.E326G|ZHX1_ENST00000297857.2_Missense_Mutation_p.E326G|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	326	Required for dimerization.|Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CTTGATCTGTTCCTCTGTATA	0.393																																																0			8											207	205	205					8																	124267210		2203	4300	6503	124336391	SO:0001583	missense	11244			AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.977A>G	8.37:g.124267210T>C	ENSP00000428821:p.Glu326Gly		124336391	Q8IWD8	Missense_Mutation	SNP	ENST00000522655.1	37	CCDS6342.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.99|16.99	3.273340|3.273340	0.59649|0.59649	.|.	.|.	ENSG00000165156|ENSG00000165156	ENST00000297857;ENST00000395571;ENST00000522655|ENST00000520474	D;D;D|.	0.96365|.	-3.99;-3.99;-3.99|.	5.8|5.8	4.63|4.63	0.57726|0.57726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.63721|0.63721	0.2535|0.2535	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.61080|.	0.989|.	P|.	0.59221|.	0.854|.	T|T	0.61073|0.61073	-0.7136|-0.7136	9|4	0.87932|.	D|.	0|.	-7.5121|-7.5121	12.2546|12.2546	0.54617|0.54617	0.1275:0.0:0.0:0.8725|0.1275:0.0:0.0:0.8725	.|.	326|.	Q9UKY1|.	ZHX1_HUMAN|.	G|D	326|11	ENSP00000297857:E326G;ENSP00000378938:E326G;ENSP00000428821:E326G|.	ENSP00000297857:E326G|.	E|N	-|-	2|1	0|0	ZHX1|ZHX1	124336391|124336391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.136000|6.136000	0.71703|0.71703	0.997000|0.997000	0.38969|0.38969	0.454000|0.454000	0.30748|0.30748	GAA|AAC		0.393	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			C	124267210	T	C	124267210	3	2	106	1	0	0	0	0	1	0	0	0	17714	1783	62	4	1648	4	ZHX1	8	124267210	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	33290557	124267210	22096812	94	27966										
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124818328	124818328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttctgtttgtagagttcactCgtgtcaatatgggtgttcat	10	6	4	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:124818328C>T	ENST00000334705.7	+	20	2137	c.1891C>T	c.(1891-1893)Cgt>Tgt	p.R631C	FAM91A1_ENST00000521166.1_Missense_Mutation_p.R631C	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	631										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			AGAGTTCACTCGTGTCAATAT	0.383																																																0			8											125	110	115					8																	124818328		1898	4141	6039	124887509	SO:0001583	missense	157769			AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.1891C>T	8.37:g.124818328C>T	ENSP00000335082:p.Arg631Cys		124887509	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	C	13.37	2.215463	0.39102	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	T;T	0.31769	1.48;1.48	5.65	5.65	0.86999	.	0.212494	0.51477	D	0.000085	T	0.28034	0.0691	N	0.22421	0.69	0.46798	D	0.999209	D;D	0.60160	0.987;0.987	B;P	0.47705	0.431;0.555	T	0.01375	-1.1371	10	0.39692	T	0.17	.	14.5508	0.68065	0.1463:0.8537:0.0:0.0	.	631;631	E7ER68;Q658Y4	.;F91A1_HUMAN	C	631	ENSP00000429491:R631C;ENSP00000335082:R631C	ENSP00000335082:R631C	R	+	1	0	FAM91A1	124887509	1.000000	0.71417	0.987000	0.45799	0.164000	0.22412	4.330000	0.59266	2.667000	0.90743	0.655000	0.94253	CGT		0.383	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		T	124818328	C	T	124818328	3	4	106	1	0	0	0	0	1	0	0	0	5670	884	31	1	1969	1	FAM91A1	8	124818328	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	551118	124818328	21545694	95	27967										
FLJ43860	389690	hgsc.bcm.edu	37	chr8	142505557	142505557	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gaaggggtcagcactgttcaTgtcctgcagcatcttgaagc	12	10	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr8:142505557T>C	ENST00000430863.1	-	0	369					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GCACTGTTCATGTCCTGCAGC	0.532																																																0			8											121	120	120					8																	142505557		2157	4262	6419	142574739			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142505557T>C			142574739		Missense_Mutation	SNP	ENST00000430863.1	37		.	.	.	.	.	.	.	.	.	.	T	2.896	-0.228657	0.06022	.	.	ENSG00000226807	ENST00000521161	.	.	.	4.47	1.32	0.21799	.	.	.	.	.	T	0.21718	0.0523	N	0.14661	0.345	.	.	.	B	0.09022	0.002	B	0.06405	0.002	T	0.19614	-1.0300	7	0.66056	D	0.02	.	2.0537	0.03576	0.1278:0.1429:0.4716:0.2578	.	97	Q6ZUA9	.	V	62	.	ENSP00000431031:M97V	M	-	1	0	AC100803.1	142574739	0.106000	0.21978	0.896000	0.35187	0.040000	0.13550	0.212000	0.17497	0.324000	0.23333	0.379000	0.24179	ATG		0.532	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		C	142505557	T	C	142505557	1	2	106	0	1	0	0	0	0	0	0	0	5949	1464	51	4		4	FLJ43860	8	142505557	RNA	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	17687229	142505557	3858465	96	27968										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32630932	32630932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caaacttcttattaactgggTgatgaaatggccaagaatct	8	7	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:32630932T>C	ENST00000242310.4	-	1	4735	c.4646A>G	c.(4645-4647)cAc>cGc	p.H1549R	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1549	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.		H -> Y (in a glioblastoma multiforme sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ATTAACTGGGTGATGAAATGG	0.398																																																0			9											125	118	120					9																	32630932		2203	4300	6503	32620932	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4646A>G	9.37:g.32630932T>C	ENSP00000418379:p.His1549Arg		32620932	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	14.09	2.432677	0.43224	.	.	ENSG00000122728	ENST00000242310	T	0.27402	1.67	0.489	0.489	0.16854	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	N	0.04508	-0.205	0.42291	D	0.992135	P	0.42337	0.776	B	0.40165	0.321	T	0.10917	-1.0609	10	0.27082	T	0.32	.	5.2121	0.15322	0.0:1.0E-4:0.0:0.9999	.	1549	Q8IZX4	TAF1L_HUMAN	R	1549	ENSP00000418379:H1549R	ENSP00000418379:H1549R	H	-	2	0	TAF1L	32620932	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	4.846000	0.62860	0.431000	0.26258	0.172000	0.16884	CAC		0.398	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			C	32630932	T	C	32630932	3	2	106	1	0	0	0	0	1	0	0	0	15562	1696	59	4	838	4	TAF1L	9	32630932	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10		32630932	108582499	97	27969										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34490391	34490391	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctgaaaaagtgactgaagaaGaattgatgactcctaagcag	10	6	0	7			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:34490391G>C	ENST00000242317.4	+	7	697	c.526G>C	c.(526-528)Gaa>Caa	p.E176Q	DNAI1_ENST00000488369.1_3'UTR	NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	176					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GACTGAAGAAGAATTGATGAC	0.498									Kartagener syndrome																																							0			9											158	169	165					9																	34490391		2203	4300	6503	34480391	SO:0001583	missense	27019	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.526G>C	9.37:g.34490391G>C	ENSP00000242317:p.Glu176Gln		34480391	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285146	0.59867	.	.	ENSG00000122735	ENST00000396929;ENST00000242317;ENST00000437363	T;T	0.75050	-0.9;-0.9	5.79	5.79	0.91817	.	0.166767	0.53938	D	0.000043	T	0.75391	0.3843	L	0.38531	1.155	0.80722	D	1	D	0.55172	0.97	P	0.53912	0.737	T	0.73871	-0.3846	10	0.38643	T	0.18	.	15.5341	0.75990	0.0:0.0:1.0:0.0	.	176	Q9UI46	DNAI1_HUMAN	Q	165;176;165	ENSP00000242317:E176Q;ENSP00000395396:E165Q	ENSP00000242317:E176Q	E	+	1	0	DNAI1	34480391	1.000000	0.71417	0.998000	0.56505	0.502000	0.33828	3.465000	0.53064	2.749000	0.94314	0.655000	0.94253	GAA		0.498	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			C	34490391	G	C	34490391	3	2	106	1	0	0	0	0	1	0	0	0	4620	943	33	5	552	5	DNAI1	9	34490391	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	1859459	34490391	106723040	98	27970										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73151436	73151436	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gaaaacataaagctatgagaTttcacaatgggagcctcttc	8	8	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:73151436T>C	ENST00000377110.3	-	25	4800	c.4557A>G	c.(4555-4557)aaA>aaG	p.K1519K	TRPM3_ENST00000360823.2_Silent_p.K1381K|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000377105.1_Silent_p.K1378K|TRPM3_ENST00000377106.1_Silent_p.K1391K|TRPM3_ENST00000423814.3_Silent_p.K1546K|TRPM3_ENST00000408909.2_Silent_p.K1378K|TRPM3_ENST00000396292.4_Silent_p.K1391K|TRPM3_ENST00000358082.3_Silent_p.K1381K|TRPM3_ENST00000357533.2_Silent_p.K1523K|TRPM3_ENST00000396285.1_Silent_p.K1378K|TRPM3_ENST00000396280.5_Silent_p.K1368K			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1544					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AGCTATGAGATTTCACAATGG	0.463																																																0			9											102	110	107					9																	73151436		2203	4300	6503	72341256	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4557A>G	9.37:g.73151436T>C			72341256	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377110.3	37	CCDS43835.1	.	.	.	.	.	.	.	.	.	.	T	3.206	-0.162751	0.06502	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.9	-1.14	0.09741	.	.	.	.	.	T	0.57829	0.2080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52909	-0.8512	4	.	.	.	-23.5125	11.3931	0.49825	0.0:0.5004:0.0:0.4996	.	.	.	.	V	1368	.	.	I	-	1	0	TRPM3	72341256	0.752000	0.28338	0.593000	0.28771	0.934000	0.57294	-0.181000	0.09740	-0.440000	0.07211	0.533000	0.62120	ATC		0.463	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		C	73151436	T	C	73151436	2	2	106	1	0	0	0	0	0	0	0	1	16627	1490	52	4		4	TRPM3	9	73151436	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	38661045	73151436	68061995	99	27971										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90312050	90312050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtctagaagagccctatgagAtccagctgaaccaagtgatt	10	9	1	5			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:90312050A>G	ENST00000408954.3	+	22	2877	c.2542A>G	c.(2542-2544)Atc>Gtc	p.I848V	DAPK1_ENST00000358077.5_Missense_Mutation_p.I848V|DAPK1_ENST00000491893.1_Intron|DAPK1_ENST00000472284.1_Missense_Mutation_p.I848V|DAPK1_ENST00000469640.2_Missense_Mutation_p.I848V	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	848					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GCCCTATGAGATCCAGCTGAA	0.458									Chronic Lymphocytic Leukemia, Familial Clustering of																																							0			9											174	164	167					9																	90312050		1904	4133	6037	89501870	SO:0001583	missense	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2542A>G	9.37:g.90312050A>G	ENSP00000386135:p.Ile848Val		89501870	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	A	9.624	1.134582	0.21123	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	5.65	5.65	0.86999	.	0.000000	0.52532	D	0.000067	T	0.08626	0.0214	N	0.16903	0.455	0.45979	D	0.998794	B	0.18461	0.028	B	0.16722	0.016	T	0.08411	-1.0723	10	0.05721	T	0.95	.	15.7104	0.77623	1.0:0.0:0.0:0.0	.	848	P53355	DAPK1_HUMAN	V	848	ENSP00000350785:I848V;ENSP00000417076:I848V;ENSP00000418885:I848V;ENSP00000386135:I848V	ENSP00000350785:I848V	I	+	1	0	DAPK1	89501870	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.069000	0.93967	2.371000	0.80710	0.533000	0.62120	ATC		0.458	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		G	90312050	A	G	90312050	3	3	106	1	0	0	0	0	1	0	0	0	4241	333	12	4	2624	4	DAPK1	9	90312050	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	17160614	90312050	50901381	100	27972										
ZNF169	169841	hgsc.bcm.edu	37	chr9	97062462	97062462	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgaagggagcagacacttcaGaatctggagcagtcatacgt	12	8	3	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:97062462G>C	ENST00000395395.2	+	5	712	c.622G>C	c.(622-624)Gaa>Caa	p.E208Q	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				AGACACTTCAGAATCTGGAGC	0.512																																																0			9											61	56	58					9																	97062462		2203	4300	6503	96102283	SO:0001583	missense	169841			U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"Zinc fingers, C2H2-type", "-"	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.622G>C	9.37:g.97062462G>C	ENSP00000378792:p.Glu208Gln		96102283	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	.	.	.	.	.	.	.	.	.	.	G	6.539	0.467671	0.12402	.	.	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.06933	3.24	2.44	1.35	0.21983	.	.	.	.	.	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	P	0.37955	0.612	B	0.33042	0.157	T	0.40979	-0.9534	9	0.22706	T	0.39	.	4.005	0.09597	0.2713:0.0:0.7287:0.0	.	208	Q14929	ZN169_HUMAN	Q	208;17	ENSP00000378792:E208Q	ENSP00000340711:E17Q	E	+	1	0	ZNF169	96102283	0.000000	0.05858	0.108000	0.21378	0.622000	0.37654	0.329000	0.19698	0.449000	0.26747	0.505000	0.49811	GAA		0.512	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		C	97062462	G	C	97062462	3	2	106	1	0	0	0	0	1	0	0	0	17781	943	33	5	636	5	ZNF169	9	97062462	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	6750412	97062462	44150969	101	27973										
ROD1	9991	hgsc.bcm.edu	37	chr9	115060128	115060128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcaccatacacacctgtagaAggagtagaactattcatggt	8	9	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:115060128A>G	ENST00000374255.2	-	3	258	c.111T>C	c.(109-111)ccT>ccC	p.P37P	PTBP3_ENST00000374257.1_Silent_p.P6P|PTBP3_ENST00000487997.1_Intron|PTBP3_ENST00000334318.6_Silent_p.P37P|PTBP3_ENST00000343327.2_5'UTR|PTBP3_ENST00000458258.1_Silent_p.P43P			O95758	PTBP3_HUMAN	polypyrimidine tract binding protein 3	37					anatomical structure morphogenesis (GO:0009653)|erythrocyte maturation (GO:0043249)|mRNA processing (GO:0006397)|negative regulation of RNA splicing (GO:0033119)|regulation of cell differentiation (GO:0045595)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										CACCTGTAGAAGGAGTAGAAC	0.318																																																0			9											95	99	98					9																	115060128		2203	4300	6503	114099949	SO:0001819	synonymous_variant	9991			AB023967	CCDS6784.1, CCDS55332.1, CCDS55333.1, CCDS59140.1, CCDS59141.1	9q32	2013-07-16	2011-11-16	2011-11-16	ENSG00000119314	ENSG00000119314		"RNA binding motif (RRM) containing"	10253	protein-coding gene	gene with protein product		607527	"regulator of differentiation (in S. pombe) 1", "ROD1 regulator of differentiation 1 (S. pombe)"	ROD1		10207106	Standard	NM_005156		Approved	DKFZp781I1117	uc004bfx.3	O95758	OTTHUMG00000020503	ENST00000374255.2:c.111T>C	9.37:g.115060128A>G			114099949	B1ALY2|B1ALY3|B1ALY5|B1ALY6|B3KME7|Q68DB9|Q86YB3|Q86YH9	Silent	SNP	ENST00000374255.2	37	CCDS6784.1																																																																																				0.318	PTBP3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053679.1			G	115060128	A	G	115060128	2	3	106	1	0	0	0	0	0	0	0	1	13556	59	3	4		4	ROD1	9	115060128	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	17997666	115060128	26153303	102	27974										
OR1L1	26737	hgsc.bcm.edu	37	chr9	125424242	125424242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cattatccctaagatgctggTgaacttcttatcagagacaa	7	9	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr9:125424242T>C	ENST00000373686.1	+	1	398	c.398T>C	c.(397-399)gTg>gCg	p.V133A	OR1L1_ENST00000309623.1_Missense_Mutation_p.V83A			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						AAGATGCTGGTGAACTTCTTA	0.438																																																0			9											192	187	188					9																	125424242		2203	4300	6503	124464063	SO:0001583	missense	26737				CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"GPCR / Class A : Olfactory receptors"	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.398T>C	9.37:g.125424242T>C	ENSP00000362790:p.Val133Ala		124464063	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		.	.	.	.	.	.	.	.	.	.	T	0.989	-0.694754	0.03303	.	.	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.01947	4.54;4.54	3.11	-4.62	0.03370	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01156	0.0038	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.48490	-0.9031	9	0.17832	T	0.49	.	5.8432	0.18645	0.2819:0.4891:0.0:0.229	.	133	Q8NH94	OR1L1_HUMAN	A	133;83	ENSP00000362790:V133A;ENSP00000310773:V83A	ENSP00000310773:V83A	V	+	2	0	OR1L1	124464063	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.624000	0.02038	-1.263000	0.02455	-0.736000	0.03550	GTG		0.438	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				C	125424242	T	C	125424242	3	2	106	1	0	0	0	0	1	0	0	0	10994	1696	59	4	250	4	OR1L1	9	125424242	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	10364114	125424242	15789189	103	27975										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3207667	3207667	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaatacaccgagaggagattCtgaaagtccttgggattttg	11	6	1	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:3207667C>G	ENST00000224949.4	-	5	505	c.471G>C	c.(469-471)caG>caC	p.Q157H	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q157H|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q125H			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	157					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AGAGGAGATTCTGAAAGTCCT	0.363																																																0			10											100	102	102					10																	3207667		1837	4084	5921	3197667	SO:0001583	missense	10531			AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.471G>C	10.37:g.3207667C>G	ENSP00000224949:p.Gln157His		3197667	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	c	14.51	2.557344	0.45590	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.18016	2.24;2.24;2.24	5.37	3.47	0.39725	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.159849	0.56097	D	0.000025	T	0.12518	0.0304	N	0.21142	0.635	0.37109	D	0.900277	B;B;B;B;B;B	0.21381	0.028;0.017;0.026;0.032;0.032;0.055	B;B;B;B;B;B	0.28305	0.015;0.057;0.034;0.088;0.088;0.088	T	0.11131	-1.0600	10	0.49607	T	0.09	.	9.955	0.41661	0.0:0.7843:0.0:0.2157	.	150;125;157;157;157;150	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	H	157;150;157;125	ENSP00000224949:Q157H;ENSP00000370377:Q157H;ENSP00000401201:Q125H	ENSP00000224949:Q157H	Q	-	3	2	PITRM1	3197667	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.339000	0.43965	1.235000	0.43724	0.586000	0.80456	CAG		0.363	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			G	3207667	C	G	3207667	3	3	106	1	0	0	0	0	1	0	0	0	11984	912	32	5	2734	5	PITRM1	10	3207667	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		3207667	132327080	104	27976										
GRID1	2894	hgsc.bcm.edu	37	chr10	87487712	87487712	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaatctcatatttaaagcccAgagccttggccagtgcatcc	7	12	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:87487712A>T	ENST00000327946.7	-	10	1518	c.1433T>A	c.(1432-1434)cTg>cAg	p.L478Q	GRID1_ENST00000536331.1_Missense_Mutation_p.L49Q	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	478					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						TTTAAAGCCCAGAGCCTTGGC	0.537										Multiple Myeloma(13;0.14)																																						0			10											174	167	169					10																	87487712		2203	4300	6503	87477692	SO:0001583	missense	2894			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1433T>A	10.37:g.87487712A>T	ENSP00000330148:p.Leu478Gln		87477692	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.645409	0.87859	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.41400	1.0;1.0	5.7	5.7	0.88788	Extracellular solute-binding protein, family 3 (1);Glutamate receptor, L-glutamate/glycine-binding (1);Ionotropic glutamate receptor (1);	0.067535	0.64402	D	0.000009	T	0.61350	0.2340	M	0.77406	2.37	0.80722	D	1	D	0.57257	0.979	P	0.57468	0.821	T	0.66956	-0.5792	10	0.87932	D	0	.	15.1306	0.72520	1.0:0.0:0.0:0.0	.	478	Q9ULK0	GRID1_HUMAN	Q	478;49	ENSP00000330148:L478Q;ENSP00000444455:L49Q	ENSP00000330148:L478Q	L	-	2	0	GRID1	87477692	1.000000	0.71417	0.988000	0.46212	0.993000	0.82548	9.323000	0.96364	2.170000	0.68504	0.491000	0.48974	CTG		0.537	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		T	87487712	A	T	87487712	3	4	106	1	0	0	0	0	1	0	0	0	6792	188	7	5	1624	5	GRID1	10	87487712	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	84280045	87487712	48047035	105	27977										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624300	89624300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggatggattcgacttagactTgacctgtatccatttctgcg	10	9	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:89624300T>C	ENST00000371953.3	+	1	1431	c.74T>C	c.(73-75)tTg>tCg	p.L25S	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	25	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.D24_L25del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GACTTAGACTTGACCTGTATC	0.458		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	51	Whole gene deletion(37)|Unknown(13)|Deletion - In frame(1)	prostate(14)|central_nervous_system(10)|skin(7)|lung(6)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											163	155	158					10																	89624300		2203	4300	6503	89614280	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.74T>C	10.37:g.89624300T>C	ENSP00000361021:p.Leu25Ser		89614280	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.510116	0.85282	.	.	ENSG00000171862	ENST00000371953	D	0.98792	-5.14	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.164389	0.41605	D	0.000848	D	0.98346	0.9451	M	0.90870	3.155	0.80722	D	1	P	0.47191	0.891	B	0.41412	0.356	D	0.98638	1.0674	9	.	.	.	-0.0822	14.1807	0.65572	0.0:0.0:0.0:1.0	.	25	P60484	PTEN_HUMAN	S	25	ENSP00000361021:L25S	.	L	+	2	0	PTEN	89614280	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.216000	0.77974	1.996000	0.58369	0.459000	0.35465	TTG		0.458	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89624300	T	C	89624300	3	2	106	1	0	0	0	0	1	0	0	0	12772	1821	63	4	76	4	PTEN	10	89624300	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	2136588	89624300	45910447	106	27978										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91497203	91497203	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agaaaagtgaagaagtgcgaCcgaacattgcagaaattgaa	11	5	0	5			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:91497203C>G	ENST00000371728.3	+	20	2670	c.2605C>G	c.(2605-2607)Ccg>Gcg	p.P869A	KIF20B_ENST00000260753.4_Missense_Mutation_p.P829A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000416354.1_Missense_Mutation_p.P899A|KIF20B_ENST00000394289.2_Missense_Mutation_p.P869A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	869					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AGAAGTGCGACCGAACATTGC	0.318																																																0			10											48	55	53					10																	91497203		2202	4293	6495	91487183	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.2605C>G	10.37:g.91497203C>G	ENSP00000360793:p.Pro869Ala		91487183	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	C	0.072	-1.201267	0.01581	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.65364	-0.1;-0.15;-0.14;-0.07	5.5	-1.57	0.08506	.	1.011510	0.07941	N	0.979309	T	0.33089	0.0851	N	0.03608	-0.345	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.09377	0.004;0.004	T	0.20207	-1.0282	10	0.11485	T	0.65	6.2784	9.0622	0.36442	0.1105:0.2886:0.5362:0.0646	.	869;829	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	A	829;899;869;869	ENSP00000260753:P829A;ENSP00000411545:P899A;ENSP00000377830:P869A;ENSP00000360793:P869A	ENSP00000260753:P829A	P	+	1	0	KIF20B	91487183	0.000000	0.05858	0.005000	0.12908	0.282000	0.26991	-0.954000	0.03873	-0.620000	0.05641	0.591000	0.81541	CCG		0.318	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91497203	C	G	91497203	3	3	106	1	0	0	0	0	1	0	0	0	8308	507	18	5	2559	5	KIF20B	10	91497203	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	1872903	91497203	44037544	107	27979										
IDE	3416	hgsc.bcm.edu	37	chr10	94234621	94234621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccagagcttcttttaactcaTctttagtccaggccacttca	5	13	4	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:94234621T>C	ENST00000265986.6	-	17	2149	c.2093A>G	c.(2092-2094)gAt>gGt	p.D698G	IDE_ENST00000371581.5_Missense_Mutation_p.D143G|IDE_ENST00000496903.1_5'UTR	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	698					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.D698A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TTTTAACTCATCTTTAGTCCA	0.393																																																1	Substitution - Missense(1)	ovary(1)	10											93	92	93					10																	94234621		2203	4300	6503	94224601	SO:0001583	missense	3416			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2093A>G	10.37:g.94234621T>C	ENSP00000265986:p.Asp698Gly		94224601	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.326565	0.60743	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.31769	1.48;1.48	5.65	5.65	0.86999	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.174186	0.49305	D	0.000153	T	0.36441	0.0967	M	0.70275	2.135	0.58432	D	0.999999	B;B	0.29571	0.249;0.154	B;B	0.33254	0.095;0.16	T	0.13176	-1.0519	10	0.30078	T	0.28	-11.9137	14.109	0.65111	0.0:0.0:0.0:1.0	.	698;143	P14735;B3KSB8	IDE_HUMAN;.	G	698;143	ENSP00000265986:D698G;ENSP00000360637:D143G	ENSP00000265986:D698G	D	-	2	0	IDE	94224601	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.936000	0.87665	2.154000	0.67381	0.477000	0.44152	GAT		0.393	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94234621	T	C	94234621	3	2	106	1	0	0	0	0	1	0	0	0	7514	1435	50	4	1002	4	IDE	10	94234621	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	2737418	94234621	41300126	108	27980										
CC2D2B	387707	hgsc.bcm.edu	37	chr10	97791678	97791678	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gctgaatttccccagacagaAtttgctttagctgtatacat	7	9	0	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:97791678A>G	ENST00000344386.3	+	9	1046	c.882A>G	c.(880-882)gaA>gaG	p.E294E	ENTPD1-AS1_ENST00000458228.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|CC2D2B_ENST00000410012.2_Silent_p.E373E|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|RP11-690P14.4_ENST00000475252.2_3'UTR|CC2D2B_ENST00000371198.2_3'UTR	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	294								p.E294D(1)		large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		CCCAGACAGAATTTGCTTTAG	0.393																																																1	Substitution - Missense(1)	ovary(1)	10											155	138	143					10																	97791678		1849	4101	5950	97781668	SO:0001819	synonymous_variant	387707			BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 130"	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.882A>G	10.37:g.97791678A>G			97781668	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Silent	SNP	ENST00000344386.3	37	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.788037	0.31593	.	.	ENSG00000188649	ENST00000410012	.	.	.	6.04	1.25	0.21368	.	.	.	.	.	T	0.69531	0.3121	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69213	-0.5204	5	0.87932	D	0	.	10.7126	0.45993	0.6877:0.0:0.3123:0.0	.	.	.	.	S	374	.	ENSP00000386988:N374S	N	+	2	0	CC2D2B	97781668	1.000000	0.71417	0.998000	0.56505	0.117000	0.20001	2.138000	0.42140	-0.039000	0.13602	-2.026000	0.00426	AAT		0.393	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		G	97791678	A	G	97791678	2	3	106	1	0	0	0	0	0	0	0	1	2735	98	4	4		4	CC2D2B	10	97791678	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	3557057	97791678	37743069	109	27981										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98773528	98773528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccggggtgcccacacactggGcctcgtgttgacatgggttc	14	13	0	1	rs371409196		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr10:98773528G>A	ENST00000266058.4	-	30	3418	c.3173C>T	c.(3172-3174)gCc>gTc	p.A1058V	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.A1058V	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1058	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CACACACTGGGCCTCGTGTTG	0.622																																																0			10						G	VAL/ALA	1,3871		0,1,1935	59	46	50		3173	3.3	0.6	10		50	0,7234		0,0,3617	no	missense	SLIT1	NM_003061.2	64	0,1,5552	AA,AG,GG		0.0,0.0258,0.0090	benign	1058/1535	98773528	1,11105	1936	3617	5553	98763518	SO:0001583	missense	6586			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3173C>T	10.37:g.98773528G>A	ENSP00000266058:p.Ala1058Val		98763518	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355746	0.61293	2.58E-4	0.0	ENSG00000187122	ENST00000266058;ENST00000371070	D;D	0.94376	-3.41;-3.41	4.28	3.35	0.38373	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.053925	0.85682	D	0.000000	D	0.91573	0.7338	M	0.64260	1.97	0.80722	D	1	P	0.39717	0.684	B	0.38378	0.272	D	0.91334	0.5092	10	0.87932	D	0	.	14.0485	0.64719	0.0:0.1525:0.8475:0.0	.	1058	O75093	SLIT1_HUMAN	V	1058	ENSP00000266058:A1058V;ENSP00000360109:A1058V	ENSP00000266058:A1058V	A	-	2	0	SLIT1	98763518	1.000000	0.71417	0.565000	0.28409	0.700000	0.40528	6.769000	0.74985	0.982000	0.38575	0.561000	0.74099	GCC		0.622	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98773528	G	A	98773528	3	1	106	1	0	0	0	0	1	0	0	0	14776	1203	42	3	1463	3	SLIT1	10	98773528	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	981850	98773528	36761219	110	27982										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1269544	1269544	+	Frame_Shift_Del	DEL	A	A	-													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cctggacccgcctatcacagAccaccacacccacggccacc							TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:1269544delA	ENST00000529681.1	+	31	11492	c.11434delA	c.(11434-11436)accfs	p.T3814fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.T3817fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3814	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CCTATCACAGACCACCACACC	0.627																																																0			11								10,3416		0,10,1703	33	42	39			0.1	0	11		39	50,7272		3,44,3614	no	frameshift	MUC5B	NM_002458.2		3,54,5317	A1A1,A1R,RR		0.6829,0.2919,0.5582			1269544	60,10688	1903	4065	5968	1226120	SO:0001589	frameshift_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.11434delA	11.37:g.1269544delA	ENSP00000436812:p.Thr3814fs		1226120	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	37	CCDS44515.2																																																																																				0.627	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1269544	A	-	1269544	7	5	106	1	0	1	0	1	0	0	0	0	10009	275	10	0	11565	0	MUC5B	11	1269544	Frame_Shift_Del	DEL	A	TCGA-DY-A1DF-01A-11D-A152-10		1269544	133736972	111	27983										
SBF2	81846	hgsc.bcm.edu	37	chr11	9983537	9983537	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttcatcatccttattatgtaGtcaaactgttgatggtctaa	6	7	4	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:9983537G>C	ENST00000256190.8	-	16	1964	c.1827C>G	c.(1825-1827)gaC>gaG	p.D609E		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	609					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TTATTATGTAGTCAAACTGTT	0.358																																																0			11											140	120	126					11																	9983537		2201	4294	6495	9940113	SO:0001583	missense	81846			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.1827C>G	11.37:g.9983537G>C	ENSP00000256190:p.Asp609Glu		9940113	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.44|15.44	2.834833|2.834833	0.50951|0.50951	.|.	.|.	ENSG00000133812|ENSG00000133812	ENST00000256190|ENST00000420722	T|.	0.65178|.	-0.14|.	5.56|5.56	3.68|3.68	0.42216|0.42216	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.65626|0.65626	0.2709|0.2709	M|M	0.70275|0.70275	2.135|2.135	0.52099|0.52099	D|D	0.999944|0.999944	D;P|.	0.89917|.	1.0;0.938|.	D;P|.	0.91635|.	0.999;0.874|.	T|T	0.65261|0.65261	-0.6211|-0.6211	10|5	0.31617|.	T|.	0.26|.	.|.	10.6448|10.6448	0.45613|0.45613	0.2075:0.0:0.7925:0.0|0.2075:0.0:0.7925:0.0	.|.	609;609|.	Q86WG5-3;Q86WG5|.	.;MTMRD_HUMAN|.	E|V	609|216	ENSP00000256190:D609E|.	ENSP00000256190:D609E|.	D|L	-|-	3|1	2|2	SBF2|SBF2	9940113|9940113	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.903000|1.903000	0.39858|0.39858	1.338000|1.338000	0.45544|0.45544	0.557000|0.557000	0.71058|0.71058	GAC|CTA		0.358	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		C	9983537	G	C	9983537	3	2	106	1	0	0	0	0	1	0	0	0	13896	1020	36	5	3822	5	SBF2	11	9983537	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	8713993	9983537	125022979	112	27984										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17417398	17417398	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggtgcccgccttacaactcaCcttcgaacgtgtccaccatg	8	16	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:17417398C>T	ENST00000389817.3	-	34	4267		c.e34+1		ABCC8_ENST00000302539.4_Splice_Site			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8						carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TTACAACTCACCTTCGAACGT	0.617																																																0			11											45	39	41					11																	17417398		2193	4283	6476	17373974	SO:0001630	splice_region_variant	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4198+1G>A	11.37:g.17417398C>T			17373974	A6NMX8|E3UYX6|O75948|Q16583	Splice_Site	SNP	ENST00000389817.3	37	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542131	0.65198	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4271	0.90612	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCC8	17373974	1.000000	0.71417	0.998000	0.56505	0.635000	0.38103	7.818000	0.86416	2.368000	0.80403	0.484000	0.47621	.		0.617	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	Intron	T	17417398	C	T	17417398	5	4	106	1	0	0	0	0	0	0	1	0	58	521	18	3	570	3	ABCC8	11	17417398	Splice_Site	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	7433861	17417398	117589118	113	27985										
FOLH1	2346	hgsc.bcm.edu	37	chr11	49221878	49221878	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgggtaggacaacaggacatCataatgtgctagctcaacag	11	8	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:49221878C>A	ENST00000256999.2	-	3	600	c.340G>T	c.(340-342)Gat>Tat	p.D114Y	FOLH1_ENST00000340334.7_Missense_Mutation_p.D99Y|FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000533034.1_Missense_Mutation_p.D99Y|FOLH1_ENST00000356696.3_Missense_Mutation_p.D114Y	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	114					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	AACAGGACATCATAATGTGCT	0.343																																																0			11											68	67	68					11																	49221878		2199	4298	6497	49178454	SO:0001583	missense	2346			M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"glutamate carboxylase II", "glutamate carboxypeptidase II"	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.340G>T	11.37:g.49221878C>A	ENSP00000256999:p.Asp114Tyr		49178454	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.849409	0.71603	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724;ENST00000529117	T;T;T;T;T	0.41065	1.08;1.11;1.01;1.03;1.04	4.79	4.79	0.61399	.	0.000000	0.56097	D	0.000031	T	0.67221	0.2870	M	0.83483	2.645	0.80722	D	1	D;D;D;D;B	0.89917	1.0;1.0;0.963;0.999;0.379	D;D;P;D;B	0.87578	0.994;0.998;0.519;0.972;0.111	T	0.72811	-0.4180	10	0.87932	D	0	.	15.3664	0.74526	0.0:1.0:0.0:0.0	.	99;99;99;114;114	Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609	.;.;.;.;FOLH1_HUMAN	Y	114;114;99;99;114;57	ENSP00000256999:D114Y;ENSP00000349129:D114Y;ENSP00000344131:D99Y;ENSP00000431463:D99Y;ENSP00000431577:D57Y	ENSP00000256999:D114Y	D	-	1	0	FOLH1	49178454	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	5.176000	0.65026	2.501000	0.84356	0.514000	0.50259	GAT		0.343	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		A	49221878	C	A	49221878	3	1	106	1	0	0	0	0	1	0	0	0	5998	826	29	2	1980	2	FOLH1	11	49221878	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	31804480	49221878	85784638	114	27986										
OR4C12	283093	hgsc.bcm.edu	37	chr11	50003839	50003839	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agaagaataaactgtgtctaTcaaagaaaggtgggtcagga	12	4	3	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:50003839T>C	ENST00000335238.4	-	1	232	c.199A>G	c.(199-201)Ata>Gta	p.I67V		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						ACTGTGTCTATCAAAGAAAGG	0.438																																																0			11											63	66	65					11																	50003839		2201	4296	6497	49960415	SO:0001583	missense	283093			BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"GPCR / Class A : Olfactory receptors"	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.199A>G	11.37:g.50003839T>C	ENSP00000334418:p.Ile67Val		49960415	B2RNF0|Q6IF49	Missense_Mutation	SNP	ENST00000335238.4	37	CCDS31496.1	.	.	.	.	.	.	.	.	.	.	.	11.08	1.534626	0.27475	.	.	ENSG00000221954	ENST00000335238	T	0.03035	4.07	3.31	3.31	0.37934	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	U	0.000240	T	0.02418	0.0074	N	0.13140	0.3	0.24800	N	0.992708	B	0.22346	0.068	B	0.27608	0.081	T	0.47262	-0.9131	10	0.10377	T	0.69	.	10.0552	0.42241	0.0:0.0:0.0:1.0	.	67	Q96R67	OR4CC_HUMAN	V	67	ENSP00000334418:I67V	ENSP00000334418:I67V	I	-	1	0	OR4C12	49960415	0.000000	0.05858	0.420000	0.26596	0.982000	0.71751	-0.202000	0.09451	1.528000	0.49103	0.325000	0.21440	ATA		0.438	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1	NM_001005270		C	50003839	T	C	50003839	3	2	106	1	0	0	0	0	1	0	0	0	11077	1435	50	4	734	4	OR4C12	11	50003839	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	781961	50003839	85002677	115	27987										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418785	55418785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	attatatgaccatcatgaacCgggagacatgcaataaaatg	8	7	1	3	rs148733636		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:55418785C>T	ENST00000312422.2	+	1	406	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R136W(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				CATCATGAACCGGGAGACATG	0.433																																																1	Substitution - Missense(1)	ovary(1)	11						C	TRP/ARG	1,4363		0,1,2181	197	166	177		406	-1.1	0	11	dbSNP_134	177	1,8077		0,1,4038	no	missense	OR4S2	NM_001004059.2	101	0,2,6219	TT,TC,CC		0.0124,0.0229,0.0161	benign	136/312	55418785	2,12440	2182	4039	6221	55175361	SO:0001583	missense	219431			BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.406C>T	11.37:g.55418785C>T	ENSP00000310337:p.Arg136Trp		55175361	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	C	4.357	0.065803	0.08388	2.29E-4	1.24E-4	ENSG00000174982	ENST00000312422	T	0.00949	5.51	5.09	-1.09	0.09904	GPCR, rhodopsin-like superfamily (1);	0.270733	0.25205	N	0.032358	T	0.00998	0.0033	L	0.50333	1.59	0.09310	N	1	B	0.14805	0.011	B	0.09377	0.004	T	0.44757	-0.9307	10	0.44086	T	0.13	.	5.7679	0.18237	0.5214:0.3235:0.0:0.1551	.	136	Q8NH73	OR4S2_HUMAN	W	136	ENSP00000310337:R136W	ENSP00000310337:R136W	R	+	1	2	OR4S2	55175361	0.000000	0.05858	0.001000	0.08648	0.162000	0.22319	-2.203000	0.01234	0.129000	0.18514	0.542000	0.68232	CGG		0.433	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55418785	C	T	55418785	3	4	106	1	0	0	0	0	1	0	0	0	11114	643	23	1	408	1	OR4S2	11	55418785	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5414946	55418785	79587731	116	27988										
MS4A2	2206	hgsc.bcm.edu	37	chr11	59860307	59860307	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caattatatctgaaaggagaAatgcaacatatctggtgagt	9	5	2	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:59860307A>T	ENST00000278888.3	+	4	466	c.364A>T	c.(364-366)Aat>Tat	p.N122Y		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	122					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	TGAAAGGAGAAATGCAACATA	0.348																																																0			11											129	121	124					11																	59860307		2201	4295	6496	59616883	SO:0001583	missense	2206			M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.364A>T	11.37:g.59860307A>T	ENSP00000278888:p.Asn122Tyr		59616883	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	37	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.928428	0.00054	.	.	ENSG00000149534	ENST00000278888	T	0.02280	4.36	4.28	0.675	0.17952	.	1.319970	0.04632	N	0.403856	T	0.05777	0.0151	L	0.54323	1.7	0.09310	N	1	P;P	0.50943	0.94;0.94	P;P	0.51742	0.678;0.678	T	0.48364	-0.9042	10	0.15499	T	0.54	3.0E-4	10.4883	0.44735	0.7741:0.2259:0.0:0.0	.	52;122	Q14298;Q01362	.;FCERB_HUMAN	Y	122	ENSP00000278888:N122Y	ENSP00000278888:N122Y	N	+	1	0	MS4A2	59616883	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	0.137000	0.15995	0.110000	0.17919	0.528000	0.53228	AAT		0.348	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59860307	A	T	59860307	3	4	106	1	0	0	0	0	1	0	0	0	9890	14	1	5	378	5	MS4A2	11	59860307	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	4441522	59860307	75146209	117	27989										
CST6	1474	hgsc.bcm.edu	37	chr11	65780325	65780325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cggcatcaagtacttcctgaCgatggagatggggagcacag	14	9	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:65780325C>T	ENST00000312134.2	+	2	473	c.269C>T	c.(268-270)aCg>aTg	p.T90M		NM_001323.3	NP_001314.1	Q15828	CYTM_HUMAN	cystatin E/M	90					anatomical structure morphogenesis (GO:0009653)|epidermis development (GO:0008544)|negative regulation of endopeptidase activity (GO:0010951)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			large_intestine(1)|lung(1)|ovary(1)	3						TACTTCCTGACGATGGAGATG	0.602																																																0			11											80	66	71					11																	65780325		2201	4296	6497	65536901	SO:0001583	missense	1476			U62800	CCDS8126.1	11q13	2005-09-29			ENSG00000175315	ENSG00000175315			2478	protein-coding gene	gene with protein product		601891				9154125, 9099741	Standard	NM_001323		Approved		uc001ogr.3	Q15828	OTTHUMG00000166750	ENST00000312134.2:c.269C>T	11.37:g.65780325C>T	ENSP00000311313:p.Thr90Met		65536901	Q540N7	Missense_Mutation	SNP	ENST00000312134.2	37	CCDS8126.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.016692	0.35606	.	.	ENSG00000175315	ENST00000312134	T	0.28069	1.63	5.66	2.77	0.32553	Proteinase inhibitor I25, cystatin, conserved site (1);Proteinase inhibitor I25, cystatin (2);	0.124523	0.52532	D	0.000071	T	0.44052	0.1275	M	0.68952	2.095	0.24104	N	0.995863	D	0.76494	0.999	D	0.63703	0.917	T	0.23583	-1.0184	10	0.46703	T	0.11	-17.3569	5.4001	0.16291	0.1613:0.6795:0.0:0.1592	.	90	Q15828	CYTM_HUMAN	M	90	ENSP00000311313:T90M	ENSP00000311313:T90M	T	+	2	0	CST6	65536901	0.591000	0.26824	0.190000	0.23270	0.220000	0.24768	0.865000	0.27940	0.327000	0.23409	0.563000	0.77884	ACG		0.602	CST6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391348.1	NM_001323		T	65780325	C	T	65780325	3	4	106	1	0	0	0	0	1	0	0	0	3982	536	19	1	275	1	CST6	11	65780325	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5920018	65780325	69226191	118	27990										
NPAT	4863	hgsc.bcm.edu	37	chr11	108044481	108044481	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gaaaaattttcctggtcttcTtgtctaagcacatcatggtt	7	8	4	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:108044481T>C	ENST00000278612.8	-	13	1335	c.1230A>G	c.(1228-1230)caA>caG	p.Q410Q	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	410					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		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)		CCTGGTCTTCTTGTCTAAGCA	0.403																																																0			11											134	122	125					11																	108044481		1856	4099	5955	107549691	SO:0001819	synonymous_variant	4863			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1230A>G	11.37:g.108044481T>C			107549691	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	37	CCDS41710.1																																																																																				0.403	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		C	108044481	T	C	108044481	2	2	106	1	0	0	0	0	0	0	0	1	10597	1606	56	4		4	NPAT	11	108044481	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	42264156	108044481	26962035	119	27991										
ATM	472	hgsc.bcm.edu	37	chr11	108170479	108170479	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgggagaagtgggtcctataGatttctctaccatagctata	10	7	1	2	rs121434217		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:108170479G>A	ENST00000452508.2	+	35	5233	c.5044G>A	c.(5044-5046)Gat>Aat	p.D1682N	ATM_ENST00000278616.4_Missense_Mutation_p.D1682N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1682			D -> H (in T-prolymphocytic leukemia). {ECO:0000269|PubMed:9288106}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1682Y(2)|p.D1682H(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GGGTCCTATAGATTTCTCTAC	0.358			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	11											132	139	136					11																	108170479		2201	4298	6499	107675689	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5044G>A	11.37:g.108170479G>A	ENSP00000388058:p.Asp1682Asn		107675689	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.499135	0.85069	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.72505	-0.66;-0.66	5.2	4.28	0.50868	Armadillo-type fold (1);	0.044055	0.85682	N	0.000000	T	0.81791	0.4897	M	0.74258	2.255	0.41759	D	0.9897	D	0.89917	1.0	D	0.79108	0.992	T	0.82973	-0.0191	10	0.62326	D	0.03	.	10.8473	0.46751	0.1519:0.0:0.8481:0.0	.	1682	Q13315	ATM_HUMAN	N	1682	ENSP00000278616:D1682N;ENSP00000388058:D1682N	ENSP00000278616:D1682N	D	+	1	0	ATM	107675689	1.000000	0.71417	0.993000	0.49108	0.952000	0.60782	2.926000	0.48892	1.180000	0.42898	0.650000	0.86243	GAT		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108170479	G	A	108170479	3	1	106	1	0	0	0	0	1	0	0	0	1110	942	33	3	5174	3	ATM	11	108170479	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	125998	108170479	26836037	120	27992										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118919562	118919562	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tccctctggggctggagcgaCgccctcaggccctgcctctg	13	17	3	0	rs147081612	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr11:118919562C>T	ENST00000404233.3	-	18	2153	c.2029G>A	c.(2029-2031)Gtc>Atc	p.V677I	HYOU1_ENST00000525859.1_Missense_Mutation_p.V615I|HYOU1_ENST00000529972.1_Missense_Mutation_p.V615I|HYOU1_ENST00000543287.1_3'UTR	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	677					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GCTGGAGCGACGCCCTCAGGC	0.607													c|||	2	0.000399361	0	0	5008	,	,		17397	0		0.002	False		,,,				2504	0															0			11						T	ILE/VAL,ILE/VAL	1,4399	2.1+/-5.4	0,1,2199	62	63	63		2029,2029	-0.5	0	11	dbSNP_134	63	6,8584	5.0+/-18.6	0,6,4289	yes	missense,missense	HYOU1	NM_001130991.1,NM_006389.3	29,29	0,7,6488	TT,TC,CC		0.0698,0.0227,0.0539	benign,benign	677/1000,677/1000	118919562	7,12983	2200	4295	6495	118424772	SO:0001583	missense	10525			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2029G>A	11.37:g.118919562C>T	ENSP00000384144:p.Val677Ile		118424772	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	c	7.653	0.683284	0.14907	2.27E-4	6.98E-4	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.01335	5.0;5.0;5.0	5.23	-0.465	0.12157	.	2.272770	0.01749	N	0.029839	T	0.01454	0.0047	N	0.16790	0.44	0.09310	N	1	B;B;B;B	0.12013	0.005;0.001;0.005;0.005	B;B;B;B	0.08055	0.002;0.001;0.003;0.003	T	0.47686	-0.9098	10	0.36615	T	0.2	0.222	9.614	0.39681	0.0:0.5373:0.0:0.4626	.	668;659;677;677	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	I	677;668;615;526;615;658	ENSP00000384144:V677I;ENSP00000437313:V615I;ENSP00000433397:V615I	ENSP00000278752:V668I	V	-	1	0	HYOU1	118424772	0.000000	0.05858	0.001000	0.08648	0.296000	0.27459	0.006000	0.13152	0.065000	0.16485	-1.193000	0.01689	GTC		0.607	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		T	118919562	C	T	118919562	3	4	106	1	0	0	0	0	1	0	0	0	7491	536	19	1	1006	1	HYOU1	11	118919562	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	10749083	118919562	16086954	121	27993										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21358822	21358822	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaataatccagtgacatctcAtagagatgtaccactttctt	5	9	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr12:21358822A>G	ENST00000256958.2	+	11	1448	c.1352A>G	c.(1351-1353)cAt>cGt	p.H451R		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	451					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.H451L(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GTGACATCTCATAGAGATGTA	0.373																																																1	Substitution - Missense(1)	ovary(1)	12											97	94	95					12																	21358822		2203	4300	6503	21250089	SO:0001583	missense	10599				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1352A>G	12.37:g.21358822A>G	ENSP00000256958:p.His451Arg		21250089	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.717199	0.30413	.	.	ENSG00000134538	ENST00000256958	T	0.39056	1.1	4.06	-0.432	0.12291	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.517240	0.03380	N	0.200267	T	0.44159	0.1280	M	0.77103	2.36	0.09310	N	1	B	0.17852	0.024	B	0.25759	0.063	T	0.24728	-1.0152	10	0.25751	T	0.34	.	5.2215	0.15371	0.3418:0.4868:0.0:0.1714	.	451	Q9Y6L6	SO1B1_HUMAN	R	451	ENSP00000256958:H451R	ENSP00000256958:H451R	H	+	2	0	SLCO1B1	21250089	0.010000	0.17322	0.604000	0.28916	0.434000	0.31775	0.689000	0.25437	0.402000	0.25451	0.397000	0.26171	CAT		0.373	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21358822	A	G	21358822	3	3	106	1	0	0	0	0	1	0	0	0	14760	217	8	4	1390	4	SLCO1B1	12	21358822	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10		21358822	112493073	122	27994										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	106	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	4039459	25398281	108453614	123	27995										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81760914	81760914	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgtaaagattcttcaagattCtttctgaaagtttctgattc	6	6	5	4			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr12:81760914C>G	ENST00000549396.1	-	14	1678	c.1518G>C	c.(1516-1518)aaG>aaC	p.K506N	PPFIA2_ENST00000548586.1_Missense_Mutation_p.K506N|PPFIA2_ENST00000541017.1_5'UTR|PPFIA2_ENST00000550359.2_Missense_Mutation_p.K353N|PPFIA2_ENST00000541570.2_Missense_Mutation_p.K73N|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000552948.1_Missense_Mutation_p.K506N|PPFIA2_ENST00000550584.2_Missense_Mutation_p.K506N|PPFIA2_ENST00000333447.7_Missense_Mutation_p.K488N|PPFIA2_ENST00000549325.1_Missense_Mutation_p.K488N|PPFIA2_ENST00000407050.4_Missense_Mutation_p.K432N|PPFIA2_ENST00000443686.3_Missense_Mutation_p.K407N	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	506	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						CTTCAAGATTCTTTCTGAAAG	0.229																																																0			12											24	22	22					12																	81760914		1460	3308	4768	80285045	SO:0001583	missense	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1518G>C	12.37:g.81760914C>G	ENSP00000450337:p.Lys506Asn		80285045	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294429	0.60086	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000553058;ENST00000548670	T;T;T;T;T;T;T;T;T	0.57752	1.68;1.68;1.3;1.37;1.69;1.68;1.31;1.7;0.38	5.41	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.68796	0.3040	M	0.82323	2.585	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.69665	-0.5084	10	0.72032	D	0.01	-26.4414	8.0156	0.30379	0.0:0.5515:0.0:0.4485	.	506	O75334	LIPA2_HUMAN	N	506;488;73;432;517;488;506;407;506;87;73	ENSP00000450337:K506N;ENSP00000450298:K488N;ENSP00000438337:K73N;ENSP00000385093:K432N;ENSP00000327416:K488N;ENSP00000449338:K506N;ENSP00000388373:K407N;ENSP00000447868:K506N;ENSP00000448941:K87N	ENSP00000327416:K488N	K	-	3	2	PPFIA2	80285045	0.982000	0.34865	1.000000	0.80357	0.998000	0.95712	0.086000	0.14935	0.748000	0.32831	0.637000	0.83480	AAG		0.229	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			G	81760914	C	G	81760914	3	3	106	1	0	0	0	0	1	0	0	0	12341	912	32	5	2331	5	PPFIA2	12	81760914	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	56362633	81760914	52090981	124	27996										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123480133	123480133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccaccactgctgccaccaccGccaccgccgccaccgccacc	6	26	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr12:123480133G>A	ENST00000542749.1	-	12	1920	c.1857C>T	c.(1855-1857)ggC>ggT	p.G619G	PITPNM2_ENST00000320201.4_Silent_p.G619G|PITPNM2_ENST00000392428.1_Silent_p.G340G|PITPNM2_ENST00000280562.5_Silent_p.G619G			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	619	Gly-rich.				metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		tgccaccaccgccaccgccgc	0.667																																																0			12											34	23	27					12																	123480133		2156	4268	6424	122046086	SO:0001819	synonymous_variant	57605			AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.1857C>T	12.37:g.123480133G>A			122046086	Q9P271	Silent	SNP	ENST00000542749.1	37	CCDS9242.1																																																																																				0.667	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123480133	G	A	123480133	2	1	106	1	0	0	0	0	0	0	0	1	11982	1074	38	1		1	PITPNM2	12	123480133	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	41719219	123480133	10371762	125	27997										
XPO4	64328	hgsc.bcm.edu	37	chr13	21357920	21357920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttcttctaaactctttaagaAggccatcttctgcttccgat	5	11	5	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr13:21357920A>G	ENST00000255305.6	-	23	3468	c.3397T>C	c.(3397-3399)Ttc>Ctc	p.F1133L	XPO4_ENST00000400602.2_Missense_Mutation_p.F1133L			Q9C0E2	XPO4_HUMAN	exportin 4	1133					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		CTCTTTAAGAAGGCCATCTTC	0.408																																																0			13											162	155	157					13																	21357920		1979	4164	6143	20255920	SO:0001583	missense	64328			AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.3397T>C	13.37:g.21357920A>G	ENSP00000255305:p.Phe1133Leu		20255920	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	37	CCDS41872.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.899538	0.91962	.	.	ENSG00000132953	ENST00000400602;ENST00000255305	T;T	0.68903	-0.36;-0.36	5.84	5.84	0.93424	.	0.102150	0.64402	D	0.000002	D	0.82360	0.5020	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84676	0.0714	10	0.87932	D	0	-8.5206	16.2302	0.82332	1.0:0.0:0.0:0.0	.	1133	Q9C0E2	XPO4_HUMAN	L	1133	ENSP00000383444:F1133L;ENSP00000255305:F1133L	ENSP00000255305:F1133L	F	-	1	0	XPO4	20255920	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	8.954000	0.93051	2.228000	0.72767	0.533000	0.62120	TTC		0.408	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		G	21357920	A	G	21357920	3	3	106	1	0	0	0	0	1	0	0	0	17486	72	3	4	62	4	XPO4	13	21357920	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10		21357920	93811958	126	27998										
ATP12A	479	hgsc.bcm.edu	37	chr13	25264509	25264509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tccgagattccgagaagaagAccatcccttcagagcagctg	10	12	1	5			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr13:25264509A>G	ENST00000381946.3	+	6	747	c.580A>G	c.(580-582)Acc>Gcc	p.T194A	ATP12A_ENST00000218548.6_Missense_Mutation_p.T194A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	194					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CGAGAAGAAGACCATCCCTTC	0.567																																					Pancreas(156;1582 1935 18898 22665 26498)											0			13											119	113	115					13																	25264509		2203	4300	6503	24162509	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.580A>G	13.37:g.25264509A>G	ENSP00000371372:p.Thr194Ala		24162509	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	3.748	-0.052116	0.07362	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.91686	-2.89;-2.89	4.74	-6.64	0.01801	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	1.697610	0.03175	N	0.171294	D	0.92734	0.7690	M	0.87381	2.88	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.12837	0.008;0.008	T	0.76913	-0.2783	10	0.27082	T	0.32	.	18.5701	0.91132	0.1929:0.0:0.8071:0.0	.	194;194	P54707-2;P54707	.;AT12A_HUMAN	A	194	ENSP00000218548:T194A;ENSP00000371372:T194A	ENSP00000218548:T194A	T	+	1	0	ATP12A	24162509	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.052000	0.11865	-1.330000	0.02255	-0.263000	0.10527	ACC		0.567	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25264509	A	G	25264509	3	3	106	1	0	0	0	0	1	0	0	0	1123	275	10	4	602	4	ATP12A	13	25264509	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	3906589	25264509	89905369	127	27999										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77695607	77695607	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcttggaggaggagtttgagAattctgatccagaagagctt	14	5	1	4			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr13:77695607A>T	ENST00000544440.2	-	55	7944	c.7927T>A	c.(7927-7929)Tct>Act	p.S2643T	MYCBP2_ENST00000407578.2_Missense_Mutation_p.S2681T|MYCBP2_ENST00000360084.5_Missense_Mutation_p.S106T|MYCBP2_ENST00000482517.1_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.S2643T					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GGAGTTTGAGAATTCTGATCC	0.403																																																0			13											82	82	82					13																	77695607		2203	4300	6503	76593608	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.7927T>A	13.37:g.77695607A>T	ENSP00000444596:p.Ser2643Thr		76593608		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	A	12.41	1.929282	0.34096	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440;ENST00000360084	T;T;T;T	0.43688	1.62;1.62;1.62;0.94	5.47	1.44	0.22558	.	0.500335	0.22661	N	0.057196	T	0.25195	0.0612	L	0.29908	0.895	0.24347	N	0.994936	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20371	-1.0277	10	0.14252	T	0.57	.	8.4488	0.32858	0.5542:0.3694:0.0764:0.0	.	2643;2643	O75592-2;O75592	.;MYCB2_HUMAN	T	2643;2681;2643;106	ENSP00000349892:S2643T;ENSP00000384288:S2681T;ENSP00000444596:S2643T;ENSP00000353197:S106T	ENSP00000349892:S2643T	S	-	1	0	MYCBP2	76593608	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.075000	0.41538	0.358000	0.24211	0.460000	0.39030	TCT		0.403	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		T	77695607	A	T	77695607	3	4	106	1	0	0	0	0	1	0	0	0	10048	246	9	5	6111	5	MYCBP2	13	77695607	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	52431098	77695607	37474271	128	28000										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111862239	111862239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acatcgggctggggagtgacTccgtgtgtgcccggccctcg	16	13	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr13:111862239T>C	ENST00000375741.2	+	5	671	c.421T>C	c.(421-423)Tcc>Ccc	p.S141P	ARHGEF7_ENST00000370623.3_Intron|ARHGEF7_ENST00000426073.2_5'UTR|ARHGEF7_ENST00000375736.4_5'UTR|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.S38P|ARHGEF7_ENST00000375723.1_5'UTR|ARHGEF7_ENST00000218789.5_5'UTR|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.S91P|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000317133.5_Missense_Mutation_p.S120P	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	141					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	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)			GGGGAGTGACTCCGTGTGTGC	0.522																																																0			13											221	221	221					13																	111862239		2203	4300	6503	110660240	SO:0001583	missense	8874			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.421T>C	13.37:g.111862239T>C	ENSP00000364893:p.Ser141Pro		110660240	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	37	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	T	15.64	2.894104	0.52121	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000545635;ENST00000426768;ENST00000375737	T;T;T;T;T	0.53640	0.63;0.61;0.61;0.86;0.62	5.39	5.39	0.77823	Calponin homology domain (1);	0.055102	0.85682	D	0.000000	T	0.50446	0.1616	L	0.27053	0.805	0.80722	D	1	B;D;P;P	0.59357	0.005;0.985;0.729;0.823	B;P;B;P	0.56916	0.007;0.809;0.284;0.477	T	0.47586	-0.9106	10	0.36615	T	0.2	.	15.6936	0.77477	0.0:0.0:0.0:1.0	.	38;91;141;120	B7Z6G2;Q14155-2;Q14155;Q14155-3	.;.;ARHG7_HUMAN;.	P	120;141;91;118;38;38	ENSP00000325994:S120P;ENSP00000364893:S141P;ENSP00000364891:S91P;ENSP00000389890:S38P;ENSP00000364889:S38P	ENSP00000325994:S120P	S	+	1	0	ARHGEF7	110660240	1.000000	0.71417	0.998000	0.56505	0.332000	0.28634	4.449000	0.60034	2.162000	0.67917	0.533000	0.62120	TCC		0.522	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		C	111862239	T	C	111862239	3	2	106	1	0	0	0	0	1	0	0	0	911	1551	54	4	439	4	ARHGEF7	13	111862239	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	34166632	111862239	3307639	129	28001										
SYT16	83851	hgsc.bcm.edu	37	chr14	62541873	62541873	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atttggatggagccagccaaCggcgttattctgagaatctc	11	9	2	1	rs372127808		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr14:62541873C>A	ENST00000430451.2	+	3	954	c.757C>A	c.(757-759)Cgg>Agg	p.R253R	RP11-355I22.5_ENST00000553990.1_lincRNA|SYT16_ENST00000446982.2_Silent_p.R253R	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	253					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		AGCCAGCCAACGGCGTTATTC	0.428																																																0			14											32	30	31					14																	62541873		1898	4126	6024	61611626	SO:0001819	synonymous_variant	83851			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.757C>A	14.37:g.62541873C>A			61611626	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																				0.428	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		A	62541873	C	A	62541873	2	1	106	1	0	0	0	0	0	0	0	1	15511	527	19	2		2	SYT16	14	62541873	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		62541873	44807667	130	28002										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63416947	63416947	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgtaaggcttgtcatggtaaAgtagagagaggacacgtaca	13	5	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr14:63416947A>C	ENST00000322893.7	-	7	1541	c.1273T>G	c.(1273-1275)Ttt>Gtt	p.F425V	KCNH5_ENST00000394964.2_Missense_Mutation_p.F367V|KCNH5_ENST00000420622.2_Missense_Mutation_p.F425V|KCNH5_ENST00000394968.1_Missense_Mutation_p.F367V	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	425					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GTCATGGTAAAGTAGAGAGAG	0.468																																																0			14											126	113	117					14																	63416947		2203	4300	6503	62486700	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1273T>G	14.37:g.63416947A>C	ENSP00000321427:p.Phe425Val		62486700	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727885	0.89390	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86	5.75	5.75	0.90469	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99187	0.9718	M	0.92459	3.31	0.80722	D	1	P;D;D;D	0.89917	0.795;0.995;0.998;1.0	P;D;D;D	0.87578	0.714;0.944;0.976;0.998	D	0.99274	1.0894	10	0.87932	D	0	.	16.0707	0.80928	1.0:0.0:0.0:0.0	.	367;367;425;425	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	V	425;425;367;367	ENSP00000321427:F425V;ENSP00000395439:F425V;ENSP00000378419:F367V;ENSP00000378415:F367V	ENSP00000321427:F425V	F	-	1	0	KCNH5	62486700	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.194000	0.70268	0.533000	0.62120	TTT		0.468	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		C	63416947	A	C	63416947	3	2	106	1	0	0	0	0	1	0	0	0	8056	72	3	4	1747	4	KCNH5	14	63416947	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	875074	63416947	43932593	131	28003										
SERPINA12	145264	hgsc.bcm.edu	37	chr14	94964311	94964311	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acgctgtggctgcagcctctGgtcaatgaacagcgtgttcc	12	12	2	1	rs17090972	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr14:94964311G>A	ENST00000341228.2	-	3	1219	c.424C>T	c.(424-426)Cag>Tag	p.Q142*	SERPINA12_ENST00000556881.1_Nonsense_Mutation_p.Q142*	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	142			Q -> K (in dbSNP:rs17090972).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		TGCAGCCTCTGGTCAATGAAC	0.463																																																0			14											130	127	128					14																	94964311		2203	4300	6503	94034064	SO:0001587	stop_gained	145264			AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.424C>T	14.37:g.94964311G>A	ENSP00000342109:p.Gln142*		94034064		Nonsense_Mutation	SNP	ENST00000341228.2	37	CCDS9926.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328464	0.81690	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	.	.	.	5.49	-2.03	0.07365	.	1.613040	0.03265	N	0.183779	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	9.7051	0.40211	0.0:0.4599:0.1795:0.3606	.	.	.	.	X	142	.	ENSP00000342109:Q142X	Q	-	1	0	SERPINA12	94034064	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.521000	0.06245	-0.013000	0.14199	-0.169000	0.13324	CAG		0.463	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		A	94964311	G	A	94964311	4	1	106	1	0	0	0	0	0	1	0	0	14126	1357	47	3	836	3	SERPINA12	14	94964311	Nonsense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	31547364	94964311	12385229	132	28004										
SERPINA4	5267	hgsc.bcm.edu	37	chr14	95034606	95034606	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atccggcatcaccaaacagcAaaaactggaggcatccaaag	8	12	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr14:95034606A>C	ENST00000557004.1	+	4	1485	c.1064A>C	c.(1063-1065)cAa>cCa	p.Q355P	SERPINA4_ENST00000298841.5_Missense_Mutation_p.Q355P|SERPINA4_ENST00000555095.1_Missense_Mutation_p.Q355P|SERPINA5_ENST00000553780.1_Intron			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	355					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		ACCAAACAGCAAAAACTGGAG	0.527																																																0			14											69	67	67					14																	95034606		2203	4300	6503	94104359	SO:0001583	missense	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.1064A>C	14.37:g.95034606A>C	ENSP00000450838:p.Gln355Pro		94104359	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	37	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	A	3.669	-0.067970	0.07228	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.84442	-1.85;-1.85;-1.85	5.3	-10.6	0.00265	Serpin domain (3);	7.423570	0.00357	N	0.000032	T	0.63698	0.2533	N	0.04959	-0.14	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.0;0.002	T	0.58741	-0.7583	10	0.29301	T	0.29	.	3.8786	0.09068	0.5276:0.1504:0.2511:0.0709	.	355;355	B2R815;P29622	.;KAIN_HUMAN	P	355	ENSP00000450838:Q355P;ENSP00000451172:Q355P;ENSP00000298841:Q355P	ENSP00000298841:Q355P	Q	+	2	0	SERPINA4	94104359	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.443000	0.00469	-4.747000	0.00033	-1.136000	0.01936	CAA		0.527	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		C	95034606	A	C	95034606	3	2	106	1	0	0	0	0	1	0	0	0	14128	130	5	4	1074	4	SERPINA4	14	95034606	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	70295	95034606	12314934	133	28005										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25940054	25940054	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtcgaccgacagcagaggacGgagcggcactgcttggcaag	16	11	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr15:25940054G>A	ENST00000356865.6	-	14	3111	c.3000C>T	c.(2998-3000)tcC>tcT	p.S1000S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1000					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGCAGAGGACGGAGCGGCACT	0.597																																																0			15											76	74	75					15																	25940054		2203	4300	6503	23491147	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3000C>T	15.37:g.25940054G>A			23491147	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.597	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25940054	G	A	25940054	2	1	106	1	0	0	0	0	0	0	0	1	1117	1103	39	1		1	ATP10A	15	25940054	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		25940054	76591338	134	28006										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305899	54305899	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tttctgaactacgagggcacGtcaatgctctcaagcactcc	8	13	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr15:54305899G>C	ENST00000260323.11	+	1	799	c.799G>C	c.(799-801)Gtc>Ctc	p.V267L	UNC13C_ENST00000537900.1_Missense_Mutation_p.V267L|UNC13C_ENST00000545554.1_Missense_Mutation_p.V267L	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	267					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACGAGGGCACGTCAATGCTCT	0.458																																																0			15											95	93	93					15																	54305899		1983	4160	6143	52093191	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.799G>C	15.37:g.54305899G>C	ENSP00000260323:p.Val267Leu		52093191	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814099	0.70912	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.81415	-1.49;-1.49;-1.49	4.97	4.97	0.65823	.	.	.	.	.	T	0.79034	0.4378	N	0.11201	0.11	0.54753	D	0.999982	D	0.63880	0.993	D	0.74023	0.982	T	0.75889	-0.3158	9	0.14252	T	0.57	.	17.243	0.87019	0.0:0.0:1.0:0.0	.	267	Q8NB66	UN13C_HUMAN	L	267	ENSP00000260323:V267L;ENSP00000438156:V267L;ENSP00000442569:V267L	ENSP00000260323:V267L	V	+	1	0	UNC13C	52093191	1.000000	0.71417	0.145000	0.22337	0.963000	0.63663	9.785000	0.99042	2.281000	0.76405	0.650000	0.86243	GTC		0.458	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		C	54305899	G	C	54305899	3	2	106	1	0	0	0	0	1	0	0	0	17026	1145	40	5	801	5	UNC13C	15	54305899	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	28365845	54305899	48225493	135	28007										
UACA	55075	hgsc.bcm.edu	37	chr15	70959142	70959142	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgattgttgttaaggacttaTcacatcgttccttctgatcc	7	9	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr15:70959142T>C	ENST00000322954.6	-	16	4066	c.3881A>G	c.(3880-3882)gAt>gGt	p.D1294G	UACA_ENST00000539319.1_Missense_Mutation_p.D1185G|UACA_ENST00000379983.2_Missense_Mutation_p.D1281G|UACA_ENST00000560441.1_Missense_Mutation_p.D1279G	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1294					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.D1281G(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TAAGGACTTATCACATCGTTC	0.343																																																1	Substitution - Missense(1)	ovary(1)	15											181	155	164					15																	70959142		2199	4297	6496	68746196	SO:0001583	missense	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3881A>G	15.37:g.70959142T>C	ENSP00000314556:p.Asp1294Gly		68746196	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062390	0.76187	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.36340	1.26;1.28;1.73	5.85	5.85	0.93711	.	0.085159	0.49916	D	0.000122	T	0.60856	0.2301	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.998;0.999	T	0.64063	-0.6495	10	0.72032	D	0.01	-26.0951	16.2303	0.82332	0.0:0.0:0.0:1.0	.	1185;1294;1294;1281	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	G	1294;1281;1185	ENSP00000314556:D1294G;ENSP00000369319:D1281G;ENSP00000438667:D1185G	ENSP00000314556:D1294G	D	-	2	0	UACA	68746196	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.404000	0.79996	2.233000	0.73108	0.533000	0.62120	GAT		0.343	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			C	70959142	T	C	70959142	3	2	106	1	0	0	0	0	1	0	0	0	16864	1435	50	4	385	4	UACA	15	70959142	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	16653243	70959142	31572250	136	28008										
IFT140	9742	hgsc.bcm.edu	37	chr16	1560954	1560954	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcccaggcccctcaggggtcGtcatctgcctcttccaccac	9	19	4	0	rs61749517	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:1560954G>A	ENST00000426508.2	-	31	4743	c.4380C>T	c.(4378-4380)gaC>gaT	p.D1460D	LA16c-385E7.1_ENST00000566922.1_lincRNA|IFT140_ENST00000361339.5_Silent_p.D654D	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1460					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CTCAGGGGTCGTCATCTGCCT	0.617													G|||	91	0.0181709	0.0643	0.0086	5008	,	,		15823	0		0	False		,,,				2504	0															0			16						G		308,4082	156.3+/-189.4	15,278,1902	52	44	47		4380	-2.9	0	16	dbSNP_129	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IFT140	NM_014714.3		15,280,6200	AA,AG,GG		0.0233,7.0159,2.3865		1460/1463	1560954	310,12680	2195	4300	6495	1500955	SO:0001819	synonymous_variant	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.4380C>T	16.37:g.1560954G>A			1500955	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				0.617	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1560954	G	A	1560954	2	1	106	1	0	0	0	0	0	0	0	1	7577	1136	40	1		1	IFT140	16	1560954	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		1560954	88793799	137	28009										
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5041902	5041902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agggtacctcgcacattccgCgctggacgcctgccccagtc	11	17	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:5041902C>T	ENST00000251170.7	+	6	718	c.538C>T	c.(538-540)Cgc>Tgc	p.R180C		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	180						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GCACATTCCGCGCTGGACGCC	0.652																																																0			16											40	42	41					16																	5041902		2070	4194	6264	4981903	SO:0001583	missense	9717			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.538C>T	16.37:g.5041902C>T	ENSP00000251170:p.Arg180Cys		4981903		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693769	0.48202	.	.	ENSG00000103184	ENST00000251170	T	0.74315	-0.83	4.54	4.54	0.55810	.	0.259681	0.26927	N	0.021785	T	0.81380	0.4810	M	0.76328	2.33	0.80722	D	1	D	0.71674	0.998	P	0.55455	0.776	D	0.84040	0.0364	10	0.87932	D	0	-30.1684	12.5921	0.56449	0.1657:0.8343:0.0:0.0	.	180	O43304	S14L5_HUMAN	C	180	ENSP00000251170:R180C	ENSP00000251170:R180C	R	+	1	0	SEC14L5	4981903	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	3.835000	0.55805	2.357000	0.79964	0.650000	0.86243	CGC		0.652	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5041902	C	T	5041902	3	4	106	1	0	0	0	0	1	0	0	0	14022	768	27	1	556	1	SEC14L5	16	5041902	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	3480948	5041902	85312851	138	28010										
CACNG3	10368	hgsc.bcm.edu	37	chr16	24372717	24372717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tagtttatatatcagccaacGccggagaccccgggcagcgt	11	12	1	1	rs140935639	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:24372717G>A	ENST00000005284.3	+	4	1683	c.481G>A	c.(481-483)Gcc>Acc	p.A161T		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	161					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		ATCAGCCAACGCCGGAGACCC	0.443																																																0			16						G	THR/ALA	1,4393	2.1+/-5.4	0,1,2196	112	124	120		481	5	0.8	16	dbSNP_134	120	2,8598	2.2+/-6.3	0,2,4298	no	missense	CACNG3	NM_006539.3	58	0,3,6494	AA,AG,GG		0.0233,0.0228,0.0231	benign	161/316	24372717	3,12991	2197	4300	6497	24280218	SO:0001583	missense	10368			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.481G>A	16.37:g.24372717G>A	ENSP00000005284:p.Ala161Thr		24280218		Missense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	G	8.379	0.837053	0.16891	2.28E-4	2.33E-4	ENSG00000006116	ENST00000005284	D	0.89415	-2.51	4.96	4.96	0.65561	.	0.054811	0.64402	D	0.000001	D	0.91375	0.7279	M	0.71581	2.175	0.46478	D	0.999065	D	0.61697	0.99	P	0.55713	0.782	D	0.89126	0.3506	10	0.12766	T	0.61	-10.5168	16.81	0.85717	0.0:0.0:1.0:0.0	.	161	O60359	CCG3_HUMAN	T	161	ENSP00000005284:A161T	ENSP00000005284:A161T	A	+	1	0	CACNG3	24280218	1.000000	0.71417	0.842000	0.33263	0.392000	0.30506	4.886000	0.63149	2.274000	0.75844	0.655000	0.94253	GCC		0.443	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		A	24372717	G	A	24372717	3	1	106	1	0	0	0	0	1	0	0	0	2564	1087	38	1	495	1	CACNG3	16	24372717	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	19330815	24372717	65982036	139	28011										
PHKB	5257	hgsc.bcm.edu	37	chr16	47684505	47684505	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaaatgcatggacgtccactTttccttgttctcatccggga	8	11	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:47684505T>C	ENST00000323584.5	+	19	1872	c.1848T>C	c.(1846-1848)ctT>ctC	p.L616L	PHKB_ENST00000455779.1_Silent_p.L609L|PHKB_ENST00000299167.8_Silent_p.L616L|PHKB_ENST00000566044.1_Silent_p.L609L	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	616					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GACGTCCACTTTTCCTTGTTC	0.413																																																0			16											131	118	122					16																	47684505		2201	4300	6501	46242006	SO:0001819	synonymous_variant	5257				CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1848T>C	16.37:g.47684505T>C			46242006	Q8N4T5	Silent	SNP	ENST00000323584.5	37	CCDS10729.1																																																																																				0.413	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			C	47684505	T	C	47684505	2	2	106	1	0	0	0	0	0	0	0	1	11876	1828	64	4		4	PHKB	16	47684505	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	23311788	47684505	42670248	140	28012										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55703493	55703493	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ccaggtgccttcttgatcccGtacacactgttccttatcat	6	14	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:55703493G>A	ENST00000379906.2	+	2	546	c.291G>A	c.(289-291)ccG>ccA	p.P97P	SLC6A2_ENST00000568943.1_Silent_p.P97P|SLC6A2_ENST00000414754.3_Silent_p.P97P|SLC6A2_ENST00000566163.1_Silent_p.P97P|SLC6A2_ENST00000561820.1_Silent_p.P97P|SLC6A2_ENST00000219833.8_Silent_p.P97P|SLC6A2_ENST00000567238.1_5'Flank	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	97					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	TCTTGATCCCGTACACACTGT	0.577																																																0			16											96	82	86					16																	55703493		2198	4300	6498	54260994	SO:0001819	synonymous_variant	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.291G>A	16.37:g.55703493G>A			54260994	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	37	CCDS10754.1																																																																																				0.577	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			A	55703493	G	A	55703493	2	1	106	1	0	0	0	0	0	0	0	1	14720	1132	40	1		1	SLC6A2	16	55703493	Silent	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	8018988	55703493	34651260	141	28013										
CDH13	1012	hgsc.bcm.edu	37	chr16	83378513	83378513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tggcaaaactctcgaggggcCggtgcctctggaagtcattg	14	10	3	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr16:83378513C>T	ENST00000566620.1	+	6	973	c.683C>T	c.(682-684)cCg>cTg	p.P228L	CDH13_ENST00000569454.1_3'UTR|CDH13_ENST00000428848.3_Missense_Mutation_p.P189L|CDH13_ENST00000268613.10_Missense_Mutation_p.P275L	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	228	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CTCGAGGGGCCGGTGCCTCTG	0.473																																																0			16											83	85	84					16																	83378513		1868	4095	5963	81936014	SO:0001583	missense	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.683C>T	16.37:g.83378513C>T	ENSP00000454435:p.Pro228Leu		81936014	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618755	0.87460	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143	T	0.51817	0.69	5.76	5.76	0.90799	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.71187	0.3310	M	0.77486	2.375	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;P	0.79108	0.992;0.959;0.878	T	0.72760	-0.4196	9	0.72032	D	0.01	.	18.8872	0.92383	0.0:1.0:0.0:0.0	.	189;275;228	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	L	275;228;189	ENSP00000268613:P275L	ENSP00000268613:P275L	P	+	2	0	CDH13	81936014	1.000000	0.71417	0.630000	0.29268	0.850000	0.48378	6.212000	0.72188	2.882000	0.98803	0.655000	0.94253	CCG		0.473	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		T	83378513	C	T	83378513	3	4	106	1	0	0	0	0	1	0	0	0	3105	652	23	1	705	1	CDH13	16	83378513	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	27675020	83378513	6976240	142	28014										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7246795	7246795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acgcagaggttcccaggcgcCgggcccaggaggcagaagag	17	12	0	3	rs374334594		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr17:7246795C>T	ENST00000158762.3	+	6	648	c.442C>T	c.(442-444)Cgg>Tgg	p.R148W	ACAP1_ENST00000573893.1_3'UTR	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	148	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R148W(1)		NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						TCCCAGGCGCCGGGCCCAGGA	0.677													C|||	1	0.000199681	8e-04	0	5008	,	,		14138	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	prostate(1)	17						C	TRP/ARG	0,4406		0,0,2203	32	41	38		442	5.2	1	17		38	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACAP1	NM_014716.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	148/741	7246795	1,13005	2203	4300	6503	7187519	SO:0001583	missense	9744			D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.442C>T	17.37:g.7246795C>T	ENSP00000158762:p.Arg148Trp		7187519	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	37	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.286225	0.80803	0.0	1.16E-4	ENSG00000072818	ENST00000158762	T	0.04917	3.53	5.24	5.24	0.73138	.	0.063724	0.64402	D	0.000010	T	0.12050	0.0293	L	0.53249	1.67	0.80722	D	1	D	0.56968	0.978	P	0.49683	0.619	T	0.00189	-1.1939	10	0.87932	D	0	.	11.7309	0.51737	0.1764:0.8236:0.0:0.0	.	148	Q15027	ACAP1_HUMAN	W	148	ENSP00000158762:R148W	ENSP00000158762:R148W	R	+	1	2	ACAP1	7187519	0.886000	0.30341	1.000000	0.80357	0.979000	0.70002	1.727000	0.38095	2.618000	0.88619	0.462000	0.41574	CGG		0.677	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7246795	C	T	7246795	3	4	106	1	0	0	0	0	1	0	0	0	118	643	23	1	464	1	ACAP1	17	7246795	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		7246795	73948415	143	28015										
TP53	7157	hgsc.bcm.edu	37	chr17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcccaggacaggcacaaacaCgcacctcaaagctgttccgt	8	15	1	0	rs28934576		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0	0	5008	,	,		18620	0		0.001	False		,,,				2504	0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67	58	61					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577120	C	T	7577120	3	4	106	1	0	0	0	0	1	0	0	0	16421	536	19	1	468	1	TP53	17	7577120	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	330325	7577120	73618090	144	28016										
PER1	5187	hgsc.bcm.edu	37	chr17	8053980	8053980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggacaaaatgattccccaggCctggggtcccctcccccatc	9	17	0	1	rs550860633		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr17:8053980C>A	ENST00000317276.4	-	2	282	c.45G>T	c.(43-45)agG>agT	p.R15S	PER1_ENST00000581082.1_Missense_Mutation_p.R15S|PER1_ENST00000354903.5_Intron	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	15	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ATTCCCCAGGCCTGGGGTCCC	0.662			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																															Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	0			17											32	37	35					17																	8053980		2202	4298	6500	7994705	SO:0001583	missense	93210			AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.45G>T	17.37:g.8053980C>A	ENSP00000314420:p.Arg15Ser		7994705	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962564	0.53400	.	.	ENSG00000179094	ENST00000317276	T	0.13307	2.6	5.38	-0.402	0.12404	.	0.176318	0.36101	N	0.002781	T	0.05731	0.0150	N	0.08118	0	0.80722	D	1	B;B	0.24258	0.02;0.1	B;B	0.28139	0.086;0.014	T	0.35450	-0.9788	10	0.35671	T	0.21	-7.0107	5.1591	0.15050	0.1314:0.5385:0.0:0.3301	.	15;15	Q6IN51;O15534	.;PER1_HUMAN	S	15	ENSP00000314420:R15S	ENSP00000314420:R15S	R	-	3	2	PER1	7994705	0.351000	0.24887	0.801000	0.32222	0.736000	0.42039	-0.348000	0.07740	-0.024000	0.13941	-0.261000	0.10672	AGG		0.662	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			A	8053980	C	A	8053980	3	1	106	1	0	0	0	0	1	0	0	0	11760	738	26	2	3915	2	PER1	17	8053980	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	476860	8053980	73141230	145	28017										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18054761	18054761	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acgctcaactctgagcacttCccacagcccacacagcagat	6	17	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr17:18054761C>T	ENST00000205890.5	+	40	8045	c.7707C>T	c.(7705-7707)ttC>ttT	p.F2569F	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2569	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CTGAGCACTTCCCACAGCCCA	0.647																																																0			17											74	79	78					17																	18054761		2083	4226	6309	17995486	SO:0001819	synonymous_variant	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7707C>T	17.37:g.18054761C>T			17995486	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.647	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18054761	C	T	18054761	2	4	106	1	0	0	0	0	0	0	0	1	10093	854	30	3		3	MYO15A	17	18054761	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	10000781	18054761	63140449	146	28018										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78857615	78857615	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gggaaacctcattgccatctGcctggagcagctcaacgacc	10	14	3	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr17:78857615G>T	ENST00000306801.3	+	16	2047	c.1685G>T	c.(1684-1686)tGc>tTc	p.C562F	RPTOR_ENST00000544334.2_Intron|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	562					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						ATTGCCATCTGCCTGGAGCAG	0.647																																																0			17											87	81	83					17																	78857615		2203	4300	6503	76472210	SO:0001583	missense	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1685G>T	17.37:g.78857615G>T	ENSP00000307272:p.Cys562Phe		76472210	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122123	0.77436	.	.	ENSG00000141564	ENST00000306801	T	0.32753	1.44	4.68	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65154	0.2664	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.73000	-0.4120	10	0.42905	T	0.14	.	18.0063	0.89210	0.0:0.0:1.0:0.0	.	562	Q8N122	RPTOR_HUMAN	F	562	ENSP00000307272:C562F	ENSP00000307272:C562F	C	+	2	0	RPTOR	76472210	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.159000	0.94728	2.322000	0.78497	0.558000	0.71614	TGC		0.647	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78857615	G	T	78857615	3	4	106	1	0	0	0	0	1	0	0	0	13702	1319	46	2	1747	2	RPTOR	17	78857615	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	60802854	78857615	2337595	147	28019										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5395107	5395107	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	atcccccgtgatgactattcGcttctcaattcttgtctctg	6	13	3	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr18:5395107G>A	ENST00000341928.2	-	21	3452	c.3112C>T	c.(3112-3114)Cga>Tga	p.R1038*	EPB41L3_ENST00000544123.1_Nonsense_Mutation_p.R869*|EPB41L3_ENST00000342933.3_Nonsense_Mutation_p.R1038*|EPB41L3_ENST00000542146.1_Nonsense_Mutation_p.R343*|EPB41L3_ENST00000400111.3_Nonsense_Mutation_p.R816*|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Nonsense_Mutation_p.R816*|EPB41L3_ENST00000427684.2_Nonsense_Mutation_p.R335*	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1038	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ATGACTATTCGCTTCTCAATT	0.458																																																0			18											142	120	128					18																	5395107		2203	4300	6503	5385107	SO:0001587	stop_gained	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.3112C>T	18.37:g.5395107G>A	ENSP00000343158:p.Arg1038*		5385107	B7Z4I5|F5GX05|O95713|Q9BRP5	Nonsense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	43	10.347299	0.99388	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	.	.	.	5.93	2.9	0.33743	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9387	0.70978	0.0:0.0:0.5508:0.4492	.	.	.	.	X	1038;707;869;707;335;343;1038;816	.	ENSP00000343158:R1038X	R	-	1	2	EPB41L3	5385107	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.628000	0.37060	0.257000	0.21650	0.655000	0.94253	CGA		0.458	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5395107	G	A	5395107	4	1	106	1	0	0	0	0	0	1	0	0	5167	1095	38	1	159	1	EPB41L3	18	5395107	Nonsense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		5395107	72682141	148	28020										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591919	48591919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggacccttctggaggagatcGcttttgtttgggtcaactct	12	9	3	1	rs377767347		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr18:48591919G>A	ENST00000342988.3	+	9	1620	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	SMAD4_ENST00000588745.1_Missense_Mutation_p.R265H|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361H	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	361	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		R -> C (in JPS; dbSNP:rs80338963). {ECO:0000269|PubMed:9811934}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R361H(12)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGAGATCGCTTTTGTTTG	0.413																																																50	Whole gene deletion(36)|Substitution - Missense(12)|Unknown(2)	pancreas(26)|large_intestine(13)|lung(3)|breast(3)|upper_aerodigestive_tract(2)|stomach(2)|oesophagus(1)	18	GRCh37	CM004254	SMAD4	M							167	138	148					18																	48591919		2203	4300	6503	46845917	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1082G>A	18.37:g.48591919G>A	ENSP00000341551:p.Arg361His		46845917	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477304	0.96291	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98120	-4.73;-4.73	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99741	1.1015	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	361	Q13485	SMAD4_HUMAN	H	361	ENSP00000341551:R361H;ENSP00000381452:R361H	ENSP00000341551:R361H	R	+	2	0	SMAD4	46845917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.828000	0.86729	2.771000	0.95319	0.563000	0.77884	CGC		0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48591919	G	A	48591919	3	1	106	1	0	0	0	0	1	0	0	0	14797	1087	38	1	1112	1	SMAD4	18	48591919	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	43196812	48591919	29485329	149	28021										
MBD3	53615	hgsc.bcm.edu	37	chr19	1592612	1592612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ctgcgggagcgccgggcactCccacctcttccgctccattg	11	18	1	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr19:1592612C>T	ENST00000434436.3	-	1	148	c.19G>A	c.(19-21)Gag>Aag	p.E7K	UQCR11_ENST00000585937.1_Intron|MBD3_ENST00000592012.1_Intron|MBD3_ENST00000156825.1_Missense_Mutation_p.E7K|MBD3_ENST00000585967.1_5'Flank	NM_001281453.1	NP_001268382.1	O95983	MBD3_HUMAN	methyl-CpG binding domain protein 3	7	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				ATP-dependent chromatin remodeling (GO:0043044)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|tissue development (GO:0009888)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.179)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCGGGCACTCCCACCTCTTC	0.731																																																0			19											18	19	19					19																	1592612		2199	4289	6488	1543612	SO:0001583	missense	64180			AF072247	CCDS12072.1, CCDS62481.1	19p13	2008-07-17				ENSG00000071655			6918	protein-coding gene	gene with protein product		603573				9774669, 10441743	Standard	NM_001281454		Approved		uc002ltl.1	O95983		ENST00000434436.3:c.19G>A	19.37:g.1592612C>T	ENSP00000412302:p.Glu7Lys		1543612	A8K4B7|D6W5Z2|Q6PIL9|Q6PJZ9|Q86XF4	Missense_Mutation	SNP	ENST00000434436.3	37	CCDS12072.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072705	0.76415	.	.	ENSG00000071655	ENST00000156825	D	0.99376	-5.79	3.03	3.03	0.35002	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.565508	0.15032	U	0.284409	D	0.97964	0.9330	L	0.54323	1.7	0.50813	D	0.999891	B	0.27594	0.182	B	0.31614	0.133	D	0.99236	1.0883	10	0.56958	D	0.05	-18.8749	11.492	0.50387	0.0:1.0:0.0:0.0	.	7	O95983	MBD3_HUMAN	K	7	ENSP00000156825:E7K	ENSP00000156825:E7K	E	-	1	0	MBD3	1543612	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	3.207000	0.51106	1.540000	0.49301	0.174000	0.16983	GAG		0.731	MBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449658.2	NM_003926		T	1592612	C	T	1592612	3	4	106	1	0	0	0	0	1	0	0	0	9374	864	30	3	880	3	MBD3	19	1592612	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		1592612	57536371	150	28022										
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917848	2917848	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttccagatcattccgaggtcAtttgaggacgcacactggag	11	10	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr19:2917848A>G	ENST00000306908.5	+	4	1377	c.1229A>G	c.(1228-1230)cAt>cGt	p.H410R	ZNF57_ENST00000523428.1_Missense_Mutation_p.H378R|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCCGAGGTCATTTGAGGACG	0.428																																					NSCLC(150;910 1964 4303 10464 26498)											0			19											99	89	92					19																	2917848		2203	4300	6503	2868848	SO:0001583	missense	126295			M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"Zinc fingers, C2H2-type", "-"	13125	protein-coding gene	gene with protein product			"zinc finger protein 424"	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1229A>G	19.37:g.2917848A>G	ENSP00000303696:p.His410Arg		2868848	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.104587	0.37145	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	D;D	0.86865	-2.18;-2.18	2.25	2.25	0.28309	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94843	0.8334	H	0.97051	3.93	0.29290	N	0.869403	D	0.89917	1.0	D	0.85130	0.997	D	0.88137	0.2842	9	0.87932	D	0	.	8.0503	0.30575	1.0:0.0:0.0:0.0	.	410	Q68EA5	ZNF57_HUMAN	R	410;412;378	ENSP00000303696:H410R;ENSP00000430223:H378R	ENSP00000303696:H410R	H	+	2	0	ZNF57	2868848	0.999000	0.42202	0.005000	0.12908	0.032000	0.12392	7.535000	0.82014	1.038000	0.40049	0.418000	0.28097	CAT		0.428	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		G	2917848	A	G	2917848	3	3	106	1	0	0	0	0	1	0	0	0	18040	217	8	4	1243	4	ZNF57	19	2917848	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	1325236	2917848	56211135	151	28023										
ZNF224	7767	hgsc.bcm.edu	37	chr19	44611669	44611669	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caccagcgcgtccatacaggAgagaaactgtataattgtaa	9	9	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr19:44611669A>G	ENST00000336976.6	+	6	1610	c.1356A>G	c.(1354-1356)ggA>ggG	p.G452G	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	452					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				TCCATACAGGAGAGAAACTGT	0.448																																																0			19											76	80	78					19																	44611669		2203	4300	6503	49303509	SO:0001819	synonymous_variant	7767			AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1356A>G	19.37:g.44611669A>G			49303509	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																				0.448	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		G	44611669	A	G	44611669	2	3	106	1	0	0	0	0	0	0	0	1	17817	291	11	4		4	ZNF224	19	44611669	Silent	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	41693821	44611669	14517314	152	28024										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44831846	44831846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tttgtatggtttctctcctgTgtggactctgtgatgggctt	12	7	2	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr19:44831846T>C	ENST00000337401.4	-	5	2570	c.2482A>G	c.(2482-2484)Aca>Gca	p.T828A	ZNF112_ENST00000354340.4_Missense_Mutation_p.T822A|ZNF112_ENST00000536500.1_Missense_Mutation_p.T845A	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	828					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TTCTCTCCTGTGTGGACTCTG	0.463																																																0			19											149	147	148					19																	44831846		2203	4300	6503	49523686	SO:0001583	missense	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2482A>G	19.37:g.44831846T>C	ENSP00000337081:p.Thr828Ala		49523686	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435825	0.62955	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.26518	1.73;1.73;1.73	5.07	5.07	0.68467	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35067	N	0.003477	T	0.38799	0.1054	L	0.47078	1.49	0.33245	D	0.55771	P;P;P	0.50528	0.936;0.921;0.936	P;P;P	0.56788	0.806;0.766;0.806	T	0.53627	-0.8412	10	0.59425	D	0.04	-17.8056	14.0978	0.65034	0.0:0.0:0.0:1.0	.	827;845;828	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	A	828;828;822;845;827	ENSP00000337081:T828A;ENSP00000346305:T822A;ENSP00000441990:T845A	ENSP00000253426:T827A	T	-	1	0	ZNF285	49523686	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	1.097000	0.30988	2.039000	0.60335	0.460000	0.39030	ACA		0.463	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		C	44831846	T	C	44831846	3	2	106	1	0	0	0	0	1	0	0	0	17677	1696	59	4	263	4	ZFP112	19	44831846	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	220177	44831846	14297137	153	28025										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55144696	55144696	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcccatgcggggacctacagGtgctacggctcacagagctc	13	14	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr19:55144696G>T	ENST00000396331.1	+	8	1545	c.1188G>T	c.(1186-1188)agG>agT	p.R396S	LILRB1_ENST00000462628.1_Splice_Site|LILRB1_ENST00000396332.4_Missense_Mutation_p.R396S|LILRB1_ENST00000434867.2_Missense_Mutation_p.R396S|LILRB1_ENST00000427581.2_Missense_Mutation_p.R432S|LILRB1_ENST00000396321.2_Missense_Mutation_p.R396S|LILRB1_ENST00000396317.1_Missense_Mutation_p.R396S|LILRB1_ENST00000324602.7_Missense_Mutation_p.R396S|LILRB1_ENST00000418536.2_Missense_Mutation_p.R396S|LILRB1_ENST00000448689.1_Missense_Mutation_p.R396S|LILRB1_ENST00000396327.3_Missense_Mutation_p.R396S|LILRB1_ENST00000396315.1_Missense_Mutation_p.R396S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	396	Ig-like C2-type 4.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGACCTACAGGTGCTACGGCT	0.582										HNSCC(37;0.09)																																						0			19											108	115	113					19																	55144696		2203	4300	6503	59836508	SO:0001583	missense	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1188G>T	19.37:g.55144696G>T	ENSP00000379622:p.Arg396Ser		59836508	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	0.139	-1.104357	0.01828	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.02552	4.25;4.25;4.25;4.25;4.25;4.25;4.25;4.25;4.25;4.25;4.25	2.25	-1.44	0.08856	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.723385	0.11365	N	0.571494	T	0.11024	0.0269	M	0.82716	2.605	0.09310	N	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.955;1.0;0.997;0.997;1.0	T	0.16778	-1.0391	10	0.87932	D	0	.	2.1256	0.03738	0.3249:0.0:0.4228:0.2524	.	396;396;396;396;396	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	396;396;396;396;396;396;396;396;432;396;396	ENSP00000379614:R396S;ENSP00000391514:R396S;ENSP00000409968:R396S;ENSP00000379622:R396S;ENSP00000379618:R396S;ENSP00000315997:R396S;ENSP00000405243:R396S;ENSP00000379623:R396S;ENSP00000395004:R432S;ENSP00000379610:R396S;ENSP00000379608:R396S	ENSP00000315997:R396S	R	+	3	2	LILRB1	59836508	1.000000	0.71417	0.030000	0.17652	0.004000	0.04260	0.482000	0.22276	-0.068000	0.12953	-2.527000	0.00183	AGG		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55144696	G	T	55144696	3	4	106	1	0	0	0	0	1	0	0	0	8813	1252	44	2	1210	2	LILRB1	19	55144696	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	10312850	55144696	3984287	154	28026										
PCNA	5111	hgsc.bcm.edu	37	chr20	5099471	5099471	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tatcttcggcccttagtgtaAtgatatcttcattgccggcg	9	10	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr20:5099471A>G	ENST00000379160.3	-	3	505	c.263T>C	c.(262-264)aTt>aCt	p.I88T	SNORA26_ENST00000391215.1_RNA|PCNA_ENST00000379143.5_Missense_Mutation_p.I88T	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	88	Interaction with NUDT15.				base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CCTTAGTGTAATGATATCTTC	0.433								DNA polymerases (catalytic subunits)																																								0			20											224	217	219					20																	5099471		2203	4300	6503	5047471	SO:0001583	missense	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.263T>C	20.37:g.5099471A>G	ENSP00000368458:p.Ile88Thr		5047471	B2R897|D3DW02	Missense_Mutation	SNP	ENST00000379160.3	37	CCDS13087.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.100166	0.76983	.	.	ENSG00000132646	ENST00000379143;ENST00000379160	.	.	.	4.57	4.57	0.56435	Proliferating cell nuclear antigen, PCNA, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75989	0.3925	M	0.67569	2.06	0.80722	D	1	P;B	0.51057	0.941;0.328	D;D	0.74023	0.982;0.938	T	0.77960	-0.2391	9	0.59425	D	0.04	-13.1607	12.9032	0.58137	1.0:0.0:0.0:0.0	.	88;88	B4DUA2;P12004	.;PCNA_HUMAN	T	88	.	ENSP00000368438:I88T	I	-	2	0	PCNA	5047471	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.739000	0.91574	1.908000	0.55244	0.460000	0.39030	ATT		0.433	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			G	5099471	A	G	5099471	3	3	106	1	0	0	0	0	1	0	0	0	11619	101	4	4	542	4	PCNA	20	5099471	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10		5099471	57926049	155	28027										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45221075	45221075	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cccccgtacaggaaggagatCcagagccagcctgccaacag	11	15	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr20:45221075C>G	ENST00000279027.4	-	6	906	c.888G>C	c.(886-888)tgG>tgC	p.W296C	SLC13A3_ENST00000396360.1_Missense_Mutation_p.W249C|SLC13A3_ENST00000372121.1_Missense_Mutation_p.W246C|SLC13A3_ENST00000290317.5_Missense_Mutation_p.W249C|SLC13A3_ENST00000495082.1_Missense_Mutation_p.W249C|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000413164.2_Missense_Mutation_p.W246C|SLC13A3_ENST00000472148.1_Missense_Mutation_p.W249C	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	296					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	GGAAGGAGATCCAGAGCCAGC	0.502																																																0			20											140	110	120					20																	45221075		2203	4300	6503	44654482	SO:0001583	missense	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.888G>C	20.37:g.45221075C>G	ENSP00000279027:p.Trp296Cys		44654482	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.492508|4.492508	0.84962|0.84962	.|.	.|.	ENSG00000158296|ENSG00000158296	ENST00000450298|ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121	.|T;T;T;T;T;T;T;T;T	.|0.13538	.|4.06;4.06;4.06;4.06;3.36;4.06;4.06;2.59;2.58	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.45677|0.45677	0.1354|0.1354	M|M	0.86178|0.86178	2.8|2.8	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0	T|T	0.48387|0.48387	-0.9040|-0.9040	5|10	.|0.87932	.|D	.|0	-10.3168|-10.3168	19.8165|19.8165	0.96571|0.96571	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|246;249;249;296	.|B4DIR8;Q8WWT9-3;F6WI18;Q8WWT9	.|.;.;.;S13A3_HUMAN	H|C	126|249;249;296;249;246;249;249;209;246	.|ENSP00000290317:W249C;ENSP00000379648:W249C;ENSP00000279027:W296C;ENSP00000420177:W249C;ENSP00000415852:W246C;ENSP00000419621:W249C;ENSP00000417784:W249C;ENSP00000395095:W209C;ENSP00000361193:W246C	.|ENSP00000279027:W296C	D|W	-|-	1|3	0|0	SLC13A3|SLC13A3	44654482|44654482	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.304000|7.304000	0.78882|0.78882	2.683000|2.683000	0.91414|0.91414	0.655000|0.655000	0.94253|0.94253	GAT|TGG		0.502	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			G	45221075	C	G	45221075	3	3	106	1	0	0	0	0	1	0	0	0	14430	856	30	5	952	5	SLC13A3	20	45221075	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	40121604	45221075	17804445	156	28028										
PREX1	57580	hgsc.bcm.edu	37	chr20	47248856	47248856	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgaactttctccagggactgCgcgttgatgtcctgctgcaa	11	11	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr20:47248856C>T	ENST00000371941.3	-	35	4507	c.4485G>A	c.(4483-4485)gcG>gcA	p.A1495A	PREX1_ENST00000396220.1_Missense_Mutation_p.R1530H	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1495					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCAGGGACTGCGCGTTGATGT	0.642																																																0			20											165	156	159					20																	47248856		2203	4300	6503	46682263	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.4485G>A	20.37:g.47248856C>T			46682263	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	5.076	0.199617	0.09652	.	.	ENSG00000124126	ENST00000396220	T	0.62788	-0.0	4.48	-8.96	0.00761	.	.	.	.	.	T	0.46521	0.1397	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.52830	-0.8523	6	0.62326	D	0.03	.	2.4818	0.04589	0.17:0.1077:0.3828:0.3395	.	.	.	.	H	1530	ENSP00000379522:R1530H	ENSP00000379522:R1530H	R	-	2	0	PREX1	46682263	0.000000	0.05858	0.310000	0.25168	0.008000	0.06430	-2.584000	0.00904	-1.014000	0.03379	0.449000	0.29647	CGC		0.642	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47248856	C	T	47248856	2	4	106	1	0	0	0	0	0	0	0	1	12510	755	27	1		1	PREX1	20	47248856	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	2027781	47248856	15776664	157	28029										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58441387	58441387	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcttttaaagactgtgaatcTttttcaaaattctccagctc	4	9	4	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr20:58441387T>C	ENST00000357552.3	-	41	4506	c.4281A>G	c.(4279-4281)aaA>aaG	p.K1427K	SYCP2_ENST00000371001.2_Silent_p.K1427K			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1427					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ACTGTGAATCTTTTTCAAAAT	0.229																																																0			20											30	35	34					20																	58441387		2119	4223	6342	57874782	SO:0001819	synonymous_variant	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4281A>G	20.37:g.58441387T>C			57874782	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																				0.229	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		C	58441387	T	C	58441387	2	2	106	1	0	0	0	0	0	0	0	1	15471	1606	56	4		4	SYCP2	20	58441387	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	11192531	58441387	4584133	158	28030										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22746200	22746200	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cagagcctggacggccgtatCgaagtcaaagggcagcatgg	15	10	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr21:22746200C>T	ENST00000400546.1	+	9	1311	c.1062C>T	c.(1060-1062)atC>atT	p.I354I	NCAM2_ENST00000284894.7_Silent_p.I212I|NCAM2_ENST00000535285.1_Silent_p.I379I	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	354	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		ACGGCCGTATCGAAGTCAAAG	0.408																																																0			21											129	121	124					21																	22746200		1917	4117	6034	21668071	SO:0001819	synonymous_variant	4685				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1062C>T	21.37:g.22746200C>T			21668071	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																				0.408	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22746200	C	T	22746200	2	4	106	1	0	0	0	0	0	0	0	1	10234	874	31	1		1	NCAM2	21	22746200	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10		22746200	25383695	159	28031										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28211980	28211980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcacctgtcctttggtgagaCgccagcgtacttgggaatcc	12	12	0	1	rs201769018		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr21:28211980C>T	ENST00000284984.3	-	7	2408	c.1954G>A	c.(1954-1956)Gtc>Atc	p.V652I		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	652	Cys-rich.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V652I(2)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TTTGGTGAGACGCCAGCGTAC	0.468													C|||	1	0.000199681	0	0	5008	,	,		16223	0		0.001	False		,,,				2504	0															2	Substitution - Missense(2)	prostate(2)	21											127	121	123					21																	28211980		2203	4300	6503	27133851	SO:0001583	missense	9510			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1954G>A	21.37:g.28211980C>T	ENSP00000284984:p.Val652Ile		27133851	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	37	CCDS33524.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.29	1.308055	0.23821	.	.	ENSG00000154734	ENST00000284984	T	0.59502	0.26	5.35	5.35	0.76521	.	.	.	.	.	T	0.52645	0.1747	L	0.52905	1.665	0.54753	D	0.999989	P	0.45396	0.857	B	0.40677	0.337	T	0.50118	-0.8865	9	0.30854	T	0.27	.	13.8532	0.63510	0.0:0.9272:0.0:0.0728	.	652	Q9UHI8	ATS1_HUMAN	I	652	ENSP00000284984:V652I	ENSP00000284984:V652I	V	-	1	0	ADAMTS1	27133851	1.000000	0.71417	0.931000	0.37212	0.048000	0.14542	4.517000	0.60503	2.941000	0.99782	0.655000	0.94253	GTC		0.468	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28211980	C	T	28211980	3	4	106	1	0	0	0	0	1	0	0	0	255	536	19	1	961	1	ADAMTS1	21	28211980	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	5465780	28211980	19917915	160	28032										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744209	31744209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tcgatccatagcccagggagCggcagctgctggatccaaag	13	12	0	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr21:31744209C>T	ENST00000399889.2	-	1	348	c.323G>A	c.(322-324)cGc>cAc	p.R108H		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	108						intermediate filament (GO:0005882)		p.R108P(1)		endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GCCCAGGGAGCGGCAGCTGCT	0.607																																																1	Substitution - Missense(1)	lung(1)	21											48	49	48					21																	31744209		2203	4300	6503	30666080	SO:0001583	missense	337959			AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.323G>A	21.37:g.31744209C>T	ENSP00000382777:p.Arg108His		30666080		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	.	.	.	.	.	.	.	.	.	.	C	0.766	-0.767386	0.02974	.	.	ENSG00000182816	ENST00000399889	T	0.03358	3.96	4.48	1.15	0.20763	.	1.529090	0.04771	N	0.427941	T	0.03477	0.0100	L	0.37466	1.105	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.48293	-0.9048	10	0.13470	T	0.59	.	3.7238	0.08467	0.0:0.5126:0.1994:0.288	.	108	Q52LG2	KR132_HUMAN	H	108	ENSP00000382777:R108H	ENSP00000382777:R108H	R	-	2	0	KRTAP13-2	30666080	0.000000	0.05858	0.001000	0.08648	0.695000	0.40330	-1.349000	0.02627	0.068000	0.16574	-0.251000	0.11542	CGC		0.607	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			T	31744209	C	T	31744209	3	4	106	1	0	0	0	0	1	0	0	0	8544	768	27	1	208	1	KRTAP13-2	21	31744209	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	3532229	31744209	16385686	161	28033										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21119220	21119220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caggttgatgatagtgctgcGgagctcactcagctcagcct	12	11	3	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr22:21119220G>A	ENST00000572273.1	-	22	2649	c.2419C>T	c.(2419-2421)Cgc>Tgc	p.R807C	PI4KA_ENST00000255882.6_Missense_Mutation_p.R865C|PI4KA_ENST00000466162.1_5'UTR			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	807					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATAGTGCTGCGGAGCTCACTC	0.582																																					GBM(136;1332 1831 3115 23601 50806)											0			22											72	67	69					22																	21119220		2203	4300	6503	19449220	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2419C>T	22.37:g.21119220G>A	ENSP00000458238:p.Arg807Cys		19449220	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.074038	0.76415	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.58	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.77110	0.4082	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79792	-0.1654	9	0.87932	D	0	-21.2708	13.2018	0.59772	0.0:0.0:0.5889:0.4111	.	807	P42356	PI4KA_HUMAN	C	807	.	ENSP00000255882:R807C	R	-	1	0	PI4KA	19449220	1.000000	0.71417	0.912000	0.35992	0.977000	0.68977	3.733000	0.55029	1.328000	0.45358	0.650000	0.86243	CGC		0.582	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21119220	G	A	21119220	3	1	106	1	0	0	0	0	1	0	0	0	11904	1116	39	1	3851	1	PI4KA	22	21119220	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		21119220	30185346	162	28034										
GNAZ	2781	hgsc.bcm.edu	37	chr22	23438030	23438030	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	actcaggcaagagcaccatcGtcaaacagatgaagatcatc	8	11	3	4			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr22:23438030G>A	ENST00000248996.4	+	2	814	c.148G>A	c.(148-150)Gtc>Atc	p.V50I	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	50					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		GAGCACCATCGTCAAACAGAT	0.592																																																0			22											121	124	123					22																	23438030		2203	4300	6503	21768030	SO:0001583	missense	2781				CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.148G>A	22.37:g.23438030G>A	ENSP00000248996:p.Val50Ile		21768030	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	37	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.543284	0.65198	.	.	ENSG00000128266	ENST00000248996	D	0.88586	-2.4	5.05	4.04	0.47022	G protein alpha subunit, helical insertion (1);	0.000000	0.85682	D	0.000000	D	0.83940	0.5363	L	0.39467	1.215	0.80722	D	1	B	0.12013	0.005	B	0.04013	0.001	T	0.80398	-0.1399	10	0.52906	T	0.07	.	12.8594	0.57906	0.0791:0.0:0.9209:0.0	.	50	P19086	GNAZ_HUMAN	I	50	ENSP00000248996:V50I	ENSP00000248996:V50I	V	+	1	0	GNAZ	21768030	1.000000	0.71417	0.857000	0.33713	0.863000	0.49368	9.597000	0.98273	1.272000	0.44329	-0.136000	0.14681	GTC		0.592	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		A	23438030	G	A	23438030	3	1	106	1	0	0	0	0	1	0	0	0	6534	1145	40	1	150	1	GNAZ	22	23438030	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	2318810	23438030	27866536	163	28035										
SMTN	6525	hgsc.bcm.edu	37	chr22	31500448	31500448	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gcgcctgcgcggcaagaatgTctagcctgcccgcccgcatg	13	16	1	1	rs554451508	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr22:31500448T>A	ENST00000347557.2	+	20	2968	c.2750T>A	c.(2749-2751)gTc>gAc	p.V917D	SMTN_ENST00000333137.7_3'UTR|SELM_ENST00000465536.1_5'Flank|SMTN_ENST00000404574.1_3'UTR|SMTN_ENST00000358743.1_Missense_Mutation_p.V940D	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	917					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						GGCAAGAATGTCTAGCCTGCC	0.657																																																0			22											83	68	73					22																	31500448		2203	4300	6503	29830448	SO:0001583	missense	6525			AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.2750T>A	22.37:g.31500448T>A	ENSP00000328635:p.Val917Asp		29830448	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	37	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.147276	0.77888	.	.	ENSG00000183963	ENST00000358743;ENST00000347557	T;T	0.70516	-0.1;-0.49	5.03	5.03	0.67393	.	1.684130	0.03833	N	0.269406	T	0.73329	0.3573	N	0.08118	0	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61940	0.896;0.896	T	0.64045	-0.6499	10	0.87932	D	0	.	15.07	0.72026	0.0:0.0:0.0:1.0	.	940;917	E7EWD0;P53814	.;SMTN_HUMAN	D	940;917	ENSP00000351593:V940D;ENSP00000328635:V917D	ENSP00000328635:V917D	V	+	2	0	SMTN	29830448	0.982000	0.34865	0.998000	0.56505	0.862000	0.49288	1.992000	0.40737	2.043000	0.60533	0.448000	0.29417	GTC		0.657	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		A	31500448	T	A	31500448	3	1	106	1	0	0	0	0	1	0	0	0	14851	1667	58	5	2973	5	SMTN	22	31500448	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	8062418	31500448	19804118	164	28036										
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40257832	40257832	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tctctgaagcagaaatatccGgtgtgggggcagaagtgcac	14	8	1	3	rs148548476		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr22:40257832G>A	ENST00000325157.6	-	3	780	c.530C>T	c.(529-531)cCg>cTg	p.P177L		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	177										breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					AGAAATATCCGGTGTGGGGGC	0.413																																																0			22						G	LEU/PRO	0,4406		0,0,2203	68	71	70		530	5.2	0.3	22	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ENTHD1	NM_152512.3	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	177/608	40257832	1,13005	2203	4300	6503	38587778	SO:0001583	missense	150350			AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.530C>T	22.37:g.40257832G>A	ENSP00000317431:p.Pro177Leu		38587778	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	37	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	G	10.20	1.285004	0.23392	0.0	1.16E-4	ENSG00000176177	ENST00000325157	T	0.49720	0.77	6.17	5.15	0.70609	.	0.246918	0.34268	N	0.004109	T	0.44808	0.1311	M	0.64997	1.995	0.30145	N	0.803601	P	0.46277	0.875	B	0.41619	0.361	T	0.49051	-0.8979	10	0.19590	T	0.45	-6.6644	12.8417	0.57806	0.0:0.0:0.8368:0.1632	.	177	Q8IYW4	ENTD1_HUMAN	L	177	ENSP00000317431:P177L	ENSP00000317431:P177L	P	-	2	0	ENTHD1	38587778	0.997000	0.39634	0.318000	0.25279	0.097000	0.18754	3.396000	0.52565	1.590000	0.49995	0.655000	0.94253	CCG		0.413	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		A	40257832	G	A	40257832	3	1	106	1	0	0	0	0	1	0	0	0	5150	1116	39	1	1313	1	ENTHD1	22	40257832	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	8757384	40257832	11046734	165	28037										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656620	46656620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gctggttgataccccactttTcaactttcttgacatacatg	6	11	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chr22:46656620T>C	ENST00000253255.5	-	1	2599	c.2600A>G	c.(2599-2601)gAa>gGa	p.E867G		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	867	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACCCCACTTTTCAACTTTCTT	0.398																																																0			22											66	66	66					22																	46656620		2203	4300	6503	45035284	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2600A>G	22.37:g.46656620T>C	ENSP00000253255:p.Glu867Gly		45035284	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317425	0.60524	.	.	ENSG00000130943	ENST00000253255	T	0.42131	0.98	5.16	2.99	0.34606	Egg jelly receptor, REJ-like (1);	0.000000	0.64402	D	0.000009	T	0.35278	0.0926	M	0.68952	2.095	0.09310	N	1	B	0.34372	0.451	B	0.31101	0.124	T	0.34453	-0.9828	10	0.59425	D	0.04	-13.2984	5.2622	0.15580	0.1565:0.0835:0.0:0.76	.	867	Q9NTG1	PKDRE_HUMAN	G	867	ENSP00000253255:E867G	ENSP00000253255:E867G	E	-	2	0	PKDREJ	45035284	0.781000	0.28676	0.005000	0.12908	0.322000	0.28314	1.723000	0.38053	0.367000	0.24454	0.533000	0.62120	GAA		0.398	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		C	46656620	T	C	46656620	3	2	106	1	0	0	0	0	1	0	0	0	12001	1783	62	4	4165	4	PKDREJ	22	46656620	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	6398788	46656620	4647946	166	28038										
GYG2	8908	hgsc.bcm.edu	37	chrX	2777919	2777919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaaggtcgtccactttttggGgtccatgaaaccttggaact	10	9	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:2777919G>A	ENST00000381163.3	+	8	1025	c.743G>A	c.(742-744)gGg>gAg	p.G248E	GYG2_ENST00000398806.3_Missense_Mutation_p.G217E|GYG2_ENST00000338623.5_Missense_Mutation_p.G248E|GYG2_ENST00000542787.1_Missense_Mutation_p.G248E|GYG2_ENST00000381161.1_3'UTR	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	248					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		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)				CACTTTTTGGGGTCCATGAAA	0.498																																																0			X											70	59	62					X																	2777919		2203	4298	6501	2787919	SO:0001583	missense	8908			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"Glycosyltransferase family 8 domain containing"	4700	protein-coding gene	gene with protein product	"glycogenin glucosyltransferase"	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.743G>A	X.37:g.2777919G>A	ENSP00000370555:p.Gly248Glu		2787919	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700530	0.48307	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	3.73	3.73	0.42828	.	0.000000	0.64402	D	0.000020	D	0.90978	0.7163	H	0.98068	4.14	0.51482	D	0.999926	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999;1.0	D	0.94353	0.7581	10	0.87932	D	0	.	14.936	0.70954	0.0:0.0:1.0:0.0	.	248;248;208;217;217;248	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;.;GLYG2_HUMAN	E	217;248;248;248	ENSP00000381786:G217E;ENSP00000370555:G248E;ENSP00000341273:G248E;ENSP00000446092:G248E	ENSP00000341273:G248E	G	+	2	0	GYG2	2787919	1.000000	0.71417	0.609000	0.28983	0.067000	0.16453	6.924000	0.75823	1.500000	0.48636	0.529000	0.55759	GGG		0.498	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918		A	2777919	G	A	2777919	3	1	106	1	0	0	0	0	1	0	0	0	6927	1232	43	3	769	3	GYG2	23	2777919	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10		2777919	152492641	167	28039										
SCML1	6322	hgsc.bcm.edu	37	chrX	17764155	17764155	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caggaaccgaatattgtatcTgacgcatcctgtaatactga	8	9	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:17764155T>A	ENST00000380041.3	+	4	463	c.135T>A	c.(133-135)tcT>tcA	p.S45S	SCML1_ENST00000380045.3_5'UTR|SCML1_ENST00000398080.1_5'UTR|SCML1_ENST00000380043.3_Silent_p.S18S	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	45					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					ATATTGTATCTGACGCATCCT	0.373																																																0			X											156	147	150					X																	17764155		2203	4300	6503	17674076	SO:0001819	synonymous_variant	6322				CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"Sterile alpha motif (SAM) domain containing"	10580	protein-coding gene	gene with protein product		300227	"sex comb on midleg (Drosophila)-like 1"			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.135T>A	X.37:g.17764155T>A			17674076	B0FZN6|B2RA08|Q5H968|Q5H969	Silent	SNP	ENST00000380041.3	37	CCDS35210.1																																																																																				0.373	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746		A	17764155	T	A	17764155	2	1	106	1	0	0	0	0	0	0	0	1	13946	1567	55	5		5	SCML1	23	17764155	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	14986236	17764155	137506405	168	28040										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19379458	19379458	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	actgttttgaggctcttaccGtagtcgaaggtatcttagat	10	7	2	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:19379458G>A	ENST00000338883.4	-	28	3855	c.3856C>T	c.(3856-3858)Cgg>Tgg	p.R1286W	PDHA1_ENST00000545074.1_3'UTR|MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000359173.3_Splice_Site_p.R721W|PDHA1_ENST00000422285.2_3'UTR|PDHA1_ENST00000379806.5_3'UTR|MAP3K15_ENST00000469203.2_Splice_Site_p.R1118W|PDHA1_ENST00000540249.1_3'UTR	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1286							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					GGCTCTTACCGTAGTCGAAGG	0.388																																																0			X											53	44	47					X																	19379458		2203	4300	6503	19289379	SO:0001630	splice_region_variant	389840			AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3857+1C>T	X.37:g.19379458G>A			19289379	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	G	15.61	2.884901	0.51908	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	D;D;D	0.88586	-2.4;-2.4;-2.4	5.91	3.21	0.36854	Sterile alpha motif/pointed domain (1);	0.000000	0.64402	U	0.000005	D	0.93625	0.7964	M	0.87900	2.915	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.91385	0.5130	10	0.87932	D	0	.	6.13	0.20199	0.1404:0.0:0.5944:0.2652	.	761;1286	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	W	1286;721;1118	ENSP00000345629:R1286W;ENSP00000352093:R721W;ENSP00000428356:R1118W	ENSP00000345629:R1286W	R	-	1	2	MAP3K15	19289379	1.000000	0.71417	0.474000	0.27266	0.526000	0.34562	3.155000	0.50700	0.250000	0.21479	-0.237000	0.12165	CGG		0.388	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671	Missense_Mutation	A	19379458	G	A	19379458	5	1	106	1	0	0	0	0	0	0	1	0	9279	1159	40	1	93	1	MAP3K15	23	19379458	Splice_Site	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	1615303	19379458	135891102	169	28041										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29973736	29973736	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tactaccgaagctatgagtaCgacgtacctcctaccggcac	8	14	0	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:29973736C>T	ENST00000378993.1	+	11	2563	c.1890C>T	c.(1888-1890)taC>taT	p.Y630Y	IL1RAPL1_ENST00000302196.4_Silent_p.Y630Y	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	630	Interaction with NCS1.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)	p.Y630Y(1)		biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						GCTATGAGTACGACGTACCTC	0.517																																																1	Substitution - coding silent(1)	large_intestine(1)	X											91	44	60					X																	29973736		2202	4300	6502	29883657	SO:0001819	synonymous_variant	11141			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1890C>T	X.37:g.29973736C>T			29883657	A0AVG4|Q9UJ53	Silent	SNP	ENST00000378993.1	37	CCDS14218.1																																																																																				0.517	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29973736	C	T	29973736	2	4	106	1	0	0	0	0	0	0	0	1	7682	547	19	1		1	IL1RAPL1	23	29973736	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	10594278	29973736	125296824	170	28042										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30237240	30237240	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ggccacacttacaccttcatCgacaaggtagacctcactga	7	14	2	2	rs140291899		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:30237240C>T	ENST00000378988.4	+	2	644	c.543C>T	c.(541-543)atC>atT	p.I181I		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	181	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						ACACCTTCATCGACAAGGTAG	0.502																																																0			X											55	44	47					X																	30237240		2202	4299	6501	30147161	SO:0001819	synonymous_variant	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.543C>T	X.37:g.30237240C>T			30147161	O75860	Silent	SNP	ENST00000378988.4	37	CCDS14219.1																																																																																				0.502	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		T	30237240	C	T	30237240	2	4	106	1	0	0	0	0	0	0	0	1	9206	874	31	1		1	MAGEB2	23	30237240	Silent	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	263504	30237240	125033320	171	28043										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45017022	45017022	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caggcgcagcttgtcacggtCggtgaagtggtccatgaaga	15	9	1	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:45017022C>T	ENST00000398000.2	-	3	684	c.610G>A	c.(610-612)Gac>Aac	p.D204N	CXorf36_ENST00000477281.1_Intron	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	204						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TTGTCACGGTCGGTGAAGTGG	0.647																																																0			X											48	43	45					X																	45017022		1567	3574	5141	44901966	SO:0001583	missense	79742			AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.610G>A	X.37:g.45017022C>T	ENSP00000381086:p.Asp204Asn		44901966	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686369	0.68157	.	.	ENSG00000147113	ENST00000398000	T	0.32515	1.45	4.8	4.8	0.61643	.	0.222920	0.36482	N	0.002573	T	0.44540	0.1298	M	0.76002	2.32	0.80722	D	1	D	0.54397	0.966	P	0.48166	0.569	T	0.53244	-0.8466	10	0.59425	D	0.04	.	17.1375	0.86743	0.0:1.0:0.0:0.0	.	204	Q9H7Y0	CX036_HUMAN	N	204	ENSP00000381086:D204N	ENSP00000381086:D204N	D	-	1	0	CXorf36	44901966	1.000000	0.71417	0.107000	0.21349	0.620000	0.37586	5.240000	0.65378	1.967000	0.57214	0.429000	0.28392	GAC		0.647	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		T	45017022	C	T	45017022	3	4	106	1	0	0	0	0	1	0	0	0	4112	884	31	1	703	1	CXorf36	23	45017022	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	14779782	45017022	110253538	172	28044										
RGN	9104	hgsc.bcm.edu	37	chrX	46951191	46951191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	caatggaggaagagtgattcGtttagatcctgtgacaggta	13	5	0	4	rs138412897	byFrequency	TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:46951191G>A	ENST00000352078.4	+	5	1022	c.677G>A	c.(676-678)cGt>cAt	p.R226H	RGN_ENST00000457380.1_Missense_Mutation_p.R154H|RGN_ENST00000336169.3_Missense_Mutation_p.R226H|RGN_ENST00000397180.1_Missense_Mutation_p.R226H	NM_004683.4	NP_004674.1	Q15493	RGN_HUMAN	regucalcin	226					cellular calcium ion homeostasis (GO:0006874)|L-ascorbic acid biosynthetic process (GO:0019853)|positive regulation of ATPase activity (GO:0032781)|regulation of calcium-mediated signaling (GO:0050848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|enzyme regulator activity (GO:0030234)|gluconolactonase activity (GO:0004341)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	9						AGAGTGATTCGTTTAGATCCT	0.438																																																0			X											136	116	123					X																	46951191		2203	4300	6503	46836135	SO:0001583	missense	9104			D31815	CCDS14272.1, CCDS75968.1	Xp11.3	2014-03-14	2013-04-26		ENSG00000130988	ENSG00000130988	3.1.1.17		9989	protein-coding gene	gene with protein product	"senescence marker protein-30", "gluconolactonase"	300212	"regucalcin (senescence marker protein-30)"			7548213	Standard	NM_152869		Approved	SMP30, RC	uc004dha.1	Q15493	OTTHUMG00000021435	ENST00000352078.4:c.677G>A	X.37:g.46951191G>A	ENSP00000253303:p.Arg226His		46836135	A4FTW1|A8K271|Q53FC9|Q5JRR5	Missense_Mutation	SNP	ENST00000352078.4	37	CCDS14272.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.593148	0.66219	.	.	ENSG00000130988	ENST00000397180;ENST00000457380;ENST00000352078;ENST00000336169	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	6.02	5.14	0.70334	SMP-30/Gluconolaconase/LRE-like region (1);Six-bladed beta-propeller, TolB-like (1);	0.211612	0.49916	D	0.000135	T	0.46268	0.1384	M	0.85777	2.775	0.58432	D	0.999998	D;D	0.56968	0.978;0.962	B;B	0.41202	0.35;0.268	T	0.59721	-0.7401	10	0.66056	D	0.02	-5.8202	16.2128	0.82178	0.0:0.1294:0.8706:0.0	.	154;226	Q15493-2;Q15493	.;RGN_HUMAN	H	226;154;226;226	ENSP00000380365:R226H;ENSP00000406568:R154H;ENSP00000253303:R226H;ENSP00000338400:R226H	ENSP00000338400:R226H	R	+	2	0	RGN	46836135	1.000000	0.71417	0.623000	0.29173	0.702000	0.40608	5.556000	0.67307	1.259000	0.44117	0.591000	0.81541	CGT		0.438	RGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056385.1	NM_004683		A	46951191	G	A	46951191	3	1	106	1	0	0	0	0	1	0	0	0	13319	1145	40	1	691	1	RGN	23	46951191	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	1934169	46951191	108319369	173	28045										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53616547	53616547	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gaatcatgtcacgataatctGctccattacgtttgattgct	7	9	3	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:53616547G>C	ENST00000342160.3	-	35	4878	c.4421C>G	c.(4420-4422)gCa>gGa	p.A1474G	HUWE1_ENST00000218328.8_Missense_Mutation_p.A1474G|HUWE1_ENST00000262854.6_Missense_Mutation_p.A1474G			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1474					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ACGATAATCTGCTCCATTACG	0.478																																																0			X											219	178	192					X																	53616547		2203	4300	6503	53633272	SO:0001583	missense	10075			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.4421C>G	X.37:g.53616547G>C	ENSP00000340648:p.Ala1474Gly		53633272	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.12|15.12	2.740387|2.740387	0.49045|0.49045	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328|ENST00000427052	T;T;T|.	0.45276|.	1.21;1.21;0.9|.	5.93|5.93	5.93|5.93	0.95920|0.95920	Armadillo-like helical (1);|.	0.133058|.	0.51477|.	D|.	0.000094|.	T|T	0.46425|0.46425	0.1392|0.1392	N|N	0.08118|0.08118	0|0	0.46954|0.46954	D|D	0.999268|0.999268	P;P|.	0.46220|.	0.801;0.874|.	B;B|.	0.40477|.	0.258;0.33|.	T|T	0.43909|0.43909	-0.9362|-0.9362	10|5	0.21540|.	T|.	0.41|.	.|.	17.9436|17.9436	0.89032|0.89032	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1474;1474|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	G|R	1474|507	ENSP00000340648:A1474G;ENSP00000262854:A1474G;ENSP00000218328:A1474G|.	ENSP00000218328:A1474G|.	A|S	-|-	2|3	0|2	HUWE1|HUWE1	53633272|53633272	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	9.483000|9.483000	0.97937|0.97937	2.513000|2.513000	0.84729|0.84729	0.600000|0.600000	0.82982|0.82982	GCA|AGC		0.478	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53616547	G	C	53616547	3	2	106	1	0	0	0	0	1	0	0	0	7482	1319	46	5	8899	5	HUWE1	23	53616547	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	6665356	53616547	101654013	174	28046										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412110	63412110	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	acttcgcttggtcccatctcGgtttgctctctggcccccag	9	16	2	0	rs137852216		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:63412110G>A	ENST00000330258.3	-	2	1329	c.1057C>T	c.(1057-1059)Cga>Tga	p.R353*	AMER1_ENST00000403336.1_Nonsense_Mutation_p.R353*|AMER1_ENST00000374869.3_Nonsense_Mutation_p.R353*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	353					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.R353*(6)									GTCCCATCTCGGTTTGCTCTC	0.522																																																73	Whole gene deletion(67)|Substitution - Nonsense(6)	kidney(69)|large_intestine(3)|ovary(1)	X	GRCh37	CM090021	FAM123B	M	rs137852216						155	137	143					X																	63412110		2203	4300	6503	63328835	SO:0001587	stop_gained	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1057C>T	X.37:g.63412110G>A	ENSP00000329117:p.Arg353*		63328835	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	39	7.320143	0.98210	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.18	2.27	0.28462	.	0.134606	0.49305	D	0.000153	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3649	9.2932	0.37800	0.0:0.1375:0.572:0.2905	.	.	.	.	X	353	.	ENSP00000329117:R353X	R	-	1	2	FAM123B	63328835	1.000000	0.71417	0.986000	0.45419	0.990000	0.78478	0.950000	0.29122	0.228000	0.21019	0.529000	0.55759	CGA		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63412110	G	A	63412110	4	1	106	1	0	0	0	0	0	1	0	0	5439	1124	39	1	2354	1	FAM123B	23	63412110	Nonsense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	9795563	63412110	91858450	175	28047										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412932	63412932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gctgcctttcccagaaccttTgctccgtccccctccaaaga	6	18	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:63412932T>C	ENST00000330258.3	-	2	507	c.235A>G	c.(235-237)Aaa>Gaa	p.K79E	AMER1_ENST00000403336.1_Missense_Mutation_p.K79E|AMER1_ENST00000374869.3_Missense_Mutation_p.K79E	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	79					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CCAGAACCTTTGCTCCGTCCC	0.532																																																67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	X											124	96	106					X																	63412932		2203	4300	6503	63329657	SO:0001583	missense	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.235A>G	X.37:g.63412932T>C	ENSP00000329117:p.Lys79Glu		63329657	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	19.41	3.822139	0.71028	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.54479	0.57;0.58;0.57	4.59	4.59	0.56863	.	0.110948	0.64402	D	0.000013	T	0.63698	0.2533	M	0.73217	2.22	0.35803	D	0.823254	D	0.63046	0.992	P	0.54889	0.763	T	0.75816	-0.3184	10	0.72032	D	0.01	-15.4925	12.5155	0.56030	0.0:0.0:0.0:1.0	.	79	Q5JTC6	F123B_HUMAN	E	79	ENSP00000364003:K79E;ENSP00000329117:K79E;ENSP00000384722:K79E	ENSP00000329117:K79E	K	-	1	0	FAM123B	63329657	1.000000	0.71417	0.998000	0.56505	0.733000	0.41908	5.713000	0.68415	2.018000	0.59344	0.486000	0.48141	AAA		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63412932	T	C	63412932	3	2	106	1	0	0	0	0	1	0	0	0	5439	1821	63	4	3176	4	FAM123B	23	63412932	Missense_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	822	63412932	91857628	176	28048										
MCART6	401612	hgsc.bcm.edu	37	chrX	103349343	103349343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	ttgctctgccaggccatcctGgatggggtccttgaaagaaa	12	10	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:103349343G>T	ENST00000357421.4	-	2	778	c.598C>A	c.(598-600)Cag>Aag	p.Q200K		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	200					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											AGGCCATCCTGGATGGGGTCC	0.557																																																0			X											60	64	62					X																	103349343		2203	4300	6503	103235999	SO:0001583	missense	401612				CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"Solute carriers"	31894	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 6"	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.598C>A	X.37:g.103349343G>T	ENSP00000361681:p.Gln200Lys		103235999	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	37	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	g	0.047	-1.262223	0.01445	.	.	ENSG00000176274	ENST00000357421	T	0.72942	-0.7	4.18	3.28	0.37604	Mitochondrial carrier domain (2);	0.397969	0.22328	N	0.061516	T	0.30510	0.0767	N	0.00599	-1.345	0.26540	N	0.974102	B	0.11235	0.004	B	0.11329	0.006	T	0.37126	-0.9719	10	0.02654	T	1	-7.2573	8.4342	0.32778	0.0:0.0:0.5774:0.4225	.	200	Q5H9E4	MCAR6_HUMAN	K	200	ENSP00000361681:Q200K	ENSP00000361681:Q200K	Q	-	1	0	MCART6	103235999	0.225000	0.23685	1.000000	0.80357	0.991000	0.79684	1.485000	0.35519	0.846000	0.35142	0.594000	0.82650	CAG		0.557	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755		T	103349343	G	T	103349343	3	4	106	1	0	0	0	0	1	0	0	0	9401	1357	47	2	329	2	MCART6	23	103349343	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	39936411	103349343	51921217	177	28049										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109694990	109694990	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtcaacacaaaatgtagactCtgaaatgatgtctaatccgc	7	9	3	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:109694990C>G	ENST00000465301.2	+	3	1391	c.1145C>G	c.(1144-1146)tCt>tGt	p.S382C	RGAG1_ENST00000540313.1_Missense_Mutation_p.S382C	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	382										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						AATGTAGACTCTGAAATGATG	0.542																																																0			X											172	178	176					X																	109694990		2203	4300	6503	109581646	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1145C>G	X.37:g.109694990C>G	ENSP00000419786:p.Ser382Cys		109581646	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603492	0.66445	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.57752	0.38;0.38	4.28	4.28	0.50868	.	0.679439	0.12217	N	0.488771	T	0.58323	0.2114	L	0.29908	0.895	0.09310	N	1	D	0.71674	0.998	D	0.63113	0.911	T	0.49634	-0.8919	9	.	.	.	-0.6536	13.5825	0.61911	0.0:1.0:0.0:0.0	.	382	Q8NET4	RGAG1_HUMAN	C	382	ENSP00000419786:S382C;ENSP00000441452:S382C	.	S	+	2	0	RGAG1	109581646	0.345000	0.24835	0.009000	0.14445	0.264000	0.26372	3.768000	0.55295	2.373000	0.80994	0.600000	0.82982	TCT		0.542	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109694990	C	G	109694990	3	3	106	1	0	0	0	0	1	0	0	0	13311	913	32	5	1147	5	RGAG1	23	109694990	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	6345647	109694990	45575570	178	28050										
PAK3	5063	hgsc.bcm.edu	37	chrX	110463671	110463671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	agcaattaagaacagcagccGctaagactgcaagccttaca	8	11	0	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:110463671G>A	ENST00000372010.1	+	19	2118	c.1676G>A	c.(1675-1677)cGc>cAc	p.R559H	PAK3_ENST00000425146.1_Missense_Mutation_p.R544H|PAK3_ENST00000446737.1_Missense_Mutation_p.R544H|PAK3_ENST00000417227.1_Missense_Mutation_p.R565H|PAK3_ENST00000360648.4_Missense_Mutation_p.R580H|PAK3_ENST00000372007.5_Missense_Mutation_p.R544H|PAK3_ENST00000519681.1_Missense_Mutation_p.R565H|PAK3_ENST00000262836.4_Missense_Mutation_p.R559H|PAK3_ENST00000518291.1_Missense_Mutation_p.R580H			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	559					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						AACAGCAGCCGCTAAGACTGC	0.448										TSP Lung(19;0.15)																																						0			X											41	36	38					X																	110463671		2203	4300	6503	110350327	SO:0001583	missense	8874			AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1676G>A	X.37:g.110463671G>A	ENSP00000361080:p.Arg559His		110350327	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	37	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956313	0.92726	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.73681	-0.69;-0.69;-0.7;-0.77;-0.69;-0.72;-0.72;-0.77;-0.7	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.78407	0.4278	N	0.14661	0.345	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.999	D;D;D;D	0.77004	0.938;0.967;0.976;0.989	T	0.81986	-0.0681	10	0.87932	D	0	.	19.7362	0.96205	0.0:0.0:1.0:0.0	.	565;580;559;544	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	H	544;544;559;565;544;580;580;565;559	ENSP00000410853:R544H;ENSP00000401982:R544H;ENSP00000361080:R559H;ENSP00000429113:R565H;ENSP00000361077:R544H;ENSP00000428921:R580H;ENSP00000353864:R580H;ENSP00000389172:R565H;ENSP00000262836:R559H	ENSP00000262836:R559H	R	+	2	0	PAK3	110350327	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.564000	0.82326	2.618000	0.88619	0.600000	0.82982	CGC		0.448	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110463671	G	A	110463671	3	1	106	1	0	0	0	0	1	0	0	0	11433	1087	38	1	1801	1	PAK3	23	110463671	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	768681	110463671	44806889	179	28051										
DCX	1641	hgsc.bcm.edu	37	chrX	110653620	110653620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtcaaagtgtccaaaatcaaGttccatattttggtggaacc	8	8	2	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:110653620G>A	ENST00000338081.3	-	2	421	c.250C>T	c.(250-252)Ctt>Ttt	p.L84F	DCX_ENST00000488120.1_Missense_Mutation_p.L3F|DCX_ENST00000356220.3_Missense_Mutation_p.L3F|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000371993.2_Missense_Mutation_p.L3F|DCX_ENST00000356915.2_Missense_Mutation_p.L3F	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	84					axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						CCAAAATCAAGTTCCATATTT	0.493																																																0			X											88	81	83					X																	110653620		2203	4300	6503	110540276	SO:0001583	missense	1641			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.250C>T	X.37:g.110653620G>A	ENSP00000337697:p.Leu84Phe		110540276	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	37	CCDS14556.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016856	0.75161	.	.	ENSG00000077279	ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120;ENST00000468911	T;T;T;T;T;T	0.52057	1.57;1.57;1.35;1.57;1.57;0.68	5.37	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.42832	0.1220	N	0.08118	0	0.50039	D	0.999845	D;P	0.59357	0.985;0.568	P;B	0.57009	0.811;0.302	T	0.52909	-0.8512	10	0.87932	D	0	.	13.0652	0.59030	0.0785:0.0:0.9214:0.0	.	72;84	B4DM53;O43602	.;DCX_HUMAN	F	3;3;84;3;3;3	ENSP00000349385:L3F;ENSP00000361061:L3F;ENSP00000337697:L84F;ENSP00000348553:L3F;ENSP00000419861:L3F;ENSP00000418811:L3F	ENSP00000337697:L84F	L	-	1	0	DCX	110540276	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.808000	0.86044	1.238000	0.43771	0.513000	0.50165	CTT		0.493	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		A	110653620	G	A	110653620	3	1	106	1	0	0	0	0	1	0	0	0	4324	1029	36	3	1114	3	DCX	23	110653620	Missense_Mutation	SNP	G	TCGA-DY-A1DF-01A-11D-A152-10	189949	110653620	44616940	180	28052										
WDR44	54521	hgsc.bcm.edu	37	chrX	117576246	117576246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	aaatacatgtccgatctactAgagggcgcaacaaggttgga	11	8	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:117576246A>G	ENST00000254029.3	+	16	2601	c.2206A>G	c.(2206-2208)Aga>Gga	p.R736G	WDR44_ENST00000371822.5_Missense_Mutation_p.R647G|WDR44_ENST00000371825.3_Missense_Mutation_p.R736G	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	736						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.R736G(1)		breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						CCGATCTACTAGAGGGCGCAA	0.363																																																1	Substitution - Missense(1)	lung(1)	X											145	138	140					X																	117576246		2203	4300	6503	117460274	SO:0001583	missense	54521			AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.2206A>G	X.37:g.117576246A>G	ENSP00000254029:p.Arg736Gly		117460274	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.194334|4.194334	0.78902|0.78902	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825;ENST00000318919|ENST00000371848	T;T;T|.	0.81415|.	-1.49;-0.42;-0.3|.	5.43|5.43	5.43|5.43	0.79202|0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77184|.	0.4093|.	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.998;1.0;1.0;0.999|.	D;D;D;D|.	0.91635|.	0.982;0.982;0.999;0.978|.	T|.	0.79366|.	-0.1833|.	10|.	0.87932|.	D|.	0|.	-19.4569|-19.4569	14.5295|14.5295	0.67915|0.67915	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	647;736;736;736|.	F8W913;E9PCI7;Q5JSH3-2;Q5JSH3|.	.;.;.;WDR44_HUMAN|.	G|W	647;736;736;122|635	ENSP00000360887:R647G;ENSP00000254029:R736G;ENSP00000360890:R736G|.	ENSP00000254029:R736G|.	R|X	+|+	1|2	2|0	WDR44|WDR44	117460274|117460274	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.772000|0.772000	0.43724|0.43724	8.671000|8.671000	0.91174|0.91174	1.811000|1.811000	0.52892|0.52892	0.427000|0.427000	0.28365|0.28365	AGA|TAG		0.363	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		G	117576246	A	G	117576246	3	3	106	1	0	0	0	0	1	0	0	0	17336	412	15	4	2268	4	WDR44	23	117576246	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	6922626	117576246	37694314	181	28053										
ODZ1	10178	hgsc.bcm.edu	37	chrX	124030055	124030055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	catgtctgtttggtagccagAgcacagagtgtgagaggttt	14	6	1	3	rs151298344		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:124030055A>G	ENST00000371130.3	-	2	316	c.253T>C	c.(253-255)Tct>Cct	p.S85P	TENM1_ENST00000422452.2_Missense_Mutation_p.S85P	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	85	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TGGTAGCCAGAGCACAGAGTG	0.463																																																0			X						A	PRO/SER,PRO/SER,PRO/SER	3,3832		0,3,1629,571	134	116	122		253,253,253	4.3	1	X	dbSNP_134	122	0,6728		0,0,2428,1872	no	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	74,74,74	0,3,4057,2443	GG,GA,AA,A		0.0,0.0782,0.0284	benign,benign,benign	85/2733,85/2732,85/2726	124030055	3,10560	2203	4300	6503	123857736	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.253T>C	X.37:g.124030055A>G	ENSP00000360171:p.Ser85Pro		123857736	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.000462	0.35320	7.82E-4	0.0	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.33865	1.39;1.39	5.56	4.32	0.51571	Teneurin intracellular, N-terminal (2);	0.179213	0.35772	N	0.002982	T	0.29850	0.0746	L	0.43152	1.355	0.43522	D	0.995799	P;P;P	0.42123	0.771;0.771;0.771	B;B;B	0.39805	0.31;0.31;0.31	T	0.06698	-1.0812	10	0.45353	T	0.12	.	9.6893	0.40118	0.739:0.0:0.0:0.261	.	85;85;85	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	P	85	ENSP00000360171:S85P;ENSP00000403954:S85P	ENSP00000360171:S85P	S	-	1	0	ODZ1	123857736	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.933000	0.48948	1.972000	0.57404	0.486000	0.48141	TCT		0.463	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	124030055	A	G	124030055	3	3	106	1	0	0	0	0	1	0	0	0	10865	304	11	4	8069	4	ODZ1	23	124030055	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	6453809	124030055	31240505	182	28054										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138813814	138813814	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gtttaacactaggtacctgtTacaatacattagattcgtct	6	8	1	1			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:138813814T>A	ENST00000327569.3	-	29	3496	c.3398A>T	c.(3397-3399)tAa>tTa	p.*1133L	ATP11C_ENST00000361648.2_Intron|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000370557.1_Intron	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	0					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					AGGTACCTGTTACAATACATT	0.363																																																0			X											108	99	102					X																	138813814		2203	4299	6502	138641480	SO:0001578	stop_lost	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.3398A>T	X.37:g.138813814T>A			138641480	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.832089	0.50845	.	.	ENSG00000101974	ENST00000327569	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7301	0.57193	0.0:0.0:0.0:1.0	.	.	.	.	L	1133	.	.	X	-	2	2	ATP11C	138641480	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.104000	0.64584	1.942000	0.56320	0.483000	0.47432	TAA		0.363	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		A	138813814	T	A	138813814	4	1	106	1	0	0	0	0	0	0	0	0	1122	1761	61	5	71	5	ATP11C	23	138813814	Nonstop_Mutation	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	14783759	138813814	16456746	183	28055										
MAGEA10	4109	hgsc.bcm.edu	37	chrX	151303091	151303091	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	gctctctcttcctcatctttCaaagcctcctcataccacag	3	17	6	0			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:151303091C>G	ENST00000370323.4	-	4	1318	c.1002G>C	c.(1000-1002)ttG>ttC	p.L334F	MAGEA10_ENST00000244096.3_Missense_Mutation_p.L334F|RP11-1007I13.4_ENST00000509345.2_RNA	NM_001251828.1|NM_021048.4	NP_001238757.1|NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	334						nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCATCTTTCAAAGCCTCCT	0.488																																																0			X											183	156	165					X																	151303091		2203	4300	6503	151053747	SO:0001583	missense	4109				CCDS14705.1	Xq28	2009-03-13			ENSG00000124260	ENSG00000124260			6797	protein-coding gene	gene with protein product	"MAGE-10 antigen", "melanoma-associated antigen 10", "cancer/testis antigen family 1, member 10"	300343		MAGE10		8575766	Standard	NM_001011543		Approved	MGC10599, CT1.10	uc004ffl.3	P43363	OTTHUMG00000024180	ENST00000370323.4:c.1002G>C	X.37:g.151303091C>G	ENSP00000359347:p.Leu334Phe		151053747		Missense_Mutation	SNP	ENST00000370323.4	37	CCDS14705.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786030	0.31593	.	.	ENSG00000124260	ENST00000370323;ENST00000244096	T;T	0.02787	4.16;4.16	2.6	0.717	0.18196	.	0.706510	0.12428	N	0.469765	T	0.03739	0.0106	M	0.75264	2.295	0.09310	N	1	P	0.36577	0.558	B	0.31751	0.135	T	0.35649	-0.9780	10	0.66056	D	0.02	.	2.8416	0.05531	0.2707:0.5634:0.0:0.1659	.	334	P43363	MAGAA_HUMAN	F	334	ENSP00000359347:L334F;ENSP00000244096:L334F	ENSP00000244096:L334F	L	-	3	2	MAGEA10	151053747	0.002000	0.14202	0.001000	0.08648	0.828000	0.46876	-0.127000	0.10547	0.065000	0.16485	0.292000	0.19580	TTG		0.488	MAGEA10-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060916.3	NM_021048		G	151303091	C	G	151303091	3	3	106	1	0	0	0	0	1	0	0	0	9194	825	29	5	111	5	MAGEA10	23	151303091	Missense_Mutation	SNP	C	TCGA-DY-A1DF-01A-11D-A152-10	12489277	151303091	3967469	184	28056										
FAM50A	9130	hgsc.bcm.edu	37	chrX	153674896	153674896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cggccatgtatgaggaggagAtggaaagggaaggtgagggc	20	4	0	3			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:153674896A>G	ENST00000393600.3	+	4	540	c.430A>G	c.(430-432)Atg>Gtg	p.M144V		NM_004699.3	NP_004690.1	Q14320	FA50A_HUMAN	family with sequence similarity 50, member A	144					spermatogenesis (GO:0007283)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|lung(9)|ovary(2)|skin(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGAGGAGGAGATGGAAAGGGA	0.627																																																0			X											75	49	58					X																	153674896		2195	4290	6485	153328090	SO:0001583	missense	9130			BC000028	CCDS14751.1	Xq28	2008-02-05			ENSG00000071859	ENSG00000071859			18786	protein-coding gene	gene with protein product	"DNA segment on chromosome X (unique) 9928 expressed sequence"	300453				9339379, 9039504	Standard	NM_004699		Approved	DXS9928E, XAP5, HXC-26, 9F	uc004fll.4	Q14320	OTTHUMG00000033292	ENST00000393600.3:c.430A>G	X.37:g.153674896A>G	ENSP00000377225:p.Met144Val		153328090	A8KAQ4|B2R997|Q5HY37|Q6PJH5	Missense_Mutation	SNP	ENST00000393600.3	37	CCDS14751.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.402903	0.25291	.	.	ENSG00000071859	ENST00000393600;ENST00000158526	.	.	.	5.27	3.48	0.39840	.	1.246750	0.05468	N	0.552468	T	0.30634	0.0771	N	0.22421	0.69	0.20926	N	0.999823	B	0.02656	0.0	B	0.01281	0.0	T	0.24941	-1.0146	9	0.30078	T	0.28	-3.0724	7.1865	0.25803	0.1707:0.7381:0.0:0.0912	.	144	Q14320	FA50A_HUMAN	V	144;104	.	ENSP00000158526:M104V	M	+	1	0	FAM50A	153328090	1.000000	0.71417	0.982000	0.44146	0.963000	0.63663	0.736000	0.26130	0.429000	0.26202	-0.344000	0.07964	ATG		0.627	FAM50A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081643.2	NM_004699		G	153674896	A	G	153674896	3	3	106	1	0	0	0	0	1	0	0	0	5596	333	12	4	444	4	FAM50A	23	153674896	Missense_Mutation	SNP	A	TCGA-DY-A1DF-01A-11D-A152-10	2371805	153674896	1595664	185	28057										
F8	2157	hgsc.bcm.edu	37	chrX	154158428	154158428	+	Frame_Shift_Del	DEL	T	T	-													0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	cttttctatttcttcctgaaTttttttttcttgattgtgtg					rs387906450		TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:154158428delT	ENST00000360256.4	-	14	3837	c.3637delA	c.(3637-3639)attfs	p.I1213fs		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1213	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCTTCCTGAATTTTTTTTTCT	0.328																																																0			X	GRCh37	CD930955	F8	D							26	25	25					X																	154158428		2203	4294	6497	153811622	SO:0001589	frameshift_variant	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3637delA	X.37:g.154158428delT	ENSP00000353393:p.Ile1213fs		153811622	Q14286|Q5HY69	Frame_Shift_Del	DEL	ENST00000360256.4	37	CCDS35457.1																																																																																				0.328	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			-	154158428	T	-	154158428	7	5	106	1	0	1	0	1	0	0	0	0	5363	1493	52	0	3498	0	F8	23	154158428	Frame_Shift_Del	DEL	T	TCGA-DY-A1DF-01A-11D-A152-10	483532	154158428	1112132	186	28058										
TMLHE	55217	hgsc.bcm.edu	37	chrX	154743709	154743709	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043010752688172	8	1	0.570400500625782	2.87237394957983	0.167555147058824	0.201556064073226	0.66867542651632	0	tgagtgggagggacattttcTacgaatgcaattccatagag	12	6	1	2			TCGA-DY-A1DF-01A-11D-A152-10	TCGA-DY-A1DF-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c4a43dba-1cef-4c03-bc80-47e4a7c3b7b9	89dc6a4a-1cae-4ac7-99b8-6a6752671939	g.chrX:154743709T>C	ENST00000334398.3	-	4	721	c.576A>G	c.(574-576)gtA>gtG	p.V192V	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Silent_p.V192V	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	192					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)			breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	GGACATTTTCTACGAATGCAA	0.408																																																0			X											127	115	119					X																	154743709		2203	4300	6503	154396903	SO:0001819	synonymous_variant	55217			AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.576A>G	X.37:g.154743709T>C			154396903	A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Silent	SNP	ENST00000334398.3	37	CCDS14768.1																																																																																				0.408	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196		C	154743709	T	C	154743709	2	2	106	1	0	0	0	0	0	0	0	1	16271	1509	53	4		4	TMLHE	23	154743709	Silent	SNP	T	TCGA-DY-A1DF-01A-11D-A152-10	585281	154743709	526851	187	28059										
CCDC27	148870	hgsc.bcm.edu	37	chr1	3683865	3683865	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcagagttggacaccaaggtCagccagctgcaggagcaggt	14	10	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:3683865C>T	ENST00000294600.2	+	10	1683	c.1599C>T	c.(1597-1599)gtC>gtT	p.V533V		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	533										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		ACACCAAGGTCAGCCAGCTGC	0.567																																																0			1											56	55	55					1																	3683865		2203	4300	6503	3673725	SO:0001819	synonymous_variant	148870				CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1599C>T	1.37:g.3683865C>T			3673725	Q5TBV3|Q96M50	Silent	SNP	ENST00000294600.2	37	CCDS50.1																																																																																				0.567	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		T	3683865	C	T	3683865	2	4	107	1	0	0	0	0	0	0	0	1	2807	813	29	3		3	CCDC27	1	3683865	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		3683865	245566756	1	28060										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561700	11561700	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaggatctggcagccaaccaGagtgaagacccgcgaaacca	12	12	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:11561700G>T	ENST00000294484.6	+	2	789	c.651G>T	c.(649-651)caG>caT	p.Q217H	PTCHD2_ENST00000389575.3_Missense_Mutation_p.Q217H	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	217					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)	p.Q434H(1)		NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CAGCCAACCAGAGTGAAGACC	0.682																																																1	Substitution - Missense(1)	breast(1)	1											10	14	13					1																	11561700		1983	4138	6121	11484287	SO:0001583	missense	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.651G>T	1.37:g.11561700G>T	ENSP00000294484:p.Gln217His		11484287	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.585420	0.46110	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.25250	1.81;1.81	5.07	4.16	0.48862	.	1.017510	0.07948	U	0.980425	T	0.14356	0.0347	N	0.08118	0	0.24671	N	0.993416	P	0.41041	0.736	B	0.38712	0.28	T	0.11842	-1.0571	10	0.33940	T	0.23	-17.3318	7.9752	0.30151	0.1865:0.0:0.8135:0.0	.	217	Q9P2K9	PTHD2_HUMAN	H	217	ENSP00000294484:Q217H;ENSP00000374226:Q217H	ENSP00000294484:Q217H	Q	+	3	2	PTCHD2	11484287	0.005000	0.15991	0.780000	0.31762	0.413000	0.31143	0.722000	0.25925	1.146000	0.42352	0.491000	0.48974	CAG		0.682	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11561700	G	T	11561700	3	4	107	1	0	0	0	0	1	0	0	0	12767	933	33	2	653	2	PTCHD2	1	11561700	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	7877835	11561700	237688921	2	28061										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11562804	11562804	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgagggcctctctgcagacaAtctgaagagctccctcctgc	10	14	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:11562804A>T	ENST00000294484.6	+	3	1304	c.1166A>T	c.(1165-1167)aAt>aTt	p.N389I	PTCHD2_ENST00000389575.3_Missense_Mutation_p.N389I	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	389					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		TCTGCAGACAATCTGAAGAGC	0.577																																																0			1											69	70	69					1																	11562804		1952	4159	6111	11485391	SO:0001583	missense	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1166A>T	1.37:g.11562804A>T	ENSP00000294484:p.Asn389Ile		11485391	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.474520	0.84640	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.27256	1.68;1.68	6.08	6.08	0.98989	.	0.102011	0.64402	D	0.000003	T	0.31009	0.0783	L	0.27053	0.805	0.48452	D	0.999656	D	0.55800	0.973	P	0.52909	0.713	T	0.03268	-1.1054	10	0.62326	D	0.03	-34.3021	15.4678	0.75416	1.0:0.0:0.0:0.0	.	389	Q9P2K9	PTHD2_HUMAN	I	389	ENSP00000294484:N389I;ENSP00000374226:N389I	ENSP00000294484:N389I	N	+	2	0	PTCHD2	11485391	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.164000	0.58190	2.333000	0.79357	0.533000	0.62120	AAT		0.577	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11562804	A	T	11562804	3	4	107	1	0	0	0	0	1	0	0	0	12767	101	4	5	1172	5	PTCHD2	1	11562804	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1104	11562804	237687817	3	28062										
FBXO44	93611	hgsc.bcm.edu	37	chr1	11718862	11718862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcctgtcgtccgcgcacgcGcctctggggaccttccagcc	11	19	1	0	rs376358727		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:11718862G>A	ENST00000251547.5	+	5	640	c.558G>A	c.(556-558)gcG>gcA	p.A186A	FBXO44_ENST00000376762.4_Missense_Mutation_p.A145T|FBXO44_ENST00000376768.1_Missense_Mutation_p.A177T|FBXO44_ENST00000376770.1_Silent_p.A186A|FBXO44_ENST00000251546.4_Missense_Mutation_p.A145T|FBXO44_ENST00000376760.1_Missense_Mutation_p.A145T	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	186	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CCGCGCACGCGCCTCTGGGGA	0.682													G|||	1	0.000199681	0	0.0014	5008	,	,		14143	0		0	False		,,,				2504	0															0			1						G	,,THR/ALA,THR/ALA	0,4406		0,0,2203	57	57	57		558,558,433,433	-7.1	0.1	1		57	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,58,58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,	186/256,186/256,145/225,145/225	11718862	2,13004	2203	4300	6503	11641449	SO:0001819	synonymous_variant	93611			AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"F-boxes /  "other""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.558G>A	1.37:g.11718862G>A			11641449	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.514669	0.00975	0.0	2.33E-4	ENSG00000132879	ENST00000251546;ENST00000425796;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T;T	0.42513	0.97;1.21;1.14;0.97;0.97	5.01	-7.09	0.01553	.	1.846850	0.02431	N	0.083549	T	0.19287	0.0463	.	.	.	0.22940	N	0.99854	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.32188	-0.9916	9	0.07644	T	0.81	-25.2619	10.4287	0.44393	0.1568:0.241:0.6022:0.0	.	177;145	B7Z1P2;Q9H4M3-2	.;.	T	145;145;177;145;145	ENSP00000251546:A145T;ENSP00000389820:A145T;ENSP00000365959:A177T;ENSP00000365953:A145T;ENSP00000365951:A145T	ENSP00000251546:A145T	A	+	1	0	FBXO44	11641449	0.000000	0.05858	0.134000	0.22075	0.120000	0.20174	-2.277000	0.01160	-1.244000	0.02516	-0.350000	0.07774	GCC		0.682	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412		A	11718862	G	A	11718862	2	1	107	1	0	0	0	0	0	0	0	1	5772	1087	38	1		1	FBXO44	1	11718862	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	156058	11718862	237531759	4	28063										
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15863099	15863099	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tccatgaaaatttttattttGatgaatccttttttcacttc	3	7	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:15863099G>A	ENST00000375847.3	+	4	528	c.364G>A	c.(364-366)Gat>Aat	p.D122N	DNAJC16_ENST00000375849.1_Missense_Mutation_p.D122N|DNAJC16_ENST00000375838.1_Missense_Mutation_p.D122N	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	122	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TTTTTATTTTGATGAATCCTT	0.403																																																0			1											90	97	95					1																	15863099		2203	4300	6503	15735686	SO:0001583	missense	23341			AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.364G>A	1.37:g.15863099G>A	ENSP00000365007:p.Asp122Asn		15735686	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	37	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040898	0.75732	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.72942	-0.7;-0.7;-0.7	5.62	5.62	0.85841	Thioredoxin-like fold (1);	0.092055	0.64402	D	0.000001	T	0.70465	0.3227	L	0.44542	1.39	0.39520	D	0.968496	P;P	0.47191	0.891;0.891	P;P	0.46452	0.517;0.517	T	0.70680	-0.4805	10	0.39692	T	0.17	-23.2059	18.587	0.91194	0.0:0.0:1.0:0.0	.	122;122	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	N	122	ENSP00000365007:D122N;ENSP00000364998:D122N;ENSP00000365009:D122N	ENSP00000364998:D122N	D	+	1	0	DNAJC16	15735686	1.000000	0.71417	0.942000	0.38095	0.833000	0.47200	8.540000	0.90641	2.809000	0.96659	0.655000	0.94253	GAT		0.403	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		A	15863099	G	A	15863099	3	1	107	1	0	0	0	0	1	0	0	0	4646	1290	45	3	374	3	DNAJC16	1	15863099	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4144237	15863099	233387522	5	28064										
LYPLA2	11313	hgsc.bcm.edu	37	chr1	24120368	24120368	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggtttgacctgatggggctGagtccagatgccccagagga	15	9	0	5			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:24120368G>A	ENST00000374514.3	+	6	550	c.243G>A	c.(241-243)ctG>ctA	p.L81L	LYPLA2_ENST00000495365.1_Intron|LYPLA2_ENST00000400061.1_Silent_p.L81L|LYPLA2_ENST00000374502.3_Silent_p.L81L|LYPLA2_ENST00000374505.2_Silent_p.L81L|LYPLA2_ENST00000374503.3_Silent_p.L81L|LYPLA2_ENST00000374501.1_Silent_p.L14L	NM_007260.2	NP_009191.1	O95372	LYPA2_HUMAN	lysophospholipase II	81					fatty acid metabolic process (GO:0006631)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		TGATGGGGCTGAGTCCAGATG	0.627																																																0			1											96	99	98					1																	24120368		2203	4300	6503	23992955	SO:0001819	synonymous_variant	11313			AF098668	CCDS241.1	1p36.11	2008-08-08			ENSG00000011009	ENSG00000011009	3.1.1.5		6738	protein-coding gene	gene with protein product							Standard	NM_007260		Approved	APT-2	uc001bht.3	O95372	OTTHUMG00000002961	ENST00000374514.3:c.243G>A	1.37:g.24120368G>A			23992955	Q7Z4Z2	Silent	SNP	ENST00000374514.3	37	CCDS241.1																																																																																				0.627	LYPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008245.1			A	24120368	G	A	24120368	2	1	107	1	0	0	0	0	0	0	0	1	9147	1277	45	3		3	LYPLA2	1	24120368	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8257269	24120368	225130253	6	28065										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27057935	27057935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acagcagcacccccagagccAgcccccctactcacagccac	6	22	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:27057935A>G	ENST00000324856.7	+	3	2014	c.1643A>G	c.(1642-1644)cAg>cGg	p.Q548R	ARID1A_ENST00000374152.2_Missense_Mutation_p.Q165R|ARID1A_ENST00000457599.2_Missense_Mutation_p.Q548R	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	548					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		CCCCAGAGCCAGCCCCCCTAC	0.647			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											171	181	177					1																	27057935		2203	4300	6503	26930522	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1643A>G	1.37:g.27057935A>G	ENSP00000320485:p.Gln548Arg		26930522	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.099407	0.37048	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02656	4.45;4.21;4.24	5.44	5.44	0.79542	.	0.145657	0.47093	D	0.000260	T	0.02494	0.0076	L	0.27053	0.805	0.80722	D	1	B;B;B	0.18461	0.016;0.028;0.016	B;B;B	0.14578	0.005;0.011;0.008	T	0.53049	-0.8493	10	0.12766	T	0.61	-6.7819	11.6267	0.51149	0.8516:0.1484:0.0:0.0	.	548;548;202	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	R	548;548;165	ENSP00000320485:Q548R;ENSP00000387636:Q548R;ENSP00000363267:Q165R	ENSP00000320485:Q548R	Q	+	2	0	ARID1A	26930522	1.000000	0.71417	1.000000	0.80357	0.251000	0.25915	3.928000	0.56506	2.278000	0.76064	0.533000	0.62120	CAG		0.647	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27057935	A	G	27057935	3	3	107	1	0	0	0	0	1	0	0	0	913	188	7	4	1653	4	ARID1A	1	27057935	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2937567	27057935	222192686	7	28066										
WASF2	10163	hgsc.bcm.edu	37	chr1	27739086	27739086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctgaattctgctggtggaggAggcaagttgtcctcggagaa	15	7	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:27739086A>G	ENST00000430629.2	-	7	1019	c.804T>C	c.(802-804)ccT>ccC	p.P268P	WASF2_ENST00000536657.1_Silent_p.P268P	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	268	Poly-Pro.				actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		CTGGTGGAGGAGGCAAGTTGT	0.488																																																0			1											183	160	168					1																	27739086		2203	4300	6503	27611673	SO:0001819	synonymous_variant	10163			AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.804T>C	1.37:g.27739086A>G			27611673	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	37	CCDS304.1																																																																																				0.488	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27739086	A	G	27739086	2	3	107	1	0	0	0	0	0	0	0	1	17293	291	11	4		4	WASF2	1	27739086	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	681151	27739086	221511535	8	28067										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34076686	34076686	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccgattctgggagtggtcgcTgtggaaatacacggtggtct	15	8	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:34076686T>C	ENST00000373380.1	-	20	3137	c.2917A>G	c.(2917-2919)Agc>Ggc	p.S973G	CSMD2_ENST00000373377.1_Missense_Mutation_p.S199G|CSMD2_ENST00000373388.2_Missense_Mutation_p.S199G|CSMD2_ENST00000373381.4_Missense_Mutation_p.S2100G			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2060	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GAGTGGTCGCTGTGGAAATAC	0.562																																																0			1											120	101	108					1																	34076686		2203	4300	6503	33849273	SO:0001583	missense	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2917A>G	1.37:g.34076686T>C	ENSP00000362478:p.Ser973Gly		33849273	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37		.	.	.	.	.	.	.	.	.	.	T	26.5	4.741121	0.89573	.	.	ENSG00000121904	ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.26	5.26	0.73747	CUB (5);	0.000000	0.85682	D	0.000000	T	0.79822	0.4512	H	0.99454	4.575	0.58432	D	0.999998	D;D;D	0.76494	0.987;0.999;0.999	D;D;D	0.91635	0.992;0.999;0.999	D	0.88549	0.3115	10	0.87932	D	0	.	14.3657	0.66805	0.0:0.0:0.0:1.0	.	973;2060;2100	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	G	2100;973;199;199	ENSP00000362479:S2100G;ENSP00000362478:S973G;ENSP00000362475:S199G;ENSP00000362486:S199G	ENSP00000241312:S2060G	S	-	1	0	CSMD2	33849273	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.967000	0.87967	1.999000	0.58509	0.459000	0.35465	AGC		0.562	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		C	34076686	T	C	34076686	3	2	107	1	0	0	0	0	1	0	0	0	3951	1580	55	4	4401	4	CSMD2	1	34076686	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	6337600	34076686	215173935	9	28068										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35853091	35853091	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctgtggcaagaattgttctGatgaatataagaaaataaat	8	3	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:35853091G>A	ENST00000314607.6	+	13	2229	c.2149G>A	c.(2149-2151)Gat>Aat	p.D717N	ZMYM4_ENST00000373297.2_Missense_Mutation_p.D628N	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	717					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D717N(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GAATTGTTCTGATGAATATAA	0.318																																																1	Substitution - Missense(1)	ovary(1)	1											66	73	70					1																	35853091		2203	4300	6503	35625678	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2149G>A	1.37:g.35853091G>A	ENSP00000322915:p.Asp717Asn		35625678	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691074	0.88735	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25579	1.79;1.89	5.36	5.36	0.76844	TRASH (1);Zinc finger, MYM-type (1);	0.320878	0.32836	N	0.005589	T	0.49201	0.1543	M	0.70275	2.135	0.50632	D	0.99988	D	0.69078	0.997	D	0.67548	0.952	T	0.34129	-0.9841	10	0.26408	T	0.33	-17.0785	18.0677	0.89396	0.0:0.0:1.0:0.0	.	717	Q5VZL5	ZMYM4_HUMAN	N	717;628	ENSP00000322915:D717N;ENSP00000362394:D628N	ENSP00000322915:D717N	D	+	1	0	ZMYM4	35625678	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.189000	0.77747	2.498000	0.84270	0.655000	0.94253	GAT		0.318	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35853091	G	A	35853091	3	1	107	1	0	0	0	0	1	0	0	0	17741	1290	45	3	2199	3	ZMYM4	1	35853091	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	1776405	35853091	213397530	10	28069										
YBX1	4904	hgsc.bcm.edu	37	chr1	43162405	43162405	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaccattatagacgctatccAcgtcgtaggggtcctccacg	9	13	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:43162405A>G	ENST00000321358.7	+	5	586	c.447A>G	c.(445-447)ccA>ccG	p.P149P	YBX1_ENST00000467957.1_3'UTR	NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	149					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GACGCTATCCACGTCGTAGGG	0.517																																																0			1											76	78	77					1																	43162405		2203	4300	6503	42934992	SO:0001819	synonymous_variant	4904			BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.447A>G	1.37:g.43162405A>G			42934992	P16990|P16991|Q14972|Q15325|Q5FVF0	Silent	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	A	9.671	1.146761	0.21288	.	.	ENSG00000065978	ENST00000436427	.	.	.	5.24	4.11	0.48088	.	.	.	.	.	T	0.54515	0.1863	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52503	-0.8567	4	.	.	.	-1.9726	6.0795	0.19933	0.8169:0.0:0.1831:0.0	.	.	.	.	R	199	.	.	H	+	2	0	YBX1	42934992	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.387000	0.34430	2.101000	0.63845	0.460000	0.39030	CAC		0.517	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		G	43162405	A	G	43162405	2	3	107	1	0	0	0	0	0	0	0	1	17509	146	6	4		4	YBX1	1	43162405	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	7309314	43162405	206088216	11	28070										
TIE1	7075	hgsc.bcm.edu	37	chr1	43778930	43778930	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gttgtggaggtgcaggtggcTgggggtgcaggagacccact	20	7	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:43778930T>C	ENST00000372476.3	+	13	2131	c.2052T>C	c.(2050-2052)gcT>gcC	p.A684A	TIE1_ENST00000433781.2_Silent_p.A329A	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	684	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGCAGGTGGCTGGGGGTGCAG	0.622																																																0			1											127	97	107					1																	43778930		2203	4300	6503	43551517	SO:0001819	synonymous_variant	7075			BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2052T>C	1.37:g.43778930T>C			43551517	B5A949|B5A950	Silent	SNP	ENST00000372476.3	37	CCDS482.1																																																																																				0.622	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		C	43778930	T	C	43778930	2	2	107	1	0	0	0	0	0	0	0	1	15932	1567	55	4		4	TIE1	1	43778930	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	616525	43778930	205471691	12	28071										
KIF2C	11004	hgsc.bcm.edu	37	chr1	45228107	45228107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaagcctgctctaacggggCgctgattccaggcaatgtaa	13	10	1	1	rs199917085		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:45228107C>T	ENST00000372224.4	+	18	1954	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	RP11-269F19.2_ENST00000440985.1_RNA|KIF2C_ENST00000372217.1_Missense_Mutation_p.A560V|RP11-269F19.2_ENST00000428791.1_RNA|KIF2C_ENST00000372222.3_Missense_Mutation_p.A501V|KIF2C_ENST00000372218.4_Missense_Mutation_p.A573V	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	614					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)	p.A614V(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					TCTAACGGGGCGCTGATTCCA	0.542													C|||	1	0.000199681	0	0	5008	,	,		20268	0		0	False		,,,				2504	0.001															1	Substitution - Missense(1)	large_intestine(1)	1											65	66	66					1																	45228107		2203	4300	6503	45000694	SO:0001583	missense	11004			U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1841C>T	1.37:g.45228107C>T	ENSP00000361298:p.Ala614Val		45000694	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	.	.	.	.	.	.	.	.	.	.	C	9.678	1.148626	0.21288	.	.	ENSG00000142945	ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217	T;T;T;T	0.74842	-0.87;-0.71;-0.88;-0.88	6.08	3.14	0.36123	.	1.181470	0.06017	N	0.650594	T	0.54532	0.1864	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.41466	-0.9507	10	0.29301	T	0.29	.	6.2177	0.20663	0.2642:0.5954:0.0:0.1404	.	573;560;614	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	V	614;573;501;560	ENSP00000361298:A614V;ENSP00000361292:A573V;ENSP00000361296:A501V;ENSP00000361291:A560V	ENSP00000361291:A560V	A	+	2	0	KIF2C	45000694	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	0.502000	0.22594	0.421000	0.25980	-0.169000	0.13324	GCG		0.542	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845		T	45228107	C	T	45228107	3	4	107	1	0	0	0	0	1	0	0	0	8320	768	27	1	1911	1	KIF2C	1	45228107	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1449177	45228107	204022514	13	28072										
TOE1	114034	hgsc.bcm.edu	37	chr1	45808078	45808078	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgatgagagccagagccagtCagtacggaccctattcctgg	12	11	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:45808078C>A	ENST00000372090.5	+	6	1098	c.515C>A	c.(514-516)tCa>tAa	p.S172*	MUTYH_ENST00000355498.2_5'Flank|TOE1_ENST00000539779.1_Nonsense_Mutation_p.S92*|MUTYH_ENST00000372100.5_5'Flank|MUTYH_ENST00000456914.2_5'Flank|MUTYH_ENST00000488731.2_5'Flank|MUTYH_ENST00000531105.1_5'Flank|MUTYH_ENST00000372098.3_5'Flank|MUTYH_ENST00000448481.1_5'Flank|MUTYH_ENST00000528013.2_5'Flank|MUTYH_ENST00000372115.3_5'Flank|MUTYH_ENST00000372110.3_5'Flank|MUTYH_ENST00000354383.6_5'Flank|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000372104.1_5'Flank|MUTYH_ENST00000450313.1_5'Flank|TESK2_ENST00000486676.1_5'Flank|TOE1_ENST00000495703.1_3'UTR|MUTYH_ENST00000528332.2_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	172						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					CAGAGCCAGTCAGTACGGACC	0.547																																																0			1											95	98	97					1																	45808078		2203	4300	6503	45580665	SO:0001587	stop_gained	114034				CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.515C>A	1.37:g.45808078C>A	ENSP00000361162:p.Ser172*		45580665	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Nonsense_Mutation	SNP	ENST00000372090.5	37	CCDS521.1	.	.	.	.	.	.	.	.	.	.	C	39	7.536756	0.98345	.	.	ENSG00000132773	ENST00000372090;ENST00000539779	.	.	.	5.79	4.83	0.62350	.	0.487580	0.23468	N	0.047846	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.9134	17.4089	0.87480	0.0:0.7993:0.2007:0.0	.	.	.	.	X	172;92	.	ENSP00000361162:S172X	S	+	2	0	TOE1	45580665	0.688000	0.27680	1.000000	0.80357	0.928000	0.56348	0.426000	0.21363	2.733000	0.93635	0.655000	0.94253	TCA		0.547	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077		A	45808078	C	A	45808078	4	1	107	1	0	0	0	0	0	1	0	0	16388	838	29	2	537	2	TOE1	1	45808078	Nonsense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	579971	45808078	203442543	14	28073										
INADL	10207	hgsc.bcm.edu	37	chr1	62321734	62321734	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctacaagatcagtgattgtGatccgctccctggtagcaga	10	11	1	4	rs41289422	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:62321734G>A	ENST00000371158.2	+	18	2259	c.2145G>A	c.(2143-2145)gtG>gtA	p.V715V	INADL_ENST00000316485.6_Silent_p.V715V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	715	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CAGTGATTGTGATCCGCTCCC	0.468																																																0			1											110	107	108					1																	62321734		2203	4300	6503	62094322	SO:0001819	synonymous_variant	10207			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2145G>A	1.37:g.62321734G>A			62094322	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																				0.468	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62321734	G	A	62321734	2	1	107	1	0	0	0	0	0	0	0	1	7752	1277	45	3		3	INADL	1	62321734	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	16513656	62321734	186928887	15	28074										
LEPR	3953	hgsc.bcm.edu	37	chr1	66081844	66081844	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atactgttacggttctggccAtcaattcaattggtgcttct	8	9	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:66081844A>T	ENST00000349533.6	+	15	2334	c.2149A>T	c.(2149-2151)Atc>Ttc	p.I717F	LEPR_ENST00000344610.8_Missense_Mutation_p.I717F|LEPR_ENST00000371060.3_Missense_Mutation_p.I717F|LEPR_ENST00000371058.1_Missense_Mutation_p.I717F|LEPR_ENST00000371059.3_Missense_Mutation_p.I717F|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GGTTCTGGCCATCAATTCAAT	0.413																																																0			1											160	149	153					1																	66081844		2203	4300	6503	65854432	SO:0001583	missense	54741			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2149A>T	1.37:g.66081844A>T	ENSP00000330393:p.Ile717Phe		65854432	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.409555	0.42715	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.5	-5.83	0.02325	Fibronectin, type III (2);	0.830792	0.11351	N	0.573001	T	0.26085	0.0636	N	0.25647	0.755	0.37986	D	0.933762	P;P;P	0.44734	0.756;0.842;0.809	P;P;P	0.48400	0.475;0.452;0.576	T	0.51395	-0.8711	10	0.10111	T	0.7	-0.73	17.7553	0.88446	0.3788:0.0:0.6212:0.0	.	717;717;717	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	F	717	ENSP00000340884:I717F;ENSP00000330393:I717F;ENSP00000360099:I717F;ENSP00000360098:I717F;ENSP00000360097:I717F	ENSP00000340884:I717F	I	+	1	0	LEPR	65854432	0.000000	0.05858	0.377000	0.26055	0.352000	0.29268	-0.437000	0.06914	-0.928000	0.03761	-0.899000	0.02877	ATC		0.413	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		T	66081844	A	T	66081844	3	4	107	1	0	0	0	0	1	0	0	0	8750	217	8	5	2199	5	LEPR	1	66081844	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3760110	66081844	183168777	16	28075										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70226013	70226013	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caggtgccaaaggaggtcttTaacttcgaacgaacattaga	10	8	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:70226013T>A	ENST00000035383.5	+	1	156	c.126T>A	c.(124-126)ttT>ttA	p.F42L	LRRC7_ENST00000415775.2_5'UTR|LRRC7_ENST00000370958.1_Missense_Mutation_p.F80L|LRRC7_ENST00000310961.5_Missense_Mutation_p.F47L	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	42						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						AGGAGGTCTTTAACTTCGAAC	0.413																																																0			1											85	84	84					1																	70226013		2203	4300	6503	69998601	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.126T>A	1.37:g.70226013T>A	ENSP00000035383:p.Phe42Leu		69998601	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.158393	0.57368	.	.	ENSG00000033122	ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298	T;T;T	0.51817	2.07;0.69;1.82	5.84	3.56	0.40772	.	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	N	0.20986	0.625	0.80722	D	1	P;D	0.61080	0.955;0.989	P;D	0.74348	0.833;0.983	T	0.15464	-1.0436	10	0.27082	T	0.32	.	7.1686	0.25706	0.0:0.3373:0.0:0.6627	.	42;80	Q96NW7;B1AKT2	LRRC7_HUMAN;.	L	47;80;42;42	ENSP00000309245:F47L;ENSP00000359997:F80L;ENSP00000035383:F42L	ENSP00000035383:F42L	F	+	3	2	LRRC7	69998601	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.239000	0.32719	0.503000	0.28060	0.528000	0.53228	TTT		0.413	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70226013	T	A	70226013	3	1	107	1	0	0	0	0	1	0	0	0	9049	1751	61	5	128	5	LRRC7	1	70226013	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	4144169	70226013	179024608	17	28076										
NEXN	91624	hgsc.bcm.edu	37	chr1	78383900	78383900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaacgaaaacgcagaattgAgcaggatatgttagaaaaga	12	4	0	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:78383900A>G	ENST00000334785.7	+	5	573	c.389A>G	c.(388-390)gAg>gGg	p.E130G	NEXN_ENST00000457030.1_Missense_Mutation_p.E130G|NEXN_ENST00000330010.8_Missense_Mutation_p.E66G|NEXN_ENST00000294624.8_Missense_Mutation_p.E130G	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		CGCAGAATTGAGCAGGATATG	0.378																																																0			1											130	127	128					1																	78383900		1908	4116	6024	78156488	SO:0001583	missense	91624			AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.389A>G	1.37:g.78383900A>G	ENSP00000333938:p.Glu130Gly		78156488		Missense_Mutation	SNP	ENST00000334785.7	37	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.26|19.26	3.792549|3.792549	0.70452|0.70452	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000401035;ENST00000457030;ENST00000330010;ENST00000294624;ENST00000334785;ENST00000440324|ENST00000342754	T;T;T;T;T;T|.	0.70631|.	-0.46;0.04;-0.28;-0.5;-0.0;-0.3|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.000000|.	0.53938|.	D|.	0.000060|.	T|T	0.68467|0.68467	0.3004|0.3004	M|M	0.73962|0.73962	2.25|2.25	0.43255|0.43255	D|D	0.995187|0.995187	P;P;P;P|.	0.50819|.	0.807;0.939;0.899;0.594|.	B;P;B;B|.	0.45610|.	0.231;0.487;0.421;0.231|.	T|T	0.69580|0.69580	-0.5107|-0.5107	10|5	0.62326|.	D|.	0.03|.	-16.3273|-16.3273	15.5278|15.5278	0.75925|0.75925	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	66;130;130;66|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	G|G	66;130;66;130;130;130|30	ENSP00000383814:E66G;ENSP00000388048:E130G;ENSP00000327363:E66G;ENSP00000294624:E130G;ENSP00000333938:E130G;ENSP00000411902:E130G|.	ENSP00000294624:E130G|.	E|S	+|+	2|1	0|0	NEXN|NEXN	78156488|78156488	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	5.907000|5.907000	0.69908|0.69908	2.320000|2.320000	0.78422|0.78422	0.528000|0.528000	0.53228|0.53228	GAG|AGC		0.378	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		G	78383900	A	G	78383900	3	3	107	1	0	0	0	0	1	0	0	0	10386	304	11	4	403	4	NEXN	1	78383900	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	8157887	78383900	170866721	18	28077										
ADORA3	140	hgsc.bcm.edu	37	chr1	112045664	112045664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccgcaagtatcggtccacagCgatggccagcaaggacatga	12	12	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:112045664C>T	ENST00000241356.4	-	1	718	c.313G>A	c.(313-315)Gct>Act	p.A105T	ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000369716.4_Missense_Mutation_p.A105T|ADORA3_ENST00000486342.1_5'UTR	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	105			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)	p.A105T(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	CGGTCCACAGCGATGGCCAGC	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											65	53	57					1																	112045664		2203	4300	6503	111847187	SO:0001583	missense	140			BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.313G>A	1.37:g.112045664C>T	ENSP00000241356:p.Ala105Thr		111847187	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.920791	0.92249	.	.	ENSG00000121933	ENST00000369716;ENST00000241356	T;T	0.76186	-1.0;-1.0	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000276	D	0.82930	0.5144	M	0.70108	2.13	0.53005	D	0.999968	D;D	0.76494	0.999;0.996	D;P	0.66497	0.944;0.879	D	0.84392	0.0555	10	0.72032	D	0.01	-14.8213	18.8155	0.92075	0.0:1.0:0.0:0.0	.	105;105	P33765;P33765-2	AA3R_HUMAN;.	T	105	ENSP00000358730:A105T;ENSP00000241356:A105T	ENSP00000241356:A105T	A	-	1	0	ADORA3	111847187	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.445000	0.80570	2.613000	0.88420	0.561000	0.74099	GCT		0.552	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683		T	112045664	C	T	112045664	3	4	107	1	0	0	0	0	1	0	0	0	329	768	27	1	1365	1	ADORA3	1	112045664	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	33661764	112045664	137204957	19	28078										
TRIM33	51592	hgsc.bcm.edu	37	chr1	114948146	114948146	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagcacaccagtcttcatttGggtcatcatctttattgttg	7	10	5	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:114948146G>T	ENST00000358465.2	-	15	2737	c.2654C>A	c.(2653-2655)cCa>cAa	p.P885Q	TRIM33_ENST00000369543.2_Missense_Mutation_p.P885Q|TRIM33_ENST00000450349.2_Missense_Mutation_p.P517Q|TRIM33_ENST00000476908.1_5'UTR	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	885			P -> S (in a glioblastoma multiforme sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		GTCTTCATTTGGGTCATCATC	0.468			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	0			1											270	235	247					1																	114948146		2203	4300	6503	114749669	SO:0001583	missense	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2654C>A	1.37:g.114948146G>T	ENSP00000351250:p.Pro885Gln		114749669	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.4|27.4	4.828058|4.828058	0.90955|0.90955	.|.	.|.	ENSG00000197323|ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349|ENST00000448034	D;D;T|.	0.85013|.	-1.93;-1.93;1.01|.	5.11|5.11	5.11|5.11	0.69529|0.69529	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	0.049961|.	0.85682|.	D|.	0.000000|.	T|T	0.49338|0.49338	0.1551|0.1551	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.87578|.	0.997;0.991;0.998;0.998;0.996|.	T|T	0.43426|0.43426	-0.9392|-0.9392	10|5	0.72032|.	D|.	0.01|.	-9.1981|-9.1981	18.8931|18.8931	0.92413|0.92413	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	517;517;80;885;885|.	E7EN20;B3KN30;Q9HAL0;Q9UPN9-2;Q9UPN9|.	.;.;.;.;TRI33_HUMAN|.	Q|K	885;885;517|646	ENSP00000351250:P885Q;ENSP00000358556:P885Q;ENSP00000412077:P517Q|.	ENSP00000351250:P885Q|.	P|Q	-|-	2|1	0|0	TRIM33|TRIM33	114749669|114749669	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	9.779000|9.779000	0.99018|0.99018	2.533000|2.533000	0.85409|0.85409	0.491000|0.491000	0.48974|0.48974	CCA|CAA		0.468	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		T	114948146	G	T	114948146	3	4	107	1	0	0	0	0	1	0	0	0	16547	1348	47	2	753	2	TRIM33	1	114948146	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2902482	114948146	134302475	20	28079										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120462032	120462032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctgcacctgcatccaggagaCgcttggcagcatcagcccgt	11	15	1	1	rs201996575		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:120462032C>T	ENST00000256646.2	-	31	5903	c.5684G>A	c.(5683-5685)cGt>cAt	p.R1895H		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1895					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATCCAGGAGACGCTTGGCAGC	0.622			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome				C|||	1	0.000199681	0	0	5008	,	,		17238	0.001		0	False		,,,				2504	0						Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0			1						C	HIS/ARG	0,4406		0,0,2203	65	58	61		5684	4.7	1	1		61	2,8598	2.2+/-6.3	0,2,4298	no	missense	NOTCH2	NM_024408.3	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	1895/2472	120462032	2,13004	2203	4300	6503	120263555	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5684G>A	1.37:g.120462032C>T	ENSP00000256646:p.Arg1895His		120263555	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	29.6	5.022029	0.93462	0.0	2.33E-4	ENSG00000134250	ENST00000256646	T	0.64438	-0.1	5.64	4.7	0.59300	Ankyrin repeat-containing domain (4);	0.000000	0.38492	U	0.001671	T	0.27832	0.0685	N	0.20807	0.61	0.80722	D	1	P	0.43750	0.816	B	0.31751	0.135	T	0.35001	-0.9806	10	0.72032	D	0.01	.	12.7339	0.57212	0.0:0.9181:0.0:0.0819	.	1895	Q04721	NOTC2_HUMAN	H	1895	ENSP00000256646:R1895H	ENSP00000256646:R1895H	R	-	2	0	NOTCH2	120263555	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.099000	0.71466	1.336000	0.45506	0.655000	0.94253	CGT		0.622	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120462032	C	T	120462032	3	4	107	1	0	0	0	0	1	0	0	0	10579	536	19	1	1747	1	NOTCH2	1	120462032	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5513886	120462032	128788589	21	28080										
BCL9	607	hgsc.bcm.edu	37	chr1	147092651	147092651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcagctggcaggcatgctggCgggcccagctgctgctgctt	16	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:147092651C>T	ENST00000234739.3	+	8	3430	c.2690C>T	c.(2689-2691)gCg>gTg	p.A897V		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	897	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GGCATGCTGGCGGGCCCAGCT	0.617			T	"IGH@, IGL@"	B-ALL																																		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	0			1											77	79	78					1																	147092651		2203	4300	6503	145559275	SO:0001583	missense	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.2690C>T	1.37:g.147092651C>T	ENSP00000234739:p.Ala897Val		145559275	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.650912	0.47362	.	.	ENSG00000116128	ENST00000234739	T	0.60548	0.18	5.41	5.41	0.78517	.	0.109710	0.64402	D	0.000007	T	0.29223	0.0727	N	0.19112	0.55	0.35785	D	0.821976	P;P	0.43662	0.814;0.814	B;B	0.30943	0.122;0.122	T	0.44636	-0.9315	10	0.72032	D	0.01	-11.1779	19.3785	0.94521	0.0:1.0:0.0:0.0	.	897;897	Q1JQ81;O00512	.;BCL9_HUMAN	V	897	ENSP00000234739:A897V	ENSP00000234739:A897V	A	+	2	0	BCL9	145559275	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.510000	0.60455	2.815000	0.96918	0.561000	0.74099	GCG		0.617	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		T	147092651	C	T	147092651	3	4	107	1	0	0	0	0	1	0	0	0	1382	768	27	1	2708	1	BCL9	1	147092651	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	26630619	147092651	102157970	22	28081										
FLG	2312	hgsc.bcm.edu	37	chr1	152282661	152282661	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gagtgtctagagctgccggcCcgagtggaaggttcatggtg	17	8	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:152282661C>A	ENST00000368799.1	-	3	4736	c.4701G>T	c.(4699-4701)cgG>cgT	p.R1567R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1567	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTGCCGGCCCGAGTGGAAG	0.582									Ichthyosis																																							0			1											188	198	195					1																	152282661		2203	4300	6503	150549285	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4701G>T	1.37:g.152282661C>A			150549285	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152282661	C	A	152282661	2	1	107	1	0	0	0	0	0	0	0	1	5941	610	22	2		2	FLG	1	152282661	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5190010	152282661	96967960	23	28082										
FLG2	388698	hgsc.bcm.edu	37	chr1	152327875	152327875	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gacttgagcctgacccatgtTgtccaaagccagatgtctgt	10	11	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:152327875T>C	ENST00000388718.5	-	3	2459	c.2387A>G	c.(2386-2388)cAa>cGa	p.Q796R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	796	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGACCCATGTTGTCCAAAGCC	0.517																																																0			1											220	206	211					1																	152327875		2203	4297	6500	150594499	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2387A>G	1.37:g.152327875T>C	ENSP00000373370:p.Gln796Arg		150594499	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	4.830	0.154363	0.09236	.	.	ENSG00000143520	ENST00000388718	T	0.04970	3.52	3.67	1.23	0.21249	.	.	.	.	.	T	0.01156	0.0038	L	0.28556	0.865	0.09310	N	1	B	0.15473	0.013	B	0.14023	0.01	T	0.48364	-0.9042	9	0.15952	T	0.53	-6.4447	3.5185	0.07734	0.0:0.2297:0.1999:0.5703	.	796	Q5D862	FILA2_HUMAN	R	796	ENSP00000373370:Q796R	ENSP00000373370:Q796R	Q	-	2	0	FLG2	150594499	0.002000	0.14202	0.002000	0.10522	0.222000	0.24845	0.736000	0.26130	0.506000	0.28125	0.329000	0.21502	CAA		0.517	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		C	152327875	T	C	152327875	3	2	107	1	0	0	0	0	1	0	0	0	5942	1812	63	4	4792	4	FLG2	1	152327875	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	45214	152327875	96922746	24	28083										
SPRR1B	6699	hgsc.bcm.edu	37	chr1	153005071	153005071	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcactccagcaccagcccagCagaagaccaagcagaagtaa	8	14	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:153005071C>A	ENST00000307098.4	+	2	315	c.250C>A	c.(250-252)Cag>Aag	p.Q84K	SPRR1B_ENST00000392661.3_Missense_Mutation_p.Q68K	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	84					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACCAGCCCAGCAGAAGACCAA	0.592																																																0			1											73	71	72					1																	153005071		2203	4300	6503	151271695	SO:0001583	missense	6699			M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"cornifin"	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.250C>A	1.37:g.153005071C>A	ENSP00000306461:p.Gln84Lys		151271695	B2R5H7|P22529|P22530|Q5T524	Missense_Mutation	SNP	ENST00000307098.4	37	CCDS30863.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883964	0.72410	.	.	ENSG00000169469	ENST00000307098;ENST00000392661	T;T	0.11712	2.75;2.75	4.48	3.5	0.40072	.	.	.	.	.	T	0.09247	0.0228	.	.	.	0.22620	N	0.998923	P	0.52463	0.953	P	0.51516	0.672	T	0.06679	-1.0813	8	0.59425	D	0.04	-0.9395	10.9577	0.47366	0.0:0.8095:0.1905:0.0	.	84	P22528	SPR1B_HUMAN	K	84;68	ENSP00000306461:Q84K;ENSP00000376429:Q68K	ENSP00000306461:Q84K	Q	+	1	0	SPRR1B	151271695	0.998000	0.40836	0.976000	0.42696	0.984000	0.73092	1.329000	0.33770	2.183000	0.69458	0.655000	0.94253	CAG		0.592	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		A	153005071	C	A	153005071	3	1	107	1	0	0	0	0	1	0	0	0	15135	711	25	2	252	2	SPRR1B	1	153005071	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	677196	153005071	96245550	25	28084										
S100A2	6273	hgsc.bcm.edu	37	chr1	153533950	153533950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcagccctggaagaagtcatTgcacatgacagtgatgagtg	13	8	1	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:153533950T>C	ENST00000368708.3	-	3	631	c.259A>G	c.(259-261)Aat>Gat	p.N87D	S100A2_ENST00000368710.1_Missense_Mutation_p.N87D|S100A2_ENST00000497140.1_Missense_Mutation_p.N54D|S100A2_ENST00000368707.4_3'UTR|S100A2_ENST00000368709.1_Missense_Mutation_p.N87D|S100A2_ENST00000487430.2_Missense_Mutation_p.N87D	NM_005978.3	NP_005969.1	P29034	S10A2_HUMAN	S100 calcium binding protein A2	88					endothelial cell migration (GO:0043542)		calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Olopatadine(DB00768)	AAGAAGTCATTGCACATGACA	0.537																																																0			1											192	184	187					1																	153533950		2203	4300	6503	151800574	SO:0001583	missense	6273			BC002829	CCDS1044.1	1q21	2013-01-10	2001-11-28		ENSG00000196754	ENSG00000196754		"S100 calcium binding proteins", "EF-hand domain containing"	10492	protein-coding gene	gene with protein product		176993	"S100 calcium-binding protein A2"	S100L		8341667	Standard	NM_005978		Approved	CAN19	uc001fcb.3	P29034	OTTHUMG00000035031	ENST00000368708.3:c.259A>G	1.37:g.153533950T>C	ENSP00000357697:p.Asn87Asp		151800574	O00266|Q3KRB9|Q5RHS8|Q9BU83	Missense_Mutation	SNP	ENST00000368708.3	37	CCDS1044.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818317	0.71028	.	.	ENSG00000196754	ENST00000368708;ENST00000368710;ENST00000368709;ENST00000368707	T;T;T	0.14516	2.5;2.5;2.5	4.79	4.79	0.61399	EF-hand-like domain (1);	0.140459	0.44688	D	0.000435	T	0.15782	0.0380	.	.	.	0.31889	N	0.617405	D	0.59767	0.986	P	0.56163	0.793	T	0.02109	-1.1212	9	0.66056	D	0.02	.	11.0015	0.47609	0.0:0.0:0.0:1.0	.	88	P29034	S10A2_HUMAN	D	87;87;87;128	ENSP00000357697:N87D;ENSP00000357699:N87D;ENSP00000357698:N87D	ENSP00000357696:N128D	N	-	1	0	S100A2	151800574	1.000000	0.71417	0.993000	0.49108	0.584000	0.36387	2.325000	0.43840	1.920000	0.55613	0.533000	0.62120	AAT		0.537	S100A2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084789.1	NM_005978		C	153533950	T	C	153533950	3	2	107	1	0	0	0	0	1	0	0	0	13815	1812	63	4	38	4	S100A2	1	153533950	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	528879	153533950	95716671	26	28085										
DAP3	7818	hgsc.bcm.edu	37	chr1	155698872	155698872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atgtctggaataagagagaaAgcactgagaaagggagtcct	13	5	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:155698872A>G	ENST00000368336.5	+	8	767	c.643A>G	c.(643-645)Agc>Ggc	p.S215G	DAP3_ENST00000343043.3_Missense_Mutation_p.S215G|MSTO1_ENST00000538143.1_Intron|DAP3_ENST00000471642.2_Missense_Mutation_p.S174G|DAP3_ENST00000535183.1_Missense_Mutation_p.S174G|DAP3_ENST00000421487.2_Missense_Mutation_p.S181G|MSTO1_ENST00000452804.2_Intron	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	215					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TAAGAGAGAAAGCACTGAGAA	0.393																																																0			1											94	105	101					1																	155698872		2203	4300	6503	153965496	SO:0001583	missense	58512			X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"Mitochondrial ribosomal proteins / small subunits"	2673	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S29"	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.643A>G	1.37:g.155698872A>G	ENSP00000357320:p.Ser215Gly		153965496	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Missense_Mutation	SNP	ENST00000368336.5	37	CCDS1120.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752434	0.69533	.	.	ENSG00000132676	ENST00000368336;ENST00000343043;ENST00000421487;ENST00000535183	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.55	4.43	0.53597	.	0.356351	0.37304	N	0.002159	T	0.50154	0.1599	M	0.78801	2.425	0.47621	D	0.999473	P;D;P	0.56287	0.9;0.975;0.947	P;P;P	0.55749	0.675;0.783;0.675	T	0.58216	-0.7675	10	0.72032	D	0.01	-7.8184	9.8745	0.41195	0.9227:0.0:0.0773:0.0	.	174;181;215	B4DP59;E7EM60;P51398	.;.;RT29_HUMAN	G	215;215;181;174	ENSP00000357320:S215G;ENSP00000341692:S215G;ENSP00000412605:S181G;ENSP00000445003:S174G	ENSP00000341692:S215G	S	+	1	0	DAP3	153965496	0.981000	0.34729	0.975000	0.42487	0.983000	0.72400	2.506000	0.45433	1.127000	0.42034	-0.361000	0.07541	AGC		0.393	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632		G	155698872	A	G	155698872	3	3	107	1	0	0	0	0	1	0	0	0	4240	72	3	4	669	4	DAP3	1	155698872	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2164922	155698872	93551749	27	28086										
TTC24	164118	hgsc.bcm.edu	37	chr1	156551781	156551781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gatgtatgctgaagagtgggCggcatcgggtgggggaagtt	20	4	0	2	rs562198796	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:156551781C>T	ENST00000368237.3	+	1	625	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	TTC24_ENST00000368236.3_Missense_Mutation_p.R209W			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	209										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAAGAGTGGGCGGCATCGGGT	0.652													C|||	2	0.000399361	0	0	5008	,	,		15321	0.002		0	False		,,,				2504	0															0			1											6	7	7					1																	156551781		687	1581	2268	154818405	SO:0001583	missense	164118				CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.625C>T	1.37:g.156551781C>T	ENSP00000357220:p.Arg209Trp		154818405	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	C	9.128	1.010647	0.19277	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.25912	1.77;1.77	4.58	4.58	0.56647	.	0.779066	0.10867	N	0.625342	T	0.08670	0.0215	N	0.08118	0	0.30324	N	0.787315	.	.	.	.	.	.	T	0.18903	-1.0322	8	0.56958	D	0.05	-0.3908	11.3736	0.49715	0.1812:0.8188:0.0:0.0	.	.	.	.	W	209	ENSP00000357219:R209W;ENSP00000357220:R209W	ENSP00000357219:R209W	R	+	1	2	TTC24	154818405	0.000000	0.05858	0.964000	0.40570	0.249000	0.25844	0.171000	0.16685	2.392000	0.81423	0.462000	0.41574	CGG		0.652	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		T	156551781	C	T	156551781	3	4	107	1	0	0	0	0	1	0	0	0	16732	759	27	1	627	1	TTC24	1	156551781	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	852909	156551781	92698840	28	28087										
SLAMF8	56833	hgsc.bcm.edu	37	chr1	159799725	159799725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gggctcggtgctgctggtggCagcgcgtccccctggcttcc	16	15	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:159799725C>A	ENST00000289707.5	+	2	259	c.110C>A	c.(109-111)gCa>gAa	p.A37E	SLAMF8_ENST00000368104.4_Intron	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	37					cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					CTGCTGGTGGCAGCGCGTCCC	0.602																																																0			1											104	115	111					1																	159799725		2203	4300	6503	158066349	SO:0001583	missense	56833			AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.110C>A	1.37:g.159799725C>A	ENSP00000289707:p.Ala37Glu		158066349	Q32MC6|Q5VU15	Missense_Mutation	SNP	ENST00000289707.5	37	CCDS1188.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.655079	0.29425	.	.	ENSG00000158714	ENST00000289707	T	0.22945	1.93	4.44	3.53	0.40419	.	0.280361	0.33732	N	0.004614	T	0.19765	0.0475	L	0.32530	0.975	0.29450	N	0.858514	D	0.89917	1.0	D	0.80764	0.994	T	0.03325	-1.1048	10	0.35671	T	0.21	-7.575	8.0457	0.30547	0.0:0.8891:0.0:0.1109	.	37	Q9P0V8	SLAF8_HUMAN	E	37	ENSP00000289707:A37E	ENSP00000289707:A37E	A	+	2	0	SLAMF8	158066349	0.581000	0.26741	0.049000	0.19019	0.095000	0.18619	1.443000	0.35057	1.082000	0.41137	0.313000	0.20887	GCA		0.602	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125		A	159799725	C	A	159799725	3	1	107	1	0	0	0	0	1	0	0	0	14407	710	25	2	116	2	SLAMF8	1	159799725	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3247944	159799725	89450896	29	28088										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172520744	172520744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caactgcgcactagaaaatgAagatgtacaattccagaaaa	7	8	0	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:172520744A>G	ENST00000263688.3	+	2	374	c.155A>G	c.(154-156)gAa>gGa	p.E52G	SUCO_ENST00000610051.1_Missense_Mutation_p.E52G|SUCO_ENST00000608151.1_Missense_Mutation_p.E248G|SUCO_ENST00000367723.4_Missense_Mutation_p.E247G	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	52					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											CTAGAAAATGAAGATGTACAA	0.363																																																0			1											85	82	83					1																	172520744		2203	4300	6503	170787367	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.155A>G	1.37:g.172520744A>G	ENSP00000263688:p.Glu52Gly		170787367	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.169291	0.57584	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.69	5.69	0.88448	.	0.173923	0.40554	N	0.001076	T	0.43144	0.1234	L	0.32530	0.975	0.40970	D	0.984695	B;D;P;P	0.53885	0.18;0.963;0.953;0.9	B;P;P;P	0.53313	0.06;0.723;0.631;0.498	T	0.51505	-0.8697	9	0.72032	D	0.01	-7.2602	12.3245	0.55003	1.0:0.0:0.0:0.0	.	52;52;248;52	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	G	248;52	.	ENSP00000263688:E52G	E	+	2	0	C1orf9	170787367	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	3.914000	0.56401	2.153000	0.67306	0.477000	0.44152	GAA		0.363	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		G	172520744	A	G	172520744	3	3	107	1	0	0	0	0	1	0	0	0	2073	246	9	4	161	4	C1orf9	1	172520744	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	12721019	172520744	76729877	30	28089										
ASTN1	460	hgsc.bcm.edu	37	chr1	176845695	176845695	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgagccttgacatcatccacCacggggcatggggtcttcac	11	13	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:176845695C>T	ENST00000367654.3	-	21	3676	c.3465G>A	c.(3463-3465)gtG>gtA	p.V1155V	ASTN1_ENST00000367657.3_Silent_p.V1147V|ASTN1_ENST00000424564.2_Silent_p.V1147V|ASTN1_ENST00000361833.2_Silent_p.V1147V	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1155					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CATCATCCACCACGGGGCATG	0.582																																																0			1											150	113	125					1																	176845695		2203	4300	6503	175112318	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3465G>A	1.37:g.176845695C>T			175112318	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.582	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176845695	C	T	176845695	2	4	107	1	0	0	0	0	0	0	0	1	1065	581	21	3		3	ASTN1	1	176845695	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	4324951	176845695	72404926	31	28090										
ABL2	27	hgsc.bcm.edu	37	chr1	179078143	179078143	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtctttttgattaagcgtggTgtaaagaagcctgtgatgcc	12	6	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:179078143T>C	ENST00000502732.1	-	12	2462	c.2259A>G	c.(2257-2259)acA>acG	p.T753T	ABL2_ENST00000507173.1_Intron|ABL2_ENST00000511413.1_Intron|ABL2_ENST00000344730.3_Intron|ABL2_ENST00000408940.3_Silent_p.T717T|ABL2_ENST00000512653.1_Silent_p.T738T|ABL2_ENST00000367623.4_Silent_p.T732T|ABL2_ENST00000504405.1_Intron	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	753	F-actin-binding. {ECO:0000250}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TTAAGCGTGGTGTAAAGAAGC	0.537			T	ETV6	AML																																		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	0			1											75	73	74					1																	179078143		2203	4300	6503	177344766	SO:0001819	synonymous_variant	27			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.2259A>G	1.37:g.179078143T>C			177344766	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Silent	SNP	ENST00000502732.1	37	CCDS30947.1																																																																																				0.537	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		C	179078143	T	C	179078143	2	2	107	1	0	0	0	0	0	0	0	1	93	1683	59	4		4	ABL2	1	179078143	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2232448	179078143	70172478	32	28091										
ACBD6	84320	hgsc.bcm.edu	37	chr1	180257598	180257598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctggtctcggagagtggggTcagcaccagactggagcagc	16	11	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:180257598T>C	ENST00000367595.3	-	8	1436	c.749A>G	c.(748-750)gAc>gGc	p.D250G	ACBD6_ENST00000475338.2_5'UTR	NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	250						cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)		ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						GAGAGTGGGGTCAGCACCAGA	0.502																																																0			1											47	44	45					1																	180257598		2203	4300	6503	178524221	SO:0001583	missense	84320			BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847			"Ankyrin repeat domain containing"	23339	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 6"			18268358	Standard	NM_032360		Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.749A>G	1.37:g.180257598T>C	ENSP00000356567:p.Asp250Gly		178524221		Missense_Mutation	SNP	ENST00000367595.3	37	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757174	0.69648	.	.	ENSG00000135847	ENST00000367595	T	0.75154	-0.91	5.66	5.66	0.87406	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.89938	0.6860	M	0.94142	3.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92589	0.6081	10	0.72032	D	0.01	-13.5802	15.5553	0.76187	0.0:0.0:0.0:1.0	.	250	Q9BR61	ACBD6_HUMAN	G	250	ENSP00000356567:D250G	ENSP00000356567:D250G	D	-	2	0	ACBD6	178524221	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.890000	0.75633	2.137000	0.66172	0.528000	0.53228	GAC		0.502	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	NM_032360		C	180257598	T	C	180257598	3	2	107	1	0	0	0	0	1	0	0	0	126	1667	58	4	103	4	ACBD6	1	180257598	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1179455	180257598	68993023	33	28092										
MR1	3140	hgsc.bcm.edu	37	chr1	181021646	181021646	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tggttcttcaggtcccccagGgtaaggacggggatcgtggc	16	10	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:181021646G>C	ENST00000367580.5	+	4	885	c.880G>C	c.(880-882)Gaa>Caa	p.E294Q	MR1_ENST00000282990.6_Intron|MR1_ENST00000367579.3_Splice_Site_p.E249Q|MR1_ENST00000438435.2_Intron|MR1_ENST00000434571.2_Intron	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	294	Connecting peptide.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GGTCCCCCAGGGTAAGGACGG	0.577																																					Colon(174;1412 1962 45296 46549 47110)											0			1											43	47	46					1																	181021646		2202	4300	6502	179288269	SO:0001630	splice_region_variant	25953			AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.880+1G>C	1.37:g.181021646G>C			179288269	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	37	CCDS1342.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295785	0.60086	.	.	ENSG00000153029	ENST00000367580;ENST00000367579	T;T	0.01106	5.8;5.33	4.37	4.37	0.52481	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.132790	0.00927	N	0.002673	T	0.01835	0.0058	N	0.11560	0.145	0.80722	D	1	P;P	0.52061	0.95;0.596	P;B	0.48227	0.571;0.203	T	0.56505	-0.7968	10	0.87932	D	0	.	12.3266	0.55013	0.0:0.0:1.0:0.0	.	249;294	Q95460-2;Q95460	.;HMR1_HUMAN	Q	294;249	ENSP00000356552:E294Q;ENSP00000356551:E249Q	ENSP00000356551:E249Q	E	+	1	0	MR1	179288269	1.000000	0.71417	0.069000	0.20011	0.378000	0.30076	1.611000	0.36879	2.267000	0.75376	0.655000	0.94253	GAA		0.577	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	Missense_Mutation	C	181021646	G	C	181021646	5	2	107	1	0	0	0	0	0	0	1	0	9782	1246	43	5	894	5	MR1	1	181021646	Splice_Site	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	764048	181021646	68228975	34	28093										
SMG7	9887	hgsc.bcm.edu	37	chr1	183513620	183513620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctggagccttccctcctcttCccagcaggccaggtaaatat	8	15	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:183513620C>T	ENST00000347615.2	+	15	2094	c.1975C>T	c.(1975-1977)Ccc>Tcc	p.P659S	SMG7_ENST00000515829.2_Missense_Mutation_p.P613S|SMG7_ENST00000508461.1_Missense_Mutation_p.P617S|SMG7_ENST00000507469.1_Missense_Mutation_p.P613S|SMG7_ENST00000456731.2_Missense_Mutation_p.P571S|SMG7_ENST00000367537.3_Missense_Mutation_p.P642S	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	659	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CCCTCCTCTTCCCAGCAGGCC	0.423																																																0			1											106	104	104					1																	183513620		2203	4300	6503	181780243	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.1975C>T	1.37:g.183513620C>T	ENSP00000340766:p.Pro659Ser		181780243	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288787	0.80914	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19;0.19;0.19	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68833	0.3044	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.996;0.994;0.994;0.998;0.996;0.996	T	0.69450	-0.5142	10	0.59425	D	0.04	-11.3651	20.2985	0.98592	0.0:1.0:0.0:0.0	.	617;642;571;613;659;613	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	S	571;642;617;571;659;613;613	ENSP00000407629:P571S;ENSP00000356507:P642S;ENSP00000426915:P617S;ENSP00000388390:P571S;ENSP00000340766:P659S;ENSP00000425133:P613S;ENSP00000421358:P613S	ENSP00000340766:P659S	P	+	1	0	SMG7	181780243	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.264000	0.78432	2.793000	0.96121	0.655000	0.94253	CCC		0.423	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		T	183513620	C	T	183513620	3	4	107	1	0	0	0	0	1	0	0	0	14835	855	30	3	2033	3	SMG7	1	183513620	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2491974	183513620	65737001	35	28094										
CDC73	79577	hgsc.bcm.edu	37	chr1	193094338	193094338	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctcatcctgtttatgtccgAcgtgcagctgtaagtagaat	9	9	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:193094338A>G	ENST00000367435.3	+	2	412	c.228A>G	c.(226-228)cgA>cgG	p.R76R		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	76					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						TTTATGTCCGACGTGCAGCTG	0.388																																																0			1											139	139	139					1																	193094338		2203	4300	6503	191360961	SO:0001819	synonymous_variant	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.228A>G	1.37:g.193094338A>G			191360961	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Silent	SNP	ENST00000367435.3	37	CCDS1382.1																																																																																				0.388	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		G	193094338	A	G	193094338	2	3	107	1	0	0	0	0	0	0	0	1	3091	262	10	4		4	CDC73	1	193094338	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	9580718	193094338	56156283	36	28095										
ZNF281	23528	hgsc.bcm.edu	37	chr1	200377255	200377255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atcatcataattactacttaTctgaccttgtttgccacttg	4	10	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:200377255T>C	ENST00000294740.3	-	2	1703	c.1579A>G	c.(1579-1581)Ata>Gta	p.I527V	ZNF281_ENST00000367353.1_Missense_Mutation_p.I527V|ZNF281_ENST00000367352.3_Missense_Mutation_p.I491V	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	527			I -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						TTACTACTTATCTGACCTTGT	0.393																																																0			1											88	89	89					1																	200377255		2202	4300	6502	198643878	SO:0001583	missense	23528			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.1579A>G	1.37:g.200377255T>C	ENSP00000294740:p.Ile527Val		198643878	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	37	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	T	6.217	0.408218	0.11754	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.40476	1.03;1.03;1.03	5.63	4.46	0.54185	.	0.203364	0.53938	D	0.000057	T	0.32793	0.0841	L	0.44542	1.39	0.28383	N	0.91943	B;B	0.18863	0.017;0.031	B;B	0.14023	0.007;0.01	T	0.17806	-1.0357	10	0.42905	T	0.14	-4.2867	8.667	0.34127	0.1271:0.0:0.1329:0.74	.	491;527	A6NF48;Q9Y2X9	.;ZN281_HUMAN	V	527;527;491;232	ENSP00000294740:I527V;ENSP00000356322:I527V;ENSP00000356321:I491V	ENSP00000294740:I527V	I	-	1	0	ZNF281	198643878	0.994000	0.37717	0.796000	0.32109	0.972000	0.66771	2.349000	0.44054	2.134000	0.65973	0.528000	0.53228	ATA		0.393	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		C	200377255	T	C	200377255	3	2	107	1	0	0	0	0	1	0	0	0	17857	1435	50	4	1112	4	ZNF281	1	200377255	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	7282917	200377255	48873366	37	28096										
USH2A	7399	hgsc.bcm.edu	37	chr1	216591942	216591942	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttgcaaaccatttactgtgcGataataaaacatggtctctt	6	8	1	0	rs370653547		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:216591942G>T	ENST00000307340.3	-	3	951	c.565C>A	c.(565-567)Cgc>Agc	p.R189S	USH2A_ENST00000366943.2_Missense_Mutation_p.R189S|USH2A_ENST00000366942.3_Missense_Mutation_p.R189S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	189					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.R189C(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTTACTGTGCGATAATAAAAC	0.368										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	ovary(1)	1											130	124	126					1																	216591942		2203	4300	6503	214658565	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.565C>A	1.37:g.216591942G>T	ENSP00000305941:p.Arg189Ser		214658565	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571741	0.86542	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.73047	-0.71;-0.71;-0.71	5.62	5.62	0.85841	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.43579	U	0.000557	D	0.83207	0.5204	M	0.65975	2.015	0.41448	D	0.987962	D;D	0.71674	0.998;0.997	D;D	0.67231	0.927;0.95	D	0.84609	0.0677	10	0.87932	D	0	.	19.6478	0.95789	0.0:0.0:1.0:0.0	.	189;189	O75445-2;O75445	.;USH2A_HUMAN	S	189	ENSP00000305941:R189S;ENSP00000355910:R189S;ENSP00000355909:R189S	ENSP00000305941:R189S	R	-	1	0	USH2A	214658565	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	4.047000	0.57383	2.638000	0.89438	0.655000	0.94253	CGC		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216591942	G	T	216591942	3	4	107	1	0	0	0	0	1	0	0	0	17076	1058	37	2	15337	2	USH2A	1	216591942	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	16214687	216591942	32658679	38	28097										
MARK1	4139	hgsc.bcm.edu	37	chr1	220809268	220809268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agaggagtgggacaaagatgTggctcgaaaacttggcagca	15	6	0	2	rs200408827		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:220809268T>C	ENST00000366917.4	+	13	1636	c.1370T>C	c.(1369-1371)gTg>gCg	p.V457A	MARK1_ENST00000402574.1_Missense_Mutation_p.V322A|MARK1_ENST00000366918.4_Missense_Mutation_p.V435A					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		GACAAAGATGTGGCTCGAAAA	0.448																																																0			1						T	ALA/VAL	0,4406		0,0,2203	106	102	103		1370	3.7	0	1		103	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MARK1	NM_018650.3	64	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	457/796	220809268	1,13005	2203	4300	6503	218875891	SO:0001583	missense	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1370T>C	1.37:g.220809268T>C	ENSP00000355884:p.Val457Ala		218875891		Missense_Mutation	SNP	ENST00000366917.4	37	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	T	5.271	0.235398	0.10023	0.0	1.16E-4	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.30714	1.52;1.52;1.52	6.03	3.7	0.42460	.	0.902953	0.09402	N	0.807010	T	0.13372	0.0324	N	0.04959	-0.14	0.09310	N	1	B;B;B;B	0.14012	0.009;0.001;0.0;0.0	B;B;B;B	0.09377	0.004;0.001;0.001;0.001	T	0.33317	-0.9873	10	0.07175	T	0.84	.	7.2949	0.26387	0.0:0.0702:0.2758:0.6541	.	457;322;457;435	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	A	322;435;457	ENSP00000386017:V322A;ENSP00000355885:V435A;ENSP00000355884:V457A	ENSP00000355884:V457A	V	+	2	0	MARK1	218875891	0.189000	0.23263	0.001000	0.08648	0.997000	0.91878	1.807000	0.38902	0.512000	0.28257	0.533000	0.62120	GTG		0.448	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			C	220809268	T	C	220809268	3	2	107	1	0	0	0	0	1	0	0	0	9342	1696	59	4	1420	4	MARK1	1	220809268	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	4217326	220809268	28441353	39	28098										
LYST	1130	hgsc.bcm.edu	37	chr1	235840883	235840883	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tatctcttctgtgtgaccatAgagatgtatttgagtctcca	8	8	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:235840883A>G	ENST00000389794.3	-	49	11011	c.10837T>C	c.(10837-10839)Tat>Cat	p.Y3613H	LYST_ENST00000389793.2_Missense_Mutation_p.Y3613H|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3613					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GTGTGACCATAGAGATGTATT	0.338																																																0			1											142	126	132					1																	235840883		2203	4300	6503	233907506	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10837T>C	1.37:g.235840883A>G	ENSP00000374444:p.Tyr3613His		233907506	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.445270	0.83993	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.28069	1.63;1.63	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.45915	0.1366	L	0.41415	1.275	0.80722	D	1	D	0.61697	0.99	D	0.67382	0.951	T	0.27536	-1.0071	10	0.39692	T	0.17	.	15.9462	0.79796	1.0:0.0:0.0:0.0	.	3613	Q99698	LYST_HUMAN	H	3613	ENSP00000374444:Y3613H;ENSP00000374443:Y3613H	ENSP00000374443:Y3613H	Y	-	1	0	LYST	233907506	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.233000	0.95337	2.168000	0.68352	0.533000	0.62120	TAT		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235840883	A	G	235840883	3	3	107	1	0	0	0	0	1	0	0	0	9158	420	15	4	588	4	LYST	1	235840883	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	15031615	235840883	13409738	40	28099										
RYR2	6262	hgsc.bcm.edu	37	chr1	237806695	237806695	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agatccctcattcccctgggAgatttggtgggcgttatcag	12	10	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:237806695A>G	ENST00000366574.2	+	48	7607	c.7290A>G	c.(7288-7290)ggA>ggG	p.G2430G	RYR2_ENST00000542537.1_Silent_p.G2414G|RYR2_ENST00000360064.6_Silent_p.G2428G	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2430	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.G2428G(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCCCCTGGGAGATTTGGTGG	0.433																																																1	Substitution - coding silent(1)	central_nervous_system(1)	1											187	177	180					1																	237806695		1882	4114	5996	235873318	SO:0001819	synonymous_variant	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7290A>G	1.37:g.237806695A>G			235873318	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237806695	A	G	237806695	2	3	107	1	0	0	0	0	0	0	0	1	13806	291	11	4		4	RYR2	1	237806695	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1965812	237806695	11443926	41	28100										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggagcaggcatactccctctGccccctctacccggagcggg					rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del		238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				0.678	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		-	240370946	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	240370914	7	5	107	1	0	1	0	1	0	0	0	0	5969	1306	46	0	2820	0	FMN2	1	240370914	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	TCGA-DY-A1DG-01A-11D-A152-10	2564219	240370914	8879707	42	28101										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524967	248524968	+	Frame_Shift_Del	DEL	AT	AT	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcagacaatccaaacatccaAtggccaatatcacctggatg					rs200915140	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr1:248524967_248524968delAT	ENST00000366475.1	+	1	85_86	c.85_86delAT	c.(85-87)atgfs	p.M29fs		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAAACATCCAATGGCCAATATC	0.5																																																0			1																																								246591591	SO:0001589	frameshift_variant	127074			BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.85_86delAT	1.37:g.248524967_248524968delAT	ENSP00000355431:p.Met29fs		246591590	Q6IEZ8	Frame_Shift_Del	DEL	ENST00000366475.1	37	CCDS31113.1																																																																																				0.5	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		-	248524968	AT	-	248524967	7	5	107	1	0	1	0	1	0	0	0	0	11058	101	4	0	87	0	OR2T4	1	248524967	Frame_Shift_Del	DEL	AT	TCGA-DY-A1DG-01A-11D-A152-10	8154053	248524967	725654	43	28102										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24438975	24438975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttctgctgtaacagagctgcTccattaagctggcagctgca	10	11	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:24438975T>C	ENST00000355123.4	-	32	4376	c.3933A>G	c.(3931-3933)ggA>ggG	p.G1311G	AC009228.1_ENST00000430105.1_RNA|ITSN2_ENST00000361999.3_Silent_p.G1284G|AC009228.1_ENST00000413989.1_RNA|AC009228.1_ENST00000413254.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1311	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAGAGCTGCTCCATTAAGCT	0.522																																																0			2											79	79	79					2																	24438975		2203	4300	6503	24292479	SO:0001819	synonymous_variant	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3933A>G	2.37:g.24438975T>C			24292479	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																				0.522	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		C	24438975	T	C	24438975	2	2	107	1	0	0	0	0	0	0	0	1	7948	1538	54	4		4	ITSN2	2	24438975	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10		24438975	218760398	44	28103										
OTOF	9381	hgsc.bcm.edu	37	chr2	26693516	26693516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	accaccagtccagcatgctcTcgtctggctcctcctcctct	6	19	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:26693516T>C	ENST00000272371.2	-	32	4094	c.3968A>G	c.(3967-3969)gAg>gGg	p.E1323G	OTOF_ENST00000338581.6_Missense_Mutation_p.E556G|OTOF_ENST00000402415.3_Missense_Mutation_p.E633G|OTOF_ENST00000339598.3_Missense_Mutation_p.E556G|OTOF_ENST00000403946.3_Missense_Mutation_p.E1323G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1323			E -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGCATGCTCTCGTCTGGCTC	0.592																																					GBM(102;732 1451 20652 24062 31372)											0			2											248	212	224					2																	26693516		2203	4300	6503	26547020	SO:0001583	missense	9381			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3968A>G	2.37:g.26693516T>C	ENSP00000272371:p.Glu1323Gly		26547020	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034219	0.75617	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;D;D	0.82619	-1.34;-1.34;-1.36;-1.63;-1.63	5.79	5.79	0.91817	.	0.045134	0.85682	D	0.000000	D	0.89466	0.6723	M	0.78637	2.42	0.80722	D	1	D;D;P;D	0.64830	0.994;0.993;0.947;0.977	P;P;P;P	0.58620	0.829;0.842;0.645;0.809	D	0.90068	0.4161	10	0.52906	T	0.07	-37.313	15.7917	0.78369	0.0:0.0:0.0:1.0	.	1323;556;633;556	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	G	556;556;633;1323;1323	ENSP00000345137:E556G;ENSP00000344521:E556G;ENSP00000383906:E633G;ENSP00000272371:E1323G;ENSP00000385255:E1323G	ENSP00000272371:E1323G	E	-	2	0	OTOF	26547020	1.000000	0.71417	0.997000	0.53966	0.441000	0.31987	7.934000	0.87649	2.218000	0.71995	0.533000	0.62120	GAG		0.592	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			C	26693516	T	C	26693516	3	2	107	1	0	0	0	0	1	0	0	0	11334	1551	54	4	2270	4	OTOF	2	26693516	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2254541	26693516	216505857	45	28104										
PRKD3	23683	hgsc.bcm.edu	37	chr2	37516584	37516584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtaaagatacatttgacagaCgtctctttcttactccacta	5	10	2	3	rs201601245		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:37516584C>T	ENST00000379066.1	-	5	1394	c.632G>A	c.(631-633)cGt>cAt	p.R211H	PRKD3_ENST00000234179.2_Missense_Mutation_p.R211H			O94806	KPCD3_HUMAN	protein kinase D3	211					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				ATTTGACAGACGTCTCTTTCT	0.408																																					Melanoma(80;621 1355 8613 11814 51767)											0			2											109	104	106					2																	37516584		2203	4300	6503	37370088	SO:0001583	missense	23683			AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.632G>A	2.37:g.37516584C>T	ENSP00000368356:p.Arg211His		37370088	D6W587|Q53TR7|Q8NEL8	Missense_Mutation	SNP	ENST00000379066.1	37	CCDS1789.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778168	0.90195	.	.	ENSG00000115825	ENST00000379066;ENST00000234179;ENST00000443187	T;T;D	0.86627	-0.33;-0.33;-2.15	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.92993	0.7770	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.919	D	0.92976	0.6402	10	0.51188	T	0.08	-16.5232	18.7091	0.91649	0.0:1.0:0.0:0.0	.	211;211	O94806-2;O94806	.;KPCD3_HUMAN	H	211;211;107	ENSP00000368356:R211H;ENSP00000234179:R211H;ENSP00000401839:R107H	ENSP00000234179:R211H	R	-	2	0	PRKD3	37370088	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.089000	0.71384	2.404000	0.81709	0.655000	0.94253	CGT		0.408	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		T	37516584	C	T	37516584	3	4	107	1	0	0	0	0	1	0	0	0	12554	536	19	1	2100	1	PRKD3	2	37516584	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	10823068	37516584	205682789	46	28105										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48873741	48873741	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacaattgaatccatggtctCttcaagcaactactgaaaaa	5	10	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:48873741C>G	ENST00000403751.3	+	6	575	c.538C>G	c.(538-540)Ctt>Gtt	p.L180V	STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.L837V|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.L884V|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.L884V|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.L884V|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.L884V|LHCGR_ENST00000420913.3_5'UTR|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.L146V	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	180					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCCATGGTCTCTTCAAGCAAC	0.418																																																0			2											92	91	91					2																	48873741		2203	4300	6503	48727245	SO:0001583	missense	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.538C>G	2.37:g.48873741C>G	ENSP00000384597:p.Leu180Val		48727245	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	2.415	-0.334536	0.05278	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000448460;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.21	1.08	0.20341	.	0.320138	0.24813	N	0.035393	T	0.19525	0.0469	N	0.20483	0.58	0.21325	N	0.999721	B;B;B;B;B	0.24043	0.096;0.005;0.001;0.026;0.01	B;B;B;B;B	0.22152	0.038;0.004;0.007;0.022;0.015	T	0.16689	-1.0394	10	0.10636	T	0.68	.	4.0286	0.09698	0.1401:0.3895:0.3798:0.0905	.	146;837;884;180;884	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	V	884;884;884;884;837;179;146;189;146;180	ENSP00000385499:L884V;ENSP00000385701:L884V;ENSP00000378236:L884V;ENSP00000311493:L884V;ENSP00000378234:L837V;ENSP00000412645:L146V;ENSP00000396702:L189V;ENSP00000387896:L146V;ENSP00000384597:L180V	ENSP00000384597:L180V	L	+	1	0	STON1-GTF2A1L;GTF2A1L	48727245	0.248000	0.23930	0.009000	0.14445	0.469000	0.32828	0.636000	0.24644	0.329000	0.23460	-0.229000	0.12294	CTT		0.418	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		G	48873741	C	G	48873741	3	3	107	1	0	0	0	0	1	0	0	0	6874	913	32	5	560	5	GTF2A1L	2	48873741	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	11357157	48873741	194325632	47	28106										
C2orf86	51057	hgsc.bcm.edu	37	chr2	63714587	63714587	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aataggtactttacctggtgGatctttcttgtcataatact	7	7	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:63714587G>T	ENST00000272321.7	-	3	729	c.202C>A	c.(202-204)Cca>Aca	p.P68T	WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409562.3_Missense_Mutation_p.P68T	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	68					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						TTACCTGGTGGATCTTTCTTG	0.303																																																0			2											43	43	43					2																	63714587		1792	4056	5848	63568091	SO:0001583	missense	51057				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.202C>A	2.37:g.63714587G>T	ENSP00000272321:p.Pro68Thr		63568091	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	G	6.024	0.372852	0.11409	.	.	ENSG00000143951	ENST00000272321;ENST00000409562;ENST00000431065	T;T;T	0.77877	-0.59;0.0;-1.13	4.66	0.746	0.18365	.	0.609878	0.16642	N	0.205582	T	0.59101	0.2169	L	0.31926	0.97	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.34428	-0.9829	10	0.17832	T	0.49	0.1185	3.6268	0.08116	0.1867:0.0:0.4676:0.3457	.	68;68	O95876-2;O95876	.;FRITZ_HUMAN	T	68	ENSP00000272321:P68T;ENSP00000387222:P68T;ENSP00000396226:P68T	ENSP00000272321:P68T	P	-	1	0	WDPCP	63568091	0.092000	0.21681	0.088000	0.20740	0.995000	0.86356	0.587000	0.23909	0.123000	0.18342	-0.188000	0.12872	CCA		0.303	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		T	63714587	G	T	63714587	3	4	107	1	0	0	0	0	1	0	0	0	2207	1174	41	2	2128	2	C2orf86	2	63714587	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	14840846	63714587	179484786	48	28107										
PCYOX1	51449	hgsc.bcm.edu	37	chr2	70485397	70485397	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cgccgagctgcgtgctccgcCagataaaatcggtaggcgag	14	12	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:70485397C>A	ENST00000433351.2	+	1	129	c.101C>A	c.(100-102)cCa>cAa	p.P34Q	PCYOX1_ENST00000505044.2_Intron|PCYOX1_ENST00000545138.1_5'Flank|PCYOX1_ENST00000264441.5_Missense_Mutation_p.P34Q	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	34					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						CGTGCTCCGCCAGATAAAATC	0.731																																																0			2											18	21	20					2																	70485397		2199	4296	6495	70338901	SO:0001583	missense	51449			AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.101C>A	2.37:g.70485397C>A	ENSP00000387654:p.Pro34Gln		70338901	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Missense_Mutation	SNP	ENST00000433351.2	37	CCDS1902.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230839	0.58777	.	.	ENSG00000116005	ENST00000433351;ENST00000264441	T;T	0.46819	2.4;0.86	4.51	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.52500	0.1738	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.57877	-0.7735	10	0.87932	D	0	-12.052	12.6318	0.56661	0.0:1.0:0.0:0.0	.	34;34	B7Z8A2;Q9UHG3	.;PCYOX_HUMAN	Q	34	ENSP00000387654:P34Q;ENSP00000264441:P34Q	ENSP00000264441:P34Q	P	+	2	0	PCYOX1	70338901	0.987000	0.35691	0.559000	0.28332	0.049000	0.14656	3.473000	0.53122	2.344000	0.79699	0.499000	0.49734	CCA		0.731	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297		A	70485397	C	A	70485397	3	1	107	1	0	0	0	0	1	0	0	0	11639	594	21	2	103	2	PCYOX1	2	70485397	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	6770810	70485397	172713976	49	28108										
CD207	50489	hgsc.bcm.edu	37	chr2	71058201	71058201	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcacggttctgatgggacatAgggtcgcttacaaatgaaaa	11	7	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:71058201A>C	ENST00000410009.3	-	6	1012	c.967T>G	c.(967-969)Tat>Gat	p.Y323D		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	323					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						GATGGGACATAGGGTCGCTTA	0.483																																																0			2											90	85	87					2																	71058201		1940	4139	6079	70911709	SO:0001583	missense	50489			AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.967T>G	2.37:g.71058201A>C	ENSP00000386378:p.Tyr323Asp		70911709		Missense_Mutation	SNP	ENST00000410009.3	37		.	.	.	.	.	.	.	.	.	.	A	14.00	2.404347	0.42613	.	.	ENSG00000116031	ENST00000410009	T	0.16597	2.33	3.58	3.58	0.41010	C-type lectin fold (1);	0.309269	0.23780	N	0.044625	T	0.29850	0.0746	L	0.61036	1.89	0.09310	N	1	D	0.76494	0.999	P	0.60345	0.873	T	0.03597	-1.1021	10	0.36615	T	0.2	.	8.8378	0.35123	1.0:0.0:0.0:0.0	.	323	Q9UJ71	CLC4K_HUMAN	D	323	ENSP00000386378:Y323D	ENSP00000386378:Y323D	Y	-	1	0	CD207	70911709	0.413000	0.25400	0.037000	0.18230	0.043000	0.13939	1.780000	0.38634	1.864000	0.54056	0.523000	0.50628	TAT		0.483	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		C	71058201	A	C	71058201	3	2	107	1	0	0	0	0	1	0	0	0	2989	420	15	4	23	4	CD207	2	71058201	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	572804	71058201	172141172	50	28109										
VAX2	25806	hgsc.bcm.edu	37	chr2	71159919	71159919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaaggtctggttccagaaccGccgcaccaagcagaagaaag	12	11	1	3	rs145503713		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:71159919G>A	ENST00000234392.2	+	3	490	c.458G>A	c.(457-459)cGc>cAc	p.R153H	snoU13_ENST00000459218.1_RNA	NM_012476.2	NP_036608.1	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	153					axonogenesis (GO:0007409)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic eye morphogenesis (GO:0048048)|forebrain development (GO:0030900)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	7						TTCCAGAACCGCCGCACCAAG	0.622													G|||	1	0.000199681	8e-04	0	5008	,	,		9528	0		0	False		,,,				2504	0															0			2						G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	32	35	34		458	4.9	1	2	dbSNP_134	34	0,8600		0,0,4300	no	missense	VAX2	NM_012476.2	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	153/291	71159919	2,13004	2203	4300	6503	71013427	SO:0001583	missense	25806			Y17791	CCDS1911.1	2p13.3	2011-06-20			ENSG00000116035	ENSG00000116035		"Homeoboxes / ANTP class : NKL subclass"	12661	protein-coding gene	gene with protein product		604295				10485894	Standard	NM_012476		Approved	DRES93	uc002shh.3	Q9UIW0	OTTHUMG00000129714	ENST00000234392.2:c.458G>A	2.37:g.71159919G>A	ENSP00000234392:p.Arg153His		71013427	Q53Y33	Missense_Mutation	SNP	ENST00000234392.2	37	CCDS1911.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971841	0.92919	4.54E-4	0.0	ENSG00000116035	ENST00000234392	D	0.97553	-4.43	4.91	4.91	0.64330	Homeobox, eukaryotic (1);Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	H	0.94385	3.53	0.80722	D	1	D	0.61080	0.989	P	0.60886	0.88	D	0.99716	1.1008	10	0.87932	D	0	-19.2815	15.5791	0.76418	0.0:0.0:1.0:0.0	.	153	Q9UIW0	VAX2_HUMAN	H	153	ENSP00000234392:R153H	ENSP00000234392:R153H	R	+	2	0	VAX2	71013427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.528000	0.98046	2.250000	0.74265	0.491000	0.48974	CGC		0.622	VAX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251923.1			A	71159919	G	A	71159919	3	1	107	1	0	0	0	0	1	0	0	0	17175	1087	38	1	468	1	VAX2	2	71159919	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	101718	71159919	172039454	51	28110										
DYSF	8291	hgsc.bcm.edu	37	chr2	71801460	71801460	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtcgcatggagccactggagAagacggggcctgcagctgtg	17	10	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:71801460A>T	ENST00000258104.3	+	30	3584	c.3307A>T	c.(3307-3309)Aag>Tag	p.K1103*	DYSF_ENST00000410020.3_Nonsense_Mutation_p.K1121*|DYSF_ENST00000409762.1_Nonsense_Mutation_p.K1120*|DYSF_ENST00000413539.2_Nonsense_Mutation_p.K1134*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.K1090*|DYSF_ENST00000409582.3_Nonsense_Mutation_p.K1120*|DYSF_ENST00000429174.2_Nonsense_Mutation_p.K1103*|DYSF_ENST00000410041.1_Nonsense_Mutation_p.K1121*|DYSF_ENST00000409366.1_Nonsense_Mutation_p.K1104*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.K1104*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.K1135*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1103					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCCACTGGAGAAGACGGGGCC	0.622																																																0			2	GRCh37	CM066054	DYSF	M							76	86	83					2																	71801460		2203	4300	6503	71654968	SO:0001587	stop_gained	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3307A>T	2.37:g.71801460A>T	ENSP00000258104:p.Lys1103*		71654968	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Nonsense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	45	11.750993	0.99599	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	5.6	3.02	0.34903	.	0.114692	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.1268	10.6142	0.45441	0.6776:0.3224:0.0:0.0	.	.	.	.	X	1134;1120;1120;1103;1103;1135;1104;1090;1104;1121;1121	.	ENSP00000258104:K1103X	K	+	1	0	DYSF	71654968	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.623000	0.46435	2.123000	0.65237	0.528000	0.53228	AAG		0.622	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71801460	A	T	71801460	4	4	107	1	0	0	0	0	0	1	0	0	4870	247	9	5	3617	5	DYSF	2	71801460	Nonsense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	641541	71801460	171397913	52	28111										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676445	73676445	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	actttcttttccctgaagaaGctctgaaggtttcagctgtt	8	9	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:73676445G>T	ENST00000264448.6	+	8	2899	c.2788G>T	c.(2788-2790)Gct>Tct	p.A930S	ALMS1_ENST00000377715.1_Missense_Mutation_p.A930S|ALMS1_ENST00000409009.1_Missense_Mutation_p.A888S	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	930	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCCTGAAGAAGCTCTGAAGGT	0.463																																																0			2											71	71	71					2																	73676445		1829	4093	5922	73529953	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2788G>T	2.37:g.73676445G>T	ENSP00000264448:p.Ala930Ser		73529953	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	9.630	1.136146	0.21123	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14144	3.42;3.42;2.53	3.64	-2.46	0.06461	.	.	.	.	.	T	0.18215	0.0437	L	0.50333	1.59	0.09310	N	1	P;D;P	0.57899	0.793;0.981;0.48	B;P;B	0.53760	0.199;0.734;0.082	T	0.16482	-1.0401	9	0.31617	T	0.26	.	8.7532	0.34631	0.6703:0.0:0.3297:0.0	.	930;888;930	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	888;930;930	ENSP00000386627:A888S;ENSP00000264448:A930S;ENSP00000366944:A930S	ENSP00000264448:A930S	A	+	1	0	ALMS1	73529953	0.000000	0.05858	0.000000	0.03702	0.171000	0.22731	-2.179000	0.01259	-0.634000	0.05538	0.591000	0.81541	GCT		0.463	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73676445	G	T	73676445	3	4	107	1	0	0	0	0	1	0	0	0	535	971	34	2	2818	2	ALMS1	2	73676445	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	1874985	73676445	169522928	53	28112										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80874935	80874935	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacgagttcgacgaggttctCagaagaaacacatttcgcct	9	11	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:80874935C>A	ENST00000402739.4	+	18	2805	c.2800C>A	c.(2800-2802)Cag>Aag	p.Q934K	CTNNA2_ENST00000466387.1_Missense_Mutation_p.Q886K|CTNNA2_ENST00000540488.1_Missense_Mutation_p.Q841K|CTNNA2_ENST00000361291.4_Missense_Mutation_p.Q920K|CTNNA2_ENST00000343114.3_Missense_Mutation_p.Q565K|CTNNA2_ENST00000496558.1_Missense_Mutation_p.Q886K|CTNNA2_ENST00000541047.1_Missense_Mutation_p.Q886K	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	934					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						ACGAGGTTCTCAGAAGAAACA	0.423																																																0			2											124	123	123					2																	80874935		1844	4085	5929	80728446	SO:0001583	missense	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.2800C>A	2.37:g.80874935C>A	ENSP00000384638:p.Gln934Lys		80728446	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	C	17.70	3.453280	0.63290	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	T;T;T;T;T;T;T	0.39406	1.18;1.18;1.16;1.08;1.18;1.1;2.42	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.34978	0.0916	N	0.21282	0.65	0.80722	D	1	B;P;B;P	0.36909	0.016;0.573;0.338;0.534	B;B;B;B	0.37780	0.017;0.258;0.135;0.143	T	0.04255	-1.0965	9	.	.	.	.	20.3658	0.98878	0.0:1.0:0.0:0.0	.	518;934;841;886	F6KRI5;P26232;P26232-3;P26232-2	.;CTNA2_HUMAN;.;.	K	886;886;920;934;886;841;565	ENSP00000418191:Q886K;ENSP00000419295:Q886K;ENSP00000355398:Q920K;ENSP00000384638:Q934K;ENSP00000444675:Q886K;ENSP00000441705:Q841K;ENSP00000341500:Q565K	.	Q	+	1	0	CTNNA2	80728446	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	CAG		0.423	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80874935	C	A	80874935	3	1	107	1	0	0	0	0	1	0	0	0	4019	827	29	2	2514	2	CTNNA2	2	80874935	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	7198490	80874935	162324438	54	28113										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98804463	98804463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaacaagaagacagtccatgCaaaatattgcagcaggtttg	10	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:98804463C>T	ENST00000477737.1	+	10	1541	c.1337C>T	c.(1336-1338)gCa>gTa	p.A446V	VWA3B_ENST00000435344.1_Missense_Mutation_p.A446V|VWA3B_ENST00000451075.2_Missense_Mutation_p.A296V	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	446										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ACAGTCCATGCAAAATATTGC	0.478																																																0			2											82	80	81					2																	98804463		1935	4148	6083	98170895	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1337C>T	2.37:g.98804463C>T	ENSP00000417955:p.Ala446Val		98170895	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504768	0.85176	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.30714	1.52;2.89;2.22	4.76	4.76	0.60689	.	0.000000	0.56097	D	0.000035	T	0.54838	0.1883	M	0.66939	2.045	0.30584	N	0.762227	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	T	0.59461	-0.7450	10	0.72032	D	0.01	.	16.8999	0.86110	0.0:1.0:0.0:0.0	.	296;446;446	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	V	446;446;296	ENSP00000401959:A446V;ENSP00000417955:A446V;ENSP00000389463:A296V	ENSP00000388158:A446V	A	+	2	0	VWA3B	98170895	0.999000	0.42202	1.000000	0.80357	0.947000	0.59692	5.259000	0.65485	2.336000	0.79503	0.460000	0.39030	GCA		0.478	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98804463	C	T	98804463	3	4	107	1	0	0	0	0	1	0	0	0	17281	710	25	3	1371	3	VWA3B	2	98804463	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	17929528	98804463	144394910	55	28114										
NCK2	8440	hgsc.bcm.edu	37	chr2	106497813	106497813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agacgcgcaggaagaccagcGcgcgggatgcgtcccccacg	15	15	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:106497813G>A	ENST00000233154.4	+	4	698	c.256G>A	c.(256-258)Gcg>Acg	p.A86T	NCK2_ENST00000393349.2_Missense_Mutation_p.A86T|NCK2_ENST00000522586.1_Intron|NCK2_ENST00000451463.2_Intron	NM_003581.4	NP_003572.2	O43639	NCK2_HUMAN	NCK adaptor protein 2	86					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|lamellipodium assembly (GO:0030032)|negative regulation of cell proliferation (GO:0008285)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of translation (GO:0006417)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|lung(3)|ovary(1)	5						GAAGACCAGCGCGCGGGATGC	0.677																																																0			2											25	27	27					2																	106497813		2202	4293	6495	105864245	SO:0001583	missense	8440			AF043119	CCDS33266.1	2q12	2013-02-14			ENSG00000071051	ENSG00000071051		"SH2 domain containing"	7665	protein-coding gene	gene with protein product		604930				9737977, 16752908	Standard	NM_001004720		Approved	NCKbeta	uc002tdi.3	O43639	OTTHUMG00000153116	ENST00000233154.4:c.256G>A	2.37:g.106497813G>A	ENSP00000233154:p.Ala86Thr		105864245	D3DVK1|Q9BWN9|Q9UIC3	Missense_Mutation	SNP	ENST00000233154.4	37	CCDS33266.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.234245	0.22626	.	.	ENSG00000071051	ENST00000233154;ENST00000393348;ENST00000425756;ENST00000393349	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.64	3.82	0.43975	.	0.146868	0.64402	D	0.000007	T	0.22781	0.0550	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.05920	-1.0856	10	0.13108	T	0.6	.	10.4333	0.44419	0.209:0.0:0.791:0.0	.	86	O43639	NCK2_HUMAN	T	86	ENSP00000233154:A86T;ENSP00000377017:A86T;ENSP00000408040:A86T;ENSP00000377018:A86T	ENSP00000233154:A86T	A	+	1	0	NCK2	105864245	1.000000	0.71417	0.931000	0.37212	0.623000	0.37688	5.286000	0.65639	1.524000	0.49035	0.563000	0.77884	GCG		0.677	NCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329634.1	NM_003581		A	106497813	G	A	106497813	3	1	107	1	0	0	0	0	1	0	0	0	10251	1087	38	1	262	1	NCK2	2	106497813	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	7693350	106497813	136701560	56	28115										
SLC5A7	60482	hgsc.bcm.edu	37	chr2	108626706	108626706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggcttcggacaaagaaatcGtttgggttatgcgaatcaca	11	7	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:108626706G>A	ENST00000264047.2	+	9	1408	c.1132G>A	c.(1132-1134)Gtt>Att	p.V378I	SLC5A7_ENST00000540517.1_Missense_Mutation_p.V273I|SLC5A7_ENST00000409059.1_Missense_Mutation_p.V378I	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	378					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)	p.V378I(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	CAAAGAAATCGTTTGGGTTAT	0.443																																																2	Substitution - Missense(2)	ovary(1)|pancreas(1)	2											148	120	129					2																	108626706		2203	4300	6503	107993138	SO:0001583	missense	60482			AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.1132G>A	2.37:g.108626706G>A	ENSP00000264047:p.Val378Ile		107993138	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	37	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	G	8.887	0.953064	0.18431	.	.	ENSG00000115665	ENST00000409059;ENST00000540517;ENST00000264047	D;D;D	0.89050	-2.46;-2.46;-2.46	5.85	2.92	0.33932	.	0.168277	0.51477	N	0.000083	T	0.79724	0.4495	N	0.25647	0.755	0.49915	D	0.999832	B	0.06786	0.001	B	0.10450	0.005	T	0.70360	-0.4893	10	0.31617	T	0.26	-25.0208	8.2684	0.31829	0.1388:0.0:0.7353:0.1259	.	378	Q9GZV3	SC5A7_HUMAN	I	378;273;378	ENSP00000387346:V378I;ENSP00000445351:V273I;ENSP00000264047:V378I	ENSP00000264047:V378I	V	+	1	0	SLC5A7	107993138	1.000000	0.71417	0.256000	0.24389	0.798000	0.45092	4.104000	0.57790	0.773000	0.33404	-0.143000	0.13931	GTT		0.443	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108626706	G	A	108626706	3	1	107	1	0	0	0	0	1	0	0	0	14707	1145	40	1	1162	1	SLC5A7	2	108626706	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2128893	108626706	134572667	57	28116										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540011	133540011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctgaactcacagcatcagtcGcggttgcagaggcatctgga	12	11	3	2	rs112873686	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:133540011G>A	ENST00000409261.1	-	14	4746	c.4373C>T	c.(4372-4374)gCg>gTg	p.A1458V	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.A1458V|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1458										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						AGCATCAGTCGCGGTTGCAGA	0.502													G|||	2	0.000399361	0	0.0014	5008	,	,		17664	0.001		0	False		,,,				2504	0															0			2						G	VAL/ALA,	3,3829		0,3,1913	52	51	52		4373,	-1.7	0	2	dbSNP_132	52	0,8254		0,0,4127	no	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	64,	0,3,6040	AA,AG,GG		0.0,0.0783,0.0248	benign,	1458/1910,	133540011	3,12083	1916	4127	6043	133256481	SO:0001583	missense	0			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4373C>T	2.37:g.133540011G>A	ENSP00000387128:p.Ala1458Val		133256481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	1.996	-0.430615	0.04669	7.83E-4	0.0	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.09538	2.97;2.97	5.5	-1.71	0.08133	.	.	.	.	.	T	0.03520	0.0101	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44862	-0.9300	9	0.15499	T	0.54	.	0.1091	0.00054	0.2625:0.2602:0.2008:0.2765	.	1458	O14513	NCKP5_HUMAN	V	1458	ENSP00000387128:A1458V;ENSP00000380603:A1458V	ENSP00000380603:A1458V	A	-	2	0	NCKAP5	133256481	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.520000	0.06252	-0.269000	0.09298	-0.823000	0.03104	GCG		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133540011	G	A	133540011	3	1	107	1	0	0	0	0	1	0	0	0	10254	1087	38	1	1384	1	NCKAP5	2	133540011	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	24913305	133540011	109659362	58	28117										
LCT	3938	hgsc.bcm.edu	37	chr2	136570467	136570467	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgcccctgctgctgtgggcgAtgatggctgttgtagtggtg	17	8	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:136570467A>G	ENST00000264162.2	-	7	1777	c.1767T>C	c.(1765-1767)caT>caC	p.H589H	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	589	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.H589Q(2)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCTGTGGGCGATGATGGCTGT	0.532																																																2	Substitution - Missense(2)	lung(2)	2											51	46	48					2																	136570467		2203	4300	6503	136286937	SO:0001819	synonymous_variant	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1767T>C	2.37:g.136570467A>G			136286937	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.532	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136570467	A	G	136570467	2	3	107	1	0	0	0	0	0	0	0	1	8715	330	12	4		4	LCT	2	136570467	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3030456	136570467	106628906	59	28118										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141116394	141116394	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cattaaatgcatttaccaccAcagtgatcttcatctgaatt	4	10	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:141116394A>T	ENST00000389484.3	-	73	12224	c.11253T>A	c.(11251-11253)tgT>tgA	p.C3751*		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3751	LDL-receptor class A 31. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ATTTACCACCACAGTGATCTT	0.378										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											194	177	183					2																	141116394		2203	4299	6502	140832864	SO:0001587	stop_gained	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.11253T>A	2.37:g.141116394A>T	ENSP00000374135:p.Cys3751*		140832864	Q8WY29|Q8WY30|Q8WY31	Nonsense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	56	25.930568	0.99967	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.33	1.77	0.24775	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1094	0.30905	0.7582:0.0:0.2418:0.0	.	.	.	.	X	3751;3689	.	ENSP00000374135:C3751X	C	-	3	2	LRP1B	140832864	1.000000	0.71417	0.997000	0.53966	0.114000	0.19823	2.265000	0.43311	0.364000	0.24374	-0.250000	0.11733	TGT		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141116394	A	T	141116394	4	4	107	1	0	0	0	0	0	1	0	0	8984	157	6	5	2622	5	LRP1B	2	141116394	Nonsense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	4545927	141116394	102082979	60	28119										
EPC2	26122	hgsc.bcm.edu	37	chr2	149519493	149519493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cttaaccttagaagttgtggAgaaaaggtaacattgctcct	9	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:149519493A>G	ENST00000258484.6	+	5	843	c.809A>G	c.(808-810)gAg>gGg	p.E270G		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	270					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		GAAGTTGTGGAGAAAAGGTAA	0.353																																																0			2											75	70	72					2																	149519493		1834	4079	5913	149235963	SO:0001583	missense	26122			AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.809A>G	2.37:g.149519493A>G	ENSP00000258484:p.Glu270Gly		149235963	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	37	CCDS46422.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.822382	0.90873	.	.	ENSG00000135999	ENST00000258484	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.84556	0.5498	M	0.91406	3.205	0.80722	D	1	D	0.61697	0.99	D	0.64776	0.929	D	0.88309	0.2955	9	0.87932	D	0	-4.7282	15.772	0.78176	1.0:0.0:0.0:0.0	.	270	Q52LR7	EPC2_HUMAN	G	270	.	ENSP00000258484:E270G	E	+	2	0	EPC2	149235963	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.339000	0.96797	2.133000	0.65898	0.477000	0.44152	GAG		0.353	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		G	149519493	A	G	149519493	3	3	107	1	0	0	0	0	1	0	0	0	5174	304	11	4	827	4	EPC2	2	149519493	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	8403099	149519493	93679880	61	28120										
NEB	4703	hgsc.bcm.edu	37	chr2	152512413	152512413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	taaactggaagttgctcgggTgctggcggtatttctgatca	13	7	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:152512413T>C	ENST00000172853.10	-	50	6767	c.6620A>G	c.(6619-6621)cAc>cGc	p.H2207R	NEB_ENST00000427231.2_Missense_Mutation_p.H2207R|NEB_ENST00000603639.1_Missense_Mutation_p.H2207R|NEB_ENST00000397345.3_Missense_Mutation_p.H2207R|NEB_ENST00000604864.1_Missense_Mutation_p.H2207R|NEB_ENST00000409198.1_Missense_Mutation_p.H2207R			P20929	NEBU_HUMAN	nebulin	2207					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.H2207P(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTTGCTCGGGTGCTGGCGGTA	0.498																																																1	Substitution - Missense(1)	ovary(1)	2											154	150	152					2																	152512413		1995	4166	6161	152220659	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6620A>G	2.37:g.152512413T>C	ENSP00000172853:p.His2207Arg		152220659	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	15.81	2.944410	0.53079	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.06528	3.29;3.33;3.33;3.29	5.3	5.3	0.74995	.	0.228496	0.43579	D	0.000544	T	0.09555	0.0235	L	0.45352	1.415	0.80722	D	1	P	0.45715	0.865	P	0.46543	0.52	T	0.37709	-0.9694	10	0.15952	T	0.53	.	15.4117	0.74929	0.0:0.0:0.0:1.0	.	2207	P20929	NEBU_HUMAN	R	2207	ENSP00000386259:H2207R;ENSP00000380505:H2207R;ENSP00000416578:H2207R;ENSP00000172853:H2207R	ENSP00000172853:H2207R	H	-	2	0	NEB	152220659	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.731000	0.62022	2.225000	0.72522	0.460000	0.39030	CAC		0.498	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152512413	T	C	152512413	3	2	107	1	0	0	0	0	1	0	0	0	10333	1696	59	4	19598	4	NEB	2	152512413	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2992920	152512413	90686960	62	28121										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158156138	158156138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaacatacgaccctggcctTgatgtttggggtggggaaaa	15	7	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:158156138T>C	ENST00000259056.4	+	6	2561	c.2076T>C	c.(2074-2076)ctT>ctC	p.L692L	RN7SKP281_ENST00000410472.1_RNA	NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	692	Catalytic subdomain B.		L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						ACCCTGGCCTTGATGTTTGGG	0.373																																																0			2											90	86	87					2																	158156138		2203	4300	6503	157864384	SO:0001819	synonymous_variant	11227			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.2076T>C	2.37:g.158156138T>C			157864384	A5PKZ1|Q9UGK7|Q9UHL6	Silent	SNP	ENST00000259056.4	37	CCDS2203.1																																																																																				0.373	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		C	158156138	T	C	158156138	2	2	107	1	0	0	0	0	0	0	0	1	6236	1799	63	4		4	GALNT5	2	158156138	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	5643725	158156138	85043235	63	28122										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168099854	168099854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgagctagccagaggagatgTctgcacagctcggtggatgt	15	8	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:168099854T>C	ENST00000409195.1	+	9	2041	c.1952T>C	c.(1951-1953)gTc>gCc	p.V651A	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.V429A|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.V651A	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	476					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGAGGAGATGTCTGCACAGCT	0.428																																																0			2											66	64	65					2																	168099854		1896	4130	6026	167808100	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1952T>C	2.37:g.168099854T>C	ENSP00000386840:p.Val651Ala		167808100	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505700	0.85282	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.10668	2.88;2.88;2.85	5.93	5.93	0.95920	.	0.122287	0.53938	D	0.000050	T	0.40398	0.1115	M	0.87038	2.855	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.994;0.997;0.997	T	0.42882	-0.9425	10	0.87932	D	0	-9.3154	16.3798	0.83452	0.0:0.0:0.0:1.0	.	476;476;429	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	A	651;651;429	ENSP00000386840:V651A;ENSP00000295237:V651A;ENSP00000387255:V429A	ENSP00000295237:V651A	V	+	2	0	XIRP2	167808100	1.000000	0.71417	0.941000	0.38009	0.905000	0.53344	7.698000	0.84413	2.271000	0.75665	0.533000	0.62120	GTC		0.428	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168099854	T	C	168099854	3	2	107	1	0	0	0	0	1	0	0	0	17470	1667	58	4	1982	4	XIRP2	2	168099854	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	9943716	168099854	75099519	64	28123										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171242699	171242699	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cgctccattttctgtgccagTgcattgtcatcagcggagag	11	11	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:171242699T>A	ENST00000408978.4	+	13	1434	c.1291T>A	c.(1291-1293)Tgc>Agc	p.C431S	MYO3B_ENST00000409044.3_Splice_Site_p.C431S|MYO3B_ENST00000334231.6_Splice_Site_p.C440S|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	431	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.C431S(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TCTGTGCCAGTGCATTGTCAT	0.433																																																1	Substitution - Missense(1)	lung(1)	2											107	102	103					2																	171242699		1958	4157	6115	170950945	SO:0001630	splice_region_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1291-1T>A	2.37:g.171242699T>A			170950945	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238861	0.79800	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.45	5.45	0.79879	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.89653	0.6777	L	0.39397	1.21	0.80722	D	1	P;P;D	0.60575	0.911;0.851;0.988	P;P;D	0.65323	0.756;0.623;0.934	D	0.88729	0.3235	9	.	.	.	.	15.8205	0.78638	0.0:0.0:0.0:1.0	.	431;431;431	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	S	431;431;430;440;440	ENSP00000386497:C431S;ENSP00000386213:C431S;ENSP00000446237:C440S;ENSP00000335100:C440S	.	C	+	1	0	MYO3B	170950945	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.997000	0.88414	2.201000	0.70794	0.533000	0.62120	TGC		0.433	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		Missense_Mutation	A	171242699	T	A	171242699	5	1	107	1	0	0	0	0	0	0	1	0	10107	1710	59	5	1341	5	MYO3B	2	171242699	Splice_Site	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	3142845	171242699	71956674	65	28124										
OLA1	29789	hgsc.bcm.edu	37	chr2	174945927	174945927	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgggcctgcagtgaaaaagtAttctagttggagtgctgcaa	13	6	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:174945927A>G	ENST00000409546.1	-	9	1609	c.979T>C	c.(979-981)Tac>Cac	p.Y327H	OLA1_ENST00000284719.3_Missense_Mutation_p.Y307H|OLA1_ENST00000428402.2_Intron|OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000344357.5_Missense_Mutation_p.Y149H					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						GTGAAAAAGTATTCTAGTTGG	0.408																																																0			2											89	79	82					2																	174945927		2203	4299	6502	174654173	SO:0001583	missense	29789				CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"GTP-binding protein 9 (putative)"	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.979T>C	2.37:g.174945927A>G	ENSP00000386350:p.Tyr327His		174654173		Missense_Mutation	SNP	ENST00000409546.1	37		.	.	.	.	.	.	.	.	.	.	A	9.946	1.218956	0.22373	.	.	ENSG00000138430	ENST00000284719;ENST00000344357;ENST00000409546	T;T;T	0.17213	2.29;2.29;2.29	5.96	5.96	0.96718	Domain of unknown function DUF933 (1);TGS-like (1);Beta-grasp fold, ferredoxin-type (1);	0.000000	0.85682	D	0.000000	T	0.30070	0.0753	N	0.25060	0.705	0.80722	D	1	D;B;D	0.89917	1.0;0.219;1.0	D;B;D	0.97110	1.0;0.122;1.0	T	0.05451	-1.0884	10	0.59425	D	0.04	-5.6086	16.4277	0.83824	1.0:0.0:0.0:0.0	.	307;149;307	D7EHM2;Q9NTK5-2;Q9NTK5	.;.;OLA1_HUMAN	H	307;149;327	ENSP00000284719:Y307H;ENSP00000340167:Y149H;ENSP00000386350:Y327H	ENSP00000284719:Y307H	Y	-	1	0	OLA1	174654173	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.109000	0.94291	2.279000	0.76181	0.533000	0.62120	TAC		0.408	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341		G	174945927	A	G	174945927	3	3	107	1	0	0	0	0	1	0	0	0	10881	449	16	4	283	4	OLA1	2	174945927	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3703228	174945927	68253446	66	28125										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098832	178098832	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcatctagttgtaactgagcGaaaaaggctttctcttgctc	8	9	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:178098832G>A	ENST00000397062.3	-	2	767	c.213C>T	c.(211-213)ttC>ttT	p.F71F	NFE2L2_ENST00000397063.4_Silent_p.F55F|NFE2L2_ENST00000464747.1_Silent_p.F55F|NFE2L2_ENST00000446151.2_Silent_p.F55F|NFE2L2_ENST00000423513.1_Silent_p.F55F	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	71					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GTAACTGAGCGAAAAAGGCTT	0.448			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																													Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	0			2											159	155	157					2																	178098832		1887	4102	5989	177807078	SO:0001819	synonymous_variant	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.213C>T	2.37:g.178098832G>A			177807078	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Silent	SNP	ENST00000397062.3	37	CCDS42782.1																																																																																				0.448	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098832	G	A	178098832	2	1	107	1	0	0	0	0	0	0	0	1	10399	1049	37	1		1	NFE2L2	2	178098832	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	3152905	178098832	65100541	67	28126										
TTN	7273	hgsc.bcm.edu	37	chr2	179434540	179434540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	catcacatttttcaacaatgTatccttgaatttcacagcca	3	11	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:179434540T>C	ENST00000591111.1	-	276	71620	c.71396A>G	c.(71395-71397)tAc>tGc	p.Y23799C	TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Y16567C|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y25440C|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Y16500C|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Y22872C|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Y16375C			Q8WZ42	TITIN_HUMAN	titin	23799	Fibronectin type-III 73. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCAACAATGTATCCTTGAAT	0.393																																																0			2											143	131	135					2																	179434540		1880	4128	6008	179142786	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71396A>G	2.37:g.179434540T>C	ENSP00000465570:p.Tyr23799Cys		179142786	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.25	1.880344	0.33162	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.92163	0.7515	H	0.98786	4.33	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.95219	0.8332	9	0.87932	D	0	.	16.3526	0.83220	0.0:0.0:0.0:1.0	.	16375;16500;16567;23799	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	22872;16375;16567;16500;16373	ENSP00000343764:Y22872C;ENSP00000434586:Y16375C;ENSP00000340554:Y16567C;ENSP00000352154:Y16500C	ENSP00000340554:Y16567C	Y	-	2	0	TTN	179142786	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.255000	0.74692	0.533000	0.62120	TAC		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179434540	T	C	179434540	3	2	107	1	0	0	0	0	1	0	0	0	16775	1638	57	4	31808	4	TTN	2	179434540	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1335708	179434540	63764833	68	28127										
TTN	7273	hgsc.bcm.edu	37	chr2	179486328	179486328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttcagtcagtatttcatatcTtcctgtttcaatgatctcct	4	10	6	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:179486328T>C	ENST00000591111.1	-	195	40524	c.40300A>G	c.(40300-40302)Aga>Gga	p.R13434G	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R6202G|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R15075G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R6135G|TTN_ENST00000342992.6_Missense_Mutation_p.R12507G|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R6010G			Q8WZ42	TITIN_HUMAN	titin	13434	Ig-like 90.		R -> K (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTCATATCTTCCTGTTTCA	0.448																																																0			2											143	138	139					2																	179486328		1966	4153	6119	179194573	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40300A>G	2.37:g.179486328T>C	ENSP00000465570:p.Arg13434Gly		179194573	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.70	2.016736	0.35606	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	6.17	4.96	0.65561	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.86912	0.6047	M	0.76938	2.355	0.40106	D	0.976425	P;P;P;P	0.50819	0.939;0.939;0.939;0.939	P;P;P;P	0.56278	0.739;0.739;0.739;0.795	D	0.89065	0.3465	9	0.87932	D	0	.	13.2634	0.60120	0.0:0.0:0.132:0.868	.	6010;6135;6202;13434	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	12507;6010;6202;6135;6010	ENSP00000343764:R12507G;ENSP00000434586:R6010G;ENSP00000340554:R6202G;ENSP00000352154:R6135G	ENSP00000340554:R6202G	R	-	1	2	TTN	179194573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.449000	0.52950	2.371000	0.80710	0.533000	0.62120	AGA		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179486328	T	C	179486328	3	2	107	1	0	0	0	0	1	0	0	0	16775	1617	56	4	62942	4	TTN	2	179486328	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	51788	179486328	63713045	69	28128										
DNAJC10	54431	hgsc.bcm.edu	37	chr2	183627443	183627443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agtgaaagctggaaaagtagActgtcaggcttatgctcaga	12	6	2	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:183627443A>G	ENST00000264065.7	+	22	2595	c.2180A>G	c.(2179-2181)gAc>gGc	p.D727G		NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	727	Thioredoxin 4. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			GGAAAAGTAGACTGTCAGGCT	0.373																																					Pancreas(56;860 1183 25669 35822 48585)											0			2											93	92	92					2																	183627443		2203	4300	6503	183335688	SO:0001583	missense	54431				CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"Heat shock proteins / DNAJ (HSP40)", "Protein disulfide isomerases"	24637	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 19"	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.2180A>G	2.37:g.183627443A>G	ENSP00000264065:p.Asp727Gly		183335688	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Missense_Mutation	SNP	ENST00000264065.7	37	CCDS33345.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.038283	0.93630	.	.	ENSG00000077232	ENST00000264065;ENST00000392392	T	0.08282	3.11	5.94	5.94	0.96194	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.100338	0.64402	D	0.000003	T	0.34308	0.0893	M	0.93638	3.44	0.80722	D	1	P;P	0.49090	0.899;0.919	P;P	0.54664	0.758;0.674	T	0.44483	-0.9325	10	0.72032	D	0.01	.	16.3951	0.83601	1.0:0.0:0.0:0.0	.	681;727	Q8IXB1-2;Q8IXB1	.;DJC10_HUMAN	G	727;681	ENSP00000264065:D727G	ENSP00000264065:D727G	D	+	2	0	DNAJC10	183335688	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.117000	0.94347	2.272000	0.75746	0.460000	0.39030	GAC		0.373	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981		G	183627443	A	G	183627443	3	3	107	1	0	0	0	0	1	0	0	0	4640	275	10	4	2258	4	DNAJC10	2	183627443	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	4141115	183627443	59571930	70	28129										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212615366	212615366	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcactgatgaacacttacaaGtctggcaatgattttctgtg	8	8	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:212615366G>C	ENST00000342788.4	-	5	930	c.620C>G	c.(619-621)aCt>aGt	p.T207S	ERBB4_ENST00000402597.1_Missense_Mutation_p.T207S|ERBB4_ENST00000484474.1_5'UTR|ERBB4_ENST00000436443.1_Missense_Mutation_p.T207S	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	207	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACACTTACAAGTCTGGCAATG	0.448										TSP Lung(8;0.080)																																						0			2											137	111	120					2																	212615366		2203	4300	6503	212323611	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.620C>G	2.37:g.212615366G>C	ENSP00000342235:p.Thr207Ser		212323611	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.72|11.72	1.722861|1.722861	0.30503|0.30503	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|D;D;D	.|0.82167	.|-1.58;-1.58;-1.58	5.58|5.58	3.6|3.6	0.41247|0.41247	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.215542	.|0.53938	.|N	.|0.000042	T|T	0.66829|0.66829	0.2829|0.2829	N|N	0.10685|0.10685	0.025|0.025	0.22926|0.22926	N|N	0.998557|0.998557	.|B;B;B;B;B	.|0.06786	.|0.0;0.001;0.0;0.001;0.001	.|B;B;B;B;B	.|0.15484	.|0.001;0.013;0.001;0.001;0.001	T|T	0.43458|0.43458	-0.9390|-0.9390	5|10	.|0.15066	.|T	.|0.55	.|.	16.5715|16.5715	0.84613|0.84613	0.0:0.2982:0.7018:0.0|0.0:0.2982:0.7018:0.0	.|.	.|207;207;66;207;207	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	V|S	207|207	.|ENSP00000342235:T207S;ENSP00000403204:T207S;ENSP00000385565:T207S	.|ENSP00000342235:T207S	L|T	-|-	1|2	0|0	ERBB4|ERBB4	212323611|212323611	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	2.930000|2.930000	0.48924|0.48924	2.625000|2.625000	0.88918|0.88918	0.650000|0.650000	0.86243|0.86243	CTT|ACT		0.448	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212615366	G	C	212615366	3	2	107	1	0	0	0	0	1	0	0	0	5222	1029	36	5	3402	5	ERBB4	2	212615366	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	28987923	212615366	30584007	71	28130										
TMEM198	130612	hgsc.bcm.edu	37	chr2	220413897	220413897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcatcagccggcagcgccgaCgcgtgcaactgatgcggatt	13	13	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:220413897C>T	ENST00000344458.2	+	5	1351	c.766C>T	c.(766-768)Cgc>Tgc	p.R256C	TMEM198_ENST00000373883.3_Missense_Mutation_p.R256C|RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA			Q66K66	TM198_HUMAN	transmembrane protein 198	256	Arg-rich.				multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GCAGCGCCGACGCGTGCAACT	0.622																																																0			2											87	94	91					2																	220413897		2203	4300	6503	220122141	SO:0001583	missense	130612			BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.766C>T	2.37:g.220413897C>T	ENSP00000343507:p.Arg256Cys		220122141		Missense_Mutation	SNP	ENST00000344458.2	37	CCDS33385.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199399	0.79015	.	.	ENSG00000188760	ENST00000344458;ENST00000373883	.	.	.	4.68	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	L	0.47190	1.495	0.53688	D	0.999979	D	0.89917	1.0	D	0.78314	0.991	T	0.71290	-0.4637	9	0.66056	D	0.02	-18.2189	14.6232	0.68602	0.1459:0.8541:0.0:0.0	.	256	Q66K66	TM198_HUMAN	C	256	.	ENSP00000343507:R256C	R	+	1	0	TMEM198	220122141	0.993000	0.37304	0.133000	0.22050	0.870000	0.49936	3.147000	0.50639	2.597000	0.87782	0.561000	0.74099	CGC		0.622	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209		T	220413897	C	T	220413897	3	4	107	1	0	0	0	0	1	0	0	0	16158	536	19	1	776	1	TMEM198	2	220413897	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	7798531	220413897	22785476	72	28131										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233348873	233348873	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgcagtgcctcacggaatggCggggacaggtgttcactcag	15	10	3	0	rs374449970		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:233348873C>A	ENST00000304546.1	-	7	1455	c.1245G>T	c.(1243-1245)ccG>ccT	p.P415P	ECEL1_ENST00000409941.1_Silent_p.P415P	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	415					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CACGGAATGGCGGGGACAGGT	0.647																																																0			2											44	44	44					2																	233348873		2203	4300	6503	233057117	SO:0001819	synonymous_variant	9427			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1245G>T	2.37:g.233348873C>A			233057117	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.647	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233348873	C	A	233348873	2	1	107	1	0	0	0	0	0	0	0	1	4902	755	27	2		2	ECEL1	2	233348873	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	12934976	233348873	9850500	73	28132										
AGAP1	116987	hgsc.bcm.edu	37	chr2	236817466	236817466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaagaggccaccccgagccAcgtcagcctgcgcacccatc	11	18	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr2:236817466A>G	ENST00000304032.8	+	11	1820	c.1240A>G	c.(1240-1242)Acg>Gcg	p.T414A	AGAP1_ENST00000336665.5_Missense_Mutation_p.T414A|AGAP1_ENST00000409538.1_Missense_Mutation_p.T679A|AGAP1_ENST00000428334.2_Missense_Mutation_p.T253A	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	414	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACCCCGAGCCACGTCAGCCTG	0.483																																																0			2											89	79	83					2																	236817466		2203	4300	6503	236482205	SO:0001583	missense	116987			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1240A>G	2.37:g.236817466A>G	ENSP00000307634:p.Thr414Ala		236482205	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.32|12.32	1.902607|1.902607	0.33628|0.33628	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	.|T;T;T;T	.|0.79141	.|-1.24;-1.24;-1.24;-1.24	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Pleckstrin homology domain (3);	.|0.159471	.|0.42682	.|D	.|0.000668	D|D	0.83533|0.83533	0.5275|0.5275	L|L	0.50333|0.50333	1.59|1.59	0.37075|0.37075	D|D	0.898726|0.898726	.|B;D	.|0.62365	.|0.015;0.991	.|B;D	.|0.74023	.|0.023;0.982	D|D	0.84098|0.84098	0.0394|0.0394	5|10	.|0.29301	.|T	.|0.29	.|.	14.8075|14.8075	0.69968|0.69968	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|414;414	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	R|A	47|414;414;679;253	.|ENSP00000307634:T414A;ENSP00000338378:T414A;ENSP00000386897:T679A;ENSP00000411824:T253A	.|ENSP00000307634:T414A	H|T	+|+	2|1	0|0	AGAP1|AGAP1	236482205|236482205	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.889000|0.889000	0.51656|0.51656	4.759000|4.759000	0.62227|0.62227	2.044000|2.044000	0.60594|0.60594	0.533000|0.533000	0.62120|0.62120	CAC|ACG		0.483	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		G	236817466	A	G	236817466	3	3	107	1	0	0	0	0	1	0	0	0	366	159	6	4	1282	4	AGAP1	2	236817466	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3468593	236817466	6381907	74	28133										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9781308	9781308	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggccaactgttacacagctTtccatgtgacatgcgcccag	9	13	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:9781308T>A	ENST00000457855.1	+	2	1236	c.1225T>A	c.(1225-1227)Ttc>Atc	p.F409I	BRPF1_ENST00000424362.1_Missense_Mutation_p.F409I|BRPF1_ENST00000383829.2_Missense_Mutation_p.F409I|BRPF1_ENST00000433861.2_Missense_Mutation_p.F409I|BRPF1_ENST00000302054.3_Missense_Mutation_p.F409I			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	409					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					TTACACAGCTTTCCATGTGAC	0.587																																																0			3											56	56	56					3																	9781308		2203	4300	6503	9756308	SO:0001583	missense	23774			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.1225T>A	3.37:g.9781308T>A	ENSP00000410210:p.Phe409Ile		9756308	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	37	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.172287	0.57584	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	6.17	6.17	0.99709	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	H	0.95437	3.67	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.998;1.0	T	0.73547	-0.3948	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	409;409;409;409	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	I	409	ENSP00000402485:F409I;ENSP00000398863:F409I;ENSP00000373340:F409I;ENSP00000306297:F409I;ENSP00000410210:F409I	ENSP00000306297:F409I	F	+	1	0	BRPF1	9756308	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	7.691000	0.84191	2.371000	0.80710	0.533000	0.62120	TTC		0.587	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		A	9781308	T	A	9781308	3	1	107	1	0	0	0	0	1	0	0	0	1523	1841	64	5	1231	5	BRPF1	3	9781308	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10		9781308	188241122	75	28134										
RAB5A	5868	hgsc.bcm.edu	37	chr3	20017197	20017197	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atagcctagcaccaatgtacTacagaggagcacaagcagcc	9	12	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:20017197T>A	ENST00000273047.4	+	3	804	c.268T>A	c.(268-270)Tac>Aac	p.Y90N	RAB5A_ENST00000422242.1_Missense_Mutation_p.Y76N	NM_004162.4	NP_004153.2	P20339	RAB5A_HUMAN	RAB5A, member RAS oncogene family	90					blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|nervous system development (GO:0007399)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of endosome size (GO:0051036)|regulation of filopodium assembly (GO:0051489)|regulation of synaptic vesicle exocytosis (GO:2000300)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoplasmic side of early endosome membrane (GO:0098559)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|somatodendritic compartment (GO:0036477)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(1)|urinary_tract(1)	2						ACCAATGTACTACAGAGGAGC	0.388																																																0			3											120	110	113					3																	20017197		2203	4300	6503	19992201	SO:0001583	missense	5868				CCDS2633.1	3p24-p22	2008-07-18			ENSG00000144566	ENSG00000144566		"RAB, member RAS oncogene"	9783	protein-coding gene	gene with protein product	"RAS-associated protein RAB5A"	179512		RAB5		1999336	Standard	NM_004162		Approved		uc003cbn.3	P20339	OTTHUMG00000129889	ENST00000273047.4:c.268T>A	3.37:g.20017197T>A	ENSP00000273047:p.Tyr90Asn		19992201	B4DJA5|Q6FI44	Missense_Mutation	SNP	ENST00000273047.4	37	CCDS2633.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.698519	0.88830	.	.	ENSG00000144566	ENST00000273047;ENST00000422242	T;T	0.80653	-1.4;-1.4	5.09	5.09	0.68999	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.93517	0.7931	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95830	0.8857	9	.	.	.	-4.8489	15.1572	0.72752	0.0:0.0:0.0:1.0	.	76;90	B4DJA5;P20339	.;RAB5A_HUMAN	N	90;76	ENSP00000273047:Y90N;ENSP00000411941:Y76N	.	Y	+	1	0	RAB5A	19992201	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.960000	0.87893	2.055000	0.61198	0.460000	0.39030	TAC		0.388	RAB5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252137.2	NM_004162		A	20017197	T	A	20017197	3	1	107	1	0	0	0	0	1	0	0	0	12985	1522	53	5	274	5	RAB5A	3	20017197	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	10235889	20017197	178005233	76	28135										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37337662	37337662	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcagctggaaccacaggctGaagtcttcactaaagaagag	10	10	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:37337662G>A	ENST00000361924.2	+	7	1140	c.766G>A	c.(766-768)Gaa>Aaa	p.E256K	GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000356847.4_Missense_Mutation_p.E278K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	256	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ACCACAGGCTGAAGTCTTCAC	0.408																																																0			3											86	89	88					3																	37337662		2203	4300	6503	37312666	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.766G>A	3.37:g.37337662G>A	ENSP00000354486:p.Glu256Lys		37312666	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.410164	0.42715	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000450863;ENST00000437131	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	4.47	3.59	0.41128	.	0.000000	0.36101	N	0.002786	T	0.26666	0.0652	M	0.71581	2.175	0.21386	N	0.999709	B;B;B	0.14438	0.01;0.01;0.003	B;B;B	0.09377	0.004;0.004;0.003	T	0.34477	-0.9827	10	0.06891	T	0.86	.	8.9349	0.35693	0.0894:0.1945:0.7162:0.0	.	256;278;256	Q13439-4;F8W8Q7;Q13439	.;.;GOGA4_HUMAN	K	256;278;261;127	ENSP00000354486:E256K;ENSP00000349305:E278K;ENSP00000387633:E261K;ENSP00000405842:E127K	ENSP00000349305:E278K	E	+	1	0	GOLGA4	37312666	0.988000	0.35896	0.476000	0.27291	0.021000	0.10359	1.998000	0.40796	1.250000	0.43966	0.411000	0.27672	GAA		0.408	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37337662	G	A	37337662	3	1	107	1	0	0	0	0	1	0	0	0	6575	1291	45	3	862	3	GOLGA4	3	37337662	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	17320465	37337662	160684768	77	28136										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266106	41266106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agtcttacctggactctggaAtccattctggtgccactacc	8	13	3	0	rs121913416		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:41266106A>G	ENST00000349496.5	+	3	383	c.103A>G	c.(103-105)Atc>Gtc	p.I35V	CTNNB1_ENST00000453024.1_Missense_Mutation_p.I28V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.I35V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.I35V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.I35V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	35			I -> S (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGACTCTGGAATCCATTCTGG	0.493		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	134	Deletion - In frame(108)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(100)|large_intestine(19)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|pancreas(1)	3											94	79	84					3																	41266106		2203	4300	6503	41241110	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.103A>G	3.37:g.41266106A>G	ENSP00000344456:p.Ile35Val		41241110	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.335333	0.81801	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79614	2.46	0.80722	D	1	D	0.64830	0.994	P	0.55749	0.783	T	0.70392	-0.4884	10	0.87932	D	0	-3.5499	16.0676	0.80897	1.0:0.0:0.0:0.0	.	35	P35222	CTNB1_HUMAN	V	28;35;35;35;35;28;35;35;35	ENSP00000400508:I28V;ENSP00000385604:I35V;ENSP00000412219:I35V;ENSP00000379486:I35V;ENSP00000344456:I35V;ENSP00000411226:I28V;ENSP00000379488:I35V;ENSP00000409302:I35V;ENSP00000401599:I35V	ENSP00000344456:I35V	I	+	1	0	CTNNB1	41241110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	ATC		0.493	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266106	A	G	41266106	3	3	107	1	0	0	0	0	1	0	0	0	4022	101	4	4	109	4	CTNNB1	3	41266106	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3928444	41266106	156756324	78	28137										
USP19	10869	hgsc.bcm.edu	37	chr3	49146603	49146604	+	Frame_Shift_Ins	INS	-	-	C													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcctcagcctccagctcctgINSccaaatccgggaagcctagg							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:49146603_49146604insC	ENST00000398888.2	-	26	4062_4063	c.3744_3745insG	c.(3742-3747)tggcagfs	p.Q1249fs	USP19_ENST00000434032.2_Frame_Shift_Ins_p.Q1350fs|USP19_ENST00000398898.2_Intron|USP19_ENST00000398896.1_Intron|USP19_ENST00000417901.1_Intron|USP19_ENST00000398892.3_Frame_Shift_Ins_p.Q1289fs|USP19_ENST00000453664.1_Intron	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1249					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCAGCTCCTGCCAAATCCGGG	0.678																																																0			3																																								49121608	SO:0001589	frameshift_variant	10869			AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.3745dupG	3.37:g.49146605_49146605dupC	ENSP00000381863:p.Gln1249fs		49121607	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Frame_Shift_Ins	INS	ENST00000398888.2	37	CCDS43090.1																																																																																				0.678	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		C	49146604	-	C	49146603	7	5	107	1	0	1	1	0	0	0	0	0	17090	1328	46	0	215	0	USP19	3	49146603	Frame_Shift_Ins	INS	-	TCGA-DY-A1DG-01A-11D-A152-10	7880497	49146603	148875827	79	28138										
CADPS	8618	hgsc.bcm.edu	37	chr3	62499312	62499312	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaggaggtggtaggtactcaCgaatggttaaatccatcact	12	7	2	0	rs557590790		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:62499312C>T	ENST00000383710.4	-	17	2931				CADPS_ENST00000357948.3_Intron|CADPS_ENST00000283269.9_Splice_Site	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator						catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TAGGTACTCACGAATGGTTAA	0.433													C|||	1	0.000199681	8e-04	0	5008	,	,		18230	0		0	False		,,,				2504	0															0			3											124	98	107					3																	62499312		2203	4300	6503	62474352	SO:0001627	intron_variant	8618			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2582-869G>A	3.37:g.62499312C>T			62474352	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Splice_Site	SNP	ENST00000383710.4	37	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016081	0.54468	.	.	ENSG00000163618	ENST00000283269	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0887	0.97806	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CADPS	62474352	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.776000	0.85560	2.825000	0.97269	0.655000	0.94253	.		0.433	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62499312	C	T	62499312	1	4	107	0	1	0	0	0	0	0	0	0	2576	550	19	1		1	CADPS	3	62499312	Intron	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	13352709	62499312	135523118	80	28139										
MITF	4286	hgsc.bcm.edu	37	chr3	70014107	70014107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcaagaacccgttcttgagaActgcagccaagacctccttc	8	14	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:70014107A>G	ENST00000448226.2	+	10	1416	c.1289A>G	c.(1288-1290)aAc>aGc	p.N430S	MITF_ENST00000328528.6_Missense_Mutation_p.N423S|MITF_ENST00000394351.3_Missense_Mutation_p.N323S|MITF_ENST00000314557.6_Missense_Mutation_p.N317S|MITF_ENST00000531774.1_Missense_Mutation_p.N261S|MITF_ENST00000394355.2_Missense_Mutation_p.N399S|MITF_ENST00000314589.5_Missense_Mutation_p.N408S|MITF_ENST00000472437.1_Missense_Mutation_p.N372S|MITF_ENST00000352241.4_Missense_Mutation_p.N424S			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	430	DNA binding regulation.				bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.N323T(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GTTCTTGAGAACTGCAGCCAA	0.502			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	1	Substitution - Missense(1)	ovary(1)	3											156	131	140					3																	70014107		2203	4300	6503	70096797	SO:0001583	missense	4286				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.1289A>G	3.37:g.70014107A>G	ENSP00000391803:p.Asn430Ser		70096797	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	A	13.03	2.116533	0.37339	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000472437;ENST00000328528;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	T;T;T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01	6.17	6.17	0.99709	.	0.079220	0.85682	D	0.000000	T	0.46386	0.1390	N	0.22421	0.69	0.43141	D	0.994899	B;B;B;B;B;B;B	0.13594	0.003;0.003;0.003;0.007;0.007;0.005;0.008	B;B;B;B;B;B;B	0.17433	0.017;0.006;0.006;0.018;0.018;0.018;0.012	T	0.41698	-0.9494	9	.	.	.	.	11.0511	0.47889	0.9315:0.0:0.0685:0.0	.	372;323;317;399;408;423;424	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	S	424;430;372;423;408;399;317;323;261	ENSP00000295600:N424S;ENSP00000391803:N430S;ENSP00000418845:N372S;ENSP00000327867:N423S;ENSP00000324443:N408S;ENSP00000377884:N399S;ENSP00000324246:N317S;ENSP00000377880:N323S;ENSP00000435909:N261S	.	N	+	2	0	MITF	70096797	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.452000	0.66638	2.371000	0.80710	0.533000	0.62120	AAC		0.502	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		G	70014107	A	G	70014107	3	3	107	1	0	0	0	0	1	0	0	0	9626	43	2	4	1548	4	MITF	3	70014107	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	7514795	70014107	128008323	81	28140										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111888083	111888083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctgatttttctggctgtaatAgcgagtccaagttttagcca	9	8	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:111888083A>G	ENST00000305815.5	-	24	3264	c.3012T>C	c.(3010-3012)gcT>gcC	p.A1004A	SLC9C1_ENST00000487372.1_Silent_p.A956A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1004					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TGGCTGTAATAGCGAGTCCAA	0.343																																																0			3											108	104	105					3																	111888083		2203	4300	6503	113370773	SO:0001819	synonymous_variant	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.3012T>C	3.37:g.111888083A>G			113370773	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																				0.343	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		G	111888083	A	G	111888083	2	3	107	1	0	0	0	0	0	0	0	1	14747	407	15	4		4	SLC9A10	3	111888083	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	41873976	111888083	86134347	82	28141										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111899499	111899499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacaatcaaatgttacaactTtggctttttcctaaaagata	4	8	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:111899499T>C	ENST00000305815.5	-	22	2912	c.2660A>G	c.(2659-2661)aAa>aGa	p.K887R	SLC9C1_ENST00000487372.1_Missense_Mutation_p.K839R	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	887					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TGTTACAACTTTGGCTTTTTC	0.303																																																0			3											116	116	116					3																	111899499		2203	4300	6503	113382189	SO:0001583	missense	285335			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2660A>G	3.37:g.111899499T>C	ENSP00000306627:p.Lys887Arg		113382189	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	12.98	2.101638	0.37048	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.44482	0.92;0.92	5.39	-5.74	0.02391	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (1);	0.476070	0.19458	N	0.113774	T	0.15782	0.0380	N	0.10874	0.06	0.09310	N	1	B;B	0.19073	0.033;0.012	B;B	0.23275	0.045;0.007	T	0.04723	-1.0931	10	0.41790	T	0.15	-28.3939	2.6079	0.04883	0.1179:0.3513:0.1202:0.4106	.	839;887	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	R	887;839	ENSP00000306627:K887R;ENSP00000420688:K839R	ENSP00000306627:K887R	K	-	2	0	SLC9A10	113382189	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	-1.750000	0.01822	-1.384000	0.02103	0.327000	0.21459	AAA		0.303	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111899499	T	C	111899499	3	2	107	1	0	0	0	0	1	0	0	0	14747	1841	64	4	905	4	SLC9A10	3	111899499	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	11416	111899499	86122931	83	28142										
KALRN	8997	hgsc.bcm.edu	37	chr3	124103827	124103827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aagacttcgtgcgcagggtgGagcagcggaagcttctcctg	15	10	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:124103827G>A	ENST00000240874.3	+	11	2057	c.1900G>A	c.(1900-1902)Gag>Aag	p.E634K	KALRN_ENST00000360013.3_Missense_Mutation_p.E634K|KALRN_ENST00000460856.1_Missense_Mutation_p.E634K	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	634					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GCGCAGGGTGGAGCAGCGGAA	0.582																																																0			3											97	82	87					3																	124103827		2203	4300	6503	125586517	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1900G>A	3.37:g.124103827G>A	ENSP00000240874:p.Glu634Lys		125586517	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.615241|5.615241	0.96649|0.96649	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013;ENST00000439170|ENST00000354186	T;T;T;T|.	0.37584|.	1.19;1.19;1.19;1.19|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.065216|.	0.64402|.	D|.	0.000013|.	T|.	0.76842|.	0.4044|.	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D;D|.	0.69078|.	0.997;0.997;0.996|.	D;D;D|.	0.79108|.	0.981;0.992;0.968|.	T|.	0.76024|.	-0.3110|.	10|.	0.37606|.	T|.	0.19|.	.|.	18.9768|18.9768	0.92740|0.92740	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	634;634;634|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	K|X	634;634;634;110|611	ENSP00000418611:E634K;ENSP00000240874:E634K;ENSP00000353109:E634K;ENSP00000402950:E110K|.	ENSP00000240874:E634K|.	E|W	+|+	1|3	0|0	KALRN|KALRN	125586517|125586517	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.597000|9.597000	0.98273|0.98273	2.700000|2.700000	0.92200|0.92200	0.563000|0.563000	0.77884|0.77884	GAG|TGG		0.582	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124103827	G	A	124103827	3	1	107	1	0	0	0	0	1	0	0	0	7996	1175	41	3	1942	3	KALRN	3	124103827	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	12204328	124103827	73918603	84	28143										
CPNE4	131034	hgsc.bcm.edu	37	chr3	131261586	131261586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gacaatggcctcccgggtgtCggccatgtctgtgataacac	12	12	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:131261586C>T	ENST00000512055.1	-	19	3480	c.1354G>A	c.(1354-1356)Gac>Aac	p.D452N	CPNE4_ENST00000511604.1_Missense_Mutation_p.D452N|CPNE4_ENST00000502818.1_Missense_Mutation_p.D470N|CPNE4_ENST00000512332.1_Missense_Mutation_p.D470N|CPNE4_ENST00000429747.1_Missense_Mutation_p.D452N			Q96A23	CPNE4_HUMAN	copine IV	452	VWFA.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						TCCCGGGTGTCGGCCATGTCT	0.567																																																0			3											112	99	103					3																	131261586		2203	4300	6503	132744276	SO:0001583	missense	131034			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1354G>A	3.37:g.131261586C>T	ENSP00000421705:p.Asp452Asn		132744276	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	C	34	5.296062	0.95574	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.3	5.3	0.74995	von Willebrand factor, type A (1);Copine (1);	0.000000	0.85682	D	0.000000	T	0.47710	0.1460	L	0.49256	1.55	0.80722	D	1	D;P	0.89917	1.0;0.763	D;B	0.80764	0.994;0.274	T	0.40515	-0.9559	10	0.56958	D	0.05	-26.566	19.0375	0.92985	0.0:1.0:0.0:0.0	.	470;452	Q96A23-2;Q96A23	.;CPNE4_HUMAN	N	452;452;470;452;470	ENSP00000421705:D452N;ENSP00000411904:D452N;ENSP00000424853:D470N;ENSP00000423811:D452N;ENSP00000421646:D470N	ENSP00000411904:D452N	D	-	1	0	CPNE4	132744276	1.000000	0.71417	0.932000	0.37286	0.993000	0.82548	7.815000	0.86186	2.503000	0.84419	0.650000	0.86243	GAC		0.567	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		T	131261586	C	T	131261586	3	4	107	1	0	0	0	0	1	0	0	0	3820	884	31	1	327	1	CPNE4	3	131261586	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	7157759	131261586	66760844	85	28144										
RAB6B	51560	hgsc.bcm.edu	37	chr3	133583452	133583452	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tatgtgttgtcgaagctgtcGtacatgaacctcgtaatcag	10	8	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:133583452G>A	ENST00000285208.4	-	2	454	c.105C>T	c.(103-105)taC>taT	p.Y35Y	RAB6B_ENST00000469959.1_Intron|RAB6B_ENST00000486858.1_Silent_p.Y22Y|RAB6B_ENST00000543906.1_Silent_p.Y35Y	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	35					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	11						CGAAGCTGTCGTACATGAACC	0.512																																																0			3											247	216	226					3																	133583452		2203	4300	6503	135066142	SO:0001819	synonymous_variant	51560			AF166492	CCDS3082.1	3q22.1	2008-05-15			ENSG00000154917	ENSG00000154917		"RAB, member RAS oncogene"	14902	protein-coding gene	gene with protein product		615852					Standard	NM_016577		Approved		uc003epy.3	Q9NRW1	OTTHUMG00000159749	ENST00000285208.4:c.105C>T	3.37:g.133583452G>A			135066142	B2R5Z9|B7Z337|D3DND3|Q92929	Silent	SNP	ENST00000285208.4	37	CCDS3082.1																																																																																				0.512	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1			A	133583452	G	A	133583452	2	1	107	1	0	0	0	0	0	0	0	1	12989	1140	40	1		1	RAB6B	3	133583452	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2321866	133583452	64438978	86	28145										
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724643	138724643	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcggggtccgcgtcctcctcGtaggcctcttcctgggcggc	14	16	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:138724643G>A	ENST00000383163.2	-	1	467	c.468C>T	c.(466-468)taC>taT	p.Y156Y	MRPS22_ENST00000495075.1_5'Flank	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	156								p.Y156Y(1)		endometrium(3)|kidney(1)|lung(7)	11						CGTCCTCCTCGTAGGCCTCTT	0.632																																																1	Substitution - coding silent(1)	endometrium(1)	3											29	31	30					3																	138724643		692	1591	2283	140207333	SO:0001819	synonymous_variant	0				CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.468C>T	3.37:g.138724643G>A			140207333		Silent	SNP	ENST00000383163.2	37	CCDS46923.1																																																																																				0.632	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		A	138724643	G	A	138724643	2	1	107	1	0	0	0	0	0	0	0	1	12628	1140	40	1		1	PRR23A	3	138724643	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	5141191	138724643	59297787	87	28146										
XRN1	54464	hgsc.bcm.edu	37	chr3	142140334	142140334	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttacatctgatagtttcacaAggtatttctcaaatcgaggt	7	7	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:142140334A>G	ENST00000264951.4	-	9	1136	c.1019T>C	c.(1018-1020)cTt>cCt	p.L340P	XRN1_ENST00000544157.1_Missense_Mutation_p.L130P|XRN1_ENST00000463916.1_Missense_Mutation_p.L340P|XRN1_ENST00000392981.2_Missense_Mutation_p.L340P|RNU1-100P_ENST00000365255.1_RNA	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	340					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.L340H(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TAGTTTCACAAGGTATTTCTC	0.328																																																1	Substitution - Missense(1)	ovary(1)	3											60	59	59					3																	142140334		2202	4299	6501	143623024	SO:0001583	missense	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1019T>C	3.37:g.142140334A>G	ENSP00000264951:p.Leu340Pro		143623024	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051422	0.75960	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157	T;T	0.50277	0.75;0.76	5.27	5.27	0.74061	.	0.174438	0.51477	D	0.000089	T	0.75961	0.3921	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.992;1.0;1.0;0.999	D;D;D;D;D	0.76071	0.986;0.952;0.95;0.987;0.971	T	0.82212	-0.0569	10	0.54805	T	0.06	-17.5749	15.1465	0.72657	1.0:0.0:0.0:0.0	.	130;340;201;340;340	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	P	340;340;340;130	ENSP00000264951:L340P;ENSP00000376707:L340P	ENSP00000264951:L340P	L	-	2	0	XRN1	143623024	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.730000	0.91510	2.118000	0.64928	0.377000	0.23210	CTT		0.328	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		G	142140334	A	G	142140334	3	3	107	1	0	0	0	0	1	0	0	0	17499	72	3	4	4237	4	XRN1	3	142140334	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3415691	142140334	55882096	88	28147										
TNIK	23043	hgsc.bcm.edu	37	chr3	170819363	170819363	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	taatcagtcaccttcttcatTgggcggtttgtttcttcaat	7	9	6	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:170819363T>C	ENST00000436636.2	-	22	2810	c.2466A>G	c.(2464-2466)ccA>ccG	p.P822P	TNIK_ENST00000341852.6_Silent_p.P738P|TNIK_ENST00000538048.1_Silent_p.P774P|TNIK_ENST00000460047.1_Silent_p.P759P|TNIK_ENST00000488470.1_Silent_p.P767P|TNIK_ENST00000470834.1_Silent_p.P785P|TNIK_ENST00000369326.5_Silent_p.P800P|TNIK_ENST00000475336.1_Silent_p.P730P|TNIK_ENST00000284483.8_Silent_p.P814P|TNIK_ENST00000357327.5_Silent_p.P793P	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	822	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CCTTCTTCATTGGGCGGTTTG	0.463																																																0			3											252	238	243					3																	170819363		2051	4201	6252	172302057	SO:0001819	synonymous_variant	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2466A>G	3.37:g.170819363T>C			172302057	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																				0.463	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		C	170819363	T	C	170819363	2	2	107	1	0	0	0	0	0	0	0	1	16352	1799	63	4		4	TNIK	3	170819363	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	28679029	170819363	27203067	89	28148										
KCNMB2	10242	hgsc.bcm.edu	37	chr3	178560616	178560616	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caacgtgctgttccattcacTcttctggccaacctgtatga	7	13	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178560616T>C	ENST00000432997.1	+	5	951	c.599T>C	c.(598-600)cTc>cCc	p.L200P	KCNMB2_ENST00000452583.1_Missense_Mutation_p.L200P|RP11-385J1.2_ENST00000451742.1_RNA|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000420517.2_Missense_Mutation_p.L200P|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA|KCNMB2_ENST00000358316.3_Missense_Mutation_p.L200P	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	214					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	TTCCATTCACTCTTCTGGCCA	0.468																																																0			3											90	86	87					3																	178560616		2203	4300	6503	180043310	SO:0001583	missense	27094			AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"Potassium channels"	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.599T>C	3.37:g.178560616T>C	ENSP00000407592:p.Leu200Pro		180043310	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	37	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755417	0.69648	.	.	ENSG00000197584	ENST00000420517;ENST00000452583;ENST00000432997;ENST00000358316;ENST00000457763	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.43787	0.1263	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.32719	-0.9896	10	0.87932	D	0	-15.6833	16.8222	0.85835	0.0:0.0:0.0:1.0	.	200	Q9Y691	KCMB2_HUMAN	P	200;200;200;200;181	ENSP00000408252:L200P;ENSP00000397483:L200P;ENSP00000407592:L200P;ENSP00000351068:L200P	ENSP00000351068:L200P	L	+	2	0	KCNMB2	180043310	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.452000	0.80683	2.371000	0.80710	0.533000	0.62120	CTC		0.468	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361		C	178560616	T	C	178560616	3	2	107	1	0	0	0	0	1	0	0	0	8096	1551	54	4	613	4	KCNMB2	3	178560616	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	7741253	178560616	19461814	90	28149										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916664	178916664	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tggggcatccacttgatgccCccaagaatcctagtagaatg	10	11	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178916664C>T	ENST00000263967.3	+	2	208	c.51C>T	c.(49-51)ccC>ccT	p.P17P		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	17	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.I13_R19del(1)|p.L15_V22>PM(1)|p.P17del(1)|p.E9_R19del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ACTTGATGCCCCCAAGAATCC	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	4	Deletion - In frame(3)|Complex - deletion inframe(1)	endometrium(2)|central_nervous_system(2)	3											56	56	56					3																	178916664		1855	4093	5948	180399358	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.51C>T	3.37:g.178916664C>T			180399358	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916664	C	T	178916664	2	4	107	1	0	0	0	0	0	0	0	1	11944	610	22	3		3	PIK3CA	3	178916664	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	356048	178916664	19105766	91	28150										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178917526	178917526	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atttgatatggttaaagatcCagaagtacaggacttccgaa	9	6	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178917526C>T	ENST00000263967.3	+	3	558	c.401C>T	c.(400-402)cCa>cTa	p.P134L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	134					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTTAAAGATCCAGAAGTACAG	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											139	132	134					3																	178917526		1832	4086	5918	180400220	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.401C>T	3.37:g.178917526C>T	ENSP00000263967:p.Pro134Leu		180400220	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727978	0.69074	.	.	ENSG00000121879	ENST00000263967	T	0.46063	0.88	5.95	5.95	0.96441	.	0.105355	0.64402	N	0.000003	T	0.48370	0.1496	M	0.69823	2.125	0.80722	D	1	B	0.14805	0.011	B	0.09377	0.004	T	0.38243	-0.9670	10	0.48119	T	0.1	-27.65	20.3748	0.98911	0.0:1.0:0.0:0.0	.	134	P42336	PK3CA_HUMAN	L	134	ENSP00000263967:P134L	ENSP00000263967:P134L	P	+	2	0	PIK3CA	180400220	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.817000	0.96982	0.563000	0.77884	CCA		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178917526	C	T	178917526	3	4	107	1	0	0	0	0	1	0	0	0	11944	594	21	3	407	3	PIK3CA	3	178917526	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	862	178917526	19104904	92	28151										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178928091	178928091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atggattagaagatttgctgAaccctattggtgttactgga	11	5	0	3	rs397517200		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178928091A>G	ENST00000263967.3	+	8	1526	c.1369A>G	c.(1369-1371)Aac>Gac	p.N457D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	457	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H450fs*9(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGATTTGCTGAACCCTATTGG	0.328		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Complex - frameshift(1)	endometrium(1)	3											137	129	132					3																	178928091		1827	4088	5915	180410785	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1369A>G	3.37:g.178928091A>G	ENSP00000263967:p.Asn457Asp		180410785	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.029747	0.93518	.	.	ENSG00000121879	ENST00000263967	T	0.77098	-1.07	5.64	5.64	0.86602	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.148010	0.64402	D	0.000008	D	0.87845	0.6280	M	0.86651	2.83	0.80722	D	1	D	0.58620	0.983	P	0.59703	0.862	D	0.88643	0.3177	10	0.44086	T	0.13	-26.4061	15.8545	0.78965	1.0:0.0:0.0:0.0	.	457	P42336	PK3CA_HUMAN	D	457	ENSP00000263967:N457D	ENSP00000263967:N457D	N	+	1	0	PIK3CA	180410785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.935000	0.92923	2.160000	0.67779	0.533000	0.62120	AAC		0.328	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178928091	A	G	178928091	3	3	107	1	0	0	0	0	1	0	0	0	11944	246	9	4	1395	4	PIK3CA	3	178928091	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	10565	178928091	19094339	93	28152										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951901	178951901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggtttcaggagatgtgttacAaggcttatctagctattcga	11	6	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178951901A>G	ENST00000263967.3	+	21	3113	c.2956A>G	c.(2956-2958)Aag>Gag	p.K986E	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	986	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GATGTGTTACAAGGCTTATCT	0.368		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											120	109	112					3																	178951901		1863	4096	5959	180434595	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2956A>G	3.37:g.178951901A>G	ENSP00000263967:p.Lys986Glu		180434595	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484726	0.44147	.	.	ENSG00000121879	ENST00000263967	T	0.74315	-0.83	6.07	6.07	0.98685	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.74772	0.3760	N	0.21142	0.635	0.80722	D	1	D	0.64830	0.994	P	0.61397	0.888	T	0.70454	-0.4867	10	0.15066	T	0.55	-18.4827	16.635	0.85050	1.0:0.0:0.0:0.0	.	986	P42336	PK3CA_HUMAN	E	986	ENSP00000263967:K986E	ENSP00000263967:K986E	K	+	1	0	PIK3CA	180434595	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	2.330000	0.79161	0.477000	0.44152	AAG		0.368	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178951901	A	G	178951901	3	3	107	1	0	0	0	0	1	0	0	0	11944	131	5	4	3034	4	PIK3CA	3	178951901	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	23810	178951901	19070529	94	28153										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952066	178952066	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggctttggagtatttcatgAaacaaatgaatgatgcacat	9	5	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:178952066A>G	ENST00000263967.3	+	21	3278	c.3121A>G	c.(3121-3123)Aaa>Gaa	p.K1041E	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1041	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTATTTCATGAAACAAATGAA	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											95	85	89					3																	178952066		1899	4127	6026	180434760	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3121A>G	3.37:g.178952066A>G	ENSP00000263967:p.Lys1041Glu		180434760	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	4.902	0.167716	0.09339	.	.	ENSG00000121879	ENST00000263967	T	0.81078	-1.45	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.051080	0.85682	D	0.000000	T	0.68449	0.3002	L	0.28608	0.87	0.80722	D	1	P	0.36483	0.555	B	0.28916	0.096	T	0.67496	-0.5656	10	0.15066	T	0.55	-22.0735	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1041	P42336	PK3CA_HUMAN	E	1041	ENSP00000263967:K1041E	ENSP00000263967:K1041E	K	+	1	0	PIK3CA	180434760	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	AAA		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952066	A	G	178952066	3	3	107	1	0	0	0	0	1	0	0	0	11944	247	9	4	3199	4	PIK3CA	3	178952066	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	165	178952066	19070364	95	28154										
TCTEX1D2	255758	hgsc.bcm.edu	37	chr3	196018209	196018209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aagattcattcagtagtagaAacagccaaatgctgctacaa	7	8	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr3:196018209A>G	ENST00000325318.5	-	5	553	c.418T>C	c.(418-420)Ttc>Ctc	p.F140L	TCTEX1D2_ENST00000491186.1_5'UTR|RP11-447L10.1_ENST00000431391.1_Intron	NM_152773.4	NP_689986.2	Q8WW35	TC1D2_HUMAN	Tctex1 domain containing 2	140										breast(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	7	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		CAGTAGTAGAAACAGCCAAAT	0.323																																																0			3											72	76	74					3																	196018209		2203	4300	6503	197502606	SO:0001583	missense	255758			BC021177	CCDS33929.1	3q29	2010-07-19			ENSG00000213123	ENSG00000213123			28482	protein-coding gene	gene with protein product						12477932	Standard	NM_152773		Approved	MGC33212	uc003fwi.3	Q8WW35	OTTHUMG00000155672	ENST00000325318.5:c.418T>C	3.37:g.196018209A>G	ENSP00000324323:p.Phe140Leu		197502606	A6NCN5	Missense_Mutation	SNP	ENST00000325318.5	37	CCDS33929.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.839406	0.51057	.	.	ENSG00000213123	ENST00000325318	T	0.27720	1.65	5.28	5.28	0.74379	.	0.105285	0.40469	U	0.001095	T	0.37073	0.0990	M	0.74546	2.27	0.46437	D	0.999049	B	0.17852	0.024	B	0.26614	0.071	T	0.31447	-0.9943	10	0.72032	D	0.01	-6.8512	11.5378	0.50648	1.0:0.0:0.0:0.0	.	140	Q8WW35	TC1D2_HUMAN	L	140	ENSP00000324323:F140L	ENSP00000324323:F140L	F	-	1	0	TCTEX1D2	197502606	1.000000	0.71417	1.000000	0.80357	0.578000	0.36192	4.181000	0.58303	2.225000	0.72522	0.533000	0.62120	TTC		0.323	TCTEX1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341166.1	NM_152773		G	196018209	A	G	196018209	3	3	107	1	0	0	0	0	1	0	0	0	15759	14	1	4	14	4	TCTEX1D2	3	196018209	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	17066143	196018209	2004221	96	28155										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228435	4228435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcggccagtttctgtgggaCgctggcgcgcacaccgcccc	13	17	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:4228435C>T	ENST00000296358.4	-	1	181	c.157G>A	c.(157-159)Gtc>Atc	p.V53I		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	53					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTCTGTGGGACGCTGGCGCGC	0.751																																																0			4											6	6	6					4																	4228435		2125	4153	6278	4279336	SO:0001583	missense	133060			BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.157G>A	4.37:g.4228435C>T	ENSP00000296358:p.Val53Ile		4279336	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	C	7.694	0.691604	0.15039	.	.	ENSG00000163982	ENST00000296358	T	0.08896	3.04	4.08	-0.686	0.11324	.	0.163986	0.41605	U	0.000856	T	0.03608	0.0103	N	0.14661	0.345	0.24006	N	0.996191	B	0.27117	0.168	B	0.17722	0.019	T	0.42430	-0.9452	10	0.27082	T	0.32	.	6.6605	0.23011	0.6572:0.2365:0.0:0.1063	.	53	Q7RTM1	OTOP1_HUMAN	I	53	ENSP00000296358:V53I	ENSP00000296358:V53I	V	-	1	0	OTOP1	4279336	0.998000	0.40836	0.966000	0.40874	0.043000	0.13939	0.803000	0.27083	0.172000	0.19760	-0.719000	0.03609	GTC		0.751	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		T	4228435	C	T	4228435	3	4	107	1	0	0	0	0	1	0	0	0	11336	536	19	1	1705	1	OTOP1	4	4228435	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		4228435	186925841	97	28156										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6862994	6862994	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcttctggctccagtgaagcAggctcaagttccagtgggaa	12	10	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:6862994A>G	ENST00000307659.5	+	7	1340	c.885A>G	c.(883-885)gcA>gcG	p.A295A	KIAA0232_ENST00000425103.1_Silent_p.A295A	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	295							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						CCAGTGAAGCAGGCTCAAGTT	0.448																																																0			4											56	56	56					4																	6862994		1946	4137	6083	6913895	SO:0001819	synonymous_variant	9778			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.885A>G	4.37:g.6862994A>G			6913895	A7E2D2	Silent	SNP	ENST00000307659.5	37	CCDS43209.1																																																																																				0.448	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6862994	A	G	6862994	2	3	107	1	0	0	0	0	0	0	0	1	8184	175	7	4		4	KIAA0232	4	6862994	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2634559	6862994	184291282	98	28157										
PROM1	8842	hgsc.bcm.edu	37	chr4	16002243	16002243	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaaacttaatccaactccaCtggaaaaaaatataaagtta	5	7	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:16002243C>A	ENST00000510224.1	-	14	1703		c.e14-1		PROM1_ENST00000540805.1_Splice_Site|PROM1_ENST00000539194.1_Splice_Site|PROM1_ENST00000505450.1_Splice_Site|PROM1_ENST00000447510.2_Splice_Site|PROM1_ENST00000543373.1_Splice_Site|PROM1_ENST00000508167.1_Splice_Site			O43490	PROM1_HUMAN	prominin 1						camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						TCCAACTCCACTGGAAAAAAA	0.333																																																0			4											46	41	43					4																	16002243		1812	4069	5881	15611341	SO:0001630	splice_region_variant	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1455-1G>T	4.37:g.16002243C>A			15611341	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Splice_Site	SNP	ENST00000510224.1	37	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.314455	0.60524	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4553	0.87605	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PROM1	15611341	1.000000	0.71417	0.793000	0.32043	0.616000	0.37450	6.872000	0.75536	2.464000	0.83262	0.650000	0.86243	.		0.333	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	Intron	A	16002243	C	A	16002243	5	1	107	1	0	0	0	0	0	0	1	0	12589	579	20	2	1199	2	PROM1	4	16002243	Splice_Site	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	9139249	16002243	175152033	99	28158										
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25258231	25258231	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgcaaaatcaagaggcaaaAagtatgctttagaaaaagtg	10	4	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:25258231A>T	ENST00000264864.6	+	4	880	c.691A>T	c.(691-693)Aag>Tag	p.K231*	PI4K2B_ENST00000512921.1_Nonsense_Mutation_p.K135*	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	231	PI3K/PI4K.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				AAGAGGCAAAAAGTATGCTTT	0.373																																																0			4											118	118	118					4																	25258231		2203	4300	6503	24867329	SO:0001587	stop_gained	55300			AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.691A>T	4.37:g.25258231A>T	ENSP00000264864:p.Lys231*		24867329	Q9NUW2	Nonsense_Mutation	SNP	ENST00000264864.6	37	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	A	39	7.902783	0.98551	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	.	.	.	6.07	6.07	0.98685	.	0.041017	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0537	16.6406	0.85098	1.0:0.0:0.0:0.0	.	.	.	.	X	135;231;200	.	ENSP00000264864:K231X	K	+	1	0	PI4K2B	24867329	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.288000	0.96055	2.326000	0.78906	0.533000	0.62120	AAG		0.373	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		T	25258231	A	T	25258231	4	4	107	1	0	0	0	0	0	1	0	0	11903	15	1	5	705	5	PI4K2B	4	25258231	Nonsense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	9255988	25258231	165896045	100	28159										
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41694371	41694371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggattcgaaatggtctcctgAactgtaatgattgctacatg	10	7	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:41694371A>G	ENST00000313860.7	+	26	3250	c.3196A>G	c.(3196-3198)Aac>Gac	p.N1066D	LIMCH1_ENST00000381753.4_Missense_Mutation_p.N873D|LIMCH1_ENST00000514096.1_Missense_Mutation_p.N880D|LIMCH1_ENST00000512946.1_Missense_Mutation_p.N1040D|LIMCH1_ENST00000512820.1_Missense_Mutation_p.N1052D|LIMCH1_ENST00000503057.1_Missense_Mutation_p.N1450D|LIMCH1_ENST00000396595.3_Missense_Mutation_p.N885D|LIMCH1_ENST00000512632.1_Missense_Mutation_p.N963D|RP11-227F19.5_ENST00000506475.1_RNA|LIMCH1_ENST00000511496.1_Missense_Mutation_p.N880D|LIMCH1_ENST00000513024.1_Missense_Mutation_p.N893D|LIMCH1_ENST00000508501.1_Missense_Mutation_p.N1039D|LIMCH1_ENST00000509277.1_Missense_Mutation_p.N899D	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	1066	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.N1066H(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						TGGTCTCCTGAACTGTAATGA	0.438																																																1	Substitution - Missense(1)	ovary(1)	4											198	172	181					4																	41694371		2203	4300	6503	41389128	SO:0001583	missense	22998			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.3196A>G	4.37:g.41694371A>G	ENSP00000316891:p.Asn1066Asp		41389128	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.58|15.58	2.874960|2.874960	0.51695|0.51695	.|.	.|.	ENSG00000064042|ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405|ENST00000508466	D;D;D;D;D;D;D;D;D;D;D;D|.	0.87256|.	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23|.	4.99|4.99	4.99|4.99	0.66335|0.66335	Zinc finger, LIM-type (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.62048|.	0.2396|.	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D;D;D|.	0.89917|.	0.99;1.0;0.996;0.998;0.999;0.999;0.988;0.999;0.988;0.992;0.99;0.995|.	D;D;D;D;D;D;D;D;D;D;D;D|.	0.91635|.	0.975;0.999;0.985;0.926;0.995;0.998;0.992;0.986;0.971;0.995;0.991;0.994|.	T|.	0.59974|.	-0.7353|.	10|.	0.54805|.	T|.	0.06|.	-22.2006|-22.2006	14.8506|14.8506	0.70295|0.70295	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	880;816;899;963;873;885;1450;893;1052;1039;1040;1066|.	E7EPK0;B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0|.	.;.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN|.	D|W	893;1039;1040;1066;963;1052;1450;880;1449;880;899;885;873;392|899	ENSP00000425222:N893D;ENSP00000424825:N1039D;ENSP00000424645:N1040D;ENSP00000316891:N1066D;ENSP00000427045:N963D;ENSP00000424437:N1052D;ENSP00000425631:N1450D;ENSP00000421242:N880D;ENSP00000426334:N880D;ENSP00000422864:N899D;ENSP00000379840:N885D;ENSP00000371172:N873D|.	ENSP00000316891:N1066D|.	N|X	+|+	1|3	0|0	LIMCH1|LIMCH1	41389128|41389128	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.094000|0.094000	0.18550|0.18550	8.529000|8.529000	0.90602|0.90602	2.094000|2.094000	0.63399|0.63399	0.455000|0.455000	0.32223|0.32223	AAC|TGA		0.438	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		G	41694371	A	G	41694371	3	3	107	1	0	0	0	0	1	0	0	0	8820	246	9	4	3326	4	LIMCH1	4	41694371	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	16436140	41694371	149459905	101	28160										
GUF1	60558	hgsc.bcm.edu	37	chr4	44680652	44680652	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cccgggtcatgtggaccctcGtgggtcggggctgggggtgc	20	11	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:44680652G>C	ENST00000281543.5	+	1	207	c.13G>C	c.(13-15)Gtg>Ctg	p.V5L	GUF1_ENST00000506793.1_Intron	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						GTGGACCCTCGTGGGTCGGGG	0.716																																																0			4											5	6	6					4																	44680652		1795	3695	5490	44375409	SO:0001583	missense	60558				CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.13G>C	4.37:g.44680652G>C	ENSP00000281543:p.Val5Leu		44375409		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598968	0.28445	.	.	ENSG00000151806	ENST00000281543	T	0.68765	-0.35	4.01	0.232	0.15381	.	1.093000	0.07069	N	0.835135	T	0.42017	0.1184	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	10	0.54805	T	0.06	2.6077	2.472	0.04566	0.096:0.1639:0.4029:0.3372	.	5	Q8N442	GUF1_HUMAN	L	5	ENSP00000281543:V5L	ENSP00000281543:V5L	V	+	1	0	GUF1	44375409	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.087000	0.11215	-0.006000	0.14370	-0.899000	0.02877	GTG		0.716	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		C	44680652	G	C	44680652	3	2	107	1	0	0	0	0	1	0	0	0	6920	1145	40	5	15	5	GUF1	4	44680652	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2986281	44680652	146473624	102	28161										
KIT	3815	hgsc.bcm.edu	37	chr4	55561763	55561763	+	Silent	SNP	C	C	T													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gacttaatagtccgcgtgggCgacgagattaggctgttatg					rs147363921		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:55561763C>T	ENST00000288135.5	+	2	250	c.153C>T	c.(151-153)ggC>ggT	p.G51G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	51	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G51G(4)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCCGCGTGGGCGACGAGATTA	0.478		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	4	Substitution - coding silent(4)	haematopoietic_and_lymphoid_tissue(3)|endometrium(1)	4						C	,	1,4405	2.1+/-5.4	0,1,2202	120	106	111		153,153	-0.6	0	4	dbSNP_134	111	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	51/977,51/973	55561763	1,13005	2203	4300	6503	55256520	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.153C>T	4.37:g.55561763C>T			55256520	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.478	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55561763	C	T	55561763	2	4	107	1	0	0	0	0	0	0	0	1	8350	755	27	1		1	KIT	4	55561763	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	10881111	55561763	135592513	103	28162	50	2								
KIT	3815	hgsc.bcm.edu	37	chr4	55561765	55561765	+	Missense_Mutation	SNP	A	A	G													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cttaatagtccgcgtgggcgAcgagattaggctgttatgca							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:55561765A>G	ENST00000288135.5	+	2	252	c.155A>G	c.(154-156)gAc>gGc	p.D52G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	52	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGCGTGGGCGACGAGATTAGG	0.473		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4											123	109	114					4																	55561765		2203	4300	6503	55256522	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.155A>G	4.37:g.55561765A>G	ENSP00000288135:p.Asp52Gly		55256522	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	5.992	0.366905	0.11352	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	T;T	0.55760	0.5;0.5	5.19	-0.118	0.13547	Immunoglobulin-like fold (1);	0.500327	0.19497	N	0.112823	T	0.51227	0.1662	L	0.57536	1.79	0.09310	N	1	B;B	0.34061	0.0;0.436	B;P	0.45343	0.004;0.477	T	0.48969	-0.8987	10	0.49607	T	0.09	.	5.3253	0.15903	0.6004:0.1446:0.255:0.0	.	52;52	P10721-2;P10721	.;KIT_HUMAN	G	52	ENSP00000288135:D52G;ENSP00000390987:D52G	ENSP00000288135:D52G	D	+	2	0	KIT	55256522	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.709000	0.37909	0.089000	0.17243	-1.133000	0.01973	GAC		0.473	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55561765	A	G	55561765	3	3	107	1	0	0	0	0	1	0	0	0	8350	275	10	4	161	4	KIT	4	55561765	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2	55561765	135592511	104	28163	50	2								
LPHN3	23284	hgsc.bcm.edu	37	chr4	62936336	62936336	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagaagatctccagtcacccCatagagactctctctatacc	5	15	4	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:62936336C>A	ENST00000514591.1	+	25	4449	c.4120C>A	c.(4120-4122)Cat>Aat	p.H1374N	LPHN3_ENST00000508946.1_Missense_Mutation_p.H1417N|LPHN3_ENST00000506746.1_Missense_Mutation_p.H1476N|RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000507164.1_3'UTR|RP11-84A1.3_ENST00000509461.1_RNA|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000506700.1_3'UTR|LPHN3_ENST00000511324.1_3'UTR|LPHN3_ENST00000507625.1_Missense_Mutation_p.H1433N|LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000514157.1_3'UTR|LPHN3_ENST00000508693.1_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.H1374N|LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000506720.1_Missense_Mutation_p.H1485N|LPHN3_ENST00000509896.1_3'UTR|LPHN3_ENST00000514996.1_Missense_Mutation_p.H1408N			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1352					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CCAGTCACCCCATAGAGACTC	0.562																																																0			4											51	49	50					4																	62936336		692	1591	2283	62618931	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.4120C>A	4.37:g.62936336C>A	ENSP00000422533:p.His1374Asn		62618931	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.058|0.058	-1.230329|-1.230329	0.01518|0.01518	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000514591;ENST00000545650;ENST00000295349;ENST00000507625;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	T;T;T;T;T;T;T|T	0.67523|0.65178	-0.21;-0.21;-0.22;-0.26;-0.27;-0.27;-0.27|-0.14	5.39|5.39	4.46|4.46	0.54185|0.54185	GPCR, family 2, latrophilin, C-terminal (1);|.	0.386356|.	0.29624|.	N|.	0.011631|.	T|T	0.43500|0.43500	0.1250|0.1250	N|N	0.03324|0.03324	-0.35|-0.35	0.29448|0.29448	N|N	0.858701|0.858701	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.48103|0.48103	-0.9064|-0.9064	10|7	0.02654|0.87932	T|D	1|0	.|.	10.8544|10.8544	0.46789|0.46789	0.4225:0.5774:0.0:0.0|0.4225:0.5774:0.0:0.0	.|.	1374;1352|.	E9PE04;Q9HAR2|.	.;LPHN3_HUMAN|.	N|Q	1374;1374;1352;1433;1417;1485;1476;1408|822	ENSP00000422533:H1374N;ENSP00000439831:H1374N;ENSP00000421372:H1433N;ENSP00000421627:H1417N;ENSP00000420931:H1485N;ENSP00000425884:H1476N;ENSP00000424258:H1408N|ENSP00000424402:P822Q	ENSP00000295349:H1352N|ENSP00000424402:P822Q	H|P	+|+	1|2	0|0	LPHN3|LPHN3	62618931|62618931	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.919000|0.919000	0.55068|0.55068	4.657000|4.657000	0.61490|0.61490	2.535000|2.535000	0.85469|0.85469	0.591000|0.591000	0.81541|0.81541	CAT|CCA		0.562	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62936336	C	A	62936336	3	1	107	1	0	0	0	0	1	0	0	0	8946	594	21	2	4210	2	LPHN3	4	62936336	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	7374571	62936336	128217940	105	28164										
ODAM	54959	hgsc.bcm.edu	37	chr4	71064306	71064306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tttttggcaggtgatgccctAtgtattctccttcaaaatgc	8	9	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:71064306A>G	ENST00000396094.2	+	5	434	c.386A>G	c.(385-387)tAt>tGt	p.Y129C		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	129	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						GTGATGCCCTATGTATTCTCC	0.368																																																0			4											109	107	108					4																	71064306		2203	4300	6503	71098895	SO:0001583	missense	54959			AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.386A>G	4.37:g.71064306A>G	ENSP00000379401:p.Tyr129Cys		71098895	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	37	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	A	13.40	2.224411	0.39300	.	.	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.51325	0.71;0.71	4.82	2.5	0.30297	.	0.174973	0.27936	N	0.017244	T	0.37705	0.1013	L	0.55481	1.735	0.31290	N	0.68954	B	0.26809	0.16	B	0.26770	0.073	T	0.44528	-0.9322	10	0.62326	D	0.03	-4.6304	4.5011	0.11865	0.6717:0.2236:0.1047:0.0	.	129	A1E959	ODAM_HUMAN	C	129;115;82	ENSP00000379401:Y129C;ENSP00000426106:Y82C	ENSP00000379401:Y129C	Y	+	2	0	ODAM	71098895	0.654000	0.27367	0.857000	0.33713	0.160000	0.22226	1.144000	0.31565	0.997000	0.38969	0.374000	0.22700	TAT		0.368	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855		G	71064306	A	G	71064306	3	3	107	1	0	0	0	0	1	0	0	0	10855	449	16	4	404	4	ODAM	4	71064306	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	8127970	71064306	120089970	106	28165										
BMP3	651	hgsc.bcm.edu	37	chr4	81967252	81967252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	taacattacgtccaagggacGccagctgccaaagaggaggt	12	10	0	1	rs373752528		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:81967252G>A	ENST00000282701.2	+	2	997	c.677G>A	c.(676-678)cGc>cAc	p.R226H		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	226					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						TCCAAGGGACGCCAGCTGCCA	0.433																																																0			4						A	HIS/ARG	1,4405	825.9+/-416.6	0,1,2202	117	123	121		677	3.9	0.3	4		121	0,8600		0,0,4300	no	missense	BMP3	NM_001201.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	226/473	81967252	1,13005	2203	4300	6503	82186276	SO:0001583	missense	651			M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.677G>A	4.37:g.81967252G>A	ENSP00000282701:p.Arg226His		82186276	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	A	0.021	-1.429988	0.01117	2.27E-4	0.0	ENSG00000152785	ENST00000282701	T	0.73152	-0.72	5.08	3.91	0.45181	.	0.281576	0.41194	N	0.000936	T	0.35248	0.0925	N	0.00642	-1.3	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26360	-1.0105	10	0.21540	T	0.41	.	8.793	0.34863	0.7757:0.0:0.2243:0.0	.	226	P12645	BMP3_HUMAN	H	226	ENSP00000282701:R226H	ENSP00000282701:R226H	R	+	2	0	BMP3	82186276	0.142000	0.22610	0.316000	0.25252	0.006000	0.05464	2.180000	0.42537	0.509000	0.28195	-0.254000	0.11334	CGC		0.433	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			A	81967252	G	A	81967252	3	1	107	1	0	0	0	0	1	0	0	0	1462	1087	38	1	683	1	BMP3	4	81967252	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	10902946	81967252	109187024	107	28166										
THAP9	79725	hgsc.bcm.edu	37	chr4	83839692	83839692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcgggtcataaatatttgtgAgcgagttgtaagaacccatt	10	6	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:83839692A>G	ENST00000302236.5	+	5	2378	c.2327A>G	c.(2326-2328)gAg>gGg	p.E776G	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	776					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.E776V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AATATTTGTGAGCGAGTTGTA	0.343																																																1	Substitution - Missense(1)	ovary(1)	4											63	67	65					4																	83839692		2202	4299	6501	84058716	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.2327A>G	4.37:g.83839692A>G	ENSP00000305533:p.Glu776Gly		84058716	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	A	8.414	0.844899	0.16963	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.93019	-3.15	3.82	3.82	0.43975	.	0.525224	0.16022	N	0.233280	D	0.92218	0.7532	L	0.34521	1.04	0.80722	D	1	D	0.60160	0.987	P	0.54544	0.755	D	0.91966	0.5583	10	0.72032	D	0.01	-11.1114	11.2867	0.49226	1.0:0.0:0.0:0.0	.	776	Q9H5L6	THAP9_HUMAN	G	776	ENSP00000305533:E776G	ENSP00000305533:E776G	E	+	2	0	THAP9	84058716	1.000000	0.71417	1.000000	0.80357	0.098000	0.18820	4.878000	0.63093	1.959000	0.56917	0.533000	0.62120	GAG		0.343	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		G	83839692	A	G	83839692	3	3	107	1	0	0	0	0	1	0	0	0	15890	304	11	4	2345	4	THAP9	4	83839692	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1872440	83839692	107314584	108	28167										
HELQ	113510	hgsc.bcm.edu	37	chr4	84376732	84376732	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttcctcctcctctttcccctCatctccgggcacgagctcgg	7	19	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:84376732C>T	ENST00000295488.3	-	1	277	c.115G>A	c.(115-117)Gag>Aag	p.E39K	HELQ_ENST00000440639.2_5'UTR|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.E39K|MRPS18C_ENST00000295491.4_5'Flank|MRPS18C_ENST00000507349.1_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	39					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TCTTTCCCCTCATCTCCGGGC	0.622								Other identified genes with known or suspected DNA repair function			OREG0016254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4											109	120	116					4																	84376732		2203	4300	6503	84595756	SO:0001583	missense	113510			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.115G>A	4.37:g.84376732C>T	ENSP00000295488:p.Glu39Lys	1228	84595756	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.030851	0.54790	.	.	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.69306	-0.02;-0.39	5.12	4.28	0.50868	.	0.654924	0.13250	N	0.402143	T	0.49558	0.1564	N	0.19112	0.55	0.09310	N	1	B;P;B;B	0.37781	0.18;0.608;0.386;0.18	B;B;B;B	0.35550	0.083;0.205;0.085;0.083	T	0.39820	-0.9595	10	0.48119	T	0.1	-27.0389	9.195	0.37222	0.0:0.9032:0.0:0.0968	.	39;39;39;39	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	K	39	ENSP00000295488:E39K;ENSP00000424539:E39K	ENSP00000295488:E39K	E	-	1	0	HELQ	84595756	0.007000	0.16637	0.086000	0.20670	0.020000	0.10135	1.638000	0.37165	1.387000	0.46486	0.462000	0.41574	GAG		0.622	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		T	84376732	C	T	84376732	3	4	107	1	0	0	0	0	1	0	0	0	7068	835	29	3	3262	3	HELQ	4	84376732	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	537040	84376732	106777544	109	28168										
ADH1B	125	hgsc.bcm.edu	37	chr4	100235226	100235226	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gccaaacacagcacaggtagAgcctggggtgacctgtgttt	13	10	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr4:100235226A>G	ENST00000305046.8	-	6	647	c.580T>C	c.(580-582)Tct>Cct	p.S194P	ADH1B_ENST00000394887.3_Missense_Mutation_p.S154P			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	194					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCACAGGTAGAGCCTGGGGTG	0.468																																																0			4											107	116	113					4																	100235226		2203	4300	6503	100454249	SO:0001583	missense	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.580T>C	4.37:g.100235226A>G	ENSP00000306606:p.Ser194Pro		100454249	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Missense_Mutation	SNP	ENST00000305046.8	37	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683449	0.47991	.	.	ENSG00000196616	ENST00000305046;ENST00000394887;ENST00000412614	T;T	0.32272	1.46;1.46	3.81	3.81	0.43845	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.70482	0.3229	H	0.98996	4.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.82030	-0.0659	10	0.87932	D	0	-12.0051	12.5708	0.56337	1.0:0.0:0.0:0.0	.	181;154;194	F5HB16;A8MYN5;P00325	.;.;ADH1B_HUMAN	P	194;154;181	ENSP00000306606:S194P;ENSP00000378351:S154P	ENSP00000306606:S194P	S	-	1	0	ADH1B	100454249	1.000000	0.71417	0.981000	0.43875	0.050000	0.14768	8.453000	0.90349	1.343000	0.45638	0.459000	0.35465	TCT		0.468	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		G	100235226	A	G	100235226	3	3	107	1	0	0	0	0	1	0	0	0	308	304	11	4	563	4	ADH1B	4	100235226	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	15858494	100235226	90919050	110	28169										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13829656	13829656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctcacacagtttgtagagcGtgaaaaacttcctggccaaa	8	11	1	2	rs140690090		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:13829656G>A	ENST00000265104.4	-	38	6511	c.6407C>T	c.(6406-6408)aCg>aTg	p.T2136M		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2136	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTTGTAGAGCGTGAAAAACTT	0.448									Kartagener syndrome																																							0			5						G	MET/THR	0,4406		0,0,2203	110	99	103		6407	5.6	1	5	dbSNP_134	103	2,8598	2.2+/-6.3	0,2,4298	no	missense	DNAH5	NM_001369.2	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	2136/4625	13829656	2,13004	2203	4300	6503	13882656	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6407C>T	5.37:g.13829656G>A	ENSP00000265104:p.Thr2136Met		13882656	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.669455	0.88348	0.0	2.33E-4	ENSG00000039139	ENST00000265104	T	0.39229	1.09	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.56352	0.1979	L	0.49513	1.565	0.80722	D	1	D	0.61697	0.99	P	0.57057	0.812	T	0.57225	-0.7848	10	0.66056	D	0.02	.	19.5353	0.95251	0.0:0.0:1.0:0.0	.	2136	Q8TE73	DYH5_HUMAN	M	2136	ENSP00000265104:T2136M	ENSP00000265104:T2136M	T	-	2	0	DNAH5	13882656	1.000000	0.71417	0.959000	0.39883	0.959000	0.62525	4.936000	0.63506	2.607000	0.88179	0.655000	0.94253	ACG		0.448	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13829656	G	A	13829656	3	1	107	1	0	0	0	0	1	0	0	0	4615	1145	40	1	7635	1	DNAH5	5	13829656	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		13829656	167085604	111	28170										
FAM105B	90268	hgsc.bcm.edu	37	chr5	14681609	14681609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcagaagttcacctccataCggcgagtccgtggtgataat	10	11	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:14681609C>T	ENST00000284274.4	+	4	439	c.361C>T	c.(361-363)Cgg>Tgg	p.R121W		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		121	OTU.				canonical Wnt signaling pathway (GO:0060070)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|protein linear deubiquitination (GO:1990108)|sprouting angiogenesis (GO:0002040)	cytoplasm (GO:0005737)|LUBAC complex (GO:0071797)	cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	14	Lung NSC(4;0.00696)					CACCTCCATACGGCGAGTCCG	0.532																																																0			5											97	104	102					5																	14681609		2038	4195	6233	14734609	SO:0001583	missense	90268																														ENST00000284274.4:c.361C>T	5.37:g.14681609C>T	ENSP00000284274:p.Arg121Trp		14734609	D3DTD3|Q8NAS0|Q96IA3	Missense_Mutation	SNP	ENST00000284274.4	37	CCDS43302.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621537	0.66787	.	.	ENSG00000154124	ENST00000284274	T	0.21361	2.01	5.82	-6.14	0.02111	.	0.000000	0.85682	D	0.000000	T	0.43366	0.1244	M	0.72118	2.19	0.41634	D	0.989035	D	0.89917	1.0	D	0.91635	0.999	T	0.55147	-0.8186	10	0.87932	D	0	-23.5851	21.9729	0.99964	0.226:0.774:0.0:0.0	.	121	Q96BN8	F105B_HUMAN	W	121	ENSP00000284274:R121W	ENSP00000284274:R121W	R	+	1	2	FAM105B	14734609	0.163000	0.22920	0.005000	0.12908	0.874000	0.50279	0.375000	0.20518	-1.390000	0.02087	-0.309000	0.09137	CGG		0.532	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1			T	14681609	C	T	14681609	3	4	107	1	0	0	0	0	1	0	0	0	5404	527	19	1	375	1	FAM105B	5	14681609	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	851953	14681609	166233651	112	28171										
MGC42105	167359	hgsc.bcm.edu	37	chr5	43280529	43280529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	accctacacctttggaacctTtccaactggatcccaaacat	4	15	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:43280529T>C	ENST00000512796.1	+	4	2508	c.1009T>C	c.(1009-1011)Ttc>Ctc	p.F337L	NIM1_ENST00000326035.2_Missense_Mutation_p.F337L			Q8IY84	NIM1_HUMAN		337					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TTTGGAACCTTTCCAACTGGA	0.468																																																0			5											101	97	98					5																	43280529		2203	4300	6503	43316286	SO:0001583	missense	167359																														ENST00000512796.1:c.1009T>C	5.37:g.43280529T>C	ENSP00000420849:p.Phe337Leu		43316286	B3KVM1	Missense_Mutation	SNP	ENST00000512796.1	37	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473093	0.43942	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	T;T	0.22134	1.97;1.97	5.58	5.58	0.84498	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.13841	0.0335	N	0.25380	0.74	0.58432	D	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.13548	-1.0505	10	0.17369	T	0.5	.	10.1543	0.42814	0.0:0.0743:0.0:0.9257	.	337	Q8IY84	NIM1_HUMAN	L	337	ENSP00000313572:F337L;ENSP00000420849:F337L	ENSP00000313572:F337L	F	+	1	0	AC114947.1	43316286	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.155000	0.64900	2.135000	0.66039	0.533000	0.62120	TTC		0.468	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			C	43280529	T	C	43280529	3	2	107	1	0	0	0	0	1	0	0	0	9582	1841	64	4	1019	4	MGC42105	5	43280529	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	28598920	43280529	137634731	113	28172										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67591116	67591116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaacagcattaaaccagaccTtatccagctgagaaagacga	8	10	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:67591116T>C	ENST00000521381.1	+	13	2325	c.1709T>C	c.(1708-1710)cTt>cCt	p.L570P	PIK3R1_ENST00000521657.1_Missense_Mutation_p.L570P|PIK3R1_ENST00000274335.5_Missense_Mutation_p.L570P|PIK3R1_ENST00000336483.5_Missense_Mutation_p.L300P|PIK3R1_ENST00000396611.1_Missense_Mutation_p.L570P|PIK3R1_ENST00000523872.1_Missense_Mutation_p.L207P|PIK3R1_ENST00000320694.8_Missense_Mutation_p.L270P	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	570					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.L570_Q572del(1)|p.L570_D578del(1)|p.0?(1)|p.?(1)|p.L570P(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAACCAGACCTTATCCAGCTG	0.368			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	5	Deletion - In frame(2)|Substitution - Missense(1)|Whole gene deletion(1)|Unknown(1)	large_intestine(2)|lung(1)|ovary(1)|central_nervous_system(1)	5											147	145	146					5																	67591116		2203	4300	6503	67626872	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1709T>C	5.37:g.67591116T>C	ENSP00000428056:p.Leu570Pro		67626872	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.355975	0.82243	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	M	0.85859	2.78	0.80722	D	1	D;D;D;D	0.89917	0.998;0.997;0.991;1.0	D;D;D;D	0.85130	0.942;0.977;0.961;0.997	T	0.67577	-0.5635	10	0.87932	D	0	-12.1122	14.6505	0.68794	0.0:0.0:0.0:1.0	.	240;300;270;570	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	P	570;570;570;570;270;300;207	ENSP00000428056:L570P;ENSP00000429277:L570P;ENSP00000379855:L570P;ENSP00000274335:L570P;ENSP00000323512:L270P;ENSP00000338554:L300P;ENSP00000430098:L207P	ENSP00000274335:L570P	L	+	2	0	PIK3R1	67626872	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.825000	0.86693	2.103000	0.63969	0.477000	0.44152	CTT		0.368	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		C	67591116	T	C	67591116	3	2	107	1	0	0	0	0	1	0	0	0	11949	1609	56	4	1885	4	PIK3R1	5	67591116	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	24310587	67591116	113324144	114	28173										
APC	324	hgsc.bcm.edu	37	chr5	112116592	112116592	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctgccaggatatggaaaaaCgagcacaggtaagttacttg	11	8	0	0	rs587781392		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:112116592C>T	ENST00000457016.1	+	6	1017	c.637C>T	c.(637-639)Cga>Tga	p.R213*	RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000257430.4_Nonsense_Mutation_p.R213*|APC_ENST00000508376.2_Nonsense_Mutation_p.R213*			P25054	APC_HUMAN	adenomatous polyposis coli	213	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R213*(20)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATGGAAAAACGAGCACAGGT	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	20	Substitution - Nonsense(20)	large_intestine(19)|lung(1)	5	GRCh37	CM920027	APC	M							58	57	58					5																	112116592		2202	4300	6502	112144491	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.637C>T	5.37:g.112116592C>T	ENSP00000413133:p.Arg213*		112144491	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.046788	0.97231	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0079	14.2561	0.66053	0.4075:0.5925:0.0:0.0	.	.	.	.	X	213;223;213;213;213	.	ENSP00000257430:R213X	R	+	1	2	APC	112144491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.672000	0.46850	0.659000	0.30945	0.655000	0.94253	CGA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112116592	C	T	112116592	4	4	107	1	0	0	0	0	0	1	0	0	763	528	19	1	655	1	APC	5	112116592	Nonsense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	44525476	112116592	68798668	115	28174										
APC	324	hgsc.bcm.edu	37	chr5	112175210	112175210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ataccctgcaaatagcagaaAtaaaagaaaagattggaact	7	6	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:112175210A>G	ENST00000457016.1	+	16	4299	c.3919A>G	c.(3919-3921)Ata>Gta	p.I1307V	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.I1307V|APC_ENST00000508376.2_Missense_Mutation_p.I1307V			P25054	APC_HUMAN	adenomatous polyposis coli	1307	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		I -> K (in 6% of Ashkenazi Jews; associated with slightly increased risk of colon and breast cancer; dbSNP:rs1801155). {ECO:0000269|PubMed:9724771, ECO:0000269|PubMed:9731522, ECO:0000269|PubMed:9731533, ECO:0000269|PubMed:9973276}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.I1307fs*8(15)|p.I1307fs*1(3)|p.I1307fs*14(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AATAGCAGAAATAAAAGAAAA	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	21	Insertion - Frameshift(15)|Deletion - Frameshift(4)|Unknown(1)|Complex - frameshift(1)	large_intestine(19)|soft_tissue(1)|skin(1)	5	GRCh37	CM086766	APC	M							53	55	54					5																	112175210		2202	4300	6502	112203109	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3919A>G	5.37:g.112175210A>G	ENSP00000413133:p.Ile1307Val		112203109	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	1.436	-0.568895	0.03910	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88975	-2.45;-2.45;-2.45	5.73	3.53	0.40419	.	0.581060	0.19747	N	0.106984	T	0.78407	0.4278	N	0.19112	0.55	0.22811	N	0.99871	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.61501	-0.7050	9	.	.	.	-6.2797	8.6908	0.34264	0.6019:0.3107:0.0874:0.0	.	1309;1307	Q4LE70;P25054	.;APC_HUMAN	V	1307	ENSP00000413133:I1307V;ENSP00000257430:I1307V;ENSP00000427089:I1307V	.	I	+	1	0	APC	112203109	0.996000	0.38824	0.992000	0.48379	0.782000	0.44232	1.389000	0.34453	0.543000	0.28864	0.533000	0.62120	ATA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175210	A	G	112175210	3	3	107	1	0	0	0	0	1	0	0	0	763	101	4	4	3977	4	APC	5	112175210	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	58618	112175210	68740050	116	28175										
APC	324	hgsc.bcm.edu	37	chr5	112175242	112175242	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	attggaactaggtcagctgaAgatcctgtgagcgaagttcc	12	8	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:112175242A>G	ENST00000457016.1	+	16	4331	c.3951A>G	c.(3949-3951)gaA>gaG	p.E1317E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.E1317E|APC_ENST00000508376.2_Silent_p.E1317E			P25054	APC_HUMAN	adenomatous polyposis coli	1317	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		E -> Q (may contribute to colorectal tumor development; dbSNP:rs1801166). {ECO:0000269|PubMed:9724771}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.D1318fs*3(1)|p.K1192fs*3(1)|p.?(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGTCAGCTGAAGATCCTGTGA	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											60	62	61					5																	112175242		2202	4300	6502	112203141	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3951A>G	5.37:g.112175242A>G			112203141	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175242	A	G	112175242	2	3	107	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112175242	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	32	112175242	68740018	117	28176										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215402	140215402	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgccacatcttcactgtgtcGgcgggggacgcggacgcgca	15	13	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:140215402G>A	ENST00000525929.1	+	1	1434	c.1434G>A	c.(1432-1434)tcG>tcA	p.S478S	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.S478S|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	478	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACTGTGTCGGCGGGGGACG	0.672																																					NSCLC(160;258 2013 5070 22440 28951)											0			5											43	49	47					5																	140215402		2201	4297	6498	140195586	SO:0001819	synonymous_variant	56141			AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1434G>A	5.37:g.140215402G>A			140195586	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																				0.672	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		A	140215402	G	A	140215402	2	1	107	1	0	0	0	0	0	0	0	1	11560	1103	39	1		1	PCDHA7	5	140215402	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	28040160	140215402	40699858	118	28177										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222316	140222316	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgaaggagaacaacccgccGggctgccacatcttcacggt	12	13	2	2	rs202126810		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:140222316G>A	ENST00000531613.1	+	1	1410	c.1410G>A	c.(1408-1410)ccG>ccA	p.P470P	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACCCGCCGGGCTGCCACA	0.672																																																0			5											38	43	41					5																	140222316		2193	4252	6445	140202500	SO:0001819	synonymous_variant	56140			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1410G>A	5.37:g.140222316G>A			140202500	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																				0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222316	G	A	140222316	2	1	107	1	0	0	0	0	0	0	0	1	11561	1103	39	1		1	PCDHA8	5	140222316	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	6914	140222316	40692944	119	28178										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263464	140263464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttgcagttccaggtgagcgcGcgcgactctggcgtgccgcc	15	14	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:140263464G>A	ENST00000289272.2	+	1	1611	c.1611G>A	c.(1609-1611)gcG>gcA	p.A537A	PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Silent_p.A537A|PCDHA10_ENST00000506939.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGAGCGCGCGCGACTCTG	0.677																																					Melanoma(147;1739 1852 5500 27947 37288)											0			5											73	78	76					5																	140263464		2203	4299	6502	140243648	SO:0001819	synonymous_variant	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1611G>A	5.37:g.140263464G>A			140243648	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																				0.677	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263464	G	A	140263464	2	1	107	1	0	0	0	0	0	0	0	1	11554	1074	38	1		1	PCDHA13	5	140263464	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	41148	140263464	40651796	120	28179										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156589770	156589770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gactcctttttggtggagctGtgggtggagctcttgcgaga	16	7	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:156589770G>A	ENST00000302938.4	-	2	1601	c.1506C>T	c.(1504-1506)caC>caT	p.H502H		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	502						nucleus (GO:0005634)		p.H502H(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGTGGAGCTGTGGGTGGAGC	0.488																																																1	Substitution - coding silent(1)	ovary(1)	5											165	165	165					5																	156589770		2203	4300	6503	156522348	SO:0001819	synonymous_variant	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1506C>T	5.37:g.156589770G>A			156522348	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																				0.488	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156589770	G	A	156589770	2	1	107	1	0	0	0	0	0	0	0	1	5627	1368	48	3		3	FAM71B	5	156589770	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	16326306	156589770	24325490	121	28180										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160016682	160016682	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgtcccaaaggtaaagacatCtatatcagagcccttatagg	8	9	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:160016682C>A	ENST00000327245.5	-	24	4513	c.3667G>T	c.(3667-3669)Gat>Tat	p.D1223Y		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1223					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	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)			GTAAAGACATCTATATCAGAG	0.463																																																0			5											170	175	174					5																	160016682		1954	4144	6098	159949260	SO:0001583	missense	23120			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.3667G>T	5.37:g.160016682C>A	ENSP00000313600:p.Asp1223Tyr		159949260	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.987760	0.53934	.	.	ENSG00000118322	ENST00000327245	T	0.51071	0.72	5.4	5.4	0.78164	.	0.117031	0.56097	D	0.000034	T	0.73110	0.3545	M	0.91872	3.25	0.19300	N	0.999976	D	0.76494	0.999	P	0.59761	0.863	T	0.71318	-0.4629	9	.	.	.	.	18.242	0.89970	0.0:1.0:0.0:0.0	.	1223	O94823	AT10B_HUMAN	Y	1223	ENSP00000313600:D1223Y	.	D	-	1	0	ATP10B	159949260	0.135000	0.22499	0.151000	0.22473	0.665000	0.39181	3.944000	0.56629	2.544000	0.85801	0.650000	0.86243	GAT		0.463	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		A	160016682	C	A	160016682	3	1	107	1	0	0	0	0	1	0	0	0	1118	913	32	2	730	2	ATP10B	5	160016682	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3426912	160016682	20898578	122	28181										
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179291016	179291016	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agaacttcttccccacctctCcgatgcggagcaggaggctg	11	14	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr5:179291016C>G	ENST00000356834.3	-	22	3222	c.3185G>C	c.(3184-3186)gGa>gCa	p.G1062A	TBC1D9B_ENST00000519746.1_Missense_Mutation_p.G221A|TBC1D9B_ENST00000518085.1_5'UTR|TBC1D9B_ENST00000355235.3_Missense_Mutation_p.G1045A|TBC1D9B_ENST00000444477.2_Missense_Mutation_p.G203A	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	1062						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCCACCTCTCCGATGCGGAG	0.617																																																0			5											56	44	48					5																	179291016		2203	4300	6503	179223622	SO:0001583	missense	23061			AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.3185G>C	5.37:g.179291016C>G	ENSP00000349291:p.Gly1062Ala		179223622	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	37	CCDS43408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.3|28.3	4.912336|4.912336	0.92178|0.92178	.|.	.|.	ENSG00000197226|ENSG00000197226	ENST00000524222|ENST00000356834;ENST00000355235;ENST00000519746;ENST00000444477;ENST00000544438	.|T;T;T;T	.|0.57436	.|0.4;0.4;0.4;0.4	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76744|0.76744	0.4030|0.4030	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.999;1.0;0.999;1.0;0.999	T|T	0.79188|0.79188	-0.1906|-0.1906	5|10	.|0.52906	.|T	.|0.07	-26.077|-26.077	19.0961|19.0961	0.93251|0.93251	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1044;1045;1062;261;136	.|A1L3A9;Q66K14-2;Q66K14;B3KM54;F5H5B8	.|.;.;TBC9B_HUMAN;.;.	Q|A	105|1062;1045;221;203;136	.|ENSP00000349291:G1062A;ENSP00000347375:G1045A;ENSP00000430293:G221A;ENSP00000401585:G203A	.|ENSP00000347375:G1045A	E|G	-|-	1|2	0|0	TBC1D9B|TBC1D9B	179223622|179223622	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.960000|0.960000	0.62799|0.62799	7.743000|7.743000	0.85020|0.85020	2.506000|2.506000	0.84524|0.84524	0.462000|0.462000	0.41574|0.41574	GAG|GGA		0.617	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		G	179291016	C	G	179291016	3	3	107	1	0	0	0	0	1	0	0	0	15667	855	30	5	571	5	TBC1D9B	5	179291016	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	19274334	179291016	1624244	123	28182										
GCM2	9247	hgsc.bcm.edu	37	chr6	10874877	10874877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tactggtggaatccttataaAgggtgggatatgggcttgaa	14	4	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:10874877A>G	ENST00000379491.4	-	5	1019	c.872T>C	c.(871-873)cTt>cCt	p.L291P	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	291					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				ATCCTTATAAAGGGTGGGATA	0.418																																																0			6											202	195	198					6																	10874877		2203	4300	6503	10982863	SO:0001583	missense	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.872T>C	6.37:g.10874877A>G	ENSP00000368805:p.Leu291Pro		10982863	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	A	8.744	0.919645	0.17982	.	.	ENSG00000124827	ENST00000379491	T	0.71934	-0.61	5.5	5.5	0.81552	.	0.537761	0.19969	N	0.102035	T	0.57725	0.2073	M	0.73962	2.25	0.80722	D	1	B	0.32918	0.39	B	0.24541	0.054	T	0.67799	-0.5577	10	0.87932	D	0	-15.1929	12.9918	0.58622	0.8658:0.1342:0.0:0.0	.	291	O75603	GCM2_HUMAN	P	291	ENSP00000368805:L291P	ENSP00000368805:L291P	L	-	2	0	GCM2	10982863	0.995000	0.38212	0.032000	0.17829	0.196000	0.23810	4.205000	0.58466	2.213000	0.71641	0.528000	0.53228	CTT		0.418	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			G	10874877	A	G	10874877	3	3	107	1	0	0	0	0	1	0	0	0	6318	72	3	4	652	4	GCM2	6	10874877	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10		10874877	160240190	124	28183										
CD83	9308	hgsc.bcm.edu	37	chr6	14133902	14133902	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgccctgcacagcgtaaagaAgagacttttaagaaatacag	9	8	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:14133902A>T	ENST00000379153.3	+	4	576	c.405A>T	c.(403-405)gaA>gaT	p.E135D		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	135					defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				AGCGTAAAGAAGAGACTTTTA	0.363																																																0			6											124	127	126					6																	14133902		2203	4300	6503	14241881	SO:0001583	missense	9308			Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.405A>T	6.37:g.14133902A>T	ENSP00000368450:p.Glu135Asp		14241881	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.420332	0.25552	.	.	ENSG00000112149	ENST00000379153	T	0.46451	0.87	5.41	-0.0289	0.13920	.	0.628414	0.16448	N	0.213986	T	0.07773	0.0195	N	0.19112	0.55	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.33369	-0.9871	10	0.24483	T	0.36	-10.1907	3.9728	0.09460	0.5758:0.0:0.2736:0.1506	.	135	Q01151	CD83_HUMAN	D	135	ENSP00000368450:E135D	ENSP00000368450:E135D	E	+	3	2	CD83	14241881	0.583000	0.26757	0.007000	0.13788	0.006000	0.05464	0.466000	0.22019	0.120000	0.18254	-0.250000	0.11733	GAA		0.363	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			T	14133902	A	T	14133902	3	4	107	1	0	0	0	0	1	0	0	0	3047	69	3	5	419	5	CD83	6	14133902	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3259025	14133902	156981165	125	28184										
SCGN	10590	hgsc.bcm.edu	37	chr6	25665248	25665248	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aacccactggacagcagcgtGgagtttatgcaggtgagtgc	14	9	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:25665248G>T	ENST00000377961.2	+	4	492	c.324G>T	c.(322-324)gtG>gtT	p.V108V	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	108	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						ACAGCAGCGTGGAGTTTATGC	0.493																																																0			6											117	107	110					6																	25665248		2203	4300	6503	25773227	SO:0001819	synonymous_variant	10590			BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.324G>T	6.37:g.25665248G>T			25773227	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Silent	SNP	ENST00000377961.2	37	CCDS4561.1																																																																																				0.493	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			T	25665248	G	T	25665248	2	4	107	1	0	0	0	0	0	0	0	1	13940	1335	47	2		2	SCGN	6	25665248	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	11531346	25665248	145449819	126	28185										
CDSN	170679	hgsc.bcm.edu	37	chr6	31085067	31085067	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gacctgggaataccccgttcCtggcttaaaagatcctgcag	10	12	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:31085067C>A	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Nonsense_Mutation_p.G109*|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TACCCCGTTCCTGGCTTAAAA	0.592																																																0			6											22	17	18					6																	31085067		1904	3805	5709	31193046	SO:0001627	intron_variant	1041			AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2399C>A	6.37:g.31085067C>A			31193046	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Nonsense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.117013	0.77323	.	.	ENSG00000204539	ENST00000376288	.	.	.	4.88	4.88	0.63580	.	0.353789	0.20525	N	0.090635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	13.8605	0.63557	0.0:1.0:0.0:0.0	.	.	.	.	X	109	.	ENSP00000365465:G109X	G	-	1	0	CDSN	31193046	0.940000	0.31905	1.000000	0.80357	0.766000	0.43426	3.954000	0.56708	2.422000	0.82143	0.549000	0.68633	GGA		0.592	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		A	31085067	C	A	31085067	1	1	107	0	1	0	0	0	0	0	0	0	3185	690	24	2		2	CDSN	6	31085067	Intron	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5419819	31085067	140030000	127	28186										
POU5F1	5460	hgsc.bcm.edu	37	chr6	31132578	31132580	+	In_Frame_Del	DEL	GTT	GTT	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agcagcctcaaaatcctctcGttgtgcatagtcgctgcttg							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	GTT	GTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:31132578_31132580delGTT	ENST00000259915.8	-	5	953_955	c.881_883delAAC	c.(880-885)caacga>cga	p.Q294del	POU5F1_ENST00000441888.3_In_Frame_Del_p.Q98del|POU5F1_ENST00000471529.2_In_Frame_Del_p.Q98del|POU5F1_ENST00000512818.1_In_Frame_Del_p.Q98del|POU5F1_ENST00000606567.1_In_Frame_Del_p.Q124del|POU5F1_ENST00000513407.1_In_Frame_Del_p.Q98del	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	294					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	AAATCCTCTCGTTGTGCATAGTC	0.562			T	EWSR1	sarcoma																																		Dom	yes		6	6p21.31	5460	"POU domain, class 5, transcription factor 1"		M	0			6																																								31240559	SO:0001651	inframe_deletion	5460			Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"Homeoboxes / POU class"	9221	protein-coding gene	gene with protein product		164177	"POU domain class 5, transcription factor 1"	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.881_883delAAC	6.37:g.31132578_31132580delGTT	ENSP00000259915:p.Gln294del		31240557	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	In_Frame_Del	DEL	ENST00000259915.8	37	CCDS34391.1																																																																																				0.562	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701		-	31132580	GTT	-	31132578	7	5	107	1	0	1	0	1	0	0	0	0	12312	1153	40	0	203	0	POU5F1	6	31132578	In_Frame_Del	DEL	GTT	TCGA-DY-A1DG-01A-11D-A152-10	47511	31132578	139982489	128	28187										
BAT2	7916	hgsc.bcm.edu	37	chr6	31592061	31592061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cgatgcctcaaccgctcagcCgccggaatcgcagccactgc	10	18	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:31592061C>T	ENST00000376033.2	+	4	548	c.314C>T	c.(313-315)cCg>cTg	p.P105L	SNORA38_ENST00000363946.1_RNA|PRRC2A_ENST00000469577.1_3'UTR|PRRC2A_ENST00000376007.4_Missense_Mutation_p.P105L	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	105	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						ACCGCTCAGCCGCCGGAATCG	0.617																																																0			6											77	90	86					6																	31592061		1510	2709	4219	31700040	SO:0001583	missense	0			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.314C>T	6.37:g.31592061C>T	ENSP00000365201:p.Pro105Leu		31700040	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870238	0.33069	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.21543	2.0;2.0	4.81	0.758	0.18432	BAT2, N-terminal (1);	0.453490	0.18905	N	0.127933	T	0.04679	0.0127	N	0.20986	0.625	0.53005	D	0.999964	B	0.13594	0.008	B	0.09377	0.004	T	0.17289	-1.0374	10	0.87932	D	0	-0.8622	5.1672	0.15092	0.3985:0.4448:0.0:0.1567	.	105	P48634	PRC2A_HUMAN	L	105	ENSP00000365175:P105L;ENSP00000365201:P105L	ENSP00000365175:P105L	P	+	2	0	PRRC2A	31700040	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	0.319000	0.19522	0.233000	0.21120	-0.145000	0.13849	CCG		0.617	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31592061	C	T	31592061	3	4	107	1	0	0	0	0	1	0	0	0	1320	652	23	1	324	1	BAT2	6	31592061	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	459483	31592061	139523006	129	28188										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778941	31778941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acagggtcctcttggccctcTcgcaggcggtgcgcagccgc	14	16	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:31778941T>C	ENST00000375654.4	-	2	998	c.809A>G	c.(808-810)gAg>gGg	p.E270G	HSPA1L_ENST00000417199.3_Missense_Mutation_p.E270G	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	270					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CTTGGCCCTCTCGCAGGCGGT	0.537																																																0			6											62	68	66					6																	31778941		2203	4300	6503	31886920	SO:0001583	missense	3305			D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.809A>G	6.37:g.31778941T>C	ENSP00000364805:p.Glu270Gly		31886920	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	37	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	T	19.67	3.871028	0.72065	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653;ENST00000424494	T;T	0.18502	2.21;2.21	5.4	5.4	0.78164	.	0.000000	0.35124	N	0.003437	T	0.64394	0.2594	H	0.99997	5.47	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83492	0.0070	10	0.87932	D	0	-3.403	13.4225	0.61007	0.0:0.0:0.0:1.0	.	270	P34931	HS71L_HUMAN	G	270;270;215;160	ENSP00000364805:E270G;ENSP00000387691:E270G	ENSP00000364804:E215G	E	-	2	0	HSPA1L	31886920	1.000000	0.71417	0.974000	0.42286	0.866000	0.49608	7.868000	0.87116	2.267000	0.75376	0.477000	0.44152	GAG		0.537	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			C	31778941	T	C	31778941	3	2	107	1	0	0	0	0	1	0	0	0	7431	1551	54	4	1120	4	HSPA1L	6	31778941	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	186880	31778941	139336126	130	28189										
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44228245	44228245	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tccatgagtggttggttcttCtgaagggtggcaatgtggag	16	5	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:44228245C>A	ENST00000275015.5	-	4	1139	c.1140G>T	c.(1138-1140)caG>caT	p.Q380H	SLC35B2_ENST00000538577.1_5'Flank|SLC35B2_ENST00000537814.1_5'Flank|SLC35B2_ENST00000495706.1_5'Flank|SLC35B2_ENST00000393812.3_5'Flank|SLC35B2_ENST00000393810.1_5'Flank	NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	380					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GTTGGTTCTTCTGAAGGGTGG	0.587																																																0			6											163	156	158					6																	44228245		2203	4300	6503	44336223	SO:0001583	missense	4794			U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.1140G>T	6.37:g.44228245C>A	ENSP00000275015:p.Gln380His		44336223	Q5T9V9	Missense_Mutation	SNP	ENST00000275015.5	37	CCDS34463.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431529	0.25813	.	.	ENSG00000146232	ENST00000275015	T	0.63255	-0.03	5.05	5.05	0.67936	Ankyrin repeat-containing domain (3);	0.519021	0.19149	N	0.121482	T	0.20820	0.0501	N	0.04373	-0.215	0.35412	D	0.792505	B	0.21225	0.053	B	0.24541	0.054	T	0.09292	-1.0681	10	0.18276	T	0.48	-20.2573	10.7917	0.46436	0.0:0.9115:0.0:0.0885	.	380	O00221	IKBE_HUMAN	H	380	ENSP00000275015:Q380H	ENSP00000275015:Q380H	Q	-	3	2	NFKBIE	44336223	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.605000	0.46283	2.336000	0.79503	0.655000	0.94253	CAG		0.587	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			A	44228245	C	A	44228245	3	1	107	1	0	0	0	0	1	0	0	0	10411	912	32	2	374	2	NFKBIE	6	44228245	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	12449304	44228245	126886822	131	28190										
C6orf142	90523	hgsc.bcm.edu	37	chr6	54067033	54067033	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cgacctcttttctgaacaggTgagcacatacaagagaaaat	8	9	2	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:54067033T>C	ENST00000274897.5	+	10	1226		c.e10+2		MLIP_ENST00000358276.5_Splice_Site|MLIP_ENST00000502396.1_Splice_Site|MLIP_ENST00000370877.2_Splice_Site|MLIP_ENST00000509997.1_Splice_Site|MLIP_ENST00000370876.2_Splice_Site|MLIP_ENST00000511744.1_Splice_Site|MLIP_ENST00000514921.1_Splice_Site	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein							nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)		p.?(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						TCTGAACAGGTGAGCACATAC	0.254																																																1	Unknown(1)	ovary(1)	6											71	70	70					6																	54067033		2203	4300	6503	54174992	SO:0001630	splice_region_variant	90523			AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"muscle-enriched A-type lamin interacting protein"	614106	"chromosome 6 open reading frame 142"	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.1113+2T>C	6.37:g.54067033T>C			54174992	B7Z2N0|D6RE05|Q96H08|Q96NF7	Splice_Site	SNP	ENST00000274897.5	37	CCDS4954.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111392	0.56398	.	.	ENSG00000146147	ENST00000274897;ENST00000514921;ENST00000370877;ENST00000509997;ENST00000370876;ENST00000502396;ENST00000358276;ENST00000514433	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2533	0.54610	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MLIP	54174992	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	4.586000	0.60984	2.147000	0.66899	0.477000	0.44152	.		0.254	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	Intron	C	54067033	T	C	54067033	5	2	107	1	0	0	0	0	0	0	1	0	2339	1710	59	4	1153	4	C6orf142	6	54067033	Splice_Site	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	9838788	54067033	117048034	132	28191										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83847225	83847225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgttcaacaggtagtatttgAcctgatatgtaaagttgtaa	9	4	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:83847225A>G	ENST00000349129.2	+	21	3724	c.3464A>G	c.(3463-3465)gAc>gGc	p.D1155G	DOPEY1_ENST00000237163.5_Missense_Mutation_p.D1136G|DOPEY1_ENST00000369739.3_Missense_Mutation_p.D1146G	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1155			D -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		GTAGTATTTGACCTGATATGT	0.418																																																0			6											81	79	80					6																	83847225		2203	4299	6502	83903944	SO:0001583	missense	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.3464A>G	6.37:g.83847225A>G	ENSP00000195654:p.Asp1155Gly		83903944	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.010809	0.54361	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.26373	1.75;1.74	5.69	5.69	0.88448	.	0.054565	0.64402	D	0.000001	T	0.19805	0.0476	L	0.27053	0.805	0.80722	D	1	D;P;P	0.57899	0.981;0.935;0.935	P;B;B	0.52554	0.702;0.411;0.411	T	0.01697	-1.1293	10	0.52906	T	0.07	.	15.9429	0.79771	1.0:0.0:0.0:0.0	.	1046;1146;1155	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	G	1155;1136;1136	ENSP00000195654:D1155G;ENSP00000237163:D1136G	ENSP00000237163:D1136G	D	+	2	0	DOPEY1	83903944	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.491000	0.90468	2.161000	0.67846	0.377000	0.23210	GAC		0.418	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83847225	A	G	83847225	3	3	107	1	0	0	0	0	1	0	0	0	4718	275	10	4	3538	4	DOPEY1	6	83847225	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	29780192	83847225	87267842	133	28192										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87968047	87968047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cattgaggaatgtagcagctTgcctgtttttccaacgaatg	10	8	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:87968047T>C	ENST00000369577.3	+	8	4743	c.4700T>C	c.(4699-4701)tTg>tCg	p.L1567S	ZNF292_ENST00000339907.4_Missense_Mutation_p.L1562S	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1567						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TGTAGCAGCTTGCCTGTTTTT	0.438																																																0			6											77	75	76					6																	87968047		1965	4152	6117	88024766	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4700T>C	6.37:g.87968047T>C	ENSP00000358590:p.Leu1567Ser		88024766	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595081	0.46318	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.11063	2.81;2.82	6.07	6.07	0.98685	.	0.209202	0.30714	N	0.009035	T	0.07908	0.0198	N	0.24115	0.695	0.38974	D	0.9588	D	0.57899	0.981	P	0.49637	0.617	T	0.08554	-1.0716	10	0.72032	D	0.01	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	1567	O60281	ZN292_HUMAN	S	1567;1562	ENSP00000358590:L1567S;ENSP00000342847:L1562S	ENSP00000342847:L1562S	L	+	2	0	ZNF292	88024766	1.000000	0.71417	1.000000	0.80357	0.746000	0.42486	5.945000	0.70226	2.326000	0.78906	0.533000	0.62120	TTG		0.438	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		C	87968047	T	C	87968047	3	2	107	1	0	0	0	0	1	0	0	0	17865	1821	63	4	4730	4	ZNF292	6	87968047	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	4120822	87968047	83147020	134	28193										
HACE1	57531	hgsc.bcm.edu	37	chr6	105297107	105297107	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttaacagcaaaaccaagcatTccaccgatccacaactaaaa	3	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:105297107T>A	ENST00000262903.4	-	4	512	c.236A>T	c.(235-237)gAa>gTa	p.E79V	HACE1_ENST00000369125.2_Missense_Mutation_p.E79V	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	79					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		AACCAAGCATTCCACCGATCC	0.333																																																0			6											118	102	107					6																	105297107		2203	4300	6503	105403800	SO:0001583	missense	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.236A>T	6.37:g.105297107T>A	ENSP00000262903:p.Glu79Val		105403800	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643271	0.87859	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645;ENST00000524020	T;T;T;T	0.70516	-0.4;-0.4;-0.49;-0.4	5.84	5.84	0.93424	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.82604	0.5073	M	0.83118	2.625	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.78314	0.991;0.991	D	0.85693	0.1308	10	0.87932	D	0	.	15.8722	0.79129	0.0:0.0:0.0:1.0	.	79;79	E9PGP0;Q8IYU2	.;HACE1_HUMAN	V	79;79;79;45	ENSP00000262903:E79V;ENSP00000358121:E79V;ENSP00000429765:E79V;ENSP00000427901:E45V	ENSP00000262903:E79V	E	-	2	0	HACE1	105403800	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.130000	0.77235	2.232000	0.73038	0.533000	0.62120	GAA		0.333	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		A	105297107	T	A	105297107	3	1	107	1	0	0	0	0	1	0	0	0	6961	1783	62	5	2577	5	HACE1	6	105297107	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	17329060	105297107	65817960	135	28194										
HDAC2	3066	hgsc.bcm.edu	37	chr6	114277793	114277793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tagcacttaccaactgaaccGccagttgagagctgacaaaa	8	11	0	3	rs373430125		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:114277793G>A	ENST00000519065.1	-	4	724	c.348C>T	c.(346-348)ggC>ggT	p.G116G	HDAC2_ENST00000368632.2_Silent_p.G86G|HDAC2_ENST00000519108.1_Silent_p.G86G|HDAC2_ENST00000398283.2_Silent_p.G210G			Q92769	HDAC2_HUMAN	histone deacetylase 2	116	Histone deacetylase.				ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	CAACTGAACCGCCAGTTGAGA	0.358																																																0			6						G		0,3712		0,0,1856	71	70	70		348	3.4	1	6		70	1,8169		0,1,4084	no	coding-synonymous	HDAC2	NM_001527.3		0,1,5940	AA,AG,GG		0.0122,0.0,0.0084		116/489	114277793	1,11881	1856	4085	5941	114384486	SO:0001819	synonymous_variant	3066			U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.348C>T	6.37:g.114277793G>A			114384486	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Silent	SNP	ENST00000519065.1	37	CCDS43493.2																																																																																				0.358	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			A	114277793	G	A	114277793	2	1	107	1	0	0	0	0	0	0	0	1	7028	1074	38	1		1	HDAC2	6	114277793	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8980686	114277793	56837274	136	28195										
FRK	2444	hgsc.bcm.edu	37	chr6	116325143	116325143	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttctctgcatctgatcttccGattgctccaaagaaccacct	5	14	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:116325143G>T	ENST00000606080.1	-	2	809	c.363C>A	c.(361-363)atC>atA	p.I121I	FRK_ENST00000538210.1_5'Flank	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	121	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	CTGATCTTCCGATTGCTCCAA	0.343																																																0			6											63	63	63					6																	116325143		2203	4299	6502	116431836	SO:0001819	synonymous_variant	2444			U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.363C>A	6.37:g.116325143G>T			116431836	B4DY49|Q13128|Q9NTR5	Silent	SNP	ENST00000606080.1	37	CCDS5103.1																																																																																				0.343	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		T	116325143	G	T	116325143	2	4	107	1	0	0	0	0	0	0	0	1	6067	1048	37	2		2	FRK	6	116325143	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2047350	116325143	54789924	137	28196										
MCM9	254394	hgsc.bcm.edu	37	chr6	119238802	119238802	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcctcatccatgatgatcccTgaggactgctcattatttac	6	12	2	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:119238802T>C	ENST00000316316.6	-	5	1114	c.828A>G	c.(826-828)tcA>tcG	p.S276S	MCM9_ENST00000316068.3_Silent_p.S276S	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	276					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGATGATCCCTGAGGACTGCT	0.428																																																0			6											123	115	118					6																	119238802		2203	4300	6503	119280501	SO:0001819	synonymous_variant	254394			BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.828A>G	6.37:g.119238802T>C			119280501	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Silent	SNP	ENST00000316316.6	37	CCDS56447.1																																																																																				0.428	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255		C	119238802	T	C	119238802	2	2	107	1	0	0	0	0	0	0	0	1	9424	1567	55	4		4	MCM9	6	119238802	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2913659	119238802	51876265	138	28197										
SGK1	6446	hgsc.bcm.edu	37	chr6	134494255	134494255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaaagggtgcttcacattcTtcaacagaacattccgctcc	8	12	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:134494255T>C	ENST00000237305.7	-	6	543	c.455A>G	c.(454-456)aAg>aGg	p.K152R	SGK1_ENST00000413996.3_Missense_Mutation_p.K166R|SGK1_ENST00000367858.5_Missense_Mutation_p.K247R|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.K180R|SGK1_ENST00000367857.5_Missense_Mutation_p.K142R|SGK1_ENST00000475719.2_Intron	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	152	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			K -> R (in Ref. 4; CAR58096). {ECO:0000305}.	apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		CTTCACATTCTTCAACAGAAC	0.438																																																0			6											100	101	101					6																	134494255		2203	4300	6503	134535948	SO:0001583	missense	6446			AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.455A>G	6.37:g.134494255T>C	ENSP00000237305:p.Lys152Arg		134535948	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.166389	0.78339	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	6.04	6.04	0.98038	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64789	0.2630	N	0.17800	0.525	0.80722	D	1	B;D;B;B;B	0.76494	0.329;0.999;0.103;0.317;0.125	B;D;B;B;B	0.87578	0.196;0.998;0.074;0.247;0.296	T	0.70092	-0.4967	10	0.48119	T	0.1	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	180;166;142;247;152	O00141-5;O00141-3;O00141-4;O00141-2;O00141	.;.;.;.;SGK1_HUMAN	R	247;166;152;142;180	ENSP00000356832:K247R;ENSP00000396242:K166R;ENSP00000237305:K152R;ENSP00000356831:K142R;ENSP00000434450:K180R	ENSP00000237305:K152R	K	-	2	0	SGK1	134535948	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.988000	0.88194	2.317000	0.78254	0.460000	0.39030	AAG		0.438	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134494255	T	C	134494255	3	2	107	1	0	0	0	0	1	0	0	0	14244	1609	56	4	868	4	SGK1	6	134494255	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	15255453	134494255	36620812	139	28198										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152639268	152639268	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtctaatggtctgctggtgaAgttcagtcagttttcctatc	10	8	4	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:152639268A>G	ENST00000367255.5	-	86	17121	c.16520T>C	c.(16519-16521)cTt>cCt	p.L5507P	SYNE1_ENST00000448038.1_Missense_Mutation_p.L5436P|SYNE1_ENST00000423061.1_Missense_Mutation_p.L5436P|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.L5507P|SYNE1_ENST00000356820.4_Missense_Mutation_p.L31P	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5507			L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L5507R(3)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTGCTGGTGAAGTTCAGTCAG	0.453										HNSCC(10;0.0054)																																						3	Substitution - Missense(3)	large_intestine(3)	6											266	234	245					6																	152639268		2203	4300	6503	152680961	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16520T>C	6.37:g.152639268A>G	ENSP00000356224:p.Leu5507Pro		152680961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.973879	0.74246	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000356820	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000039	T	0.48333	0.1494	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.76071	0.987;0.971;0.971;0.986	T	0.40961	-0.9535	10	0.30854	T	0.27	.	15.8861	0.79251	1.0:0.0:0.0:0.0	.	5507;5507;5507;5436	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	P	5507;5436;5507;5436;31	ENSP00000356224:L5507P;ENSP00000396024:L5436P;ENSP00000265368:L5507P;ENSP00000390975:L5436P;ENSP00000349276:L31P	ENSP00000265368:L5507P	L	-	2	0	SYNE1	152680961	0.992000	0.36948	0.995000	0.50966	0.771000	0.43674	8.344000	0.90055	2.156000	0.67533	0.533000	0.62120	CTT		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152639268	A	G	152639268	3	3	107	1	0	0	0	0	1	0	0	0	15484	72	3	4	10190	4	SYNE1	6	152639268	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	18145013	152639268	18475799	140	28199										
PLG	5340	hgsc.bcm.edu	37	chr6	161152156	161152156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gttttaccacagaccccagcGtcaggtgggagtactgcaac	11	12	1	1	rs574500945		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:161152156G>A	ENST00000308192.9	+	11	1393	c.1330G>A	c.(1330-1332)Gtc>Atc	p.V444I		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	444	Kringle 4. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.V444I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	AGACCCCAGCGTCAGGTGGGA	0.502																																																1	Substitution - Missense(1)	endometrium(1)	6											92	93	93					6																	161152156		2203	4300	6503	161072146	SO:0001583	missense	5340			M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1330G>A	6.37:g.161152156G>A	ENSP00000308938:p.Val444Ile		161072146	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.448919	0.43531	.	.	ENSG00000122194	ENST00000308192	T	0.62788	-0.0	5.11	4.24	0.50183	Kringle (5);Kringle-like fold (1);	0.000000	0.35466	U	0.003195	T	0.37544	0.1007	L	0.50919	1.6	0.19945	N	0.999944	P	0.40638	0.725	B	0.40375	0.327	T	0.13791	-1.0496	10	0.31617	T	0.26	.	9.9467	0.41613	0.1681:0.0:0.8319:0.0	.	444	P00747	PLMN_HUMAN	I	444	ENSP00000308938:V444I	ENSP00000308938:V444I	V	+	1	0	PLG	161072146	1.000000	0.71417	0.012000	0.15200	0.487000	0.33371	4.401000	0.59716	1.139000	0.42245	0.563000	0.77884	GTC		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161152156	G	A	161152156	3	1	107	1	0	0	0	0	1	0	0	0	12117	1145	40	1	1376	1	PLG	6	161152156	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8512888	161152156	9962911	141	28200										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161530789	161530789	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctttattcctcccacaggaAgaaatgtacatcttcatgga	6	11	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr6:161530789A>G	ENST00000392142.4	+	23	4387	c.4239A>G	c.(4237-4239)gaA>gaG	p.E1413E	MAP3K4_ENST00000366919.2_Silent_p.E1363E|MAP3K4_ENST00000366920.2_Silent_p.E1409E|MAP3K4_ENST00000348824.7_Silent_p.E1359E	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1413	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> Q (in an ovarian serous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TCCCACAGGAAGAAATGTACA	0.453																																																0			6											103	98	100					6																	161530789		2203	4300	6503	161450779	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.4239A>G	6.37:g.161530789A>G			161450779	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.453	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			G	161530789	A	G	161530789	2	3	107	1	0	0	0	0	0	0	0	1	9282	69	3	4		4	MAP3K4	6	161530789	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	378633	161530789	9584278	142	28201										
RADIL	55698	hgsc.bcm.edu	37	chr7	4854989	4854989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaagtgctctccagccgcccCgaagccggcgctccgcatcc	11	19	1	0	rs375439747		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:4854989C>T	ENST00000399583.3	-	9	2246	c.2059G>A	c.(2059-2061)Ggg>Agg	p.G687R	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.G447R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	687	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CCAGCCGCCCCGAAGCCGGCG	0.687																																																0			7						C	ARG/GLY	0,3670		0,0,1835	6	8	8		2059	5.7	0.9	7		8	1,8039		0,1,4019	no	missense	RADIL	NM_018059.4	125	0,1,5854	TT,TC,CC		0.0124,0.0,0.0085	probably-damaging	687/1076	4854989	1,11709	1835	4020	5855	4821515	SO:0001583	missense	55698			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2059G>A	7.37:g.4854989C>T	ENSP00000382492:p.Gly687Arg		4821515	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.754618	0.69648	0.0	1.24E-4	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.08807	3.12;3.05	5.74	5.74	0.90152	Dilute (1);Dil domain (1);	0.116109	0.64402	D	0.000017	T	0.28433	0.0703	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00090	-1.2087	10	0.46703	T	0.11	-41.4825	17.0678	0.86564	0.0:1.0:0.0:0.0	.	687	Q96JH8	RADIL_HUMAN	R	687;658;421;447	ENSP00000382492:G687R;ENSP00000442966:G447R	ENSP00000320946:G658R	G	-	1	0	RADIL	4821515	0.998000	0.40836	0.885000	0.34714	0.021000	0.10359	7.063000	0.76714	2.719000	0.93026	0.655000	0.94253	GGG		0.687	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4854989	C	T	4854989	3	4	107	1	0	0	0	0	1	0	0	0	13034	652	23	1	1196	1	RADIL	7	4854989	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		4854989	154283674	143	28202										
GPNMB	10457	hgsc.bcm.edu	37	chr7	23296588	23296588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgacggggaaaatggcaccGgccaaagccatcataacgtc	12	11	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:23296588G>A	ENST00000381990.2	+	4	606	c.445G>A	c.(445-447)Ggc>Agc	p.G149S	GPNMB_ENST00000453162.2_Intron|GPNMB_ENST00000539136.1_Missense_Mutation_p.G50S|GPNMB_ENST00000409458.3_Missense_Mutation_p.G149S|GPNMB_ENST00000258733.4_Missense_Mutation_p.G149S	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	149					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			AAATGGCACCGGCCAAAGCCA	0.493																																																0			7											131	109	117					7																	23296588		2203	4300	6503	23263113	SO:0001583	missense	10457			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.445G>A	7.37:g.23296588G>A	ENSP00000371420:p.Gly149Ser		23263113	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	G	7.289	0.610760	0.14066	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000409458;ENST00000539136	T;T;T;T	0.16597	2.33;2.33;2.33;2.33	5.29	-1.22	0.09494	.	0.855363	0.10523	N	0.664689	T	0.03178	0.0093	N	0.00801	-1.175	0.09310	N	1	B;B;B;B	0.23891	0.093;0.056;0.015;0.093	B;B;B;B	0.17098	0.011;0.005;0.002;0.017	T	0.37641	-0.9697	10	0.08179	T	0.78	-1.0E-4	1.3244	0.02123	0.4264:0.2623:0.1828:0.1285	.	50;149;149;149	F6SKP1;Q14956;Q14956-2;Q96F58	.;GPNMB_HUMAN;.;.	S	149;184;149;149;50	ENSP00000258733:G149S;ENSP00000371420:G149S;ENSP00000386476:G149S;ENSP00000445266:G50S	ENSP00000258733:G149S	G	+	1	0	GPNMB	23263113	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.345000	0.19979	-0.370000	0.08016	-1.045000	0.02358	GGC		0.493	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		A	23296588	G	A	23296588	3	1	107	1	0	0	0	0	1	0	0	0	6640	1116	39	1	459	1	GPNMB	7	23296588	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	18441599	23296588	135842075	144	28203										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48285546	48285546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaaactccagcatatggggTggtctccagggactgttgtg	15	8	1	0	rs538791067		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:48285546T>C	ENST00000435803.1	+	13	1602	c.1578T>C	c.(1576-1578)ggT>ggC	p.G526G		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	526					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCATATGGGGTGGTCTCCAGG	0.448																																																0			7											83	77	79					7																	48285546		1877	4109	5986	48256092	SO:0001819	synonymous_variant	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1578T>C	7.37:g.48285546T>C			48256092	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																				0.448	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48285546	T	C	48285546	2	2	107	1	0	0	0	0	0	0	0	1	31	1683	59	4		4	ABCA13	7	48285546	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	24988958	48285546	110853117	145	28204										
EGFR	1956	hgsc.bcm.edu	37	chr7	55242497	55242497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agcaacatctccgaaagccaAcaaggaaatcctcgatgtga	8	11	1	1	rs121913463|rs397517100		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:55242497A>G	ENST00000275493.2	+	19	2444	c.2267A>G	c.(2266-2268)aAc>aGc	p.N756S	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Missense_Mutation_p.N703S|EGFR_ENST00000455089.1_Missense_Mutation_p.N711S	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	756	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Missing (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.S752_I759del(13)|p.T751_I759>N(8)|p.T751_I759>S(3)|p.A750_E758>P(2)|p.T751_I759del(2)|p.A750_E758del(1)|p.N756S(1)|p.T751_I759>REA(1)|p.T751_E758del(1)|p.P753_I759del(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCGAAAGCCAACAAGGAAATC	0.493		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	33	Deletion - In frame(18)|Complex - deletion inframe(14)|Substitution - Missense(1)	lung(31)|breast(2)	7											99	94	95					7																	55242497		2203	4300	6503	55209991	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2267A>G	7.37:g.55242497A>G	ENSP00000275493:p.Asn756Ser		55209991	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295521	0.60086	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	D;D;D	0.81996	-1.56;-1.56;-1.56	5.45	5.45	0.79879	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74891	0.3776	N	0.20574	0.59	0.58432	D	0.999996	B;P	0.45634	0.027;0.863	B;B	0.42827	0.007;0.399	T	0.78468	-0.2192	10	0.54805	T	0.06	.	14.3314	0.66559	1.0:0.0:0.0:0.0	.	711;756	Q504U8;P00533	.;EGFR_HUMAN	S	711;626;756;703	ENSP00000415559:N711S;ENSP00000275493:N756S;ENSP00000395243:N703S	ENSP00000275493:N756S	N	+	2	0	EGFR	55209991	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.236000	0.95360	2.068000	0.61886	0.459000	0.35465	AAC		0.493	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55242497	A	G	55242497	3	3	107	1	0	0	0	0	1	0	0	0	4978	43	2	4	2605	4	EGFR	7	55242497	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	6956951	55242497	103896166	146	28205										
EGFR	1956	hgsc.bcm.edu	37	chr7	55249140	55249140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agacaatattggctcccagtAcctgctcaactggtgtgtgc	10	11	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:55249140A>G	ENST00000275493.2	+	20	2615	c.2438A>G	c.(2437-2439)tAc>tGc	p.Y813C	EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000454757.2_Missense_Mutation_p.Y760C|EGFR_ENST00000455089.1_Missense_Mutation_p.Y768C	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	813	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.Y813C(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGCTCCCAGTACCTGCTCAAC	0.572		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	7											86	75	79					7																	55249140		2203	4300	6503	55216634	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2438A>G	7.37:g.55249140A>G	ENSP00000275493:p.Tyr813Cys		55216634	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.835742	0.50951	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	D;D;D	0.82526	-1.62;-1.62;-1.62	5.92	3.56	0.40772	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.527828	0.23224	N	0.050535	D	0.83308	0.5226	L	0.27053	0.805	0.49299	D	0.999773	P;P	0.49090	0.497;0.919	B;D	0.68192	0.276;0.956	T	0.79654	-0.1713	10	0.39692	T	0.17	.	9.4994	0.39008	0.8558:0.0:0.1442:0.0	.	768;813	Q504U8;P00533	.;EGFR_HUMAN	C	768;683;813;760	ENSP00000415559:Y768C;ENSP00000275493:Y813C;ENSP00000395243:Y760C	ENSP00000275493:Y813C	Y	+	2	0	EGFR	55216634	0.995000	0.38212	0.761000	0.31378	0.966000	0.64601	4.348000	0.59379	0.494000	0.27859	-0.290000	0.09829	TAC		0.572	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55249140	A	G	55249140	3	3	107	1	0	0	0	0	1	0	0	0	4978	391	14	4	2780	4	EGFR	7	55249140	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	6643	55249140	103889523	147	28206										
CROT	54677	hgsc.bcm.edu	37	chr7	86986890	86986890	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agagggttcttggatctcacGcgggaaggaattcaaggtga	15	6	3	2	rs575091816		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:86986890G>A	ENST00000331536.3	+	4	300				CROT_ENST00000442291.1_Intron|CROT_ENST00000412227.2_Intron|CROT_ENST00000419147.2_Silent_p.T61T	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase						carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	tggatctcacgcgggaaggaa	0.488													G|||	1	0.000199681	8e-04	0	5008	,	,		18964	0		0	False		,,,				2504	0															0			7											97	82	87					7																	86986890		692	1591	2283	86824826	SO:0001627	intron_variant	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.116-1632G>A	7.37:g.86986890G>A			86824826	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	37	CCDS5604.1																																																																																				0.488	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		A	86986890	G	A	86986890	1	1	107	0	1	0	0	0	0	0	0	0	3900	1074	38	1		1	CROT	7	86986890	Intron	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	31737750	86986890	72151773	148	28207										
HEPACAM2	253012	hgsc.bcm.edu	37	chr7	92848754	92848754	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggcactgtcaccttcagcccCgagcaagcacctgttgcaaa	9	15	2	0	rs375176875		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:92848754C>T	ENST00000394468.2	-	2	167	c.90G>A	c.(88-90)tcG>tcA	p.S30S	HEPACAM2_ENST00000440868.1_Silent_p.S18S|HEPACAM2_ENST00000341723.4_Silent_p.S18S|HEPACAM2_ENST00000453812.2_Silent_p.S53S	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	30					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)		p.S30S(1)|p.S18S(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						CCTTCAGCCCCGAGCAAGCAC	0.517																																																2	Substitution - coding silent(2)	lung(2)	7						C	,	1,4405	2.1+/-5.4	0,1,2202	138	133	135		90,54	-6	0	7		135	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HEPACAM2	NM_001039372.1,NM_198151.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	30/463,18/451	92848754	1,13005	2203	4300	6503	92686690	SO:0001819	synonymous_variant	253012			AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.90G>A	7.37:g.92848754C>T			92686690	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Silent	SNP	ENST00000394468.2	37	CCDS43616.1																																																																																				0.517	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		T	92848754	C	T	92848754	2	4	107	1	0	0	0	0	0	0	0	1	7074	639	23	1		1	HEPACAM2	7	92848754	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5861864	92848754	66289909	149	28208										
PON3	5446	hgsc.bcm.edu	37	chr7	94993256	94993256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctcccttgggctgtagaaaAgaacataagtccagcgaaga	10	10	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:94993256A>G	ENST00000265627.5	-	6	624	c.614T>C	c.(613-615)cTt>cCt	p.L205P	PON1_ENST00000542556.1_Intron|PON3_ENST00000451904.1_Missense_Mutation_p.L205P|PON3_ENST00000427422.1_Missense_Mutation_p.L205P	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	205					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GCTGTAGAAAAGAACATAAGT	0.443																																																0			7											182	187	185					7																	94993256		2203	4300	6503	94831192	SO:0001583	missense	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.614T>C	7.37:g.94993256A>G	ENSP00000265627:p.Leu205Pro		94831192	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935290	0.73442	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.47177	0.85;0.85	5.27	4.12	0.48240	Six-bladed beta-propeller, TolB-like (1);	0.387835	0.28442	N	0.015332	T	0.58032	0.2094	M	0.66939	2.045	0.28015	N	0.934745	D;P	0.54397	0.966;0.953	P;P	0.55161	0.77;0.74	T	0.56842	-0.7912	10	0.87932	D	0	-2.1494	10.806	0.46518	0.9247:0.0:0.0753:0.0	.	253;205	B4E2I0;Q15166	.;PON3_HUMAN	P	205	ENSP00000265627:L205P;ENSP00000413276:L205P	ENSP00000265627:L205P	L	-	2	0	PON3	94831192	0.999000	0.42202	0.022000	0.16811	0.325000	0.28411	6.606000	0.74159	0.958000	0.37956	0.533000	0.62120	CTT		0.443	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		G	94993256	A	G	94993256	3	3	107	1	0	0	0	0	1	0	0	0	12281	72	3	4	466	4	PON3	7	94993256	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2144502	94993256	64145407	150	28209										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98552797	98552797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggcgatggccattctgacccCggcggtgccggccaggatgg	17	13	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:98552797C>T	ENST00000359863.4	+	40	5995	c.5786C>T	c.(5785-5787)cCg>cTg	p.P1929L	TRRAP_ENST00000446306.3_Missense_Mutation_p.P1910L|TRRAP_ENST00000355540.3_Missense_Mutation_p.P1911L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1929					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ATTCTGACCCCGGCGGTGCCG	0.592																																																0			7											50	45	47					7																	98552797		2203	4300	6503	98390733	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.5786C>T	7.37:g.98552797C>T	ENSP00000352925:p.Pro1929Leu		98390733	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.300148|5.300148	0.95574|0.95574	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.56103|.	0.48;0.48|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85474|0.85474	0.5705|0.5705	M|M	0.89904|0.89904	3.07|3.07	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;0.998;0.999|.	D|D	0.87473|0.87473	0.2415|0.2415	10|5	0.87932|.	D|.	0|.	.|.	19.5376|19.5376	0.95260|0.95260	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1911;1650;1929|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	L|W	1929;1911;1909|1651	ENSP00000352925:P1929L;ENSP00000347733:P1911L|.	ENSP00000347733:P1911L|.	P|R	+|+	2|1	0|2	TRRAP|TRRAP	98390733|98390733	1.000000|1.000000	0.71417|0.71417	0.196000|0.196000	0.23383|0.23383	0.989000|0.989000	0.77384|0.77384	7.818000|7.818000	0.86416|0.86416	2.620000|2.620000	0.88729|0.88729	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.592	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98552797	C	T	98552797	3	4	107	1	0	0	0	0	1	0	0	0	16641	652	23	1	5882	1	TRRAP	7	98552797	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3559541	98552797	60585866	151	28210										
MCM7	4176	hgsc.bcm.edu	37	chr7	99697372	99697372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctgttcccgatgagccagcCgaacctcaagtggggaagag	13	12	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:99697372C>T	ENST00000303887.5	-	3	761	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	MCM7_ENST00000343023.6_Missense_Mutation_p.R39Q|AP4M1_ENST00000429084.1_5'Flank|AP4M1_ENST00000422582.1_5'Flank|AP4M1_ENST00000359593.4_5'Flank|AP4M1_ENST00000421755.1_5'Flank|MCM7_ENST00000354230.3_5'UTR	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	39					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATGAGCCAGCCGAACCTCAAG	0.532																																																0			7											71	66	68					7																	99697372		2203	4300	6503	99535308	SO:0001583	missense	4176				CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.116G>A	7.37:g.99697372C>T	ENSP00000307288:p.Arg39Gln		99535308	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.383997	0.25031	.	.	ENSG00000166508	ENST00000343023;ENST00000303887	T;T	0.10668	2.85;2.85	4.4	-8.8	0.00817	Nucleic acid-binding, OB-fold-like (1);	1.072940	0.07082	N	0.837262	T	0.05868	0.0153	N	0.11341	0.13	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.42699	-0.9436	10	0.17369	T	0.5	0.002	18.4362	0.90646	0.0:0.144:0.0:0.856	.	39	P33993	MCM7_HUMAN	Q	39	ENSP00000344006:R39Q;ENSP00000307288:R39Q	ENSP00000307288:R39Q	R	-	2	0	MCM7	99535308	0.000000	0.05858	0.000000	0.03702	0.212000	0.24457	-0.942000	0.03921	-2.666000	0.00416	-0.259000	0.10710	CGG		0.532	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			T	99697372	C	T	99697372	3	4	107	1	0	0	0	0	1	0	0	0	9422	652	23	1	2095	1	MCM7	7	99697372	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1144575	99697372	59441291	152	28211										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107790561	107790561	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtctgaaggagttcgacttcCttttttcaaaggcttgtggt	11	7	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:107790561C>A	ENST00000425651.2	-	30	3708	c.3709G>T	c.(3709-3711)Gga>Tga	p.G1237*	NRCAM_ENST00000351718.4_Nonsense_Mutation_p.G1116*|NRCAM_ENST00000522550.2_5'UTR|NRCAM_ENST00000413765.2_Nonsense_Mutation_p.G1113*|NRCAM_ENST00000379028.3_Nonsense_Mutation_p.G1237*|NRCAM_ENST00000379024.4_Nonsense_Mutation_p.G1125*	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1237					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GTTCGACTTCCTTTTTTCAAA	0.398																																																0			7											187	175	179					7																	107790561		2203	4300	6503	107577797	SO:0001587	stop_gained	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3709G>T	7.37:g.107790561C>A	ENSP00000401244:p.Gly1237*		107577797	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Nonsense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	44|44	11.024662|11.024662	0.99504|0.99504	.|.	.|.	ENSG00000091129|ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000437386;ENST00000351718;ENST00000379024;ENST00000425651|ENST00000445634	.|D	.|0.86366	.|-2.11	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.045544|.	0.85682|.	D|.	0.000000|.	.|D	.|0.93439	.|0.7907	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.92761	.|0.6224	.|6	0.87932|0.62326	D|D	0|0.03	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	1241;1237;1113;1144;81;1116;1125;1237|135	.|ENSP00000398174:K135N	ENSP00000325269:G1116X|ENSP00000398174:K135N	G|K	-|-	1|3	0|2	NRCAM|NRCAM	107577797|107577797	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.818000|7.818000	0.86416|0.86416	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGA|AAG		0.398	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107790561	C	A	107790561	4	1	107	1	0	0	0	0	0	1	0	0	10675	690	24	2	209	2	NRCAM	7	107790561	Nonsense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	8093189	107790561	51348102	153	28212										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117432608	117432608	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgcttcttcgtttctcagcGgagagttcctcttctaattc	8	11	4	1	rs138336454		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:117432608G>T	ENST00000160373.3	-	4	733	c.642C>A	c.(640-642)tcC>tcA	p.S214S	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	214					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.S214S(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GTTTCTCAGCGGAGAGTTCCT	0.478																																																1	Substitution - coding silent(1)	ovary(1)	7											134	120	125					7																	117432608		2203	4300	6503	117219844	SO:0001819	synonymous_variant	83992				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.642C>A	7.37:g.117432608G>T			117219844	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1																																																																																				0.478	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117432608	G	T	117432608	2	4	107	1	0	0	0	0	0	0	0	1	4051	1103	39	2		2	CTTNBP2	7	117432608	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	9642047	117432608	41706055	154	28213										
C7orf58	79974	hgsc.bcm.edu	37	chr7	120629703	120629703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtcgcccagtgttcccttgtCgtcggcgattttgcccccga	11	15	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:120629703C>T	ENST00000310396.5	+	2	495	c.28C>T	c.(28-30)Cgt>Tgt	p.R10C	CPED1_ENST00000495036.1_3'UTR|CPED1_ENST00000340646.5_Missense_Mutation_p.R10C|CPED1_ENST00000450913.2_Missense_Mutation_p.R10C	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	10						endoplasmic reticulum (GO:0005783)		p.R10C(1)									GTTCCCTTGTCGTCGGCGATT	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	7											127	113	117					7																	120629703		2203	4300	6503	120416939	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.28C>T	7.37:g.120629703C>T	ENSP00000309772:p.Arg10Cys		120416939	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.696073	0.48202	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000340646	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.64	4.75	0.60458	.	0.149146	0.46758	D	0.000277	T	0.41558	0.1164	L	0.46157	1.445	0.50632	D	0.999888	P;P	0.41947	0.766;0.655	B;B	0.33121	0.158;0.076	T	0.49986	-0.8880	10	0.87932	D	0	.	11.3463	0.49563	0.0:0.9173:0.0:0.0827	.	10;10	A4D0V7-2;A4D0V7	.;CG058_HUMAN	C	10	ENSP00000309772:R10C;ENSP00000398082:R10C;ENSP00000406122:R10C;ENSP00000345235:R10C	ENSP00000309772:R10C	R	+	1	0	C7orf58	120416939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.247000	0.51422	2.662000	0.90505	0.655000	0.94253	CGT		0.552	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120629703	C	T	120629703	3	4	107	1	0	0	0	0	1	0	0	0	2411	884	31	1	30	1	C7orf58	7	120629703	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3197095	120629703	38508960	155	28214										
GPR37	2861	hgsc.bcm.edu	37	chr7	124404321	124404321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gccggttcgtgctgtttcccCggcggggacccccaggctca	14	16	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:124404321C>T	ENST00000303921.2	-	1	1360	c.710G>A	c.(709-711)cGg>cAg	p.R237Q		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	237					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GCTGTTTCCCCGGCGGGGACC	0.642																																																0			7											44	46	46					7																	124404321		2203	4300	6503	124191557	SO:0001583	missense	2861				CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.710G>A	7.37:g.124404321C>T	ENSP00000306449:p.Arg237Gln		124191557	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	37	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	C	9.651	1.141680	0.21205	.	.	ENSG00000170775	ENST00000303921	T	0.37235	1.21	5.49	2.67	0.31697	.	0.485590	0.21892	N	0.067561	T	0.19846	0.0477	L	0.40543	1.245	0.09310	N	1	D	0.60160	0.987	B	0.34418	0.182	T	0.19549	-1.0302	10	0.15499	T	0.54	-6.2098	8.4741	0.33003	0.0:0.6265:0.2947:0.0788	.	237	O15354	GPR37_HUMAN	Q	237	ENSP00000306449:R237Q	ENSP00000306449:R237Q	R	-	2	0	GPR37	124191557	0.001000	0.12720	0.017000	0.16124	0.149000	0.21700	0.648000	0.24828	0.417000	0.25871	-0.195000	0.12781	CGG		0.642	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		T	124404321	C	T	124404321	3	4	107	1	0	0	0	0	1	0	0	0	6711	652	23	1	1139	1	GPR37	7	124404321	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3774618	124404321	34734342	156	28215										
MKLN1	4289	hgsc.bcm.edu	37	chr7	131128241	131128241	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgttgccttgttctgatagaTgtgtatggactcagaaaaac	10	6	2	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:131128241T>C	ENST00000352689.6	+	11	1215	c.1175T>C	c.(1174-1176)aTg>aCg	p.M392T	MKLN1_ENST00000421797.2_Splice_Site_p.M300T	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	392					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					TTCTGATAGATGTGTATGGAC	0.363																																																0			7											118	104	109					7																	131128241		2203	4300	6503	130778781	SO:0001630	splice_region_variant	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1174-1T>C	7.37:g.131128241T>C			130778781	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	37	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.335113	0.81801	.	.	ENSG00000128585	ENST00000421797;ENST00000352689	T;T	0.66815	-0.23;-0.23	5.56	5.56	0.83823	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.83917	0.5358	M	0.88310	2.945	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.75484	0.986;0.915;0.915	D	0.86192	0.1613	10	0.51188	T	0.08	-18.2761	14.8908	0.70606	0.0:0.0:0.0:1.0	.	392;369;300	Q9UL63;B4DG30;C9J7E8	MKLN1_HUMAN;.;.	T	300;392	ENSP00000398094:M300T;ENSP00000323527:M392T	ENSP00000323527:M392T	M	+	2	0	MKLN1	130778781	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.029000	0.88807	2.113000	0.64589	0.482000	0.46254	ATG		0.363	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255	Missense_Mutation	C	131128241	T	C	131128241	5	2	107	1	0	0	0	0	0	0	1	0	9633	1478	51	4	1250	4	MKLN1	7	131128241	Splice_Site	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	6723920	131128241	28010422	157	28216										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140301270	140301270	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacagaggaaggtgggggagAggagggcagaggcgggggag	25	4	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:140301270A>G	ENST00000275884.6	-	2	1345	c.928T>C	c.(928-930)Tct>Cct	p.S310P	DENND2A_ENST00000537639.1_Missense_Mutation_p.S310P|DENND2A_ENST00000496613.1_Missense_Mutation_p.S310P|DENND2A_ENST00000492720.1_Missense_Mutation_p.S310P			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	310					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.S310A(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					ggtgggggagaggagggcaga	0.597																																																1	Substitution - Missense(1)	ovary(1)	7											44	49	48					7																	140301270		1974	4151	6125	139947739	SO:0001583	missense	27147			AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.928T>C	7.37:g.140301270A>G	ENSP00000275884:p.Ser310Pro		139947739	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636863	0.47049	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000492720	T;T;T;T	0.10763	3.56;3.56;3.56;2.84	4.85	4.85	0.62838	.	0.209266	0.43260	D	0.000581	T	0.19927	0.0479	L	0.55834	1.745	0.44042	D	0.996779	D;B	0.59357	0.985;0.021	P;B	0.53809	0.735;0.029	T	0.01613	-1.1312	10	0.27785	T	0.31	-9.5576	14.5958	0.68407	1.0:0.0:0.0:0.0	.	310;310	Q9ULE3-2;Q9ULE3	.;DEN2A_HUMAN	P	310	ENSP00000275884:S310P;ENSP00000442245:S310P;ENSP00000419654:S310P;ENSP00000419464:S310P	ENSP00000275884:S310P	S	-	1	0	DENND2A	139947739	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	7.161000	0.77505	2.038000	0.60285	0.379000	0.24179	TCT		0.597	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		G	140301270	A	G	140301270	3	3	107	1	0	0	0	0	1	0	0	0	4440	304	11	4	2173	4	DENND2A	7	140301270	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	9173029	140301270	18837393	158	28217										
NOS3	4846	hgsc.bcm.edu	37	chr7	150698638	150698638	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcatctctctgcagccagacCcctggaaggggagtgccgcc	12	15	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr7:150698638C>A	ENST00000484524.1	+	11	1435	c.1435C>A	c.(1435-1437)Ccc>Acc	p.P479T	NOS3_ENST00000461406.1_Missense_Mutation_p.P273T|NOS3_ENST00000467517.1_Missense_Mutation_p.P479T|NOS3_ENST00000297494.3_Missense_Mutation_p.P479T	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAGCCAGACCCCTGGAAGGG	0.597																																																0			7											123	148	139					7																	150698638		2203	4300	6503	150329571	SO:0001583	missense	342977				CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1435C>A	7.37:g.150698638C>A	ENSP00000420215:p.Pro479Thr		150329571	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	37	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354845	0.82243	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.25749	1.78;1.89;1.78;1.78	5.19	5.19	0.71726	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.56097	D	0.000031	T	0.51941	0.1704	M	0.77486	2.375	0.53005	D	0.999969	D;P;P;D;P	0.67145	0.993;0.937;0.949;0.996;0.943	D;P;P;D;P	0.70935	0.957;0.831;0.886;0.971;0.788	T	0.53599	-0.8416	10	0.49607	T	0.09	-8.7981	16.2437	0.82429	0.0:1.0:0.0:0.0	.	479;479;479;273;479	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	T	479;273;479;479	ENSP00000297494:P479T;ENSP00000417143:P273T;ENSP00000420215:P479T;ENSP00000420551:P479T	ENSP00000297494:P479T	P	+	1	0	NOS3	150329571	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.724000	0.54962	2.411000	0.81874	0.655000	0.94253	CCC		0.597	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150698638	C	A	150698638	3	1	107	1	0	0	0	0	1	0	0	0	10575	623	22	2	1477	2	NOS3	7	150698638	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	10397368	150698638	8440025	159	28218										
SOX7	83595	hgsc.bcm.edu	37	chr8	10584033	10584033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaggaagcccgggtccacgcGcttgcacagccgcttggcct	13	15	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:10584033G>A	ENST00000304501.1	-	2	460	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	SOX7_ENST00000554914.1_Missense_Mutation_p.R180C|SOX7_ENST00000553390.1_Missense_Mutation_p.R180C|CTD-2135J3.3_ENST00000506149.2_RNA	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	128					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		GGGTCCACGCGCTTGCACAGC	0.687																																																0			8											30	35	33					8																	10584033		2203	4300	6503	10621443	SO:0001583	missense	83595			AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"SRY (sex determining region Y)-boxes"	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.382C>T	8.37:g.10584033G>A	ENSP00000301921:p.Arg128Cys		10621443	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207424	0.79240	.	.	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	D;D;D	0.99607	-5.33;-6.27;-6.27	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	D	0.99551	0.9839	M	0.79011	2.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.98030	1.0376	10	0.87932	D	0	.	16.5561	0.84485	0.0:0.0:1.0:0.0	.	180;128	B4DKV0;Q9BT81	.;SOX7_HUMAN	C	128;180;180	ENSP00000301921:R128C;ENSP00000452017:R180C;ENSP00000451145:R180C	ENSP00000346908:R180C	R	-	1	0	SOX7;CTD-2135J3.4	10621443	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.925000	0.63425	2.368000	0.80403	0.561000	0.74099	CGC		0.687	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1			A	10584033	G	A	10584033	3	1	107	1	0	0	0	0	1	0	0	0	14993	1087	38	1	788	1	SOX7	8	10584033	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		10584033	135779989	160	28219										
CHRNA6	8973	hgsc.bcm.edu	37	chr8	42611803	42611803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caatttcagctttgtcatacGtccaggaaccaaattttagg	7	9	2	0	rs200478711		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:42611803G>A	ENST00000276410.2	-	5	894	c.539C>T	c.(538-540)aCg>aTg	p.T180M	CHRNA6_ENST00000534622.1_Missense_Mutation_p.T165M|CHRNA6_ENST00000530869.1_5'Flank	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	180					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)			endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	TTTGTCATACGTCCAGGAACC	0.388																																																0			8											119	117	117					8																	42611803		2203	4300	6503	42730960	SO:0001583	missense	8973			U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.539C>T	8.37:g.42611803G>A	ENSP00000276410:p.Thr180Met		42730960	B2R8V4|B4DQH1	Missense_Mutation	SNP	ENST00000276410.2	37	CCDS6135.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.675962	0.88445	.	.	ENSG00000147434	ENST00000276410;ENST00000534622;ENST00000533810	T;T;T	0.80824	-1.42;-1.42;-1.42	5.93	5.93	0.95920	Neurotransmitter-gated ion-channel ligand-binding (3);	0.139070	0.64402	D	0.000003	D	0.92724	0.7687	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93471	0.6819	10	0.87932	D	0	.	20.4043	0.99006	0.0:0.0:1.0:0.0	.	165;180	B4DQH1;Q15825	.;ACHA6_HUMAN	M	180;165;101	ENSP00000276410:T180M;ENSP00000433871:T165M;ENSP00000434659:T101M	ENSP00000276410:T180M	T	-	2	0	CHRNA6	42730960	1.000000	0.71417	0.947000	0.38551	0.988000	0.76386	9.773000	0.98989	2.824000	0.97209	0.650000	0.86243	ACG		0.388	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			A	42611803	G	A	42611803	3	1	107	1	0	0	0	0	1	0	0	0	3393	1145	40	1	953	1	CHRNA6	8	42611803	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	32027770	42611803	103752219	161	28220										
ASPH	444	hgsc.bcm.edu	37	chr8	62415977	62415977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttccggatgccacacatccaCgatgaatatcagccggaaag	9	12	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:62415977C>T	ENST00000379454.4	-	25	2405	c.2218G>A	c.(2218-2220)Gtg>Atg	p.V740M	ASPH_ENST00000541428.1_Missense_Mutation_p.V711M	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	740					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CACACATCCACGATGAATATC	0.527																																																0			8											121	90	100					8																	62415977		2203	4300	6503	62578531	SO:0001583	missense	444			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.2218G>A	8.37:g.62415977C>T	ENSP00000368767:p.Val740Met		62578531	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	37	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	C	31	5.101518	0.94245	.	.	ENSG00000198363	ENST00000541428;ENST00000379454	T;T	0.46451	0.87;0.87	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.66346	0.2780	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.974;1.0	T	0.67158	-0.5741	10	0.62326	D	0.03	-18.4067	19.6961	0.96026	0.0:1.0:0.0:0.0	.	711;740	F5H667;Q12797	.;ASPH_HUMAN	M	711;740	ENSP00000437864:V711M;ENSP00000368767:V740M	ENSP00000368767:V740M	V	-	1	0	ASPH	62578531	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.294000	0.78760	2.745000	0.94114	0.650000	0.86243	GTG		0.527	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		T	62415977	C	T	62415977	3	4	107	1	0	0	0	0	1	0	0	0	1054	536	19	1	62	1	ASPH	8	62415977	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	19804174	62415977	83948045	162	28221										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70982042	70982042	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttctgcgggctgctctccggCgggtagcacaccttgtcctg	13	14	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:70982042C>T	ENST00000276594.2	-	2	255	c.54G>A	c.(52-54)ccG>ccA	p.P18P		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	18					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TGCTCTCCGGCGGGTAGCACA	0.657																																					NSCLC(129;99 1813 5906 40656 46114)											0			8											15	18	17					8																	70982042		2198	4298	6496	71144596	SO:0001819	synonymous_variant	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.54G>A	8.37:g.70982042C>T			71144596	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																				0.657	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70982042	C	T	70982042	2	4	107	1	0	0	0	0	0	0	0	1	12489	755	27	1		1	PRDM14	8	70982042	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	8566065	70982042	75381980	163	28222										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77761833	77761833	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atcacagcactcggtgcagcCggtcatctgctgtcctctct	9	15	4	0	rs369863550		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:77761833C>A	ENST00000521891.2	+	8	4179	c.3731C>A	c.(3730-3732)cCg>cAg	p.P1244Q	ZFHX4_ENST00000518282.1_Missense_Mutation_p.P1218Q|ZFHX4_ENST00000455469.2_Missense_Mutation_p.P1199Q|ZFHX4_ENST00000050961.6_Missense_Mutation_p.P1199Q	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1199					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TCGGTGCAGCCGGTCATCTGC	0.473										HNSCC(33;0.089)																																						0			8											127	122	124					8																	77761833		2039	4206	6245	77924388	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3731C>A	8.37:g.77761833C>A	ENSP00000430497:p.Pro1244Gln		77924388	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827414	0.71143	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55052	0.54;0.66;0.61;0.58	4.58	4.58	0.56647	.	0.000000	0.41938	U	0.000791	T	0.74596	0.3737	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.79184	-0.1908	10	0.87932	D	0	.	17.9143	0.88944	0.0:1.0:0.0:0.0	.	1199;1199;1244	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	Q	1244;1244;1199;1199;1218	ENSP00000430497:P1244Q;ENSP00000399605:P1199Q;ENSP00000050961:P1199Q;ENSP00000430848:P1218Q	ENSP00000050961:P1199Q	P	+	2	0	ZFHX4	77924388	1.000000	0.71417	0.957000	0.39632	0.992000	0.81027	7.609000	0.82925	2.524000	0.85096	0.555000	0.69702	CCG		0.473	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77761833	C	A	77761833	3	1	107	1	0	0	0	0	1	0	0	0	17674	652	23	2	3757	2	ZFHX4	8	77761833	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	6779791	77761833	68602189	164	28223										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104955049	104955049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tagatgatgagccacattggTacaaacttcagacgcatgat	9	8	1	5			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:104955049T>C	ENST00000436393.2	+	12	2171	c.1930T>C	c.(1930-1932)Tac>Cac	p.Y644H	RIMS2_ENST00000262231.10_Missense_Mutation_p.Y705H|RIMS2_ENST00000507740.1_Missense_Mutation_p.Y658H|RIMS2_ENST00000406091.3_Missense_Mutation_p.Y866H			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	928					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GCCACATTGGTACAAACTTCA	0.403										HNSCC(12;0.0054)																																						0			8											77	73	74					8																	104955049		1889	4118	6007	105024225	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1930T>C	8.37:g.104955049T>C	ENSP00000390665:p.Tyr644His		105024225	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	T	21.5	4.154139	0.78114	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	5.17	5.17	0.71159	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	D	0.86087	0.5849	L	0.61387	1.9	0.80722	D	1	P;P;D;D;D;D	0.76494	0.689;0.823;0.996;0.998;0.999;0.999	P;D;D;D;D;D	0.91635	0.851;0.91;0.999;0.996;0.999;0.999	D	0.86773	0.1974	9	0.52906	T	0.07	.	15.3133	0.74053	0.0:0.0:0.0:1.0	.	928;928;644;705;658;866	Q9UQ26;Q9UQ26-2;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.;.	H	866;881;866;928;658;705;658;658;644	ENSP00000427018:Y866H;ENSP00000384892:Y866H;ENSP00000425205:Y658H;ENSP00000262231:Y705H;ENSP00000423559:Y658H;ENSP00000386228:Y658H;ENSP00000390665:Y644H	ENSP00000262231:Y705H	Y	+	1	0	RIMS2	105024225	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.948000	0.87774	2.064000	0.61679	0.482000	0.46254	TAC		0.403	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		C	104955049	T	C	104955049	3	2	107	1	0	0	0	0	1	0	0	0	13405	1638	57	4	2776	4	RIMS2	8	104955049	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	27193216	104955049	41408973	165	28224										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121309824	121309824	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaatgctgtgaacttccaggCctggtaagaattcttccttc	8	10	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:121309824C>A	ENST00000297848.3	+	35	4581	c.4311C>A	c.(4309-4311)ggC>ggA	p.G1437G	COL14A1_ENST00000247781.3_Silent_p.G1342G|COL14A1_ENST00000309791.4_Silent_p.G1437G	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.G1437G(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	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)			AACTTCCAGGCCTGGTAAGAA	0.323																																																1	Substitution - coding silent(1)	ovary(1)	8											66	62	63					8																	121309824		2203	4298	6501	121379005	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4311C>A	8.37:g.121309824C>A			121379005		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.323	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121309824	C	A	121309824	2	1	107	1	0	0	0	0	0	0	0	1	3677	726	26	2		2	COL14A1	8	121309824	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	16354775	121309824	25054198	166	28225										
ZFAT	57623	hgsc.bcm.edu	37	chr8	135521987	135521987	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacggccgtggggtccagtcGgtcgccttaagaggaagaag	16	10	0	2	rs200421725		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr8:135521987G>A	ENST00000377838.3	-	15	3541	c.3367C>T	c.(3367-3369)Cga>Tga	p.R1123*	ZFAT_ENST00000520356.1_Intron|ZFAT_ENST00000520214.1_Nonsense_Mutation_p.R1111*|ZFAT_ENST00000517307.1_5'Flank|ZFAT_ENST00000523399.1_Nonsense_Mutation_p.R1061*|ZFAT_ENST00000520727.1_Nonsense_Mutation_p.R1111*|ZFAT_ENST00000429442.2_Nonsense_Mutation_p.R1111*	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1123					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R1123*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	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)			GGGTCCAGTCGGTCGCCTTAA	0.597													G|||	1	0.000199681	0	0.0014	5008	,	,		14795	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	kidney(1)	8											98	102	101					8																	135521987		2085	4205	6290	135591169	SO:0001587	stop_gained	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3367C>T	8.37:g.135521987G>A	ENSP00000367069:p.Arg1123*		135591169	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Nonsense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.89	3.248084	0.59103	.	.	ENSG00000066827	ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000521673;ENST00000318135;ENST00000523399	.	.	.	5.67	3.66	0.41972	.	0.294097	0.33477	N	0.004878	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9944	9.0481	0.36358	0.0:0.0981:0.5162:0.3856	.	.	.	.	X	1111;1111;1123;1111;43;1010;1061	.	ENSP00000326997:R1010X	R	-	1	2	ZFAT	135591169	1.000000	0.71417	0.988000	0.46212	0.373000	0.29922	2.283000	0.43470	0.677000	0.31305	0.557000	0.71058	CGA		0.597	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		A	135521987	G	A	135521987	4	1	107	1	0	0	0	0	0	1	0	0	17671	1124	39	1	372	1	ZFAT	8	135521987	Nonsense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	14212163	135521987	10842035	167	28226										
RFX3	5991	hgsc.bcm.edu	37	chr9	3330483	3330483	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tccagtattttggctgtacaTctgtgtctctgtgtaaggat	10	7	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:3330483T>C	ENST00000382004.3	-	5	561	c.250A>G	c.(250-252)Atg>Gtg	p.M84V	RFX3_ENST00000358730.2_Missense_Mutation_p.M84V|RFX3_ENST00000302303.1_Missense_Mutation_p.M84V	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	84					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TGGCTGTACATCTGTGTCTCT	0.403																																																0			9											104	99	101					9																	3330483		2203	4300	6503	3320483	SO:0001583	missense	5991			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.250A>G	9.37:g.3330483T>C	ENSP00000371434:p.Met84Val		3320483	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637674	0.47049	.	.	ENSG00000080298	ENST00000382004;ENST00000381992;ENST00000358730;ENST00000302303;ENST00000457373;ENST00000451859;ENST00000442560;ENST00000420720;ENST00000381985;ENST00000449190	T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.5	5.5	0.81552	RFX1 transcription activation region (1);	0.043366	0.85682	D	0.000000	T	0.19604	0.0471	N	0.12182	0.205	0.40407	D	0.979714	B;B;B;B	0.21753	0.06;0.055;0.05;0.056	B;B;B;B	0.25759	0.029;0.041;0.022;0.063	T	0.10291	-1.0636	10	0.17832	T	0.49	-20.8715	15.5703	0.76330	0.0:0.0:0.0:1.0	.	84;84;84;84	B1ANP5;P48380-3;P48380-2;P48380	.;.;.;RFX3_HUMAN	V	84;84;84;84;84;84;45;45;84;84	ENSP00000371434:M84V;ENSP00000351574:M84V;ENSP00000303847:M84V;ENSP00000405664:M84V;ENSP00000411756:M84V;ENSP00000410988:M45V;ENSP00000416189:M45V;ENSP00000399352:M84V	ENSP00000303847:M84V	M	-	1	0	RFX3	3320483	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.751000	0.55165	2.209000	0.71365	0.460000	0.39030	ATG		0.403	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		C	3330483	T	C	3330483	3	2	107	1	0	0	0	0	1	0	0	0	13301	1435	50	4	2211	4	RFX3	9	3330483	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10		3330483	137882948	168	28227										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8484163	8484163	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcaggcagttgcacagtaatCatgccatccaagttggtctt	9	10	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:8484163C>T	ENST00000381196.4	-	27	3912	c.3369G>A	c.(3367-3369)atG>atA	p.M1123I	PTPRD_ENST00000355233.5_Missense_Mutation_p.M712I|PTPRD_ENST00000397617.3_Missense_Mutation_p.M702I|PTPRD_ENST00000486161.1_Missense_Mutation_p.M712I|PTPRD_ENST00000540109.1_Missense_Mutation_p.M1123I|PTPRD_ENST00000356435.5_Missense_Mutation_p.M1123I|PTPRD_ENST00000397606.3_Missense_Mutation_p.M702I|PTPRD_ENST00000360074.4_Missense_Mutation_p.M1110I|PTPRD_ENST00000397611.3_Missense_Mutation_p.M709I|PTPRD_ENST00000537002.1_Missense_Mutation_p.M709I|PTPRD_ENST00000471274.1_5'Flank|PTPRD_ENST00000358503.5_Missense_Mutation_p.M1101I	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1123					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		GCACAGTAATCATGCCATCCA	0.453										TSP Lung(15;0.13)																																						0			9											161	142	148					9																	8484163		2203	4300	6503	8474163	SO:0001583	missense	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3369G>A	9.37:g.8484163C>T	ENSP00000370593:p.Met1123Ile		8474163	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.304319	0.60305	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.077355	0.85682	D	0.000000	T	0.44582	0.1300	L	0.27053	0.805	0.80722	D	1	B;B;P;B;B;B;B;B;B	0.35872	0.001;0.007;0.525;0.003;0.001;0.003;0.0;0.126;0.019	B;B;B;B;B;B;B;B;B	0.42214	0.008;0.001;0.38;0.003;0.022;0.013;0.001;0.08;0.004	T	0.15464	-1.0436	9	.	.	.	.	19.9087	0.97016	0.0:1.0:0.0:0.0	.	702;707;712;712;709;709;1110;1123;1123	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	I	1123;1123;1110;1101;712;702;709;709;1123;712;702	ENSP00000370593:M1123I;ENSP00000348812:M1123I;ENSP00000353187:M1110I;ENSP00000351293:M1101I;ENSP00000347373:M712I;ENSP00000380741:M702I;ENSP00000380735:M709I;ENSP00000440515:M709I;ENSP00000438164:M1123I;ENSP00000417093:M712I;ENSP00000380731:M702I	.	M	-	3	0	PTPRD	8474163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.896000	0.63222	2.802000	0.96397	0.655000	0.94253	ATG		0.453	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8484163	C	T	8484163	3	4	107	1	0	0	0	0	1	0	0	0	12836	826	29	3	2502	3	PTPRD	9	8484163	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5153680	8484163	132729268	169	28228										
IFNA5	3442	hgsc.bcm.edu	37	chr9	21304926	21304926	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttcagctgctggtaaagttcAgtgtagaatttgtctagaag	11	5	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:21304926A>G	ENST00000259555.4	-	1	386	c.330T>C	c.(328-330)acT>acC	p.T110T		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	110					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GGTAAAGTTCAGTGTAGAATT	0.468																																																0			9											119	116	117					9																	21304926		2203	4300	6503	21294926	SO:0001819	synonymous_variant	3442				CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"Interferons"	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.330T>C	9.37:g.21304926A>G			21294926	Q52LX3	Silent	SNP	ENST00000259555.4	37	CCDS6502.1																																																																																				0.468	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169		G	21304926	A	G	21304926	2	3	107	1	0	0	0	0	0	0	0	1	7561	175	7	4		4	IFNA5	9	21304926	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	12820763	21304926	119908505	170	28229										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32631469	32631469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcgccgtttcttctttggaGgaagctgctgtttaggaaac	11	9	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:32631469G>A	ENST00000242310.4	-	1	4198	c.4109C>T	c.(4108-4110)cCt>cTt	p.P1370L	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1370					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTTCTTTGGAGGAAGCTGCTG	0.458																																																0			9											206	205	205					9																	32631469		2203	4300	6503	32621469	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4109C>T	9.37:g.32631469G>A	ENSP00000418379:p.Pro1370Leu		32621469	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741215	0.69304	.	.	ENSG00000122728	ENST00000242310	T	0.08193	3.12	0.479	0.479	0.16796	.	0.000000	0.85682	D	0.000000	T	0.06781	0.0173	L	0.40543	1.245	0.80722	D	1	B	0.25521	0.128	B	0.26770	0.073	T	0.24657	-1.0154	10	0.56958	D	0.05	.	6.6915	0.23174	2.0E-4:0.0:0.9998:0.0	.	1370	Q8IZX4	TAF1L_HUMAN	L	1370	ENSP00000418379:P1370L	ENSP00000418379:P1370L	P	-	2	0	TAF1L	32621469	1.000000	0.71417	0.977000	0.42913	0.862000	0.49288	6.138000	0.71717	0.507000	0.28148	0.195000	0.17529	CCT		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32631469	G	A	32631469	3	1	107	1	0	0	0	0	1	0	0	0	15562	1000	35	3	1375	3	TAF1L	9	32631469	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	11326543	32631469	108581962	171	28230										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32635569	32635569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcagcagcaaatcgcagccGggtcgcataaaccggaaata	10	12	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:32635569G>A	ENST00000242310.4	-	1	98	c.9C>T	c.(7-9)ccC>ccT	p.P3P	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	3					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.P3P(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		AATCGCAGCCGGGTCGCATAA	0.552																																																1	Substitution - coding silent(1)	large_intestine(1)	9											47	45	46					9																	32635569		2203	4300	6503	32625569	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.9C>T	9.37:g.32635569G>A			32625569	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.552	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32635569	G	A	32635569	2	1	107	1	0	0	0	0	0	0	0	1	15562	1103	39	1		1	TAF1L	9	32635569	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4100	32635569	108577862	172	28231										
C9orf128	392307	hgsc.bcm.edu	37	chr9	35825636	35825636	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cttttcaacctctcctgcttCttcctcctgcttttcggttg	5	15	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:35825636C>T	ENST00000423537.2	-	2	792	c.523G>A	c.(523-525)Gaa>Aaa	p.E175K	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	175										endometrium(2)|kidney(1)|lung(4)	7						TCTCCTGCTTCTTCCTCCTGC	0.512											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			9											245	238	240					9																	35825636		2026	4185	6211	35815636	SO:0001583	missense	392307			BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 128"	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.523G>A	9.37:g.35825636C>T	ENSP00000415299:p.Glu175Lys	858	35815636	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	.	.	.	.	.	.	.	.	.	.	c	12.92	2.082007	0.36758	.	.	ENSG00000204930	ENST00000423537;ENST00000377984	T;T	0.34275	1.7;1.37	4.03	2.14	0.27477	.	0.811501	0.10663	N	0.648532	T	0.22859	0.0552	L	0.27053	0.805	0.23440	N	0.997679	B	0.19331	0.035	B	0.19391	0.025	T	0.29518	-1.0009	10	0.19147	T	0.46	-1.6587	6.7773	0.23626	0.0:0.768:0.0:0.232	.	175	A6H8Z2	CI128_HUMAN	K	175	ENSP00000415299:E175K;ENSP00000367222:E175K	ENSP00000367222:E175K	E	-	1	0	C9orf128	35815636	0.633000	0.27181	0.085000	0.20634	0.012000	0.07955	0.497000	0.22514	0.433000	0.26313	0.586000	0.80456	GAA		0.512	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446		T	35825636	C	T	35825636	3	4	107	1	0	0	0	0	1	0	0	0	2461	922	32	3	709	3	C9orf128	9	35825636	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3190067	35825636	105387795	173	28232										
ZNF658	26149	hgsc.bcm.edu	37	chr9	40773969	40773969	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acattcataaagtttgaatcCcacataagttccaggatgct	6	9	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:40773969C>A	ENST00000602553.1	-	5	1600	c.1306G>T	c.(1306-1308)Gga>Tga	p.G436*	ZNF658_ENST00000377626.3_Nonsense_Mutation_p.G436*|ZNF658_ENST00000441795.1_Nonsense_Mutation_p.G434*			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	436					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G436R(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		AGTTTGAATCCCACATAAGTT	0.383																																																1	Substitution - Missense(1)	ovary(1)	9											45	46	46					9																	40773969		2195	4278	6473	40763969	SO:0001587	stop_gained	26149			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1306G>T	9.37:g.40773969C>A	ENSP00000473484:p.Gly436*		40763969	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Nonsense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	c	38	6.706907	0.97776	.	.	ENSG00000196409	ENST00000441795;ENST00000377626	.	.	.	1.96	1.04	0.20106	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	6.5707	0.22537	0.0:0.8355:0.0:0.1645	.	.	.	.	X	434;436	.	ENSP00000366853:G436X	G	-	1	0	ZNF658	40763969	0.208000	0.23494	0.000000	0.03702	0.832000	0.47134	2.829000	0.48128	0.411000	0.25702	0.384000	0.25694	GGA		0.383	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		A	40773969	C	A	40773969	4	1	107	1	0	0	0	0	0	1	0	0	18108	632	22	2	1877	2	ZNF658	9	40773969	Nonsense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	4948333	40773969	100439462	174	28233										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73399068	73399068	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaggccaggatgtccgatgcCcgtccactcccatcacagac	9	16	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:73399068C>T	ENST00000377111.2	-	7	1344	c.1101G>A	c.(1099-1101)cgG>cgA	p.R367R	TRPM3_ENST00000377105.1_Silent_p.R214R|TRPM3_ENST00000360823.2_Silent_p.R239R|TRPM3_ENST00000377106.1_Silent_p.R239R|TRPM3_ENST00000377101.1_Silent_p.R214R|TRPM3_ENST00000377110.3_Silent_p.R367R|TRPM3_ENST00000358082.3_Silent_p.R239R|TRPM3_ENST00000408909.2_Silent_p.R214R|TRPM3_ENST00000396285.1_Silent_p.R214R|TRPM3_ENST00000357533.2_Silent_p.R369R|TRPM3_ENST00000396283.1_Silent_p.R239R|TRPM3_ENST00000423814.3_Silent_p.R394R|TRPM3_ENST00000396280.5_Silent_p.R214R|TRPM3_ENST00000361823.5_Silent_p.R214R|TRPM3_ENST00000396292.4_Silent_p.R239R	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	392					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGTCCGATGCCCGTCCACTCC	0.527																																																0			9											115	99	105					9																	73399068		2203	4300	6503	72588888	SO:0001819	synonymous_variant	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.1101G>A	9.37:g.73399068C>T			72588888	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	C	10.13	1.265839	0.23136	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.91	2.11	0.27256	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50524	-0.8818	4	.	.	.	-20.8719	9.684	0.40087	0.0:0.6059:0.0:0.3941	.	.	.	.	S	214	.	.	G	-	1	0	TRPM3	72588888	0.885000	0.30320	0.999000	0.59377	0.937000	0.57800	-0.051000	0.11885	0.135000	0.18707	-0.150000	0.13652	GGC		0.527	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73399068	C	T	73399068	2	4	107	1	0	0	0	0	0	0	0	1	16627	610	22	3		3	TRPM3	9	73399068	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	32625099	73399068	67814363	175	28234										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79320992	79320992	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctatccacaagtcaggcgcGgcagaggccagctgcccacc	11	16	2	1	rs372544904		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:79320992G>A	ENST00000376718.3	-	8	6321	c.6198C>T	c.(6196-6198)gcC>gcT	p.A2066A	PRUNE2_ENST00000428286.1_Silent_p.A1707A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2066					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGTCAGGCGCGGCAGAGGCCA	0.512																																																0			9						G		1,3135		0,1,1567	132	125	127		6198	-12.1	0	9		127	0,7164		0,0,3582	no	coding-synonymous	PRUNE2	NM_015225.2		0,1,5149	AA,AG,GG		0.0,0.0319,0.0097		2066/3089	79320992	1,10299	1568	3582	5150	78510812	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6198C>T	9.37:g.79320992G>A			78510812	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.372634	0.01214	3.19E-4	0.0	ENSG00000106772	ENST00000426088	.	.	.	6.03	-12.1	0.00011	.	.	.	.	.	T	0.29882	0.0747	.	.	.	0.38911	D	0.95754	.	.	.	.	.	.	T	0.38112	-0.9676	4	.	.	.	-13.4672	1.0634	0.01605	0.23:0.2987:0.2582:0.2132	.	.	.	.	C	1388	.	.	R	-	1	0	PRUNE2	78510812	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.307000	0.02733	-2.817000	0.00345	-1.740000	0.00687	CGC		0.512	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79320992	G	A	79320992	2	1	107	1	0	0	0	0	0	0	0	1	12675	1103	39	1		1	PRUNE2	9	79320992	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	5921924	79320992	61892439	176	28235										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79461456	79461456	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggcgatgagccagttgctcGgtgatgagctcaggagcctc	15	10	1	3	rs200722902		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:79461456G>A	ENST00000376718.3	-	4	606	c.483C>T	c.(481-483)acC>acT	p.T161T	PRUNE2_ENST00000376713.3_Silent_p.T161T|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	161					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CCAGTTGCTCGGTGATGAGCT	0.498																																																0			9											80	78	78					9																	79461456		2203	4300	6503	78651276	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.483C>T	9.37:g.79461456G>A			78651276	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1																																																																																				0.498	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79461456	G	A	79461456	2	1	107	1	0	0	0	0	0	0	0	1	12675	1103	39	1		1	PRUNE2	9	79461456	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	140464	79461456	61751975	177	28236										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98231361	98231361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggctgctgtagggaggtgggGggctgtagcgggtattgtcg	22	5	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:98231361G>T	ENST00000331920.6	-	14	2221	c.1922C>A	c.(1921-1923)cCc>cAc	p.P641H	PTCH1_ENST00000429896.2_Missense_Mutation_p.P490H|PTCH1_ENST00000421141.1_Missense_Mutation_p.P490H|PTCH1_ENST00000418258.1_Missense_Mutation_p.P490H|PTCH1_ENST00000375274.2_Missense_Mutation_p.P640H|PTCH1_ENST00000437951.1_Missense_Mutation_p.P575H|PTCH1_ENST00000430669.2_Missense_Mutation_p.P575H	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	641					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.P641L(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GGGAGGTGGGGGGCTGTAGCG	0.582																																																1	Substitution - Missense(1)	skin(1)	9											126	113	118					9																	98231361		2203	4300	6503	97271182	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1922C>A	9.37:g.98231361G>T	ENSP00000332353:p.Pro641His		97271182	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643077	0.67244	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.90444	-2.66;-2.65;-2.64;-2.64;-2.65;-2.64;-2.67;-2.64	4.98	4.98	0.66077	.	0.051475	0.85682	D	0.000000	D	0.94318	0.8174	M	0.73372	2.23	0.80722	D	1	B;B;D;D	0.67145	0.32;0.32;0.995;0.996	B;B;P;P	0.61592	0.192;0.206;0.826;0.891	D	0.94753	0.7929	10	0.72032	D	0.01	-25.8266	18.455	0.90717	0.0:0.0:1.0:0.0	.	490;575;640;641	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	H	641;575;490;490;77;575;490;640;306	ENSP00000332353:P641H;ENSP00000389744:P575H;ENSP00000399981:P490H;ENSP00000396135:P490H;ENSP00000410287:P575H;ENSP00000414823:P490H;ENSP00000364423:P640H;ENSP00000364420:P306H	ENSP00000332353:P641H	P	-	2	0	PTCH1	97271182	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.096000	0.94182	2.586000	0.87340	0.557000	0.71058	CCC		0.582	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98231361	G	T	98231361	3	4	107	1	0	0	0	0	1	0	0	0	12764	1232	43	2	2461	2	PTCH1	9	98231361	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	18769905	98231361	42982070	178	28237										
PRPF4	9128	hgsc.bcm.edu	37	chr9	116044950	116044950	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agaaatatcctctcagttgtCggtactgatgccttgaaaaa	8	8	1	3	rs139273131	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:116044950C>T	ENST00000374198.4	+	4	522	c.420C>T	c.(418-420)gtC>gtT	p.V140V	PRPF4_ENST00000374199.4_Silent_p.V139V|PRPF4_ENST00000488937.1_3'UTR	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	140					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						TCTCAGTTGTCGGTACTGATG	0.303																																																0			9											80	76	77					9																	116044950		2203	4300	6503	115084771	SO:0001819	synonymous_variant	9128			AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"WD repeat domain containing"	17349	protein-coding gene	gene with protein product	"PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4"	607795	"PRP4 pre-mRNA processing factor 4 homolog (yeast)"			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.420C>T	9.37:g.116044950C>T			115084771	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																				0.303	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		T	116044950	C	T	116044950	2	4	107	1	0	0	0	0	0	0	0	1	12604	871	31	1		1	PRPF4	9	116044950	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	17813589	116044950	25168481	179	28238										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131389742	131389742	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cgccaggagtttgcccagcaCgccaacgccttccaccagtg	10	17	0	0	rs372825476		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:131389742C>T	ENST00000372731.4	+	49	6749	c.6639C>T	c.(6637-6639)caC>caT	p.H2213H	SPTAN1_ENST00000372739.3_Silent_p.H2218H|SPTAN1_ENST00000358161.5_Silent_p.H2218H	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	2213					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TTGCCCAGCACGCCAACGCCT	0.647													C|||	1	0.000199681	8e-04	0	5008	,	,		18319	0		0	False		,,,				2504	0				NSCLC(120;833 1744 2558 35612 37579)											0			9						C	,,	0,4114		0,0,2057	47	28	34		6654,6579,6639	-3.9	1	9		34	1,7971		0,1,3985	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	0,1,6042	TT,TC,CC		0.0125,0.0,0.0083	,,	2218/2478,2193/2453,2213/2473	131389742	1,12085	2057	3986	6043	130429563	SO:0001819	synonymous_variant	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.6639C>T	9.37:g.131389742C>T			130429563	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																				0.647	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131389742	C	T	131389742	2	4	107	1	0	0	0	0	0	0	0	1	15156	535	19	1		1	SPTAN1	9	131389742	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	15344792	131389742	9823689	180	28239										
NUP214	8021	hgsc.bcm.edu	37	chr9	134072982	134072982	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagccaaccaagacgtcaggCgtgccctcagggtttaattt	10	12	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr9:134072982C>T	ENST00000359428.5	+	29	4245	c.4101C>T	c.(4099-4101)ggC>ggT	p.G1367G	NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Silent_p.G1368G|NUP214_ENST00000483497.2_Silent_p.G193G|NUP214_ENST00000411637.2_Silent_p.G1357G			P35658	NU214_HUMAN	nucleoporin 214kDa	1367	11 X 5 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGACGTCAGGCGTGCCCTCAG	0.542			T	"DEK, SET, ABL1"	"AML, T-ALL"																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0			9											115	116	116					9																	134072982		2203	4300	6503	133062803	SO:0001819	synonymous_variant	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4101C>T	9.37:g.134072982C>T			133062803	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																				0.542	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134072982	C	T	134072982	2	4	107	1	0	0	0	0	0	0	0	1	10793	755	27	1		1	NUP214	9	134072982	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2683240	134072982	7140449	181	28240										
TUBB8	347688	hgsc.bcm.edu	37	chr10	93294	93294	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acggctgtttttacgttgttGgggagccagtcagcaaagta	13	7	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:93294G>A	ENST00000309812.4	-	4	1100	c.1038C>T	c.(1036-1038)ccC>ccT	p.P346P	TUBB8_ENST00000413237.3_5'Flank|TUBB8_ENST00000447903.2_Silent_p.P274P	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	346					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.P346P(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		TTACGTTGTTGGGGAGCCAGT	0.502																																					Pancreas(192;2041 3010 9013 18103)											1	Substitution - coding silent(1)	lung(1)	10											93	102	99					10																	93294		2203	4300	6503	83294	SO:0001819	synonymous_variant	347688			AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"Tubulins"	20773	protein-coding gene	gene with protein product	"class VIII beta-tubulin"						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.1038C>T	10.37:g.93294G>A			83294	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																				0.502	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		A	93294	G	A	93294	2	1	107	1	0	0	0	0	0	0	0	1	16801	1335	47	3		3	TUBB8	10	93294	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		93294	135441453	182	28241										
ADARB2	105	hgsc.bcm.edu	37	chr10	1230859	1230859	+	Frame_Shift_Del	DEL	C	C	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcttgcagagccgggatgggCccccacagctcctccgccca							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:1230859delC	ENST00000381312.1	-	9	2310	c.1985delG	c.(1984-1986)ggcfs	p.G662fs	ADARB2_ENST00000381310.3_Frame_Shift_Del_p.G171fs|ADARB2_ENST00000381305.1_Frame_Shift_Del_p.G64fs	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	662	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.G662fs*21(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CCGGGATGGGCCCCCACAGCT	0.672																																																1	Deletion - Frameshift(1)	breast(1)	10											44	40	42					10																	1230859		2203	4299	6502	1220859	SO:0001589	frameshift_variant	105			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1985delG	10.37:g.1230859delC	ENSP00000370713:p.Gly662fs		1220859	B2RPJ5|Q5VUT6|Q5VW42	Frame_Shift_Del	DEL	ENST00000381312.1	37	CCDS7058.1																																																																																				0.672	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		-	1230859	C	-	1230859	7	5	107	1	0	1	0	1	0	0	0	0	283	739	26	0	242	0	ADARB2	10	1230859	Frame_Shift_Del	DEL	C	TCGA-DY-A1DG-01A-11D-A152-10	1137565	1230859	134303888	183	28242										
ACBD5	91452	hgsc.bcm.edu	37	chr10	27493474	27493474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctcgaagggccaccaagatGgtctctgagaaaatacaata	9	9	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:27493474G>T	ENST00000375888.1	-	12	1551	c.1487C>A	c.(1486-1488)cCa>cAa	p.P496Q	ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375897.3_Missense_Mutation_p.P310Q|ACBD5_ENST00000375905.4_Missense_Mutation_p.P452Q|ACBD5_ENST00000375901.1_Missense_Mutation_p.P378Q|ACBD5_ENST00000396271.3_Missense_Mutation_p.P487Q			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	496					peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						CCACCAAGATGGTCTCTGAGA	0.358																																																0			10											71	67	68					10																	27493474		2203	4300	6503	27533480	SO:0001583	missense	91452			AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 5"			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.1487C>A	10.37:g.27493474G>T	ENSP00000365049:p.Pro496Gln		27533480	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Missense_Mutation	SNP	ENST00000375888.1	37		.	.	.	.	.	.	.	.	.	.	G	33	5.280735	0.95489	.	.	ENSG00000107897	ENST00000375889;ENST00000396271;ENST00000375905;ENST00000375901;ENST00000375897;ENST00000375888	T;T;T;T;T	0.35605	2.27;2.02;1.3;1.35;2.27	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.61060	0.2317	M	0.73962	2.25	0.80722	D	1	D;P;P;D	0.56287	0.975;0.918;0.927;0.97	P;P;P;P	0.61397	0.888;0.546;0.776;0.826	T	0.62666	-0.6806	10	0.87932	D	0	-4.6729	20.0693	0.97712	0.0:0.0:1.0:0.0	.	487;310;485;496	Q5T8D3-3;B7Z2A7;B7Z2R7;Q5T8D3	.;.;.;ACBD5_HUMAN	Q	493;487;452;378;310;496	ENSP00000379568:P487Q;ENSP00000365070:P452Q;ENSP00000365066:P378Q;ENSP00000365062:P310Q;ENSP00000365049:P496Q	ENSP00000365049:P496Q	P	-	2	0	ACBD5	27533480	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.949000	0.75971	2.758000	0.94735	0.563000	0.77884	CCA		0.358	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698		T	27493474	G	T	27493474	3	4	107	1	0	0	0	0	1	0	0	0	125	1348	47	2	125	2	ACBD5	10	27493474	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	26262615	27493474	108041273	184	28243										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48371226	48371226	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agaatgctccactctgtagcActtttctgggtgcccctaca	8	13	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:48371226A>C	ENST00000395702.2	+	2	921	c.694A>C	c.(694-696)Act>Cct	p.T232P	ZNF488_ENST00000586537.1_Missense_Mutation_p.T125P|ZNF488_ENST00000494156.1_3'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	232					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						ACTCTGTAGCACTTTTCTGGG	0.567																																																0			10											105	100	102					10																	48371226		2203	4300	6503	47991232	SO:0001583	missense	118738			AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.694A>C	10.37:g.48371226A>C	ENSP00000379054:p.Thr232Pro		47991232	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	37	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	A	3.612	-0.079339	0.07141	.	.	ENSG00000165388	ENST00000395702	T	0.20598	2.06	5.55	-6.51	0.01878	.	0.454279	0.22512	N	0.059092	T	0.07818	0.0196	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23084	-1.0198	10	0.21540	T	0.41	.	9.1131	0.36741	0.4395:0.1663:0.3942:0.0	.	232	Q96MN9	ZN488_HUMAN	P	232	ENSP00000379054:T232P	ENSP00000379054:T232P	T	+	1	0	ZNF488	47991232	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.278000	0.08490	-1.216000	0.02607	-2.198000	0.00308	ACT		0.567	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		C	48371226	A	C	48371226	3	2	107	1	0	0	0	0	1	0	0	0	17979	159	6	4	696	4	ZNF488	10	48371226	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	20877752	48371226	87163521	185	28244										
RBP3	5949	hgsc.bcm.edu	37	chr10	48390677	48390677	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agcacactggccagcgtctgCgggtctgagatgctcagaat	13	11	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:48390677C>T	ENST00000224600.4	-	1	314	c.201G>A	c.(199-201)ccG>ccA	p.P67P		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	67	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CCAGCGTCTGCGGGTCTGAGA	0.612																																																0			10											54	51	52					10																	48390677		2203	4300	6503	48010683	SO:0001819	synonymous_variant	5949			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.201G>A	10.37:g.48390677C>T			48010683	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																				0.612	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		T	48390677	C	T	48390677	2	4	107	1	0	0	0	0	0	0	0	1	13194	755	27	1		1	RBP3	10	48390677	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	19451	48390677	87144070	186	28245										
SLC18A3	6572	hgsc.bcm.edu	37	chr10	50819132	50819132	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagcccttcggccccgctacCctacggagagcgaagacgtg	12	16	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:50819132C>A	ENST00000374115.3	+	1	786	c.346C>A	c.(346-348)Cct>Act	p.P116T	CHAT_ENST00000351556.3_5'Flank|CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000395559.2_5'Flank|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000339797.1_Intron	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3	116					acetylcholine transport (GO:0015870)|cation transmembrane transport (GO:0098655)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)			endometrium(6)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	43						GCCCCGCTACCCTACGGAGAG	0.662																																																0			10											68	70	69					10																	50819132		2203	4300	6503	50489138	SO:0001583	missense	6572			BC007765	CCDS7231.1	10q11.2	2013-07-18	2013-07-18		ENSG00000187714	ENSG00000187714		"Solute carriers"	10936	protein-coding gene	gene with protein product		600336				8071310	Standard	NM_003055		Approved	VACHT	uc001jhw.3	Q16572	OTTHUMG00000018196	ENST00000374115.3:c.346C>A	10.37:g.50819132C>A	ENSP00000363229:p.Pro116Thr		50489138	B2R7S1	Missense_Mutation	SNP	ENST00000374115.3	37	CCDS7231.1	.	.	.	.	.	.	.	.	.	.	C	5.974	0.363633	0.11296	.	.	ENSG00000187714	ENST00000374115	T	0.56941	0.43	4.17	4.17	0.49024	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.876201	0.09712	U	0.765505	T	0.34745	0.0908	N	0.11427	0.14	0.34555	D	0.711789	B	0.13145	0.007	B	0.20577	0.03	T	0.30679	-0.9970	10	0.20519	T	0.43	-12.6549	12.2284	0.54474	0.0:0.914:0.0:0.086	.	116	Q16572	VACHT_HUMAN	T	116	ENSP00000363229:P116T	ENSP00000363229:P116T	P	+	1	0	SLC18A3	50489138	1.000000	0.71417	0.887000	0.34795	0.838000	0.47535	5.138000	0.64795	2.148000	0.66965	0.561000	0.74099	CCT		0.662	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	NM_003055		A	50819132	C	A	50819132	3	1	107	1	0	0	0	0	1	0	0	0	14464	623	22	2	348	2	SLC18A3	10	50819132	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2428455	50819132	84715615	187	28246										
ANK3	288	hgsc.bcm.edu	37	chr10	61829385	61829385	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttcattttctaatccctgacAactggtcatcaccgcttcta	4	13	5	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:61829385A>G	ENST00000280772.2	-	37	11445	c.11254T>C	c.(11254-11256)Tgt>Cgt	p.C3752R	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3752					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.C3752S(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						AATCCCTGACAACTGGTCATC	0.398																																																1	Substitution - Missense(1)	ovary(1)	10											131	141	137					10																	61829385		2203	4300	6503	61499391	SO:0001583	missense	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11254T>C	10.37:g.61829385A>G	ENSP00000280772:p.Cys3752Arg		61499391	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	1.754	-0.488391	0.04352	.	.	ENSG00000151150	ENST00000280772	T	0.16196	2.36	5.3	-0.774	0.10991	.	0.813546	0.10352	N	0.684994	T	0.10337	0.0253	N	0.08118	0	0.80722	D	1	B	0.18863	0.031	B	0.18263	0.021	T	0.17440	-1.0369	10	0.44086	T	0.13	.	15.9271	0.79628	0.4587:0.5413:0.0:0.0	.	3752	Q12955	ANK3_HUMAN	R	3752	ENSP00000280772:C3752R	ENSP00000280772:C3752R	C	-	1	0	ANK3	61499391	0.985000	0.35326	0.997000	0.53966	0.999000	0.98932	0.620000	0.24403	-0.009000	0.14296	0.533000	0.62120	TGT		0.398	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61829385	A	G	61829385	3	3	107	1	0	0	0	0	1	0	0	0	622	130	5	4	2220	4	ANK3	10	61829385	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	11010253	61829385	73705362	188	28247										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63852513	63852513	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcaactccaggctcccggcTgggtattctcattctctgca	8	15	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:63852513T>C	ENST00000279873.7	+	10	3701	c.3291T>C	c.(3289-3291)gcT>gcC	p.A1097A	ARID5B_ENST00000309334.5_Silent_p.A854A	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1097					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					GGCTCCCGGCTGGGTATTCTC	0.542																																																0			10											68	74	72					10																	63852513		2203	4300	6503	63522519	SO:0001819	synonymous_variant	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.3291T>C	10.37:g.63852513T>C			63522519	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																				0.542	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		C	63852513	T	C	63852513	2	2	107	1	0	0	0	0	0	0	0	1	922	1567	55	4		4	ARID5B	10	63852513	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2023128	63852513	71682234	189	28248										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64936164	64936164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctttgacggagctttttgtTcacataccaactttggtcac	7	11	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:64936164T>C	ENST00000399262.2	-	24	7512	c.7294A>G	c.(7294-7296)Aac>Gac	p.N2432D	JMJD1C_ENST00000542921.1_Missense_Mutation_p.N2250D|JMJD1C_ENST00000402544.1_Missense_Mutation_p.N2195D|JMJD1C_ENST00000399251.1_3'UTR	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2432	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGCTTTTTGTTCACATACCAA	0.398																																																0			10											127	117	120					10																	64936164		1866	4086	5952	64606170	SO:0001583	missense	221037			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7294A>G	10.37:g.64936164T>C	ENSP00000382204:p.Asn2432Asp		64606170	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827337	0.32329	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.71341	-0.56;-0.56;-0.56	5.75	5.75	0.90469	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.046736	0.85682	D	0.000000	T	0.43656	0.1257	N	0.01817	-0.705	0.80722	D	1	P;B	0.40360	0.714;0.025	B;B	0.40134	0.32;0.021	T	0.57213	-0.7850	10	0.02654	T	1	-15.2545	15.7237	0.77736	0.0:0.0:0.0:1.0	.	2432;2250	Q15652;A0T124	JHD2C_HUMAN;.	D	2432;2195;2250	ENSP00000382204:N2432D;ENSP00000384990:N2195D;ENSP00000444682:N2250D	ENSP00000382204:N2432D	N	-	1	0	JMJD1C	64606170	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.204000	0.58460	2.195000	0.70347	0.533000	0.62120	AAC		0.398	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64936164	T	C	64936164	3	2	107	1	0	0	0	0	1	0	0	0	7971	1783	62	4	340	4	JMJD1C	10	64936164	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1083651	64936164	70598583	190	28249										
LRIT1	26103	hgsc.bcm.edu	37	chr10	85992226	85992226	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gccttccacaccaaggacacGctgtggtaagtgtcccccac	9	16	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:85992226G>A	ENST00000372105.3	-	4	1350	c.1329C>T	c.(1327-1329)agC>agT	p.S443S		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	443	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CCAAGGACACGCTGTGGTAAG	0.602																																																0			10											103	78	87					10																	85992226		2203	4300	6503	85982206	SO:0001819	synonymous_variant	26103			AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1329C>T	10.37:g.85992226G>A			85982206	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																				0.602	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		A	85992226	G	A	85992226	2	1	107	1	0	0	0	0	0	0	0	1	8976	1078	38	1		1	LRIT1	10	85992226	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	21056062	85992226	49542521	191	28250										
GRID1	2894	hgsc.bcm.edu	37	chr10	87484365	87484365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	actgaatagtccatgtaccgCttgctgaagtccacaacgct	8	12	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:87484365C>T	ENST00000327946.7	-	11	1687	c.1602G>A	c.(1600-1602)aaG>aaA	p.K534K	GRID1_ENST00000536331.1_Silent_p.K105K	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	534					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCATGTACCGCTTGCTGAAGT	0.502										Multiple Myeloma(13;0.14)																																						0			10											79	74	76					10																	87484365		2203	4300	6503	87474345	SO:0001819	synonymous_variant	2894			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1602G>A	10.37:g.87484365C>T			87474345	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																				0.502	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		T	87484365	C	T	87484365	2	4	107	1	0	0	0	0	0	0	0	1	6792	796	28	3		3	GRID1	10	87484365	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1492139	87484365	48050382	192	28251										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717672	89717672	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctccaattcaggacccacaCgacgggaagacaagttcatg	9	13	2	1	rs121909219		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:89717672C>T	ENST00000371953.3	+	7	2054	c.697C>T	c.(697-699)Cga>Tga	p.R233*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	233	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R233*(77)|p.0?(37)|p.R55fs*1(5)|p.R233fs*10(3)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R233fs*12(1)|p.R233fs*20(1)|p.R233fs*25(1)|p.R233fs*23(1)|p.R233R(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AGGACCCACACGACGGGAAGA	0.423	R233*(HEC59_ENDOMETRIUM)|R233*(JHUEM1_ENDOMETRIUM)|R233*(NCIH1155_LUNG)|R233*(SF295_CENTRAL_NERVOUS_SYSTEM)|R233*(SW1783_CENTRAL_NERVOUS_SYSTEM)	31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	133	Substitution - Nonsense(77)|Whole gene deletion(37)|Deletion - Frameshift(11)|Complex - frameshift(3)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1)|Substitution - coding silent(1)	endometrium(48)|central_nervous_system(21)|prostate(17)|haematopoietic_and_lymphoid_tissue(10)|lung(9)|large_intestine(6)|skin(6)|ovary(5)|cervix(3)|soft_tissue(3)|breast(3)|urinary_tract(2)	10	GRCh37	CM971277	PTEN	M	rs121909219						155	133	141					10																	89717672		2203	4300	6503	89707652	SO:0001587	stop_gained	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.697C>T	10.37:g.89717672C>T	ENSP00000361021:p.Arg233*		89707652	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	48	14.428311	0.99795	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.15	0.533	0.17121	.	0.063428	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.2458	14.4841	0.67603	0.5413:0.4587:0.0:0.0	.	.	.	.	X	233	.	.	R	+	1	2	PTEN	89707652	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.280000	0.33202	0.512000	0.28257	0.585000	0.79938	CGA		0.423	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89717672	C	T	89717672	4	4	107	1	0	0	0	0	0	1	0	0	12772	528	19	1	723	1	PTEN	10	89717672	Nonsense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2233307	89717672	45817075	193	28252										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720700	89720700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	attcttcataccaggaccagAggaaacctcagaaaaagtag	8	9	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:89720700A>G	ENST00000371953.3	+	8	2208	c.851A>G	c.(850-852)gAg>gGg	p.E284G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	284	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CCAGGACCAGAGGAAACCTCA	0.303		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											42	47	45					10																	89720700		2198	4285	6483	89710680	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.851A>G	10.37:g.89720700A>G	ENSP00000361021:p.Glu284Gly		89710680	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700943	0.68501	.	.	ENSG00000171862	ENST00000371953	D	0.85088	-1.94	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048693	0.85682	D	0.000000	D	0.83381	0.5242	M	0.66939	2.045	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.79245	-0.1883	9	.	.	.	-5.8021	14.9228	0.70854	1.0:0.0:0.0:0.0	.	284	P60484	PTEN_HUMAN	G	284	ENSP00000361021:E284G	.	E	+	2	0	PTEN	89710680	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.861000	0.92277	1.942000	0.56320	0.482000	0.46254	GAG		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720700	A	G	89720700	3	3	107	1	0	0	0	0	1	0	0	0	12772	304	11	4	881	4	PTEN	10	89720700	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	3028	89720700	45814047	194	28253										
PTEN	5728	hgsc.bcm.edu	37	chr10	89725048	89725048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aattttctttctctaggtgaAgctgtacttcacaaaaacag	6	8	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:89725048A>G	ENST00000371953.3	+	9	2388	c.1031A>G	c.(1030-1032)aAg>aGg	p.K344R		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	344	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.K344R(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CTCTAGGTGAAGCTGTACTTC	0.323		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Substitution - Missense(1)|Deletion - In frame(1)	prostate(17)|central_nervous_system(10)|skin(5)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											40	38	38					10																	89725048		2203	4300	6503	89715028	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1031A>G	10.37:g.89725048A>G	ENSP00000361021:p.Lys344Arg		89715028	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	9.150	1.016142	0.19355	.	.	ENSG00000171862	ENST00000371953	D	0.85258	-1.96	5.35	4.22	0.49857	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.085297	0.85682	D	0.000000	T	0.78342	0.4268	L	0.43923	1.385	0.58432	D	0.999999	B	0.16166	0.016	B	0.14578	0.011	T	0.70296	-0.4911	9	.	.	.	-6.6283	11.105	0.48197	0.9273:0.0:0.0727:0.0	.	344	P60484	PTEN_HUMAN	R	344	ENSP00000361021:K344R	.	K	+	2	0	PTEN	89715028	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.918000	0.92759	0.979000	0.38497	0.482000	0.46254	AAG		0.323	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89725048	A	G	89725048	3	3	107	1	0	0	0	0	1	0	0	0	12772	72	3	4	1065	4	PTEN	10	89725048	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	4348	89725048	45809699	195	28254										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93576985	93576985	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctgccaaagcagtgcttacTggtaagtctgtatactctgg	10	9	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:93576985T>C	ENST00000371627.4	+	3	898	c.519T>C	c.(517-519)acT>acC	p.T173T		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	173					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				CAGTGCTTACTGGTAAGTCTG	0.438																																																0			10											72	56	62					10																	93576985		2203	4300	6503	93566965	SO:0001630	splice_region_variant	80351			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.520+1T>C	10.37:g.93576985T>C			93566965	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	37	CCDS7417.1																																																																																				0.438	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235	Silent	C	93576985	T	C	93576985	5	2	107	1	0	0	0	0	0	0	1	0	16360	1594	55	4	529	4	TNKS2	10	93576985	Splice_Site	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	3851937	93576985	41957762	196	28255										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93586930	93586930	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaagtgctatagacttggctCccacaccacagttaaaagaa	7	10	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:93586930C>T	ENST00000371627.4	+	8	1331	c.952C>T	c.(952-954)Ccc>Tcc	p.P318S		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	318					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.P318A(1)		biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				AGACTTGGCTCCCACACCACA	0.348																																																1	Substitution - Missense(1)	lung(1)	10											104	99	101					10																	93586930		2203	4300	6503	93576910	SO:0001583	missense	80351			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.952C>T	10.37:g.93586930C>T	ENSP00000360689:p.Pro318Ser		93576910	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	37	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892494	0.91889	.	.	ENSG00000107854	ENST00000371627	T	0.13420	2.59	5.77	5.77	0.91146	Ankyrin repeat-containing domain (1);	0.000000	0.64402	D	0.000011	T	0.11452	0.0279	N	0.11560	0.145	0.80722	D	1	P	0.41131	0.739	B	0.44163	0.443	T	0.27502	-1.0072	10	0.13108	T	0.6	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	318	Q9H2K2	TNKS2_HUMAN	S	318	ENSP00000360689:P318S	ENSP00000360689:P318S	P	+	1	0	TNKS2	93576910	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.750000	0.85110	2.885000	0.99019	0.655000	0.94253	CCC		0.348	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		T	93586930	C	T	93586930	3	4	107	1	0	0	0	0	1	0	0	0	16360	855	30	3	982	3	TNKS2	10	93586930	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	9945	93586930	41947817	197	28256										
RRP12	23223	hgsc.bcm.edu	37	chr10	99123658	99123658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtcagccatctcttcatcttCgcctggagccaaaaaagaga	8	12	4	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:99123658C>T	ENST00000370992.4	-	30	3631	c.3520G>A	c.(3520-3522)Gaa>Aaa	p.E1174K	RRP12_ENST00000315563.6_Missense_Mutation_p.E1074K|RRP12_ENST00000536831.1_Missense_Mutation_p.E892K|RRP12_ENST00000414986.1_Missense_Mutation_p.E1113K|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1174						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E1174K(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCTTCATCTTCGCCTGGAGCC	0.577																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											171	148	156					10																	99123658		2203	4300	6503	99113648	SO:0001583	missense	23223				CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3520G>A	10.37:g.99123658C>T	ENSP00000360031:p.Glu1174Lys		99113648	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	c	6.650	0.488484	0.12641	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.30714	1.56;1.56;1.54;1.52	5.13	4.23	0.50019	.	0.428769	0.26935	N	0.021757	T	0.11024	0.0269	N	0.02802	-0.49	0.40560	D	0.981209	B;B;B;B	0.29037	0.068;0.231;0.231;0.148	B;B;B;B	0.20384	0.005;0.029;0.029;0.005	T	0.12734	-1.0536	10	0.06757	T	0.87	-19.7558	12.1684	0.54144	0.0:0.9201:0.0:0.0799	.	1113;1074;892;1174	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	K	1174;1074;1113;892	ENSP00000360031:E1174K;ENSP00000324315:E1074K;ENSP00000414863:E1113K;ENSP00000446184:E892K	ENSP00000324315:E1074K	E	-	1	0	RRP12	99113648	0.850000	0.29656	0.780000	0.31762	0.108000	0.19459	4.374000	0.59543	1.165000	0.42670	-0.119000	0.15052	GAA		0.577	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99123658	C	T	99123658	3	4	107	1	0	0	0	0	1	0	0	0	13723	893	31	1	393	1	RRP12	10	99123658	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5536728	99123658	36411089	198	28257										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114905790	114905790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcaaggtcaaccagtgtaccCaatcacgacaggaggattca	10	11	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:114905790C>T	ENST00000355995.4	+	8	1316	c.809C>T	c.(808-810)cCa>cTa	p.P270L	TCF7L2_ENST00000534894.1_Missense_Mutation_p.P270L|TCF7L2_ENST00000536810.1_Missense_Mutation_p.P270L|TCF7L2_ENST00000369395.1_Missense_Mutation_p.P295L|TCF7L2_ENST00000349937.2_Missense_Mutation_p.P266L|TCF7L2_ENST00000545257.1_Missense_Mutation_p.P270L|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000352065.5_Missense_Mutation_p.P247L|TCF7L2_ENST00000369389.1_5'UTR|TCF7L2_ENST00000538897.1_Missense_Mutation_p.P270L|TCF7L2_ENST00000369397.4_Missense_Mutation_p.P247L|TCF7L2_ENST00000355717.4_Missense_Mutation_p.P294L|TCF7L2_ENST00000543371.1_Missense_Mutation_p.P270L			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	270	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCAGTGTACCCAATCACGACA	0.507			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											209	191	197					10																	114905790		2203	4300	6503	114895780	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.809C>T	10.37:g.114905790C>T	ENSP00000348274:p.Pro270Leu		114895780	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	c	31	5.081650	0.94050	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000349937;ENST00000352065;ENST00000369395	D;D;D;D;D;D;D;D;D	0.99270	-5.09;-5.1;-5.1;-5.11;-5.63;-5.66;-5.62;-5.09;-5.62	5.82	5.82	0.92795	.	0.111467	0.64402	D	0.000009	D	0.99339	0.9768	M	0.67397	2.05	0.80722	D	1	P;D;D;P;D;P;D;P;B;D;D;D;P;D;D;D;D;P;P	0.89917	0.892;0.992;0.991;0.945;0.998;0.892;0.998;0.869;0.11;0.957;0.974;0.996;0.948;0.998;1.0;1.0;0.967;0.73;0.945	P;D;D;P;D;P;P;P;B;P;P;D;B;D;D;D;P;B;P	0.91635	0.652;0.909;0.916;0.788;0.954;0.621;0.858;0.66;0.068;0.71;0.9;0.933;0.437;0.923;0.999;0.983;0.839;0.356;0.468	D	0.99834	1.1056	10	0.87932	D	0	-5.3785	20.1022	0.97879	0.0:1.0:0.0:0.0	.	127;87;164;270;141;185;243;247;247;213;270;247;247;247;294;247;270;243;247	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	L	270;270;270;270;294;270;270;247;266;247;295	ENSP00000348274:P270L;ENSP00000440547:P270L;ENSP00000444972:P270L;ENSP00000446238:P270L;ENSP00000347949:P294L;ENSP00000446172:P270L;ENSP00000443626:P270L;ENSP00000358404:P247L;ENSP00000344823:P247L	ENSP00000298692:P266L	P	+	2	0	TCF7L2	114895780	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.814000	0.86154	2.759000	0.94783	0.555000	0.69702	CCA		0.507	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114905790	C	T	114905790	3	4	107	1	0	0	0	0	1	0	0	0	15737	594	21	3	984	3	TCF7L2	10	114905790	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	15782132	114905790	20628957	199	28258										
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118434446	118434446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tggtccctgtgagatccaggCggagcgtgccacacttcttc	12	13	1	1	rs555217651		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:118434446C>T	ENST00000369209.3	-	12	1978	c.1874G>A	c.(1873-1875)cGc>cAc	p.R625H	RP11-498B4.5_ENST00000433600.1_RNA	NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	625						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		GAGATCCAGGCGGAGCGTGCC	0.587													C|||	1	0.000199681	8e-04	0	5008	,	,		17238	0		0	False		,,,				2504	0															0			10											82	84	83					10																	118434446		2032	4193	6225	118424436	SO:0001583	missense	259217			AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"Heat shock proteins / HSP70"	19022	protein-coding gene	gene with protein product		610701	"heat shock 70kD protein 12A"			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.1874G>A	10.37:g.118434446C>T	ENSP00000358211:p.Arg625His		118424436		Missense_Mutation	SNP	ENST00000369209.3	37	CCDS41569.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.299989	0.23650	.	.	ENSG00000165868	ENST00000369209	T	0.44083	0.93	5.78	5.78	0.91487	.	0.050467	0.64402	D	0.000001	T	0.33990	0.0882	N	0.24115	0.695	0.48901	D	0.999721	B	0.23442	0.085	B	0.16722	0.016	T	0.04961	-1.0915	10	0.37606	T	0.19	.	20.0124	0.97464	0.0:1.0:0.0:0.0	.	625	O43301	HS12A_HUMAN	H	625	ENSP00000358211:R625H	ENSP00000358211:R625H	R	-	2	0	HSPA12A	118424436	1.000000	0.71417	1.000000	0.80357	0.519000	0.34347	5.743000	0.68655	2.749000	0.94314	0.655000	0.94253	CGC		0.587	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		T	118434446	C	T	118434446	3	4	107	1	0	0	0	0	1	0	0	0	7425	768	27	1	157	1	HSPA12A	10	118434446	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3528656	118434446	17100301	200	28259										
TACC2	10579	hgsc.bcm.edu	37	chr10	123970169	123970169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaagtccacggattccgtcCccatctctaagtctacactg	8	14	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:123970169C>T	ENST00000369005.1	+	9	6569	c.6229C>T	c.(6229-6231)Ccc>Tcc	p.P2077S	TACC2_ENST00000360561.3_Missense_Mutation_p.P155S|TACC2_ENST00000334433.3_Missense_Mutation_p.P2077S|TACC2_ENST00000369004.3_Missense_Mutation_p.P155S|TACC2_ENST00000513429.1_Missense_Mutation_p.P223S|TACC2_ENST00000515273.1_Missense_Mutation_p.P2081S|TACC2_ENST00000453444.2_Missense_Mutation_p.P2081S|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000368999.1_Missense_Mutation_p.P155S|TACC2_ENST00000515603.1_Missense_Mutation_p.P2032S|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000260733.3_Missense_Mutation_p.P155S|TACC2_ENST00000358010.1_Missense_Mutation_p.P223S	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2077					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GGATTCCGTCCCCATCTCTAA	0.572																																																0			10											103	99	100					10																	123970169		2203	4300	6503	123960159	SO:0001583	missense	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6229C>T	10.37:g.123970169C>T	ENSP00000358001:p.Pro2077Ser		123960159	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956917	0.34565	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.10477	3.84;3.31;3.9;3.87;3.84;3.31;3.9;3.15;3.17;3.14;3.17;2.87	5.64	5.64	0.86602	.	0.000000	0.36482	N	0.002575	T	0.25195	0.0612	M	0.65975	2.015	0.43814	D	0.996377	P;P;P;P;P;P;P;P;P	0.51057	0.837;0.899;0.485;0.941;0.899;0.743;0.619;0.619;0.941	B;B;B;P;B;B;B;B;P	0.51016	0.392;0.421;0.146;0.656;0.421;0.281;0.281;0.392;0.656	T	0.00192	-1.1935	10	0.48119	T	0.1	-8.2029	19.7154	0.96115	0.0:1.0:0.0:0.0	.	172;2081;155;2032;2081;155;155;223;2077	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	S	2077;223;2081;2032;2077;223;2081;2067;155;155;155;155;172	ENSP00000358001:P2077S;ENSP00000425062:P223S;ENSP00000424467:P2081S;ENSP00000427618:P2032S;ENSP00000334280:P2077S;ENSP00000350701:P223S;ENSP00000395048:P2081S;ENSP00000353763:P155S;ENSP00000357995:P155S;ENSP00000422815:P155S;ENSP00000260733:P155S;ENSP00000420967:P172S	ENSP00000260733:P155S	P	+	1	0	TACC2	123960159	1.000000	0.71417	0.163000	0.22734	0.293000	0.27360	3.133000	0.50531	2.664000	0.90586	0.655000	0.94253	CCC		0.572	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123970169	C	T	123970169	3	4	107	1	0	0	0	0	1	0	0	0	15541	623	22	3	6331	3	TACC2	10	123970169	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5535723	123970169	11564578	201	28260										
FANK1	92565	hgsc.bcm.edu	37	chr10	127697034	127697034	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	catgagagtctctgcggtgtCgggaaatcagagggtggcct	16	8	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr10:127697034C>T	ENST00000368693.1	+	8	868	c.764C>T	c.(763-765)tCg>tTg	p.S255L	FANK1_ENST00000368695.1_Missense_Mutation_p.S249L|FANK1_ENST00000477963.1_3'UTR			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	255						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TCTGCGGTGTCGGGAAATCAG	0.527																																																0			10											116	112	113					10																	127697034		2203	4300	6503	127687024	SO:0001583	missense	92565			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.764C>T	10.37:g.127697034C>T	ENSP00000357682:p.Ser255Leu		127687024	Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	37	CCDS31309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.96|13.96	2.391792|2.391792	0.42410|0.42410	.|.	.|.	ENSG00000203780|ENSG00000203780	ENST00000456942|ENST00000368695;ENST00000368693;ENST00000368691;ENST00000368692	.|T;T;T	.|0.65916	.|-0.18;-0.18;-0.11	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Ankyrin repeat-containing domain (4);	.|0.184605	.|0.36932	.|N	.|0.002325	T|T	0.48259|0.48259	0.1490|0.1490	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48589	.|0.912;0.854;0.742	.|B;B;B	.|0.37480	.|0.242;0.162;0.251	T|T	0.45963|0.45963	-0.9225|-0.9225	5|10	.|0.22109	.|T	.|0.4	-13.9202|-13.9202	18.4482|18.4482	0.90693|0.90693	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|281;255;255	.|Q8TC84-3;Q8TC84-2;Q8TC84	.|.;.;FANK1_HUMAN	W|L	150|249;255;233;281	.|ENSP00000357684:S249L;ENSP00000357682:S255L;ENSP00000357680:S233L	.|ENSP00000357680:S233L	R|S	+|+	1|2	2|0	FANK1|FANK1	127687024|127687024	0.926000|0.926000	0.31397|0.31397	0.102000|0.102000	0.21198|0.21198	0.109000|0.109000	0.19521|0.19521	5.180000|5.180000	0.65048|0.65048	2.634000|2.634000	0.89283|0.89283	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.527	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		T	127697034	C	T	127697034	3	4	107	1	0	0	0	0	1	0	0	0	5691	893	31	1	794	1	FANK1	10	127697034	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3726865	127697034	7837713	202	28261										
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6232882	6232882	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaaaatgactgcacagtagaCagcattcttgactcgaagag	10	8	1	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:6232882C>A	ENST00000449352.2	-	12	3036	c.2773G>T	c.(2773-2775)Gtc>Ttc	p.V925F	FAM160A2_ENST00000529360.1_5'UTR|FAM160A2_ENST00000265978.4_Missense_Mutation_p.V939F			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	925					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GCACAGTAGACAGCATTCTTG	0.572																																																0			11											88	92	91					11																	6232882		2201	4296	6497	6189458	SO:0001583	missense	84067				CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 56"	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.2773G>T	11.37:g.6232882C>A	ENSP00000416918:p.Val925Phe		6189458	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058117	0.76074	.	.	ENSG00000051009	ENST00000449352;ENST00000265978	T;T	0.19105	2.18;2.17	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	M	0.69823	2.125	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.47787	-0.9090	10	0.72032	D	0.01	-10.5269	17.724	0.88360	0.0:1.0:0.0:0.0	.	925;939	Q8N612;Q8N612-2	F16A2_HUMAN;.	F	925;939	ENSP00000416918:V925F;ENSP00000265978:V939F	ENSP00000265978:V939F	V	-	1	0	FAM160A2	6189458	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.175000	0.77632	2.501000	0.84356	0.650000	0.86243	GTC		0.572	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		A	6232882	C	A	6232882	3	1	107	1	0	0	0	0	1	0	0	0	5485	478	17	2	149	2	FAM160A2	11	6232882	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		6232882	128773634	203	28262										
CD44	960	hgsc.bcm.edu	37	chr11	35219752	35219752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagacacctcagtttttctgGatcaggcattgatgatgatg	10	8	3	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:35219752G>A	ENST00000428726.2	+	7	1004	c.881G>A	c.(880-882)gGa>gAa	p.G294E	CD44_ENST00000437706.2_Missense_Mutation_p.G294E|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Missense_Mutation_p.G294E|CD44_ENST00000352818.4_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.G251E|CD44_ENST00000434472.2_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000263398.6_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.G294E|CD44_ENST00000528922.1_3'UTR	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	294	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	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)		Hyaluronan(DB08818)	AGTTTTTCTGGATCAGGCATT	0.398																																																0			11											109	104	105					11																	35219752		2202	4298	6500	35176328	SO:0001583	missense	960			M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.881G>A	11.37:g.35219752G>A	ENSP00000398632:p.Gly294Glu		35176328	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	21.1|21.1|21.1	4.105268|4.105268|4.105268	0.77096|0.77096|0.77096	.|.|.	.|.|.	ENSG00000026508|ENSG00000026508|ENSG00000026508	ENST00000525685|ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000428726;ENST00000525688;ENST00000533222|ENST00000524922	.|T;T;T;T;T;T;T|.	.|0.26067|.	.|1.76;1.76;1.76;1.76;1.76;1.76;1.76|.	5.33|5.33|5.33	5.33|5.33|5.33	0.75918|0.75918|0.75918	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000015|.	T|T|.	0.68869|0.68869|.	0.3048|0.3048|.	L|L|L	0.55481|0.55481|0.55481	1.735|1.735|1.735	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.97110|.	.|1.0;0.999|.	T|T|.	0.66077|0.66077|.	-0.6013|-0.6013|.	5|10|.	.|0.48119|.	.|T|.	.|0.1|.	-8.7524|-8.7524|-8.7524	14.8749|14.8749|14.8749	0.70488|0.70488|0.70488	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|251;294|.	.|P16070-4;P16070|.	.|.;CD44_HUMAN|.	N|E|X	162|251;294;294;294;294;90;84|38	.|ENSP00000389830:G251E;ENSP00000414567:G294E;ENSP00000391008:G294E;ENSP00000403990:G294E;ENSP00000398632:G294E;ENSP00000436980:G90E;ENSP00000435321:G84E|.	.|ENSP00000389830:G251E|.	D|G|W	+|+|+	1|2|3	0|0|0	CD44|CD44|CD44	35176328|35176328|35176328	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	4.417000|4.417000|4.417000	0.59822|0.59822|0.59822	2.658000|2.658000|2.658000	0.90341|0.90341|0.90341	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAT|GGA|TGG		0.398	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		A	35219752	G	A	35219752	3	1	107	1	0	0	0	0	1	0	0	0	3023	1174	41	3	907	3	CD44	11	35219752	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	28986870	35219752	99786764	204	28263										
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798687	55798687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgtacttacagcccaccactAgctattccctagacactgat	5	14	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:55798687A>G	ENST00000313555.1	+	1	793	c.793A>G	c.(793-795)Agc>Ggc	p.S265G		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GCCCACCACTAGCTATTCCCT	0.413																																																0			11											103	88	93					11																	55798687		2201	4296	6497	55555263	SO:0001583	missense	219447			AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.793A>G	11.37:g.55798687A>G	ENSP00000324111:p.Ser265Gly		55555263	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.644271	0.29246	.	.	ENSG00000181785	ENST00000313555	T	0.00115	8.71	5.14	5.14	0.70334	GPCR, rhodopsin-like superfamily (1);	0.389671	0.18794	U	0.130989	T	0.00178	0.0005	N	0.25647	0.755	0.09310	N	1	P	0.47484	0.896	P	0.46510	0.519	T	0.66484	-0.5912	10	0.46703	T	0.11	.	13.7773	0.63062	1.0:0.0:0.0:0.0	.	265	Q8N127	O5AS1_HUMAN	G	265	ENSP00000324111:S265G	ENSP00000324111:S265G	S	+	1	0	OR5AS1	55555263	0.000000	0.05858	0.879000	0.34478	0.065000	0.16274	0.612000	0.24283	1.935000	0.56089	0.472000	0.43445	AGC		0.413	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		G	55798687	A	G	55798687	3	3	107	1	0	0	0	0	1	0	0	0	11177	420	15	4	795	4	OR5AS1	11	55798687	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	20578935	55798687	79207829	205	28264										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56057870	56057870	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtggaattaattttcaggatGgtagagagaatggacacata	12	3	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:56057870G>T	ENST00000313022.2	-	1	696	c.669C>A	c.(667-669)acC>acA	p.T223T		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T223T(1)		NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					TTTTCAGGATGGTAGAGAGAA	0.393																																																1	Substitution - coding silent(1)	ovary(1)	11											136	125	129					11																	56057870		2201	4294	6495	55814446	SO:0001819	synonymous_variant	219469			AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.669C>A	11.37:g.56057870G>T			55814446	B2RNI7|Q6IFC5	Silent	SNP	ENST00000313022.2	37	CCDS31526.1																																																																																				0.393	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		T	56057870	G	T	56057870	2	4	107	1	0	0	0	0	0	0	0	1	11268	1335	47	2		2	OR8H1	11	56057870	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	259183	56057870	78948646	206	28265										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086256	56086256	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgcacattcatttctcttctAgtcaccataaagatttttac	3	10	4	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:56086256A>G	ENST00000312711.1	+	1	474	c.474A>G	c.(472-474)ctA>ctG	p.L158L		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L158L(1)		central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TTTCTCTTCTAGTCACCATAA	0.398																																																1	Substitution - coding silent(1)	ovary(1)	11											111	113	112					11																	56086256		2201	4296	6497	55842832	SO:0001819	synonymous_variant	219473			AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.474A>G	11.37:g.56086256A>G			55842832	Q6IFC4	Silent	SNP	ENST00000312711.1	37	CCDS31527.1																																																																																				0.398	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		G	56086256	A	G	56086256	2	3	107	1	0	0	0	0	0	0	0	1	11275	407	15	4		4	OR8K3	11	56086256	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	28386	56086256	78920260	207	28266										
OR5M8	219484	hgsc.bcm.edu	37	chr11	56258344	56258344	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gattaatttcattggggccaCagaaggctaggttgtaggtc	13	6	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:56258344C>A	ENST00000327216.2	-	1	527	c.503G>T	c.(502-504)tGt>tTt	p.C168F		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					ATTGGGGCCACAGAAGGCTAG	0.488																																																0			11											90	89	89					11																	56258344		2201	4296	6497	56014920	SO:0001583	missense	219484			AB065744	CCDS31533.1	11q11	2012-08-09			ENSG00000181371	ENSG00000181371		"GPCR / Class A : Olfactory receptors"	14846	protein-coding gene	gene with protein product							Standard	NM_001005282		Approved		uc001nix.1	Q8NGP6	OTTHUMG00000166877	ENST00000327216.2:c.503G>T	11.37:g.56258344C>A	ENSP00000323354:p.Cys168Phe		56014920	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	37	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.364776	0.41902	.	.	ENSG00000181371	ENST00000327216	T	0.00249	8.44	4.35	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43747	D	0.000536	T	0.00754	0.0025	M	0.90977	3.165	0.37439	D	0.914332	D	0.89917	1.0	D	0.81914	0.995	T	0.62737	-0.6791	10	0.87932	D	0	-21.0048	14.9019	0.70687	0.0:1.0:0.0:0.0	.	168	Q8NGP6	OR5M8_HUMAN	F	168	ENSP00000323354:C168F	ENSP00000323354:C168F	C	-	2	0	OR5M8	56014920	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	3.842000	0.55858	2.153000	0.67306	0.632000	0.83419	TGT		0.488	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		A	56258344	C	A	56258344	3	1	107	1	0	0	0	0	1	0	0	0	11207	478	17	2	436	2	OR5M8	11	56258344	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	172088	56258344	78748172	208	28267										
PRPF19	27339	hgsc.bcm.edu	37	chr11	60666669	60666669	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcgccagtggcatgaaggctGaggcctgtcacagcactctc	12	13	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:60666669G>A	ENST00000227524.4	-	11	1141	c.936C>T	c.(934-936)ctC>ctT	p.L312L		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						CATGAAGGCTGAGGCCTGTCA	0.592											OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			11											57	46	49					11																	60666669		2203	4299	6502	60423245	SO:0001819	synonymous_variant	27339			BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.936C>T	11.37:g.60666669G>A		1047	60423245		Silent	SNP	ENST00000227524.4	37	CCDS7995.1																																																																																				0.592	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		A	60666669	G	A	60666669	2	1	107	1	0	0	0	0	0	0	0	1	12598	1277	45	3		3	PRPF19	11	60666669	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4408325	60666669	74339847	209	28268										
GNG3	2785	hgsc.bcm.edu	37	chr11	62475816	62475816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctatgagtattgggcaagcaCgcaagatggtggaacagctt	13	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:62475816C>T	ENST00000294117.5	+	2	308	c.49C>T	c.(49-51)Cgc>Tgc	p.R17C	BSCL2_ENST00000407022.3_5'Flank|BSCL2_ENST00000360796.5_5'Flank|BSCL2_ENST00000405837.1_Intron|BSCL2_ENST00000421906.1_5'Flank|BSCL2_ENST00000403550.1_5'Flank|BSCL2_ENST00000537604.1_5'Flank|BSCL2_ENST00000433053.1_Intron|HNRNPUL2-BSCL2_ENST00000403734.2_Intron|BSCL2_ENST00000278893.7_5'Flank	NM_012202.4	NP_036334.1	P63215	GBG3_HUMAN	guanine nucleotide binding protein (G protein), gamma 3	17					activation of MAPK activity (GO:0000187)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	5						TGGGCAAGCACGCAAGATGGT	0.552																																																0			11											163	152	156					11																	62475816		2202	4299	6501	62232392	SO:0001583	missense	2785			AF075042	CCDS8032.1	11p11	2008-07-18				ENSG00000162188			4405	protein-coding gene	gene with protein product	"guanine nucleotide-binding protein gamma-3 subunit", "NBP gamma-3"	608941				10644457	Standard	NM_012202		Approved		uc001nuv.4	P63215		ENST00000294117.5:c.49C>T	11.37:g.62475816C>T	ENSP00000294117:p.Arg17Cys		62232392	B2R4S7|P29798|Q61014	Missense_Mutation	SNP	ENST00000294117.5	37	CCDS8032.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.776453	0.70107	.	.	ENSG00000162188	ENST00000294117	T	0.35421	1.31	5.15	5.15	0.70609	G-protein gamma domain (5);	0.000000	0.85682	D	0.000000	T	0.58104	0.2099	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.61549	-0.7040	9	0.87932	D	0	-8.2157	11.6093	0.51049	0.178:0.822:0.0:0.0	.	17	P63215	GBG3_HUMAN	C	17	ENSP00000294117:R17C	ENSP00000294117:R17C	R	+	1	0	GNG3	62232392	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.560000	0.53763	2.559000	0.86315	0.558000	0.71614	CGC		0.552	GNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395020.1	NM_012202		T	62475816	C	T	62475816	3	4	107	1	0	0	0	0	1	0	0	0	6548	536	19	1	51	1	GNG3	11	62475816	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1809147	62475816	72530700	210	28269										
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64121189	64121189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccttctcactcctgccagggAccagcttaatgccctgcgcc	8	18	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:64121189A>G	ENST00000356786.5	+	23	3880	c.3836A>G	c.(3835-3837)gAc>gGc	p.D1279G	CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000359902.2_Missense_Mutation_p.D431G	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1279						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CCTGCCAGGGACCAGCTTAAT	0.647																																																0			11											126	121	123					11																	64121189		2201	4297	6498	63877765	SO:0001583	missense	283234			AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"brain leucine zipper protein", "GRP78-interacting protein induced by ER stress"	611205	"coiled-coil domain containing 88"	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.3836A>G	11.37:g.64121189A>G	ENSP00000349238:p.Asp1279Gly		63877765	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	a	14.46	2.541696	0.45280	.	.	ENSG00000168071	ENST00000377638;ENST00000356786;ENST00000359902	T;T	0.68903	-0.36;-0.36	3.11	1.92	0.25849	.	.	.	.	.	T	0.73377	0.3579	M	0.62723	1.935	0.80722	D	1	D;P;D;D	0.76494	0.999;0.905;0.995;0.999	D;B;P;D	0.65573	0.936;0.39;0.898;0.936	T	0.70999	-0.4719	9	0.72032	D	0.01	.	6.2098	0.20623	0.7393:0.2607:0.0:0.0	.	1279;1161;415;1279	B2RTU8;A6NC98-4;A6NC98-5;A6NC98	.;.;.;CC88B_HUMAN	G	1161;1279;431	ENSP00000349238:D1279G;ENSP00000352974:D431G	ENSP00000349238:D1279G	D	+	2	0	CCDC88B	63877765	0.987000	0.35691	0.986000	0.45419	0.692000	0.40212	1.187000	0.32090	0.377000	0.24735	0.379000	0.24179	GAC		0.647	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		G	64121189	A	G	64121189	3	3	107	1	0	0	0	0	1	0	0	0	2870	275	10	4	3926	4	CCDC88B	11	64121189	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1645373	64121189	70885327	211	28270										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238483	71238483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctgctgctgcaagcccgtgtGctgctgtgtgccagcctgtt	13	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:71238483G>A	ENST00000398536.4	+	1	171	c.137G>A	c.(136-138)tGc>tAc	p.C46Y		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	46	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						AAGCCCGTGTGCTGCTGTGTG	0.692																																																0			11											76	101	93					11																	71238483		2195	4286	6481	70916131	SO:0001583	missense	440050			AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.137G>A	11.37:g.71238483G>A	ENSP00000417330:p.Cys46Tyr		70916131	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	11.17	1.559049	0.27827	.	.	ENSG00000244411	ENST00000398536	T	0.02395	4.31	1.8	1.8	0.24995	.	.	.	.	.	T	0.18635	0.0447	H	0.94183	3.505	0.28807	N	0.898436	D	0.62365	0.991	D	0.68039	0.955	T	0.02877	-1.1099	9	0.87932	D	0	.	9.6322	0.39787	0.0:0.0:1.0:0.0	.	46	Q6L8G8	KRA57_HUMAN	Y	46	ENSP00000417330:C46Y	ENSP00000417330:C46Y	C	+	2	0	KRTAP5-7	70916131	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	2.307000	0.43682	1.345000	0.45676	0.281000	0.19383	TGC		0.692	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			A	71238483	G	A	71238483	3	1	107	1	0	0	0	0	1	0	0	0	8588	1319	46	3	139	3	KRTAP5-7	11	71238483	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	7117294	71238483	63768033	212	28271										
FOLR2	2350	hgsc.bcm.edu	37	chr11	71932638	71932638	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agcaactacagccgagggagCggccgctgcatccagatgtg	14	12	0	1	rs138209906		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:71932638C>T	ENST00000298223.6	+	5	787	c.600C>T	c.(598-600)agC>agT	p.S200S	FOLR2_ENST00000454954.2_Silent_p.S159S|FOLR2_ENST00000449475.2_Silent_p.S196S	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	200					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)	p.S200R(1)|p.S200S(1)		breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	GCCGAGGGAGCGGCCGCTGCA	0.572																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|breast(1)	11						C	,,,	1,4399	2.1+/-5.4	0,1,2199	93	94	94		600,600,600,600	-9.1	0.2	11	dbSNP_134	94	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FOLR2	NM_000803.4,NM_001113534.1,NM_001113535.1,NM_001113536.1	,,,	0,1,6492	TT,TC,CC		0.0,0.0227,0.0077	,,,	200/256,200/256,200/256,200/256	71932638	1,12985	2200	4293	6493	71610286	SO:0001819	synonymous_variant	2350			AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.600C>T	11.37:g.71932638C>T			71610286	Q05CA5|Q6GTE8	Silent	SNP	ENST00000298223.6	37	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	c	8.149	0.787002	0.16189	2.27E-4	0.0	ENSG00000165457	ENST00000413873	.	.	.	4.58	-9.13	0.00704	.	.	.	.	.	T	0.53867	0.1823	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.67205	-0.5729	5	0.87932	D	0	.	6.7188	0.23318	0.1092:0.5845:0.1106:0.1957	.	.	.	.	V	214	.	ENSP00000412980:A214V	A	+	2	0	FOLR2	71610286	0.000000	0.05858	0.182000	0.23118	0.945000	0.59286	-4.433000	0.00235	-2.021000	0.00939	0.462000	0.41574	GCG		0.572	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		T	71932638	C	T	71932638	2	4	107	1	0	0	0	0	0	0	0	1	6001	767	27	1		1	FOLR2	11	71932638	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	694155	71932638	63073878	213	28272										
INTS4	92105	hgsc.bcm.edu	37	chr11	77602469	77602469	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccgcaaagggttgtctgactCgcccgctggctcgatgatgg	14	12	1	2	rs1044911		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:77602469C>G	ENST00000534064.1	-	21	2522	c.2488G>C	c.(2488-2490)Gag>Cag	p.E830Q	AAMDC_ENST00000304716.8_Intron|INTS4_ENST00000535943.1_Missense_Mutation_p.E205Q|AAMDC_ENST00000527134.1_Intron|AAMDC_ENST00000532481.1_Intron	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	830					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TTGTCTGACTCGCCCGCTGGC	0.507																																																0			11											44	41	42					11																	77602469		2200	4292	6492	77280117	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.2488G>C	11.37:g.77602469C>G	ENSP00000434466:p.Glu830Gln		77280117	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.732313	0.69189	.	.	ENSG00000149262	ENST00000534064;ENST00000535943	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.74884	0.3775	L	0.52364	1.645	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.72316	-0.4330	9	0.37606	T	0.19	-20.5562	18.7604	0.91848	0.0:1.0:0.0:0.0	.	830	Q96HW7	INT4_HUMAN	Q	830;205	.	ENSP00000434466:E830Q	E	-	1	0	INTS4	77280117	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	7.540000	0.82074	2.667000	0.90743	0.585000	0.79938	GAG		0.507	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		G	77602469	C	G	77602469	3	3	107	1	0	0	0	0	1	0	0	0	7801	893	31	5	415	5	INTS4	11	77602469	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5669831	77602469	57404047	214	28273										
INTS4	92105	hgsc.bcm.edu	37	chr11	77672105	77672105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggccttctgcatcttttgtgAcacttttctccaaagagcca	7	12	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:77672105A>G	ENST00000534064.1	-	5	585	c.551T>C	c.(550-552)gTc>gCc	p.V184A	INTS4_ENST00000529807.1_Missense_Mutation_p.V184A	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	184					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ATCTTTTGTGACACTTTTCTC	0.403																																																0			11											180	171	174					11																	77672105		2200	4292	6492	77349753	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.551T>C	11.37:g.77672105A>G	ENSP00000434466:p.Val184Ala		77349753	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	A	9.608	1.130557	0.21041	.	.	ENSG00000149262	ENST00000534064;ENST00000354849;ENST00000529807	T	0.64618	-0.11	4.48	3.35	0.38373	Armadillo-like helical (1);Armadillo-type fold (1);	0.228610	0.37761	N	0.001945	T	0.29850	0.0746	N	0.02011	-0.69	0.58432	D	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.04053	-1.0981	10	0.20519	T	0.43	-15.6565	7.126	0.25471	0.6796:0.0:0.3204:0.0	.	184	Q96HW7	INT4_HUMAN	A	184;35;184	ENSP00000434466:V184A	ENSP00000346913:V35A	V	-	2	0	INTS4	77349753	0.231000	0.23751	1.000000	0.80357	0.998000	0.95712	0.269000	0.18589	0.855000	0.35359	0.528000	0.53228	GTC		0.403	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		G	77672105	A	G	77672105	3	3	107	1	0	0	0	0	1	0	0	0	7801	275	10	4	2416	4	INTS4	11	77672105	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	69636	77672105	57334411	215	28274										
C11orf88	399949	hgsc.bcm.edu	37	chr11	111404521	111404521	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttaagaaaacaaagagaagaAaggatctcggtgagaccaat	10	5	1	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:111404521A>G	ENST00000375618.4	+	4	390	c.390A>G	c.(388-390)gaA>gaG	p.E130E	C11orf88_ENST00000529167.1_Silent_p.E157E|C11orf88_ENST00000332814.6_Silent_p.E157E	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	130										endometrium(1)|large_intestine(3)|lung(2)	6						AAAGAGAAGAAAGGATCTCGG	0.348																																																0			11											81	77	78					11																	111404521		1802	4078	5880	110909731	SO:0001819	synonymous_variant	399949			BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"hypothetical gene supported by BC039505"					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.390A>G	11.37:g.111404521A>G			110909731	E9PAN0|Q6ZRL3	Silent	SNP	ENST00000375618.4	37	CCDS41713.1																																																																																				0.348	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388		G	111404521	A	G	111404521	2	3	107	1	0	0	0	0	0	0	0	1	1674	11	1	4		4	C11orf88	11	111404521	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	33732416	111404521	23601995	216	28275										
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122678801	122678801	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acatcctgattgtggcccacGcatcttcccttgaagcgtgt	9	13	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:122678801G>A	ENST00000284273.5	+	13	2104	c.1729G>A	c.(1729-1731)Gca>Aca	p.A577T		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	577	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		TGTGGCCCACGCATCTTCCCT	0.458																																																0			11											346	330	335					11																	122678801		2202	4299	6501	122184011	SO:0001583	missense	84959			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1729G>A	11.37:g.122678801G>A	ENSP00000284273:p.Ala577Thr		122184011	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	G	36	5.660298	0.96734	.	.	ENSG00000154127	ENST00000284273	T	0.31769	1.48	5.85	5.85	0.93711	Histidine phosphatase superfamily, clade-1 (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	L	0.49350	1.555	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	T	0.43475	-0.9389	10	0.66056	D	0.02	-18.5526	19.7681	0.96350	0.0:0.0:1.0:0.0	.	577	Q8TF42	UBS3B_HUMAN	T	577	ENSP00000284273:A577T	ENSP00000284273:A577T	A	+	1	0	UBASH3B	122184011	1.000000	0.71417	0.974000	0.42286	0.998000	0.95712	9.394000	0.97261	2.768000	0.95171	0.655000	0.94253	GCA		0.458	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		A	122678801	G	A	122678801	3	1	107	1	0	0	0	0	1	0	0	0	16880	1087	38	1	1779	1	UBASH3B	11	122678801	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	11274280	122678801	12327715	217	28276										
C11orf63	79864	hgsc.bcm.edu	37	chr11	122774668	122774668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agacaaatattcagacctccGctatgacccgaactggaaga	8	11	1	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:122774668G>A	ENST00000531316.1	+	2	472	c.380G>A	c.(379-381)cGc>cAc	p.R127H	C11orf63_ENST00000227349.2_Missense_Mutation_p.R127H|C11orf63_ENST00000307257.6_Missense_Mutation_p.R127H			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	127					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		TCAGACCTCCGCTATGACCCG	0.458																																																0			11											150	169	162					11																	122774668		2202	4299	6501	122279878	SO:0001583	missense	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.380G>A	11.37:g.122774668G>A	ENSP00000431669:p.Arg127His		122279878	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302189	0.81136	.	.	ENSG00000109944	ENST00000307257;ENST00000227349;ENST00000531316	T;T	0.60424	0.19;0.19	5.73	4.79	0.61399	.	0.241265	0.29040	N	0.013323	T	0.72309	0.3444	M	0.73598	2.24	0.34124	D	0.664445	D;D	0.89917	1.0;1.0	D;D	0.68765	0.947;0.96	T	0.81470	-0.0918	10	0.72032	D	0.01	-9.0668	10.0669	0.42308	0.1685:0.0:0.8315:0.0	.	127;127	Q6NUN7;Q6NUN7-2	CK063_HUMAN;.	H	127	ENSP00000227349:R127H;ENSP00000431669:R127H	ENSP00000227349:R127H	R	+	2	0	C11orf63	122279878	0.986000	0.35501	0.944000	0.38274	0.975000	0.68041	2.433000	0.44793	1.341000	0.45600	0.655000	0.94253	CGC		0.458	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		A	122774668	G	A	122774668	3	1	107	1	0	0	0	0	1	0	0	0	1658	1087	38	1	386	1	C11orf63	11	122774668	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	95867	122774668	12231848	218	28277										
ASAM	79827	hgsc.bcm.edu	37	chr11	122953916	122953916	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcgtccagggtggttgtagtCtgcacaagcagaaagaatga	13	7	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:122953916C>T	ENST00000448775.2	-	5	897		c.e5-1		CLMP_ENST00000530371.1_Splice_Site	NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein						digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						TGGTTGTAGTCTGCACAAGCA	0.433																																																0			11											127	118	121					11																	122953916		2202	4299	6501	122459126	SO:0001630	splice_region_variant	79827			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24039	protein-coding gene	gene with protein product	"adipocyte-specific adhesion molecule", "coxsackie- and adenovirus receptor-like membrane protein", "adipocyte adhesion molecule"	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.557-1G>A	11.37:g.122953916C>T			122459126		Splice_Site	SNP	ENST00000448775.2	37	CCDS8441.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.032818	0.75504	.	.	ENSG00000166250	ENST00000448775	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9501	0.86243	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLMP	122459126	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	6.378000	0.73150	2.439000	0.82584	0.563000	0.77884	.		0.433	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769	Intron	T	122953916	C	T	122953916	5	4	107	1	0	0	0	0	0	0	1	0	1010	927	32	3	577	3	ASAM	11	122953916	Splice_Site	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	179248	122953916	12052600	219	28278										
OR8B12	219858	hgsc.bcm.edu	37	chr11	124413357	124413357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aacagaaatctattaaagagAggttaaaaaggaagaagtac	9	3	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr11:124413357A>G	ENST00000306842.2	-	1	218	c.194T>C	c.(193-195)cTc>cCc	p.L65P		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0213)		TATTAAAGAGAGGTTAAAAAG	0.453																																																0			11											81	79	80					11																	124413357		2201	4299	6500	123918567	SO:0001583	missense	219858				CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"GPCR / Class A : Olfactory receptors"	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.194T>C	11.37:g.124413357A>G	ENSP00000307159:p.Leu65Pro		123918567	B2RNF6|Q6IEW8|Q96RC7	Missense_Mutation	SNP	ENST00000306842.2	37	CCDS31711.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.132326	0.37630	.	.	ENSG00000170953	ENST00000306842	T	0.00591	6.35	3.77	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	D	0.000386	T	0.05090	0.0136	H	0.97291	3.975	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	T	0.00975	-1.1494	10	0.87932	D	0	.	12.4298	0.55567	1.0:0.0:0.0:0.0	.	65	Q8NGG6	OR8BC_HUMAN	P	65	ENSP00000307159:L65P	ENSP00000307159:L65P	L	-	2	0	OR8B12	123918567	0.958000	0.32768	0.490000	0.27465	0.115000	0.19883	8.850000	0.92190	1.940000	0.56252	0.528000	0.53228	CTC		0.453	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1			G	124413357	A	G	124413357	3	3	107	1	0	0	0	0	1	0	0	0	11257	304	11	4	740	4	OR8B12	11	124413357	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1459441	124413357	10593159	220	28279										
NOP2	4839	hgsc.bcm.edu	37	chr12	6673077	6673077	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccagcagcagcttcccgggcCttctgcttccgagcagctct	10	17	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:6673077C>G	ENST00000322166.5	-	6	631	c.510G>C	c.(508-510)aaG>aaC	p.K170N	NOP2_ENST00000541778.1_Missense_Mutation_p.K166N|NOP2_ENST00000545200.1_Missense_Mutation_p.K166N|NOP2_ENST00000382421.3_Missense_Mutation_p.K203N|NOP2_ENST00000399466.2_Missense_Mutation_p.K166N|NOP2_ENST00000537442.1_Missense_Mutation_p.K170N|NOP2_ENST00000542015.1_Intron	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	170					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						CTTCCCGGGCCTTCTGCTTCC	0.537											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			12											45	46	45					12																	6673077		1877	4115	5992	6543338	SO:0001583	missense	4839				CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.510G>C	12.37:g.6673077C>G	ENSP00000313272:p.Lys170Asn	635	6543338	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	37	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.335201	0.81801	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867;ENST00000536124	T;T;T;T;T;T;T;T;T	0.61980	2.37;2.04;2.45;2.39;2.37;2.39;0.82;0.63;0.06	5.83	4.93	0.64822	.	0.294751	0.38381	N	0.001714	T	0.73992	0.3658	M	0.71581	2.175	0.80722	D	1	P;D	0.67145	0.938;0.996	B;P	0.60541	0.368;0.876	T	0.76138	-0.3069	10	0.54805	T	0.06	-32.4439	12.415	0.55488	0.0:0.9205:0.0:0.0795	.	203;166	Q3KQS4;P46087-2	.;.	N	170;203;166;166;170;166;46;166;170	ENSP00000444437:K170N;ENSP00000371858:K203N;ENSP00000439422:K166N;ENSP00000382392:K166N;ENSP00000313272:K170N;ENSP00000443150:K166N;ENSP00000440754:K46N;ENSP00000443035:K166N;ENSP00000442895:K170N	ENSP00000313272:K170N	K	-	3	2	NOP2	6543338	0.999000	0.42202	1.000000	0.80357	0.966000	0.64601	0.923000	0.28757	1.444000	0.47605	0.557000	0.71058	AAG		0.537	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		G	6673077	C	G	6673077	3	3	107	1	0	0	0	0	1	0	0	0	10569	680	24	5	1972	5	NOP2	12	6673077	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		6673077	127178818	221	28280										
KLHDC5	57542	hgsc.bcm.edu	37	chr12	27944691	27944691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaaactctatgccatcggagGgcaggccgtttctaacgttg	11	10	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:27944691G>A	ENST00000381271.2	+	2	1234	c.923G>A	c.(922-924)gGg>gAg	p.G308E		NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	308					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G308E(1)									GCCATCGGAGGGCAGGCCGTT	0.483																																																1	Substitution - Missense(1)	ovary(1)	12											216	206	210					12																	27944691		2203	4300	6503	27835958	SO:0001583	missense	57542			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"Kelch-like"	29252	protein-coding gene	gene with protein product			"kelch domain containing 5"	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.923G>A	12.37:g.27944691G>A	ENSP00000370671:p.Gly308Glu		27835958	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888575	0.91814	.	.	ENSG00000087448	ENST00000381271	D	0.99494	-6.01	4.86	4.86	0.63082	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96586	0.9434	10	0.87932	D	0	.	17.1803	0.86853	0.0:0.0:1.0:0.0	.	308	Q9P2K6	KLDC5_HUMAN	E	308	ENSP00000370671:G308E	ENSP00000370671:G308E	G	+	2	0	KLHDC5	27835958	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	9.069000	0.93967	2.505000	0.84491	0.650000	0.86243	GGG		0.483	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		A	27944691	G	A	27944691	3	1	107	1	0	0	0	0	1	0	0	0	8380	1232	43	3	929	3	KLHDC5	12	27944691	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	21271614	27944691	105907204	222	28281										
CCDC91	55297	hgsc.bcm.edu	37	chr12	28605481	28605481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aagaaaaaatttagaaaaagCgcatgctgaagaaagggaat	10	3	0	4	rs544457452		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:28605481C>T	ENST00000545336.1	+	14	1414	c.995C>T	c.(994-996)gCg>gTg	p.A332V	CCDC91_ENST00000381256.1_Missense_Mutation_p.A296V|CCDC91_ENST00000306172.5_Missense_Mutation_p.A302V|CCDC91_ENST00000539107.1_Missense_Mutation_p.A296V|CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000381259.1_Missense_Mutation_p.A332V			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	332	Homodimerization.				protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TTAGAAAAAGCGCATGCTGAA	0.303													C|||	1	0.000199681	8e-04	0	5008	,	,		13736	0		0	False		,,,				2504	0															0			12											63	73	70					12																	28605481		2201	4290	6491	28496748	SO:0001583	missense	55297			AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"GGA binding partner"					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.995C>T	12.37:g.28605481C>T	ENSP00000438040:p.Ala332Val		28496748	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.253|3.253	-0.152939|-0.152939	0.06585|0.06585	.|.	.|.	ENSG00000123106|ENSG00000123106	ENST00000536154;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000545737;ENST00000381259;ENST00000381256;ENST00000306172;ENST00000535212|ENST00000542801	T;T;T;T;T;T;T;T;T|.	0.43688|.	1.93;0.94;1.79;1.62;1.79;1.62;0.94;1.62;1.25|.	5.43|5.43	-5.23|-5.23	0.02798|0.02798	.|.	1.291780|.	0.05034|.	N|.	0.475075|.	T|T	0.14227|0.14227	0.0344|0.0344	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|T	0.31251|0.31251	-0.9950|-0.9950	10|5	0.02654|.	T|.	1|.	1.0994|1.0994	15.1195|15.1195	0.72432|0.72432	0.0:0.1658:0.0:0.8342|0.0:0.1658:0.0:0.8342	.|.	296;332;302|.	Q7Z6B0-3;Q7Z6B0;Q7Z6B0-2|.	.;CCD91_HUMAN;.|.	V|C	72;296;332;332;332;332;296;302;31|3	ENSP00000444440:A72V;ENSP00000440513:A296V;ENSP00000445660:A332V;ENSP00000438040:A332V;ENSP00000442544:A332V;ENSP00000370658:A332V;ENSP00000370655:A296V;ENSP00000305075:A302V;ENSP00000445999:A31V|.	ENSP00000305075:A302V|.	A|R	+|+	2|1	0|0	CCDC91|CCDC91	28496748|28496748	0.006000|0.006000	0.16342|0.16342	0.002000|0.002000	0.10522|0.10522	0.969000|0.969000	0.65631|0.65631	-0.162000|-0.162000	0.10012|0.10012	-0.915000|-0.915000	0.03823|0.03823	0.585000|0.585000	0.79938|0.79938	GCG|CGC		0.303	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318		T	28605481	C	T	28605481	3	4	107	1	0	0	0	0	1	0	0	0	2876	768	27	1	1033	1	CCDC91	12	28605481	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	660790	28605481	105246414	223	28282										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29628042	29628042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaagccttgtaaacgattttTaccatcacttttaaagtata	5	7	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:29628042T>C	ENST00000318184.5	-	14	1551	c.1552A>G	c.(1552-1554)Aaa>Gaa	p.K518E	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	518	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AAACGATTTTTACCATCACTT	0.333																																																0			12											55	51	52					12																	29628042		1842	4087	5929	29519309	SO:0001583	missense	341350			BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1552A>G	12.37:g.29628042T>C	ENSP00000326708:p.Lys518Glu		29519309		Missense_Mutation	SNP	ENST00000318184.5	37		.	.	.	.	.	.	.	.	.	.	T	0.016	-1.515609	0.00975	.	.	ENSG00000187950	ENST00000318184	T	0.58652	0.32	2.45	0.533	0.17121	CUB (5);	.	.	.	.	T	0.20210	0.0486	N	0.01096	-1.015	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.30387	-0.9980	9	0.02654	T	1	.	6.936	0.24466	0.0:0.7456:0.0:0.2544	.	518	Q7RTY7	OVCH1_HUMAN	E	518	ENSP00000326708:K518E	ENSP00000326708:K518E	K	-	1	0	OVCH1	29519309	0.803000	0.28956	0.114000	0.21550	0.059000	0.15707	1.221000	0.32503	0.118000	0.18165	0.260000	0.18958	AAA		0.333	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		C	29628042	T	C	29628042	3	2	107	1	0	0	0	0	1	0	0	0	11354	1763	61	4	1912	4	OVCH1	12	29628042	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1022561	29628042	104223853	224	28283										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29629219	29629219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gactaaatttgacagcaaagTcctcaaatgtcaactgtgca	7	9	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:29629219T>C	ENST00000318184.5	-	13	1390	c.1391A>G	c.(1390-1392)gAc>gGc	p.D464G	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	464	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					GACAGCAAAGTCCTCAAATGT	0.383																																																0			12											158	148	151					12																	29629219		1855	4107	5962	29520486	SO:0001583	missense	341350			BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1391A>G	12.37:g.29629219T>C	ENSP00000326708:p.Asp464Gly		29520486		Missense_Mutation	SNP	ENST00000318184.5	37		.	.	.	.	.	.	.	.	.	.	T	13.99	2.401884	0.42613	.	.	ENSG00000187950	ENST00000318184	T	0.57907	0.37	2.83	0.34	0.15985	CUB (5);	.	.	.	.	T	0.45955	0.1368	M	0.71206	2.165	0.20764	N	0.99985	B	0.18610	0.029	B	0.21708	0.036	T	0.38156	-0.9674	9	0.23891	T	0.37	.	5.1171	0.14840	0.0:0.1066:0.1822:0.7112	.	464	Q7RTY7	OVCH1_HUMAN	G	464	ENSP00000326708:D464G	ENSP00000326708:D464G	D	-	2	0	OVCH1	29520486	1.000000	0.71417	0.066000	0.19879	0.257000	0.26127	1.132000	0.31418	0.055000	0.16094	-0.323000	0.08544	GAC		0.383	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		C	29629219	T	C	29629219	3	2	107	1	0	0	0	0	1	0	0	0	11354	1667	58	4	2077	4	OVCH1	12	29629219	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1177	29629219	104222676	225	28284										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56481924	56481924	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	accaagtatcagtatggaggAgtttgtgtagccagctgtcc	12	8	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:56481924A>G	ENST00000267101.3	+	7	1292	c.852A>G	c.(850-852)ggA>ggG	p.G284G	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Silent_p.G225G	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	284					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			AGTATGGAGGAGTTTGTGTAG	0.468																																																0			12											66	62	64					12																	56481924		2203	4300	6503	54768191	SO:0001819	synonymous_variant	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.852A>G	12.37:g.56481924A>G			54768191	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																				0.468	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			G	56481924	A	G	56481924	2	3	107	1	0	0	0	0	0	0	0	1	5221	291	11	4		4	ERBB3	12	56481924	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	26852705	56481924	77369971	226	28285										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66849241	66849241	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcctcatcatggttccacgTgggctggtggagtagaggct	14	10	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:66849241T>C	ENST00000398016.3	-	10	1214	c.1146A>G	c.(1144-1146)ccA>ccG	p.P382P	GRIP1_ENST00000359742.4_Silent_p.P434P|GRIP1_ENST00000286445.7_Silent_p.P434P	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.P382P(1)		NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TGGTTCCACGTGGGCTGGTGG	0.488																																																1	Substitution - coding silent(1)	ovary(1)	12											159	156	157					12																	66849241		1949	4155	6104	65135508	SO:0001819	synonymous_variant	85329			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1146A>G	12.37:g.66849241T>C			65135508	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.958|9.958	1.222027|1.222027	0.22457|0.22457	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000543172	.|.	.|.	.|.	5.51|5.51	-1.91|-1.91	0.07641|0.07641	.|.	.|.	.|.	.|.	.|.	T|T	0.43277|0.43277	0.1240|0.1240	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.31752|0.31752	-0.9932|-0.9932	4|4	.|.	.|.	.|.	-11.5531|-11.5531	4.2799|4.2799	0.10827|0.10827	0.3275:0.1886:0.0:0.4839|0.3275:0.1886:0.0:0.4839	.|.	.|.	.|.	.|.	R|A	249|202	.|.	.|.	H|T	-|-	2|1	0|0	GRIP1|GRIP1	65135508|65135508	0.010000|0.010000	0.17322|0.17322	0.997000|0.997000	0.53966|0.53966	0.980000|0.980000	0.70556|0.70556	-1.237000|-1.237000	0.02922|0.02922	-0.137000|-0.137000	0.11455|0.11455	-0.441000|-0.441000	0.05720|0.05720	CAC|ACG		0.488	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			C	66849241	T	C	66849241	2	2	107	1	0	0	0	0	0	0	0	1	6808	1683	59	4		4	GRIP1	12	66849241	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	10367317	66849241	67002654	227	28286										
NAV3	89795	hgsc.bcm.edu	37	chr12	78522503	78522503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagatataccccatcatctcGgcaggccaaccaagaagagg	9	13	2	3	rs377221679		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:78522503G>A	ENST00000397909.2	+	18	4471	c.4298G>A	c.(4297-4299)cGg>cAg	p.R1433Q	NAV3_ENST00000536525.2_Missense_Mutation_p.R1433Q|NAV3_ENST00000266692.7_Missense_Mutation_p.R1256Q|NAV3_ENST00000228327.6_Missense_Mutation_p.R1433Q			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1433	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CCATCATCTCGGCAGGCCAAC	0.512										HNSCC(70;0.22)																																						0			12											132	129	130					12																	78522503		1982	4174	6156	77046634	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4298G>A	12.37:g.78522503G>A	ENSP00000381007:p.Arg1433Gln		77046634	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	10.69	1.422437	0.25639	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	T;T;T;T;T	0.27256	1.88;1.89;1.88;1.68;2.66	5.81	5.81	0.92471	.	0.000000	0.36778	U	0.002418	T	0.30198	0.0757	N	0.10945	0.07	0.80722	D	1	P;P;D;P	0.89917	0.614;0.626;1.0;0.897	B;B;D;B	0.83275	0.037;0.05;0.996;0.127	T	0.03086	-1.1074	10	0.02654	T	1	-14.3859	20.0755	0.97742	0.0:0.0:1.0:0.0	.	1433;1256;1433;1433	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.;.;NAV3_HUMAN;.	Q	1433;1433;1433;1256;54;62	ENSP00000446132:R1433Q;ENSP00000381007:R1433Q;ENSP00000228327:R1433Q;ENSP00000266692:R1256Q;ENSP00000448303:R62Q	ENSP00000228327:R1433Q	R	+	2	0	NAV3	77046634	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.787000	0.85759	2.749000	0.94314	0.460000	0.39030	CGG		0.512	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78522503	G	A	78522503	3	1	107	1	0	0	0	0	1	0	0	0	10215	1116	39	1	4368	1	NAV3	12	78522503	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	11673262	78522503	55329392	228	28287										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80190724	80190724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgatactggcctataacgctGgtaagtctgtgaaacattaa	9	7	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:80190724G>T	ENST00000450142.2	-	17	2565	c.2299C>A	c.(2299-2301)Cag>Aag	p.Q767K	PPP1R12A_ENST00000550107.1_Missense_Mutation_p.Q711K|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.Q680K|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.Q767K|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.Q767K	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	767	Interaction with ROCK2.				centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						CTATAACGCTGGTAAGTCTGT	0.328																																																0			12											145	137	140					12																	80190724		1872	4108	5980	78714855	SO:0001583	missense	4659			D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.2299C>A	12.37:g.80190724G>T	ENSP00000389168:p.Gln767Lys		78714855	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	G	8.279	0.815032	0.16607	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107	T;T;T;T;T	0.34667	1.39;1.39;1.4;1.41;1.35	5.79	3.94	0.45596	.	0.430705	0.27677	N	0.018303	T	0.24928	0.0605	L	0.34521	1.04	0.30250	N	0.79414	B;B;B	0.18310	0.007;0.027;0.004	B;B;B	0.19391	0.009;0.025;0.004	T	0.22277	-1.0221	10	0.06757	T	0.87	.	12.8595	0.57906	0.0:0.1247:0.7454:0.1299	.	767;711;767	O14974-2;O14974-3;O14974	.;.;MYPT1_HUMAN	K	767;767;767;711;708;767;767;680;711	ENSP00000261207:Q767K;ENSP00000389168:Q767K;ENSP00000416769:Q767K;ENSP00000449514:Q680K;ENSP00000446855:Q711K	ENSP00000261207:Q767K	Q	-	1	0	PPP1R12A	78714855	1.000000	0.71417	0.907000	0.35723	0.980000	0.70556	4.840000	0.62817	0.751000	0.32900	0.655000	0.94253	CAG		0.328	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		T	80190724	G	T	80190724	3	4	107	1	0	0	0	0	1	0	0	0	12388	1357	47	2	829	2	PPP1R12A	12	80190724	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	1668221	80190724	53661171	229	28288										
DCN	1634	hgsc.bcm.edu	37	chr12	91552212	91552212	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgattcttggacagataaagTcgttccaacttcaccaaagg	8	9	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:91552212T>C	ENST00000052754.5	-	4	900	c.399A>G	c.(397-399)cgA>cgG	p.R133R	DCN_ENST00000441303.2_Intron|DCN_ENST00000303320.3_Intron|DCN_ENST00000420120.2_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000393155.1_Silent_p.R133R|DCN_ENST00000425043.1_Intron|DCN_ENST00000547568.2_Intron|DCN_ENST00000456569.2_Intron|DCN_ENST00000552962.1_Silent_p.R133R	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	133					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						ACAGATAAAGTCGTTCCAACT	0.408																																																0			12											134	129	131					12																	91552212		2203	4300	6503	90076343	SO:0001819	synonymous_variant	1634			AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.399A>G	12.37:g.91552212T>C			90076343	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Silent	SNP	ENST00000052754.5	37	CCDS9039.1																																																																																				0.408	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		C	91552212	T	C	91552212	2	2	107	1	0	0	0	0	0	0	0	1	4303	1654	58	4		4	DCN	12	91552212	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	11361488	91552212	42299683	230	28289										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100720404	100720404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttacctcttttaataggttcGtgtaaattcattagtgtgct	7	6	2	0	rs199548769		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:100720404G>A	ENST00000360820.2	+	12	1951	c.1514G>A	c.(1513-1515)cGt>cAt	p.R505H		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	505					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)	p.R509H(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						TAATAGGTTCGTGTAAATTCA	0.279																																																1	Substitution - Missense(1)	ovary(1)	12											95	91	93					12																	100720404		2203	4299	6502	99244535	SO:0001583	missense	55681			AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1514G>A	12.37:g.100720404G>A	ENSP00000354061:p.Arg505His		99244535	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323184	0.95708	.	.	ENSG00000136021	ENST00000549687;ENST00000360820	T;T	0.55052	0.54;0.54	5.38	5.38	0.77491	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76976	0.4063	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80420	-0.1390	10	0.87932	D	0	.	19.497	0.95077	0.0:0.0:1.0:0.0	.	505	Q6P3W7	SCYL2_HUMAN	H	505	ENSP00000448366:R505H;ENSP00000354061:R505H	ENSP00000354061:R505H	R	+	2	0	SCYL2	99244535	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.672000	0.98629	2.677000	0.91161	0.563000	0.77884	CGT		0.279	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		A	100720404	G	A	100720404	3	1	107	1	0	0	0	0	1	0	0	0	13985	1145	40	1	1556	1	SCYL2	12	100720404	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	9168192	100720404	33131491	231	28290										
ALDH2	217	hgsc.bcm.edu	37	chr12	112228251	112228251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gttgcagtggaatttcccgcTcctgatgcaagcatggaagc	12	10	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:112228251T>C	ENST00000261733.2	+	6	627	c.566T>C	c.(565-567)cTc>cCc	p.L189P	ALDH2_ENST00000416293.3_Missense_Mutation_p.L142P|RP11-162P23.2_ENST00000546840.2_Missense_Mutation_p.S186P	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	189					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	AATTTCCCGCTCCTGATGCAA	0.562			T	HMGA2	leiomyoma																																		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	0			12											128	108	115					12																	112228251		2203	4300	6503	110712634	SO:0001583	missense	217			M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.566T>C	12.37:g.112228251T>C	ENSP00000261733:p.Leu189Pro		110712634	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	37	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.075643	0.76415	.	.	ENSG00000257767;ENSG00000111275;ENSG00000111275;ENSG00000111275	ENST00000546840;ENST00000416293;ENST00000261733;ENST00000552234	T;T	0.80738	-1.41;-1.41	5.58	5.58	0.84498	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.062079	0.64402	D	0.000003	D	0.92251	0.7542	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.97110	0.981;1.0	D	0.94179	0.7430	10	0.87932	D	0	.	15.7419	0.77905	0.0:0.0:0.0:1.0	.	142;189	E7EUE5;P05091	.;ALDH2_HUMAN	P	170;142;189;49	ENSP00000403349:L142P;ENSP00000261733:L189P	ENSP00000261733:L189P	L	+	2	0	ALDH2;RP11-162P23.2	110712634	1.000000	0.71417	0.372000	0.25991	0.780000	0.44128	7.698000	0.84413	2.113000	0.64589	0.460000	0.39030	CTC		0.562	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		C	112228251	T	C	112228251	3	2	107	1	0	0	0	0	1	0	0	0	496	1551	54	4	588	4	ALDH2	12	112228251	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	11507847	112228251	21623644	232	28291										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112915744	112915744	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgcctgcaaaacacggtgaaTgacttttggcggatggtgtt	13	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:112915744T>C	ENST00000351677.2	+	9	1215	c.1017T>C	c.(1015-1017)aaT>aaC	p.N339N	PTPN11_ENST00000392597.1_Silent_p.N339N	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	339	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ACACGGTGAATGACTTTTGGC	0.418			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12											70	64	66					12																	112915744		2203	4300	6503	111400127	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1017T>C	12.37:g.112915744T>C			111400127	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			C	112915744	T	C	112915744	2	2	107	1	0	0	0	0	0	0	0	1	12815	1461	51	4		4	PTPN11	12	112915744	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	687493	112915744	20936151	233	28292										
OAS1	4938	hgsc.bcm.edu	37	chr12	113355473	113355473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acccatgctttaagaattggGatgggtccccagtgagctcc	11	11	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:113355473G>A	ENST00000202917.5	+	5	1269	c.1006G>A	c.(1006-1008)Gat>Aat	p.D336N	OAS1_ENST00000452357.2_Missense_Mutation_p.D336N|RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Missense_Mutation_p.D336N|OAS1_ENST00000551241.1_Missense_Mutation_p.D336N	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	336					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						TAAGAATTGGGATGGGTCCCC	0.557																																																0			12											137	143	141					12																	113355473		2203	4300	6503	111839856	SO:0001583	missense	4938			X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1006G>A	12.37:g.113355473G>A	ENSP00000202917:p.Asp336Asn		111839856	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.688129	0.29962	.	.	ENSG00000089127	ENST00000202917;ENST00000445409;ENST00000452357;ENST00000551241;ENST00000377508;ENST00000553152	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.05	1.01	0.19927	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	3.364860	0.00649	N	0.000548	T	0.43188	0.1236	L	0.33710	1.025	0.09310	N	0.999999	B;P;B;B	0.34977	0.031;0.478;0.423;0.204	B;B;B;B	0.41813	0.032;0.363;0.367;0.248	T	0.30416	-0.9979	10	0.45353	T	0.12	-19.6819	4.0083	0.09611	0.2711:0.0:0.5652:0.1637	.	336;336;336;336	F8VXY3;P00973;P00973-3;P00973-2	.;OAS1_HUMAN;.;.	N	336;336;336;336;336;82	ENSP00000202917:D336N;ENSP00000388001:D336N;ENSP00000415721:D336N;ENSP00000448790:D336N;ENSP00000449053:D82N	ENSP00000202917:D336N	D	+	1	0	OAS1	111839856	0.000000	0.05858	0.005000	0.12908	0.075000	0.17131	0.076000	0.14712	0.328000	0.23435	0.655000	0.94253	GAT		0.557	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			A	113355473	G	A	113355473	3	1	107	1	0	0	0	0	1	0	0	0	10830	1174	41	3	1024	3	OAS1	12	113355473	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	439729	113355473	20496422	234	28293										
RASAL1	8437	hgsc.bcm.edu	37	chr12	113568721	113568721	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctcgtcgtccactttcactaGgcagtaggggtcgctgctcc	11	14	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:113568721G>T	ENST00000261729.5	-	3	406	c.91C>A	c.(91-93)Cta>Ata	p.L31I	RASAL1_ENST00000546530.1_Missense_Mutation_p.L31I|RASAL1_ENST00000446861.3_Missense_Mutation_p.L31I|RASAL1_ENST00000548055.1_Missense_Mutation_p.L31I|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	31	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)	p.L31L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						ACTTTCACTAGGCAGTAGGGG	0.617																																																1	Substitution - coding silent(1)	ovary(1)	12											62	52	55					12																	113568721		2203	4300	6503	112053104	SO:0001583	missense	8437			AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.91C>A	12.37:g.113568721G>T	ENSP00000261729:p.Leu31Ile		112053104	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	G	3.148	-0.174845	0.06421	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	4.83	1.49	0.22878	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.202424	0.39909	N	0.001231	T	0.28101	0.0693	N	0.01209	-0.955	0.24909	N	0.992059	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B	0.11329	0.006;0.006;0.004;0.006;0.001;0.006;0.004	T	0.35943	-0.9768	10	0.02654	T	1	.	7.1759	0.25744	0.1111:0.0:0.4633:0.4256	.	31;31;31;43;31;31;31	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	I	31	ENSP00000450244:L31I;ENSP00000261729:L31I;ENSP00000395920:L31I;ENSP00000448510:L31I	ENSP00000261729:L31I	L	-	1	2	RASAL1	112053104	1.000000	0.71417	0.713000	0.30519	0.762000	0.43233	1.256000	0.32921	0.128000	0.18479	0.491000	0.48974	CTA		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		T	113568721	G	T	113568721	3	4	107	1	0	0	0	0	1	0	0	0	13100	991	35	2	2403	2	RASAL1	12	113568721	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	213248	113568721	20283174	235	28294										
PRKAB1	5564	hgsc.bcm.edu	37	chr12	120111862	120111862	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tggacgcacgacccttccgaGgtactcttcctcccacctct	7	18	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:120111862G>T	ENST00000229328.5	+	3	909	c.417G>T	c.(415-417)gaG>gaT	p.E139D	PRKAB1_ENST00000540121.1_5'UTR|PRKAB1_ENST00000541640.1_Splice_Site_p.E139D	NM_006253.4	NP_006244.2	Q9Y478	AAKB1_HUMAN	protein kinase, AMP-activated, beta 1 non-catalytic subunit	139	Glycogen-binding domain. {ECO:0000250}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein kinase activity (GO:0004672)			endometrium(2)|large_intestine(3)|lung(5)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Metformin(DB00331)	ACCCTTCCGAGGTACTCTTCC	0.532																																																0			12											134	113	120					12																	120111862		2203	4300	6503	118596245	SO:0001630	splice_region_variant	5564			BC001823	CCDS9191.1	12q24.1-q24.3	2008-05-14			ENSG00000111725	ENSG00000111725			9378	protein-coding gene	gene with protein product	"AMPK beta 1"	602740				8557660	Standard	NM_006253		Approved		uc001txg.3	Q9Y478	OTTHUMG00000168954	ENST00000229328.5:c.417+1G>T	12.37:g.120111862G>T			118596245	Q9UBV0|Q9UE20|Q9UEX2|Q9Y6V8	Missense_Mutation	SNP	ENST00000229328.5	37	CCDS9191.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.776655	0.70107	.	.	ENSG00000111725	ENST00000229328;ENST00000541640;ENST00000539596	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	L	0.41710	1.295	0.80722	D	1	P	0.36789	0.57	B	0.32533	0.147	T	0.41270	-0.9518	9	0.14252	T	0.57	-15.339	20.6634	0.99662	0.0:0.0:1.0:0.0	.	139	Q9Y478	AAKB1_HUMAN	D	139;139;102	.	ENSP00000229328:E139D	E	+	3	2	PRKAB1	118596245	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.229000	0.95273	2.894000	0.99253	0.655000	0.94253	GAG		0.532	PRKAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401731.2	NM_006253	Missense_Mutation	T	120111862	G	T	120111862	5	4	107	1	0	0	0	0	0	0	1	0	12529	1014	35	2	427	2	PRKAB1	12	120111862	Splice_Site	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	6543141	120111862	13740033	236	28295										
ATP6V0A2	23545	hgsc.bcm.edu	37	chr12	124233316	124233316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cccagccagtaaaacaagtgGcctttacacagggcaggtga	11	11	0	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:124233316G>A	ENST00000330342.3	+	15	2167	c.1919G>A	c.(1918-1920)gGc>gAc	p.G640D		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	640					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		AAAACAAGTGGCCTTTACACA	0.423																																																0			12											84	86	85					12																	124233316		2203	4300	6503	122799269	SO:0001583	missense	23545			AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"ATPases / V-type"	18481	protein-coding gene	gene with protein product	"infantile malignant osteopetrosis"	611716	"infantile malignant osteopetrosis", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 2", "ATPase, H+ transporting, lysosomal V0 subunit A2"			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.1919G>A	12.37:g.124233316G>A	ENSP00000332247:p.Gly640Asp		122799269	A8K026|Q6NUM0	Missense_Mutation	SNP	ENST00000330342.3	37	CCDS9254.1	.	.	.	.	.	.	.	.	.	.	G	8.507	0.865619	0.17250	.	.	ENSG00000185344	ENST00000330342	D	0.85629	-2.01	5.47	4.57	0.56435	.	0.165435	0.53938	D	0.000060	T	0.71753	0.3377	N	0.17723	0.515	0.25919	N	0.983132	B	0.10296	0.003	B	0.15052	0.012	T	0.55970	-0.8056	10	0.30854	T	0.27	-19.8506	7.294	0.26383	0.1333:0.2729:0.5938:0.0	.	640	Q9Y487	VPP2_HUMAN	D	640	ENSP00000332247:G640D	ENSP00000332247:G640D	G	+	2	0	ATP6V0A2	122799269	0.000000	0.05858	0.357000	0.25798	0.348000	0.29142	0.198000	0.17217	2.724000	0.93272	0.561000	0.74099	GGC		0.423	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463		A	124233316	G	A	124233316	3	1	107	1	0	0	0	0	1	0	0	0	1170	1203	42	3	1977	3	ATP6V0A2	12	124233316	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4121454	124233316	9618579	237	28296										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129569055	129569055	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tacccacctcctgctggagaCgatgggcactctccaaccct	8	17	1	1	rs542855447		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:129569055C>T	ENST00000422113.2	-	6	1962	c.1636G>A	c.(1636-1638)Gtc>Atc	p.V546I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.V84I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	546					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		CTGCTGGAGACGATGGGCACT	0.587													C|||	1	0.000199681	0	0	5008	,	,		20268	0		0	False		,,,				2504	0.001															0			12											66	49	55					12																	129569055		2203	4300	6503	128135008	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1636G>A	12.37:g.129569055C>T	ENSP00000408581:p.Val546Ile		128135008	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	0.820	-0.748914	0.03065	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.13657	2.57;2.57	4.79	0.685	0.18009	.	1.123440	0.06606	N	0.754684	T	0.09512	0.0234	L	0.36672	1.1	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.09377	0.001;0.004	T	0.40942	-0.9536	9	.	.	.	-30.9012	1.3126	0.02101	0.1506:0.4031:0.1482:0.2981	.	546;84	Q14C87;Q14C87-2	T132D_HUMAN;.	I	84;546	ENSP00000374092:V84I;ENSP00000408581:V546I	.	V	-	1	0	TMEM132D	128135008	0.000000	0.05858	0.125000	0.21846	0.102000	0.19082	-0.286000	0.08399	0.058000	0.16222	0.561000	0.74099	GTC		0.587	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	129569055	C	T	129569055	3	4	107	1	0	0	0	0	1	0	0	0	16086	536	19	1	1679	1	TMEM132D	12	129569055	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5335739	129569055	4282840	238	28297										
ZNF268	10795	hgsc.bcm.edu	37	chr12	133764550	133764550	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggccaagggactcctggtctGcaacctctccctggaacacc	10	16	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr12:133764550G>A	ENST00000536435.2	+	3	456	c.126G>A	c.(124-126)ctG>ctA	p.L42L	ZNF268_ENST00000416488.1_Silent_p.L207L|ZNF268_ENST00000228289.5_Silent_p.L42L|ZNF268_ENST00000537565.1_Intron|ZNF268_ENST00000542711.2_Intron|ZNF268_ENST00000542986.2_Silent_p.L42L|ZNF268_ENST00000536899.2_Intron|ZNF268_ENST00000541009.2_Silent_p.L42L|ZNF268_ENST00000539248.2_Silent_p.L42L|CTD-2140B24.4_ENST00000540096.2_Silent_p.L207L|ZNF268_ENST00000541211.2_Silent_p.L42L|ZNF268_ENST00000592241.1_Intron	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	42					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CTCCTGGTCTGCAACCTCTCC	0.512																																																0			12											42	43	43					12																	133764550		1864	4117	5981	132274623	SO:0001819	synonymous_variant	10795			X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"Zinc fingers, C2H2-type", "-"	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.126G>A	12.37:g.133764550G>A			132274623	Q8TDG8|Q96RH4|Q9BZJ9	Silent	SNP	ENST00000536435.2	37	CCDS45012.1																																																																																				0.512	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943		A	133764550	G	A	133764550	2	1	107	1	0	0	0	0	0	0	0	1	17846	1306	46	3		3	ZNF268	12	133764550	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4195495	133764550	87345	239	28298										
ATP12A	479	hgsc.bcm.edu	37	chr13	25264509	25264509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tccgagattccgagaagaagAccatcccttcagagcagctg	10	12	1	5			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:25264509A>G	ENST00000381946.3	+	6	747	c.580A>G	c.(580-582)Acc>Gcc	p.T194A	ATP12A_ENST00000218548.6_Missense_Mutation_p.T194A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	194					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CGAGAAGAAGACCATCCCTTC	0.567																																					Pancreas(156;1582 1935 18898 22665 26498)											0			13											119	113	115					13																	25264509		2203	4300	6503	24162509	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.580A>G	13.37:g.25264509A>G	ENSP00000371372:p.Thr194Ala		24162509	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	3.748	-0.052116	0.07362	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.91686	-2.89;-2.89	4.74	-6.64	0.01801	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	1.697610	0.03175	N	0.171294	D	0.92734	0.7690	M	0.87381	2.88	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.12837	0.008;0.008	T	0.76913	-0.2783	10	0.27082	T	0.32	.	18.5701	0.91132	0.1929:0.0:0.8071:0.0	.	194;194	P54707-2;P54707	.;AT12A_HUMAN	A	194	ENSP00000218548:T194A;ENSP00000371372:T194A	ENSP00000218548:T194A	T	+	1	0	ATP12A	24162509	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.052000	0.11865	-1.330000	0.02255	-0.263000	0.10527	ACC		0.567	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25264509	A	G	25264509	3	3	107	1	0	0	0	0	1	0	0	0	1123	275	10	4	602	4	ATP12A	13	25264509	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10		25264509	89905369	240	28299										
FLT3	2322	hgsc.bcm.edu	37	chr13	28592653	28592653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcatgatatctcgagccaatCcaaagtcacatatcttcacc	4	13	5	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:28592653C>T	ENST00000241453.7	-	20	2573	c.2492G>A	c.(2491-2493)gGa>gAa	p.G831E	FLT3_ENST00000380982.4_Missense_Mutation_p.G831E|FLT3_ENST00000537084.1_Intron	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	831	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.G831E(3)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCGAGCCAATCCAAAGTCACA	0.453			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	13											192	144	160					13																	28592653		2203	4300	6503	27490653	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2492G>A	13.37:g.28592653C>T	ENSP00000241453:p.Gly831Glu		27490653	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	C	32	5.123677	0.94429	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.99264	-5.65;-5.65	5.84	5.84	0.93424	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.99576	0.9847	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98406	1.0570	10	0.87932	D	0	.	20.221	0.98325	0.0:1.0:0.0:0.0	.	831	P36888	FLT3_HUMAN	E	831	ENSP00000241453:G831E;ENSP00000370369:G831E	ENSP00000241453:G831E	G	-	2	0	FLT3	27490653	1.000000	0.71417	0.710000	0.30468	0.926000	0.56050	7.815000	0.86186	2.792000	0.96026	0.556000	0.70494	GGA		0.453	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			T	28592653	C	T	28592653	3	4	107	1	0	0	0	0	1	0	0	0	5961	855	30	3	509	3	FLT3	13	28592653	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3328144	28592653	86577225	241	28300										
BRCA2	90634	hgsc.bcm.edu	37	chr13	32972720	32972720	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agctcttttgtctggttcaaCaggagaaaaacaatttatat	7	6	3	1	rs80358388|rs397507567		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:32972720C>T	ENST00000380130.2	-	0	3046				BRCA2_ENST00000544455.1_Missense_Mutation_p.T3357I|BRCA2_ENST00000380152.3_Missense_Mutation_p.T3357I	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1									p.T3357R(1)		large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		TCTGGTTCAACAGGAGAAAAA	0.363																																																1	Substitution - Missense(1)	breast(1)	13											64	68	67					13																	32972720		2203	4300	6503	31870720	SO:0001628	intergenic_variant	675			U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		13.37:g.32972720C>T			31870720	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	C	6.392	0.440417	0.12104	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00695	5.83;5.83	5.45	2.18	0.27775	.	0.673899	0.14154	N	0.337829	T	0.00384	0.0012	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	10	0.22706	T	0.39	.	2.418	0.04441	0.142:0.5312:0.1378:0.189	.	3357	P51587	BRCA2_HUMAN	I	3357	ENSP00000369497:T3357I;ENSP00000439902:T3357I	ENSP00000369497:T3357I	T	+	2	0	BRCA2	31870720	0.260000	0.24053	0.003000	0.11579	0.762000	0.43233	0.608000	0.24223	0.086000	0.17137	-0.444000	0.05651	ACA		0.363	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818		T	32972720	C	T	32972720	1	4	107	0	1	0	0	0	0	0	0	0	1502	478	17	3		3	BRCA2	13	32972720	IGR	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	4380067	32972720	82197158	242	28301										
HTR2A	3356	hgsc.bcm.edu	37	chr13	47466581	47466582	+	Missense_Mutation	DNP	AA	AA	GG													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atgccttagttctggagttgAagcggctgtggtggatggga							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:47466581_47466582AA>GG	ENST00000378688.4	-	2	687_688	c.556_557TT>CC	c.(556-558)TTc>CCc	p.F186P	HTR2A_ENST00000542664.1_Missense_Mutation_p.F186P|HTR2A_ENST00000543956.1_Missense_Mutation_p.F102P			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	186					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.F186L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TCTGGAGTTGAAGCGGCTGTGG	0.495																																																1	Substitution - Missense(1)	ovary(1)	13																																								46364582|46364583	SO:0001583	missense	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.556_557delinsGG	13.37:g.47466581_47466582delinsGG	ENSP00000367959:p.Phe186Pro		46364582|46364583	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1																																																																																				0.495	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		GG	47466582	AA	GG	47466581	3	3	107	1	0	0	0	0	1	0	0	0	7462	246	9	4	866	4	HTR2A	13	47466581	Missense_Mutation	DNP	AA	TCGA-DY-A1DG-01A-11D-A152-10	14493861	47466581	67703297	243	28302										
RB1	5925	hgsc.bcm.edu	37	chr13	48941659	48941659	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctttctaaacgatacgaagaAatttatcttaaaaataaaga	4	5	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:48941659A>G	ENST00000267163.4	+	10	1107	c.969A>G	c.(967-969)gaA>gaG	p.E323E		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	323					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(7)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GATACGAAGAAATTTATCTTA	0.313		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	22	Whole gene deletion(15)|Unknown(7)	bone(11)|breast(5)|adrenal_gland(1)|eye(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											57	69	65					13																	48941659		2196	4281	6477	47839660	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.969A>G	13.37:g.48941659A>G			47839660	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.313	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48941659	A	G	48941659	2	3	107	1	0	0	0	0	0	0	0	1	13135	11	1	4		4	RB1	13	48941659	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	1475078	48941659	66228219	244	28303										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77740564	77740564	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgaacagatgtcaattttggTccatatcctgaattctgaac	7	8	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:77740564T>C	ENST00000544440.2	-	41	6143	c.6126A>G	c.(6124-6126)ggA>ggG	p.G2042G	MYCBP2_ENST00000407578.2_Silent_p.G2080G|MYCBP2_ENST00000357337.6_Silent_p.G2042G|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCAATTTTGGTCCATATCCTG	0.403																																																0			13											103	100	101					13																	77740564		2203	4300	6503	76638565	SO:0001819	synonymous_variant	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6126A>G	13.37:g.77740564T>C			76638565		Silent	SNP	ENST00000544440.2	37																																																																																					0.403	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77740564	T	C	77740564	2	2	107	1	0	0	0	0	0	0	0	1	10048	1654	58	4		4	MYCBP2	13	77740564	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	28798905	77740564	37429314	245	28304										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86370292	86370292	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	taaagaattgtgattgatatGaagttgtttcaggaggccaa	11	3	1	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:86370292G>A	ENST00000400286.2	-	2	950	c.352C>T	c.(352-354)Cat>Tat	p.H118Y		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	118					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TGATTGATATGAAGTTGTTTC	0.358																																																0			13											121	112	115					13																	86370292		1833	4083	5916	85268293	SO:0001583	missense	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.352C>T	13.37:g.86370292G>A	ENSP00000383143:p.His118Tyr		85268293	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123070	0.56613	.	.	ENSG00000184564	ENST00000400286	T	0.51071	0.72	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.57932	0.2087	L	0.28115	0.83	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	T	0.50056	-0.8872	10	0.30854	T	0.27	-21.3107	19.4432	0.94831	0.0:0.0:1.0:0.0	.	118	Q9H5Y7	SLIK6_HUMAN	Y	118	ENSP00000383143:H118Y	ENSP00000383143:H118Y	H	-	1	0	SLITRK6	85268293	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CAT		0.358	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		A	86370292	G	A	86370292	3	1	107	1	0	0	0	0	1	0	0	0	14784	1290	45	3	2177	3	SLITRK6	13	86370292	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8629728	86370292	28799586	246	28305										
FARP1	10160	hgsc.bcm.edu	37	chr13	99098444	99098444	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acaaacttctgcctgttcttCtacaaatcacaccaggtaag	5	12	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr13:99098444C>G	ENST00000319562.6	+	25	3154	c.2889C>G	c.(2887-2889)ttC>ttG	p.F963L	FARP1_ENST00000376586.2_Missense_Mutation_p.F994L|FARP1_ENST00000595437.1_Missense_Mutation_p.F994L	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	963	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GCCTGTTCTTCTACAAATCAC	0.547											OREG0022474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			13											100	95	97					13																	99098444		2203	4300	6503	97896445	SO:0001583	missense	10160			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.2889C>G	13.37:g.99098444C>G	ENSP00000322926:p.Phe963Leu	1341	97896445	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	C	35	5.472163	0.96274	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	T;T	0.12039	2.72;2.72	5.32	5.32	0.75619	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	M	0.66439	2.03	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.997;1.0	T	0.15321	-1.0441	10	0.87932	D	0	.	19.002	0.92838	0.0:1.0:0.0:0.0	.	963;994	Q9Y4F1;C9JME2	FARP1_HUMAN;.	L	994;963	ENSP00000365771:F994L;ENSP00000322926:F963L	ENSP00000322926:F963L	F	+	3	2	FARP1	97896445	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.037000	0.70956	2.486000	0.83907	0.561000	0.74099	TTC		0.547	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		G	99098444	C	G	99098444	3	3	107	1	0	0	0	0	1	0	0	0	5695	912	32	5	3206	5	FARP1	13	99098444	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	12728152	99098444	16071434	247	28306										
PABPN1	8106	hgsc.bcm.edu	37	chr14	23793419	23793419	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttccacgagcccgctaccgcGcccggaccaccaactacaac	7	20	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr14:23793419G>T	ENST00000216727.4	+	6	983	c.802G>T	c.(802-804)Gcc>Tcc	p.A268S	PABPN1_ENST00000556821.1_Missense_Mutation_p.A140S|BCL2L2-PABPN1_ENST00000553781.1_Missense_Mutation_p.A295S|BCL2L2-PABPN1_ENST00000557008.1_Missense_Mutation_p.A295S|PABPN1_ENST00000557702.1_Missense_Mutation_p.A140S|AL049829.1_ENST00000594872.1_5'Flank|PABPN1_ENST00000397276.2_Missense_Mutation_p.A268S	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	268	Necessary for homooligomerization.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CCGCTACCGCGCCCGGACCAC	0.567																																																0			14											77	78	78					14																	23793419		2203	4300	6503	22863259	SO:0001583	missense	0			AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"RNA binding motif (RRM) containing"	8565	protein-coding gene	gene with protein product		602279	"poly(A)-binding protein, nuclear 1"	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.802G>T	14.37:g.23793419G>T	ENSP00000216727:p.Ala268Ser		22863259	D3DS49|O43484	Missense_Mutation	SNP	ENST00000216727.4	37	CCDS9592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.14|12.14	1.847948|1.847948	0.32699|0.32699	.|.	.|.	ENSG00000258643;ENSG00000258643;ENSG00000100836;ENSG00000100836;ENSG00000100836;ENSG00000100836|ENSG00000100836	ENST00000553781;ENST00000557008;ENST00000216727;ENST00000397276;ENST00000556821;ENST00000557702|ENST00000555295	T;T;T;T;T;T|T	0.73897|0.74947	-0.79;-0.79;-0.79;-0.79;-0.79;-0.79|-0.89	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.063724|.	0.64402|.	D|.	0.000006|.	T|T	0.65780|0.65780	0.2724|0.2724	N|N	0.12182|0.12182	0.205|0.205	0.33998|0.33998	D|D	0.64991|0.64991	B;P;B|.	0.36733|.	0.047;0.567;0.228|.	B;B;B|.	0.34489|.	0.032;0.123;0.184|.	T|T	0.69862|0.69862	-0.5030|-0.5030	10|6	0.19590|.	T|.	0.45|.	-7.9693|-7.9693	18.1036|18.1036	0.89513|0.89513	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	268;268;295|.	Q86U42;Q86U42-2;G3V5R7|.	PABP2_HUMAN;.;.|.	S|L	295;295;268;268;140;140|67	ENSP00000451320:A295S;ENSP00000452479:A295S;ENSP00000216727:A268S;ENSP00000380446:A268S;ENSP00000451970:A140S;ENSP00000450724:A140S|ENSP00000451592:R67L	ENSP00000216727:A268S|.	A|R	+|+	1|2	0|0	PABPN1;RP11-124D2.2|PABPN1	22863259|22863259	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	5.232000|5.232000	0.65332|0.65332	2.581000|2.581000	0.87130|0.87130	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.567	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643		T	23793419	G	T	23793419	3	4	107	1	0	0	0	0	1	0	0	0	11399	1087	38	2	824	2	PABPN1	14	23793419	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		23793419	83556121	248	28307										
CHMP4A	29082	hgsc.bcm.edu	37	chr14	24680631	24680631	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccgtacccacatgtcctggtAggccttcttcatgctttggg	10	13	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr14:24680631A>G	ENST00000609024.1	-	3	397	c.349T>C	c.(349-351)Tac>Cac	p.Y117H	CHMP4A_ENST00000530996.1_Missense_Mutation_p.Y12H|MDP1_ENST00000532557.1_5'Flank|CHMP4A_ENST00000542700.2_5'UTR|CHMP4A_ENST00000347519.6_Missense_Mutation_p.Y160H|TM9SF1_ENST00000556387.1_Missense_Mutation_p.Y117H|AL136419.6_ENST00000565988.1_RNA|TM9SF1_ENST00000530611.1_Missense_Mutation_p.Y117H|NEDD8-MDP1_ENST00000604306.1_5'Flank			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	117	Intramolecular interaction with C- terminus. {ECO:0000250}.				endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		ATGTCCTGGTAGGCCTTCTTC	0.537																																																0			14											85	73	77					14																	24680631		2203	4300	6503	23750471	SO:0001583	missense	128866			AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"Charged multivesicular body proteins"	20274	protein-coding gene	gene with protein product		610051	"chromosome 14 open reading frame 123", "chromatin modifying protein 4A"	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.349T>C	14.37:g.24680631A>G	ENSP00000476412:p.Tyr117His		23750471	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.36|14.36	2.511028|2.511028	0.44660|0.44660	.|.	.|.	ENSG00000254505|ENSG00000100926;ENSG00000254692;ENSG00000254505;ENSG00000254505	ENST00000548308|ENST00000556387;ENST00000530611;ENST00000347519;ENST00000533011	.|T;T;T;T	.|0.71222	.|-0.55;-0.55;-0.55;-0.55	4.59|4.59	3.43|3.43	0.39272|0.39272	.|.	.|0.161391	.|0.29493	.|N	.|0.011995	T|T	0.19725|0.19725	0.0474|0.0474	N|N	0.00045|0.00045	-2.45|-2.45	0.32157|0.32157	N|N	0.583435|0.583435	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.09377	.|0.002;0.004	T|T	0.46512|0.46512	-0.9186|-0.9186	5|10	.|0.02654	.|T	.|1	-2.9377|-2.9377	4.5213|4.5213	0.11960|0.11960	0.7761:0.0:0.2239:0.0|0.7761:0.0:0.2239:0.0	.|.	.|117;160	.|Q9BY43;Q14D22	.|CHM4A_HUMAN;.	P|H	136|117;117;160;127	.|ENSP00000451949:Y117H;ENSP00000433967:Y117H;ENSP00000324205:Y160H;ENSP00000432575:Y127H	.|ENSP00000324205:Y160H	L|Y	-|-	2|1	0|0	AL096870.1|TM9SF1;AL096870.1;RP11-468E2.1	23750471|23750471	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.766000|5.766000	0.68843|0.68843	1.934000|1.934000	0.56057|0.56057	0.459000|0.459000	0.35465|0.35465	CTA|TAC		0.537	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169		G	24680631	A	G	24680631	3	3	107	1	0	0	0	0	1	0	0	0	3362	420	15	4	335	4	CHMP4A	14	24680631	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	887212	24680631	82668909	249	28308										
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32560989	32561009	+	In_Frame_Del	DEL	GCAGATTTCCAGTTATGTTTT	GCAGATTTCCAGTTATGTTTT	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgaagttaatggaaaagagaGcagatttccagttatgtttt							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	GCAGATTTCCAGTTATGTTTT	GCAGATTTCCAGTTATGTTTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr14:32560989_32561009delGCAGATTTCCAGTTATGTTTT	ENST00000345122.3	+	2	1429_1449	c.1114_1134delGCAGATTTCCAGTTATGTTTT	c.(1114-1134)gcagatttccagttatgttttdel	p.ADFQLCF372del	ARHGAP5_ENST00000432921.1_In_Frame_Del_p.ADFQLCF372del|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000556611.1_In_Frame_Del_p.ADFQLCF372del|ARHGAP5_ENST00000539826.2_In_Frame_Del_p.ADFQLCF372del	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	372	FF 2.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.D373N(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GGAAAAGAGAGCAGATTTCCAGTTATGTTTTGTGGTGCTAG	0.353																																					NSCLC(9;77 350 3443 29227 41353)											1	Substitution - Missense(1)	large_intestine(1)	14																																								31630760	SO:0001651	inframe_deletion	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1114_1134delGCAGATTTCCAGTTATGTTTT	14.37:g.32560989_32561009delGCAGATTTCCAGTTATGTTTT	ENSP00000371897:p.Ala372_Phe378del		31630740	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	In_Frame_Del	DEL	ENST00000345122.3	37	CCDS32062.1																																																																																				0.353	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		-	32561009	GCAGATTTCCAGTTATGTTTT	-	32560989	7	5	107	1	0	1	0	1	0	0	0	0	886	971	34	0	1116	0	ARHGAP5	14	32560989	In_Frame_Del	DEL	GCAGATTTCCAGTTATGTTTT	TCGA-DY-A1DG-01A-11D-A152-10	7880358	32560989	74788551	250	28309										
RTN1	6252	hgsc.bcm.edu	37	chr14	60212553	60212553	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttctcaggggtcttctcttgGgtagtggtttcaacagaagg	13	7	4	1	rs369834065		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr14:60212553G>A	ENST00000267484.5	-	2	1223	c.888C>T	c.(886-888)acC>acT	p.T296T		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	296					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCTTCTCTTGGGTAGTGGTTT	0.498																																																0			14						G		0,4406		0,0,2203	98	93	95		888	2.6	0	14		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RTN1	NM_021136.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		296/777	60212553	1,13005	2203	4300	6503	59282306	SO:0001819	synonymous_variant	6252			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.888C>T	14.37:g.60212553G>A			59282306	Q16800|Q16801|Q5BKZ4|Q9BQ59	Silent	SNP	ENST00000267484.5	37	CCDS9740.1																																																																																				0.498	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			A	60212553	G	A	60212553	2	1	107	1	0	0	0	0	0	0	0	1	13762	1219	43	3		3	RTN1	14	60212553	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	27651564	60212553	47136987	251	28310										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64518439	64518439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggaaagccagattaagcaacTtgaacatggttgggaacaag	12	6	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr14:64518439T>C	ENST00000344113.4	+	48	8020	c.7808T>C	c.(7807-7809)cTt>cCt	p.L2603P	SYNE2_ENST00000554584.1_Missense_Mutation_p.L2636P|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Missense_Mutation_p.L2603P	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2603					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.L2603P(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATTAAGCAACTTGAACATGGT	0.373																																																1	Substitution - Missense(1)	ovary(1)	14											101	95	97					14																	64518439		1874	4113	5987	63588192	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.7808T>C	14.37:g.64518439T>C	ENSP00000341781:p.Leu2603Pro		63588192	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	6.137	0.393538	0.11638	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.70282	0.63;0.63;-0.47	5.91	4.77	0.60923	.	0.000000	0.52532	D	0.000078	T	0.60715	0.2290	L	0.34521	1.04	0.80722	D	1	B;B	0.32203	0.246;0.36	B;B	0.34385	0.088;0.181	T	0.61574	-0.7035	10	0.72032	D	0.01	.	10.5827	0.45265	0.0:0.0722:0.0:0.9278	.	2603;2603	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	P	2603;2603;2636;2636	ENSP00000350719:L2603P;ENSP00000341781:L2603P;ENSP00000452570:L2636P	ENSP00000261678:L2636P	L	+	2	0	SYNE2	63588192	0.998000	0.40836	0.062000	0.19696	0.101000	0.19017	5.172000	0.65003	1.066000	0.40716	-0.250000	0.11733	CTT		0.373	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64518439	T	C	64518439	3	2	107	1	0	0	0	0	1	0	0	0	15485	1609	56	4	7994	4	SYNE2	14	64518439	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	4305886	64518439	42831101	252	28311										
UBE3A	7337	hgsc.bcm.edu	37	chr15	25620840	25620840	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acaaaactcattcgtgcaggCttcatttccacagccctcag	6	14	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:25620840C>T	ENST00000397954.2	-	3	141	c.142G>A	c.(142-144)Gcc>Acc	p.A48T	UBE3A_ENST00000232165.3_Missense_Mutation_p.A45T|UBE3A_ENST00000566215.1_Missense_Mutation_p.A25T|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Missense_Mutation_p.A25T|UBE3A_ENST00000438097.1_Missense_Mutation_p.A25T			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	48					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TTCGTGCAGGCTTCATTTCCA	0.418																																																0			15											118	116	117					15																	25620840		2203	4300	6503	23171933	SO:0001583	missense	7337			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.142G>A	15.37:g.25620840C>T	ENSP00000381045:p.Ala48Thr		23171933	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033604	0.35893	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.97	5.97	0.96955	.	0.450432	0.26808	N	0.022386	T	0.13457	0.0326	L	0.34521	1.04	0.40056	D	0.975832	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.12785	-1.0534	10	0.14252	T	0.57	.	13.5933	0.61971	0.0:0.9293:0.0:0.0707	.	45;48	Q05086-3;Q05086	.;UBE3A_HUMAN	T	45;45;48;25;25	ENSP00000232165:A45T;ENSP00000381045:A48T;ENSP00000411258:A25T;ENSP00000401265:A25T	ENSP00000232165:A45T	A	-	1	0	UBE3A	23171933	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.145000	0.50623	2.835000	0.97688	0.591000	0.81541	GCC		0.418	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		T	25620840	C	T	25620840	3	4	107	1	0	0	0	0	1	0	0	0	16919	797	28	3	2521	3	UBE3A	15	25620840	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		25620840	76910552	253	28312										
FBN1	2200	hgsc.bcm.edu	37	chr15	48764825	48764825	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atcctcctggtgcattgaggCactggccattgccacagaga	11	12	0	2	rs397515804|rs397515803|rs398122934		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:48764825C>A	ENST00000316623.5	-	35	4714	c.4259G>T	c.(4258-4260)tGc>tTc	p.C1420F		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1420	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TGCATTGAGGCACTGGCCATT	0.532																																																0			15											131	121	125					15																	48764825		2198	4296	6494	46552117	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4259G>T	15.37:g.48764825C>A	ENSP00000325527:p.Cys1420Phe		46552117	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.986071	0.93044	.	.	ENSG00000166147	ENST00000316623;ENST00000544030	D	0.99445	-5.91	5.81	5.81	0.92471	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.99325	4.515	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.96813	0.9598	10	0.87932	D	0	.	19.6746	0.95926	0.0:1.0:0.0:0.0	.	1420	P35555	FBN1_HUMAN	F	1420;310	ENSP00000325527:C1420F	ENSP00000325527:C1420F	C	-	2	0	FBN1	46552117	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.818000	0.86416	2.747000	0.94245	0.650000	0.86243	TGC		0.532	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48764825	C	A	48764825	3	1	107	1	0	0	0	0	1	0	0	0	5721	710	25	2	4484	2	FBN1	15	48764825	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	23143985	48764825	53766567	254	28313										
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50273413	50273414	+	In_Frame_Ins	INS	-	-	GAG													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtaacttacccatagtactaINSgagtattcatcaatctatca							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:50273413_50273414insGAG	ENST00000284509.6	-	11	967_968	c.826_827insCTC	c.(826-828)cta>cCTCta	p.275_276insP	RNA5SP394_ENST00000364216.1_RNA|ATP8B4_ENST00000559829.1_In_Frame_Ins_p.275_276insP|ATP8B4_ENST00000558959.1_5'UTR	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	275						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CCATAGTACTAGAGTATTCATC	0.322																																																0			15																																								48060706	SO:0001652	inframe_insertion	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.824_826dupCTC	15.37:g.50273414_50273416dupGAG	ENSP00000284509:p.Thr275_Leu276insPro		48060705	Q9H727	In_Frame_Ins	INS	ENST00000284509.6	37	CCDS32238.1																																																																																				0.322	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		GAG	50273414	-	GAG	50273413	7	5	107	1	0	1	1	0	0	0	0	0	1198	420	15	0	2823	0	ATP8B4	15	50273413	In_Frame_Ins	INS	-	TCGA-DY-A1DG-01A-11D-A152-10	1508588	50273413	52257979	255	28314										
TMOD3	29766	hgsc.bcm.edu	37	chr15	52181327	52181327	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaagtagtaatggtgttgacCaagaacatttttcaagtgag	11	4	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:52181327C>A	ENST00000308580.7	+	5	762	c.481C>A	c.(481-483)Caa>Aaa	p.Q161K	TMOD3_ENST00000544199.1_Missense_Mutation_p.Q161K|RP11-56B16.5_ENST00000558142.1_RNA	NM_014547.4	NP_055362.1	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	161						striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)	p.Q161E(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14				all cancers(107;0.00194)		TGGTGTTGACCAAGAACATTT	0.294																																					Colon(122;1837 2251 18387 22826)											1	Substitution - Missense(1)	ovary(1)	15											74	75	75					15																	52181327		2194	4278	6472	49968619	SO:0001583	missense	29766			AF177171	CCDS10145.1	15q21.1-q21.2	2008-05-14			ENSG00000138594	ENSG00000138594			11873	protein-coding gene	gene with protein product		605112				10662549	Standard	NM_014547		Approved	UTMOD	uc002abn.3	Q9NYL9	OTTHUMG00000131803	ENST00000308580.7:c.481C>A	15.37:g.52181327C>A	ENSP00000308753:p.Gln161Lys		49968619	B2R6G7|Q9NT43|Q9NZR0	Missense_Mutation	SNP	ENST00000308580.7	37	CCDS10145.1	.	.	.	.	.	.	.	.	.	.	C	1.744	-0.490947	0.04322	.	.	ENSG00000138594	ENST00000308580;ENST00000544199	T;T	0.12361	2.69;2.69	5.68	9.9E-4	0.14044	.	0.475067	0.22496	N	0.059297	T	0.03053	0.0090	N	0.01048	-1.04	0.30965	N	0.723239	B	0.02656	0.0	B	0.01281	0.0	T	0.46386	-0.9195	10	0.02654	T	1	-4.8208	9.5548	0.39332	0.389:0.3109:0.3001:0.0	.	161	Q9NYL9	TMOD3_HUMAN	K	161	ENSP00000308753:Q161K;ENSP00000438909:Q161K	ENSP00000308753:Q161K	Q	+	1	0	TMOD3	49968619	0.959000	0.32827	0.577000	0.28562	0.881000	0.50899	1.107000	0.31110	0.022000	0.15160	-0.150000	0.13652	CAA		0.294	TMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254740.3			A	52181327	C	A	52181327	3	1	107	1	0	0	0	0	1	0	0	0	16274	595	21	2	495	2	TMOD3	15	52181327	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1907914	52181327	50350065	256	28315										
ONECUT1	3175	hgsc.bcm.edu	37	chr15	53049845	53049845	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tccagactcctccttcttgcGttcatgaagaagttgctgac	8	12	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:53049845G>A	ENST00000305901.5	-	2	1432	c.1305C>T	c.(1303-1305)aaC>aaT	p.N435N	ONECUT1_ENST00000560699.2_3'UTR|ONECUT1_ENST00000561401.2_5'UTR	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	435					B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		TCCTTCTTGCGTTCATGAAGA	0.473																																																0			15											155	144	147					15																	53049845		2194	4293	6487	50837137	SO:0001819	synonymous_variant	3175			U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"Homeoboxes / CUT class"	8138	protein-coding gene	gene with protein product		604164	"one cut domain, family member 1"	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.1305C>T	15.37:g.53049845G>A			50837137	B2RTV4|Q99744|Q9UMR6	Silent	SNP	ENST00000305901.5	37	CCDS10150.1																																																																																				0.473	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2			A	53049845	G	A	53049845	2	1	107	1	0	0	0	0	0	0	0	1	10899	1136	40	1		1	ONECUT1	15	53049845	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	868518	53049845	49481547	257	28316										
RSL24D1	51187	hgsc.bcm.edu	37	chr15	55475542	55475542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gggctcggataagatggatgTtttgcttgacttctttgata	12	5	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:55475542T>C	ENST00000260443.4	-	5	565	c.389A>G	c.(388-390)aAc>aGc	p.N130S		NM_016304.2	NP_057388.1	Q9UHA3	RLP24_HUMAN	ribosomal L24 domain containing 1	130					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)				central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	7						AAGATGGATGTTTTGCTTGAC	0.353																																																0			15											82	74	77					15																	55475542		2193	4292	6485	53262834	SO:0001583	missense	51187			AF201949	CCDS10152.1	15q21	2009-02-27	2009-02-27	2009-02-27	ENSG00000137876	ENSG00000137876			18479	protein-coding gene	gene with protein product		613262	"chromosome 15 open reading frame 15"	C15orf15		12808088, 11707418	Standard	NM_016304		Approved	HRP-L30-iso, L30, RPL24L, RPL24	uc002acn.3	Q9UHA3	OTTHUMG00000131957	ENST00000260443.4:c.389A>G	15.37:g.55475542T>C	ENSP00000260443:p.Asn130Ser		53262834	B2RD72|Q561V8|Q8N6S8|Q96B04|Q96C76|Q96HJ1	Missense_Mutation	SNP	ENST00000260443.4	37	CCDS10152.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.394849	0.42512	.	.	ENSG00000137876	ENST00000260443	.	.	.	5.46	3.16	0.36331	.	0.185032	0.56097	N	0.000022	T	0.56963	0.2021	M	0.72624	2.21	0.54753	D	0.999984	B	0.16166	0.016	B	0.12837	0.008	T	0.55042	-0.8202	9	0.44086	T	0.13	-32.6806	7.8302	0.29338	0.0:0.1709:0.0:0.8291	.	130	Q9UHA3	RLP24_HUMAN	S	130	.	ENSP00000260443:N130S	N	-	2	0	RSL24D1	53262834	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.349000	0.52217	0.887000	0.36136	-0.290000	0.09829	AAC		0.353	RSL24D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254916.1	NM_016304		C	55475542	T	C	55475542	3	2	107	1	0	0	0	0	1	0	0	0	13738	1725	60	4	110	4	RSL24D1	15	55475542	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	2425697	55475542	47055850	258	28317										
TPM1	7168	hgsc.bcm.edu	37	chr15	63335952	63335952	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aagttgctgcgggtgtcggaGgacgagcgggaccgggtgct	20	8	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:63335952G>A	ENST00000403994.3	+	2	194				TPM1_ENST00000559397.1_Silent_p.E54E|TPM1_ENST00000267996.7_Silent_p.E54E|TPM1_ENST00000357980.4_Silent_p.E54E|TPM1_ENST00000288398.6_Intron|TPM1_ENST00000559556.1_Intron|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000358278.3_Intron|RP11-244F12.3_ENST00000561241.1_RNA	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)						cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						GGGTGTCGGAGGACGAGCGGG	0.751																																																0			15											12	16	15					15																	63335952		1982	3883	5865	61123005	SO:0001627	intron_variant	7168			AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"Tropomyosins"	12010	protein-coding gene	gene with protein product		191010	"chromosome 15 open reading frame 13", "cardiomyopathy, hypertrophic 3"	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.115-274G>A	15.37:g.63335952G>A			61123005	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Silent	SNP	ENST00000403994.3	37	CCDS45273.1																																																																																				0.751	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004		A	63335952	G	A	63335952	1	1	107	0	1	0	0	0	0	0	0	0	16445	991	35	3		3	TPM1	15	63335952	Intron	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	7860410	63335952	39195440	259	28318										
NR2E3	10002	hgsc.bcm.edu	37	chr15	72106357	72106357	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgctgcttctccccagagacGcggggcctgaaggatcctga	13	13	1	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:72106357G>A	ENST00000398840.2	+	0	1189							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						CCCCAGAGACGCGGGGCCTGA	0.612																																																0			15											31	37	35					15																	72106357		2087	4212	6299	69893411			10002				CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"Nuclear hormone receptors"	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72106357G>A			69893411	B6ZGU0|Q9UHM4	Missense_Mutation	SNP	ENST00000398840.2	37																																																																																					0.612	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		A	72106357	G	A	72106357	1	1	107	0	1	0	0	0	0	0	0	0	10657	1074	38	1		1	NR2E3	15	72106357	RNA	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8770405	72106357	30425035	260	28319										
SIN3A	25942	hgsc.bcm.edu	37	chr15	75682045	75682045	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tggtaaaggcaatgtaggcaTgaatggtgaacatctctctc	11	7	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:75682045T>C	ENST00000394947.3	-	16	3283	c.2969A>G	c.(2968-2970)cAt>cGt	p.H990R	SIN3A_ENST00000360439.4_Missense_Mutation_p.H990R|SIN3A_ENST00000394949.4_Missense_Mutation_p.H990R	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						AATGTAGGCATGAATGGTGAA	0.483																																																0			15											231	172	192					15																	75682045		2197	4294	6491	73469098	SO:0001583	missense	25942			AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.2969A>G	15.37:g.75682045T>C	ENSP00000378402:p.His990Arg		73469098		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.804160	0.90623	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.44881	0.91;0.91;0.91	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.60444	0.2269	L	0.58969	1.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57481	-0.7804	10	0.34782	T	0.22	-24.0968	15.2953	0.73902	0.0:0.0:0.0:1.0	.	990	Q96ST3	SIN3A_HUMAN	R	990	ENSP00000378402:H990R;ENSP00000378403:H990R;ENSP00000353622:H990R	ENSP00000353622:H990R	H	-	2	0	SIN3A	73469098	1.000000	0.71417	0.992000	0.48379	0.999000	0.98932	7.978000	0.88095	2.214000	0.71695	0.528000	0.53228	CAT		0.483	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		C	75682045	T	C	75682045	3	2	107	1	0	0	0	0	1	0	0	0	14362	1464	51	4	876	4	SIN3A	15	75682045	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	3575688	75682045	26849347	261	28320										
SGK269	79834	hgsc.bcm.edu	37	chr15	77472051	77472051	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttctattttggccacaggctCttgagtggctctctggatct	10	10	4	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:77472051C>T	ENST00000560626.2	-	4	2693	c.2218G>A	c.(2218-2220)Gag>Aag	p.E740K	PEAK1_ENST00000558305.1_Missense_Mutation_p.E740K|PEAK1_ENST00000312493.4_Missense_Mutation_p.E740K			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	740					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.E740K(2)									GCCACAGGCTCTTGAGTGGCT	0.507																																																2	Substitution - Missense(2)	ovary(2)	15											94	90	91					15																	77472051		1957	4165	6122	75259106	SO:0001583	missense	0				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2218G>A	15.37:g.77472051C>T	ENSP00000452796:p.Glu740Lys		75259106	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.459024	0.63401	.	.	ENSG00000173517	ENST00000312493	T	0.70516	-0.49	5.89	5.89	0.94794	.	0.269388	0.16374	U	0.217216	T	0.62221	0.2410	L	0.29908	0.895	0.43076	D	0.994726	B	0.17852	0.024	B	0.15484	0.013	T	0.57063	-0.7875	10	0.51188	T	0.08	-12.7065	15.7106	0.77623	0.0:0.864:0.136:0.0	.	740	Q9H792	PEAK1_HUMAN	K	740	ENSP00000309230:E740K	ENSP00000309230:E740K	E	-	1	0	AC087465.1	75259106	1.000000	0.71417	0.693000	0.30195	0.777000	0.43975	7.161000	0.77505	2.793000	0.96121	0.655000	0.94253	GAG		0.507	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			T	77472051	C	T	77472051	3	4	107	1	0	0	0	0	1	0	0	0	14248	922	32	3	3038	3	SGK269	15	77472051	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1790006	77472051	25059341	262	28321										
LINGO1	84894	hgsc.bcm.edu	37	chr15	77908090	77908090	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttgcggtggcacagcacagcGcggtcctgggcggagcactc	16	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:77908090G>A	ENST00000355300.6	-	2	333	c.159C>T	c.(157-159)cgC>cgT	p.R53R	LINGO1_ENST00000561030.1_Silent_p.R47R	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	53	LRRNT.				central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						ACAGCACAGCGCGGTCCTGGG	0.692																																																0			15											13	15	14					15																	77908090		2109	4205	6314	75695145	SO:0001819	synonymous_variant	84894			AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.159C>T	15.37:g.77908090G>A			75695145	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																				0.692	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		A	77908090	G	A	77908090	2	1	107	1	0	0	0	0	0	0	0	1	8838	1074	38	1		1	LINGO1	15	77908090	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	436039	77908090	24623302	263	28322										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058551	79058551	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggcagcgtggagctgggtctCgggggcaggtggggtgctcc	22	9	1	0	rs540501138	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:79058551C>T	ENST00000388820.4	-	19	3912	c.3702G>A	c.(3700-3702)ccG>ccA	p.P1234P	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1234					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGCTGGGTCTCGGGGGCAGGT	0.647													c|||	2	0.000399361	0	0	5008	,	,		14816	0		0	False		,,,				2504	0.002															0			15											23	26	25					15																	79058551		2193	4290	6483	76845606	SO:0001819	synonymous_variant	11173			AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3702G>A	15.37:g.79058551C>T			76845606	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																				0.647	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79058551	C	T	79058551	2	4	107	1	0	0	0	0	0	0	0	1	271	871	31	1		1	ADAMTS7	15	79058551	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1150461	79058551	23472841	264	28323										
KLHL25	64410	hgsc.bcm.edu	37	chr15	86312925	86312925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgaacatgcagtgcttgcgAagcgtgttgaggtgggccag	17	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:86312925A>G	ENST00000337975.5	-	2	391	c.117T>C	c.(115-117)ctT>ctC	p.L39L	KLHL25_ENST00000536947.1_Silent_p.L39L|MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	39					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						AGTGCTTGCGAAGCGTGTTGA	0.642																																																0			15											74	70	72					15																	86312925		2202	4299	6501	84113929	SO:0001819	synonymous_variant	64410				CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"Kelch-like", "BTB/POZ domain containing"	25732	protein-coding gene	gene with protein product	"ectodermal-neural cortex 2"		"kelch-like 25 (Drosophila)"				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.117T>C	15.37:g.86312925A>G			84113929	B2RDH2|B3KRT7	Silent	SNP	ENST00000337975.5	37	CCDS10339.1																																																																																				0.642	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480		G	86312925	A	G	86312925	2	3	107	1	0	0	0	0	0	0	0	1	8401	233	9	4		4	KLHL25	15	86312925	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	7254374	86312925	16218467	265	28324										
IDH2	3418	hgsc.bcm.edu	37	chr15	90631879	90631879	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtccagccagggactaggcgTgggatgtttttgcagatgat	15	7	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:90631879T>C	ENST00000330062.3	-	4	587	c.474A>G	c.(472-474)ccA>ccG	p.P158P	IDH2_ENST00000539790.1_Silent_p.P28P|IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Silent_p.P106P	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	158					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			GGACTAGGCGTGGGATGTTTT	0.587			M		GBM																																		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	0			15											114	110	111					15																	90631879		2200	4298	6498	88432883	SO:0001819	synonymous_variant	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.474A>G	15.37:g.90631879T>C			88432883	B2R6L6|B4DFL2|Q96GT3	Silent	SNP	ENST00000330062.3	37	CCDS10359.1																																																																																				0.587	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			C	90631879	T	C	90631879	2	2	107	1	0	0	0	0	0	0	0	1	7516	1683	59	4		4	IDH2	15	90631879	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	4318954	90631879	11899513	266	28325										
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92988002	92988002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggcgggagaagctgctgcaaCggctgcacagcctcaatggc	15	12	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:92988002C>T	ENST00000268164.3	+	5	922	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	ST8SIA2_ENST00000539113.1_Missense_Mutation_p.R208W	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	229					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			GCTGCTGCAACGGCTGCACAG	0.602																																																0			15											58	47	51					15																	92988002		2198	4298	6496	90789006	SO:0001583	missense	8128			U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.685C>T	15.37:g.92988002C>T	ENSP00000268164:p.Arg229Trp		90789006	Q4VAZ0|Q92470|Q92746	Missense_Mutation	SNP	ENST00000268164.3	37	CCDS10372.1	.	.	.	.	.	.	.	.	.	.	C	34	5.395033	0.96009	.	.	ENSG00000140557	ENST00000268164;ENST00000539113;ENST00000555434	T;T;T	0.30981	1.51;1.51;1.51	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68256	0.2981	M	0.93550	3.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.74922	-0.3499	10	0.54805	T	0.06	-8.6569	19.9991	0.97403	0.0:1.0:0.0:0.0	.	208;229	C6G488;Q92186	.;SIA8B_HUMAN	W	229;208;186	ENSP00000268164:R229W;ENSP00000437382:R208W;ENSP00000450851:R186W	ENSP00000268164:R229W	R	+	1	2	ST8SIA2	90789006	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.857000	0.69525	2.724000	0.93272	0.655000	0.94253	CGG		0.602	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		T	92988002	C	T	92988002	3	4	107	1	0	0	0	0	1	0	0	0	15271	527	19	1	703	1	ST8SIA2	15	92988002	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2356123	92988002	9543390	267	28326										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99500330	99500330	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gctggcagtataaccccaagAtgaggccttccttcctggag	11	12	0	2	rs149148921		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr15:99500330A>G	ENST00000268035.6	+	21	4374	c.3763A>G	c.(3763-3765)Atg>Gtg	p.M1255V	IGF1R_ENST00000558762.1_Missense_Mutation_p.M1254V|RP11-654A16.3_ENST00000559468.1_RNA	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	TAACCCCAAGATGAGGCCTTC	0.582																																																0			15											88	86	87					15																	99500330		2197	4297	6494	97317853	SO:0001583	missense	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3763A>G	15.37:g.99500330A>G	ENSP00000268035:p.Met1255Val		97317853	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	A	19.67	3.871123	0.72065	.	.	ENSG00000140443	ENST00000268035	D	0.82344	-1.6	5.57	5.57	0.84162	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.75004	0.3791	N	0.10707	0.03	0.80722	D	1	P;B	0.46912	0.886;0.414	P;P	0.47118	0.467;0.538	T	0.81035	-0.1115	10	0.72032	D	0.01	.	15.7266	0.77766	1.0:0.0:0.0:0.0	.	1254;1255	C9J5X1;P08069	.;IGF1R_HUMAN	V	1255	ENSP00000268035:M1255V	ENSP00000268035:M1255V	M	+	1	0	IGF1R	97317853	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.307000	0.96226	2.114000	0.64651	0.455000	0.32223	ATG		0.582	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		G	99500330	A	G	99500330	3	3	107	1	0	0	0	0	1	0	0	0	7592	333	12	4	3845	4	IGF1R	15	99500330	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	6512328	99500330	3031062	268	28327										
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	532596	532596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gagtgtgagaccttcacggaCgaggacaccagcaccctggt	13	12	1	1	rs184050293		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:532596C>T	ENST00000262305.4	+	4	1363	c.975C>T	c.(973-975)gaC>gaT	p.D325D	RAB11FIP3_ENST00000450428.1_Silent_p.D29D|RAB11FIP3_ENST00000457159.1_Silent_p.D325D	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	325					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CCTTCACGGACGAGGACACCA	0.657													C|||	1	0.000199681	8e-04	0	5008	,	,		20381	0		0	False		,,,				2504	0				Melanoma(160;2366 2595 4474 8099)											0			16											91	73	79					16																	532596		2202	4300	6502	472597	SO:0001819	synonymous_variant	9727			AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.975C>T	16.37:g.532596C>T			472597	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																				0.657	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		T	532596	C	T	532596	2	4	107	1	0	0	0	0	0	0	0	1	12932	535	19	1		1	RAB11FIP3	16	532596	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		532596	89822157	269	28328										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11097081	11097081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	atgaggagaaagggcccaccGaggatgcccaagaagacgcc	14	11	0	4	rs201942249		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:11097081G>A	ENST00000409790.1	+	11	1452	c.1222G>A	c.(1222-1224)Gag>Aag	p.E408K	CLEC16A_ENST00000409552.3_Missense_Mutation_p.E406K	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGGGCCCACCGAGGATGCCCA	0.532																																																0			16											76	84	82					16																	11097081		1997	4141	6138	11004582	SO:0001583	missense	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1222G>A	16.37:g.11097081G>A	ENSP00000387122:p.Glu408Lys		11004582		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964781	0.74131	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.48201	0.82	5.62	5.62	0.85841	.	0.222611	0.40554	N	0.001077	T	0.51483	0.1677	L	0.54323	1.7	0.80722	D	1	D;D	0.63880	0.983;0.993	B;P	0.50082	0.356;0.63	T	0.42865	-0.9426	10	0.09338	T	0.73	-23.0153	18.6399	0.91392	0.0:0.0:1.0:0.0	.	408;406	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	K	408;408;406	ENSP00000387122:E408K	ENSP00000386495:E406K	E	+	1	0	CLEC16A	11004582	1.000000	0.71417	0.956000	0.39512	0.477000	0.33069	8.441000	0.90313	2.662000	0.90505	0.655000	0.94253	GAG		0.532	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11097081	G	A	11097081	3	1	107	1	0	0	0	0	1	0	0	0	3506	1059	37	1	1260	1	CLEC16A	16	11097081	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	10564485	11097081	79257672	270	28329										
UMOD	7369	hgsc.bcm.edu	37	chr16	20357567	20357567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caggtacatgaagaccttgtCgaagcccagactcttcagct	9	12	2	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:20357567C>T	ENST00000570689.1	-	5	1209	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N	UMOD_ENST00000396138.4_Missense_Mutation_p.D404N|UMOD_ENST00000302509.4_Missense_Mutation_p.D355N|UMOD_ENST00000396134.2_Missense_Mutation_p.D388N|UMOD_ENST00000396142.2_Missense_Mutation_p.D355N|UMOD_ENST00000424589.1_Missense_Mutation_p.D388N			P07911	UROM_HUMAN	uromodulin	355	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						AAGACCTTGTCGAAGCCCAGA	0.582																																																0			16											85	78	81					16																	20357567		2203	4300	6503	20265068	SO:0001583	missense	7369			M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"Tamm-Horsfall glycoprotein", "uromucoid"	191845	"uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.1063G>A	16.37:g.20357567C>T	ENSP00000460548:p.Asp355Asn		20265068	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Missense_Mutation	SNP	ENST00000570689.1	37	CCDS10583.1	.	.	.	.	.	.	.	.	.	.	c	13.04	2.119808	0.37436	.	.	ENSG00000169344	ENST00000396138;ENST00000396134;ENST00000424589;ENST00000302509;ENST00000429954;ENST00000396142	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	4.67	1.02	0.19986	Zona pellucida sperm-binding protein (3);	0.472674	0.17937	N	0.156969	T	0.62816	0.2459	N	0.12746	0.255	0.09310	N	1	B;B	0.12630	0.004;0.006	B;B	0.19946	0.006;0.027	T	0.47459	-0.9116	10	0.27082	T	0.32	-10.3565	3.8168	0.08818	0.0:0.3225:0.3999:0.2775	.	388;355	E9PEA4;P07911	.;UROM_HUMAN	N	355;388;388;355;333;355	ENSP00000379438:D388N;ENSP00000416346:D388N;ENSP00000306279:D355N;ENSP00000379446:D355N	ENSP00000306279:D355N	D	-	1	0	UMOD	20265068	0.001000	0.12720	0.967000	0.41034	0.886000	0.51366	-0.016000	0.12613	0.240000	0.21263	0.306000	0.20318	GAC		0.582	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1			T	20357567	C	T	20357567	3	4	107	1	0	0	0	0	1	0	0	0	17019	884	31	1	887	1	UMOD	16	20357567	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	9260486	20357567	69997186	271	28330										
TUFM	25970	hgsc.bcm.edu	37	chr16	28856082	28856082	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcccctttatagccaaactcGgtgagcagctcccggatctc	8	15	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:28856082G>A	ENST00000322610.8	+	0	0				TUFM_ENST00000313511.3_Silent_p.T207T|MIR4721_ENST00000577590.1_RNA			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						AGCCAAACTCGGTGAGCAGCT	0.592																																																0			16											110	103	106					16																	28856082		2197	4300	6497	28763583	SO:0001631	upstream_gene_variant	7284			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2			16.37:g.28856082G>A	Exception_encountered		28763583	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Silent	SNP	ENST00000322610.8	37	CCDS53996.1																																																																																				0.592	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		A	28856082	G	A	28856082	1	1	107	0	1	0	0	0	0	0	0	0	16811	1103	39	1		1	TUFM	16	28856082	5'Flank	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	8498515	28856082	61498671	272	28331										
CYLD	1540	hgsc.bcm.edu	37	chr16	50820850	50820850	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcatcaggatttacctctgaAgaaaaaggtgaccatcttaa	8	8	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:50820850A>G	ENST00000427738.3	+	12	2239	c.2034A>G	c.(2032-2034)gaA>gaG	p.E678E	CYLD_ENST00000568704.2_Silent_p.E493E|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000311559.9_Silent_p.E678E|CYLD_ENST00000569418.1_Silent_p.E675E|CYLD_ENST00000398568.2_Silent_p.E675E|CYLD_ENST00000566206.1_Silent_p.E675E|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000540145.1_Silent_p.E678E|CYLD_ENST00000564326.1_Silent_p.E675E			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	678	USP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				TTACCTCTGAAGAAAAAGGTG	0.353			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											99	103	102					16																	50820850		1840	4094	5934	49378351	SO:0001819	synonymous_variant	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.2034A>G	16.37:g.50820850A>G			49378351	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	37	CCDS45482.1																																																																																				0.353	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			G	50820850	A	G	50820850	2	3	107	1	0	0	0	0	0	0	0	1	4149	69	3	4		4	CYLD	16	50820850	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	21964768	50820850	39533903	273	28332										
CHD9	80205	hgsc.bcm.edu	37	chr16	53272302	53272302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gggtcttggcaaaactattcAatcaattacattcctctatg	6	9	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:53272302A>G	ENST00000398510.3	+	11	2768	c.2681A>G	c.(2680-2682)cAa>cGa	p.Q894R	CHD9_ENST00000566029.1_Missense_Mutation_p.Q894R|CHD9_ENST00000564845.1_Missense_Mutation_p.Q894R|CHD9_ENST00000447540.1_Missense_Mutation_p.Q894R			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	894	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				AAAACTATTCAATCAATTACA	0.348																																																0			16											97	91	93					16																	53272302		1829	4084	5913	51829803	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2681A>G	16.37:g.53272302A>G	ENSP00000381522:p.Gln894Arg		51829803	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	A	24.1	4.491233	0.84962	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.94280	-3.39;-3.39	5.02	5.02	0.67125	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.53938	D	0.000047	D	0.98406	0.9470	H	0.99815	4.805	0.80722	D	1	D;D;D;D	0.61080	0.972;0.989;0.985;0.981	D;D;D;D	0.74023	0.911;0.948;0.982;0.969	D	0.99331	1.0909	10	0.87932	D	0	-10.2449	14.7523	0.69536	1.0:0.0:0.0:0.0	.	420;894;894;894	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	R	894;894;420	ENSP00000396345:Q894R;ENSP00000381522:Q894R	ENSP00000219084:Q420R	Q	+	2	0	CHD9	51829803	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	9.281000	0.95811	1.892000	0.54788	0.377000	0.23210	CAA		0.348	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53272302	A	G	53272302	3	3	107	1	0	0	0	0	1	0	0	0	3338	130	5	4	2723	4	CHD9	16	53272302	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2451452	53272302	37082451	274	28333										
IRX6	79190	hgsc.bcm.edu	37	chr16	55363057	55363057	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggacagcctcctgcctctgcCcggcgactctcagtccccag	10	19	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:55363057C>T	ENST00000290552.7	+	5	2499	c.1167C>T	c.(1165-1167)gcC>gcT	p.A389A	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	389					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						CTGCCTCTGCCCGGCGACTCT	0.627																																																0			16											61	59	60					16																	55363057		2198	4300	6498	53920558	SO:0001819	synonymous_variant	79190			AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.1167C>T	16.37:g.55363057C>T			53920558	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																				0.627	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		T	55363057	C	T	55363057	2	4	107	1	0	0	0	0	0	0	0	1	7869	610	22	3		3	IRX6	16	55363057	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2090755	55363057	34991696	275	28334										
CDH1	999	hgsc.bcm.edu	37	chr16	68853211	68853211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tttggagagacactgccaacTggctggagattaatccggac	12	9	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:68853211T>C	ENST00000261769.5	+	11	1785	c.1594T>C	c.(1594-1596)Tgg>Cgg	p.W532R	CDH1_ENST00000422392.2_Missense_Mutation_p.W471R|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	532	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACTGCCAACTGGCTGGAGAT	0.507			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	1	Unknown(1)	breast(1)	16											106	89	95					16																	68853211		2198	4300	6498	67410712	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1594T>C	16.37:g.68853211T>C	ENSP00000261769:p.Trp532Arg		67410712	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939263	0.73557	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.51574	0.7;0.7	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.47852	D	0.000202	T	0.68842	0.3045	M	0.77616	2.38	0.80722	D	1	D;D	0.69078	0.988;0.997	D;D	0.69142	0.954;0.962	T	0.73649	-0.3916	10	0.87932	D	0	.	15.3739	0.74590	0.0:0.0:0.0:1.0	.	471;532	Q9UII8;P12830	.;CADH1_HUMAN	R	532;550;532;471	ENSP00000261769:W532R;ENSP00000414946:W471R	ENSP00000261769:W532R	W	+	1	0	CDH1	67410712	1.000000	0.71417	0.999000	0.59377	0.624000	0.37722	7.088000	0.76901	2.110000	0.64415	0.454000	0.30748	TGG		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		C	68853211	T	C	68853211	3	2	107	1	0	0	0	0	1	0	0	0	3101	1580	55	4	1636	4	CDH1	16	68853211	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	13490154	68853211	21501542	276	28335										
HAS3	3038	hgsc.bcm.edu	37	chr16	69143929	69143929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tcggcgattcggtggactacAtccaggtaagggcgcctccc	13	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:69143929A>G	ENST00000306560.1	+	2	787	c.631A>G	c.(631-633)Atc>Gtc	p.I211V	HAS3_ENST00000219322.3_Missense_Mutation_p.I211V|HAS3_ENST00000569188.1_Missense_Mutation_p.I211V	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	211					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		GGTGGACTACATCCAGGTAAG	0.602																																																0			16											57	49	52					16																	69143929		2198	4300	6498	67701430	SO:0001583	missense	3038			BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.631A>G	16.37:g.69143929A>G	ENSP00000304440:p.Ile211Val		67701430	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	37	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	A	0.539	-0.854656	0.02630	.	.	ENSG00000103044	ENST00000219322;ENST00000306560	D;T	0.84223	-1.82;0.29	5.34	5.34	0.76211	.	0.250700	0.43919	D	0.000503	T	0.61627	0.2362	N	0.02775	-0.495	0.37798	D	0.927617	B;B	0.17038	0.001;0.02	B;B	0.12156	0.007;0.003	T	0.60772	-0.7197	10	0.06236	T	0.91	-18.5114	7.725	0.28755	0.8408:0.0:0.1592:0.0	.	211;211	O00219;O00219-2	HAS3_HUMAN;.	V	211	ENSP00000219322:I211V;ENSP00000304440:I211V	ENSP00000219322:I211V	I	+	1	0	HAS3	67701430	0.955000	0.32602	1.000000	0.80357	0.855000	0.48748	0.715000	0.25822	2.027000	0.59764	0.459000	0.35465	ATC		0.602	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		G	69143929	A	G	69143929	3	3	107	1	0	0	0	0	1	0	0	0	6984	217	8	4	633	4	HAS3	16	69143929	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	290718	69143929	21210824	277	28336										
TAT	6898	hgsc.bcm.edu	37	chr16	71610250	71610250	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acagagcttctcccaccaacGttgacatgcacgtccagaat	7	14	1	3	rs370850249		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:71610250G>A	ENST00000355962.4	-	2	202	c.69C>T	c.(67-69)aaC>aaT	p.N23N	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	23					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TCCCACCAACGTTGACATGCA	0.527													G|||	1	0.000199681	0	0	5008	,	,		19449	0		0.001	False		,,,				2504	0				Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)											0			16						G		1,4395	2.1+/-5.4	0,1,2197	116	114	115		69	2	0.1	16		115	0,8600		0,0,4300	no	coding-synonymous	TAT	NM_000353.2		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		23/455	71610250	1,12995	2198	4300	6498	70167751	SO:0001819	synonymous_variant	6898				CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.69C>T	16.37:g.71610250G>A			70167751	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	CCDS10903.1																																																																																				0.527	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			A	71610250	G	A	71610250	2	1	107	1	0	0	0	0	0	0	0	1	15629	1136	40	1		1	TAT	16	71610250	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2466321	71610250	18744503	278	28337										
AP1G1	164	hgsc.bcm.edu	37	chr16	71808377	71808377	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaagtaagacttacttcttgAtacagttggtcatgagaaga	9	5	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:71808377A>G	ENST00000299980.4	-	3	761	c.320T>C	c.(319-321)aTc>aCc	p.I107T	AP1G1_ENST00000569748.1_Missense_Mutation_p.I107T|AP1G1_ENST00000393512.3_Missense_Mutation_p.I107T|AP1G1_ENST00000423132.2_Missense_Mutation_p.I107T|AP1G1_ENST00000433195.2_Missense_Mutation_p.I130T	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	107					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TTACTTCTTGATACAGTTGGT	0.373																																																0			16											146	143	144					16																	71808377		2198	4300	6498	70365878	SO:0001583	missense	164			Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.320T>C	16.37:g.71808377A>G	ENSP00000299980:p.Ile107Thr		70365878	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	37	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.409325	0.62399	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195;ENST00000425422;ENST00000450149	T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42	4.72	4.72	0.59763	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.049906	0.85682	D	0.000000	T	0.36220	0.0959	M	0.81614	2.55	0.80722	D	1	P;B;B;B	0.46064	0.872;0.01;0.067;0.001	P;B;B;B	0.52309	0.695;0.189;0.22;0.011	T	0.31503	-0.9941	10	0.66056	D	0.02	-3.099	14.6404	0.68720	1.0:0.0:0.0:0.0	.	189;107;130;107	B4DS96;O43747;B3KXW5;O43747-2	.;AP1G1_HUMAN;.;.	T	107;107;107;130;189;107	ENSP00000299980:I107T;ENSP00000377148:I107T;ENSP00000409153:I107T;ENSP00000403259:I130T;ENSP00000405836:I107T	ENSP00000299980:I107T	I	-	2	0	AP1G1	70365878	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.947000	0.93000	1.915000	0.55452	0.467000	0.42956	ATC		0.373	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			G	71808377	A	G	71808377	3	3	107	1	0	0	0	0	1	0	0	0	732	333	12	4	2245	4	AP1G1	16	71808377	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	198127	71808377	18546376	279	28338										
GLG1	2734	hgsc.bcm.edu	37	chr16	74499629	74499629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agtctagctctgggtccatcAtctctgtctcctgcagctta	8	13	5	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:74499629A>G	ENST00000422840.2	-	19	2611	c.2612T>C	c.(2611-2613)aTg>aCg	p.M871T	Y_RNA_ENST00000384794.1_RNA|GLG1_ENST00000205061.5_Missense_Mutation_p.M871T|GLG1_ENST00000447066.2_Missense_Mutation_p.M860T	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	871					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TGGGTCCATCATCTCTGTCTC	0.463																																																0			16											211	201	204					16																	74499629		2198	4300	6498	73057130	SO:0001583	missense	2734				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2612T>C	16.37:g.74499629A>G	ENSP00000405984:p.Met871Thr		73057130	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164798	0.57476	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.71676	0.3368	L	0.60455	1.87	0.80722	D	1	D;B;D;B	0.56521	0.976;0.078;0.971;0.21	P;B;P;B	0.57283	0.817;0.115;0.631;0.09	T	0.68815	-0.5309	9	0.29301	T	0.29	-16.7589	16.4101	0.83708	1.0:0.0:0.0:0.0	.	1;871;871;860	Q6ZMF1;Q92896;Q92896-2;B7Z8Y4	.;GSLG1_HUMAN;.;.	T	871;860;871	.	ENSP00000205061:M871T	M	-	2	0	GLG1	73057130	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.996000	0.93539	2.280000	0.76307	0.460000	0.39030	ATG		0.463	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		G	74499629	A	G	74499629	3	3	107	1	0	0	0	0	1	0	0	0	6456	217	8	4	1039	4	GLG1	16	74499629	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	2691252	74499629	15855124	280	28339										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81134863	81134863	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agtattttcatcagcagcaaAtctacgatctccccttcctc	4	14	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:81134863A>T	ENST00000534142.1	-	0	1632				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000533478.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCAGCAGCAAATCTACGATCT	0.512																																																0			16											50	55	53					16																	81134863		2023	4183	6206	79692364			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81134863A>T			79692364	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000534142.1	37																																																																																					0.512	PKD1L2-009	PUTATIVE	basic|exp_conf	processed_transcript	polymorphic_pseudogene	OTTHUMT00000387969.1			T	81134863	A	T	81134863	1	4	107	0	1	0	0	0	0	0	0	0	11996	98	4	5		5	PKD1L2	16	81134863	RNA	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	6635234	81134863	9219890	281	28340										
ZFPM1	161882	hgsc.bcm.edu	37	chr16	88594495	88594495	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctgcggggggactcctgagCgtgctcctcacggccgagcc	15	16	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr16:88594495C>T	ENST00000319555.3	+	6	883	c.561C>T	c.(559-561)agC>agT	p.S187S	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	187					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GACTCCTGAGCGTGCTCCTCA	0.672																																					Pancreas(49;850 1106 29641 32847 38344)											0			16											15	19	18					16																	88594495		2154	4268	6422	87121996	SO:0001819	synonymous_variant	161882			AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	19762	protein-coding gene	gene with protein product		601950	"zinc finger protein, multitype 1"				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.561C>T	16.37:g.88594495C>T			87121996		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																				0.672	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2			T	88594495	C	T	88594495	2	4	107	1	0	0	0	0	0	0	0	1	17696	767	27	1		1	ZFPM1	16	88594495	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	7459632	88594495	1760258	282	28341										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	107	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		7577094	73618116	283	28342										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7978912	7978912	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cccaggtgtccaggcccataCctgagctctcccgccccagg	10	19	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:7978912C>A	ENST00000319144.4	-	12	1915		c.e12+1		ALOX12B_ENST00000577351.1_Intron	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type						arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						CAGGCCCATACCTGAGCTCTC	0.587										Multiple Myeloma(8;0.094)																																						0			17											94	97	96					17																	7978912		2203	4300	6503	7919637	SO:0001630	splice_region_variant	242			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1654+1G>T	17.37:g.7978912C>A			7919637		Splice_Site	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	.	17.53	3.413117	0.62511	.	.	ENSG00000179477	ENST00000319144	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2286	0.82318	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ALOX12B	7919637	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	4.660000	0.61511	2.125000	0.65367	0.462000	0.41574	.		0.587	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		Intron	A	7978912	C	A	7978912	5	1	107	1	0	0	0	0	0	0	1	0	537	521	18	2	466	2	ALOX12B	17	7978912	Splice_Site	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	401818	7978912	73216298	284	28343										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18023659	18023659	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gatgcggacgaagaagaggaCgaggaggagctgcccccggt	18	9	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:18023659C>T	ENST00000205890.5	+	2	1883	c.1545C>T	c.(1543-1545)gaC>gaT	p.D515D		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	515					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AAGAAGAGGACGAGGAGGAGC	0.667																																																0			17											30	37	35					17																	18023659		2021	4164	6185	17964384	SO:0001819	synonymous_variant	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1545C>T	17.37:g.18023659C>T			17964384	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.667	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18023659	C	T	18023659	2	4	107	1	0	0	0	0	0	0	0	1	10093	535	19	1		1	MYO15A	17	18023659	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	10044747	18023659	63171551	285	28344										
PROCA1	6830	hgsc.bcm.edu	37	chr17	27030880	27030880	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccgggcttttcttcttagtcAactggcctttcttggctttt	8	11	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:27030880A>G	ENST00000314616.6	+	0	6518				PROCA1_ENST00000301039.2_Missense_Mutation_p.L236S|PROCA1_ENST00000439862.3_Missense_Mutation_p.L238S|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000579650.1_5'Flank	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L236W(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTTCTTAGTCAACTGGCCTTT	0.478																																																1	Substitution - Missense(1)	ovary(1)	17											99	104	102					17																	27030880		2203	4300	6503	24055007	SO:0001628	intergenic_variant	147011			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27030880A>G			24055007	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711603	0.48517	.	.	ENSG00000167525	ENST00000301039;ENST00000439862;ENST00000415329	T;T	0.04275	3.66;3.66	4.74	4.74	0.60224	.	0.402757	0.20110	N	0.099021	T	0.10594	0.0259	L	0.34521	1.04	0.09310	N	0.999994	P;D;D	0.61080	0.952;0.989;0.989	P;P;P	0.61722	0.521;0.858;0.893	T	0.06935	-1.0799	10	0.66056	D	0.02	-2.3458	10.8053	0.46514	1.0:0.0:0.0:0.0	.	264;238;236	Q8NCQ7;G5E9R8;Q8NCQ7-2	PRCA1_HUMAN;.;.	S	236;238;264	ENSP00000301039:L236S;ENSP00000411400:L238S	ENSP00000301039:L236S	L	-	2	0	PROCA1	24055007	0.287000	0.24315	0.378000	0.26068	0.745000	0.42441	4.909000	0.63314	2.101000	0.63845	0.533000	0.62120	TTG		0.478	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27030880	A	G	27030880	1	3	107	0	1	0	0	0	0	0	0	0	12580	131	5	4		4	PROCA1	17	27030880	IGR	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	9007221	27030880	54164330	286	28345										
CORO6	84940	hgsc.bcm.edu	37	chr17	27946079	27946079	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccctccttagcccccagaccTgcactgagcaggacattcct	7	18	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:27946079T>A	ENST00000445145.2	-	3	451	c.450A>T	c.(448-450)gcA>gcT	p.A150A	CORO6_ENST00000456796.3_5'Flank|RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000577909.1_Intron|CORO6_ENST00000345068.5_Splice_Site_p.A150A|CORO6_ENST00000584969.1_Splice_Site_p.A150A|CORO6_ENST00000580212.1_Splice_Site_p.A150A|CORO6_ENST00000388767.3_Splice_Site_p.A150A|RP11-68I3.10_ENST00000582367.1_RNA			Q6QEF8	CORO6_HUMAN	coronin 6	150					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)	actin filament binding (GO:0051015)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(2)	14						CCCCCAGACCTGCACTGAGCA	0.602																																																0			17											39	42	41					17																	27946079		2043	4224	6267	24970205	SO:0001630	splice_region_variant	84940			AF193039	CCDS11252.2	17q11.2	2013-01-10			ENSG00000167549	ENSG00000167549		"Coronins", "WD repeat domain containing"	21356	protein-coding gene	gene with protein product							Standard	NM_032854		Approved	FLJ14871	uc002hel.2	Q6QEF8	OTTHUMG00000132732	ENST00000445145.2:c.451+1A>T	17.37:g.27946079T>A			24970205	B3KU26|Q71MF3|Q8WYH7|Q96K02	Silent	SNP	ENST00000445145.2	37																																																																																					0.602	CORO6-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000447831.1	NM_032854	Silent	A	27946079	T	A	27946079	5	1	107	1	0	0	0	0	0	0	1	0	3764	1594	55	5	1000	5	CORO6	17	27946079	Splice_Site	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	915199	27946079	53249131	287	28346										
NF1	4763	hgsc.bcm.edu	37	chr17	29652986	29652986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aaacagactttctctctaagTggtttgttgtttttcctggc	8	8	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:29652986T>C	ENST00000358273.4	+	37	5367	c.4984T>C	c.(4984-4986)Tgg>Cgg	p.W1662R	NF1_ENST00000356175.3_Missense_Mutation_p.W1641R|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1662	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCTCTCTAAGTGGTTTGTTGT	0.428			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											155	141	146					17																	29652986		2203	4300	6503	26677112	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4984T>C	17.37:g.29652986T>C	ENSP00000351015:p.Trp1662Arg		26677112	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569342	0.86439	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.63255	-0.03;-0.03;-0.03	5.83	5.83	0.93111	Cellular retinaldehyde-binding/triple function, C-terminal (2);Armadillo-type fold (1);	0.131866	0.56097	D	0.000025	T	0.80276	0.4593	M	0.79805	2.47	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.83275	0.99;0.996;0.987	T	0.82878	-0.0239	10	0.72032	D	0.01	.	15.3809	0.74654	0.0:0.0:0.0:1.0	.	691;1641;1662	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	R	1662;1641;1307	ENSP00000351015:W1662R;ENSP00000348498:W1641R;ENSP00000389907:W1307R	ENSP00000348498:W1641R	W	+	1	0	NF1	26677112	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.665000	0.83852	2.240000	0.73641	0.528000	0.53228	TGG		0.428	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29652986	T	C	29652986	3	2	107	1	0	0	0	0	1	0	0	0	10387	1696	59	4	5191	4	NF1	17	29652986	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	1706907	29652986	51542224	288	28347										
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30611721	30611721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cattagcacaggcaagttccGgagtcttctggagagccaca	11	11	2	1	rs201683603		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:30611721G>A	ENST00000269051.4	+	3	193	c.179G>A	c.(178-180)cGg>cAg	p.R60Q	RHBDL3_ENST00000536287.1_Intron|RHBDL3_ENST00000538145.1_Missense_Mutation_p.R52Q	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	60	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				GGCAAGTTCCGGAGTCTTCTG	0.597																																																0			17											78	72	74					17																	30611721		2203	4300	6503	27635834	SO:0001583	missense	162494			AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.179G>A	17.37:g.30611721G>A	ENSP00000269051:p.Arg60Gln		27635834	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	37	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800390	0.70567	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145	T;T;T	0.72051	-0.62;-0.62;0.79	4.59	4.59	0.56863	EF-hand-like domain (1);	0.064498	0.64402	D	0.000010	T	0.70833	0.3269	N	0.20766	0.605	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;P;P	0.64144	0.922;0.73;0.876	T	0.66396	-0.5934	10	0.15952	T	0.53	-41.2652	17.6067	0.88040	0.0:0.0:1.0:0.0	.	60;52;60	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	Q	60;60;52	ENSP00000394849:R60Q;ENSP00000269051:R60Q;ENSP00000442092:R52Q	ENSP00000269051:R60Q	R	+	2	0	RHBDL3	27635834	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	4.671000	0.61590	2.375000	0.81037	0.563000	0.77884	CGG		0.597	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		A	30611721	G	A	30611721	3	1	107	1	0	0	0	0	1	0	0	0	13360	1116	39	1	189	1	RHBDL3	17	30611721	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	958735	30611721	50583489	289	28348										
CDK12	51755	hgsc.bcm.edu	37	chr17	37676317	37676317	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gacttccttaaagatgtcgaActcagcaaaatggctcctcc	7	12	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:37676317A>G	ENST00000447079.4	+	11	3105	c.3072A>G	c.(3070-3072)gaA>gaG	p.E1024E	CDK12_ENST00000430627.2_Silent_p.E1024E	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1024					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						AAGATGTCGAACTCAGCAAAA	0.473			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0			17											131	111	118					17																	37676317		2203	4300	6503	34929843	SO:0001819	synonymous_variant	0			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3072A>G	17.37:g.37676317A>G			34929843	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																				0.473	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		G	37676317	A	G	37676317	2	3	107	1	0	0	0	0	0	0	0	1	3134	40	2	4		4	CDK12	17	37676317	Silent	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	7064596	37676317	43518893	290	28349										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37985721	37985721	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agatttggttaaactgtagtCattcaaaaccgctgcacttt	7	8	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:37985721C>A	ENST00000346872.3	-	3	143	c.82G>T	c.(82-84)Gac>Tac	p.D28Y	IKZF3_ENST00000439016.2_Missense_Mutation_p.D28Y|IKZF3_ENST00000346243.3_Missense_Mutation_p.D28Y|IKZF3_ENST00000377952.2_Missense_Mutation_p.D28Y|IKZF3_ENST00000394189.2_Missense_Mutation_p.D28Y|IKZF3_ENST00000535189.1_Intron|IKZF3_ENST00000377945.3_Missense_Mutation_p.D28Y|IKZF3_ENST00000377944.3_Missense_Mutation_p.D28Y|IKZF3_ENST00000467757.1_Missense_Mutation_p.D28Y|IKZF3_ENST00000351680.3_Missense_Mutation_p.D28Y|IKZF3_ENST00000350532.3_Missense_Mutation_p.D28Y|IKZF3_ENST00000439167.2_Intron|IKZF3_ENST00000377958.2_Missense_Mutation_p.D28Y	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	28					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AAACTGTAGTCATTCAAAACC	0.368																																																0			17											129	109	116					17																	37985721		2203	4300	6503	35239247	SO:0001583	missense	22806			AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.82G>T	17.37:g.37985721C>A	ENSP00000344544:p.Asp28Tyr		35239247	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.267381	0.59540	.	.	ENSG00000161405	ENST00000488188;ENST00000346872;ENST00000377945;ENST00000394189;ENST00000377944;ENST00000377958;ENST00000377952;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	T;T;T;T;T;T;T;T;T;T	0.15487	3.21;2.92;2.42;2.96;2.91;2.6;3.21;3.27;3.12;4.08	5.44	4.45	0.53987	.	0.353037	0.23579	N	0.046661	T	0.24160	0.0585	N	0.24115	0.695	0.25432	N	0.988173	D;D;D;D;D;P;D;D;D;D;P	0.89917	0.998;1.0;1.0;0.999;1.0;0.94;0.999;0.972;0.995;0.999;0.952	D;D;D;P;D;P;D;P;P;D;P	0.83275	0.996;0.923;0.957;0.873;0.923;0.754;0.985;0.739;0.865;0.971;0.653	T	0.06463	-1.0825	10	0.31617	T	0.26	-15.1239	9.4108	0.38491	0.0:0.8963:0.0:0.1037	.	28;28;28;28;28;28;28;28;28;28;28	Q9UKT9-9;Q9UKT9-12;Q9UKT9-11;Q9UKT9-13;Q9UKT9-10;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9	.;.;.;.;.;.;.;.;.;.;IKZF3_HUMAN	Y	28	ENSP00000344544:D28Y;ENSP00000367180:D28Y;ENSP00000377741:D28Y;ENSP00000367179:D28Y;ENSP00000367194:D28Y;ENSP00000367188:D28Y;ENSP00000345622:D28Y;ENSP00000341977:D28Y;ENSP00000344471:D28Y;ENSP00000420463:D28Y	ENSP00000341977:D28Y	D	-	1	0	IKZF3	35239247	1.000000	0.71417	0.992000	0.48379	0.801000	0.45260	2.526000	0.45607	1.226000	0.43582	0.650000	0.86243	GAC		0.368	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		A	37985721	C	A	37985721	3	1	107	1	0	0	0	0	1	0	0	0	7637	826	29	2	1471	2	IKZF3	17	37985721	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	309404	37985721	43209489	291	28350										
KRT24	192666	hgsc.bcm.edu	37	chr17	38856477	38856477	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cagcagagaggatctacctgCttgttgaaccgctcctcagc	10	13	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:38856477C>A	ENST00000264651.2	-	4	1070	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	338	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				GATCTACCTGCTTGTTGAACC	0.532																																					GBM(61;380 1051 14702 23642 31441)											0			17											136	130	132					17																	38856477		2203	4300	6503	36110003	SO:0001583	missense	192666				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.1014G>T	17.37:g.38856477C>A	ENSP00000264651:p.Lys338Asn		36110003	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163724	0.57476	.	.	ENSG00000167916	ENST00000264651	T	0.79554	-1.28	5.86	4.89	0.63831	Prefoldin (1);Filament (1);	.	.	.	.	T	0.79329	0.4427	L	0.34521	1.04	0.38263	D	0.941945	P	0.50369	0.934	P	0.55303	0.773	T	0.80930	-0.1162	9	0.49607	T	0.09	.	9.2381	0.37479	0.0:0.7374:0.0:0.2626	.	338	Q2M2I5	K1C24_HUMAN	N	338	ENSP00000264651:K338N	ENSP00000264651:K338N	K	-	3	2	KRT24	36110003	0.014000	0.17966	1.000000	0.80357	0.539000	0.34962	-0.304000	0.08199	1.481000	0.48307	0.563000	0.77884	AAG		0.532	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		A	38856477	C	A	38856477	3	1	107	1	0	0	0	0	1	0	0	0	8482	796	28	2	583	2	KRT24	17	38856477	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	870756	38856477	42338733	292	28351										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42937325	42937325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccttgcgcaggccatcaagcAtcttgggcagctctgagggg	14	12	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:42937325A>G	ENST00000426333.2	-	18	2105	c.1808T>C	c.(1807-1809)aTg>aCg	p.M603T	EFTUD2_ENST00000402521.3_Missense_Mutation_p.M568T|EFTUD2_ENST00000591382.1_Missense_Mutation_p.M603T|EFTUD2_ENST00000592576.1_Missense_Mutation_p.M593T	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	603					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.M603K(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				GCCATCAAGCATCTTGGGCAG	0.542																																					Ovarian(10;65 485 10258 29980 30707)											1	Substitution - Missense(1)	ovary(1)	17											146	128	134					17																	42937325		2203	4300	6503	40292851	SO:0001583	missense	9343			D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1808T>C	17.37:g.42937325A>G	ENSP00000392094:p.Met603Thr		40292851	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	37	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.479213	0.84747	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.73789	-0.78;-0.78	5.45	5.45	0.79879	Elongation factor G/III/V (1);	0.000000	0.85682	D	0.000000	D	0.89125	0.6626	H	0.94222	3.51	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.63703	0.917;0.917	D	0.92245	0.5804	10	0.87932	D	0	-8.6049	15.5233	0.75881	1.0:0.0:0.0:0.0	.	593;603	B4DMC0;Q15029	.;U5S1_HUMAN	T	603;593;568	ENSP00000392094:M603T;ENSP00000385873:M568T	ENSP00000262414:M593T	M	-	2	0	EFTUD2	40292851	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.297000	0.96120	2.071000	0.62044	0.454000	0.30748	ATG		0.542	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		G	42937325	A	G	42937325	3	3	107	1	0	0	0	0	1	0	0	0	4972	217	8	4	1154	4	EFTUD2	17	42937325	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	4080848	42937325	38257885	293	28352										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43912051	43912051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caagcactcgatccgtgcccGagtggcccgtgccatgtcca	11	16	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:43912051G>A	ENST00000398285.3	+	14	1256	c.1256G>A	c.(1255-1257)cGa>cAa	p.R419Q	CRHR1_ENST00000352855.5_Missense_Mutation_p.R350Q|CRHR1_ENST00000577353.1_Missense_Mutation_p.R376Q|CRHR1_ENST00000339069.5_Missense_Mutation_p.E244K|CRHR1_ENST00000293493.7_Missense_Mutation_p.R215Q|CRHR1_ENST00000314537.5_Missense_Mutation_p.R390Q	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	419					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)	p.R390L(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		ATCCGTGCCCGAGTGGCCCGT	0.632																																					Ovarian(110;57 1568 10207 38216 49865)											1	Substitution - Missense(1)	lung(1)	17											63	78	73					17																	43912051		2194	4295	6489	41267832	SO:0001583	missense	1394			L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.1256G>A	17.37:g.43912051G>A	ENSP00000381333:p.Arg419Gln		41267832	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	37	CCDS45712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.501542|5.501542	0.96371|0.96371	.|.	.|.	ENSG00000120088|ENSG00000120088	ENST00000339069|ENST00000293493;ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855	T|T;T;T;T	0.47869|0.68624	0.83|-0.34;-0.34;-0.34;-0.34	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	.|0.056668	.|0.64402	.|D	.|0.000001	T|T	0.80243|0.80243	0.4587|0.4587	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	B|D;D;D;D;D	0.21688|0.89917	0.059|1.0;1.0;0.996;1.0;0.999	B|D;D;P;D;D	0.14023|0.71184	0.01|0.972;0.97;0.783;0.958;0.939	T|T	0.80346|0.80346	-0.1421|-0.1421	9|10	0.87932|0.45353	D|T	0|0.12	.|.	16.3315|16.3315	0.83023|0.83023	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	244|376;419;289;350;390	B4DMR5|P34998-4;P34998;B3TIK8;P34998-3;P34998-2	.|.;CRFR1_HUMAN;.;.;.	K|Q	244|215;419;390;376;350	ENSP00000340522:E244K|ENSP00000293493:R215Q;ENSP00000381333:R419Q;ENSP00000326060:R390Q;ENSP00000344068:R350Q	ENSP00000340522:E244K|ENSP00000293493:R215Q	E|R	+|+	1|2	0|0	CRHR1|CRHR1	41267832|41267832	1.000000|1.000000	0.71417|0.71417	0.913000|0.913000	0.36048|0.36048	0.875000|0.875000	0.50365|0.50365	9.793000|9.793000	0.99091|0.99091	2.451000|2.451000	0.82905|0.82905	0.555000|0.555000	0.69702|0.69702	GAG|CGA		0.632	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			A	43912051	G	A	43912051	3	1	107	1	0	0	0	0	1	0	0	0	3877	1058	37	1	1310	1	CRHR1	17	43912051	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	974726	43912051	37283159	294	28353										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48687292	48687292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggcagctcagccagcgctgcGtcaggtactgcgtctggggt	16	12	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:48687292G>A	ENST00000359106.5	+	26	4755	c.4755G>A	c.(4753-4755)gcG>gcA	p.A1585A	CACNA1G_ENST00000510115.1_Intron|CACNA1G_ENST00000510366.1_Intron|CACNA1G_ENST00000507896.1_Intron|CACNA1G_ENST00000513964.1_Intron|CACNA1G_ENST00000505165.1_Silent_p.A1585A|CACNA1G_ENST00000514717.1_Silent_p.A1528A|CACNA1G_ENST00000515411.1_Intron|CACNA1G_ENST00000352832.5_Intron|CACNA1G_ENST00000503485.1_Silent_p.A1551A|CACNA1G_ENST00000442258.2_Intron|CACNA1G_ENST00000358244.5_Intron|CACNA1G_ENST00000502264.1_Silent_p.A1562A|CACNA1G_ENST00000507510.2_Silent_p.A1585A|CACNA1G_ENST00000515165.1_Silent_p.A1585A|CACNA1G_ENST00000360761.4_Silent_p.A1562A|CACNA1G_ENST00000514079.1_Silent_p.A1592A|CACNA1G_ENST00000512389.1_Intron|CACNA1G_ENST00000507609.1_Silent_p.A1585A|CACNA1G_ENST00000515765.1_Intron|CACNA1G_ENST00000513689.2_Intron|CACNA1G_ENST00000354983.4_Intron|CACNA1G_ENST00000514181.1_Intron|CACNA1G_ENST00000507336.1_Intron|CACNA1G_ENST00000429973.2_Intron	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1585					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CCAGCGCTGCGTCAGGTACTG	0.572																																																0			17											62	73	69					17																	48687292		2170	4260	6430	46042291	SO:0001819	synonymous_variant	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4755G>A	17.37:g.48687292G>A			46042291	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																				0.572	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48687292	G	A	48687292	2	1	107	1	0	0	0	0	0	0	0	1	2550	1132	40	1		1	CACNA1G	17	48687292	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	4775241	48687292	32507918	295	28354										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901682	51901682	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ccaggagccatgcagtgttcCagatcatcctgaagtcagga	11	11	2	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:51901682C>A	ENST00000268919.4	+	1	1444	c.1288C>A	c.(1288-1290)Cag>Aag	p.Q430K		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	430	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGCAGTGTTCCAGATCATCCT	0.507																																																0			17											81	65	70					17																	51901682		2203	4300	6503	49256681	SO:0001583	missense	84643			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1288C>A	17.37:g.51901682C>A	ENSP00000268919:p.Gln430Lys		49256681	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.207479	0.58343	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.17854	2.25	5.73	5.73	0.89815	Kinesin, motor domain (5);	0.000000	0.42682	D	0.000678	T	0.46171	0.1379	M	0.88570	2.965	0.58432	D	0.999995	P	0.46706	0.883	P	0.55011	0.766	T	0.50363	-0.8837	10	0.87932	D	0	.	19.2577	0.93952	0.0:1.0:0.0:0.0	.	430	Q8N4N8	KIF2B_HUMAN	K	430;318	ENSP00000268919:Q430K	ENSP00000268919:Q430K	Q	+	1	0	KIF2B	49256681	1.000000	0.71417	1.000000	0.80357	0.084000	0.17831	7.675000	0.84002	2.854000	0.98071	0.655000	0.94253	CAG		0.507	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		A	51901682	C	A	51901682	3	1	107	1	0	0	0	0	1	0	0	0	8319	595	21	2	1290	2	KIF2B	17	51901682	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3214390	51901682	29293528	296	28355										
MPO	4353	hgsc.bcm.edu	37	chr17	56348030	56348030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctggcctctaggaggcttccCtccaggaagccaggttcaat	11	13	2	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr17:56348030C>T	ENST00000225275.3	-	12	2401	c.2225G>A	c.(2224-2226)aGg>aAg	p.R742K	MPO_ENST00000340482.3_Missense_Mutation_p.R774K	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	742					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R742M(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	GGAGGCTTCCCTCCAGGAAGC	0.542																																																1	Substitution - Missense(1)	ovary(1)	17											84	74	77					17																	56348030		2203	4300	6503	53703029	SO:0001583	missense	4353				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.2225G>A	17.37:g.56348030C>T	ENSP00000225275:p.Arg742Lys		53703029	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	7.850	0.723869	0.15439	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.72942	-0.7;-0.7	5.46	2.4	0.29515	.	0.150054	0.64402	N	0.000016	T	0.50205	0.1602	L	0.28192	0.835	0.26527	N	0.974324	B	0.02656	0.0	B	0.04013	0.001	T	0.27088	-1.0084	10	0.22706	T	0.39	-21.5625	5.3532	0.16047	0.1338:0.5748:0.0:0.2914	.	742	P05164	PERM_HUMAN	K	774;742	ENSP00000344419:R774K;ENSP00000225275:R742K	ENSP00000225275:R742K	R	-	2	0	MPO	53703029	0.030000	0.19436	0.862000	0.33874	0.244000	0.25665	0.302000	0.19192	0.354000	0.24105	-0.136000	0.14681	AGG		0.542	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56348030	C	T	56348030	3	4	107	1	0	0	0	0	1	0	0	0	9762	681	24	3	16	3	MPO	17	56348030	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	4446348	56348030	24847180	297	28356										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9254261	9254261	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agtgttgatgaaaatattgaCtctgaaacagagaaagactc	9	5	1	6			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr18:9254261C>T	ENST00000262126.4	+	9	1236	c.996C>T	c.(994-996)gaC>gaT	p.D332D	ANKRD12_ENST00000400020.3_Silent_p.D309D|ANKRD12_ENST00000383440.2_Silent_p.D309D	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	332						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AAAATATTGACTCTGAAACAG	0.368																																																0			18											84	88	87					18																	9254261		2203	4300	6503	9244261	SO:0001819	synonymous_variant	23253			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.996C>T	18.37:g.9254261C>T			9244261	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	37	CCDS11843.1																																																																																				0.368	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9254261	C	T	9254261	2	4	107	1	0	0	0	0	0	0	0	1	640	564	20	3		3	ANKRD12	18	9254261	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		9254261	68822987	298	28357										
ZNF396	252884	hgsc.bcm.edu	37	chr18	32954210	32954210	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaatcccattacactcctctGaagtttgtgttaggagtgat	9	8	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr18:32954210G>T	ENST00000589332.1	-	2	178	c.47C>A	c.(46-48)tCa>tAa	p.S16*	ZNF396_ENST00000586687.1_Nonsense_Mutation_p.S16*|ZNF396_ENST00000306346.1_Nonsense_Mutation_p.S16*			Q96N95	ZN396_HUMAN	zinc finger protein 396	16					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						ACACTCCTCTGAAGTTTGTGT	0.463																																																0			18											71	65	67					18																	32954210		2203	4300	6503	31208208	SO:0001587	stop_gained	252884			AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"-", "Zinc fingers, C2H2-type"	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.47C>A	18.37:g.32954210G>T	ENSP00000466500:p.Ser16*		31208208	A1L3V0|Q8NF98|Q8TD80	Nonsense_Mutation	SNP	ENST00000589332.1	37		.	.	.	.	.	.	.	.	.	.	G	16.36	3.101667	0.56183	.	.	ENSG00000186496	ENST00000306346;ENST00000399057	.	.	.	3.91	2.09	0.27110	.	1.377880	0.05520	U	0.561865	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	5.7107	0.17933	0.2509:0.0:0.7491:0.0	.	.	.	.	X	16	.	ENSP00000302310:S16X	S	-	2	0	ZNF396	31208208	0.012000	0.17670	0.001000	0.08648	0.047000	0.14425	1.890000	0.39728	0.602000	0.29896	0.555000	0.69702	TCA		0.463	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756		T	32954210	G	T	32954210	4	4	107	1	0	0	0	0	0	1	0	0	17921	1294	45	2	970	2	ZNF396	18	32954210	Nonsense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	23699949	32954210	45123038	299	28358										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48573537	48573537	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	catttgcaaaaagagcaattGaaagtttggtaaagaagctg	10	4	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr18:48573537G>T	ENST00000342988.3	+	2	659	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.E41*|SMAD4_ENST00000588745.1_Nonsense_Mutation_p.E41*|SMAD4_ENST00000452201.2_Nonsense_Mutation_p.E41*	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	41	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(5)|p.E41fs*8(1)|p.A36_K45delAKRAIESLVK(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AAGAGCAATTGAAAGTTTGGT	0.363																																																43	Whole gene deletion(36)|Unknown(5)|Complex - frameshift(1)|Deletion - In frame(1)	pancreas(26)|large_intestine(4)|stomach(3)|breast(3)|lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|NS(1)	18											128	126	127					18																	48573537		2203	4300	6503	46827535	SO:0001587	stop_gained	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.121G>T	18.37:g.48573537G>T	ENSP00000341551:p.Glu41*		46827535	A8K405	Nonsense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	43	9.853670	0.99280	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9469	0.92625	0.0:0.0:1.0:0.0	.	.	.	.	X	41	.	ENSP00000341551:E41X	E	+	1	0	SMAD4	46827535	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.869000	0.99810	2.774000	0.95407	0.655000	0.94253	GAA		0.363	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48573537	G	T	48573537	4	4	107	1	0	0	0	0	0	1	0	0	14797	1291	45	2	123	2	SMAD4	18	48573537	Nonsense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	15619327	48573537	29503711	300	28359										
DOK6	220164	hgsc.bcm.edu	37	chr18	67425052	67425052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caatatctcttcctcgcagcGcgtactggcatcacatcact	6	15	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr18:67425052G>A	ENST00000382713.5	+	7	989	c.799G>A	c.(799-801)Gcg>Acg	p.A267T		NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	267								p.A267T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TCCTCGCAGCGCGTACTGGCA	0.413																																																1	Substitution - Missense(1)	prostate(1)	18											132	111	118					18																	67425052		2203	4300	6503	65576032	SO:0001583	missense	220164			AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.799G>A	18.37:g.67425052G>A	ENSP00000372160:p.Ala267Thr		65576032	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	37	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127972	0.94473	.	.	ENSG00000206052	ENST00000382713	T	0.81415	-1.49	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.81602	0.4857	L	0.38175	1.15	0.58432	D	0.999999	D	0.62365	0.991	P	0.56398	0.797	T	0.76424	-0.2964	10	0.15499	T	0.54	-19.0242	18.4033	0.90525	0.0:0.0:1.0:0.0	.	267	Q6PKX4	DOK6_HUMAN	T	267	ENSP00000372160:A267T	ENSP00000372160:A267T	A	+	1	0	DOK6	65576032	1.000000	0.71417	0.394000	0.26270	0.974000	0.67602	7.786000	0.85741	2.681000	0.91329	0.561000	0.74099	GCG		0.413	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		A	67425052	G	A	67425052	3	1	107	1	0	0	0	0	1	0	0	0	4712	1087	38	1	825	1	DOK6	18	67425052	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	18851515	67425052	10652196	301	28360										
SH3GL1	6455	hgsc.bcm.edu	37	chr19	4362366	4362366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cggatgggcttgtcggaagaTcggaaagacgatgaagctaa	15	6	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:4362366T>C	ENST00000269886.3	-	9	1048	c.870A>G	c.(868-870)cgA>cgG	p.R290R	AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000598564.1_Silent_p.R226R|SH3GL1_ENST00000417295.2_Silent_p.R242R	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	290					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		TGTCGGAAGATCGGAAAGACG	0.627			T	MLL	AL																																NSCLC(94;1152 2133 30346 33362)		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	0			19											73	73	73					19																	4362366		2203	4300	6503	4313366	SO:0001819	synonymous_variant	6455				CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"extra 11-19 leukemia fusion", "fusion partner of MLL", "SH3-containing Grb-2-like 1 protein", "SH3-containing protein EEN", "SH3 domain GRB2-like 1"	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.870A>G	19.37:g.4362366T>C			4313366	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	37	CCDS32874.1																																																																																				0.627	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025		C	4362366	T	C	4362366	2	2	107	1	0	0	0	0	0	0	0	1	14287	1422	50	4		4	SH3GL1	19	4362366	Silent	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10		4362366	54766617	302	28361										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11123640	11123640	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgcagatcaaaggtttggagTggctggtgtccctgtacaac	13	8	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:11123640T>C	ENST00000429416.3	+	17	2571	c.2290T>C	c.(2290-2292)Tgg>Cgg	p.W764R	SMARCA4_ENST00000413806.3_Missense_Mutation_p.W764R|SMARCA4_ENST00000450717.3_Missense_Mutation_p.W764R|RN7SL192P_ENST00000584303.1_RNA|SMARCA4_ENST00000344626.4_Missense_Mutation_p.W764R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.W764R|SMARCA4_ENST00000541122.2_Missense_Mutation_p.W764R|SMARCA4_ENST00000444061.3_Missense_Mutation_p.W764R|SMARCA4_ENST00000358026.2_Missense_Mutation_p.W764R|CTC-215O4.4_ENST00000587831.1_RNA|SMARCA4_ENST00000589677.1_Missense_Mutation_p.W764R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	764					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.W764R(2)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AGGTTTGGAGTGGCTGGTGTC	0.592			"F, N, Mis"		NSCLC																																		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	3	Substitution - Missense(2)|Unknown(1)	lung(3)	19											108	88	95					19																	11123640		2203	4300	6503	10984640	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2290T>C	19.37:g.11123640T>C	ENSP00000395654:p.Trp764Arg		10984640	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331506	0.81690	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73;-3.73;-3.73;-3.73	4.73	4.73	0.59995	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98670	0.9554	H	0.98802	4.335	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.99184	1.0868	10	0.87932	D	0	-19.8408	13.3423	0.60551	0.0:0.0:0.0:1.0	.	764;764;764;764;764;764;764	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	R	764;764;828;764;764;764;764;764	ENSP00000395654:W764R;ENSP00000350720:W764R;ENSP00000343896:W764R;ENSP00000445036:W764R;ENSP00000392837:W764R;ENSP00000397783:W764R;ENSP00000414727:W764R	ENSP00000343896:W764R	W	+	1	0	SMARCA4	10984640	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.868000	0.87116	1.988000	0.58038	0.533000	0.62120	TGG		0.592	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11123640	T	C	11123640	3	2	107	1	0	0	0	0	1	0	0	0	14807	1696	59	4	2348	4	SMARCA4	19	11123640	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	6761274	11123640	48005343	303	28362										
JAK3	3718	hgsc.bcm.edu	37	chr19	17953854	17953854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acctgacagtcttcagcagcTctcccggccgctgggcctgc	11	17	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:17953854T>C	ENST00000527670.1	-	4	577	c.548A>G	c.(547-549)gAg>gGg	p.E183G	JAK3_ENST00000534444.1_Missense_Mutation_p.E183G|JAK3_ENST00000458235.1_Missense_Mutation_p.E183G|JAK3_ENST00000526008.1_5'UTR			P52333	JAK3_HUMAN	Janus kinase 3	183	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.E183G(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CTTCAGCAGCTCTCCCGGCCG	0.682		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	19											23	24	24					19																	17953854		2175	4247	6422	17814854	SO:0001583	missense	3718			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.548A>G	19.37:g.17953854T>C	ENSP00000432511:p.Glu183Gly		17814854	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736147	0.49045	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.71341	-0.56;-0.56;-0.56	4.92	3.85	0.44370	Band 4.1 domain (1);FERM domain (1);	0.801760	0.11245	N	0.584231	T	0.63260	0.2496	L	0.46741	1.465	0.21627	N	0.999612	P;B;B	0.34724	0.465;0.409;0.265	B;B;B	0.34242	0.178;0.138;0.08	T	0.57213	-0.7850	10	0.52906	T	0.07	-17.1319	9.2695	0.37661	0.1606:0.0:0.0:0.8394	.	183;183;183	B4DK43;P52333-2;P52333	.;.;JAK3_HUMAN	G	183	ENSP00000391676:E183G;ENSP00000432511:E183G;ENSP00000436421:E183G	ENSP00000413248:E183G	E	-	2	0	JAK3	17814854	0.949000	0.32298	0.086000	0.20670	0.039000	0.13416	5.410000	0.66381	1.866000	0.54105	0.397000	0.26171	GAG		0.682	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		C	17953854	T	C	17953854	3	2	107	1	0	0	0	0	1	0	0	0	7960	1551	54	4	2906	4	JAK3	19	17953854	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	6830214	17953854	41175129	304	28363										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440552	37440552	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gaaaatatttcctctgagttCagacattgttacttcaagac	6	8	3	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:37440552C>T	ENST00000333987.7	+	7	1003	c.497C>T	c.(496-498)tCa>tTa	p.S166L	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.S102L	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	166					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S166*(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTCTGAGTTCAGACATTGTT	0.343																																																1	Substitution - Nonsense(1)	ovary(1)	19											89	82	84					19																	37440552		1839	4084	5923	42132392	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.497C>T	19.37:g.37440552C>T	ENSP00000334685:p.Ser166Leu		42132392	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	C	9.572	1.121224	0.20877	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.11930	2.73;2.73	4.39	2.2	0.27929	.	0.000000	0.30890	N	0.008675	T	0.12008	0.0292	L	0.46157	1.445	0.20196	N	0.999922	B	0.02656	0.0	B	0.04013	0.001	T	0.19418	-1.0306	10	0.48119	T	0.1	.	9.0015	0.36085	0.0:0.8198:0.0:0.1802	.	166	Q3ZCX4	ZN568_HUMAN	L	166;102	ENSP00000334685:S166L;ENSP00000394514:S102L	ENSP00000334685:S166L	S	+	2	0	ZNF568	42132392	0.024000	0.19004	0.033000	0.17914	0.744000	0.42396	2.547000	0.45786	0.561000	0.29186	0.655000	0.94253	TCA		0.343	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37440552	C	T	37440552	3	4	107	1	0	0	0	0	1	0	0	0	18038	838	29	3	515	3	ZNF568	19	37440552	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	19486698	37440552	21688431	305	28364										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38861248	38861248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cctcgtggtgaagggctgcaCgatgatccggtggaagataa	15	8	0	3			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:38861248C>T	ENST00000409235.3	+	29	3411	c.3296C>T	c.(3295-3297)aCg>aTg	p.T1099M	CATSPERG_ENST00000410018.1_Missense_Mutation_p.T1059M|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	1099					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						AAGGGCTGCACGATGATCCGG	0.542																																																0			19											240	179	200					19																	38861248		2203	4300	6503	43553088	SO:0001583	missense	0			AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.3296C>T	19.37:g.38861248C>T	ENSP00000386962:p.Thr1099Met		43553088	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747547	0.49257	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	T;T	0.24151	1.88;1.87	5.43	-2.18	0.07037	.	0.709470	0.12700	N	0.446436	T	0.11580	0.0282	N	0.19112	0.55	0.09310	N	0.999999	D;P	0.52996	0.957;0.929	B;B	0.41691	0.364;0.276	T	0.14172	-1.0482	10	0.62326	D	0.03	-12.5893	0.3829	0.00398	0.321:0.2737:0.1572:0.2481	.	1099;1059	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	M	1059;1099;1099	ENSP00000387057:T1059M;ENSP00000386962:T1099M	ENSP00000386962:T1099M	T	+	2	0	CATSPERG	43553088	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.419000	0.07071	-0.770000	0.04614	-0.410000	0.06199	ACG		0.542	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		T	38861248	C	T	38861248	3	4	107	1	0	0	0	0	1	0	0	0	2698	536	19	1	3406	1	CATSPERG	19	38861248	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	1420696	38861248	20267735	306	28365										
RYR1	6261	hgsc.bcm.edu	37	chr19	39008158	39008158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	catgctatgcagctacctgcCccgatggtgggagcgcgggc	15	13	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:39008158C>A	ENST00000359596.3	+	66	9845	c.9845C>A	c.(9844-9846)cCc>cAc	p.P3282H	RYR1_ENST00000360985.3_Missense_Mutation_p.P3282H|RYR1_ENST00000355481.4_Missense_Mutation_p.P3282H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3282					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AGCTACCTGCCCCGATGGTGG	0.682																																																0			19											42	35	37					19																	39008158		2203	4299	6502	43699998	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9845C>A	19.37:g.39008158C>A	ENSP00000352608:p.Pro3282His		43699998	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385608	0.25031	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.91237	-2.81;-2.81;-2.81	3.64	3.64	0.41730	.	0.078945	0.50627	U	0.000101	D	0.94049	0.8093	M	0.75264	2.295	0.48135	D	0.999593	D;D;D	0.71674	0.998;0.998;0.997	P;P;P	0.62740	0.906;0.906;0.808	D	0.94876	0.8034	10	0.72032	D	0.01	.	15.0583	0.71933	0.0:1.0:0.0:0.0	.	3282;3282;3282	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	H	3282;3282;3282;202	ENSP00000352608:P3282H;ENSP00000347667:P3282H;ENSP00000354254:P3282H	ENSP00000347667:P3282H	P	+	2	0	RYR1	43699998	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	7.603000	0.82811	1.859000	0.53934	0.205000	0.17691	CCC		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39008158	C	A	39008158	3	1	107	1	0	0	0	0	1	0	0	0	13805	623	22	2	10107	2	RYR1	19	39008158	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	146910	39008158	20120825	307	28366										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39913401	39913401	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	catgacattcccaagttcccCggagactcccaggtgcctgg	10	15	0	2	rs145859648	byFrequency	TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:39913401C>G	ENST00000409794.3	+	18	2557	c.1707C>G	c.(1705-1707)ccC>ccG	p.P569P	PLEKHG2_ENST00000458508.2_Silent_p.P510P|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Silent_p.P540P|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	569					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCAAGTTCCCCGGAGACTCCC	0.587																																																0			19											71	59	63					19																	39913401		2203	4300	6503	44605241	SO:0001819	synonymous_variant	64857			AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1707C>G	19.37:g.39913401C>G			44605241	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	0.280	-0.986944	0.02180	.	.	ENSG00000090924	ENST00000205135	T	0.69806	-0.43	5.43	-10.1	0.00402	.	0.492114	0.17349	N	0.177442	T	0.52980	0.1768	.	.	.	0.19575	N	0.999963	.	.	.	.	.	.	T	0.53265	-0.8463	7	0.87932	D	0	.	5.3799	0.16186	0.105:0.1913:0.1036:0.6001	.	.	.	.	R	437	ENSP00000205135:P437R	ENSP00000205135:P437R	P	+	2	0	PLEKHG2	44605241	0.002000	0.14202	0.003000	0.11579	0.012000	0.07955	-1.273000	0.02823	-1.260000	0.02465	-0.948000	0.02665	CCG		0.587	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		G	39913401	C	G	39913401	2	3	107	1	0	0	0	0	0	0	0	1	12100	639	23	5		5	PLEKHG2	19	39913401	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	905243	39913401	19215582	308	28367										
PSG3	5671	hgsc.bcm.edu	37	chr19	43233350	43233350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aacagagcaagcatagagccCgctatgctttgtagtaatct	9	9	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:43233350C>T	ENST00000327495.5	-	5	1352	c.1168G>A	c.(1168-1170)Ggg>Agg	p.G390R	PSG3_ENST00000595140.1_Missense_Mutation_p.G390R	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	390	Ig-like C2-type 3.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G390W(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				GCATAGAGCCCGCTATGCTTT	0.468																																																1	Substitution - Missense(1)	lung(1)	19											184	190	188					19																	43233350		2203	4300	6503	47925190	SO:0001583	missense	5671				CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.1168G>A	19.37:g.43233350C>T	ENSP00000332215:p.Gly390Arg		47925190	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	N	11.34	1.610399	0.28712	.	.	ENSG00000221826	ENST00000327495	T	0.57595	0.39	1.11	1.11	0.20524	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.77425	0.4128	H	0.96691	3.865	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.986;1.0	T	0.62914	-0.6753	9	0.87932	D	0	.	5.5059	0.16854	0.0:1.0:0.0:0.0	.	314;390;390	Q08266;P11464-2;Q16557	.;.;PSG3_HUMAN	R	390	ENSP00000332215:G390R	ENSP00000332215:G390R	G	-	1	0	PSG3	47925190	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.133000	0.10451	0.549000	0.28973	0.393000	0.25936	GGG		0.468	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		T	43233350	C	T	43233350	3	4	107	1	0	0	0	0	1	0	0	0	12690	652	23	1	126	1	PSG3	19	43233350	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3319949	43233350	15895633	309	28368										
PVR	5817	hgsc.bcm.edu	37	chr19	45162043	45162043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tgagcactcaggcatatcccGtaacgccatcatcttcctgg	8	14	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:45162043G>A	ENST00000425690.3	+	6	1324	c.1025G>A	c.(1024-1026)cGt>cAt	p.R342H	PVR_ENST00000344956.4_Intron|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000403059.4_Intron|PVR_ENST00000406449.4_Missense_Mutation_p.R342H	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	342					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GGCATATCCCGTAACGCCATC	0.468																																																0			19											167	155	159					19																	45162043		2203	4300	6503	49853883	SO:0001583	missense	5817			BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.1025G>A	19.37:g.45162043G>A	ENSP00000402060:p.Arg342His		49853883	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	G	1.842	-0.467115	0.04476	.	.	ENSG00000073008	ENST00000425690;ENST00000406449	D;D	0.87650	-2.25;-2.28	2.85	-5.7	0.02421	.	9.596360	0.00616	U	0.000432	T	0.70535	0.3235	N	0.22421	0.69	0.09310	N	1	B;P	0.35714	0.0;0.517	B;B	0.29353	0.0;0.101	T	0.67440	-0.5670	10	0.19147	T	0.46	.	0.2158	0.00162	0.3367:0.1446:0.233:0.2858	.	342;342	P15151-4;P15151	.;PVR_HUMAN	H	342	ENSP00000402060:R342H;ENSP00000383907:R342H	ENSP00000383907:R342H	R	+	2	0	PVR	49853883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.469000	0.00460	-2.561000	0.00473	-1.102000	0.02115	CGT		0.468	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		A	45162043	G	A	45162043	3	1	107	1	0	0	0	0	1	0	0	0	12874	1145	40	1	1047	1	PVR	19	45162043	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	1928693	45162043	13966940	310	28369										
SULT2A1	6822	hgsc.bcm.edu	37	chr19	48386926	48386926	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ctccgtttcactgagtgctgTatacccaatctcactctcta	5	14	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:48386926T>A	ENST00000222002.3	-	2	392	c.253A>T	c.(253-255)Aca>Tca	p.T85S		NM_003167.3	NP_003158.2	Q06520	ST2A1_HUMAN	sulfotransferase family, cytosolic, 2A, dehydroepiandrosterone (DHEA)-preferring, member 1	85					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|bile acid catabolic process (GO:0030573)|cellular lipid metabolic process (GO:0044255)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	bile-salt sulfotransferase activity (GO:0047704)|sulfotransferase activity (GO:0008146)	p.T85A(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)	Abiraterone(DB05812)|Acetaminophen(DB00316)	CTGAGTGCTGTATACCCAATC	0.527																																																1	Substitution - Missense(1)	ovary(1)	19											142	106	118					19																	48386926		2203	4300	6503	53078738	SO:0001583	missense	6822			X70222	CCDS12707.1	19q13.3	2014-05-21			ENSG00000105398	ENSG00000105398	2.8.2.2	"Sulfotransferases, cytosolic"	11458	protein-coding gene	gene with protein product		125263		STD		1588921, 7736787	Standard	NM_003167		Approved	DHEA-ST	uc002phr.2	Q06520	OTTHUMG00000162469	ENST00000222002.3:c.253A>T	19.37:g.48386926T>A	ENSP00000222002:p.Thr85Ser		53078738		Missense_Mutation	SNP	ENST00000222002.3	37	CCDS12707.1	.	.	.	.	.	.	.	.	.	.	T	1.387	-0.581704	0.03854	.	.	ENSG00000105398	ENST00000222002	T	0.01599	4.74	2.83	-4.92	0.03075	Sulfotransferase domain (1);	2.385940	0.01781	N	0.031738	T	0.00936	0.0031	N	0.02345	-0.59	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48340	-0.9044	10	0.22706	T	0.39	.	7.0836	0.25245	0.0:0.5335:0.1476:0.319	.	85	Q06520	ST2A1_HUMAN	S	85	ENSP00000222002:T85S	ENSP00000222002:T85S	T	-	1	0	SULT2A1	53078738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.940000	0.01543	-1.299000	0.02344	-0.269000	0.10298	ACA		0.527	SULT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369044.1	NM_003167		A	48386926	T	A	48386926	3	1	107	1	0	0	0	0	1	0	0	0	15420	1638	57	5	624	5	SULT2A1	19	48386926	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	3224883	48386926	10742057	311	28370										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49363681	49363681	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aggtcttctaaggtgtcagcGgccaaaacgtaggtcctcat	11	10	4	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:49363681G>A	ENST00000263265.6	-	6	957	c.402C>T	c.(400-402)gcC>gcT	p.A134A	PLEKHA4_ENST00000355496.5_Silent_p.A134A|PLEKHA4_ENST00000596713.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	134	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		AGGTGTCAGCGGCCAAAACGT	0.652																																																0			19											59	60	60					19																	49363681		2203	4300	6503	54055493	SO:0001819	synonymous_variant	57664			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.402C>T	19.37:g.49363681G>A			54055493	Q8N4M8|Q8N658	Silent	SNP	ENST00000263265.6	37	CCDS12737.1																																																																																				0.652	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			A	49363681	G	A	49363681	2	1	107	1	0	0	0	0	0	0	0	1	12089	1103	39	1		1	PLEKHA4	19	49363681	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	976755	49363681	9765302	312	28371										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52034594	52034594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ggtctcctcctgcacttcttCgtctgggtcgtttgtggcca	11	13	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:52034594C>T	ENST00000425629.3	-	2	401	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K	SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.E83K|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.E47K|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.E83K|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.E83K|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.E83K	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	83	Ig-like V-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		TGCACTTCTTCGTCTGGGTCG	0.582																																																0			19											68	73	71					19																	52034594		2196	4299	6495	56726406	SO:0001583	missense	946			D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.247G>A	19.37:g.52034594C>T	ENSP00000401502:p.Glu83Lys		56726406	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	.	.	.	.	.	.	.	.	.	.	C	7.332	0.619123	0.14129	.	.	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300;ENST00000426829	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	2.89	-5.78	0.02362	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	3.177270	0.01482	N	0.016736	T	0.28001	0.0690	N	0.02315	-0.6	0.09310	N	1	B;B;B;B;B;B;B	0.09022	0.001;0.002;0.0;0.0;0.001;0.0;0.001	B;B;B;B;B;B;B	0.09377	0.003;0.004;0.004;0.001;0.001;0.002;0.004	T	0.11084	-1.0602	10	0.19590	T	0.45	.	0.4345	0.00476	0.2172:0.2928:0.1999:0.2901	.	83;47;83;83;83;83;83	F8WA78;C9JBE5;C9JUT6;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;.;SIGL6_HUMAN	K	72;83;83;83;47;83;83	ENSP00000375674:E83K;ENSP00000401502:E83K;ENSP00000353071:E83K;ENSP00000410679:E47K;ENSP00000345907:E83K	ENSP00000345907:E83K	E	-	1	0	SIGLEC6	56726406	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.186000	0.03070	-1.169000	0.02772	-2.155000	0.00331	GAA		0.582	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		T	52034594	C	T	52034594	3	4	107	1	0	0	0	0	1	0	0	0	14349	893	31	1	1175	1	SIGLEC6	19	52034594	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	2670913	52034594	7094389	313	28372										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55493981	55493981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gcgctgatcgaggacatctgCggggactgggagaagaagaa	17	7	1	4	rs370946962		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:55493981C>T	ENST00000543010.1	+	6	1058	c.915C>T	c.(913-915)tgC>tgT	p.C305C	NLRP2_ENST00000538819.1_Silent_p.C281C|NLRP2_ENST00000537859.1_Silent_p.C283C|NLRP2_ENST00000263437.6_Silent_p.C302C|NLRP2_ENST00000339757.7_Silent_p.C283C|NLRP2_ENST00000391721.4_Silent_p.C281C|NLRP2_ENST00000448584.2_Silent_p.C305C|NLRP2_ENST00000427260.2_Silent_p.C282C	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	305	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		AGGACATCTGCGGGGACTGGG	0.602																																																0			19						C	,,,	0,4406		0,0,2203	50	49	50		915,849,846,915	-2.8	0	19		50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	305/1063,283/1041,282/1040,305/1063	55493981	1,13005	2203	4300	6503	60185793	SO:0001819	synonymous_variant	55655			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.915C>T	19.37:g.55493981C>T			60185793	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																				0.602	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55493981	C	T	55493981	2	4	107	1	0	0	0	0	0	0	0	1	10508	776	27	1		1	NLRP2	19	55493981	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	3459387	55493981	3635002	314	28373										
SBK2	646643	hgsc.bcm.edu	37	chr19	56041622	56041622	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cggtacaccaggccgcgggcGtggatgtactccagggcgga	17	12	0	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:56041622G>A	ENST00000413299.1	-	4	562	c.525C>T	c.(523-525)caC>caT	p.H175H	SBK2_ENST00000344158.3_Silent_p.H175H	NM_001101401.2	NP_001094871.2	P0C263	SBK2_HUMAN	SH3 domain binding kinase family, member 2	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9						GGCCGCGGGCGTGGATGTACT	0.741																																																0			19											2	3	2					19																	56041622		1508	3111	4619	60733434	SO:0001819	synonymous_variant	646643				CCDS42631.1	19q13.42	2013-09-27	2013-09-27		ENSG00000187550	ENSG00000187550			34416	protein-coding gene	gene with protein product			"SH3-binding domain kinase family, member 2"				Standard	NM_001101401		Approved	SGK069	uc010ygc.2	P0C263	OTTHUMG00000155830	ENST00000413299.1:c.525C>T	19.37:g.56041622G>A			60733434		Silent	SNP	ENST00000413299.1	37	CCDS42631.1																																																																																				0.741	SBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341919.1	NM_001101401		A	56041622	G	A	56041622	2	1	107	1	0	0	0	0	0	0	0	1	13898	1136	40	1		1	SBK2	19	56041622	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	547641	56041622	3087361	315	28374										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953450	56953450	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cattttcagggattttctctCcagcatgaattcttttatgt	6	8	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:56953450C>G	ENST00000504904.3	-	7	1633	c.914G>C	c.(913-915)gGa>gCa	p.G305A	ZNF667_ENST00000292069.6_Missense_Mutation_p.G305A|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.G433A			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		GATTTTCTCTCCAGCATGAAT	0.333																																																0			19											87	91	90					19																	56953450		2200	4300	6500	61645262	SO:0001583	missense	63934				CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.914G>C	19.37:g.56953450C>G	ENSP00000439402:p.Gly305Ala		61645262	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723401	0.30503	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518	T;T;T	0.05025	3.51;3.55;3.55	4.96	3.94	0.45596	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.162786	0.29348	N	0.012410	T	0.11067	0.0270	M	0.69823	2.125	0.32667	N	0.517304	P;P	0.52316	0.952;0.914	P;B	0.44422	0.449;0.43	T	0.14868	-1.0457	10	0.62326	D	0.03	-6.1867	10.9162	0.47137	0.0:0.9089:0.0:0.0911	.	433;305	E7EPS0;Q5HYK9	.;ZN667_HUMAN	A	433;305;305;87	ENSP00000344699:G433A;ENSP00000439402:G305A;ENSP00000292069:G305A	ENSP00000292069:G305A	G	-	2	0	ZNF667	61645262	0.034000	0.19679	0.887000	0.34795	0.354000	0.29330	0.787000	0.26858	1.323000	0.45263	0.591000	0.81541	GGA		0.333	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		G	56953450	C	G	56953450	3	3	107	1	0	0	0	0	1	0	0	0	18113	855	30	5	922	5	ZNF667	19	56953450	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	911828	56953450	2175533	316	28375										
PEG3	5178	hgsc.bcm.edu	37	chr19	57325432	57325432	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttcagctctttcttctgggtCttcaatacctgcaccatctg	6	13	7	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr19:57325432C>A	ENST00000326441.9	-	10	4741	c.4378G>T	c.(4378-4380)Gac>Tac	p.D1460Y	ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.D1460Y|PEG3_ENST00000593695.1_Missense_Mutation_p.D1334Y|PEG3_ENST00000598410.1_Missense_Mutation_p.D1336Y|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1460	Glu-rich.				apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.D1460N(1)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCTTCTGGGTCTTCAATACCT	0.562																																																1	Substitution - Missense(1)	ovary(1)	19											111	101	104					19																	57325432		2203	4300	6503	62017244	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4378G>T	19.37:g.57325432C>A	ENSP00000326581:p.Asp1460Tyr		62017244	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650694	0.67472	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02863	4.13;4.13	4.07	4.07	0.47477	.	0.000000	0.47852	D	0.000210	T	0.06781	0.0173	L	0.27053	0.805	.	.	.	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65573	0.936;0.936;0.936	T	0.24297	-1.0164	9	0.62326	D	0.03	-33.8222	12.0647	0.53581	0.0:1.0:0.0:0.0	.	1336;1460;1395	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	Y	1460	ENSP00000326581:D1460Y;ENSP00000403051:D1460Y	ENSP00000326581:D1460Y	D	-	1	0	ZIM2	62017244	0.961000	0.32948	1.000000	0.80357	0.929000	0.56500	2.188000	0.42612	2.555000	0.86185	0.650000	0.86243	GAC		0.562	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57325432	C	A	57325432	3	1	107	1	0	0	0	0	1	0	0	0	11751	913	32	2	392	2	PEG3	19	57325432	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	371982	57325432	1803551	317	28376										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8769134	8769134	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gatgtcgcagaagagtgtcaGaacaatcagttaaagaagct	11	6	2	4			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr20:8769134G>A	ENST00000338037.6	+	28	3177	c.3150G>A	c.(3148-3150)caG>caA	p.Q1050Q	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Silent_p.Q1050Q|PLCB1_ENST00000378637.2_Silent_p.Q1050Q	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1050					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AAGAGTGTCAGAACAATCAGT	0.378																																																0			20											70	68	69					20																	8769134		2203	4300	6503	8717134	SO:0001819	synonymous_variant	23236			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3150G>A	20.37:g.8769134G>A			8717134	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																				0.378	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			A	8769134	G	A	8769134	2	1	107	1	0	0	0	0	0	0	0	1	12058	933	33	3		3	PLCB1	20	8769134	Silent	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10		8769134	54256386	318	28377										
PLK1S1	55857	hgsc.bcm.edu	37	chr20	21209692	21209692	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	aagaaggccacccttcaggaTaatacaaatcaaactgaaaa	6	9	2	2	rs372337969		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr20:21209692T>C	ENST00000457464.1	+	0	1319																											CCCTTCAGGATAATACAAATC	0.408																																																0			20											65	60	62					20																	21209692		1883	4107	5990	21157692			0																															20.37:g.21209692T>C			21157692		Missense_Mutation	SNP	ENST00000457464.1	37																																																																																					0.408	PLK1S1-003	KNOWN	not_organism_supported|sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000078262.2			C	21209692	T	C	21209692	1	2	107	0	1	0	0	0	0	0	0	0	12126	1403	49	4		4	PLK1S1	20	21209692	RNA	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	12440558	21209692	41815828	319	28378										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45192160	45192160	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gactgtgcccggaatcatcaGatacagggggtgcactctca	12	11	3	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr20:45192160G>T	ENST00000279027.4	-	12	1543	c.1525C>A	c.(1525-1527)Ctg>Atg	p.L509M	SLC13A3_ENST00000495082.1_Missense_Mutation_p.L462M|SLC13A3_ENST00000290317.5_Missense_Mutation_p.L462M|SLC13A3_ENST00000435032.1_Missense_Mutation_p.L94M|SLC13A3_ENST00000472148.1_Missense_Mutation_p.L427M|SLC13A3_ENST00000413164.2_Missense_Mutation_p.L459M|SLC13A3_ENST00000396360.1_Missense_Mutation_p.L427M	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	509					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	GGAATCATCAGATACAGGGGG	0.612																																																0			20											41	37	38					20																	45192160		2203	4300	6503	44625567	SO:0001583	missense	64849			AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1525C>A	20.37:g.45192160G>T	ENSP00000279027:p.Leu509Met		44625567	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459264	0.43634	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000435032;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082	T;T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02;4.02	5.36	-1.7	0.08159	.	0.191130	0.47093	N	0.000252	T	0.05868	0.0153	M	0.72576	2.205	0.80722	D	1	P;P;P;B;B;P	0.37636	0.603;0.548;0.532;0.184;0.219;0.587	B;B;B;B;P;P	0.44359	0.363;0.281;0.319;0.319;0.447;0.447	T	0.31138	-0.9954	10	0.52906	T	0.07	-6.7871	2.8675	0.05605	0.3187:0.1125:0.4559:0.113	.	459;94;427;462;411;509	B4DIR8;B4E181;Q8WWT9-3;F6WI18;B4DF27;Q8WWT9	.;.;.;.;.;S13A3_HUMAN	M	462;427;94;509;427;459;462	ENSP00000290317:L462M;ENSP00000379648:L427M;ENSP00000403394:L94M;ENSP00000279027:L509M;ENSP00000420177:L427M;ENSP00000415852:L459M;ENSP00000419621:L462M	ENSP00000279027:L509M	L	-	1	2	SLC13A3	44625567	0.037000	0.19845	0.078000	0.20375	0.832000	0.47134	0.236000	0.17967	-0.599000	0.05798	0.561000	0.74099	CTG		0.612	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45192160	G	T	45192160	3	4	107	1	0	0	0	0	1	0	0	0	14430	933	33	2	291	2	SLC13A3	20	45192160	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	23982468	45192160	17833360	320	28379										
AURKA	6790	hgsc.bcm.edu	37	chr20	54958085	54958085	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tctcttctgagctgatgctcCactccggctttctccagctg	8	15	3	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr20:54958085C>T	ENST00000347343.2	-	5	789	c.522G>A	c.(520-522)gtG>gtA	p.V174V	AURKA_ENST00000395911.1_Silent_p.V174V|AURKA_ENST00000395914.1_Silent_p.V174V|AURKA_ENST00000371356.2_Silent_p.V174V|AURKA_ENST00000312783.6_Silent_p.V174V|AURKA_ENST00000395907.1_Silent_p.V174V|AURKA_ENST00000395909.4_Silent_p.V174V|AURKA_ENST00000395915.3_Silent_p.V174V|AURKA_ENST00000395913.3_Silent_p.V174V	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	174	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> M (in a metastatic melanoma sample; somatic mutation; constitutively enhanced kinase activity). {ECO:0000269|PubMed:17344846}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			GCTGATGCTCCACTCCGGCTT	0.428																																					Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)											0			20											113	106	108					20																	54958085		2203	4300	6503	54391492	SO:0001819	synonymous_variant	6790			BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11393	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 47", "Aurora-A kinase"	603072	"serine/threonine kinase 15", " serine/threonine kinase 6"	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.522G>A	20.37:g.54958085C>T			54391492	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Silent	SNP	ENST00000347343.2	37	CCDS13451.1																																																																																				0.428	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600		T	54958085	C	T	54958085	2	4	107	1	0	0	0	0	0	0	0	1	1222	581	21	3		3	AURKA	20	54958085	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	9765925	54958085	8067435	321	28380										
TFAP2C	7022	hgsc.bcm.edu	37	chr20	55211794	55211794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agatggcagctaggaagaacAtgctattggcggcccagtaa	13	8	0	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr20:55211794A>G	ENST00000201031.2	+	6	1294	c.1051A>G	c.(1051-1053)Atg>Gtg	p.M351V	TFAP2C_ENST00000544508.1_Missense_Mutation_p.M182V	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	351	H-S-H (helix-span-helix), dimerization.				cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			TAGGAAGAACATGCTATTGGC	0.463																																																0			20											124	107	113					20																	55211794		2203	4300	6503	54645201	SO:0001583	missense	7022				CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"estrogen receptor factor 1"	601602	"transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.1051A>G	20.37:g.55211794A>G	ENSP00000201031:p.Met351Val		54645201	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Missense_Mutation	SNP	ENST00000201031.2	37	CCDS13454.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.863715	0.32884	.	.	ENSG00000087510	ENST00000201031;ENST00000544508	D;D	0.96885	-4.16;-4.16	5.6	3.31	0.37934	Transcription factor AP-2, C-terminal (1);	0.111502	0.85682	N	0.000000	D	0.95802	0.8634	M	0.88842	2.985	0.58432	D	0.999999	B	0.06786	0.001	B	0.09377	0.004	D	0.92353	0.5891	10	0.72032	D	0.01	-27.5451	10.0427	0.42169	0.8622:0.0:0.1378:0.0	.	351	Q92754	AP2C_HUMAN	V	351;182	ENSP00000201031:M351V;ENSP00000442274:M182V	ENSP00000201031:M351V	M	+	1	0	TFAP2C	54645201	1.000000	0.71417	0.991000	0.47740	0.644000	0.38419	4.927000	0.63440	0.387000	0.25024	0.482000	0.46254	ATG		0.463	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222		G	55211794	A	G	55211794	3	3	107	1	0	0	0	0	1	0	0	0	15828	217	8	4	1073	4	TFAP2C	20	55211794	Missense_Mutation	SNP	A	TCGA-DY-A1DG-01A-11D-A152-10	253709	55211794	7813726	322	28381										
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34721523	34721523	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	caaaaaggaatttaccttctCcgcgtacaagcatctgatgg	8	10	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr21:34721523C>G	ENST00000270139.3	+	7	1067	c.915C>G	c.(913-915)ctC>ctG	p.L305L	IFNAR1_ENST00000416947.2_Silent_p.L236L|IFNAR1_ENST00000442357.2_Silent_p.L305L	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	305	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	TTTACCTTCTCCGCGTACAAG	0.353																																					Esophageal Squamous(73;817 1211 32990 35667 42746)											0			21											111	113	113					21																	34721523		2203	4300	6503	33643393	SO:0001819	synonymous_variant	3454				CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"Interferons"	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.915C>G	21.37:g.34721523C>G			33643393	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	37	CCDS13624.1																																																																																				0.353	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			G	34721523	C	G	34721523	2	3	107	1	0	0	0	0	0	0	0	1	7565	842	30	5		5	IFNAR1	21	34721523	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		34721523	13408372	323	28382										
SLC5A3	6526	hgsc.bcm.edu	37	chr21	35468950	35468950	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ttgttcttggagcagtccgtTtgatactggcctttgcctac	10	10	1	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr21:35468950T>A	ENST00000381151.3	+	2	1965	c.1453T>A	c.(1453-1455)Ttg>Atg	p.L485M	AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.L485M|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	485					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						AGCAGTCCGTTTGATACTGGC	0.498																																																0			21											101	94	96					21																	35468950		2203	4300	6503	34390820	SO:0001583	missense	6526				CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1453T>A	21.37:g.35468950T>A	ENSP00000370543:p.Leu485Met		34390820	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	T	3.875	-0.027164	0.07589	.	.	ENSG00000198743	ENST00000381151	T	0.63913	-0.07	5.87	2.03	0.26663	.	0.000000	0.64402	D	0.000006	T	0.36082	0.0954	N	0.11427	0.14	0.41129	D	0.985874	P	0.44044	0.825	B	0.43445	0.42	T	0.43015	-0.9417	10	0.02654	T	1	.	7.7139	0.28694	0.0:0.4674:0.0:0.5326	.	485	P53794	SC5A3_HUMAN	M	485	ENSP00000370543:L485M	ENSP00000370543:L485M	L	+	1	2	SLC5A3	34390820	0.926000	0.31397	0.782000	0.31804	0.994000	0.84299	1.359000	0.34113	0.402000	0.25451	0.529000	0.55759	TTG		0.498	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			A	35468950	T	A	35468950	3	1	107	1	0	0	0	0	1	0	0	0	14703	1838	64	5	1455	5	SLC5A3	21	35468950	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	747427	35468950	12660945	324	28383										
CLDN5	7122	hgsc.bcm.edu	37	chr22	19511817	19511817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacccgaaggcccgcagaacCcccaaggccgtgctgcgcgg	13	18	0	1	rs533679011		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr22:19511817C>T	ENST00000406028.1	-	2	1277	c.217G>A	c.(217-219)Ggt>Agt	p.G73S	CLDN5_ENST00000413119.2_Missense_Mutation_p.G73S|CLDN5_ENST00000403084.1_Missense_Mutation_p.G73S			O00501	CLD5_HUMAN	claudin 5	0					calcium-independent cell-cell adhesion (GO:0016338)|myelination (GO:0042552)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			liver(1)|lung(2)|prostate(1)	4	Colorectal(54;0.0993)					CCCGCAGAACCCCCAAGGCCG	0.741																																																0			22											6	10	9					22																	19511817		2045	3950	5995	17891817	SO:0001583	missense	7122			AF000959	CCDS13763.2	22q11.21	2008-08-01	2008-08-01		ENSG00000184113	ENSG00000184113		"Claudins"	2047	protein-coding gene	gene with protein product		602101	"transmembrane protein deleted in velocardiofacial syndrome"	AWAL, TMVCF		9441748, 9192844	Standard	NM_003277		Approved	CPETRL1, BEC1	uc002zpu.2	O00501	OTTHUMG00000150441	ENST00000406028.1:c.217G>A	22.37:g.19511817C>T	ENSP00000385477:p.Gly73Ser		17891817	B3KS11|Q53XW2|Q8WUW3	Missense_Mutation	SNP	ENST00000406028.1	37	CCDS13763.2	.	.	.	.	.	.	.	.	.	.	C	13.06	2.123818	0.37436	.	.	ENSG00000184113	ENST00000406028;ENST00000403084;ENST00000413119	D;D;D	0.87103	-2.21;-2.21;-2.21	4.96	-2.65	0.06095	.	.	.	.	.	T	0.68769	0.3037	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.52939	-0.8508	9	0.23891	T	0.37	.	6.0378	0.19718	0.0:0.5179:0.1212:0.3609	.	73	D3DX19	.	S	73	ENSP00000385477:G73S;ENSP00000384554:G73S;ENSP00000400612:G73S	ENSP00000384554:G73S	G	-	1	0	CLDN5	17891817	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.033000	0.12246	-0.701000	0.05063	-1.012000	0.02466	GGT		0.741	CLDN5-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318122.3	NM_003277		T	19511817	C	T	19511817	3	4	107	1	0	0	0	0	1	0	0	0	3494	623	22	3	698	3	CLDN5	22	19511817	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10		19511817	31792749	325	28384										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26176132	26176132	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtgatgtcgctggacttcaaCgctacaggccgcatcacagc	11	13	2	1	rs374300047		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr22:26176132C>T	ENST00000407587.2	+	9	2347	c.2178C>T	c.(2176-2178)aaC>aaT	p.N726N	MYO18B_ENST00000536101.1_Silent_p.N726N|MYO18B_ENST00000335473.7_Silent_p.N726N			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	726	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGGACTTCAACGCTACAGGCC	0.647													C|||	1	0.000199681	0	0	5008	,	,		19100	0.001		0	False		,,,				2504	0															0			22						C		0,4258		0,0,2129	21	23	22		2178	-9.6	0.1	22		22	1,8481		0,1,4240	no	coding-synonymous	MYO18B	NM_032608.5		0,1,6369	TT,TC,CC		0.0118,0.0,0.0078		726/2568	26176132	1,12739	2129	4241	6370	24506132	SO:0001819	synonymous_variant	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2178C>T	22.37:g.26176132C>T			24506132	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																					0.647	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26176132	C	T	26176132	2	4	107	1	0	0	0	0	0	0	0	1	10096	535	19	1		1	MYO18B	22	26176132	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	6664315	26176132	25128434	326	28385										
LIMK2	3985	hgsc.bcm.edu	37	chr22	31663887	31663887	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	acactgaaggactttctgcgCagtatggtgagcacaccacc	10	12	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chr22:31663887C>T	ENST00000331728.4	+	10	1368	c.1254C>T	c.(1252-1254)cgC>cgT	p.R418R	LIMK2_ENST00000333611.4_Silent_p.R397R|LIMK2_ENST00000340552.4_Silent_p.R397R|LIMK2_ENST00000444929.2_Silent_p.R172R|LIMK2_ENST00000406516.1_Silent_p.R340R	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> C (in dbSNP:rs35422808). {ECO:0000269|PubMed:17344846}.		phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						ACTTTCTGCGCAGTATGGTGA	0.532																																																0			22											77	70	72					22																	31663887		2203	4300	6503	29993887	SO:0001819	synonymous_variant	3985			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1254C>T	22.37:g.31663887C>T			29993887	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Silent	SNP	ENST00000331728.4	37	CCDS13891.1																																																																																				0.532	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		T	31663887	C	T	31663887	2	4	107	1	0	0	0	0	0	0	0	1	8825	697	25	3		3	LIMK2	22	31663887	Silent	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	5487755	31663887	19640679	327	28386										
VCX3B	425054	hgsc.bcm.edu	37	chrX	8434287	8434316	+	In_Frame_Del	DEL	GAACCACTGAGTCAGGAGAGCGAGATGGAA	GAACCACTGAGTCAGGAGAGCGAGATGGAA	-													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gtcaggagagccaggtggagGaaccactgagtcaggagagc					rs377669206|rs369681806|rs374799202		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	GAACCACTGAGTCAGGAGAGCGAGATGGAA	GAACCACTGAGTCAGGAGAGCGAGATGGAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:8434287_8434316delGAACCACTGAGTCAGGAGAGCGAGATGGAA	ENST00000381032.1	+	3	911_940	c.604_633delGAACCACTGAGTCAGGAGAGCGAGATGGAA	c.(604-633)gaaccactgagtcaggagagcgagatggaadel	p.EPLSQESEME202del	VCX3B_ENST00000440654.2_In_Frame_Del_p.EPLSQESEME152del|VCX3B_ENST00000381029.4_In_Frame_Del_p.EPLSQESEME170del|VCX3B_ENST00000444481.1_In_Frame_Del_p.EPLSQESEME172del|VCX3B_ENST00000453306.1_Intron	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	202	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)		p.M180V(2)		NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						CCAGGTGGAGGAACCACTGAGTCAGGAGAGCGAGATGGAAGAACCACTGA	0.565																																																2	Substitution - Missense(2)	prostate(1)|skin(1)	X																																								8394316	SO:0001651	inframe_deletion	425054				CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.604_633delGAACCACTGAGTCAGGAGAGCGAGATGGAA	X.37:g.8434287_8434316delGAACCACTGAGTCAGGAGAGCGAGATGGAA	ENSP00000370420:p.Glu202_Glu211del		8394287	C9JS46|Q4KN12	In_Frame_Del	DEL	ENST00000381032.1	37	CCDS48077.2																																																																																				0.565	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1			-	8434316	GAACCACTGAGTCAGGAGAGCGAGATGGAA	-	8434287	7	5	107	1	0	1	0	1	0	0	0	0	17185	1175	41	0	524	0	VCX3B	23	8434287	In_Frame_Del	DEL	GAACCACTGAGTCAGGAGAGCGAGATGGAA	TCGA-DY-A1DG-01A-11D-A152-10		8434287	146836273	328	28387										
MAGIX	79917	hgsc.bcm.edu	37	chrX	49022416	49022416	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cccaatctaatccgtagtccCgtcatggccagatcgcagcc	8	16	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:49022416C>T	ENST00000412696.2	+	6	683	c.683C>T	c.(682-684)cCg>cTg	p.P228L	MAGIX_ENST00000376339.1_Intron|MAGIX_ENST00000376338.3_Missense_Mutation_p.P169L|MAGIX_ENST00000498742.1_Intron|MAGIX_ENST00000425661.2_Missense_Mutation_p.P152L	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	228																	TCCGTAGTCCCGTCATGGCCA	0.602																																																0			X											42	46	45					X																	49022416		2117	4213	6330	48909360	SO:0001583	missense	79917			AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.683C>T	X.37:g.49022416C>T	ENSP00000387928:p.Pro228Leu		48909360	A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	37	CCDS48106.1	.	.	.	.	.	.	.	.	.	.	.	6.852	0.526445	0.13066	.	.	ENSG00000017621	ENST00000425661;ENST00000412696;ENST00000376338	T;T;T	0.29397	2.29;1.66;1.57	3.86	-1.14	0.09741	.	.	.	.	.	T	0.11067	0.0270	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.0;0.0;0.001	T	0.29212	-1.0019	9	0.32370	T	0.25	.	7.1581	0.25649	0.0:0.5438:0.0:0.4562	.	152;228;169	F8WCY7;Q9H6Y5;Q9H6Y5-2	.;MAGIX_HUMAN;.	L	152;228;169	ENSP00000403515:P152L;ENSP00000387928:P228L;ENSP00000365516:P169L	ENSP00000365516:P169L	P	+	2	0	MAGIX	48909360	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.200000	0.09478	-0.203000	0.10251	-0.306000	0.09157	CCG		0.602	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859		T	49022416	C	T	49022416	3	4	107	1	0	0	0	0	1	0	0	0	9223	652	23	1	745	1	MAGIX	23	49022416	Missense_Mutation	SNP	C	TCGA-DY-A1DG-01A-11D-A152-10	40588129	49022416	106248144	329	28388										
FAAH2	158584	hgsc.bcm.edu	37	chrX	57474964	57474965	+	Missense_Mutation	DNP	TT	TT	AA													0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	tatcattctgtaggactggcTttgttggaagaaaagctcag							TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:57474964_57474965TT>AA	ENST00000374900.4	+	10	1356_1357	c.1236_1237TT>AA	c.(1234-1239)gcTTtg>gcAAtg	p.L413M	FAAH2_ENST00000491179.1_Intron	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	413						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TAGGACTGGCTTTGTTGGAAGA	0.342										HNSCC(52;0.14)																																						0			X																																								57491689|57491690	SO:0001583	missense	158584			AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"amidase domain containing"	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	Exception_encountered	X.37:g.57474964_57474965delinsAA	ENSP00000364035:p.Leu413Met		57491689|57491690	Q86VT2|Q96N98	Silent|Missense_Mutation	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																				0.342	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		AA	57474965	TT	AA	57474964	3	1	107	1	0	0	0	0	1	0	0	0	5370	1596	56	5	1274	5	FAAH2	23	57474964	Missense_Mutation	DNP	TT	TCGA-DY-A1DG-01A-11D-A152-10	8452548	57474964	97795596	330	28389										
AWAT2	158835	hgsc.bcm.edu	37	chrX	69262938	69262938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cccatgctgaagggccatgcGcacaaagccagaccggttct	11	14	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:69262938G>A	ENST00000276101.3	-	5	633	c.628C>T	c.(628-630)Cgc>Tgc	p.R210C		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	210					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						AGGGCCATGCGCACAAAGCCA	0.537																																					NSCLC(80;1334 1436 9350 24214 26427)											0			X											39	29	32					X																	69262938		2203	4295	6498	69179663	SO:0001583	missense	158835			BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"multifunctional O-acyltransferase"	300925	"diacylglycerol O-acyltransferase 2-like 4"	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.628C>T	X.37:g.69262938G>A	ENSP00000421172:p.Arg210Cys		69179663	Q6IEE3|Q6P437	Missense_Mutation	SNP	ENST00000276101.3	37	CCDS35320.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.825292	0.32237	.	.	ENSG00000147160	ENST00000276101	T	0.18810	2.19	4.95	1.99	0.26369	.	0.311546	0.27986	N	0.017052	T	0.50548	0.1622	M	0.93678	3.445	0.25604	N	0.986561	D	0.89917	1.0	D	0.78314	0.991	T	0.45804	-0.9236	10	0.87932	D	0	.	7.4258	0.27098	0.3282:0.0:0.6718:0.0	.	210	Q6E213	AWAT2_HUMAN	C	210	ENSP00000421172:R210C	ENSP00000421172:R210C	R	-	1	0	AWAT2	69179663	0.000000	0.05858	0.002000	0.10522	0.471000	0.32888	0.303000	0.19210	0.098000	0.17522	0.513000	0.50165	CGC		0.537	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		A	69262938	G	A	69262938	3	1	107	1	0	0	0	0	1	0	0	0	1236	1087	38	1	385	1	AWAT2	23	69262938	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	11787974	69262938	86007622	331	28390										
RGAG4	340526	hgsc.bcm.edu	37	chrX	71350067	71350067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	ataggtctcctcagtccctgGatcctgctgtggctctcctt	9	14	3	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:71350067G>T	ENST00000545866.1	-	1	1691	c.1324C>A	c.(1324-1326)Cca>Aca	p.P442T	NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Missense_Mutation_p.P442T	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	442										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					TCAGTCCCTGGATCCTGCTGT	0.527																																																0			X											204	204	204					X																	71350067		2142	4236	6378	71266792	SO:0001583	missense	340526			AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1324C>A	X.37:g.71350067G>T	ENSP00000441366:p.Pro442Thr		71266792	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	G	8.800	0.932644	0.18131	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.13538	2.58;2.58	2.8	2.8	0.32819	.	.	.	.	.	T	0.08891	0.0220	N	0.19112	0.55	0.09310	N	1	P	0.40970	0.734	B	0.39617	0.305	T	0.21348	-1.0248	8	.	.	.	.	8.395	0.32550	0.0:0.0:1.0:0.0	.	442	Q5HYW3	RGAG4_HUMAN	T	442	ENSP00000441366:P442T;ENSP00000418667:P442T	.	P	-	1	0	RGAG4	71266792	0.000000	0.05858	0.012000	0.15200	0.010000	0.07245	0.211000	0.17474	1.700000	0.51204	0.513000	0.50165	CCA		0.527	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		T	71350067	G	T	71350067	3	4	107	1	0	0	0	0	1	0	0	0	13312	1174	41	2	389	2	RGAG4	23	71350067	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2087129	71350067	83920493	332	28391										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71359119	71359119	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gccttccccacccacacgcaGtgtctcactggtcaaagatg	8	16	2	1			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:71359119G>T	ENST00000373677.1	+	2	1885	c.623G>T	c.(622-624)aGt>aTt	p.S208I	NHSL2_ENST00000510661.1_Missense_Mutation_p.S343I|NHSL2_ENST00000540800.1_Missense_Mutation_p.S574I|NHSL2_ENST00000535692.1_Missense_Mutation_p.S208I			Q5HYW2	NHSL2_HUMAN	NHS-like 2	208										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCCACACGCAGTGTCTCACTG	0.567																																																0			X											80	58	65					X																	71359119		2202	4297	6499	71275844	SO:0001583	missense	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.623G>T	X.37:g.71359119G>T	ENSP00000362781:p.Ser208Ile		71275844	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	37		.	.	.	.	.	.	.	.	.	.	G	11.40	1.626940	0.28978	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.65178	0.61;-0.14;-0.14;-0.14	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.79251	0.4414	M	0.74647	2.275	0.47819	D	0.999522	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.81625	-0.0848	10	0.87932	D	0	-8.3869	16.0173	0.80450	0.0:0.0:1.0:0.0	.	574;343;208	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	I	574;208;343;208	ENSP00000444617:S574I;ENSP00000362781:S208I;ENSP00000424079:S343I;ENSP00000444914:S208I	ENSP00000362781:S208I	S	+	2	0	NHSL2	71275844	1.000000	0.71417	0.996000	0.52242	0.050000	0.14768	7.958000	0.87877	2.383000	0.81215	0.600000	0.82982	AGT		0.567	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		T	71359119	G	T	71359119	3	4	107	1	0	0	0	0	1	0	0	0	10443	1029	36	2	1743	2	NHSL2	23	71359119	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	9052	71359119	83911441	333	28392										
RLIM	51132	hgsc.bcm.edu	37	chrX	73811648	73811648	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	cacctgatgagcctgatgatGagcttccttcattactgcct	8	12	1	5	rs200629905		TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:73811648G>A	ENST00000332687.6	-	4	1720	c.1502C>T	c.(1501-1503)tCa>tTa	p.S501L	RLIM_ENST00000349225.2_Missense_Mutation_p.S501L	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	501	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S501L(3)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTGATGATGAGCTTCCTTC	0.488																																					Esophageal Squamous(169;1899 1923 14997 18818 32118)											3	Substitution - Missense(3)	prostate(2)|ovary(1)	X											45	38	40					X																	73811648		2203	4300	6503	73728373	SO:0001583	missense	51132			AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1502C>T	X.37:g.73811648G>A	ENSP00000328059:p.Ser501Leu		73728373	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	7.117	0.577275	0.13686	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.08984	3.03;3.03	5.41	4.55	0.56014	.	0.666655	0.15400	N	0.264373	T	0.10121	0.0248	L	0.49126	1.545	0.38573	D	0.949983	B	0.02656	0.0	B	0.01281	0.0	T	0.08764	-1.0706	10	0.23891	T	0.37	-0.2985	13.4694	0.61273	0.0772:0.0:0.9228:0.0	.	501	Q9NVW2	RNF12_HUMAN	L	501	ENSP00000328059:S501L;ENSP00000253571:S501L	ENSP00000328059:S501L	S	-	2	0	RLIM	73728373	0.997000	0.39634	0.969000	0.41365	0.831000	0.47069	2.664000	0.46783	1.072000	0.40860	-0.192000	0.12808	TCA		0.488	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811648	G	A	73811648	3	1	107	1	0	0	0	0	1	0	0	0	13427	1294	45	3	376	3	RLIM	23	73811648	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	2452529	73811648	81458912	334	28393										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517634	123517634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	agcaacaacatcataatcccTttgccccaggtgcactaatt	5	13	1	0			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:123517634T>C	ENST00000371130.3	-	29	7189	c.7126A>G	c.(7126-7128)Agg>Ggg	p.R2376G	TENM1_ENST00000422452.2_Missense_Mutation_p.R2383G|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2376					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TCATAATCCCTTTGCCCCAGG	0.418																																																0			X											136	129	131					X																	123517634		2203	4300	6503	123345315	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7126A>G	X.37:g.123517634T>C	ENSP00000360171:p.Arg2376Gly		123345315	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898859	0.52227	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.93426	-3.22;-3.18	5.58	3.19	0.36642	.	0.000000	0.85682	D	0.000000	D	0.97324	0.9125	H	0.94847	3.59	0.58432	D	0.999997	D;D;P	0.76494	0.993;0.999;0.539	D;D;B	0.78314	0.977;0.991;0.085	D	0.97057	0.9768	10	0.87932	D	0	.	12.8937	0.58087	0.0:0.0:0.4489:0.5511	.	2382;2383;2376	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	G	2376;2383	ENSP00000360171:R2376G;ENSP00000403954:R2383G	ENSP00000360171:R2376G	R	-	1	2	ODZ1	123345315	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.438000	0.44837	0.320000	0.23234	0.486000	0.48141	AGG		0.418	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123517634	T	C	123517634	3	2	107	1	0	0	0	0	1	0	0	0	10865	1608	56	4	1063	4	ODZ1	23	123517634	Missense_Mutation	SNP	T	TCGA-DY-A1DG-01A-11D-A152-10	49705986	123517634	31752926	335	28394										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718465	142718465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0537313432835821	18	1	0.862126736966591	1.27141922825376	0.828776978417266	0.000114104820121922	0.00348019701371862	0	gagaactttcagtttgtggaGcttattgaaggctcctcgtt	11	7	1	2			TCGA-DY-A1DG-01A-11D-A152-10	TCGA-DY-A1DG-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	06466ebf-1edd-4444-9c9e-f66389499b4f	26850a7c-1c9b-4697-9aeb-b609afb454d9	g.chrX:142718465G>T	ENST00000381779.4	-	2	685	c.460C>A	c.(460-462)Ctc>Atc	p.L154I	SLITRK4_ENST00000356928.1_Missense_Mutation_p.L154I|SLITRK4_ENST00000338017.4_Missense_Mutation_p.L154I	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	154						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					AGTTTGTGGAGCTTATTGAAG	0.398																																																0			X											82	82	82					X																	142718465		2203	4300	6503	142546131	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.460C>A	X.37:g.142718465G>T	ENSP00000371198:p.Leu154Ile		142546131	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.970953	0.53614	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.70749	-0.51;-0.51;-0.51	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	D	0.86176	0.5870	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88400	0.3014	10	0.62326	D	0.03	-7.6672	16.593	0.84772	0.0:0.0:1.0:0.0	.	154	Q8IW52	SLIK4_HUMAN	I	154	ENSP00000371198:L154I;ENSP00000349400:L154I;ENSP00000336627:L154I	ENSP00000336627:L154I	L	-	1	0	SLITRK4	142546131	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.408000	0.73285	2.231000	0.72958	0.600000	0.82982	CTC		0.398	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		T	142718465	G	T	142718465	3	4	107	1	0	0	0	0	1	0	0	0	14782	971	34	2	2057	2	SLITRK4	23	142718465	Missense_Mutation	SNP	G	TCGA-DY-A1DG-01A-11D-A152-10	19200831	142718465	12552095	336	28395										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3413269	3413269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tggggcagcggcaggcccccGtggccgcatcacaggagccc	16	16	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:3413269G>A	ENST00000356575.4	-	29	3918	c.3692C>T	c.(3691-3693)aCg>aTg	p.T1231M	MEGF6_ENST00000294599.4_Missense_Mutation_p.T996M	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1231	EGF-like 22. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GCAGGCCCCCGTGGCCGCATC	0.682																																					Ovarian(73;978 3658)											0			1											8	13	12					1																	3413269		1974	4107	6081	3403129	SO:0001583	missense	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3692C>T	1.37:g.3413269G>A	ENSP00000348982:p.Thr1231Met		3403129	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.81|14.81	2.647924|2.647924	0.47258|0.47258	.|.	.|.	ENSG00000162591|ENSG00000162591	ENST00000491842|ENST00000294599;ENST00000356575	.|T;T	.|0.33865	.|1.39;1.39	4.25|4.25	4.25|4.25	0.50352|0.50352	.|Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.|0.058769	.|0.64402	.|D	.|0.000003	T|T	0.73040|0.73040	0.3536|0.3536	H|H	0.97365|0.97365	3.99|3.99	0.34173|0.34173	D|D	0.670019|0.670019	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.79784	.|0.991;0.993	D|D	0.87393|0.87393	0.2364|0.2364	5|10	.|0.56958	.|D	.|0.05	-4.0308|-4.0308	16.4653|16.4653	0.84077|0.84077	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1231;996	.|O75095;O75095-2	.|MEGF6_HUMAN;.	W|M	5|996;1231	.|ENSP00000294599:T996M;ENSP00000348982:T1231M	.|ENSP00000294599:T996M	R|T	-|-	1|2	2|0	MEGF6|MEGF6	3403129|3403129	0.992000|0.992000	0.36948|0.36948	0.131000|0.131000	0.22000|0.22000	0.153000|0.153000	0.21895|0.21895	2.281000|2.281000	0.43452|0.43452	2.209000|2.209000	0.71365|0.71365	0.655000|0.655000	0.94253|0.94253	CGG|ACG		0.682	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3413269	G	A	3413269	3	1	108	1	0	0	0	0	1	0	0	0	9492	1145	40	1	969	1	MEGF6	1	3413269	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		3413269	245837352	1	28396										
PADI6	353238	hgsc.bcm.edu	37	chr1	17708469	17708469	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtcttttgcccagaaataacGaatctgtcccagatgactct	7	11	3	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:17708469G>A	ENST00000434762.2	+	0	611							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CAGAAATAACGAATCTGTCCC	0.507																																																0			1											87	84	85					1																	17708469		1887	4112	5999	17581056			353238			AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17708469G>A			17581056	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																					0.507	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		A	17708469	G	A	17708469	1	1	108	0	1	0	0	0	0	0	0	0	11412	1045	37	1		1	PADI6	1	17708469	RNA	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	14295200	17708469	231542152	2	28397										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120512251	120512251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctcactgcagtcatctccacTccagccgttgacacatacac	5	17	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:120512251T>C	ENST00000256646.2	-	6	1210	c.991A>G	c.(991-993)Agt>Ggt	p.S331G		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	331	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCATCTCCACTCCAGCCGTTG	0.557			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0			1											162	114	130					1																	120512251		2203	4300	6503	120313774	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.991A>G	1.37:g.120512251T>C	ENSP00000256646:p.Ser331Gly		120313774	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.979832	0.92982	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	T	0.61392	0.11	5.73	5.73	0.89815	EGF-like region, conserved site (2);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.164832	0.28612	U	0.014733	T	0.50514	0.1620	N	0.21508	0.67	0.80722	D	1	P;P;P	0.50710	0.811;0.938;0.645	P;P;B	0.58210	0.597;0.835;0.371	T	0.58064	-0.7702	10	0.56958	D	0.05	.	15.1985	0.73116	0.0:0.0:0.0:1.0	.	292;331;331	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	G	331;292	ENSP00000256646:S331G	ENSP00000256646:S331G	S	-	1	0	NOTCH2	120313774	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.698000	0.84413	2.186000	0.69663	0.533000	0.62120	AGT		0.557	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		C	120512251	T	C	120512251	3	2	108	1	0	0	0	0	1	0	0	0	10579	1551	54	4	6540	4	NOTCH2	1	120512251	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	102803782	120512251	128738370	3	28398										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158626363	158626363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gttagtcttacctggcaggcGtttgcctgattccgcagagc	12	11	1	2	rs371639635	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:158626363G>A	ENST00000368147.4	-	20	3069	c.2889C>T	c.(2887-2889)aaC>aaT	p.N963N		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	963					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.N963N(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTGGCAGGCGTTTGCCTGAT	0.398													G|||	4	0.000798722	0.003	0	5008	,	,		16668	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	1						G		2,3722		0,2,1860	168	171	170		2889	-5.2	1	1		170	1,8185		0,1,4092	no	coding-synonymous	SPTA1	NM_003126.2		0,3,5952	AA,AG,GG		0.0122,0.0537,0.0252		963/2420	158626363	3,11907	1862	4093	5955	156892987	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2889C>T	1.37:g.158626363G>A			156892987	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158626363	G	A	158626363	2	1	108	1	0	0	0	0	0	0	0	1	15155	1136	40	1		1	SPTA1	1	158626363	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	38114112	158626363	90624258	4	28399										
CD84	8832	hgsc.bcm.edu	37	chr1	160535332	160535332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cggacctaaggcatgtatccGttcataataatttctgtggg	10	8	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:160535332G>A	ENST00000311224.4	-	2	316	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	CD84_ENST00000368051.3_Missense_Mutation_p.R84W|CD84_ENST00000368047.3_5'UTR|CD84_ENST00000534968.1_Intron|CD84_ENST00000368054.3_Missense_Mutation_p.R84W|CD84_ENST00000368048.3_Missense_Mutation_p.R84W|RP11-528G1.2_ENST00000446952.1_RNA	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	84	Ig-like V-type.				blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R84W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GCATGTATCCGTTCATAATAA	0.433																																																1	Substitution - Missense(1)	ovary(1)	1											255	224	234					1																	160535332		2203	4300	6503	158801956	SO:0001583	missense	8832			AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1704	protein-coding gene	gene with protein product		604513	"CD84 antigen (leukocyte antigen)", "CD84 molecule "			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.250C>T	1.37:g.160535332G>A	ENSP00000312367:p.Arg84Trp		158801956	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	37	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169431	0.57584	.	.	ENSG00000066294	ENST00000368054;ENST00000368048;ENST00000311224;ENST00000368051;ENST00000360056;ENST00000368047	T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41	5.11	3.14	0.36123	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	M	0.87971	2.92	0.27201	N	0.960175	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	T	0.42050	-0.9474	10	0.87932	D	0	-12.0244	10.2737	0.43497	0.0:0.0:0.5938:0.4062	.	84;84;84;84;84;84	Q9UIB8-5;Q9UIB8-6;Q9UIB8-4;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;.;.;SLAF5_HUMAN;.;.	W	84	ENSP00000357033:R84W;ENSP00000357027:R84W;ENSP00000312367:R84W;ENSP00000357030:R84W;ENSP00000353163:R84W;ENSP00000357026:R84W	ENSP00000312367:R84W	R	-	1	2	CD84	158801956	0.702000	0.27816	0.028000	0.17463	0.074000	0.17049	2.042000	0.41222	0.764000	0.33197	0.591000	0.81541	CGG		0.433	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874		A	160535332	G	A	160535332	3	1	108	1	0	0	0	0	1	0	0	0	3048	1144	40	1	815	1	CD84	1	160535332	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1908969	160535332	88715289	5	28400										
DDR2	4921	hgsc.bcm.edu	37	chr1	162750028	162750028	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttctgctccttcaacaaggcGacgagtgatgctgtcagtgc	11	11	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:162750028G>A	ENST00000367922.3	+	19	2998	c.2560G>A	c.(2560-2562)Gac>Aac	p.D854N	DDR2_ENST00000367921.3_Missense_Mutation_p.D854N|RN7SL861P_ENST00000473793.2_RNA	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	854					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TCAACAAGGCGACGAGTGATG	0.522																																					NSCLC(161;314 2006 8283 19651 23192)											0			1											126	111	116					1																	162750028		2203	4300	6503	161016652	SO:0001583	missense	4921			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.2560G>A	1.37:g.162750028G>A	ENSP00000356899:p.Asp854Asn		161016652	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	37	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.568659	0.28003	.	.	ENSG00000162733	ENST00000367922;ENST00000367921	D;D	0.83755	-1.76;-1.76	5.66	3.47	0.39725	.	0.735654	0.12776	N	0.440056	T	0.64692	0.2621	L	0.42245	1.32	0.22656	N	0.998888	B	0.02656	0.0	B	0.01281	0.0	T	0.61613	-0.7027	9	0.51188	T	0.08	.	10.3688	0.44042	0.1827:0.0:0.8173:0.0	.	854	Q16832	DDR2_HUMAN	N	854	ENSP00000356899:D854N;ENSP00000356898:D854N	ENSP00000356898:D854N	D	+	1	0	DDR2	161016652	0.102000	0.21896	0.005000	0.12908	0.728000	0.41692	2.423000	0.44705	1.399000	0.46721	0.650000	0.86243	GAC		0.522	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		A	162750028	G	A	162750028	3	1	108	1	0	0	0	0	1	0	0	0	4343	1058	37	1	2622	1	DDR2	1	162750028	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2214696	162750028	86500593	6	28401										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179603694	179603695	+	Frame_Shift_Ins	INS	-	-	A													0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	actgtatggaattgcccttcINSaaaaaaacaaaaagagccac					rs78052645		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:179603694_179603695insA	ENST00000367614.1	+	8	1588_1589	c.1229_1230insA	c.(1228-1233)tcaaaafs	p.SK410fs	TDRD5_ENST00000444136.1_Frame_Shift_Ins_p.SK410fs|TDRD5_ENST00000294848.8_Frame_Shift_Ins_p.SK410fs	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	410					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AATTGCCCTTCAAAAAAACAAA	0.421																																																0			1																																								177870318	SO:0001589	frameshift_variant	163589			AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1236dupA	1.37:g.179603701_179603701dupA	ENSP00000356586:p.Ser410fs		177870317	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Frame_Shift_Ins	INS	ENST00000367614.1	37	CCDS1332.1																																																																																				0.421	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		A	179603695	-	A	179603694	7	5	108	1	0	1	1	0	0	0	0	0	15772	838	29	0	1255	0	TDRD5	1	179603694	Frame_Shift_Ins	INS	-	TCGA-DY-A1H8-01A-21D-A152-10	16853666	179603694	69646927	7	28402										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186045604	186045604	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gggaaataggaaacatgctaGatactggcaggaatggtgaa	14	4	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:186045604G>C	ENST00000271588.4	+	54	8564	c.8335G>C	c.(8335-8337)Gat>Cat	p.D2779H	HMCN1_ENST00000367492.2_Missense_Mutation_p.D2779H	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2779	Ig-like C2-type 26.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAACATGCTAGATACTGGCAG	0.403																																																0			1											118	95	103					1																	186045604		2203	4300	6503	184312227	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8335G>C	1.37:g.186045604G>C	ENSP00000271588:p.Asp2779His		184312227	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551505	0.65311	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.65364	-0.14;-0.15	5.2	5.2	0.72013	Immunoglobulin-like (1);	0.264757	0.37348	N	0.002140	T	0.68842	0.3045	L	0.29908	0.895	0.37546	D	0.91851	D	0.89917	1.0	D	0.87578	0.998	T	0.72040	-0.4410	10	0.45353	T	0.12	.	14.6879	0.69062	0.0:0.1449:0.8551:0.0	.	2779	Q96RW7	HMCN1_HUMAN	H	2779	ENSP00000271588:D2779H;ENSP00000356462:D2779H	ENSP00000271588:D2779H	D	+	1	0	HMCN1	184312227	1.000000	0.71417	0.965000	0.40720	0.941000	0.58515	4.498000	0.60373	2.567000	0.86603	0.655000	0.94253	GAT		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186045604	G	C	186045604	3	2	108	1	0	0	0	0	1	0	0	0	7241	942	33	5	8549	5	HMCN1	1	186045604	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	6441910	186045604	63205017	8	28403										
BTG2	7832	hgsc.bcm.edu	37	chr1	203274815	203274815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tccagcctcctgaggacccgGggctgcgtgagcgagcagag	16	13	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:203274815G>A	ENST00000290551.4	+	1	152	c.81G>A	c.(79-81)cgG>cgA	p.R27R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	27					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R27R(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			TGAGGACCCGGGGCTGCGTGA	0.716																																																1	Substitution - coding silent(1)	skin(1)	1											16	16	16					1																	203274815		2168	4261	6429	201541438	SO:0001819	synonymous_variant	7832				CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.81G>A	1.37:g.203274815G>A			201541438	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																				0.716	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274815	G	A	203274815	2	1	108	1	0	0	0	0	0	0	0	1	1557	1219	43	3		3	BTG2	1	203274815	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	17229211	203274815	45975806	9	28404										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204399104	204399104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agatgtaaccgtttagctccTccctccgccgctcggccacc	8	18	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:204399104T>C	ENST00000367187.3	-	30	4899	c.4343A>G	c.(4342-4344)gAg>gGg	p.E1448G	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Missense_Mutation_p.E1420G	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1448	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			GTTTAGCTCCTCCCTCCGCCG	0.682																																																0			1											77	66	70					1																	204399104		2203	4300	6503	202665727	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4343A>G	1.37:g.204399104T>C	ENSP00000356155:p.Glu1448Gly		202665727	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.195850	0.58126	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.40756	1.02;1.02	5.43	5.43	0.79202	Phox homologous domain (5);	0.245918	0.39020	N	0.001482	T	0.30947	0.0781	L	0.33485	1.01	0.36309	D	0.857534	B;B	0.25048	0.005;0.117	B;B	0.24701	0.039;0.055	T	0.31971	-0.9924	10	0.24483	T	0.36	.	10.3944	0.44192	0.1461:0.0:0.0:0.8539	.	1420;1448	F5GWN5;O00750	.;P3C2B_HUMAN	G	1448;1420	ENSP00000356155:E1448G;ENSP00000400561:E1420G	ENSP00000356155:E1448G	E	-	2	0	PIK3C2B	202665727	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	3.779000	0.55379	2.056000	0.61249	0.533000	0.62120	GAG		0.682	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204399104	T	C	204399104	3	2	108	1	0	0	0	0	1	0	0	0	11941	1551	54	4	581	4	PIK3C2B	1	204399104	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	1124289	204399104	44851517	10	28405										
WDR26	80232	hgsc.bcm.edu	37	chr1	224585850	224585850	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atggcctccaaaacatgaatGaattgtataaaacccttgtg	7	8	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:224585850G>T	ENST00000414423.2	-	12	1916	c.1723C>A	c.(1723-1725)Cat>Aat	p.H575N	MIR4742_ENST00000581069.1_RNA|WDR26_ENST00000479727.1_5'UTR|WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000295024.6_Missense_Mutation_p.H428N	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	575						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		AAACATGAATGAATTGTATAA	0.368																																																0			1											104	100	101					1																	224585850		2203	4300	6503	222652473	SO:0001583	missense	80232			AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1723C>A	1.37:g.224585850G>T	ENSP00000408108:p.His575Asn		222652473	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	37	CCDS31037.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.7|28.7	4.946321|4.946321	0.92593|0.92593	.|.	.|.	ENSG00000162923|ENSG00000162923	ENST00000414423;ENST00000295024|ENST00000480676	T;T|.	0.80393|.	-1.37;-1.37|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.65365|.	0.2684|.	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	D|.	0.65815|.	0.995|.	D|.	0.65233|.	0.933|.	T|.	0.60999|.	-0.7151|.	10|.	0.26408|.	T|.	0.33|.	.|.	18.8958|18.8958	0.92423|0.92423	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	559|.	Q9H7D7-2|.	.|.	N|X	575;428|208	ENSP00000408108:H575N;ENSP00000295024:H428N|.	ENSP00000295024:H428N|.	H|S	-|-	1|2	0|0	WDR26|WDR26	222652473|222652473	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.721000|9.721000	0.98766|0.98766	2.539000|2.539000	0.85634|0.85634	0.591000|0.591000	0.81541|0.81541	CAT|TCA		0.368	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		T	224585850	G	T	224585850	3	4	108	1	0	0	0	0	1	0	0	0	17323	1290	45	2	274	2	WDR26	1	224585850	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	20186746	224585850	24664771	11	28406										
RYR2	6262	hgsc.bcm.edu	37	chr1	237958597	237958597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgtatattttaggtcatttcCcaacaactactgggacaaat	6	8	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:237958597C>T	ENST00000366574.2	+	96	14239	c.13922C>T	c.(13921-13923)cCc>cTc	p.P4641L	RYR2_ENST00000542537.1_Missense_Mutation_p.P4625L|RYR2_ENST00000360064.6_Missense_Mutation_p.P4647L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4641					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGTCATTTCCCAACAACTAC	0.249																																																0			1											34	33	33					1																	237958597		1784	4036	5820	236025220	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13922C>T	1.37:g.237958597C>T	ENSP00000355533:p.Pro4641Leu		236025220	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106513	0.94292	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.99507	-6.04;-6.04;-6.04	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000007	D	0.99530	0.9832	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	D	0.98710	1.0704	10	0.87932	D	0	-16.0779	19.6346	0.95724	0.0:1.0:0.0:0.0	.	74;4641	F5H3C7;Q92736	.;RYR2_HUMAN	L	4641;4647;4625;74	ENSP00000355533:P4641L;ENSP00000353174:P4647L;ENSP00000443798:P4625L	ENSP00000353174:P4647L	P	+	2	0	RYR2	236025220	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.691000	0.84191	2.720000	0.93068	0.491000	0.48974	CCC		0.249	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237958597	C	T	237958597	3	4	108	1	0	0	0	0	1	0	0	0	13806	623	22	3	14304	3	RYR2	1	237958597	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	13372747	237958597	11292024	12	28407										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248551009	248551009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttttcggtgtcatttgtgccGtcttcttcatggccatgata	9	9	4	1	rs41308164	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr1:248551009G>A	ENST00000355728.2	+	1	100	c.100G>A	c.(100-102)Gtc>Atc	p.V34I		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATTTGTGCCGTCTTCTTCAT	0.463													g|||	28	0.00559105	8e-04	0.0058	5008	,	,		15251	0		0.0149	False		,,,				2504	0.0082															0			1						G	ILE/VAL	20,4386	27.2+/-55.0	0,20,2183	192	168	176		100	-1.8	0.5	1	dbSNP_127	176	153,8447	75.1+/-137.7	0,153,4147	yes	missense	OR2T6	NM_001005471.1	29	0,173,6330	AA,AG,GG		1.7791,0.4539,1.3302	benign	34/309	248551009	173,12833	2203	4300	6503	246617632	SO:0001583	missense	254879			AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.100G>A	1.37:g.248551009G>A	ENSP00000347965:p.Val34Ile		246617632	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	0.009	-1.857046	0.00558	0.004539	0.017791	ENSG00000198104	ENST00000355728	T	0.01745	4.66	4.9	-1.82	0.07857	.	1.264950	0.05597	N	0.575585	T	0.00468	0.0015	N	0.03050	-0.425	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45483	-0.9258	10	0.02654	T	1	.	10.5868	0.45288	0.4891:0.0:0.5109:0.0	rs41308164	34	Q8NHC8	OR2T6_HUMAN	I	34	ENSP00000347965:V34I	ENSP00000347965:V34I	V	+	1	0	OR2T6	246617632	0.000000	0.05858	0.547000	0.28179	0.331000	0.28603	-0.915000	0.04033	-0.544000	0.06232	-1.062000	0.02293	GTC		0.463	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		A	248551009	G	A	248551009	3	1	108	1	0	0	0	0	1	0	0	0	11060	1145	40	1	102	1	OR2T6	1	248551009	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	10592412	248551009	699612	13	28408										
TTC7A	57217	hgsc.bcm.edu	37	chr2	47233826	47233826	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtttggagaatttcacctttGgtaccaggtggccctctcca	10	11	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:47233826G>A	ENST00000319190.5	+	10	1618	c.1250G>A	c.(1249-1251)tGg>tAg	p.W417*	TTC7A_ENST00000394850.2_Nonsense_Mutation_p.W417*|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000263737.6_Nonsense_Mutation_p.W63*|TTC7A_ENST00000409245.1_Nonsense_Mutation_p.W383*	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	417					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TTTCACCTTTGGTACCAGGTG	0.612																																																0			2											120	101	107					2																	47233826		2203	4300	6503	47087330	SO:0001587	stop_gained	57217			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.1250G>A	2.37:g.47233826G>A	ENSP00000316699:p.Trp417*		47087330	Q6PIX4|Q8ND67|Q9BUS3	Nonsense_Mutation	SNP	ENST00000319190.5	37	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	G	37	6.102078	0.97286	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000263737;ENST00000434093	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.5873	16.9289	0.86184	0.0:0.0:1.0:0.0	.	.	.	.	X	383;417;417;63;244	.	ENSP00000263737:W63X	W	+	2	0	TTC7A	47087330	1.000000	0.71417	1.000000	0.80357	0.041000	0.13682	9.467000	0.97671	2.297000	0.77311	0.467000	0.42956	TGG		0.612	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		A	47233826	G	A	47233826	4	1	108	1	0	0	0	0	0	1	0	0	16752	1357	47	3	1288	3	TTC7A	2	47233826	Nonsense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		47233826	195965547	14	28409										
TTC7A	57217	hgsc.bcm.edu	37	chr2	47256376	47256376	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcaacagatctccagtgccaTggagcagctgcaggaggccc	12	13	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:47256376T>G	ENST00000319190.5	+	15	2023	c.1655T>G	c.(1654-1656)aTg>aGg	p.M552R	TTC7A_ENST00000394850.2_Missense_Mutation_p.M552R|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000263737.6_Missense_Mutation_p.M198R|TTC7A_ENST00000409245.1_Missense_Mutation_p.M518R	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	552					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TCCAGTGCCATGGAGCAGCTG	0.622																																																0			2											102	89	94					2																	47256376		2203	4300	6503	47109880	SO:0001583	missense	57217			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.1655T>G	2.37:g.47256376T>G	ENSP00000316699:p.Met552Arg		47109880	Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	37	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.912574	0.33721	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000263737;ENST00000434093	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.53	4.39	0.52855	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.337631	0.38897	N	0.001527	T	0.38401	0.1039	L	0.34521	1.04	0.49130	D	0.999758	B;B;B;P;B	0.37612	0.116;0.008;0.213;0.602;0.006	B;B;B;B;B	0.41332	0.054;0.045;0.213;0.354;0.026	T	0.18178	-1.0345	10	0.33940	T	0.23	-7.3124	10.0102	0.41981	0.0:0.08:0.0:0.92	.	552;518;552;380;518	Q2T9J9;B3KPK7;Q9ULT0;Q6P0M3;G5E9G4	.;.;TTC7A_HUMAN;.;.	R	518;552;552;198;379	ENSP00000386307:M518R;ENSP00000316699:M552R;ENSP00000378320:M552R;ENSP00000263737:M198R	ENSP00000263737:M198R	M	+	2	0	TTC7A	47109880	1.000000	0.71417	1.000000	0.80357	0.185000	0.23345	4.503000	0.60407	2.107000	0.64212	0.533000	0.62120	ATG		0.622	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		G	47256376	T	G	47256376	3	3	108	1	0	0	0	0	1	0	0	0	16752	1464	51	4	1713	4	TTC7A	2	47256376	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	22550	47256376	195942997	15	28410										
USP34	9736	hgsc.bcm.edu	37	chr2	61436103	61436103	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcatcagattctaatagtatTctgaaggcactagaagaaaa	7	6	4	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:61436103T>C	ENST00000398571.2	-	70	8926	c.8850A>G	c.(8848-8850)agA>agG	p.R2950R	USP34_ENST00000472689.1_5'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2950					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CTAATAGTATTCTGAAGGCAC	0.294																																																0			2											75	74	74					2																	61436103		1813	4052	5865	61289607	SO:0001819	synonymous_variant	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.8850A>G	2.37:g.61436103T>C			61289607	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	9.915	1.210533	0.22289	.	.	ENSG00000115464	ENST00000411912	.	.	.	6.0	6.0	0.97389	.	.	.	.	.	T	0.73458	0.3589	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72297	-0.4335	4	.	.	.	.	16.5044	0.84266	0.0:0.0:0.0:1.0	.	.	.	.	D	710	.	.	N	-	1	0	USP34	61289607	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.140000	0.42159	2.295000	0.77249	0.528000	0.53228	AAT		0.294	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61436103	T	C	61436103	2	2	108	1	0	0	0	0	0	0	0	1	17105	1780	62	4		4	USP34	2	61436103	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	14179727	61436103	181763270	16	28411										
SCTR	6344	hgsc.bcm.edu	37	chr2	120231099	120231099	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gcctggggaaggtttctgacCagccatcctgtgtgcagttt	13	10	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:120231099C>T	ENST00000019103.5	-	4	602	c.335G>A	c.(334-336)tGg>tAg	p.W112*	AC013275.2_ENST00000413602.1_RNA	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	112					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	GGTTTCTGACCAGCCATCCTG	0.542																																																0			2											108	94	99					2																	120231099		2203	4300	6503	119947569	SO:0001587	stop_gained	6344				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"GPCR / Class B : Glucagon receptors"	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.335G>A	2.37:g.120231099C>T	ENSP00000019103:p.Trp112*		119947569	Q12961|Q13213|Q53T00	Nonsense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	C	39	7.600055	0.98381	.	.	ENSG00000080293	ENST00000019103	.	.	.	4.9	4.9	0.64082	.	0.000000	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.8007	0.85613	0.0:1.0:0.0:0.0	.	.	.	.	X	112	.	ENSP00000019103:W112X	W	-	2	0	SCTR	119947569	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.046000	0.64226	2.539000	0.85634	0.561000	0.74099	TGG		0.542	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			T	120231099	C	T	120231099	4	4	108	1	0	0	0	0	0	1	0	0	13980	595	21	3	1027	3	SCTR	2	120231099	Nonsense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	58794996	120231099	122968274	17	28412										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125175154	125175154	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggcatgagagtcgaggtctaCggatgttcctatagtaagta	13	6	1	1	rs368252422		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:125175154C>T	ENST00000431078.1	+	4	880	c.516C>T	c.(514-516)taC>taT	p.Y172Y		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	172	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.Y172*(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TCGAGGTCTACGGATGTTCCT	0.473																																																1	Substitution - Nonsense(1)	lung(1)	2						C		0,3980		0,0,1990	79	82	81		516	-4	0.9	2		81	1,8349		0,1,4174	no	coding-synonymous	CNTNAP5	NM_130773.2		0,1,6164	TT,TC,CC		0.012,0.0,0.0081		172/1307	125175154	1,12329	1990	4175	6165	124891624	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.516C>T	2.37:g.125175154C>T			124891624	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.473	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125175154	C	T	125175154	2	4	108	1	0	0	0	0	0	0	0	1	3656	547	19	1		1	CNTNAP5	2	125175154	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	4944055	125175154	118024219	18	28413										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540967	133540967	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggcgagttttcagtcctttCtcatgagcactttgacaacc	8	11	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:133540967C>A	ENST00000409261.1	-	14	3790	c.3417G>T	c.(3415-3417)gaG>gaT	p.E1139D	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Missense_Mutation_p.E1139D|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1139										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TCAGTCCTTTCTCATGAGCAC	0.498																																																0			2											129	130	130					2																	133540967		2038	4193	6231	133257437	SO:0001583	missense	0			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3417G>T	2.37:g.133540967C>A	ENSP00000387128:p.Glu1139Asp		133257437	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	C	9.801	1.180518	0.21787	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.13420	2.59;2.59	5.26	-0.00896	0.14002	.	0.190308	0.24933	U	0.034442	T	0.06917	0.0176	N	0.20986	0.625	0.80722	D	1	B	0.24043	0.096	B	0.22152	0.038	T	0.29549	-1.0008	10	0.42905	T	0.14	.	2.7979	0.05406	0.1267:0.5146:0.1258:0.2329	.	1139	O14513	NCKP5_HUMAN	D	1139	ENSP00000387128:E1139D;ENSP00000380603:E1139D	ENSP00000380603:E1139D	E	-	3	2	NCKAP5	133257437	0.994000	0.37717	0.994000	0.49952	0.453000	0.32348	0.193000	0.17116	0.079000	0.16929	-0.143000	0.13931	GAG		0.498	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133540967	C	A	133540967	3	1	108	1	0	0	0	0	1	0	0	0	10254	912	32	2	2340	2	NCKAP5	2	133540967	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	8365813	133540967	109658406	19	28414										
HOXD1	3231	hgsc.bcm.edu	37	chr2	177054695	177054695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctgcttgcacctgaatgacaCgcaagtcaaaatctggttcc	8	12	2	2	rs545375951		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:177054695C>T	ENST00000331462.4	+	2	1035	c.812C>T	c.(811-813)aCg>aTg	p.T271M	HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000425005.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	271					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		CTGAATGACACGCAAGTCAAA	0.493																																																0			2											143	156	152					2																	177054695		2203	4300	6503	176762941	SO:0001583	missense	3231				CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.812C>T	2.37:g.177054695C>T	ENSP00000328598:p.Thr271Met		176762941	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022072	0.93462	.	.	ENSG00000128645	ENST00000331462	D	0.96396	-4.0	5.66	5.66	0.87406	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.49305	D	0.000144	D	0.97932	0.9320	M	0.70108	2.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98260	1.0498	10	0.59425	D	0.04	.	19.3354	0.94316	0.0:1.0:0.0:0.0	.	271;271	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	M	271	ENSP00000328598:T271M	ENSP00000328598:T271M	T	+	2	0	HOXD1	176762941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.793000	0.85851	2.652000	0.90054	0.655000	0.94253	ACG		0.493	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			T	177054695	C	T	177054695	3	4	108	1	0	0	0	0	1	0	0	0	7339	536	19	1	818	1	HOXD1	2	177054695	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	43513728	177054695	66144678	20	28415										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226273691	226273691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tatggggatgaaggcctatgAtggcttggttattcagaatg	14	4	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:226273691A>G	ENST00000272907.6	+	2	508	c.95A>G	c.(94-96)gAt>gGt	p.D32G	NYAP2_ENST00000409269.2_Missense_Mutation_p.D32G	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	32					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AAGGCCTATGATGGCTTGGTT	0.408																																																0			2											147	132	137					2																	226273691		1902	4119	6021	225981935	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.95A>G	2.37:g.226273691A>G	ENSP00000272907:p.Asp32Gly		225981935	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390572	0.82902	.	.	ENSG00000144460	ENST00000272907;ENST00000409269	T	0.45668	0.89	5.92	5.92	0.95590	.	0.133715	0.48767	D	0.000166	T	0.63757	0.2538	M	0.69823	2.125	0.47905	D	0.999544	D;D	0.76494	0.999;0.995	D;P	0.66716	0.946;0.84	T	0.66905	-0.5805	10	0.72032	D	0.01	-24.6172	16.3594	0.83251	1.0:0.0:0.0:0.0	.	32;32	Q9P242-2;Q9P242	.;K1486_HUMAN	G	32	ENSP00000272907:D32G	ENSP00000272907:D32G	D	+	2	0	KIAA1486	225981935	1.000000	0.71417	0.983000	0.44433	0.908000	0.53690	8.330000	0.90019	2.266000	0.75297	0.455000	0.32223	GAT		0.408	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		G	226273691	A	G	226273691	3	3	108	1	0	0	0	0	1	0	0	0	8258	333	12	4	97	4	KIAA1486	2	226273691	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	49218996	226273691	16925682	21	28416										
IRS1	3667	hgsc.bcm.edu	37	chr2	227660499	227660499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	catggtcatgtagtcaccccGgctgctgggcactgcccggg	14	14	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:227660499G>A	ENST00000305123.5	-	1	3976	c.2956C>T	c.(2956-2958)Cgg>Tgg	p.R986W	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	986					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TAGTCACCCCGGCTGCTGGGC	0.632																																																0			2											52	56	54					2																	227660499		2203	4300	6503	227368743	SO:0001583	missense	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2956C>T	2.37:g.227660499G>A	ENSP00000304895:p.Arg986Trp		227368743		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390188	0.25118	.	.	ENSG00000169047	ENST00000305123	T	0.58210	0.35	5.39	3.61	0.41365	.	0.749453	0.11766	N	0.531641	T	0.35038	0.0918	N	0.14661	0.345	0.26105	N	0.980763	D	0.61697	0.99	B	0.43623	0.425	T	0.13282	-1.0515	10	0.66056	D	0.02	-5.6941	6.0027	0.19529	0.0751:0.1356:0.6491:0.1402	.	986	P35568	IRS1_HUMAN	W	986	ENSP00000304895:R986W	ENSP00000304895:R986W	R	-	1	2	IRS1	227368743	0.573000	0.26676	0.728000	0.30774	0.327000	0.28475	1.772000	0.38552	0.846000	0.35142	-0.152000	0.13540	CGG		0.632	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		A	227660499	G	A	227660499	3	1	108	1	0	0	0	0	1	0	0	0	7861	1115	39	1	776	1	IRS1	2	227660499	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1386808	227660499	15538874	22	28417										
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238668758	238668758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctaccaatggagagacttccGacaccctcaataatgttgga	8	11	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr2:238668758G>A	ENST00000392000.4	+	10	916	c.799G>A	c.(799-801)Gac>Aac	p.D267N	LRRFIP1_ENST00000244815.5_Missense_Mutation_p.D243N|LRRFIP1_ENST00000308482.9_Missense_Mutation_p.D457N|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.D211N	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	267					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		AGAGACTTCCGACACCCTCAA	0.398																																																0			2											111	107	108					2																	238668758		2203	4300	6503	238333497	SO:0001583	missense	9208			AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.799G>A	2.37:g.238668758G>A	ENSP00000375857:p.Asp267Asn		238333497	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818885	0.71028	.	.	ENSG00000124831	ENST00000308482;ENST00000289175;ENST00000391999;ENST00000244815;ENST00000392000	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.37	2.5	0.30297	.	0.417639	0.27027	N	0.021299	T	0.54935	0.1889	M	0.65498	2.005	0.09310	N	1	P;D;D;D;P	0.65815	0.823;0.995;0.993;0.995;0.723	B;P;P;P;B	0.62184	0.329;0.837;0.899;0.837;0.41	T	0.44050	-0.9353	10	0.38643	T	0.18	-10.3275	3.3125	0.07021	0.1492:0.1366:0.5729:0.1413	.	211;211;267;243;457	B4DPC0;Q32MZ4-3;Q32MZ4;Q32MZ4-2;E9PGZ2	.;.;LRRF1_HUMAN;.;.	N	457;211;447;243;267	ENSP00000310109:D457N;ENSP00000289175:D211N;ENSP00000244815:D243N;ENSP00000375857:D267N	ENSP00000244815:D243N	D	+	1	0	LRRFIP1	238333497	0.002000	0.14202	0.001000	0.08648	0.215000	0.24574	1.243000	0.32767	0.303000	0.22785	0.655000	0.94253	GAC		0.398	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		A	238668758	G	A	238668758	3	1	108	1	0	0	0	0	1	0	0	0	9056	1058	37	1	1513	1	LRRFIP1	2	238668758	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	11008259	238668758	4530615	23	28418										
HHATL	57467	hgsc.bcm.edu	37	chr3	42739770	42739770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccagtgcaaagctggtgcaaCgcagcactgtgaagctgctg	13	11	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:42739770C>T	ENST00000441594.1	-	6	818	c.557G>A	c.(556-558)cGt>cAt	p.R186H	HHATL_ENST00000310417.5_Missense_Mutation_p.R186H	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	186					negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		GCTGGTGCAACGCAGCACTGT	0.547																																																0			3											144	130	135					3																	42739770		2203	4300	6503	42714774	SO:0001583	missense	57467			AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"membrane bound O-acyltransferase domain containing 3"	608116	"chromosome 3 open reading frame 3", "GUP1, glycerol uptake/transporter homolog (yeast)"	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.557G>A	3.37:g.42739770C>T	ENSP00000405423:p.Arg186His		42714774	Q8TBG3|Q9ULP7	Missense_Mutation	SNP	ENST00000441594.1	37	CCDS2704.1	.	.	.	.	.	.	.	.	.	.	c	34	5.372727	0.95923	.	.	ENSG00000010282	ENST00000310417;ENST00000441594;ENST00000341477;ENST00000457462;ENST00000416756;ENST00000455195	D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43	5.07	5.07	0.68467	.	0.047476	0.85682	D	0.000000	D	0.94013	0.8082	M	0.72576	2.205	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.94081	0.7344	10	0.59425	D	0.04	-16.0452	18.6476	0.91416	0.0:1.0:0.0:0.0	.	186	Q9HCP6	HHATL_HUMAN	H	186;186;95;121;186;186	ENSP00000310621:R186H;ENSP00000405423:R186H;ENSP00000403787:R121H;ENSP00000395779:R186H;ENSP00000415351:R186H	ENSP00000310621:R186H	R	-	2	0	HHATL	42714774	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.588000	0.82629	2.643000	0.89663	0.556000	0.70494	CGT		0.547	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707		T	42739770	C	T	42739770	3	4	108	1	0	0	0	0	1	0	0	0	7111	536	19	1	985	1	HHATL	3	42739770	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		42739770	155282660	24	28419										
TLR9	54106	hgsc.bcm.edu	37	chr3	52255756	52255756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cctcatctcgcccactttgcCgcccccgccagggaagccag	9	20	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:52255756C>T	ENST00000360658.2	-	2	3209	c.2576G>A	c.(2575-2577)cGg>cAg	p.R859Q	TLR9_ENST00000597542.1_Missense_Mutation_p.R883Q|TLR9_ENST00000494383.1_Silent_p.A1012A	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	859					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	CCCACTTTGCCGCCCCCGCCA	0.637																																																0			3											59	59	59					3																	52255756		2203	4300	6503	52230796	SO:0001583	missense	54106			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2576G>A	3.37:g.52255756C>T	ENSP00000353874:p.Arg859Gln		52230796	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	C	2.043	-0.419589	0.04734	.	.	ENSG00000239732	ENST00000360658	T	0.28895	1.59	5.1	1.23	0.21249	.	1.100210	0.07297	U	0.873373	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B;B	0.24768	0.037;0.111	B;B	0.12837	0.006;0.008	T	0.30208	-0.9986	10	0.13108	T	0.6	.	2.3301	0.04233	0.1399:0.5235:0.1366:0.2	.	956;859	B4E0A1;Q9NR96	.;TLR9_HUMAN	Q	859	ENSP00000353874:R859Q	ENSP00000353874:R859Q	R	-	2	0	TLR9	52230796	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	0.032000	0.13732	-0.058000	0.13177	0.655000	0.94253	CGG		0.637	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			T	52255756	C	T	52255756	3	4	108	1	0	0	0	0	1	0	0	0	15997	652	23	1	526	1	TLR9	3	52255756	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	9515986	52255756	145766674	25	28420										
PSMD6	9861	hgsc.bcm.edu	37	chr3	64008049	64008049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccatcattgcatcgcgaattTcgctctctcctagattcttc	5	14	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:64008049T>C	ENST00000295901.4	-	2	436	c.296A>G	c.(295-297)gAa>gGa	p.E99G	PSMD6_ENST00000492933.1_Missense_Mutation_p.E152G|PSMD6_ENST00000394431.2_Missense_Mutation_p.E61G|PSMD6_ENST00000482510.1_Missense_Mutation_p.E60G|RP11-245J9.6_ENST00000605919.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	99					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		ATCGCGAATTTCGCTCTCTCC	0.453																																																0			3											177	169	172					3																	64008049		2203	4300	6503	63983089	SO:0001583	missense	9861			AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.296A>G	3.37:g.64008049T>C	ENSP00000295901:p.Glu99Gly		63983089	A8K2E0|E9PHI9|Q6UV22	Missense_Mutation	SNP	ENST00000295901.4	37	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	T	30	5.049784	0.93740	.	.	ENSG00000163636	ENST00000295901;ENST00000492933;ENST00000394431;ENST00000482510;ENST00000497323;ENST00000478185	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.19	5.19	0.71726	.	0.090629	0.85682	D	0.000000	D	0.91307	0.7259	H	0.95328	3.655	0.80722	D	1	D;D;D;D	0.71674	0.992;0.998;0.998;0.975	D;D;D;D	0.81914	0.938;0.981;0.995;0.936	D	0.93742	0.7051	10	0.72032	D	0.01	.	15.2232	0.73330	0.0:0.0:0.0:1.0	.	61;60;152;99	Q6UV22;E9PHI9;C9IZE4;Q15008	.;.;.;PSMD6_HUMAN	G	99;152;61;60;113;120	ENSP00000295901:E99G;ENSP00000418695:E152G;ENSP00000377952:E61G;ENSP00000419227:E60G;ENSP00000418887:E113G	ENSP00000295901:E99G	E	-	2	0	PSMD6	63983089	1.000000	0.71417	0.980000	0.43619	0.970000	0.65996	7.786000	0.85741	2.184000	0.69523	0.533000	0.62120	GAA		0.453	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814		C	64008049	T	C	64008049	3	2	108	1	0	0	0	0	1	0	0	0	12736	1783	62	4	901	4	PSMD6	3	64008049	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	11752293	64008049	134014381	26	28421										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77147227	77147227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agcatccttccgatgtcatcGtctctaagggcgagcccacg	10	14	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:77147227G>A	ENST00000461745.1	+	2	1024	c.124G>A	c.(124-126)Gtc>Atc	p.V42I	ROBO2_ENST00000332191.8_Missense_Mutation_p.V42I|ROBO2_ENST00000487694.3_Missense_Mutation_p.V58I	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	42	Ig-like C2-type 1.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.V42I(1)|p.V58I(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CGATGTCATCGTCTCTAAGGG	0.547																																																2	Substitution - Missense(2)	prostate(2)	3											46	50	49					3																	77147227		1960	4140	6100	77229917	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.124G>A	3.37:g.77147227G>A	ENSP00000417164:p.Val42Ile		77229917	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962860	0.74016	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191	T;T;T	0.70282	-0.47;-0.47;-0.47	4.96	4.96	0.65561	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.34879	U	0.003604	T	0.79064	0.4383	L	0.38953	1.18	0.43107	D	0.994806	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.995;0.998	T	0.81611	-0.0854	9	0.72032	D	0.01	.	18.2024	0.89843	0.0:0.0:1.0:0.0	.	58;42;42	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	I	58;58;58;42;42	ENSP00000417335:V58I;ENSP00000417164:V42I;ENSP00000327536:V42I	ENSP00000327536:V42I	V	+	1	0	ROBO2	77229917	1.000000	0.71417	0.983000	0.44433	0.027000	0.11550	9.864000	0.99589	2.283000	0.76528	0.655000	0.94253	GTC		0.547	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77147227	G	A	77147227	3	1	108	1	0	0	0	0	1	0	0	0	13551	1145	40	1	132	1	ROBO2	3	77147227	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	13139178	77147227	120875203	27	28422										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89445025	89445025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cgattaagaaagatcggaccTccagaaatagcatctctttg	8	9	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:89445025T>C	ENST00000336596.2	+	6	1570	c.1345T>C	c.(1345-1347)Tcc>Ccc	p.S449P	EPHA3_ENST00000494014.1_Missense_Mutation_p.S449P|EPHA3_ENST00000452448.2_Missense_Mutation_p.S449P	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	449	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> F (in a lung neuroendocrine carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AGATCGGACCTCCAGAAATAG	0.453										TSP Lung(6;0.00050)																																						0			3											172	163	166					3																	89445025		2203	4300	6503	89527715	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1345T>C	3.37:g.89445025T>C	ENSP00000337451:p.Ser449Pro		89527715	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481398	0.84747	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.59772	0.24;0.24;0.24	5.96	5.96	0.96718	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.052601	0.85682	D	0.000000	T	0.74527	0.3728	M	0.79805	2.47	0.80722	D	1	D;D	0.55800	0.97;0.973	P;P	0.58928	0.8;0.848	T	0.76421	-0.2965	9	.	.	.	.	16.4277	0.83824	0.0:0.0:0.0:1.0	.	449;449	P29320;P29320-2	EPHA3_HUMAN;.	P	449	ENSP00000337451:S449P;ENSP00000399926:S449P;ENSP00000419190:S449P	.	S	+	1	0	EPHA3	89527715	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	5.057000	0.64294	2.279000	0.76181	0.533000	0.62120	TCC		0.453	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89445025	T	C	89445025	3	2	108	1	0	0	0	0	1	0	0	0	5181	1551	54	4	1367	4	EPHA3	3	89445025	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	12297798	89445025	108577405	28	28423										
PLA1A	51365	hgsc.bcm.edu	37	chr3	119334871	119334871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cctttcagatttgggtattcGgattcccgttggacatgtgg	12	8	1	1	rs200921577		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:119334871G>A	ENST00000273371.4	+	6	749	c.677G>A	c.(676-678)cGg>cAg	p.R226Q	PLA1A_ENST00000495992.1_Missense_Mutation_p.R210Q|PLA1A_ENST00000488919.1_Missense_Mutation_p.R53Q|PLA1A_ENST00000494440.1_Missense_Mutation_p.R210Q	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	226					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTGGGTATTCGGATTCCCGTT	0.537													G|||	1	0.000199681	0	0.0014	5008	,	,		17662	0		0	False		,,,				2504	0															0			3											142	110	121					3																	119334871		2203	4300	6503	120817561	SO:0001583	missense	51365			AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.677G>A	3.37:g.119334871G>A	ENSP00000273371:p.Arg226Gln		120817561	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	13.81	2.347005	0.41599	.	.	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65	4.95	4.08	0.47627	Lipase, N-terminal (1);	0.431727	0.27447	N	0.019327	D	0.83468	0.5261	L	0.38692	1.165	0.35892	D	0.82971	B;B	0.20988	0.032;0.05	B;B	0.24974	0.024;0.057	T	0.76950	-0.2769	10	0.07482	T	0.82	-20.4672	10.6981	0.45911	0.0889:0.0:0.9111:0.0	.	210;226	Q53H76-3;Q53H76	.;PLA1A_HUMAN	Q	226;53;210;210;92	ENSP00000273371:R226Q;ENSP00000420625:R53Q;ENSP00000417326:R210Q;ENSP00000418793:R210Q;ENSP00000417295:R92Q	ENSP00000273371:R226Q	R	+	2	0	PLA1A	120817561	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	4.859000	0.62954	1.336000	0.45506	-0.263000	0.10527	CGG		0.537	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			A	119334871	G	A	119334871	3	1	108	1	0	0	0	0	1	0	0	0	12019	1116	39	1	699	1	PLA1A	3	119334871	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	29889846	119334871	78687559	29	28424										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121630513	121630513	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gggaggacaagtggtacacaCgtgagtaaaatcatggaatc	13	6	1	1	rs371513641		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:121630513C>T	ENST00000489711.1	+	4	816	c.428C>T	c.(427-429)aCa>aTa	p.T143I	SLC15A2_ENST00000295605.2_Intron	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	143					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GTGGTACACACGTGAGTAAAA	0.383																																																0			3						C	,ILE/THR	0,4406		0,0,2203	169	136	147		,428	4.4	1	3		147	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense-near-splice	SLC15A2	NM_001145998.1,NM_021082.3	,89	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,benign	,143/730	121630513	1,13005	2203	4300	6503	123113203	SO:0001630	splice_region_variant	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.428+1C>T	3.37:g.121630513C>T			123113203	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	C	9.732	1.162446	0.21538	0.0	1.16E-4	ENSG00000163406	ENST00000489711;ENST00000469013	T;T	0.56776	0.44;0.44	5.31	4.43	0.53597	Major facilitator superfamily domain, general substrate transporter (1);	0.300767	0.37809	N	0.001924	T	0.25754	0.0627	N	0.04686	-0.185	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.08207	-1.0733	10	0.12430	T	0.62	-3.2419	7.1616	0.25667	0.0:0.7219:0.1882:0.0899	.	143	Q16348	S15A2_HUMAN	I	143;81	ENSP00000417085:T143I;ENSP00000418704:T81I	ENSP00000418704:T81I	T	+	2	0	SLC15A2	123113203	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	1.850000	0.39328	1.463000	0.47967	0.655000	0.94253	ACA		0.383	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	Missense_Mutation	T	121630513	C	T	121630513	5	4	108	1	0	0	0	0	0	0	1	0	14436	550	19	1	442	1	SLC15A2	3	121630513	Splice_Site	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	2295642	121630513	76391917	30	28425										
PDIA5	10954	hgsc.bcm.edu	37	chr3	122869111	122869111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cccccgcccccagagcccacGtgggaagagcagcagacaag	12	17	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:122869111G>A	ENST00000316218.7	+	14	1268	c.1173G>A	c.(1171-1173)acG>acA	p.T391T	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	391	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.		T -> M (in dbSNP:rs2292661).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CAGAGCCCACGTGGGAAGAGC	0.592																																																0			3											62	65	64					3																	122869111		2203	4300	6503	124351801	SO:0001819	synonymous_variant	10954			AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1173G>A	3.37:g.122869111G>A			124351801	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	37	CCDS3020.1																																																																																				0.592	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		A	122869111	G	A	122869111	2	1	108	1	0	0	0	0	0	0	0	1	11702	1132	40	1		1	PDIA5	3	122869111	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1238598	122869111	75153319	31	28426										
HLTF	6596	hgsc.bcm.edu	37	chr3	148792068	148792068	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgaaaccgcttttctattttCttcttttccccaaaaagtca	3	11	4	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:148792068C>A	ENST00000310053.5	-	4	656	c.463G>T	c.(463-465)Gaa>Taa	p.E155*	HLTF_ENST00000465259.1_Nonsense_Mutation_p.E155*|HLTF_ENST00000392912.2_Nonsense_Mutation_p.E155*|HLTF_ENST00000494055.1_Nonsense_Mutation_p.E155*	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	155					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TTTCTATTTTCTTCTTTTCCC	0.348																																																0			3											99	96	97					3																	148792068		2203	4299	6502	150274758	SO:0001587	stop_gained	6596			L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"RING-type (C3HC4) zinc fingers"	11099	protein-coding gene	gene with protein product		603257	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.463G>T	3.37:g.148792068C>A	ENSP00000308944:p.Glu155*		150274758	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Nonsense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	C	38	6.937812	0.97948	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000416117;ENST00000392913	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	1.7746	14.3204	0.66482	0.0:0.8505:0.1495:0.0	.	.	.	.	X	155;155;155;155;152;152	.	ENSP00000308944:E155X	E	-	1	0	HLTF	150274758	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.212000	0.65225	2.550000	0.86006	0.555000	0.69702	GAA		0.348	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			A	148792068	C	A	148792068	4	1	108	1	0	0	0	0	0	1	0	0	7236	922	32	2	2654	2	HLTF	3	148792068	Nonsense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	25922957	148792068	49230362	32	28427										
DHX36	170506	hgsc.bcm.edu	37	chr3	154011585	154011585	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctattttccgaacaccaggaGgggttcttttaaacacctgt	8	10	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:154011585G>A	ENST00000496811.1	-	14	1702	c.1622C>T	c.(1621-1623)cCt>cTt	p.P541L	DHX36_ENST00000329463.5_Missense_Mutation_p.P527L|DHX36_ENST00000544526.1_Missense_Mutation_p.P527L|DHX36_ENST00000308361.6_Missense_Mutation_p.P541L	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	541	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AACACCAGGAGGGGTTCTTTT	0.294																																																0			3											71	75	74					3																	154011585		2203	4294	6497	155494279	SO:0001583	missense	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1622C>T	3.37:g.154011585G>A	ENSP00000417078:p.Pro541Leu		155494279	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.811986|4.811986	0.90707|0.90707	.|.	.|.	ENSG00000174953|ENSG00000174953	ENST00000469977|ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	.|T;T;T;T;T	.|0.03272	.|3.99;3.99;3.99;3.99;3.99	5.92|5.92	5.92|5.92	0.95590|0.95590	.|Helicase, C-terminal (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.21631|0.21631	0.0521|0.0521	M|M	0.82823|0.82823	2.61|2.61	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.50617	.|0.922;0.922;0.937	.|P;P;D	.|0.63877	.|0.868;0.868;0.919	T|T	0.00023|0.00023	-1.2330|-1.2330	5|10	.|0.59425	.|D	.|0.04	.|.	20.3138|20.3138	0.98647|0.98647	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|527;541;541	.|Q9H2U1-2;Q9H2U1-3;Q9H2U1	.|.;.;DHX36_HUMAN	F|L	21|541;541;527;527;455	.|ENSP00000417078:P541L;ENSP00000309296:P541L;ENSP00000444247:P527L;ENSP00000330113:P527L;ENSP00000419862:P455L	.|ENSP00000309296:P541L	L|P	-|-	1|2	0|0	DHX36|DHX36	155494279|155494279	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	7.158000|7.158000	0.77470|0.77470	2.814000|2.814000	0.96858|0.96858	0.585000|0.585000	0.79938|0.79938	CTC|CCT		0.294	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154011585	G	A	154011585	3	1	108	1	0	0	0	0	1	0	0	0	4520	1000	35	3	1452	3	DHX36	3	154011585	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	5219517	154011585	44010845	33	28428										
CPN2	1370	hgsc.bcm.edu	37	chr3	194062471	194062471	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtgggtaatggcattgtatgAgagcatgagggaacgcaggt	17	4	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr3:194062471A>G	ENST00000323830.3	-	2	1050	c.961T>C	c.(961-963)Tca>Cca	p.S321P	CPN2_ENST00000429275.1_Missense_Mutation_p.S321P	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	321					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		GCATTGTATGAGAGCATGAGG	0.587																																																0			3											50	46	47					3																	194062471		2203	4300	6503	195544166	SO:0001583	missense	221184			J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.961T>C	3.37:g.194062471A>G	ENSP00000319464:p.Ser321Pro		195544166	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.741166	0.49151	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.63744	-0.06;-0.06	5.29	5.29	0.74685	.	0.000000	0.32819	N	0.005615	T	0.79058	0.4382	M	0.82517	2.595	0.42364	D	0.992426	D	0.89917	1.0	D	0.79784	0.993	T	0.80797	-0.1222	10	0.45353	T	0.12	.	12.6808	0.56920	0.8628:0.1371:0.0:0.0	.	321	P22792	CPN2_HUMAN	P	321	ENSP00000319464:S321P;ENSP00000402232:S321P	ENSP00000319464:S321P	S	-	1	0	CPN2	195544166	0.109000	0.22037	0.772000	0.31596	0.491000	0.33493	1.532000	0.36029	2.129000	0.65627	0.533000	0.62120	TCA		0.587	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		G	194062471	A	G	194062471	3	3	108	1	0	0	0	0	1	0	0	0	3816	304	11	4	680	4	CPN2	3	194062471	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	40050886	194062471	3959959	34	28429										
RBPJ	3516	hgsc.bcm.edu	37	chr4	26407829	26407829	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aaattatttaaaagagcgagGggatcaaacagtacttattc	8	5	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:26407829G>A	ENST00000361572.6	+	3	325	c.131G>A	c.(130-132)gGg>gAg	p.G44E	RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000342295.1_Missense_Mutation_p.G44E|RBPJ_ENST00000504907.1_Missense_Mutation_p.G30E|RBPJ_ENST00000507561.1_Missense_Mutation_p.G9E|RBPJ_ENST00000345843.3_Missense_Mutation_p.G29E|RBPJ_ENST00000355476.3_Missense_Mutation_p.G30E|RBPJ_ENST00000348160.4_Missense_Mutation_p.G31E|RBPJ_ENST00000342320.4_Missense_Mutation_p.G30E			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	44					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G30E(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				AAAGAGCGAGGGGATCAAACA	0.308																																																1	Substitution - Missense(1)	central_nervous_system(1)	4											108	118	115					4																	26407829		2203	4299	6502	26016927	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.131G>A	4.37:g.26407829G>A	ENSP00000354528:p.Gly44Glu		26016927	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907826	0.33721	.	.	ENSG00000168214	ENST00000512351;ENST00000510778;ENST00000506956;ENST00000512671;ENST00000345843;ENST00000342295;ENST00000361572;ENST00000514807;ENST00000348160;ENST00000509158;ENST00000355476;ENST00000507561;ENST00000514730;ENST00000507574;ENST00000514675;ENST00000515573;ENST00000511546;ENST00000504907;ENST00000342320;ENST00000504938	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.4	5.4	0.78164	LAG1, DNA binding (1);p53-like transcription factor, DNA-binding (1);	0.095123	0.64402	D	0.000001	T	0.76877	0.4049	L	0.36672	1.1	0.80722	D	1	B;B;B;B;B;B	0.19583	0.009;0.037;0.009;0.015;0.015;0.015	B;B;B;B;B;B	0.29663	0.035;0.035;0.049;0.105;0.105;0.049	T	0.70517	-0.4850	10	0.06099	T	0.92	-10.8904	18.7556	0.91832	0.0:0.0:1.0:0.0	.	44;30;31;30;29;44	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	E	30;67;30;44;29;44;44;30;31;30;30;9;30;9;30;9;30;30;30;9	ENSP00000424789:G30E;ENSP00000427170:G67E;ENSP00000425750:G30E;ENSP00000423644:G44E;ENSP00000305815:G29E;ENSP00000345206:G44E;ENSP00000354528:G44E;ENSP00000424989:G30E;ENSP00000339699:G31E;ENSP00000424804:G30E;ENSP00000347659:G30E;ENSP00000423907:G9E;ENSP00000425061:G30E;ENSP00000422617:G9E;ENSP00000423575:G30E;ENSP00000423406:G9E;ENSP00000422838:G30E;ENSP00000423703:G30E;ENSP00000340124:G30E;ENSP00000424459:G9E	ENSP00000345206:G44E	G	+	2	0	RBPJ	26016927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.178000	0.71968	2.517000	0.84864	0.591000	0.81541	GGG		0.308	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		A	26407829	G	A	26407829	3	1	108	1	0	0	0	0	1	0	0	0	13198	1232	43	3	204	3	RBPJ	4	26407829	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		26407829	164746447	35	28430										
KDR	3791	hgsc.bcm.edu	37	chr4	55981159	55981159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atagtaaagcccttcttgctGtcccaggaaattctgttacc	7	11	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:55981159G>A	ENST00000263923.4	-	5	835	c.540C>T	c.(538-540)gaC>gaT	p.D180D		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	180	Ig-like C2-type 2.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCTTCTTGCTGTCCCAGGAAA	0.368			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0			4											64	64	64					4																	55981159		2203	4300	6503	55675916	SO:0001819	synonymous_variant	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.540C>T	4.37:g.55981159G>A			55675916	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																				0.368	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55981159	G	A	55981159	2	1	108	1	0	0	0	0	0	0	0	1	8160	1368	48	3		3	KDR	4	55981159	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	29573330	55981159	135173117	36	28431										
ENAM	10117	hgsc.bcm.edu	37	chr4	71508196	71508196	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cagaataggcctttttacagAaatcaacaagttcaaagggg	9	7	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:71508196A>G	ENST00000396073.3	+	9	1334	c.1053A>G	c.(1051-1053)agA>agG	p.R351R	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	351					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTTTTTACAGAAATCAACAAG	0.413																																																0			4											97	100	99					4																	71508196		2203	4300	6503	71727060	SO:0001819	synonymous_variant	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1053A>G	4.37:g.71508196A>G			71727060	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																				0.413	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		G	71508196	A	G	71508196	2	3	108	1	0	0	0	0	0	0	0	1	5125	243	9	4		4	ENAM	4	71508196	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	15527037	71508196	119646080	37	28432										
FAM190A	401145	hgsc.bcm.edu	37	chr4	92519969	92519969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cagacgttacacagaacttaCgggccaccgttgggcagagc	12	12	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:92519969C>T	ENST00000509176.1	+	11	2752	c.2464C>T	c.(2464-2466)Cgg>Tgg	p.R822W	CCSER1_ENST00000333691.8_Missense_Mutation_p.R822W	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	822																	ACAGAACTTACGGGCCACCGT	0.468																																																0			4											89	79	82					4																	92519969		692	1591	2283	92738992	SO:0001583	missense	0				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2464C>T	4.37:g.92519969C>T	ENSP00000425040:p.Arg822Trp		92738992	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.833459	0.32421	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	T;T	0.37752	1.18;1.18	5.67	-4.18	0.03846	.	.	.	.	.	T	0.15609	0.0376	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.22068	-1.0227	9	0.62326	D	0.03	-2.0381	0.3357	0.00326	0.3708:0.1986:0.1637:0.2668	.	822	Q9C0I3	F190A_HUMAN	W	822	ENSP00000425040:R822W;ENSP00000329482:R822W	ENSP00000329482:R822W	R	+	1	2	FAM190A	92738992	0.001000	0.12720	0.001000	0.08648	0.501000	0.33797	-0.362000	0.07602	-0.733000	0.04850	-0.142000	0.14014	CGG		0.468	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	92519969	C	T	92519969	3	4	108	1	0	0	0	0	1	0	0	0	5537	527	19	1	2530	1	FAM190A	4	92519969	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	21011773	92519969	98634307	38	28433										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113538777	113538777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctaggattccagtattgtttGccttctctggcagtttcaac	8	10	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:113538777G>A	ENST00000505019.1	-	6	2546	c.2421C>T	c.(2419-2421)ggC>ggT	p.G807G	C4orf21_ENST00000309071.5_Silent_p.G807G|C4orf21_ENST00000445203.2_Silent_p.G776G	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		807						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		AGTATTGTTTGCCTTCTCTGG	0.383																																																0			4											77	72	74					4																	113538777		2203	4300	6503	113758226	SO:0001819	synonymous_variant	55345																														ENST00000505019.1:c.2421C>T	4.37:g.113538777G>A			113758226	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	37																																																																																					0.383	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113538777	G	A	113538777	2	1	108	1	0	0	0	0	0	0	0	1	2260	1306	46	3		3	C4orf21	4	113538777	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	21018808	113538777	77615499	39	28434										
HSPA4L	22824	hgsc.bcm.edu	37	chr4	128744011	128744011	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atgtatatgattttagagacAggctgggcactgtctatgaa	11	5	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:128744011A>G	ENST00000296464.4	+	15	2311	c.1900A>G	c.(1900-1902)Agg>Ggg	p.R634G	HSPA4L_ENST00000505726.1_Missense_Mutation_p.R608G|HSPA4L_ENST00000508776.1_Missense_Mutation_p.R634G|HSPA4L_ENST00000439123.2_Missense_Mutation_p.R665G	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	634					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TTTTAGAGACAGGCTGGGCAC	0.343																																																0			4											66	70	68					4																	128744011		2203	4299	6502	128963461	SO:0001583	missense	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1900A>G	4.37:g.128744011A>G	ENSP00000296464:p.Arg634Gly		128963461	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.410054	0.62399	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000505726	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	4.97	4.97	0.65823	.	0.105144	0.64402	D	0.000006	T	0.14917	0.0360	L	0.36672	1.1	0.36364	D	0.860892	B;B	0.22480	0.07;0.024	B;B	0.29176	0.099;0.037	T	0.10474	-1.0628	10	0.87932	D	0	.	14.8163	0.70036	1.0:0.0:0.0:0.0	.	608;634	E9PDE8;O95757	.;HS74L_HUMAN	G	634;665;634;608	ENSP00000422482:R634G;ENSP00000393926:R665G;ENSP00000296464:R634G;ENSP00000425645:R608G	ENSP00000296464:R634G	R	+	1	2	HSPA4L	128963461	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.281000	0.89905	2.098000	0.63641	0.477000	0.44152	AGG		0.343	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		G	128744011	A	G	128744011	3	3	108	1	0	0	0	0	1	0	0	0	7434	179	7	4	1958	4	HSPA4L	4	128744011	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	15205234	128744011	62410265	40	28435										
ENPP6	133121	hgsc.bcm.edu	37	chr4	185138883	185138883	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tctgagcgaaaaccatccagCagaaacaccagcagcttccg	8	14	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr4:185138883C>A	ENST00000296741.2	-	1	231	c.90G>T	c.(88-90)ctG>ctT	p.L30L		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	30					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-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;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		AACCATCCAGCAGAAACACCA	0.577																																																0			4											50	50	50					4																	185138883		2203	4300	6503	185375877	SO:0001819	synonymous_variant	133121			AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.90G>T	4.37:g.185138883C>A			185375877	Q4W5Q1|Q96M57	Silent	SNP	ENST00000296741.2	37	CCDS3834.1																																																																																				0.577	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343		A	185138883	C	A	185138883	2	1	108	1	0	0	0	0	0	0	0	1	5147	697	25	2		2	ENPP6	4	185138883	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	56394872	185138883	6015393	41	28436										
SDHA	6389	hgsc.bcm.edu	37	chr5	225588	225588	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggacaactggaggtggcatTtctacgacaccgtgaagggc	14	9	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:225588T>A	ENST00000264932.6	+	4	482	c.367T>A	c.(367-369)Ttc>Atc	p.F123I	SDHA_ENST00000504309.1_Missense_Mutation_p.F123I|SDHA_ENST00000510361.1_Intron	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	123					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GAGGTGGCATTTCTACGACAC	0.607									Familial Paragangliomas																																							0			5											60	66	64					5																	225588		2203	4297	6500	278588	SO:0001583	missense	6389	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.367T>A	5.37:g.225588T>A	ENSP00000264932:p.Phe123Ile		278588	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	-	18.47	3.630004	0.67015	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309	T;T	0.70516	-0.49;-0.49	5.27	5.27	0.74061	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.62612	0.2442	L	0.35542	1.07	0.80722	D	1	B;B;B;B	0.33512	0.254;0.415;0.236;0.236	B;B;B;B	0.35859	0.212;0.212;0.212;0.212	T	0.66148	-0.5996	10	0.62326	D	0.03	.	13.4858	0.61364	0.0:0.0:0.0:1.0	.	123;123;123;129	B4DYN5;D6RFM5;P31040;Q59GW8	.;.;DHSA_HUMAN;.	I	123	ENSP00000264932:F123I;ENSP00000426514:F123I	ENSP00000264932:F123I	F	+	1	0	SDHA	278588	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.450000	0.80656	2.136000	0.66102	0.524000	0.50904	TTC		0.607	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		A	225588	T	A	225588	3	1	108	1	0	0	0	0	1	0	0	0	14000	1841	64	5	381	5	SDHA	5	225588	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10		225588	180689672	42	28437										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13809285	13809285	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgggtacgcgtgttccagtgCgtccatgtacctaaggtgag	14	9	0	1	rs541631905	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:13809285C>T	ENST00000265104.4	-	46	7724	c.7620G>A	c.(7618-7620)acG>acA	p.T2540T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2540					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGTTCCAGTGCGTCCATGTAC	0.448									Kartagener syndrome				C|||	2	0.000399361	0	0	5008	,	,		16908	0.002		0	False		,,,				2504	0															0			5											154	144	148					5																	13809285		2203	4300	6503	13862285	SO:0001819	synonymous_variant	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.7620G>A	5.37:g.13809285C>T			13862285	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.448	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13809285	C	T	13809285	2	4	108	1	0	0	0	0	0	0	0	1	4615	755	27	1		1	DNAH5	5	13809285	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	13583697	13809285	167105975	43	28438										
APC	324	hgsc.bcm.edu	37	chr5	112128145	112128145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tttcttgttttattttagcgAagaatagccagaattcagca	7	6	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:112128145A>G	ENST00000457016.1	+	7	1028	c.648A>G	c.(646-648)cgA>cgG	p.R216R	APC_ENST00000257430.4_Silent_p.R216R|APC_ENST00000508376.2_Silent_p.R216R			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATTTTAGCGAAGAATAGCCA	0.323		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	0			5											57	55	56					5																	112128145		2202	4300	6502	112156044	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.648A>G	5.37:g.112128145A>G			112156044	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112128145	A	G	112128145	2	3	108	1	0	0	0	0	0	0	0	1	763	233	9	4		4	APC	5	112128145	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	98318860	112128145	68787115	44	28439										
APC	324	hgsc.bcm.edu	37	chr5	112174235	112174235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aaagaggtcaaatgaaacccTcgattgaatcctattctgaa	7	8	2	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:112174235T>C	ENST00000457016.1	+	16	3324	c.2944T>C	c.(2944-2946)Tcg>Ccg	p.S982P	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S982P|APC_ENST00000508376.2_Missense_Mutation_p.S982P			P25054	APC_HUMAN	adenomatous polyposis coli	982	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AATGAAACCCTCGATTGAATC	0.353		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											80	75	76					5																	112174235		2202	4300	6502	112202134	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2944T>C	5.37:g.112174235T>C	ENSP00000413133:p.Ser982Pro		112202134	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	16.80	3.222028	0.58560	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.95853	-3.05;-3.83;-3.05;-3.05;-3.24	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.93298	0.7864	L	0.55481	1.735	0.58432	D	0.999996	B;B	0.31968	0.349;0.349	B;B	0.31442	0.13;0.13	D	0.91736	0.5400	10	0.29301	T	0.29	-11.855	15.2326	0.73404	0.0:0.0:0.0:1.0	.	984;982	Q4LE70;P25054	.;APC_HUMAN	P	982;964;982;982;982	ENSP00000413133:S982P;ENSP00000423224:S964P;ENSP00000257430:S982P;ENSP00000427089:S982P;ENSP00000423828:S982P	ENSP00000257430:S982P	S	+	1	0	APC	112202134	1.000000	0.71417	0.957000	0.39632	0.949000	0.60115	7.303000	0.78871	2.197000	0.70478	0.528000	0.53228	TCG		0.353	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112174235	T	C	112174235	3	2	108	1	0	0	0	0	1	0	0	0	763	1551	54	4	3002	4	APC	5	112174235	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	46090	112174235	68741025	45	28440			1	28		3	3	1069	N	T_C_A	1.731737e-05
APC	324	hgsc.bcm.edu	37	chr5	112175172	112175172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggatgtaatcagacgacacAggaagcagattctgctaata	10	7	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:112175172A>G	ENST00000457016.1	+	16	4261	c.3881A>G	c.(3880-3882)cAg>cGg	p.Q1294R	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1294R|APC_ENST00000508376.2_Missense_Mutation_p.Q1294R			P25054	APC_HUMAN	adenomatous polyposis coli	1294	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1293fs*2(1)|p.Q1294fs*11(1)|p.K1192fs*3(1)|p.?(1)|p.Q1294fs*6(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGACGACACAGGAAGCAGAT	0.378		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	5	Deletion - Frameshift(4)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5											55	57	56					5																	112175172		2202	4300	6502	112203071	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3881A>G	5.37:g.112175172A>G	ENSP00000413133:p.Gln1294Arg		112203071	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	3.953	-0.011958	0.07727	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.89810	-2.38;-2.38;-2.38;-2.57	5.73	4.42	0.53409	.	0.122222	0.53938	D	0.000054	T	0.71239	0.3316	N	0.04880	-0.145	0.29307	N	0.868295	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.58020	-0.7710	9	.	.	.	-3.559	3.8814	0.09080	0.7086:0.0:0.2914:0.0	.	1296;1294	Q4LE70;P25054	.;APC_HUMAN	R	1294	ENSP00000413133:Q1294R;ENSP00000257430:Q1294R;ENSP00000427089:Q1294R;ENSP00000423828:Q1294R	.	Q	+	2	0	APC	112203071	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.532000	0.53553	2.308000	0.77769	0.533000	0.62120	CAG		0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175172	A	G	112175172	3	3	108	1	0	0	0	0	1	0	0	0	763	188	7	4	3939	4	APC	5	112175172	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	937	112175172	68740088	46	28441			1	28		3	3	1069	N	T_C_A	1.731737e-05
APC	324	hgsc.bcm.edu	37	chr5	112175303	112175303	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaaccaaatccagcagactgCagggttctagtttatcttca	8	10	3	1	rs121913327		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:112175303C>T	ENST00000457016.1	+	16	4392	c.4012C>T	c.(4012-4014)Cag>Tag	p.Q1338*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1338*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1338*			P25054	APC_HUMAN	adenomatous polyposis coli	1338	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1338*(30)|p.L1337fs*76(4)|p.?(1)|p.K1192fs*3(1)|p.V1326fs*3(1)|p.S1335fs*70(1)|p.L1337>?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCAGACTGCAGGGTTCTAG	0.458	Q1338*(SW480_LARGE_INTESTINE)|Q1338*(SW620_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	39	Substitution - Nonsense(30)|Deletion - Frameshift(7)|Unknown(1)|Complex(1)	large_intestine(34)|thyroid(1)|biliary_tract(1)|stomach(1)|soft_tissue(1)|skin(1)	5	GRCh37	CM930029	APC	M	rs121913327						57	60	59					5																	112175303		2202	4300	6502	112203202	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4012C>T	5.37:g.112175303C>T	ENSP00000413133:p.Gln1338*		112203202	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.909540	0.98557	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.226724	0.46145	D	0.000316	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.6325	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1338	.	.	Q	+	1	0	APC	112203202	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	4.607000	0.61133	2.861000	0.98227	0.655000	0.94253	CAG		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175303	C	T	112175303	4	4	108	1	0	0	0	0	0	1	0	0	763	711	25	3	4070	3	APC	5	112175303	Nonsense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	131	112175303	68739957	47	28442			1	28		3	3	1069	N	T_C_A	1.731737e-05
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129072906	129072906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cccaaaagctgcagcagaagAgttgacctctagcaggctgg	12	11	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:129072906A>G	ENST00000274487.4	+	23	3764	c.3619A>G	c.(3619-3621)Agt>Ggt	p.S1207G	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	1207						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		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)		GCAGCAGAAGAGTTGACCTCT	0.443																																																0			5											60	51	54					5																	129072906		2203	4300	6503	129100805	SO:0001583	missense	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.3619A>G	5.37:g.129072906A>G	ENSP00000274487:p.Ser1207Gly		129100805		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240555	0.58995	.	.	ENSG00000145808	ENST00000274487	T	0.67345	-0.26	3.99	3.99	0.46301	.	0.077421	0.52532	D	0.000068	T	0.59662	0.2210	N	0.19112	0.55	0.42771	D	0.993832	D	0.53151	0.958	P	0.51550	0.673	T	0.59231	-0.7493	9	.	.	.	.	13.9532	0.64131	1.0:0.0:0.0:0.0	.	1207	Q8TE59	ATS19_HUMAN	G	1207	ENSP00000274487:S1207G	.	S	+	1	0	ADAMTS19	129100805	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	6.190000	0.72057	2.047000	0.60756	0.455000	0.32223	AGT		0.443	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	129072906	A	G	129072906	3	3	108	1	0	0	0	0	1	0	0	0	264	304	11	4	3709	4	ADAMTS19	5	129072906	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	16897603	129072906	51842354	48	28443										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140228183	140228183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gcggccagctccactactccGtcccggaggaagccgaacac	11	17	0	0	rs71588636		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:140228183G>A	ENST00000532602.1	+	1	1136	c.103G>A	c.(103-105)Gtc>Atc	p.V35I	PCDHA9_ENST00000378122.3_Missense_Mutation_p.V35I|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	35	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACTACTCCGTCCCGGAGGA	0.637																																					Melanoma(55;1800 1972 14909)											0			5											59	61	61					5																	140228183		2197	4270	6467	140208367	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.103G>A	5.37:g.140228183G>A	ENSP00000436042:p.Val35Ile		140208367	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	8.895	0.954905	0.18431	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.35789	1.29;1.29	3.73	2.84	0.33178	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.28034	0.0691	L	0.41236	1.265	0.21967	N	0.999444	B;B	0.29909	0.261;0.178	B;B	0.31016	0.123;0.025	T	0.17289	-1.0374	9	0.34782	T	0.22	.	7.4976	0.27498	0.2034:0.0:0.7966:0.0	.	35;35	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	I	35	ENSP00000436042:V35I;ENSP00000367362:V35I	ENSP00000367362:V35I	V	+	1	0	PCDHA9	140208367	0.002000	0.14202	0.795000	0.32087	0.505000	0.33919	-0.003000	0.12901	0.853000	0.35312	0.591000	0.81541	GTC		0.637	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140228183	G	A	140228183	3	1	108	1	0	0	0	0	1	0	0	0	11562	1145	40	1	105	1	PCDHA9	5	140228183	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	11155277	140228183	40687077	49	28444										
STK32A	202374	hgsc.bcm.edu	37	chr5	146703500	146703500	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaagacatgttcatggtggtGgacctcctgctgggtggaga	16	7	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:146703500G>A	ENST00000397936.3	+	5	633	c.300G>A	c.(298-300)gtG>gtA	p.V100V	STK32A_ENST00000398523.3_Silent_p.V100V|STK32A_ENST00000541094.1_Silent_p.V100V|STK32A_ENST00000398521.3_Silent_p.V100V	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCATGGTGGTGGACCTCCTGC	0.443																																																0			5											62	66	64					5																	146703500		2158	4294	6452	146683693	SO:0001819	synonymous_variant	202374				CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.300G>A	5.37:g.146703500G>A			146683693	B3KSY0	Silent	SNP	ENST00000397936.3	37	CCDS47299.1																																																																																				0.443	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001		A	146703500	G	A	146703500	2	1	108	1	0	0	0	0	0	0	0	1	15336	1335	47	3		3	STK32A	5	146703500	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	6475317	146703500	34211760	50	28445										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156593120	156593120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcccccatggaggttttgaaCgcactcattgaagagtagct	10	10	1	3	rs144795715	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:156593120C>T	ENST00000302938.4	-	1	155	c.60G>A	c.(58-60)gcG>gcA	p.A20A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	20						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGGTTTTGAACGCACTCATTG	0.418																																																0			5						C		1,4405	2.1+/-5.4	0,1,2202	116	112	113		60	2.8	0.8	5	dbSNP_134	113	36,8564	24.6+/-71.5	0,36,4264	no	coding-synonymous	FAM71B	NM_130899.2		0,37,6466	TT,TC,CC		0.4186,0.0227,0.2845		20/606	156593120	37,12969	2203	4300	6503	156525698	SO:0001819	synonymous_variant	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.60G>A	5.37:g.156593120C>T			156525698	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																				0.418	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156593120	C	T	156593120	2	4	108	1	0	0	0	0	0	0	0	1	5627	523	19	1		1	FAM71B	5	156593120	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	9889620	156593120	24322140	51	28446										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161524809	161524809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctgatgcacactggatcaccAcccccaacaggatgctgaga	9	14	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:161524809A>G	ENST00000361925.4	+	4	713	c.493A>G	c.(493-495)Acc>Gcc	p.T165A	GABRG2_ENST00000393933.4_Missense_Mutation_p.T70A|GABRG2_ENST00000414552.2_Missense_Mutation_p.T165A|GABRG2_ENST00000356592.3_Missense_Mutation_p.T165A			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	165					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	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)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGGATCACCACCCCCAACAG	0.423																																																0			5											98	98	98					5																	161524809		2203	4300	6503	161457387	SO:0001583	missense	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.493A>G	5.37:g.161524809A>G	ENSP00000354651:p.Thr165Ala		161457387	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684448	0.88639	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	M	0.80028	2.48	0.80722	D	1	D;P;P	0.56035	0.974;0.904;0.883	P;P;P	0.60117	0.869;0.826;0.734	D	0.89711	0.3912	10	0.56958	D	0.05	.	16.19	0.81981	1.0:0.0:0.0:0.0	.	165;165;165	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	A	165;165;165;70;70	ENSP00000349000:T165A;ENSP00000410732:T165A;ENSP00000354651:T165A;ENSP00000377510:T70A;ENSP00000430182:T70A	ENSP00000349000:T165A	T	+	1	0	GABRG2	161457387	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.168000	0.94781	2.225000	0.72522	0.460000	0.39030	ACC		0.423	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			G	161524809	A	G	161524809	3	3	108	1	0	0	0	0	1	0	0	0	6191	159	6	4	507	4	GABRG2	5	161524809	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	4931689	161524809	19390451	52	28447										
HK3	3101	hgsc.bcm.edu	37	chr5	176315471	176315471	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cagcccgcgtgcacacggccGcacagacgtgctgcacaagc	12	17	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr5:176315471G>A	ENST00000292432.5	-	10	1257	c.1166C>T	c.(1165-1167)gCg>gTg	p.A389V		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	389	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			GCACACGGCCGCACAGACGTG	0.657																																																0			5											20	19	20					5																	176315471		2154	4227	6381	176248077	SO:0001583	missense	84376				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1166C>T	5.37:g.176315471G>A	ENSP00000292432:p.Ala389Val		176248077	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	6.373	0.437015	0.12104	.	.	ENSG00000160883	ENST00000292432	D	0.96459	-4.02	5.14	-4.53	0.03462	Hexokinase, C-terminal (1);	1.336330	0.04827	N	0.438132	D	0.89392	0.6702	N	0.22421	0.69	0.09310	N	1	B	0.16166	0.016	B	0.13407	0.009	T	0.78458	-0.2196	10	0.33940	T	0.23	.	0.5431	0.00649	0.3976:0.1726:0.1621:0.2677	.	389	P52790	HXK3_HUMAN	V	389	ENSP00000292432:A389V	ENSP00000292432:A389V	A	-	2	0	HK3	176248077	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.160000	0.00145	-0.623000	0.05618	-1.126000	0.01995	GCG		0.657	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			A	176315471	G	A	176315471	3	1	108	1	0	0	0	0	1	0	0	0	7213	1087	38	1	1645	1	HK3	5	176315471	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	14790662	176315471	4599789	53	28448										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13053618	13053618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgaggaagtggagaggctggCggcgatgcgttctgactccc	17	9	1	3	rs200804785		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:13053618C>T	ENST00000379350.1	+	4	401	c.272C>T	c.(271-273)gCg>gTg	p.A91V	PHACTR1_ENST00000457702.2_5'UTR|PHACTR1_ENST00000482982.1_3'UTR|PHACTR1_ENST00000379345.2_5'UTR|PHACTR1_ENST00000332995.7_Missense_Mutation_p.A91V			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	91					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			GAGAGGCTGGCGGCGATGCGT	0.498																																																0			6											30	32	31					6																	13053618		1943	4150	6093	13161604	SO:0001583	missense	221692			AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.272C>T	6.37:g.13053618C>T	ENSP00000368655:p.Ala91Val		13161604	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	37		.	.	.	.	.	.	.	.	.	.	C	20.9	4.068465	0.76301	.	.	ENSG00000112137	ENST00000379350;ENST00000332995;ENST00000432934	T;T	0.34859	1.34;1.36	5.84	4.98	0.66077	.	0.274234	0.33515	N	0.004823	T	0.15912	0.0383	L	0.32530	0.975	0.80722	D	1	B;B;B	0.18013	0.021;0.008;0.025	B;B;B	0.11329	0.004;0.003;0.006	T	0.03534	-1.1027	10	0.46703	T	0.11	-12.9976	14.0076	0.64473	0.0:0.9278:0.0:0.0722	.	91;91;91	E7ESR5;Q9C0D0;Q9C0D0-2	.;PHAR1_HUMAN;.	V	91	ENSP00000368655:A91V;ENSP00000329880:A91V	ENSP00000329880:A91V	A	+	2	0	PHACTR1	13161604	1.000000	0.71417	0.992000	0.48379	0.828000	0.46876	4.912000	0.63335	1.494000	0.48533	0.609000	0.83330	GCG		0.498	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		T	13053618	C	T	13053618	3	4	108	1	0	0	0	0	1	0	0	0	11840	768	27	1	282	1	PHACTR1	6	13053618	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		13053618	158061449	54	28449										
CDC5L	988	hgsc.bcm.edu	37	chr6	44374091	44374091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaagagatagaaaaaaagacAaacagcatttgaaaaggaaa	9	3	0	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:44374091A>G	ENST00000371477.3	+	7	1089	c.790A>G	c.(790-792)Aaa>Gaa	p.K264E		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	264	Interaction with PPP1R8.|Nuclear localization signal. {ECO:0000255}.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAAAAAAGACAAACAGCATTT	0.294																																																0			6											68	71	70					6																	44374091		2203	4299	6502	44482069	SO:0001583	missense	988			D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.790A>G	6.37:g.44374091A>G	ENSP00000360532:p.Lys264Glu		44482069	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	37	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.469486	0.63625	.	.	ENSG00000096401	ENST00000371477	T	0.48201	0.82	5.62	5.62	0.85841	.	0.192563	0.56097	D	0.000038	T	0.26810	0.0656	L	0.46741	1.465	0.58432	D	0.999994	B	0.12630	0.006	B	0.18263	0.021	T	0.09422	-1.0675	10	0.25751	T	0.34	-22.1518	14.3835	0.66926	1.0:0.0:0.0:0.0	.	264	Q99459	CDC5L_HUMAN	E	264	ENSP00000360532:K264E	ENSP00000360532:K264E	K	+	1	0	CDC5L	44482069	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.809000	0.91944	2.138000	0.66242	0.455000	0.32223	AAA		0.294	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			G	44374091	A	G	44374091	3	3	108	1	0	0	0	0	1	0	0	0	3088	131	5	4	816	4	CDC5L	6	44374091	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	31320473	44374091	126740976	55	28450										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75833987	75833987	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ataccatctgcagggcttagTtttagcctgtaggaggtggc	13	8	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:75833987T>C	ENST00000322507.8	-	41	7017	c.6708A>G	c.(6706-6708)aaA>aaG	p.K2236K	COL12A1_ENST00000483888.2_Silent_p.K2236K|COL12A1_ENST00000345356.6_Silent_p.K1072K|COL12A1_ENST00000416123.2_Silent_p.K2236K	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2236	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.K2236K(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAGGGCTTAGTTTTAGCCTGT	0.378																																																1	Substitution - coding silent(1)	ovary(1)	6											62	60	61					6																	75833987		1843	4102	5945	75890707	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.6708A>G	6.37:g.75833987T>C			75890707	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.378	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75833987	T	C	75833987	2	2	108	1	0	0	0	0	0	0	0	1	3675	1722	60	4		4	COL12A1	6	75833987	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	31459896	75833987	95281080	56	28451										
ZBTB24	9841	hgsc.bcm.edu	37	chr6	109796640	109796640	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtttctttagctgagacacaTccatgaatttgcgatggcag	10	8	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:109796640T>C	ENST00000230122.3	-	5	1417	c.1250A>G	c.(1249-1251)gAt>gGt	p.D417G		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	417					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		CTGAGACACATCCATGAATTT	0.458																																																0			6											225	183	197					6																	109796640		2203	4300	6503	109903333	SO:0001583	missense	9841			AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1250A>G	6.37:g.109796640T>C	ENSP00000230122:p.Asp417Gly		109903333	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091401	0.76756	.	.	ENSG00000112365	ENST00000230122	T	0.07327	3.2	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	L	0.46614	1.455	0.54753	D	0.999988	D	0.89917	1.0	D	0.87578	0.998	T	0.01202	-1.1420	10	0.42905	T	0.14	-33.7729	16.8222	0.85835	0.0:0.0:0.0:1.0	.	417	O43167	ZBT24_HUMAN	G	417	ENSP00000230122:D417G	ENSP00000230122:D417G	D	-	2	0	ZBTB24	109903333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.542000	0.82095	2.371000	0.80710	0.533000	0.62120	GAT		0.458	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		C	109796640	T	C	109796640	3	2	108	1	0	0	0	0	1	0	0	0	17570	1435	50	4	855	4	ZBTB24	6	109796640	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	33962653	109796640	61318427	57	28452										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112461971	112461971	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtatggctgaccttgaagttGgaaggcactccaccaacata	10	10	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:112461971G>T	ENST00000230538.7	-	22	3364	c.2967C>A	c.(2965-2967)tcC>tcA	p.S989S	LAMA4_ENST00000389463.4_Silent_p.S982S|LAMA4_ENST00000424408.2_Silent_p.S982S|LAMA4_ENST00000522006.1_Silent_p.S982S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	989	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		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)		CCTTGAAGTTGGAAGGCACTC	0.408																																																0			6											77	71	73					6																	112461971		2203	4300	6503	112568664	SO:0001819	synonymous_variant	3910				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.2967C>A	6.37:g.112461971G>T			112568664	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																				0.408	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		T	112461971	G	T	112461971	2	4	108	1	0	0	0	0	0	0	0	1	8630	1335	47	2		2	LAMA4	6	112461971	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2665331	112461971	58653096	58	28453										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154360660	154360660	+	5'UTR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggctacctcgcacagcggtgCccgcccggccgtcagtacca	12	18	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr6:154360660C>G	ENST00000330432.7	+	0	218				OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000428397.2_5'UTR|OPRM1_ENST00000414028.2_5'UTR|OPRM1_ENST00000524163.1_5'UTR|OPRM1_ENST00000337049.4_5'UTR|OPRM1_ENST00000434900.2_Missense_Mutation_p.A87G|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000419506.2_5'UTR|OPRM1_ENST00000360422.4_5'UTR|OPRM1_ENST00000452687.2_5'UTR|OPRM1_ENST00000229768.5_5'UTR|OPRM1_ENST00000435918.2_5'UTR	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CACAGCGGTGCCCGCCCGGCC	0.632																																																0			6											21	29	26					6																	154360660		2037	4172	6209	154402353	SO:0001623	5_prime_UTR_variant	4988			L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.-20C>G	6.37:g.154360660C>G			154402353	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	C	9.856	1.194939	0.22037	.	.	ENSG00000112038	ENST00000520282;ENST00000434900	T;T	0.70749	3.87;-0.51	3.44	0.317	0.15861	.	25.302500	0.00357	N	0.000033	T	0.29588	0.0738	N	0.08118	0	0.21325	N	0.999722	B	0.13145	0.007	B	0.13407	0.009	T	0.18147	-1.0346	10	0.48119	T	0.1	.	7.2158	0.25959	0.3599:0.4845:0.1556:0.0	.	87	P35372-10	.	G	42;87	ENSP00000430247:A42G;ENSP00000394624:A87G	ENSP00000394624:A87G	A	+	2	0	OPRM1	154402353	0.004000	0.15560	0.009000	0.14445	0.019000	0.09904	1.230000	0.32612	0.034000	0.15491	-0.995000	0.02519	GCC		0.632	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		G	154360660	C	G	154360660	1	3	108	0	1	0	0	0	0	0	0	0	10918	739	26	5		5	OPRM1	6	154360660	5'UTR	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	41898689	154360660	16754407	59	28454										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50514773	50514773	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccagattcaacattgtcagaAtcaataattgcagaatattt	5	7	3	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr7:50514773A>G	ENST00000419119.1	-	2	1766	c.213T>C	c.(211-213)gaT>gaC	p.D71D	FIGNL1_ENST00000433017.1_Silent_p.D71D|FIGNL1_ENST00000395556.2_Silent_p.D71D|FIGNL1_ENST00000435566.1_Intron|FIGNL1_ENST00000356889.4_Silent_p.D71D			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	71					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				CATTGTCAGAATCAATAATTG	0.368																																																0			7											86	82	84					7																	50514773		2203	4300	6503	50482267	SO:0001819	synonymous_variant	63979			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.213T>C	7.37:g.50514773A>G			50482267	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Silent	SNP	ENST00000419119.1	37	CCDS5510.1																																																																																				0.368	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		G	50514773	A	G	50514773	2	3	108	1	0	0	0	0	0	0	0	1	5911	98	4	4		4	FIGNL1	7	50514773	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10		50514773	108623890	60	28455										
CROT	54677	hgsc.bcm.edu	37	chr7	86986858	86986858	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	accagataaggggtcttgatCcagatgctaagagagggttc	13	7	1	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr7:86986858C>T	ENST00000331536.3	+	4	300				CROT_ENST00000419147.2_Missense_Mutation_p.P51S|CROT_ENST00000442291.1_Intron|CROT_ENST00000412227.2_Intron	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase						carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	gggtcttgatccagatgctaa	0.478																																																0			7											155	131	138					7																	86986858		692	1591	2283	86824794	SO:0001627	intron_variant	54677				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.116-1664C>T	7.37:g.86986858C>T			86824794	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	.	.	.	.	.	.	.	.	.	.	C	5.823	0.336153	0.11013	.	.	ENSG00000005469	ENST00000419147	D	0.83506	-1.73	0.235	0.235	0.15431	.	.	.	.	.	T	0.69351	0.3101	N	0.03608	-0.345	0.09310	N	1	P	0.48350	0.909	P	0.50440	0.641	T	0.61826	-0.6983	8	0.62326	D	0.03	.	.	.	.	.	51	E7EQF2	.	S	51	ENSP00000413575:P51S	ENSP00000413575:P51S	P	+	1	0	CROT	86824794	0.082000	0.21442	0.052000	0.19188	0.052000	0.14988	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	CCA		0.478	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		T	86986858	C	T	86986858	1	4	108	0	1	0	0	0	0	0	0	0	3900	855	30	3		3	CROT	7	86986858	Intron	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	36472085	86986858	72151805	61	28456										
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92762907	92762907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaagcacaggaatgtaatccTgatggctctttgccctatag	10	9	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr7:92762907T>C	ENST00000318238.4	-	5	3594	c.2378A>G	c.(2377-2379)cAg>cGg	p.Q793R	SAMD9L_ENST00000411955.1_Missense_Mutation_p.Q793R|SAMD9L_ENST00000437805.1_Missense_Mutation_p.Q793R	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	793					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			AATGTAATCCTGATGGCTCTT	0.378																																																0			7											112	108	109					7																	92762907		2203	4300	6503	92600843	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.2378A>G	7.37:g.92762907T>C	ENSP00000326247:p.Gln793Arg		92600843	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	T	3.937	-0.014951	0.07681	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.80393	-1.37;-1.37;-1.37	4.77	3.6	0.41247	.	1.265160	0.05623	N	0.580253	T	0.71031	0.3292	L	0.48642	1.525	0.09310	N	1	P	0.38504	0.634	B	0.33521	0.165	T	0.60924	-0.7166	10	0.40728	T	0.16	-0.7688	1.3328	0.02138	0.3266:0.086:0.1537:0.4337	.	793	Q8IVG5	SAM9L_HUMAN	R	793	ENSP00000326247:Q793R;ENSP00000405760:Q793R;ENSP00000408796:Q793R	ENSP00000326247:Q793R	Q	-	2	0	SAMD9L	92600843	0.000000	0.05858	0.372000	0.25991	0.826000	0.46750	0.433000	0.21477	0.831000	0.34780	0.383000	0.25322	CAG		0.378	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		C	92762907	T	C	92762907	3	2	108	1	0	0	0	0	1	0	0	0	13864	1580	55	4	2380	4	SAMD9L	7	92762907	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	5776049	92762907	66375756	62	28457										
ADRA1A	148	hgsc.bcm.edu	37	chr8	26627845	26627845	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tttggacactgtaatcctggCagatccacggggcatggaag	13	9	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:26627845C>A	ENST00000519229.1	-	2	1228	c.1222G>T	c.(1222-1224)Gcc>Tcc	p.A408S	ADRA1A_ENST00000276393.4_Missense_Mutation_p.A408S|ADRA1A_ENST00000380586.1_Missense_Mutation_p.A408S|ADRA1A_ENST00000354550.4_Missense_Mutation_p.A408S|ADRA1A_ENST00000380573.3_Missense_Mutation_p.A408S|ADRA1A_ENST00000380582.3_Missense_Mutation_p.A408S|ADRA1A_ENST00000380587.1_Intron|ADRA1A_ENST00000380581.2_Intron			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	0					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GTAATCCTGGCAGATCCACGG	0.532																																																0			8											118	118	118					8																	26627845		2203	4300	6503	26683762	SO:0001583	missense	148			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"GPCR / Class A : Adrenoceptors : alpha"	277	protein-coding gene	gene with protein product		104221	"adrenergic, alpha-1A-, receptor"	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.1222G>T	8.37:g.26627845C>A	ENSP00000430793:p.Ala408Ser		26683762	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	C	10.69	1.419793	0.25552	.	.	ENSG00000120907	ENST00000380586;ENST00000380582;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573	T;T;T;T;T;T	0.63255	2.23;0.07;0.03;-0.03;0.12;0.12	5.85	2.6	0.31112	.	0.439260	0.21710	N	0.070295	T	0.50120	0.1597	L	0.51422	1.61	0.80722	D	1	B;B;B;B	0.15473	0.01;0.003;0.001;0.013	B;B;B;B	0.13407	0.004;0.004;0.003;0.009	T	0.34825	-0.9813	10	0.19590	T	0.45	.	7.9479	0.29998	0.1279:0.6703:0.0:0.2018	.	408;408;408;408	P35348;P35348-4;P35348-3;B0ZBD3	ADA1A_HUMAN;.;.;.	S	408	ENSP00000369960:A408S;ENSP00000369956:A408S;ENSP00000430793:A408S;ENSP00000346557:A408S;ENSP00000276393:A408S;ENSP00000369947:A408S	ENSP00000276393:A408S	A	-	1	0	ADRA1A	26683762	0.027000	0.19231	0.998000	0.56505	0.972000	0.66771	0.019000	0.13444	0.788000	0.33755	0.655000	0.94253	GCC		0.532	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303		A	26627845	C	A	26627845	3	1	108	1	0	0	0	0	1	0	0	0	334	710	25	2	473	2	ADRA1A	8	26627845	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		26627845	119736177	63	28458										
TEX15	56154	hgsc.bcm.edu	37	chr8	30700211	30700211	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaaatgaaaaagaagccattTtttcttggcactgaaccagc	8	8	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:30700211T>G	ENST00000256246.2	-	1	6397	c.6323A>C	c.(6322-6324)aAa>aCa	p.K2108T		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2108					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGAAGCCATTTTTTCTTGGCA	0.363																																																0			8											54	54	54					8																	30700211		2203	4300	6503	30819753	SO:0001583	missense	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.6323A>C	8.37:g.30700211T>G	ENSP00000256246:p.Lys2108Thr		30819753		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	5.784	0.328922	0.10956	.	.	ENSG00000133863	ENST00000256246	T	0.12039	2.72	5.67	3.13	0.36017	.	0.406216	0.23543	N	0.047050	T	0.10680	0.0261	L	0.41236	1.265	0.24255	N	0.995302	B	0.27351	0.176	B	0.23419	0.046	T	0.21348	-1.0248	10	0.87932	D	0	.	6.5177	0.22256	0.0:0.0775:0.3016:0.6209	.	2108	Q9BXT5	TEX15_HUMAN	T	2108	ENSP00000256246:K2108T	ENSP00000256246:K2108T	K	-	2	0	TEX15	30819753	1.000000	0.71417	0.996000	0.52242	0.757000	0.42996	1.359000	0.34113	0.959000	0.37980	0.477000	0.44152	AAA		0.363	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30700211	T	G	30700211	3	3	108	1	0	0	0	0	1	0	0	0	15818	1841	64	4	2062	4	TEX15	8	30700211	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	4072366	30700211	115663811	64	28459										
STAR	6770	hgsc.bcm.edu	37	chr8	38006255	38006255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctcctggctgatggccatcaCagcctgttgcctcagccctg	10	16	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:38006255C>T	ENST00000276449.4	-	2	528	c.82G>A	c.(82-84)Gtg>Atg	p.V28M	RP11-90P5.2_ENST00000520598.1_RNA	NM_000349.2	NP_000340.2	P49675	STAR_HUMAN	steroidogenic acute regulatory protein	28					bile acid biosynthetic process (GO:0006699)|biphenyl metabolic process (GO:0018879)|brain development (GO:0007420)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth hormone stimulus (GO:0071378)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-alpha (GO:0035457)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to luteinizing hormone stimulus (GO:0071373)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cholesterol metabolic process (GO:0008203)|circadian sleep/wake cycle, REM sleep (GO:0042747)|dibenzo-p-dioxin metabolic process (GO:0018894)|diterpenoid metabolic process (GO:0016101)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|glucocorticoid metabolic process (GO:0008211)|insecticide metabolic process (GO:0017143)|intracellular cholesterol transport (GO:0032367)|male gonad development (GO:0008584)|negative regulation of neuron apoptotic process (GO:0043524)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of gene expression (GO:0010628)|positive regulation of neurogenesis (GO:0050769)|progesterone biosynthetic process (GO:0006701)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of steroid biosynthetic process (GO:0050810)|response to activity (GO:0014823)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to hydrogen peroxide (GO:0042542)|response to ionizing radiation (GO:0010212)|response to lead ion (GO:0010288)|response to leptin (GO:0044321)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytosol (GO:0005829)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	cholesterol binding (GO:0015485)			breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		ATGGCCATCACAGCCTGTTGC	0.597																																																0			8											32	34	33					8																	38006255		2203	4300	6503	38125412	SO:0001583	missense	92002			BC010550	CCDS6102.1	8p11.2	2011-09-13	2007-05-15		ENSG00000147465	ENSG00000147465		"StAR-related lipid transfer (START) domain containing"	11359	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 1"	600617	"steroidogenic acute regulator"			7761400	Standard	NM_000349		Approved	StAR, STARD1	uc003xkv.1	P49675	OTTHUMG00000164058	ENST00000276449.4:c.82G>A	8.37:g.38006255C>T	ENSP00000276449:p.Val28Met		38125412	Q16396	Missense_Mutation	SNP	ENST00000276449.4	37	CCDS6102.1	.	.	.	.	.	.	.	.	.	.	C	4.269	0.049038	0.08243	.	.	ENSG00000147465	ENST00000276449	D	0.87966	-2.32	5.28	-0.098	0.13630	.	0.710749	0.14761	N	0.299965	T	0.73110	0.3545	N	0.21142	0.635	0.09310	N	0.999997	B	0.02656	0.0	B	0.10450	0.005	T	0.55503	-0.8131	10	0.15952	T	0.53	-7.9645	6.2879	0.21043	0.1201:0.5905:0.0:0.2894	.	28	P49675	STAR_HUMAN	M	28	ENSP00000276449:V28M	ENSP00000276449:V28M	V	-	1	0	STAR	38125412	0.004000	0.15560	0.059000	0.19551	0.340000	0.28889	0.257000	0.18369	0.278000	0.22164	0.462000	0.41574	GTG		0.597	STAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376990.2	NM_000349		T	38006255	C	T	38006255	3	4	108	1	0	0	0	0	1	0	0	0	15293	478	17	3	799	3	STAR	8	38006255	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	7306044	38006255	108357767	65	28460										
CHD7	55636	hgsc.bcm.edu	37	chr8	61769343	61769343	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggcatctccttaatggctccCtagtggatggagagcctccc	11	13	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:61769343C>G	ENST00000423902.2	+	34	7983	c.7504C>G	c.(7504-7506)Cta>Gta	p.L2502V	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000529472.1_3'UTR	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2502					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		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)			TAATGGCTCCCTAGTGGATGG	0.512																																																0			8											114	112	113					8																	61769343		1943	4141	6084	61931897	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.7504C>G	8.37:g.61769343C>G	ENSP00000392028:p.Leu2502Val		61931897	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.982659	0.74474	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.86366	-2.11	5.2	4.24	0.50183	.	0.089265	0.46442	D	0.000294	T	0.82047	0.4952	L	0.49126	1.545	0.46798	D	0.999207	P	0.47841	0.901	P	0.44696	0.458	T	0.80296	-0.1442	10	0.44086	T	0.13	-11.2105	4.2381	0.10635	0.0:0.7103:0.0:0.2897	.	2502	Q9P2D1	CHD7_HUMAN	V	2502	ENSP00000392028:L2502V	ENSP00000307304:L2502V	L	+	1	2	CHD7	61931897	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.289000	0.51747	2.698000	0.92095	0.655000	0.94253	CTA		0.512	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		G	61769343	C	G	61769343	3	3	108	1	0	0	0	0	1	0	0	0	3336	680	24	5	7634	5	CHD7	8	61769343	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	23763088	61769343	84594679	66	28461										
NBN	4683	hgsc.bcm.edu	37	chr8	90958456	90958456	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tagagtttttaatcaccagtGatctaaattcagtcaataac	5	7	4	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:90958456G>T	ENST00000265433.3	-	13	2136	c.1982C>A	c.(1981-1983)tCa>tAa	p.S661*	NBN_ENST00000409330.1_Nonsense_Mutation_p.S579*	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	661					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			AATCACCAGTGATCTAAATTC	0.323								Homologous recombination																																								0			8											120	122	121					8																	90958456		2203	4298	6501	91027632	SO:0001587	stop_gained	9048			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1982C>A	8.37:g.90958456G>T	ENSP00000265433:p.Ser661*		91027632	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Nonsense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	G	40	8.048006	0.98627	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	.	.	.	5.65	3.87	0.44632	.	0.137053	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4442	12.2048	0.54346	0.1395:0.0:0.8605:0.0	.	.	.	.	X	661;579	.	ENSP00000265433:S661X	S	-	2	0	NBN	91027632	1.000000	0.71417	0.948000	0.38648	0.949000	0.60115	3.753000	0.55180	0.870000	0.35726	0.650000	0.86243	TCA		0.323	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		T	90958456	G	T	90958456	4	4	108	1	0	0	0	0	0	1	0	0	10221	1294	45	2	298	2	NBN	8	90958456	Nonsense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	29189113	90958456	55405566	67	28462										
RGS22	26166	hgsc.bcm.edu	37	chr8	101075775	101075775	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcctttctattgccaatgtcAtaagtcctatgagaaataca	5	9	2	1	rs373041410		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:101075775A>G	ENST00000360863.6	-	8	1415	c.1221T>C	c.(1219-1221)taT>taC	p.Y407Y	RGS22_ENST00000523287.1_Silent_p.Y226Y|RGS22_ENST00000523437.1_Silent_p.Y395Y	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	407					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.Y407*(1)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TGCCAATGTCATAAGTCCTAT	0.393													A|||	1	0.000199681	8e-04	0	5008	,	,		15404	0		0	False		,,,				2504	0															1	Substitution - Nonsense(1)	ovary(1)	8						A		4,3724		0,4,1860	154	139	144		1221	-5	0.3	8		144	0,8210		0,0,4105	no	coding-synonymous	RGS22	NM_015668.3		0,4,5965	GG,GA,AA		0.0,0.1073,0.0335		407/1265	101075775	4,11934	1864	4105	5969	101144951	SO:0001819	synonymous_variant	26166			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.1221T>C	8.37:g.101075775A>G			101144951	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																				0.393	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101075775	A	G	101075775	2	3	108	1	0	0	0	0	0	0	0	1	13342	224	8	4		4	RGS22	8	101075775	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	10117319	101075775	45288247	68	28463										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125580672	125580672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agaatcggccacgttcttcaAtcaaagccttccggacagcc	8	14	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:125580672A>G	ENST00000518547.1	-	7	1039	c.566T>C	c.(565-567)aTt>aCt	p.I189T	MTSS1_ENST00000431961.2_5'UTR|NDUFB9_ENST00000522532.1_3'UTR|MTSS1_ENST00000395508.2_5'Flank|MTSS1_ENST00000325064.5_Missense_Mutation_p.I193T|MTSS1_ENST00000524090.1_Missense_Mutation_p.I79T|MTSS1_ENST00000378017.3_Missense_Mutation_p.I189T|MTSS1_ENST00000354184.4_5'UTR	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	189	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ACGTTCTTCAATCAAAGCCTT	0.448																																					Esophageal Squamous(160;622 1893 3862 8546 12509)											0			8											110	94	100					8																	125580672		2203	4300	6503	125649853	SO:0001583	missense	9788			AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.566T>C	8.37:g.125580672A>G	ENSP00000429064:p.Ile189Thr		125649853	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.630867	0.87660	.	.	ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000325064;ENST00000524090	T;T;T;T	0.42513	1.31;1.37;1.34;0.97	5.55	5.55	0.83447	IRSp53/MIM homology domain (IMD) (3);	0.072630	0.64402	D	0.000002	T	0.53690	0.1812	L	0.48362	1.52	0.80722	D	1	D;P;B;B	0.57571	0.98;0.942;0.299;0.258	P;P;B;B	0.62649	0.871;0.905;0.328;0.314	T	0.43734	-0.9373	10	0.19147	T	0.46	-18.4336	15.9844	0.80138	1.0:0.0:0.0:0.0	.	79;189;189;189	E7EWW5;A5YM41;O43312;O43312-4	.;.;MTSS1_HUMAN;.	T	189;189;193;79	ENSP00000367256:I189T;ENSP00000429064:I189T;ENSP00000322804:I193T;ENSP00000428319:I79T	ENSP00000322804:I193T	I	-	2	0	MTSS1	125649853	1.000000	0.71417	0.682000	0.30024	0.818000	0.46254	9.181000	0.94874	2.233000	0.73108	0.533000	0.62120	ATT		0.448	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		G	125580672	A	G	125580672	3	3	108	1	0	0	0	0	1	0	0	0	9992	101	4	4	1733	4	MTSS1	8	125580672	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	24504897	125580672	20783350	69	28464										
ZNF572	137209	hgsc.bcm.edu	37	chr8	125989231	125989231	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atcacagatcacatacaggtGaaaaaccatatgaatgttct	6	8	3	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:125989231G>A	ENST00000319286.5	+	3	875	c.721G>A	c.(721-723)Gaa>Aaa	p.E241K		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ACATACAGGTGAAAAACCATA	0.448										HNSCC(60;0.17)																																						0			8											67	65	66					8																	125989231		2203	4299	6502	126058412	SO:0001583	missense	137209			BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"Zinc fingers, C2H2-type"	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.721G>A	8.37:g.125989231G>A	ENSP00000319305:p.Glu241Lys		126058412	A1L4F1|Q8N1Q0	Missense_Mutation	SNP	ENST00000319286.5	37	CCDS6354.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.729262	0.89390	.	.	ENSG00000180938	ENST00000319286	T	0.24350	1.86	5.19	5.19	0.71726	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000122	T	0.44222	0.1283	L	0.43554	1.36	0.46279	D	0.998968	D	0.89917	1.0	D	0.97110	1.0	T	0.23868	-1.0176	10	0.59425	D	0.04	-17.7539	16.2371	0.82381	0.0:0.0:1.0:0.0	.	241	Q7Z3I7	ZN572_HUMAN	K	241	ENSP00000319305:E241K	ENSP00000319305:E241K	E	+	1	0	ZNF572	126058412	1.000000	0.71417	0.981000	0.43875	0.955000	0.61496	6.857000	0.75455	2.698000	0.92095	0.655000	0.94253	GAA		0.448	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		A	125989231	G	A	125989231	3	1	108	1	0	0	0	0	1	0	0	0	18043	1291	45	3	727	3	ZNF572	8	125989231	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	408559	125989231	20374791	70	28465										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131127886	131127886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	acactcactttgtcatccagAtcatcatcgctctcatctat	3	14	6	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:131127886A>G	ENST00000518721.1	-	23	2387	c.2160T>C	c.(2158-2160)gaT>gaC	p.D720D	ASAP1_ENST00000357668.1_Silent_p.D720D	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	720					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TGTCATCCAGATCATCATCGC	0.418																																																0			8											320	271	288					8																	131127886		2203	4300	6503	131197068	SO:0001819	synonymous_variant	50807			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2160T>C	8.37:g.131127886A>G			131197068	B2RNV3	Silent	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.290238	0.23478	.	.	ENSG00000153317	ENST00000524124;ENST00000519483	.	.	.	5.17	-1.89	0.07689	.	.	.	.	.	T	0.57607	0.2065	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54173	-0.8333	4	.	.	.	.	11.5213	0.50553	0.5138:0.0:0.4862:0.0	.	.	.	.	P	541;134	.	.	S	-	1	0	ASAP1	131197068	0.802000	0.28943	0.976000	0.42696	0.994000	0.84299	0.002000	0.13061	-0.489000	0.06716	0.528000	0.53228	TCT		0.418	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		G	131127886	A	G	131127886	2	3	108	1	0	0	0	0	0	0	0	1	1011	330	12	4		4	ASAP1	8	131127886	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	5138655	131127886	15236136	71	28466										
ST3GAL1	6482	hgsc.bcm.edu	37	chr8	134472027	134472027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcatctccccttgaagatccGgattttattgatggaggcca	9	10	2	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr8:134472027G>A	ENST00000319914.5	-	9	2030	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W	ST3GAL1_ENST00000521180.1_Missense_Mutation_p.R335W|ST3GAL1_ENST00000399640.2_Missense_Mutation_p.R335W|ST3GAL1_ENST00000522652.1_Missense_Mutation_p.R335W			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	335					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			TTGAAGATCCGGATTTTATTG	0.572																																																0			8											159	119	133					8																	134472027		2203	4300	6503	134541209	SO:0001583	missense	6482			L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"Sialyltransferases"	10862	protein-coding gene	gene with protein product	"ST3Gal I"	607187	"sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.1003C>T	8.37:g.134472027G>A	ENSP00000318445:p.Arg335Trp		134541209	O60677|Q9UN51	Missense_Mutation	SNP	ENST00000319914.5	37	CCDS6373.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363777	0.82353	.	.	ENSG00000008513	ENST00000319914;ENST00000399640;ENST00000521180;ENST00000522652	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	5.13	5.13	0.70059	.	0.469539	0.24561	N	0.037474	T	0.46171	0.1379	L	0.60455	1.87	0.37119	D	0.900705	D	0.76494	0.999	P	0.57846	0.828	T	0.54241	-0.8323	10	0.72032	D	0.01	-24.7509	13.5465	0.61707	0.0:0.0:0.8342:0.1658	.	335	Q11201	SIA4A_HUMAN	W	335	ENSP00000318445:R335W;ENSP00000414073:R335W;ENSP00000428540:R335W;ENSP00000430515:R335W	ENSP00000318445:R335W	R	-	1	2	ST3GAL1	134541209	0.994000	0.37717	0.998000	0.56505	0.994000	0.84299	2.355000	0.44107	2.558000	0.86282	0.555000	0.69702	CGG		0.572	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033		A	134472027	G	A	134472027	3	1	108	1	0	0	0	0	1	0	0	0	15253	1115	39	1	23	1	ST3GAL1	8	134472027	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	3344141	134472027	11891995	72	28467										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2058432	2058432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agcagaagaaggagacagagCggattgaaaaggagagaatg	16	3	0	6			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:2058432C>T	ENST00000382203.1	+	8	1698	c.1489C>T	c.(1489-1491)Cgg>Tgg	p.R497W	SMARCA2_ENST00000357248.2_Missense_Mutation_p.R497W|SMARCA2_ENST00000349721.2_Missense_Mutation_p.R497W|SMARCA2_ENST00000382194.1_Missense_Mutation_p.R497W			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	497	HSA. {ECO:0000255|PROSITE- ProRule:PRU00549}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GGAGACAGAGCGGATTGAAAA	0.512																																																0			9											125	111	116					9																	2058432		2203	4300	6503	2048432	SO:0001583	missense	6595			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1489C>T	9.37:g.2058432C>T	ENSP00000371638:p.Arg497Trp		2048432	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.848231	0.51164	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89	5.52	2.55	0.30701	Helicase/SANT-associated, DNA binding (1);HAS subgroup (1);HSA (1);	0.064020	0.64402	D	0.000010	D	0.88265	0.6390	M	0.91406	3.205	0.80722	D	1	P;D;D	0.89917	0.562;1.0;1.0	B;D;D	0.87578	0.26;0.996;0.998	D	0.89830	0.3995	10	0.87932	D	0	-13.9838	14.9479	0.71047	0.5637:0.4363:0.0:0.0	.	98;497;497	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	W	497	ENSP00000265773:R497W;ENSP00000349788:R497W;ENSP00000392081:R497W;ENSP00000371638:R497W;ENSP00000371629:R497W	ENSP00000265773:R497W	R	+	1	2	SMARCA2	2048432	0.811000	0.29063	0.974000	0.42286	0.961000	0.63080	-0.034000	0.12225	0.241000	0.21283	-0.182000	0.12963	CGG		0.512	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		T	2058432	C	T	2058432	3	4	108	1	0	0	0	0	1	0	0	0	14806	759	27	1	1515	1	SMARCA2	9	2058432	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		2058432	139154999	73	28468										
JAK2	3717	hgsc.bcm.edu	37	chr9	5070031	5070031	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	caaatggtgtttcacaaaatCagaaatgaagatttgatatt	7	4	2	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:5070031C>T	ENST00000381652.3	+	12	2114	c.1620C>T	c.(1618-1620)atC>atT	p.I540I	JAK2_ENST00000539801.1_Silent_p.I540I|JAK2_ENST00000544510.1_Silent_p.I391I	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	540					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.I540_E543>MK(7)|p.I540fs*3(1)|p.I540_E543>KK(1)|p.I540I(1)|p.I540_D544>MK(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTCACAAAATCAGAAATGAAG	0.338		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	11	Complex - deletion inframe(9)|Deletion - Frameshift(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(11)	9											88	83	84					9																	5070031		2202	4300	6502	5060031	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1620C>T	9.37:g.5070031C>T			5060031	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.338	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5070031	C	T	5070031	2	4	108	1	0	0	0	0	0	0	0	1	7959	816	29	3		3	JAK2	9	5070031	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	3011599	5070031	136143400	74	28469										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32541757	32541757	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctattgtcacattctgtatcCtcctttacttcagaatcctt	3	12	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:32541757C>T	ENST00000360538.2	-	3	2882	c.2766G>A	c.(2764-2766)gaG>gaA	p.E922E	TOPORS_ENST00000379858.1_Silent_p.E857E	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	922				E -> G (in Ref. 1; AAD23379). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E922E(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ATTCTGTATCCTCCTTTACTT	0.383																																																1	Substitution - coding silent(1)	skin(1)	9											207	190	196					9																	32541757		2203	4300	6503	32531757	SO:0001819	synonymous_variant	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2766G>A	9.37:g.32541757C>T			32531757	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																				0.383	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32541757	C	T	32541757	2	4	108	1	0	0	0	0	0	0	0	1	16410	680	24	3		3	TOPORS	9	32541757	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	27471726	32541757	108671674	75	28470										
OMD	4958	hgsc.bcm.edu	37	chr9	95179006	95179006	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gagttctacaatgttgggaaGattaaaaatattatatggga	10	2	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:95179006G>T	ENST00000375550.4	-	2	1110	c.835C>A	c.(835-837)Ctt>Att	p.L279I	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	279					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						ATGTTGGGAAGATTAAAAATA	0.318			T	USP6	aneurysmal bone cysts																																		Dom	yes		9	9q22.31	4958	osteomodulin		M	0			9											67	73	71					9																	95179006		2199	4299	6498	94218827	SO:0001583	missense	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.835C>A	9.37:g.95179006G>T	ENSP00000364700:p.Leu279Ile		94218827	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	37	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	g	6.190	0.403252	0.11754	.	.	ENSG00000127083	ENST00000375550	T	0.71934	-0.61	5.46	3.47	0.39725	.	0.093605	0.42964	D	0.000629	T	0.60090	0.2242	L	0.46947	1.48	0.35285	D	0.781696	B	0.27166	0.17	B	0.26310	0.068	T	0.62243	-0.6895	10	0.17369	T	0.5	-11.168	11.5432	0.50677	0.0:0.1166:0.6542:0.2292	.	279	Q99983	OMD_HUMAN	I	279	ENSP00000364700:L279I	ENSP00000364700:L279I	L	-	1	0	OMD	94218827	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.055000	0.30467	1.402000	0.46780	0.650000	0.86243	CTT		0.318	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		T	95179006	G	T	95179006	3	4	108	1	0	0	0	0	1	0	0	0	10896	942	33	2	438	2	OMD	9	95179006	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	62637249	95179006	46034425	76	28471										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98229511	98229511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtaggtcgtaaagtaagtgcTggatattcgggtagtctgct	14	5	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:98229511T>C	ENST00000331920.6	-	15	2746	c.2447A>G	c.(2446-2448)cAg>cGg	p.Q816R	PTCH1_ENST00000437951.1_Missense_Mutation_p.Q750R|PTCH1_ENST00000421141.1_Missense_Mutation_p.Q665R|PTCH1_ENST00000429896.2_Missense_Mutation_p.Q665R|PTCH1_ENST00000418258.1_Missense_Mutation_p.Q665R|PTCH1_ENST00000375274.2_Missense_Mutation_p.Q815R|PTCH1_ENST00000430669.2_Missense_Mutation_p.Q750R	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	816			Missing (in BCNS). {ECO:0000269|PubMed:8840969}.		brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.Q816L(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AAGTAAGTGCTGGATATTCGG	0.398																																																1	Substitution - Missense(1)	oesophagus(1)	9	GRCh37	CI962341	PTCH1	I							200	189	193					9																	98229511		2203	4300	6503	97269332	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2447A>G	9.37:g.98229511T>C	ENSP00000332353:p.Gln816Arg		97269332	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715078	0.89112	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68;-2.68;-2.68	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.94335	0.8179	M	0.64997	1.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.988;0.999	D	0.94214	0.7461	10	0.49607	T	0.09	-20.2032	16.0121	0.80409	0.0:0.0:0.0:1.0	.	750;815;816	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	R	816;750;665;665;252;750;665;815	ENSP00000332353:Q816R;ENSP00000389744:Q750R;ENSP00000399981:Q665R;ENSP00000396135:Q665R;ENSP00000410287:Q750R;ENSP00000414823:Q665R;ENSP00000364423:Q815R	ENSP00000332353:Q816R	Q	-	2	0	PTCH1	97269332	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.180000	0.69256	0.482000	0.46254	CAG		0.398	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98229511	T	C	98229511	3	2	108	1	0	0	0	0	1	0	0	0	12764	1580	55	4	1932	4	PTCH1	9	98229511	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	3050505	98229511	42983920	77	28472										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767111	105767111	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctcaaaccaactcgtactgtCgaggtggattctaaagcagc	9	11	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:105767111C>T	ENST00000374798.3	+	4	385	c.315C>T	c.(313-315)gtC>gtT	p.V105V	CYLC2_ENST00000487798.1_Silent_p.V105V	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	105	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				CTCGTACTGTCGAGGTGGATT	0.368																																																0			9											59	59	59					9																	105767111		2203	4300	6503	104806932	SO:0001819	synonymous_variant	1539			Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.315C>T	9.37:g.105767111C>T			104806932	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	37	CCDS35085.1																																																																																				0.368	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		T	105767111	C	T	105767111	2	4	108	1	0	0	0	0	0	0	0	1	4148	871	31	1		1	CYLC2	9	105767111	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	7537600	105767111	35446320	78	28473										
ACTL7B	10880	hgsc.bcm.edu	37	chr9	111617966	111617966	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cgtcggccgcctcggggcagCgtttgcccacggtggaggag	18	13	0	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:111617966C>T	ENST00000374667.3	-	1	1273	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	82						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTCGGGGCAGCGTTTGCCCAC	0.647																																																0			9											85	85	85					9																	111617966		2203	4300	6503	110657787	SO:0001583	missense	10880			BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.245G>A	9.37:g.111617966C>T	ENSP00000363799:p.Arg82His		110657787	B2R9Q2|Q5JSV1	Missense_Mutation	SNP	ENST00000374667.3	37	CCDS6771.1	.	.	.	.	.	.	.	.	.	.	C	8.418	0.845624	0.16963	.	.	ENSG00000148156	ENST00000374667	D	0.97161	-4.27	4.27	-0.171	0.13331	.	.	.	.	.	D	0.88544	0.6465	N	0.02247	-0.625	0.25928	N	0.983037	B	0.11235	0.004	B	0.06405	0.002	T	0.81814	-0.0760	9	0.87932	D	0	.	5.6417	0.17567	0.0:0.29:0.4992:0.2108	.	82	Q9Y614	ACL7B_HUMAN	H	82	ENSP00000363799:R82H	ENSP00000363799:R82H	R	-	2	0	ACTL7B	110657787	0.000000	0.05858	0.799000	0.32177	0.229000	0.25112	-0.497000	0.06428	0.086000	0.17137	0.655000	0.94253	CGC		0.647	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686		T	111617966	C	T	111617966	3	4	108	1	0	0	0	0	1	0	0	0	201	768	27	1	1006	1	ACTL7B	9	111617966	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	5850855	111617966	29595465	79	28474										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131353800	131353800	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gatcgtcagggttttgtgccGgctgcgtacgtgaagaaatt	14	7	1	2	rs140279996	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:131353800G>A	ENST00000372731.4	+	22	3161	c.3051G>A	c.(3049-3051)ccG>ccA	p.P1017P	SPTAN1_ENST00000358161.5_Silent_p.P1017P|SPTAN1_ENST00000372739.3_Silent_p.P1017P	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1017	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		P -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GTTTTGTGCCGGCTGCGTACG	0.527													g|||	10	0.00199681	0	0	5008	,	,		18251	0.0099		0	False		,,,				2504	0				NSCLC(120;833 1744 2558 35612 37579)											0			9						A	,,	19,4387	27.2+/-55.0	0,19,2184	139	136	137		3051,3051,3051	-11.8	0.3	9	dbSNP_134	137	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	0,21,6482	AA,AG,GG		0.0233,0.4312,0.1615	,,	1017/2478,1017/2453,1017/2473	131353800	21,12985	2203	4300	6503	130393621	SO:0001819	synonymous_variant	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3051G>A	9.37:g.131353800G>A			130393621	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																				0.527	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131353800	G	A	131353800	2	1	108	1	0	0	0	0	0	0	0	1	15156	1103	39	1		1	SPTAN1	9	131353800	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	19735834	131353800	9859631	80	28475										
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135554146	135554146	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atcaaatgtgtgccactttaTcatccttaccagaagtgtag	7	9	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:135554146T>C	ENST00000372146.4	+	2	1704	c.1140T>C	c.(1138-1140)taT>taC	p.Y380Y	GTF3C4_ENST00000483873.2_Intron	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	380					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TGCCACTTTATCATCCTTACC	0.428																																					Pancreas(142;417 1875 11086 31973 47667)											0			9											152	150	151					9																	135554146		2203	4300	6503	134543967	SO:0001819	synonymous_variant	9329			AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.1140T>C	9.37:g.135554146T>C			134543967	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																				0.428	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			C	135554146	T	C	135554146	2	2	108	1	0	0	0	0	0	0	0	1	6896	1442	50	4		4	GTF3C4	9	135554146	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	4200346	135554146	5659285	81	28476										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138657014	138657014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cttctcatggacttcctgaaCgagttctacgcccacccccg	7	17	2	1	rs374015551		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr9:138657014C>T	ENST00000263604.3	+	12	1116	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N	KCNT1_ENST00000371757.2_Silent_p.N391N|KCNT1_ENST00000486577.2_Silent_p.N352N|KCNT1_ENST00000491806.2_Silent_p.N358N|KCNT1_ENST00000488444.2_Silent_p.N372N|KCNT1_ENST00000298480.5_Silent_p.N391N|KCNT1_ENST00000490355.2_Silent_p.N372N|KCNT1_ENST00000487664.1_Silent_p.N346N			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	372					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		ACTTCCTGAACGAGTTCTACG	0.642																																																0			9						T		0,4406		0,0,2203	185	170	175		1173	-7.7	0.7	9		175	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	KCNT1	NM_020822.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		391/1236	138657014	2,13004	2203	4300	6503	137796835	SO:0001819	synonymous_variant	57582			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1116C>T	9.37:g.138657014C>T			137796835	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																					0.642	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		T	138657014	C	T	138657014	2	4	108	1	0	0	0	0	0	0	0	1	8112	535	19	1		1	KCNT1	9	138657014	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	3102868	138657014	2556417	82	28477										
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30317347	30317347	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aaaccaagcaaaatatagtcTcgttcatttttttctttgaa	4	7	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr10:30317347T>C	ENST00000375377.1	-	3	1831	c.1730A>G	c.(1729-1731)gAg>gGg	p.E577G		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	577					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AAATATAGTCTCGTTCATTTT	0.418																																																0			10											99	98	99					10																	30317347		1833	4085	5918	30357353	SO:0001583	missense	57608			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1730A>G	10.37:g.30317347T>C	ENSP00000364526:p.Glu577Gly		30357353	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.504251	0.44558	.	.	ENSG00000165757	ENST00000375377	T	0.18960	2.18	5.62	3.23	0.37069	.	0.159020	0.53938	D	0.000053	T	0.40398	0.1115	M	0.72894	2.215	0.48395	D	0.999647	D	0.89917	1.0	D	0.71414	0.973	T	0.11767	-1.0574	10	0.66056	D	0.02	-29.8284	8.3572	0.32338	0.0:0.0697:0.1372:0.793	.	577	Q9P266	K1462_HUMAN	G	577	ENSP00000364526:E577G	ENSP00000364526:E577G	E	-	2	0	KIAA1462	30357353	1.000000	0.71417	0.254000	0.24359	0.003000	0.03518	4.569000	0.60865	0.397000	0.25310	-0.441000	0.05720	GAG		0.418	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		C	30317347	T	C	30317347	3	2	108	1	0	0	0	0	1	0	0	0	8255	1551	54	4	2357	4	KIAA1462	10	30317347	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10		30317347	105217400	83	28478										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72462145	72462145	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cagcaggagaaggaggccagCgggaggacacatgtggtgta	18	7	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr10:72462145C>T	ENST00000373207.1	+	3	600	c.600C>T	c.(598-600)agC>agT	p.S200S	ADAMTS14_ENST00000373208.1_Silent_p.S200S	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	200					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						AGGAGGCCAGCGGGAGGACAC	0.647																																																0			10											64	70	68					10																	72462145		2203	4300	6503	72132151	SO:0001819	synonymous_variant	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.600C>T	10.37:g.72462145C>T			72132151	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																				0.647	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72462145	C	T	72462145	2	4	108	1	0	0	0	0	0	0	0	1	259	767	27	1		1	ADAMTS14	10	72462145	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	42144798	72462145	63072602	84	28479										
MYST4	23522	hgsc.bcm.edu	37	chr10	76788700	76788700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agaggaaggggaagaagaagAaggaggaggaaatgtagaaa	18	0	0	5	rs373140884		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr10:76788700A>G	ENST00000287239.4	+	18	4607	c.4118A>G	c.(4117-4119)gAa>gGa	p.E1373G	KAT6B_ENST00000372725.1_Missense_Mutation_p.E1081G|KAT6B_ENST00000372724.1_Missense_Mutation_p.E1081G|KAT6B_ENST00000372714.1_Missense_Mutation_p.E1081G|KAT6B_ENST00000372711.1_Missense_Mutation_p.E1190G	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1373	Poly-Glu.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.E1373G(1)									gaagaagaagaaggaggagga	0.448																																																1	Substitution - Missense(1)	ovary(1)	10						A	GLY/GLU	1,4405	2.1+/-5.4	0,1,2202	51	50	50		4118	2.5	0	10		50	0,8600		0,0,4300	no	missense	KAT6B	NM_012330.2	98	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	1373/2074	76788700	1,13005	2203	4300	6503	76458706	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4118A>G	10.37:g.76788700A>G	ENSP00000287239:p.Glu1373Gly		76458706	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.671003	0.00758	2.27E-4	0.0	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.78924	1.12;1.12;-1.22;1.12;-1.21	3.69	2.5	0.30297	.	0.141093	0.31963	N	0.006799	T	0.59142	0.2172	N	0.19112	0.55	0.19300	N	0.999979	B;P;B	0.40731	0.275;0.728;0.18	B;B;B	0.36186	0.088;0.219;0.04	T	0.52366	-0.8585	10	0.48119	T	0.1	-2.877	8.4038	0.32603	0.8007:0.1992:0.0:0.0	.	1190;1081;1373	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	G	1081;1081;1373;1081;1190	ENSP00000361810:E1081G;ENSP00000361809:E1081G;ENSP00000287239:E1373G;ENSP00000361799:E1081G;ENSP00000361796:E1190G	ENSP00000287239:E1373G	E	+	2	0	KAT6B	76458706	0.428000	0.25522	0.007000	0.13788	0.001000	0.01503	0.602000	0.24134	0.415000	0.25817	-0.622000	0.04023	GAA		0.448	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76788700	A	G	76788700	3	3	108	1	0	0	0	0	1	0	0	0	10135	246	9	4	4180	4	MYST4	10	76788700	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	4326555	76788700	58746047	85	28480										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692958	89692958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atcggggcaaatttttaaagGcacaagaggccctagatttc	10	8	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr10:89692958G>T	ENST00000371953.3	+	5	1799	c.442G>T	c.(442-444)Gca>Tca	p.A148S		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	148	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.A148T(2)|p.K147fs*5(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATTTTTAAAGGCACAAGAGGC	0.383		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)|Substitution - Missense(2)	prostate(16)|central_nervous_system(13)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											71	72	72					10																	89692958		2203	4300	6503	89682938	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.442G>T	10.37:g.89692958G>T	ENSP00000361021:p.Ala148Ser		89682938	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.853104	0.91355	.	.	ENSG00000171862	ENST00000371953	D	0.85861	-2.04	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87759	0.6258	M	0.83603	2.65	0.80722	D	1	P	0.43938	0.822	B	0.41946	0.371	D	0.88677	0.3199	9	.	.	.	-10.9741	18.7776	0.91918	0.0:0.0:1.0:0.0	.	148	P60484	PTEN_HUMAN	S	148	ENSP00000361021:A148S	.	A	+	1	0	PTEN	89682938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.546000	0.82137	2.411000	0.81874	0.655000	0.94253	GCA		0.383	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89692958	G	T	89692958	3	4	108	1	0	0	0	0	1	0	0	0	12772	1203	42	2	460	2	PTEN	10	89692958	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	12904258	89692958	45841789	86	28481										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717763	89717763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gttcttccacaaacagaacaAgatgctaaaaaaggtttgta	7	7	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr10:89717763A>G	ENST00000371953.3	+	7	2145	c.788A>G	c.(787-789)aAg>aGg	p.K263R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	263	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AAACAGAACAAGATGCTAAAA	0.368		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											95	87	89					10																	89717763		2203	4300	6503	89707743	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.788A>G	10.37:g.89717763A>G	ENSP00000361021:p.Lys263Arg		89707743	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.615978	0.66672	.	.	ENSG00000171862	ENST00000371953	D	0.85955	-2.05	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093551	0.64402	D	0.000001	D	0.84410	0.5466	L	0.55743	1.74	0.80722	D	1	P	0.47191	0.891	P	0.45753	0.492	D	0.84155	0.0425	9	.	.	.	-10.1303	14.9657	0.71193	1.0:0.0:0.0:0.0	.	263	P60484	PTEN_HUMAN	R	263	ENSP00000361021:K263R	.	K	+	2	0	PTEN	89707743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.918000	0.92759	1.928000	0.55862	0.477000	0.44152	AAG		0.368	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717763	A	G	89717763	3	3	108	1	0	0	0	0	1	0	0	0	12772	72	3	4	814	4	PTEN	10	89717763	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	24805	89717763	45816984	87	28482										
SLC22A18	5002	hgsc.bcm.edu	37	chr11	2946381	2946381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	caatacccttgtcctcctggTcctctggaggaaacctatgc	8	14	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:2946381T>C	ENST00000380574.1	+	11	1660	c.1229T>C	c.(1228-1230)gTc>gCc	p.V410A	SLC22A18_ENST00000347936.2_Missense_Mutation_p.V410A|SLC22A18_ENST00000441077.1_3'UTR|SLC22A18_ENST00000312221.5_Missense_Mutation_p.V410A|SLC22A18_ENST00000449793.2_Missense_Mutation_p.V312A			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	410					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		GTCCTCCTGGTCCTCTGGAGG	0.592																																																0			11											95	82	87					11																	2946381		2202	4299	6501	2902957	SO:0001583	missense	5002			AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"Solute carriers"	10964	protein-coding gene	gene with protein product		602631	"solute carrier family 22 (organic cation transporter), member 1-like"	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.1229T>C	11.37:g.2946381T>C	ENSP00000369948:p.Val410Ala		2902957	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692775	0.30052	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.80994	-1.44;-1.44;0.34;-1.44	4.65	-2.94	0.05581	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.629830	0.03651	N	0.241059	T	0.69672	0.3137	L	0.44542	1.39	0.09310	N	1	B;B	0.23128	0.08;0.002	B;B	0.20384	0.029;0.005	T	0.47787	-0.9090	10	0.20519	T	0.43	-23.0371	4.7809	0.13201	0.2441:0.3891:0.0:0.3667	.	312;410	E9PRM7;Q96BI1	.;S22AI_HUMAN	A	410;410;312;410	ENSP00000307859:V410A;ENSP00000311139:V410A;ENSP00000392072:V312A;ENSP00000369948:V410A	ENSP00000311139:V410A	V	+	2	0	SLC22A18	2902957	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.062000	0.11674	-0.359000	0.08150	-0.379000	0.06801	GTC		0.592	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233		C	2946381	T	C	2946381	3	2	108	1	0	0	0	0	1	0	0	0	14486	1667	58	4	1267	4	SLC22A18	11	2946381	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10		2946381	132060135	88	28483										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681187	55681187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcacatccttgttcctcaggCtataaatcagggggttcaac	8	11	4	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:55681187C>T	ENST00000344514.1	-	1	871	c.872G>A	c.(871-873)aGc>aAc	p.S291N		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTTCCTCAGGCTATAAATCAG	0.343																																					Melanoma(48;171 1190 15239 43886 49348)											0			11											37	41	40					11																	55681187		2201	4296	6497	55437763	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.872G>A	11.37:g.55681187C>T	ENSP00000342448:p.Ser291Asn		55437763		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098728	0.56183	.	.	ENSG00000187612	ENST00000344514	T	0.39056	1.1	5.01	5.01	0.66863	.	0.000000	0.47852	D	0.000219	T	0.78742	0.4331	H	0.99026	4.405	0.35965	D	0.834863	D	0.89917	1.0	D	0.77004	0.989	D	0.90443	0.4433	10	0.87932	D	0	.	15.8124	0.78576	0.0:1.0:0.0:0.0	.	291	Q8NH69	OR5W2_HUMAN	N	291	ENSP00000342448:S291N	ENSP00000342448:S291N	S	-	2	0	OR5W2	55437763	0.020000	0.18652	0.648000	0.29521	0.206000	0.24218	1.509000	0.35780	2.311000	0.77944	0.549000	0.68633	AGC		0.343	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		T	55681187	C	T	55681187	3	4	108	1	0	0	0	0	1	0	0	0	11216	797	28	3	62	3	OR5W2	11	55681187	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	52734806	55681187	79325329	89	28484										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681277	55681277	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gagaataggaagaacttggcCggaaatacataaagagcaga	12	5	0	4	rs202102548		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:55681277C>T	ENST00000344514.1	-	1	781	c.782G>A	c.(781-783)cGg>cAg	p.R261Q		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R261Q(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGAACTTGGCCGGAAATACAT	0.443													C|||	1	0.000199681	0	0	5008	,	,		15067	0		0	False		,,,				2504	0.001				Melanoma(48;171 1190 15239 43886 49348)											1	Substitution - Missense(1)	pancreas(1)	11						C	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	80	92	88		782	5	0	11		88	1,8591	1.2+/-3.3	0,1,4295	yes	missense	OR5W2	NM_001001960.1	43	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	261/311	55681277	2,12992	2201	4296	6497	55437853	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.782G>A	11.37:g.55681277C>T	ENSP00000342448:p.Arg261Gln		55437853		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.026923	0.35797	2.27E-4	1.16E-4	ENSG00000187612	ENST00000344514	T	0.37235	1.21	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36167	N	0.002753	T	0.31857	0.0810	L	0.56199	1.76	0.09310	N	1	P	0.41524	0.753	B	0.42188	0.379	T	0.16748	-1.0392	10	0.10636	T	0.68	.	9.4436	0.38684	0.0:0.9031:0.0:0.0969	.	261	Q8NH69	OR5W2_HUMAN	Q	261	ENSP00000342448:R261Q	ENSP00000342448:R261Q	R	-	2	0	OR5W2	55437853	0.000000	0.05858	0.047000	0.18901	0.876000	0.50452	-0.083000	0.11286	2.311000	0.77944	0.549000	0.68633	CGG		0.443	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		T	55681277	C	T	55681277	3	4	108	1	0	0	0	0	1	0	0	0	11216	652	23	1	152	1	OR5W2	11	55681277	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	90	55681277	79325239	90	28485										
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67260480	67260480	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggggacagccccagcgccgcGtatacagccacatctttggg	13	14	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:67260480G>A	ENST00000534749.1	-	22	3584	c.3396C>T	c.(3394-3396)taC>taT	p.Y1132Y	PITPNM1_ENST00000356404.3_Silent_p.Y1132Y|PITPNM1_ENST00000436757.2_Silent_p.Y1131Y|PITPNM1_ENST00000526450.1_5'Flank			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	1132					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CCAGCGCCGCGTATACAGCCA	0.642																																					GBM(28;144 709 4607 5525)											0			11											97	106	102					11																	67260480		2200	4295	6495	67017056	SO:0001819	synonymous_variant	9600			X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.3396C>T	11.37:g.67260480G>A			67017056	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																				0.642	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67260480	G	A	67260480	2	1	108	1	0	0	0	0	0	0	0	1	11981	1140	40	1		1	PITPNM1	11	67260480	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	11579203	67260480	67746036	91	28486										
GRM5	2915	hgsc.bcm.edu	37	chr11	88338110	88338110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	attttggaatcctgaacatgAtgtgttttcagagtcagaga	10	5	2	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:88338110A>C	ENST00000305447.4	-	4	1319	c.1170T>G	c.(1168-1170)caT>caG	p.H390Q	GRM5_ENST00000418177.2_Missense_Mutation_p.H390Q|GRM5_ENST00000393297.1_Missense_Mutation_p.H390Q|GRM5_ENST00000455756.2_Missense_Mutation_p.H390Q|GRM5_ENST00000305432.5_Missense_Mutation_p.H390Q	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	390					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	CCTGAACATGATGTGTTTTCA	0.453																																																0			11											96	84	88					11																	88338110		2201	4299	6500	87977758	SO:0001583	missense	2915			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1170T>G	11.37:g.88338110A>C	ENSP00000306138:p.His390Gln		87977758	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.617003	0.28801	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	5.59	3.1	0.35709	Extracellular ligand-binding receptor (1);	0.141948	0.64402	D	0.000003	T	0.54175	0.1842	N	0.01009	-1.055	0.32290	N	0.566441	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.50783	-0.8787	9	.	.	.	.	2.856	0.05572	0.481:0.318:0.0874:0.1136	.	390;390	P41594-2;P41594	.;GRM5_HUMAN	Q	390	ENSP00000402912:H390Q;ENSP00000405690:H390Q;ENSP00000305905:H390Q;ENSP00000306138:H390Q;ENSP00000376975:H390Q	.	H	-	3	2	GRM5	87977758	0.626000	0.27120	1.000000	0.80357	0.988000	0.76386	-0.105000	0.10907	1.055000	0.40461	0.445000	0.29226	CAT		0.453	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		C	88338110	A	C	88338110	3	2	108	1	0	0	0	0	1	0	0	0	6821	330	12	4	2492	4	GRM5	11	88338110	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	21077630	88338110	46668406	92	28487										
SESN3	143686	hgsc.bcm.edu	37	chr11	94911901	94911901	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cggaatgttggcaaatgctcTtctcctcgtctggcaaagtc	10	11	3	0	rs548384430		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:94911901T>C	ENST00000536441.1	-	7	1365	c.1029A>G	c.(1027-1029)gaA>gaG	p.E343E	SESN3_ENST00000278499.2_Silent_p.E204E|RP11-712B9.2_ENST00000534864.1_RNA|RP11-712B9.2_ENST00000534891.1_RNA	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	343					glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)				endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		GCAAATGCTCTTCTCCTCGTC	0.348													T|||	1	0.000199681	0	0	5008	,	,		19041	0		0	False		,,,				2504	0.001															0			11											108	104	105					11																	94911901		2201	4298	6499	94551549	SO:0001819	synonymous_variant	143686			AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212			23060	protein-coding gene	gene with protein product		607768				12607115	Standard	NM_144665		Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.1029A>G	11.37:g.94911901T>C			94551549	B7Z7P9|Q96AD1	Silent	SNP	ENST00000536441.1	37	CCDS8303.1																																																																																				0.348	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396475.3	NM_144665		C	94911901	T	C	94911901	2	2	108	1	0	0	0	0	0	0	0	1	14163	1606	56	4		4	SESN3	11	94911901	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	6573791	94911901	40094615	93	28488										
PGR	5241	hgsc.bcm.edu	37	chr11	100922294	100922294	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtcatcaatatgtaagtttcGaaaacctacaaaacaaattt	4	7	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:100922294G>A	ENST00000325455.5	-	5	3671	c.2218C>T	c.(2218-2220)Cga>Tga	p.R740*	PGR_ENST00000534013.1_Nonsense_Mutation_p.R146*|PGR_ENST00000263463.5_Nonsense_Mutation_p.R638*	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	740	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TGTAAGTTTCGAAAACCTACA	0.323																																					Pancreas(124;2271 2354 21954 22882)											0			11											72	74	73					11																	100922294		2203	4300	6503	100427504	SO:0001587	stop_gained	5241			M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2218C>T	11.37:g.100922294G>A	ENSP00000325120:p.Arg740*		100427504	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Nonsense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	40	8.184911	0.98696	.	.	ENSG00000082175	ENST00000325455;ENST00000534013;ENST00000263463;ENST00000537623	.	.	.	5.24	3.33	0.38152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1701	0.59593	0.0:0.0:0.5806:0.4194	.	.	.	.	X	740;146;638;638	.	ENSP00000263463:R638X	R	-	1	2	PGR	100427504	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	3.982000	0.56909	0.554000	0.29061	0.650000	0.86243	CGA		0.323	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			A	100922294	G	A	100922294	4	1	108	1	0	0	0	0	0	1	0	0	11836	1066	37	1	599	1	PGR	11	100922294	Nonsense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	6010393	100922294	34084222	94	28489										
CASP4	837	hgsc.bcm.edu	37	chr11	104821812	104821812	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtgtgcggttgtttctctccTttattggatagatctgcagg	12	7	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:104821812T>C	ENST00000444739.2	-	4	1296	c.386A>G	c.(385-387)aAg>aGg	p.K129R	CASP4_ENST00000393150.3_Missense_Mutation_p.K73R|CASP4_ENST00000531333.1_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	129					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		GTTTCTCTCCTTTATTGGATA	0.433																																																0			11											170	159	163					11																	104821812		2202	4299	6501	104327022	SO:0001583	missense	837			U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.386A>G	11.37:g.104821812T>C	ENSP00000388566:p.Lys129Arg		104327022	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	T	2.828	-0.243184	0.05906	.	.	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546;ENST00000417440	T;T;T	0.43294	0.95;0.95;0.95	4.1	2.88	0.33553	Peptidase C14, caspase precursor p45, core (1);	0.800156	0.11608	N	0.547138	T	0.36026	0.0952	M	0.65975	2.015	0.30853	N	0.73433	B;B	0.20671	0.047;0.023	B;B	0.22880	0.028;0.042	T	0.35992	-0.9766	10	0.28530	T	0.3	.	2.9652	0.05906	0.2315:0.1213:0.0:0.6472	.	129;129	B4E2D2;P49662	.;CASP4_HUMAN	R	129;73;82;129	ENSP00000388566:K129R;ENSP00000376857:K73R;ENSP00000401673:K129R	ENSP00000347741:K82R	K	-	2	0	CASP4	104327022	0.086000	0.21541	0.941000	0.38009	0.187000	0.23431	-0.027000	0.12371	1.690000	0.51089	0.528000	0.53228	AAG		0.433	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		C	104821812	T	C	104821812	3	2	108	1	0	0	0	0	1	0	0	0	2679	1609	56	4	767	4	CASP4	11	104821812	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	3899518	104821812	30184704	95	28490										
ATM	472	hgsc.bcm.edu	37	chr11	108143300	108143300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atatatattctctgtaagaaTggccctagtaaattgcctta	6	7	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:108143300T>C	ENST00000452508.2	+	22	3308	c.3119T>C	c.(3118-3120)aTg>aCg	p.M1040T	ATM_ENST00000278616.4_Missense_Mutation_p.M1040T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1040			M -> V (in B-cell non-Hodgkin lymphoma; dbSNP:rs3092857). {ECO:0000269|PubMed:9288106}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCTGTAAGAATGGCCCTAGTA	0.299			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											114	118	117					11																	108143300		2201	4298	6499	107648510	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3119T>C	11.37:g.108143300T>C	ENSP00000388058:p.Met1040Thr		107648510	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	5.907	0.351510	0.11182	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.71222	-0.55;-0.55;-0.55	5.43	4.3	0.51218	Armadillo-type fold (1);	0.532223	0.22706	N	0.056633	T	0.62600	0.2441	L	0.56769	1.78	0.22620	N	0.998926	B	0.20887	0.049	B	0.15870	0.014	T	0.50101	-0.8867	10	0.23891	T	0.37	.	8.8454	0.35168	0.0:0.1458:0.0:0.8542	.	1040	Q13315	ATM_HUMAN	T	1040	ENSP00000435747:M1040T;ENSP00000278616:M1040T;ENSP00000388058:M1040T	ENSP00000278616:M1040T	M	+	2	0	ATM	107648510	1.000000	0.71417	0.995000	0.50966	0.516000	0.34256	3.048000	0.49862	0.984000	0.38629	-0.290000	0.09829	ATG		0.299	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108143300	T	C	108143300	3	2	108	1	0	0	0	0	1	0	0	0	1110	1464	51	4	3197	4	ATM	11	108143300	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	3321488	108143300	26863216	96	28491										
VPS26B	112936	hgsc.bcm.edu	37	chr11	134114944	134114944	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctcaacctggtgctgatagaCgaggaggagcggcgctactt	14	10	1	2	rs144967670	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr11:134114944C>T	ENST00000281187.5	+	5	1312	c.834C>T	c.(832-834)gaC>gaT	p.D278D	VPS26B_ENST00000525095.2_Silent_p.D278D	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	278					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		TGCTGATAGACGAGGAGGAGC	0.597											OREG0021548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	39	0.00778754	0.028	0.0029	5008	,	,		20828	0		0	False		,,,				2504	0				Colon(171;1263 1952 15904 45703 47982)											0			11						C		93,4309	76.2+/-114.5	1,91,2109	78	68	71		834	-9.5	0.3	11	dbSNP_134	71	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous	VPS26B	NM_052875.3		1,93,6404	TT,TC,CC		0.0233,2.1127,0.731		278/337	134114944	95,12901	2201	4297	6498	133620154	SO:0001819	synonymous_variant	112936				CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"vacuolar protein sorting 26 homolog B (yeast)"			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.834C>T	11.37:g.134114944C>T		1608	133620154	Q96A55	Silent	SNP	ENST00000281187.5	37	CCDS8495.1																																																																																				0.597	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875		T	134114944	C	T	134114944	2	4	108	1	0	0	0	0	0	0	0	1	17238	535	19	1		1	VPS26B	11	134114944	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	25971644	134114944	891572	97	28492										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22622720	22622720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	attgtaaaagttcttcattaTctgttgaggctagaaaggca	9	5	3	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:22622720T>C	ENST00000333957.4	-	22	2711	c.2456A>G	c.(2455-2457)gAt>gGt	p.D819G	C2CD5_ENST00000545552.1_Missense_Mutation_p.D832G|C2CD5_ENST00000536386.1_Missense_Mutation_p.D821G|C2CD5_ENST00000542676.1_Missense_Mutation_p.D819G|C2CD5_ENST00000544930.1_Missense_Mutation_p.D634G|C2CD5_ENST00000396028.2_Missense_Mutation_p.D810G|C2CD5_ENST00000446597.1_Missense_Mutation_p.D819G	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	819					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										TTCTTCATTATCTGTTGAGGC	0.313																																																0			12											86	88	87					12																	22622720		2203	4300	6503	22513987	SO:0001583	missense	9847			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2456A>G	12.37:g.22622720T>C	ENSP00000334229:p.Asp819Gly		22513987	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	37	CCDS31758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.20|14.20	2.464272|2.464272	0.43736|0.43736	.|.	.|.	ENSG00000111731|ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930|ENST00000539615	T;T;T;T;T;T|.	0.65916|.	-0.13;-0.17;-0.18;-0.17;-0.17;-0.12|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	0.060005|.	0.64402|.	D|.	0.000003|.	T|T	0.56877|0.56877	0.2015|0.2015	L|L	0.38175|0.38175	1.15|1.15	0.45087|0.45087	D|D	0.998101|0.998101	P;B;P;P;B|.	0.52842|.	0.835;0.19;0.956;0.95;0.156|.	P;B;P;P;B|.	0.50708|.	0.466;0.107;0.648;0.555;0.049|.	T|T	0.54043|0.54043	-0.8352|-0.8352	10|5	0.41790|.	T|.	0.15|.	-24.2712|-24.2712	13.8047|13.8047	0.63223|0.63223	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	821;819;634;810;819|.	F5H2A1;B4DRN7;F5H3N1;Q86YS7-2;Q86YS7|.	.;.;.;.;K0528_HUMAN|.	G|V	819;819;821;810;819;832;634|103	ENSP00000334229:D819G;ENSP00000388756:D819G;ENSP00000439392:D821G;ENSP00000379345:D810G;ENSP00000441951:D819G;ENSP00000443204:D832G|.	ENSP00000334229:D819G|.	D|I	-|-	2|1	0|0	KIAA0528|KIAA0528	22513987|22513987	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.449000|5.449000	0.66619|0.66619	2.054000|2.054000	0.61138|0.61138	0.528000|0.528000	0.53228|0.53228	GAT|ATA		0.313	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22622720	T	C	22622720	3	2	108	1	0	0	0	0	1	0	0	0	8203	1435	50	4	562	4	KIAA0528	12	22622720	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10		22622720	111229175	98	28493										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398259	25398259	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgattctgaattagctgtatCgtcaaggcactcttgcctac	8	10	3	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:25398259C>A	ENST00000256078.4	-	2	123	c.60G>T	c.(58-60)acG>acT	p.T20T	KRAS_ENST00000556131.1_Silent_p.T20T|KRAS_ENST00000311936.3_Silent_p.T20T|KRAS_ENST00000557334.1_Silent_p.T20T	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	20					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			TTAGCTGTATCGTCAAGGCAC	0.363		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											89	77	81					12																	25398259		2203	4300	6503	25289526	SO:0001819	synonymous_variant	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.60G>T	12.37:g.25398259C>A			25289526	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.363	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398259	C	A	25398259	2	1	108	1	0	0	0	0	0	0	0	1	8459	871	31	2		2	KRAS	12	25398259	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	2775539	25398259	108453636	99	28494										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000311936.3_Missense_Mutation_p.G12C|KRAS_ENST00000557334.1_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93	83	86					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	12.37:g.25398285C>A	ENSP00000256078:p.Gly12Cys		25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398285	C	A	25398285	3	1	108	1	0	0	0	0	1	0	0	0	8459	594	21	2	672	2	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	26	25398285	108453610	100	28495										
KLHDC5	57542	hgsc.bcm.edu	37	chr12	27933702	27933702	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	acgggctgcccgacctgcagGaggcctgcctgcgcttcatg	14	15	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:27933702G>T	ENST00000381271.2	+	1	750	c.439G>T	c.(439-441)Gag>Tag	p.E147*	RP11-860B13.1_ENST00000545904.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	147					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGACCTGCAGGAGGCCTGCCT	0.652																																																0			12											45	49	48					12																	27933702		2203	4300	6503	27824969	SO:0001587	stop_gained	57542			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"Kelch-like"	29252	protein-coding gene	gene with protein product			"kelch domain containing 5"	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.439G>T	12.37:g.27933702G>T	ENSP00000370671:p.Glu147*		27824969	Q2VPK1|Q8N334	Nonsense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	.	.	.	.	.	.	.	.	.	.	G	39	7.645244	0.98409	.	.	ENSG00000087448	ENST00000381271	.	.	.	4.57	4.57	0.56435	.	0.625996	0.17545	N	0.170378	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	12.0381	0.53438	0.0:0.0:0.8276:0.1724	.	.	.	.	X	147	.	ENSP00000370671:E147X	E	+	1	0	KLHDC5	27824969	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.735000	0.55044	2.515000	0.84797	0.591000	0.81541	GAG		0.652	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		T	27933702	G	T	27933702	4	4	108	1	0	0	0	0	0	1	0	0	8380	1175	41	2	441	2	KLHDC5	12	27933702	Nonsense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2535417	27933702	105918193	101	28496										
PFKM	5213	hgsc.bcm.edu	37	chr12	48535840	48535840	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gctgacacagcactcaatacTatctgcacagtgagagccta	8	12	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:48535840T>C	ENST00000312352.7	+	17	1683	c.1644T>C	c.(1642-1644)acT>acC	p.T548T	PFKM_ENST00000395233.2_Silent_p.T517T|PFKM_ENST00000359794.5_Silent_p.T548T|PFKM_ENST00000340802.6_Silent_p.T619T|PFKM_ENST00000551804.1_Silent_p.T517T|PFKM_ENST00000547587.1_Silent_p.T548T	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	548	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CACTCAATACTATCTGCACAG	0.473																																																0			12											176	149	158					12																	48535840		2203	4300	6503	46822107	SO:0001819	synonymous_variant	5213			M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.1644T>C	12.37:g.48535840T>C			46822107	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	37	CCDS8760.1	.	.	.	.	.	.	.	.	.	.	T	9.661	1.144248	0.21205	.	.	ENSG00000152556	ENST00000553055	.	.	.	4.83	-1.98	0.07480	.	.	.	.	.	T	0.38081	0.1027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28106	-1.0054	4	.	.	.	-21.0569	0.5333	0.00632	0.2493:0.3365:0.1229:0.2912	.	.	.	.	H	29	.	.	Y	+	1	0	PFKM	46822107	0.007000	0.16637	0.967000	0.41034	0.993000	0.82548	-1.053000	0.03500	-0.459000	0.07013	0.533000	0.62120	TAT		0.473	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		C	48535840	T	C	48535840	2	2	108	1	0	0	0	0	0	0	0	1	11796	1509	53	4		4	PFKM	12	48535840	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	20602138	48535840	85316055	102	28497										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81732978	81732978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cggagctgcccaagtcgagcTttttcttttttaccaaacaa	7	11	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:81732978T>C	ENST00000549396.1	-	21	2689	c.2529A>G	c.(2527-2529)aaA>aaG	p.K843K	PPFIA2_ENST00000548586.1_Silent_p.K843K|PPFIA2_ENST00000550359.2_Silent_p.K690K|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000541017.1_Silent_p.K60K|PPFIA2_ENST00000550584.2_Silent_p.K843K|PPFIA2_ENST00000549325.1_Silent_p.K825K|PPFIA2_ENST00000552948.1_Silent_p.K843K|PPFIA2_ENST00000333447.7_Silent_p.K825K|PPFIA2_ENST00000443686.3_Silent_p.K744K|PPFIA2_ENST00000541570.2_Silent_p.K410K|PPFIA2_ENST00000407050.4_Silent_p.K769K	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	843					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						CAAGTCGAGCTTTTTCTTTTT	0.423																																																0			12											201	197	198					12																	81732978		1855	4105	5960	80257109	SO:0001819	synonymous_variant	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2529A>G	12.37:g.81732978T>C			80257109	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	T	7.426	0.637774	0.14386	.	.	ENSG00000139220	ENST00000551147	.	.	.	5.64	0.609	0.17575	.	.	.	.	.	T	0.55784	0.1942	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48068	-0.9067	4	.	.	.	-30.2066	9.063	0.36447	0.0:0.6762:0.0:0.3238	.	.	.	.	G	6	.	.	S	-	1	0	PPFIA2	80257109	1.000000	0.71417	0.999000	0.59377	0.694000	0.40290	1.180000	0.32005	0.106000	0.17784	-0.441000	0.05720	AGC		0.423	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			C	81732978	T	C	81732978	2	2	108	1	0	0	0	0	0	0	0	1	12341	1606	56	4		4	PPFIA2	12	81732978	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	33197138	81732978	52118917	103	28498										
PAH	5053	hgsc.bcm.edu	37	chr12	103232978	103232978	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttattttctggagggcactgCaaaggattccaatttcacct	8	9	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:103232978C>A	ENST00000553106.1	-	13	1806	c.1334G>T	c.(1333-1335)tGc>tTc	p.C445F	PAH_ENST00000307000.2_Missense_Mutation_p.C440F	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	445					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GAGGGCACTGCAAAGGATTCC	0.398																																																0			12											85	84	85					12																	103232978		2203	4300	6503	101757108	SO:0001583	missense	5053			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1334G>T	12.37:g.103232978C>A	ENSP00000448059:p.Cys445Phe		101757108	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041656	0.35989	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99511	-6.05;-6.05	5.31	4.42	0.53409	Aromatic amino acid hydroxylase, C-terminal (3);	0.043685	0.85682	D	0.000000	D	0.98333	0.9447	L	0.49350	1.555	0.80722	D	1	B	0.22541	0.071	B	0.29267	0.1	D	0.98221	1.0478	10	0.54805	T	0.06	-10.2823	13.165	0.59565	0.0:0.9209:0.0:0.0791	.	445	P00439	PH4H_HUMAN	F	445;440	ENSP00000448059:C445F;ENSP00000303500:C440F	ENSP00000303500:C440F	C	-	2	0	PAH	101757108	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.492000	0.66893	1.381000	0.46364	0.585000	0.79938	TGC		0.398	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			A	103232978	C	A	103232978	3	1	108	1	0	0	0	0	1	0	0	0	11425	710	25	2	28	2	PAH	12	103232978	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	21500000	103232978	30618917	104	28499										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108634180	108634180	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccatctgcatcaagacgcacGaaagcggccagaaagagatc	10	12	2	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:108634180G>A	ENST00000332082.4	+	9	2022	c.1204G>A	c.(1204-1206)Gaa>Aaa	p.E402K	WSCD2_ENST00000549903.1_Missense_Mutation_p.E402K|WSCD2_ENST00000261400.3_Missense_Mutation_p.E402K|WSCD2_ENST00000547525.1_Missense_Mutation_p.E402K			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	402						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						CAAGACGCACGAAAGCGGCCA	0.612																																																0			12											130	139	136					12																	108634180		2058	4203	6261	107158310	SO:0001583	missense	9671				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1204G>A	12.37:g.108634180G>A	ENSP00000331933:p.Glu402Lys		107158310	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586001	0.86748	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.33865	1.39;4.64;1.39;4.64	4.9	4.9	0.64082	.	0.118519	0.64402	D	0.000008	T	0.42944	0.1225	M	0.86178	2.8	0.80722	D	1	P;P	0.43352	0.804;0.571	B;B	0.34138	0.176;0.032	T	0.57751	-0.7757	10	0.54805	T	0.06	-32.8549	17.3052	0.87192	0.0:0.0:1.0:0.0	.	402;402	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	K	402	ENSP00000448047:E402K;ENSP00000261400:E402K;ENSP00000331933:E402K;ENSP00000447272:E402K	ENSP00000261400:E402K	E	+	1	0	WSCD2	107158310	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.097000	0.94193	2.551000	0.86045	0.644000	0.83932	GAA		0.612	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		A	108634180	G	A	108634180	3	1	108	1	0	0	0	0	1	0	0	0	17447	1059	37	1	1230	1	WSCD2	12	108634180	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	5401202	108634180	25217715	105	28500										
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108686005	108686006	+	Missense_Mutation	DNP	GC	GC	CA													0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggcggttgcgctgcagtttGcacacgatggtgaggtagca							TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:108686005_108686006GC>CA	ENST00000312143.7	-	3	1097_1098	c.734_735GC>TG	c.(733-735)tGC>tTG	p.C245L	CMKLR1_ENST00000397688.2_Missense_Mutation_p.C243L|CMKLR1_ENST00000550402.1_Missense_Mutation_p.C245L|CMKLR1_ENST00000552995.1_Missense_Mutation_p.C243L|CMKLR1_ENST00000412676.1_Missense_Mutation_p.C245L	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	245					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GCTGCAGTTTGCACACGATGGT	0.554																																																0			12																																								107210135|107210136	SO:0001583	missense	1240			U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"GPCR / Class A : Resolvin receptors"	2121	protein-coding gene	gene with protein product	"resolvin E1 receptor", "chemerin receptor"	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.734_735delinsCA	12.37:g.108686005_108686006delinsCA	ENSP00000311733:p.Cys245Leu		107210135|107210136	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																				0.554	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			CA	108686006	GC	CA	108686005	3	2	108	1	0	0	0	0	1	0	0	0	3585	1311	46	5	390	5	CMKLR1	12	108686005	Missense_Mutation	DNP	GC	TCGA-DY-A1H8-01A-21D-A152-10	51825	108686005	25165890	106	28501										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926884	112926884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agatggtgcggtctcagaggTcagggatggtccagacagaa	16	7	2	4	rs121918458		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:112926884T>C	ENST00000351677.2	+	13	1702	c.1504T>C	c.(1504-1506)Tca>Cca	p.S502P		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	506	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		R -> L (in LEOPARD1). {ECO:0000269|PubMed:15121796}.|R -> W (in LEOPARD1; reduced phosphatase activity). {ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:24891296}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.S502P(6)|p.S502A(1)|p.S502T(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GTCTCAGAGGTCAGGGATGGT	0.468			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	8	Substitution - Missense(8)	haematopoietic_and_lymphoid_tissue(8)	12	GRCh37	CM022450|CM055504	PTPN11	M	rs121918458						179	167	171					12																	112926884		2203	4300	6503	111411267	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1504T>C	12.37:g.112926884T>C	ENSP00000340944:p.Ser502Pro		111411267	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	T	32	5.127809	0.94473	.	.	ENSG00000179295	ENST00000351677	D	0.98978	-5.29	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.97892	0.9307	L	0.41573	1.285	0.80722	D	1	P	0.41214	0.742	P	0.46479	0.518	D	0.98427	1.0580	10	0.45353	T	0.12	.	15.2256	0.73348	0.0:0.0:0.0:1.0	.	502	Q06124-2	.	P	502	ENSP00000340944:S502P	ENSP00000340944:S502P	S	+	1	0	PTPN11	111411267	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.655000	0.83696	2.064000	0.61679	0.528000	0.53228	TCA		0.468	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			C	112926884	T	C	112926884	3	2	108	1	0	0	0	0	1	0	0	0	12815	1667	58	4	1554	4	PTPN11	12	112926884	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	4240879	112926884	20925011	107	28502										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119419797	119419797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	catcattgtcgccagtatcaCggcccgcaagccgctgccaa	9	16	2	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:119419797C>T	ENST00000267260.4	+	1	498	c.110C>T	c.(109-111)aCg>aTg	p.T37M		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	37					cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.T37M(2)|p.T134M(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GCCAGTATCACGGCCCGCAAG	0.592																																																3	Substitution - Missense(3)	endometrium(3)	12											17	21	20					12																	119419797		1951	4131	6082	117904180	SO:0001583	missense	0			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.110C>T	12.37:g.119419797C>T	ENSP00000267260:p.Thr37Met		117904180	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746189	0.69418	.	.	ENSG00000139767	ENST00000267260	T	0.36520	1.25	4.61	4.61	0.57282	.	0.203120	0.39759	N	0.001280	T	0.51924	0.1703	L	0.38175	1.15	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.55939	-0.8061	10	0.87932	D	0	-10.4393	18.0011	0.89198	0.0:1.0:0.0:0.0	.	37	A7MD48	SRRM4_HUMAN	M	37	ENSP00000267260:T37M	ENSP00000267260:T37M	T	+	2	0	SRRM4	117904180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.784000	0.75084	2.534000	0.85438	0.643000	0.83706	ACG		0.592	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		T	119419797	C	T	119419797	3	4	108	1	0	0	0	0	1	0	0	0	15210	536	19	1	112	1	SRRM4	12	119419797	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	6492913	119419797	14432098	108	28503										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120602182	120602182	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttcagctcctccaagagtccGtgcgccagcttaaagccccc	8	17	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:120602182G>A	ENST00000300648.6	-	18	1818	c.1806C>T	c.(1804-1806)caC>caT	p.H602H		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	602					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCAAGAGTCCGTGCGCCAGCT	0.607																																																0			12											89	94	92					12																	120602182		1966	4157	6123	119086565	SO:0001819	synonymous_variant	10985			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1806C>T	12.37:g.120602182G>A			119086565	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																				0.607	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120602182	G	A	120602182	2	1	108	1	0	0	0	0	0	0	0	1	6319	1136	40	1		1	GCN1L1	12	120602182	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1182385	120602182	13249713	109	28504										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121431483	121431483	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aaccctagcaaggaggagcgAgagacgctagtggaggagtg	17	7	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:121431483A>G	ENST00000257555.6	+	3	913	c.687A>G	c.(685-687)cgA>cgG	p.R229R	HNF1A_ENST00000543427.1_Silent_p.R112R|HNF1A_ENST00000400024.2_Silent_p.R229R|HNF1A_ENST00000402929.1_Silent_p.R229R|HNF1A_ENST00000541395.1_Silent_p.R229R|HNF1A_ENST00000544413.1_Silent_p.R229R|HNF1A_ENST00000538626.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	229			R -> Q (in MODY3). {ECO:0000269|PubMed:9032114}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AGGAGGAGCGAGAGACGCTAG	0.602									Hepatic Adenoma, Familial Clustering of																																							0			12											93	90	91					12																	121431483		2203	4300	6503	119915866	SO:0001819	synonymous_variant	6927	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.687A>G	12.37:g.121431483A>G			119915866	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																				0.602	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121431483	A	G	121431483	2	3	108	1	0	0	0	0	0	0	0	1	7272	291	11	4		4	HNF1A	12	121431483	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	829301	121431483	12420412	110	28505										
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691535	122691535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggacctcctggtgggagatgTcatccgccaagccctgccca	12	15	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:122691535T>C	ENST00000324189.4	+	3	1093	c.737T>C	c.(736-738)gTc>gCc	p.V246A	B3GNT4_ENST00000546192.1_Missense_Mutation_p.V221A|B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000535274.1_Missense_Mutation_p.V221A	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	246					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		GTGGGAGATGTCATCCGCCAA	0.562																																																0			12											79	68	72					12																	122691535		2203	4300	6503	121257488	SO:0001583	missense	79369			AB049586	CCDS9227.1	12q24	2013-02-19						"Beta 3-glycosyltransferases"	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.737T>C	12.37:g.122691535T>C	ENSP00000319636:p.Val246Ala		121257488	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	37	CCDS9227.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.758288	0.69763	.	.	ENSG00000176383	ENST00000324189;ENST00000546192;ENST00000535274	T;T;T	0.46063	0.88;0.88;0.88	5.5	5.5	0.81552	.	0.000000	0.50627	D	0.000111	T	0.48447	0.1500	M	0.77313	2.365	0.39255	D	0.9641	B	0.22211	0.066	B	0.24394	0.053	T	0.53450	-0.8437	10	0.66056	D	0.02	.	15.2784	0.73760	0.0:0.0:0.0:1.0	.	246	Q9C0J1	B3GN4_HUMAN	A	246;221;221	ENSP00000319636:V246A;ENSP00000438840:V221A;ENSP00000444534:V221A	ENSP00000319636:V246A	V	+	2	0	B3GNT4	121257488	0.995000	0.38212	0.990000	0.47175	0.949000	0.60115	3.345000	0.52182	2.091000	0.63221	0.533000	0.62120	GTC		0.562	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		C	122691535	T	C	122691535	3	2	108	1	0	0	0	0	1	0	0	0	1260	1667	58	4	743	4	B3GNT4	12	122691535	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	1260052	122691535	11160360	111	28506										
EP400	57634	hgsc.bcm.edu	37	chr12	132445290	132445290	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccgtcccccgcagctcccttCgctccctcagcaagcccgtc	7	23	1	0	rs139666996		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr12:132445290C>T	ENST00000333577.4	+	2	235	c.126C>T	c.(124-126)ttC>ttT	p.F42F	EP400_ENST00000332482.4_Silent_p.F42F|EP400_ENST00000389561.2_Silent_p.F42F|EP400_ENST00000330386.6_Silent_p.F42F|EP400_ENST00000389562.2_Silent_p.F42F			Q96L91	EP400_HUMAN	E1A binding protein p400	42					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.F42F(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		CAGCTCCCTTCGCTCCCTCAG	0.652																																																1	Substitution - coding silent(1)	skin(1)	12											24	27	26					12																	132445290		2196	4273	6469	131011243	SO:0001819	synonymous_variant	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.126C>T	12.37:g.132445290C>T			131011243	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																					0.652	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132445290	C	T	132445290	2	4	108	1	0	0	0	0	0	0	0	1	5162	883	31	1		1	EP400	12	132445290	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	9753755	132445290	1406605	112	28507										
WASF3	10810	hgsc.bcm.edu	37	chr13	27241676	27241677	+	Frame_Shift_Ins	INS	-	-	A													0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cactacaggatatcaacatgINSaaaaaagctttcaaaagttc							TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr13:27241676_27241677insA	ENST00000335327.5	+	5	469_470	c.291_292insA	c.(292-294)aaafs	p.K98fs	WASF3_ENST00000361042.4_Frame_Shift_Ins_p.K98fs|WASF3_ENST00000496788.1_3'UTR	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	98					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		ATATCAACATGAAAAAAGCTTT	0.351																																																0			13																																								26139677	SO:0001589	frameshift_variant	10810			AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.297dupA	13.37:g.27241682_27241682dupA	ENSP00000335055:p.Lys98fs		26139676	O94974|Q86VQ2	Frame_Shift_Ins	INS	ENST00000335327.5	37	CCDS9318.1																																																																																				0.351	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			A	27241677	-	A	27241676	7	5	108	1	0	1	1	0	0	0	0	0	17294	1290	45	0	301	0	WASF3	13	27241676	Frame_Shift_Ins	INS	-	TCGA-DY-A1H8-01A-21D-A152-10		27241676	87928202	113	28508										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46619620	46619620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcttggtattttccactgtgAccttccttctaatttttgac	5	10	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr13:46619620A>G	ENST00000242848.4	-	2	371	c.23T>C	c.(22-24)gTc>gCc	p.V8A	ZC3H13_ENST00000282007.3_Missense_Mutation_p.V8A			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	8							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		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)		TTCCACTGTGACCTTCCTTCT	0.408																																					Esophageal Squamous(187;747 2077 11056 31291 44172)											0			13											197	201	199					13																	46619620		2203	4300	6503	45517621	SO:0001583	missense	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.23T>C	13.37:g.46619620A>G	ENSP00000242848:p.Val8Ala		45517621	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	A	15.08	2.728530	0.48833	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000428921	T;T	0.45668	1.86;0.89	5.5	5.5	0.81552	.	0.000000	0.49916	D	0.000136	T	0.45637	0.1352	N	0.08118	0	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.77557	0.978;0.99	T	0.58148	-0.7687	10	0.87932	D	0	.	15.6151	0.76760	1.0:0.0:0.0:0.0	.	8;8	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	A	8	ENSP00000242848:V8A;ENSP00000282007:V8A	ENSP00000242848:V8A	V	-	2	0	ZC3H13	45517621	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.930000	0.92872	2.096000	0.63516	0.477000	0.44152	GTC		0.408	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		G	46619620	A	G	46619620	3	3	108	1	0	0	0	0	1	0	0	0	17604	275	10	4	4735	4	ZC3H13	13	46619620	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	19377944	46619620	68550258	114	28509										
RB1	5925	hgsc.bcm.edu	37	chr13	48951156	48951156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctgtgggacagggttgtgtcGaaattggatcacaggtaact	14	6	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr13:48951156G>A	ENST00000267163.4	+	13	1456	c.1318G>A	c.(1318-1320)Gaa>Aaa	p.E440K		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	440	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.E440*(3)|p.E440K(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GGGTTGTGTCGAAATTGGATC	0.343		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	27	Whole gene deletion(15)|Unknown(8)|Substitution - Nonsense(3)|Substitution - Missense(1)	bone(11)|breast(5)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	13											108	116	113					13																	48951156		2203	4299	6502	47849157	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1318G>A	13.37:g.48951156G>A	ENSP00000267163:p.Glu440Lys		47849157	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.670860	0.67814	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.88046	-2.33	5.93	5.93	0.95920	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.338832	0.34700	N	0.003741	D	0.86548	0.5959	M	0.68593	2.085	0.49130	D	0.99975	B	0.33612	0.419	B	0.28232	0.087	D	0.84758	0.0760	10	0.45353	T	0.12	.	20.3495	0.98807	0.0:0.0:1.0:0.0	.	440	P06400	RB_HUMAN	K	419;440	ENSP00000267163:E440K	ENSP00000267163:E440K	E	+	1	0	RB1	47849157	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	6.496000	0.73670	2.814000	0.96858	0.591000	0.81541	GAA		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48951156	G	A	48951156	3	1	108	1	0	0	0	0	1	0	0	0	13135	1059	37	1	1368	1	RB1	13	48951156	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2331536	48951156	66218722	115	28510										
RBM26	64062	hgsc.bcm.edu	37	chr13	79896553	79896553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gttactggtttattccatgcCagttttagatcttgcccttt	7	9	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr13:79896553C>T	ENST00000438737.2	-	21	3305	c.2865G>A	c.(2863-2865)ctG>ctA	p.L955L	RBM26_ENST00000438724.1_Silent_p.L931L|RBM26_ENST00000267229.7_Silent_p.L928L			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	955	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		TATTCCATGCCAGTTTTAGAT	0.308																																																0			13											118	115	116					13																	79896553		2203	4300	6503	78794554	SO:0001819	synonymous_variant	64062			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.2865G>A	13.37:g.79896553C>T			78794554	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Silent	SNP	ENST00000438737.2	37																																																																																					0.308	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		T	79896553	C	T	79896553	2	4	108	1	0	0	0	0	0	0	0	1	13163	581	21	3		3	RBM26	13	79896553	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	30945397	79896553	35273325	116	28511										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111102776	111102776	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gggcctccaggaccccccggGctccctggaccacctggacc	12	20	0	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr13:111102776G>C	ENST00000360467.5	+	20	1620	c.1314G>C	c.(1312-1314)ggG>ggC	p.G438G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	438	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GACCCCCCGGGCTCCCTGGAC	0.622																																																0			13											28	33	32					13																	111102776		1847	4085	5932	109900777	SO:0001819	synonymous_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1314G>C	13.37:g.111102776G>C			109900777	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																				0.622	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		C	111102776	G	C	111102776	2	2	108	1	0	0	0	0	0	0	0	1	3696	1190	42	5		5	COL4A2	13	111102776	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	31206223	111102776	4067102	117	28512										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215706	20215706	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttttacattgctattgtcctGggaaacctcttgatagtggt	9	7	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:20215706G>A	ENST00000331723.1	+	1	120	c.120G>A	c.(118-120)ctG>ctA	p.L40L		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L40L(3)		NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTATTGTCCTGGGAAACCTCT	0.398																																																3	Substitution - coding silent(3)	breast(3)	14																																								19285546	SO:0001819	synonymous_variant	441669			AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.120G>A	14.37:g.20215706G>A			19285546	Q6IEX4	Silent	SNP	ENST00000331723.1	37	CCDS32020.1																																																																																				0.398	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			A	20215706	G	A	20215706	2	1	108	1	0	0	0	0	0	0	0	1	11112	1335	47	3		3	OR4Q3	14	20215706	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		20215706	87133834	118	28513										
OR4K13	390433	hgsc.bcm.edu	37	chr14	20502056	20502056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tacctcttgatttcttaatgTataaataataggatttaaga	5	4	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:20502056T>C	ENST00000315693.2	-	1	863	c.862A>G	c.(862-864)Aca>Gca	p.T288A	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTTCTTAATGTATAAATAATA	0.318																																																0			14											18	20	20					14																	20502056		2198	4295	6493	19571896	SO:0001583	missense	390433				CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"GPCR / Class A : Olfactory receptors"	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.862A>G	14.37:g.20502056T>C	ENSP00000319322:p.Thr288Ala		19571896	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	.	.	.	.	.	.	.	.	.	.	.	9.547	1.114901	0.20795	.	.	ENSG00000176253	ENST00000315693	T	0.35605	1.3	3.61	3.61	0.41365	.	0.000000	0.40144	U	0.001163	T	0.46444	0.1393	M	0.91196	3.185	0.22771	N	0.998751	P	0.35192	0.489	B	0.34138	0.176	T	0.53788	-0.8389	10	0.87932	D	0	.	11.3118	0.49368	0.0:0.0:0.0:1.0	.	288	Q8NH42	OR4KD_HUMAN	A	288	ENSP00000319322:T288A	ENSP00000319322:T288A	T	-	1	0	OR4K13	19571896	0.097000	0.21791	0.665000	0.29768	0.022000	0.10575	0.573000	0.23699	1.509000	0.48786	0.421000	0.28195	ACA		0.318	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1			C	20502056	T	C	20502056	3	2	108	1	0	0	0	0	1	0	0	0	11099	1638	57	4	54	4	OR4K13	14	20502056	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	286350	20502056	86847484	119	28514										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23559778	23559778	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cacgttccagacgctgcctaAgtagctcctgctgcttttcc	8	15	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:23559778A>C	ENST00000262710.1	-	3	770	c.443T>G	c.(442-444)cTt>cGt	p.L148R	ACIN1_ENST00000555053.1_Missense_Mutation_p.L148R|ACIN1_ENST00000605057.1_Missense_Mutation_p.L90R|ACIN1_ENST00000457657.1_Missense_Mutation_p.L148R	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	148	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ACGCTGCCTAAGTAGCTCCTG	0.443																																																0			14											91	86	88					14																	23559778		2203	4300	6503	22629618	SO:0001583	missense	22985			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.443T>G	14.37:g.23559778A>C	ENSP00000262710:p.Leu148Arg		22629618	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330203	0.81690	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.52983	0.65;1.54;0.64	5.24	5.24	0.73138	.	0.000000	0.34314	N	0.004078	T	0.62732	0.2452	L	0.54323	1.7	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.60662	-0.7219	10	0.34782	T	0.22	-6.4157	14.1256	0.65217	1.0:0.0:0.0:0.0	.	148;148	G3V3M7;Q9UKV3	.;ACINU_HUMAN	R	148	ENSP00000262710:L148R;ENSP00000405677:L148R;ENSP00000451328:L148R	ENSP00000262710:L148R	L	-	2	0	ACIN1	22629618	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.081000	0.89511	1.999000	0.58509	0.533000	0.62120	CTT		0.443	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23559778	A	C	23559778	3	2	108	1	0	0	0	0	1	0	0	0	142	72	3	4	3797	4	ACIN1	14	23559778	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	3057722	23559778	83789762	120	28515										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24806435	24806435	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgtccaggcttgtggaacctGctcctcttgtgccctgctcc	10	15	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:24806435G>A	ENST00000216274.5	-	8	1350	c.1132C>T	c.(1132-1134)Cag>Tag	p.Q378*	RP11-934B9.3_ENST00000555591.1_Nonsense_Mutation_p.Q52*|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank|ADCY4_ENST00000558563.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	378	Pro-rich.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TGTGGAACCTGCTCCTCTTGT	0.537																																					Pancreas(58;918 1191 4668 13304 15331)											0			14											160	158	159					14																	24806435		2203	4300	6503	23876275	SO:0001587	stop_gained	11035			AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1132C>T	14.37:g.24806435G>A	ENSP00000216274:p.Gln378*		23876275	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Nonsense_Mutation	SNP	ENST00000216274.5	37	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474280	0.43942	.	.	ENSG00000258973;ENSG00000129465	ENST00000555591;ENST00000216274	.	.	.	4.58	1.6	0.23607	.	1.285430	0.05366	N	0.534583	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.668	4.8194	0.13383	0.1046:0.0:0.4861:0.4093	.	.	.	.	X	52;378	.	ENSP00000216274:Q378X	Q	-	1	0	RIPK3;RP11-934B9.3	23876275	0.001000	0.12720	0.000000	0.03702	0.152000	0.21847	0.911000	0.28584	0.353000	0.24079	0.655000	0.94253	CAG		0.537	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		A	24806435	G	A	24806435	4	1	108	1	0	0	0	0	0	1	0	0	13419	1328	46	3	436	3	RIPK3	14	24806435	Nonsense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1246657	24806435	82543105	121	28516										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917922	26917922	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccactggacctgtcacattgGcataactgatattgagacag	9	10	1	2	rs267603974		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:26917922G>T	ENST00000539517.2	-	5	1084	c.767C>A	c.(766-768)gCc>gAc	p.A256D	NOVA1_ENST00000465357.2_Missense_Mutation_p.A232D|NOVA1_ENST00000267422.7_Missense_Mutation_p.A134D	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	259					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A256D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		TGTCACATTGGCATAACTGAT	0.458																																																1	Substitution - Missense(1)	skin(1)	14											200	179	186					14																	26917922		2203	4300	6503	25987762	SO:0001583	missense	4857			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.767C>A	14.37:g.26917922G>T	ENSP00000438875:p.Ala256Asp		25987762	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	37	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645349	0.67358	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422;ENST00000449198	T;T;T;T	0.35605	1.36;1.3;1.32;1.39	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	L	0.52905	1.665	0.80722	D	1	D;B;P	0.63046	0.992;0.281;0.557	P;B;B	0.55545	0.778;0.027;0.06	T	0.21415	-1.0246	10	0.21540	T	0.41	-0.0673	19.8956	0.96956	0.0:0.0:1.0:0.0	.	259;232;256	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	D	232;256;134;215	ENSP00000447391:A232D;ENSP00000438875:A256D;ENSP00000267422:A134D;ENSP00000408914:A215D	ENSP00000267422:A134D	A	-	2	0	NOVA1	25987762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.833000	0.86765	2.708000	0.92522	0.563000	0.77884	GCC		0.458	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		T	26917922	G	T	26917922	3	4	108	1	0	0	0	0	1	0	0	0	10585	1203	42	2	760	2	NOVA1	14	26917922	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2111487	26917922	80431618	122	28517										
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35295263	35295263	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtttctgaatcatcactatcActgatgataatagtttctcc	5	9	5	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:35295263A>G	ENST00000382422.2	-	3	819	c.492T>C	c.(490-492)agT>agC	p.S164S	BAZ1A_ENST00000553853.1_5'Flank|BAZ1A_ENST00000358716.4_Silent_p.S164S|BAZ1A_ENST00000360310.1_Silent_p.S164S			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	164					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		CATCACTATCACTGATGATAA	0.343																																																0			14											88	72	77					14																	35295263		2203	4300	6503	34365014	SO:0001819	synonymous_variant	11177			AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.492T>C	14.37:g.35295263A>G			34365014	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																				0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35295263	A	G	35295263	2	3	108	1	0	0	0	0	0	0	0	1	1330	156	6	4		4	BAZ1A	14	35295263	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	8377341	35295263	72054277	123	28518										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64457275	64457275	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gcaaagattcaagaagctaaAgagaaagtccaggtctctct	9	8	3	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:64457275A>G	ENST00000344113.4	+	20	2672	c.2460A>G	c.(2458-2460)aaA>aaG	p.K820K	SYNE2_ENST00000358025.3_Silent_p.K820K|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.K820K	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	820					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.K820K(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAGAAGCTAAAGAGAAAGTCC	0.413																																																1	Substitution - coding silent(1)	ovary(1)	14											90	87	88					14																	64457275		1830	4085	5915	63527028	SO:0001819	synonymous_variant	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2460A>G	14.37:g.64457275A>G			63527028	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																				0.413	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64457275	A	G	64457275	2	3	108	1	0	0	0	0	0	0	0	1	15485	69	3	4		4	SYNE2	14	64457275	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	29162012	64457275	42892265	124	28519										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92047342	92047342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tcctccacggatggatgcctTgcagttgaaacataaatgct	9	10	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:92047342T>C	ENST00000256343.3	-	27	3398	c.3242A>G	c.(3241-3243)cAa>cGa	p.Q1081R		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	1081					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				ATGGATGCCTTGCAGTTGAAA	0.438																																																0			14											120	109	113					14																	92047342		2203	4300	6503	91117095	SO:0001583	missense	79820			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.3242A>G	14.37:g.92047342T>C	ENSP00000256343:p.Gln1081Arg		91117095	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	0.325	-0.959480	0.02267	.	.	ENSG00000133962	ENST00000256343	T	0.40476	1.03	5.63	-7.98	0.01135	.	0.893008	0.09568	N	0.784563	T	0.10380	0.0254	N	0.00621	-1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43734	-0.9373	10	0.13108	T	0.6	-0.4751	10.5076	0.44842	0.0949:0.2424:0.0:0.6626	.	1081	Q9H7T0	CTSRB_HUMAN	R	1081	ENSP00000256343:Q1081R	ENSP00000256343:Q1081R	Q	-	2	0	CATSPERB	91117095	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-1.651000	0.01989	-1.237000	0.02539	-1.239000	0.01543	CAA		0.438	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		C	92047342	T	C	92047342	3	2	108	1	0	0	0	0	1	0	0	0	2697	1812	63	4	112	4	CATSPERB	14	92047342	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	27590067	92047342	15302198	125	28520										
SERPINA3	12	hgsc.bcm.edu	37	chr14	95090100	95090100	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atgatcattgtccctacagaCacccagaacatcttcttcat	4	13	4	3	rs376051867		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr14:95090100C>T	ENST00000467132.1	+	5	2369	c.1221C>T	c.(1219-1221)gaC>gaT	p.D407D	RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393078.3_Silent_p.D407D|SERPINA3_ENST00000393080.4_Silent_p.D407D|SERPINA3_ENST00000482740.1_Silent_p.D189D			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	407			D -> G (in dbSNP:rs10956).		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		TCCCTACAGACACCCAGAACA	0.493																																																0			14											195	170	178					14																	95090100		2203	4300	6503	94159853	SO:0001819	synonymous_variant	12			K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.1221C>T	14.37:g.95090100C>T			94159853	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Silent	SNP	ENST00000467132.1	37	CCDS32150.1																																																																																				0.493	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		T	95090100	C	T	95090100	2	4	108	1	0	0	0	0	0	0	0	1	14127	477	17	3		3	SERPINA3	14	95090100	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	3042758	95090100	12259440	126	28521										
AQR	9716	hgsc.bcm.edu	37	chr15	35166925	35166925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggtcaacagtcggaactccAacgcgaacaaagcgagtgaa	11	10	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:35166925A>G	ENST00000156471.5	-	29	3603	c.3378T>C	c.(3376-3378)gtT>gtC	p.V1126V		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1126					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCGGAACTCCAACGCGAACAA	0.433																																																0			15											134	125	128					15																	35166925		1906	4124	6030	32954217	SO:0001819	synonymous_variant	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3378T>C	15.37:g.35166925A>G			32954217	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	37	CCDS42013.1																																																																																				0.433	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35166925	A	G	35166925	2	3	108	1	0	0	0	0	0	0	0	1	835	117	5	4		4	AQR	15	35166925	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10		35166925	67364467	127	28522										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43689445	43689445	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctttcaacagtcagcacacaAggtattgctagatgatgaca	8	9	2	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:43689445A>G	ENST00000260383.7	+	12	1459	c.1205A>G	c.(1204-1206)aAg>aGg	p.K402R	TUBGCP4_ENST00000399460.3_Missense_Mutation_p.K266R|TUBGCP4_ENST00000564079.1_Missense_Mutation_p.K402R			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	402					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		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)		TCAGCACACAAGGTATTGCTA	0.493																																																0			15											178	180	179					15																	43689445		2135	4245	6380	41476737	SO:0001583	missense	27229			AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.1205A>G	15.37:g.43689445A>G	ENSP00000260383:p.Lys402Arg		41476737	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	37		.	.	.	.	.	.	.	.	.	.	A	18.82	3.705428	0.68615	.	.	ENSG00000137822	ENST00000260383;ENST00000399460	T;T	0.07567	3.18;3.18	5.64	5.64	0.86602	.	0.041966	0.85682	D	0.000000	T	0.14787	0.0357	M	0.71871	2.18	0.46927	D	0.999259	B;B	0.27229	0.045;0.172	B;B	0.33521	0.12;0.165	T	0.03315	-1.1049	10	0.26408	T	0.33	-20.5908	15.3298	0.74200	1.0:0.0:0.0:0.0	.	402;402	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	R	402;266	ENSP00000260383:K402R;ENSP00000382387:K266R	ENSP00000260383:K402R	K	+	2	0	TUBGCP4	41476737	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.285000	0.78660	2.272000	0.75746	0.460000	0.39030	AAG		0.493	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		G	43689445	A	G	43689445	3	3	108	1	0	0	0	0	1	0	0	0	16808	72	3	4	1251	4	TUBGCP4	15	43689445	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	8522520	43689445	58841947	128	28523										
SPG11	80208	hgsc.bcm.edu	37	chr15	44921511	44921511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gcaattgttctgaaaagtgtTtgctttggggttcagaataa	11	4	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:44921511T>C	ENST00000261866.7	-	9	1827	c.1811A>G	c.(1810-1812)aAa>aGa	p.K604R	SPG11_ENST00000427534.2_Missense_Mutation_p.K604R|SPG11_ENST00000535302.2_Missense_Mutation_p.K604R|SPG11_ENST00000558319.1_Missense_Mutation_p.K604R|SPG11_ENST00000559193.1_Missense_Mutation_p.K604R	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	604					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		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)		TGAAAAGTGTTTGCTTTGGGG	0.368																																																0			15											145	131	135					15																	44921511		2198	4298	6496	42708803	SO:0001583	missense	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1811A>G	15.37:g.44921511T>C	ENSP00000261866:p.Lys604Arg		42708803	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.182532	0.38511	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.80123	-1.34;-1.08;-1.08	5.7	4.56	0.56223	.	0.127798	0.52532	D	0.000075	T	0.71013	0.3290	L	0.43152	1.355	0.44555	D	0.997511	B;B;B;B	0.27997	0.027;0.027;0.197;0.027	B;B;B;B	0.25140	0.019;0.019;0.058;0.018	T	0.66952	-0.5793	10	0.26408	T	0.33	.	10.2845	0.43558	0.0:0.0769:0.0:0.9231	.	604;604;604;604	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	R	604	ENSP00000261866:K604R;ENSP00000445278:K604R;ENSP00000396110:K604R	ENSP00000261866:K604R	K	-	2	0	SPG11	42708803	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.613000	0.54152	2.178000	0.69098	0.533000	0.62120	AAA		0.368	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			C	44921511	T	C	44921511	3	2	108	1	0	0	0	0	1	0	0	0	15080	1841	64	4	5648	4	SPG11	15	44921511	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	1232066	44921511	57609881	129	28524										
MYEF2	50804	hgsc.bcm.edu	37	chr15	48458145	48458145	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cttacctctttaatattaagGggtcttccactaagatcata	5	9	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:48458145G>T	ENST00000324324.7	-	5	789	c.510C>A	c.(508-510)ccC>ccA	p.P170P	MYEF2_ENST00000267836.6_Silent_p.P170P	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	170	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TAATATTAAGGGGTCTTCCAC	0.274																																																0			15											54	67	63					15																	48458145		2181	4241	6422	46245437	SO:0001819	synonymous_variant	50804			AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"RNA binding motif (RRM) containing"	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.510C>A	15.37:g.48458145G>T			46245437	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Silent	SNP	ENST00000324324.7	37	CCDS32230.1																																																																																				0.274	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132		T	48458145	G	T	48458145	2	4	108	1	0	0	0	0	0	0	0	1	10054	1219	43	2		2	MYEF2	15	48458145	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	3536634	48458145	54073247	130	28525										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52517286	52517286	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gattacctgcttcttacatcTtcaatgtcatagctttcgag	6	10	4	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:52517286T>C	ENST00000261839.7	-	27	3512	c.3351A>G	c.(3349-3351)gaA>gaG	p.E1117E		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1117						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E1117D(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TTCTTACATCTTCAATGTCAT	0.318																																																1	Substitution - Missense(1)	ovary(1)	15											139	122	127					15																	52517286		1849	4094	5943	50304578	SO:0001819	synonymous_variant	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.3351A>G	15.37:g.52517286T>C			50304578	Q6P1W8	Silent	SNP	ENST00000261839.7	37	CCDS42036.1																																																																																				0.318	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		C	52517286	T	C	52517286	2	2	108	1	0	0	0	0	0	0	0	1	10110	1606	56	4		4	MYO5C	15	52517286	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	4059141	52517286	50014106	131	28526										
CHRNA5	1138	hgsc.bcm.edu	37	chr15	78880659	78880659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atttctttgttttaaaggaaTggatagatgtaaaattaaga	8	1	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:78880659T>C	ENST00000299565.5	+	4	507	c.307T>C	c.(307-309)Tgg>Cgg	p.W103R	CHRNA5_ENST00000559554.1_Missense_Mutation_p.W103R|RP11-650L12.2_ENST00000567141.1_RNA	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	103					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	TTTAAAGGAATGGATAGATGT	0.333																																																0			15											83	85	84					15																	78880659		2196	4293	6489	76667714	SO:0001583	missense	1138				CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1959	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 5 (neuronal)"	118505	"cholinergic receptor, nicotinic, alpha polypeptide 5"			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.307T>C	15.37:g.78880659T>C	ENSP00000299565:p.Trp103Arg		76667714	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.264798	0.80358	.	.	ENSG00000169684	ENST00000299565;ENST00000394802	D	0.98684	-5.07	5.08	5.08	0.68730	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.99585	0.9850	H	0.99609	4.655	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97415	1.0005	10	0.72032	D	0.01	.	15.2098	0.73214	0.0:0.0:0.0:1.0	.	103	P30532	ACHA5_HUMAN	R	103;54	ENSP00000299565:W103R	ENSP00000299565:W103R	W	+	1	0	CHRNA5	76667714	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.977000	0.88081	2.041000	0.60428	0.454000	0.30748	TGG		0.333	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1			C	78880659	T	C	78880659	3	2	108	1	0	0	0	0	1	0	0	0	3392	1464	51	4	321	4	CHRNA5	15	78880659	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	26363373	78880659	23650733	132	28527										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90168898	90168898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	caaggaagaagctgaccgtgGagccaaaaggatctgtgacc	13	9	1	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:90168898G>A	ENST00000268138.7	+	20	5462	c.5357G>A	c.(5356-5358)gGa>gAa	p.G1786E	TICRR_ENST00000560985.1_Missense_Mutation_p.G1785E|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1786					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										GCTGACCGTGGAGCCAAAAGG	0.532																																																0			15											44	46	45					15																	90168898		2200	4299	6499	87969902	SO:0001583	missense	90381			AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.5357G>A	15.37:g.90168898G>A	ENSP00000268138:p.Gly1786Glu		87969902	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	G	0.534	-0.856391	0.02630	.	.	ENSG00000140534	ENST00000268138	T	0.06608	3.28	5.2	-5.01	0.02991	.	0.891295	0.10013	N	0.726934	T	0.03178	0.0093	N	0.14661	0.345	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.48258	-0.9051	10	0.13853	T	0.58	1.7211	10.071	0.42332	0.5468:0.091:0.3622:0.0	.	1786	Q7Z2Z1	TICRR_HUMAN	E	1786	ENSP00000268138:G1786E	ENSP00000268138:G1786E	G	+	2	0	C15orf42	87969902	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.505000	0.06367	-0.948000	0.03668	-0.136000	0.14681	GGA		0.532	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90168898	G	A	90168898	3	1	108	1	0	0	0	0	1	0	0	0	1800	1174	41	3	5435	3	C15orf42	15	90168898	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	11288239	90168898	12362494	133	28528										
KIF7	374654	hgsc.bcm.edu	37	chr15	90188650	90188650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gcagactccctgggcgtgccCccgccctctgactgcagttg	12	17	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr15:90188650C>T	ENST00000394412.3	-	9	2031	c.1955G>A	c.(1954-1956)gGg>gAg	p.G652E		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	652	Sufficient for interaction with NPHP1.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			TGGGCGTGCCCCCGCCCTCTG	0.637																																																0			15											72	61	65					15																	90188650		2200	4299	6499	87989654	SO:0001583	missense	374654			AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.1955G>A	15.37:g.90188650C>T	ENSP00000377934:p.Gly652Glu		87989654	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	c	8.540	0.873020	0.17322	.	.	ENSG00000166813	ENST00000394412	T	0.69435	-0.4	4.38	-0.114	0.13564	.	0.654979	0.15689	N	0.249518	T	0.37919	0.1021	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.21999	-1.0229	10	0.02654	T	1	.	1.7511	0.02972	0.1412:0.451:0.1392:0.2686	.	139;652	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	E	652	ENSP00000377934:G652E	ENSP00000377934:G652E	G	-	2	0	KIF7	87989654	0.000000	0.05858	0.002000	0.10522	0.065000	0.16274	0.092000	0.15066	0.081000	0.16988	0.454000	0.30748	GGG		0.637	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		T	90188650	C	T	90188650	3	4	108	1	0	0	0	0	1	0	0	0	8330	623	22	3	2120	3	KIF7	15	90188650	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	19752	90188650	12342742	134	28529										
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5061267	5061267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtgaggtgctcgcctctgagGacttcaggtaggagggctcc	16	10	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr16:5061267G>T	ENST00000251170.7	+	15	2152	c.1972G>T	c.(1972-1974)Gac>Tac	p.D658Y	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	658						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						CGCCTCTGAGGACTTCAGGTA	0.642																																																0			16											24	26	25					16																	5061267		1926	4128	6054	5001268	SO:0001583	missense	9717			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1972G>T	16.37:g.5061267G>T	ENSP00000251170:p.Asp658Tyr		5001268		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032987	0.75504	.	.	ENSG00000103184	ENST00000251170	T	0.43294	0.95	4.45	4.45	0.53987	GOLD (1);	0.000000	0.85682	D	0.000000	T	0.66858	0.2832	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.73075	-0.4097	10	0.87932	D	0	-5.8533	17.6471	0.88151	0.0:0.0:1.0:0.0	.	658	O43304	S14L5_HUMAN	Y	658	ENSP00000251170:D658Y	ENSP00000251170:D658Y	D	+	1	0	SEC14L5	5001268	1.000000	0.71417	0.994000	0.49952	0.705000	0.40729	7.295000	0.78780	2.490000	0.84030	0.561000	0.74099	GAC		0.642	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5061267	G	T	5061267	3	4	108	1	0	0	0	0	1	0	0	0	14022	1174	41	2	2026	2	SEC14L5	16	5061267	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		5061267	85293486	135	28530										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67991647	67991647	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgggtggcgctcactgacctGgaaccacaccgttggtggcg	15	12	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr16:67991647G>T	ENST00000316341.3	-	5	682	c.542C>A	c.(541-543)cCa>cAa	p.P181Q	SLC12A4_ENST00000537830.2_Missense_Mutation_p.P175Q|SLC12A4_ENST00000572037.1_Missense_Mutation_p.P133Q|SLC12A4_ENST00000572010.1_5'UTR|SLC12A4_ENST00000541864.2_Missense_Mutation_p.P150Q|SLC12A4_ENST00000422611.2_Missense_Mutation_p.P183Q|SLC12A4_ENST00000338335.3_Missense_Mutation_p.P181Q|SLC12A4_ENST00000576616.1_Missense_Mutation_p.P181Q	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	181					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCACTGACCTGGAACCACACC	0.627																																																0			16											104	90	94					16																	67991647		2198	4300	6498	66549148	SO:0001583	missense	6560				CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.542C>A	16.37:g.67991647G>T	ENSP00000318557:p.Pro181Gln		66549148	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429975	0.62844	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	4.97	4.0	0.46444	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98520	0.9506	M	0.64080	1.96	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.987;0.993;0.999;1.0;0.984;0.979;0.996	D;D;D;D;P;P;D	0.91635	0.941;0.963;0.997;0.999;0.839;0.907;0.987	D	0.99372	1.0920	10	0.66056	D	0.02	.	14.9214	0.70841	0.0:0.0:0.8556:0.1444	.	183;181;150;133;175;181;181	F5H3C0;B4DF30;F5H066;B4DF69;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;.;S12A4_HUMAN	Q	183;150;175;181;181	ENSP00000395983:P183Q;ENSP00000438334:P150Q;ENSP00000445962:P175Q;ENSP00000343374:P181Q;ENSP00000318557:P181Q	ENSP00000318557:P181Q	P	-	2	0	SLC12A4	66549148	1.000000	0.71417	1.000000	0.80357	0.184000	0.23303	9.813000	0.99286	1.198000	0.43158	0.591000	0.81541	CCA		0.627	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		T	67991647	G	T	67991647	3	4	108	1	0	0	0	0	1	0	0	0	14422	1348	47	2	2795	2	SLC12A4	16	67991647	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	62930380	67991647	22363106	136	28531										
KARS	3735	hgsc.bcm.edu	37	chr16	75662509	75662509	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agaaacatggcgactcgatcAatgcccatgccccagccagc	9	15	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr16:75662509A>G	ENST00000302445.3	-	13	1692	c.1653T>C	c.(1651-1653)atT>atC	p.I551I	KARS_ENST00000568378.1_Intron|KARS_ENST00000319410.5_Silent_p.I579I	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	551					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	CGACTCGATCAATGCCCATGC	0.542																																																0			16											94	91	92					16																	75662509		2198	4300	6498	74220010	SO:0001819	synonymous_variant	3735			AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"Aminoacyl tRNA synthetases / Class II"	6215	protein-coding gene	gene with protein product	"lysine tRNA ligase"	601421	"deafness, autosomal recessive 89"	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.1653T>C	16.37:g.75662509A>G			74220010	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	37	CCDS10923.1																																																																																				0.542	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		G	75662509	A	G	75662509	2	3	108	1	0	0	0	0	0	0	0	1	8001	126	5	4		4	KARS	16	75662509	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	7670862	75662509	14692244	137	28532										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81922793	81922793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	taaggagcattgggctcaggAtctgaacaaagtccgtgagc	13	8	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr16:81922793A>G	ENST00000359376.3	+	10	996	c.782A>G	c.(781-783)gAt>gGt	p.D261G		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	261					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TGGGCTCAGGATCTGAACAAA	0.463																																																0			16											148	137	140					16																	81922793		1975	4154	6129	80480294	SO:0001583	missense	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.782A>G	16.37:g.81922793A>G	ENSP00000352336:p.Asp261Gly		80480294	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281878	0.80692	.	.	ENSG00000197943	ENST00000359376	T	0.18338	2.22	4.74	4.74	0.60224	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.095649	0.64402	D	0.000001	T	0.34454	0.0898	L	0.61218	1.895	0.80722	D	1	P;D	0.63046	0.562;0.992	B;P	0.59056	0.366;0.851	T	0.11494	-1.0585	10	0.72032	D	0.01	.	14.1961	0.65672	1.0:0.0:0.0:0.0	.	128;261	B4E3H3;P16885	.;PLCG2_HUMAN	G	261	ENSP00000352336:D261G	ENSP00000352336:D261G	D	+	2	0	PLCG2	80480294	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	8.474000	0.90413	1.900000	0.55004	0.460000	0.39030	GAT		0.463	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81922793	A	G	81922793	3	3	108	1	0	0	0	0	1	0	0	0	12067	333	12	4	816	4	PLCG2	16	81922793	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	6260284	81922793	8431960	138	28533										
OR1E2	8388	hgsc.bcm.edu	37	chr17	3337127	3337131	+	Frame_Shift_Del	DEL	TCCCA	TCCCA	-													0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gagatgctggtttgattttgTcccatcatgctctgtctcca							TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	TCCCA	TCCCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:3337127_3337131delTCCCA	ENST00000248384.1	-	1	4_8	c.5_9delTGGGA	c.(4-9)atgggafs	p.MG2fs		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	2					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						TTTGATTTTGTCCCATCATGCTCTG	0.429																																																0			17																																								3283881	SO:0001589	frameshift_variant	8388			U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"GPCR / Class A : Olfactory receptors"	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.5_9delTGGGA	17.37:g.3337127_3337131delTCCCA	ENSP00000248384:p.Met2fs		3283877	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Frame_Shift_Del	DEL	ENST00000248384.1	37	CCDS11026.1																																																																																				0.429	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			-	3337131	TCCCA	-	3337127	7	5	108	1	0	1	0	1	0	0	0	0	10986	1654	58	0	965	0	OR1E2	17	3337127	Frame_Shift_Del	DEL	TCCCA	TCGA-DY-A1H8-01A-21D-A152-10		3337127	77858083	139	28534										
PLD2	5338	hgsc.bcm.edu	37	chr17	4720029	4720029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggactgggtgcagctggacCggcctttcgaaggtgaagcc	16	10	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:4720029C>T	ENST00000263088.6	+	15	1701	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W	PLD2_ENST00000572940.1_Missense_Mutation_p.R524W	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	524	Catalytic.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	GCAGCTGGACCGGCCTTTCGA	0.592																																																0			17											123	118	120					17																	4720029		2203	4300	6503	4666995	SO:0001583	missense	5338			AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1570C>T	17.37:g.4720029C>T	ENSP00000263088:p.Arg524Trp		4666995	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352337	0.41700	.	.	ENSG00000129219	ENST00000263088	T	0.07114	3.22	4.62	2.54	0.30619	.	0.468291	0.22734	N	0.056290	T	0.20251	0.0487	M	0.78049	2.395	0.40608	D	0.981646	D;D;D	0.67145	0.996;0.989;0.991	B;P;P	0.54924	0.409;0.764;0.586	T	0.01966	-1.1238	10	0.72032	D	0.01	-12.1604	10.3667	0.44028	0.5195:0.4805:0.0:0.0	.	381;524;524	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	W	524	ENSP00000263088:R524W	ENSP00000263088:R524W	R	+	1	2	PLD2	4666995	0.998000	0.40836	1.000000	0.80357	0.436000	0.31835	1.004000	0.29822	0.515000	0.28320	-0.310000	0.09108	CGG		0.592	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		T	4720029	C	T	4720029	3	4	108	1	0	0	0	0	1	0	0	0	12077	643	23	1	1624	1	PLD2	17	4720029	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	1382902	4720029	76475181	140	28535										
ALOX12	239	hgsc.bcm.edu	37	chr17	6913446	6913446	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gtcgccgccagccagacatgGtgagaggggactctcgggag	17	11	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:6913446G>A	ENST00000251535.6	+	13	1865		c.e13+1		AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000573939.1_Intron|AC027763.2_ENST00000574377.1_5'UTR|RNASEK_ENST00000548577.1_5'Flank|RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399540.2_Intron|RNASEK_ENST00000402093.1_5'Flank	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase						aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						GCCAGACATGGTGAGAGGGGA	0.547																																																0			17											39	39	39					17																	6913446		2203	4300	6503	6854170	SO:0001630	splice_region_variant	239			M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"Arachidonate lipoxygenases"	429	protein-coding gene	gene with protein product	"platelet 12-LOX"	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1812+1G>A	17.37:g.6913446G>A			6854170	O95569|Q6ISF8|Q9UQM4	Splice_Site	SNP	ENST00000251535.6	37	CCDS11084.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427162	0.62733	.	.	ENSG00000108839	ENST00000251535;ENST00000406228	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.582	0.61909	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ALOX12	6854170	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	7.819000	0.86621	2.587000	0.87381	0.460000	0.39030	.		0.547	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		Intron	A	6913446	G	A	6913446	5	1	108	1	0	0	0	0	0	0	1	0	536	1275	44	3	1863	3	ALOX12	17	6913446	Splice_Site	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	2193417	6913446	74281764	141	28536										
CHD3	1107	hgsc.bcm.edu	37	chr17	7810508	7810508	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cttgagaaggaggaagctgaAaaccaggaggaaaagccaga	14	6	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:7810508A>G	ENST00000330494.7	+	31	4881	c.4731A>G	c.(4729-4731)gaA>gaG	p.E1577E	CHD3_ENST00000380358.4_Silent_p.E1636E|SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Silent_p.E1577E	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1577	Required for interaction with PCNT.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				AGGAAGCTGAAAACCAGGAGG	0.537																																																0			17											103	107	105					17																	7810508		2203	4300	6503	7751233	SO:0001819	synonymous_variant	1107			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.4731A>G	17.37:g.7810508A>G			7751233	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	37	CCDS32554.1																																																																																				0.537	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7810508	A	G	7810508	2	3	108	1	0	0	0	0	0	0	0	1	3332	11	1	4		4	CHD3	17	7810508	Silent	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	897062	7810508	73384702	142	28537										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33482457	33482457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ggaggacaagcgggagcatcGagggaaggaggaggccctgg	21	7	0	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:33482457G>A	ENST00000268876.5	+	7	879	c.782G>A	c.(781-783)cGa>cAa	p.R261Q	UNC45B_ENST00000378449.1_Missense_Mutation_p.R261Q|UNC45B_ENST00000394570.2_Missense_Mutation_p.R261Q|UNC45B_ENST00000433649.1_Missense_Mutation_p.R261Q|UNC45B_ENST00000591048.1_Missense_Mutation_p.R261Q	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	261					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CGGGAGCATCGAGGGAAGGAG	0.527																																																0			17											200	140	161					17																	33482457		2203	4300	6503	30506570	SO:0001583	missense	146862			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.782G>A	17.37:g.33482457G>A	ENSP00000268876:p.Arg261Gln		30506570	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995021	0.54041	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.07021	3.24;3.24;3.24;3.23	5.97	1.76	0.24704	Armadillo-like helical (1);Armadillo-type fold (1);	0.243876	0.41294	N	0.000917	T	0.06962	0.0177	L	0.47190	1.495	0.09310	N	0.999998	P;P;P	0.45902	0.868;0.579;0.796	B;B;B	0.39339	0.297;0.049;0.104	T	0.27773	-1.0064	10	0.52906	T	0.07	0.031	5.2115	0.15318	0.3131:0.1387:0.5483:0.0	.	261;261;261	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	Q	261	ENSP00000378071:R261Q;ENSP00000268876:R261Q;ENSP00000412840:R261Q;ENSP00000367710:R261Q	ENSP00000268876:R261Q	R	+	2	0	UNC45B	30506570	0.040000	0.19996	0.845000	0.33349	0.988000	0.76386	1.007000	0.29860	0.128000	0.18479	0.561000	0.74099	CGA		0.527	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		A	33482457	G	A	33482457	3	1	108	1	0	0	0	0	1	0	0	0	17029	1058	37	1	804	1	UNC45B	17	33482457	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	25671949	33482457	47712753	143	28538										
AOC3	8639	hgsc.bcm.edu	37	chr17	41004241	41004241	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgtggtgctgatcccagacaAtggcacaggtgggtcctggt	15	9	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:41004241A>T	ENST00000308423.2	+	1	1041	c.881A>T	c.(880-882)aAt>aTt	p.N294I	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	294					amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	ATCCCAGACAATGGCACAGGT	0.622																																					NSCLC(3;192 220 10664 11501 16477)											0			17											14	15	15					17																	41004241		2200	4294	6494	38257767	SO:0001583	missense	8639			AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.881A>T	17.37:g.41004241A>T	ENSP00000312326:p.Asn294Ile		38257767	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	.	.	.	.	.	.	.	.	.	.	A	7.628	0.678254	0.14841	.	.	ENSG00000131471	ENST00000308423	T	0.18174	2.23	4.15	4.15	0.48705	Copper amine oxidase, N-terminal (1);	0.271361	0.35970	N	0.002878	T	0.10337	0.0253	N	0.24115	0.695	0.09310	N	1	B	0.23735	0.09	B	0.23150	0.044	T	0.16571	-1.0398	10	0.35671	T	0.21	.	6.6096	0.22743	0.8513:0.0:0.1487:0.0	.	294	Q16853	AOC3_HUMAN	I	294	ENSP00000312326:N294I	ENSP00000312326:N294I	N	+	2	0	AOC3	38257767	0.025000	0.19082	0.999000	0.59377	0.952000	0.60782	2.246000	0.43142	1.890000	0.54733	0.402000	0.26972	AAT		0.622	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		T	41004241	A	T	41004241	3	4	108	1	0	0	0	0	1	0	0	0	728	101	4	5	883	5	AOC3	17	41004241	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	7521784	41004241	40190969	144	28539										
CYTH1	9267	hgsc.bcm.edu	37	chr17	76694351	76694351	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tgactcagaggtgcgcttacCgagtttcaatagccagcctt	10	11	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:76694351C>T	ENST00000446868.3	-	9	881	c.811G>A	c.(811-813)Gga>Aga	p.G271R	RNU6-638P_ENST00000516582.1_RNA|CYTH1_ENST00000585509.1_Splice_Site_p.G212R|CYTH1_ENST00000361101.4_Splice_Site_p.G271R|CYTH1_ENST00000589297.1_Splice_Site_p.G212R|CYTH1_ENST00000589296.1_Intron|CYTH1_ENST00000591455.1_Splice_Site_p.G271S			Q15438	CYH1_HUMAN	cytohesin 1	271	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Phosphatidylinositol 3,4,5-trisphosphate binding. {ECO:0000250}.				establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						GTGCGCTTACCGAGTTTCAAT	0.517																																																0			17											128	120	122					17																	76694351		2203	4300	6503	74205946	SO:0001630	splice_region_variant	9267			M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"Pleckstrin homology (PH) domain containing"	9501	protein-coding gene	gene with protein product		182115	"pleckstrin homology, Sec7 and coiled-coil domains 1"	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.811+1G>A	17.37:g.76694351C>T			74205946	A6NFW7|B7Z1T4|Q9P123|Q9P124	Missense_Mutation	SNP	ENST00000446868.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	23.1|23.1|23.1	4.376277|4.376277|4.376277	0.82682|0.82682|0.82682	.|.|.	.|.|.	ENSG00000108669|ENSG00000108669|ENSG00000108669	ENST00000392453|ENST00000446868;ENST00000361101;ENST00000539525;ENST00000537048|ENST00000262763	.|T;T|.	.|0.76186|.	.|-1.0;-1.0|.	4.65|4.65|4.65	4.65|4.65|4.65	0.58169|0.58169|0.58169	.|.|.	9.163480|.|.	0.04994|.|.	U|.|.	0.467853|.|.	T|T|T	0.64886|0.64886|0.64886	0.2639|0.2639|0.2639	L|L|L	0.55481|0.55481|0.55481	1.735|1.735|1.735	0.48511|0.48511|0.48511	D|D|D	0.999667|0.999667|0.999667	.|.|D	.|.|0.58268	.|.|0.982	.|.|P	.|.|0.52109	.|.|0.69	T|T|T	0.68546|0.68546|0.68546	-0.5380|-0.5380|-0.5380	7|7|8	0.17369|0.51188|0.54805	T|T|T	0.5|0.08|0.06	.|.|.	17.7221|17.7221|17.7221	0.88355|0.88355|0.88355	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|271	.|.|Q15438-2	.|.|.	T|R|S	108|271;271;212;212|271	.|ENSP00000389095:G271R;ENSP00000354398:G271R|.	ENSP00000376247:A108T|ENSP00000354398:G271R|ENSP00000262763:G271S	A|G|G	-|-|-	1|1|1	0|0|0	CYTH1|CYTH1|CYTH1	74205946|74205946|74205946	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.687000|0.687000|0.687000	0.40016|0.40016|0.40016	7.500000|7.500000|7.500000	0.81588|0.81588|0.81588	2.388000|2.388000|2.388000	0.81334|0.81334|0.81334	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GCA|GGA|GGT		0.517	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1	NM_004762	Missense_Mutation	T	76694351	C	T	76694351	5	4	108	1	0	0	0	0	0	0	1	0	4209	666	23	1	405	1	CYTH1	17	76694351	Splice_Site	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	35690110	76694351	4500859	145	28540										
CBX2	84733	hgsc.bcm.edu	37	chr17	77757651	77757651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctaagaggggtccccggggcCgcgagacccacccagtgccg	15	16	0	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr17:77757651C>T	ENST00000310942.4	+	5	513	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	137					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R137C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TCCCCGGGGCCGCGAGACCCA	0.602																																																1	Substitution - Missense(1)	endometrium(1)	17											40	36	38					17																	77757651		2194	4299	6493	75372246	SO:0001583	missense	84733			BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"Pc class homolog (Drosophila)"	602770	"chromobox homolog 2 (Drosophila Pc class)", "cell division cycle associated 6"	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.409C>T	17.37:g.77757651C>T	ENSP00000308750:p.Arg137Cys		75372246	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149625	0.57151	.	.	ENSG00000173894	ENST00000310942	.	.	.	5.47	5.47	0.80525	.	0.651748	0.16150	N	0.227282	T	0.67078	0.2855	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67473	-0.5662	9	0.66056	D	0.02	2.4041	14.1022	0.65065	0.1875:0.8125:0.0:0.0	.	137	Q14781	CBX2_HUMAN	C	137	.	ENSP00000308750:R137C	R	+	1	0	CBX2	75372246	1.000000	0.71417	0.998000	0.56505	0.467000	0.32768	1.729000	0.38115	2.577000	0.86979	0.655000	0.94253	CGC		0.602	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647		T	77757651	C	T	77757651	3	4	108	1	0	0	0	0	1	0	0	0	2724	652	23	1	775	1	CBX2	17	77757651	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	1063300	77757651	3437559	146	28541										
DSG1	1828	hgsc.bcm.edu	37	chr18	28916353	28916353	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctatgcagagtctgcaactcAgtattggtgtcagaaataaa	9	7	3	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr18:28916353A>G	ENST00000257192.4	+	9	1254	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	348	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TCTGCAACTCAGTATTGGTGT	0.308																																																0			18											69	67	68					18																	28916353		2203	4300	6503	27170351	SO:0001583	missense	1828			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.1042A>G	18.37:g.28916353A>G	ENSP00000257192:p.Ser348Gly		27170351	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.974439	0.34848	.	.	ENSG00000134760	ENST00000257192	T	0.53640	0.61	5.9	4.74	0.60224	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.38878	0.1057	L	0.39085	1.19	0.80722	D	1	B	0.19935	0.04	B	0.26864	0.074	T	0.13202	-1.0518	10	0.30078	T	0.28	.	11.7815	0.52018	0.9306:0.0:0.0694:0.0	.	348	Q02413	DSG1_HUMAN	G	348	ENSP00000257192:S348G	ENSP00000257192:S348G	S	+	1	0	DSG1	27170351	1.000000	0.71417	0.785000	0.31869	0.509000	0.34042	4.637000	0.61346	1.043000	0.40175	0.460000	0.39030	AGT		0.308	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		G	28916353	A	G	28916353	3	3	108	1	0	0	0	0	1	0	0	0	4787	188	7	4	1076	4	DSG1	18	28916353	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10		28916353	49160895	147	28542										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48573543	48573543	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	caaaaagagcaattgaaagtTtggtaaagaagctgaaggag	12	3	0	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr18:48573543T>C	ENST00000342988.3	+	2	665	c.127T>C	c.(127-129)Ttg>Ctg	p.L43L	SMAD4_ENST00000398417.2_Silent_p.L43L|SMAD4_ENST00000588745.1_Silent_p.L43L|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_Silent_p.L43L	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	43	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(5)|p.E41fs*8(1)|p.A36_K45delAKRAIESLVK(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AATTGAAAGTTTGGTAAAGAA	0.368																																																43	Whole gene deletion(36)|Unknown(5)|Complex - frameshift(1)|Deletion - In frame(1)	pancreas(26)|large_intestine(4)|stomach(3)|breast(3)|lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|NS(1)	18											126	125	126					18																	48573543		2203	4300	6503	46827541	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.127T>C	18.37:g.48573543T>C			46827541	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48573543	T	C	48573543	2	2	108	1	0	0	0	0	0	0	0	1	14797	1838	64	4		4	SMAD4	18	48573543	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	19657190	48573543	29503705	148	28543										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56202992	56202992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaatttgttcagcctcctgcTtcatactgccttcttggctt	7	12	3	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr18:56202992T>C	ENST00000361673.3	-	5	4640	c.4427A>G	c.(4426-4428)aAg>aGg	p.K1476R	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1476			K -> T (in a melanoma metastatic sample; somatic mutation). {ECO:0000269|PubMed:17344846}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K837T(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						AGCCTCCTGCTTCATACTGCC	0.493																																																1	Substitution - Missense(1)	ovary(1)	18											57	59	58					18																	56202992		2203	4300	6503	54353972	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4427A>G	18.37:g.56202992T>C	ENSP00000354991:p.Lys1476Arg		54353972	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.456971	0.01071	.	.	ENSG00000198796	ENST00000361673	T	0.37411	1.2	3.9	2.0	0.26442	.	156.464000	0.00166	N	0.000000	T	0.19685	0.0473	N	0.13098	0.295	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24225	-1.0166	10	0.02654	T	1	-0.5955	4.7766	0.13182	0.0:0.6527:0.222:0.1254	.	1471;1476	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	R	1476	ENSP00000354991:K1476R	ENSP00000354991:K1476R	K	-	2	0	ALPK2	54353972	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.134000	0.10436	0.534000	0.28695	-0.456000	0.05471	AAG		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56202992	T	C	56202992	3	2	108	1	0	0	0	0	1	0	0	0	545	1609	56	4	2121	4	ALPK2	18	56202992	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	7629449	56202992	21874256	149	28544										
FZR1	51343	hgsc.bcm.edu	37	chr19	3527642	3527642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tctgcagccagaagctgctcCggtccccccggaaacccacc	9	19	1	1	rs200022187		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:3527642C>T	ENST00000395095.3	+	6	484	c.484C>T	c.(484-486)Cgg>Tgg	p.R162W	FZR1_ENST00000313639.8_Intron|FZR1_ENST00000441788.2_Missense_Mutation_p.R162W	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	162					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGCTGCTCCGGTCCCCCCG	0.627													C|||	1	0.000199681	0	0.0014	5008	,	,		16449	0		0	False		,,,				2504	0															0			19											47	42	44					19																	3527642		2198	4296	6494	3478642	SO:0001583	missense	51343			AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.484C>T	19.37:g.3527642C>T	ENSP00000378529:p.Arg162Trp		3478642	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	37	CCDS45916.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	19.80	3.895191	0.72639	.	.	ENSG00000105325	ENST00000441788;ENST00000395095	T;T	0.29142	1.58;1.58	5.14	4.1	0.47936	WD40 repeat-like-containing domain (1);	0.053128	0.64402	D	0.000001	T	0.51312	0.1667	M	0.76838	2.35	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.64595	0.676;0.927	T	0.50964	-0.8765	10	0.37606	T	0.19	-47.6071	11.5059	0.50466	0.3471:0.6529:0.0:0.0	.	162;162	Q9UM11;Q9UM11-2	FZR_HUMAN;.	W	162	ENSP00000410369:R162W;ENSP00000378529:R162W	ENSP00000378529:R162W	R	+	1	2	FZR1	3478642	1.000000	0.71417	0.991000	0.47740	0.949000	0.60115	2.604000	0.46274	1.106000	0.41623	0.655000	0.94253	CGG		0.627	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		T	3527642	C	T	3527642	3	4	108	1	0	0	0	0	1	0	0	0	6157	643	23	1	506	1	FZR1	19	3527642	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		3527642	55601341	150	28545										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5047543	5047543	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	atcctggacatggtggagcgCgagtgcggcaccatcatcga	14	11	1	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:5047543C>T	ENST00000159111.4	+	6	707	c.489C>T	c.(487-489)cgC>cgT	p.R163R	KDM4B_ENST00000592175.1_3'UTR|KDM4B_ENST00000381759.4_Silent_p.R163R|KDM4B_ENST00000536461.1_Silent_p.R163R	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	163	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TGGTGGAGCGCGAGTGCGGCA	0.662																																																0			19											104	83	90					19																	5047543		2203	4300	6503	4998543	SO:0001819	synonymous_variant	23030			AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.489C>T	19.37:g.5047543C>T			4998543	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																				0.662	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		T	5047543	C	T	5047543	2	4	108	1	0	0	0	0	0	0	0	1	8150	755	27	1		1	KDM4B	19	5047543	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	1519901	5047543	54081440	151	28546										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087386	9087386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	catgggtgaacttggacttgAaatatcaaggtctgttgaag	12	5	2	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:9087386A>G	ENST00000397910.4	-	1	4632	c.4429T>C	c.(4429-4431)Tca>Cca	p.S1477P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1477	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTGGACTTGAAATATCAAGG	0.463																																																0			19											146	143	144					19																	9087386		1942	4141	6083	8948386	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4429T>C	19.37:g.9087386A>G	ENSP00000381008:p.Ser1477Pro		8948386	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	4.619	0.114990	0.08831	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.01	1.01	0.19927	.	.	.	.	.	T	0.03739	0.0106	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.43491	-0.9388	8	0.87932	D	0	.	4.2429	0.10658	1.0:0.0:0.0:0.0	.	1477	B5ME49	.	P	1477	ENSP00000381008:S1477P	ENSP00000381008:S1477P	S	-	1	0	MUC16	8948386	0.004000	0.15560	0.050000	0.19076	0.294000	0.27393	0.287000	0.18920	0.708000	0.31955	0.260000	0.18958	TCA		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9087386	A	G	9087386	3	3	108	1	0	0	0	0	1	0	0	0	10003	246	9	4	39430	4	MUC16	19	9087386	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	4039843	9087386	50041597	152	28547										
PSG5	5673	hgsc.bcm.edu	37	chr19	43690506	43690506	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctcctcacctgtgagcaggaGccccttccaggtgatgtgct	11	14	1	2	rs8107936	byFrequency	TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:43690506G>C	ENST00000366175.3	-	1	182	c.52C>G	c.(52-54)Ctc>Gtc	p.L18V	PSG5_ENST00000407568.1_Missense_Mutation_p.L18V|PSG5_ENST00000404580.1_Missense_Mutation_p.L18V|PSG5_ENST00000342951.6_Missense_Mutation_p.L18V|PSG5_ENST00000599812.1_Missense_Mutation_p.L18V|PSG5_ENST00000407356.1_Missense_Mutation_p.L18V|PSG5_ENST00000401992.1_5'UTR			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	18			L -> V (in dbSNP:rs8107936). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907, ECO:0000269|PubMed:2789512}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GTGAGCAGGAGCCCCTTCCAG	0.582													G|||	3659	0.730631	0.7481	0.5749	5008	,	,		18212	0.9762		0.6123	False		,,,				2504	0.6861															0			19						G	VAL/LEU,VAL/LEU	3185,1221		1179,827,197	91	91	91		52,52	0.3	0	19	dbSNP_116	91	5160,3426		1603,1954,736	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	32,32	2782,2781,933	CC,CG,GG		39.9022,27.7122,35.7682	benign,benign	18/336,18/336	43690506	8345,4647	2203	4293	6496	48382346	SO:0001583	missense	5673				CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9522	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta 1 glycoprotein"	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.52C>G	19.37:g.43690506G>C	ENSP00000382334:p.Leu18Val		48382346	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	1393	0.6378205128205128	289	0.5873983739837398	177	0.4889502762430939	518	0.9055944055944056	409	0.5395778364116095	N	3.655	-0.070693	0.07228	0.722878	0.600978	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	T;T;T;T;T	0.01665	5.01;5.01;4.7;5.01;4.99	1.41	0.325	0.15903	.	.	.	.	.	T	0.00012	0.0000	L	0.33753	1.03	0.80722	P	0.0	B;B	0.29671	0.254;0.14	B;B	0.43575	0.424;0.35	T	0.02639	-1.1130	8	0.49607	T	0.09	.	3.7117	0.08423	0.2559:0.0:0.7441:0.0	rs8107936;rs11549987;rs17856401;rs59769041	18;18	E9PC55;Q15238	.;PSG5_HUMAN	V	18	ENSP00000382334:L18V;ENSP00000386008:L18V;ENSP00000386053:L18V;ENSP00000344413:L18V;ENSP00000385250:L18V	ENSP00000344413:L18V	L	-	1	0	PSG5	48382346	0.117000	0.22190	0.003000	0.11579	0.030000	0.12068	0.008000	0.13197	0.166000	0.19597	0.184000	0.17185	CTC		0.582	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781		C	43690506	G	C	43690506	3	2	108	1	0	0	0	0	1	0	0	0	12692	971	34	5	975	5	PSG5	19	43690506	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	34603120	43690506	15438477	153	28548										
LILRB4	11006	hgsc.bcm.edu	37	chr19	55179203	55179203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ctggggaattcctggacacaAaggacagacaggcagaagag	14	8	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:55179203A>G	ENST00000391736.1	+	13	1474	c.1159A>G	c.(1159-1161)Aag>Gag	p.K387E	LILRB4_ENST00000270452.2_Missense_Mutation_p.K387E|LILRB4_ENST00000391733.3_Missense_Mutation_p.K388E|LILRB4_ENST00000430952.2_Missense_Mutation_p.K386E|LILRB4_ENST00000391734.3_Intron	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	387					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.K387*(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CCTGGACACAAAGGACAGACA	0.592																																																1	Substitution - Nonsense(1)	ovary(1)	19											74	71	72					19																	55179203		2198	4298	6496	59871015	SO:0001583	missense	11006			U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1159A>G	19.37:g.55179203A>G	ENSP00000375616:p.Lys387Glu		59871015	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	A	4.483	0.089542	0.08632	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391733;ENST00000434286	T;T;T;T;T	0.00498	7.23;7.23;7.23;7.25;6.97	2.18	-3.18	0.05186	.	.	.	.	.	T	0.00552	0.0018	L	0.58669	1.825	0.09310	N	1	B;B;P;B	0.39022	0.009;0.016;0.655;0.435	B;B;P;B	0.44394	0.001;0.003;0.448;0.101	T	0.32079	-0.9920	9	0.49607	T	0.09	.	4.2792	0.10824	0.3082:0.2213:0.4705:0.0	.	386;388;386;387	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	E	387;387;386;388;386	ENSP00000375616:K387E;ENSP00000270452:K387E;ENSP00000408995:K386E;ENSP00000375613:K388E;ENSP00000401962:K386E	ENSP00000270452:K387E	K	+	1	0	LILRB4	59871015	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.414000	0.07114	-0.801000	0.04427	-0.466000	0.05196	AAG		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			G	55179203	A	G	55179203	3	3	108	1	0	0	0	0	1	0	0	0	8816	15	1	4	1201	4	LILRB4	19	55179203	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	11488697	55179203	3949780	154	28549										
KIR3DP1	3811	hgsc.bcm.edu	37	chr19	55299851	55299851	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cttctccatcggtcgcatgaCgcaagaccttgcagggacct	10	14	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:55299851C>T	ENST00000538269.1	+	2	61				KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GGTCGCATGACGCAAGACCTT	0.532																																																0			19											1	1	1					19																	55299851		423	815	1238	59991663	SO:0001627	intron_variant	768329			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-29138C>T	19.37:g.55299851C>T			59991663	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37																																																																																					0.532	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		T	55299851	C	T	55299851	1	4	108	0	1	0	0	0	0	0	0	0	8344	536	19	1		1	KIR3DP1	19	55299851	Intron	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	120648	55299851	3829132	155	28550										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55450708	55450708	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	acgtccccgatgtcccaggcGtggccgtccctgtcctcccc	10	20	0	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:55450708G>A	ENST00000590030.1	-	3	1519	c.1479C>T	c.(1477-1479)caC>caT	p.H493H	NLRP7_ENST00000448121.2_Silent_p.H493H|NLRP7_ENST00000446217.1_Silent_p.H521H|NLRP7_ENST00000592784.1_Silent_p.H493H|NLRP7_ENST00000588756.1_Silent_p.H493H|NLRP7_ENST00000340844.2_Silent_p.H493H|NLRP7_ENST00000328092.5_Silent_p.H493H			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	493							ATP binding (GO:0005524)	p.H493H(4)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TGTCCCAGGCGTGGCCGTCCC	0.567																																																4	Substitution - coding silent(4)	large_intestine(2)|kidney(2)	19											65	63	64					19																	55450708		2203	4300	6503	60142520	SO:0001819	synonymous_variant	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1479C>T	19.37:g.55450708G>A			60142520	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																				0.567	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55450708	G	A	55450708	2	1	108	1	0	0	0	0	0	0	0	1	10513	1136	40	1		1	NLRP7	19	55450708	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	150857	55450708	3678275	156	28551										
AURKC	6795	hgsc.bcm.edu	37	chr19	57746636	57746636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tagatgtgaggtttccactaTcaatgcctctgggggcccgg	13	10	2	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr19:57746636T>C	ENST00000302804.7	+	7	967	c.781T>C	c.(781-783)Tca>Cca	p.S261P	AURKC_ENST00000598785.1_Missense_Mutation_p.S227P|AURKC_ENST00000415300.2_Missense_Mutation_p.S242P|AURKC_ENST00000448930.1_Missense_Mutation_p.S227P|AURKC_ENST00000599062.1_Missense_Mutation_p.S258P	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.S227A(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		GTTTCCACTATCAATGCCTCT	0.512																																																1	Substitution - Missense(1)	ovary(1)	19											72	76	75					19																	57746636		2203	4300	6503	62438448	SO:0001583	missense	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.781T>C	19.37:g.57746636T>C	ENSP00000302898:p.Ser261Pro		62438448	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Missense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	T	7.163	0.586118	0.13749	.	.	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	T;T;T	0.64618	-0.11;-0.11;-0.11	3.88	1.7	0.24286	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.656563	0.15500	N	0.259090	T	0.64023	0.2561	L	0.54323	1.7	0.09310	N	1	P;P;P	0.48294	0.908;0.863;0.511	P;P;B	0.53062	0.717;0.56;0.35	T	0.53229	-0.8468	10	0.46703	T	0.11	-2.4644	7.6119	0.28135	0.3702:0.0:0.0:0.6298	.	258;261;242	Q5Y191;Q9UQB9;Q9UQB9-3	.;AURKC_HUMAN;.	P	242;227;261	ENSP00000407162:S242P;ENSP00000406798:S227P;ENSP00000302898:S261P	ENSP00000302898:S261P	S	+	1	0	AURKC	62438448	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.055000	0.11807	0.279000	0.22186	-0.336000	0.08194	TCA		0.512	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		C	57746636	T	C	57746636	3	2	108	1	0	0	0	0	1	0	0	0	1225	1435	50	4	812	4	AURKC	19	57746636	Missense_Mutation	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	2295928	57746636	1382347	157	28552										
SMOX	54498	hgsc.bcm.edu	37	chr20	4163144	4163144	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cgctaggtgtgctaaagaggCagtacaccagtttcttccgg	12	10	1	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr20:4163144C>T	ENST00000305958.4	+	5	1243	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	SMOX_ENST00000379460.2_Nonsense_Mutation_p.Q340*|SMOX_ENST00000339123.6_Nonsense_Mutation_p.Q287*|SMOX_ENST00000278795.3_Nonsense_Mutation_p.Q287*|SMOX_ENST00000346595.2_Intron	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	340			Q -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)	p.Q340K(1)		breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GCTAAAGAGGCAGTACACCAG	0.587																																																1	Substitution - Missense(1)	breast(1)	20											94	85	88					20																	4163144		2203	4300	6503	4111144	SO:0001587	stop_gained	54498			AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.1018C>T	20.37:g.4163144C>T	ENSP00000307252:p.Gln340*		4111144	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Nonsense_Mutation	SNP	ENST00000305958.4	37	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	C	37	6.609998	0.97705	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	.	.	.	5.37	4.42	0.53409	.	0.458821	0.27076	N	0.021046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-20.8228	7.2969	0.26397	0.0:0.8184:0.0:0.1816	.	.	.	.	X	287;340;287;340;197	.	ENSP00000278795:Q287X	Q	+	1	0	SMOX	4111144	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.091000	0.30915	2.533000	0.85409	0.558000	0.71614	CAG		0.587	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		T	4163144	C	T	4163144	4	4	108	1	0	0	0	0	0	1	0	0	14840	711	25	3	1032	3	SMOX	20	4163144	Nonsense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10		4163144	58862376	158	28553										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32828529	32828529	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	acaagatgtagatctctgcaAtctgcccacattccgagaaa	7	11	2	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chr22:32828529A>G	ENST00000397452.1	-	11	1090	c.980T>C	c.(979-981)aTt>aCt	p.I327T	BPIFC_ENST00000300399.3_Splice_Site_p.I327T|BPIFC_ENST00000534972.1_Splice_Site_p.I51T|BPIFC_ENST00000432451.2_Intron			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	327						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GATCTCTGCAATCTGCCCACA	0.473																																																0			22											166	156	160					22																	32828529		2203	4300	6503	31158529	SO:0001630	splice_region_variant	254240			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.979-1T>C	22.37:g.32828529A>G			31158529	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	A	16.91	3.253221	0.59212	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972	T;T;T	0.10192	2.9;2.9;2.9	6.07	6.07	0.98685	.	0.145674	0.64402	D	0.000016	T	0.33411	0.0862	M	0.84219	2.685	0.44587	D	0.997556	D	0.56968	0.978	P	0.60473	0.875	T	0.08994	-1.0695	10	0.72032	D	0.01	-9.7689	14.1509	0.65384	1.0:0.0:0.0:0.0	.	327	Q8NFQ6	BPIFC_HUMAN	T	327;327;51	ENSP00000380594:I327T;ENSP00000300399:I327T;ENSP00000439123:I51T	ENSP00000300399:I327T	I	-	2	0	BPIFC	31158529	1.000000	0.71417	0.990000	0.47175	0.268000	0.26511	4.779000	0.62375	2.330000	0.79161	0.528000	0.53228	ATT		0.473	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	Missense_Mutation	G	32828529	A	G	32828529	5	3	108	1	0	0	0	0	0	0	1	0	1495	115	4	4	567	4	BPIL2	22	32828529	Splice_Site	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10		32828529	18476037	159	28554										
STS	412	hgsc.bcm.edu	37	chrX	7175602	7175602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cctttgctaagcttctgaagGatcaaggttattcaacagca	8	9	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:7175602G>A	ENST00000217961.4	+	4	590	c.370G>A	c.(370-372)Gat>Aat	p.D124N		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	124					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)	p.D124Y(1)|p.D124N(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	GCTTCTGAAGGATCAAGGTTA	0.483									Ichthyosis																																							2	Substitution - Missense(2)	lung(1)|central_nervous_system(1)	X											117	100	106					X																	7175602		2203	4299	6502	7185602	SO:0001583	missense	412	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"Arylsulfatase family"	11425	protein-coding gene	gene with protein product	"arylsulfatase C"	300747	"steroid sulfatase (microsomal), arylsulfatase C, isozyme S"	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.370G>A	X.37:g.7175602G>A	ENSP00000217961:p.Asp124Asn		7185602	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	37	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	G	2.343	-0.350641	0.05173	.	.	ENSG00000101846	ENST00000217961	D	0.94138	-3.36	3.76	-1.62	0.08372	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.556550	0.03488	N	0.216128	D	0.86863	0.6035	L	0.28274	0.84	0.27858	N	0.940487	B	0.06786	0.001	B	0.09377	0.004	T	0.72537	-0.4263	10	0.25106	T	0.35	.	5.5406	0.17036	0.4475:0.1506:0.4019:0.0	.	124	P08842	STS_HUMAN	N	124	ENSP00000217961:D124N	ENSP00000217961:D124N	D	+	1	0	STS	7185602	0.058000	0.20735	0.089000	0.20774	0.122000	0.20287	-0.280000	0.08468	-0.897000	0.03910	-0.340000	0.08031	GAT		0.483	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351		A	7175602	G	A	7175602	3	1	108	1	0	0	0	0	1	0	0	0	15371	1174	41	3	384	3	STS	23	7175602	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10		7175602	148094958	160	28555										
RAI2	10742	hgsc.bcm.edu	37	chrX	17819079	17819079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cagggggaggctcggatttcCggtgggctgccactgacagg	18	10	0	1	rs140631545		TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:17819079C>T	ENST00000545871.1	-	3	1512	c.1052G>A	c.(1051-1053)cGg>cAg	p.R351Q	RAI2_ENST00000451717.1_Missense_Mutation_p.R351Q|RAI2_ENST00000415486.3_Missense_Mutation_p.R301Q|RAI2_ENST00000331511.1_Missense_Mutation_p.R351Q|RAI2_ENST00000360011.1_Missense_Mutation_p.R351Q	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	351					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					CTCGGATTTCCGGTGGGCTGC	0.552																																																0			X							GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,3835		0,0,1632,571	62	60	60		902,1052,1052,1052	5.3	1	X	dbSNP_134	60	1,6727		0,1,2427,1872	no	missense,missense,missense,missense	RAI2	NM_001172732.1,NM_001172739.1,NM_001172743.1,NM_021785.4	43,43,43,43	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging	301/481,351/531,351/531,351/531	17819079	1,10562	2203	4300	6503	17729000	SO:0001583	missense	10742			Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1052G>A	X.37:g.17819079C>T	ENSP00000444210:p.Arg351Gln		17729000	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	37	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	c	18.38	3.611504	0.66558	0.0	1.49E-4	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.38077	1.18;1.18;1.18;1.18;1.16	5.29	5.29	0.74685	.	0.074690	0.49305	D	0.000142	T	0.54532	0.1864	L	0.55481	1.735	0.37167	D	0.902861	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.62364	-0.6870	10	0.72032	D	0.01	-24.2176	15.8108	0.78561	0.0:1.0:0.0:0.0	.	301;351	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	Q	351;351;351;351;301	ENSP00000333456:R351Q;ENSP00000353106:R351Q;ENSP00000444210:R351Q;ENSP00000401323:R351Q;ENSP00000392578:R301Q	ENSP00000333456:R351Q	R	-	2	0	RAI2	17729000	0.979000	0.34478	0.999000	0.59377	0.942000	0.58702	2.626000	0.46460	2.457000	0.83068	0.597000	0.82753	CGG		0.552	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785		T	17819079	C	T	17819079	3	4	108	1	0	0	0	0	1	0	0	0	13046	652	23	1	544	1	RAI2	23	17819079	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	10643477	17819079	137451481	161	28556										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411777	23411777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ttgttcctgctcttcttctcGgcattcctggtggcagattc	9	12	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:23411777G>A	ENST00000379361.4	+	3	3002	c.2142G>A	c.(2140-2142)tcG>tcA	p.S714S		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	714					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)	p.S609S(1)		NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						TCTTCTTCTCGGCATTCCTGG	0.483																																																1	Substitution - coding silent(1)	ovary(1)	X											114	102	106					X																	23411777		2203	4300	6503	23321698	SO:0001819	synonymous_variant	139411			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2142G>A	X.37:g.23411777G>A			23321698	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	37	CCDS35215.2																																																																																				0.483	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		A	23411777	G	A	23411777	2	1	108	1	0	0	0	0	0	0	0	1	12766	1103	39	1		1	PTCHD1	23	23411777	Silent	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	5592698	23411777	131858783	162	28557										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820649	35820649	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	aggaatgtgcccgcagatgcTctcgaccagaaagtggcttt	12	10	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:35820649T>C	ENST00000399989.1	+	2	615	c.336T>C	c.(334-336)gcT>gcC	p.A112A	MAGEB16_ENST00000399988.1_Silent_p.A112A|MAGEB16_ENST00000399987.1_Silent_p.A112A|MAGEB16_ENST00000399992.1_Silent_p.A144A|MAGEB16_ENST00000399985.1_Silent_p.A112A	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	112										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CCGCAGATGCTCTCGACCAGA	0.438																																																0			X											56	52	54					X																	35820649		1959	4153	6112	35730570	SO:0001819	synonymous_variant	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.336T>C	X.37:g.35820649T>C			35730570	A8MU30	Silent	SNP	ENST00000399989.1	37	CCDS43927.1																																																																																				0.438	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			C	35820649	T	C	35820649	2	2	108	1	0	0	0	0	0	0	0	1	9204	1538	54	4		4	MAGEB16	23	35820649	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	12408872	35820649	119449911	163	28558										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028324	37028324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	cccggagcctccagagactcGcgtatctcatctccgcccag	9	18	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:37028324G>A	ENST00000358047.3	+	1	1893	c.1841G>A	c.(1840-1842)cGc>cAc	p.R614H		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	614										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						CCAGAGACTCGCGTATCTCAT	0.657																																																0			X											26	30	28					X																	37028324		2197	4290	6487	36938245	SO:0001583	missense	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1841G>A	X.37:g.37028324G>A	ENSP00000367913:p.Arg614His		36938245	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	4.944	0.175459	0.09391	.	.	ENSG00000198173	ENST00000358047	T	0.14022	2.54	1.64	-3.28	0.05033	.	.	.	.	.	T	0.22322	0.0538	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.65323	0.934	T	0.41448	-0.9508	9	0.54805	T	0.06	.	0.3479	0.00344	0.3399:0.1405:0.2703:0.2493	.	614	Q5HY64	FA47C_HUMAN	H	614	ENSP00000367913:R614H	ENSP00000367913:R614H	R	+	2	0	FAM47C	36938245	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.473000	0.06615	-3.995000	0.00083	-4.223000	0.00009	CGC		0.657	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37028324	G	A	37028324	3	1	108	1	0	0	0	0	1	0	0	0	5590	1087	38	1	1843	1	FAM47C	23	37028324	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	1207675	37028324	118242236	164	28559										
KIF4A	24137	hgsc.bcm.edu	37	chrX	69510411	69510411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gccagatgtgcctttccttcGtgcccggagagcctcaggtg	13	13	1	2			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:69510411G>A	ENST00000374403.3	+	2	185	c.103G>A	c.(103-105)Gtg>Atg	p.V35M	PDZD11_ENST00000374454.1_5'Flank|KIF4A_ENST00000485406.1_3'UTR|PDZD11_ENST00000473667.1_5'Flank|KIF4A_ENST00000374388.3_Missense_Mutation_p.V35M|PDZD11_ENST00000239666.4_5'Flank	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	35	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						CCTTTCCTTCGTGCCCGGAGA	0.562																																																0			X											67	52	57					X																	69510411		2203	4300	6503	69427136	SO:0001583	missense	24137			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.103G>A	X.37:g.69510411G>A	ENSP00000363524:p.Val35Met		69427136	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	g	19.87	3.908123	0.72868	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.75367	-0.93;-0.93	6.16	5.3	0.74995	Kinesin, motor domain (4);	0.110082	0.40302	N	0.001130	T	0.78489	0.4291	L	0.45228	1.405	0.58432	D	0.999995	P;D	0.53462	0.954;0.96	P;P	0.58210	0.835;0.795	T	0.79222	-0.1892	10	0.54805	T	0.06	.	13.3963	0.60856	0.0759:0.0:0.9241:0.0	.	35;35	O95239;O95239-2	KIF4A_HUMAN;.	M	35	ENSP00000363509:V35M;ENSP00000363524:V35M	ENSP00000363509:V35M	V	+	1	0	KIF4A	69427136	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.697000	0.54764	1.354000	0.45846	0.597000	0.82753	GTG		0.562	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		A	69510411	G	A	69510411	3	1	108	1	0	0	0	0	1	0	0	0	8324	1145	40	1	105	1	KIF4A	23	69510411	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	32482087	69510411	85760149	165	28560										
OGT	8473	hgsc.bcm.edu	37	chrX	70757809	70757809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agcattatcgacatgcattgCgtctcaaacctgatttcatc	6	11	2	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:70757809C>T	ENST00000373719.3	+	3	566	c.349C>T	c.(349-351)Cgt>Tgt	p.R117C	OGT_ENST00000373701.3_Missense_Mutation_p.R107C|OGT_ENST00000498566.1_3'UTR	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	117					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)	p.R107C(1)|p.R117C(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					ACATGCATTGCGTCTCAAACC	0.493																																																2	Substitution - Missense(2)	ovary(2)	X											162	130	141					X																	70757809		2203	4300	6503	70674534	SO:0001583	missense	8473			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.349C>T	X.37:g.70757809C>T	ENSP00000362824:p.Arg117Cys		70674534	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	37	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	c	18.55	3.647248	0.67358	.	.	ENSG00000147162	ENST00000373719;ENST00000373701;ENST00000444774	T;T;T	0.61040	0.14;0.14;0.14	4.86	4.86	0.63082	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.105470	0.64402	D	0.000011	T	0.79257	0.4415	M	0.91768	3.24	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.73708	0.981;0.937;0.941	D	0.83643	0.0151	10	0.72032	D	0.01	-19.0221	12.3845	0.55325	0.1679:0.8321:0.0:0.0	.	117;107;117	B4DTL6;O15294-3;O15294	.;.;OGT1_HUMAN	C	117;107;100	ENSP00000362824:R117C;ENSP00000362805:R107C;ENSP00000399729:R100C	ENSP00000362805:R107C	R	+	1	0	OGT	70674534	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.807000	0.47955	2.259000	0.74868	0.525000	0.51046	CGT		0.493	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		T	70757809	C	T	70757809	3	4	108	1	0	0	0	0	1	0	0	0	10878	768	27	1	359	1	OGT	23	70757809	Missense_Mutation	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	1247398	70757809	84512751	166	28561										
MAGEE2	139599	hgsc.bcm.edu	37	chrX	75004573	75004573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	actgctggatagacccctccGtctggcttttcattctcatg	8	13	3	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:75004573G>A	ENST00000373359.2	-	1	506	c.314C>T	c.(313-315)aCg>aTg	p.T105M		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	105	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.T105M(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGACCCCTCCGTCTGGCTTTT	0.537																																																1	Substitution - Missense(1)	pancreas(1)	X											34	31	32					X																	75004573		2203	4300	6503	74921298	SO:0001583	missense	139599			AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.314C>T	X.37:g.75004573G>A	ENSP00000362457:p.Thr105Met		74921298	Q5JSI5	Missense_Mutation	SNP	ENST00000373359.2	37	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	T	9.578	1.122695	0.20877	.	.	ENSG00000186675	ENST00000373359	T	0.04603	3.59	3.14	-4.36	0.03645	.	.	.	.	.	T	0.01695	0.0054	N	0.11284	0.12	0.09310	N	1	P	0.38167	0.621	B	0.37833	0.259	T	0.32745	-0.9895	9	0.05351	T	0.99	.	1.0479	0.01573	0.2077:0.1197:0.3:0.3726	.	105	Q8TD90	MAGE2_HUMAN	M	105	ENSP00000362457:T105M	ENSP00000362457:T105M	T	-	2	0	MAGEE2	74921298	0.001000	0.12720	0.000000	0.03702	0.197000	0.23852	-1.042000	0.03539	-2.017000	0.00944	-1.907000	0.00523	ACG		0.537	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703		A	75004573	G	A	75004573	3	1	108	1	0	0	0	0	1	0	0	0	9216	1145	40	1	1261	1	MAGEE2	23	75004573	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	4246764	75004573	80265987	167	28562										
POU3F4	5456	hgsc.bcm.edu	37	chrX	82763668	82763668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	ccgcacactaaccaccccaaCgcctggggggccagcccggc	11	20	0	0			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:82763668C>T	ENST00000373200.2	+	1	400	c.336C>T	c.(334-336)aaC>aaT	p.N112N	RP3-326L13.2_ENST00000607095.1_RNA|RP3-326L13.3_ENST00000607789.1_lincRNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	112					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						ACCACCCCAACGCCTGGGGGG	0.657																																																0			X											33	32	32					X																	82763668		2195	4298	6493	82650324	SO:0001819	synonymous_variant	5456			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.336C>T	X.37:g.82763668C>T			82650324	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	37	CCDS14450.1																																																																																				0.657	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82763668	C	T	82763668	2	4	108	1	0	0	0	0	0	0	0	1	12308	535	19	1		1	POU3F4	23	82763668	Silent	SNP	C	TCGA-DY-A1H8-01A-21D-A152-10	7759095	82763668	72506892	168	28563										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91090628	91090628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	agaaaacgtcctgataggcgActtgttgaaagaccttaact	9	8	0	4			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:91090628A>G	ENST00000373094.1	+	1	970	c.125A>G	c.(124-126)gAc>gGc	p.D42G	PCDH11X_ENST00000504220.2_Missense_Mutation_p.D42G|PCDH11X_ENST00000406881.1_Missense_Mutation_p.D42G|PCDH11X_ENST00000373088.1_Missense_Mutation_p.D42G|PCDH11X_ENST00000298274.8_Missense_Mutation_p.D42G|PCDH11X_ENST00000361724.1_Missense_Mutation_p.D42G|PCDH11X_ENST00000361655.2_Missense_Mutation_p.D42G|PCDH11X_ENST00000395337.2_Missense_Mutation_p.D42G|PCDH11X_ENST00000373097.1_Missense_Mutation_p.D42G	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	42	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> G (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D42G(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CTGATAGGCGACTTGTTGAAA	0.483																																					NSCLC(38;925 1092 2571 38200 45895)											1	Substitution - Missense(1)	large_intestine(1)	X											172	127	142					X																	91090628		2203	4300	6503	90977284	SO:0001583	missense	83259			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.125A>G	X.37:g.91090628A>G	ENSP00000362186:p.Asp42Gly		90977284	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.725815	0.69074	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62	3.93	3.93	0.45458	Cadherin, N-terminal (1);Cadherin (2);	0.058953	0.64402	D	0.000005	T	0.43211	0.1237	L	0.53249	1.67	0.37930	D	0.931999	P;P;D;D;D;D;P;P	0.56287	0.917;0.564;0.969;0.969;0.969;0.975;0.846;0.846	P;B;P;P;P;P;P;P	0.57244	0.508;0.391;0.719;0.719;0.719;0.816;0.508;0.508	T	0.51252	-0.8729	10	0.72032	D	0.01	.	11.4509	0.50151	1.0:0.0:0.0:0.0	.	42;42;42;42;42;42;42;42	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	G	42	ENSP00000378746:D42G;ENSP00000362186:D42G;ENSP00000362189:D42G;ENSP00000355040:D42G;ENSP00000362180:D42G;ENSP00000423762:D42G;ENSP00000355105:D42G;ENSP00000384758:D42G;ENSP00000298274:D42G	ENSP00000298274:D42G	D	+	2	0	PCDH11X	90977284	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.349000	0.90067	1.555000	0.49500	0.339000	0.21740	GAC		0.483	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		G	91090628	A	G	91090628	3	3	108	1	0	0	0	0	1	0	0	0	11539	275	10	4	127	4	PCDH11X	23	91090628	Missense_Mutation	SNP	A	TCGA-DY-A1H8-01A-21D-A152-10	8326960	91090628	64179932	169	28564										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107846223	107846223	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	gaattccaggacctccaggaGcacctgggacacctggaaga	12	12	0	1			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:107846223G>T	ENST00000361603.2	+	28	2420	c.2176G>T	c.(2176-2178)Gca>Tca	p.A726S	COL4A5_ENST00000328300.6_Missense_Mutation_p.A726S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	726	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						ACCTCCAGGAGCACCTGGGAC	0.448									Alport syndrome with Diffuse Leiomyomatosis																																							0			X											18	16	17					X																	107846223		2202	4298	6500	107732879	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2176G>T	X.37:g.107846223G>T	ENSP00000354505:p.Ala726Ser		107732879	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	8.307	0.821201	0.16678	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.93307	-3.2;-3.2	5.84	1.83	0.25207	.	0.571100	0.17049	N	0.189009	D	0.87462	0.6183	L	0.39020	1.185	0.22171	N	0.99931	B;B;B	0.13594	0.008;0.008;0.008	B;B;B	0.16289	0.009;0.015;0.009	T	0.68796	-0.5314	10	0.08837	T	0.75	.	13.2264	0.59916	0.0679:0.5185:0.4136:0.0	.	726;334;726	E7EVY4;Q49AM6;P29400	.;.;CO4A5_HUMAN	S	726	ENSP00000331902:A726S;ENSP00000354505:A726S	ENSP00000331902:A726S	A	+	1	0	COL4A5	107732879	0.998000	0.40836	1.000000	0.80357	0.966000	0.64601	1.178000	0.31981	0.583000	0.29574	-0.218000	0.12543	GCA		0.448	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107846223	G	T	107846223	3	4	108	1	0	0	0	0	1	0	0	0	3700	971	34	2	2286	2	COL4A5	23	107846223	Missense_Mutation	SNP	G	TCGA-DY-A1H8-01A-21D-A152-10	16755595	107846223	47424337	170	28565										
CCDC160	347475	hgsc.bcm.edu	37	chrX	133379031	133379031	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0175438596491228	3	1	0.246315941055057	1.36294820717131	0.174736949637348	1	1	0	tttaagaggaaaaaatatatTttccaactaaatgaaataga	5	3	0	3			TCGA-DY-A1H8-01A-21D-A152-10	TCGA-DY-A1H8-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	8c79787f-511e-4f2e-83e1-639a2e411ed4	63452874-515e-4d43-9a18-acf647371b39	g.chrX:133379031T>C	ENST00000517294.1	+	3	584	c.201T>C	c.(199-201)atT>atC	p.I67I	CCDC160_ENST00000370809.4_Silent_p.I67I			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	67										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						AAAAATATATTTTCCAACTAA	0.299																																																0			X											16	14	14					X																	133379031		1772	4012	5784	133206697	SO:0001819	synonymous_variant	0			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.201T>C	X.37:g.133379031T>C			133206697		Silent	SNP	ENST00000517294.1	37	CCDS48171.1																																																																																				0.299	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		C	133379031	T	C	133379031	2	2	108	1	0	0	0	0	0	0	0	1	2798	1829	64	4		4	CCDC160	23	133379031	Silent	SNP	T	TCGA-DY-A1H8-01A-21D-A152-10	25532808	133379031	21891529	171	28566										
PLEKHN1	84069	hgsc.bcm.edu	37	chr1	908564	908564	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggaaggtttgtggtccccacAggaccaggccaactctgacc	12	13	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:908564A>G	ENST00000379409.2	+	11	1338		c.e11-1		PLEKHN1_ENST00000379407.3_Intron|PLEKHN1_ENST00000379410.3_Splice_Site			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1											central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		TGGTCCCCACAGGACCAGGCC	0.657																																																0			1											6	8	7					1																	908564		2029	4033	6062	898427	SO:0001630	splice_region_variant	84069			AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"Pleckstrin homology (PH) domain containing"	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1309-1A>G	1.37:g.908564A>G			898427	Q494U2|Q5SV98|Q9H0M7	Splice_Site	SNP	ENST00000379409.2	37		.	.	.	.	.	.	.	.	.	.	.	7.908	0.735960	0.15574	.	.	ENSG00000187583	ENST00000379410;ENST00000379409	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5714	0.39431	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLEKHN1	898427	0.997000	0.39634	0.846000	0.33378	0.162000	0.22319	2.152000	0.42272	1.770000	0.52166	0.386000	0.25728	.		0.657	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	Intron	G	908564	A	G	908564	5	3	109	1	0	0	0	0	0	0	1	0	12114	202	7	4	1233	4	PLEKHN1	1	908564	Splice_Site	SNP	A	TCGA-EF-5830-01A-01D-1657-10		908564	248342057	1	28567										
TNFRSF9	3604	hgsc.bcm.edu	37	chr1	7980913	7980913	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tttcacagttcacatcctccTtcttcttcttctggaaatcg	4	13	6	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:7980913T>C	ENST00000377507.3	-	8	916	c.750A>G	c.(748-750)gaA>gaG	p.E250E		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	250	Interaction with LRR-1.		E -> G (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		CACATCCTCCTTCTTCTTCTT	0.378																																																0			1											137	142	140					1																	7980913		2203	4300	6503	7903500	SO:0001819	synonymous_variant	3604			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"Tumor necrosis factor receptor superfamily", "CD molecules"	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.750A>G	1.37:g.7980913T>C			7903500		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																				0.378	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1			C	7980913	T	C	7980913	2	2	109	1	0	0	0	0	0	0	0	1	16339	1606	56	4		4	TNFRSF9	1	7980913	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	7072349	7980913	241269708	2	28568										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10699176	10699176	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcgtcgtcgtcctcgtcgtcGtcgtcctcgtcgtcgtcctc	10	17	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:10699176G>C	ENST00000377022.3	-	21	5420	c.5103C>G	c.(5101-5103)gaC>gaG	p.D1701E	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1701	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	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)		cctcgtcgtcgtcgtcctcgt	0.731																																																0			1											6	6	6					1																	10699176		1801	3652	5453	10621763	SO:0001583	missense	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5103C>G	1.37:g.10699176G>C	ENSP00000366221:p.Asp1701Glu		10621763	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689008	0.48097	.	.	ENSG00000130940	ENST00000377022	T	0.20463	2.07	2.95	-2.01	0.07410	.	0.000000	0.41500	U	0.000865	T	0.09379	0.0231	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09058	-1.0692	10	0.62326	D	0.03	-11.0431	5.6169	0.17436	0.3393:0.4577:0.203:0.0	.	1701	Q86V15	CASZ1_HUMAN	E	1701	ENSP00000366221:D1701E	ENSP00000366221:D1701E	D	-	3	2	CASZ1	10621763	0.017000	0.18338	0.885000	0.34714	0.524000	0.34500	-1.781000	0.01774	-0.050000	0.13356	0.195000	0.17529	GAC		0.731	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		C	10699176	G	C	10699176	3	2	109	1	0	0	0	0	1	0	0	0	2691	1136	40	5	180	5	CASZ1	1	10699176	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	2718263	10699176	238551445	3	28569										
MTOR	2475	hgsc.bcm.edu	37	chr1	11188061	11188061	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccacagtggctccgacccacCatcatggcctgctggaccag	10	17	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:11188061C>T	ENST00000361445.4	-	43	6109	c.6033G>A	c.(6031-6033)atG>atA	p.M2011I	MTOR_ENST00000376838.1_Splice_Site_p.M216I	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2011			M -> V (in an ovarian mucinous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCCGACCCACCATCATGGCCT	0.557																																																0			1											105	106	106					1																	11188061		2203	4300	6503	11110648	SO:0001630	splice_region_variant	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6033+1G>A	1.37:g.11188061C>T			11110648	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835988	0.71373	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.09630	3.21;2.96	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.11922	0.0290	L	0.37561	1.115	0.80722	D	1	B	0.28880	0.226	B	0.28709	0.093	T	0.15435	-1.0437	9	.	.	.	-20.5682	20.063	0.97692	0.0:1.0:0.0:0.0	.	2011	P42345	MTOR_HUMAN	I	2011;216	ENSP00000354558:M2011I;ENSP00000366034:M216I	.	M	-	3	0	MTOR	11110648	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.431000	0.80335	2.735000	0.93741	0.655000	0.94253	ATG		0.557	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	Missense_Mutation	T	11188061	C	T	11188061	5	4	109	1	0	0	0	0	0	0	1	0	9984	608	21	3	1680	3	MTOR	1	11188061	Splice_Site	SNP	C	TCGA-EF-5830-01A-01D-1657-10	488885	11188061	238062560	4	28570										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12387773	12387773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgaagtctctttccttggccTccaccagccgagatagccca	8	15	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:12387773T>C	ENST00000358136.3	+	36	8189	c.8059T>C	c.(8059-8061)Tcc>Ccc	p.S2687P	VPS13D_ENST00000356315.4_Missense_Mutation_p.S2687P	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TTCCTTGGCCTCCACCAGCCG	0.483																																																0			1											159	161	160					1																	12387773		2203	4300	6503	12310360	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8059T>C	1.37:g.12387773T>C	ENSP00000350854:p.Ser2687Pro		12310360		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.805632	0.31961	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.43688	0.94;0.94	5.51	0.127	0.14727	.	2.095450	0.01699	N	0.027116	T	0.43500	0.1250	L	0.57536	1.79	0.27388	N	0.955214	B;P;B	0.36315	0.0;0.547;0.412	B;B;B	0.41088	0.001;0.347;0.188	T	0.17471	-1.0368	9	.	.	.	.	4.0221	0.09670	0.1182:0.0651:0.2468:0.5698	.	594;2687;2687	B1AJZ2;Q5THJ4-2;Q5THJ4	.;.;VP13D_HUMAN	P	2687	ENSP00000348666:S2687P;ENSP00000350854:S2687P	.	S	+	1	0	VPS13D	12310360	0.000000	0.05858	0.530000	0.27963	0.382000	0.30200	0.030000	0.13688	-0.152000	0.11156	0.533000	0.62120	TCC		0.483	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12387773	T	C	12387773	3	2	109	1	0	0	0	0	1	0	0	0	17232	1551	54	4	8197	4	VPS13D	1	12387773	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1199712	12387773	236862848	5	28571										
NBL1	4681	hgsc.bcm.edu	37	chr1	19983484	19983484	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaggggctgagcgtctatgtGcagggcgaggacgggccggg	22	8	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:19983484G>T	ENST00000375136.3	+	4	711	c.408G>T	c.(406-408)gtG>gtT	p.V136V	NBL1_ENST00000548815.1_Silent_p.V135V|NBL1_ENST00000289749.2_Silent_p.V171V|MINOS1-NBL1_ENST00000602662.1_Silent_p.V136V	NM_001204085.1|NM_001204089.1|NM_001278164.1|NM_001278166.1	NP_001191014.1|NP_001191018.1|NP_001265093.1|NP_001265095.1	P41271	NBL1_HUMAN	neuroblastoma 1, DAN family BMP antagonist	136					determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of monocyte chemotaxis (GO:0090027)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)|positive regulation of neuron differentiation (GO:0045666)|sequestering of BMP from receptor via BMP binding (GO:0038098)|sequestering of BMP in extracellular matrix (GO:0035582)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00043)|Ovarian(437;0.00373)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.9e-05)|Kidney(64;0.000173)|GBM - Glioblastoma multiforme(114;0.0012)|KIRC - Kidney renal clear cell carcinoma(64;0.0026)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCGTCTATGTGCAGGGCGAGG	0.697																																																0			1											42	37	39					1																	19983484		2197	4299	6496	19856071	SO:0001819	synonymous_variant	4681				CCDS196.1, CCDS41278.1, CCDS196.2, CCDS72720.1	1p36.3-p36.2	2013-02-26	2013-02-26		ENSG00000158747	ENSG00000158747			7650	protein-coding gene	gene with protein product	"neuroblastoma candidate region, suppression of tumorigenicity 1", "neuroblastoma suppressor of tumorigenicity 1", "differential screening-selected gene aberrant in neuroblastoma"	600613	"neuroblastoma, suppression of tumorigenicity 1"			7633401	Standard	NM_182744		Approved	D1S1733E, NB, DAN, NO3, DAND1	uc001bcj.2	P41271	OTTHUMG00000002700	ENST00000375136.3:c.408G>T	1.37:g.19983484G>T			19856071	A3KFI7|Q5TGZ2|Q5U0N4|Q96L68	Silent	SNP	ENST00000375136.3	37	CCDS196.2																																																																																				0.697	NBL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007681.4	NM_005380		T	19983484	G	T	19983484	2	4	109	1	0	0	0	0	0	0	0	1	10220	1306	46	2		2	NBL1	1	19983484	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	7595711	19983484	229267137	6	28572										
SEPN1	57190	hgsc.bcm.edu	37	chr1	26138348	26138348	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggctgcccggcgcctggaggTggccatgtaccccttcaaga	14	14	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:26138348T>G	ENST00000374315.1	+	8	1195	c.1157T>G	c.(1156-1158)gTg>gGg	p.V386G	SEPN1_ENST00000361547.2_Missense_Mutation_p.V420G|SEPN1_ENST00000354177.4_Missense_Mutation_p.V386G|RP1-317E23.6_ENST00000527604.1_5'Flank	NM_206926.1	NP_996809.1	Q9NZV5	SELN_HUMAN	selenoprotein N, 1	420						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		CGCCTGGAGGTGGCCATGTAC	0.652																																																0			1											16	17	17					1																	26138348		2091	4219	6310	26010935	SO:0001583	missense	57190			AF166125	CCDS41282.1, CCDS41283.1	1p36.13	2014-09-17	2004-02-13		ENSG00000162430	ENSG00000162430		"EF-hand domain containing"	15999	protein-coding gene	gene with protein product		606210	"rigid spine muscular dystrophy 1"	RSMD1, MDRS1		10608886	Standard	NM_020451		Approved	selN, RSS	uc021ojl.1	Q9NZV5	OTTHUMG00000007375	ENST00000374315.1:c.1157T>G	1.37:g.26138348T>G	ENSP00000363434:p.Val386Gly		26010935	A6NJG8|A8MQ64|Q6PI70|Q969F6|Q9NUI6	Missense_Mutation	SNP	ENST00000374315.1	37	CCDS41283.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560498	0.86335	.	.	ENSG00000162430	ENST00000361547;ENST00000354177;ENST00000374315	D;D;D	0.89415	-2.51;-2.49;-2.49	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.92711	0.7683	M	0.65975	2.015	0.80722	D	1	D;D	0.71674	0.996;0.998	D;P	0.63877	0.919;0.897	D	0.92752	0.6217	10	0.48119	T	0.1	-27.4748	14.7338	0.69402	0.0:0.0:0.0:1.0	.	386;420	Q9NZV5-2;Q9NZV5	.;SELN_HUMAN	G	420;386;386	ENSP00000355141:V420G;ENSP00000346109:V386G;ENSP00000363434:V386G	ENSP00000346109:V386G	V	+	2	0	SEPN1	26010935	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.008000	0.88588	1.888000	0.54679	0.254000	0.18369	GTG		0.652	SEPN1-002	KNOWN	basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000019315.2	NM_020451		G	26138348	T	G	26138348	3	3	109	1	0	0	0	0	1	0	0	0	14093	1696	59	4	1293	4	SEPN1	1	26138348	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6154864	26138348	223112273	7	28573										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101398	27101398	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccatatggtccctctgccccTgtgccccccatgacaaggcc	8	19	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:27101398T>C	ENST00000324856.7	+	18	5051	c.4680T>C	c.(4678-4680)ccT>ccC	p.P1560P	ARID1A_ENST00000374152.2_Silent_p.P1177P|ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000540690.1_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1560					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		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)		CCTCTGCCCCTGTGCCCCCCA	0.617			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											38	39	39					1																	27101398		2203	4300	6503	26973985	SO:0001819	synonymous_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4680T>C	1.37:g.27101398T>C			26973985	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	1.713	-0.498624	0.04291	.	.	ENSG00000117713	ENST00000430799	.	.	.	5.18	-4.79	0.03200	.	.	.	.	.	T	0.51635	0.1686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52793	-0.8528	4	.	.	.	-8.5123	9.4962	0.38989	0.0962:0.32:0.0:0.5838	.	.	.	.	R	457	.	.	C	+	1	0	ARID1A	26973985	0.002000	0.14202	0.800000	0.32199	0.788000	0.44548	-1.665000	0.01965	-0.707000	0.05022	-1.556000	0.00890	TGT		0.617	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27101398	T	C	27101398	2	2	109	1	0	0	0	0	0	0	0	1	913	1567	55	4		4	ARID1A	1	27101398	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	963050	27101398	222149223	8	28574										
C1orf38	9473	hgsc.bcm.edu	37	chr1	28209271	28209271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctgggcctgcggctggaggAgaagatcacagagccattct	14	11	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:28209271A>G	ENST00000373921.3	+	4	1440	c.1436A>G	c.(1435-1437)gAg>gGg	p.E479G	THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000328928.7_Missense_Mutation_p.E350G|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	479	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGGCTGGAGGAGAAGATCACA	0.597																																																0			1											81	82	82					1																	28209271		2084	4209	6293	28081858	SO:0001583	missense	9473			AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"induced by contact to basement membrane 1"		"chromosome 1 open reading frame 38"	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1436A>G	1.37:g.28209271A>G	ENSP00000363031:p.Glu479Gly		28081858	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.33|17.33	3.363391|3.363391	0.61513|0.61513	.|.	.|.	ENSG00000130775|ENSG00000130775	ENST00000328928;ENST00000373921|ENST00000456990	T;T|.	0.14266|.	2.52;2.52|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.297287|.	0.36555|.	N|.	0.002538|.	T|T	0.61324|0.61324	0.2338|0.2338	M|M	0.81341|0.81341	2.54|2.54	0.24955|0.24955	N|N	0.991766|0.991766	D;P;B|.	0.63880|.	0.993;0.607;0.4|.	P;B;B|.	0.55871|.	0.786;0.299;0.212|.	T|T	0.57277|0.57277	-0.7839|-0.7839	10|5	0.72032|.	D|.	0.01|.	-34.0508|-34.0508	11.1673|11.1673	0.48550|0.48550	0.8004:0.1996:0.0:0.0|0.8004:0.1996:0.0:0.0	.|.	350;283;479|.	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8|.	.;.;THMS2_HUMAN|.	G|G	350;479|227	ENSP00000329862:E350G;ENSP00000363031:E479G|.	ENSP00000329862:E350G|.	E|R	+|+	2|1	0|2	C1orf38|C1orf38	28081858|28081858	0.975000|0.975000	0.34042|0.34042	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	2.280000|2.280000	0.43443|0.43443	2.014000|2.014000	0.59158|0.59158	0.454000|0.454000	0.30748|0.30748	GAG|AGA		0.597	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848		G	28209271	A	G	28209271	3	3	109	1	0	0	0	0	1	0	0	0	2045	304	11	4	1450	4	C1orf38	1	28209271	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1107873	28209271	221041350	9	28575										
PHC2	1912	hgsc.bcm.edu	37	chr1	33836171	33836171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gagctgggctgctgctggggAggctgccaggttgatctaat	17	8	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:33836171A>G	ENST00000257118.5	-	4	480	c.427T>C	c.(427-429)Tcc>Ccc	p.S143P	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Missense_Mutation_p.S143P|PHC2_ENST00000419414.2_Missense_Mutation_p.S143P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	143					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GCTGCTGGGGAGGCTGCCAGG	0.582																																																0			1											47	39	42					1																	33836171		2203	4300	6503	33608758	SO:0001583	missense	1912			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.427T>C	1.37:g.33836171A>G	ENSP00000257118:p.Ser143Pro		33608758	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179624	0.57800	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.39229	1.38;1.09;1.49	4.84	4.84	0.62591	.	0.066272	0.64402	D	0.000008	T	0.44008	0.1273	M	0.75777	2.31	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.41088	-0.9528	10	0.45353	T	0.12	-19.2188	12.3836	0.55322	1.0:0.0:0.0:0.0	.	143;143;143	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	P	143	ENSP00000389436:S143P;ENSP00000257118:S143P;ENSP00000391440:S143P	ENSP00000257118:S143P	S	-	1	0	PHC2	33608758	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.576000	0.67437	1.801000	0.52704	0.460000	0.39030	TCC		0.582	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		G	33836171	A	G	33836171	3	3	109	1	0	0	0	0	1	0	0	0	11848	304	11	4	2193	4	PHC2	1	33836171	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	5626900	33836171	215414450	10	28576										
CAP1	5538	hgsc.bcm.edu	37	chr1	40536642	40536642	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtcctcattcctacagaaggCggtgactttgtaagtttctt	9	9	2	2	rs377481764		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:40536642C>A	ENST00000433473.3	-	0	2740				CAP1_ENST00000372797.3_Silent_p.G445G|CAP1_ENST00000372792.2_Silent_p.G445G|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Silent_p.G444G|CAP1_ENST00000372802.1_Silent_p.G444G|PPT1_ENST00000372775.2_5'Flank|CAP1_ENST00000372798.1_Silent_p.G444G|CAP1_ENST00000372805.3_Silent_p.G445G	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTACAGAAGGCGGTGACTTTG	0.398																																																0			1											149	136	140					1																	40536642		1853	4100	5953	40309229	SO:0001628	intergenic_variant	10487			U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40536642C>A			40309229	B4DY24|Q6FGQ4	Silent	SNP	ENST00000433473.3	37	CCDS447.1																																																																																				0.398	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		A	40536642	C	A	40536642	1	1	109	0	1	0	0	0	0	0	0	0	2625	755	27	2		2	CAP1	1	40536642	IGR	SNP	C	TCGA-EF-5830-01A-01D-1657-10	6700471	40536642	208713979	11	28577										
SLFNL1	200172	hgsc.bcm.edu	37	chr1	41481833	41481833	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gctgctgcagctgctgctggAgctgctccttctccatcatc	10	15	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:41481833A>G	ENST00000359345.1	-	4	3745	c.1169T>C	c.(1168-1170)cTc>cCc	p.L390P	SLFNL1_ENST00000302946.8_Missense_Mutation_p.L390P|SLFNL1_ENST00000439569.2_Missense_Mutation_p.L390P|SLFNL1_ENST00000372611.1_Missense_Mutation_p.L331P|SLFNL1_ENST00000397197.2_Missense_Mutation_p.L342P|SLFNL1_ENST00000372613.2_Missense_Mutation_p.L342P	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	390							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				CTGCTGCTGGAGCTGCTCCTT	0.632																																																0			1											86	79	81					1																	41481833		2203	4300	6503	41254420	SO:0001583	missense	200172			BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1169T>C	1.37:g.41481833A>G	ENSP00000352299:p.Leu390Pro		41254420	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.800276	0.70567	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.52526	0.66;1.63;1.01;0.66;0.66;1.63	5.25	5.25	0.73442	.	0.000000	0.44483	D	0.000460	T	0.56601	0.1996	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	T	0.60291	-0.7292	10	0.87932	D	0	-46.1824	11.5599	0.50769	1.0:0.0:0.0:0.0	.	342;331;390	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	P	390;342;331;390;390;342	ENSP00000304401:L390P;ENSP00000361696:L342P;ENSP00000361694:L331P;ENSP00000352299:L390P;ENSP00000398938:L390P;ENSP00000380381:L342P	ENSP00000304401:L390P	L	-	2	0	SLFNL1	41254420	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.308000	0.65768	1.991000	0.58162	0.459000	0.35465	CTC		0.632	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990		G	41481833	A	G	41481833	3	3	109	1	0	0	0	0	1	0	0	0	14775	304	11	4	58	4	SLFNL1	1	41481833	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	945191	41481833	207768788	12	28578										
MPL	4352	hgsc.bcm.edu	37	chr1	43815006	43815006	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctgggcctgctgctgctgaGgtggcagtttcctgcacact	13	13	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:43815006G>T	ENST00000372470.3	+	10	1583	c.1541G>T	c.(1540-1542)aGg>aTg	p.R514M	MPL_ENST00000413998.2_Missense_Mutation_p.R514M	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	514					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)	p.R514K(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	CTGCTGCTGAGGTGGCAGTTT	0.617			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											99	99	99					1																	43815006		2203	4300	6503	43587593	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1541G>T	1.37:g.43815006G>T	ENSP00000361548:p.Arg514Met		43587593	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.987670	0.74589	.	.	ENSG00000117400	ENST00000372470;ENST00000413998	D;T	0.81659	-1.52;-1.25	4.53	2.58	0.30949	.	1.779270	0.02274	N	0.068782	D	0.83450	0.5257	L	0.53249	1.67	0.22354	N	0.99918	P;P;D	0.63046	0.468;0.528;0.992	B;B;P	0.52710	0.079;0.116;0.707	T	0.63444	-0.6636	10	0.56958	D	0.05	-0.0063	6.2546	0.20867	0.1053:0.1891:0.7057:0.0	.	507;514;514	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	M	514	ENSP00000361548:R514M;ENSP00000414004:R514M	ENSP00000361548:R514M	R	+	2	0	MPL	43587593	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.240000	0.43088	0.424000	0.26061	0.430000	0.28490	AGG		0.617	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		T	43815006	G	T	43815006	3	4	109	1	0	0	0	0	1	0	0	0	9760	1000	35	2	1579	2	MPL	1	43815006	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	2333173	43815006	205435615	13	28579										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334298	77334298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagcagcagcagcagcagcaGcaacagcagcagcaggcgtc	13	14	0	0	rs554217920	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:77334298G>A	ENST00000477717.1	+	2	367	c.132G>A	c.(130-132)caG>caA	p.Q44Q	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	44	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcagcaacagcagc	0.711													G|||	2	0.000399361	0	0	5008	,	,		11676	0.002		0	False		,,,				2504	0															0			1											12	12	12					1																	77334298		2054	3972	6026	77106886	SO:0001819	synonymous_variant	81849				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.132G>A	1.37:g.77334298G>A			77106886	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																				0.711	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77334298	G	A	77334298	2	1	109	1	0	0	0	0	0	0	0	1	15266	962	34	3		3	ST6GALNAC5	1	77334298	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	33519292	77334298	171916323	14	28580										
RHOC	389	hgsc.bcm.edu	37	chr1	113244242	113244242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggccatctcaaacacctcccGcactccctccttggtcttgg	7	18	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:113244242G>A	ENST00000285735.2	-	6	1711	c.502C>T	c.(502-504)Cgg>Tgg	p.R168W	RHOC_ENST00000369633.2_Missense_Mutation_p.R168W|RHOC_ENST00000369642.3_Missense_Mutation_p.R168W|RHOC_ENST00000369632.2_Missense_Mutation_p.R168W|RHOC_ENST00000369637.1_Missense_Mutation_p.R168W|RHOC_ENST00000369636.2_Silent_p.C147C|RP11-426L16.10_ENST00000471038.2_5'Flank|RHOC_ENST00000369638.2_Missense_Mutation_p.R168W|RHOC_ENST00000339083.7_Missense_Mutation_p.R168W			P08134	RHOC_HUMAN	ras homolog family member C	168					apical junction assembly (GO:0043297)|axon guidance (GO:0007411)|cytokinesis (GO:0000910)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AACACCTCCCGCACTCCCTCC	0.607																																																0			1											123	108	113					1																	113244242		2203	4300	6503	113045765	SO:0001583	missense	389			BC052808	CCDS854.1	1p13.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000155366	ENSG00000155366			669	protein-coding gene	gene with protein product		165380	"ras homolog gene family, member C"	ARH9, ARHC		3283705	Standard	NM_001042678		Approved	RhoC	uc001ecp.1	P08134	OTTHUMG00000011905	ENST00000285735.2:c.502C>T	1.37:g.113244242G>A	ENSP00000285735:p.Arg168Trp		113045765	B3KSW1|Q6ICN3	Missense_Mutation	SNP	ENST00000285735.2	37	CCDS854.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.217183	0.58560	.	.	ENSG00000155366	ENST00000339083;ENST00000369633;ENST00000369642;ENST00000285735;ENST00000369638;ENST00000369637;ENST00000369632;ENST00000484054;ENST00000425265;ENST00000534717	T;T;T;T;T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	5.13	3.17	0.36434	.	.	.	.	.	T	0.81678	0.4873	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.83633	0.0146	9	0.87932	D	0	10.5575	12.5942	0.56459	0.0:0.0:0.5395:0.4605	.	168	P08134	RHOC_HUMAN	W	168;168;168;168;168;168;168;205;168;168	ENSP00000345236:R168W;ENSP00000358647:R168W;ENSP00000358656:R168W;ENSP00000285735:R168W;ENSP00000358652:R168W;ENSP00000358651:R168W;ENSP00000358646:R168W;ENSP00000434877:R205W;ENSP00000390823:R168W;ENSP00000436240:R168W	ENSP00000285735:R168W	R	-	1	2	RHOC	113045765	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.972000	0.49256	0.498000	0.27948	0.563000	0.77884	CGG		0.607	RHOC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032904.2	NM_175744		A	113244242	G	A	113244242	3	1	109	1	0	0	0	0	1	0	0	0	13373	1086	38	1	83	1	RHOC	1	113244242	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	35909944	113244242	136006379	15	28581										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144994637	144994637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctcatacttctgttgcatgCgctcctccaggaagtagatg	9	12	2	1	rs372978033		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:144994637C>T	ENST00000369354.3	-	1	284	c.95G>A	c.(94-96)cGc>cAc	p.R32H	PDE4DIP_ENST00000369349.3_Missense_Mutation_p.R32H|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R169H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R32H|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.R169H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R98H|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.R32H|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R169H|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.R32H			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	32					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTGTTGCATGCGCTCCTCCAG	0.587			T	PDGFRB	MPD																																		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			1						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,	0,4406		0,0,2203	162	140	148		95,95,104,293,95,95,506,	4.9	1	1		148	2,8598		0,2,4298	no	missense,missense,missense,missense,missense,missense,missense,utr-5	PDE4DIP	NM_001002810.3,NM_001002812.1,NM_001195261.1,NM_001198832.1,NM_001198834.2,NM_014644.4,NM_022359.5,NM_001195260.1	29,29,29,29,29,29,29,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	32/174,32/970,35/177,98/2241,32/2363,32/2347,169/311,	144994637	2,13004	2203	4300	6503	143705994	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.95G>A	1.37:g.144994637C>T	ENSP00000358360:p.Arg32His		143705994	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.985239	0.93044	0.0	2.33E-4	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000530078;ENST00000534536;ENST00000369347;ENST00000369348;ENST00000531369	T;T;T;T;T;T;T;T;T;T;T	0.79940	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;-1.32	5.78	4.86	0.63082	Spindle associated (1);	.	.	.	.	D	0.85843	0.5791	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.966;0.985;0.991;0.998;0.995;0.996;0.992	D	0.86795	0.1988	9	0.87932	D	0	.	11.8519	0.52415	0.0:0.9164:0.0:0.0836	.	32;98;32;169;98;35;32	Q5VU43-7;Q5VU43-3;Q5VU43;E9PJ64;E9PQH9;E9PS60;Q5VU43-10	.;.;MYOME_HUMAN;.;.;.;.	H	98;32;32;169;169;32;32;98;35;32;169;99	ENSP00000327209:R98H;ENSP00000358360:R32H;ENSP00000358363:R32H;ENSP00000435654:R169H;ENSP00000358366:R169H;ENSP00000358357:R32H;ENSP00000358355:R32H;ENSP00000435920:R35H;ENSP00000358353:R32H;ENSP00000358354:R169H;ENSP00000435616:R99H	ENSP00000327209:R98H	R	-	2	0	PDE4DIP	143705994	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.196000	0.51020	2.731000	0.93534	0.650000	0.86243	CGC		0.587	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144994637	C	T	144994637	3	4	109	1	0	0	0	0	1	0	0	0	11674	768	27	1	8264	1	PDE4DIP	1	144994637	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	31750395	144994637	104255984	16	28582										
RBM8A	9939	hgsc.bcm.edu	37	chr1	145509017	145509017	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagcccatcagcgttgactgGtgttttgttcggggtccacc	12	12	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:145509017G>C	ENST00000330165.8	+	5	513	c.444G>C	c.(442-444)tgG>tgC	p.W148C	RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RBM8A_ENST00000369307.3_Missense_Mutation_p.W147C|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	148	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCGTTGACTGGTGTTTTGTTC	0.473																																																0			1											107	107	107					1																	145509017		2203	4300	6503	144220374	SO:0001583	missense	9939			AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"RNA binding motif (RRM) containing"	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.444G>C	1.37:g.145509017G>C	ENSP00000333001:p.Trp148Cys		144220374	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	Missense_Mutation	SNP	ENST00000330165.8	37	CCDS916.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468310	0.63625	.	.	ENSG00000131795	ENST00000330165;ENST00000369307	T;T	0.75367	-0.93;-0.93	4.02	3.09	0.35607	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.85057	0.5610	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.87017	0.2126	9	.	.	.	-6.6545	9.8054	0.40791	0.1048:0.0:0.8952:0.0	.	147;148	Q9Y5S9-2;Q9Y5S9	.;RBM8A_HUMAN	C	148;147	ENSP00000333001:W148C;ENSP00000358313:W147C	.	W	+	3	0	RBM8A	144220374	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.883000	0.75595	0.880000	0.35969	0.561000	0.74099	TGG		0.473	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2	NM_005105		C	145509017	G	C	145509017	3	2	109	1	0	0	0	0	1	0	0	0	13183	1270	44	5	462	5	RBM8A	1	145509017	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	514380	145509017	103741604	17	28583										
FLG	2312	hgsc.bcm.edu	37	chr1	152282812	152282812	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgtggtgtggctgtgatggTaccctgagtgtccagaccta	15	8	0	3	rs146433981	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152282812T>G	ENST00000368799.1	-	3	4585	c.4550A>C	c.(4549-4551)tAc>tCc	p.Y1517S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1517	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGTGATGGTACCCTGAGTG	0.562									Ichthyosis				t|||	21	0.00419329	0.0159	0	5008	,	,		19489	0		0	False		,,,				2504	0															0			1						T	SER/TYR	60,4346	56.8+/-93.2	0,60,2143	324	307	313		4550	0	0	1	dbSNP_134	313	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	144	0,60,6443	GG,GT,TT		0.0,1.3618,0.4613	benign	1517/4062	152282812	60,12946	2203	4300	6503	150549436	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4550A>C	1.37:g.152282812T>G	ENSP00000357789:p.Tyr1517Ser		150549436	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	21	0.009615384615384616	9	0.018292682926829267	1	0.0027624309392265192	5	0.008741258741258742	6	0.0079155672823219	t	8.034	0.762413	0.15914	0.013618	0.0	ENSG00000143631	ENST00000368799	T	0.04454	3.62	3.26	1.16E-4	0.14041	.	.	.	.	.	T	0.00241	0.0007	N	0.00034	-2.555	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38564	-0.9655	9	0.10636	T	0.68	.	5.727	0.18018	0.0:0.192:0.4108:0.3973	.	1517	P20930	FILA_HUMAN	S	1517	ENSP00000357789:Y1517S	ENSP00000357789:Y1517S	Y	-	2	0	FLG	150549436	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-0.173000	0.09854	-0.085000	0.12573	-0.343000	0.07986	TAC		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152282812	T	G	152282812	3	3	109	1	0	0	0	0	1	0	0	0	5941	1638	57	4	7639	4	FLG	1	152282812	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6773795	152282812	96967809	18	28584										
FLG	2312	hgsc.bcm.edu	37	chr1	152284628	152284628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agaggaagcttcatggtgacGtgaccctgagtgcctggagc	15	9	1	4	rs147145635		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152284628G>A	ENST00000368799.1	-	3	2769	c.2734C>T	c.(2734-2736)Cgt>Tgt	p.R912C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	912	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCATGGTGACGTGACCCTGAG	0.567									Ichthyosis				-|||	1	0.000199681	0	0	5008	,	,		21118	0		0.001	False		,,,				2504	0															0			1						G	CYS/ARG	1,4405		0,1,2202	385	363	370		2734	-2.3	0	1	dbSNP_134	370	17,8583		0,17,4283	yes	missense	FLG	NM_002016.1	180	0,18,6485	AA,AG,GG		0.1977,0.0227,0.1384	probably-damaging	912/4062	152284628	18,12988	2203	4300	6503	150551252	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2734C>T	1.37:g.152284628G>A	ENSP00000357789:p.Arg912Cys		150551252	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	-	4.416	0.076815	0.08485	2.27E-4	0.001977	ENSG00000143631	ENST00000368799	T	0.02446	4.29	2.3	-2.27	0.06846	.	.	.	.	.	T	0.01835	0.0058	M	0.65975	2.015	0.09310	N	1	D	0.76494	0.999	P	0.46659	0.523	T	0.40701	-0.9549	9	0.41790	T	0.15	.	9.1447	0.36925	0.0:0.6868:0.3132:0.0	.	912	P20930	FILA_HUMAN	C	912	ENSP00000357789:R912C	ENSP00000357789:R912C	R	-	1	0	FLG	150551252	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.326000	0.07965	-0.352000	0.08237	0.479000	0.44913	CGT		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152284628	G	A	152284628	3	1	109	1	0	0	0	0	1	0	0	0	5941	1145	40	1	9455	1	FLG	1	152284628	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	1816	152284628	96965993	19	28585										
IVL	3713	hgsc.bcm.edu	37	chr1	152883253	152883253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggggcagcctaagcatctggAgcagcaggaggggcaactgg	18	9	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152883253A>G	ENST00000368764.3	+	2	1044	c.980A>G	c.(979-981)gAg>gGg	p.E327G	IVL_ENST00000392667.2_Missense_Mutation_p.E181G			P07476	INVO_HUMAN	involucrin	327	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			aagcatctggagcagcaggag	0.642																																																0			1											17	17	17					1																	152883253		2114	4160	6274	151149877	SO:0001583	missense	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.980A>G	1.37:g.152883253A>G	ENSP00000357753:p.Glu327Gly		151149877	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	9.475	1.096584	0.20552	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10477	3.04;2.87	3.82	-0.483	0.12075	.	.	.	.	.	T	0.01730	0.0055	N	0.14661	0.345	0.09310	N	1	B	0.27286	0.174	B	0.29176	0.099	T	0.46261	-0.9204	9	0.51188	T	0.08	.	4.3193	0.11009	0.5239:0.0:0.1122:0.3639	.	327	P07476	INVO_HUMAN	G	327;181	ENSP00000357753:E327G;ENSP00000376435:E181G	ENSP00000357753:E327G	E	+	2	0	IVL	151149877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.366000	0.20365	-0.360000	0.08138	-0.648000	0.03929	GAG		0.642	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		G	152883253	A	G	152883253	3	3	109	1	0	0	0	0	1	0	0	0	7950	304	11	4	982	4	IVL	1	152883253	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	598625	152883253	96367368	20	28586										
NPR1	4881	hgsc.bcm.edu	37	chr1	153657499	153657499	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcgggtgcgctgggaggacgTtgagcccagtagccttgaga	18	9	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:153657499T>G	ENST00000368680.3	+	8	2016	c.1544T>G	c.(1543-1545)gTt>gGt	p.V515G		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	515					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TGGGAGGACGTTGAGCCCAGT	0.627																																					Pancreas(141;1349 1870 15144 15830 40702)											0			1											62	60	60					1																	153657499		2203	4300	6503	151924123	SO:0001583	missense	4881			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1544T>G	1.37:g.153657499T>G	ENSP00000357669:p.Val515Gly		151924123	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.161524	0.57368	.	.	ENSG00000169418	ENST00000368680;ENST00000428723	T	0.57107	0.42	4.86	4.86	0.63082	.	0.633338	0.14462	N	0.318124	T	0.41511	0.1162	L	0.46819	1.47	0.80722	D	1	P;P	0.49185	0.92;0.547	P;B	0.46543	0.52;0.282	T	0.47522	-0.9111	10	0.87932	D	0	.	12.4638	0.55747	0.0:0.0:0.0:1.0	.	20;515	B7Z4Y7;P16066	.;ANPRA_HUMAN	G	515;20	ENSP00000357669:V515G	ENSP00000357669:V515G	V	+	2	0	NPR1	151924123	1.000000	0.71417	0.444000	0.26895	0.252000	0.25951	7.496000	0.81526	2.043000	0.60533	0.533000	0.62120	GTT		0.627	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		G	153657499	T	G	153657499	3	3	109	1	0	0	0	0	1	0	0	0	10625	1725	60	4	1574	4	NPR1	1	153657499	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	774246	153657499	95593122	21	28587										
SHC1	6464	hgsc.bcm.edu	37	chr1	154942755	154942755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	catcagctgcccttcctggcTcccccttagaccctgggcgc	9	19	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:154942755T>C	ENST00000368445.5	-	1	462	c.248A>G	c.(247-249)gAg>gGg	p.E83G	SHC1_ENST00000606391.1_Intron|SHC1_ENST00000368453.4_Intron|SHC1_ENST00000368449.4_Intron|SHC1_ENST00000448116.2_Missense_Mutation_p.E83G|SHC1_ENST00000368450.1_Intron	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	83					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCTTCCTGGCTCCCCCTTAGA	0.652																																					NSCLC(4;32 234 1864 2492 3259 13747 17376)											0			1											24	29	28					1																	154942755		2203	4299	6502	153209379	SO:0001583	missense	6464			U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.248A>G	1.37:g.154942755T>C	ENSP00000357430:p.Glu83Gly		153209379	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Missense_Mutation	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.449519	0.26074	.	.	ENSG00000160691	ENST00000368445;ENST00000448116;ENST00000368443	T;T	0.50548	0.74;0.74	4.27	4.27	0.50696	.	0.226724	0.42420	D	0.000713	T	0.19886	0.0478	L	0.51422	1.61	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.08513	-1.0718	10	0.15499	T	0.54	.	7.5658	0.27879	0.0:0.0975:0.0:0.9025	.	83;83	P29353-6;P29353	.;SHC1_HUMAN	G	83;83;19	ENSP00000357430:E83G;ENSP00000401303:E83G	ENSP00000357428:E19G	E	-	2	0	SHC1	153209379	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.539000	0.36104	1.922000	0.55676	0.454000	0.30748	GAG		0.652	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		C	154942755	T	C	154942755	3	2	109	1	0	0	0	0	1	0	0	0	14307	1551	54	4	1554	4	SHC1	1	154942755	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1285256	154942755	94307866	22	28588										
C1orf104	23623	hgsc.bcm.edu	37	chr1	155291183	155291183	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gccagattgcggcagcagggAcctggaggtccattctgggc	16	11	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:155291183A>G	ENST00000368352.5	+	2	65				RUSC1_ENST00000368354.3_Intron|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	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)			GGCAGCAGGGACCTGGAGGTC	0.677																																																0			1											14	16	15					1																	155291183		1850	4087	5937	153557807	SO:0001627	intron_variant	284618			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-86-296A>G	1.37:g.155291183A>G			153557807	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																				0.677	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			G	155291183	A	G	155291183	1	3	109	0	1	0	0	0	0	0	0	0	1984	275	10	4		4	C1orf104	1	155291183	Intron	SNP	A	TCGA-EF-5830-01A-01D-1657-10	348428	155291183	93959438	23	28589										
ASTN1	460	hgsc.bcm.edu	37	chr1	176998807	176998807	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctccttgaaggatccgtgtaAaaggtcagctgggggtcgtt	14	8	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:176998807A>G	ENST00000367654.3	-	5	1294	c.1083T>C	c.(1081-1083)ttT>ttC	p.F361F	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Silent_p.F361F|ASTN1_ENST00000361833.2_Silent_p.F361F|MIR488_ENST00000365739.2_RNA|ASTN1_ENST00000367657.3_Silent_p.F361F	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	361					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GATCCGTGTAAAAGGTCAGCT	0.542																																																0			1											70	66	67					1																	176998807		2203	4300	6503	175265430	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1083T>C	1.37:g.176998807A>G			175265430	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.542	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		G	176998807	A	G	176998807	2	3	109	1	0	0	0	0	0	0	0	1	1065	11	1	4		4	ASTN1	1	176998807	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	21707624	176998807	72251814	24	28590										
B3GALT2	8707	hgsc.bcm.edu	37	chr1	193150027	193150027	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atggtcaaattatagtacgtAtctaagtattcctgttgaat	7	5	2	1	rs376102979	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:193150027A>G	ENST00000367434.4	-	2	1421	c.666T>C	c.(664-666)gaT>gaC	p.D222D	CDC73_ENST00000367435.3_Intron	NM_003783.3	NP_003774.1	O43825	B3GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	222					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	16						TATAGTACGTATCTAAGTATT	0.348													A|||	4	0.000798722	0	0	5008	,	,		20480	0.004		0	False		,,,				2504	0															0			1											123	122	122					1																	193150027		2203	4299	6502	191416650	SO:0001819	synonymous_variant	8707			Y15060	CCDS1383.1	1q31	2013-02-19			ENSG00000162630	ENSG00000162630		"Beta 3-glycosyltransferases"	917	protein-coding gene	gene with protein product		603018				9582303, 9417100	Standard	NM_003783		Approved	beta3Gal-T2	uc001gtc.4	O43825	OTTHUMG00000035687	ENST00000367434.4:c.666T>C	1.37:g.193150027A>G			191416650	B2RAB1|Q9BZQ9	Silent	SNP	ENST00000367434.4	37	CCDS1383.1																																																																																				0.348	B3GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086759.1	NM_003783		G	193150027	A	G	193150027	2	3	109	1	0	0	0	0	0	0	0	1	1249	446	16	4		4	B3GALT2	1	193150027	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	16151220	193150027	56100594	25	28591										
NFASC	23114	hgsc.bcm.edu	37	chr1	204985634	204985634	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aacgaaagctcagaggccacGtcacctgtcaatgctatcta	8	12	4	1	rs143897854	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:204985634G>A	ENST00000401399.1	+	29	3889	c.3690G>A	c.(3688-3690)acG>acA	p.T1230T	NFASC_ENST00000513543.1_Silent_p.T1159T|NFASC_ENST00000539706.1_Silent_p.T1164T|NFASC_ENST00000339876.6_Silent_p.T1230T|NFASC_ENST00000367170.4_Silent_p.T1258T|NFASC_ENST00000367171.4_Silent_p.T1322T|NFASC_ENST00000338515.6_Silent_p.T1247T|NFASC_ENST00000367169.4_Silent_p.T1061T|NFASC_ENST00000338586.6_Silent_p.T1214T|NFASC_ENST00000404907.1_Silent_p.T1164T|NFASC_ENST00000404076.1_Silent_p.T1147T|NFASC_ENST00000360049.4_Silent_p.T1159T|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000367172.4_Silent_p.T1337T			O94856	NFASC_HUMAN	neurofascin	1337					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CAGAGGCCACGTCACCTGTCA	0.562													G|||	18	0.00359425	0.0015	0.0043	5008	,	,		19173	0		0.005	False		,,,				2504	0.0082															0			1						G	,,,	5,4401	9.9+/-24.2	0,5,2198	163	142	149		3690,3537,3492,3477	-4.4	0.5	1	dbSNP_134	149	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	0,59,6444	AA,AG,GG		0.6279,0.1135,0.4536	,,,	1230/1241,1179/1190,1164/1175,1159/1170	204985634	59,12947	2203	4300	6503	203252257	SO:0001819	synonymous_variant	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3690G>A	1.37:g.204985634G>A			203252257	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	9	0.004120879120879121	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	9.318	1.057210	0.19907	0.001135	0.006279	ENSG00000163531	ENST00000367173;ENST00000425360	.	.	.	5.34	-4.44	0.03557	.	.	.	.	.	T	0.43942	0.1270	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49504	-0.8933	4	.	.	.	.	9.6176	0.39701	0.6087:0.1038:0.2874:0.0	.	.	.	.	H	1031;288	.	.	R	+	2	0	NFASC	203252257	0.001000	0.12720	0.522000	0.27862	0.993000	0.82548	-1.532000	0.02217	-0.900000	0.03896	-0.251000	0.11542	CGT		0.562	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204985634	G	A	204985634	2	1	109	1	0	0	0	0	0	0	0	1	10390	1132	40	1		1	NFASC	1	204985634	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	11835607	204985634	44264987	26	28592										
MAPKAPK2	9261	hgsc.bcm.edu	37	chr1	206902139	206902139	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgcacatcgtacggatcgtgGatgtgtacgagaatctgtac	12	9	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:206902139G>T	ENST00000367103.3	+	2	557	c.364G>T	c.(364-366)Gat>Tat	p.D122Y	MAPKAPK2_ENST00000294981.4_Missense_Mutation_p.D122Y	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			ACGGATCGTGGATGTGTACGA	0.612																																																0			1											52	58	56					1																	206902139		2203	4300	6503	204968762	SO:0001583	missense	9261			U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.364G>T	1.37:g.206902139G>T	ENSP00000356070:p.Asp122Tyr		204968762	Q5SY30|Q5SY41|Q8IYD6	Missense_Mutation	SNP	ENST00000367103.3	37	CCDS31001.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064922	0.93898	.	.	ENSG00000162889	ENST00000294981;ENST00000367103	T;T	0.55234	0.53;0.53	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.71451	0.3341	L	0.61387	1.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.73442	-0.3981	9	0.87932	D	0	-26.8459	18.1381	0.89627	0.0:0.0:1.0:0.0	.	122;122	P49137;P49137-2	MAPK2_HUMAN;.	Y	122	ENSP00000294981:D122Y;ENSP00000356070:D122Y	ENSP00000294981:D122Y	D	+	1	0	MAPKAPK2	204968762	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	9.869000	0.99810	2.611000	0.88343	0.655000	0.94253	GAT		0.612	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		T	206902139	G	T	206902139	3	4	109	1	0	0	0	0	1	0	0	0	9319	1174	41	2	370	2	MAPKAPK2	1	206902139	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	1916505	206902139	42348482	27	28593										
USH2A	7399	hgsc.bcm.edu	37	chr1	215802379	215802379	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttggtatcggctaaccccTgagaaggaagttgctgtgag	13	7	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:215802379T>C	ENST00000307340.3	-	71	15684		c.e71-2		USH2A_ENST00000366943.2_Splice_Site|SNORD116_ENST00000365628.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)						hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGCTAACCCCTGAGAAGGAAG	0.473										HNSCC(13;0.011)																																						0			1											76	80	79					1																	215802379		2203	4300	6503	213869002	SO:0001630	splice_region_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15298-2A>G	1.37:g.215802379T>C			213869002	Q5VVM9|Q6S362|Q9NS27	Splice_Site	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.006405	0.54361	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9132	0.79488	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	USH2A	213869002	1.000000	0.71417	0.994000	0.49952	0.524000	0.34500	7.162000	0.77515	2.154000	0.67381	0.482000	0.46254	.		0.473	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	Intron	C	215802379	T	C	215802379	5	2	109	1	0	0	0	0	0	0	1	0	17076	1594	55	4	320	4	USH2A	1	215802379	Splice_Site	SNP	T	TCGA-EF-5830-01A-01D-1657-10	8900240	215802379	33448242	28	28594										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223568115	223568115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctcatcaattaccaggcccGgaaggtcctcatggactgcc	9	15	3	0	rs560005249		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:223568115G>A	ENST00000366875.3	+	1	1401	c.1298G>A	c.(1297-1299)cGg>cAg	p.R433Q		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		433										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		TACCAGGCCCGGAAGGTCCTC	0.602													G|||	1	0.000199681	0	0	5008	,	,		18052	0		0	False		,,,				2504	0.001															0			1											39	34	36					1																	223568115		2203	4299	6502	221634738	SO:0001583	missense	164127																														ENST00000366875.3:c.1298G>A	1.37:g.223568115G>A	ENSP00000355840:p.Arg433Gln		221634738	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.724736	0.68959	.	.	ENSG00000178395	ENST00000366875	T	0.26518	1.73	5.59	3.69	0.42338	.	.	.	.	.	T	0.36580	0.0972	M	0.66939	2.045	0.32537	N	0.534194	D	0.71674	0.998	P	0.57371	0.819	T	0.47420	-0.9119	9	0.39692	T	0.17	.	4.2902	0.10874	0.0845:0.1579:0.5942:0.1634	.	433	Q8N715	CA065_HUMAN	Q	433	ENSP00000355840:R433Q	ENSP00000355840:R433Q	R	+	2	0	C1orf65	221634738	0.999000	0.42202	0.845000	0.33349	0.984000	0.73092	4.841000	0.62824	0.695000	0.31675	0.655000	0.94253	CGG		0.602	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			A	223568115	G	A	223568115	3	1	109	1	0	0	0	0	1	0	0	0	2061	1116	39	1	1300	1	C1orf65	1	223568115	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	7765736	223568115	25682506	29	28595										
TRIM11	81559	hgsc.bcm.edu	37	chr1	228588858	228588858	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aacggcgaagacgctcgaacTcacccagcacgttctgccgc	10	16	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:228588858T>C	ENST00000284551.6	-	3	820	c.542A>G	c.(541-543)gAg>gGg	p.E181G	TRIM11_ENST00000460651.1_5'UTR|TRIM11_ENST00000493030.2_Missense_Mutation_p.E56G|TRIM11_ENST00000366699.3_Missense_Mutation_p.E181G	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	181					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				ACGCTCGAACTCACCCAGCAC	0.662																																																0			1											33	34	33					1																	228588858		2203	4300	6503	226655481	SO:0001583	missense	81559			AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16281	protein-coding gene	gene with protein product		607868	"tripartite motif-containing 11"			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.542A>G	1.37:g.228588858T>C	ENSP00000284551:p.Glu181Gly		226655481	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	t	14.89	2.669573	0.47677	.	.	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.05025	3.51;3.51	4.86	4.86	0.63082	.	0.336267	0.21519	N	0.073242	T	0.20455	0.0492	M	0.70108	2.13	0.27717	N	0.94525	D;D;D	0.89917	0.998;1.0;0.983	D;D;P	0.74348	0.957;0.983;0.862	T	0.03259	-1.1055	10	0.52906	T	0.07	.	9.0393	0.36307	0.0:0.0:0.1859:0.8141	.	180;181;181	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	G	181	ENSP00000284551:E181G;ENSP00000355660:E181G	ENSP00000284551:E181G	E	-	2	0	TRIM11	226655481	1.000000	0.71417	0.980000	0.43619	0.062000	0.15995	6.626000	0.74253	1.958000	0.56883	0.255000	0.18592	GAG		0.662	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		C	228588858	T	C	228588858	3	2	109	1	0	0	0	0	1	0	0	0	16527	1551	54	4	880	4	TRIM11	1	228588858	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	5020743	228588858	20661763	30	28596										
COG2	22796	hgsc.bcm.edu	37	chr1	230827217	230827217	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaacaagccagaaaaaccacTcccgccaaccccgtcggtcc	6	18	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:230827217T>C	ENST00000366669.4	+	17	2137	c.2022T>C	c.(2020-2022)acT>acC	p.T674T	COG2_ENST00000546013.1_Silent_p.T363T|COG2_ENST00000366668.3_Silent_p.T673T|COG2_ENST00000534989.1_Silent_p.T615T|COG2_ENST00000535166.1_Silent_p.T558T	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	674					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAAAAACCACTCCCGCCAACC	0.498																																																0			1											67	69	69					1																	230827217		2203	4300	6503	228893840	SO:0001819	synonymous_variant	22796			Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"Components of oligomeric golgi complex"	6546	protein-coding gene	gene with protein product		606974	"low density lipoprotein receptor defect C complementing"	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.2022T>C	1.37:g.230827217T>C			228893840	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																				0.498	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		C	230827217	T	C	230827217	2	2	109	1	0	0	0	0	0	0	0	1	3664	1538	54	4		4	COG2	1	230827217	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2238359	230827217	18423404	31	28597										
APOB	338	hgsc.bcm.edu	37	chr2	21233813	21233813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtttccaggtgcctgtctgcTcagctggagtaagcagggca	14	10	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:21233813T>C	ENST00000233242.1	-	26	6054	c.5927A>G	c.(5926-5928)gAg>gGg	p.E1976G		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1976					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCTGTCTGCTCAGCTGGAGT	0.448																																																0			2											147	137	140					2																	21233813		2203	4300	6503	21087318	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5927A>G	2.37:g.21233813T>C	ENSP00000233242:p.Glu1976Gly		21087318	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976297	0.53720	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01279	5.06	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000023	T	0.08846	0.0219	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.00800	-1.1561	10	0.72032	D	0.01	.	15.5233	0.75881	0.0:0.0:0.0:1.0	.	1976	P04114	APOB_HUMAN	G	1976	ENSP00000233242:E1976G	ENSP00000233242:E1976G	E	-	2	0	APOB	21087318	0.996000	0.38824	1.000000	0.80357	0.914000	0.54420	4.726000	0.61986	2.065000	0.61736	0.454000	0.30748	GAG		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21233813	T	C	21233813	3	2	109	1	0	0	0	0	1	0	0	0	785	1551	54	4	7780	4	APOB	2	21233813	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10		21233813	221965560	32	28598										
MAPRE3	22924	hgsc.bcm.edu	37	chr2	27248575	27248575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgaaatggcggccatgagacTgatgcccaaattcttgaact	10	10	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:27248575T>C	ENST00000233121.2	+	5	792	c.594T>C	c.(592-594)acT>acC	p.T198T	MAPRE3_ENST00000405074.3_Silent_p.T183T|MAPRE3_ENST00000402218.1_Silent_p.T183T			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	198	EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCATGAGACTGATGCCCAAA	0.572																																																0			2											53	51	52					2																	27248575		2203	4300	6503	27102079	SO:0001819	synonymous_variant	22924			Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.594T>C	2.37:g.27248575T>C			27102079	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Silent	SNP	ENST00000233121.2	37	CCDS1731.1																																																																																				0.572	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326		C	27248575	T	C	27248575	2	2	109	1	0	0	0	0	0	0	0	1	9326	1567	55	4		4	MAPRE3	2	27248575	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6014762	27248575	215950798	33	28599										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29294302	29294302	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggtggccttctctgcctgActccaagtcccacccttcac	7	18	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:29294302A>G	ENST00000331664.5	-	1	2825	c.2826T>C	c.(2824-2826)agT>agC	p.S942S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	942					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCTCTGCCTGACTCCAAGTCC	0.657																																																0			2											28	32	30					2																	29294302		2049	4199	6248	29147806	SO:0001819	synonymous_variant	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2826T>C	2.37:g.29294302A>G			29147806		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																				0.657	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		G	29294302	A	G	29294302	2	3	109	1	0	0	0	0	0	0	0	1	2197	272	10	4		4	C2orf71	2	29294302	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2045727	29294302	213905071	34	28600										
SULT6B1	391365	hgsc.bcm.edu	37	chr2	37398687	37398687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaatttgctccccagttagaAagaatcccaagaactcagca	7	11	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:37398687A>G	ENST00000535679.1	-	6	670	c.671T>C	c.(670-672)tTt>tCt	p.F224S	SULT6B1_ENST00000407963.1_Missense_Mutation_p.F186S|SULT6B1_ENST00000260637.3_Missense_Mutation_p.F186S|SULT6B1_ENST00000379149.2_Missense_Mutation_p.F120S			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	224						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCCAGTTAGAAAGAATCCCAA	0.423																																																0			2											112	110	111					2																	37398687		2203	4300	6503	37252191	SO:0001583	missense	391365			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"Sulfotransferases, cytosolic"	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.671T>C	2.37:g.37398687A>G	ENSP00000444081:p.Phe224Ser		37252191	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		.	.	.	.	.	.	.	.	.	.	A	0.011	-1.727283	0.00694	.	.	ENSG00000138068	ENST00000535679;ENST00000379149;ENST00000260637;ENST00000407963	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	4.87	3.0	0.34707	Sulfotransferase domain (1);	0.462043	0.24518	N	0.037832	T	0.01189	0.0039	N	0.00010	-3.02	0.24009	N	0.996182	B	0.02656	0.0	B	0.01281	0.0	T	0.42682	-0.9437	10	0.02654	T	1	.	8.5685	0.33554	0.0883:0.1543:0.7573:0.0	.	224	Q6IMI4	ST6B1_HUMAN	S	224;120;186;186	ENSP00000444081:F224S;ENSP00000368444:F120S;ENSP00000260637:F186S;ENSP00000384950:F186S	ENSP00000260637:F186S	F	-	2	0	SULT6B1	37252191	1.000000	0.71417	0.768000	0.31515	0.197000	0.23852	1.251000	0.32862	0.600000	0.29862	-0.462000	0.05337	TTT		0.423	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		G	37398687	A	G	37398687	3	3	109	1	0	0	0	0	1	0	0	0	15423	14	1	4	248	4	SULT6B1	2	37398687	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	8104385	37398687	205800686	35	28601										
MSH2	4436	hgsc.bcm.edu	37	chr2	47707837	47707837	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tccccaaatttcttataggtGtctgtgatcaaagttttggg	9	7	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:47707837G>T	ENST00000233146.2	+	15	2684	c.2461G>T	c.(2461-2463)Gtc>Ttc	p.V821F	MSH2_ENST00000406134.1_Missense_Mutation_p.V821F|MSH2_ENST00000543555.1_Missense_Mutation_p.V755F	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	821					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTTATAGGTGTCTGTGATCA	0.398			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	2											77	74	75					2																	47707837		2203	4300	6503	47561341	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.2461G>T	2.37:g.47707837G>T	ENSP00000233146:p.Val821Phe		47561341	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062062	0.76187	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000413880	D;D;D	0.86230	-2.09;-2.09;-2.09	5.62	4.75	0.60458	DNA mismatch repair protein MutS, C-terminal (2);	0.107611	0.64402	D	0.000006	D	0.92440	0.7600	M	0.71296	2.17	0.80722	D	1	D;D;D	0.89917	1.0;0.98;0.997	D;D;D	0.87578	0.998;0.929;0.985	D	0.92435	0.5957	10	0.49607	T	0.09	-4.0305	14.5562	0.68101	0.07:0.0:0.93:0.0	.	755;821;821	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	F	821;755;821;607	ENSP00000233146:V821F;ENSP00000442697:V755F;ENSP00000384199:V821F	ENSP00000233146:V821F	V	+	1	0	MSH2	47561341	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.075000	0.71261	1.394000	0.46624	0.563000	0.77884	GTC		0.398	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			T	47707837	G	T	47707837	3	4	109	1	0	0	0	0	1	0	0	0	9900	1377	48	2	2519	2	MSH2	2	47707837	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	10309150	47707837	195491536	36	28602										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74776631	74776631	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcctgacttccaccagccccTccgtcacgggcaggggtcgt	12	17	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:74776631T>C	ENST00000264094.3	-	4	628	c.557A>G	c.(556-558)gAg>gGg	p.E186G	LOXL3_ENST00000484369.1_5'UTR|LOXL3_ENST00000393937.2_Intron|LOXL3_ENST00000409549.1_Missense_Mutation_p.E186G|LOXL3_ENST00000409249.1_Missense_Mutation_p.E186G|DOK1_ENST00000409429.1_Intron|LOXL3_ENST00000409986.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	186	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CACCAGCCCCTCCGTCACGGG	0.662																																																0			2											34	30	31					2																	74776631		2203	4299	6502	74630139	SO:0001583	missense	84695			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.557A>G	2.37:g.74776631T>C	ENSP00000264094:p.Glu186Gly		74630139	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016823	0.93404	.	.	ENSG00000115318	ENST00000264094;ENST00000409249;ENST00000409549;ENST00000413469	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.26	5.26	0.73747	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	T	0.72153	0.3425	M	0.93283	3.4	0.80722	D	1	D;D	0.76494	0.973;0.999	P;D	0.87578	0.795;0.998	T	0.79928	-0.1596	10	0.87932	D	0	.	13.1704	0.59595	0.0:0.0:0.0:1.0	.	186;186	E7END4;P58215	.;LOXL3_HUMAN	G	186	ENSP00000264094:E186G;ENSP00000387103:E186G;ENSP00000386696:E186G;ENSP00000398260:E186G	ENSP00000264094:E186G	E	-	2	0	LOXL3	74630139	1.000000	0.71417	0.999000	0.59377	0.737000	0.42083	7.834000	0.86773	2.201000	0.70794	0.460000	0.39030	GAG		0.662	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		C	74776631	T	C	74776631	3	2	109	1	0	0	0	0	1	0	0	0	8930	1551	54	4	1748	4	LOXL3	2	74776631	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	27068794	74776631	168422742	37	28603										
TEKT4	150483	hgsc.bcm.edu	37	chr2	95540621	95540621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	acctgcgggtgctggtggacTgcatccttcgcgacacctcc	12	15	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:95540621T>C	ENST00000295201.4	+	4	951	c.814T>C	c.(814-816)Tgc>Cgc	p.C272R	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	272			C -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.C272S(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTGGTGGACTGCATCCTTCG	0.701																																																1	Substitution - Missense(1)	breast(1)	2											26	31	29					2																	95540621		2198	4297	6495	94904348	SO:0001583	missense	150483			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.814T>C	2.37:g.95540621T>C	ENSP00000295201:p.Cys272Arg		94904348		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	4.426	0.078825	0.08533	.	.	ENSG00000163060	ENST00000295201	T	0.02236	4.38	2.18	-1.28	0.09318	.	0.853589	0.10277	N	0.694098	T	0.01222	0.0040	N	0.16201	0.385	0.44685	D	0.997676	B	0.16166	0.016	B	0.10450	0.005	T	0.49254	-0.8959	10	0.15499	T	0.54	-1.76	2.6206	0.04915	0.4084:0.0:0.2215:0.3701	.	272	Q8WW24	TEKT4_HUMAN	R	272	ENSP00000295201:C272R	ENSP00000295201:C272R	C	+	1	0	TEKT4	94904348	0.065000	0.20965	0.931000	0.37212	0.541000	0.35023	0.814000	0.27239	0.087000	0.17167	0.382000	0.24955	TGC		0.701	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		C	95540621	T	C	95540621	3	2	109	1	0	0	0	0	1	0	0	0	15794	1580	55	4	828	4	TEKT4	2	95540621	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	20763990	95540621	147658752	38	28604										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101874388	101874388	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaacatgggccagtctgtggAcattagtgggcttcagttag	13	7	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:101874388A>G	ENST00000289382.3	+	2	813	c.650A>G	c.(649-651)gAc>gGc	p.D217G		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	217					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											CAGTCTGTGGACATTAGTGGG	0.502																																																0			2											113	89	97					2																	101874388		2203	4300	6503	101240820	SO:0001583	missense	55571			AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.650A>G	2.37:g.101874388A>G	ENSP00000289382:p.Asp217Gly		101240820	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	37	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357882	0.82243	.	.	ENSG00000158435	ENST00000289382	T	0.38560	1.13	6.14	6.14	0.99180	.	0.156059	0.56097	D	0.000026	T	0.65112	0.2660	M	0.69823	2.125	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.66878	-0.5812	10	0.62326	D	0.03	-21.637	16.806	0.85666	1.0:0.0:0.0:0.0	.	217	Q9UKZ1	CB029_HUMAN	G	217	ENSP00000289382:D217G	ENSP00000289382:D217G	D	+	2	0	C2orf29	101240820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.030000	0.93725	2.367000	0.80283	0.529000	0.55759	GAC		0.502	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		G	101874388	A	G	101874388	3	3	109	1	0	0	0	0	1	0	0	0	2167	275	10	4	656	4	C2orf29	2	101874388	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6333767	101874388	141324985	39	28605										
C2orf40	84417	hgsc.bcm.edu	37	chr2	106690440	106690440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agcggcagctgtgggaccggActcggcccgaggtgcagcag	18	12	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:106690440A>G	ENST00000238044.3	+	3	335	c.226A>G	c.(226-228)Act>Gct	p.T76A	C2orf40_ENST00000409944.1_Missense_Mutation_p.T40A|C2orf40_ENST00000489174.1_3'UTR	NM_032411.2	NP_115787.1	Q9H1Z8	AUGN_HUMAN	chromosome 2 open reading frame 40	76					cellular senescence (GO:0090398)|cyclin catabolic process (GO:0008054)|G1 to G0 transition (GO:0070314)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				lung(7)|urinary_tract(1)	8						GTGGGACCGGACTCGGCCCGA	0.572																																																0			2											79	88	85					2																	106690440		2203	4300	6503	106056872	SO:0001583	missense	84417			BC021742	CCDS2072.1	2q12.2	2014-01-28			ENSG00000119147	ENSG00000119147			24642	protein-coding gene	gene with protein product	"esophageal cancer related gene 4 protein"	611752				12800218	Standard	NM_032411		Approved	ECRG4, augurin	uc010fjf.3	Q9H1Z8	OTTHUMG00000130921	ENST00000238044.3:c.226A>G	2.37:g.106690440A>G	ENSP00000238044:p.Thr76Ala		106056872	D3DVK2	Missense_Mutation	SNP	ENST00000238044.3	37	CCDS2072.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673505	0.47781	.	.	ENSG00000119147	ENST00000409944;ENST00000238044;ENST00000437659	T;T;T	0.44083	0.93;0.93;0.93	5.62	3.1	0.35709	.	0.317197	0.36519	N	0.002560	T	0.36853	0.0982	L	0.51422	1.61	0.09310	N	1	B	0.26195	0.144	B	0.26094	0.066	T	0.36841	-0.9731	10	0.62326	D	0.03	-15.1452	10.974	0.47454	0.7515:0.0:0.0:0.2485	.	76	Q9H1Z8	AUGN_HUMAN	A	40;76;78	ENSP00000386421:T40A;ENSP00000238044:T76A;ENSP00000388664:T78A	ENSP00000238044:T76A	T	+	1	0	C2orf40	106056872	0.002000	0.14202	0.414000	0.26521	0.879000	0.50718	1.356000	0.34079	0.932000	0.37266	0.533000	0.62120	ACT		0.572	C2orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253515.2	NM_032411		G	106690440	A	G	106690440	3	3	109	1	0	0	0	0	1	0	0	0	2171	275	10	4	236	4	C2orf40	2	106690440	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4816052	106690440	136508933	40	28606										
CHCHD5	84269	hgsc.bcm.edu	37	chr2	113343592	113343592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgctcgctactgtggccgggAgctggagcagtatggccagt	16	11	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:113343592A>G	ENST00000324913.5	+	2	251	c.44A>G	c.(43-45)gAg>gGg	p.E15G	CHCHD5_ENST00000409719.1_Missense_Mutation_p.E15G|CHCHD5_ENST00000489052.1_3'UTR	NM_032309.2	NP_115685.1	Q9BSY4	CHCH5_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 5	15						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(4)|urinary_tract(1)	7						TGTGGCCGGGAGCTGGAGCAG	0.602																																																0			2											50	54	53					2																	113343592		2203	4300	6503	113060063	SO:0001583	missense	84269			BC004498	CCDS2098.1	2q14.1	2012-10-15	2004-01-19	2004-01-21	ENSG00000125611	ENSG00000125611		"Coiled-coil-helix-coiled-coil-helix domain containing"	17840	protein-coding gene	gene with protein product	"mitochondrial intermembrane space cysteine motif protein of 14 kDa homolog (S. cerevisiae)"		"chromosome 2 open reading frame 9"	C2orf9		22842048	Standard	NM_032309		Approved	MGC11104, MIC14	uc002thz.1	Q9BSY4	OTTHUMG00000131312	ENST00000324913.5:c.44A>G	2.37:g.113343592A>G	ENSP00000325655:p.Glu15Gly		113060063	Q585T4|Q8N8C4	Missense_Mutation	SNP	ENST00000324913.5	37	CCDS2098.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.911595	0.92178	.	.	ENSG00000125611	ENST00000324913;ENST00000409719	T;T	0.16897	2.31;2.31	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000003	T	0.31606	0.0802	L	0.36672	1.1	0.53005	D	0.999969	D;D	0.89917	1.0;0.997	D;D	0.71184	0.972;0.916	T	0.02610	-1.1134	10	0.87932	D	0	-23.6804	14.1064	0.65093	1.0:0.0:0.0:0.0	.	15;15	Q8N8C4;Q9BSY4	.;CHCH5_HUMAN	G	15	ENSP00000325655:E15G;ENSP00000386994:E15G	ENSP00000325655:E15G	E	+	2	0	CHCHD5	113060063	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.360000	0.79487	2.285000	0.76669	0.528000	0.53228	GAG		0.602	CHCHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254081.2	NM_032309		G	113343592	A	G	113343592	3	3	109	1	0	0	0	0	1	0	0	0	3325	304	11	4	50	4	CHCHD5	2	113343592	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6653152	113343592	129855781	41	28607										
FOXD4L1	200350	hgsc.bcm.edu	37	chr2	114257866	114257866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caggggctgcgcagagtttgTccccgaccgcgtggagctac	15	13	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:114257866T>C	ENST00000306507.5	+	1	1206	c.1033T>C	c.(1033-1035)Tcc>Ccc	p.S345P		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	345					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GCAGAGTTTGTCCCCGACCGC	0.627																																																0			2											12	16	15					2																	114257866		2052	3973	6025	113974336	SO:0001583	missense	200350			AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.1033T>C	2.37:g.114257866T>C	ENSP00000302756:p.Ser345Pro		113974336	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	2.545	-0.305358	0.05495	.	.	ENSG00000184492	ENST00000306507	D	0.94687	-3.49	1.64	-0.538	0.11868	.	0.891937	0.09041	N	0.857344	D	0.84835	0.5560	N	0.11560	0.145	0.24829	N	0.992535	B	0.02656	0.0	B	0.04013	0.001	T	0.72465	-0.4285	10	0.33141	T	0.24	.	4.3512	0.11157	0.0:0.5798:0.0:0.4202	.	345	Q9NU39	FX4L1_HUMAN	P	345	ENSP00000302756:S345P	ENSP00000302756:S345P	S	+	1	0	FOXD4L1	113974336	0.000000	0.05858	0.038000	0.18304	0.355000	0.29361	-0.168000	0.09925	-0.158000	0.11040	0.155000	0.16302	TCC		0.627	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184		C	114257866	T	C	114257866	3	2	109	1	0	0	0	0	1	0	0	0	6019	1667	58	4	1035	4	FOXD4L1	2	114257866	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	914274	114257866	128941507	42	28608										
POTEF	728378	hgsc.bcm.edu	37	chr2	130869607	130869607	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	catttaaattcgcttttttcTtaattaaaaatttcacgact	2	7	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:130869607T>A	ENST00000409914.2	-	6	1277	c.878A>T	c.(877-879)aAg>aTg	p.K293M	POTEF_ENST00000360967.5_Missense_Mutation_p.K293M|POTEF_ENST00000357462.5_Missense_Mutation_p.K293M|AC018804.3_ENST00000433507.1_RNA|POTEF_ENST00000361163.4_Missense_Mutation_p.K303M|RNU6-1049P_ENST00000516414.1_RNA	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	293					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CGCTTTTTTCTTAATTAAAAA	0.338																																																0			2											38	48	45					2																	130869607		1508	3580	5088	130586077	SO:0001583	missense	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.878A>T	2.37:g.130869607T>A	ENSP00000386786:p.Lys293Met		130586077	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	9.788	1.177175	0.21787	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.2	1.16	-0.0886	0.13672	Ankyrin repeat-containing domain (4);	0.193103	0.24547	N	0.037595	T	0.68742	0.3034	M	0.70903	2.155	0.09310	N	1	D	0.71674	0.998	P	0.56612	0.802	T	0.60301	-0.7290	10	0.87932	D	0	.	3.0851	0.06275	0.0:0.2815:0.0:0.7185	.	293	A5A3E0	POTEF_HUMAN	M	293;293;293;303	ENSP00000350052:K293M;ENSP00000386786:K293M;ENSP00000354232:K293M;ENSP00000355012:K303M	ENSP00000350052:K293M	K	-	2	0	POTEF	130586077	0.005000	0.15991	0.001000	0.08648	0.033000	0.12548	0.863000	0.27913	-0.027000	0.13873	0.136000	0.15936	AAG		0.338	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		A	130869607	T	A	130869607	3	1	109	1	0	0	0	0	1	0	0	0	12296	1609	56	5	2397	5	POTEF	2	130869607	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	16611741	130869607	112329766	43	28609										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131519679	131519679	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaggaaagaccttcatcaagTccagcctgcaggtttcccac	9	13	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:131519679T>C	ENST00000423981.1	+	2	144	c.34T>C	c.(34-36)Tcc>Ccc	p.S12P	AMER3_ENST00000321420.4_Missense_Mutation_p.S12P	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	12					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CTTCATCAAGTCCAGCCTGCA	0.617																																																0			2											18	21	20					2																	131519679		2198	4295	6493	131236149	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.34T>C	2.37:g.131519679T>C	ENSP00000392700:p.Ser12Pro		131236149	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.255113	0.80135	.	.	ENSG00000178171	ENST00000321420;ENST00000431758;ENST00000458606;ENST00000423981	T;T	0.61510	0.1;0.1	5.28	5.28	0.74379	.	0.000000	0.53938	D	0.000059	T	0.65312	0.2679	L	0.34521	1.04	0.35748	D	0.819234	D	0.89917	1.0	D	0.83275	0.996	T	0.74503	-0.3644	10	0.87932	D	0	.	11.8905	0.52626	0.0:0.0:0.0:1.0	.	12	Q8N944	F123C_HUMAN	P	12	ENSP00000314914:S12P;ENSP00000392700:S12P	ENSP00000314914:S12P	S	+	1	0	FAM123C	131236149	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.219000	0.51200	2.133000	0.65898	0.459000	0.35465	TCC		0.617	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		C	131519679	T	C	131519679	3	2	109	1	0	0	0	0	1	0	0	0	5440	1667	58	4	36	4	FAM123C	2	131519679	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	650072	131519679	111679694	44	28610										
LCT	3938	hgsc.bcm.edu	37	chr2	136581530	136581530	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggtggaggggcagtctgggAgttttaggttgaagatgaaa	18	2	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:136581530A>G	ENST00000264162.2	-	4	858	c.848T>C	c.(847-849)cTc>cCc	p.L283P	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	283	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCAGTCTGGGAGTTTTAGGTT	0.468																																																0			2											120	113	115					2																	136581530		2203	4300	6503	136298000	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.848T>C	2.37:g.136581530A>G	ENSP00000264162:p.Leu283Pro		136298000	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	A	8.022	0.759852	0.15846	.	.	ENSG00000115850	ENST00000264162	T	0.32023	1.47	5.35	4.16	0.48862	.	0.368126	0.25558	N	0.029856	T	0.27798	0.0684	L	0.59436	1.845	0.50813	D	0.999894	B	0.02656	0.0	B	0.06405	0.002	T	0.06110	-1.0845	10	0.34782	T	0.22	-12.4698	8.1891	0.31357	0.9098:0.0:0.0902:0.0	.	283	P09848	LPH_HUMAN	P	283	ENSP00000264162:L283P	ENSP00000264162:L283P	L	-	2	0	LCT	136298000	0.995000	0.38212	0.978000	0.43139	0.044000	0.14063	3.432000	0.52824	1.007000	0.39238	0.454000	0.30748	CTC		0.468	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136581530	A	G	136581530	3	3	109	1	0	0	0	0	1	0	0	0	8715	304	11	4	4991	4	LCT	2	136581530	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	5061851	136581530	106617843	45	28611										
ITGB6	3694	hgsc.bcm.edu	37	chr2	161051922	161051922	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggtgttgttttcacaaaaGgggatacaggtttttccaca	10	7	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:161051922G>A	ENST00000283249.2	-	4	788	c.551C>T	c.(550-552)cCt>cTt	p.P184L	ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000409872.1_Missense_Mutation_p.P184L|ITGB6_ENST00000409967.2_Missense_Mutation_p.P184L|ITGB6_ENST00000428609.2_Missense_Mutation_p.P142L	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	184	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						TTTCACAAAAGGGGATACAGG	0.438																																																0			2											102	107	106					2																	161051922		2203	4300	6503	160760168	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.551C>T	2.37:g.161051922G>A	ENSP00000283249:p.Pro184Leu		160760168	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.080368	0.55753	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94	6.05	5.17	0.71159	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.051908	0.85682	N	0.000000	D	0.98409	0.9471	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99517	1.0957	10	0.87932	D	0	.	15.3846	0.74687	0.0665:0.0:0.9335:0.0	.	142;184	E9PEE8;P18564	.;ITB6_HUMAN	L	184;142;184;184	ENSP00000283249:P184L;ENSP00000408024:P142L;ENSP00000386828:P184L;ENSP00000386367:P184L	ENSP00000283249:P184L	P	-	2	0	ITGB6	160760168	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	7.908000	0.87438	1.577000	0.49804	-0.145000	0.13849	CCT		0.438	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		A	161051922	G	A	161051922	3	1	109	1	0	0	0	0	1	0	0	0	7920	1000	35	3	1863	3	ITGB6	2	161051922	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	24470392	161051922	82147451	46	28612										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166172175	166172175	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aatgacagagtccgaaaatcGgaatctgaagacagcataag	10	7	1	4	rs141269163		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:166172175G>A	ENST00000375437.2	+	11	1868	c.1578G>A	c.(1576-1578)tcG>tcA	p.S526S	SCN2A_ENST00000357398.3_Silent_p.S526S|SCN2A_ENST00000283256.6_Silent_p.S526S|SCN2A_ENST00000375427.2_Silent_p.S526S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	526					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCCGAAAATCGGAATCTGAAG	0.373																																																0			2						G	,,	1,4405	2.1+/-5.4	0,1,2202	59	61	60		1578,1578,1578	-8.2	0.2	2	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	526/2006,526/2006,526/2006	166172175	1,13005	2203	4300	6503	165880421	SO:0001819	synonymous_variant	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1578G>A	2.37:g.166172175G>A			165880421	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																				0.373	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		A	166172175	G	A	166172175	2	1	109	1	0	0	0	0	0	0	0	1	13953	1103	39	1		1	SCN2A	2	166172175	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	5120253	166172175	77027198	47	28613										
PPIG	9360	hgsc.bcm.edu	37	chr2	170489711	170489711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgcttcataccagagacgacTtttagttactagatctggca	8	9	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:170489711T>C	ENST00000260970.3	+	12	1191	c.971T>C	c.(970-972)cTt>cCt	p.L324P	PPIG_ENST00000448752.2_Missense_Mutation_p.L324P|PPIG_ENST00000409714.3_Missense_Mutation_p.L309P|PPIG_ENST00000462903.1_Missense_Mutation_p.L324P|PPIG_ENST00000482772.1_3'UTR	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	324					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CAGAGACGACTTTTAGTTACT	0.388																																																0			2											70	69	69					2																	170489711		2203	4300	6503	170197957	SO:0001583	missense	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.971T>C	2.37:g.170489711T>C	ENSP00000260970:p.Leu324Pro		170197957	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.128964	0.77549	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752	T;T;T;T;T	0.21031	2.46;2.03;2.46;2.15;2.46	5.38	5.38	0.77491	.	0.068748	0.64402	D	0.000015	T	0.30135	0.0755	N	0.17564	0.495	0.80722	D	1	P;P;D;D;P	0.76494	0.952;0.844;0.996;0.999;0.844	P;P;P;D;P	0.85130	0.641;0.543;0.853;0.997;0.543	T	0.11155	-1.0599	10	0.49607	T	0.09	-4.2688	13.6124	0.62088	0.0:0.0:0.0:1.0	.	317;309;309;324;324	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	P	324;324;317;309;324;324	ENSP00000260970:L324P;ENSP00000408683:L317P;ENSP00000386245:L309P;ENSP00000435987:L324P;ENSP00000407083:L324P	ENSP00000260970:L324P	L	+	2	0	PPIG	170197957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.042000	0.76565	2.013000	0.59113	0.460000	0.39030	CTT		0.388	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			C	170489711	T	C	170489711	3	2	109	1	0	0	0	0	1	0	0	0	12358	1609	56	4	1009	4	PPIG	2	170489711	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4317536	170489711	72709662	48	28614										
TTN	7273	hgsc.bcm.edu	37	chr2	179473354	179473354	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaatggatctttagccacaaGtggctttgaaacacatggtg	10	7	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179473354G>C	ENST00000591111.1	-	224	47685	c.47461C>G	c.(47461-47463)Ctt>Gtt	p.L15821V	TTN_ENST00000342175.6_Missense_Mutation_p.L8589V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L17462V|TTN_ENST00000342992.6_Missense_Mutation_p.L14894V|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L8522V|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L8397V|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15821	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAGCCACAAGTGGCTTTGAA	0.368																																																0			2											59	57	58					2																	179473354		1863	4102	5965	179181599	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.47461C>G	2.37:g.179473354G>C	ENSP00000465570:p.Leu15821Val		179181599	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	3.628	-0.076041	0.07184	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.72	-0.16	0.13375	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14227	0.0344	N	0.00554	-1.385	0.28813	N	0.898122	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.17899	-1.0354	9	0.87932	D	0	.	2.9286	0.05792	0.3673:0.1349:0.4039:0.0938	.	8397;8522;8589;15821	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	14894;8397;8589;8522;8397	ENSP00000343764:L14894V;ENSP00000434586:L8397V;ENSP00000340554:L8589V;ENSP00000352154:L8522V	ENSP00000340554:L8589V	L	-	1	0	TTN	179181599	0.340000	0.24792	0.184000	0.23157	0.950000	0.60333	-0.146000	0.10250	-0.339000	0.08401	-1.008000	0.02478	CTT		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179473354	G	C	179473354	3	2	109	1	0	0	0	0	1	0	0	0	16775	1029	36	5	55665	5	TTN	2	179473354	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	8983643	179473354	63726019	49	28615										
TTN	7273	hgsc.bcm.edu	37	chr2	179635207	179635207	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cataaacagactcatccacgAtggcacagtttttaatcctc	5	12	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179635207A>G	ENST00000591111.1	-	35	8536	c.8312T>C	c.(8311-8313)aTc>aCc	p.I2771T	TTN_ENST00000342175.6_Missense_Mutation_p.I2725T|TTN_ENST00000589042.1_Missense_Mutation_p.I2771T|TTN_ENST00000342992.6_Missense_Mutation_p.I2771T|TTN_ENST00000359218.5_Missense_Mutation_p.I2725T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I2725T|TTN_ENST00000360870.5_Missense_Mutation_p.I2771T|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13097			I -> M (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCATCCACGATGGCACAGTT	0.433																																																0			2											113	112	112					2																	179635207		2203	4300	6503	179343452	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8312T>C	2.37:g.179635207A>G	ENSP00000465570:p.Ile2771Thr		179343452	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	9.934	1.215677	0.22373	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	6.06	4.9	0.64082	Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55226	0.1907	N	0.04018	-0.295	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.0;0.0;0.0;0.0;0.002	T	0.52147	-0.8614	9	0.87932	D	0	.	12.3952	0.55380	0.9338:0.0:0.0662:0.0	.	2725;2725;2725;2771;2771	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	2771;2725;2725;2725;2725;2771	ENSP00000343764:I2771T;ENSP00000434586:I2725T;ENSP00000340554:I2725T;ENSP00000352154:I2725T;ENSP00000354117:I2771T	ENSP00000340554:I2725T	I	-	2	0	TTN	179343452	0.933000	0.31639	0.017000	0.16124	0.939000	0.58152	5.275000	0.65575	2.315000	0.78130	0.533000	0.62120	ATC		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179635207	A	G	179635207	3	3	109	1	0	0	0	0	1	0	0	0	16775	333	12	4	102988	4	TTN	2	179635207	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	161853	179635207	63564166	50	28616										
TTN	7273	hgsc.bcm.edu	37	chr2	179636187	179636187	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctgatctgtgagtggcttggAgatggccccacctttggaac	13	10	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179636187A>G	ENST00000591111.1	-	34	8091	c.7867T>C	c.(7867-7869)Tcc>Ccc	p.S2623P	TTN_ENST00000342175.6_Missense_Mutation_p.S2577P|TTN_ENST00000589042.1_Missense_Mutation_p.S2623P|TTN_ENST00000342992.6_Missense_Mutation_p.S2623P|TTN_ENST00000359218.5_Missense_Mutation_p.S2577P|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S2577P|TTN_ENST00000360870.5_Missense_Mutation_p.S2623P|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12948	Ig-like 15.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTGGCTTGGAGATGGCCCCA	0.423																																																0			2											99	87	91					2																	179636187		2203	4300	6503	179344432	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7867T>C	2.37:g.179636187A>G	ENSP00000465570:p.Ser2623Pro		179344432	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	14.81	2.646855	0.47258	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78672	0.4320	M	0.64997	1.995	0.26093	N	0.980923	D;D;D;D;D	0.76494	0.988;0.988;0.988;0.996;0.999	P;P;P;P;D	0.71656	0.856;0.856;0.856;0.898;0.974	T	0.72557	-0.4257	9	0.87932	D	0	.	11.8437	0.52371	0.8695:0.0:0.0:0.1305	.	2577;2577;2577;2623;2623	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	P	2623;2577;2577;2577;2577;2623	ENSP00000343764:S2623P;ENSP00000434586:S2577P;ENSP00000340554:S2577P;ENSP00000352154:S2577P;ENSP00000354117:S2623P	ENSP00000340554:S2577P	S	-	1	0	TTN	179344432	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.671000	0.68095	2.371000	0.80710	0.533000	0.62120	TCC		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179636187	A	G	179636187	3	3	109	1	0	0	0	0	1	0	0	0	16775	304	11	4	103437	4	TTN	2	179636187	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	980	179636187	63563186	51	28617										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197866500	197866500	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcacagtgcagtggagtaaaGggattaccgataaatttgcg	13	6	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:197866500G>T	ENST00000328737.2	-	22	2413	c.2337C>A	c.(2335-2337)ccC>ccA	p.P779P	ANKRD44_ENST00000337207.5_Silent_p.P779P|ANKRD44_ENST00000450567.1_Silent_p.P779P|ANKRD44_ENST00000282272.8_Silent_p.P796P			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	804										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTGGAGTAAAGGGATTACCGA	0.338																																																0			2											108	109	109					2																	197866500		2203	4300	6503	197574745	SO:0001819	synonymous_variant	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.2337C>A	2.37:g.197866500G>T			197574745	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																					0.338	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		T	197866500	G	T	197866500	2	4	109	1	0	0	0	0	0	0	0	1	672	987	35	2		2	ANKRD44	2	197866500	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	18230313	197866500	45332873	52	28618										
COQ10B	80219	hgsc.bcm.edu	37	chr2	198318329	198318329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gccttgagaagggtagtctcGggatgccgtccgaagtcggc	16	10	1	1	rs375808557		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:198318329G>A	ENST00000263960.2	+	1	183	c.45G>A	c.(43-45)tcG>tcA	p.S15S	COQ10B_ENST00000545340.1_5'Flank|COQ10B_ENST00000409010.1_5'Flank|COQ10B_ENST00000409398.1_Silent_p.S15S	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	15						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			GGGTAGTCTCGGGATGCCGTC	0.652																																																0			2											41	50	47					2																	198318329		2203	4300	6503	198026574	SO:0001819	synonymous_variant	80219			AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"coenzyme Q10 homolog B (yeast)"				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.45G>A	2.37:g.198318329G>A			198026574	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																				0.652	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147		A	198318329	G	A	198318329	2	1	109	1	0	0	0	0	0	0	0	1	3750	1103	39	1		1	COQ10B	2	198318329	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	451829	198318329	44881044	53	28619										
SATB2	23314	hgsc.bcm.edu	37	chr2	200213525	200213525	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gatatctggagagacttccaCggaagagttggttggctctg	14	7	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:200213525C>A	ENST00000417098.1	-	7	1888	c.1072G>T	c.(1072-1074)Gtg>Ttg	p.V358L	SATB2_ENST00000443023.1_Missense_Mutation_p.V299L|SATB2_ENST00000260926.5_Missense_Mutation_p.V358L|SATB2_ENST00000457245.1_Missense_Mutation_p.V358L|SATB2_ENST00000428695.1_Missense_Mutation_p.V240L	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	358					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.V358M(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAGACTTCCACGGAAGAGTTG	0.547																																					Colon(30;262 767 11040 24421 36230)											1	Substitution - Missense(1)	lung(1)	2											176	168	171					2																	200213525		2203	4300	6503	199921770	SO:0001583	missense	23314			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1072G>T	2.37:g.200213525C>A	ENSP00000401112:p.Val358Leu		199921770	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.631068	0.67015	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.43294	0.95;0.96;0.95;0.95;0.95	5.72	5.72	0.89469	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (1);	0.142736	0.46145	D	0.000313	T	0.32675	0.0837	N	0.08118	0	0.42555	D	0.993128	B;P;P	0.49447	0.301;0.924;0.802	B;P;P	0.46659	0.189;0.523;0.494	T	0.12243	-1.0555	10	0.26408	T	0.33	-13.7282	19.8861	0.96913	0.0:1.0:0.0:0.0	.	240;106;358	Q3ZB87;Q9H726;Q9UPW6	.;.;SATB2_HUMAN	L	358;299;358;240;358	ENSP00000401112:V358L;ENSP00000388764:V299L;ENSP00000260926:V358L;ENSP00000388581:V240L;ENSP00000405420:V358L	ENSP00000260926:V358L	V	-	1	0	SATB2	199921770	0.998000	0.40836	0.999000	0.59377	0.984000	0.73092	3.734000	0.55037	2.711000	0.92665	0.655000	0.94253	GTG		0.547	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		A	200213525	C	A	200213525	3	1	109	1	0	0	0	0	1	0	0	0	13891	536	19	2	1149	2	SATB2	2	200213525	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1895196	200213525	42985848	54	28620										
KCTD18	130535	hgsc.bcm.edu	37	chr2	201371657	201371657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccttgaagcggcacaaggacTcccgccgggctgtgtaaata	12	12	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:201371657T>C	ENST00000359878.3	-	2	593	c.83A>G	c.(82-84)gAg>gGg	p.E28G	KCTD18_ENST00000468413.1_5'UTR|KCTD18_ENST00000409157.1_Missense_Mutation_p.E28G	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	28	BTB.				protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GCACAAGGACTCCCGCCGGGC	0.512																																																0			2											69	77	74					2																	201371657		2203	4300	6503	201079902	SO:0001583	missense	130535			AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.83A>G	2.37:g.201371657T>C	ENSP00000352941:p.Glu28Gly		201079902	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529668	0.64860	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.42513	0.97;0.97	5.46	4.3	0.51218	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.285799	0.30519	N	0.009447	T	0.34454	0.0898	N	0.20685	0.6	0.33487	D	0.588168	B;P	0.40000	0.02;0.698	B;P	0.45276	0.034;0.475	T	0.48969	-0.8987	10	0.38643	T	0.18	-15.072	12.4828	0.55854	0.0:0.0:0.1398:0.8602	.	28;28	Q6PI47-2;Q6PI47	.;KCD18_HUMAN	G	28	ENSP00000352941:E28G;ENSP00000386751:E28G	ENSP00000352941:E28G	E	-	2	0	KCTD18	201079902	0.940000	0.31905	0.960000	0.40013	0.995000	0.86356	3.182000	0.50910	1.068000	0.40764	0.533000	0.62120	GAG		0.512	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		C	201371657	T	C	201371657	3	2	109	1	0	0	0	0	1	0	0	0	8126	1551	54	4	1221	4	KCTD18	2	201371657	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1158132	201371657	41827716	55	28621										
SPEG	10290	hgsc.bcm.edu	37	chr2	220337720	220337720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgggcagccacagggctgcGtaagggggtccagcacatct	16	11	1	0	rs376367804		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:220337720G>A	ENST00000312358.7	+	16	4181	c.4049G>A	c.(4048-4050)cGt>cAt	p.R1350H	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1350	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACAGGGCTGCGTAAGGGGGTC	0.657																																																0			2											41	49	46					2																	220337720		2083	4210	6293	220045964	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4049G>A	2.37:g.220337720G>A	ENSP00000311684:p.Arg1350His		220045964	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	9.020	0.984686	0.18889	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.54866	0.55	5.11	4.22	0.49857	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.232949	0.22510	N	0.059116	T	0.39835	0.1093	L	0.52905	1.665	0.80722	D	1	P	0.43024	0.798	B	0.35182	0.197	T	0.28364	-1.0046	10	0.38643	T	0.18	.	5.1143	0.14825	0.1883:0.1731:0.6386:0.0	.	1350	Q15772	SPEG_HUMAN	H	1350	ENSP00000311684:R1350H	ENSP00000265327:R1350H	R	+	2	0	SPEG	220045964	0.999000	0.42202	0.933000	0.37362	0.177000	0.22998	3.420000	0.52735	1.120000	0.41904	0.561000	0.74099	CGT		0.657	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220337720	G	A	220337720	3	1	109	1	0	0	0	0	1	0	0	0	15075	1145	40	1	4123	1	SPEG	2	220337720	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	18966063	220337720	22861653	56	28622										
NGEF	25791	hgsc.bcm.edu	37	chr2	233839512	233839512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctgggagtaactcaggtttcAccttggctggttcattatca	10	9	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:233839512A>G	ENST00000264051.3	-	2	367	c.89T>C	c.(88-90)gTg>gCg	p.V30A		NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	30	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V30A(1)		central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		CTCAGGTTTCACCTTGGCTGG	0.448																																																1	Substitution - Missense(1)	central_nervous_system(1)	2											225	204	211					2																	233839512		2203	4300	6503	233547756	SO:0001583	missense	25791			AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"Rho guanine nucleotide exchange factors"	7807	protein-coding gene	gene with protein product	"ephexin"	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.89T>C	2.37:g.233839512A>G	ENSP00000264051:p.Val30Ala		233547756	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	37	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.586841	0.28268	.	.	ENSG00000066248	ENST00000264051	T	0.71461	-0.57	5.05	-1.6	0.08426	.	0.993583	0.08151	N	0.990107	T	0.43853	0.1266	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	10	0.02654	T	1	-8.203	0.8436	0.01155	0.3356:0.2229:0.2868:0.1547	.	30	Q8N5V2	NGEF_HUMAN	A	30	ENSP00000264051:V30A	ENSP00000264051:V30A	V	-	2	0	NGEF	233547756	0.000000	0.05858	0.006000	0.13384	0.087000	0.18053	0.111000	0.15458	-0.138000	0.11434	0.533000	0.62120	GTG		0.448	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		G	233839512	A	G	233839512	3	3	109	1	0	0	0	0	1	0	0	0	10425	159	6	4	2210	4	NGEF	2	233839512	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	13501792	233839512	9359861	57	28623										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241494338	241494338	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcttcatgttcaacccaaacTccccctggtacatgcaacca	5	16	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:241494338T>C	ENST00000272972.3	-	2	228	c.14A>G	c.(13-15)gAg>gGg	p.E5G	ANKMY1_ENST00000373318.2_Missense_Mutation_p.E94G|ANKMY1_ENST00000536462.1_Missense_Mutation_p.E47G|ANKMY1_ENST00000405002.1_Missense_Mutation_p.E5G|ANKMY1_ENST00000401804.1_Missense_Mutation_p.E94G|ANKMY1_ENST00000405523.3_Missense_Mutation_p.E94G|ANKMY1_ENST00000403283.1_Missense_Mutation_p.E173G|ANKMY1_ENST00000391987.1_Missense_Mutation_p.E5G|ANKMY1_ENST00000373320.4_Missense_Mutation_p.E5G|ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000361678.4_Missense_Mutation_p.E94G|ANKMY1_ENST00000406958.1_Missense_Mutation_p.E94G	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	5							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		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)		CAACCCAAACTCCCCCTGGTA	0.592																																																0			2											179	157	165					2																	241494338		2203	4300	6503	241143011	SO:0001583	missense	51281			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.14A>G	2.37:g.241494338T>C	ENSP00000272972:p.Glu5Gly		241143011	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.337889	0.41398	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002;ENST00000539830;ENST00000441168;ENST00000418708;ENST00000418505	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61859	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.85;0.07;0.07;0.07;0.07;0.07;0.07	3.85	3.85	0.44370	.	0.775582	0.10788	N	0.634025	T	0.69513	0.3119	M	0.80982	2.52	0.31570	N	0.656429	B;P;P;P;P;B	0.43826	0.322;0.782;0.818;0.611;0.782;0.322	B;P;P;B;P;B	0.50314	0.156;0.503;0.637;0.422;0.503;0.156	T	0.72516	-0.4269	10	0.72032	D	0.01	-0.8773	11.2478	0.49006	0.0:0.0:0.0:1.0	.	5;5;94;94;94;5	Q4ZFV3;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	G	94;94;5;94;5;5;173;94;47;94;5;5;47;5;5	ENSP00000362415:E94G;ENSP00000384555:E94G;ENSP00000272972:E5G;ENSP00000355097:E94G;ENSP00000375847:E5G;ENSP00000362417:E5G;ENSP00000383968:E173G;ENSP00000385887:E94G;ENSP00000444707:E47G;ENSP00000385635:E94G;ENSP00000385145:E5G;ENSP00000405938:E47G;ENSP00000407015:E5G;ENSP00000412094:E5G	ENSP00000272972:E5G	E	-	2	0	ANKMY1	241143011	0.862000	0.29867	0.872000	0.34217	0.064000	0.16182	4.171000	0.58236	1.971000	0.57363	0.533000	0.62120	GAG		0.592	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		C	241494338	T	C	241494338	3	2	109	1	0	0	0	0	1	0	0	0	634	1551	54	4	2875	4	ANKMY1	2	241494338	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	7654826	241494338	1705035	58	28624										
VHL	7428	hgsc.bcm.edu	37	chr3	10188214	10188214	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ataggtcacctttggctcttCagagatgcagggacacacga	11	10	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188214C>A	ENST00000256474.2	+	2	1197	c.357C>A	c.(355-357)ttC>ttA	p.F119L	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	119	Involved in binding to CCT complex.		F -> L (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816}.|F -> S (in VHLD; type II). {ECO:0000269|PubMed:8825918}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.F119L(3)|p.?(1)|p.L118_G123>P(1)|p.W117fs*1(1)|p.F119fs*40(1)|p.F119fs*11(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGGCTCTTCAGAGATGCAG	0.502		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	8	Substitution - Missense(3)|Deletion - Frameshift(3)|Unknown(1)|Complex - deletion inframe(1)	kidney(8)	3	GRCh37	CM951287	VHL	M							178	165	170					3																	10188214		2203	4300	6503	10163214	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.357C>A	3.37:g.10188214C>A	ENSP00000256474:p.Phe119Leu		10163214	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988860	0.74589	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99677	-6.37	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	L	0.56340	1.77	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.98181	1.0457	10	0.66056	D	0.02	-6.0328	16.3181	0.82935	0.0:1.0:0.0:0.0	.	119	P40337	VHL_HUMAN	L	119;37	ENSP00000256474:F119L	ENSP00000256474:F119L	F	+	3	2	VHL	10163214	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	5.803000	0.69129	2.530000	0.85305	0.563000	0.77884	TTC		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10188214	C	A	10188214	3	1	109	1	0	0	0	0	1	0	0	0	17202	825	29	2	363	2	VHL	3	10188214	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		10188214	187834216	59	28625			1	29		4	3	105	N	T_C	5.161624e-07
VHL	7428	hgsc.bcm.edu	37	chr3	10188240	10188240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgcagggacacacgatgggcTtctggttaaccaaactgaat	11	9	1	1	rs5030649		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188240T>C	ENST00000256474.2	+	2	1223	c.383T>C	c.(382-384)cTt>cCt	p.L128P	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	128	Involved in binding to CCT complex.		L -> F (in VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L128H(4)|p.L128P(4)|p.L128R(2)|p.H125fs*27(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CACGATGGGCTTCTGGTTAAC	0.488		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	11	Substitution - Missense(10)|Deletion - Frameshift(1)	kidney(11)	3	GRCh37	CM040270	VHL	M							204	188	194					3																	10188240		2203	4300	6503	10163240	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.383T>C	3.37:g.10188240T>C	ENSP00000256474:p.Leu128Pro		10163240	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.515896	0.44763	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.070012	0.64402	D	0.000019	D	0.99729	0.9894	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.97047	0.9761	10	0.87932	D	0	-11.7092	13.0887	0.59156	0.0:0.0:0.0:1.0	.	128	P40337	VHL_HUMAN	P	128;46	ENSP00000256474:L128P	ENSP00000256474:L128P	L	+	2	0	VHL	10163240	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	5.965000	0.70387	2.047000	0.60756	0.460000	0.39030	CTT		0.488	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188240	T	C	10188240	3	2	109	1	0	0	0	0	1	0	0	0	17202	1609	56	4	389	4	VHL	3	10188240	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	26	10188240	187834190	60	28626			1	29		4	3	105	N	T_C	5.161624e-07
VHL	7428	hgsc.bcm.edu	37	chr3	10188309	10188309	+	Missense_Mutation	SNP	T	T	C													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	acagcctatttttgccaataTcacactgccaggtactgacg							TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188309T>C	ENST00000256474.2	+	2	1292	c.452T>C	c.(451-453)aTc>aCc	p.I151T	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	151	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.I151T(7)|p.I151S(6)|p.I151N(3)|p.I151>?(1)|p.?(1)|p.N150fs*7(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGCCAATATCACACTGCCA	0.398		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	22	Substitution - Missense(16)|Deletion - Frameshift(3)|Complex(1)|Deletion - In frame(1)|Unknown(1)	kidney(22)	3	GRCh37	CM994244	VHL	M							195	182	187					3																	10188309		2203	4300	6503	10163309	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.452T>C	3.37:g.10188309T>C	ENSP00000256474:p.Ile151Thr		10163309	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.915471	0.73098	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99876	-7.41	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99796	0.9913	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96623	0.9461	10	0.87932	D	0	0.0775	12.7607	0.57363	0.0:0.0:0.0:1.0	.	151	P40337	VHL_HUMAN	T	151;69	ENSP00000256474:I151T	ENSP00000256474:I151T	I	+	2	0	VHL	10163309	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.968000	0.70413	1.966000	0.57179	0.460000	0.39030	ATC		0.398	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188309	T	C	10188309	3	2	109	1	0	0	0	0	1	0	0	0	17202	1435	50	4	458	4	VHL	3	10188309	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	69	10188309	187834121	61	28627	51	2	1	29		4	3	105	N	T_C	5.161624e-07
VHL	7428	hgsc.bcm.edu	37	chr3	10188318	10188318	+	Missense_Mutation	SNP	C	C	T													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttgccaatatcacactgcCaggtactgacgttttacttt							TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188318C>T	ENST00000256474.2	+	2	1301	c.461C>T	c.(460-462)cCa>cTa	p.P154L	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	154	Involved in binding to CCT complex.		P -> L (in VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(2)|p.P154L(2)|p.P154fs*5(1)|p.L153fs*4(1)|p.?fs(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ATCACACTGCCAGGTACTGAC	0.403		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	7	Substitution - Missense(2)|Unknown(2)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	kidney(7)	3	GRCh37	CM941378	VHL	M							173	164	167					3																	10188318		2203	4300	6503	10163318	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.461C>T	3.37:g.10188318C>T	ENSP00000256474:p.Pro154Leu		10163318	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511774	0.85389	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99841	-7.09	4.79	4.79	0.61399	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.055625	0.64402	D	0.000001	D	0.99757	0.9902	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96868	0.9637	10	0.87932	D	0	-3.2366	15.7004	0.77538	0.0:1.0:0.0:0.0	.	154	P40337	VHL_HUMAN	L	154;72	ENSP00000256474:P154L	ENSP00000256474:P154L	P	+	2	0	VHL	10163318	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.806000	0.69150	2.380000	0.81148	0.563000	0.77884	CCA		0.403	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		T	10188318	C	T	10188318	3	4	109	1	0	0	0	0	1	0	0	0	17202	594	21	3	467	3	VHL	3	10188318	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	9	10188318	187834112	62	28628	51	2	1	29		4	3	105	N	T_C	5.161624e-07
TSEN2	80746	hgsc.bcm.edu	37	chr3	12558136	12558136	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttcttggtctatgctctgggAtgtttaagtatttactatga	9	5	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:12558136A>G	ENST00000284995.6	+	7	1323	c.936A>G	c.(934-936)ggA>ggG	p.G312G	TSEN2_ENST00000314571.7_Silent_p.G286G|C3orf83_ENST00000567514.1_Intron|TSEN2_ENST00000454502.2_Silent_p.G253G|TSEN2_ENST00000444864.1_Silent_p.G286G|TSEN2_ENST00000415684.1_Silent_p.G286G|RNU6-377P_ENST00000515965.1_RNA|TSEN2_ENST00000383797.5_Intron|TSEN2_ENST00000402228.3_Silent_p.G312G	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	312					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						ATGCTCTGGGATGTTTAAGTA	0.328																																																0			3											158	133	141					3																	12558136		2203	4299	6502	12533136	SO:0001819	synonymous_variant	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"tRNA splicing endonuclease subunits"	28422	protein-coding gene	gene with protein product		608753	"tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)", "tRNA splicing endonuclease 2 homolog (S. cerevisiae)"			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.936A>G	3.37:g.12558136A>G			12533136	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Silent	SNP	ENST00000284995.6	37	CCDS2611.1																																																																																				0.328	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265		G	12558136	A	G	12558136	2	3	109	1	0	0	0	0	0	0	0	1	16652	320	12	4		4	TSEN2	3	12558136	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2369818	12558136	185464294	63	28629										
MLH1	4292	hgsc.bcm.edu	37	chr3	37053590	37053590	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctttggaaatgctgttagtcGgtatgtcgataacctatata	9	6	0	0	rs63751711|rs587779032|rs587779033|rs267607779		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:37053590G>A	ENST00000231790.2	+	8	893	c.677G>A	c.(676-678)cGa>cAa	p.R226Q	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000435176.1_Splice_Site_p.R128Q|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000536378.1_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	226			Missing (in HNPCC2).|R -> L (in HNPCC2). {ECO:0000269|PubMed:8566964}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						GCTGTTAGTCGGTATGTCGAT	0.348		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	1	Whole gene deletion(1)	ovary(1)	3	GRCh37	CM045463|CM082944|CS951471|CS961616	MLH1	M|S							111	101	105					3																	37053590		2203	4300	6503	37028594	SO:0001630	splice_region_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.677+1G>A	3.37:g.37053590G>A			37028594	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.267885|6.267885	0.97426|0.97426	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000456676|ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	.|D;D	.|0.90788	.|-2.73;-2.73	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93223|0.93223	0.7841|0.7841	L|L	0.49126|0.49126	1.545|1.545	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.67145	.|0.996;0.989;0.991	.|P;P;P	.|0.59643	.|0.861;0.832;0.832	D|D	0.93288|0.93288	0.6666|0.6666	5|10	.|0.62326	.|D	.|0.03	-5.9319|-5.9319	19.6609|19.6609	0.95871|0.95871	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|128;226;226	.|E9PCU2;Q53GX1;P40692	.|.;.;MLH1_HUMAN	K|Q	218|226;192;192;90;128	.|ENSP00000231790:R226Q;ENSP00000402564:R128Q	.|ENSP00000231790:R226Q	E|R	+|+	1|2	0|0	MLH1|MLH1	37028594|37028594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	9.270000|9.270000	0.95690|0.95690	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.348	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	Missense_Mutation	A	37053590	G	A	37053590	5	1	109	1	0	0	0	0	0	0	1	0	9647	1130	39	1	707	1	MLH1	3	37053590	Splice_Site	SNP	G	TCGA-EF-5830-01A-01D-1657-10	24495454	37053590	160968840	64	28630										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38104250	38104250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgtttttcctccaaagaagcCagcaccgataggagaattcc	8	11	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:38104250C>T	ENST00000308059.6	+	5	1073	c.1052C>T	c.(1051-1053)cCa>cTa	p.P351L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P351L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P351L					deleted in lung and esophageal cancer 1									p.P351R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCAAAGAAGCCAGCACCGATA	0.463																																																1	Substitution - Missense(1)	breast(1)	3											77	74	75					3																	38104250		1846	4093	5939	38079254	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1052C>T	3.37:g.38104250C>T	ENSP00000308597:p.Pro351Leu		38079254		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	6.499	0.460334	0.12342	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05649	3.42;3.41;3.65	4.67	3.8	0.43715	.	0.850025	0.10774	N	0.635668	T	0.07863	0.0197	L	0.56769	1.78	0.27107	N	0.962483	B;P;B;P	0.34864	0.344;0.473;0.335;0.473	B;B;B;B	0.31751	0.054;0.088;0.135;0.088	T	0.23190	-1.0195	10	0.26408	T	0.33	-3.0099	8.914	0.35570	0.0:0.8974:0.0:0.1026	.	351;351;351;351	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	351	ENSP00000308597:P351L;ENSP00000315914:P351L;ENSP00000410427:P351L	ENSP00000308597:P351L	P	+	2	0	DLEC1	38079254	0.071000	0.21146	0.175000	0.22980	0.200000	0.23975	0.735000	0.26115	1.324000	0.45282	-0.140000	0.14226	CCA		0.463	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38104250	C	T	38104250	3	4	109	1	0	0	0	0	1	0	0	0	4563	594	21	3	1070	3	DLEC1	3	38104250	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1050660	38104250	159918180	65	28631										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266135	41266135	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggtgccactaccacagctccTtctctgagtggtaaaggcaa	10	12	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:41266135T>C	ENST00000349496.5	+	3	412	c.132T>C	c.(130-132)ccT>ccC	p.P44P	CTNNB1_ENST00000405570.1_Silent_p.P44P|CTNNB1_ENST00000396185.3_Silent_p.P44P|CTNNB1_ENST00000396183.3_Silent_p.P44P|CTNNB1_ENST00000453024.1_Silent_p.P37P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	44					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_S45insAP(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S45del(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.P44del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCACAGCTCCTTCTCTGAGTG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	124	Deletion - In frame(98)|Complex - deletion inframe(18)|Unknown(7)|Insertion - In frame(1)	liver(88)|large_intestine(17)|stomach(7)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|skin(2)|kidney(2)|haematopoietic_and_lymphoid_tissue(1)	3											85	75	78					3																	41266135		2203	4300	6503	41241139	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.132T>C	3.37:g.41266135T>C			41241139	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266135	T	C	41266135	2	2	109	1	0	0	0	0	0	0	0	1	4022	1596	56	4		4	CTNNB1	3	41266135	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	3161885	41266135	156756295	66	28632										
BSN	8927	hgsc.bcm.edu	37	chr3	49698674	49698674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	accacacagagcacccttttTccagtccccgctgatagccg	7	17	0	2	rs146469841		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:49698674T>C	ENST00000296452.4	+	6	9510	c.9396T>C	c.(9394-9396)ttT>ttC	p.F3132F		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3132					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCACCCTTTTTCCAGTCCCCG	0.607																																																0			3											64	53	57					3																	49698674		2203	4300	6503	49673678	SO:0001819	synonymous_variant	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.9396T>C	3.37:g.49698674T>C			49673678	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																				0.607	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		C	49698674	T	C	49698674	2	2	109	1	0	0	0	0	0	0	0	1	1533	1780	62	4		4	BSN	3	49698674	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	8432539	49698674	148323756	67	28633										
TMEM115	11070	hgsc.bcm.edu	37	chr3	50396032	50396032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cactcgcaggaccacacagtCccccatggtttgcttgagtg	10	14	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:50396032C>T	ENST00000266025.3	-	1	1009	c.463G>A	c.(463-465)Gac>Aac	p.D155N	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	155					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ACCACACAGTCCCCCATGGTT	0.637																																																0			3											36	34	35					3																	50396032		2202	4300	6502	50371036	SO:0001583	missense	11070			BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"placental protein 6"	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.463G>A	3.37:g.50396032C>T	ENSP00000266025:p.Asp155Asn		50371036	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	37	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708013	0.96821	.	.	ENSG00000126062	ENST00000266025	T	0.10860	2.83	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.33847	0.0877	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.01330	-1.1383	10	0.27785	T	0.31	-0.1149	18.3837	0.90459	0.0:1.0:0.0:0.0	.	155	Q12893	TM115_HUMAN	N	155	ENSP00000266025:D155N	ENSP00000266025:D155N	D	-	1	0	TMEM115	50371036	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.708000	0.84633	2.622000	0.88805	0.563000	0.77884	GAC		0.637	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024		T	50396032	C	T	50396032	3	4	109	1	0	0	0	0	1	0	0	0	16068	855	30	3	600	3	TMEM115	3	50396032	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	697358	50396032	147626398	68	28634										
ABHD14B	84836	hgsc.bcm.edu	37	chr3	52004110	52004110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcacaaccggggggcccagcTccaaggcatccaccacagcc	10	18	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:52004110T>C	ENST00000483233.1	-	4	808	c.302A>G	c.(301-303)gAg>gGg	p.E101G	PCBP4_ENST00000355852.2_5'Flank|PCBP4_ENST00000395013.3_5'Flank|PCBP4_ENST00000428823.2_5'Flank|ABHD14B_ENST00000461108.1_Missense_Mutation_p.E101G|PCBP4_ENST00000461554.1_5'Flank|ABHD14B_ENST00000315877.10_Missense_Mutation_p.E99G|ABHD14B_ENST00000395008.2_Missense_Mutation_p.E101G|RP11-155D18.14_ENST00000489595.2_Intron|ABHD14B_ENST00000525795.1_Missense_Mutation_p.E101G|RP11-155D18.12_ENST00000488257.1_RNA|ABHD14B_ENST00000487005.1_5'UTR|ABHD14B_ENST00000361143.5_Missense_Mutation_p.E101G|PCBP4_ENST00000484633.1_5'Flank			Q96IU4	ABHEB_HUMAN	abhydrolase domain containing 14B	101					metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000548)|KIRC - Kidney renal clear cell carcinoma(197;0.00072)		GGGGCCCAGCTCCAAGGCATC	0.662																																																0			3											39	41	40					3																	52004110		2203	4300	6503	51979150	SO:0001583	missense	84836			AK075112	CCDS2842.1	3p21.2	2009-01-12			ENSG00000114779	ENSG00000114779		"Abhydrolase domain containing"	28235	protein-coding gene	gene with protein product							Standard	NM_032750		Approved	MGC15429, CIB	uc011bdy.2	Q96IU4	OTTHUMG00000157816	ENST00000483233.1:c.302A>G	3.37:g.52004110T>C	ENSP00000420065:p.Glu101Gly		51979150	Q86VK8|Q8N8W5	Missense_Mutation	SNP	ENST00000483233.1	37	CCDS2842.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307142	0.23821	.	.	ENSG00000114779	ENST00000483233;ENST00000315877;ENST00000395008;ENST00000361143;ENST00000439982;ENST00000461108;ENST00000525795	T;T;T;T;T;T	0.61392	2.1;2.1;2.1;2.1;0.11;2.1	5.58	1.82	0.25136	.	0.780131	0.12732	N	0.443770	T	0.19406	0.0466	N	0.00707	-1.245	0.09310	N	0.999995	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.30357	-0.9981	10	0.02654	T	1	-5.9318	7.7429	0.28851	0.0:0.0695:0.2631:0.6674	.	101;101	B4DQI4;Q96IU4	.;ABHEB_HUMAN	G	101;99;101;101;101;101;101	ENSP00000420065:E101G;ENSP00000318248:E99G;ENSP00000378455:E101G;ENSP00000354841:E101G;ENSP00000417564:E101G;ENSP00000433388:E101G	ENSP00000318248:E99G	E	-	2	0	ABHD14B	51979150	0.000000	0.05858	0.837000	0.33122	0.998000	0.95712	0.473000	0.22132	0.361000	0.24292	0.533000	0.62120	GAG		0.662	ABHD14B-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349673.1	NM_032750		C	52004110	T	C	52004110	3	2	109	1	0	0	0	0	1	0	0	0	80	1551	54	4	338	4	ABHD14B	3	52004110	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1608078	52004110	146018320	69	28635										
ACY1	95	hgsc.bcm.edu	37	chr3	52023006	52023006	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccacgatgaacggctgcatgAggctgtgttcctccgtgggg	15	11	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:52023006A>G	ENST00000404366.2	+	15	1288	c.1142A>G	c.(1141-1143)gAg>gGg	p.E381G	ACY1_ENST00000458031.2_Missense_Mutation_p.E471G|ACY1_ENST00000476854.1_Missense_Mutation_p.E316G|ACY1_ENST00000494103.1_Missense_Mutation_p.E309G|ACY1_ENST00000476351.1_Missense_Mutation_p.E346G|ABHD14A-ACY1_ENST00000463937.1_Missense_Mutation_p.E482G	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	381			E -> D (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CGGCTGCATGAGGCTGTGTTC	0.622																																																0			3											127	114	119					3																	52023006		2203	4300	6503	51998046	SO:0001583	missense	95			L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1142A>G	3.37:g.52023006A>G	ENSP00000384296:p.Glu381Gly		51998046	C9J6I6|C9J9D8|C9JWD4	Missense_Mutation	SNP	ENST00000404366.2	37	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.908681	0.92107	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;3.14;0.55	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.76849	0.4045	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79572	-0.1748	10	0.38643	T	0.18	-0.6713	15.3398	0.74287	1.0:0.0:0.0:0.0	.	471;381	B4DNW0;Q03154	.;ACY1_HUMAN	G	471;482;381;316;346;309;381	ENSP00000390557:E471G;ENSP00000420487:E482G;ENSP00000419262:E316G;ENSP00000417056:E346G;ENSP00000417618:E309G;ENSP00000384296:E381G	ENSP00000384296:E381G	E	+	2	0	ACY1;RP11-155D18.11	51998046	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	8.187000	0.89708	2.145000	0.66743	0.533000	0.62120	GAG		0.622	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666		G	52023006	A	G	52023006	3	3	109	1	0	0	0	0	1	0	0	0	226	304	11	4	1196	4	ACY1	3	52023006	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	18896	52023006	145999424	70	28636										
FLNB	2317	hgsc.bcm.edu	37	chr3	58135604	58135604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggcatatccttggcggtggAaggccccagcaaagtggaca	14	10	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:58135604A>G	ENST00000295956.4	+	37	6284	c.6119A>G	c.(6118-6120)gAa>gGa	p.E2040G	FLNB_ENST00000429972.2_Missense_Mutation_p.E2029G|FLNB_ENST00000348383.5_Missense_Mutation_p.E2040G|FLNB_ENST00000490882.1_Missense_Mutation_p.E2071G|FLNB_ENST00000419752.2_Missense_Mutation_p.E1860G|FLNB_ENST00000493452.1_Missense_Mutation_p.E1847G|FLNB_ENST00000357272.4_Missense_Mutation_p.E2040G|FLNB_ENST00000358537.3_Missense_Mutation_p.E2016G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2040	Interaction with the cytoplasmic tail of GP1BA.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TTGGCGGTGGAAGGCCCCAGC	0.567																																																0			3											121	109	113					3																	58135604		2203	4300	6503	58110644	SO:0001583	missense	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.6119A>G	3.37:g.58135604A>G	ENSP00000295956:p.Glu2040Gly		58110644	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	33	5.204497	0.95033	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82	6.08	6.08	0.98989	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.96662	3.86	0.80722	D	1	D;D;D;P;D;D	0.89917	0.997;0.957;1.0;0.78;1.0;1.0	D;P;D;P;D;D	0.87578	0.973;0.788;0.998;0.464;0.998;0.998	D	0.96689	0.9509	10	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	2016;2071;1847;1860;2029;2040	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	G	2040;2071;2016;2029;2040;2040;1847;1860	ENSP00000295956:E2040G;ENSP00000420213:E2071G;ENSP00000351339:E2016G;ENSP00000415599:E2029G;ENSP00000232447:E2040G;ENSP00000349819:E2040G;ENSP00000418510:E1847G;ENSP00000414532:E1860G	ENSP00000295956:E2040G	E	+	2	0	FLNB	58110644	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.233000	0.95337	2.333000	0.79357	0.533000	0.62120	GAA		0.567	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58135604	A	G	58135604	3	3	109	1	0	0	0	0	1	0	0	0	5953	246	9	4	6362	4	FLNB	3	58135604	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6112598	58135604	139886826	71	28637										
PTPRG	5793	hgsc.bcm.edu	37	chr3	62153747	62153747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cacagcagcgtctgcatgacAgggtggtgtccaagtccgcc	13	13	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:62153747A>G	ENST00000474889.1	+	8	1320	c.943A>G	c.(943-945)Agg>Ggg	p.R315G	PTPRG_ENST00000295874.10_Missense_Mutation_p.R315G	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	315	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCTGCATGACAGGGTGGTGTC	0.502																																																0			3											82	79	80					3																	62153747		2203	4300	6503	62128787	SO:0001583	missense	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.943A>G	3.37:g.62153747A>G	ENSP00000418112:p.Arg315Gly		62128787	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235482	0.39498	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.79749	-1.3;-1.3	5.2	4.01	0.46588	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.044132	0.85682	D	0.000000	D	0.90116	0.6912	M	0.89534	3.04	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.89080	0.3475	10	0.30854	T	0.27	.	12.3494	0.55141	0.8587:0.1413:0.0:0.0	.	315;315	P23470-2;P23470	.;PTPRG_HUMAN	G	315	ENSP00000418112:R315G;ENSP00000295874:R315G	ENSP00000295874:R315G	R	+	1	2	PTPRG	62128787	1.000000	0.71417	0.974000	0.42286	0.166000	0.22503	2.711000	0.47177	0.882000	0.36016	0.533000	0.62120	AGG		0.502	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		G	62153747	A	G	62153747	3	3	109	1	0	0	0	0	1	0	0	0	12839	179	7	4	973	4	PTPRG	3	62153747	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4018143	62153747	135868683	72	28638										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69244257	69244257	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggaggcttctcgcctatgttCaggggatactcctttggcat	12	10	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:69244257C>G	ENST00000398540.3	-	16	1487	c.1404G>C	c.(1402-1404)ctG>ctC	p.L468L	FRMD4B_ENST00000478263.1_Silent_p.L120L|FRMD4B_ENST00000542259.1_Silent_p.L414L	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	468					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CGCCTATGTTCAGGGGATACT	0.468																																																0			3											114	109	110					3																	69244257		1922	4127	6049	69326947	SO:0001819	synonymous_variant	23150			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1404G>C	3.37:g.69244257C>G			69326947	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																				0.468	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			G	69244257	C	G	69244257	2	3	109	1	0	0	0	0	0	0	0	1	6071	813	29	5		5	FRMD4B	3	69244257	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	7090510	69244257	128778173	73	28639										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89480460	89480460	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgtaaggtttctgatttcgGactttcgcgtgtcctggagg	14	7	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:89480460G>T	ENST00000336596.2	+	13	2522	c.2297G>T	c.(2296-2298)gGa>gTa	p.G766V	EPHA3_ENST00000494014.1_Missense_Mutation_p.G766V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	766	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> E (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.G766E(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCTGATTTCGGACTTTCGCGT	0.438										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	lung(1)	3											142	133	136					3																	89480460		2203	4300	6503	89563150	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2297G>T	3.37:g.89480460G>T	ENSP00000337451:p.Gly766Val		89563150	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650500	0.67472	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.92858	-3.12;-3.12	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98397	0.9467	H	0.99894	4.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99605	1.0979	9	.	.	.	.	19.3726	0.94495	0.0:0.0:1.0:0.0	.	766	P29320	EPHA3_HUMAN	V	766	ENSP00000337451:G766V;ENSP00000419190:G766V	.	G	+	2	0	EPHA3	89563150	1.000000	0.71417	1.000000	0.80357	0.245000	0.25701	9.813000	0.99286	2.648000	0.89879	0.585000	0.79938	GGA		0.438	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89480460	G	T	89480460	3	4	109	1	0	0	0	0	1	0	0	0	5181	1174	41	2	2373	2	EPHA3	3	89480460	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	20236203	89480460	108541970	74	28640										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108391419	108391419	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tatttcagatctcagtgggaAatggaaaaacataatctgga	9	5	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:108391419A>G	ENST00000361582.3	+	23	2735	c.2505A>G	c.(2503-2505)gaA>gaG	p.E835E	DZIP3_ENST00000463306.1_Silent_p.E835E	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	835					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						CTCAGTGGGAAATGGAAAAAC	0.373																																																0			3											100	96	97					3																	108391419		2203	4299	6502	109874109	SO:0001819	synonymous_variant	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2505A>G	3.37:g.108391419A>G			109874109	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Silent	SNP	ENST00000361582.3	37	CCDS2952.1																																																																																				0.373	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		G	108391419	A	G	108391419	2	3	109	1	0	0	0	0	0	0	0	1	4876	11	1	4		4	DZIP3	3	108391419	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	18910959	108391419	89631011	75	28641										
MYLK	4638	hgsc.bcm.edu	37	chr3	123333149	123333149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggaagtggcgggactcccTgattgactggtcatctttga	13	9	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:123333149T>C	ENST00000475616.1	-	31	5547	c.5548A>G	c.(5548-5550)Agg>Ggg	p.R1850G	MYLK_ENST00000418370.2_Missense_Mutation_p.R90G|MYLK_ENST00000360304.3_Missense_Mutation_p.R1850G|MYLK_ENST00000578202.1_Missense_Mutation_p.R89G|MYLK_ENST00000359169.1_Missense_Mutation_p.R1799G|MYLK-AS1_ENST00000463408.1_RNA|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000583087.1_Missense_Mutation_p.R90G|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000354792.5_Missense_Mutation_p.R650G|MYLK_ENST00000346322.5_Missense_Mutation_p.R1781G|MYLK_ENST00000360772.3_Missense_Mutation_p.R1799G			Q15746	MYLK_HUMAN	myosin light chain kinase	1850	Ig-like C2-type 9.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CGGGACTCCCTGATTGACTGG	0.473																																																0			3											104	103	103					3																	123333149		2203	4300	6503	124815839	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.5548A>G	3.37:g.123333149T>C	ENSP00000418335:p.Arg1850Gly		124815839	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640826	0.47153	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000418370;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-0.32	5.27	1.38	0.22167	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67126	0.2860	L	0.31664	0.95	0.35488	D	0.798739	P;D;P;P;P;B	0.54601	0.837;0.967;0.837;0.935;0.866;0.05	P;P;P;P;P;B	0.59115	0.637;0.852;0.637;0.755;0.752;0.008	T	0.72786	-0.4188	9	0.72032	D	0.01	.	12.0458	0.53479	0.0:0.0:0.4248:0.5752	.	1849;1730;1799;1781;1850;162	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746;Q05D81	.;.;.;.;MYLK_HUMAN;.	G	1799;1850;1799;90;1781;650;1850	ENSP00000354004:R1799G;ENSP00000353452:R1850G;ENSP00000352088:R1799G;ENSP00000428967:R90G;ENSP00000320622:R1781G;ENSP00000346846:R650G;ENSP00000418335:R1850G	ENSP00000320622:R1781G	R	-	1	2	MYLK	124815839	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.710000	0.37920	0.079000	0.16929	0.528000	0.53228	AGG		0.473	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		C	123333149	T	C	123333149	3	2	109	1	0	0	0	0	1	0	0	0	10086	1579	55	4	200	4	MYLK	3	123333149	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	14941730	123333149	74689281	76	28642										
ZNF148	7707	hgsc.bcm.edu	37	chr3	125032365	125032365	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agtactgaatcctgtagctcTccagacacagtagactggcc	9	12	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:125032365T>C	ENST00000360647.4	-	4	605	c.120A>G	c.(118-120)ggA>ggG	p.G40G	ZNF148_ENST00000485866.1_Silent_p.G40G|ZNF148_ENST00000484491.1_Silent_p.G40G|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000492394.1_Silent_p.G40G	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	40					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						CCTGTAGCTCTCCAGACACAG	0.453																																																0			3											193	173	179					3																	125032365		2203	4300	6503	126515055	SO:0001819	synonymous_variant	7707			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.120A>G	3.37:g.125032365T>C			126515055	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Silent	SNP	ENST00000360647.4	37	CCDS3031.1																																																																																				0.453	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		C	125032365	T	C	125032365	2	2	109	1	0	0	0	0	0	0	0	1	17773	1538	54	4		4	ZNF148	3	125032365	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1699216	125032365	72990065	77	28643										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126732873	126732873	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cacctaacagtactcctacgAggggaacgatgtcagcgacc	10	13	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:126732873A>G	ENST00000393409.2	+	10	2324	c.2324A>G	c.(2323-2325)gAg>gGg	p.E775G	PLXNA1_ENST00000251772.4_Missense_Mutation_p.E752G	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	775					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TACTCCTACGAGGGGAACGAT	0.607																																																0			3											143	143	143					3																	126732873		2203	4300	6503	128215563	SO:0001583	missense	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2324A>G	3.37:g.126732873A>G	ENSP00000377061:p.Glu775Gly		128215563		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	A	13.66	2.302485	0.40795	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.55760	0.5;0.5	2.87	2.87	0.33458	.	2.623400	0.01687	N	0.026449	T	0.64316	0.2587	M	0.82823	2.61	0.44098	D	0.996867	B	0.27932	0.194	B	0.32677	0.15	T	0.57820	-0.7745	10	0.72032	D	0.01	.	11.6038	0.51020	1.0:0.0:0.0:0.0	.	775	Q9UIW2	PLXA1_HUMAN	G	775;752	ENSP00000377061:E775G;ENSP00000251772:E752G	ENSP00000251772:E752G	E	+	2	0	PLXNA1	128215563	1.000000	0.71417	0.997000	0.53966	0.350000	0.29205	7.252000	0.78309	1.558000	0.49541	0.402000	0.26972	GAG		0.607	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		G	126732873	A	G	126732873	3	3	109	1	0	0	0	0	1	0	0	0	12150	304	11	4	2362	4	PLXNA1	3	126732873	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1700508	126732873	71289557	78	28644										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126752816	126752816	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgcggcggcagcggctgcggAgcaagctggagcaggtggtg	21	10	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:126752816A>G	ENST00000393409.2	+	31	5647	c.5647A>G	c.(5647-5649)Agc>Ggc	p.S1883G	PLXNA1_ENST00000251772.4_Missense_Mutation_p.S1860G|PLXNA1_ENST00000505278.1_3'UTR	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1883					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GCGGCTGCGGAGCAAGCTGGA	0.662																																																0			3											27	27	27					3																	126752816		2200	4296	6496	128235506	SO:0001583	missense	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.5647A>G	3.37:g.126752816A>G	ENSP00000377061:p.Ser1883Gly		128235506		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	A	11.77	1.738510	0.30774	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.09911	2.93;2.93	4.02	1.48	0.22813	.	0.085846	0.47852	N	0.000210	T	0.05823	0.0152	N	0.16903	0.455	0.28092	N	0.931742	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.24048	-1.0171	10	0.54805	T	0.06	.	5.4193	0.16392	0.7575:0.0:0.0884:0.1541	.	497;1883	Q6ZTY7;Q9UIW2	.;PLXA1_HUMAN	G	1883;1860	ENSP00000377061:S1883G;ENSP00000251772:S1860G	ENSP00000251772:S1860G	S	+	1	0	PLXNA1	128235506	0.918000	0.31147	0.775000	0.31657	0.947000	0.59692	1.211000	0.32382	0.114000	0.18032	0.260000	0.18958	AGC		0.662	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		G	126752816	A	G	126752816	3	3	109	1	0	0	0	0	1	0	0	0	12150	304	11	4	5769	4	PLXNA1	3	126752816	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	19943	126752816	71269614	79	28645										
ISY1	57461	hgsc.bcm.edu	37	chr3	128852986	128852986	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcctcttccttttctcctctTgccagccgagcctctctctc	4	19	5	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:128852986T>C	ENST00000393295.3	-	9	911	c.594A>G	c.(592-594)gcA>gcG	p.A198A	ISY1_ENST00000471497.1_Intron|ISY1-RAB43_ENST00000418265.1_Silent_p.A198A|ISY1_ENST00000273541.8_Silent_p.A220A|ISY1_ENST00000393292.3_Missense_Mutation_p.K200E	NM_001199469.1|NM_020701.3	NP_001186398.1|NP_065752.1	Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	198					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						TTTCTCCTCTTGCCAGCCGAG	0.507																																																0			3											102	106	105					3																	128852986		1971	4171	6142	130335676	SO:0001819	synonymous_variant	339122				CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682			29201	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 33"	612764				16103217	Standard	NM_020701		Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393295.3:c.594A>G	3.37:g.128852986T>C			130335676	Q96IL2|Q9BT05	Silent	SNP	ENST00000393295.3	37	CCDS43149.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742324	0.30865	.	.	ENSG00000240682	ENST00000393292	.	.	.	5.64	0.267	0.15622	.	.	.	.	.	T	0.09862	0.0242	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30966	-0.9960	5	0.07325	T	0.83	.	1.203	0.01889	0.1478:0.1656:0.1537:0.5329	.	.	.	.	E	200	.	ENSP00000376970:K200E	K	-	1	0	ISY1	130335676	0.469000	0.25846	0.994000	0.49952	0.983000	0.72400	-0.404000	0.07205	-0.174000	0.10743	-0.449000	0.05564	AAG		0.507	ISY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267856.1	NM_020701		C	128852986	T	C	128852986	2	2	109	1	0	0	0	0	0	0	0	1	7887	1799	63	4		4	ISY1	3	128852986	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2100170	128852986	69169444	80	28646										
NCK1	4690	hgsc.bcm.edu	37	chr3	136646963	136646963	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gattctaagtcctggtggcgAgttcgaaattccatgaataa	10	7	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:136646963A>G	ENST00000481752.1	+	2	284	c.120A>G	c.(118-120)cgA>cgG	p.R40R	NCK1_ENST00000288986.2_Silent_p.R40R|NCK1_ENST00000469404.1_5'Flank			P16333	NCK1_HUMAN	NCK adaptor protein 1	40	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						CCTGGTGGCGAGTTCGAAATT	0.388																																																0			3											113	105	108					3																	136646963		2203	4300	6503	138129653	SO:0001819	synonymous_variant	4690			X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"SH2 domain containing"	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.120A>G	3.37:g.136646963A>G			138129653	B7Z751|D3DNE3	Silent	SNP	ENST00000481752.1	37	CCDS3092.1	.	.	.	.	.	.	.	.	.	.	A	9.799	1.179994	0.21787	.	.	ENSG00000158092	ENST00000496489	.	.	.	5.98	3.64	0.41730	.	.	.	.	.	T	0.52565	0.1742	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48103	-0.9064	4	.	.	.	-6.6777	4.7045	0.12842	0.6758:0.162:0.1622:0.0	.	.	.	.	G	28	.	.	E	+	2	0	NCK1	138129653	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.129000	0.42055	1.082000	0.41137	-0.263000	0.10527	GAG		0.388	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153		G	136646963	A	G	136646963	2	3	109	1	0	0	0	0	0	0	0	1	10250	291	11	4		4	NCK1	3	136646963	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	7793977	136646963	61375467	81	28647										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281734	140281734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tccggcttcccttgaggcccGgcgtttccggattaagtgct	12	13	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:140281734G>A	ENST00000458420.3	+	14	2484	c.2294G>A	c.(2293-2295)cGg>cAg	p.R765Q		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	765			R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.R765Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CTTGAGGCCCGGCGTTTCCGG	0.572										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)	large_intestine(1)	3											54	52	53					3																	140281734		2203	4300	6503	141764424	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2294G>A	3.37:g.140281734G>A	ENSP00000402460:p.Arg765Gln		141764424	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226507	0.95173	.	.	ENSG00000158258	ENST00000458420	T	0.35236	1.32	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.63931	0.2553	M	0.85630	2.765	0.58432	D	0.999997	D	0.89917	1.0	D	0.79108	0.992	T	0.69194	-0.5209	9	.	.	.	-25.2099	15.766	0.78126	0.0:0.0:1.0:0.0	.	765	Q9H4D0	CSTN2_HUMAN	Q	765	ENSP00000402460:R765Q	.	R	+	2	0	CLSTN2	141764424	1.000000	0.71417	0.727000	0.30756	0.871000	0.50021	9.813000	0.99286	2.377000	0.81083	0.563000	0.77884	CGG		0.572	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140281734	G	A	140281734	3	1	109	1	0	0	0	0	1	0	0	0	3568	1116	39	1	2348	1	CLSTN2	3	140281734	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	3634771	140281734	57740696	82	28648										
ATR	545	hgsc.bcm.edu	37	chr3	142176491	142176491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcatcagcctcattgtaactTcacatgctcttcgaaaaaga	6	11	4	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:142176491T>C	ENST00000350721.4	-	45	7731	c.7610A>G	c.(7609-7611)gAa>gGa	p.E2537G	ATR_ENST00000383101.3_Missense_Mutation_p.E2473G	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2537	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		E -> Q (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATTGTAACTTCACATGCTCT	0.388								Other conserved DNA damage response genes																																								0			3											105	99	101					3																	142176491		2203	4300	6503	143659181	SO:0001583	missense	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7610A>G	3.37:g.142176491T>C	ENSP00000343741:p.Glu2537Gly		143659181	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.6|27.6	4.846962|4.846962	0.91277|0.91277	.|.	.|.	ENSG00000175054|ENSG00000175054	ENST00000350721;ENST00000383101|ENST00000513291	T;T|.	0.78003|.	-1.14;-1.14|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.87759|.	0.6258|.	H|H	0.96833|0.96833	3.89|3.89	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|.	0.91921|.	0.5547|.	10|.	0.87932|.	D|.	0|.	-20.4584|-20.4584	15.3539|15.3539	0.74412|0.74412	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2537|.	Q13535|.	ATR_HUMAN|.	G|W	2537;2473|383	ENSP00000343741:E2537G;ENSP00000372581:E2473G|.	ENSP00000343741:E2537G|.	E|X	-|-	2|3	0|0	ATR|ATR	143659181|143659181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.997000|7.997000	0.88414|0.88414	2.102000|2.102000	0.63906|0.63906	0.397000|0.397000	0.26171|0.26171	GAA|TGA		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142176491	T	C	142176491	3	2	109	1	0	0	0	0	1	0	0	0	1205	1783	62	4	336	4	ATR	3	142176491	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1894757	142176491	55845939	83	28649										
ATR	545	hgsc.bcm.edu	37	chr3	142204012	142204012	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaagaactatataccggatgAgatcaccttgcttttccatt	7	9	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:142204012A>T	ENST00000350721.4	-	36	6312	c.6191T>A	c.(6190-6192)cTc>cAc	p.L2064H	ATR_ENST00000383101.3_Missense_Mutation_p.L2000H	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2064	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATACCGGATGAGATCACCTTG	0.388								Other conserved DNA damage response genes																																								0			3											212	198	203					3																	142204012		2203	4300	6503	143686702	SO:0001583	missense	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6191T>A	3.37:g.142204012A>T	ENSP00000343741:p.Leu2064His		143686702	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.527922	0.64860	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.68479	-0.33;-0.33	5.2	5.2	0.72013	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.133808	0.51477	D	0.000097	T	0.70771	0.3262	L	0.56199	1.76	0.80722	D	1	P	0.49961	0.93	P	0.52159	0.691	T	0.68640	-0.5355	10	0.28530	T	0.3	-7.7811	15.343	0.74311	1.0:0.0:0.0:0.0	.	2064	Q13535	ATR_HUMAN	H	2064;2000	ENSP00000343741:L2064H;ENSP00000372581:L2000H	ENSP00000343741:L2064H	L	-	2	0	ATR	143686702	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.128000	0.94424	2.088000	0.63022	0.377000	0.23210	CTC		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142204012	A	T	142204012	3	4	109	1	0	0	0	0	1	0	0	0	1205	304	11	5	1791	5	ATR	3	142204012	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	27521	142204012	55818418	84	28650										
MED12L	116931	hgsc.bcm.edu	37	chr3	150883639	150883639	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atttctgcctataggggtgaCtattagtcgggttttgcaca	11	7	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:150883639C>A	ENST00000474524.1	+	10	1402	c.1364C>A	c.(1363-1365)aCt>aAt	p.T455N	MED12L_ENST00000273432.4_Missense_Mutation_p.T315N|MED12L_ENST00000422248.2_Missense_Mutation_p.T455N|MED12L_ENST00000309237.4_Missense_Mutation_p.T455N	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	455						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATAGGGGTGACTATTAGTCGG	0.378																																																0			3											157	150	152					3																	150883639		2203	4300	6503	152366329	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.1364C>A	3.37:g.150883639C>A	ENSP00000417235:p.Thr455Asn		152366329	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089802	0.94149	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.69	5.69	0.88448	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	M	0.64170	1.965	0.52501	D	0.999954	P;D;D;P	0.76494	0.936;0.999;0.997;0.873	P;D;P;P	0.69824	0.756;0.966;0.9;0.461	T	0.55464	-0.8137	10	0.87932	D	0	-22.2358	19.3996	0.94623	0.0:1.0:0.0:0.0	.	315;455;455;455	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	N	455;455;455;315	ENSP00000403308:T455N;ENSP00000310760:T455N;ENSP00000417235:T455N;ENSP00000273432:T315N	ENSP00000273432:T315N	T	+	2	0	MED12L	152366329	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.831000	0.75324	2.676000	0.91093	0.655000	0.94253	ACT		0.378	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	150883639	C	A	150883639	3	1	109	1	0	0	0	0	1	0	0	0	9459	565	20	2	1402	2	MED12L	3	150883639	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	8679627	150883639	47138791	85	28651										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157823550	157823550	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cggacgggagagcgccctccTccagctcctccgcctgctcc	11	20	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:157823550T>C	ENST00000425436.3	-	1	289	c.264A>G	c.(262-264)ggA>ggG	p.G88G	SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Silent_p.G88G|SHOX2_ENST00000441443.2_5'UTR|RSRC1_ENST00000480820.1_5'Flank|SHOX2_ENST00000490689.2_5'Flank|SHOX2_ENST00000483851.2_Silent_p.G88G	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	88					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AGCGCcctcctccagctcctc	0.751																																																0			3											5	8	7					3																	157823550		1797	3830	5627	159306244	SO:0001819	synonymous_variant	6474			AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.264A>G	3.37:g.157823550T>C			159306244	O60465|O60467|O60903	Silent	SNP	ENST00000425436.3	37	CCDS43164.1																																																																																				0.751	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			C	157823550	T	C	157823550	2	2	109	1	0	0	0	0	0	0	0	1	14326	1538	54	4		4	SHOX2	3	157823550	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6939911	157823550	40198880	86	28652										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178937020	178937020	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atccccgaaattctacccaaAttgcttctgtctgttaaatg	5	11	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:178937020A>G	ENST00000263967.3	+	11	1858	c.1701A>G	c.(1699-1701)aaA>aaG	p.K567K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	567	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTCTACCCAAATTGCTTCTGT	0.353		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											121	110	113					3																	178937020		1835	4079	5914	180419714	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1701A>G	3.37:g.178937020A>G			180419714	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178937020	A	G	178937020	2	3	109	1	0	0	0	0	0	0	0	1	11944	98	4	4		4	PIK3CA	3	178937020	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	21113470	178937020	19085410	87	28653										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178941879	178941879	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttaatcaggtacagatgaAgtttttagttgagcaaatga	9	3	1	4	rs181194055	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:178941879A>G	ENST00000263967.3	+	15	2355	c.2198A>G	c.(2197-2199)aAg>aGg	p.K733R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	733					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.K733R(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTACAGATGAAGTTTTTAGTT	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)			A|||	4	0.000798722	0	0	5008	,	,		17323	0.004		0	False		,,,				2504	0				Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	large_intestine(1)	3											131	117	121					3																	178941879		1817	4083	5900	180424573	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2198A>G	3.37:g.178941879A>G	ENSP00000263967:p.Lys733Arg		180424573	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	17.47	3.397526	0.62177	.	.	ENSG00000121879	ENST00000263967	T	0.81330	-1.48	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.111337	0.64402	D	0.000005	T	0.78091	0.4229	L	0.60455	1.87	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.72239	-0.4351	10	0.27082	T	0.32	-18.203	16.542	0.84395	1.0:0.0:0.0:0.0	.	733	P42336	PK3CA_HUMAN	R	733	ENSP00000263967:K733R	ENSP00000263967:K733R	K	+	2	0	PIK3CA	180424573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.890000	0.63178	2.304000	0.77564	0.528000	0.53228	AAG		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178941879	A	G	178941879	3	3	109	1	0	0	0	0	1	0	0	0	11944	72	3	4	2252	4	PIK3CA	3	178941879	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4859	178941879	19080551	88	28654										
UBXN7	26043	hgsc.bcm.edu	37	chr3	196088743	196088743	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tagcttgctctggaagagtgAtctgttccctttttccatct	8	10	3	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:196088743A>T	ENST00000296328.4	-	10	1354	c.1280T>A	c.(1279-1281)aTc>aAc	p.I427N	UBXN7_ENST00000535858.1_Missense_Mutation_p.I279N|UBXN7_ENST00000428095.1_Missense_Mutation_p.I265N	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	427	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TGGAAGAGTGATCTGTTCCCT	0.418																																																0			3											135	124	128					3																	196088743		1881	4109	5990	197573140	SO:0001583	missense	26043			AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.1280T>A	3.37:g.196088743A>T	ENSP00000296328:p.Ile427Asn		197573140	D3DXB3|Q6ZP77|Q86X20|Q8N327	Missense_Mutation	SNP	ENST00000296328.4	37	CCDS43191.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460848	0.84317	.	.	ENSG00000163960	ENST00000296328;ENST00000428095;ENST00000535858	.	.	.	5.19	5.19	0.71726	UBX (3);	0.000000	0.85682	D	0.000000	T	0.61726	0.2370	L	0.40543	1.245	0.80722	D	1	P	0.49559	0.925	P	0.53401	0.725	T	0.64525	-0.6387	9	0.56958	D	0.05	-9.1729	15.3445	0.74324	1.0:0.0:0.0:0.0	.	427	O94888	UBXN7_HUMAN	N	427;265;279	.	ENSP00000296328:I427N	I	-	2	0	UBXN7	197573140	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.561000	0.90715	2.096000	0.63516	0.533000	0.62120	ATC		0.418	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		T	196088743	A	T	196088743	3	4	109	1	0	0	0	0	1	0	0	0	16958	333	12	5	197	5	UBXN7	3	196088743	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	17146864	196088743	1933687	89	28655										
KIT	3815	hgsc.bcm.edu	37	chr4	55593601	55593601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaaacccatgtatgaagtacAgtggaaggttgttgaggaga	14	4	0	3	rs121913234		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593601A>G	ENST00000288135.5	+	11	1764	c.1667A>G	c.(1666-1668)cAg>cGg	p.Q556R		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	556			Missing (in GIST; somatic mutation). {ECO:0000269|PubMed:15824741, ECO:0000269|PubMed:9438854}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y553_K558>(8)|p.E554_K558del(8)|p.W557_K558del(8)|p.M552_W557del(8)|p.K550_K558del(7)|p.Q556_V560del(6)|p.Y553_Q556del(4)|p.Y553_K558del(4)|p.V555_K558del(3)|p.Y553_W557del(3)|p.Y553_T574>S(3)|p.P551_Q556del(3)|p.V555_I571del(3)|p.V555_V560del(3)|p.V555_P573del(3)|p.V555_V559del(3)|p.V555_Q556del(2)|p.W557_E561del(2)|p.Q556_L576del(2)|p.K550_V559del(2)|p.K550fs*6(2)|p.Q556_K558del(2)|p.V555_E562del(2)|p.Q556_V559del(2)|p.M552_Q556del(2)|p.V555_G565del(1)|p.M552_W557>R(1)|p.P551_K558del(1)|p.M552_E561>K(1)|p.E554_I571del(1)|p.Q556_V560>F(1)|p.V555_Y570del(1)|p.Q556_N566>SNNLQLY(1)|p.M552_T574>TESA(1)|p.Q556_D572>PS(1)|p.Q556_D572del(1)|p.Q556R(1)|p.V555_N566>D(1)|p.M552_Q556>(1)|p.V555_V560>V(1)|p.Q556_W557del(1)|p.M552_K558del(1)|p.Q556_E561del(1)|p.Q556_E561>HH(1)|p.Q556_K558>R(1)|p.K550_Q556del(1)|p.Q556_W557>R(1)|p.E554_E562del(1)|p.E554_N564del(1)|p.Q556_V560>TTF(1)|p.K550_W557del(1)|p.V555_I563del(1)|p.M552_D572del(1)|p.Y553_V559>E(1)|p.Q556_T574del(1)|p.P551_V559del>L(1)|p.K550_Q556>II(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.Y553_V559del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TATGAAGTACAGTGGAAGGTT	0.383		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	130	Deletion - In frame(101)|Complex - deletion inframe(26)|Deletion - Frameshift(2)|Substitution - Missense(1)	soft_tissue(127)|skin(2)|testis(1)	4											80	82	82					4																	55593601		2203	4300	6503	55288358	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1667A>G	4.37:g.55593601A>G	ENSP00000288135:p.Gln556Arg		55288358	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006138	0.54361	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.92965	-3.14;-3.14	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000015	D	0.91905	0.7437	L	0.31752	0.955	0.80722	D	1	P;D;D	0.60575	0.928;0.988;0.963	B;D;P	0.67103	0.411;0.949;0.861	D	0.88088	0.2811	10	0.06099	T	0.92	.	16.6003	0.84812	1.0:0.0:0.0:0.0	.	63;552;556	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	R	556;552	ENSP00000288135:Q556R;ENSP00000390987:Q552R	ENSP00000288135:Q556R	Q	+	2	0	KIT	55288358	1.000000	0.71417	0.999000	0.59377	0.884000	0.51177	6.200000	0.72118	2.319000	0.78375	0.533000	0.62120	CAG		0.383	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55593601	A	G	55593601	3	3	109	1	0	0	0	0	1	0	0	0	8350	188	7	4	1709	4	KIT	4	55593601	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10		55593601	135560675	90	28656			2	30		3	3	65	N	T_C_A	1.943346e-07
KIT	3815	hgsc.bcm.edu	37	chr4	55593632	55593632	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gttgaggagataaatggaaaCaattatgtttacatagaccc	9	5	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593632C>T	ENST00000288135.5	+	11	1795	c.1698C>T	c.(1696-1698)aaC>aaT	p.N566N		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	566					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V560_L576del(4)|p.N566N(4)|p.Y553_T574>S(3)|p.V555_I571del(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.W557_P573>S(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I563_D572del(1)|p.E562_V569>D(1)|p.E562_P573del(1)|p.N564_T574del(1)|p.E554_I571del(1)|p.K558_Q575del(1)|p.V555_Y570del(1)|p.M552_T574>TESA(1)|p.Q556_T574del(1)|p.Q556_D572>PS(1)|p.E561_P577del(1)|p.Q556_D572del(1)|p.N564_P573>T(1)|p.K558_L576>NV(1)|p.V559_P573>A(1)|p.V560_I571del(1)|p.W557_I571del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.K558_D572del(1)|p.Q556_D572>H(1)|p.K558_Y570>N(1)|p.N567_L576>E(1)|p.M552_D572del(1)|p.V559_I571del(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.N564_P573>TS(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TAAATGGAAACAATTATGTTT	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	57	Deletion - In frame(38)|Complex - deletion inframe(15)|Substitution - coding silent(4)	soft_tissue(52)|haematopoietic_and_lymphoid_tissue(4)|testis(1)	4											80	81	81					4																	55593632		2203	4300	6503	55288389	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1698C>T	4.37:g.55593632C>T			55288389	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55593632	C	T	55593632	2	4	109	1	0	0	0	0	0	0	0	1	8350	477	17	3		3	KIT	4	55593632	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	31	55593632	135560644	91	28657			2	30		3	3	65	N	T_C_A	1.943346e-07
KIT	3815	hgsc.bcm.edu	37	chr4	55593665	55593665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atagacccaacacaacttccTtatgatcacaaatgggagtt	6	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593665T>C	ENST00000288135.5	+	11	1828	c.1731T>C	c.(1729-1731)ccT>ccC	p.P577P		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	577					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N564_Y578del(2)|p.P577_D579del(1)|p.P577_Y578del(1)|p.E561_P577del(1)|p.Q575_P577>T(1)|p.N564_P577del(1)|p.I571_N587del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CACAACTTCCTTATGATCACA	0.418		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	8	Deletion - In frame(7)|Complex - deletion inframe(1)	soft_tissue(6)|thymus(1)|skin(1)	4											73	72	73					4																	55593665		2203	4300	6503	55288422	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1731T>C	4.37:g.55593665T>C			55288422	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.418	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55593665	T	C	55593665	2	2	109	1	0	0	0	0	0	0	0	1	8350	1596	56	4		4	KIT	4	55593665	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	33	55593665	135560611	92	28658			2	30		3	3	65	N	T_C_A	1.943346e-07
IGFBP7	3490	hgsc.bcm.edu	37	chr4	57898691	57898691	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgcatggcactcatattctcCagcatcttccttacttagag	6	12	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:57898691C>T	ENST00000295666.4	-	4	763	c.730G>A	c.(730-732)Gga>Aga	p.G244R	IGFBP7_ENST00000537922.1_Missense_Mutation_p.G244R|IGFBP7_ENST00000512512.1_5'UTR	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	244	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCATATTCTCCAGCATCTTCC	0.418																																																0			4											121	111	115					4																	57898691		2203	4300	6503	57593448	SO:0001583	missense	3490			S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"Immunoglobulin superfamily / I-set domain containing"	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.730G>A	4.37:g.57898691C>T	ENSP00000295666:p.Gly244Arg		57593448	B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Missense_Mutation	SNP	ENST00000295666.4	37	CCDS3512.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400640	0.83120	.	.	ENSG00000163453	ENST00000295666;ENST00000537922	T;T	0.81247	-1.47;-1.47	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94391	0.8196	H	0.98996	4.395	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96390	0.9288	10	0.87932	D	0	-8.058	18.043	0.89324	0.0:1.0:0.0:0.0	.	244;244	B4E1N2;Q16270	.;IBP7_HUMAN	R	244	ENSP00000295666:G244R;ENSP00000444146:G244R	ENSP00000295666:G244R	G	-	1	0	IGFBP7	57593448	1.000000	0.71417	0.998000	0.56505	0.766000	0.43426	6.968000	0.76086	2.689000	0.91719	0.655000	0.94253	GGA		0.418	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250693.1			T	57898691	C	T	57898691	3	4	109	1	0	0	0	0	1	0	0	0	7605	603	21	3	126	3	IGFBP7	4	57898691	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	2305026	57898691	133255585	93	28659										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66286178	66286178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccttttcaaaatacttgattTcatactctaggatgattcca	4	9	3	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:66286178T>C	ENST00000273854.3	-	6	2108	c.1508A>G	c.(1507-1509)gAa>gGa	p.E503G	EPHA5_ENST00000432638.2_Missense_Mutation_p.E339G|EPHA5_ENST00000511294.1_Missense_Mutation_p.E503G|EPHA5_ENST00000354839.4_Missense_Mutation_p.E503G	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	503	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATACTTGATTTCATACTCTAG	0.338										TSP Lung(17;0.13)																																						0			4											148	142	144					4																	66286178		2203	4300	6503	65968773	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1508A>G	4.37:g.66286178T>C	ENSP00000273854:p.Glu503Gly		65968773	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.348405	0.82132	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000024	D	0.85186	0.5639	H	0.98407	4.225	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.91635	0.999;0.986;0.999;0.999	D	0.91065	0.4888	10	0.87932	D	0	.	15.0155	0.71581	0.0:0.0:0.0:1.0	.	503;503;503;503	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	G	503;339;503;503	ENSP00000273854:E503G;ENSP00000389208:E339G;ENSP00000346899:E503G;ENSP00000427638:E503G	ENSP00000273854:E503G	E	-	2	0	EPHA5	65968773	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.005000	0.88553	1.957000	0.56846	0.383000	0.25322	GAA		0.338	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		C	66286178	T	C	66286178	3	2	109	1	0	0	0	0	1	0	0	0	5183	1783	62	4	1657	4	EPHA5	4	66286178	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	8387487	66286178	124868098	94	28660										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535013	88535013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaaaggcaacgaaggtaaagAggataaaggacaacatggaa	13	4	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:88535013A>G	ENST00000282478.7	+	4	1232	c.1199A>G	c.(1198-1200)gAg>gGg	p.E400G	DSPP_ENST00000399271.1_Missense_Mutation_p.E400G|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	400					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		GAAGGTAAAGAGGATAAAGGA	0.438																																																0			4											131	121	124					4																	88535013		1942	4139	6081	88754037	SO:0001583	missense	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1199A>G	4.37:g.88535013A>G	ENSP00000282478:p.Glu400Gly		88754037	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419733	0.25552	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90069	-2.61;-2.61	4.2	1.67	0.24075	.	0.811716	0.10029	N	0.725009	D	0.82318	0.5011	L	0.42245	1.32	0.09310	N	1	B	0.20052	0.041	B	0.16289	0.015	T	0.68116	-0.5494	10	0.33141	T	0.24	-3.9603	5.8433	0.18645	0.7724:0.0:0.2276:0.0	.	400	Q9NZW4	DSPP_HUMAN	G	400	ENSP00000382213:E400G;ENSP00000282478:E400G	ENSP00000282478:E400G	E	+	2	0	DSPP	88754037	0.000000	0.05858	0.004000	0.12327	0.019000	0.09904	0.055000	0.14229	0.652000	0.30806	-0.490000	0.04691	GAG		0.438	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88535013	A	G	88535013	3	3	109	1	0	0	0	0	1	0	0	0	4793	304	11	4	1213	4	DSPP	4	88535013	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	22248835	88535013	102619263	95	28661										
ANK2	287	hgsc.bcm.edu	37	chr4	114275325	114275325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagtatcaccatcaagtaaaActgagaaacactcacctgtg	6	11	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:114275325A>G	ENST00000357077.4	+	38	5604	c.5551A>G	c.(5551-5553)Act>Gct	p.T1851A	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.T1818A	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1851	Repeat-rich region.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATCAAGTAAAACTGAGAAACA	0.473																																																0			4											171	170	171					4																	114275325		2203	4300	6503	114494774	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.5551A>G	4.37:g.114275325A>G	ENSP00000349588:p.Thr1851Ala		114494774	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.658739	0.29515	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.68331	-0.31;-0.32	5.62	5.62	0.85841	.	0.147317	0.31859	N	0.006948	T	0.56529	0.1991	L	0.38175	1.15	0.80722	D	1	B;B	0.23185	0.022;0.081	B;B	0.24541	0.024;0.054	T	0.52335	-0.8589	9	.	.	.	.	13.7834	0.63094	1.0:0.0:0.0:0.0	.	1818;1851	Q01484;Q01484-4	ANK2_HUMAN;.	A	1851;1818	ENSP00000349588:T1851A;ENSP00000264366:T1818A	.	T	+	1	0	ANK2	114494774	0.857000	0.29778	0.407000	0.26434	0.907000	0.53573	1.721000	0.38032	2.144000	0.66660	0.533000	0.62120	ACT		0.473	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114275325	A	G	114275325	3	3	109	1	0	0	0	0	1	0	0	0	621	43	2	4	5766	4	ANK2	4	114275325	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	25740312	114275325	76878951	96	28662										
NDST3	9348	hgsc.bcm.edu	37	chr4	118975856	118975856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tatacatgacctggggcttcAtgatggaattcaaagggttc	11	7	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:118975856A>G	ENST00000296499.5	+	2	1194	c.791A>G	c.(790-792)cAt>cGt	p.H264R	NDST3_ENST00000433996.2_Missense_Mutation_p.H264R	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	264	Heparan sulfate N-deacetylase 3.		H -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CTGGGGCTTCATGATGGAATT	0.418																																																0			4											142	135	137					4																	118975856		2203	4299	6502	119195304	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.791A>G	4.37:g.118975856A>G	ENSP00000296499:p.His264Arg		119195304	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.646527	0.47258	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.44482	1.26;0.92	5.23	5.23	0.72850	.	0.217832	0.48286	D	0.000183	T	0.57975	0.2090	M	0.66939	2.045	0.50813	D	0.999897	B;P;P	0.40230	0.085;0.708;0.617	B;P;B	0.53518	0.091;0.728;0.23	T	0.58983	-0.7539	10	0.49607	T	0.09	.	15.1164	0.72407	1.0:0.0:0.0:0.0	.	264;264;264	B4DI67;O95803;O95803-2	.;NDST3_HUMAN;.	R	264	ENSP00000296499:H264R;ENSP00000396625:H264R	ENSP00000296499:H264R	H	+	2	0	NDST3	119195304	0.999000	0.42202	0.998000	0.56505	0.953000	0.61014	6.152000	0.71812	1.963000	0.57068	0.533000	0.62120	CAT		0.418	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		G	118975856	A	G	118975856	3	3	109	1	0	0	0	0	1	0	0	0	10288	217	8	4	793	4	NDST3	4	118975856	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4700531	118975856	72178420	97	28663										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125592728	125592728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcttctatctctaaatctgcTcccctagagacaagtaaatt	4	11	4	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:125592728T>C	ENST00000504087.1	-	4	2741	c.1704A>G	c.(1702-1704)ggA>ggG	p.G568G	ANKRD50_ENST00000515641.1_Silent_p.G389G	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	568										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CTAAATCTGCTCCCCTAGAGA	0.428																																																0			4											105	95	99					4																	125592728		2203	4300	6503	125812178	SO:0001819	synonymous_variant	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1704A>G	4.37:g.125592728T>C			125812178	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																				0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		C	125592728	T	C	125592728	2	2	109	1	0	0	0	0	0	0	0	1	677	1538	54	4		4	ANKRD50	4	125592728	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6616872	125592728	65561548	98	28664										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tttcatgaagatgcatacaaCgcacagtggaagtatgccca	9	9	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	114	Substitution - Missense(113)|Unknown(1)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	4											253	218	230					4																	153249384		2203	4300	6503	153468834	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His		153468834	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153249384	C	T	153249384	3	4	109	1	0	0	0	0	1	0	0	0	5788	536	19	1	745	1	FBXW7	4	153249384	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	27656656	153249384	37904892	99	28665										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249456	153249456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cattccacactttgagtgtcCgatctgtagatccactaatg	7	11	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:153249456C>A	ENST00000281708.4	-	9	2551	c.1322G>T	c.(1321-1323)cGg>cTg	p.R441L	FBXW7_ENST00000393956.3_Missense_Mutation_p.R265L|FBXW7_ENST00000263981.5_Missense_Mutation_p.R361L|FBXW7_ENST00000603841.1_Missense_Mutation_p.R441L|FBXW7_ENST00000296555.5_Missense_Mutation_p.R323L|FBXW7_ENST00000603548.1_Missense_Mutation_p.R441L	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	441					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R441L(2)|p.R441Q(2)|p.R202L(1)|p.?(1)|p.R361Q(1)|p.R323Q(1)|p.R361L(1)|p.R202Q(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TTTGAGTGTCCGATCTGTAGA	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	10	Substitution - Missense(9)|Unknown(1)	endometrium(5)|breast(4)|haematopoietic_and_lymphoid_tissue(1)	4											306	258	275					4																	153249456		2203	4300	6503	153468906	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1322G>T	4.37:g.153249456C>A	ENSP00000281708:p.Arg441Leu		153468906	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.157370	0.94686	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.65709	0.2717	M	0.67517	2.055	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.72982	0.972;0.979;0.974;0.974	T	0.65977	-0.6037	10	0.87932	D	0	-19.4947	20.2787	0.98501	0.0:1.0:0.0:0.0	.	265;441;323;361	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	L	441;323;361;265	ENSP00000281708:R441L;ENSP00000296555:R323L;ENSP00000263981:R361L;ENSP00000377528:R265L	ENSP00000263981:R361L	R	-	2	0	FBXW7	153468906	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	CGG		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153249456	C	A	153249456	3	1	109	1	0	0	0	0	1	0	0	0	5788	652	23	2	817	2	FBXW7	4	153249456	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	72	153249456	37904820	100	28666										
RXFP1	59350	hgsc.bcm.edu	37	chr4	159568118	159568118	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttactgttaacatttctgacAttggaaaaatacatctgcat	5	7	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:159568118A>G	ENST00000307765.5	+	16	1772	c.1521A>G	c.(1519-1521)acA>acG	p.T507T	RXFP1_ENST00000470033.1_Silent_p.T474T|RXFP1_ENST00000460056.2_Silent_p.T426T|RXFP1_ENST00000343542.5_Silent_p.T459T|RXFP1_ENST00000448688.2_Silent_p.T402T	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	507					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CATTTCTGACATTGGAAAAAT	0.388																																																0			4											127	117	120					4																	159568118		1881	4116	5997	159787568	SO:0001819	synonymous_variant	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1521A>G	4.37:g.159568118A>G			159787568	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Silent	SNP	ENST00000307765.5	37	CCDS43276.1																																																																																				0.388	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		G	159568118	A	G	159568118	2	3	109	1	0	0	0	0	0	0	0	1	13796	204	8	4		4	RXFP1	4	159568118	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6318662	159568118	31586158	101	28667										
NKD2	85409	hgsc.bcm.edu	37	chr5	1038205	1038205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agccttcagctactacctgcCggccgtcctgccgccccagg	10	19	1	0	rs182715653	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:1038205C>T	ENST00000296849.5	+	10	1302	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	NKD2_ENST00000382730.2_Intron|NKD2_ENST00000274150.4_3'UTR	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	358	Interaction with TGFA.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			TACTACCTGCCGGCCGTCCTG	0.706													C|||	6	0.00119808	0.0045	0	5008	,	,		11134	0		0	False		,,,				2504	0															0			5											7	8	8					5																	1038205		2062	4066	6128	1091205	SO:0001583	missense	85409			AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1073C>T	5.37:g.1038205C>T	ENSP00000296849:p.Pro358Leu		1091205	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	6.092	0.385173	0.11524	.	.	ENSG00000145506	ENST00000296849	T	0.49720	0.77	3.84	2.92	0.33932	.	0.234568	0.35585	N	0.003111	T	0.26195	0.0639	L	0.36672	1.1	0.80722	D	1	B	0.17465	0.022	B	0.09377	0.004	T	0.06516	-1.0822	10	0.35671	T	0.21	-9.349	8.2376	0.31636	0.2503:0.7497:0.0:0.0	.	358	Q969F2	NKD2_HUMAN	L	358	ENSP00000296849:P358L	ENSP00000296849:P358L	P	+	2	0	NKD2	1091205	0.016000	0.18221	0.032000	0.17829	0.466000	0.32739	0.563000	0.23547	0.545000	0.28902	0.305000	0.20034	CCG		0.706	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		T	1038205	C	T	1038205	3	4	109	1	0	0	0	0	1	0	0	0	10473	652	23	1	1111	1	NKD2	5	1038205	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		1038205	179877055	102	28668										
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937619	33937619	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccggacaagttgctgggccgCgacaggcagttctggctggg	17	11	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:33937619C>T	ENST00000330120.3	+	1	1129	c.774C>T	c.(772-774)cgC>cgT	p.R258R		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	258					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						TGCTGGGCCGCGACAGGCAGT	0.637																																																0			5											45	35	39					5																	33937619		2200	4299	6499	33973376	SO:0001819	synonymous_variant	51289			D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.774C>T	5.37:g.33937619C>T			33973376	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																				0.637	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		T	33937619	C	T	33937619	2	4	109	1	0	0	0	0	0	0	0	1	13798	755	27	1		1	RXFP3	5	33937619	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	32899414	33937619	146977641	103	28669										
UGT3A1	133688	hgsc.bcm.edu	37	chr5	35954453	35954453	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atgccaaggctgctggaaggCatagggcttgaggtgcgtcg	17	8	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:35954453C>T	ENST00000274278.3	-	7	1780	c.1423G>A	c.(1423-1425)Gcc>Acc	p.A475T	UGT3A1_ENST00000513233.1_5'Flank	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	475				A -> V (in Ref. 1; BAB71358). {ECO:0000305}.		integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCTGGAAGGCATAGGGCTTG	0.602																																																0			5											105	80	89					5																	35954453		2203	4300	6503	35990210	SO:0001583	missense	133688				CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"UDP glucuronosyltransferases"	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.1423G>A	5.37:g.35954453C>T	ENSP00000274278:p.Ala475Thr		35990210	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Missense_Mutation	SNP	ENST00000274278.3	37	CCDS3913.1	.	.	.	.	.	.	.	.	.	.	.	13.80	2.346564	0.41599	.	.	ENSG00000145626	ENST00000274278	T	0.67523	-0.27	3.6	1.77	0.24775	.	0.203527	0.30800	U	0.008845	T	0.69958	0.3169	M	0.85542	2.76	0.80722	D	1	B	0.31859	0.343	B	0.41666	0.363	T	0.67333	-0.5697	10	0.87932	D	0	.	4.6533	0.12605	0.1709:0.6287:0.0:0.2005	.	475	Q6NUS8	UD3A1_HUMAN	T	475	ENSP00000274278:A475T	ENSP00000274278:A475T	A	-	1	0	UGT3A1	35990210	0.006000	0.16342	0.882000	0.34594	0.637000	0.38172	0.853000	0.27777	0.292000	0.22492	0.411000	0.27672	GCC		0.602	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404		T	35954453	C	T	35954453	3	4	109	1	0	0	0	0	1	0	0	0	17003	710	25	3	152	3	UGT3A1	5	35954453	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	2016834	35954453	144960807	104	28670										
SLC1A3	6507	hgsc.bcm.edu	37	chr5	36680574	36680574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcgcgtcaccagattcgtgcTccccgtaggagccaccatta	10	15	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:36680574T>C	ENST00000265113.4	+	8	1648	c.1172T>C	c.(1171-1173)cTc>cCc	p.L391P	SLC1A3_ENST00000381918.3_Missense_Mutation_p.L391P|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	391					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGATTCGTGCTCCCCGTAGGA	0.507																																																0			5											105	92	97					5																	36680574		2203	4300	6503	36716331	SO:0001583	missense	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1172T>C	5.37:g.36680574T>C	ENSP00000265113:p.Leu391Pro		36716331	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242749	0.79912	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.64618	-0.11;-0.11	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.86268	0.5892	H	0.97240	3.965	0.80722	D	1	D;D	0.62365	0.959;0.991	P;D	0.69307	0.738;0.963	D	0.91154	0.4955	10	0.87932	D	0	-21.3719	16.1502	0.81611	0.0:0.0:0.0:1.0	.	391;391	Q4JCQ8;P43003	.;EAA1_HUMAN	P	391;339;391	ENSP00000265113:L391P;ENSP00000371343:L391P	ENSP00000265113:L391P	L	+	2	0	SLC1A3	36716331	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	8.033000	0.88852	2.224000	0.72417	0.533000	0.62120	CTC		0.507	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		C	36680574	T	C	36680574	3	2	109	1	0	0	0	0	1	0	0	0	14470	1551	54	4	1215	4	SLC1A3	5	36680574	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	726121	36680574	144234686	105	28671										
NNT	23530	hgsc.bcm.edu	37	chr5	43649358	43649358	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gggtatcataccgtctggggAgtgacccctgctctccactc	11	14	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:43649358A>G	ENST00000264663.5	+	11	1775	c.1554A>G	c.(1552-1554)ggA>ggG	p.G518G	NNT_ENST00000512996.2_Silent_p.G387G|NNT_ENST00000344920.4_Silent_p.G518G	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	518					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CCGTCTGGGGAGTGACCCCTG	0.498																																																0			5											296	279	284					5																	43649358		2203	4300	6503	43685115	SO:0001819	synonymous_variant	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.1554A>G	5.37:g.43649358A>G			43685115	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																				0.498	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		G	43649358	A	G	43649358	2	3	109	1	0	0	0	0	0	0	0	1	10541	291	11	4		4	NNT	5	43649358	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6968784	43649358	137265902	106	28672										
DIMT1L	27292	hgsc.bcm.edu	37	chr5	61694695	61694695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctactagccttgggtcaagtTcacaagcaacaacctaattt	6	11	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:61694695T>C	ENST00000199320.4	-	4	414	c.254A>G	c.(253-255)gAa>gGa	p.E85G	KIF2A_ENST00000509663.2_Intron|DIMT1_ENST00000506390.1_Missense_Mutation_p.E85G	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	85						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)										TGGGTCAAGTTCACAAGCAAC	0.299																																																0			5											50	50	50					5																	61694695		2203	4300	6503	61730452	SO:0001583	missense	27292			AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189			30217	protein-coding gene	gene with protein product		612499	"DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)"	DIMT1L		11124703	Standard	NM_014473		Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.254A>G	5.37:g.61694695T>C	ENSP00000199320:p.Glu85Gly		61730452	O76025|Q9BU77|Q9UES1	Missense_Mutation	SNP	ENST00000199320.4	37	CCDS3981.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.011245	0.75046	.	.	ENSG00000086189	ENST00000199320;ENST00000506390	T;T	0.54479	0.57;0.57	5.5	5.5	0.81552	.	0.090319	0.85682	D	0.000000	D	0.83285	0.5221	H	0.99582	4.64	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.89193	0.3552	10	0.87932	D	0	-20.5441	11.7321	0.51744	0.0:0.0:0.1471:0.8529	.	85	Q9UNQ2	DIM1_HUMAN	G	85	ENSP00000199320:E85G;ENSP00000421754:E85G	ENSP00000199320:E85G	E	-	2	0	DIMT1L	61730452	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.525000	0.81892	2.313000	0.78055	0.454000	0.30748	GAA		0.299	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253967.1	NM_014473		C	61694695	T	C	61694695	3	2	109	1	0	0	0	0	1	0	0	0	4534	1783	62	4	723	4	DIMT1L	5	61694695	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	18045337	61694695	119220565	107	28673										
POLK	51426	hgsc.bcm.edu	37	chr5	74880616	74880616	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aggaaaagttacagagaaaaTgttaaaggcccttggaatta	10	4	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:74880616T>C	ENST00000241436.4	+	9	1263	c.1091T>C	c.(1090-1092)aTg>aCg	p.M364T	POLK_ENST00000504026.1_Missense_Mutation_p.M364T|POLK_ENST00000352007.5_Intron|POLK_ENST00000508526.1_Intron|POLK_ENST00000515295.1_Missense_Mutation_p.M364T|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000380481.3_Missense_Mutation_p.M274T	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	364					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		ACAGAGAAAATGTTAAAGGCC	0.313								DNA polymerases (catalytic subunits)																																								0			5											99	101	100					5																	74880616		2203	4300	6503	74916372	SO:0001583	missense	51426			AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1091T>C	5.37:g.74880616T>C	ENSP00000241436:p.Met364Thr		74916372	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.407081	0.42715	.	.	ENSG00000122008	ENST00000241436;ENST00000515295;ENST00000504026;ENST00000380481	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46	5.4	5.4	0.78164	DNA polymerase type-Y, HhH motif (1);	0.035385	0.85682	D	0.000000	T	0.69691	0.3139	N	0.16656	0.425	0.80722	D	1	B;B;D	0.76494	0.037;0.036;0.999	B;B;D	0.73380	0.034;0.023;0.98	T	0.73560	-0.3944	10	0.51188	T	0.08	-17.9987	15.7002	0.77536	0.0:0.0:0.0:1.0	.	364;364;364	Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;POLK_HUMAN	T	364;364;364;274	ENSP00000241436:M364T;ENSP00000424174:M364T;ENSP00000425075:M364T;ENSP00000369848:M274T	ENSP00000241436:M364T	M	+	2	0	POLK	74916372	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.981000	0.88123	2.174000	0.68829	0.402000	0.26972	ATG		0.313	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74880616	T	C	74880616	3	2	109	1	0	0	0	0	1	0	0	0	12235	1464	51	4	1121	4	POLK	5	74880616	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	13185921	74880616	106034644	108	28674										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77523997	77523997	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcgctgaaaagtgcttatggAcaggagtgcaagatcctgct	12	8	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:77523997A>G	ENST00000255194.6	-	4	521	c.346T>C	c.(346-348)Tcc>Ccc	p.S116P	AP3B1_ENST00000519295.1_Missense_Mutation_p.S67P	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	116					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GTGCTTATGGACAGGAGTGCA	0.383									Hermansky-Pudlak syndrome																																							0			5											102	97	98					5																	77523997		2203	4300	6503	77559753	SO:0001583	missense	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.346T>C	5.37:g.77523997A>G	ENSP00000255194:p.Ser116Pro		77559753	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.008176	0.75046	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.66280	-0.2;-0.2	5.48	5.48	0.80851	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.053891	0.85682	N	0.000000	T	0.74604	0.3738	M	0.89478	3.035	0.80722	D	1	B	0.24675	0.109	B	0.37451	0.25	T	0.76664	-0.2876	10	0.87932	D	0	-2.6242	15.9032	0.79400	1.0:0.0:0.0:0.0	.	116	O00203	AP3B1_HUMAN	P	116;67;116	ENSP00000255194:S116P;ENSP00000430597:S67P	ENSP00000255194:S116P	S	-	1	0	AP3B1	77559753	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.287000	0.95975	2.211000	0.71520	0.472000	0.43445	TCC		0.383	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			G	77523997	A	G	77523997	3	3	109	1	0	0	0	0	1	0	0	0	744	275	10	4	3034	4	AP3B1	5	77523997	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2643381	77523997	103391263	109	28675										
CHD1	1105	hgsc.bcm.edu	37	chr5	98216997	98216997	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttacctggggctcttgttCttctccttcaggttccttaa	7	11	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:98216997C>T	ENST00000284049.3	-	20	3099	c.2950G>A	c.(2950-2952)Gaa>Aaa	p.E984K		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	984					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GGCTCTTGTTCTTCTCCTTCA	0.318																																																0			5											17	16	16					5																	98216997		2181	4277	6458	98244897	SO:0001583	missense	1105			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.2950G>A	5.37:g.98216997C>T	ENSP00000284049:p.Glu984Lys		98244897	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	33	5.205815	0.95033	.	.	ENSG00000153922	ENST00000284049	D	0.90133	-2.62	5.23	5.23	0.72850	.	0.000000	0.34245	U	0.004127	D	0.91153	0.7214	L	0.55743	1.74	0.80722	D	1	P	0.51449	0.945	P	0.47402	0.546	D	0.92132	0.5713	10	0.72032	D	0.01	.	19.1612	0.93533	0.0:1.0:0.0:0.0	.	984	O14646	CHD1_HUMAN	K	984	ENSP00000284049:E984K	ENSP00000284049:E984K	E	-	1	0	CHD1	98244897	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.818000	0.86416	2.600000	0.87896	0.585000	0.79938	GAA		0.318	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		T	98216997	C	T	98216997	3	4	109	1	0	0	0	0	1	0	0	0	3329	922	32	3	2246	3	CHD1	5	98216997	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	20693000	98216997	82698263	110	28676										
APC	324	hgsc.bcm.edu	37	chr5	112173849	112173849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgaaaaagatagaagtttggAgagagaacgcggaattggtc	14	3	0	5			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112173849A>G	ENST00000457016.1	+	16	2938	c.2558A>G	c.(2557-2559)gAg>gGg	p.E853G	APC_ENST00000257430.4_Missense_Mutation_p.E853G|APC_ENST00000508376.2_Missense_Mutation_p.E853G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	853	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAGTTTGGAGAGAGAACGC	0.448		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											66	67	66					5																	112173849		2202	4300	6502	112201748	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2558A>G	5.37:g.112173849A>G	ENSP00000413133:p.Glu853Gly		112201748	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778440	0.31502	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94330	-2.67;-3.4;-2.67;-2.67;-2.85	6.16	6.16	0.99307	.	0.073236	0.56097	D	0.000021	D	0.89234	0.6657	L	0.34521	1.04	0.36291	D	0.856434	B;B	0.23937	0.0;0.094	B;B	0.16722	0.001;0.016	D	0.87781	0.2612	10	0.33940	T	0.23	-17.3326	15.3771	0.74615	1.0:0.0:0.0:0.0	.	855;853	Q4LE70;P25054	.;APC_HUMAN	G	853;835;853;853;853	ENSP00000413133:E853G;ENSP00000423224:E835G;ENSP00000257430:E853G;ENSP00000427089:E853G;ENSP00000423828:E853G	ENSP00000257430:E853G	E	+	2	0	APC	112201748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.742000	0.74843	2.367000	0.80283	0.528000	0.53228	GAG		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173849	A	G	112173849	3	3	109	1	0	0	0	0	1	0	0	0	763	304	11	4	2616	4	APC	5	112173849	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	13956852	112173849	68741411	111	28677			3	31		4	4	1641	N	T_A	6.86602e-07
APC	324	hgsc.bcm.edu	37	chr5	112175148	112175148	+	Frame_Shift_Del	DEL	A	A	-													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tttgtcatcagctgaagatgAaataggatgtaatcagacga							TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175148delA	ENST00000457016.1	+	16	4237	c.3857delA	c.(3856-3858)gaafs	p.E1286fs	APC_ENST00000257430.4_Frame_Shift_Del_p.E1286fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1286fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1286	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.I1287fs*1(1)|p.K1192fs*3(1)|p.?(1)|p.E1286G(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCTGAAGATGAAATAGGATGT	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	ovary(1)|large_intestine(1)|soft_tissue(1)|skin(1)	5											55	57	56					5																	112175148		2202	4300	6502	112203047	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3857delA	5.37:g.112175148delA	ENSP00000413133:p.Glu1286fs		112203047	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175148	A	-	112175148	7	5	109	1	0	1	0	1	0	0	0	0	763	246	9	0	3915	0	APC	5	112175148	Frame_Shift_Del	DEL	A	TCGA-EF-5830-01A-01D-1657-10	1299	112175148	68740112	112	28678			3	31		4	4	1641	N	T_A	6.86602e-07
APC	324	hgsc.bcm.edu	37	chr5	112175215	112175215	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctgcaaatagcagaaataaaAgaaaagattggaactaggtc	9	5	0	3	rs121913224		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175215A>G	ENST00000457016.1	+	16	4304	c.3924A>G	c.(3922-3924)aaA>aaG	p.K1308K	APC_ENST00000257430.4_Silent_p.K1308K|APC_ENST00000508376.2_Silent_p.K1308K|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1308	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*6(50)|p.E1309fs*4(37)|p.I1307fs*6(12)|p.?(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.K1308fs*4(1)|p.I1307fs*13(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGAAATAAAAGAAAAGATTG	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	104	Deletion - Frameshift(53)|Insertion - Frameshift(50)|Unknown(1)	large_intestine(100)|stomach(2)|soft_tissue(1)|skin(1)	5	GRCh37	CD972006	APC	D							53	55	54					5																	112175215		2202	4300	6502	112203114	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3924A>G	5.37:g.112175215A>G			112203114	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175215	A	G	112175215	2	3	109	1	0	0	0	0	0	0	0	1	763	69	3	4		4	APC	5	112175215	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	67	112175215	68740045	113	28679			3	31		4	4	1641	N	T_A	6.86602e-07
APC	324	hgsc.bcm.edu	37	chr5	112175489	112175489	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttgatagttttgagagtcgtTcgattgccagctccgttcag	11	8	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175489T>C	ENST00000457016.1	+	16	4578	c.4198T>C	c.(4198-4200)Tcg>Ccg	p.S1400P	APC_ENST00000257430.4_Missense_Mutation_p.S1400P|APC_ENST00000508376.2_Missense_Mutation_p.S1400P|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1400	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1400fs*15(2)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)|p.S1400fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGAGAGTCGTTCGATTGCCAG	0.478		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											110	102	105					5																	112175489		2202	4300	6502	112203388	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4198T>C	5.37:g.112175489T>C	ENSP00000413133:p.Ser1400Pro		112203388	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.745490	0.69418	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91945	-2.94;-2.94;-2.94	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94997	0.8381	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.94352	0.7580	9	.	.	.	-9.695	16.4957	0.84242	0.0:0.0:0.0:1.0	.	1402;1400	Q4LE70;P25054	.;APC_HUMAN	P	1400	ENSP00000413133:S1400P;ENSP00000257430:S1400P;ENSP00000427089:S1400P	.	S	+	1	0	APC	112203388	1.000000	0.71417	0.735000	0.30896	0.777000	0.43975	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	TCG		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175489	T	C	112175489	3	2	109	1	0	0	0	0	1	0	0	0	763	1783	62	4	4256	4	APC	5	112175489	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	274	112175489	68739771	114	28680			3	31		4	4	1641	N	T_A	6.86602e-07
SNX2	6643	hgsc.bcm.edu	37	chr5	122154636	122154636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgaggagaagatagaccagtTacatcaagaacaagcttttg	10	6	1	5			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:122154636T>C	ENST00000379516.2	+	11	1238	c.1130T>C	c.(1129-1131)tTa>tCa	p.L377S	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Missense_Mutation_p.L260S	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	377					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.L377*(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		ATAGACCAGTTACATCAAGAA	0.388																																																1	Substitution - Nonsense(1)	kidney(1)	5											140	129	133					5																	122154636		2203	4300	6503	122182535	SO:0001583	missense	6643			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1130T>C	5.37:g.122154636T>C	ENSP00000368831:p.Leu377Ser		122182535	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Missense_Mutation	SNP	ENST00000379516.2	37	CCDS34217.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577589	0.86645	.	.	ENSG00000205302	ENST00000379516;ENST00000514949	T;T	0.32515	1.45;1.45	5.81	5.81	0.92471	Vps5 C-terminal (1);	0.076783	0.56097	D	0.000036	T	0.57359	0.2048	M	0.88377	2.95	0.80722	D	1	P	0.48764	0.915	P	0.55161	0.77	T	0.66232	-0.5975	10	0.87932	D	0	-14.176	16.1708	0.81812	0.0:0.0:0.0:1.0	.	377	O60749	SNX2_HUMAN	S	377;260	ENSP00000368831:L377S;ENSP00000421663:L260S	ENSP00000368831:L377S	L	+	2	0	SNX2	122182535	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.982000	0.88131	2.225000	0.72522	0.533000	0.62120	TTA		0.388	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		C	122154636	T	C	122154636	3	2	109	1	0	0	0	0	1	0	0	0	14928	1764	61	4	1172	4	SNX2	5	122154636	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	9979147	122154636	58760624	115	28681										
SMAD5	4090	hgsc.bcm.edu	37	chr5	135498971	135498971	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttcctcttagctgatacgccTcctcctgcctatatgccacc	5	17	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:135498971T>C	ENST00000545279.1	+	5	1026	c.666T>C	c.(664-666)ccT>ccC	p.P222P	SMAD5_ENST00000545620.1_Silent_p.P222P|SMAD5_ENST00000514641.2_3'UTR	NM_001001419.1|NM_005903.5	NP_001001419.1|NP_005894.3	Q99717	SMAD5_HUMAN	SMAD family member 5	222					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle contraction (GO:0060048)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|embryonic pattern specification (GO:0009880)|erythrocyte differentiation (GO:0030218)|germ cell development (GO:0007281)|intracellular signal transduction (GO:0035556)|Mullerian duct regression (GO:0001880)|osteoblast fate commitment (GO:0002051)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|large_intestine(4)|lung(3)	8			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGATACGCCTCCTCCTGCCT	0.343																																																0			5											106	101	102					5																	135498971		1937	4157	6094	135526870	SO:0001819	synonymous_variant	4090			U59913	CCDS75308.1	5q31	2008-02-05	2006-11-06	2004-05-26		ENSG00000113658		"SMADs"	6771	protein-coding gene	gene with protein product		603110	"MAD, mothers against decapentaplegic homolog 5 (Drosophila)", "SMAD, mothers against DPP homolog 5 (Drosophila)"	MADH5		8673135	Standard	NM_005903		Approved	Dwfc, JV5-1	uc003lbl.1	Q99717		ENST00000545279.1:c.666T>C	5.37:g.135498971T>C			135526870	O14688|Q15798|Q9UQA1	Silent	SNP	ENST00000545279.1	37		.	.	.	.	.	.	.	.	.	.	T	9.215	1.031997	0.19590	.	.	ENSG00000113658	ENST00000507637	.	.	.	6.04	4.7	0.59300	.	.	.	.	.	T	0.57154	0.2034	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55438	-0.8141	4	.	.	.	.	7.169	0.25708	0.1652:0.0804:0.0:0.7544	.	.	.	.	P	45	.	.	S	+	1	0	SMAD5	135526870	0.997000	0.39634	1.000000	0.80357	0.932000	0.56968	0.350000	0.20079	2.317000	0.78254	0.460000	0.39030	TCC		0.343	SMAD5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005903		C	135498971	T	C	135498971	2	2	109	1	0	0	0	0	0	0	0	1	14798	1538	54	4		4	SMAD5	5	135498971	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	13344335	135498971	45416289	116	28682										
SRA1	8637	hgsc.bcm.edu	37	chr5	139931709	139931709	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caggtggggacctgggagccTtacttgaaggaggtggaggc	19	7	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:139931709T>C	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Missense_Mutation_p.K83R	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGGAGCCTTACTTGAAGG	0.582																																																0			5											34	30	31					5																	139931709		2203	4300	6503	139911893	SO:0001628	intergenic_variant	58506			AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931709T>C			139911893		Missense_Mutation	SNP	ENST00000310331.2	37	CCDS4226.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.047069	0.36085	.	.	ENSG00000213523	ENST00000336283;ENST00000520427	T	0.45668	0.89	5.75	3.18	0.36537	.	1.236330	0.05768	U	0.606128	T	0.43478	0.1249	L	0.53249	1.67	0.25508	N	0.987487	B	0.30851	0.297	B	0.35413	0.202	T	0.38023	-0.9680	9	.	.	.	.	9.5417	0.39255	0.0:0.0:0.3455:0.6545	.	83	Q9HD15	SRA1_HUMAN	R	83;9	ENSP00000337513:K83R	.	K	-	2	0	SRA1	139911893	0.835000	0.29415	0.902000	0.35471	0.994000	0.84299	0.856000	0.27818	0.979000	0.38497	0.533000	0.62120	AAG		0.582	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732		C	139931709	T	C	139931709	1	2	109	0	1	0	0	0	0	0	0	0	15171	1609	56	4		4	SRA1	5	139931709	IGR	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4432738	139931709	40983551	117	28683										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794729	140794729	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccctctctccgccactgtcAcgctcaccgtggccgtggcc	9	21	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:140794729A>C	ENST00000398610.2	+	1	1987	c.1987A>C	c.(1987-1989)Acg>Ccg	p.T663P	PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	663	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCACTGTCACGCTCACCGT	0.657																																																0			5											34	44	41					5																	140794729		2167	4229	6396	140774913	SO:0001583	missense	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1987A>C	5.37:g.140794729A>C	ENSP00000381611:p.Thr663Pro		140774913	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	a	11.22	1.573219	0.28092	.	.	ENSG00000253846	ENST00000398610	T	0.55234	0.53	5.57	4.39	0.52855	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.71443	0.3340	M	0.82193	2.58	0.23893	N	0.996544	D;D	0.71674	0.976;0.998	D;D	0.76575	0.952;0.988	T	0.62115	-0.6922	9	0.87932	D	0	.	7.9393	0.29948	0.7885:0.1391:0.0724:0.0	.	663;663	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	P	663	ENSP00000381611:T663P	ENSP00000381611:T663P	T	+	1	0	PCDHGA10	140774913	0.002000	0.14202	0.905000	0.35620	0.005000	0.04900	1.895000	0.39778	0.927000	0.37143	-0.313000	0.08912	ACG		0.657	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		C	140794729	A	C	140794729	3	2	109	1	0	0	0	0	1	0	0	0	11582	159	6	4	1989	4	PCDHGA10	5	140794729	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	863020	140794729	40120531	118	28684										
YIPF5	81555	hgsc.bcm.edu	37	chr5	143545033	143545033	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcatcctcaaagttgtttccAtagaaaggctgaggtgaagc	10	8	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:143545033A>T	ENST00000274496.5	-	3	380	c.246T>A	c.(244-246)taT>taA	p.Y82*	YIPF5_ENST00000513112.1_Nonsense_Mutation_p.Y28*|YIPF5_ENST00000448443.2_Nonsense_Mutation_p.Y82*	NM_001271732.1|NM_030799.7	NP_001258661.1|NP_110426.4	Q969M3	YIPF5_HUMAN	Yip1 domain family, member 5	82	Interaction with Sec23.				protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum exit site (GO:0070971)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)				large_intestine(2)|lung(5)|ovary(1)|skin(1)	9		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGTTGTTTCCATAGAAAGGCT	0.428																																																0			5											192	169	177					5																	143545033		2203	4300	6503	143525226	SO:0001587	stop_gained	81555			AF318329	CCDS4279.1, CCDS64277.1	5q31.3	2009-01-12			ENSG00000145817	ENSG00000145817		"Yip1 domain family"	24877	protein-coding gene	gene with protein product		611483				12975309, 18718466	Standard	NM_001024947		Approved	SMAP-5, FinGER5	uc003lnl.5	Q969M3	OTTHUMG00000129679	ENST00000274496.5:c.246T>A	5.37:g.143545033A>T	ENSP00000274496:p.Tyr82*		143525226	D3DQF5|Q4VSN6|Q53EX4|Q8NHE5|Q9H338|Q9H3U4	Nonsense_Mutation	SNP	ENST00000274496.5	37	CCDS4279.1	.	.	.	.	.	.	.	.	.	.	A	36	5.704482	0.96812	.	.	ENSG00000145817	ENST00000274496;ENST00000377986;ENST00000448443;ENST00000513112;ENST00000519064;ENST00000522203;ENST00000536767	.	.	.	6.02	3.69	0.42338	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1914	9.7802	0.40643	0.8631:0.0:0.1369:0.0	.	.	.	.	X	82;82;82;28;28;28;82	.	ENSP00000274496:Y82X	Y	-	3	2	YIPF5	143525226	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.988000	0.40697	1.110000	0.41699	0.528000	0.53228	TAT		0.428	YIPF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251882.1	NM_030799		T	143545033	A	T	143545033	4	4	109	1	0	0	0	0	0	1	0	0	17521	224	8	5	543	5	YIPF5	5	143545033	Nonsense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2750304	143545033	37370227	119	28685										
GABRP	2568	hgsc.bcm.edu	37	chr5	170239185	170239185	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaaaccccagtaatgttgatCactattccaaactactgttt	4	10	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:170239185C>T	ENST00000518525.1	+	11	1710	c.1246C>T	c.(1246-1248)Cac>Tac	p.H416Y	GABRP_ENST00000519385.1_3'UTR|GABRP_ENST00000265294.4_Missense_Mutation_p.H416Y			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	416			H -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TAATGTTGATCACTATTCCAA	0.348																																																0			5											120	110	114					5																	170239185		2203	4300	6503	170171763	SO:0001583	missense	2568			U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4089	protein-coding gene	gene with protein product	"GABA(A) receptor, pi"	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1246C>T	5.37:g.170239185C>T	ENSP00000430100:p.His416Tyr		170171763	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549247	0.45383	.	.	ENSG00000094755	ENST00000518525;ENST00000265294	T;T	0.81415	-1.49;-1.49	5.74	4.87	0.63330	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.234387	0.41396	D	0.000893	T	0.66499	0.2795	N	0.08118	0	0.23063	N	0.998356	B	0.16166	0.016	B	0.12837	0.008	T	0.61686	-0.7012	10	0.87932	D	0	.	15.8208	0.78644	0.1372:0.8628:0.0:0.0	.	416	O00591	GBRP_HUMAN	Y	416	ENSP00000430100:H416Y;ENSP00000265294:H416Y	ENSP00000265294:H416Y	H	+	1	0	GABRP	170171763	0.179000	0.23135	0.996000	0.52242	0.874000	0.50279	1.600000	0.36762	1.402000	0.46780	0.655000	0.94253	CAC		0.348	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		T	170239185	C	T	170239185	3	4	109	1	0	0	0	0	1	0	0	0	6193	826	29	3	1280	3	GABRP	5	170239185	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	26694152	170239185	10676075	120	28686										
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171773255	171773255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgggcggcttcggcaggttgAggcctcgaggctggtacgat	18	9	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:171773255A>G	ENST00000311601.5	-	12	1243	c.1073T>C	c.(1072-1074)cTc>cCc	p.L358P	SH3PXD2B_ENST00000519643.1_Missense_Mutation_p.L358P	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	358					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGCAGGTTGAGGCCTCGAGG	0.592																																																0			5											175	168	170					5																	171773255		2203	4300	6503	171705860	SO:0001583	missense	285590			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1073T>C	5.37:g.171773255A>G	ENSP00000309714:p.Leu358Pro		171705860	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.32|13.32	2.201556|2.201556	0.38905|0.38905	.|.	.|.	ENSG00000174705|ENSG00000174705	ENST00000519643;ENST00000311601|ENST00000518522	T;T|.	0.62788|.	0.23;0.0|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Src homology-3 domain (1);|.	0.247490|.	0.35615|.	N|.	0.003093|.	T|T	0.69691|0.69691	0.3139|0.3139	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.69078|.	0.997|.	D|.	0.64042|.	0.921|.	T|T	0.69217|0.69217	-0.5203|-0.5203	10|5	0.56958|.	D|.	0.05|.	-20.5633|-20.5633	13.2115|13.2115	0.59828|0.59828	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	358|.	A1X283|.	SPD2B_HUMAN|.	P|P	358|29	ENSP00000430890:L358P;ENSP00000309714:L358P|.	ENSP00000309714:L358P|.	L|S	-|-	2|1	0|0	SH3PXD2B|SH3PXD2B	171705860|171705860	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.176000|0.176000	0.22953|0.22953	6.844000|6.844000	0.75390|0.75390	2.014000|2.014000	0.59158|0.59158	0.374000|0.374000	0.22700|0.22700	CTC|TCA		0.592	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		G	171773255	A	G	171773255	3	3	109	1	0	0	0	0	1	0	0	0	14294	304	11	4	1670	4	SH3PXD2B	5	171773255	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1534070	171773255	9142005	121	28687										
DBN1	1627	hgsc.bcm.edu	37	chr5	176884464	176884464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccctcgaagccctcctcctcTtctggaactgggtctgcatc	8	17	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:176884464T>C	ENST00000309007.5	-	14	2139	c.1920A>G	c.(1918-1920)gaA>gaG	p.E640E	DBN1_ENST00000393563.4_Silent_p.E372E|DBN1_ENST00000292385.5_Silent_p.E642E|DBN1_ENST00000512501.1_3'UTR|DBN1_ENST00000393565.1_Silent_p.E686E	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	640			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			CCTCCTCCTCTTCTGGAACTG	0.622											OREG0016462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			5											141	123	129					5																	176884464		2203	4300	6503	176817070	SO:0001819	synonymous_variant	1627				CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1920A>G	5.37:g.176884464T>C		1934	176817070	A8MV58|B2RBG0|Q9UFZ5	Silent	SNP	ENST00000309007.5	37	CCDS4420.1																																																																																				0.622	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		C	176884464	T	C	176884464	2	2	109	1	0	0	0	0	0	0	0	1	4258	1606	56	4		4	DBN1	5	176884464	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	5111209	176884464	4030796	122	28688										
FLOT1	8870	hgsc.bcm.edu	37	chr6	30709588	30709588	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctctggatctgttggatgcAgggcaggacaaagacacgcc	13	11	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:30709588A>G	ENST00000259874.5	-	0	1244				FLOT1_ENST00000470643.1_5'UTR|FLOT1_ENST00000376389.3_Missense_Mutation_p.C34R|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000456573.2_Missense_Mutation_p.C34R	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						TGTTGGATGCAGGGCAGGACA	0.562																																																0			6											66	66	66					6																	30709588		1509	2708	4217	30817567	SO:0001628	intergenic_variant	10211			AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		6.37:g.30709588A>G			30817567	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	37	CCDS4689.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789314	0.49997	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000438162;ENST00000445853;ENST00000416018;ENST00000454845	D;T;D;D;D;D	0.94417	-3.42;1.05;-3.42;-3.42;-3.42;-3.42	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	D	0.91935	0.7446	L	0.49350	1.555	0.80722	D	1	B;D	0.58620	0.26;0.983	B;P	0.50860	0.163;0.652	D	0.92272	0.5826	10	0.56958	D	0.05	-13.5039	11.6627	0.51356	1.0:0.0:0.0:0.0	.	34;34	B4DVY7;O75955	.;FLOT1_HUMAN	R	34	ENSP00000365569:C34R;ENSP00000394375:C34R;ENSP00000400615:C34R;ENSP00000398834:C34R;ENSP00000412058:C34R;ENSP00000391341:C34R	ENSP00000365569:C34R	C	-	1	0	FLOT1	30817567	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.082000	0.71318	1.909000	0.55274	0.379000	0.24179	TGC		0.562	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			G	30709588	A	G	30709588	1	3	109	0	1	0	0	0	0	0	0	0	5955	188	7	4		4	FLOT1	6	30709588	IGR	SNP	A	TCGA-EF-5830-01A-01D-1657-10		30709588	140405479	123	28689										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918665	30918665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	acagaacacgcagaaaggacTccactggccaatgagaacac	9	12	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:30918665T>C	ENST00000462446.1	+	2	2452	c.2424T>C	c.(2422-2424)acT>acC	p.T808T	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	0						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CAGAAAGGACTCCACTGGCCA	0.488																																																0			6											62	62	62					6																	30918665		692	1591	2283	31026644	SO:0001819	synonymous_variant	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2424T>C	6.37:g.30918665T>C			31026644	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																				0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		C	30918665	T	C	30918665	2	2	109	1	0	0	0	0	0	0	0	1	4723	1538	54	4		4	DPCR1	6	30918665	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	209077	30918665	140196402	124	28690										
HLA-B	3106	hgsc.bcm.edu	37	chr6	31323116	31323116	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	catctcagggtgaggggcttCggcagcccctcatgctgtac	13	13	2	1	rs1131446	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:31323116C>T	ENST00000412585.2	-	4	901	c.873G>A	c.(871-873)ccG>ccA	p.P291P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	291	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGAGGGGCTTCGGCAGCCCCT	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	485	0.096845	0.0749	0.0922	5008	,	,		21693	0.0754		0.1074	False		,,,				2504	0.1411															0			6											60	57	58					6																	31323116		2203	4300	6503	31431095	SO:0001819	synonymous_variant	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.873G>A	6.37:g.31323116C>T			31431095	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																				0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		T	31323116	C	T	31323116	2	4	109	1	0	0	0	0	0	0	0	1	7217	871	31	1		1	HLA-B	6	31323116	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	404451	31323116	139791951	125	28691										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33171369	33171369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gggcactggcaggcacagccTgtgcccttctcactgaagga	13	13	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:33171369T>C	ENST00000374677.3	+	7	1562	c.1189T>C	c.(1189-1191)Tgt>Cgt	p.C397R	SLC39A7_ENST00000463972.1_3'UTR|RXRB_ENST00000374685.4_5'Flank|HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.C397R|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|RXRB_ENST00000413614.2_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	397				CALLTEGGAVGSEIAGGAGPGWVLPFTAGGFIYVATVSVLP ELLREASPLQSLLEVLGLLGGVIMMVLIAHLE -> VPFSL KEEQWTVKLQVVQVLAGSCHLLQVALST (in Ref. 1; BAA11528 and 2; AAD12305). {ECO:0000305}.	transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						AGGCACAGCCTGTGCCCTTCT	0.532																																																0			6											67	71	70					6																	33171369		2028	4167	6195	33279347	SO:0001583	missense	7922			AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1189T>C	6.37:g.33171369T>C	ENSP00000363809:p.Cys397Arg		33279347	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	37	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	T	18.20	3.570233	0.65765	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.47528	0.84;0.84	4.79	4.79	0.61399	.	0.105696	0.64402	D	0.000003	T	0.34279	0.0892	M	0.63843	1.955	0.80722	D	1	B;P	0.49090	0.072;0.919	B;B	0.41723	0.028;0.365	T	0.44329	-0.9335	10	0.87932	D	0	-22.1958	12.3302	0.55035	0.0:0.0:0.0:1.0	.	378;397	B4DVK8;Q92504	.;S39A7_HUMAN	R	397;378;302;397	ENSP00000363807:C397R;ENSP00000363809:C397R	ENSP00000363807:C397R	C	+	1	0	SLC39A7	33279347	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.050000	0.71063	2.018000	0.59344	0.448000	0.29417	TGT		0.532	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		C	33171369	T	C	33171369	3	2	109	1	0	0	0	0	1	0	0	0	14660	1580	55	4	1215	4	SLC39A7	6	33171369	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1848253	33171369	137943698	126	28692										
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35048831	35048831	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agaatgattcctgcactgggCggtcggcagatctgctgctg	14	10	1	3	rs541932194		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:35048831C>T	ENST00000360359.3	+	17	2743	c.2605C>T	c.(2605-2607)Cgg>Tgg	p.R869W	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	869					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CTGCACTGGGCGGTCGGCAGA	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		19518	0		0	False		,,,				2504	0															0			6											118	101	107					6																	35048831		2203	4300	6503	35156809	SO:0001583	missense	23294			D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2605C>T	6.37:g.35048831C>T	ENSP00000353518:p.Arg869Trp		35156809	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600636	0.46423	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.39056	1.1	5.28	0.668	0.17912	.	0.163313	0.28119	N	0.016535	T	0.40322	0.1112	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	P;P;P	0.58266	0.836;0.676;0.781	T	0.39121	-0.9629	10	0.56958	D	0.05	-11.4128	9.5806	0.39486	0.5006:0.4004:0.099:0.0	.	195;195;869	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	W	869;195	ENSP00000353518:R869W	ENSP00000353518:R869W	R	+	1	2	ANKS1A	35156809	0.558000	0.26554	0.003000	0.11579	0.127000	0.20565	0.958000	0.29227	0.175000	0.19841	-0.181000	0.13052	CGG		0.607	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		T	35048831	C	T	35048831	3	4	109	1	0	0	0	0	1	0	0	0	688	759	27	1	2671	1	ANKS1A	6	35048831	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1877462	35048831	136066236	127	28693										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41556431	41556431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	accggagtacagcccagtgcCgggtacagatgcaggtggtg	16	10	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:41556431C>T	ENST00000307972.4	+	8	1039	c.1027C>T	c.(1027-1029)Cgg>Tgg	p.R343W	FOXP4_ENST00000373063.3_Missense_Mutation_p.R342W|FOXP4_ENST00000373060.1_Missense_Mutation_p.R343W|FOXP4_ENST00000409208.1_Missense_Mutation_p.R343W|FOXP4_ENST00000373057.3_Missense_Mutation_p.R341W			Q8IVH2	FOXP4_HUMAN	forkhead box P4	343					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGCCCAGTGCCGGGTACAGAT	0.627																																																0			6											139	123	128					6																	41556431		2203	4300	6503	41664409	SO:0001583	missense	116113			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1027C>T	6.37:g.41556431C>T	ENSP00000309823:p.Arg343Trp		41664409	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.303430	0.40795	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02	4.92	3.04	0.35103	.	0.000000	0.64402	D	0.000001	T	0.37517	0.1006	M	0.84948	2.725	0.80722	D	1	D;D;P	0.89917	1.0;0.999;0.878	D;D;B	0.72075	0.965;0.976;0.261	T	0.43925	-0.9361	10	0.66056	D	0.02	.	13.0015	0.58679	0.2947:0.7052:0.0:0.0	.	342;341;343	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	W	343;342;343;341;343	ENSP00000362151:R343W;ENSP00000362154:R342W;ENSP00000386958:R343W;ENSP00000362148:R341W;ENSP00000309823:R343W	ENSP00000309823:R343W	R	+	1	2	FOXP4	41664409	0.997000	0.39634	0.999000	0.59377	0.997000	0.91878	1.282000	0.33226	0.432000	0.26286	0.561000	0.74099	CGG		0.627	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		T	41556431	C	T	41556431	3	4	109	1	0	0	0	0	1	0	0	0	6048	643	23	1	1057	1	FOXP4	6	41556431	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	6507600	41556431	129558636	128	28694										
EYS	346007	hgsc.bcm.edu	37	chr6	64436546	64436546	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tccaggataactcattgcttCtgaaagatggatcacttatg	8	8	3	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:64436546C>T	ENST00000370621.3	-	43	8688	c.8162G>A	c.(8161-8163)aGa>aAa	p.R2721K	EYS_ENST00000370616.2_Missense_Mutation_p.R2721K|EYS_ENST00000503581.1_Missense_Mutation_p.R2700K			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2721	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTCATTGCTTCTGAAAGATGG	0.383																																																0			6											64	53	56					6																	64436546		692	1591	2283	64494505	SO:0001583	missense	346007				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.8162G>A	6.37:g.64436546C>T	ENSP00000359655:p.Arg2721Lys		64494505	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	C	12.55	1.972146	0.34754	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.78816	-1.21;-0.35;-0.35	3.55	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.37461	0.1004	N	0.08118	0	0.80722	D	1	B;B	0.19331	0.035;0.005	B;B	0.20767	0.031;0.014	T	0.12889	-1.0530	9	0.29301	T	0.29	.	8.3091	0.32060	0.0:0.8784:0.0:0.1216	.	2700;2721	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	K	2700;2721;2721	ENSP00000424243:R2700K;ENSP00000359655:R2721K;ENSP00000359650:R2721K	ENSP00000359650:R2721K	R	-	2	0	EYS	64494505	1.000000	0.71417	0.995000	0.50966	0.708000	0.40852	4.791000	0.62460	0.416000	0.25844	0.491000	0.48974	AGA		0.383	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	64436546	C	T	64436546	3	4	109	1	0	0	0	0	1	0	0	0	5345	913	32	3	1343	3	EYS	6	64436546	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	22880115	64436546	106678521	129	28695										
CD109	135228	hgsc.bcm.edu	37	chr6	74517810	74517810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctttttttcttccaagcctaAcattgatgtgcaagagtcta	6	9	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:74517810A>G	ENST00000287097.5	+	26	3306	c.3194A>G	c.(3193-3195)aAc>aGc	p.N1065S	CD109_ENST00000422508.2_Missense_Mutation_p.N988S|CD109_ENST00000437994.2_Missense_Mutation_p.N1065S			Q6YHK3	CD109_HUMAN	CD109 molecule	1065			N -> K (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCAAGCCTAACATTGATGTG	0.313																																																0			6											66	63	64					6																	74517810		2203	4300	6503	74574531	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3194A>G	6.37:g.74517810A>G	ENSP00000287097:p.Asn1065Ser		74574531	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	8.192	0.796197	0.16327	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.31510	1.49;1.49;1.49	5.02	3.86	0.44501	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.659654	0.16401	N	0.216016	T	0.04543	0.0124	N	0.03224	-0.385	0.26399	N	0.976458	B;B;B	0.13594	0.004;0.008;0.001	B;B;B	0.15052	0.008;0.012;0.01	T	0.35001	-0.9806	10	0.13108	T	0.6	.	11.448	0.50136	0.7456:0.2544:0.0:0.0	.	988;1065;1065	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	1065;988;1065	ENSP00000388062:N1065S;ENSP00000404475:N988S;ENSP00000287097:N1065S	ENSP00000287097:N1065S	N	+	2	0	CD109	74574531	0.998000	0.40836	1.000000	0.80357	0.806000	0.45545	1.090000	0.30902	2.110000	0.64415	0.528000	0.53228	AAC		0.313	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		G	74517810	A	G	74517810	3	3	109	1	0	0	0	0	1	0	0	0	2969	43	2	4	3296	4	CD109	6	74517810	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	10081264	74517810	96597257	130	28696										
SENP6	26054	hgsc.bcm.edu	37	chr6	76373083	76373083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttatggcaacaatgtggaAaaggttccaattgatattat	8	4	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:76373083A>G	ENST00000447266.2	+	9	1321	c.843A>G	c.(841-843)gaA>gaG	p.E281E	SENP6_ENST00000370010.2_Silent_p.E274E|SENP6_ENST00000327284.8_Silent_p.E274E|SENP6_ENST00000370014.3_Silent_p.E281E	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	281					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ACAATGTGGAAAAGGTTCCAA	0.348																																																0			6											119	114	115					6																	76373083		1851	4099	5950	76429803	SO:0001819	synonymous_variant	26054				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.843A>G	6.37:g.76373083A>G			76429803	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																				0.348	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76373083	A	G	76373083	2	3	109	1	0	0	0	0	0	0	0	1	14087	11	1	4		4	SENP6	6	76373083	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1855273	76373083	94741984	131	28697										
REV3L	5980	hgsc.bcm.edu	37	chr6	111634650	111634650	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagtgtttcatacatgtaacCcacatacctcttttttgttt	4	10	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:111634650C>A	ENST00000358835.3	-	29	8963	c.8509G>T	c.(8509-8511)Ggt>Tgt	p.G2837C	REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000435970.1_Missense_Mutation_p.G2759C|REV3L_ENST00000368802.3_Missense_Mutation_p.G2837C|REV3L_ENST00000368805.1_Missense_Mutation_p.G2837C|RP5-1112D6.8_ENST00000607434.1_RNA			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2837					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.G2759S(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TACATGTAACCCACATACCTC	0.378								DNA polymerases (catalytic subunits)																																								1	Substitution - Missense(1)	skin(1)	6											108	106	107					6																	111634650		2203	4300	6503	111741343	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8509G>T	6.37:g.111634650C>A	ENSP00000351697:p.Gly2837Cys		111741343	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	28.0	4.884216	0.91814	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.29	5.29	0.74685	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.244012	0.42172	D	0.000753	T	0.52837	0.1759	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64546	-0.6382	10	0.87932	D	0	-8.722	19.1263	0.93386	0.0:1.0:0.0:0.0	.	2837	O60673	DPOLZ_HUMAN	C	2837;2837;2837;2759	ENSP00000357792:G2837C;ENSP00000357795:G2837C;ENSP00000351697:G2837C;ENSP00000402003:G2759C	ENSP00000351697:G2837C	G	-	1	0	REV3L	111741343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.610000	0.82949	2.736000	0.93811	0.650000	0.86243	GGT		0.378	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111634650	C	A	111634650	3	1	109	1	0	0	0	0	1	0	0	0	13277	623	22	2	903	2	REV3L	6	111634650	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	35261567	111634650	59480417	132	28698										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146276034	146276034	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	actgattgcttgactctgaaCtcatcaatgtaatactcctt	5	10	3	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:146276034C>A	ENST00000367505.2	-	2	689	c.425G>T	c.(424-426)aGt>aTt	p.S142I	SHPRH_ENST00000438092.2_Missense_Mutation_p.S142I|SHPRH_ENST00000367503.3_Missense_Mutation_p.S142I|SHPRH_ENST00000275233.7_Missense_Mutation_p.S142I			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	142					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TGACTCTGAACTCATCAATGT	0.343																																																0			6											77	70	72					6																	146276034		1828	4084	5912	146317727	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.425G>T	6.37:g.146276034C>A	ENSP00000356475:p.Ser142Ile		146317727	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	11.68	1.712070	0.30322	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.66	1.55	0.23275	.	0.349704	0.28901	N	0.013764	T	0.33847	0.0877	L	0.44542	1.39	0.09310	N	1	B;B	0.32071	0.242;0.355	B;B	0.32864	0.074;0.154	T	0.16364	-1.0405	10	0.38643	T	0.18	-4.1426	6.8362	0.23937	0.0:0.4926:0.238:0.2695	.	142;142	Q149N8;Q149N8-4	SHPRH_HUMAN;.	I	142	ENSP00000356475:S142I;ENSP00000356473:S142I;ENSP00000412797:S142I;ENSP00000275233:S142I	ENSP00000275233:S142I	S	-	2	0	SHPRH	146317727	1.000000	0.71417	0.351000	0.25721	0.976000	0.68499	1.015000	0.29963	0.329000	0.23460	0.655000	0.94253	AGT		0.343	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146276034	C	A	146276034	3	1	109	1	0	0	0	0	1	0	0	0	14328	565	20	2	4786	2	SHPRH	6	146276034	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	34641384	146276034	24839033	133	28699										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152461141	152461141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtcagtgctgagttccagacGctggagctgttccaactcct	11	12	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152461141G>A	ENST00000367255.5	-	140	26003	c.25402C>T	c.(25402-25404)Cgt>Tgt	p.R8468C	SYNE1_ENST00000423061.1_Missense_Mutation_p.R8420C|SYNE1_ENST00000341594.5_Missense_Mutation_p.R8080C|SYNE1_ENST00000539504.1_Missense_Mutation_p.R623C|SYNE1_ENST00000265368.4_Missense_Mutation_p.R8468C|SYNE1_ENST00000356820.4_Missense_Mutation_p.R2992C|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.R8420C|SYNE1_ENST00000354674.4_Missense_Mutation_p.R646C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8468			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGTTCCAGACGCTGGAGCTGT	0.557										HNSCC(10;0.0054)																																						0			6											121	99	106					6																	152461141		2203	4300	6503	152502834	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25402C>T	6.37:g.152461141G>A	ENSP00000356224:p.Arg8468Cys		152502834	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	7.411	0.634666	0.14322	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.92	5.04	0.67666	.	0.227351	0.31156	N	0.008147	T	0.27063	0.0663	M	0.64997	1.995	0.09310	N	0.999999	B;B;B;B;B	0.19073	0.033;0.033;0.027;0.033;0.008	B;B;B;B;B	0.17433	0.018;0.018;0.011;0.018;0.013	T	0.20739	-1.0266	10	0.51188	T	0.08	.	10.5768	0.45231	0.0683:0.0:0.7974:0.1342	.	8468;8468;8420;8420;670	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	C	8468;623;1114;8420;8468;8420;8080;2992;653;648;1413;646	ENSP00000356224:R8468C;ENSP00000441052:R623C;ENSP00000356226:R1114C;ENSP00000396024:R8420C;ENSP00000265368:R8468C;ENSP00000390975:R8420C;ENSP00000341887:R8080C;ENSP00000349276:R2992C;ENSP00000356220:R1413C;ENSP00000346701:R646C	ENSP00000265368:R8468C	R	-	1	0	SYNE1	152502834	0.000000	0.05858	0.037000	0.18230	0.206000	0.24218	0.727000	0.25999	1.465000	0.48006	0.561000	0.74099	CGT		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152461141	G	A	152461141	3	1	109	1	0	0	0	0	1	0	0	0	15484	1087	38	1	1019	1	SYNE1	6	152461141	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	6185107	152461141	18653926	134	28700										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152674796	152674796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caacccattctgctgttcacGtggctctcgtccagtatctc	7	15	4	0	rs143673038		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152674796G>A	ENST00000367255.5	-	68	11611	c.11010C>T	c.(11008-11010)caC>caT	p.H3670H	SYNE1_ENST00000423061.1_Silent_p.H3655H|SYNE1_ENST00000341594.5_Silent_p.H3641H|SYNE1_ENST00000265368.4_Silent_p.H3670H|SYNE1_ENST00000448038.1_Silent_p.H3655H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3670					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGCTGTTCACGTGGCTCTCGT	0.527										HNSCC(10;0.0054)																																						0			6											155	127	137					6																	152674796		2203	4300	6503	152716489	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.11010C>T	6.37:g.152674796G>A			152716489	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.527	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152674796	G	A	152674796	2	1	109	1	0	0	0	0	0	0	0	1	15484	1136	40	1		1	SYNE1	6	152674796	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	213655	152674796	18440271	135	28701										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152737961	152737961	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atggctctggaggaattctgCcaaatgggacagggcaagct	14	8	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152737961C>A	ENST00000367255.5	-	41	6212	c.5611G>T	c.(5611-5613)Gca>Tca	p.A1871S	SYNE1_ENST00000423061.1_Missense_Mutation_p.A1878S|SYNE1_ENST00000341594.5_Missense_Mutation_p.A1908S|SYNE1_ENST00000265368.4_Missense_Mutation_p.A1871S|SYNE1_ENST00000448038.1_Missense_Mutation_p.A1878S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1871					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGGAATTCTGCCAAATGGGAC	0.562										HNSCC(10;0.0054)																																						0			6											81	79	80					6																	152737961		2203	4300	6503	152779654	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5611G>T	6.37:g.152737961C>A	ENSP00000356224:p.Ala1871Ser		152779654	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457586	0.26161	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52754	0.74;0.74;0.65;0.7;0.82	6.16	2.92	0.33932	.	0.566781	0.17102	N	0.186955	T	0.09598	0.0236	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.22003	0.02;0.025;0.025;0.063	B;B;B;B	0.20767	0.016;0.015;0.015;0.031	T	0.34650	-0.9820	10	0.06236	T	0.91	.	7.0183	0.24900	0.0:0.5632:0.1355:0.3014	.	1854;1871;1871;1878	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	S	1871;1878;1871;1878;1908	ENSP00000356224:A1871S;ENSP00000396024:A1878S;ENSP00000265368:A1871S;ENSP00000390975:A1878S;ENSP00000341887:A1908S	ENSP00000265368:A1871S	A	-	1	0	SYNE1	152779654	0.001000	0.12720	0.653000	0.29593	0.970000	0.65996	0.942000	0.29017	0.875000	0.35847	0.650000	0.86243	GCA		0.562	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152737961	C	A	152737961	3	1	109	1	0	0	0	0	1	0	0	0	15484	739	26	2	21279	2	SYNE1	6	152737961	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	63165	152737961	18377106	136	28702										
C7orf27	221927	hgsc.bcm.edu	37	chr7	2578946	2578946	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gctgcagggccagctgaggcAcctctgaagccaagagtgcg	15	12	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:2578946A>C	ENST00000340611.4	-	13	1893	c.1637T>G	c.(1636-1638)gTg>gGg	p.V546G	BRAT1_ENST00000473879.1_Intron	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	546					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CAGCTGAGGCACCTCTGAAGC	0.652																																																0			7											29	29	29					7																	2578946		2203	4300	6503	2545472	SO:0001583	missense	221927			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"BRCA1-associated protein required for ATM activation protein 1"	614506	"chromosome 7 open reading frame 27"	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1637T>G	7.37:g.2578946A>C	ENSP00000339637:p.Val546Gly		2545472	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.579362	0.46006	.	.	ENSG00000106009	ENST00000340611	T	0.70164	-0.46	5.74	3.38	0.38709	Armadillo-like helical (1);Armadillo-type fold (1);	0.666018	0.15652	N	0.251380	T	0.69780	0.3149	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.67581	-0.5634	10	0.87932	D	0	-14.6006	9.8164	0.40856	0.861:0.0:0.139:0.0	.	546	Q6PJG6	BRAT1_HUMAN	G	546	ENSP00000339637:V546G	ENSP00000339637:V546G	V	-	2	0	BRAT1	2545472	0.261000	0.24063	0.188000	0.23233	0.035000	0.12851	2.406000	0.44557	0.460000	0.27045	0.459000	0.35465	GTG		0.652	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		C	2578946	A	C	2578946	3	2	109	1	0	0	0	0	1	0	0	0	2388	159	6	4	836	4	C7orf27	7	2578946	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10		2578946	156559717	137	28703										
CARD11	84433	hgsc.bcm.edu	37	chr7	2984051	2984051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcatctgcttcttctcatccTccagctgccgcaacctggcc	6	18	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:2984051T>C	ENST00000396946.4	-	5	882	c.479A>G	c.(478-480)gAg>gGg	p.E160G	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	160					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CTTCTCATCCTCCAGCTGCCG	0.577			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	0			7											110	89	96					7																	2984051		2203	4300	6503	2950577	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.479A>G	7.37:g.2984051T>C	ENSP00000380150:p.Glu160Gly		2950577	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.104150	0.76983	.	.	ENSG00000198286	ENST00000396946	T	0.35605	1.3	4.38	4.38	0.52667	.	0.055849	0.64402	D	0.000001	T	0.54240	0.1846	M	0.67397	2.05	0.58432	D	0.999997	D	0.89917	1.0	D	0.70935	0.971	T	0.57917	-0.7728	10	0.87932	D	0	-32.0181	10.1448	0.42758	0.0:0.0:0.1677:0.8323	.	160	Q9BXL7	CAR11_HUMAN	G	160	ENSP00000380150:E160G	ENSP00000380150:E160G	E	-	2	0	CARD11	2950577	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.484000	0.81180	1.750000	0.51863	0.533000	0.62120	GAG		0.577	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2984051	T	C	2984051	3	2	109	1	0	0	0	0	1	0	0	0	2651	1551	54	4	3069	4	CARD11	7	2984051	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	405105	2984051	156154612	138	28704										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7413179	7413179	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttgcatttgggcccacaaccTaaaagatgaatgttgagaga	10	7	0	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:7413179T>C	ENST00000399429.3	-	32	2500		c.e32-2			NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1						cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		GCCCACAACCTAAAAGATGAA	0.423																																																0			7											53	54	54					7																	7413179		1858	4108	5966	7379704	SO:0001630	splice_region_variant	340267			AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2360-2A>G	7.37:g.7413179T>C			7379704	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Splice_Site	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.846109	0.51164	.	.	ENSG00000215018	ENST00000399429	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9056	0.63834	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL28A1	7379704	1.000000	0.71417	0.923000	0.36655	0.503000	0.33858	7.406000	0.80017	1.925000	0.55765	0.528000	0.53228	.		0.423	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	Intron	C	7413179	T	C	7413179	5	2	109	1	0	0	0	0	0	0	1	0	3692	1536	53	4	1035	4	COL28A1	7	7413179	Splice_Site	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4429128	7413179	151725484	139	28705										
WIPF3	644150	hgsc.bcm.edu	37	chr7	29923977	29923977	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcgcaagatgcgcaggagccTcccgccccgccgcccccgct	12	21	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:29923977T>C	ENST00000409290.1	+	4	867	c.867T>C	c.(865-867)ccT>ccC	p.P289P	WIPF3_ENST00000409123.1_Silent_p.P289P|WIPF3_ENST00000242140.5_Silent_p.P289P	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	289	Poly-Pro.				cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						CGCAGGAGCCTCCCGCCCCGC	0.687																																																0			7											3	3	3					7																	29923977		1482	3505	4987	29890502	SO:0001819	synonymous_variant	644150			AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.867T>C	7.37:g.29923977T>C			29890502	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																				0.687	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			C	29923977	T	C	29923977	2	2	109	1	0	0	0	0	0	0	0	1	17409	1538	54	4		4	WIPF3	7	29923977	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	22510798	29923977	129214686	140	28706										
POU6F2	11281	hgsc.bcm.edu	37	chr7	39379423	39379423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccagcagccaccacccgccTctcagcagccgccagctcct	7	23	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:39379423T>C	ENST00000403058.1	+	6	848	c.694T>C	c.(694-696)Tct>Cct	p.S232P	POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Missense_Mutation_p.S224P|POU6F2_ENST00000518318.2_Missense_Mutation_p.S232P	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	232	Gln-rich.|Pro-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						accacccgcctctcagcagcc	0.682																																																0			7											47	52	51					7																	39379423		2185	4262	6447	39345948	SO:0001583	missense	11281			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.694T>C	7.37:g.39379423T>C	ENSP00000384004:p.Ser232Pro		39345948	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585129	0.28268	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.85556	0.96;-2.0	3.56	2.38	0.29361	.	2.806260	0.03871	N	0.275598	T	0.74876	0.3774	N	0.19112	0.55	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.09377	0.004;0.0	T	0.61138	-0.7123	10	0.33940	T	0.23	.	5.2419	0.15477	0.0:0.2103:0.0:0.7897	.	232;232	P78424-2;P78424	.;PO6F2_HUMAN	P	232	ENSP00000384004:S232P;ENSP00000430514:S232P	ENSP00000384004:S232P	S	+	1	0	POU6F2	39345948	0.994000	0.37717	0.969000	0.41365	0.981000	0.71138	1.390000	0.34464	1.474000	0.48178	0.455000	0.32223	TCT		0.682	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		C	39379423	T	C	39379423	3	2	109	1	0	0	0	0	1	0	0	0	12316	1551	54	4	712	4	POU6F2	7	39379423	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	9455446	39379423	119759240	141	28707										
HECW1	23072	hgsc.bcm.edu	37	chr7	43531697	43531697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcagaagtttctagaaacagAggagcctctttactggccag	10	9	3	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:43531697A>G	ENST00000395891.2	+	18	3863	c.3258A>G	c.(3256-3258)agA>agG	p.R1086R	HECW1_ENST00000453890.1_Silent_p.R1052R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1086					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CTAGAAACAGAGGAGCCTCTT	0.398																																																0			7											58	58	58					7																	43531697		1835	4086	5921	43498222	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3258A>G	7.37:g.43531697A>G			43498222	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.398	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		G	43531697	A	G	43531697	2	3	109	1	0	0	0	0	0	0	0	1	7063	301	11	4		4	HECW1	7	43531697	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4152274	43531697	115606966	142	28708										
HECW1	23072	hgsc.bcm.edu	37	chr7	43591929	43591929	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcggaataacactgagtacCggggaggtgagtgggcagga	19	6	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:43591929C>A	ENST00000395891.2	+	28	5109	c.4504C>A	c.(4504-4506)Cgg>Agg	p.R1502R	HECW1_ENST00000453890.1_Silent_p.R1468R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1502	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CACTGAGTACCGGGGAGGTGA	0.483																																																0			7											89	93	92					7																	43591929		2028	4174	6202	43558454	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4504C>A	7.37:g.43591929C>A			43558454	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.483	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43591929	C	A	43591929	2	1	109	1	0	0	0	0	0	0	0	1	7063	643	23	2		2	HECW1	7	43591929	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	60232	43591929	115546734	143	28709										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103987	53103987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agacagcaagggtggcaggcGgaacctgcagccccggccct	15	14	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:53103987G>A	ENST00000408890.4	+	1	639	c.623G>A	c.(622-624)cGg>cAg	p.R208Q		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	208										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTGGCAGGCGGAACCTGCAG	0.667																																																0			7											45	55	52					7																	53103987		1990	4134	6124	53071481	SO:0001583	missense	285877				CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.623G>A	7.37:g.53103987G>A	ENSP00000386133:p.Arg208Gln		53071481	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	7.868	0.727502	0.15439	.	.	ENSG00000221900	ENST00000408890	T	0.11063	2.81	1.84	-2.29	0.06805	.	.	.	.	.	T	0.04634	0.0126	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.42749	-0.9433	9	0.22706	T	0.39	.	2.9968	0.06001	0.4771:0.2402:0.2827:0.0	.	208	Q8N7R1	P1L12_HUMAN	Q	208	ENSP00000386133:R208Q	ENSP00000386133:R208Q	R	+	2	0	POM121L12	53071481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.364000	0.01080	-0.707000	0.05022	-0.258000	0.10820	CGG		0.667	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		A	53103987	G	A	53103987	3	1	109	1	0	0	0	0	1	0	0	0	12272	1116	39	1	625	1	POM121L12	7	53103987	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	9512058	53103987	106034676	144	28710										
EGFR	1956	hgsc.bcm.edu	37	chr7	55210077	55210077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ataactgtgaggtggtccttGggaatttggaaattacctat	11	5	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:55210077G>A	ENST00000275493.2	+	2	364	c.187G>A	c.(187-189)Ggg>Agg	p.G63R	EGFR_ENST00000420316.2_Missense_Mutation_p.G63R|EGFR_ENST00000442591.1_Missense_Mutation_p.G63R|EGFR_ENST00000455089.1_Missense_Mutation_p.G63R|EGFR_ENST00000344576.2_Missense_Mutation_p.G63R|EGFR_ENST00000454757.2_Missense_Mutation_p.G10R|EGFR_ENST00000342916.3_Missense_Mutation_p.G63R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	63			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.G63R(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGTGGTCCTTGGGAATTTGGA	0.398		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	1	Substitution - Missense(1)	central_nervous_system(1)	7											174	167	169					7																	55210077		2203	4300	6503	55177571	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.187G>A	7.37:g.55210077G>A	ENSP00000275493:p.Gly63Arg		55177571	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325432	0.81580	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000450046;ENST00000454757	D;D;D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	6.05	6.05	0.98169	EGF receptor, L domain (1);	0.096922	0.64402	D	0.000001	D	0.96002	0.8698	H	0.95187	3.635	0.37218	D	0.905126	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.993;0.999;0.973;0.993;0.999	D	0.97967	1.0341	10	0.87932	D	0	.	13.4187	0.60985	0.0752:0.0:0.9248:0.0	.	63;63;63;63;63	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	R	63;63;63;63;63;63;10;10	ENSP00000415559:G63R;ENSP00000342376:G63R;ENSP00000345973:G63R;ENSP00000413843:G63R;ENSP00000275493:G63R;ENSP00000410031:G63R;ENSP00000413354:G10R;ENSP00000395243:G10R	ENSP00000275493:G63R	G	+	1	0	EGFR	55177571	1.000000	0.71417	0.998000	0.56505	0.695000	0.40330	7.677000	0.84024	2.878000	0.98634	0.650000	0.86243	GGG		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55210077	G	A	55210077	3	1	109	1	0	0	0	0	1	0	0	0	4978	1348	47	3	193	3	EGFR	7	55210077	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	2106090	55210077	103928586	145	28711										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94052425	94052425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtccctctggagaggctggtActgctgtaagtgatttccaa	12	9	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:94052425A>G	ENST00000297268.6	+	40	3031	c.2560A>G	c.(2560-2562)Act>Gct	p.T854A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	854			Missing (in OI2). {ECO:0000269|PubMed:1339453}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	AGAGGCTGGTACTGCTGTAAG	0.483										HNSCC(75;0.22)																																						0			7											114	105	108					7																	94052425		2203	4300	6503	93890361	SO:0001583	missense	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2560A>G	7.37:g.94052425A>G	ENSP00000297268:p.Thr854Ala		93890361	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440086	0.43326	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93133	-3.17	5.32	2.92	0.33932	.	0.268284	0.38605	N	0.001638	T	0.81800	0.4899	N	0.10972	0.075	0.26343	N	0.977322	B	0.02656	0.0	B	0.01281	0.0	T	0.67856	-0.5562	10	0.25751	T	0.34	.	4.1071	0.10041	0.5647:0.1801:0.2552:0.0	.	854	P08123	CO1A2_HUMAN	A	854;855	ENSP00000297268:T854A	ENSP00000297268:T854A	T	+	1	0	COL1A2	93890361	0.977000	0.34250	1.000000	0.80357	0.933000	0.57130	0.542000	0.23222	0.974000	0.38366	0.460000	0.39030	ACT		0.483	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		G	94052425	A	G	94052425	3	3	109	1	0	0	0	0	1	0	0	0	3684	391	14	4	2718	4	COL1A2	7	94052425	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	38842348	94052425	65086238	146	28712										
EPHB4	2050	hgsc.bcm.edu	37	chr7	100417812	100417812	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgtgcccggaagtacccgacGcggcactggcagacggctga	15	14	0	2	rs139571805		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:100417812G>A	ENST00000358173.3	-	5	1383	c.915C>T	c.(913-915)cgC>cgT	p.R305R	EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Silent_p.R305R|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	305	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGTACCCGACGCGGCACTGGC	0.642																																					GBM(200;2113 3072 25865 52728)											0			7						G		1,4405	2.1+/-5.4	0,1,2202	92	103	100		915	-0.3	0.1	7	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous	EPHB4	NM_004444.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		305/988	100417812	1,13005	2203	4300	6503	100255748	SO:0001819	synonymous_variant	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.915C>T	7.37:g.100417812G>A			100255748	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																				0.642	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100417812	G	A	100417812	2	1	109	1	0	0	0	0	0	0	0	1	5190	1074	38	1		1	EPHB4	7	100417812	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	6365387	100417812	58720851	147	28713										
MUC17	140453	hgsc.bcm.edu	37	chr7	100678232	100678232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggtcagttctgaggctaacAccctttcaacaactcctgtg	8	12	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:100678232A>C	ENST00000306151.4	+	3	3599	c.3535A>C	c.(3535-3537)Acc>Ccc	p.T1179P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1179	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TGAGGCTAACACCCTTTCAAC	0.527																																																0			7											348	297	314					7																	100678232		2203	4300	6503	100464952	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3535A>C	7.37:g.100678232A>C	ENSP00000302716:p.Thr1179Pro		100464952	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.435	-0.901363	0.02453	.	.	ENSG00000169876	ENST00000306151	T	0.02525	4.26	0.838	-1.68	0.08212	.	.	.	.	.	T	0.01661	0.0053	N	0.24115	0.695	0.09310	N	1	B	0.21225	0.053	B	0.11329	0.006	T	0.48456	-0.9034	9	0.23891	T	0.37	.	0.0783	0.00029	0.3202:0.2406:0.1996:0.2396	.	1179	Q685J3	MUC17_HUMAN	P	1179	ENSP00000302716:T1179P	ENSP00000302716:T1179P	T	+	1	0	MUC17	100464952	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.575000	0.00910	-1.133000	0.02903	0.113000	0.15668	ACC		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100678232	A	C	100678232	3	2	109	1	0	0	0	0	1	0	0	0	10004	159	6	4	3545	4	MUC17	7	100678232	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	260420	100678232	58460431	148	28714										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106513212	106513212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgagaagtgagatagcccagTccagacactatcagcagagg	12	9	1	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:106513212T>C	ENST00000359195.3	+	4	2426	c.2116T>C	c.(2116-2118)Tcc>Ccc	p.S706P	PIK3CG_ENST00000440650.2_Missense_Mutation_p.S706P|PIK3CG_ENST00000496166.1_Missense_Mutation_p.S706P	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	706	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GATAGCCCAGTCCAGACACTA	0.438																																																0			7											109	108	108					7																	106513212		2203	4300	6503	106300448	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2116T>C	7.37:g.106513212T>C	ENSP00000352121:p.Ser706Pro		106300448	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	T	32	5.191435	0.94923	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.62498	0.02;0.02;0.02	5.92	5.92	0.95590	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68833	0.3044	L	0.39633	1.23	0.80722	D	1	D	0.58970	0.984	P	0.61132	0.884	T	0.64803	-0.6321	10	0.25751	T	0.34	-26.9448	16.3631	0.83280	0.0:0.0:0.0:1.0	.	706	P48736	PK3CG_HUMAN	P	706	ENSP00000392258:S706P;ENSP00000419260:S706P;ENSP00000352121:S706P	ENSP00000352121:S706P	S	+	1	0	PIK3CG	106300448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.266000	0.75297	0.533000	0.62120	TCC		0.438	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			C	106513212	T	C	106513212	3	2	109	1	0	0	0	0	1	0	0	0	11947	1667	58	4	2126	4	PIK3CG	7	106513212	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	5834980	106513212	52625451	149	28715										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107743551	107743551	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgtagaagaggggtctgcagCggtcgcagtgctgcccctca	15	11	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:107743551C>T	ENST00000388781.3	-	10	1201	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	LAMB4_ENST00000414450.2_Missense_Mutation_p.R373H|LAMB4_ENST00000418464.1_Missense_Mutation_p.R373H|LAMB4_ENST00000205386.4_Missense_Mutation_p.R373H|LAMB4_ENST00000388780.3_Missense_Mutation_p.R373H	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	373	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GGGTCTGCAGCGGTCGCAGTG	0.612																																																0			7											63	55	57					7																	107743551		2203	4300	6503	107530787	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1118G>A	7.37:g.107743551C>T	ENSP00000373433:p.Arg373His		107530787	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	7.750	0.703221	0.15172	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	4.02	-3.68	0.04463	EGF-like, laminin (4);	0.670359	0.13321	N	0.396717	T	0.45736	0.1357	L	0.58583	1.82	0.09310	N	1	B	0.25169	0.119	B	0.22386	0.039	T	0.35301	-0.9794	10	0.15066	T	0.55	.	4.0425	0.09758	0.105:0.2626:0.1038:0.5286	.	373	A4D0S4	LAMB4_HUMAN	H	373	ENSP00000205386:R373H;ENSP00000373433:R373H;ENSP00000373432:R373H;ENSP00000402353:R373H;ENSP00000402265:R373H	ENSP00000205386:R373H	R	-	2	0	LAMB4	107530787	0.000000	0.05858	0.002000	0.10522	0.829000	0.46940	-1.150000	0.03178	-0.752000	0.04728	-0.150000	0.13652	CGC		0.612	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		T	107743551	C	T	107743551	3	4	109	1	0	0	0	0	1	0	0	0	8635	768	27	1	4267	1	LAMB4	7	107743551	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1230339	107743551	51395112	150	28716										
PARP12	64761	hgsc.bcm.edu	37	chr7	139724562	139724562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cctccttggccggcggacggAcaaaggaggcattgcccctg	14	14	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:139724562A>G	ENST00000263549.3	-	12	2777	c.1904T>C	c.(1903-1905)gTc>gCc	p.V635A		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	635	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CGGCGGACGGACAAAGGAGGC	0.582																																																0			7											107	89	95					7																	139724562		2203	4300	6503	139371031	SO:0001583	missense	64761			AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	21919	protein-coding gene	gene with protein product		612481	"zinc finger CCCH-type domain containing 1"	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1904T>C	7.37:g.139724562A>G	ENSP00000263549:p.Val635Ala		139371031	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.115212	0.77210	.	.	ENSG00000059378	ENST00000263549;ENST00000541746	T	0.12672	2.66	5.18	5.18	0.71444	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.145410	0.45606	D	0.000352	T	0.22475	0.0542	L	0.53561	1.675	0.42048	D	0.991108	P	0.39404	0.672	P	0.46110	0.504	T	0.01188	-1.1424	10	0.52906	T	0.07	.	15.0413	0.71793	1.0:0.0:0.0:0.0	.	635	Q9H0J9	PAR12_HUMAN	A	635;19	ENSP00000263549:V635A	ENSP00000263549:V635A	V	-	2	0	PARP12	139371031	0.446000	0.25665	0.967000	0.41034	0.546000	0.35178	4.154000	0.58125	1.958000	0.56883	0.533000	0.62120	GTC		0.582	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		G	139724562	A	G	139724562	3	3	109	1	0	0	0	0	1	0	0	0	11488	275	10	4	205	4	PARP12	7	139724562	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	31981011	139724562	19414101	151	28717										
BRAF	673	hgsc.bcm.edu	37	chr7	140453127	140453127	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	actgatgggacccactccatCgagatttcactgtagctaga	9	11	1	3	rs372569965		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:140453127C>A	ENST00000288602.6	-	15	1868	c.1808G>T	c.(1807-1809)cGa>cTa	p.R603L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.W604del(2)|p.T599_R603>I(2)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.V600_S605>EK(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CCCACTCCATCGAGATTTCAC	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	7	Complex - deletion inframe(5)|Deletion - In frame(2)	thyroid(3)|small_intestine(2)|ovary(1)|skin(1)	7											107	100	102					7																	140453127		2203	4300	6503	140099596	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1808G>T	7.37:g.140453127C>A	ENSP00000288602:p.Arg603Leu		140099596	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.0|22.0	4.234378|4.234378	0.79800|0.79800	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.82803	.|-1.65	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76586|0.76586	0.4008|0.4008	N|N	0.20881|0.20881	0.62|0.62	0.80722|0.80722	D|D	1|1	.|B	.|0.27117	.|0.168	.|B	.|0.24701	.|0.055	T|T	0.74266|0.74266	-0.3721|-0.3721	5|10	.|0.87932	.|D	.|0	.|.	19.7917|19.7917	0.96461|0.96461	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|603	.|P15056	.|BRAF_HUMAN	Y|L	211|603	.|ENSP00000288602:R603L	.|ENSP00000288602:R603L	D|R	-|-	1|2	0|0	BRAF|BRAF	140099596|140099596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.702000|7.702000	0.84576|0.84576	2.686000|2.686000	0.91538|0.91538	0.650000|0.650000	0.86243|0.86243	GAT|CGA		0.383	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		A	140453127	C	A	140453127	3	1	109	1	0	0	0	0	1	0	0	0	1499	884	31	2	508	2	BRAF	7	140453127	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	728565	140453127	18685536	152	28718										
BRAF	673	hgsc.bcm.edu	37	chr7	140481406	140481406	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcccttgtagactgttccaaAtgatccagatccaattcttt	5	11	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:140481406A>G	ENST00000288602.6	-	11	1462	c.1402T>C	c.(1402-1404)Ttt>Ctt	p.F468L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	468	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		F -> S (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:18042262}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACTGTTCCAAATGATCCAGAT	0.378		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											173	149	157					7																	140481406		2203	4300	6503	140127875	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1402T>C	7.37:g.140481406A>G	ENSP00000288602:p.Phe468Leu		140127875	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124417	0.77436	.	.	ENSG00000157764	ENST00000288602	D	0.89196	-2.48	5.62	5.62	0.85841	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095786	0.85682	D	0.000000	D	0.90345	0.6979	M	0.82716	2.605	0.80722	D	1	B	0.22080	0.064	B	0.28553	0.091	D	0.88758	0.3255	10	0.87932	D	0	.	14.394	0.66999	1.0:0.0:0.0:0.0	.	468	P15056	BRAF_HUMAN	L	468	ENSP00000288602:F468L	ENSP00000288602:F468L	F	-	1	0	BRAF	140127875	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.130000	0.65690	0.477000	0.44152	TTT		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		G	140481406	A	G	140481406	3	3	109	1	0	0	0	0	1	0	0	0	1499	101	4	4	930	4	BRAF	7	140481406	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	28279	140481406	18657257	153	28719										
ZYX	7791	hgsc.bcm.edu	37	chr7	143080008	143080008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cttggaagtccccttccagcTcccagcctctgccccaggtt	8	18	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:143080008T>C	ENST00000322764.5	+	5	961	c.616T>C	c.(616-618)Tcc>Ccc	p.S206P	ZYX_ENST00000477373.1_3'UTR|ZYX_ENST00000449423.2_Missense_Mutation_p.S119P|ZYX_ENST00000392910.2_Missense_Mutation_p.S49P|AC093673.5_ENST00000429630.1_RNA	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	206					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					CCCTTCCAGCTCCCAGCCTCT	0.642																																																0			7											58	65	63					7																	143080008		2203	4300	6503	142790130	SO:0001583	missense	7791			X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.616T>C	7.37:g.143080008T>C	ENSP00000324422:p.Ser206Pro		142790130	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.265038	0.23136	.	.	ENSG00000159840	ENST00000322764;ENST00000449630;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T;T	0.54279	0.67;0.73;0.59;0.58;0.58	3.67	0.689	0.18033	.	0.589031	0.15010	N	0.285623	T	0.38612	0.1047	L	0.50919	1.6	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18967	-1.0320	10	0.23302	T	0.38	.	4.4542	0.11635	0.0:0.152:0.3594:0.4886	.	119;206	B4DQR8;Q15942	.;ZYX_HUMAN	P	206;175;174;119;49	ENSP00000324422:S206P;ENSP00000413467:S175P;ENSP00000346417:S174P;ENSP00000394158:S119P;ENSP00000376642:S49P	ENSP00000324422:S206P	S	+	1	0	ZYX	142790130	0.001000	0.12720	0.425000	0.26659	0.818000	0.46254	0.035000	0.13797	0.370000	0.24538	0.459000	0.35465	TCC		0.642	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461		C	143080008	T	C	143080008	3	2	109	1	0	0	0	0	1	0	0	0	18293	1551	54	4	630	4	ZYX	7	143080008	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2598602	143080008	16058655	154	28720										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143094439	143094439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtcacgctgcctctgctgccTctgccgctgggctctcctgt	11	17	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:143094439T>C	ENST00000275815.3	-	10	1815	c.1729A>G	c.(1729-1731)Agg>Ggg	p.R577G		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	577					activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				CTCTGCTGCCTCTGCCGCTGG	0.657																																																0			7											23	16	19					7																	143094439		1995	3837	5832	142804561	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1729A>G	7.37:g.143094439T>C	ENSP00000275815:p.Arg577Gly		142804561	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	T	9.124	1.009734	0.19277	.	.	ENSG00000146904	ENST00000275815	T	0.10668	2.85	5.96	0.208	0.15221	.	0.786081	0.10813	N	0.631358	T	0.08179	0.0204	L	0.35854	1.095	0.18873	N	0.999988	B	0.20887	0.049	B	0.19148	0.024	T	0.39187	-0.9626	10	0.25106	T	0.35	.	7.7353	0.28810	0.0836:0.0:0.2973:0.6191	.	577	P21709	EPHA1_HUMAN	G	577	ENSP00000275815:R577G	ENSP00000275815:R577G	R	-	1	2	EPHA1	142804561	0.002000	0.14202	0.075000	0.20258	0.311000	0.27955	0.401000	0.20948	0.341000	0.23771	-0.168000	0.13345	AGG		0.657	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			C	143094439	T	C	143094439	3	2	109	1	0	0	0	0	1	0	0	0	5178	1550	54	4	1237	4	EPHA1	7	143094439	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	14431	143094439	16044224	155	28721										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150649725	150649725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caccacagccagcggctggcAggcgtagccacactcggtag	13	15	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:150649725A>G	ENST00000262186.5	-	6	1746	c.1345T>C	c.(1345-1347)Tgc>Cgc	p.C449R	KCNH2_ENST00000392968.2_Missense_Mutation_p.C353R|KCNH2_ENST00000330883.4_Missense_Mutation_p.C109R|KCNH2_ENST00000430723.3_Missense_Mutation_p.C449R	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	449					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGCGGCTGGCAGGCGTAGCCA	0.587																																					GBM(137;110 1844 13671 20123 45161)											0			7											116	115	115					7																	150649725		2203	4300	6503	150280658	SO:0001583	missense	3757			U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1345T>C	7.37:g.150649725A>G	ENSP00000262186:p.Cys449Arg		150280658	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.908433	0.72868	.	.	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186;ENST00000350328;ENST00000430723	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	4.8	4.8	0.61643	.	0.101742	0.64402	D	0.000001	D	0.97071	0.9043	M	0.85710	2.77	0.80722	D	1	D;D;P;D;P	0.89917	0.998;1.0;0.928;0.988;0.883	D;D;P;P;P	0.81914	0.982;0.995;0.573;0.837;0.681	D	0.97443	1.0023	10	0.66056	D	0.02	.	12.3181	0.54969	1.0:0.0:0.0:0.0	.	353;449;109;449;109	C4PFH9;G5E9I0;Q708S9;Q12809;Q12809-2	.;.;.;KCNH2_HUMAN;.	R	109;353;449;109;449	ENSP00000328531:C109R;ENSP00000376695:C353R;ENSP00000262186:C449R;ENSP00000387657:C449R	ENSP00000262186:C449R	C	-	1	0	KCNH2	150280658	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	7.185000	0.77714	1.812000	0.52913	0.448000	0.29417	TGC		0.587	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		G	150649725	A	G	150649725	3	3	109	1	0	0	0	0	1	0	0	0	8053	188	7	4	2443	4	KCNH2	7	150649725	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	7555286	150649725	8488938	156	28722										
ATG9B	285973	hgsc.bcm.edu	37	chr7	150713872	150713872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcagatctctcggaggcaggAgagggtgcacgaagaggttg	17	7	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:150713872A>G	ENST00000377974.2	-	11	2399	c.2324T>C	c.(2323-2325)cTc>cCc	p.L775P	ATG9B_ENST00000605938.1_Missense_Mutation_p.S776P|ATG9B_ENST00000444312.1_Missense_Mutation_p.L261P|ATG9B_ENST00000494791.1_5'UTR			Q674R7	ATG9B_HUMAN	autophagy related 9B	776					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGGAGGCAGGAGAGGGTGCAC	0.617																																																0			7											40	45	43					7																	150713872		2041	4208	6249	150344805	SO:0001583	missense	285973			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"nitric oxide synthase 3 antisense", "ATG9 autophagy related 9 homolog B (S. cerevisiae)"	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.2324T>C	7.37:g.150713872A>G	ENSP00000475005:p.Leu775Pro		150344805	A1A5D3|Q6JRW5|Q8N8I8	Missense_Mutation	SNP	ENST00000377974.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.656|8.656	0.899512|0.899512	0.17686|0.17686	.|.	.|.	ENSG00000248602|ENSG00000248602	ENST00000377974;ENST00000444312|ENST00000397266	.|.	.|.	.|.	5.33|5.33	4.16|4.16	0.48862|0.48862	.|.	0.440664|.	0.24081|.	N|.	0.041725|.	T|T	0.53769|0.53769	0.1817|0.1817	.|.	.|.	.|.	.|.	.|.	.|.	P|.	0.49447|.	0.924|.	B|.	0.41619|.	0.361|.	T|T	0.62378|0.62378	-0.6867|-0.6867	7|3	0.33141|.	T|.	0.24|.	-6.9931|-6.9931	10.3366|10.3366	0.43854|0.43854	0.8274:0.1726:0.0:0.0|0.8274:0.1726:0.0:0.0	.|.	776|.	Q674R7|.	ATG9B_HUMAN|.	P|P	775;261|776	.|.	ENSP00000444232:L775P|.	L|S	-|-	2|1	0|0	AC010973.1|AC010973.1	150344805|150344805	0.001000|0.001000	0.12720|0.12720	0.057000|0.057000	0.19452|0.19452	0.347000|0.347000	0.29111|0.29111	0.383000|0.383000	0.20651|0.20651	0.837000|0.837000	0.34925|0.34925	0.459000|0.459000	0.35465|0.35465	CTC|TCC		0.617	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173681		G	150713872	A	G	150713872	3	3	109	1	0	0	0	0	1	0	0	0	1104	304	11	4	463	4	ATG9B	7	150713872	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	64147	150713872	8424791	157	28723										
MLL3	58508	hgsc.bcm.edu	37	chr7	151845973	151845973	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tctccattttttattgagcgGcctgcaatcttcaaacccac	5	13	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:151845973G>T	ENST00000262189.6	-	52	13257	c.13039C>A	c.(13039-13041)Ccg>Acg	p.P4347T	KMT2C_ENST00000355193.2_Missense_Mutation_p.P4404T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4347					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTATTGAGCGGCCTGCAATCT	0.468																																																0			7											65	61	63					7																	151845973		2203	4300	6503	151476906	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13039C>A	7.37:g.151845973G>T	ENSP00000262189:p.Pro4347Thr		151476906	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.366|7.366	0.625793|0.625793	0.14257|0.14257	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193;ENST00000424877	.|D;D;D	.|0.88818	.|-1.77;-1.75;-2.43	5.67|5.67	4.78|4.78	0.61160|0.61160	.|.	.|0.159293	.|0.29212	.|U	.|0.012816	D|D	0.88702|0.88702	0.6508|0.6508	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.42456	.|0.78;0.775;0.775	.|B;B;B	.|0.42282	.|0.335;0.382;0.382	D|D	0.88927|0.88927	0.3370|0.3370	5|10	.|0.66056	.|D	.|0.02	.|.	12.4842|12.4842	0.55863|0.55863	0.1393:0.0:0.8607:0.0|0.1393:0.0:0.8607:0.0	.|.	.|4347;3465;4404	.|Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	.|MLL3_HUMAN;.;.	D|T	1907|4347;4404;964	.|ENSP00000262189:P4347T;ENSP00000347325:P4404T;ENSP00000410411:P964T	.|ENSP00000262189:P4347T	A|P	-|-	2|1	0|0	MLL3|MLL3	151476906|151476906	1.000000|1.000000	0.71417|0.71417	0.481000|0.481000	0.27354|0.27354	0.034000|0.034000	0.12701|0.12701	6.333000|6.333000	0.72939|0.72939	1.384000|1.384000	0.46424|0.46424	0.650000|0.650000	0.86243|0.86243	GCC|CCG		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151845973	G	T	151845973	3	4	109	1	0	0	0	0	1	0	0	0	9652	1203	42	2	1728	2	MLL3	7	151845973	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	1132101	151845973	7292690	158	28724										
TEX15	56154	hgsc.bcm.edu	37	chr8	30704020	30704020	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcttgccttatattatcaacTttatcttcacatggataatc	3	9	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:30704020T>C	ENST00000256246.2	-	1	2588	c.2514A>G	c.(2512-2514)aaA>aaG	p.K838K	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	838					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TATTATCAACTTTATCTTCAC	0.363																																																0			8											64	60	62					8																	30704020		2203	4299	6502	30823562	SO:0001819	synonymous_variant	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2514A>G	8.37:g.30704020T>C			30823562		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																				0.363	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30704020	T	C	30704020	2	2	109	1	0	0	0	0	0	0	0	1	15818	1606	56	4		4	TEX15	8	30704020	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10		30704020	115660002	159	28725										
SGK3	23678	hgsc.bcm.edu	37	chr8	67726110	67726110	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tttattaaacaaagacgagcAggactaaacgaattcattca	6	7	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:67726110A>G	ENST00000396596.1	+	5	490	c.276A>G	c.(274-276)gcA>gcG	p.A92A	SGK3_ENST00000345714.4_Silent_p.A92A|SGK3_ENST00000520976.1_Silent_p.A92A|SGK3_ENST00000521198.2_Silent_p.A92A|C8orf44-SGK3_ENST00000519289.1_Silent_p.A92A|SGK3_ENST00000522398.1_Silent_p.A92A	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	92	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		A -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			AAAGACGAGCAGGACTAAACG	0.303																																																0			8											70	74	73					8																	67726110		2202	4292	6494	67888664	SO:0001819	synonymous_variant	23678				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"serum/glucocorticoid regulated kinase-like"	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.276A>G	8.37:g.67726110A>G			67888664	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Silent	SNP	ENST00000396596.1	37	CCDS6195.1																																																																																				0.303	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3			G	67726110	A	G	67726110	2	3	109	1	0	0	0	0	0	0	0	1	14249	175	7	4		4	SGK3	8	67726110	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	37022090	67726110	78637912	160	28726										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848940	73848940	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaaaggaacggaagcatcgtTtctatgaacttaaaagatgc	9	6	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:73848940T>C	ENST00000523207.1	+	3	1938	c.1350T>C	c.(1348-1350)gtT>gtC	p.V450V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	450			V -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAGCATCGTTTCTATGAACT	0.478																																																0			8											77	82	80					8																	73848940		2203	4300	6503	74011494	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1350T>C	8.37:g.73848940T>C			74011494	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.478	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73848940	T	C	73848940	2	2	109	1	0	0	0	0	0	0	0	1	8034	1828	64	4		4	KCNB2	8	73848940	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6122830	73848940	72515082	161	28727										
NBN	4683	hgsc.bcm.edu	37	chr8	90990529	90990529	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggctttacaattggacgtCcacaaatgagtgcacatatt	8	9	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:90990529C>A	ENST00000265433.3	-	5	657	c.503G>T	c.(502-504)gGa>gTa	p.G168V	NBN_ENST00000409330.1_Missense_Mutation_p.G86V	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	168	BRCT.|Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			AATTGGACGTCCACAAATGAG	0.303								Homologous recombination																																								0			8											78	78	78					8																	90990529		2203	4300	6503	91059705	SO:0001583	missense	9048			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.503G>T	8.37:g.90990529C>A	ENSP00000265433:p.Gly168Val		91059705	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983360	0.74474	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000517772;ENST00000517337	T;T;D;T	0.82255	0.47;0.47;-1.59;0.47	5.96	5.96	0.96718	BRCT (2);	0.046520	0.85682	D	0.000000	D	0.88581	0.6475	M	0.61703	1.905	0.58432	D	0.999999	D;D	0.65815	0.995;0.995	P;P	0.59595	0.86;0.86	D	0.88006	0.2759	10	0.51188	T	0.08	-29.2814	17.3038	0.87189	0.0:0.8751:0.1249:0.0	.	168;168	A6H8Y5;O60934	.;NBN_HUMAN	V	168;86;168;86;86	ENSP00000265433:G168V;ENSP00000386924:G86V;ENSP00000428717:G86V;ENSP00000429971:G86V	ENSP00000265433:G168V	G	-	2	0	NBN	91059705	0.999000	0.42202	0.991000	0.47740	0.998000	0.95712	2.505000	0.45424	2.826000	0.97356	0.655000	0.94253	GGA		0.303	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		A	90990529	C	A	90990529	3	1	109	1	0	0	0	0	1	0	0	0	10221	855	30	2	1809	2	NBN	8	90990529	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	17141589	90990529	55373493	162	28728										
PDP1	54704	hgsc.bcm.edu	37	chr8	94934247	94934247	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tctaatttgctgtctaggaaTcccagtcagaagttccagcc	8	11	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:94934247T>C	ENST00000297598.4	+	0	229				PDP1_ENST00000396200.3_Missense_Mutation_p.I12T|PDP1_ENST00000517764.1_5'UTR|PDP1_ENST00000520728.1_5'UTR	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1						cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TGTCTAGGAATCCCAGTCAGA	0.413																																																0			8											86	87	86					8																	94934247		2203	4300	6503	95003423	SO:0001623	5_prime_UTR_variant	54704			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.-41T>C	8.37:g.94934247T>C			95003423	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017187	0.35606	.	.	ENSG00000164951	ENST00000396200	T	0.49139	0.79	5.45	5.45	0.79879	.	.	.	.	.	T	0.29556	0.0737	N	0.08118	0	0.34064	D	0.657619	B	0.30482	0.281	B	0.22753	0.041	T	0.44802	-0.9304	9	0.52906	T	0.07	-12.0246	15.6958	0.77494	0.0:0.0:0.0:1.0	.	38	B4DYX8	.	T	12	ENSP00000379503:I12T	ENSP00000379503:I12T	I	+	2	0	PDP1	95003423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.030000	0.49720	2.288000	0.76882	0.528000	0.53228	ATC		0.413	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		C	94934247	T	C	94934247	1	2	109	0	1	0	0	0	0	0	0	0	11716	1435	50	4		4	PDP1	8	94934247	5'UTR	SNP	T	TCGA-EF-5830-01A-01D-1657-10	3943718	94934247	51429775	163	28729										
RAD21	5885	hgsc.bcm.edu	37	chr8	117864237	117864237	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agcttttcgcttaactccctGaggtggtggtggaggcatag	14	8	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:117864237G>T	ENST00000297338.2	-	11	1707	c.1420C>A	c.(1420-1422)Cag>Aag	p.Q474K	RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000518055.1_Missense_Mutation_p.Q19K	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	474	Pro-rich.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.Q474*(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TTAACTCCCTGAGGTGGTGGT	0.473																																																1	Substitution - Nonsense(1)	lung(1)	8											133	119	124					8																	117864237		2203	4300	6503	117933418	SO:0001583	missense	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1420C>A	8.37:g.117864237G>T	ENSP00000297338:p.Gln474Lys		117933418	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171209	0.57584	.	.	ENSG00000164754	ENST00000297338;ENST00000518055	T;T	0.65178	0.7;-0.14	5.71	5.71	0.89125	.	0.108239	0.64402	D	0.000005	T	0.54334	0.1852	L	0.44542	1.39	0.42186	D	0.991704	B	0.06786	0.001	B	0.04013	0.001	T	0.53725	-0.8398	10	0.07175	T	0.84	-21.6355	19.8625	0.96789	0.0:0.0:1.0:0.0	.	474	O60216	RAD21_HUMAN	K	474;19	ENSP00000297338:Q474K;ENSP00000428003:Q19K	ENSP00000297338:Q474K	Q	-	1	0	RAD21	117933418	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.429000	0.97481	2.689000	0.91719	0.655000	0.94253	CAG		0.473	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		T	117864237	G	T	117864237	3	4	109	1	0	0	0	0	1	0	0	0	13018	1299	45	2	491	2	RAD21	8	117864237	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	22929990	117864237	28499785	164	28730										
FLJ43860	389690	hgsc.bcm.edu	37	chr8	142476614	142476614	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcttttccttggcttgcgggAtgtggacagagcacaggcgg	15	9	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:142476614A>G	ENST00000430863.1	-	0	2452					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GGCTTGCGGGATGTGGACAGA	0.652																																																0			8											72	83	80					8																	142476614		2128	4230	6358	142545796			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142476614A>G			142545796		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																					0.652	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		G	142476614	A	G	142476614	1	3	109	0	1	0	0	0	0	0	0	0	5949	333	12	4		4	FLJ43860	8	142476614	RNA	SNP	A	TCGA-EF-5830-01A-01D-1657-10	24612377	142476614	3887408	165	28731										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144946730	144946730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggagcggaaggtgatcttgAggggcagcaaggctagcccc	17	9	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:144946730A>G	ENST00000525985.1	-	2	763	c.692T>C	c.(691-693)cTc>cCc	p.L231P				P58107	EPIPL_HUMAN	epiplakin 1	231						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	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)			GGTGATCTTGAGGGGCAGCAA	0.677																																																0			8											17	21	20					8																	144946730		2133	4223	6356	145018718	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.692T>C	8.37:g.144946730A>G	ENSP00000436337:p.Leu231Pro		145018718	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	10.29	1.308701	0.23821	.	.	ENSG00000227184	ENST00000525985	T	0.70749	-0.51	4.23	4.23	0.50019	.	.	.	.	.	T	0.81034	0.4739	M	0.76727	2.345	0.51012	D	0.999904	D	0.89917	1.0	D	0.70716	0.97	T	0.80374	-0.1409	9	0.36615	T	0.2	.	11.575	0.50856	1.0:0.0:0.0:0.0	.	231	E9PPU0	.	P	231	ENSP00000436337:L231P	ENSP00000436337:L231P	L	-	2	0	EPPK1	145018718	0.910000	0.30920	0.626000	0.29213	0.016000	0.09150	7.710000	0.84655	1.895000	0.54865	0.334000	0.21626	CTC		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144946730	A	G	144946730	3	3	109	1	0	0	0	0	1	0	0	0	5203	304	11	4	6574	4	EPPK1	8	144946730	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2470116	144946730	1417292	166	28732										
GPR172A	79581	hgsc.bcm.edu	37	chr8	145584592	145584592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tccaggtgggctctctgctcGgcgctgttgctatgttcccc	12	14	1	0	rs397514658		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:145584592G>A	ENST00000532887.1	+	5	1838	c.1255G>A	c.(1255-1257)Ggc>Agc	p.G419S	SLC52A2_ENST00000540505.1_Missense_Mutation_p.G331S|SLC52A2_ENST00000527078.1_Missense_Mutation_p.G419S|SLC52A2_ENST00000402965.1_Missense_Mutation_p.G419S|FBXL6_ENST00000455319.2_5'Flank|SLC52A2_ENST00000329994.2_Missense_Mutation_p.G419S|SLC52A2_ENST00000530047.1_Missense_Mutation_p.G419S|FBXL6_ENST00000331890.5_5'Flank|SLC52A2_ENST00000526752.1_Missense_Mutation_p.R87Q			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	419					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	CTCTCTGCTCGGCGCTGTTGC	0.652																																																0			8											111	104	106					8																	145584592		2203	4300	6503	145555400	SO:0001583	missense	79581			AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"Solute carriers"	30224	protein-coding gene	gene with protein product		607882	"G protein-coupled receptor 172A"	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.1255G>A	8.37:g.145584592G>A	ENSP00000436768:p.Gly419Ser		145555400	A8K6B6|D3DWL8|G1UCY1|Q86UT1	Missense_Mutation	SNP	ENST00000532887.1	37	CCDS6423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.810462|4.810462	0.90707|0.90707	.|.	.|.	ENSG00000185803|ENSG00000185803	ENST00000530047;ENST00000527078;ENST00000402965;ENST00000532887;ENST00000329994;ENST00000540505|ENST00000526752	D;D;D;D;D;D|D	0.86956|0.90504	-2.19;-2.19;-2.19;-2.19;-2.19;-1.94|-2.68	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.94142|0.94142	0.8121|0.8121	M|M	0.86502|0.86502	2.82|2.82	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.92514|0.92514	0.6019|0.6019	10|7	0.87932|0.13470	D|T	0|0.59	.|.	16.4138|16.4138	0.83727|0.83727	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	419|.	Q9HAB3|.	RFT3_HUMAN|.	S|Q	419;419;419;419;419;331|87	ENSP00000435820:G419S;ENSP00000434728:G419S;ENSP00000385961:G419S;ENSP00000436768:G419S;ENSP00000333638:G419S;ENSP00000440400:G331S|ENSP00000433796:R87Q	ENSP00000333638:G419S|ENSP00000433796:R87Q	G|R	+|+	1|2	0|0	GPR172A|GPR172A	145555400|145555400	1.000000|1.000000	0.71417|0.71417	0.190000|0.190000	0.23270|0.23270	0.731000|0.731000	0.41821|0.41821	7.543000|7.543000	0.82106|0.82106	2.480000|2.480000	0.83734|0.83734	0.456000|0.456000	0.33151|0.33151	GGC|CGG		0.652	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1	NM_024531		A	145584592	G	A	145584592	3	1	109	1	0	0	0	0	1	0	0	0	6689	1116	39	1	1269	1	GPR172A	8	145584592	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	637862	145584592	779430	167	28733										
AK3	50808	hgsc.bcm.edu	37	chr9	4719198	4719198	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggcgggatgaatccagcgAgcagtaaggcgttgtttaat	14	7	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:4719198A>G	ENST00000381809.3	-	3	611	c.381T>C	c.(379-381)gcT>gcC	p.A127A	AK3_ENST00000447596.4_Silent_p.A87A|AK3_ENST00000359883.2_Silent_p.A57A	NM_016282.3	NP_057366.2	P27144	KAD4_HUMAN	adenylate kinase 3	125	LID.				ADP biosynthetic process (GO:0006172)|AMP metabolic process (GO:0046033)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|GTP metabolic process (GO:0046039)|liver development (GO:0001889)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|response to drug (GO:0042493)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside triphosphate adenylate kinase activity (GO:0046899)			large_intestine(2)|lung(1)|ovary(2)	5	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0302)	Adefovir Dipivoxil(DB00718)|Tenofovir(DB00300)	GAATCCAGCGAGCAGTAAGGC	0.478																																																0			9											98	84	88					9																	4719198		2203	4300	6503	4709198	SO:0001819	synonymous_variant	50808			BC013771	CCDS6455.1, CCDS56561.1, CCDS56562.1	9p24.1	2010-09-29	2004-06-11	2005-04-07	ENSG00000147853	ENSG00000147853			17376	protein-coding gene	gene with protein product		609290	"adenylate kinase 6", "adenylate kinase 3 like 1"	AK6, AK3L1		8288, 182062	Standard	NM_001199852		Approved	AKL3L1	uc003ziq.2	Q9UIJ7	OTTHUMG00000019472	ENST00000381809.3:c.381T>C	9.37:g.4719198A>G			4709198	B2R927|D3DQ62|Q6IBH4|Q6NXQ5|Q8IUU9	Silent	SNP	ENST00000381809.3	37	CCDS6455.1																																																																																				0.478	AK3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051585.1	NM_016282		G	4719198	A	G	4719198	2	3	109	1	0	0	0	0	0	0	0	1	441	291	11	4		4	AK3	9	4719198	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10		4719198	136494233	168	28734										
JAK2	3717	hgsc.bcm.edu	37	chr9	5070030	5070030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccaaatggtgtttcacaaaaTcagaaatgaagatttgatat	7	5	2	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:5070030T>C	ENST00000381652.3	+	12	2113	c.1619T>C	c.(1618-1620)aTc>aCc	p.I540T	JAK2_ENST00000539801.1_Missense_Mutation_p.I540T|JAK2_ENST00000544510.1_Missense_Mutation_p.I391T	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	540					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.I540T(1)|p.I540_E543>KK(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTTCACAAAATCAGAAATGAA	0.333		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	2	Substitution - Missense(1)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(2)	9											88	82	84					9																	5070030		2202	4300	6502	5060030	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1619T>C	9.37:g.5070030T>C	ENSP00000371067:p.Ile540Thr		5060030	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234067	0.79688	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.27557	1.66;1.66;1.66	5.07	5.07	0.68467	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	P	0.59546	0.859	T	0.63256	-0.6678	10	0.87932	D	0	-9.0565	14.4823	0.67592	0.0:0.0:0.0:1.0	.	540	O60674	JAK2_HUMAN	T	540;540;391	ENSP00000440387:I540T;ENSP00000371067:I540T;ENSP00000443103:I391T	ENSP00000371067:I540T	I	+	2	0	JAK2	5060030	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.656000	0.83736	1.892000	0.54788	0.455000	0.32223	ATC		0.333	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5070030	T	C	5070030	3	2	109	1	0	0	0	0	1	0	0	0	7959	1435	50	4	1657	4	JAK2	9	5070030	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	350832	5070030	136143401	169	28735										
JAK2	3717	hgsc.bcm.edu	37	chr9	5070046	5070046	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaaatcagaaatgaagatttGatatttgtaagtcattagat	7	2	2	5			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:5070046G>A	ENST00000381652.3	+	12	2129	c.1635G>A	c.(1633-1635)ttG>ttA	p.L545L	JAK2_ENST00000539801.1_Silent_p.L545L|JAK2_ENST00000544510.1_Silent_p.L396L	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	545	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATGAAGATTTGATATTTGTAA	0.323		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											83	78	79					9																	5070046		2202	4298	6500	5060046	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1635G>A	9.37:g.5070046G>A			5060046	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.323	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			A	5070046	G	A	5070046	2	1	109	1	0	0	0	0	0	0	0	1	7959	1281	45	3		3	JAK2	9	5070046	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	16	5070046	136143385	170	28736										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21970944	21970944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atgcgggcatggttactgccTctggtgccccccgcagccgc	13	16	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:21970944T>C	ENST00000304494.5	-	2	684	c.414A>G	c.(412-414)agA>agG	p.R138R	CDKN2A_ENST00000497750.1_Silent_p.R87R|CDKN2A_ENST00000498628.2_Silent_p.R87R|CDKN2A_ENST00000494262.1_Silent_p.R87R|CDKN2A_ENST00000579122.1_Intron|CDKN2A_ENST00000498124.1_Silent_p.R138R|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000578845.2_Silent_p.R87R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000446177.1_Silent_p.R138R|CDKN2A_ENST00000479692.2_Silent_p.R87R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	138					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(13)|p.R128fs*12(3)|p.A118fs*10(1)|p.0(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GGTTACTGCCTCTGGTGCCCC	0.632		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1333	Whole gene deletion(1316)|Unknown(13)|Deletion - Frameshift(4)	haematopoietic_and_lymphoid_tissue(278)|skin(168)|central_nervous_system(164)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|upper_aerodigestive_tract(49)|oesophagus(48)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											30	33	32					9																	21970944		2203	4300	6503	21960944	SO:0001819	synonymous_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.414A>G	9.37:g.21970944T>C			21960944	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Silent	SNP	ENST00000304494.5	37	CCDS6510.1																																																																																				0.632	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		C	21970944	T	C	21970944	2	2	109	1	0	0	0	0	0	0	0	1	3167	1548	54	4		4	CDKN2A	9	21970944	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	16900898	21970944	119242487	171	28737										
CLTA	1211	hgsc.bcm.edu	37	chr9	36191149	36191149	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gccggcgaagaagacccggcTgcggccttcttggcgcagca	15	14	1	2	rs2274524	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:36191149T>C	ENST00000242285.6	+	1	216	c.96T>C	c.(94-96)gcT>gcC	p.A32A	CLTA_ENST00000396603.2_Silent_p.A32A|CLTA_ENST00000466396.1_Silent_p.A32A|CLTA_ENST00000538225.1_Silent_p.A32A|CLTA_ENST00000470744.1_Silent_p.A32A|CLTA_ENST00000345519.5_Silent_p.A32A|CLTA_ENST00000433436.2_Silent_p.A32A|CLTA_ENST00000540080.1_Silent_p.A32A			P09496	CLCA_HUMAN	clathrin, light chain A	32					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			AAGACCCGGCTGCGGCCTTCT	0.746													C|||	673	0.134385	0.1747	0.0634	5008	,	,		11673	0.1806		0.0497	False		,,,				2504	0.1697															0			9						C	,,,,,	525,3703		24,477,1613	8	9	9		96,96,96,96,96,96	4.5	1	9	dbSNP_100	9	447,7817		9,429,3694	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLTA	NM_001076677.2,NM_001184760.1,NM_001184761.1,NM_001184762.1,NM_001833.3,NM_007096.3	,,,,,	33,906,5307	CC,CT,TT		5.409,12.4172,7.781	,,,,,	32/237,32/231,32/169,32/167,32/219,32/249	36191149	972,11520	2114	4132	6246	36181149	SO:0001819	synonymous_variant	1211				CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"clathrin, light polypeptide (Lca)"			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.96T>C	9.37:g.36191149T>C			36181149	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																				0.746	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		C	36191149	T	C	36191149	2	2	109	1	0	0	0	0	0	0	0	1	3570	1567	55	4		4	CLTA	9	36191149	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	14220205	36191149	105022282	172	28738										
ECM2	1842	hgsc.bcm.edu	37	chr9	95285114	95285114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agtcagtttgaaaaatgataAgcagaaaaaaacaaaacaaa	6	4	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:95285114A>G	ENST00000344604.5	-	2	184	c.35T>C	c.(34-36)cTt>cCt	p.L12P	ECM2_ENST00000375540.1_Missense_Mutation_p.L12P|CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Missense_Mutation_p.L12P	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	12					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						AAAAATGATAAGCAGAAAAAA	0.333																																																0			9											46	49	48					9																	95285114		2202	4300	6502	94324935	SO:0001583	missense	1842			AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"matrix glycoprotein SC1/ECM2"	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.35T>C	9.37:g.95285114A>G	ENSP00000344758:p.Leu12Pro		94324935	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729281	0.69074	.	.	ENSG00000106823	ENST00000444490;ENST00000344604;ENST00000375540;ENST00000395534	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.28	4.28	0.50868	.	0.303544	0.27340	N	0.019818	T	0.42063	0.1186	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.76494	0.998;0.998;0.997;0.999	D;P;P;D	0.66351	0.909;0.831;0.831;0.943	T	0.39800	-0.9596	10	0.87932	D	0	.	13.5504	0.61728	1.0:0.0:0.0:0.0	.	12;12;12;12	Q5T9F3;O94769;B4DK93;O94769-2	.;ECM2_HUMAN;.;.	P	12	ENSP00000393971:L12P;ENSP00000344758:L12P;ENSP00000364690:L12P;ENSP00000378905:L12P	ENSP00000344758:L12P	L	-	2	0	ECM2	94324935	1.000000	0.71417	0.602000	0.28890	0.943000	0.58893	5.725000	0.68507	1.948000	0.56530	0.528000	0.53228	CTT		0.333	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		G	95285114	A	G	95285114	3	3	109	1	0	0	0	0	1	0	0	0	4909	72	3	4	2100	4	ECM2	9	95285114	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	59093965	95285114	45928317	173	28739										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98239882	98239882	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caatgagcacaggcccagtcCtgcagccactgacagtgcaa	10	14	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:98239882C>A	ENST00000331920.6	-	10	1749	c.1450G>T	c.(1450-1452)Gga>Tga	p.G484*	PTCH1_ENST00000421141.1_Nonsense_Mutation_p.G333*|PTCH1_ENST00000429896.2_Nonsense_Mutation_p.G333*|PTCH1_ENST00000375274.2_Nonsense_Mutation_p.G483*|PTCH1_ENST00000437951.1_Nonsense_Mutation_p.G418*|PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000430669.2_Nonsense_Mutation_p.G418*|PTCH1_ENST00000418258.1_Nonsense_Mutation_p.G333*	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	484	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.G484R(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGGCCCAGTCCTGCAGCCACT	0.572																																																1	Substitution - Missense(1)	skin(1)	9	GRCh37	CM032341	PTCH1	M							50	53	52					9																	98239882		2203	4300	6503	97279703	SO:0001587	stop_gained	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1450G>T	9.37:g.98239882C>A	ENSP00000332353:p.Gly484*		97279703	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Nonsense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	42	9.412021	0.99163	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274	.	.	.	5.06	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.8386	13.802	0.63206	0.0:0.9261:0.0:0.0739	.	.	.	.	X	484;418;333;333;418;333;483	.	ENSP00000332353:G484X	G	-	1	0	PTCH1	97279703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.320000	0.79064	1.351000	0.45789	0.655000	0.94253	GGA		0.572	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98239882	C	A	98239882	4	1	109	1	0	0	0	0	0	1	0	0	12764	690	24	2	2949	2	PTCH1	9	98239882	Nonsense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	2954768	98239882	42973549	174	28740										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98248086	98248086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggggtctgtatcatgagttgAggattaaacatagcctcttc	11	7	3	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:98248086A>G	ENST00000331920.6	-	3	764	c.465T>C	c.(463-465)ccT>ccC	p.P155P	PTCH1_ENST00000421141.1_Silent_p.P4P|PTCH1_ENST00000429896.2_Silent_p.P4P|PTCH1_ENST00000375274.2_Silent_p.P154P|PTCH1_ENST00000468211.2_Silent_p.P89P|PTCH1_ENST00000437951.1_Silent_p.P89P|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000430669.2_Silent_p.P89P|PTCH1_ENST00000418258.1_Silent_p.P4P	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	155					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TCATGAGTTGAGGATTAAACA	0.453																																																0			9											218	229	225					9																	98248086		2203	4300	6503	97287907	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.465T>C	9.37:g.98248086A>G			97287907	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.453	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		G	98248086	A	G	98248086	2	3	109	1	0	0	0	0	0	0	0	1	12764	291	11	4		4	PTCH1	9	98248086	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	8204	98248086	42965345	175	28741										
ABCA1	19	hgsc.bcm.edu	37	chr9	107584854	107584854	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	taaaaattcagtgccaggccAtcgacagccaccttcatccc	6	15	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:107584854A>G	ENST00000374736.3	-	19	3145	c.2751T>C	c.(2749-2751)gaT>gaC	p.D917D		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	917	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		D -> Y (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GTGCCAGGCCATCGACAGCCA	0.552																																																0			9											142	133	136					9																	107584854		2203	4300	6503	106624675	SO:0001819	synonymous_variant	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2751T>C	9.37:g.107584854A>G			106624675	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																				0.552	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		G	107584854	A	G	107584854	2	3	109	1	0	0	0	0	0	0	0	1	28	214	8	4		4	ABCA1	9	107584854	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	9336768	107584854	33628577	176	28742										
ABL1	25	hgsc.bcm.edu	37	chr9	133760130	133760130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caacctgactccaaaaccccTccggcggcaggtcaccgtgg	10	17	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:133760130T>C	ENST00000318560.5	+	11	2834	c.2453T>C	c.(2452-2454)cTc>cCc	p.L818P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	818	Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCAAAACCCCTCCGGCGGCAG	0.622			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	0			9											14	18	17					9																	133760130		2198	4289	6487	132749951	SO:0001583	missense	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2453T>C	9.37:g.133760130T>C	ENSP00000323315:p.Leu818Pro		132749951	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	T	9.064	0.995133	0.19043	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.16457	2.34;2.34	5.54	3.17	0.36434	.	0.800466	0.11693	N	0.538717	T	0.09774	0.0240	N	0.19112	0.55	0.54753	D	0.999983	B;B	0.32128	0.357;0.357	B;B	0.33620	0.167;0.167	T	0.24368	-1.0162	10	0.28530	T	0.3	.	2.7618	0.05308	0.1489:0.0819:0.1525:0.6167	.	818;855	P00519;Q59FK4	ABL1_HUMAN;.	P	633;837;818	ENSP00000361423:L837P;ENSP00000323315:L818P	ENSP00000323315:L818P	L	+	2	0	ABL1	132749951	0.751000	0.28327	0.116000	0.21606	0.642000	0.38348	1.223000	0.32527	0.894000	0.36317	0.459000	0.35465	CTC		0.622	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		C	133760130	T	C	133760130	3	2	109	1	0	0	0	0	1	0	0	0	92	1551	54	4	2635	4	ABL1	9	133760130	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	26175276	133760130	7453301	177	28743										
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133787222	133787222	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctgccaaagccgtctcggtaCgcatcccagccccggaagaa	10	16	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:133787222C>T	ENST00000372338.4	-	5	1145	c.903G>A	c.(901-903)gcG>gcA	p.A301A	FIBCD1_ENST00000253018.4_Silent_p.A143A|FIBCD1_ENST00000372337.2_Silent_p.A143A|FIBCD1_ENST00000448616.1_Silent_p.A301A	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	301	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CGTCTCGGTACGCATCCCAGC	0.677																																																0			9											46	39	42					9																	133787222		2198	4300	6498	132777043	SO:0001819	synonymous_variant	84929			AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"Fibrinogen C domain containing"	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.903G>A	9.37:g.133787222C>T			132777043	A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	C	1.277	-0.611303	0.03690	.	.	ENSG00000130720	ENST00000444139	.	.	.	5.17	-10.3	0.00346	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.76610	-0.2896	4	.	.	.	.	10.9936	0.47563	0.0607:0.123:0.5413:0.275	.	.	.	.	H	255	.	.	R	-	2	0	FIBCD1	132777043	0.000000	0.05858	0.001000	0.08648	0.195000	0.23768	-9.652000	0.00010	-6.722000	0.00003	-1.464000	0.01018	CGT		0.677	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		T	133787222	C	T	133787222	2	4	109	1	0	0	0	0	0	0	0	1	5903	523	19	1		1	FIBCD1	9	133787222	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	27092	133787222	7426209	178	28744										
C9orf171	389799	hgsc.bcm.edu	37	chr9	135374875	135374875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcctggtgactgcccgggagAacttgctctaccgtcagctc	12	14	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:135374875A>G	ENST00000343036.2	+	4	568	c.520A>G	c.(520-522)Aac>Gac	p.N174D	C9orf171_ENST00000393215.3_Missense_Mutation_p.N138D|C9orf171_ENST00000393216.2_Missense_Mutation_p.N138D	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	174										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TGCCCGGGAGAACTTGCTCTA	0.597																																																0			9											87	87	87					9																	135374875		2203	4300	6503	134364696	SO:0001583	missense	389799			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.520A>G	9.37:g.135374875A>G	ENSP00000343290:p.Asn174Asp		134364696	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.537613	0.65085	.	.	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.22743	1.94;1.94;1.94	5.26	4.07	0.47477	.	0.394558	0.24904	N	0.034664	T	0.15305	0.0369	L	0.40543	1.245	0.26124	N	0.980506	B;P	0.40515	0.413;0.719	B;B	0.38985	0.098;0.287	T	0.10660	-1.0620	10	0.35671	T	0.21	.	5.7025	0.17891	0.5359:0.3145:0.0:0.1496	.	138;174	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	D	138;174;138	ENSP00000376908:N138D;ENSP00000343290:N174D;ENSP00000376909:N138D	ENSP00000343290:N174D	N	+	1	0	C9orf171	134364696	0.970000	0.33590	0.991000	0.47740	0.818000	0.46254	2.327000	0.43858	2.116000	0.64780	0.459000	0.35465	AAC		0.597	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		G	135374875	A	G	135374875	3	3	109	1	0	0	0	0	1	0	0	0	2476	246	9	4	534	4	C9orf171	9	135374875	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1587653	135374875	5838556	179	28745										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135983446	135983446	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaggtgaggcttctcctcacTcagcccgttctctgcaacca	9	15	4	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:135983446T>G	ENST00000372050.3	-	6	1147	c.1126A>C	c.(1126-1128)Agt>Cgt	p.S376R	RALGDS_ENST00000372062.3_Missense_Mutation_p.S347R|RALGDS_ENST00000542690.1_Missense_Mutation_p.S447R|RALGDS_ENST00000393157.3_Missense_Mutation_p.S375R|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000372047.3_Missense_Mutation_p.S364R|RALGDS_ENST00000393160.3_Missense_Mutation_p.S321R	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	376					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTCTCCTCACTCAGCCCGTTC	0.577			T	CIITA	"PMBL, Hodgkin Lymphona, "																																Melanoma(189;762 2088 15384 21931 52515)		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	0			9											98	86	90					9																	135983446		2203	4300	6503	134973267	SO:0001583	missense	5900			AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1126A>C	9.37:g.135983446T>G	ENSP00000361120:p.Ser376Arg		134973267	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643125	0.67244	.	.	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000372051;ENST00000393157;ENST00000542690;ENST00000372062;ENST00000424572	T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.39	-1.73	0.08081	Ras guanine nucleotide exchange factor, domain (1);	1.108720	0.06691	N	0.769766	T	0.15132	0.0365	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B;P;P	0.46952	0.372;0.08;0.344;0.146;0.0;0.421;0.887;0.815	B;B;B;B;B;B;B;B	0.35931	0.118;0.029;0.088;0.024;0.005;0.095;0.214;0.214	T	0.18366	-1.0339	10	0.16420	T	0.52	.	0.8645	0.01200	0.3018:0.3306:0.1541:0.2136	.	447;347;376;364;321;375;364;376	F5H6M6;E7ER93;Q12967-2;Q8TEK9;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;.;.;GNDS_HUMAN	R	376;364;321;145;375;447;347;8	ENSP00000361120:S376R;ENSP00000361117:S364R;ENSP00000376867:S321R;ENSP00000376864:S375R;ENSP00000437518:S447R;ENSP00000361132:S347R;ENSP00000391814:S8R	ENSP00000361117:S364R	S	-	1	0	RALGDS	134973267	0.000000	0.05858	0.008000	0.14137	0.936000	0.57629	-0.704000	0.05058	-0.229000	0.09854	0.533000	0.62120	AGT		0.577	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		G	135983446	T	G	135983446	3	3	109	1	0	0	0	0	1	0	0	0	13053	1551	54	4	1670	4	RALGDS	9	135983446	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	608571	135983446	5229985	180	28746										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137623961	137623961	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggccaaaagggagaaccagcGattatcgagccggtgaggac	15	9	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:137623961G>A	ENST00000371817.3	+	9	1791	c.1377G>A	c.(1375-1377)gcG>gcA	p.A459A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	459	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GAGAACCAGCGATTATCGAGC	0.557																																																0			9											110	95	101					9																	137623961		2203	4300	6503	136763782	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1377G>A	9.37:g.137623961G>A			136763782	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.557	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137623961	G	A	137623961	2	1	109	1	0	0	0	0	0	0	0	1	3702	1045	37	1		1	COL5A1	9	137623961	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	1640515	137623961	3589470	181	28747										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24835175	24835175	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcaccaggaccatccatacTcccagcctcaccagctacaa	6	18	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:24835175T>C	ENST00000376454.3	+	21	5784	c.5754T>C	c.(5752-5754)acT>acC	p.T1918T	KIAA1217_ENST00000376462.1_Silent_p.T1239T|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000458595.1_Silent_p.T1324T|KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.T1349T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1918					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CCATCCATACTCCCAGCCTCA	0.532																																																0			10											76	71	72					10																	24835175		2203	4300	6503	24875181	SO:0001819	synonymous_variant	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5754T>C	10.37:g.24835175T>C			24875181	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																				0.532	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24835175	T	C	24835175	2	2	109	1	0	0	0	0	0	0	0	1	8237	1538	54	4		4	KIAA1217	10	24835175	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10		24835175	110699572	182	28748										
MYPN	84665	hgsc.bcm.edu	37	chr10	69933946	69933946	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	actgttttgaactccaatgcTcccccagcggtgacaacatc	7	14	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:69933946T>C	ENST00000358913.5	+	11	2585	c.2097T>C	c.(2095-2097)gcT>gcC	p.A699A	MYPN_ENST00000540630.1_Silent_p.A699A|MYPN_ENST00000354393.2_Silent_p.A424A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	699					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACTCCAATGCTCCCCCAGCGG	0.493																																																0			10											138	126	130					10																	69933946		2203	4300	6503	69603952	SO:0001819	synonymous_variant	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2097T>C	10.37:g.69933946T>C			69603952	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																				0.493	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		C	69933946	T	C	69933946	2	2	109	1	0	0	0	0	0	0	0	1	10128	1538	54	4		4	MYPN	10	69933946	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	45098771	69933946	65600801	183	28749										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692910	89692910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aagctggaaagggacgaactGgtgtaatgatatgtgcatat	13	4	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:89692910G>T	ENST00000371953.3	+	5	1751	c.394G>T	c.(394-396)Ggt>Tgt	p.G132C		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	132	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		G -> V (in one patient with clinical findings suggesting hamartoma tumor syndrome). {ECO:0000269|PubMed:16752378}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.G132S(3)|p.Y27fs*1(2)|p.A121_F145del(1)|p.R130fs*2(1)|p.T131fs*42(1)|p.F56fs*2(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GGGACGAACTGGTGTAATGAT	0.398		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	57	Whole gene deletion(37)|Deletion - Frameshift(11)|Unknown(5)|Substitution - Missense(3)|Deletion - In frame(1)	prostate(16)|central_nervous_system(13)|skin(6)|endometrium(5)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											137	128	131					10																	89692910		2203	4300	6503	89682890	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.394G>T	10.37:g.89692910G>T	ENSP00000361021:p.Gly132Cys		89682890	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.255594	0.80135	.	.	ENSG00000171862	ENST00000371953	D	0.99552	-6.15	5.22	4.3	0.51218	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99816	0.9919	H	0.99026	4.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96700	0.9517	9	.	.	.	-10.5526	15.1176	0.72416	0.0:0.0:0.8573:0.1427	.	132	P60484	PTEN_HUMAN	C	132	ENSP00000361021:G132C	.	G	+	1	0	PTEN	89682890	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.429000	0.97481	1.157000	0.42530	-0.182000	0.12963	GGT		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89692910	G	T	89692910	3	4	109	1	0	0	0	0	1	0	0	0	12772	1348	47	2	412	2	PTEN	10	89692910	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	19758964	89692910	45841837	184	28750										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692960	89692960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cggggcaaatttttaaaggcAcaagaggccctagatttcta	10	8	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:89692960A>G	ENST00000371953.3	+	5	1801	c.444A>G	c.(442-444)gcA>gcG	p.A148A		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	148	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.K147fs*5(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TTTTAAAGGCACAAGAGGCCC	0.378		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	51	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											69	70	70					10																	89692960		2203	4300	6503	89682940	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.444A>G	10.37:g.89692960A>G			89682940	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.378	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692960	A	G	89692960	2	3	109	1	0	0	0	0	0	0	0	1	12772	146	6	4		4	PTEN	10	89692960	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	50	89692960	45841787	185	28751										
CWF19L1	55280	hgsc.bcm.edu	37	chr10	101993030	101993030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gctcaaagtctttccggaagCggcgagccagggtctcctcg	13	13	3	0	rs375717897		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:101993030C>T	ENST00000354105.4	-	14	1657	c.1571G>A	c.(1570-1572)cGc>cAc	p.R524H	CWF19L1_ENST00000370379.1_Missense_Mutation_p.R239H|CWF19L1_ENST00000478047.1_5'UTR|RP11-316M21.6_ENST00000444359.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	524							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		TTTCCGGAAGCGGCGAGCCAG	0.468																																																0			10						C	HIS/ARG	0,4406		0,0,2203	88	91	90		1571	3.4	1	10		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	CWF19L1	NM_018294.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	524/539	101993030	1,13005	2203	4300	6503	101983020	SO:0001583	missense	55280			AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1571G>A	10.37:g.101993030C>T	ENSP00000326411:p.Arg524His		101983020	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.119088	0.56505	0.0	1.16E-4	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.30448	1.53;1.53	5.38	3.36	0.38483	Histidine triad motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.577194	0.18770	N	0.131623	T	0.28067	0.0692	L	0.34521	1.04	0.20975	N	0.999811	D;D;P	0.58268	0.982;0.958;0.943	P;P;P	0.52710	0.707;0.467;0.586	T	0.08806	-1.0704	10	0.45353	T	0.12	-0.0378	3.0391	0.06132	0.2155:0.545:0.1426:0.0969	.	228;387;524	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	H	524;239	ENSP00000326411:R524H;ENSP00000359405:R239H	ENSP00000326411:R524H	R	-	2	0	CWF19L1	101983020	0.890000	0.30428	0.997000	0.53966	0.604000	0.37047	1.202000	0.32271	1.255000	0.44051	0.561000	0.74099	CGC		0.468	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		T	101993030	C	T	101993030	3	4	109	1	0	0	0	0	1	0	0	0	4077	768	27	1	49	1	CWF19L1	10	101993030	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	12300070	101993030	33541717	186	28752										
SEMA4G	57715	hgsc.bcm.edu	37	chr10	102737414	102737414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgctttaaccatgtgcggtTcctgcagcggctcaattcta	10	11	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:102737414T>C	ENST00000370250.4	+	4	735	c.362T>C	c.(361-363)tTc>tCc	p.F121S	SEMA4G_ENST00000210633.3_Missense_Mutation_p.F121S|SEMA4G_ENST00000517724.1_Missense_Mutation_p.F121S|SEMA4G_ENST00000519756.1_3'UTR|RP11-108L7.4_ENST00000447344.1_RNA|MIR608_ENST00000384820.1_RNA	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	121	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		CATGTGCGGTTCCTGCAGCGG	0.552																																																0			10											237	197	211					10																	102737414		2203	4300	6503	102727404	SO:0001583	missense	57715			AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.362T>C	10.37:g.102737414T>C	ENSP00000359270:p.Phe121Ser		102727404	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.859485	0.91433	.	.	ENSG00000095539	ENST00000519649;ENST00000518124;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83	5.32	5.32	0.75619	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.154036	0.64402	D	0.000015	T	0.34279	0.0892	M	0.78801	2.425	0.51482	D	0.999929	D;D;P	0.71674	0.996;0.998;0.579	D;D;B	0.76575	0.95;0.988;0.305	T	0.12218	-1.0556	10	0.87932	D	0	.	14.4545	0.67407	0.0:0.0:0.0:1.0	.	121;121;121	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	S	121	ENSP00000428896:F121S;ENSP00000430103:F121S;ENSP00000359270:F121S;ENSP00000430175:F121S;ENSP00000210633:F121S	ENSP00000210633:F121S	F	+	2	0	SEMA4G	102727404	1.000000	0.71417	0.944000	0.38274	0.981000	0.71138	7.482000	0.81143	2.014000	0.59158	0.402000	0.26972	TTC		0.552	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			C	102737414	T	C	102737414	3	2	109	1	0	0	0	0	1	0	0	0	14073	1783	62	4	376	4	SEMA4G	10	102737414	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	744384	102737414	32797333	187	28753										
VWA2	340706	hgsc.bcm.edu	37	chr10	116038577	116038577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gagaggatcgcggcggacccTtgcggtgctggctgcacact	16	12	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:116038577T>C	ENST00000392982.3	+	8	1050	c.800T>C	c.(799-801)cTt>cCt	p.L267P	VWA2_ENST00000603594.1_Missense_Mutation_p.L267P			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	267		Cleavage.			calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CGGCGGACCCTTGCGGTGCTG	0.667																																																0			10											127	96	107					10																	116038577		2203	4300	6503	116028567	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.800T>C	10.37:g.116038577T>C	ENSP00000376708:p.Leu267Pro		116028567	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	T	0.881	-0.728643	0.03135	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.67345	-0.26	5.55	-2.95	0.05564	.	1.151880	0.06035	N	0.653756	T	0.39118	0.1066	N	0.08118	0	0.21020	N	0.99981	B;B	0.10296	0.002;0.003	B;B	0.06405	0.001;0.002	T	0.06917	-1.0800	10	0.29301	T	0.29	.	2.2623	0.04070	0.3312:0.2311:0.3261:0.1117	.	267;267	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	P	267	ENSP00000376708:L267P	ENSP00000298715:L267P	L	+	2	0	VWA2	116028567	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.710000	0.25748	-1.242000	0.02523	-4.184000	0.00009	CTT		0.667	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		C	116038577	T	C	116038577	3	2	109	1	0	0	0	0	1	0	0	0	17279	1609	56	4	826	4	VWA2	10	116038577	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	13301163	116038577	19496170	188	28754										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117059717	117059717	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcttaaaagctaatccttgTacatctatggcaaatggcct	8	9	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:117059717T>C	ENST00000355044.3	+	16	2715	c.2589T>C	c.(2587-2589)tgT>tgC	p.C863C	ATRNL1_ENST00000423111.2_5'Flank|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	863	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTAATCCTTGTACATCTATGG	0.428																																																0			10											78	77	78					10																	117059717		2203	4300	6503	117049707	SO:0001819	synonymous_variant	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2589T>C	10.37:g.117059717T>C			117049707	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																				0.428	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117059717	T	C	117059717	2	2	109	1	0	0	0	0	0	0	0	1	1208	1644	57	4		4	ATRNL1	10	117059717	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1021140	117059717	18475030	189	28755										
BAG3	9531	hgsc.bcm.edu	37	chr10	121432094	121432094	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgcatcgagccgggagggcTcaccagccaggagcagcacg	16	13	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:121432094T>C	ENST00000369085.3	+	3	1141	c.835T>C	c.(835-837)Tca>Cca	p.S279P		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	279					brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		CCGGGAGGGCTCACCAGCCAG	0.662																																																0			10											43	50	48					10																	121432094		2203	4299	6502	121422084	SO:0001583	missense	9531			AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.835T>C	10.37:g.121432094T>C	ENSP00000358081:p.Ser279Pro		121422084	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	T	17.04	3.287175	0.59867	.	.	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.79247	-1.07;-1.25	5.81	4.68	0.58851	.	0.380637	0.30620	N	0.009229	T	0.78830	0.4345	L	0.34521	1.04	0.45025	D	0.998042	D;D	0.63880	0.993;0.993	P;P	0.60949	0.881;0.881	T	0.77233	-0.2663	10	0.40728	T	0.16	-14.6173	11.546	0.50694	0.0:0.0695:0.0:0.9305	.	279;279	O95817;Q53GY1	BAG3_HUMAN;.	P	279;221	ENSP00000358081:S279P;ENSP00000410036:S221P	ENSP00000358081:S279P	S	+	1	0	BAG3	121422084	1.000000	0.71417	0.827000	0.32855	0.177000	0.22998	5.852000	0.69488	1.041000	0.40125	0.383000	0.25322	TCA		0.662	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281		C	121432094	T	C	121432094	3	2	109	1	0	0	0	0	1	0	0	0	1289	1551	54	4	845	4	BAG3	10	121432094	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4372377	121432094	14102653	190	28756										
TACC2	10579	hgsc.bcm.edu	37	chr10	123842777	123842777	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtgacccctgaggcccctgcTgcagcccagcagggcacaga	13	16	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:123842777T>C	ENST00000369005.1	+	4	1102	c.762T>C	c.(760-762)gcT>gcC	p.A254A	TACC2_ENST00000515273.1_Silent_p.A254A|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000334433.3_Silent_p.A254A|TACC2_ENST00000515603.1_Silent_p.A254A|TACC2_ENST00000453444.2_Silent_p.A254A|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	254					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGGCCCCTGCTGCAGCCCAGC	0.612																																																0			10											39	46	44					10																	123842777		2203	4299	6502	123832767	SO:0001819	synonymous_variant	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.762T>C	10.37:g.123842777T>C			123832767	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																				0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123842777	T	C	123842777	2	2	109	1	0	0	0	0	0	0	0	1	15541	1567	55	4		4	TACC2	10	123842777	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2410683	123842777	11691970	191	28757										
BCCIP	56647	hgsc.bcm.edu	37	chr10	127515180	127515180	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gaagtgaatattgaatttgaAgcttattccctatcagataa	7	5	1	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:127515180A>G	ENST00000278100.6	+	2	198	c.186A>G	c.(184-186)gaA>gaG	p.E62E	BCCIP_ENST00000368759.5_Silent_p.E62E|BCCIP_ENST00000299130.3_Silent_p.E62E|BCCIP_ENST00000478798.1_3'UTR|BCCIP_ENST00000429863.2_Silent_p.E62E	NM_078468.2	NP_510868.1	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A interacting protein	62	Interaction with BRCA2.				cell cycle (GO:0007049)|DNA repair (GO:0006281)|neuroendocrine cell differentiation (GO:0061101)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nucleus (GO:0005634)	kinase regulator activity (GO:0019207)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)	8		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTGAATTTGAAGCTTATTCCC	0.294																																																0			10											83	86	85					10																	127515180		2202	4299	6501	127505170	SO:0001819	synonymous_variant	56647			AB040451	CCDS7649.1, CCDS7650.1, CCDS7651.1	10q26.2	2008-05-14	2001-11-29		ENSG00000107949	ENSG00000107949			978	protein-coding gene	gene with protein product		611883	"BRCA2 and CDKN1A-interacting protein"			11313963, 10878006	Standard	NM_016567		Approved	BCCIPalpha, TOK-1	uc001ljd.4	Q9P287	OTTHUMG00000019237	ENST00000278100.6:c.186A>G	10.37:g.127515180A>G			127505170	B3KP45|Q8ND15|Q96GC4|Q9P288	Silent	SNP	ENST00000278100.6	37	CCDS7651.1																																																																																				0.294	BCCIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050941.1			G	127515180	A	G	127515180	2	3	109	1	0	0	0	0	0	0	0	1	1357	69	3	4		4	BCCIP	10	127515180	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	3672403	127515180	8019567	192	28758										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	379598	379598	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcagacggagaaagtcccgaAcccgctcccgccgcctccgt	11	18	0	2	rs1134699	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:379598A>G	ENST00000329962.6	+	15	2385	c.2385A>G	c.(2383-2385)gaA>gaG	p.E795E		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	795					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		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;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAAGTCCCGAACCCGCTCCCG	0.731													.|||	2497	0.498602	0.6664	0.464	5008	,	,		10232	0.4911		0.4026	False		,,,				2504	0.4029															0			11						G		2237,1841		675,887,477	5	7	7		2385	2.7	0.3	11	dbSNP_86	7	2925,5275		621,1683,1796	no	coding-synonymous	B4GALNT4	NM_178537.4		1296,2570,2273	GG,GA,AA		35.6707,45.1447,42.0427		795/1040	379598	5162,7116	2039	4100	6139	369598	SO:0001819	synonymous_variant	338707			AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2385A>G	11.37:g.379598A>G			369598	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																				0.731	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		G	379598	A	G	379598	2	3	109	1	0	0	0	0	0	0	0	1	1270	40	2	4		4	B4GALNT4	11	379598	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10		379598	134626918	193	28759										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253733	1253733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccgatcccaacagtgccttcTcgcgctgccactccatcatc	6	19	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1253733T>C	ENST00000529681.1	+	16	1955	c.1897T>C	c.(1897-1899)Tcg>Ccg	p.S633P	MUC5B_ENST00000447027.1_Missense_Mutation_p.S636P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	633	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CAGTGCCTTCTCGCGCTGCCA	0.667																																																0			11											38	44	42					11																	1253733		2108	4208	6316	1210309	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1897T>C	11.37:g.1253733T>C	ENSP00000436812:p.Ser633Pro		1210309	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	10.32	1.318377	0.23994	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.78707	-1.2;-1.2	4.32	-1.52	0.08637	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	D	0.85890	0.5802	M	0.83312	2.635	0.09310	N	1	D;D;D	0.76494	0.984;0.999;0.999	P;D;D	0.72338	0.825;0.977;0.977	T	0.76121	-0.3075	9	0.87932	D	0	.	8.862	0.35263	0.0921:0.0:0.5806:0.3274	.	633;1292;636	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	P	633;636;634;669	ENSP00000436812:S633P;ENSP00000415793:S636P	ENSP00000343037:S634P	S	+	1	0	MUC5B	1210309	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	-0.074000	0.11450	-0.320000	0.08640	0.379000	0.24179	TCG		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1253733	T	C	1253733	3	2	109	1	0	0	0	0	1	0	0	0	10009	1551	54	4	1968	4	MUC5B	11	1253733	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	874135	1253733	133752783	194	28760										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1270938	1270938	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcctccaccccgggaacagcTccccctcccaaagtgctgac	7	20	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1270938T>C	ENST00000529681.1	+	31	12886	c.12828T>C	c.(12826-12828)gcT>gcC	p.A4276A	MUC5B_ENST00000447027.1_Silent_p.A4279A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4276	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		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)		CGGGAACAGCTCCCCCTCCCA	0.637																																																0			11											122	142	136					11																	1270938		2103	4198	6301	1227514	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.12828T>C	11.37:g.1270938T>C			1227514	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1270938	T	C	1270938	2	2	109	1	0	0	0	0	0	0	0	1	10009	1538	54	4		4	MUC5B	11	1270938	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	17205	1270938	133735578	195	28761										
KRTAP5-1	387264	hgsc.bcm.edu	37	chr11	1606443	1606443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggagccacagcccccacagcTggagccacagcctccggagc	12	18	0	0	rs541535366		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1606443T>C	ENST00000382171.2	-	1	70	c.37A>G	c.(37-39)Agc>Ggc	p.S13G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	13						keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCACAGCTGGAGCCACAG	0.672													T|||	1	0.000199681	0	0	5008	,	,		10249	0.001		0	False		,,,				2504	0															0			11											50	59	56					11																	1606443		2191	4292	6483	1563019	SO:0001583	missense	387264			AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"Keratin associated proteins"	23596	protein-coding gene	gene with protein product		148022	"keratin, cuticle, ultrahigh sulphur 1-like"	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.37A>G	11.37:g.1606443T>C	ENSP00000371606:p.Ser13Gly		1563019		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	T	0.020	-1.442712	0.01089	.	.	ENSG00000205869	ENST00000382171	T	0.05786	3.39	3.68	-0.313	0.12754	.	.	.	.	.	T	0.04363	0.0120	N	0.21448	0.665	0.09310	N	0.999997	B	0.11235	0.004	B	0.09377	0.004	T	0.39522	-0.9610	9	0.62326	D	0.03	.	5.381	0.16192	0.1575:0.1056:0.0:0.7369	.	13	Q6L8H4	KRA51_HUMAN	G	13	ENSP00000371606:S13G	ENSP00000371606:S13G	S	-	1	0	KRTAP5-1	1563019	0.013000	0.17824	0.972000	0.41901	0.013000	0.08279	-1.124000	0.03260	-0.420000	0.07427	-0.748000	0.03510	AGC		0.672	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922		C	1606443	T	C	1606443	3	2	109	1	0	0	0	0	1	0	0	0	8580	1580	55	4	803	4	KRTAP5-1	11	1606443	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	335505	1606443	133400073	196	28762										
TSPAN32	10077	hgsc.bcm.edu	37	chr11	2337867	2337867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccgctgtggctgcagcttggAccgcaagggcaaatacaccc	12	14	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:2337867A>G	ENST00000182290.4	+	8	826	c.689A>G	c.(688-690)gAc>gGc	p.D230G	TSPAN32_ENST00000451520.2_Missense_Mutation_p.D219G|TSPAN32_ENST00000381121.3_Missense_Mutation_p.D230G	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	230					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		TGCAGCTTGGACCGCAAGGGC	0.662																																																0			11											107	86	93					11																	2337867		2202	4299	6501	2294443	SO:0001583	missense	10077			AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"Tetraspanins"	13410	protein-coding gene	gene with protein product		603853	"pan-hematopoietic expression"	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.689A>G	11.37:g.2337867A>G	ENSP00000182290:p.Asp230Gly		2294443	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Missense_Mutation	SNP	ENST00000182290.4	37	CCDS7733.1	.	.	.	.	.	.	.	.	.	.	.	12.28	1.891076	0.33348	.	.	ENSG00000064201	ENST00000182290;ENST00000381121;ENST00000451520;ENST00000444307;ENST00000381117	T;T;T	0.51071	0.73;0.8;0.72	3.5	3.5	0.40072	.	0.501194	0.16044	U	0.232280	T	0.51584	0.1683	L	0.27053	0.805	0.27197	N	0.960276	D;D;D;D	0.89917	1.0;0.998;1.0;0.997	D;D;D;P	0.87578	0.964;0.943;0.998;0.878	T	0.33979	-0.9847	10	0.41790	T	0.15	-12.9163	8.7151	0.34405	1.0:0.0:0.0:0.0	.	219;175;230;230	D3YTD1;G3XAG6;Q96QS1-3;Q96QS1	.;.;.;TSN32_HUMAN	G	230;230;219;166;175	ENSP00000182290:D230G;ENSP00000370513:D230G;ENSP00000405205:D219G	ENSP00000182290:D230G	D	+	2	0	TSPAN32	2294443	0.964000	0.33143	0.688000	0.30117	0.041000	0.13682	2.369000	0.44231	1.389000	0.46526	0.260000	0.18958	GAC		0.662	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024		G	2337867	A	G	2337867	3	3	109	1	0	0	0	0	1	0	0	0	16687	275	10	4	719	4	TSPAN32	11	2337867	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	731424	2337867	132668649	197	28763										
NAV2	89797	hgsc.bcm.edu	37	chr11	19968013	19968013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgatctgcggcagaatttggAggaaaccatgtccagtttaa	11	7	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:19968013A>G	ENST00000396087.3	+	10	2381	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G	NAV2_ENST00000349880.4_Missense_Mutation_p.E738G|NAV2_ENST00000527559.2_Missense_Mutation_p.E690G|NAV2_ENST00000540292.1_Missense_Mutation_p.E692G|NAV2_ENST00000396085.1_Missense_Mutation_p.E738G|NAV2_ENST00000360655.4_Missense_Mutation_p.E674G	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	761					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CAGAATTTGGAGGAAACCATG	0.458																																																0			11											91	82	85					11																	19968013		2199	4293	6492	19924589	SO:0001583	missense	89797			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.2282A>G	11.37:g.19968013A>G	ENSP00000379396:p.Glu761Gly		19924589	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	A	32	5.187293	0.94923	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39;2.39	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000002	T	0.42607	0.1210	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.18023	-1.0350	9	.	.	.	.	16.3668	0.83335	1.0:0.0:0.0:0.0	.	738;674	Q8IVL1-3;Q8IVL1-4	.;.	G	674;738;738;761;690;692	ENSP00000353871:E674G;ENSP00000379394:E738G;ENSP00000309577:E738G;ENSP00000379396:E761G;ENSP00000435395:E690G;ENSP00000443489:E692G	.	E	+	2	0	NAV2	19924589	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.268000	0.75426	0.454000	0.30748	GAG		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		G	19968013	A	G	19968013	3	3	109	1	0	0	0	0	1	0	0	0	10214	304	11	4	2326	4	NAV2	11	19968013	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	17630146	19968013	115038503	198	28764										
C11orf9	745	hgsc.bcm.edu	37	chr11	61539374	61539374	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagtccatcaagtggcagccTcatcagcagaacaagtgggc	11	12	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:61539374T>C	ENST00000278836.5	+	7	1161	c.1065T>C	c.(1063-1065)ccT>ccC	p.P355P	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000327797.1_5'Flank|MYRF_ENST00000265460.5_Silent_p.P346P	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	355					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGTGGCAGCCTCATCAGCAGA	0.612																																																0			11											152	148	150					11																	61539374		2202	4299	6501	61295950	SO:0001819	synonymous_variant	745				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.1065T>C	11.37:g.61539374T>C			61295950	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																				0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		C	61539374	T	C	61539374	2	2	109	1	0	0	0	0	0	0	0	1	1675	1538	54	4		4	C11orf9	11	61539374	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	41571361	61539374	73467142	199	28765										
ROM1	6094	hgsc.bcm.edu	37	chr11	62381295	62381295	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caaggattggtttggggtccAgtgggtcagcagccgttacc	15	9	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:62381295A>G	ENST00000278833.3	+	1	1083	c.542A>G	c.(541-543)cAg>cGg	p.Q181R	EML3_ENST00000494176.2_5'Flank|ROM1_ENST00000534093.1_Intron|EML3_ENST00000278845.4_5'Flank|EML3_ENST00000529309.1_5'Flank|EML3_ENST00000531557.1_5'Flank|EML3_ENST00000394773.2_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	181					camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						TTTGGGGTCCAGTGGGTCAGC	0.622																																																0			11											71	81	78					11																	62381295		2202	4299	6501	62137871	SO:0001583	missense	6094			L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"Tetraspanins"	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.542A>G	11.37:g.62381295A>G	ENSP00000278833:p.Gln181Arg		62137871	B2R978	Missense_Mutation	SNP	ENST00000278833.3	37	CCDS8024.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289141	0.80914	.	.	ENSG00000149489	ENST00000278833	T	0.80123	-1.34	4.74	4.74	0.60224	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.89371	0.6696	M	0.82823	2.61	0.58432	D	0.999998	D	0.76494	0.999	D	0.87578	0.998	D	0.90627	0.4564	10	0.72032	D	0.01	-28.5236	12.2478	0.54581	1.0:0.0:0.0:0.0	.	181	Q03395	ROM1_HUMAN	R	181	ENSP00000278833:Q181R	ENSP00000278833:Q181R	Q	+	2	0	ROM1	62137871	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	5.610000	0.67668	1.994000	0.58287	0.260000	0.18958	CAG		0.622	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327		G	62381295	A	G	62381295	3	3	109	1	0	0	0	0	1	0	0	0	13558	188	7	4	544	4	ROM1	11	62381295	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	841921	62381295	72625221	200	28766										
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64129168	64129168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcgagctgctgacgggggccTcgcccttcaccctggagggc	15	15	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:64129168T>C	ENST00000334205.4	+	7	771	c.706T>C	c.(706-708)Tcg>Ccg	p.S236P	RPS6KA4_ENST00000528057.1_Missense_Mutation_p.S236P|RPS6KA4_ENST00000294261.4_Missense_Mutation_p.S236P	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	236	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> L (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GACGGGGGCCTCGCCCTTCAC	0.697																																																0			11											21	22	22					11																	64129168		2199	4294	6493	63885744	SO:0001583	missense	8986			AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.706T>C	11.37:g.64129168T>C	ENSP00000333896:p.Ser236Pro		63885744	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	37	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	N	11.25	1.583050	0.28268	.	.	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000294261;ENST00000530504	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.12	2.98	0.34508	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.155416	0.43747	D	0.000523	T	0.12944	0.0314	N	0.00507	-1.42	0.49915	D	0.999836	B;D;D;D	0.89917	0.011;0.995;1.0;0.999	B;D;D;D	0.85130	0.003;0.964;0.997;0.99	T	0.37103	-0.9720	10	0.32370	T	0.25	.	7.8104	0.29228	0.0:0.1028:0.0:0.8972	.	236;236;236;236	G3XAA9;E9PJN1;O75676;O75676-2	.;.;KS6A4_HUMAN;.	P	236;236;236;220	ENSP00000435580:S236P;ENSP00000333896:S236P;ENSP00000294261:S236P;ENSP00000432945:S220P	ENSP00000294261:S236P	S	+	1	0	RPS6KA4	63885744	0.999000	0.42202	0.520000	0.27837	0.524000	0.34500	3.456000	0.53000	0.743000	0.32719	0.418000	0.28097	TCG		0.697	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		C	64129168	T	C	64129168	3	2	109	1	0	0	0	0	1	0	0	0	13690	1551	54	4	732	4	RPS6KA4	11	64129168	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1747873	64129168	70877348	201	28767										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66466117	66466117	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cagcactgctcaccttgtccAccttgtccagccagtctttg	7	16	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:66466117A>C	ENST00000533211.1	-	20	4338	c.4007T>G	c.(4006-4008)gTg>gGg	p.V1336G	SPTBN2_ENST00000529997.1_Missense_Mutation_p.V1336G|SPTBN2_ENST00000309996.2_Missense_Mutation_p.V1336G			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1336					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CACCTTGTCCACCTTGTCCAG	0.602																																																0			11											83	79	80					11																	66466117		2200	4295	6495	66222693	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4007T>G	11.37:g.66466117A>C	ENSP00000432568:p.Val1336Gly		66222693	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044054	0.55110	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.55234	0.53;0.53;0.53	4.72	4.72	0.59763	.	0.077294	0.53938	D	0.000042	T	0.66499	0.2795	M	0.80616	2.505	0.80722	D	1	P	0.50272	0.933	P	0.53313	0.723	T	0.72959	-0.4133	10	0.87932	D	0	.	13.341	0.60545	1.0:0.0:0.0:0.0	.	1336	O15020	SPTN2_HUMAN	G	1336	ENSP00000432568:V1336G;ENSP00000311489:V1336G;ENSP00000433593:V1336G	ENSP00000311489:V1336G	V	-	2	0	SPTBN2	66222693	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	9.081000	0.94049	1.981000	0.57761	0.533000	0.62120	GTG		0.602	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		C	66466117	A	C	66466117	3	2	109	1	0	0	0	0	1	0	0	0	15159	159	6	4	3241	4	SPTBN2	11	66466117	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2336949	66466117	68540399	202	28768										
MYEOV	26579	hgsc.bcm.edu	37	chr11	69063156	69063156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cggcagatcccggggccgccTctgtctctcccaggccctgc	12	19	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:69063156T>C	ENST00000308946.3	+	3	689	c.239T>C	c.(238-240)cTc>cCc	p.L80P	MYEOV_ENST00000441339.2_Missense_Mutation_p.L80P|MYEOV_ENST00000535407.1_Missense_Mutation_p.L22P	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	80										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		CGGGGCCGCCTCTGTCTCTCC	0.617																																																0			11											59	67	64					11																	69063156		2200	4294	6494	68819732	SO:0001583	missense	26579			AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.239T>C	11.37:g.69063156T>C	ENSP00000308330:p.Leu80Pro		68819732	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	T	8.387	0.838868	0.16891	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.27402	1.68;1.68;1.67	1.69	-0.752	0.11072	.	.	.	.	.	T	0.13415	0.0325	N	0.08118	0	0.09310	N	0.999999	B	0.23540	0.087	B	0.19148	0.024	T	0.21621	-1.0240	9	0.87932	D	0	.	4.1942	0.10435	0.0:0.4299:0.0:0.5701	.	80	Q96EZ4	MYEOV_HUMAN	P	80;80;22	ENSP00000412482:L80P;ENSP00000308330:L80P;ENSP00000438100:L22P	ENSP00000308330:L80P	L	+	2	0	MYEOV	68819732	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.018000	0.13422	-0.214000	0.10078	0.402000	0.26972	CTC		0.617	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1			C	69063156	T	C	69063156	3	2	109	1	0	0	0	0	1	0	0	0	10055	1551	54	4	245	4	MYEOV	11	69063156	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2597039	69063156	65943360	203	28769										
FAM86C	55199	hgsc.bcm.edu	37	chr11	71498591	71498591	+	Silent	SNP	C	C	G													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccgcccccgtcatggcgccCgaggagaacgcggggagcga					rs12270466	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:71498591C>G	ENST00000359244.4	+	1	32	c.9C>G	c.(7-9)ccC>ccG	p.P3P	FAM86C1_ENST00000346333.6_Silent_p.P3P|FAM86C1_ENST00000426628.2_Silent_p.P3P	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	3										lung(1)	1						TCATGGCGCCCGAGGAGAACG	0.746													.|||	2240	0.447284	0.3328	0.3458	5008	,	,		9232	0.3403		0.5646	False		,,,				2504	0.6636															0			11											4	4	4					11																	71498591		1963	3674	5637	71176239	SO:0001819	synonymous_variant	55199			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.9C>G	11.37:g.71498591C>G			71176239	Q8N5D3	Silent	SNP	ENST00000359244.4	37	CCDS41686.1																																																																																				0.746	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		G	71498591	C	G	71498591	2	3	109	1	0	0	0	0	0	0	0	1	5665	639	23	5		5	FAM86C	11	71498591	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	2435435	71498591	63507925	204	28770	52	2								
FAM86C	55199	hgsc.bcm.edu	37	chr11	71498601	71498601	+	Missense_Mutation	SNP	G	G	T													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcatggcgcccgaggagaacGcggggagcgaactcttgctg					rs12283300	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:71498601G>T	ENST00000359244.4	+	1	42	c.19G>T	c.(19-21)Gcg>Tcg	p.A7S	FAM86C1_ENST00000346333.6_Missense_Mutation_p.A7S|FAM86C1_ENST00000426628.2_Missense_Mutation_p.A7S	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	7			A -> S (in dbSNP:rs12283300). {ECO:0000269|PubMed:14702039}.							lung(1)	1						CGAGGAGAACGCGGGGAGCGA	0.736													.|||	2243	0.447883	0.3328	0.3458	5008	,	,		9168	0.3423		0.5646	False		,,,				2504	0.6646															0			11											5	5	5					11																	71498601		2022	3792	5814	71176249	SO:0001583	missense	55199			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.19G>T	11.37:g.71498601G>T	ENSP00000352182:p.Ala7Ser		71176249	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	838	0.3836996336996337	160	0.3252032520325203	130	0.35911602209944754	166	0.2902097902097902	382	0.503957783641161	.	11.43	1.635370	0.29068	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	1.78	0.792	0.18625	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	D;D;P	0.61080	0.961;0.989;0.561	P;D;B	0.74674	0.537;0.984;0.053	T	0.47611	-0.9104	8	0.72032	D	0.01	.	3.6282	0.08121	0.2602:0.0:0.7398:0.0	rs12283300;rs12283300	7;7;7	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	S	7	ENSP00000325662:A7S;ENSP00000352182:A7S;ENSP00000391329:A7S;ENSP00000436598:A7S	ENSP00000325662:A7S	A	+	1	0	FAM86C1	71176249	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	0.154000	0.16343	0.968000	0.38212	0.184000	0.17185	GCG		0.736	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		T	71498601	G	T	71498601	3	4	109	1	0	0	0	0	1	0	0	0	5665	1087	38	2	21	2	FAM86C	11	71498601	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	10	71498601	63507915	205	28771	52	2								
RPS3	6188	hgsc.bcm.edu	37	chr11	75115084	75115084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcctgctatggtgtgctgcGgttcatcatggagagtgggg	18	7	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:75115084G>A	ENST00000531188.1	+	5	433	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	SNORD15B_ENST00000384714.1_RNA|RPS3_ENST00000534440.1_Intron|RPS3_ENST00000527446.1_Missense_Mutation_p.R124Q|RPS3_ENST00000529285.1_Intron|RPS3_ENST00000526608.1_Missense_Mutation_p.R112Q|RPS3_ENST00000278572.6_Missense_Mutation_p.R140Q|RPS3_ENST00000524851.1_Missense_Mutation_p.R124Q	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	124					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						GGTGTGCTGCGGTTCATCATG	0.488																																																0			11											106	101	103					11																	75115084		2200	4293	6493	74792732	SO:0001583	missense	6188				CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.371G>A	11.37:g.75115084G>A	ENSP00000434643:p.Arg124Gln		74792732	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	37	CCDS8236.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.35|18.35	3.605329|3.605329	0.66445|0.66445	.|.	.|.	ENSG00000149273|ENSG00000149273	ENST00000525933|ENST00000531188;ENST00000530689;ENST00000278572;ENST00000527446;ENST00000526608;ENST00000524851	.|.	.|.	.|.	5.01|5.01	4.1|4.1	0.47936|0.47936	.|Ribosomal protein S3, C-terminal (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63105|0.63105	0.2483|0.2483	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|B	.|0.21753	.|0.06	.|B	.|0.23419	.|0.046	T|T	0.65541|0.65541	-0.6143|-0.6143	5|9	.|0.87932	.|D	.|0	-4.3954|-4.3954	11.3838|11.3838	0.49773|0.49773	0.0881:0.0:0.9119:0.0|0.0881:0.0:0.9119:0.0	.|.	.|124	.|P23396	.|RS3_HUMAN	S|Q	52|124;124;140;124;112;124	.|.	.|ENSP00000278572:R140Q	G|R	+|+	1|2	0|0	RPS3|RPS3	74792732|74792732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.801000|0.801000	0.45260|0.45260	9.626000|9.626000	0.98410|0.98410	1.353000|1.353000	0.45828|0.45828	-0.162000|-0.162000	0.13425|0.13425	GGT|CGG		0.488	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		A	75115084	G	A	75115084	3	1	109	1	0	0	0	0	1	0	0	0	13680	1116	39	1	389	1	RPS3	11	75115084	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	3616483	75115084	59891432	206	28772										
KLHL35	283212	hgsc.bcm.edu	37	chr11	75137623	75137623	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccttgtgcagagaggctaccTtgatccaggtgtgcagatgg	14	9	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:75137623T>C	ENST00000539798.1	-	3	1126	c.1127A>G	c.(1126-1128)aAg>aGg	p.K376R	KLHL35_ENST00000376292.4_Missense_Mutation_p.K156R	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	376										lung(2)|stomach(1)	3						AGAGGCTACCTTGATCCAGGT	0.577																																					Colon(77;683 1691 18820 23811)											0			11											43	45	44					11																	75137623		2085	4227	6312	74815271	SO:0001583	missense	283212				CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1127A>G	11.37:g.75137623T>C	ENSP00000438526:p.Lys376Arg		74815271	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	37	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	T	7.387	0.630027	0.14257	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.78595	-1.19;-1.19	5.23	4.09	0.47781	Kelch-type beta propeller (1);	0.141052	0.46442	D	0.000291	T	0.54095	0.1837	N	0.13272	0.32	0.35672	D	0.813373	B	0.16396	0.017	B	0.19666	0.026	T	0.52638	-0.8549	10	0.08599	T	0.76	.	5.1321	0.14915	0.0:0.1911:0.0:0.8088	.	156	Q6PF15	KLH35_HUMAN	R	156;376	ENSP00000365469:K156R;ENSP00000438526:K376R	ENSP00000365469:K156R	K	-	2	0	KLHL35	74815271	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	1.860000	0.39428	2.191000	0.70037	0.533000	0.62120	AAG		0.577	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		C	75137623	T	C	75137623	3	2	109	1	0	0	0	0	1	0	0	0	8409	1609	56	4	640	4	KLHL35	11	75137623	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	22539	75137623	59868893	207	28773										
CCDC81	60494	hgsc.bcm.edu	37	chr11	86126334	86126334	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccagaggcgggatttgcaaaTgcttcagaggacacaaagag	13	8	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:86126334T>A	ENST00000445632.2	+	13	1942	c.1670T>A	c.(1669-1671)aTg>aAg	p.M557K	CCDC81_ENST00000278487.3_Missense_Mutation_p.M292K|CCDC81_ENST00000354755.1_Missense_Mutation_p.M467K|CCDC81_ENST00000528728.1_Missense_Mutation_p.M292K	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	557										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				GATTTGCAAATGCTTCAGAGG	0.483																																																0			11											66	67	67					11																	86126334		2202	4299	6501	85803982	SO:0001583	missense	60494			AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1670T>A	11.37:g.86126334T>A	ENSP00000415528:p.Met557Lys		85803982	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.385379	0.61956	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.56	4.43	0.53597	.	0.326334	0.36374	N	0.002638	T	0.51312	0.1667	M	0.74258	2.255	0.40019	D	0.975386	P;P;D	0.71674	0.908;0.887;0.998	B;P;D	0.68943	0.436;0.638;0.961	T	0.52434	-0.8576	9	.	.	.	-10.3624	10.2948	0.43618	0.0:0.0792:0.0:0.9208	.	292;557;467	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	K	467;292;557;292	ENSP00000346800:M467K;ENSP00000278487:M292K;ENSP00000415528:M557K;ENSP00000437165:M292K	.	M	+	2	0	CCDC81	85803982	1.000000	0.71417	0.934000	0.37439	0.763000	0.43281	3.128000	0.50492	0.940000	0.37473	0.528000	0.53228	ATG		0.483	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		A	86126334	T	A	86126334	3	1	109	1	0	0	0	0	1	0	0	0	2861	1464	51	5	1720	5	CCDC81	11	86126334	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	10988711	86126334	48880182	208	28774										
ATM	472	hgsc.bcm.edu	37	chr11	108139301	108139301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	taatgttaattgattctagcAcgctagaacctaccaaatcc	5	10	1	2	rs35813135		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:108139301A>G	ENST00000452508.2	+	19	2992	c.2803A>G	c.(2803-2805)Acg>Gcg	p.T935A	ATM_ENST00000278616.4_Missense_Mutation_p.T935A|AP001925.1_ENST00000596081.1_5'Flank			Q13315	ATM_HUMAN	ATM serine/threonine kinase	935			T -> A. {ECO:0000269|PubMed:17344846}.|T -> M (in dbSNP:rs3218708).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGATTCTAGCACGCTAGAACC	0.393			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			A|||	1	0.000199681	0	0	5008	,	,		18115	0.001		0	False		,,,				2504	0					yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											159	146	150					11																	108139301		2201	4298	6499	107644511	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2803A>G	11.37:g.108139301A>G	ENSP00000388058:p.Thr935Ala		107644511	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.655957	0.00779	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70516	-0.49;-0.49;-0.49	5.5	3.14	0.36123	Armadillo-type fold (1);	0.774747	0.12455	N	0.467361	T	0.43010	0.1228	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28933	-1.0028	10	0.08179	T	0.78	.	4.8104	0.13340	0.6646:0.0:0.2072:0.1282	rs35813135	935	Q13315	ATM_HUMAN	A	935	ENSP00000435747:T935A;ENSP00000278616:T935A;ENSP00000388058:T935A	ENSP00000278616:T935A	T	+	1	0	ATM	107644511	0.654000	0.27367	0.559000	0.28332	0.132000	0.20833	1.343000	0.33930	0.375000	0.24679	-0.333000	0.08304	ACG		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108139301	A	G	108139301	3	3	109	1	0	0	0	0	1	0	0	0	1110	159	6	4	2869	4	ATM	11	108139301	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	22012967	108139301	26867215	209	28775										
ATM	472	hgsc.bcm.edu	37	chr11	108180983	108180983	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcttgtgctgctcactttacAgctttactctatgcagaaat	6	10	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:108180983A>G	ENST00000452508.2	+	40	6048	c.5859A>G	c.(5857-5859)acA>acG	p.T1953T	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.T1953T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1953			T -> R (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10397742}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTCACTTTACAGCTTTACTCT	0.328			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											84	86	85					11																	108180983		2201	4297	6498	107686193	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5859A>G	11.37:g.108180983A>G			107686193	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108180983	A	G	108180983	2	3	109	1	0	0	0	0	0	0	0	1	1110	175	7	4		4	ATM	11	108180983	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	41682	108180983	26825533	210	28776										
PDZD3	79849	hgsc.bcm.edu	37	chr11	119059156	119059156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggctgtggctggggagagcGtggaggggctgggccatgag	23	6	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:119059156G>A	ENST00000531114.1	+	6	1702	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	PDZD3_ENST00000525131.1_Missense_Mutation_p.V306M|PDZD3_ENST00000392817.2_Missense_Mutation_p.V385M|PDZD3_ENST00000322712.4_Missense_Mutation_p.V305M|PDZD3_ENST00000355547.5_Missense_Mutation_p.V319M			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	385	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		TGGGGAGAGCGTGGAGGGGCT	0.672																																																0			11											40	41	40					11																	119059156		2199	4294	6493	118564366	SO:0001583	missense	79849			AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"PDZ domain containing 2"	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1153G>A	11.37:g.119059156G>A	ENSP00000431164:p.Val385Met		118564366	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		.	.	.	.	.	.	.	.	.	.	G	19.08	3.758644	0.69763	.	.	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	5.66	2.59	0.31030	PDZ/DHR/GLGF (4);	0.501532	0.20802	N	0.085402	T	0.40222	0.1108	M	0.76328	2.33	0.39671	D	0.970752	D;D;P;P	0.56035	0.974;0.974;0.942;0.953	P;P;B;B	0.51135	0.66;0.532;0.25;0.365	T	0.37596	-0.9699	10	0.62326	D	0.03	-12.5467	7.2772	0.26292	0.2225:0.1245:0.653:0.0	.	306;385;319;305	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	M	306;385;319;305;319;385	ENSP00000434559:V306M;ENSP00000431164:V385M;ENSP00000347742:V319M;ENSP00000327107:V305M;ENSP00000376564:V385M	ENSP00000327107:V305M	V	+	1	0	PDZD3	118564366	1.000000	0.71417	0.972000	0.41901	0.933000	0.57130	4.672000	0.61597	0.742000	0.32697	-0.208000	0.12717	GTG		0.672	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791		A	119059156	G	A	119059156	3	1	109	1	0	0	0	0	1	0	0	0	11733	1145	40	1	985	1	PDZD3	11	119059156	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	10878173	119059156	15947360	211	28777										
CBL	867	hgsc.bcm.edu	37	chr11	119149245	119149245	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agaaggtcagggctgtccttTctgccgatgtgaaattaaag	12	7	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:119149245T>C	ENST00000264033.4	+	9	1629	c.1253T>C	c.(1252-1254)tTc>tCc	p.F418S		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	418	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F418S(4)|p.G397_I429del(1)|p.E366_K477del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GGCTGTCCTTTCTGCCGATGT	0.433			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																														"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	6	Substitution - Missense(4)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(6)	11											126	123	124					11																	119149245		2199	4295	6494	118654455	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1253T>C	11.37:g.119149245T>C	ENSP00000264033:p.Phe418Ser		118654455	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040706	0.75732	.	.	ENSG00000110395	ENST00000264033	D	0.95788	-3.81	5.96	5.96	0.96718	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.97090	0.9049	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97729	1.0201	10	0.87932	D	0	-26.8748	16.4484	0.83959	0.0:0.0:0.0:1.0	.	418	P22681	CBL_HUMAN	S	418	ENSP00000264033:F418S	ENSP00000264033:F418S	F	+	2	0	CBL	118654455	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	TTC		0.433	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119149245	T	C	119149245	3	2	109	1	0	0	0	0	1	0	0	0	2706	1783	62	4	1287	4	CBL	11	119149245	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	90089	119149245	15857271	212	28778										
SCN3B	55800	hgsc.bcm.edu	37	chr11	123516432	123516432	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctccgtctccgagggcacttCcacacacacagggaagcaga	10	15	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:123516432C>A	ENST00000392770.2	-	2	884	c.82G>T	c.(82-84)Gaa>Taa	p.E28*	SCN3B_ENST00000299333.3_Nonsense_Mutation_p.E28*|SCN3B_ENST00000530277.1_Nonsense_Mutation_p.E28*	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	28					atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGGGCACTTCCACACACACA	0.607																																																0			11											90	86	88					11																	123516432		2202	4299	6501	123021642	SO:0001587	stop_gained	55800			AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.82G>T	11.37:g.123516432C>A	ENSP00000376523:p.Glu28*		123021642	A5H1I5|Q17RL3|Q9ULR2	Nonsense_Mutation	SNP	ENST00000392770.2	37	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	C	41	8.829637	0.98970	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836;ENST00000528267	.	.	.	5.96	5.96	0.96718	.	0.086699	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-4.3832	20.4182	0.99029	0.0:1.0:0.0:0.0	.	.	.	.	X	28	.	ENSP00000299333:E28X	E	-	1	0	SCN3B	123021642	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.481000	0.81124	2.820000	0.97059	0.609000	0.83330	GAA		0.607	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		A	123516432	C	A	123516432	4	1	109	1	0	0	0	0	0	1	0	0	13956	864	30	2	581	2	SCN3B	11	123516432	Nonsense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	4367187	123516432	11490084	213	28779										
ETS1	2113	hgsc.bcm.edu	37	chr11	128354817	128354817	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtctgtctggagagggtctcGgagaatgaccgaggggtagt	18	6	3	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:128354817G>A	ENST00000319397.6	-	5	940	c.631C>T	c.(631-633)Cga>Tga	p.R211*	ETS1_ENST00000392668.4_Nonsense_Mutation_p.R255*|ETS1_ENST00000526145.2_Nonsense_Mutation_p.R211*|ETS1_ENST00000345075.4_Nonsense_Mutation_p.R211*|ETS1_ENST00000531611.1_Nonsense_Mutation_p.R211*|ETS1_ENST00000535549.1_Intron	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	211	Activation domain; required for transcription activation.				angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R211*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		AGAGGGTCTCGGAGAATGACC	0.532																																																1	Substitution - Nonsense(1)	pleura(1)	11											140	125	130					11																	128354817		2201	4297	6498	127860027	SO:0001587	stop_gained	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.631C>T	11.37:g.128354817G>A	ENSP00000324578:p.Arg211*		127860027	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Nonsense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	G	39	7.648207	0.98409	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	.	.	.	5.67	4.68	0.58851	.	0.250164	0.40818	N	0.001002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	17.3427	0.87301	0.0:0.0:0.8664:0.1336	.	.	.	.	X	211;255;211;211;211	.	ENSP00000324578:R211X	R	-	1	2	ETS1	127860027	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.876000	0.87215	2.673000	0.90976	0.561000	0.74099	CGA		0.532	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		A	128354817	G	A	128354817	4	1	109	1	0	0	0	0	0	1	0	0	5288	1124	39	1	710	1	ETS1	11	128354817	Nonsense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	4838385	128354817	6651699	214	28780										
MLF2	8079	hgsc.bcm.edu	37	chr12	6859909	6859909	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atcatgtcattcatcatcccAaacatgtccatgaaaccacc	3	14	4	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:6859909A>G	ENST00000203630.5	-	5	884	c.240T>C	c.(238-240)ttT>ttC	p.F80F	MLF2_ENST00000435120.1_Silent_p.F80F|MLF2_ENST00000542154.1_Silent_p.F80F|MLF2_ENST00000564181.1_5'UTR|MLF2_ENST00000539187.1_Silent_p.F80F			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	80			F -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						TCATCATCCCAAACATGTCCA	0.478																																																0			12											159	128	139					12																	6859909		2203	4300	6503	6730170	SO:0001819	synonymous_variant	8079			U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.240T>C	12.37:g.6859909A>G			6730170		Silent	SNP	ENST00000203630.5	37	CCDS8559.1																																																																																				0.478	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2			G	6859909	A	G	6859909	2	3	109	1	0	0	0	0	0	0	0	1	9646	127	5	4		4	MLF2	12	6859909	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10		6859909	126991986	215	28781										
LRP6	4040	hgsc.bcm.edu	37	chr12	12397443	12397443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcttcttcgctgacatcacTccagtatatcaagccatgac	7	13	3	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:12397443T>C	ENST00000261349.4	-	2	278	c.202A>G	c.(202-204)Agt>Ggt	p.S68G	LRP6_ENST00000543091.1_Missense_Mutation_p.S68G	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	68	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CTGACATCACTCCAGTATATC	0.448																																																0			12											121	101	108					12																	12397443		2203	4300	6503	12288710	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.202A>G	12.37:g.12397443T>C	ENSP00000261349:p.Ser68Gly		12288710	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.631983	0.87660	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91996	-2.95;-2.95	5.04	5.04	0.67666	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000007	D	0.93035	0.7783	M	0.82630	2.6	0.80722	D	1	P;P	0.50943	0.94;0.893	B;P	0.44897	0.21;0.463	D	0.94160	0.7413	10	0.87932	D	0	.	14.9552	0.71107	0.0:0.0:0.0:1.0	.	68;68	F5H7J9;O75581	.;LRP6_HUMAN	G	68	ENSP00000261349:S68G;ENSP00000442472:S68G	ENSP00000261349:S68G	S	-	1	0	LRP6	12288710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.868000	0.87116	2.123000	0.65237	0.377000	0.23210	AGT		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12397443	T	C	12397443	3	2	109	1	0	0	0	0	1	0	0	0	8991	1551	54	4	4727	4	LRP6	12	12397443	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	5537534	12397443	121454452	216	28782										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	109	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	13000841	25398284	108453611	217	28783										
BICD1	636	hgsc.bcm.edu	37	chr12	32481358	32481358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctcgtcaaagagcagcggctCgggagctagcccccatgatt	12	13	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:32481358C>T	ENST00000281474.5	+	5	2072	c.1969C>T	c.(1969-1971)Cgg>Tgg	p.R657W	BICD1_ENST00000548411.1_Missense_Mutation_p.R657W	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	657					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.R657W(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AGCAGCGGCTCGGGAGCTAGC	0.507																																																1	Substitution - Missense(1)	ovary(1)	12											73	78	76					12																	32481358		2203	4300	6503	32372625	SO:0001583	missense	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1969C>T	12.37:g.32481358C>T	ENSP00000281474:p.Arg657Trp		32372625	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	37	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.183320	0.57800	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.47869	0.83;0.83	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.74348	0.897;0.983	T	0.67428	-0.5673	10	0.72032	D	0.01	.	13.3962	0.60853	0.1573:0.8427:0.0:0.0	.	657;657	F8W113;Q96G01	.;BICD1_HUMAN	W	657	ENSP00000446793:R657W;ENSP00000281474:R657W	ENSP00000281474:R657W	R	+	1	2	BICD1	32372625	0.959000	0.32827	0.991000	0.47740	0.883000	0.51084	2.247000	0.43151	2.333000	0.79357	0.655000	0.94253	CGG		0.507	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32481358	C	T	32481358	3	4	109	1	0	0	0	0	1	0	0	0	1429	875	31	1	1987	1	BICD1	12	32481358	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	7083074	32481358	101370537	218	28784										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42854287	42854287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctggcttctcttcaggcaggAttttctctggacacaactct	8	12	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:42854287A>G	ENST00000455697.1	-	8	2105	c.1820T>C	c.(1819-1821)aTc>aCc	p.I607T	PRICKLE1_ENST00000548696.1_Missense_Mutation_p.I607T|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.I607T|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.I607T|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.I607T	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	607					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TTCAGGCAGGATTTTCTCTGG	0.458																																																0			12											124	119	120					12																	42854287		2203	4300	6503	41140554	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1820T>C	12.37:g.42854287A>G	ENSP00000401060:p.Ile607Thr		41140554	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.552347	0.27739	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	5.53	3.17	0.36434	.	0.369538	0.30159	N	0.010264	T	0.35770	0.0943	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16394	-1.0404	10	0.24483	T	0.36	0.001	8.9118	0.35557	0.6587:0.0:0.3413:0.0	.	607	Q96MT3	PRIC1_HUMAN	T	607	ENSP00000401060:I607T;ENSP00000398947:I607T;ENSP00000448359:I607T;ENSP00000345064:I607T;ENSP00000449819:I607T	ENSP00000345064:I607T	I	-	2	0	PRICKLE1	41140554	0.103000	0.21917	0.413000	0.26509	0.988000	0.76386	2.644000	0.46613	0.476000	0.27440	0.528000	0.53228	ATC		0.458	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			G	42854287	A	G	42854287	3	3	109	1	0	0	0	0	1	0	0	0	12520	333	12	4	679	4	PRICKLE1	12	42854287	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	10372929	42854287	90997608	219	28785										
TWF1	5756	hgsc.bcm.edu	37	chr12	44191532	44191532	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aactgcacatagttgagctgTctattattcaatttttccaa	5	8	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:44191532T>C	ENST00000395510.2	-	6	717	c.588A>G	c.(586-588)agA>agG	p.R196R	TWF1_ENST00000552521.1_Silent_p.R98R|TWF1_ENST00000325127.4_Silent_p.R230R|TWF1_ENST00000548315.1_Silent_p.R203R	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	196	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		AGTTGAGCTGTCTATTATTCA	0.373																																																0			12											92	95	94					12																	44191532		2203	4300	6503	42477799	SO:0001819	synonymous_variant	5756			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"protein tyrosine kinase 9", "PTK9 protein tyrosine kinase 9", "twinfilin, actin-binding protein, homolog 1 (Drosophila)"	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.588A>G	12.37:g.44191532T>C			42477799	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																				0.373	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822		C	44191532	T	C	44191532	2	2	109	1	0	0	0	0	0	0	0	1	16821	1664	58	4		4	TWF1	12	44191532	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1337245	44191532	89660363	220	28786										
OR6C4	341418	hgsc.bcm.edu	37	chr12	55945194	55945194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccccatgtatttcttcctcCggaatttctccttcttagaa	4	14	3	1	rs139634367		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:55945194C>T	ENST00000394256.2	+	1	212	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R62W(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TTTCTTCCTCCGGAATTTCTC	0.428																																																1	Substitution - Missense(1)	endometrium(1)	12											141	146	144					12																	55945194		2202	4300	6502	54231461	SO:0001583	missense	341418			BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.184C>T	12.37:g.55945194C>T	ENSP00000377799:p.Arg62Trp		54231461	A8MZG7|B2RNN2|Q6IFK1	Missense_Mutation	SNP	ENST00000394256.2	37	CCDS31827.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726383	0.30593	.	.	ENSG00000179626	ENST00000394256	T	0.01092	5.35	4.77	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44097	D	0.000492	T	0.02418	0.0074	M	0.84326	2.69	0.09310	N	0.999999	B	0.22683	0.073	B	0.17098	0.017	T	0.25187	-1.0139	10	0.66056	D	0.02	.	10.1441	0.42753	0.2718:0.5967:0.1315:0.0	.	62	Q8NGE1	OR6C4_HUMAN	W	62	ENSP00000377799:R62W	ENSP00000377799:R62W	R	+	1	2	OR6C4	54231461	0.000000	0.05858	0.998000	0.56505	0.982000	0.71751	-2.251000	0.01186	0.685000	0.31468	-0.153000	0.13522	CGG		0.428	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			T	55945194	C	T	55945194	3	4	109	1	0	0	0	0	1	0	0	0	11224	643	23	1	186	1	OR6C4	12	55945194	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	11753662	55945194	77906701	221	28787										
NACA	4666	hgsc.bcm.edu	37	chr12	57111608	57111608	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgtgggggcccctttgggggAtggggtagccagacctcctt	17	10	0	1	rs12822307		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57111608A>G	ENST00000454682.1	-	3	3987	c.3706T>C	c.(3706-3708)Tcc>Ccc	p.S1236P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1236	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CCTTTGGGGGATGGGGTAGCC	0.667			T	BCL6	NHL																																		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0			12											58	78	72					12																	57111608		1230	2824	4054	55397875	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3706T>C	12.37:g.57111608A>G	ENSP00000403817:p.Ser1236Pro		55397875		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	A	6.444	0.450025	0.12223	.	.	ENSG00000196531	ENST00000454682	T	0.43688	0.94	3.89	-4.59	0.03400	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19910	-1.0291	7	.	.	.	.	3.5713	0.07918	0.364:0.0:0.2606:0.3754	rs12822307	1236	E9PAV3	.	P	1236	ENSP00000403817:S1236P	.	S	-	1	0	NACA	55397875	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.237000	0.00138	-1.100000	0.03030	-1.185000	0.01705	TCC		0.667	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		G	57111608	A	G	57111608	3	3	109	1	0	0	0	0	1	0	0	0	10163	333	12	4	2558	4	NACA	12	57111608	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1166414	57111608	76740287	222	28788			4	32		3	3	415	N	T_A	8.222142e-06
NACA	4666	hgsc.bcm.edu	37	chr12	57111932	57111932	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gggaggagttgcagctggggTtgtgggtgcccctttgtggg	21	6	0	0	rs558038375	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57111932T>G	ENST00000454682.1	-	3	3663	c.3382A>C	c.(3382-3384)Acc>Ccc	p.T1128P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1128	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T1127fs*215(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GCAGCTGGGGTTGTGGGTGCC	0.637			T	BCL6	NHL								-|||	294	0.0587061	0.0159	0.0519	5008	,	,		4348	0.0377		0.0408	False		,,,				2504	0.1616						Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	1	Deletion - Frameshift(1)	prostate(1)	12																																								55398199	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3382A>C	12.37:g.57111932T>G	ENSP00000403817:p.Thr1128Pro		55398199		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	N	1.204	-0.631660	0.03584	.	.	ENSG00000196531	ENST00000454682	T	0.48522	0.81	2.51	-5.02	0.02982	.	.	.	.	.	T	0.23054	0.0557	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	7	.	.	.	.	0.4619	0.00518	0.334:0.1221:0.1737:0.3702	.	1128	E9PAV3	.	P	1128	ENSP00000403817:T1128P	.	T	-	1	0	NACA	55398199	0.031000	0.19500	0.000000	0.03702	0.012000	0.07955	-0.022000	0.12480	-3.442000	0.00162	-1.928000	0.00512	ACC		0.637	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		G	57111932	T	G	57111932	3	3	109	1	0	0	0	0	1	0	0	0	10163	1725	60	4	2882	4	NACA	12	57111932	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	324	57111932	76739963	223	28789			4	32		3	3	415	N	T_A	8.222142e-06
NACA	4666	hgsc.bcm.edu	37	chr12	57112022	57112022	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	catgggggcccctttgggggAtggggtagctgggcctcctt	18	10	0	0	rs560117011	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57112022A>G	ENST00000454682.1	-	3	3573	c.3292T>C	c.(3292-3294)Tcc>Ccc	p.S1098P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1098	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CCTTTGGGGGATGGGGTAGCT	0.667			T	BCL6	NHL								-|||	4	0.000798722	8e-04	0	5008	,	,		6986	0		0.003	False		,,,				2504	0						Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0			12											46	56	53					12																	57112022		1330	2920	4250	55398289	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3292T>C	12.37:g.57112022A>G	ENSP00000403817:p.Ser1098Pro		55398289		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	a	6.029	0.373746	0.11409	.	.	ENSG00000196531	ENST00000454682	T	0.50813	0.73	3.67	-4.92	0.03075	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.20405	-1.0276	7	.	.	.	.	7.5955	0.28046	0.2853:0.2822:0.4325:0.0	.	1098	E9PAV3	.	P	1098	ENSP00000403817:S1098P	.	S	-	1	0	NACA	55398289	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-9.909000	0.00008	-1.295000	0.02357	-0.923000	0.02734	TCC		0.667	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		G	57112022	A	G	57112022	3	3	109	1	0	0	0	0	1	0	0	0	10163	333	12	4	2972	4	NACA	12	57112022	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	90	57112022	76739873	224	28790			4	32		3	3	415	N	T_A	8.222142e-06
NR1H4	9971	hgsc.bcm.edu	37	chr12	100904822	100904822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caaagaagccccgcatgggcGcgtcagcagggaggatcaaa	14	11	2	1	rs375599105	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:100904822G>A	ENST00000551379.1	+	2	404	c.376G>A	c.(376-378)Gcg>Acg	p.A126T	NR1H4_ENST00000548884.1_Missense_Mutation_p.A116T|NR1H4_ENST00000549996.1_Missense_Mutation_p.A116T|NR1H4_ENST00000188403.7_Missense_Mutation_p.A126T|NR1H4_ENST00000392986.3_Missense_Mutation_p.A116T			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	126					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	CCGCATGGGCGCGTCAGCAGG	0.522													G|||	2	0.000399361	0.0015	0	5008	,	,		17385	0		0	False		,,,				2504	0															0			12						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	97	102	100		346,346,346,376,376,346	-8.7	0	12		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	NR1H4	NM_001206977.1,NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1,NM_005123.3	58,58,58,58,58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	116/477,116/426,116/477,126/483,126/487,116/473	100904822	1,13005	2203	4300	6503	99428953	SO:0001583	missense	9971			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.376G>A	12.37:g.100904822G>A	ENSP00000447149:p.Ala126Thr		99428953	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	37	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	G	5.280	0.237135	0.10023	0.0	1.16E-4	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.93133	-2.95;-3.0;-3.17;-3.01;-2.95	5.9	-8.68	0.00859	.	1.496650	0.03088	N	0.159433	D	0.83908	0.5356	N	0.20685	0.6	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.0;0.002;0.001;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.001	T	0.72197	-0.4363	10	0.30078	T	0.28	.	5.5969	0.17331	0.5244:0.1889:0.2149:0.0717	.	116;126;126;116;116	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	T	116;116;116;126;126	ENSP00000448506:A116T;ENSP00000376712:A116T;ENSP00000448978:A116T;ENSP00000447149:A126T;ENSP00000188403:A126T	ENSP00000188403:A126T	A	+	1	0	NR1H4	99428953	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	-1.660000	0.01974	-1.431000	0.01982	-0.312000	0.09012	GCG		0.522	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		A	100904822	G	A	100904822	3	1	109	1	0	0	0	0	1	0	0	0	10650	1087	38	1	352	1	NR1H4	12	100904822	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	43792800	100904822	32947073	225	28791										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017442	109017442	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcctccatggctgctggtggAgtggtctgtgcttccatggc	15	11	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:109017442A>G	ENST00000550948.1	-	2	866	c.642T>C	c.(640-642)acT>acC	p.T214T	SELPLG_ENST00000388962.3_Silent_p.T204T|SELPLG_ENST00000228463.6_Silent_p.T230T			Q14242	SELPL_HUMAN	selectin P ligand	214	12 X 10 AA tandem repeats.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CTGCTGGTGGAGTGGTCTGTG	0.612																																																0			12											169	150	157					12																	109017442		2201	4300	6501	107541571	SO:0001819	synonymous_variant	6404				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.642T>C	12.37:g.109017442A>G			107541571	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	37	CCDS31895.2																																																																																				0.612	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			G	109017442	A	G	109017442	2	3	109	1	0	0	0	0	0	0	0	1	14057	291	11	4		4	SELPLG	12	109017442	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	8112620	109017442	24834453	226	28792										
TCHP	84260	hgsc.bcm.edu	37	chr12	110340935	110340935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccggcttcggcagcagtgggAgcagaacagccgttacttca	13	12	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:110340935A>G	ENST00000312777.5	+	2	318	c.104A>G	c.(103-105)gAg>gGg	p.E35G	TCHP_ENST00000405876.4_Missense_Mutation_p.E35G	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						CAGCAGTGGGAGCAGAACAGC	0.597																																																0			12											76	72	73					12																	110340935		2203	4300	6503	108825318	SO:0001583	missense	84260			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"mitostatin"	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.104A>G	12.37:g.110340935A>G	ENSP00000324404:p.Glu35Gly		108825318		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.448888	0.63178	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.51574	1.35;1.35;0.7	4.7	4.7	0.59300	.	0.237506	0.40728	N	0.001035	T	0.39759	0.1090	L	0.47716	1.5	0.80722	D	1	P	0.34522	0.455	B	0.31016	0.123	T	0.38067	-0.9678	10	0.51188	T	0.08	-3.4974	12.1862	0.54241	1.0:0.0:0.0:0.0	.	35	Q9BT92	TCHP_HUMAN	G	35	ENSP00000384520:E35G;ENSP00000324404:E35G;ENSP00000441835:E35G	ENSP00000324404:E35G	E	+	2	0	TCHP	108825318	1.000000	0.71417	0.924000	0.36721	0.979000	0.70002	5.789000	0.69029	1.775000	0.52247	0.369000	0.22263	GAG		0.597	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300		G	110340935	A	G	110340935	3	3	109	1	0	0	0	0	1	0	0	0	15741	304	11	4	106	4	TCHP	12	110340935	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1323493	110340935	23510960	227	28793										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126137096	126137096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gctcgtagctggcatgtctcTctccctgcagccacaccgag	10	16	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:126137096T>C	ENST00000299308.3	+	8	2017	c.2009T>C	c.(2008-2010)cTc>cCc	p.L670P	TMEM132B_ENST00000535886.1_Missense_Mutation_p.L182P	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	670						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		GGCATGTCTCTCTCCCTGCAG	0.607																																																0			12											54	58	57					12																	126137096		2137	4257	6394	124703049	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2009T>C	12.37:g.126137096T>C	ENSP00000299308:p.Leu670Pro		124703049	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869499	0.72065	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.59906	0.23;0.23	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000021	T	0.76335	0.3973	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.79974	-0.1577	10	0.87932	D	0	.	15.6483	0.77070	0.0:0.0:0.0:1.0	.	670	Q14DG7	T132B_HUMAN	P	670;182	ENSP00000299308:L670P;ENSP00000440436:L182P	ENSP00000299308:L670P	L	+	2	0	TMEM132B	124703049	1.000000	0.71417	0.160000	0.22671	0.526000	0.34562	7.700000	0.84556	2.081000	0.62600	0.533000	0.62120	CTC		0.607	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		C	126137096	T	C	126137096	3	2	109	1	0	0	0	0	1	0	0	0	16085	1551	54	4	2039	4	TMEM132B	12	126137096	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	15796161	126137096	7714799	228	28794										
MTUS2	23281	hgsc.bcm.edu	37	chr13	30062047	30062047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tctcctccaggtggaagatcTcaccgccagccatgatgctg	10	14	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:30062047T>C	ENST00000380808.2	+	4	563	c.347T>C	c.(346-348)cTc>cCc	p.L116P	MTUS2-AS1_ENST00000323380.5_RNA|MTUS2-AS1_ENST00000587588.1_RNA|MTUS2_ENST00000542829.1_Missense_Mutation_p.L26P|MTUS2_ENST00000431530.3_Missense_Mutation_p.L1147P	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1137						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GTGGAAGATCTCACCGCCAGC	0.512																																																0			13											95	98	97					13																	30062047		2090	4219	6309	28960047	SO:0001583	missense	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.347T>C	13.37:g.30062047T>C	ENSP00000370186:p.Leu116Pro		28960047	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000380808.2	37	CCDS41874.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573034	0.65765	.	.	ENSG00000132938	ENST00000431530;ENST00000380808;ENST00000542829;ENST00000417109	T;T;T	0.23754	2.37;1.89;2.96	4.72	4.72	0.59763	.	0.321095	0.36815	N	0.002391	T	0.38532	0.1044	M	0.67397	2.05	0.80722	D	1	P;D	0.61080	0.942;0.989	P;P	0.53450	0.684;0.726	T	0.18366	-1.0339	9	.	.	.	.	11.6673	0.51381	0.0:0.0:0.0:1.0	.	116;1137	Q5JR59-3;Q5JR59	.;MTUS2_HUMAN	P	1147;116;26;73	ENSP00000392057:L1147P;ENSP00000370186:L116P;ENSP00000445403:L26P	.	L	+	2	0	MTUS2	28960047	1.000000	0.71417	0.908000	0.35775	0.877000	0.50540	5.668000	0.68074	1.981000	0.57761	0.533000	0.62120	CTC		0.512	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270		C	30062047	T	C	30062047	3	2	109	1	0	0	0	0	1	0	0	0	9996	1551	54	4	3532	4	MTUS2	13	30062047	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10		30062047	85107831	229	28795										
WBP4	11193	hgsc.bcm.edu	37	chr13	41639401	41639401	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aaagcataccaagaggatttGaaaagacttggcttagagtc	10	6	0	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:41639401G>A	ENST00000379487.3	+	4	640	c.240G>A	c.(238-240)ttG>ttA	p.L80L	WBP4_ENST00000542082.1_Silent_p.L59L	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	80					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AAGAGGATTTGAAAAGACTTG	0.378																																																0			13											48	52	51					13																	41639401		2203	4300	6503	40537401	SO:0001819	synonymous_variant	11193			AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"formin binding protein 21"	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.240G>A	13.37:g.41639401G>A			40537401	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																				0.378	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		A	41639401	G	A	41639401	2	1	109	1	0	0	0	0	0	0	0	1	17301	1281	45	3		3	WBP4	13	41639401	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	11577354	41639401	73530477	230	28796										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328216	88328216	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aatgacaatcttttgtccagTttacccaacaatcttttccg	4	11	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:88328216T>A	ENST00000325089.6	+	2	792	c.573T>A	c.(571-573)agT>agA	p.S191R	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	191					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTTTGTCCAGTTTACCCAACA	0.483																																																0			13											85	86	86					13																	88328216		2203	4300	6503	87126217	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.573T>A	13.37:g.88328216T>A	ENSP00000366283:p.Ser191Arg		87126217	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461566	0.26248	.	.	ENSG00000165300	ENST00000325089	T	0.55052	0.54	5.88	5.88	0.94601	.	0.296155	0.37219	N	0.002197	T	0.43656	0.1257	L	0.46157	1.445	0.80722	D	1	P	0.36647	0.563	B	0.36378	0.223	T	0.38735	-0.9647	9	.	.	.	-1.8733	8.7309	0.34498	0.0:0.0835:0.0:0.9165	.	191	O94991	SLIK5_HUMAN	R	191	ENSP00000366283:S191R	.	S	+	3	2	SLITRK5	87126217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.735000	0.38176	2.257000	0.74773	0.459000	0.35465	AGT		0.483	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88328216	T	A	88328216	3	1	109	1	0	0	0	0	1	0	0	0	14783	1722	60	5	575	5	SLITRK5	13	88328216	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	46688815	88328216	26841662	231	28797										
TMTC4	84899	hgsc.bcm.edu	37	chr13	101316492	101316492	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tacctgaaagtcaggacggtGagaggccggtaggacttgtg	16	7	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:101316492G>A	ENST00000376234.3	-	3	450	c.261C>T	c.(259-261)ctC>ctT	p.L87L	TMTC4_ENST00000328767.5_Intron|TMTC4_ENST00000342624.5_Silent_p.L106L	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	87						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TCAGGACGGTGAGAGGCCGGT	0.567																																																0			13											63	72	69					13																	101316492		2016	4174	6190	100114493	SO:0001819	synonymous_variant	84899				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.261C>T	13.37:g.101316492G>A			100114493	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																				0.567	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		A	101316492	G	A	101316492	2	1	109	1	0	0	0	0	0	0	0	1	16302	1277	45	3		3	TMTC4	13	101316492	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	12988276	101316492	13853386	232	28798										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111545496	111545496	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccccatttaagatgccattGttatagaaatggttcagatg	8	8	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:111545496G>A	ENST00000267339.2	-	4	704	c.570C>T	c.(568-570)aaC>aaT	p.N190N	ANKRD10_ENST00000310847.4_3'UTR|ANKRD10-IT1_ENST00000426991.1_RNA|ANKRD10_ENST00000489973.2_5'UTR|ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	190										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			AGATGCCATTGTTATAGAAAT	0.433																																																0			13											127	127	127					13																	111545496		2203	4300	6503	110343497	SO:0001819	synonymous_variant	55608			AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.570C>T	13.37:g.111545496G>A			110343497	Q5VW12|Q9BV12	Silent	SNP	ENST00000267339.2	37	CCDS9520.1																																																																																				0.433	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			A	111545496	G	A	111545496	2	1	109	1	0	0	0	0	0	0	0	1	638	1368	48	3		3	ANKRD10	13	111545496	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	10229004	111545496	3624382	233	28799										
C14orf119	55017	hgsc.bcm.edu	37	chr14	23567258	23567258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	acttcgtggcaaagttttacCaagcagtggctgctacagct	10	10	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:23567258C>A	ENST00000319074.4	+	2	1247	c.391C>A	c.(391-393)Caa>Aaa	p.Q131K	C14orf119_ENST00000554203.1_Missense_Mutation_p.Q131K|ACIN1_ENST00000605057.1_5'Flank|ACIN1_ENST00000457657.1_5'Flank|ACIN1_ENST00000262710.1_5'Flank|ACIN1_ENST00000555053.1_5'Flank	NM_017924.3	NP_060394.1	Q9NWQ9	CN119_HUMAN	chromosome 14 open reading frame 119	131						mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(1)|lung(1)	3	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00649)		AAAGTTTTACCAAGCAGTGGC	0.478																																																0			14											77	78	78					14																	23567258		2203	4300	6503	22637098	SO:0001583	missense	55017				CCDS9588.1	14q11.2	2012-09-25			ENSG00000179933	ENSG00000179933			20270	protein-coding gene	gene with protein product							Standard	NM_017924		Approved	FLJ20671	uc001wiu.3	Q9NWQ9	OTTHUMG00000028717	ENST00000319074.4:c.391C>A	14.37:g.23567258C>A	ENSP00000322238:p.Gln131Lys		22637098	Q6IAA7	Missense_Mutation	SNP	ENST00000319074.4	37	CCDS9588.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026283	0.75390	.	.	ENSG00000179933	ENST00000319074;ENST00000554203	T;T	0.45276	0.9;0.9	6.07	6.07	0.98685	.	0.265262	0.43919	D	0.000503	T	0.44393	0.1291	M	0.67953	2.075	0.33916	D	0.64027	B	0.16396	0.017	B	0.15484	0.013	T	0.52711	-0.8539	10	0.49607	T	0.09	-17.1923	15.0234	0.71650	0.0:0.8579:0.1421:0.0	.	131	Q9NWQ9	CN119_HUMAN	K	131	ENSP00000322238:Q131K;ENSP00000450861:Q131K	ENSP00000322238:Q131K	Q	+	1	0	C14orf119	22637098	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.725000	0.38074	2.902000	0.99343	0.650000	0.86243	CAA		0.478	C14orf119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071713.3	NM_017924		A	23567258	C	A	23567258	3	1	109	1	0	0	0	0	1	0	0	0	1746	595	21	2	393	2	C14orf119	14	23567258	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		23567258	83782282	234	28800										
EFS	10278	hgsc.bcm.edu	37	chr14	23828606	23828606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcctgctgggtcatcctccaTctccctgccctctggatccc	7	19	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:23828606T>C	ENST00000216733.3	-	4	1688	c.1081A>G	c.(1081-1083)Atg>Gtg	p.M361V	RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Missense_Mutation_p.M192V|EFS_ENST00000351354.3_Missense_Mutation_p.M268V	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	361			M -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		TCATCCTCCATCTCCCTGCCC	0.652																																																0			14											78	70	72					14																	23828606		2201	4297	6498	22898446	SO:0001583	missense	10278			AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1081A>G	14.37:g.23828606T>C	ENSP00000216733:p.Met361Val		22898446	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.639489	0.00112	.	.	ENSG00000100842	ENST00000216733;ENST00000351354;ENST00000429593	T;T;T	0.54675	0.56;1.07;1.05	4.69	3.76	0.43208	.	0.920027	0.09175	N	0.838226	T	0.26484	0.0647	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.07290	-1.0780	10	0.08837	T	0.75	-1.8724	11.7367	0.51769	0.0:0.9118:0.0:0.0882	.	192;268;361	B4DJ56;O43281-2;O43281	.;.;EFS_HUMAN	V	361;268;192	ENSP00000216733:M361V;ENSP00000340607:M268V;ENSP00000416684:M192V	ENSP00000216733:M361V	M	-	1	0	EFS	22898446	0.026000	0.19158	0.003000	0.11579	0.019000	0.09904	1.697000	0.37784	1.188000	0.43014	-0.177000	0.13119	ATG		0.652	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			C	23828606	T	C	23828606	3	2	109	1	0	0	0	0	1	0	0	0	4970	1435	50	4	616	4	EFS	14	23828606	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	261348	23828606	83520934	235	28801										
C14orf115	55237	hgsc.bcm.edu	37	chr14	74825081	74825081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tttctgccgcttccgcctccGctaccccagcctgtcacctt	6	20	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:74825081G>A	ENST00000256362.4	+	2	1836	c.1595G>A	c.(1594-1596)cGc>cAc	p.R532H		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	532					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						TTCCGCCTCCGCTACCCCAGC	0.647																																																0			14											71	73	72					14																	74825081		2203	4300	6503	73894834	SO:0001583	missense	0			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1595G>A	14.37:g.74825081G>A	ENSP00000256362:p.Arg532His		73894834	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233517	0.58886	.	.	ENSG00000133980	ENST00000256362	T	0.54479	0.57	4.29	2.41	0.29592	.	0.167734	0.38272	U	0.001744	T	0.37404	0.1002	L	0.32530	0.975	0.36627	D	0.876102	B	0.23490	0.086	B	0.17098	0.017	T	0.33828	-0.9853	10	0.72032	D	0.01	-6.4676	7.2197	0.25979	0.0873:0.0:0.7451:0.1676	.	532	Q9H8Y1	VRTN_HUMAN	H	532	ENSP00000256362:R532H	ENSP00000256362:R532H	R	+	2	0	VRTN	73894834	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	3.062000	0.49971	0.428000	0.26173	-0.500000	0.04577	CGC		0.647	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		A	74825081	G	A	74825081	3	1	109	1	0	0	0	0	1	0	0	0	1744	1087	38	1	1597	1	C14orf115	14	74825081	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	50996475	74825081	32524459	236	28802										
PSMC1	5700	hgsc.bcm.edu	37	chr14	90731462	90731462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctgaatattatgaagagatgGgtataaagcctcctaagggg	12	5	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:90731462G>A	ENST00000261303.8	+	7	746	c.643G>A	c.(643-645)Ggt>Agt	p.G215S	PSMC1_ENST00000543772.2_Missense_Mutation_p.G142S	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	215					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		TGAAGAGATGGGTATAAAGCC	0.433																																																0			14											89	91	90					14																	90731462		2203	4297	6500	89801215	SO:0001583	missense	5700			L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.643G>A	14.37:g.90731462G>A	ENSP00000261303:p.Gly215Ser		89801215	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	Missense_Mutation	SNP	ENST00000261303.8	37	CCDS32139.1	.	.	.	.	.	.	.	.	.	.	G	35	5.455305	0.96223	.	.	ENSG00000100764	ENST00000261303;ENST00000553835;ENST00000543772	D;D;D	0.95980	-3.75;-3.87;-3.75	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.98024	0.9349	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98860	1.0762	10	0.87932	D	0	-18.7785	18.8979	0.92430	0.0:0.0:1.0:0.0	.	215	P62191	PRS4_HUMAN	S	215;52;142	ENSP00000261303:G215S;ENSP00000452049:G52S;ENSP00000445147:G142S	ENSP00000261303:G215S	G	+	1	0	PSMC1	89801215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.802000	0.99131	2.546000	0.85860	0.561000	0.74099	GGT		0.433	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802		A	90731462	G	A	90731462	3	1	109	1	0	0	0	0	1	0	0	0	12719	1232	43	3	669	3	PSMC1	14	90731462	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	15906381	90731462	16618078	237	28803										
EVL	51466	hgsc.bcm.edu	37	chr14	100589881	100589881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cttctctgcccacaggccccTccagccagcgtcaggtgcag	10	18	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:100589881T>C	ENST00000402714.2	+	4	962	c.358T>C	c.(358-360)Tcc>Ccc	p.S120P	EVL_ENST00000544450.2_Missense_Mutation_p.S126P|EVL_ENST00000392920.3_Missense_Mutation_p.S122P			Q9UI08	EVL_HUMAN	Enah/Vasp-like	120					actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				CACAGGCCCCTCCAGCCAGCG	0.587																																																0			14											42	39	40					14																	100589881		2203	4300	6503	99659634	SO:0001583	missense	51466			AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530	ENST00000402714.2:c.358T>C	14.37:g.100589881T>C	ENSP00000384720:p.Ser120Pro		99659634	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Missense_Mutation	SNP	ENST00000402714.2	37		.	.	.	.	.	.	.	.	.	.	T	11.86	1.764720	0.31228	.	.	ENSG00000196405	ENST00000402714;ENST00000544450;ENST00000392920;ENST00000555706;ENST00000539470;ENST00000557153;ENST00000557384	T;T;T;T;T;T	0.77877	-0.57;-0.6;-0.58;-1.13;-0.5;0.92	5.22	4.09	0.47781	.	0.301734	0.30269	N	0.010012	T	0.49712	0.1573	N	0.05351	-0.065	0.34952	D	0.751376	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.001	T	0.49790	-0.8902	10	0.09843	T	0.71	-24.7806	3.19	0.06614	0.0:0.1478:0.2483:0.6039	.	126;122;120	B7Z3I5;Q9UI08-2;Q9UI08	.;.;EVL_HUMAN	P	120;126;122;107;122;107;16	ENSP00000384720:S120P;ENSP00000437904:S126P;ENSP00000376652:S122P;ENSP00000450723:S107P;ENSP00000452327:S107P;ENSP00000450979:S16P	ENSP00000376652:S122P	S	+	1	0	EVL	99659634	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.594000	0.24014	1.968000	0.57251	0.459000	0.35465	TCC		0.587	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1			C	100589881	T	C	100589881	3	2	109	1	0	0	0	0	1	0	0	0	5304	1551	54	4	378	4	EVL	14	100589881	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	9858419	100589881	6759659	238	28804										
WDR20	91833	hgsc.bcm.edu	37	chr14	102675499	102675499	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tatggagtttagtggcagcgAtgaggacttccaagaccttc	12	8	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:102675499A>G	ENST00000342702.3	+	3	1023	c.992A>G	c.(991-993)gAt>gGt	p.D331G	WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556511.2_Missense_Mutation_p.D270G|WDR20_ENST00000335263.5_Missense_Mutation_p.D331G|WDR20_ENST00000545563.1_Missense_Mutation_p.D158G|WDR20_ENST00000556807.1_Missense_Mutation_p.D270G|WDR20_ENST00000424963.2_Missense_Mutation_p.D207G|WDR20_ENST00000499851.2_Missense_Mutation_p.D74G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Missense_Mutation_p.D362G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	331										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AGTGGCAGCGATGAGGACTTC	0.517																																																0			14											83	81	82					14																	102675499		2203	4300	6503	101745252	SO:0001583	missense	91833			BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.992A>G	14.37:g.102675499A>G	ENSP00000341037:p.Asp331Gly		101745252	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	37	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143467	0.57044	.	.	ENSG00000140153	ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	T;T;T;T;T;T;T	0.74632	0.09;0.09;0.09;-0.12;1.32;-0.12;-0.86	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83589	0.5287	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D;D;P	0.89917	0.998;0.997;1.0;0.999;0.995;0.997;0.895	D;P;D;D;D;D;P	0.87578	0.947;0.89;0.998;0.945;0.931;0.98;0.579	T	0.83265	-0.0046	10	0.41790	T	0.15	.	15.722	0.77718	1.0:0.0:0.0:0.0	.	362;343;270;331;270;207;331	E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.;.;.;.;.;.;WDR20_HUMAN	G	331;270;207;331;270;74;362;261;158	ENSP00000335434:D331G;ENSP00000395793:D207G;ENSP00000341037:D331G;ENSP00000450636:D270G;ENSP00000443641:D74G;ENSP00000406084:D362G;ENSP00000437927:D158G	ENSP00000299135:D270G	D	+	2	0	WDR20	101745252	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	8.953000	0.93041	2.133000	0.65898	0.533000	0.62120	GAT		0.517	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		G	102675499	A	G	102675499	3	3	109	1	0	0	0	0	1	0	0	0	17320	333	12	4	1019	4	WDR20	14	102675499	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2085618	102675499	4674041	239	28805										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105418345	105418345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccttgtcggccagggacagtTccccctccagccgcgcactg	11	18	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:105418345T>C	ENST00000333244.5	-	7	3562	c.3443A>G	c.(3442-3444)gAa>gGa	p.E1148G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1148						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			CAGGGACAGTTCCCCCTCCAG	0.632																																																0			14											162	184	177					14																	105418345		1971	4148	6119	104489390	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3443A>G	14.37:g.105418345T>C	ENSP00000353114:p.Glu1148Gly		104489390	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	12.99	2.102033	0.37048	.	.	ENSG00000185567	ENST00000333244	T	0.00711	5.8	4.22	4.22	0.49857	.	.	.	.	.	T	0.00998	0.0033	L	0.48877	1.53	0.09310	N	1	B	0.22146	0.065	B	0.22601	0.04	T	0.45891	-0.9230	9	0.26408	T	0.33	.	7.8851	0.29646	0.0:0.1024:0.0:0.8976	.	1148	Q8IVF2	AHNK2_HUMAN	G	1148	ENSP00000353114:E1148G	ENSP00000353114:E1148G	E	-	2	0	AHNAK2	104489390	0.033000	0.19621	0.004000	0.12327	0.002000	0.02628	1.169000	0.31871	1.542000	0.49330	0.402000	0.26972	GAA		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105418345	T	C	105418345	3	2	109	1	0	0	0	0	1	0	0	0	415	1783	62	4	13948	4	AHNAK2	14	105418345	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2742846	105418345	1931195	240	28806										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105423028	105423028	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcctgccgggggcgtcttccTgcagccacaagtgttgggag	16	12	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:105423028T>C	ENST00000333244.5	-	4	333		c.e4-2		AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2							costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		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)			GGCGTCTTCCTGCAGCCACAA	0.622																																																0			14											59	64	63					14																	105423028		1976	4165	6141	104494073	SO:0001630	splice_region_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.214-2A>G	14.37:g.105423028T>C			104494073	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Splice_Site	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.137324	0.37728	.	.	ENSG00000185567	ENST00000333244	.	.	.	3.44	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.5098	0.33211	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AHNAK2	104494073	1.000000	0.71417	0.980000	0.43619	0.133000	0.20885	2.212000	0.42835	1.581000	0.49865	0.533000	0.62120	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	Intron	C	105423028	T	C	105423028	5	2	109	1	0	0	0	0	0	0	1	0	415	1594	55	4	17191	4	AHNAK2	14	105423028	Splice_Site	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4683	105423028	1926512	241	28807										
CASC5	57082	hgsc.bcm.edu	37	chr15	40920343	40920343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	taaaaaacctgagcaggaccCcatctagttgcagcagctct	8	12	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:40920343C>T	ENST00000346991.5	+	12	5920	c.5530C>T	c.(5530-5532)Cca>Tca	p.P1844S	CASC5_ENST00000399668.2_Missense_Mutation_p.P1818S			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1844	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GAGCAGGACCCCATCTAGTTG	0.403																																																0			15											84	86	85					15																	40920343		1847	4090	5937	38707635	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5530C>T	15.37:g.40920343C>T	ENSP00000335463:p.Pro1844Ser		38707635	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921669	0.73213	.	.	ENSG00000137812	ENST00000346991;ENST00000399668	T;T	0.05649	3.41;3.41	5.59	4.68	0.58851	.	0.132262	0.34986	N	0.003521	T	0.10637	0.0260	L	0.60455	1.87	0.49389	D	0.999788	P;P	0.46142	0.873;0.873	P;P	0.45310	0.476;0.476	T	0.09818	-1.0657	10	0.33940	T	0.23	.	12.2836	0.54779	0.0:0.9209:0.0:0.0791	.	1818;1844	Q8NG31-2;Q8NG31	.;CASC5_HUMAN	S	1844;1818	ENSP00000335463:P1844S;ENSP00000382576:P1818S	ENSP00000335463:P1844S	P	+	1	0	CASC5	38707635	0.290000	0.24343	0.998000	0.56505	0.985000	0.73830	2.091000	0.41691	1.367000	0.46095	0.650000	0.86243	CCA		0.403	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40920343	C	T	40920343	3	4	109	1	0	0	0	0	1	0	0	0	2669	623	22	3	5572	3	CASC5	15	40920343	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		40920343	61611049	242	28808										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42167130	42167130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gggcagccatcttggcagccAgggtccggctctcactctcc	12	16	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:42167130A>G	ENST00000320955.6	-	23	4639	c.4412T>C	c.(4411-4413)cTg>cCg	p.L1471P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1471					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTTGGCAGCCAGGGTCCGGCT	0.667																																																0			15											36	42	40					15																	42167130		2004	4158	6162	39954422	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4412T>C	15.37:g.42167130A>G	ENSP00000317790:p.Leu1471Pro		39954422		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	14.09	2.431409	0.43122	.	.	ENSG00000137877	ENST00000320955	T	0.75367	-0.93	4.77	4.77	0.60923	.	0.000000	0.53938	D	0.000047	D	0.84365	0.5456	M	0.74258	2.255	0.46678	D	0.999155	D	0.89917	1.0	D	0.87578	0.998	D	0.84835	0.0804	10	0.46703	T	0.11	.	12.2624	0.54658	1.0:0.0:0.0:0.0	.	1471	Q9NRC6	SPTN5_HUMAN	P	1471	ENSP00000317790:L1471P	ENSP00000317790:L1471P	L	-	2	0	SPTBN5	39954422	1.000000	0.71417	0.717000	0.30585	0.011000	0.07611	6.288000	0.72679	1.771000	0.52183	0.454000	0.30748	CTG		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42167130	A	G	42167130	3	3	109	1	0	0	0	0	1	0	0	0	15161	188	7	4	6796	4	SPTBN5	15	42167130	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1246787	42167130	60364262	243	28809										
TGM5	9333	hgsc.bcm.edu	37	chr15	43527820	43527820	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caggacaaagcatatatcctGgcccatgttgggcgggtcga	13	10	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:43527820G>C	ENST00000220420.5	-	10	1568	c.1561C>G	c.(1561-1563)Cag>Gag	p.Q521E	TGM5_ENST00000349114.4_Missense_Mutation_p.Q439E	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	521			Q -> R (in dbSNP:rs35985214).		cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		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)	CATATATCCTGGCCCATGTTG	0.577																																																0			15											100	81	88					15																	43527820		2203	4299	6502	41315112	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1561C>G	15.37:g.43527820G>C	ENSP00000220420:p.Gln521Glu		41315112	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	6.964	0.547755	0.13312	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69926	-0.44;-0.44	5.58	4.67	0.58626	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.134279	0.47852	D	0.000201	T	0.54549	0.1865	L	0.37800	1.135	0.28500	N	0.914064	B;B	0.18013	0.002;0.025	B;B	0.23150	0.011;0.044	T	0.52525	-0.8564	10	0.49607	T	0.09	-8.616	8.215	0.31505	0.0839:0.1569:0.7592:0.0	.	439;521	O43548-2;O43548	.;TGM5_HUMAN	E	521;439;520	ENSP00000220420:Q521E;ENSP00000220419:Q439E	ENSP00000220420:Q521E	Q	-	1	0	TGM5	41315112	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	1.827000	0.39102	1.368000	0.46115	-0.137000	0.14449	CAG		0.577	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		C	43527820	G	C	43527820	3	2	109	1	0	0	0	0	1	0	0	0	15872	1357	47	5	617	5	TGM5	15	43527820	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	1360690	43527820	59003572	244	28810										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82533623	82533623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tccattacctgtggacagacTccttccacagcatctaccac	5	16	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:82533623T>C	ENST00000268206.7	-	5	534	c.366A>G	c.(364-366)ggA>ggG	p.G122G	EFTUD1_ENST00000359445.3_Silent_p.G71G	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	122	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						GTGGACAGACTCCTTCCACAG	0.443																																																0			15											79	74	75					15																	82533623		1911	4119	6030	80320678	SO:0001819	synonymous_variant	79631			AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.366A>G	15.37:g.82533623T>C			80320678	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																				0.443	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		C	82533623	T	C	82533623	2	2	109	1	0	0	0	0	0	0	0	1	4971	1538	54	4		4	EFTUD1	15	82533623	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	39005803	82533623	19997769	245	28811										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88678529	88678529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcagaggctgcccattgtgcAgccagtgcagcgttggtggg	17	10	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:88678529A>G	ENST00000360948.2	-	9	1168	c.1007T>C	c.(1006-1008)cTg>cCg	p.L336P	NTRK3_ENST00000394480.2_Missense_Mutation_p.L336P|NTRK3_ENST00000558676.1_Missense_Mutation_p.L336P|NTRK3_ENST00000317501.3_Missense_Mutation_p.L336P|NTRK3_ENST00000540489.2_Missense_Mutation_p.L336P|NTRK3_ENST00000557856.1_Missense_Mutation_p.L336P|NTRK3_ENST00000542733.2_Missense_Mutation_p.L238P|NTRK3_ENST00000355254.2_Missense_Mutation_p.L336P|NTRK3_ENST00000357724.2_Missense_Mutation_p.L336P	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	336	Ig-like C2-type 2.		L -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L336Q(2)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCCATTGTGCAGCCAGTGCAG	0.607			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	2	Substitution - Missense(2)	lung(2)	15											82	84	83					15																	88678529		2201	4299	6500	86479533	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1007T>C	15.37:g.88678529A>G	ENSP00000354207:p.Leu336Pro		86479533	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858573	0.71834	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.223524	0.40222	N	0.001151	D	0.89767	0.6810	H	0.95816	3.725	0.80722	D	1	D;D;P;D;D;P	0.89917	0.997;0.966;0.956;1.0;0.967;0.956	D;P;D;D;P;D	0.72338	0.93;0.77;0.936;0.977;0.73;0.936	D	0.92618	0.6105	10	0.72032	D	0.01	.	14.4172	0.67158	1.0:0.0:0.0:0.0	.	238;336;336;336;336;336	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	P	336;336;336;336;238;336;336	ENSP00000377990:L336P;ENSP00000354207:L336P;ENSP00000350356:L336P;ENSP00000347397:L336P;ENSP00000437773:L238P;ENSP00000444673:L336P;ENSP00000318328:L336P	ENSP00000318328:L336P	L	-	2	0	NTRK3	86479533	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.874000	0.75546	1.988000	0.58038	0.460000	0.39030	CTG		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				G	88678529	A	G	88678529	3	3	109	1	0	0	0	0	1	0	0	0	10739	188	7	4	1818	4	NTRK3	15	88678529	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	6144906	88678529	13852863	246	28812										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94910857	94910857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	taaagtggatatctcggcacTccctctgaagcaagccaact	8	12	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:94910857T>C	ENST00000357742.4	+	10	1325	c.1325T>C	c.(1324-1326)cTc>cCc	p.L442P	MCTP2_ENST00000451018.3_Missense_Mutation_p.L442P|MCTP2_ENST00000331706.4_Missense_Mutation_p.L30P|MCTP2_ENST00000557742.1_Missense_Mutation_p.L30P	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	442					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			ATCTCGGCACTCCCTCTGAAG	0.522																																																0			15											102	104	103					15																	94910857		2197	4298	6495	92711861	SO:0001583	missense	55784			AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1325T>C	15.37:g.94910857T>C	ENSP00000350377:p.Leu442Pro		92711861	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943464	0.73672	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.75154	2.61;-0.91;2.61	5.33	5.33	0.75918	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.137404	0.48767	D	0.000169	D	0.86130	0.5859	M	0.77313	2.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.988;0.987	D	0.88097	0.2817	10	0.87932	D	0	.	15.3122	0.74042	0.0:0.0:0.0:1.0	.	442;30;442	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	P	442;30;442	ENSP00000395109:L442P;ENSP00000329646:L30P;ENSP00000350377:L442P	ENSP00000329646:L30P	L	+	2	0	MCTP2	92711861	1.000000	0.71417	0.846000	0.33378	0.996000	0.88848	6.664000	0.74437	2.016000	0.59253	0.528000	0.53228	CTC		0.522	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		C	94910857	T	C	94910857	3	2	109	1	0	0	0	0	1	0	0	0	9431	1551	54	4	1363	4	MCTP2	15	94910857	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	6232328	94910857	7620535	247	28813										
SYNM	23336	hgsc.bcm.edu	37	chr15	99672941	99672941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	accagggcccaaagaaacttCgtttacctttcagatggatg	9	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:99672941C>T	ENST00000336292.6	+	5	4493	c.4373C>T	c.(4372-4374)tCg>tTg	p.S1458L	SYNM_ENST00000560674.1_Intron|SYNM_ENST00000561323.1_3'UTR|RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000328642.7_Intron	NM_145728.2	NP_663780.2	O15061	SYNEM_HUMAN	synemin, intermediate filament protein	1459	Interaction with DMD and UTRN.|Interaction with TLN1 and VCL.|Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						AAAGAAACTTCGTTTACCTTT	0.552																																					Pancreas(125;1071 1762 21750 40003 40381)											0			15											177	182	181					15																	99672941		2075	4208	6283	97490464	SO:0001583	missense	23336			AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000336292.6:c.4373C>T	15.37:g.99672941C>T	ENSP00000336775:p.Ser1458Leu		97490464	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000336292.6	37		.	.	.	.	.	.	.	.	.	.	C	16.17	3.046579	0.55110	.	.	ENSG00000182253	ENST00000336292	T	0.15834	2.39	5.55	2.67	0.31697	.	.	.	.	.	T	0.12092	0.0294	.	.	.	0.80722	D	1	P	0.34412	0.453	B	0.17722	0.019	T	0.06625	-1.0816	8	0.87932	D	0	.	9.9826	0.41821	0.0:0.7838:0.0:0.2162	.	1459	O15061	SYNEM_HUMAN	L	1458	ENSP00000336775:S1458L	ENSP00000336775:S1458L	S	+	2	0	SYNM	97490464	0.779000	0.28652	0.261000	0.24466	0.981000	0.71138	1.588000	0.36633	0.311000	0.23014	0.655000	0.94253	TCG		0.552	SYNM-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_145728		T	99672941	C	T	99672941	3	4	109	1	0	0	0	0	1	0	0	0	15494	893	31	1	4389	1	SYNM	15	99672941	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	4762084	99672941	2858451	248	28814										
TMEM8A	58986	hgsc.bcm.edu	37	chr16	425425	425425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccactacgacggtctcgttcCgcatctctgtctggaaaggg	11	13	3	0	rs370004240		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:425425C>T	ENST00000431232.2	-	7	1395	c.1235G>A	c.(1234-1236)cGg>cAg	p.R412Q	TMEM8A_ENST00000250930.3_Missense_Mutation_p.R219Q|TMEM8A_ENST00000476735.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	412					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GGTCTCGTTCCGCATCTCTGT	0.637																																																0			16						C	GLN/ARG	0,4402		0,0,2201	95	78	84		1235	-3.3	0	16		84	1,8595	1.2+/-3.3	0,1,4297	no	missense	TMEM8A	NM_021259.2	43	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	412/772	425425	1,12997	2201	4298	6499	365426	SO:0001583	missense	58986			AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1235G>A	16.37:g.425425C>T	ENSP00000401338:p.Arg412Gln		365426	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	C	5.338	0.247696	0.10130	0.0	1.16E-4	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.29655	1.97;1.56	4.17	-3.31	0.04988	.	2.138010	0.01884	N	0.038028	T	0.15565	0.0375	N	0.11427	0.14	0.09310	N	1	B	0.18166	0.026	B	0.06405	0.002	T	0.19289	-1.0310	10	0.12766	T	0.61	0.7189	9.039	0.36305	0.0:0.3632:0.3138:0.323	.	412	Q9HCN3	TMM8A_HUMAN	Q	412;219	ENSP00000401338:R412Q;ENSP00000250930:R219Q	ENSP00000250930:R219Q	R	-	2	0	TMEM8A	365426	0.014000	0.17966	0.000000	0.03702	0.000000	0.00434	0.638000	0.24674	-0.373000	0.07979	-1.751000	0.00678	CGG		0.637	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		T	425425	C	T	425425	3	4	109	1	0	0	0	0	1	0	0	0	16253	652	23	1	1108	1	TMEM8A	16	425425	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		425425	89929328	249	28815										
ZP2	7783	hgsc.bcm.edu	37	chr16	21213466	21213466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	attcaggggtatgtggaaccGtaccagcccctgagactgag	13	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:21213466G>A	ENST00000574002.1	-	12	1728	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	ZP2_ENST00000219593.4_Missense_Mutation_p.R416W|ZP2_ENST00000574091.1_Missense_Mutation_p.R416W|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	416	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		ATGTGGAACCGTACCAGCCCC	0.507																																																0			16											88	78	81					16																	21213466		2200	4300	6500	21120967	SO:0001583	missense	7783			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1246C>T	16.37:g.21213466G>A	ENSP00000460971:p.Arg416Trp		21120967	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.384048	0.25031	.	.	ENSG00000103310	ENST00000219593	D	0.82984	-1.67	5.83	-0.0239	0.13941	Zona pellucida sperm-binding protein (3);	0.917115	0.09272	N	0.824992	T	0.70159	0.3192	L	0.38531	1.155	0.09310	N	1	P;B	0.35844	0.524;0.205	B;B	0.28916	0.096;0.096	T	0.54622	-0.8266	10	0.36615	T	0.2	0.2289	6.6004	0.22697	0.1381:0.0:0.3582:0.5037	.	416;416	Q4VAP1;Q05996	.;ZP2_HUMAN	W	416	ENSP00000219593:R416W	ENSP00000219593:R416W	R	-	1	2	ZP2	21120967	0.000000	0.05858	0.000000	0.03702	0.665000	0.39181	0.200000	0.17257	-0.203000	0.10251	0.467000	0.42956	CGG		0.507	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			A	21213466	G	A	21213466	3	1	109	1	0	0	0	0	1	0	0	0	18255	1144	40	1	1027	1	ZP2	16	21213466	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	20788041	21213466	69141287	250	28816										
ATP2A1	487	hgsc.bcm.edu	37	chr16	28912087	28912087	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gagaacgaggaggtggccgaTcgcgcctacacgggccgaga	17	11	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:28912087T>C	ENST00000357084.3	+	15	2217	c.1950T>C	c.(1948-1950)gaT>gaC	p.D650D	ATP2A1_ENST00000536376.1_Silent_p.D525D|ATP2A1_ENST00000395503.4_Silent_p.D650D	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	650					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGTGGCCGATCGCGCCTACA	0.647																																																0			16											90	73	79					16																	28912087		2197	4300	6497	28819588	SO:0001819	synonymous_variant	487				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"ATPases / P-type"	811	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 1", "calcium pump 1"	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1950T>C	16.37:g.28912087T>C			28819588	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																				0.647	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		C	28912087	T	C	28912087	2	2	109	1	0	0	0	0	0	0	0	1	1137	1432	50	4		4	ATP2A1	16	28912087	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10	7698621	28912087	61442666	251	28817										
CA7	766	hgsc.bcm.edu	37	chr16	66885460	66885460	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgtggttggtgtttttttggAggtgagtggtggtttgctgg	19	1	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:66885460A>G	ENST00000338437.2	+	4	561	c.452A>G	c.(451-453)gAg>gGg	p.E151G	CA7_ENST00000394069.3_Splice_Site_p.E95G|RP11-61A14.1_ENST00000551187.1_RNA	NM_005182.2	NP_005173.1	P43166	CAH7_HUMAN	carbonic anhydrase VII	151					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of chloride transport (GO:2001225)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(4)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)	Acetazolamide(DB00819)|Diclofenamide(DB01144)|Methazolamide(DB00703)|Zonisamide(DB00909)	GTTTTTTTGGAGGTGAGTGGT	0.592																																																0			16											167	154	158					16																	66885460		2200	4300	6500	65442961	SO:0001630	splice_region_variant	766				CCDS10821.1, CCDS42173.1	16q22.1	2008-02-05			ENSG00000168748	ENSG00000168748	4.2.1.1	"Carbonic anhydrases"	1381	protein-coding gene	gene with protein product		114770				1783392	Standard	XM_005256135		Approved		uc002eqi.3	P43166	OTTHUMG00000137524	ENST00000338437.2:c.453+1A>G	16.37:g.66885460A>G			65442961	Q541F0|Q86YU0	Missense_Mutation	SNP	ENST00000338437.2	37	CCDS10821.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.332686	0.60853	.	.	ENSG00000168748	ENST00000338437;ENST00000394069	T;T	0.66815	-0.23;-0.23	5.87	5.87	0.94306	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.90369	3.11	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	D	0.87565	0.2474	10	0.87932	D	0	-28.3879	15.1012	0.72279	1.0:0.0:0.0:0.0	.	151	P43166	CAH7_HUMAN	G	151;95	ENSP00000345659:E151G;ENSP00000377632:E95G	ENSP00000345659:E151G	E	+	2	0	CA7	65442961	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	9.026000	0.93700	2.247000	0.74100	0.528000	0.53228	GAG		0.592	CA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268847.1		Missense_Mutation	G	66885460	A	G	66885460	5	3	109	1	0	0	0	0	0	0	1	0	2528	318	11	4	466	4	CA7	16	66885460	Splice_Site	SNP	A	TCGA-EF-5830-01A-01D-1657-10	37973373	66885460	23469293	252	28818										
CDH1	999	hgsc.bcm.edu	37	chr16	68844110	68844110	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gttctttcagctcttctctcAcgctgtgtcatccaacggga	8	13	6	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:68844110A>G	ENST00000261769.5	+	6	889	c.698A>G	c.(697-699)cAc>cGc	p.H233R	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.H233R	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	233	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CTCTTCTCTCACGCTGTGTCA	0.532			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	4	Unknown(4)	breast(4)	16											154	144	148					16																	68844110		2198	4300	6498	67401611	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.698A>G	16.37:g.68844110A>G	ENSP00000261769:p.His233Arg		67401611	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243615	0.79912	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.68765	-0.35;-0.35	5.22	5.22	0.72569	Cadherin (4);Cadherin-like (1);	0.000000	0.51477	D	0.000100	T	0.74696	0.3750	L	0.39467	1.215	0.80722	D	1	D;P	0.89917	1.0;0.941	D;B	0.73708	0.981;0.441	T	0.77159	-0.2690	10	0.66056	D	0.02	.	14.391	0.66978	1.0:0.0:0.0:0.0	.	233;233	Q9UII8;P12830	.;CADH1_HUMAN	R	233	ENSP00000261769:H233R;ENSP00000414946:H233R	ENSP00000261769:H233R	H	+	2	0	CDH1	67401611	1.000000	0.71417	0.996000	0.52242	0.885000	0.51271	8.671000	0.91174	2.096000	0.63516	0.455000	0.32223	CAC		0.532	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68844110	A	G	68844110	3	3	109	1	0	0	0	0	1	0	0	0	3101	159	6	4	720	4	CDH1	16	68844110	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1958650	68844110	21510643	253	28819										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77389967	77389967	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccttctccatcgtgaatcaTaccaaagctgaaacagaatg	6	12	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:77389967T>G	ENST00000282849.5	-	9	1748	c.1330A>C	c.(1330-1332)Atg>Ctg	p.M444L		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	444	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TCGTGAATCATACCAAAGCTG	0.403																																																0			16											96	88	91					16																	77389967		2198	4300	6498	75947468	SO:0001583	missense	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.1330A>C	16.37:g.77389967T>G	ENSP00000282849:p.Met444Leu		75947468	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.683950	0.68157	.	.	ENSG00000140873	ENST00000282849	T	0.61980	0.06	5.19	5.19	0.71726	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.77922	0.4203	M	0.76170	2.325	0.58432	D	0.999999	P;D	0.60575	0.909;0.988	P;D	0.70227	0.646;0.968	T	0.80654	-0.1286	10	0.72032	D	0.01	.	14.6804	0.69012	0.0:0.0:0.0:1.0	.	444;444	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	L	444	ENSP00000282849:M444L	ENSP00000282849:M444L	M	-	1	0	ADAMTS18	75947468	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	7.825000	0.86693	2.311000	0.77944	0.533000	0.62120	ATG		0.403	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			G	77389967	T	G	77389967	3	3	109	1	0	0	0	0	1	0	0	0	263	1406	49	4	2395	4	ADAMTS18	16	77389967	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	8545857	77389967	12964786	254	28820										
BANP	54971	hgsc.bcm.edu	37	chr16	88039785	88039785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggacggggagagcggctcggAggccagcgactctgtgtcca	18	11	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:88039785A>G	ENST00000393207.1	+	6	766	c.545A>G	c.(544-546)gAg>gGg	p.E182G	BANP_ENST00000355022.4_Missense_Mutation_p.E151G|BANP_ENST00000286122.7_Missense_Mutation_p.E182G|BANP_ENST00000393208.2_Missense_Mutation_p.E151G|BANP_ENST00000355163.5_Missense_Mutation_p.E157G|BANP_ENST00000538234.1_Missense_Mutation_p.E190G|BANP_ENST00000479780.2_Missense_Mutation_p.E151G	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	182	Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		AGCGGCTCGGAGGCCAGCGAC	0.652																																																0			16											71	70	70					16																	88039785		2198	4299	6497	86597286	SO:0001583	missense	54971			AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.545A>G	16.37:g.88039785A>G	ENSP00000376902:p.Glu182Gly		86597286	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846486	0.91277	.	.	ENSG00000172530	ENST00000439677;ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.43	5.43	0.79202	.	0.045450	0.85682	D	0.000000	T	0.38852	0.1056	L	0.27053	0.805	0.58432	D	0.999999	D;D;P;D;D;D	0.89917	0.993;1.0;0.948;0.994;0.969;1.0	D;D;P;D;P;D	0.85130	0.968;0.993;0.452;0.979;0.556;0.997	T	0.28776	-1.0033	10	0.72032	D	0.01	.	14.9579	0.71131	1.0:0.0:0.0:0.0	.	190;157;151;182;151;151	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	G	157;182;157;147;151;151;151;151;190;182	ENSP00000411479:E157G;ENSP00000286122:E182G;ENSP00000347290:E157G;ENSP00000432508:E151G;ENSP00000376903:E151G;ENSP00000347125:E151G;ENSP00000444352:E190G;ENSP00000376902:E182G	ENSP00000286122:E182G	E	+	2	0	BANP	86597286	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	8.101000	0.89546	2.186000	0.69663	0.533000	0.62120	GAG		0.652	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		G	88039785	A	G	88039785	3	3	109	1	0	0	0	0	1	0	0	0	1311	304	11	4	605	4	BANP	16	88039785	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	10649818	88039785	2314968	255	28821										
TP53	7157	hgsc.bcm.edu	37	chr17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	attctcttcctctgtgcgccGgtctctcccaggacaggcac	9	16	3	0	rs28934574		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577094	G	A	7577094	3	1	109	1	0	0	0	0	1	0	0	0	16421	1115	39	1	442	1	TP53	17	7577094	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10		7577094	73618116	256	28822										
KDM6B	23135	hgsc.bcm.edu	37	chr17	7749471	7749471	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caggcattgctccgggagccAgcccagccagggctttggga	15	13	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:7749471A>G	ENST00000448097.2	+	6	643	c.312A>G	c.(310-312)ccA>ccG	p.P104P	KDM6B_ENST00000254846.5_Silent_p.P104P			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	104					cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						TCCGGGAGCCAGCCCAGCCAG	0.627																																																0			17											42	42	42					17																	7749471		2203	4300	6503	7690196	SO:0001819	synonymous_variant	23135			AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.312A>G	17.37:g.7749471A>G			7690196	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																					0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		G	7749471	A	G	7749471	2	3	109	1	0	0	0	0	0	0	0	1	8159	175	7	4		4	KDM6B	17	7749471	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	172377	7749471	73445739	257	28823										
NF1	4763	hgsc.bcm.edu	37	chr17	29527558	29527558	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agcaagtacttacatcaattGggaagataactctgtcattt	7	7	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:29527558G>T	ENST00000358273.4	+	9	1390	c.1007G>T	c.(1006-1008)tGg>tTg	p.W336L	NF1_ENST00000356175.3_Missense_Mutation_p.W336L|NF1_ENST00000431387.4_Missense_Mutation_p.W336L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	336					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.W336*(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TACATCAATTGGGAAGATAAC	0.393			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	17	Whole gene deletion(8)|Unknown(6)|Substitution - Nonsense(3)	soft_tissue(8)|lung(3)|autonomic_ganglia(3)|central_nervous_system(3)	17	GRCh37	CM003946|CS001840	NF1	M|S							122	107	112					17																	29527558		2203	4300	6503	26551684	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1007G>T	17.37:g.29527558G>T	ENSP00000351015:p.Trp336Leu		26551684	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836698	0.91117	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	T;T;T;T	0.62364	3.04;0.03;0.03;3.08	5.39	5.39	0.77823	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73369	0.3578	L	0.54323	1.7	0.80722	D	1	B;D;B;P;B	0.57899	0.038;0.981;0.011;0.782;0.397	B;D;B;B;B	0.70487	0.013;0.969;0.011;0.423;0.24	T	0.66106	-0.6006	10	0.09843	T	0.71	.	19.1503	0.93485	0.0:0.0:1.0:0.0	.	336;336;336;336;336	E1P657;P21359-2;P21359;Q14931;P21359-3	.;.;NF1_HUMAN;.;.	L	336;336;336;2	ENSP00000412921:W336L;ENSP00000351015:W336L;ENSP00000348498:W336L;ENSP00000389907:W2L	ENSP00000348498:W336L	W	+	2	0	NF1	26551684	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.082000	0.94059	2.542000	0.85734	0.591000	0.81541	TGG		0.393	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29527558	G	T	29527558	3	4	109	1	0	0	0	0	1	0	0	0	10387	1357	47	2	1041	2	NF1	17	29527558	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	21778087	29527558	51667652	258	28824										
NF1	4763	hgsc.bcm.edu	37	chr17	29664408	29664408	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gagaccaagcaagttttgagActcagtctgacagagttctc	10	9	3	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:29664408A>G	ENST00000358273.4	+	43	6833	c.6450A>G	c.(6448-6450)agA>agG	p.R2150R	NF1_ENST00000356175.3_Silent_p.R2129R|NF1_ENST00000444181.2_5'Flank|NF1_ENST00000417592.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2150					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.R2150S(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAGTTTTGAGACTCAGTCTGA	0.368			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(8)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											86	75	79					17																	29664408		2203	4300	6503	26688534	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.6450A>G	17.37:g.29664408A>G			26688534	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29664408	A	G	29664408	2	3	109	1	0	0	0	0	0	0	0	1	10387	272	10	4		4	NF1	17	29664408	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	136850	29664408	51530802	259	28825										
TUBG2	27175	hgsc.bcm.edu	37	chr17	40811902	40811902	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccgagcatggtatcagccccGagggcatcgtggaggaattc	14	11	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:40811902G>T	ENST00000251412.7	+	2	299	c.100G>T	c.(100-102)Gag>Tag	p.E34*		NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	34					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TATCAGCCCCGAGGGCATCGT	0.652																																																0			17											43	55	51					17																	40811902		2203	4298	6501	38065428	SO:0001587	stop_gained	27175			AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"Tubulins"	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.100G>T	17.37:g.40811902G>T	ENSP00000251412:p.Glu34*		38065428	A6NDI4|Q32NB2	Nonsense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	.	.	.	.	.	.	.	.	.	.	G	38	6.768235	0.97825	.	.	ENSG00000037042	ENST00000251412	.	.	.	5.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-32.4097	13.162	0.59550	0.0:0.0:0.84:0.16	.	.	.	.	X	34	.	ENSP00000251412:E34X	E	+	1	0	TUBG2	38065428	1.000000	0.71417	0.999000	0.59377	0.811000	0.45836	6.404000	0.73268	1.254000	0.44035	0.655000	0.94253	GAG		0.652	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437		T	40811902	G	T	40811902	4	4	109	1	0	0	0	0	0	1	0	0	16805	1059	37	2	106	2	TUBG2	17	40811902	Nonsense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	11147494	40811902	40383308	260	28826										
WNT3	7473	hgsc.bcm.edu	37	chr17	44851144	44851144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggatgcccagcttcacgcccTcggccacgctgggcatgatc	12	16	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:44851144T>C	ENST00000225512.5	-	2	374	c.212A>G	c.(211-213)gAg>gGg	p.E71G		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	71					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CTTCACGCCCTCGGCCACGCT	0.652																																																0			17											52	56	55					17																	44851144		2203	4300	6503	42206307	SO:0001583	missense	7473			AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.212A>G	17.37:g.44851144T>C	ENSP00000225512:p.Glu71Gly		42206307	Q2M237|Q9H1J9	Missense_Mutation	SNP	ENST00000225512.5	37	CCDS11505.1	.	.	.	.	.	.	.	.	.	.	T	31	5.098801	0.94197	.	.	ENSG00000108379	ENST00000225512	T	0.77358	-1.09	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.83801	0.5333	M	0.77313	2.365	0.80722	D	1	D	0.53151	0.958	P	0.54174	0.744	D	0.85399	0.1130	10	0.49607	T	0.09	.	13.8223	0.63329	0.0:0.0:0.0:1.0	.	71	P56703	WNT3_HUMAN	G	71	ENSP00000225512:E71G	ENSP00000225512:E71G	E	-	2	0	WNT3	42206307	1.000000	0.71417	0.782000	0.31804	0.991000	0.79684	5.923000	0.70045	1.852000	0.53769	0.379000	0.24179	GAG		0.652	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		C	44851144	T	C	44851144	3	2	109	1	0	0	0	0	1	0	0	0	17428	1551	54	4	867	4	WNT3	17	44851144	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4039242	44851144	36344066	261	28827										
EVPL	2125	hgsc.bcm.edu	37	chr17	74014586	74014586	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atgcagaagcaggcggcgggAgcacgcttggtctccccgcc	15	14	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:74014586A>G	ENST00000301607.3	-	12	1633	c.1380T>C	c.(1378-1380)gcT>gcC	p.A460A	EVPL_ENST00000586740.1_Silent_p.A460A	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	460	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGGCGGCGGGAGCACGCTTGG	0.662																																																0			17											20	20	20					17																	74014586		2202	4300	6502	71526181	SO:0001819	synonymous_variant	2125			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1380T>C	17.37:g.74014586A>G			71526181	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																				0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		G	74014586	A	G	74014586	2	3	109	1	0	0	0	0	0	0	0	1	5305	291	11	4		4	EVPL	17	74014586	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	29163442	74014586	7180624	262	28828										
CANT1	124583	hgsc.bcm.edu	37	chr17	76993398	76993398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aactgcgattcgataccgaaTcccagccggtgtcctttgtg	10	12	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:76993398T>C	ENST00000302345.2	-	2	801	c.307A>G	c.(307-309)Att>Gtt	p.I103V	CANT1_ENST00000591732.1_5'Flank|CANT1_ENST00000392446.5_Missense_Mutation_p.I103V|CANT1_ENST00000591773.1_Missense_Mutation_p.I103V	NM_001159773.1|NM_138793.3	NP_001153245.1|NP_620148.1	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	103					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|proteoglycan biosynthetic process (GO:0030166)|signal transduction (GO:0007165)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|signal transducer activity (GO:0004871)|uridine-diphosphatase activity (GO:0045134)		CANT1/ETV4(3)	cervix(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			CGATACCGAATCCCAGCCGGT	0.577			T	ETV4	prostate																																		Dom	yes		17	17q25	124583	calcium activated nucleotidase 1		E	0			17											105	115	112					17																	76993398		2203	4300	6503	74504993	SO:0001583	missense	124583			AJ312208	CCDS11760.1	17q25.3	2008-02-05	2004-10-12	2004-10-15		ENSG00000171302			19721	protein-coding gene	gene with protein product	"Soluble Ca-Activated Nucleotidase, isozyme 1"	613165				12167635	Standard	NM_138793		Approved	SHAPY, SCAN-1	uc002jwk.3	Q8WVQ1		ENST00000302345.2:c.307A>G	17.37:g.76993398T>C	ENSP00000307674:p.Ile103Val		74504993	B4DJ54|Q7Z2J7|Q8NG05|Q8NHP0|Q9BSD5	Missense_Mutation	SNP	ENST00000302345.2	37	CCDS11760.1	.	.	.	.	.	.	.	.	.	.	T	0.421	-0.908095	0.02434	.	.	ENSG00000171302	ENST00000302345;ENST00000392446;ENST00000537282;ENST00000339300	D;D	0.85484	-1.99;-1.99	5.17	-0.112	0.13572	.	0.646879	0.16807	N	0.198759	T	0.64182	0.2575	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48833	-0.9000	10	0.13853	T	0.58	-2.1482	5.5721	0.17202	0.0:0.2459:0.5215:0.2326	.	103	Q8WVQ1	CANT1_HUMAN	V	103;103;103;52	ENSP00000307674:I103V;ENSP00000376241:I103V	ENSP00000307674:I103V	I	-	1	0	CANT1	74504993	0.010000	0.17322	0.050000	0.19076	0.163000	0.22366	0.886000	0.28241	0.278000	0.22164	0.459000	0.35465	ATT		0.577	CANT1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437723.2	NM_138793		C	76993398	T	C	76993398	3	2	109	1	0	0	0	0	1	0	0	0	2623	1435	50	4	910	4	CANT1	17	76993398	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	2978812	76993398	4201812	263	28829										
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79974392	79974392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tctggtgcacttgggagccgAggagccggcaggtgagtgtc	18	9	1	1	rs112054193		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:79974392A>G	ENST00000306739.4	+	13	1491	c.1394A>G	c.(1393-1395)gAg>gGg	p.E465G	ASPSCR1_ENST00000582404.1_3'UTR|STRA13_ENST00000583767.1_5'Flank|ASPSCR1_ENST00000306729.7_Missense_Mutation_p.E559G|ASPSCR1_ENST00000580534.1_Missense_Mutation_p.E413G	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	465					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			TTGGGAGCCGAGGAGCCGGCA	0.706			T	TFE3	alveolar soft part sarcoma																																		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	0			17											20	22	21					17																	79974392		2060	4087	6147	77567681	SO:0001583	missense	79058			AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"UBX domain containing"	13825	protein-coding gene	gene with protein product	"UBX domain protein 9"	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.1394A>G	17.37:g.79974392A>G	ENSP00000302176:p.Glu465Gly		77567681	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	37	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	A	5.720	0.317268	0.10845	.	.	ENSG00000169696	ENST00000306739;ENST00000306729	T;T	0.30182	1.77;1.54	3.76	2.62	0.31277	.	0.633971	0.15827	N	0.242716	T	0.35682	0.0940	M	0.63428	1.95	0.19300	N	0.999978	D;D;D	0.57257	0.979;0.978;0.974	P;P;B	0.50109	0.631;0.546;0.422	T	0.12116	-1.0560	9	.	.	.	-16.2532	7.1134	0.25403	0.8866:0.0:0.1134:0.0	.	413;559;465	Q9BZE9-3;Q9BZE9-2;Q9BZE9	.;.;ASPC1_HUMAN	G	465;559	ENSP00000302176:E465G;ENSP00000306625:E559G	.	E	+	2	0	ASPSCR1	77567681	0.479000	0.25925	0.348000	0.25681	0.074000	0.17049	2.581000	0.46077	1.581000	0.49865	0.460000	0.39030	GAG		0.706	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		G	79974392	A	G	79974392	3	3	109	1	0	0	0	0	1	0	0	0	1060	304	11	4	1444	4	ASPSCR1	17	79974392	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	2980994	79974392	1220818	264	28830										
CD7	924	hgsc.bcm.edu	37	chr17	80274179	80274179	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gctggcgggtcagggagggcAgaggctgtctgcgggtcagg	22	8	3	1	rs560319694		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80274179A>G	ENST00000312648.3	-	3	610	c.504T>C	c.(502-504)tcT>tcC	p.S168S	CD7_ENST00000583376.1_Silent_p.S68S|CD7_ENST00000578509.1_Silent_p.S68S|CD7_ENST00000584284.1_Silent_p.S168S	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	168	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			CAGGGAGGGCAGAGGCTGTCT	0.716																																					Pancreas(45;804 1068 19702 28207 28798)											0			17											14	17	16					17																	80274179		2168	4265	6433	77867468	SO:0001819	synonymous_variant	924			X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1695	protein-coding gene	gene with protein product	"p41 protein", "T-cell antigen CD7", "T-cell leukemia antigen"	186820	"CD7 antigen (p41)"			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.504T>C	17.37:g.80274179A>G			77867468		Silent	SNP	ENST00000312648.3	37	CCDS11807.1																																																																																				0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		G	80274179	A	G	80274179	2	3	109	1	0	0	0	0	0	0	0	1	3038	175	7	4		4	CD7	17	80274179	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	299787	80274179	921031	265	28831										
ZNF750	79755	hgsc.bcm.edu	37	chr17	80789936	80789936	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgcagggtgatgccctgtggAgggctggcttctgtcccagg	17	10	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80789936A>G	ENST00000269394.3	-	2	1228	c.395T>C	c.(394-396)cTc>cCc	p.L132P	ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	132					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	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)			TGCCCTGTGGAGGGCTGGCTT	0.632																																																0			17											33	35	34					17																	80789936		2203	4300	6503	78383225	SO:0001583	missense	79755			AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.395T>C	17.37:g.80789936A>G	ENSP00000269394:p.Leu132Pro		78383225	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	A	5.038	0.192741	0.09599	.	.	ENSG00000141579	ENST00000269394	T	0.25085	1.82	5.86	0.873	0.19118	.	0.693133	0.13492	N	0.383930	T	0.16514	0.0397	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.14023	0.01	T	0.27502	-1.0072	9	.	.	.	-21.9099	9.3124	0.37912	0.6777:0.0:0.3223:0.0	.	132	Q32MQ0	ZN750_HUMAN	P	132	ENSP00000269394:L132P	.	L	-	2	0	ZNF750	78383225	0.014000	0.17966	0.004000	0.12327	0.023000	0.10783	1.466000	0.35310	0.380000	0.24823	0.533000	0.62120	CTC		0.632	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		G	80789936	A	G	80789936	3	3	109	1	0	0	0	0	1	0	0	0	18171	304	11	4	1784	4	ZNF750	17	80789936	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	515757	80789936	405274	266	28832										
ATP5A1	498	hgsc.bcm.edu	37	chr18	43669870	43669870	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggaacgtccacaatggctccTgtcctcttcactatatctcc	6	15	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:43669870T>C	ENST00000398752.6	-	4	523	c.402A>G	c.(400-402)acA>acG	p.T134T	ATP5A1_ENST00000593152.2_Silent_p.T84T|ATP5A1_ENST00000282050.2_Silent_p.T134T|ATP5A1_ENST00000590665.1_Silent_p.T134T	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	134					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CAATGGCTCCTGTCCTCTTCA	0.433																																																0			18											127	98	108					18																	43669870		2203	4300	6503	41923868	SO:0001819	synonymous_variant	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.402A>G	18.37:g.43669870T>C			41923868	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Silent	SNP	ENST00000398752.6	37	CCDS11927.1																																																																																				0.433	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		C	43669870	T	C	43669870	2	2	109	1	0	0	0	0	0	0	0	1	1148	1567	55	4		4	ATP5A1	18	43669870	Silent	SNP	T	TCGA-EF-5830-01A-01D-1657-10		43669870	34407378	267	28833										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591827	48591827	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgttccattgcttactttgaAatggatgttcaggtaggaga	11	5	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:48591827A>G	ENST00000342988.3	+	9	1528	c.990A>G	c.(988-990)gaA>gaG	p.E330E	SMAD4_ENST00000398417.2_Silent_p.E330E|SMAD4_ENST00000588745.1_Silent_p.E234E	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	330	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		E -> G (in JPS; dbSNP:rs281875324). {ECO:0000269|PubMed:12417513}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CTTACTTTGAAATGGATGTTC	0.423																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											259	224	236					18																	48591827		2203	4300	6503	46845825	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.990A>G	18.37:g.48591827A>G			46845825	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.423	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48591827	A	G	48591827	2	3	109	1	0	0	0	0	0	0	0	1	14797	11	1	4		4	SMAD4	18	48591827	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4921957	48591827	29485421	268	28834										
CDH7	1005	hgsc.bcm.edu	37	chr18	63489414	63489414	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	atggttggtcaaaatggaggActgtcaggaactacatcagt	12	6	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:63489414A>G	ENST00000397968.2	+	5	1149	c.723A>G	c.(721-723)ggA>ggG	p.G241G	CDH7_ENST00000536984.2_Silent_p.G241G|CDH7_ENST00000323011.3_Silent_p.G241G	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	241	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				AAAATGGAGGACTGTCAGGAA	0.443																																																0			18											171	124	140					18																	63489414		2203	4300	6503	61640394	SO:0001819	synonymous_variant	28513			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.723A>G	18.37:g.63489414A>G			61640394	Q9H157	Silent	SNP	ENST00000397968.2	37	CCDS11993.1																																																																																				0.443	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		G	63489414	A	G	63489414	2	3	109	1	0	0	0	0	0	0	0	1	3121	262	10	4		4	CDH7	18	63489414	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	14897587	63489414	14587834	269	28835										
CNDP2	55748	hgsc.bcm.edu	37	chr18	72178204	72178204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggctgggaaagaagaagcccTgcatcacctacggcctcagg	13	12	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:72178204T>C	ENST00000324262.4	+	6	929	c.613T>C	c.(613-615)Tgc>Cgc	p.C205R	CNDP2_ENST00000324301.8_Missense_Mutation_p.C121R|CNDP2_ENST00000579847.1_Missense_Mutation_p.C205R	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	205					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GAAGAAGCCCTGCATCACCTA	0.493																																																0			18											121	102	109					18																	72178204		2203	4300	6503	70329184	SO:0001583	missense	55748			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.613T>C	18.37:g.72178204T>C	ENSP00000325548:p.Cys205Arg		70329184	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.165232	0.38217	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T	0.20598	2.06	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	H	0.95365	3.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.73547	-0.3948	10	0.87932	D	0	0.0	16.8222	0.85835	0.0:0.0:0.0:1.0	.	110;121;205	B4DPF1;Q96KP4-2;Q96KP4	.;.;CNDP2_HUMAN	R	205;121	ENSP00000325548:C205R	ENSP00000325548:C205R	C	+	1	0	CNDP2	70329184	1.000000	0.71417	0.988000	0.46212	0.702000	0.40608	6.222000	0.72249	2.371000	0.80710	0.533000	0.62120	TGC		0.493	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		C	72178204	T	C	72178204	3	2	109	1	0	0	0	0	1	0	0	0	3600	1580	55	4	631	4	CNDP2	18	72178204	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	8688790	72178204	5899044	270	28836										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066829	9066829	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggcttctatagctgtggtgtCttcatctgttgtcagtatct	10	8	6	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:9066829C>T	ENST00000397910.4	-	3	20820	c.20617G>A	c.(20617-20619)Gac>Aac	p.D6873N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6875	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTGTGGTGTCTTCATCTGTT	0.488																																																0			19											199	188	192					19																	9066829		2106	4233	6339	8927829	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20617G>A	19.37:g.9066829C>T	ENSP00000381008:p.Asp6873Asn		8927829	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	8.470	0.857363	0.17106	.	.	ENSG00000181143	ENST00000397910	T	0.24350	1.86	2.05	2.05	0.26809	.	.	.	.	.	T	0.14270	0.0345	N	0.22421	0.69	.	.	.	P	0.50710	0.938	B	0.37451	0.25	T	0.15407	-1.0438	8	0.87932	D	0	.	7.593	0.28031	0.0:1.0:0.0:0.0	.	6873	B5ME49	.	N	6873	ENSP00000381008:D6873N	ENSP00000381008:D6873N	D	-	1	0	MUC16	8927829	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.236000	0.02925	1.444000	0.47605	0.407000	0.27541	GAC		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9066829	C	T	9066829	3	4	109	1	0	0	0	0	1	0	0	0	10003	913	32	3	23234	3	MUC16	19	9066829	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		9066829	50062154	271	28837										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10403920	10403920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggacgtaacgctaacggtggAgtgtgagtgggggtgcgcag	20	6	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:10403920A>G	ENST00000221980.4	+	6	1526	c.1463A>G	c.(1462-1464)gAg>gGg	p.E488G		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	488			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CTAACGGTGGAGTGTGAGTGG	0.607																																																0			19											73	54	61					19																	10403920		2194	4289	6483	10264920	SO:0001583	missense	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1463A>G	19.37:g.10403920A>G	ENSP00000221980:p.Glu488Gly		10264920	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807692	0.70797	.	.	ENSG00000105376	ENST00000221980	T	0.15718	2.4	4.84	3.83	0.44106	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.207799	0.33572	N	0.004768	T	0.26195	0.0639	L	0.55990	1.75	0.36635	D	0.876495	D	0.67145	0.996	P	0.58331	0.837	T	0.15492	-1.0435	10	0.31617	T	0.26	-20.9806	6.9864	0.24731	0.8978:0.0:0.1022:0.0	.	488	Q9UMF0	ICAM5_HUMAN	G	488	ENSP00000221980:E488G	ENSP00000221980:E488G	E	+	2	0	ICAM5	10264920	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	3.210000	0.51129	0.891000	0.36235	0.402000	0.26972	GAG		0.607	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		G	10403920	A	G	10403920	3	3	109	1	0	0	0	0	1	0	0	0	7504	304	11	4	1485	4	ICAM5	19	10403920	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1337091	10403920	48725063	272	28838										
LDLR	3949	hgsc.bcm.edu	37	chr19	11230864	11230864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgttggctgaaaacctactgTccccagaggatatggttctc	10	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:11230864T>C	ENST00000558518.1	+	13	2129	c.1942T>C	c.(1942-1944)Tcc>Ccc	p.S648P	LDLR_ENST00000558013.1_Missense_Mutation_p.S648P|LDLR_ENST00000545707.1_Missense_Mutation_p.S521P|LDLR_ENST00000557933.1_Missense_Mutation_p.S648P|LDLR_ENST00000535915.1_Missense_Mutation_p.S607P|LDLR_ENST00000455727.2_Missense_Mutation_p.S480P	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	648					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	AAACCTACTGTCCCCAGAGGA	0.502																																					GBM(18;201 575 7820 21545)											1	Unknown(1)	lung(1)	19	GRCh37	CM074324	LDLR	M							117	89	98					19																	11230864		2203	4300	6503	11091864	SO:0001583	missense	3949			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1942T>C	19.37:g.11230864T>C	ENSP00000454071:p.Ser648Pro		11091864	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	T	5.227	0.227401	0.09916	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.96168	-3.93;-3.93;-3.93	5.37	4.35	0.52113	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.228496	0.29752	N	0.011284	D	0.96303	0.8794	M	0.66506	2.035	0.18873	N	0.999984	B;D;B;B;B;B	0.54964	0.018;0.969;0.049;0.043;0.018;0.018	B;P;B;B;B;B	0.61940	0.078;0.896;0.129;0.061;0.121;0.078	D	0.90836	0.4720	10	0.38643	T	0.18	.	10.3077	0.43691	0.0:0.0788:0.0:0.9212	.	480;521;527;607;660;648	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	P	648;521;607;480	ENSP00000437639:S521P;ENSP00000440520:S607P;ENSP00000397829:S480P	ENSP00000252444:S648P	S	+	1	0	LDLR	11091864	0.015000	0.18098	0.017000	0.16124	0.011000	0.07611	1.737000	0.38197	0.900000	0.36469	-0.262000	0.10625	TCC		0.502	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			C	11230864	T	C	11230864	3	2	109	1	0	0	0	0	1	0	0	0	8726	1667	58	4	1992	4	LDLR	19	11230864	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	826944	11230864	47898119	273	28839										
RAD23A	5886	hgsc.bcm.edu	37	chr19	13059032	13059032	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tcagcacccccagaggcctcAcccacagctgccccagagtc	8	20	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:13059032A>C	ENST00000586534.1	+	3	337	c.276A>C	c.(274-276)tcA>tcC	p.S92S	RAD23A_ENST00000592268.1_Silent_p.S92S|RAD23A_ENST00000588826.2_3'UTR|RAD23A_ENST00000316856.3_Silent_p.S92S|RAD23A_ENST00000541222.1_5'UTR			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	92					nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						CAGAGGCCTCACCCACAGCTG	0.627								Nucleotide excision repair (NER)																																								0			19											54	67	63					19																	13059032		2203	4300	6503	12920032	SO:0001819	synonymous_variant	5886				CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"RAD23, yeast homolog, A"	600061	"RAD23 (S. cerevisiae) homolog A"			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.276A>C	19.37:g.13059032A>C			12920032	K7ESE3|Q59EU8|Q5M7Z1	Silent	SNP	ENST00000586534.1	37	CCDS12289.1																																																																																				0.627	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053		C	13059032	A	C	13059032	2	2	109	1	0	0	0	0	0	0	0	1	13019	146	6	4		4	RAD23A	19	13059032	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1828168	13059032	46069951	274	28840										
NFIX	4784	hgsc.bcm.edu	37	chr19	13186419	13186419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttgatgacgtgttctatcccGggacaggccgttccccagca	11	13	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:13186419G>A	ENST00000592199.1	+	6	889	c.889G>A	c.(889-891)Ggg>Agg	p.G297R	NFIX_ENST00000588228.1_Missense_Mutation_p.G250R|NFIX_ENST00000587260.1_Missense_Mutation_p.G296R|NFIX_ENST00000358552.3_Missense_Mutation_p.G296R|NFIX_ENST00000397661.2_Missense_Mutation_p.G297R|NFIX_ENST00000360105.4_Missense_Mutation_p.G300R|NFIX_ENST00000585575.1_Missense_Mutation_p.G289R|NFIX_ENST00000587760.1_Missense_Mutation_p.G289R			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	297					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GTTCTATCCCGGGACAGGCCG	0.617																																																0			19											44	50	48					19																	13186419		2052	4196	6248	13047419	SO:0001583	missense	4784			U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.889G>A	19.37:g.13186419G>A	ENSP00000467512:p.Gly297Arg		13047419	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Missense_Mutation	SNP	ENST00000592199.1	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.977771	0.74360	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000358552	T;T	0.44482	0.92;0.97	4.69	4.69	0.59074	.	0.000000	0.64402	D	0.000016	T	0.58061	0.2096	L	0.51422	1.61	0.46823	D	0.999218	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.996;0.999;0.999	T	0.53272	-0.8462	10	0.31617	T	0.26	.	16.5244	0.84327	0.0:0.0:1.0:0.0	.	305;296;300;297;297	B4DHW2;Q14938-5;F8W8H9;Q14938;Q14938-3	.;.;.;NFIX_HUMAN;.	R	297;297;300;296	ENSP00000380781:G297R;ENSP00000351354:G296R	ENSP00000264825:G300R	G	+	1	0	NFIX	13047419	1.000000	0.71417	0.980000	0.43619	0.814000	0.46013	6.453000	0.73488	2.440000	0.82611	0.561000	0.74099	GGG		0.617	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501		A	13186419	G	A	13186419	3	1	109	1	0	0	0	0	1	0	0	0	10405	1116	39	1	911	1	NFIX	19	13186419	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	127387	13186419	45942564	275	28841										
SFRS14	10147	hgsc.bcm.edu	37	chr19	19115059	19115059	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttgctgctgatcctcttccgAgggaagcaggtacctgagga	13	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:19115059A>G	ENST00000601879.1	-	7	3144	c.2847T>C	c.(2845-2847)ccT>ccC	p.P949P	SUGP2_ENST00000600377.1_Silent_p.P963P|SUGP2_ENST00000456085.2_Silent_p.P718P|SUGP2_ENST00000452918.2_Silent_p.P949P|SUGP2_ENST00000337018.6_Silent_p.P949P			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	949					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCCTCTTCCGAGGGAAGCAGG	0.622																																																0			19											70	70	70					19																	19115059		2203	4300	6503	18976059	SO:0001819	synonymous_variant	0			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2847T>C	19.37:g.19115059A>G			18976059	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	37	CCDS12392.1																																																																																				0.622	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		G	19115059	A	G	19115059	2	3	109	1	0	0	0	0	0	0	0	1	14207	291	11	4		4	SFRS14	19	19115059	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	5928640	19115059	40013924	276	28842										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37416131	37416131	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctcaagagtctgccctttccGaggaagaagaggatacaacc	10	11	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:37416131G>A	ENST00000333987.7	+	4	612	c.106G>A	c.(106-108)Gag>Aag	p.E36K	ZNF568_ENST00000415168.1_Intron|ZNF568_ENST00000427117.1_Missense_Mutation_p.E36K|ZNF568_ENST00000455427.2_5'UTR	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	36					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGCCCTTTCCGAGGAAGAAGA	0.413																																																0			19											141	126	131					19																	37416131		1878	4112	5990	42107971	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.106G>A	19.37:g.37416131G>A	ENSP00000334685:p.Glu36Lys		42107971	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	G	8.439	0.850363	0.17034	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000444991	T;T;T	0.06449	5.83;3.51;3.3	3.74	-7.48	0.01360	.	.	.	.	.	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.01;0.0	B;B	0.04013	0.001;0.0	T	0.47497	-0.9113	9	0.09338	T	0.73	.	9.6374	0.39817	0.186:0.2588:0.5552:0.0	.	36;36	C9JZ58;Q3ZCX4	.;ZN568_HUMAN	K	36	ENSP00000407012:E36K;ENSP00000334685:E36K;ENSP00000389794:E36K	ENSP00000334685:E36K	E	+	1	0	ZNF568	42107971	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-3.302000	0.00520	-2.153000	0.00793	-0.796000	0.03273	GAG		0.413	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		A	37416131	G	A	37416131	3	1	109	1	0	0	0	0	1	0	0	0	18038	1059	37	1	112	1	ZNF568	19	37416131	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	18301072	37416131	21712852	277	28843										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38590741	38590741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ccactgcctgcggctggcccTcaacacccccaaggtgacgg	11	18	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:38590741T>C	ENST00000222345.6	+	5	2314	c.1805T>C	c.(1804-1806)cTc>cCc	p.L602P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	602					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGGCTGGCCCTCAACACCCCC	0.647																																																0			19											52	47	49					19																	38590741		2203	4300	6503	43282581	SO:0001583	missense	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1805T>C	19.37:g.38590741T>C	ENSP00000222345:p.Leu602Pro		43282581	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380306	0.82682	.	.	ENSG00000105738	ENST00000222345	D	0.94457	-3.43	5.88	5.88	0.94601	.	0.062740	0.64402	D	0.000004	D	0.93220	0.7840	M	0.61703	1.905	0.80722	D	1	B	0.15141	0.012	B	0.17098	0.017	D	0.90301	0.4330	10	0.56958	D	0.05	-40.9922	15.2813	0.73787	0.0:0.0:0.0:1.0	.	602	O60292	SI1L3_HUMAN	P	602	ENSP00000222345:L602P	ENSP00000222345:L602P	L	+	2	0	SIPA1L3	43282581	0.992000	0.36948	1.000000	0.80357	0.988000	0.76386	4.966000	0.63715	2.257000	0.74773	0.459000	0.35465	CTC		0.647	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38590741	T	C	38590741	3	2	109	1	0	0	0	0	1	0	0	0	14368	1551	54	4	1815	4	SIPA1L3	19	38590741	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	1174610	38590741	20538242	278	28844										
IRGQ	126298	hgsc.bcm.edu	37	chr19	44097454	44097454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggccgccggtctcaaaggccTcacgcacagcctctagctct	10	17	4	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:44097454T>C	ENST00000602269.1	-	2	781	c.596A>G	c.(595-597)gAg>gGg	p.E199G	L34079.2_ENST00000594374.1_5'Flank|IRGQ_ENST00000422989.1_Missense_Mutation_p.E199G|IRGQ_ENST00000601520.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	199										endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				CTCAAAGGCCTCACGCACAGC	0.667																																																0			19											37	37	37					19																	44097454		2203	4297	6500	48789294	SO:0001583	missense	126298			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"immunity-related GTPase family, Q1"	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.596A>G	19.37:g.44097454T>C	ENSP00000472250:p.Glu199Gly		48789294	B2RNP3	Missense_Mutation	SNP	ENST00000602269.1	37	CCDS33040.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446635	0.63178	.	.	ENSG00000167378	ENST00000422989	T	0.51071	0.72	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000001	T	0.60301	0.2258	M	0.64997	1.995	0.31376	N	0.679564	D	0.76494	0.999	D	0.68943	0.961	T	0.63545	-0.6613	10	0.33141	T	0.24	-5.9844	9.3454	0.38104	0.0:0.0:0.1803:0.8197	.	199	Q8WZA9	IRGQ_HUMAN	G	199	ENSP00000387535:E199G	ENSP00000387535:E199G	E	-	2	0	IRGQ	48789294	1.000000	0.71417	0.994000	0.49952	0.627000	0.37826	3.612000	0.54142	2.291000	0.77112	0.533000	0.62120	GAG		0.667	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		C	44097454	T	C	44097454	3	2	109	1	0	0	0	0	1	0	0	0	7860	1551	54	4	1279	4	IRGQ	19	44097454	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	5506713	44097454	15031529	279	28845										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55597841	55597841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cccgctgggacaggccccgcTgggacagctgcgatagcctc	14	16	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:55597841T>C	ENST00000201647.6	+	17	1788	c.1732T>C	c.(1732-1734)Tgg>Cgg	p.W578R	EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000245618.5_Missense_Mutation_p.W451R|EPS8L1_ENST00000540810.1_Missense_Mutation_p.W514R|EPS8L1_ENST00000588359.1_Missense_Mutation_p.W264R	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	578					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CAGGCCCCGCTGGGACAGCTG	0.682																																					Ovarian(149;255 1863 3636 27051 29647)											0			19											23	19	21					19																	55597841		2043	4009	6052	60289653	SO:0001583	missense	54869			AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1732T>C	19.37:g.55597841T>C	ENSP00000201647:p.Trp578Arg		60289653	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	T	9.529	1.110275	0.20714	.	.	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.05081	3.75;3.51;3.5	3.97	2.93	0.34026	.	3.431930	0.02776	U	0.120307	T	0.04679	0.0127	N	0.14661	0.345	0.25758	N	0.984976	B;B;B	0.14805	0.011;0.002;0.0	B;B;B	0.12156	0.007;0.006;0.001	T	0.41179	-0.9523	10	0.10377	T	0.69	-6.0143	6.9123	0.24342	0.2187:0.0:0.0:0.7813	.	357;451;578	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	R	578;514;451;264	ENSP00000201647:W578R;ENSP00000437541:W514R;ENSP00000245618:W451R	ENSP00000201647:W578R	W	+	1	0	EPS8L1	60289653	0.264000	0.24093	0.974000	0.42286	0.574000	0.36063	0.373000	0.20484	0.663000	0.31027	0.240000	0.17902	TGG		0.682	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		C	55597841	T	C	55597841	3	2	109	1	0	0	0	0	1	0	0	0	5208	1580	55	4	1846	4	EPS8L1	19	55597841	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	11500387	55597841	3531142	280	28846										
TBC1D20	128637	hgsc.bcm.edu	37	chr20	419927	419927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gtccaggacttcctgctcgcGatacaacacaatctgtgggg	11	12	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:419927G>A	ENST00000354200.4	-	7	928	c.781C>T	c.(781-783)Cgc>Tgc	p.R261C	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	261					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				TCCTGCTCGCGATACAACACA	0.547																																																0			20											119	104	109					20																	419927		2203	4300	6503	367927	SO:0001583	missense	128637			AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.781C>T	20.37:g.419927G>A	ENSP00000346139:p.Arg261Cys		367927	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	37	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760441	0.49468	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.22134	1.97	5.54	4.57	0.56435	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.28566	0.0707	M	0.86420	2.815	0.80722	D	1	P	0.39847	0.691	B	0.34093	0.175	T	0.24154	-1.0168	10	0.48119	T	0.1	-12.238	12.6821	0.56928	0.0:0.0:0.7006:0.2994	.	261	Q96BZ9	TBC20_HUMAN	C	261;286	ENSP00000346139:R261C	ENSP00000246077:R286C	R	-	1	0	TBC1D20	367927	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	4.590000	0.61013	1.526000	0.49068	0.655000	0.94253	CGC		0.547	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		A	419927	G	A	419927	3	1	109	1	0	0	0	0	1	0	0	0	15648	1058	37	1	438	1	TBC1D20	20	419927	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10		419927	62605593	281	28847										
CDS2	8760	hgsc.bcm.edu	37	chr20	5154229	5154229	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cggacagtgagagccgggcaGaatccgcacccctgccagtc	13	15	0	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:5154229G>A	ENST00000460006.1	+	2	425	c.118G>A	c.(118-120)Gaa>Aaa	p.E40K	CDS2_ENST00000379062.4_Intron	NM_003818.3	NP_003809.1	O95674	CDS2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	40					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	phosphatidate cytidylyltransferase activity (GO:0004605)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|stomach(1)	14						GAGCCGGGCAGAATCCGCACC	0.507																																																0			20											159	161	160					20																	5154229		2203	4300	6503	5102229	SO:0001583	missense	8760			AF069532	CCDS13088.1	20p13	2006-03-28			ENSG00000101290	ENSG00000101290	2.7.7.41		1801	protein-coding gene	gene with protein product		603549				9806839, 9889000	Standard	NM_003818		Approved		uc002wls.3	O95674	OTTHUMG00000031801	ENST00000460006.1:c.118G>A	20.37:g.5154229G>A	ENSP00000419879:p.Glu40Lys		5102229	B2RDC6|D3DW04|Q5TDY2|Q5TDY3|Q5TDY4|Q5TDY5|Q9BYK5|Q9NTT2	Missense_Mutation	SNP	ENST00000460006.1	37	CCDS13088.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858355	0.32791	.	.	ENSG00000101290	ENST00000460006	T	0.43294	0.95	5.39	5.39	0.77823	.	0.107189	0.64402	D	0.000006	T	0.32941	0.0846	L	0.38838	1.175	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.16719	-1.0393	10	0.06891	T	0.86	-13.2875	18.0708	0.89405	0.0:0.0:1.0:0.0	.	40	O95674	CDS2_HUMAN	K	40	ENSP00000419879:E40K	ENSP00000419879:E40K	E	+	1	0	CDS2	5102229	1.000000	0.71417	0.095000	0.20976	0.165000	0.22458	8.174000	0.89682	2.676000	0.91093	0.655000	0.94253	GAA		0.507	CDS2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077858.2			A	5154229	G	A	5154229	3	1	109	1	0	0	0	0	1	0	0	0	3184	943	33	3	124	3	CDS2	20	5154229	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	4734302	5154229	57871291	282	28848										
BPIL1	80341	hgsc.bcm.edu	37	chr20	31600614	31600614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	attactaccctgcaggatccGgattctgaatgtccatgtgc	9	11	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:31600614G>A	ENST00000170150.3	+	4	404	c.209G>A	c.(208-210)cGg>cAg	p.R70Q		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	70						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										TGCAGGATCCGGATTCTGAAT	0.522																																																0			20											199	186	191					20																	31600614		2203	4300	6503	31064275	SO:0001583	missense	80341			AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.209G>A	20.37:g.31600614G>A	ENSP00000170150:p.Arg70Gln		31064275	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	1.932	-0.445795	0.04604	.	.	ENSG00000078898	ENST00000170150	T	0.05025	3.51	4.41	1.98	0.26296	.	0.703635	0.12548	N	0.459345	T	0.01835	0.0058	N	0.02247	-0.625	0.22050	N	0.999396	B	0.09022	0.002	B	0.04013	0.001	T	0.46925	-0.9156	10	0.02654	T	1	-6.1992	2.9411	0.05830	0.6653:0.0:0.1202:0.2145	.	70	Q8N4F0	BPIB2_HUMAN	Q	70	ENSP00000170150:R70Q	ENSP00000170150:R70Q	R	+	2	0	BPIFB2	31064275	0.999000	0.42202	0.998000	0.56505	0.537000	0.34900	1.188000	0.32102	0.848000	0.35191	-0.302000	0.09304	CGG		0.522	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		A	31600614	G	A	31600614	3	1	109	1	0	0	0	0	1	0	0	0	1494	1116	39	1	219	1	BPIL1	20	31600614	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	26446385	31600614	31424906	283	28849										
CDK5RAP1	51654	hgsc.bcm.edu	37	chr20	31954784	31954784	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttttacctcttccgggacatCatccttcagcctatgatatg	6	12	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:31954784C>A	ENST00000357886.4	-	13	1618	c.1465G>T	c.(1465-1467)Gat>Tat	p.D489Y	CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.D385Y|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.D475Y|CDK5RAP1_ENST00000544843.1_3'UTR|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.D398Y			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	489	CDK5R1-binding.				brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)	p.D475N(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						TCCGGGACATCATCCTTCAGC	0.418																																																1	Substitution - Missense(1)	skin(1)	20											167	156	160					20																	31954784		2203	4300	6503	31418445	SO:0001583	missense	51654			AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"chromosome 20 open reading frame 34"	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.1465G>T	20.37:g.31954784C>A	ENSP00000350558:p.Asp489Tyr		31418445	A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.78|18.78	3.697846|3.697846	0.68386|0.68386	.|.	.|.	ENSG00000101391|ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000339269;ENST00000452723;ENST00000375351|ENST00000427097	T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0|.	5.17|5.17	4.23|4.23	0.50019|0.50019	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);|.	0.150326|.	0.64402|.	D|.	0.000013|.	D|D	0.85826|0.85826	0.5787|0.5787	H|H	0.96365|0.96365	3.81|3.81	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	0.999;0.998;0.998;1.0;0.999;1.0;0.998|.	D;D;D;D;D;D;D|.	0.76071|.	0.944;0.95;0.95;0.979;0.97;0.987;0.964|.	D|D	0.89190|0.89190	0.3550|0.3550	10|5	0.87932|.	D|.	0|.	-7.0046|-7.0046	11.6915|11.6915	0.51519|0.51519	0.0:0.9144:0.0:0.0856|0.0:0.9144:0.0:0.0856	.|.	398;489;475;215;474;475;385|.	Q96SZ6-4;Q96SZ6;Q675N5;E9PF14;Q53H36;Q96SZ6-3;Q96SZ6-2|.	.;CK5P1_HUMAN;.;.;.;.;.|.	Y|I	475;489;398;385;215|143	ENSP00000217372:D475Y;ENSP00000350558:D489Y;ENSP00000341840:D398Y;ENSP00000408133:D385Y|.	ENSP00000341840:D398Y|.	D|M	-|-	1|3	0|0	CDK5RAP1|CDK5RAP1	31418445|31418445	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.884000|0.884000	0.51177|0.51177	4.180000|4.180000	0.58296|0.58296	1.403000|1.403000	0.46800|0.46800	0.655000|0.655000	0.94253|0.94253	GAT|ATG		0.418	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408		A	31954784	C	A	31954784	3	1	109	1	0	0	0	0	1	0	0	0	3151	826	29	2	352	2	CDK5RAP1	20	31954784	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	354170	31954784	31070736	284	28850										
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33632316	33632316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggagactttaccttgattgAtttcagctgcagaaggcccc	10	10	1	4			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:33632316A>G	ENST00000252015.2	-	7	946	c.857T>C	c.(856-858)aTc>aCc	p.I286T	TRPC4AP_ENST00000451813.2_Missense_Mutation_p.I286T|TRPC4AP_ENST00000432634.2_Missense_Mutation_p.I247T			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	286	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			ACCTTGATTGATTTCAGCTGC	0.378																																																0			20											93	95	94					20																	33632316		2203	4300	6503	33095977	SO:0001583	missense	26133			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.857T>C	20.37:g.33632316A>G	ENSP00000252015:p.Ile286Thr		33095977	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440645	0.43326	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	T;T;T	0.28895	1.59;1.59;1.59	5.74	5.74	0.90152	.	0.191113	0.47852	D	0.000214	T	0.21631	0.0521	N	0.22421	0.69	0.80722	D	1	B;B;B	0.29716	0.118;0.156;0.255	B;B;B	0.19666	0.018;0.026;0.026	T	0.03673	-1.1014	10	0.30078	T	0.28	.	16.043	0.80698	1.0:0.0:0.0:0.0	.	247;286;286	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	T	286;286;247;271	ENSP00000252015:I286T;ENSP00000400614:I286T;ENSP00000400497:I247T	ENSP00000252015:I286T	I	-	2	0	TRPC4AP	33095977	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.035000	0.93752	2.187000	0.69744	0.477000	0.44152	ATC		0.378	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		G	33632316	A	G	33632316	3	3	109	1	0	0	0	0	1	0	0	0	16621	333	12	4	1588	4	TRPC4AP	20	33632316	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1677532	33632316	29393204	285	28851										
NFS1	9054	hgsc.bcm.edu	37	chr20	34286486	34286486	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agcggctgtatctgcgggaaCcgcagactgaggagcacggt	16	10	1	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:34286486C>A	ENST00000374092.4	-	2	194	c.124G>T	c.(124-126)Gtt>Ttt	p.V42F	NFS1_ENST00000540053.1_5'UTR|NFS1_ENST00000306750.3_Missense_Mutation_p.V42F|ROMO1_ENST00000374072.1_5'Flank|NFS1_ENST00000541387.1_Missense_Mutation_p.V42F|ROMO1_ENST00000397416.1_5'Flank|ROMO1_ENST00000374078.1_5'Flank|NFS1_ENST00000397425.1_5'UTR|NFS1_ENST00000374085.1_5'UTR|ROMO1_ENST00000374077.3_5'Flank|ROMO1_ENST00000336695.4_5'Flank	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase	42					cysteine metabolic process (GO:0006534)|iron incorporation into metallo-sulfur cluster (GO:0018283)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|protein complex assembly (GO:0006461)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine desulfurase activity (GO:0031071)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)	TCTGCGGGAACCGCAGACTGA	0.532																																																0			20											40	44	43					20																	34286486		2203	4300	6503	33749900	SO:0001583	missense	9054			AF097025	CCDS13262.1, CCDS56185.1	20q11.22	2013-08-06	2013-08-06		ENSG00000244005	ENSG00000244005	2.8.1.7		15910	protein-coding gene	gene with protein product		603485	"nitrogen fixation 1 (S. cerevisiae, homolog)", "NFS1 nitrogen fixation 1 homolog (S. cerevisiae)"			9885568, 16847322	Standard	NM_021100		Approved	NifS, IscS	uc002xdw.2	Q9Y697	OTTHUMG00000032361	ENST00000374092.4:c.124G>T	20.37:g.34286486C>A	ENSP00000363205:p.Val42Phe		33749900	B3KMA5|B4DXK9|E1P5R8|F5GYK5|Q6P0L8|Q9NTZ5|Q9Y481	Missense_Mutation	SNP	ENST00000374092.4	37	CCDS13262.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.236109	0.39498	.	.	ENSG00000244005	ENST00000374092;ENST00000541387;ENST00000537772;ENST00000306750	T;T;T	0.33216	1.87;1.85;1.42	5.09	1.94	0.25998	.	0.834306	0.11116	N	0.598001	T	0.15046	0.0363	N	0.08118	0	0.09310	N	0.999992	B;B;B	0.21309	0.018;0.046;0.054	B;B;B	0.17722	0.019;0.009;0.015	T	0.20472	-1.0274	10	0.72032	D	0.01	.	5.4787	0.16710	0.0:0.6552:0.1632:0.1816	.	42;42;42	F5GYK5;Q8WV90;Q9Y697	.;.;NFS1_HUMAN	F	42	ENSP00000363205:V42F;ENSP00000440897:V42F;ENSP00000304740:V42F	ENSP00000304740:V42F	V	-	1	0	NFS1	33749900	0.042000	0.20092	0.052000	0.19188	0.005000	0.04900	0.174000	0.16743	0.731000	0.32448	0.563000	0.77884	GTT		0.532	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078936.4	NM_021100		A	34286486	C	A	34286486	3	1	109	1	0	0	0	0	1	0	0	0	10416	507	18	2	1297	2	NFS1	20	34286486	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	654170	34286486	28739034	286	28852										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40730859	40730859	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aggcagcacgtccatacttcGattcttatcatggttccggg	10	11	2	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:40730859G>A	ENST00000373187.1	-	26	3618	c.3619C>T	c.(3619-3621)Cga>Tga	p.R1207*	PTPRT_ENST00000373201.1_Nonsense_Mutation_p.R1197*|PTPRT_ENST00000356100.2_Nonsense_Mutation_p.R1216*|PTPRT_ENST00000373190.1_Nonsense_Mutation_p.R1206*|PTPRT_ENST00000373198.4_Nonsense_Mutation_p.R1226*|PTPRT_ENST00000373184.1_Nonsense_Mutation_p.R1217*|PTPRT_ENST00000373193.3_Nonsense_Mutation_p.R1210*			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1207	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.R1229*(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCCATACTTCGATTCTTATCA	0.552																																																1	Substitution - Nonsense(1)	large_intestine(1)	20											78	82	81					20																	40730859		2146	4269	6415	40164273	SO:0001587	stop_gained	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3619C>T	20.37:g.40730859G>A	ENSP00000362283:p.Arg1207*		40164273	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Nonsense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	45	11.689647	0.99591	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.354	0.94404	0.0:0.0:1.0:0.0	.	.	.	.	X	1206;1207;1210;1216;1229;1217;1197	.	ENSP00000348408:R1216X	R	-	1	2	PTPRT	40164273	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	8.013000	0.88655	2.588000	0.87417	0.650000	0.86243	CGA		0.552	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40730859	G	A	40730859	4	1	109	1	0	0	0	0	0	1	0	0	12849	1066	37	1	730	1	PTPRT	20	40730859	Nonsense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10	6444373	40730859	22294661	287	28853										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46264449	46264450	+	Missense_Mutation	DNP	CT	CT	AC													0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	agcctcacatcagttttctcCtgttgcaggtatttgtgttg							TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C|T	C|T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:46264449_46264450CT>AC	ENST00000371998.3	+	11	1687_1688	c.1496_1497CT>AC	c.(1495-1497)cCT>cAC	p.P499H	NCOA3_ENST00000341724.6_Missense_Mutation_p.P509H|NCOA3_ENST00000372004.3_Missense_Mutation_p.P499H|NCOA3_ENST00000371997.3_Missense_Mutation_p.P509H			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	499					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.P499L(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CAGTTTTCTCCTGTTGCAGGTA	0.361																																																1	Substitution - Missense(1)	lung(1)	20																																								45697856|45697857	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	Exception_encountered	20.37:g.46264449_46264450delinsAC	ENSP00000361066:p.Pro499His		45697856|45697857	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation|Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																				0.361	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		AC	46264450	CT	AC	46264449	3	1	109	1	0	0	0	0	1	0	0	0	10261	681	24	2	1560	2	NCOA3	20	46264449	Missense_Mutation	DNP	CT	TCGA-EF-5830-01A-01D-1657-10	5533590	46264449	16761071	288	28854										
ADRM1	11047	hgsc.bcm.edu	37	chr20	60882692	60882692	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cggtcaccccgtcatccaccAcctcttccacccgtgccacc	5	23	3	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:60882692A>C	ENST00000253003.2	+	7	710	c.664A>C	c.(664-666)Acc>Ccc	p.T222P	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'Flank	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	222	Ser-rich.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GTCATCCACCACCTCTTCCAC	0.697																																																0			20											37	37	37					20																	60882692		2196	4296	6492	60316087	SO:0001583	missense	11047			D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.664A>C	20.37:g.60882692A>C	ENSP00000253003:p.Thr222Pro		60316087	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.883900	0.51908	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	5.25	-2.74	0.05932	.	0.486350	0.24530	N	0.037739	T	0.45337	0.1337	L	0.53249	1.67	0.39955	D	0.974594	B	0.10296	0.003	B	0.15870	0.014	T	0.26189	-1.0110	9	0.72032	D	0.01	-13.293	7.4044	0.26983	0.7243:0.0:0.1684:0.1072	.	222	Q16186	ADRM1_HUMAN	P	201;222	.	ENSP00000253003:T222P	T	+	1	0	ADRM1	60316087	0.441000	0.25626	0.995000	0.50966	0.919000	0.55068	0.090000	0.15025	-0.274000	0.09232	0.459000	0.35465	ACC		0.697	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			C	60882692	A	C	60882692	3	2	109	1	0	0	0	0	1	0	0	0	345	159	6	4	686	4	ADRM1	20	60882692	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	14618243	60882692	2142828	289	28855										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981238	61981238	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggtgttgcgagaggccagggCgccggcagcctggccatctg	18	12	1	1	rs142137599		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:61981238C>T	ENST00000370263.4	-	5	1746	c.1525G>A	c.(1525-1527)Gcc>Acc	p.A509T	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	509					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GAGGCCAGGGCGCCGGCAGCC	0.682																																																0			20						C	THR/ALA	0,4374		0,0,2187	20	21	21		1525	1	0	20	dbSNP_134	21	1,8577		0,1,4288	no	missense	CHRNA4	NM_000744.5	58	0,1,6475	TT,TC,CC		0.0117,0.0,0.0077	benign	509/628	61981238	1,12951	2187	4289	6476	61451682	SO:0001583	missense	1137				CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1525G>A	20.37:g.61981238C>T	ENSP00000359285:p.Ala509Thr		61451682	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	C	8.643	0.896519	0.17686	0.0	1.17E-4	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.77877	-1.13	4.67	1.04	0.20106	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.580257	0.12578	U	0.456707	T	0.52403	0.1732	N	0.11560	0.145	0.28591	N	0.909628	P;B	0.39520	0.676;0.006	B;B	0.35413	0.202;0.002	T	0.45920	-0.9228	10	0.13108	T	0.6	.	7.6129	0.28142	0.4812:0.4414:0.0774:0.0	.	438;509	Q4VAQ5;P43681	.;ACHA4_HUMAN	T	415;509;438	ENSP00000359285:A509T	ENSP00000359280:A415T	A	-	1	0	CHRNA4	61451682	0.555000	0.26530	0.007000	0.13788	0.013000	0.08279	1.127000	0.31357	-0.099000	0.12263	-0.467000	0.05162	GCC		0.682	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			T	61981238	C	T	61981238	3	4	109	1	0	0	0	0	1	0	0	0	3391	768	27	1	366	1	CHRNA4	20	61981238	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1098546	61981238	1044282	290	28856										
KRTAP6-3	337968	hgsc.bcm.edu	37	chr21	31964985	31964985	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cttctgtggctgtggctacaGaggcctggactgtggctatg	15	9	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:31964985G>A	ENST00000391624.1	+	1	227	c.200G>A	c.(199-201)aGa>aAa	p.R67K	KRTAP22-2_ENST00000382830.2_5'Flank	NM_181605.3	NP_853636.3	Q3LI67	KRA63_HUMAN	keratin associated protein 6-3	67						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(7)	10						tgtggctacagaggcctggac	0.607																																																0			21											52	64	60					21																	31964985		2203	4300	6503	30886856	SO:0001583	missense	337968			AP001708		21q22.1	2012-04-19			ENSG00000212938	ENSG00000212938		"Keratin associated proteins"	18933	protein-coding gene	gene with protein product						12359730	Standard	NM_181605		Approved	KAP6.3	uc002yom.3	Q3LI67	OTTHUMG00000057791	ENST00000391624.1:c.200G>A	21.37:g.31964985G>A	ENSP00000375482:p.Arg67Lys		30886856	A4IF26	Missense_Mutation	SNP	ENST00000391624.1	37		.	.	.	.	.	.	.	.	.	.	G	3.589	-0.083957	0.07141	.	.	ENSG00000212938	ENST00000391624	T	0.34072	1.38	3.62	2.74	0.32292	.	.	.	.	.	T	0.27027	0.0662	L	0.39898	1.24	0.09310	N	1	B	0.31290	0.318	B	0.26770	0.073	T	0.21143	-1.0254	9	0.87932	D	0	.	7.3391	0.26627	0.12:0.0:0.88:0.0	.	67	Q3LI67	KRA63_HUMAN	K	67	ENSP00000375482:R67K	ENSP00000375482:R67K	R	+	2	0	KRTAP6-3	30886856	0.002000	0.14202	0.035000	0.18076	0.022000	0.10575	1.139000	0.31504	1.097000	0.41459	0.650000	0.86243	AGA		0.607	KRTAP6-3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128243.2	NM_181605		A	31964985	G	A	31964985	3	1	109	1	0	0	0	0	1	0	0	0	8593	942	33	3	223	3	KRTAP6-3	21	31964985	Missense_Mutation	SNP	G	TCGA-EF-5830-01A-01D-1657-10		31964985	16164910	291	28857										
RUNX1	861	hgsc.bcm.edu	37	chr21	36259150	36259150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gggccagtaccttgaaagcgAtgggcagggtcttgttgcag	16	8	1	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:36259150A>G	ENST00000344691.4	-	1	1837	c.260T>C	c.(259-261)aTc>aCc	p.I87T	RUNX1_ENST00000300305.3_Missense_Mutation_p.I114T|RUNX1_ENST00000325074.5_Missense_Mutation_p.I102T|RUNX1_ENST00000358356.5_Missense_Mutation_p.I87T|RUNX1_ENST00000437180.1_Missense_Mutation_p.I114T|RUNX1_ENST00000399240.1_Missense_Mutation_p.I87T|RUNX1_ENST00000486278.2_Missense_Mutation_p.I90T	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	87	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.V90_K117del(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						CTTGAAAGCGATGGGCAGGGT	0.726			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	21											53	51	51					21																	36259150		2203	4300	6503	35181020	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.260T>C	21.37:g.36259150A>G	ENSP00000340690:p.Ile87Thr		35181020	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892310	0.52121	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278;ENST00000455571	D;D;D;D;D;D;D;D;D	0.99462	-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94	4.45	4.45	0.53987	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98966	0.9648	L	0.29908	0.895	0.80722	D	1	D;B;D;P;D	0.71674	0.987;0.413;0.998;0.807;0.966	D;B;D;P;D	0.87578	0.946;0.272;0.998;0.565;0.925	D	0.99802	1.1036	10	0.87932	D	0	-23.3958	13.8867	0.63712	1.0:0.0:0.0:0.0	.	114;87;114;102;87	Q2TAM6;Q01196-3;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	T	87;114;114;102;87;90;87;102;90;101	ENSP00000340690:I87T;ENSP00000300305:I114T;ENSP00000409227:I114T;ENSP00000319459:I102T;ENSP00000382184:I87T;ENSP00000351123:I87T;ENSP00000382182:I102T;ENSP00000438019:I90T;ENSP00000388189:I101T	ENSP00000300305:I114T	I	-	2	0	RUNX1	35181020	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.587000	0.90810	1.862000	0.54008	0.460000	0.39030	ATC		0.726	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			G	36259150	A	G	36259150	3	3	109	1	0	0	0	0	1	0	0	0	13783	333	12	4	1158	4	RUNX1	21	36259150	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4294165	36259150	11870745	292	28858										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45924704	45924704	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gagaaggtacgcccatcgaaGgagttggccaccaccaggaa	13	11	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:45924704G>T	ENST00000323084.4	-	11	1880	c.1815C>A	c.(1813-1815)tcC>tcA	p.S605S	TSPEAR-AS1_ENST00000451035.1_RNA	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	605					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GCCCATCGAAGGAGTTGGCCA	0.537																																																0			21											88	83	85					21																	45924704		2203	4300	6503	44749132	SO:0001819	synonymous_variant	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1815C>A	21.37:g.45924704G>T			44749132		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																				0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		T	45924704	G	T	45924704	2	4	109	1	0	0	0	0	0	0	0	1	2130	987	35	2		2	C21orf29	21	45924704	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	9665554	45924704	2205191	293	28859										
UBE2G2	7327	hgsc.bcm.edu	37	chr21	46207991	46207991	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ttacctgctacaattccttcCggaggattcagtgttaattc	7	10	1	0	rs546573694		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:46207991C>A	ENST00000345496.2	-	2	333	c.63G>T	c.(61-63)ccG>ccT	p.P21P	UBE2G2_ENST00000330942.5_5'UTR|UBE2G2_ENST00000477954.1_5'UTR	NM_003343.5	NP_003334.2	P60604	UB2G2_HUMAN	ubiquitin-conjugating enzyme E2G 2	21					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K48-linked ubiquitination (GO:0070936)|protein N-linked glycosylation via asparagine (GO:0018279)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|central_nervous_system(1)|lung(1)	5				Colorectal(79;0.0638)		CAATTCCTTCCGGAGGATTCA	0.269																																																0			21											44	47	46					21																	46207991		2201	4300	6501	45032419	SO:0001819	synonymous_variant	7327			BC008351	CCDS13714.1, CCDS33586.1	21q22.3	2011-05-19	2011-05-19		ENSG00000184787	ENSG00000184787		"Ubiquitin-conjugating enzymes E2"	12483	protein-coding gene	gene with protein product		603124	"ubiquitin-conjugating enzyme E2G 2 (homologous to yeast UBC7)", "ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast)"			9693041, 9925943	Standard	NM_003343		Approved	UBC7	uc002zfy.3	P60604	OTTHUMG00000089179	ENST00000345496.2:c.63G>T	21.37:g.46207991C>A			45032419	A6NMQ7|A8K3L4|D3DSL7|P56554	Silent	SNP	ENST00000345496.2	37	CCDS13714.1																																																																																				0.269	UBE2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202647.2	NM_182688		A	46207991	C	A	46207991	2	1	109	1	0	0	0	0	0	0	0	1	16897	639	23	2		2	UBE2G2	21	46207991	Silent	SNP	C	TCGA-EF-5830-01A-01D-1657-10	283287	46207991	1921904	294	28860										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47544566	47544566	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tgttcttgttccttctcaggCggatcctggtccccctggtg	11	13	2	0	rs376303610		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:47544566C>T	ENST00000300527.4	+	22	1777	c.1673C>T	c.(1672-1674)gCg>gTg	p.A558V	COL6A2_ENST00000357838.4_Splice_Site_p.A558V|COL6A2_ENST00000310645.5_Splice_Site_p.A558V|COL6A2_ENST00000409416.1_Splice_Site_p.A558V|COL6A2_ENST00000397763.1_Splice_Site_p.A558V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	558	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)		p.A558V(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CCTTCTCAGGCGGATCCTGGT	0.672																																																1	Substitution - Missense(1)	central_nervous_system(1)	21						C	VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	49	59	55		1673,1673,1673	4.1	1	21		55	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	64,64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	558/1020,558/919,558/829	47544566	1,13005	2203	4300	6503	46368994	SO:0001630	splice_region_variant	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1672-1C>T	21.37:g.47544566C>T			46368994	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662467	0.67700	0.0	1.16E-4	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	D;D;D;D;D;D	0.93906	-3.31;-2.48;-3.31;-3.31;-2.48;-3.27	4.08	4.08	0.47627	.	0.055737	0.64402	D	0.000001	D	0.90573	0.7045	N	0.19112	0.55	0.40611	D	0.981674	D;D;D	0.56035	0.974;0.968;0.968	P;P;P	0.53185	0.72;0.598;0.598	D	0.90399	0.4401	10	0.39692	T	0.17	-9.0304	12.5266	0.56089	0.0:0.6896:0.3104:0.0	.	558;558;558	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	V	558;558;558;558;558;99	ENSP00000300527:A558V;ENSP00000350497:A558V;ENSP00000312529:A558V;ENSP00000387115:A558V;ENSP00000380870:A558V;ENSP00000395751:A99V	ENSP00000300527:A558V	A	+	2	0	COL6A2	46368994	1.000000	0.71417	0.993000	0.49108	0.607000	0.37147	4.099000	0.57755	1.852000	0.53769	0.585000	0.79938	GCG		0.672	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		Missense_Mutation	T	47544566	C	T	47544566	5	4	109	1	0	0	0	0	0	0	1	0	3706	782	27	1	1755	1	COL6A2	21	47544566	Splice_Site	SNP	C	TCGA-EF-5830-01A-01D-1657-10	1336575	47544566	585329	295	28861										
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24175874	24175874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	tggagaagaagatccgcgacCaggacaggaacacgaggtac	14	9	0	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:24175874C>A	ENST00000263121.7	+	8	1298	c.1102C>A	c.(1102-1104)Cag>Aag	p.Q368K	SMARCB1_ENST00000407422.3_Missense_Mutation_p.Q359K|SMARCB1_ENST00000407082.3_Missense_Mutation_p.Q322K|SMARCB1_ENST00000344921.6_Missense_Mutation_p.Q377K|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	368					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.Q368*(2)|p.Q377*(1)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GATCCGCGACCAGGACAGGAA	0.622			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																																yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	6	Substitution - Nonsense(3)|Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)|kidney(2)|haematopoietic_and_lymphoid_tissue(1)	22											122	105	111					22																	24175874		2203	4300	6503	22505874	SO:0001583	missense	6598			U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1102C>A	22.37:g.24175874C>A	ENSP00000263121:p.Gln368Lys		22505874	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	37	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606407	0.87157	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92	4.76	4.76	0.60689	.	0.108664	0.64402	D	0.000004	T	0.81861	0.4912	L	0.45228	1.405	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.997;0.999	T	0.82141	-0.0604	10	0.46703	T	0.11	-31.4772	17.2148	0.86940	0.0:1.0:0.0:0.0	.	377;359;368	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	K	377;368;359;322	ENSP00000340883:Q377K;ENSP00000263121:Q368K;ENSP00000383984:Q359K;ENSP00000385226:Q322K	ENSP00000263121:Q368K	Q	+	1	0	SMARCB1	22505874	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.569000	0.82380	2.387000	0.81309	0.543000	0.68304	CAG		0.622	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		A	24175874	C	A	24175874	3	1	109	1	0	0	0	0	1	0	0	0	14811	595	21	2	1132	2	SMARCB1	22	24175874	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		24175874	27128692	296	28862										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32239741	32239741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ctcccacgaacggctggaggAgtacaagtggaattacttag	12	9	0	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:32239741A>G	ENST00000382112.3	+	28	2787	c.2717A>G	c.(2716-2718)gAg>gGg	p.E906G	DEPDC5_ENST00000382105.2_Missense_Mutation_p.E837G|DEPDC5_ENST00000535622.1_Missense_Mutation_p.E837G|DEPDC5_ENST00000266091.3_Missense_Mutation_p.E915G|DEPDC5_ENST00000400249.2_Missense_Mutation_p.E906G|DEPDC5_ENST00000382111.2_Missense_Mutation_p.E915G|DEPDC5_ENST00000400246.1_Missense_Mutation_p.E915G|DEPDC5_ENST00000400248.2_Missense_Mutation_p.E906G	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	915					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CGGCTGGAGGAGTACAAGTGG	0.512																																																0			22											83	80	81					22																	32239741		1881	4099	5980	30569741	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2717A>G	22.37:g.32239741A>G	ENSP00000371546:p.Glu906Gly		30569741	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599602	0.87055	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T	0.34667	1.38;1.81;1.81;1.79;1.35;1.8;1.79;1.81	5.91	5.91	0.95273	.	0.104113	0.64402	D	0.000004	T	0.38558	0.1045	L	0.40543	1.245	0.80722	D	1	B;P;P;P;P;P	0.45396	0.054;0.856;0.857;0.787;0.536;0.799	B;B;P;B;B;B	0.46275	0.099;0.285;0.51;0.298;0.11;0.156	T	0.11916	-1.0568	10	0.45353	T	0.12	.	15.5312	0.75964	1.0:0.0:0.0:0.0	.	236;915;837;915;906;906	B4DSS1;B9EGN9;B4DH93;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	G	837;915;906;837;915;837;906;915;906	ENSP00000440210:E837G;ENSP00000266091:E915G;ENSP00000383108:E906G;ENSP00000383105:E915G;ENSP00000371539:E837G;ENSP00000371546:E906G;ENSP00000371545:E915G;ENSP00000383107:E906G	ENSP00000266091:E915G	E	+	2	0	DEPDC5	30569741	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.327000	0.90012	2.270000	0.75569	0.528000	0.53228	GAG		0.512	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32239741	A	G	32239741	3	3	109	1	0	0	0	0	1	0	0	0	4453	304	11	4	2845	4	DEPDC5	22	32239741	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	8063867	32239741	19064825	297	28863										
C22orf28	51493	hgsc.bcm.edu	37	chr22	32792108	32792108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gcggttgacccaggcatagtTcccagcagctgccattccct	10	15	0	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:32792108T>C	ENST00000216038.5	-	8	1041	c.943A>G	c.(943-945)Aac>Gac	p.N315D	RTCB_ENST00000476619.1_5'Flank|RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		CAGGCATAGTTCCCAGCAGCT	0.488																																																0			22											233	221	225					22																	32792108		2203	4300	6503	31122108	SO:0001583	missense	51493			BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"focal adhesion-associated protein"	613901	"chromosome 22 open reading frame 28"	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.943A>G	22.37:g.32792108T>C	ENSP00000216038:p.Asn315Asp		31122108		Missense_Mutation	SNP	ENST00000216038.5	37	CCDS13905.1	.	.	.	.	.	.	.	.	.	.	T	33	5.274181	0.95459	.	.	ENSG00000100220	ENST00000216038	T	0.32753	1.44	5.64	5.64	0.86602	.	0.080350	0.85682	D	0.000000	T	0.54046	0.1834	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.56950	-0.7894	10	0.87932	D	0	-10.6085	15.8531	0.78952	0.0:0.0:0.0:1.0	.	315	Q9Y3I0	RTCB_HUMAN	D	315	ENSP00000216038:N315D	ENSP00000216038:N315D	N	-	1	0	C22orf28	31122108	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.995000	0.70631	2.149000	0.67028	0.459000	0.35465	AAC		0.488	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306		C	32792108	T	C	32792108	3	2	109	1	0	0	0	0	1	0	0	0	2146	1783	62	4	594	4	C22orf28	22	32792108	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	552367	32792108	18512458	298	28864										
DDX17	10521	hgsc.bcm.edu	37	chr22	38891910	38891910	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gccacctgctgtacttgctgGgcaagctctctggtaggagc	13	12	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:38891910G>A	ENST00000396821.3	-	6	870	c.771C>T	c.(769-771)gcC>gcT	p.A257A	DDX17_ENST00000432525.1_5'UTR|DDX17_ENST00000381633.3_Silent_p.A178A	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	257	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)	p.A257A(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					GTACTTGCTGGGCAAGCTCTC	0.413																																					Ovarian(55;1085 1454 6392 21425)											1	Substitution - coding silent(1)	skin(1)	22											96	101	99					22																	38891910		2203	4300	6503	37221856	SO:0001819	synonymous_variant	10521			U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.771C>T	22.37:g.38891910G>A			37221856	B1AHM0|Q69YT1|Q6ICD6	Silent	SNP	ENST00000396821.3	37	CCDS46706.1																																																																																				0.413	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		A	38891910	G	A	38891910	2	1	109	1	0	0	0	0	0	0	0	1	4350	1219	43	3		3	DDX17	22	38891910	Silent	SNP	G	TCGA-EF-5830-01A-01D-1657-10	6099802	38891910	12412656	299	28865										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42269974	42269974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	acgatatcgctcctccatcaAtgacaaaatcatcgaattga	5	11	2	2			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:42269974A>G	ENST00000361204.4	+	5	1206	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	347	Interaction with LMNA. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		N -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TCCTCCATCAATGACAAAATC	0.488																																																0			22											93	78	83					22																	42269974		2203	4300	6503	40599920	SO:0001583	missense	6721			U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1040A>G	22.37:g.42269974A>G	ENSP00000354476:p.Asn347Ser		40599920	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	A	32	5.162495	0.94727	.	.	ENSG00000198911	ENST00000361204;ENST00000444813;ENST00000457567	D	0.99369	-5.78	6.17	6.17	0.99709	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	M	0.88181	2.935	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98496	1.0612	10	0.87932	D	0	-25.217	16.8222	0.85835	1.0:0.0:0.0:0.0	.	347	Q12772	SRBP2_HUMAN	S	347	ENSP00000354476:N347S	ENSP00000354476:N347S	N	+	2	0	SREBF2	40599920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.329000	0.96413	2.371000	0.80710	0.533000	0.62120	AAT		0.488	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		G	42269974	A	G	42269974	3	3	109	1	0	0	0	0	1	0	0	0	15181	101	4	4	1058	4	SREBF2	22	42269974	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	3378064	42269974	9034592	300	28866										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46704749	46704749	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cactgctcatgctgcaagtcAggcagcgactcagaggaagc	12	12	3	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:46704749A>G	ENST00000454366.1	+	4	883	c.671A>G	c.(670-672)cAg>cGg	p.Q224R		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	205					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GCTGCAAGTCAGGCAGCGACT	0.642																																					GBM(153;542 1915 12487 29016 50495)											0			22											53	62	59					22																	46704749		2203	4299	6502	45083413	SO:0001583	missense	51512			AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.671A>G	22.37:g.46704749A>G	ENSP00000415430:p.Gln224Arg		45083413	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.782093	0.49891	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07688	3.17	4.88	0.019	0.14119	.	1.133970	0.06283	N	0.697782	T	0.07369	0.0186	L	0.46157	1.445	0.09310	N	1	P	0.46142	0.873	B	0.43225	0.412	T	0.25641	-1.0126	10	0.10377	T	0.69	-1.276	1.857	0.03181	0.412:0.3343:0.0923:0.1614	.	205	Q9NYZ3	GTSE1_HUMAN	R	224;184	ENSP00000415430:Q224R	ENSP00000354634:Q184R	Q	+	2	0	GTSE1	45083413	0.036000	0.19791	0.017000	0.16124	0.026000	0.11368	0.239000	0.18023	-0.034000	0.13713	-0.313000	0.08912	CAG		0.642	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		G	46704749	A	G	46704749	3	3	109	1	0	0	0	0	1	0	0	0	6906	188	7	4	681	4	GTSE1	22	46704749	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	4434775	46704749	4599817	301	28867										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50721555	50721555	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	caggtgggtgccgtggatggTcagtgtggtgccgcccgcct	18	11	1	0			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:50721555T>G	ENST00000449103.1	-	17	2880	c.2740A>C	c.(2740-2742)Acc>Ccc	p.T914P	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.T914P			O15031	PLXB2_HUMAN	plexin B2	914	IPT/TIG 2.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-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)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCGTGGATGGTCAGTGTGGTG	0.687																																																0			22											13	18	17					22																	50721555		1991	4133	6124	49063682	SO:0001583	missense	23654				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2740A>C	22.37:g.50721555T>G	ENSP00000409171:p.Thr914Pro		49063682	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.228434	0.58777	.	.	ENSG00000196576	ENST00000449103;ENST00000359337	D;D	0.84223	-1.82;-1.82	3.96	2.85	0.33270	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.265720	0.26631	N	0.023308	D	0.92348	0.7572	M	0.93763	3.455	0.49213	D	0.999762	D	0.71674	0.998	D	0.69824	0.966	D	0.91770	0.5427	10	0.72032	D	0.01	.	6.5693	0.22529	0.0:0.1326:0.0:0.8674	.	914	O15031	PLXB2_HUMAN	P	914	ENSP00000409171:T914P;ENSP00000352288:T914P	ENSP00000352288:T914P	T	-	1	0	PLXNB2	49063682	1.000000	0.71417	0.994000	0.49952	0.403000	0.30841	3.013000	0.49582	1.654000	0.50703	0.459000	0.35465	ACC		0.687	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		G	50721555	T	G	50721555	3	3	109	1	0	0	0	0	1	0	0	0	12155	1667	58	4	2860	4	PLXNB2	22	50721555	Missense_Mutation	SNP	T	TCGA-EF-5830-01A-01D-1657-10	4016806	50721555	583011	302	28868										
ADM2	79924	hgsc.bcm.edu	37	chr22	50921164	50921164	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	cgccaacactcgggcccccgAagacactcgggcccccgcag	11	20	0	1	rs72438078|rs3840963	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:50921164A>C	ENST00000395738.2	+	2	571	c.279A>C	c.(277-279)cgA>cgC	p.R93R	ADM2_ENST00000362068.2_Missense_Mutation_p.E10A|ADM2_ENST00000395737.1_Silent_p.R93R	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	93					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGGGCCCCCGAAGACACTCGG	0.697																																																1	Deletion - In frame(1)	breast(1)	22																																								49268030	SO:0001819	synonymous_variant	79924			AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"Endogenous ligands"	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.279A>C	22.37:g.50921164A>C			49268030	Q3LFQ0	Silent	SNP	ENST00000395738.2	37	CCDS33682.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058801	0.55325	.	.	ENSG00000128165	ENST00000362068	.	.	.	4.21	-5.89	0.02282	.	.	.	.	.	T	0.08670	0.0215	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35151	-0.9800	5	0.08381	T	0.77	.	0.8616	0.01194	0.2188:0.3176:0.2553:0.2083	.	.	.	.	A	10	.	ENSP00000354955:E10A	E	+	2	0	ADM2	49268030	0.000000	0.05858	0.002000	0.10522	0.479000	0.33129	-1.143000	0.03200	-0.430000	0.07318	0.368000	0.22195	GAA		0.697	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866		C	50921164	A	C	50921164	2	2	109	1	0	0	0	0	0	0	0	1	322	233	9	4		4	ADM2	22	50921164	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	199609	50921164	383402	303	28869										
PHKA2	5256	hgsc.bcm.edu	37	chrX	18954250	18954250	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	gatgagtattccctccagggCctctcggtattcttggacct	10	12	2	1			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:18954250C>A	ENST00000379942.4	-	11	1725	c.1060G>T	c.(1060-1062)Gcc>Tcc	p.A354S		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	354					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CCCTCCAGGGCCTCTCGGTAT	0.542																																																0			X											82	58	67					X																	18954250		2203	4300	6503	18864171	SO:0001583	missense	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1060G>T	X.37:g.18954250C>A	ENSP00000369274:p.Ala354Ser		18864171	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	C	33	5.210827	0.95069	.	.	ENSG00000044446	ENST00000379942	D	0.92965	-3.14	5.41	5.41	0.78517	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.96002	0.8698	M	0.87456	2.885	0.80722	D	1	D	0.55385	0.971	P	0.59357	0.856	D	0.95571	0.8638	10	0.41790	T	0.15	-18.9081	18.5226	0.90959	0.0:1.0:0.0:0.0	.	354	P46019	KPB2_HUMAN	S	354	ENSP00000369274:A354S	ENSP00000369274:A354S	A	-	1	0	PHKA2	18864171	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.731000	0.84895	2.402000	0.81655	0.600000	0.82982	GCC		0.542	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		A	18954250	C	A	18954250	3	1	109	1	0	0	0	0	1	0	0	0	11875	739	26	2	2739	2	PHKA2	23	18954250	Missense_Mutation	SNP	C	TCGA-EF-5830-01A-01D-1657-10		18954250	136316310	304	28870										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20213211	20213211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	aacttgacaataaaaggatgAttaacctctaccaagatatc	5	8	1	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:20213211A>G	ENST00000379565.3	-	5	585	c.378T>C	c.(376-378)aaT>aaC	p.N126N	RPS6KA3_ENST00000540702.1_Silent_p.N98N|RPS6KA3_ENST00000544447.1_Silent_p.N98N|RPS6KA3_ENST00000379548.4_Silent_p.N97N	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	126	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TAAAAGGATGATTAACCTCTA	0.378																																																0			X	GRCh37	CD060659	RPS6KA3	D							182	141	155					X																	20213211		2203	4300	6503	20123132	SO:0001819	synonymous_variant	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.378T>C	X.37:g.20213211A>G			20123132	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Silent	SNP	ENST00000379565.3	37	CCDS14197.1																																																																																				0.378	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		G	20213211	A	G	20213211	2	3	109	1	0	0	0	0	0	0	0	1	13689	330	12	4		4	RPS6KA3	23	20213211	Silent	SNP	A	TCGA-EF-5830-01A-01D-1657-10	1258961	20213211	135057349	305	28871										
CNGA2	1260	hgsc.bcm.edu	37	chrX	150908071	150908071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0328947368421053	10	1	1.21592565597668	1.70229591836735	1.1785125588697	0.0036074841836048	0.0628732957713979	0	ggatcatcagagaatgggccAacaagaatttccgagaggag	13	7	2	3			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:150908071A>G	ENST00000329903.4	+	3	274	c.241A>G	c.(241-243)Aac>Gac	p.N81D		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	81					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					AGAATGGGCCAACAAGAATTT	0.527																																																0			X											112	88	96					X																	150908071		2203	4300	6503	150658727	SO:0001583	missense	1260			S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.241A>G	X.37:g.150908071A>G	ENSP00000328478:p.Asn81Asp		150658727	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480601	0.44044	.	.	ENSG00000183862	ENST00000329903	T	0.41758	0.99	5.25	2.82	0.32997	.	0.225320	0.47455	D	0.000234	T	0.29850	0.0746	L	0.47190	1.495	0.27562	N	0.950163	B	0.14805	0.011	B	0.14023	0.01	T	0.30149	-0.9988	10	0.54805	T	0.06	.	1.8247	0.03118	0.5705:0.1699:0.0928:0.1669	.	81	Q16280	CNGA2_HUMAN	D	81	ENSP00000328478:N81D	ENSP00000328478:N81D	N	+	1	0	CNGA2	150658727	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	5.244000	0.65400	0.251000	0.21505	0.430000	0.28490	AAC		0.527	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		G	150908071	A	G	150908071	3	3	109	1	0	0	0	0	1	0	0	0	3603	130	5	4	251	4	CNGA2	23	150908071	Missense_Mutation	SNP	A	TCGA-EF-5830-01A-01D-1657-10	130694860	150908071	4362489	306	28872										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7724489	7724489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccagcaaacccctccccgtcGagcagaacacccacagcagc	7	20	0	1	rs200762060		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:7724489G>A	ENST00000303635.7	+	9	2089	c.1882G>A	c.(1882-1884)Gag>Aag	p.E628K	CAMTA1_ENST00000439411.2_Missense_Mutation_p.E628K	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	628					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CCTCCCCGTCGAGCAGAACAC	0.647			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0			1						G	LYS/GLU	0,4406		0,0,2203	105	122	116		1882	5.1	0.6	1		116	2,8596	2.2+/-6.3	0,2,4297	no	missense	CAMTA1	NM_015215.2	56	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	628/1674	7724489	2,13002	2203	4299	6502	7647076	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.1882G>A	1.37:g.7724489G>A	ENSP00000306522:p.Glu628Lys		7647076	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	g	11.68	1.710735	0.30322	0.0	2.33E-4	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.20332	2.08;2.08	5.12	5.12	0.69794	.	0.407506	0.27371	N	0.019669	T	0.18087	0.0434	L	0.36672	1.1	0.41711	D	0.989457	B	0.33073	0.396	B	0.25614	0.062	T	0.03761	-1.1006	10	0.30078	T	0.28	-23.5781	18.5592	0.91094	0.0:0.0:1.0:0.0	.	628	Q9Y6Y1	CMTA1_HUMAN	K	628	ENSP00000306522:E628K;ENSP00000402561:E628K	ENSP00000306522:E628K	E	+	1	0	CAMTA1	7647076	1.000000	0.71417	0.560000	0.28344	0.434000	0.31775	7.660000	0.83776	2.408000	0.81797	0.498000	0.49722	GAG		0.647	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		A	7724489	G	A	7724489	3	1	110	1	0	0	0	0	1	0	0	0	2619	1059	37	1	1916	1	CAMTA1	1	7724489	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10		7724489	241526132	1	28873										
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9100202	9100202	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagaagggcagcagaaggagCtgcagcgccgcggggacccc	17	12	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:9100202C>T	ENST00000377424.4	-	6	797	c.618G>A	c.(616-618)caG>caA	p.Q206Q	SLC2A5_ENST00000536305.1_Silent_p.Q147Q|SLC2A5_ENST00000535586.1_Silent_p.Q91Q|SLC2A5_ENST00000377414.3_3'UTR	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	206					carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)			endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGAAGGAGCTGCAGCGCCG	0.687																																																0			1											23	27	26					1																	9100202		2186	4282	6468	9022789	SO:0001819	synonymous_variant	6518			BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.618G>A	1.37:g.9100202C>T			9022789	Q14770|Q5T977|Q8IVB3	Silent	SNP	ENST00000377424.4	37	CCDS99.1																																																																																				0.687	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		T	9100202	C	T	9100202	2	4	110	1	0	0	0	0	0	0	0	1	14585	796	28	3		3	SLC2A5	1	9100202	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1375713	9100202	240150419	2	28874										
TAF12	6883	hgsc.bcm.edu	37	chr1	28931967	28931967	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgggatccacatgttccactGgcgctctgcaaggaagaagc	12	11	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:28931967G>A	ENST00000263974.4	-	5	801	c.367C>T	c.(367-369)Cag>Tag	p.Q123*	TAF12_ENST00000373824.4_Nonsense_Mutation_p.Q123*|TAF12_ENST00000471683.1_5'UTR	NM_001135218.1	NP_001128690.1	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa	123					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			ovary(1)|upper_aerodigestive_tract(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		ATGTTCCACTGGCGCTCTGCA	0.512																																																0			1											99	98	99					1																	28931967		2203	4300	6503	28804554	SO:0001587	stop_gained	6883			BC011986	CCDS326.1	1p35	2008-02-05	2002-08-29	2001-12-07	ENSG00000120656	ENSG00000120656			11545	protein-coding gene	gene with protein product		600773	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD"	TAF2J		7729427	Standard	NM_005644		Approved	TAFII20	uc001bqy.3	Q16514	OTTHUMG00000003655	ENST00000263974.4:c.367C>T	1.37:g.28931967G>A	ENSP00000263974:p.Gln123*		28804554	D3DPM5|Q15775|Q5T077	Nonsense_Mutation	SNP	ENST00000263974.4	37	CCDS326.1	.	.	.	.	.	.	.	.	.	.	G	37	6.204716	0.97376	.	.	ENSG00000120656	ENST00000373824;ENST00000263974	.	.	.	5.65	5.65	0.86999	.	0.053759	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-4.3712	18.4761	0.90793	0.0:0.0:1.0:0.0	.	.	.	.	X	123	.	ENSP00000263974:Q123X	Q	-	1	0	TAF12	28804554	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.303000	0.96183	2.666000	0.90696	0.585000	0.79938	CAG		0.512	TAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010367.1	NM_005644		A	28931967	G	A	28931967	4	1	110	1	0	0	0	0	0	1	0	0	15555	1357	47	3	126	3	TAF12	1	28931967	Nonsense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	19831765	28931967	220318654	3	28875										
INADL	10207	hgsc.bcm.edu	37	chr1	62330030	62330030	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gcaaggaggcctgggagatgCatgaatttctgactcctaga	13	8	1	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:62330030C>G	ENST00000371158.2	+	20	2674	c.2560C>G	c.(2560-2562)Cat>Gat	p.H854D	INADL_ENST00000316485.6_Missense_Mutation_p.H854D	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	854					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CTGGGAGATGCATGAATTTCT	0.388																																																0			1											100	97	98					1																	62330030		2203	4300	6503	62102618	SO:0001583	missense	10207			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2560C>G	1.37:g.62330030C>G	ENSP00000360200:p.His854Asp		62102618	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	13.38	2.218800	0.39201	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.12879	2.78;2.64	5.31	4.41	0.53225	.	0.493769	0.18541	N	0.138191	T	0.14227	0.0344	L	0.60455	1.87	0.80722	D	1	P;B;P	0.36465	0.554;0.09;0.554	B;B;B	0.29785	0.107;0.024;0.107	T	0.02721	-1.1119	10	0.49607	T	0.09	.	11.9298	0.52839	0.0:0.8554:0.0:0.1446	.	854;854;854	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	D	854	ENSP00000360200:H854D;ENSP00000326199:H854D	ENSP00000255202:H854D	H	+	1	0	INADL	62102618	0.964000	0.33143	0.982000	0.44146	0.980000	0.70556	1.356000	0.34079	1.249000	0.43950	0.555000	0.69702	CAT		0.388	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62330030	C	G	62330030	3	3	110	1	0	0	0	0	1	0	0	0	7752	710	25	5	2634	5	INADL	1	62330030	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	33398063	62330030	186920591	4	28876										
CCBL2	56267	hgsc.bcm.edu	37	chr1	89414923	89414923	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aacattctgggtcatccatgCgcttgatgtcaatccagaaa	8	10	3	2	rs377683877		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:89414923C>T	ENST00000260508.4	-	11	1329	c.992G>A	c.(991-993)cGc>cAc	p.R331H	CCBL2_ENST00000446900.2_5'UTR|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Missense_Mutation_p.R297H	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	331					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		GTCATCCATGCGCTTGATGTC	0.363																																																0			1						C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	72	67	69		992,890	4.4	1	1		69	0,8600		0,0,4300	no	missense,missense	CCBL2	NM_001008661.2,NM_001008662.2	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	331/455,297/421	89414923	1,13005	2203	4300	6503	89187511	SO:0001583	missense	56267			AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.992G>A	1.37:g.89414923C>T	ENSP00000260508:p.Arg331His		89187511	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	37	CCDS30766.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.250968	0.22880	2.27E-4	0.0	ENSG00000137944	ENST00000370491;ENST00000260508	D;D	0.90844	-2.74;-2.74	5.34	4.42	0.53409	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.170503	0.51477	D	0.000092	T	0.69913	0.3164	N	0.16903	0.455	0.80722	D	1	P	0.36162	0.54	B	0.27262	0.078	T	0.73544	-0.3949	10	0.14656	T	0.56	-43.8821	14.2692	0.66140	0.0:0.9268:0.0:0.0732	.	331	Q6YP21	KAT3_HUMAN	H	297;331	ENSP00000359522:R297H;ENSP00000260508:R331H	ENSP00000260508:R331H	R	-	2	0	CCBL2	89187511	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.523000	0.45580	2.515000	0.84797	0.467000	0.42956	CGC		0.363	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		T	89414923	C	T	89414923	3	4	110	1	0	0	0	0	1	0	0	0	2739	768	27	1	388	1	CCBL2	1	89414923	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	27084893	89414923	159835698	5	28877										
NTNG1	22854	hgsc.bcm.edu	37	chr1	107867468	107867468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taaggctgttaagaccagccGttggggaaatatttgtagat	12	5	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:107867468G>A	ENST00000370068.1	+	3	1657	c.811G>A	c.(811-813)Gtt>Att	p.V271I	NTNG1_ENST00000370065.1_Missense_Mutation_p.V271I|NTNG1_ENST00000370074.4_Missense_Mutation_p.V271I|NTNG1_ENST00000370067.1_Missense_Mutation_p.V271I|NTNG1_ENST00000542803.1_Missense_Mutation_p.V271I|NTNG1_ENST00000370061.3_Missense_Mutation_p.V271I|NTNG1_ENST00000370070.2_Missense_Mutation_p.V271I|NTNG1_ENST00000370066.1_Missense_Mutation_p.V271I|NTNG1_ENST00000477948.1_3'UTR|NTNG1_ENST00000370072.3_Missense_Mutation_p.V271I|NTNG1_ENST00000370073.2_Missense_Mutation_p.V271I|NTNG1_ENST00000370071.2_Missense_Mutation_p.V271I			Q9Y2I2	NTNG1_HUMAN	netrin G1	271	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)		p.V271I(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		AAGACCAGCCGTTGGGGAAAT	0.458																																																2	Substitution - Missense(2)	large_intestine(2)	1											54	56	56					1																	107867468		2203	4299	6502	107668991	SO:0001583	missense	84628			AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.811G>A	1.37:g.107867468G>A	ENSP00000359085:p.Val271Ile		107668991	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	37	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.630818	0.28978	.	.	ENSG00000162631	ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370064;ENST00000370062;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065	T;T;T;T;T;T;T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91	5.94	3.92	0.45320	Laminin, N-terminal (3);	0.336633	0.24492	N	0.038046	T	0.29850	0.0746	N	0.04508	-0.205	0.33178	D	0.549223	B;B;B;B;B	0.25772	0.001;0.134;0.007;0.021;0.076	B;B;B;B;B	0.28709	0.007;0.093;0.019;0.024;0.046	T	0.05435	-1.0885	10	0.40728	T	0.16	.	4.7071	0.12855	0.6449:0.0:0.3551:0.0	.	271;271;271;271;271	B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1	.;NTNG1_HUMAN;.;.;.	I	271;271;271;271;271;271;271;271;32;32;271;271;271;271;271;271	ENSP00000359090:V271I;ENSP00000359088:V271I;ENSP00000440561:V271I;ENSP00000359078:V271I;ENSP00000359089:V271I;ENSP00000359087:V271I;ENSP00000359091:V271I;ENSP00000359085:V271I;ENSP00000359084:V271I;ENSP00000359083:V271I;ENSP00000359082:V271I	ENSP00000294649:V271I	V	+	1	0	NTNG1	107668991	1.000000	0.71417	0.787000	0.31911	0.994000	0.84299	7.637000	0.83313	0.752000	0.32923	0.655000	0.94253	GTT		0.458	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		A	107867468	G	A	107867468	3	1	110	1	0	0	0	0	1	0	0	0	10735	1145	40	1	817	1	NTNG1	1	107867468	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	18452545	107867468	141383153	6	28878										
GPSM2	29899	hgsc.bcm.edu	37	chr1	109444503	109444503	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atacatatactttacttcaaGactatgaaaaggccattgat	5	7	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:109444503G>T	ENST00000406462.2	+	9	1662	c.889G>T	c.(889-891)Gac>Tac	p.D297Y	GPSM2_ENST00000264126.3_Missense_Mutation_p.D297Y|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	297					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		TTTACTTCAAGACTATGAAAA	0.378																																																0			1											87	83	84					1																	109444503		2203	4300	6503	109246026	SO:0001583	missense	29899			AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.889G>T	1.37:g.109444503G>T	ENSP00000385510:p.Asp297Tyr		109246026	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447744	0.84101	.	.	ENSG00000121957	ENST00000406462;ENST00000264126	D;D	0.95137	-3.62;-3.62	5.9	5.9	0.94986	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.97284	0.9112	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.97232	0.9885	10	0.87932	D	0	-22.2125	20.2723	0.98479	0.0:0.0:1.0:0.0	.	297	P81274	GPSM2_HUMAN	Y	297	ENSP00000385510:D297Y;ENSP00000264126:D297Y	ENSP00000264126:D297Y	D	+	1	0	GPSM2	109246026	1.000000	0.71417	0.998000	0.56505	0.590000	0.36582	9.869000	0.99810	2.793000	0.96121	0.563000	0.77884	GAC		0.378	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		T	109444503	G	T	109444503	3	4	110	1	0	0	0	0	1	0	0	0	6756	942	33	2	915	2	GPSM2	1	109444503	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1577035	109444503	139806118	7	28879										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060544	111060544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgctggggcagaccacgaacCggagcaccagctcgaaggtg	15	12	0	1	rs571676088		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:111060544C>T	ENST00000369771.2	-	1	1253	c.866G>A	c.(865-867)cGg>cAg	p.R289Q		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	289					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	GACCACGAACCGGAGCACCAG	0.502													C|||	1	0.000199681	0	0.0014	5008	,	,		22390	0		0	False		,,,				2504	0															0			1											144	122	130					1																	111060544		2203	4300	6503	110862067	SO:0001583	missense	3744			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.866G>A	1.37:g.111060544C>T	ENSP00000358786:p.Arg289Gln		110862067		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.537519	0.85917	.	.	ENSG00000143105	ENST00000369771	D	0.98567	-5.0	5.8	5.8	0.92144	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	H	0.99911	4.935	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	D	0.97403	0.9997	10	0.87932	D	0	.	18.6105	0.91283	0.0:1.0:0.0:0.0	.	289	Q16322	KCA10_HUMAN	Q	289	ENSP00000358786:R289Q	ENSP00000358786:R289Q	R	-	2	0	KCNA10	110862067	0.997000	0.39634	0.983000	0.44433	0.813000	0.45954	7.818000	0.86416	2.749000	0.94314	0.655000	0.94253	CGG		0.502	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060544	C	T	111060544	3	4	110	1	0	0	0	0	1	0	0	0	8023	652	23	1	673	1	KCNA10	1	111060544	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1616041	111060544	138190077	8	28880										
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957638	111957638	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acagattgatgacccacaggGgtcagggccttctctccagg	12	12	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:111957638G>T	ENST00000369732.3	-	11	1540	c.1485C>A	c.(1483-1485)acC>acA	p.T495T		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	495					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		GACCCACAGGGGTCAGGGCCT	0.557																																																0			1											91	79	83					1																	111957638		2203	4300	6503	111759161	SO:0001819	synonymous_variant	5016			U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1485C>A	1.37:g.111957638G>T			111759161	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	37	CCDS834.1																																																																																				0.557	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		T	111957638	G	T	111957638	2	4	110	1	0	0	0	0	0	0	0	1	11356	1219	43	2		2	OVGP1	1	111957638	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	897094	111957638	137292983	9	28881										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120437576	120437576	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctctgcaaggtcacattcatTtccttcctgcctacacacgt	5	15	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:120437576T>A	ENST00000369400.1	-	1	1542	c.1384A>T	c.(1384-1386)Aat>Tat	p.N462Y		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	462	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N462D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		TCACATTCATTTCCTTCCTGC	0.468																																																1	Substitution - Missense(1)	ovary(1)	1											148	131	137					1																	120437576		2203	4300	6503	120239099	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.1384A>T	1.37:g.120437576T>A	ENSP00000358407:p.Asn462Tyr		120239099	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.621640	0.66787	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.12774	2.65	4.97	4.97	0.65823	Blood coagulation inhibitor, Disintegrin (5);	0.270220	0.26007	N	0.026920	T	0.27629	0.0679	M	0.85945	2.785	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.15983	-1.0418	10	0.87932	D	0	.	11.0032	0.47618	0.0:0.0:0.0:1.0	.	462	Q9UKF2	ADA30_HUMAN	Y	462	ENSP00000358407:N462Y	ENSP00000358407:N462Y	N	-	1	0	ADAM30	120239099	0.009000	0.17119	0.073000	0.20177	0.397000	0.30659	2.086000	0.41643	2.090000	0.63153	0.460000	0.39030	AAT		0.468	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		A	120437576	T	A	120437576	3	1	110	1	0	0	0	0	1	0	0	0	248	1841	64	5	992	5	ADAM30	1	120437576	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	8479938	120437576	128813045	10	28882										
FLG	2312	hgsc.bcm.edu	37	chr1	152277472	152277472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atccgtgtctctctcctggaCttgatcttgcctgttcatgg	9	12	4	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:152277472C>A	ENST00000368799.1	-	3	9925	c.9890G>T	c.(9889-9891)aGt>aTt	p.S3297I	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3297	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCCTGGACTTGATCTTGC	0.577									Ichthyosis																																							0			1											394	385	388					1																	152277472		2203	4300	6503	150544096	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9890G>T	1.37:g.152277472C>A	ENSP00000357789:p.Ser3297Ile		150544096	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	9.439	1.087605	0.20390	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.09255	3.0	3.05	-0.392	0.12442	.	.	.	.	.	T	0.09158	0.0226	L	0.47716	1.5	0.09310	N	1	D	0.76494	0.999	D	0.91635	0.999	T	0.14227	-1.0480	9	0.41790	T	0.15	.	5.0151	0.14331	0.0:0.4455:0.4215:0.1329	.	3297	P20930	FILA_HUMAN	I	3297;235	ENSP00000357789:S3297I	ENSP00000357786:S235I	S	-	2	0	FLG	150544096	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.341000	0.07811	-0.190000	0.10465	0.298000	0.19748	AGT		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152277472	C	A	152277472	3	1	110	1	0	0	0	0	1	0	0	0	5941	565	20	2	2299	2	FLG	1	152277472	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	31839896	152277472	96973149	11	28883										
SPRR2E	6704	hgsc.bcm.edu	37	chr1	153066109	153066109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtgggcagggctgtggacacTttggtggtgggcagggctca	20	7	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:153066109T>C	ENST00000368751.1	-	2	193	c.119A>G	c.(118-120)aAg>aGg	p.K40R	SPRR2B_ENST00000368752.4_Intron|SPRR2E_ENST00000368750.3_Missense_Mutation_p.K40R			P22531	SPR2E_HUMAN	small proline-rich protein 2E	40	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGTGGACACTTTGGTGGTGG	0.622																																																0			1											151	148	149					1																	153066109		2203	4298	6501	151332733	SO:0001583	missense	6704			AF333955	CCDS30866.1	1q21-q22	2008-02-05			ENSG00000203785	ENSG00000203785			11265	protein-coding gene	gene with protein product						8325635	Standard	NM_001024209		Approved		uc001fbh.3	P22531	OTTHUMG00000014397	ENST00000368751.1:c.119A>G	1.37:g.153066109T>C	ENSP00000357740:p.Lys40Arg		151332733	Q5T9T4|Q96RM2	Missense_Mutation	SNP	ENST00000368751.1	37	CCDS30866.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483727	0.26598	.	.	ENSG00000203785	ENST00000368751;ENST00000368750	T;T	0.32753	1.44;1.44	4.3	1.89	0.25635	.	0.942785	0.08679	N	0.909641	T	0.05181	0.0138	.	.	.	0.09310	N	1	P	0.36909	0.573	B	0.33521	0.165	T	0.35599	-0.9782	9	0.21014	T	0.42	.	3.6516	0.08205	0.191:0.1085:0.0:0.7004	.	40	P22531	SPR2E_HUMAN	R	40	ENSP00000357740:K40R;ENSP00000357739:K40R	ENSP00000357739:K40R	K	-	2	0	SPRR2E	151332733	0.166000	0.22962	0.005000	0.12908	0.446000	0.32137	0.850000	0.27737	0.088000	0.17205	0.333000	0.21579	AAG		0.622	SPRR2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040054.1			C	153066109	T	C	153066109	3	2	110	1	0	0	0	0	1	0	0	0	15139	1609	56	4	103	4	SPRR2E	1	153066109	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	788637	153066109	96184512	12	28884										
ADAR	103	hgsc.bcm.edu	37	chr1	154574369	154574369	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgtgctggttccaagcctgaGctgagactgcaataaaaggc	12	9	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:154574369G>T	ENST00000368474.4	-	2	948	c.749C>A	c.(748-750)gCt>gAt	p.A250D	ADAR_ENST00000471068.1_5'Flank|ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000292205.5_Missense_Mutation_p.A293D	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	250					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A250V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CCAAGCCTGAGCTGAGACTGC	0.517																																																1	Substitution - Missense(1)	ovary(1)	1											121	124	123					1																	154574369		2203	4300	6503	152840993	SO:0001583	missense	103			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.749C>A	1.37:g.154574369G>T	ENSP00000357459:p.Ala250Asp		152840993	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.668073	0.47677	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.12465	2.68;2.7;2.73	2.09	-4.17	0.03857	.	1.204520	0.07030	U	0.828319	T	0.02047	0.0064	N	0.22421	0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45160	-0.9280	10	0.46703	T	0.11	.	2.574	0.04801	0.5054:0.0:0.2903:0.2043	.	250;250;250	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	D	293;250;245	ENSP00000292205:A293D;ENSP00000357459:A250D;ENSP00000431794:A245D	ENSP00000292205:A293D	A	-	2	0	ADAR	152840993	0.659000	0.27411	0.140000	0.22221	0.142000	0.21351	1.720000	0.38022	-1.131000	0.02910	-0.339000	0.08088	GCT		0.517	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		T	154574369	G	T	154574369	3	4	110	1	0	0	0	0	1	0	0	0	281	971	34	2	2987	2	ADAR	1	154574369	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1508260	154574369	94676252	13	28885										
UBQLN4	56893	hgsc.bcm.edu	37	chr1	156018300	156018300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccttgatcccacctgttcccGggcagcactgaacatgggct	10	15	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:156018300G>A	ENST00000368309.3	-	5	984	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	UBQLN4_ENST00000472638.1_5'UTR	NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4	298				R -> Q (in Ref. 1; AAF80171). {ECO:0000305}.	regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|polyubiquitin binding (GO:0031593)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)	16	Hepatocellular(266;0.133)|all_neural(408;0.195)					ACCTGTTCCCGGGCAGCACTG	0.622																																																0			1											43	41	42					1																	156018300		2203	4300	6503	154284924	SO:0001583	missense	56893			BC018403	CCDS1127.1	1q21	2013-02-12	2004-11-05	2004-11-06	ENSG00000160803	ENSG00000160803		"Ubiquilin family"	1237	protein-coding gene	gene with protein product	"ataxin-1 ubiquitin-like interacting protein"	605440	"chromosome 1 open reading frame 6"	C1orf6		10575211, 11001934	Standard	NM_020131		Approved	A1U, UBIN	uc001fna.3	Q9NRR5	OTTHUMG00000017461	ENST00000368309.3:c.892C>T	1.37:g.156018300G>A	ENSP00000357292:p.Arg298Trp		154284924	A6ND44|B2RAY7|Q5VYA0|Q5VYA1|Q9BR98|Q9UHX4	Missense_Mutation	SNP	ENST00000368309.3	37	CCDS1127.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.662911	0.67700	.	.	ENSG00000160803	ENST00000368309	T	0.80909	-1.43	4.35	2.39	0.29439	.	0.000000	0.85682	D	0.000000	D	0.82609	0.5074	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.96;0.973	D	0.83610	0.0133	10	0.72032	D	0.01	-10.9081	11.1779	0.48610	0.0:0.0:0.3841:0.6158	.	278;298	B4DZF6;Q9NRR5	.;UBQL4_HUMAN	W	298	ENSP00000357292:R298W	ENSP00000357292:R298W	R	-	1	2	UBQLN4	154284924	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.328000	0.43867	0.428000	0.26173	0.561000	0.74099	CGG		0.622	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046193.1	NM_020131		A	156018300	G	A	156018300	3	1	110	1	0	0	0	0	1	0	0	0	16939	1115	39	1	941	1	UBQLN4	1	156018300	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1443931	156018300	93232321	14	28886										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158648254	158648254	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtctctggagagccaaaccaCgaaggcgctcccaggcagca	12	14	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:158648254C>T	ENST00000368147.4	-	6	929	c.749G>A	c.(748-750)cGt>cAt	p.R250H		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	250					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R250H(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCCAAACCACGAAGGCGCTC	0.438																																																1	Substitution - Missense(1)	prostate(1)	1											101	94	96					1																	158648254		1873	4116	5989	156914878	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.749G>A	1.37:g.158648254C>T	ENSP00000357129:p.Arg250His		156914878	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	9.621	1.133833	0.21123	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52526	0.66;0.66	4.66	0.629	0.17687	.	1.398420	0.05344	N	0.530647	T	0.08582	0.0213	N	0.05383	-0.06	0.24646	N	0.993547	B	0.02656	0.0	B	0.04013	0.001	T	0.18398	-1.0338	10	0.25106	T	0.35	.	3.4954	0.07653	0.1633:0.2271:0.0:0.6095	.	250	P02549	SPTA1_HUMAN	H	250	ENSP00000357130:R250H;ENSP00000357129:R250H	ENSP00000357129:R250H	R	-	2	0	SPTA1	156914878	0.986000	0.35501	0.003000	0.11579	0.299000	0.27559	2.102000	0.41796	0.048000	0.15891	-0.300000	0.09419	CGT		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158648254	C	T	158648254	3	4	110	1	0	0	0	0	1	0	0	0	15155	536	19	1	6698	1	SPTA1	1	158648254	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2629954	158648254	90602367	15	28887										
F5	2153	hgsc.bcm.edu	37	chr1	169483638	169483638	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acacggataaacctggaaatGattggggggttgaaaaagtt	13	4	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:169483638G>T	ENST00000367797.3	-	25	6789	c.6588C>A	c.(6586-6588)atC>atA	p.I2196I	F5_ENST00000367796.3_Silent_p.I2201I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	2196	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	ACCTGGAAATGATTGGGGGGT	0.343																																																0			1											76	80	79					1																	169483638		2203	4300	6503	167750262	SO:0001819	synonymous_variant	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.6588C>A	1.37:g.169483638G>T			167750262	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																				0.343	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		T	169483638	G	T	169483638	2	4	110	1	0	0	0	0	0	0	0	1	5361	1280	45	2		2	F5	1	169483638	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	10835384	169483638	79766983	16	28888										
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185267298	185267298	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gttccctacagttgcaatccCagcattgctccttggtgaag	9	12	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:185267298C>T	ENST00000367498.3	-	15	2420	c.1798G>A	c.(1798-1800)Ggg>Agg	p.G600R	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.G382R	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	600					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						GTTGCAATCCCAGCATTGCTC	0.413																																																0			1											304	267	280					1																	185267298		2203	4300	6503	183533921	SO:0001583	missense	10625			AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1798G>A	1.37:g.185267298C>T	ENSP00000356468:p.Gly600Arg		183533921	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373565	0.82573	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	D;D	0.82711	-1.64;-1.64	5.38	5.38	0.77491	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.92341	0.7570	M	0.85710	2.77	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.965;1.0	D	0.92967	0.6394	10	0.72032	D	0.01	.	19.5013	0.95095	0.0:1.0:0.0:0.0	.	382;600	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	R	600;382	ENSP00000356468:G600R;ENSP00000375864:G382R	ENSP00000356468:G600R	G	-	1	0	IVNS1ABP	183533921	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.637000	0.83313	2.677000	0.91161	0.563000	0.77884	GGG		0.413	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		T	185267298	C	T	185267298	3	4	110	1	0	0	0	0	1	0	0	0	7951	594	21	3	134	3	IVNS1ABP	1	185267298	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	15783660	185267298	63983323	17	28889										
CDC73	79577	hgsc.bcm.edu	37	chr1	193094274	193094274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggccaacccagagagtactAcacattggattccattttat	7	10	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:193094274A>G	ENST00000367435.3	+	2	348	c.164A>G	c.(163-165)tAc>tGc	p.Y55C		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	55					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						AGAGAGTACTACACATTGGAT	0.358																																																0			1											146	146	146					1																	193094274		2203	4300	6503	191360897	SO:0001583	missense	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.164A>G	1.37:g.193094274A>G	ENSP00000356405:p.Tyr55Cys		191360897	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.609513	0.87258	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.93953	-3.32	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.97081	0.9046	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97749	1.0213	10	0.87932	D	0	-8.2692	16.3009	0.82811	1.0:0.0:0.0:0.0	.	55	Q6P1J9	CDC73_HUMAN	C	55	ENSP00000356405:Y55C	ENSP00000356405:Y55C	Y	+	2	0	CDC73	191360897	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.086000	0.94088	2.246000	0.74042	0.533000	0.62120	TAC		0.358	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		G	193094274	A	G	193094274	3	3	110	1	0	0	0	0	1	0	0	0	3091	391	14	4	170	4	CDC73	1	193094274	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	7826976	193094274	56156347	18	28890										
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203024713	203024713	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gccctgtccctggccagcgcGtccccaccactcagcggccg	11	21	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:203024713G>A	ENST00000447715.2	+	21	2358	c.1917G>A	c.(1915-1917)gcG>gcA	p.A639A	PPFIA4_ENST00000272198.6_Silent_p.A155A|PPFIA4_ENST00000599966.1_Silent_p.A155A|PPFIA4_ENST00000414050.2_Silent_p.A368A|PPFIA4_ENST00000367240.2_Silent_p.A640A|PPFIA4_ENST00000295706.4_Silent_p.A155A			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	639					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						TGGCCAGCGCGTCCCCACCAC	0.652																																																0			1											47	57	54					1																	203024713		2157	4252	6409	201291336	SO:0001819	synonymous_variant	8497			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.1917G>A	1.37:g.203024713G>A			201291336	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																					0.652	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203024713	G	A	203024713	2	1	110	1	0	0	0	0	0	0	0	1	12343	1132	40	1		1	PPFIA4	1	203024713	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	9930439	203024713	46225908	19	28891										
USH2A	7399	hgsc.bcm.edu	37	chr1	216256830	216256830	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggtccatctttgttataaaCgaaaagaagcaatccattta	6	7	1	1	rs143208990		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:216256830C>A	ENST00000307340.3	-	26	5652	c.5266G>T	c.(5266-5268)Gtt>Ttt	p.V1756F	RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.V1756F|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1756	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.V1756I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTGTTATAAACGAAAAGAAGC	0.303										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	ovary(1)	1											96	100	99					1																	216256830		2202	4299	6501	214323453	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5266G>T	1.37:g.216256830C>A	ENSP00000305941:p.Val1756Phe		214323453	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.093858	0.56075	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.78595	-1.19;-1.19	4.38	-1.89	0.07689	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.783880	0.10646	N	0.650406	T	0.79828	0.4513	M	0.63843	1.955	0.20403	N	0.999906	P	0.48834	0.916	P	0.52267	0.694	T	0.72478	-0.4281	10	0.66056	D	0.02	.	11.0688	0.47991	0.0:0.2969:0.0:0.7031	.	1756	O75445	USH2A_HUMAN	F	1756	ENSP00000305941:V1756F;ENSP00000355910:V1756F	ENSP00000305941:V1756F	V	-	1	0	USH2A	214323453	0.008000	0.16893	0.367000	0.25926	0.938000	0.57974	-0.574000	0.05868	-0.673000	0.05259	-0.136000	0.14681	GTT		0.303	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216256830	C	A	216256830	3	1	110	1	0	0	0	0	1	0	0	0	17076	536	19	2	10530	2	USH2A	1	216256830	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	13232117	216256830	32993791	20	28892										
USH2A	7399	hgsc.bcm.edu	37	chr1	216373185	216373185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agctgaggtttcatgaccttCgtaggaaacacatggctgac	11	9	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:216373185C>T	ENST00000307340.3	-	17	3981	c.3595G>A	c.(3595-3597)Gaa>Aaa	p.E1199K	RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.E1199K|USH2A_ENST00000366942.3_Missense_Mutation_p.E1199K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1199	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCATGACCTTCGTAGGAAACA	0.468										HNSCC(13;0.011)																																						0			1											103	108	106					1																	216373185		2203	4300	6503	214439808	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3595G>A	1.37:g.216373185C>T	ENSP00000305941:p.Glu1199Lys		214439808	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055730	0.75960	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.56275	0.47;0.47;0.47	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46145	D	0.000308	T	0.69797	0.3151	M	0.78223	2.4	0.34997	D	0.755624	D;D	0.76494	0.962;0.999	B;P	0.61477	0.239;0.889	T	0.71889	-0.4456	10	0.22706	T	0.39	.	17.0531	0.86525	0.0:0.8734:0.1266:0.0	.	1199;1199	O75445-2;O75445	.;USH2A_HUMAN	K	1199	ENSP00000305941:E1199K;ENSP00000355910:E1199K;ENSP00000355909:E1199K	ENSP00000305941:E1199K	E	-	1	0	USH2A	214439808	1.000000	0.71417	0.990000	0.47175	0.966000	0.64601	3.256000	0.51492	2.941000	0.99782	0.655000	0.94253	GAA		0.468	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216373185	C	T	216373185	3	4	110	1	0	0	0	0	1	0	0	0	17076	893	31	1	12251	1	USH2A	1	216373185	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	116355	216373185	32877436	21	28893										
GALNT2	2590	hgsc.bcm.edu	37	chr1	230386265	230386265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctattttgaagaactggggaAgtacgacatgatgatggatg	13	4	0	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:230386265A>G	ENST00000366672.4	+	10	1040	c.968A>G	c.(967-969)aAg>aGg	p.K323R	GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Missense_Mutation_p.K285R	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	323	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.K323M(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				GAACTGGGGAAGTACGACATG	0.502																																																1	Substitution - Missense(1)	ovary(1)	1											182	166	171					1																	230386265		2203	4300	6503	228452888	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.968A>G	1.37:g.230386265A>G	ENSP00000355632:p.Lys323Arg		228452888	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.484686	0.63962	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291	T;T	0.58797	0.31;0.31	4.43	4.43	0.53597	.	0.136038	0.64402	D	0.000007	T	0.57257	0.2041	M	0.74647	2.275	0.80722	D	1	B;B	0.23316	0.083;0.08	B;B	0.17722	0.014;0.019	T	0.58572	-0.7613	10	0.41790	T	0.15	.	13.6391	0.62239	1.0:0.0:0.0:0.0	.	323;285	Q10471;G3V1S6	GALT2_HUMAN;.	R	285;323;204	ENSP00000445017:K285R;ENSP00000355632:K323R	ENSP00000355632:K323R	K	+	2	0	GALNT2	228452888	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	7.001000	0.76297	1.761000	0.52028	0.379000	0.24179	AAG		0.502	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		G	230386265	A	G	230386265	3	3	110	1	0	0	0	0	1	0	0	0	6233	72	3	4	1006	4	GALNT2	1	230386265	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	14013080	230386265	18864356	22	28894										
HNRNPU	3192	hgsc.bcm.edu	37	chr1	245021006	245021008	+	In_Frame_Del	DEL	ATC	ATC	-													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttccagctcctggcaagccaAtcatcatcacaacctagtga							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	ATC	ATC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr1:245021006_245021008delATC	ENST00000283179.9	-	8	1669_1671	c.1506_1508delGAT	c.(1504-1509)atgatt>att	p.M502del	HNRNPU-AS1_ENST00000475997.1_RNA|HNRNPU_ENST00000444376.2_In_Frame_Del_p.M483del			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	502					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			TGGCAAGCCAATCATCATCACAA	0.345																																					NSCLC(33;911 1010 3329 23631 49995)											0			1																																								243087631	SO:0001651	inframe_deletion	3192			X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.1506_1508delGAT	1.37:g.245021012_245021014delATC	ENSP00000283179:p.Met502del		243087629	O75507|Q8N174|Q96HY9|Q9BQ09	In_Frame_Del	DEL	ENST00000283179.9	37	CCDS41479.1																																																																																				0.345	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844		-	245021008	ATC	-	245021006	7	5	110	1	0	1	0	1	0	0	0	0	7294	101	4	0	997	0	HNRNPU	1	245021006	In_Frame_Del	DEL	ATC	TCGA-EI-6506-01A-11D-1733-10	14634741	245021006	4229615	23	28895										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9695705	9695705	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gccagcacgaaaggaaccacGctggtcaggaataggagaga	14	9	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:9695705G>T	ENST00000310823.3	-	1	212	c.30C>A	c.(28-30)agC>agA	p.S10R	ADAM17_ENST00000497134.1_Missense_Mutation_p.S10R|RP11-214N9.1_ENST00000607241.1_lincRNA	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	10					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		AAGGAACCACGCTGGTCAGGA	0.647											OREG0014419	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			2											42	44	43					2																	9695705		2201	4298	6499	9613156	SO:0001583	missense	6868			U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.30C>A	2.37:g.9695705G>T	ENSP00000309968:p.Ser10Arg	658	9613156	O60226	Missense_Mutation	SNP	ENST00000310823.3	37	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.376453	0.61735	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	T;T	0.64803	2.01;-0.12	4.71	0.933	0.19471	.	0.800808	0.12004	N	0.508585	T	0.45135	0.1327	L	0.27053	0.805	0.09310	N	1	P;B;P;B	0.44380	0.834;0.065;0.834;0.065	B;B;B;B	0.44044	0.439;0.052;0.322;0.052	T	0.24764	-1.0151	10	0.22109	T	0.4	.	3.841	0.08914	0.2948:0.1858:0.5194:0.0	.	10;10;10;10	A8K1B4;B2RNB2;Q6P5T8;P78536	.;.;.;ADA17_HUMAN	R	10	ENSP00000309968:S10R;ENSP00000418728:S10R	ENSP00000309968:S10R	S	-	3	2	ADAM17	9613156	0.041000	0.20044	0.020000	0.16555	0.993000	0.82548	0.141000	0.16076	0.058000	0.16222	0.655000	0.94253	AGC		0.647	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			T	9695705	G	T	9695705	3	4	110	1	0	0	0	0	1	0	0	0	238	1078	38	2	2520	2	ADAM17	2	9695705	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10		9695705	233503668	24	28896										
GREB1	9687	hgsc.bcm.edu	37	chr2	11706632	11706632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gccaggccgggaaggacctgCgccttgtctccatttccaac	11	15	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:11706632C>T	ENST00000381486.2	+	4	604	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	GREB1_ENST00000234142.5_Missense_Mutation_p.R102C|GREB1_ENST00000381483.2_Missense_Mutation_p.R102C|GREB1_ENST00000263834.5_Missense_Mutation_p.R102C|GREB1_ENST00000389825.3_5'UTR	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	102						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAAGGACCTGCGCCTTGTCTC	0.647																																					Ovarian(39;850 945 2785 23371 33093)											0			2											63	61	62					2																	11706632		2203	4300	6503	11624083	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.304C>T	2.37:g.11706632C>T	ENSP00000370896:p.Arg102Cys		11624083	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321580	0.81580	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000381483;ENST00000234142	T;T;T;T	0.45668	1.82;0.89;0.91;1.82	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.63570	0.2522	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.67369	-0.5688	10	0.87932	D	0	-42.6783	12.8833	0.58030	0.2742:0.7258:0.0:0.0	.	102;102;102	Q4ZG55-2;Q4ZG55-3;Q4ZG55	.;.;GREB1_HUMAN	C	102	ENSP00000370896:R102C;ENSP00000263834:R102C;ENSP00000370892:R102C;ENSP00000234142:R102C	ENSP00000234142:R102C	R	+	1	0	GREB1	11624083	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.154000	0.50693	2.397000	0.81536	0.655000	0.94253	CGC		0.647	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11706632	C	T	11706632	3	4	110	1	0	0	0	0	1	0	0	0	6781	768	27	1	314	1	GREB1	2	11706632	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2010927	11706632	231492741	25	28897										
GREB1	9687	hgsc.bcm.edu	37	chr2	11716493	11716493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctccaggtttctctgggaatTgtgttggctgtggaaagaaa	13	6	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:11716493T>C	ENST00000381486.2	+	5	769	c.469T>C	c.(469-471)Tgt>Cgt	p.C157R	GREB1_ENST00000234142.5_Missense_Mutation_p.C157R|GREB1_ENST00000381483.2_Missense_Mutation_p.C157R|GREB1_ENST00000263834.5_Missense_Mutation_p.C157R|GREB1_ENST00000389825.3_Missense_Mutation_p.C47R	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	157						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CTCTGGGAATTGTGTTGGCTG	0.383																																					Ovarian(39;850 945 2785 23371 33093)											0			2											143	147	146					2																	11716493		2203	4300	6503	11633944	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.469T>C	2.37:g.11716493T>C	ENSP00000370896:p.Cys157Arg		11633944	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018271	0.75275	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;T;T;T;T	0.79033	1.34;0.31;-1.23;0.46;1.34	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.87253	0.6131	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	D	0.88958	0.3391	10	0.87932	D	0	-8.5931	14.6441	0.68748	0.0:0.0:0.0:1.0	.	157;47;157;157	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	R	157;157;47;157;157	ENSP00000370896:C157R;ENSP00000263834:C157R;ENSP00000374475:C47R;ENSP00000370892:C157R;ENSP00000234142:C157R	ENSP00000234142:C157R	C	+	1	0	GREB1	11633944	1.000000	0.71417	0.966000	0.40874	0.987000	0.75469	7.726000	0.84824	2.049000	0.60858	0.533000	0.62120	TGT		0.383	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		C	11716493	T	C	11716493	3	2	110	1	0	0	0	0	1	0	0	0	6781	1812	63	4	483	4	GREB1	2	11716493	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	9861	11716493	231482880	26	28898										
RHOB	388	hgsc.bcm.edu	37	chr2	20647736	20647736	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaggaaggcgtgcgcgaggtCttcgagacggccacgcgcgc	17	12	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:20647736C>G	ENST00000272233.4	+	1	902	c.510C>G	c.(508-510)gtC>gtG	p.V170V		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	170					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	TGCGCGAGGTCTTCGAGACGG	0.682																																																0			2											56	59	58					2																	20647736		2197	4295	6492	20511217	SO:0001819	synonymous_variant	388				CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.510C>G	2.37:g.20647736C>G			20511217	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Silent	SNP	ENST00000272233.4	37	CCDS1699.1																																																																																				0.682	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		G	20647736	C	G	20647736	2	3	110	1	0	0	0	0	0	0	0	1	13369	900	32	5		5	RHOB	2	20647736	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	8931243	20647736	222551637	27	28899										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37310491	37310491	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccattcaaagatgaaaactgGtctttttgcttcggtgattt	8	7	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:37310491G>C	ENST00000233099.5	-	2	162	c.67C>G	c.(67-69)Cca>Gca	p.P23A	HEATR5B_ENST00000354531.2_Missense_Mutation_p.P23A|GPATCH11_ENST00000281932.5_5'Flank|GPATCH11_ENST00000608836.1_5'Flank|GPATCH11_ENST00000409774.1_5'Flank	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	23						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ATGAAAACTGGTCTTTTTGCT	0.378																																																0			2											136	123	127					2																	37310491		2203	4300	6503	37163995	SO:0001583	missense	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.67C>G	2.37:g.37310491G>C	ENSP00000233099:p.Pro23Ala		37163995	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	7.354	0.623522	0.14193	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.68181	-0.31;-0.31	5.63	5.63	0.86233	Armadillo-type fold (1);	0.057213	0.64402	D	0.000001	T	0.41143	0.1146	N	0.02736	-0.51	0.58432	D	0.999999	B	0.09022	0.002	B	0.15052	0.012	T	0.37888	-0.9686	10	0.18710	T	0.47	-14.1998	12.951	0.58401	0.0737:0.0:0.9263:0.0	.	23	Q9P2D3	HTR5B_HUMAN	A	23	ENSP00000233099:P23A;ENSP00000346531:P23A	ENSP00000233099:P23A	P	-	1	0	HEATR5B	37163995	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	5.694000	0.68272	2.637000	0.89404	0.561000	0.74099	CCA		0.378	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37310491	G	C	37310491	3	2	110	1	0	0	0	0	1	0	0	0	7053	1261	44	5	6288	5	HEATR5B	2	37310491	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	16662755	37310491	205888882	28	28900										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103274048	103274048	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	catctgtatcacaagttgccCacaatagtgcctgagagctg	9	11	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:103274048C>T	ENST00000233969.2	+	2	457	c.315C>T	c.(313-315)ccC>ccT	p.P105P		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	105					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						ACAAGTTGCCCACAATAGTGC	0.428																																																0			2											76	73	74					2																	103274048		2203	4300	6503	102640480	SO:0001819	synonymous_variant	6549				CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.315C>T	2.37:g.103274048C>T			102640480	B2RMS2	Silent	SNP	ENST00000233969.2	37	CCDS2062.1																																																																																				0.428	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			T	103274048	C	T	103274048	2	4	110	1	0	0	0	0	0	0	0	1	14749	581	21	3		3	SLC9A2	2	103274048	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	65963557	103274048	139925325	29	28901										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113074148	113074148	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atctgtaaatacttcctggaAgggaggtgtattaaggtaaa	11	4	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:113074148A>G	ENST00000409871.1	+	6	1250	c.849A>G	c.(847-849)gaA>gaG	p.E283E	ZC3H6_ENST00000343936.4_Silent_p.E283E	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	283							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						ACTTCCTGGAAGGGAGGTGTA	0.303																																																0			2											45	43	43					2																	113074148		1802	4064	5866	112790619	SO:0001819	synonymous_variant	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.849A>G	2.37:g.113074148A>G			112790619	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	37	CCDS46393.1																																																																																				0.303	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		G	113074148	A	G	113074148	2	3	110	1	0	0	0	0	0	0	0	1	17610	69	3	4		4	ZC3H6	2	113074148	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	9800100	113074148	130125225	30	28902										
DPP10	57628	hgsc.bcm.edu	37	chr2	116485450	116485450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tataaagagcagttcattgcGactgacatcttctggaaaag	9	7	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:116485450G>A	ENST00000410059.1	+	8	1115	c.635G>A	c.(634-636)cGa>cAa	p.R212Q	DPP10_ENST00000393147.2_Missense_Mutation_p.R216Q|DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000310323.8_Missense_Mutation_p.R205Q|DPP10_ENST00000409163.1_Missense_Mutation_p.R162Q	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	212						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGTTCATTGCGACTGACATCT	0.308																																																0			2											53	56	55					2																	116485450		2203	4293	6496	116201920	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.635G>A	2.37:g.116485450G>A	ENSP00000386565:p.Arg212Gln		116201920	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	32	5.134072	0.94517	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.46	5.46	0.80206	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.47284	0.1437	L	0.38733	1.17	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.83275	0.91;0.996;0.968;0.946	T	0.26360	-1.0105	10	0.37606	T	0.19	-23.7844	18.2953	0.90143	0.0:0.0:1.0:0.0	.	205;216;208;212	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	Q	212;162;208;216;205;162	ENSP00000386565:R212Q;ENSP00000387038:R162Q;ENSP00000376854:R208Q;ENSP00000376855:R216Q;ENSP00000309066:R205Q	ENSP00000309066:R205Q	R	+	2	0	DPP10	116201920	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.631000	0.98424	2.570000	0.86706	0.591000	0.81541	CGA		0.308	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116485450	G	A	116485450	3	1	110	1	0	0	0	0	1	0	0	0	4738	1058	37	1	836	1	DPP10	2	116485450	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3411302	116485450	126713923	31	28903										
DPP10	57628	hgsc.bcm.edu	37	chr2	116534805	116534805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtaaaagtgagcaaattaccGtgcggcatctgacatcagga	11	8	2	2	rs150929011		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:116534805G>A	ENST00000410059.1	+	14	1723	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M	DPP10_ENST00000393147.2_Missense_Mutation_p.V419M|DPP10_ENST00000310323.8_Missense_Mutation_p.V408M|DPP10_ENST00000409163.1_Missense_Mutation_p.V365M	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	415						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.V408M(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GCAAATTACCGTGCGGCATCT	0.378																																																1	Substitution - Missense(1)	ovary(1)	2						G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	3,4403	6.2+/-15.9	0,3,2200	108	105	106		1222,1255,1093,1231,1243	4.1	0.9	2	dbSNP_134	106	0,8598		0,0,4299	no	missense,missense,missense,missense,missense	DPP10	NM_001004360.3,NM_001178034.1,NM_001178036.1,NM_001178037.1,NM_020868.3	21,21,21,21,21	0,3,6499	AA,AG,GG		0.0,0.0681,0.0231	benign,benign,benign,benign,benign	408/790,419/801,365/747,411/793,415/797	116534805	3,13001	2203	4299	6502	116251275	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1243G>A	2.37:g.116534805G>A	ENSP00000386565:p.Val415Met		116251275	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493314	0.44352	6.81E-4	0.0	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.97	4.1	0.47936	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.202355	0.42548	N	0.000696	T	0.20536	0.0494	L	0.29908	0.895	0.44946	D	0.997961	B;P;B;P	0.38677	0.385;0.524;0.439;0.642	B;B;B;B	0.36378	0.063;0.086;0.104;0.223	T	0.04115	-1.0976	10	0.62326	D	0.03	-14.5709	7.6174	0.28167	0.1874:0.0:0.8126:0.0	.	408;419;411;415	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	M	415;365;419;408;365	ENSP00000386565:V415M;ENSP00000387038:V365M;ENSP00000376855:V419M;ENSP00000309066:V408M	ENSP00000309066:V408M	V	+	1	0	DPP10	116251275	1.000000	0.71417	0.893000	0.35052	0.992000	0.81027	3.538000	0.53597	1.452000	0.47756	0.655000	0.94253	GTG		0.378	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116534805	G	A	116534805	3	1	110	1	0	0	0	0	1	0	0	0	4738	1145	40	1	1468	1	DPP10	2	116534805	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	49355	116534805	126664568	32	28904										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141665450	141665450	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	attaaacatgcaataccacaGagatagccttcatcagagcc	6	11	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:141665450G>T	ENST00000389484.3	-	22	4487	c.3516C>A	c.(3514-3516)ctC>ctA	p.L1172L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1172	LDL-receptor class A 10. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CAATACCACAGAGATAGCCTT	0.408										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											174	181	179					2																	141665450		2203	4300	6503	141381920	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3516C>A	2.37:g.141665450G>T			141381920	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141665450	G	T	141665450	2	4	110	1	0	0	0	0	0	0	0	1	8984	929	33	2		2	LRP1B	2	141665450	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	25130645	141665450	101533923	33	28905										
TTN	7273	hgsc.bcm.edu	37	chr2	179432537	179432537	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atacacaggtttggtccactGtaaagtgatttcatttcttt	7	7	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:179432537G>A	ENST00000591111.1	-	276	73623	c.73399C>T	c.(73399-73401)Cag>Tag	p.Q24467*	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.Q17043*|TTN_ENST00000359218.5_Nonsense_Mutation_p.Q17168*|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Q23540*|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Q17235*|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Q26108*|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24467	Fibronectin type-III 78. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGGTCCACTGTAAAGTGATT	0.423																																																0			2											142	133	136					2																	179432537		1887	4109	5996	179140783	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73399C>T	2.37:g.179432537G>A	ENSP00000465570:p.Gln24467*		179140783	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	63	77.918022	0.99993	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.58	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.3151	0.60403	0.0:0.0:0.7124:0.2876	.	.	.	.	X	23540;17043;17235;17168;17041	.	ENSP00000340554:Q17235X	Q	-	1	0	TTN	179140783	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.246000	0.58740	1.282000	0.44496	0.555000	0.69702	CAG		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179432537	G	A	179432537	4	1	110	1	0	0	0	0	0	1	0	0	16775	1386	48	3	29805	3	TTN	2	179432537	Nonsense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	37767087	179432537	63766836	34	28906										
TTN	7273	hgsc.bcm.edu	37	chr2	179629528	179629528	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agctcctgcagaacttggggCggttcaggagctaggagtaa	15	8	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:179629528C>T	ENST00000591111.1	-	42	9938	c.9714G>A	c.(9712-9714)ccG>ccA	p.P3238P	TTN_ENST00000460472.2_Silent_p.P3192P|TTN_ENST00000359218.5_Silent_p.P3192P|TTN_ENST00000360870.5_Silent_p.P3238P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342992.6_Silent_p.P3238P|TTN_ENST00000342175.6_Silent_p.P3192P|TTN_ENST00000589042.1_Silent_p.P3238P|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13566			P -> L (in a bladder carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAACTTGGGGCGGTTCAGGAG	0.483																																																0			2											50	54	52					2																	179629528		2203	4300	6503	179337773	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9714G>A	2.37:g.179629528C>T			179337773	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179629528	C	T	179629528	2	4	110	1	0	0	0	0	0	0	0	1	16775	755	27	1		1	TTN	2	179629528	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	196991	179629528	63569845	35	28907										
SSFA2	6744	hgsc.bcm.edu	37	chr2	182783548	182783548	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttagaacacaaatgatggatTtagaattggcaatgctgcgt	10	5	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:182783548T>G	ENST00000431877.2	+	13	3111	c.2932T>G	c.(2932-2934)Tta>Gta	p.L978V	SSFA2_ENST00000409136.1_Missense_Mutation_p.L487V|SSFA2_ENST00000409001.1_Missense_Mutation_p.L978V|SSFA2_ENST00000428267.2_Missense_Mutation_p.L825V|SSFA2_ENST00000320370.7_Missense_Mutation_p.L978V	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	978						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			AATGATGGATTTAGAATTGGC	0.373																																																0			2											69	71	70					2																	182783548		2203	4300	6503	182491793	SO:0001583	missense	6744			M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.2932T>G	2.37:g.182783548T>G	ENSP00000388731:p.Leu978Val		182491793	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.8|21.8	4.198544|4.198544	0.79015|0.79015	.|.	.|.	ENSG00000138434|ENSG00000138434	ENST00000457421|ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	.|T;T;T;T;T	.|0.38077	.|1.16;1.16;1.16;1.16;1.16	6.11|6.11	6.11|6.11	0.99139|0.99139	.|.	.|0.065407	.|0.64402	.|D	.|0.000008	T|T	0.62122|0.62122	0.2402|0.2402	M|M	0.74881|0.74881	2.28|2.28	0.49483|0.49483	D|D	0.999792|0.999792	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.85130	.|0.997;0.996;0.997;0.997;0.997	T|T	0.64478|0.64478	-0.6398|-0.6398	5|10	.|0.62326	.|D	.|0.03	-11.6741|-11.6741	16.7021|16.7021	0.85357|0.85357	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|825;487;978;978;978	.|E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.|.;.;.;SSFA2_HUMAN;.	C|V	16|978;978;978;825;487	.|ENSP00000388731:L978V;ENSP00000314669:L978V;ENSP00000387319:L978V;ENSP00000409867:L825V;ENSP00000386916:L487V	.|ENSP00000314669:L978V	F|L	+|+	2|1	0|2	SSFA2|SSFA2	182491793|182491793	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	2.272000|2.272000	0.43373|0.43373	2.343000|2.343000	0.79666|0.79666	0.533000|0.533000	0.62120|0.62120	TTT|TTA		0.373	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		G	182783548	T	G	182783548	3	3	110	1	0	0	0	0	1	0	0	0	15222	1838	64	4	2982	4	SSFA2	2	182783548	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	3154020	182783548	60415825	36	28908										
DUSP19	142679	hgsc.bcm.edu	37	chr2	183960271	183960271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taccagtgctttttctttggTgaaaaatgcaagaccttcca	7	9	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:183960271T>C	ENST00000354221.4	+	4	714	c.539T>C	c.(538-540)gTg>gCg	p.V180A	AC064871.3_ENST00000413954.1_RNA|DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Missense_Mutation_p.V129A|AC064871.3_ENST00000444562.1_RNA	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	180	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						TTTTCTTTGGTGAAAAATGCA	0.408																																																0			2											133	135	134					2																	183960271		2203	4300	6503	183668516	SO:0001583	missense	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.539T>C	2.37:g.183960271T>C	ENSP00000346160:p.Val180Ala		183668516	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.647117	0.67358	.	.	ENSG00000162999	ENST00000342619;ENST00000354221	D;D	0.89270	-2.49;-2.49	5.74	5.74	0.90152	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.107189	0.64402	D	0.000005	D	0.93533	0.7936	M	0.83118	2.625	0.80722	D	1	P;P	0.46578	0.778;0.88	B;P	0.55087	0.399;0.768	D	0.94081	0.7344	10	0.62326	D	0.03	.	16.0247	0.80536	0.0:0.0:0.0:1.0	.	129;180	Q8WTR2-2;Q8WTR2	.;DUS19_HUMAN	A	129;180	ENSP00000343905:V129A;ENSP00000346160:V180A	ENSP00000343905:V129A	V	+	2	0	DUSP19	183668516	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.193000	0.77780	2.189000	0.69895	0.482000	0.46254	GTG		0.408	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			C	183960271	T	C	183960271	3	2	110	1	0	0	0	0	1	0	0	0	4829	1696	59	4	553	4	DUSP19	2	183960271	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	1176723	183960271	59239102	37	28909										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187626640	187626640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taatgaggaggcgtatgggcGttcccatattcctgaacagc	12	9	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:187626640G>A	ENST00000304698.5	+	8	1774	c.1571G>A	c.(1570-1572)cGt>cAt	p.R524H		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	524						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCGTATGGGCGTTCCCATATT	0.413																																																0			2											96	86	89					2																	187626640		2203	4300	6503	187334885	SO:0001583	missense	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1571G>A	2.37:g.187626640G>A	ENSP00000304108:p.Arg524His		187334885	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	G	7.176	0.588699	0.13812	.	.	ENSG00000144369	ENST00000304698	T	0.43688	0.94	5.79	-1.6	0.08426	.	0.601209	0.19035	N	0.124449	T	0.16041	0.0386	N	0.08118	0	0.21984	N	0.999436	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.18178	-1.0345	10	0.17832	T	0.49	2.0E-4	5.0873	0.14689	0.4883:0.0:0.2936:0.2181	.	524;525	Q6P995;A8K122	F171B_HUMAN;.	H	524	ENSP00000304108:R524H	ENSP00000304108:R524H	R	+	2	0	FAM171B	187334885	0.719000	0.27986	0.492000	0.27490	0.664000	0.39144	0.582000	0.23834	-0.176000	0.10707	-0.140000	0.14226	CGT		0.413	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187626640	G	A	187626640	3	1	110	1	0	0	0	0	1	0	0	0	5507	1145	40	1	1601	1	FAM171B	2	187626640	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3666369	187626640	55572733	38	28910										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189876400	189876400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtctttgaatatcgaacacGcaaggctgtgagactaccta	9	9	1	2	rs138533702		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:189876400G>A	ENST00000304636.3	+	51	4471	c.4301G>A	c.(4300-4302)cGc>cAc	p.R1434H	COL3A1_ENST00000317840.5_Missense_Mutation_p.R1131H	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1434	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.		R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TATCGAACACGCAAGGCTGTG	0.393																																																0			2						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	224	201	209		4301	4.8	1	2	dbSNP_134	209	0,8600		0,0,4300	no	missense	COL3A1	NM_000090.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1434/1467	189876400	1,13005	2203	4300	6503	189584645	SO:0001583	missense	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.4301G>A	2.37:g.189876400G>A	ENSP00000304408:p.Arg1434His		189584645	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544019	0.45280	2.27E-4	0.0	ENSG00000168542	ENST00000304636;ENST00000317840	T;T	0.73681	-0.77;-0.77	5.7	4.82	0.62117	Fibrillar collagen, C-terminal (4);	0.000000	0.52532	D	0.000072	T	0.75332	0.3835	M	0.77313	2.365	0.25222	N	0.989896	B	0.16396	0.017	B	0.15484	0.013	T	0.68519	-0.5387	10	0.59425	D	0.04	.	14.8672	0.70425	0.0691:0.0:0.9309:0.0	.	1434	P02461	CO3A1_HUMAN	H	1434;1131	ENSP00000304408:R1434H;ENSP00000315243:R1131H	ENSP00000304408:R1434H	R	+	2	0	COL3A1	189584645	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.130000	0.50508	1.409000	0.46915	0.591000	0.81541	CGC		0.393	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189876400	G	A	189876400	3	1	110	1	0	0	0	0	1	0	0	0	3694	1087	38	1	4503	1	COL3A1	2	189876400	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2249760	189876400	53322973	39	28911										
PGAP1	80055	hgsc.bcm.edu	37	chr2	197757952	197757952	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tacaaaactgacagtttcttCttggaattttgagttatcta	6	6	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:197757952C>A	ENST00000354764.4	-	8	1059	c.945G>T	c.(943-945)aaG>aaT	p.K315N	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.K273N|PGAP1_ENST00000409475.1_Missense_Mutation_p.K315N	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	315					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						ACAGTTTCTTCTTGGAATTTT	0.313																																																0			2											105	109	108					2																	197757952		2203	4299	6502	197466197	SO:0001583	missense	80055				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.945G>T	2.37:g.197757952C>A	ENSP00000346809:p.Lys315Asn		197466197	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.440661	0.43326	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000409188;ENST00000374738	.	.	.	4.9	3.94	0.45596	.	0.195026	0.48767	D	0.000172	T	0.47563	0.1452	N	0.19112	0.55	0.34611	D	0.717604	B;B;D	0.71674	0.024;0.383;0.998	B;B;D	0.76071	0.014;0.151;0.987	T	0.48186	-0.9057	9	0.17832	T	0.49	-9.6702	10.5792	0.45246	0.0:0.8984:0.0:0.1016	.	273;315;315	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	N	95;315;315;273;95	.	ENSP00000346809:K315N	K	-	3	2	PGAP1	197466197	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.213000	0.42844	2.552000	0.86080	0.563000	0.77884	AAG		0.313	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		A	197757952	C	A	197757952	3	1	110	1	0	0	0	0	1	0	0	0	11808	912	32	2	1903	2	PGAP1	2	197757952	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	7881552	197757952	45441421	40	28912										
HSPD1	3329	hgsc.bcm.edu	37	chr2	198362021	198362021	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtttagctccaatgtttttGtatttatcttttaagtcaat	5	5	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:198362021G>T	ENST00000388968.3	-	3	537	c.270C>A	c.(268-270)taC>taA	p.Y90*	HSPE1_ENST00000233893.5_5'Flank|HSPD1_ENST00000345042.2_Nonsense_Mutation_p.Y90*|HSPE1_ENST00000409729.1_5'Flank|HSPD1_ENST00000544407.1_Nonsense_Mutation_p.Y90*	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	90					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CAATGTTTTTGTATTTATCTT	0.403																																																0			2											100	95	97					2																	198362021		2203	4300	6503	198070266	SO:0001587	stop_gained	3329			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"Heat Shock Proteins / Chaperonins"	5261	protein-coding gene	gene with protein product		118190	"heat shock 60kD protein 1 (chaperonin)", "spastic paraplegia 13 (autosomal dominant)"	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.270C>A	2.37:g.198362021G>T	ENSP00000373620:p.Tyr90*		198070266	B2R5M6|B7Z712|Q38L19|Q9UCR6	Nonsense_Mutation	SNP	ENST00000388968.3	37	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	g	15.78	2.933021	0.52866	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000430176;ENST00000452200;ENST00000544407;ENST00000426480;ENST00000428204	.	.	.	4.24	-0.0211	0.13953	.	0.057615	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-18.1988	10.7303	0.46093	0.3921:0.0:0.6079:0.0	.	.	.	.	X	90;90;90;90;90;132;90	.	ENSP00000340019:Y90X	Y	-	3	2	HSPD1	198070266	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	1.640000	0.37186	-0.084000	0.12595	-0.302000	0.09304	TAC		0.403	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		T	198362021	G	T	198362021	4	4	110	1	0	0	0	0	0	1	0	0	7449	1372	48	2	1491	2	HSPD1	2	198362021	Nonsense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	604069	198362021	44837352	41	28913										
KCTD18	130535	hgsc.bcm.edu	37	chr2	201371645	201371645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccaacatggagtccttgaagCggcacaaggactcccgccgg	12	14	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:201371645C>T	ENST00000359878.3	-	2	605	c.95G>A	c.(94-96)cGc>cAc	p.R32H	KCTD18_ENST00000468413.1_5'UTR|KCTD18_ENST00000409157.1_Missense_Mutation_p.R32H	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	32	BTB.				protein homooligomerization (GO:0051260)			p.R32L(1)|p.R32H(1)|p.R32P(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GTCCTTGAAGCGGCACAAGGA	0.483																																																3	Substitution - Missense(3)	ovary(1)|lung(1)|endometrium(1)	2											75	81	79					2																	201371645		2203	4300	6503	201079890	SO:0001583	missense	130535			AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.95G>A	2.37:g.201371645C>T	ENSP00000352941:p.Arg32His		201079890	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633365	0.87660	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.48522	0.81;0.81	5.46	5.46	0.80206	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	D	0.000004	T	0.71022	0.3291	M	0.84846	2.72	0.41654	D	0.989142	D;D	0.89917	0.997;1.0	P;D	0.77004	0.796;0.989	T	0.75385	-0.3336	10	0.87932	D	0	-18.4704	14.0045	0.64453	0.1512:0.8488:0.0:0.0	.	32;32	Q6PI47-2;Q6PI47	.;KCD18_HUMAN	H	32	ENSP00000352941:R32H;ENSP00000386751:R32H	ENSP00000352941:R32H	R	-	2	0	KCTD18	201079890	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.085000	0.50151	2.840000	0.97914	0.655000	0.94253	CGC		0.483	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		T	201371645	C	T	201371645	3	4	110	1	0	0	0	0	1	0	0	0	8126	768	27	1	1209	1	KCTD18	2	201371645	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	3009624	201371645	41827728	42	28914										
FZD7	8324	hgsc.bcm.edu	37	chr2	202900224	202900224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	catgcggcgcttcagctaccCagagcggcccatcatcttcc	9	17	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:202900224C>T	ENST00000286201.1	+	1	915	c.854C>T	c.(853-855)cCa>cTa	p.P285L	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	285					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	31						TTCAGCTACCCAGAGCGGCCC	0.662											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			2											112	113	113					2																	202900224		2203	4300	6503	202608469	SO:0001583	missense	8324			AB010881	CCDS2351.1	2q33	2014-01-29	2014-01-29		ENSG00000155760	ENSG00000155760		"GPCR / Class F : Frizzled receptors"	4045	protein-coding gene	gene with protein product		603410	"frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7"			9707618, 9813155	Standard	NM_003507		Approved	FzE3	uc002uyw.1	O75084	OTTHUMG00000132841	ENST00000286201.1:c.854C>T	2.37:g.202900224C>T	ENSP00000286201:p.Pro285Leu	2133	202608469	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	37	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472127	0.84533	.	.	ENSG00000155760	ENST00000286201	D	0.91740	-2.9	5.13	5.13	0.70059	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.97629	0.9223	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98732	1.0713	10	0.87932	D	0	.	18.7816	0.91934	0.0:1.0:0.0:0.0	.	285	O75084	FZD7_HUMAN	L	285	ENSP00000286201:P285L	ENSP00000286201:P285L	P	+	2	0	FZD7	202608469	1.000000	0.71417	0.974000	0.42286	0.992000	0.81027	7.580000	0.82523	2.678000	0.91216	0.563000	0.77884	CCA		0.662	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		T	202900224	C	T	202900224	3	4	110	1	0	0	0	0	1	0	0	0	6154	594	21	3	856	3	FZD7	2	202900224	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1528579	202900224	40299149	43	28915										
MDH1B	130752	hgsc.bcm.edu	37	chr2	207619951	207619951	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gcctgcagagaggcaccctgCttcggaggcagtcctccaga	13	14	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:207619951C>A	ENST00000374412.3	-	5	967	c.692G>T	c.(691-693)aGc>aTc	p.S231I	MDH1B_ENST00000454776.2_Missense_Mutation_p.S231I|MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000449792.1_Missense_Mutation_p.S133I	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	231					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		AGGCACCCTGCTTCGGAGGCA	0.552																																					Pancreas(76;29 1355 28675 37177 51207)											0			2											62	58	60					2																	207619951		2203	4300	6503	207328196	SO:0001583	missense	130752				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.692G>T	2.37:g.207619951C>A	ENSP00000363533:p.Ser231Ile		207328196	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247907	0.22880	.	.	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.08370	3.1;3.1;3.1	5.68	0.83	0.18854	NAD(P)-binding domain (1);	0.655088	0.17294	N	0.179530	T	0.09512	0.0234	M	0.63428	1.95	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.13407	0.009;0.004	T	0.21621	-1.0240	10	0.62326	D	0.03	-8.3295	7.373	0.26813	0.0:0.4647:0.1126:0.4227	.	231;231	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	I	231;133;231	ENSP00000363533:S231I;ENSP00000416577:S133I;ENSP00000389916:S231I	ENSP00000363533:S231I	S	-	2	0	MDH1B	207328196	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	0.049000	0.14099	0.149000	0.19098	-0.808000	0.03180	AGC		0.552	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		A	207619951	C	A	207619951	3	1	110	1	0	0	0	0	1	0	0	0	9439	797	28	2	896	2	MDH1B	2	207619951	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4719727	207619951	35579422	44	28916										
NGEF	25791	hgsc.bcm.edu	37	chr2	233752756	233752756	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gactcaccatttccagctccTtgtgagcatccaaagcagtg	8	13	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:233752756T>A	ENST00000264051.3	-	9	1612	c.1334A>T	c.(1333-1335)aAg>aTg	p.K445M	NGEF_ENST00000373552.4_Missense_Mutation_p.K353M|NGEF_ENST00000539537.1_Missense_Mutation_p.K168M	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	445	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K445R(1)		central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TTCCAGCTCCTTGTGAGCATC	0.512																																																1	Substitution - Missense(1)	ovary(1)	2											173	145	154					2																	233752756		2203	4300	6503	233461000	SO:0001583	missense	25791			AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"Rho guanine nucleotide exchange factors"	7807	protein-coding gene	gene with protein product	"ephexin"	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.1334A>T	2.37:g.233752756T>A	ENSP00000264051:p.Lys445Met		233461000	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	37	CCDS2500.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	16.02|16.02	3.004661|3.004661	0.54254|0.54254	.|.	.|.	ENSG00000066248|ENSG00000066248	ENST00000264051;ENST00000373552;ENST00000541023;ENST00000539537;ENST00000416114|ENST00000424488	T;T;T;T|.	0.65916|.	-0.18;-0.18;-0.18;-0.18|.	5.21|5.21	-2.83|-2.83	0.05769|0.05769	Dbl homology (DH) domain (5);|.	0.417418|.	0.27531|.	N|.	0.018945|.	T|T	0.51346|0.51346	0.1669|0.1669	M|M	0.67397|0.67397	2.05|2.05	0.22873|0.22873	N|N	0.998623|0.998623	D;D|.	0.55800|.	0.973;0.963|.	P;P|.	0.60345|.	0.852;0.873|.	T|T	0.54070|0.54070	-0.8348|-0.8348	10|5	0.54805|.	T|.	0.06|.	-17.1457|-17.1457	11.7917|11.7917	0.52073|0.52073	0.0:0.4609:0.0:0.5391|0.0:0.4609:0.0:0.5391	.|.	353;445|.	E9PC42;Q8N5V2|.	.;NGEF_HUMAN|.	M|W	445;353;335;168;168|37	ENSP00000264051:K445M;ENSP00000362653:K353M;ENSP00000439035:K168M;ENSP00000401063:K168M|.	ENSP00000264051:K445M|.	K|R	-|-	2|1	0|2	NGEF|NGEF	233461000|233461000	0.274000|0.274000	0.24191|0.24191	0.229000|0.229000	0.23960|0.23960	0.842000|0.842000	0.47809|0.47809	0.722000|0.722000	0.25925|0.25925	-0.425000|-0.425000	0.07371|0.07371	-0.402000|-0.402000	0.06365|0.06365	AAG|AGG		0.512	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		A	233752756	T	A	233752756	3	1	110	1	0	0	0	0	1	0	0	0	10425	1609	56	5	826	5	NGEF	2	233752756	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	26132805	233752756	9446617	45	28917										
PER2	8864	hgsc.bcm.edu	37	chr2	239162195	239162195	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gctgtggcgttcaagcccacCagcgggggccgggcggacac	17	14	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr2:239162195C>T	ENST00000254657.3	-	19	2748	c.2469G>A	c.(2467-2469)ctG>ctA	p.L823L	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	823			L -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		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)		TCAAGCCCACCAGCGGGGGCC	0.622																																																0			2											14	15	15					2																	239162195		2198	4294	6492	238826934	SO:0001819	synonymous_variant	8864			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2469G>A	2.37:g.239162195C>T			238826934	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																				0.622	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		T	239162195	C	T	239162195	2	4	110	1	0	0	0	0	0	0	0	1	11761	581	21	3		3	PER2	2	239162195	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5409439	239162195	4037178	46	28918										
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38307447	38307447	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgtgttctcaacttcctgtcTcccttctacttttttgccca	4	14	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:38307447T>C	ENST00000311856.4	+	1	145	c.96T>C	c.(94-96)tcT>tcC	p.S32S	SLC22A13_ENST00000450935.2_5'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	32					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		ACTTCCTGTCTCCCTTCTACT	0.498																																																0			3											219	183	195					3																	38307447		2203	4300	6503	38282451	SO:0001819	synonymous_variant	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.96T>C	3.37:g.38307447T>C			38282451	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																				0.498	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38307447	T	C	38307447	2	2	110	1	0	0	0	0	0	0	0	1	14481	1538	54	4		4	SLC22A13	3	38307447	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10		38307447	159714983	47	28919										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38640450	38640450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cgctgactgcgctgagggccCgctgccgtgctcctggctcc	14	17	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:38640450C>T	ENST00000333535.4	-	13	2131	c.1982G>A	c.(1981-1983)cGg>cAg	p.R661Q	SCN5A_ENST00000451551.2_Missense_Mutation_p.R661Q|SCN5A_ENST00000413689.1_Missense_Mutation_p.R661Q|SCN5A_ENST00000423572.2_Missense_Mutation_p.R661Q|SCN5A_ENST00000414099.2_Missense_Mutation_p.R661Q|SCN5A_ENST00000455624.2_Missense_Mutation_p.R661Q|SCN5A_ENST00000443581.1_Missense_Mutation_p.R661Q|SCN5A_ENST00000425664.1_Missense_Mutation_p.R661Q|SCN5A_ENST00000450102.2_Missense_Mutation_p.R661Q|SCN5A_ENST00000449557.2_Missense_Mutation_p.R661Q			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	661					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GCTGAGGGCCCGCTGCCGTGC	0.642																																																0			3											56	64	62					3																	38640450		2199	4298	6497	38615454	SO:0001583	missense	6331			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1982G>A	3.37:g.38640450C>T	ENSP00000328968:p.Arg661Gln		38615454	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220265	0.95139	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93	4.08	4.08	0.47627	Domain of unknown function DUF3451 (1);	0.066433	0.64402	D	0.000018	D	0.96374	0.8817	M	0.87381	2.88	0.49051	D	0.999742	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.995;0.99;0.996;1.0;0.998	D;D;P;P;P;D;P	0.85130	0.997;0.909;0.661;0.695;0.771;0.975;0.742	D	0.97317	0.9941	10	0.87932	D	0	.	16.4426	0.83906	0.0:1.0:0.0:0.0	.	661;661;661;661;661;661;661	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	Q	661	ENSP00000398962:R661Q;ENSP00000398266:R661Q;ENSP00000410257:R661Q;ENSP00000388797:R661Q;ENSP00000397915:R661Q;ENSP00000416634:R661Q;ENSP00000328968:R661Q;ENSP00000399524:R661Q;ENSP00000403355:R661Q;ENSP00000413996:R661Q	ENSP00000328968:R661Q	R	-	2	0	SCN5A	38615454	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.604000	0.82830	2.117000	0.64856	0.561000	0.74099	CGG		0.642	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38640450	C	T	38640450	3	4	110	1	0	0	0	0	1	0	0	0	13959	652	23	1	4132	1	SCN5A	3	38640450	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	333003	38640450	159381980	48	28920										
ANO10	55129	hgsc.bcm.edu	37	chr3	43618188	43618188	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagcctcaagtcttaccccaTgaagttaaaaactcggcagc	7	12	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:43618188T>C	ENST00000292246.3	-	6	1328	c.1158A>G	c.(1156-1158)tcA>tcG	p.S386S	ANO10_ENST00000350459.4_Intron|ANO10_ENST00000451430.2_Silent_p.S275S|ANO10_ENST00000414522.2_Silent_p.S386S|ANO10_ENST00000396091.3_Silent_p.S320S	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	386					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						TCTTACCCCATGAAGTTAAAA	0.423																																																0			3											48	46	47					3																	43618188		2203	4300	6503	43593192	SO:0001819	synonymous_variant	55129			AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.1158A>G	3.37:g.43618188T>C			43593192	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Silent	SNP	ENST00000292246.3	37	CCDS2710.2																																																																																				0.423	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		C	43618188	T	C	43618188	2	2	110	1	0	0	0	0	0	0	0	1	696	1451	51	4		4	ANO10	3	43618188	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4977738	43618188	154404242	49	28921										
SETD2	29072	hgsc.bcm.edu	37	chr3	47162349	47162349	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttttcttgagagaagtcccaAcctaagtttctgagctcttc	7	10	3	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:47162349A>G	ENST00000409792.3	-	3	3819	c.3777T>C	c.(3775-3777)ggT>ggC	p.G1259G		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1259					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AGAAGTCCCAACCTAAGTTTC	0.438			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0			3											101	100	101					3																	47162349		2203	4300	6503	47137353	SO:0001819	synonymous_variant	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3777T>C	3.37:g.47162349A>G			47137353	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.438	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47162349	A	G	47162349	2	3	110	1	0	0	0	0	0	0	0	1	14168	30	2	4		4	SETD2	3	47162349	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	3544161	47162349	150860081	50	28922										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69267496	69267496	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tactgcataataatggacacCgtaagtcggtagagcttcta	9	8	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:69267496C>A	ENST00000398540.3	-	10	849	c.766G>T	c.(766-768)Ggt>Tgt	p.G256C	FRMD4B_ENST00000542259.1_Missense_Mutation_p.G202C	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	256	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TAATGGACACCGTAAGTCGGT	0.313																																																0			3											44	43	43					3																	69267496		1816	4076	5892	69350186	SO:0001583	missense	23150			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.766G>T	3.37:g.69267496C>A	ENSP00000381549:p.Gly256Cys		69350186	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085231	0.76642	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880	D;D;D	0.96396	-4.0;-4.0;-4.0	5.87	5.87	0.94306	Band 4.1 domain (1);FERM central domain (1);FERM domain (1);Pleckstrin homology-type (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98523	0.9507	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99208	1.0875	10	0.87932	D	0	-15.953	18.9896	0.92786	0.0:1.0:0.0:0.0	.	100;256	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	C	256;202;147	ENSP00000381549:G256C;ENSP00000437658:G202C;ENSP00000418962:G147C	ENSP00000381549:G256C	G	-	1	0	FRMD4B	69350186	1.000000	0.71417	0.989000	0.46669	0.663000	0.39108	6.678000	0.74508	2.785000	0.95823	0.655000	0.94253	GGT		0.313	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69267496	C	A	69267496	3	1	110	1	0	0	0	0	1	0	0	0	6071	652	23	2	2394	2	FRMD4B	3	69267496	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	22105147	69267496	128754934	51	28923										
FOXP1	27086	hgsc.bcm.edu	37	chr3	71101700	71101701	+	Frame_Shift_Del	DEL	TT	TT	-													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtcggtacctctttaggctgTtttccagcatgttgttgttg							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	TT	TT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:71101700_71101701delTT	ENST00000318789.4	-	9	1022_1023	c.497_498delAA	c.(496-498)aaafs	p.K166fs	FOXP1_ENST00000493089.1_Frame_Shift_Del_p.K166fs|FOXP1_ENST00000498215.1_Frame_Shift_Del_p.K166fs|FOXP1_ENST00000491238.1_Frame_Shift_Del_p.K168fs|FOXP1_ENST00000472382.1_5'UTR|FOXP1_ENST00000484350.1_Intron|FOXP1_ENST00000468577.1_Frame_Shift_Del_p.K166fs|FOXP1_ENST00000475937.1_Frame_Shift_Del_p.K166fs	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	166	Gln-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CTTTAGGCTGTTTTCCAGCATG	0.371			T	PAX5	ALL																																		Dom	yes		3	3p14.1	27086	forkhead box P1		L	0			3																																								71184391	SO:0001589	frameshift_variant	27086			AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"Forkhead boxes"	3823	protein-coding gene	gene with protein product	"fork head-related protein like B", "glutamine-rich factor 1", "PAX5/FOXP1 fusion protein"	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.497_498delAA	3.37:g.71101702_71101703delTT	ENSP00000318902:p.Lys166fs		71184390	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Frame_Shift_Del	DEL	ENST00000318789.4	37	CCDS2914.1																																																																																				0.371	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		-	71101701	TT	-	71101700	7	5	110	1	0	1	0	1	0	0	0	0	6045	1722	60	0	1587	0	FOXP1	3	71101700	Frame_Shift_Del	DEL	TT	TCGA-EI-6506-01A-11D-1733-10	1834204	71101700	126920730	52	28924										
CLDND1	56650	hgsc.bcm.edu	37	chr3	98235672	98235672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggagctctagtttctggtggAgtagttcaattccagcaaca	11	8	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:98235672A>G	ENST00000503004.1	-	5	1472	c.593T>C	c.(592-594)cTc>cCc	p.L198P	CLDND1_ENST00000507874.1_Intron|CLDND1_ENST00000394180.2_Missense_Mutation_p.L198P|CLDND1_ENST00000394185.2_Missense_Mutation_p.L198P|CLDND1_ENST00000508503.1_5'UTR|CLDND1_ENST00000394181.2_Missense_Mutation_p.L198P|CLDND1_ENST00000437922.1_Missense_Mutation_p.L221P|CLDND1_ENST00000341181.6_Missense_Mutation_p.L198P|CLDND1_ENST00000511081.1_Missense_Mutation_p.L103P|CLDND1_ENST00000502288.1_Intron|CLDND1_ENST00000513287.1_Missense_Mutation_p.L198P|CLDND1_ENST00000510545.1_Missense_Mutation_p.L198P			Q9NY35	CLDN1_HUMAN	claudin domain containing 1	198						apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	9						TTTCTGGTGGAGTAGTTCAAT	0.448																																																0			3											132	114	120					3																	98235672		2203	4300	6503	99718362	SO:0001583	missense	56650			AF116664	CCDS2930.1, CCDS43116.1	3q12.1	2005-12-23	2005-12-23	2005-12-23		ENSG00000080822			1322	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 4"	C3orf4			Standard	NM_001040181		Approved		uc003dst.3	Q9NY35		ENST00000503004.1:c.593T>C	3.37:g.98235672A>G	ENSP00000421226:p.Leu198Pro		99718362	B3KQR1|D3DN36|F2Z2D9|Q502Y8|Q6UVX2|Q9BUZ9|Q9NZZ5|Q9Y4S9	Missense_Mutation	SNP	ENST00000503004.1	37	CCDS2930.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.218442	0.58560	.	.	ENSG00000080822	ENST00000341181;ENST00000437922;ENST00000394180;ENST00000503004;ENST00000394185;ENST00000394181;ENST00000513873;ENST00000510545;ENST00000511081;ENST00000513287;ENST00000511667;ENST00000513452;ENST00000502299;ENST00000512147;ENST00000508902;ENST00000510541;ENST00000514537	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.93	5.93	0.95920	.	0.196730	0.42964	D	0.000629	T	0.79907	0.4527	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.77004	0.989;0.971;0.989	T	0.78807	-0.2059	10	0.35671	T	0.21	-10.8966	14.3286	0.66537	1.0:0.0:0.0:0.0	.	198;103;198	D6RCR8;F2Z2D9;Q9NY35	.;.;CLDN1_HUMAN	P	198;221;198;198;198;198;54;198;103;198;176;198;198;83;198;83;198	ENSP00000340247:L198P;ENSP00000388457:L221P;ENSP00000377734:L198P;ENSP00000421226:L198P;ENSP00000377739:L198P;ENSP00000377735:L198P;ENSP00000426164:L54P;ENSP00000423590:L198P;ENSP00000424669:L103P;ENSP00000426869:L198P;ENSP00000423732:L176P;ENSP00000425539:L198P;ENSP00000420913:L198P;ENSP00000427119:L83P;ENSP00000421413:L198P;ENSP00000424484:L83P;ENSP00000423151:L198P	ENSP00000340247:L198P	L	-	2	0	CLDND1	99718362	1.000000	0.71417	0.995000	0.50966	0.797000	0.45037	8.696000	0.91302	2.263000	0.75096	0.533000	0.62120	CTC		0.448	CLDND1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359071.1	NM_019895		G	98235672	A	G	98235672	3	3	110	1	0	0	0	0	1	0	0	0	3499	304	11	4	172	4	CLDND1	3	98235672	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	27133972	98235672	99786758	53	28925										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111795730	111795730	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	actgttctatcaggctgtcaGatcccacaccatggactgca	8	13	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:111795730G>T	ENST00000452346.2	+	16	1966	c.1963G>T	c.(1963-1965)Gat>Tat	p.D655Y	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.D529Y			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	655	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D384H(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CAGGCTGTCAGATCCCACACC	0.448																																																1	Substitution - Missense(1)	ovary(1)	3											172	166	168					3																	111795730		1982	4180	6162	113278420	SO:0001583	missense	344805			BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1963G>T	3.37:g.111795730G>T	ENSP00000398236:p.Asp655Tyr		113278420	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	37		.	.	.	.	.	.	.	.	.	.	G	22.5	4.303394	0.81136	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	D;D	0.89810	-2.57;-2.57	6.11	6.11	0.99139	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.93485	0.7921	L	0.58354	1.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.93415	0.6772	10	0.87932	D	0	.	17.651	0.88164	0.0:0.0:1.0:0.0	.	655;529	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	Y	655;643;629;529	ENSP00000398236:D655Y;ENSP00000411645:D529Y	ENSP00000411645:D529Y	D	+	1	0	TMPRSS7	113278420	1.000000	0.71417	0.987000	0.45799	0.837000	0.47467	6.964000	0.76061	2.906000	0.99361	0.655000	0.94253	GAT		0.448	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111795730	G	T	111795730	3	4	110	1	0	0	0	0	1	0	0	0	16291	942	33	2	1635	2	TMPRSS7	3	111795730	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	13560058	111795730	86226700	54	28926										
BOC	91653	hgsc.bcm.edu	37	chr3	112969433	112969433	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	caggtcaccgtccagcctgcGtccaccgtccagaagcccgg	11	18	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:112969433G>A	ENST00000495514.1	+	4	833	c.129G>A	c.(127-129)gcG>gcA	p.A43A	BOC_ENST00000484034.1_Silent_p.A43A|BOC_ENST00000485230.1_Silent_p.A43A|BOC_ENST00000355385.3_Silent_p.A43A|BOC_ENST00000273395.4_Silent_p.A43A			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	43	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TCCAGCCTGCGTCCACCGTCC	0.552																																																0			3											112	106	108					3																	112969433		2203	4300	6503	114452123	SO:0001819	synonymous_variant	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.129G>A	3.37:g.112969433G>A			114452123	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																				0.552	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		A	112969433	G	A	112969433	2	1	110	1	0	0	0	0	0	0	0	1	1482	1132	40	1		1	BOC	3	112969433	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1173703	112969433	85052997	55	28927										
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113634568	113634568	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaaatgttcctgagaaagatCttcatggaagactttttatc	7	6	2	3	rs199895173		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:113634568C>A	ENST00000358160.4	+	10	1465	c.973C>A	c.(973-975)Ctt>Att	p.L325I	GRAMD1C_ENST00000440446.2_Missense_Mutation_p.L120I|GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_Missense_Mutation_p.L54I|GRAMD1C_ENST00000472026.1_Missense_Mutation_p.L158I	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	325						integral component of membrane (GO:0016021)		p.L325V(1)		NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						TGAGAAAGATCTTCATGGAAG	0.358																																																1	Substitution - Missense(1)	ovary(1)	3											79	80	80					3																	113634568		2203	4296	6499	115117258	SO:0001583	missense	54762				CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.973C>A	3.37:g.113634568C>A	ENSP00000350881:p.Leu325Ile		115117258	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	37	CCDS33826.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.280356	0.59758	.	.	ENSG00000178075	ENST00000358160;ENST00000452134;ENST00000472026;ENST00000462838;ENST00000440446	T;T;T;T	0.56444	1.03;0.54;0.46;0.48	5.98	5.98	0.97165	.	0.199004	0.44483	D	0.000452	T	0.47154	0.1430	L	0.49350	1.555	0.33973	D	0.647005	B;D	0.54397	0.314;0.966	B;B	0.38880	0.05;0.284	T	0.61237	-0.7103	10	0.34782	T	0.22	.	17.3601	0.87347	0.0:1.0:0.0:0.0	.	158;325	E9PHT3;Q8IYS0	.;GRM1C_HUMAN	I	325;54;158;120;120	ENSP00000350881:L325I;ENSP00000399844:L54I;ENSP00000419132:L158I;ENSP00000408135:L120I	ENSP00000350881:L325I	L	+	1	0	GRAMD1C	115117258	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.609000	0.61148	2.838000	0.97847	0.655000	0.94253	CTT		0.358	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		A	113634568	C	A	113634568	3	1	110	1	0	0	0	0	1	0	0	0	6770	913	32	2	1011	2	GRAMD1C	3	113634568	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	665135	113634568	84387862	56	28928										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157099073	157099073	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaggagaaggtgtcggtgatGcttttaatctccagcaggag	15	6	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:157099073G>A	ENST00000362010.2	-	7	1306	c.999C>T	c.(997-999)agC>agT	p.S333S	VEPH1_ENST00000392832.2_Silent_p.S333S|VEPH1_ENST00000392833.2_Silent_p.S333S|VEPH1_ENST00000543418.1_Silent_p.S333S|RP11-550I24.2_ENST00000487238.1_RNA	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	333						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TGTCGGTGATGCTTTTAATCT	0.517																																																0			3											151	146	148					3																	157099073		2203	4300	6503	158581767	SO:0001819	synonymous_variant	79674			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.999C>T	3.37:g.157099073G>A			158581767	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Silent	SNP	ENST00000362010.2	37	CCDS3179.1																																																																																				0.517	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		A	157099073	G	A	157099073	2	1	110	1	0	0	0	0	0	0	0	1	17194	1310	46	3		3	VEPH1	3	157099073	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	43464505	157099073	40923357	57	28929										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178951999	178951999	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaactacaatcttttgatgaCattgcatacattcgaaagac	6	8	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:178951999C>T	ENST00000263967.3	+	21	3211	c.3054C>T	c.(3052-3054)gaC>gaT	p.D1018D	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1018	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTTTTGATGACATTGCATACA	0.398		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											108	95	99					3																	178951999		1878	4117	5995	180434693	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3054C>T	3.37:g.178951999C>T			180434693	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.398	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178951999	C	T	178951999	2	4	110	1	0	0	0	0	0	0	0	1	11944	477	17	3		3	PIK3CA	3	178951999	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	21852926	178951999	19070431	58	28930										
TFRC	7037	hgsc.bcm.edu	37	chr3	195798995	195798995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tttttgagatccagcctcacGagggacatatgaattttcat	8	8	2	2	rs377519674		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr3:195798995G>A	ENST00000360110.4	-	5	632	c.463C>T	c.(463-465)Cgt>Tgt	p.R155C	RNU7-18P_ENST00000516365.1_RNA|TFRC_ENST00000535031.1_5'UTR|TFRC_ENST00000392396.3_Missense_Mutation_p.R155C|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000420415.1_Missense_Mutation_p.R74C	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	155					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	CCAGCCTCACGAGGGACATAT	0.333			T	BCL6	NHL																																		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	0			3						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	70	70	70		463,463	4.8	1	3		70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TFRC	NM_001128148.1,NM_003234.2	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	155/761,155/761	195798995	1,13005	2203	4300	6503	197283392	SO:0001583	missense	7037			X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"CD molecules"	11763	protein-coding gene	gene with protein product		190010	"transferrin receptor (p90, CD71)"				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.463C>T	3.37:g.195798995G>A	ENSP00000353224:p.Arg155Cys		197283392	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	37	CCDS3312.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134924	0.77662	0.0	1.16E-4	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396	T;T;T	0.65916	-0.18;-0.18;-0.18	5.68	4.79	0.61399	.	0.306462	0.40640	N	0.001058	T	0.79528	0.4461	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	P	0.61201	0.885	D	0.83999	0.0342	10	0.87932	D	0	-10.3439	14.6289	0.68643	0.0:0.1467:0.8533:0.0	.	155	P02786	TFR1_HUMAN	C	155;74;155	ENSP00000353224:R155C;ENSP00000390133:R74C;ENSP00000376197:R155C	ENSP00000353224:R155C	R	-	1	0	TFRC	197283392	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.079000	0.50104	1.497000	0.48584	0.591000	0.81541	CGT		0.333	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			A	195798995	G	A	195798995	3	1	110	1	0	0	0	0	1	0	0	0	15851	1058	37	1	1879	1	TFRC	3	195798995	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	16846996	195798995	2223435	59	28931										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tggagtgccacctgctcacaCacgtgcccatgtggagtgcc					rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																																1	Substitution - Missense(1)	pancreas(1)	4																																								1378622	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs		1378594	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388622	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	1388594	7	5	110	1	0	1	0	1	0	0	0	0	3883	478	17	0	297	0	CRIPAK	4	1388594	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	TCGA-EI-6506-01A-11D-1733-10		1388594	189765682	60	28932										
NOP14	8602	hgsc.bcm.edu	37	chr4	2955244	2955244	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tacttggctcccaccttgggTttttcctttttgtctctgtt	7	11	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:2955244T>A	ENST00000314262.6	-	5	789	c.741A>T	c.(739-741)aaA>aaT	p.K247N	NOP14_ENST00000502735.1_Missense_Mutation_p.K247N|NOP14_ENST00000398071.4_Missense_Mutation_p.K247N|NOP14_ENST00000416614.2_Missense_Mutation_p.K247N|NOP14-AS1_ENST00000503709.1_RNA|NOP14-AS1_ENST00000515194.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	247					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CCACCTTGGGTTTTTCCTTTT	0.507																																																0			4											217	195	203					4																	2955244		2203	4300	6503	2925042	SO:0001583	missense	8602			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.741A>T	4.37:g.2955244T>A	ENSP00000315674:p.Lys247Asn		2925042	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.760723	0.31137	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	4.94	-6.93	0.01638	.	0.000000	0.85682	D	0.000000	T	0.39809	0.1092	M	0.89904	3.07	0.53005	D	0.999962	B;B	0.27450	0.107;0.179	B;B	0.30943	0.122;0.104	T	0.46034	-0.9220	10	0.87932	D	0	-23.6138	17.7494	0.88430	0.0:0.7074:0.0:0.2926	.	247;247	E9PFK5;P78316	.;NOP14_HUMAN	N	247;247;247;247;146	ENSP00000405068:K247N;ENSP00000315674:K247N;ENSP00000427415:K247N;ENSP00000381146:K247N	ENSP00000315674:K247N	K	-	3	2	NOP14	2925042	0.108000	0.22018	0.573000	0.28510	0.129000	0.20672	-0.666000	0.05280	-1.534000	0.01743	-0.415000	0.06103	AAA		0.507	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		A	2955244	T	A	2955244	3	1	110	1	0	0	0	0	1	0	0	0	10567	1722	60	5	1888	5	NOP14	4	2955244	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	1566650	2955244	188199032	61	28933										
STIM2	57620	hgsc.bcm.edu	37	chr4	27010417	27010417	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgagttgacaacttgtttaCgagaacgactttttcgctgg	10	8	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:27010417C>T	ENST00000467011.1	+	10	1707	c.1282C>T	c.(1282-1284)Cga>Tga	p.R428*	STIM2_ENST00000467087.1_Nonsense_Mutation_p.R428*|STIM2_ENST00000237364.5_Nonsense_Mutation_p.R515*|STIM2_ENST00000412829.2_Nonsense_Mutation_p.R515*|STIM2_ENST00000465503.1_Nonsense_Mutation_p.R436*|STIM2_ENST00000382009.3_Nonsense_Mutation_p.R523*	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	428					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AACTTGTTTACGAGAACGACT	0.413																																																0			4											71	73	72					4																	27010417		2203	4300	6503	26619515	SO:0001587	stop_gained	57620			AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.1282C>T	4.37:g.27010417C>T	ENSP00000419383:p.Arg428*		26619515	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Nonsense_Mutation	SNP	ENST00000467011.1	37	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	C	43	9.836158	0.99276	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503;ENST00000473519;ENST00000477474	.	.	.	5.95	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8551	0.63522	0.3926:0.6074:0.0:0.0	.	.	.	.	X	428;523;515;428;515;436;136;30	.	ENSP00000237364:R515X	R	+	1	2	STIM2	26619515	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.254000	0.32897	1.507000	0.48752	0.563000	0.77884	CGA		0.413	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		T	27010417	C	T	27010417	4	4	110	1	0	0	0	0	0	1	0	0	15323	528	19	1	1348	1	STIM2	4	27010417	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	24055173	27010417	164143859	62	28934										
LNX1	84708	hgsc.bcm.edu	37	chr4	54344828	54344828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tctatgtgatgctccccctgCgacggtcatgccgagagatt	11	12	2	2	rs531904689		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:54344828C>T	ENST00000263925.7	-	8	1881	c.1567G>A	c.(1567-1569)Gca>Aca	p.A523T	FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Missense_Mutation_p.A427T	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	523	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A427T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			GCTCCCCCTGCGACGGTCATG	0.468																																																1	Substitution - Missense(1)	central_nervous_system(1)	4											154	148	150					4																	54344828		2203	4300	6503	54039585	SO:0001583	missense	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1567G>A	4.37:g.54344828C>T	ENSP00000263925:p.Ala523Thr		54039585	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.915949	0.73098	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.28255	1.62;1.62	4.83	3.06	0.35304	PDZ/DHR/GLGF (4);	0.152046	0.64402	D	0.000016	T	0.44623	0.1302	L	0.53561	1.675	0.58432	D	0.999999	D;D	0.60160	0.987;0.985	P;P	0.58172	0.834;0.793	T	0.46076	-0.9217	10	0.87932	D	0	.	13.9864	0.64339	0.2763:0.7237:0.0:0.0	.	523;427	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	T	427;361;523	ENSP00000302879:A427T;ENSP00000263925:A523T	ENSP00000263925:A523T	A	-	1	0	LNX1	54039585	0.999000	0.42202	0.829000	0.32907	0.676000	0.39594	4.216000	0.58540	0.715000	0.32103	-0.169000	0.13324	GCA		0.468	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			T	54344828	C	T	54344828	3	4	110	1	0	0	0	0	1	0	0	0	8889	768	27	1	635	1	LNX1	4	54344828	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	27334411	54344828	136809448	63	28935										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489581	76489581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agccattttattggccacacCgttaccttacttataggtat	6	10	0	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:76489581C>T	ENST00000311623.4	+	2	360	c.325C>T	c.(325-327)Cgt>Tgt	p.R109C	C4orf26_ENST00000435974.2_Silent_p.T123T	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	109			R -> H (in dbSNP:rs2306174).			extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTGGCCACACCGTTACCTTAC	0.458																																																0			4											181	192	188					4																	76489581		2203	4300	6503	76708605	SO:0001583	missense	152816			AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.325C>T	4.37:g.76489581C>T	ENSP00000311307:p.Arg109Cys		76708605	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	37	CCDS3569.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703585	0.48412	.	.	ENSG00000174792	ENST00000311623	T	0.35605	1.3	4.72	-9.45	0.00600	.	2.870760	0.01103	N	0.005427	T	0.20129	0.0484	N	0.19112	0.55	0.09310	N	1	D	0.56521	0.976	B	0.41723	0.365	T	0.44697	-0.9311	9	.	.	.	.	8.2179	0.31524	0.2408:0.4138:0.3455:0.0	.	109	Q17RF5	CD026_HUMAN	C	109	ENSP00000311307:R109C	.	R	+	1	0	C4orf26	76708605	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.558000	0.02164	-2.426000	0.00560	-0.971000	0.02607	CGT		0.458	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		T	76489581	C	T	76489581	3	4	110	1	0	0	0	0	1	0	0	0	2263	652	23	1	331	1	C4orf26	4	76489581	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	22144753	76489581	114664695	64	28936										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797630	76797630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gcccgtccagggaaccgctgCaggggatgctggaggacctg	17	12	0	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:76797630C>T	ENST00000286719.7	-	11	1486	c.1130G>A	c.(1129-1131)tGc>tAc	p.C377Y		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	377	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GGAACCGCTGCAGGGGATGCT	0.657																																					NSCLC(105;1359 1603 15961 44567 47947)											0			4											35	36	35					4																	76797630		2203	4300	6503	77016654	SO:0001583	missense	5470			AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1130G>A	4.37:g.76797630C>T	ENSP00000286719:p.Cys377Tyr		77016654	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	8.743	0.919360	0.17982	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.41400	1.0	5.02	5.02	0.67125	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	2.105260	0.01974	N	0.044318	T	0.46560	0.1399	N	0.14661	0.345	0.32122	N	0.587821	P;D	0.61697	0.948;0.99	B;P	0.59288	0.438;0.855	T	0.41215	-0.9521	10	0.21014	T	0.42	-8.0322	11.679	0.51446	0.0:0.8207:0.1792:0.0	.	377;377	O14830-2;O14830	.;PPE2_HUMAN	Y	377	ENSP00000286719:C377Y	ENSP00000286719:C377Y	C	-	2	0	PPEF2	77016654	0.990000	0.36364	0.935000	0.37517	0.180000	0.23129	0.816000	0.27267	2.349000	0.79799	0.491000	0.48974	TGC		0.657	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		T	76797630	C	T	76797630	3	4	110	1	0	0	0	0	1	0	0	0	12339	710	25	3	1159	3	PPEF2	4	76797630	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	308049	76797630	114356646	65	28937										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87655980	87655980	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gatgatgagacttccttattGctggcatccttggctctcca	9	11	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:87655980G>C	ENST00000411767.2	+	14	2166	c.2103G>C	c.(2101-2103)ttG>ttC	p.L701F	PTPN13_ENST00000316707.6_Missense_Mutation_p.L701F|PTPN13_ENST00000436978.1_Missense_Mutation_p.L701F|PTPN13_ENST00000511467.1_Missense_Mutation_p.L701F|PTPN13_ENST00000427191.2_Missense_Mutation_p.L701F			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	701	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CTTCCTTATTGCTGGCATCCT	0.408																																																0			4											202	195	197					4																	87655980		1917	4137	6054	87875004	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.2103G>C	4.37:g.87655980G>C	ENSP00000407249:p.Leu701Phe		87875004	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	g	14.17	2.456654	0.43634	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	5.85	0.0376	0.14197	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.38111	N	0.001813	D	0.83390	0.5244	M	0.72624	2.21	0.41668	D	0.98922	B;P;D;D	0.89917	0.376;0.859;0.999;1.0	B;P;D;D	0.77004	0.268;0.542;0.989;0.989	T	0.77424	-0.2593	10	0.38643	T	0.18	.	2.17	0.03847	0.2938:0.1964:0.4091:0.1007	.	701;701;701;701	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	F	701;701;701;701;701;669	ENSP00000408368:L701F;ENSP00000394794:L701F;ENSP00000322675:L701F;ENSP00000407249:L701F;ENSP00000426626:L701F	ENSP00000322675:L701F	L	+	3	2	PTPN13	87875004	0.121000	0.22262	0.149000	0.22428	0.991000	0.79684	-0.113000	0.10774	-0.095000	0.12351	-0.119000	0.15052	TTG		0.408	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87655980	G	C	87655980	3	2	110	1	0	0	0	0	1	0	0	0	12817	1310	46	5	2153	5	PTPN13	4	87655980	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	10858350	87655980	103498296	66	28938										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87680197	87680197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgaagatgtgacacttgttaTctctcagccaaaagaaaaga	8	7	2	5			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:87680197T>C	ENST00000411767.2	+	23	3587	c.3524T>C	c.(3523-3525)aTc>aCc	p.I1175T	PTPN13_ENST00000316707.6_Missense_Mutation_p.I984T|PTPN13_ENST00000436978.1_Missense_Mutation_p.I1175T|PTPN13_ENST00000511467.1_Missense_Mutation_p.I1175T|PTPN13_ENST00000427191.2_Missense_Mutation_p.I1156T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1175	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ACACTTGTTATCTCTCAGCCA	0.383																																																0			4											86	89	88					4																	87680197		2033	4205	6238	87899221	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3524T>C	4.37:g.87680197T>C	ENSP00000407249:p.Ile1175Thr		87899221	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.425718	0.83667	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.42	5.42	0.78866	PDZ/DHR/GLGF (4);	0.000000	0.51477	D	0.000087	T	0.70369	0.3216	M	0.86028	2.79	0.49915	D	0.999836	D;P;P;P	0.55605	0.972;0.936;0.955;0.887	P;P;P;P	0.62813	0.742;0.669;0.907;0.763	T	0.76094	-0.3085	10	0.72032	D	0.01	.	15.7586	0.78058	0.0:0.0:0.0:1.0	.	984;1156;1175;1175	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	1156;1175;984;1175;1175;1124	ENSP00000408368:I1156T;ENSP00000394794:I1175T;ENSP00000322675:I984T;ENSP00000407249:I1175T;ENSP00000426626:I1175T	ENSP00000322675:I984T	I	+	2	0	PTPN13	87899221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.256000	0.78350	2.175000	0.68902	0.477000	0.44152	ATC		0.383	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87680197	T	C	87680197	3	2	110	1	0	0	0	0	1	0	0	0	12817	1435	50	4	3610	4	PTPN13	4	87680197	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	24217	87680197	103474079	67	28939										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123302158	123302158	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgtttttaggtaattttccaGagccgttgctttccaagaat	8	7	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:123302158G>A	ENST00000296513.2	+	4	369	c.184G>A	c.(184-186)Gag>Aag	p.E62K	ADAD1_ENST00000492454.1_3'UTR|ADAD1_ENST00000388725.2_Missense_Mutation_p.E44K|ADAD1_ENST00000388724.2_Missense_Mutation_p.E62K	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	62					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TAATTTTCCAGAGCCGTTGCT	0.323																																																0			4											60	63	62					4																	123302158		2202	4300	6502	123521608	SO:0001583	missense	132612			AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.184G>A	4.37:g.123302158G>A	ENSP00000296513:p.Glu62Lys		123521608	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	37	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081063	0.36758	.	.	ENSG00000164113	ENST00000446706;ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	T;T;T	0.37411	1.2;1.21;1.22	5.23	5.23	0.72850	.	0.082845	0.49305	D	0.000152	T	0.32376	0.0827	L	0.29908	0.895	0.36460	D	0.8666	P;P	0.43826	0.818;0.722	B;B	0.43082	0.407;0.231	T	0.22730	-1.0208	10	0.27082	T	0.32	-22.7296	17.5703	0.87933	0.0:0.0:1.0:0.0	.	62;62	Q96M93-2;Q96M93	.;ADAD1_HUMAN	K	62;62;62;62;44	ENSP00000296513:E62K;ENSP00000373376:E62K;ENSP00000373377:E44K	ENSP00000296513:E62K	E	+	1	0	ADAD1	123521608	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	6.530000	0.73816	2.423000	0.82170	0.563000	0.77884	GAG		0.323	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		A	123302158	G	A	123302158	3	1	110	1	0	0	0	0	1	0	0	0	231	943	33	3	190	3	ADAD1	4	123302158	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	35621961	123302158	67852118	68	28940										
FAT1	2195	hgsc.bcm.edu	37	chr4	187539013	187539013	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggtggactatcgttgacatcGgtgacggtaacatccacaat	11	9	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr4:187539013G>A	ENST00000441802.2	-	10	8936	c.8727C>T	c.(8725-8727)acC>acT	p.T2909T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2909	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CGTTGACATCGGTGACGGTAA	0.473										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											157	146	150					4																	187539013		2012	4176	6188	187776007	SO:0001819	synonymous_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8727C>T	4.37:g.187539013G>A			187776007		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.473	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187539013	G	A	187539013	2	1	110	1	0	0	0	0	0	0	0	1	5708	1103	39	1		1	FAT1	4	187539013	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	64236855	187539013	3615263	69	28941										
ADCY2	108	hgsc.bcm.edu	37	chr5	7766870	7766870	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaacacaagcttttcagcctCaaataatcaggtggcgattc	7	10	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:7766870C>G	ENST00000338316.4	+	17	2254	c.2165C>G	c.(2164-2166)tCa>tGa	p.S722*	ADCY2_ENST00000537121.1_Nonsense_Mutation_p.S542*	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	722					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TTTTCAGCCTCAAATAATCAG	0.423																																																0			5											153	151	151					5																	7766870		2203	4300	6503	7819870	SO:0001587	stop_gained	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2165C>G	5.37:g.7766870C>G	ENSP00000342952:p.Ser722*		7819870	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Nonsense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	40	8.304944	0.98752	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	.	.	.	5.46	1.61	0.23674	.	1.434830	0.04022	N	0.299916	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	7.5499	0.27790	0.0:0.6018:0.0:0.3982	.	.	.	.	X	722;555;542	.	ENSP00000342952:S722X	S	+	2	0	ADCY2	7819870	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	0.018000	0.13422	0.249000	0.21456	0.655000	0.94253	TCA		0.423	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7766870	C	G	7766870	4	3	110	1	0	0	0	0	0	1	0	0	294	838	29	5	2231	5	ADCY2	5	7766870	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10		7766870	173148390	70	28942										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37169590	37169590	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagtggatggtaagttttgaGatgatggaattggtcctttt	13	2	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:37169590G>T	ENST00000508244.1	-	33	6629	c.6536C>A	c.(6535-6537)tCt>tAt	p.S2179Y	C5orf42_ENST00000274258.7_Missense_Mutation_p.S1059Y|C5orf42_ENST00000425232.2_Missense_Mutation_p.S2179Y			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2179						integral component of membrane (GO:0016021)		p.S1059Y(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TAAGTTTTGAGATGATGGAAT	0.408																																																1	Substitution - Missense(1)	ovary(1)	5											75	76	76					5																	37169590		2203	4300	6503	37205347	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6536C>A	5.37:g.37169590G>T	ENSP00000421690:p.Ser2179Tyr		37205347	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980334	0.74474	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.26223	1.78;1.78;1.75;1.76	5.53	4.63	0.57726	.	0.528900	0.18498	N	0.139460	T	0.39462	0.1079	L	0.52573	1.65	0.09310	N	1	D;D	0.63046	0.986;0.992	P;P	0.62813	0.684;0.907	T	0.14643	-1.0465	10	0.87932	D	0	.	9.2506	0.37554	0.077:0.1459:0.7771:0.0	.	2179;1059	E9PH94;Q9H799	.;CE042_HUMAN	Y	2179;2179;1059;1227;1059	ENSP00000421690:S2179Y;ENSP00000389014:S2179Y;ENSP00000274258:S1059Y;ENSP00000424223:S1227Y	ENSP00000274258:S1059Y	S	-	2	0	C5orf42	37205347	0.034000	0.19679	0.813000	0.32504	0.193000	0.23685	1.220000	0.32491	2.587000	0.87381	0.655000	0.94253	TCT		0.408	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37169590	G	T	37169590	3	4	110	1	0	0	0	0	1	0	0	0	2307	942	33	2	3133	2	C5orf42	5	37169590	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	29402720	37169590	143745670	71	28943										
FYB	2533	hgsc.bcm.edu	37	chr5	39202865	39202865	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttttcctcagaagaaggtttGactgccacaggtggctttgg	12	8	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:39202865G>T	ENST00000351578.6	-	2	388	c.198C>A	c.(196-198)gtC>gtA	p.V66V	FYB_ENST00000505428.1_Silent_p.V66V|FYB_ENST00000540520.1_Silent_p.V76V|FYB_ENST00000512982.1_Silent_p.V66V|FYB_ENST00000515010.1_Silent_p.V66V	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	66					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			AAGAAGGTTTGACTGCCACAG	0.517																																																0			5											51	49	49					5																	39202865		1883	4131	6014	39238622	SO:0001819	synonymous_variant	2533			U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.198C>A	5.37:g.39202865G>T			39238622	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	CCDS47200.1																																																																																				0.517	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		T	39202865	G	T	39202865	2	4	110	1	0	0	0	0	0	0	0	1	6143	1277	45	2		2	FYB	5	39202865	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2033275	39202865	141712395	72	28944										
APC	324	hgsc.bcm.edu	37	chr5	112175136	112175136	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttcattatcatctttgtcatCagctgaagatgaaataggat	7	6	5	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:112175136C>A	ENST00000457016.1	+	16	4225	c.3845C>A	c.(3844-3846)tCa>tAa	p.S1282*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.S1282*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1282*			P25054	APC_HUMAN	adenomatous polyposis coli	1282	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1282*(4)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTTTGTCATCAGCTGAAGAT	0.338		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Substitution - Nonsense(4)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											54	56	55					5																	112175136		2202	4300	6502	112203035	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3845C>A	5.37:g.112175136C>A	ENSP00000413133:p.Ser1282*		112203035	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.061518	0.98635	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.056000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6145	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1282	.	.	S	+	2	0	APC	112203035	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.861000	0.98227	0.655000	0.94253	TCA		0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175136	C	A	112175136	4	1	110	1	0	0	0	0	0	1	0	0	763	838	29	2	3903	2	APC	5	112175136	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	72972271	112175136	68740124	73	28945										
MCC	4163	hgsc.bcm.edu	37	chr5	112403879	112403879	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtaggcttcgatgcactgctCgctgaaacaaagcacatggg	12	10	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:112403879C>T	ENST00000302475.4	-	11	1920	c.1357G>A	c.(1357-1359)Gag>Aag	p.E453K	MCC_ENST00000515367.2_Splice_Site_p.E390K|MCC_ENST00000408903.3_Splice_Site_p.E643K|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	453					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ATGCACTGCTCGCTGAAACAA	0.632																																																0			5											49	48	48					5																	112403879		2202	4300	6502	112431778	SO:0001630	splice_region_variant	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1356-1G>A	5.37:g.112403879C>T			112431778	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.147496	0.77888	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.54479	0.57;0.57;0.57	5.1	5.1	0.69264	Usher syndrome type-1C protein-binding protein 1, PDZ domain (1);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	N	0.24115	0.695	0.80722	D	1	D;D;P	0.67145	0.996;0.995;0.824	D;D;B	0.71656	0.974;0.97;0.278	T	0.60398	-0.7271	10	0.37606	T	0.19	-25.3901	18.5226	0.90959	0.0:1.0:0.0:0.0	.	453;643;453	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	K	453;390;643	ENSP00000305617:E453K;ENSP00000421615:E390K;ENSP00000386227:E643K	ENSP00000305617:E453K	E	-	1	0	MCC	112431778	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.216000	0.72212	2.394000	0.81467	0.467000	0.42956	GAG		0.632	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	Missense_Mutation	T	112403879	C	T	112403879	5	4	110	1	0	0	0	0	0	0	1	0	9403	898	31	1	1160	1	MCC	5	112403879	Splice_Site	SNP	C	TCGA-EI-6506-01A-11D-1733-10	228743	112403879	68511381	74	28946										
SNX2	6643	hgsc.bcm.edu	37	chr5	122110863	122110864	+	Frame_Shift_Ins	INS	-	-	GG													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	accgactttgaggatctggaINSggacggagaggacctgttca							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:122110863_122110864insGG	ENST00000379516.2	+	1	173_174	c.65_66insGG	c.(64-69)gaggacfs	p.D23fs	SNX2_ENST00000514949.1_5'Flank|AC093267.1_ENST00000390825.1_RNA	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	23					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		GAGGATCTGGAGGACGGAGAGG	0.668																																																0			5																																								122138763	SO:0001589	frameshift_variant	6643			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.66_67dupGG	5.37:g.122110864_122110865dupGG	ENSP00000368831:p.Asp23fs		122138762	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Frame_Shift_Ins	INS	ENST00000379516.2	37	CCDS34217.1																																																																																				0.668	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		GG	122110864	-	GG	122110863	7	5	110	1	0	1	1	0	0	0	0	0	14928	304	11	0	67	0	SNX2	5	122110863	Frame_Shift_Ins	INS	-	TCGA-EI-6506-01A-11D-1733-10	9706984	122110863	58804397	75	28947										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140230198	140230198	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgatcatcgccatctgcgcGgtgtctagcctgttggttct	11	12	4	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:140230198G>A	ENST00000532602.1	+	1	3151	c.2118G>A	c.(2116-2118)gcG>gcA	p.A706A	PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.A706A|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	706					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCATCTGCGCGGTGTCTAGCC	0.667																																					Melanoma(55;1800 1972 14909)											0			5											82	74	77					5																	140230198		2196	4274	6470	140210382	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2118G>A	5.37:g.140230198G>A			140210382	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.667	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140230198	G	A	140230198	2	1	110	1	0	0	0	0	0	0	0	1	11562	1103	39	1		1	PCDHA9	5	140230198	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	18119335	140230198	40685062	76	28948										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140710662	140710662	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccccaattccagttagaggaActggagtttaaaatgaatga	9	7	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:140710662A>G	ENST00000517417.1	+	1	411	c.411A>G	c.(409-411)gaA>gaG	p.E137E	PCDHGA1_ENST00000378105.3_Silent_p.E137E|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTTAGAGGAACTGGAGTTTA	0.383																																																0			5											94	105	102					5																	140710662		2202	4300	6502	140690846	SO:0001819	synonymous_variant	56114			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.411A>G	5.37:g.140710662A>G			140690846	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																				0.383	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140710662	A	G	140710662	2	3	110	1	0	0	0	0	0	0	0	1	11581	40	2	4		4	PCDHGA1	5	140710662	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	480464	140710662	40204598	77	28949										
CCNG1	900	hgsc.bcm.edu	37	chr5	162869134	162869134	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acagaaggaatagaatgtctTcagaaacattccaaggtatg	9	6	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr5:162869134T>C	ENST00000340828.2	+	5	905	c.681T>C	c.(679-681)ctT>ctC	p.L227L	CCNG1_ENST00000511683.2_Silent_p.L93L|CCNG1_ENST00000510664.1_Silent_p.L99L|CCNG1_ENST00000504553.1_Silent_p.L93L|CCNG1_ENST00000512163.1_Silent_p.L93L|CCNG1_ENST00000393929.1_Silent_p.L227L|AC112205.1_ENST00000599797.1_Intron	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	227					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		TAGAATGTCTTCAGAAACATT	0.363																																																0			5											78	77	77					5																	162869134		2203	4299	6502	162801712	SO:0001819	synonymous_variant	900			D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.681T>C	5.37:g.162869134T>C			162801712	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Silent	SNP	ENST00000340828.2	37	CCDS4360.1																																																																																				0.363	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		C	162869134	T	C	162869134	2	2	110	1	0	0	0	0	0	0	0	1	2929	1770	62	4		4	CCNG1	5	162869134	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	22158472	162869134	18046126	78	28950										
GCM2	9247	hgsc.bcm.edu	37	chr6	10875153	10875153	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgaaatgaccactgctgtctTgattttcttctgcctagaaa	7	9	3	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:10875153T>A	ENST00000379491.4	-	5	743	c.596A>T	c.(595-597)cAa>cTa	p.Q199L	SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	199					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				ACTGCTGTCTTGATTTTCTTC	0.413																																																0			6											89	85	86					6																	10875153		2203	4300	6503	10983139	SO:0001583	missense	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.596A>T	6.37:g.10875153T>A	ENSP00000368805:p.Gln199Leu		10983139	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.524344	0.27299	.	.	ENSG00000124827	ENST00000379491	T	0.69175	-0.38	5.72	1.92	0.25849	.	0.591630	0.19001	N	0.125359	T	0.41050	0.1142	L	0.56769	1.78	0.80722	D	1	P	0.42409	0.779	B	0.35470	0.203	T	0.29610	-1.0006	10	0.51188	T	0.08	-3.4057	8.7699	0.34726	0.0:0.0643:0.3648:0.5708	.	199	O75603	GCM2_HUMAN	L	199	ENSP00000368805:Q199L	ENSP00000368805:Q199L	Q	-	2	0	GCM2	10983139	1.000000	0.71417	0.111000	0.21465	0.300000	0.27592	1.035000	0.30216	0.092000	0.17331	0.482000	0.46254	CAA		0.413	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			A	10875153	T	A	10875153	3	1	110	1	0	0	0	0	1	0	0	0	6318	1812	63	5	928	5	GCM2	6	10875153	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10		10875153	160239914	79	28951										
RNF182	221687	hgsc.bcm.edu	37	chr6	13977523	13977523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	catagactttggggactcccCacaaggtgtcattgtctgtc	10	11	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:13977523C>T	ENST00000488300.1	+	3	696	c.173C>T	c.(172-174)cCa>cTa	p.P58L	RNF182_ENST00000537388.1_Missense_Mutation_p.P58L|RNF182_ENST00000544682.1_Missense_Mutation_p.P58L|RNF182_ENST00000537663.1_Missense_Mutation_p.P58L	NM_152737.3	NP_689950.1	Q8N6D2	RN182_HUMAN	ring finger protein 182	58			P -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P58L(1)		cervix(1)|large_intestine(7)|liver(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			GGGGACTCCCCACAAGGTGTC	0.463																																																1	Substitution - Missense(1)	large_intestine(1)	6											159	151	153					6																	13977523		2203	4300	6503	14085502	SO:0001583	missense	221687			AK090576	CCDS4531.1	6p23	2013-01-09			ENSG00000180537	ENSG00000180537		"RING-type (C3HC4) zinc fingers"	28522	protein-coding gene	gene with protein product						12477932	Standard	NM_152737		Approved	MGC33993	uc003nbg.3	Q8N6D2	OTTHUMG00000014280	ENST00000488300.1:c.173C>T	6.37:g.13977523C>T	ENSP00000420465:p.Pro58Leu		14085502	B2RDG2|Q8NBG3	Missense_Mutation	SNP	ENST00000488300.1	37	CCDS4531.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426921	0.83667	.	.	ENSG00000180537	ENST00000537663;ENST00000488300;ENST00000544682;ENST00000420478;ENST00000423553;ENST00000537388	D;D;D;T;T;D	0.87966	-2.32;-2.32;-2.32;-0.18;-0.18;-2.32	5.52	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.229579	0.44688	D	0.000424	T	0.81427	0.4820	L	0.45744	1.44	0.58432	D	0.999999	P	0.45044	0.849	P	0.45998	0.5	T	0.80845	-0.1200	9	.	.	.	-9.9645	14.7335	0.69399	0.0:0.9288:0.0:0.0712	.	58	Q8N6D2	RN182_HUMAN	L	58	ENSP00000443228:P58L;ENSP00000420465:P58L;ENSP00000442021:P58L;ENSP00000419329:P58L;ENSP00000418717:P58L;ENSP00000441271:P58L	.	P	+	2	0	RNF182	14085502	0.999000	0.42202	0.942000	0.38095	0.986000	0.74619	4.552000	0.60747	2.600000	0.87896	0.563000	0.77884	CCA		0.463	RNF182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039911.2	NM_152737		T	13977523	C	T	13977523	3	4	110	1	0	0	0	0	1	0	0	0	13503	594	21	3	175	3	RNF182	6	13977523	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	3102370	13977523	157137544	80	28952										
HIST1H1T	3010	hgsc.bcm.edu	37	chr6	26107987	26107987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atttaggaatcaccttcttaCtaagcttaaaggaaccggaa	7	8	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:26107987C>T	ENST00000338379.4	-	1	377	c.335G>A	c.(334-336)aGt>aAt	p.S112N		NM_005323.3	NP_005314.2	P22492	H1T_HUMAN	histone cluster 1, H1t	112	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|nucleosome assembly (GO:0006334)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S112T(1)		breast(2)|endometrium(1)|lung(3)|ovary(2)|prostate(1)	9						CACCTTCTTACTAAGCTTAAA	0.458																																																1	Substitution - Missense(1)	ovary(1)	6											93	90	91					6																	26107987		2203	4300	6503	26215966	SO:0001583	missense	3010			M60094	CCDS34349.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000187475	ENSG00000187475		"Histones / Replication-dependent"	4720	protein-coding gene	gene with protein product		142712	"H1 histone family, member T (testis-specific)", "histone 1, H1t"	H1FT		8175896, 12408966	Standard	NM_005323		Approved	H1t	uc003ngj.3	P22492	OTTHUMG00000014430	ENST00000338379.4:c.335G>A	6.37:g.26107987C>T	ENSP00000341214:p.Ser112Asn		26215966	Q6ISI1|Q8IUE8	Missense_Mutation	SNP	ENST00000338379.4	37	CCDS34349.1	.	.	.	.	.	.	.	.	.	.	.	0.017	-1.497194	0.01001	.	.	ENSG00000187475	ENST00000338379	T	0.10099	2.91	5.38	1.3	0.21679	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.360243	0.30714	N	0.009030	T	0.00815	0.0027	N	0.02403	-0.565	0.26339	N	0.977393	B	0.11235	0.004	B	0.15484	0.013	T	0.47636	-0.9102	10	0.02654	T	1	-19.109	8.6391	0.33966	0.0:0.5711:0.0:0.4289	.	112	P22492	H1T_HUMAN	N	112	ENSP00000341214:S112N	ENSP00000341214:S112N	S	-	2	0	HIST1H1T	26215966	0.000000	0.05858	0.614000	0.29051	0.091000	0.18340	-2.693000	0.00829	0.380000	0.24823	0.655000	0.94253	AGT		0.458	HIST1H1T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040093.2	NM_005323		T	26107987	C	T	26107987	3	4	110	1	0	0	0	0	1	0	0	0	7148	565	20	3	292	3	HIST1H1T	6	26107987	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	12130464	26107987	145007080	81	28953										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323192	29323192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgagtaagttgagatgggccGtacatatgtaaagatggcgc	14	5	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:29323192G>A	ENST00000377154.1	-	4	1080	c.781C>T	c.(781-783)Cgg>Tgg	p.R261W	OR5V1_ENST00000543825.1_Missense_Mutation_p.R261W			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GAGATGGGCCGTACATATGTA	0.438																																					Ovarian(32;43 883 21137 32120 42650)											0			6											88	86	87					6																	29323192		2203	4299	6502	29431171	SO:0001583	missense	81696				CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.781C>T	6.37:g.29323192G>A	ENSP00000366359:p.Arg261Trp		29431171	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.337124	0.41398	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.37915	1.17;1.17	4.53	1.48	0.22813	GPCR, rhodopsin-like superfamily (1);	0.279943	0.18565	N	0.137514	T	0.44074	0.1276	M	0.79805	2.47	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.31194	-0.9952	10	0.72032	D	0.01	-6.5251	9.3018	0.37851	0.0:0.1216:0.417:0.4614	.	261	Q9UGF6	OR5V1_HUMAN	W	261	ENSP00000366359:R261W;ENSP00000443309:R261W	ENSP00000366356:R261W	R	-	1	2	OR5V1	29431171	0.000000	0.05858	0.019000	0.16419	0.675000	0.39556	-2.036000	0.01421	0.168000	0.19655	0.543000	0.68304	CGG		0.438	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			A	29323192	G	A	29323192	3	1	110	1	0	0	0	0	1	0	0	0	11215	1144	40	1	187	1	OR5V1	6	29323192	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3215205	29323192	141791875	82	28954										
C6orf106	64771	hgsc.bcm.edu	37	chr6	34574605	34574605	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgcggctgtgtgttgaactcCgtttcaaaagatgacagctg	12	8	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:34574605C>A	ENST00000374023.3	-	4	831	c.588G>T	c.(586-588)acG>acT	p.T196T	C6orf106_ENST00000374026.3_Silent_p.T130T|C6orf106_ENST00000374021.1_Silent_p.T122T	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	196								p.T196T(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						TGTTGAACTCCGTTTCAAAAG	0.438																																																1	Substitution - coding silent(1)	ovary(1)	6											85	76	79					6																	34574605		2203	4300	6503	34682583	SO:0001819	synonymous_variant	64771			AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.588G>T	6.37:g.34574605C>A			34682583	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Silent	SNP	ENST00000374023.3	37	CCDS4796.1																																																																																				0.438	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040251.1	NM_022758		A	34574605	C	A	34574605	2	1	110	1	0	0	0	0	0	0	0	1	2325	639	23	2		2	C6orf106	6	34574605	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5251413	34574605	136540462	83	28955										
KCNK17	89822	hgsc.bcm.edu	37	chr6	39271748	39271748	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctcaccaatcacgtagtcgcCgaagcccacggtgctgaggg	12	14	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:39271748C>T	ENST00000373231.4	-	4	905	c.673G>A	c.(673-675)Ggc>Agc	p.G225S	KCNK17_ENST00000453413.2_Missense_Mutation_p.G225S	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	225					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						ACGTAGTCGCCGAAGCCCACG	0.622																																																0			6											96	91	93					6																	39271748		2203	4300	6503	39379726	SO:0001583	missense	89822			AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.673G>A	6.37:g.39271748C>T	ENSP00000362328:p.Gly225Ser		39379726	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430356	0.83776	.	.	ENSG00000124780	ENST00000373231;ENST00000453413	D;D	0.90133	-1.65;-2.62	4.31	3.42	0.39159	Ion transport 2 (1);	0.000000	0.56097	D	0.000025	D	0.96175	0.8753	H	0.97540	4.025	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96582	0.9431	10	0.87932	D	0	.	11.6011	0.51003	0.0:0.9089:0.0:0.0911	.	225;225	E9PB46;Q96T54	.;KCNKH_HUMAN	S	225	ENSP00000362328:G225S;ENSP00000401271:G225S	ENSP00000362328:G225S	G	-	1	0	KCNK17	39379726	1.000000	0.71417	0.988000	0.46212	0.737000	0.42083	5.137000	0.64789	0.980000	0.38523	0.561000	0.74099	GGC		0.622	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		T	39271748	C	T	39271748	3	4	110	1	0	0	0	0	1	0	0	0	8085	652	23	1	465	1	KCNK17	6	39271748	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4697143	39271748	131843319	84	28956										
POLH	5429	hgsc.bcm.edu	37	chr6	43555194	43555194	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cattgaagggttgccccaagGccctacaacggcagaagaga	12	11	0	3	rs367709714		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:43555194G>T	ENST00000372236.4	+	4	753	c.458G>T	c.(457-459)gGc>gTc	p.G153V	POLH_ENST00000535400.1_Missense_Mutation_p.G91V|POLH_ENST00000372226.1_Missense_Mutation_p.G153V|RP3-337H4.8_ENST00000417591.1_RNA	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.G153D(2)		breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			TTGCCCCAAGGCCCTACAACG	0.488								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																																							2	Substitution - Missense(2)	breast(2)	6											102	87	92					6																	43555194		2203	4300	6503	43663172	SO:0001583	missense	10721	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.458G>T	6.37:g.43555194G>T	ENSP00000361310:p.Gly153Val		43663172	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	G	1.119	-0.655736	0.03480	.	.	ENSG00000170734	ENST00000372236;ENST00000535400;ENST00000372226	T;T;T	0.69806	-0.43;-0.43;-0.43	5.63	2.92	0.33932	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	1.057510	0.07300	N	0.873957	T	0.24236	0.0587	N	0.08118	0	0.20563	N	0.999888	P	0.36010	0.532	B	0.33960	0.173	T	0.15838	-1.0423	10	0.26408	T	0.33	-12.9737	10.1928	0.43037	0.2127:0.0:0.7873:0.0	.	153	Q9Y253	POLH_HUMAN	V	153;91;153	ENSP00000361310:G153V;ENSP00000442102:G91V;ENSP00000361300:G153V	ENSP00000361300:G153V	G	+	2	0	POLH	43663172	0.060000	0.20803	0.017000	0.16124	0.158000	0.22134	0.742000	0.26216	0.330000	0.23485	-0.225000	0.12378	GGC		0.488	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502		T	43555194	G	T	43555194	3	4	110	1	0	0	0	0	1	0	0	0	12233	1203	42	2	468	2	POLH	6	43555194	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	4283446	43555194	127559873	85	28957										
GPR115	221393	hgsc.bcm.edu	37	chr6	47682172	47682172	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgtcctccaaatcgatgacCgacaaagttctggactacat	7	11	1	1	rs367867105		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:47682172C>T	ENST00000283303.2	+	6	1449	c.1191C>T	c.(1189-1191)acC>acT	p.T397T	RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Silent_p.T454T|GPR115_ENST00000327753.3_Silent_p.T397T	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	397					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						AATCGATGACCGACAAAGTTC	0.483																																					GBM(22;431 510 9010 26644 32828)											0			6						C		0,4406		0,0,2203	154	119	131		1191	-10.5	0	6		131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR115	NM_153838.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		397/696	47682172	1,13005	2203	4300	6503	47790131	SO:0001819	synonymous_variant	221393			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1191C>T	6.37:g.47682172C>T			47790131	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	37	CCDS4922.2																																																																																				0.483	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		T	47682172	C	T	47682172	2	4	110	1	0	0	0	0	0	0	0	1	6652	639	23	1		1	GPR115	6	47682172	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4126978	47682172	123432895	86	28958										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51497506	51497506	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cagcaaatggcttggatcgaGctgtaaaattgactcctgtg	11	8	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:51497506G>T	ENST00000371117.3	-	65	11797	c.11522C>A	c.(11521-11523)gCt>gAt	p.A3841D		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3841					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.A3841V(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTTGGATCGAGCTGTAAAATT	0.418																																																1	Substitution - Missense(1)	ovary(1)	6											76	76	76					6																	51497506		2203	4300	6503	51605465	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11522C>A	6.37:g.51497506G>T	ENSP00000360158:p.Ala3841Asp		51605465	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.694061	0.48202	.	.	ENSG00000170927	ENST00000371117	D	0.87571	-2.27	5.69	3.58	0.41010	.	0.162496	0.41712	D	0.000834	T	0.81740	0.4886	M	0.62723	1.935	0.80722	D	1	P	0.50272	0.933	P	0.48030	0.564	D	0.83429	0.0037	10	0.72032	D	0.01	.	7.7796	0.29058	0.2521:0.0:0.7479:0.0	.	3841	P08F94	PKHD1_HUMAN	D	3841	ENSP00000360158:A3841D	ENSP00000360158:A3841D	A	-	2	0	PKHD1	51605465	0.998000	0.40836	1.000000	0.80357	0.321000	0.28281	0.621000	0.24418	1.403000	0.46800	0.650000	0.86243	GCT		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51497506	G	T	51497506	3	4	110	1	0	0	0	0	1	0	0	0	12002	971	34	2	714	2	PKHD1	6	51497506	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3815334	51497506	119617561	87	28959										
KLHL31	401265	hgsc.bcm.edu	37	chr6	53518999	53518999	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atccatcacagccacacactGattaaaacttttggctggca	6	12	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:53518999G>T	ENST00000407079.1	-	1	1071	c.1072C>A	c.(1072-1074)Cag>Aag	p.Q358K	KLHL31_ENST00000370905.3_Missense_Mutation_p.Q358K			Q9H511	KLH31_HUMAN	kelch-like family member 31	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.Q358*(1)		autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					GCCACACACTGATTAAAACTT	0.458																																																1	Substitution - Nonsense(1)	ovary(1)	6											114	109	111					6																	53518999		2203	4300	6503	53626958	SO:0001583	missense	401265				CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"Kelch-like", "BTB/POZ domain containing"	21353	protein-coding gene	gene with protein product		610749	"kelch repeat and BTB (POZ) domain containing 1", "kelch-like 31 (Drosophila)"	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1072C>A	6.37:g.53518999G>T	ENSP00000384644:p.Gln358Lys		53626958	A6N9J2|B2RP49	Missense_Mutation	SNP	ENST00000407079.1	37	CCDS34478.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895610	0.72639	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.66280	-0.2;-0.2	5.25	5.25	0.73442	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.67059	0.2853	L	0.42245	1.32	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.63097	-0.6713	10	0.31617	T	0.26	.	18.8839	0.92367	0.0:0.0:1.0:0.0	.	358	Q9H511	KLH31_HUMAN	K	358	ENSP00000359942:Q358K;ENSP00000384644:Q358K	ENSP00000359942:Q358K	Q	-	1	0	KLHL31	53626958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.467000	0.83353	0.561000	0.74099	CAG		0.458	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760		T	53518999	G	T	53518999	3	4	110	1	0	0	0	0	1	0	0	0	8406	1299	45	2	840	2	KLHL31	6	53518999	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2021493	53518999	117596068	88	28960										
DST	667	hgsc.bcm.edu	37	chr6	56497760	56497760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gacttgggattcctggctatCttccagaaaatcttcaaaac	7	10	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:56497760C>A	ENST00000361203.3	-	24	3071	c.3064G>T	c.(3064-3066)Gat>Tat	p.D1022Y	DST_ENST00000244364.6_Missense_Mutation_p.D696Y|DST_ENST00000370769.4_Missense_Mutation_p.D1022Y|DST_ENST00000421834.2_Missense_Mutation_p.D1022Y|DST_ENST00000518935.1_Missense_Mutation_p.D696Y|DST_ENST00000370754.5_Missense_Mutation_p.D1200Y|DST_ENST00000370788.2_Missense_Mutation_p.D1022Y|DST_ENST00000370765.6_Missense_Mutation_p.D696Y|DST_ENST00000312431.6_Missense_Mutation_p.D1022Y|DST_ENST00000446842.2_Missense_Mutation_p.D696Y			Q03001	DYST_HUMAN	dystonin	1022					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCCTGGCTATCTTCCAGAAAA	0.368																																																0			6											112	109	110					6																	56497760		2203	4300	6503	56605719	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3064G>T	6.37:g.56497760C>A	ENSP00000354508:p.Asp1022Tyr		56605719	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	27.9	4.870441	0.91587	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000028	T	0.62551	0.2437	M	0.84683	2.71	0.37157	D	0.902431	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.999;1.0;1.0;0.998	D;D;D;D;D;D;D;D	0.85130	0.95;0.997;0.95;0.929;0.993;0.997;0.95;0.964	T	0.66488	-0.5911	9	0.87932	D	0	.	20.2602	0.98440	0.0:1.0:0.0:0.0	.	1022;1022;1200;696;696;696;1022;696	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	Y	696;1200;1022;1022;696;1022;1022;1022;696;1062;696;696	ENSP00000244364:D696Y;ENSP00000359790:D1200Y;ENSP00000359805:D1022Y;ENSP00000400883:D1022Y;ENSP00000393645:D696Y;ENSP00000307959:D1022Y;ENSP00000359824:D1022Y;ENSP00000354508:D1022Y;ENSP00000404924:D696Y;ENSP00000431030:D1062Y;ENSP00000359801:D696Y;ENSP00000431003:D696Y	ENSP00000244364:D696Y	D	-	1	0	DST	56605719	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.427000	0.80284	2.861000	0.98227	0.655000	0.94253	GAT		0.368	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56497760	C	A	56497760	3	1	110	1	0	0	0	0	1	0	0	0	4794	913	32	2	18353	2	DST	6	56497760	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2978761	56497760	114617307	89	28961										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70900047	70900047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtttcatttgaagaaataaAgaagtatattaatcaagagg	8	2	2	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:70900047A>G	ENST00000322773.4	+	48	3158	c.3056A>G	c.(3055-3057)aAg>aGg	p.K1019R	COL19A1_ENST00000393344.1_Missense_Mutation_p.K641R	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	1019			K -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GAAGAAATAAAGAAGTATATT	0.313																																																0			6											66	67	67					6																	70900047		2203	4300	6503	70956768	SO:0001583	missense	1310				CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.3056A>G	6.37:g.70900047A>G	ENSP00000316030:p.Lys1019Arg		70956768	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.970916	0.53614	.	.	ENSG00000082293	ENST00000322773;ENST00000393344;ENST00000393333	D;D	0.91464	-2.85;-2.78	5.46	5.46	0.80206	.	0.058605	0.64402	D	0.000005	T	0.75384	0.3842	N	0.16790	0.44	0.30518	N	0.768761	B	0.34200	0.441	B	0.32465	0.146	T	0.75269	-0.3377	10	0.49607	T	0.09	.	14.6407	0.68723	1.0:0.0:0.0:0.0	.	1019	Q14993	COJA1_HUMAN	R	1019;641;94	ENSP00000316030:K1019R;ENSP00000377013:K641R	ENSP00000316030:K1019R	K	+	2	0	COL19A1	70956768	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.001000	0.63946	2.197000	0.70478	0.533000	0.62120	AAG		0.313	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			G	70900047	A	G	70900047	3	3	110	1	0	0	0	0	1	0	0	0	3682	72	3	4	3242	4	COL19A1	6	70900047	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	14402287	70900047	100215020	90	28962										
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83667113	83667113	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acagcagctccaagcaggttGcagagggcagggttagcggg	17	9	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:83667113G>T	ENST00000369747.3	-	9	1189	c.1067C>A	c.(1066-1068)gCa>gAa	p.A356E		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	356	HECT-like.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)	p.A356V(1)									CAAGCAGGTTGCAGAGGGCAG	0.463																																																1	Substitution - Missense(1)	ovary(1)	6											121	98	106					6																	83667113		2203	4300	6503	83723832	SO:0001583	missense	90025			AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1067C>A	6.37:g.83667113G>T	ENSP00000358762:p.Ala356Glu		83723832	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	37	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	G	4.893	0.166003	0.09339	.	.	ENSG00000118420	ENST00000369747	T	0.28454	1.61	5.57	4.62	0.57501	.	0.622429	0.17964	N	0.156098	T	0.06917	0.0176	N	0.22421	0.69	0.43890	D	0.996515	B	0.14438	0.01	B	0.10450	0.005	T	0.09552	-1.0669	10	0.02654	T	1	-4.8493	10.2709	0.43483	0.0:0.0:0.7082:0.2918	.	356	Q7Z6J8	UB2CB_HUMAN	E	356	ENSP00000358762:A356E	ENSP00000358762:A356E	A	-	2	0	UBE2CBP	83723832	0.937000	0.31787	0.893000	0.35052	0.982000	0.71751	3.490000	0.53245	2.628000	0.89032	0.462000	0.41574	GCA		0.463	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		T	83667113	G	T	83667113	3	4	110	1	0	0	0	0	1	0	0	0	16887	1319	46	2	110	2	UBE2CBP	6	83667113	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	12767066	83667113	87447954	91	28963										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87968046	87968046	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccattgaggaatgtagcagcTtgcctgtttttccaacgaat	9	9	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:87968046T>C	ENST00000369577.3	+	8	4742	c.4699T>C	c.(4699-4701)Ttg>Ctg	p.L1567L	ZNF292_ENST00000339907.4_Silent_p.L1562L	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1567						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		ATGTAGCAGCTTGCCTGTTTT	0.433																																																0			6											77	75	76					6																	87968046		1970	4154	6124	88024765	SO:0001819	synonymous_variant	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4699T>C	6.37:g.87968046T>C			88024765	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	37	CCDS47457.1																																																																																				0.433	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		C	87968046	T	C	87968046	2	2	110	1	0	0	0	0	0	0	0	1	17865	1606	56	4		4	ZNF292	6	87968046	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4300933	87968046	83147021	92	28964										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112508764	112508764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cgatggagagcgctgctaacCgcagtgcatcagtcaggtcc	13	12	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:112508764C>T	ENST00000230538.7	-	8	1251	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	LAMA4_ENST00000424408.2_Missense_Mutation_p.R278Q|LAMA4_ENST00000522006.1_Missense_Mutation_p.R278Q|LAMA4_ENST00000389463.4_Missense_Mutation_p.R278Q	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	285	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)	p.R278Q(1)		NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		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)		CGCTGCTAACCGCAGTGCATC	0.537																																																1	Substitution - Missense(1)	lung(1)	6											78	64	69					6																	112508764		2203	4300	6503	112615457	SO:0001583	missense	3910				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.854G>A	6.37:g.112508764C>T	ENSP00000230538:p.Arg285Gln		112615457	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.8|24.8	4.576317|4.576317	0.86645|0.86645	.|.	.|.	ENSG00000112769|ENSG00000112769	ENST00000368640|ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408;ENST00000454881;ENST00000521398;ENST00000542588	.|T;T;T;T;T	.|0.27256	.|2.6;2.63;2.63;2.63;1.68	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|0.124420	.|0.51477	.|D	.|0.000099	T|T	0.29423|0.29423	0.0733|0.0733	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	.|D;D	.|0.67145	.|0.994;0.996	.|P;P	.|0.54174	.|0.559;0.744	T|T	0.00331|0.00331	-1.1811|-1.1811	5|10	.|0.28530	.|T	.|0.3	.|.	20.2822|20.2822	0.98520|0.98520	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|285;278	.|Q16363;Q16363-2	.|LAMA4_HUMAN;.	S|Q	89|285;278;278;278;285;285;278	.|ENSP00000230538:R285Q;ENSP00000429488:R278Q;ENSP00000374114:R278Q;ENSP00000416470:R278Q;ENSP00000430336:R285Q	.|ENSP00000230538:R285Q	G|R	-|-	1|2	0|0	LAMA4|LAMA4	112615457|112615457	0.892000|0.892000	0.30473|0.30473	0.965000|0.965000	0.40720|0.40720	0.558000|0.558000	0.35554|0.35554	1.735000|1.735000	0.38176|0.38176	2.806000|2.806000	0.96561|0.96561	0.655000|0.655000	0.94253|0.94253	GGT|CGG		0.537	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		T	112508764	C	T	112508764	3	4	110	1	0	0	0	0	1	0	0	0	8630	652	23	1	4745	1	LAMA4	6	112508764	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	24540718	112508764	58606303	93	28965										
FRK	2444	hgsc.bcm.edu	37	chr6	116325073	116325073	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttctcctttttggctttcacTttctctgattagaaaggaac	6	9	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:116325073T>C	ENST00000606080.1	-	2	879	c.433A>G	c.(433-435)Agt>Ggt	p.S145G	FRK_ENST00000538210.1_5'Flank	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	145	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	TGGCTTTCACTTTCTCTGATT	0.388																																																0			6											92	85	87					6																	116325073		2203	4300	6503	116431766	SO:0001583	missense	2444			U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.433A>G	6.37:g.116325073T>C	ENSP00000476145:p.Ser145Gly		116431766	B4DY49|Q13128|Q9NTR5	Missense_Mutation	SNP	ENST00000606080.1	37	CCDS5103.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.443095	0.83993	.	.	ENSG00000111816	ENST00000368626	D	0.95035	-3.59	5.97	5.97	0.96955	SH2 motif (5);	0.000000	0.85682	D	0.000000	D	0.96744	0.8937	H	0.97829	4.085	0.80722	D	1	P	0.46859	0.885	P	0.45610	0.487	D	0.97478	1.0045	10	0.62326	D	0.03	.	16.0825	0.81014	0.0:0.0:0.0:1.0	.	145	P42685	FRK_HUMAN	G	145	ENSP00000357615:S145G	ENSP00000357615:S145G	S	-	1	0	FRK	116431766	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.897000	0.48664	2.278000	0.76064	0.533000	0.62120	AGT		0.388	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		C	116325073	T	C	116325073	3	2	110	1	0	0	0	0	1	0	0	0	6067	1609	56	4	1112	4	FRK	6	116325073	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	3816309	116325073	54789994	94	28966										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130376383	130376383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaggaaaagacgaggggattCggctgtactaaagcagggtg	17	5	0	1	rs368839890		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:130376383C>T	ENST00000529410.1	+	10	1129	c.650C>T	c.(649-651)tCg>tTg	p.S217L	L3MBTL3_ENST00000526019.1_Missense_Mutation_p.S192L|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.S192L|L3MBTL3_ENST00000361794.2_Missense_Mutation_p.S217L|L3MBTL3_ENST00000533560.1_Missense_Mutation_p.S192L|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.S217L			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	217					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.S217L(1)		cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		CGAGGGGATTCGGCTGTACTA	0.398																																																1	Substitution - Missense(1)	endometrium(1)	6						C	LEU/SER,LEU/SER	0,4406		0,0,2203	108	115	113		575,650	5.4	0	6		113	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	L3MBTL3	NM_001007102.2,NM_032438.2	145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	192/756,217/781	130376383	1,13005	2203	4300	6503	130418076	SO:0001583	missense	84456			AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.650C>T	6.37:g.130376383C>T	ENSP00000431962:p.Ser217Leu		130418076	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	37	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799260	0.50208	0.0	1.16E-4	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T	0.14766	2.49;2.48;2.49;2.48;2.48;2.49	5.39	5.39	0.77823	.	0.871122	0.10202	N	0.703320	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	B;B	0.13594	0.008;0.0	B;B	0.13407	0.009;0.0	T	0.41875	-0.9484	10	0.29301	T	0.29	.	9.1245	0.36807	0.0:0.8698:0.0:0.1302	.	192;217	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	L	217;192;217;192;192;217	ENSP00000431962:S217L;ENSP00000437185:S192L;ENSP00000354526:S217L;ENSP00000357121:S192L;ENSP00000436706:S192L;ENSP00000357118:S217L	ENSP00000354526:S217L	S	+	2	0	L3MBTL3	130418076	0.005000	0.15991	0.007000	0.13788	0.676000	0.39594	2.074000	0.41529	2.703000	0.92315	0.447000	0.29281	TCG		0.398	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		T	130376383	C	T	130376383	3	4	110	1	0	0	0	0	1	0	0	0	8615	893	31	1	672	1	L3MBTL3	6	130376383	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	14051310	130376383	40738684	95	28967										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152590380	152590380	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acgccggggctctgcgtggcTgttaggtcaacatcgctctc	13	13	3	0	rs552884641		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr6:152590380T>A	ENST00000367255.5	-	99	19216	c.18615A>T	c.(18613-18615)acA>acT	p.T6205T	SYNE1_ENST00000356820.4_Silent_p.T729T|SYNE1_ENST00000423061.1_Silent_p.T6134T|SYNE1_ENST00000448038.1_Silent_p.T6134T|SYNE1_ENST00000265368.4_Silent_p.T6205T|SYNE1_ENST00000341594.5_Silent_p.T5817T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6205					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTGCGTGGCTGTTAGGTCAA	0.542										HNSCC(10;0.0054)																																						0			6											160	125	137					6																	152590380		2203	4300	6503	152632073	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18615A>T	6.37:g.152590380T>A			152632073	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.542	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152590380	T	A	152590380	2	1	110	1	0	0	0	0	0	0	0	1	15484	1567	55	5		5	SYNE1	6	152590380	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	22213997	152590380	18524687	96	28968										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21788302	21788302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	caggctggcagcttaccttcGtggccttgaggtctttcaga	12	11	2	2	rs374342102		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:21788302G>A	ENST00000409508.3	+	52	8646	c.8615G>A	c.(8614-8616)cGt>cAt	p.R2872H	DNAH11_ENST00000328843.6_Missense_Mutation_p.R2879H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2879	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GCTTACCTTCGTGGCCTTGAG	0.572									Kartagener syndrome																																							0			7						G	HIS/ARG	0,4020		0,0,2010	101	104	103		8637	5.7	0.1	7		103	1,8361		0,1,4180	no	missense	DNAH11	NM_003777.3	29	0,1,6190	AA,AG,GG		0.012,0.0,0.0081	benign	2879/4524	21788302	1,12381	2010	4181	6191	21754827	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8615G>A	7.37:g.21788302G>A	ENSP00000475939:p.Arg2872His		21754827	Q9UJ82	Silent	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	14.28	2.489327	0.44249	0.0	1.2E-4	ENSG00000105877	ENST00000328843	T	0.39229	1.09	5.73	5.73	0.89815	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	0.146619	0.64402	D	0.000009	T	0.36608	0.0973	.	.	.	0.23841	N	0.996698	B	0.24920	0.114	B	0.14023	0.01	T	0.36792	-0.9733	9	0.87932	D	0	.	16.875	0.86050	0.0:0.1279:0.8721:0.0	.	2879	Q96DT5	DYH11_HUMAN	H	2879	ENSP00000330671:R2879H	ENSP00000330671:R2879H	R	+	2	0	DNAH11	21754827	0.786000	0.28738	0.088000	0.20740	0.153000	0.21895	4.258000	0.58822	2.692000	0.91855	0.650000	0.86243	CGT		0.572	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21788302	G	A	21788302	3	1	110	1	0	0	0	0	1	0	0	0	4610	1145	40	1	8843	1	DNAH11	7	21788302	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10		21788302	137350361	97	28969										
STARD3NL	83930	hgsc.bcm.edu	37	chr7	38256633	38256633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgtgtcttgcagttgacaaCggcagtgaccagtgcctttt	11	9	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:38256633C>T	ENST00000009041.7	+	5	646	c.389C>T	c.(388-390)aCg>aTg	p.T130M	STARD3NL_ENST00000396013.1_Missense_Mutation_p.T130M|STARD3NL_ENST00000434197.1_Intron|STARD3NL_ENST00000544203.1_Missense_Mutation_p.T123M	NM_032016.3	NP_114405.1	O95772	MENTO_HUMAN	STARD3 N-terminal like	130	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.					endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.T130M(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10						CAGTTGACAACGGCAGTGACC	0.478																																																1	Substitution - Missense(1)	ovary(1)	7											298	259	272					7																	38256633		2203	4300	6503	38223158	SO:0001583	missense	83930			AJ492267	CCDS5455.1	7p14-p13	2003-02-06			ENSG00000010270	ENSG00000010270			19169	protein-coding gene	gene with protein product		611759				12393907	Standard	NM_032016		Approved	MENTHO, MGC3251	uc003tfr.3	O95772	OTTHUMG00000023659	ENST00000009041.7:c.389C>T	7.37:g.38256633C>T	ENSP00000009041:p.Thr130Met		38223158	A4D1X0	Missense_Mutation	SNP	ENST00000009041.7	37	CCDS5455.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.884854	0.91814	.	.	ENSG00000010270	ENST00000009041;ENST00000544203;ENST00000396013;ENST00000440144;ENST00000453225;ENST00000429075	T;T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16;0.16	5.79	5.79	0.91817	MENTAL domain (2);	0.000000	0.85682	D	0.000000	T	0.81029	0.4738	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83524	0.0087	10	0.66056	D	0.02	-19.5212	18.8126	0.92064	0.0:1.0:0.0:0.0	.	130	O95772	MENTO_HUMAN	M	130;123;130;130;130;130	ENSP00000009041:T130M;ENSP00000439436:T123M;ENSP00000379334:T130M;ENSP00000411933:T130M;ENSP00000395455:T130M;ENSP00000402028:T130M	ENSP00000009041:T130M	T	+	2	0	STARD3NL	38223158	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.202000	0.77856	2.739000	0.93911	0.655000	0.94253	ACG		0.478	STARD3NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226929.2			T	38256633	C	T	38256633	3	4	110	1	0	0	0	0	1	0	0	0	15297	536	19	1	403	1	STARD3NL	7	38256633	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	16468331	38256633	120882030	98	28970										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44560626	44560626	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgttgggccggtcgttcagGaaccagggaagatacttatg	14	7	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:44560626G>C	ENST00000289547.4	-	13	3100	c.3045C>G	c.(3043-3045)ttC>ttG	p.F1015L	NPC1L1_ENST00000381160.3_Missense_Mutation_p.F1015L|NPC1L1_ENST00000546276.1_Missense_Mutation_p.F969L	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1015					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GGTCGTTCAGGAACCAGGGAA	0.537																																																0			7											159	162	161					7																	44560626		2203	4300	6503	44527151	SO:0001583	missense	29881				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3045C>G	7.37:g.44560626G>C	ENSP00000289547:p.Phe1015Leu		44527151	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	37	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253233	0.59212	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.96940	-4.18;-4.17;-4.17	5.35	1.98	0.26296	.	0.115066	0.64402	D	0.000016	D	0.97974	0.9333	M	0.93550	3.43	0.42774	D	0.993849	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.983;0.996;0.997	D	0.96551	0.9408	10	0.66056	D	0.02	-32.5644	5.5738	0.17212	0.5377:0.0:0.4623:0.0	.	969;1015;1015;1015	B7ZLE6;Q17RV5;D3DVK9;Q9UHC9	.;.;.;NPCL1_HUMAN	L	1015;1015;969	ENSP00000289547:F1015L;ENSP00000370552:F1015L;ENSP00000438033:F969L	ENSP00000289547:F1015L	F	-	3	2	NPC1L1	44527151	0.997000	0.39634	0.996000	0.52242	0.495000	0.33615	0.347000	0.20014	0.591000	0.29711	0.650000	0.86243	TTC		0.537	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		C	44560626	G	C	44560626	3	2	110	1	0	0	0	0	1	0	0	0	10602	1165	41	5	1066	5	NPC1L1	7	44560626	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	6303993	44560626	114578037	99	28971										
GTF2IRD2	84163	hgsc.bcm.edu	37	chr7	74211463	74211463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agattattcctcgtcaaatgAgtctcccagaggcacagttt	8	10	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:74211463A>G	ENST00000405086.2	-	16	2577	c.2388T>C	c.(2386-2388)acT>acC	p.T796T	GTF2IRD2_ENST00000451013.2_Silent_p.T343T	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	796					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						tcgtcaaatgagtctcccaga	0.493																																					NSCLC(40;560 1096 7501 40315 49546)											0			7											58	61	60					7																	74211463		2198	4293	6491	73849399	SO:0001819	synonymous_variant	84163			BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"transcription factor GTF2IRD2"	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.2388T>C	7.37:g.74211463A>G			73849399	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Silent	SNP	ENST00000405086.2	37	CCDS5576.1																																																																																				0.493	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537		G	74211463	A	G	74211463	2	3	110	1	0	0	0	0	0	0	0	1	6890	291	11	4		4	GTF2IRD2	7	74211463	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	29650837	74211463	84927200	100	28972										
SRCRB4D	136853	hgsc.bcm.edu	37	chr7	76024570	76024570	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tggagggctgagctctttacCggacggatctgtctgccaag	14	10	3	1	rs199812860		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:76024570C>T	ENST00000275560.3	-	7	1293	c.946G>A	c.(946-948)Gct>Act	p.A316T	SRCRB4D_ENST00000492979.2_5'Flank|ZP3_ENST00000336517.4_5'Flank	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						AGCTCTTTACCGGACGGATCT	0.627																																																0			7											75	71	72					7																	76024570		2203	4300	6503	75862506	SO:0001630	splice_region_variant	136853																														ENST00000275560.3:c.946+1G>A	7.37:g.76024570C>T			75862506		Missense_Mutation	SNP	ENST00000275560.3	37	CCDS5585.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.255471	0.22965	.	.	ENSG00000146700	ENST00000275560	T	0.01221	5.15	4.03	4.03	0.46877	.	0.499017	0.19682	N	0.108481	T	0.01320	0.0043	L	0.27053	0.805	0.32662	N	0.51801	B	0.22480	0.07	B	0.08055	0.003	T	0.37056	-0.9722	9	.	.	.	.	11.9696	0.53055	0.0:1.0:0.0:0.0	.	316	Q8WTU2	SRB4D_HUMAN	T	316	ENSP00000275560:A316T	.	A	-	1	0	SRCRB4D	75862506	0.994000	0.37717	0.860000	0.33809	0.040000	0.13550	3.481000	0.53179	2.523000	0.85059	0.655000	0.94253	GCT		0.627	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3		Missense_Mutation	T	76024570	C	T	76024570	5	4	110	1	0	0	0	0	0	0	1	0	15176	666	23	1	801	1	SRCRB4D	7	76024570	Splice_Site	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1813107	76024570	83114093	101	28973										
DTX2	113878	hgsc.bcm.edu	37	chr7	76111908	76111908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tctgggagtggctgagcgacGatggctcctggactgcctat	15	10	1	1	rs146593354		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:76111908G>A	ENST00000324432.5	+	5	862	c.352G>A	c.(352-354)Gat>Aat	p.D118N	DTX2_ENST00000446820.2_Missense_Mutation_p.D118N|DTX2_ENST00000472426.1_3'UTR|DTX2_ENST00000413936.2_Missense_Mutation_p.D118N|DTX2_ENST00000446600.1_Missense_Mutation_p.D27N|DTX2_ENST00000307569.8_Missense_Mutation_p.D118N|DTX2_ENST00000430490.2_Missense_Mutation_p.D118N	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	118	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.				Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D118Y(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCTGAGCGACGATGGCTCCTG	0.617																																																1	Substitution - Missense(1)	ovary(1)	7											52	51	51					7																	76111908		2203	4300	6503	75949844	SO:0001583	missense	113878				CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"RING-type (C3HC4) zinc fingers"	15973	protein-coding gene	gene with protein product		613141	"deltex (Drosophila) homolog 2", "deltex homolog 2 (Drosophila)"			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.352G>A	7.37:g.76111908G>A	ENSP00000322885:p.Asp118Asn		75949844	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	10.77	1.445270	0.25987	.	.	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000423646;ENST00000430490;ENST00000446820	T;T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23;1.23	5.41	5.41	0.78517	WWE domain (2);WWE domain, subgroup (1);	0.054241	0.64402	D	0.000001	T	0.24470	0.0593	N	0.19112	0.55	0.41193	D	0.98631	B;B;B	0.27286	0.174;0.165;0.153	B;B;B	0.24006	0.011;0.03;0.05	T	0.07424	-1.0773	10	0.09084	T	0.74	-18.442	18.1599	0.89705	0.0:0.0:1.0:0.0	.	27;118;118	F5GX89;Q86UW9-2;Q86UW9	.;.;DTX2_HUMAN	N	118;118;27;27;118;118;118;118	ENSP00000322885:D118N;ENSP00000305242:D118N;ENSP00000397648:D27N;ENSP00000390218:D118N;ENSP00000415838:D118N;ENSP00000411986:D118N;ENSP00000392545:D118N	ENSP00000305242:D118N	D	+	1	0	AC005522.1	75949844	1.000000	0.71417	0.954000	0.39281	0.247000	0.25773	6.399000	0.73248	2.552000	0.86080	0.561000	0.74099	GAT		0.617	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			A	76111908	G	A	76111908	3	1	110	1	0	0	0	0	1	0	0	0	4805	1058	37	1	358	1	DTX2	7	76111908	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	87338	76111908	83026755	102	28974										
PCLO	27445	hgsc.bcm.edu	37	chr7	82580730	82580730	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtggaatactgtggggtactAatcccagctcctgaaatgac	11	9	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:82580730A>C	ENST00000333891.9	-	6	9511	c.9174T>G	c.(9172-9174)atT>atG	p.I3058M	PCLO_ENST00000423517.2_Missense_Mutation_p.I3058M|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTGGGGTACTAATCCCAGCTC	0.448																																																0			7											101	94	96					7																	82580730		1908	4122	6030	82418666	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9174T>G	7.37:g.82580730A>C	ENSP00000334319:p.Ile3058Met		82418666		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	6.321	0.427415	0.11987	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20200	2.09;2.09	5.58	5.58	0.84498	.	.	.	.	.	T	0.29158	0.0725	L	0.35723	1.085	0.80722	D	1	P;D;D	0.59357	0.838;0.985;0.985	B;P;P	0.58391	0.293;0.838;0.838	T	0.03597	-1.1021	9	0.87932	D	0	.	8.7176	0.34421	0.8817:0.0:0.1183:0.0	.	2989;3058;3058	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	M	2989;3058;3058	ENSP00000334319:I3058M;ENSP00000388393:I3058M	ENSP00000334319:I3058M	I	-	3	3	PCLO	82418666	0.994000	0.37717	1.000000	0.80357	0.995000	0.86356	0.426000	0.21363	2.128000	0.65567	0.460000	0.39030	ATT		0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82580730	A	C	82580730	3	2	110	1	0	0	0	0	1	0	0	0	11614	358	13	4	6351	4	PCLO	7	82580730	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	6468822	82580730	76557933	103	28975										
SGCE	8910	hgsc.bcm.edu	37	chr7	94248262	94248262	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	attctgcttgatatggcaacGggaagtctaattttggtgaa	11	5	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:94248262G>T	ENST00000265735.7	-	5	580	c.470C>A	c.(469-471)cCg>cAg	p.P157Q	SGCE_ENST00000437425.2_Missense_Mutation_p.P116Q|SGCE_ENST00000428696.2_Missense_Mutation_p.P157Q|SGCE_ENST00000445866.2_Missense_Mutation_p.P157Q|SGCE_ENST00000447873.1_Missense_Mutation_p.P157Q|SGCE_ENST00000415788.2_Missense_Mutation_p.P193Q	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	157					cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)	p.P157L(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	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)			ATATGGCAACGGGAAGTCTAA	0.358																																																1	Substitution - Missense(1)	ovary(1)	7											82	75	77					7																	94248262		2203	4300	6503	94086198	SO:0001583	missense	8910			AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.470C>A	7.37:g.94248262G>T	ENSP00000265735:p.Pro157Gln		94086198	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Missense_Mutation	SNP	ENST00000265735.7	37	CCDS5637.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575715	0.45902	.	.	ENSG00000127990	ENST00000265735;ENST00000445866;ENST00000437425;ENST00000447873;ENST00000428696;ENST00000415788	D;D;D;D;D;D	0.98264	-4.44;-4.45;-4.83;-4.49;-4.49;-4.45	5.54	4.64	0.57946	Dystroglycan-type cadherin-like (1);	0.047393	0.85682	D	0.000000	D	0.97583	0.9208	L	0.31664	0.95	0.80722	D	1	D;D;P;B;D	0.89917	1.0;0.996;0.467;0.355;1.0	D;D;P;B;D	0.97110	1.0;0.93;0.527;0.191;0.999	D	0.96248	0.9181	10	0.18710	T	0.47	-9.3439	13.8781	0.63665	0.0767:0.0:0.9233:0.0	.	193;116;157;157;157	B7Z2R4;E9PEH6;E9PF60;G5E9K6;O43556	.;.;.;.;SGCE_HUMAN	Q	157;157;116;157;157;193	ENSP00000265735:P157Q;ENSP00000398930:P157Q;ENSP00000394061:P116Q;ENSP00000388734:P157Q;ENSP00000397536:P157Q;ENSP00000405313:P193Q	ENSP00000265735:P157Q	P	-	2	0	SGCE	94086198	1.000000	0.71417	0.974000	0.42286	0.977000	0.68977	5.770000	0.68873	1.418000	0.47098	0.655000	0.94253	CCG		0.358	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			T	94248262	G	T	94248262	3	4	110	1	0	0	0	0	1	0	0	0	14239	1116	39	2	1023	2	SGCE	7	94248262	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	11667532	94248262	64890401	104	28976										
CNPY4	245812	hgsc.bcm.edu	37	chr7	99722184	99722184	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gacattgtgggagactggtaCttccaccatcaggagcagcc	12	11	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:99722184C>T	ENST00000262932.3	+	5	645	c.513C>T	c.(511-513)taC>taT	p.Y171Y	CNPY4_ENST00000480692.1_3'UTR|RP11-506M12.1_ENST00000494221.1_RNA|MBLAC1_ENST00000398075.2_5'Flank	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	171	Glu-rich.					extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAGACTGGTACTTCCACCATC	0.507																																																0			7											105	103	104					7																	99722184		2203	4300	6503	99560120	SO:0001819	synonymous_variant	245812			AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"protein associated with TLR4"	610047	"canopy 4 homolog (zebrafish)"			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.513C>T	7.37:g.99722184C>T			99560120	Q8WUN9	Silent	SNP	ENST00000262932.3	37	CCDS34701.1																																																																																				0.507	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		T	99722184	C	T	99722184	2	4	110	1	0	0	0	0	0	0	0	1	3636	576	20	3		3	CNPY4	7	99722184	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5473922	99722184	59416479	105	28977										
EPHB4	2050	hgsc.bcm.edu	37	chr7	100410422	100410422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaactctgtgagaatcatgaCgggcatgctgttggtgacca	13	8	2	3	rs529340542		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:100410422C>T	ENST00000358173.3	-	12	2533	c.2065G>A	c.(2065-2067)Gtc>Atc	p.V689I	EPHB4_ENST00000360620.3_Missense_Mutation_p.V689I|EPHB4_ENST00000477446.1_5'Flank	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	689	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V689I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGAATCATGACGGGCATGCTG	0.627																																					GBM(200;2113 3072 25865 52728)											1	Substitution - Missense(1)	ovary(1)	7											88	84	85					7																	100410422		2203	4300	6503	100248358	SO:0001583	missense	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.2065G>A	7.37:g.100410422C>T	ENSP00000350896:p.Val689Ile		100248358	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048239	0.55110	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.61859	0.07;0.07	4.79	4.79	0.61399	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000166	T	0.53916	0.1826	N	0.02802	-0.49	0.54753	D	0.999981	D;D	0.89917	0.996;1.0	D;D	0.79108	0.97;0.992	T	0.67730	-0.5595	10	0.56958	D	0.05	.	15.6721	0.77286	0.0:1.0:0.0:0.0	.	689;689	Q96L35;P54760	.;EPHB4_HUMAN	I	689	ENSP00000353833:V689I;ENSP00000350896:V689I	ENSP00000350896:V689I	V	-	1	0	EPHB4	100248358	0.997000	0.39634	0.934000	0.37439	0.028000	0.11728	3.649000	0.54417	2.368000	0.80403	0.650000	0.86243	GTC		0.627	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		T	100410422	C	T	100410422	3	4	110	1	0	0	0	0	1	0	0	0	5190	536	19	1	922	1	EPHB4	7	100410422	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	688238	100410422	58728241	106	28978										
MYL10	93408	hgsc.bcm.edu	37	chr7	101267528	101267528	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cggtgccttctgctcttttcCgagctcttctcggtgcctgc	10	15	4	0	rs143165987		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:101267528C>A	ENST00000223167.4	-	2	272	c.95G>T	c.(94-96)cGg>cTg	p.R32L		NM_138403.4	NP_612412.2	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	32						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)	p.R32Q(1)		breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	12						TGCTCTTTTCCGAGCTCTTCT	0.612																																					Esophageal Squamous(24;575 709 17516 40384 51639)											1	Substitution - Missense(1)	ovary(1)	7											113	109	111					7																	101267528		2203	4300	6503	101054248	SO:0001583	missense	93408			BC002778	CCDS34713.1	7q22.1	2013-01-10			ENSG00000106436	ENSG00000106436		"Myosins / Light chain", "EF-hand domain containing"	29825	protein-coding gene	gene with protein product						1628631	Standard	NM_138403		Approved	MGC3479, MYLC2PL, PLRLC	uc003uyr.3	Q9BUA6	OTTHUMG00000157137	ENST00000223167.4:c.95G>T	7.37:g.101267528C>A	ENSP00000223167:p.Arg32Leu		101054248		Missense_Mutation	SNP	ENST00000223167.4	37	CCDS34713.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403682	0.62288	.	.	ENSG00000106436	ENST00000223167	T	0.72942	-0.7	4.71	3.56	0.40772	.	0.088290	0.42964	D	0.000638	T	0.64216	0.2578	L	0.46157	1.445	0.33134	D	0.543545	B	0.33826	0.427	B	0.42214	0.38	T	0.72017	-0.4417	10	0.66056	D	0.02	.	4.1434	0.10205	0.0:0.6769:0.0:0.3231	.	32	Q9BUA6	MYL10_HUMAN	L	32	ENSP00000223167:R32L	ENSP00000223167:R32L	R	-	2	0	MYL10	101054248	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	5.783000	0.68982	2.339000	0.79563	0.561000	0.74099	CGG		0.612	MYL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347575.1	NM_138403		A	101267528	C	A	101267528	3	1	110	1	0	0	0	0	1	0	0	0	10074	652	23	2	613	2	MYL10	7	101267528	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	857106	101267528	57871135	107	28979										
TFEC	22797	hgsc.bcm.edu	37	chr7	115594643	115594643	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaaaaatatatactcactgaGgttgtggttgtccttttttt	8	5	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:115594643G>T	ENST00000265440.7	-	5	616	c.436C>A	c.(436-438)Ctc>Atc	p.L146I	TFEC_ENST00000393485.1_Missense_Mutation_p.L117I|TFEC_ENST00000484212.1_Missense_Mutation_p.L236I|TFEC_ENST00000320239.7_Missense_Mutation_p.L117I|TFEC_ENST00000457268.1_Missense_Mutation_p.L79I	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	146	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		L -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.L146V(1)		NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			TACTCACTGAGGTTGTGGTTG	0.303																																																1	Substitution - Missense(1)	large_intestine(1)	7											143	140	141					7																	115594643		2202	4300	6502	115381879	SO:0001583	missense	22797			D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"Basic helix-loop-helix proteins"	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.436C>A	7.37:g.115594643G>T	ENSP00000265440:p.Leu146Ile		115381879	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Missense_Mutation	SNP	ENST00000265440.7	37	CCDS5762.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733275	0.89482	.	.	ENSG00000105967	ENST00000265440;ENST00000457268;ENST00000320239;ENST00000393485;ENST00000484212	D;D;D;D;D	0.97772	-4.53;-4.53;-4.53;-4.53;-4.53	5.66	5.66	0.87406	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.97870	0.9300	L	0.33093	0.98	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.984;0.999	D;D;D;D	0.91635	0.999;0.998;0.926;0.999	D	0.98611	1.0663	10	0.56958	D	0.05	.	20.1225	0.97967	0.0:0.0:1.0:0.0	.	236;117;117;146	B7Z757;O14948-3;O14948-2;O14948	.;.;.;TFEC_HUMAN	I	146;79;117;117;236	ENSP00000265440:L146I;ENSP00000387650:L79I;ENSP00000318676:L117I;ENSP00000377125:L117I;ENSP00000417432:L236I	ENSP00000265440:L146I	L	-	1	0	TFEC	115381879	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.034000	0.64152	2.831000	0.97527	0.650000	0.86243	CTC		0.303	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252		T	115594643	G	T	115594643	3	4	110	1	0	0	0	0	1	0	0	0	15841	1000	35	2	623	2	TFEC	7	115594643	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	14327115	115594643	43544020	108	28980										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136699656	136699656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taacaatagcctggctcttaCaagtccttataagacatttg	6	9	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:136699656C>T	ENST00000445907.2	+	3	572	c.44C>T	c.(43-45)aCa>aTa	p.T15I	hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.T15I|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.T15I|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.T15I|CHRM2_ENST00000401861.1_Missense_Mutation_p.T15I|CHRM2_ENST00000320658.5_Missense_Mutation_p.T15I	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	15					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.T15R(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CTGGCTCTTACAAGTCCTTAT	0.398																																																1	Substitution - Missense(1)	ovary(1)	7											100	99	99					7																	136699656		2203	4300	6503	136350196	SO:0001583	missense	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.44C>T	7.37:g.136699656C>T	ENSP00000399745:p.Thr15Ile		136350196	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	C	4.467	0.086539	0.08583	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.33	2.32	0.28847	.	0.788603	0.11693	N	0.538671	T	0.19886	0.0478	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.20107	-1.0285	10	0.29301	T	0.29	-8.0095	11.8381	0.52338	0.1273:0.4324:0.4402:0.0	.	15	P08172	ACM2_HUMAN	I	15	ENSP00000399745:T15I;ENSP00000415386:T15I;ENSP00000319984:T15I;ENSP00000380733:T15I;ENSP00000384937:T15I;ENSP00000384401:T15I	ENSP00000319984:T15I	T	+	2	0	CHRM2	136350196	0.749000	0.28305	0.996000	0.52242	0.806000	0.45545	-0.067000	0.11579	0.614000	0.30107	-1.250000	0.01514	ACA		0.398	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136699656	C	T	136699656	3	4	110	1	0	0	0	0	1	0	0	0	3383	478	17	3	46	3	CHRM2	7	136699656	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	21105013	136699656	22439007	109	28981										
OR6B1	135946	hgsc.bcm.edu	37	chr7	143701918	143701918	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaattatttccatcttctatGccattgtcactccttctctc	2	13	4	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr7:143701918G>A	ENST00000408922.2	+	1	897	c.829G>A	c.(829-831)Gcc>Acc	p.A277T		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					CATCTTCTATGCCATTGTCAC	0.423																																																0			7											104	99	100					7																	143701918		1940	4128	6068	143332851	SO:0001583	missense	135946				CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"GPCR / Class A : Olfactory receptors"	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.829G>A	7.37:g.143701918G>A	ENSP00000386151:p.Ala277Thr		143332851	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	.	.	.	.	.	.	.	.	.	.	G	1.397	-0.579286	0.03854	.	.	ENSG00000221813	ENST00000408922	T	0.00021	9.02	5.15	3.3	0.37823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36665	U	0.002475	T	0.00039	0.0001	N	0.00554	-1.385	0.23533	N	0.997478	B	0.06786	0.001	B	0.14578	0.011	T	0.24870	-1.0148	10	0.02654	T	1	.	7.3069	0.26453	0.2674:0.0:0.7326:0.0	.	277	O95007	OR6B1_HUMAN	T	277	ENSP00000386151:A277T	ENSP00000386151:A277T	A	+	1	0	OR6B1	143332851	0.000000	0.05858	1.000000	0.80357	0.999000	0.98932	-0.347000	0.07750	1.397000	0.46682	0.655000	0.94253	GCC		0.423	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1			A	143701918	G	A	143701918	3	1	110	1	0	0	0	0	1	0	0	0	11218	1319	46	3	831	3	OR6B1	7	143701918	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	7002262	143701918	15436745	110	28982										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3245034	3245034	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	accgtcgcagctgggcaaggCgtggttccactggtggttcc	15	12	0	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:3245034C>T	ENST00000520002.1	-	19	3322	c.2767G>A	c.(2767-2769)Gcc>Acc	p.A923T	CSMD1_ENST00000602723.1_Missense_Mutation_p.A923T|CSMD1_ENST00000537824.1_Missense_Mutation_p.A922T|CSMD1_ENST00000602557.1_Missense_Mutation_p.A923T|CSMD1_ENST00000539096.1_Missense_Mutation_p.A922T|CSMD1_ENST00000542608.1_Missense_Mutation_p.A922T|CSMD1_ENST00000400186.3_Missense_Mutation_p.A923T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	923	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.A409S(3)		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)		CTGGGCAAGGCGTGGTTCCAC	0.582																																																3	Substitution - Missense(3)	breast(3)	8											40	46	44					8																	3245034		2112	4223	6335	3232441	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2767G>A	8.37:g.3245034C>T	ENSP00000430733:p.Ala923Thr		3232441	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.38|18.38	3.610420|3.610420	0.66558|0.66558	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.64803|.	-0.12;-0.12;-0.12;-0.12;-0.12|.	5.11|5.11	5.11|5.11	0.69529|0.69529	Complement control module (2);Sushi/SCR/CCP (3);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.48732|0.48732	0.1516|0.1516	N|N	0.17474|0.17474	0.49|0.49	0.42742|0.42742	D|D	0.993749|0.993749	D;D;P|.	0.89917|.	1.0;0.974;0.952|.	D;P;B|.	0.87578|.	0.998;0.766;0.388|.	T|T	0.45366|0.45366	-0.9266|-0.9266	10|5	0.30078|.	T|.	0.28|.	.|.	14.1803|14.1803	0.65568|0.65568	0.0:0.8502:0.1497:0.0|0.0:0.8502:0.1497:0.0	.|.	923;923;923|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	T|H	923;923;785;922;922;922|402	ENSP00000383047:A923T;ENSP00000430733:A923T;ENSP00000441462:A922T;ENSP00000446243:A922T;ENSP00000441675:A922T|.	ENSP00000320445:A785T|.	A|R	-|-	1|2	0|0	CSMD1|CSMD1	3232441|3232441	0.976000|0.976000	0.34144|0.34144	0.744000|0.744000	0.31058|0.31058	0.736000|0.736000	0.42039|0.42039	2.452000|2.452000	0.44961|0.44961	2.374000|2.374000	0.81015|0.81015	0.650000|0.650000	0.86243|0.86243	GCC|CGC		0.582	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3245034	C	T	3245034	3	4	110	1	0	0	0	0	1	0	0	0	3950	768	27	1	8142	1	CSMD1	8	3245034	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10		3245034	143118988	111	28983										
CSGALNACT1	55790	hgsc.bcm.edu	37	chr8	19362934	19362934	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgcatactctgtggccagctTgacgccagcattcacctctg	9	14	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:19362934T>G	ENST00000454498.2	-	4	1425	c.412A>C	c.(412-414)Aag>Cag	p.K138Q	CSGALNACT1_ENST00000311540.4_Missense_Mutation_p.K138Q|CSGALNACT1_ENST00000544602.1_Missense_Mutation_p.K138Q|CSGALNACT1_ENST00000522854.1_Missense_Mutation_p.K138Q|CSGALNACT1_ENST00000332246.6_Missense_Mutation_p.K138Q	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	138					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		GTGGCCAGCTTGACGCCAGCA	0.607																																																0			8											71	69	69					8																	19362934		2203	4300	6503	19407214	SO:0001583	missense	55790			AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"Beta 4-glycosyltransferases"	24290	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase"					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.412A>C	8.37:g.19362934T>G	ENSP00000411816:p.Lys138Gln		19407214	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Missense_Mutation	SNP	ENST00000454498.2	37	CCDS6010.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.097428	0.37048	.	.	ENSG00000147408	ENST00000454498;ENST00000332246;ENST00000311540;ENST00000522854;ENST00000544602	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	5.74	5.74	0.90152	.	0.176323	0.51477	D	0.000088	T	0.41259	0.1151	M	0.79123	2.44	0.40918	D	0.98428	P	0.44429	0.835	P	0.49477	0.612	T	0.28299	-1.0048	10	0.23891	T	0.37	-45.7961	15.1655	0.72821	0.0:0.0:0.0:1.0	.	138	Q8TDX6	CGAT1_HUMAN	Q	138	ENSP00000411816:K138Q;ENSP00000330805:K138Q;ENSP00000310891:K138Q;ENSP00000429809:K138Q;ENSP00000442155:K138Q	ENSP00000310891:K138Q	K	-	1	0	CSGALNACT1	19407214	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.874000	0.48483	2.317000	0.78254	0.460000	0.39030	AAG		0.607	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371		G	19362934	T	G	19362934	3	3	110	1	0	0	0	0	1	0	0	0	3944	1821	63	4	1214	4	CSGALNACT1	8	19362934	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	16117900	19362934	127001088	112	28984										
NPBWR1	2831	hgsc.bcm.edu	37	chr8	53853198	53853198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccacgccaaggccctggagcGcgccaagaagcgggtgacct	14	15	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:53853198G>A	ENST00000331251.3	+	1	2208	c.731G>A	c.(730-732)cGc>cAc	p.R244H		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	244					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCCTGGAGCGCGCCAAGAAG	0.667																																																0			8											40	22	28					8																	53853198		2202	4295	6497	54015751	SO:0001583	missense	2831			BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"GPCR / Class A : Neuropeptide receptors : W/B"	4522	protein-coding gene	gene with protein product		600730	"G protein-coupled receptor 7"	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.731G>A	8.37:g.53853198G>A	ENSP00000330284:p.Arg244His		54015751	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	g	27.4	4.828504	0.90955	.	.	ENSG00000183729	ENST00000331251	T	0.41400	1.0	5.32	5.32	0.75619	GPCR, rhodopsin-like superfamily (1);	0.156269	0.28977	N	0.013528	T	0.57227	0.2039	M	0.69523	2.12	0.42411	D	0.992608	D	0.89917	1.0	D	0.67548	0.952	T	0.61671	-0.7015	10	0.87932	D	0	.	6.389	0.21576	0.209:0.0:0.791:0.0	.	244	P48145	NPBW1_HUMAN	H	244	ENSP00000330284:R244H	ENSP00000330284:R244H	R	+	2	0	NPBWR1	54015751	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.997000	0.76270	2.769000	0.95229	0.651000	0.88453	CGC		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285		A	53853198	G	A	53853198	3	1	110	1	0	0	0	0	1	0	0	0	10599	1087	38	1	733	1	NPBWR1	8	53853198	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	34490264	53853198	92510824	113	28985										
ASPH	444	hgsc.bcm.edu	37	chr8	62556507	62556507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttttaacatttacaaacctgGattttcctgctcagacatca	4	10	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:62556507G>A	ENST00000379454.4	-	8	893	c.706C>T	c.(706-708)Cca>Tca	p.P236S	ASPH_ENST00000522835.1_Missense_Mutation_p.P179S|ASPH_ENST00000518068.1_Missense_Mutation_p.P193S|ASPH_ENST00000517847.2_Missense_Mutation_p.P222S|ASPH_ENST00000445642.3_Missense_Mutation_p.P222S|ASPH_ENST00000523897.1_5'Flank|ASPH_ENST00000541428.1_Missense_Mutation_p.P207S|ASPH_ENST00000517903.1_Missense_Mutation_p.P222S|ASPH_ENST00000356457.5_Missense_Mutation_p.P236S|ASPH_ENST00000522919.1_Missense_Mutation_p.P49S	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	236	Glu-rich.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	TACAAACCTGGATTTTCCTGC	0.343																																																0			8											77	75	76					8																	62556507		2203	4298	6501	62719061	SO:0001583	missense	444			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.706C>T	8.37:g.62556507G>A	ENSP00000368767:p.Pro236Ser		62719061	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	37	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	G	6.383	0.438689	0.12104	.	.	ENSG00000198363	ENST00000541428;ENST00000379454;ENST00000522919;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000445642;ENST00000517847;ENST00000522835	T;T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.22	2.41	0.29592	Aspartyl beta-hydroxylase/Triadin domain (1);	0.583989	0.17262	N	0.180736	T	0.38878	0.1057	L	0.34521	1.04	0.24473	N	0.994383	B;P;B;P;B;B;B	0.39601	0.407;0.68;0.072;0.549;0.06;0.34;0.147	B;P;B;B;B;B;B	0.44860	0.338;0.462;0.04;0.18;0.046;0.364;0.067	T	0.15607	-1.0431	10	0.33141	T	0.24	.	7.3229	0.26539	0.2626:0.0:0.7374:0.0	.	179;222;207;193;236;222;236	B4DIC9;B7ZM95;F5H667;Q8TB28;Q12797-2;Q9H291;Q12797	.;.;.;.;.;.;ASPH_HUMAN	S	207;236;49;236;251;193;222;222;222;179	ENSP00000437864:P207S;ENSP00000368767:P236S;ENSP00000430516:P49S;ENSP00000348841:P236S;ENSP00000427823:P251S;ENSP00000429286:P193S;ENSP00000430245:P222S;ENSP00000394013:P222S;ENSP00000429954:P222S;ENSP00000429160:P179S	ENSP00000348841:P236S	P	-	1	0	ASPH	62719061	0.986000	0.35501	0.186000	0.23195	0.135000	0.20990	1.184000	0.32053	0.284000	0.22305	0.655000	0.94253	CCA		0.343	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		A	62556507	G	A	62556507	3	1	110	1	0	0	0	0	1	0	0	0	1054	1174	41	3	1654	3	ASPH	8	62556507	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	8703309	62556507	83807515	114	28986										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766388	77766388	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	caaaacctgaatatcccgcaGaaaagccaaagcagagtgac	8	11	0	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:77766388G>T	ENST00000521891.2	+	10	7679	c.7231G>T	c.(7231-7233)Gaa>Taa	p.E2411*	ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.E2366*|ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.E2366*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.E2385*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2366	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATATCCCGCAGAAAAGCCAAA	0.567										HNSCC(33;0.089)																																						0			8											33	49	44					8																	77766388		1980	4152	6132	77928943	SO:0001587	stop_gained	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7231G>T	8.37:g.77766388G>T	ENSP00000430497:p.Glu2411*		77928943	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	50	16.622759	0.99868	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	5.23	5.23	0.72850	.	0.000000	0.45867	U	0.000336	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	18.9988	0.92824	0.0:0.0:1.0:0.0	.	.	.	.	X	2411;2395;2366;2366;2385	.	ENSP00000050961:E2366X	E	+	1	0	ZFHX4	77928943	1.000000	0.71417	0.996000	0.52242	0.941000	0.58515	7.786000	0.85741	2.721000	0.93114	0.650000	0.86243	GAA		0.567	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766388	G	T	77766388	4	4	110	1	0	0	0	0	0	1	0	0	17674	943	33	2	7265	2	ZFHX4	8	77766388	Nonsense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	15209881	77766388	68597634	115	28987										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101299934	101299934	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taaatattgtcgtaagcaatCcacacaagatctgtgatgac	7	8	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:101299934C>A	ENST00000519449.1	-	3	785	c.469G>T	c.(469-471)Gat>Tat	p.D157Y	RNF19A_ENST00000341084.2_Missense_Mutation_p.D157Y	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	157					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.D157N(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			CGTAAGCAATCCACACAAGAT	0.378																																																1	Substitution - Missense(1)	central_nervous_system(1)	8											107	109	108					8																	101299934		2203	4300	6503	101369110	SO:0001583	missense	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.469G>T	8.37:g.101299934C>A	ENSP00000428968:p.Asp157Tyr		101369110	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551245	0.86127	.	.	ENSG00000034677	ENST00000519449;ENST00000341084;ENST00000519527	D;D	0.85171	-1.95;-1.95	5.57	5.57	0.84162	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.93867	0.8038	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94558	0.7760	10	0.87932	D	0	.	19.1651	0.93553	0.0:1.0:0.0:0.0	.	157	Q9NV58	RN19A_HUMAN	Y	157	ENSP00000428968:D157Y;ENSP00000342667:D157Y	ENSP00000342667:D157Y	D	-	1	0	RNF19A	101369110	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.606000	0.88127	0.650000	0.86243	GAT		0.378	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101299934	C	A	101299934	3	1	110	1	0	0	0	0	1	0	0	0	13507	855	30	2	2083	2	RNF19A	8	101299934	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	23533546	101299934	45064088	116	28988										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113314167	113314167	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccaatcttatttccatttggAggtgtaggtagttctccaca	8	9	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:113314167A>G	ENST00000297405.5	-	53	8539	c.8295T>C	c.(8293-8295)ccT>ccC	p.P2765P	CSMD3_ENST00000343508.3_Silent_p.P2725P|CSMD3_ENST00000352409.3_Silent_p.P2695P|CSMD3_ENST00000455883.2_Silent_p.P2596P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2765	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTCCATTTGGAGGTGTAGGTA	0.368										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											97	98	98					8																	113314167		2203	4300	6503	113383343	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8295T>C	8.37:g.113314167A>G			113383343	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.368	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113314167	A	G	113314167	2	3	110	1	0	0	0	0	0	0	0	1	3952	291	11	4		4	CSMD3	8	113314167	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	12014233	113314167	33049855	117	28989										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113702256	113702256	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atataagggtgtaccaggatCaccacaactttctttctcaa	6	10	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:113702256C>T	ENST00000297405.5	-	14	2240	c.1996G>A	c.(1996-1998)Gat>Aat	p.D666N	CSMD3_ENST00000343508.3_Missense_Mutation_p.D626N|CSMD3_ENST00000352409.3_Missense_Mutation_p.D666N|CSMD3_ENST00000455883.2_Missense_Mutation_p.D562N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	666	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D666N(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTACCAGGATCACCACAACTT	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	large_intestine(1)	8											131	140	137					8																	113702256		2203	4300	6503	113771432	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1996G>A	8.37:g.113702256C>T	ENSP00000297405:p.Asp666Asn		113771432	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182518	0.78677	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.09	5.09	0.68999	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.70684	0.3252	L	0.39467	1.215	0.45621	D	0.998559	D;D;D	0.60160	0.968;0.987;0.958	P;D;P	0.67382	0.755;0.951;0.815	T	0.64791	-0.6324	10	0.20519	T	0.43	.	18.8569	0.92255	0.0:1.0:0.0:0.0	.	562;666;626	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	N	626;666;6;562;666	ENSP00000345799:D626N;ENSP00000297405:D666N;ENSP00000341558:D6N;ENSP00000412263:D562N;ENSP00000343124:D666N	ENSP00000297405:D666N	D	-	1	0	CSMD3	113771432	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.525000	0.85131	0.585000	0.79938	GAT		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113702256	C	T	113702256	3	4	110	1	0	0	0	0	1	0	0	0	3952	826	29	3	9359	3	CSMD3	8	113702256	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	388089	113702256	32661766	118	28990										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116430677	116430677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaaaacaccggagcctctacGcctctgaaacaggggaaaaa	9	11	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:116430677G>A	ENST00000220888.5	-	5	2824	c.2665C>T	c.(2665-2667)Cgt>Tgt	p.R889C	TRPS1_ENST00000519076.1_Missense_Mutation_p.R643C|TRPS1_ENST00000395715.3_Missense_Mutation_p.R902C|TRPS1_ENST00000520276.1_Missense_Mutation_p.R893C			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	889					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R889C(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GAGCCTCTACGCCTCTGAAAC	0.473									Langer-Giedion syndrome																																							1	Substitution - Missense(1)	ovary(1)	8											88	89	89					8																	116430677		1909	4120	6029	116499853	SO:0001583	missense	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2665C>T	8.37:g.116430677G>A	ENSP00000220888:p.Arg889Cys		116499853	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.71|17.71	3.455925|3.455925	0.63401|0.63401	.|.	.|.	ENSG00000104447|ENSG00000104447	ENST00000518018|ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	.|D;D;D;D	.|0.99695	.|-6.43;-6.43;-6.43;-6.43	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99402|0.99402	0.9789|0.9789	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.996;0.998	D|D	0.99585|0.99585	1.0974|1.0974	5|10	.|0.87932	.|D	.|0	.|.	20.0805|20.0805	0.97772|0.97772	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|893;889;902	.|Q9UHF7-3;Q9UHF7;Q9UHF7-2	.|.;TRPS1_HUMAN;.	V|C	13|902;889;643;893	.|ENSP00000379065:R902C;ENSP00000220888:R889C;ENSP00000428910:R643C;ENSP00000428680:R893C	.|ENSP00000220888:R889C	A|R	-|-	2|1	0|0	TRPS1|TRPS1	116499853|116499853	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.586000|7.586000	0.82596|0.82596	2.755000|2.755000	0.94549|0.94549	0.650000|0.650000	0.86243|0.86243	GCG|CGT		0.473	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116430677	G	A	116430677	3	1	110	1	0	0	0	0	1	0	0	0	16633	1087	38	1	1188	1	TRPS1	8	116430677	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2728421	116430677	29933345	119	28991										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124340475	124340475	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgtattatctgagagctagAagcatctccattacaagcaa	7	8	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:124340475A>T	ENST00000287394.5	-	25	3930	c.3823T>A	c.(3823-3825)Tct>Act	p.S1275T	ATAD2_ENST00000521903.1_Missense_Mutation_p.S593T	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1275					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S1275T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TGAGAGCTAGAAGCATCTCCA	0.294																																																1	Substitution - Missense(1)	ovary(1)	8											73	69	70					8																	124340475		2203	4299	6502	124409656	SO:0001583	missense	29028			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.3823T>A	8.37:g.124340475A>T	ENSP00000287394:p.Ser1275Thr		124409656	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	4.286	0.052304	0.08291	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;T	0.91843	-2.92;1.5	5.08	-0.599	0.11645	.	1.760250	0.02605	N	0.101461	D	0.86981	0.6064	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.70615	-0.4823	10	0.25751	T	0.34	-4.1646	5.3878	0.16227	0.4622:0.2727:0.0:0.2652	.	1275	Q6PL18	ATAD2_HUMAN	T	1275;593	ENSP00000287394:S1275T;ENSP00000429213:S593T	ENSP00000287394:S1275T	S	-	1	0	ATAD2	124409656	0.000000	0.05858	0.006000	0.13384	0.057000	0.15508	0.265000	0.18515	0.301000	0.22738	0.528000	0.53228	TCT		0.294	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124340475	A	T	124340475	3	4	110	1	0	0	0	0	1	0	0	0	1072	246	9	5	365	5	ATAD2	8	124340475	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	7909798	124340475	22023547	120	28992										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133192501	133192501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tctgcaggaagcgcaggcttCgcagggaggtggccagaaca	16	10	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr8:133192501C>T	ENST00000388996.4	-	4	1100	c.680G>A	c.(679-681)cGa>cAa	p.R227Q	KCNQ3_ENST00000519445.1_Missense_Mutation_p.R227Q|KCNQ3_ENST00000521134.1_Missense_Mutation_p.R107Q	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	227					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCGCAGGCTTCGCAGGGAGGT	0.587																																																0			8											105	93	97					8																	133192501		2203	4300	6503	133261683	SO:0001583	missense	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.680G>A	8.37:g.133192501C>T	ENSP00000373648:p.Arg227Gln		133261683	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759950	0.89932	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.98028	-4.67;-4.67;-4.67	5.52	5.52	0.82312	Ion transport (1);	0.123529	0.52532	D	0.000061	D	0.98131	0.9383	L	0.58810	1.83	0.54753	D	0.999987	D;D	0.76494	0.999;0.999	P;P	0.62560	0.904;0.904	D	0.99198	1.0872	10	0.87932	D	0	-4.5406	18.4101	0.90549	0.0:1.0:0.0:0.0	.	227;227	E7ET42;O43525	.;KCNQ3_HUMAN	Q	227;107;227;216;106	ENSP00000373648:R227Q;ENSP00000429799:R107Q;ENSP00000428790:R227Q	ENSP00000373648:R227Q	R	-	2	0	KCNQ3	133261683	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	7.729000	0.84864	2.610000	0.88304	0.561000	0.74099	CGA		0.587	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133192501	C	T	133192501	3	4	110	1	0	0	0	0	1	0	0	0	8105	884	31	1	1986	1	KCNQ3	8	133192501	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	8852026	133192501	13171521	121	28993										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19063008	19063008	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	attacagtcttttctcacctCttctaccagatgatcttgct	4	12	5	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:19063008C>A	ENST00000380502.3	-	14	2094	c.1627G>T	c.(1627-1629)Gag>Tag	p.E543*	HAUS6_ENST00000380496.1_Nonsense_Mutation_p.E407*|SCARNA8_ENST00000515924.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	543					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.E543K(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TTTCTCACCTCTTCTACCAGA	0.413																																																1	Substitution - Missense(1)	ovary(1)	9											164	149	154					9																	19063008		2203	4300	6503	19053008	SO:0001587	stop_gained	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1627G>T	9.37:g.19063008C>A	ENSP00000369871:p.Glu543*		19053008	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Nonsense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	C	33	5.231171	0.95207	.	.	ENSG00000147874	ENST00000380502;ENST00000380496;ENST00000415524	.	.	.	5.54	5.54	0.83059	.	0.101103	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-7.6635	16.2177	0.82239	0.0:1.0:0.0:0.0	.	.	.	.	X	543;407;59	.	ENSP00000369865:E407X	E	-	1	0	HAUS6	19053008	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	2.950000	0.49081	2.606000	0.88127	0.563000	0.77884	GAG		0.413	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		A	19063008	C	A	19063008	4	1	110	1	0	0	0	0	0	1	0	0	6991	922	32	2	1256	2	HAUS6	9	19063008	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10		19063008	122150423	122	28994										
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39178351	39178351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtccatcaaaataaaccaccTcagattctaggaaagaagat	6	9	3	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:39178351T>C	ENST00000297668.6	-	5	618	c.545A>G	c.(544-546)gAg>gGg	p.E182G	CNTNAP3_ENST00000377653.2_5'UTR|CNTNAP3_ENST00000358144.2_Missense_Mutation_p.E94G|CNTNAP3_ENST00000323947.7_Missense_Mutation_p.E182G|CNTNAP3_ENST00000377656.2_Missense_Mutation_p.E182G|CNTNAP3_ENST00000377659.1_Missense_Mutation_p.E182G	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	182					cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		ATAAACCACCTCAGATTCTAG	0.323																																																0			9											63	74	70					9																	39178351		2187	4289	6476	39168351	SO:0001583	missense	79937			AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.545A>G	9.37:g.39178351T>C	ENSP00000297668:p.Glu182Gly		39168351	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.356909	0.41801	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000323947;ENST00000377659;ENST00000377653	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	3.16	3.16	0.36331	Concanavalin A-like lectin/glucanase (2);Concanavalin A-like lectin/glucanase, subgroup (2);	.	.	.	.	T	0.78413	0.4279	L	0.46157	1.445	0.26749	N	0.97024	P;B;B;P;B	0.52316	0.952;0.389;0.016;0.645;0.389	P;B;B;B;B	0.53266	0.722;0.138;0.008;0.368;0.098	T	0.68006	-0.5523	9	0.45353	T	0.12	.	10.6771	0.45792	0.0:0.0:0.0:1.0	.	182;182;182;182;182	E2QRH2;Q96NU0;Q9BZ76-2;A6NC89;Q9BZ76	.;CNT3B_HUMAN;.;.;CNTP3_HUMAN	G	182;182;94;182;182;94	ENSP00000297668:E182G;ENSP00000366884:E182G;ENSP00000350863:E94G;ENSP00000320728:E182G;ENSP00000366887:E182G	ENSP00000297668:E182G	E	-	2	0	CNTNAP3	39168351	0.908000	0.30866	0.436000	0.26797	0.736000	0.42039	6.442000	0.73443	1.422000	0.47177	0.460000	0.39030	GAG		0.323	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		C	39178351	T	C	39178351	3	2	110	1	0	0	0	0	1	0	0	0	3654	1551	54	4	3401	4	CNTNAP3	9	39178351	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	20115343	39178351	102035080	123	28995										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90500388	90500388	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acatggcaaatcccagccacGgcatcttcccgaccacacct	6	18	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:90500388G>A	ENST00000325643.5	+	4	1052	c.986G>A	c.(985-987)cGg>cAg	p.R329Q		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	329					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCCCAGCCACGGCATCTTCCC	0.617																																																0			9											50	52	51					9																	90500388		2203	4300	6503	89690208	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.986G>A	9.37:g.90500388G>A	ENSP00000322640:p.Arg329Gln		89690208	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	.	8.144	0.785808	0.16189	.	.	ENSG00000177992	ENST00000325643	T	0.03330	3.97	2.72	-1.19	0.09585	.	1.435330	0.04726	N	0.420210	T	0.01254	0.0041	N	0.00538	-1.39	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.45366	-0.9266	10	0.24483	T	0.36	.	5.806	0.18440	0.5422:0.0:0.4578:0.0	.	329	Q6ZUB1	CI079_HUMAN	Q	329	ENSP00000322640:R329Q	ENSP00000322640:R329Q	R	+	2	0	C9orf79	89690208	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.338000	0.07842	-0.098000	0.12285	-0.416000	0.06073	CGG		0.617	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		A	90500388	G	A	90500388	3	1	110	1	0	0	0	0	1	0	0	0	2503	1116	39	1	1000	1	C9orf79	9	90500388	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	51322037	90500388	50713043	124	28996										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98248148	98248148	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atttaattcacgacttactcGtcctccaactgacaaatatg	4	11	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:98248148G>A	ENST00000331920.6	-	3	702	c.403C>T	c.(403-405)Cga>Tga	p.R135*	PTCH1_ENST00000429896.2_De_novo_Start_OutOfFrame|PTCH1_ENST00000430669.2_Nonsense_Mutation_p.R69*|PTCH1_ENST00000375274.2_Nonsense_Mutation_p.R134*|PTCH1_ENST00000468211.2_Nonsense_Mutation_p.R69*|PTCH1_ENST00000418258.1_De_novo_Start_OutOfFrame|PTCH1_ENST00000421141.1_De_novo_Start_OutOfFrame|PTCH1_ENST00000437951.1_Nonsense_Mutation_p.R69*|PTCH1_ENST00000548379.1_5'UTR	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	135					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.R135*(2)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CGACTTACTCGTCCTCCAACT	0.373																																																2	Substitution - Nonsense(2)	bone(2)	9	GRCh37	CM971257	PTCH1	M							128	132	130					9																	98248148		2203	4300	6503	97287969	SO:0001587	stop_gained	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.403C>T	9.37:g.98248148G>A	ENSP00000332353:p.Arg135*		97287969	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Nonsense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	38	6.805447	0.97853	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000430669;ENST00000375274;ENST00000468211	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9287	14.7486	0.69508	0.0:0.0:0.8554:0.1446	.	.	.	.	X	135;69;69;134;69	.	ENSP00000332353:R135X	R	-	1	2	PTCH1	97287969	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.916000	0.63362	2.719000	0.93026	0.655000	0.94253	CGA		0.373	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98248148	G	A	98248148	4	1	110	1	0	0	0	0	0	1	0	0	12764	1153	40	1	4024	1	PTCH1	9	98248148	Nonsense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	7747760	98248148	42965283	125	28997										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119770416	119770416	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acaggcatctgtcgtcctttGtccacagaggtccctcaccc	8	16	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:119770416G>T	ENST00000313400.4	-	7	1646	c.1546C>A	c.(1546-1548)Caa>Aaa	p.Q516K	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.Q465K|ASTN2_ENST00000373996.3_Missense_Mutation_p.Q516K			O75129	ASTN2_HUMAN	astrotactin 2	516	EGF-like 1.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GTCGTCCTTTGTCCACAGAGG	0.577																																																0			9											95	86	89					9																	119770416		2203	4300	6503	118810237	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1546C>A	9.37:g.119770416G>T	ENSP00000314038:p.Gln516Lys		118810237	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	18.56	3.649398	0.67358	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.11385	2.95;2.95;2.78;2.98	5.67	5.67	0.87782	.	0.073084	0.56097	D	0.000024	T	0.12817	0.0311	N	0.24115	0.695	0.53688	D	0.999972	P;P;B	0.52170	0.681;0.951;0.39	B;P;B	0.47299	0.276;0.543;0.208	T	0.07597	-1.0764	9	.	.	.	-22.8811	19.7848	0.96432	0.0:0.0:1.0:0.0	.	465;516;516	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	K	516;516;243;465	ENSP00000314038:Q516K;ENSP00000363108:Q516K;ENSP00000363098:Q243K;ENSP00000354504:Q465K	.	Q	-	1	0	ASTN2	118810237	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.708000	0.84633	2.673000	0.90976	0.655000	0.94253	CAA		0.577	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119770416	G	T	119770416	3	4	110	1	0	0	0	0	1	0	0	0	1066	1386	48	2	2773	2	ASTN2	9	119770416	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	21522268	119770416	21443015	126	28998										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119976922	119976922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgagtggcttctgtgcttgCgctcttctgggggatgcggc	16	9	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:119976922C>T	ENST00000313400.4	-	3	830	c.730G>A	c.(730-732)Gca>Aca	p.A244T	ASTN2_ENST00000361209.2_Missense_Mutation_p.A244T|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.A244T			O75129	ASTN2_HUMAN	astrotactin 2	244					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TCTGTGCTTGCGCTCTTCTGG	0.637																																																0			9											63	58	60					9																	119976922		2203	4300	6503	119016743	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.730G>A	9.37:g.119976922C>T	ENSP00000314038:p.Ala244Thr		119016743	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	24.6	4.545304	0.86022	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.14144	2.61;2.61;2.53	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.25717	0.0626	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.99;0.983	T	0.02751	-1.1115	9	.	.	.	-15.5834	19.0397	0.92993	0.0:1.0:0.0:0.0	.	244;244;244	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	T	244	ENSP00000314038:A244T;ENSP00000363108:A244T;ENSP00000354504:A244T	.	A	-	1	0	ASTN2	119016743	1.000000	0.71417	0.979000	0.43373	0.991000	0.79684	7.783000	0.85696	2.599000	0.87857	0.655000	0.94253	GCA		0.637	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119976922	C	T	119976922	3	4	110	1	0	0	0	0	1	0	0	0	1066	768	27	1	3448	1	ASTN2	9	119976922	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	206506	119976922	21236509	127	28999										
ZBTB43	23099	hgsc.bcm.edu	37	chr9	129594890	129594890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cagcaaggacaattatgtgaCgtctccattgttgtccaagg	10	9	1	1	rs371516295		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:129594890C>T	ENST00000373464.4	+	3	366	c.102C>T	c.(100-102)gaC>gaT	p.D34D	ZBTB43_ENST00000449886.1_Silent_p.D34D|ZBTB43_ENST00000373457.1_Silent_p.D34D	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	34	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AATTATGTGACGTCTCCATTG	0.478													C|||	1	0.000199681	8e-04	0	5008	,	,		19820	0		0	False		,,,				2504	0															0			9						C	,	1,4405	2.1+/-5.4	0,1,2202	105	92	96		102,102	-1.6	1	9		96	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	ZBTB43	NM_001135776.1,NM_014007.3	,	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	,	34/468,34/468	129594890	6,13000	2203	4300	6503	128634711	SO:0001819	synonymous_variant	23099			AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	17908	protein-coding gene	gene with protein product			"zinc finger protein 297B"	ZNF297B			Standard	NM_014007		Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.102C>T	9.37:g.129594890C>T			128634711	Q5JU96	Silent	SNP	ENST00000373464.4	37	CCDS6867.1																																																																																				0.478	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054124.1	NM_001135776		T	129594890	C	T	129594890	2	4	110	1	0	0	0	0	0	0	0	1	17583	535	19	1		1	ZBTB43	9	129594890	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	9617968	129594890	11618541	128	29000										
LCN9	392399	hgsc.bcm.edu	37	chr9	138557188	138557188	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aacgggaccgagacccacacGctggcgctctatggtacctc	11	15	1	1	rs367648675		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:138557188G>A	ENST00000277526.3	+	4	405	c.405G>A	c.(403-405)acG>acA	p.T135T	LCN9_ENST00000430290.2_3'UTR	NM_001001676.1	NP_001001676.1	Q8WX39	LCN9_HUMAN	lipocalin 9	135						extracellular region (GO:0005576)	pheromone binding (GO:0005550)|transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	6		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;3.43e-07)|Epithelial(140;1.97e-06)|all cancers(34;6.1e-05)		AGACCCACACGCTGGCGCTCT	0.642																																																0			9						G		1,4175		0,1,2087	61	69	66		405	2.2	0.8	9		66	0,8372		0,0,4186	no	coding-synonymous	LCN9	NM_001001676.1		0,1,6273	AA,AG,GG		0.0,0.0239,0.0080		135/177	138557188	1,12547	2088	4186	6274	137697009	SO:0001819	synonymous_variant	392399			AY301270	CCDS56593.1	9q34	2011-11-14			ENSG00000148386	ENSG00000148386		"Lipocalins"	17442	protein-coding gene	gene with protein product	"MUP-like lipocalin", "epididymal-specific lipocalin-9"	612903				15363845	Standard	NM_001001676		Approved		uc004cgk.2	Q8WX39	OTTHUMG00000020916	ENST00000277526.3:c.405G>A	9.37:g.138557188G>A			137697009	C9J5F0|Q6JVE7	Silent	SNP	ENST00000277526.3	37	CCDS56593.1																																																																																				0.642	LCN9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410711.1	NM_001001676		A	138557188	G	A	138557188	2	1	110	1	0	0	0	0	0	0	0	1	8709	1074	38	1		1	LCN9	9	138557188	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	8962298	138557188	2656243	129	29001										
CACNA1B	774	hgsc.bcm.edu	37	chr9	141016272	141016272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgaggacactctcactttcGaggaggctgtggccaccaac	11	13	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr9:141016272G>A	ENST00000371372.1	+	47	6986	c.6841G>A	c.(6841-6843)Gag>Aag	p.E2281K	CACNA1B_ENST00000277551.2_Silent_p.S2218S|CACNA1B_ENST00000371357.1_Missense_Mutation_p.E2280K|CACNA1B_ENST00000277549.5_Missense_Mutation_p.E1475K|CACNA1B_ENST00000371355.4_Missense_Mutation_p.E2282K|CACNA1B_ENST00000371363.1_Missense_Mutation_p.E2279K	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	2281					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTCACTTTCGAGGAGGCTGT	0.647																																																0			9											48	53	51					9																	141016272		2082	4200	6282	140136093	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.6841G>A	9.37:g.141016272G>A	ENSP00000360423:p.Glu2281Lys		140136093	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201561	0.79015	.	.	ENSG00000148408	ENST00000371372;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.97888	-4.35;-4.59;-4.35;-4.34;-4.34	5.11	5.11	0.69529	.	0.527437	0.19548	N	0.111627	D	0.96577	0.8883	M	0.68952	2.095	0.50813	D	0.999895	D;P	0.55605	0.972;0.939	B;B	0.39805	0.31;0.31	D	0.97286	0.9921	10	0.66056	D	0.02	.	18.5267	0.90975	0.0:0.0:1.0:0.0	.	2280;2279	B1AQK7;B1AQK6	.;.	K	2281;1475;2279;2280;2282	ENSP00000360423:E2281K;ENSP00000277549:E1475K;ENSP00000360414:E2279K;ENSP00000360408:E2280K;ENSP00000360406:E2282K	ENSP00000277549:E1475K	E	+	1	0	CACNA1B	140136093	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.520000	0.73773	2.381000	0.81170	0.555000	0.69702	GAG		0.647	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	141016272	G	A	141016272	3	1	110	1	0	0	0	0	1	0	0	0	2545	1059	37	1	7023	1	CACNA1B	9	141016272	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2459084	141016272	197159	130	29002										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50678650	50678650	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttccactaatcactgacaacTcttctggtccagatactgca	5	13	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:50678650T>C	ENST00000355832.5	-	18	3434	c.3356A>G	c.(3355-3357)gAg>gGg	p.E1119G	ERCC6_ENST00000542458.1_Missense_Mutation_p.E489G|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1119			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|E -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.E1119L(1)|p.E1119V(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CACTGACAACTCTTCTGGTCC	0.398								Direct reversal of damage;Nucleotide excision repair (NER)																																								2	Substitution - Missense(2)	breast(2)	10											162	153	156					10																	50678650		2203	4300	6503	50348656	SO:0001583	missense	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3356A>G	10.37:g.50678650T>C	ENSP00000348089:p.Glu1119Gly		50348656	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.729034	0.30684	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83419	-1.72;-1.45	5.95	0.933	0.19471	.	.	.	.	.	T	0.74839	0.3769	L	0.53249	1.67	0.09310	N	1	B;B	0.20887	0.049;0.001	B;B	0.16722	0.016;0.001	T	0.58059	-0.7703	9	0.27082	T	0.32	-0.1099	5.3758	0.16164	0.0:0.3612:0.1514:0.4874	.	1119;496	Q03468;Q59FF6	ERCC6_HUMAN;.	G	1119;496;489	ENSP00000348089:E1119G;ENSP00000445134:E489G	ENSP00000348089:E1119G	E	-	2	0	ERCC6	50348656	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.463000	0.21972	-0.076000	0.12775	0.533000	0.62120	GAG		0.398	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50678650	T	C	50678650	3	2	110	1	0	0	0	0	1	0	0	0	5230	1551	54	4	1141	4	ERCC6	10	50678650	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10		50678650	84856097	131	29003										
CSTF2T	23283	hgsc.bcm.edu	37	chr10	53459173	53459173	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tctctctatcgtataccagcCggaaactgacaacagaacca	6	13	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:53459173C>A	ENST00000331173.4	-	1	182	c.137G>T	c.(136-138)cGg>cTg	p.R46L	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	46	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				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)		GTATACCAGCCGGAAACTGAC	0.522																																																0			10											143	146	145					10																	53459173		2203	4300	6503	53129179	SO:0001583	missense	23283			AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.137G>T	10.37:g.53459173C>A	ENSP00000332444:p.Arg46Leu		53129179	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	37	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546161	0.86022	.	.	ENSG00000177613	ENST00000331173	T	0.17691	2.26	5.09	5.09	0.68999	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.22589	0.0545	L	0.52905	1.665	0.80722	D	1	B	0.20368	0.044	B	0.28305	0.088	T	0.03008	-1.1083	10	0.87932	D	0	-5.4288	16.3988	0.83632	0.0:1.0:0.0:0.0	.	46	Q9H0L4	CSTFT_HUMAN	L	46	ENSP00000332444:R46L	ENSP00000332444:R46L	R	-	2	0	CSTF2T	53129179	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.130000	0.77235	2.826000	0.97356	0.491000	0.48974	CGG		0.522	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		A	53459173	C	A	53459173	3	1	110	1	0	0	0	0	1	0	0	0	3991	652	23	2	1717	2	CSTF2T	10	53459173	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2780523	53459173	82075574	132	29004										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624235	89624235	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggctcccagacatgacagcCatcatcaaagagatcgttag	9	11	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:89624235C>T	ENST00000371953.3	+	1	1366	c.9C>T	c.(7-9)gcC>gcT	p.A3A	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	3					activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.A3fs*21(2)|p.I4fs*6(1)|p.M1fs*24(1)|p.A3fs*14(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ACATGACAGCCATCATCAAAG	0.498		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	55	Whole gene deletion(37)|Unknown(13)|Complex - frameshift(3)|Deletion - Frameshift(2)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											150	149	149					10																	89624235		2203	4300	6503	89614215	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.9C>T	10.37:g.89624235C>T			89614215	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.498	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624235	C	T	89624235	2	4	110	1	0	0	0	0	0	0	0	1	12772	581	21	3		3	PTEN	10	89624235	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	36165062	89624235	45910512	133	29005										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692923	89692924	+	Missense_Mutation	DNP	GT	GT	AC													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acgaactggtgtaatgatatGtgcatatttattacatcggg							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G|T	G|T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:89692923_89692924GT>AC	ENST00000371953.3	+	5	1764_1765	c.407_408GT>AC	c.(406-408)tGT>tAC	p.C136Y		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	136	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		C -> Y (in CWS1; loss of phosphatase activity towards Ins(1,3,4,5)P3). {ECO:0000269|PubMed:9735393}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.C136Y(8)|p.C136F(5)|p.?(5)|p.R55fs*1(5)|p.C136fs*1(2)|p.Y27fs*1(2)|p.I135_A137>T(1)|p.A121_F145del(1)|p.I135fs*6(1)|p.C136_A137insGM(1)|p.C136W(1)|p.T131fs*42(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GTAATGATATGTGCATATTTAT	0.391		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	71	Whole gene deletion(37)|Substitution - Missense(14)|Deletion - Frameshift(10)|Unknown(5)|Insertion - Frameshift(2)|Deletion - In frame(1)|Insertion - In frame(1)|Complex - deletion inframe(1)	prostate(16)|central_nervous_system(14)|endometrium(11)|breast(8)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|upper_aerodigestive_tract(1)|meninges(1)|soft_tissue(1)|urinary_tract(1)	10	GRCh37	CM983501	PTEN	M																																				89682903|89682904	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	Exception_encountered	10.37:g.89692923_89692924delinsAC	ENSP00000361021:p.Cys136Tyr		89682903|89682904	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation|Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.391	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		AC	89692924	GT	AC	89692923	3	1	110	1	0	0	0	0	1	0	0	0	12772	1377	48	3	425	3	PTEN	10	89692923	Missense_Mutation	DNP	GT	TCGA-EI-6506-01A-11D-1733-10	68688	89692923	45841824	134	29006										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720865	89720865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agccaaccgatacttttctcCaaattttaaggtcagttaaa	5	9	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:89720865C>T	ENST00000371953.3	+	8	2373	c.1016C>T	c.(1015-1017)cCa>cTa	p.P339L	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	339	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.P339L(1)|p.W274_F341del(1)|p.S338fs*1(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TACTTTTCTCCAAATTTTAAG	0.333		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(3)|Unknown(2)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|skin(7)|lung(4)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	10											49	52	51					10																	89720865		2203	4299	6502	89710845	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1016C>T	10.37:g.89720865C>T	ENSP00000361021:p.Pro339Leu		89710845	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949132	0.92660	.	.	ENSG00000171862	ENST00000371953	D	0.86432	-2.12	5.37	5.37	0.77165	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.93125	0.7811	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.92697	0.6171	9	.	.	.	-4.5206	19.0916	0.93228	0.0:1.0:0.0:0.0	.	339	P60484	PTEN_HUMAN	L	339	ENSP00000361021:P339L	.	P	+	2	0	PTEN	89710845	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.405000	0.80007	2.516000	0.84829	0.591000	0.81541	CCA		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720865	C	T	89720865	3	4	110	1	0	0	0	0	1	0	0	0	12772	594	21	3	1046	3	PTEN	10	89720865	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	27942	89720865	45813882	135	29007										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	116889144	116889144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggaagtgtacaactagtgtcTctgttccaagtcaagtatat	9	7	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:116889144T>C	ENST00000355044.3	+	5	802	c.676T>C	c.(676-678)Tct>Cct	p.S226P	ATRNL1_ENST00000529665.1_3'UTR|ATRNL1_ENST00000527407.1_Missense_Mutation_p.S226P	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	226	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AACTAGTGTCTCTGTTCCAAG	0.363																																																0			10											155	144	148					10																	116889144		2203	4300	6503	116879134	SO:0001583	missense	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.676T>C	10.37:g.116889144T>C	ENSP00000347152:p.Ser226Pro		116879134	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.850837	0.91277	.	.	ENSG00000107518	ENST00000526946;ENST00000355044	T;T	0.32515	1.45;2.47	5.47	5.47	0.80525	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.052476	0.85682	D	0.000000	T	0.48095	0.1481	L	0.51422	1.61	0.80722	D	1	D;D;D	0.71674	0.998;0.99;0.998	P;P;D	0.63381	0.896;0.676;0.914	T	0.48433	-0.9036	10	0.72032	D	0.01	-22.8684	15.5419	0.76057	0.0:0.0:0.0:1.0	.	159;226;226	E9PL90;Q5VV63;Q5VV63-2	.;ATRN1_HUMAN;.	P	159;226	ENSP00000431423:S159P;ENSP00000347152:S226P	ENSP00000347152:S226P	S	+	1	0	ATRNL1	116879134	1.000000	0.71417	0.953000	0.39169	0.974000	0.67602	6.272000	0.72575	2.085000	0.62840	0.383000	0.25322	TCT		0.363	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	116889144	T	C	116889144	3	2	110	1	0	0	0	0	1	0	0	0	1208	1551	54	4	694	4	ATRNL1	10	116889144	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	27168279	116889144	18645603	136	29008										
PNLIP	5406	hgsc.bcm.edu	37	chr10	118313342	118313342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaccaatgggaccattggacGcatcacaggttggtgaaaac	11	9	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:118313342G>A	ENST00000369221.2	+	6	591	c.563G>A	c.(562-564)cGc>cAc	p.R188H		NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	188					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	ACCATTGGACGCATCACAGGT	0.552																																																0			10											80	65	70					10																	118313342		2203	4300	6503	118303332	SO:0001583	missense	5406			BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.563G>A	10.37:g.118313342G>A	ENSP00000358223:p.Arg188His		118303332	Q5VSQ2	Missense_Mutation	SNP	ENST00000369221.2	37	CCDS7594.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158779	0.78226	.	.	ENSG00000175535	ENST00000369221	D	0.97209	-4.29	6.07	6.07	0.98685	Lipase, N-terminal (1);	0.000000	0.64402	D	0.000010	D	0.98848	0.9611	M	0.91818	3.245	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.99387	1.0924	10	0.87932	D	0	.	19.4308	0.94765	0.0:0.0:1.0:0.0	.	188	P16233	LIPP_HUMAN	H	188	ENSP00000358223:R188H	ENSP00000358223:R188H	R	+	2	0	PNLIP	118303332	0.990000	0.36364	0.547000	0.28179	0.840000	0.47671	6.262000	0.72514	2.885000	0.99019	0.655000	0.94253	CGC		0.552	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936		A	118313342	G	A	118313342	3	1	110	1	0	0	0	0	1	0	0	0	12180	1087	38	1	581	1	PNLIP	10	118313342	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1424198	118313342	17221405	137	29009										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123247573	123247573	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tccaaagtctgctattttcaTcacattgttttctgttacca	4	10	4	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:123247573T>C	ENST00000358487.5	-	14	2190	c.1918A>G	c.(1918-1920)Atg>Gtg	p.M640V	FGFR2_ENST00000360144.3_Missense_Mutation_p.M552V|FGFR2_ENST00000357555.5_Missense_Mutation_p.M551V|FGFR2_ENST00000346997.2_Missense_Mutation_p.M638V|FGFR2_ENST00000369060.4_Missense_Mutation_p.M524V|FGFR2_ENST00000356226.4_Missense_Mutation_p.M523V|FGFR2_ENST00000369061.4_Missense_Mutation_p.M528V|FGFR2_ENST00000369059.1_Missense_Mutation_p.M526V|FGFR2_ENST00000457416.2_Missense_Mutation_p.M641V|FGFR2_ENST00000369056.1_Missense_Mutation_p.M641V|FGFR2_ENST00000351936.6_Missense_Mutation_p.M638V|FGFR2_ENST00000478859.1_Missense_Mutation_p.M412V	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	640	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GCTATTTTCATCACATTGTTT	0.373		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											181	181	181					10																	123247573		2203	4300	6503	123237563	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1918A>G	10.37:g.123247573T>C	ENSP00000351276:p.Met640Val		123237563	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.061194	0.76187	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.37	4.22	0.49857	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61887	0.2383	N	0.00277	-1.72	0.80722	D	1	B;B;D;P;P;P;D;P	0.61080	0.281;0.194;0.989;0.727;0.956;0.543;0.989;0.861	B;B;D;P;P;B;P;P	0.65773	0.373;0.234;0.938;0.557;0.842;0.289;0.809;0.762	T	0.78041	-0.2359	10	0.87932	D	0	.	11.9114	0.52741	0.1307:0.0:0.0:0.8693	.	657;639;551;523;640;552;641;543	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	V	551;641;528;640;523;524;526;232;638;641;638;552;641;641;549	ENSP00000350166:M551V;ENSP00000358057:M528V;ENSP00000351276:M640V;ENSP00000348559:M523V;ENSP00000358056:M524V;ENSP00000358055:M526V;ENSP00000404219:M232V;ENSP00000263451:M638V;ENSP00000410294:M641V;ENSP00000309878:M638V;ENSP00000353262:M552V;ENSP00000358052:M641V;ENSP00000358054:M641V;ENSP00000337665:M549V	ENSP00000337665:M549V	M	-	1	0	FGFR2	123237563	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.873000	0.87193	0.951000	0.37770	0.533000	0.62120	ATG		0.373	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		C	123247573	T	C	123247573	3	2	110	1	0	0	0	0	1	0	0	0	5885	1435	50	4	671	4	FGFR2	10	123247573	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4934231	123247573	12287174	138	29010										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127753558	127753558	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggagtccctgcacgctgttcCtgcaggcttcagctggaagg	14	12	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr10:127753558C>A	ENST00000368679.4	-	14	1744	c.1435G>T	c.(1435-1437)Gga>Tga	p.G479*	ADAM12_ENST00000467145.1_5'UTR|ADAM12_ENST00000368676.4_Nonsense_Mutation_p.G479*	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	479	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		G -> E (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CACGCTGTTCCTGCAGGCTTC	0.607																																																0			10											60	59	59					10																	127753558		2203	4300	6503	127743548	SO:0001587	stop_gained	8038			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1435G>T	10.37:g.127753558C>A	ENSP00000357668:p.Gly479*		127743548	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Nonsense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	38	7.089505	0.98055	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.0783	0.93171	0.0:1.0:0.0:0.0	.	.	.	.	X	479	.	ENSP00000357665:G479X	G	-	1	0	ADAM12	127743548	1.000000	0.71417	0.079000	0.20413	0.142000	0.21351	7.558000	0.82253	2.731000	0.93534	0.650000	0.86243	GGA		0.607	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			A	127753558	C	A	127753558	4	1	110	1	0	0	0	0	0	1	0	0	236	690	24	2	1442	2	ADAM12	10	127753558	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4505985	127753558	7781189	139	29011										
IFITM3	10410	hgsc.bcm.edu	37	chr11	319855	319855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gatctatccataggcctggaAgatcagcactgggatgacga	12	9	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:319855A>G	ENST00000399808.4	-	2	621	c.385T>C	c.(385-387)Ttc>Ctc	p.F129L	RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.F108L|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.F108L|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	129	Interaction with VAPA.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.F129V(1)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TAGGCCTGGAAGATCAGCACT	0.587																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											68	70	70					11																	319855		2029	4178	6207	309855	SO:0001583	missense	10410			X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"interferon induced transmembrane protein 3 (1-8U)"			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.385T>C	11.37:g.319855A>G	ENSP00000382707:p.Phe129Leu		309855	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.348|0.348	-0.946328|-0.946328	0.02304|0.02304	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000399808;ENST00000526811|ENST00000270031	T;T|.	0.78126|.	-0.9;-1.15|.	2.58|2.58	-5.16|-5.16	0.02857|0.02857	.|.	.|0.215683	.|0.25981	.|U	.|0.027064	T|T	0.07503|0.07503	0.0189|0.0189	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.11665|0.11665	-1.0578|-1.0578	9|7	0.05833|0.51188	T|T	0.94|0.08	1.4325|1.4325	2.1432|2.1432	0.03780|0.03780	0.1561:0.2923:0.4058:0.1459|0.1561:0.2923:0.4058:0.1459	.|.	129|.	Q01628|.	IFM3_HUMAN|.	L|P	129;108|109	ENSP00000382707:F129L;ENSP00000432108:F108L|.	ENSP00000382707:F129L|ENSP00000372047:L109P	F|L	-|-	1|2	0|0	IFITM3|IFITM3	309855|309855	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-6.554000|-6.554000	0.00061|0.00061	-2.050000|-2.050000	0.00905|0.00905	-0.420000|-0.420000	0.06012|0.06012	TTC|CTT		0.587	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		G	319855	A	G	319855	3	3	110	1	0	0	0	0	1	0	0	0	7549	72	3	4	20	4	IFITM3	11	319855	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10		319855	134686661	140	29012										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17172174	17172174	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atagcctgggtttgtgcggtGattggtatatggaaatttgg	15	3	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:17172174G>A	ENST00000265970.7	-	3	1197	c.1198C>T	c.(1198-1200)Cac>Tac	p.H400Y	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.H20Y	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	400					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTTGTGCGGTGATTGGTATAT	0.363																																																0			11											165	148	154					11																	17172174		2200	4293	6493	17128750	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.1198C>T	11.37:g.17172174G>A	ENSP00000265970:p.His400Tyr		17128750	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	0.512	-0.866065	0.02590	.	.	ENSG00000011405	ENST00000265970;ENST00000540361;ENST00000544896	T;T	0.41758	0.99;0.99	5.94	5.94	0.96194	.	0.393472	0.28398	N	0.015486	T	0.23289	0.0563	N	0.19112	0.55	0.28425	N	0.91756	P;P	0.44578	0.838;0.476	B;B	0.37550	0.253;0.062	T	0.23868	-1.0176	10	0.02654	T	1	-2.7413	13.5446	0.61695	0.0709:0.0:0.9291:0.0	.	400;400	F5H5W9;O00443	.;P3C2A_HUMAN	Y	400;20;400	ENSP00000265970:H400Y;ENSP00000438687:H20Y	ENSP00000265970:H400Y	H	-	1	0	PIK3C2A	17128750	1.000000	0.71417	0.948000	0.38648	0.215000	0.24574	3.846000	0.55888	2.807000	0.96579	0.591000	0.81541	CAC		0.363	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		A	17172174	G	A	17172174	3	1	110	1	0	0	0	0	1	0	0	0	11940	1290	45	3	3982	3	PIK3C2A	11	17172174	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	16852319	17172174	117834342	141	29013										
API5	8539	hgsc.bcm.edu	37	chr11	43343566	43343566	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gggttgttcagccaaatactTcaaggagaggacattgttag	12	6	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:43343566T>C	ENST00000531273.1	+	5	562	c.423T>C	c.(421-423)ctT>ctC	p.L141L	API5_ENST00000378852.3_Silent_p.L141L|API5_ENST00000534695.1_Intron|API5_ENST00000455725.2_Silent_p.L130L|API5_ENST00000420461.2_Silent_p.L87L|API5_ENST00000534600.1_Silent_p.L141L			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	141	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						GCCAAATACTTCAAGGAGAGG	0.368																																					Pancreas(1;98 122 5625 20895 49453)											0			11											118	116	117					11																	43343566		2203	4300	6503	43300142	SO:0001819	synonymous_variant	8539			U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.423T>C	11.37:g.43343566T>C			43300142	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Silent	SNP	ENST00000531273.1	37	CCDS44572.1																																																																																				0.368	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		C	43343566	T	C	43343566	2	2	110	1	0	0	0	0	0	0	0	1	773	1770	62	4		4	API5	11	43343566	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	26171392	43343566	91662950	142	29014										
PTPMT1	114971	hgsc.bcm.edu	37	chr11	47593119	47593119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agctggatgttcttaaagagTtccacaagcagattactgca	9	8	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:47593119T>C	ENST00000326674.9	+	4	566	c.544T>C	c.(544-546)Ttc>Ctc	p.F182L	PTPMT1_ENST00000326656.8_Missense_Mutation_p.F118L|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000426530.2_3'UTR|PTPMT1_ENST00000534775.1_3'UTR|NDUFS3_ENST00000533507.1_3'UTR	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	182	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						TCTTAAAGAGTTCCACAAGCA	0.478																																																0			11											122	113	116					11																	47593119		1901	4129	6030	47549695	SO:0001583	missense	114971			BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.544T>C	11.37:g.47593119T>C	ENSP00000325958:p.Phe182Leu		47549695	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.940835	0.92526	.	.	ENSG00000110536	ENST00000326656;ENST00000326674	T;T	0.61274	1.82;0.12	5.93	5.93	0.95920	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.075144	0.53938	U	0.000046	T	0.70482	0.3229	M	0.63428	1.95	0.49130	D	0.999757	D;D	0.69078	0.995;0.997	P;P	0.61800	0.894;0.865	T	0.71603	-0.4543	10	0.49607	T	0.09	-8.3213	14.6096	0.68507	0.0:0.0:0.0:1.0	.	118;182	Q8WUK0-2;Q8WUK0	.;PTPM1_HUMAN	L	118;182	ENSP00000325882:F118L;ENSP00000325958:F182L	ENSP00000325882:F118L	F	+	1	0	PTPMT1	47549695	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	6.376000	0.73141	2.271000	0.75665	0.533000	0.62120	TTC		0.478	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879		C	47593119	T	C	47593119	3	2	110	1	0	0	0	0	1	0	0	0	12813	1725	60	4	663	4	PTPMT1	11	47593119	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4249553	47593119	87413397	143	29015										
OR5R1	219479	hgsc.bcm.edu	37	chr11	56184842	56184842	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tctttgttccttagactataGattagggggtttaacatggg	11	5	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:56184842G>T	ENST00000312253.1	-	1	866	c.867C>A	c.(865-867)atC>atA	p.I289I		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					TTAGACTATAGATTAGGGGGT	0.358																																																0			11											120	120	120					11																	56184842		2201	4296	6497	55941418	SO:0001819	synonymous_variant	219479			AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"GPCR / Class A : Olfactory receptors"	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.867C>A	11.37:g.56184842G>T			55941418		Silent	SNP	ENST00000312253.1	37	CCDS31530.1																																																																																				0.358	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744		T	56184842	G	T	56184842	2	4	110	1	0	0	0	0	0	0	0	1	11211	932	33	2		2	OR5R1	11	56184842	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	8591723	56184842	78821674	144	29016										
VWCE	220001	hgsc.bcm.edu	37	chr11	61041993	61041993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggcaaacacaggtggtacacTcgtcaccacccccactgaac	8	16	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:61041993T>C	ENST00000335613.5	-	12	1945	c.1559A>G	c.(1558-1560)gAg>gGg	p.E520G	VWCE_ENST00000535710.1_5'Flank	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	520	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GGTGGTACACTCGTCACCACC	0.552																																																0			11											221	134	163					11																	61041993		2203	4299	6502	60798569	SO:0001583	missense	220001			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1559A>G	11.37:g.61041993T>C	ENSP00000334186:p.Glu520Gly		60798569	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	T	19.45	3.830811	0.71258	.	.	ENSG00000167992	ENST00000335613	T	0.64438	-0.1	4.94	3.82	0.43975	von Willebrand factor, type C (3);	0.147353	0.31210	N	0.008041	T	0.48484	0.1502	N	0.14661	0.345	0.80722	D	1	P	0.45348	0.856	P	0.48454	0.578	T	0.45716	-0.9242	10	0.39692	T	0.17	.	7.7717	0.29012	0.0:0.0966:0.0:0.9034	.	520	Q96DN2	VWCE_HUMAN	G	520	ENSP00000334186:E520G	ENSP00000334186:E520G	E	-	2	0	VWCE	60798569	0.809000	0.29036	0.983000	0.44433	0.981000	0.71138	1.370000	0.34238	1.854000	0.53819	0.459000	0.35465	GAG		0.552	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		C	61041993	T	C	61041993	3	2	110	1	0	0	0	0	1	0	0	0	17285	1551	54	4	1344	4	VWCE	11	61041993	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4857151	61041993	73964523	145	29017										
PLA2G16	11145	hgsc.bcm.edu	37	chr11	63357674	63357674	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgccccaccagctcctccgcCcgctggatgattttgctgca	9	17	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:63357674C>T	ENST00000323646.5	-	3	639	c.285G>A	c.(283-285)cgG>cgA	p.R95R	PLA2G16_ENST00000415826.1_Silent_p.R95R|PLA2G16_ENST00000394613.3_5'UTR	NM_007069.3	NP_009000.2	P53816	HRSL3_HUMAN	phospholipase A2, group XVI	95					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|negative regulation of cell cycle (GO:0045786)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	1-acyl-2-lysophosphatidylserine acylhydrolase activity (GO:0052740)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phosphatidylserine 1-acylhydrolase activity (GO:0052739)|phospholipase A2 activity (GO:0004623)			kidney(2)|lung(1)|ovary(1)|skin(1)	5						GCTCCTCCGCCCGCTGGATGA	0.562																																																0			11											119	100	106					11																	63357674		2201	4298	6499	63114250	SO:0001819	synonymous_variant	11145			X92814	CCDS8047.1	11q12.3	2014-03-14	2008-09-19	2008-09-19	ENSG00000176485	ENSG00000176485	3.1.1.4		17825	protein-coding gene	gene with protein product	"adipose-specific PLA2"	613867	"HRAS-like suppressor 3"	HRASLS3		9771974, 18614531	Standard	NM_007069		Approved	HREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA	uc009you.1	P53816	OTTHUMG00000167852	ENST00000323646.5:c.285G>A	11.37:g.63357674C>T			63114250	B2R7Q4|B7XAK5|Q3SYI3|Q9HDD1	Silent	SNP	ENST00000323646.5	37	CCDS8047.1																																																																																				0.562	PLA2G16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396632.1	NM_001128203		T	63357674	C	T	63357674	2	4	110	1	0	0	0	0	0	0	0	1	12024	610	22	3		3	PLA2G16	11	63357674	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2315681	63357674	71648842	146	29018										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64416248	64416248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cccaatgcggtgcagggcgtCggcgatgaggtctgggagac	18	10	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:64416248C>T	ENST00000377551.1	-	15	3452	c.3241G>A	c.(3241-3243)Gac>Aac	p.D1081N	NRXN2_ENST00000409571.1_Missense_Mutation_p.D1074N|NRXN2_ENST00000377559.3_Missense_Mutation_p.D1041N|NRXN2_ENST00000265459.6_Missense_Mutation_p.D1081N|AP001092.4_ENST00000433606.1_RNA			Q9P2S2	NRX2A_HUMAN	neurexin 2	1081	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)	p.D1081N(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TGCAGGGCGTCGGCGATGAGG	0.642																																																1	Substitution - Missense(1)	ovary(1)	11											91	78	83					11																	64416248		2201	4297	6498	64172824	SO:0001583	missense	9379				CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.3241G>A	11.37:g.64416248C>T	ENSP00000366774:p.Asp1081Asn		64172824	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	.	.	.	.	.	.	.	.	.	.	C	31	5.094373	0.94149	.	.	ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	4.52	4.52	0.55395	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.44097	U	0.000496	D	0.88347	0.6412	M	0.72624	2.21	0.80722	D	1	D;D;D	0.89917	1.0;0.993;1.0	D;P;D	0.77557	0.977;0.701;0.99	D	0.89717	0.3916	10	0.87932	D	0	.	14.7847	0.69793	0.0:1.0:0.0:0.0	.	1041;1081;827	Q9P2S2-2;Q9P2S2;E7EV67	.;NRX2A_HUMAN;.	N	1081;1041;1081;1041;1074	ENSP00000366774:D1081N;ENSP00000366782:D1041N;ENSP00000265459:D1081N;ENSP00000386416:D1074N	ENSP00000265459:D1081N	D	-	1	0	NRXN2	64172824	1.000000	0.71417	0.936000	0.37596	0.930000	0.56654	7.620000	0.83070	2.345000	0.79718	0.561000	0.74099	GAC		0.642	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64416248	C	T	64416248	3	4	110	1	0	0	0	0	1	0	0	0	10697	884	31	1	2198	1	NRXN2	11	64416248	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1058574	64416248	70590268	147	29019										
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67201684	67201684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tacagagacatccctttttcCggcacatgaattgggacgac	9	11	0	2	rs376762664		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:67201684C>T	ENST00000312629.5	+	12	1030	c.985C>T	c.(985-987)Cgg>Tgg	p.R329W	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	329	AGC-kinase C-terminal.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			TCCCTTTTTCCGGCACATGAA	0.647																																																0			11						C	TRP/ARG	2,4140		0,2,2069	261	290	280		985	3.7	1	11		280	0,8404		0,0,4202	no	missense	RPS6KB2	NM_003952.2	101	0,2,6271	TT,TC,CC		0.0,0.0483,0.0159	probably-damaging	329/483	67201684	2,12544	2071	4202	6273	66958260	SO:0001583	missense	6199			AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.985C>T	11.37:g.67201684C>T	ENSP00000308413:p.Arg329Trp		66958260	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.510221	0.44660	4.83E-4	0.0	ENSG00000175634	ENST00000312629	T	0.54479	0.57	4.63	3.71	0.42584	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.072300	0.52532	D	0.000078	T	0.73845	0.3639	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.67548	0.941;0.952	T	0.78545	-0.2163	10	0.87932	D	0	.	10.9313	0.47220	0.3404:0.6596:0.0:0.0	.	329;329	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	W	329	ENSP00000308413:R329W	ENSP00000308413:R329W	R	+	1	2	RPS6KB2	66958260	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	1.471000	0.35365	1.140000	0.42260	0.462000	0.41574	CGG		0.647	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		T	67201684	C	T	67201684	3	4	110	1	0	0	0	0	1	0	0	0	13694	643	23	1	1031	1	RPS6KB2	11	67201684	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2785436	67201684	67804832	148	29020										
ALDH3B2	222	hgsc.bcm.edu	37	chr11	67433013	67433013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtagcagaaccaggccacgCggttggccacggtctggggg	17	11	1	1	rs150455483		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:67433013C>T	ENST00000349015.3	-	7	887	c.449G>A	c.(448-450)cGc>cAc	p.R150H	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Missense_Mutation_p.R150H	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	150					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CCAGGCCACGCGGTTGGCCAC	0.667													C|||	1	0.000199681	0	0	5008	,	,		18499	0.001		0	False		,,,				2504	0															0			11						C	HIS/ARG,HIS/ARG	8,4392	14.3+/-33.2	0,8,2192	109	119	116		449,449	2.1	0.6	11	dbSNP_134	116	0,8588		0,0,4294	no	missense,missense	ALDH3B2	NM_000695.3,NM_001031615.1	29,29	0,8,6486	TT,TC,CC		0.0,0.1818,0.0616	probably-damaging,probably-damaging	150/386,150/386	67433013	8,12980	2200	4294	6494	67189589	SO:0001583	missense	222			U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"Aldehyde dehydrogenases"	411	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 8", "acetaldehyde dehydrogenase 8"	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.449G>A	11.37:g.67433013C>T	ENSP00000255084:p.Arg150His		67189589	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	37	CCDS31622.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	21.6	4.173277	0.78452	0.001818	0.0	ENSG00000132746	ENST00000530069;ENST00000349015	T;T	0.76578	-1.03;-1.03	4.06	2.13	0.27403	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	U	0.000000	D	0.89385	0.6700	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	D	0.89438	0.3721	10	0.87932	D	0	.	10.4571	0.44557	0.1513:0.703:0.1457:0.0	.	35;150	B4DSX1;P48448	.;AL3B2_HUMAN	H	150	ENSP00000431595:R150H;ENSP00000255084:R150H	ENSP00000255084:R150H	R	-	2	0	ALDH3B2	67189589	0.997000	0.39634	0.625000	0.29200	0.665000	0.39181	3.696000	0.54757	0.460000	0.27045	-0.359000	0.07587	CGC		0.667	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695		T	67433013	C	T	67433013	3	4	110	1	0	0	0	0	1	0	0	0	500	768	27	1	724	1	ALDH3B2	11	67433013	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	231329	67433013	67573503	149	29021										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92714759	92714759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cctttgtgatgggcctgagcGtcatcggctctgtcttcaat	11	11	4	2	rs145440211	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:92714759G>A	ENST00000257068.2	+	2	376	c.370G>A	c.(370-372)Gtc>Atc	p.V124I		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	124					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	GGGCCTGAGCGTCATCGGCTC	0.592																																																0			11						G	ILE/VAL	2,4400	4.2+/-10.8	0,2,2199	146	131	136		370	4	1	11	dbSNP_134	136	10,8586	7.7+/-29.5	0,10,4288	yes	missense	MTNR1B	NM_005959.3	29	0,12,6487	AA,AG,GG		0.1163,0.0454,0.0923	probably-damaging	124/363	92714759	12,12986	2201	4298	6499	92354407	SO:0001583	missense	4544			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.370G>A	11.37:g.92714759G>A	ENSP00000257068:p.Val124Ile		92354407		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139846	0.77775	4.54E-4	0.001163	ENSG00000134640	ENST00000257068	T	0.72394	-0.65	3.97	3.97	0.46021	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.82986	0.5156	M	0.76574	2.34	0.58432	D	0.999993	D	0.89917	1.0	D	0.76575	0.988	D	0.84356	0.0535	10	0.46703	T	0.11	-49.6579	16.6059	0.84828	0.0:0.0:1.0:0.0	.	124	P49286	MTR1B_HUMAN	I	124	ENSP00000257068:V124I	ENSP00000257068:V124I	V	+	1	0	MTNR1B	92354407	1.000000	0.71417	0.953000	0.39169	0.933000	0.57130	5.751000	0.68720	2.220000	0.72140	0.491000	0.48974	GTC		0.592	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92714759	G	A	92714759	3	1	110	1	0	0	0	0	1	0	0	0	9982	1145	40	1	376	1	MTNR1B	11	92714759	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	25281746	92714759	42291757	150	29022										
MMP10	4319	hgsc.bcm.edu	37	chr11	102650015	102650015	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agaatgtgagtggagtcaccTcttcccagactttcagagct	10	10	3	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:102650015T>C	ENST00000279441.4	-	3	461	c.425A>G	c.(424-426)gAg>gGg	p.E142G		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	142			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TGGAGTCACCTCTTCCCAGAC	0.408																																																0			11											169	167	168					11																	102650015		2203	4299	6502	102155225	SO:0001583	missense	4319			X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.425A>G	11.37:g.102650015T>C	ENSP00000279441:p.Glu142Gly		102155225	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	t	8.855	0.945541	0.18356	.	.	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.53423	2.2;0.62	4.38	3.23	0.37069	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.487757	0.19607	N	0.110241	T	0.51517	0.1679	L	0.49256	1.55	0.23314	N	0.99793	D	0.57899	0.981	P	0.57283	0.817	T	0.35968	-0.9767	10	0.46703	T	0.11	.	6.0888	0.19983	0.0:0.1282:0.1515:0.7203	.	142	P09238	MMP10_HUMAN	G	142	ENSP00000279441:E142G;ENSP00000441485:E142G	ENSP00000279441:E142G	E	-	2	0	MMP10	102155225	0.000000	0.05858	1.000000	0.80357	0.459000	0.32528	-0.082000	0.11304	0.800000	0.34041	0.482000	0.46254	GAG		0.408	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			C	102650015	T	C	102650015	3	2	110	1	0	0	0	0	1	0	0	0	9679	1551	54	4	1037	4	MMP10	11	102650015	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	9935256	102650015	32356501	151	29023										
MMP13	4322	hgsc.bcm.edu	37	chr11	102826346	102826346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggaggtcttcctcagacaaaTcatcttcatcaccaccactg	6	14	6	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:102826346T>C	ENST00000260302.3	-	1	117	c.89A>G	c.(88-90)gAt>gGt	p.D30G	MMP13_ENST00000340273.4_Missense_Mutation_p.D30G	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	30					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CTCAGACAAATCATCTTCATC	0.502																																																0			11											113	101	105					11																	102826346		2202	4299	6501	102331556	SO:0001583	missense	4322			X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.89A>G	11.37:g.102826346T>C	ENSP00000260302:p.Asp30Gly		102331556	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	T	8.414	0.844909	0.16963	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.36520	1.25;1.25	5.62	4.49	0.54785	Metallopeptidase, catalytic domain (1);	0.422167	0.28742	N	0.014293	T	0.18759	0.0450	N	0.08118	0	0.24237	N	0.995371	B	0.31026	0.304	B	0.26693	0.072	T	0.11817	-1.0572	10	0.33141	T	0.24	.	11.8916	0.52633	0.0:0.0686:0.0:0.9314	.	30	P45452	MMP13_HUMAN	G	30	ENSP00000260302:D30G;ENSP00000339672:D30G	ENSP00000260302:D30G	D	-	2	0	MMP13	102331556	0.671000	0.27521	0.040000	0.18447	0.120000	0.20174	3.454000	0.52986	1.052000	0.40392	0.533000	0.62120	GAT		0.502	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		C	102826346	T	C	102826346	3	2	110	1	0	0	0	0	1	0	0	0	9682	1435	50	4	1366	4	MMP13	11	102826346	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	176331	102826346	32180170	152	29024										
ATM	472	hgsc.bcm.edu	37	chr11	108200957	108200957	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	caagatacacagtaaaggttCagcgagagctggagttggat	13	6	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:108200957C>T	ENST00000452508.2	+	51	7513	c.7324C>T	c.(7324-7326)Cag>Tag	p.Q2442*	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Nonsense_Mutation_p.Q2442*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2442	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.		Q -> P (in T-prolymphocytic leukemia; also in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9288106}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AGTAAAGGTTCAGCGAGAGCT	0.348			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											83	88	86					11																	108200957		2201	4298	6499	107706167	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7324C>T	11.37:g.108200957C>T	ENSP00000388058:p.Gln2442*		107706167	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	49	15.217711	0.99826	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	.	.	.	4.7	4.7	0.59300	.	0.105878	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.9756	0.86312	0.0:1.0:0.0:0.0	.	.	.	.	X	2442	.	ENSP00000278616:Q2442X	Q	+	1	0	ATM	107706167	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.430000	0.66501	2.293000	0.77203	0.561000	0.74099	CAG		0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108200957	C	T	108200957	4	4	110	1	0	0	0	0	0	1	0	0	1110	827	29	3	7518	3	ATM	11	108200957	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5374611	108200957	26805559	153	29025										
CCDC84	338657	hgsc.bcm.edu	37	chr11	118886110	118886110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgcaggctggctgccctcttTtggccgcgtctggaataatg	13	11	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr11:118886110T>C	ENST00000334418.1	+	10	955	c.899T>C	c.(898-900)tTt>tCt	p.F300S	RPS25_ENST00000528547.1_5'Flank	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	300										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CTGCCCTCTTTTGGCCGCGTC	0.542																																																0			11											38	40	40					11																	118886110		2200	4294	6494	118391320	SO:0001583	missense	338657			AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.899T>C	11.37:g.118886110T>C	ENSP00000334767:p.Phe300Ser		118391320		Missense_Mutation	SNP	ENST00000334418.1	37	CCDS8405.1	.	.	.	.	.	.	.	.	.	.	T	32	5.161437	0.94727	.	.	ENSG00000186166	ENST00000334418	T	0.73258	-0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.84447	0.5474	M	0.79011	2.435	0.54753	D	0.999985	D	0.89917	1.0	D	0.87578	0.998	D	0.86476	0.1788	10	0.87932	D	0	-12.6706	16.0796	0.80995	0.0:0.0:0.0:1.0	.	300	Q86UT8	CCD84_HUMAN	S	300	ENSP00000334767:F300S	ENSP00000334767:F300S	F	+	2	0	CCDC84	118391320	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.539000	0.82063	2.206000	0.71126	0.533000	0.62120	TTT		0.542	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		C	118886110	T	C	118886110	3	2	110	1	0	0	0	0	1	0	0	0	2864	1841	64	4	937	4	CCDC84	11	118886110	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	10685153	118886110	16120406	154	29026										
CD163	9332	hgsc.bcm.edu	37	chr12	7636010	7636010	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgtgcccacactcactatggCcccagcgtctggcaggacaa	10	15	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:7636010C>G	ENST00000359156.4	-	12	3243	c.3041G>C	c.(3040-3042)gGc>gCc	p.G1014A	CD163_ENST00000432237.2_Missense_Mutation_p.G1014A|CD163_ENST00000539632.1_5'UTR|CD163_ENST00000541972.1_Missense_Mutation_p.G1002A|CD163_ENST00000396620.3_Missense_Mutation_p.G1047A	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	1014	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.G1014D(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CTCACTATGGCCCCAGCGTCT	0.532																																																1	Substitution - Missense(1)	ovary(1)	12											111	97	102					12																	7636010		2203	4300	6503	7527277	SO:0001583	missense	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.3041G>C	12.37:g.7636010C>G	ENSP00000352071:p.Gly1014Ala		7527277	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.80|19.80	3.895357|3.895357	0.72639|0.72639	.|.	.|.	ENSG00000177575|ENSG00000177575	ENST00000537626|ENST00000359156;ENST00000542280;ENST00000541972;ENST00000396620;ENST00000432237	.|T;T;T;T;T	.|0.53206	.|0.63;0.63;0.63;0.63;0.63	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.|0.371003	.|0.25854	.|N	.|0.027878	T|T	0.67878|0.67878	0.2940|0.2940	M|M	0.89715|0.89715	3.055|3.055	0.31683|0.31683	N|N	0.64282|0.64282	.|D;D;D	.|0.60575	.|0.983;0.988;0.983	.|P;P;P	.|0.60286	.|0.872;0.814;0.832	T|T	0.74592|0.74592	-0.3614|-0.3614	5|10	.|0.36615	.|T	.|0.2	.|.	10.4935|10.4935	0.44764|0.44764	0.0:0.9112:0.0:0.0887|0.0:0.9112:0.0:0.0887	.|.	.|1047;1014;1014	.|C9JHR8;Q86VB7-3;Q86VB7	.|.;.;C163A_HUMAN	P|A	27|1014;54;1002;1047;1014	.|ENSP00000352071:G1014A;ENSP00000445438:G54A;ENSP00000444071:G1002A;ENSP00000379863:G1047A;ENSP00000403885:G1014A	.|ENSP00000352071:G1014A	A|G	-|-	1|2	0|0	CD163|CD163	7527277|7527277	0.039000|0.039000	0.19947|0.19947	0.997000|0.997000	0.53966|0.53966	0.871000|0.871000	0.50021|0.50021	0.833000|0.833000	0.27504|0.27504	2.707000|2.707000	0.92482|0.92482	0.555000|0.555000	0.69702|0.69702	GCC|GGC		0.532	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		G	7636010	C	G	7636010	3	3	110	1	0	0	0	0	1	0	0	0	2973	739	26	5	449	5	CD163	12	7636010	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10		7636010	126215885	155	29027										
CD163	9332	hgsc.bcm.edu	37	chr12	7640085	7640085	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctccagatctgaccatttccTtttccaaaacgtgctcctcc	4	16	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:7640085T>C	ENST00000359156.4	-	8	2122	c.1920A>G	c.(1918-1920)aaA>aaG	p.K640K	CD163_ENST00000432237.2_Silent_p.K640K|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000541972.1_Silent_p.K628K|CD163_ENST00000396620.3_Silent_p.K673K	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	640	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GACCATTTCCTTTTCCAAAAC	0.478																																																0			12											154	140	145					12																	7640085		2203	4300	6503	7531352	SO:0001819	synonymous_variant	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1920A>G	12.37:g.7640085T>C			7531352	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																				0.478	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		C	7640085	T	C	7640085	2	2	110	1	0	0	0	0	0	0	0	1	2973	1606	56	4		4	CD163	12	7640085	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4075	7640085	126211810	156	29028										
FOXJ2	55810	hgsc.bcm.edu	37	chr12	8200496	8200496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggcttttcttctctcctggGggacatcccaccctcgaaca	8	15	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:8200496G>T	ENST00000162391.3	+	7	1981	c.836G>T	c.(835-837)gGg>gTg	p.G279V	FOXJ2_ENST00000428177.2_Missense_Mutation_p.G279V	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	279					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		TCTCTCCTGGGGGACATCCCA	0.552																																																0			12											50	58	55					12																	8200496		2203	4300	6503	8091763	SO:0001583	missense	55810			AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"Forkhead boxes"	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.836G>T	12.37:g.8200496G>T	ENSP00000162391:p.Gly279Val		8091763	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Missense_Mutation	SNP	ENST00000162391.3	37	CCDS8587.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685712	0.68157	.	.	ENSG00000065970	ENST00000162391;ENST00000428177	D;D	0.95137	-3.37;-3.62	5.42	5.42	0.78866	.	2.072210	0.02298	N	0.070893	D	0.96713	0.8927	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.87812	0.2632	10	0.19590	T	0.45	.	15.0867	0.72158	0.0:0.0:1.0:0.0	.	279;279	Q9P0K8;Q9P0K8-2	FOXJ2_HUMAN;.	V	279	ENSP00000162391:G279V;ENSP00000403411:G279V	ENSP00000162391:G279V	G	+	2	0	FOXJ2	8091763	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	5.915000	0.69973	2.702000	0.92279	0.462000	0.41574	GGG		0.552	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		T	8200496	G	T	8200496	3	4	110	1	0	0	0	0	1	0	0	0	6031	1232	43	2	858	2	FOXJ2	12	8200496	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	560411	8200496	125651399	157	29029										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380243	25380243	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaaagccctccccagtcctcAtgtactggtccctcattgca	7	16	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:25380243A>G	ENST00000256078.4	-	3	278	c.215T>C	c.(214-216)aTg>aCg	p.M72T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.M72T	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	72					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCCAGTCCTCATGTACTGGTC	0.388		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											117	107	110					12																	25380243		2203	4300	6503	25271510	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.215T>C	12.37:g.25380243A>G	ENSP00000256078:p.Met72Thr		25271510	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.901136	0.72754	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	T;T	0.76839	-1.05;-1.05	5.77	4.62	0.57501	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.86781	0.6015	M	0.76838	2.35	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79784	0.979;0.993	D	0.87530	0.2452	10	0.87932	D	0	.	11.4078	0.49908	0.9291:0.0:0.0709:0.0	.	72;72	P01116-2;P01116	.;RASK_HUMAN	T	72	ENSP00000308495:M72T;ENSP00000256078:M72T	ENSP00000256078:M72T	M	-	2	0	KRAS	25271510	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.271000	0.95698	1.107000	0.41642	0.533000	0.62120	ATG		0.388	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		G	25380243	A	G	25380243	3	3	110	1	0	0	0	0	1	0	0	0	8459	217	8	4	487	4	KRAS	12	25380243	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	17179747	25380243	108471652	158	29030										
C12orf11	55726	hgsc.bcm.edu	37	chr12	27077412	27077412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cttcactggttaaaaccgggGacaactacagaaaaacatac	7	10	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:27077412G>A	ENST00000261191.7	-	7	1216	c.680C>T	c.(679-681)tCc>tTc	p.S227F	ASUN_ENST00000539625.1_Missense_Mutation_p.S126F	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	227			S -> P (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TAAAACCGGGGACAACTACAG	0.318																																																0			12											75	78	77					12																	27077412		2203	4300	6503	26968679	SO:0001583	missense	55726			AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.680C>T	12.37:g.27077412G>A	ENSP00000261191:p.Ser227Phe		26968679	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Missense_Mutation	SNP	ENST00000261191.7	37	CCDS8708.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.854292	0.91355	.	.	ENSG00000064102	ENST00000261191;ENST00000539625	T;T	0.55413	0.52;0.52	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73892	0.3645	M	0.71036	2.16	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	T	0.75133	-0.3425	10	0.87932	D	0	-4.738	20.0759	0.97745	0.0:0.0:1.0:0.0	.	227	Q9NVM9	M89BB_HUMAN	F	227;126	ENSP00000261191:S227F;ENSP00000443724:S126F	ENSP00000261191:S227F	S	-	2	0	C12orf11	26968679	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.795000	0.91872	2.814000	0.96858	0.655000	0.94253	TCC		0.318	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		A	27077412	G	A	27077412	3	1	110	1	0	0	0	0	1	0	0	0	1679	1174	41	3	1484	3	C12orf11	12	27077412	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1697169	27077412	106774483	159	29031										
C12orf40	283461	hgsc.bcm.edu	37	chr12	40044119	40044119	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttttcagtccatcacataaaActacacgatttgggacatta	5	9	2	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:40044119A>G	ENST00000324616.5	+	7	803	c.649A>G	c.(649-651)Act>Gct	p.T217A	C12orf40_ENST00000405531.3_Missense_Mutation_p.T217A|C12orf40_ENST00000398716.1_Missense_Mutation_p.T140A	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	217										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATCACATAAAACTACACGATT	0.313																																																0			12											76	69	71					12																	40044119		1814	4071	5885	38330386	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.649A>G	12.37:g.40044119A>G	ENSP00000317671:p.Thr217Ala		38330386	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	A	0.798	-0.756296	0.03019	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.46063	0.88;0.89	3.53	-2.51	0.06365	.	0.544584	0.15415	N	0.263534	T	0.23014	0.0556	L	0.27053	0.805	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.10636	-1.0621	10	0.51188	T	0.08	.	4.312	0.10976	0.4376:0.1867:0.3757:0.0	.	217	Q86WS4	CL040_HUMAN	A	217;140;217	ENSP00000383897:T217A;ENSP00000317671:T217A	ENSP00000317671:T217A	T	+	1	0	C12orf40	38330386	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.603000	0.05674	-0.451000	0.07097	0.528000	0.53228	ACT		0.313	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		G	40044119	A	G	40044119	3	3	110	1	0	0	0	0	1	0	0	0	1690	43	2	4	675	4	C12orf40	12	40044119	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	12966707	40044119	93807776	160	29032										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43847820	43847820	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccatttacaggacgtgtttcCgtttctttgtttacacatag	7	9	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:43847820C>T	ENST00000389420.3	-	12	1649	c.1650G>A	c.(1648-1650)acG>acA	p.T550T	ADAMTS20_ENST00000553158.1_Silent_p.T550T	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	550	Disintegrin.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		GACGTGTTTCCGTTTCTTTGT	0.398																																																0			12											119	97	104					12																	43847820		2203	4300	6503	42134087	SO:0001819	synonymous_variant	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1650G>A	12.37:g.43847820C>T			42134087	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																				0.398	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43847820	C	T	43847820	2	4	110	1	0	0	0	0	0	0	0	1	266	639	23	1		1	ADAMTS20	12	43847820	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	3803701	43847820	90004075	161	29033										
TMEM106C	79022	hgsc.bcm.edu	37	chr12	48360513	48360513	+	Frame_Shift_Del	DEL	G	G	-													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggaggaccgttttcctatgtGtagtaaggacactgttctct							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:48360513delG	ENST00000429772.2	+	6	713	c.600delG	c.(598-600)gtgfs	p.V200fs	TMEM106C_ENST00000550552.1_Frame_Shift_Del_p.V181fs|TMEM106C_ENST00000552546.1_Frame_Shift_Del_p.V129fs|TMEM106C_ENST00000449758.2_Frame_Shift_Del_p.V181fs|TMEM106C_ENST00000256686.6_Frame_Shift_Del_p.V181fs|TMEM106C_ENST00000549288.1_Intron|TMEM106C_ENST00000552561.1_Frame_Shift_Del_p.V200fs	NM_001143842.1	NP_001137314.1	Q9BVX2	T106C_HUMAN	transmembrane protein 106C	200						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)		TTTCCTATGTGTAGTAAGGAC	0.488																																																0			12											163	152	156					12																	48360513		2203	4300	6503	46646780	SO:0001589	frameshift_variant	79022			BC000854	CCDS8758.1, CCDS44867.1	12q13.1	2005-12-19				ENSG00000134291			28775	protein-coding gene	gene with protein product							Standard	NM_024056		Approved	MGC5576	uc001rqr.3	Q9BVX2	OTTHUMG00000169892	ENST00000429772.2:c.600delG	12.37:g.48360513delG	ENSP00000400471:p.Val200fs		46646780	B2R998|B7Z5M4|Q3B761	Frame_Shift_Del	DEL	ENST00000429772.2	37	CCDS8758.1																																																																																				0.488	TMEM106C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406452.1	NM_024056		-	48360513	G	-	48360513	7	5	110	1	0	1	0	1	0	0	0	0	16061	1364	48	0	618	0	TMEM106C	12	48360513	Frame_Shift_Del	DEL	G	TCGA-EI-6506-01A-11D-1733-10	4512693	48360513	85491382	162	29034										
NAV3	89795	hgsc.bcm.edu	37	chr12	78582114	78582114	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttagatggtgtaataagacgTctctttaaggtatgttgtgc	11	4	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:78582114T>C	ENST00000397909.2	+	32	6050	c.5877T>C	c.(5875-5877)cgT>cgC	p.R1959R	NAV3_ENST00000228327.6_Silent_p.R1937R|NAV3_ENST00000536525.2_Silent_p.R1937R|NAV3_ENST00000266692.7_Silent_p.R1760R|NAV3_ENST00000552300.1_3'UTR			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1959						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TAATAAGACGTCTCTTTAAGG	0.343										HNSCC(70;0.22)																																						0			12											111	107	108					12																	78582114		1851	4089	5940	77106245	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5877T>C	12.37:g.78582114T>C			77106245	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	T	9.779	1.174675	0.21704	.	.	ENSG00000067798	ENST00000552895	.	.	.	5.74	3.2	0.36748	.	.	.	.	.	T	0.57799	0.2078	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53279	-0.8461	4	.	.	.	-4.2121	8.311	0.32071	0.1208:0.0:0.2433:0.6359	.	.	.	.	P	832	.	.	S	+	1	0	NAV3	77106245	0.994000	0.37717	1.000000	0.80357	0.984000	0.73092	0.200000	0.17257	0.971000	0.38288	0.482000	0.46254	TCT		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		C	78582114	T	C	78582114	2	2	110	1	0	0	0	0	0	0	0	1	10215	1654	58	4		4	NAV3	12	78582114	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	30221601	78582114	55269781	163	29035										
UTP20	27340	hgsc.bcm.edu	37	chr12	101764871	101764871	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagctgttggtcccagaaatCgatgaggtcatgcggaaagt	13	7	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:101764871C>T	ENST00000261637.4	+	51	6897	c.6723C>T	c.(6721-6723)atC>atT	p.I2241I		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2241					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TCCCAGAAATCGATGAGGTCA	0.448																																																0			12											154	147	149					12																	101764871		2203	4300	6503	100289002	SO:0001819	synonymous_variant	27340			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6723C>T	12.37:g.101764871C>T			100289002	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																				0.448	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101764871	C	T	101764871	2	4	110	1	0	0	0	0	0	0	0	1	17139	874	31	1		1	UTP20	12	101764871	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	23182757	101764871	32087024	164	29036										
STAB2	55576	hgsc.bcm.edu	37	chr12	104155080	104155080	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctcttctcatttccctagacGgagaccaggtttgttgatgg	10	10	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:104155080G>T	ENST00000388887.2	+	66	7455	c.7251G>T	c.(7249-7251)acG>acT	p.T2417T	RP11-341G23.4_ENST00000550029.1_RNA|RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.T2417T(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTCCCTAGACGGAGACCAGGT	0.512																																																1	Substitution - coding silent(1)	lung(1)	12											148	127	134					12																	104155080		2203	4300	6503	102679210	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7251G>T	12.37:g.104155080G>T			102679210		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.512	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104155080	G	T	104155080	2	4	110	1	0	0	0	0	0	0	0	1	15277	1103	39	2		2	STAB2	12	104155080	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2390209	104155080	29696815	165	29037										
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104208740	104208740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gttcattgatgagaaggtccCgtgcagcattaaatatcagc	10	8	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:104208740C>T	ENST00000392876.3	-	2	408	c.368G>A	c.(367-369)cGg>cAg	p.R123Q		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	123						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						GAGAAGGTCCCGTGCAGCATT	0.458																																																0			12											167	156	160					12																	104208740		2203	4300	6503	102732870	SO:0001583	missense	51559			AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.368G>A	12.37:g.104208740C>T	ENSP00000376615:p.Arg123Gln		102732870	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	37	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	C	36	5.794816	0.96952	.	.	ENSG00000111696	ENST00000392876	T	0.23147	1.92	5.87	5.87	0.94306	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.86651	2.83	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.59542	-0.7435	10	0.49607	T	0.09	-34.9703	20.5827	0.99408	0.0:1.0:0.0:0.0	.	123	Q86UY8	NT5D3_HUMAN	Q	123	ENSP00000376615:R123Q	ENSP00000376615:R123Q	R	-	2	0	NT5DC3	102732870	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.419000	0.80179	2.941000	0.99782	0.655000	0.94253	CGG		0.458	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		T	104208740	C	T	104208740	3	4	110	1	0	0	0	0	1	0	0	0	10723	652	23	1	1330	1	NT5DC3	12	104208740	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	53660	104208740	29643155	166	29038										
SART3	9733	hgsc.bcm.edu	37	chr12	108920086	108920086	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcgaagagtggcctgagcttCgtgtccggctcctgcatgct	13	12	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr12:108920086C>T	ENST00000228284.3	-	16	2394	c.2160G>A	c.(2158-2160)acG>acA	p.T720T	SART3_ENST00000431469.2_Silent_p.T684T	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	720	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						GCCTGAGCTTCGTGTCCGGCT	0.587									Porokeratosis																																							0			12											98	81	87					12																	108920086		2203	4300	6503	107444216	SO:0001819	synonymous_variant	9733	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"RNA binding motif (RRM) containing"	16860	protein-coding gene	gene with protein product		611684	"squamous cell carcinoma antigen recognised by T cells 3"			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.2160G>A	12.37:g.108920086C>T			107444216	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	37	CCDS9117.1	.	.	.	.	.	.	.	.	.	.	C	0.041	-1.282901	0.01398	.	.	ENSG00000075856	ENST00000412617	.	.	.	5.81	-6.58	0.01836	.	.	.	.	.	T	0.45135	0.1327	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.27905	-1.0060	7	0.87932	D	0	-0.5482	20.5985	0.99450	0.0734:0.1292:0.747:0.0505	.	667	E7EMI4	.	K	667	.	ENSP00000400292:E667K	E	-	1	0	SART3	107444216	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.677000	0.05215	-1.220000	0.02594	-0.951000	0.02657	GAA		0.587	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1			T	108920086	C	T	108920086	2	4	110	1	0	0	0	0	0	0	0	1	13884	871	31	1		1	SART3	12	108920086	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4711346	108920086	24931809	167	29039										
NUPL1	9818	hgsc.bcm.edu	37	chr13	25911115	25911115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttagttttggaacgccattcGgctcaggtattggcactggc	12	9	1	0	rs373360958		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr13:25911115G>A	ENST00000381736.3	+	14	1727	c.1477G>A	c.(1477-1479)Ggc>Agc	p.G493S	NUPL1_ENST00000381718.3_Missense_Mutation_p.G481S|NUPL1_ENST00000466694.1_3'UTR	NM_001008564.1|NM_014089.3	NP_001008564.1|NP_054808.1	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1	493	14 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	nucleocytoplasmic transporter activity (GO:0005487)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|stomach(1)|urinary_tract(1)	16		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		AACGCCATTCGGCTCAGGTAT	0.378																																					Pancreas(166;1040 2004 4560 4728 37041)|GBM(109;1045 1520 7614 9308 19618)											0			13						G	SER/GLY,SER/GLY	0,4406		0,0,2203	84	80	81		1477,1441	4.9	1	13		81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NUPL1	NM_014089.3,NM_001008564.1	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	493/600,481/588	25911115	1,13005	2203	4300	6503	24809115	SO:0001583	missense	9818			AB007870	CCDS9314.1, CCDS31949.1	13q12.12	2011-04-12			ENSG00000139496	ENSG00000139496			20261	protein-coding gene	gene with protein product		607615				9455477	Standard	NM_014089		Approved	KIAA0410	uc001uqi.3	Q9BVL2	OTTHUMG00000016608	ENST00000381736.3:c.1477G>A	13.37:g.25911115G>A	ENSP00000371155:p.Gly493Ser		24809115	A6NI12|B4DZJ1|O43160|Q5JRG2|Q5JRG5	Missense_Mutation	SNP	ENST00000381736.3	37	CCDS9314.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643806	0.67244	0.0	1.16E-4	ENSG00000139496	ENST00000381736;ENST00000313619;ENST00000381718	T;T	0.33654	1.4;1.44	5.78	4.94	0.65067	.	0.227351	0.45606	N	0.000346	T	0.27866	0.0686	L	0.31664	0.95	0.44937	D	0.997953	B;B	0.24186	0.014;0.099	B;B	0.20577	0.01;0.03	T	0.03706	-1.1011	10	0.25751	T	0.34	-1.1943	14.9374	0.70967	0.0687:0.0:0.9313:0.0	.	481;493	A6NI12;Q9BVL2	.;NUPL1_HUMAN	S	493;470;481	ENSP00000371155:G493S;ENSP00000371137:G481S	ENSP00000318459:G470S	G	+	1	0	NUPL1	24809115	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.949000	0.70257	1.451000	0.47736	0.585000	0.79938	GGC		0.378	NUPL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044228.2			A	25911115	G	A	25911115	3	1	110	1	0	0	0	0	1	0	0	0	10805	1116	39	1	1531	1	NUPL1	13	25911115	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10		25911115	89258763	168	29040										
SPG20	23111	hgsc.bcm.edu	37	chr13	36888471	36888471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtttttcttctggttgaatcCgctctcggagtttagaagca	10	8	3	2	rs7321457	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr13:36888471C>T	ENST00000451493.1	-	6	1593	c.1376G>A	c.(1375-1377)cGg>cAg	p.R459Q	SPG20_ENST00000494062.2_Missense_Mutation_p.R459Q|SPG20_ENST00000438666.2_Missense_Mutation_p.R459Q|SPG20_ENST00000355182.4_Missense_Mutation_p.R459Q	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	459					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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)		TGGTTGAATCCGCTCTCGGAG	0.463													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		14771	0		0	False		,,,				2504	0															0			13						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	4,4402	9.9+/-24.2	0,4,2199	111	111	111		1376,1376,1376,1376	3.2	1	13	dbSNP_116	111	0,8600		0,0,4300	yes	missense,missense,missense,missense	SPG20	NM_001142294.1,NM_001142295.1,NM_001142296.1,NM_015087.4	43,43,43,43	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging,probably-damaging,probably-damaging	459/667,459/667,459/667,459/667	36888471	4,13002	2203	4300	6503	35786471	SO:0001583	missense	23111			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1376G>A	13.37:g.36888471C>T	ENSP00000414147:p.Arg459Gln		35786471	O60349|Q86Y67|Q9H1T2|Q9H1T3	Missense_Mutation	SNP	ENST00000451493.1	37	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524314	0.85600	9.08E-4	0.0	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	D;D;D	0.89050	-2.46;-2.46;-2.46	5.85	3.15	0.36227	Senescence/spartin-associated (1);	0.126087	0.53938	D	0.000057	D	0.86364	0.5915	L	0.47190	1.495	0.31888	N	0.61756	D;D	0.64830	0.994;0.994	P;P	0.50791	0.65;0.65	D	0.85868	0.1414	10	0.51188	T	0.08	-12.7412	6.1141	0.20117	0.0:0.5895:0.0:0.4105	rs7321457;rs7321457	459;459	A8K6Q9;Q8N0X7	.;SPG20_HUMAN	Q	459	ENSP00000406061:R459Q;ENSP00000347314:R459Q;ENSP00000414147:R459Q	ENSP00000347314:R459Q	R	-	2	0	SPG20	35786471	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.265000	0.43311	1.467000	0.48044	0.563000	0.77884	CGG		0.463	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			T	36888471	C	T	36888471	3	4	110	1	0	0	0	0	1	0	0	0	15081	652	23	1	640	1	SPG20	13	36888471	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	10977356	36888471	78281407	169	29041										
CDADC1	81602	hgsc.bcm.edu	37	chr13	49854742	49854742	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttaaaggtgcaggcataaaaCaaatctatgcaggagatgta	10	5	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr13:49854742C>A	ENST00000251108.6	+	8	1431	c.1318C>A	c.(1318-1320)Caa>Aaa	p.Q440K	CDADC1_ENST00000444959.1_Missense_Mutation_p.Q242K	NM_001193478.1|NM_030911.3	NP_001180407.1|NP_112173.1	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	440							hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	16		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		AGGCATAAAACAAATCTATGC	0.388																																																0			13											111	107	108					13																	49854742		2203	4300	6503	48752743	SO:0001583	missense	81602			AY027525	CCDS9415.1	13q14.11	2008-02-05			ENSG00000102543	ENSG00000102543			20299	protein-coding gene	gene with protein product							Standard	NM_001193478		Approved	NYD-SP15	uc001vcu.3	Q9BWV3	OTTHUMG00000016913	ENST00000251108.6:c.1318C>A	13.37:g.49854742C>A	ENSP00000251108:p.Gln440Lys		48752743	Q49A08|Q4G119|Q5TAW9|Q7Z764|Q9NT36	Missense_Mutation	SNP	ENST00000251108.6	37	CCDS9415.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.823859	0.90873	.	.	ENSG00000102543	ENST00000251108;ENST00000444959	T;T	0.37915	1.17;1.17	5.64	5.64	0.86602	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.051153	0.85682	D	0.000000	T	0.33876	0.0878	N	0.02697	-0.525	0.80722	D	1	P	0.50066	0.931	P	0.57283	0.817	T	0.48801	-0.9003	10	0.46703	T	0.11	-16.993	19.0502	0.93039	0.0:1.0:0.0:0.0	.	440	Q9BWV3	CDAC1_HUMAN	K	440;242	ENSP00000251108:Q440K;ENSP00000407226:Q242K	ENSP00000251108:Q440K	Q	+	1	0	CDADC1	48752743	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.062000	0.76706	2.816000	0.96949	0.561000	0.74099	CAA		0.388	CDADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044902.2	NM_030911		A	49854742	C	A	49854742	3	1	110	1	0	0	0	0	1	0	0	0	3059	479	17	2	1348	2	CDADC1	13	49854742	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	12966271	49854742	65315136	170	29042										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207643	58207643	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gggatgctggagattgacgtGcaggcccgagacctggggcc	18	10	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr13:58207643G>C	ENST00000377918.3	+	1	989	c.963G>C	c.(961-963)gtG>gtC	p.V321V		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	321	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		AGATTGACGTGCAGGCCCGAG	0.592																																					Melanoma(72;952 1291 1619 12849 33676)											0			13											81	77	78					13																	58207643		2203	4300	6503	57105644	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.963G>C	13.37:g.58207643G>C			57105644	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.592	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		C	58207643	G	C	58207643	2	2	110	1	0	0	0	0	0	0	0	1	11543	1306	46	5		5	PCDH17	13	58207643	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	8352901	58207643	56962235	171	29043										
KLF12	11278	hgsc.bcm.edu	37	chr13	74289528	74289528	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tatgtgtcctccggtgagccTtcaggtgagaactttttgtg	12	8	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr13:74289528T>C	ENST00000377669.2	-	6	1030	c.1004A>G	c.(1003-1005)aAg>aGg	p.K335R	KLF12_ENST00000377666.4_Missense_Mutation_p.K335R	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	335					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		CCGGTGAGCCTTCAGGTGAGA	0.537																																																0			13											173	141	152					13																	74289528		2203	4300	6503	73187529	SO:0001583	missense	11278			AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.1004A>G	13.37:g.74289528T>C	ENSP00000366897:p.Lys335Arg		73187529	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.038950	0.93630	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.36157	1.27;1.27	5.81	5.81	0.92471	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.45458	0.1343	N	0.25485	0.75	0.80722	D	1	D	0.76494	0.999	D	0.65573	0.936	T	0.33523	-0.9865	10	0.36615	T	0.2	.	15.3448	0.74327	0.0:0.0:0.0:1.0	.	335	Q9Y4X4	KLF12_HUMAN	R	335	ENSP00000366897:K335R;ENSP00000366894:K335R	ENSP00000344057:K335R	K	-	2	0	KLF12	73187529	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.978000	0.88095	2.216000	0.71823	0.533000	0.62120	AAG		0.537	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		C	74289528	T	C	74289528	3	2	110	1	0	0	0	0	1	0	0	0	8361	1609	56	4	212	4	KLF12	13	74289528	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	16081885	74289528	40880350	172	29044										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215705	20215705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tttttacattgctattgtccTgggaaacctcttgatagtgg	9	7	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:20215705T>C	ENST00000331723.1	+	1	119	c.119T>C	c.(118-120)cTg>cCg	p.L40P		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCTATTGTCCTGGGAAACCTC	0.393																																																0			14											188	193	191					14																	20215705		2203	4300	6503	19285545	SO:0001583	missense	441669			AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.119T>C	14.37:g.20215705T>C	ENSP00000330049:p.Leu40Pro		19285545	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	37	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	15.29	2.789857	0.50102	.	.	ENSG00000182652	ENST00000331723	T	0.02552	4.25	4.32	4.32	0.51571	.	0.000000	0.31859	U	0.006947	T	0.09949	0.0244	M	0.90483	3.12	0.53005	D	0.999962	P	0.47409	0.895	P	0.49561	0.615	T	0.00214	-1.1912	10	0.87932	D	0	.	6.379	0.21523	0.0:0.1101:0.0:0.8899	.	40	Q8NH05	OR4Q3_HUMAN	P	40	ENSP00000330049:L40P	ENSP00000330049:L40P	L	+	2	0	OR4Q3	19285545	0.000000	0.05858	0.992000	0.48379	0.861000	0.49209	0.821000	0.27338	1.814000	0.52955	0.416000	0.27883	CTG		0.393	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			C	20215705	T	C	20215705	3	2	110	1	0	0	0	0	1	0	0	0	11112	1580	55	4	121	4	OR4Q3	14	20215705	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10		20215705	87133835	173	29045										
RNASE2	6036	hgsc.bcm.edu	37	chr14	21424040	21424040	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acagtttacctgggctcaatGgtttgaaacccagcacatca	8	11	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:21424040G>T	ENST00000304625.2	+	2	200	c.110G>T	c.(109-111)tGg>tTg	p.W37L		NM_002934.2	NP_002925.1	P10153	RNAS2_HUMAN	ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)	37				W -> R (in Ref. 10; AA sequence). {ECO:0000305}.	chemotaxis (GO:0006935)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)|ribonuclease activity (GO:0004540)			breast(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	17	all_cancers(95;0.00381)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)		TGGGCTCAATGGTTTGAAACC	0.453																																																0			14											87	82	83					14																	21424040		2203	4300	6503	20493880	SO:0001583	missense	6036			X55988	CCDS9561.1	14q11.2	2014-03-13			ENSG00000169385	ENSG00000169385		"Ribonucleases, RNase A"	10045	protein-coding gene	gene with protein product		131410		RNS2		1577491, 2734298	Standard	NM_002934		Approved	EDN	uc001vyl.1	P10153	OTTHUMG00000029607	ENST00000304625.2:c.110G>T	14.37:g.21424040G>T	ENSP00000303276:p.Trp37Leu		20493880	Q52M39|Q9H2B7|Q9UCG7	Missense_Mutation	SNP	ENST00000304625.2	37	CCDS9561.1	.	.	.	.	.	.	.	.	.	.	g	16.01	3.001443	0.54254	.	.	ENSG00000169385	ENST00000304625	T	0.73047	-0.71	2.78	2.78	0.32641	Ribonuclease A, domain (4);	1.760720	0.03567	U	0.227943	T	0.78610	0.4310	M	0.87682	2.9	0.33107	D	0.540013	D	0.54964	0.969	P	0.45343	0.477	T	0.75442	-0.3316	10	0.72032	D	0.01	.	9.1968	0.37233	0.0:0.0:1.0:0.0	.	37	P10153	RNAS2_HUMAN	L	37	ENSP00000303276:W37L	ENSP00000303276:W37L	W	+	2	0	RNASE2	20493880	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	3.413000	0.52686	1.865000	0.54081	0.455000	0.32223	TGG		0.453	RNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073799.2			T	21424040	G	T	21424040	3	4	110	1	0	0	0	0	1	0	0	0	13441	1357	47	2	112	2	RNASE2	14	21424040	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1208335	21424040	85925500	174	29046										
WDHD1	11169	hgsc.bcm.edu	37	chr14	55433311	55433311	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggttgtgaaatataactgaaCgccaaaattgctcctataaa	7	7	0	2	rs145612447		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:55433311C>A	ENST00000360586.3	-	18	2257	c.2192G>T	c.(2191-2193)cGt>cTt	p.R731L	WDHD1_ENST00000420358.2_Missense_Mutation_p.R608L|WDHD1_ENST00000359167.4_Missense_Mutation_p.R249L|WDHD1_ENST00000421192.1_Missense_Mutation_p.R608L	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	731					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						TATAACTGAACGCCAAAATTG	0.313																																																0			14											84	75	78					14																	55433311		2200	4295	6495	54503061	SO:0001583	missense	11169			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2192G>T	14.37:g.55433311C>A	ENSP00000353793:p.Arg731Leu		54503061	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.533711	0.64972	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.70045	-0.05;0.47;-0.45	5.63	2.81	0.32909	.	0.109437	0.64402	D	0.000005	T	0.77644	0.4161	M	0.76002	2.32	0.80722	D	1	D;D	0.76494	0.999;0.988	D;P	0.70935	0.971;0.876	T	0.74694	-0.3579	10	0.42905	T	0.14	.	10.0057	0.41955	0.0:0.7799:0.0:0.2201	.	249;731	F8W7P7;O75717	.;WDHD1_HUMAN	L	731;249;608	ENSP00000353793:R731L;ENSP00000352085:R249L;ENSP00000391049:R608L	ENSP00000352085:R249L	R	-	2	0	WDHD1	54503061	1.000000	0.71417	0.945000	0.38365	0.652000	0.38707	4.511000	0.60462	0.319000	0.23209	0.591000	0.81541	CGT		0.313	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		A	55433311	C	A	55433311	3	1	110	1	0	0	0	0	1	0	0	0	17311	536	19	2	1233	2	WDHD1	14	55433311	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	34009271	55433311	51916229	175	29047										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60591813	60591813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agacttttatgttcatacagTaatgacttgttattttagtt	6	4	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:60591813T>C	ENST00000406854.1	+	9	3478	c.2924T>C	c.(2923-2925)gTa>gCa	p.V975A	PCNXL4_ENST00000404681.2_Missense_Mutation_p.V975A|PCNXL4_ENST00000317623.4_Missense_Mutation_p.V741A|PCNXL4_ENST00000535349.1_Missense_Mutation_p.V182A|PCNXL4_ENST00000406949.1_Missense_Mutation_p.V741A			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	975						integral component of membrane (GO:0016021)											GTTCATACAGTAATGACTTGT	0.363																																																0			14											84	86	85					14																	60591813		2202	4300	6502	59661566	SO:0001583	missense	64430			AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.2924T>C	14.37:g.60591813T>C	ENSP00000384801:p.Val975Ala		59661566	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		.	.	.	.	.	.	.	.	.	.	T	13.27	2.186025	0.38609	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.39592	1.65;1.65;1.61;1.65;1.07	4.91	3.76	0.43208	.	0.244211	0.41500	N	0.000864	T	0.52306	0.1726	L	0.59436	1.845	0.45056	D	0.998076	B;D	0.63046	0.248;0.992	B;P	0.61328	0.079;0.887	T	0.44651	-0.9314	10	0.24483	T	0.36	.	10.4562	0.44553	0.0:0.0773:0.0:0.9227	.	975;741	Q63HM2;B5MC47	CN135_HUMAN;.	A	741;975;741;975;182	ENSP00000317396:V741A;ENSP00000384801:V975A;ENSP00000385201:V741A;ENSP00000385713:V975A;ENSP00000445644:V182A	ENSP00000317396:V741A	V	+	2	0	C14orf135	59661566	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.970000	0.49240	0.827000	0.34685	0.254000	0.18369	GTA		0.363	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		C	60591813	T	C	60591813	3	2	110	1	0	0	0	0	1	0	0	0	1749	1638	57	4	2248	4	C14orf135	14	60591813	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	5158502	60591813	46757727	176	29048										
SIX1	6495	hgsc.bcm.edu	37	chr14	61115504	61115504	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	actcccgcaggacacccctcGacttctccttgaagcagtag	8	16	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:61115504G>A	ENST00000247182.6	-	1	676	c.404C>T	c.(403-405)tCg>tTg	p.S135L	SIX1_ENST00000554986.1_Intron	NM_005982.3	NP_005973.1	Q15475	SIX1_HUMAN	SIX homeobox 1	135					aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|branching involved in ureteric bud morphogenesis (GO:0001658)|cochlea morphogenesis (GO:0090103)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial cell differentiation (GO:0030855)|facial nerve morphogenesis (GO:0021610)|generation of neurons (GO:0048699)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesonephric tubule formation (GO:0072172)|metanephric mesenchyme development (GO:0072075)|middle ear morphogenesis (GO:0042474)|myoblast migration (GO:0051451)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|organ induction (GO:0001759)|otic vesicle development (GO:0071599)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|protein localization to nucleus (GO:0034504)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of neuron differentiation (GO:0045664)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		GACACCCCTCGACTTCTCCTT	0.662																																																0			14											64	60	61					14																	61115504		2203	4300	6503	60185257	SO:0001583	missense	6495			X91868	CCDS9748.1	14q23.1	2011-06-20	2007-07-13		ENSG00000126778	ENSG00000126778		"Homeoboxes / SINE class"	10887	protein-coding gene	gene with protein product		601205	"sine oculis homeobox (Drosophila) homolog 1", "sine oculis homeobox homolog 1 (Drosophila)", "deafness, autosomal dominant 23"	DFNA23		8617500, 15141091	Standard	NM_005982		Approved		uc001xfb.4	Q15475	OTTHUMG00000140334	ENST00000247182.6:c.404C>T	14.37:g.61115504G>A	ENSP00000247182:p.Ser135Leu		60185257	Q53Y16|Q96H64	Missense_Mutation	SNP	ENST00000247182.6	37	CCDS9748.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960885	0.92791	.	.	ENSG00000126778	ENST00000247182	D	0.96200	-3.94	5.97	5.03	0.67393	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97517	0.9187	M	0.88377	2.95	0.80722	D	1	D	0.65815	0.995	D	0.63488	0.915	D	0.97509	1.0065	10	0.87932	D	0	-8.9345	12.1441	0.54014	0.0:0.1289:0.7377:0.1333	.	135	Q15475	SIX1_HUMAN	L	135	ENSP00000247182:S135L	ENSP00000247182:S135L	S	-	2	0	SIX1	60185257	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.842000	0.48230	2.828000	0.97474	0.655000	0.94253	TCG		0.662	SIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276951.3			A	61115504	G	A	61115504	3	1	110	1	0	0	0	0	1	0	0	0	14383	1059	37	1	458	1	SIX1	14	61115504	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	523691	61115504	46234036	177	29049										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68250183	68250183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	caaggggctcacagcagcagCtgacgatgacctgtggcaca	13	12	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:68250183C>T	ENST00000347230.4	-	21	3824	c.3686G>A	c.(3685-3687)aGc>aAc	p.S1229N	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.S1229N	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1229					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		ACAGCAGCAGCTGACGATGAC	0.572																																																0			14											67	62	63					14																	68250183		2203	4300	6503	67319936	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.3686G>A	14.37:g.68250183C>T	ENSP00000251119:p.Ser1229Asn		67319936	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	1.547	-0.540306	0.04053	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.27104	1.83;1.69	5.63	0.518	0.17030	.	0.514237	0.22527	N	0.058900	T	0.08758	0.0217	N	0.04043	-0.29	0.25886	N	0.983533	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39099	-0.9630	10	0.02654	T	1	-5.0458	10.0562	0.42246	0.0:0.3703:0.0:0.6297	.	1229;1229	G3V2D8;Q68DK2	.;ZFY26_HUMAN	N	1229;1208;1229	ENSP00000251119:S1229N;ENSP00000450603:S1229N	ENSP00000251119:S1229N	S	-	2	0	ZFYVE26	67319936	0.998000	0.40836	0.937000	0.37676	0.851000	0.48451	0.385000	0.20685	0.089000	0.17243	-0.312000	0.09012	AGC		0.572	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68250183	C	T	68250183	3	4	110	1	0	0	0	0	1	0	0	0	17707	797	28	3	4021	3	ZFYVE26	14	68250183	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	7134679	68250183	39099357	178	29050										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74999244	74999244	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggcccagggtcaagcactcGttgatatctgcagggttgga	14	9	2	1	rs149576879	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr14:74999244G>A	ENST00000261978.4	-	10	2258	c.1872C>T	c.(1870-1872)aaC>aaT	p.N624N	LTBP2_ENST00000556690.1_Silent_p.N624N	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	624	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		TCAAGCACTCGTTGATATCTG	0.592																																																0			14						A		0,4406		0,0,2203	99	68	79		1872	-4.9	0.7	14	dbSNP_134	79	3,8597	818.4+/-406.9	0,3,4297	no	coding-synonymous	LTBP2	NM_000428.2		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		624/1822	74999244	3,13003	2203	4300	6503	74068997	SO:0001819	synonymous_variant	4054				CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1872C>T	14.37:g.74999244G>A			74068997	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																				0.592	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74999244	G	A	74999244	2	1	110	1	0	0	0	0	0	0	0	1	9103	1136	40	1		1	LTBP2	14	74999244	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	6749061	74999244	32350296	179	29051										
TJP1	7082	hgsc.bcm.edu	37	chr15	30012114	30012114	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aaggagctggggtgggctccTccagtctgacattagttaaa	13	8	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:30012114T>A	ENST00000346128.6	-	20	3344	c.2870A>T	c.(2869-2871)gAg>gTg	p.E957V	TJP1_ENST00000400011.2_Intron|TJP1_ENST00000545208.2_Intron|TJP1_ENST00000356107.6_Missense_Mutation_p.E957V	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	957					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.E957V(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		GGTGGGCTCCTCCAGTCTGAC	0.443																																					Melanoma(77;681 1843 6309 6570)											1	Substitution - Missense(1)	ovary(1)	15											139	133	135					15																	30012114		1908	4117	6025	27799406	SO:0001583	missense	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2870A>T	15.37:g.30012114T>A	ENSP00000281537:p.Glu957Val		27799406	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156564	0.57259	.	.	ENSG00000104067	ENST00000346128;ENST00000545208	T	0.08807	3.05	6.17	5.05	0.67936	.	0.051117	0.85682	D	0.000000	T	0.18173	0.0436	L	0.53249	1.67	0.80722	D	1	D;P	0.71674	0.998;0.919	P;B	0.56343	0.796;0.371	T	0.00512	-1.1696	10	0.44086	T	0.13	.	12.3964	0.55386	0.0:0.0652:0.0:0.9348	.	950;957	A9CQZ8;Q07157	.;ZO1_HUMAN	V	957	ENSP00000281537:E957V	ENSP00000281537:E957V	E	-	2	0	TJP1	27799406	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.293000	0.65680	1.148000	0.42385	0.533000	0.62120	GAG		0.443	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30012114	T	A	30012114	3	1	110	1	0	0	0	0	1	0	0	0	15968	1551	54	5	2412	5	TJP1	15	30012114	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10		30012114	72519278	180	29052										
HDC	3067	hgsc.bcm.edu	37	chr15	50534631	50534631	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	accctggaggagcccccattCttcacagaggcctctgtggg	12	14	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:50534631C>G	ENST00000267845.3	-	12	2217	c.1815G>C	c.(1813-1815)aaG>aaC	p.K605N	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.K572N	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGCCCCCATTCTTCACAGAGG	0.498																																					GBM(95;1627 1936 6910 9570)											0			15											134	152	146					15																	50534631		2196	4295	6491	48321923	SO:0001583	missense	51696				CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1815G>C	15.37:g.50534631C>G	ENSP00000267845:p.Lys605Asn		48321923		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.612497	0.28712	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.14391	2.8;2.51	5.48	5.48	0.80851	.	0.806022	0.11263	N	0.582329	T	0.12008	0.0292	L	0.29908	0.895	0.46149	D	0.998894	B;B	0.32245	0.361;0.181	B;B	0.26969	0.075;0.075	T	0.09164	-1.0687	10	0.87932	D	0	-17.1927	12.6613	0.56815	0.0:0.9245:0.0:0.0755	.	572;605	B7ZM01;P19113	.;DCHS_HUMAN	N	605;572	ENSP00000267845:K605N;ENSP00000440252:K572N	ENSP00000267845:K605N	K	-	3	2	HDC	48321923	1.000000	0.71417	0.982000	0.44146	0.087000	0.18053	3.352000	0.52239	2.570000	0.86706	0.563000	0.77884	AAG		0.498	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			G	50534631	C	G	50534631	3	3	110	1	0	0	0	0	1	0	0	0	7036	912	32	5	177	5	HDC	15	50534631	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	20522517	50534631	51996761	181	29053										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54919114	54919114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ccagagaagatcgaattatcGgaatgacagtcattcagcta	9	8	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:54919114G>A	ENST00000260323.11	+	32	6448	c.6448G>A	c.(6448-6450)Gga>Aga	p.G2150R	UNC13C_ENST00000539562.2_Missense_Mutation_p.G71R|UNC13C_ENST00000537900.1_Missense_Mutation_p.G2148R|UNC13C_ENST00000545554.1_Missense_Mutation_p.G2150R	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2150	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.G2150*(2)|p.G2150R(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCGAATTATCGGAATGACAGT	0.418																																																3	Substitution - Nonsense(2)|Substitution - Missense(1)	lung(2)|pancreas(1)	15											105	98	101					15																	54919114		1879	4102	5981	52706406	SO:0001583	missense	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6448G>A	15.37:g.54919114G>A	ENSP00000260323:p.Gly2150Arg		52706406	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.729280	0.89390	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900;ENST00000539562	D;D;D;D	0.94931	-3.28;-3.28;-3.28;-3.56	5.85	5.85	0.93711	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.051321	0.85682	D	0.000000	D	0.97958	0.9328	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98457	1.0594	10	0.87932	D	0	.	19.1612	0.93533	0.0:0.0:1.0:0.0	.	2150	Q8NB66	UN13C_HUMAN	R	2150;2150;2148;71	ENSP00000260323:G2150R;ENSP00000438156:G2150R;ENSP00000442569:G2148R;ENSP00000443886:G71R	ENSP00000260323:G2150R	G	+	1	0	UNC13C	52706406	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.751000	0.98889	2.768000	0.95171	0.655000	0.94253	GGA		0.418	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54919114	G	A	54919114	3	1	110	1	0	0	0	0	1	0	0	0	17026	1117	39	1	6570	1	UNC13C	15	54919114	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	4384483	54919114	47612278	182	29054										
MAP2K1	5604	hgsc.bcm.edu	37	chr15	66727441	66727441	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agcgaaagcgccttgaggccTttcttacccagaagcagaag	11	11	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:66727441T>G	ENST00000307102.5	+	2	688	c.157T>G	c.(157-159)Ttt>Gtt	p.F53V		NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	53			F -> S (in CFC3). {ECO:0000269|PubMed:16439621}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.F53L(2)|p.F53S(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	CCTTGAGGCCTTTCTTACCCA	0.547																																																3	Substitution - Missense(3)	lung(2)|large_intestine(1)	15											155	146	149					15																	66727441		2201	4299	6500	64514495	SO:0001583	missense	5604			L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.157T>G	15.37:g.66727441T>G	ENSP00000302486:p.Phe53Val		64514495		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.813069	0.90707	.	.	ENSG00000169032	ENST00000307102	D	0.92495	-3.05	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.66847	0.928;0.947	D	0.94530	0.7735	10	0.39692	T	0.17	-14.6287	14.0473	0.64712	0.0:0.0:0.0:1.0	.	31;53	B4DFY5;Q02750	.;MP2K1_HUMAN	V	53	ENSP00000302486:F53V	ENSP00000302486:F53V	F	+	1	0	MAP2K1	64514495	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.924000	0.87555	1.911000	0.55334	0.383000	0.25322	TTT		0.547	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4			G	66727441	T	G	66727441	3	3	110	1	0	0	0	0	1	0	0	0	9266	1609	56	4	163	4	MAP2K1	15	66727441	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	11808327	66727441	35803951	183	29055										
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78893717	78893717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atcaacagattcagaactagAgcttctcgtgaggttagcac	9	9	3	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:78893717A>G	ENST00000326828.5	-	5	1651	c.1267T>C	c.(1267-1269)Tct>Cct	p.S423P	CHRNA3_ENST00000348639.3_Missense_Mutation_p.S423P	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	423					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TCAGAACTAGAGCTTCTCGTG	0.473																																																0			15											159	144	149					15																	78893717		2196	4293	6489	76680772	SO:0001583	missense	1136				CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1267T>C	15.37:g.78893717A>G	ENSP00000315602:p.Ser423Pro		76680772	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Missense_Mutation	SNP	ENST00000326828.5	37	CCDS10305.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109889	0.37242	.	.	ENSG00000080644	ENST00000348639;ENST00000326828	D;D	0.86030	-2.06;-2.06	5.79	3.37	0.38596	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.402626	0.26307	N	0.025124	D	0.84529	0.5492	L	0.43598	1.365	0.53005	D	0.999969	P;P	0.51147	0.916;0.942	P;P	0.55871	0.756;0.786	T	0.78984	-0.1988	10	0.26408	T	0.33	.	8.9876	0.36003	0.7436:0.1313:0.0:0.1251	.	423;423	P32297;P32297-3	ACHA3_HUMAN;.	P	423	ENSP00000267951:S423P;ENSP00000315602:S423P	ENSP00000315602:S423P	S	-	1	0	CHRNA3	76680772	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	2.781000	0.47750	0.396000	0.25283	-0.435000	0.05868	TCT		0.473	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			G	78893717	A	G	78893717	3	3	110	1	0	0	0	0	1	0	0	0	3390	304	11	4	343	4	CHRNA3	15	78893717	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	12166276	78893717	23637675	184	29056										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79750551	79750551	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggtgctgctctgatgctagcGggagcaacagtgaaagcctg	15	9	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:79750551G>A	ENST00000305428.3	+	2	2137	c.2062G>A	c.(2062-2064)Ggg>Agg	p.G688R		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	688						integral component of membrane (GO:0016021)		p.G688R(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						TGATGCTAGCGGGAGCAACAG	0.557																																																1	Substitution - Missense(1)	lung(1)	15											157	155	156					15																	79750551		2196	4293	6489	77537606	SO:0001583	missense	23251			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.2062G>A	15.37:g.79750551G>A	ENSP00000307461:p.Gly688Arg		77537606	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.861749	0.32884	.	.	ENSG00000169330	ENST00000305428	T	0.37915	1.17	5.59	4.67	0.58626	.	0.178123	0.52532	D	0.000067	T	0.48804	0.1520	M	0.65975	2.015	0.24941	N	0.991859	D	0.71674	0.998	P	0.55999	0.789	T	0.44112	-0.9349	9	.	.	.	.	10.4174	0.44329	0.1495:0.0:0.8505:0.0	.	688	Q9UPX6	K1024_HUMAN	R	688	ENSP00000307461:G688R	.	G	+	1	0	KIAA1024	77537606	1.000000	0.71417	0.252000	0.24328	0.345000	0.29048	5.331000	0.65905	1.356000	0.45884	0.591000	0.81541	GGG		0.557	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		A	79750551	G	A	79750551	3	1	110	1	0	0	0	0	1	0	0	0	8226	1116	39	1	2064	1	KIAA1024	15	79750551	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	856834	79750551	22780841	185	29057										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99251010	99251010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cctcttccccaacctcacggTcatccgcggctggaaactct	7	18	4	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr15:99251010T>C	ENST00000268035.6	+	2	925	c.314T>C	c.(313-315)gTc>gCc	p.V105A	IGF1R_ENST00000558762.1_Missense_Mutation_p.V105A	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	105			V -> L (in a renal chromophobe sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	AACCTCACGGTCATCCGCGGC	0.547																																																0			15											78	63	68					15																	99251010		2197	4297	6494	97068533	SO:0001583	missense	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.314T>C	15.37:g.99251010T>C	ENSP00000268035:p.Val105Ala		97068533	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360039	0.82353	.	.	ENSG00000140443	ENST00000268035	T	0.80994	-1.44	5.36	5.36	0.76844	EGF receptor, L domain (1);	0.000000	0.48767	D	0.000172	D	0.92561	0.7637	H	0.95402	3.665	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.966;0.999	D	0.94605	0.7799	10	0.87932	D	0	.	14.824	0.70097	0.0:0.0:0.0:1.0	.	105;105	C9J5X1;P08069	.;IGF1R_HUMAN	A	105	ENSP00000268035:V105A	ENSP00000268035:V105A	V	+	2	0	IGF1R	97068533	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.880000	0.87243	2.148000	0.66965	0.460000	0.39030	GTC		0.547	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		C	99251010	T	C	99251010	3	2	110	1	0	0	0	0	1	0	0	0	7592	1667	58	4	320	4	IGF1R	15	99251010	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	19500459	99251010	3280382	186	29058										
MSLNL	401827	hgsc.bcm.edu	37	chr16	830194	830194	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgggctgtgagggtcccggcGggagcaggggccggggcatc	22	10	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:830194G>A	ENST00000442466.1	-	2	37				MSLNL_ENST00000293892.3_Silent_p.P269P			Q96KJ4	MSLNL_HUMAN	mesothelin-like						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(15)|ovary(2)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	36						GGGTCCCGGCGGGAGCAGGGG	0.687																																																0			16											17	22	21					16																	830194		1895	4107	6002	770195	SO:0001627	intron_variant	401827					16p13.3	2008-08-06	2008-07-04	2008-07-04	ENSG00000162006	ENSG00000162006			14170	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 37"	C16orf37			Standard	NG_032123		Approved	MPFL		Q96KJ4		ENST00000442466.1:c.38-32C>T	16.37:g.830194G>A			770195		Silent	SNP	ENST00000442466.1	37																																																																																					0.687	MSLNL-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001025190		A	830194	G	A	830194	1	1	110	0	1	0	0	0	0	0	0	0	9912	1103	39	1		1	MSLNL	16	830194	Intron	SNP	G	TCGA-EI-6506-01A-11D-1733-10		830194	89524559	187	29059										
ZNF200	7752	hgsc.bcm.edu	37	chr16	3274543	3274547	+	Frame_Shift_Del	DEL	TTCTC	TTCTC	-													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcatcatcatctgaagacttTtctctataatcttcattttc							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	TTCTC	TTCTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:3274543_3274547delTTCTC	ENST00000431561.3	-	5	1145_1149	c.533_537delGAGAA	c.(532-537)agagaafs	p.RE178fs	ZNF200_ENST00000396868.3_Frame_Shift_Del_p.RE177fs|AJ003147.9_ENST00000576468.1_RNA|ZNF200_ENST00000414144.2_Frame_Shift_Del_p.RE178fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.RE177fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.RE177fs|ZNF200_ENST00000396871.4_Frame_Shift_Del_p.RE177fs	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTGAAGACTTTTCTCTATAATCTTC	0.395																																																0			16																																								3214548	SO:0001589	frameshift_variant	7752			AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.533_537delGAGAA	16.37:g.3274543_3274547delTTCTC	ENSP00000395723:p.Arg178fs		3214544	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	37	CCDS10497.1																																																																																				0.395	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			-	3274547	TTCTC	-	3274543	7	5	110	1	0	1	0	1	0	0	0	0	17801	1838	64	0	654	0	ZNF200	16	3274543	Frame_Shift_Del	DEL	TTCTC	TCGA-EI-6506-01A-11D-1733-10	2444349	3274543	87080210	188	29060										
SRL	6345	hgsc.bcm.edu	37	chr16	4254547	4254547	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tggttaccagagtagtcatcGgatggcttgtcctcattcag	11	9	3	1	rs186123843	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:4254547G>A	ENST00000399609.3	-	2	162	c.150C>T	c.(148-150)tcC>tcT	p.S50S	SRL_ENST00000537996.1_Silent_p.S8S	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	509	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.S50S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						AGTAGTCATCGGATGGCTTGT	0.602													G|||	8	0.00159744	0	0	5008	,	,		17599	0.0069		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	16						G		0,3834		0,0,1917	127	126	126		150	-11.2	0	16		126	1,8239		0,1,4119	no	coding-synonymous	SRL	NM_001098814.1		0,1,6036	AA,AG,GG		0.0121,0.0,0.0083		50/474	4254547	1,12073	1917	4120	6037	4194548	SO:0001819	synonymous_variant	6345			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.150C>T	16.37:g.4254547G>A			4194548		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																				0.602	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		A	4254547	G	A	4254547	2	1	110	1	0	0	0	0	0	0	0	1	15189	1103	39	1		1	SRL	16	4254547	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	980004	4254547	86100206	189	29061										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16216007	16216007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggacgagaaccagaaggcctAttaccccagcatcgtggcca	11	13	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:16216007A>G	ENST00000399410.3	+	24	3741	c.3566A>G	c.(3565-3567)tAt>tGt	p.Y1189C	ABCC1_ENST00000345148.5_Missense_Mutation_p.Y1189C|ABCC1_ENST00000346370.5_Missense_Mutation_p.Y1133C|ABCC1_ENST00000349029.5_Missense_Mutation_p.Y1074C|ABCC1_ENST00000399408.2_Missense_Mutation_p.Y1199C|ABCC1_ENST00000351154.5_Missense_Mutation_p.Y1130C	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1189	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CAGAAGGCCTATTACCCCAGC	0.597																																																0			16											52	59	56					16																	16216007		2152	4266	6418	16123508	SO:0001583	missense	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.3566A>G	16.37:g.16216007A>G	ENSP00000382342:p.Tyr1189Cys		16123508	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.501561	0.44455	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54;-2.54	5.08	5.08	0.68730	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.92821	0.7717	M	0.64404	1.975	0.46798	D	0.999202	B;D;D;D;D;D	0.89917	0.364;1.0;1.0;1.0;1.0;1.0	B;D;D;D;D;D	0.97110	0.233;1.0;1.0;0.999;1.0;1.0	D	0.92046	0.5644	10	0.36615	T	0.2	-15.7422	14.0596	0.64790	1.0:0.0:0.0:0.0	.	1074;1189;1133;1130;1189;1199	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	C	1189;1199;1133;1130;1189;1074;873	ENSP00000382342:Y1189C;ENSP00000382340:Y1199C;ENSP00000263019:Y1133C;ENSP00000263017:Y1130C;ENSP00000263014:Y1189C;ENSP00000263016:Y1074C	ENSP00000263014:Y1189C	Y	+	2	0	ABCC1	16123508	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.276000	0.78559	1.919000	0.55581	0.459000	0.35465	TAT		0.597	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		G	16216007	A	G	16216007	3	3	110	1	0	0	0	0	1	0	0	0	49	449	16	4	3660	4	ABCC1	16	16216007	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	11961460	16216007	74138746	190	29062										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30750596	30750596	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagcagaaggaatgcgaggaCggaagagtggagggtccatg	18	5	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:30750596C>T	ENST00000262518.4	+	34	9620	c.9235C>T	c.(9235-9237)Cgg>Tgg	p.R3079W	SRCAP_ENST00000395059.2_Missense_Mutation_p.R3017W|SRCAP_ENST00000344771.4_Missense_Mutation_p.R2921W|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3079					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AATGCGAGGACGGAAGAGTGG	0.607																																																0			16											68	64	65					16																	30750596		2197	4300	6497	30658097	SO:0001583	missense	10847			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.9235C>T	16.37:g.30750596C>T	ENSP00000262518:p.Arg3079Trp		30658097	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	10.45	1.353584	0.24512	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.96856	-4.14;-4.15;-4.15	4.97	4.97	0.65823	.	0.000000	0.39083	N	0.001474	D	0.95220	0.8450	N	0.08118	0	0.32750	N	0.506465	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.96029	0.9015	10	0.87932	D	0	-6.3718	15.2431	0.73485	0.0:1.0:0.0:0.0	.	3017;3079	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	W	3079;3017;2921	ENSP00000262518:R3079W;ENSP00000378499:R3017W;ENSP00000343042:R2921W	ENSP00000262518:R3079W	R	+	1	2	SRCAP	30658097	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.698000	0.37794	2.584000	0.87258	0.462000	0.41574	CGG		0.607	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30750596	C	T	30750596	3	4	110	1	0	0	0	0	1	0	0	0	15174	527	19	1	9361	1	SRCAP	16	30750596	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	14534589	30750596	59604157	191	29063										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70955014	70955014	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgctgacatcgcccatgttcCttttcttcttatttagctct	5	12	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:70955014C>A	ENST00000393567.2	-	46	7415	c.7265G>T	c.(7264-7266)aGg>aTg	p.R2422M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2422					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCCCATGTTCCTTTTCTTCTT	0.488																																																0			16											50	45	46					16																	70955014		1806	4066	5872	69512515	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7265G>T	16.37:g.70955014C>A	ENSP00000377197:p.Arg2422Met		69512515	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.725654	0.30593	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00912	5.55	5.89	-2.23	0.06930	.	0.526148	0.13186	U	0.407157	T	0.00875	0.0029	N	0.08118	0	0.23962	N	0.996332	P	0.51351	0.944	P	0.47981	0.563	T	0.54990	-0.8210	10	0.51188	T	0.08	.	12.1066	0.53816	0.0:0.4161:0.0:0.5839	.	2421	F8WD23	.	M	2422;2421	ENSP00000377197:R2422M	ENSP00000313052:R2421M	R	-	2	0	HYDIN	69512515	0.002000	0.14202	0.000000	0.03702	0.005000	0.04900	-0.281000	0.08456	-0.307000	0.08804	-0.908000	0.02827	AGG		0.488	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70955014	C	A	70955014	3	1	110	1	0	0	0	0	1	0	0	0	7488	681	24	2	8264	2	HYDIN	16	70955014	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	40204418	70955014	19399739	192	29064										
ATMIN	23300	hgsc.bcm.edu	37	chr16	81077779	81077779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taagactttaaatcaagataTtgagaaatctgcaccaatta	5	6	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr16:81077779T>C	ENST00000299575.4	+	4	1700	c.1676T>C	c.(1675-1677)aTt>aCt	p.I559T	ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000566488.1_Missense_Mutation_p.I403T|ATMIN_ENST00000564241.1_Missense_Mutation_p.I403T	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	559					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						AATCAAGATATTGAGAAATCT	0.338																																																0			16											43	43	43					16																	81077779		2202	4299	6501	79635280	SO:0001583	missense	23300			BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.1676T>C	16.37:g.81077779T>C	ENSP00000299575:p.Ile559Thr		79635280	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	37	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	T	6.056	0.378647	0.11466	.	.	ENSG00000166454	ENST00000299575;ENST00000539819	T	0.30448	1.53	6.17	5.07	0.68467	.	0.967508	0.08595	N	0.922386	T	0.23766	0.0575	L	0.41236	1.265	0.09310	N	0.999993	B	0.06786	0.001	B	0.06405	0.002	T	0.35773	-0.9775	10	0.17832	T	0.49	-2.3609	5.2669	0.15603	0.0:0.1055:0.1776:0.717	.	559	O43313	ATMIN_HUMAN	T	559;330	ENSP00000299575:I559T	ENSP00000299575:I559T	I	+	2	0	ATMIN	79635280	0.063000	0.20901	0.796000	0.32109	0.638000	0.38207	1.000000	0.29770	1.138000	0.42230	0.533000	0.62120	ATT		0.338	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		C	81077779	T	C	81077779	3	2	110	1	0	0	0	0	1	0	0	0	1111	1493	52	4	1690	4	ATMIN	16	81077779	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	10122765	81077779	9276974	193	29065										
TRPV3	162514	hgsc.bcm.edu	37	chr17	3448549	3448549	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gggttcaaacccttctatctCcaggaagaagtgtgcactga	10	10	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:3448549C>G	ENST00000576742.1	-	3	457	c.136G>C	c.(136-138)Gag>Cag	p.E46Q	TRPV3_ENST00000572519.1_Missense_Mutation_p.E46Q|TRPV3_ENST00000301365.4_Missense_Mutation_p.E46Q	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	46					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	CCTTCTATCTCCAGGAAGAAG	0.597																																																0			17											110	93	99					17																	3448549		2203	4300	6503	3395299	SO:0001583	missense	162514			AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.136G>C	17.37:g.3448549C>G	ENSP00000461518:p.Glu46Gln		3395299	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362981	0.61403	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	T	0.43294	0.95	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000006	T	0.51329	0.1668	N	0.24115	0.695	0.35234	D	0.777163	D;D;B;D;D;B;B	0.67145	0.996;0.993;0.376;0.993;0.996;0.295;0.419	D;D;B;D;D;B;B	0.78314	0.991;0.979;0.1;0.979;0.991;0.123;0.244	T	0.63413	-0.6643	10	0.72032	D	0.01	-15.5485	16.2359	0.82375	0.0:1.0:0.0:0.0	.	30;30;46;30;46;46;46	E7EV24;B7ZKP9;Q2M3L1;B7ZKP6;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;.;.;.;TRPV3_HUMAN;.	Q	46;46;30	ENSP00000301365:E46Q	ENSP00000301365:E46Q	E	-	1	0	TRPV3	3395299	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.257000	0.58816	2.579000	0.87056	0.561000	0.74099	GAG		0.597	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		G	3448549	C	G	3448549	3	3	110	1	0	0	0	0	1	0	0	0	16637	864	30	5	2300	5	TRPV3	17	3448549	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10		3448549	77746661	194	29066										
TP53	7157	hgsc.bcm.edu	37	chr17	7574018	7574018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctctcggaacatctcgaagcGctcacgcccacggatctgca	9	16	4	0	rs587782529		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:7574018G>T	ENST00000269305.4	-	10	1198	c.1009C>A	c.(1009-1011)Cgc>Agc	p.R337S	TP53_ENST00000420246.2_3'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.R337S|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000359597.4_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	337	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9452042}.|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11481490}.|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R337C(18)|p.0?(8)|p.R337fs*8(2)|p.R337G(1)|p.?(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATCTCGAAGCGCTCACGCCCA	0.522		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	31	Substitution - Missense(19)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(1)	central_nervous_system(6)|large_intestine(5)|ovary(4)|bone(4)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|stomach(1)|liver(1)|peritoneum(1)|lung(1)|kidney(1)	17	GRCh37	CM981929	TP53	M							56	44	48					17																	7574018		2203	4300	6503	7514743	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1009C>A	17.37:g.7574018G>T	ENSP00000269305:p.Arg337Ser		7514743	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306095	0.40795	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.95069	-3.6;-3.6	5.43	3.38	0.38709	p53, tetramerisation domain (3);	0.000000	0.85682	D	0.000000	D	0.96762	0.8943	M	0.82323	2.585	0.37100	D	0.899832	D	0.62365	0.991	D	0.66716	0.946	D	0.97762	1.0221	10	0.72032	D	0.01	-7.3279	12.447	0.55657	0.0:0.0:0.6947:0.3053	.	337	P04637	P53_HUMAN	S	337;337;326	ENSP00000269305:R337S;ENSP00000391478:R337S	ENSP00000269305:R337S	R	-	1	0	TP53	7514743	0.558000	0.26554	0.006000	0.13384	0.274000	0.26718	1.012000	0.29924	0.615000	0.30124	0.561000	0.74099	CGC		0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7574018	G	T	7574018	3	4	110	1	0	0	0	0	1	0	0	0	16421	1087	38	2	180	2	TP53	17	7574018	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	4125469	7574018	73621192	195	29067										
TP53	7157	hgsc.bcm.edu	37	chr17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cccaggacaggcacaaacacGcacctcaaagctgttccgtc	8	16	1	0	rs121913343		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	17	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65	56	59					17																	7577121		2203	4300	6503	7517846	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		7517846	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577121	G	A	7577121	3	1	110	1	0	0	0	0	1	0	0	0	16421	1087	38	1	469	1	TP53	17	7577121	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3103	7577121	73618089	196	29068										
TP53	7157	hgsc.bcm.edu	37	chr17	7579404	7579404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tttctgggaagggacagaagAtgacaggggccaggaggggg	20	5	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:7579404A>G	ENST00000269305.4	-	4	472	c.283T>C	c.(283-285)Tct>Cct	p.S95P	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.S95P|TP53_ENST00000445888.2_Missense_Mutation_p.S95P|TP53_ENST00000413465.2_Missense_Mutation_p.S95P|TP53_ENST00000455263.2_Missense_Mutation_p.S95P|TP53_ENST00000359597.4_Missense_Mutation_p.S95P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	95	Interaction with WWOX.		S -> F (in sporadic cancers; somatic mutation).|S -> T (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.G59fs*23(3)|p.V73fs*9(1)|p.A88fs*52(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGGACAGAAGATGACAGGGGC	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	16	Whole gene deletion(8)|Deletion - Frameshift(8)	bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|breast(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)	17											47	51	50					17																	7579404		2203	4300	6503	7520129	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.283T>C	17.37:g.7579404A>G	ENSP00000269305:p.Ser95Pro		7520129	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554526	0.65425	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99769	-6.7;-6.7;-6.7;-6.7;-6.7;-6.7;-6.7;-6.7	4.62	4.62	0.57501	p53, DNA-binding domain (1);	0.175915	0.51477	D	0.000099	D	0.99456	0.9807	L	0.43554	1.36	0.42374	D	0.992466	B;D;B;B;P;B;B	0.89917	0.135;1.0;0.252;0.018;0.491;0.157;0.018	B;D;B;B;P;P;B	0.97110	0.041;1.0;0.326;0.045;0.577;0.458;0.024	D	0.98427	1.0580	10	0.27785	T	0.31	-25.4213	12.2903	0.54815	1.0:0.0:0.0:0.0	.	56;95;95;95;95;95;95	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	95	ENSP00000410739:S95P;ENSP00000352610:S95P;ENSP00000269305:S95P;ENSP00000398846:S95P;ENSP00000391127:S95P;ENSP00000391478:S95P;ENSP00000424104:S95P;ENSP00000426252:S95P	ENSP00000269305:S95P	S	-	1	0	TP53	7520129	0.997000	0.39634	0.958000	0.39756	0.823000	0.46562	2.946000	0.49050	2.070000	0.61991	0.459000	0.35465	TCT		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7579404	A	G	7579404	3	3	110	1	0	0	0	0	1	0	0	0	16421	333	12	4	1019	4	TP53	17	7579404	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	2283	7579404	73615806	197	29069										
MYH8	4626	hgsc.bcm.edu	37	chr17	10302911	10302911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgtgaggtcattgatcagccGctgctgctcctcttccttgg	11	12	3	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:10302911G>A	ENST00000403437.2	-	28	3905	c.3811C>T	c.(3811-3813)Cgg>Tgg	p.R1271W	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1271					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TTGATCAGCCGCTGCTGCTCC	0.483									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							0			17											142	130	134					17																	10302911		2203	4300	6503	10243636	SO:0001583	missense	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3811C>T	17.37:g.10302911G>A	ENSP00000384330:p.Arg1271Trp		10243636	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.341871	0.81911	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.84146	-1.81	5.38	3.29	0.37713	Myosin tail (1);	0.000000	0.38548	U	0.001656	D	0.94486	0.8225	H	0.96720	3.87	0.50171	D	0.99985	D	0.89917	1.0	D	0.79784	0.993	D	0.95274	0.8380	10	0.87932	D	0	.	13.1896	0.59702	0.0:0.0:0.5817:0.4183	.	1271	P13535	MYH8_HUMAN	W	1271	ENSP00000384330:R1271W	ENSP00000252173:R1271W	R	-	1	2	MYH8	10243636	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.080000	0.50112	0.758000	0.33059	0.655000	0.94253	CGG		0.483	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10302911	G	A	10302911	3	1	110	1	0	0	0	0	1	0	0	0	10071	1086	38	1	2054	1	MYH8	17	10302911	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	2723507	10302911	70892299	198	29070										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12639605	12639605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcagcgggatccccgccagaCgctaaagcctcagatacccc	9	17	2	2	rs368720240		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:12639605C>T	ENST00000343344.4	+	6	543	c.543C>T	c.(541-543)gaC>gaT	p.D181D	MYOCD_ENST00000425538.1_Silent_p.D181D|MYOCD_ENST00000395988.1_3'UTR|AC005358.1_ENST00000609971.1_Silent_p.D85D			Q8IZQ8	MYCD_HUMAN	myocardin	181	HDAC5-binding. {ECO:0000250}.				cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		CCCCGCCAGACGCTAAAGCCT	0.488																																																0			17											89	97	95					17																	12639605		2203	4300	6503	12580330	SO:0001819	synonymous_variant	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.543C>T	17.37:g.12639605C>T			12580330	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																				0.488	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		T	12639605	C	T	12639605	2	4	110	1	0	0	0	0	0	0	0	1	10117	535	19	1		1	MYOCD	17	12639605	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2336694	12639605	68555605	199	29071										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27000471	27000471	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtcagaggaagaatacaatGatgaaggcgaggtggtaccc	14	6	1	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:27000471G>A	ENST00000314616.6	+	2	335	c.52G>A	c.(52-54)Gat>Aat	p.D18N	SUPT6H_ENST00000347486.4_Missense_Mutation_p.D18N|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	18	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D18N(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGAATACAATGATGAAGGCGA	0.493																																																1	Substitution - Missense(1)	ovary(1)	17											89	84	86					17																	27000471		2203	4300	6503	24024598	SO:0001583	missense	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.52G>A	17.37:g.27000471G>A	ENSP00000319104:p.Asp18Asn		24024598	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076597	0.36662	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.75	4.76	0.60689	.	0.149195	0.64402	D	0.000018	T	0.27594	0.0678	N	0.08118	0	0.32563	N	0.530893	B	0.17667	0.023	B	0.14023	0.01	T	0.27020	-1.0086	9	0.40728	T	0.16	-14.4731	11.0059	0.47633	0.0:0.2844:0.5911:0.1245	.	18	Q7KZ85	SPT6H_HUMAN	N	18	.	ENSP00000319104:D18N	D	+	1	0	SUPT6H	24024598	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.609000	0.61148	1.390000	0.46547	0.655000	0.94253	GAT		0.493	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		A	27000471	G	A	27000471	3	1	110	1	0	0	0	0	1	0	0	0	15439	1290	45	3	54	3	SUPT6H	17	27000471	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	14360866	27000471	54194739	200	29072										
NF1	4763	hgsc.bcm.edu	37	chr17	29665756	29665756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cttaaaaggacctgacacttAcaacagtcaagttctgatag	7	9	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:29665756A>G	ENST00000358273.4	+	46	7237	c.6854A>G	c.(6853-6855)tAc>tGc	p.Y2285C	NF1_ENST00000444181.2_Missense_Mutation_p.Y78C|NF1_ENST00000356175.3_Missense_Mutation_p.Y2264C|NF1_ENST00000417592.2_Intron	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2285					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.Y2285fs*5(4)|p.?(3)|p.Y2285fs*16(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCTGACACTTACAACAGTCAA	0.308			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	16	Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(3)	soft_tissue(8)|central_nervous_system(4)|autonomic_ganglia(2)|lung(1)|haematopoietic_and_lymphoid_tissue(1)	17	GRCh37	CI962317	NF1	I							86	85	85					17																	29665756		2203	4296	6499	26689882	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.6854A>G	17.37:g.29665756A>G	ENSP00000351015:p.Tyr2285Cys		26689882	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012434	0.54468	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181	T;T;T;T	0.65178	3.17;3.32;3.02;-0.14	5.91	5.91	0.95273	Armadillo-type fold (2);	0.056060	0.85682	D	0.000000	T	0.56543	0.1992	N	0.22421	0.69	0.80722	D	1	P;B	0.42123	0.771;0.001	P;B	0.45829	0.494;0.002	T	0.57347	-0.7827	10	0.39692	T	0.17	.	16.35	0.83199	1.0:0.0:0.0:0.0	.	2264;2285	P21359-2;P21359	.;NF1_HUMAN	C	2285;2264;1930;78	ENSP00000351015:Y2285C;ENSP00000348498:Y2264C;ENSP00000389907:Y1930C;ENSP00000396481:Y78C	ENSP00000348498:Y2264C	Y	+	2	0	NF1	26689882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.826000	0.75298	2.270000	0.75569	0.528000	0.53228	TAC		0.308	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29665756	A	G	29665756	3	3	110	1	0	0	0	0	1	0	0	0	10387	391	14	4	7097	4	NF1	17	29665756	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	2665285	29665756	51529454	201	29073										
ACCN1	40	hgsc.bcm.edu	37	chr17	31352990	31352990	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgctgctcaggggtacaaaaAggggcatcccctgcaaagaa	12	10	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:31352990A>T	ENST00000359872.6	-	5	1757	c.996T>A	c.(994-996)ccT>ccA	p.P332P	ASIC2_ENST00000448983.1_5'UTR|ASIC2_ENST00000225823.2_Silent_p.P383P	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	332					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GGGTACAAAAAGGGGCATCCC	0.557																																																0			17											98	76	84					17																	31352990		2203	4300	6503	28377103	SO:0001819	synonymous_variant	40			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.996T>A	17.37:g.31352990A>T			28377103	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																				0.557	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		T	31352990	A	T	31352990	2	4	110	1	0	0	0	0	0	0	0	1	128	59	3	5		5	ACCN1	17	31352990	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	1687234	31352990	49842220	202	29074										
RDM1	201299	hgsc.bcm.edu	37	chr17	34251749	34251749	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	catgctatcttcattttcccTttcttcaaggtcagaaagct	5	11	5	1	rs148466061	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:34251749T>A	ENST00000293273.6	-	4	472	c.427A>T	c.(427-429)Agg>Tgg	p.R143W	RDM1_ENST00000431884.2_Missense_Mutation_p.R143W|RDM1_ENST00000425909.3_Intron|RDM1_ENST00000430160.2_Missense_Mutation_p.R120W|RDM1_ENST00000394529.3_Missense_Mutation_p.R120W|RDM1_ENST00000419453.2_Missense_Mutation_p.R120W|RDM1_ENST00000394527.1_Intron|RDM1_ENST00000591402.1_Intron|RDM1_ENST00000394528.3_Missense_Mutation_p.R143W	NM_145654.3	NP_663629.1	Q8NG50	RDM1_HUMAN	RAD52 motif containing 1	143					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|kidney(3)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)	9		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TCATTTTCCCTTTCTTCAAGG	0.423								Other identified genes with known or suspected DNA repair function																																								0			17											79	74	76					17																	34251749		2203	4300	6503	31275862	SO:0001583	missense	201299			AB080728	CCDS11301.1, CCDS42299.1, CCDS54111.1, CCDS54108.1, CCDS54109.1, CCDS54110.1, CCDS59280.1, CCDS59281.1	17q11.2	2014-04-10	2014-04-10	2005-10-20	ENSG00000187456	ENSG00000278023		"RNA binding motif (RRM) containing"	19950	protein-coding gene	gene with protein product		612896	"RAD52 homolog B (S. cerevisiae)", "RAD52 motif 1"	RAD52B		15611051	Standard	NM_001163120		Approved	MGC33977	uc002hkh.3	Q8NG50	OTTHUMG00000188399	ENST00000293273.6:c.427A>T	17.37:g.34251749T>A	ENSP00000293273:p.Arg143Trp		31275862	A0JP55|A8MV46|A8MY68|A8MZ92|A8RCS5|A8RCT0|A8RCT5|A8RCT8|A8RCU3|A8RCU8|A8RCW0|A8RCW5	Missense_Mutation	SNP	ENST00000293273.6	37	CCDS11301.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.604389	0.28623	.	.	ENSG00000187456	ENST00000293273;ENST00000419453;ENST00000394529;ENST00000431884;ENST00000430160;ENST00000394528	T;T;T;T;T	0.30981	1.51;1.51;1.52;1.51;1.51	3.29	3.29	0.37713	.	0.987576	0.08255	N	0.974026	T	0.43964	0.1271	L	0.51422	1.61	0.21697	N	0.999585	D;D;D;D;D;D	0.63880	0.993;0.992;0.992;0.993;0.993;0.992	P;P;P;P;P;P	0.62813	0.907;0.792;0.895;0.868;0.868;0.895	T	0.23297	-1.0192	10	0.62326	D	0.03	-0.7718	5.2319	0.15426	0.0:0.1338:0.0:0.8662	.	120;143;120;143;143;120	B4DZ74;Q8NG50-5;Q8NG50-2;A8MY68;Q8NG50;Q8NG50-6	.;.;.;.;RDM1_HUMAN;.	W	143;22;120;143;120;143	ENSP00000293273:R143W;ENSP00000378037:R120W;ENSP00000391290:R143W;ENSP00000413421:R120W;ENSP00000378036:R143W	ENSP00000293273:R143W	R	-	1	2	RDM1	31275862	0.398000	0.25279	0.716000	0.30569	0.283000	0.27025	1.012000	0.29924	1.503000	0.48686	0.477000	0.44152	AGG		0.423	RDM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256588.2	NM_145654		A	34251749	T	A	34251749	3	1	110	1	0	0	0	0	1	0	0	0	13234	1608	56	5	487	5	RDM1	17	34251749	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	2898759	34251749	46943461	203	29075										
JUP	3728	hgsc.bcm.edu	37	chr17	39913781	39913781	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cggaacaggacggcagcagcGtaggtggctgagcagagagg	19	8	0	2	rs201704572		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:39913781G>A	ENST00000393931.3	-	12	2050	c.1932C>T	c.(1930-1932)taC>taT	p.Y644Y	JUP_ENST00000310706.5_Silent_p.Y644Y|JUP_ENST00000393930.1_Silent_p.Y644Y|JUP_ENST00000540235.1_Intron	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	644	Interaction with DSC1.				adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		CGGCAGCAGCGTAGGTGGCTG	0.632													G|||	1	0.000199681	0	0	5008	,	,		17992	0.001		0	False		,,,				2504	0				Colon(16;42 520 6044 17852 28530)											0			17											78	79	78					17																	39913781		2203	4300	6503	37167307	SO:0001819	synonymous_variant	3728			AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"Armadillo repeat containing"	6207	protein-coding gene	gene with protein product		173325	"catenin (cadherin-associated protein), gamma 80kDa"	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.1932C>T	17.37:g.39913781G>A			37167307	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Silent	SNP	ENST00000393931.3	37	CCDS11407.1																																																																																				0.632	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			A	39913781	G	A	39913781	2	1	110	1	0	0	0	0	0	0	0	1	7993	1140	40	1		1	JUP	17	39913781	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	5662032	39913781	41281429	204	29076										
BRCA1	672	hgsc.bcm.edu	37	chr17	41197783	41197783	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cactgtccaacacccactctCgggtcaccacaggtgcctca	7	18	3	0	rs80359883|rs273902775|rs273902776|rs397509290|rs397509291|rs80359873		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:41197783C>A	ENST00000357654.3	-	23	5622	c.5504G>T	c.(5503-5505)cGa>cTa	p.R1835L	BRCA1_ENST00000493795.1_Missense_Mutation_p.R1788L|BRCA1_ENST00000491747.2_Missense_Mutation_p.R731L|BRCA1_ENST00000354071.3_Missense_Mutation_p.R1570L|BRCA1_ENST00000591534.1_Missense_Mutation_p.R326L|BRCA1_ENST00000471181.2_Missense_Mutation_p.R1856L|BRCA1_ENST00000468300.1_3'UTR|BRCA1_ENST00000309486.4_Missense_Mutation_p.R1539L|BRCA1_ENST00000351666.3_Missense_Mutation_p.R652L|BRCA1_ENST00000352993.3_Missense_Mutation_p.R693L|BRCA1_ENST00000346315.3_Missense_Mutation_p.R1596L|BRCA1_ENST00000591849.1_Missense_Mutation_p.R68L|BRCA1_ENST00000586385.1_Missense_Mutation_p.R145L	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1835	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CACCCACTCTCGGGTCACCAC	0.542			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0			17											103	86	91					17																	41197783		2203	4300	6503	38451309	SO:0001583	missense	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5504G>T	17.37:g.41197783C>A	ENSP00000350283:p.Arg1835Leu		38451309	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667139	0.88251	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000309486;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747	T;T;T;T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23	5.32	5.32	0.75619	BRCT (4);	0.158509	0.29624	N	0.011630	D	0.86756	0.6009	M	0.71581	2.175	0.38555	D	0.94955	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.983;0.954;0.989;0.989;0.986	D	0.88168	0.2862	10	0.62326	D	0.03	.	14.3724	0.66849	0.0:1.0:0.0:0.0	.	684;145;730;1857;1835;1835	B4DES0;C6YB45;E7ETR2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	L	1835;1856;1570;693;1596;652;1539;684;1857;1788;730	ENSP00000350283:R1835L;ENSP00000326002:R1570L;ENSP00000312236:R693L;ENSP00000246907:R1596L;ENSP00000338007:R652L;ENSP00000310938:R1539L;ENSP00000377294:R684L;ENSP00000418775:R1788L	ENSP00000310938:R1539L	R	-	2	0	BRCA1	38451309	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.360000	0.59455	2.770000	0.95276	0.563000	0.77884	CGA		0.542	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		A	41197783	C	A	41197783	3	1	110	1	0	0	0	0	1	0	0	0	1501	884	31	2	91	2	BRCA1	17	41197783	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1284002	41197783	39997427	205	29077										
GFAP	2670	hgsc.bcm.edu	37	chr17	42991127	42991127	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcttcctcaagaaccggatcTcctcctccagcgactcaatc	5	17	4	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:42991127T>A	ENST00000253408.5	-	3	652	c.587A>T	c.(586-588)gAg>gTg	p.E196V	GFAP_ENST00000588735.1_Intron|GFAP_ENST00000591327.1_5'UTR|GFAP_ENST00000435360.2_Missense_Mutation_p.E196V|GFAP_ENST00000586793.1_Missense_Mutation_p.E196V	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	196	Coil 1B.|Rod.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				GAACCGGATCTCCTCCTCCAG	0.582																																																0			17											174	175	175					17																	42991127		2203	4300	6503	40346653	SO:0001583	missense	2670			S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"Intermediate filaments type III"	4235	protein-coding gene	gene with protein product	"intermediate filament protein"	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.587A>T	17.37:g.42991127T>A	ENSP00000253408:p.Glu196Val		40346653	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.153227|5.153227	0.94645|0.94645	.|.	.|.	ENSG00000131095|ENSG00000131095	ENST00000253408;ENST00000421021;ENST00000435360|ENST00000376990	D;D|.	0.93307|.	-3.2;-3.2|.	4.71|4.71	4.71|4.71	0.59529|0.59529	Filament (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.88687|.	0.6504|.	H|H	0.98918|0.98918	4.37|4.37	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.87578|.	0.998;0.997|.	D|.	0.92740|.	0.6207|.	10|.	0.87932|0.87932	D|D	0|0	.|.	13.5904|13.5904	0.61957|0.61957	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	196;196|.	E9PAX3;P14136|.	.;GFAP_HUMAN|.	V|X	196;171;196|176	ENSP00000253408:E196V;ENSP00000403962:E196V|.	ENSP00000253408:E196V|ENSP00000366189:R176X	E|R	-|-	2|1	0|2	GFAP|GFAP	40346653|40346653	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	6.095000|6.095000	0.71439|0.71439	2.100000|2.100000	0.63781|0.63781	0.379000|0.379000	0.24179|0.24179	GAG|AGA		0.582	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		A	42991127	T	A	42991127	3	1	110	1	0	0	0	0	1	0	0	0	6357	1551	54	5	868	5	GFAP	17	42991127	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	1793344	42991127	38204083	206	29078										
PPM1E	22843	hgsc.bcm.edu	37	chr17	57047048	57047048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggccctgtgcagggccttccGggtcactgatgagcggtttg	16	11	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:57047048G>A	ENST00000308249.2	+	4	1061	c.932G>A	c.(931-933)cGg>cAg	p.R311Q	RP11-579O24.3_ENST00000582080.1_RNA	NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	36					protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			AGGGCCTTCCGGGTCACTGAT	0.522																																																0			17											81	73	76					17																	57047048		2203	4300	6503	54401830	SO:0001583	missense	22843			AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.932G>A	17.37:g.57047048G>A	ENSP00000312411:p.Arg311Gln		54401830	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.001867	0.74932	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.16743	2.32	5.49	5.49	0.81192	.	0.052050	0.85682	D	0.000000	T	0.14700	0.0355	N	0.17674	0.51	0.44289	D	0.997156	B;B	0.33549	0.417;0.395	B;B	0.34346	0.119;0.18	T	0.07214	-1.0784	10	0.33940	T	0.23	-6.2566	19.7268	0.96166	0.0:0.0:1.0:0.0	.	320;311	Q8WY54-3;Q8WY54-2	.;.	Q	311;162	ENSP00000312411:R311Q	ENSP00000312411:R311Q	R	+	2	0	PPM1E	54401830	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.291000	0.65667	2.727000	0.93392	0.563000	0.77884	CGG		0.522	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	57047048	G	A	57047048	3	1	110	1	0	0	0	0	1	0	0	0	12372	1116	39	1	946	1	PPM1E	17	57047048	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	14055921	57047048	24148162	207	29079										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57126578	57126578	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atcttctcctcatcttcttcAtcctctttggcctctcttac	2	16	8	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:57126578A>G	ENST00000262294.7	-	15	1750	c.1491T>C	c.(1489-1491)gaT>gaC	p.D497D	TRIM37_ENST00000376149.3_Silent_p.D375D|TRIM37_ENST00000393065.2_Silent_p.D463D|TRIM37_ENST00000393066.3_Silent_p.D497D	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	497					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CATCTTCTTCATCCTCTTTGG	0.398									Mulibrey Nanism																																							0			17											125	110	115					17																	57126578		2203	4300	6503	54481360	SO:0001819	synonymous_variant	4591	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1491T>C	17.37:g.57126578A>G			54481360	Q7Z3E6|Q8IYF7|Q8WYF7	Silent	SNP	ENST00000262294.7	37	CCDS32694.1																																																																																				0.398	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		G	57126578	A	G	57126578	2	3	110	1	0	0	0	0	0	0	0	1	16551	214	8	4		4	TRIM37	17	57126578	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	79530	57126578	24068632	208	29080										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74277973	74277973	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggagcttggccttcttggagGgtcgggagacggccaggctg	19	9	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr17:74277973G>A	ENST00000262765.5	-	8	3916	c.3737C>T	c.(3736-3738)cCc>cTc	p.P1246L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1246								p.P1246L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTTCTTGGAGGGTCGGGAGAC	0.637																																																1	Substitution - Missense(1)	central_nervous_system(1)	17											66	50	56					17																	74277973		2203	4300	6503	71789568	SO:0001583	missense	84074			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.3737C>T	17.37:g.74277973G>A	ENSP00000262765:p.Pro1246Leu		71789568	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966413	0.74131	.	.	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.48836	2.86;0.8	5.55	5.55	0.83447	.	.	.	.	.	T	0.57519	0.2059	L	0.32530	0.975	0.44388	D	0.997297	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.973	T	0.58154	-0.7686	9	0.56958	D	0.05	-16.7834	15.0104	0.71545	0.0:0.0:1.0:0.0	.	1246;1246	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	1246;254;1246	ENSP00000262765:P1246L;ENSP00000394461:P254L	ENSP00000262765:P1246L	P	-	2	0	QRICH2	71789568	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	3.550000	0.53691	2.617000	0.88574	0.650000	0.86243	CCC		0.637	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74277973	G	A	74277973	3	1	110	1	0	0	0	0	1	0	0	0	12917	1232	43	3	1302	3	QRICH2	17	74277973	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	17151395	74277973	6917237	209	29081										
DSG2	1829	hgsc.bcm.edu	37	chr18	29121187	29121187	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttactgctgatgtgccattgCggaaagggcgccaaaggctt	13	9	0	1	rs201654341	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr18:29121187C>T	ENST00000261590.8	+	13	2120	c.1911C>T	c.(1909-1911)tgC>tgT	p.C637C	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	637					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C637C(1)		breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			TGTGCCATTGCGGAAAGGGCG	0.428													C|||	23	0.00459265	0	0	5008	,	,		21181	0.001		0	False		,,,				2504	0.0225															1	Substitution - coding silent(1)	ovary(1)	18											127	110	116					18																	29121187		1912	4131	6043	27375185	SO:0001819	synonymous_variant	1829			Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1911C>T	18.37:g.29121187C>T			27375185	Q4KKU6	Silent	SNP	ENST00000261590.8	37	CCDS42423.1																																																																																				0.428	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		T	29121187	C	T	29121187	2	4	110	1	0	0	0	0	0	0	0	1	4788	776	27	1		1	DSG2	18	29121187	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10		29121187	48956061	210	29082										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48586262	48586262	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttcacaatgagcttgcattcCagcctcccatttccaatcat	4	14	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr18:48586262C>T	ENST00000342988.3	+	8	1469	c.931C>T	c.(931-933)Cag>Tag	p.Q311*	SMAD4_ENST00000398417.2_Nonsense_Mutation_p.Q311*|SMAD4_ENST00000588745.1_Intron	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	311	SAD.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)|p.Q311*(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GCTTGCATTCCAGCCTCCCAT	0.333																																																41	Whole gene deletion(36)|Unknown(3)|Substitution - Nonsense(2)	pancreas(27)|large_intestine(4)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											121	116	118					18																	48586262		2203	4300	6503	46840260	SO:0001587	stop_gained	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.931C>T	18.37:g.48586262C>T	ENSP00000341551:p.Gln311*		46840260	A8K405	Nonsense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	42	9.410002	0.99163	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	18.3351	0.90285	0.0:1.0:0.0:0.0	.	.	.	.	X	311	.	ENSP00000341551:Q311X	Q	+	1	0	SMAD4	46840260	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.500000	0.81588	2.616000	0.88540	0.650000	0.86243	CAG		0.333	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		T	48586262	C	T	48586262	4	4	110	1	0	0	0	0	0	1	0	0	14797	595	21	3	957	3	SMAD4	18	48586262	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	19465075	48586262	29490986	211	29083										
MBD2	8932	hgsc.bcm.edu	37	chr18	51729417	51729417	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agagcaaacagcgtatgagcAagcagagtcttgaaagcgca	12	8	1	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr18:51729417A>T	ENST00000256429.3	-	2	931				MBD2_ENST00000583046.1_Nonsense_Mutation_p.L253*|MBD2_ENST00000398398.2_3'UTR	NM_003927.4	NP_003918.1	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2						ATP-dependent chromatin remodeling (GO:0043044)|cellular protein complex assembly (GO:0043623)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|protein domain specific binding (GO:0019904)|satellite DNA binding (GO:0003696)|siRNA binding (GO:0035197)			breast(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)		gcgtatgagcaagcagagtct	0.493																																																0			18											142	143	143					18																	51729417		2167	4267	6434	49983415	SO:0001627	intron_variant	64174			AF072242	CCDS11953.1, CCDS45871.1	18q21	2008-08-01			ENSG00000134046	ENSG00000134046			6917	protein-coding gene	gene with protein product		603547				9774669, 10441743	Standard	NM_003927		Approved		uc002lfg.2	Q9UBB5	OTTHUMG00000132705	ENST00000256429.3:c.702+1950T>A	18.37:g.51729417A>T			49983415	O95242|Q9UIS8	Nonsense_Mutation	SNP	ENST00000256429.3	37	CCDS11953.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.458116	0.84317	.	.	ENSG00000134046	ENST00000398398	.	.	.	4.6	3.45	0.39498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1166	0.25421	0.9008:0.0:0.0992:0.0	.	.	.	.	X	253	.	ENSP00000381435:L253X	L	-	2	0	MBD2	49983415	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	3.612000	0.54142	1.086000	0.41228	0.533000	0.62120	TTG		0.493	MBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256003.2	NM_003927		T	51729417	A	T	51729417	1	4	110	0	1	0	0	0	0	0	0	0	9373	131	5	5		5	MBD2	18	51729417	Intron	SNP	A	TCGA-EI-6506-01A-11D-1733-10	3143155	51729417	26347831	212	29084										
MALT1	10892	hgsc.bcm.edu	37	chr18	56390338	56390338	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taccgggagcaccccaagctCaaagctcctttggtggatgt	11	12	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr18:56390338C>A	ENST00000348428.3	+	10	1335	c.1077C>A	c.(1075-1077)ctC>ctA	p.L359L	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Silent_p.L348L	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	359	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)	p.L348L(1)		central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						ACCCCAAGCTCAAAGCTCCTT	0.403			T	BIRC3	MALT																																		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	1	Substitution - coding silent(1)	ovary(1)	18											133	126	128					18																	56390338		2203	4300	6503	54541318	SO:0001819	synonymous_variant	10892				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1077C>A	18.37:g.56390338C>A			54541318	Q9NTB7|Q9ULX4	Silent	SNP	ENST00000348428.3	37	CCDS11967.1																																																																																				0.403	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			A	56390338	C	A	56390338	2	1	110	1	0	0	0	0	0	0	0	1	9232	813	29	2		2	MALT1	18	56390338	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	4660921	56390338	21686910	213	29085										
NFATC1	4772	hgsc.bcm.edu	37	chr18	77193580	77193580	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgctctgttcccttccagcCcgaccctgcccgccctggac	8	21	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr18:77193580C>T	ENST00000427363.2	+	3	1228	c.1228C>T	c.(1228-1230)Ccg>Tcg	p.P410S	NFATC1_ENST00000318065.5_Splice_Site_p.P397S|NFATC1_ENST00000545796.1_5'UTR|NFATC1_ENST00000329101.4_Splice_Site_p.P397S|NFATC1_ENST00000397790.2_5'UTR|NFATC1_ENST00000587635.1_Splice_Site_p.P410S|NFATC1_ENST00000586434.1_Splice_Site_p.P397S|NFATC1_ENST00000592223.1_Splice_Site_p.P397S|NFATC1_ENST00000591814.1_Splice_Site_p.P410S|NFATC1_ENST00000253506.5_Splice_Site_p.P410S|NFATC1_ENST00000542384.1_Splice_Site_p.P410S			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	410	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CCCTTCCAGCCCGACCCTGCC	0.662																																					GBM(151;1210 2593 28719 45011)											0			18											80	84	82					18																	77193580		2203	4300	6503	75294568	SO:0001630	splice_region_variant	4772			U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1227-1C>T	18.37:g.77193580C>T			75294568	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		.	.	.	.	.	.	.	.	.	.	C	2.465	-0.323288	0.05350	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T	0.12361	3.13;2.69;2.93	4.6	4.6	0.57074	Rel homology (1);	0.111065	0.64402	D	0.000007	T	0.05364	0.0142	N	0.01800	-0.715	0.80722	D	1	P;P;P;B;B;B;P	0.48911	0.917;0.917;0.745;0.102;0.102;0.047;0.745	B;B;B;B;B;B;B	0.41440	0.357;0.357;0.298;0.05;0.05;0.04;0.298	T	0.32534	-0.9903	10	0.02654	T	1	-24.2885	17.4139	0.87494	0.0:1.0:0.0:0.0	.	397;397;410;410;410;397;410	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	S	410;410;410;397;397;374	ENSP00000253506:P410S;ENSP00000442435:P410S;ENSP00000327850:P397S	ENSP00000253506:P410S	P	+	1	0	NFATC1	75294568	1.000000	0.71417	0.988000	0.46212	0.110000	0.19582	4.341000	0.59335	2.097000	0.63578	0.561000	0.74099	CCG		0.662	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	Missense_Mutation	T	77193580	C	T	77193580	5	4	110	1	0	0	0	0	0	0	1	0	10392	637	22	3	1330	3	NFATC1	18	77193580	Splice_Site	SNP	C	TCGA-EI-6506-01A-11D-1733-10	20803242	77193580	883668	214	29086										
STK11	6794	hgsc.bcm.edu	37	chr19	1207092	1207092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgctgggggaaggctcttaCggcaaggtgaaggaggtgct	18	7	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:1207092C>T	ENST00000326873.7	+	1	1353	c.180C>T	c.(178-180)taC>taT	p.Y60Y	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	60	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)|p.Y60fs*1(3)|p.Y60*(2)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGGCTCTTACGGCAAGGTGA	0.622		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																												yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	28	Whole gene deletion(20)|Deletion - Frameshift(4)|Substitution - Nonsense(2)|Unknown(2)	cervix(15)|lung(8)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19	GRCh37	CD064644|CM981863|CM991149	STK11	D|M							42	46	45					19																	1207092		2088	4198	6286	1158092	SO:0001819	synonymous_variant	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.180C>T	19.37:g.1207092C>T			1158092	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																				0.622	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1207092	C	T	1207092	2	4	110	1	0	0	0	0	0	0	0	1	15326	547	19	1		1	STK11	19	1207092	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10		1207092	57921891	215	29087										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877893	2877893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgagaattcacaacggggagAaaccctataagtgtggaaaa	11	6	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:2877893A>G	ENST00000307635.2	+	4	1024	c.937A>G	c.(937-939)Aaa>Gaa	p.K313E	ZNF556_ENST00000586426.1_Missense_Mutation_p.K312E	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		CAACGGGGAGAAACCCTATAA	0.522																																																0			19											53	51	52					19																	2877893		2203	4300	6503	2828893	SO:0001583	missense	80032			BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.937A>G	19.37:g.2877893A>G	ENSP00000302603:p.Lys313Glu		2828893	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.748750	0.30955	.	.	ENSG00000172000	ENST00000307635	T	0.27104	1.69	2.3	2.3	0.28687	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36963	0.0986	M	0.64080	1.96	0.21355	N	0.999713	P	0.52316	0.952	P	0.54460	0.753	T	0.11397	-1.0589	9	0.72032	D	0.01	.	7.8561	0.29483	1.0:0.0:0.0:0.0	.	313	Q9HAH1	ZN556_HUMAN	E	313	ENSP00000302603:K313E	ENSP00000302603:K313E	K	+	1	0	ZNF556	2828893	0.933000	0.31639	0.246000	0.24233	0.184000	0.23303	3.050000	0.49877	0.902000	0.36520	0.334000	0.21626	AAA		0.522	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		G	2877893	A	G	2877893	3	3	110	1	0	0	0	0	1	0	0	0	18026	247	9	4	951	4	ZNF556	19	2877893	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	1670801	2877893	56251090	216	29088										
UHRF1	29128	hgsc.bcm.edu	37	chr19	4954680	4954681	+	RNA	INS	-	-	T													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggaggtggcccgagcagggcINSgggtccccgcgccggacatc							TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:4954680_4954681insT	ENST00000592666.1	+	0	2552_2553							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		CCGAGCAGGGCGGGTCCCCGCG	0.683																																																0			19																																								4905681			29128			AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"RING-type (C3HC4) zinc fingers"	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4954680_4954681insT			4905680	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Frame_Shift_Ins	INS	ENST00000592666.1	37																																																																																					0.683	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1	NM_001048201		T	4954681	-	T	4954680	6	5	110	0	1	1	1	0	0	0	0	0	17007	768	27	0		0	UHRF1	19	4954680	RNA	INS	-	TCGA-EI-6506-01A-11D-1733-10	2076787	4954680	54174303	217	29089										
MUC16	94025	hgsc.bcm.edu	37	chr19	9075296	9075296	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	attctcttagaggaggtaatTtctgttctaggccccttggt	10	8	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:9075296T>A	ENST00000397910.4	-	3	12353	c.12150A>T	c.(12148-12150)gaA>gaT	p.E4050D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4052	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E4050D(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGAGGTAATTTCTGTTCTAG	0.507																																																1	Substitution - Missense(1)	ovary(1)	19											152	139	143					19																	9075296		1923	4123	6046	8936296	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12150A>T	19.37:g.9075296T>A	ENSP00000381008:p.Glu4050Asp		8936296	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	7.785	0.710247	0.15239	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	2.23	-2.88	0.05682	.	.	.	.	.	T	0.01800	0.0057	N	0.22421	0.69	.	.	.	B	0.28713	0.22	B	0.20184	0.028	T	0.43507	-0.9387	8	0.87932	D	0	.	2.3664	0.04320	0.4117:0.2891:0.0:0.2991	.	4050	B5ME49	.	D	4050	ENSP00000381008:E4050D	ENSP00000381008:E4050D	E	-	3	2	MUC16	8936296	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-3.551000	0.00433	-0.943000	0.03691	0.260000	0.18958	GAA		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9075296	T	A	9075296	3	1	110	1	0	0	0	0	1	0	0	0	10003	1838	64	5	31701	5	MUC16	19	9075296	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	4120616	9075296	50053687	218	29090										
MUC16	94025	hgsc.bcm.edu	37	chr19	9083247	9083247	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	acaggtgttaggaggcctgaCtcagcactggtgggcttcac	14	10	2	1	rs371108545		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:9083247C>G	ENST00000397910.4	-	1	8771	c.8568G>C	c.(8566-8568)gaG>gaC	p.E2856D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2856	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAGGCCTGACTCAGCACTGG	0.542																																																0			19											88	85	86					19																	9083247		2010	4185	6195	8944247	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8568G>C	19.37:g.9083247C>G	ENSP00000381008:p.Glu2856Asp		8944247	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	0	-2.715322	0.00093	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	0.869	-1.74	0.08056	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.45963	-0.9225	8	0.87932	D	0	.	2.0553	0.03579	0.2553:0.3442:0.0:0.4005	.	2856	B5ME49	.	D	2856	ENSP00000381008:E2856D	ENSP00000381008:E2856D	E	-	3	2	MUC16	8944247	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.811000	0.01728	-1.413000	0.02027	-0.678000	0.03780	GAG		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9083247	C	G	9083247	3	3	110	1	0	0	0	0	1	0	0	0	10003	564	20	5	35291	5	MUC16	19	9083247	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	7951	9083247	50045736	219	29091										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15063753	15063753	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cactcacaggaaccagtccaCggcaatgatgagcgtgatgt	11	11	1	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:15063753C>T	ENST00000221742.3	-	8	1493	c.1486G>A	c.(1486-1488)Gtg>Atg	p.V496M	SLC1A6_ENST00000430939.2_Missense_Mutation_p.V432M|SLC1A6_ENST00000600144.1_Missense_Mutation_p.V418M	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	496					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						AACCAGTCCACGGCAATGATG	0.582																																																0			19											193	145	162					19																	15063753		2203	4300	6503	14924753	SO:0001583	missense	6511				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1486G>A	19.37:g.15063753C>T	ENSP00000221742:p.Val496Met		14924753	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	-	21.2	4.119758	0.77323	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.66638	-0.03;-0.22	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	D	0.85392	0.5686	M	0.93763	3.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73708	0.968;0.981	D	0.89274	0.3607	10	0.87932	D	0	-31.9452	14.8789	0.70516	0.0:1.0:0.0:0.0	.	432;496	E7EV13;P48664	.;EAA4_HUMAN	M	432;496	ENSP00000409386:V432M;ENSP00000221742:V496M	ENSP00000221742:V496M	V	-	1	0	SLC1A6	14924753	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	7.455000	0.80726	2.451000	0.82905	0.446000	0.29264	GTG		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15063753	C	T	15063753	3	4	110	1	0	0	0	0	1	0	0	0	14473	536	19	1	216	1	SLC1A6	19	15063753	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5980506	15063753	44065230	220	29092										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17058029	17058029	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cccttgggaaccgagagcttCatgtacacctgcagagggtg	13	11	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:17058029C>T	ENST00000443236.1	-	21	2689	c.2658G>A	c.(2656-2658)atG>atA	p.M886I		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	839						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCGAGAGCTTCATGTACACCT	0.602																																																0			19											143	144	144					19																	17058029		2078	4214	6292	16919029	SO:0001583	missense	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2658G>A	19.37:g.17058029C>T	ENSP00000402505:p.Met886Ile		16919029	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.537735	0.27475	.	.	ENSG00000160111	ENST00000291440	.	.	.	3.46	3.46	0.39613	Alpha-2-macroglobulin (1);	0.355253	0.25296	N	0.031693	T	0.34687	0.0906	N	0.04686	-0.185	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.13980	-1.0489	9	0.34782	T	0.22	.	11.8444	0.52376	0.0:0.8221:0.1779:0.0	.	839	Q8IZJ3	CPMD8_HUMAN	I	886	.	ENSP00000291440:M886I	M	-	3	0	CPAMD8	16919029	0.998000	0.40836	0.076000	0.20297	0.948000	0.59901	0.473000	0.22132	1.510000	0.48803	0.491000	0.48974	ATG		0.602	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17058029	C	T	17058029	3	4	110	1	0	0	0	0	1	0	0	0	3801	826	29	3	3228	3	CPAMD8	19	17058029	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1994276	17058029	42070954	221	29093										
C19orf46	163183	hgsc.bcm.edu	37	chr19	36498129	36498129	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agcaggcacaggtgcaggctGttctgctcagcctctagtac	12	12	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:36498129G>A	ENST00000324444.3	-	3	432	c.321C>T	c.(319-321)aaC>aaT	p.N107N	SYNE4_ENST00000340477.5_Intron|AC002116.8_ENST00000473572.2_RNA|ALKBH6_ENST00000495116.2_5'Flank	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	107					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											GGTGCAGGCTGTTCTGCTCAG	0.652																																																0			19											13	16	15					19																	36498129		1967	4145	6112	41189969	SO:0001819	synonymous_variant	163183			BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"chromosome 19 open reading frame 46", "deafness, autosomal recessive 76"	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.321C>T	19.37:g.36498129G>A			41189969	A8MRS0|A8MYE3|Q7Z7L3	Silent	SNP	ENST00000324444.3	37	CCDS42553.1																																																																																				0.652	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876		A	36498129	G	A	36498129	2	1	110	1	0	0	0	0	0	0	0	1	1935	1368	48	3		3	C19orf46	19	36498129	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	19440100	36498129	22630854	222	29094										
LGALS7B	653499	hgsc.bcm.edu	37	chr19	39281365	39281365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctgtgcggggaggagcagggCtccgatgccgccctgcattt	16	12	0	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:39281365C>T	ENST00000314980.4	+	3	148	c.132C>T	c.(130-132)ggC>ggT	p.G44G		NM_001042507.3	NP_001035972.1	P47929	LEG7_HUMAN	lectin, galactoside-binding, soluble, 7B	44	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|heterophilic cell-cell adhesion (GO:0007157)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carbohydrate binding (GO:0030246)										AGGAGCAGGGCTCCGATGCCG	0.642																																																0			19											34	37	36					19																	39281365		2201	4298	6499	43973205	SO:0001819	synonymous_variant	653499				CCDS42565.1	19q13.2	2011-08-04			ENSG00000178934	ENSG00000178934		"Lectins, galactoside-binding"	34447	protein-coding gene	gene with protein product	"galectin 7B"						Standard	NM_001042507		Approved	GAL7	uc002ojf.4	P47929		ENST00000314980.4:c.132C>T	19.37:g.39281365C>T			43973205	Q6IB87	Silent	SNP	ENST00000314980.4	37	CCDS42565.1																																																																																				0.642	LGALS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462638.1			T	39281365	C	T	39281365	2	4	110	1	0	0	0	0	0	0	0	1	8769	784	28	3		3	LGALS7B	19	39281365	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	2783236	39281365	19847618	223	29095										
LGALS13	29124	hgsc.bcm.edu	37	chr19	40095882	40095882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aggattcagatattgccttcCgtttccgagtgcactttggc	10	10	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:40095882C>T	ENST00000221797.4	+	3	202	c.157C>T	c.(157-159)Cgt>Tgt	p.R53C		NM_013268.2	NP_037400.1	Q9UHV8	PP13_HUMAN	lectin, galactoside-binding, soluble, 13	53	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			TATTGCCTTCCGTTTCCGAGT	0.512																																																0			19											241	178	199					19																	40095882		2203	4300	6503	44787722	SO:0001583	missense	29124			AF117383	CCDS33024.1	19q13.2	2014-03-19	2008-07-25		ENSG00000105198	ENSG00000105198		"Lectins, galactoside-binding"	15449	protein-coding gene	gene with protein product	"galectin 13"	608717				6856484, 10527825	Standard	NM_013268		Approved	PP13, PLAC8	uc002omb.3	Q9UHV8	OTTHUMG00000183073	ENST00000221797.4:c.157C>T	19.37:g.40095882C>T	ENSP00000221797:p.Arg53Cys		44787722	C5HZ15	Missense_Mutation	SNP	ENST00000221797.4	37	CCDS33024.1	.	.	.	.	.	.	.	.	.	.	.	11.79	1.743078	0.30865	.	.	ENSG00000105198	ENST00000221797	T	0.06371	3.31	0.744	0.744	0.18353	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.10337	0.0253	L	0.34521	1.04	0.09310	N	1	D	0.65815	0.995	P	0.56916	0.809	T	0.25082	-1.0142	8	0.87932	D	0	.	.	.	.	.	53	Q9UHV8	PP13_HUMAN	C	53	ENSP00000221797:R53C	ENSP00000221797:R53C	R	+	1	0	LGALS13	44787722	0.001000	0.12720	0.006000	0.13384	0.022000	0.10575	-1.105000	0.03323	0.658000	0.30925	0.305000	0.20034	CGT		0.512	LGALS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464968.1	NM_013268		T	40095882	C	T	40095882	3	4	110	1	0	0	0	0	1	0	0	0	8762	652	23	1	167	1	LGALS13	19	40095882	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	814517	40095882	19033101	224	29096										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40408807	40408807	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgggaggcacggatctggccGttggccagcaccacgggcag	17	12	1	0	rs587708149	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:40408807G>A	ENST00000221347.6	-	8	4039	c.4032C>T	c.(4030-4032)aaC>aaT	p.N1344N		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1344	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			GGATCTGGCCGTTGGCCAGCA	0.587													G|||	2	0.000399361	0	0.0014	5008	,	,		19942	0		0	False		,,,				2504	0.001															0			19											23	20	21					19																	40408807		2203	4294	6497	45100647	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4032C>T	19.37:g.40408807G>A			45100647	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40408807	G	A	40408807	2	1	110	1	0	0	0	0	0	0	0	1	5797	1136	40	1		1	FCGBP	19	40408807	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	312925	40408807	18720176	225	29097										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51986278	51986278	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cctgtctctacagatgggccCgactatgtgctgctgaggag	13	11	1	2	rs112143229		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:51986278C>T	ENST00000396477.4	+	4	702	c.681C>T	c.(679-681)ccC>ccT	p.P227P	CEACAM18_ENST00000451626.1_Silent_p.P288P	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	227	Ig-like C2-type.							p.P227P(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAGATGGGCCCGACTATGTGC	0.557																																																1	Substitution - coding silent(1)	skin(1)	19											153	147	149					19																	51986278		1963	4158	6121	56678090	SO:0001819	synonymous_variant	729767					19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.681C>T	19.37:g.51986278C>T			56678090	C9JN24	Silent	SNP	ENST00000396477.4	37																																																																																					0.557	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2			T	51986278	C	T	51986278	2	4	110	1	0	0	0	0	0	0	0	1	3195	639	23	1		1	CEACAM18	19	51986278	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	11577471	51986278	7142705	226	29098										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249968	52249968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gaatttgcacaggaaccagcCgaaaggccaatgtcctccca	9	13	0	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:52249968C>T	ENST00000595042.1	-	3	421	c.280G>A	c.(280-282)Ggc>Agc	p.G94S	FPR1_ENST00000304748.4_Missense_Mutation_p.G94S	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	94					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	AGGAACCAGCCGAAAGGCCAA	0.517																																																0			19											137	105	116					19																	52249968		2203	4300	6503	56941780	SO:0001583	missense	2357			M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"GPCR / Class A : Formyl peptide receptors"	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.280G>A	19.37:g.52249968C>T	ENSP00000471493:p.Gly94Ser		56941780	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	17.49	3.401969	0.62288	.	.	ENSG00000171051	ENST00000304748	T	0.40225	1.04	3.66	3.66	0.41972	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.67998	0.2953	M	0.89030	3	0.49130	D	0.999756	D	0.89917	1.0	D	0.79108	0.992	T	0.76141	-0.3068	10	0.87932	D	0	.	13.6424	0.62260	0.0:1.0:0.0:0.0	.	94	P21462	FPR1_HUMAN	S	94	ENSP00000302707:G94S	ENSP00000302707:G94S	G	-	1	0	FPR1	56941780	1.000000	0.71417	0.916000	0.36221	0.077000	0.17291	7.043000	0.76572	1.960000	0.56953	0.655000	0.94253	GGC		0.517	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		T	52249968	C	T	52249968	3	4	110	1	0	0	0	0	1	0	0	0	6057	652	23	1	776	1	FPR1	19	52249968	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	263690	52249968	6879015	227	29099										
ZNF649	65251	hgsc.bcm.edu	37	chr19	52399807	52399807	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttggtgagggcatcaggtttGccggcttgataccctgtttg	14	8	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:52399807G>A	ENST00000354957.3	-	4	440	c.156C>T	c.(154-156)ggC>ggT	p.G52G	ZNF649_ENST00000600738.1_Silent_p.G52G|CTC-429C10.2_ENST00000600329.1_RNA	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	52	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		CATCAGGTTTGCCGGCTTGAT	0.493																																																0			19											158	120	133					19																	52399807		2203	4300	6503	57091619	SO:0001819	synonymous_variant	65251			BC005368	CCDS12843.1	19q13.41	2013-01-08				ENSG00000198093		"Zinc fingers, C2H2-type", "-"	25741	protein-coding gene	gene with protein product		611903				15950191	Standard	NM_023074		Approved	FLJ12644	uc002pxy.3	Q9BS31		ENST00000354957.3:c.156C>T	19.37:g.52399807G>A			57091619	A8MYJ5|B2RDC4|Q9H9N2	Silent	SNP	ENST00000354957.3	37	CCDS12843.1																																																																																				0.493	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		A	52399807	G	A	52399807	2	1	110	1	0	0	0	0	0	0	0	1	18103	1306	46	3		3	ZNF649	19	52399807	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	149839	52399807	6729176	228	29100										
CNOT3	4849	hgsc.bcm.edu	37	chr19	54651930	54651930	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtccacagcaaccagcacccTcagtccccagctgtgccgcc	8	20	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:54651930T>G	ENST00000406403.1	+	10	2545	c.942T>G	c.(940-942)ccT>ccG	p.P314P	CNOT3_ENST00000358389.3_Silent_p.P133P|CNOT3_ENST00000221232.5_Silent_p.P314P			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	314	Pro-rich.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ACCAGCACCCTCAGTCCCCAG	0.687																																																0			19											32	33	32					19																	54651930		2193	4289	6482	59343742	SO:0001819	synonymous_variant	4849			AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"NOT3 (negative regulator of transcription 3, yeast) homolog"	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.942T>G	19.37:g.54651930T>G			59343742	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	37	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.450466	0.26074	.	.	ENSG00000088038	ENST00000440571	.	.	.	3.43	-0.942	0.10398	.	.	.	.	.	T	0.38983	0.1061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28713	-1.0035	4	.	.	.	-10.2197	0.503	0.00582	0.2964:0.1586:0.3232:0.2217	.	.	.	.	R	236	.	.	L	+	2	0	CNOT3	59343742	0.999000	0.42202	1.000000	0.80357	0.984000	0.73092	0.370000	0.20433	0.061000	0.16311	0.379000	0.24179	CTC		0.687	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		G	54651930	T	G	54651930	2	3	110	1	0	0	0	0	0	0	0	1	3626	1538	54	4		4	CNOT3	19	54651930	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	2252123	54651930	4477053	229	29101										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56241220	56241220	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agttttcggagtttacaaacAggctgagccagcgctttgca	11	9	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:56241220A>T	ENST00000332836.2	-	3	1998	c.1971T>A	c.(1969-1971)ccT>ccA	p.P657P		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	657						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.P657P(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		GTTTACAAACAGGCTGAGCCA	0.418																																																1	Substitution - coding silent(1)	ovary(1)	19											82	81	81					19																	56241220		2203	4300	6503	60933032	SO:0001819	synonymous_variant	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1971T>A	19.37:g.56241220A>T			60933032	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																				0.418	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56241220	A	T	56241220	2	4	110	1	0	0	0	0	0	0	0	1	10515	175	7	5		5	NLRP9	19	56241220	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	1589290	56241220	2887763	230	29102										
NLRP5	126206	hgsc.bcm.edu	37	chr19	56539847	56539847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcttcccaagagatgagtccGctgaggcatgtcctgtggtc	12	11	1	3	rs61745533	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:56539847G>A	ENST00000390649.3	+	7	2248	c.2248G>A	c.(2248-2250)Gct>Act	p.A750T		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	750					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AGATGAGTCCGCTGAGGCATG	0.522													G|||	4	0.000798722	0	0	5008	,	,		18567	0		0	False		,,,				2504	0.0041															0			19						G	THR/ALA	1,4055		0,1,2027	144	144	144		2248	-5.4	0	19	dbSNP_129	144	5,8385		0,5,4190	yes	missense	NLRP5	NM_153447.4	58	0,6,6217	AA,AG,GG		0.0596,0.0247,0.0482	benign	750/1201	56539847	6,12440	2028	4195	6223	61231659	SO:0001583	missense	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2248G>A	19.37:g.56539847G>A	ENSP00000375063:p.Ala750Thr		61231659	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	3.389	-0.124674	0.06795	2.47E-4	5.96E-4	ENSG00000171487	ENST00000390649	D	0.88896	-2.44	2.72	-5.45	0.02616	.	1.278590	0.05974	N	0.642867	T	0.74359	0.3706	N	0.17474	0.49	0.09310	N	1	B	0.15141	0.012	B	0.08055	0.003	T	0.60777	-0.7196	10	0.13853	T	0.58	.	5.4198	0.16394	0.1865:0.4322:0.3813:0.0	rs61745533	750	P59047	NALP5_HUMAN	T	750	ENSP00000375063:A750T	ENSP00000375063:A750T	A	+	1	0	NLRP5	61231659	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.786000	0.04623	-1.005000	0.03417	0.313000	0.20887	GCT		0.522	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56539847	G	A	56539847	3	1	110	1	0	0	0	0	1	0	0	0	10511	1087	38	1	2274	1	NLRP5	19	56539847	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	298627	56539847	2589136	231	29103										
PEG3	5178	hgsc.bcm.edu	37	chr19	57328632	57328632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	catctgtgtcaaaatgatagCgcctctttctttcaagaact	6	10	5	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr19:57328632C>T	ENST00000326441.9	-	10	1541	c.1178G>A	c.(1177-1179)cGc>cAc	p.R393H	PEG3_ENST00000598410.1_Missense_Mutation_p.R269H|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R393H|PEG3_ENST00000593695.1_Missense_Mutation_p.R267H|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000599935.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	393					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AAAATGATAGCGCCTCTTTCT	0.453																																																0			19											107	112	110					19																	57328632		2203	4300	6503	62020444	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.1178G>A	19.37:g.57328632C>T	ENSP00000326581:p.Arg393His		62020444	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520664	0.64747	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02606	4.23;4.23	4.35	2.18	0.27775	.	0.000000	0.45361	D	0.000378	T	0.05593	0.0147	L	0.34521	1.04	.	.	.	P;P;D	0.89917	0.627;0.454;1.0	B;B;D	0.68621	0.065;0.036;0.959	T	0.40608	-0.9554	9	0.22109	T	0.4	-26.0019	6.4559	0.21930	0.0:0.5439:0.3586:0.0975	.	269;393;328	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	H	393;393;363	ENSP00000326581:R393H;ENSP00000403051:R393H	ENSP00000292074:R363H	R	-	2	0	ZIM2	62020444	0.196000	0.23350	0.996000	0.52242	0.935000	0.57460	0.300000	0.19156	0.748000	0.32831	0.655000	0.94253	CGC		0.453	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57328632	C	T	57328632	3	4	110	1	0	0	0	0	1	0	0	0	11751	768	27	1	3592	1	PEG3	19	57328632	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	788785	57328632	1800351	232	29104										
CHGB	1114	hgsc.bcm.edu	37	chr20	5902992	5902992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcattataggtagaaaagacGtcaaagacaaagagacaact	8	6	2	4	rs370206314		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:5902992G>A	ENST00000378961.4	+	4	406	c.202G>A	c.(202-204)Gtc>Atc	p.V68I		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	68						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						TAGAAAAGACGTCAAAGACAA	0.408																																																0			20						G	ILE/VAL	0,4406		0,0,2203	47	48	48		202	1.7	1	20		48	1,8599	1.2+/-3.3	0,1,4299	no	missense	CHGB	NM_001819.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	68/678	5902992	1,13005	2203	4300	6503	5850992	SO:0001583	missense	1114				CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.202G>A	20.37:g.5902992G>A	ENSP00000368244:p.Val68Ile		5850992	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	G	2.933	-0.220639	0.06061	0.0	1.16E-4	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01548	4.78;4.78	5.77	1.66	0.24008	.	0.642918	0.14144	N	0.338490	T	0.02193	0.0068	M	0.62723	1.935	0.26383	N	0.976705	B	0.26081	0.141	B	0.17722	0.019	T	0.43147	-0.9409	10	0.28530	T	0.3	-6.5147	5.2658	0.15597	0.2325:0.2966:0.4709:0.0	.	68	P05060	SCG1_HUMAN	I	68;48	ENSP00000368244:V68I;ENSP00000416643:V48I	ENSP00000368244:V68I	V	+	1	0	CHGB	5850992	0.914000	0.31030	0.993000	0.49108	0.055000	0.15305	0.490000	0.22403	0.087000	0.17167	-0.878000	0.02970	GTC		0.408	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		A	5902992	G	A	5902992	3	1	110	1	0	0	0	0	1	0	0	0	3345	1145	40	1	216	1	CHGB	20	5902992	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10		5902992	57122528	233	29105										
CST4	1472	hgsc.bcm.edu	37	chr20	23667836	23667836	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagtaattcacccccccaaaGgtctgcacacaggagaaaac	7	13	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:23667836G>A	ENST00000217423.3	-	2	301	c.231C>T	c.(229-231)acC>acT	p.T77T		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	77			T -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CCCCCCCAAAGGTCTGCACAC	0.562																																																0			20											209	192	198					20																	23667836		2203	4300	6503	23615836	SO:0001819	synonymous_variant	1472				CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.231C>T	20.37:g.23667836G>A			23615836	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																				0.562	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899		A	23667836	G	A	23667836	2	1	110	1	0	0	0	0	0	0	0	1	3980	987	35	3		3	CST4	20	23667836	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	17764844	23667836	39357684	234	29106										
C20orf114	92747	hgsc.bcm.edu	37	chr20	31889044	31889044	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gctctgtctcctcaggccaaGttgttggactcacagggaaa	11	11	4	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:31889044G>A	ENST00000253354.1	+	9	914	c.753G>A	c.(751-753)aaG>aaA	p.K251K	BPIFB1_ENST00000464032.1_3'UTR	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	251					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CTCAGGCCAAGTTGTTGGACT	0.498																																																0			20											115	103	107					20																	31889044		2203	4300	6503	31352705	SO:0001819	synonymous_variant	92747			BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"BPI fold containing"	16108	protein-coding gene	gene with protein product	"von Ebner minor salivary gland protein"		"chromosome 20 open reading frame 114"	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.753G>A	20.37:g.31889044G>A			31352705	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Silent	SNP	ENST00000253354.1	37	CCDS13218.1																																																																																				0.498	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197		A	31889044	G	A	31889044	2	1	110	1	0	0	0	0	0	0	0	1	2088	1020	36	3		3	C20orf114	20	31889044	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	8221208	31889044	31136476	235	29107										
UBE2C	11065	hgsc.bcm.edu	37	chr20	44445347	44445347	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gacctgcctgttctcttccaGcttttaagaagtacctgcaa	7	12	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:44445347G>C	ENST00000356455.4	+	6	601		c.e6-1		UBE2C_ENST00000372568.4_Splice_Site|UBE2C_ENST00000243893.6_Splice_Site|UBE2C_ENST00000496085.1_Splice_Site|UBE2C_ENST00000335046.3_Splice_Site|UBE2C_ENST00000352551.5_Splice_Site|UBE2C_ENST00000405520.1_Splice_Site	NM_007019.2	NP_008950.1	O00762	UBE2C_HUMAN	ubiquitin-conjugating enzyme E2C						activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cyclin catabolic process (GO:0008054)|exit from mitosis (GO:0010458)|free ubiquitin chain polymerization (GO:0010994)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(2)|lung(2)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				TTCTCTTCCAGCTTTTAAGAA	0.458																																																0			20											75	74	74					20																	44445347		2203	4300	6503	43878754	SO:0001630	splice_region_variant	11065			U73379	CCDS13370.1, CCDS13371.1, CCDS13372.1, CCDS13374.1, CCDS74733.1, CCDS74734.1	20q13.12	2007-02-05			ENSG00000175063	ENSG00000175063		"Ubiquitin-conjugating enzymes E2"	15937	protein-coding gene	gene with protein product		605574				9122200	Standard	NM_007019		Approved	UBCH10	uc002xpm.3	O00762	OTTHUMG00000033038	ENST00000356455.4:c.482-1G>C	20.37:g.44445347G>C			43878754	A6NP33|E1P5N7|G3XAB7	Splice_Site	SNP	ENST00000356455.4	37	CCDS13370.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.715332	0.68844	.	.	ENSG00000175063	ENST00000356455;ENST00000405520;ENST00000335046;ENST00000352551;ENST00000372568	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1365	0.86742	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2C	43878754	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.781000	0.68964	2.382000	0.81193	0.655000	0.94253	.		0.458	UBE2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080309.2	NM_007019	Intron	C	44445347	G	C	44445347	5	2	110	1	0	0	0	0	0	0	1	0	16886	985	34	5	654	5	UBE2C	20	44445347	Splice_Site	SNP	G	TCGA-EI-6506-01A-11D-1733-10	12556303	44445347	18580173	236	29108										
NCOA5	57727	hgsc.bcm.edu	37	chr20	44698924	44698924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ctcgctgatctcgaaaatccCtagagtctcttagatcacga	7	12	3	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:44698924C>T	ENST00000290231.6	-	3	454	c.290G>A	c.(289-291)aGg>aAg	p.R97K		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	97	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TCGAAAATCCCTAGAGTCTCT	0.488																																																0			20											115	105	108					20																	44698924		2203	4300	6503	44132331	SO:0001583	missense	57727				CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"coactivator independent of AF-2"					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.290G>A	20.37:g.44698924C>T	ENSP00000290231:p.Arg97Lys		44132331	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320134	0.81469	.	.	ENSG00000124160	ENST00000290231	T	0.51574	0.7	5.17	5.17	0.71159	.	0.123708	0.53938	D	0.000044	T	0.67116	0.2859	M	0.68317	2.08	0.41092	D	0.985606	D	0.56035	0.974	D	0.67725	0.953	T	0.69143	-0.5223	10	0.62326	D	0.03	-12.0168	17.8426	0.88719	0.0:1.0:0.0:0.0	.	97	Q9HCD5	NCOA5_HUMAN	K	97	ENSP00000290231:R97K	ENSP00000290231:R97K	R	-	2	0	NCOA5	44132331	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.956000	0.56722	2.684000	0.91462	0.650000	0.86243	AGG		0.488	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967		T	44698924	C	T	44698924	3	4	110	1	0	0	0	0	1	0	0	0	10263	681	24	3	1473	3	NCOA5	20	44698924	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	253577	44698924	18326596	237	29109										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51870661	51870661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tccgatgccgacagtgcagcGcggcctatgacaccctagtc	11	15	0	1	rs141167641	byFrequency	TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:51870661G>A	ENST00000371497.5	+	2	1551	c.664G>A	c.(664-666)Gcg>Acg	p.A222T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A219T|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A219T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	222					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A222T(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			ACAGTGCAGCGCGGCCTATGA	0.562													G|||	4	0.000798722	0	0	5008	,	,		19301	0		0.001	False		,,,				2504	0.0031															1	Substitution - Missense(1)	ovary(1)	20											57	52	53					20																	51870661		2203	4300	6503	51304068	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.664G>A	20.37:g.51870661G>A	ENSP00000360552:p.Ala222Thr		51304068	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.9	4.584970	0.86748	.	.	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.16073	2.37;2.37	5.2	5.2	0.72013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.41213	0.1149	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.17715	-1.0360	10	0.66056	D	0.02	-21.8975	19.0899	0.93223	0.0:0.0:1.0:0.0	.	222	Q9NRE2	TSH2_HUMAN	T	222;219	ENSP00000360552:A222T;ENSP00000333114:A219T	ENSP00000333114:A219T	A	+	1	0	TSHZ2	51304068	1.000000	0.71417	0.730000	0.30809	0.640000	0.38277	9.414000	0.97362	2.579000	0.87056	0.643000	0.83706	GCG		0.562	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51870661	G	A	51870661	3	1	110	1	0	0	0	0	1	0	0	0	16664	1087	38	1	670	1	TSHZ2	20	51870661	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	7171737	51870661	11154859	238	29110										
GNAS	2778	hgsc.bcm.edu	37	chr20	57415590	57415590	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cccgagaccgagcctgaagaCgatcgcggcccggtggtgcc	15	15	0	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:57415590C>T	ENST00000313949.7	+	1	818	c.429C>T	c.(427-429)gaC>gaT	p.D143D	GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000371075.3_Silent_p.D143D|GNAS_ENST00000371098.2_Silent_p.D143D|GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000443966.1_RNA			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			AGCCTGAAGACGATCGCGGCC	0.662			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	0			20											75	70	71					20																	57415590		2203	4300	6503	56848985	SO:0001819	synonymous_variant	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000313949.7:c.429C>T	20.37:g.57415590C>T			56848985	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000313949.7	37	CCDS13471.1	.	.	.	.	.	.	.	.	.	.	C	8.995	0.978738	0.18812	.	.	ENSG00000087460	ENST00000419558	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	T	0.64583	0.2611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62353	-0.6872	4	.	.	.	.	13.15	0.59484	0.0:1.0:0.0:0.0	.	.	.	.	M	11	.	.	T	+	2	0	GNAS	56848985	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	1.154000	0.31688	2.566000	0.86566	0.585000	0.79938	ACG		0.662	GNAS-002	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080418.7	NM_000516		T	57415590	C	T	57415590	2	4	110	1	0	0	0	0	0	0	0	1	6530	535	19	1		1	GNAS	20	57415590	Silent	SNP	C	TCGA-EI-6506-01A-11D-1733-10	5544929	57415590	5609930	239	29111										
C20orf151	140893	hgsc.bcm.edu	37	chr20	60991872	60991872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agctctcgaactcctgctgcCgcttcctggccagctcctgg	10	17	1	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr20:60991872C>T	ENST00000252998.1	-	5	413	c.257G>A	c.(256-258)cGg>cAg	p.R86Q		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	86						extracellular space (GO:0005615)											CTCCTGCTGCCGCTTCCTGGC	0.682																																																0			20											42	38	40					20																	60991872		2194	4291	6485	60425267	SO:0001583	missense	140893			AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"hypothetical protein LOC140893"		"chromosome 20 open reading frame 151"	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.257G>A	20.37:g.60991872C>T	ENSP00000252998:p.Arg86Gln		60425267	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.552452	0.45487	.	.	ENSG00000130701	ENST00000252998	T	0.18960	2.18	4.46	0.928	0.19443	Tumour-suppressor protein CtIP N-terminal (1);	0.195483	0.41938	D	0.000788	T	0.13072	0.0317	L	0.43152	1.355	0.21697	N	0.999585	P	0.42993	0.797	B	0.31946	0.138	T	0.13764	-1.0497	10	0.59425	D	0.04	-25.2442	8.0339	0.30480	0.0:0.2265:0.0:0.7735	.	86	Q8NC74	CT151_HUMAN	Q	86	ENSP00000252998:R86Q	ENSP00000252998:R86Q	R	-	2	0	C20orf151	60425267	1.000000	0.71417	0.996000	0.52242	0.252000	0.25951	0.897000	0.28390	-0.111000	0.12001	-0.367000	0.07326	CGG		0.682	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		T	60991872	C	T	60991872	3	4	110	1	0	0	0	0	1	0	0	0	2097	652	23	1	1777	1	C20orf151	20	60991872	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	3576282	60991872	2033648	240	29112										
GGT5	2687	hgsc.bcm.edu	37	chr22	24622043	24622043	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cttcccccaggccctacgcaCggtgtgttgatggtgctggt	13	13	0	1	rs372682332		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr22:24622043C>T	ENST00000327365.4	-	8	1646		c.e8+1		GGT5_ENST00000418439.2_Splice_Site|GGT5_ENST00000263112.7_Splice_Site|GGT5_ENST00000398292.3_Splice_Site	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5						arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GCCCTACGCACGGTGTGTTGA	0.682																																																0			22						C	,,	0,4406		0,0,2203	20	20	20		,,	3.3	1	22		20	1,8595		0,1,4297	no	splice-5,splice-5,splice-5	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,	,,	24622043	1,13001	2203	4298	6501	22952043	SO:0001630	splice_region_variant	2687			M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.1229+1G>A	22.37:g.24622043C>T			22952043	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Splice_Site	SNP	ENST00000327365.4	37	CCDS13825.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044628	0.55110	0.0	1.16E-4	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292;ENST00000425408;ENST00000418439	.	.	.	3.3	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.4019	0.44235	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GGT5	22952043	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	4.615000	0.61190	2.175000	0.68902	0.485000	0.47835	.		0.682	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	Intron	T	24622043	C	T	24622043	5	4	110	1	0	0	0	0	0	0	1	0	6382	550	19	1	553	1	GGT5	22	24622043	Splice_Site	SNP	C	TCGA-EI-6506-01A-11D-1733-10		24622043	26682523	241	29113										
NF2	4771	hgsc.bcm.edu	37	chr22	30035156	30035156	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttttatcctgagaatgctgaAgaggagctggttcaggagat	13	5	1	4	rs535626069		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr22:30035156A>G	ENST00000338641.4	+	3	759	c.318A>G	c.(316-318)gaA>gaG	p.E106E	NF2_ENST00000353887.4_Intron|NF2_ENST00000403435.1_Silent_p.E106E|NF2_ENST00000361166.4_Silent_p.E106E|NF2_ENST00000413209.2_Silent_p.E106E|NF2_ENST00000403999.3_Silent_p.E106E|NF2_ENST00000361676.4_Silent_p.E64E|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Intron|NF2_ENST00000397789.3_Silent_p.E106E|NF2_ENST00000334961.7_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	106	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		E -> G (in NF2). {ECO:0000269|PubMed:8081368, ECO:0000269|PubMed:9643284}.		actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.H95fs*3(1)|p.V86_Q111>E(1)|p.A105fs*20(1)|p.L97fs*17(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AGAATGCTGAAGAGGAGCTGG	0.448			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2				A|||	1	0.000199681	8e-04	0	5008	,	,		20266	0		0	False		,,,				2504	0					yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	7	Unknown(3)|Deletion - Frameshift(3)|Complex - deletion inframe(1)	soft_tissue(3)|stomach(1)|large_intestine(1)|lung(1)|kidney(1)	22											137	120	126					22																	30035156		2203	4300	6503	28365156	SO:0001819	synonymous_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.318A>G	22.37:g.30035156A>G			28365156	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Silent	SNP	ENST00000338641.4	37	CCDS13861.1																																																																																				0.448	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		G	30035156	A	G	30035156	2	3	110	1	0	0	0	0	0	0	0	1	10388	69	3	4		4	NF2	22	30035156	Silent	SNP	A	TCGA-EI-6506-01A-11D-1733-10	5413113	30035156	21269410	242	29114										
PIK3IP1	113791	hgsc.bcm.edu	37	chr22	31679153	31679153	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	agtctggctggtgtggaccaCgacagtcttctcatccacaa	10	12	3	0			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr22:31679153C>T	ENST00000215912.5	-	6	892	c.709G>A	c.(709-711)Gtg>Atg	p.V237M	PIK3IP1_ENST00000441972.1_3'UTR|PIK3IP1_ENST00000487265.2_Missense_Mutation_p.V158M	NM_052880.4	NP_443112.2	Q96FE7	P3IP1_HUMAN	phosphoinositide-3-kinase interacting protein 1	237					negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase catalytic subunit binding (GO:0036313)			large_intestine(2)|lung(1)|ovary(1)	4						GTGTGGACCACGACAGTCTTC	0.607																																																0			22											99	71	80					22																	31679153		2203	4300	6503	30009153	SO:0001583	missense	113791			BC011049	CCDS13893.1, CCDS46690.1	22q12.2	2007-04-13			ENSG00000100100	ENSG00000100100			24942	protein-coding gene	gene with protein product						12477932	Standard	NM_052880		Approved	HGFL, MGC17330	uc003akm.3	Q96FE7	OTTHUMG00000151256	ENST00000215912.5:c.709G>A	22.37:g.31679153C>T	ENSP00000215912:p.Val237Met		30009153	B4DRR9|D1MEI0|O00318|Q49A94|Q86YW2|Q8NCJ9	Missense_Mutation	SNP	ENST00000215912.5	37	CCDS13893.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.155795	0.78114	.	.	ENSG00000100100	ENST00000215912;ENST00000416925;ENST00000487265	T;T	0.51071	0.72;0.72	5.67	3.59	0.41128	.	0.177739	0.49916	D	0.000132	T	0.49133	0.1539	L	0.61218	1.895	0.80722	D	1	D;P	0.59767	0.986;0.902	P;B	0.46825	0.528;0.15	T	0.52808	-0.8526	10	0.87932	D	0	-11.678	10.6888	0.45858	0.0:0.8444:0.0:0.1556	.	158;237	D1MEI0;Q96FE7	.;P3IP1_HUMAN	M	237;215;158	ENSP00000215912:V237M;ENSP00000441361:V158M	ENSP00000215912:V237M	V	-	1	0	PIK3IP1	30009153	0.994000	0.37717	0.625000	0.29200	0.983000	0.72400	4.463000	0.60128	0.738000	0.32606	0.561000	0.74099	GTG		0.607	PIK3IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321939.1	NM_052880		T	31679153	C	T	31679153	3	4	110	1	0	0	0	0	1	0	0	0	11948	536	19	1	86	1	PIK3IP1	22	31679153	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	1643997	31679153	19625413	243	29115										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50279381	50279381	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgcttgaatacttgaaacctCagtactccctccccgcccct	5	17	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chr22:50279381C>T	ENST00000216268.5	+	2	2548	c.2071C>T	c.(2071-2073)Cag>Tag	p.Q691*		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	691						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q691K(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		CTTGAAACCTCAGTACTCCCT	0.443																																																1	Substitution - Missense(1)	ovary(1)	22											111	116	114					22																	50279381		2203	4300	6503	48665385	SO:0001587	stop_gained	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2071C>T	22.37:g.50279381C>T	ENSP00000216268:p.Gln691*		48665385	B2RZH1|Q1ECU0|Q9UGG8	Nonsense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	43	10.068848	0.99330	.	.	ENSG00000100426	ENST00000216268	.	.	.	5.36	5.36	0.76844	.	0.065867	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-28.2004	19.0818	0.93186	0.0:1.0:0.0:0.0	.	.	.	.	X	691	.	ENSP00000216268:Q691X	Q	+	1	0	ZBED4	48665385	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.361000	0.79497	2.492000	0.84095	0.655000	0.94253	CAG		0.443	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50279381	C	T	50279381	4	4	110	1	0	0	0	0	0	1	0	0	17559	827	29	3	2073	3	ZBED4	22	50279381	Nonsense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	18600228	50279381	1025185	244	29116										
MID1	4281	hgsc.bcm.edu	37	chrX	10427780	10427780	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttggtgccgctctgcagaccGtgcaccgtgtagtggttctg	14	11	2	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:10427780G>A	ENST00000317552.4	-	8	1753	c.1353C>T	c.(1351-1353)caC>caT	p.H451H	MID1_ENST00000453318.2_Silent_p.H451H|MID1_ENST00000380782.2_Silent_p.H451H|MID1_ENST00000380785.1_Silent_p.H451H|MID1_ENST00000380787.1_Silent_p.H451H|MID1_ENST00000380779.1_Silent_p.H451H|MID1_ENST00000380780.1_Silent_p.H451H|MID1_ENST00000479925.1_5'UTR	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	451	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGCAGACCGTGCACCGTGT	0.517																																																0			X											262	182	209					X																	10427780		2203	4300	6503	10387780	SO:0001819	synonymous_variant	4281			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1353C>T	X.37:g.10427780G>A			10387780	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	37	CCDS14138.1																																																																																				0.517	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10427780	G	A	10427780	2	1	110	1	0	0	0	0	0	0	0	1	9606	1136	40	1		1	MID1	23	10427780	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10		10427780	144842780	245	29117										
ACE2	59272	hgsc.bcm.edu	37	chrX	15593883	15593883	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	taacatgtaagtaaatggcaGagtcccaacaatcgtgagtg	10	7	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:15593883G>A	ENST00000252519.3	-	10	1450	c.1348C>T	c.(1348-1350)Ctg>Ttg	p.L450L	ACE2_ENST00000427411.1_Silent_p.L450L			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	450					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	GTAAATGGCAGAGTCCCAACA	0.388																																																0			X											165	138	147					X																	15593883		2203	4300	6503	15503804	SO:0001819	synonymous_variant	59272			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.1348C>T	X.37:g.15593883G>A			15503804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Silent	SNP	ENST00000252519.3	37	CCDS14169.1																																																																																				0.388	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1			A	15593883	G	A	15593883	2	1	110	1	0	0	0	0	0	0	0	1	137	933	33	3		3	ACE2	23	15593883	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	5166103	15593883	139676677	246	29118										
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15821892	15821892	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aagaaggaaaaggaagaggcGgctaaaaaacggcaagaaga	14	4	0	4			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:15821892G>A	ENST00000307771.7	+	4	309	c.285G>A	c.(283-285)gcG>gcA	p.A95A	ZRSR2_ENST00000468028.1_3'UTR	NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	95					mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					AGGAAGAGGCGGCTAAAAAAC	0.388			"F, S, Mis"		"MDS, CLL"																																NSCLC(197;1631 3042 5741 31152)		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	0			X											85	65	72					X																	15821892		2202	4298	6500	15731813	SO:0001819	synonymous_variant	8233			BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.285G>A	X.37:g.15821892G>A			15731813	Q14D69	Silent	SNP	ENST00000307771.7	37	CCDS14172.1																																																																																				0.388	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		A	15821892	G	A	15821892	2	1	110	1	0	0	0	0	0	0	0	1	18264	1103	39	1		1	ZRSR2	23	15821892	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	228009	15821892	139448668	247	29119										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028523	37028523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ggagtgtcccatctctgcccGgagcctccagagactcgcgt	12	15	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:37028523G>A	ENST00000358047.3	+	1	2092	c.2040G>A	c.(2038-2040)ccG>ccA	p.P680P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	680										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ATCTCTGCCCGGAGCCTCCAG	0.642																																																0			X											24	23	24					X																	37028523		2162	4235	6397	36938444	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2040G>A	X.37:g.37028523G>A			36938444	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.642	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37028523	G	A	37028523	2	1	110	1	0	0	0	0	0	0	0	1	5590	1103	39	1		1	FAM47C	23	37028523	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	21206631	37028523	118242037	248	29120										
KCND1	3750	hgsc.bcm.edu	37	chrX	48819870	48819870	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atgagatcttgacagtctcgGggaagaggcaaggggtaccc	15	8	2	3			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:48819870G>T	ENST00000218176.3	-	6	3213	c.1916C>A	c.(1915-1917)cCc>cAc	p.P639H	KCND1_ENST00000376477.1_Missense_Mutation_p.P262H	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	639					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	GACAGTCTCGGGGAAGAGGCA	0.587																																																0			X											23	21	22					X																	48819870		2203	4300	6503	48704814	SO:0001583	missense	3750			AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1916C>A	X.37:g.48819870G>T	ENSP00000218176:p.Pro639His		48704814	A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	37	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	g	0.061	-1.224109	0.01530	.	.	ENSG00000102057	ENST00000376477;ENST00000218176	D;D	0.95690	-3.25;-3.78	5.32	4.37	0.52481	.	0.137128	0.46442	D	0.000297	T	0.81664	0.4870	N	0.00538	-1.39	0.32481	N	0.541485	B	0.02656	0.0	B	0.01281	0.0	T	0.79838	-0.1634	10	0.23891	T	0.37	.	9.4069	0.38466	0.0:0.0:0.5513:0.4487	.	639	Q9NSA2	KCND1_HUMAN	H	262;639	ENSP00000365660:P262H;ENSP00000218176:P639H	ENSP00000218176:P639H	P	-	2	0	KCND1	48704814	0.999000	0.42202	0.692000	0.30179	0.061000	0.15899	3.038000	0.49783	2.220000	0.72140	0.431000	0.28591	CCC		0.587	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		T	48819870	G	T	48819870	3	4	110	1	0	0	0	0	1	0	0	0	8039	1232	43	2	31	2	KCND1	23	48819870	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	11791347	48819870	106450690	249	29121										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49074243	49074243	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgaggggtgtgtttggcctcGtccgtgcaggtgtagaattt	16	6	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:49074243G>A	ENST00000376265.2	-	26	3154	c.3093C>T	c.(3091-3093)gaC>gaT	p.D1031D	CACNA1F_ENST00000376251.1_Silent_p.D966D|CACNA1F_ENST00000323022.5_Silent_p.D1020D	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1031					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GTTTGGCCTCGTCCGTGCAGG	0.567																																																0			X											177	142	154					X																	49074243		2203	4300	6503	48961187	SO:0001819	synonymous_variant	778			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.3093C>T	X.37:g.49074243G>A			48961187	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																				0.567	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		A	49074243	G	A	49074243	2	1	110	1	0	0	0	0	0	0	0	1	2549	1136	40	1		1	CACNA1F	23	49074243	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	254373	49074243	106196317	250	29122										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	110	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-EI-6506-01A-11D-1733-10	1276515	50350758	104919802	251	29123										
ARHGEF9	23229	hgsc.bcm.edu	37	chrX	62898439	62898439	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tacaatactcagagtatatcCagaatccatcttgctgtggg	8	9	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:62898439C>G	ENST00000253401.6	-	5	1375	c.575G>C	c.(574-576)tGg>tCg	p.W192S	ARHGEF9_ENST00000374870.4_Missense_Mutation_p.W90S|ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374872.1_Missense_Mutation_p.W171S|ARHGEF9_ENST00000433323.2_5'Flank|ARHGEF9_ENST00000437457.2_Missense_Mutation_p.W139S|ARHGEF9_ENST00000374878.1_Missense_Mutation_p.W190S	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	192	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						AGAGTATATCCAGAATCCATC	0.438																																																0			X											47	40	43					X																	62898439		2203	4300	6503	62815164	SO:0001583	missense	23229			AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.575G>C	X.37:g.62898439C>G	ENSP00000253401:p.Trp192Ser		62815164	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Missense_Mutation	SNP	ENST00000253401.6	37	CCDS35315.1	.	.	.	.	.	.	.	.	.	.	C	7.852	0.724275	0.15439	.	.	ENSG00000131089	ENST00000253401;ENST00000374878;ENST00000437457;ENST00000374870;ENST00000374872	T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11	5.08	5.08	0.68730	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	N	0.00155	-1.965	0.80722	D	1	B;B;B;B	0.20988	0.05;0.018;0.05;0.05	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.38023	-0.9680	10	0.08837	T	0.75	.	16.0426	0.80695	0.0:1.0:0.0:0.0	.	139;190;192;192	B4DHC7;B1AMR4;O43307;A8K1S8	.;.;ARHG9_HUMAN;.	S	192;190;139;90;171	ENSP00000253401:W192S;ENSP00000364012:W190S;ENSP00000399994:W139S;ENSP00000364004:W90S;ENSP00000364006:W171S	ENSP00000253401:W192S	W	-	2	0	ARHGEF9	62815164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.425000	0.59875	2.087000	0.62958	0.600000	0.82982	TGG		0.438	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			G	62898439	C	G	62898439	3	3	110	1	0	0	0	0	1	0	0	0	912	595	21	5	999	5	ARHGEF9	23	62898439	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	12547681	62898439	92372121	252	29124										
EDA	1896	hgsc.bcm.edu	37	chrX	69247710	69247710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tgaatcctatttttcaggaaAgaaagcaggacctcctggac	9	9	1	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:69247710A>G	ENST00000374552.4	+	4	772	c.530A>G	c.(529-531)aAg>aGg	p.K177R	EDA_ENST00000374553.2_Missense_Mutation_p.K177R|EDA_ENST00000524573.1_Missense_Mutation_p.K177R	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	177					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						TTTTCAGGAAAGAAAGCAGGA	0.547																																																0			X											11	10	11					X																	69247710		2107	4105	6212	69164435	SO:0001583	missense	1896			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.530A>G	X.37:g.69247710A>G	ENSP00000363680:p.Lys177Arg		69164435	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	A	7.485	0.649523	0.14516	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573;ENST00000503592	D;D;D;D	0.93547	-3.24;-3.24;-3.24;-2.88	4.55	4.55	0.56014	.	0.069640	0.56097	D	0.000036	D	0.90051	0.6893	L	0.35487	1.065	0.80722	D	1	P;P;P	0.42078	0.728;0.77;0.728	B;B;B	0.43508	0.297;0.422;0.297	D	0.90435	0.4427	10	0.59425	D	0.04	-9.3543	12.3423	0.55101	1.0:0.0:0.0:0.0	.	177;177;177	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	R	177;177;177;45	ENSP00000363680:K177R;ENSP00000363681:K177R;ENSP00000432585:K177R;ENSP00000423037:K45R	ENSP00000363680:K177R	K	+	2	0	EDA	69164435	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	7.858000	0.86971	1.703000	0.51240	0.483000	0.47432	AAG		0.547	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		G	69247710	A	G	69247710	3	3	110	1	0	0	0	0	1	0	0	0	4914	72	3	4	680	4	EDA	23	69247710	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	6349271	69247710	86022850	253	29125										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83129020	83129020	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttcaaagacagataataaaaAgtctgtcaagaatgatgaag	8	4	3	5			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:83129020A>T	ENST00000329312.4	+	4	1341	c.1304A>T	c.(1303-1305)aAg>aTg	p.K435M		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	435					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						GATAATAAAAAGTCTGTCAAG	0.343																																																0			X											20	17	18					X																	83129020		2195	4290	6485	83015676	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1304A>T	X.37:g.83129020A>T	ENSP00000331556:p.Lys435Met		83015676	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	11.99	1.802190	0.31869	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.26660	1.72	3.88	3.88	0.44766	.	.	.	.	.	T	0.47637	0.1456	M	0.73962	2.25	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	T	0.26815	-1.0092	9	0.87932	D	0	-1.13	8.1399	0.31078	1.0:0.0:0.0:0.0	.	435;435	P35663;F5H4V5	CYLC1_HUMAN;.	M	435	ENSP00000331556:K435M	ENSP00000331556:K435M	K	+	2	0	CYLC1	83015676	0.235000	0.23794	0.015000	0.15790	0.251000	0.25915	2.502000	0.45398	1.739000	0.51704	0.486000	0.48141	AAG		0.343	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83129020	A	T	83129020	3	4	110	1	0	0	0	0	1	0	0	0	4147	72	3	5	1318	5	CYLC1	23	83129020	Missense_Mutation	SNP	A	TCGA-EI-6506-01A-11D-1733-10	13881310	83129020	72141540	254	29126										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86772920	86772920	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tcagtgtctggcaagaaagaGtttgatgtgaaacagatcct	11	6	2	5			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:86772920G>C	ENST00000373119.4	+	1	169	c.24G>C	c.(22-24)gaG>gaC	p.E8D	KLHL4_ENST00000373114.4_Missense_Mutation_p.E8D	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	8						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GCAAGAAAGAGTTTGATGTGA	0.458																																																0			X											115	106	109					X																	86772920		2203	4300	6503	86659576	SO:0001583	missense	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.24G>C	X.37:g.86772920G>C	ENSP00000362211:p.Glu8Asp		86659576	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	5.760	0.324565	0.10900	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.73789	-0.78;-0.75	4.95	1.26	0.21427	.	0.000000	0.64402	D	0.000004	T	0.58807	0.2148	L	0.38953	1.18	0.44155	D	0.996959	B;B	0.25667	0.131;0.086	B;B	0.29942	0.079;0.109	T	0.38779	-0.9645	10	0.09084	T	0.74	.	8.5209	0.33275	0.3307:0.0:0.6693:0.0	.	8;8	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	D	8	ENSP00000362211:E8D;ENSP00000362206:E8D	ENSP00000362206:E8D	E	+	3	2	KLHL4	86659576	1.000000	0.71417	0.997000	0.53966	0.590000	0.36582	2.003000	0.40844	-0.068000	0.12953	-0.322000	0.08575	GAG		0.458	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			C	86772920	G	C	86772920	3	2	110	1	0	0	0	0	1	0	0	0	8412	1020	36	5	26	5	KLHL4	23	86772920	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	3643900	86772920	68497640	255	29127										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99661861	99661861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	gtagcctatgccagagttgcGgggtatgtagacctcggcag	15	9	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:99661861G>A	ENST00000373034.4	-	1	3410	c.1735C>T	c.(1735-1737)Cgc>Tgc	p.R579C	PCDH19_ENST00000255531.7_Missense_Mutation_p.R579C|PCDH19_ENST00000420881.2_Missense_Mutation_p.R579C	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	579	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CCAGAGTTGCGGGGTATGTAG	0.582																																																0			X											85	83	84					X																	99661861		2097	4182	6279	99548517	SO:0001583	missense	57575			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1735C>T	X.37:g.99661861G>A	ENSP00000362125:p.Arg579Cys		99548517	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.263472	0.39995	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.51574	0.7;0.7;0.7	5.64	5.64	0.86602	Cadherin (3);Cadherin-like (1);	0.057280	0.64402	D	0.000002	T	0.74412	0.3713	M	0.91663	3.23	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.97;0.987;0.992	T	0.80630	-0.1297	10	0.87932	D	0	.	14.112	0.65126	0.0:0.0:0.773:0.227	.	579;579;579	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	C	579	ENSP00000400327:R579C;ENSP00000362125:R579C;ENSP00000255531:R579C	ENSP00000255531:R579C	R	-	1	0	PCDH19	99548517	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	2.847000	0.48270	2.362000	0.80069	0.513000	0.50165	CGC		0.582	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99661861	G	A	99661861	3	1	110	1	0	0	0	0	1	0	0	0	11545	1116	39	1	1735	1	PCDH19	23	99661861	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	12888941	99661861	55608699	256	29128										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101138613	101138613	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	atggctttttttcttttttcGatgcttaagctttcctgaac	6	8	1	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:101138613G>T	ENST00000372782.3	-	7	1833	c.1786C>A	c.(1786-1788)Cga>Aga	p.R596R	ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Silent_p.R425R|ZMAT1_ENST00000540921.1_Silent_p.R596R	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	596						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						TTCTTTTTTCGATGCTTAAGC	0.378																																																0			X											197	167	177					X																	101138613		2203	4299	6502	101025269	SO:0001819	synonymous_variant	84460			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1786C>A	X.37:g.101138613G>T			101025269	Q8NDS3|Q96JN6	Silent	SNP	ENST00000372782.3	37	CCDS35348.1																																																																																				0.378	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			T	101138613	G	T	101138613	2	4	110	1	0	0	0	0	0	0	0	1	17730	1066	37	2		2	ZMAT1	23	101138613	Silent	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1476752	101138613	54131947	257	29129										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114245297	114245297	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	aatatagaaatctttatagtCtgatgcctccaaatagggaa	7	6	2	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:114245297C>A	ENST00000371936.1	-	7	865	c.616G>T	c.(616-618)Gac>Tac	p.D206Y	IL13RA2_ENST00000243213.1_Missense_Mutation_p.D206Y			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	206	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						TCTTTATAGTCTGATGCCTCC	0.358																																																0			X											104	97	100					X																	114245297		2203	4300	6503	114151553	SO:0001583	missense	3598			X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.616G>T	X.37:g.114245297C>A	ENSP00000361004:p.Asp206Tyr		114151553	A8K7E2|O00667	Missense_Mutation	SNP	ENST00000371936.1	37	CCDS14565.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413124	0.62511	.	.	ENSG00000123496	ENST00000371936;ENST00000243213	D;D	0.83755	-1.76;-1.76	5.15	5.15	0.70609	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.510248	0.22438	N	0.060050	D	0.85835	0.5789	L	0.54323	1.7	0.43879	D	0.99649	D;D	0.71674	0.998;0.996	D;D	0.69307	0.963;0.93	T	0.81371	-0.0963	10	0.06891	T	0.86	-8.1165	12.6771	0.56901	0.0:1.0:0.0:0.0	.	206;206	D0EFR8;Q14627	.;I13R2_HUMAN	Y	206	ENSP00000361004:D206Y;ENSP00000243213:D206Y	ENSP00000243213:D206Y	D	-	1	0	IL13RA2	114151553	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.551000	0.60740	2.388000	0.81334	0.544000	0.68410	GAC		0.358	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		A	114245297	C	A	114245297	3	1	110	1	0	0	0	0	1	0	0	0	7651	913	32	2	546	2	IL13RA2	23	114245297	Missense_Mutation	SNP	C	TCGA-EI-6506-01A-11D-1733-10	13106684	114245297	41025263	258	29130										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123514664	123514664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttcgacagttgtcccataccGgatgttgaagcacagggctc	11	11	0	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:123514664G>A	ENST00000371130.3	-	31	7963	c.7900C>T	c.(7900-7902)Cgg>Tgg	p.R2634W	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.R2641W	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2634					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTCCCATACCGGATGTTGAAG	0.517																																																0			X											101	87	92					X																	123514664		2203	4300	6503	123342345	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7900C>T	X.37:g.123514664G>A	ENSP00000360171:p.Arg2634Trp		123342345	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759462	0.69763	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87491	-2.26;-2.23	5.82	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.92805	0.7712	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.993;0.976;0.994	D	0.93568	0.6901	10	0.87932	D	0	.	15.3958	0.74790	0.0:0.0:0.8606:0.1394	.	2640;2641;2634	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	W	2634;2641	ENSP00000360171:R2634W;ENSP00000403954:R2641W	ENSP00000360171:R2634W	R	-	1	2	ODZ1	123342345	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.586000	0.74067	2.455000	0.83008	0.594000	0.82650	CGG		0.517	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123514664	G	A	123514664	3	1	110	1	0	0	0	0	1	0	0	0	10865	1115	39	1	281	1	ODZ1	23	123514664	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	9269367	123514664	31755896	259	29131										
ODZ1	10178	hgsc.bcm.edu	37	chrX	124029955	124029955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	tccacattcttagtgcatggTcaggtgaggcagcaccttct	10	11	3	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:124029955T>C	ENST00000371130.3	-	2	416	c.353A>G	c.(352-354)gAc>gGc	p.D118G	TENM1_ENST00000422452.2_Missense_Mutation_p.D118G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	118	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TAGTGCATGGTCAGGTGAGGC	0.502																																																0			X											277	225	242					X																	124029955		2203	4300	6503	123857636	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.353A>G	X.37:g.124029955T>C	ENSP00000360171:p.Asp118Gly		123857636	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665041	0.47677	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.30714	1.52;1.52	5.56	5.56	0.83823	Teneurin intracellular, N-terminal (2);	0.240686	0.33309	N	0.005054	T	0.25082	0.0609	N	0.22421	0.69	0.44789	D	0.997792	B;B;B	0.16396	0.017;0.017;0.017	B;B;B	0.22152	0.038;0.038;0.038	T	0.04178	-1.0971	10	0.72032	D	0.01	.	14.9145	0.70785	0.0:0.0:0.0:1.0	.	118;118;118	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	G	118	ENSP00000360171:D118G;ENSP00000403954:D118G	ENSP00000360171:D118G	D	-	2	0	ODZ1	123857636	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	3.853000	0.55941	1.972000	0.57404	0.486000	0.48141	GAC		0.502	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	124029955	T	C	124029955	3	2	110	1	0	0	0	0	1	0	0	0	10865	1667	58	4	7969	4	ODZ1	23	124029955	Missense_Mutation	SNP	T	TCGA-EI-6506-01A-11D-1733-10	515291	124029955	31240605	260	29132										
DCAF12L2	340578	hgsc.bcm.edu	37	chrX	125299499	125299499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	cagcccggcctccttgtcccGcatgagggggatgcgcgtga	15	14	0	2			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:125299499G>A	ENST00000360028.2	-	1	435	c.409C>T	c.(409-411)Cgg>Tgg	p.R137W	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.R137W			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	137										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						TCCTTGTCCCGCATGAGGGGG	0.642																																																0			X											82	79	80					X																	125299499		2203	4300	6503	125127180	SO:0001583	missense	0			AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.409C>T	X.37:g.125299499G>A	ENSP00000353128:p.Arg137Trp		125127180	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	g	9.501	1.103254	0.20632	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.35789	1.29;1.29	3.75	-1.73	0.08081	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.36799	0.0980	M	0.64997	1.995	0.20403	N	0.999908	D	0.67145	0.996	P	0.50791	0.65	T	0.26360	-1.0105	9	0.87932	D	0	.	1.8557	0.03178	0.1076:0.3139:0.2557:0.3228	.	137	Q5VW00	DC122_HUMAN	W	137	ENSP00000441489:R137W;ENSP00000353128:R137W	ENSP00000353128:R137W	R	-	1	2	DCAF12L2	125127180	0.997000	0.39634	0.000000	0.03702	0.002000	0.02628	1.557000	0.36299	-0.547000	0.06207	-0.337000	0.08149	CGG		0.642	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		A	125299499	G	A	125299499	3	1	110	1	0	0	0	0	1	0	0	0	4271	1086	38	1	986	1	DCAF12L2	23	125299499	Missense_Mutation	SNP	G	TCGA-EI-6506-01A-11D-1733-10	1269544	125299499	29971061	261	29133										
MAGEA1	4100	hgsc.bcm.edu	37	chrX	152482177	152482177	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0419847328244275	11	1	0.526090471465844	1.44504071058475	0.424788870303129	0.175080710726683	0.633238627089555	0	ttgatcacatactcaaggacTttcacatagctggtttcagc	7	10	4	1			TCGA-EI-6506-01A-11D-1733-10	TCGA-EI-6506-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f8ed5279-0909-4495-854d-e5230bba7006	fae20a20-3163-4c5f-b5e7-e3feb9e03945	g.chrX:152482177T>C	ENST00000356661.5	-	3	1052	c.834A>G	c.(832-834)aaA>aaG	p.K278K		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	278	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACTCAAGGACTTTCACATAGC	0.537																																																0			X											137	130	133					X																	152482177		2203	4300	6503	152135371	SO:0001819	synonymous_variant	4100				CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"melanoma-associated antigen 1", "melanoma-associated antigen MZ2-E", "melanoma antigen MAGE-1", "melanoma antigen family A 1", "cancer/testis antigen family 1, member 1"	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.834A>G	X.37:g.152482177T>C			152135371	B2RC81|O00346	Silent	SNP	ENST00000356661.5	37	CCDS14720.1																																																																																				0.537	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988		C	152482177	T	C	152482177	2	2	110	1	0	0	0	0	0	0	0	1	9193	1606	56	4		4	MAGEA1	23	152482177	Silent	SNP	T	TCGA-EI-6506-01A-11D-1733-10	27182678	152482177	2788383	262	29134										
MORN1	79906	hgsc.bcm.edu	37	chr1	2290147	2290147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagatctgcaggacccggccGctctcgccttccaggagaga	13	14	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:2290147G>A	ENST00000378531.3	-	9	926	c.753C>T	c.(751-753)agC>agT	p.S251S	MORN1_ENST00000378529.3_Silent_p.S251S|MORN1_ENST00000606372.1_5'UTR	NM_024848.1	NP_079124.1	Q5T089	MORN1_HUMAN	MORN repeat containing 1	251										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2)	9	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		GGACCCGGCCGCTCTCGCCTT	0.602																																																0			1											56	53	54					1																	2290147		2203	4300	6503	2280007	SO:0001819	synonymous_variant	79906			AK024003	CCDS40.1, CCDS72688.1	1p36.33-p36.32	2008-02-05			ENSG00000116151	ENSG00000116151			25852	protein-coding gene	gene with protein product						12477932	Standard	XM_005244798		Approved	FLJ13941	uc001ajb.1	Q5T089	OTTHUMG00000001402	ENST00000378531.3:c.753C>T	1.37:g.2290147G>A			2280007	A6NKZ6|Q8WW30|Q9H852	Silent	SNP	ENST00000378531.3	37	CCDS40.1																																																																																				0.602	MORN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004055.1	NM_024848		A	2290147	G	A	2290147	2	1	111	1	0	0	0	0	0	0	0	1	9738	1078	38	1		1	MORN1	1	2290147	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10		2290147	246960474	1	29135										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6534578	6534578	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggacaggggtgtgttggaCtggtccaggtagatgtccac	17	7	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:6534578C>A	ENST00000400915.3	-	7	606	c.540G>T	c.(538-540)caG>caT	p.Q180H	PLEKHG5_ENST00000400913.1_Missense_Mutation_p.Q124H|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.Q124H|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.Q124H|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.Q193H|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.Q124H|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.Q161H|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.Q203H|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.Q201H|PLEKHG5_ENST00000377740.3_Missense_Mutation_p.Q201H|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.Q124H|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.Q124H	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	180					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GTGTGTTGGACTGGTCCAGGT	0.592																																																0			1											125	86	99					1																	6534578		2203	4299	6502	6457165	SO:0001583	missense	57449			AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.540G>T	1.37:g.6534578C>A	ENSP00000383706:p.Gln180His		6457165	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	37	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	c	20.3	3.971364	0.74246	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T;T	0.71341	-0.53;-0.53;-0.53;-0.54;-0.44;-0.54;-0.53;-0.52;-0.56;-0.53;-0.54;-0.52	4.41	2.49	0.30216	.	0.000000	0.64402	D	0.000001	T	0.78811	0.4342	L	0.59436	1.845	0.48452	D	0.999654	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.998	T	0.77718	-0.2483	10	0.72032	D	0.01	-31.1873	9.856	0.41086	0.0:0.826:0.0:0.174	.	193;124;201;201;180	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	H	201;124;124;180;201;161;124;124;193;124;30;203;124	ENSP00000366977:Q201H;ENSP00000344570:Q124H;ENSP00000383704:Q124H;ENSP00000383706:Q180H;ENSP00000366969:Q201H;ENSP00000366961:Q161H;ENSP00000366957:Q124H;ENSP00000366954:Q124H;ENSP00000441445:Q193H;ENSP00000366966:Q124H;ENSP00000439625:Q203H;ENSP00000437710:Q124H	ENSP00000344570:Q124H	Q	-	3	2	PLEKHG5	6457165	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.753000	0.47524	0.466000	0.27193	0.457000	0.33378	CAG		0.592	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		A	6534578	C	A	6534578	3	1	111	1	0	0	0	0	1	0	0	0	12104	564	20	2	2712	2	PLEKHG5	1	6534578	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4244431	6534578	242716043	2	29136										
TNFRSF9	3604	hgsc.bcm.edu	37	chr1	7993346	7993346	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaaagaaggagatgatctgCggagagtgtcctgcaaaaca	13	6	1	5	rs150424591		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:7993346C>T	ENST00000377507.3	-	7	721	c.555G>A	c.(553-555)ccG>ccA	p.P185P		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	185					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		AGATGATCTGCGGAGAGTGTC	0.453																																																0			1											90	76	81					1																	7993346		2203	4300	6503	7915933	SO:0001819	synonymous_variant	3604			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"Tumor necrosis factor receptor superfamily", "CD molecules"	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.555G>A	1.37:g.7993346C>T			7915933		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																				0.453	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1			T	7993346	C	T	7993346	2	4	111	1	0	0	0	0	0	0	0	1	16339	755	27	1		1	TNFRSF9	1	7993346	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1458768	7993346	241257275	3	29137										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10318717	10318717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaagaagaaagccaggctgGcatcattccacaggtgaaaa	10	9	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:10318717G>A	ENST00000377086.1	+	4	552	c.350G>A	c.(349-351)gGc>gAc	p.G117D	KIF1B_ENST00000377093.4_Missense_Mutation_p.G117D|KIF1B_ENST00000377083.1_Missense_Mutation_p.G117D|KIF1B_ENST00000263934.6_Missense_Mutation_p.G117D|KIF1B_ENST00000377081.1_Missense_Mutation_p.G117D			O60333	KIF1B_HUMAN	kinesin family member 1B	117	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		AGCCAGGCTGGCATCATTCCA	0.358																																																0			1											87	84	85					1																	10318717		2203	4300	6503	10241304	SO:0001583	missense	23095			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.350G>A	1.37:g.10318717G>A	ENSP00000366290:p.Gly117Asp		10241304	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	G	32	5.109208	0.94292	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7	5.69	5.69	0.88448	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.97952	0.9326	H	0.99619	4.66	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.999;0.999	D	0.99342	1.0912	10	0.87932	D	0	.	19.8093	0.96541	0.0:0.0:1.0:0.0	.	117;117;117;117;117;117;117	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	D	117	ENSP00000263934:G117D;ENSP00000366297:G117D;ENSP00000366290:G117D;ENSP00000366287:G117D;ENSP00000366284:G117D	ENSP00000263934:G117D	G	+	2	0	KIF1B	10241304	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.776000	0.99001	2.688000	0.91661	0.460000	0.39030	GGC		0.358	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10318717	G	A	10318717	3	1	111	1	0	0	0	0	1	0	0	0	8305	1203	42	3	360	3	KIF1B	1	10318717	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2325371	10318717	238931904	4	29138										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10709168	10709168	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaaggtgctgaagagcgcGccgcattcctccaccacgca	10	16	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:10709168G>A	ENST00000377022.3	-	15	3434	c.3117C>T	c.(3115-3117)ggC>ggT	p.G1039G	CASZ1_ENST00000344008.5_Silent_p.G1039G|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1039					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	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)		TGAAGAGCGCGCCGCATTCCT	0.617																																																0			1											45	44	44					1																	10709168		2203	4300	6503	10631755	SO:0001819	synonymous_variant	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.3117C>T	1.37:g.10709168G>A			10631755	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																				0.617	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10709168	G	A	10709168	2	1	111	1	0	0	0	0	0	0	0	1	2691	1074	38	1		1	CASZ1	1	10709168	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	390451	10709168	238541453	5	29139										
MIIP	60672	hgsc.bcm.edu	37	chr1	12089331	12089331	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcagcggcgtggaggaagaCcatgaatgtgagtgcgggcc	19	8	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:12089331C>T	ENST00000235332.4	+	6	877	c.708C>T	c.(706-708)gaC>gaT	p.D236D	MIIP_ENST00000466860.1_3'UTR|MIIP_ENST00000436478.2_Silent_p.D236D	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	236										autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						TGGAGGAAGACCATGAATGTG	0.682																																																0			1											22	27	26					1																	12089331		2203	4300	6503	12011918	SO:0001819	synonymous_variant	60672			AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"invasion inhibitory protein 45"	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.708C>T	1.37:g.12089331C>T			12011918	C0KL22|Q96HU6|Q9H839|Q9HA00	Silent	SNP	ENST00000235332.4	37	CCDS143.1																																																																																				0.682	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933		T	12089331	C	T	12089331	2	4	111	1	0	0	0	0	0	0	0	1	9615	506	18	3		3	MIIP	1	12089331	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1380163	12089331	237161290	6	29140										
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12183838	12183838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acgctgcccatcccaaccagCgctcccgtcgctctctcctc	6	22	1	0	rs202227728	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:12183838C>T	ENST00000263932.2	+	10	1329	c.1107C>T	c.(1105-1107)agC>agT	p.S369S	TNFRSF8_ENST00000417814.2_Silent_p.S258S|TNFRSF8_ENST00000413146.2_5'Flank	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	369	Pro/Ser/Thr-rich.				cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	TCCCAACCAGCGCTCCCGTCG	0.647													C|||	3	0.000599042	0	0	5008	,	,		15042	0.003		0	False		,,,				2504	0															0			1											35	27	30					1																	12183838		2199	4293	6492	12106425	SO:0001819	synonymous_variant	943			M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.1107C>T	1.37:g.12183838C>T			12106425	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	CCDS144.1																																																																																				0.647	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			T	12183838	C	T	12183838	2	4	111	1	0	0	0	0	0	0	0	1	16338	767	27	1		1	TNFRSF8	1	12183838	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	94507	12183838	237066783	7	29141										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12333174	12333174	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgtggatctaggaagaatgCttttgacgaacacccaaggt	11	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:12333174C>A	ENST00000358136.3	+	18	2348	c.2218C>A	c.(2218-2220)Ctt>Att	p.L740I	VPS13D_ENST00000356315.4_Missense_Mutation_p.L740I	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		AGGAAGAATGCTTTTGACGAA	0.398																																																0			1											146	142	143					1																	12333174		2203	4300	6503	12255761	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.2218C>A	1.37:g.12333174C>A	ENSP00000350854:p.Leu740Ile		12255761		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561554	0.45590	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.53206	0.63;0.64	5.27	4.27	0.50696	.	0.000000	0.64402	D	0.000006	T	0.35740	0.0942	L	0.57536	1.79	0.80722	D	1	P;P	0.43287	0.802;0.702	B;B	0.36719	0.231;0.116	T	0.15150	-1.0447	10	0.23891	T	0.37	.	4.9976	0.14247	0.0:0.5327:0.0:0.4673	.	740;740	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	I	740	ENSP00000348666:L740I;ENSP00000350854:L740I	ENSP00000348666:L740I	L	+	1	0	VPS13D	12255761	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	2.809000	0.47971	1.070000	0.40811	0.585000	0.79938	CTT		0.398	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		A	12333174	C	A	12333174	3	1	111	1	0	0	0	0	1	0	0	0	17232	797	28	2	2284	2	VPS13D	1	12333174	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	149336	12333174	236917447	8	29142										
CROCC	9696	hgsc.bcm.edu	37	chr1	17277573	17277573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcctctctgcgggagcagCgggcagctcacgaggaggac	17	12	2	0	rs3969856		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:17277573C>T	ENST00000375541.5	+	20	3031	c.2962C>T	c.(2962-2964)Cgg>Tgg	p.R988W	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCGGGAGCAGCGGGCAGCTCA	0.592																																																0			1											15	16	16					1																	17277573		2201	4293	6494	17150160	SO:0001583	missense	9696			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2962C>T	1.37:g.17277573C>T	ENSP00000364691:p.Arg988Trp		17150160		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.183903	0.57800	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.23147	1.92	4.83	3.91	0.45181	.	.	.	.	.	T	0.41581	0.1165	L	0.50333	1.59	0.32100	N	0.59074	D;D	0.76494	0.999;0.999	D;D	0.66196	0.942;0.942	T	0.51810	-0.8658	9	0.72032	D	0.01	.	11.1907	0.48683	0.1842:0.8158:0.0:0.0	rs3969856	291;988	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	W	988;869	ENSP00000364691:R988W	ENSP00000364691:R988W	R	+	1	2	CROCC	17150160	0.999000	0.42202	1.000000	0.80357	0.970000	0.65996	1.759000	0.38420	1.347000	0.45714	0.556000	0.70494	CGG		0.592	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17277573	C	T	17277573	3	4	111	1	0	0	0	0	1	0	0	0	3899	759	27	1	3040	1	CROCC	1	17277573	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4944399	17277573	231973048	9	29143										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17314834	17314834	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacctgatgaccatgggcacGcactcaatactggccatgct	9	13	1	2	rs372361807		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:17314834G>A	ENST00000326735.8	-	24	2778	c.2745C>T	c.(2743-2745)tgC>tgT	p.C915C	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.C871C|ATP13A2_ENST00000452699.1_Silent_p.C910C			Q9NQ11	AT132_HUMAN	ATPase type 13A2	915					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		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)		CCATGGGCACGCACTCAATAC	0.637																																																0			1						G	,,	0,4406		0,0,2203	138	132	134		2730,2613,2745	1	1	1		134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	910/1176,871/1159,915/1181	17314834	1,13005	2203	4300	6503	17187421	SO:0001819	synonymous_variant	23400			AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2745C>T	1.37:g.17314834G>A			17187421	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																				0.637	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		A	17314834	G	A	17314834	2	1	111	1	0	0	0	0	0	0	0	1	1125	1079	38	1		1	ATP13A2	1	17314834	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	37261	17314834	231935787	10	29144										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17323636	17323636	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagtagggccccagcccctcCggcagtgccgtcttcagcac	11	18	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:17323636C>T	ENST00000326735.8	-	12	1107	c.1074G>A	c.(1072-1074)ccG>ccA	p.P358P	ATP13A2_ENST00000502860.1_5'UTR|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.P353P|ATP13A2_ENST00000452699.1_Silent_p.P353P			Q9NQ11	AT132_HUMAN	ATPase type 13A2	358					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		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)		CCAGCCCCTCCGGCAGTGCCG	0.647																																																0			1											70	70	70					1																	17323636		2203	4300	6503	17196223	SO:0001819	synonymous_variant	23400			AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.1074G>A	1.37:g.17323636C>T			17196223	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																				0.647	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17323636	C	T	17323636	2	4	111	1	0	0	0	0	0	0	0	1	1125	639	23	1		1	ATP13A2	1	17323636	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	8802	17323636	231926985	11	29145										
UBR4	23352	hgsc.bcm.edu	37	chr1	19467922	19467922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcaggtgggatgtccagcaTgggggggaagccctctgcgc	17	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:19467922T>C	ENST00000375254.3	-	57	8434	c.8407A>G	c.(8407-8409)Atg>Gtg	p.M2803V	UBR4_ENST00000375226.2_Missense_Mutation_p.M2814V|UBR4_ENST00000375267.2_Missense_Mutation_p.M2803V|UBR4_ENST00000375217.2_Missense_Mutation_p.M2831V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2803					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ATGTCCAGCATGGGGGGGAAG	0.587																																																0			1											81	80	80					1																	19467922		2203	4300	6503	19340509	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.8407A>G	1.37:g.19467922T>C	ENSP00000364403:p.Met2803Val		19340509	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	13.64	2.296259	0.40594	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	T;T;T;T	0.22743	1.94;1.94;1.94;1.96	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.20047	0.0482	N	0.14661	0.345	0.80722	D	1	B	0.31435	0.323	B	0.41332	0.354	T	0.15093	-1.0449	10	0.72032	D	0.01	.	15.4939	0.75634	0.0:0.0:0.0:1.0	.	2803	Q5T4S7	UBR4_HUMAN	V	2803;2803;2831;2814;446;1524	ENSP00000364403:M2803V;ENSP00000364416:M2803V;ENSP00000364365:M2831V;ENSP00000364374:M2814V	ENSP00000364365:M2831V	M	-	1	0	UBR4	19340509	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.477000	0.81069	2.243000	0.73865	0.482000	0.46254	ATG		0.587	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19467922	T	C	19467922	3	2	111	1	0	0	0	0	1	0	0	0	16944	1464	51	4	7344	4	UBR4	1	19467922	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2144286	19467922	229782699	12	29146										
CELA3A	10136	hgsc.bcm.edu	37	chr1	22333381	22333381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctccccagcaatgacatcGccctcatcaagctctcacgc	5	19	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:22333381G>A	ENST00000290122.3	+	5	392	c.373G>A	c.(373-375)Gcc>Acc	p.A125T		NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CAATGACATCGCCCTCATCAA	0.622																																																0			1											85	77	80					1																	22333381		2199	4300	6499	22205968	SO:0001583	missense	10136			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"protease E"		"elastase 3A, pancreatic (protease E)", "elastase 3A, pancreatic"	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.373G>A	1.37:g.22333381G>A	ENSP00000290122:p.Ala125Thr		22205968	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.378138	0.82682	.	.	ENSG00000142789	ENST00000290122;ENST00000374661	T	0.40756	1.02	3.83	1.88	0.25563	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.53546	0.1803	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	P	0.56751	0.805	T	0.52837	-0.8522	9	0.72032	D	0.01	-54.2737	6.5062	0.22196	0.1014:0.0:0.7206:0.178	.	125	P09093	CEL3A_HUMAN	T	125;141	ENSP00000290122:A125T	ENSP00000290122:A125T	A	+	1	0	CELA3A	22205968	1.000000	0.71417	0.993000	0.49108	0.910000	0.53928	5.086000	0.64474	0.267000	0.21916	0.400000	0.26472	GCC		0.622	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		A	22333381	G	A	22333381	3	1	111	1	0	0	0	0	1	0	0	0	3219	1087	38	1	391	1	CELA3A	1	22333381	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2865459	22333381	226917240	13	29147										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23385581	23385581	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctaggagggaatcctatggCtgtggtcagcaaacaagtaa	12	7	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:23385581C>A	ENST00000356634.3	+	8	1177	c.1028C>A	c.(1027-1029)gCt>gAt	p.A343D	KDM1A_ENST00000542151.1_Missense_Mutation_p.A363D|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Missense_Mutation_p.A363D|MIR4419A_ENST00000583845.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	343	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AATCCTATGGCTGTGGTCAGC	0.358																																																0			1											78	72	74					1																	23385581		2203	4300	6503	23258168	SO:0001583	missense	0			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1028C>A	1.37:g.23385581C>A	ENSP00000349049:p.Ala343Asp		23258168	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	37	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871458	0.72065	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	D;D;D	0.92699	-3.09;-3.09;-3.09	5.91	5.91	0.95273	Amine oxidase (1);	0.051448	0.85682	D	0.000000	D	0.85952	0.5817	N	0.25426	0.745	0.80722	D	1	P;B	0.34546	0.456;0.079	B;B	0.24269	0.052;0.051	D	0.83628	0.0143	10	0.24483	T	0.36	-19.1135	19.2767	0.94034	0.0:1.0:0.0:0.0	.	363;343	O60341-2;O60341	.;KDM1A_HUMAN	D	343;363;363	ENSP00000349049:A343D;ENSP00000383042:A363D;ENSP00000439072:A363D	ENSP00000349049:A343D	A	+	2	0	KDM1A	23258168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.791000	0.96007	0.650000	0.86243	GCT		0.358	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23385581	C	A	23385581	3	1	111	1	0	0	0	0	1	0	0	0	8143	797	28	2	1122	2	KDM1A	1	23385581	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1052200	23385581	225865040	14	29148										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27436136	27436136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatcgggaggtgaaggctgCgatgaccccgtagaccacgc	14	11	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:27436136C>T	ENST00000263980.3	-	3	1521	c.946G>A	c.(946-948)Gca>Aca	p.A316T	SLC9A1_ENST00000545949.1_5'UTR|SLC9A1_ENST00000374086.3_Missense_Mutation_p.A316T	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	316					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				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)	GTGAAGGCTGCGATGACCCCG	0.602																																																0			1											171	158	162					1																	27436136		2203	4300	6503	27308723	SO:0001583	missense	6548			M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.946G>A	1.37:g.27436136C>T	ENSP00000263980:p.Ala316Thr		27308723	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	37	CCDS295.1	.	.	.	.	.	.	.	.	.	.	c	23.3	4.405387	0.83230	.	.	ENSG00000090020	ENST00000263980;ENST00000374086	T;T	0.14893	2.47;2.47	5.96	5.03	0.67393	Cation/H+ exchanger (1);	0.045838	0.85682	D	0.000000	T	0.18045	0.0433	L	0.36672	1.1	0.80722	D	1	D;P	0.53462	0.96;0.673	P;B	0.45881	0.496;0.265	T	0.02546	-1.1143	10	0.23891	T	0.37	.	15.0582	0.71930	0.1432:0.8568:0.0:0.0	.	316;316	P19634-2;P19634	.;SL9A1_HUMAN	T	316	ENSP00000263980:A316T;ENSP00000363199:A316T	ENSP00000263980:A316T	A	-	1	0	SLC9A1	27308723	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.815000	0.86186	1.489000	0.48450	0.651000	0.88453	GCA		0.602	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		T	27436136	C	T	27436136	3	4	111	1	0	0	0	0	1	0	0	0	14746	768	27	1	1541	1	SLC9A1	1	27436136	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4050555	27436136	221814485	15	29149										
WDTC1	23038	hgsc.bcm.edu	37	chr1	27631523	27631523	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atatcgtcagtggctctgacGatggctccttcttcatctgg	10	11	5	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:27631523G>A	ENST00000319394.3	+	15	2210	c.1675G>A	c.(1675-1677)Gat>Aat	p.D559N	WDTC1_ENST00000361771.3_Missense_Mutation_p.D558N	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	559					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		TGGCTCTGACGATGGCTCCTT	0.587																																																0			1											72	58	63					1																	27631523		2203	4300	6503	27504110	SO:0001583	missense	23038			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.1675G>A	1.37:g.27631523G>A	ENSP00000317971:p.Asp559Asn		27504110	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	G	27.5	4.833158	0.91036	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	D;D	0.88046	-2.33;-2.33	4.82	3.9	0.45041	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.92760	0.7698	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.91738	0.5402	10	0.33141	T	0.24	.	12.6205	0.56600	0.0808:0.0:0.9192:0.0	.	559;558	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	N	559;558	ENSP00000317971:D559N;ENSP00000355317:D558N	ENSP00000317971:D559N	D	+	1	0	WDTC1	27504110	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	7.453000	0.80700	1.243000	0.43853	0.455000	0.32223	GAT		0.587	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27631523	G	A	27631523	3	1	111	1	0	0	0	0	1	0	0	0	17382	1058	37	1	1726	1	WDTC1	1	27631523	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	195387	27631523	221619098	16	29150										
KHDRBS1	10657	hgsc.bcm.edu	37	chr1	32503459	32503459	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgtggtgttggaccacctcGgggggctttggtacgtggta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:32503459delG	ENST00000327300.7	+	6	1096	c.929delG	c.(928-930)cggfs	p.R310fs	KHDRBS1_ENST00000492989.1_Frame_Shift_Del_p.R271fs|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1											endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GGACCACCTCGGGGGGCTTTG	0.502																																					Ovarian(173;401 1982 12359 31110 42403)											0			1											90	100	97					1																	32503459		2203	4300	6503	32276046	SO:0001589	frameshift_variant	10657			U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"GAP-associated tyrosine phosphoprotein p62 (Sam68)"	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.929delG	1.37:g.32503459delG	ENSP00000313829:p.Arg310fs		32276046		Frame_Shift_Del	DEL	ENST00000327300.7	37	CCDS350.1																																																																																				0.502	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		-	32503459	G	-	32503459	7	5	111	1	0	1	0	1	0	0	0	0	8167	1116	39	0	951	0	KHDRBS1	1	32503459	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	4871936	32503459	216747162	17	29151										
ZNF362	149076	hgsc.bcm.edu	37	chr1	33747200	33747200	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccgcaggtgtaaggtatgCccactgacctttttcaccaa	8	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:33747200C>G	ENST00000539719.1	+	6	866	c.696C>G	c.(694-696)tgC>tgG	p.C232W	ZNF362_ENST00000373428.5_Missense_Mutation_p.C232W	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTAAGGTATGCCCACTGACCT	0.562																																					Pancreas(162;1431 2676 35353 38425)											0			1											115	100	105					1																	33747200		2203	4300	6503	33519787	SO:0001583	missense	149076				CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"Zinc fingers, C2H2-type"	18079	protein-coding gene	gene with protein product	"rotund homolog (Drosophila)"						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.696C>G	1.37:g.33747200C>G	ENSP00000446335:p.Cys232Trp		33519787	Q8WYU4	Missense_Mutation	SNP	ENST00000539719.1	37	CCDS377.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.122662	0.56613	.	.	ENSG00000160094	ENST00000539719;ENST00000373428	D;D	0.98947	-5.26;-5.26	5.48	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.299519	0.24180	N	0.040812	D	0.98732	0.9574	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.98683	1.0693	10	0.72032	D	0.01	-21.7464	9.6262	0.39752	0.0:0.8315:0.0:0.1685	.	232	Q5T0B9	ZN362_HUMAN	W	232	ENSP00000446335:C232W;ENSP00000362527:C232W	ENSP00000362527:C232W	C	+	3	2	ZNF362	33519787	0.998000	0.40836	0.998000	0.56505	0.922000	0.55478	0.711000	0.25764	0.684000	0.31448	0.561000	0.74099	TGC		0.562	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493		G	33747200	C	G	33747200	3	3	111	1	0	0	0	0	1	0	0	0	17907	747	26	5	714	5	ZNF362	1	33747200	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1243741	33747200	215503421	18	29152										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35972480	35972480	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatcatctgcagtttggaaTttttttaaaaacaccagcat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:35972480delT	ENST00000325722.3	-	3	633	c.399delA	c.(397-399)aaafs	p.K133fs		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	133						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAGTTTGGAATTTTTTTAAAA	0.512																																																0			1											72	81	78					1																	35972480		2203	4300	6503	35745067	SO:0001589	frameshift_variant	79932			AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.399delA	1.37:g.35972480delT	ENSP00000318406:p.Lys133fs		35745067	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Frame_Shift_Del	DEL	ENST00000325722.3	37	CCDS390.1																																																																																				0.512	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		-	35972480	T	-	35972480	7	5	111	1	0	1	0	1	0	0	0	0	8190	1490	52	0	2826	0	KIAA0319L	1	35972480	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	2225280	35972480	213278141	19	29153										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38219959	38219959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcacacgcagaaggtggaggCgttttccagggcccggctgt	16	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:38219959C>T	ENST00000373048.4	-	4	933	c.934G>A	c.(934-936)Gcc>Acc	p.A312T	EPHA10_ENST00000427468.2_Missense_Mutation_p.A312T|EPHA10_ENST00000330210.7_Intron|EPHA10_ENST00000540011.1_5'Flank|EPHA10_ENST00000446149.2_Intron	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	312					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AAGGTGGAGGCGTTTTCCAGG	0.697																																																0			1											23	31	28					1																	38219959		1943	4096	6039	37992546	SO:0001583	missense	284656			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.934G>A	1.37:g.38219959C>T	ENSP00000362139:p.Ala312Thr		37992546	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	c	25.5	4.644881	0.87859	.	.	ENSG00000183317	ENST00000427468;ENST00000373048	D;D	0.97404	-4.37;-4.37	3.98	3.98	0.46160	.	0.249563	0.20990	N	0.082041	D	0.98018	0.9347	M	0.81942	2.565	0.80722	D	1	D	0.76494	0.999	P	0.61800	0.894	D	0.98917	1.0782	10	0.87932	D	0	.	15.2231	0.73330	0.0:1.0:0.0:0.0	.	312	Q5JZY3	EPHAA_HUMAN	T	312	ENSP00000397746:A312T;ENSP00000362139:A312T	ENSP00000362139:A312T	A	-	1	0	EPHA10	37992546	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.644000	0.74338	2.054000	0.61138	0.493000	0.49557	GCC		0.697	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		T	38219959	C	T	38219959	3	4	111	1	0	0	0	0	1	0	0	0	5179	768	27	1	2148	1	EPHA10	1	38219959	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2247479	38219959	211030662	20	29154										
ZNF684	127396	hgsc.bcm.edu	37	chr1	41012494	41012494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatgcagtgaatgcgggaaaGccttcaaaaagaagtttcat	10	6	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:41012494G>A	ENST00000372699.3	+	5	750	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			ATGCGGGAAAGCCTTCAAAAA	0.333																																																0			1											39	42	41					1																	41012494		2200	4300	6500	40785081	SO:0001583	missense	127396				CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"Zinc fingers, C2H2-type", "-"	28418	protein-coding gene	gene with protein product	"hypothetical protein MGC27466"					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.499G>A	1.37:g.41012494G>A	ENSP00000361784:p.Ala167Thr		40785081	Q2NKY4	Missense_Mutation	SNP	ENST00000372699.3	37	CCDS454.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.752378	0.31046	.	.	ENSG00000117010	ENST00000372699	T	0.48836	0.8	4.05	-1.41	0.08941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.738509	0.11129	N	0.596523	T	0.24509	0.0594	N	0.21508	0.67	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.21314	-1.0249	10	0.26408	T	0.33	.	0.6665	0.00851	0.3822:0.1687:0.2776:0.1715	.	167	Q5T5D7	ZN684_HUMAN	T	167	ENSP00000361784:A167T	ENSP00000361784:A167T	A	+	1	0	ZNF684	40785081	0.000000	0.05858	0.947000	0.38551	0.563000	0.35712	-0.446000	0.06837	-0.120000	0.11809	0.591000	0.81541	GCC		0.333	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		A	41012494	G	A	41012494	3	1	111	1	0	0	0	0	1	0	0	0	18130	971	34	3	513	3	ZNF684	1	41012494	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2792535	41012494	208238127	21	29155										
CLDN19	149461	hgsc.bcm.edu	37	chr1	43200781	43200781	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acacccagggggcccttggcGgaggcgggcaatttaacaac	14	12	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:43200781G>A	ENST00000296387.1	-	5	841	c.651C>T	c.(649-651)tcC>tcT	p.S217S	CLDN19_ENST00000539749.1_3'UTR|CLDN19_ENST00000372539.3_3'UTR	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	217					apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCCCTTGGCGGAGGCGGGCA	0.552																																																0			1											70	72	71					1																	43200781		2203	4300	6503	42973368	SO:0001819	synonymous_variant	149461			AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007		"Claudins"	2040	protein-coding gene	gene with protein product		610036					Standard	NM_148960		Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.651C>T	1.37:g.43200781G>A			42973368	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Silent	SNP	ENST00000296387.1	37	CCDS471.1																																																																																				0.552	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960		A	43200781	G	A	43200781	2	1	111	1	0	0	0	0	0	0	0	1	3486	1103	39	1		1	CLDN19	1	43200781	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2188287	43200781	206049840	22	29156										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43909271	43909271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatctttactctcatagcggCgccatcgccctgagtcaggg	11	13	3	1	rs543404828		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:43909271C>T	ENST00000562955.1	+	61	8458	c.8458C>T	c.(8458-8460)Cgc>Tgc	p.R2820C	SZT2_ENST00000372442.1_Missense_Mutation_p.R1978C	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2877					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTCATAGCGGCGCCATCGCCC	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		17748	0		0	False		,,,				2504	0															0			1											54	56	55					1																	43909271		2203	4300	6503	43681858	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.8458C>T	1.37:g.43909271C>T	ENSP00000457168:p.Arg2820Cys		43681858	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305275	0.60305	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.36	5.36	0.76844	.	0.054620	0.64402	D	0.000001	T	0.74558	0.3732	L	0.43152	1.355	0.41169	D	0.986151	D	0.89917	1.0	D	0.79108	0.992	T	0.76860	-0.2803	9	0.72032	D	0.01	.	19.1475	0.93475	0.0:1.0:0.0:0.0	.	2820	Q5T011-5	.	C	1978	.	ENSP00000361519:R1978C	R	+	1	0	SZT2	43681858	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.591000	0.53986	2.514000	0.84764	0.650000	0.86243	CGC		0.607	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43909271	C	T	43909271	3	4	111	1	0	0	0	0	1	0	0	0	8199	768	27	1	6110	1	KIAA0467	1	43909271	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	708490	43909271	205341350	23	29157										
PTPRF	5792	hgsc.bcm.edu	37	chr1	44071004	44071004	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcagcacctggtgtccatCcgcacagcccccgacctcct	8	20	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:44071004C>T	ENST00000359947.4	+	18	3619	c.3279C>T	c.(3277-3279)atC>atT	p.I1093I	PTPRF_ENST00000372413.3_Silent_p.I1084I|PTPRF_ENST00000372414.3_Silent_p.I1093I|PTPRF_ENST00000438120.1_Silent_p.I1084I|PTPRF_ENST00000422171.2_Silent_p.I441I|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1093	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGGTGTCCATCCGCACAGCCC	0.632																																																0			1											53	56	55					1																	44071004		2203	4300	6503	43843591	SO:0001819	synonymous_variant	5792			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3279C>T	1.37:g.44071004C>T			43843591	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.29|10.29	1.310518|1.310518	0.23821|0.23821	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.31|5.31	1.26|1.26	0.21427|0.21427	.|.	.|.	.|.	.|.	.|.	T|T	0.51466|0.51466	0.1676|0.1676	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35624|0.35624	-0.9781|-0.9781	4|4	.|.	.|.	.|.	.|.	5.1938|5.1938	0.15225|0.15225	0.1318:0.59:0.0:0.2782|0.1318:0.59:0.0:0.2782	.|.	.|.	.|.	.|.	S|F	466;507|739	.|.	.|.	P|S	+|+	1|2	0|0	PTPRF|PTPRF	43843591|43843591	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.939000|0.939000	0.58152|0.58152	1.000000|1.000000	0.29770|0.29770	0.056000|0.056000	0.16144|0.16144	-0.229000|-0.229000	0.12294|0.12294	CCG|TCC		0.632	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44071004	C	T	44071004	2	4	111	1	0	0	0	0	0	0	0	1	12838	845	30	3		3	PTPRF	1	44071004	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	161733	44071004	205179617	24	29158										
MAST2	23139	hgsc.bcm.edu	37	chr1	46290200	46290200	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttaaacttcagcgacaactGagtcaggatgattgtaagtt	10	6	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:46290200G>A	ENST00000361297.2	+	2	556	c.273G>A	c.(271-273)ctG>ctA	p.L91L	MAST2_ENST00000372009.2_Silent_p.L91L	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					AGCGACAACTGAGTCAGGATG	0.413																																																0			1											165	147	153					1																	46290200		1850	4092	5942	46062787	SO:0001819	synonymous_variant	23139			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.273G>A	1.37:g.46290200G>A			46062787		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																				0.413	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46290200	G	A	46290200	2	1	111	1	0	0	0	0	0	0	0	1	9355	1277	45	3		3	MAST2	1	46290200	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2219196	46290200	202960421	25	29159										
MKNK1	8569	hgsc.bcm.edu	37	chr1	47046209	47046209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgagacactcactttgacgGcatactctttgccattctgt	7	12	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:47046209G>T	ENST00000371946.4	-	4	390	c.227C>A	c.(226-228)gCc>gAc	p.A76D	MKNK1_ENST00000428112.2_Missense_Mutation_p.A76D|MKNK1_ENST00000371944.4_Missense_Mutation_p.P6T|MKNK1_ENST00000341183.5_Missense_Mutation_p.A76D|MKNK1_ENST00000545730.1_Missense_Mutation_p.A76D|MKNK1_ENST00000371945.4_Missense_Mutation_p.A76D|MKNK1_ENST00000465783.1_Missense_Mutation_p.A76D	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	76	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					CACTTTGACGGCATACTCTTT	0.433																																																0			1											146	116	126					1																	47046209		2203	4300	6503	46818796	SO:0001583	missense	8569			AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.227C>A	1.37:g.47046209G>T	ENSP00000361014:p.Ala76Asp		46818796	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	37	CCDS538.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.186223|5.186223	0.94885|0.94885	.|.	.|.	ENSG00000079277|ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000341183;ENST00000428112;ENST00000532783;ENST00000496619;ENST00000528237;ENST00000545730;ENST00000529170;ENST00000531769;ENST00000465783|ENST00000371944	T;T;T;T;T;T;T;T;T;T;T|T	0.72394|0.59224	0.45;0.45;0.45;0.45;-0.65;-0.02;-0.65;1.62;-0.65;-0.65;1.62|0.28	5.49|5.49	5.49|5.49	0.81192|0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73697|0.73697	0.3620|0.3620	H|H	0.97516|0.97516	4.02|4.02	0.80722|0.80722	D|D	1|1	D;D;D;D|B;B	0.89917|0.13145	1.0;1.0;1.0;1.0|0.007;0.007	D;D;D;D|B;B	0.97110|0.12837	1.0;1.0;0.995;0.999|0.008;0.008	T|T	0.76833|0.76833	-0.2813|-0.2813	10|9	0.87932|0.87932	D|D	0|0	.|.	16.9239|16.9239	0.86170|0.86170	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	76;76;76;76|6;6	B4E1V9;Q9BUB5-3;Q9BUB5-2;Q9BUB5|B4DQK5;Q7Z319	.;.;.;MKNK1_HUMAN|.;.	D|T	76;76;76;76;64;76;70;76;76;76;76|6	ENSP00000361014:A76D;ENSP00000361013:A76D;ENSP00000339573:A76D;ENSP00000411135:A76D;ENSP00000431837:A64D;ENSP00000436709:A76D;ENSP00000432665:A70D;ENSP00000440974:A76D;ENSP00000435163:A76D;ENSP00000434021:A76D;ENSP00000434834:A76D|ENSP00000361012:P6T	ENSP00000339573:A76D|ENSP00000361012:P6T	A|P	-|-	2|1	0|0	MKNK1|MKNK1	46818796|46818796	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	8.854000|8.854000	0.92228|0.92228	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	GCC|CCG		0.433	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684		T	47046209	G	T	47046209	3	4	111	1	0	0	0	0	1	0	0	0	9634	1203	42	2	1214	2	MKNK1	1	47046209	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	756009	47046209	202204412	26	29160										
NRD1	4898	hgsc.bcm.edu	37	chr1	52285470	52285470	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttaaacttttggttcacaaAcctctataaagtttgttaaa	4	6	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:52285470A>C	ENST00000354831.7	-	11	1685		c.e11+1		NRD1_ENST00000485608.1_Splice_Site|NRD1_ENST00000539524.1_Splice_Site|NRD1_ENST00000352171.7_Splice_Site|NRD1_ENST00000544028.1_Splice_Site	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)						cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TGGTTCACAAACCTCTATAAA	0.328																																																0			1											53	51	52					1																	52285470		2202	4300	6502	52058058	SO:0001630	splice_region_variant	4898			X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.1495+1T>G	1.37:g.52285470A>C			52058058	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Splice_Site	SNP	ENST00000354831.7	37	CCDS559.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370167	0.82573	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8637	0.63576	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NRD1	52058058	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.300000	0.72776	2.083000	0.62718	0.533000	0.62120	.		0.328	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	Intron	C	52285470	A	C	52285470	5	2	111	1	0	0	0	0	0	0	1	0	10676	57	2	4	2254	4	NRD1	1	52285470	Splice_Site	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5239261	52285470	196965151	27	29161										
NRD1	4898	hgsc.bcm.edu	37	chr1	52344009	52344009	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccccagcattactgagagaCcccctccgtccctcttcctc					rs143307071	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:52344009delC	ENST00000354831.7	-	1	468	c.279delG	c.(277-279)gggfs	p.G93fs	NRD1_ENST00000539524.1_5'Flank|NRD1_ENST00000352171.7_Frame_Shift_Del_p.G93fs|NRD1_ENST00000544028.1_Intron	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	93					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TACTGAGAGACCCCCTCCGTC	0.612																																																0			1											70	72	72					1																	52344009		2203	4300	6503	52116597	SO:0001589	frameshift_variant	4898			X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.279delG	1.37:g.52344009delC	ENSP00000346890:p.Gly93fs		52116597	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Frame_Shift_Del	DEL	ENST00000354831.7	37	CCDS559.1																																																																																				0.612	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		-	52344009	C	-	52344009	7	5	111	1	0	1	0	1	0	0	0	0	10676	494	18	0	3512	0	NRD1	1	52344009	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	58539	52344009	196906612	28	29162										
C1orf177	163747	hgsc.bcm.edu	37	chr1	55277593	55277593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgagcaacaagccacaccccCggccttatcaggtaccccct	7	18	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:55277593C>T	ENST00000371273.3	+	5	622	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	C1orf177_ENST00000358193.3_Missense_Mutation_p.R203W	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	203										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GCCACACCCCCGGCCTTATCA	0.637																																																0			1											63	62	63					1																	55277593		2203	4300	6503	55050181	SO:0001583	missense	163747			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.607C>T	1.37:g.55277593C>T	ENSP00000360320:p.Arg203Trp		55050181	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.322951	0.41096	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.24151	1.87;1.87	4.66	-9.32	0.00643	.	1.106640	0.07143	N	0.847768	T	0.10594	0.0259	N	0.08118	0	0.09310	N	1	P;P	0.51933	0.949;0.949	P;P	0.44696	0.458;0.458	T	0.37407	-0.9707	10	0.66056	D	0.02	.	3.0915	0.06295	0.1741:0.3798:0.2879:0.1582	.	203;203	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	W	203	ENSP00000350924:R203W;ENSP00000360320:R203W	ENSP00000350924:R203W	R	+	1	2	C1orf177	55050181	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.469000	0.00992	-2.699000	0.00399	-1.099000	0.02127	CGG		0.637	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		T	55277593	C	T	55277593	3	4	111	1	0	0	0	0	1	0	0	0	2023	643	23	1	625	1	C1orf177	1	55277593	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2933584	55277593	193973028	29	29163										
C1orf177	163747	hgsc.bcm.edu	37	chr1	55307313	55307313	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggctgttttgttggaaaggCctagaagtcatcaattttgg	12	5	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:55307313C>T	ENST00000371273.3	+	10	1199				C1orf177_ENST00000358193.3_Silent_p.G403G	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177											breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						gttggaaaggcctagaagtca	0.463																																																0			1											185	156	165					1																	55307313		2203	4300	6503	55079901	SO:0001627	intron_variant	163747			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.1185-161C>T	1.37:g.55307313C>T			55079901	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																				0.463	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		T	55307313	C	T	55307313	1	4	111	0	1	0	0	0	0	0	0	0	2023	726	26	3		3	C1orf177	1	55307313	Intron	SNP	C	TCGA-EI-6507-01A-11D-1733-10	29720	55307313	193943308	30	29164										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55509560	55509560	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacgtggtggtgctgaaggaGgagacccacctctcgcagtc	14	11	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:55509560G>A	ENST00000302118.5	+	2	542	c.252G>A	c.(250-252)gaG>gaA	p.E84E	PCSK9_ENST00000452118.2_Silent_p.E84E|PCSK9_ENST00000543384.1_Intron	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	84					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TGCTGAAGGAGGAGACCCACC	0.627																																					Pancreas(137;1454 1827 5886 22361 42375)											0			1											58	50	53					1																	55509560		2203	4300	6503	55282148	SO:0001819	synonymous_variant	255738			AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.252G>A	1.37:g.55509560G>A			55282148	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																				0.627	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		A	55509560	G	A	55509560	2	1	111	1	0	0	0	0	0	0	0	1	11637	991	35	3		3	PCSK9	1	55509560	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	202247	55509560	193741061	31	29165										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62923331	62923331	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccctttgatactccttttgAtccggcccaattaagctctt	5	13	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:62923331A>T	ENST00000340370.5	-	48	6182	c.6165T>A	c.(6163-6165)gaT>gaA	p.D2055E	DOCK7_ENST00000251157.5_Missense_Mutation_p.D2075E	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	2086	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ACTCCTTTTGATCCGGCCCAA	0.408																																																0			1											191	186	188					1																	62923331		2203	4300	6503	62695919	SO:0001583	missense	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.6165T>A	1.37:g.62923331A>T	ENSP00000340742:p.Asp2055Glu		62695919	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	32|32	5.180652|5.180652	0.94846|0.94846	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441|ENST00000454575	T;T|.	0.16324|.	2.35;2.35|.	5.99|5.99	3.69|3.69	0.42338|0.42338	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61173|0.61173	0.2326|0.2326	M|M	0.70903|0.70903	2.155|2.155	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.996;0.966;1.0;0.98;0.98;0.981|.	D;P;D;D;P;P|.	0.87578|.	0.991;0.872;0.998;0.952;0.789;0.86|.	T|T	0.59852|0.59852	-0.7376|-0.7376	10|5	0.66056|.	D|.	0.02|.	.|.	4.4891|4.4891	0.11805|0.11805	0.5633:0.0:0.4367:0.0|0.5633:0.0:0.4367:0.0	.|.	2086;2075;2055;2044;2046;2077|.	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6|.	DOCK7_HUMAN;.;.;.;.;.|.	E|T	2086;2075;2055;816|1249	ENSP00000251157:D2075E;ENSP00000340742:D2055E|.	ENSP00000251157:D2075E|.	D|S	-|-	3|1	2|0	DOCK7|DOCK7	62695919|62695919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	2.756000|2.756000	0.47549|0.47549	1.100000|1.100000	0.41517|0.41517	0.533000|0.533000	0.62120|0.62120	GAT|TCA		0.408	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	62923331	A	T	62923331	3	4	111	1	0	0	0	0	1	0	0	0	4703	330	12	5	172	5	DOCK7	1	62923331	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	7413771	62923331	186327290	32	29166										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65098317	65098317	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacagtccggccgcagtcaaAgcacatagtagtgattctgg	11	10	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:65098317A>C	ENST00000371073.2	+	6	680	c.680A>C	c.(679-681)aAg>aCg	p.K227T	CACHD1_ENST00000290039.5_Missense_Mutation_p.K176T|CACHD1_ENST00000495994.1_Intron			Q5VU97	CAHD1_HUMAN	cache domain containing 1	227					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCGCAGTCAAAGCACATAGTA	0.532																																																0			1											103	105	104					1																	65098317		2058	4190	6248	64870905	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.680A>C	1.37:g.65098317A>C	ENSP00000360113:p.Lys227Thr		64870905	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	A	19.64	3.865331	0.71949	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.21543	2.0;2.0	5.67	5.67	0.87782	von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	T	0.25568	0.0622	L	0.34521	1.04	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.02781	-1.1111	10	0.56958	D	0.05	-27.9969	15.9204	0.79562	1.0:0.0:0.0:0.0	.	227	Q5VU97	CAHD1_HUMAN	T	227;176	ENSP00000360113:K227T;ENSP00000290039:K176T	ENSP00000290039:K176T	K	+	2	0	CACHD1	64870905	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	8.923000	0.92808	2.164000	0.68074	0.533000	0.62120	AAG		0.532	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		C	65098317	A	C	65098317	3	2	111	1	0	0	0	0	1	0	0	0	2543	72	3	4	549	4	CACHD1	1	65098317	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2174986	65098317	184152304	33	29167										
JAK1	3716	hgsc.bcm.edu	37	chr1	65312354	65312354	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccacgtcgcggacacagacGccatagaggtacacgatgtg	12	12	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:65312354G>A	ENST00000342505.4	-	14	2213	c.1965C>T	c.(1963-1965)ggC>ggT	p.G655G	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	655	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGACACAGACGCCATAGAGGT	0.582			Mis		ALL																																		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	0			1											91	99	96					1																	65312354		2149	4277	6426	65084942	SO:0001819	synonymous_variant	3716			M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1965C>T	1.37:g.65312354G>A			65084942	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																				0.582	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65312354	G	A	65312354	2	1	111	1	0	0	0	0	0	0	0	1	7958	1074	38	1		1	JAK1	1	65312354	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	214037	65312354	183938267	34	29168										
JAK1	3716	hgsc.bcm.edu	37	chr1	65325833	65325833	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtatgttgtggacgatcaacGggggggccacgtcggtgcag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:65325833delG	ENST00000342505.4	-	9	1537	c.1289delC	c.(1288-1290)ccgfs	p.P430fs		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	430					cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GACGATCAACGGGGGGGCCAC	0.542			Mis		ALL																																		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	0			1											95	99	98					1																	65325833		2012	4160	6172	65098421	SO:0001589	frameshift_variant	3716			M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1289delC	1.37:g.65325833delG	ENSP00000343204:p.Pro430fs		65098421	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	37	CCDS41346.1																																																																																				0.542	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		-	65325833	G	-	65325833	7	5	111	1	0	1	0	1	0	0	0	0	7958	1116	39	0	2243	0	JAK1	1	65325833	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	13479	65325833	183924788	35	29169										
LEPR	3953	hgsc.bcm.edu	37	chr1	66102459	66102460	+	Frame_Shift_Ins	INS	-	-	AG													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggggtcacctcaatcaaaaINSagagagagagtggtgtgctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:66102459_66102460insAG	ENST00000349533.6	+	20	3444_3445	c.3259_3260insAG	c.(3259-3261)aagfs	p.K1087fs	LEPR_ENST00000406510.3_Frame_Shift_Ins_p.K154fs	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTCAATCAAAAAGAGAGAGAGT	0.421																																																0			1																																								65875048	SO:0001589	frameshift_variant	54741			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3268_3269dupAG	1.37:g.66102468_66102469dupAG	ENSP00000330393:p.Lys1087fs		65875047	Q6FHL5	Frame_Shift_Ins	INS	ENST00000349533.6	37	CCDS631.1																																																																																				0.421	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		AG	66102460	-	AG	66102459	7	5	111	1	0	1	1	0	0	0	0	0	8750	15	1	0	3559	0	LEPR	1	66102459	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	776626	66102459	183148162	36	29170										
WDR78	79819	hgsc.bcm.edu	37	chr1	67370934	67370934	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctacagttttcagttcagGtggaataagcacggttttgg	11	6	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:67370934G>A	ENST00000371026.3	-	2	350	c.295C>T	c.(295-297)Cct>Tct	p.P99S	WDR78_ENST00000431318.1_5'UTR|WDR78_ENST00000488333.1_Missense_Mutation_p.P27S|WDR78_ENST00000371022.3_Missense_Mutation_p.P99S|WDR78_ENST00000371023.3_Missense_Mutation_p.P99S	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	99					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TTCAGTTCAGGTGGAATAAGC	0.353																																																0			1											169	165	166					1																	67370934		2203	4300	6503	67143522	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.295C>T	1.37:g.67370934G>A	ENSP00000360065:p.Pro99Ser		67143522	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	G	8.645	0.896910	0.17686	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022;ENST00000488333	T;T;T	0.57273	0.41;2.17;1.42	3.99	0.916	0.19373	.	0.864181	0.09984	N	0.730633	T	0.16685	0.0401	L	0.57536	1.79	0.21325	N	0.999723	B;B;B	0.32653	0.379;0.024;0.024	B;B;B	0.31686	0.134;0.005;0.005	T	0.28839	-1.0031	10	0.06757	T	0.87	-3.7865	3.0691	0.06224	0.2455:0.0:0.5467:0.2077	.	99;99;99	Q5TAD8;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	S	99;99;99;27	ENSP00000360065:P99S;ENSP00000360062:P99S;ENSP00000360061:P99S	ENSP00000360061:P99S	P	-	1	0	WDR78	67143522	0.089000	0.21612	0.017000	0.16124	0.008000	0.06430	0.186000	0.16978	0.196000	0.20367	0.555000	0.69702	CCT		0.353	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		A	67370934	G	A	67370934	3	1	111	1	0	0	0	0	1	0	0	0	17368	1261	44	3	2372	3	WDR78	1	67370934	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1268475	67370934	181879687	37	29171										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67787453	67787453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagaatcaattttcaccatgGccactccctcaattctcaag	4	13	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:67787453G>A	ENST00000262345.1	+	3	885	c.245G>A	c.(244-246)gGc>gAc	p.G82D	IL12RB2_ENST00000541374.1_Missense_Mutation_p.G82D|IL12RB2_ENST00000371000.1_Missense_Mutation_p.G82D|IL12RB2_ENST00000544434.1_Missense_Mutation_p.G82D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	82					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TTTCACCATGGCCACTCCCTC	0.413																																																0			1											176	168	170					1																	67787453		2203	4300	6503	67560041	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.245G>A	1.37:g.67787453G>A	ENSP00000262345:p.Gly82Asp		67560041	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.855432	0.51376	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.41758	0.99;1.06;1.06;1.95	5.81	4.89	0.63831	Immunoglobulin C2-set-like, ligand-binding (1);	0.669659	0.16657	N	0.204940	T	0.33527	0.0866	L	0.32530	0.975	0.09310	N	1	B;D;P;D	0.67145	0.171;0.996;0.804;0.961	B;D;B;P	0.64237	0.181;0.923;0.308;0.602	T	0.08554	-1.0716	10	0.30854	T	0.27	-12.3366	9.8164	0.40856	0.091:0.0:0.909:0.0	.	82;82;82;82	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	D	82	ENSP00000262345:G82D;ENSP00000360039:G82D;ENSP00000445276:G82D;ENSP00000442443:G82D	ENSP00000262345:G82D	G	+	2	0	IL12RB2	67560041	0.111000	0.22076	0.021000	0.16686	0.005000	0.04900	3.202000	0.51067	2.739000	0.93911	0.650000	0.86243	GGC		0.413	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		A	67787453	G	A	67787453	3	1	111	1	0	0	0	0	1	0	0	0	7648	1203	42	3	251	3	IL12RB2	1	67787453	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	416519	67787453	181463168	38	29172										
WLS	79971	hgsc.bcm.edu	37	chr1	68619317	68619317	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaaccacaccttggtgaagCctccattttggtggatcccc	8	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:68619317C>A	ENST00000262348.4	-	5	939	c.686G>T	c.(685-687)gGc>gTc	p.G229V	GNG12-AS1_ENST00000413628.1_RNA|WLS_ENST00000370976.3_Missense_Mutation_p.G138V|WLS_ENST00000354777.2_Missense_Mutation_p.G227V|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000491811.1_5'UTR|WLS_ENST00000540432.1_Missense_Mutation_p.G229V	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	229	Interacts with Wnt proteins. {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						CTTGGTGAAGCCTCCATTTTG	0.463																																																0			1											125	103	110					1																	68619317		2203	4300	6503	68391905	SO:0001583	missense	79971			BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"wntless homolog"	611514	"chromosome 1 open reading frame 139", "G protein-coupled receptor 177", "wntless homolog (Drosophila)"	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.686G>T	1.37:g.68619317C>A	ENSP00000262348:p.Gly229Val		68391905	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Missense_Mutation	SNP	ENST00000262348.4	37	CCDS642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.556091|4.556091	0.86231|0.86231	.|.	.|.	ENSG00000116729|ENSG00000116729	ENST00000534713|ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976;ENST00000533537;ENST00000530486;ENST00000370973	.|T;T;T;T;T;T;T	.|0.45276	.|0.9;0.9;0.9;0.9;0.9;0.9;0.9	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62233|0.62233	0.2411|0.2411	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0	T|T	0.67292|0.67292	-0.5707|-0.5707	5|10	.|0.87932	.|D	.|0	-3.929|-3.929	18.9753|18.9753	0.92733|0.92733	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|229;138;229;227	.|F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2	.|.;.;WLS_HUMAN;.	S|V	132|229;227;229;138;96;184;96	.|ENSP00000446112:G229V;ENSP00000346829:G227V;ENSP00000262348:G229V;ENSP00000360015:G138V;ENSP00000433690:G96V;ENSP00000433111:G184V;ENSP00000360012:G96V	.|ENSP00000262348:G229V	A|G	-|-	1|2	0|0	WLS|WLS	68391905|68391905	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.629000|7.629000	0.83207|0.83207	2.480000|2.480000	0.83734|0.83734	0.563000|0.563000	0.77884|0.77884	GCT|GGC		0.463	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911		A	68619317	C	A	68619317	3	1	111	1	0	0	0	0	1	0	0	0	17416	739	26	2	1097	2	WLS	1	68619317	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	831864	68619317	180631304	39	29173										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504434	70504434	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctttcccccctaatgaaagAtatcaagtctaataaattca	4	10	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:70504434A>G	ENST00000035383.5	+	19	2843	c.2813A>G	c.(2812-2814)gAt>gGt	p.D938G	LRRC7_ENST00000415775.2_Missense_Mutation_p.D222G|LRRC7_ENST00000310961.5_Missense_Mutation_p.D943G	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	938						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CTAATGAAAGATATCAAGTCT	0.368																																																0			1											57	58	58					1																	70504434		2203	4300	6503	70277022	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2813A>G	1.37:g.70504434A>G	ENSP00000035383:p.Asp938Gly		70277022	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	A	8.668	0.902252	0.17760	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.37058	1.22;1.3;2.39	5.67	5.67	0.87782	.	0.053861	0.64402	D	0.000001	T	0.24890	0.0604	L	0.47716	1.5	0.54753	D	0.999987	B;P;P	0.50272	0.161;0.933;0.89	B;P;B	0.44811	0.075;0.461;0.272	T	0.02126	-1.1209	10	0.35671	T	0.21	.	15.0844	0.72138	1.0:0.0:0.0:0.0	.	222;938;938	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	G	943;938;222;761	ENSP00000309245:D943G;ENSP00000035383:D938G;ENSP00000394867:D222G	ENSP00000035383:D938G	D	+	2	0	LRRC7	70277022	1.000000	0.71417	0.997000	0.53966	0.170000	0.22686	8.703000	0.91344	2.169000	0.68431	0.383000	0.25322	GAT		0.368	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70504434	A	G	70504434	3	3	111	1	0	0	0	0	1	0	0	0	9049	333	12	4	2887	4	LRRC7	1	70504434	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1885117	70504434	178746187	40	29174										
FPGT	8790	hgsc.bcm.edu	37	chr1	74665348	74665348	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccttgctttttccaaatagGcaaacttgtagcacgtggag	9	9	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:74665348G>A	ENST00000609362.1	+	2	120	c.83G>A	c.(82-84)gGc>gAc	p.G28D	FPGT_ENST00000370898.3_Splice_Site_p.G41D|FPGT-TNNI3K_ENST00000533006.1_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Splice_Site_p.G28D|FPGT_ENST00000482102.2_Splice_Site_p.G50D|FPGT_ENST00000370894.5_Splice_Site_p.G28D|LRRIQ3_ENST00000370911.3_5'Flank|FPGT-TNNI3K_ENST00000370893.1_Splice_Site_p.G28D|LRRIQ3_ENST00000354431.4_5'Flank|LRRIQ3_ENST00000370909.2_5'Flank|FPGT_ENST00000524915.1_3'UTR|FPGT-TNNI3K_ENST00000370899.3_Splice_Site_p.G28D|FPGT_ENST00000534056.1_Splice_Site_p.G28D|FPGT_ENST00000467578.2_Splice_Site_p.G41D|FPGT-TNNI3K_ENST00000557284.2_Splice_Site_p.G41D|TNNI3K_ENST00000370891.2_Splice_Site_p.G28D	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	28					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TTCCAAATAGGCAAACTTGTA	0.378																																																0			1											82	82	82					1																	74665348		2203	4300	6503	74437936	SO:0001630	splice_region_variant	8790			AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.83-1G>A	1.37:g.74665348G>A			74437936	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	CCDS663.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.797894	0.50208	.	.	ENSG00000254685;ENSG00000254685;ENSG00000254685;ENSG00000254685;ENSG00000254685;ENSG00000254685;ENSG00000254685;ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000467578;ENST00000524915;ENST00000482102;ENST00000370898;ENST00000370894;ENST00000534056;ENST00000472069;ENST00000370899;ENST00000370895;ENST00000534632;ENST00000557284;ENST00000370891;ENST00000370893	T;T;T;T;T;T	0.75938	1.4;0.86;-0.97;-0.68;-0.98;-0.98	4.9	4.9	0.64082	.	0.073118	0.53938	U	0.000051	D	0.82591	0.5070	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.984;0.978	D;D;D;D;P;P	0.91635	0.972;0.998;0.999;0.999;0.742;0.46	T	0.82504	-0.0424	9	.	.	.	.	17.2321	0.86987	0.0:0.0:1.0:0.0	.	28;28;28;28;28;28	B4DH62;E9PNQ2;Q59H18-1;Q59H18-4;Q59H18-3;O14772	.;.;.;.;.;FPGT_HUMAN	D	28;28;50;28;28;28;26;28;28;28;28;28;28	ENSP00000359935:G28D;ENSP00000432819:G28D;ENSP00000359936:G28D;ENSP00000359932:G28D;ENSP00000450895:G28D;ENSP00000359928:G28D	.	G	+	2	0	RP11-653A5.2;TNNI3K;AC093158.1	74437936	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	6.247000	0.72411	2.417000	0.82017	0.585000	0.79938	GGC		0.378	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	A	74665348	G	A	74665348	5	1	111	1	0	0	0	0	0	0	1	0	6056	1217	42	3	89	3	FPGT	1	74665348	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4160914	74665348	174585273	41	29175										
TYW3	127253	hgsc.bcm.edu	37	chr1	75218076	75218076	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctgttaaatgtggcaaatcAaaaaatggaggaaaacaaga					rs200408383		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:75218076delA	ENST00000370867.3	+	5	616	c.527delA	c.(526-528)caafs	p.Q176fs	TYW3_ENST00000479111.1_Frame_Shift_Del_p.Q56fs|TYW3_ENST00000457880.2_Frame_Shift_Del_p.Q143fs|TYW3_ENST00000421739.2_Frame_Shift_Del_p.Q92fs	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	176					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						GTGGCAAATCAAAAAATGGAG	0.348																																																0			1											82	88	86					1																	75218076		2203	4300	6503	74990664	SO:0001589	frameshift_variant	127253			BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"chromosome 1 open reading frame 171"	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.527delA	1.37:g.75218076delA	ENSP00000359904:p.Gln176fs		74990664	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Frame_Shift_Del	DEL	ENST00000370867.3	37	CCDS666.1																																																																																				0.348	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467		-	75218076	A	-	75218076	7	5	111	1	0	1	0	1	0	0	0	0	16860	130	5	0	545	0	TYW3	1	75218076	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	552728	75218076	174032545	42	29176										
GBP4	115361	hgsc.bcm.edu	37	chr1	89651001	89651001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggaagccccaggtagagtgAcaatcattatgttgctagcc	11	9	1	2	rs61746918		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:89651001A>G	ENST00000355754.6	-	11	1956	c.1859T>C	c.(1858-1860)gTc>gCc	p.V620A	GBP4_ENST00000471938.1_5'UTR	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	620						cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		AGGTAGAGTGACAATCATTAT	0.348																																																0			1											128	113	118					1																	89651001		2203	4300	6503	89423589	SO:0001583	missense	115361			AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1859T>C	1.37:g.89651001A>G	ENSP00000359490:p.Val620Ala		89423589	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	A	0.077	-1.191681	0.01607	.	.	ENSG00000162654	ENST00000355754	T	0.56444	0.46	4.0	-8.0	0.01126	.	1.419030	0.04801	N	0.433511	T	0.06280	0.0162	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05784	-1.0864	10	0.15952	T	0.53	.	2.2661	0.04079	0.4915:0.1797:0.1532:0.1755	.	620	Q96PP9	GBP4_HUMAN	A	620	ENSP00000359490:V620A	ENSP00000359490:V620A	V	-	2	0	GBP4	89423589	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.968000	0.00669	-3.553000	0.00142	-1.957000	0.00481	GTC		0.348	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941		G	89651001	A	G	89651001	3	3	111	1	0	0	0	0	1	0	0	0	6296	275	10	4	67	4	GBP4	1	89651001	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	14432925	89651001	159599620	43	29177										
GBP5	115362	hgsc.bcm.edu	37	chr1	89732028	89732028	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatcctaaaaataatactcaCgagatccattgaccatgatg	5	9	1	3	rs140405391		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:89732028C>T	ENST00000370459.3	-	6	996		c.e6+1		RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Splice_Site			Q96PP8	GBP5_HUMAN	guanylate binding protein 5							cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATAATACTCACGAGATCCATT	0.363																																																0			1						C	,	0,4406		0,0,2203	69	68	68		,	4.4	0.2	1	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	splice-5,splice-5	GBP5	NM_001134486.2,NM_052942.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,	89732028	1,13005	2203	4300	6503	89504616	SO:0001630	splice_region_variant	115362			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.868+1G>A	1.37:g.89732028C>T			89504616	B2RCE1|Q86TM5	Splice_Site	SNP	ENST00000370459.3	37	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	4.947	0.176000	0.09443	0.0	1.16E-4	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	.	.	.	5.3	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0571	0.42252	0.0:0.9095:0.0:0.0905	.	.	.	.	.	-1	.	.	.	-	.	.	GBP5	89504616	0.917000	0.31117	0.218000	0.23776	0.005000	0.04900	2.135000	0.42112	1.624000	0.50355	0.644000	0.83932	.		0.363	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	Intron	T	89732028	C	T	89732028	5	4	111	1	0	0	0	0	0	0	1	0	6297	550	19	1	915	1	GBP5	1	89732028	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	81027	89732028	159518593	44	29178										
EPHX4	253152	hgsc.bcm.edu	37	chr1	92511122	92511122	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttcttattggccatgactGggggggcatgattgcttggc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:92511122delG	ENST00000370383.4	+	4	607	c.509delG	c.(508-510)tggfs	p.W170fs		NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	170						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			central_nervous_system(1)|large_intestine(3)|lung(8)	12						GGCCATGACTGGGGGGGCATG	0.388																																					GBM(140;473 1857 5172 22066 49719)											0			1											213	184	194					1																	92511122		2203	4300	6503	92283710	SO:0001589	frameshift_variant	253152			AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"Abhydrolase domain containing"	23758	protein-coding gene	gene with protein product			"abhydrolase domain containing 7"	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.509delG	1.37:g.92511122delG	ENSP00000359410:p.Trp170fs		92283710	Q8NCC6	Frame_Shift_Del	DEL	ENST00000370383.4	37	CCDS736.1																																																																																				0.388	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567		-	92511122	G	-	92511122	7	5	111	1	0	1	0	1	0	0	0	0	5195	1357	47	0	523	0	EPHX4	1	92511122	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	2779094	92511122	156739499	45	29179										
DPYD	1806	hgsc.bcm.edu	37	chr1	98165012	98165012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgcaggcccagcaccaaaaAgagcaatctttgcagaatag	9	10	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:98165012A>G	ENST00000370192.3	-	6	675	c.575T>C	c.(574-576)cTt>cCt	p.L192P	DPYD_ENST00000474241.1_5'UTR|DPYD_ENST00000423006.2_3'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	192					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AGCACCAAAAAGAGCAATCTT	0.433																																																0			1											158	158	158					1																	98165012		2203	4300	6503	97937600	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.575T>C	1.37:g.98165012A>G	ENSP00000359211:p.Leu192Pro		97937600	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286559	0.80803	.	.	ENSG00000188641	ENST00000370192	D	0.82893	-1.66	5.5	5.5	0.81552	Alpha-helical ferredoxin (1);	0.067190	0.64402	D	0.000009	D	0.90748	0.7096	M	0.86343	2.81	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.92572	0.6067	10	0.87932	D	0	-18.4137	15.5975	0.76599	1.0:0.0:0.0:0.0	.	192	Q12882	DPYD_HUMAN	P	192	ENSP00000359211:L192P	ENSP00000359211:L192P	L	-	2	0	DPYD	97937600	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.920000	0.92779	2.094000	0.63399	0.477000	0.44152	CTT		0.433	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		G	98165012	A	G	98165012	3	3	111	1	0	0	0	0	1	0	0	0	4756	72	3	4	2574	4	DPYD	1	98165012	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5653890	98165012	151085609	46	29180										
AGL	178	hgsc.bcm.edu	37	chr1	100343239	100343239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaacttatttgctggggagAcagtgttaaattacgctatg	11	5	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:100343239A>G	ENST00000294724.4	+	12	1944	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	AGL_ENST00000370165.3_Missense_Mutation_p.D489G|AGL_ENST00000370163.3_Missense_Mutation_p.D489G|AGL_ENST00000361302.3_Missense_Mutation_p.D473G|AGL_ENST00000370161.2_Missense_Mutation_p.D473G|AGL_ENST00000361522.4_Missense_Mutation_p.D472G|AGL_ENST00000361915.3_Missense_Mutation_p.D489G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGCTGGGGAGACAGTGTTAAA	0.363																																																0			1											102	99	100					1																	100343239		2203	4300	6503	100115827	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1466A>G	1.37:g.100343239A>G	ENSP00000294724:p.Asp489Gly		100115827	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838082	0.91117	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12;-3.12;-3.12	5.97	5.97	0.96955	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97687	1.0176	10	0.87932	D	0	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	472;473;489	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	489;489;489;489;473;473;472	ENSP00000355106:D489G;ENSP00000359184:D489G;ENSP00000359182:D489G;ENSP00000294724:D489G;ENSP00000354971:D473G;ENSP00000359180:D473G;ENSP00000354635:D472G	ENSP00000294724:D489G	D	+	2	0	AGL	100115827	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.896000	0.92521	2.288000	0.76882	0.533000	0.62120	GAC		0.363	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100343239	A	G	100343239	3	3	111	1	0	0	0	0	1	0	0	0	384	275	10	4	1577	4	AGL	1	100343239	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2178227	100343239	148907382	47	29181										
MYBPHL	343263	hgsc.bcm.edu	37	chr1	109837737	109837737	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcctcttgcccttacctttCacatccacccgacagtccac	3	20	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:109837737C>T	ENST00000357155.1	-	7	1099	c.1050G>A	c.(1048-1050)gtG>gtA	p.V350V	MYBPHL_ENST00000477962.1_5'UTR	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	350										central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		CCTTACCTTTCACATCCACCC	0.587																																																0			1											101	94	96					1																	109837737		2203	4300	6503	109639260	SO:0001819	synonymous_variant	343263			AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.1050G>A	1.37:g.109837737C>T			109639260	B7ZME5|Q5T2Z7	Silent	SNP	ENST00000357155.1	37	CCDS30793.1																																																																																				0.587	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985		T	109837737	C	T	109837737	2	4	111	1	0	0	0	0	0	0	0	1	10045	813	29	3		3	MYBPHL	1	109837737	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9494498	109837737	139412884	48	29182										
GPR61	83873	hgsc.bcm.edu	37	chr1	110086222	110086222	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggagctcccagtgtcccccCaggctgttcactccagtgga	11	15	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:110086222C>A	ENST00000527748.1	+	2	1261	c.578C>A	c.(577-579)cCa>cAa	p.P193Q	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGTGTCCCCCCAGGCTGTTCA	0.582																																																0			1											161	152	155					1																	110086222		2203	4300	6503	109887745	SO:0001583	missense	83873			AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"GPCR / Class A : Orphans"	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.578C>A	1.37:g.110086222C>A	ENSP00000432456:p.Pro193Gln		109887745	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	37	CCDS801.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.676267	0.29783	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.36157	1.27	5.68	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.190927	0.42548	D	0.000698	T	0.12433	0.0302	L	0.35854	1.095	0.41312	D	0.987119	B	0.32350	0.366	B	0.30855	0.121	T	0.05886	-1.0858	10	0.18710	T	0.47	-2.3848	10.4248	0.44371	0.0:0.7518:0.1728:0.0754	.	193	Q9BZJ8	GPR61_HUMAN	Q	193;321	ENSP00000432456:P193Q	ENSP00000286603:P321Q	P	+	2	0	GPR61	109887745	0.032000	0.19561	0.998000	0.56505	0.979000	0.70002	1.554000	0.36266	1.393000	0.46605	0.655000	0.94253	CCA		0.582	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1			A	110086222	C	A	110086222	3	1	111	1	0	0	0	0	1	0	0	0	6722	594	21	2	580	2	GPR61	1	110086222	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	248485	110086222	139164399	49	29183										
FAM40A	85369	hgsc.bcm.edu	37	chr1	110587643	110587643	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctttattctccagtgacacGaacacagtggtggggctgcc	11	11	2	1	rs143183603	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:110587643G>A	ENST00000369795.3	+	12	1381	c.1359G>A	c.(1357-1359)acG>acA	p.T453T	STRIP1_ENST00000369796.1_Silent_p.T358T	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	453					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.T453T(1)									CCAGTGACACGAACACAGTGG	0.512													G|||	4	0.000798722	0.003	0	5008	,	,		15888	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	1						G		8,4398	14.3+/-33.2	0,8,2195	114	113	113		1359	-10.2	0.4	1	dbSNP_134	113	0,8600		0,0,4300	no	coding-synonymous	FAM40A	NM_033088.2		0,8,6495	AA,AG,GG		0.0,0.1816,0.0615		453/838	110587643	8,12998	2203	4300	6503	110389166	SO:0001819	synonymous_variant	85369			AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.1359G>A	1.37:g.110587643G>A			110389166	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Silent	SNP	ENST00000369795.3	37	CCDS30798.1																																																																																				0.512	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		A	110587643	G	A	110587643	2	1	111	1	0	0	0	0	0	0	0	1	5579	1045	37	1		1	FAM40A	1	110587643	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	501421	110587643	138662978	50	29184										
KCNC4	3749	hgsc.bcm.edu	37	chr1	110766275	110766275	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgctggtaggggcactgtgTgcactggctggcgtgctcac	16	10	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:110766275T>C	ENST00000369787.3	+	2	1395	c.1368T>C	c.(1366-1368)tgT>tgC	p.C456C	KCNC4_ENST00000438661.2_Silent_p.C456C|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000413138.3_Silent_p.C456C	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	456					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGGCACTGTGTGCACTGGCTG	0.602																																																0			1											119	101	107					1																	110766275		2203	4300	6503	110567798	SO:0001819	synonymous_variant	3749			BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.1368T>C	1.37:g.110766275T>C			110567798	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	37	CCDS821.1																																																																																				0.602	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		C	110766275	T	C	110766275	2	2	111	1	0	0	0	0	0	0	0	1	8038	1702	59	4		4	KCNC4	1	110766275	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	178632	110766275	138484346	51	29185										
CEPT1	10390	hgsc.bcm.edu	37	chr1	111703836	111703836	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggacaaaccctgattggatgTttttttgttgttttgcgggg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:111703836delT	ENST00000545121.1	+	4	755	c.547delT	c.(547-549)tttfs	p.F184fs	CEPT1_ENST00000357172.4_Frame_Shift_Del_p.F184fs	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	184					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)	p.C185fs*26(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TGATTGGATGTTTTTTTGTTG	0.383																																																1	Deletion - Frameshift(1)	large_intestine(1)	1											234	234	234					1																	111703836		2203	4300	6503	111505359	SO:0001589	frameshift_variant	10390			AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.547delT	1.37:g.111703836delT	ENSP00000441980:p.Phe184fs		111505359	Q69YJ9|Q9P0Y8	Frame_Shift_Del	DEL	ENST00000545121.1	37	CCDS830.1																																																																																				0.383	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090		-	111703836	T	-	111703836	7	5	111	1	0	1	0	1	0	0	0	0	3270	1725	60	0	557	0	CEPT1	1	111703836	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	937561	111703836	137546785	52	29186										
KCND3	3752	hgsc.bcm.edu	37	chr1	112524649	112524649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccacggtgaagatcatgaCgcacgccgtgtccaggcaga	12	13	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:112524649C>T	ENST00000315987.2	-	2	1179	c.700G>A	c.(700-702)Gtc>Atc	p.V234I	KCND3_ENST00000369697.1_Missense_Mutation_p.V234I|KCND3_ENST00000302127.4_Missense_Mutation_p.V234I	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	234					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.V234I(2)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AAGATCATGACGCACGCCGTG	0.667																																																2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|endometrium(1)	1											36	36	36					1																	112524649		2203	4300	6503	112326172	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.700G>A	1.37:g.112524649C>T	ENSP00000319591:p.Val234Ile		112326172	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146250	0.77888	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.98512	-4.97;-4.97;-4.97	5.51	5.51	0.81932	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97117	0.9058	L	0.28776	0.89	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.70227	0.968;0.968	D	0.95496	0.8573	10	0.10111	T	0.7	.	18.9981	0.92821	0.0:1.0:0.0:0.0	.	234;234	Q14D71;Q9UK17	.;KCND3_HUMAN	I	234	ENSP00000358711:V234I;ENSP00000319591:V234I;ENSP00000306923:V234I	ENSP00000306923:V234I	V	-	1	0	KCND3	112326172	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	6.089000	0.71384	2.590000	0.87494	0.563000	0.77884	GTC		0.667	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112524649	C	T	112524649	3	4	111	1	0	0	0	0	1	0	0	0	8041	536	19	1	1295	1	KCND3	1	112524649	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	820813	112524649	136725972	53	29187										
TRIM33	51592	hgsc.bcm.edu	37	chr1	114944078	114944078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaggtaaagcagaagacgtTcacatttctggcccaaacaa	9	9	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:114944078T>C	ENST00000358465.2	-	17	2983	c.2900A>G	c.(2899-2901)gAa>gGa	p.E967G	TRIM33_ENST00000450349.2_Missense_Mutation_p.E599G|TRIM33_ENST00000476908.1_5'Flank|TRIM33_ENST00000369543.2_Missense_Mutation_p.E967G	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	967					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		CAGAAGACGTTCACATTTCTG	0.398			T	RET	papillary thyroid																																		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	0			1											69	67	68					1																	114944078		2203	4300	6503	114745601	SO:0001583	missense	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2900A>G	1.37:g.114944078T>C	ENSP00000351250:p.Glu967Gly		114745601	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.4|29.4	5.005235|5.005235	0.93287|0.93287	.|.	.|.	ENSG00000197323|ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349|ENST00000448034	T;T;T|.	0.33654|.	1.4;1.4;1.4|.	5.86|5.86	5.86|5.86	0.93980|0.93980	Bromodomain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71467|0.71467	0.3343|0.3343	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0|.	T|T	0.72959|0.72959	-0.4133|-0.4133	10|5	0.87932|.	D|.	0|.	-19.1923|-19.1923	16.5602|16.5602	0.84551|0.84551	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	599;599;967;967|.	E7EN20;B3KN30;Q9UPN9-2;Q9UPN9|.	.;.;.;TRI33_HUMAN|.	G|D	967;967;599|728	ENSP00000351250:E967G;ENSP00000358556:E967G;ENSP00000412077:E599G|.	ENSP00000351250:E967G|.	E|N	-|-	2|1	0|0	TRIM33|TRIM33	114745601|114745601	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.621000|7.621000	0.83083|0.83083	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	GAA|AAC		0.398	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		C	114944078	T	C	114944078	3	2	111	1	0	0	0	0	1	0	0	0	16547	1783	62	4	499	4	TRIM33	1	114944078	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2419429	114944078	134306543	54	29188										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120438430	120438430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatctgccattctatttcaTcatcacttaagccacaaacc	2	15	5	0	rs144018958		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:120438430T>C	ENST00000369400.1	-	1	688	c.530A>G	c.(529-531)gAt>gGt	p.D177G		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	177					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		TTCTATTTCATCATCACTTAA	0.448													T|||	1	0.000199681	0	0	5008	,	,		19656	0.001		0	False		,,,				2504	0															0			1											87	85	85					1																	120438430		2203	4300	6503	120239953	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.530A>G	1.37:g.120438430T>C	ENSP00000358407:p.Asp177Gly		120239953	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	11.03	1.518271	0.27211	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01192	5.2	5.2	1.69	0.24217	.	0.636430	0.13646	N	0.372604	T	0.00412	0.0013	N	0.19112	0.55	0.09310	N	1	P	0.42649	0.786	B	0.41860	0.368	T	0.51212	-0.8734	10	0.72032	D	0.01	.	6.3583	0.21414	0.0:0.2814:0.0:0.7186	.	177	Q9UKF2	ADA30_HUMAN	G	177	ENSP00000358407:D177G	ENSP00000358407:D177G	D	-	2	0	ADAM30	120239953	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.304000	0.19228	0.319000	0.23209	-0.468000	0.05107	GAT		0.448	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		C	120438430	T	C	120438430	3	2	111	1	0	0	0	0	1	0	0	0	248	1435	50	4	1846	4	ADAM30	1	120438430	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	5494352	120438430	128812191	55	29189										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144880809	144880809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caagtctcatagcccaggtcCtggaggtccacctggatctg	11	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:144880809C>A	ENST00000369354.3	-	26	4008	c.3819G>T	c.(3817-3819)caG>caT	p.Q1273H	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q1409H|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q1409H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q1273H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1229H|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1273					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGCCCAGGTCCTGGAGGTCCA	0.552			T	PDGFRB	MPD																																		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			1											228	196	207					1																	144880809		2203	4297	6500	143592166	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3819G>T	1.37:g.144880809C>A	ENSP00000358360:p.Gln1273His		143592166	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.7|27.7	4.858679|4.858679	0.91433|0.91433	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000530592|ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.|T;T;T;T;T	.|0.03330	.|3.97;4.16;4.12;4.16;4.18	6.07|6.07	4.17|4.17	0.49024|0.49024	.|.	.|.	.|.	.|.	.|.	.|T	.|0.08313	.|0.0207	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.998	.|D;D	.|0.81914	.|0.943;0.995	.|T	.|0.02004	.|-1.1231	.|9	.|0.72032	.|D	.|0.01	.|.	11.7519|11.7519	0.51853|0.51853	0.0:0.8517:0.0:0.1483|0.0:0.8517:0.0:0.1483	.|.	.|1229;1273	.|Q5VU43-3;Q5VU43	.|.;MYOME_HUMAN	X|H	167|1229;1273;1273;1409;1409	.|ENSP00000327209:Q1229H;ENSP00000358360:Q1273H;ENSP00000358363:Q1273H;ENSP00000435654:Q1409H;ENSP00000358366:Q1409H	.|ENSP00000327209:Q1229H	G|Q	-|-	1|3	0|2	PDE4DIP|PDE4DIP	143592166|143592166	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.903000|1.903000	0.39858|0.39858	1.547000|1.547000	0.49401|0.49401	0.655000|0.655000	0.94253|0.94253	GGA|CAG		0.552	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144880809	C	A	144880809	3	1	111	1	0	0	0	0	1	0	0	0	11674	680	24	2	3297	2	PDE4DIP	1	144880809	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	24442379	144880809	104369812	56	29190										
HIST2H2AB	317772	hgsc.bcm.edu	37	chr1	149859099	149859100	+	Frame_Shift_Del	DEL	CT	CT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttcttgccaggcttgtgaCtctccgttttcttgggcaac							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:149859099_149859100delCT	ENST00000331128.3	-	1	366_367	c.367_368delAG	c.(367-369)agtfs	p.S123fs	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_175065.2	NP_778235.1	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	123						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			AGGCTTGTGACTCTCCGTTTTC	0.505																																																0			1																																								148125724	SO:0001589	frameshift_variant	317772			AY131972	CCDS938.1	1q21.2	2011-01-27	2006-10-11		ENSG00000184270	ENSG00000184270		"Histones / Replication-dependent"	20508	protein-coding gene	gene with protein product		615014	"histone 2, H2ab"			12408966	Standard	NM_175065		Approved		uc001ete.3	Q8IUE6	OTTHUMG00000012085	ENST00000331128.3:c.367_368delAG	1.37:g.149859101_149859102delCT	ENSP00000332790:p.Ser123fs		148125723		Frame_Shift_Del	DEL	ENST00000331128.3	37	CCDS938.1																																																																																				0.505	HIST2H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033440.1	NM_175065		-	149859100	CT	-	149859099	7	5	111	1	0	1	0	1	0	0	0	0	7198	565	20	0	28	0	HIST2H2AB	1	149859099	Frame_Shift_Del	DEL	CT	TCGA-EI-6507-01A-11D-1733-10	4978290	149859099	99391522	57	29191										
MTMR11	10903	hgsc.bcm.edu	37	chr1	149908497	149908498	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catctctggctcctccttctINSggggggcaatgttgaaactc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:149908497_149908498insG	ENST00000439741.2	-	1	293_294	c.43_44insC	c.(43-45)cagfs	p.Q15fs	MTMR11_ENST00000369140.3_5'Flank|MTMR11_ENST00000361405.6_Frame_Shift_Ins_p.Q15fs|MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000406732.3_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	15							phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|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)			ctcctccttctGGGGGGCAATG	0.579																																																0			1																																								148175122	SO:0001589	frameshift_variant	10903			AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	24307	protein-coding gene	gene with protein product	"cisplatin resistance associated"					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.44dupC	1.37:g.149908503_149908503dupG	ENSP00000391668:p.Gln15fs		148175121	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Frame_Shift_Ins	INS	ENST00000439741.2	37	CCDS53360.1																																																																																				0.579	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873		G	149908498	-	G	149908497	7	5	111	1	0	1	1	0	0	0	0	0	9970	1580	55	0	2192	0	MTMR11	1	149908497	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	49398	149908497	99342124	58	29192										
RPRD2	23248	hgsc.bcm.edu	37	chr1	150444062	150444062	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtccagttatagccacagaGcccaagaatttggggtaaag	11	8	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:150444062G>A	ENST00000369068.4	+	11	2642	c.2638G>A	c.(2638-2640)Gcc>Acc	p.A880T	RPRD2_ENST00000539519.1_Missense_Mutation_p.A854T|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.A854T	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	880	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TAGCCACAGAGCCCAAGAATT	0.493																																																0			1											85	83	83					1																	150444062		1930	4117	6047	148710686	SO:0001583	missense	23248			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.2638G>A	1.37:g.150444062G>A	ENSP00000358064:p.Ala880Thr		148710686	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	G	6.918	0.538959	0.13250	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.51325	0.75;0.71;0.75	5.32	3.33	0.38152	.	0.247111	0.35151	N	0.003406	T	0.07548	0.0190	N	0.04508	-0.205	0.23120	N	0.998266	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.0;0.002;0.004	T	0.20405	-1.0276	10	0.23302	T	0.38	-3.2925	4.4286	0.11517	0.1852:0.0:0.5096:0.3052	.	854;880;854	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	T	854;854;880	ENSP00000383785:A854T;ENSP00000445482:A854T;ENSP00000358064:A880T	ENSP00000358064:A880T	A	+	1	0	RPRD2	148710686	0.999000	0.42202	1.000000	0.80357	0.971000	0.66376	0.453000	0.21811	1.486000	0.48398	-0.143000	0.13931	GCC		0.493	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		A	150444062	G	A	150444062	3	1	111	1	0	0	0	0	1	0	0	0	13654	971	34	3	2680	3	RPRD2	1	150444062	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	535565	150444062	98806559	59	29193										
TNFAIP8L2	79626	hgsc.bcm.edu	37	chr1	151131303	151131303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggtgctagatgagctctacCgtgtgtccaaggagtacacg	13	9	1	2	rs374028247		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:151131303C>T	ENST00000368910.3	+	2	256	c.130C>T	c.(130-132)Cgt>Tgt	p.R44C		NM_024575.4	NP_078851.2	Q6P589	TP8L2_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 2	44					innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)				lung(1)|skin(2)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			TGAGCTCTACCGTGTGTCCAA	0.562																																																0			1											67	64	65					1																	151131303		2203	4300	6503	149397927	SO:0001583	missense	79626			BC063014	CCDS985.1	1q21.2	2008-02-05			ENSG00000163154	ENSG00000163154			26277	protein-coding gene	gene with protein product		612112					Standard	NM_024575		Approved	FLJ23467	uc001ewx.2	Q6P589	OTTHUMG00000012259	ENST00000368910.3:c.130C>T	1.37:g.151131303C>T	ENSP00000357906:p.Arg44Cys		149397927	Q6I9Y0|Q9H2H7|Q9H5G2	Missense_Mutation	SNP	ENST00000368910.3	37	CCDS985.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943118	0.73672	.	.	ENSG00000163154	ENST00000368910	T	0.37411	1.2	5.67	4.68	0.58851	.	0.051900	0.64402	D	0.000001	T	0.52964	0.1767	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.57493	-0.7802	10	0.87932	D	0	-10.9942	14.6121	0.68522	0.2179:0.7821:0.0:0.0	.	44	Q6P589	TP8L2_HUMAN	C	44	ENSP00000357906:R44C	ENSP00000357906:R44C	R	+	1	0	TNFAIP8L2	149397927	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.430000	0.44766	2.673000	0.90976	0.655000	0.94253	CGT		0.562	TNFAIP8L2-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034069.2	NM_024575		T	151131303	C	T	151131303	3	4	111	1	0	0	0	0	1	0	0	0	16317	652	23	1	132	1	TNFAIP8L2	1	151131303	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	687241	151131303	98119318	60	29194										
CELF3	11189	hgsc.bcm.edu	37	chr1	151678795	151678795	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgaccagggctggaggctgcGggaacgcaggtgcaaccagg	18	11	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:151678795G>A	ENST00000290583.4	-	10	1824	c.1031C>T	c.(1030-1032)cCg>cTg	p.P344L	CELF3_ENST00000290585.4_Missense_Mutation_p.P294L|CELF3_ENST00000470688.1_5'UTR|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Missense_Mutation_p.P139L	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	344					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						TGGAGGCTGCGGGAACGCAGG	0.642																																																0			1											36	40	38					1																	151678795		2164	4244	6408	149945419	SO:0001583	missense	11189			U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1031C>T	1.37:g.151678795G>A	ENSP00000290583:p.Pro344Leu		149945419	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.57|18.57	3.653396|3.653396	0.67472|0.67472	.|.	.|.	ENSG00000159409|ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000392706|ENST00000420342	T;T;T|.	0.31247|.	2.26;2.2;1.5|.	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	0.062472|.	0.64402|.	D|.	0.000004|.	T|T	0.47303|0.47303	0.1438|0.1438	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.33748|.	0.206;0.035;0.423;0.021;0.021|.	B;B;B;B;B|.	0.33690|.	0.041;0.006;0.168;0.002;0.006|.	T|T	0.40079|0.40079	-0.9582|-0.9582	10|5	0.49607|.	T|.	0.09|.	-16.4417|-16.4417	15.4996|15.4996	0.75687|0.75687	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	139;294;343;344;343|.	B4DQL3;Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3|.	.;.;.;CELF3_HUMAN;.|.	L|C	294;344;139|345	ENSP00000290585:P294L;ENSP00000290583:P344L;ENSP00000376470:P139L|.	ENSP00000290583:P344L|.	P|R	-|-	2|1	0|0	CELF3|CELF3	149945419|149945419	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	2.691000|2.691000	0.47010|0.47010	2.524000|2.524000	0.85096|0.85096	0.655000|0.655000	0.94253|0.94253	CCG|CGC		0.642	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		A	151678795	G	A	151678795	3	1	111	1	0	0	0	0	1	0	0	0	3223	1116	39	1	378	1	CELF3	1	151678795	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	547492	151678795	97571826	61	29195										
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154544280	154544280	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgcaccaccgctcgcccacCacgcacaccatggcgccctg	9	21	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:154544280C>T	ENST00000368476.3	+	5	1245	c.981C>T	c.(979-981)acC>acT	p.T327T		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	327					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	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)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	GCTCGCCCACCACGCACACCA	0.637																																																0			1											83	61	68					1																	154544280		2203	4300	6503	152810904	SO:0001819	synonymous_variant	1141			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.981C>T	1.37:g.154544280C>T			152810904	Q9UEH9	Silent	SNP	ENST00000368476.3	37	CCDS1070.1																																																																																				0.637	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		T	154544280	C	T	154544280	2	4	111	1	0	0	0	0	0	0	0	1	3397	581	21	3		3	CHRNB2	1	154544280	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2865485	154544280	94706341	62	29196										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154680615	154680615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgctggcgcagggtgtcgGcgatgagcagcggcagggag	21	9	0	1	rs371429880		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:154680615G>A	ENST00000271915.4	-	8	2348	c.2033C>T	c.(2032-2034)gCc>gTc	p.A678V	KCNN3_ENST00000515643.1_5'UTR|KCNN3_ENST00000358505.2_Missense_Mutation_p.A365V|KCNN3_ENST00000361147.4_Missense_Mutation_p.A373V	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	683					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	CAGGGTGTCGGCGATGAGCAG	0.637																																																0			1						G	VAL/ALA,VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	72	81	78		1118,2033,2078	5.1	1	1		78	0,8598		0,0,4299	no	missense,missense,missense	KCNN3	NM_170782.2,NM_002249.5,NM_001204087.1	64,64,64	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	373/427,678/732,693/747	154680615	1,13003	2203	4299	6502	152947239	SO:0001583	missense	3782			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.2033C>T	1.37:g.154680615G>A	ENSP00000271915:p.Ala678Val		152947239	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507618	0.64410	2.27E-4	0.0	ENSG00000143603	ENST00000361147;ENST00000271915;ENST00000358505	D;D;D	0.98585	-5.01;-3.81;-5.01	5.09	5.09	0.68999	.	0.000000	0.56097	D	0.000024	D	0.92652	0.7665	N	0.11255	0.115	0.40864	D	0.983859	B;B	0.27594	0.002;0.182	B;B	0.34180	0.005;0.177	D	0.91601	0.5295	10	0.66056	D	0.02	-20.4554	11.74	0.51788	0.0812:0.0:0.9188:0.0	.	683;373	Q9UGI6;Q9UGI6-2	KCNN3_HUMAN;.	V	373;678;365	ENSP00000354764:A373V;ENSP00000271915:A678V;ENSP00000351295:A365V	ENSP00000271915:A678V	A	-	2	0	KCNN3	152947239	1.000000	0.71417	0.982000	0.44146	0.978000	0.69477	5.172000	0.65003	2.642000	0.89623	0.655000	0.94253	GCC		0.637	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154680615	G	A	154680615	3	1	111	1	0	0	0	0	1	0	0	0	8101	1203	42	3	166	3	KCNN3	1	154680615	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	136335	154680615	94570006	63	29197										
THBS3	7059	hgsc.bcm.edu	37	chr1	155171335	155171335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggttgcccaggaaacccaggCggcagggaccacacttgaaa	13	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:155171335C>T	ENST00000368378.3	-	11	1222	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000457183.2_Missense_Mutation_p.R281H|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000541576.1_5'UTR|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	401	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)			GAAACCCAGGCGGCAGGGACC	0.637																																																0			1											41	45	44					1																	155171335		2203	4300	6503	153437959	SO:0001583	missense	7059			L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1202G>A	1.37:g.155171335C>T	ENSP00000357362:p.Arg401His		153437959	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	37	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058286	0.76074	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	D;D;D	0.92397	-3.03;-3.03;-2.25	4.71	4.71	0.59529	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.065257	0.64402	D	0.000013	D	0.86401	0.5924	N	0.17474	0.49	0.37210	D	0.904781	D;D;D;D	0.59357	0.985;0.985;0.985;0.985	P;P;P;P	0.53760	0.734;0.652;0.652;0.652	D	0.87713	0.2568	10	0.45353	T	0.12	-23.3163	13.3465	0.60575	0.0:1.0:0.0:0.0	.	281;401;401;401	B4DQ20;Q53FK6;Q2HIZ0;P49746	.;.;.;TSP3_HUMAN	H	401;281;251	ENSP00000357362:R401H;ENSP00000392207:R281H;ENSP00000404040:R251H	ENSP00000357362:R401H	R	-	2	0	THBS3	153437959	0.993000	0.37304	1.000000	0.80357	0.983000	0.72400	2.633000	0.46519	2.618000	0.88619	0.591000	0.81541	CGC		0.637	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		T	155171335	C	T	155171335	3	4	111	1	0	0	0	0	1	0	0	0	15894	768	27	1	1720	1	THBS3	1	155171335	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	490720	155171335	94079286	64	29198										
GON4L	54856	hgsc.bcm.edu	37	chr1	155727042	155727042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctagctgctgggcgcaagtGgtcaaagaagatagaaaact	13	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:155727042G>T	ENST00000368331.1	-	26	5374	c.5326C>A	c.(5326-5328)Cac>Aac	p.H1776N	GON4L_ENST00000271883.5_Missense_Mutation_p.H1776N|GON4L_ENST00000437809.1_Missense_Mutation_p.H1776N	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1776	PAH 2. {ECO:0000255|PROSITE- ProRule:PRU00810}.				regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGGCGCAAGTGGTCAAAGAAG	0.512																																																0			1											74	77	76					1																	155727042		1998	4161	6159	153993666	SO:0001583	missense	54856			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5326C>A	1.37:g.155727042G>T	ENSP00000357315:p.His1776Asn		153993666	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	G	20.7	4.034818	0.75617	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.10099	2.91;2.91;2.91	5.39	5.39	0.77823	.	0.085080	0.50627	D	0.000118	T	0.09113	0.0225	N	0.03608	-0.345	0.40720	D	0.982652	D;D;D	0.71674	0.993;0.997;0.998	D;D;D	0.78314	0.968;0.98;0.991	T	0.53641	-0.8410	10	0.41790	T	0.15	.	18.7775	0.91916	0.0:0.0:1.0:0.0	.	972;1776;1776	Q1ED43;Q3T8J9;Q3T8J9-3	.;GON4L_HUMAN;.	N	1776	ENSP00000396117:H1776N;ENSP00000357315:H1776N;ENSP00000271883:H1776N	ENSP00000271883:H1776N	H	-	1	0	GON4L	153993666	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	6.780000	0.75063	2.531000	0.85337	0.484000	0.47621	CAC		0.512	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		T	155727042	G	T	155727042	3	4	111	1	0	0	0	0	1	0	0	0	6592	1348	47	2	1424	2	GON4L	1	155727042	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	555707	155727042	93523579	65	29199										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156503578	156503578	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacgtaccaataaggtcaggGatggtgggcagctccccaag	13	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:156503578G>A	ENST00000361170.2	-	31	3973	c.3963C>T	c.(3961-3963)atC>atT	p.I1321I		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1321					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TAAGGTCAGGGATGGTGGGCA	0.632																																																0			1											60	47	52					1																	156503578		2203	4300	6503	154770202	SO:0001819	synonymous_variant	128239			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3963C>T	1.37:g.156503578G>A			154770202	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																				0.632	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		A	156503578	G	A	156503578	2	1	111	1	0	0	0	0	0	0	0	1	7837	1164	41	3		3	IQGAP3	1	156503578	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	776536	156503578	92747043	66	29200										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815041	156815041	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctcgaaatccgagctgttgCcccccagccggaggggccca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:156815041delC	ENST00000368195.3	-	12	2660	c.2264delG	c.(2263-2265)ggcfs	p.G755fs	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	755					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CGAGCTGTTGCCCCCCAGCCG	0.687																																																0			1											17	19	18					1																	156815041		2200	4295	6495	155081665	SO:0001589	frameshift_variant	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2264delG	1.37:g.156815041delC	ENSP00000357178:p.Gly755fs		155081665	O60724|Q5VZS3	Frame_Shift_Del	DEL	ENST00000368195.3	37	CCDS1160.1																																																																																				0.687	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		-	156815041	C	-	156815041	7	5	111	1	0	1	0	1	0	0	0	0	7795	739	26	0	1672	0	INSRR	1	156815041	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	311463	156815041	92435580	67	29201										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156843698	156843698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggcctccgcctccatcaTggctgccttcatggacaacc	8	18	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:156843698T>C	ENST00000524377.1	+	8	1165	c.1124T>C	c.(1123-1125)aTg>aCg	p.M375T	NTRK1_ENST00000368196.3_Missense_Mutation_p.M375T|NTRK1_ENST00000358660.3_Missense_Mutation_p.M375T|NTRK1_ENST00000392302.2_Missense_Mutation_p.M345T	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	375					activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCCTCCATCATGGCTGCCTTC	0.657			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																													Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	0			1											57	38	44					1																	156843698		2196	4295	6491	155110322	SO:0001583	missense	4914			Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1124T>C	1.37:g.156843698T>C	ENSP00000431418:p.Met375Thr		155110322	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	T	4.265	0.048341	0.08243	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.95	3.68	0.42216	Immunoglobulin-like fold (1);	0.464740	0.22245	N	0.062623	T	0.07234	0.0183	L	0.41236	1.265	0.20764	N	0.999852	B;B;B;B	0.21688	0.0;0.022;0.004;0.059	B;B;B;B	0.29663	0.001;0.035;0.007;0.105	T	0.28202	-1.0051	9	.	.	.	.	4.1372	0.10176	0.0:0.2377:0.1687:0.5936	.	375;375;375;345	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	T	345;375;375;375	ENSP00000376120:M345T;ENSP00000357179:M375T;ENSP00000431418:M375T;ENSP00000351486:M375T	.	M	+	2	0	NTRK1	155110322	0.000000	0.05858	0.816000	0.32577	0.362000	0.29581	-0.488000	0.06497	1.090000	0.41315	0.533000	0.62120	ATG		0.657	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		C	156843698	T	C	156843698	3	2	111	1	0	0	0	0	1	0	0	0	10737	1464	51	4	1284	4	NTRK1	1	156843698	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	28657	156843698	92406923	68	29202										
OR10K1	391109	hgsc.bcm.edu	37	chr1	158435793	158435793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtatgggactaatggctgctGcctgtgcctgtggcttcact	13	10	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:158435793G>A	ENST00000289451.2	+	1	522	c.442G>A	c.(442-444)Gcc>Acc	p.A148T		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					AATGGCTGCTGCCTGTGCCTG	0.547																																																0			1											194	182	186					1																	158435793		2203	4300	6503	156702417	SO:0001583	missense	391109			AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"GPCR / Class A : Olfactory receptors"	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.442G>A	1.37:g.158435793G>A	ENSP00000289451:p.Ala148Thr		156702417	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	37	CCDS30897.1	.	.	.	.	.	.	.	.	.	.	g	15.64	2.893248	0.52121	.	.	ENSG00000173285	ENST00000289451	T	0.37584	1.19	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000657	T	0.41373	0.1156	L	0.35644	1.08	0.34377	D	0.692703	D	0.89917	1.0	D	0.97110	1.0	T	0.44345	-0.9334	10	0.66056	D	0.02	.	16.1284	0.81410	0.0:0.0:1.0:0.0	.	148	Q8NGX5	O10K1_HUMAN	T	148	ENSP00000289451:A148T	ENSP00000289451:A148T	A	+	1	0	OR10K1	156702417	0.780000	0.28664	0.962000	0.40283	0.212000	0.24457	3.270000	0.51600	2.311000	0.77944	0.557000	0.71058	GCC		0.547	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			A	158435793	G	A	158435793	3	1	111	1	0	0	0	0	1	0	0	0	10944	1319	46	3	444	3	OR10K1	1	158435793	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1592095	158435793	90814828	69	29203										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158639317	158639317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagcaatctacgtctagtggCagccttttcacgtagggcat	10	11	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:158639317C>T	ENST00000368147.4	-	14	1894	c.1714G>A	c.(1714-1716)Gcc>Acc	p.A572T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	572					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CGTCTAGTGGCAGCCTTTTCA	0.453																																																0			1											153	143	146					1																	158639317		1942	4142	6084	156905941	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1714G>A	1.37:g.158639317C>T	ENSP00000357129:p.Ala572Thr		156905941	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.679437	0.29783	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.42131	0.98;0.98	4.72	3.8	0.43715	.	0.266050	0.19957	N	0.102291	T	0.29850	0.0746	L	0.53780	1.695	0.24110	N	0.995842	P	0.51653	0.947	P	0.57720	0.826	T	0.10132	-1.0643	10	0.15499	T	0.54	.	7.5865	0.27995	0.0:0.6977:0.1392:0.1632	.	572	P02549	SPTA1_HUMAN	T	572	ENSP00000357130:A572T;ENSP00000357129:A572T	ENSP00000357129:A572T	A	-	1	0	SPTA1	156905941	0.991000	0.36638	0.812000	0.32479	0.028000	0.11728	2.169000	0.42434	0.727000	0.32360	-0.797000	0.03246	GCC		0.453	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158639317	C	T	158639317	3	4	111	1	0	0	0	0	1	0	0	0	15155	710	25	3	5701	3	SPTA1	1	158639317	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	203524	158639317	90611304	70	29204										
B4GALT3	8703	hgsc.bcm.edu	37	chr1	161145720	161145720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtgagaatagtcaaatgtcGgtccctgatctcggccaaat	11	9	2	2	rs367870203		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:161145720G>A	ENST00000319769.5	-	3	353	c.131C>T	c.(130-132)cCg>cTg	p.P44L	B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|B4GALT3_ENST00000367998.1_Missense_Mutation_p.P44L	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	44					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	GTCAAATGTCGGTCCCTGATC	0.592																																																0			1											95	96	96					1																	161145720		2203	4300	6503	159412344	SO:0001583	missense	8703			BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"Beta 4-glycosyltransferases"	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.131C>T	1.37:g.161145720G>A	ENSP00000320965:p.Pro44Leu		159412344	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.336597	0.81801	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000541560;ENST00000310413;ENST00000367998;ENST00000367997	T;T	0.51071	0.72;0.72	5.37	5.37	0.77165	.	0.059722	0.64402	D	0.000002	T	0.35770	0.0943	L	0.32530	0.975	0.80722	D	1	D;D	0.58268	0.982;0.982	P;P	0.47299	0.462;0.543	T	0.24584	-1.0156	10	0.56958	D	0.05	-18.4129	17.888	0.88863	0.0:0.0:1.0:0.0	.	44;44	B3KPV4;O60512	.;B4GT3_HUMAN	L	44;21;44;44;44;44	ENSP00000320965:P44L;ENSP00000356977:P44L	ENSP00000308551:P44L	P	-	2	0	B4GALT3	159412344	1.000000	0.71417	0.974000	0.42286	0.476000	0.33039	8.884000	0.92432	2.511000	0.84671	0.467000	0.42956	CCG		0.592	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779		A	161145720	G	A	161145720	3	1	111	1	0	0	0	0	1	0	0	0	1273	1116	39	1	1074	1	B4GALT3	1	161145720	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2506403	161145720	88104901	71	29205										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161954715	161954715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggccccttcattccgcccAtatgtgttctgggtggtcgg	12	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:161954715A>G	ENST00000294794.3	-	7	1953	c.1530T>C	c.(1528-1530)taT>taC	p.Y510Y	OLFML2B_ENST00000367940.2_Silent_p.Y511Y|OLFML2B_ENST00000367938.1_5'UTR	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	510	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CATTCCGCCCATATGTGTTCT	0.547																																																0			1											190	168	176					1																	161954715		2203	4300	6503	160221339	SO:0001819	synonymous_variant	25903			BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.1530T>C	1.37:g.161954715A>G			160221339	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	37	CCDS1236.1																																																																																				0.547	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		G	161954715	A	G	161954715	2	3	111	1	0	0	0	0	0	0	0	1	10889	224	8	4		4	OLFML2B	1	161954715	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	808995	161954715	87295906	72	29206										
NUF2	83540	hgsc.bcm.edu	37	chr1	163310215	163310215	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcagagaaaaccaagcgttTggtaaacatcttttcttttc	6	8	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:163310215T>C	ENST00000271452.3	+	9	947	c.668T>C	c.(667-669)tTg>tCg	p.L223S	NUF2_ENST00000524800.1_Splice_Site_p.L223S|NUF2_ENST00000367900.3_Splice_Site_p.L223S	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	223	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					ACCAAGCGTTTGGTAAACATC	0.333																																																0			1											99	107	104					1																	163310215		2203	4300	6503	161576839	SO:0001630	splice_region_variant	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.669+1T>C	1.37:g.163310215T>C			161576839	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.156354	0.38119	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.37058	1.22;1.24;1.24	5.07	5.07	0.68467	.	0.073983	0.56097	D	0.000028	T	0.37732	0.1014	L	0.55481	1.735	0.47778	D	0.999514	D;D	0.76494	0.999;0.999	P;P	0.59643	0.861;0.861	T	0.40534	-0.9558	9	0.54805	T	0.06	-2.1981	11.141	0.48402	0.0:0.0:0.0:1.0	.	223;223	E9PQC4;Q9BZD4	.;NUF2_HUMAN	S	223	ENSP00000436888:L223S;ENSP00000356875:L223S;ENSP00000271452:L223S	ENSP00000271452:L223S	L	+	2	0	NUF2	161576839	1.000000	0.71417	0.995000	0.50966	0.922000	0.55478	4.005000	0.57075	2.124000	0.65301	0.533000	0.62120	TTG		0.333	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	Missense_Mutation	C	163310215	T	C	163310215	5	2	111	1	0	0	0	0	0	0	1	0	10778	1826	63	4	698	4	NUF2	1	163310215	Splice_Site	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1355500	163310215	85940406	73	29207										
GPR161	23432	hgsc.bcm.edu	37	chr1	168065765	168065765	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctgtgatcctgttggaaatGctgaagagcctggaagtcct	12	9	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:168065765G>A	ENST00000367838.1	-	5	1393	c.1080C>T	c.(1078-1080)agC>agT	p.S360S	GPR161_ENST00000539777.1_Silent_p.S282S|GPR161_ENST00000546300.1_Silent_p.S246S|GPR161_ENST00000367835.1_Silent_p.S360S|GPR161_ENST00000271357.5_Silent_p.S360S|GPR161_ENST00000361697.2_Silent_p.S360S|GPR161_ENST00000367836.1_Silent_p.S228S|GPR161_ENST00000537209.1_Silent_p.S380S	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	360					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					TGTTGGAAATGCTGAAGAGCC	0.517																																																0			1											78	77	77					1																	168065765		2203	4300	6503	166332389	SO:0001819	synonymous_variant	23432			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1080C>T	1.37:g.168065765G>A			166332389	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Silent	SNP	ENST00000367838.1	37	CCDS1268.1																																																																																				0.517	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		A	168065765	G	A	168065765	2	1	111	1	0	0	0	0	0	0	0	1	6685	1310	46	3		3	GPR161	1	168065765	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4755550	168065765	81184856	74	29208										
GPR161	23432	hgsc.bcm.edu	37	chr1	168065808	168065808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtcgttgcacaaatggttccCgataataccggtccccaaag	9	12	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:168065808C>T	ENST00000367838.1	-	5	1350	c.1037G>A	c.(1036-1038)cGg>cAg	p.R346Q	GPR161_ENST00000539777.1_Missense_Mutation_p.R268Q|GPR161_ENST00000546300.1_Missense_Mutation_p.R232Q|GPR161_ENST00000367835.1_Missense_Mutation_p.R346Q|GPR161_ENST00000271357.5_Missense_Mutation_p.R346Q|GPR161_ENST00000361697.2_Missense_Mutation_p.R346Q|GPR161_ENST00000367836.1_Missense_Mutation_p.R214Q|GPR161_ENST00000537209.1_Missense_Mutation_p.R366Q	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	346					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					AAATGGTTCCCGATAATACCG	0.527																																																0			1											88	86	86					1																	168065808		2203	4300	6503	166332432	SO:0001583	missense	23432			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1037G>A	1.37:g.168065808C>T	ENSP00000356812:p.Arg346Gln		166332432	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.499326	0.85069	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.61	4.7	0.59300	.	0.053503	0.64402	D	0.000001	T	0.47600	0.1454	M	0.63843	1.955	0.40801	D	0.983346	D;D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;0.999;0.921	D;D;D;D;P;B	0.83275	0.979;0.992;0.996;0.944;0.889;0.211	T	0.56836	-0.7913	9	0.87932	D	0	-24.6889	14.2282	0.65873	0.0:0.9275:0.0:0.0725	.	366;232;268;366;346;346	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8-2;Q8N6U8	.;.;.;.;.;GP161_HUMAN	Q	346;346;214;346;232;268;366;346	ENSP00000356812:R346Q;ENSP00000271357:R346Q;ENSP00000356810:R214Q;ENSP00000356809:R346Q;ENSP00000444348:R232Q;ENSP00000437576:R268Q;ENSP00000441039:R366Q;ENSP00000355194:R346Q	ENSP00000271357:R346Q	R	-	2	0	GPR161	166332432	1.000000	0.71417	0.999000	0.59377	0.527000	0.34593	7.637000	0.83313	1.500000	0.48636	0.655000	0.94253	CGG		0.527	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		T	168065808	C	T	168065808	3	4	111	1	0	0	0	0	1	0	0	0	6685	652	23	1	568	1	GPR161	1	168065808	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	43	168065808	81184813	75	29209										
SELL	6402	hgsc.bcm.edu	37	chr1	169672532	169672532	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagctggccaggggatggctAcagttcatgatccccaaatc	11	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:169672532A>G	ENST00000236147.4	-	6	1015	c.855T>C	c.(853-855)tgT>tgC	p.C285C	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	272	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					GGGGATGGCTACAGTTCATGA	0.398																																																0			1											48	45	46					1																	169672532		1913	4144	6057	167939156	SO:0001819	synonymous_variant	6402			M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.855T>C	1.37:g.169672532A>G			167939156	B2R6Q8|P15023|Q9UJ43	Silent	SNP	ENST00000236147.4	37	CCDS53427.1																																																																																				0.398	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		G	169672532	A	G	169672532	2	3	111	1	0	0	0	0	0	0	0	1	14053	389	14	4		4	SELL	1	169672532	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1606724	169672532	79578089	76	29210										
MYOC	4653	hgsc.bcm.edu	37	chr1	171621330	171621330	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcggaggaggttgctgtagGcagtctccaactctctggtt	13	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:171621330G>A	ENST00000037502.6	-	1	493	c.422C>T	c.(421-423)gCc>gTc	p.A141V		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	141					bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GTTGCTGTAGGCAGTCTCCAA	0.597																																																0			1											109	118	115					1																	171621330		2203	4300	6503	169887953	SO:0001583	missense	4653			BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.422C>T	1.37:g.171621330G>A	ENSP00000037502:p.Ala141Val		169887953	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	G	9.519	1.107729	0.20714	.	.	ENSG00000034971	ENST00000037502;ENST00000536591;ENST00000537133	D	0.83163	-1.69	5.55	2.25	0.28309	.	0.264920	0.42682	D	0.000663	T	0.64283	0.2584	M	0.64997	1.995	0.27215	N	0.95981	B;B	0.14805	0.004;0.011	B;B	0.15484	0.007;0.013	T	0.61053	-0.7140	10	0.52906	T	0.07	.	7.351	0.26691	0.0867:0.0:0.6057:0.3075	.	83;141	B4DV44;Q99972	.;MYOC_HUMAN	V	141;74;141	ENSP00000037502:A141V	ENSP00000037502:A141V	A	-	2	0	MYOC	169887953	0.989000	0.36119	0.588000	0.28705	0.443000	0.32047	1.393000	0.34497	0.673000	0.31224	0.655000	0.94253	GCC		0.597	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		A	171621330	G	A	171621330	3	1	111	1	0	0	0	0	1	0	0	0	10116	1203	42	3	1104	3	MYOC	1	171621330	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1948798	171621330	77629291	77	29211										
CEP350	9857	hgsc.bcm.edu	37	chr1	180010311	180010311	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaagagacttggccctcttGaaactaaaggctgaacaaga	10	8	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:180010311G>A	ENST00000367607.3	+	18	4567	c.4149G>A	c.(4147-4149)ttG>ttA	p.L1383L		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1383					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TGGCCCTCTTGAAACTAAAGG	0.398																																																0			1											38	36	37					1																	180010311		2203	4300	6503	178276934	SO:0001819	synonymous_variant	9857			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4149G>A	1.37:g.180010311G>A			178276934	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1																																																																																				0.398	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	180010311	G	A	180010311	2	1	111	1	0	0	0	0	0	0	0	1	3260	1281	45	3		3	CEP350	1	180010311	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8388981	180010311	69240310	78	29212										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190250770	190250770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgctgaagggtaggtcgaCgtcccaaaagtcttatgttg	12	7	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:190250770C>T	ENST00000367462.3	-	3	578	c.347G>A	c.(346-348)cGt>cAt	p.R116H	RP11-547I7.1_ENST00000452178.1_RNA|BRINP3_ENST00000534846.1_Intron	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	116	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											GGTAGGTCGACGTCCCAAAAG	0.448																																																0			1											94	89	91					1																	190250770		2203	4300	6503	188517393	SO:0001583	missense	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.347G>A	1.37:g.190250770C>T	ENSP00000356432:p.Arg116His		188517393	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	C	34	5.299071	0.95574	.	.	ENSG00000162670	ENST00000367462	D	0.84298	-1.83	5.67	5.67	0.87782	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.85682	D	0.000000	D	0.91835	0.7416	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.92329	0.5872	10	0.87932	D	0	.	17.2529	0.87047	0.0:1.0:0.0:0.0	.	116	Q76B58	FAM5C_HUMAN	H	116	ENSP00000356432:R116H	ENSP00000356432:R116H	R	-	2	0	FAM5C	188517393	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.794000	0.85869	2.677000	0.91161	0.585000	0.79938	CGT		0.448	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190250770	C	T	190250770	3	4	111	1	0	0	0	0	1	0	0	0	5613	536	19	1	1977	1	FAM5C	1	190250770	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10240459	190250770	58999851	79	29213										
CDC73	79577	hgsc.bcm.edu	37	chr1	193094275	193094275	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggccaacccagagagtactaCacattggattccattttatt	7	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:193094275C>T	ENST00000367435.3	+	2	349	c.165C>T	c.(163-165)taC>taT	p.Y55Y		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	55					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.Y55fs*1(2)|p.Y55*(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						GAGAGTACTACACATTGGATT	0.358																																																3	Deletion - Frameshift(2)|Substitution - Nonsense(1)	parathyroid(3)	1	GRCh37	CM023088	CDC73	M							147	147	147					1																	193094275		2203	4300	6503	191360898	SO:0001819	synonymous_variant	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.165C>T	1.37:g.193094275C>T			191360898	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Silent	SNP	ENST00000367435.3	37	CCDS1382.1																																																																																				0.358	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		T	193094275	C	T	193094275	2	4	111	1	0	0	0	0	0	0	0	1	3091	489	17	3		3	CDC73	1	193094275	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2843505	193094275	56156346	80	29214										
CFH	3075	hgsc.bcm.edu	37	chr1	196696040	196696040	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatcaattacgtgtattcatGgagtatggacccaacttccc	8	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:196696040G>A	ENST00000367429.4	+	14	2446	c.2206G>A	c.(2206-2208)Gga>Aga	p.G736R		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	736	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						GTGTATTCATGGAGTATGGAC	0.353																																																0			1											102	101	101					1																	196696040		2203	4299	6502	194962663	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2206G>A	1.37:g.196696040G>A	ENSP00000356399:p.Gly736Arg		194962663	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.791785	0.50102	.	.	ENSG00000000971	ENST00000367429	T	0.72615	-0.67	5.6	5.6	0.85130	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.86715	0.5999	M	0.89658	3.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89020	0.3434	9	0.87932	D	0	.	15.1081	0.72336	0.0:0.0:1.0:0.0	.	736	P08603	CFAH_HUMAN	R	736	ENSP00000356399:G736R	ENSP00000356399:G736R	G	+	1	0	CFH	194962663	0.997000	0.39634	0.649000	0.29536	0.007000	0.05969	3.304000	0.51866	2.637000	0.89404	0.655000	0.94253	GGA		0.353	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		A	196696040	G	A	196696040	3	1	111	1	0	0	0	0	1	0	0	0	3289	1349	47	3	2278	3	CFH	1	196696040	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3601765	196696040	52554581	81	29215										
LHX9	56956	hgsc.bcm.edu	37	chr1	197887102	197887102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaggcccgtctggccaaagGcgcccagctcaacggccgcg	14	16	2	1	rs577856015		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:197887102G>A	ENST00000367387.4	+	1	574	c.149G>A	c.(148-150)gGc>gAc	p.G50D	LHX9_ENST00000606127.1_3'UTR|LHX9_ENST00000337020.2_Missense_Mutation_p.G50D|LHX9_ENST00000367390.3_Missense_Mutation_p.G41D|LHX9_ENST00000561173.1_Missense_Mutation_p.G56D|LHX9_ENST00000367391.1_Missense_Mutation_p.G41D	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	50					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CTGGCCAAAGGCGCCCAGCTC	0.672													G|||	1	0.000199681	8e-04	0	5008	,	,		13943	0		0	False		,,,				2504	0															0			1											61	65	63					1																	197887102		2203	4300	6503	196153725	SO:0001583	missense	56956			AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.149G>A	1.37:g.197887102G>A	ENSP00000356357:p.Gly50Asp		196153725	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	ENST00000367387.4	37	CCDS1393.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432614	0.62844	.	.	ENSG00000143355	ENST00000367391;ENST00000367390;ENST00000367388;ENST00000337020;ENST00000367387	T;D;T;D	0.87729	0.67;-2.29;0.59;-2.29	5.06	5.06	0.68205	.	0.107874	0.64402	D	0.000005	D	0.85915	0.5808	L	0.36672	1.1	0.50313	D	0.999868	B;B;B	0.25486	0.078;0.068;0.127	B;B;B	0.37650	0.066;0.139;0.255	D	0.83707	0.0185	10	0.49607	T	0.09	.	17.7666	0.88480	0.0:0.0:1.0:0.0	.	50;41;41	Q9NQ69;Q9NQ69-3;Q9NQ69-2	LHX9_HUMAN;.;.	D	41;41;93;50;50	ENSP00000356361:G41D;ENSP00000356360:G41D;ENSP00000337969:G50D;ENSP00000356357:G50D	ENSP00000337969:G50D	G	+	2	0	LHX9	196153725	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.764000	0.68826	2.506000	0.84524	0.655000	0.94253	GGC		0.672	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		A	197887102	G	A	197887102	3	1	111	1	0	0	0	0	1	0	0	0	8800	1203	42	3	183	3	LHX9	1	197887102	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1191062	197887102	51363519	82	29216										
ZNF281	23528	hgsc.bcm.edu	37	chr1	200376876	200376876	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catttgaaggtgtttgggtgCctgggctcaaattttcttct	11	7	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:200376876C>T	ENST00000294740.3	-	2	2082	c.1958G>A	c.(1957-1959)gGc>gAc	p.G653D	ZNF281_ENST00000367352.3_Missense_Mutation_p.G617D|ZNF281_ENST00000367353.1_Missense_Mutation_p.G653D	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	653					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						TGTTTGGGTGCCTGGGCTCAA	0.398																																																0			1											120	125	124					1																	200376876		2203	4300	6503	198643499	SO:0001583	missense	23528			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.1958G>A	1.37:g.200376876C>T	ENSP00000294740:p.Gly653Asp		198643499	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	37	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	C	7.887	0.731499	0.15507	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.39997	1.05;1.05;1.05	5.54	5.54	0.83059	.	0.140571	0.43579	D	0.000546	T	0.27349	0.0671	N	0.19112	0.55	0.32074	N	0.594093	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.19976	-1.0289	10	0.39692	T	0.17	-14.3522	9.7279	0.40344	0.0:0.8409:0.0:0.1591	.	617;653	A6NF48;Q9Y2X9	.;ZN281_HUMAN	D	653;653;617;358	ENSP00000294740:G653D;ENSP00000356322:G653D;ENSP00000356321:G617D	ENSP00000294740:G653D	G	-	2	0	ZNF281	198643499	0.985000	0.35326	1.000000	0.80357	1.000000	0.99986	1.411000	0.34702	2.597000	0.87782	0.655000	0.94253	GGC		0.398	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		T	200376876	C	T	200376876	3	4	111	1	0	0	0	0	1	0	0	0	17857	739	26	3	733	3	ZNF281	1	200376876	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2489774	200376876	48873745	83	29217										
DDX59	83479	hgsc.bcm.edu	37	chr1	200633156	200633156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaattctttagcttgtctcTctatctgaatggctaactct	5	10	6	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:200633156T>C	ENST00000331314.6	-	3	1076	c.863A>G	c.(862-864)gAg>gGg	p.E288G	DDX59_ENST00000367348.3_Missense_Mutation_p.E288G|DDX59_ENST00000447706.2_Missense_Mutation_p.E288G	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	288	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						AGCTTGTCTCTCTATCTGAAT	0.438																																																0			1											143	126	132					1																	200633156		2203	4300	6503	198899779	SO:0001583	missense	83479			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.863A>G	1.37:g.200633156T>C	ENSP00000330460:p.Glu288Gly		198899779	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	37	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	T	31	5.076176	0.94000	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314	T;T;T	0.14893	2.47;2.47;2.47	5.75	5.75	0.90469	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.35740	0.0942	L	0.42581	1.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.05468	-1.0883	10	0.72032	D	0.01	-37.1631	16.0519	0.80769	0.0:0.0:0.0:1.0	.	288;288	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	G	288	ENSP00000394367:E288G;ENSP00000356317:E288G;ENSP00000330460:E288G	ENSP00000330460:E288G	E	-	2	0	DDX59	198899779	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.752000	0.85141	2.196000	0.70406	0.533000	0.62120	GAG		0.438	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		C	200633156	T	C	200633156	3	2	111	1	0	0	0	0	1	0	0	0	4382	1551	54	4	1020	4	DDX59	1	200633156	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	256280	200633156	48617465	84	29218										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201046242	201046242	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggatgccaccaggttgctcaGcgacgtccaatatctgaagg	12	11	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:201046242G>A	ENST00000362061.3	-	12	1859	c.1633C>T	c.(1633-1635)Ctg>Ttg	p.L545L	CACNA1S_ENST00000367338.3_Silent_p.L545L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	545					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGGTTGCTCAGCGACGTCCAA	0.597																																																0			1											84	78	80					1																	201046242		2203	4300	6503	199312865	SO:0001819	synonymous_variant	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1633C>T	1.37:g.201046242G>A			199312865	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																				0.597	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201046242	G	A	201046242	2	1	111	1	0	0	0	0	0	0	0	1	2553	962	34	3		3	CACNA1S	1	201046242	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	413086	201046242	48204379	85	29219										
LGR6	59352	hgsc.bcm.edu	37	chr1	202287206	202287206	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtgttcgctggcgggcctgTccccctgcccccggtcaagt					rs788795|rs113146160	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:202287206delT	ENST00000367278.3	+	18	1864	c.1775delT	c.(1774-1776)gtcfs	p.V592fs	LGR6_ENST00000255432.7_Frame_Shift_Del_p.V540fs|LGR6_ENST00000439764.2_Frame_Shift_Del_p.V453fs	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	592			V -> A (in dbSNP:rs788795). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.5}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						GGCGGGCCTGTCCCCCTGCCC	0.622																																																0			1											87	75	79					1																	202287206		2203	4300	6503	200553829	SO:0001589	frameshift_variant	59352			AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1775delT	1.37:g.202287206delT	ENSP00000356247:p.Val592fs		200553829	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Frame_Shift_Del	DEL	ENST00000367278.3	37	CCDS30971.1																																																																																				0.622	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		-	202287206	T	-	202287206	7	5	111	1	0	1	0	1	0	0	0	0	8781	1667	58	0	1992	0	LGR6	1	202287206	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	1240964	202287206	46963415	86	29220										
KLHL12	59349	hgsc.bcm.edu	37	chr1	202880212	202880212	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attacatctgtgatatacctGggggttagtaggggcatccg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:202880212delG	ENST00000367261.3	-	5	905	c.687delC	c.(685-687)cccfs	p.P229fs	KLHL12_ENST00000435533.3_Frame_Shift_Del_p.P267fs|KLHL12_ENST00000367259.1_5'Flank	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	229	BACK.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			TGATATACCTGGGGGTTAGTA	0.453																																																0			1											153	149	150					1																	202880212		2203	4300	6503	201146835	SO:0001589	frameshift_variant	59349			AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"Kelch-like", "BTB/POZ domain containing"	19360	protein-coding gene	gene with protein product		614522	"kelch-like 12 (Drosophila)"			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.687delC	1.37:g.202880212delG	ENSP00000356230:p.Pro229fs		201146835	A6NEN8|B7Z7B8|Q9HBX5	Frame_Shift_Del	DEL	ENST00000367261.3	37	CCDS1429.1																																																																																				0.453	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633		-	202880212	G	-	202880212	7	5	111	1	0	1	0	1	0	0	0	0	8389	1335	47	0	1051	0	KLHL12	1	202880212	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	593006	202880212	46370409	87	29221										
LAX1	54900	hgsc.bcm.edu	37	chr1	203743525	203743525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagcagcagatcccagtggaAgccagcagcaggctgagaaa	13	11	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:203743525A>G	ENST00000442561.2	+	5	1303	c.913A>G	c.(913-915)Agc>Ggc	p.S305G	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Missense_Mutation_p.S289G	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	305					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)	p.S305C(1)		central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TCCCAGTGGAAGCCAGCAGCA	0.522																																																1	Substitution - Missense(1)	central_nervous_system(1)	1											83	78	79					1																	203743525		2203	4300	6503	202010148	SO:0001583	missense	54900			AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"LAT-like membrane associated protein", "linker for activation of x cells"					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.913A>G	1.37:g.203743525A>G	ENSP00000406970:p.Ser305Gly		202010148	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	37	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	A	10.69	1.420687	0.25639	.	.	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	4.79	3.63	0.41609	.	1.221100	0.05327	N	0.527691	T	0.35422	0.0931	L	0.34521	1.04	0.09310	N	1	B;B	0.25809	0.073;0.135	B;B	0.27887	0.084;0.045	T	0.29971	-0.9994	9	0.40728	T	0.16	-3.6849	7.6659	0.28430	0.812:0.0:0.0:0.188	.	289;305	B7Z744;Q8IWV1	.;LAX1_HUMAN	G	305;289	.	ENSP00000356186:S289G	S	+	1	0	LAX1	202010148	0.001000	0.12720	0.017000	0.16124	0.286000	0.27126	1.104000	0.31074	0.920000	0.36970	0.533000	0.62120	AGC		0.522	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773		G	203743525	A	G	203743525	3	3	111	1	0	0	0	0	1	0	0	0	8670	72	3	4	976	4	LAX1	1	203743525	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	863313	203743525	45507096	88	29222										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204419065	204419065	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctctgaggagctccccggtGgggggatgggcagagcatag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:204419065delG	ENST00000367187.3	-	14	2703	c.2147delC	c.(2146-2148)ccafs	p.P717fs	PIK3C2B_ENST00000424712.2_Frame_Shift_Del_p.P717fs	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	717	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	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)			GCTCCCCGGTGGGGGGATGGG	0.617																																																0			1											25	28	27					1																	204419065		2203	4300	6503	202685688	SO:0001589	frameshift_variant	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2147delC	1.37:g.204419065delG	ENSP00000356155:p.Pro717fs		202685688	O95666|Q5SW99	Frame_Shift_Del	DEL	ENST00000367187.3	37	CCDS1446.1																																																																																				0.617	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		-	204419065	G	-	204419065	7	5	111	1	0	1	0	1	0	0	0	0	11941	1348	47	0	2841	0	PIK3C2B	1	204419065	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	675540	204419065	44831556	89	29223										
FCAMR	83953	hgsc.bcm.edu	37	chr1	207134158	207134158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccctctatgtcctcccttgGcctatcagccttggtagttg	8	15	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:207134158G>A	ENST00000324852.4	-	6	1537	c.1063C>T	c.(1063-1065)Cca>Tca	p.P355S	FCAMR_ENST00000486178.1_5'UTR|FCAMR_ENST00000400962.3_Intron|FCAMR_ENST00000450945.2_Intron	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	310					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TCCTCCCTTGGCCTATCAGCC	0.542																																					Ovarian(199;1883 2142 16966 44409 45154)											0			1											224	188	199					1																	207134158		692	1591	2283	205200781	SO:0001583	missense	83953			AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.1063C>T	1.37:g.207134158G>A	ENSP00000316491:p.Pro355Ser		205200781	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.786976	0.49997	.	.	ENSG00000162897	ENST00000324852;ENST00000367087	T	0.05649	3.41	5.09	2.12	0.27331	.	0.659026	0.14179	N	0.336145	T	0.08223	0.0205	L	0.48642	1.525	0.09310	N	1	P;P	0.49185	0.92;0.689	P;B	0.46685	0.524;0.286	T	0.22765	-1.0207	10	0.62326	D	0.03	-1.6253	5.6627	0.17678	0.1875:0.1667:0.6458:0.0	.	330;310	D2KTA8;Q8WWV6	.;FCAMR_HUMAN	S	355;331	ENSP00000316491:P355S	ENSP00000316491:P355S	P	-	1	0	FCAMR	205200781	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.640000	0.24705	0.637000	0.30526	0.561000	0.74099	CCA		0.542	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		A	207134158	G	A	207134158	3	1	111	1	0	0	0	0	1	0	0	0	5791	1203	42	3	682	3	FCAMR	1	207134158	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2715093	207134158	42116463	90	29224										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208218009	208218009	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccgccggccgcgatgctgaCgatggctggcagggtcagca	17	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:208218009C>T	ENST00000367033.3	-	20	4475	c.3718G>A	c.(3718-3720)Gtc>Atc	p.V1240I		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1240					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GCGATGCTGACGATGGCTGGC	0.572																																																0			1											72	67	69					1																	208218009		2203	4300	6503	206284632	SO:0001583	missense	5362			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.3718G>A	1.37:g.208218009C>T	ENSP00000356000:p.Val1240Ile		206284632	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.563759	0.27915	.	.	ENSG00000076356	ENST00000367033	T	0.00808	5.67	4.95	0.849	0.18972	.	0.180161	0.47852	N	0.000203	T	0.00524	0.0017	N	0.04297	-0.235	0.49483	D	0.999793	B	0.26081	0.141	B	0.16722	0.016	T	0.62407	-0.6861	10	0.13470	T	0.59	.	9.5171	0.39113	0.0:0.7006:0.0:0.2994	.	1240	O75051	PLXA2_HUMAN	I	1240	ENSP00000356000:V1240I	ENSP00000356000:V1240I	V	-	1	0	PLXNA2	206284632	0.990000	0.36364	0.998000	0.56505	0.988000	0.76386	2.372000	0.44257	0.132000	0.18615	0.467000	0.42956	GTC		0.572	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208218009	C	T	208218009	3	4	111	1	0	0	0	0	1	0	0	0	12151	536	19	1	2018	1	PLXNA2	1	208218009	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1083851	208218009	41032612	91	29225										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209806041	209806041	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgggacacagcatagtaggCgctgggagggtggtagcccc	17	10	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:209806041C>T	ENST00000356082.4	-	8	843	c.709G>A	c.(709-711)Gcc>Acc	p.A237T	LAMB3_ENST00000391911.1_Missense_Mutation_p.A237T|LAMB3_ENST00000367030.3_Missense_Mutation_p.A237T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	237	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCATAGTAGGCGCTGGGAGGG	0.627																																																0			1											45	50	48					1																	209806041		2203	4300	6503	207872664	SO:0001583	missense	3914			D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.709G>A	1.37:g.209806041C>T	ENSP00000348384:p.Ala237Thr		207872664	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	1.441	-0.567546	0.03910	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.37058	1.22;1.22;1.22	4.76	2.81	0.32909	Laminin, N-terminal (2);	0.732438	0.13398	N	0.390865	T	0.21468	0.0517	L	0.38175	1.15	0.22562	N	0.998985	B;B	0.19583	0.013;0.037	B;B	0.15484	0.013;0.012	T	0.31530	-0.9940	10	0.07813	T	0.8	.	4.3522	0.11160	0.1649:0.5875:0.0:0.2476	.	237;237	B4DL55;Q13751	.;LAMB3_HUMAN	T	237	ENSP00000375778:A237T;ENSP00000348384:A237T;ENSP00000355997:A237T	ENSP00000348384:A237T	A	-	1	0	LAMB3	207872664	0.963000	0.33076	0.982000	0.44146	0.721000	0.41392	1.531000	0.36018	0.572000	0.29383	0.456000	0.33151	GCC		0.627	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209806041	C	T	209806041	3	4	111	1	0	0	0	0	1	0	0	0	8634	768	27	1	2873	1	LAMB3	1	209806041	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1588032	209806041	39444580	92	29226										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212550912	212550912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagccacctacctcctgccGgaactccactgcttcccgcc	7	20	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:212550912G>A	ENST00000261455.4	-	6	912	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W	TMEM206_ENST00000535273.1_Missense_Mutation_p.R320W	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	259						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		ACCTCCTGCCGGAACTCCACT	0.552																																																0			1											135	125	128					1																	212550912		2203	4300	6503	210617535	SO:0001583	missense	55248			AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.775C>T	1.37:g.212550912G>A	ENSP00000261455:p.Arg259Trp		210617535	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004348	0.74932	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.83	4.9	0.64082	.	0.050661	0.85682	D	0.000000	T	0.66327	0.2778	L	0.32530	0.975	0.50171	D	0.99985	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.95	T	0.69921	-0.5014	9	0.87932	D	0	-20.036	13.8221	0.63329	0.0:0.0:0.6055:0.3945	.	320;259	B7Z4D6;Q9H813	.;TM206_HUMAN	W	259;320	.	ENSP00000261455:R259W	R	-	1	2	TMEM206	210617535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.719000	0.54926	1.425000	0.47237	0.655000	0.94253	CGG		0.552	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		A	212550912	G	A	212550912	3	1	111	1	0	0	0	0	1	0	0	0	16170	1115	39	1	289	1	TMEM206	1	212550912	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2744871	212550912	36699709	93	29227										
FAM71A	149647	hgsc.bcm.edu	37	chr1	212799707	212799707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cataaaggtgtcagccacacGcccatctcaaaggagtccag	9	13	2	0	rs376011969		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:212799707G>A	ENST00000294829.3	+	1	1919	c.1488G>A	c.(1486-1488)acG>acA	p.T496T	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	496						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		TCAGCCACACGCCCATCTCAA	0.557																																																0			1						G		0,4406		0,0,2203	85	77	80		1488	-8.5	0	1		80	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM71A	NM_153606.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		496/595	212799707	2,13004	2203	4300	6503	210866330	SO:0001819	synonymous_variant	149647				CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1488G>A	1.37:g.212799707G>A			210866330	Q5VTZ1	Silent	SNP	ENST00000294829.3	37	CCDS1507.1																																																																																				0.557	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		A	212799707	G	A	212799707	2	1	111	1	0	0	0	0	0	0	0	1	5626	1074	38	1		1	FAM71A	1	212799707	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	248795	212799707	36450914	94	29228										
PROX1	5629	hgsc.bcm.edu	37	chr1	214178556	214178556	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaaaaaagcaaagctcatgTttttttatacccgttatccc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:214178556delT	ENST00000366958.4	+	3	2382	c.1774delT	c.(1774-1776)tttfs	p.F593fs	PROX1_ENST00000261454.4_Frame_Shift_Del_p.F593fs|PROX1_ENST00000498508.2_Frame_Shift_Del_p.F593fs|PROX1_ENST00000435016.1_Frame_Shift_Del_p.F593fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	593					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		AAAGCTCATGTTTTTTTATAC	0.383																																																0			1											120	120	120					1																	214178556		2203	4300	6503	212245179	SO:0001589	frameshift_variant	5629			U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.1774delT	1.37:g.214178556delT	ENSP00000355925:p.Phe593fs		212245179	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Del	DEL	ENST00000366958.4	37	CCDS31021.1																																																																																				0.383	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		-	214178556	T	-	214178556	7	5	111	1	0	1	0	1	0	0	0	0	12594	1725	60	0	1780	0	PROX1	1	214178556	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	1378849	214178556	35072065	95	29229										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222717148	222717148	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacaccactcctacctgctcGgcaacaaagaagcgatgggt	9	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:222717148G>A	ENST00000343410.6	-	2	763	c.705C>T	c.(703-705)gcC>gcT	p.A235A		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	235					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CTACCTGCTCGGCAACAAAGA	0.622																																																0			1											72	65	68					1																	222717148		2203	4300	6503	220783771	SO:0001819	synonymous_variant	79802			BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.705C>T	1.37:g.222717148G>A			220783771	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																				0.622	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		A	222717148	G	A	222717148	2	1	111	1	0	0	0	0	0	0	0	1	7115	1103	39	1		1	HHIPL2	1	222717148	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8538592	222717148	26533473	96	29230										
WDR26	80232	hgsc.bcm.edu	37	chr1	224612245	224612245	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagaacatgaatgcgctctgTattgtatttcagcggcgtca	10	8	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:224612245T>C	ENST00000414423.2	-	4	932	c.739A>G	c.(739-741)Aca>Gca	p.T247A	WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000295024.6_Missense_Mutation_p.T100A	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	247						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		ATGCGCTCTGTATTGTATTTC	0.423																																																0			1											111	99	103					1																	224612245		2203	4300	6503	222678868	SO:0001583	missense	80232			AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.739A>G	1.37:g.224612245T>C	ENSP00000408108:p.Thr247Ala		222678868	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	37	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	T	26.4	4.733008	0.89482	.	.	ENSG00000162923	ENST00000414423;ENST00000295024;ENST00000445239	T;T	0.69561	-0.41;-0.09	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.71213	0.3313	M	0.79805	2.47	0.80722	D	1	P;P	0.46220	0.874;0.724	P;B	0.45343	0.477;0.284	T	0.70382	-0.4887	10	0.12430	T	0.62	.	16.3798	0.83452	0.0:0.0:0.0:1.0	.	247;231	Q9H7D7;Q9H7D7-2	WDR26_HUMAN;.	A	247;100;100	ENSP00000408108:T247A;ENSP00000295024:T100A	ENSP00000295024:T100A	T	-	1	0	WDR26	222678868	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.271000	0.75665	0.533000	0.62120	ACA		0.423	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		C	224612245	T	C	224612245	3	2	111	1	0	0	0	0	1	0	0	0	17323	1638	57	4	1290	4	WDR26	1	224612245	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1895097	224612245	24638376	97	29231										
PARP1	142	hgsc.bcm.edu	37	chr1	226578195	226578195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaagcccttgagctgactcGcactgtactcgggccggaaa	12	12	0	3	rs202057244		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:226578195G>A	ENST00000366794.5	-	4	676	c.533C>T	c.(532-534)gCg>gTg	p.A178V		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	178					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GAGCTGACTCGCACTGTACTC	0.577								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	1	0.000199681	0	0.0014	5008	,	,		18332	0		0	False		,,,				2504	0															0			1											69	66	67					1																	226578195		2203	4300	6503	224644818	SO:0001583	missense	142			BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.533C>T	1.37:g.226578195G>A	ENSP00000355759:p.Ala178Val		224644818	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959772	0.74016	.	.	ENSG00000143799	ENST00000432338;ENST00000366794	T	0.28255	1.62	5.13	4.22	0.49857	Zinc finger, PARP-type (3);	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	N	0.24115	0.695	0.80722	D	1	P	0.47191	0.891	P	0.47376	0.545	T	0.02877	-1.1099	10	0.39692	T	0.17	.	13.9012	0.63804	0.0738:0.0:0.9262:0.0	.	178	P09874	PARP1_HUMAN	V	178	ENSP00000355759:A178V	ENSP00000355759:A178V	A	-	2	0	PARP1	224644818	1.000000	0.71417	0.469000	0.27204	0.613000	0.37349	5.699000	0.68310	1.277000	0.44412	0.655000	0.94253	GCG		0.577	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		A	226578195	G	A	226578195	3	1	111	1	0	0	0	0	1	0	0	0	11485	1087	38	1	2591	1	PARP1	1	226578195	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1965950	226578195	22672426	98	29232										
JMJD4	65094	hgsc.bcm.edu	37	chr1	227920209	227920209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggggtgcgcaaccaaggaggCcagcacctctgtgatgcgcc	15	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:227920209C>T	ENST00000366758.3	-	6	1275	c.1276G>A	c.(1276-1278)Gcc>Acc	p.A426T	SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|SNAP47_ENST00000480897.1_3'UTR|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Missense_Mutation_p.A410T	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	426										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				ACCAAGGAGGCCAGCACCTCT	0.617																																																0			1											98	80	86					1																	227920209		2203	4300	6503	225986832	SO:0001583	missense	65094			AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1276G>A	1.37:g.227920209C>T	ENSP00000355720:p.Ala426Thr		225986832	Q5TBZ1|Q5TBZ6|Q9H970	Missense_Mutation	SNP	ENST00000366758.3	37	CCDS1561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.571|8.571	0.880005|0.880005	0.17467|0.17467	.|.	.|.	ENSG00000081692|ENSG00000081692	ENST00000366758|ENST00000438896	T|.	0.18016|.	2.24|.	4.75|4.75	2.89|2.89	0.33648|0.33648	.|.	0.245573|.	0.40469|.	N|.	0.001085|.	T|.	0.36524|.	0.0970|.	L|L	0.48362|0.48362	1.52|1.52	0.24619|0.24619	N|N	0.993682|0.993682	B;B|.	0.17038|.	0.02;0.011|.	B;B|.	0.17098|.	0.017;0.008|.	T|.	0.26189|.	-1.0110|.	10|.	0.14656|.	T|.	0.56|.	-11.8711|-11.8711	4.1738|4.1738	0.10343|0.10343	0.1823:0.6261:0.0:0.1915|0.1823:0.6261:0.0:0.1915	.|.	410;426|.	Q9H9V9-2;Q9H9V9|.	.;JMJD4_HUMAN|.	T|X	426|402	ENSP00000355720:A426T|.	ENSP00000355720:A426T|.	A|W	-|-	1|3	0|0	JMJD4|JMJD4	225986832|225986832	0.959000|0.959000	0.32827|0.32827	0.790000|0.790000	0.31976|0.31976	0.198000|0.198000	0.23893|0.23893	1.835000|1.835000	0.39181|0.39181	0.620000|0.620000	0.30215|0.30215	0.462000|0.462000	0.41574|0.41574	GCC|TGG		0.617	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007		T	227920209	C	T	227920209	3	4	111	1	0	0	0	0	1	0	0	0	7972	739	26	3	119	3	JMJD4	1	227920209	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1342014	227920209	21330412	99	29233										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494622	228494622	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcgcctgtgcggttcctcCgagagctgcagcaccaggag	14	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:228494622C>T	ENST00000422127.1	+	45	11991	c.11947C>T	c.(11947-11949)Cga>Tga	p.R3983*	OBSCN_ENST00000284548.11_Nonsense_Mutation_p.R3983*|OBSCN_ENST00000570156.2_Nonsense_Mutation_p.R4940*|OBSCN_ENST00000366707.4_Nonsense_Mutation_p.R1617*|OBSCN_ENST00000366709.4_Nonsense_Mutation_p.R1102*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3983	Ig-like 41.		R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGGTTCCTCCGAGAGCTGCA	0.652																																																0			1											11	13	13					1																	228494622		2076	4198	6274	226561245	SO:0001587	stop_gained	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11947C>T	1.37:g.228494622C>T	ENSP00000409493:p.Arg3983*		226561245	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	62	71.054468	0.99992	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.	.	.	5.75	2.5	0.30297	.	0.744078	0.12001	N	0.508834	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	9.7265	0.40335	0.611:0.2855:0.1035:0.0	.	.	.	.	X	3983;3983;1617;1102	.	ENSP00000284548:R3983X	R	+	1	2	OBSCN	226561245	0.000000	0.05858	0.034000	0.17996	0.011000	0.07611	-1.013000	0.03645	0.730000	0.32425	0.462000	0.41574	CGA		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228494622	C	T	228494622	4	4	111	1	0	0	0	0	0	1	0	0	10843	644	23	1	12121	1	OBSCN	1	228494622	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	574413	228494622	20755999	100	29234										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228528808	228528808	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcccccagggccacttcatcGtgtgggagggtgcaccgggg	16	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:228528808G>A	ENST00000422127.1	+	73	17754	c.17710G>A	c.(17710-17712)Gtg>Atg	p.V5904M	OBSCN_ENST00000284548.11_Missense_Mutation_p.V5904M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V6861M|OBSCN_ENST00000366707.4_Missense_Mutation_p.V3538M|OBSCN_ENST00000366709.4_Missense_Mutation_p.V3023M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5904	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCACTTCATCGTGTGGGAGGG	0.677																																																0			1											17	20	19					1																	228528808		2023	4167	6190	226595431	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17710G>A	1.37:g.228528808G>A	ENSP00000409493:p.Val5904Met		226595431	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.194017|4.194017	0.78902|0.78902	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.21191	.|2.02;2.02;2.02;2.02	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.53883|0.53883	0.1824|0.1824	M|M	0.85462|0.85462	2.755|2.755	0.53005|0.53005	D|D	0.99996|0.99996	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.76575	.|0.974;0.988	T|T	0.59726|0.59726	-0.7400|-0.7400	5|10	.|0.87932	.|D	.|0	.|.	19.5555|19.5555	0.95345|0.95345	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|5904;5904	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	H|M	520|5904;5904;3538;3023	.|ENSP00000284548:V5904M;ENSP00000409493:V5904M;ENSP00000355668:V3538M;ENSP00000355670:V3023M	.|ENSP00000284548:V5904M	R|V	+|+	2|1	0|0	OBSCN|OBSCN	226595431|226595431	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.383000|0.383000	0.30230|0.30230	9.799000|9.799000	0.99117|0.99117	2.638000|2.638000	0.89438|0.89438	0.561000|0.561000	0.74099|0.74099	CGT|GTG		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228528808	G	A	228528808	3	1	111	1	0	0	0	0	1	0	0	0	10843	1145	40	1	17996	1	OBSCN	1	228528808	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	34186	228528808	20721813	101	29235										
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472265	231472265	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaactgctctgcgagtagcCttcggaccacctctcaggga	11	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:231472265C>A	ENST00000360394.2	-	1	1313	c.1227G>T	c.(1225-1227)aaG>aaT	p.K409N	SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.K405N|SPRTN_ENST00000391858.4_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	409					cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				TGCGAGTAGCCTTCGGACCAC	0.537																																																0			1											60	59	59					1																	231472265		2203	4300	6503	229538888	SO:0001583	missense	149371			AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.1227G>T	1.37:g.231472265C>A	ENSP00000353564:p.Lys409Asn		229538888	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	37	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.181346	0.38511	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.78126	-1.15;-1.15	5.86	1.88	0.25563	Cullin repeat-like-containing domain (1);	0.056198	0.64402	D	0.000002	T	0.61515	0.2353	L	0.39397	1.21	0.58432	D	0.999999	B	0.30482	0.281	B	0.26969	0.075	T	0.45175	-0.9279	10	0.18710	T	0.47	-23.0336	5.6787	0.17763	0.0:0.5348:0.1263:0.3389	.	409	Q8IYI6	EXOC8_HUMAN	N	409;405	ENSP00000353564:K409N;ENSP00000355605:K405N	ENSP00000353564:K409N	K	-	3	2	EXOC8	229538888	1.000000	0.71417	0.993000	0.49108	0.940000	0.58332	1.282000	0.33226	0.093000	0.17368	0.655000	0.94253	AAG		0.537	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472265	C	A	231472265	3	1	111	1	0	0	0	0	1	0	0	0	5324	680	24	2	954	2	EXOC8	1	231472265	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2943457	231472265	17778356	102	29236										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232600867	232600867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccaatgctaaacaagtgggCatccttccttggctttacct	7	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:232600867C>T	ENST00000366630.1	-	8	2897	c.2539G>A	c.(2539-2541)Gcc>Acc	p.A847T	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A847T|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	847					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AACAAGTGGGCATCCTTCCTT	0.512																																																0			1											131	126	128					1																	232600867		1993	4174	6167	230667490	SO:0001583	missense	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2539G>A	1.37:g.232600867C>T	ENSP00000355589:p.Ala847Thr		230667490	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809170	0.90707	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.57595	0.39;0.39	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.71508	0.3348	M	0.62266	1.93	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	T	0.70339	-0.4899	10	0.56958	D	0.05	-32.8437	20.3658	0.98878	0.0:1.0:0.0:0.0	.	847	Q9P2F8	SI1L2_HUMAN	T	847	ENSP00000355589:A847T;ENSP00000262861:A847T	ENSP00000262861:A847T	A	-	1	0	SIPA1L2	230667490	1.000000	0.71417	0.919000	0.36401	0.674000	0.39518	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	GCC		0.512	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232600867	C	T	232600867	3	4	111	1	0	0	0	0	1	0	0	0	14367	710	25	3	2689	3	SIPA1L2	1	232600867	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1128602	232600867	16649754	103	29237										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233344392	233344393	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aataaggccacacagcacacINSaaaaatagattggtctgcta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:233344392_233344393insA	ENST00000258229.9	-	13	2968_2969	c.2734_2735insT	c.(2734-2736)tgtfs	p.C912fs	PCNXL2_ENST00000430153.1_Frame_Shift_Ins_p.C211fs|PCNXL2_ENST00000488780.2_Frame_Shift_Ins_p.C45fs	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	912						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				ACACAGCACACAAAAATAGATT	0.406																																																0			1																																								231411016	SO:0001589	frameshift_variant	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2735dupT	1.37:g.233344397_233344397dupA	ENSP00000258229:p.Cys912fs		231411015	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Frame_Shift_Ins	INS	ENST00000258229.9	37	CCDS44335.1																																																																																				0.406	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233344393	-	A	233344392	7	5	111	1	0	1	1	0	0	0	0	0	11623	478	17	0	3766	0	PCNXL2	1	233344392	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	743525	233344392	15906229	104	29238										
NID1	4811	hgsc.bcm.edu	37	chr1	236157153	236157153	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgtgttctcgctcgtgctgGcaccgggttttctccacctc	10	14	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:236157153G>A	ENST00000264187.6	-	13	2629	c.2547C>T	c.(2545-2547)tgC>tgT	p.C849C	NID1_ENST00000366595.3_Silent_p.C716C	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	849	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GCTCGTGCTGGCACCGGGTTT	0.642																																																0			1											27	27	27					1																	236157153		2203	4300	6503	234223776	SO:0001819	synonymous_variant	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2547C>T	1.37:g.236157153G>A			234223776	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																				0.642	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236157153	G	A	236157153	2	1	111	1	0	0	0	0	0	0	0	1	10445	1195	42	3		3	NID1	1	236157153	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2812761	236157153	13093468	105	29239										
ZP4	57829	hgsc.bcm.edu	37	chr1	238053843	238053843	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccacggcccacagtggagCacactggaataatctggtgc	11	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:238053843C>T	ENST00000366570.4	-	1	251	c.93G>A	c.(91-93)gtG>gtA	p.V31V	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	31					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CACAGTGGAGCACACTGGAAT	0.507																																					NSCLC(166;160 2029 11600 18754 19936)											0			1											59	56	57					1																	238053843		2203	4300	6503	236120466	SO:0001819	synonymous_variant	57829			U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.93G>A	1.37:g.238053843C>T			236120466	B2RAE1	Silent	SNP	ENST00000366570.4	37	CCDS1615.1																																																																																				0.507	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238053843	C	T	238053843	2	4	111	1	0	0	0	0	0	0	0	1	18257	697	25	3		3	ZP4	1	238053843	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1896690	238053843	11196778	106	29240										
FH	2271	hgsc.bcm.edu	37	chr1	241663756	241663756	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctatatgaggattgagagcTgtcaccaacattagagactc	9	9	1	3	rs199747704		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:241663756T>C	ENST00000366560.3	-	9	1409	c.1371A>G	c.(1369-1371)acA>acG	p.T457T		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	457					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)	p.T457T(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		GATTGAGAGCTGTCACCAACA	0.368			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	1	Substitution - coding silent(1)	lung(1)	1											158	152	154					1																	241663756		2203	4300	6503	239730379	SO:0001819	synonymous_variant	3949	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1371A>G	1.37:g.241663756T>C			239730379	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																				0.368	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		C	241663756	T	C	241663756	2	2	111	1	0	0	0	0	0	0	0	1	5894	1567	55	4		4	FH	1	241663756	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3609913	241663756	7586865	107	29241										
OPN3	23596	hgsc.bcm.edu	37	chr1	241761112	241761112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgatttagcaaagaggtacGaaacaatagatattgttgga	10	4	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:241761112G>A	ENST00000366554.2	-	3	987	c.881C>T	c.(880-882)tCg>tTg	p.S294L	OPN3_ENST00000331838.5_Missense_Mutation_p.S215L|OPN3_ENST00000469376.1_5'UTR	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	294					detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			AAAGAGGTACGAAACAATAGA	0.398																																																0			1											159	147	151					1																	241761112		2203	4300	6503	239827735	SO:0001583	missense	23596			AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"GPCR / Class A : Opsin receptors"	14007	protein-coding gene	gene with protein product	"panopsin", "protein phosphatase 1, regulatory subunit 116"	606695	"encephalopsin"	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691	ENST00000366554.2:c.881C>T	1.37:g.241761112G>A	ENSP00000355512:p.Ser294Leu		239827735	Q8IX08|Q9Y344	Missense_Mutation	SNP	ENST00000366554.2	37	CCDS31072.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719365	0.48728	.	.	ENSG00000054277	ENST00000366554;ENST00000331838	T;T	0.71222	-0.55;-0.55	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.150622	0.45126	D	0.000396	T	0.56514	0.1990	L	0.27053	0.805	0.46478	D	0.99906	P	0.48407	0.91	B	0.35413	0.202	T	0.67499	-0.5655	10	0.87932	D	0	.	17.1598	0.86801	0.0:0.0:1.0:0.0	.	294	Q9H1Y3	OPN3_HUMAN	L	294;215	ENSP00000355512:S294L;ENSP00000328018:S215L	ENSP00000328018:S215L	S	-	2	0	OPN3	239827735	1.000000	0.71417	0.760000	0.31359	0.027000	0.11550	5.778000	0.68940	2.210000	0.71456	0.655000	0.94253	TCG		0.398	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322		A	241761112	G	A	241761112	3	1	111	1	0	0	0	0	1	0	0	0	10912	1059	37	1	335	1	OPN3	1	241761112	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	97356	241761112	7489509	108	29242										
PLD5	200150	hgsc.bcm.edu	37	chr1	242277236	242277236	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcaggtagtccatgacagcGatgtacacatactgcttggc	12	10	0	1	rs576261716	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:242277236G>A	ENST00000536534.2	-	7	1267	c.1026C>T	c.(1024-1026)atC>atT	p.I342I	PLD5_ENST00000442594.2_Silent_p.I250I|PLD5_ENST00000427495.1_Silent_p.I280I			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	342						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.I250M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CCATGACAGCGATGTACACAT	0.458													G|||	2	0.000399361	0.0015	0	5008	,	,		18193	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	skin(1)	1											190	142	159					1																	242277236		2203	4300	6503	240343859	SO:0001819	synonymous_variant	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1026C>T	1.37:g.242277236G>A			240343859	A1KXV0|B7Z324|Q494U9|Q8NB22	Silent	SNP	ENST00000536534.2	37	CCDS1621.2																																																																																				0.458	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		A	242277236	G	A	242277236	2	1	111	1	0	0	0	0	0	0	0	1	12080	1048	37	1		1	PLD5	1	242277236	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	516124	242277236	6973385	109	29243										
PLD5	200150	hgsc.bcm.edu	37	chr1	242383405	242383405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagcggtcatgttcatgtacGtcacctcggctcctaggagt	11	11	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:242383405G>A	ENST00000536534.2	-	5	861	c.620C>T	c.(619-621)aCg>aTg	p.T207M	PLD5_ENST00000442594.2_Missense_Mutation_p.T115M|PLD5_ENST00000427495.1_Missense_Mutation_p.T145M			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	207						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.T115M(3)|p.T207M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GTTCATGTACGTCACCTCGGC	0.557																																																4	Substitution - Missense(4)	lung(2)|ovary(1)|large_intestine(1)	1											131	118	123					1																	242383405		2203	4300	6503	240450028	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.620C>T	1.37:g.242383405G>A	ENSP00000440896:p.Thr207Met		240450028	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226328	0.39300	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.13778	2.56;2.56;2.56	5.52	4.6	0.57074	.	0.238118	0.43747	D	0.000527	T	0.07548	0.0190	N	0.17474	0.49	0.33978	D	0.647606	B;B;B	0.33694	0.421;0.297;0.421	B;B;B	0.21360	0.034;0.015;0.023	T	0.14420	-1.0473	10	0.54805	T	0.06	-20.8238	10.7734	0.46336	0.0909:0.0:0.9091:0.0	.	115;207;145	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	M	145;115;207	ENSP00000401285:T145M;ENSP00000414188:T115M;ENSP00000440896:T207M	ENSP00000401285:T145M	T	-	2	0	PLD5	240450028	0.983000	0.35010	0.999000	0.59377	0.995000	0.86356	1.828000	0.39111	2.591000	0.87537	0.655000	0.94253	ACG		0.557	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		A	242383405	G	A	242383405	3	1	111	1	0	0	0	0	1	0	0	0	12080	1145	40	1	1014	1	PLD5	1	242383405	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	106169	242383405	6867216	110	29244										
CEP170	9859	hgsc.bcm.edu	37	chr1	243388560	243388560	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtgcctccactgctcaccAaaaaccaggatgttaagctc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:243388560delA	ENST00000366542.1	-	2	74	c.23delT	c.(22-24)ttgfs	p.L8fs	CEP170_ENST00000366544.1_Frame_Shift_Del_p.L8fs|CEP170_ENST00000366543.1_Frame_Shift_Del_p.L8fs|AC092782.1_ENST00000596590.1_Intron	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	8						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			ACTGCTCACCAAAAACCAGGA	0.428																																																0			1											54	55	55					1																	243388560		1937	4149	6086	241455183	SO:0001589	frameshift_variant	9859			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.23delT	1.37:g.243388560delA	ENSP00000355500:p.Leu8fs		241455183	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Frame_Shift_Del	DEL	ENST00000366542.1	37	CCDS44339.1																																																																																				0.428	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		-	243388560	A	-	243388560	7	5	111	1	0	1	0	1	0	0	0	0	3256	131	5	0	4837	0	CEP170	1	243388560	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	1005155	243388560	5862061	111	29245										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243471392	243471392	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacttgtaaccgtgttggtgGtctttgtttgaaatgtgctc	11	6	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:243471392G>C	ENST00000366541.3	+	8	960	c.842G>C	c.(841-843)gGt>gCt	p.G281A	SDCCAG8_ENST00000355875.4_Missense_Mutation_p.G238A|SDCCAG8_ENST00000391846.1_Missense_Mutation_p.G281A|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.G136A	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	281	Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		CGTGTTGGTGGTCTTTGTTTG	0.383																																																0			1											250	211	224					1																	243471392		2203	4300	6503	241538015	SO:0001583	missense	10806			AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.842G>C	1.37:g.243471392G>C	ENSP00000355499:p.Gly281Ala		241538015	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	37	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186848	0.78789	.	.	ENSG00000054282	ENST00000355875;ENST00000391846;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68	5.6	5.6	0.85130	.	0.049229	0.85682	D	0.000000	T	0.50616	0.1626	M	0.74258	2.255	0.58432	D	0.999999	D;D	0.89917	1.0;0.997	D;P	0.91635	0.999;0.893	T	0.32052	-0.9921	10	0.18276	T	0.48	-11.8835	17.7577	0.88455	0.0:0.0:1.0:0.0	.	238;281	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	A	238;281;281;136;61	ENSP00000348137:G238A;ENSP00000375721:G281A;ENSP00000355499:G281A;ENSP00000341260:G136A;ENSP00000410200:G61A	ENSP00000341260:G136A	G	+	2	0	SDCCAG8	241538015	1.000000	0.71417	0.997000	0.53966	0.800000	0.45204	7.525000	0.81892	2.805000	0.96524	0.650000	0.86243	GGT		0.383	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		C	243471392	G	C	243471392	3	2	111	1	0	0	0	0	1	0	0	0	13996	1261	44	5	872	5	SDCCAG8	1	243471392	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	82832	243471392	5779229	112	29246										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243589845	243589845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagcatgggagagtacatgAgacgatgaagcaaaggtaat	13	6	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:243589845A>G	ENST00000366541.3	+	16	2088	c.1970A>G	c.(1969-1971)gAg>gGg	p.E657G	SDCCAG8_ENST00000355875.4_Missense_Mutation_p.E614G|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.E512G	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	657	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		AGAGTACATGAGACGATGAAG	0.398																																																0			1											154	133	140					1																	243589845		2203	4300	6503	241656468	SO:0001583	missense	10806			AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1970A>G	1.37:g.243589845A>G	ENSP00000355499:p.Glu657Gly		241656468	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	37	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	17.26	3.343967	0.61073	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.53423	0.71;0.68;0.7;0.62	6.02	6.02	0.97574	.	0.186098	0.46145	D	0.000310	T	0.57577	0.2063	L	0.27053	0.805	0.48135	D	0.999593	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.58730	-0.7585	10	0.48119	T	0.1	-15.349	16.5446	0.84426	1.0:0.0:0.0:0.0	.	614;657	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	G	614;657;512;358	ENSP00000348137:E614G;ENSP00000355499:E657G;ENSP00000341260:E512G;ENSP00000410200:E358G	ENSP00000341260:E512G	E	+	2	0	SDCCAG8	241656468	1.000000	0.71417	0.986000	0.45419	0.202000	0.24057	6.790000	0.75115	2.311000	0.77944	0.533000	0.62120	GAG		0.398	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		G	243589845	A	G	243589845	3	3	111	1	0	0	0	0	1	0	0	0	13996	304	11	4	2032	4	SDCCAG8	1	243589845	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	118453	243589845	5660776	113	29247										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245530620	245530620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctcaccagtacctggatgGcacctggtccctgtcgagaa	12	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:245530620G>A	ENST00000407071.2	+	3	1390	c.950G>A	c.(949-951)gGc>gAc	p.G317D	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	317					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TACCTGGATGGCACCTGGTCC	0.597																																																0			1											21	27	25					1																	245530620		2122	4229	6351	243597243	SO:0001583	missense	55083			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.950G>A	1.37:g.245530620G>A	ENSP00000385545:p.Gly317Asp		243597243	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228638	0.58777	.	.	ENSG00000162849	ENST00000407071	T	0.80653	-1.4	5.75	4.79	0.61399	.	0.000000	0.85682	D	0.000000	D	0.85835	0.5789	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.67382	0.951;0.921	D	0.87008	0.2121	10	0.87932	D	0	.	16.273	0.82630	0.0:0.1324:0.8676:0.0	.	317;317	B4DF75;Q2KJY2	.;KI26B_HUMAN	D	317	ENSP00000385545:G317D	ENSP00000385545:G317D	G	+	2	0	KIF26B	243597243	1.000000	0.71417	0.995000	0.50966	0.836000	0.47400	4.692000	0.61746	2.716000	0.92895	0.655000	0.94253	GGC		0.597	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245530620	G	A	245530620	3	1	111	1	0	0	0	0	1	0	0	0	8316	1203	42	3	960	3	KIF26B	1	245530620	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1940775	245530620	3720001	114	29248										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224426	248224426	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgatgataacagggtcttGgatcataggctcgatcaatg	12	7	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr1:248224426G>A	ENST00000359959.3	+	1	443	c.443G>A	c.(442-444)tGg>tAg	p.W148*	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ACAGGGTCTTGGATCATAGGC	0.433																																																0			1											197	220	213					1																	248224426		2203	4300	6503	246291049	SO:0001587	stop_gained	391192			AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.443G>A	1.37:g.248224426G>A	ENSP00000353044:p.Trp148*		246291049	B9EH44	Nonsense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	.	13.77	2.336290	0.41398	.	.	ENSG00000198128	ENST00000359959	.	.	.	1.91	0.933	0.19471	.	0.000000	0.30293	U	0.009952	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4659	0.32956	0.1435:0.0:0.8565:0.0	.	.	.	.	X	148	.	ENSP00000353044:W148X	W	+	2	0	OR2L3	246291049	0.004000	0.15560	0.543000	0.28128	0.054000	0.15201	-0.058000	0.11750	1.031000	0.39867	0.462000	0.41574	TGG		0.433	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		A	248224426	G	A	248224426	4	1	111	1	0	0	0	0	0	1	0	0	11039	1357	47	3	445	3	OR2L3	1	248224426	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2693806	248224426	1026195	115	29249										
TPO	7173	hgsc.bcm.edu	37	chr2	1426879	1426879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaagcgcctggtggacaccGccatgtacgccacgatgcag	13	14	0	0	rs199694732		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:1426879G>A	ENST00000345913.4	+	3	248	c.157G>A	c.(157-159)Gcc>Acc	p.A53T	TPO_ENST00000382201.3_Missense_Mutation_p.A53T|TPO_ENST00000346956.3_Missense_Mutation_p.A53T|TPO_ENST00000382269.3_Missense_Mutation_p.A53T|TPO_ENST00000349624.3_Missense_Mutation_p.A53T|TPO_ENST00000329066.4_Missense_Mutation_p.A53T|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Missense_Mutation_p.A53T|TPO_ENST00000539820.1_Missense_Mutation_p.A53T|TPO_ENST00000337415.3_Missense_Mutation_p.A53T	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	53			A -> P (in TDH2A). {ECO:0000269|PubMed:12213873}.		cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GGTGGACACCGCCATGTACGC	0.602																																																0			2	GRCh37	CM022257	TPO	M							92	77	82					2																	1426879		2203	4300	6503	1405886	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.157G>A	2.37:g.1426879G>A	ENSP00000318820:p.Ala53Thr		1405886	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973506	0.53720	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33	3.72	2.82	0.32997	.	0.117057	0.37857	N	0.001914	T	0.65133	0.2662	M	0.81341	2.54	0.09310	N	1	D;P;D;D;D	0.61697	0.99;0.931;0.99;0.972;0.962	P;B;P;P;B	0.51895	0.665;0.356;0.683;0.552;0.427	T	0.59836	-0.7379	10	0.87932	D	0	-22.8934	8.6299	0.33913	0.0:0.0:0.7718:0.2282	.	53;53;53;53;53	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	T	53	ENSP00000371704:A53T;ENSP00000337263:A53T;ENSP00000318820:A53T;ENSP00000263886:A53T;ENSP00000332044:A53T;ENSP00000444840:A53T;ENSP00000329869:A53T;ENSP00000371636:A53T;ENSP00000390994:A53T;ENSP00000371633:A53T	ENSP00000329869:A53T	A	+	1	0	TPO	1405886	0.112000	0.22096	0.006000	0.13384	0.020000	0.10135	1.448000	0.35112	1.105000	0.41606	0.467000	0.42956	GCC		0.602	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1426879	G	A	1426879	3	1	111	1	0	0	0	0	1	0	0	0	16450	1087	38	1	163	1	TPO	2	1426879	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10		1426879	241772494	116	29250										
TPO	7173	hgsc.bcm.edu	37	chr2	1507747	1507748	+	Frame_Shift_Ins	INS	-	-	C													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtgtgcagacggtgcccaINSccccccctgccacgcctctg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:1507747_1507748insC	ENST00000345913.4	+	14	2505_2506	c.2414_2415insC	c.(2413-2418)caccccfs	p.HP805fs	TPO_ENST00000337415.3_Frame_Shift_Ins_p.HP805fs|TPO_ENST00000382201.3_Frame_Shift_Ins_p.HP748fs|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000329066.4_Frame_Shift_Ins_p.HP805fs|TPO_ENST00000346956.3_Intron|TPO_ENST00000349624.3_Frame_Shift_Ins_p.HP632fs|TPO_ENST00000382198.1_Frame_Shift_Ins_p.HP632fs	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	805	EGF-like; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.H805L(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GACGGTGCCCACCCCCCCTGCC	0.644																																																1	Substitution - Missense(1)	ovary(1)	2																																								1486755	SO:0001589	frameshift_variant	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2421dupC	2.37:g.1507754_1507754dupC	ENSP00000318820:p.His805fs		1486754	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Frame_Shift_Ins	INS	ENST00000345913.4	37	CCDS1643.1																																																																																				0.644	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		C	1507748	-	C	1507747	7	5	111	1	0	1	1	0	0	0	0	0	16450	159	6	0	2464	0	TPO	2	1507747	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	80868	1507747	241691626	117	29251										
TSSC1	7260	hgsc.bcm.edu	37	chr2	3197910	3197910	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggtcccgcaccagctgtccGtgggcattctctatgcagta	11	13	1	0	rs148611386		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:3197910G>A	ENST00000382125.4	-	7	873	c.681C>T	c.(679-681)caC>caT	p.H227H	TSSC1_ENST00000478754.1_5'UTR|TSSC1_ENST00000398659.4_Silent_p.H254H	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	227								p.H227Q(1)		breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CCAGCTGTCCGTGGGCATTCT	0.507													G|||	1	0.000199681	8e-04	0	5008	,	,		19761	0		0	False		,,,				2504	0				Colon(140;1261 1762 4183 34270 49743)											1	Substitution - Missense(1)	lung(1)	2						G		1,4405	2.1+/-5.4	0,1,2202	86	91	90		681	-1.5	1	2	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous	TSSC1	NM_003310.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		227/388	3197910	1,13005	2203	4300	6503	3176917	SO:0001819	synonymous_variant	7260			AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"WD repeat domain containing"	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.681C>T	2.37:g.3197910G>A			3176917	D6W4Y1|O43179|Q53S19|Q53SG2	Silent	SNP	ENST00000382125.4	37	CCDS1651.1																																																																																				0.507	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		A	3197910	G	A	3197910	2	1	111	1	0	0	0	0	0	0	0	1	16706	1136	40	1		1	TSSC1	2	3197910	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1690163	3197910	240001463	118	29252										
SOX11	6664	hgsc.bcm.edu	37	chr2	5832916	5832916	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccccgggaggcgctggacacGgaggagggcgaattcatggc	18	11	1	0	rs139885563	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:5832916G>C	ENST00000322002.3	+	1	118	c.63G>C	c.(61-63)acG>acC	p.T21T	AC107057.2_ENST00000458264.1_RNA|AC108025.2_ENST00000420221.1_RNA|AC108025.2_ENST00000453678.1_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	21					cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)			central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		CGCTGGACACGGAGGAGGGCG	0.682																																																0			2											28	30	29					2																	5832916		2202	4300	6502	5750367	SO:0001819	synonymous_variant	6664				CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.63G>C	2.37:g.5832916G>C			5750367	Q4ZFV8	Silent	SNP	ENST00000322002.3	37	CCDS1654.1																																																																																				0.682	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		C	5832916	G	C	5832916	2	2	111	1	0	0	0	0	0	0	0	1	14979	1103	39	5		5	SOX11	2	5832916	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2635006	5832916	237366457	119	29253										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9528650	9528650	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcaccaccagcgcccccccGcttcctccacggaatgttgg	9	19	0	0	rs200458713		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:9528650G>A	ENST00000281419.3	+	22	2698	c.2358G>A	c.(2356-2358)ccG>ccA	p.P786P	ASAP2_ENST00000491413.1_3'UTR|ASAP2_ENST00000315273.4_Silent_p.P786P	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	786	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GCGCCCCCCCGCTTCCTCCAC	0.582													G|||	1	0.000199681	0	0	5008	,	,		13524	0		0.001	False		,,,				2504	0															0			2						G	,	0,4406		0,0,2203	27	30	29		2358,2358	-11.2	0	2		29	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	ASAP2	NM_001135191.1,NM_003887.2	,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,	786/962,786/1007	9528650	1,13003	2203	4299	6502	9446101	SO:0001819	synonymous_variant	8853			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2358G>A	2.37:g.9528650G>A			9446101	D6W4Y8	Silent	SNP	ENST00000281419.3	37	CCDS1661.1																																																																																				0.582	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		A	9528650	G	A	9528650	2	1	111	1	0	0	0	0	0	0	0	1	1012	1074	38	1		1	ASAP2	2	9528650	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3695734	9528650	233670723	120	29254										
TRIB2	28951	hgsc.bcm.edu	37	chr2	12880639	12880639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtacaccatgttggtggggCggtaccctttccatgacatt	11	10	0	1	rs186204534		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:12880639C>T	ENST00000155926.4	+	3	2170	c.751C>T	c.(751-753)Cgg>Tgg	p.R251W	TRIB2_ENST00000381465.2_Missense_Mutation_p.R115W	NM_021643.3	NP_067675.1			tribbles pseudokinase 2											breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GTTGGTGGGGCGGTACCCTTT	0.572																																																0			2											105	75	85					2																	12880639		2203	4300	6503	12798090	SO:0001583	missense	28951			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000155926.4:c.751C>T	2.37:g.12880639C>T	ENSP00000155926:p.Arg251Trp		12798090		Missense_Mutation	SNP	ENST00000155926.4	37	CCDS1683.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.509770	0.85282	.	.	ENSG00000071575	ENST00000155926;ENST00000381465	T;T	0.68025	-0.3;-0.3	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86447	0.5935	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88437	0.3039	10	0.87932	D	0	-10.6335	19.354	0.94404	0.0:1.0:0.0:0.0	.	251	Q92519	TRIB2_HUMAN	W	251;115	ENSP00000155926:R251W;ENSP00000370874:R115W	ENSP00000155926:R251W	R	+	1	2	TRIB2	12798090	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	CGG		0.572	TRIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207114.2	NM_021643		T	12880639	C	T	12880639	3	4	111	1	0	0	0	0	1	0	0	0	16523	759	27	1	761	1	TRIB2	2	12880639	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3351989	12880639	230318734	121	29255										
NBAS	51594	hgsc.bcm.edu	37	chr2	15330512	15330512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcggttctcttcattctcaaTgtcagctatgtctacctgga	8	11	5	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:15330512T>C	ENST00000281513.5	-	49	6473	c.6448A>G	c.(6448-6450)Att>Gtt	p.I2150V	NBAS_ENST00000441750.1_Missense_Mutation_p.I2030V	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2150					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.I2150F(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TCATTCTCAATGTCAGCTATG	0.378																																																1	Substitution - Missense(1)	ovary(1)	2											103	104	104					2																	15330512		2203	4300	6503	15247963	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6448A>G	2.37:g.15330512T>C	ENSP00000281513:p.Ile2150Val		15247963	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	T	5.944	0.358197	0.11239	.	.	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000433283;ENST00000423602	T;T	0.08720	3.06;3.23	5.47	-4.32	0.03688	.	0.555420	0.20111	N	0.099008	T	0.06872	0.0175	L	0.38838	1.175	0.09310	N	1	B;B	0.20052	0.041;0.0	B;B	0.22386	0.039;0.001	T	0.20840	-1.0263	10	0.87932	D	0	.	12.5309	0.56115	0.0:0.4952:0.0:0.5048	.	2030;2150	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	V	2030;2150;6;4	ENSP00000413201:I2030V;ENSP00000281513:I2150V	ENSP00000281513:I2150V	I	-	1	0	NBAS	15247963	0.036000	0.19791	0.000000	0.03702	0.489000	0.33432	0.040000	0.13905	-1.003000	0.03425	-0.263000	0.10527	ATT		0.378	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		C	15330512	T	C	15330512	3	2	111	1	0	0	0	0	1	0	0	0	10216	1464	51	4	683	4	NBAS	2	15330512	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2449873	15330512	227868861	122	29256										
MYCN	4613	hgsc.bcm.edu	37	chr2	16085728	16085728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccacattcaccatcactgtgCgtcccaagaacgcagccctg	7	17	2	1	rs144939456		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:16085728C>T	ENST00000281043.3	+	3	1201	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	302					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			CATCACTGTGCGTCCCAAGAA	0.582			A		neuroblastoma																																		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	0			2						C	CYS/ARG	0,4406		0,0,2203	103	83	90		904	4.1	0.9	2	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYCN	NM_005378.4	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	302/465	16085728	1,13005	2203	4300	6503	16003179	SO:0001583	missense	4613			BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.904C>T	2.37:g.16085728C>T	ENSP00000281043:p.Arg302Cys		16003179	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	37	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.896675	0.52121	0.0	1.16E-4	ENSG00000134323	ENST00000281043;ENST00000426211	D	0.81908	-1.55	4.94	4.05	0.47172	Transcription regulator Myc, N-terminal (1);	1.323720	0.05292	U	0.521372	D	0.91506	0.7318	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.82255	-0.0548	10	0.87932	D	0	-8.6368	14.9038	0.70703	0.1445:0.8555:0.0:0.0	.	302	P04198	MYCN_HUMAN	C	302;220	ENSP00000281043:R302C	ENSP00000281043:R302C	R	+	1	0	MYCN	16003179	1.000000	0.71417	0.862000	0.33874	0.447000	0.32167	2.112000	0.41892	1.203000	0.43233	0.655000	0.94253	CGT		0.582	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		T	16085728	C	T	16085728	3	4	111	1	0	0	0	0	1	0	0	0	10051	768	27	1	910	1	MYCN	2	16085728	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	755216	16085728	227113645	123	29257										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	23977138	23977138	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctctcaagctgatcaactgCcagattgttgcttttatcca	6	11	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:23977138C>T	ENST00000238789.5	-	27	4589	c.4246G>A	c.(4246-4248)Gca>Aca	p.A1416T	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1416						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGATCAACTGCCAGATTGTTG	0.318																																																0			2											38	36	37					2																	23977138		1831	4080	5911	23830642	SO:0001583	missense	54454			AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.4246G>A	2.37:g.23977138C>T	ENSP00000238789:p.Ala1416Thr		23830642	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.448|6.448	0.450796|0.450796	0.12223|0.12223	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000238789;ENST00000546030|ENST00000381024	D|.	0.90844|.	-2.74|.	5.47|5.47	3.65|3.65	0.41850|0.41850	.|.	0.204155|.	0.33075|.	N|.	0.005310|.	T|.	0.14700|.	0.0355|.	N|N	0.03115|0.03115	-0.41|-0.41	0.25785|0.25785	N|N	0.984684|0.984684	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|.	0.23261|.	-1.0193|.	10|.	0.07030|.	T|.	0.85|.	.|.	6.8287|6.8287	0.23897|0.23897	0.0:0.6029:0.0:0.3971|0.0:0.6029:0.0:0.3971	.|.	1416;1411|.	Q9ULI0;Q9ULI0-2|.	ATD2B_HUMAN;.|.	T|X	1416;584|691	ENSP00000238789:A1416T|.	ENSP00000238789:A1416T|.	A|W	-|-	1|3	0|0	ATAD2B|ATAD2B	23830642|23830642	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.727000|1.727000	0.38095|0.38095	0.779000|0.779000	0.33543|0.33543	0.655000|0.655000	0.94253|0.94253	GCA|TGG		0.318	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		T	23977138	C	T	23977138	3	4	111	1	0	0	0	0	1	0	0	0	1073	739	26	3	138	3	ATAD2B	2	23977138	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7891410	23977138	219222235	124	29258										
GPR113	165082	hgsc.bcm.edu	37	chr2	26536276	26536276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaacaaggccaggagcctcGcatctgtgcagctgctgtgg	14	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:26536276G>A	ENST00000311519.1	-	9	1441	c.1442C>T	c.(1441-1443)gCg>gTg	p.A481V	GPR113_ENST00000421160.2_Missense_Mutation_p.A412V|GPR113_ENST00000541401.1_Missense_Mutation_p.A84V|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000333478.6_Missense_Mutation_p.A282V	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	481					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGGAGCCTCGCATCTGTGCA	0.642																																																0			2											26	26	26					2																	26536276		2202	4300	6502	26389780	SO:0001583	missense	165082			AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"-", "GPCR / Class B : Orphans"	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.1442C>T	2.37:g.26536276G>A	ENSP00000307831:p.Ala481Val		26389780	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571388	0.45798	.	.	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.28666	1.6;2.98;2.98;2.98	5.84	-6.74	0.01743	.	.	.	.	.	T	0.19685	0.0473	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.24483	0.104;0.068;0.027;0.005	B;B;B;B	0.19391	0.025;0.021;0.025;0.005	T	0.35822	-0.9773	9	0.56958	D	0.05	2.5799	5.2899	0.15721	0.3904:0.0:0.2271:0.3825	.	412;282;481;84	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	V	84;282;412;481	ENSP00000445729:A84V;ENSP00000327396:A282V;ENSP00000388537:A412V;ENSP00000307831:A481V	ENSP00000307831:A481V	A	-	2	0	GPR113	26389780	0.000000	0.05858	0.000000	0.03702	0.339000	0.28857	-1.207000	0.03008	-0.909000	0.03852	-0.397000	0.06425	GCG		0.642	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		A	26536276	G	A	26536276	3	1	111	1	0	0	0	0	1	0	0	0	6650	1087	38	1	1906	1	GPR113	2	26536276	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2559138	26536276	216663097	125	29259										
SLC5A6	8884	hgsc.bcm.edu	37	chr2	27423973	27423973	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggttcagggaccggcctcGcattctccctgaatggaaat	12	11	2	1	rs546600819		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:27423973G>A	ENST00000310574.3	-	16	2130	c.1657C>T	c.(1657-1659)Cga>Tga	p.R553*	SLC5A6_ENST00000461319.1_5'UTR|SLC5A6_ENST00000408041.1_Nonsense_Mutation_p.R553*	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	553					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GACCGGCCTCGCATTCTCCCT	0.607																																																0			2											86	84	85					2																	27423973		2203	4300	6503	27277477	SO:0001587	stop_gained	8884			AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.1657C>T	2.37:g.27423973G>A	ENSP00000310208:p.Arg553*		27277477	B2RB85|D6W549|Q969Y5	Nonsense_Mutation	SNP	ENST00000310574.3	37	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	G	36	5.930168	0.97116	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	.	.	.	5.73	4.77	0.60923	.	0.242069	0.39544	N	0.001334	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	12.7062	0.57061	0.0:0.0:0.8249:0.1751	.	.	.	.	X	553	.	ENSP00000310208:R553X	R	-	1	2	SLC5A6	27277477	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.404000	0.34623	2.698000	0.92095	0.650000	0.86243	CGA		0.607	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		A	27423973	G	A	27423973	4	1	111	1	0	0	0	0	0	1	0	0	14706	1095	38	1	258	1	SLC5A6	2	27423973	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	887697	27423973	215775400	126	29260										
CAD	51374	hgsc.bcm.edu	37	chr2	27440847	27440848	+	IGR	INS	-	-	C													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgatcggcaactatggcatINSccccccagatgaaatggatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:27440847_27440848insC	ENST00000606999.1	+	0	956				CAD_ENST00000403525.1_Frame_Shift_Ins_p.IP62fs|CAD_ENST00000264705.4_Frame_Shift_Ins_p.IP62fs	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor						cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											AACTATGGCATCCCCCCAGATG	0.495																																																0			2																																								27294352	SO:0001628	intergenic_variant	1677			BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405		2.37:g.27440853_27440853dupC			27294351	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Frame_Shift_Ins	INS	ENST00000606999.1	37																																																																																					0.495	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		C	27440848	-	C	27440847	6	5	111	0	1	1	1	0	0	0	0	0	2571	1435	50	0		0	CAD	2	27440847	IGR	INS	-	TCGA-EI-6507-01A-11D-1733-10	16874	27440847	215758526	127	29261										
IFT172	26160	hgsc.bcm.edu	37	chr2	27684212	27684212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttggctagcagttcctctCgggtcagcaccagccgagca	12	13	2	0	rs148237432		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:27684212C>T	ENST00000260570.3	-	22	2469	c.2366G>A	c.(2365-2367)cGa>cAa	p.R789Q		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	789					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					CAGTTCCTCTCGGGTCAGCAC	0.567																																																0			2						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	109	97	101		2366	2.9	1	2	dbSNP_134	101	0,8600		0,0,4300	no	missense	IFT172	NM_015662.1	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	789/1750	27684212	1,13005	2203	4300	6503	27537716	SO:0001583	missense	26160			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.2366G>A	2.37:g.27684212C>T	ENSP00000260570:p.Arg789Gln		27537716	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	37	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.021570	0.35701	2.27E-4	0.0	ENSG00000138002	ENST00000260570	T	0.62941	-0.01	5.68	2.93	0.34026	Tetratricopeptide-like helical (1);	0.576140	0.19450	N	0.113947	T	0.41743	0.1172	N	0.25647	0.755	0.80722	D	1	B	0.18610	0.029	B	0.09377	0.004	T	0.11991	-1.0565	10	0.10902	T	0.67	-1.6506	7.833	0.29353	0.0:0.6806:0.0:0.3194	.	789	Q9UG01	IF172_HUMAN	Q	789	ENSP00000260570:R789Q	ENSP00000260570:R789Q	R	-	2	0	IFT172	27537716	0.418000	0.25440	0.999000	0.59377	0.878000	0.50629	0.750000	0.26334	0.772000	0.33382	0.585000	0.79938	CGA		0.567	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		T	27684212	C	T	27684212	3	4	111	1	0	0	0	0	1	0	0	0	7578	884	31	1	2991	1	IFT172	2	27684212	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	243365	27684212	215515161	128	29262										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29226542	29226542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacaggcctgagggccccacGcacgcggtaagagctccaag	13	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:29226542G>A	ENST00000379558.4	+	6	1175	c.824G>A	c.(823-825)cGc>cAc	p.R275H	FAM179A_ENST00000403861.2_Missense_Mutation_p.R275H	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	275										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGGGCCCCACGCACGCGGTAA	0.642																																																0			2											21	23	22					2																	29226542		1995	4148	6143	29080046	SO:0001583	missense	165186			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.824G>A	2.37:g.29226542G>A	ENSP00000368876:p.Arg275His		29080046	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	1.318	-0.600366	0.03744	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.10192	3.1;2.9	4.34	-8.67	0.00863	.	.	.	.	.	T	0.04861	0.0131	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.38067	-0.9678	9	0.40728	T	0.16	.	8.3695	0.32406	0.3943:0.3068:0.2989:0.0	.	275;275	F8W8E4;Q6ZUX3	.;F179A_HUMAN	H	275	ENSP00000368876:R275H;ENSP00000384699:R275H	ENSP00000368876:R275H	R	+	2	0	FAM179A	29080046	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.463000	0.02361	-3.964000	0.00086	-1.579000	0.00862	CGC		0.642	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		A	29226542	G	A	29226542	3	1	111	1	0	0	0	0	1	0	0	0	5521	1087	38	1	842	1	FAM179A	2	29226542	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1542330	29226542	213972831	129	29263										
MEMO1	51072	hgsc.bcm.edu	37	chr2	32157135	32157135	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaacaaaactacattacttaCgtaatagacggatccacttg	5	9	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:32157135C>T	ENST00000295065.5	-	3	522		c.e3+1		MEMO1_ENST00000407893.3_Splice_Site|MEMO1_ENST00000379383.3_Splice_Site|MEMO1_ENST00000490459.1_Splice_Site|DPY30_ENST00000446765.1_Splice_Site|MEMO1_ENST00000404530.1_Splice_Site|MEMO1_ENST00000426310.2_Intron	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1						regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					ACATTACTTACGTAATAGACG	0.313																																																0			2											78	79	78					2																	32157135		2203	4300	6503	32010639	SO:0001630	splice_region_variant	51072			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.212+1G>A	2.37:g.32157135C>T			32010639	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Splice_Site	SNP	ENST00000295065.5	37	CCDS1776.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.995277	0.74703	.	.	ENSG00000162959	ENST00000295065;ENST00000379383;ENST00000404530;ENST00000407893	.	.	.	5.71	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4281	0.83831	0.0:0.8683:0.1317:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MEMO1	32010639	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.661000	0.68025	1.396000	0.46663	0.563000	0.77884	.		0.313	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955	Intron	T	32157135	C	T	32157135	5	4	111	1	0	0	0	0	0	0	1	0	9501	550	19	1	708	1	MEMO1	2	32157135	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2930593	32157135	211042238	130	29264										
PRKD3	23683	hgsc.bcm.edu	37	chr2	37480453	37480453	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taatgtaacgttctccaatgCgagtttcaaattctctaagg	7	8	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:37480453C>T	ENST00000379066.1	-	19	3302	c.2540G>A	c.(2539-2541)cGc>cAc	p.R847H	PRKD3_ENST00000234179.2_Missense_Mutation_p.R847H			O94806	KPCD3_HUMAN	protein kinase D3	847					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				TTCTCCAATGCGAGTTTCAAA	0.373																																					Melanoma(80;621 1355 8613 11814 51767)											0			2											126	113	117					2																	37480453		2203	4300	6503	37333957	SO:0001583	missense	23683			AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.2540G>A	2.37:g.37480453C>T	ENSP00000368356:p.Arg847His		37333957	D6W587|Q53TR7|Q8NEL8	Missense_Mutation	SNP	ENST00000379066.1	37	CCDS1789.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644598	0.87859	.	.	ENSG00000115825	ENST00000379066;ENST00000234179	T;T	0.39787	1.06;1.06	5.94	5.07	0.68467	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.42291	0.1196	L	0.38175	1.15	0.47819	D	0.999524	D	0.53745	0.962	P	0.50049	0.629	T	0.38373	-0.9664	10	0.66056	D	0.02	-5.0643	11.3806	0.49754	0.0:0.8617:0.0:0.1383	.	847	O94806	KPCD3_HUMAN	H	847	ENSP00000368356:R847H;ENSP00000234179:R847H	ENSP00000234179:R847H	R	-	2	0	PRKD3	37333957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.982000	0.63825	1.522000	0.49001	0.650000	0.86243	CGC		0.373	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		T	37480453	C	T	37480453	3	4	111	1	0	0	0	0	1	0	0	0	12554	768	27	1	136	1	PRKD3	2	37480453	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5323318	37480453	205718920	131	29265										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452581	43452582	+	Frame_Shift_Ins	INS	-	-	C													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttctcgctaaacgagcggtINScccggaatttgttctccttg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:43452581_43452582insC	ENST00000282388.3	-	2	654_655	c.361_362insG	c.(361-363)gacfs	p.D121fs	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	121					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				AAACGAGCGGTCCCGGAATTTG	0.688																																																0			2																																								43306086	SO:0001589	frameshift_variant	678			X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.362dupG	2.37:g.43452584_43452584dupC	ENSP00000282388:p.Asp121fs		43306085	Q53TB4|Q9BSJ3	Frame_Shift_Ins	INS	ENST00000282388.3	37	CCDS1811.1																																																																																				0.688	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		C	43452582	-	C	43452581	7	5	111	1	0	1	1	0	0	0	0	0	17686	1667	58	0	1126	0	ZFP36L2	2	43452581	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	5972128	43452581	199746792	132	29266										
THADA	63892	hgsc.bcm.edu	37	chr2	43571279	43571279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctcttggccagccagagtTtggctttggtacaaacagtg	11	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:43571279T>C	ENST00000405006.4	-	30	4676	c.4325A>G	c.(4324-4326)aAa>aGa	p.K1442R	THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.K1442R|THADA_ENST00000415080.2_Missense_Mutation_p.K1123R|THADA_ENST00000485353.1_5'Flank	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1442										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CAGCCAGAGTTTGGCTTTGGT	0.443																																																0			2											75	70	72					2																	43571279		1916	4130	6046	43424783	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4325A>G	2.37:g.43571279T>C	ENSP00000385995:p.Lys1442Arg		43424783	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.50|15.50	2.853423|2.853423	0.51270|0.51270	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.12879|.	2.8;2.64;2.8|.	4.8|4.8	3.64|3.64	0.41730|0.41730	.|.	0.116052|.	0.56097|.	D|.	0.000031|.	T|T	0.34337|0.34337	0.0894|0.0894	L|L	0.33485|0.33485	1.01|1.01	0.30213|0.30213	N|N	0.79752|0.79752	B;B;B|.	0.23806|.	0.091;0.065;0.055|.	B;B;B|.	0.26202|.	0.067;0.01;0.008|.	T|T	0.28776|0.28776	-1.0033|-1.0033	10|5	0.12766|.	T|.	0.61|.	.|.	7.7623|7.7623	0.28959|0.28959	0.0:0.1642:0.0:0.8358|0.0:0.1642:0.0:0.8358	.|.	1369;1123;1442|.	B6ZDQ0;C9JJB1;Q6YHU6|.	.;.;THADA_HUMAN|.	R|D	1442;1369;1123;1442|682	ENSP00000386088:K1442R;ENSP00000416048:K1123R;ENSP00000385995:K1442R|.	ENSP00000349464:K1369R|.	K|N	-|-	2|1	0|0	THADA|THADA	43424783|43424783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.306000|2.306000	0.43673|0.43673	0.858000|0.858000	0.35431|0.35431	0.477000|0.477000	0.44152|0.44152	AAA|AAC		0.443	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		C	43571279	T	C	43571279	3	2	111	1	0	0	0	0	1	0	0	0	15879	1841	64	4	1572	4	THADA	2	43571279	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	118698	43571279	199628094	133	29267										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50733738	50733738	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggttatagccagcaaaaaGagtctcgggacctttgcctg	12	9	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:50733738G>T	ENST00000406316.2	-	13	3868	c.2392C>A	c.(2392-2394)Ctt>Att	p.L798I	NRXN1_ENST00000402717.3_Missense_Mutation_p.L790I|NRXN1_ENST00000406859.3_Missense_Mutation_p.L798I|NRXN1_ENST00000405472.3_Missense_Mutation_p.L790I|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Missense_Mutation_p.L798I|NRXN1_ENST00000404971.1_Missense_Mutation_p.L838I	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	798	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CCAGCAAAAAGAGTCTCGGGA	0.443																																																0			2											114	108	109					2																	50733738		1902	4124	6026	50587242	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2392C>A	2.37:g.50733738G>T	ENSP00000384311:p.Leu798Ile		50587242	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.125562	0.56721	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;-1.34;-1.34	5.7	5.7	0.88788	.	0.057967	0.64402	D	0.000002	T	0.80076	0.4557	L	0.45470	1.425	0.36741	D	0.882236	B;B;B	0.21071	0.051;0.024;0.011	B;B;B	0.31869	0.137;0.087;0.044	T	0.77335	-0.2626	10	0.38643	T	0.18	.	19.8388	0.96673	0.0:0.0:1.0:0.0	.	838;798;790	Q9ULB1-3;F8WB18;A7E294	.;.;.	I	838;798;790;798;839;790;798	ENSP00000385142:L838I;ENSP00000384311:L798I;ENSP00000434015:L790I;ENSP00000385017:L798I;ENSP00000385434:L790I;ENSP00000385681:L798I	ENSP00000385017:L798I	L	-	1	0	NRXN1	50587242	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.155000	0.71833	2.695000	0.91970	0.561000	0.74099	CTT		0.443	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50733738	G	T	50733738	3	4	111	1	0	0	0	0	1	0	0	0	10696	942	33	2	2438	2	NRXN1	2	50733738	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7162459	50733738	192465635	134	29268										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50779939	50779939	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatggctaaataagatgagGccatttggctctgttgtacg	11	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:50779939G>A	ENST00000406316.2	-	9	3021	c.1545C>T	c.(1543-1545)ggC>ggT	p.G515G	NRXN1_ENST00000402717.3_Silent_p.G507G|NRXN1_ENST00000406859.3_Silent_p.G515G|NRXN1_ENST00000405472.3_Silent_p.G507G|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Silent_p.G515G|NRXN1_ENST00000404971.1_Silent_p.G555G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	515	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATAAGATGAGGCCATTTGGCT	0.433																																																0			2											162	151	154					2																	50779939		1904	4114	6018	50633443	SO:0001819	synonymous_variant	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1545C>T	2.37:g.50779939G>A			50633443	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50779939	G	A	50779939	2	1	111	1	0	0	0	0	0	0	0	1	10696	1190	42	3		3	NRXN1	2	50779939	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	46201	50779939	192419434	135	29269										
RTN4	57142	hgsc.bcm.edu	37	chr2	55253949	55253949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttcgtgattagtttgctcaAggctatctgcaaaacatttt	7	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:55253949A>G	ENST00000337526.6	-	3	1529	c.1286T>C	c.(1285-1287)cTt>cCt	p.L429P	RTN4_ENST00000405240.1_Missense_Mutation_p.L223P|RTN4_ENST00000394611.2_Missense_Mutation_p.L223P|RTN4_ENST00000357376.3_Missense_Mutation_p.L223P|RTN4_ENST00000404909.1_Missense_Mutation_p.L223P|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000354474.6_Missense_Mutation_p.L197P|RTN4_ENST00000317610.7_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	429			L -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						AGTTTGCTCAAGGCTATCTGC	0.383																																																0			2											247	238	241					2																	55253949		2202	4299	6501	55107453	SO:0001583	missense	57142			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1286T>C	2.37:g.55253949A>G	ENSP00000337838:p.Leu429Pro		55107453	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	A	4.705	0.131049	0.08981	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.23950	1.88;1.88;2.31;1.88;1.88;1.9	6.06	2.42	0.29668	.	1.733500	0.02514	N	0.091842	T	0.32224	0.0822	M	0.66939	2.045	0.19575	N	0.999966	B	0.18461	0.028	B	0.15870	0.014	T	0.27938	-1.0059	10	0.44086	T	0.13	0.1938	9.0099	0.36135	0.6632:0.0:0.3368:0.0	.	429	Q9NQC3	RTN4_HUMAN	P	223;223;429;223;223;197	ENSP00000384471:L223P;ENSP00000349944:L223P;ENSP00000337838:L429P;ENSP00000378109:L223P;ENSP00000385650:L223P;ENSP00000346465:L197P	ENSP00000337838:L429P	L	-	2	0	RTN4	55107453	0.829000	0.29322	0.028000	0.17463	0.441000	0.31987	1.274000	0.33132	0.180000	0.19960	0.528000	0.53228	CTT		0.383	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			G	55253949	A	G	55253949	3	3	111	1	0	0	0	0	1	0	0	0	13765	72	3	4	2358	4	RTN4	2	55253949	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	4474010	55253949	187945424	136	29270										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55561838	55561838	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaagattctacattccttcGcagttctaagttttcctcat	4	11	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:55561838G>A	ENST00000436346.1	-	15	2960	c.2119C>T	c.(2119-2121)Cga>Tga	p.R707*	CCDC88A_ENST00000336838.6_Nonsense_Mutation_p.R707*|AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000600219.1_RNA|CCDC88A_ENST00000263630.8_Nonsense_Mutation_p.R707*|AC012358.8_ENST00000599352.1_RNA|CCDC88A_ENST00000413716.2_Nonsense_Mutation_p.R707*|AC012358.8_ENST00000594078.1_RNA|AC012358.8_ENST00000608103.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	707					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.R707*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						ACATTCCTTCGCAGTTCTAAG	0.348																																																1	Substitution - Nonsense(1)	large_intestine(1)	2											80	82	82					2																	55561838		2202	4299	6501	55415342	SO:0001587	stop_gained	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.2119C>T	2.37:g.55561838G>A	ENSP00000410608:p.Arg707*		55415342	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Nonsense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	G	39	7.676002	0.98428	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	.	.	.	4.9	3.96	0.45880	.	0.000000	0.40818	U	0.001009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8176	14.4226	0.67193	0.0:0.0:0.7525:0.2475	.	.	.	.	X	707	.	ENSP00000263630:R707X	R	-	1	2	CCDC88A	55415342	0.993000	0.37304	1.000000	0.80357	0.969000	0.65631	1.493000	0.35605	2.421000	0.82119	0.462000	0.41574	CGA		0.348	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		A	55561838	G	A	55561838	4	1	111	1	0	0	0	0	0	1	0	0	2869	1095	38	1	3568	1	CCDC88A	2	55561838	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	307889	55561838	187637535	137	29271										
FAM161A	84140	hgsc.bcm.edu	37	chr2	62067077	62067077	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggaatgggtctggctttaaaTcgatttgttttctttttata	9	4	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:62067077T>A	ENST00000405894.3	-	3	1163	c.1062A>T	c.(1060-1062)cgA>cgT	p.R354R	FAM161A_ENST00000404929.1_Silent_p.R354R	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	354					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TGGCTTTAAATCGATTTGTTT	0.403																																																0			2											117	113	114					2																	62067077		1855	4106	5961	61920581	SO:0001819	synonymous_variant	84140				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1062A>T	2.37:g.62067077T>A			61920581	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																				0.403	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62067077	T	A	62067077	2	1	111	1	0	0	0	0	0	0	0	1	5488	1422	50	5		5	FAM161A	2	62067077	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	6505239	62067077	181132296	138	29272										
C2orf86	51057	hgsc.bcm.edu	37	chr2	63486507	63486507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcttgccacttcagctagtGccaattcacctttatctagt	5	12	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:63486507G>A	ENST00000272321.7	-	14	2377	c.1850C>T	c.(1849-1851)gCa>gTa	p.A617V	WDPCP_ENST00000398544.3_Missense_Mutation_p.A458V|WDPCP_ENST00000409120.1_Missense_Mutation_p.A425V|WDPCP_ENST00000409199.1_Missense_Mutation_p.A425V|WDPCP_ENST00000409562.3_Intron	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	617					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						TTCAGCTAGTGCCAATTCACC	0.358																																																0			2											130	124	126					2																	63486507		1829	4083	5912	63340011	SO:0001583	missense	51057				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.1850C>T	2.37:g.63486507G>A	ENSP00000272321:p.Ala617Val		63340011	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.897897	0.52227	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.42	4.53	0.55603	.	0.075573	0.52532	D	0.000078	T	0.42245	0.1194	L	0.41710	1.295	0.80722	D	1	P;P	0.51537	0.889;0.946	B;P	0.48677	0.426;0.586	T	0.19192	-1.0313	10	0.36615	T	0.2	-10.4156	14.5339	0.67947	0.072:0.0:0.928:0.0	.	617;458	O95876;O95876-3	FRITZ_HUMAN;.	V	617;425;425;458	ENSP00000272321:A617V;ENSP00000386592:A425V;ENSP00000386769:A425V;ENSP00000381552:A458V	ENSP00000272321:A617V	A	-	2	0	WDPCP	63340011	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.430000	0.59907	2.545000	0.85829	0.591000	0.81541	GCA		0.358	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		A	63486507	G	A	63486507	3	1	111	1	0	0	0	0	1	0	0	0	2207	1319	46	3	410	3	C2orf86	2	63486507	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1419430	63486507	179712866	139	29273										
FBXO48	554251	hgsc.bcm.edu	37	chr2	68691402	68691403	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcatccattgggtacatgaINSttttttctggtaggctaatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:68691402_68691403insT	ENST00000377957.3	-	4	813_814	c.406_407insA	c.(406-408)atcfs	p.I136fs		NM_001024680.1	NP_001019851.1	Q5FWF7	FBX48_HUMAN	F-box protein 48	136										endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TGGGTACATGATTTTTTCTGGT	0.401																																																0			2																																								68544907	SO:0001589	frameshift_variant	554251			BC089423	CCDS33213.1	2p13.3	2011-03-09			ENSG00000204923	ENSG00000204923		"F-boxes /  "other""	33857	protein-coding gene	gene with protein product							Standard	XM_005264407		Approved		uc002seo.3	Q5FWF7	OTTHUMG00000152585	ENST00000377957.3:c.407dupA	2.37:g.68691408_68691408dupT	ENSP00000367193:p.Ile136fs		68544906		Frame_Shift_Ins	INS	ENST00000377957.3	37	CCDS33213.1																																																																																				0.401	FBXO48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326900.2	NM_001024680		T	68691403	-	T	68691402	7	5	111	1	0	1	1	0	0	0	0	0	5776	333	12	0	64	0	FBXO48	2	68691402	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	5204895	68691402	174507971	140	29274										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71577132	71577132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catctgtaagccagcaagagCggatcccacatgaacctgtg	10	12	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:71577132C>T	ENST00000409544.1	+	2	1678	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W	ZNF638_ENST00000377802.2_Missense_Mutation_p.R350W|ZNF638_ENST00000264447.4_Missense_Mutation_p.R350W|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000355812.3_Missense_Mutation_p.R350W	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	350					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CCAGCAAGAGCGGATCCCACA	0.423																																																0			2											127	126	126					2																	71577132		2203	4300	6503	71430640	SO:0001583	missense	27332			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1048C>T	2.37:g.71577132C>T	ENSP00000386433:p.Arg350Trp		71430640	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.925108	0.34002	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.78003	-0.55;-1.14;0.01;-0.54;0.99;0.99	5.88	2.78	0.32641	.	0.171583	0.48767	D	0.000161	T	0.78880	0.4353	N	0.24115	0.695	0.31602	N	0.652565	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.995;0.995;0.997;0.993;0.995	T	0.80336	-0.1425	10	0.87932	D	0	-2.9758	11.5861	0.50918	0.5869:0.4131:0.0:0.0	.	456;350;350;350;350	F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;ZN638_HUMAN;.	W	350;456;350;350;350;350	ENSP00000386669:R350W;ENSP00000438189:R456W;ENSP00000348066:R350W;ENSP00000367033:R350W;ENSP00000264447:R350W;ENSP00000386433:R350W	ENSP00000264447:R350W	R	+	1	2	ZNF638	71430640	0.426000	0.25506	0.642000	0.29436	0.654000	0.38779	1.015000	0.29963	0.789000	0.33779	-0.181000	0.13052	CGG		0.423	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71577132	C	T	71577132	3	4	111	1	0	0	0	0	1	0	0	0	18094	759	27	1	1050	1	ZNF638	2	71577132	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2885730	71577132	171622241	141	29275										
EXOC6B	23233	hgsc.bcm.edu	37	chr2	72945272	72945272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caattttgtctgaatgtttgCggatgctctccagaaagtct	9	8	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:72945272C>T	ENST00000272427.6	-	6	759	c.629G>A	c.(628-630)cGc>cAc	p.R210H	EXOC6B_ENST00000410104.1_Missense_Mutation_p.R210H	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	210					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						TGAATGTTTGCGGATGCTCTC	0.423																																																0			2											133	130	131					2																	72945272		1883	4111	5994	72798780	SO:0001583	missense	23233			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.629G>A	2.37:g.72945272C>T	ENSP00000272427:p.Arg210His		72798780	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	37	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300842	0.95601	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.32753	1.44;1.44	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.63200	0.2491	M	0.87971	2.92	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.976;0.999	T	0.69146	-0.5222	10	0.87932	D	0	.	18.2035	0.89847	0.0:1.0:0.0:0.0	.	210;210	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	H	210	ENSP00000272427:R210H;ENSP00000386698:R210H	ENSP00000272427:R210H	R	-	2	0	EXOC6B	72798780	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.632000	0.89209	0.655000	0.94253	CGC		0.423	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		T	72945272	C	T	72945272	3	4	111	1	0	0	0	0	1	0	0	0	5322	768	27	1	1874	1	EXOC6B	2	72945272	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1368140	72945272	170254101	142	29276										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73677074	73677074	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actggcacaccaactgtaacCtcaacttcctactcacaaca	3	16	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:73677074C>A	ENST00000264448.6	+	8	3528	c.3417C>A	c.(3415-3417)acC>acA	p.T1139T	ALMS1_ENST00000409009.1_Silent_p.T1097T|ALMS1_ENST00000377715.1_Silent_p.T1139T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1139	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CAACTGTAACCTCAACTTCCT	0.483																																																0			2											153	150	151					2																	73677074		1864	4113	5977	73530582	SO:0001819	synonymous_variant	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.3417C>A	2.37:g.73677074C>A			73530582	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																				0.483	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73677074	C	A	73677074	2	1	111	1	0	0	0	0	0	0	0	1	535	668	24	2		2	ALMS1	2	73677074	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	731802	73677074	169522299	143	29277										
AUP1	165545	hgsc.bcm.edu	37	chr2	74755993	74755993	+	5'Flank	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttgagtgactccaccaactCcccccgcccattcatctcca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:74755993delC	ENST00000404568.3	-	0	0				HTRA2_ENST00000352222.3_5'Flank|DQX1_ENST00000393951.2_5'Flank|AUP1_ENST00000377526.3_Frame_Shift_Del_p.E137fs|HTRA2_ENST00000258080.3_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TCCACCAACTCCCCCCGCCCA	0.577																																																0			2											44	46	45					2																	74755993		1884	4111	5995	74609501	SO:0001631	upstream_gene_variant	550			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		2.37:g.74755993delC	Exception_encountered		74609501	Q6B017|Q8NAM8	Frame_Shift_Del	DEL	ENST00000404568.3	37	CCDS1949.2																																																																																				0.577	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		-	74755993	C	-	74755993	6	5	111	0	1	1	0	1	0	0	0	0	1221	864	30	0		0	AUP1	2	74755993	5'Flank	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1078919	74755993	168443380	144	29278										
SMYD1	150572	hgsc.bcm.edu	37	chr2	88383972	88383972	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccacaagaatgaatgttcggCcatcaagagatatgggaagg	12	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:88383972C>G	ENST00000419482.2	+	2	360	c.275C>G	c.(274-276)gCc>gGc	p.A92G	MIR4780_ENST00000584268.1_RNA|SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000444564.2_Missense_Mutation_p.A92G|SMYD1_ENST00000438570.1_Missense_Mutation_p.A92G	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	92	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						GAATGTTCGGCCATCAAGAGA	0.537																																																0			2											98	83	88					2																	88383972		2203	4300	6503	88165087	SO:0001583	missense	150572			AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.275C>G	2.37:g.88383972C>G	ENSP00000393453:p.Ala92Gly		88165087	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	37	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529922	0.85706	.	.	ENSG00000115593	ENST00000419482;ENST00000444564;ENST00000438570	T;T;T	0.14516	2.5;2.5;2.5	5.63	5.63	0.86233	SET domain (2);	0.000000	0.85682	D	0.000000	T	0.30916	0.0780	L	0.54965	1.715	0.80722	D	1	D;D	0.59357	0.969;0.985	P;P	0.58820	0.846;0.797	T	0.00254	-1.1874	10	0.49607	T	0.09	-17.6667	18.6665	0.91492	0.0:1.0:0.0:0.0	.	92;92	Q8NB12;C9JUP3	SMYD1_HUMAN;.	G	92	ENSP00000393453:A92G;ENSP00000407888:A92G;ENSP00000387482:A92G	ENSP00000393453:A92G	A	+	2	0	SMYD1	88165087	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	7.441000	0.80485	2.655000	0.90218	0.555000	0.69702	GCC		0.537	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		G	88383972	C	G	88383972	3	3	111	1	0	0	0	0	1	0	0	0	14858	739	26	5	281	5	SMYD1	2	88383972	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	13627979	88383972	154815401	145	29279										
C2orf51	200523	hgsc.bcm.edu	37	chr2	88828791	88828791	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcacatatccagcttcccaCgatctgcacctggcccaggg	8	16	2	0	rs151127650	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:88828791C>T	ENST00000303254.3	+	4	484	c.342C>T	c.(340-342)caC>caT	p.H114H		NM_152670.2	NP_689883.1	Q96LM6	TEX37_HUMAN	testis expressed 37	114						nucleus (GO:0005634)											CAGCTTCCCACGATCTGCACC	0.602													C|||	8	0.00159744	0.0061	0	5008	,	,		19817	0		0	False		,,,				2504	0															0			2						C		18,4388	25.3+/-52.1	0,18,2185	130	118	122		342	-8.2	0	2	dbSNP_134	122	0,8600		0,0,4300	yes	coding-synonymous	C2orf51	NM_152670.2		0,18,6485	TT,TC,CC		0.0,0.4085,0.1384		114/181	88828791	18,12988	2203	4300	6503	88609906	SO:0001819	synonymous_variant	200523			AK058098	CCDS2003.1	2p11.2	2014-01-28	2012-09-14	2012-09-14	ENSG00000172073	ENSG00000172073			26341	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 21kDa"		"chromosome 2 open reading frame 51"	C2orf51		17091336	Standard	NM_152670		Approved	FLJ25369, TSC21	uc002stb.2	Q96LM6	OTTHUMG00000130332	ENST00000303254.3:c.342C>T	2.37:g.88828791C>T			88609906		Silent	SNP	ENST00000303254.3	37	CCDS2003.1																																																																																				0.602	TEX37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252682.1	NM_152670		T	88828791	C	T	88828791	2	4	111	1	0	0	0	0	0	0	0	1	2179	535	19	1		1	C2orf51	2	88828791	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	444819	88828791	154370582	146	29280										
MRPS5	64969	hgsc.bcm.edu	37	chr2	95753233	95753233	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atccttcctcaagggcccccGgggggacgcaaccacaatgg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:95753233delG	ENST00000272418.2	-	12	1370	c.1162delC	c.(1162-1164)cggfs	p.R388fs		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	388					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						AAGGGCCCCCGGGGGGACGCA	0.557																																																0			2											74	69	71					2																	95753233		2203	4300	6503	95116960	SO:0001589	frameshift_variant	64969			AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"Mitochondrial ribosomal proteins / small subunits"	14498	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S5"	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.1162delC	2.37:g.95753233delG	ENSP00000272418:p.Arg388fs		95116960	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Frame_Shift_Del	DEL	ENST00000272418.2	37	CCDS2010.1																																																																																				0.557	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902		-	95753233	G	-	95753233	7	5	111	1	0	1	0	1	0	0	0	0	9876	1115	39	0	134	0	MRPS5	2	95753233	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	6924442	95753233	147446140	147	29281										
FAHD2A	51011	hgsc.bcm.edu	37	chr2	96078466	96078466	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggatgtcatcctaactgggaCccccccaggtgtcggtgtat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:96078466delC	ENST00000233379.4	+	7	989	c.836delC	c.(835-837)accfs	p.T279fs	FAHD2A_ENST00000447036.1_Frame_Shift_Del_p.T279fs	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						CTAACTGGGACCCCCCCAGGT	0.562																																																0			2											43	43	43					2																	96078466		2203	4298	6501	95442193	SO:0001589	frameshift_variant	51011			AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.836delC	2.37:g.96078466delC	ENSP00000233379:p.Thr279fs		95442193	Q9Y3B0	Frame_Shift_Del	DEL	ENST00000233379.4	37	CCDS2014.1																																																																																				0.562	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044		-	96078466	C	-	96078466	7	5	111	1	0	1	0	1	0	0	0	0	5389	507	18	0	858	0	FAHD2A	2	96078466	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	325233	96078466	147120907	148	29282										
ADRA2B	151	hgsc.bcm.edu	37	chr2	96780980	96780980	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggggttcacactcttcctcCtcctcctcctcctcttcagc	5	19	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:96780980C>T	ENST00000409345.3	-	1	1004	c.909G>A	c.(907-909)gaG>gaA	p.E303E		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	303	Asp/Glu-rich (acidic).				activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	Actcttcctcctcctcctcct	0.652																																																0			2											11	15	14					2																	96780980		2105	4196	6301	96144707	SO:0001819	synonymous_variant	151			M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.909G>A	2.37:g.96780980C>T			96144707	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																				0.652	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			T	96780980	C	T	96780980	2	4	111	1	0	0	0	0	0	0	0	1	338	680	24	3		3	ADRA2B	2	96780980	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	702514	96780980	146418393	149	29283										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97274706	97274708	+	In_Frame_Del	DEL	CTT	CTT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcgggccacatcgcggggCttcttcttcttctcagcatc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	CTT	CTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:97274706_97274708delCTT	ENST00000431828.1	-	13	1553_1555	c.1477_1479delAAG	c.(1477-1479)aagdel	p.K493del	KANSL3_ENST00000440133.1_In_Frame_Del_p.K287del|KANSL3_ENST00000441706.2_In_Frame_Del_p.K406del|KANSL3_ENST00000599854.1_In_Frame_Del_p.K406del|KANSL3_ENST00000487070.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	493					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CATCGCGGGGCTTCTTCTTCTTC	0.601																																																0			2																																								96638435	SO:0001651	inframe_deletion	55683			BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1477_1479delAAG	2.37:g.97274715_97274717delCTT	ENSP00000396749:p.Lys493del		96638433	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	In_Frame_Del	DEL	ENST00000431828.1	37	CCDS46361.1																																																																																				0.601	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		-	97274708	CTT	-	97274706	7	5	111	1	0	1	0	1	0	0	0	0	8243	796	28	0	1193	0	KIAA1310	2	97274706	In_Frame_Del	DEL	CTT	TCGA-EI-6507-01A-11D-1733-10	493726	97274706	145924667	150	29284										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105886127	105886127	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagcttcccgtgcaggatggCgctctccatgggcaggccag	14	14	1	0	rs199861425		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:105886127C>T	ENST00000393359.2	-	11	2434	c.2008G>A	c.(2008-2010)Gcc>Acc	p.A670T	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.A670T			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	670					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TGCAGGATGGCGCTCTCCATG	0.652													C|||	1	0.000199681	0	0	5008	,	,		17125	0.001		0	False		,,,				2504	0				Esophageal Squamous(183;794 2019 9730 21801 48859)											0			2						C	THR/ALA,THR/ALA	1,4405		0,1,2202	20	21	21		2008,2008	5.2	1	2		21	0,8600		0,0,4300	no	missense,missense	TGFBRAP1	NM_001142621.1,NM_004257.4	58,58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	670/861,670/861	105886127	1,13005	2203	4300	6503	105252559	SO:0001583	missense	9392			AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2008G>A	2.37:g.105886127C>T	ENSP00000377027:p.Ala670Thr		105252559	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	33	5.237625	0.95240	2.27E-4	0.0	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19806	2.12;2.12	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.57154	0.2034	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.66948	-0.5794	10	0.56958	D	0.05	-28.7463	18.6511	0.91430	0.0:1.0:0.0:0.0	.	125;670	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	T	670;670;125	ENSP00000377027:A670T;ENSP00000258449:A670T	ENSP00000258449:A670T	A	-	1	0	TGFBRAP1	105252559	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.487000	0.81328	2.423000	0.82170	0.462000	0.41574	GCC		0.652	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		T	105886127	C	T	105886127	3	4	111	1	0	0	0	0	1	0	0	0	15863	768	27	1	582	1	TGFBRAP1	2	105886127	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	8611421	105886127	137313246	151	29285										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107460162	107460162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgcaggtctccaggccccGcatgaaaggaaccggctggg	14	13	2	1	rs80079355	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:107460162G>A	ENST00000409382.3	-	2	882	c.272C>T	c.(271-273)gCg>gTg	p.A91V	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.A91V|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.A91V	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	91					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						TCCAGGCCCCGCATGAAAGGA	0.622													G|||	254	0.0507188	0.1755	0.0216	5008	,	,		14128	0.005		0.002	False		,,,				2504	0															0			2						G	VAL/ALA,VAL/ALA,VAL/ALA	611,3739		41,529,1605	30	36	34		272,272,272	-1.4	0	2	dbSNP_131	34	18,8526		0,18,4254	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	64,64,64	41,547,5859	AA,AG,GG		0.2107,14.046,4.8782	benign,benign,benign	91/530,91/467,91/530	107460162	629,12265	2175	4272	6447	106826594	SO:0001583	missense	84620			AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.272C>T	2.37:g.107460162G>A	ENSP00000386942:p.Ala91Val		106826594	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	106	0.048534798534798536	91	0.18495934959349594	8	0.022099447513812154	6	0.01048951048951049	1	0.0013192612137203166	G	10.52	1.374099	0.24857	0.14046	0.002107	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.29655	2.56;2.56;1.56	5.35	-1.35	0.09114	.	1.615520	0.03144	N	0.166966	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.20261	0.043;0.001	B;B	0.08055	0.003;0.001	T	0.13124	-1.0521	9	0.05525	T	0.97	-0.9807	5.443	0.16519	0.3548:0.2384:0.4068:0.0	.	91;91	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	V	91	ENSP00000355273:A91V;ENSP00000386942:A91V;ENSP00000387332:A91V	ENSP00000355273:A91V	A	-	2	0	ST6GAL2	106826594	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.979000	0.03774	-0.003000	0.14444	-0.150000	0.13652	GCG		0.622	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		A	107460162	G	A	107460162	3	1	111	1	0	0	0	0	1	0	0	0	15261	1087	38	1	1424	1	ST6GAL2	2	107460162	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1574035	107460162	135739211	152	29286										
GCC2	9648	hgsc.bcm.edu	37	chr2	109087884	109087884	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaacaataaactcagttcagAaaaaaaacagttgagtaggg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:109087884delA	ENST00000309863.6	+	6	2813	c.2099delA	c.(2098-2100)gaafs	p.E700fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	700					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						CTCAGTTCAGAAAAAAAACAG	0.308																																																0			2											114	144	134					2																	109087884		2203	4297	6500	108454316	SO:0001589	frameshift_variant	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2099delA	2.37:g.109087884delA	ENSP00000307939:p.Glu700fs		108454316	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Del	DEL	ENST00000309863.6	37	CCDS33268.1																																																																																				0.308	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		-	109087884	A	-	109087884	7	5	111	1	0	1	0	1	0	0	0	0	6306	246	9	0	2121	0	GCC2	2	109087884	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	1627722	109087884	134111489	153	29287										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112839024	112839024	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttctggattgcagctgttaTttttttgggaatgcttgaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:112839024delT	ENST00000283206.4	+	8	1136	c.767delT	c.(766-768)attfs	p.I256fs		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	256						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						GCAGCTGTTATTTTTTTGGGA	0.343																																																0			2											131	142	138					2																	112839024		2203	4300	6503	112555495	SO:0001589	frameshift_variant	84910			AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.767delT	2.37:g.112839024delT	ENSP00000283206:p.Ile256fs		112555495	A8K2M9|Q1RLN2|Q53R54	Frame_Shift_Del	DEL	ENST00000283206.4	37	CCDS33275.1																																																																																				0.343	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		-	112839024	T	-	112839024	7	5	111	1	0	1	0	1	0	0	0	0	16250	1493	52	0	797	0	TMEM87B	2	112839024	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	3751140	112839024	130360349	154	29288										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112847235	112847235	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acagtcatgcaccgggtgatCggactggggcttctatactt	12	10	2	1	rs547196638		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:112847235C>T	ENST00000283206.4	+	10	1341	c.972C>T	c.(970-972)atC>atT	p.I324I	TMEM87B_ENST00000463427.1_3'UTR	NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	324						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						ACCGGGTGATCGGACTGGGGC	0.438													C|||	1	0.000199681	0	0	5008	,	,		19437	0.001		0	False		,,,				2504	0															0			2											137	128	131					2																	112847235		2203	4300	6503	112563706	SO:0001819	synonymous_variant	84910			AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.972C>T	2.37:g.112847235C>T			112563706	A8K2M9|Q1RLN2|Q53R54	Silent	SNP	ENST00000283206.4	37	CCDS33275.1																																																																																				0.438	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		T	112847235	C	T	112847235	2	4	111	1	0	0	0	0	0	0	0	1	16250	874	31	1		1	TMEM87B	2	112847235	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	8211	112847235	130352138	155	29289										
FBLN7	129804	hgsc.bcm.edu	37	chr2	112917331	112917331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggccaggagacacgcttcGccgagggcatccgccacatg	14	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:112917331G>A	ENST00000331203.2	+	2	425	c.154G>A	c.(154-156)Gcc>Acc	p.A52T	FBLN7_ENST00000409667.3_Missense_Mutation_p.A52T|FBLN7_ENST00000409450.3_Missense_Mutation_p.A52T|FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409903.1_Missense_Mutation_p.A52T	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	52					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GACACGCTTCGCCGAGGGCAT	0.662																																																0			2											28	28	28					2																	112917331		2203	4299	6502	112633802	SO:0001583	missense	129804				CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.154G>A	2.37:g.112917331G>A	ENSP00000331411:p.Ala52Thr		112633802	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	37	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	G	6.352	0.433020	0.12045	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409667;ENST00000409450;ENST00000441565	T;T;T;T;D	0.82711	-1.46;-1.38;1.44;-1.4;-1.64	5.66	1.27	0.21489	.	0.173163	0.51477	N	0.000093	T	0.64000	0.2559	N	0.05383	-0.06	0.28186	N	0.927965	B;B;B;B	0.21147	0.006;0.004;0.001;0.052	B;B;B;B	0.10450	0.003;0.002;0.001;0.005	T	0.53578	-0.8419	10	0.29301	T	0.29	-20.6785	11.2158	0.48825	0.3134:0.0:0.6866:0.0	.	52;52;52;52	Q53RD9-4;Q53RD9-2;Q53RD9;B8ZZC1	.;.;FBLN7_HUMAN;.	T	52;52;52;52;3	ENSP00000331411:A52T;ENSP00000386295:A52T;ENSP00000386822:A52T;ENSP00000387000:A52T;ENSP00000388025:A3T	ENSP00000331411:A52T	A	+	1	0	FBLN7	112633802	0.234000	0.23783	0.999000	0.59377	0.994000	0.84299	0.710000	0.25748	0.336000	0.23639	-0.226000	0.12346	GCC		0.662	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		A	112917331	G	A	112917331	3	1	111	1	0	0	0	0	1	0	0	0	5720	1087	38	1	160	1	FBLN7	2	112917331	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	70096	112917331	130282042	156	29290										
POLR1B	84172	hgsc.bcm.edu	37	chr2	113309416	113309416	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaaggaaaagaggatgattCtttccttaggaactctgttt	9	6	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:113309416C>A	ENST00000263331.5	+	6	1407	c.827C>A	c.(826-828)tCt>tAt	p.S276Y	POLR1B_ENST00000409894.3_Missense_Mutation_p.S276Y|POLR1B_ENST00000417433.2_Missense_Mutation_p.S220Y|POLR1B_ENST00000541869.1_Missense_Mutation_p.S314Y|POLR1B_ENST00000537335.1_Missense_Mutation_p.S65Y	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	276					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						GAGGATGATTCTTTCCTTAGG	0.373																																					Ovarian(16;256 576 9537 23969 41147)											0			2											112	111	112					2																	113309416		2203	4300	6503	113025887	SO:0001583	missense	84172			AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.827C>A	2.37:g.113309416C>A	ENSP00000263331:p.Ser276Tyr		113025887	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731318	0.89390	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.21	5.21	0.72293	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.053146	0.85682	D	0.000000	T	0.81004	0.4733	M	0.83118	2.625	0.80722	D	1	D;D;B;D	0.76494	0.998;0.999;0.399;0.993	D;D;P;D	0.74674	0.929;0.984;0.577;0.942	D	0.83650	0.0155	10	0.72032	D	0.01	-23.214	17.8986	0.88897	0.0:1.0:0.0:0.0	.	314;276;220;276	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	Y	276;314;276;65;220	ENSP00000263331:S276Y;ENSP00000444136:S314Y;ENSP00000387143:S276Y;ENSP00000437914:S65Y;ENSP00000405358:S220Y	ENSP00000263331:S276Y	S	+	2	0	POLR1B	113025887	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.962000	0.70364	2.604000	0.88044	0.591000	0.81541	TCT		0.373	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		A	113309416	C	A	113309416	3	1	111	1	0	0	0	0	1	0	0	0	12241	913	32	2	849	2	POLR1B	2	113309416	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	392085	113309416	129889957	157	29291										
DPP10	57628	hgsc.bcm.edu	37	chr2	116447456	116447456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccagaagtagaggactccGtcttgcagtacgcggcctgg	13	12	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:116447456G>A	ENST00000410059.1	+	7	1015	c.535G>A	c.(535-537)Gtc>Atc	p.V179I	DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000393147.2_Missense_Mutation_p.V183I|DPP10_ENST00000310323.8_Missense_Mutation_p.V172I|DPP10_ENST00000409163.1_Missense_Mutation_p.V129I	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	179						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGAGGACTCCGTCTTGCAGTA	0.438																																																0			2											84	91	89					2																	116447456		2203	4300	6503	116163926	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.535G>A	2.37:g.116447456G>A	ENSP00000386565:p.Val179Ile		116163926	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.164856	0.38217	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.44	-2.02	0.07388	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.225321	0.36778	N	0.002414	T	0.22859	0.0552	L	0.55481	1.735	0.24648	N	0.993537	B;B;B;B	0.22800	0.027;0.075;0.034;0.034	B;B;B;B	0.20955	0.013;0.018;0.032;0.022	T	0.33650	-0.9860	10	0.15499	T	0.54	-12.1613	11.1686	0.48558	0.491:0.0:0.509:0.0	.	172;183;175;179	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	I	179;129;175;183;172;129	ENSP00000386565:V179I;ENSP00000387038:V129I;ENSP00000376854:V175I;ENSP00000376855:V183I;ENSP00000309066:V172I	ENSP00000309066:V172I	V	+	1	0	DPP10	116163926	0.323000	0.24643	0.908000	0.35775	0.965000	0.64279	0.668000	0.25127	-0.308000	0.08792	-0.237000	0.12165	GTC		0.438	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116447456	G	A	116447456	3	1	111	1	0	0	0	0	1	0	0	0	4738	1145	40	1	732	1	DPP10	2	116447456	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3138040	116447456	126751917	158	29292										
GPR17	2840	hgsc.bcm.edu	37	chr2	128409270	128409270	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaaaaggctcaagggcccgCcccccagcttcgaagggaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:128409270delC	ENST00000272644.3	+	3	1119	c.1045delC	c.(1045-1047)cccfs	p.P350fs	LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000324938.5_Intron|GPR17_ENST00000544369.1_Frame_Shift_Del_p.P350fs|LIMS2_ENST00000410011.1_Intron|GPR17_ENST00000393018.3_Frame_Shift_Del_p.P350fs|LIMS2_ENST00000409254.1_5'Flank|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000409808.2_Intron|GPR17_ENST00000486700.1_3'UTR	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	350					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		CAAGGGCCCGCCCCCCAGCTT	0.617																																																0			2											57	70	66					2																	128409270		2203	4299	6502	128125740	SO:0001589	frameshift_variant	2840				CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"GPCR / Class A : Orphans"	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.1045delC	2.37:g.128409270delC	ENSP00000272644:p.Pro350fs		128125740	A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Frame_Shift_Del	DEL	ENST00000272644.3	37	CCDS2148.1																																																																																				0.617	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1			-	128409270	C	-	128409270	7	5	111	1	0	1	0	1	0	0	0	0	6687	739	26	0	1051	0	GPR17	2	128409270	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	11961814	128409270	114790103	159	29293										
POTEF	728378	hgsc.bcm.edu	37	chr2	130872806	130872806	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctttatcagagctgtcctcTttttgttgtcaaggacatta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:130872806delT	ENST00000409914.2	-	4	1016	c.617delA	c.(616-618)aagfs	p.K206fs	POTEF_ENST00000361163.4_Frame_Shift_Del_p.K206fs|POTEF_ENST00000357462.5_Frame_Shift_Del_p.K206fs|POTEF_ENST00000360967.5_Frame_Shift_Del_p.K206fs	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	206					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K206R(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						AGCTGTCCTCTTTTTGTTGTC	0.403																																																2	Substitution - Missense(2)	lung(2)	2											12	14	13					2																	130872806		1993	3901	5894	130589276	SO:0001589	frameshift_variant	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.617delA	2.37:g.130872806delT	ENSP00000386786:p.Lys206fs		130589276	A6NC34	Frame_Shift_Del	DEL	ENST00000409914.2	37	CCDS46409.1																																																																																				0.403	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		-	130872806	T	-	130872806	7	5	111	1	0	1	0	1	0	0	0	0	12296	1609	56	0	2666	0	POTEF	2	130872806	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	2463536	130872806	112326567	160	29294										
LCT	3938	hgsc.bcm.edu	37	chr2	136564710	136564710	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcctcacctgatatgcagcAgaagctgcactccagatgaa	8	13	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:136564710A>G	ENST00000264162.2	-	9	4171	c.4161T>C	c.(4159-4161)tcT>tcC	p.S1387S		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1387	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GATATGCAGCAGAAGCTGCAC	0.567																																																0			2											123	99	107					2																	136564710		2203	4300	6503	136281180	SO:0001819	synonymous_variant	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4161T>C	2.37:g.136564710A>G			136281180	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.567	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136564710	A	G	136564710	2	3	111	1	0	0	0	0	0	0	0	1	8715	175	7	4		4	LCT	2	136564710	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5691904	136564710	106634663	161	29295										
RBM43	375287	hgsc.bcm.edu	37	chr2	152107556	152107556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atctcgaacttaattgttcaCatgcccttttgatcattctt	4	10	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:152107556C>T	ENST00000331426.5	-	4	1089	c.938G>A	c.(937-939)tGt>tAt	p.C313Y		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	313							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		TAATTGTTCACATGCCCTTTT	0.333																																																0			2											156	151	153					2																	152107556		2203	4300	6503	151815802	SO:0001583	missense	375287			AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"RNA binding motif (RRM) containing"	24790	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 38"	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.938G>A	2.37:g.152107556C>T	ENSP00000331211:p.Cys313Tyr		151815802	B2RMT5	Missense_Mutation	SNP	ENST00000331426.5	37	CCDS2191.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846864	0.51164	.	.	ENSG00000184898	ENST00000331426	T	0.52295	0.67	5.48	4.58	0.56647	.	0.488971	0.22393	N	0.060659	T	0.54319	0.1851	L	0.32530	0.975	0.58432	D	0.999999	D	0.69078	0.997	D	0.69654	0.965	T	0.49184	-0.8966	10	0.30078	T	0.28	-1.1375	12.7871	0.57512	0.1693:0.8307:0.0:0.0	.	313	Q6ZSC3	RBM43_HUMAN	Y	313	ENSP00000331211:C313Y	ENSP00000331211:C313Y	C	-	2	0	RBM43	151815802	0.464000	0.25807	0.059000	0.19551	0.006000	0.05464	1.393000	0.34497	1.484000	0.48361	0.655000	0.94253	TGT		0.333	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557		T	152107556	C	T	152107556	3	4	111	1	0	0	0	0	1	0	0	0	13174	478	17	3	139	3	RBM43	2	152107556	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	15542846	152107556	91091817	162	29296										
NEB	4703	hgsc.bcm.edu	37	chr2	152506778	152506778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtttctgtctggaggctgaCgatatttcttctcactgatg	10	8	4	2	rs373589529		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:152506778C>T	ENST00000172853.10	-	54	7490	c.7343G>A	c.(7342-7344)cGt>cAt	p.R2448H	NEB_ENST00000409198.1_Missense_Mutation_p.R2448H|NEB_ENST00000427231.2_Missense_Mutation_p.R2448H|NEB_ENST00000397345.3_Missense_Mutation_p.R2448H|NEB_ENST00000603639.1_Missense_Mutation_p.R2448H|NEB_ENST00000604864.1_Missense_Mutation_p.R2448H			P20929	NEBU_HUMAN	nebulin	2448					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGAGGCTGACGATATTTCTT	0.463																																																0			2						C	HIS/ARG,HIS/ARG,HIS/ARG	1,3839		0,1,1919	159	150	153		7343,7343,7343	5.2	1	2		153	0,8262		0,0,4131	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	29,29,29	0,1,6050	TT,TC,CC		0.0,0.026,0.0083	probably-damaging,probably-damaging,probably-damaging	2448/8526,2448/8526,2448/6670	152506778	1,12101	1920	4131	6051	152215024	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7343G>A	2.37:g.152506778C>T	ENSP00000172853:p.Arg2448His		152215024	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	33	5.255863	0.95336	2.6E-4	0.0	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.09538	3.0;3.0;3.0;2.97	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.38931	0.1059	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.30822	-0.9965	10	0.59425	D	0.04	.	18.7871	0.91960	0.0:1.0:0.0:0.0	.	2448	P20929	NEBU_HUMAN	H	2448	ENSP00000386259:R2448H;ENSP00000380505:R2448H;ENSP00000416578:R2448H;ENSP00000172853:R2448H	ENSP00000172853:R2448H	R	-	2	0	NEB	152215024	1.000000	0.71417	0.980000	0.43619	0.989000	0.77384	7.770000	0.85390	2.456000	0.83038	0.650000	0.86243	CGT		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152506778	C	T	152506778	3	4	111	1	0	0	0	0	1	0	0	0	10333	536	19	1	18859	1	NEB	2	152506778	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	399222	152506778	90692595	163	29297										
UPP2	151531	hgsc.bcm.edu	37	chr2	158980303	158980303	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actgtgctccttttccagagAaaaaaagttagactacttga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:158980303delA	ENST00000005756.4	+	6	901	c.707delA	c.(706-708)gaafs	p.E236fs	UPP2_ENST00000605860.1_Frame_Shift_Del_p.E293fs|UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Frame_Shift_Del_p.E293fs	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	236					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	TTTTCCAGAGAAAAAAAGTTA	0.468																																																0			2											93	92	93					2																	158980303		2203	4300	6503	158688549	SO:0001589	frameshift_variant	151531			AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.707delA	2.37:g.158980303delA	ENSP00000005756:p.Glu236fs		158688549	B3KV87	Frame_Shift_Del	DEL	ENST00000005756.4	37	CCDS2207.1																																																																																				0.468	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		-	158980303	A	-	158980303	7	5	111	1	0	1	0	1	0	0	0	0	17053	246	9	0	908	0	UPP2	2	158980303	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	6473525	158980303	84219070	164	29298										
TANC1	85461	hgsc.bcm.edu	37	chr2	160053150	160053150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggataagaagggccagtgtgCgcttgtccacagtgccctac	13	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:160053150C>T	ENST00000263635.6	+	18	3248	c.3011C>T	c.(3010-3012)gCg>gTg	p.A1004V	TANC1_ENST00000454300.1_Missense_Mutation_p.A898V	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1004					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GGCCAGTGTGCGCTTGTCCAC	0.602																																																0			2											61	65	64					2																	160053150		2086	4204	6290	159761396	SO:0001583	missense	85461			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3011C>T	2.37:g.160053150C>T	ENSP00000263635:p.Ala1004Val		159761396	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	C	35	5.487758	0.96323	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.70399	-0.48;2.13	6.06	6.06	0.98353	Ankyrin repeat-containing domain (4);	0.049671	0.85682	D	0.000000	D	0.82365	0.5021	L	0.60067	1.865	0.80722	D	1	D;D;D	0.69078	0.996;0.997;0.995	D;P;P	0.64410	0.925;0.842;0.846	T	0.82319	-0.0516	10	0.87932	D	0	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	996;898;1004	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	V	898;1004	ENSP00000396339:A898V;ENSP00000263635:A1004V	ENSP00000263635:A1004V	A	+	2	0	TANC1	159761396	1.000000	0.71417	0.974000	0.42286	0.935000	0.57460	6.042000	0.70996	2.880000	0.98712	0.650000	0.86243	GCG		0.602	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160053150	C	T	160053150	3	4	111	1	0	0	0	0	1	0	0	0	15583	768	27	1	3073	1	TANC1	2	160053150	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1072847	160053150	83146223	165	29299										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167108273	167108273	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaggtctcaatttttgtcttAccatctgtgaaacaggcctc	7	10	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:167108273A>G	ENST00000409435.1	-	17	3472		c.e17+1		AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000375387.4_Splice_Site|SCN9A_ENST00000303354.6_Splice_Site|SCN9A_ENST00000409672.1_Splice_Site			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit						behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTTTGTCTTACCATCTGTGA	0.453																																																0			2											103	98	100					2																	167108273		1887	4116	6003	166816519	SO:0001630	splice_region_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3472+1T>C	2.37:g.167108273A>G			166816519	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Splice_Site	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917298	0.73098	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1632	0.72801	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCN9A	166816519	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	8.678000	0.91211	2.221000	0.72209	0.528000	0.53228	.		0.453	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	Intron	G	167108273	A	G	167108273	5	3	111	1	0	0	0	0	0	0	1	0	13962	405	14	4	2532	4	SCN9A	2	167108273	Splice_Site	SNP	A	TCGA-EI-6507-01A-11D-1733-10	7055123	167108273	76091100	166	29300										
LRP2	4036	hgsc.bcm.edu	37	chr2	170003400	170003400	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctcgaaaaccaggatgttGcggtcctctccattcatcca	7	14	2	0	rs375138694		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:170003400G>A	ENST00000263816.3	-	69	12945	c.12660C>T	c.(12658-12660)cgC>cgT	p.R4220R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4220				R -> P (in Ref. 3; AAB02882). {ECO:0000305}.	cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCAGGATGTTGCGGTCCTCTC	0.458																																																0			2						G		1,4405	2.1+/-5.4	0,1,2202	105	84	91		12660	1.7	0.1	2		91	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		4220/4656	170003400	1,13005	2203	4300	6503	169711646	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12660C>T	2.37:g.170003400G>A			169711646	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170003400	G	A	170003400	2	1	111	1	0	0	0	0	0	0	0	1	8985	1306	46	3		3	LRP2	2	170003400	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2895127	170003400	73195973	167	29301										
KBTBD10	10324	hgsc.bcm.edu	37	chr2	170374733	170374734	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggtgtttatcttcaaccccINSaaaaaaggagattggaaaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:170374733_170374734insA	ENST00000284669.1	+	4	1487_1488	c.1410_1411insA	c.(1411-1413)aaafs	p.K471fs	KLHL41_ENST00000463400.1_3'UTR|BBS5_ENST00000554017.1_Frame_Shift_Ins_p.K409fs|RP11-724O16.1_ENST00000513963.1_Frame_Shift_Ins_p.K409fs	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	471					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)											TCTTCAACCCCAAAAAAGGAGA	0.376																																																0			2																																								170082980	SO:0001589	frameshift_variant	10324			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1416dupA	2.37:g.170374739_170374739dupA	ENSP00000284669:p.Lys471fs		170082979	Q53R42	Frame_Shift_Ins	INS	ENST00000284669.1	37	CCDS2234.1																																																																																				0.376	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		A	170374734	-	A	170374733	7	5	111	1	0	1	1	0	0	0	0	0	8011	581	21	0	1424	0	KBTBD10	2	170374733	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	371333	170374733	72824640	168	29302										
PPIG	9360	hgsc.bcm.edu	37	chr2	170493349	170493349	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaacagttagaatcaaagagTaatgagcatgatcacagtaa	8	5	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:170493349T>C	ENST00000260970.3	+	14	1801	c.1581T>C	c.(1579-1581)agT>agC	p.S527S	PPIG_ENST00000409714.3_Silent_p.S512S|PPIG_ENST00000448752.2_Silent_p.S527S	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	527					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AATCAAAGAGTAATGAGCATG	0.333																																																0			2											56	55	55					2																	170493349		2203	4300	6503	170201595	SO:0001819	synonymous_variant	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1581T>C	2.37:g.170493349T>C			170201595	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																				0.333	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			C	170493349	T	C	170493349	2	2	111	1	0	0	0	0	0	0	0	1	12358	1635	57	4		4	PPIG	2	170493349	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	118616	170493349	72706024	169	29303										
UBR3	130507	hgsc.bcm.edu	37	chr2	170843230	170843230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgaggcagtatatgactgtgTtatttgtggacagagtggcc	14	6	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:170843230T>C	ENST00000272793.5	+	25	3760	c.3710T>C	c.(3709-3711)gTt>gCt	p.V1237A	UBR3_ENST00000418381.1_Missense_Mutation_p.V1237A|UBR3_ENST00000392631.1_Missense_Mutation_p.V58A			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1237					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TATGACTGTGTTATTTGTGGA	0.423																																																0			2											107	105	106					2																	170843230		2203	4300	6503	170551476	SO:0001583	missense	130507			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3710T>C	2.37:g.170843230T>C	ENSP00000272793:p.Val1237Ala		170551476	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	T	26.6	4.756753	0.89843	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631	T;T;T	0.56444	0.85;0.85;0.46	5.27	5.27	0.74061	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.67887	0.2941	L	0.60455	1.87	0.43360	D	0.995436	D;D;P	0.61697	0.984;0.99;0.924	D;D;P	0.73380	0.956;0.98;0.9	T	0.67043	-0.5770	10	0.38643	T	0.18	.	15.1979	0.73108	0.0:0.0:0.0:1.0	.	1237;58;1237	Q6ZT12;Q6ZT12-2;E7EVK3	UBR3_HUMAN;.;.	A	1237;1237;1237;58	ENSP00000272793:V1237A;ENSP00000396068:V1237A;ENSP00000376408:V58A	ENSP00000272793:V1237A	V	+	2	0	UBR3	170551476	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.679000	0.84048	1.992000	0.58205	0.477000	0.44152	GTT		0.423	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		C	170843230	T	C	170843230	3	2	111	1	0	0	0	0	1	0	0	0	16943	1725	60	4	3808	4	UBR3	2	170843230	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	349881	170843230	72356143	170	29304										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175287696	175287696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggagaattcctgaccactGcaagcatggtttctatttta	9	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:175287696G>A	ENST00000272732.6	+	6	920	c.838G>A	c.(838-840)Gca>Aca	p.A280T	SCRN3_ENST00000409673.3_Missense_Mutation_p.A273T|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	280							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			CCTGACCACTGCAAGCATGGT	0.378																																																0			2											113	112	112					2																	175287696		2203	4300	6503	174995942	SO:0001583	missense	79634			AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.838G>A	2.37:g.175287696G>A	ENSP00000272732:p.Ala280Thr		174995942	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	37	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	G	34	5.333634	0.95758	.	.	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.11063	2.81;2.81	5.16	5.16	0.70880	.	0.051146	0.85682	D	0.000000	T	0.15609	0.0376	M	0.66297	2.02	0.50313	D	0.999861	B;B	0.32939	0.391;0.22	B;B	0.25140	0.058;0.039	T	0.02574	-1.1139	10	0.87932	D	0	-17.1647	18.6679	0.91499	0.0:0.0:1.0:0.0	.	273;280	B4DI11;Q0VDG4	.;SCRN3_HUMAN	T	273;280	ENSP00000387142:A273T;ENSP00000272732:A280T	ENSP00000272732:A280T	A	+	1	0	SCRN3	174995942	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.475000	0.73582	2.420000	0.82092	0.561000	0.74099	GCA		0.378	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		A	175287696	G	A	175287696	3	1	111	1	0	0	0	0	1	0	0	0	13977	1319	46	3	856	3	SCRN3	2	175287696	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4444466	175287696	67911677	171	29305										
HOXD9	3235	hgsc.bcm.edu	37	chr2	176988295	176988295	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcagcattcgcagccgcagCagcagcaacttgacccaagt	10	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:176988295C>T	ENST00000249499.6	+	1	1208	c.799C>T	c.(799-801)Cag>Tag	p.Q267*	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	267					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GCAGCCGCAGCAGCAGCAACT	0.542																																					GBM(47;924 952 7959 9248 12176)											0			2											17	17	17					2																	176988295		2188	4245	6433	176696541	SO:0001587	stop_gained	3235				CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"Homeoboxes / ANTP class : HOXL subclass"	5140	protein-coding gene	gene with protein product		142982	"homeo box D9"	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.799C>T	2.37:g.176988295C>T	ENSP00000249499:p.Gln267*		176696541	Q86ST1	Nonsense_Mutation	SNP	ENST00000249499.6	37	CCDS2267.2	.	.	.	.	.	.	.	.	.	.	C	37	6.461883	0.97585	.	.	ENSG00000128709	ENST00000249499	.	.	.	4.91	4.91	0.64330	.	3.234920	0.00941	N	0.002823	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.514	0.90928	0.0:1.0:0.0:0.0	.	.	.	.	X	267	.	ENSP00000249499:Q267X	Q	+	1	0	HOXD9	176696541	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	5.028000	0.64115	2.418000	0.82041	0.555000	0.69702	CAG		0.542	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			T	176988295	C	T	176988295	4	4	111	1	0	0	0	0	0	1	0	0	7347	711	25	3	801	3	HOXD9	2	176988295	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1700599	176988295	66211078	172	29306										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179214085	179214085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaacagattatacaaagctGcaagaagaattttgtctaat	6	6	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:179214085G>A	ENST00000190611.4	+	12	1498	c.1122G>A	c.(1120-1122)ctG>ctA	p.L374L	OSBPL6_ENST00000409631.1_Silent_p.L374L|OSBPL6_ENST00000409045.3_Silent_p.L343L|OSBPL6_ENST00000315022.2_Silent_p.L378L|OSBPL6_ENST00000392505.2_Silent_p.L399L|OSBPL6_ENST00000357080.4_Silent_p.L343L|OSBPL6_ENST00000359685.3_Silent_p.L374L	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	374					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			ATACAAAGCTGCAAGAAGAAT	0.398																																																0			2											105	108	107					2																	179214085		2203	4300	6503	178922331	SO:0001819	synonymous_variant	114880			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1122G>A	2.37:g.179214085G>A			178922331	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																				0.398	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		A	179214085	G	A	179214085	2	1	111	1	0	0	0	0	0	0	0	1	11312	1306	46	3		3	OSBPL6	2	179214085	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2225790	179214085	63985288	173	29307										
TTN	7273	hgsc.bcm.edu	37	chr2	179395463	179395463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atctctttagaagcttctgcTttcaggaactgagtaatctt	7	8	4	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:179395463T>C	ENST00000591111.1	-	308	101180	c.100956A>G	c.(100954-100956)aaA>aaG	p.K33652K	TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN_ENST00000359218.5_Silent_p.K26353K|TTN_ENST00000460472.2_Silent_p.K26228K|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.K26420K|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.K35293K|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342992.6_Silent_p.K32725K|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591867.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33652	Ig-like 148.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGCTTCTGCTTTCAGGAACT	0.458																																																0			2											105	100	102					2																	179395463		1893	4107	6000	179103709	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100956A>G	2.37:g.179395463T>C			179103709	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179395463	T	C	179395463	2	2	111	1	0	0	0	0	0	0	0	1	16775	1606	56	4		4	TTN	2	179395463	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	181378	179395463	63803910	174	29308										
TTN	7273	hgsc.bcm.edu	37	chr2	179464487	179464487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctttaaaccaggttagtgtcGggaatggcacacctttaatt	9	8	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:179464487G>A	ENST00000591111.1	-	239	51442	c.51218C>T	c.(51217-51219)cCg>cTg	p.P17073L	TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P9774L|TTN_ENST00000460472.2_Missense_Mutation_p.P9649L|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P9841L|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P18714L|TTN_ENST00000342992.6_Missense_Mutation_p.P16146L			Q8WZ42	TITIN_HUMAN	titin	17073	Ig-like 102.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P16144L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTTAGTGTCGGGAATGGCAC	0.408																																																1	Substitution - Missense(1)	ovary(1)	2											121	111	114					2																	179464487		1867	4104	5971	179172732	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51218C>T	2.37:g.179464487G>A	ENSP00000465570:p.Pro17073Leu		179172732	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	15.34	2.805555	0.50315	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.90817	0.7116	H	0.98048	4.135	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.93846	0.7141	9	0.87932	D	0	.	19.6238	0.95670	0.0:0.0:1.0:0.0	.	9649;9774;9841;17073	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	16146;9649;9841;9774;9647	ENSP00000343764:P16146L;ENSP00000434586:P9649L;ENSP00000340554:P9841L;ENSP00000352154:P9774L	ENSP00000340554:P9841L	P	-	2	0	TTN	179172732	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.793000	0.99091	2.642000	0.89623	0.557000	0.71058	CCG		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179464487	G	A	179464487	3	1	111	1	0	0	0	0	1	0	0	0	16775	1116	39	1	51848	1	TTN	2	179464487	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	69024	179464487	63734886	175	29309										
TTN	7273	hgsc.bcm.edu	37	chr2	179485519	179485519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acacattatagttggcttggTcatctaagtgtgcatctcta	8	8	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:179485519T>C	ENST00000591111.1	-	197	41119	c.40895A>G	c.(40894-40896)gAc>gGc	p.D13632G	TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D6333G|TTN_ENST00000460472.2_Missense_Mutation_p.D6208G|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D6400G|TTN_ENST00000589042.1_Missense_Mutation_p.D15273G|TTN_ENST00000342992.6_Missense_Mutation_p.D12705G			Q8WZ42	TITIN_HUMAN	titin	13632	Ig-like 92.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGGCTTGGTCATCTAAGTG	0.348																																																0			2											186	183	184					2																	179485519		1858	4095	5953	179193764	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40895A>G	2.37:g.179485519T>C	ENSP00000465570:p.Asp13632Gly		179193764	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.43	1.936754	0.34189	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.83	5.83	0.93111	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.92609	0.7652	H	0.94345	3.525	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.94497	0.7706	9	0.87932	D	0	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	6208;6333;6400;13632	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	12705;6208;6400;6333;6208	ENSP00000343764:D12705G;ENSP00000434586:D6208G;ENSP00000340554:D6400G;ENSP00000352154:D6333G	ENSP00000340554:D6400G	D	-	2	0	TTN	179193764	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	7.991000	0.88244	2.225000	0.72522	0.533000	0.62120	GAC		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179485519	T	C	179485519	3	2	111	1	0	0	0	0	1	0	0	0	16775	1667	58	4	62339	4	TTN	2	179485519	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	21032	179485519	63713854	176	29310										
TTN	7273	hgsc.bcm.edu	37	chr2	179486228	179486228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctttgactttgccatcggttCgagagcttgggagtcgacag	13	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:179486228C>T	ENST00000591111.1	-	195	40624	c.40400G>A	c.(40399-40401)cGa>cAa	p.R13467Q	TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R6168Q|TTN_ENST00000460472.2_Missense_Mutation_p.R6043Q|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R6235Q|TTN_ENST00000589042.1_Missense_Mutation_p.R15108Q|TTN_ENST00000342992.6_Missense_Mutation_p.R12540Q			Q8WZ42	TITIN_HUMAN	titin	13467	Ig-like 90.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCATCGGTTCGAGAGCTTGG	0.393																																																0			2											122	121	121					2																	179486228		1997	4159	6156	179194473	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40400G>A	2.37:g.179486228C>T	ENSP00000465570:p.Arg13467Gln		179194473	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.00	2.403437	0.42613	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62639	0.01;0.22;0.19;0.19	6.17	3.13	0.36017	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.48150	0.1484	L	0.27975	0.815	0.30517	N	0.768792	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.48736	-0.9009	9	0.87932	D	0	.	9.3991	0.38422	0.0:0.6945:0.0:0.3055	.	6043;6168;6235;13467	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	12540;6043;6235;6168;6043	ENSP00000343764:R12540Q;ENSP00000434586:R6043Q;ENSP00000340554:R6235Q;ENSP00000352154:R6168Q	ENSP00000340554:R6235Q	R	-	2	0	TTN	179194473	0.990000	0.36364	0.998000	0.56505	0.992000	0.81027	1.711000	0.37930	0.345000	0.23873	0.655000	0.94253	CGA		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179486228	C	T	179486228	3	4	111	1	0	0	0	0	1	0	0	0	16775	884	31	1	62842	1	TTN	2	179486228	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	709	179486228	63713145	177	29311										
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183848087	183848087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgcagatcttaaaaacttgCgtctttctctgtgcattgaa	8	8	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:183848087C>T	ENST00000361354.4	-	11	1400	c.1028G>A	c.(1027-1029)cGc>cAc	p.R343H	NCKAP1_ENST00000360982.2_Missense_Mutation_p.R349H	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	343					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)	p.R349L(1)		breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TAAAAACTTGCGTCTTTCTCT	0.343																																																1	Substitution - Missense(1)	ovary(1)	2											107	103	105					2																	183848087		2203	4300	6503	183556332	SO:0001583	missense	10787			AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1028G>A	2.37:g.183848087C>T	ENSP00000355348:p.Arg343His		183556332	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	C	34	5.390589	0.95988	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.57595	0.39;0.39	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.76659	0.4018	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68765	0.96;0.932	T	0.81600	-0.0859	10	0.87932	D	0	-6.3069	18.7206	0.91691	0.0:1.0:0.0:0.0	.	343;349	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	H	343;349	ENSP00000355348:R343H;ENSP00000354251:R349H	ENSP00000354251:R349H	R	-	2	0	NCKAP1	183556332	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.794000	0.85869	2.417000	0.82017	0.555000	0.69702	CGC		0.343	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		T	183848087	C	T	183848087	3	4	111	1	0	0	0	0	1	0	0	0	10252	768	27	1	2442	1	NCKAP1	2	183848087	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4361859	183848087	59351286	178	29312										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196651819	196651819	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cataaggaatattccaccctAggggtccaaatttccgtctt	7	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:196651819A>T	ENST00000312428.6	-	58	10893	c.10793T>A	c.(10792-10794)cTa>cAa	p.L3598Q	DNAH7_ENST00000409063.1_Missense_Mutation_p.L81Q	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3598	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ATTCCACCCTAGGGGTCCAAA	0.408																																																0			2											119	113	115					2																	196651819		1936	4156	6092	196360064	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.10793T>A	2.37:g.196651819A>T	ENSP00000311273:p.Leu3598Gln		196360064	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.165632	0.78339	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.09630	2.96;2.96	4.34	4.34	0.51931	Dynein heavy chain (1);	0.000000	0.64402	D	0.000007	T	0.31358	0.0794	M	0.74546	2.27	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.03364	-1.1044	10	0.44086	T	0.13	.	13.6272	0.62173	1.0:0.0:0.0:0.0	.	3598	Q8WXX0	DYH7_HUMAN	Q	3598;81	ENSP00000311273:L3598Q;ENSP00000386912:L81Q	ENSP00000311273:L3598Q	L	-	2	0	DNAH7	196360064	1.000000	0.71417	0.995000	0.50966	0.709000	0.40893	8.963000	0.93385	1.936000	0.56123	0.454000	0.30748	CTA		0.408	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196651819	A	T	196651819	3	4	111	1	0	0	0	0	1	0	0	0	4617	420	15	5	1313	5	DNAH7	2	196651819	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	12803732	196651819	46547554	179	29313										
HECW2	57520	hgsc.bcm.edu	37	chr2	197183694	197183694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcattgcaggagctgtcagcGcattccaggtcactctctcc	9	14	4	0	rs370830289		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:197183694G>A	ENST00000260983.3	-	9	2102	c.1920C>T	c.(1918-1920)tgC>tgT	p.C640C	HECW2_ENST00000409111.1_Silent_p.C284C	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	640					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						AGCTGTCAGCGCATTCCAGGT	0.587																																																0			2											98	75	83					2																	197183694		2203	4300	6503	196891939	SO:0001819	synonymous_variant	57520			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.1920C>T	2.37:g.197183694G>A			196891939	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																				0.587	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197183694	G	A	197183694	2	1	111	1	0	0	0	0	0	0	0	1	7064	1079	38	1		1	HECW2	2	197183694	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	531875	197183694	46015679	180	29314										
CASP8	841	hgsc.bcm.edu	37	chr2	202139625	202139626	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgcaggggaggagttgtgtINSggggtaatgacaatctcgga					rs577264458		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:202139625_202139626insG	ENST00000432109.2	+	7	798_799	c.609_610insG	c.(610-612)gggfs	p.G204fs	CASP8_ENST00000392258.3_Intron|CASP8_ENST00000264275.5_Frame_Shift_Ins_p.G221fs|CASP8_ENST00000264274.9_Intron|CASP8_ENST00000392266.3_Intron|CASP8_ENST00000392259.2_Intron|CASP8_ENST00000358485.4_Frame_Shift_Ins_p.G263fs|CASP8_ENST00000323492.7_Frame_Shift_Ins_p.G189fs	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	204					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						AGGAGTTGTGTGGGGTAATGAC	0.411										HNSCC(4;0.00038)																											Melanoma(82;831 1348 20716 36952 40159)											0			2																																								201847871	SO:0001589	frameshift_variant	841			U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"Caspases"	1509	protein-coding gene	gene with protein product		601763	"caspase 8, apoptosis-related cysteine protease"			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.613dupG	2.37:g.202139629_202139629dupG	ENSP00000412523:p.Gly204fs		201847870	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Frame_Shift_Ins	INS	ENST00000432109.2	37	CCDS2342.1																																																																																				0.411	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		G	202139626	-	G	202139625	7	5	111	1	0	1	1	0	0	0	0	0	2683	1702	59	0	908	0	CASP8	2	202139625	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	4955931	202139625	41059748	181	29315										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203972179	203972179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaattggttatacacatatgCttgaagtattaaaatccctg	7	6	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:203972179C>T	ENST00000449802.1	+	12	1552	c.1219C>T	c.(1219-1221)Ctt>Ttt	p.L407F		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	407										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TACACATATGCTTGAAGTATT	0.303																																																0			2											78	72	74					2																	203972179		692	1589	2281	203680424	SO:0001583	missense	65065			AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.1219C>T	2.37:g.203972179C>T	ENSP00000399903:p.Leu407Phe		203680424	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	C	2.313	-0.357441	0.05138	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.60548	0.18	5.54	4.38	0.52667	Armadillo-type fold (1);	.	.	.	.	T	0.27027	0.0662	N	0.02225	-0.63	0.27351	N	0.956235	B	0.02656	0.0	B	0.01281	0.0	T	0.18935	-1.0321	9	0.06625	T	0.88	.	8.8524	0.35208	0.0:0.1456:0.0:0.8544	.	407	Q6ZS30	NBEL1_HUMAN	F	407	ENSP00000399903:L407F	ENSP00000344985:L407F	L	+	1	0	NBEAL1	203680424	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.831000	0.62752	1.048000	0.40298	-0.351000	0.07748	CTT		0.303	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	203972179	C	T	203972179	3	4	111	1	0	0	0	0	1	0	0	0	10218	797	28	3	1261	3	NBEAL1	2	203972179	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1832554	203972179	39227194	182	29316										
VIL1	7429	hgsc.bcm.edu	37	chr2	219296776	219296776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atactggccctaggtgtggcGcattgagaacctagagctgg	14	9	0	2	rs369865042		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:219296776G>A	ENST00000248444.5	+	12	1299	c.1211G>A	c.(1210-1212)cGc>cAc	p.R404H	VIL1_ENST00000392114.2_Missense_Mutation_p.R93H	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	404	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TAGGTGTGGCGCATTGAGAAC	0.602																																																0			2						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	101	82	89		1211	5	1	2		89	0,8600		0,0,4300	no	missense	VIL1	NM_007127.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	404/828	219296776	1,13005	2203	4300	6503	219005020	SO:0001583	missense	7429			X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.1211G>A	2.37:g.219296776G>A	ENSP00000248444:p.Arg404His		219005020	B2R9A7|Q53S11|Q96AC8	Missense_Mutation	SNP	ENST00000248444.5	37	CCDS2417.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541636	0.65085	2.27E-4	0.0	ENSG00000127831	ENST00000248444;ENST00000392114	T;T	0.15834	2.39;2.39	5.03	5.03	0.67393	.	0.068810	0.52532	D	0.000068	T	0.54565	0.1866	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68311	-0.5442	10	0.66056	D	0.02	-16.6743	18.3616	0.90376	0.0:0.0:1.0:0.0	.	404	P09327	VILI_HUMAN	H	404;93	ENSP00000248444:R404H;ENSP00000375962:R93H	ENSP00000248444:R404H	R	+	2	0	VIL1	219005020	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	9.860000	0.99555	2.351000	0.79841	0.561000	0.74099	CGC		0.602	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		A	219296776	G	A	219296776	3	1	111	1	0	0	0	0	1	0	0	0	17204	1087	38	1	1253	1	VIL1	2	219296776	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	15324597	219296776	23902597	183	29317										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219903670	219903672	+	In_Frame_Del	DEL	AGG	AGG	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgaacactcttgcctcttAggagaagaggaataaggggg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AGG	AGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:219903670_219903672delAGG	ENST00000341552.5	-	3	182_184	c.99_101delCCT	c.(97-102)ctccta>cta	p.33_34LL>L	CCDC108_ENST00000295729.2_Intron|CCDC108_ENST00000441968.1_In_Frame_Del_p.33_34LL>L|CCDC108_ENST00000409865.3_Intron|CCDC108_ENST00000453220.1_In_Frame_Del_p.33_34LL>L|CCDC108_ENST00000410037.1_Intron|CCDC108_ENST00000324264.6_5'UTR	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	33						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		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)		CTTGCCTCTTAGGAGAAGAGGAA	0.458																																																0			2																																								219611916	SO:0001651	inframe_deletion	255101			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.99_101delCCT	2.37:g.219903670_219903672delAGG	ENSP00000340776:p.Leu34del		219611914	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	In_Frame_Del	DEL	ENST00000341552.5	37	CCDS2430.2																																																																																				0.458	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		-	219903672	AGG	-	219903670	7	5	111	1	0	1	0	1	0	0	0	0	2749	420	15	0	5956	0	CCDC108	2	219903670	In_Frame_Del	DEL	AGG	TCGA-EI-6507-01A-11D-1733-10	606894	219903670	23295703	184	29318										
ATG9A	79065	hgsc.bcm.edu	37	chr2	220085973	220085973	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccactctcatcactctcccGgcggtgccatacatgccgct	7	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:220085973G>A	ENST00000409618.1	-	14	2636	c.2197C>T	c.(2197-2199)Cgg>Tgg	p.R733W	ATG9A_ENST00000409422.1_Missense_Mutation_p.R672W|ABCB6_ENST00000265316.3_5'Flank|ATG9A_ENST00000396761.2_Missense_Mutation_p.R733W|ABCB6_ENST00000439002.2_5'Flank|ATG9A_ENST00000361242.4_Missense_Mutation_p.R733W|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	733					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCACTCTCCCGGCGGTGCCAT	0.637																																																0			2											18	20	19					2																	220085973		1928	4124	6052	219794217	SO:0001583	missense	79065			AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.2197C>T	2.37:g.220085973G>A	ENSP00000386710:p.Arg733Trp		219794217	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080836	0.76528	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.3	5.3	0.74995	.	0.134893	0.52532	D	0.000071	T	0.64405	0.2595	L	0.36672	1.1	0.49915	D	0.999833	D	0.61697	0.99	B	0.41299	0.353	T	0.70722	-0.4794	10	0.66056	D	0.02	-15.5601	19.1489	0.93479	0.0:0.0:1.0:0.0	.	733	Q7Z3C6	ATG9A_HUMAN	W	733;733;733;672	ENSP00000379983:R733W;ENSP00000386710:R733W;ENSP00000355173:R733W;ENSP00000386535:R672W	ENSP00000355173:R733W	R	-	1	2	ATG9A	219794217	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.294000	0.78760	2.757000	0.94681	0.591000	0.81541	CGG		0.637	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		A	220085973	G	A	220085973	3	1	111	1	0	0	0	0	1	0	0	0	1103	1115	39	1	334	1	ATG9A	2	220085973	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	182303	220085973	23113400	185	29319										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220470776	220470776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtggctgctggctgagctcCgcaaggtgagatgggaatgc	17	8	0	2	rs145811191		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:220470776C>T	ENST00000456909.1	+	9	934	c.844C>T	c.(844-846)Cgc>Tgc	p.R282C	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Missense_Mutation_p.R293C			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	293					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCTGAGCTCCGCAAGGTGAG	0.607											OREG0003992	type=REGULATORY REGION|Gene=STK11IP|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			2											23	29	27					2																	220470776		2144	4268	6412	220179020	SO:0001583	missense	114790			AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.844C>T	2.37:g.220470776C>T	ENSP00000389383:p.Arg282Cys	2267	220179020	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	C	15.96	2.985992	0.53934	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.24908	1.83;1.83	4.9	4.03	0.46877	.	0.381149	0.27522	N	0.018998	T	0.50000	0.1590	M	0.80982	2.52	0.41643	D	0.989082	P;P;P;D	0.89917	0.617;0.537;0.617;1.0	B;B;B;D	0.72075	0.048;0.034;0.048;0.976	T	0.55528	-0.8127	10	0.87932	D	0	-6.5791	10.7562	0.46239	0.0:0.9086:0.0:0.0914	.	293;293;293;293	B4DUE4;B4DII2;Q8N1F8-2;Q8N1F8	.;.;.;S11IP_HUMAN	C	282;293;293	ENSP00000389383:R282C;ENSP00000295641:R293C	ENSP00000295641:R293C	R	+	1	0	STK11IP	220179020	0.896000	0.30565	1.000000	0.80357	0.871000	0.50021	1.730000	0.38125	1.296000	0.44742	0.655000	0.94253	CGC		0.607	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220470776	C	T	220470776	3	4	111	1	0	0	0	0	1	0	0	0	15327	652	23	1	911	1	STK11IP	2	220470776	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	384803	220470776	22728597	186	29320										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220480910	220480910	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagaggcgctggcccttgacCgatgagggtcccacgctgac	14	13	0	4	rs202148315		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:220480910C>T	ENST00000456909.1	+	25	3352	c.3262C>T	c.(3262-3264)Cga>Tga	p.R1088*	STK11IP_ENST00000295641.10_Nonsense_Mutation_p.R1099*			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	1099					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCCCTTGACCGATGAGGGTC	0.627													C|||	1	0.000199681	0	0.0014	5008	,	,		18323	0		0	False		,,,				2504	0															0			2						C	stop/ARG	0,4340		0,0,2170	31	35	33		3295	2.7	1	2		33	1,8551		0,1,4275	yes	stop-gained	STK11IP	NM_052902.2		0,1,6445	TT,TC,CC		0.0117,0.0,0.0078		1099/1100	220480910	1,12891	2170	4276	6446	220189154	SO:0001587	stop_gained	114790			AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.3262C>T	2.37:g.220480910C>T	ENSP00000389383:p.Arg1088*		220189154	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Nonsense_Mutation	SNP	ENST00000456909.1	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	38	6.846000	0.97881	0.0	1.17E-4	ENSG00000144589	ENST00000456909;ENST00000295641	.	.	.	4.51	2.72	0.32119	.	0.158257	0.29558	N	0.011811	.	.	.	.	.	.	0.26801	N	0.969197	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8685	0.24106	0.0:0.791:0.0:0.209	.	.	.	.	X	1088;1099	.	ENSP00000295641:R1099X	R	+	1	2	STK11IP	220189154	0.191000	0.23288	0.951000	0.38953	0.596000	0.36781	0.065000	0.14466	0.546000	0.28920	-0.137000	0.14449	CGA		0.627	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220480910	C	T	220480910	4	4	111	1	0	0	0	0	0	1	0	0	15327	644	23	1	3393	1	STK11IP	2	220480910	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10134	220480910	22718463	187	29321										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222365809	222365809	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaggtgcacgaggtggctcCttcccagacagagtagctgt	13	11	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:222365809C>A	ENST00000281821.2	-	4	948	c.907G>T	c.(907-909)Gga>Tga	p.G303*	EPHA4_ENST00000409938.1_Nonsense_Mutation_p.G303*|EPHA4_ENST00000392071.4_Nonsense_Mutation_p.G252*|EPHA4_ENST00000409854.1_Nonsense_Mutation_p.G303*	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	303	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GAGGTGGCTCCTTCCCAGACA	0.532																																																0			2											118	103	108					2																	222365809		2203	4300	6503	222074053	SO:0001587	stop_gained	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.907G>T	2.37:g.222365809C>A	ENSP00000281821:p.Gly303*		222074053	A8K2P1|B2R601|B7Z6Q8|Q2M380	Nonsense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.168126|8.168126	0.98686|0.98686	.|.	.|.	ENSG00000116106|ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071|ENST00000441679	.|.	.|.	.|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.81103	.|0.4753	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.78437	.|-0.2204	.|3	0.59425|.	D|.	0.04|.	.|.	20.6439|20.6439	0.99570|0.99570	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|N	303;303;303;252|39	.|.	ENSP00000281821:G303X|.	G|K	-|-	1|3	0|2	EPHA4|EPHA4	222074053|222074053	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.487000|7.487000	0.81328|0.81328	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GGA|AAG		0.532	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			A	222365809	C	A	222365809	4	1	111	1	0	0	0	0	0	1	0	0	5182	690	24	2	2109	2	EPHA4	2	222365809	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1884899	222365809	20833564	188	29322										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228884641	228884641	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcccattccccacagcttctCttttccactgtgatggcttg	6	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:228884641C>A	ENST00000392056.3	-	7	975	c.929G>T	c.(928-930)aGa>aTa	p.R310I	SPHKAP_ENST00000344657.5_Missense_Mutation_p.R310I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	310						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		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)		CACAGCTTCTCTTTTCCACTG	0.418																																																0			2											207	212	210					2																	228884641		2203	4300	6503	228592885	SO:0001583	missense	80309				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.929G>T	2.37:g.228884641C>A	ENSP00000375909:p.Arg310Ile		228592885	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	4.499	0.092515	0.08632	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11821	2.74;2.74	5.6	2.84	0.33178	.	0.770176	0.13127	N	0.411773	T	0.06554	0.0168	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.35375	-0.9791	10	0.34782	T	0.22	.	6.1774	0.20451	0.0:0.6344:0.0:0.3656	.	310;310	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	I	310	ENSP00000375909:R310I;ENSP00000339886:R310I	ENSP00000339886:R310I	R	-	2	0	SPHKAP	228592885	0.001000	0.12720	0.128000	0.21923	0.002000	0.02628	0.515000	0.22801	0.730000	0.32425	-0.142000	0.14014	AGA		0.418	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228884641	C	A	228884641	3	1	111	1	0	0	0	0	1	0	0	0	15087	913	32	2	4197	2	SPHKAP	2	228884641	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6518832	228884641	14314732	189	29323										
CHRNG	1146	hgsc.bcm.edu	37	chr2	233408008	233408008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggggccagaagtgtaccgtcGccatcaacgtgctcctggcc	13	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:233408008G>A	ENST00000389494.3	+	8	850	c.829G>A	c.(829-831)Gcc>Acc	p.A277T	CHRNG_ENST00000389492.3_Missense_Mutation_p.A225T	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	277					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		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;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	GTGTACCGTCGCCATCAACGT	0.592																																																0			2											97	90	93					2																	233408008		2203	4300	6503	233116252	SO:0001583	missense	1146			X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1967	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, gamma (muscle)"	100730	"cholinergic receptor, nicotinic, gamma"	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.829G>A	2.37:g.233408008G>A	ENSP00000374145:p.Ala277Thr		233116252	B3KWM8|Q14DU4|Q53RG2	Missense_Mutation	SNP	ENST00000389494.3	37	CCDS33400.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.356769	0.82243	.	.	ENSG00000196811	ENST00000389494;ENST00000541596;ENST00000389492	D;D	0.85861	-2.04;-2.04	5.61	3.6	0.41247	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.190165	0.46442	D	0.000286	T	0.75228	0.3821	N	0.16708	0.43	0.37046	D	0.897359	P;P	0.50617	0.937;0.787	B;P	0.44561	0.225;0.453	T	0.76198	-0.3047	10	0.23891	T	0.37	.	13.4005	0.60881	0.0:0.0:0.5644:0.4356	.	225;277	Q14DU4;P07510	.;ACHG_HUMAN	T	277;277;225	ENSP00000374145:A277T;ENSP00000374143:A225T	ENSP00000374143:A225T	A	+	1	0	CHRNG	233116252	1.000000	0.71417	0.988000	0.46212	0.990000	0.78478	3.836000	0.55813	1.353000	0.45828	0.462000	0.41574	GCC		0.592	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199		A	233408008	G	A	233408008	3	1	111	1	0	0	0	0	1	0	0	0	3402	1087	38	1	859	1	CHRNG	2	233408008	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4523367	233408008	9791365	190	29324										
PER2	8864	hgsc.bcm.edu	37	chr2	239162337	239162337	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggaagtatttcttagtccaGgggcagctaatgcagaaaaa	11	7	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:239162337G>T	ENST00000254657.3	-	19	2606	c.2327C>A	c.(2326-2328)cCt>cAt	p.P776H	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	776					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		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)		TCTTAGTCCAGGGGCAGCTAA	0.413																																																0			2											9	10	10					2																	239162337		2005	4148	6153	238827076	SO:0001583	missense	8864			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2327C>A	2.37:g.239162337G>T	ENSP00000254657:p.Pro776His		238827076	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.587113	0.28268	.	.	ENSG00000132326	ENST00000254657	T	0.12039	2.72	4.2	2.09	0.27110	.	0.236902	0.25063	U	0.033430	T	0.10937	0.0267	L	0.53561	1.675	0.26829	N	0.968626	B;B	0.30741	0.012;0.293	B;B	0.28638	0.007;0.092	T	0.19778	-1.0295	10	0.20046	T	0.44	-5.651	6.5994	0.22693	0.0:0.3741:0.4612:0.1647	.	776;776	B4DH14;O15055	.;PER2_HUMAN	H	776	ENSP00000254657:P776H	ENSP00000254657:P776H	P	-	2	0	PER2	238827076	0.119000	0.22226	0.123000	0.21794	0.585000	0.36419	0.758000	0.26447	0.866000	0.35629	0.655000	0.94253	CCT		0.413	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		T	239162337	G	T	239162337	3	4	111	1	0	0	0	0	1	0	0	0	11761	1000	35	2	1460	2	PER2	2	239162337	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5754329	239162337	4037036	191	29325										
ASB1	51665	hgsc.bcm.edu	37	chr2	239353021	239353021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtcaaccaccacctgactcCtgatgtccagcctcgattct	6	17	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:239353021C>A	ENST00000264607.4	+	4	780	c.533C>A	c.(532-534)cCt>cAt	p.P178H	ASB1_ENST00000409297.1_Missense_Mutation_p.P77H	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	178					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		CACCTGACTCCTGATGTCCAG	0.602																																																0			2											62	51	55					2																	239353021		2203	4300	6503	239017760	SO:0001583	missense	51665			AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"Ankyrin repeat domain containing"	16011	protein-coding gene	gene with protein product		605758	"ankyrin repeat and SOCS box-containing 1"				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.533C>A	2.37:g.239353021C>A	ENSP00000264607:p.Pro178His		239017760	A6NL50|Q4ZG29|Q9ULS4	Missense_Mutation	SNP	ENST00000264607.4	37	CCDS33416.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820900	0.71028	.	.	ENSG00000065802	ENST00000264607;ENST00000409297	T;T	0.54866	0.55;1.94	5.63	5.63	0.86233	Ankyrin repeat-containing domain (3);	0.699256	0.15056	N	0.283011	T	0.47192	0.1432	N	0.13003	0.285	0.38062	D	0.936097	P	0.42203	0.773	P	0.50791	0.65	T	0.40646	-0.9552	9	.	.	.	.	12.9623	0.58466	0.0:0.9267:0.0:0.0733	.	178	Q9Y576	ASB1_HUMAN	H	178;77	ENSP00000264607:P178H;ENSP00000387025:P77H	.	P	+	2	0	ASB1	239017760	0.167000	0.22975	0.997000	0.53966	0.842000	0.47809	3.459000	0.53021	2.652000	0.90054	0.655000	0.94253	CCT		0.602	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445		A	239353021	C	A	239353021	3	1	111	1	0	0	0	0	1	0	0	0	1014	681	24	2	547	2	ASB1	2	239353021	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	190684	239353021	3846352	192	29326										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240024584	240024584	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccagggtggccttgcgtccGcggatgcactgtggggacag	17	11	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:240024584G>A	ENST00000345617.3	-	16	2897	c.2106C>T	c.(2104-2106)cgC>cgT	p.R702R	HDAC4_ENST00000543185.1_Silent_p.R286R|HDAC4_ENST00000541256.1_Silent_p.R676R	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	702	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R702R(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CCTTGCGTCCGCGGATGCACT	0.587																																																1	Substitution - coding silent(1)	ovary(1)	2											116	93	101					2																	240024584		2203	4300	6503	239689521	SO:0001819	synonymous_variant	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2106C>T	2.37:g.240024584G>A			239689521	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																				0.587	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240024584	G	A	240024584	2	1	111	1	0	0	0	0	0	0	0	1	7030	1074	38	1		1	HDAC4	2	240024584	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	671563	240024584	3174789	193	29327										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463399	241463399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagcaagctgtgggactgggCgcttctctccagcatggcct	13	13	1	0	rs141510821	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:241463399C>T	ENST00000272972.3	-	7	1682	c.1468G>A	c.(1468-1470)Gcc>Acc	p.A490T	ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000391987.1_Missense_Mutation_p.A490T|ANKMY1_ENST00000536462.1_Missense_Mutation_p.A302T|ANKMY1_ENST00000406958.1_Missense_Mutation_p.A251T|ANKMY1_ENST00000405002.1_Missense_Mutation_p.A260T|ANKMY1_ENST00000361678.4_Missense_Mutation_p.A349T|ANKMY1_ENST00000403283.1_Missense_Mutation_p.A428T|ANKMY1_ENST00000405523.3_Missense_Mutation_p.A349T|ANKMY1_ENST00000401804.1_Missense_Mutation_p.A579T|ANKMY1_ENST00000373320.4_Missense_Mutation_p.A260T|ANKMY1_ENST00000373318.2_Missense_Mutation_p.A349T	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	490							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		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)		TGGGACTGGGCGCTTCTCTCC	0.592																																																0			2											98	89	92					2																	241463399		2203	4300	6503	241112072	SO:0001583	missense	51281			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1468G>A	2.37:g.241463399C>T	ENSP00000272972:p.Ala490Thr		241112072	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.762900	0.69763	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T;T	0.75938	1.42;3.36;-0.97;0.69;-0.97;3.02;0.88;-0.98;0.48;0.15;0.95	4.06	4.06	0.47325	Ankyrin repeat-containing domain (1);	0.247388	0.31290	N	0.007901	T	0.79131	0.4394	L	0.36672	1.1	0.09310	N	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.99;0.992;0.974;0.994;0.999	T	0.70107	-0.4963	10	0.72032	D	0.01	-34.0637	12.4117	0.55471	0.0:1.0:0.0:0.0	.	490;302;260;349;251;349;490	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;.;ANKY1_HUMAN	T	349;251;490;349;490;260;428;579;302;349;260	ENSP00000362415:A349T;ENSP00000384555:A251T;ENSP00000272972:A490T;ENSP00000355097:A349T;ENSP00000375847:A490T;ENSP00000362417:A260T;ENSP00000383968:A428T;ENSP00000385887:A579T;ENSP00000444707:A302T;ENSP00000385635:A349T;ENSP00000385145:A260T	ENSP00000272972:A490T	A	-	1	0	ANKMY1	241112072	0.381000	0.25140	0.051000	0.19133	0.040000	0.13550	2.006000	0.40874	2.197000	0.70478	0.491000	0.48974	GCC		0.592	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		T	241463399	C	T	241463399	3	4	111	1	0	0	0	0	1	0	0	0	634	768	27	1	1401	1	ANKMY1	2	241463399	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1438815	241463399	1735974	194	29328										
SNED1	25992	hgsc.bcm.edu	37	chr2	241979558	241979558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggtggagaatggctctgCggtgtgtgtgtgccaggccg	18	9	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:241979558C>T	ENST00000310397.8	+	7	1112	c.1112C>T	c.(1111-1113)gCg>gTg	p.A371V	SNED1_ENST00000401884.1_Missense_Mutation_p.A371V|SNED1_ENST00000342631.6_Missense_Mutation_p.A371V|SNED1_ENST00000405547.3_Missense_Mutation_p.A371V|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	371	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Follistatin-like 1.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|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;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		AATGGCTCTGCGGTGTGTGTG	0.617																																																0			2											32	38	36					2																	241979558		2133	4248	6381	241628231	SO:0001583	missense	25992			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1112C>T	2.37:g.241979558C>T	ENSP00000308893:p.Ala371Val		241628231	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.34|13.34	2.206799|2.206799	0.39003|0.39003	.|.	.|.	ENSG00000162804|ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631;ENST00000420591|ENST00000431690	D;D;D;D;D|.	0.91180|.	-2.8;-2.8;-2.8;-2.8;-2.03|.	4.73|4.73	4.73|4.73	0.59995|0.59995	Follistatin-like, N-terminal (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);|.	0.119854|.	0.37012|.	N|.	0.002283|.	T|T	0.57548|0.57548	0.2061|0.2061	L|L	0.58669|0.58669	1.825|1.825	0.21147|0.21147	N|N	0.999772|0.999772	P|.	0.52061|.	0.95|.	P|.	0.46076|.	0.503|.	T|T	0.52253|0.52253	-0.8600|-0.8600	10|5	0.37606|.	T|.	0.19|.	.|.	17.3185|17.3185	0.87230|0.87230	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	371|.	Q8TER0|.	SNED1_HUMAN|.	V|W	371;371;371;371;9|29	ENSP00000384871:A371V;ENSP00000386007:A371V;ENSP00000308893:A371V;ENSP00000342992:A371V;ENSP00000394324:A9V|.	ENSP00000308893:A371V|.	A|R	+|+	2|1	0|2	SNED1|SNED1	241628231|241628231	0.989000|0.989000	0.36119|0.36119	0.012000|0.012000	0.15200|0.15200	0.011000|0.011000	0.07611|0.07611	4.082000|4.082000	0.57635|0.57635	2.137000|2.137000	0.66172|0.66172	0.591000|0.591000	0.81541|0.81541	GCG|CGG		0.617	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	241979558	C	T	241979558	3	4	111	1	0	0	0	0	1	0	0	0	14882	768	27	1	1138	1	SNED1	2	241979558	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	516159	241979558	1219815	195	29329										
FARP2	9855	hgsc.bcm.edu	37	chr2	242350516	242350516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacctgtgctgacaccacagCggcccttctcacgtcccatc	8	18	1	1	rs555590124		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr2:242350516C>T	ENST00000264042.3	+	6	649	c.479C>T	c.(478-480)gCg>gTg	p.A160V	FARP2_ENST00000373287.4_Missense_Mutation_p.A160V|FARP2_ENST00000545004.1_Missense_Mutation_p.A160V	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	160	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GACACCACAGCGGCCCTTCTC	0.507													C|||	1	0.000199681	0	0	5008	,	,		19505	0.001		0	False		,,,				2504	0															0			2											112	96	101					2																	242350516		2203	4300	6503	241999189	SO:0001583	missense	9855			AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.479C>T	2.37:g.242350516C>T	ENSP00000264042:p.Ala160Val		241999189	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.626218	0.66901	.	.	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;T	0.80123	-1.34;-1.34;-1.34	5.44	5.44	0.79542	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.134533	0.51477	D	0.000095	D	0.84406	0.5465	M	0.86343	2.81	0.54753	D	0.999989	B;B;B	0.20780	0.048;0.032;0.024	B;B;B	0.17433	0.01;0.017;0.018	T	0.82542	-0.0405	10	0.56958	D	0.05	.	19.2456	0.93901	0.0:1.0:0.0:0.0	.	160;160;160	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	V	160	ENSP00000264042:A160V;ENSP00000443876:A160V;ENSP00000362384:A160V	ENSP00000264042:A160V	A	+	2	0	FARP2	241999189	1.000000	0.71417	0.054000	0.19295	0.906000	0.53458	4.980000	0.63812	2.544000	0.85801	0.655000	0.94253	GCG		0.507	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			T	242350516	C	T	242350516	3	4	111	1	0	0	0	0	1	0	0	0	5696	768	27	1	497	1	FARP2	2	242350516	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	370958	242350516	848857	196	29330										
NUP210	23225	hgsc.bcm.edu	37	chr3	13407493	13407493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatcttggcactcaggtggaCgtggccgtgtctgtagctca	14	10	4	0	rs141744656	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:13407493C>T	ENST00000254508.5	-	14	1967	c.1885G>A	c.(1885-1887)Gtc>Atc	p.V629I		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	629					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CTCAGGTGGACGTGGCCGTGT	0.647													C|||	3	0.000599042	0.0023	0	5008	,	,		16721	0		0	False		,,,				2504	0															0			3						C	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	121	111	115		1885	-2	0.9	3	dbSNP_134	115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NUP210	NM_024923.2	29	0,5,6498	TT,TC,CC		0.0116,0.0908,0.0384	benign	629/1888	13407493	5,13001	2203	4300	6503	13382493	SO:0001583	missense	23225			AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.1885G>A	3.37:g.13407493C>T	ENSP00000254508:p.Val629Ile		13382493	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	7.289	0.610705	0.14066	9.08E-4	1.16E-4	ENSG00000132182	ENST00000254508	T	0.04917	3.53	5.21	-2.04	0.07343	.	0.532272	0.19600	N	0.110401	T	0.03959	0.0111	N	0.16790	0.44	0.40431	D	0.979948	B;B	0.21821	0.061;0.009	B;B	0.17098	0.017;0.005	T	0.41502	-0.9505	10	0.30078	T	0.28	.	13.1731	0.59611	0.0:0.7401:0.0:0.2599	.	629;629	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	I	629	ENSP00000254508:V629I	ENSP00000254508:V629I	V	-	1	0	NUP210	13382493	0.794000	0.28838	0.901000	0.35422	0.262000	0.26303	-0.021000	0.12504	-0.308000	0.08792	0.655000	0.94253	GTC		0.647	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		T	13407493	C	T	13407493	3	4	111	1	0	0	0	0	1	0	0	0	10791	536	19	1	3886	1	NUP210	3	13407493	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		13407493	184614937	197	29331										
GALNTL2	117248	hgsc.bcm.edu	37	chr3	16237352	16237352	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcctggtccactctcctgCggactgtacacagcatcctc	9	16	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:16237352C>T	ENST00000339732.5	+	2	1128	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	GALNT15_ENST00000437509.1_Missense_Mutation_p.R209W	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	209	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CACTCTCCTGCGGACTGTACA	0.607																																																0			3											103	77	86					3																	16237352		2203	4300	6503	16212356	SO:0001583	missense	117248			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.625C>T	3.37:g.16237352C>T	ENSP00000344260:p.Arg209Trp		16212356	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	c	19.06	3.753121	0.69648	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.63913	-0.07;-0.07	4.88	3.72	0.42706	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	D	0.86024	0.5834	H	0.98682	4.3	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.88998	0.3419	10	0.87932	D	0	.	11.9178	0.52776	0.8539:0.1461:0.0:0.0	.	209	Q8N3T1	GLTL2_HUMAN	W	209	ENSP00000344260:R209W;ENSP00000395873:R209W	ENSP00000344260:R209W	R	+	1	2	GALNTL2	16212356	1.000000	0.71417	0.995000	0.50966	0.944000	0.59088	1.566000	0.36396	0.715000	0.32103	-0.387000	0.06579	CGG		0.607	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		T	16237352	C	T	16237352	3	4	111	1	0	0	0	0	1	0	0	0	6242	759	27	1	631	1	GALNTL2	3	16237352	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2829859	16237352	181785078	198	29332										
TRIM71	131405	hgsc.bcm.edu	37	chr3	32932173	32932173	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaccaaggccacaggcgatGgcctcaagcgtgccctccag	11	16	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:32932173G>T	ENST00000383763.5	+	4	1540	c.1477G>T	c.(1477-1479)Ggc>Tgc	p.G493C		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	493					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CACAGGCGATGGCCTCAAGCG	0.597																																																0			3											47	50	49					3																	32932173		2047	4195	6242	32907177	SO:0001583	missense	131405				CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.1477G>T	3.37:g.32932173G>T	ENSP00000373272:p.Gly493Cys		32907177		Missense_Mutation	SNP	ENST00000383763.5	37	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034007	0.75504	.	.	ENSG00000206557	ENST00000383763	D	0.92446	-3.04	5.71	5.71	0.89125	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.047605	0.85682	D	0.000000	D	0.96617	0.8896	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96409	0.9303	10	0.52906	T	0.07	-37.4963	18.4247	0.90605	0.0:0.0:1.0:0.0	.	493	Q2Q1W2	LIN41_HUMAN	C	493	ENSP00000373272:G493C	ENSP00000373272:G493C	G	+	1	0	TRIM71	32907177	1.000000	0.71417	0.966000	0.40874	0.968000	0.65278	9.869000	0.99810	2.700000	0.92200	0.650000	0.86243	GGC		0.597	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		T	32932173	G	T	32932173	3	4	111	1	0	0	0	0	1	0	0	0	16584	1348	47	2	1491	2	TRIM71	3	32932173	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	16694821	32932173	165090257	199	29333										
FBXL2	7342	hgsc.bcm.edu	37	chr3	33427020	33427020	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccctcatgtcaaagtccacGcctactttgctcccgtcacc	5	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:33427020G>A	ENST00000283629.3	-	0	4148				FBXL2_ENST00000484457.1_Missense_Mutation_p.A398T|FBXL2_ENST00000542085.1_Missense_Mutation_p.A108T|FBXL2_ENST00000446237.3_Missense_Mutation_p.A139T|FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000538892.1_Missense_Mutation_p.A330T|FBXL2_ENST00000538181.1_Missense_Mutation_p.A314T|FBXL2_ENST00000507198.1_Missense_Mutation_p.A330T	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)						angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						CAAAGTCCACGCCTACTTTGC	0.488																																																0			3											161	157	158					3																	33427020		2203	4300	6503	33402024	SO:0001628	intergenic_variant	25827			AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749		3.37:g.33427020G>A			33402024	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	37	6.121416	0.97300	.	.	ENSG00000153558	ENST00000484457;ENST00000538892;ENST00000538181;ENST00000446237;ENST00000507198;ENST00000542085	T;T;T;T;T;T	0.34472	2.66;3.42;2.63;1.36;3.42;2.42	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.63768	0.2539	M	0.77406	2.37	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.995	T	0.64271	-0.6447	10	0.52906	T	0.07	.	19.6921	0.96007	0.0:0.0:1.0:0.0	.	314;293;398	B4E1B8;B4DMM3;Q9UKC9	.;.;FBXL2_HUMAN	T	398;330;314;139;330;108	ENSP00000417601:A398T;ENSP00000441228:A330T;ENSP00000440794:A314T;ENSP00000389251:A139T;ENSP00000426163:A330T;ENSP00000445039:A108T	ENSP00000389251:A139T	A	+	1	0	FBXL2	33402024	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	9.753000	0.98904	2.830000	0.97506	0.655000	0.94253	GCC		0.488	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		A	33427020	G	A	33427020	1	1	111	0	1	0	0	0	0	0	0	0	5735	1087	38	1		1	FBXL2	3	33427020	IGR	SNP	G	TCGA-EI-6507-01A-11D-1733-10	494847	33427020	164595410	200	29334										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38645239	38645239	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctagcatcacagggcggagGaggtggcttcctggggatgt	17	8	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:38645239G>A	ENST00000333535.4	-	12	2003	c.1854C>T	c.(1852-1854)ctC>ctT	p.L618L	SCN5A_ENST00000414099.2_Silent_p.L618L|SCN5A_ENST00000449557.2_Silent_p.L618L|SCN5A_ENST00000451551.2_Silent_p.L618L|SCN5A_ENST00000425664.1_Silent_p.L618L|SCN5A_ENST00000443581.1_Silent_p.L618L|SCN5A_ENST00000450102.2_Silent_p.L618L|SCN5A_ENST00000455624.2_Silent_p.L618L|SCN5A_ENST00000413689.1_Silent_p.L618L|SCN5A_ENST00000423572.2_Silent_p.L618L			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	618			L -> F (in drug-induced LQT syndrome; also found in patients with atrial fibrillation; dbSNP:rs45488304). {ECO:0000269|PubMed:15840476, ECO:0000269|PubMed:18378609}.	L -> I (in Ref. 4; AAO91669). {ECO:0000305}.	AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGGGCGGAGGAGGTGGCTTC	0.622																																																0			3											34	37	36					3																	38645239		2057	4207	6264	38620243	SO:0001819	synonymous_variant	6331			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1854C>T	3.37:g.38645239G>A			38620243	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																				0.622	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38645239	G	A	38645239	2	1	111	1	0	0	0	0	0	0	0	1	13959	1161	41	3		3	SCN5A	3	38645239	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5218219	38645239	159377191	201	29335										
GORASP1	64689	hgsc.bcm.edu	37	chr3	39142260	39142260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccctctccaccccaggctgCgttgggagttacagtcacct	10	16	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:39142260C>T	ENST00000319283.3	-	5	1365	c.544G>A	c.(544-546)Gca>Aca	p.A182T	GORASP1_ENST00000422110.2_Intron|GORASP1_ENST00000479927.1_Missense_Mutation_p.A87T|GORASP1_ENST00000476334.1_5'Flank	NM_031899.2	NP_114105.1	Q9BQQ3	GORS1_HUMAN	golgi reassembly stacking protein 1, 65kDa	182					Golgi organization (GO:0007030)|mitotic cell cycle (GO:0000278)|negative regulation of dendrite morphogenesis (GO:0050774)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)		p.A182T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(1)|ovary(3)|urinary_tract(1)	14				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CCCCAGGCTGCGTTGGGAGTT	0.587											OREG0015486	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	large_intestine(1)	3											103	104	104					3																	39142260		2203	4300	6503	39117264	SO:0001583	missense	64689			AJ409349	CCDS2681.1, CCDS63596.1, CCDS63597.1	3p22-p21.33	2008-04-23	2002-08-29	2002-05-24	ENSG00000114745	ENSG00000114745			16769	protein-coding gene	gene with protein product		606867	"golgi phosphoprotein 5"	GOLPH5			Standard	NM_001278789		Approved	GRASP65, P65, FLJ23443	uc003ciw.1	Q9BQQ3	OTTHUMG00000131292	ENST00000319283.3:c.544G>A	3.37:g.39142260C>T	ENSP00000313869:p.Ala182Thr	883	39117264	B3KWC8|Q3SYG7|Q8N272|Q96H42	Missense_Mutation	SNP	ENST00000319283.3	37	CCDS2681.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.619547	0.87460	.	.	ENSG00000114745	ENST00000319283;ENST00000479927	T;T	0.44083	0.94;0.93	5.26	4.38	0.52667	PDZ/DHR/GLGF (1);	0.270103	0.41938	D	0.000785	T	0.23014	0.0556	N	0.04880	-0.145	0.40202	D	0.97752	B;B	0.31680	0.3;0.335	B;B	0.34824	0.19;0.112	T	0.11567	-1.0582	10	0.44086	T	0.13	-8.4738	9.6389	0.39826	0.0:0.8444:0.0:0.1556	.	87;182	B4E1H8;Q9BQQ3	.;GORS1_HUMAN	T	182;87	ENSP00000313869:A182T;ENSP00000419123:A87T	ENSP00000313869:A182T	A	-	1	0	GORASP1	39117264	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	3.321000	0.51999	2.460000	0.83146	0.655000	0.94253	GCA		0.587	GORASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254060.1			T	39142260	C	T	39142260	3	4	111	1	0	0	0	0	1	0	0	0	6595	768	27	1	798	1	GORASP1	3	39142260	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	497021	39142260	158880170	202	29336										
LZTFL1	54585	hgsc.bcm.edu	37	chr3	45879492	45879492	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctctttgaacgagcaaaacGcatataattaataacttcat	4	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:45879492G>A	ENST00000296135.6	-	2	229	c.55C>T	c.(55-57)Cgt>Tgt	p.R19C	LZTFL1_ENST00000536047.1_Missense_Mutation_p.R2C|LZTFL1_ENST00000490463.1_5'UTR|LZTFL1_ENST00000539217.1_Intron	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	19					establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CGAGCAAAACGCATATAATTA	0.393																																																0			3											76	77	77					3																	45879492		2203	4300	6503	45854496	SO:0001583	missense	54585			AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.55C>T	3.37:g.45879492G>A	ENSP00000296135:p.Arg19Cys		45854496	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	37	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208307	0.79240	.	.	ENSG00000163818	ENST00000296135;ENST00000536047;ENST00000445698	T;T	0.32753	1.44;1.44	5.63	3.85	0.44370	.	0.103141	0.64402	D	0.000002	T	0.52092	0.1713	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	P	0.62382	0.901	T	0.56691	-0.7937	10	0.87932	D	0	-0.3867	12.4918	0.55905	0.1189:0.0:0.8811:0.0	.	19	Q9NQ48	LZTL1_HUMAN	C	19;2;2	ENSP00000296135:R19C;ENSP00000439522:R2C	ENSP00000296135:R19C	R	-	1	0	LZTFL1	45854496	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.303000	0.78871	0.746000	0.32786	0.655000	0.94253	CGT		0.393	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		A	45879492	G	A	45879492	3	1	111	1	0	0	0	0	1	0	0	0	9166	1087	38	1	880	1	LZTFL1	3	45879492	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	6737232	45879492	152142938	203	29337										
IMPDH2	54870	hgsc.bcm.edu	37	chr3	49065922	49065922	+	IGR	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatgggagaggaaaccagtGgggtcttaagagtgattttc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:49065922delG	ENST00000395443.2	-	0	3549				RP13-131K19.6_ENST00000607245.1_RNA|IMPDH2_ENST00000326739.4_Frame_Shift_Del_p.P64fs	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1							nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GGAAACCAGTGGGGTCTTAAG	0.542																																																0			3											72	72	72					3																	49065922		2203	4300	6503	49040926	SO:0001628	intergenic_variant	3615				CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772		3.37:g.49065922delG			49040926	Q4G0F7|Q7L621|Q8TEA5	Frame_Shift_Del	DEL	ENST00000395443.2	37	CCDS2787.1																																																																																				0.542	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		-	49065922	G	-	49065922	6	5	111	0	1	1	0	1	0	0	0	0	7748	1348	47	0		0	IMPDH2	3	49065922	IGR	DEL	G	TCGA-EI-6507-01A-11D-1733-10	3186430	49065922	148956508	204	29338										
BSN	8927	hgsc.bcm.edu	37	chr3	49689007	49689007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caagccttactctcaggatgCgtctcggagcccacagagcc	10	15	2	1	rs147953739	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:49689007C>T	ENST00000296452.4	+	5	2132	c.2018C>T	c.(2017-2019)gCg>gTg	p.A673V		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	673					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.A673V(2)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TCTCAGGATGCGTCTCGGAGC	0.582													C|||	2	0.000399361	0	0	5008	,	,		19044	0		0.002	False		,,,				2504	0															2	Substitution - Missense(2)	lung(1)|endometrium(1)	3						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	86	79	81		2018	4	1	3	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	yes	missense	BSN	NM_003458.3	64	0,12,6491	TT,TC,CC		0.1279,0.0227,0.0923	benign	673/3927	49689007	12,12994	2203	4300	6503	49664011	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.2018C>T	3.37:g.49689007C>T	ENSP00000296452:p.Ala673Val		49664011	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	c	4.937	0.174109	0.09391	2.27E-4	0.001279	ENSG00000164061	ENST00000296452	T	0.17054	2.3	5.16	4.0	0.46444	.	0.725738	0.12749	N	0.442348	T	0.09423	0.0232	N	0.08118	0	0.22819	N	0.998698	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	10	0.29301	T	0.29	.	10.7481	0.46191	0.0:0.0755:0.0:0.9245	.	673	Q9UPA5	BSN_HUMAN	V	673	ENSP00000296452:A673V	ENSP00000296452:A673V	A	+	2	0	BSN	49664011	1.000000	0.71417	0.996000	0.52242	0.177000	0.22998	4.655000	0.61476	0.809000	0.34255	-0.349000	0.07799	GCG		0.582	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49689007	C	T	49689007	3	4	111	1	0	0	0	0	1	0	0	0	1533	768	27	1	2036	1	BSN	3	49689007	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	623085	49689007	148333423	205	29339										
BSN	8927	hgsc.bcm.edu	37	chr3	49692058	49692058	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catggacctcacctctcttgCtgtggaagcgaggaagtatg	12	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:49692058C>T	ENST00000296452.4	+	5	5183	c.5069C>T	c.(5068-5070)gCt>gTt	p.A1690V		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1690					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACCTCTCTTGCTGTGGAAGCG	0.602																																																0			3											98	92	94					3																	49692058		2203	4300	6503	49667062	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.5069C>T	3.37:g.49692058C>T	ENSP00000296452:p.Ala1690Val		49667062	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.926552	0.52759	.	.	ENSG00000164061	ENST00000296452	T	0.28069	1.63	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.71184	0.972	T	0.59941	-0.7359	10	0.66056	D	0.02	.	18.6541	0.91441	0.0:1.0:0.0:0.0	.	1690	Q9UPA5	BSN_HUMAN	V	1690	ENSP00000296452:A1690V	ENSP00000296452:A1690V	A	+	2	0	BSN	49667062	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	5.999000	0.70665	2.420000	0.82092	0.561000	0.74099	GCT		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49692058	C	T	49692058	3	4	111	1	0	0	0	0	1	0	0	0	1533	797	28	3	5087	3	BSN	3	49692058	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3051	49692058	148330372	206	29340										
APEH	327	hgsc.bcm.edu	37	chr3	49720019	49720019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggaggaacactttgatgCaagccatgtggcccttatgg	12	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:49720019C>T	ENST00000296456.5	+	19	2133	c.1733C>T	c.(1732-1734)gCa>gTa	p.A578V	APEH_ENST00000438011.1_Missense_Mutation_p.A578V|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	578					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CACTTTGATGCAAGCCATGTG	0.582																																																0			3											204	189	194					3																	49720019		2203	4300	6503	49695023	SO:0001583	missense	327			D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1733C>T	3.37:g.49720019C>T	ENSP00000296456:p.Ala578Val		49695023	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126707	0.37533	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.32272	1.46;1.46	5.48	3.59	0.41128	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	1.123640	0.06327	N	0.705574	T	0.29126	0.0724	L	0.34521	1.04	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.18263	0.021;0.013	T	0.10941	-1.0608	10	0.49607	T	0.09	-1.5691	13.3776	0.60747	0.123:0.7579:0.1192:0.0	.	578;578	C9JIF9;P13798	.;ACPH_HUMAN	V	578	ENSP00000296456:A578V;ENSP00000415862:A578V	ENSP00000296456:A578V	A	+	2	0	APEH	49695023	0.000000	0.05858	0.037000	0.18230	0.995000	0.86356	0.662000	0.25038	2.566000	0.86566	0.655000	0.94253	GCA		0.582	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49720019	C	T	49720019	3	4	111	1	0	0	0	0	1	0	0	0	768	710	25	3	1807	3	APEH	3	49720019	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	27961	49720019	148302411	207	29341										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49831425	49831425	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatgggtgtcaccatcaccaGtaccggcacctcagctggaa	11	13	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:49831425G>A	ENST00000412678.2	-	11	1302	c.1294C>T	c.(1294-1296)Ctg>Ttg	p.L432L	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	432	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						ACCATCACCAGTACCGGCACC	0.627																																																0			3											54	54	54					3																	49831425		692	1591	2283	49806429	SO:0001819	synonymous_variant	0				CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1294C>T	3.37:g.49831425G>A			49806429	Q6UXT0	Silent	SNP	ENST00000412678.2	37	CCDS46829.1																																																																																				0.627	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		A	49831425	G	A	49831425	2	1	111	1	0	0	0	0	0	0	0	1	3127	1020	36	3		3	CDHR4	3	49831425	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	111406	49831425	148191005	208	29342										
HYAL2	8692	hgsc.bcm.edu	37	chr3	50357347	50357347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgcactgccttgacataacGcagtgtctccagcatgaact	8	14	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:50357347G>A	ENST00000447092.1	-	1	2866	c.574C>T	c.(574-576)Cgt>Tgt	p.R192C	HYAL2_ENST00000395139.3_Missense_Mutation_p.R192C|TUSC2_ENST00000462137.1_5'Flank|HYAL2_ENST00000442581.1_Missense_Mutation_p.R192C|HYAL2_ENST00000357750.4_Missense_Mutation_p.R192C			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	192					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)			breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TTGACATAACGCAGTGTCTCC	0.542																																																0			3											84	84	84					3																	50357347		2203	4300	6503	50332351	SO:0001583	missense	8692			AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"lysosomal hyaluronidase", "PH-20 homolog", "hyaluronidase 2"	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.574C>T	3.37:g.50357347G>A	ENSP00000401853:p.Arg192Cys		50332351	B3KRZ2|O15177|Q9BW29	Missense_Mutation	SNP	ENST00000447092.1	37	CCDS2818.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.047394	0.36085	.	.	ENSG00000068001	ENST00000447092;ENST00000357750;ENST00000395139;ENST00000442581	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	5.81	4.93	0.64822	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.206543	0.49305	D	0.000148	T	0.56171	0.1967	M	0.86953	2.85	0.58432	D	0.99999	D;D	0.89917	1.0;0.998	D;D	0.72075	0.976;0.954	T	0.65298	-0.6202	10	0.72032	D	0.01	-23.4133	14.9793	0.71301	0.0:0.0:0.856:0.144	.	192;192	B3KRZ2;Q12891	.;HYAL2_HUMAN	C	192	ENSP00000401853:R192C;ENSP00000350387:R192C;ENSP00000378571:R192C;ENSP00000406657:R192C	ENSP00000350387:R192C	R	-	1	0	HYAL2	50332351	0.998000	0.40836	0.041000	0.18516	0.001000	0.01503	3.985000	0.56930	1.445000	0.47624	-0.321000	0.08615	CGT		0.542	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773		A	50357347	G	A	50357347	3	1	111	1	0	0	0	0	1	0	0	0	7485	1087	38	1	859	1	HYAL2	3	50357347	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	525922	50357347	147665083	209	29343										
HYAL2	8692	hgsc.bcm.edu	37	chr3	50357873	50357873	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agctccatggcccatgacacCgccagcaccagggccaatgt	10	16	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:50357873C>A	ENST00000447092.1	-	1	2340	c.48G>T	c.(46-48)gcG>gcT	p.A16A	HYAL2_ENST00000395139.3_Silent_p.A16A|TUSC2_ENST00000462137.1_5'UTR|HYAL2_ENST00000442581.1_Silent_p.A16A|HYAL2_ENST00000357750.4_Silent_p.A16A			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	16					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)			breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CCCATGACACCGCCAGCACCA	0.662																																																0			3											27	24	25					3																	50357873		2198	4300	6498	50332877	SO:0001819	synonymous_variant	8692			AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"lysosomal hyaluronidase", "PH-20 homolog", "hyaluronidase 2"	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.48G>T	3.37:g.50357873C>A			50332877	B3KRZ2|O15177|Q9BW29	Silent	SNP	ENST00000447092.1	37	CCDS2818.1																																																																																				0.662	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773		A	50357873	C	A	50357873	2	1	111	1	0	0	0	0	0	0	0	1	7485	639	23	2		2	HYAL2	3	50357873	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	526	50357873	147664557	210	29344										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51418780	51418780	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agccactcagccccagggtgCgtcatccctcaggaccccat	9	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:51418780C>T	ENST00000266037.9	+	53	5906	c.5883C>T	c.(5881-5883)tgC>tgT	p.C1961C		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1961					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CCCCAGGGTGCGTCATCCCTC	0.682																																																0			3											55	64	61					3																	51418780		2142	4250	6392	51393820	SO:0001819	synonymous_variant	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.5883C>T	3.37:g.51418780C>T			51393820	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																				0.682	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51418780	C	T	51418780	2	4	111	1	0	0	0	0	0	0	0	1	4699	776	27	1		1	DOCK3	3	51418780	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1060907	51418780	146603650	211	29345										
GRM2	2912	hgsc.bcm.edu	37	chr3	51743379	51743379	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgccccgacggctcttatgCgacccatggtgatgctccca	10	16	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:51743379C>T	ENST00000395052.3	+	2	614	c.380C>T	c.(379-381)gCg>gTg	p.A127V	GRM2_ENST00000442933.2_Missense_Mutation_p.A127V|GRM2_ENST00000475478.1_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	127					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGCTCTTATGCGACCCATGGT	0.587																																																0			3											59	46	50					3																	51743379		2203	4297	6500	51718419	SO:0001583	missense	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.380C>T	3.37:g.51743379C>T	ENSP00000378492:p.Ala127Val		51718419	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.981130	0.93044	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.84589	-1.87;-1.87	5.42	5.42	0.78866	Extracellular ligand-binding receptor (1);	0.062472	0.64402	D	0.000006	D	0.85500	0.5711	L	0.37630	1.12	0.80722	D	1	P	0.48230	0.907	P	0.49887	0.625	D	0.86902	0.2055	10	0.66056	D	0.02	.	19.2362	0.93861	0.0:1.0:0.0:0.0	.	127	Q14416	GRM2_HUMAN	V	127	ENSP00000378492:A127V;ENSP00000408906:A127V	ENSP00000296479:A127V	A	+	2	0	GRM2	51718419	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	6.026000	0.70873	2.555000	0.86185	0.655000	0.94253	GCG		0.587	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51743379	C	T	51743379	3	4	111	1	0	0	0	0	1	0	0	0	6818	768	27	1	382	1	GRM2	3	51743379	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	324599	51743379	146279051	212	29346										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436345	52436345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggggcgagagcgtttccgccGgtcaggcttccgctgcttgt	16	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:52436345G>A	ENST00000460680.1	-	17	2620	c.2149C>T	c.(2149-2151)Cgg>Tgg	p.R717W	BAP1_ENST00000296288.5_Missense_Mutation_p.R699W	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				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)		CGTTTCCGCCGGTCAGGCTTC	0.662			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															GBM(101;493 1458 7992 21037 25532)		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0			3											23	26	25					3																	52436345		2202	4294	6496	52411385	SO:0001583	missense	9223			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.2149C>T	3.37:g.52436345G>A	ENSP00000417132:p.Arg717Trp		52411385	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.898773	0.72639	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368	T;T;T	0.47177	0.85;0.85;0.85	5.52	-2.12	0.07165	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.222920	0.46442	D	0.000286	T	0.33818	0.0876	L	0.36672	1.1	0.80722	D	1	B	0.18310	0.027	B	0.09377	0.004	T	0.17684	-1.0361	10	0.87932	D	0	.	12.1302	0.53938	0.0583:0.0:0.4445:0.4971	.	717	Q92560	BAP1_HUMAN	W	717;699;241	ENSP00000417132:R717W;ENSP00000296288:R699W;ENSP00000420647:R241W	ENSP00000296288:R699W	R	-	1	2	BAP1	52411385	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	3.332000	0.52083	-0.232000	0.09811	0.561000	0.74099	CGG		0.662	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52436345	G	A	52436345	3	1	111	1	0	0	0	0	1	0	0	0	1312	1115	39	1	44	1	BAP1	3	52436345	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	692966	52436345	145586085	213	29347										
NISCH	11188	hgsc.bcm.edu	37	chr3	52518632	52518632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagggatgttctgattccttGgagtccatccctgcgggaca	12	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:52518632G>A	ENST00000479054.1	+	15	1704	c.1632G>A	c.(1630-1632)ttG>ttA	p.L544L	NISCH_ENST00000345716.4_Silent_p.L544L			Q9Y2I1	NISCH_HUMAN	nischarin	544	Interaction with PAK1. {ECO:0000250}.|Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CTGATTCCTTGGAGTCCATCC	0.582																																																0			3											101	92	95					3																	52518632		2203	4300	6503	52493672	SO:0001819	synonymous_variant	11188			AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.1632G>A	3.37:g.52518632G>A			52493672	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																				0.582	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		A	52518632	G	A	52518632	2	1	111	1	0	0	0	0	0	0	0	1	10463	1339	47	3		3	NISCH	3	52518632	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	82287	52518632	145503798	214	29348										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52840932	52840932	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcaggcctcacagttaatgGgcagatcactggcgacaaga	13	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:52840932G>A	ENST00000449956.2	+	19	2078	c.2072G>A	c.(2071-2073)gGg>gAg	p.G691E	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	691					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		ACAGTTAATGGGCAGATCACT	0.547																																																0			3											24	25	25					3																	52840932		2050	4186	6236	52815972	SO:0001583	missense	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.2072G>A	3.37:g.52840932G>A	ENSP00000415769:p.Gly691Glu		52815972	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605799	0.66445	.	.	ENSG00000162267	ENST00000273291;ENST00000449956	T	0.57752	0.38	5.41	5.41	0.78517	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76990	0.4065	M	0.88842	2.985	0.44547	D	0.997508	D	0.89917	1.0	D	0.97110	1.0	T	0.80823	-0.1210	10	0.59425	D	0.04	-29.9651	16.113	0.81275	0.0:0.0:1.0:0.0	.	691	Q06033	ITIH3_HUMAN	E	686;691	ENSP00000415769:G691E	ENSP00000273291:G686E	G	+	2	0	ITIH3	52815972	1.000000	0.71417	0.996000	0.52242	0.374000	0.29953	6.321000	0.72881	2.547000	0.85894	0.555000	0.69702	GGG		0.547	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		A	52840932	G	A	52840932	3	1	111	1	0	0	0	0	1	0	0	0	7926	1232	43	3	2146	3	ITIH3	3	52840932	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	322300	52840932	145181498	215	29349										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56598018	56598018	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taggtaaacagaagcctcacAaaaaacacatcacagctgaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:56598018delA	ENST00000394672.3	+	4	479	c.409delA	c.(409-411)aaafs	p.K138fs	CCDC66_ENST00000442522.2_3'UTR|CCDC66_ENST00000436465.2_Frame_Shift_Del_p.K138fs|CCDC66_ENST00000538560.1_Frame_Shift_Del_p.K138fs|CCDC66_ENST00000326595.7_Frame_Shift_Del_p.K104fs	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	138					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		GAAGCCTCACAAAAAACACAT	0.388																																																0			3											100	88	92					3																	56598018		2203	4300	6503	56573058	SO:0001589	frameshift_variant	285331			AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.409delA	3.37:g.56598018delA	ENSP00000378167:p.Lys138fs		56573058	B3KWL8|Q4VC34|Q8N949	Frame_Shift_Del	DEL	ENST00000394672.3	37	CCDS46852.1																																																																																				0.388	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		-	56598018	A	-	56598018	7	5	111	1	0	1	0	1	0	0	0	0	2844	131	5	0	423	0	CCDC66	3	56598018	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	3757086	56598018	141424412	216	29350										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56680557	56680557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgatattttaccttcataCagatggcaattttcagataa	5	7	3	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:56680557C>T	ENST00000493960.2	-	14	2218	c.2208G>A	c.(2206-2208)ctG>ctA	p.L736L	FAM208A_ENST00000355628.5_Silent_p.L736L|FAM208A_ENST00000431842.2_Silent_p.L340L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	736							poly(A) RNA binding (GO:0044822)	p.L340L(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TACCTTCATACAGATGGCAAT	0.368																																																1	Substitution - coding silent(1)	kidney(1)	3											92	95	94					3																	56680557		2202	4300	6502	56655597	SO:0001819	synonymous_variant	23272			AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.2208G>A	3.37:g.56680557C>T			56655597	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	ENST00000493960.2	37	CCDS46853.1																																																																																				0.368	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		T	56680557	C	T	56680557	2	4	111	1	0	0	0	0	0	0	0	1	2245	465	17	3		3	C3orf63	3	56680557	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	82539	56680557	141341873	217	29351										
IL17RD	54756	hgsc.bcm.edu	37	chr3	57132118	57132118	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgacgtatagggaccggcctGacttgctccggaagtagttc	13	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:57132118G>A	ENST00000296318.7	-	12	1701	c.1613C>T	c.(1612-1614)tCa>tTa	p.S538L	IL17RD_ENST00000463523.1_Missense_Mutation_p.S394L|IL17RD_ENST00000427856.2_Missense_Mutation_p.S514L|IL17RD_ENST00000320057.5_Missense_Mutation_p.S394L	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	538					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		GGACCGGCCTGACTTGCTCCG	0.592																																																0			3											88	78	82					3																	57132118		2203	4300	6503	57107158	SO:0001583	missense	54756			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.1613C>T	3.37:g.57132118G>A	ENSP00000296318:p.Ser538Leu		57107158	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092571	0.76756	.	.	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.15139	2.45;2.45;2.46;2.45	5.64	5.64	0.86602	.	0.447919	0.26213	N	0.025675	T	0.22205	0.0535	L	0.50333	1.59	0.41412	D	0.987743	P;P;B	0.43352	0.577;0.804;0.342	B;B;B	0.39660	0.202;0.17;0.306	T	0.01697	-1.1293	10	0.87932	D	0	-29.6195	19.7154	0.96115	0.0:0.0:1.0:0.0	.	394;538;514	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	L	538;394;514;394	ENSP00000296318:S538L;ENSP00000322250:S394L;ENSP00000399209:S514L;ENSP00000417516:S394L	ENSP00000296318:S538L	S	-	2	0	IL17RD	57107158	1.000000	0.71417	0.088000	0.20740	0.962000	0.63368	9.195000	0.94971	2.664000	0.90586	0.655000	0.94253	TCA		0.592	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		A	57132118	G	A	57132118	3	1	111	1	0	0	0	0	1	0	0	0	7663	1294	45	3	614	3	IL17RD	3	57132118	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	451561	57132118	140890312	218	29352										
ASB14	142686	hgsc.bcm.edu	37	chr3	57312659	57312659	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atagttgcccatcctgagggCtatctggaggcagttaaccg	12	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:57312659C>A	ENST00000389601.3	-	9	1297	c.1177G>T	c.(1177-1179)Gcc>Tcc	p.A393S	ASB14_ENST00000487349.1_Missense_Mutation_p.A393S	NM_130387.5	NP_569058.1	A6NK59	ASB14_HUMAN	ankyrin repeat and SOCS box containing 14	393					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		ATCCTGAGGGCTATCTGGAGG	0.478																																																0			3											103	98	100					3																	57312659		2203	4300	6503	57287699	SO:0001583	missense	142686			AF403032	CCDS46856.1, CCDS46856.2	3p21.1	2013-01-10	2011-01-25			ENSG00000239388		"Ankyrin repeat domain containing"	19766	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 14"			12076535	Standard	NM_130387		Approved	DKFZp313L0121	uc021wzs.1	A6NK59		ENST00000389601.3:c.1177G>T	3.37:g.57312659C>A	ENSP00000374252:p.Ala393Ser		57287699	C9JX97|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000389601.3	37		.	.	.	.	.	.	.	.	.	.	C	27.8	4.862015	0.91433	.	.	ENSG00000239388	ENST00000487349;ENST00000389601;ENST00000438870	D;D	0.90324	-2.65;-1.51	6.07	6.07	0.98685	.	.	.	.	.	D	0.95677	0.8594	M	0.82716	2.605	0.58432	D	0.999998	D;D	0.76494	0.999;0.982	D;D	0.65573	0.936;0.936	D	0.94963	0.8110	9	0.56958	D	0.05	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	393;108	C9JX97;A6NK59-2	.;.	S	393;393;229	ENSP00000419199:A393S;ENSP00000374252:A393S	ENSP00000374252:A393S	A	-	1	0	ASB14	57287699	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.431000	0.80335	2.885000	0.99019	0.655000	0.94253	GCC		0.478	ASB14-201	KNOWN	basic	protein_coding	protein_coding				A	57312659	C	A	57312659	3	1	111	1	0	0	0	0	1	0	0	0	1019	797	28	2	598	2	ASB14	3	57312659	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	180541	57312659	140709771	219	29353										
MAGI1	9223	hgsc.bcm.edu	37	chr3	65422910	65422912	+	In_Frame_Del	DEL	TCT	TCT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggcacaagggctgagtgaTcttctgtccattctatgaaa					rs144417292		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	TCT	TCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:65422910_65422912delTCT	ENST00000497477.2	-	10	1280_1282	c.1281_1283delAGA	c.(1279-1284)gaagat>gat	p.E427del	MAGI1_ENST00000402939.2_In_Frame_Del_p.E427del|MAGI1_ENST00000330909.8_In_Frame_Del_p.E427del|MAGI1_ENST00000483466.1_In_Frame_Del_p.E427del|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	427					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		GGCTGAGTGATCTTCTGTCCATT	0.389																																																0			3																																								65397952	SO:0001651	inframe_deletion	154043			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1281_1283delAGA	3.37:g.65422913_65422915delTCT	ENSP00000424369:p.Glu427del		65397950	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	In_Frame_Del	DEL	ENST00000497477.2	37																																																																																					0.389	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		-	65422912	TCT	-	65422910	7	5	111	1	0	1	0	1	0	0	0	0	9220	1435	50	0	3395	0	MAGI1	3	65422910	In_Frame_Del	DEL	TCT	TCGA-EI-6507-01A-11D-1733-10	8110251	65422910	132599520	220	29354										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66430822	66430822	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcaagtactgggcttccgcGcgctctggactgcctgaagt	13	12	1	1	rs138156364	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:66430822G>A	ENST00000273261.3	-	19	3671	c.3147C>T	c.(3145-3147)cgC>cgT	p.R1049R	LRIG1_ENST00000383703.3_Silent_p.R1026R|LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1049					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GGGCTTCCGCGCGCTCTGGAC	0.562													G|||	2	0.000399361	0.0015	0	5008	,	,		18813	0		0	False		,,,				2504	0															0			3						G		3,4403	6.2+/-15.9	0,3,2200	111	112	112		3147	1.9	0	3	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LRIG1	NM_015541.2		0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308		1049/1094	66430822	4,13002	2203	4300	6503	66513512	SO:0001819	synonymous_variant	26018			AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3147C>T	3.37:g.66430822G>A			66513512	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																				0.562	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66430822	G	A	66430822	2	1	111	1	0	0	0	0	0	0	0	1	8973	1074	38	1		1	LRIG1	3	66430822	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1007912	66430822	131591608	221	29355										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89445016	89445016	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgtcctgacgattaagaaaGatcggacctccagaaatagc	9	10	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:89445016G>A	ENST00000336596.2	+	6	1561	c.1336G>A	c.(1336-1338)Gat>Aat	p.D446N	EPHA3_ENST00000494014.1_Missense_Mutation_p.D446N|EPHA3_ENST00000452448.2_Missense_Mutation_p.D446N	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	446	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.D446Y(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GATTAAGAAAGATCGGACCTC	0.453										TSP Lung(6;0.00050)																																						1	Substitution - Missense(1)	lung(1)	3											165	158	160					3																	89445016		2203	4300	6503	89527706	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1336G>A	3.37:g.89445016G>A	ENSP00000337451:p.Asp446Asn		89527706	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052428	0.75960	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.57273	0.41;0.41;0.41	5.96	5.96	0.96718	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.149213	0.64402	D	0.000013	T	0.45498	0.1345	L	0.31578	0.945	0.80722	D	1	P;B	0.35493	0.505;0.062	B;B	0.35770	0.21;0.085	T	0.23762	-1.0179	9	.	.	.	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	446;446	P29320;P29320-2	EPHA3_HUMAN;.	N	446	ENSP00000337451:D446N;ENSP00000399926:D446N;ENSP00000419190:D446N	.	D	+	1	0	EPHA3	89527706	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	GAT		0.453	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89445016	G	A	89445016	3	1	111	1	0	0	0	0	1	0	0	0	5181	942	33	3	1358	3	EPHA3	3	89445016	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	23014194	89445016	108577414	222	29356										
OR5H2	79310	hgsc.bcm.edu	37	chr3	98002008	98002008	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttggttaatttcttggccAaaaacaggatgatatctctg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:98002008delA	ENST00000355273.2	+	1	277	c.277delA	c.(277-279)aaafs	p.K93fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						TTTCTTGGCCAAAAACAGGAT	0.373																																																0			3											163	160	161					3																	98002008		2203	4300	6503	99484698	SO:0001589	frameshift_variant	79310				CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.277delA	3.37:g.98002008delA	ENSP00000347418:p.Lys93fs		99484698	Q6IF87	Frame_Shift_Del	DEL	ENST00000355273.2	37	CCDS33801.1																																																																																				0.373	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			-	98002008	A	-	98002008	7	5	111	1	0	1	0	1	0	0	0	0	11193	131	5	0	279	0	OR5H2	3	98002008	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	8556992	98002008	100020422	223	29357										
IFT57	55081	hgsc.bcm.edu	37	chr3	107884331	107884331	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccatttccctgctggtatcGctcctttgcctgagaggaaa	9	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:107884331G>A	ENST00000264538.3	-	9	1238	c.991C>T	c.(991-993)Cga>Tga	p.R331*	IFT57_ENST00000468021.1_5'UTR	NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	331					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			TGCTGGTATCGCTCCTTTGCC	0.478																																																0			3											195	133	154					3																	107884331		2203	4300	6503	109367021	SO:0001587	stop_gained	55081			AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.991C>T	3.37:g.107884331G>A	ENSP00000264538:p.Arg331*		109367021	Q96DA9	Nonsense_Mutation	SNP	ENST00000264538.3	37	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361190	0.82353	.	.	ENSG00000114446	ENST00000264538	.	.	.	5.92	4.97	0.65823	.	0.179469	0.46758	D	0.000277	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	13.5745	0.61866	0.0:0.0:0.7597:0.2403	.	.	.	.	X	331	.	ENSP00000264538:R331X	R	-	1	2	IFT57	109367021	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	3.198000	0.51035	2.818000	0.97014	0.655000	0.94253	CGA		0.478	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		A	107884331	G	A	107884331	4	1	111	1	0	0	0	0	0	1	0	0	7583	1095	38	1	310	1	IFT57	3	107884331	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	9882323	107884331	90138099	224	29358										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108324275	108324275	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggattctctaccagatgaaTtttttgtgaggtaaggccac							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:108324275delT	ENST00000361582.3	+	2	252	c.22delT	c.(22-24)tttfs	p.F9fs	DZIP3_ENST00000463306.1_Frame_Shift_Del_p.F9fs	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	9					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						ACCAGATGAATTTTTTGTGAG	0.443																																																0			3											111	116	114					3																	108324275		2203	4300	6503	109806965	SO:0001589	frameshift_variant	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.22delT	3.37:g.108324275delT	ENSP00000355028:p.Phe9fs		109806965	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Frame_Shift_Del	DEL	ENST00000361582.3	37	CCDS2952.1																																																																																				0.443	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		-	108324275	T	-	108324275	7	5	111	1	0	1	0	1	0	0	0	0	4876	1493	52	0	24	0	DZIP3	3	108324275	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	439944	108324275	89698155	225	29359										
MORC1	27136	hgsc.bcm.edu	37	chr3	108677968	108677968	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggtcaccttctggaccaccCtggaaaagagaagcaacagt	10	11	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:108677968C>A	ENST00000483760.1	-	27	2780		c.e27-1		MORC1_ENST00000232603.5_Splice_Site					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CTGGACCACCCTGGAAAAGAG	0.428																																																0			3											38	40	39					3																	108677968		2202	4298	6500	110160658	SO:0001630	splice_region_variant	27136			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2737-1G>T	3.37:g.108677968C>A			110160658		Splice_Site	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	C	19.69	3.875444	0.72180	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8227	0.63333	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MORC1	110160658	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.298000	0.51818	2.648000	0.89879	0.557000	0.71058	.		0.428	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		Intron	A	108677968	C	A	108677968	5	1	111	1	0	0	0	0	0	0	1	0	9731	695	24	2	159	2	MORC1	3	108677968	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	353693	108677968	89344462	226	29360										
ATG3	64422	hgsc.bcm.edu	37	chr3	112260669	112260669	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccttccatatctgcagcttcTccttcatcttcatcttcttc	2	16	7	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:112260669T>G	ENST00000283290.5	-	7	890	c.456A>C	c.(454-456)ggA>ggC	p.G152G	ATG3_ENST00000402314.2_Silent_p.G152G|ATG3_ENST00000495756.1_5'UTR	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	152					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						CTGCAGCTTCTCCTTCATCTT	0.303																																																0			3											158	147	151					3																	112260669		2203	4299	6502	113743359	SO:0001819	synonymous_variant	64422				CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"APG3 autophagy 3-like (S. cerevisiae)", "ATG3 autophagy related 3 homolog (S. cerevisiae)"	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.456A>C	3.37:g.112260669T>G			113743359	Q6PKC5|Q9H6L9	Silent	SNP	ENST00000283290.5	37	CCDS2966.1																																																																																				0.303	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488		G	112260669	T	G	112260669	2	3	111	1	0	0	0	0	0	0	0	1	1096	1538	54	4		4	ATG3	3	112260669	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3582701	112260669	85761761	227	29361										
UPK1B	7348	hgsc.bcm.edu	37	chr3	118917947	118917947	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaatgaaccgacacgcctGgggggttgcctggtttggat					rs368682621		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:118917947delG	ENST00000264234.3	+	7	841	c.692delG	c.(691-693)tggfs	p.W231fs	UPK1B_ENST00000497685.1_Frame_Shift_Del_p.W151fs|UPK1B_ENST00000460625.1_Frame_Shift_Del_p.W223fs	NM_006952.3	NP_008883.2	O75841	UPK1B_HUMAN	uroplakin 1B	231					epithelial cell differentiation (GO:0030855)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	14				GBM - Glioblastoma multiforme(114;0.222)		CGACACGCCTGGGGGGTTGCC	0.483																																																0			3											112	107	109					3																	118917947		2203	4300	6503	120400637	SO:0001589	frameshift_variant	7348			AF082888	CCDS2985.1	3q13.32	2013-02-14			ENSG00000114638	ENSG00000114638		"Tetraspanins"	12578	protein-coding gene	gene with protein product		602380		UPK1		9935153, 9846985	Standard	NM_006952		Approved	TSPAN20	uc003ecc.3	O75841	OTTHUMG00000159354	ENST00000264234.3:c.692delG	3.37:g.118917947delG	ENSP00000264234:p.Trp231fs		120400637	O60753|Q9UIM2|Q9UNX6	Frame_Shift_Del	DEL	ENST00000264234.3	37	CCDS2985.1																																																																																				0.483	UPK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354883.2			-	118917947	G	-	118917947	7	5	111	1	0	1	0	1	0	0	0	0	17048	1357	47	0	714	0	UPK1B	3	118917947	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	6657278	118917947	79104483	228	29362										
DTX3L	151636	hgsc.bcm.edu	37	chr3	122287438	122287438	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtatcagaaaaatggaaggtCacgatggaattgagaaggtg	14	3	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:122287438C>T	ENST00000296161.4	+	3	691	c.502C>T	c.(502-504)Cac>Tac	p.H168Y	DTX3L_ENST00000383661.3_Intron	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	168					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		AATGGAAGGTCACGATGGAAT	0.418																																																0			3											105	92	97					3																	122287438		2203	4300	6503	123770128	SO:0001583	missense	151636				CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"RING-type (C3HC4) zinc fingers"	30323	protein-coding gene	gene with protein product	"rhysin 2"	613143	"deltex 3-like (Drosophila)"			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.502C>T	3.37:g.122287438C>T	ENSP00000296161:p.His168Tyr		123770128	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	C	7.408	0.634207	0.14322	.	.	ENSG00000163840	ENST00000296161	T	0.30981	1.51	5.5	-0.298	0.12814	.	1.640760	0.03209	N	0.175982	T	0.15349	0.0370	N	0.24115	0.695	0.09310	N	1	P	0.44877	0.845	B	0.31016	0.123	T	0.15780	-1.0425	10	0.56958	D	0.05	-34.0349	1.3847	0.02237	0.3409:0.358:0.1254:0.1757	.	168	Q8TDB6	DTX3L_HUMAN	Y	168	ENSP00000296161:H168Y	ENSP00000296161:H168Y	H	+	1	0	DTX3L	123770128	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-1.520000	0.02241	-0.265000	0.09352	0.655000	0.94253	CAC		0.418	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		T	122287438	C	T	122287438	3	4	111	1	0	0	0	0	1	0	0	0	4807	826	29	3	512	3	DTX3L	3	122287438	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3369491	122287438	75734992	229	29363										
PARP14	54625	hgsc.bcm.edu	37	chr3	122446781	122446781	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catgggacagatgccggctcCgtgccacacgtcaatcgaaa	11	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:122446781C>T	ENST00000474629.2	+	16	5330	c.5064C>T	c.(5062-5064)tcC>tcT	p.S1688S		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1688	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		ATGCCGGCTCCGTGCCACACG	0.483																																																0			3											67	67	67					3																	122446781		1993	4172	6165	123929471	SO:0001819	synonymous_variant	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.5064C>T	3.37:g.122446781C>T			123929471	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																				0.483	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122446781	C	T	122446781	2	4	111	1	0	0	0	0	0	0	0	1	11489	639	23	1		1	PARP14	3	122446781	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	159343	122446781	75575649	230	29364										
KALRN	8997	hgsc.bcm.edu	37	chr3	124390543	124390543	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgagtatcaacggaaagaaaGgagcacagctgtgatgaggt	14	5	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:124390543G>T	ENST00000291478.5	+	15	1809	c.1646G>T	c.(1645-1647)aGg>aTg	p.R549M	KALRN_ENST00000393496.1_Missense_Mutation_p.R587M|KALRN_ENST00000428018.2_Missense_Mutation_p.R517M|KALRN_ENST00000360013.3_Missense_Mutation_p.R2246M|KALRN_ENST00000459915.1_Missense_Mutation_p.R338M	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2245					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CGGAAAGAAAGGAGCACAGCT	0.562																																																0			3											97	106	103					3																	124390543		2203	4300	6503	125873233	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.1646G>T	3.37:g.124390543G>T	ENSP00000291478:p.Arg549Met		125873233	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	37	CCDS3028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.80|14.80	2.642575|2.642575	0.47153|0.47153	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000360013;ENST00000393496;ENST00000291478;ENST00000428018;ENST00000459915	.|T;T;T;T;T	.|0.44083	.|0.93;0.93;0.93;0.93;0.93	4.35|4.35	4.35|4.35	0.52113|0.52113	.|Pleckstrin homology-type (1);	.|0.724812	.|0.12578	.|N	.|0.456657	.|T	.|0.26159	.|0.0638	N|N	0.08118|0.08118	0|0	0.33900|0.33900	D|D	0.638353|0.638353	.|B;P;P;B	.|0.38711	.|0.099;0.511;0.643;0.327	.|B;B;B;B	.|0.37346	.|0.019;0.087;0.247;0.053	.|T	.|0.41592	.|-0.9500	.|10	.|0.56958	.|D	.|0.05	.|.	12.4232|12.4232	0.55532|0.55532	0.0847:0.0:0.9153:0.0|0.0847:0.0:0.9153:0.0	.|.	.|338;549;587;2245	.|E7EUZ8;C9JQ37;O60229-5;O60229	.|.;.;.;KALRN_HUMAN	X|M	2215|2246;587;549;517;338	.|ENSP00000353109:R2246M;ENSP00000377134:R587M;ENSP00000291478:R549M;ENSP00000402419:R517M;ENSP00000420318:R338M	.|ENSP00000291478:R549M	G|R	+|+	1|2	0|0	KALRN|KALRN	125873233|125873233	0.161000|0.161000	0.22892|0.22892	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	1.507000|1.507000	0.35758|0.35758	1.968000|1.968000	0.57251|0.57251	0.557000|0.557000	0.71058|0.71058	GGA|AGG		0.562	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		T	124390543	G	T	124390543	3	4	111	1	0	0	0	0	1	0	0	0	7996	1000	35	2	7083	2	KALRN	3	124390543	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1943762	124390543	73631887	231	29365										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126137577	126137577	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgccttgttcgacgagttcGtcagggagaatgactgcagc	13	11	1	2	rs371120376		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:126137577G>A	ENST00000352312.1	+	7	709	c.610G>A	c.(610-612)Gtc>Atc	p.V204I	CCDC37_ENST00000393425.1_Missense_Mutation_p.V205I|CCDC37_ENST00000505024.1_Missense_Mutation_p.V205I	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	204										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		CGACGAGTTCGTCAGGGAGAA	0.662													G|||	1	0.000199681	0	0	5008	,	,		13951	0		0	False		,,,				2504	0.001															0			3											41	45	44					3																	126137577		2197	4299	6496	127620267	SO:0001583	missense	348807			AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.610G>A	3.37:g.126137577G>A	ENSP00000344749:p.Val204Ile		127620267	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	37	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.610683	0.28712	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.14766	2.48;2.48;2.48	5.09	3.28	0.37604	.	0.066263	0.64402	D	0.000008	T	0.06280	0.0162	N	0.08118	0	0.20489	N	0.999897	B;B	0.12013	0.004;0.005	B;B	0.06405	0.001;0.002	T	0.26224	-1.0109	10	0.48119	T	0.1	-18.6468	6.0203	0.19625	0.0:0.6707:0.1605:0.1688	.	205;204	Q494V2-2;Q494V2	.;CCD37_HUMAN	I	204;205;205	ENSP00000344749:V204I;ENSP00000377076:V205I;ENSP00000423046:V205I	ENSP00000344749:V204I	V	+	1	0	CCDC37	127620267	1.000000	0.71417	0.990000	0.47175	0.078000	0.17371	2.369000	0.44231	1.161000	0.42604	-0.339000	0.08088	GTC		0.662	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126137577	G	A	126137577	3	1	111	1	0	0	0	0	1	0	0	0	2815	1145	40	1	632	1	CCDC37	3	126137577	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1747034	126137577	71884853	232	29366										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670256	134670256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaaaacctgaacaccatccGcacctaccaggtgtgcaatg	8	13	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:134670256G>A	ENST00000398015.3	+	3	537	c.167G>A	c.(166-168)cGc>cAc	p.R56H	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	56	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.R56L(2)|p.R56P(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						AACACCATCCGCACCTACCAG	0.517																																																3	Substitution - Missense(3)	lung(3)	3											38	43	41					3																	134670256		2155	4278	6433	136152946	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.167G>A	3.37:g.134670256G>A	ENSP00000381097:p.Arg56His		136152946	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469822	0.84533	.	.	ENSG00000154928	ENST00000460895;ENST00000398015;ENST00000497173;ENST00000473867;ENST00000474732	T;T;T;T;T	0.04360	3.64;3.64;3.64;3.64;3.64	5.64	5.64	0.86602	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.19366	0.0465	L	0.57130	1.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00563	-1.1669	10	0.29301	T	0.29	.	19.7209	0.96143	0.0:0.0:1.0:0.0	.	56;56	B5A969;P54762	.;EPHB1_HUMAN	H	34;56;34;34;34	ENSP00000417435:R34H;ENSP00000381097:R56H;ENSP00000419688:R34H;ENSP00000417216:R34H;ENSP00000418352:R34H	ENSP00000381097:R56H	R	+	2	0	EPHB1	136152946	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.651000	0.90000	0.650000	0.86243	CGC		0.517	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134670256	G	A	134670256	3	1	111	1	0	0	0	0	1	0	0	0	5187	1087	38	1	177	1	EPHB1	3	134670256	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8532679	134670256	63352174	233	29367										
COPB2	9276	hgsc.bcm.edu	37	chr3	139077104	139077104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtaggagaagcaggtttccCatcaagttcctgaaaccaca	9	10	1	2	rs560518160		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:139077104C>A	ENST00000333188.5	-	21	2744	c.2563G>T	c.(2563-2565)Ggg>Tgg	p.G855W	COPB2_ENST00000507777.1_Missense_Mutation_p.G826W	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	855					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.G855R(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						GCAGGTTTCCCATCAAGTTCC	0.433																																																1	Substitution - Missense(1)	ovary(1)	3											110	96	100					3																	139077104		2203	4300	6503	140559794	SO:0001583	missense	9276			BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.2563G>T	3.37:g.139077104C>A	ENSP00000329419:p.Gly855Trp		140559794	B4DZI8	Missense_Mutation	SNP	ENST00000333188.5	37	CCDS3108.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.78|13.78	2.338314|2.338314	0.41398|0.41398	.|.	.|.	ENSG00000184432|ENSG00000184432	ENST00000333188;ENST00000507777|ENST00000503326	T;T|.	0.62941|.	-0.01;0.1|.	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	0.717399|.	0.13055|.	N|.	0.417385|.	T|T	0.41259|0.41259	0.1151|0.1151	N|N	0.24115|0.24115	0.695|0.695	0.31506|0.31506	N|N	0.664213|0.664213	B|.	0.26147|.	0.143|.	B|.	0.23852|.	0.049|.	T|T	0.43015|0.43015	-0.9417|-0.9417	10|5	0.72032|.	D|.	0.01|.	-21.3713|-21.3713	13.8059|13.8059	0.63230|0.63230	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	855|.	P35606|.	COPB2_HUMAN|.	W|L	855;826|68	ENSP00000329419:G855W;ENSP00000422295:G826W|.	ENSP00000329419:G855W|.	G|W	-|-	1|2	0|0	COPB2|COPB2	140559794|140559794	0.797000|0.797000	0.28877|0.28877	0.936000|0.936000	0.37596|0.37596	0.765000|0.765000	0.43378|0.43378	3.232000|3.232000	0.51302|0.51302	2.634000|2.634000	0.89283|0.89283	0.650000|0.650000	0.86243|0.86243	GGG|TGG		0.433	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		A	139077104	C	A	139077104	3	1	111	1	0	0	0	0	1	0	0	0	3735	594	21	2	165	2	COPB2	3	139077104	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4406848	139077104	58945326	234	29368										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401871	140401871	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcatcatcgagtactgccgCaatgacaacaaattgctctg	8	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:140401871C>T	ENST00000286349.3	+	2	1100	c.909C>T	c.(907-909)cgC>cgT	p.R303R		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	303						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R303R(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGTACTGCCGCAATGACAACA	0.567																																																1	Substitution - coding silent(1)	lung(1)	3											244	209	221					3																	140401871		2203	4300	6503	141884561	SO:0001819	synonymous_variant	287015			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.909C>T	3.37:g.140401871C>T			141884561	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																				0.567	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140401871	C	T	140401871	2	4	111	1	0	0	0	0	0	0	0	1	16557	697	25	3		3	TRIM42	3	140401871	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1324767	140401871	57620559	235	29369										
GRK7	131890	hgsc.bcm.edu	37	chr3	141497143	141497143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agccatggtggacatgggggCcctggacaacctgatcgcca	14	12	0	1	rs377464259		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:141497143C>T	ENST00000264952.2	+	1	154	c.17C>T	c.(16-18)gCc>gTc	p.A6V		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	6					protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GACATGGGGGCCCTGGACAAC	0.677																																																0			3											46	55	52					3																	141497143		2197	4299	6496	142979833	SO:0001583	missense	131890				CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.17C>T	3.37:g.141497143C>T	ENSP00000264952:p.Ala6Val		142979833		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.800522	0.50315	.	.	ENSG00000114124	ENST00000264952	T	0.61274	0.12	4.5	1.61	0.23674	.	0.133015	0.50627	D	0.000109	T	0.48259	0.1490	L	0.38175	1.15	0.23859	N	0.996649	B	0.14805	0.011	B	0.14578	0.011	T	0.44997	-0.9291	10	0.59425	D	0.04	-6.801	15.8711	0.79119	0.0:0.3053:0.6947:0.0	.	6	Q8WTQ7	GRK7_HUMAN	V	6	ENSP00000264952:A6V	ENSP00000264952:A6V	A	+	2	0	GRK7	142979833	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.498000	0.53302	0.009000	0.14813	-0.176000	0.13171	GCC		0.677	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		T	141497143	C	T	141497143	3	4	111	1	0	0	0	0	1	0	0	0	6815	739	26	3	19	3	GRK7	3	141497143	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1095272	141497143	56525287	236	29370										
XRN1	54464	hgsc.bcm.edu	37	chr3	142140334	142140334	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttacatctgatagtttcacaAggtatttctcaaatcgaggt	7	7	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:142140334A>G	ENST00000264951.4	-	9	1136	c.1019T>C	c.(1018-1020)cTt>cCt	p.L340P	XRN1_ENST00000392981.2_Missense_Mutation_p.L340P|XRN1_ENST00000463916.1_Missense_Mutation_p.L340P|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Missense_Mutation_p.L130P	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	340					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.L340H(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TAGTTTCACAAGGTATTTCTC	0.328																																																1	Substitution - Missense(1)	ovary(1)	3											60	59	59					3																	142140334		2202	4299	6501	143623024	SO:0001583	missense	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1019T>C	3.37:g.142140334A>G	ENSP00000264951:p.Leu340Pro		143623024	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051422	0.75960	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157	T;T	0.50277	0.75;0.76	5.27	5.27	0.74061	.	0.174438	0.51477	D	0.000089	T	0.75961	0.3921	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.992;1.0;1.0;0.999	D;D;D;D;D	0.76071	0.986;0.952;0.95;0.987;0.971	T	0.82212	-0.0569	10	0.54805	T	0.06	-17.5749	15.1465	0.72657	1.0:0.0:0.0:0.0	.	130;340;201;340;340	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	P	340;340;340;130	ENSP00000264951:L340P;ENSP00000376707:L340P	ENSP00000264951:L340P	L	-	2	0	XRN1	143623024	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.730000	0.91510	2.118000	0.64928	0.377000	0.23210	CTT		0.328	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		G	142140334	A	G	142140334	3	3	111	1	0	0	0	0	1	0	0	0	17499	72	3	4	4237	4	XRN1	3	142140334	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	643191	142140334	55882096	237	29371										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840585	142840585	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ataaagggtgtgcgcgtcttCgacgtggcggtcttggcgcc	16	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:142840585C>T	ENST00000309575.3	+	2	2311	c.927C>T	c.(925-927)ttC>ttT	p.F309F		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	309					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						TGCGCGTCTTCGACGTGGCGG	0.652																																																0			3											23	24	24					3																	142840585		2198	4300	6498	144323275	SO:0001819	synonymous_variant	9435			BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.927C>T	3.37:g.142840585C>T			144323275	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Silent	SNP	ENST00000309575.3	37	CCDS3129.1																																																																																				0.652	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		T	142840585	C	T	142840585	2	4	111	1	0	0	0	0	0	0	0	1	3410	883	31	1		1	CHST2	3	142840585	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	700251	142840585	55181845	238	29372										
WWTR1	25937	hgsc.bcm.edu	37	chr3	149245632	149245632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tattaacttacccattgaggAaaggatctgagctattatta	7	6	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:149245632A>G	ENST00000465804.1	-	6	1152	c.896T>C	c.(895-897)tTc>tCc	p.F299S	WWTR1_ENST00000360632.3_Missense_Mutation_p.F299S|WWTR1_ENST00000467467.1_Missense_Mutation_p.F299S|RNU6-1098P_ENST00000516772.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	299					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CCCATTGAGGAAAGGATCTGA	0.428			T	CAMTA1	epitheliod hemangioendothelioma																																		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	0			3											189	200	196					3																	149245632		2203	4300	6503	150728322	SO:0001583	missense	25937			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.896T>C	3.37:g.149245632A>G	ENSP00000419465:p.Phe299Ser		150728322	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	37	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443368	0.83993	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000472417	T;T;T	0.63255	-0.03;-0.03;-0.03	5.09	5.09	0.68999	.	0.493259	0.23241	N	0.050353	T	0.63988	0.2558	M	0.79123	2.44	0.54753	D	0.999985	B	0.32573	0.376	B	0.29267	0.1	T	0.69316	-0.5177	10	0.87932	D	0	-10.8866	15.2181	0.73285	1.0:0.0:0.0:0.0	.	299	Q9GZV5	WWTR1_HUMAN	S	299;299;299;157	ENSP00000419465:F299S;ENSP00000353847:F299S;ENSP00000419234:F299S	ENSP00000353847:F299S	F	-	2	0	WWTR1	150728322	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.678000	0.91211	2.046000	0.60703	0.524000	0.50904	TTC		0.428	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		G	149245632	A	G	149245632	3	3	111	1	0	0	0	0	1	0	0	0	17457	246	9	4	318	4	WWTR1	3	149245632	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	6405047	149245632	48776798	239	29373										
EIF2A	83939	hgsc.bcm.edu	37	chr3	150299509	150299510	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggggaccctgagatagacINSaaaaaaatcaagaacctaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:150299509_150299510insA	ENST00000460851.1	+	12	1711_1712	c.1602_1603insA	c.(1603-1605)aaafs	p.K535fs	EIF2A_ENST00000273435.5_Frame_Shift_Ins_p.K530fs|EIF2A_ENST00000482471.1_3'UTR|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000406576.3_Frame_Shift_Ins_p.K474fs|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000383043.3_Frame_Shift_Ins_p.K321fs|EIF2A_ENST00000487799.1_Frame_Shift_Ins_p.K510fs			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	535					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CTGAGATAGACAAAAAAATCAA	0.406																																																0			3																																								151782200	SO:0001589	frameshift_variant	83939			AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.1609dupA	3.37:g.150299516_150299516dupA	ENSP00000417229:p.Lys535fs		151782199	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Frame_Shift_Ins	INS	ENST00000460851.1	37	CCDS46935.1																																																																																				0.406	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025		A	150299510	-	A	150299509	7	5	111	1	0	1	1	0	0	0	0	0	5006	477	17	0	1648	0	EIF2A	3	150299509	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	1053877	150299509	47722921	240	29374										
SIAH2	6478	hgsc.bcm.edu	37	chr3	150460160	150460160	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggtgccaatgagcaggacgAtggcaaaaaactgctggtgg	16	7	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:150460160A>G	ENST00000312960.3	-	2	1270	c.743T>C	c.(742-744)aTc>aCc	p.I248T		NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2	248	SBD.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|cellular protein catabolic process (GO:0044257)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|regulation of protein ubiquitination (GO:0031396)|regulation of RNA biosynthetic process (GO:2001141)|small GTPase mediated signal transduction (GO:0007264)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I248N(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)	16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GAGCAGGACGATGGCAAAAAA	0.552																																																1	Substitution - Missense(1)	lung(1)	3											95	82	86					3																	150460160		2203	4300	6503	151942850	SO:0001583	missense	6478			U76248	CCDS3152.1	3q25	2012-02-23	2012-02-23		ENSG00000181788	ENSG00000181788	6.3.2.1		10858	protein-coding gene	gene with protein product		602213	"seven in absentia (Drosophila) homolog 2", "seven in absentia homolog 2 (Drosophila)"			9334332	Standard	NM_005067		Approved		uc003eyi.3	O43255	OTTHUMG00000159847	ENST00000312960.3:c.743T>C	3.37:g.150460160A>G	ENSP00000322457:p.Ile248Thr		151942850	O43270	Missense_Mutation	SNP	ENST00000312960.3	37	CCDS3152.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893385	0.72524	.	.	ENSG00000181788	ENST00000312960	T	0.25250	1.81	5.81	5.81	0.92471	TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);	0.058931	0.64402	D	0.000003	T	0.30978	0.0782	N	0.16656	0.425	0.50171	D	0.999852	B	0.24368	0.102	P	0.48840	0.592	T	0.39643	-0.9604	10	0.35671	T	0.21	.	12.0037	0.53246	0.9312:0.0:0.0688:0.0	.	248	O43255	SIAH2_HUMAN	T	248	ENSP00000322457:I248T	ENSP00000322457:I248T	I	-	2	0	SIAH2	151942850	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	7.520000	0.81821	2.217000	0.71921	0.482000	0.46254	ATC		0.552	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	NM_005067		G	150460160	A	G	150460160	3	3	111	1	0	0	0	0	1	0	0	0	14337	333	12	4	235	4	SIAH2	3	150460160	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	160651	150460160	47562270	241	29375										
DHX36	170506	hgsc.bcm.edu	37	chr3	153998375	153998375	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcaatgcttacatttttcTttttttacccaaatttagtc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:153998375delT	ENST00000496811.1	-	22	2640	c.2560delA	c.(2560-2562)agafs	p.R854fs	DHX36_ENST00000308361.6_Frame_Shift_Del_p.R825fs|DHX36_ENST00000329463.5_Frame_Shift_Del_p.R840fs|DHX36_ENST00000544526.1_Frame_Shift_Del_p.R840fs	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	854					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TACATTTTTCTTTTTTTACCC	0.294																																																0			3											73	77	75					3																	153998375		2201	4296	6497	155481069	SO:0001589	frameshift_variant	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2560delA	3.37:g.153998375delT	ENSP00000417078:p.Arg854fs		155481069	B2RB00|Q70JU3|Q8IYE5|Q9P240	Frame_Shift_Del	DEL	ENST00000496811.1	37	CCDS3171.1																																																																																				0.294	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		-	153998375	T	-	153998375	7	5	111	1	0	1	0	1	0	0	0	0	4520	1617	56	0	482	0	DHX36	3	153998375	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	3538215	153998375	44024055	242	29376										
SI	6476	hgsc.bcm.edu	37	chr3	164785145	164785145	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacaaagttttaccgttgctTttcctaataacttggatgct	6	8	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:164785145T>C	ENST00000264382.3	-	6	680	c.618A>G	c.(616-618)aaA>aaG	p.K206K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	206	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.K206N(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TACCGTTGCTTTTCCTAATAA	0.308										HNSCC(35;0.089)																																						1	Substitution - Missense(1)	ovary(1)	3											86	85	85					3																	164785145		2203	4298	6501	166267839	SO:0001819	synonymous_variant	6490			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.618A>G	3.37:g.164785145T>C			166267839	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																				0.308	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164785145	T	C	164785145	2	2	111	1	0	0	0	0	0	0	0	1	14334	1838	64	4		4	SI	3	164785145	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	10786770	164785145	33237285	243	29377										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906123	164906123	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgagggtgatggtgattcacCgtcactatggtgttaagctg	14	6	2	3	rs377111636		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:164906123C>T	ENST00000475390.1	-	2	2939	c.2496G>A	c.(2494-2496)acG>acA	p.T832T	SLITRK3_ENST00000241274.3_Silent_p.T832T			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	832					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GGTGATTCACCGTCACTATGG	0.547										HNSCC(40;0.11)																																						0			3											106	104	105					3																	164906123		2203	4300	6503	166388817	SO:0001819	synonymous_variant	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.2496G>A	3.37:g.164906123C>T			166388817	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																				0.547	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164906123	C	T	164906123	2	4	111	1	0	0	0	0	0	0	0	1	14781	639	23	1		1	SLITRK3	3	164906123	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	120978	164906123	33116307	244	29378										
TNIK	23043	hgsc.bcm.edu	37	chr3	170781745	170781745	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctccagatcgcacggatgcAaaaaatacctgtttgaaatt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:170781745delA	ENST00000436636.2	-	33	4352	c.4008delT	c.(4006-4008)tttfs	p.F1336fs	TNIK_ENST00000475336.1_Frame_Shift_Del_p.F1244fs|TNIK_ENST00000538048.1_Frame_Shift_Del_p.F1288fs|TNIK_ENST00000357327.5_Frame_Shift_Del_p.F1307fs|TNIK_ENST00000284483.8_Frame_Shift_Del_p.F1328fs|TNIK_ENST00000460047.1_Frame_Shift_Del_p.F1273fs|TNIK_ENST00000464785.1_5'UTR|TNIK_ENST00000470834.1_Frame_Shift_Del_p.F1299fs|TNIK_ENST00000488470.1_Frame_Shift_Del_p.F1281fs|TNIK_ENST00000369326.5_Frame_Shift_Del_p.F1314fs|TNIK_ENST00000341852.6_Frame_Shift_Del_p.F1252fs	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1336					actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GCACGGATGCAAAAAATACCT	0.403																																																0			3											92	88	89					3																	170781745		1857	4099	5956	172264439	SO:0001589	frameshift_variant	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.4008delT	3.37:g.170781745delA	ENSP00000399511:p.Phe1336fs		172264439	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Frame_Shift_Del	DEL	ENST00000436636.2	37	CCDS46956.1																																																																																				0.403	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		-	170781745	A	-	170781745	7	5	111	1	0	1	0	1	0	0	0	0	16352	127	5	0	78	0	TNIK	3	170781745	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	5875622	170781745	27240685	245	29379										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952114	178952114	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctggacaacaaaaatggatTggatcttccacacaattaaa	7	8	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:178952114T>C	ENST00000263967.3	+	21	3326	c.3169T>C	c.(3169-3171)Tgg>Cgg	p.W1057R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1057	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.W1057R(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAAAATGGATTGGATCTTCCA	0.383		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	1	Substitution - Missense(1)	stomach(1)	3											97	87	90					3																	178952114		1920	4136	6056	180434808	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3169T>C	3.37:g.178952114T>C	ENSP00000263967:p.Trp1057Arg		180434808	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425160	0.62733	.	.	ENSG00000121879	ENST00000263967	D	0.81579	-1.51	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.85682	D	0.000000	D	0.89076	0.6612	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88861	0.3326	10	0.48119	T	0.1	-8.4726	16.6512	0.85203	0.0:0.0:0.0:1.0	.	1057	P42336	PK3CA_HUMAN	R	1057	ENSP00000263967:W1057R	ENSP00000263967:W1057R	W	+	1	0	PIK3CA	180434808	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.611000	0.82962	2.333000	0.79357	0.482000	0.46254	TGG		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178952114	T	C	178952114	3	2	111	1	0	0	0	0	1	0	0	0	11944	1812	63	4	3247	4	PIK3CA	3	178952114	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	8170369	178952114	19070316	246	29380										
MCF2L2	23101	hgsc.bcm.edu	37	chr3	182897469	182897469	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgactgtcgtccgactggaaAaggcccgcgagctggaaggg	16	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:182897469A>G	ENST00000328913.3	-	29	3414	c.3117T>C	c.(3115-3117)ctT>ctC	p.L1039L	MCF2L2_ENST00000473233.1_Silent_p.L1039L|MCF2L2_ENST00000468976.1_5'Flank	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	1039			L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CCGACTGGAAAAGGCCCGCGA	0.602																																																0			3											73	81	78					3																	182897469		2203	4300	6503	184380163	SO:0001819	synonymous_variant	23101			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.3117T>C	3.37:g.182897469A>G			184380163	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	37	CCDS3243.1																																																																																				0.602	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		G	182897469	A	G	182897469	2	3	111	1	0	0	0	0	0	0	0	1	9410	1	1	4		4	MCF2L2	3	182897469	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3945355	182897469	15124961	247	29381										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184044407	184044407	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggaggctcaggagccaagccCtcagacgcaggtatggaggc	16	11	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:184044407C>A	ENST00000346169.2	+	22	3586	c.3315C>A	c.(3313-3315)ccC>ccA	p.P1105P	EIF4G1_ENST00000434061.2_Silent_p.P910P|EIF4G1_ENST00000342981.4_Silent_p.P1106P|EIF4G1_ENST00000350481.5_Silent_p.P941P|EIF4G1_ENST00000352767.3_Silent_p.P1112P|EIF4G1_ENST00000414031.1_Silent_p.P1065P|EIF4G1_ENST00000435046.2_Silent_p.P909P|EIF4G1_ENST00000319274.6_Silent_p.P1105P|EIF4G1_ENST00000424196.1_Silent_p.P1112P|EIF4G1_ENST00000411531.1_Silent_p.P1066P|EIF4G1_ENST00000427845.1_Silent_p.P1019P|EIF4G1_ENST00000392537.2_Silent_p.P1018P|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.P942P|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000382330.3_Silent_p.P1112P	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1105					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGCCAAGCCCTCAGACGCAG	0.587																																																0			3											70	66	67					3																	184044407		2203	4300	6503	185527101	SO:0001819	synonymous_variant	1981			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.3315C>A	3.37:g.184044407C>A			185527101	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	C	8.894	0.954599	0.18431	.	.	ENSG00000114867	ENST00000448284	T	0.46063	0.88	5.05	1.3	0.21679	.	0.058143	0.64402	D	0.000001	T	0.45256	0.1333	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38824	-0.9643	7	0.87932	D	0	-7.4415	4.5363	0.12032	0.2241:0.4298:0.0:0.3461	.	.	.	.	H	159	ENSP00000392908:P159H	ENSP00000392908:P159H	P	+	2	0	EIF4G1	185527101	0.161000	0.22892	1.000000	0.80357	0.983000	0.72400	-0.489000	0.06490	0.408000	0.25621	-0.150000	0.13652	CCT		0.587	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184044407	C	A	184044407	2	1	111	1	0	0	0	0	0	0	0	1	5049	668	24	2		2	EIF4G1	3	184044407	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1146938	184044407	13978023	248	29382										
MASP1	5648	hgsc.bcm.edu	37	chr3	187003668	187003668	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaagttgaagtgcatgaagTaaagcttgatccgaaaccca	9	9	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:187003668T>C	ENST00000337774.5	-	2	571	c.182A>G	c.(181-183)tAc>tGc	p.Y61C	MASP1_ENST00000392470.2_Missense_Mutation_p.Y35C|MASP1_ENST00000296280.6_Missense_Mutation_p.Y61C|MASP1_ENST00000392472.2_Intron|MASP1_ENST00000169293.6_Missense_Mutation_p.Y61C|MASP1_ENST00000495249.1_Intron	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	61	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.|Homodimerization. {ECO:0000250}.|Interaction with FCN2.|Interaction with MBL2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GTGCATGAAGTAAAGCTTGAT	0.488																																																0			3											136	127	130					3																	187003668		2203	4300	6503	188486362	SO:0001583	missense	5648			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.182A>G	3.37:g.187003668T>C	ENSP00000336792:p.Tyr61Cys		188486362	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	37	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.959653	0.74016	.	.	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000169293;ENST00000392470;ENST00000392475;ENST00000439271;ENST00000425937	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.15	5.15	0.70609	CUB (5);	0.000000	0.85682	D	0.000000	T	0.50000	0.1590	M	0.91612	3.225	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.995;1.0;0.997	T	0.59830	-0.7380	10	0.51188	T	0.08	.	14.453	0.67397	0.0:0.0:0.0:1.0	.	35;61;61;61	F8W876;P48740-3;P48740-2;P48740	.;.;.;MASP1_HUMAN	C	61;61;61;35;68;87;35	ENSP00000336792:Y61C;ENSP00000296280:Y61C;ENSP00000169293:Y61C;ENSP00000376262:Y35C;ENSP00000376267:Y68C;ENSP00000412021:Y87C;ENSP00000409047:Y35C	ENSP00000169293:Y61C	Y	-	2	0	MASP1	188486362	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.679000	0.68160	2.073000	0.62155	0.383000	0.25322	TAC		0.488	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		C	187003668	T	C	187003668	3	2	111	1	0	0	0	0	1	0	0	0	9352	1638	57	4	2922	4	MASP1	3	187003668	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2959261	187003668	11018762	249	29383										
OPA1	4976	hgsc.bcm.edu	37	chr3	193361790	193361790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgtggatgctgaacgcagtAttgttacagacttggtcagt	12	7	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:193361790A>G	ENST00000392438.3	+	14	1573	c.1339A>G	c.(1339-1341)Att>Gtt	p.I447V	OPA1_ENST00000361510.2_Missense_Mutation_p.I502V|OPA1_ENST00000361715.2_Missense_Mutation_p.I466V|OPA1_ENST00000361908.3_Missense_Mutation_p.I484V|OPA1_ENST00000361150.2_Missense_Mutation_p.I448V|OPA1_ENST00000361828.2_Missense_Mutation_p.I465V	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	447	Dynamin-type G.				apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TGAACGCAGTATTGTTACAGA	0.368																																																0			3											85	79	81					3																	193361790		2203	4300	6503	194844484	SO:0001583	missense	9968			AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.1339A>G	3.37:g.193361790A>G	ENSP00000376233:p.Ile447Val		194844484	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103520	0.56291	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150	D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.8	5.8	0.92144	Dynamin, GTPase domain (2);	0.044653	0.85682	D	0.000000	D	0.91727	0.7384	L	0.31578	0.945	0.80722	D	1	B;P;B;B;P;B;B;B	0.35684	0.24;0.454;0.24;0.24;0.515;0.24;0.267;0.372	B;B;B;B;B;B;B;B	0.39771	0.232;0.266;0.309;0.309;0.266;0.309;0.127;0.309	D	0.91988	0.5600	10	0.62326	D	0.03	-20.0082	15.3361	0.74255	1.0:0.0:0.0:0.0	.	411;447;429;448;465;484;466;502	E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.;OPA1_HUMAN;.;.;.;.;.;.	V	484;447;502;466;465;448	ENSP00000354681:I484V;ENSP00000376233:I447V;ENSP00000355324:I502V;ENSP00000355311:I466V;ENSP00000354429:I465V;ENSP00000354781:I448V	ENSP00000354781:I448V	I	+	1	0	OPA1	194844484	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.307000	0.96226	2.209000	0.71365	0.533000	0.62120	ATT		0.368	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		G	193361790	A	G	193361790	3	3	111	1	0	0	0	0	1	0	0	0	10902	449	16	4	1566	4	OPA1	3	193361790	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	6358122	193361790	4660640	250	29384										
BDH1	622	hgsc.bcm.edu	37	chr3	197239178	197239178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgaacttggtgatgcagtacGgggagcgggccgggttggcc	19	9	0	1	rs200605471		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr3:197239178G>A	ENST00000392378.2	-	7	930	c.620C>T	c.(619-621)cCg>cTg	p.P207L	BDH1_ENST00000441275.1_Missense_Mutation_p.P120L|BDH1_ENST00000392379.1_Missense_Mutation_p.P207L|BDH1_ENST00000358186.2_Missense_Mutation_p.P207L	NM_004051.4	NP_004042.1	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	207					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|response to cadmium ion (GO:0046686)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to growth hormone (GO:0060416)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|phospholipid binding (GO:0005543)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)		GATGCAGTACGGGGAGCGGGC	0.627													G|||	1	0.000199681	0	0	5008	,	,		20559	0.001		0	False		,,,				2504	0															0			3											38	40	39					3																	197239178		2203	4300	6503	198723575	SO:0001583	missense	622			M93107	CCDS3328.1	3q29	2011-09-14	2005-11-15	2005-11-15	ENSG00000161267	ENSG00000161267	1.1.1.30	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	1027	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 1"	603063	"3-hydroxybutyrate dehydrogenase (heart, mitochondrial)"	BDH		1639787, 19027726	Standard	XM_005269352		Approved	SDR9C1	uc003fxs.3	Q02338	OTTHUMG00000155478	ENST00000392378.2:c.620C>T	3.37:g.197239178G>A	ENSP00000376183:p.Pro207Leu		198723575	D3DXC0|Q96ET1|Q9BRZ4	Missense_Mutation	SNP	ENST00000392378.2	37	CCDS3328.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	G|G	19.60|19.60	3.857702|3.857702	0.71834|0.71834	.|.	.|.	ENSG00000161267|ENSG00000161267	ENST00000392378;ENST00000358186;ENST00000392379;ENST00000441275;ENST00000446746|ENST00000455876	D;D;D;D;D|.	0.87103|.	-2.21;-2.21;-2.21;-2.21;-2.21|.	5.21|5.21	5.21|5.21	0.72293|0.72293	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);|.	0.049760|.	0.85682|.	D|.	0.000000|.	T|T	0.61009|0.61009	0.2313|0.2313	L|L	0.41906|0.41906	1.305|1.305	0.80722|0.80722	D|D	1|1	D|.	0.62365|.	0.991|.	P|.	0.55667|.	0.781|.	T|T	0.56335|0.56335	-0.7996|-0.7996	10|5	0.46703|.	T|.	0.11|.	.|.	16.6264|16.6264	0.84971|0.84971	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	207|.	Q02338|.	BDH_HUMAN|.	L|C	207;207;207;120;120|101	ENSP00000376183:P207L;ENSP00000350914:P207L;ENSP00000376184:P207L;ENSP00000411014:P120L;ENSP00000387648:P120L|.	ENSP00000350914:P207L|.	P|R	-|-	2|1	0|0	BDH1|BDH1	198723575|198723575	1.000000|1.000000	0.71417|0.71417	0.844000|0.844000	0.33320|0.33320	0.018000|0.018000	0.09664|0.09664	7.771000|7.771000	0.85420|0.85420	2.587000|2.587000	0.87381|0.87381	0.591000|0.591000	0.81541|0.81541	CCG|CGT		0.627	BDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340267.1	NM_004051		A	197239178	G	A	197239178	3	1	111	1	0	0	0	0	1	0	0	0	1391	1116	39	1	415	1	BDH1	3	197239178	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3877388	197239178	783252	251	29385										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggagtgccacctgctcacaCacgtgcccatgtggagtgcc					rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																																1	Substitution - Missense(1)	pancreas(1)	4																																								1378622	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs		1378594	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388622	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	1388594	7	5	111	1	0	1	0	1	0	0	0	0	3883	478	17	0	297	0	CRIPAK	4	1388594	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	TCGA-EI-6507-01A-11D-1733-10		1388594	189765682	252	29386										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25671332	25671332	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgtgttggtgctcttgccCgtggaggtggccacccatta	13	12	1	0	rs116552692	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:25671332C>T	ENST00000382051.3	+	7	749	c.699C>T	c.(697-699)ccC>ccT	p.P233P	SLC34A2_ENST00000504570.1_Silent_p.P232P|SLC34A2_ENST00000503434.1_Silent_p.P232P	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	233					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TGCTCTTGCCCGTGGAGGTGG	0.517			T	ROS1	NSCLC								C|||	17	0.00339457	0	0	5008	,	,		19720	0.0079		0.005	False		,,,				2504	0.0041						Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	0			4						C	,,	1,4405	2.1+/-5.4	0,1,2202	209	201	203		696,696,699	-7.4	0	4	dbSNP_132	203	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC34A2	NM_001177998.1,NM_001177999.1,NM_006424.2	,,	0,7,6496	TT,TC,CC		0.0698,0.0227,0.0538	,,	232/690,232/690,233/691	25671332	7,12999	2203	4300	6503	25280430	SO:0001819	synonymous_variant	10568			AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.699C>T	4.37:g.25671332C>T			25280430	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	37	CCDS3435.1																																																																																				0.517	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		T	25671332	C	T	25671332	2	4	111	1	0	0	0	0	0	0	0	1	14605	639	23	1		1	SLC34A2	4	25671332	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	24282738	25671332	165482944	253	29387										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36069878	36069878	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acttttcactgagccgcagcCtttcaagttctgctcttgca	7	13	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:36069878C>A	ENST00000303965.4	-	33	5255	c.4766G>T	c.(4765-4767)aGg>aTg	p.R1589M		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1589					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						GAGCCGCAGCCTTTCAAGTTC	0.428																																																0			4											57	61	60					4																	36069878		2203	4299	6502	35746273	SO:0001583	missense	116984			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.4766G>T	4.37:g.36069878C>A	ENSP00000302895:p.Arg1589Met		35746273	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.763288	0.69763	.	.	ENSG00000047365	ENST00000303965	T	0.09817	2.94	6.08	2.21	0.28008	.	0.330039	0.32802	N	0.005633	T	0.12050	0.0293	L	0.29908	0.895	0.27390	N	0.955152	D	0.61697	0.99	P	0.52710	0.707	T	0.04708	-1.0932	10	0.66056	D	0.02	.	7.3603	0.26742	0.0:0.6381:0.0:0.3619	.	1589	Q8WZ64	ARAP2_HUMAN	M	1589	ENSP00000302895:R1589M	ENSP00000302895:R1589M	R	-	2	0	ARAP2	35746273	0.952000	0.32445	1.000000	0.80357	0.966000	0.64601	0.351000	0.20096	0.796000	0.33947	0.655000	0.94253	AGG		0.428	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36069878	C	A	36069878	3	1	111	1	0	0	0	0	1	0	0	0	839	681	24	2	352	2	ARAP2	4	36069878	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10398546	36069878	155084398	254	29388										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40104571	40104571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtggaatccaatgattcctgCttttgacctcttccaaggaa	8	10	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:40104571C>T	ENST00000261435.6	+	4	1522	c.1106C>T	c.(1105-1107)gCt>gTt	p.A369V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	369					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ATGATTCCTGCTTTTGACCTC	0.502																																																0			4											138	129	132					4																	40104571		2203	4300	6503	39780966	SO:0001583	missense	55728			AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.1106C>T	4.37:g.40104571C>T	ENSP00000261435:p.Ala369Val		39780966	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.016459	0.35606	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.20069	2.1	6.07	5.24	0.73138	.	0.458810	0.21585	N	0.072181	T	0.16214	0.0390	L	0.29908	0.895	0.32926	D	0.516518	B;B	0.29590	0.25;0.162	B;B	0.24848	0.056;0.025	T	0.14448	-1.0472	10	0.36615	T	0.2	-4.057	12.9956	0.58644	0.0:0.8674:0.0:0.1326	.	369;369	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	V	369;289	ENSP00000261435:A369V	ENSP00000261435:A369V	A	+	2	0	N4BP2	39780966	0.110000	0.22057	1.000000	0.80357	0.160000	0.22226	0.984000	0.29565	1.582000	0.49881	0.655000	0.94253	GCT		0.502	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		T	40104571	C	T	40104571	3	4	111	1	0	0	0	0	1	0	0	0	10140	797	28	3	1112	3	N4BP2	4	40104571	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4034693	40104571	151049705	255	29389										
RBM47	54502	hgsc.bcm.edu	37	chr4	40440535	40440535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttgagctcacgcactgcgcGcttggcctcgtgcttgtggc	14	13	1	1	rs201192048		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:40440535G>A	ENST00000381793.2	-	3	772	c.376C>T	c.(376-378)Cgc>Tgc	p.R126C	RBM47_ENST00000381795.6_Missense_Mutation_p.R126C|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000295971.7_Missense_Mutation_p.R126C|RBM47_ENST00000514014.1_Missense_Mutation_p.R88C|RBM47_ENST00000319592.4_Missense_Mutation_p.R126C			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	126	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CGCACTGCGCGCTTGGCCTCG	0.652																																																0			4						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	62	52	55		376,376	4.7	1	4		55	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RBM47	NM_001098634.1,NM_019027.3	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	126/594,126/525	40440535	1,13005	2203	4300	6503	40135292	SO:0001583	missense	54502			AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.376C>T	4.37:g.40440535G>A	ENSP00000371212:p.Arg126Cys		40135292	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368869	0.61624	0.0	1.16E-4	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014;ENST00000515053;ENST00000513473;ENST00000505414;ENST00000514782	T;T;T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.58	4.73	0.59995	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.053221	0.85682	D	0.000000	T	0.36110	0.0955	M	0.73598	2.24	0.80722	D	1	D;D	0.76494	0.999;0.995	P;P	0.60682	0.878;0.849	T	0.08994	-1.0695	10	0.72032	D	0.01	-19.002	11.1459	0.48430	0.0686:0.0:0.8053:0.1262	.	126;126	A0AV96-2;A0AV96	.;RBM47_HUMAN	C	126;126;126;126;88;126;126;126;126	ENSP00000320108:R126C;ENSP00000371212:R126C;ENSP00000371214:R126C;ENSP00000295971:R126C;ENSP00000423243:R88C;ENSP00000422564:R126C;ENSP00000421589:R126C;ENSP00000423527:R126C;ENSP00000426542:R126C	ENSP00000295971:R126C	R	-	1	0	RBM47	40135292	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	3.045000	0.49838	2.635000	0.89317	0.313000	0.20887	CGC		0.652	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		A	40440535	G	A	40440535	3	1	111	1	0	0	0	0	1	0	0	0	13178	1087	38	1	1421	1	RBM47	4	40440535	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	335964	40440535	150713741	256	29390										
APBB2	323	hgsc.bcm.edu	37	chr4	40947013	40947013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatgtgccaataataggtccCggcaatgtcactgactcttt	9	10	2	1	rs373320430		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:40947013C>A	ENST00000295974.8	-	7	1539	c.910G>T	c.(910-912)Ggg>Tgg	p.G304W	APBB2_ENST00000513140.1_Missense_Mutation_p.G304W|APBB2_ENST00000506352.1_Missense_Mutation_p.G304W|APBB2_ENST00000508593.1_Missense_Mutation_p.G305W	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	304	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						TAATAGGTCCCGGCAATGTCA	0.527																																					Ovarian(3;20 75 16686 49997)											0			4											93	97	95					4																	40947013		1966	4163	6129	40641770	SO:0001583	missense	323			U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.910G>T	4.37:g.40947013C>A	ENSP00000295974:p.Gly304Trp		40641770	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.3|23.3	4.404571|4.404571	0.83230|0.83230	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352|ENST00000513611	D;D;D;D|.	0.94931|.	-3.56;-3.56;-3.56;-3.56|.	5.82|5.82	5.82|5.82	0.92795|0.92795	WW/Rsp5/WWP (6);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78052|0.78052	0.4223|0.4223	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.991;0.996;0.991|.	T|T	0.76219|0.76219	-0.3039|-0.3039	10|5	0.87932|.	D|.	0|.	-11.9713|-11.9713	20.0853|20.0853	0.97797|0.97797	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	287;305;304;304|.	B4DJ88;E9PG87;Q92870-2;Q92870|.	.;.;.;APBB2_HUMAN|.	W|L	304;303;304;305;304|294	ENSP00000295974:G304W;ENSP00000426018:G304W;ENSP00000427211:G305W;ENSP00000421539:G304W|.	ENSP00000295974:G304W|.	G|R	-|-	1|2	0|0	APBB2|APBB2	40641770|40641770	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.774000|0.774000	0.43823|0.43823	7.421000|7.421000	0.80204|0.80204	2.761000|2.761000	0.94854|0.94854	0.591000|0.591000	0.81541|0.81541	GGG|CGG		0.527	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	40947013	C	A	40947013	3	1	111	1	0	0	0	0	1	0	0	0	761	652	23	2	1414	2	APBB2	4	40947013	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	506478	40947013	150207263	257	29391										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060366	46060366	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgctcaggtcaaaaaaaaTtgtcatgataacataatccc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:46060366delT	ENST00000295452.4	-	7	951	c.784delA	c.(784-786)attfs	p.I262fs		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	262					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCAAAAAAAATTGTCATGATA	0.289																																																0			4											92	97	95					4																	46060366		2203	4300	6503	45755123	SO:0001589	frameshift_variant	2565			BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.784delA	4.37:g.46060366delT	ENSP00000295452:p.Ile262fs		45755123	Q5H9T8	Frame_Shift_Del	DEL	ENST00000295452.4	37	CCDS3470.1																																																																																				0.289	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		-	46060366	T	-	46060366	7	5	111	1	0	1	0	1	0	0	0	0	6190	1493	52	0	625	0	GABRG1	4	46060366	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	5113353	46060366	145093910	258	29392										
USP46	64854	hgsc.bcm.edu	37	chr4	53468064	53468064	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaaccaagtcatacatgcgGtccaggttcactgcatcact	8	13	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:53468064G>A	ENST00000441222.3	-	7	1063	c.879C>T	c.(877-879)gaC>gaT	p.D293D	USP46_ENST00000451218.2_Silent_p.D266D|USP46_ENST00000508499.1_Silent_p.D286D	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	293	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			CATACATGCGGTCCAGGTTCA	0.537																																																0			4											111	108	109					4																	53468064		2084	4216	6300	53162821	SO:0001819	synonymous_variant	64854			AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"Ubiquitin-specific peptidases"	20075	protein-coding gene	gene with protein product		612849	"ubiquitin specific protease 46"			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.879C>T	4.37:g.53468064G>A			53162821	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Silent	SNP	ENST00000441222.3	37	CCDS47053.1																																																																																				0.537	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832		A	53468064	G	A	53468064	2	1	111	1	0	0	0	0	0	0	0	1	17117	1252	44	3		3	USP46	4	53468064	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7407698	53468064	137686212	259	29393										
KIT	3815	hgsc.bcm.edu	37	chr4	55594177	55594177	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgcatgtttccaattttagCgagtgcccatttgacagaac	8	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:55594177C>T	ENST00000288135.5	+	13	1977	c.1880C>T	c.(1879-1881)cCg>cTg	p.P627L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	627	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P627L(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCAATTTTAGCGAGTGCCCAT	0.433		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	1	Substitution - Missense(1)	soft_tissue(1)	4											145	134	137					4																	55594177		2203	4300	6503	55288934	SO:0001630	splice_region_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1880-1C>T	4.37:g.55594177C>T			55288934	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903525	0.72754	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.82711	-1.64;-1.64	6.06	5.22	0.72569	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000013	D	0.82314	0.5010	N	0.13327	0.33	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.999	P;P;D	0.66084	0.818;0.898;0.941	T	0.81947	-0.0700	9	.	.	.	.	15.2169	0.73274	0.0:0.933:0.0:0.067	.	134;623;627	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	L	627;623	ENSP00000288135:P627L;ENSP00000390987:P623L	.	P	+	2	0	KIT	55288934	1.000000	0.71417	0.997000	0.53966	0.170000	0.22686	7.743000	0.85020	1.576000	0.49790	0.655000	0.94253	CCG		0.433	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		Missense_Mutation	T	55594177	C	T	55594177	5	4	111	1	0	0	0	0	0	0	1	0	8350	782	27	1	1930	1	KIT	4	55594177	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2126113	55594177	135560099	260	29394										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181417	57181417	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaagccagcccagtccagcaCgccctaccgtcgtccctgag	9	18	0	1	rs534115460	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:57181417C>T	ENST00000504228.1	+	6	1854	c.1749C>T	c.(1747-1749)caC>caT	p.H583H	KIAA1211_ENST00000264229.6_Silent_p.H583H|KIAA1211_ENST00000541073.1_Silent_p.H576H			Q6ZU35	K1211_HUMAN	KIAA1211	583										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CAGTCCAGCACGCCCTACCGT	0.662													C|||	3	0.000599042	0	0	5008	,	,		13945	0		0	False		,,,				2504	0.0031															0			4											17	24	22					4																	57181417		2025	4168	6193	56876174	SO:0001819	synonymous_variant	57482			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1749C>T	4.37:g.57181417C>T			56876174	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																				0.662	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57181417	C	T	57181417	2	4	111	1	0	0	0	0	0	0	0	1	8236	535	19	1		1	KIAA1211	4	57181417	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1587240	57181417	133972859	261	29395										
AMTN	401138	hgsc.bcm.edu	37	chr4	71388495	71388495	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaaacctgctttgggactCcctcccacaaaactggctcc	6	17	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:71388495C>T	ENST00000339336.4	+	3	208	c.78C>T	c.(76-78)ctC>ctT	p.L26L	AMTN_ENST00000504451.1_Silent_p.L25L	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	26					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			CTTTGGGACTCCCTCCCACAA	0.423																																																0			4											203	210	208					4																	71388495		2203	4300	6503	71423084	SO:0001819	synonymous_variant	401138			AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.78C>T	4.37:g.71388495C>T			71423084	Q0P503|Q0P506	Silent	SNP	ENST00000339336.4	37	CCDS3542.1																																																																																				0.423	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557		T	71388495	C	T	71388495	2	4	111	1	0	0	0	0	0	0	0	1	590	842	30	3		3	AMTN	4	71388495	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	14207078	71388495	119765781	262	29396										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73956582	73956582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgttttcaaacaatgtgcTaaagggcccaaatggtaagg	11	7	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:73956582T>C	ENST00000358602.4	-	29	6879	c.6763A>G	c.(6763-6765)Agc>Ggc	p.S2255G	ANKRD17_ENST00000330838.6_Missense_Mutation_p.S2004G|ANKRD17_ENST00000509867.2_Missense_Mutation_p.S2142G	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2255					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AACAATGTGCTAAAGGGCCCA	0.438																																																0			4											218	224	222					4																	73956582		2203	4300	6503	74175446	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6763A>G	4.37:g.73956582T>C	ENSP00000351416:p.Ser2255Gly		74175446	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.261927	0.39995	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000426917	T;T;T	0.80824	-1.42;-1.41;-0.75	5.65	5.65	0.86999	.	0.150425	0.45361	D	0.000374	T	0.78717	0.4327	L	0.57536	1.79	0.32208	N	0.57695	B;B;B;B	0.31817	0.341;0.341;0.231;0.231	B;B;B;B	0.30495	0.116;0.116;0.054;0.037	D	0.83740	0.0203	10	0.87932	D	0	.	15.8715	0.79122	0.0:0.0:0.0:1.0	.	2254;2004;2255;2142	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	G	2255;1662;2004;2142;639	ENSP00000351416:S2255G;ENSP00000332265:S2004G;ENSP00000427151:S2142G	ENSP00000332265:S2004G	S	-	1	0	ANKRD17	74175446	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.926000	0.70070	2.155000	0.67459	0.533000	0.62120	AGC		0.438	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	73956582	T	C	73956582	3	2	111	1	0	0	0	0	1	0	0	0	646	1522	53	4	1072	4	ANKRD17	4	73956582	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2568087	73956582	117197694	263	29397										
AFM	173	hgsc.bcm.edu	37	chr4	74347520	74347521	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actaaaacttacaggttttaINStttttttcttgttttttttg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:74347520_74347521insT	ENST00000226355.3	+	1	121_122	c.28_29insT	c.(28-30)attfs	p.I10fs		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	10					vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TACAGGTTTTATTTTTTTCTTG	0.317																																																0			4																																								74566385	SO:0001589	frameshift_variant	173			L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.35dupT	4.37:g.74347527_74347527dupT	ENSP00000226355:p.Ile10fs		74566384	A8K3E1|Q32MR3|Q4W5C5	Frame_Shift_Ins	INS	ENST00000226355.3	37	CCDS3557.1																																																																																				0.317	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			T	74347521	-	T	74347520	7	5	111	1	0	1	1	0	0	0	0	0	361	449	16	0	30	0	AFM	4	74347520	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	390938	74347520	116806756	264	29398										
NUP54	53371	hgsc.bcm.edu	37	chr4	77051838	77051838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtttgatgctgcttagtcaTctgatcttgaaccttcagtc	9	9	4	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:77051838T>C	ENST00000264883.3	-	8	1167	c.1027A>G	c.(1027-1029)Atg>Gtg	p.M343V	NUP54_ENST00000458189.2_Missense_Mutation_p.M163V|NUP54_ENST00000342467.6_Missense_Mutation_p.M163V|NUP54_ENST00000514987.1_Missense_Mutation_p.M295V	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	343	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TGCTTAGTCATCTGATCTTGA	0.383																																																0			4											95	76	83					4																	77051838		2203	4300	6503	77270862	SO:0001583	missense	53371			AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"nucleoporin 54kD"			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.1027A>G	4.37:g.77051838T>C	ENSP00000264883:p.Met343Val		77270862	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.482885	0.63962	.	.	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	L	0.38175	1.15	0.58432	D	0.999996	P;P;B	0.43662	0.719;0.814;0.386	B;P;B	0.45195	0.244;0.473;0.308	T	0.45745	-0.9240	9	0.16420	T	0.52	-17.6058	15.713	0.77646	0.0:0.0:0.0:1.0	.	295;163;343	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	V	343;163;295;163	.	ENSP00000264883:M343V	M	-	1	0	NUP54	77270862	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.610000	0.82949	2.114000	0.64651	0.460000	0.39030	ATG		0.383	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3			C	77051838	T	C	77051838	3	2	111	1	0	0	0	0	1	0	0	0	10798	1435	50	4	516	4	NUP54	4	77051838	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2704318	77051838	114102438	265	29399										
PAQR3	152559	hgsc.bcm.edu	37	chr4	79851421	79851422	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccatccatcttcgacatgINSttttttctgaccgatggcag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:79851421_79851422insT	ENST00000512733.1	-	3	619_620	c.406_407insA	c.(406-408)acafs	p.T136fs	PAQR3_ENST00000380645.4_Frame_Shift_Ins_p.T136fs|PAQR3_ENST00000295462.3_Frame_Shift_Ins_p.H82fs	NM_001040202.1	NP_001035292.1	Q6TCH7	PAQR3_HUMAN	progestin and adipoQ receptor family member III	136					negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein phosphorylation (GO:0001933)|protein localization to Golgi apparatus (GO:0034067)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	8						TCTTCGACATGTTTTTTCTGAC	0.356																																																0			4																																								80070446	SO:0001589	frameshift_variant	152559			AK055774	CCDS34020.1	4q21	2008-02-05				ENSG00000163291			30130	protein-coding gene	gene with protein product		614577				16044242	Standard	XM_006714104		Approved		uc003hlp.1	Q6TCH7		ENST00000512733.1:c.407dupA	4.37:g.79851427_79851427dupT	ENSP00000421981:p.Thr136fs		80070445	A8K5B7|B3KP59|Q6PIQ1|Q86X05|Q8NCP9	Frame_Shift_Ins	INS	ENST00000512733.1	37	CCDS34020.1																																																																																				0.356	PAQR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363442.1	NM_177453		T	79851422	-	T	79851421	7	5	111	1	0	1	1	0	0	0	0	0	11467	1377	48	0	544	0	PAQR3	4	79851421	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	2799583	79851421	111302855	266	29400										
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80899192	80899192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtaccattttgtctgaggaGgctggtgtgtgggtttgggt	17	4	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:80899192G>T	ENST00000307333.7	-	15	1318	c.1316C>A	c.(1315-1317)cCt>cAt	p.P439H	ANTXR2_ENST00000346652.6_Missense_Mutation_p.P336H|ANTXR2_ENST00000403729.2_Missense_Mutation_p.P439H|ANTXR2_ENST00000404191.1_Missense_Mutation_p.P362H	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	439					reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						TGTCTGAGGAGGCTGGTGTGT	0.438									Juvenile Hyaline Fibromatosis																																							0			4											272	263	266					4																	80899192		1909	4126	6035	81118216	SO:0001583	missense	118429	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.1316C>A	4.37:g.80899192G>T	ENSP00000306185:p.Pro439His		81118216	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Missense_Mutation	SNP	ENST00000307333.7	37	CCDS47086.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222513	0.39300	.	.	ENSG00000163297	ENST00000403729;ENST00000404191;ENST00000346652;ENST00000307333	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.78	5.78	0.91487	Anthrax toxin receptor, C-terminal (2);	0.478792	0.24098	N	0.041563	T	0.76765	0.4033	L	0.32530	0.975	0.80722	D	1	P;P;P	0.48764	0.904;0.915;0.895	B;P;P	0.52424	0.439;0.663;0.698	T	0.77940	-0.2399	10	0.62326	D	0.03	-5.4066	12.3215	0.54987	0.0768:0.0:0.9232:0.0	.	336;439;439	P58335-2;P58335;P58335-4	.;ANTR2_HUMAN;.	H	439;362;336;439	ENSP00000385575:P439H;ENSP00000384028:P362H;ENSP00000314883:P336H;ENSP00000306185:P439H	ENSP00000306185:P439H	P	-	2	0	ANTXR2	81118216	0.799000	0.28903	0.951000	0.38953	0.016000	0.09150	2.020000	0.41010	2.737000	0.93849	0.585000	0.79938	CCT		0.438	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		T	80899192	G	T	80899192	3	4	111	1	0	0	0	0	1	0	0	0	712	1000	35	2	204	2	ANTXR2	4	80899192	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1047771	80899192	110255084	267	29401										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83745800	83745800	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggaataggtttcttggtaaTtttttttgttggcaaagact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:83745800delT	ENST00000395310.2	-	25	3501	c.3319delA	c.(3319-3321)attfs	p.I1107fs	SEC31A_ENST00000513858.1_Frame_Shift_Del_p.I954fs|SEC31A_ENST00000355196.2_Frame_Shift_Del_p.I1107fs|SEC31A_ENST00000348405.4_Frame_Shift_Del_p.I1068fs|SEC31A_ENST00000508502.1_Frame_Shift_Del_p.I1092fs|SEC31A_ENST00000505984.1_Frame_Shift_Del_p.I1053fs|SEC31A_ENST00000505472.1_Frame_Shift_Del_p.I1138fs|SEC31A_ENST00000448323.1_Frame_Shift_Del_p.I1107fs|SEC31A_ENST00000432794.1_Frame_Shift_Del_p.I1120fs|SEC31A_ENST00000311785.7_Frame_Shift_Del_p.I993fs|SEC31A_ENST00000326950.5_Frame_Shift_Del_p.I1068fs|SEC31A_ENST00000264405.5_Frame_Shift_Del_p.I856fs|SEC31A_ENST00000509142.1_Frame_Shift_Del_p.I993fs|SEC31A_ENST00000443462.2_Frame_Shift_Del_p.I1087fs|SEC31A_ENST00000500777.2_Frame_Shift_Del_p.I954fs	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	1107	Interaction with PDCD6.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TTCTTGGTAATTTTTTTTGTT	0.388																																																0			4											147	145	145					4																	83745800		2203	4300	6503	83964824	SO:0001589	frameshift_variant	22872			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.3319delA	4.37:g.83745800delT	ENSP00000378721:p.Ile1107fs		83964824	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Frame_Shift_Del	DEL	ENST00000395310.2	37	CCDS3596.1																																																																																				0.388	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		-	83745800	T	-	83745800	7	5	111	1	0	1	0	1	0	0	0	0	14035	1493	52	0	355	0	SEC31A	4	83745800	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	2846608	83745800	107408476	268	29402										
LIN54	132660	hgsc.bcm.edu	37	chr4	83905824	83905824	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggttccgtggaaatgggcgtGgctgtagagtcaccagtaga	16	7	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:83905824G>T	ENST00000340417.3	-	2	551	c.174C>A	c.(172-174)gcC>gcA	p.A58A	LIN54_ENST00000506560.1_Silent_p.A58A|LIN54_ENST00000395283.2_Silent_p.A58A|LIN54_ENST00000446851.2_Intron|LIN54_ENST00000510557.1_Intron|LIN54_ENST00000442461.2_Intron|LIN54_ENST00000505397.1_Silent_p.A58A|LIN54_ENST00000395282.2_Silent_p.A58A	NM_194282.2	NP_919258.2	Q6MZP7	LIN54_HUMAN	lin-54 DREAM MuvB core complex component	58					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)	14		Hepatocellular(203;0.114)				AAATGGGCGTGGCTGTAGAGT	0.408																																																0			4											242	228	233					4																	83905824		2203	4300	6503	84124848	SO:0001819	synonymous_variant	132660			BX537919	CCDS3599.1, CCDS47089.1, CCDS75157.1	4q21.22	2014-07-17	2014-07-17		ENSG00000189308	ENSG00000189308			25397	protein-coding gene	gene with protein product	"CXC domain containing 1"	613367	"lin-54 homolog (C. elegans)"			21498570	Standard	XM_005262749		Approved	MIP120, DKFZp686L1814, JC8.6, CXCDC1	uc003hnx.3	Q6MZP7	OTTHUMG00000130287	ENST00000340417.3:c.174C>A	4.37:g.83905824G>T			84124848	Q32M68|Q32M69|Q6N071|Q76B60	Silent	SNP	ENST00000340417.3	37	CCDS3599.1																																																																																				0.408	LIN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252626.2	NM_194282		T	83905824	G	T	83905824	2	4	111	1	0	0	0	0	0	0	0	1	8833	1335	47	2		2	LIN54	4	83905824	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	160024	83905824	107248452	269	29403										
CYP2U1	113612	hgsc.bcm.edu	37	chr4	108853210	108853210	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcgacttccacagcgtgcgCgaggcgctggtgcagcaggc	16	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:108853210C>T	ENST00000332884.6	+	1	686	c.411C>T	c.(409-411)cgC>cgT	p.R137R	CYP2U1_ENST00000508453.1_5'UTR|CYP2U1_ENST00000513302.1_3'UTR|RP11-286E11.1_ENST00000499098.1_RNA|RP11-286E11.1_ENST00000513071.1_RNA	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	137					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		ACAGCGTGCGCGAGGCGCTGG	0.652																																																0			4											12	12	12					4																	108853210		2194	4294	6488	109072659	SO:0001819	synonymous_variant	113612			BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"Cytochrome P450s"	20582	protein-coding gene	gene with protein product	"spastic paraplegia 49"	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.411C>T	4.37:g.108853210C>T			109072659	B2RMV7|Q96EQ6	Silent	SNP	ENST00000332884.6	37	CCDS34047.1																																																																																				0.652	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075		T	108853210	C	T	108853210	2	4	111	1	0	0	0	0	0	0	0	1	4181	755	27	1		1	CYP2U1	4	108853210	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	24947386	108853210	82301066	270	29404										
EGF	1950	hgsc.bcm.edu	37	chr4	110882121	110882121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccctgtaggatttgttctgCttcctgatgggaaacgatgt	12	8	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:110882121C>T	ENST00000265171.5	+	7	1610	c.1165C>T	c.(1165-1167)Ctt>Ttt	p.L389F	EGF_ENST00000503392.1_Missense_Mutation_p.L389F|EGF_ENST00000509793.1_Missense_Mutation_p.L347F	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	389	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	ATTTGTTCTGCTTCCTGATGG	0.388																																																0			4											252	222	232					4																	110882121		2203	4300	6503	111101570	SO:0001583	missense	1950			X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1165C>T	4.37:g.110882121C>T	ENSP00000265171:p.Leu389Phe		111101570	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300652	0.81136	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.92048	-2.96;-2.96;-2.96	4.82	4.82	0.62117	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.94169	0.8129	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.91540	0.5249	10	0.09843	T	0.71	.	17.9396	0.89023	0.0:1.0:0.0:0.0	.	389;347;389	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	F	347;389;389	ENSP00000424316:L347F;ENSP00000265171:L389F;ENSP00000421384:L389F	ENSP00000265171:L389F	L	+	1	0	EGF	111101570	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	5.218000	0.65257	2.225000	0.72522	0.561000	0.74099	CTT		0.388	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110882121	C	T	110882121	3	4	111	1	0	0	0	0	1	0	0	0	4973	797	28	3	1191	3	EGF	4	110882121	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2028911	110882121	80272155	271	29405										
LARP7	51574	hgsc.bcm.edu	37	chr4	113570732	113570732	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaagagtatttagcgctacAaaaagctagcatggcttctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:113570732delA	ENST00000344442.5	+	9	1462	c.1184delA	c.(1183-1185)caafs	p.Q395fs	MIR302B_ENST00000362188.1_RNA|MIR302C_ENST00000362232.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302D_ENST00000362275.1_RNA|MIR302A_ENST00000385192.1_RNA|LARP7_ENST00000324052.6_Frame_Shift_Del_p.Q395fs|MIR302B_ENST00000509938.1_RNA|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000509061.1_Frame_Shift_Del_p.Q402fs	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	395					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		TTAGCGCTACAAAAAGCTAGC	0.328																																																0			4											45	43	43					4																	113570732		2202	4296	6498	113790181	SO:0001589	frameshift_variant	51574			AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.1184delA	4.37:g.113570732delA	ENSP00000344950:p.Gln395fs		113790181	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Frame_Shift_Del	DEL	ENST00000344442.5	37	CCDS3701.2																																																																																				0.328	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		-	113570732	A	-	113570732	7	5	111	1	0	1	0	1	0	0	0	0	8655	130	5	0	1214	0	LARP7	4	113570732	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	2688611	113570732	77583544	272	29406										
ANK2	287	hgsc.bcm.edu	37	chr4	114276086	114276087	+	Frame_Shift_Ins	INS	-	-	CA													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagtgcctgaagaagaaagcINScacagagagagcgaagtgcc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:114276086_114276087insCA	ENST00000357077.4	+	38	6365_6366	c.6312_6313insCA	c.(6313-6315)cacfs	p.H2105fs	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000264366.6_Frame_Shift_Ins_p.H2072fs|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2105					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AAGAAGAAAGCCACAGAGAGAG	0.475																																																0			4																																								114495536	SO:0001589	frameshift_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6315_6316dupCA	4.37:g.114276089_114276090dupCA	ENSP00000349588:p.His2105fs		114495535	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Ins	INS	ENST00000357077.4	37	CCDS3702.1																																																																																				0.475	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		CA	114276087	-	CA	114276086	7	5	111	1	0	1	1	0	0	0	0	0	621	738	26	0	6527	0	ANK2	4	114276086	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	705354	114276086	76878190	273	29407										
FAT4	79633	hgsc.bcm.edu	37	chr4	126238751	126238751	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcggccaacgggaacatctcCgtgcaaattctcgggggcaa	13	12	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:126238751C>T	ENST00000394329.3	+	1	1198	c.1185C>T	c.(1183-1185)tcC>tcT	p.S395S		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	395	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGAACATCTCCGTGCAAATTC	0.607											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			4											28	32	30					4																	126238751		2020	4167	6187	126458201	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1185C>T	4.37:g.126238751C>T		1548	126458201	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.607	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126238751	C	T	126238751	2	4	111	1	0	0	0	0	0	0	0	1	5711	639	23	1		1	FAT4	4	126238751	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	11962665	126238751	64915525	274	29408										
FAT4	79633	hgsc.bcm.edu	37	chr4	126371860	126371860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggaacaaatgctgtgattgCgtatactgtacagtcatctg	10	7	2	1	rs373873722		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:126371860C>T	ENST00000394329.3	+	9	9702	c.9689C>T	c.(9688-9690)gCg>gTg	p.A3230V	FAT4_ENST00000335110.5_Missense_Mutation_p.A1528V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3230	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCTGTGATTGCGTATACTGTA	0.433																																																0			4						C	VAL/ALA	0,4406		0,0,2203	87	81	83		9689	5.6	0.9	4		83	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAT4	NM_024582.4	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	3230/4982	126371860	1,13005	2203	4300	6503	126591310	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9689C>T	4.37:g.126371860C>T	ENSP00000377862:p.Ala3230Val		126591310	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	13.16	2.155536	0.38021	0.0	1.16E-4	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01804	4.63;4.63	5.63	5.63	0.86233	Cadherin (4);Cadherin-like (1);	0.000000	0.34088	U	0.004271	T	0.02727	0.0082	N	0.01649	-0.78	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.994;0.991;0.997	T	0.78386	-0.2224	10	0.18710	T	0.47	.	19.7096	0.96089	0.0:1.0:0.0:0.0	.	1528;3230;3230	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	3230;1528	ENSP00000377862:A3230V;ENSP00000335169:A1528V	ENSP00000335169:A1528V	A	+	2	0	FAT4	126591310	1.000000	0.71417	0.935000	0.37517	0.088000	0.18126	5.942000	0.70203	2.652000	0.90054	0.655000	0.94253	GCG		0.433	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126371860	C	T	126371860	3	4	111	1	0	0	0	0	1	0	0	0	5711	768	27	1	9723	1	FAT4	4	126371860	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	133109	126371860	64782416	275	29409										
PGRMC2	10424	hgsc.bcm.edu	37	chr4	129208629	129208629	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtcgtactggcgcagctgcTccaagctgaagtcccgcttc	11	15	0	1	rs149247614	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:129208629T>G	ENST00000296425.5	-	1	337	c.317A>C	c.(316-318)gAg>gCg	p.E106A	PGRMC2_ENST00000520121.1_Missense_Mutation_p.E130A|PGRMC2_ENST00000512483.1_Intron|PGRMC2_ENST00000503872.1_5'Flank|PGRMC2_ENST00000503588.1_5'Flank			O15173	PGRC2_HUMAN	progesterone receptor membrane component 2	106	Cytochrome b5 heme-binding.				steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)										GCGCAGCTGCTCCAAGCTGAA	0.697																																					Colon(78;371 1268 8296 41305 53030)											0			4											27	23	25					4																	129208629		2178	4239	6417	129428079	SO:0001583	missense	10424				CCDS3739.1, CCDS3739.2	4q26	2008-08-29			ENSG00000164040	ENSG00000164040			16089	protein-coding gene	gene with protein product		607735				9705155	Standard	NM_006320		Approved	PMBP, DG6	uc003igg.3	O15173	OTTHUMG00000133342	ENST00000296425.5:c.317A>C	4.37:g.129208629T>G	ENSP00000296425:p.Glu106Ala		129428079	Q569H1	Missense_Mutation	SNP	ENST00000296425.5	37		.	.	.	.	.	.	.	.	.	.	T	13.24	2.178231	0.38511	.	.	ENSG00000164040	ENST00000296425;ENST00000520121	T;T	0.81415	-1.49;-1.49	4.06	4.06	0.47325	Cytochrome b5 (3);	0.292790	0.37437	N	0.002096	T	0.65719	0.2718	N	0.12637	0.245	0.58432	D	0.999998	P	0.37370	0.592	B	0.37091	0.241	T	0.68606	-0.5364	10	0.40728	T	0.16	-10.4615	13.1584	0.59531	0.0:0.0:0.0:1.0	.	106	O15173	PGRC2_HUMAN	A	106;130	ENSP00000296425:E106A;ENSP00000429301:E130A	ENSP00000296425:E106A	E	-	2	0	PGRMC2	129428079	1.000000	0.71417	1.000000	0.80357	0.148000	0.21650	3.819000	0.55686	1.831000	0.53308	0.459000	0.35465	GAG		0.697	PGRMC2-007	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470697.1			G	129208629	T	G	129208629	3	3	111	1	0	0	0	0	1	0	0	0	11838	1551	54	4	366	4	PGRMC2	4	129208629	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2836769	129208629	61945647	276	29410										
SETD7	80854	hgsc.bcm.edu	37	chr4	140432892	140432892	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcttcaggcccactcttcccGggggggctgtggtcatagcc					rs368140697		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:140432892delG	ENST00000274031.3	-	8	1662	c.1026delC	c.(1024-1026)cccfs	p.P342fs	SETD7_ENST00000506866.2_Intron	NM_030648.2	NP_085151.1	Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	342					chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					CACTCTTCCCGGGGGGGCTGT	0.607																																																0			4											63	65	64					4																	140432892		2203	4300	6503	140652342	SO:0001589	frameshift_variant	80854			AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391		"Chromatin-modifying enzymes / K-methyltransferases"	30412	protein-coding gene	gene with protein product		606594				11850410, 11779497	Standard	NM_030648		Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000274031.3:c.1026delC	4.37:g.140432892delG	ENSP00000274031:p.Pro342fs		140652342	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	Frame_Shift_Del	DEL	ENST00000274031.3	37	CCDS3748.1																																																																																				0.607	SETD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257236.1	NM_030648		-	140432892	G	-	140432892	7	5	111	1	0	1	0	1	0	0	0	0	14173	1103	39	0	78	0	SETD7	4	140432892	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	11224263	140432892	50721384	277	29411										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141543531	141543531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaggtgatggcccagtcccGgtccaggctggtgctccggg	17	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:141543531G>A	ENST00000442267.2	-	21	3693	c.3619C>T	c.(3619-3621)Cgg>Tgg	p.R1207W		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1207							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GCCCAGTCCCGGTCCAGGCTG	0.647																																																0			4											37	42	41					4																	141543531		2085	4188	6273	141762981	SO:0001583	missense	23158			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.3619C>T	4.37:g.141543531G>A	ENSP00000411197:p.Arg1207Trp		141762981	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466754	0.63625	.	.	ENSG00000109436	ENST00000442267	T	0.30981	1.51	5.01	3.03	0.35002	.	0.109676	0.64402	D	0.000010	T	0.32912	0.0845	L	0.44542	1.39	0.45648	D	0.998576	D	0.65815	0.995	P	0.48677	0.586	T	0.17198	-1.0377	10	0.66056	D	0.02	.	12.5589	0.56269	0.0:0.0:0.5352:0.4648	.	1207	Q6ZT07	TBCD9_HUMAN	W	1207	ENSP00000411197:R1207W	ENSP00000411197:R1207W	R	-	1	2	TBC1D9	141762981	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.471000	0.60182	1.077000	0.40990	0.655000	0.94253	CGG		0.647	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141543531	G	A	141543531	3	1	111	1	0	0	0	0	1	0	0	0	15666	1115	39	1	185	1	TBC1D9	4	141543531	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1110639	141543531	49610745	278	29412										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245445	153245445	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agttccattccacttgttaaCgactggtgccctgttaacgt	8	11	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:153245445C>T	ENST00000281708.4	-	11	2975	c.1746G>A	c.(1744-1746)tcG>tcA	p.S582S	FBXW7_ENST00000603841.1_Silent_p.S582S|FBXW7_ENST00000603548.1_Silent_p.S582S|FBXW7_ENST00000263981.5_Silent_p.S502S|FBXW7_ENST00000393956.3_Silent_p.S406S|FBXW7_ENST00000296555.5_Silent_p.S464S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	582			S -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CACTTGTTAACGACTGGTGCC	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											149	126	133					4																	153245445		2203	4300	6503	153464895	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1746G>A	4.37:g.153245445C>T			153464895	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153245445	C	T	153245445	2	4	111	1	0	0	0	0	0	0	0	1	5788	523	19	1		1	FBXW7	4	153245445	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	11701914	153245445	37908831	279	29413										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249360	153249361	+	Splice_Site	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgacaagattttcccttaccINSttttttcatgaagatgcata							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:153249360_153249361insT	ENST00000281708.4	-	9	2646_2647	c.1417_1418insA	c.(1417-1419)aga>aAga	p.R473fs	FBXW7_ENST00000603841.1_Splice_Site_p.R473fs|FBXW7_ENST00000603548.1_Splice_Site_p.R473fs|FBXW7_ENST00000263981.5_Splice_Site_p.R393fs|FBXW7_ENST00000393956.3_Splice_Site_p.R297fs|FBXW7_ENST00000296555.5_Splice_Site_p.R355fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	473					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R473fs*25(4)|p.R473fs*4(3)|p.R234fs*25(1)|p.R393fs*25(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TTTCCCTTACCTTTTTTCATGA	0.416			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	10	Deletion - Frameshift(6)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(6)|NS(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|endometrium(1)	4																																								153468811	SO:0001630	splice_region_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1418+1->A	4.37:g.153249366_153249366dupT			153468810	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Ins	INS	ENST00000281708.4	37	CCDS3777.1																																																																																				0.416	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		Frame_Shift_Ins	T	153249361	-	T	153249360	8	5	111	1	0	1	1	0	0	0	1	0	5788	695	24	0	721	0	FBXW7	4	153249360	Splice_Site	INS	-	TCGA-EI-6507-01A-11D-1733-10	3915	153249360	37904916	280	29414										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153249466	153249466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgagtgtccgatctgtagAtccactaatgatgatgttgt	10	6	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:153249466A>G	ENST00000281708.4	-	9	2541	c.1312T>C	c.(1312-1314)Tct>Cct	p.S438P	FBXW7_ENST00000603841.1_Missense_Mutation_p.S438P|FBXW7_ENST00000603548.1_Missense_Mutation_p.S438P|FBXW7_ENST00000263981.5_Missense_Mutation_p.S358P|FBXW7_ENST00000393956.3_Missense_Mutation_p.S262P|FBXW7_ENST00000296555.5_Missense_Mutation_p.S320P	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	438					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CGATCTGTAGATCCACTAATG	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											316	267	284					4																	153249466		2203	4300	6503	153468916	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1312T>C	4.37:g.153249466A>G	ENSP00000281708:p.Ser438Pro		153468916	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.603572	0.87157	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.92583	0.7644	H	0.99475	4.585	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;P;D;D	0.81914	0.994;0.869;0.995;0.995	D	0.95737	0.8780	10	0.87932	D	0	-11.5446	16.3291	0.83001	1.0:0.0:0.0:0.0	.	262;438;320;358	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	P	438;320;358;262	ENSP00000281708:S438P;ENSP00000296555:S320P;ENSP00000263981:S358P;ENSP00000377528:S262P	ENSP00000263981:S358P	S	-	1	0	FBXW7	153468916	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	9.339000	0.96797	2.257000	0.74773	0.528000	0.53228	TCT		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153249466	A	G	153249466	3	3	111	1	0	0	0	0	1	0	0	0	5788	333	12	4	827	4	FBXW7	4	153249466	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	106	153249466	37904810	281	29415										
FAM198B	51313	hgsc.bcm.edu	37	chr4	159052022	159052022	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtctataaaaaccaaatgcCttgggtcatgctttcgctgg	9	9	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:159052022C>A	ENST00000296530.8	-	4	1889	c.1268G>T	c.(1267-1269)aGg>aTg	p.R423M	FAM198B_ENST00000393807.5_Missense_Mutation_p.R431M|FAM198B_ENST00000585682.1_Missense_Mutation_p.R423M|FAM198B_ENST00000589306.1_5'UTR	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	423						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						AACCAAATGCCTTGGGTCATG	0.403																																																0			4											111	105	107					4																	159052022		2203	4300	6503	159271472	SO:0001583	missense	0				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 18"	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.1268G>T	4.37:g.159052022C>A	ENSP00000296530:p.Arg423Met		159271472	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723076	0.68959	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000505460	T;T	0.32753	1.44;1.44	5.71	4.84	0.62591	.	0.159131	0.53938	D	0.000046	T	0.52008	0.1708	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.974	T	0.55617	-0.8113	10	0.72032	D	0.01	-0.5356	14.2087	0.65750	0.0:0.9255:0.0:0.0745	.	431;423	Q6UWH4-2;Q6UWH4	.;F198B_HUMAN	M	423;423;431;129	ENSP00000296530:R423M;ENSP00000377396:R431M	ENSP00000296530:R423M	R	-	2	0	FAM198B	159271472	0.999000	0.42202	0.988000	0.46212	0.989000	0.77384	3.308000	0.51896	1.491000	0.48482	0.650000	0.86243	AGG		0.403	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		A	159052022	C	A	159052022	3	1	111	1	0	0	0	0	1	0	0	0	5545	681	24	2	299	2	FAM198B	4	159052022	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5802556	159052022	32102254	282	29416										
PALLD	23022	hgsc.bcm.edu	37	chr4	169824954	169824954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatctctccaaagagtgatcActacaccattcaaagagatc	6	11	3	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:169824954A>G	ENST00000505667.1	+	15	2692	c.2519A>G	c.(2518-2520)cAc>cGc	p.H840R	PALLD_ENST00000261509.6_Missense_Mutation_p.H823R|PALLD_ENST00000512127.1_Missense_Mutation_p.H441R|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000507735.1_Missense_Mutation_p.H336R|PALLD_ENST00000335742.7_Missense_Mutation_p.H665R			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1047	Interaction with ACTN.|Pro-rich.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AAGAGTGATCACTACACCATT	0.408									Pancreatic Cancer, Familial Clustering of																												Esophageal Squamous(109;1482 1532 18347 40239 51172)											0			4											103	99	101					4																	169824954		2203	4300	6503	170061529	SO:0001583	missense	23022	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2519A>G	4.37:g.169824954A>G	ENSP00000425556:p.His840Arg		170061529	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.696378	0.48202	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000393726;ENST00000507735	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;1.98;-0.02	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.33712	U	0.004627	T	0.48804	0.1520	N	0.04994	-0.135	0.80722	D	1	P;B;B;P	0.47034	0.889;0.071;0.4;0.889	P;B;B;P	0.49799	0.622;0.077;0.332;0.622	T	0.47774	-0.9091	10	0.14252	T	0.57	.	15.5185	0.75846	1.0:0.0:0.0:0.0	.	840;1047;441;823	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	R	823;665;840;441;116;336	ENSP00000261509:H823R;ENSP00000336735:H665R;ENSP00000425556:H840R;ENSP00000426947:H441R;ENSP00000377327:H116R;ENSP00000424016:H336R	ENSP00000261509:H823R	H	+	2	0	PALLD	170061529	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	7.385000	0.79763	2.246000	0.74042	0.533000	0.62120	CAC		0.408	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		G	169824954	A	G	169824954	3	3	111	1	0	0	0	0	1	0	0	0	11438	159	6	4	3080	4	PALLD	4	169824954	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	10772932	169824954	21329322	283	29417										
C4orf27	54969	hgsc.bcm.edu	37	chr4	170663195	170663195	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgtgagtttttcatctatGtttttcaagagattgatttt	7	4	4	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:170663195G>A	ENST00000393381.2	-	5	636	c.561C>T	c.(559-561)aaC>aaT	p.N187N		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	187						nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		TTTCATCTATGTTTTTCAAGA	0.353																																																0			4											145	132	137					4																	170663195		2202	4300	6502	170899770	SO:0001819	synonymous_variant	54969			BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.561C>T	4.37:g.170663195G>A			170899770		Silent	SNP	ENST00000393381.2	37	CCDS3813.1																																																																																				0.353	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867		A	170663195	G	A	170663195	2	1	111	1	0	0	0	0	0	0	0	1	2264	1368	48	3		3	C4orf27	4	170663195	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	838241	170663195	20491081	284	29418										
WDR17	116966	hgsc.bcm.edu	37	chr4	177069341	177069341	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcaatattcttaatggacaCactgcacctgtgagaggatt	8	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:177069341C>T	ENST00000280190.4	+	14	1980	c.1824C>T	c.(1822-1824)caC>caT	p.H608H	WDR17_ENST00000393643.2_Silent_p.H584H|WDR17_ENST00000507824.2_Silent_p.H591H|WDR17_ENST00000508596.1_Silent_p.H584H			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	608										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		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;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TTAATGGACACACTGCACCTG	0.388																																																0			4											172	169	170					4																	177069341		2203	4300	6503	177306335	SO:0001819	synonymous_variant	116966			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1824C>T	4.37:g.177069341C>T			177306335	E7EQX0|Q0QD35	Silent	SNP	ENST00000280190.4	37	CCDS3825.1																																																																																				0.388	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177069341	C	T	177069341	2	4	111	1	0	0	0	0	0	0	0	1	17317	477	17	3		3	WDR17	4	177069341	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6406146	177069341	14084935	285	29419										
STOX2	56977	hgsc.bcm.edu	37	chr4	184828090	184828090	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccttcgcgccccaggcttcGcggggctacatgacatcagg	13	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr4:184828090G>A	ENST00000308497.4	+	1	1582	c.147G>A	c.(145-147)tcG>tcA	p.S49S	STOX2_ENST00000438269.1_Silent_p.S49S|STOX2_ENST00000511250.1_Intron	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	49					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CCCAGGCTTCGCGGGGCTACA	0.706																																																0			4											17	20	19					4																	184828090		1521	3229	4750	185065084	SO:0001819	synonymous_variant	56977			AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.147G>A	4.37:g.184828090G>A			185065084	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																				0.706	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		A	184828090	G	A	184828090	2	1	111	1	0	0	0	0	0	0	0	1	15359	1074	38	1		1	STOX2	4	184828090	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7758749	184828090	6326186	286	29420										
LPCAT1	79888	hgsc.bcm.edu	37	chr5	1463838	1463838	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgaaatcggcacagaagccGtttgggattggcgcaggtga	15	8	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:1463838G>A	ENST00000283415.3	-	14	1665	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	511					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CACAGAAGCCGTTTGGGATTG	0.572																																																0			5											89	89	89					5																	1463838		2203	4300	6503	1516838	SO:0001819	synonymous_variant	79888			BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1533C>T	5.37:g.1463838G>A			1516838	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																				0.572	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		A	1463838	G	A	1463838	2	1	111	1	0	0	0	0	0	0	0	1	8939	1136	40	1		1	LPCAT1	5	1463838	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10		1463838	179451422	287	29421										
ADCY2	108	hgsc.bcm.edu	37	chr5	7802415	7802415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aattttatacagaatccgacGtgaacaaggagggcttggaa	11	6	0	2	rs368187458		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:7802415G>A	ENST00000338316.4	+	21	2802	c.2713G>A	c.(2713-2715)Gtg>Atg	p.V905M	ADCY2_ENST00000537121.1_Missense_Mutation_p.V725M	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	905					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						AGAATCCGACGTGAACAAGGA	0.493																																																0			5						G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	91	90	90		2713	5.2	1	5		90	0,8600		0,0,4300	no	missense	ADCY2	NM_020546.2	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	905/1092	7802415	1,13005	2203	4300	6503	7855415	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2713G>A	5.37:g.7802415G>A	ENSP00000342952:p.Val905Met		7855415	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630636	0.87660	2.27E-4	0.0	ENSG00000078295	ENST00000338316;ENST00000382532;ENST00000541993;ENST00000537121	T;T	0.30714	1.52;1.52	5.24	5.24	0.73138	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	T	0.50871	0.1641	L	0.49350	1.555	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.74023	0.973;0.982	T	0.41574	-0.9501	10	0.39692	T	0.17	.	18.8415	0.92186	0.0:0.0:1.0:0.0	.	725;905	B7Z2C1;Q08462	.;ADCY2_HUMAN	M	905;58;738;725	ENSP00000342952:V905M;ENSP00000444803:V725M	ENSP00000342952:V905M	V	+	1	0	ADCY2	7855415	1.000000	0.71417	0.958000	0.39756	0.748000	0.42578	6.423000	0.73361	2.447000	0.82792	0.591000	0.81541	GTG		0.493	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7802415	G	A	7802415	3	1	111	1	0	0	0	0	1	0	0	0	294	1145	40	1	2795	1	ADCY2	5	7802415	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	6338577	7802415	173112845	288	29422										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13913866	13913866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caatacctggtatttagtggCcatgtcttccagcccttcaa	7	12	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:13913866C>T	ENST00000265104.4	-	11	1626	c.1522G>A	c.(1522-1524)Gcc>Acc	p.A508T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	508	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TATTTAGTGGCCATGTCTTCC	0.353									Kartagener syndrome																																							0			5											111	113	112					5																	13913866		2203	4300	6503	13966866	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.1522G>A	5.37:g.13913866C>T	ENSP00000265104:p.Ala508Thr		13966866	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.503763	0.26949	.	.	ENSG00000039139	ENST00000265104	T	0.55588	0.51	5.8	2.97	0.34412	Dynein heavy chain, domain-1 (1);	0.530986	0.20432	N	0.092454	T	0.37433	0.1003	L	0.35288	1.05	0.28706	N	0.903828	B	0.02656	0.0	B	0.15484	0.013	T	0.23547	-1.0185	10	0.23302	T	0.38	.	8.3981	0.32570	0.0:0.5685:0.0:0.4315	.	508	Q8TE73	DYH5_HUMAN	T	508	ENSP00000265104:A508T	ENSP00000265104:A508T	A	-	1	0	DNAH5	13966866	1.000000	0.71417	0.010000	0.14722	0.819000	0.46315	2.687000	0.46976	0.317000	0.23160	0.650000	0.86243	GCC		0.353	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13913866	C	T	13913866	3	4	111	1	0	0	0	0	1	0	0	0	4615	739	26	3	12628	3	DNAH5	5	13913866	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6111451	13913866	167001394	289	29423										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32052764	32052764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctccttaagcacgactcaGgtggaatctccttggaggct	11	12	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:32052764G>T	ENST00000438447.1	+	9	2101	c.1713G>T	c.(1711-1713)caG>caT	p.Q571H	PDZD2_ENST00000282493.3_Missense_Mutation_p.Q571H			O15018	PDZD2_HUMAN	PDZ domain containing 2	571					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCACGACTCAGGTGGAATCTC	0.468																																																0			5											177	166	170					5																	32052764		2203	4300	6503	32088521	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.1713G>T	5.37:g.32052764G>T	ENSP00000402033:p.Gln571His		32088521	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829348	0.32329	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.38401	1.14;1.14	5.57	-0.492	0.12041	PDZ/DHR/GLGF (1);	0.215240	0.23777	N	0.044671	T	0.15609	0.0376	N	0.19112	0.55	0.36364	D	0.860869	B;B	0.19445	0.036;0.022	B;B	0.14578	0.01;0.011	T	0.10019	-1.0648	10	0.29301	T	0.29	.	0.3233	0.00306	0.2321:0.1753:0.2642:0.3285	.	397;571	B4E3P2;O15018	.;PDZD2_HUMAN	H	571;390;571	ENSP00000402033:Q571H;ENSP00000282493:Q571H	ENSP00000282493:Q571H	Q	+	3	2	PDZD2	32088521	1.000000	0.71417	0.873000	0.34254	0.942000	0.58702	0.821000	0.27338	-0.446000	0.07149	0.655000	0.94253	CAG		0.468	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32052764	G	T	32052764	3	4	111	1	0	0	0	0	1	0	0	0	11732	991	35	2	1743	2	PDZD2	5	32052764	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	18138898	32052764	148862496	290	29424										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32058122	32058122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgggggagcctcagcgggaGgttccgatgaaggcagttct	18	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:32058122G>T	ENST00000438447.1	+	12	2501	c.2113G>T	c.(2113-2115)Ggt>Tgt	p.G705C	PDZD2_ENST00000282493.3_Missense_Mutation_p.G705C			O15018	PDZD2_HUMAN	PDZ domain containing 2	705					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTCAGCGGGAGGTTCCGATGA	0.572																																																0			5																																								32093879	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2113G>T	5.37:g.32058122G>T	ENSP00000402033:p.Gly705Cys		32093879	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.412461	0.42817	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.09073	3.02;3.02	5.84	5.84	0.93424	PDZ/DHR/GLGF (1);	0.457721	0.18586	N	0.136870	T	0.19886	0.0478	L	0.29908	0.895	0.38730	D	0.953641	D;D	0.89917	0.999;1.0	D;D	0.69142	0.921;0.962	T	0.00945	-1.1505	10	0.66056	D	0.02	.	17.6508	0.88163	0.0:0.0:1.0:0.0	.	531;705	B4E3P2;O15018	.;PDZD2_HUMAN	C	705;524;705	ENSP00000402033:G705C;ENSP00000282493:G705C	ENSP00000282493:G705C	G	+	1	0	PDZD2	32093879	1.000000	0.71417	0.063000	0.19743	0.013000	0.08279	3.398000	0.52579	2.768000	0.95171	0.650000	0.86243	GGT		0.572	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32058122	G	T	32058122	3	4	111	1	0	0	0	0	1	0	0	0	11732	1000	35	2	2155	2	PDZD2	5	32058122	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5358	32058122	148857138	291	29425										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37019433	37019433	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtttcaggaggggaagatgaAatccaacaattacaaaaagc	10	6	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:37019433A>G	ENST00000282516.8	+	25	5440	c.4941A>G	c.(4939-4941)gaA>gaG	p.E1647E	NIPBL_ENST00000448238.2_Silent_p.E1647E	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1647			E -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			GGGAAGATGAAATCCAACAAT	0.343																																																0			5											100	95	97					5																	37019433		2203	4299	6502	37055190	SO:0001819	synonymous_variant	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4941A>G	5.37:g.37019433A>G			37055190	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																				0.343	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37019433	A	G	37019433	2	3	111	1	0	0	0	0	0	0	0	1	10459	11	1	4		4	NIPBL	5	37019433	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	4961311	37019433	143895827	292	29426										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37064899	37064899	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagagtcagacattatttacAaaaaaattgctctaacgagt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:37064899delA	ENST00000282516.8	+	47	8819	c.8320delA	c.(8320-8322)aaafs	p.K2775fs		NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2775					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	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)			CATTATTTACAAAAAAATTGC	0.463																																																0			5											57	58	58					5																	37064899		2203	4300	6503	37100656	SO:0001589	frameshift_variant	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.8320delA	5.37:g.37064899delA	ENSP00000282516:p.Lys2775fs		37100656	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	37	CCDS3920.1																																																																																				0.463	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	37064899	A	-	37064899	7	5	111	1	0	1	0	1	0	0	0	0	10459	131	5	0	8547	0	NIPBL	5	37064899	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	45466	37064899	143850361	293	29427										
FYB	2533	hgsc.bcm.edu	37	chr5	39202038	39202038	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggcaatggcttctgtttcGgggtggctgaattcttgtct					rs374928648		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:39202038delG	ENST00000351578.6	-	2	1215	c.1025delC	c.(1024-1026)ccgfs	p.P342fs	FYB_ENST00000515010.1_Frame_Shift_Del_p.P342fs|FYB_ENST00000540520.1_Frame_Shift_Del_p.P352fs|FYB_ENST00000512982.1_Frame_Shift_Del_p.P342fs|FYB_ENST00000505428.1_Frame_Shift_Del_p.P342fs	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	342					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)	p.P342L(3)|p.P352L(1)		endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CTTCTGTTTCGGGGTGGCTGA	0.532																																																4	Substitution - Missense(4)	lung(4)	5											138	141	140					5																	39202038		1926	4121	6047	39237795	SO:0001589	frameshift_variant	2533			U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1025delC	5.37:g.39202038delG	ENSP00000316460:p.Pro342fs		39237795	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Frame_Shift_Del	DEL	ENST00000351578.6	37	CCDS47200.1																																																																																				0.532	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		-	39202038	G	-	39202038	7	5	111	1	0	1	0	1	0	0	0	0	6143	1116	39	0	1536	0	FYB	5	39202038	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	2137139	39202038	141713222	294	29428										
GZMA	3001	hgsc.bcm.edu	37	chr5	54401317	54401317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacagatgtctgtgaaaaaaTtattggaggaaatgaagtaa	10	2	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:54401317T>A	ENST00000274306.6	+	2	121	c.86T>A	c.(85-87)aTt>aAt	p.I29N		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	29	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				TGTGAAAAAATTATTGGAGGA	0.413																																																0			5											91	87	88					5																	54401317		2203	4300	6503	54437074	SO:0001583	missense	3001				CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.86T>A	5.37:g.54401317T>A	ENSP00000274306:p.Ile29Asn		54437074	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	37	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138255	0.56936	.	.	ENSG00000145649	ENST00000274306	T	0.67171	-0.25	5.07	5.07	0.68467	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.89008	0.6593	H	0.99042	4.41	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.93256	0.6639	10	0.87932	D	0	.	14.6564	0.68835	0.0:0.0:0.0:1.0	.	29	P12544	GRAA_HUMAN	N	29	ENSP00000274306:I29N	ENSP00000274306:I29N	I	+	2	0	GZMA	54437074	1.000000	0.71417	0.983000	0.44433	0.384000	0.30261	6.180000	0.71981	2.114000	0.64651	0.533000	0.62120	ATT		0.413	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144		A	54401317	T	A	54401317	3	1	111	1	0	0	0	0	1	0	0	0	6936	1493	52	5	92	5	GZMA	5	54401317	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	15199279	54401317	126513943	295	29429										
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56176939	56176939	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtattggtggtgttgattatGtcttaaattgtattcttgga	11	2	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:56176939G>T	ENST00000399503.3	+	13	2209	c.2209G>T	c.(2209-2211)Gtc>Ttc	p.V737F		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	737					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		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)		TGTTGATTATGTCTTAAATTG	0.308																																																0			5											112	98	102					5																	56176939		1825	4079	5904	56212696	SO:0001583	missense	4214			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2209G>T	5.37:g.56176939G>T	ENSP00000382423:p.Val737Phe		56212696		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328426	0.81690	.	.	ENSG00000095015	ENST00000399503	T	0.65549	-0.16	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.75744	0.3891	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.75414	-0.3326	10	0.72032	D	0.01	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	737	Q13233	M3K1_HUMAN	F	737	ENSP00000382423:V737F	ENSP00000382423:V737F	V	+	1	0	MAP3K1	56212696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.122000	0.64697	2.941000	0.99782	0.655000	0.94253	GTC		0.308	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		T	56176939	G	T	56176939	3	4	111	1	0	0	0	0	1	0	0	0	9273	1377	48	2	2259	2	MAP3K1	5	56176939	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1775622	56176939	124738321	296	29430										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67576772	67576772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagctctgataatactgaaaAcctcataaaagttatagaaa	5	7	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:67576772A>G	ENST00000521381.1	+	7	1470	c.854A>G	c.(853-855)aAc>aGc	p.N285S	PIK3R1_ENST00000274335.5_Missense_Mutation_p.N285S|PIK3R1_ENST00000521657.1_Missense_Mutation_p.N285S|PIK3R1_ENST00000396611.1_Missense_Mutation_p.N285S	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	285	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AATACTGAAAACCTCATAAAA	0.328			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	5											53	59	57					5																	67576772		2203	4300	6503	67612528	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.854A>G	5.37:g.67576772A>G	ENSP00000428056:p.Asn285Ser		67612528	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	A	9.624	1.134633	0.21123	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000522084	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;2.03;2.03	5.24	1.39	0.22231	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	1.002750	0.08029	N	0.993168	T	0.24509	0.0594	N	0.24115	0.695	0.22693	N	0.998842	B	0.02656	0.0	B	0.01281	0.0	T	0.25502	-1.0130	10	0.22109	T	0.4	-1.7464	2.9431	0.05837	0.5089:0.2818:0.0738:0.1355	.	285	P27986	P85A_HUMAN	S	285;285;285;285;15;15	ENSP00000428056:N285S;ENSP00000429277:N285S;ENSP00000379855:N285S;ENSP00000274335:N285S;ENSP00000430126:N15S;ENSP00000429766:N15S	ENSP00000274335:N285S	N	+	2	0	PIK3R1	67612528	0.999000	0.42202	0.998000	0.56505	0.971000	0.66376	1.309000	0.33539	0.272000	0.22027	0.460000	0.39030	AAC		0.328	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67576772	A	G	67576772	3	3	111	1	0	0	0	0	1	0	0	0	11949	43	2	4	876	4	PIK3R1	5	67576772	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	11399833	67576772	113338488	297	29431										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71496022	71496022	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagcgggcttgaaagaatcCtcggataaagtgtccagggt	13	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:71496022C>A	ENST00000296755.7	+	5	7138	c.6840C>A	c.(6838-6840)tcC>tcA	p.S2280S		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2280					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		TGAAAGAATCCTCGGATAAAG	0.502																																					Melanoma(17;367 822 11631 31730 47712)											0			5											97	108	104					5																	71496022		2203	4300	6503	71531778	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6840C>A	5.37:g.71496022C>A			71531778	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.502	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71496022	C	A	71496022	2	1	111	1	0	0	0	0	0	0	0	1	9258	668	24	2		2	MAP1B	5	71496022	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3919250	71496022	109419238	298	29432										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75866460	75866460	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtccagtggttaagagcgaTggagtctattggtctaccca	12	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:75866460T>C	ENST00000274364.6	+	4	656	c.359T>C	c.(358-360)aTg>aCg	p.M120T	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	120	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TTAAGAGCGATGGAGTCTATT	0.448																																																0			5											168	158	162					5																	75866460		2203	4300	6503	75902216	SO:0001583	missense	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.359T>C	5.37:g.75866460T>C	ENSP00000274364:p.Met120Thr		75902216	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.285025	0.80803	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.43294	0.95;0.95;0.95	5.52	5.52	0.82312	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	T	0.68035	0.2957	M	0.83953	2.67	0.80722	D	1	D	0.62365	0.991	D	0.87578	0.998	T	0.73652	-0.3915	10	0.87932	D	0	-33.1508	15.6418	0.77009	0.0:0.0:0.0:1.0	.	120	Q13576	IQGA2_HUMAN	T	120;93;70	ENSP00000274364:M120T;ENSP00000423672:M93T;ENSP00000421097:M70T	ENSP00000274364:M120T	M	+	2	0	IQGAP2	75902216	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	7.874000	0.87199	2.103000	0.63969	0.533000	0.62120	ATG		0.448	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		C	75866460	T	C	75866460	3	2	111	1	0	0	0	0	1	0	0	0	7836	1464	51	4	373	4	IQGAP2	5	75866460	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	4370438	75866460	105048800	299	29433										
PDE8B	8622	hgsc.bcm.edu	37	chr5	76717755	76717755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgacgtggccaacccatgccGccccttggacctgtgcattg	11	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:76717755G>A	ENST00000264917.5	+	20	2405	c.2360G>A	c.(2359-2361)cGc>cAc	p.R787H	PDE8B_ENST00000346042.3_Missense_Mutation_p.R690H|PDE8B_ENST00000342343.4_Missense_Mutation_p.R767H|PDE8B_ENST00000340978.3_Missense_Mutation_p.R740H|PDE8B_ENST00000333194.4_Missense_Mutation_p.R732H|PDE8B_ENST00000505283.1_Missense_Mutation_p.R252H	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	787	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	AACCCATGCCGCCCCTTGGAC	0.532																																																0			5											118	107	111					5																	76717755		2203	4300	6503	76753511	SO:0001583	missense	8622			AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.2360G>A	5.37:g.76717755G>A	ENSP00000264917:p.Arg787His		76753511	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Missense_Mutation	SNP	ENST00000264917.5	37	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.591947	0.86953	.	.	ENSG00000113231	ENST00000340978;ENST00000346042;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000505283	D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	4.85	3.96	0.45880	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.161807	0.53938	D	0.000058	D	0.94059	0.8096	H	0.97214	3.96	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;0.999;1.0;1.0	D	0.95826	0.8854	10	0.87932	D	0	.	14.4612	0.67450	0.0:0.0:0.8516:0.1484	.	690;740;732;767;787	O95263-2;O95263-6;O95263-3;O95263-4;O95263	.;.;.;.;PDE8B_HUMAN	H	740;690;787;767;732;252	ENSP00000345446:R740H;ENSP00000330428:R690H;ENSP00000264917:R787H;ENSP00000345646:R767H;ENSP00000331336:R732H;ENSP00000423461:R252H	ENSP00000264917:R787H	R	+	2	0	PDE8B	76753511	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	1.243000	0.43853	0.561000	0.74099	CGC		0.532	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		A	76717755	G	A	76717755	3	1	111	1	0	0	0	0	1	0	0	0	11685	1087	38	1	2438	1	PDE8B	5	76717755	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	851295	76717755	104197505	300	29434										
JMY	133746	hgsc.bcm.edu	37	chr5	78533002	78533002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcgcccagagaggcccagGtgtcctctgtacggatagtg	15	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:78533002G>A	ENST00000396137.4	+	1	991	c.529G>A	c.(529-531)Gtg>Atg	p.V177M	DMGDH_ENST00000520388.1_5'Flank	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	177					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		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)		AGAGGCCCAGGTGTCCTCTGT	0.657																																																0			5											12	17	15					5																	78533002		692	1590	2282	78568758	SO:0001583	missense	133746			AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.529G>A	5.37:g.78533002G>A	ENSP00000379441:p.Val177Met		78568758	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	G	9.177	1.022514	0.19433	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.08193	3.12	3.25	1.39	0.22231	.	1.672870	0.04729	U	0.420775	T	0.06826	0.0174	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.37079	-0.9721	10	0.40728	T	0.16	.	6.2736	0.20969	0.2591:0.0:0.7409:0.0	.	177	Q8N9B5	JMY_HUMAN	M	177	ENSP00000379441:V177M	ENSP00000282259:V177M	V	+	1	0	JMY	78568758	0.003000	0.15002	0.029000	0.17559	0.169000	0.22640	0.692000	0.25482	0.651000	0.30788	0.462000	0.41574	GTG		0.657	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		A	78533002	G	A	78533002	3	1	111	1	0	0	0	0	1	0	0	0	7978	1261	44	3	531	3	JMY	5	78533002	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1815247	78533002	102382258	301	29435										
ATG10	83734	hgsc.bcm.edu	37	chr5	81283461	81283461	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaattcattaaacattcacaAcagataggtgatagttggga	9	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:81283461A>T	ENST00000282185.3	+	2	366	c.72A>T	c.(70-72)caA>caT	p.Q24H	ATG10_ENST00000458350.3_Missense_Mutation_p.Q24H|ATG10_ENST00000355178.4_Missense_Mutation_p.Q24H|ATG10_ENST00000513634.1_Missense_Mutation_p.Q24H|ATG10_ENST00000513443.1_Missense_Mutation_p.Q24H	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	24					autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		AACATTCACAACAGATAGGTG	0.318																																																0			5											125	136	133					5																	81283461		2203	4299	6502	81319217	SO:0001583	missense	83734			AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"APG10 autophagy 10-like (S. cerevisiae)", "ATG10 autophagy related 10 homolog (S. cerevisiae)"	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.72A>T	5.37:g.81283461A>T	ENSP00000282185:p.Gln24His		81319217	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	37	CCDS4057.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.546348	0.27652	.	.	ENSG00000152348	ENST00000355178;ENST00000282185;ENST00000458350;ENST00000510085;ENST00000513443;ENST00000513634	T;T;T;T;T	0.47177	1.27;1.85;1.85;1.27;0.85	5.71	-0.273	0.12915	.	0.297264	0.35585	N	0.003111	T	0.60104	0.2243	M	0.62723	1.935	0.39026	D	0.959848	P;P;D	0.76494	0.917;0.952;0.999	P;P;D	0.70935	0.671;0.753;0.971	T	0.58549	-0.7617	10	0.35671	T	0.21	-8.6822	13.2969	0.60303	0.2431:0.0:0.7569:0.0	.	24;24;24	D6RDX3;Q9H0Y0;Q9H0Y0-2	.;ATG10_HUMAN;.	H	24	ENSP00000347309:Q24H;ENSP00000282185:Q24H;ENSP00000404938:Q24H;ENSP00000425182:Q24H;ENSP00000425225:Q24H	ENSP00000282185:Q24H	Q	+	3	2	ATG10	81319217	0.999000	0.42202	0.993000	0.49108	0.438000	0.31896	0.829000	0.27449	-0.258000	0.09446	-0.924000	0.02725	CAA		0.318	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028		T	81283461	A	T	81283461	3	4	111	1	0	0	0	0	1	0	0	0	1090	40	2	5	74	5	ATG10	5	81283461	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2750459	81283461	99631799	302	29436										
VCAN	1462	hgsc.bcm.edu	37	chr5	82785939	82785939	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaagtgggaaaaagcccaccGgtgaggggctccctctctgg	14	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:82785939G>A	ENST00000265077.3	+	3	658	c.93G>A	c.(91-93)ccG>ccA	p.P31P	VCAN_ENST00000512590.2_De_novo_Start_InFrame|VCAN_ENST00000502527.2_Silent_p.P31P|VCAN_ENST00000513984.1_Silent_p.P31P|VCAN_ENST00000343200.5_Silent_p.P31P|VCAN_ENST00000342785.4_Silent_p.P31P	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	31	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		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)	Hyaluronan(DB08818)	AAAGCCCACCGGTGAGGGGCT	0.408																																																0			5											48	49	49					5																	82785939		2201	4290	6491	82821695	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.93G>A	5.37:g.82785939G>A			82821695	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.408	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82785939	G	A	82785939	2	1	111	1	0	0	0	0	0	0	0	1	17178	1103	39	1		1	VCAN	5	82785939	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1502478	82785939	98129321	303	29437										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83402565	83402565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggataccatttttggagtcCaaaaagagctcggtgagtag	13	6	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:83402565C>T	ENST00000296591.5	-	6	971	c.553G>A	c.(553-555)Gga>Aga	p.G185R	EDIL3_ENST00000380138.3_Missense_Mutation_p.G175R	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	185	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.G185*(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		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)		TTTTGGAGTCCAAAAAGAGCT	0.448																																																1	Substitution - Nonsense(1)	kidney(1)	5											187	194	192					5																	83402565		2203	4300	6503	83438321	SO:0001583	missense	10085			U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.553G>A	5.37:g.83402565C>T	ENSP00000296591:p.Gly185Arg		83438321	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	37	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264859	0.95399	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.98419	-4.92;-4.92	5.55	5.55	0.83447	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.050150	0.85682	D	0.000000	D	0.99020	0.9665	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.99833	1.1055	10	0.87932	D	0	-18.9715	19.5157	0.95162	0.0:1.0:0.0:0.0	.	175;185	O43854-2;O43854	.;EDIL3_HUMAN	R	185;175	ENSP00000296591:G185R;ENSP00000369483:G175R	ENSP00000296591:G185R	G	-	1	0	EDIL3	83438321	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.277000	0.78572	2.630000	0.89119	0.650000	0.86243	GGA		0.448	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		T	83402565	C	T	83402565	3	4	111	1	0	0	0	0	1	0	0	0	4926	603	21	3	913	3	EDIL3	5	83402565	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	616626	83402565	97512695	304	29438										
GPR98	84059	hgsc.bcm.edu	37	chr5	90106134	90106134	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatatcatagtgtcagaagaTacacagatgatcagattaca	7	6	3	5			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:90106134T>A	ENST00000405460.2	+	74	15153	c.15057T>A	c.(15055-15057)gaT>gaA	p.D5019E	GPR98_ENST00000425867.2_Missense_Mutation_p.D680E	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5019	Calx-beta 33. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGTCAGAAGATACACAGATGA	0.393																																																0			5											43	41	41					5																	90106134		1844	4095	5939	90141890	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15057T>A	5.37:g.90106134T>A	ENSP00000384582:p.Asp5019Glu		90141890	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	7.053	0.564755	0.13498	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.36699	1.24;1.24	5.47	-3.68	0.04463	Na-Ca exchanger/integrin-beta4 (2);	0.269242	0.46758	N	0.000270	T	0.18882	0.0453	L	0.45422	1.42	0.09310	N	0.999996	B;B;B	0.21606	0.058;0.003;0.047	B;B;B	0.19666	0.026;0.016;0.015	T	0.08743	-1.0707	9	.	.	.	.	0.596	0.00736	0.3222:0.1898:0.1105:0.3775	.	680;5019;680	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	E	5019;5019;680	ENSP00000384582:D5019E;ENSP00000392618:D680E	.	D	+	3	2	GPR98	90141890	0.067000	0.21026	0.013000	0.15412	0.246000	0.25737	0.285000	0.18883	-0.406000	0.07588	0.455000	0.32223	GAT		0.393	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90106134	T	A	90106134	3	1	111	1	0	0	0	0	1	0	0	0	6742	1403	49	5	15351	5	GPR98	5	90106134	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	6703569	90106134	90809126	305	29439										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93788720	93788720	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccaatataatggttgcttAaaaaatgattttaaggaatc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:93788720delA	ENST00000513200.3	-	12	2373	c.2301delT	c.(2299-2301)tttfs	p.F767fs	KIAA0825_ENST00000312498.7_Frame_Shift_Del_p.F767fs|KIAA0825_ENST00000427991.2_Frame_Shift_Del_p.F767fs	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	767										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						ATGGTTGCTTAAAAAATGATT	0.343																																																0			5											56	52	53					5																	93788720		692	1590	2282	93814476	SO:0001589	frameshift_variant	285600			BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2301delT	5.37:g.93788720delA	ENSP00000424618:p.Phe767fs		93814476	O94914|Q6ZNN2	Frame_Shift_Del	DEL	ENST00000513200.3	37																																																																																					0.343	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		-	93788720	A	-	93788720	7	5	111	1	0	1	0	1	0	0	0	0	2301	359	13	0	1562	0	C5orf36	5	93788720	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	3682586	93788720	87126540	306	29440										
PHAX	51808	hgsc.bcm.edu	37	chr5	125939833	125939833	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggtcgatacgagatcacagCggaagattctcaagagaaag	12	7	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:125939833C>T	ENST00000297540.4	+	2	1363	c.668C>T	c.(667-669)gCg>gTg	p.A223V		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	223	Necessary for interaction with CBP80. {ECO:0000250}.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						GAGATCACAGCGGAAGATTCT	0.403																																																0			5											55	53	54					5																	125939833		2203	4300	6503	125967732	SO:0001583	missense	51808			AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.668C>T	5.37:g.125939833C>T	ENSP00000297540:p.Ala223Val		125967732	Q9H8W1	Missense_Mutation	SNP	ENST00000297540.4	37	CCDS4138.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.173669	0.57584	.	.	ENSG00000164902	ENST00000297540;ENST00000456348	T	0.44083	0.93	5.74	4.58	0.56647	.	0.046754	0.85682	D	0.000000	T	0.26122	0.0637	N	0.14661	0.345	0.27215	N	0.959804	B	0.28880	0.226	B	0.20577	0.03	T	0.13124	-1.0521	10	0.49607	T	0.09	-36.4872	13.1106	0.59270	0.8647:0.1353:0.0:0.0	.	223	Q9H814	PHAX_HUMAN	V	223;188	ENSP00000297540:A223V	ENSP00000297540:A223V	A	+	2	0	PHAX	125967732	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.940000	0.63533	1.008000	0.39264	-0.256000	0.11100	GCG		0.403	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177		T	125939833	C	T	125939833	3	4	111	1	0	0	0	0	1	0	0	0	11844	768	27	1	674	1	PHAX	5	125939833	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	32151113	125939833	54975427	307	29441										
KIF3A	11127	hgsc.bcm.edu	37	chr5	132037846	132037846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaagctcccggctaagttgcCgaatgttctccagtaggcct	11	12	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:132037846C>T	ENST00000378746.4	-	13	1954	c.1736G>A	c.(1735-1737)cGg>cAg	p.R579Q	KIF3A_ENST00000403231.1_Missense_Mutation_p.R606Q|KIF3A_ENST00000378735.1_Missense_Mutation_p.R582Q|AC004237.1_ENST00000431165.1_RNA|KIF3A_ENST00000487055.1_5'UTR	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	579					anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)			endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCTAAGTTGCCGAATGTTCTC	0.403																																																0			5											81	83	82					5																	132037846		2203	4300	6503	132065745	SO:0001583	missense	11127			AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"Kinesins"	6319	protein-coding gene	gene with protein product	"kinesin family protein 3A"	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.1736G>A	5.37:g.132037846C>T	ENSP00000368020:p.Arg579Gln		132065745	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Missense_Mutation	SNP	ENST00000378746.4	37	CCDS34235.1	.	.	.	.	.	.	.	.	.	.	C	37	6.040565	0.97226	.	.	ENSG00000131437	ENST00000378746;ENST00000378735;ENST00000541316;ENST00000403231	T;T;T	0.09163	3.01;3.01;3.01	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.39253	0.1071	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;P;P	0.64042	0.921;0.921;0.598;0.885	T	0.19353	-1.0308	10	0.72032	D	0.01	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	606;606;579;605	E9PES4;B4DHG8;Q9Y496;Q2UVF2	.;.;KIF3A_HUMAN;.	Q	579;582;606;606	ENSP00000368020:R579Q;ENSP00000368009:R582Q;ENSP00000385808:R606Q	ENSP00000368009:R582Q	R	-	2	0	KIF3A	132065745	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.487000	0.81328	2.824000	0.97209	0.655000	0.94253	CGG		0.403	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054		T	132037846	C	T	132037846	3	4	111	1	0	0	0	0	1	0	0	0	8321	652	23	1	383	1	KIF3A	5	132037846	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6098013	132037846	48877414	308	29442										
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132159097	132159097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgaggggcacaggcctggcGcactgcagcctccagagccg	15	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:132159097G>A	ENST00000378679.3	-	9	2875	c.2071C>T	c.(2071-2073)Cgc>Tgc	p.R691C	SHROOM1_ENST00000488072.1_5'UTR|SHROOM1_ENST00000319854.3_Missense_Mutation_p.R691C|SHROOM1_ENST00000378676.1_Missense_Mutation_p.R622C	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	691	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGGCCTGGCGCACTGCAGCC	0.677																																																0			5											14	16	15					5																	132159097		2188	4279	6467	132186996	SO:0001583	missense	134549			AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.2071C>T	5.37:g.132159097G>A	ENSP00000367950:p.Arg691Cys		132186996	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389641	0.42410	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676	T;T;T	0.31247	1.5;1.5;1.5	4.91	-3.18	0.05186	Apx/shroom, ASD2 (2);	0.891913	0.09934	N	0.736875	T	0.27765	0.0683	L	0.27053	0.805	0.25495	N	0.987606	D;D	0.71674	0.998;0.992	P;P	0.54174	0.627;0.744	T	0.28427	-1.0044	10	0.62326	D	0.03	-2.3471	7.159	0.25652	0.0:0.1929:0.4769:0.3302	.	691;691	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	C	691;691;622	ENSP00000367950:R691C;ENSP00000324245:R691C;ENSP00000367947:R622C	ENSP00000324245:R691C	R	-	1	0	SHROOM1	132186996	0.011000	0.17503	0.028000	0.17463	0.433000	0.31745	0.573000	0.23699	-0.371000	0.08004	-0.410000	0.06199	CGC		0.677	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		A	132159097	G	A	132159097	3	1	111	1	0	0	0	0	1	0	0	0	14330	1087	38	1	495	1	SHROOM1	5	132159097	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	121251	132159097	48756163	309	29443										
AFF4	27125	hgsc.bcm.edu	37	chr5	132232053	132232053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgttggaaactttttctgAggcttgtttctgagcctctc	9	8	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:132232053A>G	ENST00000265343.5	-	11	2648	c.2269T>C	c.(2269-2271)Tca>Cca	p.S757P	AFF4_ENST00000378595.3_Missense_Mutation_p.S757P	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	757			S -> T (found in a clear cell renal carcinoma case; somatic mutation). {ECO:0000269|PubMed:21248752}.		spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S757T(2)	SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACTTTTTCTGAGGCTTGTTTC	0.423																																					Ovarian(126;889 1733 2942 10745 11605)											2	Substitution - Missense(2)	kidney(2)	5											111	113	112					5																	132232053		2203	4300	6503	132259952	SO:0001583	missense	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2269T>C	5.37:g.132232053A>G	ENSP00000265343:p.Ser757Pro		132259952	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087475	0.55968	.	.	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.69306	-0.39;-0.39	5.03	5.03	0.67393	.	0.386006	0.26658	N	0.023173	T	0.72236	0.3435	L	0.36672	1.1	0.52099	D	0.999948	D;B	0.63046	0.992;0.012	D;B	0.73708	0.981;0.023	T	0.68876	-0.5293	10	0.26408	T	0.33	-7.6975	13.6284	0.62181	1.0:0.0:0.0:0.0	.	757;757	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	P	757	ENSP00000265343:S757P;ENSP00000367858:S757P	ENSP00000265343:S757P	S	-	1	0	AFF4	132259952	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.773000	0.62331	2.012000	0.59069	0.533000	0.62120	TCA		0.423	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		G	132232053	A	G	132232053	3	3	111	1	0	0	0	0	1	0	0	0	359	304	11	4	1266	4	AFF4	5	132232053	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	72956	132232053	48683207	310	29444										
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134332023	134332023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtccatgaaggtctatgtgGaccccatcaactactggaag	10	10	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:134332023G>T	ENST00000282611.6	+	3	399	c.313G>T	c.(313-315)Gac>Tac	p.D105Y		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	105					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGTCTATGTGGACCCCATCAA	0.488																																																0			5											243	195	211					5																	134332023		2203	4300	6503	134359922	SO:0001583	missense	347732			AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"Voltage-gated ion channels / Cation channels, sperm associated"	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.313G>T	5.37:g.134332023G>T	ENSP00000282611:p.Asp105Tyr		134359922	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.746188	0.30955	.	.	ENSG00000152705	ENST00000282611	D	0.97256	-4.31	4.14	3.27	0.37495	Ion transport (1);	0.110360	0.40640	N	0.001044	D	0.97002	0.9021	L	0.51422	1.61	0.37036	D	0.896928	D	0.89917	1.0	D	0.79108	0.992	D	0.97070	0.9777	10	0.59425	D	0.04	-28.0523	7.7351	0.28810	0.1116:0.0:0.8884:0.0	.	105	Q86XQ3	CTSR3_HUMAN	Y	105	ENSP00000282611:D105Y	ENSP00000282611:D105Y	D	+	1	0	CATSPER3	134359922	1.000000	0.71417	0.998000	0.56505	0.055000	0.15305	2.505000	0.45424	1.329000	0.45376	0.561000	0.74099	GAC		0.488	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		T	134332023	G	T	134332023	3	4	111	1	0	0	0	0	1	0	0	0	2695	1174	41	2	323	2	CATSPER3	5	134332023	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2099970	134332023	46583237	311	29445										
PITX1	5307	hgsc.bcm.edu	37	chr5	134364640	134364640	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgtacgggcaagcgcccggCgacatggccgagttgagcga	16	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:134364640C>T	ENST00000265340.7	-	3	1190	c.774G>A	c.(772-774)tcG>tcA	p.S258S	PITX1_ENST00000506438.1_Silent_p.S258S	NM_002653.4	NP_002644.4	P78337	PITX1_HUMAN	paired-like homeodomain 1	258	Interacts with PIT-1. {ECO:0000250}.				anatomical structure morphogenesis (GO:0009653)|branchiomeric skeletal muscle development (GO:0014707)|cartilage development (GO:0051216)|embryonic hindlimb morphogenesis (GO:0035116)|myoblast fate commitment (GO:0048625)|pituitary gland development (GO:0021983)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)			central_nervous_system(1)|cervix(3)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)		AAGCGCCCGGCGACATGGCCG	0.667																																																0			5											59	57	58					5																	134364640		2203	4299	6502	134392539	SO:0001819	synonymous_variant	5307			AF009648	CCDS4182.1	5q31.1	2011-06-20	2007-07-12		ENSG00000069011	ENSG00000069011		"Homeoboxes / PRD class"	9004	protein-coding gene	gene with protein product		602149	"paired-like homeodomain transcription factor 1"	BFT		9337397, 9070926	Standard	NM_002653		Approved	PTX1, POTX	uc010jea.3	P78337	OTTHUMG00000149983	ENST00000265340.7:c.774G>A	5.37:g.134364640C>T			134392539	A8K3M0|D3DQB0|O14677|O60425|Q9BTI5	Silent	SNP	ENST00000265340.7	37	CCDS4182.1																																																																																				0.667	PITX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251195.3			T	134364640	C	T	134364640	2	4	111	1	0	0	0	0	0	0	0	1	11985	755	27	1		1	PITX1	5	134364640	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	32617	134364640	46550620	312	29446										
H2AFY	9555	hgsc.bcm.edu	37	chr5	134724634	134724634	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtcaggtattccaggacggcGgccatgtacacgggtgcccc	14	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:134724634G>A	ENST00000511689.1	-	2	743	c.150C>T	c.(148-150)gcC>gcT	p.A50A	H2AFY_ENST00000304332.4_Silent_p.A50A|H2AFY_ENST00000312469.4_Silent_p.A50A|H2AFY_ENST00000510038.1_Silent_p.A50A|H2AFY_ENST00000423969.2_Silent_p.A50A	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	50	Histone H2A.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAGGACGGCGGCCATGTACA	0.542																																																0			5											102	91	95					5																	134724634		2203	4300	6503	134752533	SO:0001819	synonymous_variant	9555			AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.150C>T	5.37:g.134724634G>A			134752533	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																				0.542	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		A	134724634	G	A	134724634	2	1	111	1	0	0	0	0	0	0	0	1	6950	1103	39	1		1	H2AFY	5	134724634	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	359994	134724634	46190626	313	29447										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692533	135692533	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgcccttgagcagcaggatGtgcacgatctcatactcctg	11	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:135692533G>A	ENST00000513104.1	-	2	825	c.543C>T	c.(541-543)caC>caT	p.H181H	TRPC7_ENST00000355180.3_Silent_p.H181H|TRPC7_ENST00000426057.2_Silent_p.H181H	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	181					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCAGCAGGATGTGCACGATCT	0.602																																																0			5											114	122	119					5																	135692533		2203	4296	6499	135720432	SO:0001819	synonymous_variant	57113			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.543C>T	5.37:g.135692533G>A			135720432	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	37	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	8.574	0.880666	0.17467	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	T;T;T	0.70516	-0.49;-0.49;-0.49	5.26	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.75162	0.3812	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75068	-0.3448	7	0.72032	D	0.01	-25.8699	8.7666	0.34706	0.2909:0.0:0.7091:0.0	.	.	.	.	Y	181	ENSP00000330322:H181Y;ENSP00000367720:H181Y;ENSP00000424854:H181Y	ENSP00000330322:H181Y	H	-	1	0	TRPC7	135720432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.351000	0.44071	0.762000	0.33152	0.650000	0.86243	CAT		0.602	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692533	G	A	135692533	2	1	111	1	0	0	0	0	0	0	0	1	16624	1368	48	3		3	TRPC7	5	135692533	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	967899	135692533	45222727	314	29448										
KLHL3	26249	hgsc.bcm.edu	37	chr5	137034039	137034039	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagtcaatcagcttactcagCgtctgcccatccacgtcctt	6	15	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:137034039C>T	ENST00000309755.4	-	4	743	c.300G>A	c.(298-300)acG>acA	p.T100T	KLHL3_ENST00000508657.1_Silent_p.T68T|KLHL3_ENST00000506491.1_Silent_p.T18T|KLHL3_ENST00000541417.1_5'UTR|KLHL3_ENST00000394937.3_Silent_p.T100T	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	100	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		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)		GCTTACTCAGCGTCTGCCCAT	0.413																																																0			5											329	296	307					5																	137034039		2203	4300	6503	137061938	SO:0001819	synonymous_variant	26249			AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.300G>A	5.37:g.137034039C>T			137061938	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																				0.413	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			T	137034039	C	T	137034039	2	4	111	1	0	0	0	0	0	0	0	1	8404	755	27	1		1	KLHL3	5	137034039	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1341506	137034039	43881221	315	29449										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139907857	139907857	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aactggaagacttgattcctAaaaatcatatcagaacacct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:139907857delA	ENST00000360839.2	+	29	5480	c.5326delA	c.(5326-5328)aaafs	p.K1776fs	SNORD45_ENST00000363181.1_RNA|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1776fs|ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.K1776fs|ANKHD1_ENST00000544120.1_Frame_Shift_Del_p.K159fs	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1776						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGATTCCTAAAAATCATAT	0.403																																																0			5											103	99	101					5																	139907857		2203	4300	6503	139888041	SO:0001589	frameshift_variant	54882			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.5326delA	5.37:g.139907857delA	ENSP00000354085:p.Lys1776fs		139888041	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Frame_Shift_Del	DEL	ENST00000360839.2	37	CCDS4225.1																																																																																				0.403	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		-	139907857	A	-	139907857	7	5	111	1	0	1	0	1	0	0	0	0	628	363	13	0	5546	0	ANKHD1	5	139907857	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	2873818	139907857	41007403	316	29450										
WDR55	54853	hgsc.bcm.edu	37	chr5	140049101	140049102	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggatgactaccgtcggcgcINSaaaaaaaagggaggaccact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140049101_140049102insA	ENST00000358337.5	+	7	1251_1252	c.1014_1015insA	c.(1015-1017)aaafs	p.K339fs	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	339					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)		p.K341fs*8(1)		NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCGTCGGCGCAAAAAAAAGGG	0.589																																																1	Deletion - Frameshift(1)	large_intestine(1)	5								6,4258		0,6,2126						1	1			45	11,8243		0,11,4116	no	frameshift	WDR55	NM_017706.4		0,17,6242	A1A1,A1R,RR		0.1333,0.1407,0.1358				17,12501				140029286	SO:0001589	frameshift_variant	54853			AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.1022dupA	5.37:g.140049109_140049109dupA	ENSP00000351100:p.Lys339fs		140029285	Q9NXK4	Frame_Shift_Ins	INS	ENST00000358337.5	37	CCDS4235.1																																																																																				0.589	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		A	140049102	-	A	140049101	7	5	111	1	0	1	1	0	0	0	0	0	17347	697	25	0	1040	0	WDR55	5	140049101	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	141244	140049101	40866159	317	29451										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215694	140215694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggtgggtggcactggtggcGcagtgagagagcttgtgccg	21	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140215694G>A	ENST00000525929.1	+	1	1726	c.1726G>A	c.(1726-1728)Gca>Aca	p.A576T	PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.A576T|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	576					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTGGTGGCGCAGTGAGAGA	0.662																																					NSCLC(160;258 2013 5070 22440 28951)											0			5											95	97	96					5																	140215694		2203	4300	6503	140195878	SO:0001583	missense	56141			AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1726G>A	5.37:g.140215694G>A	ENSP00000436426:p.Ala576Thr		140195878	O75282	Missense_Mutation	SNP	ENST00000525929.1	37	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	G	1.242	-0.620930	0.03636	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.37235	1.21;1.21	4.2	-4.94	0.03057	Cadherin-like (1);	0.839395	0.09050	U	0.855921	T	0.11067	0.0270	N	0.03608	-0.345	0.09310	N	1	B;B	0.21452	0.056;0.043	B;B	0.15870	0.014;0.009	T	0.26573	-1.0099	10	0.17832	T	0.49	.	2.885	0.05659	0.1511:0.3407:0.3221:0.186	.	576;576	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	T	576	ENSP00000436426:A576T;ENSP00000367365:A576T	ENSP00000367365:A576T	A	+	1	0	PCDHA7	140195878	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.168000	0.09925	-0.652000	0.05408	0.462000	0.41574	GCA		0.662	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		A	140215694	G	A	140215694	3	1	111	1	0	0	0	0	1	0	0	0	11560	1087	38	1	1728	1	PCDHA7	5	140215694	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	166593	140215694	40699566	318	29452										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262567	140262567	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attctggacgtgaatgacaaCgccccggaattttaccaatc	8	11	1	2	rs139888237	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140262567C>T	ENST00000289272.2	+	1	714	c.714C>T	c.(712-714)aaC>aaT	p.N238N	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.N238N|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	238	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N238N(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAATGACAACGCCCCGGAAT	0.453													.|||	2	0.000399361	0	0	5008	,	,		19765	0.002		0	False		,,,				2504	0				Melanoma(147;1739 1852 5500 27947 37288)											1	Substitution - coding silent(1)	ovary(1)	5											67	65	66					5																	140262567		2203	4300	6503	140242751	SO:0001819	synonymous_variant	56136			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.714C>T	5.37:g.140262567C>T			140242751	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																				0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140262567	C	T	140262567	2	4	111	1	0	0	0	0	0	0	0	1	11554	535	19	1		1	PCDHA13	5	140262567	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	46873	140262567	40652693	319	29453										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140503131	140503131	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacctgttcgccctcaggtcGctggactacgaggccctgca	11	16	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140503131G>T	ENST00000194152.1	+	1	1551	c.1551G>T	c.(1549-1551)tcG>tcT	p.S517S	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	517	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTCAGGTCGCTGGACTACG	0.692																																																0			5											58	65	63					5																	140503131		2197	4288	6485	140483315	SO:0001819	synonymous_variant	56131			AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1551G>T	5.37:g.140503131G>T			140483315	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																				0.692	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140503131	G	T	140503131	2	4	111	1	0	0	0	0	0	0	0	1	11575	1074	38	2		2	PCDHB4	5	140503131	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	240564	140503131	40412129	320	29454										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559696	140559696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caccgtctacctggtggtggCgttggcctcggtgtcttcgc	14	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140559696C>T	ENST00000239444.2	+	1	2326	c.2081C>T	c.(2080-2082)gCg>gTg	p.A694V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	694					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGGTGGTGGCGTTGGCCTCG	0.672																																																0			5											90	87	88					5																	140559696		2202	4298	6500	140539880	SO:0001583	missense	56128			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.2081C>T	5.37:g.140559696C>T	ENSP00000239444:p.Ala694Val		140539880	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.437343	0.83885	.	.	ENSG00000120322	ENST00000239444	T	0.25250	1.81	4.22	3.34	0.38264	.	.	.	.	.	T	0.59059	0.2166	H	0.97051	3.93	0.09310	N	1	D	0.71674	0.998	P	0.62813	0.907	T	0.55373	-0.8151	9	0.87932	D	0	.	8.7671	0.34708	0.0:0.7627:0.1494:0.0879	.	694	Q9UN66	PCDB8_HUMAN	V	694	ENSP00000239444:A694V	ENSP00000239444:A694V	A	+	2	0	PCDHB8	140539880	0.003000	0.15002	0.007000	0.13788	0.455000	0.32408	2.044000	0.41241	1.915000	0.55452	0.298000	0.19748	GCG		0.672	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140559696	C	T	140559696	3	4	111	1	0	0	0	0	1	0	0	0	11579	768	27	1	2083	1	PCDHB8	5	140559696	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	56565	140559696	40355564	321	29455										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140712129	140712129	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtctgcacacgggcgaggtGcgcacggcgcgagccctgct	17	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140712129G>A	ENST00000517417.1	+	1	1878	c.1878G>A	c.(1876-1878)gtG>gtA	p.V626V	PCDHGA1_ENST00000378105.3_Silent_p.V626V	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	626	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGCGAGGTGCGCACGGCGC	0.701																																																0			5											23	28	26					5																	140712129		2180	4254	6434	140692313	SO:0001819	synonymous_variant	56114			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1878G>A	5.37:g.140712129G>A			140692313	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																				0.701	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140712129	G	A	140712129	2	1	111	1	0	0	0	0	0	0	0	1	11581	1306	46	3		3	PCDHGA1	5	140712129	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	152433	140712129	40203131	322	29456										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140754304	140754304	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttactgccatggatggcggCgaccctgtccgctcaagcgt	12	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140754304C>T	ENST00000517434.1	+	1	654	c.654C>T	c.(652-654)ggC>ggT	p.G218G	PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	218	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGATGGCGGCGACCCTGTCC	0.562																																																0			5											25	29	28					5																	140754304		2017	4170	6187	140734488	SO:0001819	synonymous_variant	56109			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.654C>T	5.37:g.140754304C>T			140734488	A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	37	CCDS54926.1																																																																																				0.562	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140754304	C	T	140754304	2	4	111	1	0	0	0	0	0	0	0	1	11589	755	27	1		1	PCDHGA6	5	140754304	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	42175	140754304	40160956	323	29457										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140812235	140812235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagccctgctggacagagacGcgctcaagcagagcctcgta	13	13	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:140812235G>A	ENST00000252085.3	+	1	2051	c.1909G>A	c.(1909-1911)Gcg>Acg	p.A637T	PCDHGA11_ENST00000518882.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	637	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACAGAGACGCGCTCAAGCA	0.697																																																0			5											43	52	49					5																	140812235		2198	4293	6491	140792419	SO:0001583	missense	26025			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1909G>A	5.37:g.140812235G>A	ENSP00000252085:p.Ala637Thr		140792419	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	14.05	2.420342	0.42918	.	.	ENSG00000253159	ENST00000252085	T	0.51325	0.71	5.06	3.24	0.37175	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.33818	0.0876	N	0.25890	0.77	0.19775	N	0.999958	B;P	0.35481	0.448;0.504	B;B	0.33568	0.103;0.166	T	0.19647	-1.0299	9	0.56958	D	0.05	.	9.5179	0.39117	0.2332:0.0:0.7668:0.0	.	637;637	O60330-2;O60330	.;PCDGC_HUMAN	T	637	ENSP00000252085:A637T	ENSP00000252085:A637T	A	+	1	0	PCDHGA12	140792419	0.000000	0.05858	0.267000	0.24556	0.886000	0.51366	0.113000	0.15499	1.271000	0.44313	0.556000	0.70494	GCG		0.697	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140812235	G	A	140812235	3	1	111	1	0	0	0	0	1	0	0	0	11584	1087	38	1	1911	1	PCDHGA12	5	140812235	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	57931	140812235	40103025	324	29458										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142661457	142661457	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cattcttattaaggcagtcaCttttgatgaaacagaagttt	7	6	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:142661457C>T	ENST00000343796.2	-	9	3324	c.2331G>A	c.(2329-2331)aaG>aaA	p.K777K	NR3C1_ENST00000424646.2_Silent_p.K751K|NR3C1_ENST00000503201.1_Silent_p.K777K|NR3C1_ENST00000394464.2_Silent_p.K777K|NR3C1_ENST00000394466.2_Silent_p.K778K|NR3C1_ENST00000416954.2_Silent_p.K380K|NR3C1_ENST00000504572.1_Silent_p.K778K|NR3C1_ENST00000415690.2_Intron|NR3C1_ENST00000231509.3_Silent_p.K778K	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	777	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	AAGGCAGTCACTTTTGATGAA	0.313																																																0			5											80	82	81					5																	142661457		2201	4300	6501	142641650	SO:0001819	synonymous_variant	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2331G>A	5.37:g.142661457C>T			142641650	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Silent	SNP	ENST00000343796.2	37	CCDS4278.1																																																																																				0.313	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			T	142661457	C	T	142661457	2	4	111	1	0	0	0	0	0	0	0	1	10661	564	20	3		3	NR3C1	5	142661457	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1849222	142661457	38253803	325	29459										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145887465	145887465	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acatccacgtggaaagaagtAaaaaaaatcattaaggaaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:145887465delA	ENST00000296702.5	+	20	2978	c.2940delA	c.(2938-2940)gtafs	p.V980fs	TCERG1_ENST00000394421.2_Frame_Shift_Del_p.V959fs	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	980	FF 5.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAAAGAAGTAAAAAAAATCA	0.338																																																0			5											89	84	86					5																	145887465		2203	4299	6502	145867658	SO:0001589	frameshift_variant	10915			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.2940delA	5.37:g.145887465delA	ENSP00000296702:p.Val980fs		145867658	Q2NKN2|Q59EA1	Frame_Shift_Del	DEL	ENST00000296702.5	37	CCDS4282.1																																																																																				0.338	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		-	145887465	A	-	145887465	7	5	111	1	0	1	0	1	0	0	0	0	15724	349	13	0	3018	0	TCERG1	5	145887465	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	3226008	145887465	35027795	326	29460										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147449939	147449939	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatggaaaactgttctgtccCcaggataagaaattttttca	7	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:147449939C>T	ENST00000256084.7	+	3	177	c.135C>T	c.(133-135)ccC>ccT	p.P45P	SPINK5_ENST00000398454.1_Silent_p.P45P|SPINK5_ENST00000359874.3_Silent_p.P45P	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	45	Kazal-like 1; atypical. {ECO:0000255|PROSITE-ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTCTGTCCCCAGGATAAGA	0.323																																																0			5											69	68	68					5																	147449939		1827	4073	5900	147430132	SO:0001819	synonymous_variant	11005			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.135C>T	5.37:g.147449939C>T			147430132	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																				0.323	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147449939	C	T	147449939	2	4	111	1	0	0	0	0	0	0	0	1	15101	610	22	3		3	SPINK5	5	147449939	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1562474	147449939	33465321	327	29461										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148687138	148687138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaagcgtttcgggcagtggGccaagcagctgacggtcatc	14	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:148687138G>A	ENST00000296721.4	+	7	807	c.709G>A	c.(709-711)Gcc>Acc	p.A237T	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.A237T|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	237	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGCAGTGGGCCAAGCAGCT	0.617																																																0			5											65	52	56					5																	148687138		2203	4300	6503	148667331	SO:0001583	missense	134265			AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.709G>A	5.37:g.148687138G>A	ENSP00000296721:p.Ala237Thr		148667331	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618541	0.87460	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.11712	2.75;2.75	4.89	4.89	0.63831	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.100619	0.64402	D	0.000002	T	0.19604	0.0471	N	0.25201	0.72	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.998	P;D;D	0.91635	0.895;0.999;0.995	T	0.12066	-1.0562	10	0.14656	T	0.56	-26.4255	18.243	0.89974	0.0:0.0:1.0:0.0	.	237;237;237	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	T	237	ENSP00000296721:A237T;ENSP00000424427:A237T	ENSP00000296721:A237T	A	+	1	0	AFAP1L1	148667331	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.567000	0.73983	2.543000	0.85770	0.561000	0.74099	GCC		0.617	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		A	148687138	G	A	148687138	3	1	111	1	0	0	0	0	1	0	0	0	354	1203	42	3	735	3	AFAP1L1	5	148687138	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1237199	148687138	32228122	328	29462										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167626066	167626066	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatcatctcctccccactgTccaccttctttagtgctgcc	4	18	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:167626066T>G	ENST00000518659.1	+	16	3148	c.3109T>G	c.(3109-3111)Tcc>Gcc	p.S1037A	TENM2_ENST00000519204.1_Missense_Mutation_p.S916A|TENM2_ENST00000520394.1_Missense_Mutation_p.S805A|TENM2_ENST00000545108.1_Missense_Mutation_p.S1037A|TENM2_ENST00000403607.2_Missense_Mutation_p.S861A	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1037					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CTCCCCACTGTCCACCTTCTT	0.582																																																0			5											69	72	71					5																	167626066		2061	4203	6264	167558644	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3109T>G	5.37:g.167626066T>G	ENSP00000429430:p.Ser1037Ala		167558644	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	T	18.42	3.620047	0.66787	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89196	-2.0;-2.0;-2.1;-2.46;-2.48	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.92828	0.7719	M	0.68317	2.08	0.45747	D	0.998645	D;D;D	0.71674	0.998;0.996;0.959	D;D;D	0.85130	0.997;0.992;0.909	D	0.90708	0.4625	10	0.15499	T	0.54	.	15.4567	0.75321	0.0:0.0:0.0:1.0	.	1037;1037;805	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	A	1037;1037;916;805;861	ENSP00000429430:S1037A;ENSP00000438635:S1037A;ENSP00000428964:S916A;ENSP00000427874:S805A;ENSP00000384905:S861A	ENSP00000384905:S861A	S	+	1	0	ODZ2	167558644	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	6.289000	0.72696	2.058000	0.61347	0.460000	0.39030	TCC		0.582	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		G	167626066	T	G	167626066	3	3	111	1	0	0	0	0	1	0	0	0	10866	1667	58	4	3144	4	ODZ2	5	167626066	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	18938928	167626066	13289194	329	29463										
STK10	6793	hgsc.bcm.edu	37	chr5	171488267	171488267	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctgcttggctacaaagtcCcggtcctgtggggagagagg	15	9	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:171488267C>A	ENST00000176763.5	-	14	2431	c.2088G>T	c.(2086-2088)cgG>cgT	p.R696R		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	696					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTACAAAGTCCCGGTCCTGTG	0.587																																																0			5											117	108	111					5																	171488267		2203	4300	6503	171420872	SO:0001819	synonymous_variant	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.2088G>T	5.37:g.171488267C>A			171420872	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																				0.587	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171488267	C	A	171488267	2	1	111	1	0	0	0	0	0	0	0	1	15325	610	22	2		2	STK10	5	171488267	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3862201	171488267	9426993	330	29464										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172341786	172341786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcgacaactccatgaagaTcccgctgaacaatggggcag	10	12	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:172341786T>C	ENST00000393784.3	+	5	459	c.320T>C	c.(319-321)aTc>aCc	p.I107T	ERGIC1_ENST00000326654.2_Missense_Mutation_p.I62T|ERGIC1_ENST00000523291.1_Missense_Mutation_p.I107T	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	107					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCATGAAGATCCCGCTGAAC	0.567																																																0			5											65	63	64					5																	172341786		2203	4300	6503	172274392	SO:0001583	missense	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.320T>C	5.37:g.172341786T>C	ENSP00000377374:p.Ile107Thr		172274392	Q9H0L0|Q9H2J2|Q9ULN9	Missense_Mutation	SNP	ENST00000393784.3	37	CCDS34292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.474|6.474	0.455566|0.455566	0.12283|0.12283	.|.	.|.	ENSG00000113719|ENSG00000113719	ENST00000393784;ENST00000520326;ENST00000523291;ENST00000518247;ENST00000326654|ENST00000519567	.|.	.|.	.|.	5.37|5.37	5.37|5.37	0.77165|0.77165	Domain of unknown function DUF1692 (1);|.	0.105585|.	0.64402|.	D|.	0.000004|.	T|T	0.47820|0.47820	0.1466|0.1466	N|N	0.13098|0.13098	0.295|0.295	0.80722|0.80722	D|D	1|1	B;D;B|.	0.69078|.	0.01;0.997;0.001|.	B;D;B|.	0.63283|.	0.01;0.913;0.005|.	T|T	0.44726|0.44726	-0.9309|-0.9309	9|5	0.12766|.	T|.	0.61|.	-21.8449|-21.8449	15.0738|15.0738	0.72059|0.72059	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	52;62;107|.	B4E0N6;Q969X5-3;Q969X5|.	.;.;ERGI1_HUMAN|.	T|P	107;107;107;62;62|96	.|.	ENSP00000325127:I62T|.	I|S	+|+	2|1	0|0	ERGIC1|ERGIC1	172274392|172274392	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.831000|0.831000	0.47069|0.47069	7.638000|7.638000	0.83328|0.83328	2.028000|2.028000	0.59812|0.59812	0.533000|0.533000	0.62120|0.62120	ATC|TCC		0.567	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		C	172341786	T	C	172341786	3	2	111	1	0	0	0	0	1	0	0	0	5236	1435	50	4	338	4	ERGIC1	5	172341786	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	853519	172341786	8573474	331	29465										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173372101	173372101	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaagagtggaacgatattctCgaaaggtgtttgtaggcgga	14	4	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:173372101C>T	ENST00000265085.5	+	5	2868	c.1414C>T	c.(1414-1416)Cga>Tga	p.R472*	CPEB4_ENST00000520867.1_Nonsense_Mutation_p.R447*|CPEB4_ENST00000334035.5_Nonsense_Mutation_p.R455*|CPEB4_ENST00000519835.1_Nonsense_Mutation_p.R447*|CPEB4_ENST00000522336.1_Nonsense_Mutation_p.R82*|CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000517880.1_Nonsense_Mutation_p.R65*	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	472	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			ACGATATTCTCGAAAGGTGTT	0.488																																																0			5											159	144	149					5																	173372101		2203	4300	6503	173304707	SO:0001587	stop_gained	80315			BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.1414C>T	5.37:g.173372101C>T	ENSP00000265085:p.Arg472*		173304707	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Nonsense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911728	0.92178	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835;ENST00000522336;ENST00000517880	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.029	19.4739	0.94976	0.0:1.0:0.0:0.0	.	.	.	.	X	472;447;455;447;82;65	.	ENSP00000265085:R472X	R	+	1	2	CPEB4	173304707	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.034000	0.70933	2.697000	0.92050	0.655000	0.94253	CGA		0.488	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		T	173372101	C	T	173372101	4	4	111	1	0	0	0	0	0	1	0	0	3809	876	31	1	1432	1	CPEB4	5	173372101	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1030315	173372101	7543159	332	29466										
DBN1	1627	hgsc.bcm.edu	37	chr5	176886218	176886218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgctggagtcagacgggctcCgcgtggggatgggagtgggc	21	8	1	1	rs144418852		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:176886218C>T	ENST00000309007.5	-	11	1226	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	DBN1_ENST00000292385.5_Missense_Mutation_p.R338Q|DBN1_ENST00000512501.1_Missense_Mutation_p.R68Q|DBN1_ENST00000393563.4_Missense_Mutation_p.R68Q|DBN1_ENST00000393565.1_Missense_Mutation_p.R382Q	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	336					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			AGACGGGCTCCGCGTGGGGAT	0.692																																																0			5						C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	72	74	73		1007,1013	4.6	1	5	dbSNP_134	73	0,8600		0,0,4300	no	missense,missense	DBN1	NM_004395.3,NM_080881.2	43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	336/650,338/652	176886218	2,13004	2203	4300	6503	176818824	SO:0001583	missense	1627				CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1007G>A	5.37:g.176886218C>T	ENSP00000308532:p.Arg336Gln		176818824	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847571	0.71603	4.54E-4	0.0	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.35973	1.46;1.44;1.46;1.28;1.42	4.58	4.58	0.56647	.	0.569295	0.17171	N	0.184295	T	0.43456	0.1248	N	0.24115	0.695	0.39161	D	0.962419	D;D;D;D	0.76494	0.999;0.998;0.997;0.998	P;P;P;P	0.62649	0.905;0.788;0.728;0.86	T	0.43212	-0.9405	10	0.48119	T	0.1	-10.4558	14.6573	0.68844	0.0:1.0:0.0:0.0	.	286;382;336;338	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	Q	336;338;382;68;68	ENSP00000308532:R336Q;ENSP00000292385:R338Q;ENSP00000377195:R382Q;ENSP00000423208:R68Q;ENSP00000377193:R68Q	ENSP00000292385:R338Q	R	-	2	0	DBN1	176818824	1.000000	0.71417	1.000000	0.80357	0.509000	0.34042	4.361000	0.59461	2.260000	0.74910	0.462000	0.41574	CGG		0.692	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		T	176886218	C	T	176886218	3	4	111	1	0	0	0	0	1	0	0	0	4258	652	23	1	958	1	DBN1	5	176886218	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3514117	176886218	4029042	333	29467										
HNRNPAB	85007	hgsc.bcm.edu	37	chr5	177633743	177633745	+	IGR	DEL	AGA	AGA	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttggaacaggtcctagaccAgaaggagcacaggctggatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AGA	AGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:177633743_177633745delAGA	ENST00000308158.5	-	0	2038				HNRNPAB_ENST00000514633.1_In_Frame_Del_p.K131del|PHYKPL_ENST00000481811.1_5'Flank|HNRNPAB_ENST00000506339.1_In_Frame_Del_p.K131del|HNRNPAB_ENST00000515193.1_In_Frame_Del_p.K131del|HNRNPAB_ENST00000506259.1_In_Frame_Del_p.K131del|HNRNPAB_ENST00000358344.3_In_Frame_Del_p.K131del|HNRNPAB_ENST00000355836.5_In_Frame_Del_p.K131del|HNRNPAB_ENST00000504898.1_In_Frame_Del_p.K131del	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GTCCTAGACCAGAAGGAGCACAG	0.522																																																0			5																																								177566351	SO:0001628	intergenic_variant	3182			BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892		5.37:g.177633743_177633745delAGA			177566349	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	In_Frame_Del	DEL	ENST00000308158.5	37	CCDS4434.1																																																																																				0.522	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		-	177633745	AGA	-	177633743	6	5	111	0	1	1	0	1	0	0	0	0	7282	188	7	0		0	HNRNPAB	5	177633743	IGR	DEL	AGA	TCGA-EI-6507-01A-11D-1733-10	747525	177633743	3281517	334	29468										
GRM6	2916	hgsc.bcm.edu	37	chr5	178413302	178413302	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccaggaagagcctgcgggcGgcacagaccgcggccccagg	16	16	0	2	rs62638620	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:178413302G>A	ENST00000517717.1	-	9	1991	c.1953C>T	c.(1951-1953)gcC>gcT	p.A651A	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.A651A			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	651					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		GCCTGCGGGCGGCACAGACCG	0.642													G|||	19	0.00379393	0.003	0.0086	5008	,	,		17274	0		0.0089	False		,,,				2504	0															0			5						G		10,4396	16.8+/-37.8	0,10,2193	39	41	40	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1953	-10	0	5	dbSNP_129	40	59,8539	36.4+/-91.3	0,59,4240	no	coding-synonymous	GRM6	NM_000843.3		0,69,6433	AA,AG,GG		0.6862,0.227,0.5306		651/878	178413302	69,12935	2203	4299	6502	178345908	SO:0001819	synonymous_variant	2916			U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1953C>T	5.37:g.178413302G>A			178345908		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																				0.642	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			A	178413302	G	A	178413302	2	1	111	1	0	0	0	0	0	0	0	1	6822	1103	39	1		1	GRM6	5	178413302	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	779559	178413302	2501958	335	29469										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178506725	178506725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcatcctttaatgaacatcGgaaaattcatactggggaaa	7	7	2	1	rs545360275		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:178506725G>A	ENST00000315475.6	+	5	1598	c.1292G>A	c.(1291-1293)cGg>cAg	p.R431Q		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	431					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		AATGAACATCGGAAAATTCAT	0.388																																																0			5											75	81	79					5																	178506725		2203	4300	6503	178439331	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1292G>A	5.37:g.178506725G>A	ENSP00000324064:p.Arg431Gln		178439331	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	G	3.175	-0.169108	0.06461	.	.	ENSG00000177932	ENST00000315475	T	0.17691	2.26	4.22	1.45	0.22620	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06508	0.0167	N	0.11106	0.095	0.28601	N	0.909138	B	0.18741	0.03	B	0.13407	0.009	T	0.40961	-0.9535	9	0.02654	T	1	-6.8972	5.8484	0.18679	0.4174:0.0:0.5826:0.0	.	431	Q86Y25	Z354C_HUMAN	Q	431	ENSP00000324064:R431Q	ENSP00000324064:R431Q	R	+	2	0	ZNF354C	178439331	0.002000	0.14202	0.902000	0.35471	0.945000	0.59286	1.153000	0.31676	0.531000	0.28639	0.591000	0.81541	CGG		0.388	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			A	178506725	G	A	178506725	3	1	111	1	0	0	0	0	1	0	0	0	17905	1116	39	1	1306	1	ZNF354C	5	178506725	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	93423	178506725	2408535	336	29470										
BTNL9	153579	hgsc.bcm.edu	37	chr5	180475111	180475111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccctggcaggcagatgccGgcgttccggaacaggaccaa	13	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:180475111G>A	ENST00000327705.9	+	3	525	c.294G>A	c.(292-294)ccG>ccA	p.P98P	BTNL9_ENST00000376842.3_Silent_p.P98P|BTNL9_ENST00000515271.1_Silent_p.P29P|BTNL9_ENST00000376841.2_Silent_p.P98P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	98	Ig-like V-type.					integral component of membrane (GO:0016021)		p.P98P(1)		breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	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)			GGCAGATGCCGGCGTTCCGGA	0.582																																																1	Substitution - coding silent(1)	central_nervous_system(1)	5											64	53	57					5																	180475111		2203	4300	6503	180407717	SO:0001819	synonymous_variant	153579			AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.294G>A	5.37:g.180475111G>A			180407717	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																				0.582	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		A	180475111	G	A	180475111	2	1	111	1	0	0	0	0	0	0	0	1	1571	1103	39	1		1	BTNL9	5	180475111	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1968386	180475111	440149	337	29471										
TRIM52	84851	hgsc.bcm.edu	37	chr5	180687262	180687262	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtaaagctctttcggcactGggggcaggtgaactgccctg	14	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr5:180687262G>A	ENST00000327767.4	-	1	857	c.553C>T	c.(553-555)Cag>Tag	p.Q185*	CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA|CTC-338M12.4_ENST00000511331.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|TRIM52-AS1_ENST00000507434.1_RNA|TRIM52_ENST00000514805.1_5'UTR	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	185					positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		TTTCGGCACTGGGGGCAGGTG	0.552																																																0			5											115	102	106					5																	180687262		2203	4300	6503	180619868	SO:0001587	stop_gained	84851				CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19024	protein-coding gene	gene with protein product			"tripartite motif-containing 52"				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.553C>T	5.37:g.180687262G>A	ENSP00000332152:p.Gln185*		180619868		Nonsense_Mutation	SNP	ENST00000327767.4	37	CCDS4467.1	.	.	.	.	.	.	.	.	.	.	g	38	7.065139	0.98040	.	.	ENSG00000183718	ENST00000327767	.	.	.	3.5	1.6	0.23607	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8539	0.24030	0.1089:0.1789:0.7121:0.0	.	.	.	.	X	185	.	.	Q	-	1	0	TRIM52	180619868	1.000000	0.71417	0.995000	0.50966	0.671000	0.39405	2.857000	0.48349	0.247000	0.21414	0.511000	0.50034	CAG		0.552	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765		A	180687262	G	A	180687262	4	1	111	1	0	0	0	0	0	1	0	0	16567	1357	47	3	348	3	TRIM52	5	180687262	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	212151	180687262	227998	338	29472										
GMDS	2762	hgsc.bcm.edu	37	chr6	1961101	1961101	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttgaggcttggtagaactTcacagagttgataaggccac	12	7	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:1961101T>A	ENST00000380815.4	-	5	714	c.445A>T	c.(445-447)Aag>Tag	p.K149*	GMDS_ENST00000530927.1_Nonsense_Mutation_p.K119*	NM_001500.3	NP_001491.1	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	149					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|GDP-mannose metabolic process (GO:0019673)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	GDP-mannose 4,6-dehydratase activity (GO:0008446)|NADP+ binding (GO:0070401)		GMDS/PDE8B(2)	breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|prostate(1)	21	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TGGTAGAACTTCACAGAGTTG	0.488																																																0			6											135	134	134					6																	1961101		2203	4300	6503	1906100	SO:0001587	stop_gained	2762			AF042377	CCDS4474.1, CCDS58994.1	6p25	2011-09-14			ENSG00000112699	ENSG00000112699	4.2.1.47	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	4369	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 3E, member 1"	602884				9525924, 19027726	Standard	NM_001500		Approved	GMD, SDR3E1	uc003mtq.3	O60547	OTTHUMG00000016143	ENST00000380815.4:c.445A>T	6.37:g.1961101T>A	ENSP00000370194:p.Lys149*		1906100	E9PI88|O75357|Q5T954|Q6FH09|Q9UGZ3|Q9UJK9	Nonsense_Mutation	SNP	ENST00000380815.4	37	CCDS4474.1	.	.	.	.	.	.	.	.	.	.	T	40	8.061346	0.98635	.	.	ENSG00000112699	ENST00000530927;ENST00000380815	.	.	.	5.26	4.08	0.47627	.	0.286229	0.32328	N	0.006241	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-15.1508	12.3047	0.54895	0.0:0.0:0.1417:0.8583	.	.	.	.	X	119;149	.	ENSP00000370194:K149X	K	-	1	0	GMDS	1906100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.892000	0.39748	0.823000	0.34589	0.533000	0.62120	AAG		0.488	GMDS-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043380.3			A	1961101	T	A	1961101	4	1	111	1	0	0	0	0	0	1	0	0	6506	1792	62	5	701	5	GMDS	6	1961101	Nonsense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10		1961101	169153966	339	29473										
C6orf145	221749	hgsc.bcm.edu	37	chr6	3727804	3727804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaatgctctgttgggtccaCgcccagctgctggtctcttc	10	14	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:3727804C>T	ENST00000380283.4	-	4	1053	c.559G>A	c.(559-561)Gtg>Atg	p.V187M	PXDC1_ENST00000477592.2_5'UTR	NM_183373.3	NP_899229.2	Q5TGL8	PXDC1_HUMAN	PX domain containing 1	187							phosphatidylinositol binding (GO:0035091)										GTTGGGTCCACGCCCAGCTGC	0.428																																																0			6											122	112	115					6																	3727804		2203	4300	6503	3672803	SO:0001583	missense	221749			AJ420534	CCDS4486.1	6p25.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000168994	ENSG00000168994			21361	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 145"	C6orf145			Standard	NM_183373		Approved		uc003mvt.2	Q5TGL8	OTTHUMG00000014146	ENST00000380283.4:c.559G>A	6.37:g.3727804C>T	ENSP00000369636:p.Val187Met		3672803	A8K0N3|Q6PGP0|Q86XB7	Missense_Mutation	SNP	ENST00000380283.4	37	CCDS4486.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.344329	0.41498	.	.	ENSG00000168994	ENST00000380283	T	0.35048	1.33	5.41	3.64	0.41730	.	0.360024	0.31772	N	0.007092	T	0.13286	0.0322	L	0.40543	1.245	0.25272	N	0.989502	B	0.12630	0.006	B	0.08055	0.003	T	0.19484	-1.0304	10	0.62326	D	0.03	-14.4166	10.4036	0.44243	0.1321:0.7959:0.0:0.0719	.	187	Q5TGL8	CF145_HUMAN	M	187	ENSP00000369636:V187M	ENSP00000369636:V187M	V	-	1	0	C6orf145	3672803	0.298000	0.24417	0.102000	0.21198	0.250000	0.25880	2.172000	0.42463	0.635000	0.30488	-0.205000	0.12727	GTG		0.428	PXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039688.1	NM_183373		T	3727804	C	T	3727804	3	4	111	1	0	0	0	0	1	0	0	0	2340	536	19	1	144	1	C6orf145	6	3727804	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1766703	3727804	167387263	340	29474										
NRN1	51299	hgsc.bcm.edu	37	chr6	6002607	6002607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcacacggtcttgatgttcGtcttgtcgtccaggccctgc	11	13	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:6002607G>A	ENST00000244766.2	-	2	396	c.179C>T	c.(178-180)aCg>aTg	p.T60M	NRN1_ENST00000495850.1_5'UTR	NM_001278710.1|NM_016588.2	NP_001265639.1|NP_057672.1	Q9NPD7	NRN1_HUMAN	neuritin 1	60					nervous system development (GO:0007399)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|anchored component of membrane (GO:0031225)|cell junction (GO:0030054)|synapse (GO:0045202)				endometrium(2)|large_intestine(2)|lung(4)	8	Ovarian(93;0.0816)	all_hematologic(90;0.151)		OV - Ovarian serous cystadenocarcinoma(45;0.00415)		CTTGATGTTCGTCTTGTCGTC	0.622																																																0			6											160	133	142					6																	6002607		2203	4300	6503	5947606	SO:0001583	missense	51299			AF136631	CCDS4495.1, CCDS75393.1	6p25.1	2008-02-05			ENSG00000124785	ENSG00000124785			17972	protein-coding gene	gene with protein product		607409				9122250	Standard	NM_016588		Approved	NRN	uc003mwu.3	Q9NPD7	OTTHUMG00000014184	ENST00000244766.2:c.179C>T	6.37:g.6002607G>A	ENSP00000244766:p.Thr60Met		5947606	B2RA93|Q7Z4Y1	Missense_Mutation	SNP	ENST00000244766.2	37	CCDS4495.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795126	0.31777	.	.	ENSG00000124785	ENST00000244766	.	.	.	4.24	3.35	0.38373	.	0.365932	0.28047	N	0.016803	T	0.09247	0.0228	N	0.08118	0	0.28989	N	0.888189	B	0.25390	0.125	B	0.16722	0.016	T	0.15838	-1.0423	9	0.42905	T	0.14	-12.1762	10.9187	0.47152	0.0:0.4041:0.5959:0.0	.	60	Q9NPD7	NRN1_HUMAN	M	60	.	ENSP00000244766:T60M	T	-	2	0	NRN1	5947606	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.123000	0.57917	0.967000	0.38186	0.462000	0.41574	ACG		0.622	NRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039753.1			A	6002607	G	A	6002607	3	1	111	1	0	0	0	0	1	0	0	0	10689	1145	40	1	257	1	NRN1	6	6002607	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2274803	6002607	165112460	341	29475										
NRN1	51299	hgsc.bcm.edu	37	chr6	6002686	6002686	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtccgaaaagcccttgaagaCcgcatcgcacttgcccgctg	10	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:6002686C>A	ENST00000244766.2	-	2	317	c.100G>T	c.(100-102)Gtc>Ttc	p.V34F	NRN1_ENST00000495850.1_5'UTR	NM_001278710.1|NM_016588.2	NP_001265639.1|NP_057672.1	Q9NPD7	NRN1_HUMAN	neuritin 1	34					nervous system development (GO:0007399)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|anchored component of membrane (GO:0031225)|cell junction (GO:0030054)|synapse (GO:0045202)				endometrium(2)|large_intestine(2)|lung(4)	8	Ovarian(93;0.0816)	all_hematologic(90;0.151)		OV - Ovarian serous cystadenocarcinoma(45;0.00415)		CCCTTGAAGACCGCATCGCAC	0.647																																																0			6											135	113	121					6																	6002686		2203	4300	6503	5947685	SO:0001583	missense	51299			AF136631	CCDS4495.1, CCDS75393.1	6p25.1	2008-02-05			ENSG00000124785	ENSG00000124785			17972	protein-coding gene	gene with protein product		607409				9122250	Standard	NM_016588		Approved	NRN	uc003mwu.3	Q9NPD7	OTTHUMG00000014184	ENST00000244766.2:c.100G>T	6.37:g.6002686C>A	ENSP00000244766:p.Val34Phe		5947685	B2RA93|Q7Z4Y1	Missense_Mutation	SNP	ENST00000244766.2	37	CCDS4495.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518947	0.85495	.	.	ENSG00000124785	ENST00000244766	.	.	.	4.24	4.24	0.50183	.	0.076848	0.51477	D	0.000090	T	0.61937	0.2387	L	0.53249	1.67	0.54753	D	0.999985	D	0.65815	0.995	D	0.63877	0.919	T	0.66760	-0.5842	9	0.72032	D	0.01	-13.1752	13.9329	0.64007	0.0:1.0:0.0:0.0	.	34	Q9NPD7	NRN1_HUMAN	F	34	.	ENSP00000244766:V34F	V	-	1	0	NRN1	5947685	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.429000	0.73387	2.185000	0.69588	0.462000	0.41574	GTC		0.647	NRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039753.1			A	6002686	C	A	6002686	3	1	111	1	0	0	0	0	1	0	0	0	10689	507	18	2	336	2	NRN1	6	6002686	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	79	6002686	165112381	342	29476										
BMP6	654	hgsc.bcm.edu	37	chr6	7862555	7862555	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtccacgtccacccccgagCcgcaggcctggtgggcagag	14	16	0	1	rs150526011	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:7862555C>A	ENST00000283147.6	+	4	1187	c.1028C>A	c.(1027-1029)gCc>gAc	p.A343D		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	343			A -> D (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)	p.A343D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					CACCCCCGAGCCGCAGGCCTG	0.532																																																1	Substitution - Missense(1)	large_intestine(1)	6											83	91	88					6																	7862555		2203	4300	6503	7807554	SO:0001583	missense	654			AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"Bone morphogenetic proteins", "Endogenous ligands"	1073	protein-coding gene	gene with protein product		112266	"vegetal related growth factor (TGFB-related)"	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1028C>A	6.37:g.7862555C>A	ENSP00000283147:p.Ala343Asp		7807554	Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	37	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	C	2.638	-0.284899	0.05605	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	T	0.65178	-0.14	5.8	4.93	0.64822	Transforming growth factor-beta, N-terminal (1);	0.178088	0.49305	D	0.000154	T	0.24699	0.0599	N	0.24115	0.695	0.46011	D	0.998811	B	0.14012	0.009	B	0.15052	0.012	T	0.13335	-1.0513	10	0.11794	T	0.64	.	9.6259	0.39750	0.1736:0.752:0.0:0.0744	.	343	P22004	BMP6_HUMAN	D	265;343;306	ENSP00000283147:A343D	ENSP00000283147:A343D	A	+	2	0	BMP6	7807554	0.963000	0.33076	0.172000	0.22920	0.197000	0.23852	2.322000	0.43814	1.451000	0.47736	0.655000	0.94253	GCC		0.532	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718		A	7862555	C	A	7862555	3	1	111	1	0	0	0	0	1	0	0	0	1465	739	26	2	1042	2	BMP6	6	7862555	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1859869	7862555	163252512	343	29477										
GCM2	9247	hgsc.bcm.edu	37	chr6	10874878	10874878	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actggtggaatccttataaaGggtgggatatgggcttgaat	14	4	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:10874878G>T	ENST00000379491.4	-	5	1018	c.871C>A	c.(871-873)Ctt>Att	p.L291I	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	291					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.L291V(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				TCCTTATAAAGGGTGGGATAT	0.423																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											203	196	199					6																	10874878		2203	4300	6503	10982864	SO:0001583	missense	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.871C>A	6.37:g.10874878G>T	ENSP00000368805:p.Leu291Ile		10982864	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	G	9.569	1.120637	0.20877	.	.	ENSG00000124827	ENST00000379491	T	0.70399	-0.48	5.5	3.71	0.42584	.	0.537761	0.19969	N	0.102035	T	0.55305	0.1912	M	0.73962	2.25	0.47441	D	0.999421	P	0.42456	0.78	B	0.38106	0.265	T	0.60747	-0.7202	10	0.66056	D	0.02	-15.1929	9.1306	0.36843	0.2809:0.0:0.7191:0.0	.	291	O75603	GCM2_HUMAN	I	291	ENSP00000368805:L291I	ENSP00000368805:L291I	L	-	1	0	GCM2	10982864	0.814000	0.29104	0.031000	0.17742	0.207000	0.24258	0.734000	0.26101	0.788000	0.33755	0.650000	0.86243	CTT		0.423	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			T	10874878	G	T	10874878	3	4	111	1	0	0	0	0	1	0	0	0	6318	1000	35	2	653	2	GCM2	6	10874878	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3012323	10874878	160240189	344	29478										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327163	16327163	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctcaggtagccgatgacaGggggttgagtccctgcgtag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:16327163delG	ENST00000244769.4	-	8	2315	c.1379delC	c.(1378-1380)cctfs	p.P460fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P460fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	460					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GCCGATGACAGGGGGTTGAGT	0.657																																																0			6											90	97	95					6																	16327163		2203	4300	6503	16435142	SO:0001589	frameshift_variant	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1379delC	6.37:g.16327163delG	ENSP00000244769:p.Pro460fs		16435142	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	37	CCDS34342.1																																																																																				0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		-	16327163	G	-	16327163	7	5	111	1	0	1	0	1	0	0	0	0	1210	1000	35	0	1076	0	ATXN1	6	16327163	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	5452285	16327163	154787904	345	29479										
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775621	27775621	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttgccatccttcttctgggCcttggtcaccgccttcttgg	9	15	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:27775621C>A	ENST00000377401.2	-	1	88	c.64G>T	c.(64-66)Gcc>Tcc	p.A22S	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	22					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						TTCTTCTGGGCCTTGGTCACC	0.572																																																0			6											130	127	128					6																	27775621		2203	4300	6503	27883600	SO:0001583	missense	8340			Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"Histones / Replication-dependent"	4748	protein-coding gene	gene with protein product		602800	"H2B histone family, member C", "histone 1, H2bl"	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.64G>T	6.37:g.27775621C>A	ENSP00000366618:p.Ala22Ser		27883600	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	.	.	.	.	.	.	.	.	.	.	.	12.12	1.843577	0.32606	.	.	ENSG00000185130	ENST00000377401	T	0.20069	2.1	4.35	4.35	0.52113	Histone-fold (2);	.	.	.	.	T	0.10121	0.0248	M	0.67953	2.075	0.29830	N	0.830072	B	0.30851	0.297	B	0.24701	0.055	T	0.10019	-1.0648	9	0.59425	D	0.04	.	6.9145	0.24352	0.0:0.7967:0.0:0.2033	.	22	Q99880	H2B1L_HUMAN	S	22	ENSP00000366618:A22S	ENSP00000366618:A22S	A	-	1	0	HIST1H2BL	27883600	1.000000	0.71417	0.992000	0.48379	0.087000	0.18053	1.334000	0.33827	2.331000	0.79229	0.650000	0.86243	GCC		0.572	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		A	27775621	C	A	27775621	3	1	111	1	0	0	0	0	1	0	0	0	7172	739	26	2	320	2	HIST1H2BL	6	27775621	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	11448458	27775621	143339446	346	29480										
HIST1H2BM	8342	hgsc.bcm.edu	37	chr6	27783059	27783059	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtatcgccggagaagcgtcaCgcctggcgcattacaacaag	12	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:27783059C>T	ENST00000359465.4	+	1	238	c.238C>T	c.(238-240)Cgc>Tgc	p.R80C	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	80					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						AGAAGCGTCACGCCTGGCGCA	0.592																																																0			6											114	105	108					6																	27783059		2203	4300	6503	27891038	SO:0001583	missense	8342			Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"Histones / Replication-dependent"	4750	protein-coding gene	gene with protein product		602802	"H2B histone family, member E", "histone 1, H2bm"	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.238C>T	6.37:g.27783059C>T	ENSP00000352442:p.Arg80Cys		27891038	Q6NWQ3	Missense_Mutation	SNP	ENST00000359465.4	37	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	12.74	2.027612	0.35797	.	.	ENSG00000196374	ENST00000359465	T	0.32753	1.44	4.17	4.17	0.49024	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000013	T	0.32912	0.0845	M	0.92367	3.3	0.80722	D	1	B	0.25169	0.119	B	0.19666	0.026	T	0.47328	-0.9126	10	0.49607	T	0.09	.	15.9934	0.80223	0.0:1.0:0.0:0.0	.	80	Q99879	H2B1M_HUMAN	C	80	ENSP00000352442:R80C	ENSP00000352442:R80C	R	+	1	0	HIST1H2BM	27891038	1.000000	0.71417	0.953000	0.39169	0.535000	0.34838	5.377000	0.66184	2.308000	0.77769	0.563000	0.77884	CGC		0.592	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		T	27783059	C	T	27783059	3	4	111	1	0	0	0	0	1	0	0	0	7173	536	19	1	240	1	HIST1H2BM	6	27783059	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7438	27783059	143332008	347	29481										
EGFL8	80864	hgsc.bcm.edu	37	chr6	32134573	32134573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaagaagcggcacccgggggCgctcacctgtgaaggtgagg	18	10	1	3	rs371176366		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:32134573C>T	ENST00000395512.1	+	4	425	c.320C>T	c.(319-321)gCg>gTg	p.A107V	EGFL8_ENST00000333845.6_Missense_Mutation_p.A107V|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000490711.1_5'Flank			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	107	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						CACCCGGGGGCGCTCACCTGT	0.667																																																0			6						C	VAL/ALA	0,4406		0,0,2203	30	36	34		320	5.2	1	6		34	1,8599	1.2+/-3.3	0,1,4299	no	missense	EGFL8	NM_030652.3	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	107/294	32134573	1,13005	2203	4300	6503	32242551	SO:0001583	missense	80864			U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"chromosome 6 open reading frame 8"	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.320C>T	6.37:g.32134573C>T	ENSP00000378888:p.Ala107Val		32242551	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	37	CCDS4743.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.417883	0.83449	0.0	1.16E-4	ENSG00000241404	ENST00000333845;ENST00000395512;ENST00000432129	D;D;T	0.89810	-2.57;-2.57;2.09	6.08	5.21	0.72293	EMI domain (1);	.	.	.	.	D	0.87947	0.6306	L	0.60455	1.87	0.32719	N	0.51057	D	0.76494	0.999	P	0.60415	0.874	D	0.85539	0.1214	9	0.30854	T	0.27	-12.1407	11.3236	0.49436	0.0:0.9172:0.0:0.0828	.	107	Q99944	EGFL8_HUMAN	V	107	ENSP00000333380:A107V;ENSP00000378888:A107V;ENSP00000401694:A107V	ENSP00000333380:A107V	A	+	2	0	EGFL8	32242551	0.867000	0.29959	0.992000	0.48379	0.966000	0.64601	1.447000	0.35101	1.595000	0.50050	-0.136000	0.14681	GCG		0.667	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652		T	32134573	C	T	32134573	3	4	111	1	0	0	0	0	1	0	0	0	4976	768	27	1	330	1	EGFL8	6	32134573	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4351514	32134573	138980494	348	29482										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33658852	33658852	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaaggatgacttcattctCgaggtcgaccggctgcccaa	10	13	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:33658852C>T	ENST00000374316.5	+	53	8251	c.7191C>T	c.(7189-7191)ctC>ctT	p.L2397L	ITPR3_ENST00000605930.1_Silent_p.L2397L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2397					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACTTCATTCTCGAGGTCGACC	0.587																																																0			6											119	111	114					6																	33658852		2203	4300	6503	33766830	SO:0001819	synonymous_variant	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7191C>T	6.37:g.33658852C>T			33766830	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																				0.587	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33658852	C	T	33658852	2	4	111	1	0	0	0	0	0	0	0	1	7943	871	31	1		1	ITPR3	6	33658852	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1524279	33658852	137456215	349	29483										
MAPK14	1432	hgsc.bcm.edu	37	chr6	36020512	36020512	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaacggggttacgtgtggcAgtgaagaagctctccagacc	13	9	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:36020512A>G	ENST00000229794.4	+	2	541	c.153A>G	c.(151-153)gcA>gcG	p.A51A	MAPK14_ENST00000468133.1_5'UTR|MAPK14_ENST00000229795.3_Silent_p.A51A|MAPK14_ENST00000310795.4_Silent_p.A51A	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> V (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						TACGTGTGGCAGTGAAGAAGC	0.378																																					Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)											0			6											122	119	120					6																	36020512		2203	4300	6503	36128490	SO:0001819	synonymous_variant	1432			L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.153A>G	6.37:g.36020512A>G			36128490	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Silent	SNP	ENST00000229794.4	37	CCDS4816.1																																																																																				0.378	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		G	36020512	A	G	36020512	2	3	111	1	0	0	0	0	0	0	0	1	9306	175	7	4		4	MAPK14	6	36020512	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2361660	36020512	135094555	350	29484										
UNC5CL	222643	hgsc.bcm.edu	37	chr6	41002498	41002498	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccgcggtgatccacctctcGagccgaaaacaccaacagtt	9	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:41002498G>A	ENST00000373164.1	-	1	376	c.316C>T	c.(316-318)Cga>Tga	p.R106*	UNC5CL_ENST00000470102.1_5'Flank|UNC5CL_ENST00000244565.3_Nonsense_Mutation_p.R106*			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	106	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCCACCTCTCGAGCCGAAAAC	0.567																																																0			6											181	159	167					6																	41002498		2203	4300	6503	41110476	SO:0001587	stop_gained	222643			BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.316C>T	6.37:g.41002498G>A	ENSP00000362258:p.Arg106*		41110476	Q5TGU1	Nonsense_Mutation	SNP	ENST00000373164.1	37	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300471	0.95601	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	.	.	.	4.66	3.78	0.43462	.	0.197821	0.25768	N	0.028440	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-5.0956	9.9892	0.41860	0.0:0.0:0.7979:0.2021	.	.	.	.	X	106	.	ENSP00000244565:R106X	R	-	1	2	UNC5CL	41110476	0.080000	0.21391	0.989000	0.46669	0.919000	0.55068	0.913000	0.28611	1.177000	0.42855	0.563000	0.77884	CGA		0.567	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		A	41002498	G	A	41002498	4	1	111	1	0	0	0	0	0	1	0	0	17034	1066	37	1	1272	1	UNC5CL	6	41002498	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4981986	41002498	130112569	351	29485										
RUNX2	860	hgsc.bcm.edu	37	chr6	45514707	45514707	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcacctcaggcatgtccctcGgtatgtccgccaccactcac	7	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:45514707G>A	ENST00000371438.1	+	8	1589	c.1231G>A	c.(1231-1233)Ggt>Agt	p.G411S	RUNX2_ENST00000576263.1_Intron|RUNX2_ENST00000352853.5_Missense_Mutation_p.G479S|RUNX2_ENST00000371436.6_Missense_Mutation_p.G389S|RUNX2_ENST00000541979.1_Missense_Mutation_p.G457S|RUNX2_ENST00000465038.2_Missense_Mutation_p.G411S|RUNX2_ENST00000371432.3_Missense_Mutation_p.G375S|RUNX2_ENST00000359524.5_Missense_Mutation_p.G397S	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	411	Interaction with KAT6A. {ECO:0000250}.|Interaction with KAT6B.|Pro/Ser/Thr-rich.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G411S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CATGTCCCTCGGTATGTCCGC	0.577																																																1	Substitution - Missense(1)	ovary(1)	6											147	116	126					6																	45514707		2203	4300	6503	45622685	SO:0001583	missense	860			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.1231G>A	6.37:g.45514707G>A	ENSP00000360493:p.Gly411Ser		45622685	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.109934	0.77210	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	D;D;D;D;D;D;D	0.97328	-4.29;-4.34;-4.26;-4.29;-4.25;-4.3;-4.27	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.96781	0.8949	L	0.41710	1.295	0.80722	D	1	D;D;D	0.76494	0.986;0.998;0.999	P;P;P	0.62560	0.555;0.762;0.904	D	0.95328	0.8427	10	0.31617	T	0.26	-6.6236	19.922	0.97089	0.0:0.0:1.0:0.0	.	457;411;397	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	S	411;479;457;411;389;397;375	ENSP00000420707:G411S;ENSP00000319087:G479S;ENSP00000446290:G457S;ENSP00000360493:G411S;ENSP00000360491:G389S;ENSP00000352514:G397S;ENSP00000360486:G375S	ENSP00000319087:G479S	G	+	1	0	RUNX2	45622685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.780000	0.95670	0.655000	0.94253	GGT		0.577	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		A	45514707	G	A	45514707	3	1	111	1	0	0	0	0	1	0	0	0	13785	1116	39	1	1277	1	RUNX2	6	45514707	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4512209	45514707	125600360	352	29486										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72596775	72596775	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcgcccacccacggtgcctCcccccatgcaagagctgccc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:72596775delC	ENST00000521978.1	+	1	49	c.49delC	c.(49-51)cccfs	p.P18fs	RIMS1_ENST00000520567.1_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000517960.1_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000264839.7_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000522291.1_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000518273.1_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000491071.2_Frame_Shift_Del_p.P18fs|RIMS1_ENST00000348717.5_Frame_Shift_Del_p.P18fs	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	18					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.M19fs*7(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CACGGTGCCTCCCCCCATGCA	0.637																																																1	Deletion - Frameshift(1)	large_intestine(1)	6											28	34	32					6																	72596775		2033	4171	6204	72653496	SO:0001589	frameshift_variant	22999			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.49delC	6.37:g.72596775delC	ENSP00000428417:p.Pro18fs		72653496	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Frame_Shift_Del	DEL	ENST00000521978.1	37	CCDS47449.1																																																																																				0.637	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			-	72596775	C	-	72596775	7	5	111	1	0	1	0	1	0	0	0	0	13404	855	30	0	51	0	RIMS1	6	72596775	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	27082068	72596775	98518292	353	29487										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75890797	75890797	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctggctccaccacagtgacCtcatcatccccagccgcttc	7	19	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:75890797C>T	ENST00000322507.8	-	11	2331	c.2022G>A	c.(2020-2022)gaG>gaA	p.E674E	COL12A1_ENST00000416123.2_Silent_p.E674E|COL12A1_ENST00000483888.2_Silent_p.E674E|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	674	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCACAGTGACCTCATCATCCC	0.483																																																0			6											95	97	97					6																	75890797		2001	4188	6189	75947517	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2022G>A	6.37:g.75890797C>T			75947517	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																				0.483	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75890797	C	T	75890797	2	4	111	1	0	0	0	0	0	0	0	1	3675	680	24	3		3	COL12A1	6	75890797	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3294022	75890797	95224270	354	29488										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76022694	76022694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggtgatggaataatggttaTtcttggtttctgattcccta	10	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:76022694T>C	ENST00000237172.7	-	5	3184	c.2854A>G	c.(2854-2856)Ata>Gta	p.I952V	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000393004.2_Missense_Mutation_p.I952V|FILIP1_ENST00000370020.1_Missense_Mutation_p.I853V	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	952										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						ATAATGGTTATTCTTGGTTTC	0.423																																																0			6											153	151	152					6																	76022694		2203	4300	6503	76079414	SO:0001583	missense	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2854A>G	6.37:g.76022694T>C	ENSP00000237172:p.Ile952Val		76079414	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.442735	0.83993	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.25579	1.79;1.79;1.79	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.39733	0.1089	M	0.65975	2.015	0.80722	D	1	D;D;D	0.71674	0.991;0.996;0.998	P;D;D	0.75020	0.82;0.966;0.985	T	0.10109	-1.0644	10	0.33141	T	0.24	-28.2046	16.5582	0.84512	0.0:0.0:0.0:1.0	.	952;952;952	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	V	952;952;853	ENSP00000376728:I952V;ENSP00000237172:I952V;ENSP00000359037:I853V	ENSP00000237172:I952V	I	-	1	0	FILIP1	76079414	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.768000	0.85345	2.308000	0.77769	0.533000	0.62120	ATA		0.423	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		C	76022694	T	C	76022694	3	2	111	1	0	0	0	0	1	0	0	0	5913	1493	52	4	795	4	FILIP1	6	76022694	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	131897	76022694	95092373	355	29489										
PGM3	5238	hgsc.bcm.edu	37	chr6	83892563	83892563	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catgttcaataaacttttcaCctgtttggtgagttccacaa	6	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:83892563C>T	ENST00000283977.4	-	4	475		c.e4+1		PGM3_ENST00000513973.1_Splice_Site|PGM3_ENST00000506587.1_Splice_Site|PGM3_ENST00000512866.1_Splice_Site					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		AAACTTTTCACCTGTTTGGTG	0.378																																																0			6											108	108	108					6																	83892563		2203	4300	6503	83949282	SO:0001630	splice_region_variant	5238			BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"acetylglucosamine phosphomutase"	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.348+1G>A	6.37:g.83892563C>T			83949282		Splice_Site	SNP	ENST00000283977.4	37		.	.	.	.	.	.	.	.	.	.	C	25.0	4.597524	0.87055	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000510258	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6376	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PGM3	83949282	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	7.419000	0.80179	2.647000	0.89833	0.557000	0.71058	.		0.378	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599	Intron	T	83892563	C	T	83892563	5	4	111	1	0	0	0	0	0	0	1	0	11831	521	18	3	1072	3	PGM3	6	83892563	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7869869	83892563	87222504	356	29490										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87967280	87967280	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actaattcctcctttctaaaGgggggtaatggtgaaaatgc					rs571636248		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:87967280delG	ENST00000369577.3	+	8	3976	c.3933delG	c.(3931-3933)aagfs	p.K1311fs	ZNF292_ENST00000339907.4_Frame_Shift_Del_p.K1306fs	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1311						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CCTTTCTAAAGGGGGGTAATG	0.373																																																0			6											28	27	28					6																	87967280		1846	4091	5937	88023999	SO:0001589	frameshift_variant	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.3933delG	6.37:g.87967280delG	ENSP00000358590:p.Lys1311fs		88023999	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Frame_Shift_Del	DEL	ENST00000369577.3	37	CCDS47457.1																																																																																				0.373	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		-	87967280	G	-	87967280	7	5	111	1	0	1	0	1	0	0	0	0	17865	991	35	0	3963	0	ZNF292	6	87967280	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	4074717	87967280	83147787	357	29491										
AKIRIN2	55122	hgsc.bcm.edu	37	chr6	88385637	88385637	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catgcgtaaacttcacaaacGcatcatattgttctataaat	4	9	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:88385637G>A	ENST00000257787.5	-	4	1066	c.542C>T	c.(541-543)gCg>gTg	p.A181V		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	181					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)			large_intestine(4)	4						CTTCACAAACGCATCATATTG	0.313																																																0			6											78	75	76					6																	88385637		2203	4299	6502	88442356	SO:0001583	missense	55122			BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"chromosome 6 open reading frame 166"	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.542C>T	6.37:g.88385637G>A	ENSP00000257787:p.Ala181Val		88442356	Q9BQB1	Missense_Mutation	SNP	ENST00000257787.5	37	CCDS5013.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997557	0.74818	.	.	ENSG00000135334	ENST00000257787	.	.	.	5.77	5.77	0.91146	.	0.046361	0.85682	D	0.000000	T	0.43545	0.1252	L	0.58428	1.81	0.80722	D	1	P	0.47034	0.889	B	0.36922	0.236	T	0.43556	-0.9384	9	0.29301	T	0.29	-10.9035	20.3473	0.98799	0.0:0.0:1.0:0.0	.	181	Q53H80	AKIR2_HUMAN	V	181	.	ENSP00000257787:A181V	A	-	2	0	AKIRIN2	88442356	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.420000	0.97426	2.884000	0.98904	0.655000	0.94253	GCG		0.313	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064		A	88385637	G	A	88385637	3	1	111	1	0	0	0	0	1	0	0	0	462	1087	38	1	77	1	AKIRIN2	6	88385637	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	418357	88385637	82729430	358	29492										
RRAGD	58528	hgsc.bcm.edu	37	chr6	90097037	90097037	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgagtcaatgacaaatatcaGtgctcctgttccccggaaga	9	10	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:90097037G>A	ENST00000369415.4	-	2	697	c.421C>T	c.(421-423)Ctg>Ttg	p.L141L	RRAGD_ENST00000359203.3_Intron|RRAGD_ENST00000492783.1_5'UTR	NM_021244.4	NP_067067.1			Ras-related GTP binding D											breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(2)	15		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)		ACAAATATCAGTGCTCCTGTT	0.473																																																0			6											109	104	106					6																	90097037		2203	4300	6503	90153756	SO:0001819	synonymous_variant	58528			AF272036	CCDS5022.1	6q15-q16	2008-02-05			ENSG00000025039	ENSG00000025039			19903	protein-coding gene	gene with protein product		608268				11073942	Standard	NM_021244		Approved	DKFZP761H171, bA11D8.2.1	uc003pnd.4	Q9NQL2	OTTHUMG00000015200	ENST00000369415.4:c.421C>T	6.37:g.90097037G>A			90153756		Silent	SNP	ENST00000369415.4	37	CCDS5022.1																																																																																				0.473	RRAGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041484.1	NM_021244		A	90097037	G	A	90097037	2	1	111	1	0	0	0	0	0	0	0	1	13712	1020	36	3		3	RRAGD	6	90097037	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1711400	90097037	81018030	359	29493										
GJA10	84694	hgsc.bcm.edu	37	chr6	90604469	90604469	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccttctttggtctatatgggCcatgcactttataggctcag	9	10	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:90604469C>T	ENST00000369352.1	+	1	282	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	94					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		TCTATATGGGCCATGCACTTT	0.443																																																0			6											102	88	93					6																	90604469		2203	4300	6503	90661190	SO:0001819	synonymous_variant	84694			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.282C>T	6.37:g.90604469C>T			90661190	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000369352.1	37	CCDS5025.1																																																																																				0.443	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90604469	C	T	90604469	2	4	111	1	0	0	0	0	0	0	0	1	6421	726	26	3		3	GJA10	6	90604469	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	507432	90604469	80510598	360	29494										
MANEA	79694	hgsc.bcm.edu	37	chr6	96053716	96053716	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgattcctatattaccaagcCtgaaaaatgggccaatctgt	7	9	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:96053716C>A	ENST00000358812.4	+	5	958	c.824C>A	c.(823-825)cCt>cAt	p.P275H	MANEA_ENST00000474553.1_3'UTR	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	275	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		ATTACCAAGCCTGAAAAATGG	0.403																																																0			6											116	112	113					6																	96053716		2203	4300	6503	96160437	SO:0001583	missense	79694			AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.824C>A	6.37:g.96053716C>A	ENSP00000351669:p.Pro275His		96160437	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	37	CCDS5032.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.349973	0.61183	.	.	ENSG00000172469	ENST00000358812	D	0.91996	-2.95	6.16	5.3	0.74995	.	0.148484	0.64402	D	0.000007	D	0.94896	0.8350	M	0.83953	2.67	0.54753	D	0.999985	D	0.61697	0.99	P	0.60473	0.875	D	0.95019	0.8159	10	0.54805	T	0.06	-9.3726	16.9401	0.86215	0.0:0.8724:0.1276:0.0	.	275	Q5SRI9	MANEA_HUMAN	H	275	ENSP00000351669:P275H	ENSP00000351669:P275H	P	+	2	0	MANEA	96160437	1.000000	0.71417	0.921000	0.36526	0.506000	0.33950	5.700000	0.68318	1.635000	0.50512	-0.133000	0.14855	CCT		0.403	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		A	96053716	C	A	96053716	3	1	111	1	0	0	0	0	1	0	0	0	9251	681	24	2	838	2	MANEA	6	96053716	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5449247	96053716	75061351	361	29495										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97562260	97562260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgggggcagaaatgaactgcGccaggttctgcctacagttg	14	9	1	2	rs150244885		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:97562260G>A	ENST00000369261.4	+	7	1592	c.1229G>A	c.(1228-1230)cGc>cAc	p.R410H	KLHL32_ENST00000536676.1_Missense_Mutation_p.R374H|KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Missense_Mutation_p.R341H	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	410										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		AATGAACTGCGCCAGGTTCTG	0.498																																																0			6						G	HIS/ARG	0,4406		0,0,2203	66	58	61		1229	5.7	1	6	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLHL32	NM_052904.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	410/621	97562260	1,13005	2203	4300	6503	97668981	SO:0001583	missense	114792			AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1229G>A	6.37:g.97562260G>A	ENSP00000358265:p.Arg410His		97668981	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569826	0.86439	0.0	1.16E-4	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.77229	-1.08;-1.08;-1.08	5.65	5.65	0.86999	Kelch-type beta propeller (1);	0.044535	0.85682	D	0.000000	T	0.79890	0.4524	L	0.31926	0.97	0.80722	D	1	D;D;B;D	0.89917	1.0;0.972;0.003;0.998	D;P;B;P	0.65874	0.939;0.786;0.01;0.896	T	0.79167	-0.1915	10	0.51188	T	0.08	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	341;374;410;410	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	H	410;374;341	ENSP00000358265:R410H;ENSP00000440382:R374H;ENSP00000441527:R341H	ENSP00000358265:R410H	R	+	2	0	KLHL32	97668981	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	9.229000	0.95273	2.941000	0.99782	0.655000	0.94253	CGC		0.498	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		A	97562260	G	A	97562260	3	1	111	1	0	0	0	0	1	0	0	0	8407	1087	38	1	1251	1	KLHL32	6	97562260	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1508544	97562260	73552807	362	29496										
SIM1	6492	hgsc.bcm.edu	37	chr6	100838725	100838725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgttggtagtttgcaaaacAcagggagtgttttttcccag	11	7	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:100838725A>G	ENST00000369208.3	-	12	2595	c.1813T>C	c.(1813-1815)Tgt>Cgt	p.C605R	SIM1_ENST00000262901.4_Missense_Mutation_p.C605R			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	605	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.C605S(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		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)		TTTGCAAAACACAGGGAGTGT	0.488																																																1	Substitution - Missense(1)	ovary(1)	6											78	80	79					6																	100838725		2203	4300	6503	100945446	SO:0001583	missense	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1813T>C	6.37:g.100838725A>G	ENSP00000358210:p.Cys605Arg		100945446	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.555142	0.45487	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.03831	3.79;3.79	5.82	5.82	0.92795	Single-minded, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.01940	0.0061	N	0.19112	0.55	0.80722	D	1	P	0.34412	0.453	B	0.30316	0.114	T	0.53739	-0.8396	10	0.59425	D	0.04	.	16.1986	0.82053	1.0:0.0:0.0:0.0	.	605	P81133	SIM1_HUMAN	R	605	ENSP00000358210:C605R;ENSP00000262901:C605R	ENSP00000262901:C605R	C	-	1	0	SIM1	100945446	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.912000	0.63335	2.227000	0.72691	0.455000	0.32223	TGT		0.488	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		G	100838725	A	G	100838725	3	3	111	1	0	0	0	0	1	0	0	0	14360	159	6	4	491	4	SIM1	6	100838725	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3276465	100838725	70276342	363	29497										
WASF1	8936	hgsc.bcm.edu	37	chr6	110423411	110423411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcgattttctatcaaacctGtagcagaactgaaatgacaa	8	8	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:110423411G>A	ENST00000392589.1	-	10	1738	c.902C>T	c.(901-903)aCa>aTa	p.T301I	WASF1_ENST00000392586.1_Missense_Mutation_p.T301I|WASF1_ENST00000392588.1_Missense_Mutation_p.T301I|WASF1_ENST00000392587.2_Missense_Mutation_p.T301I|WASF1_ENST00000359451.2_Missense_Mutation_p.T301I	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	301					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		TATCAAACCTGTAGCAGAACT	0.433																																																0			6											103	99	101					6																	110423411		2203	4300	6503	110530104	SO:0001583	missense	8936			D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.902C>T	6.37:g.110423411G>A	ENSP00000376368:p.Thr301Ile		110530104	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790423	0.70337	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.64	5.64	0.86602	.	0.305475	0.35407	N	0.003228	T	0.18425	0.0442	N	0.14661	0.345	0.43647	D	0.996056	B	0.14438	0.01	B	0.12156	0.007	T	0.03000	-1.1084	10	0.37606	T	0.19	.	19.7561	0.96291	0.0:0.0:1.0:0.0	.	301	Q92558	WASF1_HUMAN	I	301	ENSP00000376365:T301I;ENSP00000376366:T301I;ENSP00000376368:T301I;ENSP00000376367:T301I;ENSP00000352425:T301I	ENSP00000352425:T301I	T	-	2	0	WASF1	110530104	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.154000	0.94694	2.672000	0.90937	0.539000	0.68188	ACA		0.433	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		A	110423411	G	A	110423411	3	1	111	1	0	0	0	0	1	0	0	0	17292	1377	48	3	785	3	WASF1	6	110423411	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	9584686	110423411	60691656	364	29498										
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114379277	114379277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcagcaggccacgcttaaacTgcagggcgcgaagtgggaat	15	10	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:114379277T>C	ENST00000312719.5	-	5	1373	c.185A>G	c.(184-186)cAg>cGg	p.Q62R	RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.Q62R|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000523087.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	62					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		ACGCTTAAACTGCAGGGCGCG	0.587																																																0			6											38	35	36					6																	114379277		2203	4300	6503	114485970	SO:0001583	missense	222537			AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.185A>G	6.37:g.114379277T>C	ENSP00000427888:p.Gln62Arg		114485970	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	37	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927431	0.34002	.	.	ENSG00000249853	ENST00000312719;ENST00000411826	T;T	0.46451	0.87;0.87	5.77	5.77	0.91146	.	0.115717	0.64402	D	0.000012	T	0.32255	0.0823	N	0.19112	0.55	0.52501	D	0.999958	P	0.39094	0.659	P	0.55391	0.775	T	0.17899	-1.0354	10	0.15499	T	0.54	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	62	Q8IZT8	HS3S5_HUMAN	R	62	ENSP00000427888:Q62R;ENSP00000440332:Q62R	ENSP00000427888:Q62R	Q	-	2	0	HS3ST5	114485970	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	7.231000	0.78106	2.326000	0.78906	0.533000	0.62120	CAG		0.587	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		C	114379277	T	C	114379277	3	2	111	1	0	0	0	0	1	0	0	0	7389	1580	55	4	859	4	HS3ST5	6	114379277	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3955866	114379277	56735790	365	29499										
GOPC	57120	hgsc.bcm.edu	37	chr6	117884480	117884480	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgaagcaccgtcatctagCggagtttcacttgcagtgcc	10	11	3	1	rs146035577		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:117884480C>T	ENST00000368498.2	-	9	1401	c.1326G>A	c.(1324-1326)ccG>ccA	p.P442P	GOPC_ENST00000535237.1_Silent_p.P442P|GOPC_ENST00000467125.1_Intron|GOPC_ENST00000052569.6_Silent_p.P434P|DCBLD1_ENST00000296955.8_Intron	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	442					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		CGTCATCTAGCGGAGTTTCAC	0.368			O	ROS1	glioblastoma								C|||	1	0.000199681	0	0.0014	5008	,	,		18881	0		0	False		,,,				2504	0						Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	0			6						C	,,	0,4406		0,0,2203	149	139	142		1302,1326,	-11.6	0	6	dbSNP_134	142	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,intron	GOPC,DCBLD1	NM_001017408.2,NM_020399.3,NM_173674.1	,,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,,	434/455,442/463,	117884480	3,13003	2203	4300	6503	117991173	SO:0001819	synonymous_variant	57120			AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.1326G>A	6.37:g.117884480C>T			117991173	A6NM30|Q59FS4|Q969U8	Silent	SNP	ENST00000368498.2	37	CCDS5117.1																																																																																				0.368	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		T	117884480	C	T	117884480	2	4	111	1	0	0	0	0	0	0	0	1	6593	755	27	1		1	GOPC	6	117884480	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3505203	117884480	53230587	366	29500										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128294818	128294818	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccctactcacaggcagtggAtaatcgtccggccttcccct	9	16	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:128294818A>T	ENST00000368215.3	-	28	4120	c.4121T>A	c.(4120-4122)aTc>aAc	p.I1374N	PTPRK_ENST00000368207.3_Missense_Mutation_p.I1407N|PTPRK_ENST00000368210.3_Missense_Mutation_p.I1393N|PTPRK_ENST00000532331.1_Missense_Mutation_p.I1397N|PTPRK_ENST00000368226.4_Missense_Mutation_p.I1375N|PTPRK_ENST00000368213.5_Missense_Mutation_p.I1381N|PTPRK_ENST00000368227.3_Missense_Mutation_p.I1392N			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	1374	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CAGGCAGTGGATAATCGTCCG	0.478																																																0			6											113	99	104					6																	128294818		2203	4300	6503	128336511	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.4121T>A	6.37:g.128294818A>T	ENSP00000357198:p.Ile1374Asn		128336511	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	A	28.5	4.927180	0.92389	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207	T;T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;2.31;2.31	5.82	5.82	0.92795	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.054664	0.64402	D	0.000001	T	0.27866	0.0686	M	0.69358	2.11	0.80722	D	1	D;D;D;D	0.55385	0.971;0.964;0.971;0.965	P;P;P;P	0.58331	0.808;0.709;0.837;0.748	T	0.02417	-1.1162	10	0.87932	D	0	.	16.1614	0.81721	1.0:0.0:0.0:0.0	.	1397;1381;1374;1375	B7ZMG0;Q15262-3;Q15262;Q15262-2	.;.;PTPRK_HUMAN;.	N	1375;1392;1397;1381;1393;1374;1407	ENSP00000357209:I1375N;ENSP00000357210:I1392N;ENSP00000432973:I1397N;ENSP00000357196:I1381N;ENSP00000357193:I1393N;ENSP00000357198:I1374N;ENSP00000357190:I1407N	ENSP00000357190:I1407N	I	-	2	0	PTPRK	128336511	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.284000	0.95882	2.219000	0.72066	0.533000	0.62120	ATC		0.478	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			T	128294818	A	T	128294818	3	4	111	1	0	0	0	0	1	0	0	0	12842	333	12	5	210	5	PTPRK	6	128294818	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	10410338	128294818	42820249	367	29501										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128326362	128326362	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctgccgggtattccccatGgcatctttgcgttttttagc	9	12	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:128326362G>A	ENST00000368215.3	-	15	2357	c.2358C>T	c.(2356-2358)gcC>gcT	p.A786A	PTPRK_ENST00000368207.3_Silent_p.A797A|PTPRK_ENST00000368210.3_Silent_p.A787A|PTPRK_ENST00000532331.1_Silent_p.A787A|PTPRK_ENST00000368226.4_Silent_p.A787A|PTPRK_ENST00000368213.5_Silent_p.A787A|PTPRK_ENST00000368227.3_Silent_p.A787A|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	786					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TATTCCCCATGGCATCTTTGC	0.453																																																0			6											89	74	79					6																	128326362		2203	4299	6502	128368055	SO:0001819	synonymous_variant	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2358C>T	6.37:g.128326362G>A			128368055	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	G	7.715	0.695950	0.15106	.	.	ENSG00000152894	ENST00000415046	.	.	.	5.87	-9.38	0.00623	.	.	.	.	.	T	0.33177	0.0854	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56044	-0.8044	4	.	.	.	.	10.3092	0.43699	0.1004:0.0:0.5666:0.333	.	.	.	.	L	68	.	.	P	-	2	0	PTPRK	128368055	0.765000	0.28485	0.298000	0.25002	0.995000	0.86356	-0.180000	0.09754	-1.914000	0.01078	-0.157000	0.13467	CCA		0.453	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128326362	G	A	128326362	2	1	111	1	0	0	0	0	0	0	0	1	12842	1335	47	3		3	PTPRK	6	128326362	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	31544	128326362	42788705	368	29502										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132006591	132006591	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctacatgtacgaagggcctgCcccccgcatccgagctcata							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:132006591delC	ENST00000414305.1	+	14	1536	c.1208delC	c.(1207-1209)gccfs	p.A403fs	ENPP3_ENST00000358229.5_Frame_Shift_Del_p.A403fs|ENPP3_ENST00000357639.3_Frame_Shift_Del_p.A403fs			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	403	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GAAGGGCCTGCCCCCCGCATC	0.363																																																0			6											133	151	145					6																	132006591		2203	4300	6503	132048284	SO:0001589	frameshift_variant	5169			AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.1208delC	6.37:g.132006591delC	ENSP00000406261:p.Ala403fs		132048284	Q5JTL3	Frame_Shift_Del	DEL	ENST00000414305.1	37	CCDS5148.1																																																																																				0.363	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			-	132006591	C	-	132006591	7	5	111	1	0	1	0	1	0	0	0	0	5144	739	26	0	1258	0	ENPP3	6	132006591	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	3680229	132006591	39108476	369	29503										
OR2A4	79541	hgsc.bcm.edu	37	chr6	132022010	132022010	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagaacagccaagatttcacAaaaaaagtgataaattttct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:132022010delA	ENST00000315453.2	-	1	625	c.532delT	c.(532-534)tgtfs	p.C178fs	ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000357639.3_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	178					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		AAGATTTCACAAAAAAAGTGA	0.458																																																0			6											4	6	6					6																	132022010		1296	3636	4932	132063703	SO:0001589	frameshift_variant	79541			AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"GPCR / Class A : Olfactory receptors"	14729	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 10"	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.532delT	6.37:g.132022010delA	ENSP00000319546:p.Cys178fs		132063703	Q0VAR3|Q6IF18|Q9NQN0	Frame_Shift_Del	DEL	ENST00000315453.2	37	CCDS5149.1																																																																																				0.458	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908		-	132022010	A	-	132022010	7	5	111	1	0	1	0	1	0	0	0	0	11010	130	5	0	403	0	OR2A4	6	132022010	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	15419	132022010	39093057	370	29504										
MYB	4602	hgsc.bcm.edu	37	chr6	135521306	135521306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaacatgcacttgcagctcAagaaattaaatacggtcccc	6	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:135521306A>G	ENST00000367814.4	+	11	1616	c.1430A>G	c.(1429-1431)cAa>cGa	p.Q477R	MYB_ENST00000341911.5_Missense_Mutation_p.Q598R|MYB_ENST00000534044.1_Missense_Mutation_p.Q477R|MYB_ENST00000528774.1_Missense_Mutation_p.Q595R|MYB_ENST00000442647.2_Missense_Mutation_p.Q474R|MYB_ENST00000525369.1_Missense_Mutation_p.Q392R|MYB_ENST00000316528.8_Missense_Mutation_p.Q477R|MYB_ENST00000527615.1_Missense_Mutation_p.Q477R|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000534121.1_Missense_Mutation_p.Q582R|MYB_ENST00000533624.1_Missense_Mutation_p.Q442R	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	477					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		CTTGCAGCTCAAGAAATTAAA	0.363			T	NFIB	adenoid cystic carcinoma																																		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	0			6											93	98	96					6																	135521306		2203	4300	6503	135562999	SO:0001583	missense	4602				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1430A>G	6.37:g.135521306A>G	ENSP00000356788:p.Gln477Arg		135562999	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.078246	0.76528	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.8	5.8	0.92144	C-myb, C-terminal (1);	0.109871	0.64402	D	0.000002	T	0.53417	0.1795	M	0.75777	2.31	0.40590	D	0.981475	P;P;P;D;D;D;D;D;P	0.76494	0.863;0.863;0.763;0.996;0.994;0.999;0.995;0.975;0.863	P;P;B;D;D;D;D;P;P	0.87578	0.497;0.697;0.382;0.994;0.988;0.998;0.99;0.856;0.697	T	0.57825	-0.7744	10	0.54805	T	0.06	-13.0562	16.1461	0.81569	1.0:0.0:0.0:0.0	.	442;477;474;595;392;582;598;477;477	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	R	598;474;477;477;477;477;392;595;582;477;442	ENSP00000339992:Q598R;ENSP00000410825:Q474R;ENSP00000326328:Q477R;ENSP00000356788:Q477R;ENSP00000433227:Q477R;ENSP00000435938:Q392R;ENSP00000434723:Q595R;ENSP00000432851:Q582R;ENSP00000435055:Q477R;ENSP00000436605:Q442R	ENSP00000237302:Q477R	Q	+	2	0	MYB	135562999	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.715000	0.91416	2.219000	0.72066	0.533000	0.62120	CAA		0.363	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			G	135521306	A	G	135521306	3	3	111	1	0	0	0	0	1	0	0	0	10037	130	5	4	1839	4	MYB	6	135521306	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3499296	135521306	35593761	371	29505										
IL20RA	53832	hgsc.bcm.edu	37	chr6	137330519	137330519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attggagtatatttgttgcaTggaaacaggaaggtcttctg	12	4	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:137330519T>C	ENST00000316649.5	-	4	749	c.514A>G	c.(514-516)Atg>Gtg	p.M172V	IL20RA_ENST00000367748.1_Missense_Mutation_p.M61V|IL20RA_ENST00000468393.1_5'UTR|IL20RA_ENST00000367746.3_Missense_Mutation_p.M172V|IL20RA_ENST00000541547.1_Missense_Mutation_p.M123V	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	172	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		ATTTGTTGCATGGAAACAGGA	0.433																																																0			6											204	189	194					6																	137330519		2203	4300	6503	137372212	SO:0001583	missense	53832			AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.514A>G	6.37:g.137330519T>C	ENSP00000314976:p.Met172Val		137372212	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.691768	0.48097	.	.	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547;ENST00000367746	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.92	4.75	0.60458	Fibronectin, type III (1);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.337690	0.35739	N	0.003011	T	0.42698	0.1214	M	0.79475	2.455	0.35188	D	0.773127	D;P	0.71674	0.998;0.906	D;P	0.76071	0.987;0.542	T	0.52170	-0.8611	10	0.52906	T	0.07	-16.4203	10.6339	0.45554	0.0:0.0:0.3082:0.6918	.	61;172	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	V	172;61;123;172	ENSP00000314976:M172V;ENSP00000356722:M61V;ENSP00000437843:M123V;ENSP00000356720:M172V	ENSP00000314976:M172V	M	-	1	0	IL20RA	137372212	1.000000	0.71417	0.998000	0.56505	0.763000	0.43281	1.574000	0.36482	1.064000	0.40671	0.528000	0.53228	ATG		0.433	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		C	137330519	T	C	137330519	3	2	111	1	0	0	0	0	1	0	0	0	7689	1464	51	4	1163	4	IL20RA	6	137330519	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1809213	137330519	33784548	372	29506										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146276446	146276446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactggaggagcacgtttccGtcggctgctcattttcaagt	11	11	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:146276446G>A	ENST00000367505.2	-	2	277	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	SHPRH_ENST00000367503.3_Missense_Mutation_p.R5W|SHPRH_ENST00000275233.7_Missense_Mutation_p.R5W|SHPRH_ENST00000438092.2_Missense_Mutation_p.R5W			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	5					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GCACGTTTCCGTCGGCTGCTC	0.423																																																0			6											118	114	115					6																	146276446		1929	4140	6069	146318139	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.13C>T	6.37:g.146276446G>A	ENSP00000356475:p.Arg5Trp		146318139	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	16.17	3.047594	0.55110	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.66	2.82	0.32997	.	0.000000	0.64402	D	0.000002	T	0.72961	0.3526	M	0.61703	1.905	0.47214	D	0.999352	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.76873	-0.2798	10	0.87932	D	0	-21.543	16.2659	0.82579	0.0:0.0:0.5512:0.4488	.	5;5;5	Q149N8-2;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	W	5	ENSP00000356475:R5W;ENSP00000356473:R5W;ENSP00000412797:R5W;ENSP00000275233:R5W	ENSP00000275233:R5W	R	-	1	2	SHPRH	146318139	0.973000	0.33851	0.944000	0.38274	0.723000	0.41478	1.724000	0.38064	0.036000	0.15547	-0.808000	0.03180	CGG		0.423	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146276446	G	A	146276446	3	1	111	1	0	0	0	0	1	0	0	0	14328	1144	40	1	5198	1	SHPRH	6	146276446	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8945927	146276446	24838621	373	29507										
GRM1	2911	hgsc.bcm.edu	37	chr6	146755713	146755713	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaagggaacacggaagaagaCgaactggaagaggaggagga	18	4	0	3	rs138460952		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:146755713C>T	ENST00000282753.1	+	8	3601	c.3366C>T	c.(3364-3366)gaC>gaT	p.D1122D	GRM1_ENST00000361719.2_Silent_p.D1122D|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000392299.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1122	Asp/Glu-rich (acidic).				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CGGAAGAAGACGAACTGGAAG	0.637																																																0			6											63	70	67					6																	146755713		2203	4300	6503	146797406	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3366C>T	6.37:g.146755713C>T			146797406	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																				0.637	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146755713	C	T	146755713	2	4	111	1	0	0	0	0	0	0	0	1	6817	535	19	1		1	GRM1	6	146755713	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	479267	146755713	24359354	374	29508										
SASH1	23328	hgsc.bcm.edu	37	chr6	148865342	148865342	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgacaactaagaaactggaGggctcaatcgcagcctctgg	11	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:148865342G>T	ENST00000367467.3	+	18	3211	c.2736G>T	c.(2734-2736)gaG>gaT	p.E912D		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	912					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		AGAAACTGGAGGGCTCAATCG	0.522																																																0			6											85	98	94					6																	148865342		2203	4300	6503	148907035	SO:0001583	missense	23328			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.2736G>T	6.37:g.148865342G>T	ENSP00000356437:p.Glu912Asp		148907035	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	G	0.098	-1.156426	0.01686	.	.	ENSG00000111961	ENST00000367467;ENST00000535767;ENST00000537769	T	0.36340	1.26	5.03	-10.1	0.00402	.	1.127930	0.06438	N	0.725354	T	0.02571	0.0078	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08472	-1.0720	10	0.14252	T	0.57	-0.0969	7.8789	0.29610	0.1275:0.3227:0.4687:0.0811	.	893;912	Q6P4R9;O94885	.;SASH1_HUMAN	D	912;673;322	ENSP00000356437:E912D	ENSP00000356437:E912D	E	+	3	2	SASH1	148907035	0.000000	0.05858	0.000000	0.03702	0.681000	0.39784	-2.925000	0.00691	-5.218000	0.00019	-0.188000	0.12872	GAG		0.522	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		T	148865342	G	T	148865342	3	4	111	1	0	0	0	0	1	0	0	0	13885	991	35	2	2806	2	SASH1	6	148865342	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2109629	148865342	22249725	375	29509										
PPP1R14C	81706	hgsc.bcm.edu	37	chr6	150569938	150569938	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgaggaaactgagccctccGcagaagaagagtgtatgatt	12	7	0	6	rs372465064		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:150569938G>A	ENST00000361131.4	+	4	597	c.480G>A	c.(478-480)ccG>ccA	p.P160P		NM_030949.2	NP_112211.1	Q8TAE6	PP14C_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14C	160					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)|membrane (GO:0016020)	protein serine/threonine phosphatase inhibitor activity (GO:0004865)			endometrium(1)|large_intestine(1)|prostate(1)	3		Ovarian(120;0.0284)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;9.14e-12)		TGAGCCCTCCGCAGAAGAAGA	0.403																																					Melanoma(165;1879 1941 2052 16588 48349)											0			6						G		2,4404	4.2+/-10.8	0,2,2201	54	55	54		480	-11.2	0.7	6		54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PPP1R14C	NM_030949.2		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		160/166	150569938	3,13003	2203	4300	6503	150611631	SO:0001819	synonymous_variant	81706			AF308297	CCDS5226.1	6q24.3-q25.3	2012-04-17			ENSG00000198729	ENSG00000198729		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14952	protein-coding gene	gene with protein product	"kinase C-enhanced PP1 inhibitor"	613242				11948623	Standard	NM_030949		Approved	CPI17-like, NY-BR-81, KEPI	uc003qnt.3	Q8TAE6	OTTHUMG00000015818	ENST00000361131.4:c.480G>A	6.37:g.150569938G>A			150611631	Q5VY83|Q96BB1|Q9H277	Silent	SNP	ENST00000361131.4	37	CCDS5226.1																																																																																				0.403	PPP1R14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042685.1	NM_030949		A	150569938	G	A	150569938	2	1	111	1	0	0	0	0	0	0	0	1	12395	1074	38	1		1	PPP1R14C	6	150569938	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1704596	150569938	20545129	376	29510										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151671330	151671330	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagctacttccgatggagagAaaaaaagagaaggtgtcact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:151671330delA	ENST00000253332.1	+	3	1993	c.1804delA	c.(1804-1806)aaafs	p.K603fs	AKAP12_ENST00000354675.6_Frame_Shift_Del_p.K505fs|AKAP12_ENST00000359755.5_Frame_Shift_Del_p.K498fs|AKAP12_ENST00000402676.2_Frame_Shift_Del_p.K603fs			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	603					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		CGATGGAGAGAAAAAAAGAGA	0.517																																					Melanoma(141;1616 1805 10049 24534 51979)											0			6											51	51	51					6																	151671330		2203	4300	6503	151713023	SO:0001589	frameshift_variant	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.1804delA	6.37:g.151671330delA	ENSP00000253332:p.Lys603fs		151713023	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Frame_Shift_Del	DEL	ENST00000253332.1	37	CCDS5229.1																																																																																				0.517	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			-	151671330	A	-	151671330	7	5	111	1	0	1	0	1	0	0	0	0	448	247	9	0	1843	0	AKAP12	6	151671330	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	1101392	151671330	19443737	377	29511										
ESR1	2099	hgsc.bcm.edu	37	chr6	152163847	152163847	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctactgtgcagtgtgcaatGactatgcttcaggctaccat	10	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:152163847G>A	ENST00000206249.3	+	2	930	c.568G>A	c.(568-570)Gac>Aac	p.D190N	ESR1_ENST00000443427.1_Missense_Mutation_p.D190N|ESR1_ENST00000427531.2_Missense_Mutation_p.D17N|ESR1_ENST00000440973.1_Missense_Mutation_p.D190N|ESR1_ENST00000456483.2_Missense_Mutation_p.D190N|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000338799.5_Missense_Mutation_p.D190N	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	190	Mediates interaction with DNTTIP2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	AGTGTGCAATGACTATGCTTC	0.488																																																0			6											143	124	130					6																	152163847		2203	4300	6503	152205540	SO:0001583	missense	2099			X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.568G>A	6.37:g.152163847G>A	ENSP00000206249:p.Asp190Asn		152205540	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	37	CCDS5234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.533378|5.533378	0.96460|0.96460	.|.	.|.	ENSG00000091831|ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000443427;ENST00000206249;ENST00000347491;ENST00000431590;ENST00000544394|ENST00000427531	D;D;D;D;D;D|.	0.98329|.	-4.87;-4.87;-4.87;-4.87;-4.87;-4.87|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82774|0.82774	0.5110|0.5110	M|M	0.87097|0.87097	2.86|2.86	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;0.999;1.0|.	T|T	0.82810|0.82810	-0.0273|-0.0273	10|5	0.87932|.	D|.	0|.	.|.	20.6525|20.6525	0.99598|0.99598	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	190;190;190|.	A8KAF4;G4XH65;P03372|.	.;.;ESR1_HUMAN|.	N|I	190;190;190;190;190;15;118;17|94	ENSP00000405330:D190N;ENSP00000342630:D190N;ENSP00000415934:D190N;ENSP00000387500:D190N;ENSP00000206249:D190N;ENSP00000445454:D17N|.	ENSP00000206249:D190N|.	D|M	+|+	1|3	0|0	ESR1|ESR1	152205540|152205540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.869000|9.869000	0.99810|0.99810	2.890000|2.890000	0.99128|0.99128	0.585000|0.585000	0.79938|0.79938	GAC|ATG		0.488	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			A	152163847	G	A	152163847	3	1	111	1	0	0	0	0	1	0	0	0	5269	1290	45	3	574	3	ESR1	6	152163847	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	492517	152163847	18951220	378	29512										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152639316	152639316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagtggcttacccagttggCcattctgttccaagaatttc	8	12	1	1	rs530429418		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:152639316C>T	ENST00000367255.5	-	86	17073	c.16472G>A	c.(16471-16473)gGc>gAc	p.G5491D	SYNE1_ENST00000356820.4_Missense_Mutation_p.G15D|SYNE1_ENST00000448038.1_Missense_Mutation_p.G5420D|SYNE1_ENST00000423061.1_Missense_Mutation_p.G5420D|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.G5491D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5491					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACCCAGTTGGCCATTCTGTTC	0.443										HNSCC(10;0.0054)																																						0			6											201	176	184					6																	152639316		2203	4300	6503	152681009	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16472G>A	6.37:g.152639316C>T	ENSP00000356224:p.Gly5491Asp		152681009	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.06	1.823208	0.32237	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000356820	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.66	3.87	0.44632	.	0.520576	0.18799	N	0.130837	T	0.06600	0.0169	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.32071	0.118;0.112;0.112;0.355	B;B;B;B	0.21360	0.034;0.015;0.015;0.031	T	0.28267	-1.0049	10	0.12430	T	0.62	.	2.8755	0.05629	0.1415:0.4685:0.2441:0.1458	.	5491;5491;5491;5420	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	D	5491;5420;5491;5420;15	ENSP00000356224:G5491D;ENSP00000396024:G5420D;ENSP00000265368:G5491D;ENSP00000390975:G5420D;ENSP00000349276:G15D	ENSP00000265368:G5491D	G	-	2	0	SYNE1	152681009	0.000000	0.05858	0.154000	0.22540	0.860000	0.49131	0.470000	0.22084	0.723000	0.32274	0.655000	0.94253	GGC		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152639316	C	T	152639316	3	4	111	1	0	0	0	0	1	0	0	0	15484	739	26	3	10238	3	SYNE1	6	152639316	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	475469	152639316	18475751	379	29513										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155578072	155578072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attaaacgaaaagccaacagCaccaagagggacagaggaac	10	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:155578072C>T	ENST00000461783.3	+	29	6196	c.4923C>T	c.(4921-4923)agC>agT	p.S1641S	RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000318981.5_Silent_p.S1641S|TIAM2_ENST00000456877.2_Silent_p.S953S|TIAM2_ENST00000360366.4_Silent_p.S1665S|TIAM2_ENST00000528391.2_Silent_p.S985S|TIAM2_ENST00000456144.1_Silent_p.S1670S|TIAM2_ENST00000529824.2_Silent_p.S1670S|TIAM2_ENST00000367174.2_Silent_p.S1017S|TIAM2_ENST00000275246.7_Silent_p.S566S			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1641					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AAGCCAACAGCACCAAGAGGG	0.557																																																0			6											68	64	65					6																	155578072		2203	4300	6503	155619764	SO:0001819	synonymous_variant	26230				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4923C>T	6.37:g.155578072C>T			155619764	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																				0.557	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155578072	C	T	155578072	2	4	111	1	0	0	0	0	0	0	0	1	15930	709	25	3		3	TIAM2	6	155578072	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2938756	155578072	15536995	380	29514										
TFB1M	51106	hgsc.bcm.edu	37	chr6	155579134	155579134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgtgagatggagagctggcGgggccgaagagtagggtcta	20	5	1	3	rs368405074		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:155579134G>A	ENST00000367166.4	-	7	932	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C	RP11-477D19.2_ENST00000435295.1_RNA	NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)	p.R293S(1)		lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		GAGAGCTGGCGGGGCCGAAGA	0.478																																																1	Substitution - Missense(1)	lung(1)	6						G	CYS/ARG	0,4406		0,0,2203	114	124	120		877	-6.1	0	6		120	1,8599	1.2+/-3.3	0,1,4299	no	missense	TFB1M	NM_016020.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	293/347	155579134	1,13005	2203	4300	6503	155620826	SO:0001583	missense	51106			AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"dimethyladenosine transferase 1, mitochondrial"	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.877C>T	6.37:g.155579134G>A	ENSP00000356134:p.Arg293Cys		155620826	Q05DR0|Q9Y384	Missense_Mutation	SNP	ENST00000367166.4	37	CCDS5248.1	.	.	.	.	.	.	.	.	.	.	G	6.564	0.472395	0.12461	0.0	1.16E-4	ENSG00000029639	ENST00000367166	T	0.30714	1.52	5.91	-6.1	0.02138	rRNA adenine dimethylase-like (1);	1.357460	0.04419	N	0.367238	T	0.04952	0.0133	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.26430	-1.0103	10	0.44086	T	0.13	0.2086	0.3051	0.00279	0.2783:0.1584:0.2475:0.3158	.	293	Q8WVM0	TFB1M_HUMAN	C	293	ENSP00000356134:R293C	ENSP00000356134:R293C	R	-	1	0	TFB1M	155620826	0.000000	0.05858	0.017000	0.16124	0.038000	0.13279	-0.881000	0.04179	-0.688000	0.05155	-1.104000	0.02111	CGC		0.478	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1			A	155579134	G	A	155579134	3	1	111	1	0	0	0	0	1	0	0	0	15832	1116	39	1	167	1	TFB1M	6	155579134	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1062	155579134	15535933	381	29515										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157528201	157528201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggcctggtgctgatcctgGggaagctgattcttcttcac	12	11	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:157528201G>A	ENST00000350026.5	+	19	5888	c.5887G>A	c.(5887-5889)Ggg>Agg	p.G1963R	ARID1B_ENST00000275248.4_Missense_Mutation_p.G1958R|ARID1B_ENST00000367148.1_Missense_Mutation_p.G2016R|ARID1B_ENST00000346085.5_Missense_Mutation_p.G1976R	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1963					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GCTGATCCTGGGGAAGCTGAT	0.527																																																0			6											110	111	111					6																	157528201		2203	4296	6499	157569893	SO:0001583	missense	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.5887G>A	6.37:g.157528201G>A	ENSP00000055163:p.Gly1963Arg		157569893	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300750	0.60195	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43	5.28	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.52629	0.1746	M	0.83483	2.645	0.80722	D	1	P;P;P	0.48350	0.909;0.889;0.889	P;B;B	0.47015	0.534;0.399;0.399	T	0.64437	-0.6408	10	0.87932	D	0	.	14.2606	0.66083	0.072:0.0:0.928:0.0	.	1963;1976;1958	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	R	1976;1963;2016;1958;1485	ENSP00000344546:G1976R;ENSP00000055163:G1963R;ENSP00000356116:G2016R;ENSP00000275248:G1958R;ENSP00000412835:G1485R	ENSP00000275248:G1958R	G	+	1	0	ARID1B	157569893	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.813000	0.99286	1.360000	0.45960	0.563000	0.77884	GGG		0.527	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157528201	G	A	157528201	3	1	111	1	0	0	0	0	1	0	0	0	914	1232	43	3	6004	3	ARID1B	6	157528201	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1949067	157528201	13586866	382	29516										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159457199	159457199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgccctcatgctccccaccGtcatgctccccacggtctgg	8	20	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:159457199G>A	ENST00000367066.3	-	10	2187	c.1856C>T	c.(1855-1857)aCg>aTg	p.T619M	RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.T441M|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	619					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GCTCCCCACCGTCATGCTCCC	0.642																																																0			6											53	52	53					6																	159457199		2203	4300	6503	159377187	SO:0001583	missense	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1856C>T	6.37:g.159457199G>A	ENSP00000356033:p.Thr619Met		159377187	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.238583	0.58886	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	T;T	0.20881	2.04;2.26	2.76	2.76	0.32466	.	.	.	.	.	T	0.36220	0.0959	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.43621	-0.9380	9	0.87932	D	0	-26.3246	13.8482	0.63481	0.0:0.0:1.0:0.0	.	619	Q8N103	TAGAP_HUMAN	M	619;441	ENSP00000356033:T619M;ENSP00000322650:T441M	ENSP00000322650:T441M	T	-	2	0	TAGAP	159377187	1.000000	0.71417	0.760000	0.31359	0.096000	0.18686	8.088000	0.89523	1.465000	0.48006	0.563000	0.77884	ACG		0.642	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159457199	G	A	159457199	3	1	111	1	0	0	0	0	1	0	0	0	15576	1145	40	1	343	1	TAGAP	6	159457199	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1928998	159457199	11657868	383	29517										
LPA	4018	hgsc.bcm.edu	37	chr6	161026186	161026186	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtatgtgccttgataactcTgtccatttccgtggtagcac	9	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:161026186T>C	ENST00000316300.5	-	18	2881	c.2837A>G	c.(2836-2838)cAg>cGg	p.Q946R	LPA_ENST00000447678.1_Missense_Mutation_p.Q946R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3454	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TTGATAACTCTGTCCATTTCC	0.468																																																0			6											302	313	309					6																	161026186		2203	4300	6503	160946176	SO:0001583	missense	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2837A>G	6.37:g.161026186T>C	ENSP00000321334:p.Gln946Arg		160946176	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	t	0.048	-1.260207	0.01445	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.66099	-0.19;-0.19	2.16	2.16	0.27623	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.30510	0.0767	N	0.21240	0.645	0.09310	N	1	P	0.47545	0.897	P	0.48488	0.579	T	0.05257	-1.0896	9	0.19590	T	0.45	.	6.2159	0.20656	0.0:0.0:0.0:1.0	.	3454	P08519	APOA_HUMAN	R	946	ENSP00000321334:Q946R;ENSP00000395608:Q946R	ENSP00000321334:Q946R	Q	-	2	0	LPA	160946176	0.001000	0.12720	0.012000	0.15200	0.078000	0.17371	0.967000	0.29344	0.999000	0.39023	0.155000	0.16302	CAG		0.468	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		C	161026186	T	C	161026186	3	2	111	1	0	0	0	0	1	0	0	0	8932	1580	55	4	3373	4	LPA	6	161026186	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1568987	161026186	10088881	384	29518										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168352692	168352692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatccaggagctccagagcaAaccggaccgcagcgccgagg	14	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr6:168352692A>G	ENST00000447894.2	+	29	4637	c.4637A>G	c.(4636-4638)aAa>aGa	p.K1546R	MLLT4_ENST00000366806.2_Missense_Mutation_p.K1546R|MLLT4_ENST00000400822.3_Missense_Mutation_p.K1545R|MLLT4_ENST00000344191.4_Missense_Mutation_p.K1546R|MLLT4_ENST00000392112.1_Missense_Mutation_p.K1529R|MLLT4_ENST00000392108.3_Missense_Mutation_p.K1546R|MLLT4_ENST00000351017.4_Missense_Mutation_p.K1553R			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1546					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		CTCCAGAGCAAACCGGACCGC	0.612			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	0			6											50	54	52					6																	168352692		2203	4300	6503	168095541	SO:0001583	missense	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.4637A>G	6.37:g.168352692A>G	ENSP00000404595:p.Lys1546Arg		168095541	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.492|9.492	1.101038|1.101038	0.20552|0.20552	.|.	.|.	ENSG00000130396|ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894|ENST00000507704;ENST00000476946	T;T;T;T;T;T;T|.	0.46819|.	3.76;0.9;3.75;0.9;0.9;0.86;0.9|.	5.34|5.34	1.64|1.64	0.23874|0.23874	.|.	0.114017|.	0.64402|.	N|.	0.000018|.	T|T	0.36441|0.36441	0.0967|0.0967	M|M	0.73962|0.73962	2.25|2.25	0.09310|0.09310	N|N	1|1	B;P;P;B|.	0.39131|.	0.15;0.661;0.547;0.22|.	B;B;B;B|.	0.35312|.	0.039;0.2;0.162;0.162|.	T|T	0.31696|0.31696	-0.9934|-0.9934	10|5	0.42905|.	T|.	0.14|.	-27.2154|-27.2154	8.5621|8.5621	0.33516|0.33516	0.7716:0.0:0.2284:0.0|0.7716:0.0:0.2284:0.0	.|.	1546;1545;1546;1530|.	P55196;P55196-5;P55196-6;P55196-2|.	AFAD_HUMAN;.;.;.|.	R|D	1546;1553;1546;1546;1529;1546;1545;1546|37;22	ENSP00000341118:K1546R;ENSP00000252692:K1553R;ENSP00000375956:K1546R;ENSP00000355771:K1546R;ENSP00000375960:K1529R;ENSP00000383623:K1545R;ENSP00000404595:K1546R|.	ENSP00000345834:K1546R|.	K|N	+|+	2|1	0|0	MLLT4|MLLT4	168095541|168095541	1.000000|1.000000	0.71417|0.71417	0.001000|0.001000	0.08648|0.08648	0.564000|0.564000	0.35744|0.35744	3.244000|3.244000	0.51399|0.51399	0.043000|0.043000	0.15746|0.15746	0.533000|0.533000	0.62120|0.62120	AAA|AAC		0.612	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		G	168352692	A	G	168352692	3	3	111	1	0	0	0	0	1	0	0	0	9659	14	1	4	4751	4	MLLT4	6	168352692	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	7326506	168352692	2762375	385	29519										
CYP2W1	54905	hgsc.bcm.edu	37	chr7	1024057	1024057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atccctgccagctctcagaaCgctacgggccggtgttcacc	10	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:1024057C>T	ENST00000308919.7	+	2	197	c.184C>T	c.(184-186)Cgc>Tgc	p.R62C	CYP2W1_ENST00000340150.6_Missense_Mutation_p.R6C	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	62					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GCTCTCAGAACGCTACGGGCC	0.711																																																0			7											13	14	14					7																	1024057		2009	3970	5979	990583	SO:0001583	missense	54905			AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"Cytochrome P450s"	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.184C>T	7.37:g.1024057C>T	ENSP00000310149:p.Arg62Cys		990583		Missense_Mutation	SNP	ENST00000308919.7	37	CCDS5319.2	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258128	0.39896	.	.	ENSG00000073067	ENST00000308919;ENST00000340150	T;T	0.69435	-0.4;-0.4	5.45	-0.381	0.12485	.	0.894418	0.09644	N	0.774635	T	0.75034	0.3795	M	0.78456	2.415	0.09310	N	1	D;D	0.61697	0.99;0.981	P;P	0.59595	0.86;0.806	T	0.62062	-0.6933	10	0.59425	D	0.04	.	5.858	0.18730	0.5784:0.248:0.0:0.1735	.	6;62	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	C	62;6	ENSP00000310149:R62C;ENSP00000344178:R6C	ENSP00000310149:R62C	R	+	1	0	CYP2W1	990583	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.030000	0.13688	-0.001000	0.14495	0.478000	0.44815	CGC		0.711	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781		T	1024057	C	T	1024057	3	4	111	1	0	0	0	0	1	0	0	0	4182	536	19	1	190	1	CYP2W1	7	1024057	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		1024057	158114606	386	29520										
GPER	2852	hgsc.bcm.edu	37	chr7	1131796	1131796	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggtcaacatgtacagcagCgtcttcttcctcacctggat	8	13	4	0	rs143366301	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:1131796C>T	ENST00000297469.3	+	2	1123	c.432C>T	c.(430-432)agC>agT	p.S144S	GPER1_ENST00000397092.1_Silent_p.S144S|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron|GPER1_ENST00000401670.1_Silent_p.S144S|GPER1_ENST00000397088.3_Silent_p.S144S|C7orf50_ENST00000357429.6_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	144				NMYSSVF -> QHVQAASS (in Ref. 7; AAB02736). {ECO:0000305}.	apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										TGTACAGCAGCGTCTTCTTCC	0.602																																																0			7							,,,,,	0,4406		0,0,2203	146	106	119		432,432,,,432,	0.9	1	7	dbSNP_134	119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	,,,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,,,	144/376,144/376,,,144/376,	1131796	2,13004	2203	4300	6503	1098322	SO:0001819	synonymous_variant	2852			U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"G protein-coupled receptor 30"	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.432C>T	7.37:g.1131796C>T			1098322	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																				0.602	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966		T	1131796	C	T	1131796	2	4	111	1	0	0	0	0	0	0	0	1	6627	767	27	1		1	GPER	7	1131796	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	107739	1131796	158006867	387	29521										
INTS1	26173	hgsc.bcm.edu	37	chr7	1539638	1539638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agttgatggaggcgtcccgcCgcaggaggctacacagagcc	15	12	0	2	rs373727561		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:1539638C>T	ENST00000404767.3	-	5	651	c.566G>A	c.(565-567)cGg>cAg	p.R189Q	INTS1_ENST00000389470.4_Missense_Mutation_p.R317Q|INTS1_ENST00000493531.1_5'UTR	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	189					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGCGTCCCGCCGCAGGAGGCT	0.647													C|||	1	0.000199681	0	0	5008	,	,		15902	0		0.001	False		,,,				2504	0															0			7							GLN/ARG	0,4036		0,0,2018	41	47	45		566	4.2	1	7		45	1,8345		0,1,4172	no	missense	INTS1	NM_001080453.2	43	0,1,6190	TT,TC,CC		0.012,0.0,0.0081	probably-damaging	189/2191	1539638	1,12381	2018	4173	6191	1506164	SO:0001583	missense	26173			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.566G>A	7.37:g.1539638C>T	ENSP00000385722:p.Arg189Gln		1506164	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	37	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892502	0.91889	0.0	1.2E-4	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.47528	0.84;0.85	4.24	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.62660	0.2446	L	0.53249	1.67	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.65323	0.934;0.905	T	0.67284	-0.5709	10	0.66056	D	0.02	.	16.8596	0.86014	0.0:1.0:0.0:0.0	.	317;189	A4D212;Q8N201	.;INT1_HUMAN	Q	189;317	ENSP00000385722:R189Q;ENSP00000374121:R317Q	ENSP00000374121:R317Q	R	-	2	0	INTS1	1506164	1.000000	0.71417	0.998000	0.56505	0.741000	0.42261	7.455000	0.80726	2.204000	0.70986	0.655000	0.94253	CGG		0.647	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			T	1539638	C	T	1539638	3	4	111	1	0	0	0	0	1	0	0	0	7796	652	23	1	6182	1	INTS1	7	1539638	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	407842	1539638	157599025	388	29522										
GNA12	2768	hgsc.bcm.edu	37	chr7	2834612	2834612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccctgatgccagaatcccTccagagtgcgctcagggccg	11	16	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:2834612T>C	ENST00000275364.3	-	2	637	c.475A>G	c.(475-477)Agg>Ggg	p.R159G	GNA12_ENST00000544127.1_Missense_Mutation_p.R83G|GNA12_ENST00000407904.3_Missense_Mutation_p.R100G	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	159					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		CCAGAATCCCTCCAGAGTGCG	0.582																																																0			7											80	79	79					7																	2834612		2203	4300	6503	2801138	SO:0001583	missense	2768			L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.475A>G	7.37:g.2834612T>C	ENSP00000275364:p.Arg159Gly		2801138	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Missense_Mutation	SNP	ENST00000275364.3	37	CCDS5335.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.977033	0.34848	.	.	ENSG00000146535	ENST00000275364;ENST00000407904;ENST00000544127;ENST00000447791	D;D;D	0.88509	-2.39;-2.39;-2.39	5.45	-3.52	0.04682	G protein alpha subunit, helical insertion (2);	0.374258	0.32416	N	0.006138	T	0.75376	0.3841	L	0.31420	0.93	0.80722	D	1	B;B;B	0.14012	0.0;0.009;0.0	B;B;B	0.10450	0.001;0.005;0.002	T	0.52328	-0.8590	10	0.18710	T	0.47	.	5.8379	0.18617	0.0:0.2124:0.386:0.4016	.	159;159;100	Q5PPR5;Q03113;B3KXS2	.;GNA12_HUMAN;.	G	159;100;83;74	ENSP00000275364:R159G;ENSP00000385935:R100G;ENSP00000437469:R83G	ENSP00000275364:R159G	R	-	1	2	GNA12	2801138	0.912000	0.30974	0.988000	0.46212	0.893000	0.52053	0.432000	0.21461	-0.489000	0.06716	0.379000	0.24179	AGG		0.582	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353		C	2834612	T	C	2834612	3	2	111	1	0	0	0	0	1	0	0	0	6520	1550	54	4	682	4	GNA12	7	2834612	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1294974	2834612	156304051	389	29523										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4794936	4794936	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atctcctccgcccaggaccgGcagctgaccctgagcgggat	12	16	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:4794936G>A	ENST00000328914.4	+	4	972	c.972G>A	c.(970-972)cgG>cgA	p.R324R	FOXK1_ENST00000446823.1_Silent_p.R161R	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CCCAGGACCGGCAGCTGACCC	0.642																																																0			7											67	59	62					7																	4794936		2203	4300	6503	4761462	SO:0001819	synonymous_variant	221937			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.972G>A	7.37:g.4794936G>A			4761462		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																				0.642	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			A	4794936	G	A	4794936	2	1	111	1	0	0	0	0	0	0	0	1	6033	1190	42	3		3	FOXK1	7	4794936	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1960324	4794936	154343727	390	29524										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4823955	4823955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggccttctctatgctgcgggCgtggctgctgcacagcggcc	15	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:4823955C>T	ENST00000348624.4	+	6	837	c.743C>T	c.(742-744)gCg>gTg	p.A248V	AP5Z1_ENST00000401897.1_Missense_Mutation_p.A248V	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	248					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											ATGCTGCGGGCGTGGCTGCTG	0.682																																																0			7											10	12	11					7																	4823955		2045	4182	6227	4790481	SO:0001583	missense	9907			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.743C>T	7.37:g.4823955C>T	ENSP00000297562:p.Ala248Val		4790481	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	C	6.003	0.369014	0.11352	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.46819	0.86;0.86	4.31	-0.942	0.10398	.	0.671962	0.14578	N	0.311068	T	0.30417	0.0764	L	0.38531	1.155	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.15150	-1.0447	10	0.30854	T	0.27	.	5.2447	0.15490	0.3738:0.4352:0.0:0.191	.	248	O43299	K0415_HUMAN	V	248	ENSP00000297562:A248V;ENSP00000384980:A248V	ENSP00000297562:A248V	A	+	2	0	KIAA0415	4790481	0.002000	0.14202	0.049000	0.19019	0.193000	0.23685	1.055000	0.30467	0.031000	0.15407	-0.448000	0.05591	GCG		0.682	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4823955	C	T	4823955	3	4	111	1	0	0	0	0	1	0	0	0	8196	768	27	1	765	1	KIAA0415	7	4823955	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	29019	4823955	154314708	391	29525										
PHF14	9678	hgsc.bcm.edu	37	chr7	11030370	11030370	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtcaaaactggagctctcAaaaaatggaccatattctga					rs188488010		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:11030370delA	ENST00000403050.3	+	4	1393	c.941delA	c.(940-942)caafs	p.Q314fs	PHF14_ENST00000445996.2_Frame_Shift_Del_p.Q29fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	314					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		TGGAGCTCTCAAAAAATGGAC	0.323																																																0			7											112	98	102					7																	11030370		1839	4094	5933	10996895	SO:0001589	frameshift_variant	9678			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.941delA	7.37:g.11030370delA	ENSP00000385795:p.Gln314fs		10996895	A7MCZ3|B4DI82	Frame_Shift_Del	DEL	ENST00000403050.3	37	CCDS47542.1																																																																																				0.323	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		-	11030370	A	-	11030370	7	5	111	1	0	1	0	1	0	0	0	0	11856	130	5	0	955	0	PHF14	7	11030370	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	6206415	11030370	148108293	392	29526										
PHF14	9678	hgsc.bcm.edu	37	chr7	11101436	11101436	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagaaccagaggacgaaaaCgaagcttcgttcctgaggaa	12	8	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:11101436C>T	ENST00000403050.3	+	15	2952	c.2500C>T	c.(2500-2502)Cga>Tga	p.R834*	PHF14_ENST00000445996.2_Nonsense_Mutation_p.R549*	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	834					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		AGGACGAAAACGAAGCTTCGT	0.284																																																0			7											51	52	51					7																	11101436		1775	4011	5786	11067961	SO:0001587	stop_gained	9678			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.2500C>T	7.37:g.11101436C>T	ENSP00000385795:p.Arg834*		11067961	A7MCZ3|B4DI82	Nonsense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	C	44	10.748378	0.99460	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	.	.	.	5.28	3.25	0.37280	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3153	0.66446	0.2801:0.7199:0.0:0.0	.	.	.	.	X	834;549	.	ENSP00000385795:R834X	R	+	1	2	PHF14	11067961	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.637000	0.24659	1.198000	0.43158	0.655000	0.94253	CGA		0.284	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		T	11101436	C	T	11101436	4	4	111	1	0	0	0	0	0	1	0	0	11856	528	19	1	2558	1	PHF14	7	11101436	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	71066	11101436	148037227	393	29527										
TMEM106B	54664	hgsc.bcm.edu	37	chr7	12258129	12258129	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gattccatatagtgatcagaGattaaggccaagaagaacgt	10	6	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:12258129G>T	ENST00000396667.3	+	4	585	c.263G>T	c.(262-264)aGa>aTa	p.R88I	TMEM106B_ENST00000396668.3_Missense_Mutation_p.R88I	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	88					cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AGTGATCAGAGATTAAGGCCA	0.279																																																0			7											105	105	105					7																	12258129		2203	4300	6503	12224654	SO:0001583	missense	54664			BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.263G>T	7.37:g.12258129G>T	ENSP00000379901:p.Arg88Ile		12224654	A4D108|Q53FL9|Q8N4L0	Missense_Mutation	SNP	ENST00000396667.3	37	CCDS5358.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.844387	0.91197	.	.	ENSG00000106460	ENST00000396668;ENST00000444443;ENST00000396667	T;T;T	0.41758	0.99;0.99;0.99	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.70622	0.3245	M	0.87900	2.915	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.76772	-0.2836	10	0.87932	D	0	.	18.882	0.92358	0.0:0.0:1.0:0.0	.	88	Q9NUM4	T106B_HUMAN	I	88	ENSP00000379902:R88I;ENSP00000401302:R88I;ENSP00000379901:R88I	ENSP00000379901:R88I	R	+	2	0	TMEM106B	12224654	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.621000	0.88768	0.650000	0.86243	AGA		0.279	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374		T	12258129	G	T	12258129	3	4	111	1	0	0	0	0	1	0	0	0	16060	942	33	2	269	2	TMEM106B	7	12258129	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1156693	12258129	146880534	394	29528										
TSPAN13	27075	hgsc.bcm.edu	37	chr7	16816718	16816718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcagttttctgtatcttgcGcttgtttagccctgaaccag	8	10	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:16816718G>A	ENST00000262067.4	+	3	716	c.283G>A	c.(283-285)Gct>Act	p.A95T	TSPAN13_ENST00000466195.1_3'UTR	NM_014399.3	NP_055214.1	O95857	TSN13_HUMAN	tetraspanin 13	95						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	7	Lung NSC(10;0.0494)|all_lung(11;0.109)			UCEC - Uterine corpus endometrioid carcinoma (126;0.188)		TGTATCTTGCGCTTGTTTAGC	0.328																																																0			7											119	113	115					7																	16816718		2203	4300	6503	16783243	SO:0001583	missense	27075			AF100759	CCDS5363.1	7p21.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000106537	ENSG00000106537		"Tetraspanins"	21643	protein-coding gene	gene with protein product		613139	"transmembrane 4 superfamily member 13"	TM4SF13			Standard	NM_014399		Approved	NET-6	uc003stq.3	O95857	OTTHUMG00000022968	ENST00000262067.4:c.283G>A	7.37:g.16816718G>A	ENSP00000262067:p.Ala95Thr		16783243		Missense_Mutation	SNP	ENST00000262067.4	37	CCDS5363.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915856	0.92178	.	.	ENSG00000106537	ENST00000262067	T	0.79940	-1.32	5.61	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.90721	0.7088	M	0.87682	2.9	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.91481	0.5204	10	0.46703	T	0.11	-22.7223	16.6208	0.84929	0.0:0.1301:0.8699:0.0	.	95	O95857	TSN13_HUMAN	T	95	ENSP00000262067:A95T	ENSP00000262067:A95T	A	+	1	0	TSPAN13	16783243	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.623000	0.83113	1.359000	0.45940	0.561000	0.74099	GCT		0.328	TSPAN13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250178.2	NM_014399		A	16816718	G	A	16816718	3	1	111	1	0	0	0	0	1	0	0	0	16677	1087	38	1	293	1	TSPAN13	7	16816718	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4558589	16816718	142321945	395	29529										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20371449	20371450	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgtgcggctcggccctggcINStttttttaccgctgcatttg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:20371449_20371450insT	ENST00000222573.4	+	1	704_705	c.20_21insT	c.(19-24)gcttttfs	p.AF7fs	ITGB8_ENST00000537992.1_Intron|CTA-293F17.1_ENST00000605357.1_RNA|CTA-293F17.1_ENST00000603156.1_RNA	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	7					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						TCGGCCCTGGCTTTTTTTACCG	0.668																																																0			7																																								20337975	SO:0001589	frameshift_variant	3696				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.27dupT	7.37:g.20371456_20371456dupT	ENSP00000222573:p.Ala7fs		20337974	A4D133|B4DHD4	Frame_Shift_Ins	INS	ENST00000222573.4	37	CCDS5370.1																																																																																				0.668	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		T	20371450	-	T	20371449	7	5	111	1	0	1	1	0	0	0	0	0	7922	797	28	0	22	0	ITGB8	7	20371449	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	3554731	20371449	138767214	396	29530										
HOXA2	3199	hgsc.bcm.edu	37	chr7	27140497	27140497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaggaatctgtggagaaaaCgctaaagtcctgcaaagagg	13	7	1	2	rs143043350		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:27140497C>T	ENST00000222718.5	-	2	1289	c.979G>A	c.(979-981)Gtt>Att	p.V327I	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000428939.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	327					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						GTGGAGAAAACGCTAAAGTCC	0.512													C|||	1	0.000199681	0	0.0014	5008	,	,		18540	0		0	False		,,,				2504	0															0			7						C	ILE/VAL	0,4406		0,0,2203	77	77	77		979	5	1	7	dbSNP_134	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	HOXA2	NM_006735.3	29	0,8,6495	TT,TC,CC		0.093,0.0,0.0615	probably-damaging	327/377	27140497	8,12998	2203	4300	6503	27107022	SO:0001583	missense	3199				CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.979G>A	7.37:g.27140497C>T	ENSP00000222718:p.Val327Ile		27107022	A1L4K3|B2RMW3	Missense_Mutation	SNP	ENST00000222718.5	37	CCDS5403.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976840	0.34848	0.0	9.3E-4	ENSG00000105996	ENST00000222718	T	0.10960	2.82	5.04	5.04	0.67666	.	0.128331	0.52532	D	0.000076	T	0.16300	0.0392	M	0.80616	2.505	0.43457	D	0.995654	P	0.38863	0.65	B	0.30855	0.121	T	0.07654	-1.0761	10	0.33141	T	0.24	.	18.3861	0.90466	0.0:1.0:0.0:0.0	.	327	O43364	HXA2_HUMAN	I	327	ENSP00000222718:V327I	ENSP00000222718:V327I	V	-	1	0	HOXA2	27107022	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	4.605000	0.61119	2.492000	0.84095	0.655000	0.94253	GTT		0.512	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			T	27140497	C	T	27140497	3	4	111	1	0	0	0	0	1	0	0	0	7313	536	19	1	155	1	HOXA2	7	27140497	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6769048	27140497	131998166	397	29531										
HOXA3	3200	hgsc.bcm.edu	37	chr7	27150132	27150132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcgggtcggtggtactcgCcgtcggcgcccaaagcggcg	18	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:27150132C>T	ENST00000396352.4	-	2	327	c.128G>A	c.(127-129)gGc>gAc	p.G43D	HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA3_ENST00000317201.2_Missense_Mutation_p.G43D	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	43					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						GTGGTACTCGCCGTCGGCGCC	0.682																																					Esophageal Squamous(136;1368 1743 5685 7935 50360)											0			7											16	15	15					7																	27150132		2124	4194	6318	27116657	SO:0001583	missense	3200				CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.128G>A	7.37:g.27150132C>T	ENSP00000379640:p.Gly43Asp		27116657	A4D181	Missense_Mutation	SNP	ENST00000396352.4	37	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589842	0.66105	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000522788;ENST00000522456	T;T;T;T	0.41758	3.38;3.38;0.99;0.99	5.49	5.49	0.81192	.	0.232519	0.49916	D	0.000134	T	0.43411	0.1246	N	0.24115	0.695	0.45216	D	0.998221	D	0.60160	0.987	P	0.54544	0.755	T	0.12372	-1.0550	10	0.13853	T	0.58	.	19.3654	0.94460	0.0:1.0:0.0:0.0	.	43	O43365	HXA3_HUMAN	D	43	ENSP00000379640:G43D;ENSP00000324884:G43D;ENSP00000429426:G43D;ENSP00000430566:G43D	ENSP00000324884:G43D	G	-	2	0	HOXA3	27116657	1.000000	0.71417	0.997000	0.53966	0.760000	0.43138	4.712000	0.61888	2.595000	0.87683	0.462000	0.41574	GGC		0.682	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			T	27150132	C	T	27150132	3	4	111	1	0	0	0	0	1	0	0	0	7314	739	26	3	1211	3	HOXA3	7	27150132	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9635	27150132	131988531	398	29532										
FAM188B	84182	hgsc.bcm.edu	37	chr7	30830903	30830903	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caacaggacattctggcttcGagcaacagctccccctccag	8	16	1	0	rs61741901		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:30830903G>A	ENST00000265299.6	+	5	863	c.786G>A	c.(784-786)tcG>tcA	p.S262S	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	262			S -> L (in dbSNP:rs17159453).							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTCTGGCTTCGAGCAACAGCT	0.592																																																0			7											81	89	87					7																	30830903		1966	4154	6120	30797428	SO:0001819	synonymous_variant	84182			AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 67"	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.786G>A	7.37:g.30830903G>A			30797428	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																				0.592	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		A	30830903	G	A	30830903	2	1	111	1	0	0	0	0	0	0	0	1	5531	1045	37	1		1	FAM188B	7	30830903	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3680771	30830903	128307760	399	29533										
FAM188B	84182	hgsc.bcm.edu	37	chr7	30898883	30898883	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccctcccagtttgaagtggGcccctatggctgcatcctgc	10	16	0	1	rs561526056		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:30898883G>A	ENST00000265299.6	+	13	1765	c.1688G>A	c.(1687-1689)gGc>gAc	p.G563D	INMT-FAM188B_ENST00000458257.1_3'UTR|AQP1_ENST00000509504.1_Missense_Mutation_p.G26D|AQP1_ENST00000434909.2_5'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	563										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTTGAAGTGGGCCCCTATGGC	0.592													G|||	0	0	0	0	5008	,	,		20712	0		0	False		,,,				2504	0															0			7											107	117	114					7																	30898883		2039	4196	6235	30865408	SO:0001583	missense	84182			AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 67"	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1688G>A	7.37:g.30898883G>A	ENSP00000265299:p.Gly563Asp		30865408	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390768	0.62066	.	.	ENSG00000106125;ENSG00000106125;ENSG00000250424	ENST00000265299;ENST00000409881;ENST00000509504	T;T	0.31769	1.48;1.48	5.26	5.26	0.73747	.	0.051282	0.85682	D	0.000000	T	0.46560	0.1399	L	0.41824	1.3	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.982;0.989	T	0.43376	-0.9395	10	0.87932	D	0	-21.7232	14.3483	0.66682	0.0:0.0:1.0:0.0	.	83;563	B8ZZX1;Q4G0A6	.;F188B_HUMAN	D	563;83;26	ENSP00000265299:G563D;ENSP00000421315:G26D	ENSP00000265299:G563D	G	+	2	0	RP5-877J2.1;FAM188B	30865408	1.000000	0.71417	0.798000	0.32154	0.713000	0.41058	6.005000	0.70716	2.458000	0.83093	0.561000	0.74099	GGC		0.592	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		A	30898883	G	A	30898883	3	1	111	1	0	0	0	0	1	0	0	0	5531	1203	42	3	1738	3	FAM188B	7	30898883	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	67980	30898883	128239780	400	29534										
BMPER	168667	hgsc.bcm.edu	37	chr7	34118715	34118715	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctcaccgtgcgctggaacgGctcgcgcatcgcgctcccct	11	19	1	0	rs368059451		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:34118715G>A	ENST00000297161.2	+	13	1699	c.1325G>A	c.(1324-1326)gGc>gAc	p.G442D	BMPER_ENST00000426693.1_Missense_Mutation_p.G442D	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	442	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CGCTGGAACGGCTCGCGCATC	0.672																																																0			7						G	ASP/GLY	0,4406		0,0,2203	65	67	66		1325	5.9	1	7		66	1,8597	1.2+/-3.3	0,1,4298	no	missense	BMPER	NM_133468.3	94	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	442/686	34118715	1,13003	2203	4299	6502	34085240	SO:0001583	missense	168667				CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.1325G>A	7.37:g.34118715G>A	ENSP00000297161:p.Gly442Asp		34085240	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	37	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	G	34	5.380988	0.95945	0.0	1.16E-4	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.61980	0.06;0.06	5.87	5.87	0.94306	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.78553	0.4301	M	0.67397	2.05	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	T	0.75121	-0.3429	10	0.38643	T	0.18	.	20.2079	0.98282	0.0:0.0:1.0:0.0	.	442	Q8N8U9	BMPER_HUMAN	D	442	ENSP00000297161:G442D;ENSP00000393950:G442D	ENSP00000297161:G442D	G	+	2	0	BMPER	34085240	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.461000	0.97646	2.781000	0.95711	0.655000	0.94253	GGC		0.672	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		A	34118715	G	A	34118715	3	1	111	1	0	0	0	0	1	0	0	0	1469	1203	42	3	1371	3	BMPER	7	34118715	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3219832	34118715	125019948	401	29535										
ANLN	54443	hgsc.bcm.edu	37	chr7	36489339	36489340	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagaaccagccaacagagaaINSttttgtgcaagacgcaacac							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:36489339_36489340insT	ENST00000265748.2	+	23	3365_3366	c.3144_3145insT	c.(3145-3147)tttfs	p.F1049fs	ANLN_ENST00000396068.2_Frame_Shift_Ins_p.F1012fs	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	1049	Localization to the cleavage furrow.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						CCAACAGAGAATTTTGTGCAAG	0.391																																																0			7																																								36455865	SO:0001589	frameshift_variant	54443			AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.3148dupT	7.37:g.36489343_36489343dupT	ENSP00000265748:p.Phe1049fs		36455864	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Frame_Shift_Ins	INS	ENST00000265748.2	37	CCDS5447.1																																																																																				0.391	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		T	36489340	-	T	36489339	7	5	111	1	0	1	1	0	0	0	0	0	694	98	4	0	3234	0	ANLN	7	36489339	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	2370624	36489339	122649324	402	29536										
ELMO1	9844	hgsc.bcm.edu	37	chr7	36910015	36910015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taccttgttttgtttaagggCacctttctctttcatatgag	7	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:36910015C>T	ENST00000310758.4	-	20	2535	c.1888G>A	c.(1888-1890)Gcc>Acc	p.A630T	ELMO1_ENST00000396040.2_Missense_Mutation_p.A150T|ELMO1_ENST00000442504.1_Missense_Mutation_p.A630T|ELMO1_ENST00000448602.1_Missense_Mutation_p.A630T|ELMO1_ENST00000396045.3_Missense_Mutation_p.A150T|ELMO1_ENST00000341056.3_Missense_Mutation_p.A332T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	630	PH.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						TGTTTAAGGGCACCTTTCTCT	0.453																																																0			7											190	170	177					7																	36910015		2203	4300	6503	36876540	SO:0001583	missense	9844			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1888G>A	7.37:g.36910015C>T	ENSP00000312185:p.Ala630Thr		36876540	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	37	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.287465	0.80803	.	.	ENSG00000155849	ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.41	5.41	0.78517	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.44623	0.1302	M	0.62723	1.935	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.28202	-1.0051	10	0.30078	T	0.28	.	19.568	0.95403	0.0:1.0:0.0:0.0	.	630	Q92556	ELMO1_HUMAN	T	332;150;630;534;150;630;630	ENSP00000342142:A332T;ENSP00000379360:A150T;ENSP00000312185:A630T;ENSP00000379355:A150T;ENSP00000406952:A630T;ENSP00000394458:A630T	ENSP00000312185:A630T	A	-	1	0	ELMO1	36876540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.709000	0.92574	0.655000	0.94253	GCC		0.453	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		T	36910015	C	T	36910015	3	4	111	1	0	0	0	0	1	0	0	0	5078	710	25	3	307	3	ELMO1	7	36910015	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	420676	36910015	122228648	403	29537										
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37901718	37901718	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatcgatgaggagagaaaaaTtgcagcaggtgaaatggctc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:37901718delT	ENST00000199447.4	+	7	731	c.359delT	c.(358-360)attfs	p.I120fs	NME8_ENST00000440017.1_Frame_Shift_Del_p.I120fs|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	120					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										GAGAGAAAAATTGCAGCAGGT	0.348																																																0			7											55	59	57					7																	37901718		2203	4300	6503	37868243	SO:0001589	frameshift_variant	51314			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.359delT	7.37:g.37901718delT	ENSP00000199447:p.Ile120fs		37868243	Q9NZH1	Frame_Shift_Del	DEL	ENST00000199447.4	37	CCDS5452.1																																																																																				0.348	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		-	37901718	T	-	37901718	7	5	111	1	0	1	0	1	0	0	0	0	16838	1493	52	0	377	0	TXNDC3	7	37901718	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	991703	37901718	121236945	404	29538										
SFRP4	6424	hgsc.bcm.edu	37	chr7	37955923	37955923	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcacagaggaagaagcgcaGcacggcgctgcagttcacgt	15	11	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:37955923G>A	ENST00000436072.2	-	1	594	c.217C>T	c.(217-219)Ctg>Ttg	p.L73L	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	73	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						AAGAAGCGCAGCACGGCGCTG	0.637																																																0			7											148	117	127					7																	37955923		2203	4300	6503	37922448	SO:0001819	synonymous_variant	6424			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.217C>T	7.37:g.37955923G>A			37922448	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Silent	SNP	ENST00000436072.2	37	CCDS5453.1																																																																																				0.637	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		A	37955923	G	A	37955923	2	1	111	1	0	0	0	0	0	0	0	1	14200	962	34	3		3	SFRP4	7	37955923	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	54205	37955923	121182740	405	29539										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729928	41729928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagagcaacagttcactccTctccccctttaagcccactt	5	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:41729928T>C	ENST00000242208.4	-	3	847	c.601A>G	c.(601-603)Agg>Ggg	p.R201G	INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_Missense_Mutation_p.R201G	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	201					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						AGTTCACTCCTCTCCCCCTTT	0.587										TSP Lung(11;0.080)																																						0			7											82	74	77					7																	41729928		2203	4300	6503	41696453	SO:0001583	missense	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.601A>G	7.37:g.41729928T>C	ENSP00000242208:p.Arg201Gly		41696453	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	15.46	2.839553	0.51057	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.64260	-0.09;-0.09	6.06	4.88	0.63580	Transforming growth factor-beta, N-terminal (1);	0.503516	0.23021	N	0.052848	T	0.48960	0.1529	L	0.29908	0.895	0.41012	D	0.985016	B	0.06786	0.001	B	0.06405	0.002	T	0.36163	-0.9759	10	0.19590	T	0.45	-14.8981	13.4032	0.60896	0.0:0.0:0.1312:0.8688	.	201	P08476	INHBA_HUMAN	G	201	ENSP00000242208:R201G;ENSP00000397197:R201G	ENSP00000242208:R201G	R	-	1	2	INHBA	41696453	0.363000	0.24989	1.000000	0.80357	0.998000	0.95712	2.722000	0.47269	1.079000	0.41038	0.533000	0.62120	AGG		0.587	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			C	41729928	T	C	41729928	3	2	111	1	0	0	0	0	1	0	0	0	7762	1550	54	4	683	4	INHBA	7	41729928	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3774005	41729928	117408735	406	29540										
URGCP	55665	hgsc.bcm.edu	37	chr7	43917500	43917500	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctcagccctgtgcttctcaGgggggtccacggcccactgg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:43917500delG	ENST00000453200.1	-	6	2055	c.1562delC	c.(1561-1563)cctfs	p.P521fs	URGCP_ENST00000336086.6_Frame_Shift_Del_p.P478fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.P478fs|URGCP_ENST00000497914.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Frame_Shift_Del_p.P512fs|URGCP_ENST00000447717.3_Frame_Shift_Del_p.P478fs|URGCP_ENST00000443736.1_Frame_Shift_Del_p.P478fs			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	521					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GTGCTTCTCAGGGGGGTCCAC	0.642																																																0			7											52	56	55					7																	43917500		1972	4162	6134	43884025	SO:0001589	frameshift_variant	0				CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1562delC	7.37:g.43917500delG	ENSP00000396918:p.Pro521fs		43884025	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	37	CCDS47578.1																																																																																				0.642	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		-	43917500	G	-	43917500	7	5	111	1	0	1	0	1	0	0	0	0	17066	1000	35	0	1237	0	URGCP	7	43917500	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	2187572	43917500	115221163	407	29541										
GCK	2645	hgsc.bcm.edu	37	chr7	44184795	44184795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagaccagggccgcgccccgGccactgccctcctccgactc	11	21	0	1	rs193922274		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:44184795G>A	ENST00000403799.3	-	10	1807	c.1338C>T	c.(1336-1338)ggC>ggT	p.G446G	GCK_ENST00000395796.3_Silent_p.G445G|GCK_ENST00000345378.2_Silent_p.G447G|GCK_ENST00000437084.1_Silent_p.G429G	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	446	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						CCGCGCCCCGGCCACTGCCCT	0.667																																																0			7											19	22	21					7																	44184795		2203	4298	6501	44151320	SO:0001819	synonymous_variant	5871			AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.1338C>T	7.37:g.44184795G>A			44151320	A4D2J2|A4D2J3|Q05810	Silent	SNP	ENST00000403799.3	37	CCDS5479.1																																																																																				0.667	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			A	44184795	G	A	44184795	2	1	111	1	0	0	0	0	0	0	0	1	6313	1190	42	3		3	GCK	7	44184795	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	267295	44184795	114953868	408	29542										
TBRG4	9238	hgsc.bcm.edu	37	chr7	45140958	45140958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaagttggggaactcccaccGcaagaacgctagcctggaag	13	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:45140958G>A	ENST00000258770.3	-	10	1814	c.1693C>T	c.(1693-1695)Cgg>Tgg	p.R565W	TBRG4_ENST00000395655.4_Missense_Mutation_p.R455W|SNORA5A_ENST00000384111.1_RNA|TBRG4_ENST00000361278.3_Missense_Mutation_p.R455W|TBRG4_ENST00000494076.1_Missense_Mutation_p.R565W	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	565	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						AACTCCCACCGCAAGAACGCT	0.557																																																0			7											63	65	64					7																	45140958		2202	4300	6502	45107483	SO:0001583	missense	9238			AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"FAST kinase domains 4", "cell cycle progression 2 protein"	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.1693C>T	7.37:g.45140958G>A	ENSP00000258770:p.Arg565Trp		45107483	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Missense_Mutation	SNP	ENST00000258770.3	37	CCDS5501.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910751	0.52439	.	.	ENSG00000136270	ENST00000258770;ENST00000361278;ENST00000395655;ENST00000494076	T;T;T;T	0.17528	3.11;2.27;2.27;3.11	4.79	2.86	0.33363	RAP domain (2);	0.247435	0.31381	N	0.007754	T	0.25901	0.0631	L	0.36672	1.1	0.09310	N	0.999998	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.72338	0.91;0.977;0.809	T	0.03566	-1.1024	10	0.39692	T	0.17	.	7.9073	0.29769	0.0:0.1435:0.3609:0.4956	.	576;455;565	B4DU42;Q969Z0-2;Q969Z0	.;.;TBRG4_HUMAN	W	565;455;455;565	ENSP00000258770:R565W;ENSP00000354992:R455W;ENSP00000379016:R455W;ENSP00000420597:R565W	ENSP00000258770:R565W	R	-	1	2	TBRG4	45107483	0.000000	0.05858	0.705000	0.30386	0.994000	0.84299	0.225000	0.17757	0.523000	0.28482	0.591000	0.81541	CGG		0.557	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900		A	45140958	G	A	45140958	3	1	111	1	0	0	0	0	1	0	0	0	15688	1086	38	1	210	1	TBRG4	7	45140958	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	956163	45140958	113997705	409	29543										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50450341	50450341	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggggagaagcccttcaaatgCcacctctgcaactacgcctg	10	14	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:50450341C>T	ENST00000331340.3	+	5	680	c.525C>T	c.(523-525)tgC>tgT	p.C175C	IKZF1_ENST00000343574.5_Silent_p.C88C|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000438033.1_Silent_p.C88C|IKZF1_ENST00000439701.1_Silent_p.C175C|IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000359197.5_Silent_p.C175C|IKZF1_ENST00000440768.2_Silent_p.C175C|IKZF1_ENST00000357364.4_Silent_p.C175C	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	175					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				CCTTCAAATGCCACCTCTGCA	0.642			"D,T"	BCL6	"ALL, DLBCL"																																		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	7											27	33	31					7																	50450341		2159	4274	6433	50417835	SO:0001819	synonymous_variant	10320			U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.525C>T	7.37:g.50450341C>T			50417835	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																					0.642	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50450341	C	T	50450341	2	4	111	1	0	0	0	0	0	0	0	1	7635	747	26	3		3	IKZF1	7	50450341	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5309383	50450341	108688322	410	29544										
COBL	23242	hgsc.bcm.edu	37	chr7	51092918	51092918	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctggaggccgtccttggtGcagagagagcctgggagggt	18	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:51092918G>T	ENST00000265136.7	-	12	3821	c.3656C>A	c.(3655-3657)gCa>gAa	p.A1219E	COBL_ENST00000395542.2_Missense_Mutation_p.A1301E|RP4-724E13.2_ENST00000582616.1_RNA	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1219					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CGTCCTTGGTGCAGAGAGAGC	0.647																																					NSCLC(189;2119 2138 12223 30818 34679)											0			7											39	37	38					7																	51092918		2203	4300	6503	51060412	SO:0001583	missense	23242			AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3656C>A	7.37:g.51092918G>T	ENSP00000265136:p.Ala1219Glu		51060412	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	G	7.628	0.678268	0.14841	.	.	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.17528	2.67;2.27;2.67;2.66	5.14	3.0	0.34707	.	1.348390	0.05507	N	0.559453	T	0.20536	0.0494	L	0.47716	1.5	0.09310	N	1	B;B;B;B;P	0.42620	0.13;0.13;0.112;0.178;0.785	B;B;B;B;B	0.43103	0.149;0.149;0.036;0.053;0.408	T	0.22277	-1.0221	10	0.56958	D	0.05	.	7.1426	0.25564	0.2887:0.0:0.7113:0.0	.	1172;1229;1219;1301;761	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	E	1219;1064;1104;1301	ENSP00000265136:A1219E;ENSP00000401204:A1064E;ENSP00000413498:A1104E;ENSP00000378912:A1301E	ENSP00000265136:A1219E	A	-	2	0	COBL	51060412	0.000000	0.05858	0.002000	0.10522	0.146000	0.21551	0.878000	0.28126	1.059000	0.40554	0.650000	0.86243	GCA		0.647	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51092918	G	T	51092918	3	4	111	1	0	0	0	0	1	0	0	0	3659	1319	46	2	137	2	COBL	7	51092918	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	642577	51092918	108045745	411	29545										
ZNF716	441234	hgsc.bcm.edu	37	chr7	57528706	57528706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagacacaagacaagacataCtggaaagaaacatttcaaat	6	7	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:57528706C>T	ENST00000420713.1	+	4	651	c.539C>T	c.(538-540)aCt>aTt	p.T180I		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						ACAAGACATACTGGAAAGAAA	0.338																																																0			7											77	67	70					7																	57528706		692	1591	2283	57532648	SO:0001583	missense	441234			AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"Zinc fingers, C2H2-type", "-"	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.539C>T	7.37:g.57528706C>T	ENSP00000394248:p.Thr180Ile		57532648		Missense_Mutation	SNP	ENST00000420713.1	37	CCDS55112.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751760	0.31046	.	.	ENSG00000182111	ENST00000420713;ENST00000418732	T	0.19105	2.17	0.195	0.195	0.15151	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31358	0.0794	L	0.54863	1.705	0.27546	N	0.950642	D	0.69078	0.997	P	0.60012	0.867	T	0.13019	-1.0525	9	0.62326	D	0.03	.	6.2336	0.20750	0.0:0.9997:0.0:3.0E-4	.	168	A6NP11	ZN716_HUMAN	I	180;168	ENSP00000394248:T180I	ENSP00000387687:T168I	T	+	2	0	ZNF716	57532648	0.000000	0.05858	0.075000	0.20258	0.075000	0.17131	0.608000	0.24223	0.300000	0.22699	0.306000	0.20318	ACT		0.338	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279		T	57528706	C	T	57528706	3	4	111	1	0	0	0	0	1	0	0	0	18158	565	20	3	553	3	ZNF716	7	57528706	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6435788	57528706	101609957	412	29546										
DTX2	113878	hgsc.bcm.edu	37	chr7	76129798	76129798	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagagccagagcaggtcatAaaaaactacacggaagagct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:76129798delA	ENST00000324432.5	+	8	1701	c.1191delA	c.(1189-1191)atafs	p.I397fs	DTX2_ENST00000446600.1_Frame_Shift_Del_p.I306fs|DTX2_ENST00000446820.2_Frame_Shift_Del_p.I350fs|DTX2_ENST00000413936.2_Frame_Shift_Del_p.I397fs|DTX2_ENST00000307569.8_Frame_Shift_Del_p.I350fs|DTX2_ENST00000430490.2_Frame_Shift_Del_p.I397fs	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	397					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						AGCAGGTCATAAAAAACTACA	0.527																																																0			7											3	4	4					7																	76129798		1495	3503	4998	75967734	SO:0001589	frameshift_variant	113878				CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"RING-type (C3HC4) zinc fingers"	15973	protein-coding gene	gene with protein product		613141	"deltex (Drosophila) homolog 2", "deltex homolog 2 (Drosophila)"			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1191delA	7.37:g.76129798delA	ENSP00000322885:p.Ile397fs		75967734	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Frame_Shift_Del	DEL	ENST00000324432.5	37	CCDS5587.1																																																																																				0.527	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			-	76129798	A	-	76129798	7	5	111	1	0	1	0	1	0	0	0	0	4805	352	13	0	1209	0	DTX2	7	76129798	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	18601092	76129798	83008865	413	29547										
GRM3	2913	hgsc.bcm.edu	37	chr7	86493618	86493618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctctgcaagcacgtatgtgCcaacggtgtgcaatgggcgg	14	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:86493618C>T	ENST00000361669.2	+	6	3686	c.2587C>T	c.(2587-2589)Cca>Tca	p.P863S	GRM3_ENST00000439827.1_Missense_Mutation_p.A507V|GRM3_ENST00000394720.2_Missense_Mutation_p.A505V|GRM3_ENST00000536043.1_Missense_Mutation_p.P735S|GRM3_ENST00000546348.1_Missense_Mutation_p.P455S	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	863					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CACGTATGTGCCAACGGTGTG	0.448																																					GBM(52;969 1098 3139 52280)											0			7											263	217	233					7																	86493618		2203	4300	6503	86331554	SO:0001583	missense	2913				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2587C>T	7.37:g.86493618C>T	ENSP00000355316:p.Pro863Ser		86331554	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.0|28.0	4.879377|4.879377	0.91740|0.91740	.|.	.|.	ENSG00000198822|ENSG00000198822	ENST00000439827;ENST00000394720|ENST00000361669;ENST00000546348;ENST00000536043	D;D|D;D;D	0.89050|0.88201	-2.46;-2.46|-2.35;-2.24;-2.13	5.99|5.99	5.99|5.99	0.97316|0.97316	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91623|0.91623	0.7353|0.7353	L|L	0.32530|0.32530	0.975|0.975	0.31519|0.31519	N|N	0.662644|0.662644	B|D;D;D	0.17038|0.89917	0.02|0.999;1.0;1.0	B|D;D;D	0.16289|0.91635	0.015|0.972;0.999;0.998	D|D	0.89127|0.89127	0.3507|0.3507	9|10	0.32370|0.32370	T|T	0.25|0.25	.|.	19.4659|19.4659	0.94939|0.94939	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	507|455;735;863	G5E9K2|B7Z204;F5GYZ2;Q14832	.|.;.;GRM3_HUMAN	V|S	507;505|863;455;735	ENSP00000398767:A507V;ENSP00000378209:A505V|ENSP00000355316:P863S;ENSP00000444064:P455S;ENSP00000441407:P735S	ENSP00000378209:A505V|ENSP00000355316:P863S	A|P	+|+	2|1	0|0	GRM3|GRM3	86331554|86331554	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.961000|0.961000	0.63080|0.63080	6.741000|6.741000	0.74837|0.74837	2.840000|2.840000	0.97914|0.97914	0.655000|0.655000	0.94253|0.94253	GCC|CCA		0.448	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			T	86493618	C	T	86493618	3	4	111	1	0	0	0	0	1	0	0	0	6819	739	26	3	2605	3	GRM3	7	86493618	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10363820	86493618	72645045	414	29548										
FZD1	8321	hgsc.bcm.edu	37	chr7	90895699	90895699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcttcgtgtacctgtttatcGgcacgtcctttctgctggcc	9	13	2	0	rs368484423		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:90895699G>A	ENST00000287934.2	+	1	1917	c.1504G>A	c.(1504-1506)Ggc>Agc	p.G502S		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	502					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.G502C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			CCTGTTTATCGGCACGTCCTT	0.602																																																1	Substitution - Missense(1)	lung(1)	7											173	153	159					7																	90895699		2203	4300	6503	90733635	SO:0001583	missense	8321			AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1504G>A	7.37:g.90895699G>A	ENSP00000287934:p.Gly502Ser		90733635	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.013112	0.93346	.	.	ENSG00000157240	ENST00000287934	D	0.92099	-2.97	4.79	4.79	0.61399	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000003	D	0.97263	0.9105	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98397	1.0566	10	0.87932	D	0	.	18.0221	0.89258	0.0:0.0:1.0:0.0	.	502	Q9UP38	FZD1_HUMAN	S	502	ENSP00000287934:G502S	ENSP00000287934:G502S	G	+	1	0	FZD1	90733635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.491000	0.84063	0.655000	0.94253	GGC		0.602	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		A	90895699	G	A	90895699	3	1	111	1	0	0	0	0	1	0	0	0	6147	1116	39	1	1506	1	FZD1	7	90895699	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4402081	90895699	68242964	415	29549										
NPTX2	4885	hgsc.bcm.edu	37	chr7	98254334	98254334	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagacgctgcctgagctgtaCgccttcaccatctgcctgtg	10	14	2	2	rs201376730	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:98254334C>T	ENST00000265634.3	+	3	909	c.744C>T	c.(742-744)taC>taT	p.Y248Y		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	248	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			CTGAGCTGTACGCCTTCACCA	0.587													C|||	2	0.000399361	0	0.0014	5008	,	,		19127	0		0	False		,,,				2504	0.001															0			7						C		0,4406		0,0,2203	193	151	165		744	-5.5	0.9	7		165	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NPTX2	NM_002523.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		248/432	98254334	1,13005	2203	4300	6503	98092270	SO:0001819	synonymous_variant	4885				CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.744C>T	7.37:g.98254334C>T			98092270	A4D267|Q86XV7|Q96G70	Silent	SNP	ENST00000265634.3	37	CCDS5657.1																																																																																				0.587	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		T	98254334	C	T	98254334	2	4	111	1	0	0	0	0	0	0	0	1	10634	547	19	1		1	NPTX2	7	98254334	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7358635	98254334	60884329	416	29550										
ZKSCAN5	23660	hgsc.bcm.edu	37	chr7	99103706	99103706	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgagaagttatagacttagaCcccccagctgagacttccca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:99103706delC	ENST00000394170.2	+	2	290	c.39delC	c.(37-39)gacfs	p.D13fs	ZKSCAN5_ENST00000451158.1_Frame_Shift_Del_p.D13fs|ZKSCAN5_ENST00000326775.5_Frame_Shift_Del_p.D13fs	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TAGACTTAGACCCCCCAGCTG	0.483																																																0			7											85	88	87					7																	99103706		2203	4300	6503	98941642	SO:0001589	frameshift_variant	23660			AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.39delC	7.37:g.99103706delC	ENSP00000377725:p.Asp13fs		98941642	A4D280|D6W5S9	Frame_Shift_Del	DEL	ENST00000394170.2	37	CCDS5667.1																																																																																				0.483	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		-	99103706	C	-	99103706	7	5	111	1	0	1	0	1	0	0	0	0	17729	506	18	0	41	0	ZKSCAN5	7	99103706	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	849372	99103706	60034957	417	29551										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100084616	100084616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccgcagcgccatggccccaCgctccctctcctgccactcg	9	22	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:100084616C>T	ENST00000300179.2	+	3	400	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C	NYAP1_ENST00000423930.1_Missense_Mutation_p.R81C|NYAP1_ENST00000454988.1_Missense_Mutation_p.R24C	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	81	Involved in CYFIP1- and NCKAP1-binding. {ECO:0000250}.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CATGGCCCCACGCTCCCTCTC	0.711																																																0			7											11	14	13					7																	100084616		2153	4238	6391	99922552	SO:0001583	missense	222950			AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.241C>T	7.37:g.100084616C>T	ENSP00000300179:p.Arg81Cys		99922552	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911831	0.92178	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.58210	0.35;0.35;0.35	5.03	5.03	0.67393	.	0.000000	0.51477	D	0.000086	T	0.70789	0.3264	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.73711	-0.3897	10	0.87932	D	0	-19.1738	15.8881	0.79269	0.0:1.0:0.0:0.0	.	81	Q6ZVC0	CG051_HUMAN	C	81;81;24	ENSP00000300179:R81C;ENSP00000411861:R81C;ENSP00000394424:R24C	ENSP00000300179:R81C	R	+	1	0	C7orf51	99922552	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	6.628000	0.74262	2.606000	0.88127	0.462000	0.41574	CGC		0.711	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100084616	C	T	100084616	3	4	111	1	0	0	0	0	1	0	0	0	2406	536	19	1	247	1	C7orf51	7	100084616	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	980910	100084616	59054047	418	29552										
MOSPD3	64598	hgsc.bcm.edu	37	chr7	100212789	100212789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccaggcctcctcaccatgGtgttcctccggacctgagct	9	17	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:100212789G>A	ENST00000393950.2	+	5	973	c.691G>A	c.(691-693)Gtg>Atg	p.V231M	MOSPD3_ENST00000223054.4_Missense_Mutation_p.V231M|MOSPD3_ENST00000379527.2_Missense_Mutation_p.V231M|MOSPD3_ENST00000424091.2_Missense_Mutation_p.V221M	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	231					heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CCTCACCATGGTGTTCCTCCG	0.617																																																0			7											111	103	106					7																	100212789		2203	4300	6503	100050725	SO:0001583	missense	64598			BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.691G>A	7.37:g.100212789G>A	ENSP00000377522:p.Val231Met		100050725	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Missense_Mutation	SNP	ENST00000393950.2	37	CCDS5701.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.041079	0.75732	.	.	ENSG00000106330	ENST00000223054;ENST00000379527;ENST00000393950;ENST00000424091;ENST00000393953	.	.	.	4.92	4.92	0.64577	.	0.000000	0.48286	D	0.000189	T	0.69602	0.3129	L	0.49778	1.585	0.45676	D	0.998599	D;D	0.71674	0.998;0.998	D;D	0.81914	0.987;0.995	T	0.71663	-0.4525	9	0.72032	D	0.01	-11.6933	13.4794	0.61326	0.0:0.0:1.0:0.0	.	221;231	C9JE89;O75425	.;MSPD3_HUMAN	M	231;231;231;221;217	.	ENSP00000223054:V231M	V	+	1	0	MOSPD3	100050725	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.921000	0.48852	2.559000	0.86315	0.655000	0.94253	GTG		0.617	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	NM_023948		A	100212789	G	A	100212789	3	1	111	1	0	0	0	0	1	0	0	0	9747	1261	44	3	709	3	MOSPD3	7	100212789	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	128173	100212789	58925874	419	29553										
ZAN	7455	hgsc.bcm.edu	37	chr7	100363155	100363155	+	RNA	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcccagtgtgggtgcctccAccctgcaggcagctacttca					rs201491474		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:100363155delA	ENST00000348028.3	+	0	4613				ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GGGTGCCTCCACCCTGCAGGC	0.622																																																0			7											28	31	30					7																	100363155		2081	4211	6292	100201091			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100363155delA			100201091	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Frame_Shift_Del	DEL	ENST00000348028.3	37																																																																																					0.622	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		-	100363155	A	-	100363155	6	5	111	0	1	1	0	1	0	0	0	0	17553	159	6	0		0	ZAN	7	100363155	RNA	DEL	A	TCGA-EI-6507-01A-11D-1733-10	150366	100363155	58775508	420	29554										
MUC17	140453	hgsc.bcm.edu	37	chr7	100679543	100679543	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagccagttcatctacaaccGctgaaggtagcagcatgaca	9	11	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:100679543G>A	ENST00000306151.4	+	3	4910	c.4846G>A	c.(4846-4848)Gct>Act	p.A1616T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1616	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.A1616T(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ATCTACAACCGCTGAAGGTAG	0.502																																																1	Substitution - Missense(1)	lung(1)	7											200	203	202					7																	100679543		2203	4300	6503	100466263	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4846G>A	7.37:g.100679543G>A	ENSP00000302716:p.Ala1616Thr		100466263	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	3.466	-0.109007	0.06924	.	.	ENSG00000169876	ENST00000306151	T	0.02085	4.46	0.806	0.806	0.18708	.	.	.	.	.	T	0.00998	0.0033	N	0.14661	0.345	0.09310	N	1	B	0.33171	0.4	B	0.17098	0.017	T	0.39143	-0.9628	9	0.02654	T	1	.	5.0545	0.14525	0.0:0.0:1.0:0.0	.	1616	Q685J3	MUC17_HUMAN	T	1616	ENSP00000302716:A1616T	ENSP00000302716:A1616T	A	+	1	0	MUC17	100466263	0.000000	0.05858	0.005000	0.12908	0.020000	0.10135	-4.472000	0.00228	0.772000	0.33382	0.064000	0.15345	GCT		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100679543	G	A	100679543	3	1	111	1	0	0	0	0	1	0	0	0	10004	1087	38	1	4856	1	MUC17	7	100679543	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	316388	100679543	58459120	421	29555										
CUX1	1523	hgsc.bcm.edu	37	chr7	101839974	101839974	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgcccgggatctttgccggCcccccctccttctcagttgc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:101839974delC	ENST00000292535.7	+	15	1321	c.1283delC	c.(1282-1284)gccfs	p.A428fs	CUX1_ENST00000550008.2_Frame_Shift_Del_p.A428fs|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000292538.4_Intron|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Frame_Shift_Del_p.A439fs|CUX1_ENST00000549414.2_Frame_Shift_Del_p.A428fs	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	428					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TCTTTGCCGGCCCCCCCTCCT	0.567																																																0			7											38	49	45					7																	101839974		2200	4299	6499	101626694	SO:0001589	frameshift_variant	1523			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1283delC	7.37:g.101839974delC	ENSP00000292535:p.Ala428fs		101626694	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Frame_Shift_Del	DEL	ENST00000292535.7	37	CCDS5721.1																																																																																				0.567	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		-	101839974	C	-	101839974	7	5	111	1	0	1	0	1	0	0	0	0	4070	739	26	0	1408	0	CUX1	7	101839974	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1160431	101839974	57298689	422	29556										
FBXL13	222235	hgsc.bcm.edu	37	chr7	102523814	102523814	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtgaaagggatctgaggctGctgtctgttattcccttgca	13	8	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:102523814G>A	ENST00000313221.4	-	14	1752	c.1326C>T	c.(1324-1326)agC>agT	p.S442S	FBXL13_ENST00000455112.2_Silent_p.S442S|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000379308.3_Silent_p.S442S|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379305.3_Silent_p.S442S|FBXL13_ENST00000393772.2_Silent_p.S442S|FBXL13_ENST00000436908.1_Silent_p.S442S	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	442										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						ATCTGAGGCTGCTGTCTGTTA	0.363																																																0			7											120	113	115					7																	102523814		2203	4300	6503	102311050	SO:0001819	synonymous_variant	222235			BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.1326C>T	7.37:g.102523814G>A			102311050	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	37	CCDS5726.1																																																																																				0.363	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		A	102523814	G	A	102523814	2	1	111	1	0	0	0	0	0	0	0	1	5728	1310	46	3		3	FBXL13	7	102523814	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	683840	102523814	56614849	423	29557										
RELN	5649	hgsc.bcm.edu	37	chr7	103234167	103234167	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaggtttcagggtcaaatCtcgagttactgcaaatcgat	9	9	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:103234167C>T	ENST00000428762.1	-	27	4033	c.3874G>A	c.(3874-3876)Gat>Aat	p.D1292N	RELN_ENST00000343529.5_Missense_Mutation_p.D1292N|RELN_ENST00000424685.2_Missense_Mutation_p.D1292N	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1292					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGGGTCAAATCTCGAGTTACT	0.393																																					NSCLC(146;835 1944 15585 22231 52158)											0			7											170	159	163					7																	103234167		2203	4300	6503	103021403	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.3874G>A	7.37:g.103234167C>T	ENSP00000392423:p.Asp1292Asn		103021403	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175135	0.94807	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.26957	1.7;1.7;1.7	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.54870	0.1885	M	0.76170	2.325	0.58432	D	0.999999	P;D	0.69078	0.929;0.997	B;D	0.73380	0.399;0.98	T	0.51949	-0.8640	10	0.62326	D	0.03	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	1292;1292	P78509-2;P78509	.;RELN_HUMAN	N	1292	ENSP00000392423:D1292N;ENSP00000345694:D1292N;ENSP00000388446:D1292N	ENSP00000345694:D1292N	D	-	1	0	RELN	103021403	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.270000	0.78493	2.885000	0.99019	0.655000	0.94253	GAT		0.393	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103234167	C	T	103234167	3	4	111	1	0	0	0	0	1	0	0	0	13257	913	32	3	6664	3	RELN	7	103234167	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	710353	103234167	55904496	424	29558										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106508432	106508432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacctggtgcagcggcacccGccctccgaggagtcccaagc	12	18	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:106508432G>A	ENST00000359195.3	+	2	736	c.426G>A	c.(424-426)ccG>ccA	p.P142P	PIK3CG_ENST00000496166.1_Silent_p.P142P|PIK3CG_ENST00000440650.2_Silent_p.P142P	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	142					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						AGCGGCACCCGCCCTCCGAGG	0.637																																																0			7											16	19	18					7																	106508432		2200	4286	6486	106295668	SO:0001819	synonymous_variant	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.426G>A	7.37:g.106508432G>A			106295668	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	CCDS5739.1																																																																																				0.637	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			A	106508432	G	A	106508432	2	1	111	1	0	0	0	0	0	0	0	1	11947	1074	38	1		1	PIK3CG	7	106508432	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3274265	106508432	52630231	425	29559										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112090792	112090792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccaccgcggtagcagtgctGgcggcggcgggtcaggagca	18	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:112090792G>A	ENST00000403825.3	+	1	310	c.49G>A	c.(49-51)Ggc>Agc	p.G17S	IFRD1_ENST00000429071.1_Missense_Mutation_p.G17S|IFRD1_ENST00000005558.4_Missense_Mutation_p.G17S|IFRD1_ENST00000535603.1_5'Flank	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	17	Poly-Gly.				adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						tagcagtgctggcggcggcgg	0.692																																																0			7											17	20	19					7																	112090792		2085	4095	6180	111878028	SO:0001583	missense	3475			Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.49G>A	7.37:g.112090792G>A	ENSP00000384477:p.Gly17Ser		111878028	B7Z5G1|O75234|Q5U013|Q9BVE4	Missense_Mutation	SNP	ENST00000403825.3	37	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942021	0.73557	.	.	ENSG00000006652	ENST00000432734;ENST00000005558;ENST00000445335;ENST00000417662;ENST00000403825;ENST00000429071	T;T	0.42513	0.97;0.97	4.98	4.11	0.48088	.	.	.	.	.	T	0.19208	0.0461	N	0.08118	0	0.80722	D	1	B;P	0.42908	0.002;0.793	B;B	0.35655	0.004;0.207	T	0.04664	-1.0935	9	0.11794	T	0.64	-2.3695	12.2318	0.54492	0.0842:0.0:0.9158:0.0	.	17;17	C9JA65;O00458	.;IFRD1_HUMAN	S	17	ENSP00000005558:G17S;ENSP00000384477:G17S	ENSP00000005558:G17S	G	+	1	0	IFRD1	111878028	0.981000	0.34729	0.982000	0.44146	0.993000	0.82548	0.639000	0.24690	1.328000	0.45358	0.591000	0.81541	GGC		0.692	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		A	112090792	G	A	112090792	3	1	111	1	0	0	0	0	1	0	0	0	7574	1348	47	3	51	3	IFRD1	7	112090792	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5582360	112090792	47047871	426	29560										
WNT2	7472	hgsc.bcm.edu	37	chr7	116960704	116960704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctggcggaactggtgctggCattctgctgtccactcggcc	14	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:116960704C>T	ENST00000265441.3	-	2	526	c.227G>A	c.(226-228)tGc>tAc	p.C76Y	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	76					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CTGGTGCTGGCATTCTGCTGT	0.597																																																0			7											80	62	68					7																	116960704		2203	4300	6503	116747940	SO:0001583	missense	7472			X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.227G>A	7.37:g.116960704C>T	ENSP00000265441:p.Cys76Tyr		116747940	A4D0V1|Q75N05|Q9UDP9	Missense_Mutation	SNP	ENST00000265441.3	37	CCDS5771.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373323	0.82573	.	.	ENSG00000105989	ENST00000265441;ENST00000491214	D;D	0.91740	-2.9;-2.9	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.97707	0.9248	H	0.97390	3.995	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99023	1.0818	10	0.87932	D	0	.	18.2752	0.90080	0.0:1.0:0.0:0.0	.	76	P09544	WNT2_HUMAN	Y	76	ENSP00000265441:C76Y;ENSP00000419466:C76Y	ENSP00000265441:C76Y	C	-	2	0	WNT2	116747940	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.419000	0.80179	2.604000	0.88044	0.655000	0.94253	TGC		0.597	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		T	116960704	C	T	116960704	3	4	111	1	0	0	0	0	1	0	0	0	17426	710	25	3	871	3	WNT2	7	116960704	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4869912	116960704	42177959	427	29561										
CFTR	1080	hgsc.bcm.edu	37	chr7	117227809	117227809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ataggacatctccaagtttgCagagaaagacaatatagttc	8	7	1	2	rs387906368		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:117227809C>T	ENST00000003084.6	+	12	1733	c.1601C>T	c.(1600-1602)gCa>gTa	p.A534V	CFTR_ENST00000454343.1_Missense_Mutation_p.A473V	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	534	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TCCAAGTTTGCAGAGAAAGAC	0.353									Cystic Fibrosis																																							0			7	GRCh37	CM930112	CFTR	M							107	109	109					7																	117227809		2203	4300	6503	117015045	SO:0001583	missense	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1601C>T	7.37:g.117227809C>T	ENSP00000003084:p.Ala534Val		117015045	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034510	0.75617	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.90620	-2.7;-2.7;-2.7	5.06	5.06	0.68205	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.098818	0.64402	D	0.000001	D	0.88183	0.6368	L	0.43701	1.375	0.30372	N	0.782799	B	0.06786	0.001	B	0.04013	0.001	D	0.84410	0.0565	10	0.72032	D	0.01	-7.2422	18.8008	0.92016	0.0:1.0:0.0:0.0	.	534	P13569	CFTR_HUMAN	V	534;473;504	ENSP00000003084:A534V;ENSP00000403677:A473V;ENSP00000389119:A504V	ENSP00000003084:A534V	A	+	2	0	CFTR	117015045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.901000	0.75693	2.512000	0.84698	0.655000	0.94253	GCA		0.353	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117227809	C	T	117227809	3	4	111	1	0	0	0	0	1	0	0	0	3300	710	25	3	1647	3	CFTR	7	117227809	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	267105	117227809	41910854	428	29562										
GCC1	79571	hgsc.bcm.edu	37	chr7	127222472	127222472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggccgctgcaagttgtaatgCttgggtcaggctatcagagg	15	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:127222472C>A	ENST00000321407.2	-	2	2348	c.1924G>T	c.(1924-1926)Gca>Tca	p.A642S	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	642					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AGTTGTAATGCTTGGGTCAGG	0.582																																																0			7											120	118	119					7																	127222472		2203	4300	6503	127009708	SO:0001583	missense	79571			AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.1924G>T	7.37:g.127222472C>A	ENSP00000318821:p.Ala642Ser		127009708	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	37	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.249717	0.39797	.	.	ENSG00000179562	ENST00000321407	T	0.13196	2.61	5.49	5.49	0.81192	.	0.105501	0.64402	D	0.000005	T	0.19846	0.0477	L	0.41236	1.265	0.58432	D	0.999998	D	0.67145	0.996	P	0.55923	0.787	T	0.01829	-1.1265	10	0.08381	T	0.77	-5.8489	15.2337	0.73411	0.0:1.0:0.0:0.0	.	642	Q96CN9	GCC1_HUMAN	S	642	ENSP00000318821:A642S	ENSP00000318821:A642S	A	-	1	0	GCC1	127009708	1.000000	0.71417	0.996000	0.52242	0.020000	0.10135	5.219000	0.65262	2.733000	0.93635	0.655000	0.94253	GCA		0.582	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		A	127222472	C	A	127222472	3	1	111	1	0	0	0	0	1	0	0	0	6305	797	28	2	407	2	GCC1	7	127222472	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9994663	127222472	31916191	429	29563										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135412191	135412191	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcagcagcaggagcgggacGcagacgaccagcagcagctt	16	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:135412191G>A	ENST00000354042.4	-	1	743	c.54C>T	c.(52-54)tgC>tgT	p.C18C	FAM180A_ENST00000435869.1_5'Flank	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	18					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GGAGCGGGACGCAGACGACCA	0.701																																																0			7											28	25	26					7																	135412191		1914	3663	5577	135062731	SO:0001819	synonymous_variant	26266			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.54C>T	7.37:g.135412191G>A			135062731	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																				0.701	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		A	135412191	G	A	135412191	2	1	111	1	0	0	0	0	0	0	0	1	14431	1079	38	1		1	SLC13A4	7	135412191	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8189719	135412191	23726472	430	29564										
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139719863	139719863	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaaatctgccctaggtccAaaaaatggtgtctatatcaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:139719863delA	ENST00000336425.5	+	17	1955	c.1566delA	c.(1564-1566)ccafs	p.P522fs	TBXAS1_ENST00000458722.1_Frame_Shift_Del_p.P568fs|TBXAS1_ENST00000263552.6_Frame_Shift_Del_p.P523fs|TBXAS1_ENST00000416849.2_Frame_Shift_Del_p.P569fs|TBXAS1_ENST00000411653.1_3'UTR|TBXAS1_ENST00000414508.2_3'UTR|TBXAS1_ENST00000448866.1_Frame_Shift_Del_p.P522fs|TBXAS1_ENST00000436047.2_Frame_Shift_Del_p.P523fs|TBXAS1_ENST00000425687.1_Frame_Shift_Del_p.P455fs			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	522					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	CCCTAGGTCCAAAAAATGGTG	0.438																																																0			7											87	88	88					7																	139719863		2203	4300	6503	139366332	SO:0001589	frameshift_variant	6916			L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"Cytochrome P450s"	11609	protein-coding gene	gene with protein product	"cytochrome P450, family 5, subfamily A, polypeptide 1"	274180	"thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1566delA	7.37:g.139719863delA	ENSP00000338087:p.Pro522fs		139366332	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Frame_Shift_Del	DEL	ENST00000336425.5	37																																																																																					0.438	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			-	139719863	A	-	139719863	7	5	111	1	0	1	0	1	0	0	0	0	15703	117	5	0	1761	0	TBXAS1	7	139719863	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	4307672	139719863	19418800	431	29565										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142566291	142566291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccgcctgcagccacggggaCggagggagcagactgtggcc	18	13	0	1	rs56021232		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:142566291C>T	ENST00000392957.2	+	15	2867	c.2080C>T	c.(2080-2082)Cgg>Tgg	p.R694W	EPHB6_ENST00000411471.2_Missense_Mutation_p.R417W|EPHB6_ENST00000442129.1_Missense_Mutation_p.R694W	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	694	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GCCACGGGGACGGAGGGAGCA	0.662																																																0			7											24	25	24					7																	142566291		2193	4288	6481	142276413	SO:0001583	missense	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.2080C>T	7.37:g.142566291C>T	ENSP00000376684:p.Arg694Trp		142276413	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675241	0.29783	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	D;D;D	0.83163	-1.69;-1.69;-1.69	4.99	0.433	0.16534	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.41001	D	0.000978	D	0.86740	0.6005	L	0.50919	1.6	0.20489	N	0.999892	D;D	0.89917	1.0;1.0	D;P	0.65323	0.934;0.891	T	0.82364	-0.0494	10	0.87932	D	0	.	15.5848	0.76473	0.701:0.299:0.0:0.0	rs56021232	694;417	O15197;O15197-2	EPHB6_HUMAN;.	W	694;694;417	ENSP00000376684:R694W;ENSP00000410789:R694W;ENSP00000409061:R417W	ENSP00000376684:R694W	R	+	1	2	EPHB6	142276413	0.000000	0.05858	0.516000	0.27786	0.039000	0.13416	-0.004000	0.12878	-0.257000	0.09459	-0.448000	0.05591	CGG		0.662	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142566291	C	T	142566291	3	4	111	1	0	0	0	0	1	0	0	0	5191	527	19	1	2122	1	EPHB6	7	142566291	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2846428	142566291	16572372	432	29566										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142569516	142569516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccctgttgattatcccacGcaggtctctcctcagggtcc	8	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:142569516G>A	ENST00000359396.3	-	15	2367	c.2122C>T	c.(2122-2124)Cgt>Tgt	p.R708C		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	708	Interaction with calmodulin.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					ATTATCCCACGCAGGTCTCTC	0.567																																																0			7											72	72	72					7																	142569516		2203	4300	6503	142279638	SO:0001583	missense	55503			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.2122C>T	7.37:g.142569516G>A	ENSP00000352358:p.Arg708Cys		142279638	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369247	0.24771	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.57273	0.41	5.41	-1.3	0.09259	.	1.216240	0.05804	N	0.612710	T	0.47414	0.1444	L	0.47716	1.5	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.47636	-0.9102	10	0.46703	T	0.11	-4.4072	12.767	0.57396	0.0841:0.0:0.7625:0.1534	.	708	Q9H1D0	TRPV6_HUMAN	C	708;540	ENSP00000352358:R708C	ENSP00000310825:R540C	R	-	1	0	TRPV6	142279638	0.000000	0.05858	0.051000	0.19133	0.471000	0.32888	0.158000	0.16422	-0.085000	0.12573	0.561000	0.74099	CGT		0.567	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		A	142569516	G	A	142569516	3	1	111	1	0	0	0	0	1	0	0	0	16640	1087	38	1	59	1	TRPV6	7	142569516	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3225	142569516	16569147	433	29567										
ZYX	7791	hgsc.bcm.edu	37	chr7	143086972	143086972	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtacgccccgaggtgctccGtctgctctgagcccatcatg	11	15	3	1	rs569088357	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:143086972G>A	ENST00000322764.5	+	9	1861	c.1516G>A	c.(1516-1518)Gtc>Atc	p.V506I	ZYX_ENST00000449423.2_Missense_Mutation_p.V419I|EPHA1_ENST00000458129.1_5'Flank|ZYX_ENST00000392910.2_Missense_Mutation_p.V349I	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	506	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					GAGGTGCTCCGTCTGCTCTGA	0.607													G|||	9	0.00179712	0	0	5008	,	,		20108	0		0	False		,,,				2504	0.0092															0			7											99	83	88					7																	143086972		2203	4300	6503	142797094	SO:0001583	missense	7791			X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.1516G>A	7.37:g.143086972G>A	ENSP00000324422:p.Val506Ile		142797094	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.695800	0.68386	.	.	ENSG00000159840	ENST00000322764;ENST00000354434;ENST00000449423;ENST00000392910	D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22	4.69	2.87	0.33458	Zinc finger, LIM-type (4);	0.266734	0.31601	U	0.007367	D	0.84795	0.5551	L	0.50993	1.605	0.35379	D	0.789768	P;P	0.51449	0.927;0.945	P;P	0.46208	0.449;0.507	D	0.87051	0.2147	10	0.72032	D	0.01	.	10.9017	0.47056	0.1549:0.0:0.8451:0.0	.	419;506	B4DQR8;Q15942	.;ZYX_HUMAN	I	506;474;419;349	ENSP00000324422:V506I;ENSP00000346417:V474I;ENSP00000394158:V419I;ENSP00000376642:V349I	ENSP00000324422:V506I	V	+	1	0	ZYX	142797094	1.000000	0.71417	0.037000	0.18230	0.844000	0.47949	6.100000	0.71473	0.502000	0.28037	0.313000	0.20887	GTC		0.607	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461		A	143086972	G	A	143086972	3	1	111	1	0	0	0	0	1	0	0	0	18293	1145	40	1	1546	1	ZYX	7	143086972	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	517456	143086972	16051691	434	29568										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096942	144096942	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttcgccacttggcccggcgAttctggaaccacacctatgg	10	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:144096942A>G	ENST00000467773.1	-	6	1061	c.1062T>C	c.(1060-1062)aaT>aaC	p.N354N	NOBOX_ENST00000223140.5_Silent_p.N237N|NOBOX_ENST00000483238.1_Silent_p.N322N	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	354					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					TGGCCCGGCGATTCTGGAACC	0.547																																																0			7											69	73	71					7																	144096942		1952	4147	6099	143727875	SO:0001819	synonymous_variant	135935					7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1062T>C	7.37:g.144096942A>G			143727875	A6NCD3|A8MZN5	Silent	SNP	ENST00000467773.1	37																																																																																					0.547	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		G	144096942	A	G	144096942	2	3	111	1	0	0	0	0	0	0	0	1	10543	330	12	4		4	NOBOX	7	144096942	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1009970	144096942	15041721	435	29569										
EZH2	2146	hgsc.bcm.edu	37	chr7	148523604	148523604	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaacatcgcctacagaaaagCgtatgaaaggagtgtaagct	10	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:148523604C>T	ENST00000460911.1	-	8	937	c.849G>A	c.(847-849)acG>acA	p.T283T	EZH2_ENST00000476773.1_Silent_p.T274T|EZH2_ENST00000536783.1_Silent_p.T174T|EZH2_ENST00000483967.1_Silent_p.T274T|EZH2_ENST00000350995.2_Silent_p.T244T|EZH2_ENST00000541220.1_Silent_p.T274T|EZH2_ENST00000478654.1_Silent_p.T274T|EZH2_ENST00000320356.2_Silent_p.T283T			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	283	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TACAGAAAAGCGTATGAAAGG	0.398			Mis		DLBCL																																		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	0			7											160	133	142					7																	148523604		2203	4300	6503	148154537	SO:0001819	synonymous_variant	2146				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.849G>A	7.37:g.148523604C>T			148154537	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	37	CCDS56516.1																																																																																				0.398	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		T	148523604	C	T	148523604	2	4	111	1	0	0	0	0	0	0	0	1	5347	755	27	1		1	EZH2	7	148523604	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4426662	148523604	10615059	436	29570										
ZNF425	155054	hgsc.bcm.edu	37	chr7	148801598	148801598	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctggtgggcgcgcatggcGttcctccagaagaagcccct	14	14	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:148801598G>A	ENST00000378061.2	-	4	1497	c.1365C>T	c.(1363-1365)aaC>aaT	p.N455N		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	455					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N455N(1)		breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CGCGCATGGCGTTCCTCCAGA	0.662																																																1	Substitution - coding silent(1)	endometrium(1)	7											33	34	34					7																	148801598		2203	4300	6503	148432531	SO:0001819	synonymous_variant	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1365C>T	7.37:g.148801598G>A			148432531	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																				0.662	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		A	148801598	G	A	148801598	2	1	111	1	0	0	0	0	0	0	0	1	17938	1136	40	1		1	ZNF425	7	148801598	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	277994	148801598	10337065	437	29571										
ACTR3B	57180	hgsc.bcm.edu	37	chr7	152513582	152513582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggcagtgctggccttggCggcatcttggacatctcgac	13	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:152513582C>T	ENST00000256001.8	+	6	583	c.449C>T	c.(448-450)gCg>gTg	p.A150V	ACTR3B_ENST00000537264.1_Missense_Mutation_p.A62V|ACTR3B_ENST00000488782.1_3'UTR|ACTR3B_ENST00000377776.3_Missense_Mutation_p.A150V|ACTR3B_ENST00000397282.2_Missense_Mutation_p.A62V	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	150						cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		CTGGCCTTGGCGGCATCTTGG	0.512																																																0			7											41	32	35					7																	152513582		2203	4299	6502	152144515	SO:0001583	missense	57180				CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627			17256	protein-coding gene	gene with protein product						10806390	Standard	NM_001040135		Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.449C>T	7.37:g.152513582C>T	ENSP00000256001:p.Ala150Val		152144515	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Missense_Mutation	SNP	ENST00000256001.8	37	CCDS5934.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.418667	0.83559	.	.	ENSG00000133627	ENST00000377776;ENST00000256001;ENST00000397282;ENST00000537264	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	4.65	4.65	0.58169	.	0.000000	0.64402	U	0.000008	D	0.95146	0.8427	M	0.83603	2.65	0.58432	D	0.999995	D;D	0.67145	0.996;0.972	P;P	0.51193	0.662;0.621	D	0.95400	0.8489	10	0.51188	T	0.08	-9.5975	16.5322	0.84364	0.0:1.0:0.0:0.0	.	150;150	Q9P1U1-3;Q9P1U1	.;ARP3B_HUMAN	V	150;150;62;62	ENSP00000367007:A150V;ENSP00000256001:A150V;ENSP00000380452:A62V;ENSP00000446157:A62V	ENSP00000256001:A150V	A	+	2	0	ACTR3B	152144515	1.000000	0.71417	0.037000	0.18230	0.859000	0.49053	7.510000	0.81708	2.132000	0.65825	0.484000	0.47621	GCG		0.512	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445		T	152513582	C	T	152513582	3	4	111	1	0	0	0	0	1	0	0	0	213	768	27	1	471	1	ACTR3B	7	152513582	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3711984	152513582	6625081	438	29572										
DPP6	1804	hgsc.bcm.edu	37	chr7	154237664	154237664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaggaacagtgagactgtggAatgttgaaacaaatacttct	10	5	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:154237664A>G	ENST00000377770.3	+	4	646	c.505A>G	c.(505-507)Aat>Gat	p.N169D	DPP6_ENST00000496611.1_3'UTR|DPP6_ENST00000427557.1_Missense_Mutation_p.N107D|DPP6_ENST00000404039.1_Missense_Mutation_p.N105D|DPP6_ENST00000332007.3_Missense_Mutation_p.N107D|DPP6_ENST00000406326.1_Missense_Mutation_p.N169D			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	169					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GAGACTGTGGAATGTTGAAAC	0.358																																					NSCLC(125;1384 1783 2490 7422 34254)											0			7											75	71	72					7																	154237664		1830	4082	5912	153868597	SO:0001583	missense	1804			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.505A>G	7.37:g.154237664A>G	ENSP00000367001:p.Asn169Asp		153868597		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	A	13.65	2.299756	0.40694	.	.	ENSG00000130226	ENST00000404039;ENST00000406326;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.2	4.05	0.47172	.	0.044236	0.85682	N	0.000000	T	0.37598	0.1009	.	.	.	0.49389	D	0.999788	B;B;B;B;B	0.34255	0.005;0.016;0.009;0.445;0.009	B;B;B;B;B	0.36418	0.042;0.032;0.009;0.224;0.014	T	0.28202	-1.0051	9	0.87932	D	0	-27.1198	8.9297	0.35663	0.916:0.0:0.084:0.0	.	107;107;169;169;105	E9PDL2;P42658-2;P42658;Q8IYG9;E9PF59	.;.;DPP6_HUMAN;.;.	D	105;169;169;107;107	ENSP00000385578:N105D;ENSP00000384393:N169D;ENSP00000367001:N169D;ENSP00000328226:N107D;ENSP00000397303:N107D	ENSP00000328226:N107D	N	+	1	0	DPP6	153868597	1.000000	0.71417	0.963000	0.40424	0.944000	0.59088	3.434000	0.52841	0.937000	0.37394	0.460000	0.39030	AAT		0.358	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		G	154237664	A	G	154237664	3	3	111	1	0	0	0	0	1	0	0	0	4741	246	9	4	635	4	DPP6	7	154237664	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1724082	154237664	4900999	439	29573										
DPP6	1804	hgsc.bcm.edu	37	chr7	154585824	154585824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catggtgaagtgggccaccaGcaccaaggtcgccgtgacct	13	13	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:154585824G>A	ENST00000377770.3	+	11	1313	c.1172G>A	c.(1171-1173)aGc>aAc	p.S391N	DPP6_ENST00000427557.1_Missense_Mutation_p.S284N|DPP6_ENST00000404039.1_Missense_Mutation_p.S327N|DPP6_ENST00000332007.3_Missense_Mutation_p.S329N			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	391					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGGGCCACCAGCACCAAGGTC	0.642																																					NSCLC(125;1384 1783 2490 7422 34254)											0			7											42	49	47					7																	154585824		2154	4246	6400	154216757	SO:0001583	missense	1804			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1172G>A	7.37:g.154585824G>A	ENSP00000367001:p.Ser391Asn		154216757		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	G	10.64	1.406185	0.25378	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	4.21	3.32	0.38043	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.041014	0.85682	D	0.000000	T	0.14270	0.0345	N	0.05608	-0.01	0.46725	D	0.999178	B;B;B;B	0.25609	0.024;0.027;0.13;0.034	B;B;B;B	0.28011	0.085;0.046;0.076;0.076	T	0.06807	-1.0806	10	0.06757	T	0.87	-14.9994	11.8691	0.52511	0.0876:0.0:0.9124:0.0	.	284;329;391;327	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	N	327;391;329;284	ENSP00000385578:S327N;ENSP00000367001:S391N;ENSP00000328226:S329N;ENSP00000397303:S284N	ENSP00000328226:S329N	S	+	2	0	DPP6	154216757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.201000	0.51059	0.899000	0.36444	0.650000	0.86243	AGC		0.642	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	154585824	G	A	154585824	3	1	111	1	0	0	0	0	1	0	0	0	4741	971	34	3	1330	3	DPP6	7	154585824	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	348160	154585824	4552839	440	29574										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154746105	154746105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcacttctgtgcagactccGcaacctctccaccaagaatg	7	15	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr7:154746105G>A	ENST00000404141.1	-	16	2835	c.2681C>T	c.(2680-2682)gCg>gTg	p.A894V	RP11-5C23.2_ENST00000609134.1_RNA|RP11-5C23.1_ENST00000608064.1_RNA|PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.A894V			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	894	BRCT 5. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		TGCAGACTCCGCAACCTCTCC	0.498																																																0			7											47	50	49					7																	154746105		2086	4234	6320	154377038	SO:0001583	missense	22976			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2681C>T	7.37:g.154746105G>A	ENSP00000384048:p.Ala894Val		154377038	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627179	0.28978	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.79749	-1.3;-1.3	4.91	3.99	0.46301	BRCT (4);	0.000000	0.51477	U	0.000081	T	0.71417	0.3337	N	0.17901	0.54	0.51012	D	0.999903	D;D;B	0.63880	0.993;0.976;0.351	P;B;B	0.47044	0.535;0.292;0.029	T	0.71119	-0.4685	10	0.41790	T	0.15	-13.5095	11.7897	0.52063	0.0906:0.0:0.9094:0.0	.	847;860;894	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	V	894;894;718;847	ENSP00000384048:A894V;ENSP00000380376:A894V	ENSP00000319149:A847V	A	-	2	0	PAXIP1	154377038	1.000000	0.71417	0.144000	0.22314	0.004000	0.04260	7.612000	0.82975	0.984000	0.38629	0.650000	0.86243	GCG		0.498	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		A	154746105	G	A	154746105	3	1	111	1	0	0	0	0	1	0	0	0	11518	1087	38	1	552	1	PAXIP1	7	154746105	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	160281	154746105	4392558	441	29575										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1842705	1842705	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcgtttccgagtgggactcCgtggaaatgataggcgatgt	15	8	0	1	rs147974725		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:1842705C>T	ENST00000398564.1	+	13	1482	c.1482C>T	c.(1480-1482)tcC>tcT	p.S494S	ARHGEF10_ENST00000262112.6_Silent_p.S494S|ARHGEF10_ENST00000349830.3_Silent_p.S469S|ARHGEF10_ENST00000520359.1_Silent_p.S431S|ARHGEF10_ENST00000518288.1_Silent_p.S494S|ARHGEF10_ENST00000398560.1_Silent_p.S455S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	494	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AGTGGGACTCCGTGGAAATGA	0.547																																																0			8											84	78	80					8																	1842705		2203	4300	6503	1830112	SO:0001819	synonymous_variant	9639			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.1482C>T	8.37:g.1842705C>T			1830112	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																					0.547	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1842705	C	T	1842705	2	4	111	1	0	0	0	0	0	0	0	1	894	639	23	1		1	ARHGEF10	8	1842705	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10		1842705	144521317	442	29576										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3087702	3087702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctctctgctgtctccatagCgggtgccattttggggcata	11	12	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:3087702C>T	ENST00000520002.1	-	28	4763	c.4208G>A	c.(4207-4209)cGc>cAc	p.R1403H	CSMD1_ENST00000400186.3_Missense_Mutation_p.R1403H|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1403H|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1402H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1402H|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1403H|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1402H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1403	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				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)		GTCTCCATAGCGGGTGCCATT	0.522																																																0			8											65	66	66					8																	3087702		1992	4179	6171	3075109	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4208G>A	8.37:g.3087702C>T	ENSP00000430733:p.Arg1403His		3075109	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	33	5.275374	0.95459	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	6.1	6.1	0.99115	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000003	T	0.52025	0.1709	M	0.64080	1.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.993;1.0	T	0.32798	-0.9893	10	0.46703	T	0.11	.	20.7146	0.99709	0.0:1.0:0.0:0.0	.	1403;1403;1403	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	H	1403;1403;1265;1402;1402;1402	ENSP00000383047:R1403H;ENSP00000430733:R1403H;ENSP00000441462:R1402H;ENSP00000446243:R1402H;ENSP00000441675:R1402H	ENSP00000320445:R1265H	R	-	2	0	CSMD1	3075109	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	7.634000	0.83273	2.902000	0.99343	0.650000	0.86243	CGC		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3087702	C	T	3087702	3	4	111	1	0	0	0	0	1	0	0	0	3950	768	27	1	6665	1	CSMD1	8	3087702	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1244997	3087702	143276320	443	29577										
ANGPT2	285	hgsc.bcm.edu	37	chr8	6372270	6372270	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctgaataattgtccacccGcctcctccagcttccatgtc	6	17	0	1	rs139416191		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:6372270G>C	ENST00000325203.5	-	6	1434	c.960C>G	c.(958-960)ggC>ggG	p.G320G	ANGPT2_ENST00000338312.6_Silent_p.G268G|MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000523120.1_Silent_p.G319G|ANGPT2_ENST00000415216.1_Silent_p.G319G			O15123	ANGP2_HUMAN	angiopoietin 2	320	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		TTGTCCACCCGCCTCCTCCAG	0.502																																																0			8											150	161	158					8																	6372270		2203	4300	6503	6359678	SO:0001819	synonymous_variant	285			AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"Fibrinogen C domain containing"	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.960C>G	8.37:g.6372270G>C			6359678	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																				0.502	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147		C	6372270	G	C	6372270	2	2	111	1	0	0	0	0	0	0	0	1	611	1074	38	5		5	ANGPT2	8	6372270	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3284568	6372270	139991752	444	29578										
TNKS	8658	hgsc.bcm.edu	37	chr8	9567544	9567544	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaaggagcaaatgttaatgAaaaaaataaagagtaagtat					rs200458028		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:9567544delA	ENST00000310430.6	+	10	1684	c.1658delA	c.(1657-1659)gaafs	p.E553fs	TNKS_ENST00000518281.1_Frame_Shift_Del_p.E316fs|TNKS_ENST00000520408.1_Frame_Shift_Del_p.E553fs	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	553					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		AATGTTAATGAAAAAAATAAA	0.338																																																0			8											72	68	69					8																	9567544		2203	4300	6503	9604954	SO:0001589	frameshift_variant	8658			AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.1658delA	8.37:g.9567544delA	ENSP00000311579:p.Glu553fs		9604954	O95272|Q4G0F2	Frame_Shift_Del	DEL	ENST00000310430.6	37	CCDS5974.1																																																																																				0.338	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		-	9567544	A	-	9567544	7	5	111	1	0	1	0	1	0	0	0	0	16358	246	9	0	1696	0	TNKS	8	9567544	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	3195274	9567544	136796478	445	29579										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10467948	10467948	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccctgtgtcaccagggtgccGtccatggcacagggtacgct	13	14	1	0	rs375441998		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:10467948G>A	ENST00000382483.3	-	4	3883	c.3660C>T	c.(3658-3660)gaC>gaT	p.D1220D		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1220					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.D1220D(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCAGGGTGCCGTCCATGGCAC	0.582																																																1	Substitution - coding silent(1)	breast(1)	8						G		0,4092		0,0,2046	37	40	39		3660	-1.7	0	8		39	3,8367		0,3,4182	no	coding-synonymous	RP1L1	NM_178857.5		0,3,6228	AA,AG,GG		0.0358,0.0,0.0241		1220/2401	10467948	3,12459	2046	4185	6231	10505358	SO:0001819	synonymous_variant	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3660C>T	8.37:g.10467948G>A			10505358	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.582	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10467948	G	A	10467948	2	1	111	1	0	0	0	0	0	0	0	1	13570	1136	40	1		1	RP1L1	8	10467948	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	900404	10467948	135896074	446	29580										
DLC1	10395	hgsc.bcm.edu	37	chr8	12960306	12960306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgtatactcactcgtttcCgatgaggactaatttctagc	7	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:12960306C>T	ENST00000276297.4	-	8	1968	c.1559G>A	c.(1558-1560)cGg>cAg	p.R520Q	DLC1_ENST00000520226.1_Missense_Mutation_p.R9Q|DLC1_ENST00000512044.2_Missense_Mutation_p.R117Q|DLC1_ENST00000358919.2_Missense_Mutation_p.R83Q	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	520					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CACTCGTTTCCGATGAGGACT	0.368																																																0			8											186	180	182					8																	12960306		2203	4300	6503	13004677	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1559G>A	8.37:g.12960306C>T	ENSP00000276297:p.Arg520Gln		13004677	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034995	0.93575	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.46451	0.87;0.87;0.87;3.16	5.85	5.85	0.93711	.	0.052329	0.85682	D	0.000000	T	0.64494	0.2603	L	0.58810	1.83	0.80722	D	1	D;P;P	0.89917	1.0;0.788;0.954	D;B;P	0.85130	0.997;0.317;0.727	T	0.63070	-0.6719	10	0.72032	D	0.01	.	20.5471	0.99284	0.0:1.0:0.0:0.0	.	520;117;83	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	Q	520;83;117;9	ENSP00000276297:R520Q;ENSP00000351797:R83Q;ENSP00000422595:R117Q;ENSP00000428028:R9Q	ENSP00000276297:R520Q	R	-	2	0	DLC1	13004677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.113000	0.50376	2.941000	0.99782	0.655000	0.94253	CGG		0.368	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	12960306	C	T	12960306	3	4	111	1	0	0	0	0	1	0	0	0	4561	652	23	1	3071	1	DLC1	8	12960306	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2492358	12960306	133403716	447	29581										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17581321	17581322	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacccatgacgactgtgcagINSttttcaaggatgtaggcttt					rs369762682|rs535166254		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:17581321_17581322insT	ENST00000262102.6	-	4	2532_2533	c.2308_2309insA	c.(2308-2310)actfs	p.T770fs	MTUS1_ENST00000544260.1_5'Flank|MTUS1_ENST00000519263.1_Intron|MTUS1_ENST00000381861.3_5'Flank|MTUS1_ENST00000381869.3_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	770					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CGACTGTGCAGTTTTCAAGGAT	0.441																																																0			8																																								17625602	SO:0001589	frameshift_variant	57509			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2309dupA	8.37:g.17581325_17581325dupT	ENSP00000262102:p.Thr770fs		17625601	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Frame_Shift_Ins	INS	ENST00000262102.6	37	CCDS43717.1																																																																																				0.441	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17581322	-	T	17581321	7	5	111	1	0	1	1	0	0	0	0	0	9995	1029	36	0	1870	0	MTUS1	8	17581321	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	4621015	17581321	128782701	448	29582										
PSD3	23362	hgsc.bcm.edu	37	chr8	18393367	18393367	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgggttcagcgaaggactCgagtgcgacttcttcagtcc	12	12	3	0	rs547134848		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:18393367C>T	ENST00000327040.8	-	16	3132	c.3030G>A	c.(3028-3030)tcG>tcA	p.S1010S	PSD3_ENST00000428502.2_Silent_p.S339S|PSD3_ENST00000286485.8_Silent_p.S476S|PSD3_ENST00000440756.2_Silent_p.S1012S|PSD3_ENST00000523619.1_Silent_p.S945S	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	1011					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		GCGAAGGACTCGAGTGCGACT	0.493													C|||	1	0.000199681	0	0	5008	,	,		18399	0.001		0	False		,,,				2504	0															0			8											194	156	169					8																	18393367		2203	4300	6503	18437647	SO:0001819	synonymous_variant	23362			AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.3030G>A	8.37:g.18393367C>T			18437647	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	37	CCDS43720.1																																																																																				0.493	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		T	18393367	C	T	18393367	2	4	111	1	0	0	0	0	0	0	0	1	12682	871	31	1		1	PSD3	8	18393367	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	812046	18393367	127970655	449	29583										
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22472454	22472454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgacccgcaggtgctggtgcGtaccgccatccgctgtgcgc	14	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:22472454G>A	ENST00000308511.4	+	11	1394	c.1145G>A	c.(1144-1146)cGt>cAt	p.R382H	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Missense_Mutation_p.R57H|CCAR2_ENST00000389279.3_Missense_Mutation_p.R382H			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	382					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GTGCTGGTGCGTACCGCCATC	0.627																																																0			8											50	39	42					8																	22472454		2202	4300	6502	22528399	SO:0001583	missense	57805			AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1145G>A	8.37:g.22472454G>A	ENSP00000310670:p.Arg382His		22528399	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	28.8|28.8|28.8	4.947511|4.947511|4.947511	0.92593|0.92593|0.92593	.|.|.	.|.|.	ENSG00000253200|ENSG00000158941|ENSG00000158941	ENST00000521025|ENST00000308511;ENST00000389279;ENST00000520861;ENST00000522599|ENST00000520738	.|T;T;T;T|.	.|0.51071|.	.|0.72;0.72;0.72;0.72|.	5.53|5.53|5.53	5.53|5.53|5.53	0.82687|0.82687|0.82687	.|.|.	0.226227|0.226227|.	0.38663|0.38663|.	N|N|.	0.001617|0.001617|.	T|T|T	0.73575|0.73575|0.73575	0.3604|0.3604|0.3604	M|M|M	0.64170|0.64170|0.64170	1.965|1.965|1.965	0.44736|0.44736|0.44736	D|D|D	0.997733|0.997733|0.997733	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.81914|.	.|0.995;0.986|.	T|T|T	0.70360|0.70360|0.70360	-0.4893|-0.4893|-0.4893	7|10|5	0.87932|0.72032|.	D|D|.	0|0.01|.	-16.5872|-16.5872|-16.5872	18.396|18.396|18.396	0.90499|0.90499|0.90499	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|57;382|.	.|G3V119;Q8N163|.	.|.;K1967_HUMAN|.	C|H|I	13|382;382;57;200|74	.|ENSP00000310670:R382H;ENSP00000373930:R382H;ENSP00000429773:R57H;ENSP00000429739:R200H|.	ENSP00000429254:R13C|ENSP00000310670:R382H|.	R|R|V	-|+|+	1|2|1	0|0|0	RP11-582J16.5|KIAA1967|KIAA1967	22528399|22528399|22528399	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.952000|0.952000|0.952000	0.60782|0.60782|0.60782	4.225000|4.225000|4.225000	0.58600|0.58600|0.58600	2.882000|2.882000|2.882000	0.98803|0.98803|0.98803	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	CGC|CGT|GTA		0.627	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22472454	G	A	22472454	3	1	111	1	0	0	0	0	1	0	0	0	8286	1145	40	1	1183	1	KIAA1967	8	22472454	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4079087	22472454	123891568	450	29584										
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22473324	22473324	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atctcccagaggcccctccaCcccccctagaacctgctgtc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:22473324delC	ENST00000308511.4	+	13	1756	c.1507delC	c.(1507-1509)cccfs	p.P504fs	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Frame_Shift_Del_p.P179fs|CCAR2_ENST00000389279.3_Frame_Shift_Del_p.P504fs			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	504					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GGCCCCTCCACCCCCCCTAGA	0.572																																																0			8											84	95	91					8																	22473324		2203	4300	6503	22529269	SO:0001589	frameshift_variant	57805			AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1507delC	8.37:g.22473324delC	ENSP00000310670:p.Pro504fs		22529269	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Frame_Shift_Del	DEL	ENST00000308511.4	37	CCDS34863.1																																																																																				0.572	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		-	22473324	C	-	22473324	7	5	111	1	0	1	0	1	0	0	0	0	8286	507	18	0	1553	0	KIAA1967	8	22473324	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	870	22473324	123890698	451	29585										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24350675	24350675	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tactgtcaaatgcaaaactaTttttttataccatgattcta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:24350675delT	ENST00000175238.6	+	16	1858	c.1775delT	c.(1774-1776)attfs	p.I592fs	ADAM7_ENST00000520720.1_Frame_Shift_Del_p.I364fs|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000380789.1_Frame_Shift_Del_p.I592fs	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	592	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		TGCAAAACTATTTTTTTATAC	0.413																																																0			8											94	93	93					8																	24350675		2203	4299	6502	24406565	SO:0001589	frameshift_variant	8756			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1775delT	8.37:g.24350675delT	ENSP00000175238:p.Ile592fs		24406565	A8K8X7|O75959|Q6PEJ6	Frame_Shift_Del	DEL	ENST00000175238.6	37	CCDS6045.1																																																																																				0.413	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		-	24350675	T	-	24350675	7	5	111	1	0	1	0	1	0	0	0	0	251	1493	52	0	1837	0	ADAM7	8	24350675	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	1877351	24350675	122013347	452	29586										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25174578	25174580	+	In_Frame_Del	DEL	GAA	GAA	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacggtgagtttgacaaaggGaagaagaagacgccaaagaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:25174578_25174580delGAA	ENST00000276440.7	+	14	1418_1420	c.1374_1376delGAA	c.(1372-1377)gggaag>ggg	p.K461del		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	461	DHR-1.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TTGACAAAGGGAAGAAGAAGACG	0.502																																					Pancreas(145;34 1887 3271 10937 30165)											0			8																																								25230497	SO:0001651	inframe_deletion	80005				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.1374_1376delGAA	8.37:g.25174584_25174586delGAA	ENSP00000276440:p.Lys461del		25230495	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	In_Frame_Del	DEL	ENST00000276440.7	37	CCDS6047.1																																																																																				0.502	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		-	25174580	GAA	-	25174578	7	5	111	1	0	1	0	1	0	0	0	0	4701	1161	41	0	1428	0	DOCK5	8	25174578	In_Frame_Del	DEL	GAA	TCGA-EI-6507-01A-11D-1733-10	823903	25174578	121189444	453	29587										
SCARA5	286133	hgsc.bcm.edu	37	chr8	27737221	27737221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccggtcgtggtacacttccaCgcggccctcgtgcggacctg	13	16	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:27737221C>T	ENST00000354914.3	-	8	1701	c.1216G>A	c.(1216-1218)Gtg>Atg	p.V406M	SCARA5_ENST00000380385.2_Missense_Mutation_p.V181M	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	406	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TACACTTCCACGCGGCCCTCG	0.652																																																0			8											88	74	79					8																	27737221		2203	4300	6503	27793140	SO:0001583	missense	286133			AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.1216G>A	8.37:g.27737221C>T	ENSP00000346990:p.Val406Met		27793140	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	C	35	5.437083	0.96168	.	.	ENSG00000168079	ENST00000354914;ENST00000380385	T;T	0.55930	0.49;0.49	4.96	4.96	0.65561	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.000000	0.64402	D	0.000001	T	0.82231	0.4992	H	0.97587	4.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.88713	0.3224	10	0.87932	D	0	.	16.0591	0.80826	0.0:1.0:0.0:0.0	.	181;406	Q6ZMJ2-4;Q6ZMJ2	.;SCAR5_HUMAN	M	406;181	ENSP00000346990:V406M;ENSP00000369746:V181M	ENSP00000346990:V406M	V	-	1	0	SCARA5	27793140	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	4.809000	0.62591	2.454000	0.82982	0.655000	0.94253	GTG		0.652	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		T	27737221	C	T	27737221	3	4	111	1	0	0	0	0	1	0	0	0	13917	536	19	1	279	1	SCARA5	8	27737221	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2562643	27737221	118626801	454	29588										
ZNF395	55893	hgsc.bcm.edu	37	chr8	28218518	28218518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtggtgaaaggctggggagCggccccttctagcagtggct	18	9	1	1	rs142226591		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:28218518C>T	ENST00000344423.5	-	2	255	c.124G>A	c.(124-126)Gct>Act	p.A42T	ZNF395_ENST00000523202.1_Missense_Mutation_p.A42T|ZNF395_ENST00000523095.1_Missense_Mutation_p.A42T	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	42					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GGCTGGGGAGCGGCCCCTTCT	0.677																																																0			8											23	26	25					8																	28218518		2203	4300	6503	28274437	SO:0001583	missense	55893			AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.124G>A	8.37:g.28218518C>T	ENSP00000340494:p.Ala42Thr		28274437	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	37	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	C	5.299	0.240616	0.10023	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095;ENST00000521912;ENST00000520290;ENST00000521185;ENST00000522795;ENST00000517459	T;T;T	0.44482	0.92;0.92;0.92	5.0	-2.12	0.07165	.	0.647835	0.14707	N	0.303176	T	0.20536	0.0494	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19386	-1.0307	10	0.19147	T	0.46	-0.2495	6.0804	0.19938	0.0:0.3702:0.4066:0.2232	.	42	Q9H8N7	ZN395_HUMAN	T	42	ENSP00000340494:A42T;ENSP00000429640:A42T;ENSP00000428452:A42T	ENSP00000340494:A42T	A	-	1	0	ZNF395	28274437	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.880000	0.04183	-0.221000	0.09973	-0.175000	0.13238	GCT		0.677	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			T	28218518	C	T	28218518	3	4	111	1	0	0	0	0	1	0	0	0	17920	768	27	1	1453	1	ZNF395	8	28218518	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	481297	28218518	118145504	455	29589										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33361280	33361280	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctcacctgttcacgaaagcCggcaggtttcttgcgtaggt	11	12	3	0	rs17850186	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:33361280C>T	ENST00000431156.2	-	5	1719	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	TTI2_ENST00000520636.1_Silent_p.P336P|TTI2_ENST00000360742.5_Silent_p.P367P|TTI2_ENST00000519356.1_5'UTR	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	367																	TCACGAAAGCCGGCAGGTTTC	0.527													C|||	43	0.00858626	0.0023	0.0058	5008	,	,		17510	0.002		0.0229	False		,,,				2504	0.0112															0			8						C	,	17,4389	24.3+/-50.5	0,17,2186	33	31	32		1101,1101	-8.6	0.2	8	dbSNP_123	32	172,8428	78.4+/-141.0	3,166,4131	no	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	3,183,6317	TT,TC,CC		2.0,0.3858,1.4532	,	367/509,367/509	33361280	189,12817	2203	4300	6503	33480822	SO:0001819	synonymous_variant	80185			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1101G>A	8.37:g.33361280C>T			33480822	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																				0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33361280	C	T	33361280	2	4	111	1	0	0	0	0	0	0	0	1	2433	639	23	1		1	C8orf41	8	33361280	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5142762	33361280	113002742	456	29590										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35579744	35579744	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaggcattgagaatgccagCgacattgctttgtactcggg	12	9	1	1	rs188758803	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:35579744C>T	ENST00000404895.2	+	9	1462	c.1134C>T	c.(1132-1134)agC>agT	p.S378S	UNC5D_ENST00000287272.2_Silent_p.S322S|UNC5D_ENST00000420357.1_Silent_p.S311S|UNC5D_ENST00000449677.1_5'Flank|UNC5D_ENST00000453357.2_Silent_p.S373S|UNC5D_ENST00000416672.1_Silent_p.S383S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	378					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		AGAATGCCAGCGACATTGCTT	0.502													C|||	3	0.000599042	0	0	5008	,	,		20616	0.003		0	False		,,,				2504	0															0			8											227	201	209					8																	35579744		2203	4300	6503	35699286	SO:0001819	synonymous_variant	137970			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1134C>T	8.37:g.35579744C>T			35699286	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																				0.502	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35579744	C	T	35579744	2	4	111	1	0	0	0	0	0	0	0	1	17035	767	27	1		1	UNC5D	8	35579744	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2218464	35579744	110784278	457	29591										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36768480	36768480	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tattctggagacctccatgcGgccaacatagagcaatgctc	9	12	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:36768480G>A	ENST00000399881.3	+	22	2401	c.2364G>A	c.(2362-2364)gcG>gcA	p.A788A		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	788					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		ACCTCCATGCGGCCAACATAG	0.527																																																0			8											100	104	103					8																	36768480		1991	4171	6162	36887638	SO:0001819	synonymous_variant	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2364G>A	8.37:g.36768480G>A			36887638		Silent	SNP	ENST00000399881.3	37	CCDS55220.1																																																																																				0.527	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36768480	G	A	36768480	2	1	111	1	0	0	0	0	0	0	0	1	8114	1103	39	1		1	KCNU1	8	36768480	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1188736	36768480	109595542	458	29592										
LSM1	27257	hgsc.bcm.edu	37	chr8	38027332	38027332	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcacttactatttctcctagTaggaccacattttctcctct	3	13	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:38027332T>C	ENST00000311351.4	-	3	614	c.219A>G	c.(217-219)ctA>ctG	p.L73L	LSM1_ENST00000520755.1_Intron|LSM1_ENST00000522515.1_5'UTR	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated	73					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					TTTCTCCTAGTAGGACCACAT	0.358																																																0			8											137	130	132					8																	38027332		2203	4300	6503	38146489	SO:0001819	synonymous_variant	27257			AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.219A>G	8.37:g.38027332T>C			38146489	B2R5E6	Silent	SNP	ENST00000311351.4	37	CCDS6103.1																																																																																				0.358	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462		C	38027332	T	C	38027332	2	2	111	1	0	0	0	0	0	0	0	1	9079	1625	57	4		4	LSM1	8	38027332	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1258852	38027332	108336690	459	29593										
DDHD2	23259	hgsc.bcm.edu	37	chr8	38099780	38099780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttttccagttaatgattttcGcagtgtttccttgaacttgc	7	8	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:38099780G>A	ENST00000397166.2	+	7	1250	c.725G>A	c.(724-726)cGc>cAc	p.R242H	DDHD2_ENST00000528888.1_3'UTR|DDHD2_ENST00000520272.2_Missense_Mutation_p.R242H	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	242					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			AATGATTTTCGCAGTGTTTCC	0.358																																																0			8											84	83	83					8																	38099780		2203	4300	6503	38218937	SO:0001583	missense	23259			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"Sterile alpha motif (SAM) domain containing"	29106	protein-coding gene	gene with protein product		615003	"SAM, WWE and DDHD domain containing 1"	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.725G>A	8.37:g.38099780G>A	ENSP00000380352:p.Arg242His		38218937	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.95|18.95	3.731673|3.731673	0.69189|0.69189	.|.	.|.	ENSG00000085788|ENSG00000085788	ENST00000532106|ENST00000397166;ENST00000532222;ENST00000520272;ENST00000440212	.|T;T;T	.|0.60040	.|1.07;0.22;1.07	5.48|5.48	4.58|4.58	0.56647|0.56647	.|.	.|0.056769	.|0.64402	.|D	.|0.000002	T|T	0.59046|0.59046	0.2165|0.2165	M|M	0.77712|0.77712	2.385|2.385	0.80722|0.80722	D|D	1|1	.|P;P	.|0.52316	.|0.952;0.812	.|P;B	.|0.44518	.|0.452;0.317	T|T	0.64206|0.64206	-0.6462|-0.6462	5|10	.|0.72032	.|D	.|0.01	-10.6745|-10.6745	8.191|8.191	0.31368|0.31368	0.0783:0.0:0.7637:0.158|0.0783:0.0:0.7637:0.158	.|.	.|54;242	.|B4DSR3;O94830	.|.;DDHD2_HUMAN	T|H	35|242;212;242;54	.|ENSP00000380352:R242H;ENSP00000433578:R212H;ENSP00000429932:R242H	.|ENSP00000380352:R242H	A|R	+|+	1|2	0|0	DDHD2|DDHD2	38218937|38218937	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.840000|7.840000	0.86819|0.86819	1.260000|1.260000	0.44134|0.44134	0.467000|0.467000	0.42956|0.42956	GCA|CGC		0.358	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291		A	38099780	G	A	38099780	3	1	111	1	0	0	0	0	1	0	0	0	4333	1087	38	1	809	1	DDHD2	8	38099780	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	72448	38099780	108264242	460	29594										
LETM2	137994	hgsc.bcm.edu	37	chr8	38257891	38257891	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggaacagagccaagatgggCgatgcctctacacagctctc	11	12	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:38257891C>T	ENST00000379957.4	+	5	874	c.747C>T	c.(745-747)ggC>ggT	p.G249G	LETM2_ENST00000524874.1_Silent_p.G201G|LETM2_ENST00000527710.1_Silent_p.G35G|RP11-350N15.3_ENST00000533301.1_RNA|LETM2_ENST00000523983.2_Silent_p.G202G|LETM2_ENST00000297720.5_Silent_p.G154G	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	249	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			CCAAGATGGGCGATGCCTCTA	0.438																																																0			8											127	103	111					8																	38257891		2203	4300	6503	38377048	SO:0001819	synonymous_variant	137994			AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"EF-hand domain containing"	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.747C>T	8.37:g.38257891C>T			38377048	A6NMG3|Q8NCR2|Q96LL1	Silent	SNP	ENST00000379957.4	37																																																																																					0.438	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652		T	38257891	C	T	38257891	2	4	111	1	0	0	0	0	0	0	0	1	8757	755	27	1		1	LETM2	8	38257891	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	158111	38257891	108106131	461	29595										
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42294776	42294776	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttggagtaggacacggtgtcGcccaccagcttctcactgtc	11	13	1	0	rs115234947	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:42294776G>A	ENST00000342228.3	-	8	1623	c.1254C>T	c.(1252-1254)ggC>ggT	p.G418G	SLC20A2_ENST00000520179.1_Silent_p.G418G|SLC20A2_ENST00000520262.1_Silent_p.G418G	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	418					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)	p.G418G(1)		breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ACACGGTGTCGCCCACCAGCT	0.632													G|||	108	0.0215655	0.0809	0.0014	5008	,	,		17338	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	8						G		254,4152	146.5+/-181.1	7,240,1956	69	63	65		1254	-11.7	0	8	dbSNP_132	65	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SLC20A2	NM_006749.3		7,245,6251	AA,AG,GG		0.0581,5.7649,1.9914		418/653	42294776	259,12747	2203	4300	6503	42413933	SO:0001819	synonymous_variant	6575				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"Solute carriers"	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1254C>T	8.37:g.42294776G>A			42413933		Silent	SNP	ENST00000342228.3	37	CCDS6132.1																																																																																				0.632	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			A	42294776	G	A	42294776	2	1	111	1	0	0	0	0	0	0	0	1	14476	1074	38	1		1	SLC20A2	8	42294776	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4036885	42294776	104069246	462	29596										
CHRNA6	8973	hgsc.bcm.edu	37	chr8	42611740	42611741	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcccattcactgttttcccINSaaaaatcattcatatccact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:42611740_42611741insA	ENST00000276410.2	-	5	956_957	c.601_602insT	c.(601-603)tggfs	p.W201fs	CHRNA6_ENST00000530869.1_5'Flank|CHRNA6_ENST00000534622.1_Frame_Shift_Ins_p.W186fs	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	201					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)			endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	ACTGTTTTCCCAAAAATCATTC	0.347																																																0			8																																								42730898	SO:0001589	frameshift_variant	8973			U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.602dupT	8.37:g.42611745_42611745dupA	ENSP00000276410:p.Trp201fs		42730897	B2R8V4|B4DQH1	Frame_Shift_Ins	INS	ENST00000276410.2	37	CCDS6135.1																																																																																				0.347	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			A	42611741	-	A	42611740	7	5	111	1	0	1	1	0	0	0	0	0	3393	595	21	0	890	0	CHRNA6	8	42611740	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	316964	42611740	103752282	463	29597										
TGS1	96764	hgsc.bcm.edu	37	chr8	56723473	56723473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tatcgatcctgttaagattgCccttgctcgcaataatgcag	8	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:56723473C>T	ENST00000260129.5	+	11	2654	c.2177C>T	c.(2176-2178)gCc>gTc	p.A726V		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	726	Sufficient for catalytic activity.				7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)	p.A726G(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			GTTAAGATTGCCCTTGCTCGC	0.353																																					Esophageal Squamous(34;275 823 4842 34837 48447)											1	Substitution - Missense(1)	ovary(1)	8											206	208	207					8																	56723473		2203	4300	6503	56886027	SO:0001583	missense	286826			AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.2177C>T	8.37:g.56723473C>T	ENSP00000260129:p.Ala726Val		56886027	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706204	0.48412	.	.	ENSG00000137574	ENST00000260129	T	0.53206	0.63	5.57	4.42	0.53409	.	0.269103	0.39985	N	0.001217	T	0.40347	0.1113	L	0.60845	1.875	0.34928	D	0.749055	B	0.32031	0.352	B	0.31946	0.138	T	0.50693	-0.8798	10	0.40728	T	0.16	-21.6624	5.8816	0.18858	0.7161:0.1743:0.1096:0.0	.	726	Q96RS0	TGS1_HUMAN	V	726	ENSP00000260129:A726V	ENSP00000260129:A726V	A	+	2	0	TGS1	56886027	0.985000	0.35326	1.000000	0.80357	0.982000	0.71751	2.459000	0.45023	0.952000	0.37798	-0.262000	0.10625	GCC		0.353	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		T	56723473	C	T	56723473	3	4	111	1	0	0	0	0	1	0	0	0	15876	739	26	3	2219	3	TGS1	8	56723473	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	14111733	56723473	89640549	464	29598										
ADHFE1	137872	hgsc.bcm.edu	37	chr8	67356834	67356834	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taggttttcttgtaggacctAaaaaacatgggtgctaaaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:67356834delA	ENST00000396623.3	+	5	235	c.204delA	c.(202-204)ctafs	p.L68fs	ADHFE1_ENST00000379385.4_Frame_Shift_Del_p.L68fs|ADHFE1_ENST00000496501.1_3'UTR|ADHFE1_ENST00000415254.1_Frame_Shift_Del_p.L20fs	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	68					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		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)			TGTAGGACCTAAAAAACATGG	0.408																																																0			8											151	147	148					8																	67356834		2203	4300	6503	67519388	SO:0001589	frameshift_variant	137872			AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"Alcohol dehydrogenases"	16354	protein-coding gene	gene with protein product	"hydroxyacid-oxoacid transhydrogenase"	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.204delA	8.37:g.67356834delA	ENSP00000379865:p.Leu68fs		67519388	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Frame_Shift_Del	DEL	ENST00000396623.3	37	CCDS6190.2																																																																																				0.408	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650		-	67356834	A	-	67356834	7	5	111	1	0	1	0	1	0	0	0	0	314	349	13	0	222	0	ADHFE1	8	67356834	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	10633361	67356834	79007188	465	29599										
LRRC67	286187	hgsc.bcm.edu	37	chr8	67929897	67929897	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaaatttatatgagttattTtcttcaggcactgtgaaatg	7	4	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:67929897T>G	ENST00000324682.5	-	2	230	c.86A>C	c.(85-87)aAa>aCa	p.K29T	PPP1R42_ENST00000522909.1_Missense_Mutation_p.K29T|PPP1R42_ENST00000517834.1_5'UTR	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	29					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										ATGAGTTATTTTCTTCAGGCA	0.269																																																0			8											62	60	61					8																	67929897		2201	4300	6501	68092451	SO:0001583	missense	286187			BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	33732	protein-coding gene	gene with protein product	"testis leucine-rich repeat"		"leucine rich repeat containing 67"	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.86A>C	8.37:g.67929897T>G	ENSP00000315035:p.Lys29Thr		68092451		Missense_Mutation	SNP	ENST00000324682.5	37	CCDS34902.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.394807	0.42512	.	.	ENSG00000178125	ENST00000522909;ENST00000421742;ENST00000324682	T;T	0.40756	2.22;1.02	5.05	5.05	0.67936	.	0.143330	0.64402	D	0.000007	T	0.25232	0.0613	N	0.12611	0.24	0.46701	D	0.999167	B	0.13145	0.007	B	0.24394	0.053	T	0.07927	-1.0747	10	0.33141	T	0.24	-15.2332	9.3595	0.38186	0.0:0.0805:0.0:0.9195	.	29	Q7Z4L9-2	.	T	29	ENSP00000429721:K29T;ENSP00000315035:K29T	ENSP00000315035:K29T	K	-	2	0	LRRC67	68092451	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.250000	0.51445	1.883000	0.54544	0.533000	0.62120	AAA		0.269	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		G	67929897	T	G	67929897	3	3	111	1	0	0	0	0	1	0	0	0	9048	1841	64	4	620	4	LRRC67	8	67929897	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	573063	67929897	78434125	466	29600										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68151106	68151106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggtaaatcttgctagtgccTggacatatgcatctctctcc	8	11	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:68151106T>C	ENST00000262215.3	-	21	3391	c.3002A>G	c.(3001-3003)cAg>cGg	p.Q1001R	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.Q455R|ARFGEF1_ENST00000518230.1_5'Flank	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1001					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TGCTAGTGCCTGGACATATGC	0.368																																																0			8											142	125	131					8																	68151106		2203	4300	6503	68313660	SO:0001583	missense	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.3002A>G	8.37:g.68151106T>C	ENSP00000262215:p.Gln1001Arg		68313660	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358055	0.82243	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.52057	0.68;0.68	5.32	5.32	0.75619	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;0.991	D;P	0.85130	0.997;0.885	T	0.71666	-0.4524	10	0.66056	D	0.02	.	15.5798	0.76425	0.0:0.0:0.0:1.0	.	1001;455	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	R	455;1001	ENSP00000428429:Q455R;ENSP00000262215:Q1001R	ENSP00000262215:Q1001R	Q	-	2	0	ARFGEF1	68313660	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.986000	0.88173	2.123000	0.65237	0.528000	0.53228	CAG		0.368	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68151106	T	C	68151106	3	2	111	1	0	0	0	0	1	0	0	0	852	1580	55	4	2623	4	ARFGEF1	8	68151106	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	221209	68151106	78212916	467	29601										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480416	73480416	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaaaaaaagaacaaatgaaCgaagaactgaggcgagaggc	11	6	0	5			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:73480416C>T	ENST00000523207.1	+	2	1035	c.447C>T	c.(445-447)aaC>aaT	p.N149N		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	149					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	AACAAATGAACGAAGAACTGA	0.458																																																0			8											123	130	128					8																	73480416		2203	4300	6503	73642970	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.447C>T	8.37:g.73480416C>T			73642970	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.458	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73480416	C	T	73480416	2	4	111	1	0	0	0	0	0	0	0	1	8034	535	19	1		1	KCNB2	8	73480416	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5329310	73480416	72883606	468	29602										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77763302	77763302	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agatcaattaaatgaacagcAaaaaaggcaaccgctctctg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:77763302delA	ENST00000521891.2	+	10	4593	c.4145delA	c.(4144-4146)caafs	p.Q1382fs	ZFHX4_ENST00000518282.1_Frame_Shift_Del_p.Q1356fs|ZFHX4_ENST00000050961.6_Frame_Shift_Del_p.Q1337fs|ZFHX4_ENST00000455469.2_Frame_Shift_Del_p.Q1337fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AATGAACAGCAAAAAAGGCAA	0.403										HNSCC(33;0.089)																																						0			8											107	100	102					8																	77763302		1865	4111	5976	77925857	SO:0001589	frameshift_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4145delA	8.37:g.77763302delA	ENSP00000430497:p.Gln1382fs		77925857	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Del	DEL	ENST00000521891.2	37	CCDS47878.2																																																																																				0.403	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		-	77763302	A	-	77763302	7	5	111	1	0	1	0	1	0	0	0	0	17674	130	5	0	4179	0	ZFHX4	8	77763302	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	4282886	77763302	68600720	469	29603										
ZNF704	619279	hgsc.bcm.edu	37	chr8	81571827	81571827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttttctacttactgggatgCctgtgaaagtgaccggagga	12	7	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:81571827C>T	ENST00000327835.3	-	7	1256	c.1025G>A	c.(1024-1026)gGc>gAc	p.G342D		NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	342							metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TACTGGGATGCCTGTGAAAGT	0.468																																																0			8											185	197	193					8																	81571827		2203	4300	6503	81734382	SO:0001583	missense	619279			AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.1025G>A	8.37:g.81571827C>T	ENSP00000331462:p.Gly342Asp		81734382	B2RNE6|B9EGW6	Missense_Mutation	SNP	ENST00000327835.3	37	CCDS34913.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.973035	0.92919	.	.	ENSG00000164684	ENST00000327835	T	0.31510	1.49	5.62	5.62	0.85841	.	0.045882	0.85682	D	0.000000	T	0.53690	0.1812	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.34229	-0.9837	10	0.30078	T	0.28	-35.4145	20.0114	0.97452	0.0:1.0:0.0:0.0	.	342	Q6ZNC4	ZN704_HUMAN	D	342	ENSP00000331462:G342D	ENSP00000331462:G342D	G	-	2	0	ZNF704	81734382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.221000	0.78016	2.795000	0.96236	0.655000	0.94253	GGC		0.468	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2	NM_001033723		T	81571827	C	T	81571827	3	4	111	1	0	0	0	0	1	0	0	0	18146	739	26	3	225	3	ZNF704	8	81571827	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3808525	81571827	64792195	470	29604										
SLC10A5	347051	hgsc.bcm.edu	37	chr8	82606597	82606597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttacaactccaaaagcttgcGcctcaggcaatgccacaatc	6	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:82606597G>A	ENST00000518568.1	-	1	1812	c.611C>T	c.(610-612)gCg>gTg	p.A204V		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	204						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						AAAAGCTTGCGCCTCAGGCAA	0.483																																																0			8											84	91	89					8																	82606597		2203	4300	6503	82769152	SO:0001583	missense	347051				CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.611C>T	8.37:g.82606597G>A	ENSP00000428612:p.Ala204Val		82769152	B2RN26	Missense_Mutation	SNP	ENST00000518568.1	37	CCDS34915.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.163952	0.38217	.	.	ENSG00000253598	ENST00000518568	T	0.12569	2.67	6.1	4.21	0.49690	.	0.247697	0.28382	N	0.015544	T	0.09774	0.0240	L	0.35723	1.085	0.35543	D	0.803248	P	0.37276	0.589	B	0.32980	0.156	T	0.28522	-1.0041	10	0.29301	T	0.29	-6.4121	8.9787	0.35953	0.0776:0.0:0.7742:0.1482	.	204	Q5PT55	NTCP5_HUMAN	V	204	ENSP00000428612:A204V	ENSP00000428612:A204V	A	-	2	0	SLC10A5	82769152	0.993000	0.37304	0.663000	0.29738	0.316000	0.28119	4.032000	0.57274	1.587000	0.49959	0.650000	0.86243	GCG		0.483	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		A	82606597	G	A	82606597	3	1	111	1	0	0	0	0	1	0	0	0	14414	1087	38	1	707	1	SLC10A5	8	82606597	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1034770	82606597	63757425	471	29605										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86057694	86057695	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacaaaaaaacaatggaagcINSaaaaattaagcaacttgctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:86057694_86057695insA	ENST00000360375.3	+	19	3196_3197	c.3047_3048insA	c.(3046-3051)gcaaaafs	p.AK1016fs	LRRCC1_ENST00000414626.2_Frame_Shift_Ins_p.AK996fs	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1016					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ACAATGGAAGCAAAAATTAAGC	0.297																																																0			8																																								86244947	SO:0001589	frameshift_variant	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3052dupA	8.37:g.86057699_86057699dupA	ENSP00000353538:p.Ala1016fs		86244946	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Frame_Shift_Ins	INS	ENST00000360375.3	37	CCDS43750.1																																																																																				0.297	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		A	86057695	-	A	86057694	7	5	111	1	0	1	1	0	0	0	0	0	9055	710	25	0	3121	0	LRRCC1	8	86057694	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	3451097	86057694	60306328	472	29606										
SNX31	169166	hgsc.bcm.edu	37	chr8	101642568	101642568	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcttaccagctgcgccagtTttaaaaactcaacgaagaca	7	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:101642568T>A	ENST00000311812.2	-	4	458	c.308A>T	c.(307-309)aAa>aTa	p.K103I		NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	103	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			CTGCGCCAGTTTTAAAAACTC	0.502																																																0			8											94	77	83					8																	101642568		2203	4300	6503	101711744	SO:0001583	missense	169166				CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"Sorting nexins"	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.308A>T	8.37:g.101642568T>A	ENSP00000312368:p.Lys103Ile		101711744	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.195576	0.38806	.	.	ENSG00000174226	ENST00000311812;ENST00000520352;ENST00000520661	T;T;T	0.40476	1.03;1.03;1.03	5.23	2.68	0.31781	Phox homologous domain (5);	0.080070	0.50627	D	0.000110	T	0.41282	0.1152	L	0.37630	1.12	0.43421	D	0.99557	D	0.54772	0.968	P	0.55087	0.768	T	0.27054	-1.0085	10	0.62326	D	0.03	-11.3116	5.7639	0.18215	0.0:0.0891:0.3464:0.5645	.	103	Q8N9S9	SNX31_HUMAN	I	103;37;104	ENSP00000312368:K103I;ENSP00000428210:K37I;ENSP00000428855:K104I	ENSP00000312368:K103I	K	-	2	0	SNX31	101711744	0.444000	0.25649	0.407000	0.26434	0.421000	0.31385	0.482000	0.22276	0.804000	0.34136	0.454000	0.30748	AAA		0.502	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628		A	101642568	T	A	101642568	3	1	111	1	0	0	0	0	1	0	0	0	14938	1841	64	5	1058	5	SNX31	8	101642568	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	15584874	101642568	44721454	473	29607										
GRHL2	79977	hgsc.bcm.edu	37	chr8	102505016	102505019	+	Splice_Site	DEL	AAGT	AAGT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acatgtcacaagagtcggacAagtaagtggatcacacgcgc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AAGT	AAGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:102505016_102505019delAAGT	ENST00000251808.3	+	1	357_358	c.19_20delAAGT	c.(19-21)aag>g	p.K7fs	KB-1562D12.1_ENST00000520268.1_RNA|GRHL2_ENST00000395927.1_5'UTR	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	7	Transcription activation.				brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			AGAGTCGGACAAGTAAGTGGATCA	0.461																																																0			8																																								102574195	SO:0001630	splice_region_variant	79977			AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.20+1AAGT>-	8.37:g.102505020_102505023delAAGT			102574192	A1L303|Q6NT03|Q9H8B8	In_Frame_Del	DEL	ENST00000251808.3	37	CCDS34931.1																																																																																				0.461	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	Frame_Shift_Del	-	102505019	AAGT	-	102505016	8	5	111	1	0	1	0	1	0	0	1	0	6785	144	5	0	21	0	GRHL2	8	102505016	Splice_Site	DEL	AAGT	TCGA-EI-6507-01A-11D-1733-10	862448	102505016	43859006	474	29608										
FZD6	8323	hgsc.bcm.edu	37	chr8	104340566	104340566	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatgacattaattgttggcaTctctgctgtcttctgggttg	11	7	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:104340566T>C	ENST00000358755.4	+	5	1780	c.1463T>C	c.(1462-1464)aTc>aCc	p.I488T	FZD6_ENST00000540287.1_Missense_Mutation_p.I183T|FZD6_ENST00000522566.1_Missense_Mutation_p.I488T|FZD6_ENST00000523739.1_Missense_Mutation_p.I456T	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	488					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			ATTGTTGGCATCTCTGCTGTC	0.348																																																0			8											108	112	111					8																	104340566		2203	4300	6503	104409742	SO:0001583	missense	8323			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.1463T>C	8.37:g.104340566T>C	ENSP00000351605:p.Ile488Thr		104409742	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.593014	0.86953	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000540287;ENST00000539487	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.45	5.45	0.79879	GPCR, family 2-like (1);	0.169147	0.53938	D	0.000046	D	0.94591	0.8257	M	0.90019	3.08	0.58432	D	0.99999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.87578	0.992;0.997;0.998;0.992	D	0.95592	0.8655	10	0.87932	D	0	.	15.8118	0.78571	0.0:0.0:0.0:1.0	.	433;183;488;488	B4E236;F5H831;B2R9H9;O60353	.;.;.;FZD6_HUMAN	T	488;488;456;183;433	ENSP00000429055:I488T;ENSP00000351605:I488T;ENSP00000429528:I456T;ENSP00000443757:I183T	ENSP00000351605:I488T	I	+	2	0	FZD6	104409742	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.798000	0.85924	2.194000	0.70268	0.383000	0.25322	ATC		0.348	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		C	104340566	T	C	104340566	3	2	111	1	0	0	0	0	1	0	0	0	6153	1435	50	4	1477	4	FZD6	8	104340566	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1835550	104340566	42023456	475	29609										
LRP12	29967	hgsc.bcm.edu	37	chr8	105509439	105509440	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggttggcaaaaaaagcagINStttttttcatctgagccatt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:105509439_105509440insT	ENST00000276654.5	-	5	1448_1449	c.1340_1341insA	c.(1339-1341)aacfs	p.N447fs	LRP12_ENST00000518375.1_5'Flank|LRP12_ENST00000424843.2_Frame_Shift_Ins_p.N428fs	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	447	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AAAAAAAGCAGTTTTTTTCATC	0.421																																																0			8																																								105578616	SO:0001589	frameshift_variant	29967			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1341dupA	8.37:g.105509446_105509446dupT	ENSP00000276654:p.Asn447fs		105578615	A8K137|B4DRQ2	Frame_Shift_Ins	INS	ENST00000276654.5	37	CCDS6303.1																																																																																				0.421	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		T	105509440	-	T	105509439	7	5	111	1	0	1	1	0	0	0	0	0	8983	1020	36	0	1250	0	LRP12	8	105509439	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	1168873	105509439	40854583	476	29610										
LRP12	29967	hgsc.bcm.edu	37	chr8	105511547	105511548	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttatttaaaaacacacctgINSaaaaatatgccagtctgaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:105511547_105511548insA	ENST00000276654.5	-	4	580_581	c.472_473insT	c.(472-474)tcafs	p.S158fs	LRP12_ENST00000424843.2_Frame_Shift_Ins_p.S139fs	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	158	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AAACACACCTGAAAAATATGCC	0.356																																																0			8																																								105580724	SO:0001589	frameshift_variant	29967			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.473dupT	8.37:g.105511552_105511552dupA	ENSP00000276654:p.Ser158fs		105580723	A8K137|B4DRQ2	Frame_Shift_Ins	INS	ENST00000276654.5	37	CCDS6303.1																																																																																				0.356	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		A	105511548	-	A	105511547	7	5	111	1	0	1	1	0	0	0	0	0	8983	1294	45	0	2122	0	LRP12	8	105511547	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	2108	105511547	40852475	477	29611										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106813577	106813577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagaagcgaacttccccagAgccaaaaggccatgcagact	9	14	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:106813577A>G	ENST00000407775.2	+	8	1517	c.1267A>G	c.(1267-1269)Agc>Ggc	p.S423G	RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.S291G|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.S291G|ZFPM2_ENST00000378472.4_Missense_Mutation_p.S154G	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	423					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ACTTCCCCAGAGCCAAAAGGC	0.488																																																0			8											63	64	64					8																	106813577		1965	4168	6133	106882753	SO:0001583	missense	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1267A>G	8.37:g.106813577A>G	ENSP00000384179:p.Ser423Gly		106882753	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	A	9.039	0.989232	0.18966	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.21031	2.03;2.5;2.5;3.7	5.91	2.29	0.28610	.	0.168138	0.64402	N	0.000003	T	0.15869	0.0382	L	0.43152	1.355	0.43283	D	0.995255	B	0.14012	0.009	B	0.14578	0.011	T	0.10222	-1.0639	10	0.17832	T	0.49	.	9.7369	0.40392	0.7361:0.0:0.2639:0.0	.	423	Q8WW38	FOG2_HUMAN	G	423;291;291;154	ENSP00000384179:S423G;ENSP00000430757:S291G;ENSP00000428720:S291G;ENSP00000367733:S154G	ENSP00000367733:S154G	S	+	1	0	ZFPM2	106882753	1.000000	0.71417	0.967000	0.41034	0.692000	0.40212	1.066000	0.30604	0.164000	0.19529	-0.256000	0.11100	AGC		0.488	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			G	106813577	A	G	106813577	3	3	111	1	0	0	0	0	1	0	0	0	17697	304	11	4	1297	4	ZFPM2	8	106813577	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1302030	106813577	39550445	478	29612										
KCNV1	27012	hgsc.bcm.edu	37	chr8	110986388	110986388	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcggccagggccccggggCggcggtaggaagccaccacc	18	16	0	0	rs112430047		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:110986388C>A	ENST00000524391.1	-	2	1262	c.230G>T	c.(229-231)cGc>cTc	p.R77L	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Missense_Mutation_p.R77L			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	77					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			GGCCCCGGGGCGGCGGTAGGA	0.697																																																0			8											15	15	15					8																	110986388		2192	4283	6475	111055564	SO:0001583	missense	27012			AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.230G>T	8.37:g.110986388C>A	ENSP00000435954:p.Arg77Leu		111055564	Q9UHJ4	Missense_Mutation	SNP	ENST00000524391.1	37	CCDS6314.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.670431	0.47677	.	.	ENSG00000164794	ENST00000524391;ENST00000297404	D;D	0.97505	-4.41;-4.41	4.95	3.99	0.46301	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.115933	0.39834	N	0.001256	D	0.92564	0.7638	L	0.27053	0.805	0.36563	D	0.872536	B	0.31383	0.321	B	0.32677	0.15	D	0.91970	0.5586	10	0.56958	D	0.05	.	7.391	0.26909	0.0:0.8814:0.0:0.1186	.	77	Q6PIU1	KCNV1_HUMAN	L	77	ENSP00000435954:R77L;ENSP00000297404:R77L	ENSP00000297404:R77L	R	-	2	0	KCNV1	111055564	0.885000	0.30320	1.000000	0.80357	0.776000	0.43924	0.018000	0.13422	2.554000	0.86153	0.655000	0.94253	CGC		0.697	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		A	110986388	C	A	110986388	3	1	111	1	0	0	0	0	1	0	0	0	8115	768	27	2	1284	2	KCNV1	8	110986388	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4172811	110986388	35377634	479	29613										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116599330	116599330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgccagctggcgccccctgCaggaatcccttggtttccac	10	18	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:116599330C>T	ENST00000220888.5	-	4	2718	c.2559G>A	c.(2557-2559)ctG>ctA	p.L853L	TRPS1_ENST00000519674.1_Silent_p.L853L|TRPS1_ENST00000395715.3_Silent_p.L866L|TRPS1_ENST00000519076.1_Silent_p.L607L|TRPS1_ENST00000520276.1_Silent_p.L857L			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	853					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GCGCCCCCTGCAGGAATCCCT	0.577									Langer-Giedion syndrome																																							0			8											32	34	33					8																	116599330		1819	4072	5891	116668505	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2559G>A	8.37:g.116599330C>T			116668505	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.577	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116599330	C	T	116599330	2	4	111	1	0	0	0	0	0	0	0	1	16633	697	25	3		3	TRPS1	8	116599330	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5612942	116599330	29764692	480	29614										
MRPL13	28998	hgsc.bcm.edu	37	chr8	121444364	121444364	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacatgatccccacagtcacCtacattttaaaaagaaacaa	3	11	1	2	rs376034901		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:121444364C>G	ENST00000306185.3	-	3	443		c.e3-1			NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13						translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CCACAGTCACCTACATTTTAA	0.308																																																0			8											92	89	90					8																	121444364		2203	4296	6499	121513545	SO:0001630	splice_region_variant	28998			AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.152-1G>C	8.37:g.121444364C>G			121513545	B2R4R8|Q9UI04	Splice_Site	SNP	ENST00000306185.3	37	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.574559	0.65878	.	.	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	6.05	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1468	0.65355	0.0:0.9274:0.0:0.0726	.	.	.	.	.	-1	.	.	.	-	.	.	MRPL13	121513545	1.000000	0.71417	0.988000	0.46212	0.807000	0.45602	7.093000	0.76937	1.580000	0.49851	0.573000	0.79308	.		0.308	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078	Intron	G	121444364	C	G	121444364	5	3	111	1	0	0	0	0	0	0	1	0	9808	695	24	5	405	5	MRPL13	8	121444364	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4845034	121444364	24919658	481	29615										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964088	123964088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaccccctctacgtgtgtgCagaatgtaacttcacaacca	6	14	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:123964088C>T	ENST00000314393.4	+	3	1173	c.338C>T	c.(337-339)gCa>gTa	p.A113V		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	113					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TACGTGTGTGCAGAATGTAAC	0.498																																					Esophageal Squamous(94;1056 1388 11767 13799 49639)											0			8											103	93	96					8																	123964088		2203	4300	6503	124033269	SO:0001583	missense	22882			AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.338C>T	8.37:g.123964088C>T	ENSP00000314709:p.Ala113Val		124033269		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748986	0.49257	.	.	ENSG00000178764	ENST00000314393	T	0.51071	0.72	5.56	5.56	0.83823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.55847	0.1946	N	0.25144	0.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48456	-0.9034	10	0.19590	T	0.45	-21.352	19.5336	0.95240	0.0:1.0:0.0:0.0	.	113	Q9Y6X8	ZHX2_HUMAN	V	113	ENSP00000314709:A113V	ENSP00000314709:A113V	A	+	2	0	ZHX2	124033269	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.724000	0.68500	2.637000	0.89404	0.455000	0.32223	GCA		0.498	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		T	123964088	C	T	123964088	3	4	111	1	0	0	0	0	1	0	0	0	17715	710	25	3	340	3	ZHX2	8	123964088	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2519724	123964088	22399934	482	29616										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133150233	133150233	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcctcaaagtctccttgaaTttttttttatagagacggaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:133150233delT	ENST00000388996.4	-	12	2019	c.1599delA	c.(1597-1599)aaafs	p.K533fs	KCNQ3_ENST00000521134.1_Frame_Shift_Del_p.K413fs|KCNQ3_ENST00000519445.1_Frame_Shift_Del_p.K533fs	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	533					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCTCCTTGAATTTTTTTTTAT	0.453																																																0			8											103	101	102					8																	133150233		2203	4300	6503	133219415	SO:0001589	frameshift_variant	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1599delA	8.37:g.133150233delT	ENSP00000373648:p.Lys533fs		133219415	A2VCT8|B4DJY4|E7EQ89	Frame_Shift_Del	DEL	ENST00000388996.4	37	CCDS34943.1																																																																																				0.453	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		-	133150233	T	-	133150233	7	5	111	1	0	1	0	1	0	0	0	0	8105	1490	52	0	1035	0	KCNQ3	8	133150233	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	9186145	133150233	13213789	483	29617										
TG	7038	hgsc.bcm.edu	37	chr8	133984918	133984918	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagaatggaggagcctggcGcattttggactgtggctctc	16	8	1	1	rs573866267		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:133984918G>A	ENST00000220616.4	+	34	6171	c.6131G>A	c.(6130-6132)cGc>cAc	p.R2044H	TG_ENST00000519543.1_Missense_Mutation_p.R198H|TG_ENST00000542445.1_Missense_Mutation_p.R414H|TG_ENST00000377869.1_Missense_Mutation_p.R1987H|TG_ENST00000522523.1_3'UTR	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2044					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		GGAGCCTGGCGCATTTTGGAC	0.488																																																0			8											165	148	154					8																	133984918		2203	4300	6503	134054100	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.6131G>A	8.37:g.133984918G>A	ENSP00000220616:p.Arg2044His		134054100	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399079	0.62177	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	T;T;T;T	0.71103	-0.33;-0.34;-0.54;-0.42	5.74	3.0	0.34707	.	0.421904	0.23360	N	0.049025	T	0.80132	0.4567	M	0.77616	2.38	0.26929	N	0.966517	D;D;D	0.89917	1.0;0.999;0.999	D;P;P	0.66979	0.948;0.891;0.88	T	0.70443	-0.4870	10	0.87932	D	0	.	7.0978	0.25319	0.2687:0.0:0.7313:0.0	.	198;414;2044	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	H	1987;850;2044;414;198	ENSP00000367100:R1987H;ENSP00000220616:R2044H;ENSP00000441693:R414H;ENSP00000430430:R198H	ENSP00000220616:R2044H	R	+	2	0	TG	134054100	0.990000	0.36364	0.481000	0.27354	0.844000	0.47949	2.316000	0.43761	0.785000	0.33685	-0.136000	0.14681	CGC		0.488	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133984918	G	A	133984918	3	1	111	1	0	0	0	0	1	0	0	0	15852	1087	38	1	6265	1	TG	8	133984918	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	834685	133984918	12379104	484	29618										
ZFAT	57623	hgsc.bcm.edu	37	chr8	135614700	135614700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccgtggaccagcatatggCggtcacggtccagctcgttc	12	14	1	0	rs141961813		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:135614700C>T	ENST00000377838.3	-	6	1436	c.1262G>A	c.(1261-1263)cGc>cAc	p.R421H	ZFAT_ENST00000520727.1_Missense_Mutation_p.R409H|ZFAT_ENST00000429442.2_Missense_Mutation_p.R409H|ZFAT_ENST00000520214.1_Missense_Mutation_p.R409H|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520356.1_Missense_Mutation_p.R409H|ZFAT_ENST00000523399.1_Missense_Mutation_p.R359H	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	421					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	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)			CAGCATATGGCGGTCACGGTC	0.592																																																0			8											47	51	49					8																	135614700		2064	4218	6282	135683882	SO:0001583	missense	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.1262G>A	8.37:g.135614700C>T	ENSP00000367069:p.Arg421His		135683882	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397280	0.83120	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18	5.74	5.74	0.90152	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.28863	0.0716	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.992;0.995	T	0.00135	-1.2007	10	0.34782	T	0.22	-33.6203	18.9218	0.92528	0.0:1.0:0.0:0.0	.	359;409;409;421	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	H	409;409;409;421;409;359;409	ENSP00000427879:R409H;ENSP00000427831:R409H;ENSP00000394501:R409H;ENSP00000367069:R421H;ENSP00000428483:R409H;ENSP00000429091:R359H	ENSP00000367069:R421H	R	-	2	0	ZFAT	135683882	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.079000	0.71291	2.717000	0.92951	0.563000	0.77884	CGC		0.592	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		T	135614700	C	T	135614700	3	4	111	1	0	0	0	0	1	0	0	0	17671	768	27	1	2513	1	ZFAT	8	135614700	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1629782	135614700	10749322	485	29619										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139180283	139180283	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccagggacagctggctgtgCgtctgtatcctggggagcac	15	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:139180283C>T	ENST00000395297.1	-	12	1283	c.1113G>A	c.(1111-1113)acG>acA	p.T371T		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	371										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GCTGGCTGTGCGTCTGTATCC	0.597										HNSCC(54;0.14)																																						0			8											86	93	91					8																	139180283		2105	4230	6335	139249465	SO:0001819	synonymous_variant	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1113G>A	8.37:g.139180283C>T			139249465	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																				0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139180283	C	T	139180283	2	4	111	1	0	0	0	0	0	0	0	1	5465	755	27	1		1	FAM135B	8	139180283	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3565583	139180283	7183739	486	29620										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142229024	142229024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggacaccgtgaagatgatggCggcaaagaagaagagcacct	14	8	0	6	rs539535235	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:142229024C>T	ENST00000024061.3	-	4	869	c.562G>A	c.(562-564)Gcc>Acc	p.A188T	SLC45A4_ENST00000433583.2_Missense_Mutation_p.A181T|SLC45A4_ENST00000517878.1_Missense_Mutation_p.A239T|SLC45A4_ENST00000519067.1_Missense_Mutation_p.A188T	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|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;0.0493)			AAGATGATGGCGGCAAAGAAG	0.662													C|||	9	0.00179712	0	0	5008	,	,		16769	0		0	False		,,,				2504	0.0092															0			8											93	97	95					8																	142229024		2203	4300	6503	142298206	SO:0001583	missense	57210			AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.562G>A	8.37:g.142229024C>T	ENSP00000024061:p.Ala188Thr		142298206	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275776	0.59649	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000520137	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	5.3	5.3	0.74995	.	0.100250	0.64402	D	0.000002	D	0.93354	0.7881	L	0.33093	0.98	0.46499	D	0.999071	D;D;B	0.69078	0.997;0.997;0.369	D;P;B	0.65684	0.937;0.859;0.249	D	0.92826	0.6276	10	0.38643	T	0.18	-35.8864	19.0189	0.92905	0.0:1.0:0.0:0.0	.	239;188;188	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	T	188;239;181;188;46	ENSP00000429059:A188T;ENSP00000428137:A239T;ENSP00000400799:A181T;ENSP00000024061:A188T;ENSP00000429033:A46T	ENSP00000024061:A188T	A	-	1	0	SLC45A4	142298206	0.999000	0.42202	0.995000	0.50966	0.983000	0.72400	4.358000	0.59442	2.479000	0.83701	0.555000	0.69702	GCC		0.662	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		T	142229024	C	T	142229024	3	4	111	1	0	0	0	0	1	0	0	0	14680	768	27	1	1854	1	SLC45A4	8	142229024	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3048741	142229024	4134998	487	29621										
PTP4A3	11156	hgsc.bcm.edu	37	chr8	142437905	142437905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgggatgaagtacgaggacGccatccagttcatccgccag	13	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:142437905G>A	ENST00000521578.1	+	5	1330	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	PTP4A3_ENST00000329397.1_Missense_Mutation_p.A129T|PTP4A3_ENST00000520105.1_Intron|PTP4A3_ENST00000349124.1_Intron|PTP4A3_ENST00000524028.1_Missense_Mutation_p.A43T			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	129	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			GTACGAGGACGCCATCCAGTT	0.682																																																0			8											44	34	37					8																	142437905		2115	4181	6296	142507087	SO:0001583	missense	11156			AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.385G>A	8.37:g.142437905G>A	ENSP00000428976:p.Ala129Thr		142507087	Q8IVN5|Q99849|Q9BTW5	Missense_Mutation	SNP	ENST00000521578.1	37	CCDS6383.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653096	0.88056	.	.	ENSG00000184489	ENST00000521578;ENST00000329397;ENST00000524028	D;D	0.82984	-1.67;-1.67	5.22	3.39	0.38822	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.91365	0.7276	M	0.91818	3.245	0.80722	D	1	D	0.69078	0.997	D	0.71414	0.973	D	0.92054	0.5651	10	0.87932	D	0	-24.6015	10.1961	0.43056	0.1659:0.0:0.8341:0.0	.	129	O75365	TP4A3_HUMAN	T	129;129;43	ENSP00000428976:A129T;ENSP00000332274:A129T	ENSP00000332274:A129T	A	+	1	0	PTP4A3	142507087	1.000000	0.71417	0.635000	0.29338	0.984000	0.73092	6.579000	0.74036	1.327000	0.45338	0.407000	0.27541	GCC		0.682	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611		A	142437905	G	A	142437905	3	1	111	1	0	0	0	0	1	0	0	0	12807	1087	38	1	399	1	PTP4A3	8	142437905	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	208881	142437905	3926117	488	29622										
JRK	8629	hgsc.bcm.edu	37	chr8	143746339	143746339	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccacagcttcctccaggccCgcctgaagacgtggctaggg	13	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:143746339C>T	ENST00000507178.2	-	0	1471							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				cctccaggcccgcctgaagac	0.632																																																0			8											10	11	11					8																	143746339		2082	4218	6300	143743341			8629			AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746339C>T			143743341	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																					0.632	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		T	143746339	C	T	143746339	1	4	111	0	1	0	0	0	0	0	0	0	7985	652	23	1		1	JRK	8	143746339	RNA	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1308434	143746339	2617683	489	29623										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145109542	145109542	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgttgcagcatggtggagtGggggggcatggagcctggtg					rs539582965	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:145109542delG	ENST00000426825.1	-	19	2689	c.2608delC	c.(2608-2610)cacfs	p.H870fs	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	870					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ATGGTGGAGTGGGGGGGCATG	0.642																																																0			8											41	48	46					8																	145109542		2102	4221	6323	145181530	SO:0001589	frameshift_variant	26873			AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.2608delC	8.37:g.145109542delG	ENSP00000475943:p.His870fs		145181530	A5PKY8|Q75W65|Q9Y4Q0	Frame_Shift_Del	DEL	ENST00000426825.1	37																																																																																					0.642	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		-	145109542	G	-	145109542	7	5	111	1	0	1	0	1	0	0	0	0	10907	1348	47	0	1296	0	OPLAH	8	145109542	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1363203	145109542	1254480	490	29624										
GPAA1	8733	hgsc.bcm.edu	37	chr8	145139400	145139400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggttctgcggcaggcctccGgccgcccccacggctcccat	12	19	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:145139400G>A	ENST00000355091.4	+	7	1019	c.898G>A	c.(898-900)Ggc>Agc	p.G300S	GPAA1_ENST00000527144.1_3'UTR|GPAA1_ENST00000361036.6_Missense_Mutation_p.G240S	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	300					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCAGGCCTCCGGCCGCCCCCA	0.627																																																0			8											31	36	34					8																	145139400		2028	4173	6201	145211388	SO:0001583	missense	8733			AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"GPI transamidase subunit"	603048	"anchor attachment protein 1 (Gaa1p, yeast) homolog", "GPAA1P anchor attachment protein 1 homolog (yeast)", "glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.898G>A	8.37:g.145139400G>A	ENSP00000347206:p.Gly300Ser		145211388	Q9NSS0|Q9UQ31	Missense_Mutation	SNP	ENST00000355091.4	37	CCDS43776.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.317906	0.81469	.	.	ENSG00000197858	ENST00000355091;ENST00000525087;ENST00000361036	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.78685	0.4322	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.993	T	0.77544	-0.2548	9	0.38643	T	0.18	-21.4343	16.7392	0.85454	0.0:0.0:1.0:0.0	.	300;240	O43292;O43292-2	GPAA1_HUMAN;.	S	300;228;240	.	ENSP00000347206:G300S	G	+	1	0	GPAA1	145211388	1.000000	0.71417	0.976000	0.42696	0.423000	0.31445	7.082000	0.76851	2.551000	0.86045	0.561000	0.74099	GGC		0.627	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801		A	145139400	G	A	145139400	3	1	111	1	0	0	0	0	1	0	0	0	6607	1116	39	1	924	1	GPAA1	8	145139400	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	29858	145139400	1224622	491	29625										
GPR172A	79581	hgsc.bcm.edu	37	chr8	145583598	145583598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcttacggtcattcttccTgggtcaaggcctgagtgccc	10	13	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:145583598T>C	ENST00000532887.1	+	3	1029	c.446T>C	c.(445-447)cTg>cCg	p.L149P	SLC52A2_ENST00000402965.1_Missense_Mutation_p.L149P|SLC52A2_ENST00000526891.1_3'UTR|FBXL6_ENST00000526524.1_5'Flank|SLC52A2_ENST00000329994.2_Missense_Mutation_p.L149P|FBXL6_ENST00000455319.2_5'Flank|FBXL6_ENST00000331890.5_5'Flank|SLC52A2_ENST00000540505.1_Missense_Mutation_p.L61P|SLC52A2_ENST00000530047.1_Missense_Mutation_p.L149P|SLC52A2_ENST00000526752.1_Intron|SLC52A2_ENST00000527078.1_Missense_Mutation_p.L149P			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	149					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	TCATTCTTCCTGGGTCAAGGC	0.647																																																0			8											135	137	136					8																	145583598		2203	4300	6503	145554406	SO:0001583	missense	79581			AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"Solute carriers"	30224	protein-coding gene	gene with protein product		607882	"G protein-coupled receptor 172A"	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.446T>C	8.37:g.145583598T>C	ENSP00000436768:p.Leu149Pro		145554406	A8K6B6|D3DWL8|G1UCY1|Q86UT1	Missense_Mutation	SNP	ENST00000532887.1	37	CCDS6423.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.761597	0.69763	.	.	ENSG00000185803	ENST00000530047;ENST00000527078;ENST00000402965;ENST00000534725;ENST00000532887;ENST00000329994;ENST00000540505	D;D;D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7	3.82	3.82	0.43975	.	0.178860	0.39909	N	0.001240	D	0.93785	0.8013	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	D	0.93276	0.6656	9	.	.	.	.	10.58	0.45250	0.0:0.0:0.0:1.0	.	149	Q9HAB3	RFT3_HUMAN	P	149;149;149;149;149;149;61	ENSP00000435820:L149P;ENSP00000434728:L149P;ENSP00000385961:L149P;ENSP00000431965:L149P;ENSP00000436768:L149P;ENSP00000333638:L149P;ENSP00000440400:L61P	.	L	+	2	0	GPR172A	145554406	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.692000	0.84203	1.600000	0.50102	0.379000	0.24179	CTG		0.647	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1	NM_024531		C	145583598	T	C	145583598	3	2	111	1	0	0	0	0	1	0	0	0	6689	1580	55	4	452	4	GPR172A	8	145583598	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	444198	145583598	780424	492	29626										
GPT	2875	hgsc.bcm.edu	37	chr8	145732004	145732004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatgtactccttcccgcgcGtgcagctgcccccgcgggcg	12	19	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr8:145732004G>A	ENST00000528431.1	+	10	1409	c.1252G>A	c.(1252-1254)Gtg>Atg	p.V418M	MFSD3_ENST00000301327.4_5'Flank|GPT_ENST00000394955.2_Missense_Mutation_p.V418M			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	418					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	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)		L-Alanine(DB00160)|Phenelzine(DB00780)	CTTCCCGCGCGTGCAGCTGCC	0.721																																																0			8											9	7	7					8																	145732004		2064	4071	6135	145702812	SO:0001583	missense	2875				CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	ENST00000528431.1:c.1252G>A	8.37:g.145732004G>A	ENSP00000433586:p.Val418Met		145702812	B0YJ18|D3DWM7|P78398|Q93076	Missense_Mutation	SNP	ENST00000528431.1	37	CCDS6430.1	.	.	.	.	.	.	.	.	.	.	G	7.518	0.656084	0.14580	.	.	ENSG00000167701	ENST00000528431;ENST00000394955	T;T	0.24538	1.85;1.85	4.54	-4.94	0.03057	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.192570	0.42964	N	0.000639	T	0.19446	0.0467	L	0.48260	1.515	0.18873	N	0.999985	B	0.27997	0.197	B	0.28784	0.094	T	0.13098	-1.0522	10	0.66056	D	0.02	-1.6278	12.529	0.56104	0.7825:0.0:0.2175:0.0	.	418	P24298	ALAT1_HUMAN	M	418	ENSP00000433586:V418M;ENSP00000378408:V418M	ENSP00000378408:V418M	V	+	1	0	GPT	145702812	0.180000	0.23148	0.001000	0.08648	0.024000	0.10985	0.679000	0.25291	-0.981000	0.03520	-1.069000	0.02264	GTG		0.721	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			A	145732004	G	A	145732004	3	1	111	1	0	0	0	0	1	0	0	0	6758	1145	40	1	1286	1	GPT	8	145732004	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	148406	145732004	632018	493	29627										
KANK1	23189	hgsc.bcm.edu	37	chr9	740854	740854	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatcatgttggcggccctcGccgctgtggaagcagagaag	14	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:740854G>A	ENST00000382303.1	+	13	4268	c.3616G>A	c.(3616-3618)Gcc>Acc	p.A1206T	KANK1_ENST00000382293.3_Missense_Mutation_p.A1048T|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.A1206T	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1206	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		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)		GGCGGCCCTCGCCGCTGTGGA	0.498																																																0			9											127	112	117					9																	740854		2203	4300	6503	730854	SO:0001583	missense	23189			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3616G>A	9.37:g.740854G>A	ENSP00000371740:p.Ala1206Thr		730854	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457514	0.63401	.	.	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293;ENST00000382289;ENST00000382286	T;T;T	0.53206	0.63;0.63;0.63	5.52	5.52	0.82312	Ankyrin repeat-containing domain (3);	0.000000	0.52532	D	0.000070	T	0.58850	0.2151	L	0.28400	0.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.991;0.967;0.994	T	0.53236	-0.8467	10	0.32370	T	0.25	-2.4989	19.8119	0.96549	0.0:0.0:1.0:0.0	.	252;118;1206	F5H7I5;Q5W0W2;Q14678	.;.;KANK1_HUMAN	T	1206;252;1206;1048;184;118	ENSP00000371740:A1206T;ENSP00000371734:A1206T;ENSP00000371730:A1048T	ENSP00000371723:A118T	A	+	1	0	KANK1	730854	1.000000	0.71417	0.221000	0.23827	0.102000	0.19082	9.700000	0.98707	2.756000	0.94617	0.563000	0.77884	GCC		0.498	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	740854	G	A	740854	3	1	111	1	0	0	0	0	1	0	0	0	7997	1087	38	1	3646	1	KANK1	9	740854	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10		740854	140472577	494	29628										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20874701	20874701	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taagaccagaaattcccattCctgaagagttagatgacgat	8	8	0	6			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:20874701C>T	ENST00000380249.1	+	21	2576	c.2212C>T	c.(2212-2214)Cct>Tct	p.P738S	FOCAD_ENST00000604828.1_3'UTR|FOCAD_ENST00000605086.1_Missense_Mutation_p.P174S|FOCAD_ENST00000338382.6_Missense_Mutation_p.P738S	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	738						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.P738A(1)									AATTCCCATTCCTGAAGAGTT	0.368																																																1	Substitution - Missense(1)	ovary(1)	9											177	162	167					9																	20874701		2203	4300	6503	20864701	SO:0001583	missense	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2212C>T	9.37:g.20874701C>T	ENSP00000369599:p.Pro738Ser		20864701	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	C	4.124	0.021313	0.08006	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.67171	-0.25;-0.25	5.21	2.02	0.26589	Armadillo-type fold (1);	0.434923	0.26525	N	0.023893	T	0.46268	0.1384	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.14337	-1.0476	10	0.08599	T	0.76	-18.8689	2.0074	0.03480	0.1345:0.488:0.1314:0.2461	.	738	Q5VW36	K1797_HUMAN	S	738	ENSP00000369599:P738S;ENSP00000344307:P738S	ENSP00000344307:P738S	P	+	1	0	KIAA1797	20864701	0.004000	0.15560	0.255000	0.24374	0.103000	0.19146	0.164000	0.16542	0.618000	0.30179	-0.157000	0.13467	CCT		0.368	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20874701	C	T	20874701	3	4	111	1	0	0	0	0	1	0	0	0	8279	855	30	3	2282	3	KIAA1797	9	20874701	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	20133847	20874701	120338730	495	29629										
IFNA1	3439	hgsc.bcm.edu	37	chr9	21440948	21440948	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggctgtgaagaaatacttcCgaagaatcactctctatctg	8	9	3	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:21440948C>T	ENST00000276927.1	+	1	509	c.442C>T	c.(442-444)Cga>Tga	p.R148*		NM_024013.2	NP_076918.1	P01562	IFNA1_HUMAN	interferon, alpha 1	148					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.R148G(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(2)	7				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		GAAATACTTCCGAAGAATCAC	0.478																																																1	Substitution - Missense(1)	ovary(1)	9											31	38	35					9																	21440948		2135	4234	6369	21430948	SO:0001587	stop_gained	3439				CCDS6508.1	9p22	2010-12-10			ENSG00000197919	ENSG00000197919		"Interferons"	5417	protein-coding gene	gene with protein product	"IFN-alpha 1b", "interferon alpha 1b"	147660				1385305	Standard	NM_024013		Approved	IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD	uc003zpd.2	P01562	OTTHUMG00000019673	ENST00000276927.1:c.442C>T	9.37:g.21440948C>T	ENSP00000276927:p.Arg148*		21430948	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Nonsense_Mutation	SNP	ENST00000276927.1	37	CCDS6508.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299895	0.81136	.	.	ENSG00000197919	ENST00000276927	.	.	.	3.12	1.2	0.21068	.	0.522676	0.20658	N	0.088072	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	6.5509	0.22433	0.0:0.7352:0.0:0.2648	.	.	.	.	X	148	.	ENSP00000276927:R148X	R	+	1	2	IFNA1	21430948	0.195000	0.23338	0.666000	0.29783	0.610000	0.37248	0.300000	0.19156	0.632000	0.30432	0.536000	0.68110	CGA		0.478	IFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051902.1	NM_024013		T	21440948	C	T	21440948	4	4	111	1	0	0	0	0	0	1	0	0	7552	644	23	1	444	1	IFNA1	9	21440948	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	566247	21440948	119772483	496	29630										
C9orf72	203228	hgsc.bcm.edu	37	chr9	27556578	27556578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaatcaggagtaaagctttCgtcagtgtagatgatcgtat	10	6	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:27556578C>T	ENST00000380003.3	-	8	1135	c.1072G>A	c.(1072-1074)Gaa>Aaa	p.E358K	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	358					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GTAAAGCTTTCGTCAGTGTAG	0.403																																																0			9											117	108	111					9																	27556578		2203	4300	6503	27546578	SO:0001583	missense	203228			AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1072G>A	9.37:g.27556578C>T	ENSP00000369339:p.Glu358Lys		27546578	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946044	0.73672	.	.	ENSG00000147894	ENST00000380003	T	0.48522	0.81	5.79	5.79	0.91817	.	0.045975	0.85682	D	0.000000	T	0.41003	0.1140	L	0.44542	1.39	0.80722	D	1	P	0.50710	0.938	B	0.36666	0.23	T	0.30995	-0.9959	9	.	.	.	.	20.0308	0.97536	0.0:1.0:0.0:0.0	.	358	Q96LT7	CI072_HUMAN	K	358	ENSP00000369339:E358K	.	E	-	1	0	C9orf72	27546578	1.000000	0.71417	0.983000	0.44433	0.916000	0.54674	7.487000	0.81328	2.732000	0.93576	0.585000	0.79938	GAA		0.403	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		T	27556578	C	T	27556578	3	4	111	1	0	0	0	0	1	0	0	0	2501	893	31	1	389	1	C9orf72	9	27556578	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6115630	27556578	113656853	497	29631										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543427	32543427	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcatgctggtcaaaggctgCcatgttaaaaggagatcggg	15	7	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:32543427C>A	ENST00000360538.2	-	3	1212	c.1096G>T	c.(1096-1098)Gca>Tca	p.A366S	TOPORS_ENST00000379858.1_Missense_Mutation_p.A301S	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	366	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TCAAAGGCTGCCATGTTAAAA	0.403																																																0			9											65	68	67					9																	32543427		2203	4300	6503	32533427	SO:0001583	missense	10210			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1096G>T	9.37:g.32543427C>A	ENSP00000353735:p.Ala366Ser		32533427	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	5.343	0.248580	0.10130	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.14266	2.52;2.53	5.93	5.03	0.67393	.	0.131087	0.35436	N	0.003203	T	0.08268	0.0206	N	0.17082	0.46	0.34910	D	0.747428	B	0.30406	0.278	B	0.24974	0.057	T	0.26224	-1.0109	10	0.13108	T	0.6	-8.5287	13.7922	0.63148	0.0:0.9256:0.0:0.0744	.	366	Q9NS56	TOPRS_HUMAN	S	366;301	ENSP00000353735:A366S;ENSP00000369187:A301S	ENSP00000353735:A366S	A	-	1	0	TOPORS	32533427	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	3.815000	0.55651	1.503000	0.48686	0.655000	0.94253	GCA		0.403	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		A	32543427	C	A	32543427	3	1	111	1	0	0	0	0	1	0	0	0	16410	739	26	2	2045	2	TOPORS	9	32543427	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4986849	32543427	108670004	498	29632										
NOL6	65083	hgsc.bcm.edu	37	chr9	33463383	33463383	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggcggtgccgcgggatatgGcgaggagacaggcgaatcag	19	8	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:33463383G>A	ENST00000455041.2	-	23	2954	c.2895C>T	c.(2893-2895)cgC>cgT	p.R965R	NOL6_ENST00000379471.2_Intron|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	1017					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		GCGGGATATGGCGAGGAGACA	0.662																																																0			9											48	48	48					9																	33463383		2203	4300	6503	33453383	SO:0001819	synonymous_variant	65083			AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000455041.2:c.2895C>T	9.37:g.33463383G>A			33453383	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000455041.2	37																																																																																					0.662	NOL6-201	KNOWN	basic	protein_coding	protein_coding		NM_022917		A	33463383	G	A	33463383	2	1	111	1	0	0	0	0	0	0	0	1	10556	1190	42	3		3	NOL6	9	33463383	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	919956	33463383	107750048	499	29633										
RUSC2	9853	hgsc.bcm.edu	37	chr9	35547974	35547974	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagtatacacgaatacttcaCcccccaacctcagcactgga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:35547974delC	ENST00000455600.1	+	2	2025	c.1456delC	c.(1456-1458)cccfs	p.P487fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	487						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GAATACTTCACCCCCCAACCT	0.602																																																0			9											68	74	72					9																	35547974		2203	4300	6503	35537974	SO:0001589	frameshift_variant	9853			AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1456delC	9.37:g.35547974delC	ENSP00000393922:p.Pro487fs		35537974	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	37	CCDS35008.1																																																																																				0.602	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		-	35547974	C	-	35547974	7	5	111	1	0	1	0	1	0	0	0	0	13788	507	18	0	1458	0	RUSC2	9	35547974	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	2084591	35547974	105665457	500	29634										
CCIN	881	hgsc.bcm.edu	37	chr9	36169700	36169700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacatgaagaccgctgatgaGcttttcatcaccattgacac	8	11	2	5			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:36169700G>T	ENST00000335119.2	+	1	312	c.201G>T	c.(199-201)gaG>gaT	p.E67D		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	67	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			CCGCTGATGAGCTTTTCATCA	0.527																																																0			9											101	94	97					9																	36169700		2203	4300	6503	36159700	SO:0001583	missense	881			Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.201G>T	9.37:g.36169700G>T	ENSP00000334996:p.Glu67Asp		36159700	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	37	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335645	0.41398	.	.	ENSG00000185972	ENST00000335119	T	0.67523	-0.27	5.56	3.7	0.42460	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.53938	D	0.000041	T	0.68979	0.3060	L	0.39326	1.205	0.29905	N	0.824077	D	0.57257	0.979	D	0.71414	0.973	T	0.62511	-0.6839	10	0.21540	T	0.41	.	7.6748	0.28480	0.1961:0.0:0.8039:0.0	.	67	Q13939	CALI_HUMAN	D	67	ENSP00000334996:E67D	ENSP00000334996:E67D	E	+	3	2	CCIN	36159700	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	0.876000	0.28092	0.697000	0.31718	0.462000	0.41574	GAG		0.527	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36169700	G	T	36169700	3	4	111	1	0	0	0	0	1	0	0	0	2884	962	34	2	203	2	CCIN	9	36169700	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	621726	36169700	105043731	501	29635										
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37304241	37304241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccagcggtactattcagcCaacaaaaacattatctgtag	6	11	2	0	rs267602236		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:37304241C>T	ENST00000336755.5	+	4	817	c.711C>T	c.(709-711)gcC>gcT	p.A237A	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_5'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	237						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		ACTATTCAGCCAACAAAAACA	0.383																																																0			9											97	94	95					9																	37304241		2203	4300	6503	37294241	SO:0001819	synonymous_variant	84186			AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"Zinc fingers, CCHC domain containing"	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.711C>T	9.37:g.37304241C>T			37294241	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Silent	SNP	ENST00000336755.5	37	CCDS6608.2																																																																																				0.383	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226		T	37304241	C	T	37304241	2	4	111	1	0	0	0	0	0	0	0	1	17632	581	21	3		3	ZCCHC7	9	37304241	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1134541	37304241	103909190	502	29636										
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37442272	37442272	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacatccattacattgctctCccccagcatgagggtggagg					rs369892279		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:37442272delC	ENST00000307750.4	-	2	465	c.277delG	c.(277-279)gagfs	p.E93fs		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	93	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		ACATTGCTCTCCCCCAGCATG	0.483																																																0			9											174	129	144					9																	37442272		2203	4300	6503	37432272	SO:0001589	frameshift_variant	9925			AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.277delG	9.37:g.37442272delC	ENSP00000307604:p.Glu93fs		37432272		Frame_Shift_Del	DEL	ENST00000307750.4	37	CCDS6610.1																																																																																				0.483	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		-	37442272	C	-	37442272	7	5	111	1	0	1	0	1	0	0	0	0	17590	864	30	0	1760	0	ZBTB5	9	37442272	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	138031	37442272	103771159	503	29637										
C9orf41	138199	hgsc.bcm.edu	37	chr9	77631201	77631202	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accatctctcttttggaaaaINSttttttaaaatttctttaat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:77631201_77631202insT	ENST00000376834.3	-	3	724_725	c.572_573insA	c.(571-573)aatfs	p.N191fs	C9orf41_ENST00000376837.3_Frame_Shift_Ins_p.N191fs|RP11-197P3.5_ENST00000455336.2_RNA	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	191								p.N191K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						CTTTTGGAAAATTTTTTAAAAT	0.342																																																1	Substitution - Missense(1)	endometrium(1)	9																																								76821022	SO:0001589	frameshift_variant	138199			AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.573dupA	9.37:g.77631207_77631207dupT	ENSP00000366030:p.Asn191fs		76821021	Q7Z383|Q8N7C5	Frame_Shift_Ins	INS	ENST00000376834.3	37	CCDS6649.1																																																																																				0.342	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		T	77631202	-	T	77631201	7	5	111	1	0	1	1	0	0	0	0	0	2488	98	4	0	680	0	C9orf41	9	77631201	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	40188929	77631201	63582230	504	29638										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79931126	79931128	+	In_Frame_Del	DEL	TTA	TTA	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtgaagtgggaaattaatgTtattattaaaaatcctgaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	TTA	TTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:79931126_79931128delTTA	ENST00000360280.3	+	39	4927_4929	c.4667_4669delTTA	c.(4666-4671)gttatt>gtt	p.I1558del	VPS13A_ENST00000376636.3_In_Frame_Del_p.I1519del|VPS13A_ENST00000376634.4_In_Frame_Del_p.I1558del|VPS13A_ENST00000357409.5_In_Frame_Del_p.I1558del|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1558					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAAATTAATGTTATTATTAAAAA	0.251																																																0			9																																								79120948	SO:0001651	inframe_deletion	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.4667_4669delTTA	9.37:g.79931132_79931134delTTA	ENSP00000353422:p.Ile1558del		79120946	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	In_Frame_Del	DEL	ENST00000360280.3	37	CCDS6655.1																																																																																				0.251	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		-	79931128	TTA	-	79931126	7	5	111	1	0	1	0	1	0	0	0	0	17229	1725	60	0	4821	0	VPS13A	9	79931126	In_Frame_Del	DEL	TTA	TCGA-EI-6507-01A-11D-1733-10	2299925	79931126	61282305	505	29639										
SPTLC1	10558	hgsc.bcm.edu	37	chr9	94794788	94794788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacctccttgatggtggacgCagctctctccagttcttcct	8	14	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:94794788C>T	ENST00000262554.2	-	15	1386	c.1381G>A	c.(1381-1383)Gcg>Acg	p.A461T		NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	461					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	ATGGTGGACGCAGCTCTCTCC	0.562																																																0			9											178	143	155					9																	94794788		2203	4300	6503	93834609	SO:0001583	missense	10558			Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.1381G>A	9.37:g.94794788C>T	ENSP00000262554:p.Ala461Thr		93834609	A8K681|Q5VWB4|Q96IX6	Missense_Mutation	SNP	ENST00000262554.2	37	CCDS6692.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799030	0.50208	.	.	ENSG00000090054	ENST00000262554	D	0.91577	-2.87	5.18	4.29	0.51040	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.152438	0.64402	N	0.000018	D	0.86585	0.5968	L	0.47716	1.5	0.80722	D	1	B	0.17465	0.022	B	0.24848	0.056	T	0.81147	-0.1065	10	0.19590	T	0.45	.	12.6055	0.56521	0.0:0.9192:0.0:0.0808	.	461	O15269	SPTC1_HUMAN	T	461	ENSP00000262554:A461T	ENSP00000262554:A461T	A	-	1	0	SPTLC1	93834609	1.000000	0.71417	0.621000	0.29145	0.993000	0.82548	5.734000	0.68580	1.425000	0.47237	0.655000	0.94253	GCG		0.562	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415		T	94794788	C	T	94794788	3	4	111	1	0	0	0	0	1	0	0	0	15162	710	25	3	44	3	SPTLC1	9	94794788	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	14863662	94794788	46418643	506	29640										
PHF2	5253	hgsc.bcm.edu	37	chr9	96436063	96436063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaaacgactgctgaagaggGctgccaagaacagtgtcgac	13	10	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:96436063G>A	ENST00000359246.4	+	18	2912	c.2545G>A	c.(2545-2547)Gct>Act	p.A849T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	849				A -> T (in Ref. 1; AAD21791). {ECO:0000305}.	liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GCTGAAGAGGGCTGCCAAGAA	0.617																																																0			9											103	86	92					9																	96436063		2203	4300	6503	95475884	SO:0001583	missense	5253			AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2545G>A	9.37:g.96436063G>A	ENSP00000352185:p.Ala849Thr		95475884	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	G	8.344	0.829449	0.16749	.	.	ENSG00000197724	ENST00000359246	T	0.56941	0.43	5.03	-3.26	0.05064	.	0.644956	0.15419	N	0.263345	T	0.22936	0.0554	N	0.08118	0	0.80722	D	1	B;B	0.16603	0.018;0.002	B;B	0.12156	0.007;0.001	T	0.06643	-1.0815	10	0.17369	T	0.5	-5.2194	6.017	0.19608	0.4788:0.2617:0.2595:0.0	.	268;849	Q8N359;O75151	.;PHF2_HUMAN	T	849	ENSP00000352185:A849T	ENSP00000352185:A849T	A	+	1	0	PHF2	95475884	0.994000	0.37717	0.867000	0.34043	0.895000	0.52256	0.543000	0.23237	-0.526000	0.06383	0.561000	0.74099	GCT		0.617	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		A	96436063	G	A	96436063	3	1	111	1	0	0	0	0	1	0	0	0	11861	1203	42	3	2615	3	PHF2	9	96436063	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1641275	96436063	44777368	507	29641										
PHF2	5253	hgsc.bcm.edu	37	chr9	96436080	96436080	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggctgccaagaacagtgtCgacctggacgactacgagga	14	10	0	1	rs201272131	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:96436080C>T	ENST00000359246.4	+	18	2929	c.2562C>T	c.(2560-2562)gtC>gtT	p.V854V	PHF2_ENST00000375376.4_Silent_p.V85V	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	854					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		AGAACAGTGTCGACCTGGACG	0.617													C|||	2	0.000399361	0	0	5008	,	,		19683	0.002		0	False		,,,				2504	0															0			9											101	86	92					9																	96436080		2203	4300	6503	95475901	SO:0001819	synonymous_variant	5253			AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2562C>T	9.37:g.96436080C>T			95475901	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																				0.617	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		T	96436080	C	T	96436080	2	4	111	1	0	0	0	0	0	0	0	1	11861	871	31	1		1	PHF2	9	96436080	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	17	96436080	44777351	508	29642										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98231216	98231216	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgtcctgtgtcacggtgacGggctgcacagagatctcgga	15	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:98231216G>T	ENST00000331920.6	-	14	2366	c.2067C>A	c.(2065-2067)ccC>ccA	p.P689P	PTCH1_ENST00000418258.1_Silent_p.P538P|PTCH1_ENST00000429896.2_Silent_p.P538P|PTCH1_ENST00000421141.1_Silent_p.P538P|PTCH1_ENST00000437951.1_Silent_p.P623P|PTCH1_ENST00000375274.2_Silent_p.P688P|PTCH1_ENST00000430669.2_Silent_p.P623P	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	689					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TCACGGTGACGGGCTGCACAG	0.637																																																0			9											123	116	118					9																	98231216		2203	4300	6503	97271037	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2067C>A	9.37:g.98231216G>T			97271037	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.637	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98231216	G	T	98231216	2	4	111	1	0	0	0	0	0	0	0	1	12764	1103	39	2		2	PTCH1	9	98231216	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1795136	98231216	42982215	509	29643										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100420956	100420956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcgtatattagatattgttCctcctaccttctcagctctg	6	11	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:100420956C>T	ENST00000375147.3	+	15	1664	c.1408C>T	c.(1408-1410)Cct>Tct	p.P470S		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	470					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				AGATATTGTTCCTCCTACCTT	0.393																																					Ovarian(36;879 898 2893 44212 50307)											0			9											236	203	214					9																	100420956		2203	4300	6503	99460777	SO:0001583	missense	4686			BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1408C>T	9.37:g.100420956C>T	ENSP00000364289:p.Pro470Ser		99460777	B2R718|Q59G76|Q5T1V0|Q5T7X2	Missense_Mutation	SNP	ENST00000375147.3	37	CCDS6728.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.899740	0.91962	.	.	ENSG00000136937	ENST00000375147	.	.	.	5.56	5.56	0.83823	MIF4G-like, type 1 (1);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	D	0.86772	0.6013	M	0.92604	3.325	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.89087	0.3480	9	0.72032	D	0.01	-17.6701	19.5096	0.95135	0.0:1.0:0.0:0.0	.	470	Q09161	NCBP1_HUMAN	S	470	.	ENSP00000364289:P470S	P	+	1	0	NCBP1	99460777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.546000	0.73887	2.781000	0.95711	0.555000	0.69702	CCT		0.393	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		T	100420956	C	T	100420956	3	4	111	1	0	0	0	0	1	0	0	0	10242	855	30	3	1466	3	NCBP1	9	100420956	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2189740	100420956	40792475	510	29644										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101216433	101216433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatgccatcgtaggcgtaccCgtggaacttgctgggcccca	13	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:101216433C>T	ENST00000259455.2	-	7	1525	c.1066G>A	c.(1066-1068)Ggg>Agg	p.G356R		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	356					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TAGGCGTACCCGTGGAACTTG	0.577																																																0			9											155	132	140					9																	101216433		2203	4300	6503	100256254	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1066G>A	9.37:g.101216433C>T	ENSP00000259455:p.Gly356Arg		100256254	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	C	32	5.170014	0.94768	.	.	ENSG00000136928	ENST00000259455	D	0.83591	-1.74	5.79	5.79	0.91817	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89480	0.6727	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89861	0.4016	10	0.87932	D	0	.	17.5351	0.87827	0.0:1.0:0.0:0.0	.	356	O75899	GABR2_HUMAN	R	356	ENSP00000259455:G356R	ENSP00000259455:G356R	G	-	1	0	GABBR2	100256254	1.000000	0.71417	0.985000	0.45067	0.975000	0.68041	7.818000	0.86416	2.751000	0.94390	0.650000	0.86243	GGG		0.577	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			T	101216433	C	T	101216433	3	4	111	1	0	0	0	0	1	0	0	0	6175	652	23	1	1811	1	GABBR2	9	101216433	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	795477	101216433	39996998	511	29645										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101470737	101470737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggtcgaggaagtaggggcGcaggagtgactcgttgcgga	19	7	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:101470737G>A	ENST00000259455.2	-	1	742	c.283C>T	c.(283-285)Cgc>Tgc	p.R95C		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	95					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	AAGTAGGGGCGCAGGAGTGAC	0.677																																																0			9											46	43	44					9																	101470737		2203	4299	6502	100510558	SO:0001583	missense	9568			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.283C>T	9.37:g.101470737G>A	ENSP00000259455:p.Arg95Cys		100510558	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.677975	0.29783	.	.	ENSG00000136928	ENST00000259455	D	0.83837	-1.77	3.14	2.09	0.27110	Extracellular ligand-binding receptor (1);	0.174274	0.25253	U	0.032002	T	0.65004	0.2650	L	0.34521	1.04	0.44816	D	0.997821	P	0.42248	0.774	B	0.25291	0.059	T	0.66172	-0.5990	10	0.46703	T	0.11	.	7.1027	0.25346	0.1619:0.0:0.838:0.0	.	95	O75899	GABR2_HUMAN	C	95	ENSP00000259455:R95C	ENSP00000259455:R95C	R	-	1	0	GABBR2	100510558	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.748000	0.38308	1.605000	0.50152	0.456000	0.33151	CGC		0.677	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101470737	G	A	101470737	3	1	111	1	0	0	0	0	1	0	0	0	6175	1087	38	1	2618	1	GABBR2	9	101470737	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	254304	101470737	39742694	512	29646										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109688688	109688688	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgggactgagcacaatagtgAaaacacagactttggtgact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:109688688delA	ENST00000277225.5	+	3	2784	c.2495delA	c.(2494-2496)gaafs	p.E832fs	ZNF462_ENST00000457913.1_Frame_Shift_Del_p.E832fs|ZNF462_ENST00000441147.2_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	832					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CACAATAGTGAAAACACAGAC	0.423																																																0			9											105	103	104					9																	109688688		2203	4300	6503	108728509	SO:0001589	frameshift_variant	58499			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.2495delA	9.37:g.109688688delA	ENSP00000277225:p.Glu832fs		108728509	Q5T0T4|Q8N408	Frame_Shift_Del	DEL	ENST00000277225.5	37	CCDS35096.1																																																																																				0.423	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		-	109688688	A	-	109688688	7	5	111	1	0	1	0	1	0	0	0	0	17965	246	9	0	2501	0	ZNF462	9	109688688	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	8217951	109688688	31524743	513	29647										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	111979393	111979393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccaaaaggcaaccggtccGagctgctaagcactggggaa	13	11	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:111979393G>A	ENST00000374566.3	-	16	1959	c.1442C>T	c.(1441-1443)tCg>tTg	p.S481L		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	481					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)	p.S481L(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CAACCGGTCCGAGCTGCTAAG	0.557																																																1	Substitution - Missense(1)	ovary(1)	9											68	68	68					9																	111979393		2120	4246	6366	111019214	SO:0001583	missense	54566			AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1442C>T	9.37:g.111979393G>A	ENSP00000363694:p.Ser481Leu		111019214	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	37	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702960	0.30232	.	.	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.83837	-1.77	5.91	5.91	0.95273	.	0.481175	0.15664	N	0.250746	T	0.74520	0.3727	N	0.24115	0.695	0.80722	D	1	B	0.24426	0.103	B	0.14023	0.01	T	0.68754	-0.5325	10	0.44086	T	0.13	.	15.7986	0.78433	0.0:0.0:1.0:0.0	.	481	Q9H329	E41LB_HUMAN	L	166;481	ENSP00000363694:S481L	ENSP00000262536:S166L	S	-	2	0	EPB41L4B	111019214	0.953000	0.32496	0.822000	0.32727	0.078000	0.17371	2.382000	0.44345	2.793000	0.96121	0.655000	0.94253	TCG		0.557	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		A	111979393	G	A	111979393	3	1	111	1	0	0	0	0	1	0	0	0	5169	1059	37	1	1304	1	EPB41L4B	9	111979393	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2290705	111979393	29234038	514	29648										
ZNF483	158399	hgsc.bcm.edu	37	chr9	114289709	114289709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcccttgaacaagatgacaGccatctcaccagaacctcaa	6	14	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:114289709G>A	ENST00000309235.5	+	2	192	c.34G>A	c.(34-36)Gcc>Acc	p.A12T	ZNF483_ENST00000374374.3_Missense_Mutation_p.A12T|ZNF483_ENST00000355824.3_Missense_Mutation_p.A12T|ZNF483_ENST00000358151.4_Missense_Mutation_p.A12T	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	12					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						CAAGATGACAGCCATCTCACC	0.478																																																0			9											104	99	101					9																	114289709		2203	4300	6503	113329530	SO:0001583	missense	158399			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.34G>A	9.37:g.114289709G>A	ENSP00000311679:p.Ala12Thr		113329530	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.320868	0.60634	.	.	ENSG00000173258	ENST00000358151;ENST00000355824;ENST00000374374;ENST00000309235	T;T;T;T	0.05513	5.71;5.66;3.43;3.56	5.55	3.7	0.42460	.	0.326910	0.22360	N	0.061088	T	0.03220	0.0094	N	0.16656	0.425	0.09310	N	1	B;B;B;B	0.32031	0.064;0.029;0.352;0.011	B;B;B;B	0.27170	0.053;0.008;0.077;0.012	T	0.43540	-0.9385	10	0.09338	T	0.73	-2.7258	7.4743	0.27368	0.085:0.0:0.7508:0.1642	.	12;12;12;12	Q6P088;Q5VZN3;Q8NAE1;Q8TF39	.;.;.;ZN483_HUMAN	T	12	ENSP00000350871:A12T;ENSP00000438048:A12T;ENSP00000363494:A12T;ENSP00000311679:A12T	ENSP00000311679:A12T	A	+	1	0	ZNF483	113329530	0.001000	0.12720	0.053000	0.19242	0.996000	0.88848	0.572000	0.23684	0.805000	0.34159	0.609000	0.83330	GCC		0.478	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		A	114289709	G	A	114289709	3	1	111	1	0	0	0	0	1	0	0	0	17975	971	34	3	36	3	ZNF483	9	114289709	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2310316	114289709	26923722	515	29649										
ZNF483	158399	hgsc.bcm.edu	37	chr9	114305009	114305009	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatgccttacccggcatcaGagaattcacactggagaaaa	8	11	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:114305009G>T	ENST00000309235.5	+	6	1952	c.1794G>T	c.(1792-1794)caG>caT	p.Q598H	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	598					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						CCCGGCATCAGAGAATTCACA	0.398																																																0			9											57	61	59					9																	114305009		2203	4300	6503	113344830	SO:0001583	missense	158399			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1794G>T	9.37:g.114305009G>T	ENSP00000311679:p.Gln598His		113344830	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684424	0.47991	.	.	ENSG00000173258	ENST00000309235	T	0.18502	2.21	3.84	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.161504	0.29822	N	0.011101	T	0.25827	0.0629	L	0.53561	1.675	0.80722	D	1	D	0.59767	0.986	P	0.56088	0.791	T	0.00431	-1.1743	10	0.34782	T	0.22	-12.5621	9.0271	0.36236	0.0:0.0:0.7803:0.2197	.	598	Q8TF39	ZN483_HUMAN	H	598	ENSP00000311679:Q598H	ENSP00000311679:Q598H	Q	+	3	2	ZNF483	113344830	0.001000	0.12720	1.000000	0.80357	0.996000	0.88848	0.935000	0.28924	2.436000	0.82500	0.655000	0.94253	CAG		0.398	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		T	114305009	G	T	114305009	3	4	111	1	0	0	0	0	1	0	0	0	17975	933	33	2	1812	2	ZNF483	9	114305009	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	15300	114305009	26908422	516	29650										
SUSD1	64420	hgsc.bcm.edu	37	chr9	114820789	114820789	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcattataatattccccataGtacagcctgtctcctatagg	6	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:114820789G>A	ENST00000374270.3	-	14	2200	c.2028C>T	c.(2026-2028)taC>taT	p.Y676Y	SUSD1_ENST00000374263.3_Silent_p.Y676Y|SUSD1_ENST00000374264.2_Silent_p.Y676Y	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	676						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ATTCCCCATAGTACAGCCTGT	0.423																																																0			9											125	111	116					9																	114820789		2203	4300	6503	113860610	SO:0001819	synonymous_variant	64420			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.2028C>T	9.37:g.114820789G>A			113860610	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	37	CCDS6783.1																																																																																				0.423	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		A	114820789	G	A	114820789	2	1	111	1	0	0	0	0	0	0	0	1	15446	1024	36	3		3	SUSD1	9	114820789	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	515780	114820789	26392642	517	29651										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117020870	117020870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catgaggggagcaaagggacGtcgggtaagtcgagcccagc	17	9	0	1	rs368823650		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:117020870G>A	ENST00000356083.3	+	28	3582	c.3191G>A	c.(3190-3192)cGt>cAt	p.R1064H		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1064	Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GCAAAGGGACGTCGGGTAAGT	0.617																																																0			9						G	HIS/ARG	0,4406		0,0,2203	44	42	43		3191	-1.8	0.7	9		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL27A1	NM_032888.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	1064/1861	117020870	1,13005	2203	4300	6503	116060691	SO:0001583	missense	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3191G>A	9.37:g.117020870G>A	ENSP00000348385:p.Arg1064His		116060691	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.172905	0.57584	0.0	1.16E-4	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.94497	-3.44	5.24	-1.75	0.08031	.	.	.	.	.	D	0.88381	0.6421	L	0.38175	1.15	0.23813	N	0.996771	B	0.09022	0.002	B	0.06405	0.002	T	0.74794	-0.3544	9	0.38643	T	0.18	.	5.4014	0.16299	0.17:0.0:0.2605:0.5695	.	1064	Q8IZC6	CORA1_HUMAN	H	1064	ENSP00000348385:R1064H	ENSP00000348385:R1064H	R	+	2	0	COL27A1	116060691	0.025000	0.19082	0.729000	0.30791	0.782000	0.44232	-0.225000	0.09151	-0.737000	0.04824	0.462000	0.41574	CGT		0.617	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117020870	G	A	117020870	3	1	111	1	0	0	0	0	1	0	0	0	3691	1145	40	1	3301	1	COL27A1	9	117020870	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2200081	117020870	24192561	518	29652										
AKNA	80709	hgsc.bcm.edu	37	chr9	117099535	117099535	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtgggggagaggctgtgggCggccacttggcagctggttg	22	7	0	1	rs375027878		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:117099535C>T	ENST00000307564.4	-	22	4280	c.4119G>A	c.(4117-4119)ccG>ccA	p.P1373P	AKNA_ENST00000374079.4_Silent_p.P318P|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000223791.3_Silent_p.P833P|AKNA_ENST00000374088.3_Silent_p.P1373P|AKNA_ENST00000374075.5_Silent_p.P1292P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1373					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						AGGCTGTGGGCGGCCACTTGG	0.662																																																0			9						C		0,4406		0,0,2203	43	47	45		4119	-2.2	0	9		45	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	AKNA	NM_030767.4		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		1373/1440	117099535	1,13003	2203	4299	6502	116139356	SO:0001819	synonymous_variant	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.4119G>A	9.37:g.117099535C>T			116139356	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	3.630	-0.075806	0.07184	0.0	1.16E-4	ENSG00000106948	ENST00000320310	.	.	.	3.92	-2.15	0.07102	.	.	.	.	.	T	0.38799	0.1054	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.46721	-0.9171	5	0.87932	D	0	3.4487	6.9188	0.24376	0.0:0.4332:0.2424:0.3244	.	.	.	.	H	384	.	ENSP00000314538:R384H	R	-	2	0	AKNA	116139356	0.000000	0.05858	0.003000	0.11579	0.013000	0.08279	-0.252000	0.08806	-0.101000	0.12219	-1.328000	0.01277	CGC		0.662	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		T	117099535	C	T	117099535	2	4	111	1	0	0	0	0	0	0	0	1	463	755	27	1		1	AKNA	9	117099535	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	78665	117099535	24113896	519	29653										
DBC1	1620	hgsc.bcm.edu	37	chr9	121930148	121930148	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgatgaaggtggtgtggacGtagaggcgtgagtccatctt	16	6	1	4	rs142482414		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:121930148G>A	ENST00000265922.3	-	8	1961	c.1500C>T	c.(1498-1500)taC>taT	p.Y500Y	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	500					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											TGGTGTGGACGTAGAGGCGTG	0.567																																																0			9						G		2,4404	2.1+/-5.4	0,2,2201	280	196	224		1500	-2.6	1	9	dbSNP_134	224	0,8600		0,0,4300	no	coding-synonymous	DBC1	NM_014618.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		500/762	121930148	2,13004	2203	4300	6503	120969969	SO:0001819	synonymous_variant	57805			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1500C>T	9.37:g.121930148G>A			120969969	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																				0.567	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	121930148	G	A	121930148	2	1	111	1	0	0	0	0	0	0	0	1	4253	1140	40	1		1	DBC1	9	121930148	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4830613	121930148	19283283	520	29654										
OR1Q1	158131	hgsc.bcm.edu	37	chr9	125377563	125377563	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acttcttctgtgacctctacGctctgatgaagatctcctgc	7	13	5	4	rs116701890	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:125377563G>A	ENST00000297913.2	+	1	616	c.547G>A	c.(547-549)Gct>Act	p.A183T	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	183					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A183F(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						TGACCTCTACGCTCTGATGAA	0.488													G|||	39	0.00778754	0.0295	0	5008	,	,		22872	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	9						G	THR/ALA	101,4305	80.4+/-118.8	1,99,2103	168	157	161		547	3.7	0.9	9	dbSNP_132	161	0,8600		0,0,4300	yes	missense	OR1Q1	NM_012364.1	58	1,99,6403	AA,AG,GG		0.0,2.2923,0.7766	benign	183/315	125377563	101,12905	2203	4300	6503	124417384	SO:0001583	missense	158131				CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"GPCR / Class A : Olfactory receptors"	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.547G>A	9.37:g.125377563G>A	ENSP00000297913:p.Ala183Thr		124417384	Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	37	CCDS35125.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	14.00	2.405621	0.42715	0.022923	0.0	ENSG00000165202	ENST00000297913	T	0.00130	8.69	5.57	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.136171	0.34178	N	0.004194	T	0.00039	0.0001	L	0.45352	1.415	0.09310	N	1	P	0.39847	0.691	B	0.34346	0.18	T	0.48456	-0.9034	10	0.22706	T	0.39	-16.5007	15.1948	0.73078	0.0:0.5806:0.4194:0.0	.	183	Q15612	OR1Q1_HUMAN	T	183	ENSP00000297913:A183T	ENSP00000297913:A183T	A	+	1	0	OR1Q1	124417384	0.000000	0.05858	0.903000	0.35520	0.916000	0.54674	0.115000	0.15540	0.878000	0.35920	-0.171000	0.13296	GCT		0.488	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1			A	125377563	G	A	125377563	3	1	111	1	0	0	0	0	1	0	0	0	11002	1087	38	1	549	1	OR1Q1	9	125377563	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3447415	125377563	15835868	521	29655										
ANGPTL2	23452	hgsc.bcm.edu	37	chr9	129870930	129870930	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagccctcctcagtgccctcAaaaccgtcctcctggcctgc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:129870930delA	ENST00000373425.3	-	2	698	c.81delT	c.(79-81)tttfs	p.F27fs	ANGPTL2_ENST00000373417.1_Intron|ANGPTL2_ENST00000491991.1_5'Flank|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000424082.2_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	27					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CAGTGCCCTCAAAACCGTCCT	0.582																																																0			9											63	54	57					9																	129870930		2203	4300	6503	128910751	SO:0001589	frameshift_variant	51129			AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"Fibrinogen C domain containing"	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.81delT	9.37:g.129870930delA	ENSP00000362524:p.Phe27fs		128910751	Q5JT58|Q8NCH7	Frame_Shift_Del	DEL	ENST00000373425.3	37	CCDS6868.1																																																																																				0.582	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		-	129870930	A	-	129870930	7	5	111	1	0	1	0	1	0	0	0	0	614	127	5	0	1416	0	ANGPTL2	9	129870930	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	4493367	129870930	11342501	522	29656										
SLC2A8	29988	hgsc.bcm.edu	37	chr9	130165010	130165011	+	Frame_Shift_Ins	INS	-	-	C													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgagcagggctgggaagaINScccccccatcggggctgagc					rs199808560		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:130165010_130165011insC	ENST00000373371.3	+	5	790_791	c.701_702insC	c.(700-705)gaccccfs	p.DP234fs	SLC2A8_ENST00000373360.3_Frame_Shift_Ins_p.DP234fs|SLC2A8_ENST00000373352.1_Intron	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	234					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						GGCTGGGAAGACCCCCCCATCG	0.673																																																0			9								5,4101		0,5,2048						4	1			12	9,7993		2,5,3994	no	frameshift	SLC2A8	NM_014580.3		2,10,6042	A1A1,A1R,RR		0.1125,0.1218,0.1156				14,12094				129204832	SO:0001589	frameshift_variant	29988			AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"Solute carriers"	13812	protein-coding gene	gene with protein product		605245	"solute carrier family 2 (facilitated glucose transporter) member 8"			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.708dupC	9.37:g.130165017_130165017dupC	ENSP00000362469:p.Asp234fs		129204831	Q8WUZ9|Q9NSC4	Frame_Shift_Ins	INS	ENST00000373371.3	37	CCDS6870.1																																																																																				0.673	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		C	130165011	-	C	130165010	7	5	111	1	0	1	1	0	0	0	0	0	14588	275	10	0	719	0	SLC2A8	9	130165010	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	294080	130165010	11048421	523	29657										
TBC1D13	54662	hgsc.bcm.edu	37	chr9	131554840	131554840	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acgaggtgctgctgcagatcGacaaagatgtccggtaggca	14	9	0	2	rs148490755		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:131554840G>A	ENST00000372648.5	+	6	520	c.370G>A	c.(370-372)Gac>Aac	p.D124N	TBC1D13_ENST00000223865.8_Missense_Mutation_p.D124N|TBC1D13_ENST00000466056.1_3'UTR|TBC1D13_ENST00000539497.1_Intron	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	124	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						GCTGCAGATCGACAAAGATGT	0.597																																																0			9						G	ASN/ASP	0,4406		0,0,2203	85	63	71		370	4.9	1	9	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense	TBC1D13	NM_018201.3	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	124/401	131554840	1,13005	2203	4300	6503	130594661	SO:0001583	missense	54662			AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.370G>A	9.37:g.131554840G>A	ENSP00000361731:p.Asp124Asn		130594661	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Missense_Mutation	SNP	ENST00000372648.5	37	CCDS6911.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389028	0.95988	0.0	1.16E-4	ENSG00000107021	ENST00000372648;ENST00000223865	T;T	0.04809	3.55;3.55	4.95	4.95	0.65309	Rab-GAP/TBC domain (3);	0.105878	0.64402	D	0.000006	T	0.13415	0.0325	L	0.42487	1.325	0.80722	D	1	D;D	0.65815	0.995;0.975	D;P	0.66716	0.946;0.691	T	0.25117	-1.0141	10	0.17832	T	0.49	-18.2339	16.7747	0.85548	0.0:0.0:1.0:0.0	.	124;124	Q9NVG8-2;Q9NVG8	.;TBC13_HUMAN	N	124	ENSP00000361731:D124N;ENSP00000223865:D124N	ENSP00000223865:D124N	D	+	1	0	TBC1D13	130594661	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	9.869000	0.99810	2.309000	0.77851	0.561000	0.74099	GAC		0.597	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201		A	131554840	G	A	131554840	3	1	111	1	0	0	0	0	1	0	0	0	15641	1058	37	1	392	1	TBC1D13	9	131554840	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1389830	131554840	9658591	524	29658										
FAM73B	84895	hgsc.bcm.edu	37	chr9	131832593	131832593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgctacacgtcactgcccgCgctggcagacgacatcctgc	11	17	1	1	rs202169772		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:131832593C>T	ENST00000358369.4	+	16	1869	c.1643C>T	c.(1642-1644)gCg>gTg	p.A548V	FAM73B_ENST00000406926.2_3'UTR|FAM73B_ENST00000277475.5_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	548					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						TCACTGCCCGCGCTGGCAGAC	0.672													C|||	1	0.000199681	0	0.0014	5008	,	,		19096	0		0	False		,,,				2504	0															0			9						C	VAL/ALA	0,4404		0,0,2202	61	48	53		1643	5.7	0.2	9		53	1,8597		0,1,4298	no	missense	FAM73B	NM_032809.2	64	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	548/594	131832593	1,13001	2202	4299	6501	130872414	SO:0001583	missense	84895			AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 54"	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.1643C>T	9.37:g.131832593C>T	ENSP00000351138:p.Ala548Val		130872414	Q8NBM3|Q8TEJ6|Q969E6	Missense_Mutation	SNP	ENST00000358369.4	37	CCDS6917.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	13.86	2.362229	0.41902	0.0	1.16E-4	ENSG00000148343	ENST00000358369	T	0.23552	1.9	5.67	5.67	0.87782	.	0.276732	0.35772	N	0.002986	T	0.24699	0.0599	L	0.40543	1.245	0.50632	D	0.999888	P;B	0.49358	0.923;0.35	P;B	0.44518	0.452;0.164	T	0.00839	-1.1545	10	0.37606	T	0.19	.	12.0548	0.53529	0.0:0.9131:0.0:0.0869	.	124;548	Q96NP4;Q7L4E1	.;FA73B_HUMAN	V	548	ENSP00000351138:A548V	ENSP00000351138:A548V	A	+	2	0	FAM73B	130872414	0.905000	0.30787	0.210000	0.23637	0.518000	0.34316	2.271000	0.43364	2.668000	0.90789	0.655000	0.94253	GCG		0.672	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809		T	131832593	C	T	131832593	3	4	111	1	0	0	0	0	1	0	0	0	5637	768	27	1	1701	1	FAM73B	9	131832593	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	277753	131832593	9380838	525	29659										
DDX31	64794	hgsc.bcm.edu	37	chr9	135501082	135501082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcgtttccctttaaaacaaTcatctcttgtcagaacacac	3	12	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:135501082T>C	ENST00000372159.3	-	17	2148	c.1997A>G	c.(1996-1998)gAt>gGt	p.D666G	DDX31_ENST00000438527.3_Missense_Mutation_p.D537G|DDX31_ENST00000372153.1_Intron	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	666						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		TTTAAAACAATCATCTCTTGT	0.408																																																0			9											125	121	122					9																	135501082		2203	4300	6503	134490903	SO:0001583	missense	158067			AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"DEAD-boxes", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16715	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 25"		"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1997A>G	9.37:g.135501082T>C	ENSP00000361232:p.Asp666Gly		134490903	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.408493	0.62399	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000438527	T;T	0.02579	4.27;4.24	5.87	3.55	0.40652	.	0.292405	0.41294	N	0.000904	T	0.10078	0.0247	M	0.72118	2.19	0.80722	D	1	D	0.63046	0.992	P	0.59825	0.864	T	0.00619	-1.1641	10	0.72032	D	0.01	-6.2493	9.4868	0.38935	0.0:0.1415:0.0:0.8585	.	666	Q9H8H2	DDX31_HUMAN	G	666;666;537	ENSP00000361232:D666G;ENSP00000387730:D537G	ENSP00000361228:D666G	D	-	2	0	DDX31	134490903	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	3.737000	0.55060	0.497000	0.27926	0.529000	0.55759	GAT		0.408	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		C	135501082	T	C	135501082	3	2	111	1	0	0	0	0	1	0	0	0	4362	1435	50	4	574	4	DDX31	9	135501082	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3668489	135501082	5712349	526	29660										
FCN2	2220	hgsc.bcm.edu	37	chr9	137777132	137777132	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accgagggcacttcctgagcGgctggcacaccatctacctg	11	15	1	1	rs12684476	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:137777132G>A	ENST00000291744.6	+	5	359	c.349G>A	c.(349-351)Ggc>Agc	p.G117S	FCN2_ENST00000350339.2_Missense_Mutation_p.G79S	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	117	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		G -> S (in dbSNP:rs12684476).		complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CTTCCTGAGCGGCTGGCACAC	0.682													G|||	15	0.00299521	0	0	5008	,	,		16231	0.0149		0	False		,,,				2504	0															0			9						G	SER/GLY,SER/GLY	1,4405	2.1+/-5.4	0,1,2202	62	60	61		349,235	3.6	0.9	9	dbSNP_120	61	0,8600		0,0,4300	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	117/314,79/276	137777132	1,13005	2203	4300	6503	136916953	SO:0001583	missense	2220			D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"Fibrinogen C domain containing"	3624	protein-coding gene	gene with protein product	"hucolin", "collagen/fibrinogen domain-containing protein 2", "ficolin B", "serum lectin p35", "L-ficolin"	601624	"ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.349G>A	9.37:g.137777132G>A	ENSP00000291744:p.Gly117Ser		136916953	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	13	0.005952380952380952	0	0.0	0	0.0	13	0.022727272727272728	0	0.0	G	18.58	3.654017	0.67472	2.27E-4	0.0	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.36157	1.27;1.27	3.59	3.59	0.41128	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.41097	U	0.000942	T	0.54759	0.1878	H	0.96142	3.775	0.52099	D	0.999946	D;D	0.89917	1.0;1.0	D;D	0.83275	0.952;0.996	T	0.75414	-0.3326	10	0.62326	D	0.03	.	12.6783	0.56908	0.0:0.0:1.0:0.0	rs12684476;rs52823359;rs12684476	79;117	Q15485-2;Q15485	.;FCN2_HUMAN	S	79;117	ENSP00000291741:G79S;ENSP00000291744:G117S	ENSP00000291744:G117S	G	+	1	0	FCN2	136916953	0.985000	0.35326	0.945000	0.38365	0.388000	0.30384	2.790000	0.47821	1.524000	0.49035	0.462000	0.41574	GGC		0.682	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108		A	137777132	G	A	137777132	3	1	111	1	0	0	0	0	1	0	0	0	5811	1116	39	1	367	1	FCN2	9	137777132	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2276050	137777132	3436299	527	29661										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139395241	139395241	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgtcctcctcttcctcgctGttgcccgtctccaggccgcc	9	20	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:139395241G>A	ENST00000277541.6	-	31	5772	c.5697C>T	c.(5695-5697)aaC>aaT	p.N1899N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1899					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CTTCCTCGCTGTTGCCCGTCT	0.682			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	0			9											26	33	31					9																	139395241		2067	4207	6274	138515062	SO:0001819	synonymous_variant	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5697C>T	9.37:g.139395241G>A			138515062	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																				0.682	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139395241	G	A	139395241	2	1	111	1	0	0	0	0	0	0	0	1	10578	1368	48	3		3	NOTCH1	9	139395241	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1618109	139395241	1818190	528	29662										
C9orf86	55684	hgsc.bcm.edu	37	chr9	139733732	139733732	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcccacgaggaccgcagcaCccccctggccaggcggtgtc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:139733732delC	ENST00000311502.7	+	12	1788	c.1552delC	c.(1552-1554)cccfs	p.P519fs	RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371663.4_Frame_Shift_Del_p.P520fs|RABL6_ENST00000371675.3_Frame_Shift_Del_p.P404fs|RABL6_ENST00000432842.2_Intron			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	519					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GACCGCAGCACCCCCCTGGCC	0.667																																																0			9											22	30	27					9																	139733732		2077	4205	6282	138853553	SO:0001589	frameshift_variant	55684			AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1552delC	9.37:g.139733732delC	ENSP00000311134:p.Pro519fs		138853553	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Frame_Shift_Del	DEL	ENST00000311502.7	37	CCDS48058.1																																																																																				0.667	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		-	139733732	C	-	139733732	7	5	111	1	0	1	0	1	0	0	0	0	2508	507	18	0	1845	0	C9orf86	9	139733732	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	338491	139733732	1479699	529	29663										
ABCA2	20	hgsc.bcm.edu	37	chr9	139917204	139917204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcccgggcccgcactgaggGcctccagatgctggcgtagg	16	14	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:139917204G>A	ENST00000371605.3	-	4	533	c.386C>T	c.(385-387)gCc>gTc	p.A129V	ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000341511.6_Missense_Mutation_p.A130V|ABCA2_ENST00000265662.5_Missense_Mutation_p.A130V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	129					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGCACTGAGGGCCTCCAGATG	0.692																																																0			9											13	18	17					9																	139917204		1940	4127	6067	139037025	SO:0001583	missense	20			U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.386C>T	9.37:g.139917204G>A	ENSP00000360666:p.Ala129Val		139037025	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	37		.	.	.	.	.	.	.	.	.	.	g	16.30	3.084396	0.55861	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.86956	-2.19;-2.19;-2.19	4.25	4.25	0.50352	.	1.583810	0.04437	U	0.370162	T	0.74581	0.3735	N	0.04508	-0.205	0.25158	N	0.990373	B;P;B	0.35433	0.361;0.501;0.0	B;B;B	0.30646	0.075;0.118;0.001	T	0.65376	-0.6183	10	0.28530	T	0.3	.	11.3361	0.49505	0.094:0.0:0.906:0.0	.	129;159;160	Q9BZC7;E7EU84;E7ETC3	ABCA2_HUMAN;.;.	V	130;129;160;130	ENSP00000265662:A130V;ENSP00000360666:A129V;ENSP00000344155:A130V	ENSP00000265662:A130V	A	-	2	0	ABCA2	139037025	1.000000	0.71417	0.998000	0.56505	0.909000	0.53808	4.384000	0.59607	1.921000	0.55644	0.486000	0.48141	GCC		0.692	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		A	139917204	G	A	139917204	3	1	111	1	0	0	0	0	1	0	0	0	32	1203	42	3	7101	3	ABCA2	9	139917204	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	183472	139917204	1296227	530	29664										
SLC34A3	142680	hgsc.bcm.edu	37	chr9	140127250	140127250	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgtaggcaaagtggccggaGacatcttcaaggacaacgtg	14	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:140127250G>T	ENST00000538474.1	+	5	543	c.319G>T	c.(319-321)Gac>Tac	p.D107Y	SLC34A3_ENST00000361134.2_Missense_Mutation_p.D107Y	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	107					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGTGGCCGGAGACATCTTCAA	0.647																																																0			9											100	76	84					9																	140127250		2203	4300	6503	139247071	SO:0001583	missense	142680			AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"Solute carriers"	20305	protein-coding gene	gene with protein product		609826	"solute carrier family 34 (sodium phosphate), member 3"			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.319G>T	9.37:g.140127250G>T	ENSP00000442397:p.Asp107Tyr		139247071	A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	37	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	g	16.73	3.204951	0.58234	.	.	ENSG00000198569	ENST00000538474;ENST00000361134	D;D	0.86097	-2.07;-2.07	3.65	3.65	0.41850	.	0.000000	0.64402	D	0.000017	D	0.91119	0.7204	M	0.74546	2.27	0.45342	D	0.998338	D	0.89917	1.0	D	0.87578	0.998	D	0.92051	0.5648	10	0.72032	D	0.01	-34.3397	13.2753	0.60184	0.0:0.0:1.0:0.0	.	107	Q8N130	NPT2C_HUMAN	Y	107	ENSP00000442397:D107Y;ENSP00000355353:D107Y	ENSP00000355353:D107Y	D	+	1	0	SLC34A3	139247071	1.000000	0.71417	0.989000	0.46669	0.283000	0.27025	6.424000	0.73366	2.046000	0.60703	0.537000	0.68136	GAC		0.647	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877		T	140127250	G	T	140127250	3	4	111	1	0	0	0	0	1	0	0	0	14606	942	33	2	333	2	SLC34A3	9	140127250	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	210046	140127250	1086181	531	29665										
TUBB2C	10383	hgsc.bcm.edu	37	chr9	140137888	140137888	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcgagggcatggacgagatGgagttcaccgaggccgagag	19	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:140137888G>T	ENST00000340384.4	+	4	1366	c.1218G>T	c.(1216-1218)atG>atT	p.M406I		NM_006088.5	NP_006079.1	P68371	TBB4B_HUMAN	tubulin, beta 4B class IVb	406					'de novo' posttranslational protein folding (GO:0051084)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|unfolded protein binding (GO:0051082)									Albendazole(DB00518)|Mebendazole(DB00643)	TGGACGAGATGGAGTTCACCG	0.617																																																0			9											102	99	100					9																	140137888		2203	4296	6499	139257709	SO:0001583	missense	10383			BC019359	CCDS7039.1	9q34.3	2011-10-10	2011-10-10	2011-10-10	ENSG00000188229	ENSG00000188229		"Tubulins"	20771	protein-coding gene	gene with protein product	"class IVb beta-tubulin"	602660	"tubulin, beta 2C"	TUBB2C		3999141	Standard	NM_006088		Approved	Beta2	uc004cmh.1	P68371	OTTHUMG00000131783	ENST00000340384.4:c.1218G>T	9.37:g.140137888G>T	ENSP00000341289:p.Met406Ile		139257709	A2BFA2|P05217	Missense_Mutation	SNP	ENST00000340384.4	37	CCDS7039.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.569898	0.45798	.	.	ENSG00000188229	ENST00000340384	T	0.72615	-0.67	5.57	5.57	0.84162	.	0.049321	0.85682	D	0.000000	T	0.78654	0.4317	M	0.90082	3.085	0.80722	D	1	B	0.14012	0.009	B	0.20955	0.032	T	0.77945	-0.2397	10	0.87932	D	0	.	18.1378	0.89627	0.0:0.0:1.0:0.0	.	406	P68371	TBB4B_HUMAN	I	406	ENSP00000341289:M406I	ENSP00000341289:M406I	M	+	3	0	TUBB2C	139257709	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.678000	0.98647	2.625000	0.88918	0.655000	0.94253	ATG		0.617	TUBB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254715.1	NM_006088		T	140137888	G	T	140137888	3	4	111	1	0	0	0	0	1	0	0	0	16796	1348	47	2	1232	2	TUBB2C	9	140137888	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	10638	140137888	1075543	532	29666										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140611267	140611267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caacacactaactcggatagCggaaaatggggtttcagaaa	10	8	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr9:140611267C>T	ENST00000460843.1	+	3	302	c.275C>T	c.(274-276)gCg>gTg	p.A92V	EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000334856.6_Missense_Mutation_p.A61V|EHMT1_ENST00000462484.1_Missense_Mutation_p.A92V	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	92					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACTCGGATAGCGGAAAATGGG	0.532																																																0			9											118	119	119					9																	140611267		2203	4300	6503	139731088	SO:0001583	missense	79813			AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.275C>T	9.37:g.140611267C>T	ENSP00000417980:p.Ala92Val		139731088	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	c	15.48	2.845662	0.51164	.	.	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.72394	1.42;0.63;-0.65	5.87	4.98	0.66077	.	0.076845	0.53938	D	0.000049	D	0.82499	0.5050	M	0.65975	2.015	0.09310	N	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.991;0.998;0.992	T	0.76416	-0.2967	10	0.66056	D	0.02	.	15.287	0.73835	0.0:0.9327:0.0:0.0673	.	92;61;92	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	V	61;61;92;92	ENSP00000334476:A61V;ENSP00000417328:A92V;ENSP00000417980:A92V	ENSP00000334476:A61V	A	+	2	0	EHMT1	139731088	0.999000	0.42202	0.004000	0.12327	0.076000	0.17211	5.237000	0.65360	1.508000	0.48769	0.546000	0.68486	GCG		0.532	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140611267	C	T	140611267	3	4	111	1	0	0	0	0	1	0	0	0	4994	768	27	1	285	1	EHMT1	9	140611267	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	473379	140611267	602164	533	29667										
ADARB2	105	hgsc.bcm.edu	37	chr10	1230914	1230914	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatctccaggtccgcgctgcCcacgacccagttcatgctga	9	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:1230914C>A	ENST00000381312.1	-	9	2255	c.1930G>T	c.(1930-1932)Ggc>Tgc	p.G644C	ADARB2_ENST00000381305.1_Missense_Mutation_p.G46C|ADARB2_ENST00000381310.3_Missense_Mutation_p.G153C	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	644	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		TCCGCGCTGCCCACGACCCAG	0.677																																																0			10											40	38	38					10																	1230914		2203	4299	6502	1220914	SO:0001583	missense	105			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1930G>T	10.37:g.1230914C>A	ENSP00000370713:p.Gly644Cys		1220914	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499134	0.64298	.	.	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.94497	-3.44;-3.44;-3.44	4.81	4.81	0.61882	Adenosine deaminase/editase (3);	0.000000	0.85682	D	0.000000	D	0.97564	0.9202	M	0.87758	2.905	0.80722	D	1	D;P;D	0.89917	0.99;0.891;1.0	D;P;D	0.91635	0.936;0.821;0.999	D	0.98576	1.0648	10	0.87932	D	0	-33.5067	17.8992	0.88898	0.0:1.0:0.0:0.0	.	644;46;153	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	C	644;153;46	ENSP00000370713:G644C;ENSP00000370711:G153C;ENSP00000370706:G46C	ENSP00000370706:G46C	G	-	1	0	ADARB2	1220914	1.000000	0.71417	0.860000	0.33809	0.084000	0.17831	5.983000	0.70540	2.220000	0.72140	0.561000	0.74099	GGC		0.677	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1230914	C	A	1230914	3	1	111	1	0	0	0	0	1	0	0	0	283	623	22	2	297	2	ADARB2	10	1230914	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		1230914	134303833	534	29668										
IL2RA	3559	hgsc.bcm.edu	37	chr10	6063498	6063498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagctggggctgggtccaccTtgtcttcccgtgggtcattt	14	11	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:6063498T>C	ENST00000379959.3	-	4	699	c.526A>G	c.(526-528)Agg>Ggg	p.R176G	IL2RA_ENST00000379954.1_Intron|IL2RA_ENST00000256876.6_Missense_Mutation_p.R176G	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	176	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	TGGGTCCACCTTGTCTTCCCG	0.557																																																0			10											199	176	184					10																	6063498		2203	4300	6503	6103504	SO:0001583	missense	3559			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.526A>G	10.37:g.6063498T>C	ENSP00000369293:p.Arg176Gly		6103504	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	37	CCDS7076.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220819	0.22457	.	.	ENSG00000134460	ENST00000379959;ENST00000256876	T;T	0.64803	-0.12;-0.12	4.41	0.63	0.17693	Complement control module (2);Sushi/SCR/CCP (3);	0.683107	0.13866	N	0.357333	T	0.46678	0.1405	L	0.47716	1.5	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.25745	-1.0123	10	0.23891	T	0.37	-36.2391	3.5929	0.07995	0.0:0.2095:0.1961:0.5944	.	176	P01589	IL2RA_HUMAN	G	176	ENSP00000369293:R176G;ENSP00000256876:R176G	ENSP00000256876:R176G	R	-	1	2	IL2RA	6103504	0.000000	0.05858	0.003000	0.11579	0.064000	0.16182	-0.138000	0.10374	0.265000	0.21872	0.528000	0.53228	AGG		0.557	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		C	6063498	T	C	6063498	3	2	111	1	0	0	0	0	1	0	0	0	7707	1608	56	4	312	4	IL2RA	10	6063498	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	4832584	6063498	129471249	535	29669										
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6540492	6540492	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcaaagcaaagaagccttcCgtctcaaattcattcatgtc	6	11	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:6540492C>A	ENST00000263125.5	-	5	507	c.408G>T	c.(406-408)acG>acT	p.T136T	PRKCQ_ENST00000397176.2_Silent_p.T136T|PRKCQ_ENST00000539722.1_Silent_p.T11T	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	136					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	AGAAGCCTTCCGTCTCAAATT	0.517																																					Ovarian(50;572 1126 10530 25349 30594)											0			10											169	142	151					10																	6540492		2203	4300	6503	6580498	SO:0001819	synonymous_variant	5588			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.408G>T	10.37:g.6540492C>A			6580498	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1																																																																																				0.517	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		A	6540492	C	A	6540492	2	1	111	1	0	0	0	0	0	0	0	1	12549	639	23	2		2	PRKCQ	10	6540492	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	476994	6540492	128994255	536	29670										
GATA3	2625	hgsc.bcm.edu	37	chr10	8115750	8115750	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaggcatccagaccagaaacCgaaaaatgtctagcaaatcc	7	11	1	2	rs104894164		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:8115750C>A	ENST00000346208.3	+	6	1551	c.1096C>A	c.(1096-1098)Cga>Aga	p.R366R	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.R367R			P23771	GATA3_HUMAN	GATA binding protein 3	366			R -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:17224074}.		anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.R367*(1)		NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						GACCAGAAACCGAAAAATGTC	0.413			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																																Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	1	Substitution - Nonsense(1)	breast(1)	10	GRCh37	CM011940	GATA3	M	rs104894164						57	62	60					10																	8115750		2203	4300	6503	8155756	SO:0001819	synonymous_variant	2625			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.1096C>A	10.37:g.8115750C>A			8155756	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																				0.413	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8115750	C	A	8115750	2	1	111	1	0	0	0	0	0	0	0	1	6275	644	23	2		2	GATA3	10	8115750	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1575258	8115750	127418997	537	29671										
C10orf47	254427	hgsc.bcm.edu	37	chr10	11908747	11908747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccagcacctggcgccggggAagccgagggccttccagagg	17	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:11908747A>G	ENST00000277570.5	+	3	510	c.356A>G	c.(355-357)gAa>gGa	p.E119G	PROSER2_ENST00000379200.1_5'Flank|PROSER2-AS1_ENST00000445498.1_RNA|PROSER2-AS1_ENST00000453242.1_RNA|PROSER2_ENST00000474155.1_3'UTR	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	119																	GGCGCCGGGGAAGCCGAGGGC	0.632																																																0			10											31	31	31					10																	11908747		2203	4300	6503	11948753	SO:0001583	missense	254427			BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 47", "proline and serine-rich protein 2"	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.356A>G	10.37:g.11908747A>G	ENSP00000277570:p.Glu119Gly		11948753	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Missense_Mutation	SNP	ENST00000277570.5	37	CCDS7085.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.657979	0.67586	.	.	ENSG00000148426	ENST00000379208;ENST00000277570;ENST00000379202	T	0.07114	3.22	5.34	4.17	0.49024	.	0.474225	0.21001	N	0.081867	T	0.11922	0.0290	L	0.49126	1.545	0.35781	D	0.821642	P	0.46784	0.884	P	0.45377	0.478	T	0.11155	-1.0599	10	0.87932	D	0	-28.4284	10.5026	0.44815	0.8371:0.1629:0.0:0.0	.	119	Q86WR7	CJ047_HUMAN	G	119	ENSP00000277570:E119G	ENSP00000277570:E119G	E	+	2	0	C10orf47	11948753	0.530000	0.26330	0.215000	0.23724	0.008000	0.06430	2.321000	0.43805	0.930000	0.37217	0.460000	0.39030	GAA		0.632	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256		G	11908747	A	G	11908747	3	3	111	1	0	0	0	0	1	0	0	0	1609	246	9	4	362	4	C10orf47	10	11908747	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3792997	11908747	123626000	538	29672										
PHYH	5264	hgsc.bcm.edu	37	chr10	13325835	13325835	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtggaacattttgttaactCccccctagaacaagaggcaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:13325835delC	ENST00000263038.4	-	7	741	c.683delG	c.(682-684)ggafs	p.G228fs	PHYH_ENST00000396920.3_Frame_Shift_Del_p.G211fs|PHYH_ENST00000396913.2_Frame_Shift_Del_p.G128fs	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	228					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	TTTGTTAACTCCCCCCTAGAA	0.463																																																0			10											229	238	235					10																	13325835		2203	4300	6503	13365841	SO:0001589	frameshift_variant	5264				CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"Refsum disease", "phytanoyl-CoA dioxygenase"	602026	"phytanoyl-CoA hydroxylase (Refsum disease)", "phytanoyl-CoA hydroxylase"			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.683delG	10.37:g.13325835delC	ENSP00000263038:p.Gly228fs		13365841	A8MTS8|B1ALH5	Frame_Shift_Del	DEL	ENST00000263038.4	37	CCDS7097.1																																																																																				0.463	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			-	13325835	C	-	13325835	7	5	111	1	0	1	0	1	0	0	0	0	11895	855	30	0	345	0	PHYH	10	13325835	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1417088	13325835	122208912	539	29673										
BEND7	222389	hgsc.bcm.edu	37	chr10	13538824	13538824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcttgtagaatggcctgcaaCgttgactggcagttacaagt	11	8	1	2	rs568550072		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:13538824C>T	ENST00000396900.2	-	4	512	c.513G>A	c.(511-513)acG>acA	p.T171T	BEND7_ENST00000378605.3_Silent_p.T132T|BEND7_ENST00000396898.2_Silent_p.T184T|BEND7_ENST00000341083.3_Silent_p.T119T			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	171						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						TGGCCTGCAACGTTGACTGGC	0.413																																																0			10											140	136	137					10																	13538824		2203	4300	6503	13578830	SO:0001819	synonymous_variant	222389			BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"BEN domain containing"	23514	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 30"	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.513G>A	10.37:g.13538824C>T			13578830	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																					0.413	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		T	13538824	C	T	13538824	2	4	111	1	0	0	0	0	0	0	0	1	1404	523	19	1		1	BEND7	10	13538824	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	212989	13538824	121995923	540	29674										
FRMD4A	55691	hgsc.bcm.edu	37	chr10	13743445	13743445	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacgtgtgcactgcaatgccGctgtgcccaaacgtcctcct	9	16	0	0	rs188864146	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:13743445G>A	ENST00000357447.2	-	14	1238	c.870C>T	c.(868-870)agC>agT	p.S290S	FRMD4A_ENST00000378503.1_Silent_p.S290S|FRMD4A_ENST00000492155.1_5'UTR|FRMD4A_ENST00000342409.2_Silent_p.S306S|FRMD4A_ENST00000358621.4_Silent_p.S275S	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	290	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CTGCAATGCCGCTGTGCCCAA	0.498													G|||	5	0.000998403	0	0	5008	,	,		23021	0.004		0.001	False		,,,				2504	0															0			10											194	164	174					10																	13743445		2203	4300	6503	13783451	SO:0001819	synonymous_variant	55691			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"FERM domain containing 4"	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.870C>T	10.37:g.13743445G>A			13783451	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																				0.498	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		A	13743445	G	A	13743445	2	1	111	1	0	0	0	0	0	0	0	1	6070	1078	38	1		1	FRMD4A	10	13743445	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	204621	13743445	121791302	541	29675										
CACNB2	783	hgsc.bcm.edu	37	chr10	18828645	18828645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggaacagggatgtttacatcCgccaatgagttttgcccgtt	11	9	0	1	rs77141223	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:18828645C>T	ENST00000324631.7	+	14	2035	c.1975C>T	c.(1975-1977)Cgc>Tgc	p.R659C	CACNB2_ENST00000377319.3_Missense_Mutation_p.R566C|RP11-499P20.2_ENST00000425669.1_RNA|CACNB2_ENST00000377315.4_Missense_Mutation_p.R611C|CACNB2_ENST00000377331.2_Missense_Mutation_p.R607C|CACNB2_ENST00000377328.1_Missense_Mutation_p.R409C|CACNB2_ENST00000352115.6_Missense_Mutation_p.R635C|CACNB2_ENST00000282343.8_Missense_Mutation_p.R631C|CACNB2_ENST00000396576.2_Missense_Mutation_p.R604C|RP11-499P20.2_ENST00000436485.1_RNA|CACNB2_ENST00000377329.4_Missense_Mutation_p.R605C	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	659				R -> P (in Ref. 2; AAB53332, 3; AAG01473/ AAL16948/AAL16951/AAL16950, 4; AAQ97606/ AAQ97607/AAQ97608/AAQ97609/AAQ97610 and 6; AAL73495). {ECO:0000305}.	axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTTTACATCCGCCAATGAGT	0.408													C|||	5	0.000998403	0.003	0	5008	,	,		16461	0		0.001	False		,,,				2504	0															0			10						C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	13,4389		0,13,2188	57	55	56		1810,1777,1831,1891,1819,1813,1861,1975,1903	5.2	1	10	dbSNP_131	56	0,8592		0,0,4296	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNB2	NM_000724.3,NM_001167945.1,NM_201570.2,NM_201571.3,NM_201572.3,NM_201590.2,NM_201593.2,NM_201596.2,NM_201597.2	180,180,180,180,180,180,180,180,180	0,13,6484	TT,TC,CC		0.0,0.2953,0.1	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	604/606,593/595,611/613,631/633,607/609,605/607,621/623,659/661,635/637	18828645	13,12981	2201	4296	6497	18868651	SO:0001583	missense	783			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"Calcium channel subunits"	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.1975C>T	10.37:g.18828645C>T	ENSP00000320025:p.Arg659Cys		18868651	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	37	CCDS7125.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	16.35	3.099996	0.56183	0.002953	0.0	ENSG00000165995	ENST00000324631;ENST00000352115;ENST00000377328;ENST00000282343;ENST00000377331;ENST00000396576;ENST00000377319;ENST00000377329;ENST00000377315	D;D;D;D;D;D;D;D;D	0.85088	-1.89;-1.86;-1.94;-1.87;-1.87;-1.88;-1.87;-1.88;-1.88	5.17	5.17	0.71159	.	0.352416	0.34067	N	0.004291	D	0.88890	0.6560	L	0.32530	0.975	0.58432	D	0.999998	P;D;D;D;D;D;D;D;D;D;D	0.89917	0.946;1.0;0.992;0.984;0.992;0.987;0.994;0.984;0.997;0.998;0.972	B;D;P;P;P;P;P;P;P;P;B	0.74348	0.333;0.983;0.513;0.59;0.513;0.534;0.724;0.59;0.736;0.857;0.386	D	0.90011	0.4121	10	0.87932	D	0	-14.5433	18.8737	0.92327	0.0:1.0:0.0:0.0	.	573;409;611;605;615;566;607;631;621;635;659	B7Z1U5;A6PVM6;Q5VVH1;Q08289-3;Q59H42;Q08289-6;A6PVM7;Q08289-4;Q08289-7;Q08289-8;Q08289	.;.;.;.;.;.;.;.;.;.;CACB2_HUMAN	C	659;635;409;631;607;604;566;605;611	ENSP00000320025:R659C;ENSP00000344474:R635C;ENSP00000366545:R409C;ENSP00000282343:R631C;ENSP00000366548:R607C;ENSP00000379821:R604C;ENSP00000366536:R566C;ENSP00000366546:R605C;ENSP00000366532:R611C	ENSP00000282343:R631C	R	+	1	0	CACNB2	18868651	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.380000	0.66202	2.703000	0.92315	0.655000	0.94253	CGC		0.408	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724		T	18828645	C	T	18828645	3	4	111	1	0	0	0	0	1	0	0	0	2559	652	23	1	2339	1	CACNB2	10	18828645	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5085200	18828645	116706102	542	29676										
MPP7	143098	hgsc.bcm.edu	37	chr10	28420579	28420579	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ataggaggcaacactgggtcGtaattcttctgagccacagt	11	9	2	1	rs145809120		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:28420579G>A	ENST00000375732.1	-	6	616	c.357C>T	c.(355-357)taC>taT	p.Y119Y	MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000375719.3_Silent_p.Y119Y|MPP7_ENST00000445954.2_De_novo_Start_OutOfFrame|MPP7_ENST00000540098.1_Silent_p.Y119Y|MPP7_ENST00000337532.5_Silent_p.Y119Y			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	119	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						ACACTGGGTCGTAATTCTTCT	0.353													G|||	1	0.000199681	0	0	5008	,	,		15557	0		0.001	False		,,,				2504	0															0			10						G		1,4405	2.1+/-5.4	0,1,2202	106	97	100		357	-8.1	0.3	10	dbSNP_134	100	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	MPP7	NM_173496.3		0,13,6490	AA,AG,GG		0.1395,0.0227,0.1		119/577	28420579	13,12993	2203	4300	6503	28460585	SO:0001819	synonymous_variant	143098			BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.357C>T	10.37:g.28420579G>A			28460585	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	37	CCDS7158.1																																																																																				0.353	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		A	28420579	G	A	28420579	2	1	111	1	0	0	0	0	0	0	0	1	9769	1140	40	1		1	MPP7	10	28420579	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	9591934	28420579	107114168	543	29677										
WAC	51322	hgsc.bcm.edu	37	chr10	28900837	28900837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgatcagtactcctcctgttTcatcacagccaaaggtatgt	7	11	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:28900837T>C	ENST00000354911.4	+	10	1584	c.1423T>C	c.(1423-1425)Tca>Cca	p.S475P	WAC_ENST00000347934.4_Missense_Mutation_p.S372P|WAC_ENST00000375664.4_Missense_Mutation_p.S430P|WAC_ENST00000375646.1_Missense_Mutation_p.S323P	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	475			S -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						TCCTCCTGTTTCATCACAGCC	0.383																																																0			10											138	114	122					10																	28900837		2203	4300	6503	28940843	SO:0001583	missense	51322			AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1423T>C	10.37:g.28900837T>C	ENSP00000346986:p.Ser475Pro		28940843	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	37	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762842	0.69763	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911;ENST00000338396	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.12	5.12	0.69794	.	0.193793	0.45606	D	0.000352	T	0.35799	0.0944	L	0.27053	0.805	0.80722	D	1	P;P;B	0.52316	0.578;0.952;0.442	B;P;B	0.47075	0.264;0.536;0.135	T	0.22103	-1.0226	10	0.72032	D	0.01	-15.5392	10.5959	0.45338	0.1435:0.0:0.0:0.8565	.	430;372;475	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	P	430;323;372;475;38	ENSP00000364816:S430P;ENSP00000364797:S323P;ENSP00000311106:S372P;ENSP00000346986:S475P	ENSP00000341462:S38P	S	+	1	0	WAC	28940843	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.157000	0.50716	2.275000	0.75901	0.528000	0.53228	TCA		0.383	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		C	28900837	T	C	28900837	3	2	111	1	0	0	0	0	1	0	0	0	17287	1783	62	4	1461	4	WAC	10	28900837	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	480258	28900837	106633910	544	29678										
SVIL	6840	hgsc.bcm.edu	37	chr10	29760116	29760116	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccccgagtgcaccaccatCcccccctggaaacactgcag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:29760116delC	ENST00000355867.4	-	31	6338	c.5586delG	c.(5584-5586)gggfs	p.G1862fs	SVIL_ENST00000460007.1_5'Flank|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Frame_Shift_Del_p.G776fs|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|SVIL_ENST00000375398.2_Frame_Shift_Del_p.G1862fs|SVIL_ENST00000375400.3_Frame_Shift_Del_p.G1436fs	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1862					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GCACCACCATCCCCCCCTGGA	0.527																																																0			10											75	62	67					10																	29760116		2203	4300	6503	29800122	SO:0001589	frameshift_variant	6840			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5586delG	10.37:g.29760116delC	ENSP00000348128:p.Gly1862fs		29800122	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Frame_Shift_Del	DEL	ENST00000355867.4	37	CCDS7164.1																																																																																				0.527	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			-	29760116	C	-	29760116	7	5	111	1	0	1	0	1	0	0	0	0	15460	842	30	0	1090	0	SVIL	10	29760116	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	859279	29760116	105774631	545	29679										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31809187	31809187	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaagaacaggactcaagacAtctcagtgttcttcaccgtc	7	13	4	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:31809187A>G	ENST00000320985.10	+	7	1034	c.924A>G	c.(922-924)acA>acG	p.T308T	ZEB1_ENST00000361642.5_Silent_p.T309T|ZEB1_ENST00000446923.2_Silent_p.T292T|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Silent_p.T241T|ZEB1_ENST00000560721.2_Silent_p.T288T			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	308					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GACTCAAGACATCTCAGTGTT	0.453																																					Ovarian(40;423 959 14296 36701 49589)											0			10											134	129	131					10																	31809187		2203	4300	6503	31849193	SO:0001819	synonymous_variant	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.924A>G	10.37:g.31809187A>G			31849193	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Silent	SNP	ENST00000320985.10	37	CCDS7169.1																																																																																				0.453	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		G	31809187	A	G	31809187	2	3	111	1	0	0	0	0	0	0	0	1	17662	204	8	4		4	ZEB1	10	31809187	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2049071	31809187	103725560	546	29680										
ITGB1	3688	hgsc.bcm.edu	37	chr10	33208969	33208969	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttttaaagctgtcagaatccTtttttggacacttatttgaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:33208969delT	ENST00000396033.2	-	11	1448	c.1313delA	c.(1312-1314)aagfs	p.K438fs	ITGB1_ENST00000374956.4_Frame_Shift_Del_p.K438fs|ITGB1_ENST00000423113.1_Frame_Shift_Del_p.K438fs|ITGB1_ENST00000302278.3_Frame_Shift_Del_p.K438fs	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	438					axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	GTCAGAATCCTTTTTTGGACA	0.338																																																0			10											122	130	128					10																	33208969		2203	4300	6503	33248975	SO:0001589	frameshift_variant	3688			BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1313delA	10.37:g.33208969delT	ENSP00000379350:p.Lys438fs		33248975	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Frame_Shift_Del	DEL	ENST00000396033.2	37	CCDS7174.1																																																																																				0.338	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		-	33208969	T	-	33208969	7	5	111	1	0	1	0	1	0	0	0	0	7911	1609	56	0	1345	0	ITGB1	10	33208969	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	1399782	33208969	102325778	547	29681										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38126605	38126605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggctcttctccttgctcgaTcttaaagatcacttctggtt	8	11	5	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:38126605T>C	ENST00000395867.3	-	5	728	c.178A>G	c.(178-180)Atc>Gtc	p.I60V	ZNF248_ENST00000357328.4_Missense_Mutation_p.I60V|ZNF248_ENST00000494133.1_5'UTR|ZNF248_ENST00000374648.3_Missense_Mutation_p.I60V	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	60	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						CCTTGCTCGATCTTAAAGATC	0.433																																																0			10											105	93	97					10																	38126605		2203	4300	6503	38166611	SO:0001583	missense	57209			AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.178A>G	10.37:g.38126605T>C	ENSP00000379208:p.Ile60Val		38166611	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	T	8.932	0.963669	0.18583	.	.	ENSG00000198105	ENST00000395867;ENST00000374648;ENST00000357328;ENST00000395873;ENST00000395874	T;T;T;T;T	0.40756	5.74;1.02;5.74;1.02;1.02	4.74	2.2	0.27929	Krueppel-associated box (3);	0.000000	0.50627	D	0.000104	T	0.20007	0.0481	N	0.10629	0.01	0.28536	N	0.912334	B;P	0.36874	0.041;0.572	B;B	0.34038	0.043;0.174	T	0.12553	-1.0543	10	0.59425	D	0.04	.	8.5136	0.33233	0.3059:0.0:0.0:0.694	.	60;60	Q8NDW4;Q8NDV8	ZN248_HUMAN;.	V	60	ENSP00000379208:I60V;ENSP00000363778:I60V;ENSP00000349882:I60V;ENSP00000379214:I60V;ENSP00000379215:I60V	ENSP00000349882:I60V	I	-	1	0	ZNF248	38166611	0.975000	0.34042	0.996000	0.52242	0.024000	0.10985	0.807000	0.27140	0.920000	0.36970	-0.327000	0.08410	ATC		0.433	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		C	38126605	T	C	38126605	3	2	111	1	0	0	0	0	1	0	0	0	17832	1435	50	4	1569	4	ZNF248	10	38126605	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	4917636	38126605	97408142	548	29682										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999897	46999897	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggatgctggtgtgcaggcGgccccagtggcggcctgcaa	17	12	0	0	rs141986818	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:46999897G>A	ENST00000374317.1	+	3	1290	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	GPRIN2_ENST00000374314.4_Silent_p.A339A	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	339										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GTGTGCAGGCGGCCCCAGTGG	0.647													G|||	87	0.0173722	8e-04	0.0072	5008	,	,		31557	0.0794		0	False		,,,				2504	0.001															0			10						G		5,4399		0,5,2197	39	44	43		1017	-9.7	0	10	dbSNP_134	43	3,8573		0,3,4285	yes	coding-synonymous	GPRIN2	NM_014696.3		0,8,6482	AA,AG,GG		0.035,0.1135,0.0616		339/459	46999897	8,12972	2202	4288	6490	46419903	SO:0001819	synonymous_variant	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1017G>A	10.37:g.46999897G>A			46419903	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																				0.647	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46999897	G	A	46999897	2	1	111	1	0	0	0	0	0	0	0	1	6751	1103	39	1		1	GPRIN2	10	46999897	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	8873292	46999897	88534850	549	29683										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48371212	48371212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaagcattgccacagaatgCtccactctgtagcacttttc	7	13	1	1	rs138808688		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:48371212C>T	ENST00000395702.2	+	2	907	c.680C>T	c.(679-681)gCt>gTt	p.A227V	ZNF488_ENST00000586537.1_Missense_Mutation_p.A120V|ZNF488_ENST00000494156.1_3'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	227					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						CCACAGAATGCTCCACTCTGT	0.557																																																0			10						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	120	114	116		680	2.6	0	10	dbSNP_134	116	0,8600		0,0,4300	no	missense	ZNF488	NM_153034.2	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	227/341	48371212	1,13005	2203	4300	6503	47991218	SO:0001583	missense	118738			AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.680C>T	10.37:g.48371212C>T	ENSP00000379054:p.Ala227Val		47991218	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	37	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	C	4.877	0.163073	0.09287	2.27E-4	0.0	ENSG00000165388	ENST00000395702	T	0.22134	1.97	5.55	2.59	0.31030	.	0.849249	0.10575	N	0.658637	T	0.19248	0.0462	L	0.51422	1.61	0.09310	N	1	B	0.25719	0.132	B	0.17098	0.017	T	0.19745	-1.0296	10	0.44086	T	0.13	.	8.1138	0.30930	0.0:0.6246:0.0:0.3754	.	227	Q96MN9	ZN488_HUMAN	V	227	ENSP00000379054:A227V	ENSP00000379054:A227V	A	+	2	0	ZNF488	47991218	0.000000	0.05858	0.002000	0.10522	0.419000	0.31324	0.662000	0.25038	0.253000	0.21552	0.561000	0.74099	GCT		0.557	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		T	48371212	C	T	48371212	3	4	111	1	0	0	0	0	1	0	0	0	17979	797	28	3	682	3	ZNF488	10	48371212	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1371315	48371212	87163535	550	29684										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49395324	49395324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactcttcagctgctcccggCcagtgcaggggctgccggga	14	15	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:49395324C>T	ENST00000374201.3	-	17	2479	c.2177G>A	c.(2176-2178)gGc>gAc	p.G726D	FRMPD2_ENST00000305531.3_Missense_Mutation_p.G701D|FRMPD2_ENST00000407470.4_Missense_Mutation_p.G694D	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	726					tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTGCTCCCGGCCAGTGCAGGG	0.562																																																0			10											57	53	54					10																	49395324		2203	4300	6503	49065330	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2177G>A	10.37:g.49395324C>T	ENSP00000363317:p.Gly726Asp		49065330	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.248178	0.39697	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.63417	0.0;-0.04;-0.03	4.06	2.21	0.28008	.	.	.	.	.	T	0.42381	0.1200	L	0.27053	0.805	0.09310	N	1	B;B;B	0.13594	0.008;0.003;0.008	B;B;B	0.17433	0.018;0.003;0.018	T	0.25676	-1.0125	9	0.10902	T	0.67	.	6.275	0.20975	0.0:0.7759:0.0:0.2241	.	701;726;694	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	D	726;701;694	ENSP00000363317:G726D;ENSP00000307079:G701D;ENSP00000384339:G694D	ENSP00000307079:G701D	G	-	2	0	FRMPD2	49065330	0.282000	0.24268	0.246000	0.24233	0.901000	0.52897	0.780000	0.26760	0.681000	0.31386	0.655000	0.94253	GGC		0.562	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		T	49395324	C	T	49395324	3	4	111	1	0	0	0	0	1	0	0	0	6077	739	26	3	1804	3	FRMPD2	10	49395324	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1024112	49395324	86139423	551	29685										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50954813	50954813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacctggttgttgacgacgaCgtgcacggtaccattggtcg	13	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:50954813C>T	ENST00000374103.4	-	10	1364	c.1279G>A	c.(1279-1281)Gtc>Atc	p.V427I	OGDHL_ENST00000432695.1_Missense_Mutation_p.V218I|OGDHL_ENST00000419399.1_Missense_Mutation_p.V370I	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	427					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						TTGACGACGACGTGCACGGTA	0.602																																																0			10											148	98	115					10																	50954813		2203	4300	6503	50624819	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1279G>A	10.37:g.50954813C>T	ENSP00000363216:p.Val427Ile		50624819	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.828916	0.00584	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;D	0.96365	2.52;2.52;-3.99	5.76	0.112	0.14623	Dehydrogenase, E1 component (1);	0.359209	0.28977	N	0.013532	D	0.86644	0.5982	N	0.04724	-0.175	0.21064	N	0.999795	B;B;B	0.12013	0.005;0.005;0.002	B;B;B	0.18263	0.016;0.007;0.021	T	0.73579	-0.3938	10	0.02654	T	1	.	10.932	0.47224	0.0:0.5809:0.0:0.4191	.	370;218;427	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	I	427;370;218	ENSP00000363216:V427I;ENSP00000401356:V370I;ENSP00000390240:V218I	ENSP00000363216:V427I	V	-	1	0	OGDHL	50624819	0.099000	0.21834	0.001000	0.08648	0.004000	0.04260	0.643000	0.24750	0.094000	0.17404	-0.137000	0.14449	GTC		0.602	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		T	50954813	C	T	50954813	3	4	111	1	0	0	0	0	1	0	0	0	10871	536	19	1	1809	1	OGDHL	10	50954813	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1559489	50954813	84579934	552	29686										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55626441	55626441	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcagtcccttcccatagtcGtcagttgcaataacttgaaa	6	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:55626441G>A	ENST00000320301.6	-	27	4072	c.3678C>T	c.(3676-3678)gaC>gaT	p.D1226D	PCDH15_ENST00000409834.1_Silent_p.D837D|PCDH15_ENST00000373965.2_Silent_p.D1233D|PCDH15_ENST00000395433.1_Silent_p.D1204D|PCDH15_ENST00000361849.3_Silent_p.D1226D|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000414778.1_Silent_p.D1231D|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Silent_p.D1189D|PCDH15_ENST00000395438.1_Silent_p.D1226D|PCDH15_ENST00000395445.1_Silent_p.D1233D|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395430.1_Silent_p.D1226D|PCDH15_ENST00000437009.1_Silent_p.D1155D|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1226	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCCCATAGTCGTCAGTTGCAA	0.413										HNSCC(58;0.16)																																						0			10											127	109	115					10																	55626441		2203	4300	6503	55296447	SO:0001819	synonymous_variant	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3678C>T	10.37:g.55626441G>A			55296447	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.413	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55626441	G	A	55626441	2	1	111	1	0	0	0	0	0	0	0	1	11542	1136	40	1		1	PCDH15	10	55626441	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4671628	55626441	79908306	553	29687										
ANK3	288	hgsc.bcm.edu	37	chr10	61865700	61865701	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtaactcggttaaatcttcaINStttttgctgtcaaactgatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:61865700_61865701insT	ENST00000280772.2	-	28	3481_3482	c.3290_3291insA	c.(3289-3291)aatfs	p.N1097fs	ANK3_ENST00000503366.1_Frame_Shift_Ins_p.N1098fs|ANK3_ENST00000373827.2_Frame_Shift_Ins_p.N1091fs|ANK3_ENST00000355288.2_Frame_Shift_Ins_p.N231fs	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1097	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTAAATCTTCATTTTTGCTGTC	0.396																																																0			10																																								61535707	SO:0001589	frameshift_variant	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.3291dupA	10.37:g.61865705_61865705dupT	ENSP00000280772:p.Asn1097fs		61535706	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Ins	INS	ENST00000280772.2	37	CCDS7258.1																																																																																				0.396	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61865701	-	T	61865700	7	5	111	1	0	1	1	0	0	0	0	0	622	214	8	0	10219	0	ANK3	10	61865700	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	6239259	61865700	73669047	554	29688										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63845642	63845642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaaagaaaatgccccaaagCcccaggatgcagcagaggtg	11	10	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:63845642C>T	ENST00000279873.7	+	9	1791	c.1381C>T	c.(1381-1383)Ccc>Tcc	p.P461S	ARID5B_ENST00000309334.5_Missense_Mutation_p.P218S	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	461					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					TGCCCCAAAGCCCCAGGATGC	0.448																																																0			10											107	116	113					10																	63845642		2203	4300	6503	63515648	SO:0001583	missense	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1381C>T	10.37:g.63845642C>T	ENSP00000279873:p.Pro461Ser		63515648	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	37	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.573951	0.45902	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.12361	2.69;2.69	5.66	4.73	0.59995	.	0.222920	0.40302	N	0.001123	T	0.10165	0.0249	L	0.32530	0.975	0.40270	D	0.978276	P;B	0.43938	0.822;0.057	B;B	0.30855	0.121;0.035	T	0.08493	-1.0719	10	0.51188	T	0.08	-14.3497	15.5066	0.75745	0.0:0.6125:0.3875:0.0	.	218;461	Q14865-2;Q14865	.;ARI5B_HUMAN	S	461;218	ENSP00000279873:P461S;ENSP00000308862:P218S	ENSP00000279873:P461S	P	+	1	0	ARID5B	63515648	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.178000	0.31981	1.468000	0.48064	0.655000	0.94253	CCC		0.448	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63845642	C	T	63845642	3	4	111	1	0	0	0	0	1	0	0	0	922	739	26	3	1415	3	ARID5B	10	63845642	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1979942	63845642	71689105	555	29689										
SLC25A16	8034	hgsc.bcm.edu	37	chr10	70276587	70276587	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaactgttgttttggcacaGcatccagcaatacctaaaaa	7	10	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:70276587G>T	ENST00000609923.1	-	2	242	c.144C>A	c.(142-144)tgC>tgA	p.C48*	SLC25A16_ENST00000539557.1_De_novo_Start_OutOfFrame|SLC25A16_ENST00000265870.3_5'UTR	NM_152707.3	NP_689920.1	P16260	GDC_HUMAN	solute carrier family 25 (mitochondrial carrier), member 16	48					coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	antiporter activity (GO:0015297)			endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	7						TTTTGGCACAGCATCCAGCAA	0.378																																																0			10											111	105	107					10																	70276587		2203	4300	6503	69946593	SO:0001587	stop_gained	8034			M31659	CCDS7280.1	10q21.3-q22.1	2014-06-17	2014-06-17		ENSG00000122912	ENSG00000122912		"Solute carriers"	10986	protein-coding gene	gene with protein product	"Graves disease autoantigen"	139080				8444471, 2575220	Standard	NM_152707		Approved	GDA, D10S105E, HGT.1, ML7	uc001joi.3	P16260	OTTHUMG00000018354	ENST00000609923.1:c.144C>A	10.37:g.70276587G>T	ENSP00000476815:p.Cys48*		69946593	Q8N2U1	Nonsense_Mutation	SNP	ENST00000609923.1	37	CCDS7280.1	.	.	.	.	.	.	.	.	.	.	G	35	5.522027	0.96416	.	.	ENSG00000122912	ENST00000265870	.	.	.	5.63	4.53	0.55603	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-13.2954	10.9319	0.47222	0.1482:0.0:0.8518:0.0	.	.	.	.	X	48	.	ENSP00000265870:C48X	C	-	3	2	SLC25A16	69946593	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.557000	0.45871	2.636000	0.89361	0.655000	0.94253	TGC		0.378	SLC25A16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048347.2			T	70276587	G	T	70276587	4	4	111	1	0	0	0	0	0	1	0	0	14515	963	34	2	886	2	SLC25A16	10	70276587	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	6430945	70276587	65258160	556	29690										
STOX1	219736	hgsc.bcm.edu	37	chr10	70652358	70652358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctttaggacacagagtctgGgatctaataattcagtcatt	8	7	5	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:70652358G>A	ENST00000298596.6	+	4	2919	c.2836G>A	c.(2836-2838)Gga>Aga	p.G946R	STOX1_ENST00000399162.2_Nonsense_Mutation_p.W159*|STOX1_ENST00000421961.2_Missense_Mutation_p.G836R|STOX1_ENST00000399165.4_Missense_Mutation_p.G226E|STOX1_ENST00000399169.4_Missense_Mutation_p.G946R	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	946						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						ACAGAGTCTGGGATCTAATAA	0.353																																																0			10											92	90	91					10																	70652358		1855	4099	5954	70322364	SO:0001583	missense	219736			AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2836G>A	10.37:g.70652358G>A	ENSP00000298596:p.Gly946Arg		70322364	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Nonsense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.59|15.59|15.59	2.877836|2.877836|2.877836	0.51801|0.51801|0.51801	.|.|.	.|.|.	ENSG00000165730|ENSG00000165730|ENSG00000165730	ENST00000399165|ENST00000399169;ENST00000298596;ENST00000421961|ENST00000399162	D|T;T;T|.	0.83419|0.73681|.	-1.72|-0.77;-0.77;-0.45|.	6.07|6.07|6.07	1.08|1.08|1.08	0.20341|0.20341|0.20341	.|.|.	0.480009|0.480009|.	0.21919|0.21919|.	N|N|.	0.067192|0.067192|.	T|T|.	0.46249|0.46249|.	0.1383|0.1383|.	.|.|.	.|.|.	.|.|.	0.22389|0.22389|0.22389	N|N|N	0.999144|0.999144|0.999144	P|P|.	0.42620|0.38335|.	0.785|0.627|.	P|B|.	0.44897|0.28638|.	0.463|0.092|.	T|T|.	0.43360|0.43360|.	-0.9396|-0.9396|.	9|9|.	0.87932|0.72032|0.72032	D|D|D	0|0.01|0.01	.|.|.	11.0572|11.0572|11.0572	0.47925|0.47925|0.47925	0.3909:0.0:0.6091:0.0|0.3909:0.0:0.6091:0.0|0.3909:0.0:0.6091:0.0	.|.|.	226|946|.	Q6ZVD7-2|Q6ZVD7|.	.|STOX1_HUMAN|.	E|R|X	226|946;946;836|159	ENSP00000382118:G226E|ENSP00000382121:G946R;ENSP00000298596:G946R;ENSP00000394509:G836R|.	ENSP00000382118:G226E|ENSP00000298596:G946R|ENSP00000382115:W159X	G|G|W	+|+|+	2|1|3	0|0|0	STOX1|STOX1|STOX1	70322364|70322364|70322364	0.943000|0.943000|0.943000	0.32029|0.32029|0.32029	0.986000|0.986000|0.986000	0.45419|0.45419|0.45419	0.982000|0.982000|0.982000	0.71751|0.71751|0.71751	1.018000|1.018000|1.018000	0.30002|0.30002|0.30002	0.163000|0.163000|0.163000	0.19507|0.19507|0.19507	-0.150000|-0.150000|-0.150000	0.13652|0.13652|0.13652	GGG|GGA|TGG		0.353	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		A	70652358	G	A	70652358	3	1	111	1	0	0	0	0	1	0	0	0	15358	1242	43	3	2850	3	STOX1	10	70652358	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	375771	70652358	64882389	557	29691										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72493710	72493710	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcctgggcagcgtcatggcGcccctggtgcaggctgcctt	15	14	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:72493710G>A	ENST00000373207.1	+	8	1278	c.1278G>A	c.(1276-1278)gcG>gcA	p.A426A	ADAMTS14_ENST00000373208.1_Silent_p.A429A	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	426	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GCGTCATGGCGCCCCTGGTGC	0.627																																																0			10											69	61	63					10																	72493710		2203	4300	6503	72163716	SO:0001819	synonymous_variant	140766			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1278G>A	10.37:g.72493710G>A			72163716	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																				0.627	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		A	72493710	G	A	72493710	2	1	111	1	0	0	0	0	0	0	0	1	259	1074	38	1		1	ADAMTS14	10	72493710	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1841352	72493710	63041037	558	29692										
UNC5B	219699	hgsc.bcm.edu	37	chr10	73039667	73039667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctgcaggagccacaggacGcctacattgtgaagaacaag	11	11	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:73039667G>A	ENST00000335350.6	+	2	585	c.169G>A	c.(169-171)Gcc>Acc	p.A57T	UNC5B_ENST00000373192.4_Missense_Mutation_p.A57T	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	57	Ig-like.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GCCACAGGACGCCTACATTGT	0.617																																																0			10											69	66	67					10																	73039667		2203	4300	6503	72709673	SO:0001583	missense	219699			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.169G>A	10.37:g.73039667G>A	ENSP00000334329:p.Ala57Thr		72709673	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	G	34	5.333512	0.95758	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.25414	1.8;1.8	4.52	4.52	0.55395	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.45074	0.1324	L	0.52011	1.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.25152	-1.0140	10	0.29301	T	0.29	-32.4997	17.2464	0.87029	0.0:0.0:1.0:0.0	.	57;57	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	T	57	ENSP00000334329:A57T;ENSP00000362288:A57T	ENSP00000334329:A57T	A	+	1	0	UNC5B	72709673	1.000000	0.71417	0.992000	0.48379	0.905000	0.53344	9.869000	0.99810	2.051000	0.60960	0.561000	0.74099	GCC		0.617	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		A	73039667	G	A	73039667	3	1	111	1	0	0	0	0	1	0	0	0	17032	1087	38	1	175	1	UNC5B	10	73039667	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	545957	73039667	62495080	559	29693										
UNC5B	219699	hgsc.bcm.edu	37	chr10	73051241	73051241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctgacctgacagccagcgcCggcatctaccgcggacccgt	11	18	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:73051241C>T	ENST00000335350.6	+	10	1763	c.1347C>T	c.(1345-1347)gcC>gcT	p.A449A	UNC5B_ENST00000373192.4_Silent_p.A438A	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	449					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						CAGCCAGCGCCGGCATCTACC	0.612																																																0			10											73	72	73					10																	73051241		2203	4300	6503	72721247	SO:0001819	synonymous_variant	219699			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1347C>T	10.37:g.73051241C>T			72721247	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																				0.612	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73051241	C	T	73051241	2	4	111	1	0	0	0	0	0	0	0	1	17032	639	23	1		1	UNC5B	10	73051241	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	11574	73051241	62483506	560	29694										
CDH23	64072	hgsc.bcm.edu	37	chr10	73405673	73405673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacctccgtccaggggaaggCggacattcgtattcgggtgg	16	10	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:73405673C>T	ENST00000224721.6	+	12	1246	c.1241C>T	c.(1240-1242)gCg>gTg	p.A414V	CDH23_ENST00000461841.3_Missense_Mutation_p.A454V|CDH23_ENST00000299366.7_Missense_Mutation_p.A454V|CDH23_ENST00000398809.4_Missense_Mutation_p.A409V|CDH23_ENST00000398842.3_Missense_Mutation_p.A409V	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	409	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A414V(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CAGGGGAAGGCGGACATTCGT	0.577																																																1	Substitution - Missense(1)	large_intestine(1)	10											70	74	73					10																	73405673		2025	4171	6196	73075679	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1241C>T	10.37:g.73405673C>T	ENSP00000224721:p.Ala414Val		73075679	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	19.70	3.876103	0.72180	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.59224	0.28;0.32	4.91	4.91	0.64330	Cadherin (3);Cadherin-like (1);	0.000000	0.64402	D	0.000006	T	0.70988	0.3287	L	0.50333	1.59	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.989;0.994;0.995;0.994	T	0.69083	-0.5239	10	0.34782	T	0.22	.	18.1099	0.89532	0.0:1.0:0.0:0.0	.	409;412;409;409	Q6P152;G3XCN8;Q9H251;Q9H251-5	.;.;CAD23_HUMAN;.	V	414;409;409;409;409;412;412;324	ENSP00000381789:A409V;ENSP00000381822:A409V	ENSP00000224721:A414V	A	+	2	0	CDH23	73075679	1.000000	0.71417	0.777000	0.31699	0.337000	0.28794	7.456000	0.80751	2.280000	0.76307	0.561000	0.74099	GCG		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73405673	C	T	73405673	3	4	111	1	0	0	0	0	1	0	0	0	3114	768	27	1	1355	1	CDH23	10	73405673	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	354432	73405673	62129074	561	29695										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85964307	85964307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggaggtactgaaggtggtcGccatggatggagaccggggc	19	8	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:85964307G>A	ENST00000372117.3	+	9	911	c.808G>A	c.(808-810)Gcc>Acc	p.A270T	CDHR1_ENST00000440770.2_Missense_Mutation_p.A29T|CDHR1_ENST00000332904.3_Missense_Mutation_p.A270T	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	270	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						GAAGGTGGTCGCCATGGATGG	0.562																																																0			10											118	112	114					10																	85964307		2203	4300	6503	85954287	SO:0001583	missense	0			AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.808G>A	10.37:g.85964307G>A	ENSP00000361189:p.Ala270Thr		85954287	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724539	0.89298	.	.	ENSG00000148600	ENST00000332904;ENST00000372117;ENST00000440770	T;T;T	0.61392	0.11;0.11;0.11	5.48	5.48	0.80851	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.83839	0.5341	H	0.96333	3.805	0.80722	D	1	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.91635	0.999;0.93;0.975	D	0.88876	0.3336	10	0.87932	D	0	-36.4018	16.8514	0.85995	0.0:0.0:1.0:0.0	.	29;270;270	E7EN47;Q96JP9-2;Q96JP9	.;.;CDHR1_HUMAN	T	270;270;29	ENSP00000331063:A270T;ENSP00000361189:A270T;ENSP00000415980:A29T	ENSP00000331063:A270T	A	+	1	0	CDHR1	85954287	1.000000	0.71417	0.986000	0.45419	0.506000	0.33950	8.922000	0.92789	2.571000	0.86741	0.561000	0.74099	GCC		0.562	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85964307	G	A	85964307	3	1	111	1	0	0	0	0	1	0	0	0	3124	1087	38	1	842	1	CDHR1	10	85964307	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	12558634	85964307	49570440	562	29696										
FAM190B	54462	hgsc.bcm.edu	37	chr10	86230175	86230176	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacttaaagacgaaataaagINSaaaaaagatgaaaagatcca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:86230175_86230176insA	ENST00000224756.8	+	8	2381_2382	c.2196_2197insA	c.(2197-2199)aaafs	p.K733fs	CCSER2_ENST00000494144.1_3'UTR|CCSER2_ENST00000372088.2_Frame_Shift_Ins_p.K733fs|CCSER2_ENST00000543283.1_Frame_Shift_Ins_p.K160fs	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	733					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											ACGAAATAAAGAAAAAAGATGA	0.248																																																0			10																																								86220156	SO:0001589	frameshift_variant	0				CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.2202dupA	10.37:g.86230181_86230181dupA	ENSP00000224756:p.Lys733fs		86220155	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Frame_Shift_Ins	INS	ENST00000224756.8	37	CCDS31235.1																																																																																				0.248	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		A	86230176	-	A	86230175	7	5	111	1	0	1	1	0	0	0	0	0	5538	933	33	0	2222	0	FAM190B	10	86230175	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	265868	86230175	49304572	563	29697										
MMRN2	79812	hgsc.bcm.edu	37	chr10	88703092	88703092	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcacgtacttgatgaggtcGgcatggccaccctgcaggtg	13	11	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:88703092G>A	ENST00000372027.5	-	6	1770	c.1449C>T	c.(1447-1449)gcC>gcT	p.A483A	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	483					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						TGATGAGGTCGGCATGGCCAC	0.597																																																0			10											62	55	57					10																	88703092		2203	4300	6503	88693072	SO:0001819	synonymous_variant	79812			AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"EMI domain containing"	19888	protein-coding gene	gene with protein product		608925	"elastin microfibril interfacer 3"	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.1449C>T	10.37:g.88703092G>A			88693072	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	37	CCDS7379.1																																																																																				0.597	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756		A	88703092	G	A	88703092	2	1	111	1	0	0	0	0	0	0	0	1	9701	1103	39	1		1	MMRN2	10	88703092	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2472917	88703092	46831655	564	29698										
PTEN	5728	hgsc.bcm.edu	37	chr10	89690812	89690812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttttcttttagttgtgctgaAagacattatgacaccgccaa	7	8	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:89690812A>G	ENST00000371953.3	+	4	1576	c.219A>G	c.(217-219)gaA>gaG	p.E73E		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	73	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y27fs*1(2)|p.E73fs*25(1)|p.E73fs*4(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GTTGTGCTGAAAGACATTATG	0.308		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	59	Whole gene deletion(37)|Deletion - Frameshift(16)|Unknown(6)	prostate(16)|central_nervous_system(14)|breast(6)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10	GRCh37	CD041930	PTEN	D							75	71	72					10																	89690812		2202	4294	6496	89680792	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.219A>G	10.37:g.89690812A>G			89680792	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.308	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89690812	A	G	89690812	2	3	111	1	0	0	0	0	0	0	0	1	12772	11	1	4		4	PTEN	10	89690812	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	987720	89690812	45843935	565	29699										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692804	89692804	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttgaagaccataacccaccAcagctagaacttatcaaacc	4	13	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:89692804A>G	ENST00000371953.3	+	5	1645	c.288A>G	c.(286-288)ccA>ccG	p.P96P		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	96	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.H93fs*5(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATAACCCACCACAGCTAGAAC	0.358		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	51	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											108	100	102					10																	89692804		2203	4300	6503	89682784	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.288A>G	10.37:g.89692804A>G			89682784	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.358	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692804	A	G	89692804	2	3	111	1	0	0	0	0	0	0	0	1	12772	146	6	4		4	PTEN	10	89692804	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1992	89692804	45841943	566	29700										
FRA10AC1	118924	hgsc.bcm.edu	37	chr10	95445007	95445007	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctaaaatcaacttacttaaTttaacaagtgcatttctctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:95445007delT	ENST00000359204.4	-	9	818	c.621delA	c.(619-621)aaafs	p.K207fs	FRA10AC1_ENST00000536233.1_Frame_Shift_Del_p.K207fs|FRA10AC1_ENST00000394100.2_Frame_Shift_Del_p.K207fs|FRA10AC1_ENST00000371430.2_Frame_Shift_Del_p.K207fs	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	207	Lys-rich.					nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						ACTTACTTAATTTAACAAGTG	0.264																																																0			10											97	110	106					10																	95445007		2201	4295	6496	95434997	SO:0001589	frameshift_variant	118924			AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"chromosome 10 open reading frame 4"	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.621delA	10.37:g.95445007delT	ENSP00000360488:p.Lys207fs		95434997	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Frame_Shift_Del	DEL	ENST00000359204.4	37	CCDS7430.1																																																																																				0.264	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246		-	95445007	T	-	95445007	7	5	111	1	0	1	0	1	0	0	0	0	6060	1490	52	0	350	0	FRA10AC1	10	95445007	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	5752203	95445007	40089740	567	29701										
NOC3L	64318	hgsc.bcm.edu	37	chr10	96106304	96106304	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gattcttaggcataaaaatgTttttaacatctaatattgga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:96106304delT	ENST00000371361.3	-	11	1367	c.1267delA	c.(1267-1269)acafs	p.T423fs	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000543788.1_Frame_Shift_Del_p.T161fs|NOC3L_ENST00000371350.1_Frame_Shift_Del_p.T423fs	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	423					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CATAAAAATGTTTTTAACATC	0.244																																																0			10											46	45	45					10																	96106304		2168	4237	6405	96096294	SO:0001589	frameshift_variant	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1267delA	10.37:g.96106304delT	ENSP00000360412:p.Thr423fs		96096294	Q9H5M6|Q9H9D8	Frame_Shift_Del	DEL	ENST00000371361.3	37	CCDS7433.1																																																																																				0.244	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		-	96106304	T	-	96106304	7	5	111	1	0	1	0	1	0	0	0	0	10545	1725	60	0	1179	0	NOC3L	10	96106304	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	661297	96106304	39428443	568	29702										
ENTPD1	953	hgsc.bcm.edu	37	chr10	97599530	97599530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaaaaggagaatgacacagGcgtggtgcatcaagtagaag	14	5	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:97599530G>A	ENST00000371205.4	+	3	510	c.227G>A	c.(226-228)gGc>gAc	p.G76D	ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000371203.5_5'UTR|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000543964.1_5'UTR|ENTPD1_ENST00000453258.2_Missense_Mutation_p.G83D|ENTPD1_ENST00000539125.1_Intron|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000371207.3_Missense_Mutation_p.G88D			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	76					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		AATGACACAGGCGTGGTGCAT	0.478																																																0			10											175	164	168					10																	97599530		2203	4300	6503	97589520	SO:0001583	missense	953			S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.227G>A	10.37:g.97599530G>A	ENSP00000360248:p.Gly76Asp		97589520	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	37	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776837	0.90195	.	.	ENSG00000138185	ENST00000453258;ENST00000371206;ENST00000371207;ENST00000371205	T;T;T	0.11385	2.78;2.78;2.78	5.51	4.61	0.57282	.	0.049140	0.85682	D	0.000000	T	0.33818	0.0876	M	0.85373	2.75	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.987;1.0;1.0	D;D;P;D;D	0.97110	1.0;0.999;0.618;1.0;0.997	T	0.15578	-1.0432	10	0.27082	T	0.32	-16.8582	12.0868	0.53702	0.0821:0.0:0.9179:0.0	.	88;88;83;76;83	B4DWB9;G3XAF6;P49961-2;P49961;P49961-3	.;.;.;ENTP1_HUMAN;.	D	83;83;88;76	ENSP00000390955:G83D;ENSP00000360250:G88D;ENSP00000360248:G76D	ENSP00000360248:G76D	G	+	2	0	ENTPD1	97589520	1.000000	0.71417	0.897000	0.35233	0.949000	0.60115	9.353000	0.97080	1.572000	0.49736	0.557000	0.71058	GGC		0.478	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776		A	97599530	G	A	97599530	3	1	111	1	0	0	0	0	1	0	0	0	5151	1203	42	3	334	3	ENTPD1	10	97599530	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1493226	97599530	37935217	569	29703										
CC2D2B	387707	hgsc.bcm.edu	37	chr10	97787006	97787006	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagtaaagtgatggaatggCgacctaaacacccaacacat	9	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:97787006C>T	ENST00000344386.3	+	9	944				ENTPD1-AS1_ENST00000416301.1_RNA|RP11-690P14.4_ENST00000475252.2_3'UTR|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000458228.1_RNA|CC2D2B_ENST00000371198.2_3'UTR|ENTPD1-AS1_ENST00000449197.1_RNA|CC2D2B_ENST00000410012.2_Nonsense_Mutation_p.R293*|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B											large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		GATGGAATGGCGACCTAAACA	0.363																																																0			10											205	166	178					10																	97787006		692	1591	2283	97776996	SO:0001627	intron_variant	387707			BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 130"	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.781-4571C>T	10.37:g.97787006C>T			97776996	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Nonsense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	C	31	5.075502	0.94000	.	.	ENSG00000188649	ENST00000451649;ENST00000410012	.	.	.	5.67	-4.73	0.03259	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.8691	0.88806	0.6996:0.3004:0.0:0.0	.	.	.	.	X	293	.	ENSP00000386988:R293X	R	+	1	2	CC2D2B	97776996	1.000000	0.71417	0.947000	0.38551	0.751000	0.42716	1.416000	0.34759	-0.557000	0.06126	-0.321000	0.08615	CGA		0.363	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		T	97787006	C	T	97787006	1	4	111	0	1	0	0	0	0	0	0	0	2735	760	27	1		1	CC2D2B	10	97787006	Intron	SNP	C	TCGA-EI-6507-01A-11D-1733-10	187476	97787006	37747741	570	29704										
ZNF518A	9849	hgsc.bcm.edu	37	chr10	97916340	97916341	+	RNA	DEL	AA	AA	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaagaaaatctatcagtatAaagactgtaagctgtgtaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:97916340_97916341delAA	ENST00000534948.1	+	0	1118_1119							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		CTATCAGTATAAAGACTGTAAG	0.337																																																0			10																																								97906331			9849			AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"Zinc fingers, C2H2-type"	29009	protein-coding gene	gene with protein product			"zinc finger protein 518"	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97916340_97916341delAA			97906330	A0PJI5|O15044|Q32MP4	Frame_Shift_Del	DEL	ENST00000534948.1	37																																																																																					0.337	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		-	97916341	AA	-	97916340	6	5	111	0	1	1	0	1	0	0	0	0	18001	352	13	0		0	ZNF518A	10	97916340	RNA	DEL	AA	TCGA-EI-6507-01A-11D-1733-10	129334	97916340	37618407	571	29705										
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99683051	99683051	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acacaggccacagagcgtccGgcaaagaggctggccacacc	12	15	0	2	rs150915829		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:99683051G>A	ENST00000370597.3	-	4	883	c.528C>T	c.(526-528)gcC>gcT	p.A176A	CRTAC1_ENST00000298819.4_Silent_p.A176A|CRTAC1_ENST00000370591.2_Silent_p.A176A	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	176						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CAGAGCGTCCGGCAAAGAGGC	0.592																																																0			10						G	,	1,4405	2.1+/-5.4	0,1,2202	78	62	67		528,528	-2.4	1	10	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	176/646,176/662	99683051	2,13004	2203	4300	6503	99673041	SO:0001819	synonymous_variant	55118			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.528C>T	10.37:g.99683051G>A			99673041	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																				0.592	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		A	99683051	G	A	99683051	2	1	111	1	0	0	0	0	0	0	0	1	3902	1103	39	1		1	CRTAC1	10	99683051	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1766711	99683051	35851696	572	29706										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101578954	101578954	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatcctacagtgctctcctgGccaaaaaaggagagtttgct	10	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:101578954G>T	ENST00000370449.4	+	19	2661	c.2548G>T	c.(2548-2550)Gcc>Tcc	p.A850S		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	850	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TGCTCTCCTGGCCAAAAAAGG	0.433																																																0			10											99	101	100					10																	101578954		2203	4300	6503	101568944	SO:0001583	missense	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.2548G>T	10.37:g.101578954G>T	ENSP00000359478:p.Ala850Ser		101568944	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	G	6.571	0.473585	0.12521	.	.	ENSG00000023839	ENST00000370449	T	0.78246	-1.16	5.45	5.45	0.79879	ABC transporter-like (1);	0.048372	0.85682	D	0.000000	T	0.57740	0.2074	N	0.04387	-0.21	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.54977	-0.8212	10	0.28530	T	0.3	-9.349	13.56	0.61784	0.0748:0.0:0.9252:0.0	.	850	Q92887	MRP2_HUMAN	S	850	ENSP00000359478:A850S	ENSP00000359478:A850S	A	+	1	0	ABCC2	101568944	1.000000	0.71417	0.979000	0.43373	0.015000	0.08874	3.665000	0.54532	2.543000	0.85770	0.561000	0.74099	GCC		0.433	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		T	101578954	G	T	101578954	3	4	111	1	0	0	0	0	1	0	0	0	53	1203	42	2	2622	2	ABCC2	10	101578954	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1895903	101578954	33955793	573	29707										
PDZD7	79955	hgsc.bcm.edu	37	chr10	102783745	102783745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggccatgctctgagccccCgcgcacgctgaagcccagcc	11	19	1	2	rs148695069		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:102783745C>T	ENST00000370215.3	-	3	532	c.307G>A	c.(307-309)Ggg>Agg	p.G103R	PDZD7_ENST00000470414.1_Missense_Mutation_p.G103R	NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	103	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		TCTGAGCCCCCGCGCACGCTG	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		21090	0		0	False		,,,				2504	0															0			10											99	91	94					10																	102783745		2203	4300	6503	102773735	SO:0001583	missense	79955			AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.307G>A	10.37:g.102783745C>T	ENSP00000359234:p.Gly103Arg		102773735	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737050	0.89482	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.25085	1.82	5.07	5.07	0.68467	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.59918	0.2229	M	0.89163	3.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.68712	-0.5336	10	0.87932	D	0	.	18.8027	0.92025	0.0:1.0:0.0:0.0	.	103;103	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	R	103	ENSP00000359234:G103R	ENSP00000359234:G103R	G	-	1	0	PDZD7	102773735	1.000000	0.71417	0.223000	0.23860	0.723000	0.41478	7.675000	0.84002	2.498000	0.84270	0.491000	0.48974	GGG		0.577	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		T	102783745	C	T	102783745	3	4	111	1	0	0	0	0	1	0	0	0	11735	652	23	1	1278	1	PDZD7	10	102783745	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1204791	102783745	32751002	574	29708										
TLX1	3195	hgsc.bcm.edu	37	chr10	102894060	102894060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggcctcggccgagcgcgccGccctggccaaggcgctcaaa	14	17	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:102894060G>A	ENST00000370196.6	+	2	2739	c.697G>A	c.(697-699)Gcc>Acc	p.A233T	RP11-31L23.3_ENST00000411459.1_RNA|TLX1_ENST00000467928.2_Missense_Mutation_p.A233T			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	233					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CGAGCGCGCCGCCCTGGCCAA	0.657			T	"TRB@, TRD@"	T-ALL																																		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	0			10											26	27	27					10																	102894060		2198	4298	6496	102884050	SO:0001583	missense	3195			M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"Homeoboxes / ANTP class : NKL subclass"	5056	protein-coding gene	gene with protein product	"Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)", "homeo box 11 (T-cell lymphoma 3-associated breakpoint)"	186770	"homeo box 11 (T-cell lymphoma 3-associated breakpoint)", "T-cell leukemia, homeobox 1"	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.697G>A	10.37:g.102894060G>A	ENSP00000359215:p.Ala233Thr		102884050	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Missense_Mutation	SNP	ENST00000370196.6	37	CCDS7510.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180111	0.94846	.	.	ENSG00000107807	ENST00000370196;ENST00000467928	D;D	0.96200	-3.94;-3.94	5.8	5.8	0.92144	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.049134	0.85682	D	0.000000	D	0.92896	0.7740	N	0.11427	0.14	0.80722	D	1	D	0.56521	0.976	P	0.50490	0.642	D	0.93637	0.6961	10	0.51188	T	0.08	.	20.0537	0.97638	0.0:0.0:1.0:0.0	.	233	P31314	TLX1_HUMAN	T	233	ENSP00000359215:A233T;ENSP00000434914:A233T	ENSP00000359215:A233T	A	+	1	0	TLX1	102884050	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.176000	0.58269	2.758000	0.94735	0.561000	0.74099	GCC		0.657	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		A	102894060	G	A	102894060	3	1	111	1	0	0	0	0	1	0	0	0	15998	1087	38	1	703	1	TLX1	10	102894060	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	110315	102894060	32640687	575	29709										
CALHM1	255022	hgsc.bcm.edu	37	chr10	105217977	105217977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagatgcagcggaggtaacGcacggccacctctcgggcca	15	13	1	1	rs368218776		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:105217977G>A	ENST00000329905.5	-	1	668	c.532C>T	c.(532-534)Cgt>Tgt	p.R178C	RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	178					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CGGAGGTAACGCACGGCCACC	0.692																																																0			10						G	CYS/ARG	1,4405		0,1,2202	40	49	46		532	4.6	1	10		46	0,8594		0,0,4297	no	missense	CALHM1	NM_001001412.3	180	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	178/347	105217977	1,12999	2203	4297	6500	105207967	SO:0001583	missense	255022			BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"family with sequence similarity 26, member C"	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.532C>T	10.37:g.105217977G>A	ENSP00000329926:p.Arg178Cys		105207967	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	37	CCDS7550.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.778742	0.70107	2.27E-4	0.0	ENSG00000185933	ENST00000329905	T	0.19669	2.13	5.49	4.55	0.56014	.	0.048431	0.85682	D	0.000000	T	0.47173	0.1431	M	0.80183	2.485	0.58432	D	0.999999	D	0.89917	1.0	D	0.74023	0.982	T	0.49899	-0.8890	10	0.66056	D	0.02	-41.0963	13.6457	0.62279	0.0:0.0:0.7409:0.2591	.	178	Q8IU99	CAHM1_HUMAN	C	178	ENSP00000329926:R178C	ENSP00000329926:R178C	R	-	1	0	CALHM1	105207967	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	1.389000	0.34453	2.582000	0.87167	0.462000	0.41574	CGT		0.692	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		A	105217977	G	A	105217977	3	1	111	1	0	0	0	0	1	0	0	0	2588	1087	38	1	516	1	CALHM1	10	105217977	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2323917	105217977	30316770	576	29710										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105793886	105793886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcagcttcaccaaaggcacCgcctgcacccagggagcctg	11	16	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:105793886C>T	ENST00000353479.5	-	52	4263	c.3973G>A	c.(3973-3975)Ggt>Agt	p.G1325S	COL17A1_ENST00000369733.3_Missense_Mutation_p.G1243S	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1325	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CCAAAGGCACCGCCTGCACCC	0.632																																																0			10											46	44	45					10																	105793886		2203	4300	6503	105783876	SO:0001583	missense	1308			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.3973G>A	10.37:g.105793886C>T	ENSP00000340937:p.Gly1325Ser		105783876	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.597750	0.28445	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	T;D	0.90844	-0.77;-2.74	4.66	4.66	0.58398	.	0.414645	0.17976	N	0.155686	T	0.81851	0.4910	N	0.16368	0.405	0.80722	D	1	P	0.43662	0.814	B	0.32583	0.148	D	0.85338	0.1094	10	0.72032	D	0.01	-0.2304	15.726	0.77761	0.0:1.0:0.0:0.0	.	1325	Q9UMD9	COHA1_HUMAN	S	1325;1243	ENSP00000340937:G1325S;ENSP00000358748:G1243S	ENSP00000340937:G1325S	G	-	1	0	COL17A1	105783876	0.007000	0.16637	0.590000	0.28732	0.003000	0.03518	1.397000	0.34543	2.148000	0.66965	0.561000	0.74099	GGT		0.632	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		T	105793886	C	T	105793886	3	4	111	1	0	0	0	0	1	0	0	0	3680	652	23	1	540	1	COL17A1	10	105793886	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	575909	105793886	29740861	577	29711										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108489870	108489870	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctttatttgaccccatcacaGacctaaaaaatggagaaaca	5	10	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:108489870G>A	ENST00000263054.6	-	6	969	c.962C>T	c.(961-963)tCt>tTt	p.S321F	SORCS1_ENST00000344440.6_Missense_Mutation_p.S321F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	321					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CCCCATCACAGACCTAAAAAA	0.408																																																0			10											106	90	95					10																	108489870		2203	4300	6503	108479860	SO:0001583	missense	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.962C>T	10.37:g.108489870G>A	ENSP00000263054:p.Ser321Phe		108479860	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.093322	0.76756	.	.	ENSG00000108018	ENST00000263054;ENST00000344440	T;T	0.40756	1.02;1.02	5.89	5.89	0.94794	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	M	0.68952	2.095	0.48571	D	0.999671	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.79784	0.984;0.986;0.993;0.984;0.993	T	0.60239	-0.7302	9	.	.	.	-16.645	15.7619	0.78091	0.0:0.0:1.0:0.0	.	321;321;321;321;321	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	F	321	ENSP00000263054:S321F;ENSP00000345964:S321F	.	S	-	2	0	SORCS1	108479860	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.353000	0.66034	2.793000	0.96121	0.655000	0.94253	TCT		0.408	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108489870	G	A	108489870	3	1	111	1	0	0	0	0	1	0	0	0	14967	942	33	3	2862	3	SORCS1	10	108489870	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2695984	108489870	27044877	578	29712										
ACSL5	51703	hgsc.bcm.edu	37	chr10	114176724	114176724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtaaattcaaagagcttcaaAagggtatcatcaggcatgat	9	6	4	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:114176724A>G	ENST00000393081.1	+	13	1469	c.1162A>G	c.(1162-1164)Aag>Gag	p.K388E	ACSL5_ENST00000433418.1_Missense_Mutation_p.K388E|ACSL5_ENST00000356116.1_Missense_Mutation_p.K444E|RP11-324O2.6_ENST00000424422.1_RNA|ACSL5_ENST00000354655.4_Missense_Mutation_p.K388E|ACSL5_ENST00000369410.3_Missense_Mutation_p.K170E|ACSL5_ENST00000354273.4_Missense_Mutation_p.K388E	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	388			K -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		AGAGCTTCAAAAGGGTATCAT	0.463																																																0			10											120	114	116					10																	114176724		2203	4300	6503	114166714	SO:0001583	missense	51703			AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"Acyl-CoA synthetase family"	16526	protein-coding gene	gene with protein product	"FACL5 for fatty acid coenzyme A ligase 5", "long-chain acyl-CoA synthetase 5", "long-chain fatty acid coenzyme A ligase 5", "fatty-acid-Coenzyme A ligase, long-chain 5"	605677	"fatty-acid-Coenzyme A ligase, long-chain 5"	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.1162A>G	10.37:g.114176724A>G	ENSP00000376796:p.Lys388Glu		114166714	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	.	.	.	.	.	.	.	.	.	.	A	4.529	0.098208	0.08681	.	.	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273;ENST00000369410	T;T;T;T;T;T	0.39997	1.82;1.82;1.81;1.05;1.82;1.5	5.79	3.48	0.39840	AMP-dependent synthetase/ligase (1);	0.613940	0.18293	N	0.145668	T	0.29620	0.0739	N	0.25144	0.715	0.25009	N	0.991418	B;B;B;B	0.25955	0.001;0.001;0.138;0.014	B;B;B;B	0.27170	0.008;0.004;0.077;0.053	T	0.17930	-1.0353	10	0.36615	T	0.2	-0.7129	11.8005	0.52124	0.4652:0.5347:0.0:0.0	.	170;388;444;388	B4DX30;A6GV77;Q9ULC5-3;Q9ULC5	.;.;.;ACSL5_HUMAN	E	388;388;444;388;388;170	ENSP00000346680:K388E;ENSP00000376796:K388E;ENSP00000348429:K444E;ENSP00000403647:K388E;ENSP00000346223:K388E;ENSP00000358418:K170E	ENSP00000346223:K388E	K	+	1	0	ACSL5	114166714	0.991000	0.36638	0.476000	0.27291	0.003000	0.03518	1.347000	0.33975	1.011000	0.39340	-0.323000	0.08544	AAG		0.463	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234		G	114176724	A	G	114176724	3	3	111	1	0	0	0	0	1	0	0	0	180	15	1	4	1380	4	ACSL5	10	114176724	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5686854	114176724	21358023	579	29713										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117154169	117154169	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attttggttttgacttacagCttgtacatgcagtggccatg	10	7	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:117154169C>T	ENST00000355044.3	+	20	3302	c.3176C>T	c.(3175-3177)gCt>gTt	p.A1059V	ATRNL1_ENST00000423111.2_Splice_Site_p.A110V|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1059	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.A1059G(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGACTTACAGCTTGTACATGC	0.333																																																1	Substitution - Missense(1)	ovary(1)	10											136	123	127					10																	117154169		2203	4300	6503	117144159	SO:0001630	splice_region_variant	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3176-1C>T	10.37:g.117154169C>T			117144159	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.592994	0.66219	.	.	ENSG00000107518	ENST00000355044;ENST00000423111	T;T	0.63580	-0.05;1.82	5.61	5.61	0.85477	EGF-like, laminin (2);	0.097167	0.64402	D	0.000001	T	0.69142	0.3078	L	0.35542	1.07	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	T	0.66396	-0.5934	9	.	.	.	.	15.1377	0.72583	0.0:1.0:0.0:0.0	.	110;1059	B4DH41;Q5VV63	.;ATRN1_HUMAN	V	1059;110	ENSP00000347152:A1059V;ENSP00000409624:A110V	.	A	+	2	0	ATRNL1	117144159	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.442000	0.59988	2.640000	0.89533	0.655000	0.94253	GCT		0.333	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	Missense_Mutation	T	117154169	C	T	117154169	5	4	111	1	0	0	0	0	0	0	1	0	1208	811	28	3	3254	3	ATRNL1	10	117154169	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2977445	117154169	18380578	580	29714										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118231354	118231354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgtctttcttcgtgtaggcGgggcagttaggaaaactggg	15	7	2	0	rs61729308		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:118231354G>A	ENST00000369230.3	+	10	1281	c.1135G>A	c.(1135-1137)Ggg>Agg	p.G379R		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	379	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		TCGTGTAGGCGGGGCAGTTAG	0.473																																																0			10											145	154	151					10																	118231354		2203	4300	6503	118221344	SO:0001583	missense	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1135G>A	10.37:g.118231354G>A	ENSP00000358232:p.Gly379Arg		118221344		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.330278	0.60743	.	.	ENSG00000203837	ENST00000369230	D	0.88741	-2.42	4.18	4.18	0.49190	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.329027	0.21304	N	0.076742	D	0.94241	0.8151	M	0.82517	2.595	0.09310	N	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.87864	0.2666	10	0.87932	D	0	.	14.0858	0.64954	0.0:0.0:1.0:0.0	rs61729308	379	Q17RR3	LIPR3_HUMAN	R	379	ENSP00000358232:G379R	ENSP00000358232:G379R	G	+	1	0	PNLIPRP3	118221344	0.997000	0.39634	0.079000	0.20413	0.018000	0.09664	4.017000	0.57167	2.279000	0.76181	0.591000	0.81541	GGG		0.473	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		A	118231354	G	A	118231354	3	1	111	1	0	0	0	0	1	0	0	0	12183	1116	39	1	1173	1	PNLIPRP3	10	118231354	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1077185	118231354	17303393	581	29715										
INPP5F	22876	hgsc.bcm.edu	37	chr10	121582687	121582687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acacattgcgagctgtaatgCgtaatcctgaagaggatgga	12	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:121582687C>T	ENST00000361976.2	+	18	2303	c.2137C>T	c.(2137-2139)Cgt>Tgt	p.R713C	INPP5F_ENST00000490818.1_3'UTR|INPP5F_ENST00000369080.3_Missense_Mutation_p.R103C	NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0					cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AGCTGTAATGCGTAATCCTGA	0.408																																																0			10											96	89	91					10																	121582687		2203	4300	6503	121572677	SO:0001583	missense	22876			AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.2137C>T	10.37:g.121582687C>T	ENSP00000354519:p.Arg713Cys		121572677	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	37	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.523704	0.85600	.	.	ENSG00000198825	ENST00000361976;ENST00000369080	T;T	0.52526	0.95;0.66	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.61912	0.2385	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.926	T	0.58923	-0.7550	10	0.52906	T	0.07	-16.5405	20.8598	0.99761	0.0:1.0:0.0:0.0	.	103;713	Q5W135;Q9Y2H2	.;SAC2_HUMAN	C	713;103	ENSP00000354519:R713C;ENSP00000358076:R103C	ENSP00000354519:R713C	R	+	1	0	INPP5F	121572677	1.000000	0.71417	0.945000	0.38365	0.448000	0.32197	7.786000	0.85741	2.937000	0.99478	0.650000	0.86243	CGT		0.408	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		T	121582687	C	T	121582687	3	4	111	1	0	0	0	0	1	0	0	0	7779	768	27	1	2207	1	INPP5F	10	121582687	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3351333	121582687	13952060	582	29716										
DHX32	55760	hgsc.bcm.edu	37	chr10	127527574	127527574	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccccaccccttctcacctgcAtaaagtaaccggacagaaga	6	16	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:127527574A>G	ENST00000284690.3	-	9	2367	c.1877T>C	c.(1876-1878)aTg>aCg	p.M626T	BCCIP_ENST00000429863.2_Intron|DHX32_ENST00000368721.1_Missense_Mutation_p.M250T|BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000284688.6_Missense_Mutation_p.M545T|BCCIP_ENST00000299130.3_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	626						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TCTCACCTGCATAAAGTAACC	0.448																																																0			10											230	230	230					10																	127527574		2203	4300	6503	127517564	SO:0001583	missense	55760				CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1877T>C	10.37:g.127527574A>G	ENSP00000284690:p.Met626Thr		127517564	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation	SNP	ENST00000284690.3	37	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.632323	0.67015	.	.	ENSG00000089876	ENST00000368721;ENST00000284690;ENST00000284688	T;T;T	0.17213	2.29;4.09;3.79	5.02	5.02	0.67125	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.27765	0.0683	M	0.84585	2.705	0.80722	D	1	B	0.33940	0.433	B	0.34093	0.175	T	0.15896	-1.0421	10	0.87932	D	0	-43.1841	14.0776	0.64900	1.0:0.0:0.0:0.0	.	626	Q7L7V1	DHX32_HUMAN	T	250;626;545	ENSP00000357710:M250T;ENSP00000284690:M626T;ENSP00000284688:M545T	ENSP00000284688:M545T	M	-	2	0	DHX32	127517564	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.051000	0.76627	2.099000	0.63709	0.533000	0.62120	ATG		0.448	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		G	127527574	A	G	127527574	3	3	111	1	0	0	0	0	1	0	0	0	4516	217	8	4	366	4	DHX32	10	127527574	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5944887	127527574	8007173	583	29717										
PTPRE	5791	hgsc.bcm.edu	37	chr10	129868630	129868630	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacggggacacagagctggaCgtgtcctccctggagaagca	14	11	0	2	rs140843679		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:129868630C>T	ENST00000254667.3	+	14	1488	c.1209C>T	c.(1207-1209)gaC>gaT	p.D403D	PTPRE_ENST00000306042.5_Silent_p.D345D|PTPRE_ENST00000419012.2_Silent_p.D403D	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	403					negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	CAGAGCTGGACGTGTCCTCCC	0.587																																					Colon(52;977 1184 20575 41685)											0			10						T	,	1,4405	2.1+/-5.4	0,1,2202	137	105	116		1209,1035	-1.7	1	10	dbSNP_134	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PTPRE	NM_006504.4,NM_130435.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	403/701,345/643	129868630	1,13005	2203	4300	6503	129758620	SO:0001819	synonymous_variant	5791			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1209C>T	10.37:g.129868630C>T			129758620	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																				0.587	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			T	129868630	C	T	129868630	2	4	111	1	0	0	0	0	0	0	0	1	12837	535	19	1		1	PTPRE	10	129868630	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2341056	129868630	5666117	584	29718										
MKI67	4288	hgsc.bcm.edu	37	chr10	129903302	129903302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctcctgctggtttgggtgTgtccatagctttccctactg	10	12	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:129903302T>C	ENST00000368654.3	-	13	7177	c.6802A>G	c.(6802-6804)Aca>Gca	p.T2268A	MKI67_ENST00000368653.3_Missense_Mutation_p.T1908A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2268	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGTTTGGGTGTGTCCATAGCT	0.473																																																0			10											301	273	282					10																	129903302		2203	4300	6503	129793292	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6802A>G	10.37:g.129903302T>C	ENSP00000357643:p.Thr2268Ala		129793292	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053516	0.36181	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03065	4.06;4.06	2.91	0.477	0.16784	.	0.419884	0.17486	N	0.172501	T	0.06325	0.0163	M	0.63843	1.955	0.09310	N	1	P;D;D	0.55800	0.762;0.961;0.973	B;P;P	0.56163	0.348;0.793;0.754	T	0.22977	-1.0201	10	0.08599	T	0.76	.	2.4224	0.04451	0.3502:0.0:0.21:0.4398	.	2267;1908;2268	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	2268;1908;2267	ENSP00000357643:T2268A;ENSP00000357642:T1908A	ENSP00000357642:T1908A	T	-	1	0	MKI67	129793292	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.759000	0.01808	0.301000	0.22738	0.533000	0.62120	ACA		0.473	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129903302	T	C	129903302	3	2	111	1	0	0	0	0	1	0	0	0	9628	1696	59	4	2980	4	MKI67	10	129903302	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	34672	129903302	5631445	585	29719										
MKI67	4288	hgsc.bcm.edu	37	chr10	129906252	129906252	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatggcattagattcctgcaCgctaagagttctccctctac	8	12	2	2	rs141076241	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:129906252C>T	ENST00000368654.3	-	13	4227	c.3852G>A	c.(3850-3852)gcG>gcA	p.A1284A	MKI67_ENST00000368653.3_Silent_p.A924A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1284	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.A1284A(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GATTCCTGCACGCTAAGAGTT	0.498													T|||	2	0.000399361	0	0	5008	,	,		21875	0		0	False		,,,				2504	0.002															1	Substitution - coding silent(1)	large_intestine(1)	10						T	,	0,4406		0,0,2203	263	247	253		2772,3852	-2.8	0	10	dbSNP_134	253	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	924/2897,1284/3257	129906252	2,13004	2203	4300	6503	129796242	SO:0001819	synonymous_variant	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3852G>A	10.37:g.129906252C>T			129796242	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																				0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129906252	C	T	129906252	2	4	111	1	0	0	0	0	0	0	0	1	9628	523	19	1		1	MKI67	10	129906252	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2950	129906252	5628495	586	29720										
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134013933	134013933	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactactggagcaagaactgGgccaaggccgcagccttcgt	12	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:134013933G>T	ENST00000338492.4	+	9	1049	c.885G>T	c.(883-885)tgG>tgT	p.W295C	DPYSL4_ENST00000368629.1_Missense_Mutation_p.W195C|DPYSL4_ENST00000368627.1_Missense_Mutation_p.W195C	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	295					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		GCAAGAACTGGGCCAAGGCCG	0.647																																																0			10											133	119	124					10																	134013933		2203	4300	6503	133863923	SO:0001583	missense	10570			AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.885G>T	10.37:g.134013933G>T	ENSP00000339850:p.Trp295Cys		133863923	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Missense_Mutation	SNP	ENST00000338492.4	37	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.918813	0.73098	.	.	ENSG00000151640	ENST00000338492;ENST00000368629;ENST00000368627	D;D;D	0.90133	-2.62;-2.62;-2.62	4.58	3.68	0.42216	Amidohydrolase 1 (1);	0.138738	0.52532	D	0.000068	D	0.95987	0.8693	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96546	0.9404	10	0.87932	D	0	-23.1401	12.8327	0.57754	0.0792:0.0:0.9208:0.0	.	295	O14531	DPYL4_HUMAN	C	295;195;195	ENSP00000339850:W295C;ENSP00000357618:W195C;ENSP00000357616:W195C	ENSP00000339850:W295C	W	+	3	0	DPYSL4	133863923	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.118000	0.94355	1.304000	0.44892	0.555000	0.69702	TGG		0.647	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			T	134013933	G	T	134013933	3	4	111	1	0	0	0	0	1	0	0	0	4760	1241	43	2	919	2	DPYSL4	10	134013933	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4107681	134013933	1520814	587	29721										
KNDC1	85442	hgsc.bcm.edu	37	chr10	134999821	134999821	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggccaccctctgcctgccGctgacccgcgggaaaagcca	12	17	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:134999821G>A	ENST00000304613.3	+	6	990	c.969G>A	c.(967-969)ccG>ccA	p.P323P	KNDC1_ENST00000368572.2_Silent_p.P323P|KNDC1_ENST00000368571.2_Silent_p.P258P			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	323					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TCTGCCTGCCGCTGACCCGCG	0.622																																																0			10											17	19	19					10																	134999821		2198	4294	6492	134849811	SO:0001819	synonymous_variant	85442			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.969G>A	10.37:g.134999821G>A			134849811	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																				0.622	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	134999821	G	A	134999821	2	1	111	1	0	0	0	0	0	0	0	1	8447	1074	38	1		1	KNDC1	10	134999821	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	985888	134999821	534926	588	29722										
ECHS1	1892	hgsc.bcm.edu	37	chr10	135179533	135179534	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aattttagaattgctggcaaINSttttttctgcacactggatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr10:135179533_135179534insT	ENST00000368547.3	-	6	1040_1041	c.685_686insA	c.(685-687)attfs	p.I229fs		NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	229					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		ATTGCTGGCAATTTTTTCTGCA	0.47																																					GBM(132;1720 1771 5373 10277 21402)											0			10																																								135029524	SO:0001589	frameshift_variant	1892				CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.686dupA	10.37:g.135179539_135179539dupT	ENSP00000357535:p.Ile229fs		135029523	O00739|Q5VWY1|Q96H54	Frame_Shift_Ins	INS	ENST00000368547.3	37	CCDS7681.1																																																																																				0.47	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			T	135179534	-	T	135179533	7	5	111	1	0	1	1	0	0	0	0	0	4907	101	4	0	198	0	ECHS1	10	135179533	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	179712	135179533	355214	589	29723										
ODF3	113746	hgsc.bcm.edu	37	chr11	199942	199942	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcatagcccctcctctcccAggtgaccctgaccaagccct	6	19	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:199942A>G	ENST00000325113.4	+	7	992		c.e7-1		ODF3_ENST00000525282.1_Splice_Site|BET1L_ENST00000410108.1_Intron	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)				biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTCCTCTCCCAGGTGACCCTG	0.622																																																0			11											109	81	90					11																	199942		2203	4300	6503	189942	SO:0001630	splice_region_variant	113746			AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"cancer/testis antigen 135"	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.676-1A>G	11.37:g.199942A>G			189942	B7ZLT0|Q69YX0	Splice_Site	SNP	ENST00000325113.4	37	CCDS7688.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497708	0.64186	.	.	ENSG00000177947	ENST00000325113;ENST00000540150;ENST00000525282	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9361	0.47247	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ODF3	189942	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.735000	0.55044	2.072000	0.62099	0.454000	0.30748	.		0.622	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1		Intron	G	199942	A	G	199942	5	3	111	1	0	0	0	0	0	0	1	0	10860	202	7	4	696	4	ODF3	11	199942	Splice_Site	SNP	A	TCGA-EI-6507-01A-11D-1733-10		199942	134806574	590	29724										
OR52E2	119678	hgsc.bcm.edu	37	chr11	5080306	5080306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caagatagatgagcaagaccCatgtgctcacagtaggtgtg	12	8	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:5080306C>A	ENST00000321522.2	-	1	551	c.552G>T	c.(550-552)atG>atT	p.M184I		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		GAGCAAGACCCATGTGCTCAC	0.398																																																0			11											91	83	86					11																	5080306		2201	4298	6499	5036882	SO:0001583	missense	119678			AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"GPCR / Class A : Olfactory receptors"	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.552G>T	11.37:g.5080306C>A	ENSP00000322088:p.Met184Ile		5036882		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.962624	0.34659	.	.	ENSG00000176787	ENST00000321522	T	0.00069	8.77	3.76	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	T	0.00241	0.0007	M	0.78049	2.395	0.09310	N	0.999998	P	0.43392	0.805	P	0.44811	0.461	T	0.37361	-0.9709	10	0.38643	T	0.18	.	10.8757	0.46909	0.0:0.9037:0.0:0.0963	.	184	Q8NGJ4	O52E2_HUMAN	I	184	ENSP00000322088:M184I	ENSP00000322088:M184I	M	-	3	0	OR52E2	5036882	0.000000	0.05858	0.993000	0.49108	0.765000	0.43378	0.433000	0.21477	1.197000	0.43143	0.644000	0.83932	ATG		0.398	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		A	5080306	C	A	5080306	3	1	111	1	0	0	0	0	1	0	0	0	11146	594	21	2	428	2	OR52E2	11	5080306	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4880364	5080306	129926210	591	29725										
OR51B2	79345	hgsc.bcm.edu	37	chr11	5345234	5345234	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggagtgaataaagtaagcCtgtaggaagcagcccacact	12	8	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:5345234C>A	ENST00000328813.2	-	1	348	c.294G>T	c.(292-294)caG>caT	p.Q98H	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAAAGTAAGCCTGTAGGAAGC	0.478																																																0			11											89	75	80					11																	5345234		2201	4297	6498	5301810	SO:0001583	missense	79345			AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"GPCR / Class A : Olfactory receptors"	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.294G>T	11.37:g.5345234C>A	ENSP00000327540:p.Gln98His		5301810	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	.	.	.	.	.	.	.	.	.	.	C	7.625	0.677544	0.14841	.	.	ENSG00000184881	ENST00000328813	T	0.00472	7.19	4.39	-2.26	0.06867	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36482	U	0.002564	T	0.00845	0.0028	H	0.98133	4.155	0.27359	N	0.956016	B	0.31859	0.343	B	0.33620	0.167	T	0.32903	-0.9889	10	0.87932	D	0	.	5.475	0.16690	0.1244:0.498:0.0:0.3776	.	98	Q9Y5P1	O51B2_HUMAN	H	98	ENSP00000327540:Q98H	ENSP00000327540:Q98H	Q	-	3	2	OR51B2	5301810	0.011000	0.17503	0.065000	0.19835	0.141000	0.21300	0.183000	0.16919	-0.337000	0.08426	-0.152000	0.13540	CAG		0.478	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180		A	5345234	C	A	5345234	3	1	111	1	0	0	0	0	1	0	0	0	11120	680	24	2	648	2	OR51B2	11	5345234	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	264928	5345234	129661282	592	29726										
OR52B6	340980	hgsc.bcm.edu	37	chr11	5602883	5602883	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctccaaggccctgagtacCtgtggatcccatatctgtgt	10	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:5602883C>A	ENST00000345043.2	+	1	777	c.777C>A	c.(775-777)acC>acA	p.T259T	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCCTGAGTACCTGTGGATCCC	0.507																																																0			11											243	256	252					11																	5602883		1997	4171	6168	5559459	SO:0001819	synonymous_variant	340980			AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.777C>A	11.37:g.5602883C>A			5559459	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																				0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		A	5602883	C	A	5602883	2	1	111	1	0	0	0	0	0	0	0	1	11144	668	24	2		2	OR52B6	11	5602883	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	257649	5602883	129403633	593	29727										
CCKBR	887	hgsc.bcm.edu	37	chr11	6291979	6291979	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acttagggcttcgctttgacGgcgacagtgacagcgacagc	13	11	0	2	rs375063663		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6291979G>T	ENST00000334619.2	+	4	950	c.757G>T	c.(757-759)Ggc>Tgc	p.G253C	CCKBR_ENST00000525462.1_Missense_Mutation_p.G253C|CCKBR_ENST00000532715.1_Missense_Mutation_p.G169C	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	253					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		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)	TCGCTTTGACGGCGACAGTGA	0.602																																																0			11											107	83	91					11																	6291979		2201	4296	6497	6248555	SO:0001583	missense	887			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.757G>T	11.37:g.6291979G>T	ENSP00000335544:p.Gly253Cys		6248555	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959526	0.34565	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.72282	-0.64;-0.64;-0.64	5.66	-3.56	0.04626	GPCR, rhodopsin-like superfamily (1);	0.894418	0.09798	N	0.754401	T	0.68522	0.3010	L	0.58510	1.815	0.09310	N	1	P;B;B	0.41784	0.762;0.271;0.317	P;B;P	0.47346	0.544;0.348;0.479	T	0.63386	-0.6649	10	0.44086	T	0.13	.	9.3392	0.38069	0.6134:0.103:0.2835:0.0	.	253;187;253	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	C	253;169;253	ENSP00000335544:G253C;ENSP00000432079:G169C;ENSP00000435534:G253C	ENSP00000335544:G253C	G	+	1	0	CCKBR	6248555	0.140000	0.22579	0.004000	0.12327	0.765000	0.43378	0.408000	0.21065	-0.483000	0.06772	-0.440000	0.05779	GGC		0.602	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		T	6291979	G	T	6291979	3	4	111	1	0	0	0	0	1	0	0	0	2887	1116	39	2	771	2	CCKBR	11	6291979	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	689096	6291979	128714537	594	29728										
APBB1	322	hgsc.bcm.edu	37	chr11	6417179	6417179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacgcacccgacactctcccAgcactgcctctgtctgcatg	7	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6417179A>G	ENST00000609360.1	-	14	1901	c.1802T>C	c.(1801-1803)cTg>cCg	p.L601P	APBB1_ENST00000526240.1_5'UTR|APBB1_ENST00000311051.3_Missense_Mutation_p.L599P|APBB1_ENST00000299402.6_Missense_Mutation_p.L599P|APBB1_ENST00000529519.1_Missense_Mutation_p.L126P|APBB1_ENST00000608645.1_Missense_Mutation_p.L342P|APBB1_ENST00000389906.2_Missense_Mutation_p.L601P|APBB1_ENST00000608704.1_Missense_Mutation_p.L342P|APBB1_ENST00000609331.1_Missense_Mutation_p.L366P|APBB1_ENST00000530885.1_Missense_Mutation_p.L379P|APBB1_ENST00000608655.1_Missense_Mutation_p.L381P|APBB1_ENST00000608394.1_Missense_Mutation_p.L342P	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	601	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		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)		ACACTCTCCCAGCACTGCCTC	0.577																																					GBM(147;1810 2556 5672 39622)											0			11											76	77	77					11																	6417179		2201	4296	6497	6373755	SO:0001583	missense	322			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1802T>C	11.37:g.6417179A>G	ENSP00000477213:p.Leu601Pro		6373755	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	A	13.89	2.371091	0.42003	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906;ENST00000539758;ENST00000536523;ENST00000544288;ENST00000530885	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	4.9	4.9	0.64082	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.64402	D	0.000017	T	0.49779	0.1577	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.994;0.988	T	0.54282	-0.8317	10	0.87932	D	0	-8.6947	12.4735	0.55799	1.0:0.0:0.0:0.0	.	601;379;599	O00213;B7Z2Y0;O00213-2	APBB1_HUMAN;.;.	P	599;599;601;450;342;366;379	ENSP00000299402:L599P;ENSP00000311912:L599P;ENSP00000374556:L601P;ENSP00000433338:L379P	ENSP00000299402:L599P	L	-	2	0	APBB1	6373755	1.000000	0.71417	0.997000	0.53966	0.128000	0.20619	7.257000	0.78362	1.836000	0.53414	0.477000	0.44152	CTG		0.577	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		G	6417179	A	G	6417179	3	3	111	1	0	0	0	0	1	0	0	0	759	188	7	4	338	4	APBB1	11	6417179	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	125200	6417179	128589337	595	29729										
TRIM3	10612	hgsc.bcm.edu	37	chr11	6477620	6477620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctacgcactgccttctggcGcacatggctgccggggccgc	13	17	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6477620G>A	ENST00000525074.1	-	6	1730	c.1336C>T	c.(1336-1338)Cgc>Tgc	p.R446C	TRIM3_ENST00000345851.3_Missense_Mutation_p.R446C|TRIM3_ENST00000537602.1_Missense_Mutation_p.R368C|TRIM3_ENST00000529058.1_Intron|TRIM3_ENST00000536344.1_Missense_Mutation_p.R327C|TRIM3_ENST00000359518.3_Missense_Mutation_p.R446C	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	446					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCCTTCTGGCGCACATGGCTG	0.647																																					Melanoma(6;5 510 1540 25169 29084)											0			11											49	46	47					11																	6477620		2201	4296	6497	6434196	SO:0001583	missense	10612			AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1336C>T	11.37:g.6477620G>A	ENSP00000433102:p.Arg446Cys		6434196	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	37	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468449	0.63625	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;D	0.84146	-0.67;-0.67;-0.87;-0.67;-1.81	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.86560	0.5962	L	0.27053	0.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.68943	0.961;0.95;0.953	D	0.87090	0.2172	10	0.56958	D	0.05	-20.7659	13.2185	0.59873	0.0:0.0:0.8408:0.1592	.	327;327;446	F5H2Q8;D3DQT4;O75382	.;.;TRIM3_HUMAN	C	446;446;446;446;435;368;446;327	ENSP00000433102:R446C;ENSP00000340797:R446C;ENSP00000441091:R368C;ENSP00000352508:R446C;ENSP00000445460:R327C	ENSP00000337094:R435C	R	-	1	0	TRIM3	6434196	0.005000	0.15991	1.000000	0.80357	0.996000	0.88848	0.654000	0.24918	2.648000	0.89879	0.563000	0.77884	CGC		0.647	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		A	6477620	G	A	6477620	3	1	111	1	0	0	0	0	1	0	0	0	16544	1087	38	1	926	1	TRIM3	11	6477620	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	60441	6477620	128528896	596	29730										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6568740	6568740	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctggtgcctgcaacattgCgattcctcacctgccaaggt	9	13	2	0	rs368557562		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6568740C>T	ENST00000527990.2	+	19	6571	c.6571C>T	c.(6571-6573)Cga>Tga	p.R2191*	DNHD1_ENST00000254579.6_Nonsense_Mutation_p.R2191*			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2191					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TGCAACATTGCGATTCCTCAC	0.572																																																0			11						C	stop/ARG	0,1384		0,0,692	60	50	53		6571	2	0.1	11		53	1,3181		0,1,1590	no	stop-gained	DNHD1	NM_144666.2		0,1,2282	TT,TC,CC		0.0314,0.0,0.0219		2191/4754	6568740	1,4565	692	1591	2283	6525316	SO:0001587	stop_gained	144132			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.6571C>T	11.37:g.6568740C>T	ENSP00000436180:p.Arg2191*		6525316	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Nonsense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	43	9.873687	0.99285	0.0	3.14E-4	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000533649	.	.	.	6.17	2.04	0.26737	.	1.100630	0.06807	N	0.789664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	9.1967	0.37233	0.2904:0.4587:0.2509:0.0	.	.	.	.	X	2191;2191;482	.	ENSP00000254579:R2191X	R	+	1	2	DNHD1	6525316	0.000000	0.05858	0.131000	0.22000	0.047000	0.14425	-0.033000	0.12246	0.116000	0.18110	-0.165000	0.13383	CGA		0.572	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6568740	C	T	6568740	4	4	111	1	0	0	0	0	0	1	0	0	4679	760	27	1	6654	1	DNHD1	11	6568740	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	91120	6568740	128437776	597	29731										
RRP8	23378	hgsc.bcm.edu	37	chr11	6622647	6622648	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacacctctgtcttctctgtINSgggggcctcagctggggcct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6622647_6622648insG	ENST00000254605.6	-	3	765_766	c.648_649insC	c.(646-651)cccacafs	p.T217fs	RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000537806.1_5'Flank|RRP8_ENST00000534343.1_Intron|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000420936.2_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	217					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						GTCTTCTCTGTGGGGGCCTCAG	0.614																																																0			11																																								6579224	SO:0001589	frameshift_variant	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.649dupC	11.37:g.6622652_6622652dupG	ENSP00000254605:p.Thr217fs		6579223	Q7KZ78|Q9BVM6	Frame_Shift_Ins	INS	ENST00000254605.6	37	CCDS31411.1																																																																																				0.614	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		G	6622648	-	G	6622647	7	5	111	1	0	1	1	0	0	0	0	0	13727	1696	59	0	741	0	RRP8	11	6622647	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	53907	6622647	128383869	598	29732										
TAF10	6881	hgsc.bcm.edu	37	chr11	6633003	6633003	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcagtacgtaaaccccgttAgatatggccccctccggggg	13	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:6633003A>G	ENST00000299424.4	-	2	756	c.279T>C	c.(277-279)tcT>tcC	p.S93S	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'UTR	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa	93					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AAACCCCGTTAGATATGGCCC	0.642																																																0			11											21	25	24					11																	6633003		2201	4295	6496	6589579	SO:0001819	synonymous_variant	6881			U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402	ENST00000299424.4:c.279T>C	11.37:g.6633003A>G			6589579	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																				0.642	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284		G	6633003	A	G	6633003	2	3	111	1	0	0	0	0	0	0	0	1	15553	407	15	4		4	TAF10	11	6633003	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	10356	6633003	128373513	599	29733										
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7614411	7614411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtaatgaaacctaccaggaaCgcttggcacgtctagaaggg	12	9	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:7614411C>T	ENST00000299492.4	+	4	716	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	PPFIBP2_ENST00000533792.1_5'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	110					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTACCAGGAACGCTTGGCACG	0.433																																																0			11											108	100	103					11																	7614411		2201	4296	6497	7570987	SO:0001583	missense	8495			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.328C>T	11.37:g.7614411C>T	ENSP00000299492:p.Arg110Cys		7570987	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218038	0.79352	.	.	ENSG00000166387	ENST00000299492;ENST00000527790;ENST00000541115	T;T	0.52057	0.68;0.68	5.83	5.83	0.93111	.	0.000000	0.50627	D	0.000102	T	0.68366	0.2993	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.961	T	0.71341	-0.4622	10	0.87932	D	0	-14.7306	12.5428	0.56182	0.1663:0.8337:0.0:0.0	.	33;110	F5GWB0;Q8ND30	.;LIPB2_HUMAN	C	110;110;33	ENSP00000299492:R110C;ENSP00000434981:R110C	ENSP00000299492:R110C	R	+	1	0	PPFIBP2	7570987	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.891000	0.48617	2.761000	0.94854	0.650000	0.86243	CGC		0.433	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		T	7614411	C	T	7614411	3	4	111	1	0	0	0	0	1	0	0	0	12345	536	19	1	338	1	PPFIBP2	11	7614411	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	981408	7614411	127392105	600	29734										
DKK3	27122	hgsc.bcm.edu	37	chr11	11986055	11986055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcagcggcggcagccgcagGctccctcagcgccatctctt	12	17	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:11986055G>A	ENST00000396505.2	-	8	1247	c.1009C>T	c.(1009-1011)Cct>Tct	p.P337S	DKK3_ENST00000326932.4_Missense_Mutation_p.P337S|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000450094.2_Missense_Mutation_p.P309S|DKK3_ENST00000525493.1_Missense_Mutation_p.P351S	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	337					adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		GCAGCCGCAGGCTCCCTCAGC	0.572																																																0			11											78	101	93					11																	11986055		2201	4294	6495	11942631	SO:0001583	missense	27122			AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.1009C>T	11.37:g.11986055G>A	ENSP00000379762:p.Pro337Ser		11942631	A8K1I2|D3DQW1|Q9ULB7	Missense_Mutation	SNP	ENST00000396505.2	37	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455774	0.26161	.	.	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000450094	T;T;T;T	0.30981	2.22;2.22;2.2;1.51	5.53	3.63	0.41609	.	0.275863	0.32041	N	0.006674	T	0.27731	0.0682	L	0.47716	1.5	0.31625	N	0.649785	B;B;B	0.32829	0.386;0.267;0.267	B;B;B	0.34242	0.178;0.06;0.06	T	0.31364	-0.9946	10	0.62326	D	0.03	-0.3131	10.1785	0.42952	0.0:0.1477:0.6987:0.1536	.	351;309;337	F6SYF8;E7EUD0;Q9UBP4	.;.;DKK3_HUMAN	S	337;337;280;351;309	ENSP00000379762:P337S;ENSP00000314910:P337S;ENSP00000433112:P351S;ENSP00000398365:P309S	ENSP00000314910:P337S	P	-	1	0	DKK3	11942631	0.995000	0.38212	0.694000	0.30210	0.064000	0.16182	2.764000	0.47613	0.672000	0.31204	-0.181000	0.13052	CCT		0.572	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		A	11986055	G	A	11986055	3	1	111	1	0	0	0	0	1	0	0	0	4557	1203	42	3	47	3	DKK3	11	11986055	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4371644	11986055	123020461	601	29735										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17190789	17190789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gattgaagccattttggaatGcagcctgtttactgtaagta	10	6	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:17190789G>A	ENST00000265970.7	-	1	499	c.500C>T	c.(499-501)gCa>gTa	p.A167V	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	167					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ATTTTGGAATGCAGCCTGTTT	0.413																																																0			11											77	81	80					11																	17190789		2200	4293	6493	17147365	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.500C>T	11.37:g.17190789G>A	ENSP00000265970:p.Ala167Val		17147365	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.495425	0.44352	.	.	ENSG00000011405	ENST00000265970;ENST00000544896	T	0.63096	-0.02	5.53	3.66	0.41972	.	0.488658	0.24162	N	0.040977	T	0.42607	0.1210	N	0.14661	0.345	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.001	T	0.23655	-1.0182	10	0.51188	T	0.08	-1.7492	8.947	0.35764	0.2834:0.0:0.7166:0.0	.	167;167	F5H5W9;O00443	.;P3C2A_HUMAN	V	167	ENSP00000265970:A167V	ENSP00000265970:A167V	A	-	2	0	PIK3C2A	17147365	0.974000	0.33945	0.997000	0.53966	0.940000	0.58332	3.326000	0.52037	0.699000	0.31761	0.591000	0.81541	GCA		0.413	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		A	17190789	G	A	17190789	3	1	111	1	0	0	0	0	1	0	0	0	11940	1319	46	3	4688	3	PIK3C2A	11	17190789	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5204734	17190789	117815727	602	29736										
KCNC1	3746	hgsc.bcm.edu	37	chr11	17757801	17757801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcccagccgacgtgtgcggGccgctctacgaggaggagct	16	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:17757801G>A	ENST00000379472.3	+	1	282	c.252G>A	c.(250-252)ggG>ggA	p.G84G	KCNC1_ENST00000265969.6_Silent_p.G84G	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	84					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	ACGTGTGCGGGCCGCTCTACG	0.672																																																0			11											43	43	43					11																	17757801		2200	4292	6492	17714377	SO:0001819	synonymous_variant	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.252G>A	11.37:g.17757801G>A			17714377	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																				0.672	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		A	17757801	G	A	17757801	2	1	111	1	0	0	0	0	0	0	0	1	8035	1190	42	3		3	KCNC1	11	17757801	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	567012	17757801	117248715	603	29737										
MRGPRX4	117196	hgsc.bcm.edu	37	chr11	18195357	18195357	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcccagtcgcgtggctgaTttttttatgtgtggttctct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:18195357delT	ENST00000314254.3	+	1	974	c.554delT	c.(553-555)attfs	p.I185fs	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GCGTGGCTGATTTTTTTATGT	0.507																																																0			11											180	173	176					11																	18195357		2199	4293	6492	18151933	SO:0001589	frameshift_variant	117196			AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.554delT	11.37:g.18195357delT	ENSP00000314042:p.Ile185fs		18151933	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Frame_Shift_Del	DEL	ENST00000314254.3	37	CCDS7831.1																																																																																				0.507	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		-	18195357	T	-	18195357	7	5	111	1	0	1	0	1	0	0	0	0	9799	1493	52	0	556	0	MRGPRX4	11	18195357	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	437556	18195357	116811159	604	29738										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26714123	26714123	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaaaggtcactgttgccaAggcattgatgctggaagcca	11	10	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:26714123A>G	ENST00000396005.3	-	9	1375	c.1066T>C	c.(1066-1068)Ttg>Ctg	p.L356L	SLC5A12_ENST00000280467.6_Silent_p.L356L	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	356					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						ACTGTTGCCAAGGCATTGATG	0.488																																																0			11											99	86	90					11																	26714123		2203	4299	6502	26670699	SO:0001819	synonymous_variant	159963			BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1066T>C	11.37:g.26714123A>G			26670699	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																				0.488	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26714123	A	G	26714123	2	3	111	1	0	0	0	0	0	0	0	1	14701	69	3	4		4	SLC5A12	11	26714123	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	8518766	26714123	108292393	605	29739										
KIF18A	81930	hgsc.bcm.edu	37	chr11	28119255	28119255	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gactgagttgacgtttcatcAaaaacagcatcaaatacaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:28119255delA	ENST00000263181.6	-	2	530	c.240delT	c.(238-240)tttfs	p.F80fs		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	80	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						ACGTTTCATCAAAAACAGCAT	0.289																																																0			11											58	57	57					11																	28119255		2201	4298	6499	28075831	SO:0001589	frameshift_variant	81930			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.240delT	11.37:g.28119255delA	ENSP00000263181:p.Phe80fs		28075831	Q4VPE3|Q86VS5|Q9H0F3	Frame_Shift_Del	DEL	ENST00000263181.6	37	CCDS7867.1																																																																																				0.289	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		-	28119255	A	-	28119255	7	5	111	1	0	1	0	1	0	0	0	0	8301	127	5	0	2520	0	KIF18A	11	28119255	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	1405132	28119255	106887261	606	29740										
SLC1A2	6506	hgsc.bcm.edu	37	chr11	35302521	35302521	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcactggggatactggccgcGccgacgcttgccagggtggc	17	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:35302521G>A	ENST00000278379.3	-	9	1596	c.1314C>T	c.(1312-1314)ggC>ggT	p.G438G	SLC1A2_ENST00000395750.1_Silent_p.G429G|RP1-68D18.3_ENST00000532760.1_RNA|SLC1A2_ENST00000606205.1_Silent_p.G438G|SLC1A2_ENST00000395753.1_Silent_p.G429G|SLC1A2_ENST00000479543.1_5'UTR	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	438					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			TACTGGCCGCGCCGACGCTTG	0.562																																					NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)											0			11											36	37	37					11																	35302521		2202	4298	6500	35259097	SO:0001819	synonymous_variant	6506			AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.1314C>T	11.37:g.35302521G>A			35259097	B4DQE9|Q14417|Q541G6|U3KQQ4	Silent	SNP	ENST00000278379.3	37	CCDS31459.1																																																																																				0.562	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		A	35302521	G	A	35302521	2	1	111	1	0	0	0	0	0	0	0	1	14469	1074	38	1		1	SLC1A2	11	35302521	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7183266	35302521	99703995	607	29741										
PAMR1	25891	hgsc.bcm.edu	37	chr11	35496275	35496275	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatctgaccctttggggctcGcagaacctggccacatccta	9	14	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:35496275G>A	ENST00000378880.2	-	4	842	c.397C>T	c.(397-399)Cga>Tga	p.R133*	PAMR1_ENST00000278360.3_Nonsense_Mutation_p.R133*|PAMR1_ENST00000532848.1_Nonsense_Mutation_p.R93*|PAMR1_ENST00000378878.3_Intron|PAMR1_ENST00000534803.1_5'UTR	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	133	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TTTGGGGCTCGCAGAACCTGG	0.438																																																0			11											69	69	69					11																	35496275		2202	4298	6500	35452851	SO:0001587	stop_gained	25891				CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.397C>T	11.37:g.35496275G>A	ENSP00000368158:p.Arg133*		35452851	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Nonsense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	42	9.410116	0.99163	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000532848;ENST00000527605	.	.	.	5.2	3.26	0.37387	.	0.151084	0.44688	D	0.000438	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.0362	0.64646	0.0:0.0:0.7248:0.2752	.	.	.	.	X	133;133;93;93	.	ENSP00000278360:R133X	R	-	1	2	PAMR1	35452851	0.885000	0.30320	0.898000	0.35279	0.985000	0.73830	3.259000	0.51515	0.528000	0.28580	0.462000	0.41574	CGA		0.438	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35496275	G	A	35496275	4	1	111	1	0	0	0	0	0	1	0	0	11444	1095	38	1	1852	1	PAMR1	11	35496275	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	193754	35496275	99510241	608	29742										
PAMR1	25891	hgsc.bcm.edu	37	chr11	35513593	35513593	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctaggtcaaggtctacttacGcatgcagtctcctccgtacc	8	14	3	0	rs201076075		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:35513593G>A	ENST00000378880.2	-	3	824	c.379C>T	c.(379-381)Cga>Tga	p.R127*	PAMR1_ENST00000278360.3_Splice_Site_p.R127*|PAMR1_ENST00000532848.1_Splice_Site_p.R87*|PAMR1_ENST00000378878.3_Splice_Site_p.P127S|PAMR1_ENST00000534803.1_5'UTR	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	127						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						GTCTACTTACGCATGCAGTCT	0.493																																																0			11											157	147	150					11																	35513593		2202	4298	6500	35470169	SO:0001630	splice_region_variant	25891				CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.379+1C>T	11.37:g.35513593G>A			35470169	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Nonsense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.514385|7.514385	0.98332|0.98332	.|.	.|.	ENSG00000149090|ENSG00000149090	ENST00000378878;ENST00000529303|ENST00000278360;ENST00000378880;ENST00000532848;ENST00000527605	T;T|.	0.61859|.	0.07;0.07|.	5.38|5.38	3.35|3.35	0.38373|0.38373	.|.	.|0.061993	.|0.64402	.|D	.|0.000007	T|.	0.36358|.	0.0964|.	.|.	.|.	.|.	0.29015|0.29015	N|N	0.886669|0.886669	P|.	0.37176|.	0.586|.	B|.	0.32465|.	0.146|.	T|.	0.21211|.	-1.0252|.	7|.	.|.	.|.	.|.	.|.	8.2641|8.2641	0.31804|0.31804	0.0892:0.0:0.6471:0.2637|0.0892:0.0:0.6471:0.2637	.|.	127|.	A8MQ58|.	.|.	S|X	127|127;127;87;87	ENSP00000368156:P127S;ENSP00000433024:P127S|.	.|.	P|R	-|-	1|1	0|2	PAMR1|PAMR1	35470169|35470169	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.233000|0.233000	0.25261|0.25261	2.072000|2.072000	0.41510|0.41510	1.285000|1.285000	0.44548|0.44548	-0.229000|-0.229000	0.12294|0.12294	CCA|CGA		0.493	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	Nonsense_Mutation	A	35513593	G	A	35513593	5	1	111	1	0	0	0	0	0	0	1	0	11444	1101	38	1	1874	1	PAMR1	11	35513593	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	17318	35513593	99492923	609	29743										
COMMD9	29099	hgsc.bcm.edu	37	chr11	36296246	36296246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggccatctaacatggtgtccAgtgtttctttgctcagctcc	9	12	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:36296246A>G	ENST00000263401.5	-	6	549	c.533T>C	c.(532-534)cTg>cCg	p.L178P	COMMD9_ENST00000533308.1_5'Flank|LINC00610_ENST00000355500.1_lincRNA|COMMD9_ENST00000532705.1_Silent_p.T166T|COMMD9_ENST00000452374.2_Missense_Mutation_p.L136P	NM_014186.3	NP_054905.2	Q9P000	COMD9_HUMAN	COMM domain containing 9	178	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	5	all_lung(20;0.211)	all_hematologic(20;0.107)				CATGGTGTCCAGTGTTTCTTT	0.567																																																0			11											175	144	155					11																	36296246		2202	4298	6500	36252822	SO:0001583	missense	29099			AY542164	CCDS7900.1, CCDS44571.1	11p13	2008-02-05			ENSG00000110442	ENSG00000110442			25014	protein-coding gene	gene with protein product		612299				15799966	Standard	NM_014186		Approved	HSPC166, FLJ31106	uc001mwn.4	Q9P000	OTTHUMG00000166333	ENST00000263401.5:c.533T>C	11.37:g.36296246A>G	ENSP00000263401:p.Leu178Pro		36252822	E9PAN2|Q96FI2|Q9H0R0	Missense_Mutation	SNP	ENST00000263401.5	37	CCDS7900.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.499930	0.85176	.	.	ENSG00000110442	ENST00000263401;ENST00000452374	T;T	0.18810	2.19;2.19	5.66	5.66	0.87406	COMM domain (1);	0.000000	0.85682	D	0.000000	T	0.50565	0.1623	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.977	T	0.56944	-0.7895	10	0.87932	D	0	-15.346	14.8828	0.70545	1.0:0.0:0.0:0.0	.	136;178	Q9P000-2;Q9P000	.;COMD9_HUMAN	P	178;136	ENSP00000263401:L178P;ENSP00000392510:L136P	ENSP00000263401:L178P	L	-	2	0	COMMD9	36252822	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	7.895000	0.87343	2.147000	0.66899	0.533000	0.62120	CTG		0.567	COMMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389196.1	NM_014186		G	36296246	A	G	36296246	3	3	111	1	0	0	0	0	1	0	0	0	3729	188	7	4	67	4	COMMD9	11	36296246	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	782653	36296246	98710270	610	29744										
EXT2	2132	hgsc.bcm.edu	37	chr11	44146398	44146398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatcctgagtacagagaggAcctagaagccctccaggtca	10	13	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:44146398A>G	ENST00000343631.3	+	5	932	c.803A>G	c.(802-804)gAc>gGc	p.D268G	EXT2_ENST00000358681.4_Missense_Mutation_p.D268G|EXT2_ENST00000395673.3_Missense_Mutation_p.D301G|EXT2_ENST00000533608.1_Missense_Mutation_p.D268G			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	268					carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						TACAGAGAGGACCTAGAAGCC	0.502			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																													yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	0			11											80	69	73					11																	44146398		2203	4300	6503	44102974	SO:0001583	missense	2133	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.803A>G	11.37:g.44146398A>G	ENSP00000342656:p.Asp268Gly		44102974	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	37	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.785399	0.49997	.	.	ENSG00000151348	ENST00000533608;ENST00000358681;ENST00000395673;ENST00000343631	D;D;D;D	0.94793	-3.51;-3.51;-3.52;-3.51	5.81	5.81	0.92471	.	0.247416	0.47093	D	0.000251	D	0.91040	0.7181	L	0.34521	1.04	0.46416	D	0.999035	B;B;B;B;B	0.22746	0.024;0.012;0.01;0.022;0.074	B;B;B;B;B	0.26310	0.052;0.068;0.04;0.068;0.068	D	0.87516	0.2443	10	0.25751	T	0.34	0.0107	16.1699	0.81801	1.0:0.0:0.0:0.0	.	268;268;268;268;281	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	G	268;268;301;268	ENSP00000431173:D268G;ENSP00000351509:D268G;ENSP00000379032:D301G;ENSP00000342656:D268G	ENSP00000342656:D268G	D	+	2	0	EXT2	44102974	1.000000	0.71417	0.891000	0.34965	0.942000	0.58702	8.733000	0.91539	2.217000	0.71921	0.533000	0.62120	GAC		0.502	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		G	44146398	A	G	44146398	3	3	111	1	0	0	0	0	1	0	0	0	5337	275	10	4	920	4	EXT2	11	44146398	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	7850152	44146398	90860118	611	29745										
SLC39A13	91252	hgsc.bcm.edu	37	chr11	47431937	47431937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagagatggggaccatgctgCgctcagaaggtaggtgactc	15	8	1	3	rs369854018		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:47431937C>T	ENST00000362021.4	+	2	334	c.292C>T	c.(292-294)Cgc>Tgc	p.R98C	SLC39A13_ENST00000533076.1_Missense_Mutation_p.R98C|RP11-750H9.5_ENST00000532340.1_RNA|SLC39A13_ENST00000524928.1_Missense_Mutation_p.R98C|SLC39A13_ENST00000354884.4_Missense_Mutation_p.R98C|SLC39A13_ENST00000531974.1_Missense_Mutation_p.R98C|RP11-750H9.5_ENST00000532943.1_RNA	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	98					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		GACCATGCTGCGCTCAGAAGG	0.617																																																0			11						C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	49	49	49		292,292	3.7	1	11		49	2,8594	2.2+/-6.3	0,2,4296	no	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	180,180	0,2,6497	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	98/372,98/365	47431937	2,12996	2201	4298	6499	47388513	SO:0001583	missense	91252				CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"Solute carriers"	20859	protein-coding gene	gene with protein product		608735	"solute carrier family 39 (metal ion transporter), member 13"			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.292C>T	11.37:g.47431937C>T	ENSP00000354689:p.Arg98Cys		47388513	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165995	0.38217	0.0	2.33E-4	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.72282	-0.64;0.8;0.84;-0.63;-0.5;-0.31;-0.14;0.8;0.83	4.58	3.67	0.42095	.	0.206913	0.41605	D	0.000846	T	0.53562	0.1804	L	0.36672	1.1	0.50171	D	0.999852	B;B;P	0.36712	0.075;0.033;0.566	B;B;B	0.28139	0.056;0.02;0.086	T	0.51317	-0.8721	10	0.39692	T	0.17	-0.255	8.6537	0.34051	0.15:0.7694:0.0:0.0806	.	98;98;98	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	C	98	ENSP00000434290:R98C;ENSP00000435845:R98C;ENSP00000432302:R98C;ENSP00000434684:R98C;ENSP00000354689:R98C;ENSP00000346956:R98C;ENSP00000432499:R98C;ENSP00000435076:R98C;ENSP00000437186:R98C	ENSP00000346956:R98C	R	+	1	0	SLC39A13	47388513	0.998000	0.40836	0.998000	0.56505	0.950000	0.60333	2.271000	0.43364	0.913000	0.36797	-0.254000	0.11334	CGC		0.617	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264		T	47431937	C	T	47431937	3	4	111	1	0	0	0	0	1	0	0	0	14653	768	27	1	294	1	SLC39A13	11	47431937	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3285539	47431937	87574579	612	29746										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418785	55418785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attatatgaccatcatgaacCgggagacatgcaataaaatg	8	7	1	3	rs148733636		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:55418785C>T	ENST00000312422.2	+	1	406	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R136W(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				CATCATGAACCGGGAGACATG	0.433																																																1	Substitution - Missense(1)	ovary(1)	11						C	TRP/ARG	1,4363		0,1,2181	197	166	177		406	-1.1	0	11	dbSNP_134	177	1,8077		0,1,4038	no	missense	OR4S2	NM_001004059.2	101	0,2,6219	TT,TC,CC		0.0124,0.0229,0.0161	benign	136/312	55418785	2,12440	2182	4039	6221	55175361	SO:0001583	missense	219431			BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.406C>T	11.37:g.55418785C>T	ENSP00000310337:p.Arg136Trp		55175361	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	C	4.357	0.065803	0.08388	2.29E-4	1.24E-4	ENSG00000174982	ENST00000312422	T	0.00949	5.51	5.09	-1.09	0.09904	GPCR, rhodopsin-like superfamily (1);	0.270733	0.25205	N	0.032358	T	0.00998	0.0033	L	0.50333	1.59	0.09310	N	1	B	0.14805	0.011	B	0.09377	0.004	T	0.44757	-0.9307	10	0.44086	T	0.13	.	5.7679	0.18237	0.5214:0.3235:0.0:0.1551	.	136	Q8NH73	OR4S2_HUMAN	W	136	ENSP00000310337:R136W	ENSP00000310337:R136W	R	+	1	2	OR4S2	55175361	0.000000	0.05858	0.001000	0.08648	0.162000	0.22319	-2.203000	0.01234	0.129000	0.18514	0.542000	0.68232	CGG		0.433	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55418785	C	T	55418785	3	4	111	1	0	0	0	0	1	0	0	0	11114	643	23	1	408	1	OR4S2	11	55418785	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7986848	55418785	79587731	613	29747										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57563201	57563201	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actcggcgcacagagaccacGgtaaactaagacgtgtgtaa	11	10	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:57563201G>A	ENST00000399050.4	+	5	956	c.420G>A	c.(418-420)acG>acA	p.T140T	CTNND1_ENST00000360682.6_Splice_Site_p.T140T|CTNND1_ENST00000532245.1_Splice_Site_p.T39T|CTNND1_ENST00000530748.1_Splice_Site_p.T86T|CTNND1_ENST00000532787.1_Splice_Site_p.T39T|CTNND1_ENST00000528621.1_Splice_Site_p.T86T|CTNND1_ENST00000399039.4_Splice_Site_p.T140T|CTNND1_ENST00000426142.2_Splice_Site_p.T39T|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000361796.4_Splice_Site_p.T140T|CTNND1_ENST00000529873.1_Splice_Site_p.T86T|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000361332.4_Splice_Site_p.T140T|CTNND1_ENST00000361391.6_Splice_Site_p.T140T|CTNND1_ENST00000534579.1_Splice_Site_p.T86T|CTNND1_ENST00000530094.1_Splice_Site_p.T39T|CTNND1_ENST00000528232.1_Splice_Site_p.T39T|CTNND1_ENST00000358694.6_Splice_Site_p.T140T|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000529526.1_Splice_Site_p.T86T|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000526357.1_Splice_Site_p.T86T|CTNND1_ENST00000415361.2_Splice_Site_p.T39T|CTNND1_ENST00000428599.2_Splice_Site_p.T140T|CTNND1_ENST00000526938.1_Splice_Site_p.T140T|CTNND1_ENST00000532463.1_Splice_Site_p.T39T|CTNND1_ENST00000529919.1_Splice_Site_p.T140T|CTNND1_ENST00000524630.1_Splice_Site_p.T140T|CTNND1_ENST00000532844.1_Splice_Site_p.T86T|CTNND1_ENST00000532649.1_Splice_Site_p.T86T|CTNND1_ENST00000529986.1_Splice_Site_p.T39T|CTNND1_ENST00000531014.1_Intron	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	140					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CAGAGACCACGGTAAACTAAG	0.488																																																0			11											37	40	39					11																	57563201		1911	4124	6035	57319777	SO:0001630	splice_region_variant	1500			AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.420+1G>A	11.37:g.57563201G>A			57319777	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	37	CCDS44604.1																																																																																				0.488	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	Silent	A	57563201	G	A	57563201	5	1	111	1	0	0	0	0	0	0	1	0	4025	1130	39	1	430	1	CTNND1	11	57563201	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2144416	57563201	77443315	614	29748										
MS4A14	84689	hgsc.bcm.edu	37	chr11	60183562	60183562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaagatatgctgtttcatgAcatgacatcccaagatatgc	7	9	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:60183562A>G	ENST00000300187.6	+	5	1398	c.1121A>G	c.(1120-1122)gAc>gGc	p.D374G	MS4A14_ENST00000531783.1_Missense_Mutation_p.D407G|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.D262G|MS4A14_ENST00000395005.2_Missense_Mutation_p.D357G	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	374						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						ctgtttcatgacatgacatcc	0.453																																																0			11											145	111	123					11																	60183562		2203	4300	6503	59940138	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1121A>G	11.37:g.60183562A>G	ENSP00000300187:p.Asp374Gly		59940138	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.153018	0.38021	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.36520	1.25;2.45;1.27;2.74	2.6	0.107	0.14544	.	2.504800	0.01886	N	0.038218	T	0.24774	0.0601	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.01;0.006	B;B	0.11329	0.006;0.003	T	0.07947	-1.0746	10	0.25106	T	0.35	-0.0069	2.0841	0.03641	0.5894:0.0:0.1534:0.2572	.	357;374	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	G	262;374;357;407	ENSP00000437222:D262G;ENSP00000300187:D374G;ENSP00000378453:D357G;ENSP00000433761:D407G	ENSP00000300187:D374G	D	+	2	0	MS4A14	59940138	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.397000	0.07269	0.005000	0.14708	0.254000	0.18369	GAC		0.453	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			G	60183562	A	G	60183562	3	3	111	1	0	0	0	0	1	0	0	0	9888	275	10	4	1139	4	MS4A14	11	60183562	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2620361	60183562	74822954	615	29749										
ZP1	22917	hgsc.bcm.edu	37	chr11	60642643	60642643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accgtaatgacactgccaggCcccaggacatcgtgagctct	10	14	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:60642643C>T	ENST00000278853.5	+	11	1696	c.1696C>T	c.(1696-1698)Ccc>Tcc	p.P566S		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	566					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CACTGCCAGGCCCCAGGACAT	0.627																																																0			11											64	67	66					11																	60642643		2203	4299	6502	60399219	SO:0001583	missense	57829			BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1696C>T	11.37:g.60642643C>T	ENSP00000278853:p.Pro566Ser		60399219		Missense_Mutation	SNP	ENST00000278853.5	37	CCDS31572.1	.	.	.	.	.	.	.	.	.	.	C	6.669	0.492003	0.12702	.	.	ENSG00000149506	ENST00000278853;ENST00000544498	T	0.22134	1.97	5.57	-0.351	0.12602	.	1.008750	0.07949	N	0.980520	T	0.10294	0.0252	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.39623	-0.9605	10	0.09338	T	0.73	-9.8057	7.0678	0.25161	0.0:0.2434:0.5335:0.2231	.	566	P60852	ZP1_HUMAN	S	566;273	ENSP00000278853:P566S	ENSP00000278853:P566S	P	+	1	0	ZP1	60399219	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	0.207000	0.17395	0.221000	0.20879	0.561000	0.74099	CCC		0.627	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		T	60642643	C	T	60642643	3	4	111	1	0	0	0	0	1	0	0	0	18254	739	26	3	1738	3	ZP1	11	60642643	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	459081	60642643	74363873	616	29750										
SCGB1D4	404552	hgsc.bcm.edu	37	chr11	62066429	62066429	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatgactgatgtactcaccCtggtagcagcaaagggccag	11	11	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:62066429C>A	ENST00000358585.1	-	1	107	c.54G>T	c.(52-54)caG>caT	p.Q18H		NM_206998.1	NP_996881.1	Q6XE38	SG1D4_HUMAN	secretoglobin, family 1D, member 4	18						extracellular region (GO:0005576)				lung(1)|prostate(1)	2						TGTACTCACCCTGGTAGCAGC	0.532																																																0			11											162	115	131					11																	62066429		2202	4299	6501	61823005	SO:0001630	splice_region_variant	404552			AY236538	CCDS31583.1	11q12.3	2011-12-14			ENSG00000197745	ENSG00000197745		"Secretoglobins"	31748	protein-coding gene	gene with protein product		615062				15034037, 15340161, 22155607	Standard	NM_206998		Approved	IIS	uc001ntd.1	Q6XE38	OTTHUMG00000167510	ENST00000358585.1:c.55+1G>T	11.37:g.62066429C>A			61823005	A1L4Q8	Missense_Mutation	SNP	ENST00000358585.1	37	CCDS31583.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091799	0.55968	.	.	ENSG00000197745	ENST00000358585	T	0.23754	1.89	2.27	1.33	0.21861	.	2.837800	0.02530	U	0.093554	T	0.35970	0.0950	.	.	.	0.21220	N	0.999757	D	0.61080	0.989	P	0.53809	0.735	T	0.11743	-1.0575	9	0.72032	D	0.01	.	4.5849	0.12277	0.0:0.8064:0.0:0.1936	.	18	Q6XE38	SG1D4_HUMAN	H	18	ENSP00000351395:Q18H	ENSP00000351395:Q18H	Q	-	3	2	SCGB1D4	61823005	0.012000	0.17670	0.987000	0.45799	0.357000	0.29423	-1.158000	0.03153	0.497000	0.27926	0.491000	0.48974	CAG		0.532	SCGB1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394862.1	NM_206998	Missense_Mutation	A	62066429	C	A	62066429	5	1	111	1	0	0	0	0	0	0	1	0	13935	695	24	2	209	2	SCGB1D4	11	62066429	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1423786	62066429	72940087	617	29751										
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63176247	63176247	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tattctccacccctgccctgGatcatctatggagtcttccc	6	16	4	0	rs374697464		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:63176247G>T	ENST00000279178.3	+	9	1746	c.1497G>T	c.(1495-1497)tgG>tgT	p.W499C	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	499					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						CCCTGCCCTGGATCATCTATG	0.502																																																0			11											148	134	139					11																	63176247		2201	4298	6499	62932823	SO:0001583	missense	114571			AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"Solute carriers"	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.1497G>T	11.37:g.63176247G>T	ENSP00000279178:p.Trp499Cys		62932823	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	37	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332095	0.60853	.	.	ENSG00000149742	ENST00000279178	T	0.59083	0.29	2.63	2.63	0.31362	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.474187	0.21591	N	0.072094	T	0.76350	0.3975	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77688	-0.2494	10	0.40728	T	0.16	.	10.974	0.47454	0.0:0.0:1.0:0.0	.	499	Q8IVM8	S22A9_HUMAN	C	499	ENSP00000279178:W499C	ENSP00000279178:W499C	W	+	3	0	SLC22A9	62932823	1.000000	0.71417	0.995000	0.50966	0.688000	0.40055	3.326000	0.52037	1.492000	0.48499	0.205000	0.17691	TGG		0.502	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		T	63176247	G	T	63176247	3	4	111	1	0	0	0	0	1	0	0	0	14498	1183	41	2	1531	2	SLC22A9	11	63176247	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1109818	63176247	71830269	618	29752										
STIP1	10963	hgsc.bcm.edu	37	chr11	63964984	63964984	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcggtatactttgaaaagggCgactacaataagtgccggga	13	7	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:63964984C>T	ENST00000305218.4	+	7	966	c.819C>T	c.(817-819)ggC>ggT	p.G273G	STIP1_ENST00000538945.1_Silent_p.G249G|STIP1_ENST00000358794.5_Silent_p.G320G	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	273					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						TTGAAAAGGGCGACTACAATA	0.502																																																0			11											73	73	73					11																	63964984		2201	4297	6498	63721560	SO:0001819	synonymous_variant	10963			BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.819C>T	11.37:g.63964984C>T			63721560	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Silent	SNP	ENST00000305218.4	37	CCDS8058.1																																																																																				0.502	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		T	63964984	C	T	63964984	2	4	111	1	0	0	0	0	0	0	0	1	15324	755	27	1		1	STIP1	11	63964984	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	788737	63964984	71041532	619	29753										
NUDT22	84304	hgsc.bcm.edu	37	chr11	63994436	63994436	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcagctgcctggctgcgacaGcagggtgccaccgactgggg	16	13	1	0	rs374116646		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:63994436G>A	ENST00000279206.3	+	2	468	c.312G>A	c.(310-312)caG>caA	p.Q104Q	TRPT1_ENST00000546133.1_5'Flank|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000394547.3_5'Flank|TRPT1_ENST00000540472.1_5'Flank|NUDT22_ENST00000441250.2_Silent_p.Q104Q|TRPT1_ENST00000546089.1_5'Flank|TRPT1_ENST00000317459.6_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|TRPT1_ENST00000394546.2_5'Flank	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	104							hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						GGCTGCGACAGCAGGGTGCCA	0.657																																																0			11						G	,,	0,4396		0,0,2198	24	27	26		312,312,312	3.6	1	11		26	1,8585		0,1,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	NUDT22	NM_001128612.1,NM_001128613.1,NM_032344.2	,,	0,1,6490	AA,AG,GG		0.0116,0.0,0.0077	,,	104/304,104/271,104/304	63994436	1,12981	2198	4293	6491	63751012	SO:0001819	synonymous_variant	84304			BC006129	CCDS8061.1, CCDS44640.1	11q13.1	2008-02-05			ENSG00000149761	ENSG00000149761		"Nudix motif containing"	28189	protein-coding gene	gene with protein product						12477932	Standard	NM_032344		Approved	MGC13045	uc009ype.4	Q9BRQ3	OTTHUMG00000167791	ENST00000279206.3:c.312G>A	11.37:g.63994436G>A			63751012	C9JY06|Q71RD5	Silent	SNP	ENST00000279206.3	37	CCDS8061.1																																																																																				0.657	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344		A	63994436	G	A	63994436	2	1	111	1	0	0	0	0	0	0	0	1	10770	962	34	3		3	NUDT22	11	63994436	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	29452	63994436	71012080	620	29754										
ESRRA	2101	hgsc.bcm.edu	37	chr11	64074667	64074667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgccatgtccagccaggtgGtgggcattgagcctctctac	13	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:64074667G>A	ENST00000405666.1	+	2	250	c.16G>A	c.(16-18)Gtg>Atg	p.V6M	ESRRA_ENST00000000442.6_Missense_Mutation_p.V6M|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000406310.1_Missense_Mutation_p.V6M	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	6	Repressor domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						CAGCCAGGTGGTGGGCATTGA	0.632																																																0			11											50	56	54					11																	64074667		2085	4214	6299	63831243	SO:0001583	missense	2101			X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"Nuclear hormone receptors"	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.16G>A	11.37:g.64074667G>A	ENSP00000384851:p.Val6Met		63831243	Q14514	Missense_Mutation	SNP	ENST00000405666.1	37	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567246	0.65651	.	.	ENSG00000173153	ENST00000406310;ENST00000000442;ENST00000405666;ENST00000468670	D;D;D;D	0.96041	-3.02;-3.07;-3.07;-3.89	4.29	3.3	0.37823	.	0.305321	0.30510	N	0.009470	D	0.84786	0.5549	N	0.08118	0	0.30293	N	0.790172	B;B	0.31519	0.327;0.22	B;B	0.19946	0.027;0.012	T	0.79706	-0.1691	10	0.31617	T	0.26	.	5.5688	0.17184	0.1085:0.2026:0.6889:0.0	.	6;6	P11474-2;P11474	.;ERR1_HUMAN	M	6	ENSP00000385971:V6M;ENSP00000000442:V6M;ENSP00000384851:V6M;ENSP00000441970:V6M	ENSP00000000442:V6M	V	+	1	0	ESRRA	63831243	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.489000	0.35562	2.380000	0.81148	0.561000	0.74099	GTG		0.632	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		A	64074667	G	A	64074667	3	1	111	1	0	0	0	0	1	0	0	0	5273	1261	44	3	18	3	ESRRA	11	64074667	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	80231	64074667	70931849	621	29755										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64591974	64591974	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctctccaattcaggggataGggggaggcttcggggccgtt					rs557823416		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:64591974delG	ENST00000342711.5	-	37	4626	c.4627delC	c.(4627-4629)ctafs	p.L1543fs		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						TCAGGGGATAGGGGGAGGCTT	0.562																																																0			11											51	55	54					11																	64591974		2201	4297	6498	64348550	SO:0001589	frameshift_variant	55561			AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4627delC	11.37:g.64591974delG	ENSP00000345133:p.Leu1543fs		64348550		Frame_Shift_Del	DEL	ENST00000342711.5	37	CCDS31601.1																																																																																				0.562	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		-	64591974	G	-	64591974	7	5	111	1	0	1	0	1	0	0	0	0	3080	991	35	0	32	0	CDC42BPG	11	64591974	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	517307	64591974	70414542	622	29756										
GPHA2	170589	hgsc.bcm.edu	37	chr11	64702829	64702829	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccggtcccagaggtactcaCggtgcaagtggcagcctggg	15	12	1	1	rs528889811		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:64702829C>T	ENST00000279168.2	-	2	158		c.e2+1		GPHA2_ENST00000533257.1_Splice_Site|GPHA2_ENST00000532246.1_Splice_Site	NM_130769.3	NP_570125.1	Q96T91	GPHA2_HUMAN	glycoprotein hormone alpha 2							extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|prostate(1)	3						GAGGTACTCACGGTGCAAGTG	0.637													C|||	1	0.000199681	0	0	5008	,	,		18772	0.001		0	False		,,,				2504	0															0			11											42	38	39					11																	64702829		2201	4297	6498	64459405	SO:0001630	splice_region_variant	170589			AF260739	CCDS8086.1	11q13.1	2008-07-18				ENSG00000149735			18054	protein-coding gene	gene with protein product	"glycoprotein alpha 2", "cysteine knot protein"	609651				11809971	Standard	NM_130769		Approved	GPA2, ZSIG51, A2, MGC126572	uc001oca.3	Q96T91		ENST00000279168.2:c.103+1G>A	11.37:g.64702829C>T			64459405	Q52LE2	Splice_Site	SNP	ENST00000279168.2	37	CCDS8086.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991563	0.74703	.	.	ENSG00000149735	ENST00000279168;ENST00000533257;ENST00000532246	.	.	.	4.1	4.1	0.47936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2376	0.65937	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPHA2	64459405	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.730000	0.68546	2.298000	0.77334	0.655000	0.94253	.		0.637	GPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385470.1	NM_130769	Intron	T	64702829	C	T	64702829	5	4	111	1	0	0	0	0	0	0	1	0	6628	550	19	1	297	1	GPHA2	11	64702829	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	110855	64702829	70303687	623	29757										
KAT5	10524	hgsc.bcm.edu	37	chr11	65481116	65481116	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccagtgcccagcgagacagCcccggcctcggtttttcccc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:65481116delC	ENST00000377046.3	+	6	766	c.494delC	c.(493-495)gccfs	p.A165fs	KAT5_ENST00000525204.1_3'UTR|KAT5_ENST00000352980.4_Frame_Shift_Del_p.A113fs|KAT5_ENST00000534650.1_5'UTR|KAT5_ENST00000530446.1_Frame_Shift_Del_p.A146fs|KAT5_ENST00000341318.4_Frame_Shift_Del_p.A198fs	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	165					androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						AGCGAGACAGCCCCGGCCTCG	0.537																																																0			11											66	67	66					11																	65481116		2201	4297	6498	65237692	SO:0001589	frameshift_variant	10524			U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.494delC	11.37:g.65481116delC	ENSP00000366245:p.Ala165fs		65237692	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Frame_Shift_Del	DEL	ENST00000377046.3	37	CCDS31610.1																																																																																				0.537	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		-	65481116	C	-	65481116	7	5	111	1	0	1	0	1	0	0	0	0	8004	739	26	0	611	0	KAT5	11	65481116	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	778287	65481116	69525400	624	29758										
EFEMP2	30008	hgsc.bcm.edu	37	chr11	65638093	65638093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tatggcagtcctggctggggCgacagtcgtgcagggcctgg	18	10	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:65638093C>T	ENST00000307998.6	-	5	634	c.404G>A	c.(403-405)cGc>cAc	p.R135H	EFEMP2_ENST00000528176.1_Missense_Mutation_p.R135H|EFEMP2_ENST00000532648.1_5'Flank	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	135	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		CTGGCTGGGGCGACAGTCGTG	0.612																																																0			11											81	69	73					11																	65638093		2201	4296	6497	65394669	SO:0001583	missense	30008			AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"Fibulins"	3219	protein-coding gene	gene with protein product	"fibulin 4"	604633	"EGF-containing fibulin-like extracellular matrix protein 2"			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.404G>A	11.37:g.65638093C>T	ENSP00000309953:p.Arg135His		65394669	A8K7R4|B3KM31|B3KQT1|O75967	Missense_Mutation	SNP	ENST00000307998.6	37	CCDS8116.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419745	0.62622	.	.	ENSG00000172638	ENST00000528176;ENST00000307998;ENST00000526624;ENST00000527378	D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95	5.3	5.3	0.74995	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.43110	D	0.000612	D	0.89047	0.6604	N	0.11673	0.155	0.29377	N	0.863611	D;D	0.65815	0.995;0.965	P;P	0.59703	0.862;0.615	D	0.83964	0.0323	10	0.36615	T	0.2	.	11.3737	0.49715	0.1806:0.8194:0.0:0.0	.	135;135	E9PRU1;O95967	.;FBLN4_HUMAN	H	135	ENSP00000434151:R135H;ENSP00000309953:R135H;ENSP00000435419:R135H;ENSP00000435963:R135H	ENSP00000309953:R135H	R	-	2	0	EFEMP2	65394669	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.070000	0.41491	2.761000	0.94854	0.561000	0.74099	CGC		0.612	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938		T	65638093	C	T	65638093	3	4	111	1	0	0	0	0	1	0	0	0	4953	768	27	1	955	1	EFEMP2	11	65638093	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	156977	65638093	69368423	625	29759										
DRAP1	10589	hgsc.bcm.edu	37	chr11	65688868	65688868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagcgcccccgggcccctcaGcacctgatgaagaggacgaa	12	16	1	3	rs143922438		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:65688868G>A	ENST00000312515.2	+	7	825	c.580G>A	c.(580-582)Gca>Aca	p.A194T	DRAP1_ENST00000376991.2_Missense_Mutation_p.A201T|DRAP1_ENST00000532933.1_Missense_Mutation_p.A174T|C11orf68_ENST00000438576.2_5'Flank|DRAP1_ENST00000527119.1_Missense_Mutation_p.A150T|C11orf68_ENST00000449692.3_5'Flank	NM_006442.3	NP_006433.2	Q14919	NC2A_HUMAN	DR1-associated protein 1 (negative cofactor 2 alpha)	194	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	5				READ - Rectum adenocarcinoma(159;0.166)		GGGCCCCTCAGCACCTGATGA	0.622																																																0			11						G	THR/ALA	0,4402		0,0,2201	72	83	79		580	4.9	0.9	11	dbSNP_134	79	1,8591	1.2+/-3.3	0,1,4295	no	missense	DRAP1	NM_006442.3	58	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	194/206	65688868	1,12993	2201	4296	6497	65445444	SO:0001583	missense	10589			U41843	CCDS8123.1	11q13	2010-09-29			ENSG00000175550	ENSG00000175550			3019	protein-coding gene	gene with protein product	"negative cofactor 2 alpha", "DR1-associated corepressor"	602289				8608938	Standard	NM_006442		Approved	NC2-alpha	uc001ogj.2	Q14919	OTTHUMG00000166723	ENST00000312515.2:c.580G>A	11.37:g.65688868G>A	ENSP00000307850:p.Ala194Thr		65445444	Q13448	Missense_Mutation	SNP	ENST00000312515.2	37	CCDS8123.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577207	0.45902	0.0	1.16E-4	ENSG00000175550	ENST00000312515;ENST00000525501;ENST00000376991;ENST00000527119;ENST00000532933	.	.	.	4.9	4.9	0.64082	.	0.502377	0.18057	N	0.153065	T	0.37489	0.1005	L	0.29908	0.895	0.31476	N	0.667792	B	0.31100	0.308	B	0.30029	0.11	T	0.48031	-0.9070	9	0.48119	T	0.1	-4.9075	13.9561	0.64150	0.0:0.0:1.0:0.0	.	194	Q14919	NC2A_HUMAN	T	194;155;201;150;174	.	ENSP00000307850:A194T	A	+	1	0	DRAP1	65445444	1.000000	0.71417	0.950000	0.38849	0.350000	0.29205	4.555000	0.60767	2.450000	0.82876	0.655000	0.94253	GCA		0.622	DRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391197.2	NM_006442		A	65688868	G	A	65688868	3	1	111	1	0	0	0	0	1	0	0	0	4766	971	34	3	606	3	DRAP1	11	65688868	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	50775	65688868	69317648	626	29760										
TSGA10IP	9092	hgsc.bcm.edu	37	chr11	65726679	65726679	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggccaatgcccggctcaccGtcactcggcgcttctcccag	10	18	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:65726679G>T	ENST00000312397.5	+	0	0				TSGA10IP_ENST00000608857.1_RNA|TSGA10IP_ENST00000532620.1_RNA	NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells						cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCGGCTCACCGTCACTCGGCG	0.647																																																0			11											24	28	27					11																	65726679		2055	4199	6254	65483255	SO:0001631	upstream_gene_variant	254187			AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"	605941	"squamous cell carcinoma antigen recognised by T cells"			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771		11.37:g.65726679G>T	Exception_encountered		65483255	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	37	CCDS31611.1																																																																																				0.647	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1			T	65726679	G	T	65726679	1	4	111	0	1	0	0	0	0	0	0	0	16658	1145	40	2		2	TSGA10IP	11	65726679	5'Flank	SNP	G	TCGA-EI-6507-01A-11D-1733-10	37811	65726679	69279837	627	29761										
YIF1A	10897	hgsc.bcm.edu	37	chr11	66052190	66052190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtcaggtagagctggagaCgctgccgggggacggggccc	20	10	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66052190C>T	ENST00000376901.4	-	8	984	c.800G>A	c.(799-801)cGt>cAt	p.R267H	YIF1A_ENST00000359461.6_Missense_Mutation_p.R215H|YIF1A_ENST00000496746.1_Missense_Mutation_p.R53H|YIF1A_ENST00000526497.1_5'UTR|CNIH2_ENST00000530519.1_Intron|YIF1A_ENST00000471387.2_Missense_Mutation_p.V154I	NM_020470.2	NP_065203.2	O95070	YIF1A_HUMAN	Yip1 interacting factor homolog A (S. cerevisiae)	267					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	9						GAGCTGGAGACGCTGCCGGGG	0.657																																																0			11											19	22	21					11																	66052190		2192	4279	6471	65808766	SO:0001583	missense	10897			AF004876	CCDS8132.1, CCDS73325.1	11q13	2009-01-05	2005-06-07	2005-06-07	ENSG00000174851	ENSG00000174851			16688	protein-coding gene	gene with protein product		611484	"Yip1 interacting factor homolog (S. cerevisiae)"	YIF1		8824393, 10970842, 18718466	Standard	NM_020470		Approved	YIF1P, 54TM, FinGER7	uc001ohk.4	O95070	OTTHUMG00000102079	ENST00000376901.4:c.800G>A	11.37:g.66052190C>T	ENSP00000366098:p.Arg267His		65808766	A6NM00|Q96G83|Q9BVD0	Missense_Mutation	SNP	ENST00000376901.4	37	CCDS8132.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.07|14.07	2.427073|2.427073	0.43122|0.43122	.|.	.|.	ENSG00000174851|ENSG00000174851	ENST00000496746;ENST00000359461;ENST00000376901;ENST00000376904|ENST00000471387	T;T|.	0.48522|.	0.85;0.81|.	5.66|5.66	0.541|0.541	0.17168|0.17168	.|.	0.271361|.	0.37955|.	N|.	0.001879|.	T|T	0.54791|0.54791	0.1880|0.1880	L|L	0.40543|0.40543	1.245|1.245	0.42496|0.42496	D|D	0.992914|0.992914	B|.	0.15719|.	0.014|.	B|.	0.13407|.	0.009|.	T|T	0.54193|0.54193	-0.8330|-0.8330	10|6	0.45353|0.87932	T|D	0.12|0	-19.8096|-19.8096	9.5367|9.5367	0.39226|0.39226	0.0:0.5712:0.0:0.4288|0.0:0.5712:0.0:0.4288	.|.	267|.	O95070|.	YIF1A_HUMAN|.	H|I	53;215;267;271|154	ENSP00000352437:R215H;ENSP00000366098:R267H|.	ENSP00000352437:R215H|ENSP00000437042:V154I	R|V	-|-	2|1	0|0	YIF1A|YIF1A	65808766|65808766	0.094000|0.094000	0.21725|0.21725	0.867000|0.867000	0.34043|0.34043	0.948000|0.948000	0.59901|0.59901	0.394000|0.394000	0.20834|0.20834	-0.143000|-0.143000	0.11334|0.11334	-0.254000|-0.254000	0.11334|0.11334	CGT|GTC		0.657	YIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219903.3	NM_020470		T	66052190	C	T	66052190	3	4	111	1	0	0	0	0	1	0	0	0	17515	536	19	1	85	1	YIF1A	11	66052190	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	325511	66052190	68954326	628	29762										
RIN1	9610	hgsc.bcm.edu	37	chr11	66102239	66102239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatggaccgaagcagaggtCgtcggcggcccaggtggggt	18	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66102239C>T	ENST00000311320.4	-	6	1157	c.1031G>A	c.(1030-1032)cGa>cAa	p.R344Q	RIN1_ENST00000424433.2_Missense_Mutation_p.R239Q|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000530056.1_Missense_Mutation_p.R239Q	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	344	Ras and 14-3-3 protein binding region.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						AAGCAGAGGTCGTCGGCGGCC	0.716																																																0			11											4	4	4					11																	66102239		2015	3967	5982	65858815	SO:0001583	missense	9610			L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1031G>A	11.37:g.66102239C>T	ENSP00000310406:p.Arg344Gln		65858815	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	37	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960230	0.74016	.	.	ENSG00000174791	ENST00000311320;ENST00000424433;ENST00000530056	T;T;T	0.15487	2.97;2.83;2.42	3.96	3.03	0.35002	.	0.172194	0.37219	N	0.002185	T	0.24967	0.0606	L	0.47716	1.5	0.30174	N	0.801031	D;P;D	0.76494	0.961;0.955;0.999	B;B;P	0.60236	0.342;0.207;0.871	T	0.06770	-1.0808	10	0.17832	T	0.49	-12.7206	9.8172	0.40860	0.0:0.7893:0.2107:0.0	.	239;37;344	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	Q	344;239;239	ENSP00000310406:R344Q;ENSP00000400560:R239Q;ENSP00000432798:R239Q	ENSP00000310406:R344Q	R	-	2	0	RIN1	65858815	0.025000	0.19082	0.943000	0.38184	0.536000	0.34869	0.356000	0.20181	0.786000	0.33708	0.462000	0.41574	CGA		0.716	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		T	66102239	C	T	66102239	3	4	111	1	0	0	0	0	1	0	0	0	13408	884	31	1	1340	1	RIN1	11	66102239	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	50049	66102239	68904277	629	29763										
DPP3	10072	hgsc.bcm.edu	37	chr11	66249709	66249709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcctgcccaatgacatcgGcgtgtctagcctggactgcc	10	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66249709G>A	ENST00000360510.2	+	2	103	c.38G>A	c.(37-39)gGc>gAc	p.G13D	CTD-3074O7.5_ENST00000525142.1_RNA|CTD-3074O7.5_ENST00000527274.2_RNA|DPP3_ENST00000530165.1_Missense_Mutation_p.G13D|DPP3_ENST00000531863.1_Missense_Mutation_p.G33D|DPP3_ENST00000453114.1_Missense_Mutation_p.G13D|CTD-3074O7.5_ENST00000527092.1_RNA|DPP3_ENST00000541961.1_Missense_Mutation_p.G13D|CTD-3074O7.5_ENST00000533502.1_RNA|DPP3_ENST00000532677.1_Missense_Mutation_p.G32D			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	13					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						AATGACATCGGCGTGTCTAGC	0.602																																																0			11											121	79	93					11																	66249709		2200	4295	6495	66006285	SO:0001583	missense	10072			AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.38G>A	11.37:g.66249709G>A	ENSP00000353701:p.Gly13Asp		66006285	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535000	0.85812	.	.	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000526515;ENST00000530165;ENST00000347422;ENST00000531314;ENST00000531354	T;T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.71	5.71	0.89125	.	0.105321	0.64402	D	0.000004	T	0.56485	0.1988	L	0.51422	1.61	0.44711	D	0.997709	D;P	0.58620	0.983;0.589	D;P	0.71656	0.974;0.638	T	0.51772	-0.8663	10	0.40728	T	0.16	.	13.0001	0.58670	0.0:0.162:0.838:0.0	.	32;13	G3V1D3;Q9NY33	.;DPP3_HUMAN	D	33;32;13;13;13;13;13;13;13;13	ENSP00000432782:G33D;ENSP00000435284:G32D;ENSP00000353701:G13D;ENSP00000389943:G13D;ENSP00000440502:G13D;ENSP00000431606:G13D;ENSP00000436941:G13D;ENSP00000436820:G13D;ENSP00000432618:G13D	ENSP00000309957:G13D	G	+	2	0	DPP3	66006285	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.339000	0.72969	2.691000	0.91804	0.561000	0.74099	GGC		0.602	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			A	66249709	G	A	66249709	3	1	111	1	0	0	0	0	1	0	0	0	4739	1203	42	3	40	3	DPP3	11	66249709	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	147470	66249709	68756807	630	29764										
CCDC87	55231	hgsc.bcm.edu	37	chr11	66360164	66360164	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcttccgcagcttctggttgTttttgtggctcagactaagt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66360164delT	ENST00000333861.3	-	1	390	c.323delA	c.(322-324)aacfs	p.N109fs	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	109					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CTTCTGGTTGTTTTTGTGGCT	0.617											OREG0021111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			11											46	50	49					11																	66360164		2200	4295	6495	66116740	SO:0001589	frameshift_variant	55231			BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.323delA	11.37:g.66360164delT	ENSP00000328487:p.Asn109fs	1091	66116740	Q8NE76	Frame_Shift_Del	DEL	ENST00000333861.3	37	CCDS8145.1																																																																																				0.617	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		-	66360164	T	-	66360164	7	5	111	1	0	1	0	1	0	0	0	0	2868	1725	60	0	2230	0	CCDC87	11	66360164	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	110455	66360164	68646352	631	29765										
RBM14	10432	hgsc.bcm.edu	37	chr11	66391769	66391769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaagaagtgaagggcaagcGcatcaacgtggaactctcca	11	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66391769G>A	ENST00000310137.4	+	2	561	c.422G>A	c.(421-423)cGc>cAc	p.R141H	RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14_ENST00000443702.1_3'UTR|RBM14_ENST00000393979.3_Missense_Mutation_p.R141H|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000409372.1_3'UTR|RBM14_ENST00000461478.1_3'UTR|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000412278.2_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	141	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						AAGGGCAAGCGCATCAACGTG	0.567																																																0			11											75	70	72					11																	66391769		2200	4295	6495	66148345	SO:0001583	missense	10432			AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.422G>A	11.37:g.66391769G>A	ENSP00000311747:p.Arg141His		66148345	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	37	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.634145	0.67130	.	.	ENSG00000239306	ENST00000310137;ENST00000393979	T;T	0.17054	2.3;2.3	5.67	5.67	0.87782	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.298817	0.22643	N	0.057427	T	0.30978	0.0782	L	0.28776	0.89	0.80722	D	1	D;D	0.76494	0.992;0.999	P;D	0.67725	0.674;0.953	T	0.01604	-1.1314	10	0.66056	D	0.02	-2.4154	17.2666	0.87088	0.0:0.0:1.0:0.0	.	141;141	Q96PK6-2;Q96PK6	.;RBM14_HUMAN	H	141	ENSP00000311747:R141H;ENSP00000377548:R141H	ENSP00000311747:R141H	R	+	2	0	RBM14	66148345	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.507000	0.60434	2.687000	0.91594	0.655000	0.94253	CGC		0.567	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66391769	G	A	66391769	3	1	111	1	0	0	0	0	1	0	0	0	13152	1087	38	1	428	1	RBM14	11	66391769	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	31605	66391769	68614747	632	29766										
C11orf80	79703	hgsc.bcm.edu	37	chr11	66595782	66595782	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaaactgcacaaagtatttCgtgagatcacccaacaccaa	5	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66595782C>T	ENST00000360962.4	+	14	1622	c.1615C>T	c.(1615-1617)Cgt>Tgt	p.R539C	C11orf80_ENST00000527634.1_Missense_Mutation_p.R322C|C11orf80_ENST00000525449.2_Missense_Mutation_p.R347C|C11orf80_ENST00000532565.2_Missense_Mutation_p.R321C|C11orf80_ENST00000346672.4_Missense_Mutation_p.R348C|C11orf80_ENST00000540737.1_Missense_Mutation_p.R374C	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	539										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						CAAAGTATTTCGTGAGATCAC	0.438																																																0			11											82	81	81					11																	66595782		1920	4117	6037	66352358	SO:0001583	missense	79703					11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.1615C>T	11.37:g.66595782C>T	ENSP00000354227:p.Arg539Cys		66352358	Q9H677	Missense_Mutation	SNP	ENST00000360962.4	37	CCDS53664.1	.	.	.	.	.	.	.	.	.	.	C	4.189	0.033752	0.08101	.	.	ENSG00000173715	ENST00000360962;ENST00000346672;ENST00000527634;ENST00000528340;ENST00000540737;ENST00000525449	T	0.32753	1.44	5.3	-0.0247	0.13938	.	1.186920	0.06254	N	0.692655	T	0.14787	0.0357	N	0.08118	0	0.20307	N	0.999917	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.25433	-1.0132	10	0.38643	T	0.18	0.74	4.1238	0.10118	0.1703:0.4782:0.0:0.3515	.	374;348;322;384;375	B4DXL1;C9JZP8;E9PKM2;Q8N6T0;E9PKZ8	.;.;.;CK080_HUMAN;.	C	539;348;322;375;374;348	ENSP00000354227:R539C	ENSP00000317408:R348C	R	+	1	0	C11orf80	66352358	0.536000	0.26378	0.246000	0.24233	0.101000	0.19017	0.226000	0.17776	-0.171000	0.10797	-0.181000	0.13052	CGT		0.438	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		T	66595782	C	T	66595782	3	4	111	1	0	0	0	0	1	0	0	0	1668	884	31	1	1669	1	C11orf80	11	66595782	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	204013	66595782	68410734	633	29767										
PC	5091	hgsc.bcm.edu	37	chr11	66616566	66616566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaccttcccaggcatgggcGccccgatctggcccttcacg	10	18	3	0	rs148492494		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:66616566G>A	ENST00000393958.2	-	22	3434	c.3341C>T	c.(3340-3342)gCg>gTg	p.A1114V	PC_ENST00000528224.1_5'UTR|PC_ENST00000393955.2_Missense_Mutation_p.A1114V|PC_ENST00000393960.1_Missense_Mutation_p.A1114V|PC_ENST00000529047.1_Missense_Mutation_p.A234V	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1114	Biotinyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AGGCATGGGCGCCCCGATCTG	0.612													G|||	1	0.000199681	0	0	5008	,	,		20113	0		0.001	False		,,,				2504	0															0			11						G	VAL/ALA,VAL/ALA,VAL/ALA	1,4399	2.1+/-5.4	0,1,2199	71	71	71		3341,3341,3341	4.7	1	11	dbSNP_134	71	3,8587	3.0+/-9.4	0,3,4292	yes	missense,missense,missense	PC	NM_000920.3,NM_001040716.1,NM_022172.2	64,64,64	0,4,6491	AA,AG,GG		0.0349,0.0227,0.0308	probably-damaging,probably-damaging,probably-damaging	1114/1179,1114/1179,1114/1179	66616566	4,12986	2200	4295	6495	66373142	SO:0001583	missense	5624			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.3341C>T	11.37:g.66616566G>A	ENSP00000377530:p.Ala1114Val		66373142	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	27.6	4.846019	0.91277	2.27E-4	3.49E-4	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	4.66	4.66	0.58398	Single hybrid motif (1);Biotin/lipoyl attachment (2);	0.000000	0.85682	D	0.000000	D	0.94072	0.8100	M	0.92555	3.32	0.80722	D	1	D	0.76494	0.999	P	0.61201	0.885	D	0.95372	0.8465	10	0.87932	D	0	-16.7783	15.072	0.72046	0.0:0.0:1.0:0.0	.	1114	P11498	PYC_HUMAN	V	234;1114;1114;1114	ENSP00000435905:A234V;ENSP00000377527:A1114V;ENSP00000377530:A1114V;ENSP00000377532:A1114V	ENSP00000377527:A1114V	A	-	2	0	PC	66373142	1.000000	0.71417	0.992000	0.48379	0.981000	0.71138	7.147000	0.77382	2.414000	0.81942	0.462000	0.41574	GCG		0.612	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		A	66616566	G	A	66616566	3	1	111	1	0	0	0	0	1	0	0	0	11528	1087	38	1	199	1	PC	11	66616566	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	20784	66616566	68389950	634	29768										
CARNS1	57571	hgsc.bcm.edu	37	chr11	67191150	67191150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatggcccaccctggcctgCgccctccctccatgctgtgc	9	21	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:67191150C>T	ENST00000307823.3	+	9	2014	c.1562C>T	c.(1561-1563)gCg>gTg	p.A521V	CARNS1_ENST00000524740.1_3'UTR|CARNS1_ENST00000423745.2_Missense_Mutation_p.A521V|CARNS1_ENST00000445895.2_Missense_Mutation_p.A644V|CARNS1_ENST00000531040.1_Missense_Mutation_p.A618V	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	521	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						CCCTGGCCTGCGCCCTCCCTC	0.657																																																0			11											18	21	20					11																	67191150		2124	4235	6359	66947726	SO:0001583	missense	0				CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1562C>T	11.37:g.67191150C>T	ENSP00000308268:p.Ala521Val		66947726	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849837	0.32699	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52	5.37	4.39	0.52855	ATP-grasp fold (1);	0.165132	0.28618	N	0.014716	D	0.93956	0.8065	L	0.29908	0.895	0.09310	N	1	P;P	0.51791	0.873;0.948	B;B	0.39503	0.27;0.301	D	0.88518	0.3094	10	0.29301	T	0.29	-20.3516	14.4366	0.67284	0.0:0.8514:0.1486:0.0	.	521;660	A5YM72;A5YM72-3	CRNS1_HUMAN;.	V	618;521;618;521;644	ENSP00000431670:A618V;ENSP00000308268:A521V;ENSP00000401519:A521V;ENSP00000389009:A644V	ENSP00000308268:A521V	A	+	2	0	CARNS1	66947726	0.638000	0.27225	0.772000	0.31596	0.919000	0.55068	3.924000	0.56476	2.515000	0.84797	0.549000	0.68633	GCG		0.657	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		T	67191150	C	T	67191150	3	4	111	1	0	0	0	0	1	0	0	0	2662	768	27	1	1965	1	CARNS1	11	67191150	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	574584	67191150	67815366	635	29769										
TBX10	347853	hgsc.bcm.edu	37	chr11	67401769	67401769	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtcggggtggaagtgcacgCggccaggtgtggctgggtct	20	8	1	0	rs372763899		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:67401769C>T	ENST00000335385.3	-	4	527	c.440G>A	c.(439-441)cGc>cAc	p.R147H		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	147					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						GAAGTGCACGCGGCCAGGTGT	0.642																																																0			11						C	HIS/ARG	1,4399	2.1+/-5.4	0,1,2199	67	63	64		440	3.6	0.2	11		64	0,8586		0,0,4293	no	missense	TBX10	NM_005995.4	29	0,1,6492	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	147/386	67401769	1,12985	2200	4293	6493	67158345	SO:0001583	missense	347853			AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"T-boxes"	11593	protein-coding gene	gene with protein product		604648	"T-box 7"	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.440G>A	11.37:g.67401769C>T	ENSP00000335191:p.Arg147His		67158345	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845782	0.71603	2.27E-4	0.0	ENSG00000167800	ENST00000335385	D	0.90563	-2.69	3.56	3.56	0.40772	p53-like transcription factor, DNA-binding (1);	0.000000	0.56097	D	0.000034	D	0.96204	0.8762	M	0.93978	3.48	0.53005	D	0.999969	D	0.89917	1.0	D	0.85130	0.997	D	0.97196	0.9861	10	0.87932	D	0	.	14.0846	0.64947	0.0:1.0:0.0:0.0	.	147	O75333	TBX10_HUMAN	H	147	ENSP00000335191:R147H	ENSP00000335191:R147H	R	-	2	0	TBX10	67158345	0.999000	0.42202	0.243000	0.24186	0.490000	0.33462	7.302000	0.78861	1.839000	0.53478	0.305000	0.20034	CGC		0.642	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995		T	67401769	C	T	67401769	3	4	111	1	0	0	0	0	1	0	0	0	15690	768	27	1	737	1	TBX10	11	67401769	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	210619	67401769	67604747	636	29770										
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70202304	70202304	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gataactcatctcaggatgcCttgggacttagcaaattggg	11	8	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:70202304C>A	ENST00000253925.7	+	19	2741	c.2526C>A	c.(2524-2526)gcC>gcA	p.A842A	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Silent_p.A842A|AP000487.4_ENST00000324630.5_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	842					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CTCAGGATGCCTTGGGACTTA	0.398																																																0			11											136	143	141					11																	70202304		2200	4294	6494	69879952	SO:0001819	synonymous_variant	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2526C>A	11.37:g.70202304C>A			69879952	A6NLE3|Q13135|Q14567|Q8N4I2	Silent	SNP	ENST00000253925.7	37	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.747|9.747	1.166544|1.166544	0.21621|0.21621	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000530798|ENST00000528750	.|.	.|.	.|.	5.15|5.15	3.22|3.22	0.36961|0.36961	.|.	.|.	.|.	.|.	.|.	T|T	0.59197|0.59197	0.2176|0.2176	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.56001|0.56001	-0.8051|-0.8051	4|4	.|.	.|.	.|.	.|.	9.503|9.503	0.39028|0.39028	0.2673:0.6598:0.0:0.0728|0.2673:0.6598:0.0:0.0728	.|.	.|.	.|.	.|.	I|H	235|285	.|.	.|.	L|P	+|+	1|2	0|0	PPFIA1|PPFIA1	69879952|69879952	0.914000|0.914000	0.31030|0.31030	0.879000|0.879000	0.34478|0.34478	0.925000|0.925000	0.55904|0.55904	1.927000|1.927000	0.40094|0.40094	1.280000|1.280000	0.44463|0.44463	0.655000|0.655000	0.94253|0.94253	CTT|CCT		0.398	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		A	70202304	C	A	70202304	2	1	111	1	0	0	0	0	0	0	0	1	12340	668	24	2		2	PPFIA1	11	70202304	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2800535	70202304	64804212	637	29771										
CTTN	2017	hgsc.bcm.edu	37	chr11	70277323	70277323	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccagagccaaaacgcaaacGccccctgtgtcgcccgcacc	9	19	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:70277323G>A	ENST00000301843.8	+	15	1409	c.1203G>A	c.(1201-1203)acG>acA	p.T401T	CTTN_ENST00000538675.1_Silent_p.T85T|CTTN_ENST00000346329.3_Silent_p.T364T|CTTN_ENST00000376561.3_Silent_p.T364T	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	401					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		AAACGCAAACGCCCCCTGTGT	0.552																																																0			11											121	131	128					11																	70277323		2200	4294	6494	69954971	SO:0001819	synonymous_variant	2017			AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.1203G>A	11.37:g.70277323G>A			69954971	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1																																																																																				0.552	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		A	70277323	G	A	70277323	2	1	111	1	0	0	0	0	0	0	0	1	4050	1074	38	1		1	CTTN	11	70277323	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	75019	70277323	64729193	638	29772										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70333475	70333475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctcttgttgcggaagttggCttgcgggccggcattccgac	14	11	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:70333475C>A	ENST00000423696.2	-	15	1822	c.1786G>T	c.(1786-1788)Gcc>Tcc	p.A596S	SHANK2_ENST00000338508.4_Missense_Mutation_p.A976S|SHANK2_ENST00000409161.1_Missense_Mutation_p.A379S|SHANK2_ENST00000449833.2_Missense_Mutation_p.A380S			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	596					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CGGAAGTTGGCTTGCGGGCCG	0.592																																																0			11											107	109	108					11																	70333475		2200	4294	6494	70011123	SO:0001583	missense	22941			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.1786G>T	11.37:g.70333475C>A	ENSP00000394536:p.Ala596Ser		70011123	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	C	4.799	0.148511	0.09134	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.38722	2.41;2.41;3.13;1.12;2.53;2.53	4.85	3.87	0.44632	.	0.452856	0.24044	N	0.042063	T	0.33265	0.0857	L	0.35414	1.06	0.80722	D	1	B;P;B	0.45348	0.227;0.856;0.218	B;B;B	0.43536	0.079;0.423;0.167	T	0.03981	-1.0987	10	0.18710	T	0.47	.	13.2864	0.60245	0.0:0.7061:0.2939:0.0	.	596;975;380	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	S	380;379;254;976;596;614;599	ENSP00000399423:A380S;ENSP00000386491:A379S;ENSP00000402944:A254S;ENSP00000345193:A976S;ENSP00000394536:A596S;ENSP00000294018:A599S	ENSP00000294018:A599S	A	-	1	0	SHANK2	70011123	1.000000	0.71417	0.989000	0.46669	0.059000	0.15707	1.353000	0.34045	2.250000	0.74265	0.655000	0.94253	GCC		0.592	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		A	70333475	C	A	70333475	3	1	111	1	0	0	0	0	1	0	0	0	14302	797	28	2	2634	2	SHANK2	11	70333475	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	56152	70333475	64673041	639	29773										
INPPL1	3636	hgsc.bcm.edu	37	chr11	71948748	71948748	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggccccctggagctgcagCccccccggggactgccctcg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:71948748delC	ENST00000298229.2	+	26	3664	c.3460delC	c.(3460-3462)cccfs	p.P1155fs	INPPL1_ENST00000538751.1_Frame_Shift_Del_p.P913fs|PHOX2A_ENST00000544057.1_5'Flank|INPPL1_ENST00000541756.1_Frame_Shift_Del_p.P913fs	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1155					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GGAGCTGCAGCCCCCCCGGGG	0.697																																																0			11											10	12	12					11																	71948748		2120	4190	6310	71626396	SO:0001589	frameshift_variant	3636			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3460delC	11.37:g.71948748delC	ENSP00000298229:p.Pro1155fs		71626396	B2RTX5|Q13577|Q13578	Frame_Shift_Del	DEL	ENST00000298229.2	37	CCDS8213.1																																																																																				0.697	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		-	71948748	C	-	71948748	7	5	111	1	0	1	0	1	0	0	0	0	7782	739	26	0	3562	0	INPPL1	11	71948748	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1615273	71948748	63057768	640	29774										
CLPB	81570	hgsc.bcm.edu	37	chr11	72028249	72028249	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcctcagcctcacgcttccGctgcttctcttggtactgtg	8	16	3	0	rs148534573	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:72028249G>A	ENST00000294053.3	-	8	1152	c.979C>T	c.(979-981)Cgg>Tgg	p.R327W	CLPB_ENST00000437826.2_Missense_Mutation_p.R282W|CLPB_ENST00000538039.1_Missense_Mutation_p.R297W|CLPB_ENST00000340729.5_Missense_Mutation_p.R268W|CLPB_ENST00000543042.1_Missense_Mutation_p.R126W	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	327					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						TCACGCTTCCGCTGCTTCTCT	0.617																																																0			11						G	TRP/ARG	1,4399	2.1+/-5.4	0,1,2199	68	58	61		979	5	1	11	dbSNP_134	61	8,8578	6.4+/-24.3	0,8,4285	yes	missense	CLPB	NM_030813.3	101	0,9,6484	AA,AG,GG		0.0932,0.0227,0.0693	probably-damaging	327/708	72028249	9,12977	2200	4293	6493	71705897	SO:0001583	missense	81570			BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"Ankyrin repeat domain containing"	30664	protein-coding gene	gene with protein product	"suppressor of potassium transport defect 3"					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.979C>T	11.37:g.72028249G>A	ENSP00000294053:p.Arg327Trp		71705897	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	37	CCDS8215.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998773	0.74818	2.27E-4	9.32E-4	ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000535990;ENST00000340729;ENST00000437826;ENST00000543042;ENST00000544683	T;T;T;T;T;T;T	0.68025	1.76;0.99;1.99;-0.3;2.24;0.28;0.73	5.9	4.97	0.65823	Ankyrin repeat-containing domain (1);	0.137925	0.48767	D	0.000172	T	0.69151	0.3079	N	0.22421	0.69	0.42406	D	0.992583	D;D;D;D;D	0.89917	0.996;0.999;0.999;0.999;1.0	P;D;P;D;D	0.65684	0.617;0.933;0.859;0.933;0.937	T	0.73745	-0.3886	10	0.87932	D	0	-21.5125	12.6773	0.56901	0.0:0.0:0.6903:0.3097	.	126;268;282;297;327	B4DXW4;F8W7P6;E7EWN6;Q9H078-2;Q9H078	.;.;.;.;CLPB_HUMAN	W	327;297;332;268;282;126;151	ENSP00000294053:R327W;ENSP00000441518:R297W;ENSP00000443822:R332W;ENSP00000340385:R268W;ENSP00000407296:R282W;ENSP00000439746:R126W;ENSP00000442651:R151W	ENSP00000294053:R327W	R	-	1	2	CLPB	71705897	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	4.227000	0.58612	1.448000	0.47680	0.655000	0.94253	CGG		0.617	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813		A	72028249	G	A	72028249	3	1	111	1	0	0	0	0	1	0	0	0	3557	1086	38	1	1184	1	CLPB	11	72028249	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	79501	72028249	62978267	641	29775										
ARAP1	116985	hgsc.bcm.edu	37	chr11	72437975	72437975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggggccggtgaggtatgggCacggagcaggccagccagga	20	9	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:72437975C>T	ENST00000393609.3	-	3	401	c.199G>A	c.(199-201)Gcc>Acc	p.A67T	ARAP1_ENST00000455638.2_Missense_Mutation_p.A67T|ARAP1_ENST00000359373.5_Missense_Mutation_p.A67T	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	67	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GAGGTATGGGCACGGAGCAGG	0.692																																					Ovarian(102;1198 1520 13195 17913 37529)											0			11											12	20	17					11																	72437975		2105	4200	6305	72115623	SO:0001583	missense	116985			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.199G>A	11.37:g.72437975C>T	ENSP00000377233:p.Ala67Thr		72115623	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	0.631	-0.817314	0.02776	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393609	T;T;T	0.06294	3.33;3.33;3.32	4.56	3.65	0.41850	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);	0.126528	0.36066	N	0.002818	T	0.04815	0.0130	L	0.41824	1.3	0.29801	N	0.832404	B;B	0.33883	0.376;0.43	B;B	0.30572	0.071;0.117	T	0.23332	-1.0191	10	0.15499	T	0.54	.	7.1762	0.25747	0.0:0.7331:0.1733:0.0936	.	67;67	Q96P48-3;Q96P48	.;ARAP1_HUMAN	T	67	ENSP00000352332:A67T;ENSP00000390461:A67T;ENSP00000377233:A67T	ENSP00000352332:A67T	A	-	1	0	ARAP1	72115623	0.450000	0.25697	0.985000	0.45067	0.091000	0.18340	0.705000	0.25675	1.131000	0.42111	0.555000	0.69702	GCC		0.692	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		T	72437975	C	T	72437975	3	4	111	1	0	0	0	0	1	0	0	0	838	710	25	3	4285	3	ARAP1	11	72437975	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	409726	72437975	62568541	642	29776										
PCF11	51585	hgsc.bcm.edu	37	chr11	82878210	82878210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtaaacctcctcatctgaggCatagggagagctggtcaagc	12	10	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:82878210C>T	ENST00000298281.4	+	6	2313	c.1861C>T	c.(1861-1863)Cat>Tat	p.H621Y		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	621					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TCATCTGAGGCATAGGGAGAG	0.388																																																0			11											136	132	133					11																	82878210		1915	4146	6061	82555858	SO:0001583	missense	51585			AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1861C>T	11.37:g.82878210C>T	ENSP00000298281:p.His621Tyr		82555858	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824550	0.71143	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.57273	1.33;0.41;0.5	5.98	5.98	0.97165	.	0.000000	0.64402	D	0.000011	T	0.64778	0.2629	L	0.32530	0.975	0.51233	D	0.999917	D;D	0.69078	0.997;0.981	D;D	0.75484	0.986;0.954	T	0.58567	-0.7614	9	.	.	.	.	20.452	0.99131	0.0:1.0:0.0:0.0	.	621;621	E9PQ01;O94913	.;PCF11_HUMAN	Y	621	ENSP00000298281:H621Y;ENSP00000434540:H621Y;ENSP00000431567:H621Y	.	H	+	1	0	PCF11	82555858	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.610000	0.74178	2.838000	0.97847	0.591000	0.81541	CAT		0.388	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82878210	C	T	82878210	3	4	111	1	0	0	0	0	1	0	0	0	11604	710	25	3	1883	3	PCF11	11	82878210	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10440235	82878210	52128306	643	29777										
FAT3	120114	hgsc.bcm.edu	37	chr11	92532199	92532199	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agttgctattgtcaatgcagTtggaaatcgccttaatgagc	10	7	1	1	rs563450153		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:92532199T>A	ENST00000298047.6	+	9	6037	c.6020T>A	c.(6019-6021)gTt>gAt	p.V2007D	FAT3_ENST00000525166.1_Missense_Mutation_p.V1857D|FAT3_ENST00000409404.2_Missense_Mutation_p.V2007D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2007	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GTCAATGCAGTTGGAAATCGC	0.423										TCGA Ovarian(4;0.039)																																						0			11											136	133	134					11																	92532199		1901	4123	6024	92171847	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6020T>A	11.37:g.92532199T>A	ENSP00000298047:p.Val2007Asp		92171847	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	T	16.99	3.274450	0.59649	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.28069	1.63;1.63;1.63	5.82	5.82	0.92795	.	.	.	.	.	T	0.35393	0.0930	N	0.25380	0.74	0.80722	D	1	P	0.46621	0.881	P	0.53185	0.72	T	0.03945	-1.0990	9	0.28530	T	0.3	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	2007	Q8TDW7-3	.	D	2007;2007;1857	ENSP00000298047:V2007D;ENSP00000387040:V2007D;ENSP00000432586:V1857D	ENSP00000298047:V2007D	V	+	2	0	FAT3	92171847	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	7.975000	0.88055	2.228000	0.72767	0.533000	0.62120	GTT		0.423	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92532199	T	A	92532199	3	1	111	1	0	0	0	0	1	0	0	0	5710	1725	60	5	6054	5	FAT3	11	92532199	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	9653989	92532199	42474317	644	29778										
FAT3	120114	hgsc.bcm.edu	37	chr11	92534950	92534950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatgacaatgcaccagtctTcgcgcaggaagtgtaccgag	11	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:92534950T>G	ENST00000298047.6	+	9	8788	c.8771T>G	c.(8770-8772)tTc>tGc	p.F2924C	FAT3_ENST00000525166.1_Missense_Mutation_p.F2774C|FAT3_ENST00000409404.2_Missense_Mutation_p.F2924C			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2924	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GCACCAGTCTTCGCGCAGGAA	0.552										TCGA Ovarian(4;0.039)																																						0			11											103	101	102					11																	92534950		2033	4196	6229	92174598	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.8771T>G	11.37:g.92534950T>G	ENSP00000298047:p.Phe2924Cys		92174598	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	T	15.87	2.961071	0.53400	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.03413	3.94;3.94;3.94	6.04	6.04	0.98038	.	.	.	.	.	T	0.25975	0.0633	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.07290	-1.0780	9	0.87932	D	0	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	2924	Q8TDW7-3	.	C	2924;2924;2774	ENSP00000298047:F2924C;ENSP00000387040:F2924C;ENSP00000432586:F2774C	ENSP00000298047:F2924C	F	+	2	0	FAT3	92174598	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	7.975000	0.88055	2.317000	0.78254	0.460000	0.39030	TTC		0.552	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92534950	T	G	92534950	3	3	111	1	0	0	0	0	1	0	0	0	5710	1783	62	4	8805	4	FAT3	11	92534950	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2751	92534950	42471566	645	29779										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92715053	92715053	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgtgtccttctgctacctgCgcatctgggtgctggtgctt	12	12	2	0	rs549634756		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:92715053C>T	ENST00000257068.2	+	2	670	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	222					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CTGCTACCTGCGCATCTGGGT	0.597																																																0			11											65	57	60					11																	92715053		2201	4298	6499	92354701	SO:0001583	missense	4544			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.664C>T	11.37:g.92715053C>T	ENSP00000257068:p.Arg222Cys		92354701		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118553	0.37436	.	.	ENSG00000134640	ENST00000257068	T	0.39592	1.07	4.21	2.18	0.27775	GPCR, rhodopsin-like superfamily (1);	0.128742	0.52532	D	0.000067	T	0.49558	0.1564	M	0.89785	3.06	0.58432	D	0.999998	P	0.37525	0.598	B	0.39419	0.299	T	0.56625	-0.7948	10	0.49607	T	0.09	-11.5791	9.3531	0.38151	0.1425:0.7773:0.0:0.0802	.	222	P49286	MTR1B_HUMAN	C	222	ENSP00000257068:R222C	ENSP00000257068:R222C	R	+	1	0	MTNR1B	92354701	1.000000	0.71417	0.993000	0.49108	0.253000	0.25986	1.493000	0.35605	1.122000	0.41944	-0.424000	0.05967	CGC		0.597	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			T	92715053	C	T	92715053	3	4	111	1	0	0	0	0	1	0	0	0	9982	768	27	1	670	1	MTNR1B	11	92715053	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	180103	92715053	42291463	646	29780										
CCDC67	159989	hgsc.bcm.edu	37	chr11	93104239	93104240	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accaaactcaactaaatggtINSaaaaaacagtgcttagaaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:93104239_93104240insA	ENST00000298050.3	+	7	682_683	c.582_583insA	c.(583-585)aaafs	p.K195fs		NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	195					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				AACTAAATGGTAAAAAACAGTG	0.332																																																0			11																																								92743888	SO:0001589	frameshift_variant	159989			AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.588dupA	11.37:g.93104245_93104245dupA	ENSP00000298050:p.Lys195fs		92743887	Q8NEF1|Q96LL7	Frame_Shift_Ins	INS	ENST00000298050.3	37	CCDS44707.1																																																																																				0.332	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		A	93104240	-	A	93104239	7	5	111	1	0	1	1	0	0	0	0	0	2845	1625	57	0	604	0	CCDC67	11	93104239	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	389186	93104239	41902277	647	29781										
CCDC82	79780	hgsc.bcm.edu	37	chr11	96098144	96098144	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gattagagggaagaaaatacCtgtttatcatgtgacatgaa	10	4	1	4	rs143571415		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:96098144C>A	ENST00000278520.5	-	7	1808	c.1380G>T	c.(1378-1380)caG>caT	p.Q460H	CCDC82_ENST00000542662.1_Splice_Site_p.Q460H|CCDC82_ENST00000423339.2_Splice_Site_p.Q460H			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	460										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		AAGAAAATACCTGTTTATCAT	0.318																																																0			11											81	81	81					11																	96098144		2201	4298	6499	95737792	SO:0001630	splice_region_variant	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.1380+1G>T	11.37:g.96098144C>A			95737792	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070245	0.76301	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.27104	1.69;1.69;1.69	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000001	T	0.51007	0.1649	M	0.71581	2.175	0.58432	D	0.999995	D	0.89917	1.0	D	0.79108	0.992	T	0.48969	-0.8987	9	.	.	.	-13.1118	17.5022	0.87735	0.0:1.0:0.0:0.0	.	460	Q8N4S0	CCD82_HUMAN	H	460	ENSP00000278520:Q460H;ENSP00000444010:Q460H;ENSP00000397156:Q460H	.	Q	-	3	2	CCDC82	95737792	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.898000	0.63238	2.490000	0.84030	0.591000	0.81541	CAG		0.318	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725	Missense_Mutation	A	96098144	C	A	96098144	5	1	111	1	0	0	0	0	0	0	1	0	2862	695	24	2	266	2	CCDC82	11	96098144	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2993905	96098144	38908372	648	29782										
CCDC82	79780	hgsc.bcm.edu	37	chr11	96098232	96098232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcactgaatatttacagtagCgatgcagtccacaagcctgg	10	10	0	1	rs202142231		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:96098232C>T	ENST00000278520.5	-	7	1720	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	CCDC82_ENST00000542662.1_Missense_Mutation_p.R431H|CCDC82_ENST00000423339.2_Missense_Mutation_p.R431H			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	431										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		TTTACAGTAGCGATGCAGTCC	0.348																																																0			11											90	88	89					11																	96098232		2201	4298	6499	95737880	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.1292G>A	11.37:g.96098232C>T	ENSP00000278520:p.Arg431His		95737880	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150152	0.78001	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.47177	0.85;0.85;0.85	5.22	4.31	0.51392	.	0.000000	0.64402	D	0.000001	T	0.65123	0.2661	M	0.66939	2.045	0.48696	D	0.999695	D	0.89917	1.0	D	0.85130	0.997	T	0.66724	-0.5851	10	0.51188	T	0.08	-7.3303	12.8887	0.58058	0.0:0.9192:0.0:0.0808	.	431	Q8N4S0	CCD82_HUMAN	H	431	ENSP00000278520:R431H;ENSP00000444010:R431H;ENSP00000397156:R431H	ENSP00000278520:R431H	R	-	2	0	CCDC82	95737880	1.000000	0.71417	0.448000	0.26945	0.997000	0.91878	4.898000	0.63238	1.335000	0.45486	0.591000	0.81541	CGC		0.348	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		T	96098232	C	T	96098232	3	4	111	1	0	0	0	0	1	0	0	0	2862	768	27	1	354	1	CCDC82	11	96098232	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	88	96098232	38908284	649	29783										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101815107	101815107	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttactgaaaaattccagcgTgcccatgttcctctttcaca	6	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:101815107T>C	ENST00000263468.8	+	3	630	c.360T>C	c.(358-360)cgT>cgC	p.R120R		NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	120										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AATTCCAGCGTGCCCATGTTC	0.353																																																0			11											80	79	79					11																	101815107		2203	4299	6502	101320317	SO:0001819	synonymous_variant	57562			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.360T>C	11.37:g.101815107T>C			101320317	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																				0.353	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		C	101815107	T	C	101815107	2	2	111	1	0	0	0	0	0	0	0	1	8248	1683	59	4		4	KIAA1377	11	101815107	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	5716875	101815107	33191409	650	29784										
MMP12	4321	hgsc.bcm.edu	37	chr11	102738104	102738104	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	attgtcaggatttggcaagcGttggttctcttttgggtctc	12	7	3	0	rs202044860		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:102738104G>A	ENST00000532855.1	-	0	903							P39900	MMP12_HUMAN	matrix metallopeptidase 12 (macrophage elastase)						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|proteolysis (GO:0006508)|wound healing, spreading of epidermal cells (GO:0035313)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	26		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)|Marimastat(DB00786)	TTTGGCAAGCGTTGGTTCTCT	0.383																																																0			11											130	122	125					11																	102738104		1843	4096	5939	102243314			4321			L23808	CCDS73375.1	11q22.3	2009-02-26	2005-08-08			ENSG00000262406			7158	protein-coding gene	gene with protein product		601046	"matrix metalloproteinase 12 (macrophage elastase)"				Standard	NM_002426		Approved	HME	uc001phk.3	P39900			11.37:g.102738104G>A			102243314	B2R9X8|B7ZLF6|Q2M1L9	Silent	SNP	ENST00000532855.1	37																																																																																					0.383	MMP12-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000386646.1	NM_002426		A	102738104	G	A	102738104	1	1	111	0	1	0	0	0	0	0	0	0	9681	1145	40	1		1	MMP12	11	102738104	RNA	SNP	G	TCGA-EI-6507-01A-11D-1733-10	922997	102738104	32268412	651	29785										
ATM	472	hgsc.bcm.edu	37	chr11	108122664	108122664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtgtgaagtaaatagaagcTtttctttaaaggaatcaata	8	3	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:108122664T>C	ENST00000452508.2	+	12	1897	c.1708T>C	c.(1708-1710)Ttt>Ctt	p.F570L	ATM_ENST00000278616.4_Missense_Mutation_p.F570L			Q13315	ATM_HUMAN	ATM serine/threonine kinase	570			F -> S (in AT). {ECO:0000269|PubMed:9887333}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AAATAGAAGCTTTTCTTTAAA	0.373			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											116	119	118					11																	108122664		2201	4298	6499	107627874	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.1708T>C	11.37:g.108122664T>C	ENSP00000388058:p.Phe570Leu		107627874	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.806224	0.31961	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.56275	0.47;0.47;0.47	5.91	3.53	0.40419	Armadillo-type fold (1);	0.685523	0.15372	N	0.265783	T	0.37433	0.1003	L	0.44542	1.39	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	T	0.30090	-0.9990	10	0.11485	T	0.65	.	4.4935	0.11826	0.1334:0.2072:0.0:0.6594	.	570	Q13315	ATM_HUMAN	L	570	ENSP00000435747:F570L;ENSP00000278616:F570L;ENSP00000388058:F570L	ENSP00000278616:F570L	F	+	1	0	ATM	107627874	0.142000	0.22610	0.983000	0.44433	0.787000	0.44495	0.457000	0.21875	0.449000	0.26747	0.455000	0.32223	TTT		0.373	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108122664	T	C	108122664	3	2	111	1	0	0	0	0	1	0	0	0	1110	1609	56	4	1746	4	ATM	11	108122664	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	5384560	108122664	26883852	652	29786										
ATM	472	hgsc.bcm.edu	37	chr11	108173661	108173661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtggattcctctaagtgaaAatcatgacatttggataaag	9	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:108173661A>G	ENST00000452508.2	+	37	5590	c.5401A>G	c.(5401-5403)Aat>Gat	p.N1801D	ATM_ENST00000278616.4_Missense_Mutation_p.N1801D			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1801					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.N1801Y(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCTAAGTGAAAATCATGACAT	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											131	138	135					11																	108173661		2201	4298	6499	107678871	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5401A>G	11.37:g.108173661A>G	ENSP00000388058:p.Asn1801Asp		107678871	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	4.957	0.177716	0.09443	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.70631	-0.5;-0.5	5.1	3.96	0.45880	Armadillo-type fold (1);	0.319150	0.41823	D	0.000801	T	0.52240	0.1722	N	0.20685	0.6	0.26812	N	0.968976	B	0.02656	0.0	B	0.06405	0.002	T	0.37009	-0.9724	10	0.25751	T	0.34	.	10.4835	0.44708	0.9231:0.0:0.0769:0.0	.	1801	Q13315	ATM_HUMAN	D	1801	ENSP00000278616:N1801D;ENSP00000388058:N1801D	ENSP00000278616:N1801D	N	+	1	0	ATM	107678871	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	3.732000	0.55021	2.018000	0.59344	0.528000	0.53228	AAT		0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108173661	A	G	108173661	3	3	111	1	0	0	0	0	1	0	0	0	1110	14	1	4	5539	4	ATM	11	108173661	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	50997	108173661	26832855	653	29787										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110007988	110007988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacttggaaataaaagtgagGctgatcaaacggttagtaca	10	5	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:110007988G>A	ENST00000278590.3	+	2	673	c.622G>A	c.(622-624)Gct>Act	p.A208T	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.A177T|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.A209T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	208							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TAAAAGTGAGGCTGATCAAAC	0.373																																																0			11											64	60	61					11																	110007988		1860	4085	5945	109513198	SO:0001583	missense	85463				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.622G>A	11.37:g.110007988G>A	ENSP00000278590:p.Ala208Thr		109513198	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	g	12.31	1.899078	0.33535	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.31769	1.48;1.48;1.48	5.65	0.0442	0.14224	.	425.996000	0.02679	U	0.109496	T	0.25195	0.0612	L	0.41824	1.3	0.23773	N	0.996886	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19451	-1.0305	10	0.10902	T	0.67	-0.1325	9.022	0.36206	0.6645:0.0:0.3355:0.0	.	209;208;208	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	T	208;209;177	ENSP00000278590:A208T;ENSP00000431821:A209T;ENSP00000413094:A177T	ENSP00000278590:A208T	A	+	1	0	ZC3H12C	109513198	0.019000	0.18553	0.963000	0.40424	0.979000	0.70002	1.151000	0.31651	0.010000	0.14839	0.650000	0.86243	GCT		0.373	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		A	110007988	G	A	110007988	3	1	111	1	0	0	0	0	1	0	0	0	17602	1203	42	3	628	3	ZC3H12C	11	110007988	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1834327	110007988	24998528	654	29788										
DLAT	1737	hgsc.bcm.edu	37	chr11	111899620	111899620	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgctgccactgcttcgccacCtacaccttctgctcaggctc	7	18	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:111899620C>A	ENST00000280346.6	+	4	1270	c.611C>A	c.(610-612)cCt>cAt	p.P204H	DLAT_ENST00000393051.1_Missense_Mutation_p.P204H|DLAT_ENST00000537636.1_Intron	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	204					cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		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)		GCTTCGCCACCTACACCTTCT	0.527																																																0			11											90	88	89					11																	111899620		2201	4297	6498	111404830	SO:0001583	missense	1737			Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"E2 component of pyruvate dehydrogenase complex"	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.611C>A	11.37:g.111899620C>A	ENSP00000280346:p.Pro204His		111404830	Q16783|Q53EP3	Missense_Mutation	SNP	ENST00000280346.6	37	CCDS8354.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996562	0.54147	.	.	ENSG00000150768	ENST00000280346;ENST00000534998;ENST00000393051	T;T	0.18338	2.22;2.29	5.22	5.22	0.72569	.	0.244255	0.40728	N	0.001021	T	0.37652	0.1011	L	0.52573	1.65	0.80722	D	1	D;P	0.89917	1.0;0.856	D;B	0.68765	0.96;0.235	T	0.03969	-1.0988	10	0.54805	T	0.06	-8.6278	19.1652	0.93553	0.0:1.0:0.0:0.0	.	204;204	E9PEJ4;P10515	.;ODP2_HUMAN	H	204;172;204	ENSP00000280346:P204H;ENSP00000376771:P204H	ENSP00000280346:P204H	P	+	2	0	DLAT	111404830	0.695000	0.27747	0.033000	0.17914	0.058000	0.15608	6.156000	0.71840	2.607000	0.88179	0.585000	0.79938	CCT		0.527	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931		A	111899620	C	A	111899620	3	1	111	1	0	0	0	0	1	0	0	0	4560	681	24	2	625	2	DLAT	11	111899620	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1891632	111899620	23106896	655	29789										
CLDN25	644672	hgsc.bcm.edu	37	chr11	113650572	113650572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggggctacttctctccctcCttggctgggtctgctcctgt	12	14	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:113650572C>A	ENST00000453129.2	+	1	104	c.55C>A	c.(55-57)Ctt>Att	p.L19I		NM_001101389.1	NP_001094859.1	C9JDP6	CLD25_HUMAN	claudin 25	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			large_intestine(1)|lung(6)|ovary(1)|urinary_tract(2)	10						TCTCTCCCTCCTTGGCTGGGT	0.547																																																0			11											88	95	93					11																	113650572		2091	4225	6316	113155782	SO:0001583	missense	0				CCDS44736.1	11q23.2	2009-09-22			ENSG00000228607	ENSG00000228607			37218	protein-coding gene	gene with protein product							Standard	NM_001101389		Approved		uc009yyw.1	C9JDP6	OTTHUMG00000168193	ENST00000453129.2:c.55C>A	11.37:g.113650572C>A	ENSP00000396304:p.Leu19Ile		113155782		Missense_Mutation	SNP	ENST00000453129.2	37	CCDS44736.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.202495	0.38905	.	.	ENSG00000228607	ENST00000453129	D	0.88354	-2.37	5.04	2.04	0.26737	.	.	.	.	.	D	0.83769	0.5326	L	0.43923	1.385	0.09310	N	0.999999	P	0.50156	0.932	P	0.47346	0.544	T	0.72308	-0.4332	9	0.33141	T	0.24	.	2.3387	0.04254	0.1336:0.5093:0.13:0.2271	.	19	C9JDP6	CLD25_HUMAN	I	19	ENSP00000396304:L19I	ENSP00000396304:L19I	L	+	1	0	CLDN25	113155782	0.001000	0.12720	0.754000	0.31244	0.958000	0.62258	-0.083000	0.11286	0.267000	0.21916	0.655000	0.94253	CTT		0.547	CLDN25-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398706.1	NM_001101389		A	113650572	C	A	113650572	3	1	111	1	0	0	0	0	1	0	0	0	3491	681	24	2	57	2	CLDN25	11	113650572	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1750952	113650572	21355944	656	29790										
CLDN25	644672	hgsc.bcm.edu	37	chr11	113650938	113650938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccttccagtctcctgggtgGcccatgccacaatccaagac	8	16	1	1	rs187854554		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:113650938G>A	ENST00000453129.2	+	1	470	c.421G>A	c.(421-423)Gcc>Acc	p.A141T		NM_001101389.1	NP_001094859.1	C9JDP6	CLD25_HUMAN	claudin 25	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			large_intestine(1)|lung(6)|ovary(1)|urinary_tract(2)	10						CTCCTGGGTGGCCCATGCCAC	0.567																																																0			11											69	73	72					11																	113650938		1961	4136	6097	113156148	SO:0001583	missense	0				CCDS44736.1	11q23.2	2009-09-22			ENSG00000228607	ENSG00000228607			37218	protein-coding gene	gene with protein product							Standard	NM_001101389		Approved		uc009yyw.1	C9JDP6	OTTHUMG00000168193	ENST00000453129.2:c.421G>A	11.37:g.113650938G>A	ENSP00000396304:p.Ala141Thr		113156148		Missense_Mutation	SNP	ENST00000453129.2	37	CCDS44736.1	.	.	.	.	.	.	.	.	.	.	G	33	5.214361	0.95104	.	.	ENSG00000228607	ENST00000453129	D	0.87103	-2.21	5.1	5.1	0.69264	.	.	.	.	.	D	0.92932	0.7751	M	0.71296	2.17	0.54753	D	0.999983	D	0.89917	1.0	D	0.97110	1.0	D	0.93503	0.6846	9	0.87932	D	0	.	17.2551	0.87053	0.0:0.0:1.0:0.0	.	141	C9JDP6	CLD25_HUMAN	T	141	ENSP00000396304:A141T	ENSP00000396304:A141T	A	+	1	0	CLDN25	113156148	1.000000	0.71417	0.993000	0.49108	0.923000	0.55619	7.239000	0.78182	2.636000	0.89361	0.655000	0.94253	GCC		0.567	CLDN25-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398706.1	NM_001101389		A	113650938	G	A	113650938	3	1	111	1	0	0	0	0	1	0	0	0	3491	1203	42	3	423	3	CLDN25	11	113650938	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	366	113650938	21355578	657	29791										
HTR3A	3359	hgsc.bcm.edu	37	chr11	113853982	113853982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcgatgtccagaactgctCgctgaccttcaccagttggc	9	14	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:113853982C>T	ENST00000504030.2	+	5	960	c.515C>T	c.(514-516)tCg>tTg	p.S172L	HTR3A_ENST00000506841.2_Missense_Mutation_p.S172L|HTR3A_ENST00000299961.5_Missense_Mutation_p.S157L|HTR3A_ENST00000355556.2_Missense_Mutation_p.S178L|HTR3A_ENST00000535865.1_5'UTR|HTR3A_ENST00000375498.2_Missense_Mutation_p.S178L			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	172					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	CAGAACTGCTCGCTGACCTTC	0.587																																																0			11											192	174	180					11																	113853982		2201	4296	6497	113359192	SO:0001583	missense	3359			D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.515C>T	11.37:g.113853982C>T	ENSP00000424189:p.Ser172Leu		113359192	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	C	18.77	3.695727	0.68386	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4	5.56	5.56	0.83823	.	0.205916	0.42682	D	0.000677	D	0.89543	0.6745	M	0.82923	2.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.992;0.994	D	0.85891	0.1428	10	0.10377	T	0.69	-17.2352	19.5273	0.95212	0.0:1.0:0.0:0.0	.	157;178;178	B4DSY6;G5E986;Q7KZM7	.;.;.	L	172;178;178;172;157	ENSP00000424189:S172L;ENSP00000347754:S178L;ENSP00000364648:S178L;ENSP00000424776:S172L;ENSP00000299961:S157L	ENSP00000299961:S157L	S	+	2	0	HTR3A	113359192	1.000000	0.71417	0.900000	0.35374	0.211000	0.24417	4.176000	0.58269	2.615000	0.88500	0.555000	0.69702	TCG		0.587	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		T	113853982	C	T	113853982	3	4	111	1	0	0	0	0	1	0	0	0	7465	893	31	1	577	1	HTR3A	11	113853982	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	203044	113853982	21152534	658	29792										
FAM55A	120400	hgsc.bcm.edu	37	chr11	114400937	114400937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttgtctgtaagataagataCctctctattccgggtggtca	9	9	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:114400937C>T	ENST00000424269.1	-	2	792	c.793G>A	c.(793-795)Gta>Ata	p.V265I	NXPE1_ENST00000536271.1_5'Flank|NXPE1_ENST00000251921.2_Missense_Mutation_p.V123I|snoU13_ENST00000459372.1_RNA|NXPE1_ENST00000536312.1_Missense_Mutation_p.V265I			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	265						extracellular region (GO:0005576)											AGATAAGATACCTCTCTATTC	0.458																																																0			11											92	92	92					11																	114400937		2201	4296	6497	113906147	SO:0001583	missense	120400			BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"family with sequence similarity 55, member A"	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.793G>A	11.37:g.114400937C>T	ENSP00000411690:p.Val265Ile		113906147	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		.	.	.	.	.	.	.	.	.	.	C	0.814	-0.750895	0.03041	.	.	ENSG00000095110	ENST00000251921;ENST00000424269;ENST00000536312	T;T;T	0.44482	2.56;2.77;0.92	4.4	-1.87	0.07737	.	0.466168	0.18111	N	0.151362	T	0.17280	0.0415	N	0.05078	-0.115	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.25082	-1.0142	10	0.18710	T	0.47	.	8.9451	0.35753	0.0:0.5576:0.0:0.4424	.	265	F5H6W7	.	I	123;265;265	ENSP00000251921:V123I;ENSP00000411690:V265I;ENSP00000442984:V265I	ENSP00000251921:V123I	V	-	1	0	FAM55A	113906147	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.166000	0.16583	-0.230000	0.09840	-1.004000	0.02495	GTA		0.458	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		T	114400937	C	T	114400937	3	4	111	1	0	0	0	0	1	0	0	0	5603	507	18	3	866	3	FAM55A	11	114400937	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	546955	114400937	20605579	659	29793										
TAGLN	6876	hgsc.bcm.edu	37	chr11	117074069	117074069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtaccctgatggctccaagcCggtgaaggtgcccgagaacc	13	13	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:117074069C>T	ENST00000532870.1	+	2	1368	c.227C>T	c.(226-228)cCg>cTg	p.P76L	PCSK7_ENST00000529458.1_5'Flank|TAGLN_ENST00000392951.4_Missense_Mutation_p.P76L|TAGLN_ENST00000530649.1_Missense_Mutation_p.P76L			Q01995	TAGL_HUMAN	transgelin	76	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		GGCTCCAAGCCGGTGAAGGTG	0.577																																																0			11											93	91	92					11																	117074069		2201	4296	6497	116579279	SO:0001583	missense	6876			M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"SM22-alpha", "transgelin variant 2"	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.227C>T	11.37:g.117074069C>T	ENSP00000432282:p.Pro76Leu		116579279	O15542	Missense_Mutation	SNP	ENST00000532870.1	37	CCDS8381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.0|29.0	4.965507|4.965507	0.92855|0.92855	.|.	.|.	ENSG00000149591|ENSG00000149591	ENST00000392951;ENST00000525531;ENST00000278968;ENST00000529792;ENST00000530649;ENST00000532870|ENST00000529622	D;D;D;D;D;D|.	0.93426|.	-3.22;-3.22;-3.22;-3.22;-3.22;-3.22|.	4.84|4.84	4.84|4.84	0.62591|0.62591	Calponin homology domain (5);|.	0.365597|.	0.33419|.	N|.	0.004922|.	T|T	0.76905|0.76905	0.4053|0.4053	M|M	0.78223|0.78223	2.4|2.4	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	D|.	0.65443|.	0.935|.	T|T	0.77480|0.77480	-0.2572|-0.2572	10|5	0.72032|.	D|.	0.01|.	.|.	17.4727|17.4727	0.87650|0.87650	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	76|.	Q01995|.	TAGL_HUMAN|.	L|W	76|26	ENSP00000376678:P76L;ENSP00000432054:P76L;ENSP00000278968:P76L;ENSP00000431862:P76L;ENSP00000431941:P76L;ENSP00000432282:P76L|.	ENSP00000278968:P76L|.	P|R	+|+	2|1	0|2	TAGLN|TAGLN	116579279|116579279	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.953000|0.953000	0.61014|0.61014	7.098000|7.098000	0.76974|0.76974	2.666000|2.666000	0.90696|0.90696	0.561000|0.561000	0.74099|0.74099	CCG|CGG		0.577	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522		T	117074069	C	T	117074069	3	4	111	1	0	0	0	0	1	0	0	0	15577	652	23	1	233	1	TAGLN	11	117074069	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2673132	117074069	17932447	660	29794										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117389392	117389392	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgaccgtggggggcggggcGcccttggccgcacacatcag	18	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:117389392G>A	ENST00000321322.6	-	7	1480	c.1479C>T	c.(1477-1479)ggC>ggT	p.G493G	DSCAML1_ENST00000527706.1_Silent_p.G223G	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	433	Ig-like C2-type 5.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	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)		GGGGCGGGGCGCCCTTGGCCG	0.672																																																0			11											46	45	45					11																	117389392		2201	4296	6497	116894602	SO:0001819	synonymous_variant	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1479C>T	11.37:g.117389392G>A			116894602	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.672	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117389392	G	A	117389392	2	1	111	1	0	0	0	0	0	0	0	1	4780	1074	38	1		1	DSCAML1	11	117389392	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	315323	117389392	17617124	661	29795										
MLL	4297	hgsc.bcm.edu	37	chr11	118344186	118344186	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctgagctctcacctctcaCccccccgtcttctgtctctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:118344186delC	ENST00000389506.5	+	3	2312	c.2312delC	c.(2311-2313)accfs	p.T771fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.T771fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.T771fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	771					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TCACCTCTCACCCCCCCGTCT	0.453																																																0			11											197	169	178					11																	118344186		2200	4296	6496	117849396	SO:0001589	frameshift_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.2312delC	11.37:g.118344186delC	ENSP00000374157:p.Thr771fs		117849396	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	37	CCDS31686.1																																																																																				0.453	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118344186	C	-	118344186	7	5	111	1	0	1	0	1	0	0	0	0	9650	507	18	0	2322	0	MLL	11	118344186	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	954794	118344186	16662330	662	29796										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118773196	118773196	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccgctgcggagcagcagtCgctcaatgtctcgcagcgtc	12	15	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:118773196C>T	ENST00000334801.3	-	6	2220	c.1256G>A	c.(1255-1257)cGa>cAa	p.R419Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	419	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GAGCAGCAGTCGCTCAATGTC	0.682																																																0			11											25	28	27					11																	118773196		2198	4291	6489	118278406	SO:0001583	missense	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1256G>A	11.37:g.118773196C>T	ENSP00000335320:p.Arg419Gln		118278406	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.876449	0.91664	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	T	0.73258	-0.73	4.52	4.52	0.55395	B-cell lymphoma 9, beta-catenin binding domain (1);	0.000000	0.39407	N	0.001364	T	0.76478	0.3993	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.80480	-0.1364	10	0.87932	D	0	-16.1543	17.4217	0.87517	0.0:1.0:0.0:0.0	.	414;419	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	Q	419;382;419;419	ENSP00000335320:R419Q	ENSP00000335320:R419Q	R	-	2	0	BCL9L	118278406	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	5.816000	0.69222	2.365000	0.80145	0.305000	0.20034	CGA		0.682	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118773196	C	T	118773196	3	4	111	1	0	0	0	0	1	0	0	0	1383	884	31	1	3255	1	BCL9L	11	118773196	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	429010	118773196	16233320	663	29797										
CCDC84	338657	hgsc.bcm.edu	37	chr11	118882958	118882958	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatctctgacattcattggCcatcaggtacaaaggataag	8	10	3	1	rs376394064		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:118882958C>T	ENST00000334418.1	+	7	734	c.678C>T	c.(676-678)ggC>ggT	p.G226G	CCDC84_ENST00000580556.1_3'UTR	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	226										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CATTCATTGGCCATCAGGTAC	0.522																																																0			11						C		0,4400		0,0,2200	79	69	72		678	-1.7	1	11		72	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CCDC84	NM_198489.1		0,1,6494	TT,TC,CC		0.0116,0.0,0.0077		226/333	118882958	1,12989	2200	4295	6495	118388168	SO:0001819	synonymous_variant	338657			AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.678C>T	11.37:g.118882958C>T			118388168		Silent	SNP	ENST00000334418.1	37	CCDS8405.1																																																																																				0.522	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		T	118882958	C	T	118882958	2	4	111	1	0	0	0	0	0	0	0	1	2864	726	26	3		3	CCDC84	11	118882958	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	109762	118882958	16123558	664	29798										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118923452	118923452	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctcccgcacatcctttgctCtctgacccttgcgctgctca	6	18	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:118923452C>A	ENST00000404233.3	-	9	1008	c.884G>T	c.(883-885)aGa>aTa	p.R295I	HYOU1_ENST00000525859.1_Missense_Mutation_p.R295I|HYOU1_ENST00000543287.1_Missense_Mutation_p.R208I|HYOU1_ENST00000529972.1_Missense_Mutation_p.R295I	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	295					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		ATCCTTTGCTCTCTGACCCTT	0.592																																																0			11											71	65	67					11																	118923452		2200	4295	6495	118428662	SO:0001583	missense	10525			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.884G>T	11.37:g.118923452C>A	ENSP00000384144:p.Arg295Ile		118428662	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024480	0.35701	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.01015	5.44;5.44;5.44;5.44;5.44	5.23	1.29	0.21616	.	1.383790	0.04361	N	0.357469	T	0.01029	0.0034	N	0.20986	0.625	0.09310	N	1	B;B;B;B	0.33826	0.427;0.074;0.427;0.427	B;B;B;B	0.35655	0.207;0.15;0.207;0.207	T	0.50381	-0.8835	10	0.23891	T	0.37	2.3158	6.7999	0.23746	0.0:0.6134:0.0:0.3866	.	286;339;295;295	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	I	295;286;295;295;144;295;338;208;295	ENSP00000384144:R295I;ENSP00000437313:R295I;ENSP00000433397:R295I;ENSP00000442727:R208I;ENSP00000431874:R295I	ENSP00000278752:R286I	R	-	2	0	HYOU1	118428662	0.057000	0.20700	0.002000	0.10522	0.804000	0.45430	0.855000	0.27805	0.089000	0.17243	-0.150000	0.13652	AGA		0.592	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		A	118923452	C	A	118923452	3	1	111	1	0	0	0	0	1	0	0	0	7491	913	32	2	2187	2	HYOU1	11	118923452	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	40494	118923452	16083064	665	29799										
CCDC153	283152	hgsc.bcm.edu	37	chr11	119061086	119061086	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgctgctccttgtgcctggCgtgaagtctcagtgctgccc	12	13	1	1	rs563015042		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:119061086C>A	ENST00000503566.2	-	6	555	c.556G>T	c.(556-558)Gcc>Tcc	p.A186S	CCDC153_ENST00000415318.1_Missense_Mutation_p.A186S			Q494R4	CC153_HUMAN	coiled-coil domain containing 153	186										lung(3)|stomach(1)	4						TTGTGCCTGGCGTGAAGTCTC	0.572																																																0			11											120	105	110					11																	119061086		2200	4295	6495	118566296	SO:0001583	missense	283152				CCDS44753.1	11q23.3	2011-07-22			ENSG00000248712	ENSG00000248712			27446	protein-coding gene	gene with protein product						12477932	Standard	NM_001145018		Approved	LOC283152	uc010rze.2	Q494R4	OTTHUMG00000156903	ENST00000503566.2:c.556G>T	11.37:g.119061086C>A	ENSP00000423567:p.Ala186Ser		118566296		Missense_Mutation	SNP	ENST00000503566.2	37	CCDS44753.1	.	.	.	.	.	.	.	.	.	.	C	1.363	-0.588146	0.03799	.	.	ENSG00000248712	ENST00000503566;ENST00000415318	T;T	0.44482	0.92;0.92	4.61	1.69	0.24217	.	0.755857	0.12387	N	0.473391	T	0.24122	0.0584	L	0.39898	1.24	0.09310	N	1	P	0.38020	0.615	B	0.35727	0.209	T	0.10753	-1.0616	10	0.10111	T	0.7	-32.6832	1.012	0.01499	0.1575:0.4081:0.1537:0.2807	.	186	Q494R4	CC153_HUMAN	S	186	ENSP00000423567:A186S;ENSP00000445431:A186S	ENSP00000445431:A186S	A	-	1	0	CCDC153	118566296	0.001000	0.12720	0.004000	0.12327	0.024000	0.10985	-0.270000	0.08584	0.193000	0.20303	0.511000	0.50034	GCC		0.572	CCDC153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388331.2	NM_001033658		A	119061086	C	A	119061086	3	1	111	1	0	0	0	0	1	0	0	0	2793	768	27	2	80	2	CCDC153	11	119061086	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	137634	119061086	15945430	666	29800										
TECTA	7007	hgsc.bcm.edu	37	chr11	120996473	120996473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgcgtgtatgacctgtgcAgtgtgagggacaatggcacg	16	8	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:120996473A>G	ENST00000392793.1	+	8	1937	c.1666A>G	c.(1666-1668)Agt>Ggt	p.S556G	TECTA_ENST00000264037.2_Missense_Mutation_p.S556G			O75443	TECTA_HUMAN	tectorin alpha	556					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGACCTGTGCAGTGTGAGGGA	0.582																																																0			11											108	100	103					11																	120996473		2203	4299	6502	120501683	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1666A>G	11.37:g.120996473A>G	ENSP00000376543:p.Ser556Gly		120501683		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	A	9.704	1.155311	0.21454	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.76578	-1.03;-1.03	4.91	4.91	0.64330	Uncharacterised domain, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.59932	0.2230	N	0.16862	0.45	0.35376	D	0.789462	B	0.18013	0.025	B	0.22152	0.038	T	0.60535	-0.7244	10	0.14656	T	0.56	.	9.408	0.38473	0.9194:0.0:0.0806:0.0	.	556	O75443	TECTA_HUMAN	G	556	ENSP00000376543:S556G;ENSP00000264037:S556G	ENSP00000264037:S556G	S	+	1	0	TECTA	120501683	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.561000	0.60809	1.985000	0.57927	0.460000	0.39030	AGT		0.582	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	120996473	A	G	120996473	3	3	111	1	0	0	0	0	1	0	0	0	15786	188	7	4	1692	4	TECTA	11	120996473	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1935387	120996473	14010043	667	29801										
TECTA	7007	hgsc.bcm.edu	37	chr11	120998520	120998520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtgcacaagcagctgccccGacacatgctccgacctgacg	10	16	0	1	rs143730090	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:120998520G>A	ENST00000392793.1	+	9	2105	c.1834G>A	c.(1834-1836)Gac>Aac	p.D612N	TECTA_ENST00000264037.2_Missense_Mutation_p.D612N			O75443	TECTA_HUMAN	tectorin alpha	612	TIL 1.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CAGCTGCCCCGACACATGCTC	0.632													G|||	2	0.000399361	8e-04	0.0014	5008	,	,		18317	0		0	False		,,,				2504	0															0			11						G	ASN/ASP	22,4384	29.0+/-57.7	0,22,2181	65	67	66		1834	3.5	0.7	11	dbSNP_134	66	0,8596		0,0,4298	yes	missense	TECTA	NM_005422.2	23	0,22,6479	AA,AG,GG		0.0,0.4993,0.1692	possibly-damaging	612/2156	120998520	22,12980	2203	4298	6501	120503730	SO:0001583	missense	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1834G>A	11.37:g.120998520G>A	ENSP00000376543:p.Asp612Asn		120503730		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	14.44	2.535013	0.45073	0.004993	0.0	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.90563	-2.69;-2.69	5.52	3.47	0.39725	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.055363	0.64402	D	0.000001	D	0.82572	0.5066	L	0.28556	0.865	0.32950	D	0.519588	B	0.26081	0.141	B	0.15484	0.013	T	0.78094	-0.2338	10	0.18276	T	0.48	.	12.2846	0.54786	0.1478:0.0:0.8522:0.0	.	612	O75443	TECTA_HUMAN	N	612	ENSP00000376543:D612N;ENSP00000264037:D612N	ENSP00000264037:D612N	D	+	1	0	TECTA	120503730	1.000000	0.71417	0.716000	0.30569	0.922000	0.55478	3.068000	0.50018	0.688000	0.31529	-0.137000	0.14449	GAC		0.632	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	120998520	G	A	120998520	3	1	111	1	0	0	0	0	1	0	0	0	15786	1058	37	1	1864	1	TECTA	11	120998520	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2047	120998520	14007996	668	29802										
OR10G9	219870	hgsc.bcm.edu	37	chr11	123894346	123894347	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctagtggcctcgggctgcINStttctcctgatagtgctgtc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:123894346_123894347insT	ENST00000375024.1	+	1	627_628	c.627_628insT	c.(628-630)tttfs	p.F210fs		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CCTCGGGCTGCTTTCTCCTGAT	0.554																																																0			11																																								123399557	SO:0001589	frameshift_variant	219870			AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"GPCR / Class A : Olfactory receptors"	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.630dupT	11.37:g.123894349_123894349dupT	ENSP00000364164:p.Phe210fs		123399556		Frame_Shift_Ins	INS	ENST00000375024.1	37	CCDS31703.1																																																																																				0.554	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		T	123894347	-	T	123894346	7	5	111	1	0	1	1	0	0	0	0	0	10935	805	28	0	629	0	OR10G9	11	123894346	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	2895826	123894346	11112170	669	29803										
OR8B2	26595	hgsc.bcm.edu	37	chr11	124253130	124253130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaggttgcctaccatggtgAcaatgtagatcactagaaac	9	9	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:124253130A>G	ENST00000375013.2	-	1	128	c.110T>C	c.(109-111)gTc>gCc	p.V37A		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TACCATGGTGACAATGTAGAT	0.413																																																0			11											215	185	195					11																	124253130		2201	4299	6500	123758340	SO:0001583	missense	26595			AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"GPCR / Class A : Olfactory receptors"	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.110T>C	11.37:g.124253130A>G	ENSP00000364152:p.Val37Ala		123758340	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	37	CCDS31708.1	.	.	.	.	.	.	.	.	.	.	a	13.81	2.347884	0.41599	.	.	ENSG00000204293	ENST00000375013	T	0.00596	6.32	4.2	3.08	0.35506	.	0.669254	0.13823	N	0.360254	T	0.00496	0.0016	N	0.21448	0.665	0.09310	N	0.999998	P	0.34800	0.469	B	0.31946	0.138	T	0.52245	-0.8601	10	0.62326	D	0.03	.	7.031	0.24967	0.8062:0.0:0.1938:0.0	.	37	Q96RD0	OR8B2_HUMAN	A	37	ENSP00000364152:V37A	ENSP00000364152:V37A	V	-	2	0	OR8B2	123758340	0.003000	0.15002	0.112000	0.21494	0.217000	0.24651	1.990000	0.40717	0.789000	0.33779	0.329000	0.21502	GTC		0.413	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		G	124253130	A	G	124253130	3	3	111	1	0	0	0	0	1	0	0	0	11258	275	10	4	834	4	OR8B2	11	124253130	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	358784	124253130	10753386	670	29804										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124756449	124756449	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccgggcaaagtgagcatcaGcgaggaaggagccatcggag	16	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:124756449G>A	ENST00000306534.3	-	16	3190	c.2705C>T	c.(2704-2706)gCt>gTt	p.A902V	RP11-664I21.5_ENST00000524453.1_RNA|ROBO4_ENST00000533054.1_Missense_Mutation_p.A757V	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	902					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GTGAGCATCAGCGAGGAAGGA	0.607																																																0			11											45	47	46					11																	124756449		2201	4299	6500	124261659	SO:0001583	missense	54538			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2705C>T	11.37:g.124756449G>A	ENSP00000304945:p.Ala902Val		124261659	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800659	0.50315	.	.	ENSG00000154133	ENST00000306534;ENST00000533054	T;T	0.65364	-0.15;0.23	4.94	4.94	0.65067	.	0.000000	0.36234	N	0.002719	T	0.58509	0.2127	M	0.69823	2.125	0.09310	N	1	P;D	0.53151	0.949;0.958	P;B	0.48304	0.573;0.369	T	0.55283	-0.8165	10	0.06365	T	0.9	.	6.7326	0.23390	0.2222:0.0:0.7778:0.0	.	902;902	Q8WZ75-2;Q8WZ75	.;ROBO4_HUMAN	V	902;757	ENSP00000304945:A902V;ENSP00000437129:A757V	ENSP00000304945:A902V	A	-	2	0	ROBO4	124261659	0.912000	0.30974	0.705000	0.30386	0.965000	0.64279	3.288000	0.51739	2.435000	0.82474	0.655000	0.94253	GCT		0.607	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124756449	G	A	124756449	3	1	111	1	0	0	0	0	1	0	0	0	13553	971	34	3	330	3	ROBO4	11	124756449	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	503319	124756449	10250067	671	29805										
STT3A	3703	hgsc.bcm.edu	37	chr11	125478128	125478128	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgaagttcttttccggagcgTcatctctctggtaggctttg	11	9	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:125478128T>A	ENST00000529196.1	+	10	1111	c.905T>A	c.(904-906)gTc>gAc	p.V302D	STT3A_ENST00000531491.1_Missense_Mutation_p.V210D|STT3A_ENST00000392708.4_Missense_Mutation_p.V302D			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	302					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TTCCGGAGCGTCATCTCTCTG	0.473																																																0			11											121	115	117					11																	125478128		2201	4299	6500	124983338	SO:0001583	missense	3703			BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.905T>A	11.37:g.125478128T>A	ENSP00000436962:p.Val302Asp		124983338	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	37	CCDS8458.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.106654|5.106654	0.94292|0.94292	.|.	.|.	ENSG00000134910|ENSG00000134910	ENST00000526726|ENST00000392708;ENST00000529196;ENST00000531491	.|.	.|.	.|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.74152|0.74152	0.3679|0.3679	M|M	0.76574|0.76574	2.34|2.34	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48834	.|0.897;0.916;0.854	.|P;P;P	.|0.54590	.|0.524;0.756;0.756	T|T	0.74569|0.74569	-0.3622|-0.3622	5|9	.|0.40728	.|T	.|0.16	-22.0069|-22.0069	15.8567|15.8567	0.78983|0.78983	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|210;210;302	.|B4DJ24;E9PNQ1;P46977	.|.;.;STT3A_HUMAN	T|D	60|302;302;210	.|.	.|ENSP00000376472:V302D	S|V	+|+	1|2	0|0	STT3A|STT3A	124983338|124983338	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.948000|0.948000	0.59901|0.59901	6.178000|6.178000	0.71968|0.71968	2.228000|2.228000	0.72767|0.72767	0.533000|0.533000	0.62120|0.62120	TCA|GTC		0.473	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		A	125478128	T	A	125478128	3	1	111	1	0	0	0	0	1	0	0	0	15372	1667	58	5	935	5	STT3A	11	125478128	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	721679	125478128	9528388	672	29806										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126299107	126299107	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atggtggagtgctcctcaccCtcccgaccagaggctggttc	12	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:126299107C>T	ENST00000525144.2	-	15	2022	c.1773G>A	c.(1771-1773)gaG>gaA	p.E591E	KIRREL3_ENST00000416561.2_Silent_p.E58E|KIRREL3_ENST00000529097.2_Silent_p.E579E	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	591					hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		GCTCCTCACCCTCCCGACCAG	0.498																																																0			11											90	99	96					11																	126299107		1988	4157	6145	125804317	SO:0001819	synonymous_variant	84623			AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1773G>A	11.37:g.126299107C>T			125804317	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																				0.498	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		T	126299107	C	T	126299107	2	4	111	1	0	0	0	0	0	0	0	1	8347	680	24	3		3	KIRREL3	11	126299107	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	820979	126299107	8707409	673	29807										
NTM	50863	hgsc.bcm.edu	37	chr11	132177684	132177684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctccaatgacgtggccgcgCccgtggtacggagagtaaag	14	12	0	2	rs202188991		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:132177684C>T	ENST00000374786.1	+	4	1107	c.628C>T	c.(628-630)Ccc>Tcc	p.P210S	NTM_ENST00000474900.1_3'UTR|NTM_ENST00000427481.2_Missense_Mutation_p.P201S|NTM_ENST00000374784.1_Missense_Mutation_p.P210S|NTM_ENST00000374791.3_Missense_Mutation_p.P210S|NTM_ENST00000425719.2_Missense_Mutation_p.P210S|NTM_ENST00000539799.1_Missense_Mutation_p.P210S	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	210	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						CGTGGCCGCGCCCGTGGTACG	0.582													C|||	1	0.000199681	0	0	5008	,	,		17701	0		0.001	False		,,,				2504	0															0			11											84	73	77					11																	132177684		2201	4297	6498	131682894	SO:0001583	missense	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.628C>T	11.37:g.132177684C>T	ENSP00000363918:p.Pro210Ser		131682894	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	24.1	4.489700	0.84962	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.78	5.78	0.91487	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.72724	0.3496	L	0.42529	1.33	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.998;1.0;0.994	D;D;D;D;D;D	0.83275	0.996;0.994;0.967;0.994;0.99;0.95	T	0.62868	-0.6763	10	0.12430	T	0.62	-15.5836	20.3754	0.98918	0.0:1.0:0.0:0.0	.	210;201;210;210;210;210	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	S	210;210;201;210;210;210	ENSP00000363923:P210S;ENSP00000437668:P210S;ENSP00000416320:P201S;ENSP00000363918:P210S;ENSP00000396722:P210S;ENSP00000363916:P210S	ENSP00000363916:P210S	P	+	1	0	NTM	131682894	0.998000	0.40836	0.767000	0.31495	0.411000	0.31082	4.383000	0.59600	2.894000	0.99253	0.591000	0.81541	CCC		0.582	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		T	132177684	C	T	132177684	3	4	111	1	0	0	0	0	1	0	0	0	10730	739	26	3	728	3	NTM	11	132177684	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5878577	132177684	2828832	674	29808										
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134212845	134212845	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggcttgaacaccctcaccaCgtaggtgctgcccctgtccc	9	17	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr11:134212845C>T	ENST00000535456.2	+	2	472	c.284C>T	c.(283-285)aCc>aTc	p.T95I	GLB1L2_ENST00000339772.7_Splice_Site_p.T95I|GLB1L2_ENST00000389881.3_Splice_Site_p.T95I	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	95					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACCCTCACCACGTAGGTGCTG	0.607																																																0			11											58	53	54					11																	134212845		2201	4297	6498	133718055	SO:0001630	splice_region_variant	89944				CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.284+1C>T	11.37:g.134212845C>T			133718055	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084581	0.76642	.	.	ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881	D;D;D	0.98090	-4.71;-4.71;-4.71	4.72	4.72	0.59763	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98482	0.9494	M	0.85462	2.755	0.58432	D	0.999998	D	0.62365	0.991	P	0.58970	0.849	D	0.98701	1.0700	10	0.45353	T	0.12	-25.1206	17.8758	0.88825	0.0:1.0:0.0:0.0	.	95	Q8IW92	GLBL2_HUMAN	I	95	ENSP00000344659:T95I;ENSP00000444628:T95I;ENSP00000374531:T95I	ENSP00000344659:T95I	T	+	2	0	GLB1L2	133718055	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	5.783000	0.68982	2.460000	0.83146	0.561000	0.74099	ACC		0.607	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	Missense_Mutation	T	134212845	C	T	134212845	5	4	111	1	0	0	0	0	0	0	1	0	6449	550	19	1	290	1	GLB1L2	11	134212845	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2035161	134212845	793671	675	29809										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2676928	2676928	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcatctccgtgctcagatgCgtccggctgctgaggatttt	13	11	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:2676928C>T	ENST00000347598.4	+	13	1863	c.1863C>T	c.(1861-1863)tgC>tgT	p.C621C	CACNA1C_ENST00000399629.1_Silent_p.C621C|CACNA1C_ENST00000399641.1_Silent_p.C621C|CACNA1C_ENST00000327702.7_Silent_p.C621C|CACNA1C_ENST00000402845.3_Silent_p.C621C|CACNA1C_ENST00000399595.1_Silent_p.C621C|CACNA1C_ENST00000480911.1_Silent_p.C621C|CACNA1C_ENST00000399597.1_Silent_p.C621C|CACNA1C_ENST00000406454.3_Silent_p.C621C|CACNA1C_ENST00000399606.1_Silent_p.C621C|CACNA1C_ENST00000399638.1_Silent_p.C621C|CACNA1C_ENST00000399601.1_Silent_p.C621C|CACNA1C_ENST00000399637.1_Silent_p.C621C|CACNA1C_ENST00000399617.1_Silent_p.C621C|CACNA1C_ENST00000399591.1_Silent_p.C621C|CACNA1C_ENST00000399603.1_Silent_p.C621C|CACNA1C_ENST00000399649.1_Silent_p.C621C|CACNA1C_ENST00000344100.3_Silent_p.C621C|CACNA1C_ENST00000399655.1_Silent_p.C621C|CACNA1C_ENST00000335762.5_Silent_p.C646C|CACNA1C_ENST00000399644.1_Silent_p.C621C|CACNA1C_ENST00000399621.1_Silent_p.C621C|CACNA1C_ENST00000399634.1_Silent_p.C621C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	621					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGCTCAGATGCGTCCGGCTGC	0.572																																																0			12											34	36	36					12																	2676928		2170	4291	6461	2547189	SO:0001819	synonymous_variant	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1863C>T	12.37:g.2676928C>T			2547189	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																				0.572	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2676928	C	T	2676928	2	4	111	1	0	0	0	0	0	0	0	1	2546	776	27	1		1	CACNA1C	12	2676928	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10		2676928	131174967	676	29810										
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3726166	3726166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtgttgtgaccagagtaggCgctgcattcatagaagatca	13	7	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:3726166C>T	ENST00000440314.2	-	19	2538	c.2065G>A	c.(2065-2067)Gcc>Acc	p.A689T		NM_001144958.1	NP_001138430.1	Q9BSW2	EFC4B_HUMAN		0					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			CCAGAGTAGGCGCTGCATTCA	0.512																																																0			12											210	180	189					12																	3726166		692	1591	2283	3596427	SO:0001583	missense	84766																														ENST00000440314.2:c.2065G>A	12.37:g.3726166C>T	ENSP00000409382:p.Ala689Thr		3596427	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	37	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100186	0.76983	.	.	ENSG00000130038	ENST00000440314	D	0.88741	-2.42	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	D	0.93943	0.8061	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94427	0.7646	9	0.87932	D	0	.	12.8416	0.57806	0.0:1.0:0.0:0.0	.	689	Q9BSW2-2	.	T	689	ENSP00000409382:A689T	ENSP00000409382:A689T	A	-	1	0	EFCAB4B	3596427	1.000000	0.71417	0.988000	0.46212	0.786000	0.44442	5.401000	0.66326	2.372000	0.80975	0.563000	0.77884	GCC		0.512	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2			T	3726166	C	T	3726166	3	4	111	1	0	0	0	0	1	0	0	0	4948	768	27	1	138	1	EFCAB4B	12	3726166	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1049238	3726166	130125729	677	29811										
KCNA6	3742	hgsc.bcm.edu	37	chr12	4919445	4919445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtccgcttcttcgaccccCtgaggaacgagtacttcttc	9	14	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:4919445C>A	ENST00000280684.3	+	1	1104	c.238C>A	c.(238-240)Ctg>Atg	p.L80M	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Missense_Mutation_p.L80M			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	80					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	CTTCGACCCCCTGAGGAACGA	0.642										HNSCC(72;0.22)																																						0			12											51	53	53					12																	4919445		2203	4300	6503	4789706	SO:0001583	missense	3742			X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.238C>A	12.37:g.4919445C>A	ENSP00000280684:p.Leu80Met		4789706		Missense_Mutation	SNP	ENST00000280684.3	37	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919583	0.52653	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	T;T	0.76709	-1.04;-1.04	4.57	1.62	0.23740	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.243253	0.34906	N	0.003597	T	0.78735	0.4330	L	0.37507	1.11	0.46317	D	0.998982	D	0.56035	0.974	D	0.70935	0.971	T	0.74266	-0.3721	10	0.38643	T	0.18	.	8.6353	0.33943	0.0:0.7363:0.0:0.2637	.	80	P17658	KCNA6_HUMAN	M	80	ENSP00000408321:L80M;ENSP00000280684:L80M	ENSP00000280684:L80M	L	+	1	2	KCNA6	4789706	0.976000	0.34144	0.365000	0.25901	0.984000	0.73092	2.487000	0.45268	0.519000	0.28406	0.462000	0.41574	CTG		0.642	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		A	4919445	C	A	4919445	3	1	111	1	0	0	0	0	1	0	0	0	8028	680	24	2	240	2	KCNA6	12	4919445	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1193279	4919445	128932450	678	29812										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7551178	7551178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccttaggtccagatctgcctTatctgcaagcaagacaaaac	7	12	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:7551178T>C	ENST00000313599.3	-	7	1468	c.1411A>G	c.(1411-1413)Aag>Gag	p.K471E	CD163L1_ENST00000416109.2_Missense_Mutation_p.K481E|CD163L1_ENST00000396630.1_Missense_Mutation_p.K471E			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	471						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						AGATCTGCCTTATCTGCAAGC	0.453																																																0			12											54	48	50					12																	7551178		2203	4300	6503	7442445	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1411A>G	12.37:g.7551178T>C	ENSP00000315945:p.Lys471Glu		7442445	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.925104	0.00493	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.27890	1.64;1.64;1.64	2.11	1.16	0.20824	Speract/scavenger receptor-related (1);	.	.	.	.	T	0.08537	0.0212	N	0.01250	-0.93	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.08055	0.003;0.003	T	0.37384	-0.9708	9	0.07813	T	0.8	.	6.337	0.21302	0.0:0.8184:0.0:0.1816	.	481;471	E7EVK4;Q9NR16	.;C163B_HUMAN	E	471;481;471	ENSP00000315945:K471E;ENSP00000393474:K481E;ENSP00000379871:K471E	ENSP00000315945:K471E	K	-	1	0	CD163L1	7442445	0.001000	0.12720	0.092000	0.20876	0.048000	0.14542	0.645000	0.24782	0.390000	0.25115	-0.467000	0.05162	AAG		0.453	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7551178	T	C	7551178	3	2	111	1	0	0	0	0	1	0	0	0	2974	1763	61	4	3002	4	CD163L1	12	7551178	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2631733	7551178	126300717	679	29813										
GDF3	9573	hgsc.bcm.edu	37	chr12	7842962	7842962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcttctttgaccagtatctCcaggaataacccgaaatttt	5	10	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:7842962C>T	ENST00000329913.3	-	2	654	c.607G>A	c.(607-609)Gag>Aag	p.E203K		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	203					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.E203K(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						ACCAGTATCTCCAGGAATAAC	0.502																																																1	Substitution - Missense(1)	skin(1)	12											70	73	72					12																	7842962		2203	4300	6503	7734229	SO:0001583	missense	9573			AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"Endogenous ligands"	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.607G>A	12.37:g.7842962C>T	ENSP00000331745:p.Glu203Lys		7734229	Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	37	CCDS8581.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.272836	0.80580	.	.	ENSG00000184344	ENST00000329913	T	0.69685	-0.42	4.61	3.68	0.42216	Transforming growth factor-beta, N-terminal (1);	7.370980	0.00166	N	0.000000	D	0.84170	0.5413	M	0.80183	2.485	0.58432	D	0.999995	D	0.71674	0.998	D	0.70716	0.97	T	0.65302	-0.6201	10	0.49607	T	0.09	.	12.4582	0.55716	0.0:0.8295:0.1705:0.0	.	203	Q9NR23	GDF3_HUMAN	K	203	ENSP00000331745:E203K	ENSP00000331745:E203K	E	-	1	0	GDF3	7734229	0.999000	0.42202	0.994000	0.49952	0.884000	0.51177	4.475000	0.60210	1.022000	0.39626	0.561000	0.74099	GAG		0.502	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			T	7842962	C	T	7842962	3	4	111	1	0	0	0	0	1	0	0	0	6335	864	30	3	491	3	GDF3	12	7842962	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	291784	7842962	126008933	680	29814										
RIMKLB	57494	hgsc.bcm.edu	37	chr12	8902559	8902559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atagtgacatcactgttttgCgccatctagagaagatggga	11	7	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:8902559C>T	ENST00000538135.1	+	3	1102	c.277C>T	c.(277-279)Cgc>Tgc	p.R93C	RIMKLB_ENST00000535829.1_Missense_Mutation_p.R93C|RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000357529.3_Missense_Mutation_p.R93C			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	93					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CACTGTTTTGCGCCATCTAGA	0.488																																																0			12											72	68	69					12																	8902559		1906	4117	6023	8793826	SO:0001583	missense	57494			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"N-acetylaspartyl-glutamate synthetase"	614054	"family with sequence similarity 80, member B"	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.277C>T	12.37:g.8902559C>T	ENSP00000440943:p.Arg93Cys		8793826	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	37	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.888947	0.52014	.	.	ENSG00000166532	ENST00000541044;ENST00000539923;ENST00000537189;ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	5.47	5.47	0.80525	.	0.071421	0.53938	U	0.000048	T	0.52092	0.1713	L	0.55481	1.735	0.80722	D	1	B;B	0.33448	0.398;0.412	B;B	0.30179	0.112;0.052	T	0.57700	-0.7766	9	0.87932	D	0	.	12.9384	0.58329	0.1622:0.8378:0.0:0.0	.	93;93	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	C	93;93;154;93;93;93	.	ENSP00000350136:R93C	R	+	1	0	RIMKLB	8793826	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.469000	0.53093	2.571000	0.86741	0.591000	0.81541	CGC		0.488	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		T	8902559	C	T	8902559	3	4	111	1	0	0	0	0	1	0	0	0	13403	768	27	1	283	1	RIMKLB	12	8902559	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1059597	8902559	124949336	681	29815										
CD69	969	hgsc.bcm.edu	37	chr12	9906143	9906144	+	Frame_Shift_Ins	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatgctgctgacctctgtgINStttttcagaaaaacacactt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:9906143_9906144insT	ENST00000228434.3	-	5	613_614	c.533_534insA	c.(532-534)aacfs	p.N178fs		NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	178	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						TGACCTCTGTGTTTTTCAGAAA	0.317																																																0			12																																								9797411	SO:0001589	frameshift_variant	969			Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"C-type lectin domain containing", "CD molecules"	1694	protein-coding gene	gene with protein product		107273	"CD69 antigen (p60, early T-cell activation antigen)"			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.534dupA	12.37:g.9906148_9906148dupT	ENSP00000228434:p.Asn178fs		9797410		Frame_Shift_Ins	INS	ENST00000228434.3	37	CCDS8604.1																																																																																				0.317	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1			T	9906144	-	T	9906143	7	5	111	1	0	1	1	0	0	0	0	0	3037	1368	48	0	69	0	CD69	12	9906143	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	1003584	9906143	123945752	682	29816										
TAS2R10	50839	hgsc.bcm.edu	37	chr12	10978281	10978282	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtctccaaagggaaatgattINSaaaaaaatacatgtaattag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:10978281_10978282insA	ENST00000240619.2	-	1	675_676	c.587_588insT	c.(586-588)ttafs	p.L196fs		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	196					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GGGAAATGATTAAAAAAATACA	0.347																																																0			12																																								10869549	SO:0001589	frameshift_variant	50839			AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.588dupT	12.37:g.10978288_10978288dupA	ENSP00000240619:p.Leu196fs		10869548	Q3MIM9|Q6NTD9	Frame_Shift_Ins	INS	ENST00000240619.2	37	CCDS8634.1																																																																																				0.347	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			A	10978282	-	A	10978281	7	5	111	1	0	1	1	0	0	0	0	0	15605	1751	61	0	339	0	TAS2R10	12	10978281	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	1072138	10978281	122873614	683	29817										
TAS2R50	259296	hgsc.bcm.edu	37	chr12	11139424	11139424	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaacaaataaaaccattatTagaattgaaaaaaaaatgta	4	3	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:11139424T>A	ENST00000506868.1	-	1	87	c.36A>T	c.(34-36)ctA>ctT	p.L12L	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	12					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						AAACCATTATTAGAATTGAAA	0.323																																																0			12											32	39	37					12																	11139424		2182	4286	6468	11030691	SO:0001819	synonymous_variant	259296			AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.36A>T	12.37:g.11139424T>A			11030691	P59545|Q2M255|Q645Y0	Silent	SNP	ENST00000506868.1	37	CCDS8638.1																																																																																				0.323	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890		A	11139424	T	A	11139424	2	1	111	1	0	0	0	0	0	0	0	1	15623	1741	61	5		5	TAS2R50	12	11139424	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	161143	11139424	122712471	684	29818										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15702113	15702113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgtagtgtcaccagctttaGccatgacagccccagtgtcc	9	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:15702113G>A	ENST00000281171.4	+	14	2720	c.2390G>A	c.(2389-2391)aGc>aAc	p.S797N	PTPRO_ENST00000442921.2_5'UTR|PTPRO_ENST00000445537.2_5'UTR|PTPRO_ENST00000542557.1_5'UTR|PTPRO_ENST00000544244.1_5'UTR|PTPRO_ENST00000348962.2_Missense_Mutation_p.S797N	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	797	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				ACCAGCTTTAGCCATGACAGC	0.423																																																0			12											188	170	176					12																	15702113		2203	4300	6503	15593380	SO:0001583	missense	10076			U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2390G>A	12.37:g.15702113G>A	ENSP00000281171:p.Ser797Asn		15593380	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538556	0.85917	.	.	ENSG00000151490	ENST00000281171;ENST00000348962	T;T	0.72167	0.99;-0.63	4.93	4.93	0.64822	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000007	T	0.77219	0.4098	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.993;0.999	D;D	0.72982	0.91;0.979	T	0.79612	-0.1731	10	0.62326	D	0.03	.	18.3504	0.90336	0.0:0.0:1.0:0.0	.	797;797	Q16827-2;Q16827	.;PTPRO_HUMAN	N	797	ENSP00000281171:S797N;ENSP00000343434:S797N	ENSP00000281171:S797N	S	+	2	0	PTPRO	15593380	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	8.578000	0.90777	2.567000	0.86603	0.655000	0.94253	AGC		0.423	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15702113	G	A	15702113	3	1	111	1	0	0	0	0	1	0	0	0	12846	971	34	3	2444	3	PTPRO	12	15702113	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4562689	15702113	118149782	685	29819										
LST-3TM12	338821	hgsc.bcm.edu	37	chr12	21175856	21175856	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tatgcttcgtggcataggggAaacccccatagtaccattgg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:21175856delA	ENST00000421593.2	+	4	413	c.413delA	c.(412-414)gaafs	p.E138fs	LST3_ENST00000381541.3_Frame_Shift_Del_p.E185fs|SLCO1B3_ENST00000553473.1_Intron|SLCO1B7_ENST00000554957.1_Frame_Shift_Del_p.E185fs|LST3_ENST00000540229.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GGCATAGGGGAAACCCCCATA	0.373																																																0			12											134	133	133					12																	21175856		2203	4300	6503	21067123	SO:0001589	frameshift_variant	338821			AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"Solute carriers"	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.413delA	12.37:g.21175856delA	ENSP00000394168:p.Glu138fs		21067123	Q71QF0	Frame_Shift_Del	DEL	ENST00000421593.2	37	CCDS44843.1																																																																																				0.373	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562		-	21175856	A	-	21175856	7	5	111	1	0	1	0	1	0	0	0	0	9095	246	9	0	427	0	LST-3TM12	12	21175856	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	5473743	21175856	112676039	686	29820										
SLCO1A2	6579	hgsc.bcm.edu	37	chr12	21446892	21446892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtcttaccatgtttattcccGttccaatggatgtctcacaa	6	11	2	0	rs141238012	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:21446892G>A	ENST00000307378.6	-	12	2144	c.1424C>T	c.(1423-1425)aCg>aTg	p.T475M	SLCO1A2_ENST00000458504.1_Missense_Mutation_p.T343M|SLCO1A2_ENST00000452078.1_Missense_Mutation_p.T475M|SLCO1A2_ENST00000537524.1_Missense_Mutation_p.T343M|SLCO1A2_ENST00000390670.3_Missense_Mutation_p.T473M	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	475	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	GTTTATTCCCGTTCCAATGGA	0.383													G|||	2	0.000399361	0.0015	0	5008	,	,		16085	0		0	False		,,,				2504	0															0			12						G	MET/THR,MET/THR	0,4406		0,0,2203	118	102	108		1424,1424	4	0.6	12	dbSNP_134	108	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SLCO1A2	NM_021094.3,NM_134431.3	81,81	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	benign,benign	475/671,475/671	21446892	8,12998	2203	4300	6503	21338159	SO:0001583	missense	6579				CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"Solute carriers"	10956	protein-coding gene	gene with protein product		602883	"solute carrier family 21 (organic anion transporter), member 3"	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.1424C>T	12.37:g.21446892G>A	ENSP00000305974:p.Thr475Met		21338159	Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	37	CCDS8686.1	.	.	.	.	.	.	.	.	.	.	G	3.317	-0.139659	0.06669	0.0	9.3E-4	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000458504;ENST00000537524;ENST00000390670	T;T;T;T;T	0.04360	3.64;3.64;3.64;3.64;3.64	4.93	4.03	0.46877	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.815714	0.11565	N	0.551302	T	0.09113	0.0225	M	0.63428	1.95	0.28692	N	0.904528	B;P	0.35077	0.095;0.483	B;B	0.32583	0.067;0.148	T	0.05666	-1.0871	10	0.51188	T	0.08	.	16.6501	0.85187	0.0705:0.0:0.9295:0.0	.	473;475	P46721-2;P46721	.;SO1A2_HUMAN	M	475;475;343;343;473	ENSP00000305974:T475M;ENSP00000393973:T475M;ENSP00000394854:T343M;ENSP00000439401:T343M;ENSP00000375088:T473M	ENSP00000305974:T475M	T	-	2	0	SLCO1A2	21338159	1.000000	0.71417	0.562000	0.28370	0.065000	0.16274	3.161000	0.50747	0.607000	0.29982	-1.128000	0.01989	ACG		0.383	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		A	21446892	G	A	21446892	3	1	111	1	0	0	0	0	1	0	0	0	14759	1145	40	1	608	1	SLCO1A2	12	21446892	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	271036	21446892	112405003	687	29821										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380281	25380281	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcactgtactcctcttgaccTgctgtgtcgagaatatccaa	8	12	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:25380281T>C	ENST00000256078.4	-	3	240	c.177A>G	c.(175-177)gcA>gcG	p.A59A	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Silent_p.A59A|KRAS_ENST00000557334.1_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	59			A -> T (in bladder cancer and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:1553789}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCTCTTGACCTGCTGTGTCGA	0.418		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											108	96	100					12																	25380281		2203	4300	6503	25271548	SO:0001819	synonymous_variant	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.177A>G	12.37:g.25380281T>C			25271548	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.418	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		C	25380281	T	C	25380281	2	2	111	1	0	0	0	0	0	0	0	1	8459	1567	55	4		4	KRAS	12	25380281	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3933389	25380281	108471614	688	29822										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	111	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	18003	25398284	108453611	689	29823										
TM7SF3	51768	hgsc.bcm.edu	37	chr12	27149701	27149701	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagcctaggtttgctggggcAaacttgatagtcgtttcaaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:27149701delA	ENST00000343028.4	-	4	717	c.492delT	c.(490-492)tttfs	p.F164fs	TM7SF3_ENST00000542667.1_5'UTR	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	164						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					TTGCTGGGGCAAACTTGATAG	0.418																																																0			12											80	75	77					12																	27149701		2203	4300	6503	27040968	SO:0001589	frameshift_variant	51768			AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.492delT	12.37:g.27149701delA	ENSP00000342322:p.Phe164fs		27040968	B3KMZ3|Q9NUS4	Frame_Shift_Del	DEL	ENST00000343028.4	37	CCDS8710.1																																																																																				0.418	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551		-	27149701	A	-	27149701	7	5	111	1	0	1	0	1	0	0	0	0	16014	127	5	0	1256	0	TM7SF3	12	27149701	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	1751417	27149701	106702194	690	29824										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40704299	40704299	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgtttctgatgagaagcaaCgcaaagcctgcatgagtaaa	10	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:40704299C>T	ENST00000298910.7	+	31	4442	c.4384C>T	c.(4384-4386)Cgc>Tgc	p.R1462C		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1462	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TGAGAAGCAACGCAAAGCCTG	0.483																																																0			12											153	145	147					12																	40704299		2203	4300	6503	38990566	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4384C>T	12.37:g.40704299C>T	ENSP00000298910:p.Arg1462Cys		38990566	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.907198	0.72868	.	.	ENSG00000188906	ENST00000298910	T	0.80653	-1.4	5.63	4.73	0.59995	ROC GTPase (1);Small GTP-binding protein domain (1);	0.182649	0.49916	D	0.000136	T	0.75810	0.3900	L	0.49778	1.585	0.58432	D	0.999992	D;D	0.76494	0.998;0.999	B;B	0.41440	0.282;0.357	T	0.79381	-0.1827	10	0.52906	T	0.07	.	14.9416	0.70997	0.0:0.9302:0.0:0.0698	.	1462;1462	Q17RV3;Q5S007	.;LRRK2_HUMAN	C	1462	ENSP00000298910:R1462C	ENSP00000298910:R1462C	R	+	1	0	LRRK2	38990566	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.391000	0.52530	2.653000	0.90120	0.650000	0.86243	CGC		0.483	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40704299	C	T	40704299	3	4	111	1	0	0	0	0	1	0	0	0	9062	536	19	1	4506	1	LRRK2	12	40704299	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	13554598	40704299	93147596	691	29825										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966505	41966505	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaagattcgaaatcatggaGagtatgacctgtattactca	9	7	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:41966505G>T	ENST00000402685.2	+	10	1932	c.1924G>T	c.(1924-1926)Gag>Tag	p.E642*	PDZRN4_ENST00000298919.7_Nonsense_Mutation_p.E382*|PDZRN4_ENST00000539469.2_Nonsense_Mutation_p.E384*	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	642							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AAATCATGGAGAGTATGACCT	0.443																																																0			12											108	101	104					12																	41966505		2203	4300	6503	40252772	SO:0001587	stop_gained	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1924G>T	12.37:g.41966505G>T	ENSP00000384197:p.Glu642*		40252772	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	38	7.072673	0.98044	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	.	.	.	4.49	3.58	0.41010	.	0.258966	0.32106	N	0.006568	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-15.5719	14.7263	0.69346	0.0:0.1594:0.8406:0.0	.	.	.	.	X	642;384;382	.	ENSP00000298919:E382X	E	+	1	0	PDZRN4	40252772	1.000000	0.71417	0.959000	0.39883	0.983000	0.72400	4.695000	0.61767	1.181000	0.42912	0.650000	0.86243	GAG		0.443	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41966505	G	T	41966505	4	4	111	1	0	0	0	0	0	1	0	0	11741	943	33	2	2035	2	PDZRN4	12	41966505	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1262206	41966505	91885390	692	29826										
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42729723	42729723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatgtggtctgagggacgaTatgaatatgaaagaattccg	12	4	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:42729723T>C	ENST00000395568.2	+	2	103	c.19T>C	c.(19-21)Tat>Cat	p.Y7H	PPHLN1_ENST00000317560.9_Missense_Mutation_p.Y14H|PPHLN1_ENST00000256678.8_Intron|PPHLN1_ENST00000549190.1_Missense_Mutation_p.Y25H|PPHLN1_ENST00000432191.2_Missense_Mutation_p.Y7H|PPHLN1_ENST00000395580.3_Missense_Mutation_p.Y14H|PPHLN1_ENST00000358314.7_Missense_Mutation_p.Y7H|PPHLN1_ENST00000449194.2_Missense_Mutation_p.Y7H|PPHLN1_ENST00000337898.6_Missense_Mutation_p.Y7H|PPHLN1_ENST00000550535.1_3'UTR|PPHLN1_ENST00000552761.1_Missense_Mutation_p.Y14H	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	7					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		TGAGGGACGATATGAATATGA	0.378																																																0			12											135	138	137					12																	42729723		2203	4300	6503	41015990	SO:0001583	missense	51535			AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.19T>C	12.37:g.42729723T>C	ENSP00000378935:p.Tyr7His		41015990	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872882	0.51695	.	.	ENSG00000134283	ENST00000549190;ENST00000395580;ENST00000337898;ENST00000358314;ENST00000395568;ENST00000449194;ENST00000552761;ENST00000317560;ENST00000432191;ENST00000546750;ENST00000547847	.	.	.	5.34	4.19	0.49359	.	0.140536	0.49305	N	0.000152	T	0.62708	0.2450	M	0.68593	2.085	0.31744	N	0.635406	B;B;B;B;B;D;D;D;B;B;B;B	0.89917	0.082;0.06;0.012;0.049;0.099;0.999;0.999;1.0;0.145;0.418;0.073;0.418	B;B;B;B;B;D;D;D;B;B;B;B	0.91635	0.058;0.03;0.006;0.026;0.067;0.996;0.996;0.999;0.099;0.198;0.086;0.184	T	0.68644	-0.5354	9	0.87932	D	0	-5.0943	8.0245	0.30430	0.0:0.0903:0.0:0.9097	.	14;7;7;14;7;7;7;7;14;14;14;25	F8WF16;B7Z695;B7Z8L1;B7Z615;Q8NEY8-3;Q8NEY8;E9PAX8;Q8NEY8-8;Q8NEY8-6;Q8NEY8-2;Q8NEY8-5;F8W0Q9	.;.;.;.;.;PPHLN_HUMAN;.;.;.;.;.;.	H	25;14;7;7;7;7;14;14;7;14;7	.	ENSP00000322048:Y14H	Y	+	1	0	PPHLN1	41015990	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	2.629000	0.46485	1.152000	0.42452	0.528000	0.53228	TAT		0.378	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515		C	42729723	T	C	42729723	3	2	111	1	0	0	0	0	1	0	0	0	12346	1406	49	4	46	4	PPHLN1	12	42729723	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	763218	42729723	91122172	693	29827										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43821126	43821126	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttacttctccccaatttccGtagttccactgtggacaagg	7	13	1	0	rs536908821		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:43821126G>A	ENST00000389420.3	-	27	4091	c.4092C>T	c.(4090-4092)taC>taT	p.Y1364Y	ADAMTS20_ENST00000395541.2_Silent_p.Y482Y|ADAMTS20_ENST00000553158.1_Silent_p.Y1364Y	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1364	TSP type-1 10. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		CCCAATTTCCGTAGTTCCACT	0.413													G|||	1	0.000199681	0	0	5008	,	,		17862	0		0	False		,,,				2504	0.001															0			12											94	80	85					12																	43821126		2203	4300	6503	42107393	SO:0001819	synonymous_variant	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.4092C>T	12.37:g.43821126G>A			42107393	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																				0.413	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43821126	G	A	43821126	2	1	111	1	0	0	0	0	0	0	0	1	266	1140	40	1		1	ADAMTS20	12	43821126	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1091403	43821126	90030769	694	29828										
MLL2	8085	hgsc.bcm.edu	37	chr12	49422879	49422879	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggaatgagggggatgacaGgggagagggcccggtcctct	20	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:49422879G>T	ENST00000301067.7	-	44	14215	c.14216C>A	c.(14215-14217)cCt>cAt	p.P4739H		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4739					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGGGATGACAGGGGAGAGGGC	0.647																																																0			12											44	50	48					12																	49422879		1943	4108	6051	47709146	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.14216C>A	12.37:g.49422879G>T	ENSP00000301067:p.Pro4739His		47709146	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865489	0.51588	.	.	ENSG00000167548	ENST00000301067	D	0.95447	-3.71	4.91	4.91	0.64330	.	0.000000	0.36444	N	0.002594	D	0.97570	0.9204	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98342	1.0539	10	0.87932	D	0	.	17.2511	0.87042	0.0:0.0:1.0:0.0	.	4739	O14686	MLL2_HUMAN	H	4739	ENSP00000301067:P4739H	ENSP00000301067:P4739H	P	-	2	0	MLL2	47709146	1.000000	0.71417	0.993000	0.49108	0.979000	0.70002	9.725000	0.98778	2.454000	0.82982	0.557000	0.71058	CCT		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49422879	G	T	49422879	3	4	111	1	0	0	0	0	1	0	0	0	9651	1000	35	2	2441	2	MLL2	12	49422879	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5601753	49422879	84429016	695	29829										
MLL2	8085	hgsc.bcm.edu	37	chr12	49437986	49437986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccctcacccgtctcaccctCgtcgggctgcccatccccac	7	23	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:49437986C>T	ENST00000301067.7	-	21	5184	c.5185G>A	c.(5185-5187)Gag>Aag	p.E1729K		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1729					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GTCTCACCCTCGTCGGGCTGC	0.622											OREG0021780	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			12											38	44	42					12																	49437986		2077	4198	6275	47724253	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.5185G>A	12.37:g.49437986C>T	ENSP00000301067:p.Glu1729Lys	962	47724253	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421458	0.62622	.	.	ENSG00000167548	ENST00000301067	T	0.81163	-1.46	4.82	4.82	0.62117	.	0.000000	0.35772	N	0.002988	D	0.82829	0.5122	L	0.39898	1.24	0.45822	D	0.998692	D	0.71674	0.998	P	0.55871	0.786	D	0.85212	0.1021	10	0.87932	D	0	.	16.8327	0.85949	0.0:1.0:0.0:0.0	.	1729	O14686	MLL2_HUMAN	K	1729	ENSP00000301067:E1729K	ENSP00000301067:E1729K	E	-	1	0	MLL2	47724253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.705000	0.61838	2.498000	0.84270	0.563000	0.77884	GAG		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49437986	C	T	49437986	3	4	111	1	0	0	0	0	1	0	0	0	9651	893	31	1	11564	1	MLL2	12	49437986	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	15107	49437986	84413909	696	29830										
MLL2	8085	hgsc.bcm.edu	37	chr12	49445485	49445485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaggcggtggagacaggcGtgacaccacaggcagggggg	19	10	1	2	rs371225040		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:49445485G>A	ENST00000301067.7	-	10	1980	c.1981C>T	c.(1981-1983)Cgc>Tgc	p.R661C		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	661	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGAGACAGGCGTGACACCACA	0.642																																																0			12						G	CYS/ARG	0,4242		0,0,2121	43	49	47		1981	2.1	0.1	12		47	1,8435		0,1,4217	no	missense	MLL2	NM_003482.3	180	0,1,6338	AA,AG,GG		0.0119,0.0,0.0079	possibly-damaging	661/5538	49445485	1,12677	2121	4218	6339	47731752	SO:0001583	missense	9757			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.1981C>T	12.37:g.49445485G>A	ENSP00000301067:p.Arg661Cys		47731752	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.205656	0.39003	0.0	1.19E-4	ENSG00000167548	ENST00000301067	T	0.79845	-1.31	3.98	2.13	0.27403	.	.	.	.	.	T	0.58878	0.2153	N	0.08118	0	0.09310	N	1	P	0.34892	0.474	B	0.25140	0.058	T	0.51988	-0.8635	9	0.87932	D	0	.	8.2447	0.31682	0.2027:0.0:0.7973:0.0	.	661	O14686	MLL2_HUMAN	C	661	ENSP00000301067:R661C	ENSP00000301067:R661C	R	-	1	0	MLL2	47731752	0.038000	0.19896	0.087000	0.20705	0.822000	0.46500	1.972000	0.40540	0.476000	0.27440	0.313000	0.20887	CGC		0.642	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49445485	G	A	49445485	3	1	111	1	0	0	0	0	1	0	0	0	9651	1145	40	1	14812	1	MLL2	12	49445485	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7499	49445485	84406410	697	29831										
KRT83	3889	hgsc.bcm.edu	37	chr12	52714899	52714899	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggggctgggtccgcacacgCccccggagcggtagccgaag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:52714899delC	ENST00000293670.3	-	1	283	c.221delG	c.(220-222)ggcfs	p.G74fs		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	74	Head.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCGCACACGCCCCCGGAGCG	0.706																																					GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)											0			12											51	56	55					12																	52714899		2203	4300	6503	51001166	SO:0001589	frameshift_variant	3889			X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.221delG	12.37:g.52714899delC	ENSP00000293670:p.Gly74fs		51001166	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Frame_Shift_Del	DEL	ENST00000293670.3	37	CCDS8823.1																																																																																				0.706	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		-	52714899	C	-	52714899	7	5	111	1	0	1	0	1	0	0	0	0	8518	739	26	0	1296	0	KRT83	12	52714899	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	3269414	52714899	81136996	698	29832										
KRT6C	286887	hgsc.bcm.edu	37	chr12	52865494	52865494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcattctctgctgctgtgcGcttgttgatttcatcctcat	7	11	4	1	rs187821450	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:52865494G>A	ENST00000252250.6	-	3	825	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	260	Coil 1B.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		GCTGCTGTGCGCTTGTTGATT	0.448													G|||	2	0.000399361	0	0.0014	5008	,	,		20612	0		0	False		,,,				2504	0.001															0			12											98	94	96					12																	52865494		2203	4298	6501	51151761	SO:0001583	missense	286887			L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"-", "Intermediate filaments type II, keratins (basic)"	20406	protein-coding gene	gene with protein product		612315	"keratin 6E"	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.778C>T	12.37:g.52865494G>A	ENSP00000252250:p.Arg260Cys		51151761	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	19.45	3.829225	0.71258	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.90069	-2.61	2.96	2.96	0.34315	Filament (1);	0.000000	0.56097	D	0.000022	D	0.91047	0.7183	H	0.96142	3.775	0.58432	D	0.999998	D	0.56746	0.977	P	0.48982	0.597	D	0.92578	0.6072	10	0.87932	D	0	.	10.546	0.45060	0.0:0.0:0.8063:0.1937	.	260	P48668	K2C6C_HUMAN	C	260;245	ENSP00000252250:R260C	ENSP00000252250:R260C	R	-	1	0	KRT6C	51151761	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.523000	0.81856	1.943000	0.56356	0.462000	0.41574	CGC		0.448	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086		A	52865494	G	A	52865494	3	1	111	1	0	0	0	0	1	0	0	0	8503	1087	38	1	944	1	KRT6C	12	52865494	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	150595	52865494	80986401	699	29833										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52881579	52881579	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaactgccgcctccaacagaGctgaggccacccccaatggc	10	17	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:52881579G>A	ENST00000330722.6	-	9	1688	c.1620C>T	c.(1618-1620)agC>agT	p.S540S		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	540	Tail.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTCCAACAGAGCTGAGGCCAC	0.587																																																0			12											76	84	82					12																	52881579		2203	4296	6499	51167846	SO:0001819	synonymous_variant	3853			BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.1620C>T	12.37:g.52881579G>A			51167846	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																				0.587	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		A	52881579	G	A	52881579	2	1	111	1	0	0	0	0	0	0	0	1	8501	962	34	3		3	KRT6A	12	52881579	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	16085	52881579	80970316	700	29834										
KRT73	319101	hgsc.bcm.edu	37	chr12	53012018	53012018	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atacccccgggcgggcacaaCgacggacacacggaccccaa	11	17	0	0	rs142655706	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53012018C>T	ENST00000305748.3	-	1	325	c.291G>A	c.(289-291)tcG>tcA	p.S97S	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	97	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCGGGCACAACGACGGACACA	0.637																																																0			12						C		7,4399	12.9+/-30.5	0,7,2196	113	120	118		291	-9.3	0	12	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	KRT73	NM_175068.2		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		97/541	53012018	7,12999	2203	4300	6503	51298285	SO:0001819	synonymous_variant	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.291G>A	12.37:g.53012018C>T			51298285	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																				0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		T	53012018	C	T	53012018	2	4	111	1	0	0	0	0	0	0	0	1	8507	523	19	1		1	KRT73	12	53012018	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	130439	53012018	80839877	701	29835										
KRT8	3856	hgsc.bcm.edu	37	chr12	53292651	53292651	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccagctctccacgctgctcGgcatctgcaatggcggcctc	11	17	2	0	rs112222496	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53292651G>A	ENST00000552551.1	-	7	1446	c.1014C>T	c.(1012-1014)gcC>gcT	p.A338A	KRT8_ENST00000293308.6_Silent_p.A338A|KRT8_ENST00000546897.1_Silent_p.A338A|KRT8_ENST00000552150.1_Silent_p.A366A			P05787	K2C8_HUMAN	keratin 8	338	Coil 2.|Necessary for interaction with PNN.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	CACGCTGCTCGGCATCTGCAA	0.642													G|||	11	0.00219649	0.0083	0	5008	,	,		16632	0		0	False		,,,				2504	0															0			12						G		27,4377		0,27,2175	32	32	32		1014	-7.7	0.1	12	dbSNP_132	32	0,8600		0,0,4300	no	coding-synonymous	KRT8	NM_002273.3		0,27,6475	AA,AG,GG		0.0,0.6131,0.2076		338/484	53292651	27,12977	2202	4300	6502	51578918	SO:0001819	synonymous_variant	3856			BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"-", "Intermediate filaments type II, keratins (basic)"	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.1014C>T	12.37:g.53292651G>A			51578918	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Silent	SNP	ENST00000552551.1	37	CCDS8841.1																																																																																				0.642	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273		A	53292651	G	A	53292651	2	1	111	1	0	0	0	0	0	0	0	1	8514	1103	39	1		1	KRT8	12	53292651	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	280633	53292651	80559244	702	29836										
SPRYD3	84926	hgsc.bcm.edu	37	chr12	53461435	53461435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcagcccgctattcacctgCatgataagccacagaccctc	8	16	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53461435C>T	ENST00000301463.4	-	8	984	c.898G>A	c.(898-900)Gca>Aca	p.A300T	SPRYD3_ENST00000547837.1_Missense_Mutation_p.A337T	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	300										central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TATTCACCTGCATGATAAGCC	0.537																																																0			12											156	128	138					12																	53461435		2203	4300	6503	51747702	SO:0001583	missense	84926			AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.898G>A	12.37:g.53461435C>T	ENSP00000301463:p.Ala300Thr		51747702	B9EG99|Q96SK5	Missense_Mutation	SNP	ENST00000301463.4	37	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.136490	0.56936	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	T;T	0.15603	2.41;2.41	3.68	3.68	0.42216	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);SPla/RYanodine receptor SPRY (1);	0.203632	0.42821	D	0.000658	T	0.30417	0.0764	L	0.60067	1.865	0.51012	D	0.9999	D	0.60575	0.988	P	0.58266	0.836	T	0.02560	-1.1141	10	0.72032	D	0.01	.	11.1986	0.48728	0.0:1.0:0.0:0.0	.	300	Q8NCJ5	SPRY3_HUMAN	T	300;337	ENSP00000301463:A300T;ENSP00000449452:A337T	ENSP00000301463:A300T	A	-	1	0	SPRYD3	51747702	1.000000	0.71417	0.999000	0.59377	0.665000	0.39181	6.304000	0.72800	2.363000	0.80096	0.462000	0.41574	GCA		0.537	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840		T	53461435	C	T	53461435	3	4	111	1	0	0	0	0	1	0	0	0	15148	710	25	3	446	3	SPRYD3	12	53461435	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	168784	53461435	80390460	703	29837										
ESPL1	9700	hgsc.bcm.edu	37	chr12	53683916	53683916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaccctccagcccggaaccGtgggcaacaccctcctgctg	9	20	0	0	rs149892921	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53683916G>A	ENST00000257934.4	+	23	5252	c.5161G>A	c.(5161-5163)Gtg>Atg	p.V1721M	ESPL1_ENST00000552462.1_Missense_Mutation_p.V1721M	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1721					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						GCCCGGAACCGTGGGCAACAC	0.587																																					Colon(53;1069 1201 2587 5382)											0			12						G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75	68	71		5161	-2.4	0	12	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense	ESPL1	NM_012291.4	21	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	1721/2121	53683916	2,13004	2203	4300	6503	51970183	SO:0001583	missense	9700			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5161G>A	12.37:g.53683916G>A	ENSP00000257934:p.Val1721Met		51970183		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	G	2.436	-0.329649	0.05314	2.27E-4	1.16E-4	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12774	2.65;2.65	5.4	-2.42	0.06542	.	0.593368	0.18745	N	0.132344	T	0.04770	0.0129	N	0.19112	0.55	0.09310	N	1	P	0.34800	0.469	B	0.22601	0.04	T	0.28808	-1.0032	10	0.38643	T	0.18	.	1.8601	0.03187	0.4092:0.2141:0.2621:0.1147	.	1721	Q14674	ESPL1_HUMAN	M	1721;1396;1721	ENSP00000257934:V1721M;ENSP00000449831:V1721M	ENSP00000257934:V1721M	V	+	1	0	ESPL1	51970183	0.000000	0.05858	0.013000	0.15412	0.151000	0.21798	-0.266000	0.08631	-0.352000	0.08237	-0.793000	0.03317	GTG		0.587	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		A	53683916	G	A	53683916	3	1	111	1	0	0	0	0	1	0	0	0	5266	1145	40	1	5247	1	ESPL1	12	53683916	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	222481	53683916	80167979	704	29838										
SP7	121340	hgsc.bcm.edu	37	chr12	53722440	53722440	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaggagcgccctgccccactGcccccatatccaccactacc	7	21	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53722440G>T	ENST00000536324.2	-	3	1069	c.786C>A	c.(784-786)ggC>ggA	p.G262G	SP7_ENST00000303846.3_Silent_p.G262G|SP7_ENST00000537210.2_Silent_p.G244G	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	262					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						CTGCCCCACTGCCCCCATATC	0.632																																																0			12											27	32	31					12																	53722440		2024	4183	6207	52008707	SO:0001819	synonymous_variant	121340			AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.786C>A	12.37:g.53722440G>T			52008707	B3KY26|Q3MJ72|Q7Z718	Silent	SNP	ENST00000536324.2	37	CCDS44897.1																																																																																				0.632	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53722440	G	T	53722440	2	4	111	1	0	0	0	0	0	0	0	1	15006	1306	46	2		2	SP7	12	53722440	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	38524	53722440	80129455	705	29839										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53877706	53877708	+	In_Frame_Del	DEL	CCT	CCT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggaactcacctgagctcctcCctcctcctcatcaccagttc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	CCT	CCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:53877706_53877708delCCT	ENST00000267079.2	-	9	1471_1473	c.1246_1248delAGG	c.(1246-1248)aggdel	p.R416del	MAP3K12_ENST00000547035.1_In_Frame_Del_p.R449del|MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547488.1_In_Frame_Del_p.R449del	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	416					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						TGAGCTCCTCCCTCCTCCTCATC	0.542																																																0			12																																								52163975	SO:0001651	inframe_deletion	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1246_1248delAGG	12.37:g.53877712_53877714delCCT	ENSP00000267079:p.Arg416del		52163973	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	In_Frame_Del	DEL	ENST00000267079.2	37	CCDS8860.1																																																																																				0.542	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		-	53877708	CCT	-	53877706	7	5	111	1	0	1	0	1	0	0	0	0	9276	622	22	0	1359	0	MAP3K12	12	53877706	In_Frame_Del	DEL	CCT	TCGA-EI-6507-01A-11D-1733-10	155266	53877706	79974189	706	29840										
KIAA0748	9840	hgsc.bcm.edu	37	chr12	55356689	55356689	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccccaaatcagagtcttgCtggaggaactgcttctcttc	9	12	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:55356689C>T	ENST00000449076.1	-	9	1125	c.993G>A	c.(991-993)caG>caA	p.Q331Q	TESPA1_ENST00000316577.8_Silent_p.Q331Q|TESPA1_ENST00000524622.1_Silent_p.Q193Q|TESPA1_ENST00000531122.1_Silent_p.Q193Q|TESPA1_ENST00000532804.1_Silent_p.Q193Q|TESPA1_ENST00000524959.1_5'Flank	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	331					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											CAGAGTCTTGCTGGAGGAACT	0.517																																																0			12											68	72	71					12																	55356689		1957	4151	6108	53642956	SO:0001819	synonymous_variant	9840			AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.993G>A	12.37:g.55356689C>T			53642956	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Silent	SNP	ENST00000449076.1	37	CCDS44913.1																																																																																				0.517	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		T	55356689	C	T	55356689	2	4	111	1	0	0	0	0	0	0	0	1	8211	796	28	3		3	KIAA0748	12	55356689	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1478983	55356689	78495206	707	29841										
SARNP	84324	hgsc.bcm.edu	37	chr12	56194674	56194674	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtacatcttcttcatttgcCtcctcttcagctaaagaata	4	11	5	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:56194674C>A	ENST00000336133.3	-	3	201	c.147G>T	c.(145-147)gaG>gaT	p.E49D	SARNP_ENST00000552080.1_Missense_Mutation_p.E49D|SARNP_ENST00000444631.2_Intron|RP11-762I7.5_ENST00000552719.1_5'Flank|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.G362C	NM_033082.3	NP_149073.1	P82979	SARNP_HUMAN	SAP domain containing ribonucleoprotein	49					mRNA export from nucleus (GO:0006406)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	6						CTTCATTTGCCTCCTCTTCAG	0.388																																																0			12											239	198	212					12																	56194674		2203	4300	6503	54480941	SO:0001583	missense	84324			AJ409089	CCDS8892.1	12q13.2	2009-07-09				ENSG00000205323			24432	protein-coding gene	gene with protein product	"hepatocellular carcinoma 1", "cytokine induced protein 29 kDa"	610049				11356193, 11922608	Standard	NM_033082		Approved	THO1, Hcc-1, CIP29		P82979	OTTHUMG00000170441	ENST00000336133.3:c.147G>T	12.37:g.56194674C>A	ENSP00000337632:p.Glu49Asp		54480941	A8K393|Q9P066	Missense_Mutation	SNP	ENST00000336133.3	37	CCDS8892.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.77|11.77	1.737895|1.737895	0.30774|0.30774	.|.	.|.	ENSG00000205323|ENSG00000257390	ENST00000336133;ENST00000552080|ENST00000546837	.|.	.|.	.|.	5.32|5.32	2.41|2.41	0.29592|0.29592	DNA-binding SAP (1);|.	0.170876|.	0.52532|.	D|.	0.000076|.	T|T	0.39911|0.39911	0.1096|0.1096	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	B;B|.	0.30146|.	0.27;0.023|.	B;B|.	0.32533|.	0.147;0.011|.	T|T	0.07233|0.07233	-1.0783|-1.0783	9|5	0.31617|.	T|.	0.26|.	-14.1182|-14.1182	8.1025|8.1025	0.30865|0.30865	0.0:0.716:0.0:0.284|0.0:0.716:0.0:0.284	.|.	49;49|.	F8VZQ9;P82979|.	.;SARNP_HUMAN|.	D|C	49|362	.|.	ENSP00000337632:E49D|.	E|G	-|-	3|1	2|0	SARNP|RP11-762I7.5	54480941|54480941	0.824000|0.824000	0.29247|0.29247	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	-0.232000|-0.232000	0.09055|0.09055	0.294000|0.294000	0.22547|0.22547	-0.136000|-0.136000	0.14681|0.14681	GAG|GGC		0.388	SARNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409159.2	NM_033082		A	56194674	C	A	56194674	3	1	111	1	0	0	0	0	1	0	0	0	13880	680	24	2	521	2	SARNP	12	56194674	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	837985	56194674	77657221	708	29842										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56565715	56565715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagtcatctttgtacatttCcagtgcctggtggtagtggt	11	9	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:56565715C>T	ENST00000267064.4	-	20	1926	c.1840G>A	c.(1840-1842)Gaa>Aaa	p.E614K	SMARCC2_ENST00000394023.3_Missense_Mutation_p.E645K|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Missense_Mutation_p.E645K|SMARCC2_ENST00000550164.1_Missense_Mutation_p.E645K	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	614	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.E614K(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTGTACATTTCCAGTGCCTGG	0.507																																																1	Substitution - Missense(1)	skin(1)	12											77	65	69					12																	56565715		2203	4300	6503	54851982	SO:0001583	missense	6601			U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.1840G>A	12.37:g.56565715C>T	ENSP00000267064:p.Glu614Lys		54851982	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798517	0.90538	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	3.89	3.0	0.34707	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.122444	0.52532	D	0.000069	T	0.38134	0.1029	L	0.61387	1.9	0.58432	D	0.999994	B;B;B;B;B	0.33345	0.409;0.356;0.409;0.409;0.356	B;B;B;B;B	0.30572	0.117;0.071;0.117;0.117;0.115	T	0.40308	-0.9570	10	0.56958	D	0.05	-11.0784	11.0341	0.47791	0.0:0.9047:0.0:0.0953	.	534;645;649;614;645	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	K	645;645;645;614	ENSP00000377591:E645K;ENSP00000449396:E645K;ENSP00000302919:E645K;ENSP00000267064:E614K	ENSP00000267064:E614K	E	-	1	0	SMARCC2	54851982	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.609000	0.82925	1.211000	0.43351	0.655000	0.94253	GAA		0.507	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56565715	C	T	56565715	3	4	111	1	0	0	0	0	1	0	0	0	14813	864	30	3	1840	3	SMARCC2	12	56565715	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	371041	56565715	77286180	709	29843										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57424050	57424050	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcactggcacagagcttttcCctcaggatctctacctgctt	7	14	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:57424050C>A	ENST00000442789.2	-	25	2822	c.2535G>T	c.(2533-2535)agG>agT	p.R845S	MYO1A_ENST00000300119.3_Missense_Mutation_p.R845S|MYO1A_ENST00000544473.1_Missense_Mutation_p.R683S|TAC3_ENST00000415231.1_5'Flank	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	845					microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R845R(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						AGAGCTTTTCCCTCAGGATCT	0.572																																																1	Substitution - coding silent(1)	skin(1)	12											109	92	98					12																	57424050		2203	4300	6503	55710317	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2535G>T	12.37:g.57424050C>A	ENSP00000393392:p.Arg845Ser		55710317	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	C	40	8.369062	0.98781	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.88046	-2.27;-2.27;-2.33	4.94	4.04	0.47022	.	0.429106	0.26390	N	0.024644	T	0.81133	0.4759	L	0.47190	1.495	0.34496	D	0.705543	B	0.17038	0.02	B	0.19148	0.024	T	0.80903	-0.1174	10	0.40728	T	0.16	.	8.2433	0.31673	0.0:0.8926:0.0:0.1074	.	845	Q9UBC5	MYO1A_HUMAN	S	845;845;683	ENSP00000300119:R845S;ENSP00000393392:R845S;ENSP00000440514:R683S	ENSP00000300119:R845S	R	-	3	2	MYO1A	55710317	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	1.866000	0.39489	2.291000	0.77112	0.544000	0.68410	AGG		0.572	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57424050	C	A	57424050	3	1	111	1	0	0	0	0	1	0	0	0	10098	622	22	2	616	2	MYO1A	12	57424050	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	858335	57424050	76427845	710	29844										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57431361	57431361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcttctaatgaagatctttgTcttgccaaaggccagctccc	8	12	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:57431361T>C	ENST00000442789.2	-	20	2313	c.2026A>G	c.(2026-2028)Aca>Gca	p.T676A	MYO1A_ENST00000476795.1_5'Flank|MYO1A_ENST00000300119.3_Missense_Mutation_p.T676A|MYO1A_ENST00000544473.1_Missense_Mutation_p.T514A	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	676	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						AAGATCTTTGTCTTGCCAAAG	0.527																																																0			12											272	283	279					12																	57431361		2203	4300	6503	55717628	SO:0001583	missense	4640			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2026A>G	12.37:g.57431361T>C	ENSP00000393392:p.Thr676Ala		55717628	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135035	0.77662	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.90620	-2.7;-2.7;-2.7	4.96	4.96	0.65561	Myosin head, motor domain (2);	0.059684	0.64402	D	0.000003	D	0.95576	0.8562	H	0.96269	3.795	0.53005	D	0.999967	D	0.63046	0.992	P	0.56042	0.79	D	0.96254	0.9185	10	0.87932	D	0	.	11.0233	0.47730	0.0:0.0:0.0:1.0	.	676	Q9UBC5	MYO1A_HUMAN	A	676;676;514	ENSP00000300119:T676A;ENSP00000393392:T676A;ENSP00000440514:T514A	ENSP00000300119:T676A	T	-	1	0	MYO1A	55717628	0.993000	0.37304	1.000000	0.80357	0.965000	0.64279	2.485000	0.45250	1.882000	0.54519	0.482000	0.46254	ACA		0.527	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		C	57431361	T	C	57431361	3	2	111	1	0	0	0	0	1	0	0	0	10098	1667	58	4	1145	4	MYO1A	12	57431361	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	7311	57431361	76420534	711	29845										
GLI1	2735	hgsc.bcm.edu	37	chr12	57860075	57860075	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaggagttcgtgtgccactGggggggctgctccagggagc					rs368789621		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:57860075delG	ENST00000228682.2	+	8	906	c.815delG	c.(814-816)tggfs	p.W272fs	GLI1_ENST00000543426.1_Frame_Shift_Del_p.W144fs|GLI1_ENST00000546141.1_Frame_Shift_Del_p.W231fs	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	272					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			GTGTGCCACTGGGGGGGCTGC	0.597																																					Pancreas(157;841 1936 10503 41495 50368)											0			12											128	124	126					12																	57860075		2203	4300	6503	56146342	SO:0001589	frameshift_variant	2735				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.815delG	12.37:g.57860075delG	ENSP00000228682:p.Trp272fs		56146342	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Frame_Shift_Del	DEL	ENST00000228682.2	37	CCDS8940.1																																																																																				0.597	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		-	57860075	G	-	57860075	7	5	111	1	0	1	0	1	0	0	0	0	6457	1357	47	0	841	0	GLI1	12	57860075	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	428714	57860075	75991820	712	29846										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59267964	59267964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagtaactagtgttaagtagCttcctcacatgtgaaggcca	10	8	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:59267964C>A	ENST00000320743.3	-	18	3274	c.2988G>T	c.(2986-2988)aaG>aaT	p.K996N	LRIG3_ENST00000379141.4_Missense_Mutation_p.K936N	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	996					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TGTTAAGTAGCTTCCTCACAT	0.413			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0			12											88	87	87					12																	59267964		2203	4300	6503	57554231	SO:0001583	missense	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2988G>T	12.37:g.59267964C>A	ENSP00000326759:p.Lys996Asn		57554231	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.62|12.62	1.991999|1.991999	0.35131|0.35131	.|.	.|.	ENSG00000139263|ENSG00000139263	ENST00000550825|ENST00000379141;ENST00000320743	.|T;T	.|0.62639	.|0.06;0.01	5.83|5.83	3.01|3.01	0.34805|0.34805	.|.	.|0.000000	.|0.38897	.|N	.|0.001539	T|T	0.52322|0.52322	0.1727|0.1727	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.27559	.|0.145;0.181	.|B;B	.|0.26864	.|0.054;0.074	T|T	0.41502|0.41502	-0.9505|-0.9505	5|9	.|.	.|.	.|.	.|.	9.0667|9.0667	0.36467|0.36467	0.0:0.7017:0.0:0.2983|0.0:0.7017:0.0:0.2983	.|.	.|936;996	.|Q6UXM1-2;Q6UXM1	.|.;LRIG3_HUMAN	S|N	98|936;996	.|ENSP00000368436:K936N;ENSP00000326759:K996N	.|.	A|K	-|-	1|3	0|2	LRIG3|LRIG3	57554231|57554231	0.433000|0.433000	0.25562|0.25562	0.441000|0.441000	0.26858|0.26858	0.026000|0.026000	0.11368|0.11368	0.554000|0.554000	0.23407|0.23407	1.467000|1.467000	0.48044|0.48044	0.650000|0.650000	0.86243|0.86243	GCT|AAG		0.413	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59267964	C	A	59267964	3	1	111	1	0	0	0	0	1	0	0	0	8975	796	28	2	379	2	LRIG3	12	59267964	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1407889	59267964	74583931	713	29847										
TBK1	29110	hgsc.bcm.edu	37	chr12	64878186	64878186	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagtcttagaacctggaaggCtggcacaacatttccctaaa	8	10	1	1	rs529643988		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:64878186C>T	ENST00000331710.5	+	9	1435	c.1096C>T	c.(1096-1098)Ctg>Ttg	p.L366L		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	366	Ubiquitin-like.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		ACCTGGAAGGCTGGCACAACA	0.348													C|||	1	0.000199681	0	0	5008	,	,		17718	0		0	False		,,,				2504	0.001															0			12											60	62	61					12																	64878186		2203	4300	6503	63164453	SO:0001819	synonymous_variant	29110			AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1096C>T	12.37:g.64878186C>T			63164453	A8K4S4|Q8IYV3|Q9NUJ5	Silent	SNP	ENST00000331710.5	37	CCDS8968.1																																																																																				0.348	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		T	64878186	C	T	64878186	2	4	111	1	0	0	0	0	0	0	0	1	15676	796	28	3		3	TBK1	12	64878186	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5610222	64878186	68973709	714	29848										
MDM1	56890	hgsc.bcm.edu	37	chr12	68690735	68690735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcttcatgttgaggtaacTgcaaattgttcatccttgct	9	8	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:68690735T>C	ENST00000303145.7	-	13	2086	c.2000A>G	c.(1999-2001)cAg>cGg	p.Q667R	MDM1_ENST00000540418.1_Missense_Mutation_p.Q387R|MDM1_ENST00000411698.2_Missense_Mutation_p.Q632R	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	667					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)		p.Q667L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TTGAGGTAACTGCAAATTGTT	0.313																																																1	Substitution - Missense(1)	ovary(1)	12											128	122	124					12																	68690735		2202	4299	6501	66977002	SO:0001583	missense	56890			AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.2000A>G	12.37:g.68690735T>C	ENSP00000302537:p.Gln667Arg		66977002	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	T	6.399	0.441736	0.12164	.	.	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.24908	1.83;2.14;2.14	5.02	3.88	0.44766	.	0.537282	0.20336	N	0.094339	T	0.22742	0.0549	L	0.59436	1.845	0.80722	D	1	P;B	0.45827	0.867;0.041	B;B	0.39027	0.288;0.011	T	0.02498	-1.1150	9	.	.	.	-5.3148	7.8707	0.29565	0.0:0.0927:0.0:0.9073	.	632;667	E7EPQ3;Q8TC05	.;MDM1_HUMAN	R	387;667;632	ENSP00000443815:Q387R;ENSP00000302537:Q667R;ENSP00000391006:Q632R	.	Q	-	2	0	MDM1	66977002	1.000000	0.71417	0.922000	0.36590	0.293000	0.27360	1.280000	0.33202	1.065000	0.40693	-0.281000	0.10026	CAG		0.313	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		C	68690735	T	C	68690735	3	2	111	1	0	0	0	0	1	0	0	0	9442	1580	55	4	152	4	MDM1	12	68690735	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3812549	68690735	65161160	715	29849										
E2F7	144455	hgsc.bcm.edu	37	chr12	77419585	77419585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtcctgtgtttgggagagcaCcaagagtagaagaaaccggg	15	7	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:77419585C>T	ENST00000322886.7	-	12	2553	c.2318G>A	c.(2317-2319)gGt>gAt	p.G773D	E2F7_ENST00000416496.2_Intron	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	773					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TGGGAGAGCACCAAGAGTAGA	0.532																																																0			12											56	57	57					12																	77419585		2203	4300	6503	75943716	SO:0001583	missense	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2318G>A	12.37:g.77419585C>T	ENSP00000323246:p.Gly773Asp		75943716	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.70|12.70	2.016099|2.016099	0.35606|0.35606	.|.	.|.	ENSG00000165891|ENSG00000165891	ENST00000339887|ENST00000322886	.|T	.|0.16324	.|2.35	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	.|0.737835	.|0.13279	.|N	.|0.399860	.|T	.|0.12008	.|0.0292	L|L	0.29908|0.29908	0.895|0.895	0.36111|0.36111	D|D	0.844836|0.844836	.|B	.|0.16166	.|0.016	.|B	.|0.15052	.|0.012	.|T	.|0.13522	.|-1.0506	.|10	.|0.12103	.|T	.|0.63	.|-10.5033	9.8725|9.8725	0.41182|0.41182	0.0:0.9006:0.0:0.0994|0.0:0.9006:0.0:0.0994	.|.	.|773	.|Q96AV8	.|E2F7_HUMAN	.|D	-1|773	.|ENSP00000323246:G773D	.|ENSP00000323246:G773D	.|G	-|-	.|2	.|0	E2F7|E2F7	75943716|75943716	0.003000|0.003000	0.15002|0.15002	0.048000|0.048000	0.18961|0.18961	0.132000|0.132000	0.20833|0.20833	1.668000|1.668000	0.37481|0.37481	2.818000|2.818000	0.97014|0.97014	0.655000|0.655000	0.94253|0.94253	.|GGT		0.532	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		T	77419585	C	T	77419585	3	4	111	1	0	0	0	0	1	0	0	0	4883	507	18	3	425	3	E2F7	12	77419585	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	8728850	77419585	56432310	716	29850										
NAV3	89795	hgsc.bcm.edu	37	chr12	78516075	78516075	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctaccagtccatgactagcCtccacacgagctctgagtcc	8	16	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:78516075C>A	ENST00000397909.2	+	16	4278	c.4105C>A	c.(4105-4107)Ctc>Atc	p.L1369I	NAV3_ENST00000536525.2_Missense_Mutation_p.L1369I|NAV3_ENST00000228327.6_Missense_Mutation_p.L1369I|NAV3_ENST00000266692.7_Intron			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1369	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CATGACTAGCCTCCACACGAG	0.567										HNSCC(70;0.22)																																						0			12											122	115	117					12																	78516075		2015	4198	6213	77040206	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4105C>A	12.37:g.78516075C>A	ENSP00000381007:p.Leu1369Ile		77040206	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	C	18.96	3.733257	0.69189	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000378640;ENST00000550788	T;T;T;T	0.36878	1.23;1.27;1.23;1.95	5.96	5.96	0.96718	.	0.000000	0.35708	U	0.003035	T	0.63189	0.2490	M	0.72118	2.19	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.83275	0.936;0.996;0.915	T	0.62996	-0.6735	10	0.72032	D	0.01	-11.5003	20.4082	0.99013	0.0:1.0:0.0:0.0	.	1369;1369;1369	E7EUC6;Q8IVL0;Q8IVL0-2	.;NAV3_HUMAN;.	I	1369;1369;1369;4;12	ENSP00000446132:L1369I;ENSP00000381007:L1369I;ENSP00000228327:L1369I;ENSP00000448303:L12I	ENSP00000228327:L1369I	L	+	1	0	NAV3	77040206	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.737000	0.62066	2.814000	0.96858	0.655000	0.94253	CTC		0.567	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78516075	C	A	78516075	3	1	111	1	0	0	0	0	1	0	0	0	10215	681	24	2	4167	2	NAV3	12	78516075	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1096490	78516075	55335820	717	29851										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80214607	80214607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcttcttcactagagcagCtagactcatccttctttcct	4	14	5	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:80214607C>A	ENST00000450142.2	-	8	1327	c.1061G>T	c.(1060-1062)aGc>aTc	p.S354I	PPP1R12A_ENST00000261207.5_Missense_Mutation_p.S354I|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.S354I|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.S267I|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.S354I|RP11-530C5.2_ENST00000548469.1_RNA	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	354					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						ACTAGAGCAGCTAGACTCATC	0.378																																																0			12											199	193	195					12																	80214607		1898	4100	5998	78738738	SO:0001583	missense	4659			D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.1061G>T	12.37:g.80214607C>A	ENSP00000389168:p.Ser354Ile		78738738	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048880	0.93740	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107;ENST00000547330;ENST00000547131	T;T;T;T;T;T;T	0.62232	1.02;1.02;1.04;1.02;0.96;0.99;0.04	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.81197	0.4772	M	0.77313	2.365	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.997;0.998	D;D;D;D	0.83275	0.994;0.996;0.994;0.991	T	0.81824	-0.0755	10	0.66056	D	0.02	.	20.1392	0.98050	0.0:1.0:0.0:0.0	.	354;354;354;354	F8W8Q6;O14974-2;O14974-3;O14974	.;.;.;MYPT1_HUMAN	I	354;354;354;354;354;354;354;267;354;354;49	ENSP00000261207:S354I;ENSP00000389168:S354I;ENSP00000416769:S354I;ENSP00000449514:S267I;ENSP00000446855:S354I;ENSP00000446816:S354I;ENSP00000450061:S49I	ENSP00000261207:S354I	S	-	2	0	PPP1R12A	78738738	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.247000	0.78257	2.751000	0.94390	0.591000	0.81541	AGC		0.378	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		A	80214607	C	A	80214607	3	1	111	1	0	0	0	0	1	0	0	0	12388	797	28	2	2103	2	PPP1R12A	12	80214607	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1698532	80214607	53637288	718	29852										
EPYC	1833	hgsc.bcm.edu	37	chr12	91365683	91365683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgccttattttgttgtcaCgcaggacaagctctcgaagt	10	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:91365683C>T	ENST00000261172.3	-	5	688	c.596G>A	c.(595-597)cGt>cAt	p.R199H		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	199					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						TTTGTTGTCACGCAGGACAAG	0.383																																																0			12											95	87	90					12																	91365683		2203	4300	6503	89889814	SO:0001583	missense	1833			AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.596G>A	12.37:g.91365683C>T	ENSP00000261172:p.Arg199His		89889814	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860780	0.91433	.	.	ENSG00000083782	ENST00000261172;ENST00000551767	T;T	0.57752	0.38;0.38	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.60702	0.2289	N	0.17379	0.485	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	T	0.61978	-0.6951	10	0.48119	T	0.1	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	199	Q99645	EPYC_HUMAN	H	199	ENSP00000261172:R199H;ENSP00000448272:R199H	ENSP00000261172:R199H	R	-	2	0	EPYC	89889814	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	3.341000	0.52151	2.861000	0.98227	0.655000	0.94253	CGT		0.383	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950		T	91365683	C	T	91365683	3	4	111	1	0	0	0	0	1	0	0	0	5214	536	19	1	384	1	EPYC	12	91365683	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	11151076	91365683	42486212	719	29853										
C12orf42	374470	hgsc.bcm.edu	37	chr12	103699965	103699965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcagtaaaaatcaatggggCctcatcagtttcactggatg	11	8	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:103699965C>T	ENST00000378113.2	-	5	643	c.418G>A	c.(418-420)Gcc>Acc	p.A140T	C12orf42_ENST00000315192.8_Intron|C12orf42_ENST00000548048.1_Missense_Mutation_p.A73T|C12orf42_ENST00000548883.1_Missense_Mutation_p.A140T|C12orf42_ENST00000548789.1_5'UTR	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	140										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						ATCAATGGGGCCTCATCAGTT	0.453																																																0			12											72	74	73					12																	103699965		1858	4108	5966	102224095	SO:0001583	missense	374470			AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.418G>A	12.37:g.103699965C>T	ENSP00000367353:p.Ala140Thr		102224095	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	37	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	C	7.002	0.555066	0.13436	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113;ENST00000552578	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.34	-2.62	0.06152	.	2.083010	0.02499	N	0.090311	T	0.23133	0.0559	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09796	-1.0658	10	0.25106	T	0.35	8.8502	5.3045	0.15795	0.1577:0.2212:0.0:0.6212	.	140	Q96LP6	CL042_HUMAN	T	140;73;140;140	ENSP00000447908:A140T;ENSP00000449362:A73T;ENSP00000367353:A140T;ENSP00000447795:A140T	ENSP00000367353:A140T	A	-	1	0	C12orf42	102224095	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.315000	0.08081	-0.546000	0.06216	-0.368000	0.07277	GCC		0.453	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		T	103699965	C	T	103699965	3	4	111	1	0	0	0	0	1	0	0	0	1692	739	26	3	672	3	C12orf42	12	103699965	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	12334282	103699965	30151930	720	29854										
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104171699	104171699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgctgcagtggagtcctccGggggtagaaagtgtggctga	18	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:104171699G>A	ENST00000392876.3	-	14	1595	c.1555C>T	c.(1555-1557)Cgg>Tgg	p.R519W		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	519						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.R444G(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						GGAGTCCTCCGGGGGTAGAAA	0.622																																																1	Substitution - Missense(1)	ovary(1)	12											64	67	66					12																	104171699		2203	4300	6503	102695829	SO:0001583	missense	51559			AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1555C>T	12.37:g.104171699G>A	ENSP00000376615:p.Arg519Trp		102695829	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	37	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.498814	0.85069	.	.	ENSG00000111696	ENST00000392876	T	0.24151	1.87	5.8	-2.53	0.06326	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	M	0.86573	2.825	0.52099	D	0.999941	D	0.89917	1.0	D	0.76071	0.987	T	0.65265	-0.6210	10	0.87932	D	0	-24.1928	18.7136	0.91667	0.0:0.0:0.3514:0.6486	.	519	Q86UY8	NT5D3_HUMAN	W	519	ENSP00000376615:R519W	ENSP00000376615:R519W	R	-	1	2	NT5DC3	102695829	1.000000	0.71417	0.884000	0.34674	0.998000	0.95712	1.174000	0.31932	-0.719000	0.04942	0.655000	0.94253	CGG		0.622	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		A	104171699	G	A	104171699	3	1	111	1	0	0	0	0	1	0	0	0	10723	1115	39	1	95	1	NT5DC3	12	104171699	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	471734	104171699	29680196	721	29855										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104487253	104487253	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccagactttaaagcactgacGgattctaatgccattttata	6	9	1	2	rs142462488	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:104487253G>A	ENST00000229330.4	+	10	1478	c.1374G>A	c.(1372-1374)acG>acA	p.T458T	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	458					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AAGCACTGACGGATTCTAATG	0.338																																					Esophageal Squamous(184;1814 2036 4771 6974 15702)											0			12						G		0,4406		0,0,2203	97	91	93		1374	-0.1	0.1	12	dbSNP_134	93	1,8597		0,1,4298	no	coding-synonymous	HCFC2	NM_013320.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		458/793	104487253	1,13003	2203	4299	6502	103011383	SO:0001819	synonymous_variant	29915			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1374G>A	12.37:g.104487253G>A			103011383	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	37	CCDS9097.1																																																																																				0.338	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		A	104487253	G	A	104487253	2	1	111	1	0	0	0	0	0	0	0	1	7014	1103	39	1		1	HCFC2	12	104487253	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	315554	104487253	29364642	722	29856										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcctctgtggctgccagtgGagtggtctgtgcctccgtgg					rs200527674|rs540144714|rs368721402|rs63748999|rs372173288|rs201851784|rs377406736|rs200694582|rs200732108|rs199985195|rs558357966	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENST00000550948.1	-	2	628_657	c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	c.(403-435)caaccagtgcccacggaggcacagaccactcca>cca	p.QPVPTEAQTT135del	SELPLG_ENST00000388962.3_Splice_Site_p.NQCPR131del|SELPLG_ENST00000228463.6_In_Frame_Del_p.QPVPTEAQTT151del			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCTGCCAGTGGAGTGGTCTGTGCCTCCGTGGGCACTGGTTGAGTGGTCTG	0.617														558	0.111422	0.0817	0.0879	5008	,	,		27757	0.13		0.0835	False		,,,				2504	0.1779															1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12							,	500,3762		33,434,1664					,	-2	0		dbSNP_129	146	1398,6854		132,1134,2860	no	coding,coding	SELPLG	NM_003006.4,NM_001206609.1	,	165,1568,4524	A1A1,A1R,RR		16.9413,11.7316,15.167	,	,		1898,10616				107541809	SO:0001651	inframe_deletion	6404				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	12.37:g.109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENSP00000447752:p.Gln135_Thr144del		107541780	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Frame_Shift_Del	DEL	ENST00000550948.1	37	CCDS31895.2																																																																																				0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			-	109017680	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	109017651	7	5	111	1	0	1	0	1	0	0	0	0	14057	1174	41	0	809	0	SELPLG	12	109017651	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	TCGA-EI-6507-01A-11D-1733-10	4530398	109017651	24834244	723	29857										
USP30	84749	hgsc.bcm.edu	37	chr12	109523555	109523555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acactttgtcacttaccgacGgtccccaccttctgccagga	7	16	2	0	rs200435024		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:109523555G>A	ENST00000257548.5	+	13	1466	c.1373G>A	c.(1372-1374)cGg>cAg	p.R458Q	USP30_ENST00000392784.2_Missense_Mutation_p.R427Q	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	458	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						ACTTACCGACGGTCCCCACCT	0.567																																																0			12											160	129	140					12																	109523555		2203	4300	6503	108007938	SO:0001583	missense	84749			BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.1373G>A	12.37:g.109523555G>A	ENSP00000257548:p.Arg458Gln		108007938	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	37	CCDS9123.2	.	.	.	.	.	.	.	.	.	.	G	36	5.839967	0.97009	.	.	ENSG00000135093	ENST00000392784;ENST00000257548	T;T	0.76839	-1.05;-1.05	5.65	5.65	0.86999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.87977	0.6314	M	0.70903	2.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	D	0.88499	0.3081	10	0.72032	D	0.01	-38.7726	18.7287	0.91726	0.0:0.0:1.0:0.0	.	458;427	Q70CQ3;B3KUS5	UBP30_HUMAN;.	Q	427;458	ENSP00000376535:R427Q;ENSP00000257548:R458Q	ENSP00000257548:R458Q	R	+	2	0	USP30	108007938	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.355000	0.97087	2.655000	0.90218	0.655000	0.94253	CGG		0.567	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		A	109523555	G	A	109523555	3	1	111	1	0	0	0	0	1	0	0	0	17101	1116	39	1	1423	1	USP30	12	109523555	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	505904	109523555	24328340	724	29858										
ACACB	32	hgsc.bcm.edu	37	chr12	109704163	109704163	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catggacagcccggcctccaCctgaccgtggcccgcccagc	11	20	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:109704163C>T	ENST00000338432.7	+	53	7492	c.7373C>T	c.(7372-7374)aCc>aTc	p.T2458I	ACACB_ENST00000543201.1_3'UTR|ACACB_ENST00000377854.5_Missense_Mutation_p.T2388I|ACACB_ENST00000377848.3_Missense_Mutation_p.T2458I			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2458					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CCGGCCTCCACCTGACCGTGG	0.632																																																0			12											36	34	35					12																	109704163		2203	4300	6503	108188546	SO:0001583	missense	32			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.7373C>T	12.37:g.109704163C>T	ENSP00000341044:p.Thr2458Ile		108188546	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756879	0.49362	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000537279	D;D;D	0.95756	-3.8;-3.8;-3.8	4.93	3.06	0.35304	.	0.487974	0.21260	N	0.077484	D	0.91707	0.7378	L	0.29908	0.895	0.80722	D	1	P	0.39717	0.684	B	0.41374	0.355	D	0.89621	0.3848	10	0.87932	D	0	.	10.6842	0.45833	0.1388:0.5931:0.2681:0.0	.	2458	O00763	ACACB_HUMAN	I	2458;2458;2388;1689;152	ENSP00000341044:T2458I;ENSP00000367079:T2458I;ENSP00000367085:T2388I	ENSP00000341044:T2458I	T	+	2	0	ACACB	108188546	0.149000	0.22717	0.993000	0.49108	0.432000	0.31715	1.437000	0.34991	0.579000	0.29504	-0.165000	0.13383	ACC		0.632	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109704163	C	T	109704163	3	4	111	1	0	0	0	0	1	0	0	0	107	507	18	3	7579	3	ACACB	12	109704163	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	180608	109704163	24147732	725	29859										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109972419	109972419	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accggggacactctgggcagCgtcctccggggcttcttcac	13	15	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:109972419C>T	ENST00000342494.3	+	28	3634	c.3039C>T	c.(3037-3039)agC>agT	p.S1013S	UBE3B_ENST00000434735.2_Silent_p.S1013S	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	1013	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						CTCTGGGCAGCGTCCTCCGGG	0.647																																																0			12											43	43	43					12																	109972419		2203	4300	6503	108456802	SO:0001819	synonymous_variant	89910			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.3039C>T	12.37:g.109972419C>T			108456802	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Silent	SNP	ENST00000342494.3	37	CCDS9129.1																																																																																				0.647	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109972419	C	T	109972419	2	4	111	1	0	0	0	0	0	0	0	1	16920	767	27	1		1	UBE3B	12	109972419	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	268256	109972419	23879476	726	29860										
TCHP	84260	hgsc.bcm.edu	37	chr12	110344435	110344435	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgggaaatgcagaaagaagAaaaaaaacaggtgtggtatg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:110344435delA	ENST00000312777.5	+	5	729	c.515delA	c.(514-516)gaafs	p.E172fs	TCHP_ENST00000405876.4_Frame_Shift_Del_p.E172fs	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						CAGAAAGAAGAAAAAAAACAG	0.478																																																0			12											63	63	63					12																	110344435		2203	4300	6503	108828818	SO:0001589	frameshift_variant	84260			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"mitostatin"	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.515delA	12.37:g.110344435delA	ENSP00000324404:p.Glu172fs		108828818		Frame_Shift_Del	DEL	ENST00000312777.5	37	CCDS9137.1																																																																																				0.478	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300		-	110344435	A	-	110344435	7	5	111	1	0	1	0	1	0	0	0	0	15741	246	9	0	529	0	TCHP	12	110344435	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	372016	110344435	23507460	727	29861										
PPTC7	160760	hgsc.bcm.edu	37	chr12	110989689	110989689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accgtccttcttttactaaaCgttcacacgtccgcattaaa	4	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:110989689C>T	ENST00000354300.3	-	2	596	c.308G>A	c.(307-309)cGt>cAt	p.R103H		NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)	103	PP2C-like.					mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						TTTTACTAAACGTTCACACGT	0.443																																																0			12											141	123	129					12																	110989689		2203	4300	6503	109474072	SO:0001583	missense	160760			AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"T cell activation protein phosphatase 2C"	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.308G>A	12.37:g.110989689C>T	ENSP00000346255:p.Arg103His		109474072	B3KWC5|Q68DZ7|Q6UY82	Missense_Mutation	SNP	ENST00000354300.3	37	CCDS9149.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934588	0.92458	.	.	ENSG00000196850	ENST00000354300	.	.	.	5.96	5.96	0.96718	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.68118	0.2966	L	0.54965	1.715	0.80722	D	1	P	0.39831	0.69	P	0.45538	0.484	T	0.66830	-0.5824	9	0.51188	T	0.08	-11.113	20.4082	0.99013	0.0:1.0:0.0:0.0	.	103	Q8NI37	PPTC7_HUMAN	H	103	.	ENSP00000346255:R103H	R	-	2	0	PPTC7	109474072	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.814000	0.86154	2.814000	0.96858	0.655000	0.94253	CGT		0.443	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283		T	110989689	C	T	110989689	3	4	111	1	0	0	0	0	1	0	0	0	12447	536	19	1	626	1	PPTC7	12	110989689	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	645254	110989689	22862206	728	29862										
MAPKAPK5	8550	hgsc.bcm.edu	37	chr12	112321565	112321565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagagatggccaaagatgttGtgaggaagtgagttcacggg	16	5	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:112321565G>A	ENST00000551404.2	+	9	949	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	MAPKAPK5_ENST00000550735.2_Missense_Mutation_p.V281M			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						CAAAGATGTTGTGAGGAAGTG	0.522																																																0			12											88	85	86					12																	112321565		1989	4179	6168	110805948	SO:0001583	missense	8550			AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.841G>A	12.37:g.112321565G>A	ENSP00000449381:p.Val281Met		110805948	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Missense_Mutation	SNP	ENST00000551404.2	37	CCDS44975.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810968	0.90707	.	.	ENSG00000089022	ENST00000550735;ENST00000202788;ENST00000428907;ENST00000553053;ENST00000551404	T;T	0.68624	-0.34;-0.34	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81206	0.4774	M	0.66939	2.045	0.80722	D	1	D;D;D	0.63880	0.992;0.993;0.991	D;D;P	0.72982	0.979;0.912;0.857	T	0.82784	-0.0286	10	0.72032	D	0.01	.	18.9881	0.92780	0.0:0.0:1.0:0.0	.	275;281;281	C9J458;Q8IW41;Q8IW41-2	.;MAPK5_HUMAN;.	M	281;281;281;48;281	ENSP00000449667:V281M;ENSP00000449381:V281M	ENSP00000202788:V281M	V	+	1	0	MAPKAPK5	110805948	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.476000	0.97823	2.484000	0.83849	0.557000	0.71058	GTG		0.522	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078		A	112321565	G	A	112321565	3	1	111	1	0	0	0	0	1	0	0	0	9321	1377	48	3	875	3	MAPKAPK5	12	112321565	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1331876	112321565	21530330	729	29863										
RHOF	54509	hgsc.bcm.edu	37	chr12	122219074	122219074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttctggtaggacaggggcCgcagccggtcatagtcttct	14	10	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:122219074C>T	ENST00000267205.2	-	3	879	c.251G>A	c.(250-252)cGg>cAg	p.R84Q	TMEM120B_ENST00000449592.2_3'UTR|TMEM120B_ENST00000538055.1_Intron|RHOF_ENST00000537265.1_5'UTR|RHOF_ENST00000537171.1_Missense_Mutation_p.R84Q	NM_019034.2	NP_061907.2	Q9HBH0	RHOF_HUMAN	ras homolog family member F (in filopodia)	84					actin filament organization (GO:0007015)|GTP catabolic process (GO:0006184)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(1)|ovary(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;4.38e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.223)		GGACAGGGGCCGCAGCCGGTC	0.622																																																0			12											106	100	102					12																	122219074		2203	4300	6503	120703457	SO:0001583	missense	54509			AK000254	CCDS9222.1	12q24.31	2013-09-23	2012-02-27	2004-03-24	ENSG00000139725	ENSG00000139725			15703	protein-coding gene	gene with protein product			"ras homolog gene family, member F (in filopodia)"	ARHF		11084341	Standard	NM_019034		Approved	FLJ20247, RIF	uc001ubb.3	Q9HBH0	OTTHUMG00000169077	ENST00000267205.2:c.251G>A	12.37:g.122219074C>T	ENSP00000267205:p.Arg84Gln		120703457	Q8WVB1|Q9NXH6	Missense_Mutation	SNP	ENST00000267205.2	37	CCDS9222.1	.	.	.	.	.	.	.	.	.	.	C	36	5.813918	0.96975	.	.	ENSG00000139725	ENST00000267205;ENST00000535560	T;T	0.72167	-0.63;-0.63	5.03	5.03	0.67393	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90758	0.7099	H	0.98629	4.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94399	0.7621	10	0.87932	D	0	.	18.3082	0.90189	0.0:1.0:0.0:0.0	.	84;84	Q9HBH0-2;Q9HBH0	.;RHOF_HUMAN	Q	84	ENSP00000267205:R84Q;ENSP00000440397:R84Q	ENSP00000267205:R84Q	R	-	2	0	RHOF	120703457	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.401000	0.79962	2.488000	0.83962	0.650000	0.86243	CGG		0.622	RHOF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402165.1			T	122219074	C	T	122219074	3	4	111	1	0	0	0	0	1	0	0	0	13375	652	23	1	396	1	RHOF	12	122219074	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9897509	122219074	11632821	730	29864										
RSRC2	65117	hgsc.bcm.edu	37	chr12	123001814	123001814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actcctgcttctagtcctatGcctgtgtcttgatcttgagc	8	12	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:123001814G>A	ENST00000331738.7	-	5	707	c.562C>T	c.(562-564)Cat>Tat	p.H188Y	RSRC2_ENST00000354654.2_Missense_Mutation_p.H140Y	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2	188	Ser-rich.						poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		CTAGTCCTATGCCTGTGTCTT	0.473																																																0			12											223	184	197					12																	123001814		2203	4300	6503	121567767	SO:0001583	missense	65117			AF161432	CCDS31920.1	12q24.31	2007-02-13			ENSG00000111011	ENSG00000111011			30559	protein-coding gene	gene with protein product						17203224	Standard	NM_023012		Approved	FLJ11021	uc001ucr.3	Q7L4I2	OTTHUMG00000167572	ENST00000331738.7:c.562C>T	12.37:g.123001814G>A	ENSP00000330188:p.His188Tyr		121567767	Q6N040|Q6NW16|Q9H864	Missense_Mutation	SNP	ENST00000331738.7	37	CCDS31920.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028589	0.75390	.	.	ENSG00000111011	ENST00000331738;ENST00000354654;ENST00000418773;ENST00000344591	T;T;T	0.21734	1.99;1.99;1.99	5.48	5.48	0.80851	.	0.143804	0.64402	D	0.000005	T	0.23094	0.0558	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.56968	0.978;0.957;0.978;0.957	P;B;P;B	0.47528	0.549;0.395;0.549;0.395	T	0.01416	-1.1360	10	0.59425	D	0.04	.	19.3576	0.94421	0.0:0.0:1.0:0.0	.	188;140;188;129	F5GXM2;Q7L4I2-2;Q7L4I2;E1B6W4	.;.;RSRC2_HUMAN;.	Y	188;140;188;129	ENSP00000330188:H188Y;ENSP00000346678:H140Y;ENSP00000343315:H129Y	ENSP00000330188:H188Y	H	-	1	0	RSRC2	121567767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.700000	0.91322	2.589000	0.87451	0.655000	0.94253	CAT		0.473	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	NM_023012		A	123001814	G	A	123001814	3	1	111	1	0	0	0	0	1	0	0	0	13752	1319	46	3	766	3	RSRC2	12	123001814	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	782740	123001814	10850081	731	29865										
ABCB9	23457	hgsc.bcm.edu	37	chr12	123424719	123424719	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccgtccagcagcacccggCccccctccagggggtagaag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:123424719delC	ENST00000542678.1	-	9	4520	c.1682delG	c.(1681-1683)ggcfs	p.G561fs	ABCB9_ENST00000346530.5_Frame_Shift_Del_p.G518fs|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.G561fs|ABCB9_ENST00000540285.1_Frame_Shift_Del_p.G498fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.G561fs|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.G561fs|ABCB9_ENST00000392439.3_Frame_Shift_Del_p.G561fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.G561fs|ABCB9_ENST00000541983.1_5'UTR			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	561	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CAGCACCCGGCCCCCCTCCAG	0.657																																					Ovarian(49;786 1333 9175 38236)											0			12											26	27	27					12																	123424719		2203	4299	6502	121990672	SO:0001589	frameshift_variant	23457			U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1682delG	12.37:g.123424719delC	ENSP00000440288:p.Gly561fs		121990672	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	37	CCDS9241.1																																																																																				0.657	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123424719	C	-	123424719	7	5	111	1	0	1	0	1	0	0	0	0	48	739	26	0	634	0	ABCB9	12	123424719	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	422905	123424719	10427176	732	29866										
EP400	57634	hgsc.bcm.edu	37	chr12	132471280	132471280	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcatctgcccccaccaaaccAcagagtcctgctcagaatgc	7	17	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:132471280A>G	ENST00000333577.4	+	7	2368	c.2259A>G	c.(2257-2259)ccA>ccG	p.P753P	EP400_ENST00000389561.2_Silent_p.P717P|EP400_ENST00000332482.4_Silent_p.P680P|EP400_ENST00000389562.2_Silent_p.P716P|EP400_ENST00000330386.6_Silent_p.P717P			Q96L91	EP400_HUMAN	E1A binding protein p400	753					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		CCACCAAACCACAGAGTCCTG	0.502																																																0			12											121	124	123					12																	132471280		2203	4300	6503	131037233	SO:0001819	synonymous_variant	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.2259A>G	12.37:g.132471280A>G			131037233	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																					0.502	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		G	132471280	A	G	132471280	2	3	111	1	0	0	0	0	0	0	0	1	5162	146	6	4		4	EP400	12	132471280	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	9046561	132471280	1380615	733	29867										
DDX51	317781	hgsc.bcm.edu	37	chr12	132624675	132624675	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttctcaggtactggggggcGtcgtagttcaccaccagctc	13	12	2	0	rs531852048		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr12:132624675G>A	ENST00000397333.3	-	12	1781	c.1743C>T	c.(1741-1743)gaC>gaT	p.D581D		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	581	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		ACTGGGGGGCGTCGTAGTTCA	0.677																																																0			12											55	63	61					12																	132624675		2153	4237	6390	131190628	SO:0001819	synonymous_variant	317781			BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1743C>T	12.37:g.132624675G>A			131190628	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																				0.677	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		A	132624675	G	A	132624675	2	1	111	1	0	0	0	0	0	0	0	1	4375	1136	40	1		1	DDX51	12	132624675	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	153395	132624675	1227220	734	29868										
IFT88	8100	hgsc.bcm.edu	37	chr13	21170297	21170297	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtctttaatagcccagaggAaaaaataaagcaattagaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:21170297delA	ENST00000319980.6	+	10	761	c.434delA	c.(433-435)gaafs	p.E145fs	IFT88_ENST00000351808.5_Frame_Shift_Del_p.E136fs|IFT88_ENST00000382778.4_Frame_Shift_Del_p.E145fs|IFT88_ENST00000537103.1_Frame_Shift_Del_p.E117fs	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	145					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		AGCCCAGAGGAAAAAATAAAG	0.259																																																0			13											67	70	69					13																	21170297		2203	4295	6498	20068297	SO:0001589	frameshift_variant	8100			AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.434delA	13.37:g.21170297delA	ENSP00000323580:p.Glu145fs		20068297	A2A491|B4DUS2|Q5SZJ6|Q8N719	Frame_Shift_Del	DEL	ENST00000319980.6	37	CCDS31944.1																																																																																				0.259	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		-	21170297	A	-	21170297	7	5	111	1	0	1	0	1	0	0	0	0	7587	246	9	0	464	0	IFT88	13	21170297	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10		21170297	93999581	735	29869										
RNF6	6049	hgsc.bcm.edu	37	chr13	26788240	26788241	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcatcactttcatttagtINSaaaaaaaagtgagcaaggcg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:26788240_26788241insA	ENST00000381588.4	-	5	2530_2531	c.1778_1779insT	c.(1777-1779)ttafs	p.L593fs	RNF6_ENST00000399762.2_Frame_Shift_Ins_p.L237fs|RNF6_ENST00000468480.1_Intron|RNF6_ENST00000381570.3_Frame_Shift_Ins_p.L593fs|RNF6_ENST00000346166.3_Frame_Shift_Ins_p.L593fs	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	593					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		TTTCATTTAGTAAAAAAAAGTG	0.406																																																0			13																																								25686241	SO:0001589	frameshift_variant	6049			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1779dupT	13.37:g.26788248_26788248dupA	ENSP00000371000:p.Leu593fs		25686240	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Frame_Shift_Ins	INS	ENST00000381588.4	37	CCDS9316.1																																																																																				0.406	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		A	26788241	-	A	26788240	7	5	111	1	0	1	1	0	0	0	0	0	13535	1635	57	0	282	0	RNF6	13	26788240	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	5617943	26788240	88381638	736	29870										
FLT1	2321	hgsc.bcm.edu	37	chr13	29001900	29001900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaacttaccattgacaattAgagtggcagtgaggttttta	9	6	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:29001900A>G	ENST00000282397.4	-	9	1516	c.1265T>C	c.(1264-1266)cTa>cCa	p.L422P	FLT1_ENST00000539099.1_Missense_Mutation_p.L422P|FLT1_ENST00000541932.1_Missense_Mutation_p.L422P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	422			L -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTGACAATTAGAGTGGCAGT	0.353																																																0			13											140	127	131					13																	29001900		2203	4300	6503	27899900	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1265T>C	13.37:g.29001900A>G	ENSP00000282397:p.Leu422Pro		27899900	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740481	0.69304	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	D;D;D	0.87571	-2.27;-2.27;-2.27	5.73	5.73	0.89815	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.96178	0.8754	H	0.97852	4.09	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97789	1.0237	10	0.87932	D	0	.	16.026	0.80545	1.0:0.0:0.0:0.0	.	422;422;422;422	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	P	422	ENSP00000282397:L422P;ENSP00000437631:L422P;ENSP00000442630:L422P	ENSP00000282397:L422P	L	-	2	0	FLT1	27899900	1.000000	0.71417	0.794000	0.32065	0.746000	0.42486	8.219000	0.89770	2.189000	0.69895	0.528000	0.53228	CTA		0.353	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			G	29001900	A	G	29001900	3	3	111	1	0	0	0	0	1	0	0	0	5960	420	15	4	3102	4	FLT1	13	29001900	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2213660	29001900	86167978	737	29871										
BRCA2	675	hgsc.bcm.edu	37	chr13	32906657	32906657	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgaaaaatctaaaaaccaaGtgaaagaaaaatactcattt	5	5	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:32906657G>A	ENST00000380152.3	+	10	1275	c.1042G>A	c.(1042-1044)Gtg>Atg	p.V348M	BRCA2_ENST00000544455.1_Missense_Mutation_p.V348M			P51587	BRCA2_HUMAN	breast cancer 2, early onset	348					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAAAAACCAAGTGAAAGAAAA	0.323			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13											98	114	109					13																	32906657		2200	4298	6498	31804657	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1042G>A	13.37:g.32906657G>A	ENSP00000369497:p.Val348Met		31804657	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	0.054	-1.241707	0.01493	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00711	5.8;5.8	5.6	-6.46	0.01908	.	1.739820	0.02692	N	0.110745	T	0.00412	0.0013	N	0.05280	-0.08	0.09310	N	1	B;P	0.48640	0.013;0.913	B;B	0.37601	0.006;0.254	T	0.51733	-0.8668	10	0.20046	T	0.44	.	3.1194	0.06386	0.2644:0.1165:0.4211:0.198	.	348;348	P51587;A1YBP1	BRCA2_HUMAN;.	M	348;348;346	ENSP00000369497:V348M;ENSP00000439902:V348M	ENSP00000369497:V348M	V	+	1	0	BRCA2	31804657	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.140000	0.10342	-1.292000	0.02366	-1.292000	0.01352	GTG		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32906657	G	A	32906657	3	1	111	1	0	0	0	0	1	0	0	0	1502	1029	36	3	1076	3	BRCA2	13	32906657	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3904757	32906657	82263221	738	29872										
BRCA2	675	hgsc.bcm.edu	37	chr13	32913559	32913559	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagacttcattacttgaagcAaaaaaatggcttagagaagg					rs80359479|rs80359481		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:32913559delA	ENST00000380152.3	+	11	5300	c.5067delA	c.(5065-5067)gcafs	p.A1689fs	BRCA2_ENST00000544455.1_Frame_Shift_Del_p.A1689fs			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1689	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TACTTGAAGCAAAAAAATGGC	0.313			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13								17,4187		1,15,2086	36	39	38	http://www.ncbi.nlm.nih.gov/sites/varvu?gene		3.9	1	13	dbSNP_132	38	14,8208		1,12,4098	no	frameshift	BRCA2	NM_000059.3		2,27,6184	A1A1,A1R,RR		0.1703,0.4044,0.2495			32913559	31,12395	2181	4286	6467	31811559	SO:0001589	frameshift_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5067delA	13.37:g.32913559delA	ENSP00000369497:p.Ala1689fs		31811559	O00183|O15008|Q13879|Q5TBJ7	Frame_Shift_Del	DEL	ENST00000380152.3	37	CCDS9344.1																																																																																				0.313	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		-	32913559	A	-	32913559	7	5	111	1	0	1	0	1	0	0	0	0	1502	117	5	0	5105	0	BRCA2	13	32913559	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	6902	32913559	82256319	739	29873										
BRCA2	675	hgsc.bcm.edu	37	chr13	32945129	32945129	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catctggattatacatatttCgcaatgaaagagaggaagaa	9	5	1	3	rs80359104		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:32945129C>A	ENST00000380152.3	+	20	8757	c.8524C>A	c.(8524-8526)Cgc>Agc	p.R2842S	BRCA2_ENST00000544455.1_Missense_Mutation_p.R2842S			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2842			R -> C (in one patient with esophageal carcinoma; somatic mutation). {ECO:0000269|PubMed:11948123}.		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.R2842C(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATACATATTTCGCAATGAAAG	0.348			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	1	Substitution - Missense(1)	oesophagus(1)	13											87	86	86					13																	32945129		2203	4300	6503	31843129	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8524C>A	13.37:g.32945129C>A	ENSP00000369497:p.Arg2842Ser		31843129	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864004	0.91511	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.84589	-1.87;-1.87	5.1	5.1	0.69264	Nucleic acid-binding, OB-fold-like (1);Tower (1);	0.062472	0.64402	D	0.000003	D	0.92267	0.7547	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92967	0.6394	10	0.66056	D	0.02	.	18.5217	0.90956	0.0:1.0:0.0:0.0	.	2842	P51587	BRCA2_HUMAN	S	2842	ENSP00000369497:R2842S;ENSP00000439902:R2842S	ENSP00000369497:R2842S	R	+	1	0	BRCA2	31843129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.529000	0.60588	2.373000	0.80994	0.484000	0.47621	CGC		0.348	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32945129	C	A	32945129	3	1	111	1	0	0	0	0	1	0	0	0	1502	884	31	2	8598	2	BRCA2	13	32945129	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	31570	32945129	82224749	740	29874										
KL	9365	hgsc.bcm.edu	37	chr13	33635594	33635594	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccttatttcactgaagatgAaaaaaagctaatccagggta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:33635594delA	ENST00000380099.3	+	4	2386	c.2378delA	c.(2377-2379)gaafs	p.E793fs	KL_ENST00000426690.2_3'UTR|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	793	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		ACTGAAGATGAAAAAAAGCTA	0.393																																																0			13											64	65	65					13																	33635594		2203	4300	6503	32533594	SO:0001589	frameshift_variant	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2378delA	13.37:g.33635594delA	ENSP00000369442:p.Glu793fs		32533594	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Frame_Shift_Del	DEL	ENST00000380099.3	37	CCDS9347.1																																																																																				0.393	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			-	33635594	A	-	33635594	7	5	111	1	0	1	0	1	0	0	0	0	8352	246	9	0	2392	0	KL	13	33635594	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	690465	33635594	81534284	741	29875										
MRPS31	10240	hgsc.bcm.edu	37	chr13	41341161	41341161	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaaatatctttggatgttaTtttttgtcctggaaagatgc					rs556043646		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:41341161delT	ENST00000323563.6	-	2	197	c.161delA	c.(160-162)aatfs	p.N55fs		NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	55						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		TTGGATGTTATTTTTTGTCCT	0.323																																																0			13											51	49	50					13																	41341161		2202	4298	6500	40239161	SO:0001589	frameshift_variant	10240			Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"Mitochondrial ribosomal proteins / small subunits"	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.161delA	13.37:g.41341161delT	ENSP00000315397:p.Asn55fs		40239161	B2RCS3|Q5VYC8|Q8WTV8	Frame_Shift_Del	DEL	ENST00000323563.6	37	CCDS9372.1																																																																																				0.323	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2			-	41341161	T	-	41341161	7	5	111	1	0	1	0	1	0	0	0	0	9871	1493	52	0	1050	0	MRPS31	13	41341161	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	7705567	41341161	73828717	742	29876										
COG3	83548	hgsc.bcm.edu	37	chr13	46085968	46085969	+	Frame_Shift_Del	DEL	AG	AG	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagtccttacttggagcgtcAgagtctatcagcaaaaacaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:46085968_46085969delAG	ENST00000349995.5	+	16	1900_1901	c.1788_1789delAG	c.(1786-1791)tcagagfs	p.E597fs	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	597					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTGGAGCGTCAGAGTCTATCAG	0.406																																					Ovarian(150;1048 1859 18083 21577 42700)											0			13																																								44983970	SO:0001589	frameshift_variant	83548			AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1788_1789delAG	13.37:g.46085970_46085971delAG	ENSP00000258654:p.Glu597fs		44983969	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	37	CCDS9398.1																																																																																				0.406	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			-	46085969	AG	-	46085968	7	5	111	1	0	1	0	1	0	0	0	0	3665	175	7	0	1850	0	COG3	13	46085968	Frame_Shift_Del	DEL	AG	TCGA-EI-6507-01A-11D-1733-10	4744807	46085968	69083910	743	29877										
SPERT	220082	hgsc.bcm.edu	37	chr13	46287374	46287374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtacagcacccctcgctgcGcgcagcaggccgccctgccc	11	20	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:46287374G>A	ENST00000310521.1	+	3	294	c.214G>A	c.(214-216)Gcg>Acg	p.A72T	SPERT_ENST00000378966.3_Missense_Mutation_p.A36T	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	72						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		CCCTCGCTGCGCGCAGCAGGC	0.652																																																0			13											30	31	30					13																	46287374		2202	4299	6501	45185375	SO:0001583	missense	220082			AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.214G>A	13.37:g.46287374G>A	ENSP00000309189:p.Ala72Thr		45185375	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	G	8.728	0.916016	0.17907	.	.	ENSG00000174015	ENST00000310521;ENST00000533564;ENST00000378966	T;T	0.47869	0.89;0.83	5.1	-2.28	0.06826	.	0.690130	0.12656	N	0.450036	T	0.20455	0.0492	N	0.22421	0.69	0.09310	N	1	P;P	0.39326	0.668;0.668	B;B	0.28465	0.09;0.09	T	0.15378	-1.0439	10	0.56958	D	0.05	.	0.4051	0.00432	0.2059:0.2402:0.1976:0.3563	.	36;72	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	T	72;45;36	ENSP00000309189:A72T;ENSP00000368249:A36T	ENSP00000309189:A72T	A	+	1	0	SPERT	45185375	0.000000	0.05858	0.005000	0.12908	0.142000	0.21351	-0.200000	0.09478	-0.284000	0.09102	0.650000	0.86243	GCG		0.652	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46287374	G	A	46287374	3	1	111	1	0	0	0	0	1	0	0	0	15078	1087	38	1	224	1	SPERT	13	46287374	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	201406	46287374	68882504	744	29878										
SPERT	220082	hgsc.bcm.edu	37	chr13	46287532	46287532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgccgcgggtgcagctcagCgacgagatgttcgtgttcca	14	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:46287532C>T	ENST00000310521.1	+	3	452	c.372C>T	c.(370-372)agC>agT	p.S124S	SPERT_ENST00000378966.3_Silent_p.S88S	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	124						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		TGCAGCTCAGCGACGAGATGT	0.632																																																0			13											63	67	66					13																	46287532		2203	4300	6503	45185533	SO:0001819	synonymous_variant	220082			AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.372C>T	13.37:g.46287532C>T			45185533	A8K8I5|Q8NHV2	Silent	SNP	ENST00000310521.1	37	CCDS9399.1																																																																																				0.632	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		T	46287532	C	T	46287532	2	4	111	1	0	0	0	0	0	0	0	1	15078	767	27	1		1	SPERT	13	46287532	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	158	46287532	68882346	745	29879										
HTR2A	3356	hgsc.bcm.edu	37	chr13	47466708	47466708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gactgcacaaagcttgctcgGcagaggccaccggtacccta	11	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:47466708G>A	ENST00000378688.4	-	2	561	c.430C>T	c.(430-432)Ccg>Tcg	p.P144S	HTR2A_ENST00000543956.1_Missense_Mutation_p.P60S|HTR2A_ENST00000542664.1_Missense_Mutation_p.P144S			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	144					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	AGCTTGCTCGGCAGAGGCCAC	0.567																																																0			13											99	96	97					13																	47466708		2203	4300	6503	46364709	SO:0001583	missense	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.430C>T	13.37:g.47466708G>A	ENSP00000367959:p.Pro144Ser		46364709	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.885581	0.91814	.	.	ENSG00000102468	ENST00000378688;ENST00000543956;ENST00000542664	T;T;T	0.32515	1.45;1.45;1.45	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48554	0.1506	L	0.38531	1.155	0.80722	D	1	P;D	0.76494	0.89;0.999	P;D	0.76071	0.749;0.987	T	0.16453	-1.0402	10	0.41790	T	0.15	.	19.848	0.96722	0.0:0.0:1.0:0.0	.	60;144	F5GWE8;P28223	.;5HT2A_HUMAN	S	144;60;144	ENSP00000367959:P144S;ENSP00000441861:P60S;ENSP00000437737:P144S	ENSP00000367959:P144S	P	-	1	0	HTR2A	46364709	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.860000	0.99555	2.937000	0.99478	0.650000	0.86243	CCG		0.567	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		A	47466708	G	A	47466708	3	1	111	1	0	0	0	0	1	0	0	0	7462	1203	42	3	993	3	HTR2A	13	47466708	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1179176	47466708	67703170	746	29880										
KPNA3	3839	hgsc.bcm.edu	37	chr13	50275977	50275977	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgaaggttggctgttggatCaaaattgtaggtacctcctt	11	6	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:50275977C>G	ENST00000261667.3	-	17	1939	c.1525G>C	c.(1525-1527)Gat>Cat	p.D509H		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	509					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		GCTGTTGGATCAAAATTGTAG	0.363																																																0			13											164	181	176					13																	50275977		2203	4300	6503	49173978	SO:0001583	missense	3839			D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"Importins", "Armadillo repeat containing"	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.1525G>C	13.37:g.50275977C>G	ENSP00000261667:p.Asp509His		49173978	O00191|O43195|Q5JVM9|Q96AA7	Missense_Mutation	SNP	ENST00000261667.3	37	CCDS9421.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737185	0.89482	.	.	ENSG00000102753	ENST00000261667	T	0.29917	1.55	6.17	6.17	0.99709	.	0.042170	0.85682	D	0.000000	T	0.48132	0.1483	M	0.63843	1.955	0.80722	D	1	P	0.37466	0.596	P	0.47470	0.548	T	0.28459	-1.0043	10	0.59425	D	0.04	-13.9303	20.8794	0.99867	0.0:1.0:0.0:0.0	.	509	O00505	IMA3_HUMAN	H	509	ENSP00000261667:D509H	ENSP00000261667:D509H	D	-	1	0	KPNA3	49173978	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.868000	0.63021	2.941000	0.99782	0.655000	0.94253	GAT		0.363	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267		G	50275977	C	G	50275977	3	3	111	1	0	0	0	0	1	0	0	0	8452	826	29	5	44	5	KPNA3	13	50275977	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2809269	50275977	64893901	747	29881										
NEK3	4752	hgsc.bcm.edu	37	chr13	52707309	52707309	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaggccttgccatccagctCgcttcttcagctctgacacc	7	17	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:52707309C>T	ENST00000400357.2	-	14	2732	c.1439G>A	c.(1438-1440)cGa>cAa	p.R480Q	NEK3_ENST00000339406.3_Missense_Mutation_p.R497Q|NEK3_ENST00000378101.2_Missense_Mutation_p.R497Q|NEK3_ENST00000452082.2_Missense_Mutation_p.R501Q			P51956	NEK3_HUMAN	NIMA-related kinase 3	497					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		CCATCCAGCTCGCTTCTTCAG	0.502																																																0			13											50	51	51					13																	52707309		2068	4231	6299	51605310	SO:0001583	missense	4752			AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"serine/threonine-protein kinase NEK3", "phosphorylase B kinase kinase", "glycogen synthase A kinase", "hydroxyalkyl-protein kinase"	604044	"NIMA (never in mitosis gene a)-related kinase 3"			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1439G>A	13.37:g.52707309C>T	ENSP00000383210:p.Arg480Gln		51605310	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.360686	0.24598	.	.	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	5.38	2.7	0.31948	.	1.191300	0.06211	N	0.685035	T	0.21186	0.0510	N	0.25890	0.77	0.09310	N	1	B;B;B	0.27971	0.026;0.123;0.196	B;B;B	0.14578	0.003;0.005;0.011	T	0.24621	-1.0155	10	0.27785	T	0.31	.	8.2872	0.31935	0.0:0.7425:0.0:0.2575	.	497;501;474	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	Q	497;497;480;501;474	ENSP00000339429:R497Q;ENSP00000367341:R497Q;ENSP00000383210:R480Q;ENSP00000404197:R501Q;ENSP00000448716:R474Q	ENSP00000339429:R497Q	R	-	2	0	NEK3	51605310	0.105000	0.21958	0.005000	0.12908	0.395000	0.30598	0.854000	0.27791	0.327000	0.23409	-0.244000	0.11960	CGA		0.502	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			T	52707309	C	T	52707309	3	4	111	1	0	0	0	0	1	0	0	0	10356	884	31	1	34	1	NEK3	13	52707309	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2431332	52707309	62462569	748	29882										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86368484	86368484	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgattttcctgttccaaaagActtctttggagatgttttgc	8	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:86368484A>G	ENST00000400286.2	-	2	2758	c.2160T>C	c.(2158-2160)agT>agC	p.S720S		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	720					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GTTCCAAAAGACTTCTTTGGA	0.393																																																0			13											293	284	287					13																	86368484		1871	4112	5983	85266485	SO:0001819	synonymous_variant	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.2160T>C	13.37:g.86368484A>G			85266485	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Silent	SNP	ENST00000400286.2	37	CCDS41903.1																																																																																				0.393	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		G	86368484	A	G	86368484	2	3	111	1	0	0	0	0	0	0	0	1	14784	272	10	4		4	SLITRK6	13	86368484	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	33661175	86368484	28801394	749	29883										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99462522	99462522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagagtccatctgcgcactgCtcaaggagctccatcagcac	9	15	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:99462522C>A	ENST00000376460.1	-	47	5234	c.5154G>T	c.(5152-5154)gaG>gaT	p.E1718D	DOCK9_ENST00000339416.2_Missense_Mutation_p.E1719D|DOCK9_ENST00000448493.2_3'UTR	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1719	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTGCGCACTGCTCAAGGAGCT	0.522																																																0			13											125	120	122					13																	99462522		2013	4185	6198	98260523	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.5154G>T	13.37:g.99462522C>A	ENSP00000365643:p.Glu1718Asp		98260523	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	20.6|20.6|20.6	4.010403|4.010403|4.010403	0.75046|0.75046|0.75046	.|.|.	.|.|.	ENSG00000088387|ENSG00000088387|ENSG00000088387	ENST00000400228|ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453;ENST00000451563;ENST00000340449|ENST00000419908	.|T;T;T;T|.	.|0.51325|.	.|2.23;2.33;0.95;0.71|.	5.35|5.35|5.35	0.979|0.979|0.979	0.19745|0.19745|0.19745	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.57154|0.57154|0.57154	0.2034|0.2034|0.2034	L|L|L	0.59436|0.59436|0.59436	1.845|1.845|1.845	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;B;B;B;B;D;B;B|.	.|0.71674|.	.|0.998;0.346;0.126;0.039;0.059;0.958;0.072;0.2|.	.|D;B;B;B;B;P;B;B|.	.|0.75484|.	.|0.986;0.179;0.104;0.191;0.165;0.69;0.079;0.211|.	T|T|T	0.50259|0.50259|0.50259	-0.8849|-0.8849|-0.8849	5|10|5	.|0.56958|.	.|D|.	.|0.05|.	-27.5173|-27.5173|-27.5173	6.8862|6.8862|6.8862	0.24202|0.24202|0.24202	0.0:0.4979:0.1197:0.3824|0.0:0.4979:0.1197:0.3824|0.0:0.4979:0.1197:0.3824	.|.|.	.|1696;438;339;1718;339;1719;388;338|.	.|A8MWZ5;B7Z6H5;B7Z2J2;Q9BZ29-5;Q5JUD8;Q9BZ29;B7Z6G9;F5H1Q4|.	.|.;.;.;.;.;DOCK9_HUMAN;.;.|.	S|D|I	283|1718;1719;1711;1696;1718;626;1719;338;83;339|136	.|ENSP00000365643:E1718D;ENSP00000341086:E1719D;ENSP00000407610:E83D;ENSP00000344702:E339D|.	.|ENSP00000341086:E1719D|.	A|E|S	-|-|-	1|3|2	0|2|0	DOCK9|DOCK9|DOCK9	98260523|98260523|98260523	0.913000|0.913000|0.913000	0.31002|0.31002|0.31002	0.995000|0.995000|0.995000	0.50966|0.50966|0.50966	0.969000|0.969000|0.969000	0.65631|0.65631|0.65631	0.023000|0.023000|0.023000	0.13533|0.13533|0.13533	0.220000|0.220000|0.220000	0.20860|0.20860|0.20860	0.563000|0.563000|0.563000	0.77884|0.77884|0.77884	GCA|GAG|AGC		0.522	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		A	99462522	C	A	99462522	3	1	111	1	0	0	0	0	1	0	0	0	4705	796	28	2	1088	2	DOCK9	13	99462522	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	13094038	99462522	15707356	750	29884										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111545497	111545497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccccatttaagatgccattgTtatagaaatggttcagatga	8	7	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr13:111545497T>C	ENST00000267339.2	-	4	703	c.569A>G	c.(568-570)aAc>aGc	p.N190S	ANKRD10_ENST00000310847.4_Silent_p.*221*|ANKRD10-IT1_ENST00000426991.1_RNA|ANKRD10_ENST00000489973.2_5'UTR|ANKRD10_ENST00000375758.5_Silent_p.*221*	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	190								p.N190S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			GATGCCATTGTTATAGAAATG	0.428																																																1	Substitution - Missense(1)	central_nervous_system(1)	13											127	127	127					13																	111545497		2203	4300	6503	110343498	SO:0001583	missense	55608			AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.569A>G	13.37:g.111545497T>C	ENSP00000267339:p.Asn190Ser		110343498	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	T	0.372	-0.933221	0.02359	.	.	ENSG00000088448	ENST00000267339	T	0.52754	0.65	5.67	-5.51	0.02568	Ankyrin repeat-containing domain (1);	0.950216	0.08927	N	0.873485	T	0.19846	0.0477	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27571	-1.0070	10	0.18710	T	0.47	0.0706	7.7453	0.28864	0.0:0.2932:0.4296:0.2772	.	190	Q9NXR5	ANR10_HUMAN	S	190	ENSP00000267339:N190S	ENSP00000267339:N190S	N	-	2	0	ANKRD10	110343498	0.013000	0.17824	0.000000	0.03702	0.656000	0.38851	0.431000	0.21444	-0.480000	0.06803	-0.290000	0.09829	AAC		0.428	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			C	111545497	T	C	111545497	3	2	111	1	0	0	0	0	1	0	0	0	638	1725	60	4	705	4	ANKRD10	13	111545497	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	12082975	111545497	3624381	751	29885										
MMP14	4323	hgsc.bcm.edu	37	chr14	23315106	23315106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggacgaggagggcggcggggCggtgagcgcggctgccgtgg	25	9	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23315106C>T	ENST00000311852.6	+	10	1868	c.1607C>T	c.(1606-1608)gCg>gTg	p.A536V	MMP14_ENST00000548162.1_Intron	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	536					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	GGCGGCGGGGCGGTGAGCGCG	0.687																																																0			14											36	40	39					14																	23315106		2203	4300	6503	22384946	SO:0001583	missense	4323				CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1607C>T	14.37:g.23315106C>T	ENSP00000308208:p.Ala536Val		22384946	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	37	CCDS9577.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467360	0.26335	.	.	ENSG00000157227	ENST00000311852	T	0.32023	1.47	4.38	3.49	0.39957	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.409080	0.25546	N	0.029931	T	0.19846	0.0477	L	0.29908	0.895	0.21719	N	0.999576	B	0.15719	0.014	B	0.15052	0.012	T	0.14727	-1.0462	10	0.31617	T	0.26	.	7.4743	0.27368	0.0:0.7389:0.1678:0.0933	.	536	P50281	MMP14_HUMAN	V	536	ENSP00000308208:A536V	ENSP00000308208:A536V	A	+	2	0	MMP14	22384946	0.002000	0.14202	0.711000	0.30485	0.452000	0.32318	0.253000	0.18296	0.971000	0.38288	0.460000	0.39030	GCG		0.687	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		T	23315106	C	T	23315106	3	4	111	1	0	0	0	0	1	0	0	0	9683	768	27	1	1645	1	MMP14	14	23315106	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		23315106	84034434	752	29886										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23532747	23532747	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttccttctcttcttcctcttCttccctctgcccattctcct	1	19	6	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23532747C>A	ENST00000262710.1	-	13	3136	c.2809G>T	c.(2809-2811)Gaa>Taa	p.E937*	ACIN1_ENST00000397341.3_Nonsense_Mutation_p.E179*|ACIN1_ENST00000555053.1_Nonsense_Mutation_p.E924*|ACIN1_ENST00000338631.6_Nonsense_Mutation_p.E210*|ACIN1_ENST00000357481.2_Nonsense_Mutation_p.E179*|ACIN1_ENST00000557515.1_Nonsense_Mutation_p.E178*|ACIN1_ENST00000605057.1_Nonsense_Mutation_p.E879*|ACIN1_ENST00000457657.1_Nonsense_Mutation_p.E897*	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	937					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TCTTCCTCTTCTTCCCTCTGC	0.507																																																0			14											95	85	88					14																	23532747		2203	4300	6503	22602587	SO:0001587	stop_gained	22985			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.2809G>T	14.37:g.23532747C>A	ENSP00000262710:p.Glu937*		22602587	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Nonsense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	C	33	5.204631	0.95033	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053;ENST00000555566	.	.	.	5.16	5.16	0.70880	.	0.000000	0.41938	D	0.000788	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-11.8879	17.5916	0.87998	0.0:1.0:0.0:0.0	.	.	.	.	X	178;210;179;937;897;179;924;167	.	ENSP00000262710:E937X	E	-	1	0	ACIN1	22602587	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.148000	0.58085	2.683000	0.91414	0.655000	0.94253	GAA		0.507	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23532747	C	A	23532747	4	1	111	1	0	0	0	0	0	1	0	0	142	922	32	2	1244	2	ACIN1	14	23532747	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	217641	23532747	83816793	753	29887										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23816811	23816811	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcggccaaatcggtccacGgtgacccccaggaagacaca	12	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23816811G>A	ENST00000206544.8	-	7	1410	c.1074C>T	c.(1072-1074)acC>acT	p.T358T	SLC22A17_ENST00000397260.3_Silent_p.T247T|SLC22A17_ENST00000354772.3_Silent_p.T358T|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397267.1_Silent_p.T358T	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	358					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		ATCGGTCCACGGTGACCCCCA	0.637																																																0			14											49	56	54					14																	23816811		2203	4300	6503	22886651	SO:0001819	synonymous_variant	51310			AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1074C>T	14.37:g.23816811G>A			22886651	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Silent	SNP	ENST00000206544.8	37	CCDS9593.1																																																																																				0.637	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		A	23816811	G	A	23816811	2	1	111	1	0	0	0	0	0	0	0	1	14485	1103	39	1		1	SLC22A17	14	23816811	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	284064	23816811	83532729	754	29888										
MYH6	4624	hgsc.bcm.edu	37	chr14	23869992	23869992	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcttggtctccagggtggCgttgatgcgcgtcaccatcc	13	13	2	1	rs556536964	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23869992C>T	ENST00000356287.3	-	12	1365	c.1336G>A	c.(1336-1338)Gcc>Acc	p.A446T	MYH6_ENST00000405093.3_Missense_Mutation_p.A446T			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	446	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.A446T(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCCAGGGTGGCGTTGATGCGC	0.587													C|||	3	0.000599042	0	0	5008	,	,		21542	0.003		0	False		,,,				2504	0															1	Substitution - Missense(1)	urinary_tract(1)	14											139	109	119					14																	23869992		2203	4300	6503	22939832	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1336G>A	14.37:g.23869992C>T	ENSP00000348634:p.Ala446Thr		22939832	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	13.77	2.335706	0.41398	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.87103	-2.21;-2.21	4.03	2.1	0.27182	Myosin head, motor domain (2);	.	.	.	.	T	0.72977	0.3528	N	0.16201	0.385	0.35513	D	0.800807	B;B	0.09022	0.002;0.002	B;B	0.12837	0.008;0.008	T	0.65651	-0.6116	9	0.52906	T	0.07	.	3.7577	0.08592	0.2927:0.4802:0.1423:0.0847	.	446;446	D9YZU2;P13533	.;MYH6_HUMAN	T	446	ENSP00000386041:A446T;ENSP00000348634:A446T	ENSP00000348634:A446T	A	-	1	0	MYH6	22939832	0.687000	0.27671	0.929000	0.37066	0.947000	0.59692	0.045000	0.14013	0.267000	0.21916	-0.301000	0.09380	GCC		0.587	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23869992	C	T	23869992	3	4	111	1	0	0	0	0	1	0	0	0	10068	768	27	1	4591	1	MYH6	14	23869992	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	53181	23869992	83479548	755	29889										
MYH6	4624	hgsc.bcm.edu	37	chr14	23876383	23876383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacgctccttctctgacttgCggaggtactgggccgctgcc	13	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23876383C>T	ENST00000356287.3	-	2	79	c.50G>A	c.(49-51)cGc>cAc	p.R17H	MYH6_ENST00000405093.3_Missense_Mutation_p.R17H			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	17					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CTCTGACTTGCGGAGGTACTG	0.582																																																0			14											114	117	116					14																	23876383		2203	4300	6503	22946223	SO:0001583	missense	4624			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.50G>A	14.37:g.23876383C>T	ENSP00000348634:p.Arg17His		22946223	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	28.0	4.881508	0.91740	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.86562	-2.14;-2.14	3.53	3.53	0.40419	.	.	.	.	.	D	0.93861	0.8036	M	0.91459	3.21	0.53005	D	0.99996	D;D	0.69078	0.997;0.997	P;P	0.62740	0.906;0.906	D	0.95351	0.8447	9	0.72032	D	0.01	.	15.2325	0.73401	0.0:1.0:0.0:0.0	.	17;17	D9YZU2;P13533	.;MYH6_HUMAN	H	17	ENSP00000386041:R17H;ENSP00000348634:R17H	ENSP00000348634:R17H	R	-	2	0	MYH6	22946223	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.482000	0.81143	1.974000	0.57490	0.455000	0.32223	CGC		0.582	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23876383	C	T	23876383	3	4	111	1	0	0	0	0	1	0	0	0	10068	768	27	1	5917	1	MYH6	14	23876383	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6391	23876383	83473157	756	29890										
NGDN	25983	hgsc.bcm.edu	37	chr14	23945248	23945248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcttttgtagttgagctctgAggatgaggaggaagatgaag	15	3	2	5			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:23945248A>T	ENST00000408901.3	+	7	459	c.431A>T	c.(430-432)gAg>gTg	p.E144V	NGDN_ENST00000397154.3_Missense_Mutation_p.E144V|NGDN_ENST00000556580.1_5'Flank	NM_001042635.1|NM_015514.1	NP_001036100.1|NP_056329.1	Q8NEJ9	NGDN_HUMAN	neuroguidin, EIF4E binding protein	144	Necessary for interaction with EIF4E. {ECO:0000250}.				regulation of translation (GO:0006417)	cell projection (GO:0042995)|chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	12	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TTGAGCTCTGAGGATGAGGAG	0.453																																																0			14											90	90	90					14																	23945248		2203	4300	6503	23015088	SO:0001583	missense	25983			AK022215	CCDS32051.1, CCDS41926.1	14q11.2	2014-06-13	2006-08-02	2006-08-02	ENSG00000129460	ENSG00000129460			20271	protein-coding gene	gene with protein product		610777	"chromosome 14 open reading frame 120"	C14orf120		16705177	Standard	NM_001042635		Approved	DKFZP564O092, LCP5, lpd-2, NGD	uc001wjy.3	Q8NEJ9	OTTHUMG00000171501	ENST00000408901.3:c.431A>T	14.37:g.23945248A>T	ENSP00000386134:p.Glu144Val		23015088	A8K760|Q9Y400	Missense_Mutation	SNP	ENST00000408901.3	37	CCDS41926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.26|11.26	1.584858|1.584858	0.28268|0.28268	.|.	.|.	ENSG00000129460|ENSG00000129460	ENST00000408901;ENST00000397154;ENST00000555128|ENST00000556483	T;T|.	0.36340|.	1.26;1.26|.	5.89|5.89	4.74|4.74	0.60224|0.60224	.|.	0.342497|.	0.33180|.	N|.	0.005187|.	T|.	0.57388|.	0.2050|.	L|L	0.43923|0.43923	1.385|1.385	0.80722|0.80722	D|D	1|1	P;P|.	0.49090|.	0.919;0.868|.	B;B|.	0.43575|.	0.424;0.243|.	T|.	0.52786|.	-0.8529|.	10|.	0.30078|.	T|.	0.28|.	-15.0543|-15.0543	11.6626|11.6626	0.51356|0.51356	0.7197:0.2803:0.0:0.0|0.7197:0.2803:0.0:0.0	.|.	144;144|.	Q8NEJ9-2;Q8NEJ9|.	.;NGDN_HUMAN|.	V|C	144;144;119|91	ENSP00000386134:E144V;ENSP00000380340:E144V|.	ENSP00000380340:E144V|.	E|X	+|+	2|3	0|0	NGDN|NGDN	23015088|23015088	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.699000|0.699000	0.40488|0.40488	2.714000|2.714000	0.47202|0.47202	1.039000|1.039000	0.40074|0.40074	0.460000|0.460000	0.39030|0.39030	GAG|TGA		0.453	NGDN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413782.3	NM_001042635		T	23945248	A	T	23945248	3	4	111	1	0	0	0	0	1	0	0	0	10424	304	11	5	457	5	NGDN	14	23945248	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	68865	23945248	83404292	757	29891										
AP1G2	8906	hgsc.bcm.edu	37	chr14	24029037	24029037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaagtggtcgtaggtgaggCgcagctttagccgcaggggg	19	7	0	1	rs74849041	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:24029037C>T	ENST00000308724.5	-	21	3034	c.2279G>A	c.(2278-2280)cGc>cAc	p.R760H	RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Missense_Mutation_p.R760H|THTPA_ENST00000288014.6_3'UTR|RP11-66N24.4_ENST00000555446.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.4_ENST00000556354.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	760	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)	p.R760H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		GTAGGTGAGGCGCAGCTTTAG	0.567											OREG0022604	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	56	0.0111821	8e-04	0	5008	,	,		18127	0.0407		0.0129	False		,,,				2504	0.001															1	Substitution - Missense(1)	stomach(1)	14						C	HIS/ARG	0,4406		0,0,2203	54	45	48		2279	5	1	14	dbSNP_131	48	7,8593	5.7+/-21.5	0,7,4293	yes	missense	AP1G2	NM_003917.2	29	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	probably-damaging	760/786	24029037	7,12999	2203	4300	6503	23098877	SO:0001583	missense	8906			AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.2279G>A	14.37:g.24029037C>T	ENSP00000312442:p.Arg760His	768	23098877	D3DS51|O75504	Missense_Mutation	SNP	ENST00000308724.5	37	CCDS9602.1	46	0.021062271062271064	0	0.0	0	0.0	33	0.057692307692307696	13	0.017150395778364115	C	24.0	4.483747	0.84854	0.0	8.14E-4	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	T;T	0.51071	0.72;0.72	5.93	5.04	0.67666	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.000000	0.85682	D	0.000000	T	0.23451	0.0567	M	0.85777	2.775	0.43503	D	0.995759	D;D	0.76494	0.999;0.999	D;D	0.70716	0.945;0.97	T	0.60515	-0.7248	10	0.87932	D	0	-16.3284	13.1837	0.59670	0.0:0.8402:0.1598:0.0	.	760;615	O75843;Q86V28	AP1G2_HUMAN;.	H	760;760;529;615	ENSP00000312442:R760H;ENSP00000380309:R760H	ENSP00000312442:R760H	R	-	2	0	AP1G2	23098877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.613000	0.36900	1.506000	0.48736	0.655000	0.94253	CGC		0.567	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		T	24029037	C	T	24029037	3	4	111	1	0	0	0	0	1	0	0	0	733	768	27	1	82	1	AP1G2	14	24029037	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	83789	24029037	83320503	758	29892										
C14orf147	171546	hgsc.bcm.edu	37	chr14	34904436	34904436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatttcaaagtagtgcaataTcgccatgatgtgctggggca	12	7	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:34904436T>C	ENST00000298130.4	-	2	335	c.187A>G	c.(187-189)Ata>Gta	p.I63V		NM_138288.3	NP_612145.2	Q969W0	SPTSA_HUMAN	serine palmitoyltransferase, small subunit A	63					sphingolipid biosynthetic process (GO:0030148)	integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)											TAGTGCAATATCGCCATGATG	0.463																																																0			14											166	132	143					14																	34904436		2203	4300	6503	33974187	SO:0001583	missense	171546			AK001993	CCDS9647.2	14q13.1	2011-07-26	2011-07-26	2011-07-26	ENSG00000165389	ENSG00000165389			20361	protein-coding gene	gene with protein product	"small subunit of serine palmitoyltransferase A"	613540	"chromosome 14 open reading frame 147"	C14orf147		19416851	Standard	NM_138288		Approved	ssSPTa	uc001wsc.3	Q969W0	OTTHUMG00000140212	ENST00000298130.4:c.187A>G	14.37:g.34904436T>C	ENSP00000298130:p.Ile63Val		33974187	B2RD54|D3DS93|Q8WTZ7	Missense_Mutation	SNP	ENST00000298130.4	37	CCDS9647.2	.	.	.	.	.	.	.	.	.	.	.	15.14	2.745113	0.49151	.	.	ENSG00000165389	ENST00000298130	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.74489	0.3723	.	.	.	0.58432	D	0.999998	P	0.47604	0.898	D	0.68192	0.956	T	0.68542	-0.5381	8	0.15952	T	0.53	-5.6424	16.5317	0.84362	0.0:0.0:0.0:1.0	.	63	Q969W0	SPTSA_HUMAN	V	63	.	ENSP00000298130:I63V	I	-	1	0	SPTSSA	33974187	1.000000	0.71417	0.107000	0.21349	0.992000	0.81027	7.509000	0.81698	2.367000	0.80283	0.528000	0.53228	ATA		0.463	SPTSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276640.2	NM_138288		C	34904436	T	C	34904436	3	2	111	1	0	0	0	0	1	0	0	0	1754	1435	50	4	32	4	C14orf147	14	34904436	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	10875399	34904436	72445104	759	29893										
MIPOL1	145282	hgsc.bcm.edu	37	chr14	37777573	37777573	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacattacaggaattactgaAcagaataaacaatgcagaca	7	7	0	3	rs371476003		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:37777573A>T	ENST00000327441.7	+	10	1143	c.677A>T	c.(676-678)aAc>aTc	p.N226I	MIPOL1_ENST00000536774.1_Missense_Mutation_p.N45I|MIPOL1_ENST00000539062.2_Missense_Mutation_p.N195I|MIPOL1_ENST00000537471.1_Missense_Mutation_p.N226I|MIPOL1_ENST00000396294.2_Missense_Mutation_p.N226I|MIPOL1_ENST00000545536.1_Missense_Mutation_p.N195I|MIPOL1_ENST00000556451.1_Missense_Mutation_p.N195I	NM_001195296.1|NM_001195297.1|NM_138731.6	NP_001182225.1|NP_001182226.1|NP_620059.1	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	226						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		GAATTACTGAACAGAATAAAC	0.303																																																0			14											105	111	109					14																	37777573		2203	4299	6502	36847324	SO:0001583	missense	145282			AY059470	CCDS9664.1	14q13.3	2010-05-25			ENSG00000151338	ENSG00000151338			21460	protein-coding gene	gene with protein product		606850				11954550, 19667180	Standard	NM_001195296		Approved		uc001wuc.3	Q8TD10	OTTHUMG00000140252	ENST00000327441.7:c.677A>T	14.37:g.37777573A>T	ENSP00000333539:p.Asn226Ile		36847324	D3DSA4|Q7Z3J0|Q8IV14	Missense_Mutation	SNP	ENST00000327441.7	37	CCDS9664.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.737600	0.49045	.	.	ENSG00000151338	ENST00000327441;ENST00000536774;ENST00000539062;ENST00000556451;ENST00000396294;ENST00000537471;ENST00000545536	T;T;T;T;T;T	0.49432	0.79;0.79;0.78;0.79;0.79;0.78	5.76	5.76	0.90799	.	0.337880	0.34291	N	0.004092	T	0.62109	0.2401	M	0.71581	2.175	0.43617	D	0.995996	D;D	0.58970	0.984;0.984	P;P	0.59703	0.851;0.862	T	0.62742	-0.6790	10	0.40728	T	0.16	-9.2844	11.9888	0.53163	0.8556:0.1444:0.0:0.0	.	226;195	Q8TD10;Q49AL5	MIPO1_HUMAN;.	I	226;45;195;195;226;226;195	ENSP00000333539:N226I;ENSP00000438319:N195I;ENSP00000450479:N195I;ENSP00000379589:N226I;ENSP00000444254:N226I;ENSP00000442529:N195I	ENSP00000333539:N226I	N	+	2	0	MIPOL1	36847324	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.029000	0.57253	2.197000	0.70478	0.482000	0.46254	AAC		0.303	MIPOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276734.1	NM_138731		T	37777573	A	T	37777573	3	4	111	1	0	0	0	0	1	0	0	0	9623	43	2	5	703	5	MIPOL1	14	37777573	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2873137	37777573	69571967	760	29894										
SSTR1	6751	hgsc.bcm.edu	37	chr14	38678867	38678867	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgctatgccaagatgaagacGgccaccaacatctacatcct	7	14	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:38678867G>A	ENST00000267377.2	+	3	890	c.273G>A	c.(271-273)acG>acA	p.T91T		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	91					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	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)|Pasireotide(DB06663)	AGATGAAGACGGCCACCAACA	0.547																																																0			14											184	167	173					14																	38678867		2203	4300	6503	37748618	SO:0001819	synonymous_variant	6751				CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"GPCR / Class A : Somatostatin receptors"	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.273G>A	14.37:g.38678867G>A			37748618		Silent	SNP	ENST00000267377.2	37	CCDS9666.1																																																																																				0.547	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			A	38678867	G	A	38678867	2	1	111	1	0	0	0	0	0	0	0	1	15236	1103	39	1		1	SSTR1	14	38678867	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	901294	38678867	68670673	761	29895										
SIX4	51804	hgsc.bcm.edu	37	chr14	61186633	61186633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagtcactacagaccctccaTcttgggaagccactgtttga	8	12	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:61186633T>C	ENST00000216513.4	-	2	1453	c.1394A>G	c.(1393-1395)gAt>gGt	p.D465G		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	465					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		AGACCCTCCATCTTGGGAAGC	0.507																																																0			14											166	170	169					14																	61186633		2203	4300	6503	60256386	SO:0001583	missense	51804			AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1394A>G	14.37:g.61186633T>C	ENSP00000216513:p.Asp465Gly		60256386	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	T	14.42	2.529256	0.44969	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	D;T	0.91740	-2.9;0.65	5.72	5.72	0.89469	.	0.225560	0.45361	D	0.000362	D	0.88321	0.6405	L	0.29908	0.895	0.50813	D	0.999896	B;P	0.36282	0.449;0.546	B;B	0.37239	0.244;0.133	D	0.89104	0.3491	10	0.72032	D	0.01	.	16.0205	0.80486	0.0:0.0:0.0:1.0	.	457;465	G3V2N2;Q9UIU6	.;SIX4_HUMAN	G	465;138;457	ENSP00000216513:D465G;ENSP00000451537:D138G	ENSP00000216513:D465G	D	-	2	0	SIX4	60256386	1.000000	0.71417	0.918000	0.36340	0.949000	0.60115	5.513000	0.67037	2.194000	0.70268	0.533000	0.62120	GAT		0.507	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			C	61186633	T	C	61186633	3	2	111	1	0	0	0	0	1	0	0	0	14386	1435	50	4	959	4	SIX4	14	61186633	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	22507766	61186633	46162907	762	29896										
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61517247	61517247	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagacaaagtggagtcagaaTtactaaaaggttatagtaaa	9	4	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:61517247T>A	ENST00000267488.4	+	13	1059	c.943T>A	c.(943-945)Tta>Ata	p.L315I	SLC38A6_ENST00000354886.2_Missense_Mutation_p.L315I|SLC38A6_ENST00000456840.2_Missense_Mutation_p.L292I	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	315					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		GGAGTCAGAATTACTAAAAGG	0.308																																																0			14											112	106	108					14																	61517247		2202	4298	6500	60587000	SO:0001583	missense	145389			AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.943T>A	14.37:g.61517247T>A	ENSP00000267488:p.Leu315Ile		60587000	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	T	16.00	2.999019	0.54147	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000529212	T;T;T;T;T	0.01981	4.52;4.52;4.52;4.52;4.52	5.92	1.81	0.25067	.	0.065191	0.64402	D	0.000006	T	0.03178	0.0093	L	0.48935	1.535	0.43994	D	0.996695	P;P;B	0.45283	0.855;0.825;0.27	P;B;B	0.46208	0.507;0.373;0.198	T	0.54807	-0.8238	10	0.56958	D	0.05	-2.609	5.42	0.16396	0.2273:0.1736:0.0:0.5992	.	292;315;315	E7ETF2;Q8IZM9-2;Q8IZM9	.;.;S38A6_HUMAN	I	315;315;310;292;88	ENSP00000346959:L315I;ENSP00000267488:L315I;ENSP00000395851:L310I;ENSP00000413863:L292I;ENSP00000437190:L88I	ENSP00000267488:L315I	L	+	1	2	SLC38A6	60587000	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.133000	0.31430	0.475000	0.27415	0.528000	0.53228	TTA		0.308	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			A	61517247	T	A	61517247	3	1	111	1	0	0	0	0	1	0	0	0	14645	1490	52	5	993	5	SLC38A6	14	61517247	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	330614	61517247	45832293	763	29897										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64465637	64465637	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttcattttgcccaggtatgAtacatacagagatattcttg	7	7	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:64465637A>T	ENST00000344113.4	+	27	3571	c.3359A>T	c.(3358-3360)gAt>gTt	p.D1120V	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.D1120V|SYNE2_ENST00000358025.3_Missense_Mutation_p.D1120V	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1120					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CCCAGGTATGATACATACAGA	0.398																																																0			14											119	109	112					14																	64465637		1863	4129	5992	63535390	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.3359A>T	14.37:g.64465637A>T	ENSP00000341781:p.Asp1120Val		63535390	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	6.647	0.487781	0.12641	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.60424	0.55;0.55;0.19	5.32	2.86	0.33363	.	0.488400	0.18497	N	0.139471	T	0.49779	0.1577	L	0.50333	1.59	0.80722	D	1	B;B	0.14438	0.006;0.01	B;B	0.19391	0.011;0.025	T	0.40961	-0.9535	10	0.48119	T	0.1	.	9.2366	0.37470	0.6876:0.0:0.0:0.3124	.	1120;1120	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	V	1120	ENSP00000350719:D1120V;ENSP00000341781:D1120V;ENSP00000452570:D1120V	ENSP00000261678:D1120V	D	+	2	0	SYNE2	63535390	0.948000	0.32251	0.528000	0.27938	0.353000	0.29299	2.065000	0.41442	0.374000	0.24650	0.533000	0.62120	GAT		0.398	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64465637	A	T	64465637	3	4	111	1	0	0	0	0	1	0	0	0	15485	333	12	5	3461	5	SYNE2	14	64465637	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2948390	64465637	42883903	764	29898										
AKAP5	9495	hgsc.bcm.edu	37	chr14	64935520	64935520	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ataaaattcccaagagggccAaaaaggagtaatcattccaa					rs559697318		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:64935520delA	ENST00000394718.4	+	2	786	c.408delA	c.(406-408)ccafs	p.P136fs	AKAP5_ENST00000320636.5_Frame_Shift_Del_p.P136fs|ZBTB25_ENST00000555424.1_Intron|ZBTB25_ENST00000555220.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	136	Essential to the intracellular anchoring function. {ECO:0000250}.				energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		CAAGAGGGCCAAAAAGGAGTA	0.383																																																0			14											99	111	107					14																	64935520		2203	4300	6503	64005273	SO:0001589	frameshift_variant	9495			M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"A-kinase anchor proteins"	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.408delA	14.37:g.64935520delA	ENSP00000378207:p.Pro136fs		64005273	A2RRB8	Frame_Shift_Del	DEL	ENST00000394718.4	37	CCDS9764.1																																																																																				0.383	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3			-	64935520	A	-	64935520	7	5	111	1	0	1	0	1	0	0	0	0	454	117	5	0	410	0	AKAP5	14	64935520	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	469883	64935520	42414020	765	29899										
SPTB	6710	hgsc.bcm.edu	37	chr14	65259806	65259806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcccatccacagctcacaggCgtctgtctccccgaacaccg	7	19	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:65259806C>T	ENST00000389721.5	-	13	2607	c.2575G>A	c.(2575-2577)Gcc>Acc	p.A859T	SPTB_ENST00000556626.1_Missense_Mutation_p.A859T|SPTB_ENST00000542895.1_Missense_Mutation_p.A859T|SPTB_ENST00000389720.3_Missense_Mutation_p.A859T|SPTB_ENST00000389722.3_Missense_Mutation_p.A859T	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	859					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AGCTCACAGGCGTCTGTCTCC	0.627																																																0			14											63	51	55					14																	65259806		2203	4300	6503	64329559	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.2575G>A	14.37:g.65259806C>T	ENSP00000374371:p.Ala859Thr		64329559	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.878710	0.72294	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.63965	0.2556	M	0.69185	2.1	0.80722	D	1	P;D	0.64830	0.938;0.994	P;P	0.58820	0.745;0.846	T	0.65315	-0.6198	10	0.49607	T	0.09	.	17.5745	0.87944	0.0:1.0:0.0:0.0	.	859;863	P11277;Q59FP5	SPTB1_HUMAN;.	T	863;859;859;859;859;859	ENSP00000374372:A859T;ENSP00000451752:A859T;ENSP00000374371:A859T;ENSP00000443882:A859T;ENSP00000374370:A859T	ENSP00000374370:A859T	A	-	1	0	SPTB	64329559	1.000000	0.71417	0.956000	0.39512	0.346000	0.29079	7.792000	0.85828	2.431000	0.82371	0.555000	0.69702	GCC		0.627	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65259806	C	T	65259806	3	4	111	1	0	0	0	0	1	0	0	0	15157	768	27	1	4572	1	SPTB	14	65259806	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	324286	65259806	42089734	766	29900										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68274397	68274397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcagggccctgcaaagcccGcaatgcctttcgaatgaggt	11	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:68274397G>A	ENST00000347230.4	-	5	742	c.604C>T	c.(604-606)Cgg>Tgg	p.R202W	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.R202W	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	202					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TGCAAAGCCCGCAATGCCTTT	0.612																																																0			14											83	83	83					14																	68274397		2203	4300	6503	67344150	SO:0001583	missense	23503			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.604C>T	14.37:g.68274397G>A	ENSP00000251119:p.Arg202Trp		67344150	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.564494	0.27915	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.31769	1.63;1.48	5.51	-0.51	0.11973	.	0.809720	0.11201	N	0.588792	T	0.32882	0.0844	L	0.44542	1.39	0.09310	N	1	D;D;D	0.69078	0.997;0.995;0.985	P;P;B	0.50708	0.533;0.648;0.232	T	0.27739	-1.0065	10	0.87932	D	0	-0.0041	9.6873	0.40107	0.0:0.156:0.3128:0.5312	.	202;202;202	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	W	202	ENSP00000251119:R202W;ENSP00000450603:R202W	ENSP00000251119:R202W	R	-	1	2	ZFYVE26	67344150	0.002000	0.14202	0.000000	0.03702	0.011000	0.07611	0.813000	0.27225	-0.237000	0.09739	-2.067000	0.00394	CGG		0.612	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68274397	G	A	68274397	3	1	111	1	0	0	0	0	1	0	0	0	17707	1086	38	1	7167	1	ZFYVE26	14	68274397	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3014591	68274397	39075143	767	29901										
ACTN1	87	hgsc.bcm.edu	37	chr14	69349741	69349741	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtcggcatcagggagggtgGccttgaactgctcatgggct	16	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:69349741G>A	ENST00000193403.6	-	15	2050	c.1667C>T	c.(1666-1668)gCc>gTc	p.A556V	ACTN1_ENST00000376839.3_Missense_Mutation_p.A491V|ACTN1_ENST00000438964.2_Missense_Mutation_p.A556V|ACTN1_ENST00000538545.2_Missense_Mutation_p.A556V|ACTN1_ENST00000394419.4_Missense_Mutation_p.A556V	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	556	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AGGGAGGGTGGCCTTGAACTG	0.577																																																0			14											147	121	130					14																	69349741		2203	4300	6503	68419494	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1667C>T	14.37:g.69349741G>A	ENSP00000193403:p.Ala556Val		68419494	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633926	0.87660	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000544964	T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.69975	0.3171	M	0.80982	2.52	0.80722	D	1	P;B;B;B;B	0.49862	0.929;0.119;0.338;0.134;0.433	P;B;B;B;B	0.54060	0.741;0.078;0.182;0.182;0.226	T	0.74303	-0.3709	10	0.72032	D	0.01	.	19.0858	0.93202	0.0:0.0:1.0:0.0	.	187;556;556;556;203	B7Z2W3;P12814-2;Q1HE25;P12814;B4DFY0	.;.;.;ACTN1_HUMAN;.	V	556;556;556;491;556;146	ENSP00000193403:A556V;ENSP00000377941:A556V;ENSP00000414272:A556V;ENSP00000366035:A491V;ENSP00000439828:A556V;ENSP00000444422:A146V	ENSP00000193403:A556V	A	-	2	0	ACTN1	68419494	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.660000	0.83776	2.740000	0.93945	0.650000	0.86243	GCC		0.577	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69349741	G	A	69349741	3	1	111	1	0	0	0	0	1	0	0	0	204	1203	42	3	1109	3	ACTN1	14	69349741	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1075344	69349741	37999799	768	29902										
EXD2	55218	hgsc.bcm.edu	37	chr14	69695625	69695625	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttcgcctgcccaagctaatCtgtggaggaaaaacactacc	9	12	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:69695625C>A	ENST00000409018.3	+	3	554	c.426C>A	c.(424-426)atC>atA	p.I142I	EXD2_ENST00000409014.1_Silent_p.I17I|EXD2_ENST00000449989.1_Silent_p.I17I|EXD2_ENST00000409242.1_Silent_p.I17I|EXD2_ENST00000312994.5_Silent_p.I142I|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409949.1_Silent_p.I17I|EXD2_ENST00000409675.1_Silent_p.I17I	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	142							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)	p.I17M(1)		breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						CCAAGCTAATCTGTGGAGGAA	0.483																																																1	Substitution - Missense(1)	ovary(1)	14											109	103	105					14																	69695625		2203	4300	6503	68765378	SO:0001819	synonymous_variant	55218			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.426C>A	14.37:g.69695625C>A			68765378	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Silent	SNP	ENST00000409018.3	37	CCDS53902.1																																																																																				0.483	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			A	69695625	C	A	69695625	2	1	111	1	0	0	0	0	0	0	0	1	5311	903	32	2		2	EXD2	14	69695625	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	345884	69695625	37653915	769	29903										
EXD2	55218	hgsc.bcm.edu	37	chr14	69701517	69701517	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctggagaaaaaaacgatgAccacagtagctggagaaaag	11	7	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:69701517A>G	ENST00000409018.3	+	5	946	c.818A>G	c.(817-819)gAc>gGc	p.D273G	EXD2_ENST00000409014.1_Missense_Mutation_p.D148G|EXD2_ENST00000449989.1_Missense_Mutation_p.D148G|EXD2_ENST00000409242.1_Missense_Mutation_p.D148G|EXD2_ENST00000312994.5_Missense_Mutation_p.D273G|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409949.1_Missense_Mutation_p.D148G|EXD2_ENST00000409675.1_Missense_Mutation_p.D148G	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	273							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)	p.D148A(1)		breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						AAAAACGATGACCACAGTAGC	0.453																																																1	Substitution - Missense(1)	ovary(1)	14											60	61	61					14																	69701517		2203	4300	6503	68771270	SO:0001583	missense	55218			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.818A>G	14.37:g.69701517A>G	ENSP00000387331:p.Asp273Gly		68771270	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	37	CCDS53902.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.718|8.718	0.913745|0.913745	0.17907|0.17907	.|.	.|.	ENSG00000081177|ENSG00000081177	ENST00000409018;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000449989|ENST00000193422	T;T;T;T;T;T;T|.	0.63744|.	0.33;-0.06;-0.06;-0.06;-0.06;0.33;-0.06|.	5.42|5.42	1.32|1.32	0.21799|0.21799	.|.	0.741885|.	0.13968|.	N|.	0.350358|.	T|.	0.19366|.	0.0465|.	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.19418|.	-1.0306|.	10|.	0.42905|.	T|.	0.14|.	-7.2338|-7.2338	0.5136|0.5136	0.00599|0.00599	0.4048:0.2313:0.1876:0.1764|0.4048:0.2313:0.1876:0.1764	.|.	273;148;148|.	G5E947;B3KP95;Q9NVH0|.	.;.;EXD2_HUMAN|.	G|W	273;148;148;148;148;273;148|272	ENSP00000387331:D273G;ENSP00000386915:D148G;ENSP00000386762:D148G;ENSP00000386632:D148G;ENSP00000386839:D148G;ENSP00000313140:D273G;ENSP00000392177:D148G|.	ENSP00000313140:D273G|.	D|X	+|+	2|3	0|0	EXD2|EXD2	68771270|68771270	0.000000|0.000000	0.05858|0.05858	0.022000|0.022000	0.16811|0.16811	0.941000|0.941000	0.58515|0.58515	-0.298000|-0.298000	0.08265|0.08265	0.435000|0.435000	0.26365|0.26365	0.528000|0.528000	0.53228|0.53228	GAC|TGA		0.453	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			G	69701517	A	G	69701517	3	3	111	1	0	0	0	0	1	0	0	0	5311	275	10	4	453	4	EXD2	14	69701517	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	5892	69701517	37648023	770	29904										
PCNX	22990	hgsc.bcm.edu	37	chr14	71575352	71575352	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agctctcactctgtgcagtcGggcctggtcagacagtctcc	11	14	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:71575352G>A	ENST00000304743.2	+	34	6779	c.6333G>A	c.(6331-6333)tcG>tcA	p.S2111S	PCNX_ENST00000439984.3_Silent_p.S2000S|PCNX_ENST00000238570.5_Silent_p.S2039S|PCNX_ENST00000556272.1_3'UTR	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	2111	Ser-rich.					integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CTGTGCAGTCGGGCCTGGTCA	0.547																																																0			14											49	48	48					14																	71575352		2203	4300	6503	70645105	SO:0001819	synonymous_variant	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.6333G>A	14.37:g.71575352G>A			70645105	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	G	0.028	-1.358534	0.01245	.	.	ENSG00000100731	ENST00000554691	.	.	.	5.94	-11.9	0.00025	.	.	.	.	.	T	0.60418	0.2267	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.76512	-0.2932	4	.	.	.	.	16.7633	0.85517	0.1362:0.5548:0.309:0.0	.	.	.	.	Q	1098	.	.	R	+	2	0	PCNX	70645105	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.537000	0.00939	-2.997000	0.00277	-0.312000	0.09012	CGG		0.547	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71575352	G	A	71575352	2	1	111	1	0	0	0	0	0	0	0	1	11622	1103	39	1		1	PCNX	14	71575352	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1873835	71575352	35774188	771	29905										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72055079	72055079	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagcctaccccagctcccccAgaaaagctcttcgcagaata	6	16	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:72055079A>C	ENST00000555818.1	+	2	838	c.490A>C	c.(490-492)Aga>Cga	p.R164R	SIPA1L1_ENST00000381232.3_Silent_p.R164R|SIPA1L1_ENST00000358550.2_Silent_p.R164R	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	164					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAGCTCCCCCAGAAAAGCTCT	0.458																																																0			14											64	61	62					14																	72055079		2203	4300	6503	71124832	SO:0001819	synonymous_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.490A>C	14.37:g.72055079A>C			71124832	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.458	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72055079	A	C	72055079	2	2	111	1	0	0	0	0	0	0	0	1	14366	180	7	4		4	SIPA1L1	14	72055079	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	479727	72055079	35294461	772	29906										
ZFYVE1	53349	hgsc.bcm.edu	37	chr14	73441632	73441632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcagtgatgcttagtgtcGttatctttaaaggacgtcgc	12	8	1	1	rs151266277	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:73441632G>A	ENST00000556143.1	-	10	2562	c.1842C>T	c.(1840-1842)aaC>aaT	p.N614N	ZFYVE1_ENST00000318876.5_Silent_p.N600N|ZFYVE1_ENST00000394207.2_Silent_p.N199N|ZFYVE1_ENST00000555072.1_Silent_p.N199N|ZFYVE1_ENST00000554145.1_5'UTR|ZFYVE1_ENST00000553891.1_Silent_p.N614N	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	614					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		GCTTAGTGTCGTTATCTTTAA	0.552													G|||	3	0.000599042	0	0	5008	,	,		20643	0		0.001	False		,,,				2504	0.002															0			14						G	,	0,4406		0,0,2203	90	86	88		1842,597	-3.7	0.8	14	dbSNP_134	88	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	ZFYVE1	NM_021260.2,NM_178441.1	,	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	,	614/778,199/363	73441632	7,12999	2203	4300	6503	72511385	SO:0001819	synonymous_variant	53349			AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"Zinc fingers, FYVE domain containing"	13180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 172"	605471	"zinc finger protein, subfamily 2A (FYVE domain containing), 1"	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1842C>T	14.37:g.73441632G>A			72511385	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																				0.552	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260		A	73441632	G	A	73441632	2	1	111	1	0	0	0	0	0	0	0	1	17702	1136	40	1		1	ZFYVE1	14	73441632	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1386553	73441632	33907908	773	29907										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73965799	73965799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatggcaaaggccttgatttTccagtaaggatctctctgca	9	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:73965799T>C	ENST00000553558.1	-	13	2653	c.2332A>G	c.(2332-2334)Aaa>Gaa	p.K778E	HEATR4_ENST00000334988.2_Missense_Mutation_p.K778E|HEATR4_ENST00000560393.1_Missense_Mutation_p.K731E	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	778										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		GCCTTGATTTTCCAGTAAGGA	0.458																																																0			14											226	218	220					14																	73965799		2203	4300	6503	73035552	SO:0001583	missense	399671			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2332A>G	14.37:g.73965799T>C	ENSP00000450444:p.Lys778Glu		73035552	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	T	21.2	4.115667	0.77323	.	.	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.17691	2.26	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.49916	D	0.000127	T	0.27134	0.0665	N	0.20986	0.625	0.35647	D	0.811471	D	0.89917	1.0	D	0.80764	0.994	T	0.27739	-1.0065	10	0.42905	T	0.14	-16.1796	13.8784	0.63667	0.0:0.0:0.0:1.0	.	778	Q86WZ0	HEAT4_HUMAN	E	778;731	ENSP00000450444:K778E	ENSP00000335447:K731E	K	-	1	0	HEATR4	73035552	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.641000	0.61375	2.117000	0.64856	0.533000	0.62120	AAA		0.458	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		C	73965799	T	C	73965799	3	2	111	1	0	0	0	0	1	0	0	0	7051	1792	62	4	772	4	HEATR4	14	73965799	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	524167	73965799	33383741	774	29908										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74196464	74196464	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcccgcacagggctgaggatGgggggcggcgtgtagggagg					rs537089743		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:74196464delG	ENST00000286523.5	-	4	2756	c.1974delC	c.(1972-1974)cccfs	p.P658fs	ELMSAN1_ENST00000394071.2_Frame_Shift_Del_p.P658fs	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	658					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GGCTGAGGATGGGGGGCGGCG	0.627																																																0			14											69	63	65					14																	74196464		2203	4300	6503	73266217	SO:0001589	frameshift_variant	91748			BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1974delC	14.37:g.74196464delG	ENSP00000286523:p.Pro658fs		73266217	Q6PK13|Q6PK59|Q6ZS23	Frame_Shift_Del	DEL	ENST00000286523.5	37	CCDS9819.1																																																																																				0.627	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		-	74196464	G	-	74196464	7	5	111	1	0	1	0	1	0	0	0	0	1778	1335	47	0	1199	0	C14orf43	14	74196464	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	230665	74196464	33153076	775	29909										
COQ6	51004	hgsc.bcm.edu	37	chr14	74420233	74420233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagaaacttacagcaacaggGtcagctccatttcccctggc	8	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:74420233G>A	ENST00000334571.2	+	2	299	c.259G>A	c.(259-261)Gtc>Atc	p.V87I	COQ6_ENST00000394026.4_Missense_Mutation_p.V62I|COQ6_ENST00000555552.1_3'UTR|COQ6_ENST00000238709.4_Silent_p.G31G|COQ6_ENST00000554920.1_Missense_Mutation_p.V87I	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	87					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		CAGCAACAGGGTCAGCTCCAT	0.423																																																0			14											104	98	100					14																	74420233		2203	4300	6503	73489986	SO:0001583	missense	51004			AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.259G>A	14.37:g.74420233G>A	ENSP00000333946:p.Val87Ile		73489986	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	37	CCDS9823.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806443	0.90623	.	.	ENSG00000119723	ENST00000394026;ENST00000334571;ENST00000556300;ENST00000554920;ENST00000545052	T;T	0.42513	0.97;0.97	5.37	5.37	0.77165	.	0.056069	0.64402	D	0.000001	T	0.60104	0.2243	L	0.53617	1.68	0.80722	D	1	D;P;P	0.71674	0.998;0.944;0.938	D;P;P	0.63877	0.919;0.724;0.589	T	0.59434	-0.7455	10	0.59425	D	0.04	0.0419	19.369	0.94477	0.0:0.0:1.0:0.0	.	87;62;87	B7Z357;B7Z3K8;Q9Y2Z9	.;.;COQ6_HUMAN	I	62;87;87;87;87	ENSP00000377594:V62I;ENSP00000333946:V87I	ENSP00000333946:V87I	V	+	1	0	COQ6	73489986	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.271000	0.78506	2.822000	0.97130	0.650000	0.86243	GTC		0.423	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			A	74420233	G	A	74420233	3	1	111	1	0	0	0	0	1	0	0	0	3755	1261	44	3	265	3	COQ6	14	74420233	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	223769	74420233	32929307	776	29910										
RPS6KL1	83694	hgsc.bcm.edu	37	chr14	75386612	75386612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agttgaagatctcctctgccCgccgcaggtatttggtaatt	10	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:75386612C>T	ENST00000555647.1	-	4	613	c.326G>A	c.(325-327)cGg>cAg	p.R109Q	RPS6KL1_ENST00000554900.1_5'UTR|RPS6KL1_ENST00000358328.4_Missense_Mutation_p.R109Q|RPS6KL1_ENST00000354625.2_Missense_Mutation_p.R109Q|RPS6KL1_ENST00000557413.1_Missense_Mutation_p.R109Q			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	109	MIT.					ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		CTCCTCTGCCCGCCGCAGGTA	0.637																																																0			14											45	43	44					14																	75386612		2203	4300	6503	74456365	SO:0001583	missense	83694			BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.326G>A	14.37:g.75386612C>T	ENSP00000452027:p.Arg109Gln		74456365	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Missense_Mutation	SNP	ENST00000555647.1	37	CCDS9834.2	.	.	.	.	.	.	.	.	.	.	C	36	5.929530	0.97116	.	.	ENSG00000198208	ENST00000555647;ENST00000354625;ENST00000557413;ENST00000358328	T;T;T;T	0.58652	0.41;0.32;0.41;0.41	4.99	4.99	0.66335	MIT (2);	0.000000	0.85682	D	0.000000	T	0.76652	0.4017	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.76948	-0.2770	10	0.41790	T	0.15	-30.5216	16.2227	0.82267	0.0:1.0:0.0:0.0	.	109;109;109	Q9Y6S9;Q9Y6S9-4;Q9Y6S9-2	RPKL1_HUMAN;.;.	Q	109	ENSP00000452027:R109Q;ENSP00000346644:R109Q;ENSP00000450567:R109Q;ENSP00000351086:R109Q	ENSP00000346644:R109Q	R	-	2	0	RPS6KL1	74456365	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.170000	0.77587	2.600000	0.87896	0.655000	0.94253	CGG		0.637	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1			T	75386612	C	T	75386612	3	4	111	1	0	0	0	0	1	0	0	0	13696	652	23	1	1335	1	RPS6KL1	14	75386612	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	966379	75386612	31962928	777	29911										
C14orf179	112752	hgsc.bcm.edu	37	chr14	76455320	76455320	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctttgactctgactggagaGgtgggtgctaaaaaaaaaga	12	5	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:76455320G>A	ENST00000314067.6	+	2	181	c.147G>A	c.(145-147)gaG>gaA	p.E49E	IFT43_ENST00000553338.1_3'UTR|IFT43_ENST00000238628.6_Splice_Site_p.E49E|IFT43_ENST00000556742.1_Splice_Site_p.E49E	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43	49					cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGACTGGAGAGGTGGGTGCTA	0.433																																																0			14											85	84	84					14																	76455320		2203	4300	6503	75525073	SO:0001630	splice_region_variant	112752			BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"Intraflagellar transport homologs"	29669	protein-coding gene	gene with protein product		614068	"chromosome 14 open reading frame 179", "intraflagellar transport 43 homolog (Chlamydomonas)"	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.147+1G>A	14.37:g.76455320G>A			75525073	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Silent	SNP	ENST00000314067.6	37	CCDS41973.1																																																																																				0.433	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873	Silent	A	76455320	G	A	76455320	5	1	111	1	0	0	0	0	0	0	1	0	1766	1014	35	3	153	3	C14orf179	14	76455320	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1068708	76455320	30894220	778	29912										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76905887	76905887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcgccacccatgtttgcagGcgccgggctgggaggcaccc	14	16	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:76905887G>A	ENST00000509242.1	+	3	289	c.191G>A	c.(190-192)gGc>gAc	p.G64D	ESRRB_ENST00000556177.1_Missense_Mutation_p.G64D|ESRRB_ENST00000380887.2_Missense_Mutation_p.G64D|ESRRB_ENST00000261532.7_Missense_Mutation_p.G64D|ESRRB_ENST00000507951.1_3'UTR	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	64					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		ATGTTTGCAGGCGCCGGGCTG	0.677																																																0			14											38	37	37					14																	76905887		2203	4299	6502	75975640	SO:0001583	missense	2103			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.191G>A	14.37:g.76905887G>A	ENSP00000422488:p.Gly64Asp		75975640	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592598	0.28357	.	.	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000556177;ENST00000380887;ENST00000261532	D;D;D;D;D	0.92699	-3.08;-3.09;-3.06;-3.09;-3.05	5.22	5.22	0.72569	.	0.187585	0.45606	D	0.000349	D	0.84719	0.5534	N	0.14661	0.345	0.42176	D	0.991663	B;B	0.33512	0.415;0.415	B;B	0.32677	0.15;0.15	D	0.84467	0.0597	10	0.38643	T	0.18	.	14.4255	0.67212	0.0:0.1472:0.8528:0.0	.	64;69	Q5F0P7;E7EWD9	.;.	D	69;64;64;64;64	ENSP00000424992:G69D;ENSP00000422488:G64D;ENSP00000451658:G64D;ENSP00000370270:G64D;ENSP00000261532:G64D	ENSP00000261532:G64D	G	+	2	0	ESRRB	75975640	1.000000	0.71417	0.504000	0.27639	0.235000	0.25334	4.418000	0.59828	2.437000	0.82529	0.655000	0.94253	GGC		0.677	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			A	76905887	G	A	76905887	3	1	111	1	0	0	0	0	1	0	0	0	5274	1203	42	3	193	3	ESRRB	14	76905887	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	450567	76905887	30443653	779	29913										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77491802	77491802	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctaagatagtcgcgatttcGccctgcatgaaggcccaagg	12	11	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:77491802G>A	ENST00000238647.3	-	1	3232	c.2334C>T	c.(2332-2334)ggC>ggT	p.G778G		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	778					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						TCGCGATTTCGCCCTGCATGA	0.572																																																0			14											94	91	92					14																	77491802		2203	4300	6503	76561555	SO:0001819	synonymous_variant	64207			AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2334C>T	14.37:g.77491802G>A			76561555	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																				0.572	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		A	77491802	G	A	77491802	2	1	111	1	0	0	0	0	0	0	0	1	1777	1074	38	1		1	C14orf4	14	77491802	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	585915	77491802	29857738	780	29914										
C14orf145	145508	hgsc.bcm.edu	37	chr14	80993288	80993288	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcgaaccctgtatttggaAtatcttccatcagttctctc	6	12	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:80993288A>T	ENST00000555265.1	-	23	3372	c.2997T>A	c.(2995-2997)taT>taA	p.Y999*	CEP128_ENST00000553717.1_5'UTR|CEP128_ENST00000281129.3_Nonsense_Mutation_p.Y999*			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	999						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGTATTTGGAATATCTTCCAT	0.348																																																0			14											80	81	81					14																	80993288		2203	4300	6503	80063041	SO:0001587	stop_gained	145508			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2997T>A	14.37:g.80993288A>T	ENSP00000451162:p.Tyr999*		80063041	B9EK52|Q86X97|Q96ML4	Nonsense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	37|37	6.581512|6.581512	0.97680|0.97680	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000556061|ENST00000281129;ENST00000555265	.|.	.|.	.|.	5.64|5.64	-3.34|-3.34	0.04943|0.04943	.|.	.|0.257753	.|0.32041	.|N	.|0.006665	T|.	0.17746|.	0.0426|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.24083|.	-1.0170|.	4|.	.|0.02654	.|T	.|1	.|.	14.5718|14.5718	0.68216|0.68216	0.5059:0.0:0.4941:0.0|0.5059:0.0:0.4941:0.0	.|.	.|.	.|.	.|.	I|X	65|999	.|.	.|ENSP00000281129:Y999X	F|Y	-|-	1|3	0|2	CEP128|CEP128	80063041|80063041	0.145000|0.145000	0.22656|0.22656	0.005000|0.005000	0.12908|0.12908	0.005000|0.005000	0.04900|0.04900	-0.234000|-0.234000	0.09028|0.09028	-1.379000|-1.379000	0.02118|0.02118	-1.463000|-1.463000	0.01021|0.01021	TTC|TAT		0.348	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		T	80993288	A	T	80993288	4	4	111	1	0	0	0	0	0	1	0	0	1753	108	4	5	299	5	C14orf145	14	80993288	Nonsense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3501486	80993288	26356252	781	29915										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089235	86089235	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acatgggtgaaaatgggccaCagtttagtagggggcatcgt	15	6	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:86089235C>T	ENST00000330753.4	+	2	2144	c.1377C>T	c.(1375-1377)caC>caT	p.H459H	FLRT2_ENST00000554746.1_Silent_p.H459H	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	459	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		AAATGGGCCACAGTTTAGTAG	0.488																																																0			14											100	90	94					14																	86089235		2203	4300	6503	85158988	SO:0001819	synonymous_variant	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1377C>T	14.37:g.86089235C>T			85158988	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	37	CCDS9877.1																																																																																				0.488	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			T	86089235	C	T	86089235	2	4	111	1	0	0	0	0	0	0	0	1	5958	477	17	3		3	FLRT2	14	86089235	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5095947	86089235	21260305	782	29916										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91739787	91739787	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggggcctcggcctcagtcaGtctgaagtttggctttacgt	13	10	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:91739787G>A	ENST00000389857.6	-	30	5355	c.5269C>T	c.(5269-5271)Ctg>Ttg	p.L1757L	CCDC88C_ENST00000331194.7_Silent_p.L281L	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1757					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GCCTCAGTCAGTCTGAAGTTT	0.692																																																0			14											19	22	21					14																	91739787		1949	4110	6059	90809540	SO:0001819	synonymous_variant	440193				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.5269C>T	14.37:g.91739787G>A			90809540	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																				0.692	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		A	91739787	G	A	91739787	2	1	111	1	0	0	0	0	0	0	0	1	2871	1020	36	3		3	CCDC88C	14	91739787	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5650552	91739787	15609753	783	29917										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92461696	92461696	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagtgaccgtagagcttacCttgttggaaatgctctagta	11	7	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:92461696C>A	ENST00000267622.4	-	14	5429	c.5056G>T	c.(5056-5058)Gag>Tag	p.E1686*		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1686					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TAGAGCTTACCTTGTTGGAAA	0.428			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											107	94	98					14																	92461696		2203	4300	6503	91531449	SO:0001630	splice_region_variant	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5056+1G>T	14.37:g.92461696C>A			91531449	B2RUT2|O14689|O15154|O95949	Nonsense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.514444|10.514444	0.99419|0.99419	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	.|.	.|.	.|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80303	.|0.4598	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77755	.|-0.2469	.|3	.|.	.|.	.|.	.|.	20.3343|20.3343	0.98733|0.98733	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	1686;1422|1401	.|.	.|.	E|R	-|-	1|2	0|0	TRIP11|TRIP11	91531449|91531449	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.710000|0.710000	0.40934|0.40934	7.676000|7.676000	0.84012|0.84012	2.822000|2.822000	0.97130|0.97130	0.650000|0.650000	0.86243|0.86243	GAG|AGA		0.428	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		Nonsense_Mutation	A	92461696	C	A	92461696	5	1	111	1	0	0	0	0	0	0	1	0	16595	695	24	2	915	2	TRIP11	14	92461696	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	721909	92461696	14887844	784	29918										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92471812	92471812	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atttcattttttcttaaggcCtgagaatatttatccaattc	4	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:92471812C>A	ENST00000267622.4	-	11	2881	c.2508G>T	c.(2506-2508)caG>caT	p.Q836H		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	836					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTCTTAAGGCCTGAGAATATT	0.328			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											63	66	65					14																	92471812		2203	4300	6503	91541565	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.2508G>T	14.37:g.92471812C>A	ENSP00000267622:p.Gln836His		91541565	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.59|10.59	1.393094|1.393094	0.25118|0.25118	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000554357|ENST00000267622;ENST00000542257	.|T	.|0.04194	.|3.68	5.23|5.23	1.27|1.27	0.21489|0.21489	.|.	.|1.115110	.|0.06522	.|N	.|0.739768	T|T	0.09379|0.09379	0.0231|0.0231	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	.|P;P	.|0.47409	.|0.755;0.895	.|P;P	.|0.46940	.|0.465;0.532	T|T	0.39354|0.39354	-0.9618|-0.9618	5|10	.|0.46703	.|T	.|0.11	.|.	9.1603|9.1603	0.37019|0.37019	0.0:0.5018:0.0:0.4982|0.0:0.5018:0.0:0.4982	.|.	.|572;836	.|F5H1Z0;Q15643	.|.;TRIPB_HUMAN	C|H	552|836;572	.|ENSP00000267622:Q836H	.|ENSP00000267622:Q836H	G|Q	-|-	1|3	0|2	TRIP11|TRIP11	91541565|91541565	0.003000|0.003000	0.15002|0.15002	0.003000|0.003000	0.11579|0.11579	0.942000|0.942000	0.58702|0.58702	0.441000|0.441000	0.21611|0.21611	-0.038000|-0.038000	0.13624|0.13624	0.305000|0.305000	0.20034|0.20034	GGC|CAG		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			A	92471812	C	A	92471812	3	1	111	1	0	0	0	0	1	0	0	0	16595	680	24	2	3475	2	TRIP11	14	92471812	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10116	92471812	14877728	785	29919										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94079411	94079411	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaacttgctttaatgcattCattgcaggaattgcccaagt	7	9	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:94079411C>A	ENST00000393151.2	+	27	4023	c.4023C>A	c.(4021-4023)ttC>ttA	p.F1341L	UNC79_ENST00000555664.1_Missense_Mutation_p.F1341L|UNC79_ENST00000256339.4_Missense_Mutation_p.F1164L|UNC79_ENST00000553484.1_Missense_Mutation_p.F1363L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1341					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TTAATGCATTCATTGCAGGAA	0.423																																																0			14											108	93	98					14																	94079411		2203	4300	6503	93149164	SO:0001583	missense	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4023C>A	14.37:g.94079411C>A	ENSP00000376858:p.Phe1341Leu		93149164	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	18.19	3.569997	0.65765	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.42131	1.04;0.98;1.02;1.04	5.56	1.53	0.23141	.	0.000000	0.85682	D	0.000000	T	0.53965	0.1829	L	0.54323	1.7	0.36595	D	0.874311	D	0.58268	0.982	D	0.68943	0.961	T	0.59936	-0.7360	10	0.87932	D	0	-19.7383	10.0385	0.42144	0.0:0.4385:0.0:0.5615	.	1363	C9JQL1	.	L	1164;1341;1363;1341;1363	ENSP00000256339:F1164L;ENSP00000450868:F1341L;ENSP00000451360:F1363L;ENSP00000376858:F1341L	ENSP00000256339:F1164L	F	+	3	2	KIAA1409	93149164	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.566000	0.36396	0.111000	0.17947	-0.806000	0.03193	TTC		0.423	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94079411	C	A	94079411	3	1	111	1	0	0	0	0	1	0	0	0	8251	825	29	2	3586	2	KIAA1409	14	94079411	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1607599	94079411	13270129	786	29920										
IFI27L2	83982	hgsc.bcm.edu	37	chr14	94594997	94594997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactgagcaccacgggcacaGcccccactgccagggctgtg	12	17	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:94594997G>A	ENST00000238609.3	-	3	152	c.53C>T	c.(52-54)gCt>gTt	p.A18V	IFI27L2_ENST00000556727.1_5'UTR	NM_032036.2	NP_114425.1	Q9H2X8	I27L2_HUMAN	interferon, alpha-inducible protein 27-like 2	18						integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	8						CACGGGCACAGCCCCCACTGC	0.642																																																0			14											32	26	28					14																	94594997		2203	4300	6503	93664750	SO:0001583	missense	83982			AF208232	CCDS9920.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000119632			19753	protein-coding gene	gene with protein product		611319	"family with sequence similarity 14, member A"	FAM14A			Standard	NM_032036		Approved	TLH29	uc001ycq.3	Q9H2X8		ENST00000238609.3:c.53C>T	14.37:g.94594997G>A	ENSP00000238609:p.Ala18Val		93664750	Q8TBD7|Q9NYL0	Missense_Mutation	SNP	ENST00000238609.3	37	CCDS9920.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.448643	0.43531	.	.	ENSG00000119632	ENST00000238609	T	0.34859	1.34	4.01	3.1	0.35709	.	1.216240	0.06453	U	0.728014	T	0.49745	0.1575	M	0.78801	2.425	0.21878	N	0.999498	B	0.27013	0.166	B	0.38327	0.271	T	0.51020	-0.8758	10	0.59425	D	0.04	.	10.4407	0.44464	0.0:0.1983:0.8017:0.0	.	18	Q9H2X8	I27L2_HUMAN	V	18	ENSP00000238609:A18V	ENSP00000238609:A18V	A	-	2	0	IFI27L2	93664750	0.024000	0.19004	0.005000	0.12908	0.017000	0.09413	2.071000	0.41500	0.941000	0.37499	0.655000	0.94253	GCT		0.642	IFI27L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412935.1	NM_032036		A	94594997	G	A	94594997	3	1	111	1	0	0	0	0	1	0	0	0	7535	971	34	3	347	3	IFI27L2	14	94594997	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	515586	94594997	12754543	787	29921										
DICER1	23405	hgsc.bcm.edu	37	chr14	95582025	95582025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tattgatgtgtccaatggccGtgttgattgtgactcgtgga	13	6	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:95582025G>A	ENST00000526495.1	-	13	2177	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M	DICER1_ENST00000393063.1_Missense_Mutation_p.T629M|DICER1_ENST00000541352.1_Missense_Mutation_p.T629M|DICER1_ENST00000343455.3_Missense_Mutation_p.T629M|DICER1_ENST00000527414.1_Missense_Mutation_p.T629M			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	629					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TCCAATGGCCGTGTTGATTGT	0.433			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																													yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	0			14											285	234	251					14																	95582025		2203	4300	6503	94651778	SO:0001583	missense	23405	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.1886C>T	14.37:g.95582025G>A	ENSP00000437256:p.Thr629Met		94651778	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	37	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.927640	0.92389	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.64	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.67163	0.2864	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.67382	0.951	T	0.68610	-0.5363	10	0.52906	T	0.07	-16.4242	18.9613	0.92678	0.0:0.0:1.0:0.0	.	629	Q9UPY3	DICER_HUMAN	M	629	ENSP00000343745:T629M;ENSP00000437256:T629M;ENSP00000376783:T629M;ENSP00000435681:T629M;ENSP00000444719:T629M	ENSP00000343745:T629M	T	-	2	0	DICER1	94651778	1.000000	0.71417	0.974000	0.42286	0.963000	0.63663	9.634000	0.98435	2.554000	0.86153	0.655000	0.94253	ACG		0.433	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			A	95582025	G	A	95582025	3	1	111	1	0	0	0	0	1	0	0	0	4532	1145	40	1	3950	1	DICER1	14	95582025	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	987028	95582025	11767515	788	29922										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99697797	99697797	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggaggcagggcgggagagcGcccagggcacgcagaggtga	22	9	0	3	rs372881820		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:99697797G>A	ENST00000357195.3	-	3	534	c.525C>T	c.(523-525)ggC>ggT	p.G175G	BCL11B_ENST00000443726.2_Intron|BCL11B_ENST00000345514.2_Intron	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	175					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GCGGGAGAGCGCCCAGGGCAC	0.711			T	TLX3	T-ALL																																		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	0			14						G	,	0,4390		0,0,2195	25	29	28		,525	4.5	1	14		28	1,8599		0,1,4299	no	intron,coding-synonymous	BCL11B	NM_022898.1,NM_138576.2	,	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	,	,175/895	99697797	1,12989	2195	4300	6495	98767550	SO:0001819	synonymous_variant	64919			AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.525C>T	14.37:g.99697797G>A			98767550	Q9H162	Silent	SNP	ENST00000357195.3	37	CCDS9950.1																																																																																				0.711	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		A	99697797	G	A	99697797	2	1	111	1	0	0	0	0	0	0	0	1	1365	1074	38	1		1	BCL11B	14	99697797	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4115772	99697797	7651743	789	29923										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102481636	102481636	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcgtaagggcaaagaggaTgagggggaggaggccgcttc	20	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:102481636T>C	ENST00000360184.4	+	35	7373	c.7209T>C	c.(7207-7209)gaT>gaC	p.D2403D		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2403	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCAAAGAGGATGAGGGGGAGG	0.607																																																0			14											38	35	36					14																	102481636		2203	4300	6503	101551389	SO:0001819	synonymous_variant	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.7209T>C	14.37:g.102481636T>C			101551389	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																				0.607	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102481636	T	C	102481636	2	2	111	1	0	0	0	0	0	0	0	1	4852	1461	51	4		4	DYNC1H1	14	102481636	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	2783839	102481636	4867904	790	29924										
JAG2	3714	hgsc.bcm.edu	37	chr14	105612105	105612105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggttgaaatgcaaggtgaggCgggcacagttattgtccagg	16	6	0	2	rs372934981		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr14:105612105C>T	ENST00000331782.3	-	23	3318	c.2915G>A	c.(2914-2916)cGc>cAc	p.R972H	JAG2_ENST00000347004.2_Missense_Mutation_p.R934H	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	972					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CAAGGTGAGGCGGGCACAGTT	0.672																																																0			14						C	HIS/ARG,HIS/ARG	0,4366		0,0,2183	49	34	39		2915,2801	1.8	0.9	14		39	1,8581		0,1,4290	no	missense,missense	JAG2	NM_002226.3,NM_145159.1	29,29	0,1,6473	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	972/1239,934/1201	105612105	1,12947	2183	4291	6474	104683150	SO:0001583	missense	3714			AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.2915G>A	14.37:g.105612105C>T	ENSP00000328169:p.Arg972His		104683150	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	C	9.790	1.177563	0.21787	0.0	1.17E-4	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.89552	-2.53;-2.52	4.14	1.82	0.25136	.	0.221015	0.35772	N	0.002994	D	0.86957	0.6058	M	0.78049	2.395	0.26112	N	0.980662	B;B	0.25390	0.125;0.076	B;B	0.22601	0.04;0.018	T	0.80520	-0.1346	10	0.59425	D	0.04	.	9.9894	0.41860	0.0:0.7899:0.0:0.2101	.	934;972	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	H	972;934	ENSP00000328169:R972H;ENSP00000328566:R934H	ENSP00000328169:R972H	R	-	2	0	JAG2	104683150	0.001000	0.12720	0.882000	0.34594	0.081000	0.17604	0.491000	0.22419	0.713000	0.32060	0.436000	0.28706	CGC		0.672	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			T	105612105	C	T	105612105	3	4	111	1	0	0	0	0	1	0	0	0	7956	768	27	1	817	1	JAG2	14	105612105	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3130469	105612105	1737435	791	29925										
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31822970	31822970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtggccagaggaagaagccGtttacagctcgtgcacacag	13	10	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:31822970G>A	ENST00000307050.4	-	4	684	c.592C>T	c.(592-594)Cgg>Tgg	p.R198W	OTUD7A_ENST00000382902.1_Missense_Mutation_p.R198W	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	198	Catalytic. {ECO:0000250}.|TRAF-binding. {ECO:0000250}.				protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GGAAGAAGCCGTTTACAGCTC	0.562																																																0			15											126	103	111					15																	31822970		2201	4300	6501	29610262	SO:0001583	missense	161725			AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"OTU domain containing"	20718	protein-coding gene	gene with protein product		612024	"chromosome 15 open reading frame 16", "OTU domain containing 7", "OTU domain containing 7A"	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.592C>T	15.37:g.31822970G>A	ENSP00000305926:p.Arg198Trp		29610262	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.297361	0.81025	.	.	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.38240	1.15;1.19	6.06	4.14	0.48551	.	0.057428	0.64402	D	0.000002	T	0.53061	0.1773	L	0.52573	1.65	0.41149	D	0.986013	D;D	0.89917	1.0;0.999	D;P	0.67231	0.95;0.893	T	0.57021	-0.7882	10	0.87932	D	0	-30.6992	15.4002	0.74834	0.0:0.0:0.7387:0.2612	.	198;198	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	W	198	ENSP00000305926:R198W;ENSP00000372358:R198W	ENSP00000305926:R198W	R	-	1	2	OTUD7A	29610262	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	5.151000	0.64875	0.837000	0.34925	0.650000	0.86243	CGG		0.562	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		A	31822970	G	A	31822970	3	1	111	1	0	0	0	0	1	0	0	0	11349	1144	40	1	2220	1	OTUD7A	15	31822970	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10		31822970	70708422	792	29926										
FMN1	342184	hgsc.bcm.edu	37	chr15	33261041	33261041	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaagagtccagggggaggtGggggtgcaagtcctgggggt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:33261041delG	ENST00000559047.1	-	5	2860	c.2861delC	c.(2860-2862)ccafs	p.P957fs	FMN1_ENST00000334528.9_Frame_Shift_Del_p.P734fs|SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000561249.1_Frame_Shift_Del_p.P859fs			Q68DA7	FMN1_HUMAN	formin 1	957	FH1.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		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)		AGGGGGAGGTGGGGGTGCAAG	0.612																																																0			15											41	42	42					15																	33261041		1790	4039	5829	31048333	SO:0001589	frameshift_variant	342184			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2861delC	15.37:g.33261041delG	ENSP00000454047:p.Pro957fs		31048333	Q3B7I6|Q3ZAR4|Q6ZSY1	Frame_Shift_Del	DEL	ENST00000559047.1	37																																																																																					0.612	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		-	33261041	G	-	33261041	7	5	111	1	0	1	0	1	0	0	0	0	5968	1348	47	0	1454	0	FMN1	15	33261041	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1438071	33261041	69270351	793	29927										
PGBD4	161779	hgsc.bcm.edu	37	chr15	34396124	34396124	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcttctacacattacagtGctgaactcctacatcctgtt	4	13	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:34396124G>A	ENST00000397766.2	+	1	1851	c.1392G>A	c.(1390-1392)gtG>gtA	p.V464V	EMC7_ENST00000532113.1_5'Flank|EMC7_ENST00000256545.4_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	464										breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		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)		ACATTACAGTGCTGAACTCCT	0.408																																																0			15											76	70	72					15																	34396124		2201	4298	6499	32183416	SO:0001819	synonymous_variant	161779			AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.1392G>A	15.37:g.34396124G>A			32183416	A1L487|A8K0C6|Q8N9E8	Silent	SNP	ENST00000397766.2	37	CCDS10033.1																																																																																				0.408	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			A	34396124	G	A	34396124	2	1	111	1	0	0	0	0	0	0	0	1	11814	1306	46	3		3	PGBD4	15	34396124	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1135083	34396124	68135268	794	29928										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34640224	34640224	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctagtgccgccccgtctcCatcccctgcacttccctttc	5	21	1	0	rs528007806		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:34640224C>A	ENST00000333756.4	+	2	226	c.71C>A	c.(70-72)cCa>cAa	p.P24Q	NUTM1_ENST00000537011.1_Missense_Mutation_p.P52Q|NUTM1_ENST00000438749.3_Missense_Mutation_p.P42Q	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	24	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)											GCCCCGTCTCCATCCCCTGCA	0.532																																																0			15											126	114	118					15																	34640224		2201	4298	6499	32427516	SO:0001583	missense	256646			AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.71C>A	15.37:g.34640224C>A	ENSP00000329448:p.Pro24Gln		32427516	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674688	0.67928	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	T;T;T	0.23754	1.89;1.89;1.89	5.69	5.69	0.88448	Nuclear Testis  protein, N-terminal (1);	0.418208	0.20595	N	0.089265	T	0.47838	0.1467	M	0.67953	2.075	0.19300	N	0.99998	D;D;D	0.62365	0.991;0.989;0.991	D;P;D	0.64877	0.93;0.885;0.93	T	0.38457	-0.9660	10	0.48119	T	0.1	.	15.3253	0.74157	0.0:1.0:0.0:0.0	.	42;52;24	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	Q	52;42;24;24	ENSP00000444896:P52Q;ENSP00000407031:P42Q;ENSP00000329448:P24Q	ENSP00000329448:P24Q	P	+	2	0	C15orf55	32427516	0.041000	0.20044	0.222000	0.23844	0.005000	0.04900	1.491000	0.35583	2.692000	0.91855	0.655000	0.94253	CCA		0.532	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34640224	C	A	34640224	3	1	111	1	0	0	0	0	1	0	0	0	1807	594	21	2	77	2	C15orf55	15	34640224	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	244100	34640224	67891168	795	29929										
RPUSD2	27079	hgsc.bcm.edu	37	chr15	40866329	40866329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccactctgtgcagagtgcCggctggtgcgacaggatccc	13	14	1	1	rs532193389		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:40866329C>T	ENST00000315616.7	+	3	1545	c.1507C>T	c.(1507-1509)Cgg>Tgg	p.R503W	RPUSD2_ENST00000559271.1_Missense_Mutation_p.R442W	NM_152260.1	NP_689473.1	Q8IZ73	RUSD2_HUMAN	RNA pseudouridylate synthase domain containing 2	503					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(4)|lung(4)|skin(3)	11		all_cancers(109;2.74e-14)|all_epithelial(112;1.64e-11)|Lung NSC(122;6.69e-09)|all_lung(180;1.22e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.1e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0786)		TGCAGAGTGCCGGCTGGTGCG	0.532													C|||	1	0.000199681	0	0.0014	5008	,	,		21886	0		0	False		,,,				2504	0															0			15											71	59	63					15																	40866329		2203	4300	6503	38653621	SO:0001583	missense	27079			AK055971	CCDS10061.1, CCDS66737.1	15q13.3	2013-02-11	2005-01-31	2005-02-07	ENSG00000166133	ENSG00000166133		"RNA pseudouridylate synthase domain containing"	24180	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 19"	C15orf19		12477932	Standard	NM_001286407		Approved	C18B11, FLJ31409	uc001zmd.1	Q8IZ73	OTTHUMG00000130031	ENST00000315616.7:c.1507C>T	15.37:g.40866329C>T	ENSP00000323288:p.Arg503Trp		38653621	B4DDD1|Q7L989|Q92939|Q96IA7|Q96N50	Missense_Mutation	SNP	ENST00000315616.7	37	CCDS10061.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.390051	0.61956	.	.	ENSG00000166133	ENST00000315616;ENST00000417769	T	0.33438	1.41	5.22	5.22	0.72569	Pseudouridine synthase, catalytic domain (1);	0.271892	0.39687	N	0.001288	T	0.52273	0.1724	M	0.76002	2.32	0.42532	D	0.993045	D	0.76494	0.999	D	0.67548	0.952	T	0.55134	-0.8188	10	0.72032	D	0.01	-13.7546	11.5676	0.50815	0.2914:0.7086:0.0:0.0	.	503	Q8IZ73	RUSD2_HUMAN	W	503;482	ENSP00000323288:R503W	ENSP00000323288:R503W	R	+	1	2	RPUSD2	38653621	1.000000	0.71417	0.997000	0.53966	0.858000	0.48976	4.199000	0.58426	2.717000	0.92951	0.563000	0.77884	CGG		0.532	RPUSD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252308.2	NM_152260		T	40866329	C	T	40866329	3	4	111	1	0	0	0	0	1	0	0	0	13704	643	23	1	1517	1	RPUSD2	15	40866329	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6226105	40866329	61665063	796	29930										
CHAC1	79094	hgsc.bcm.edu	37	chr15	41247727	41247727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accaaccactgaaggcattgGcctatgtggccaccccacag	9	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:41247727G>A	ENST00000446533.3	+	3	859	c.550G>A	c.(550-552)Gcc>Acc	p.A184T	CHAC1_ENST00000444189.2_Intron|CHAC1_ENST00000487220.1_5'UTR	NM_001142776.1|NM_024111.3	NP_001136248.1|NP_077016.2	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator homolog 1 (E. coli)	184					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein processing (GO:0010955)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|trans-Golgi network (GO:0005802)	Notch binding (GO:0005112)			endometrium(1)|large_intestine(1)|skin(1)	3		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		GAAGGCATTGGCCTATGTGGC	0.597																																																0			15											179	150	159					15																	41247727		2203	4300	6503	39035019	SO:0001583	missense	79094			BC019625	CCDS10070.2, CCDS45233.1	15q15.1	2013-09-12	2006-09-12		ENSG00000128965	ENSG00000128965			28680	protein-coding gene	gene with protein product	"gamma-GCT acting on glutathione homolog 1"	614587	"ChaC, cation transport regulator-like 1 (E. coli)"			23070364	Standard	NM_024111		Approved	MGC4504	uc001znh.2	Q9BUX1	OTTHUMG00000130208	ENST00000446533.3:c.550G>A	15.37:g.41247727G>A	ENSP00000398105:p.Ala184Thr		39035019	Q0VIA0	Missense_Mutation	SNP	ENST00000446533.3	37	CCDS10070.2	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371662	0.42003	.	.	ENSG00000128965	ENST00000446533	T	0.42131	0.98	6.03	5.11	0.69529	Butirosin biosynthesis, BtrG-like (1);	0.110266	0.64402	D	0.000011	T	0.26991	0.0661	N	0.02247	-0.625	0.80722	D	1	B	0.25486	0.127	B	0.35859	0.212	T	0.19386	-1.0307	10	0.37606	T	0.19	-26.1268	17.3355	0.87280	0.0:0.1252:0.8748:0.0	.	184	Q9BUX1	CHAC1_HUMAN	T	184	ENSP00000398105:A184T	ENSP00000398105:A184T	A	+	1	0	CHAC1	39035019	1.000000	0.71417	0.995000	0.50966	0.001000	0.01503	7.826000	0.86716	1.535000	0.49220	-0.175000	0.13238	GCC		0.597	CHAC1-001	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252526.3	NM_024111		A	41247727	G	A	41247727	3	1	111	1	0	0	0	0	1	0	0	0	3314	1203	42	3	560	3	CHAC1	15	41247727	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	381398	41247727	61283665	797	29931										
MGA	23269	hgsc.bcm.edu	37	chr15	42046641	42046642	+	Frame_Shift_Del	DEL	TG	TG	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgatgtatttcagaataacTgtgtagaatacattgaggat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	TG	TG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:42046641_42046642delTG	ENST00000570161.1	+	17	7015_7016	c.7015_7016delTG	c.(7015-7017)tgtfs	p.C2339fs	MGA_ENST00000545763.1_Frame_Shift_Del_p.C2130fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.C2300fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.C2130fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.C2339fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCAGAATAACTGTGTAGAATAC	0.381																																																0			15																																								39833934	SO:0001589	frameshift_variant	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7015_7016delTG	15.37:g.42046643_42046644delTG	ENSP00000457035:p.Cys2339fs		39833933	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	37	CCDS55959.1																																																																																				0.381	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42046642	TG	-	42046641	7	5	111	1	0	1	0	1	0	0	0	0	9570	1580	55	0	7081	0	MGA	15	42046641	Frame_Shift_Del	DEL	TG	TCGA-EI-6507-01A-11D-1733-10	798914	42046641	60484751	798	29932										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42107532	42107532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttacctgctcctcagacaacAccatccgcctgtggaacaca	6	16	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:42107532A>G	ENST00000456763.2	+	12	1460	c.1264A>G	c.(1264-1266)Acc>Gcc	p.T422A	MAPKBP1_ENST00000221214.6_Missense_Mutation_p.T299A|MAPKBP1_ENST00000260357.7_Intron|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.T416A|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.T416A	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	422										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		CTCAGACAACACCATCCGCCT	0.602																																																0			15											89	83	85					15																	42107532		2203	4300	6503	39894824	SO:0001583	missense	23005			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1264A>G	15.37:g.42107532A>G	ENSP00000393099:p.Thr422Ala		39894824	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	a	32	5.132889	0.94517	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000456763;ENST00000514566	T;T;T;T	0.69435	-0.4;0.35;-0.4;-0.4	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84074	0.5392	M	0.86651	2.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.87578	0.998;0.998;0.973	D	0.86507	0.1807	10	0.59425	D	0.04	-24.2414	15.9854	0.80147	1.0:0.0:0.0:0.0	.	416;422;416	O60336-2;O60336;O60336-6	.;MABP1_HUMAN;.	A	416;299;422;416	ENSP00000397570:T416A;ENSP00000221214:T299A;ENSP00000393099:T422A;ENSP00000426154:T416A	ENSP00000221214:T299A	T	+	1	0	MAPKBP1	39894824	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.169000	0.94788	2.175000	0.68902	0.454000	0.30748	ACC		0.602	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		G	42107532	A	G	42107532	3	3	111	1	0	0	0	0	1	0	0	0	9322	159	6	4	1306	4	MAPKBP1	15	42107532	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	60891	42107532	60423860	799	29933										
CAPN3	825	hgsc.bcm.edu	37	chr15	42701572	42701574	+	In_Frame_Del	DEL	AGG	AGG	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacattttcaagcagatagcAggagatgtgagtacctccaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AGG	AGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:42701572_42701574delAGG	ENST00000397163.3	+	17	2205_2207	c.1986_1988delAGG	c.(1984-1989)gcagga>gca	p.G663del	CAPN3_ENST00000357568.3_In_Frame_Del_p.G657del|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000397204.4_5'UTR|CAPN3_ENST00000337571.4_5'UTR|CAPN3_ENST00000356316.3_In_Frame_Del_p.G570del|CAPN3_ENST00000349748.3_In_Frame_Del_p.G571del|CAPN3_ENST00000561817.1_5'UTR|CAPN3_ENST00000318023.7_In_Frame_Del_p.G657del|CAPN3_ENST00000397200.4_In_Frame_Del_p.G151del	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	663	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGCAGATAGCAGGAGATGTGAGT	0.478																																																0			15																																								40488866	SO:0001651	inframe_deletion	825			X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1986_1988delAGG	15.37:g.42701572_42701574delAGG	ENSP00000380349:p.Gly663del		40488864	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	In_Frame_Del	DEL	ENST00000397163.3	37	CCDS45245.1																																																																																				0.478	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			-	42701574	AGG	-	42701572	7	5	111	1	0	1	0	1	0	0	0	0	2634	175	7	0	2104	0	CAPN3	15	42701572	In_Frame_Del	DEL	AGG	TCGA-EI-6507-01A-11D-1733-10	594040	42701572	59829820	800	29934										
TGM7	116179	hgsc.bcm.edu	37	chr15	43568766	43568766	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccagctttggtcgggtagaGgtccagttgaatttggaggg	16	6	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:43568766G>T	ENST00000452443.2	-	13	2024	c.2020C>A	c.(2020-2022)Ctc>Atc	p.L674I		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	674					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GTCGGGTAGAGGTCCAGTTGA	0.577																																																0			15											156	134	141					15																	43568766		2202	4299	6501	41356058	SO:0001583	missense	116179			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.2020C>A	15.37:g.43568766G>T	ENSP00000389466:p.Leu674Ile		41356058		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	G	0.979	-0.697826	0.03279	.	.	ENSG00000159495	ENST00000452443	T	0.66995	-0.24	4.61	2.57	0.30868	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.147023	0.45361	D	0.000368	T	0.61299	0.2336	L	0.32530	0.975	0.28102	N	0.931383	D	0.67145	0.996	D	0.65573	0.936	T	0.54984	-0.8211	10	0.08381	T	0.77	-15.5703	3.7723	0.08646	0.2031:0.0:0.6035:0.1934	.	674	Q96PF1	TGM7_HUMAN	I	674	ENSP00000389466:L674I	ENSP00000389466:L674I	L	-	1	0	TGM7	41356058	0.992000	0.36948	0.995000	0.50966	0.072000	0.16883	1.096000	0.30976	1.067000	0.40740	0.585000	0.79938	CTC		0.577	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43568766	G	T	43568766	3	4	111	1	0	0	0	0	1	0	0	0	15874	1000	35	2	116	2	TGM7	15	43568766	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	867194	43568766	58962626	801	29935										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43720315	43720315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccggattgttctcatgtgacGatgtaagacatggccatgtg	12	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:43720315G>A	ENST00000263801.3	-	18	3964	c.3712C>T	c.(3712-3714)Cgt>Tgt	p.R1238C	TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1243C|TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1243C|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1243C	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1238					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		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)		CTCATGTGACGATGTAAGACA	0.438								Other conserved DNA damage response genes																																								0			15											228	198	208					15																	43720315		2201	4298	6499	41507607	SO:0001583	missense	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3712C>T	15.37:g.43720315G>A	ENSP00000263801:p.Arg1238Cys		41507607	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659934	0.88154	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.09255	3.12;3.12;3.0;3.11	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.993;0.997;0.999;0.999	T	0.00785	-1.1567	10	0.87932	D	0	-8.1402	19.7689	0.96353	0.0:0.0:1.0:0.0	.	1243;1238;1243;1243	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	C	1238;1243;1243;1243	ENSP00000263801:R1238C;ENSP00000371475:R1243C;ENSP00000371470:R1243C;ENSP00000393497:R1243C	ENSP00000263801:R1238C	R	-	1	0	TP53BP1	41507607	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.853000	0.62911	2.747000	0.94245	0.650000	0.86243	CGT		0.438	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43720315	G	A	43720315	3	1	111	1	0	0	0	0	1	0	0	0	16423	1058	37	1	2250	1	TP53BP1	15	43720315	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	151549	43720315	58811077	802	29936										
PPIP5K1	9677	hgsc.bcm.edu	37	chr15	43831689	43831689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaagggggcttctcagagcGctgctggagttgcaggggag	18	9	1	1	rs202101760	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:43831689G>A	ENST00000396923.3	-	29	3599	c.3478C>T	c.(3478-3480)Cgc>Tgc	p.R1160C	PPIP5K1_ENST00000334933.4_Missense_Mutation_p.R1135C|PPIP5K1_ENST00000360135.4_Missense_Mutation_p.R1093C|PPIP5K1_ENST00000381879.4_Missense_Mutation_p.R1136C|PPIP5K1_ENST00000360301.4_Missense_Mutation_p.R1135C|PPIP5K1_ENST00000348806.6_Missense_Mutation_p.R1093C|PPIP5K1_ENST00000381885.1_Missense_Mutation_p.R1156C|PPIP5K1_ENST00000420765.1_Missense_Mutation_p.R1160C			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1	1160					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			large_intestine(1)	1						TTCTCAGAGCGCTGCTGGAGT	0.507													G|||	4	0.000798722	0	0	5008	,	,		17824	0.004		0	False		,,,				2504	0															0			15											81	78	79					15																	43831689		2201	4298	6499	41618981	SO:0001583	missense	9677			AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"histidine acid phosphatase domain containing 2A"	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.3478C>T	15.37:g.43831689G>A	ENSP00000380129:p.Arg1160Cys		41618981	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Missense_Mutation	SNP	ENST00000396923.3	37	CCDS45252.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	G	16.27	3.076826	0.55753	.	.	ENSG00000168781	ENST00000381885;ENST00000360301;ENST00000360135;ENST00000334933;ENST00000396923;ENST00000304953;ENST00000381878;ENST00000420765;ENST00000381879;ENST00000348806	T;T;T;T;T;T;T;T	0.25579	1.82;1.79;2.25;1.79;1.82;1.82;1.81;2.25	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.20861	0.0502	L	0.55481	1.735	0.47123	D	0.999321	B;B;B	0.14805	0.003;0.003;0.011	B;B;B	0.14023	0.01;0.002;0.005	T	0.03043	-1.1079	10	0.54805	T	0.06	-11.7042	15.6884	0.77430	0.0:0.0:1.0:0.0	.	1093;1160;1135	Q6PFW1-7;Q6PFW1;Q6PFW1-3	.;VIP1_HUMAN;.	C	1156;1135;1093;1135;1160;1160;1135;1160;1136;1093	ENSP00000371309:R1156C;ENSP00000353446:R1135C;ENSP00000353253:R1093C;ENSP00000334779:R1135C;ENSP00000380129:R1160C;ENSP00000400887:R1160C;ENSP00000371303:R1136C;ENSP00000308773:R1093C	ENSP00000304750:R1160C	R	-	1	0	PPIP5K1	41618981	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.545000	0.53648	2.628000	0.89032	0.557000	0.71058	CGC		0.507	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659		A	43831689	G	A	43831689	3	1	111	1	0	0	0	0	1	0	0	0	12366	1087	38	1	955	1	PPIP5K1	15	43831689	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	111374	43831689	58699703	803	29937										
PRTG	283659	hgsc.bcm.edu	37	chr15	55971556	55971556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accatgacatcttgggagagGggattccttctgcctgacac	11	11	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:55971556G>T	ENST00000389286.4	-	7	1108	c.1061C>A	c.(1060-1062)cCc>cAc	p.P354H	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		CTTGGGAGAGGGGATTCCTTC	0.413																																																0			15											123	111	115					15																	55971556		1836	4091	5927	53758848	SO:0001583	missense	283659			AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1061C>A	15.37:g.55971556G>T	ENSP00000373937:p.Pro354His		53758848		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125291	0.77436	.	.	ENSG00000166450	ENST00000389286	T	0.74526	-0.85	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90390	0.6992	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91676	0.5354	10	0.51188	T	0.08	-16.8019	18.8612	0.92273	0.0:0.0:1.0:0.0	.	354	Q2VWP7	PRTG_HUMAN	H	354	ENSP00000373937:P354H	ENSP00000373937:P354H	P	-	2	0	PRTG	53758848	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	9.400000	0.97290	2.690000	0.91761	0.591000	0.81541	CCC		0.413	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		T	55971556	G	T	55971556	3	4	111	1	0	0	0	0	1	0	0	0	12672	1232	43	2	2447	2	PRTG	15	55971556	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	12139867	55971556	46559836	804	29938										
RFX7	64864	hgsc.bcm.edu	37	chr15	56385803	56385803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agagaaatcagatgcagtatTagtgagatcagatgctccct	10	7	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:56385803T>C	ENST00000559447.2	-	9	4103	c.3832A>G	c.(3832-3834)Aat>Gat	p.N1278D	RFX7_ENST00000317318.6_Intron|RFX7_ENST00000423270.1_Missense_Mutation_p.N1375D|RFX7_ENST00000422057.1_Intron			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	1278					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GATGCAGTATTAGTGAGATCA	0.433																																																0			15											74	71	72					15																	56385803		1959	4147	6106	54173095	SO:0001583	missense	64864					15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.3832A>G	15.37:g.56385803T>C	ENSP00000453281:p.Asn1278Asp		54173095	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	T	9.161	1.018661	0.19355	.	.	ENSG00000181827	ENST00000423270	T	0.53423	0.62	5.65	5.65	0.86999	.	2.300670	0.03398	U	0.202881	T	0.43567	0.1253	N	0.24115	0.695	0.09310	N	1	B	0.19817	0.039	B	0.14023	0.01	T	0.38802	-0.9644	10	0.52906	T	0.07	-4.2798	15.0116	0.71555	0.0:0.0:0.0:1.0	.	1278	Q2KHR2	RFX7_HUMAN	D	1375	ENSP00000397644:N1375D	ENSP00000397644:N1375D	N	-	1	0	RFX7	54173095	0.995000	0.38212	0.008000	0.14137	0.954000	0.61252	3.605000	0.54088	2.279000	0.76181	0.533000	0.62120	AAT		0.433	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56385803	T	C	56385803	3	2	111	1	0	0	0	0	1	0	0	0	13305	1754	61	4	263	4	RFX7	15	56385803	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	414247	56385803	46145589	805	29939										
ZNF280D	54816	hgsc.bcm.edu	37	chr15	56959017	56959017	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttgtattaggtttacttgcGttggatttgactgtattagg	11	4	0	1	rs141387666	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:56959017G>A	ENST00000267807.7	-	15	1929	c.1713C>T	c.(1711-1713)aaC>aaT	p.N571N	ZNF280D_ENST00000396245.1_Silent_p.N275N|ZNF280D_ENST00000559000.1_Silent_p.N558N|ZNF280D_ENST00000559237.1_Silent_p.N558N	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N571K(1)		endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		GTTTACTTGCGTTGGATTTGA	0.343																																																1	Substitution - Missense(1)	endometrium(1)	15						G	,	1,4383	2.1+/-5.4	0,1,2191	141	147	145		1674,1713	-1.3	0	15	dbSNP_134	145	1,8583	1.2+/-3.3	0,1,4291	no	coding-synonymous,coding-synonymous	ZNF280D	NM_001002843.1,NM_017661.2	,	0,2,6482	AA,AG,GG		0.0116,0.0228,0.0154	,	558/967,571/980	56959017	2,12966	2192	4292	6484	54746309	SO:0001819	synonymous_variant	54816			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1713C>T	15.37:g.56959017G>A			54746309	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Silent	SNP	ENST00000267807.7	37	CCDS32245.1																																																																																				0.343	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		A	56959017	G	A	56959017	2	1	111	1	0	0	0	0	0	0	0	1	17856	1136	40	1		1	ZNF280D	15	56959017	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	573214	56959017	45572375	806	29940										
NARG2	79664	hgsc.bcm.edu	37	chr15	60768348	60768349	+	De_novo_Start_OutOfFrame	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaaaaatgtcttaaggccaINStttttgggggaaatatccct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:60768348_60768349insT	ENST00000439632.1	-	0	293_294				NARG2_ENST00000561114.1_Frame_Shift_Ins_p.N20fs|NARG2_ENST00000558654.1_5'UTR|NARG2_ENST00000261520.4_Frame_Shift_Ins_p.N20fs	NM_001018089.1	NP_001018099.1														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TCTTAAGGCCATTTTTGGGGGA	0.317																																																0			15																																								58555641			79664																														ENST00000439632.1:c.-193->A	15.37:g.60768353_60768353dupT			58555640		Frame_Shift_Ins	INS	ENST00000439632.1	37																																																																																					0.317	NARG2-201	KNOWN	basic	protein_coding	protein_coding				T	60768349	-	T	60768348	6	5	111	1	0	1	1	0	0	0	0	0	10199	214	8	0		0	NARG2	15	60768348	De_novo_Start_OutOfFrame	INS	-	TCGA-EI-6507-01A-11D-1733-10	3809331	60768348	41763044	807	29941										
HERC1	8925	hgsc.bcm.edu	37	chr15	64048879	64048879	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggcccagtctcccatagctGcctttcccgcaagctctaac	7	17	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:64048879G>A	ENST00000443617.2	-	5	1377	c.1290C>T	c.(1288-1290)ggC>ggT	p.G430G		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	430					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TCCCATAGCTGCCTTTCCCGC	0.383																																																0			15											27	26	26					15																	64048879		1868	4108	5976	61835932	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.1290C>T	15.37:g.64048879G>A			61835932	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.383	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	64048879	G	A	64048879	2	1	111	1	0	0	0	0	0	0	0	1	7078	1306	46	3		3	HERC1	15	64048879	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3280531	64048879	38482513	808	29942										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68661571	68661571	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcactggacacttgtacacGtctcccgtcttctggtagcc	8	14	4	0	rs185148260	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:68661571G>A	ENST00000315757.7	-	3	302	c.216C>T	c.(214-216)gaC>gaT	p.D72D	ITGA11_ENST00000423218.2_Silent_p.D72D	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	72					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						ACTTGTACACGTCTCCCGTCT	0.552													G|||	6	0.00119808	0.0038	0.0014	5008	,	,		14674	0		0	False		,,,				2504	0															0			15						G		37,4105		0,37,2034	139	143	141		216	-0.5	1	15		141	1,8429		0,1,4214	no	coding-synonymous	ITGA11	NM_001004439.1		0,38,6248	AA,AG,GG		0.0119,0.8933,0.3023		72/1189	68661571	38,12534	2071	4215	6286	66448625	SO:0001819	synonymous_variant	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.216C>T	15.37:g.68661571G>A			66448625	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																				0.552	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		A	68661571	G	A	68661571	2	1	111	1	0	0	0	0	0	0	0	1	7895	1136	40	1		1	ITGA11	15	68661571	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4612692	68661571	33869821	809	29943										
TLE3	7090	hgsc.bcm.edu	37	chr15	70345690	70345690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agatgtctatgcagctggccCcatctgtgtggccctggaac	12	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:70345690C>T	ENST00000558939.1	-	17	3236	c.1859G>A	c.(1858-1860)gGg>gAg	p.G620E	TLE3_ENST00000451782.2_Missense_Mutation_p.G617E|TLE3_ENST00000557907.1_Missense_Mutation_p.G612E|TLE3_ENST00000558379.1_Missense_Mutation_p.G615E|TLE3_ENST00000442299.2_Missense_Mutation_p.G612E|TLE3_ENST00000317509.8_Missense_Mutation_p.G608E|TLE3_ENST00000560939.1_Missense_Mutation_p.G622E|TLE3_ENST00000557997.1_Missense_Mutation_p.G612E|TLE3_ENST00000559929.1_Missense_Mutation_p.G630E|TLE3_ENST00000559048.1_Missense_Mutation_p.G620E|TLE3_ENST00000440567.3_Missense_Mutation_p.G610E|TLE3_ENST00000560589.1_Missense_Mutation_p.G564E|TLE3_ENST00000559191.1_Missense_Mutation_p.G201E|TLE3_ENST00000539550.1_Missense_Mutation_p.G547E|TLE3_ENST00000558201.1_Missense_Mutation_p.G626E	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	620					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GCAGCTGGCCCCATCTGTGTG	0.647																																																0			15											57	60	59					15																	70345690		2106	4251	6357	68132744	SO:0001583	missense	7090			M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"WD repeat domain containing"	11839	protein-coding gene	gene with protein product		600190	"transducin-like enhancer of split 3, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1859G>A	15.37:g.70345690C>T	ENSP00000452871:p.Gly620Glu		68132744	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.659552	0.88154	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.68274	0.2983	L	0.33485	1.01	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.70357	-0.4894	10	0.62326	D	0.03	-3.0698	18.3882	0.90473	0.0:1.0:0.0:0.0	.	610;617;612;615;608;620;620;547	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	E	612;617;620;610;547	ENSP00000390007:G612E;ENSP00000394717:G617E;ENSP00000415057:G610E;ENSP00000442594:G547E	ENSP00000319233:G620E	G	-	2	0	TLE3	68132744	1.000000	0.71417	0.999000	0.59377	0.717000	0.41224	7.512000	0.81728	2.686000	0.91538	0.561000	0.74099	GGG		0.647	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		T	70345690	C	T	70345690	3	4	111	1	0	0	0	0	1	0	0	0	15979	623	22	3	475	3	TLE3	15	70345690	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1684119	70345690	32185702	810	29944										
UACA	55075	hgsc.bcm.edu	37	chr15	70987400	70987400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caactccatgtataaggatgGcattcaaacactcaagattc	6	10	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:70987400G>A	ENST00000322954.6	-	3	442	c.257C>T	c.(256-258)gCc>gTc	p.A86V	UACA_ENST00000539319.1_Missense_Mutation_p.A86V|UACA_ENST00000560441.1_Missense_Mutation_p.A73V|UACA_ENST00000379983.2_Missense_Mutation_p.A73V	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	86					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TATAAGGATGGCATTCAAACA	0.348																																																0			15											109	101	104					15																	70987400		2199	4297	6496	68774454	SO:0001583	missense	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.257C>T	15.37:g.70987400G>A	ENSP00000314556:p.Ala86Val		68774454	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	g	11.85	1.762599	0.31228	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	T;T;T	0.64618	-0.09;-0.09;-0.11	5.61	4.7	0.59300	Ankyrin repeat-containing domain (4);	0.226670	0.31145	N	0.008178	T	0.32102	0.0818	N	0.03016	-0.435	0.09310	N	0.999995	B;B;B;B	0.16603	0.001;0.005;0.013;0.018	B;B;B;B	0.20955	0.006;0.032;0.032;0.011	T	0.21042	-1.0257	10	0.02654	T	1	-6.0242	10.9183	0.47150	0.143:0.0:0.857:0.0	.	86;86;86;73	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	V	86;73;73;86	ENSP00000314556:A86V;ENSP00000369319:A73V;ENSP00000438667:A86V	ENSP00000314556:A86V	A	-	2	0	UACA	68774454	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.315000	0.51951	1.384000	0.46424	-0.127000	0.14921	GCC		0.348	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			A	70987400	G	A	70987400	3	1	111	1	0	0	0	0	1	0	0	0	16864	1203	42	3	4061	3	UACA	15	70987400	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	641710	70987400	31543992	811	29945										
TMEM202	338949	hgsc.bcm.edu	37	chr15	72691085	72691085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcacacatctacatccgaaCgctctgtggcagcctctgta	9	14	3	0	rs147492128	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:72691085C>T	ENST00000341689.3	+	2	227	c.173C>T	c.(172-174)aCg>aTg	p.T58M	TMEM202_ENST00000567679.1_Intron	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	58						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						TACATCCGAACGCTCTGTGGC	0.522													C|||	3	0.000599042	0	0.0014	5008	,	,		19497	0		0.002	False		,,,				2504	0															0			15						C	MET/THR	1,4397	2.1+/-5.4	0,1,2198	157	111	127		173	2.2	1	15	dbSNP_134	127	8,8586	6.4+/-24.3	0,8,4289	yes	missense	TMEM202	NM_001080462.1	81	0,9,6487	TT,TC,CC		0.0931,0.0227,0.0693	benign	58/274	72691085	9,12983	2199	4297	6496	70478139	SO:0001583	missense	338949				CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.173C>T	15.37:g.72691085C>T	ENSP00000340212:p.Thr58Met		70478139		Missense_Mutation	SNP	ENST00000341689.3	37	CCDS32287.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	0.003	-2.445162	0.00178	2.27E-4	9.31E-4	ENSG00000187806	ENST00000341689	T	0.42513	0.97	4.47	2.15	0.27550	.	0.427236	0.20657	N	0.088087	T	0.09468	0.0233	N	0.00392	-1.555	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21552	-1.0242	10	0.06099	T	0.92	-27.5485	5.9751	0.19373	0.0:0.2102:0.0:0.7898	.	58	A6NGA9	TM202_HUMAN	M	58	ENSP00000340212:T58M	ENSP00000340212:T58M	T	+	2	0	TMEM202	70478139	1.000000	0.71417	0.970000	0.41538	0.001000	0.01503	0.447000	0.21710	0.265000	0.21872	-0.238000	0.12139	ACG		0.522	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		T	72691085	C	T	72691085	3	4	111	1	0	0	0	0	1	0	0	0	16166	536	19	1	179	1	TMEM202	15	72691085	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1703685	72691085	29840307	812	29946										
ISLR2	57611	hgsc.bcm.edu	37	chr15	74426457	74426457	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagatcctcgcggacccggcGgaggagcagcgctgtggcaa	16	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:74426457G>A	ENST00000361742.3	+	4	2131	c.1362G>A	c.(1360-1362)gcG>gcA	p.A454A	ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Silent_p.A454A|ISLR2_ENST00000419208.1_Silent_p.A454A|ISLR2_ENST00000445793.1_Silent_p.A454A|ISLR2_ENST00000453268.2_Silent_p.A454A|ISLR2_ENST00000565540.1_Silent_p.A454A|ISLR2_ENST00000435464.1_Silent_p.A454A	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	454					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CGGACCCGGCGGAGGAGCAGC	0.657																																																0			15											31	34	33					15																	74426457		2196	4297	6493	72213510	SO:0001819	synonymous_variant	57611				CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1362G>A	15.37:g.74426457G>A			72213510	A8K352|Q9P263	Silent	SNP	ENST00000361742.3	37	CCDS10259.1																																																																																				0.657	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		A	74426457	G	A	74426457	2	1	111	1	0	0	0	0	0	0	0	1	7880	1103	39	1		1	ISLR2	15	74426457	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1735372	74426457	28104935	813	29947										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74703249	74703249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtggcgccatgagtaggtggCgtggcgggattccatggggc	20	8	0	1	rs371438755		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:74703249C>T	ENST00000261918.4	-	14	2265	c.1717G>A	c.(1717-1719)Gcc>Acc	p.A573T	SEMA7A_ENST00000543145.2_Missense_Mutation_p.A559T|SEMA7A_ENST00000542748.1_Missense_Mutation_p.A408T	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	573	Ig-like C2-type.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GAGTAGGTGGCGTGGCGGGAT	0.617																																																0			15						C	THR/ALA,THR/ALA,THR/ALA	0,4394		0,0,2197	104	104	104		1675,1222,1717	4.6	1	15		104	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense,missense	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	58,58,58	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	559/653,408/502,573/667	74703249	1,12985	2197	4296	6493	72490302	SO:0001583	missense	8482			AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1717G>A	15.37:g.74703249C>T	ENSP00000261918:p.Ala573Thr		72490302	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	37	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682258	0.88542	0.0	1.16E-4	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.12465	2.68;2.68;2.68	4.55	4.55	0.56014	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.133831	0.50627	D	0.000120	T	0.33847	0.0877	L	0.59436	1.845	0.51767	D	0.999939	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.08166	-1.0735	10	0.87932	D	0	-23.8916	15.1022	0.72288	0.0:1.0:0.0:0.0	.	559;573	F5H1S0;O75326	.;SEM7A_HUMAN	T	573;559;408	ENSP00000261918:A573T;ENSP00000438966:A559T;ENSP00000441493:A408T	ENSP00000261918:A573T	A	-	1	0	SEMA7A	72490302	0.998000	0.40836	0.996000	0.52242	0.997000	0.91878	4.873000	0.63057	2.094000	0.63399	0.555000	0.69702	GCC		0.617	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		T	74703249	C	T	74703249	3	4	111	1	0	0	0	0	1	0	0	0	14080	768	27	1	287	1	SEMA7A	15	74703249	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	276792	74703249	27828143	814	29948										
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75116785	75116785	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctgttctacctcctcattCagactgtaggcttcttcggc	7	14	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:75116785C>T	ENST00000309664.5	+	13	1556	c.1417C>T	c.(1417-1419)Cag>Tag	p.Q473*	RP11-414J4.2_ENST00000564823.1_RNA|CPLX3_ENST00000395018.4_5'Flank|LMAN1L_ENST00000379709.3_Nonsense_Mutation_p.Q461*	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	473						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.Q473E(1)		NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCTCCTCATTCAGACTGTAGG	0.597																																																1	Substitution - Missense(1)	urinary_tract(1)	15											120	117	118					15																	75116785		2197	4295	6492	72903838	SO:0001587	stop_gained	79748			AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.1417C>T	15.37:g.75116785C>T	ENSP00000310431:p.Gln473*		72903838	Q6UWN2	Nonsense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.716539	0.89205	.	.	ENSG00000140506	ENST00000309664;ENST00000379709	.	.	.	4.88	4.88	0.63580	.	0.000000	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.8981	0.63785	0.0:1.0:0.0:0.0	.	.	.	.	X	473;461	.	ENSP00000310431:Q473X	Q	+	1	0	LMAN1L	72903838	0.985000	0.35326	0.897000	0.35233	0.504000	0.33889	3.409000	0.52657	2.429000	0.82318	0.561000	0.74099	CAG		0.597	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			T	75116785	C	T	75116785	4	4	111	1	0	0	0	0	0	1	0	0	8861	827	29	3	1467	3	LMAN1L	15	75116785	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	413536	75116785	27414607	815	29949										
TSPAN3	10099	hgsc.bcm.edu	37	chr15	77339191	77339191	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtcaactatgcataggttcCgccagtgatgaggagctcgt	12	9	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:77339191C>T	ENST00000267970.4	-	7	1021	c.748G>A	c.(748-750)Gga>Aga	p.G250R	TSPAN3_ENST00000561277.1_Missense_Mutation_p.G42R|TSPAN3_ENST00000559494.1_Missense_Mutation_p.G161R|TSPAN3_ENST00000558745.1_Missense_Mutation_p.G42R|TSPAN3_ENST00000346495.2_Missense_Mutation_p.G225R|TSPAN3_ENST00000424443.3_Missense_Mutation_p.G186R|RP11-797A18.3_ENST00000560446.1_lincRNA	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	250						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		GCATAGGTTCCGCCAGTGATG	0.488																																																0			15											77	59	65					15																	77339191		2196	4294	6490	75126246	SO:0001583	missense	10099				CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"Tetraspanins"	17752	protein-coding gene	gene with protein product		613134	"transmembrane 4 superfamily member 8"	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.748G>A	15.37:g.77339191C>T	ENSP00000267970:p.Gly250Arg		75126246	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	Missense_Mutation	SNP	ENST00000267970.4	37	CCDS10292.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721184	0.89205	.	.	ENSG00000140391	ENST00000267970;ENST00000424443;ENST00000423920;ENST00000346495	T;T;T	0.53857	1.0;0.6;0.91	5.94	5.94	0.96194	.	0.102569	0.64402	D	0.000004	T	0.53384	0.1793	L	0.56769	1.78	0.58432	D	0.999999	B;B;B;P	0.48998	0.08;0.05;0.002;0.918	B;B;B;B	0.39876	0.013;0.005;0.002;0.312	T	0.58725	-0.7586	10	0.56958	D	0.05	.	20.3594	0.98849	0.0:1.0:0.0:0.0	.	186;212;225;250	B4DP19;B4DEK8;A6NEH4;O60637	.;.;.;TSN3_HUMAN	R	250;186;213;225	ENSP00000267970:G250R;ENSP00000407243:G186R;ENSP00000341329:G225R	ENSP00000267970:G250R	G	-	1	0	TSPAN3	75126246	0.999000	0.42202	0.289000	0.24876	0.749000	0.42624	4.750000	0.62162	2.816000	0.96949	0.563000	0.77884	GGA		0.488	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724		T	77339191	C	T	77339191	3	4	111	1	0	0	0	0	1	0	0	0	16685	661	23	1	17	1	TSPAN3	15	77339191	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2222406	77339191	25192201	816	29950										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82422829	82422829	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acttccgggcttggttctcaGagtcagccttctccccaaag	9	14	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:82422829G>T	ENST00000268206.7	-	20	3416	c.3248C>A	c.(3247-3249)tCt>tAt	p.S1083Y	EFTUD1_ENST00000359445.3_Missense_Mutation_p.S1032Y	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	1083					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TTGGTTCTCAGAGTCAGCCTT	0.488																																																0			15											144	136	139					15																	82422829		1948	4153	6101	80209884	SO:0001583	missense	79631			AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.3248C>A	15.37:g.82422829G>T	ENSP00000268206:p.Ser1083Tyr		80209884	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	37	CCDS42071.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082741	0.76528	.	.	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.66460	-0.21;0.05	5.07	4.14	0.48551	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (1);	0.000000	0.39615	N	0.001314	T	0.76492	0.3995	L	0.47190	1.495	0.80722	D	1	D;P	0.76494	0.999;0.93	D;P	0.77557	0.99;0.496	T	0.78031	-0.2363	10	0.52906	T	0.07	-23.267	15.9112	0.79475	0.0:0.1355:0.8645:0.0	.	1032;1083	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	Y	1083;1032	ENSP00000268206:S1083Y;ENSP00000352418:S1032Y	ENSP00000268206:S1083Y	S	-	2	0	EFTUD1	80209884	1.000000	0.71417	0.056000	0.19401	0.922000	0.55478	9.556000	0.98127	1.253000	0.44018	-0.165000	0.13383	TCT		0.488	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		T	82422829	G	T	82422829	3	4	111	1	0	0	0	0	1	0	0	0	4971	942	33	2	118	2	EFTUD1	15	82422829	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5083638	82422829	20108563	817	29951										
BNC1	646	hgsc.bcm.edu	37	chr15	83935798	83935798	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctggcttgttggatacatGggggggatccttagcttact							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:83935798delG	ENST00000345382.2	-	3	310	c.225delC	c.(223-225)cccfs	p.P75fs	BNC1_ENST00000569704.1_Frame_Shift_Del_p.P68fs|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	75					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						TTGGATACATGGGGGGGATCC	0.423																																																0			15											51	50	51					15																	83935798		2203	4300	6503	81726802	SO:0001589	frameshift_variant	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.225delC	15.37:g.83935798delG	ENSP00000307041:p.Pro75fs		81726802	Q15840	Frame_Shift_Del	DEL	ENST00000345382.2	37	CCDS10324.1																																																																																				0.423	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		-	83935798	G	-	83935798	7	5	111	1	0	1	0	1	0	0	0	0	1475	1335	47	0	2771	0	BNC1	15	83935798	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1512969	83935798	18595594	818	29952										
SH3GL3	6457	hgsc.bcm.edu	37	chr15	84241320	84241320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tatgttttctattcaaggcaAtgcattgatagaagttggtg	10	4	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:84241320A>G	ENST00000427482.2	+	5	641	c.335A>G	c.(334-336)aAt>aGt	p.N112S	SH3GL3_ENST00000535412.1_Missense_Mutation_p.N112S|SH3GL3_ENST00000434347.1_Missense_Mutation_p.N120S|SH3GL3_ENST00000324537.5_Missense_Mutation_p.N120S	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	112	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						ATTCAAGGCAATGCATTGATA	0.343																																																0			15											107	96	99					15																	84241320		2203	4300	6503	82032324	SO:0001583	missense	6457			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.335A>G	15.37:g.84241320A>G	ENSP00000391372:p.Asn112Ser		82032324	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	A	9.435	1.086563	0.20390	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	5.25	-3.71	0.04424	BAR (3);	1.168630	0.05802	N	0.612393	T	0.35364	0.0929	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20240	-1.0281	10	0.08381	T	0.77	-25.3328	4.6069	0.12382	0.2613:0.1165:0.4961:0.1261	.	112;112;120	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	S	112;112;120;120	ENSP00000391372:N112S;ENSP00000439239:N112S;ENSP00000320092:N120S;ENSP00000397871:N120S	ENSP00000320092:N120S	N	+	2	0	SH3GL3	82032324	0.000000	0.05858	0.235000	0.24058	0.972000	0.66771	0.026000	0.13599	-0.449000	0.07117	0.477000	0.44152	AAT		0.343	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		G	84241320	A	G	84241320	3	3	111	1	0	0	0	0	1	0	0	0	14289	101	4	4	353	4	SH3GL3	15	84241320	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	305522	84241320	18290072	819	29953										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89448988	89448988	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccgcacccccagcactcacCgttcagctcacagcccagta	6	21	3	0	rs148279922	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:89448988C>A	ENST00000566497.1	-	5	746	c.685G>T	c.(685-687)Gga>Tga	p.G229*	MFGE8_ENST00000268150.8_Splice_Site_p.G229*|MFGE8_ENST00000268151.7_Splice_Site_p.G229*|MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000542878.1_Splice_Site_p.G185*|MFGE8_ENST00000539437.1_Splice_Site_p.G221*			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	229					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CAGCACTCACCGTTCAGCTCA	0.612																																																0			15											83	77	79					15																	89448988		2200	4299	6499	87249992	SO:0001630	splice_region_variant	4240			U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.685+1G>T	15.37:g.89448988C>A			87249992	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Nonsense_Mutation	SNP	ENST00000566497.1	37	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789037	0.70337	.	.	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437;ENST00000542878	.	.	.	4.97	4.97	0.65823	.	0.047868	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.2886	17.8179	0.88640	0.0:1.0:0.0:0.0	.	.	.	.	X	229;229;221;185	.	.	G	-	1	0	MFGE8	87249992	1.000000	0.71417	1.000000	0.80357	0.022000	0.10575	7.465000	0.80898	2.764000	0.94973	0.555000	0.69702	GGA		0.612	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	Nonsense_Mutation	A	89448988	C	A	89448988	5	1	111	1	0	0	0	0	0	0	1	0	9550	666	23	2	494	2	MFGE8	15	89448988	Splice_Site	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5207668	89448988	13082404	820	29954										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90163022	90163022	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccttctattctgtgtctcagCcgaagtctcgaagtgtgcaa	9	11	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:90163022C>T	ENST00000268138.7	+	18	3208	c.3103C>T	c.(3103-3105)Ccg>Tcg	p.P1035S	TICRR_ENST00000560985.1_Missense_Mutation_p.P1034S|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1035					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TGTGTCTCAGCCGAAGTCTCG	0.473																																																0			15											118	113	115					15																	90163022		1943	4149	6092	87964026	SO:0001583	missense	90381			AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.3103C>T	15.37:g.90163022C>T	ENSP00000268138:p.Pro1035Ser		87964026	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	C	14.24	2.475750	0.44044	.	.	ENSG00000140534	ENST00000268138	T	0.11821	2.74	5.31	3.42	0.39159	.	0.255650	0.39909	N	0.001238	T	0.28995	0.0720	M	0.70275	2.135	0.80722	D	1	D	0.64830	0.994	P	0.58721	0.844	T	0.02184	-1.1199	10	0.72032	D	0.01	-6.6211	10.4375	0.44443	0.1342:0.7962:0.0:0.0696	.	1035	Q7Z2Z1	TICRR_HUMAN	S	1035	ENSP00000268138:P1035S	ENSP00000268138:P1035S	P	+	1	0	C15orf42	87964026	0.934000	0.31675	0.894000	0.35097	0.063000	0.16089	1.167000	0.31847	0.790000	0.33803	-0.182000	0.12963	CCG		0.473	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		T	90163022	C	T	90163022	3	4	111	1	0	0	0	0	1	0	0	0	1800	739	26	3	3173	3	C15orf42	15	90163022	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	714034	90163022	12368370	821	29955										
FURIN	5045	hgsc.bcm.edu	37	chr15	91421496	91421496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agacagtggatgggccagccCgcctcgccgaggaggccttc	15	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:91421496C>T	ENST00000268171.3	+	8	1081	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	268	Peptidase S8.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TGGGCCAGCCCGCCTCGCCGA	0.647																																																0			15											51	44	46					15																	91421496		2198	4298	6496	89222500	SO:0001583	missense	5045			X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.802C>T	15.37:g.91421496C>T	ENSP00000268171:p.Arg268Cys		89222500	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934545	0.73442	.	.	ENSG00000140564	ENST00000268171	D	0.87809	-2.3	4.58	4.58	0.56647	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.128378	0.53938	D	0.000049	D	0.89853	0.6835	L	0.58810	1.83	0.58432	D	0.999998	D	0.53312	0.959	P	0.57720	0.826	D	0.90228	0.4277	10	0.59425	D	0.04	-20.2436	12.6933	0.56988	0.1646:0.8354:0.0:0.0	.	268	P09958	FURIN_HUMAN	C	268	ENSP00000268171:R268C	ENSP00000268171:R268C	R	+	1	0	FURIN	89222500	1.000000	0.71417	0.990000	0.47175	0.806000	0.45545	4.655000	0.61476	2.383000	0.81215	0.555000	0.69702	CGC		0.647	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91421496	C	T	91421496	3	4	111	1	0	0	0	0	1	0	0	0	6118	652	23	1	828	1	FURIN	15	91421496	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1258474	91421496	11109896	822	29956										
FURIN	5045	hgsc.bcm.edu	37	chr15	91424956	91424956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcgctctggctttagttttCggggggtgaaggtgtacacc	15	8	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:91424956C>T	ENST00000268171.3	+	16	2512	c.2233C>T	c.(2233-2235)Cgg>Tgg	p.R745W	FES_ENST00000394302.1_5'Flank|FES_ENST00000414248.2_5'Flank|FES_ENST00000328850.3_5'Flank	NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	745					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CTTTAGTTTTCGGGGGGTGAA	0.617																																																0			15											130	120	123					15																	91424956		2198	4298	6496	89225960	SO:0001583	missense	5045			X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.2233C>T	15.37:g.91424956C>T	ENSP00000268171:p.Arg745Trp		89225960	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.164992	0.38217	.	.	ENSG00000140564	ENST00000268171	T	0.71579	-0.58	5.17	5.17	0.71159	.	0.404550	0.27130	N	0.020783	T	0.66025	0.2748	L	0.51422	1.61	0.38653	D	0.951881	B	0.15473	0.013	B	0.08055	0.003	T	0.67197	-0.5731	10	0.72032	D	0.01	-24.4532	14.3353	0.66584	0.0:0.8516:0.1484:0.0	.	745	P09958	FURIN_HUMAN	W	745	ENSP00000268171:R745W	ENSP00000268171:R745W	R	+	1	2	FURIN	89225960	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.061000	0.49963	2.419000	0.82065	0.555000	0.69702	CGG		0.617	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91424956	C	T	91424956	3	4	111	1	0	0	0	0	1	0	0	0	6118	875	31	1	2291	1	FURIN	15	91424956	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3460	91424956	11106436	823	29957										
FES	2242	hgsc.bcm.edu	37	chr15	91434219	91434219	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcccttgcccagctccctcCaccgctgcagctcattccgg	7	21	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr15:91434219C>A	ENST00000328850.3	+	11	1470	c.1328C>A	c.(1327-1329)cCa>cAa	p.P443Q	FES_ENST00000394302.1_Intron|FES_ENST00000394300.3_Missense_Mutation_p.P385Q|FES_ENST00000414248.2_Intron|FES_ENST00000450438.2_Intron|FES_ENST00000448367.1_3'UTR|FES_ENST00000444422.2_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	443					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CAGCTCCCTCCACCGCTGCAG	0.647																																																0			15											25	26	26					15																	91434219		2194	4290	6484	89235223	SO:0001583	missense	2242			X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"SH2 domain containing"	3657	protein-coding gene	gene with protein product	"Oncogene FES, feline sarcoma virus", "c-fes/fps protein"	190030	"feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog", "feline sarcoma oncogene"			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.1328C>A	15.37:g.91434219C>A	ENSP00000331504:p.Pro443Gln		89235223	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	37	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.097676	0.56075	.	.	ENSG00000182511	ENST00000328850;ENST00000394300	T;T	0.62788	-0.0;-0.0	4.42	4.42	0.53409	.	0.176879	0.50627	D	0.000120	T	0.75213	0.3819	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.98;0.988;0.972	T	0.77270	-0.2650	10	0.54805	T	0.06	-18.6661	17.2641	0.87081	0.0:1.0:0.0:0.0	.	425;385;443	B4DUD9;P07332-3;P07332	.;.;FES_HUMAN	Q	443;385	ENSP00000331504:P443Q;ENSP00000377837:P385Q	ENSP00000331504:P443Q	P	+	2	0	FES	89235223	0.992000	0.36948	0.846000	0.33378	0.338000	0.28826	5.275000	0.65575	2.299000	0.77371	0.478000	0.44815	CCA		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		A	91434219	C	A	91434219	3	1	111	1	0	0	0	0	1	0	0	0	5839	594	21	2	1366	2	FES	15	91434219	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9263	91434219	11097173	824	29958										
SOLH	6650	hgsc.bcm.edu	37	chr16	597763	597763	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccacggagggtggcaccagcCgcgtagaggccggcagctcc	16	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:597763C>A	ENST00000219611.2	+	4	1288	c.925C>A	c.(925-927)Cgc>Agc	p.R309S	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	309					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGGCACCAGCCGCGTAGAGGC	0.692																																																0			16											20	22	21					16																	597763		2173	4272	6445	537764	SO:0001583	missense	6650			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.925C>A	16.37:g.597763C>A	ENSP00000219611:p.Arg309Ser		537764	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	4.646	0.120143	0.08881	.	.	ENSG00000103326	ENST00000219611;ENST00000397687	D	0.88354	-2.37	4.69	2.72	0.32119	.	2.047000	0.02434	N	0.083840	T	0.80199	0.4579	N	0.14661	0.345	0.09310	N	1	B	0.28350	0.208	B	0.20384	0.029	T	0.66941	-0.5796	10	0.22706	T	0.39	.	8.4107	0.32642	0.0:0.8176:0.0:0.1824	.	309	O75808	CAN15_HUMAN	S	309	ENSP00000219611:R309S	ENSP00000219611:R309S	R	+	1	0	SOLH	537764	0.968000	0.33430	0.010000	0.14722	0.342000	0.28953	3.613000	0.54152	0.418000	0.25898	0.556000	0.70494	CGC		0.692	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		A	597763	C	A	597763	3	1	111	1	0	0	0	0	1	0	0	0	14962	652	23	2	927	2	SOLH	16	597763	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		597763	89756990	825	29959										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1254137	1254137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccgtgccctggaggacccGgagggtgagctcagcggctc	16	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:1254137G>A	ENST00000348261.5	+	10	2378	c.2130G>A	c.(2128-2130)ccG>ccA	p.P710P	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Silent_p.P710P|CACNA1H_ENST00000358590.4_Silent_p.P710P	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	710					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGGAGGACCCGGAGGGTGAGC	0.687																																																0			16											19	25	23					16																	1254137		2107	4239	6346	1194138	SO:0001819	synonymous_variant	8912			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2130G>A	16.37:g.1254137G>A			1194138	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																				0.687	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1254137	G	A	1254137	2	1	111	1	0	0	0	0	0	0	0	1	2551	1103	39	1		1	CACNA1H	16	1254137	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	656374	1254137	89100616	826	29960										
IGFALS	3483	hgsc.bcm.edu	37	chr16	1841430	1841430	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggccctcaaagctgcgctcaGccagctgccggatgcggttg	14	14	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:1841430G>C	ENST00000215539.3	-	2	1099	c.989C>G	c.(988-990)gCt>gGt	p.A330G	IGFALS_ENST00000415638.3_Missense_Mutation_p.A368G			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	330					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						GCTGCGCTCAGCCAGCTGCCG	0.662																																																0			16											29	31	30					16																	1841430		2197	4299	6496	1781431	SO:0001583	missense	3483			M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.989C>G	16.37:g.1841430G>C	ENSP00000215539:p.Ala330Gly		1781431	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.642948	0.00792	.	.	ENSG00000099769	ENST00000215539;ENST00000415638	T;T	0.22945	1.93;1.93	5.22	1.97	0.26223	.	0.571386	0.18561	N	0.137630	T	0.09512	0.0234	N	0.03281	-0.365	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.28586	-1.0039	10	0.26408	T	0.33	.	6.1707	0.20416	0.164:0.3043:0.5318:0.0	.	368;330	E9PGU3;P35858	.;ALS_HUMAN	G	330;368	ENSP00000215539:A330G;ENSP00000416683:A368G	ENSP00000215539:A330G	A	-	2	0	IGFALS	1781431	0.000000	0.05858	0.068000	0.19968	0.010000	0.07245	0.294000	0.19047	0.558000	0.29135	0.561000	0.74099	GCT		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			C	1841430	G	C	1841430	3	2	111	1	0	0	0	0	1	0	0	0	7598	971	34	5	832	5	IGFALS	16	1841430	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	587293	1841430	88513323	827	29961										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786783	3786783	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgtaatcatctccttcactTggaggacaggcccagatgtg	10	10	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:3786783T>A	ENST00000262367.5	-	27	5237	c.4428A>T	c.(4426-4428)ccA>ccT	p.P1476P	CREBBP_ENST00000382070.3_Silent_p.P1438P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1476	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTCCTTCACTTGGAGGACAGG	0.507			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											186	158	167					16																	3786783		2197	4300	6497	3726784	SO:0001819	synonymous_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4428A>T	16.37:g.3786783T>A			3726784	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.507	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3786783	T	A	3786783	2	1	111	1	0	0	0	0	0	0	0	1	3867	1799	63	5		5	CREBBP	16	3786783	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1945353	3786783	86567970	828	29962										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3801731	3801731	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaggacggtacttacgtctGgggctgtgaagggtcgtcac	15	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:3801731G>A	ENST00000262367.5	-	20	4584	c.3775C>T	c.(3775-3777)Cag>Tag	p.Q1259*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.Q1221*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1259	Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACTTACGTCTGGGGCTGTGAA	0.493			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											210	151	171					16																	3801731		2197	4300	6497	3741732	SO:0001587	stop_gained	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3775C>T	16.37:g.3801731G>A	ENSP00000262367:p.Gln1259*		3741732	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	35	5.561725	0.96527	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.3082	0.94173	0.0:0.0:1.0:0.0	.	.	.	.	X	1259;1289;1221	.	ENSP00000262367:Q1259X	Q	-	1	0	CREBBP	3741732	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.420000	0.97426	2.539000	0.85634	0.655000	0.94253	CAG		0.493	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3801731	G	A	3801731	4	1	111	1	0	0	0	0	0	1	0	0	3867	1357	47	3	3601	3	CREBBP	16	3801731	Nonsense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	14948	3801731	86553022	829	29963										
TIMM16	51025	hgsc.bcm.edu	37	chr16	4393260	4393260	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccctgcccaccacctgcacGcccatcacaatgatctgggc	8	19	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:4393260G>A	ENST00000318059.3	-	2	173	c.36C>T	c.(34-36)ggC>ggT	p.G12G	PAM16_ENST00000571941.1_Silent_p.G32G|PAM16_ENST00000573553.1_Silent_p.G32G|PAM16_ENST00000575942.1_5'Flank|PAM16_ENST00000575848.1_Silent_p.G24G|CORO7-PAM16_ENST00000572467.1_Silent_p.G935G|PAM16_ENST00000577031.1_Silent_p.G12G|PAM16_ENST00000576217.1_Silent_p.G12G|CORO7-PAM16_ENST00000572274.1_Intron	NM_016069.9	NP_057153.8	Q9Y3D7	TIM16_HUMAN	presequence translocase-associated motor 16 homolog (S. cerevisiae)	12					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane presequence translocase complex (GO:0005744)				lung(3)	3						CCACCTGCACGCCCATCACAA	0.637																																																0			16											66	48	54					16																	4393260		2192	4295	6487	4333261	SO:0001819	synonymous_variant	0			AK026514	CCDS10512.1	16p13.3	2010-10-12	2010-10-12		ENSG00000217930	ENSG00000217930			29679	protein-coding gene	gene with protein product	"mitochondria associated protein involved in granulocyte macrophage colony stimulating factor signal transduction"	614336				10810093, 11750097	Standard	NM_016069		Approved	Magmas, Tim16, TIMM16		Q9Y3D7	OTTHUMG00000129466	ENST00000318059.3:c.36C>T	16.37:g.4393260G>A			4333261	Q6I9Z3|Q9H5X3	Silent	SNP	ENST00000318059.3	37	CCDS10512.1																																																																																				0.637	PAM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251629.2	NM_016069		A	4393260	G	A	4393260	2	1	111	1	0	0	0	0	0	0	0	1	15946	1074	38	1		1	TIMM16	16	4393260	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	591529	4393260	85961493	830	29964										
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15704938	15704938	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aactcacaaacaccatattcAgtgacatcccagtcctttga	4	13	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:15704938A>T	ENST00000396368.3	-	19	3851	c.3645T>A	c.(3643-3645)acT>acA	p.T1215T	CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000540441.2_Silent_p.T1050T|KIAA0430_ENST00000551742.1_Silent_p.T1215T|KIAA0430_ENST00000548025.1_Silent_p.T1212T|KIAA0430_ENST00000602337.1_Silent_p.T1212T|KIAA0430_ENST00000344181.3_Silent_p.T817T	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1215	HTH OST-type 4. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						CACCATATTCAGTGACATCCC	0.423																																																0			16											161	148	152					16																	15704938		1928	4135	6063	15612439	SO:0001819	synonymous_variant	9665			AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3645T>A	16.37:g.15704938A>T			15612439	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Silent	SNP	ENST00000396368.3	37	CCDS10562.2																																																																																				0.423	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		T	15704938	A	T	15704938	2	4	111	1	0	0	0	0	0	0	0	1	8198	175	7	5		5	KIAA0430	16	15704938	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	11311678	15704938	74649815	831	29965										
MYH11	4629	hgsc.bcm.edu	37	chr16	15808860	15808860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcagcttcctgcggttggCgttgatgcgctgggactcct	14	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:15808860C>T	ENST00000300036.5	-	40	5801	c.5692G>A	c.(5692-5694)Gcc>Acc	p.A1898T	NDE1_ENST00000396355.1_Intron|MYH11_ENST00000452625.2_Missense_Mutation_p.A1905T|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.A1905T|MYH11_ENST00000576790.2_Missense_Mutation_p.A1898T|NDE1_ENST00000342673.5_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1898					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CTGCGGTTGGCGTTGATGCGC	0.637			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	0			16											133	125	127					16																	15808860		2197	4300	6497	15716361	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5692G>A	16.37:g.15808860C>T	ENSP00000300036:p.Ala1898Thr		15716361	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887212	0.91814	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	4.76	4.76	0.60689	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.84352	0.5453	L	0.55213	1.73	0.80722	D	1	P;D;D;D;D	0.69078	0.856;0.997;0.997;0.997;0.997	P;D;D;D;D	0.66084	0.507;0.941;0.941;0.941;0.941	D	0.84162	0.0429	10	0.40728	T	0.16	.	16.7535	0.85493	0.0:1.0:0.0:0.0	.	1905;1898;1905;1898;1905	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	T	1898;1898;1905;1905;1905	ENSP00000300036:A1898T;ENSP00000345136:A1898T;ENSP00000379616:A1905T;ENSP00000407821:A1905T	ENSP00000300036:A1898T	A	-	1	0	MYH11	15716361	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.902000	0.69869	2.177000	0.69029	0.455000	0.32223	GCC		0.637	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15808860	C	T	15808860	3	4	111	1	0	0	0	0	1	0	0	0	10061	768	27	1	269	1	MYH11	16	15808860	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	103922	15808860	74545893	832	29966										
SMG1	23049	hgsc.bcm.edu	37	chr16	18853072	18853072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaacatggtattcacaatagAtaggaactgcattattctct	6	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:18853072A>G	ENST00000446231.2	-	41	6923	c.6511T>C	c.(6511-6513)Tct>Cct	p.S2171P	SMG1_ENST00000389467.3_Missense_Mutation_p.S2171P			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2171	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		S -> C (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TTCACAATAGATAGGAACTGC	0.398																																																0			16											248	233	238					16																	18853072		1888	4110	5998	18760573	SO:0001583	missense	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6511T>C	16.37:g.18853072A>G	ENSP00000402515:p.Ser2171Pro		18760573	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121998	0.77436	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	D;D	0.82081	-1.57;-1.57	5.48	5.48	0.80851	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.64402	D	0.000003	D	0.92251	0.7542	M	0.89353	3.025	0.49483	D	0.999792	D;D	0.69078	0.997;0.997	D;D	0.81914	0.986;0.995	D	0.93505	0.6848	10	0.66056	D	0.02	.	15.8631	0.79040	1.0:0.0:0.0:0.0	.	2031;2171	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	P	2171	ENSP00000402515:S2171P;ENSP00000374118:S2171P	ENSP00000374118:S2171P	S	-	1	0	SMG1	18760573	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	9.212000	0.95126	2.198000	0.70561	0.533000	0.62120	TCT		0.398	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18853072	A	G	18853072	3	3	111	1	0	0	0	0	1	0	0	0	14832	333	12	4	4566	4	SMG1	16	18853072	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3044212	18853072	71501681	833	29967										
CRYM	1428	hgsc.bcm.edu	37	chr16	21289437	21289437	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caccggcaccacggtgcgcaCgggctgcatgacccctcctt					rs571066423		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:21289437delC	ENST00000219599.3	-	3	401	c.136delG	c.(136-138)gtgfs	p.V46fs	CRYM_ENST00000574787.1_5'Flank|CRYM_ENST00000415987.2_Frame_Shift_Del_p.V4fs|CRYM_ENST00000543948.1_Frame_Shift_Del_p.V46fs|CRYM_ENST00000396023.2_Frame_Shift_Del_p.V46fs	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	46					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sensory perception of sound (GO:0007605)|thyroid hormone metabolic process (GO:0042403)|thyroid hormone transport (GO:0070327)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|thiomorpholine-carboxylate dehydrogenase activity (GO:0047127)|thyroid hormone binding (GO:0070324)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(3)	4				GBM - Glioblastoma multiforme(48;0.0573)		ACGGTGCGCACGGGCTGCATG	0.662											OREG0023670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			16											25	22	23					16																	21289437		2105	4133	6238	21196938	SO:0001589	frameshift_variant	1428				CCDS10597.1	16p12.2	2013-02-14			ENSG00000103316	ENSG00000103316	1.5.1.25		2418	protein-coding gene	gene with protein product	"thiomorpholine-carboxylate dehydrogenase"	123740				1478656, 21332720	Standard	NM_001014444		Approved	DFNA40	uc002dim.3	Q14894	OTTHUMG00000090707	ENST00000219599.3:c.136delG	16.37:g.21289437delC	ENSP00000219599:p.Val46fs	747	21196938	D5MNX0|Q5HYB7	Frame_Shift_Del	DEL	ENST00000219599.3	37	CCDS10597.1																																																																																				0.662	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1			-	21289437	C	-	21289437	7	5	111	1	0	1	0	1	0	0	0	0	3927	536	19	0	840	0	CRYM	16	21289437	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	2436365	21289437	69065316	834	29968										
OTOA	146183	hgsc.bcm.edu	37	chr16	21693081	21693081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccacgtgtggacggatgacCtgtcccacagagtcctggcc	12	15	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:21693081C>A	ENST00000286149.4	+	5	203	c.202C>A	c.(202-204)Ctg>Atg	p.L68M	OTOA_ENST00000388956.4_5'Flank|OTOA_ENST00000388958.3_Missense_Mutation_p.L68M			Q7RTW8	OTOAN_HUMAN	otoancorin	68					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		GACGGATGACCTGTCCCACAG	0.507																																																0			16											176	131	146					16																	21693081		2199	4300	6499	21600582	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.202C>A	16.37:g.21693081C>A	ENSP00000286149:p.Leu68Met		21600582	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	C	12.13	1.846112	0.32606	.	.	ENSG00000155719	ENST00000388958;ENST00000286149	T;T	0.73789	-0.78;-0.77	5.93	3.99	0.46301	.	0.425292	0.21899	N	0.067474	T	0.70710	0.3255	L	0.52364	1.645	0.80722	D	1	P	0.52316	0.952	P	0.47673	0.554	T	0.71659	-0.4526	10	0.54805	T	0.06	-5.1637	8.1377	0.31064	0.0:0.8243:0.0:0.1757	.	68	E9PF51	.	M	68	ENSP00000373610:L68M;ENSP00000286149:L68M	ENSP00000286149:L68M	L	+	1	2	OTOA	21600582	0.993000	0.37304	0.997000	0.53966	0.027000	0.11550	0.755000	0.26405	1.527000	0.49086	-0.136000	0.14681	CTG		0.507	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			A	21693081	C	A	21693081	3	1	111	1	0	0	0	0	1	0	0	0	11333	680	24	2	220	2	OTOA	16	21693081	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	403644	21693081	68661672	835	29969										
GGA2	23062	hgsc.bcm.edu	37	chr16	23481450	23481450	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtggagcagaattctgaatCcattccggtcatacacaatg	9	9	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:23481450C>A	ENST00000309859.4	-	15	1569	c.1487G>T	c.(1486-1488)gGa>gTa	p.G496V	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	496	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		AATTCTGAATCCATTCCGGTC	0.582																																																0			16											64	64	64					16																	23481450		2197	4300	6497	23388951	SO:0001583	missense	23062			AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1487G>T	16.37:g.23481450C>A	ENSP00000311962:p.Gly496Val		23388951	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974632	0.74360	.	.	ENSG00000103365	ENST00000309859	T	0.37584	1.19	4.93	4.93	0.64822	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.000000	0.85682	D	0.000000	T	0.63896	0.2550	M	0.85373	2.75	0.80722	D	1	D	0.71674	0.998	D	0.75020	0.985	T	0.69304	-0.5180	10	0.56958	D	0.05	-19.1322	15.9976	0.80262	0.0:1.0:0.0:0.0	.	496	Q9UJY4	GGA2_HUMAN	V	496	ENSP00000311962:G496V	ENSP00000311962:G496V	G	-	2	0	GGA2	23388951	0.994000	0.37717	0.955000	0.39395	0.704000	0.40688	6.808000	0.75206	2.418000	0.82041	0.561000	0.74099	GGA		0.582	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			A	23481450	C	A	23481450	3	1	111	1	0	0	0	0	1	0	0	0	6373	855	30	2	366	2	GGA2	16	23481450	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1788369	23481450	66873303	836	29970										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24105581	24105581	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatgggatctttgtcctttGggatttctgaacttcagaaa	9	7	4	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:24105581G>T	ENST00000321728.7	+	7	959	c.784G>T	c.(784-786)Ggg>Tgg	p.G262W	PRKCB_ENST00000482000.1_3'UTR|PRKCB_ENST00000303531.7_Missense_Mutation_p.G262W	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	262					apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.G262R(2)		central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	TTTGTCCTTTGGGATTTCTGA	0.448																																																2	Substitution - Missense(2)	lung(2)	16											158	143	148					16																	24105581		2197	4300	6497	24013082	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.784G>T	16.37:g.24105581G>T	ENSP00000318315:p.Gly262Trp		24013082	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537773	0.85917	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.45276	0.9;0.9	5.52	5.52	0.82312	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.65080	0.2657	M	0.87381	2.88	0.80722	D	1	P;P	0.42620	0.785;0.68	P;P	0.52031	0.688;0.623	T	0.70857	-0.4758	10	0.87932	D	0	.	18.4466	0.90686	0.0:0.0:1.0:0.0	.	262;262	P05771-2;P05771	.;KPCB_HUMAN	W	262	ENSP00000318315:G262W;ENSP00000305355:G262W	ENSP00000305355:G262W	G	+	1	0	PRKCB	24013082	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.468000	0.97676	2.581000	0.87130	0.655000	0.94253	GGG		0.448	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		T	24105581	G	T	24105581	3	4	111	1	0	0	0	0	1	0	0	0	12542	1348	47	2	810	2	PRKCB	16	24105581	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	624131	24105581	66249172	837	29971										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24582954	24582954	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggaagagagagatttgcctAaaaaaggaacaggagattcc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:24582954delA	ENST00000319715.4	+	18	4999	c.4567delA	c.(4567-4569)aaafs	p.K1524fs	RBBP6_ENST00000381039.3_Frame_Shift_Del_p.K684fs|RBBP6_ENST00000348022.2_Frame_Shift_Del_p.K1490fs	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1524	Interaction with p53. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AGATTTGCCTAAAAAAGGAAC	0.368																																																0			16											37	37	37					16																	24582954		2197	4297	6494	24490455	SO:0001589	frameshift_variant	5930				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4567delA	16.37:g.24582954delA	ENSP00000317872:p.Lys1524fs		24490455	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Del	DEL	ENST00000319715.4	37	CCDS10621.1																																																																																				0.368	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		-	24582954	A	-	24582954	7	5	111	1	0	1	0	1	0	0	0	0	13140	363	13	0	4691	0	RBBP6	16	24582954	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	477373	24582954	65771799	838	29972										
IL21R	50615	hgsc.bcm.edu	37	chr16	27455913	27455913	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaagaagtgtctccctcctCcccctggagttccgcaaaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:27455913delC	ENST00000337929.3	+	6	1031	c.558delC	c.(556-558)ctcfs	p.L186fs	IL21R_ENST00000564089.1_Frame_Shift_Del_p.L186fs|IL21R_ENST00000395754.4_Frame_Shift_Del_p.L186fs|IL21R_ENST00000564583.1_3'UTR|IL21R_ENST00000395755.1_Frame_Shift_Del_p.L186fs	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	186	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TCTCCCTCCTCCCCCTGGAGT	0.592			T	BCL6	NHL																																		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	0			16											86	78	80					16																	27455913		2197	4300	6497	27363414	SO:0001589	frameshift_variant	50615			AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.558delC	16.37:g.27455913delC	ENSP00000338010:p.Leu186fs		27363414	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Frame_Shift_Del	DEL	ENST00000337929.3	37	CCDS10630.1																																																																																				0.592	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		-	27455913	C	-	27455913	7	5	111	1	0	1	0	1	0	0	0	0	7692	842	30	0	576	0	IL21R	16	27455913	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	2872959	27455913	62898840	839	29973										
ASPHD1	253982	hgsc.bcm.edu	37	chr16	29912629	29912629	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taggggctgggagccgagctGggggtgttcgtggtgggcct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:29912629delG	ENST00000308748.5	+	1	589	c.337delG	c.(337-339)gggfs	p.G114fs	SEZ6L2_ENST00000537485.1_5'Flank|SEZ6L2_ENST00000346932.5_5'Flank|SEZ6L2_ENST00000308713.5_5'Flank|ASPHD1_ENST00000483405.1_Intron|SEZ6L2_ENST00000350527.3_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	114	Gly-rich.				peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						GAGCCGAGCTGGGGGTGTTCG	0.682																																																0			16											32	39	37					16																	29912629		2129	4227	6356	29820130	SO:0001589	frameshift_variant	253982			AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.337delG	16.37:g.29912629delG	ENSP00000311447:p.Gly114fs		29820130	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Frame_Shift_Del	DEL	ENST00000308748.5	37	CCDS10660.1																																																																																				0.682	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718		-	29912629	G	-	29912629	7	5	111	1	0	1	0	1	0	0	0	0	1055	1348	47	0	339	0	ASPHD1	16	29912629	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	2456716	29912629	60442124	840	29974										
ZNF785	146540	hgsc.bcm.edu	37	chr16	30594477	30594477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtacctgcgctgggagaaacGcgcctgacactggccgcagg	15	13	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:30594477G>A	ENST00000395216.2	-	3	781	c.622C>T	c.(622-624)Cgt>Tgt	p.R208C	AC002310.7_ENST00000486926.1_RNA|ZNF785_ENST00000470110.1_Missense_Mutation_p.R193C|AC002310.7_ENST00000492040.1_RNA|RP11-146F11.5_ENST00000563540.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						TGGGAGAAACGCGCCTGACAC	0.692																																																0			16											40	43	42					16																	30594477		2197	4299	6496	30501978	SO:0001583	missense	146540			BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162		"Zinc fingers, C2H2-type", "-"	26496	protein-coding gene	gene with protein product						10493829	Standard	NM_152458		Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.622C>T	16.37:g.30594477G>A	ENSP00000378642:p.Arg208Cys		30501978	O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000395216.2	37	CCDS10685.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383427	0.42207	.	.	ENSG00000197162	ENST00000470110;ENST00000395222;ENST00000395216	T;T	0.29397	1.57;1.57	4.34	1.13	0.20643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16854	0.0405	N	0.20881	0.62	0.09310	N	1	B;B;B	0.31351	0.028;0.32;0.022	B;B;B	0.27500	0.008;0.08;0.005	T	0.18304	-1.0341	9	0.51188	T	0.08	.	3.9921	0.09541	0.3226:0.1743:0.5031:0.0	.	173;208;193	B4DQL1;A8K8V0;A8K8V0-2	.;ZN785_HUMAN;.	C	193;173;208	ENSP00000420340:R193C;ENSP00000378642:R208C	ENSP00000378642:R208C	R	-	1	0	ZNF785	30501978	0.000000	0.05858	0.001000	0.08648	0.145000	0.21501	-0.759000	0.04761	0.095000	0.17434	-0.374000	0.07098	CGT		0.692	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255529.2	NM_152458		A	30594477	G	A	30594477	3	1	111	1	0	0	0	0	1	0	0	0	18196	1087	38	1	599	1	ZNF785	16	30594477	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	681848	30594477	59760276	841	29975										
ADCY7	113	hgsc.bcm.edu	37	chr16	50332842	50332842	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtgcatgcgaatcaagatcCtcggcgactgctactactgt	10	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:50332842C>T	ENST00000394697.2	+	8	1316	c.976C>T	c.(976-978)Ctc>Ttc	p.L326F	ADCY7_ENST00000538642.1_Missense_Mutation_p.L326F|ADCY7_ENST00000537579.1_Missense_Mutation_p.L326F|ADCY7_ENST00000254235.3_Missense_Mutation_p.L326F|ADCY7_ENST00000566433.2_Missense_Mutation_p.L326F|ADCY7_ENST00000564044.1_3'UTR			P51828	ADCY7_HUMAN	adenylate cyclase 7	326	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		AATCAAGATCCTCGGCGACTG	0.637																																																0			16											122	93	103					16																	50332842		2198	4300	6498	48890343	SO:0001583	missense	113			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.976C>T	16.37:g.50332842C>T	ENSP00000378187:p.Leu326Phe		48890343	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	37	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820180	0.71028	.	.	ENSG00000121281	ENST00000538642;ENST00000394697;ENST00000537579;ENST00000254235	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.51	3.21	0.36854	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.35013	U	0.003519	D	0.92519	0.7624	H	0.95816	3.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92879	0.6321	10	0.87932	D	0	.	9.5236	0.39152	0.0:0.7037:0.0:0.2963	.	326;326	P51828;F5H4D1	ADCY7_HUMAN;.	F	326	ENSP00000445046:L326F;ENSP00000378187:L326F;ENSP00000437788:L326F;ENSP00000254235:L326F	ENSP00000254235:L326F	L	+	1	0	ADCY7	48890343	0.999000	0.42202	1.000000	0.80357	0.702000	0.40608	1.036000	0.30228	1.323000	0.45263	0.491000	0.48974	CTC		0.637	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50332842	C	T	50332842	3	4	111	1	0	0	0	0	1	0	0	0	299	681	24	3	1002	3	ADCY7	16	50332842	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	19738365	50332842	40021911	842	29976										
CCDC135	84229	hgsc.bcm.edu	37	chr16	57741449	57741449	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttgtgctatcggggaagcgCgaggtgcctgagaacttctt	14	9	1	1	rs368181149		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:57741449C>T	ENST00000360716.3	+	8	1157	c.936C>T	c.(934-936)cgC>cgT	p.R312R	CCDC135_ENST00000394337.4_Silent_p.R312R|CCDC135_ENST00000336825.8_Silent_p.R247R			Q8IY82	CC135_HUMAN		312					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CGGGGAAGCGCGAGGTGCCTG	0.587																																																0			16						C		0,4396		0,0,2198	76	70	72		936	-10.1	0	16		72	1,8599		0,1,4299	no	coding-synonymous	CCDC135	NM_032269.5		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		312/875	57741449	1,12995	2198	4300	6498	56298950	SO:0001819	synonymous_variant	84229																														ENST00000360716.3:c.936C>T	16.37:g.57741449C>T			56298950	A8K943|Q8NAA0|Q9H080	Silent	SNP	ENST00000360716.3	37	CCDS10787.1																																																																																				0.587	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			T	57741449	C	T	57741449	2	4	111	1	0	0	0	0	0	0	0	1	2775	755	27	1		1	CCDC135	16	57741449	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	7408607	57741449	32613304	843	29977										
MMP15	4324	hgsc.bcm.edu	37	chr16	58073969	58073969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcttccacggcgacagctcgCcgtttgatggcaccggtggc	14	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:58073969C>T	ENST00000219271.3	+	4	1416	c.631C>T	c.(631-633)Ccg>Tcg	p.P211S		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	211					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CGACAGCTCGCCGTTTGATGG	0.627																																																0			16											62	57	59					16																	58073969		2198	4300	6498	56631470	SO:0001583	missense	4324			Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.631C>T	16.37:g.58073969C>T	ENSP00000219271:p.Pro211Ser		56631470	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.979620	0.92982	.	.	ENSG00000102996	ENST00000219271	T	0.22539	1.95	4.69	4.69	0.59074	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47857	0.1468	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52586	-0.8556	10	0.66056	D	0.02	.	16.5944	0.84792	0.0:1.0:0.0:0.0	.	211	P51511	MMP15_HUMAN	S	211	ENSP00000219271:P211S	ENSP00000219271:P211S	P	+	1	0	MMP15	56631470	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	6.073000	0.71245	2.162000	0.67917	0.462000	0.41574	CCG		0.627	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		T	58073969	C	T	58073969	3	4	111	1	0	0	0	0	1	0	0	0	9684	739	26	3	645	3	MMP15	16	58073969	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	332520	58073969	32280784	844	29978										
NDRG4	65009	hgsc.bcm.edu	37	chr16	58545393	58545393	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaccagtgccagctcggtGgatggcagccgcccacaggc	13	16	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:58545393G>T	ENST00000570248.1	+	15	1078	c.972G>T	c.(970-972)gtG>gtT	p.V324V	NDRG4_ENST00000563799.1_Silent_p.V329V|NDRG4_ENST00000562999.1_Silent_p.V299V|NDRG4_ENST00000566192.1_Silent_p.V311V|NDRG4_ENST00000356752.4_Silent_p.V341V|NDRG4_ENST00000568640.1_Silent_p.V329V|NDRG4_ENST00000569923.1_Silent_p.V256V|NDRG4_ENST00000394282.4_Silent_p.V363V|NDRG4_ENST00000258187.5_Silent_p.V343V|NDRG4_ENST00000394279.2_Silent_p.V343V	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	324					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						CCAGCTCGGTGGATGGCAGCC	0.657																																																0			16											63	59	61					16																	58545393		2198	4299	6497	57102894	SO:0001819	synonymous_variant	65009			AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.972G>T	16.37:g.58545393G>T			57102894	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																				0.657	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2			T	58545393	G	T	58545393	2	4	111	1	0	0	0	0	0	0	0	1	10285	1335	47	2		2	NDRG4	16	58545393	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	471424	58545393	31809360	845	29979										
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67859872	67859872	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgcaaggagcatgagatccTcatgcagctgcacatgagca	11	11	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:67859872T>C	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.L346P|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.L277P|TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.L292P	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CATGAGATCCTCATGCAGCTG	0.617																																																0			16											59	49	53					16																	67859872		2198	4300	6498	66417373	SO:0001628	intergenic_variant	55815			AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			16.37:g.67859872T>C			66417373	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	37	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	T	13.09	2.132469	0.37630	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.8	5.8	0.92144	.	0.000000	0.50627	D	0.000109	T	0.78039	0.4221	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.80538	-0.1338	9	0.87932	D	0	-12.1782	14.3848	0.66938	0.0:0.0:0.0:1.0	.	277;346;82;292	E7ENJ7;B4DXD0;B4DY78;Q2TAA8	.;.;.;TXIP1_HUMAN	P	277;292;82	.	ENSP00000373485:L292P	L	+	2	0	TSNAXIP1	66417373	1.000000	0.71417	0.757000	0.31301	0.006000	0.05464	5.024000	0.64090	2.209000	0.71365	0.533000	0.62120	CTC		0.617	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		C	67859872	T	C	67859872	1	2	111	0	1	0	0	0	0	0	0	0	16672	1551	54	4		4	TSNAXIP1	16	67859872	IGR	SNP	T	TCGA-EI-6507-01A-11D-1733-10	9314479	67859872	22494881	846	29980										
CENPT	80152	hgsc.bcm.edu	37	chr16	67862654	67862654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcacatagtggctcagtccaGccttgtggggatcttgccgg	13	11	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:67862654G>A	ENST00000562787.1	-	14	1921	c.1373C>T	c.(1372-1374)gCt>gTt	p.A458V	CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000219172.3_Missense_Mutation_p.A458V|CENPT_ENST00000440851.2_Missense_Mutation_p.A458V|CENPT_ENST00000564817.1_Missense_Mutation_p.A403V	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	458					chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		GCTCAGTCCAGCCTTGTGGGG	0.592																																																0			16											136	137	137					16																	67862654		1880	4120	6000	66420155	SO:0001583	missense	80152			AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.1373C>T	16.37:g.67862654G>A	ENSP00000457810:p.Ala458Val		66420155	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	37	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453512	0.63290	.	.	ENSG00000102901	ENST00000440851;ENST00000436104;ENST00000219172	T;T	0.47528	0.84;0.84	5.8	3.86	0.44501	Histone-fold (2);	0.890950	0.09832	N	0.750037	T	0.44953	0.1318	L	0.47716	1.5	0.49687	D	0.999819	P;P;P	0.45531	0.86;0.573;0.573	P;B;B	0.44561	0.453;0.197;0.143	T	0.10268	-1.0637	10	0.36615	T	0.2	0.0794	8.6019	0.33749	0.1732:0.0:0.8268:0.0	.	216;458;458	F5H5A6;Q96BT3;B3KPB2	.;CENPT_HUMAN;.	V	458;216;458	ENSP00000400140:A458V;ENSP00000219172:A458V	ENSP00000219172:A458V	A	-	2	0	CENPT	66420155	0.052000	0.20516	0.475000	0.27278	0.674000	0.39518	0.648000	0.24828	0.801000	0.34066	0.655000	0.94253	GCT		0.592	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67862654	G	A	67862654	3	1	111	1	0	0	0	0	1	0	0	0	3248	971	34	3	324	3	CENPT	16	67862654	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2782	67862654	22492099	847	29981										
DPEP2	64174	hgsc.bcm.edu	37	chr16	68021797	68021797	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcagcaggtttccacgaagGacaccctgaagctcttcctc	9	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:68021797G>T	ENST00000572888.1	-	9	1814	c.1164C>A	c.(1162-1164)gtC>gtA	p.V388V	DPEP2_ENST00000393847.1_Silent_p.V388V|DPEP2_ENST00000412757.2_Silent_p.V388V			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	388					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		TTCCACGAAGGACACCCTGAA	0.562																																																0			16											132	129	130					16																	68021797		2198	4300	6498	66579298	SO:0001819	synonymous_variant	64174			AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.1164C>A	16.37:g.68021797G>T			66579298	B2RCF8|Q6UX92|Q8TC95	Silent	SNP	ENST00000572888.1	37	CCDS10857.1																																																																																				0.562	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355		T	68021797	G	T	68021797	2	4	111	1	0	0	0	0	0	0	0	1	4725	1161	41	2		2	DPEP2	16	68021797	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	159143	68021797	22332956	848	29982										
HPR	3250	hgsc.bcm.edu	37	chr16	72110329	72110329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aatctcaccacaggggccacGctgatcaatgaacaatggct	9	12	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:72110329G>A	ENST00000540303.2	+	5	428	c.396G>A	c.(394-396)acG>acA	p.T132T	HPR_ENST00000561690.1_Intron|HPR_ENST00000356967.5_Silent_p.T132T|HPR_ENST00000228226.8_Silent_p.T169T	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CAGGGGCCACGCTGATCAATG	0.512																																																0			16											93	63	73					16																	72110329		2054	4194	6248	70667830	SO:0001819	synonymous_variant	3250			BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.396G>A	16.37:g.72110329G>A			70667830	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	37	CCDS42193.1																																																																																				0.512	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		A	72110329	G	A	72110329	2	1	111	1	0	0	0	0	0	0	0	1	7358	1074	38	1		1	HPR	16	72110329	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4088532	72110329	18244424	849	29983										
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83999526	83999526	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acgccatggggccgctggccGgggacaacttcgtgaggttt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:83999526delG	ENST00000343939.2	+	7	1980	c.1597delG	c.(1597-1599)gggfs	p.G533fs	OSGIN1_ENST00000361711.3_Frame_Shift_Del_p.G450fs|OSGIN1_ENST00000393306.1_Frame_Shift_Del_p.G450fs|NECAB2_ENST00000305202.4_5'Flank			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	533					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GCCGCTGGCCGGGGACAACTT	0.657																																																0			16											20	20	20					16																	83999526		2195	4292	6487	82557027	SO:0001589	frameshift_variant	29948			AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1597delG	16.37:g.83999526delG	ENSP00000343376:p.Gly533fs		82557027	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Frame_Shift_Del	DEL	ENST00000343939.2	37																																																																																					0.657	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		-	83999526	G	-	83999526	7	5	111	1	0	1	0	1	0	0	0	0	11320	1116	39	0	1623	0	OSGIN1	16	83999526	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	11889197	83999526	6355227	850	29984										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84199422	84199422	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcctgggctaggggagggtaCgcagctgaaaaggaggagag	20	6	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:84199422C>T	ENST00000378553.5	+	7	1021	c.897C>T	c.(895-897)taC>taT	p.Y299Y	DNAAF1_ENST00000334315.5_Silent_p.Y299Y|DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	299					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						GGGGAGGGTACGCAGCTGAAA	0.512																																																0			16											146	145	146					16																	84199422		2200	4300	6500	82756923	SO:0001819	synonymous_variant	123872			BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.897C>T	16.37:g.84199422C>T			82756923	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	37	CCDS10943.2																																																																																				0.512	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		T	84199422	C	T	84199422	2	4	111	1	0	0	0	0	0	0	0	1	9038	547	19	1		1	LRRC50	16	84199422	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	199896	84199422	6155331	851	29985										
KLHL36	79786	hgsc.bcm.edu	37	chr16	84695234	84695235	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaagacttcgtgtacatctcINSggggggccacgactaccaaa					rs373757262		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:84695234_84695235insG	ENST00000564996.1	+	5	1487_1488	c.1346_1347insG	c.(1345-1350)tcggggfs	p.SG449fs	KLHL36_ENST00000258157.5_Frame_Shift_Ins_p.SG386fs	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	449					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GTGTACATCTCGGGGGGCCACG	0.639																																																0			16																																								83252736	SO:0001589	frameshift_variant	79786			AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"Kelch-like", "BTB/POZ domain containing"	17844	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 44", "kelch-like 36 (Drosophila)"	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.1352dupG	16.37:g.84695240_84695240dupG	ENSP00000456743:p.Ser449fs		83252735	Q8N5G6|Q9H9U6	Frame_Shift_Ins	INS	ENST00000564996.1	37	CCDS10948.1																																																																																				0.639	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2			G	84695235	-	G	84695234	7	5	111	1	0	1	1	0	0	0	0	0	8410	893	31	0	1360	0	KLHL36	16	84695234	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	495812	84695234	5659519	852	29986										
FOXL1	2300	hgsc.bcm.edu	37	chr16	86613231	86613231	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcctcgctcctggccgcctCctccagcctccgtccgcctt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:86613231delC	ENST00000320241.3	+	1	1117	c.902delC	c.(901-903)tccfs	p.S303fs		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	303					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						CTGGCCGCCTCCTCCAGCCTC	0.672																																					NSCLC(163;308 2020 10889 11476 18208)											0			16											21	25	24					16																	86613231		2198	4300	6498	85170732	SO:0001589	frameshift_variant	2300			AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"Forkhead boxes"	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.902delC	16.37:g.86613231delC	ENSP00000326272:p.Ser303fs		85170732	Q17RR1|Q9H242	Frame_Shift_Del	DEL	ENST00000320241.3	37	CCDS10959.1																																																																																				0.672	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250		-	86613231	C	-	86613231	7	5	111	1	0	1	0	1	0	0	0	0	6035	855	30	0	904	0	FOXL1	16	86613231	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1917997	86613231	3741522	853	29987										
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445899	87445899	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctgtgtacagagcagtccGggggtttattattgcagggg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:87445899delG	ENST00000268616.4	-	12	2234	c.2017delC	c.(2017-2019)cggfs	p.R673fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	673							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.R673R(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGAGCAGTCCGGGGGTTTATT	0.512																																																1	Substitution - coding silent(1)	lung(1)	16											77	94	88					16																	87445899		2197	4290	6487	86003400	SO:0001589	frameshift_variant	23174			AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2017delC	16.37:g.87445899delG	ENSP00000268616:p.Arg673fs		86003400	D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	37	CCDS10961.1																																																																																				0.512	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		-	87445899	G	-	87445899	7	5	111	1	0	1	0	1	0	0	0	0	17622	1115	39	0	840	0	ZCCHC14	16	87445899	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	832668	87445899	2908854	854	29988										
PABPN1L	390748	hgsc.bcm.edu	37	chr16	88932296	88932296	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcactcctggaggccgtggCgtcccctcggcctgctccat	12	17	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:88932296C>T	ENST00000419291.2	-	2	320	c.309G>A	c.(307-309)acG>acA	p.T103T	PABPN1L_ENST00000427766.1_Silent_p.T103T|PABPN1L_ENST00000411789.2_Silent_p.T103T|PABPN1L_ENST00000378358.4_Silent_p.T103T	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	103						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						GAGGCCGTGGCGTCCCCTCGG	0.687																																																0			16											24	29	28					16																	88932296		2091	4202	6293	87459797	SO:0001819	synonymous_variant	0				CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"RNA binding motif (RRM) containing"	37237	protein-coding gene	gene with protein product	"embryonic poly(A) binding protein 2"					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.309G>A	16.37:g.88932296C>T			87459797	A1L3B3|A2VDI2	Silent	SNP	ENST00000419291.2	37	CCDS45547.2																																																																																				0.687	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487		T	88932296	C	T	88932296	2	4	111	1	0	0	0	0	0	0	0	1	11400	755	27	1		1	PABPN1L	16	88932296	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1486397	88932296	1422457	855	29989										
C16orf7	9605	hgsc.bcm.edu	37	chr16	89775777	89775777	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtggggatgccaatggcggtGgggggtgcattcctgtagag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr16:89775777delG	ENST00000389386.3	-	12	1579	c.1455delC	c.(1453-1455)cccfs	p.P485fs	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Frame_Shift_Del_p.P415fs|VPS9D1-AS1_ENST00000562866.1_RNA	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	485	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CAATGGCGGTGGGGGGTGCAT	0.692																																																0			16											27	33	31					16																	89775777		1992	4142	6134	88303278	SO:0001589	frameshift_variant	9605			AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1455delC	16.37:g.89775777delG	ENSP00000374037:p.Pro485fs		88303278		Frame_Shift_Del	DEL	ENST00000389386.3	37	CCDS42220.1																																																																																				0.692	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		-	89775777	G	-	89775777	7	5	111	1	0	1	0	1	0	0	0	0	1832	1335	47	0	456	0	C16orf7	16	89775777	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	843481	89775777	578976	856	29990										
INPP5K	51763	hgsc.bcm.edu	37	chr17	1401315	1401315	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcccctcagagacaaggagAagtgtgacgccggcggtatg	15	10	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:1401315A>G	ENST00000421807.2	-	8	1266	c.878T>C	c.(877-879)tTc>tCc	p.F293S	INPP5K_ENST00000397335.3_Missense_Mutation_p.F201S|INPP5K_ENST00000542125.1_Missense_Mutation_p.F197S|INPP5K_ENST00000406424.4_Missense_Mutation_p.F217S|INPP5K_ENST00000320345.6_Missense_Mutation_p.F217S	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	293	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						AGACAAGGAGAAGTGTGACGC	0.607																																																0			17											142	136	138					17																	1401315		2203	4300	6503	1348065	SO:0001583	missense	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.878T>C	17.37:g.1401315A>G	ENSP00000413937:p.Phe293Ser		1348065	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	37	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.105232	0.56291	.	.	ENSG00000132376	ENST00000421807;ENST00000406424;ENST00000350761;ENST00000320345;ENST00000397335;ENST00000542125;ENST00000449479	T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28	5.53	5.53	0.82687	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.306737	0.38381	N	0.001703	T	0.80808	0.4694	L	0.33137	0.985	0.33636	D	0.606684	D;B	0.56287	0.975;0.002	P;B	0.55667	0.781;0.003	D	0.85944	0.1460	10	0.49607	T	0.09	-16.444	13.3184	0.60419	1.0:0.0:0.0:0.0	.	197;293	F5GXZ0;Q9BT40	.;INP5K_HUMAN	S	217;217;293;217;201;197;201	ENSP00000385177:F217S;ENSP00000318476:F217S;ENSP00000380496:F201S;ENSP00000440147:F197S;ENSP00000413259:F201S	ENSP00000318476:F217S	F	-	2	0	INPP5K	1348065	1.000000	0.71417	0.819000	0.32651	0.087000	0.18053	3.601000	0.54059	2.220000	0.72140	0.533000	0.62120	TTC		0.607	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			G	1401315	A	G	1401315	3	3	111	1	0	0	0	0	1	0	0	0	7781	246	9	4	488	4	INPP5K	17	1401315	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10		1401315	79793895	857	29991										
SGSM2	9905	hgsc.bcm.edu	37	chr17	2280079	2280079	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcagggcatgtgcgatctgCtggcgcctctcctggtcacc	13	14	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:2280079C>T	ENST00000426855.2	+	19	2702	c.2527C>T	c.(2527-2529)Ctg>Ttg	p.L843L	RP1-59D14.5_ENST00000574290.1_RNA|RP1-59D14.5_ENST00000573007.1_RNA|SGSM2_ENST00000574563.1_Silent_p.L843L|SGSM2_ENST00000268989.3_Silent_p.L888L	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	843	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		GTGCGATCTGCTGGCGCCTCT	0.627																																																0			17											161	146	151					17																	2280079		2203	4300	6503	2226829	SO:0001819	synonymous_variant	9905			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2527C>T	17.37:g.2280079C>T			2226829	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																				0.627	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		T	2280079	C	T	2280079	2	4	111	1	0	0	0	0	0	0	0	1	14260	796	28	3		3	SGSM2	17	2280079	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	878764	2280079	78915131	858	29992										
MNT	4335	hgsc.bcm.edu	37	chr17	2290383	2290383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggtgcgagagggtgtgggCgatgtggctcactgccacgg	19	9	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:2290383C>T	ENST00000174618.4	-	6	1966	c.1561G>A	c.(1561-1563)Gcc>Acc	p.A521T	RP1-59D14.1_ENST00000571775.1_RNA|MNT_ENST00000575374.1_5'Flank	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	521					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		AGGGTGTGGGCGATGTGGCTC	0.682																																																0			17											36	38	37					17																	2290383		2191	4283	6474	2237133	SO:0001583	missense	4335			Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7188	protein-coding gene	gene with protein product	"myc antagonist", "Max-interacting protein"	603039	"MAX binding protein", "MNT, MAX dimerization protein"			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1561G>A	17.37:g.2290383C>T	ENSP00000174618:p.Ala521Thr		2237133	A8K6D1|D3DTI7|Q1ED38	Missense_Mutation	SNP	ENST00000174618.4	37	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257760	0.39896	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	D	0.82255	-1.59	4.91	4.91	0.64330	.	3.902500	0.01100	N	0.005343	T	0.70587	0.3241	N	0.11560	0.145	0.48571	D	0.99967	P	0.42375	0.778	B	0.26864	0.074	T	0.59768	-0.7392	10	0.28530	T	0.3	-15.9892	17.0679	0.86564	0.0:1.0:0.0:0.0	.	521	Q99583	MNT_HUMAN	T	521	ENSP00000174618:A521T	ENSP00000174618:A521T	A	-	1	0	MNT	2237133	0.993000	0.37304	0.987000	0.45799	0.985000	0.73830	2.968000	0.49224	2.274000	0.75844	0.591000	0.81541	GCC		0.682	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310		T	2290383	C	T	2290383	3	4	111	1	0	0	0	0	1	0	0	0	9708	768	27	1	191	1	MNT	17	2290383	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	10304	2290383	78904827	859	29993										
TRPV1	7442	hgsc.bcm.edu	37	chr17	3495606	3495606	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgtccttttggagtgggtcCgcagctgcccccaagtctgt	13	12	1	0	rs201154250	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:3495606C>T	ENST00000571088.1	-	2	252	c.39G>A	c.(37-39)gcG>gcA	p.A13A	TRPV1_ENST00000425167.2_Silent_p.A13A|TRPV1_ENST00000399756.4_Silent_p.A13A|SHPK_ENST00000572705.1_Silent_p.A13A|TRPV1_ENST00000399759.3_Silent_p.A13A|TRPV1_ENST00000174621.6_5'UTR|TRPV1_ENST00000310522.5_Silent_p.A13A|TRPV1_ENST00000576351.1_Silent_p.A13A	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	13					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GGAGTGGGTCCGCAGCTGCCC	0.632													C|||	5	0.000998403	0	0	5008	,	,		17190	0.001		0	False		,,,				2504	0.0041				Melanoma(38;962 1762 15789)											0			17						C	,,,	1,4169		0,1,2084	42	46	45		39,39,39,39	4	0.4	17		45	0,8438		0,0,4219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	0,1,6303	TT,TC,CC		0.0,0.024,0.0079	,,,	13/840,13/840,13/840,13/840	3495606	1,12607	2085	4219	6304	3442355	SO:0001819	synonymous_variant	7442			AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.39G>A	17.37:g.3495606C>T			3442355	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																				0.632	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		T	3495606	C	T	3495606	2	4	111	1	0	0	0	0	0	0	0	1	16635	639	23	1		1	TRPV1	17	3495606	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1205223	3495606	77699604	860	29994										
MINK1	50488	hgsc.bcm.edu	37	chr17	4789438	4789438	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtgtgacatgcaccccatgCgagccctcttcctcattcct	7	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:4789438C>T	ENST00000355280.6	+	9	914	c.718C>T	c.(718-720)Cga>Tga	p.R240*	RN7SL784P_ENST00000577319.1_RNA|MINK1_ENST00000453408.3_Nonsense_Mutation_p.R240*|MINK1_ENST00000347992.7_Nonsense_Mutation_p.R240*	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GCACCCCATGCGAGCCCTCTT	0.607																																																0			17											79	85	83					17																	4789438		2068	4206	6274	4730221	SO:0001587	stop_gained	50488			AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.718C>T	17.37:g.4789438C>T	ENSP00000347427:p.Arg240*		4730221		Silent	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	C	37	6.310772	0.97462	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	.	.	.	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7959	0.46459	0.189:0.811:0.0:0.0	.	.	.	.	X	240	.	ENSP00000269296:R240X	R	+	1	2	MINK1	4730221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.553000	0.36255	2.680000	0.91292	0.561000	0.74099	CGA		0.607	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		T	4789438	C	T	4789438	4	4	111	1	0	0	0	0	0	1	0	0	9617	760	27	1	491	1	MINK1	17	4789438	Nonsense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1293832	4789438	76405772	861	29995										
MINK1	1145	hgsc.bcm.edu	37	chr17	4799330	4799330	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggattaagttcctggtcatcGccctcaagagctccgtggag	12	11	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:4799330G>A	ENST00000293780.4	-	0	2455				MINK1_ENST00000453408.3_Missense_Mutation_p.A1113T|MINK1_ENST00000347992.7_Missense_Mutation_p.A1104T|MINK1_ENST00000355280.6_Missense_Mutation_p.A1133T	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	CCTGGTCATCGCCCTCAAGAG	0.587											OREG0024107	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			17											52	56	55					17																	4799330		1971	4145	6116	4740106	SO:0001628	intergenic_variant	50488			X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1966	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, epsilon (muscle)"	100725	"cholinergic receptor, nicotinic, epsilon"			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778		17.37:g.4799330G>A		621	4740106	D3DTK6	Silent	SNP	ENST00000293780.4	37	CCDS11058.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.024588	0.93518	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992;ENST00000542906	T;T;T	0.09163	3.01;3.01;3.01	4.41	4.41	0.53225	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.36413	0.0966	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.74348	0.978;0.982;0.983;0.982	T	0.33624	-0.9861	10	0.87932	D	0	.	14.8844	0.70557	0.0:0.0:1.0:0.0	.	1096;1113;1133;1104	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	T	1133;1113;1104;93	ENSP00000347427:A1133T;ENSP00000406487:A1113T;ENSP00000269296:A1104T	ENSP00000269296:A1104T	A	+	1	0	MINK1	4740106	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.601000	0.98297	2.436000	0.82500	0.561000	0.74099	GCC		0.587	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3			A	4799330	G	A	4799330	1	1	111	0	1	0	0	0	0	0	0	0	9617	1087	38	1		1	MINK1	17	4799330	IGR	SNP	G	TCGA-EI-6507-01A-11D-1733-10	9892	4799330	76395880	862	29996										
GPR172B	55065	hgsc.bcm.edu	37	chr17	4937895	4937895	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagacggcccagcgtgggtgCtgccattcagcccaaagctg	13	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:4937895C>A	ENST00000424747.1	-	2	719	c.7G>T	c.(7-9)Gca>Tca	p.A3S	SLC52A1_ENST00000512825.2_Missense_Mutation_p.A3S|SLC52A1_ENST00000254853.5_Missense_Mutation_p.A3S	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	3					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										AGCGTGGGTGCTGCCATTCAG	0.602																																																0			17											46	47	47					17																	4937895		2203	4300	6503	4878619	SO:0001583	missense	55065			AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.7G>T	17.37:g.4937895C>A	ENSP00000399979:p.Ala3Ser		4878619	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	37	CCDS11066.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.042124	0.55003	.	.	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.76448	-1.02;-0.84;-1.02	1.92	-0.728	0.11162	.	0.591655	0.16928	N	0.193794	T	0.77143	0.4087	L	0.37630	1.12	0.21782	N	0.999546	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.66156	-0.5994	10	0.27785	T	0.31	.	7.1041	0.25354	0.4698:0.5302:0.0:0.0	.	3;3	F5H5Y1;Q9NWF4	.;RFT_HUMAN	S	3	ENSP00000254853:A3S;ENSP00000443026:A3S;ENSP00000399979:A3S	ENSP00000254853:A3S	A	-	1	0	GPR172B	4878619	0.975000	0.34042	0.765000	0.31456	0.846000	0.48090	2.709000	0.47160	-0.115000	0.11915	0.650000	0.86243	GCA		0.602	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		A	4937895	C	A	4937895	3	1	111	1	0	0	0	0	1	0	0	0	6690	797	28	2	1355	2	GPR172B	17	4937895	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	138565	4937895	76257315	863	29997										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6377871	6377871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctgacctcagggagctgcGgccccccagccgccggggtc	16	17	1	1	rs536434931		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:6377871G>A	ENST00000262483.8	-	10	1226	c.1139C>T	c.(1138-1140)cCg>cTg	p.P380L	PITPNM3_ENST00000421306.3_Missense_Mutation_p.P344L|PITPNM3_ENST00000576664.1_5'Flank	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	380					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGGGAGCTGCGGCCCCCCAGC	0.672													G|||	1	0.000199681	0	0	5008	,	,		16870	0		0	False		,,,				2504	0.001															0			17											24	22	23					17																	6377871		2190	4294	6484	6318595	SO:0001583	missense	83394			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1139C>T	17.37:g.6377871G>A	ENSP00000262483:p.Pro380Leu		6318595	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	G	3.518	-0.098348	0.07010	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.42513	0.97;0.97	4.3	0.0455	0.14230	.	0.580061	0.19024	N	0.124755	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.0	T	0.19160	-1.0314	10	0.23302	T	0.38	.	7.9757	0.30153	0.3626:0.0:0.6374:0.0	.	344;380	F8WEW5;Q9BZ71	.;PITM3_HUMAN	L	380;344	ENSP00000262483:P380L;ENSP00000407882:P344L	ENSP00000262483:P380L	P	-	2	0	PITPNM3	6318595	0.987000	0.35691	0.000000	0.03702	0.004000	0.04260	2.471000	0.45127	-0.033000	0.13736	-0.244000	0.11960	CCG		0.672	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		A	6377871	G	A	6377871	3	1	111	1	0	0	0	0	1	0	0	0	11983	1116	39	1	1829	1	PITPNM3	17	6377871	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1439976	6377871	74817339	864	29998										
BCL6B	255877	hgsc.bcm.edu	37	chr17	6930824	6930824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttggctgtcctcccacagtgCgacccctgtggcctgcattt	10	15	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:6930824C>T	ENST00000293805.5	+	9	1418	c.1326C>T	c.(1324-1326)tgC>tgT	p.C442C		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	442					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						TCCCACAGTGCGACCCCTGTG	0.597																																																0			17											38	45	42					17																	6930824		2073	4207	6280	6871548	SO:0001819	synonymous_variant	255877			AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1002	protein-coding gene	gene with protein product		608992	"zinc finger protein 62", "B-cell CLL/lymphoma 6, member B (zinc finger protein)"	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.1326C>T	17.37:g.6930824C>T			6871548	Q6PCB4	Silent	SNP	ENST00000293805.5	37	CCDS42248.1																																																																																				0.597	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844		T	6930824	C	T	6930824	2	4	111	1	0	0	0	0	0	0	0	1	1378	776	27	1		1	BCL6B	17	6930824	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	552953	6930824	74264386	865	29999										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7399270	7399270	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctttgcagaagcgaatgtCtgtgacggagggtggcatca	14	7	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7399270C>A	ENST00000322644.6	+	2	503	c.104C>A	c.(103-105)tCt>tAt	p.S35Y	POLR2A_ENST00000572844.1_Missense_Mutation_p.S35Y	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	35					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				AAGCGAATGTCTGTGACGGAG	0.567																																																0			17											76	82	80					17																	7399270		2203	4300	6503	7339994	SO:0001583	missense	5430					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.104C>A	17.37:g.7399270C>A	ENSP00000314949:p.Ser35Tyr		7339994	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160163	0.78226	.	.	ENSG00000181222	ENST00000322644	T	0.46063	0.88	5.33	5.33	0.75918	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.79203	0.4406	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.993	D	0.87694	0.2556	10	0.87932	D	0	.	17.783	0.88529	0.0:1.0:0.0:0.0	.	35;35	P24928;Q6NX41	RPB1_HUMAN;.	Y	35	ENSP00000314949:S35Y	ENSP00000314949:S35Y	S	+	2	0	SLC35G6	7339994	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.142000	0.77339	2.499000	0.84300	0.467000	0.42956	TCT		0.567	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		A	7399270	C	A	7399270	3	1	111	1	0	0	0	0	1	0	0	0	12245	913	32	2	110	2	POLR2A	17	7399270	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	468446	7399270	73795940	866	30000										
TP53	7157	hgsc.bcm.edu	37	chr17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccaggacaggcacaaacacGcacctcaaagctgttccgtc	8	16	1	0	rs121913343		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000420246.2_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	17	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65	56	59					17																	7577121		2203	4300	6503	7517846	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		7517846	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577121	G	A	7577121	3	1	111	1	0	0	0	0	1	0	0	0	16421	1087	38	1	469	1	TP53	17	7577121	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	177851	7577121	73618089	867	30001										
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	111	1	0	0	0	0	1	0	0	0	16421	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	417	7577538	73617672	868	30002										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7720951	7720951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtgcaatcctaccaaagtcCgggactggaacatccaaggg	11	11	0	0	rs138685987		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7720951C>T	ENST00000572933.1	+	66	11553	c.10093C>T	c.(10093-10095)Cgg>Tgg	p.R3365W	DNAH2_ENST00000389173.2_Missense_Mutation_p.R3365W			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3365	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TACCAAAGTCCGGGACTGGAA	0.562													C|||	1	0.000199681	0	0.0014	5008	,	,		19227	0		0	False		,,,				2504	0															0			17						C	TRP/ARG	0,4406		0,0,2203	88	88	88		10093	4.4	1	17	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DNAH2	NM_020877.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	3365/4428	7720951	1,13005	2203	4300	6503	7661676	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10093C>T	17.37:g.7720951C>T	ENSP00000458355:p.Arg3365Trp		7661676	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	19.94	3.920707	0.73213	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.67171	-0.25	5.36	4.39	0.52855	.	0.135740	0.48767	D	0.000168	D	0.88164	0.6363	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92133	0.5714	10	0.72032	D	0.01	.	14.4386	0.67301	0.1489:0.8511:0.0:0.0	.	3326;3365	Q9P225-2;Q9P225	.;DYH2_HUMAN	W	3326;3365	ENSP00000373825:R3365W	ENSP00000353818:R3326W	R	+	1	2	DNAH2	7661676	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	4.160000	0.58164	1.258000	0.44101	-0.270000	0.10280	CGG		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7720951	C	T	7720951	3	4	111	1	0	0	0	0	1	0	0	0	4613	643	23	1	10351	1	DNAH2	17	7720951	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	143413	7720951	73474259	869	30003										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7979578	7979579	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccacgctccacaaagtcattINSggggaggtagaggctgtcat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7979578_7979579insG	ENST00000319144.4	-	11	1706_1707	c.1446_1447insC	c.(1444-1449)cccaatfs	p.N483fs	ALOX12B_ENST00000577351.1_5'UTR	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	483	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						ACAAAGTCATTGGGGAGGTAGA	0.589										Multiple Myeloma(8;0.094)																																						0			17																																								7920304	SO:0001589	frameshift_variant	242			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1447dupC	17.37:g.7979582_7979582dupG	ENSP00000315167:p.Asn483fs		7920303		Frame_Shift_Ins	INS	ENST00000319144.4	37	CCDS11129.1																																																																																				0.589	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			G	7979579	-	G	7979578	7	5	111	1	0	1	1	0	0	0	0	0	537	1812	63	0	678	0	ALOX12B	17	7979578	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	258627	7979578	73215632	870	30004										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7982767	7982767	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaaagtgcagcaggcagaGgggggcgcagtggtgctgct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:7982767delG	ENST00000319144.4	-	8	1278	c.1018delC	c.(1018-1020)ctcfs	p.L340fs	AC129492.6_ENST00000399413.3_5'Flank|ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	340	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						AGCAGGCAGAGGGGGGCGCAG	0.667										Multiple Myeloma(8;0.094)																																						0			17											21	19	19					17																	7982767		2125	4158	6283	7923492	SO:0001589	frameshift_variant	242			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1018delC	17.37:g.7982767delG	ENSP00000315167:p.Leu340fs		7923492		Frame_Shift_Del	DEL	ENST00000319144.4	37	CCDS11129.1																																																																																				0.667	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			-	7982767	G	-	7982767	7	5	111	1	0	1	0	1	0	0	0	0	537	1000	35	0	1119	0	ALOX12B	17	7982767	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	3189	7982767	73212443	871	30005										
PFAS	5198	hgsc.bcm.edu	37	chr17	8159189	8159189	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggagctacagcggaaccCgagcactgtggaggcctttg	14	12	0	0	rs369947140		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:8159189C>A	ENST00000314666.6	+	6	774	c.641C>A	c.(640-642)cCg>cAg	p.P214Q	PFAS_ENST00000545834.1_5'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	214					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	CAGCGGAACCCGAGCACTGTG	0.547																																																0			17											102	100	101					17																	8159189		2203	4300	6503	8099914	SO:0001583	missense	5198			AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.641C>A	17.37:g.8159189C>A	ENSP00000313490:p.Pro214Gln		8099914	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067450	0.93898	.	.	ENSG00000178921	ENST00000314666	T	0.29655	1.56	5.68	5.68	0.88126	.	0.056910	0.64402	D	0.000001	T	0.72748	0.3499	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83822	0.0247	10	0.87932	D	0	-18.5456	17.2918	0.87159	0.0:1.0:0.0:0.0	.	214	O15067	PUR4_HUMAN	Q	214	ENSP00000313490:P214Q	ENSP00000313490:P214Q	P	+	2	0	PFAS	8099914	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	5.504000	0.66968	2.677000	0.91161	0.563000	0.77884	CCG		0.547	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			A	8159189	C	A	8159189	3	1	111	1	0	0	0	0	1	0	0	0	11785	652	23	2	659	2	PFAS	17	8159189	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	176422	8159189	73036021	872	30006										
PIK3R6	146850	hgsc.bcm.edu	37	chr17	8731468	8731468	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgtagtagagctgcaggctGagtctgggagtgaggcagaa	17	5	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:8731468G>A	ENST00000311434.9	-	12	1592	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	PIK3R6_ENST00000434064.2_5'UTR	NM_001010855.2	NP_001010855.1	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	451					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										GCTGCAGGCTGAGTCTGGGAG	0.642																																																0			17											92	96	94					17																	8731468		1989	4167	6156	8672193	SO:0001819	synonymous_variant	146850			AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000311434.9:c.1353C>T	17.37:g.8731468G>A			8672193	Q658R3	Silent	SNP	ENST00000311434.9	37																																																																																					0.642	PIK3R6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001010855		A	8731468	G	A	8731468	2	1	111	1	0	0	0	0	0	0	0	1	11954	1277	45	3		3	PIK3R6	17	8731468	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	572279	8731468	72463742	873	30007										
GLP2R	9340	hgsc.bcm.edu	37	chr17	9792899	9792899	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgcgaggtcttggggagctGggcgcccagccccaacagga	16	12	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:9792899G>A	ENST00000262441.5	+	13	2052	c.1539G>A	c.(1537-1539)ctG>ctA	p.L513L	GLP2R_ENST00000574745.1_Silent_p.L333L	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	513					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	TTGGGGAGCTGGGCGCCCAGC	0.637																																																0			17											37	37	37					17																	9792899		2203	4300	6503	9733624	SO:0001819	synonymous_variant	9340			AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1539G>A	17.37:g.9792899G>A			9733624	Q4VAT3	Silent	SNP	ENST00000262441.5	37	CCDS11150.1																																																																																				0.637	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9792899	G	A	9792899	2	1	111	1	0	0	0	0	0	0	0	1	6473	1335	47	3		3	GLP2R	17	9792899	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1061431	9792899	71402311	874	30008										
MYH8	4626	hgsc.bcm.edu	37	chr17	10300248	10300248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcaagggaagcacatttggCgttcacagcttctacatgtt	9	10	3	0	rs200412862		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:10300248C>T	ENST00000403437.2	-	31	4328	c.4234G>A	c.(4234-4236)Gcc>Acc	p.A1412T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1412					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GCACATTTGGCGTTCACAGCT	0.512									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							0			17											97	90	92					17																	10300248		2203	4300	6503	10240973	SO:0001583	missense	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.4234G>A	17.37:g.10300248C>T	ENSP00000384330:p.Ala1412Thr		10240973	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.753852	0.49362	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.78924	-1.22	5.15	5.15	0.70609	Myosin tail (1);	0.181065	0.26069	U	0.026527	T	0.78559	0.4302	M	0.80847	2.515	0.33432	D	0.581258	B	0.21821	0.061	B	0.19946	0.027	T	0.82376	-0.0488	10	0.59425	D	0.04	.	13.4122	0.60948	0.2698:0.7302:0.0:0.0	.	1412	P13535	MYH8_HUMAN	T	1412	ENSP00000384330:A1412T	ENSP00000252173:A1412T	A	-	1	0	MYH8	10240973	0.003000	0.15002	1.000000	0.80357	0.975000	0.68041	-0.061000	0.11693	2.673000	0.90976	0.650000	0.86243	GCC		0.512	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10300248	C	T	10300248	3	4	111	1	0	0	0	0	1	0	0	0	10071	768	27	1	1619	1	MYH8	17	10300248	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	507349	10300248	70894962	875	30009										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11865434	11865434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcatgcagtccacggctcGcaagaatgagtggccactgg	12	12	1	2	rs368954907		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:11865434G>A	ENST00000262442.4	+	68	13162	c.13094G>A	c.(13093-13095)cGc>cAc	p.R4365H	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Missense_Mutation_p.R677H|RP11-1096G20.5_ENST00000580270.1_RNA|DNAH9_ENST00000454412.2_Missense_Mutation_p.R4289H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4365					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		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)		TCCACGGCTCGCAAGAATGAG	0.557																																																0			17						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	67	64	65		13094,2030	1.8	0.9	17		65	0,8600		0,0,4300	no	missense,missense	DNAH9	NM_001372.3,NM_004662.2	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	4365/4487,677/799	11865434	1,13005	2203	4300	6503	11806159	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.13094G>A	17.37:g.11865434G>A	ENSP00000262442:p.Arg4365His		11806159	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.234034	0.22626	2.27E-4	0.0	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.14893	2.47;2.47;2.47	5.04	1.8	0.24995	Dynein heavy chain (1);	0.054502	0.64402	D	0.000002	T	0.44891	0.1315	H	0.97131	3.945	0.49798	D	0.999829	D	0.55800	0.973	P	0.54060	0.741	T	0.62191	-0.6906	10	0.72032	D	0.01	.	11.1115	0.48235	0.2349:0.0:0.7651:0.0	.	4365	Q9NYC9	DYH9_HUMAN	H	4365;4289;2871;677	ENSP00000262442:R4365H;ENSP00000414874:R4289H;ENSP00000379323:R677H	ENSP00000262442:R4365H	R	+	2	0	DNAH9	11806159	0.550000	0.26489	0.855000	0.33649	0.187000	0.23431	3.374000	0.52402	0.718000	0.32166	0.655000	0.94253	CGC		0.557	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11865434	G	A	11865434	3	1	111	1	0	0	0	0	1	0	0	0	4619	1087	38	1	13364	1	DNAH9	17	11865434	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1565186	11865434	69329776	876	30010										
RAB11FIP4	84440	hgsc.bcm.edu	37	chr17	29858706	29858706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acatggacaagattatcctcGccatcctggaccacaatccc	6	15	0	1	rs144926498		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:29858706G>A	ENST00000325874.8	+	15	2099	c.1870G>A	c.(1870-1872)Gcc>Acc	p.A624T	RAB11FIP4_ENST00000394744.2_Missense_Mutation_p.A522T	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	624	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				GATTATCCTCGCCATCCTGGA	0.562																																																0			17											158	141	147					17																	29858706		2203	4300	6503	26882826	SO:0001583	missense	84440			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"EF-hand domain containing"	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.1870G>A	17.37:g.29858706G>A	ENSP00000312837:p.Ala624Thr		26882826	Q52LI1|Q8N829|Q8NDT7|Q969D8	Missense_Mutation	SNP	ENST00000325874.8	37	CCDS11267.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.818229	0.50633	.	.	ENSG00000131242	ENST00000325874;ENST00000394744	.	.	.	5.81	5.81	0.92471	Rab-binding domain FIP-RBD (2);	0.053516	0.85682	D	0.000000	T	0.63604	0.2525	L	0.28274	0.84	0.58432	D	0.999996	D;P	0.71674	0.998;0.875	D;B	0.64595	0.927;0.188	T	0.59794	-0.7387	8	.	.	.	-26.0067	17.5764	0.87950	0.0:0.0:1.0:0.0	.	522;624	Q86YS3-2;Q86YS3	.;RFIP4_HUMAN	T	624	.	.	A	+	1	0	RAB11FIP4	26882826	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	5.142000	0.64820	2.746000	0.94184	0.655000	0.94253	GCC		0.562	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932		A	29858706	G	A	29858706	3	1	111	1	0	0	0	0	1	0	0	0	12933	1087	38	1	1928	1	RAB11FIP4	17	29858706	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	17993272	29858706	51336504	877	30011										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072928	34072928	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatggggtctctcccaagttCtgtcctgggacttccacttg	11	12	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:34072928C>T	ENST00000254466.6	-	6	1615	c.1588G>A	c.(1588-1590)Gaa>Aaa	p.E530K	GAS2L2_ENST00000587565.1_Missense_Mutation_p.E514K	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	530					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCCCAAGTTCTGTCCTGGGA	0.617																																																0			17											43	44	44					17																	34072928		2203	4300	6503	31097041	SO:0001583	missense	246176			AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1588G>A	17.37:g.34072928C>T	ENSP00000254466:p.Glu530Lys		31097041	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.688876	0.68271	.	.	ENSG00000132139	ENST00000254466	T	0.21543	2.0	4.81	3.83	0.44106	.	0.449943	0.21522	N	0.073188	T	0.15262	0.0368	L	0.29908	0.895	0.23192	N	0.998148	B	0.17038	0.02	B	0.20767	0.031	T	0.18023	-1.0350	10	0.28530	T	0.3	-8.7864	10.4654	0.44604	0.0:0.9077:0.0:0.0923	.	530	Q8NHY3	GA2L2_HUMAN	K	530	ENSP00000254466:E530K	ENSP00000254466:E530K	E	-	1	0	GAS2L2	31097041	0.004000	0.15560	0.853000	0.33588	0.922000	0.55478	0.289000	0.18957	1.238000	0.43771	0.655000	0.94253	GAA		0.617	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34072928	C	T	34072928	3	4	111	1	0	0	0	0	1	0	0	0	6267	922	32	3	1058	3	GAS2L2	17	34072928	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4214222	34072928	47122282	878	30012										
CSF3	1440	hgsc.bcm.edu	37	chr17	38173127	38173127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcctctgctttccagcgccGggcaggaggggtcctggttg	16	13	1	0	rs190847104		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:38173127G>A	ENST00000225474.2	+	5	570	c.539G>A	c.(538-540)cGg>cAg	p.R180Q	RP11-387H17.6_ENST00000583462.1_lincRNA|CSF3_ENST00000394148.3_Missense_Mutation_p.R144Q|CSF3_ENST00000577675.1_Missense_Mutation_p.R137Q|CSF3_ENST00000394149.3_Missense_Mutation_p.R177Q|CSF3_ENST00000331769.2_Missense_Mutation_p.R173Q			P09919	CSF3_HUMAN	colony stimulating factor 3 (granulocyte)	180					cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|granulocyte differentiation (GO:0030851)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of neuron death (GO:1901215)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|granulocyte colony-stimulating factor receptor binding (GO:0005130)			endometrium(1)|ovary(1)|prostate(1)	3	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)				TTCCAGCGCCGGGCAGGAGGG	0.657													G|||	1	0.000199681	0	0	5008	,	,		15617	0		0.001	False		,,,				2504	0															0			17						G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	44	42	43		539,422,530,431	3.3	0.8	17		43	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CSF3	NM_000759.3,NM_001178147.1,NM_172219.2,NM_172220.2	43,43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	180/208,141/169,177/205,144/172	38173127	1,13005	2203	4300	6503	35426653	SO:0001583	missense	1440				CCDS11357.1, CCDS11358.1, CCDS42314.1, CCDS11358.2	17q11.2-q12	2014-01-30			ENSG00000108342	ENSG00000108342		"Endogenous ligands"	2438	protein-coding gene	gene with protein product	"granulocyte colony stimulating factor", "pluripoietin", "filgrastim", "lenograstim"	138970	"chromosome 17 open reading frame 33"	GCSF, G-CSF, C17orf33		3499671, 3501046	Standard	NM_000759		Approved	MGC45931	uc002htp.3	P09919	OTTHUMG00000133247	ENST00000225474.2:c.539G>A	17.37:g.38173127G>A	ENSP00000225474:p.Arg180Gln		35426653	A8MXR7	Missense_Mutation	SNP	ENST00000225474.2	37	CCDS11357.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.65	1.408897	0.25378	0.0	1.16E-4	ENSG00000108342	ENST00000394149;ENST00000225474;ENST00000331769;ENST00000394148	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.29	3.32	0.38043	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.191913	0.45867	N	0.000329	T	0.14527	0.0351	M	0.63428	1.95	0.31491	N	0.665949	B;B;B;B	0.33000	0.393;0.358;0.144;0.144	B;B;B;B	0.23574	0.034;0.047;0.047;0.047	T	0.10894	-1.0610	10	0.31617	T	0.26	-41.3711	7.5034	0.27530	0.2646:0.0:0.7354:0.0	.	137;173;180;177	B4DNY7;Q8N4W3;P09919;Q6FH65	.;.;CSF3_HUMAN;.	Q	177;180;173;144	ENSP00000377705:R177Q;ENSP00000225474:R180Q;ENSP00000327766:R173Q;ENSP00000377704:R144Q	ENSP00000225474:R180Q	R	+	2	0	CSF3	35426653	1.000000	0.71417	0.810000	0.32431	0.109000	0.19521	2.030000	0.41108	0.631000	0.30412	-0.254000	0.11334	CGG		0.657	CSF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256988.2	NM_172220		A	38173127	G	A	38173127	3	1	111	1	0	0	0	0	1	0	0	0	3942	1116	39	1	557	1	CSF3	17	38173127	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4100199	38173127	43022083	879	30013										
RARA	5914	hgsc.bcm.edu	37	chr17	38508267	38508267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagctcattgagaaggtgcGcaaagcgcaccaggaaacct	13	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:38508267G>A	ENST00000254066.5	+	5	1030	c.575G>A	c.(574-576)cGc>cAc	p.R192H	RARA_ENST00000425707.3_Missense_Mutation_p.R95H|RARA_ENST00000394081.3_Missense_Mutation_p.R187H|RARA_ENST00000420042.1_3'UTR|RARA_ENST00000394089.2_Missense_Mutation_p.R192H|RARA_ENST00000394086.3_Missense_Mutation_p.R208H	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	192	Hinge.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GAGAAGGTGCGCAAAGCGCAC	0.602			T	"PML, ZNF145, TIF1, NUMA1, NPM1"	APL																																		Dom	yes		17	17q12	5914	"retinoic acid receptor, alpha"		L	0			17											32	32	32					17																	38508267		2202	4293	6495	35761793	SO:0001583	missense	5914			X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"Nuclear hormone receptors"	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.575G>A	17.37:g.38508267G>A	ENSP00000254066:p.Arg192His		35761793	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Missense_Mutation	SNP	ENST00000254066.5	37	CCDS11366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.781|9.781	1.175284|1.175284	0.21704|0.21704	.|.	.|.	ENSG00000131759|ENSG00000131759	ENST00000319149|ENST00000254066;ENST00000425707;ENST00000394089;ENST00000394086;ENST00000394081;ENST00000420042	.|D;D;D;D;D	.|0.92805	.|-3.09;-3.11;-3.09;-3.05;-2.95	4.38|4.38	3.41|3.41	0.39046|0.39046	.|Nuclear hormone receptor, ligand-binding (2);	0.478086|.	0.20834|.	N|.	0.084827|.	D|D	0.91270|0.91270	0.7248|0.7248	L|L	0.53561|0.53561	1.675|1.675	0.58432|0.58432	D|D	0.999999|0.999999	.|D;B;D	.|0.69078	.|0.997;0.027;0.99	.|P;B;P	.|0.52189	.|0.692;0.007;0.592	D|D	0.88153|0.88153	0.2852|0.2852	7|9	0.39692|0.24483	T|T	0.17|0.36	.|.	11.4391|11.4391	0.50086|0.50086	0.0915:0.0:0.9085:0.0|0.0915:0.0:0.9085:0.0	.|.	.|95;187;192	.|B8Y636;F1D8N9;P10276	.|.;.;RARA_HUMAN	T|H	186|192;95;192;208;187;79	.|ENSP00000254066:R192H;ENSP00000389993:R95H;ENSP00000377649:R192H;ENSP00000377648:R208H;ENSP00000377643:R187H	ENSP00000316769:A186T|ENSP00000254066:R192H	A|R	+|+	1|2	0|0	RARA|RARA	35761793|35761793	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.018000|0.018000	0.09664|0.09664	9.731000|9.731000	0.98807|0.98807	0.958000|0.958000	0.37956|0.37956	0.461000|0.461000	0.40582|0.40582	GCA|CGC		0.602	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2			A	38508267	G	A	38508267	3	1	111	1	0	0	0	0	1	0	0	0	13089	1087	38	1	756	1	RARA	17	38508267	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	335140	38508267	42686943	880	30014										
SMARCE1	6605	hgsc.bcm.edu	37	chr17	38787845	38787846	+	Splice_Site	INS	-	-	T													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacatattaaacagatacccINSttttaagttcattgttaaat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:38787845_38787846insT	ENST00000348513.6	-	9	1594_1595	c.814_815insA	c.(814-816)agg>aAgg	p.R272fs	SMARCE1_ENST00000578044.1_Splice_Site_p.R202fs|SMARCE1_ENST00000377808.4_Splice_Site_p.R237fs|SMARCE1_ENST00000544009.1_Splice_Site_p.R202fs|SMARCE1_ENST00000400122.3_Splice_Site_p.R202fs|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Splice_Site_p.R237fs|SMARCE1_ENST00000431889.2_Splice_Site_p.R254fs	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	272					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)			large_intestine(1)	1		Breast(137;0.000812)				AACAGATACCCTTTTAAGTTCA	0.312																																																0			17																																								36041372	SO:0001630	splice_region_variant	6605			AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.816+1->A	17.37:g.38787849_38787849dupT			36041371	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	Frame_Shift_Ins	INS	ENST00000348513.6	37	CCDS11370.1																																																																																				0.312	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1	NM_003079	Frame_Shift_Ins	T	38787846	-	T	38787845	8	5	111	1	0	1	1	0	0	0	1	0	14817	695	24	0	432	0	SMARCE1	17	38787845	Splice_Site	INS	-	TCGA-EI-6507-01A-11D-1733-10	279578	38787845	42407365	881	30015										
STAT5A	6776	hgsc.bcm.edu	37	chr17	40460307	40460307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catctatgtgtttcctgaccGccccaaggatgaggtcttct	9	12	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:40460307G>A	ENST00000345506.4	+	17	2660	c.2018G>A	c.(2017-2019)cGc>cAc	p.R673H	STAT5A_ENST00000588868.1_Missense_Mutation_p.R642H|STAT5A_ENST00000590949.1_Missense_Mutation_p.R673H|STAT5A_ENST00000546010.2_Missense_Mutation_p.R643H|STAT5A_ENST00000452307.2_Missense_Mutation_p.R670H|STAT5A_ENST00000587646.1_Missense_Mutation_p.R161H	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	673	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		TTTCCTGACCGCCCCAAGGAT	0.607																																																0			17											72	67	69					17																	40460307		2203	4300	6503	37713833	SO:0001583	missense	6776			U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.2018G>A	17.37:g.40460307G>A	ENSP00000341208:p.Arg673His		37713833	Q1KLZ6	Missense_Mutation	SNP	ENST00000345506.4	37	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.097455	0.76870	.	.	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	D;D;D	0.96522	-4.04;-4.04;-4.04	5.06	5.06	0.68205	SH2 motif (3);	0.000000	0.85682	D	0.000000	D	0.96494	0.8856	L	0.50333	1.59	0.80722	D	1	D;P;P;D;P	0.89917	1.0;0.951;0.951;0.966;0.951	P;B;B;P;P	0.56960	0.81;0.397;0.397;0.629;0.469	D	0.95284	0.8389	10	0.25106	T	0.35	-34.5498	18.4321	0.90630	0.0:0.0:1.0:0.0	.	673;670;643;644;673	A8K6I5;Q8WWS9;Q1KLZ6;Q59GY7;P42229	.;.;.;.;STA5A_HUMAN	H	673;643;644;670	ENSP00000341208:R673H;ENSP00000443107:R643H;ENSP00000400320:R670H	ENSP00000341208:R673H	R	+	2	0	STAT5A	37713833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.347000	0.65998	2.368000	0.80403	0.561000	0.74099	CGC		0.607	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		A	40460307	G	A	40460307	3	1	111	1	0	0	0	0	1	0	0	0	15307	1087	38	1	2076	1	STAT5A	17	40460307	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1672462	40460307	40734903	882	30016										
BRCA1	672	hgsc.bcm.edu	37	chr17	41197782	41197782	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acactgtccaacacccactcTcgggtcaccacaggtgcctc	7	18	2	0	rs397509290|rs273902775|rs80359873|rs80359883		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:41197782T>C	ENST00000357654.3	-	23	5623	c.5505A>G	c.(5503-5505)cgA>cgG	p.R1835R	BRCA1_ENST00000591534.1_Silent_p.R326R|BRCA1_ENST00000471181.2_Silent_p.R1856R|BRCA1_ENST00000468300.1_3'UTR|BRCA1_ENST00000591849.1_Silent_p.R68R|BRCA1_ENST00000309486.4_Silent_p.R1539R|BRCA1_ENST00000351666.3_Silent_p.R652R|BRCA1_ENST00000354071.3_Silent_p.R1570R|BRCA1_ENST00000346315.3_Silent_p.R1596R|BRCA1_ENST00000352993.3_Silent_p.R693R|BRCA1_ENST00000586385.1_Silent_p.R145R|BRCA1_ENST00000493795.1_Silent_p.R1788R|BRCA1_ENST00000491747.2_Silent_p.R731R	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1835	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ACACCCACTCTCGGGTCACCA	0.542			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0			17											104	86	92					17																	41197782		2203	4300	6503	38451308	SO:0001819	synonymous_variant	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5505A>G	17.37:g.41197782T>C			38451308	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																				0.542	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		C	41197782	T	C	41197782	2	2	111	1	0	0	0	0	0	0	0	1	1501	1538	54	4		4	BRCA1	17	41197782	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	737475	41197782	39997428	883	30017										
DHX8	1659	hgsc.bcm.edu	37	chr17	41570159	41570159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caagcggagacaccgatcccGctctcgatcacgttccagga	10	15	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:41570159G>A	ENST00000262415.3	+	6	686	c.614G>A	c.(613-615)cGc>cAc	p.R205H	DHX8_ENST00000540306.1_Missense_Mutation_p.R205H	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	205	Arg/Ser-rich (RS domain).				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		caCCGATCCCGCTCTCGATCA	0.552																																					NSCLC(56;1548 1661 49258 49987)											0			17											139	141	140					17																	41570159		2203	4300	6503	38925685	SO:0001583	missense	1659			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.614G>A	17.37:g.41570159G>A	ENSP00000262415:p.Arg205His		38925685		Missense_Mutation	SNP	ENST00000262415.3	37	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696420	0.30142	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.40476	1.03;1.03	5.47	3.49	0.39957	.	0.306760	0.31404	N	0.007707	T	0.31327	0.0793	L	0.32530	0.975	0.58432	D	0.999999	B;B	0.12630	0.006;0.002	B;B	0.09377	0.004;0.001	T	0.16070	-1.0415	10	0.62326	D	0.03	.	10.6547	0.45667	0.153:0.0:0.847:0.0	.	205;205	F5H658;Q14562	.;DHX8_HUMAN	H	205	ENSP00000437886:R205H;ENSP00000262415:R205H	ENSP00000262415:R205H	R	+	2	0	DHX8	38925685	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	6.268000	0.72552	1.314000	0.45095	-0.145000	0.13849	CGC		0.552	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			A	41570159	G	A	41570159	3	1	111	1	0	0	0	0	1	0	0	0	4526	1087	38	1	636	1	DHX8	17	41570159	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	372377	41570159	39625051	884	30018										
RUNDC3A	10900	hgsc.bcm.edu	37	chr17	42392949	42392949	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcgagaaacgggagctggaaGgcgtgatcctggagctgcag	18	8	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:42392949G>T	ENST00000426726.3	+	8	1199	c.925G>T	c.(925-927)Ggc>Tgc	p.G309C	RUNDC3A_ENST00000225441.7_Missense_Mutation_p.G309C|AC003102.3_ENST00000588097.1_RNA|RUNDC3A_ENST00000590941.1_Missense_Mutation_p.G304C	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	309					positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GGAGCTGGAAGGCGTGATCCT	0.682																																					Pancreas(82;1061 1416 11136 20771 23901)											0			17											3	5	4					17																	42392949		1845	3806	5651	39748475	SO:0001583	missense	10900			AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309			16984	protein-coding gene	gene with protein product		605448				9523700	Standard	NM_006695		Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.925G>T	17.37:g.42392949G>T	ENSP00000410862:p.Gly309Cys		39748475	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	Missense_Mutation	SNP	ENST00000426726.3	37	CCDS45698.1	.	.	.	.	.	.	.	.	.	.	g	19.12	3.765519	0.69878	.	.	ENSG00000108309	ENST00000426726;ENST00000225441	T;T	0.56103	0.48;0.48	4.01	4.01	0.46588	.	0.323197	0.32608	N	0.005872	T	0.46541	0.1398	N	0.22421	0.69	0.45318	D	0.99831	P;P;P;P	0.51653	0.947;0.896;0.896;0.896	B;B;P;P	0.48815	0.417;0.336;0.591;0.591	T	0.47497	-0.9113	10	0.40728	T	0.16	-20.1559	15.0634	0.71973	0.0:0.0:1.0:0.0	.	309;309;304;309	Q59EK9;Q59EK9-4;Q59EK9-2;Q59EK9-3	RUN3A_HUMAN;.;.;.	C	309	ENSP00000410862:G309C;ENSP00000225441:G309C	ENSP00000225441:G309C	G	+	1	0	RUNDC3A	39748475	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.527000	0.73803	2.060000	0.61445	0.455000	0.32223	GGC		0.682	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403173.2	NM_006695		T	42392949	G	T	42392949	3	4	111	1	0	0	0	0	1	0	0	0	13781	1000	35	2	955	2	RUNDC3A	17	42392949	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	822790	42392949	38802261	885	30019										
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42475954	42475954	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcccccctttccaagccaGactcttcacacttcttattg	3	17	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:42475954G>T	ENST00000591680.1	-	8	3521	c.3491C>A	c.(3490-3492)tCt>tAt	p.S1164Y	GPATCH8_ENST00000434000.1_Missense_Mutation_p.S1086Y	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1164							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TTCCAAGCCAGACTCTTCACA	0.542																																																0			17											116	125	122					17																	42475954		2202	4300	6502	39831480	SO:0001583	missense	23131			AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.3491C>A	17.37:g.42475954G>T	ENSP00000467556:p.Ser1164Tyr		39831480	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.447680	0.43429	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.14893	2.47	4.99	4.03	0.46877	.	0.289542	0.33419	N	0.004922	T	0.11537	0.0281	N	0.24115	0.695	0.29448	N	0.858709	B	0.13145	0.007	B	0.06405	0.002	T	0.08249	-1.0731	10	0.62326	D	0.03	-4.3848	9.1472	0.36939	0.0772:0.1463:0.7766:0.0	.	1164	Q9UKJ3	GPTC8_HUMAN	Y	1164;1086	ENSP00000395016:S1086Y	ENSP00000335486:S1164Y	S	-	2	0	GPATCH8	39831480	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.627000	0.54252	1.344000	0.45657	0.650000	0.86243	TCT		0.542	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		T	42475954	G	T	42475954	3	4	111	1	0	0	0	0	1	0	0	0	6614	942	33	2	1021	2	GPATCH8	17	42475954	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	83005	42475954	38719256	886	30020										
HEXIM2	124790	hgsc.bcm.edu	37	chr17	43246685	43246685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgagaggcagagccagaggGcctcccgggtccgcgaagag	17	11	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:43246685G>A	ENST00000307275.3	+	4	806	c.370G>A	c.(370-372)Gcc>Acc	p.A124T	HEXIM2_ENST00000592695.1_Missense_Mutation_p.A124T|RP13-890H12.2_ENST00000589451.1_RNA|RP13-890H12.2_ENST00000589796.1_RNA|HEXIM2_ENST00000591576.1_Missense_Mutation_p.A124T	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	124					negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			endometrium(1)|large_intestine(3)|lung(1)	5						GAGCCAGAGGGCCTCCCGGGT	0.637																																																0			17											31	35	34					17																	43246685		2203	4300	6503	40602468	SO:0001583	missense	124790			AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.370G>A	17.37:g.43246685G>A	ENSP00000302276:p.Ala124Thr		40602468	D3DX66	Missense_Mutation	SNP	ENST00000307275.3	37	CCDS11496.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.717284	0.89205	.	.	ENSG00000168517	ENST00000307275	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.76435	0.3987	L	0.58925	1.835	0.52099	D	0.999942	D	0.89917	1.0	D	0.87578	0.998	T	0.78590	-0.2145	9	0.87932	D	0	-22.9547	16.9989	0.86376	0.0:0.0:1.0:0.0	.	124	Q96MH2	HEXI2_HUMAN	T	124	.	ENSP00000302276:A124T	A	+	1	0	HEXIM2	40602468	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	7.544000	0.82117	2.667000	0.90743	0.561000	0.74099	GCC		0.637	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608		A	43246685	G	A	43246685	3	1	111	1	0	0	0	0	1	0	0	0	7098	1203	42	3	376	3	HEXIM2	17	43246685	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	770731	43246685	37948525	887	30021										
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46128610	46128610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccccactccgggagatcatcCtggggcccagttctgcctat	10	16	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:46128610C>A	ENST00000362042.3	+	2	746	c.130C>A	c.(130-132)Ctg>Atg	p.L44M	NFE2L1_ENST00000357480.5_Missense_Mutation_p.L44M|NFE2L1_ENST00000585291.1_Missense_Mutation_p.L44M|NFE2L1_ENST00000361665.3_Missense_Mutation_p.L44M	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	44					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGAGATCATCCTGGGGCCCAG	0.527																																																0			17											100	97	98					17																	46128610		2203	4300	6503	43483609	SO:0001583	missense	4779			AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.130C>A	17.37:g.46128610C>A	ENSP00000354855:p.Leu44Met		43483609	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	37	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467249	0.26335	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480	T;T	0.45276	0.9;0.9	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000001	T	0.61476	0.2350	M	0.71581	2.175	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.994;0.998;0.997	T	0.64445	-0.6406	10	0.66056	D	0.02	-19.3142	11.3388	0.49520	0.0:0.911:0.0:0.089	.	44;44;44	A3KMG6;Q14494-2;Q14494	.;.;NF2L1_HUMAN	M	63;44;44	ENSP00000355190:L44M;ENSP00000350072:L44M	ENSP00000350072:L44M	L	+	1	2	NFE2L1	43483609	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.034000	0.70933	2.323000	0.78572	0.462000	0.41574	CTG		0.527	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		A	46128610	C	A	46128610	3	1	111	1	0	0	0	0	1	0	0	0	10398	680	24	2	132	2	NFE2L1	17	46128610	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2881925	46128610	35066600	888	30022										
IGF2BP1	10642	hgsc.bcm.edu	37	chr17	47117401	47117401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccctgagggctgctcctccGcttgtaagatgatcttggag	12	12	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:47117401G>A	ENST00000290341.3	+	7	1100	c.766G>A	c.(766-768)Gct>Act	p.A256T	IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	256	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with ELAVL4 and binding to TAU mRNA. {ECO:0000250}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTGCTCCTCCGCTTGTAAGAT	0.512																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)											0			17											161	147	152					17																	47117401		2203	4300	6503	44472400	SO:0001583	missense	10642			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.766G>A	17.37:g.47117401G>A	ENSP00000290341:p.Ala256Thr		44472400	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	35	5.534452	0.96460	.	.	ENSG00000159217	ENST00000290341	T	0.76448	-1.02	5.65	5.65	0.86999	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.89206	0.6649	M	0.89534	3.04	0.80722	D	1	D	0.65815	0.995	P	0.59825	0.864	D	0.90494	0.4469	10	0.56958	D	0.05	-10.9207	18.512	0.90920	0.0:0.0:1.0:0.0	.	256	Q9NZI8	IF2B1_HUMAN	T	256	ENSP00000290341:A256T	ENSP00000290341:A256T	A	+	1	0	IGF2BP1	44472400	1.000000	0.71417	0.934000	0.37439	0.802000	0.45316	9.866000	0.99616	2.655000	0.90218	0.655000	0.94253	GCT		0.512	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		A	47117401	G	A	47117401	3	1	111	1	0	0	0	0	1	0	0	0	7594	1087	38	1	792	1	IGF2BP1	17	47117401	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	988791	47117401	34077809	889	30023										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48165207	48165207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgcagggctgctgctgctgGggctgatcatcctcctgctg	15	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:48165207G>T	ENST00000320031.8	+	24	3349	c.3019G>T	c.(3019-3021)Ggg>Tgg	p.G1007W	ITGA3_ENST00000007722.7_Missense_Mutation_p.G1007W	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	1007					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GCTGCTGCTGGGGCTGATCAT	0.637																																																0			17											54	56	55					17																	48165207		2202	4299	6501	45520206	SO:0001583	missense	3675			M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.3019G>T	17.37:g.48165207G>T	ENSP00000315190:p.Gly1007Trp		45520206	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.542554	0.65198	.	.	ENSG00000005884	ENST00000007722;ENST00000538917;ENST00000320031	T;T	0.58060	0.36;0.36	4.7	4.7	0.59300	.	0.052929	0.64402	D	0.000001	T	0.73071	0.3540	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.75892	-0.3157	10	0.51188	T	0.08	.	16.7594	0.85507	0.0:0.0:1.0:0.0	.	1007;1007	P26006-1;P26006	.;ITA3_HUMAN	W	1007;993;1007	ENSP00000007722:G1007W;ENSP00000315190:G1007W	ENSP00000007722:G1007W	G	+	1	0	ITGA3	45520206	1.000000	0.71417	0.944000	0.38274	0.273000	0.26683	5.785000	0.68998	2.314000	0.78098	0.455000	0.32223	GGG		0.637	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		T	48165207	G	T	48165207	3	4	111	1	0	0	0	0	1	0	0	0	7898	1232	43	2	3113	2	ITGA3	17	48165207	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1047806	48165207	33030003	890	30024										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48263786	48263786	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgggctgagtggggtacacGcaggtctcaccagtctccat	13	12	2	1	rs34940368	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:48263786G>A	ENST00000225964.5	-	49	4015	c.3897C>T	c.(3895-3897)tgC>tgT	p.C1299C		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1299	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	TGGGGTACACGCAGGTCTCAC	0.562			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta						G|||	32	0.00638978	0.0227	0.0029	5008	,	,		22768	0		0	False		,,,				2504	0						Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	0			17	GRCh37	CM012085	COL1A1	M	rs34940368	G		75,4331	66.4+/-103.9	0,75,2128	160	143	149	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3897	-0.3	1	17	dbSNP_126	149	0,8600		0,0,4300	no	coding-synonymous	COL1A1	NM_000088.3		0,75,6428	AA,AG,GG		0.0,1.7022,0.5767		1299/1465	48263786	75,12931	2203	4300	6503	45618785	SO:0001819	synonymous_variant	1277			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3897C>T	17.37:g.48263786G>A			45618785	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																				0.562	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48263786	G	A	48263786	2	1	111	1	0	0	0	0	0	0	0	1	3683	1079	38	1		1	COL1A1	17	48263786	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	98579	48263786	32931424	891	30025										
PRR11	55771	hgsc.bcm.edu	37	chr17	57247170	57247171	+	Frame_Shift_Ins	INS	-	-	A													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaaagccgaaagattattcINSaaaaaaaaagaagcctctca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:57247170_57247171insA	ENST00000262293.4	+	2	369_370	c.57_58insA	c.(58-60)aaafs	p.K20fs		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	20						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.E23fs*9(3)|p.E23fs*46(1)		breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AAAGATTATTCAAAAAAAAAGA	0.361																																																4	Deletion - Frameshift(3)|Insertion - Frameshift(1)	large_intestine(2)|ovary(1)|lung(1)	17																																								54601953	SO:0001589	frameshift_variant	55771				CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.66dupA	17.37:g.57247179_57247179dupA	ENSP00000262293:p.Lys20fs		54601952	Q9NUZ7|Q9NXE9	Frame_Shift_Ins	INS	ENST00000262293.4	37	CCDS11614.1																																																																																				0.361	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304		A	57247171	-	A	57247170	7	5	111	1	0	1	1	0	0	0	0	0	12617	825	29	0	59	0	PRR11	17	57247170	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	8983384	57247170	23948040	892	30026										
CLTC	1213	hgsc.bcm.edu	37	chr17	57761287	57761287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcgttcagttcagaaccatAacaacaaatctgtgaatgaa	7	8	3	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:57761287A>G	ENST00000269122.3	+	28	4649	c.4375A>G	c.(4375-4377)Aac>Gac	p.N1459D	CLTC_ENST00000579456.1_Missense_Mutation_p.N396D|CLTC_ENST00000393043.1_Missense_Mutation_p.N1459D	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1459	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCAGAACCATAACAACAAATC	0.318			T	"ALK, TFE3"	"ALCL, renal "																																		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	0			17											72	69	70					17																	57761287		2203	4300	6503	55116069	SO:0001583	missense	1213			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.4375A>G	17.37:g.57761287A>G	ENSP00000269122:p.Asn1459Asp		55116069	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.205454	0.79127	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.25912	1.77;1.77	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.82433	2.59	0.80722	D	1	D;B	0.71674	0.998;0.295	D;P	0.91635	0.999;0.487	T	0.60747	-0.7202	10	0.59425	D	0.04	.	15.9826	0.80125	1.0:0.0:0.0:0.0	.	1459;1459	Q00610;Q00610-2	CLH1_HUMAN;.	D	1459	ENSP00000269122:N1459D;ENSP00000376763:N1459D	ENSP00000269122:N1459D	N	+	1	0	CLTC	55116069	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.235000	0.73313	0.460000	0.39030	AAC		0.318	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57761287	A	G	57761287	3	3	111	1	0	0	0	0	1	0	0	0	3572	362	13	4	4485	4	CLTC	17	57761287	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	514117	57761287	23433923	893	30027										
CCDC47	57003	hgsc.bcm.edu	37	chr17	61829359	61829359	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gattcgctccttctctgctcTttttttctcctcccgccgag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:61829359delT	ENST00000225726.5	-	12	1694	c.1312delA	c.(1312-1314)agafs	p.R438fs	CCDC47_ENST00000403162.3_Frame_Shift_Del_p.R438fs|RP11-51F16.8_ENST00000580553.1_Frame_Shift_Del_p.K33fs|CCDC47_ENST00000582252.1_Frame_Shift_Del_p.R438fs	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	438					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						TTCTCTGCTCTTTTTTTCTCC	0.458																																																0			17											141	138	139					17																	61829359		2203	4300	6503	59183091	SO:0001589	frameshift_variant	57003			AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1312delA	17.37:g.61829359delT	ENSP00000225726:p.Arg438fs		59183091	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Frame_Shift_Del	DEL	ENST00000225726.5	37	CCDS11643.1																																																																																				0.458	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198		-	61829359	T	-	61829359	7	5	111	1	0	1	0	1	0	0	0	0	2824	1617	56	0	147	0	CCDC47	17	61829359	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	4068072	61829359	19365851	894	30028										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62049972	62049972	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaggtcctccagggggatgCcgatgacctccggcgggggg	18	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:62049972C>T	ENST00000435607.1	-	1	306	c.230G>A	c.(229-231)gGc>gAc	p.G77D	SCN4A_ENST00000578147.1_Missense_Mutation_p.G77D|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	77					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGGGGGATGCCGATGACCTC	0.587																																																0			17											27	31	29					17																	62049972		2059	4185	6244	59403704	SO:0001583	missense	6329			U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.230G>A	17.37:g.62049972C>T	ENSP00000396320:p.Gly77Asp		59403704	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941639	0.53079	.	.	ENSG00000007314	ENST00000435607	D	0.96300	-3.97	4.33	4.33	0.51752	.	0.225652	0.46758	D	0.000268	D	0.97046	0.9035	M	0.89353	3.025	0.37334	D	0.91009	D	0.56521	0.976	P	0.47786	0.557	D	0.99895	1.1146	10	0.62326	D	0.03	.	15.9897	0.80193	0.0:1.0:0.0:0.0	.	77	P35499	SCN4A_HUMAN	D	77	ENSP00000396320:G77D	ENSP00000396320:G77D	G	-	2	0	SCN4A	59403704	0.938000	0.31826	1.000000	0.80357	0.547000	0.35210	1.518000	0.35877	2.258000	0.74832	0.305000	0.20034	GGC		0.587	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62049972	C	T	62049972	3	4	111	1	0	0	0	0	1	0	0	0	13957	739	26	3	5376	3	SCN4A	17	62049972	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	220613	62049972	19145238	895	30029										
SMURF2	64750	hgsc.bcm.edu	37	chr17	62582271	62582271	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcctcctgtgcctattcggtCtctggactgaagacttacta	8	12	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:62582271C>T	ENST00000262435.9	-	6	605	c.418G>A	c.(418-420)Gac>Aac	p.D140N	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	140					BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			CCTATTCGGTCTCTGGACTGA	0.338																																																0			17											92	98	96					17																	62582271		2203	4300	6503	60012733	SO:0001583	missense	64750			AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.418G>A	17.37:g.62582271C>T	ENSP00000262435:p.Asp140Asn		60012733	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.406188	0.62288	.	.	ENSG00000108854	ENST00000262435	T	0.52754	0.65	5.45	5.45	0.79879	C2 calcium/lipid-binding domain, CaLB (1);	0.082699	0.85682	D	0.000000	T	0.58921	0.2156	M	0.70595	2.14	0.80722	D	1	P	0.50943	0.94	P	0.50754	0.649	T	0.54662	-0.8260	10	0.21014	T	0.42	.	19.2959	0.94122	0.0:1.0:0.0:0.0	.	140	Q9HAU4	SMUF2_HUMAN	N	140	ENSP00000262435:D140N	ENSP00000262435:D140N	D	-	1	0	SMURF2	60012733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.188000	0.77739	2.566000	0.86566	0.655000	0.94253	GAC		0.338	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		T	62582271	C	T	62582271	3	4	111	1	0	0	0	0	1	0	0	0	14857	913	32	3	1884	3	SMURF2	17	62582271	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	532299	62582271	18612939	896	30030										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67119400	67119400	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgatggcttcttttccttgGaattcaggagctactggttc	10	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:67119400G>A	ENST00000284425.2	-	10	1590	c.1416C>T	c.(1414-1416)ttC>ttT	p.F472F		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	472					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					CTTTTCCTTGGAATTCAGGAG	0.328																																																0			17											91	89	90					17																	67119400		2203	4300	6503	64630995	SO:0001819	synonymous_variant	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1416C>T	17.37:g.67119400G>A			64630995	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																				0.328	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67119400	G	A	67119400	2	1	111	1	0	0	0	0	0	0	0	1	36	1165	41	3		3	ABCA6	17	67119400	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	4537129	67119400	14075810	897	30031										
C17orf28	283987	hgsc.bcm.edu	37	chr17	72947704	72947704	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aacagcttcacgtcggtgtcGtaccagacaggggggtccac	13	12	1	1	rs147194757	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:72947704G>A	ENST00000425042.2	-	19	2405	c.2328C>T	c.(2326-2328)taC>taT	p.Y776Y		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	776					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											CGTCGGTGTCGTACCAGACAG	0.622																																																0			17						G		0,4406		0,0,2203	39	35	37		2328	-7.9	0.9	17	dbSNP_134	37	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	C17orf28	NM_030630.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		776/789	72947704	2,13004	2203	4300	6503	70459299	SO:0001819	synonymous_variant	283987				CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.2328C>T	17.37:g.72947704G>A			70459299	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																				0.622	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		A	72947704	G	A	72947704	2	1	111	1	0	0	0	0	0	0	0	1	1858	1140	40	1		1	C17orf28	17	72947704	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5828304	72947704	8247506	898	30032										
RECQL5	9400	hgsc.bcm.edu	37	chr17	73654466	73654466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gacggcaccaggaaggcttcCcatccctgccagcccggcca	11	18	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:73654466C>A	ENST00000317905.5	-	7	1220	c.1061G>T	c.(1060-1062)gGg>gTg	p.G354V	RECQL5_ENST00000420326.2_Missense_Mutation_p.G354V|RECQL5_ENST00000423245.2_Missense_Mutation_p.G327V|RECQL5_ENST00000340830.5_Missense_Mutation_p.G354V|RECQL5_ENST00000584999.1_Missense_Mutation_p.G354V	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	354	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GGAAGGCTTCCCATCCCTGCC	0.547								Other identified genes with known or suspected DNA repair function																																								0			17											129	126	127					17																	73654466		2203	4300	6503	71166061	SO:0001583	missense	9400			AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"RecQ protein 5"	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.1061G>T	17.37:g.73654466C>A	ENSP00000317636:p.Gly354Val		71166061	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	37	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171362	0.57584	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	T;T;T	0.10573	2.86;2.86;2.86	5.84	5.84	0.93424	Helicase, C-terminal (3);	0.049816	0.85682	D	0.000000	T	0.57373	0.2049	H	0.99516	4.605	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.77222	-0.2667	10	0.87932	D	0	-16.0714	20.1346	0.98019	0.0:1.0:0.0:0.0	.	354;327;354	O94762;Q6P4G0;O94762-3	RECQ5_HUMAN;.;.	V	354	ENSP00000317636:G354V;ENSP00000414933:G354V;ENSP00000341983:G354V	ENSP00000317636:G354V	G	-	2	0	RECQL5	71166061	1.000000	0.71417	0.992000	0.48379	0.975000	0.68041	7.818000	0.86416	2.765000	0.95021	0.655000	0.94253	GGG		0.547	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		A	73654466	C	A	73654466	3	1	111	1	0	0	0	0	1	0	0	0	13240	623	22	2	2057	2	RECQL5	17	73654466	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	706762	73654466	7540744	899	30033										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73738544	73738544	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgacctcaaggtggcccccgGctactacaccctcactgcag	9	18	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:73738544G>A	ENST00000200181.3	+	24	2943	c.2756G>A	c.(2755-2757)gGc>gAc	p.G919D	ITGB4_ENST00000449880.2_Missense_Mutation_p.G919D|ITGB4_ENST00000339591.3_Missense_Mutation_p.G919D|ITGB4_ENST00000579662.1_Missense_Mutation_p.G919D|ITGB4_ENST00000450894.3_Missense_Mutation_p.G919D|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	919					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTGGCCCCCGGCTACTACACC	0.667																																																0			17											47	32	37					17																	73738544		2201	4299	6500	71250139	SO:0001583	missense	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2756G>A	17.37:g.73738544G>A	ENSP00000200181:p.Gly919Asp		71250139	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022556	0.54683	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.82619	-1.63;-1.53;-1.53	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.87692	0.6241	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88902	0.3353	10	0.87932	D	0	.	19.3572	0.94420	0.0:0.0:1.0:0.0	.	919;919;919	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	D	919	ENSP00000200181:G919D;ENSP00000344079:G919D;ENSP00000400217:G919D	ENSP00000200181:G919D	G	+	2	0	ITGB4	71250139	1.000000	0.71417	0.981000	0.43875	0.772000	0.43724	7.913000	0.87471	2.583000	0.87209	0.650000	0.86243	GGC		0.667	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73738544	G	A	73738544	3	1	111	1	0	0	0	0	1	0	0	0	7918	1203	42	3	2846	3	ITGB4	17	73738544	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	84078	73738544	7456666	900	30034										
FOXJ1	2302	hgsc.bcm.edu	37	chr17	74136058	74136058	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggccgacagggtgatcttgGtggccttgctggcctgcatg	16	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:74136058G>A	ENST00000322957.6	-	2	773	c.419C>T	c.(418-420)aCc>aTc	p.T140I	RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157_ENST00000589912.1_5'Flank|RNF157-AS1_ENST00000585542.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	140					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			GGTGATCTTGGTGGCCTTGCT	0.627																																																0			17											81	57	65					17																	74136058		2203	4300	6503	71647653	SO:0001583	missense	2302			X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"Forkhead boxes"	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.419C>T	17.37:g.74136058G>A	ENSP00000323880:p.Thr140Ile		71647653	O00630	Missense_Mutation	SNP	ENST00000322957.6	37	CCDS32739.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.578335	0.45902	.	.	ENSG00000129654	ENST00000322957	D	0.95482	-3.72	5.35	5.35	0.76521	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.154769	0.56097	D	0.000023	D	0.89491	0.6730	N	0.11560	0.145	0.80722	D	1	B	0.18310	0.027	B	0.17433	0.018	D	0.86096	0.1553	10	0.56958	D	0.05	.	13.369	0.60703	0.0759:0.0:0.9241:0.0	.	140	Q92949	FOXJ1_HUMAN	I	140	ENSP00000323880:T140I	ENSP00000323880:T140I	T	-	2	0	FOXJ1	71647653	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.579000	0.36536	2.499000	0.84300	0.462000	0.41574	ACC		0.627	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454		A	74136058	G	A	74136058	3	1	111	1	0	0	0	0	1	0	0	0	6030	1261	44	3	854	3	FOXJ1	17	74136058	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	397514	74136058	7059152	901	30035										
UBE2O	63893	hgsc.bcm.edu	37	chr17	74392240	74392240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccagtacggagaagacctcGcccttggcgctggtgaaggt	14	11	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:74392240G>A	ENST00000319380.7	-	14	2842	c.2778C>T	c.(2776-2778)ggC>ggT	p.G926G	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	926					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						AGAAGACCTCGCCCTTGGCGC	0.637																																																0			17											36	38	37					17																	74392240		2203	4300	6503	71903835	SO:0001819	synonymous_variant	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2778C>T	17.37:g.74392240G>A			71903835	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																				0.637	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		A	74392240	G	A	74392240	2	1	111	1	0	0	0	0	0	0	0	1	16908	1074	38	1		1	UBE2O	17	74392240	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	256182	74392240	6802970	902	30036										
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74475004	74475004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggaggtgagggacaggactcCgggggtcagcggtgggtgcg	23	7	1	1	rs376555925		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:74475004C>T	ENST00000313080.4	-	6	916	c.643G>A	c.(643-645)Gga>Aga	p.G215R	RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000389760.4_Missense_Mutation_p.G186R|RHBDF2_ENST00000591885.1_Missense_Mutation_p.G186R	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	215					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						GACAGGACTCCGGGGGTCAGC	0.677																																																0			17						C	ARG/GLY,ARG/GLY	0,4406		0,0,2203	52	46	48		556,643	5.6	0.6	17		48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RHBDF2	NM_001005498.3,NM_024599.5	125,125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	186/828,215/857	74475004	1,13005	2203	4300	6503	71986599	SO:0001583	missense	79651			BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"rhomboid, veinlet-like 6 (Drosophila)", "tylosis with oesophageal cancer"	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.643G>A	17.37:g.74475004C>T	ENSP00000322775:p.Gly215Arg		71986599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475757	0.84640	0.0	1.16E-4	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.79749	-1.3;-1.3	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.89178	0.6641	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	D	0.88597	0.3147	10	0.49607	T	0.09	-36.6475	19.4888	0.95042	0.0:1.0:0.0:0.0	.	186;161;215;186	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	R	215;186;161	ENSP00000322775:G215R;ENSP00000374410:G186R	ENSP00000322775:G215R	G	-	1	0	RHBDF2	71986599	1.000000	0.71417	0.605000	0.28930	0.438000	0.31896	6.072000	0.71238	2.605000	0.88082	0.455000	0.32223	GGA		0.677	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		T	74475004	C	T	74475004	3	4	111	1	0	0	0	0	1	0	0	0	13357	661	23	1	1983	1	RHBDF2	17	74475004	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	82764	74475004	6720206	903	30037										
C17orf95	124512	hgsc.bcm.edu	37	chr17	74729392	74729392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagattttgaagacattttgGctacaatatattttttgatg	7	4	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:74729392G>A	ENST00000341249.6	+	4	672	c.340G>A	c.(340-342)Gct>Act	p.A114T	METTL23_ENST00000586200.1_5'UTR|METTL23_ENST00000590964.1_Missense_Mutation_p.A47T|METTL23_ENST00000588302.1_Missense_Mutation_p.A47T|METTL23_ENST00000589977.1_Missense_Mutation_p.A114T|METTL23_ENST00000586738.1_Missense_Mutation_p.A114T|METTL23_ENST00000586752.1_Missense_Mutation_p.A47T|METTL23_ENST00000591571.1_Missense_Mutation_p.A47T|METTL23_ENST00000588783.1_Missense_Mutation_p.A114T|METTL23_ENST00000588822.1_Missense_Mutation_p.A47T|MFSD11_ENST00000586622.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron	NM_001206984.1	NP_001193913.1	Q86XA0	MET23_HUMAN	methyltransferase like 23	114						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	methyltransferase activity (GO:0008168)			large_intestine(2)|lung(1)	3						AGACATTTTGGCTACAATATA	0.348																																																0			17											71	64	66					17																	74729392		1840	4087	5927	72240987	SO:0001583	missense	124512				CCDS45787.1, CCDS59298.1	17q25.2	2011-03-03	2011-03-03	2011-03-03	ENSG00000181038	ENSG00000181038			26988	protein-coding gene	gene with protein product		615262	"chromosome 17 open reading frame 95"	C17orf95		12477932	Standard	NM_001080510		Approved	LOC124512	uc021udl.1	Q86XA0		ENST00000341249.6:c.340G>A	17.37:g.74729392G>A	ENSP00000341543:p.Ala114Thr		72240987	H9ZYJ0|K7EK32	Missense_Mutation	SNP	ENST00000341249.6	37	CCDS45787.1	.	.	.	.	.	.	.	.	.	.	G	4.329	0.060496	0.08339	.	.	ENSG00000181038	ENST00000317409;ENST00000341249	T	0.06687	3.27	6.17	3.98	0.46160	.	0.511063	0.23354	N	0.049097	T	0.03783	0.0107	N	0.12637	0.245	0.20196	N	0.999922	B;B	0.06786	0.001;0.001	B;B	0.10450	0.002;0.005	T	0.46205	-0.9208	10	0.09338	T	0.73	-6.8963	5.2511	0.15522	0.7288:0.0:0.1403:0.1308	.	114;194	Q86XA0;Q8N712	MET23_HUMAN;.	T	193;114	ENSP00000341543:A114T	ENSP00000316862:A193T	A	+	1	0	METTL23	72240987	1.000000	0.71417	0.763000	0.31416	0.109000	0.19521	1.380000	0.34351	0.586000	0.29626	-0.238000	0.12139	GCT		0.348	METTL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451002.1	NM_001080510		A	74729392	G	A	74729392	3	1	111	1	0	0	0	0	1	0	0	0	1897	1203	42	3	350	3	C17orf95	17	74729392	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	254388	74729392	6465818	904	30038										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76462738	76462738	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtggcctcagtgactcaccGgaatcccctcagtctcctcc	9	17	4	1	rs374923749	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:76462738G>A	ENST00000585328.1	-	56	9048	c.8924C>T	c.(8923-8925)cCg>cTg	p.P2975L	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Splice_Site_p.P2966L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2966	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GTGACTCACCGGAATCCCCTC	0.637																																																0			17											30	35	33					17																	76462738		2065	4211	6276	73974333	SO:0001630	splice_region_variant	8632			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.8925+1C>T	17.37:g.76462738G>A			73974333	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	G	11.91	1.779159	0.31502	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.39997	1.05	4.64	-2.4	0.06583	.	.	.	.	.	T	0.42154	0.1190	M	0.64676	1.99	0.33918	D	0.640484	.	.	.	.	.	.	T	0.52815	-0.8525	7	0.54805	T	0.06	.	4.3957	0.11362	0.1125:0.0699:0.4019:0.4157	.	.	.	.	L	2975;2966	ENSP00000374490:P2966L	ENSP00000300671:P2975L	P	-	2	0	DNAH17	73974333	0.944000	0.32072	0.001000	0.08648	0.006000	0.05464	0.983000	0.29552	-0.718000	0.04949	-0.397000	0.06425	CCG		0.637	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	Missense_Mutation	A	76462738	G	A	76462738	5	1	111	1	0	0	0	0	0	0	1	0	4612	1130	39	1	4553	1	DNAH17	17	76462738	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1733346	76462738	4732472	905	30039										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76497340	76497340	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaatactggatttgggcatcGcagatgttggcaaagcagtg	14	6	0	1	rs370045140		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:76497340G>A	ENST00000585328.1	-	35	5518	c.5394C>T	c.(5392-5394)tgC>tgT	p.C1798C	RP11-559N14.5_ENST00000591373.1_RNA|DNAH17_ENST00000389840.5_Silent_p.C1789C|DNAH17-AS1_ENST00000598378.1_3'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1789	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TTTGGGCATCGCAGATGTTGG	0.592																																																0			17						G		0,4356		0,0,2178	108	116	113		5409	-8.5	0.7	17		113	2,8578	1.2+/-3.3	0,2,4288	no	coding-synonymous	DNAH17	NM_173628.3		0,2,6466	AA,AG,GG		0.0233,0.0,0.0155		1803/4463	76497340	2,12934	2178	4290	6468	74008935	SO:0001819	synonymous_variant	8632			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.5394C>T	17.37:g.76497340G>A			74008935	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																					0.592	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76497340	G	A	76497340	2	1	111	1	0	0	0	0	0	0	0	1	4612	1079	38	1		1	DNAH17	17	76497340	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	34602	76497340	4697870	906	30040										
RNF213	57674	hgsc.bcm.edu	37	chr17	78320610	78320610	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atcagcaccttccggcagtgCgcccgctttcagcaggggaa	12	14	2	0	rs375053532	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:78320610C>T	ENST00000582970.1	+	29	8618	c.8475C>T	c.(8473-8475)tgC>tgT	p.C2825C	RNF213_ENST00000336301.6_Silent_p.C898C|RNF213_ENST00000508628.2_Silent_p.C2874C	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2825					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TCCGGCAGTGCGCCCGCTTTC	0.607													C|||	2	0.000399361	0	0.0029	5008	,	,		18246	0		0	False		,,,				2504	0															0			17						C		0,4406		0,0,2203	51	47	48		8622	-8.2	0.7	17		48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RNF213	NM_020914.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		2874/5257	78320610	1,13005	2203	4300	6503	75935205	SO:0001819	synonymous_variant	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.8475C>T	17.37:g.78320610C>T			75935205	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																				0.607	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78320610	C	T	78320610	2	4	111	1	0	0	0	0	0	0	0	1	13514	776	27	1		1	RNF213	17	78320610	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1823270	78320610	2874600	907	30041										
RNF213	57674	hgsc.bcm.edu	37	chr17	78341582	78341582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctctgacgtgaagacgcacgGgccttttgaggccgtgatgc	14	11	1	5			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:78341582G>T	ENST00000582970.1	+	43	12049	c.11906G>T	c.(11905-11907)gGg>gTg	p.G3969V	RNF213_ENST00000336301.6_Missense_Mutation_p.G2042V|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.G4018V|CTD-2047H16.4_ENST00000575034.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3969					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AAGACGCACGGGCCTTTTGAG	0.592																																																0			17											76	70	72					17																	78341582		2203	4300	6503	75956177	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11906G>T	17.37:g.78341582G>T	ENSP00000464087:p.Gly3969Val		75956177	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.016520	0.35606	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.21361	2.01	5.08	2.02	0.26589	.	0.519406	0.20669	N	0.087876	T	0.11196	0.0273	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.17038	0.02;0.0	B;B	0.15870	0.014;0.0	T	0.20538	-1.0272	10	0.49607	T	0.09	.	1.1071	0.01696	0.2637:0.1526:0.4264:0.1572	.	4018;2042	C9JCP4;Q63HN8	.;RN213_HUMAN	V	3969;4018;2042	ENSP00000338218:G2042V	ENSP00000338218:G2042V	G	+	2	0	RNF213	75956177	0.119000	0.22226	0.256000	0.24389	0.592000	0.36648	0.737000	0.26144	0.543000	0.28864	0.655000	0.94253	GGG		0.592	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78341582	G	T	78341582	3	4	111	1	0	0	0	0	1	0	0	0	13514	1232	43	2	12391	2	RNF213	17	78341582	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	20972	78341582	2853628	908	30042										
RNF213	57674	hgsc.bcm.edu	37	chr17	78350234	78350234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcctagtgacagcaaccttgAtggaacggtgacagaaatgg	13	8	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:78350234A>G	ENST00000582970.1	+	52	13462	c.13319A>G	c.(13318-13320)gAt>gGt	p.D4440G	RNF213_ENST00000336301.6_Missense_Mutation_p.D2513G|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.D4489G|CTD-2047H16.4_ENST00000575034.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4440					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGCAACCTTGATGGAACGGTG	0.527																																																0			17											148	128	135					17																	78350234		2203	4300	6503	75964829	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13319A>G	17.37:g.78350234A>G	ENSP00000464087:p.Asp4440Gly		75964829	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.697060	0.30142	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.23348	1.91	5.47	1.95	0.26073	.	1.185250	0.05914	N	0.632297	T	0.15349	0.0370	N	0.14661	0.345	0.09310	N	1	B;B	0.14438	0.008;0.01	B;B	0.15484	0.013;0.005	T	0.30504	-0.9976	10	0.31617	T	0.26	.	5.7693	0.18243	0.7353:0.0:0.1393:0.1254	.	4489;2513	C9JCP4;Q63HN8	.;RN213_HUMAN	G	4440;4489;2513	ENSP00000338218:D2513G	ENSP00000338218:D2513G	D	+	2	0	RNF213	75964829	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.773000	0.26661	0.316000	0.23135	0.459000	0.35465	GAT		0.527	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78350234	A	G	78350234	3	3	111	1	0	0	0	0	1	0	0	0	13514	333	12	4	13840	4	RNF213	17	78350234	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	8652	78350234	2844976	909	30043										
RNF213	57674	hgsc.bcm.edu	37	chr17	78357688	78357688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cattgtggaacagaaaaatgGcaaagaaagagtgcccatcc	10	8	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr17:78357688G>A	ENST00000582970.1	+	59	14425	c.14282G>A	c.(14281-14283)gGc>gAc	p.G4761D	CTD-2047H16.4_ENST00000573394.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.G2834D|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.G4810D|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000427003.3_3'UTR	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4761					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CAGAAAAATGGCAAAGAAAGA	0.512																																																0			17											95	94	94					17																	78357688		2203	4300	6503	75972283	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.14282G>A	17.37:g.78357688G>A	ENSP00000464087:p.Gly4761Asp		75972283	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.962748	0.53507	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23147	1.92	5.08	5.08	0.68730	.	0.380686	0.26187	N	0.025834	T	0.27933	0.0688	M	0.76002	2.32	0.36158	D	0.847949	P	0.45283	0.855	B	0.38985	0.287	T	0.40403	-0.9565	10	0.51188	T	0.08	.	9.2966	0.37819	0.0808:0.1592:0.76:0.0	.	2834	Q63HN8	RN213_HUMAN	D	4761;4810;2834;111	ENSP00000338218:G2834D	ENSP00000338218:G2834D	G	+	2	0	RNF213	75972283	1.000000	0.71417	0.548000	0.28192	0.925000	0.55904	4.928000	0.63447	2.626000	0.88956	0.655000	0.94253	GGC		0.512	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78357688	G	A	78357688	3	1	111	1	0	0	0	0	1	0	0	0	13514	1203	42	3	14831	3	RNF213	17	78357688	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7454	78357688	2837522	910	30044										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7037668	7037668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgttgatgctgacctgatggCgcccgcctagtgcatcttgc	12	12	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:7037668C>T	ENST00000389658.3	-	12	1739	c.1646G>A	c.(1645-1647)cGc>cAc	p.R549H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	549	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GACCTGATGGCGCCCGCCTAG	0.547																																																0			18											101	86	91					18																	7037668		2203	4300	6503	7027668	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1646G>A	18.37:g.7037668C>T	ENSP00000374309:p.Arg549His		7027668		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	1.463	-0.561898	0.03939	.	.	ENSG00000101680	ENST00000389658	T	0.18810	2.19	5.43	-2.56	0.06268	Laminin B type IV (1);	0.503483	0.19469	N	0.113485	T	0.06280	0.0162	N	0.04508	-0.205	0.09310	N	1	B	0.15719	0.014	B	0.04013	0.001	T	0.16719	-1.0393	10	0.42905	T	0.14	.	0.8027	0.01078	0.1889:0.1742:0.2728:0.3641	.	549	P25391	LAMA1_HUMAN	H	549	ENSP00000374309:R549H	ENSP00000374309:R549H	R	-	2	0	LAMA1	7027668	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.244000	0.08903	-0.553000	0.06158	-0.221000	0.12465	CGC		0.547	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7037668	C	T	7037668	3	4	111	1	0	0	0	0	1	0	0	0	8627	768	27	1	7789	1	LAMA1	18	7037668	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		7037668	71039580	911	30045										
FAM38B	63895	hgsc.bcm.edu	37	chr18	10677755	10677755	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tacacttacactggtgttttTgaactttctgtgctgttgcc	8	9	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:10677755T>C	ENST00000503781.3	-	49	7730	c.7731A>G	c.(7729-7731)tcA>tcG	p.S2577S	PIEZO2_ENST00000581680.1_5'UTR|PIEZO2_ENST00000580640.1_Silent_p.S2602S|PIEZO2_ENST00000538948.1_Silent_p.S534S|PIEZO2_ENST00000285141.4_Silent_p.S369S|PIEZO2_ENST00000302079.6_Silent_p.S2514S	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2577					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										CTGGTGTTTTTGAACTTTCTG	0.343																																																0			18											143	134	137					18																	10677755		2202	4300	6502	10667755	SO:0001819	synonymous_variant	63895			AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7731A>G	18.37:g.10677755T>C			10667755	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	37																																																																																					0.343	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		C	10677755	T	C	10677755	2	2	111	1	0	0	0	0	0	0	0	1	5574	1799	63	4		4	FAM38B	18	10677755	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	3640087	10677755	67399493	912	30046										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12463405	12463405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actgcctcacgttagtaggcGtttccttttcaatggaatgt	9	9	2	0	rs141286455		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:12463405G>A	ENST00000409402.4	-	12	1850	c.1583C>T	c.(1582-1584)aCg>aTg	p.T528M	SPIRE1_ENST00000453447.2_Missense_Mutation_p.T394M|SPIRE1_ENST00000309836.5_Missense_Mutation_p.T317M|SPIRE1_ENST00000383356.2_Missense_Mutation_p.T355M|SPIRE1_ENST00000410092.3_Missense_Mutation_p.T514M|SPIRE1_ENST00000464481.1_5'UTR	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						GTTAGTAGGCGTTTCCTTTTC	0.502																																																0			18						G	MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	126	115	119		1583,1181,1541	5.4	1	18	dbSNP_134	119	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	SPIRE1	NM_001128626.1,NM_001128627.1,NM_020148.2	81,81,81	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging	528/757,394/623,514/743	12463405	3,13003	2203	4300	6503	12453405	SO:0001583	missense	56907			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1583C>T	18.37:g.12463405G>A	ENSP00000387266:p.Thr528Met		12453405		Missense_Mutation	SNP	ENST00000409402.4	37	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523161	0.85600	2.27E-4	2.33E-4	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.48522	0.83;1.42;1.41;0.83;0.81	5.41	5.41	0.78517	.	0.093182	0.85682	D	0.000000	T	0.69079	0.3071	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.97;0.949;0.998	T	0.70073	-0.4972	10	0.62326	D	0.03	-11.2978	19.5527	0.95328	0.0:0.0:1.0:0.0	.	514;317;528	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	M	394;528;514;317;355	ENSP00000407050:T394M;ENSP00000387266:T528M;ENSP00000387226:T514M;ENSP00000309661:T317M;ENSP00000372847:T355M	ENSP00000309661:T317M	T	-	2	0	SPIRE1	12453405	1.000000	0.71417	0.954000	0.39281	0.925000	0.55904	9.084000	0.94076	2.705000	0.92388	0.585000	0.79938	ACG		0.502	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		A	12463405	G	A	12463405	3	1	111	1	0	0	0	0	1	0	0	0	15110	1145	40	1	711	1	SPIRE1	18	12463405	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1785650	12463405	65613843	913	30047										
CEP192	55125	hgsc.bcm.edu	37	chr18	13029760	13029760	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcaaatgccaatagaggtggTtttgatctgactgaccctgt	11	8	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:13029760T>C	ENST00000325971.8	+	0	1229				CEP192_ENST00000430049.2_5'Flank|CEP192_ENST00000506447.1_Silent_p.G383G			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ATAGAGGTGGTTTTGATCTGA	0.428																																																0			18											88	72	77					18																	13029760		692	1591	2283	13019760	SO:0001623	5_prime_UTR_variant	55125			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-365T>C	18.37:g.13029760T>C			13019760	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																					0.428	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		C	13029760	T	C	13029760	1	2	111	0	1	0	0	0	0	0	0	0	3257	1712	60	4		4	CEP192	18	13029760	5'UTR	SNP	T	TCGA-EI-6507-01A-11D-1733-10	566355	13029760	65047488	914	30048										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18546988	18546988	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caatatcactctctttgctgGccaactgcatctgaagctca	6	13	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:18546988G>T	ENST00000399799.2	-	27	4182	c.3242C>A	c.(3241-3243)gCc>gAc	p.A1081D		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1081					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					CTCTTTGCTGGCCAACTGCAT	0.373																																																0			18											171	153	159					18																	18546988		2203	4300	6503	16800986	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3242C>A	18.37:g.18546988G>T	ENSP00000382697:p.Ala1081Asp		16800986	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	G	5.143	0.211996	0.09757	.	.	ENSG00000067900	ENST00000399799	T	0.14266	2.52	5.62	4.73	0.59995	.	0.109437	0.64402	D	0.000014	T	0.02767	0.0083	N	0.00223	-1.815	0.36894	D	0.890078	B	0.02656	0.0	B	0.01281	0.0	T	0.34675	-0.9819	10	0.02654	T	1	.	12.8531	0.57869	0.0:0.0:0.5518:0.4481	.	1081	Q13464	ROCK1_HUMAN	D	1081	ENSP00000382697:A1081D	ENSP00000382697:A1081D	A	-	2	0	ROCK1	16800986	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.604000	0.61112	1.351000	0.45789	0.591000	0.81541	GCC		0.373	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		T	18546988	G	T	18546988	3	4	111	1	0	0	0	0	1	0	0	0	13554	1203	42	2	850	2	ROCK1	18	18546988	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5517228	18546988	59530260	915	30049										
KCTD1	284252	hgsc.bcm.edu	37	chr18	24039635	24039635	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtggaaacctgatgacgtgCgtcgagtcgtgattccagcc	13	10	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:24039635C>T	ENST00000408011.3	-	4	1123	c.564G>A	c.(562-564)acG>acA	p.T188T	KCTD1_ENST00000317932.7_Silent_p.T188T|KCTD1_ENST00000417602.1_Silent_p.T796T|KCTD1_ENST00000580059.1_Silent_p.T188T|KCTD1_ENST00000579973.1_Silent_p.T188T	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1	188					negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			TGATGACGTGCGTCGAGTCGT	0.473																																																0			18											173	143	153					18																	24039635		2203	4300	6503	22293633	SO:0001819	synonymous_variant	284252			AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"potassium channel tetramerisation domain containing 1"	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.564G>A	18.37:g.24039635C>T			22293633	A8K1F5	Silent	SNP	ENST00000408011.3	37	CCDS11888.1																																																																																				0.473	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091		T	24039635	C	T	24039635	2	4	111	1	0	0	0	0	0	0	0	1	8117	755	27	1		1	KCTD1	18	24039635	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5492647	24039635	54037613	916	30050										
CHST9	83539	hgsc.bcm.edu	37	chr18	24496363	24496363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctttcatcggaagagtgccTatccttaaagttgggaaatt	9	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:24496363T>C	ENST00000284224.8	-	6	1469	c.1192A>G	c.(1192-1194)Agg>Ggg	p.R398G	AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000579964.1_RNA|CHST9_ENST00000580774.1_3'UTR|CHST9_ENST00000581714.1_Missense_Mutation_p.R398G|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000582605.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	398					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					GAAGAGTGCCTATCCTTAAAG	0.368																																																0			18											155	142	146					18																	24496363		1839	4091	5930	22750361	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.1192A>G	18.37:g.24496363T>C	ENSP00000284224:p.Arg398Gly		22750361	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610254	0.46527	.	.	ENSG00000154080	ENST00000284224	T	0.73681	-0.77	6.07	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.74191	0.3684	L	0.35542	1.07	0.80722	D	1	B	0.29162	0.235	P	0.45343	0.477	T	0.71111	-0.4687	10	0.38643	T	0.18	-25.1503	13.5852	0.61926	0.0:0.0:0.1297:0.8703	.	398	Q7L1S5	CHST9_HUMAN	G	398	ENSP00000284224:R398G	ENSP00000284224:R398G	R	-	1	2	CHST9	22750361	1.000000	0.71417	0.960000	0.40013	0.976000	0.68499	3.206000	0.51098	1.100000	0.41517	0.533000	0.62120	AGG		0.368	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		C	24496363	T	C	24496363	3	2	111	1	0	0	0	0	1	0	0	0	3417	1521	53	4	143	4	CHST9	18	24496363	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	456728	24496363	53580885	917	30051										
ST8SIA5	29906	hgsc.bcm.edu	37	chr18	44268805	44268805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggtgtccacctcatacttgAgctttgtccccaggggagtg	12	11	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:44268805A>G	ENST00000315087.7	-	4	1049	c.389T>C	c.(388-390)cTc>cCc	p.L130P	ST8SIA5_ENST00000538168.1_Missense_Mutation_p.L166P|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.L99P|ST8SIA5_ENST00000590497.1_5'UTR	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	130					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						CTCATACTTGAGCTTTGTCCC	0.597																																																0			18											168	143	151					18																	44268805		2203	4300	6503	42522803	SO:0001583	missense	29906			U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.389T>C	18.37:g.44268805A>G	ENSP00000321343:p.Leu130Pro		42522803	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	37	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.437410	0.83885	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.34472	1.36;1.36;1.36	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.66005	0.2746	M	0.87381	2.88	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	0.999;0.997;1.0	T	0.73030	-0.4111	10	0.87932	D	0	-8.5351	15.7574	0.78046	1.0:0.0:0.0:0.0	.	99;166;130	F5H8D1;B7Z1K9;O15466	.;.;SIA8E_HUMAN	P	130;166;99	ENSP00000321343:L130P;ENSP00000445492:L166P;ENSP00000443683:L99P	ENSP00000321343:L130P	L	-	2	0	ST8SIA5	42522803	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.932000	0.92897	2.125000	0.65367	0.459000	0.35465	CTC		0.597	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		G	44268805	A	G	44268805	3	3	111	1	0	0	0	0	1	0	0	0	15274	304	11	4	757	4	ST8SIA5	18	44268805	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	19772442	44268805	33808443	918	30052										
SMAD7	4092	hgsc.bcm.edu	37	chr18	46474795	46474795	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcgggtatctggagtaaggaGgggggggagactctgaaatt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:46474795delG	ENST00000262158.2	-	2	912	c.626delC	c.(625-627)cctfs	p.P210fs	SMAD7_ENST00000591805.1_5'UTR|SMAD7_ENST00000589634.1_Frame_Shift_Del_p.P210fs	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7	210	Important for interaction with SMURF2.|Poly-Pro.				adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					GGAGTAAGGAGGGGGGGGAGA	0.388																																																0			18											37	44	42					18																	46474795		2202	4299	6501	44728793	SO:0001589	frameshift_variant	4092			AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"SMADs"	6773	protein-coding gene	gene with protein product		602932	"MAD, mothers against decapentaplegic homolog 7 (Drosophila)", "SMAD, mothers against DPP homolog 7 (Drosophila)"	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.626delC	18.37:g.46474795delG	ENSP00000262158:p.Pro210fs		44728793	B7Z773|K7EQ10|O14740|Q6DK23	Frame_Shift_Del	DEL	ENST00000262158.2	37	CCDS11936.1																																																																																				0.388	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904		-	46474795	G	-	46474795	7	5	111	1	0	1	0	1	0	0	0	0	14800	1000	35	0	666	0	SMAD7	18	46474795	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	2205990	46474795	31602453	919	30053										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48593497	48593497	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagagttactacttagacagAgaagctgggcgtgcacctgg	13	9	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:48593497A>G	ENST00000342988.3	+	10	1786	c.1248A>G	c.(1246-1248)agA>agG	p.R416R	SMAD4_ENST00000398417.2_Silent_p.R416R|SMAD4_ENST00000588745.1_Silent_p.R320R	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	416	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.R416S(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ACTTAGACAGAGAAGCTGGGC	0.413																																																39	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)	pancreas(26)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											162	133	143					18																	48593497		2203	4300	6503	46847495	SO:0001819	synonymous_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1248A>G	18.37:g.48593497A>G			46847495	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48593497	A	G	48593497	2	3	111	1	0	0	0	0	0	0	0	1	14797	301	11	4		4	SMAD4	18	48593497	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2118702	48593497	29483751	920	30054										
POLI	11201	hgsc.bcm.edu	37	chr18	51813701	51813701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agtgagattaataatccgtcGgtattcctctgagaagcact	9	8	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:51813701G>A	ENST00000579534.1	+	8	1261	c.1118G>A	c.(1117-1119)cGg>cAg	p.R373Q	POLI_ENST00000406285.3_Missense_Mutation_p.R294Q|POLI_ENST00000582366.1_3'UTR|POLI_ENST00000217800.5_Missense_Mutation_p.R247Q|POLI_ENST00000579434.1_Missense_Mutation_p.R270Q	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	373	DNA binding.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		ATAATCCGTCGGTATTCCTCT	0.388								DNA polymerases (catalytic subunits)																																								0			18											90	84	86					18																	51813701		2203	4300	6503	50067699	SO:0001583	missense	11201				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.1118G>A	18.37:g.51813701G>A	ENSP00000462664:p.Arg373Gln		50067699	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	37	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844861	0.32606	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.48836	0.8	5.55	5.55	0.83447	DNA polymerase, Y-family, little finger domain (2);	0.146210	0.49305	D	0.000148	T	0.52322	0.1727	L	0.31926	0.97	0.39907	D	0.97397	D;D	0.76494	0.999;0.988	D;B	0.67725	0.953;0.385	T	0.53019	-0.8497	10	0.42905	T	0.14	-11.1732	8.5897	0.33679	0.1628:0.0:0.8372:0.0	.	293;373	B7Z780;Q9UNA4	.;POLI_HUMAN	Q	294;373	ENSP00000385196:R294Q	ENSP00000217800:R373Q	R	+	2	0	POLI	50067699	0.995000	0.38212	0.954000	0.39281	0.456000	0.32438	3.141000	0.50593	2.618000	0.88619	0.655000	0.94253	CGG		0.388	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		A	51813701	G	A	51813701	3	1	111	1	0	0	0	0	1	0	0	0	12234	1116	39	1	1148	1	POLI	18	51813701	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3220204	51813701	26263547	921	30055										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246440	56246440	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccctcttgctccataagtccTttccccccactctcttgtca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:56246440delT	ENST00000361673.3	-	4	1781	c.1568delA	c.(1567-1569)aagfs	p.K523fs	ALPK2_ENST00000587399.1_5'UTR	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	523						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCATAAGTCCTTTCCCCCCAC	0.522											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			18											227	226	226					18																	56246440		2203	4300	6503	54397420	SO:0001589	frameshift_variant	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1568delA	18.37:g.56246440delT	ENSP00000354991:p.Lys523fs	1014	54397420	Q6ZUX0|Q8NAT5|Q96L95	Frame_Shift_Del	DEL	ENST00000361673.3	37	CCDS11966.2																																																																																				0.522	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		-	56246440	T	-	56246440	7	5	111	1	0	1	0	1	0	0	0	0	545	1609	56	0	4984	0	ALPK2	18	56246440	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	4432739	56246440	21830808	922	30056										
PIGN	23556	hgsc.bcm.edu	37	chr18	59825011	59825011	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcacacgtgtatgagatatGccccagctgccttcatgcat	10	12	1	1	rs34096683		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:59825011G>A	ENST00000357637.5	-	5	667	c.252C>T	c.(250-252)ggC>ggT	p.G84G	PIGN_ENST00000400334.3_Silent_p.G84G	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	84					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TATGAGATATGCCCCAGCTGC	0.393																																																0			18											61	58	59					18																	59825011		1921	4154	6075	57975991	SO:0001819	synonymous_variant	23556			AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.252C>T	18.37:g.59825011G>A			57975991	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																				0.393	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		A	59825011	G	A	59825011	2	1	111	1	0	0	0	0	0	0	0	1	11924	1306	46	3		3	PIGN	18	59825011	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3578571	59825011	18252237	923	30057										
TMX3	54495	hgsc.bcm.edu	37	chr18	66364524	66364524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atacaatcaattctgaagcaGcatctatgtatttctcctat	4	9	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:66364524G>A	ENST00000299608.2	-	8	825	c.509C>T	c.(508-510)gCt>gTt	p.A170V	TMX3_ENST00000562706.1_Missense_Mutation_p.A170V|TMX3_ENST00000443099.2_Missense_Mutation_p.A143V	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	170					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TTCTGAAGCAGCATCTATGTA	0.289																																																0			18											36	36	36					18																	66364524		2199	4289	6488	64515504	SO:0001583	missense	54495			BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.509C>T	18.37:g.66364524G>A	ENSP00000299608:p.Ala170Val		64515504	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	37	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	G	4.075	0.011747	0.07912	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T	0.29142	1.58;2.75	5.52	2.34	0.29019	.	0.310261	0.34828	N	0.003649	T	0.07458	0.0188	N	0.00483	-1.445	0.48452	D	0.999651	B;B;B	0.18013	0.007;0.011;0.025	B;B;B	0.24701	0.004;0.018;0.055	T	0.10870	-1.0611	10	0.13470	T	0.59	.	5.4444	0.16527	0.4759:0.0:0.5241:0.0	.	143;170;170	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	V	170;170;143	ENSP00000299608:A170V;ENSP00000402605:A143V	ENSP00000299608:A170V	A	-	2	0	TMX3	64515504	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.282000	0.43461	0.696000	0.31696	0.655000	0.94253	GCT		0.289	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		A	66364524	G	A	66364524	3	1	111	1	0	0	0	0	1	0	0	0	16307	971	34	3	891	3	TMX3	18	66364524	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	6539513	66364524	11712724	924	30058										
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992660	67992660	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctcccatggaagtctctgcGgttcctcctcaagtgggagg	12	12	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:67992660G>A	ENST00000397942.3	+	2	1072	c.756G>A	c.(754-756)gcG>gcA	p.A252A	SOCS6_ENST00000582322.1_Silent_p.A252A	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	252					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				AAGTCTCTGCGGTTCCTCCTC	0.532																																					Melanoma(84;1024 1361 24382 36583 42651)											0			18											95	78	84					18																	67992660		2203	4300	6503	66143640	SO:0001819	synonymous_variant	9306			AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.756G>A	18.37:g.67992660G>A			66143640	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																				0.532	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			A	67992660	G	A	67992660	2	1	111	1	0	0	0	0	0	0	0	1	14955	1103	39	1		1	SOCS6	18	67992660	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1628136	67992660	10084588	925	30059										
CNDP2	55748	hgsc.bcm.edu	37	chr18	72185802	72185802	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagttcaaggtgtacatgggCcacggtgggaagccctgggt	17	8	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:72185802C>T	ENST00000324262.4	+	10	1453	c.1137C>T	c.(1135-1137)ggC>ggT	p.G379G	CNDP2_ENST00000579847.1_Silent_p.G379G|CNDP2_ENST00000324301.8_Silent_p.G295G	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	379					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		TGTACATGGGCCACGGTGGGA	0.502																																																0			18											129	121	123					18																	72185802		2203	4300	6503	70336782	SO:0001819	synonymous_variant	55748			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.1137C>T	18.37:g.72185802C>T			70336782	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																				0.502	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		T	72185802	C	T	72185802	2	4	111	1	0	0	0	0	0	0	0	1	3600	726	26	3		3	CNDP2	18	72185802	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4193142	72185802	5891446	926	30060										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77895441	77895441	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggtccacatggaggtagcGcataagcacagcgagtccaa	12	11	0	0	rs117499189	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr18:77895441G>A	ENST00000262198.4	+	4	2600	c.2145G>A	c.(2143-2145)gcG>gcA	p.A715A		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	715					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		TGGAGGTAGCGCATAAGCACA	0.522													G|||	12	0.00239617	0	0	5008	,	,		22436	0.0119		0	False		,,,				2504	0															0			18						G		2,4404	4.2+/-10.8	0,2,2201	150	140	144		2145	-6.3	0.8	18	dbSNP_132	144	0,8600		0,0,4300	no	coding-synonymous	ADNP2	NM_014913.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		715/1132	77895441	2,13004	2203	4300	6503	75996432	SO:0001819	synonymous_variant	22850			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2145G>A	18.37:g.77895441G>A			75996432	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																				0.522	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		A	77895441	G	A	77895441	2	1	111	1	0	0	0	0	0	0	0	1	324	1074	38	1		1	ADNP2	18	77895441	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	5709639	77895441	181807	927	30061										
RNF126	55658	hgsc.bcm.edu	37	chr19	648262	648263	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgaggctttttcggcagacINSggggcagctgtcgtgctttg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:648262_648263insG	ENST00000292363.5	-	9	956_957	c.801_802insC	c.(799-804)cccgtcfs	p.V268fs		NM_194460.2	NP_919442.1			ring finger protein 126											lung(1)	1		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|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)		TTTCGGCAGACGGGGCAGCTGT	0.693																																																0			19																																								599263	SO:0001589	frameshift_variant	55658			BC025374	CCDS12039.1	19p13.3	2013-01-09				ENSG00000070423		"RING-type (C3HC4) zinc fingers"	21151	protein-coding gene	gene with protein product		615177					Standard	NM_194460		Approved	FLJ20552	uc010drs.3	Q9BV68		ENST00000292363.5:c.802dupC	19.37:g.648266_648266dupG	ENSP00000292363:p.Val268fs		599262		Frame_Shift_Ins	INS	ENST00000292363.5	37	CCDS12039.1																																																																																				0.693	RNF126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452104.2	NM_017876		G	648263	-	G	648262	7	5	111	1	0	1	1	0	0	0	0	0	13472	536	19	0	137	0	RNF126	19	648262	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10		648262	58480721	928	30062										
TLE6	79816	hgsc.bcm.edu	37	chr19	2980147	2980147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctctccgacgctgaattatcAgggcattctaaatcggctca	8	12	4	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:2980147A>G	ENST00000246112.4	+	3	302	c.101A>G	c.(100-102)cAg>cGg	p.Q34R	TLE6_ENST00000452088.1_5'UTR|TLE6_ENST00000482627.1_Missense_Mutation_p.Q34R	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	34					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		CTGAATTATCAGGGCATTCTA	0.552																																																0			19											116	91	99					19																	2980147		692	1591	2283	2931147	SO:0001583	missense	79816			AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"WD repeat domain containing"	30788	protein-coding gene	gene with protein product		612399	"transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.101A>G	19.37:g.2980147A>G	ENSP00000246112:p.Gln34Arg		2931147	J3KMZ1	Missense_Mutation	SNP	ENST00000246112.4	37	CCDS45910.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.789758	0.31685	.	.	ENSG00000104953	ENST00000447920;ENST00000453329;ENST00000246112	T	0.20463	2.07	1.21	1.21	0.21127	.	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.19575	N	0.999963	P	0.40578	0.722	B	0.32211	0.142	T	0.19778	-1.0295	9	0.31617	T	0.26	.	4.6103	0.12399	1.0:0.0:0.0:0.0	.	34	C9JGZ7	.	R	34	ENSP00000246112:Q34R	ENSP00000246112:Q34R	Q	+	2	0	TLE6	2931147	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.398000	0.07259	0.801000	0.34066	0.379000	0.24179	CAG		0.552	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760		G	2980147	A	G	2980147	3	3	111	1	0	0	0	0	1	0	0	0	15981	188	7	4	107	4	TLE6	19	2980147	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2331885	2980147	56148836	929	30063										
GNA11	2767	hgsc.bcm.edu	37	chr19	3118949	3118949	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatgtggggggccagcggtcGgagcggaggaagtggatcca	21	7	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:3118949G>A	ENST00000078429.4	+	5	875	c.633G>A	c.(631-633)tcG>tcA	p.S211S	GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA|AC005262.2_ENST00000585980.1_RNA	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	211			S -> W (in HYPOC2). {ECO:0000269|PubMed:23782177}.		action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GCCAGCGGTCGGAGCGGAGGA	0.612			Mis		uveal melanoma																																		Dom	yes		19	19p13.3	2767	"guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"		E	0			19											117	97	104					19																	3118949		2203	4300	6503	3069949	SO:0001819	synonymous_variant	2767			AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"hypocalciuric hypercalcemia 2"	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.633G>A	19.37:g.3118949G>A			3069949	O15109|Q14350|Q6IB00	Silent	SNP	ENST00000078429.4	37	CCDS12103.1																																																																																				0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067		A	3118949	G	A	3118949	2	1	111	1	0	0	0	0	0	0	0	1	6519	1103	39	1		1	GNA11	19	3118949	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	138802	3118949	56010034	930	30064										
C19orf28	126321	hgsc.bcm.edu	37	chr19	3557198	3557198	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcggtgtgcacagcccgtcGgccacctggcccagcagcag	14	16	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:3557198G>T	ENST00000355415.2	-	1	373	c.204C>A	c.(202-204)gcC>gcA	p.A68A	MFSD12_ENST00000591878.1_Intron|MFSD12_ENST00000398558.4_Silent_p.A68A|AC005786.5_ENST00000592368.1_lincRNA|MFSD12_ENST00000389395.3_Silent_p.A68A|AC005786.7_ENST00000589360.1_RNA	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	68					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						ACAGCCCGTCGGCCACCTGGC	0.731																																																0			19											11	14	13					19																	3557198		2006	4136	6142	3508198	SO:0001819	synonymous_variant	126321			AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 28"	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.204C>A	19.37:g.3557198G>T			3508198	A8MXP7|D6W615|E9PAJ8|Q8N459	Silent	SNP	ENST00000355415.2	37	CCDS42465.1																																																																																				0.731	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983		T	3557198	G	T	3557198	2	4	111	1	0	0	0	0	0	0	0	1	1923	1103	39	2		2	C19orf28	19	3557198	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	438249	3557198	55571785	931	30065										
TJP3	27134	hgsc.bcm.edu	37	chr19	3746640	3746640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcccgccgcagcacccgtcGcctctacgcacaagcccaga	8	21	1	1	rs370766855		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:3746640G>A	ENST00000541714.2	+	17	2630	c.2168G>A	c.(2167-2169)cGc>cAc	p.R723H	TJP3_ENST00000539908.2_Missense_Mutation_p.R687H|TJP3_ENST00000587686.1_Missense_Mutation_p.R742H|TJP3_ENST00000382008.3_Missense_Mutation_p.R737H|TJP3_ENST00000589378.1_Missense_Mutation_p.R732H|TJP3_ENST00000262968.9_Missense_Mutation_p.R756H	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	723	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCACCCGTCGCCTCTACGCA	0.672																																																0			19						G	HIS/ARG	0,4404		0,0,2202	21	25	24		2267	4.8	1	19		24	1,8599	1.2+/-3.3	0,1,4299	no	missense	TJP3	NM_014428.1	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	756/953	3746640	1,13003	2202	4300	6502	3697640	SO:0001583	missense	27134			AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"zona occludens 3"	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2168G>A	19.37:g.3746640G>A	ENSP00000439278:p.Arg723His		3697640	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	.	.	.	.	.	.	.	.	.	.	G	21.8	4.203573	0.79127	0.0	1.16E-4	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	4.8	4.8	0.61643	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.058905	0.64402	D	0.000003	T	0.47728	0.1461	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.997;0.966;1.0;0.995	T	0.56980	-0.7889	10	0.87932	D	0	.	16.8263	0.85933	0.0:0.0:1.0:0.0	.	742;756;737;723	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	H	723;687;737;756	ENSP00000439278:R723H;ENSP00000439991:R687H;ENSP00000371438:R737H;ENSP00000262968:R756H	ENSP00000262968:R756H	R	+	2	0	TJP3	3697640	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.379000	0.59575	2.196000	0.70406	0.491000	0.48974	CGC		0.672	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			A	3746640	G	A	3746640	3	1	111	1	0	0	0	0	1	0	0	0	15970	1087	38	1	2329	1	TJP3	19	3746640	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	189442	3746640	55382343	932	30066										
EBI3	10148	hgsc.bcm.edu	37	chr19	4236988	4236988	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctgtgcggccccgagccaGgtactacgtccaagtggcgg	16	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:4236988G>T	ENST00000221847.5	+	5	646	c.593G>T	c.(592-594)aGg>aTg	p.R198M		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	198	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCGAGCCAGGTACTACGTC	0.597																																																0			19											56	56	56					19																	4236988		2203	4300	6503	4187988	SO:0001583	missense	10148			L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"Fibronectin type III domain containing"	3129	protein-coding gene	gene with protein product	"IL27 subunit", "IL35 subunit"	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.593G>T	19.37:g.4236988G>T	ENSP00000221847:p.Arg198Met		4187988	A0N0N2|O75269	Missense_Mutation	SNP	ENST00000221847.5	37	CCDS12123.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.161997	0.57368	.	.	ENSG00000105246	ENST00000221847	T	0.57752	0.38	5.41	-4.45	0.03546	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.970566	0.08493	N	0.937731	T	0.52741	0.1753	M	0.62723	1.935	0.09310	N	1	D	0.53151	0.958	P	0.51453	0.67	T	0.54309	-0.8313	10	0.51188	T	0.08	-12.789	6.537	0.22359	0.5957:0.1448:0.2596:0.0	.	198	Q14213	IL27B_HUMAN	M	198	ENSP00000221847:R198M	ENSP00000221847:R198M	R	+	2	0	EBI3	4187988	0.001000	0.12720	0.206000	0.23566	0.009000	0.06853	-0.383000	0.07398	-0.244000	0.09639	-0.142000	0.14014	AGG		0.597	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1			T	4236988	G	T	4236988	3	4	111	1	0	0	0	0	1	0	0	0	4894	1000	35	2	611	2	EBI3	19	4236988	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	490348	4236988	54891995	933	30067										
UHRF1	29128	hgsc.bcm.edu	37	chr19	4941840	4941840	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctgccacctgtgcgggggcCggcaggaccccgacaagcag	15	16	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:4941840C>T	ENST00000592666.1	+	0	1546							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		GTGCGGGGGCCGGCAGGACCC	0.672																																																0			19											11	14	13					19																	4941840		2088	4192	6280	4892840			29128			AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"RING-type (C3HC4) zinc fingers"	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4941840C>T			4892840	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Missense_Mutation	SNP	ENST00000592666.1	37		.	.	.	.	.	.	.	.	.	.	C	24.9	4.577436	0.86645	.	.	ENSG00000034063	ENST00000262952;ENST00000455180;ENST00000543616;ENST00000398240	.	.	.	4.64	3.62	0.41486	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.052776	0.85682	D	0.000000	T	0.47600	0.1454	N	0.17278	0.47	0.32099	N	0.5908359999999999	D;D	0.71674	0.998;0.994	P;D	0.64321	0.865;0.924	T	0.62072	-0.6931	8	0.87932	D	0	-25.5644	10.3721	0.44060	0.7302:0.2698:0.0:0.0	.	337;324	Q2HIX7;Q96T88	.;UHRF1_HUMAN	W	324;324;324;337	.	ENSP00000262952:R324W	R	+	1	2	UHRF1	4892840	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	6.955000	0.76007	0.983000	0.38602	0.561000	0.74099	CGG		0.672	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1	NM_001048201		T	4941840	C	T	4941840	1	4	111	0	1	0	0	0	0	0	0	0	17007	643	23	1		1	UHRF1	19	4941840	RNA	SNP	C	TCGA-EI-6507-01A-11D-1733-10	704852	4941840	54187143	934	30068										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5212404	5212404	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttgcaggtcttgactctccgCaggaaagccaggaagggcgt	14	10	2	1	rs146621666		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:5212404C>T	ENST00000587303.1	-	30	4812	c.4713G>A	c.(4711-4713)ctG>ctA	p.L1571L	PTPRS_ENST00000588012.1_Silent_p.L1533L|PTPRS_ENST00000592099.1_Silent_p.L1124L|PTPRS_ENST00000262963.6_Silent_p.L1551L|PTPRS_ENST00000353284.2_Silent_p.L1124L|PTPRS_ENST00000372412.4_Silent_p.L1572L|PTPRS_ENST00000357368.4_Silent_p.L1571L|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000348075.2_Silent_p.L1533L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1571	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TGACTCTCCGCAGGAAAGCCA	0.647																																																0			19											65	46	53					19																	5212404		2201	4300	6501	5163404	SO:0001819	synonymous_variant	5802			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4713G>A	19.37:g.5212404C>T			5163404	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																				0.647	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			T	5212404	C	T	5212404	2	4	111	1	0	0	0	0	0	0	0	1	12848	697	25	3		3	PTPRS	19	5212404	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	270564	5212404	53916579	935	30069										
FUT6	2528	hgsc.bcm.edu	37	chr19	5832407	5832407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gatcagggggatggagtgggCgggggtccctgtgctgtctg	21	7	2	0	rs112849079	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:5832407C>T	ENST00000318336.4	-	3	1366	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	FUT6_ENST00000527106.1_Missense_Mutation_p.A58T|FUT6_ENST00000524754.1_Missense_Mutation_p.A58T|FUT6_ENST00000592563.1_Missense_Mutation_p.A58T|FUT6_ENST00000286955.5_Missense_Mutation_p.A58T	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	58					fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						ATGGAGTGGGCGGGGGTCCCT	0.587																																																0			19											37	39	38					19																	5832407		2203	4300	6503	5783407	SO:0001583	missense	2528				CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"Fucosyltransferases"	4017	protein-coding gene	gene with protein product	"alpha-(1,3)-fucosyltransferase", "galactoside 3-L-fucosyltransferase"	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.172G>A	19.37:g.5832407C>T	ENSP00000313398:p.Ala58Thr		5783407	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	.	.	.	.	.	.	.	.	.	.	C	5.380	0.255349	0.10185	.	.	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165;ENST00000531085;ENST00000531199	T;T;T;T;T;T;T	0.35236	1.81;1.81;1.81;1.81;1.79;1.87;1.32	3.57	-6.97	0.01616	.	3.212480	0.01890	N	0.038509	T	0.21468	0.0517	N	0.13235	0.315	0.09310	N	1	B;B	0.14012	0.009;0.003	B;B	0.13407	0.009;0.009	T	0.22800	-1.0206	10	0.12430	T	0.62	.	14.3561	0.66738	0.0:0.6865:0.0:0.3135	.	58;58	C9J8A2;P51993	.;FUT6_HUMAN	T	58	ENSP00000431708:A58T;ENSP00000432954:A58T;ENSP00000313398:A58T;ENSP00000286955:A58T;ENSP00000436547:A58T;ENSP00000432161:A58T;ENSP00000436413:A58T	ENSP00000286955:A58T	A	-	1	0	FUT6	5783407	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.354000	0.02614	-1.732000	0.01359	-1.401000	0.01141	GCC		0.587	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150		T	5832407	C	T	5832407	3	4	111	1	0	0	0	0	1	0	0	0	6127	768	27	1	911	1	FUT6	19	5832407	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	620003	5832407	53296576	936	30070										
KHSRP	8570	hgsc.bcm.edu	37	chr19	6418029	6418029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgagatccgtactcattcCggtccccaaagccgccttgg	9	16	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:6418029C>T	ENST00000398148.3	-	10	1033	c.941G>A	c.(940-942)cGg>cAg	p.R314Q	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	314	Gly-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						GTACTCATTCCGGTCCCCAAA	0.642											OREG0025200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(55;593 1006 2067 9135 22980)											0			19											74	82	79					19																	6418029		2162	4268	6430	6369029	SO:0001583	missense	8570			U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.941G>A	19.37:g.6418029C>T	ENSP00000381216:p.Arg314Gln	633	6369029	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Missense_Mutation	SNP	ENST00000398148.3	37	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.744146	0.89663	.	.	ENSG00000088247	ENST00000398148;ENST00000201886;ENST00000424942	T	0.45668	0.89	5.11	5.11	0.69529	.	0.172348	0.48286	D	0.000189	T	0.66277	0.2773	M	0.77616	2.38	0.48395	D	0.999646	D	0.89917	1.0	D	0.81914	0.995	T	0.69476	-0.5135	10	0.54805	T	0.06	.	17.3392	0.87291	0.0:1.0:0.0:0.0	.	314	Q92945	FUBP2_HUMAN	Q	314;314;270	ENSP00000381216:R314Q	ENSP00000201886:R314Q	R	-	2	0	KHSRP	6369029	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	7.249000	0.78278	2.366000	0.80165	0.563000	0.77884	CGG		0.642	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			T	6418029	C	T	6418029	3	4	111	1	0	0	0	0	1	0	0	0	8172	652	23	1	1238	1	KHSRP	19	6418029	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	585622	6418029	52710954	937	30071										
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7607647	7607648	+	Splice_Site	INS	-	-	C													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaagcctgccccactcagaINScccccactcaggagcctcgt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:7607647_7607648insC	ENST00000221249.6	+	15	1677_1678	c.1246_1247insC	c.(1246-1248)acc>aCcc	p.T416fs	PNPLA6_ENST00000545201.2_Splice_Site_p.T416fs|PNPLA6_ENST00000450331.3_Splice_Site_p.T416fs|PNPLA6_ENST00000600737.1_Splice_Site_p.T455fs|PNPLA6_ENST00000414982.3_Splice_Site_p.T464fs	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	455					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						CCCCACTCAGACCCCCACTCAG	0.673																																																0			19																																								7513648	SO:0001630	splice_region_variant	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1246-1->C	19.37:g.7607652_7607652dupC			7513647	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Frame_Shift_Ins	INS	ENST00000221249.6	37	CCDS32891.1																																																																																				0.673	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	Frame_Shift_Ins	C	7607648	-	C	7607647	8	5	111	1	0	1	1	0	0	0	1	0	12200	289	10	0	1440	0	PNPLA6	19	7607647	Splice_Site	INS	-	TCGA-EI-6507-01A-11D-1733-10	1189618	7607647	51521336	938	30072										
LRRC8E	80131	hgsc.bcm.edu	37	chr19	7964957	7964957	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagctgcacctggaggggcTtttcccccaggagctagctc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:7964957delT	ENST00000306708.6	+	3	1651	c.1550delT	c.(1549-1551)cttfs	p.L517fs	AC010336.1_ENST00000539278.1_Frame_Shift_Del_p.S104fs|RN7SL115P_ENST00000392196.5_RNA	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	517					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						CTGGAGGGGCTTTTCCCCCAG	0.657																																																0			19											23	21	21					19																	7964957		2201	4300	6501	7870957	SO:0001589	frameshift_variant	80131				CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1550delT	19.37:g.7964957delT	ENSP00000306524:p.Leu517fs		7870957	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Frame_Shift_Del	DEL	ENST00000306708.6	37	CCDS12189.1																																																																																				0.657	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		-	7964957	T	-	7964957	7	5	111	1	0	1	0	1	0	0	0	0	9054	1609	56	0	1556	0	LRRC8E	19	7964957	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	357310	7964957	51164026	939	30073										
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7977252	7977252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggttcaaggatgtcatggCgaagactgagtcaccgcgga	14	9	3	2	rs201368825		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:7977252C>T	ENST00000397979.3	+	11	1250	c.1196C>T	c.(1195-1197)gCg>gTg	p.A399V	CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000545011.1_Missense_Mutation_p.A441V|MAP2K7_ENST00000397981.3_Missense_Mutation_p.A406V|MAP2K7_ENST00000397983.3_Missense_Mutation_p.A415V	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	399	DVD domain.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						GATGTCATGGCGAAGACTGAG	0.662																																																0			19						C	VAL/ALA	0,4286		0,0,2143	54	65	61		1196	4.5	1	19		61	1,8481		0,1,4240	yes	missense	MAP2K7	NM_145185.2	64	0,1,6383	TT,TC,CC		0.0118,0.0,0.0078	benign	399/420	7977252	1,12767	2143	4241	6384	7883252	SO:0001583	missense	5609			AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.1196C>T	19.37:g.7977252C>T	ENSP00000381066:p.Ala399Val		7883252	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Missense_Mutation	SNP	ENST00000397979.3	37	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.896063	0.52121	0.0	1.18E-4	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	T;T;T;T	0.70631	-0.4;-0.5;-0.45;-0.5	4.54	4.54	0.55810	Protein kinase-like domain (1);	0.131606	0.49916	D	0.000134	T	0.54967	0.1891	L	0.27053	0.805	0.42985	D	0.994475	B;B	0.31640	0.333;0.185	B;B	0.19148	0.024;0.007	T	0.57201	-0.7852	10	0.35671	T	0.21	-9.7287	14.8416	0.70230	0.0:1.0:0.0:0.0	.	406;399	O14733-4;O14733	.;MP2K7_HUMAN	V	406;415;441;415;399	ENSP00000381068:A406V;ENSP00000381070:A415V;ENSP00000443946:A441V;ENSP00000381066:A399V	ENSP00000381066:A399V	A	+	2	0	MAP2K7	7883252	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	4.192000	0.58378	2.356000	0.79943	0.511000	0.50034	GCG		0.662	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			T	7977252	C	T	7977252	3	4	111	1	0	0	0	0	1	0	0	0	9272	768	27	1	1238	1	MAP2K7	19	7977252	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	12295	7977252	51151731	940	30074										
FBN3	84467	hgsc.bcm.edu	37	chr19	8154511	8154511	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccatcggtgttgacacagacGccgttagtgcagacgccagg	13	12	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:8154511G>A	ENST00000600128.1	-	51	6708	c.6294C>T	c.(6292-6294)ggC>ggT	p.G2098G	FBN3_ENST00000601739.1_Silent_p.G2098G|FBN3_ENST00000270509.2_Silent_p.G2098G			Q75N90	FBN3_HUMAN	fibrillin 3	2098	EGF-like 33; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGACACAGACGCCGTTAGTGC	0.582																																																0			19											211	181	191					19																	8154511		2203	4300	6503	8060511	SO:0001819	synonymous_variant	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.6294C>T	19.37:g.8154511G>A			8060511	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																				0.582	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8154511	G	A	8154511	2	1	111	1	0	0	0	0	0	0	0	1	5723	1074	38	1		1	FBN3	19	8154511	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	177259	8154511	50974472	941	30075										
MUC16	94025	hgsc.bcm.edu	37	chr19	9047453	9047453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcaggtgagacagttattGttggaaaatctgaagtggct	12	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:9047453G>A	ENST00000397910.4	-	5	34381	c.34178C>T	c.(34177-34179)aCa>aTa	p.T11393I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11395	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACAGTTATTGTTGGAAAATC	0.453																																																0			19											228	215	219					19																	9047453		1947	4151	6098	8908453	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34178C>T	19.37:g.9047453G>A	ENSP00000381008:p.Thr11393Ile		8908453	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.661	0.490406	0.12702	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	3.47	2.43	0.29744	.	.	.	.	.	T	0.02807	0.0084	N	0.19112	0.55	.	.	.	P	0.46912	0.886	P	0.45276	0.475	T	0.37103	-0.9720	8	0.87932	D	0	.	6.7636	0.23554	0.1285:0.0:0.8715:0.0	.	11393	B5ME49	.	I	11393	ENSP00000381008:T11393I	ENSP00000381008:T11393I	T	-	2	0	MUC16	8908453	0.007000	0.16637	0.001000	0.08648	0.009000	0.06853	1.074000	0.30703	1.037000	0.40024	0.586000	0.80456	ACA		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9047453	G	A	9047453	3	1	111	1	0	0	0	0	1	0	0	0	10003	1377	48	3	9665	3	MUC16	19	9047453	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	892942	9047453	50081530	942	30076										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10402955	10402955	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggtctgcaacgtcaccctGgggggcgaaaaccgggagac							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:10402955delG	ENST00000221980.4	+	4	981	c.918delG	c.(916-918)ctgfs	p.L306fs		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	306	Ig-like C2-type 3.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			ACGTCACCCTGGGGGGCGAAA	0.647																																																0			19											26	21	23					19																	10402955		2202	4300	6502	10263955	SO:0001589	frameshift_variant	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.918delG	19.37:g.10402955delG	ENSP00000221980:p.Leu306fs		10263955	Q9Y6F3	Frame_Shift_Del	DEL	ENST00000221980.4	37	CCDS12233.1																																																																																				0.647	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		-	10402955	G	-	10402955	7	5	111	1	0	1	0	1	0	0	0	0	7504	1335	47	0	932	0	ICAM5	19	10402955	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1355502	10402955	48726028	943	30077										
PDE4A	5141	hgsc.bcm.edu	37	chr19	10571763	10571763	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caccctggggtctccaaccaGttcctcatcaacaccagtga	7	16	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:10571763G>A	ENST00000352831.6	+	11	1559	c.1449G>A	c.(1447-1449)caG>caA	p.Q483Q	PDE4A_ENST00000440014.2_Silent_p.Q422Q|PDE4A_ENST00000380702.2_Silent_p.Q461Q|PDE4A_ENST00000344979.3_Silent_p.Q244Q|PDE4A_ENST00000293683.5_Silent_p.Q457Q|PDE4A_ENST00000592685.1_Silent_p.Q461Q	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	483	Catalytic.				cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	TCTCCAACCAGTTCCTCATCA	0.637																																																0			19											47	42	43					19																	10571763		2203	4300	6503	10432763	SO:0001819	synonymous_variant	5141				CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"Phosphodiesterases"	8780	protein-coding gene	gene with protein product	"phosphodiesterase E2 dunce homolog (Drosophila)"	600126	"phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.1449G>A	19.37:g.10571763G>A			10432763	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	37	CCDS45961.1																																																																																				0.637	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			A	10571763	G	A	10571763	2	1	111	1	0	0	0	0	0	0	0	1	11670	1020	36	3		3	PDE4A	19	10571763	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	168808	10571763	48557220	944	30078										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11324971	11324971	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttggacacaagggccctctGggtggccaggccatgctgca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:11324971delG	ENST00000294618.7	-	34	4329	c.4318delC	c.(4318-4320)cagfs	p.Q1440fs	DOCK6_ENST00000319867.7_Frame_Shift_Del_p.Q779fs|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1440					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						AGGGCCCTCTGGGTGGCCAGG	0.572																																																0			19											30	32	31					19																	11324971		1998	4159	6157	11185971	SO:0001589	frameshift_variant	57572				CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4318delC	19.37:g.11324971delG	ENSP00000294618:p.Gln1440fs		11185971	A6H8X5|Q7Z7P4|Q9P2F2	Frame_Shift_Del	DEL	ENST00000294618.7	37	CCDS45975.1																																																																																				0.572	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		-	11324971	G	-	11324971	7	5	111	1	0	1	0	1	0	0	0	0	4702	1357	47	0	1885	0	DOCK6	19	11324971	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	753208	11324971	47804012	945	30079										
JUNB	3726	hgsc.bcm.edu	37	chr19	12902958	12902958	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtggaggtgcagggggcgcaGggggcggcgtcaccgaggag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:12902958delG	ENST00000302754.4	+	1	649	c.373delG	c.(373-375)gggfs	p.G127fs		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	127					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|decidualization (GO:0046697)|embryonic process involved in female pregnancy (GO:0060136)|gene expression (GO:0010467)|labyrinthine layer blood vessel development (GO:0060716)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|osteoclast differentiation (GO:0030316)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|kidney(1)|lung(3)	6						AGGGGGCGCAGGGGGCGGCGT	0.662																																																0			19											8	9	9					19																	12902958		2109	4183	6292	12763958	SO:0001589	frameshift_variant	10535			M29039	CCDS12280.1	19p13.13	2013-01-10				ENSG00000171223		"basic leucine zipper proteins"	6205	protein-coding gene	gene with protein product		165161				2513129	Standard	NM_002229		Approved		uc002mvc.3	P17275		ENST00000302754.4:c.373delG	19.37:g.12902958delG	ENSP00000303315:p.Gly127fs		12763958	Q96GH3	Frame_Shift_Del	DEL	ENST00000302754.4	37	CCDS12280.1																																																																																				0.662	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229		-	12902958	G	-	12902958	7	5	111	1	0	1	0	1	0	0	0	0	7991	1000	35	0	375	0	JUNB	19	12902958	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1577987	12902958	46226025	946	30080										
GCDH	2639	hgsc.bcm.edu	37	chr19	13007747	13007747	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccttcggctgcctgaacaaCgcccggtacggcatcgcgtg	12	16	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:13007747C>T	ENST00000222214.5	+	9	1087	c.876C>T	c.(874-876)aaC>aaT	p.N292N	GCDH_ENST00000591470.1_Silent_p.N292N|GCDH_ENST00000457854.1_Silent_p.N292N|GCDH_ENST00000422947.2_Silent_p.N248N			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	292	Substrate binding.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	GCCTGAACAACGCCCGGTACG	0.627																																					GBM(123;875 1636 7726 16444 26754)											0			19											50	44	46					19																	13007747		2203	4300	6503	12868747	SO:0001819	synonymous_variant	2639			AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.876C>T	19.37:g.13007747C>T			12868747	A8K2Z2|O14719	Silent	SNP	ENST00000222214.5	37	CCDS12286.1																																																																																				0.627	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			T	13007747	C	T	13007747	2	4	111	1	0	0	0	0	0	0	0	1	6307	535	19	1		1	GCDH	19	13007747	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	104789	13007747	46121236	947	30081										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13414640	13414640	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acaccatgccgccctgcacgCccccctgagacttgatcccg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:13414640delC	ENST00000360228.5	-	16	2044	c.2045delG	c.(2044-2046)ggcfs	p.G682fs	CACNA1A_ENST00000573710.2_Frame_Shift_Del_p.G683fs	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	683					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCCTGCACGCCCCCCTGAGA	0.557																																																0			19											172	177	175					19																	13414640		2025	4179	6204	13275640	SO:0001589	frameshift_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2045delG	19.37:g.13414640delC	ENSP00000353362:p.Gly682fs		13275640	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Frame_Shift_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																				0.557	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		-	13414640	C	-	13414640	7	5	111	1	0	1	0	1	0	0	0	0	2544	739	26	0	5714	0	CACNA1A	19	13414640	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	406893	13414640	45714343	948	30082										
GTPBP3	84705	hgsc.bcm.edu	37	chr19	17450340	17450340	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggatttcctgtgctgctgagCgacacggctgggttgcggga	17	9	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:17450340C>T	ENST00000324894.8	+	7	974	c.906C>T	c.(904-906)agC>agT	p.S302S	GTPBP3_ENST00000361619.5_Silent_p.S324S|GTPBP3_ENST00000598038.1_3'UTR|GTPBP3_ENST00000600625.1_Silent_p.S302S|GTPBP3_ENST00000358792.7_Silent_p.S334S	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	302	TrmE-type G.				tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						TGCTGCTGAGCGACACGGCTG	0.711																																																0			19											39	37	37					19																	17450340		2203	4298	6501	17311340	SO:0001819	synonymous_variant	84705			AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.906C>T	19.37:g.17450340C>T			17311340	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Silent	SNP	ENST00000324894.8	37	CCDS32951.1																																																																																				0.711	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620		T	17450340	C	T	17450340	2	4	111	1	0	0	0	0	0	0	0	1	6902	767	27	1		1	GTPBP3	19	17450340	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	4035700	17450340	41678643	949	30083										
MAST3	23031	hgsc.bcm.edu	37	chr19	18245760	18245760	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgtgcctttctttggagataCccccgaggaactcttcggtc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:18245760delC	ENST00000262811.6	+	16	1751	c.1751delC	c.(1750-1752)accfs	p.T584fs		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	584	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TTTGGAGATACCCCCGAGGAA	0.627																																																0			19											109	114	112					19																	18245760		2061	4207	6268	18106760	SO:0001589	frameshift_variant	23031			AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.1751delC	19.37:g.18245760delC	ENSP00000262811:p.Thr584fs		18106760	Q7LDZ8|Q9UPI0	Frame_Shift_Del	DEL	ENST00000262811.6	37	CCDS46014.1																																																																																				0.627	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		-	18245760	C	-	18245760	7	5	111	1	0	1	0	1	0	0	0	0	9356	507	18	0	1813	0	MAST3	19	18245760	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	795420	18245760	40883223	950	30084										
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19576354	19576354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgagggcaacagaggccaCggccatggccatgggcagag	17	11	0	3	rs370240766		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:19576354C>T	ENST00000360315.3	+	2	512	c.200C>T	c.(199-201)aCg>aTg	p.T67M	GATAD2A_ENST00000537887.1_5'UTR|GATAD2A_ENST00000404158.1_Missense_Mutation_p.T67M|GATAD2A_ENST00000252577.5_Missense_Mutation_p.T67M|GATAD2A_ENST00000429563.2_5'UTR|GATAD2A_ENST00000358713.3_Missense_Mutation_p.T67M	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	67					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						ACAGAGGCCACGGCCATGGCC	0.632																																																0			19						C	MET/THR	1,3135		0,1,1567	50	50	50		200	1.4	0	19		50	0,7164		0,0,3582	no	missense	GATAD2A	NM_017660.3	81	0,1,5149	TT,TC,CC		0.0,0.0319,0.0097	benign	67/634	19576354	1,10299	1568	3582	5150	19437354	SO:0001583	missense	54815			AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"GATA zinc finger domain containing"	29989	protein-coding gene	gene with protein product	"p66 alpha"	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.200C>T	19.37:g.19576354C>T	ENSP00000353463:p.Thr67Met		19437354	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	4.194	0.034687	0.08101	3.19E-4	0.0	ENSG00000167491	ENST00000417582;ENST00000360315;ENST00000252577;ENST00000457895;ENST00000432704;ENST00000404158;ENST00000429242;ENST00000358713;ENST00000444839	T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	3.78	1.35	0.21983	.	0.834308	0.10939	N	0.617438	T	0.18173	0.0436	N	0.02011	-0.69	0.21762	N	0.999556	B;B	0.13145	0.007;0.002	B;B	0.09377	0.004;0.001	T	0.21518	-1.0243	10	0.56958	D	0.05	-20.4195	9.1899	0.37193	0.6677:0.3323:0.0:0.0	.	86;67	B5MC40;Q86YP4	.;P66A_HUMAN	M	67;67;67;67;67;86;67;67;67	ENSP00000403703:T67M;ENSP00000353463:T67M;ENSP00000252577:T67M;ENSP00000404212:T67M;ENSP00000390495:T67M;ENSP00000414252:T67M;ENSP00000351552:T67M;ENSP00000407293:T67M	ENSP00000252577:T67M	T	+	2	0	GATAD2A	19437354	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.137000	0.15995	0.544000	0.28883	0.467000	0.42956	ACG		0.632	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19576354	C	T	19576354	3	4	111	1	0	0	0	0	1	0	0	0	6280	536	19	1	202	1	GATAD2A	19	19576354	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1330594	19576354	39552629	951	30085										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22272034	22272034	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatgtgaagaatgtggcaaAgcctttaaccggtcttcaca	9	8	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:22272034A>C	ENST00000594947.1	+	4	1626	c.1482A>C	c.(1480-1482)aaA>aaC	p.K494N		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				AATGTGGCAAAGCCTTTAACC	0.398																																																0			19											43	47	45					19																	22272034		2116	4261	6377	22063874	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.1482A>C	19.37:g.22272034A>C	ENSP00000470209:p.Lys494Asn		22063874	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.847736	0.32606	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	1.11	-0.039	0.13878	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49012	0.1532	M	0.90019	3.08	0.22581	N	0.998967	P	0.44281	0.831	B	0.43508	0.422	T	0.48375	-0.9041	8	0.72032	D	0.01	.	5.1987	0.15252	0.7893:0.0:0.2107:0.0	.	494	Q9Y2Q1	ZN257_HUMAN	N	494;466	.	ENSP00000380312:K466N	K	+	3	2	ZNF257	22063874	0.000000	0.05858	0.429000	0.26710	0.101000	0.19017	-0.329000	0.07935	0.436000	0.26393	0.260000	0.18958	AAA		0.398	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			C	22272034	A	C	22272034	3	2	111	1	0	0	0	0	1	0	0	0	17839	69	3	4	1496	4	ZNF257	19	22272034	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	2695680	22272034	36856949	952	30086										
RHPN2	85415	hgsc.bcm.edu	37	chr19	33486948	33486948	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaccaacaacactgggggcGtcgatcaggttcagcaggtc	12	12	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:33486948G>A	ENST00000254260.3	-	11	1439	c.1404C>T	c.(1402-1404)gaC>gaT	p.D468D	RHPN2_ENST00000400226.4_Silent_p.D317D	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	468					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					CACTGGGGGCGTCGATCAGGT	0.627																																																0			19											80	62	68					19																	33486948		2203	4300	6503	38178788	SO:0001819	synonymous_variant	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1404C>T	19.37:g.33486948G>A			38178788	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Silent	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																				0.627	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		A	33486948	G	A	33486948	2	1	111	1	0	0	0	0	0	0	0	1	13388	1136	40	1		1	RHPN2	19	33486948	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	11214914	33486948	25642035	953	30087										
ZNF792	126375	hgsc.bcm.edu	37	chr19	35451780	35451780	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgacagccttacccagcgagGctataagtgcaaagttttcc	9	11	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:35451780G>T	ENST00000404801.1	-	2	538	c.152C>A	c.(151-153)gCc>gAc	p.A51D	ZNF792_ENST00000605484.1_5'Flank	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			ACCCAGCGAGGCTATAAGTGC	0.567																																					GBM(1;7 183 21053 22581 22847)											0			19											120	118	119					19																	35451780		2203	4300	6503	40143620	SO:0001583	missense	126375			AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.152C>A	19.37:g.35451780G>T	ENSP00000385099:p.Ala51Asp		40143620	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	37	CCDS12440.2	.	.	.	.	.	.	.	.	.	.	g	15.68	2.904153	0.52333	.	.	ENSG00000180884	ENST00000404801	T	0.01933	4.55	2.6	2.6	0.31112	Krueppel-associated box (4);	.	.	.	.	T	0.10337	0.0253	M	0.82517	2.595	0.23563	N	0.997407	D	0.89917	1.0	D	0.72982	0.979	T	0.09292	-1.0681	9	0.56958	D	0.05	.	5.4454	0.16531	0.1539:0.0:0.8461:0.0	.	51	Q3KQV3	ZN792_HUMAN	D	51	ENSP00000385099:A51D	ENSP00000385099:A51D	A	-	2	0	ZNF792	40143620	0.008000	0.16893	0.790000	0.31976	0.858000	0.48976	0.234000	0.17930	1.768000	0.52137	0.563000	0.77884	GCC		0.567	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		T	35451780	G	T	35451780	3	4	111	1	0	0	0	0	1	0	0	0	18203	1203	42	2	1758	2	ZNF792	19	35451780	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1964832	35451780	23677203	954	30088										
LSR	51599	hgsc.bcm.edu	37	chr19	35753559	35753559	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctgctgctacgtcaggtgcCcctgctgcccagacaagtgc	12	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:35753559C>A	ENST00000361790.3	+	5	1045	c.886C>A	c.(886-888)Ccc>Acc	p.P296T	AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000602122.1_Missense_Mutation_p.P277T|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000354900.3_Missense_Mutation_p.P277T|LSR_ENST00000427250.1_Intron|LSR_ENST00000360798.3_Intron|LSR_ENST00000347609.4_Missense_Mutation_p.P259T	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	296	Cys-rich.				embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CGTCAGGTGCCCCTGCTGCCC	0.632																																																0			19											94	75	82					19																	35753559		2203	4300	6503	40445399	SO:0001583	missense	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.886C>A	19.37:g.35753559C>A	ENSP00000354575:p.Pro296Thr		40445399	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	37	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	C	19.51	3.840587	0.71488	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000347609	T;T;T	0.50548	0.74;0.74;0.74	4.74	4.74	0.60224	LISCH7 (1);	0.056734	0.64402	D	0.000001	T	0.66356	0.2781	M	0.69358	2.11	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.996	D;D;D;D	0.81914	0.988;0.992;0.995;0.957	T	0.69465	-0.5138	10	0.66056	D	0.02	-27.4288	15.256	0.73585	0.0:1.0:0.0:0.0	.	259;277;277;296	Q86X29-2;Q86X29-3;E9PHD4;Q86X29	.;.;.;LSR_HUMAN	T	296;277;259	ENSP00000354575:P296T;ENSP00000346976:P277T;ENSP00000262627:P259T	ENSP00000262627:P259T	P	+	1	0	LSR	40445399	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	4.328000	0.59253	2.448000	0.82819	0.591000	0.81541	CCC		0.632	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		A	35753559	C	A	35753559	3	1	111	1	0	0	0	0	1	0	0	0	9093	623	22	2	904	2	LSR	19	35753559	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	301779	35753559	23375424	955	30089										
FFAR2	2867	hgsc.bcm.edu	37	chr19	35940825	35940825	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcaagatcatcgaggctgCgtcgaacttccgctggtacc	10	13	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:35940825C>T	ENST00000599180.2	+	2	289	c.209C>T	c.(208-210)gCg>gTg	p.A70V	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Missense_Mutation_p.A70V			O15552	FFAR2_HUMAN	free fatty acid receptor 2	70					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	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)			ATCGAGGCTGCGTCGAACTTC	0.637																																					GBM(40;139 809 9833 23358 48736)											0			19											50	41	44					19																	35940825		2203	4300	6503	40632665	SO:0001583	missense	2867			AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.209C>T	19.37:g.35940825C>T	ENSP00000473159:p.Ala70Val		40632665	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Missense_Mutation	SNP	ENST00000599180.2	37	CCDS12461.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726572	0.30593	.	.	ENSG00000126262	ENST00000246549	T	0.37584	1.19	5.61	4.58	0.56647	GPCR, rhodopsin-like superfamily (1);	0.450275	0.23272	N	0.050009	T	0.31670	0.0804	L	0.58810	1.83	0.09310	N	1	P	0.49307	0.922	B	0.39904	0.313	T	0.21381	-1.0247	10	0.13470	T	0.59	-22.3343	12.8317	0.57750	0.0:0.9202:0.0:0.0798	.	70	O15552	FFAR2_HUMAN	V	70	ENSP00000246549:A70V	ENSP00000246549:A70V	A	+	2	0	FFAR2	40632665	0.000000	0.05858	0.063000	0.19743	0.002000	0.02628	0.405000	0.21015	1.512000	0.48834	0.655000	0.94253	GCG		0.637	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		T	35940825	C	T	35940825	3	4	111	1	0	0	0	0	1	0	0	0	5847	768	27	1	211	1	FFAR2	19	35940825	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	187266	35940825	23188158	956	30090										
MLL4	9757	hgsc.bcm.edu	37	chr19	36221688	36221688	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aattctggagtatcggccatGggggccgagggaagagccag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:36221688delG	ENST00000222270.7	+	26	5357	c.5357delG	c.(5356-5358)tggfs	p.W1786fs	KMT2B_ENST00000420124.1_Frame_Shift_Del_p.W1786fs|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1786					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TATCGGCCATGGGGGCCGAGG	0.617																																																0			19											41	48	46					19																	36221688		2052	4188	6240	40913528	SO:0001589	frameshift_variant	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5357delG	19.37:g.36221688delG	ENSP00000222270:p.Trp1786fs		40913528	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	37	CCDS46055.1																																																																																				0.617	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		-	36221688	G	-	36221688	7	5	111	1	0	1	0	1	0	0	0	0	9653	1357	47	0	5459	0	MLL4	19	36221688	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	280863	36221688	22907295	957	30091										
NFKBID	84807	hgsc.bcm.edu	37	chr19	36387423	36387423	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aggggctggttggcagcagcCgccaccaggagaggggtctg	19	10	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:36387423C>T	ENST00000396901.1	-	7	849	c.276G>A	c.(274-276)gcG>gcA	p.A92A	NFKBID_ENST00000585544.1_5'Flank|NFKBID_ENST00000606253.1_Silent_p.A92A|NFKBID_ENST00000352614.2_Silent_p.A244A	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	92					inflammatory response (GO:0006954)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|positive regulation of thymocyte apoptotic process (GO:0070245)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	14						TGGCAGCAGCCGCCACCAGGA	0.642																																																0			19											30	37	35					19																	36387423		1983	4156	6139	41079263	SO:0001819	synonymous_variant	84807			AF385434	CCDS42552.1	19q13.12	2013-01-10				ENSG00000167604		"Ankyrin repeat domain containing"	15671	protein-coding gene	gene with protein product						12477932	Standard	NM_139239		Approved	TA-NFKBH, IkappaBNS	uc002oci.1	Q8NI38		ENST00000396901.1:c.276G>A	19.37:g.36387423C>T			41079263	Q8NI39|Q9BRG9	Silent	SNP	ENST00000396901.1	37	CCDS42552.1																																																																																				0.642	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721		T	36387423	C	T	36387423	2	4	111	1	0	0	0	0	0	0	0	1	10410	639	23	1		1	NFKBID	19	36387423	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	165735	36387423	22741560	958	30092										
ZNF382	84911	hgsc.bcm.edu	37	chr19	37118175	37118176	+	Frame_Shift_Ins	INS	-	-	G													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccaccagagaattcacacINSgggggaaaaaccctatattt							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:37118175_37118176insG	ENST00000292928.2	+	5	1489_1490	c.1376_1377insG	c.(1375-1380)acggggfs	p.TG459fs	CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000435416.1_Frame_Shift_Ins_p.TG458fs|ZNF382_ENST00000423582.1_Frame_Shift_Ins_p.TG410fs|ZNF382_ENST00000439428.1_Frame_Shift_Ins_p.TG458fs	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	459	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T459T(3)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGAATTCACACGGGGGAAAAAC	0.441																																																3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	19																																								41810016	SO:0001589	frameshift_variant	84911			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1381dupG	19.37:g.37118180_37118180dupG	ENSP00000292928:p.Thr459fs		41810015	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Frame_Shift_Ins	INS	ENST00000292928.2	37	CCDS33004.1																																																																																				0.441	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		G	37118176	-	G	37118175	7	5	111	1	0	1	1	0	0	0	0	0	17912	536	19	0	1386	0	ZNF382	19	37118175	Frame_Shift_Ins	INS	-	TCGA-EI-6507-01A-11D-1733-10	730752	37118175	22010808	959	30093										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37903604	37903604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcacctgtatgttttctcatAtgaagggtaagagatgagat	10	5	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:37903604A>G	ENST00000316950.6	-	6	2513	c.1956T>C	c.(1954-1956)caT>caC	p.H652H	ZNF569_ENST00000392149.2_Silent_p.H652H|ZNF569_ENST00000392150.2_Silent_p.H493H	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	652					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTTTTCTCATATGAAGGGTAA	0.423																																																0			19											121	123	122					19																	37903604		2203	4300	6503	42595444	SO:0001819	synonymous_variant	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.1956T>C	19.37:g.37903604A>G			42595444	A8K1S2|Q15925|Q17RR6|Q96MQ2	Silent	SNP	ENST00000316950.6	37	CCDS12503.1																																																																																				0.423	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		G	37903604	A	G	37903604	2	3	111	1	0	0	0	0	0	0	0	1	18039	446	16	4		4	ZNF569	19	37903604	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	785429	37903604	21225379	960	30094										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37916782	37916782	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccactaaccttgccagtgtcTccttaatacttcttcctcca	3	16	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:37916782T>A	ENST00000316950.6	-	5	783	c.226A>T	c.(226-228)Aga>Tga	p.R76*	ZNF569_ENST00000392149.2_Nonsense_Mutation_p.R76*|ZNF569_ENST00000591073.1_5'Flank|ZNF569_ENST00000392150.2_Intron|ZNF569_ENST00000589833.1_Nonsense_Mutation_p.R100*|ZNF569_ENST00000592490.1_Intron	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	76	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGCCAGTGTCTCCTTAATACT	0.428																																																0			19											490	475	480					19																	37916782		2203	4300	6503	42608622	SO:0001587	stop_gained	148266			AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.226A>T	19.37:g.37916782T>A	ENSP00000325018:p.Arg76*		42608622	A8K1S2|Q15925|Q17RR6|Q96MQ2	Nonsense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	39	7.649913	0.98412	.	.	ENSG00000196437	ENST00000316950	.	.	.	3.39	3.39	0.38822	.	0.227351	0.22513	N	0.059078	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	8.5267	0.33309	0.0:0.0:0.0:1.0	.	.	.	.	X	76	.	ENSP00000325018:R76X	R	-	1	2	ZNF569	42608622	0.489000	0.26004	0.989000	0.46669	0.609000	0.37215	2.075000	0.41538	1.785000	0.52413	0.459000	0.35465	AGA		0.428	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		A	37916782	T	A	37916782	4	1	111	1	0	0	0	0	0	1	0	0	18039	1559	54	5	1842	5	ZNF569	19	37916782	Nonsense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	13178	37916782	21212201	961	30095										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38028091	38028091	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaattgcttcagcgtataaaTcatggtagacgacctaatgg	9	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:38028091T>A	ENST00000587143.1	+	6	766	c.531T>A	c.(529-531)aaT>aaA	p.N177K	ZNF793_ENST00000542455.1_Missense_Mutation_p.N177K|ZNF793_ENST00000445217.1_Missense_Mutation_p.N177K|ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000589319.1_Intron			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	177					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGCGTATAAATCATGGTAGAC	0.408																																					Melanoma(44;400 1431 1499 19093)											0			19											34	33	34					19																	38028091		1837	4098	5935	42719931	SO:0001583	missense	390927			AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.531T>A	19.37:g.38028091T>A	ENSP00000468605:p.Asn177Lys		42719931	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	37	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.311938	0.00237	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.14266	2.52;2.52	4.03	-3.08	0.05347	.	0.342514	0.21239	N	0.077846	T	0.03053	0.0090	N	0.05259	-0.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35400	-0.9790	10	0.02654	T	1	.	0.1194	0.00063	0.2904:0.204:0.1625:0.3432	.	177	E9PGN4	.	K	177;177;177;176	ENSP00000444355:N177K;ENSP00000396402:N177K	ENSP00000318811:N176K	N	+	3	2	ZNF793	42719931	0.000000	0.05858	0.009000	0.14445	0.040000	0.13550	-1.872000	0.01639	-0.201000	0.10284	-0.146000	0.13790	AAT		0.408	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		A	38028091	T	A	38028091	3	1	111	1	0	0	0	0	1	0	0	0	18204	1432	50	5	545	5	ZNF793	19	38028091	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	111309	38028091	21100892	962	30096										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38609985	38609985	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaagacgctcctcctttcggCccccccatccccagtggaac							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:38609985delC	ENST00000222345.6	+	9	2840	c.2331delC	c.(2329-2331)ggcfs	p.G777fs		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	777	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTCCTTTCGGCCCCCCCATCC	0.537																																																0			19											66	74	71					19																	38609985		2203	4300	6503	43301825	SO:0001589	frameshift_variant	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2331delC	19.37:g.38609985delC	ENSP00000222345:p.Gly777fs		43301825	Q2TV87	Frame_Shift_Del	DEL	ENST00000222345.6	37	CCDS33007.1																																																																																				0.537	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		-	38609985	C	-	38609985	7	5	111	1	0	1	0	1	0	0	0	0	14368	726	26	0	2357	0	SIPA1L3	19	38609985	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	581894	38609985	20518998	963	30097										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38861334	38861334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccggaatctcgagcatgccgTctctgagacattccaggatg	11	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:38861334T>C	ENST00000409235.3	+	29	3497	c.3382T>C	c.(3382-3384)Tct>Cct	p.S1128P	CATSPERG_ENST00000410018.1_Missense_Mutation_p.S1088P|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	1128					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						GAGCATGCCGTCTCTGAGACA	0.537																																																0			19											154	138	143					19																	38861334		2203	4300	6503	43553174	SO:0001583	missense	0			AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.3382T>C	19.37:g.38861334T>C	ENSP00000386962:p.Ser1128Pro		43553174	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	T	14.86	2.662100	0.47572	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	T;T	0.28666	1.61;1.6	3.57	3.57	0.40892	.	2.847580	0.01174	N	0.006938	T	0.44973	0.1319	N	0.24115	0.695	0.36230	D	0.85257	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.41805	-0.9488	10	0.66056	D	0.02	-0.7155	8.824	0.35043	0.0:0.0:0.0:1.0	.	1128;1088	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	P	1088;1128;1128	ENSP00000387057:S1088P;ENSP00000386962:S1128P	ENSP00000386962:S1128P	S	+	1	0	CATSPERG	43553174	0.001000	0.12720	0.023000	0.16930	0.014000	0.08584	0.525000	0.22956	1.874000	0.54306	0.397000	0.26171	TCT		0.537	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		C	38861334	T	C	38861334	3	2	111	1	0	0	0	0	1	0	0	0	2698	1667	58	4	3492	4	CATSPERG	19	38861334	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	251349	38861334	20267649	964	30098										
FAM98C	147965	hgsc.bcm.edu	37	chr19	38897659	38897659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcccgagccgacctgtcttGtctcgtcccagccaccagcg	10	18	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:38897659G>A	ENST00000252530.5	+	7	879	c.860G>A	c.(859-861)tGt>tAt	p.C287Y	FAM98C_ENST00000343358.7_Intron|FAM98C_ENST00000588262.1_Silent_p.L153L	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	287										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GACCTGTCTTGTCTCGTCCCA	0.617																																																0			19											105	109	108					19																	38897659		2052	4180	6232	43589499	SO:0001583	missense	147965				CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.860G>A	19.37:g.38897659G>A	ENSP00000252530:p.Cys287Tyr		43589499	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.815976	0.50527	.	.	ENSG00000130244	ENST00000252530	T	0.41065	1.01	4.9	4.9	0.64082	.	6.976200	0.00166	N	0.000004	T	0.29093	0.0723	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01528	-1.1332	10	0.23891	T	0.37	-0.6223	15.6386	0.76977	0.0:0.0:1.0:0.0	.	287	Q17RN3	FA98C_HUMAN	Y	287	ENSP00000252530:C287Y	ENSP00000252530:C287Y	C	+	2	0	FAM98C	43589499	0.142000	0.22610	0.996000	0.52242	0.959000	0.62525	1.980000	0.40618	2.274000	0.75844	0.650000	0.86243	TGT		0.617	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		A	38897659	G	A	38897659	3	1	111	1	0	0	0	0	1	0	0	0	5677	1377	48	3	886	3	FAM98C	19	38897659	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	36325	38897659	20231324	965	30099										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39334512	39334512	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagattggggtttgtgtagtCccaagtatcctgatcattct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:39334512delC	ENST00000221419.5	-	6	1216	c.850delG	c.(850-852)gacfs	p.D284fs	AC008982.2_ENST00000600473.1_RNA|HNRNPL_ENST00000600873.1_Frame_Shift_Del_p.D151fs	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	284					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TTTGTGTAGTCCCAAGTATCC	0.483																																																0			19											172	142	152					19																	39334512		2203	4300	6503	44026352	SO:0001589	frameshift_variant	3191			X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.850delG	19.37:g.39334512delC	ENSP00000221419:p.Asp284fs		44026352	A6ND69|A6NIT8|Q9H3P3	Frame_Shift_Del	DEL	ENST00000221419.5	37	CCDS33015.1																																																																																				0.483	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			-	39334512	C	-	39334512	7	5	111	1	0	1	0	1	0	0	0	0	7291	855	30	0	951	0	HNRNPL	19	39334512	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	436853	39334512	19794471	966	30100										
HIPK4	147746	hgsc.bcm.edu	37	chr19	40886833	40886833	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tagtagtgggtggtctcgtgGgcactgcgcagctgctgcat	16	9	1	0	rs570485639		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:40886833G>T	ENST00000291823.2	-	3	1349	c.1065C>A	c.(1063-1065)gcC>gcA	p.A355A		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	355					histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			TGGTCTCGTGGGCACTGCGCA	0.657																																																0			19											71	70	70					19																	40886833		2203	4300	6503	45578673	SO:0001819	synonymous_variant	147746			BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.1065C>A	19.37:g.40886833G>T			45578673	A8K863|Q96M54	Silent	SNP	ENST00000291823.2	37	CCDS12555.1																																																																																				0.657	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		T	40886833	G	T	40886833	2	4	111	1	0	0	0	0	0	0	0	1	7140	1219	43	2		2	HIPK4	19	40886833	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1552321	40886833	18242150	967	30101										
ERF	2077	hgsc.bcm.edu	37	chr19	42754536	42754536	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggggcttgcacttgcgaacGccccacagccgggccacctc	12	17	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:42754536G>A	ENST00000222329.4	-	2	361	c.204C>T	c.(202-204)ggC>ggT	p.G68G	ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000440177.2_5'UTR	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	68					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				ACTTGCGAACGCCCCACAGCC	0.647																																																0			19											45	45	45					19																	42754536		2203	4300	6503	47446376	SO:0001819	synonymous_variant	2107			U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.204C>T	19.37:g.42754536G>A			47446376	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Silent	SNP	ENST00000222329.4	37	CCDS12600.1																																																																																				0.647	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		A	42754536	G	A	42754536	2	1	111	1	0	0	0	0	0	0	0	1	5234	1074	38	1		1	ERF	19	42754536	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1867703	42754536	16374447	968	30102										
LYPD3	27076	hgsc.bcm.edu	37	chr19	43967350	43967350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggcgttgtagcagctcacgaCcggcggcgatgtaccctggc	15	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:43967350C>T	ENST00000244333.3	-	4	560	c.472G>A	c.(472-474)Gtc>Atc	p.V158I		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	158	UPAR/Ly6 2.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CAGCTCACGACCGGCGGCGAT	0.647																																																0			19											80	72	75					19																	43967350		2203	4300	6503	48659190	SO:0001583	missense	27076			AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.472G>A	19.37:g.43967350C>T	ENSP00000244333:p.Val158Ile		48659190	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025127	0.54683	.	.	ENSG00000124466	ENST00000244333	T	0.69685	-0.42	4.9	3.79	0.43588	CD59 antigen (1);	0.236088	0.29113	N	0.013101	T	0.59998	0.2235	L	0.36672	1.1	0.29119	N	0.880352	P	0.52316	0.952	P	0.48488	0.579	T	0.55010	-0.8207	10	0.24483	T	0.36	.	11.8532	0.52423	0.0:0.8228:0.1772:0.0	.	158	O95274	LYPD3_HUMAN	I	158	ENSP00000244333:V158I	ENSP00000244333:V158I	V	-	1	0	LYPD3	48659190	0.898000	0.30612	0.998000	0.56505	0.595000	0.36748	1.341000	0.33907	2.466000	0.83321	0.456000	0.33151	GTC		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		T	43967350	C	T	43967350	3	4	111	1	0	0	0	0	1	0	0	0	9141	507	18	3	576	3	LYPD3	19	43967350	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1212814	43967350	15161633	969	30103										
IRGQ	126298	hgsc.bcm.edu	37	chr19	44097061	44097061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctcgccctcgccgtctgtgCgcacgcagacaagaggcgca	12	17	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:44097061C>T	ENST00000602269.1	-	2	1174	c.989G>A	c.(988-990)cGc>cAc	p.R330H	IRGQ_ENST00000422989.1_Missense_Mutation_p.R330H|IRGQ_ENST00000601520.1_5'UTR|L34079.2_ENST00000594374.1_Missense_Mutation_p.R43H			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	330	IRG-type G.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCCGTCTGTGCGCACGCAGAC	0.632																																																0			19											128	124	125					19																	44097061		2203	4300	6503	48788901	SO:0001583	missense	126298			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"immunity-related GTPase family, Q1"	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.989G>A	19.37:g.44097061C>T	ENSP00000472250:p.Arg330His		48788901	B2RNP3	Missense_Mutation	SNP	ENST00000602269.1	37	CCDS33040.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765253	0.69878	.	.	ENSG00000167378	ENST00000422989	T	0.58358	0.34	4.26	4.26	0.50523	.	0.353444	0.19631	N	0.109661	T	0.67515	0.2901	M	0.68952	2.095	0.29488	N	0.855838	D	0.89917	1.0	D	0.79108	0.992	T	0.63260	-0.6677	10	0.72032	D	0.01	-25.8297	10.4901	0.44746	0.0:0.8034:0.1966:0.0	.	330	Q8WZA9	IRGQ_HUMAN	H	330	ENSP00000387535:R330H	ENSP00000387535:R330H	R	-	2	0	IRGQ	48788901	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.964000	0.49192	2.667000	0.90743	0.655000	0.94253	CGC		0.632	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		T	44097061	C	T	44097061	3	4	111	1	0	0	0	0	1	0	0	0	7860	768	27	1	886	1	IRGQ	19	44097061	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	129711	44097061	15031922	970	30104										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46850393	46850393	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaggactgagtgtgctgagCccccccgggacgaacccccg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:46850393delC	ENST00000012443.4	+	1	143	c.40delC	c.(40-42)cccfs	p.P15fs	PPP5C_ENST00000391919.1_5'UTR	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	15					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)	p.R16fs*7(1)		endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GTGTGCTGAGCCCCCCCGGGA	0.687											OREG0025570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Insertion - Frameshift(1)	ovary(1)	19											25	23	24					19																	46850393		2197	4298	6495	51542233	SO:0001589	frameshift_variant	5536				CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.40delC	19.37:g.46850393delC	ENSP00000012443:p.Pro15fs	942	51542233	Q16722|Q53XV2	Frame_Shift_Del	DEL	ENST00000012443.4	37	CCDS12684.1																																																																																				0.687	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		-	46850393	C	-	46850393	7	5	111	1	0	1	0	1	0	0	0	0	12440	739	26	0	42	0	PPP5C	19	46850393	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	2753332	46850393	12278590	971	30105										
PNMAL2	57469	hgsc.bcm.edu	37	chr19	46997834	46997834	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtccggggtgtctctcacagCcagcagggccactaagtcgg	14	13	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:46997834C>T	ENST00000377655.2	-	1	734				PNMAL2_ENST00000594749.1_Intron|AC011484.1_ENST00000377652.3_5'UTR|PNMAL2_ENST00000599531.1_Missense_Mutation_p.A297T			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TCTCTCACAGCCAGCAGGGCC	0.567																																																0			19											60	61	61					19																	46997834		2203	4300	6503	51689674	SO:0001627	intron_variant	57469			AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+154G>A	19.37:g.46997834C>T			51689674	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37																																																																																					0.567	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		T	46997834	C	T	46997834	1	4	111	0	1	0	0	0	0	0	0	0	12189	739	26	3		3	PNMAL2	19	46997834	Intron	SNP	C	TCGA-EI-6507-01A-11D-1733-10	147441	46997834	12131149	972	30106										
LIG1	3978	hgsc.bcm.edu	37	chr19	48657140	48657140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggggctcaccttcctcctccTtcttcctcttggcttctctg	7	17	4	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:48657140T>C	ENST00000263274.7	-	6	874	c.455A>G	c.(454-456)aAg>aGg	p.K152R	LIG1_ENST00000536218.1_Intron|LIG1_ENST00000427526.2_Missense_Mutation_p.K122R|LIG1_ENST00000599165.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	152			K -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ttcctcctccttcttcctctt	0.577								Nucleotide excision repair (NER)																																								0			19											196	113	141					19																	48657140		2203	4300	6503	53348952	SO:0001583	missense	26018				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.455A>G	19.37:g.48657140T>C	ENSP00000263274:p.Lys152Arg		53348952	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	6.386	0.439422	0.12104	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526	T;T	0.58506	0.44;0.33	3.99	2.94	0.34122	.	0.866238	0.10215	N	0.701604	T	0.48714	0.1515	L	0.54323	1.7	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.28839	-1.0031	10	0.18710	T	0.47	-18.4584	7.3918	0.26913	0.0:0.0:0.2229:0.7771	.	122;152	B4DTU4;P18858	.;DNLI1_HUMAN	R	152;184;122	ENSP00000263274:K152R;ENSP00000442841:K122R	ENSP00000263274:K152R	K	-	2	0	LIG1	53348952	0.292000	0.24362	0.892000	0.35008	0.244000	0.25665	1.067000	0.30616	0.837000	0.34925	0.496000	0.49642	AAG		0.577	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48657140	T	C	48657140	3	2	111	1	0	0	0	0	1	0	0	0	8804	1609	56	4	2396	4	LIG1	19	48657140	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1659306	48657140	10471843	973	30107										
FUT2	2524	hgsc.bcm.edu	37	chr19	49206855	49206855	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtcatgccaaaagtgtggaaGggggtggtggccgaccggcg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:49206855delG	ENST00000425340.2	+	2	759	c.642delG	c.(640-642)aagfs	p.K214fs	FUT2_ENST00000391876.4_Frame_Shift_Del_p.K214fs	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	214					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		AAGTGTGGAAGGGGGTGGTGG	0.627																																																0			19											67	70	69					19																	49206855		2203	4300	6503	53898667	SO:0001589	frameshift_variant	2524				CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"Fucosyltransferases"	4013	protein-coding gene	gene with protein product	"alpha (1,2) fucosyltransferase", "galactoside 2-alpha-L-fucosyltransferase 2", "GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2", "alpha(1,2)FT2", "secretor factor", "secretor blood group alpha-2-fucosyltransferase"	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.642delG	19.37:g.49206855delG	ENSP00000387498:p.Lys214fs		53898667	Q0VAG5|Q14338|Q5D0G2	Frame_Shift_Del	DEL	ENST00000425340.2	37	CCDS33069.1																																																																																				0.627	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511		-	49206855	G	-	49206855	7	5	111	1	0	1	0	1	0	0	0	0	6123	991	35	0	644	0	FUT2	19	49206855	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	549715	49206855	9922128	974	30108										
HSD17B14	51171	hgsc.bcm.edu	37	chr19	49334941	49334941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaccttggtcaaggtgtacGtccccagtaggttcagctcc	10	13	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:49334941G>A	ENST00000263278.4	-	5	619	c.353C>T	c.(352-354)aCg>aTg	p.T118M	HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	118					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CAAGGTGTACGTCCCCAGTAG	0.597																																																0			19											62	63	63					19																	49334941		2203	4300	6503	54026753	SO:0001583	missense	51171			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	23238	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 3", "short chain dehydrogenase/reductase family 47C, member 1"	612832	"dehydrogenase/reductase (SDR family) member 10"	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.353C>T	19.37:g.49334941G>A	ENSP00000263278:p.Thr118Met		54026753	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	G	1.815	-0.473583	0.04445	.	.	ENSG00000087076	ENST00000263278	D	0.88509	-2.39	4.26	-1.07	0.09968	NAD(P)-binding domain (1);	0.896444	0.09556	N	0.786237	T	0.76162	0.3949	L	0.31207	0.915	0.09310	N	1	P	0.39352	0.669	B	0.28784	0.094	T	0.64980	-0.6279	10	0.44086	T	0.13	.	5.1252	0.14880	0.1456:0.0:0.6758:0.1786	.	118	Q9BPX1	DHB14_HUMAN	M	118	ENSP00000263278:T118M	ENSP00000263278:T118M	T	-	2	0	HSD17B14	54026753	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.451000	0.06795	-0.052000	0.13311	-0.458000	0.05436	ACG		0.597	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246		A	49334941	G	A	49334941	3	1	111	1	0	0	0	0	1	0	0	0	7404	1145	40	1	479	1	HSD17B14	19	49334941	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	128086	49334941	9794042	975	30109										
RUVBL2	10856	hgsc.bcm.edu	37	chr19	49510281	49510281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcctccttcccaggcatggCgcaggccctgggccctgaca	12	17	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:49510281C>T	ENST00000595090.1	+	5	736	c.272C>T	c.(271-273)gCg>gTg	p.A91V	RUVBL2_ENST00000413176.2_Missense_Mutation_p.A46V|RUVBL2_ENST00000601968.1_Missense_Mutation_p.A46V	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	91					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		CCAGGCATGGCGCAGGCCCTG	0.632																																																0			19											28	32	31					19																	49510281		2046	4181	6227	54202093	SO:0001583	missense	10856			AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"INO80 complex subunits", "ATPases / AAA-type"	10475	protein-coding gene	gene with protein product	"reptin", "INO80 complex subunit J"	604788	"RuvB (E coli homolog)-like 2", "RuvB-like 2 (E. coli)"			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.272C>T	19.37:g.49510281C>T	ENSP00000473172:p.Ala91Val		54202093	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789553	0.90367	.	.	ENSG00000183207	ENST00000221413;ENST00000413176	T;T	0.59224	0.28;0.53	5.46	4.41	0.53225	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.107480	0.64402	D	0.000006	D	0.83211	0.5205	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.963;0.975	D	0.88911	0.3359	10	0.87932	D	0	-36.8523	14.2578	0.66062	0.0:0.8497:0.1502:0.0	.	91;91;57	B4DW30;Q9Y230;B3KNL2	.;RUVB2_HUMAN;.	V	91;46	ENSP00000221413:A91V;ENSP00000413890:A46V	ENSP00000221413:A91V	A	+	2	0	RUVBL2	54202093	1.000000	0.71417	0.924000	0.36721	0.919000	0.55068	7.016000	0.76393	1.403000	0.46800	0.561000	0.74099	GCG		0.632	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1			T	49510281	C	T	49510281	3	4	111	1	0	0	0	0	1	0	0	0	13790	768	27	1	290	1	RUVBL2	19	49510281	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	175340	49510281	9618702	976	30110										
RUVBL2	10856	hgsc.bcm.edu	37	chr19	49513087	49513087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagagatggagaccatctacGacctgggcaccaagatgatt	11	10	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:49513087G>A	ENST00000595090.1	+	7	981	c.517G>A	c.(517-519)Gac>Aac	p.D173N	RUVBL2_ENST00000413176.2_Missense_Mutation_p.D128N|RUVBL2_ENST00000601968.1_Missense_Mutation_p.D128N	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	173					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GACCATCTACGACCTGGGCAC	0.622																																																0			19											105	106	106					19																	49513087		2077	4208	6285	54204899	SO:0001583	missense	10856			AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"INO80 complex subunits", "ATPases / AAA-type"	10475	protein-coding gene	gene with protein product	"reptin", "INO80 complex subunit J"	604788	"RuvB (E coli homolog)-like 2", "RuvB-like 2 (E. coli)"			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.517G>A	19.37:g.49513087G>A	ENSP00000473172:p.Asp173Asn		54204899	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	G	31	5.071038	0.93950	.	.	ENSG00000183207	ENST00000221413;ENST00000413176	T;T	0.50001	0.76;0.93	4.31	4.31	0.51392	TIP49, C-terminal (1);Nucleic acid-binding, OB-fold-like (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.73791	0.3632	M	0.90870	3.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75484	0.986;0.986;0.986	T	0.80407	-0.1395	10	0.66056	D	0.02	-43.4915	14.6799	0.69009	0.0:0.0:1.0:0.0	.	173;173;139	B4DW30;Q9Y230;B3KNL2	.;RUVB2_HUMAN;.	N	173;128	ENSP00000221413:D173N;ENSP00000413890:D128N	ENSP00000221413:D173N	D	+	1	0	RUVBL2	54204899	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.645000	0.91049	2.417000	0.82017	0.655000	0.94253	GAC		0.622	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1			A	49513087	G	A	49513087	3	1	111	1	0	0	0	0	1	0	0	0	13790	1058	37	1	543	1	RUVBL2	19	49513087	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2806	49513087	9615896	977	30111										
SLC6A16	28968	hgsc.bcm.edu	37	chr19	49813001	49813001	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agactgtagactggtgacccGccatcctcgattctgtctga	10	12	2	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:49813001G>A	ENST00000335875.4	-	5	1024	c.783C>T	c.(781-783)ggC>ggT	p.G261G	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Silent_p.G261G	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	261					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		CTGGTGACCCGCCATCCTCGA	0.537																																																0			19											84	86	86					19																	49813001		1962	4148	6110	54504813	SO:0001819	synonymous_variant	28968			AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.783C>T	19.37:g.49813001G>A			54504813	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																				0.537	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		A	49813001	G	A	49813001	2	1	111	1	0	0	0	0	0	0	0	1	14716	1074	38	1		1	SLC6A16	19	49813001	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	299914	49813001	9315982	978	30112										
PRR12	57479	hgsc.bcm.edu	37	chr19	50098979	50098979	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctacgggcaagggtttggaGgggggcaggcacaggacttg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:50098979delG	ENST00000418929.2	+	4	1399	c.1387delG	c.(1387-1389)gggfs	p.G464fs		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		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)		AGGGTTTGGAGGGGGGCAGGC	0.701																																																0			19											15	17	16					19																	50098979		1732	3926	5658	54790791	SO:0001589	frameshift_variant	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.1387delG	19.37:g.50098979delG	ENSP00000394510:p.Gly464fs		54790791	E9PB06|Q8N4J6	Frame_Shift_Del	DEL	ENST00000418929.2	37	CCDS46143.1																																																																																				0.701	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		-	50098979	G	-	50098979	7	5	111	1	0	1	0	1	0	0	0	0	12618	1000	35	0	1401	0	PRR12	19	50098979	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	285978	50098979	9030004	979	30113										
POLD1	5424	hgsc.bcm.edu	37	chr19	50918238	50918238	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcctcactgcgccgcctgcTcatcgaccggtgtgtggggc	14	15	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:50918238T>G	ENST00000440232.2	+	20	2608	c.2555T>G	c.(2554-2556)cTc>cGc	p.L852R	POLD1_ENST00000599857.1_Missense_Mutation_p.L852R|CTD-2545M3.6_ENST00000599632.1_5'Flank|POLD1_ENST00000595904.1_Missense_Mutation_p.L878R	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	852					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CGCCGCCTGCTCATCGACCGG	0.701								DNA polymerases (catalytic subunits)																																								0			19											35	28	30					19																	50918238		2198	4298	6496	55610050	SO:0001583	missense	5424				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2555T>G	19.37:g.50918238T>G	ENSP00000406046:p.Leu852Arg		55610050	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.824474	0.50739	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.21932	1.98	4.45	3.41	0.39046	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.64402	D	0.000001	T	0.64832	0.2634	H	0.99811	4.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.74266	-0.3721	10	0.87932	D	0	-28.0817	9.5963	0.39576	0.1573:0.0:0.0:0.8427	.	878;852	E7EVW0;P28340	.;DPOD1_HUMAN	R	852;853	ENSP00000406046:L852R	ENSP00000366129:L853R	L	+	2	0	POLD1	55610050	1.000000	0.71417	0.931000	0.37212	0.292000	0.27327	7.358000	0.79466	0.672000	0.31204	0.235000	0.17854	CTC		0.701	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			G	50918238	T	G	50918238	3	3	111	1	0	0	0	0	1	0	0	0	12221	1551	54	4	2629	4	POLD1	19	50918238	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	819259	50918238	8210745	980	30114										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51984817	51984817	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccccagacggcaagaccctcGtcatcctcagggtcagccgc	10	18	3	2	rs144039020	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:51984817G>A	ENST00000396477.4	+	3	592	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	CEACAM18_ENST00000451626.1_Missense_Mutation_p.V252I	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	191										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAAGACCCTCGTCATCCTCAG	0.493													g|||	5	0.000998403	0	0	5008	,	,		21412	0		0.003	False		,,,				2504	0.002															0			19						G	ILE/VAL	0,3978		0,0,1989	84	78	80		754	-2.8	0	19	dbSNP_134	80	21,8333		0,21,4156	yes	missense	CEACAM18	NM_001080405.1	29	0,21,6145	AA,AG,GG		0.2514,0.0,0.1703	benign	252/399	51984817	21,12311	1989	4177	6166	56676629	SO:0001583	missense	729767					19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.571G>A	19.37:g.51984817G>A	ENSP00000379738:p.Val191Ile		56676629	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	.	0.069	-1.205756	0.01568	0.0	0.002514	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.77358	-1.09	2.72	-2.75	0.05914	Immunoglobulin-like fold (1);	.	.	.	.	T	0.53546	0.1803	N	0.13352	0.335	0.09310	N	1	B	0.17465	0.022	B	0.16289	0.015	T	0.38908	-0.9639	9	0.10377	T	0.69	-7.1095	7.1115	0.25392	0.6217:0.0:0.3783:0.0	.	252	A8MTB9	CEA18_HUMAN	I	252;191;191	ENSP00000402203:V252I	ENSP00000379738:V191I	V	+	1	0	CEACAM18	56676629	0.010000	0.17322	0.001000	0.08648	0.031000	0.12232	-0.824000	0.04438	-0.584000	0.05913	-0.259000	0.10710	GTC		0.493	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2			A	51984817	G	A	51984817	3	1	111	1	0	0	0	0	1	0	0	0	3195	1145	40	1	768	1	CEACAM18	19	51984817	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1066579	51984817	7144166	981	30115										
ZNF614	80110	hgsc.bcm.edu	37	chr19	52520436	52520436	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttgattaaacttaaacttgAtttcaaattttttctgtaca	4	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:52520436A>G	ENST00000270649.6	-	5	959	c.415T>C	c.(415-417)Tca>Cca	p.S139P	ZNF614_ENST00000356322.6_Missense_Mutation_p.S139P	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CTTAAACTTGATTTCAAATTT	0.328																																																0			19											89	85	86					19																	52520436		2203	4299	6502	57212248	SO:0001583	missense	80110			BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"Zinc fingers, C2H2-type", "-"	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.415T>C	19.37:g.52520436A>G	ENSP00000270649:p.Ser139Pro		57212248	Q494T8|Q8TCF4|Q9BSN8	Missense_Mutation	SNP	ENST00000270649.6	37	CCDS12847.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094957	0.36952	.	.	ENSG00000142556	ENST00000356322;ENST00000270649	T;T	0.07688	5.94;3.17	3.53	1.21	0.21127	.	.	.	.	.	T	0.09468	0.0233	L	0.41492	1.28	0.09310	N	1	B;D	0.55800	0.229;0.973	B;P	0.49301	0.081;0.606	T	0.29640	-1.0005	9	0.28530	T	0.3	.	5.9458	0.19217	0.7269:0.0:0.2731:0.0	.	139;139	Q8N883;Q9BSN8	ZN614_HUMAN;.	P	139	ENSP00000348674:S139P;ENSP00000270649:S139P	ENSP00000270649:S139P	S	-	1	0	ZNF614	57212248	0.025000	0.19082	0.013000	0.15412	0.306000	0.27790	0.554000	0.23407	0.432000	0.26286	0.482000	0.46254	TCA		0.328	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040		G	52520436	A	G	52520436	3	3	111	1	0	0	0	0	1	0	0	0	18078	333	12	4	1346	4	ZNF614	19	52520436	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	535619	52520436	6608547	982	30116										
DPRX	503834	hgsc.bcm.edu	37	chr19	54139893	54139893	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaaactcaagaaagcgaaatGcaagcatattcatcaaaaac	5	8	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:54139893G>A	ENST00000376650.1	+	3	278	c.227G>A	c.(226-228)tGc>tAc	p.C76Y		NM_001012728.1	NP_001012746.1	A6NFQ7	DPRX_HUMAN	divergent-paired related homeobox	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(4)|large_intestine(1)|lung(7)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)		AAAGCGAAATGCAAGCATATT	0.458																																																0			19											82	79	80					19																	54139893		2203	4300	6503	58831705	SO:0001583	missense	503834				CCDS33103.1	19q13.42	2011-06-20			ENSG00000204595	ENSG00000204595		"Homeoboxes / PRD class"	32166	protein-coding gene	gene with protein product		611165					Standard	NM_001012728		Approved		uc002qcf.1	A6NFQ7		ENST00000376650.1:c.227G>A	19.37:g.54139893G>A	ENSP00000365838:p.Cys76Tyr		58831705		Missense_Mutation	SNP	ENST00000376650.1	37	CCDS33103.1	.	.	.	.	.	.	.	.	.	.	g	3.449	-0.112386	0.06881	.	.	ENSG00000204595	ENST00000376650	D	0.94376	-3.41	1.3	-2.04	0.07343	Homeobox (1);Homeodomain-like (1);	.	.	.	.	D	0.82430	0.5035	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.68318	-0.5440	9	0.46703	T	0.11	.	1.5066	0.02487	0.3521:0.0:0.3291:0.3189	.	76	A6NFQ7	DPRX_HUMAN	Y	76	ENSP00000365838:C76Y	ENSP00000365838:C76Y	C	+	2	0	DPRX	58831705	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	-0.177000	0.09796	-0.553000	0.06158	0.561000	0.74099	TGC		0.458	DPRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409880.1	NM_001012728		A	54139893	G	A	54139893	3	1	111	1	0	0	0	0	1	0	0	0	4749	1319	46	3	237	3	DPRX	19	54139893	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1619457	54139893	4989090	983	30117										
TMC4	147798	hgsc.bcm.edu	37	chr19	54672280	54672280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgtcggggccgggagggcctGggggagcgcctcccaaccag	19	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:54672280G>A	ENST00000376591.4	-	4	718	c.587C>T	c.(586-588)cCa>cTa	p.P196L	TMC4_ENST00000301187.4_Missense_Mutation_p.P190L|TMC4_ENST00000476013.2_5'UTR	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	196					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGGAGGGCCTGGGGGAGCGCC	0.647											OREG0025670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			19											25	21	23					19																	54672280		2181	4282	6463	59364092	SO:0001583	missense	147798			AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.587C>T	19.37:g.54672280G>A	ENSP00000365776:p.Pro196Leu	1002	59364092	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243900	0.22796	.	.	ENSG00000167608	ENST00000301187;ENST00000376591;ENST00000446291	T;T;T	0.47528	0.84;0.84;0.84	4.2	3.14	0.36123	.	0.806849	0.11131	N	0.596274	T	0.38081	0.1027	L	0.54323	1.7	0.28196	N	0.927556	B;B	0.10296	0.001;0.003	B;B	0.10450	0.004;0.005	T	0.30208	-0.9986	10	0.11485	T	0.65	-33.1815	7.3095	0.26467	0.1205:0.0:0.8795:0.0	.	196;190	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	L	190;196;100	ENSP00000301187:P190L;ENSP00000365776:P196L;ENSP00000416444:P100L	ENSP00000301187:P190L	P	-	2	0	TMC4	59364092	0.960000	0.32886	0.816000	0.32577	0.683000	0.39861	1.596000	0.36718	2.071000	0.62044	0.558000	0.71614	CCA		0.647	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			A	54672280	G	A	54672280	3	1	111	1	0	0	0	0	1	0	0	0	16026	1348	47	3	1599	3	TMC4	19	54672280	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	532387	54672280	4456703	984	30118										
TMEM86B	255043	hgsc.bcm.edu	37	chr19	55738752	55738752	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggccgcgccacagcatggCcatcaggatcagcccatagg	12	15	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:55738752C>A	ENST00000327042.4	-	3	1000	c.478G>T	c.(478-480)Gcc>Tcc	p.A160S	AC010327.2_ENST00000598855.1_Silent_p.G38G	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	160					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CACAGCATGGCCATCAGGATC	0.687																																																0			19											14	15	15					19																	55738752		2188	4286	6474	60430564	SO:0001583	missense	255043			BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.478G>T	19.37:g.55738752C>A	ENSP00000321038:p.Ala160Ser		60430564		Missense_Mutation	SNP	ENST00000327042.4	37	CCDS12920.1	.	.	.	.	.	.	.	.	.	.	.	13.01	2.109887	0.37242	.	.	ENSG00000180089	ENST00000327042	T	0.22336	1.96	4.79	-9.58	0.00559	.	1.089140	0.07015	N	0.825806	T	0.10551	0.0258	L	0.31926	0.97	0.09310	N	1	B	0.31413	0.322	B	0.34536	0.185	T	0.18272	-1.0342	10	0.18276	T	0.48	.	2.9176	0.05757	0.1917:0.1045:0.18:0.5238	.	160	Q8N661	TM86B_HUMAN	S	160	ENSP00000321038:A160S	ENSP00000321038:A160S	A	-	1	0	TMEM86B	60430564	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.638000	0.00407	-1.724000	0.01373	-0.136000	0.14681	GCC		0.687	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804		A	55738752	C	A	55738752	3	1	111	1	0	0	0	0	1	0	0	0	16248	739	26	2	206	2	TMEM86B	19	55738752	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1066472	55738752	3390231	985	30119										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56466501	56466501	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acccttccggggtttaatacGatggaaaaaatcaagtattt	8	7	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:56466501G>A	ENST00000291971.3	+	3	1148	c.1077G>A	c.(1075-1077)acG>acA	p.T359T	NLRP8_ENST00000590542.1_Silent_p.T359T	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	359	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GGTTTAATACGATGGAAAAAA	0.453																																																0			19											74	73	73					19																	56466501		2203	4300	6503	61158313	SO:0001819	synonymous_variant	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1077G>A	19.37:g.56466501G>A			61158313	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																				0.453	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56466501	G	A	56466501	2	1	111	1	0	0	0	0	0	0	0	1	10514	1045	37	1		1	NLRP8	19	56466501	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	727749	56466501	2662482	986	30120										
ZSCAN5B	342933	hgsc.bcm.edu	37	chr19	56701518	56701518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agggctgcaagaagcgcttcCgacagagatcacattgaaag	12	9	1	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:56701518C>T	ENST00000586855.2	-	5	1479	c.1166G>A	c.(1165-1167)cGg>cAg	p.R389Q	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.R389Q			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	389					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R389L(1)		breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GAAGCGCTTCCGACAGAGATC	0.527																																																1	Substitution - Missense(1)	prostate(1)	19											75	79	78					19																	56701518		2177	4280	6457	61393330	SO:0001583	missense	342933				CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"-", "Zinc fingers, C2H2-type"	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.1166G>A	19.37:g.56701518C>T	ENSP00000466072:p.Arg389Gln		61393330		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	C	8.234	0.805258	0.16467	.	.	ENSG00000197213	ENST00000358992	T	0.14391	2.51	3.15	-2.74	0.05932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04003	0.0112	N	0.04373	-0.215	0.09310	N	1	P	0.34837	0.472	B	0.25987	0.065	T	0.30851	-0.9964	9	0.54805	T	0.06	.	1.5186	0.02511	0.1509:0.4449:0.1824:0.2217	.	389	A6NJL1	ZSA5B_HUMAN	Q	389	ENSP00000351883:R389Q	ENSP00000351883:R389Q	R	-	2	0	ZSCAN5B	61393330	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.041000	0.12084	-0.535000	0.06307	-0.676000	0.03789	CGG		0.527	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		T	56701518	C	T	56701518	3	4	111	1	0	0	0	0	1	0	0	0	18278	652	23	1	325	1	ZSCAN5B	19	56701518	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	235017	56701518	2427465	987	30121										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56895627	56895627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttctctccagtgtgaattcTctgatgttgcttgagttgtg	10	7	2	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:56895627T>C	ENST00000301310.4	-	5	1317	c.1159A>G	c.(1159-1161)Aga>Gga	p.R387G	ZNF582_ENST00000586929.1_Missense_Mutation_p.R387G	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GTGTGAATTCTCTGATGTTGC	0.428																																					Ovarian(183;1887 2032 4349 30507 51343)											0			19											97	96	96					19																	56895627		2203	4300	6503	61587439	SO:0001583	missense	147948			AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.1159A>G	19.37:g.56895627T>C	ENSP00000301310:p.Arg387Gly		61587439	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.132957	0.56828	.	.	ENSG00000018869	ENST00000301310	T	0.24723	1.84	4.76	2.65	0.31530	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37761	N	0.001946	T	0.49133	0.1539	M	0.84511	2.7	0.29183	N	0.876351	D;D	0.89917	0.972;1.0	P;D	0.91635	0.702;0.999	T	0.46442	-0.9191	10	0.59425	D	0.04	.	6.8217	0.23861	0.0:0.0817:0.1519:0.7664	.	387;418	Q96NG8;B4DQZ9	ZN582_HUMAN;.	G	387	ENSP00000301310:R387G	ENSP00000301310:R387G	R	-	1	2	ZNF582	61587439	0.024000	0.19004	0.892000	0.35008	0.525000	0.34531	0.774000	0.26675	0.313000	0.23062	0.533000	0.62120	AGA		0.428	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		C	56895627	T	C	56895627	3	2	111	1	0	0	0	0	1	0	0	0	18053	1559	54	4	398	4	ZNF582	19	56895627	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	194109	56895627	2233356	988	30122										
PEG3	5178	hgsc.bcm.edu	37	chr19	57328908	57328908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	catcttcacaaatcccccgcCggtgggttgattttttggct	9	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:57328908C>T	ENST00000326441.9	-	10	1265	c.902G>A	c.(901-903)cGg>cAg	p.R301Q	PEG3_ENST00000598410.1_Missense_Mutation_p.R177Q|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R175Q|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R301Q|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000593711.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	301					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AATCCCCCGCCGGTGGGTTGA	0.458																																																0			19											48	57	54					19																	57328908		2203	4298	6501	62020720	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.902G>A	19.37:g.57328908C>T	ENSP00000326581:p.Arg301Gln		62020720	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.364023	0.41902	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02525	4.26;4.26	4.27	3.24	0.37175	.	0.163819	0.29178	N	0.012918	T	0.01835	0.0058	L	0.27053	0.805	.	.	.	P;P;P	0.43885	0.82;0.82;0.669	B;B;B	0.32864	0.097;0.154;0.022	T	0.37150	-0.9718	9	0.62326	D	0.03	-16.7107	5.3052	0.15799	0.2011:0.6968:0.0:0.102	.	177;301;236	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	Q	301;301;271	ENSP00000326581:R301Q;ENSP00000403051:R301Q	ENSP00000292074:R271Q	R	-	2	0	ZIM2	62020720	0.016000	0.18221	0.417000	0.26559	0.987000	0.75469	0.419000	0.21247	1.395000	0.46643	0.561000	0.74099	CGG		0.458	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57328908	C	T	57328908	3	4	111	1	0	0	0	0	1	0	0	0	11751	652	23	1	3868	1	PEG3	19	57328908	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	433281	57328908	1800075	989	30123										
C19orf18	147685	hgsc.bcm.edu	37	chr19	58483860	58483860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcaggaatttcatggggttcGtaggggatgcagctaaaagg	15	5	2	0	rs139303329	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:58483860G>A	ENST00000314391.3	-	3	340	c.239C>T	c.(238-240)aCg>aTg	p.T80M		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	80						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)		CATGGGGTTCGTAGGGGATGC	0.463													G|||	8	0.00159744	8e-04	0.0029	5008	,	,		20372	0		0.005	False		,,,				2504	0															0			19						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	87	83	84		239	-4.1	0	19	dbSNP_134	84	46,8554	29.6+/-80.5	0,46,4254	yes	missense	C19orf18	NM_152474.4	81	0,47,6456	AA,AG,GG		0.5349,0.0227,0.3614	possibly-damaging	80/216	58483860	47,12959	2203	4300	6503	63175672	SO:0001583	missense	147685			BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.239C>T	19.37:g.58483860G>A	ENSP00000321519:p.Thr80Met		63175672		Missense_Mutation	SNP	ENST00000314391.3	37	CCDS12967.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	9.613	1.131889	0.21041	2.27E-4	0.005349	ENSG00000177025	ENST00000314391	T	0.59364	0.27	2.76	-4.1	0.03940	.	2.304190	0.02283	N	0.069571	T	0.34716	0.0907	N	0.14661	0.345	0.09310	N	1	D	0.59357	0.985	P	0.49683	0.619	T	0.34502	-0.9826	10	0.62326	D	0.03	-1.0539	1.4251	0.02321	0.1217:0.3127:0.2395:0.3261	.	80	Q8NEA5	CS018_HUMAN	M	80	ENSP00000321519:T80M	ENSP00000321519:T80M	T	-	2	0	C19orf18	63175672	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.571000	0.05889	-0.821000	0.04312	-1.094000	0.02160	ACG		0.463	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	NM_152474		A	58483860	G	A	58483860	3	1	111	1	0	0	0	0	1	0	0	0	1916	1145	40	1	424	1	C19orf18	19	58483860	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1154952	58483860	645123	990	30124										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58579256	58579256	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagagaagccctatgagtgCagtcagtgtgggaaggcctt	16	7	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:58579256C>T	ENST00000313434.5	+	5	1505	c.1404C>T	c.(1402-1404)tgC>tgT	p.C468C	ZNF135_ENST00000401053.4_Silent_p.C492C|ZNF135_ENST00000511556.1_Silent_p.C480C|ZNF135_ENST00000439855.2_Silent_p.C468C|ZNF135_ENST00000506786.1_Silent_p.C426C|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000359978.6_Intron	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	468					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		CCTATGAGTGCAGTCAGTGTG	0.567																																																0			19											91	81	84					19																	58579256		2203	4300	6503	63271068	SO:0001819	synonymous_variant	7694			U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1404C>T	19.37:g.58579256C>T			63271068	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	37		.	.	.	.	.	.	.	.	.	.	C	0.009	-1.849953	0.00563	.	.	ENSG00000176293	ENST00000391699	.	.	.	2.65	-0.777	0.10981	.	.	.	.	.	T	0.53594	0.1806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47005	-0.9150	4	.	.	.	.	7.6625	0.28410	0.0:0.6457:0.0:0.3543	.	.	.	.	V	486	.	.	A	+	2	0	ZNF135	63271068	0.000000	0.05858	0.073000	0.20177	0.002000	0.02628	-0.464000	0.06688	0.041000	0.15688	-0.259000	0.10710	GCA		0.567	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		T	58579256	C	T	58579256	2	4	111	1	0	0	0	0	0	0	0	1	17764	718	25	3		3	ZNF135	19	58579256	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	95396	58579256	549727	991	30125										
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58966975	58966975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccgccagtggtggcagggatCgcagaatgggcgcagcttgg	18	10	0	1	rs371148383		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:58966975C>T	ENST00000336614.4	+	4	771	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C	ZNF324B_ENST00000545523.1_Missense_Mutation_p.R222C|ZNF324B_ENST00000391696.1_Missense_Mutation_p.R212C	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		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;0.0164)|Lung(386;0.179)		TGGCAGGGATCGCAGAATGGG	0.667																																																0			19						C	CYS/ARG	0,4406		0,0,2203	37	35	36		664	-0.1	0	19		36	1,8599		0,1,4299	no	missense	ZNF324B	NM_207395.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	222/545	58966975	1,13005	2203	4300	6503	63658787	SO:0001583	missense	388569			AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.664C>T	19.37:g.58966975C>T	ENSP00000337473:p.Arg222Cys		63658787	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	37	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	C	8.551	0.875598	0.17395	0.0	1.16E-4	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.08370	3.27;3.27;3.1	2.31	-0.0815	0.13702	.	.	.	.	.	T	0.04272	0.0118	N	0.19112	0.55	0.09310	N	1	D;D	0.57571	0.978;0.98	B;B	0.40329	0.153;0.326	T	0.34601	-0.9822	9	0.72032	D	0.01	.	0.9151	0.01303	0.2448:0.3638:0.2391:0.1523	.	222;212	Q6AW86;C9JTQ8	Z324B_HUMAN;.	C	222;222;212	ENSP00000337473:R222C;ENSP00000438930:R222C;ENSP00000375578:R212C	ENSP00000337473:R222C	R	+	1	0	ZNF324B	63658787	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.153000	0.16323	0.041000	0.15688	0.491000	0.48974	CGC		0.667	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		T	58966975	C	T	58966975	3	4	111	1	0	0	0	0	1	0	0	0	17884	884	31	1	674	1	ZNF324B	19	58966975	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	387719	58966975	162008	992	30126										
TRIM28	10155	hgsc.bcm.edu	37	chr19	59060556	59060556	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accggccagccagggactgcGcctgcaggaacccctggtgc	14	16	0	0	rs142762100		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr19:59060556G>A	ENST00000253024.5	+	12	1900	c.1611G>A	c.(1609-1611)gcG>gcA	p.A537A	TRIM28_ENST00000341753.6_Silent_p.A455A	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	537					convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CAGGGACTGCGCCTGCAGGAA	0.582													G|||	1	0.000199681	0	0	5008	,	,		18410	0		0	False		,,,				2504	0.001															0			19								0,4394		0,0,2197	46	57	53		1611	-7.4	0	19	dbSNP_134	53	7,8567		0,7,4280	no	coding-synonymous	TRIM28	NM_005762.2		0,7,6477	AA,AG,GG		0.0816,0.0,0.054		537/836	59060556	7,12961	2197	4287	6484	63752368	SO:0001819	synonymous_variant	10155				CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.1611G>A	19.37:g.59060556G>A			63752368	O00677|Q7Z632|Q93040|Q96IM1	Silent	SNP	ENST00000253024.5	37	CCDS12985.1																																																																																				0.582	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		A	59060556	G	A	59060556	2	1	111	1	0	0	0	0	0	0	0	1	16542	1074	38	1		1	TRIM28	19	59060556	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	93581	59060556	68427	993	30127										
SIRPD	128646	hgsc.bcm.edu	37	chr20	1515073	1515073	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttccttccctgtttggattAttttgacagcaagcctgaaa	8	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:1515073A>G	ENST00000381623.3	-	4	1781	c.592T>C	c.(592-594)Taa>Caa	p.*198Q	SIRPD_ENST00000381621.1_Nonstop_Mutation_p.*199Q			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	0						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						TGTTTGGATTATTTTGACAGC	0.353																																																0			20											148	141	143					20																	1515073		2203	4300	6503	1463073	SO:0001578	stop_lost	128646			AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16248	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type substrate 1-like 2"	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.592T>C	20.37:g.1515073A>G	ENSP00000371036:p.*198Gluext*42		1463073	B3KS88|Q5TFQ6	Missense_Mutation	SNP	ENST00000381623.3	37	CCDS13018.1	.	.	.	.	.	.	.	.	.	.	A	4.458	0.084917	0.08583	.	.	ENSG00000125900	ENST00000381623;ENST00000381621	.	.	.	1.71	0.495	0.16890	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.7122	0.08424	0.6167:0.0:0.0:0.3832	.	.	.	.	Q	198;199	.	.	X	-	1	0	SIRPD	1463073	0.001000	0.12720	0.012000	0.15200	0.509000	0.34042	-0.423000	0.07034	0.100000	0.17581	0.459000	0.35465	TAA		0.353	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460		G	1515073	A	G	1515073	4	3	111	1	0	0	0	0	0	0	0	0	14372	462	16	4	5	4	SIRPD	20	1515073	Nonstop_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10		1515073	61510447	994	30128										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1559074	1559074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacacagtagtaggtgccggCgtctgctggggtgatgttac	15	9	1	1	rs201259964		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:1559074C>T	ENST00000381605.4	-	2	407	c.343G>A	c.(343-345)Gcc>Acc	p.A115T	SIRPB1_ENST00000262929.5_Missense_Mutation_p.A114T|RP4-576H24.4_ENST00000564763.1_Missense_Mutation_p.A115T|SIRPB1_ENST00000381603.3_Missense_Mutation_p.A115T	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	115	Ig-like V-type.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TAGGTGCCGGCGTCTGCTGGG	0.527																																																0			20						C	THR/ALA,THR/ALA	0,4398		0,0,2199	214	184	194		343,343	-1.2	0.2	20		194	2,8508		0,2,4253	no	missense,missense	SIRPB1	NM_001083910.2,NM_006065.3	58,58	0,2,6452	TT,TC,CC		0.0235,0.0,0.0155	benign,benign	115/182,115/399	1559074	2,12906	2199	4255	6454	1507074	SO:0001583	missense	10326			Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.343G>A	20.37:g.1559074C>T	ENSP00000371018:p.Ala115Thr		1507074	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	7.257	0.604417	0.14002	0.0	2.35E-4	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000262929	T;T;T	0.62788	-0.0;-0.0;-0.0	2.36	-1.25	0.09405	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.520465	0.19067	N	0.123609	T	0.35158	0.0922	N	0.25957	0.775	0.19300	N	0.999971	P;B	0.36144	0.539;0.158	B;B	0.27500	0.08;0.056	T	0.20605	-1.0270	10	0.22109	T	0.4	.	5.3744	0.16156	0.0:0.3344:0.0:0.6656	.	115;115	O00241;O00241-2	SIRB1_HUMAN;.	T	115;115;114	ENSP00000371018:A115T;ENSP00000371016:A115T;ENSP00000262929:A114T	ENSP00000262929:A114T	A	-	1	0	SIRPB1	1507074	0.003000	0.15002	0.171000	0.22900	0.874000	0.50279	-1.098000	0.03346	-0.136000	0.11475	0.462000	0.41574	GCC		0.527	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		T	1559074	C	T	1559074	3	4	111	1	0	0	0	0	1	0	0	0	14370	768	27	1	869	1	SIRPB1	20	1559074	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	44001	1559074	61466446	995	30129										
SIRPG	55423	hgsc.bcm.edu	37	chr20	1617037	1617037	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gctcattcccatttttgaacCatttcagggtgatgtctctg	8	10	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:1617037C>A	ENST00000303415.3	-	3	609	c.545G>T	c.(544-546)tGg>tTg	p.W182L	SIRPG_ENST00000381580.1_Missense_Mutation_p.W149L|SIRPG_ENST00000216927.4_Missense_Mutation_p.W182L|SIRPG_ENST00000344103.4_Intron|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381583.2_Missense_Mutation_p.W182L|RP11-77C3.3_ENST00000437384.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	182	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						ATTTTTGAACCATTTCAGGGT	0.567																																																0			20											179	160	167					20																	1617037		2203	4300	6503	1565037	SO:0001583	missense	55423			AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.545G>T	20.37:g.1617037C>A	ENSP00000305529:p.Trp182Leu		1565037	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	16.10	3.027743	0.54790	.	.	ENSG00000089012	ENST00000381580;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T	0.04194	3.68;3.68;3.68;3.68	2.09	2.09	0.27110	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000034	T	0.26304	0.0642	H	0.96333	3.805	0.40037	D	0.975603	D;D	0.76494	0.998;0.999	D;D	0.71656	0.935;0.974	T	0.12553	-1.0543	10	0.87932	D	0	.	7.6109	0.28129	0.0:1.0:0.0:0.0	.	182;182	Q9P1W8-4;Q9P1W8	.;SIRPG_HUMAN	L	149;182;182;182	ENSP00000370992:W149L;ENSP00000305529:W182L;ENSP00000370995:W182L;ENSP00000216927:W182L	ENSP00000216927:W182L	W	-	2	0	SIRPG	1565037	1.000000	0.71417	0.948000	0.38648	0.398000	0.30690	3.048000	0.49862	1.148000	0.42385	0.404000	0.27445	TGG		0.567	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1617037	C	A	1617037	3	1	111	1	0	0	0	0	1	0	0	0	14373	595	21	2	630	2	SIRPG	20	1617037	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	57963	1617037	61408483	996	30130										
PDYN	5173	hgsc.bcm.edu	37	chr20	1961195	1961195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agctcctcttggggtatttgCgcaaaaagcccccatagcgt	10	12	1	0	rs377075531		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:1961195C>T	ENST00000217305.2	-	4	764	c.539G>A	c.(538-540)cGc>cAc	p.R180H	PDYN_ENST00000540134.1_Missense_Mutation_p.R180H|RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000539905.1_Missense_Mutation_p.R180H	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	180					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GGGGTATTTGCGCAAAAAGCC	0.602																																																0			20											99	103	102					20																	1961195		2203	4300	6503	1909195	SO:0001583	missense	5173				CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.539G>A	20.37:g.1961195C>T	ENSP00000217305:p.Arg180His		1909195	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772531	0.90108	.	.	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	D;D;D	0.86769	-2.17;-2.17;-2.17	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.94162	0.8127	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95090	0.8221	10	0.87932	D	0	-18.2484	15.1657	0.72821	0.0:1.0:0.0:0.0	.	180	P01213	PDYN_HUMAN	H	180	ENSP00000440185:R180H;ENSP00000442259:R180H;ENSP00000217305:R180H	ENSP00000217305:R180H	R	-	2	0	PDYN	1909195	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.652000	0.61454	2.445000	0.82738	0.313000	0.20887	CGC		0.602	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			T	1961195	C	T	1961195	3	4	111	1	0	0	0	0	1	0	0	0	11730	768	27	1	229	1	PDYN	20	1961195	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	344158	1961195	61064325	997	30131										
TGM3	7053	hgsc.bcm.edu	37	chr20	2320521	2320521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgctgaacgaggctcgtgtgCggaagcctgtgaacgtgcag	16	9	0	2	rs370607077	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:2320521C>T	ENST00000381458.5	+	12	1885	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	608					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	GGCTCGTGTGCGGAAGCCTGT	0.632													C|||	2	0.000399361	8e-04	0	5008	,	,		13698	0		0	False		,,,				2504	0.001															0			20						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	89	73	78		1822	0.3	0.1	20		78	0,8600		0,0,4300	no	missense	TGM3	NM_003245.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	608/694	2320521	1,13005	2203	4300	6503	2268521	SO:0001583	missense	7053			L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.1822C>T	20.37:g.2320521C>T	ENSP00000370867:p.Arg608Trp		2268521	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.366131	0.61513	2.27E-4	0.0	ENSG00000125780	ENST00000381458	T	0.69040	-0.37	5.26	0.351	0.16042	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	1.405290	0.04301	N	0.347352	T	0.59878	0.2226	L	0.27053	0.805	0.09310	N	1	D	0.76494	0.999	P	0.47864	0.559	T	0.55730	-0.8095	10	0.72032	D	0.01	-8.4543	7.9084	0.29776	0.5464:0.3121:0.1415:0.0	.	608	Q08188	TGM3_HUMAN	W	608	ENSP00000370867:R608W	ENSP00000370867:R608W	R	+	1	2	TGM3	2268521	0.000000	0.05858	0.130000	0.21974	0.035000	0.12851	-0.450000	0.06803	0.553000	0.29044	0.561000	0.74099	CGG		0.632	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2320521	C	T	2320521	3	4	111	1	0	0	0	0	1	0	0	0	15870	759	27	1	1868	1	TGM3	20	2320521	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	359326	2320521	60704999	998	30132										
C20orf196	149840	hgsc.bcm.edu	37	chr20	5843794	5843794	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cttcggaaatccctggatagAttctatgaaatgtttggtca	9	7	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:5843794A>T	ENST00000303142.6	+	3	390	c.303A>T	c.(301-303)agA>agT	p.R101S		NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	101										endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						CCCTGGATAGATTCTATGAAA	0.488																																																0			20											72	74	74					20																	5843794		2203	4300	6503	5791794	SO:0001583	missense	149840			AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984			26318	protein-coding gene	gene with protein product						12477932	Standard	NM_152504		Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.303A>T	20.37:g.5843794A>T	ENSP00000305875:p.Arg101Ser		5791794	A8K9J3|Q5TGA9|Q96LU1	Missense_Mutation	SNP	ENST00000303142.6	37	CCDS13091.1	.	.	.	.	.	.	.	.	.	.	a	7.853	0.724334	0.15439	.	.	ENSG00000171984	ENST00000303142;ENST00000378971;ENST00000445603;ENST00000442185	T;T;T	0.46063	0.88;0.88;0.88	5.5	-1.53	0.08611	.	0.704221	0.13552	N	0.379390	T	0.31295	0.0792	L	0.42245	1.32	0.22500	N	0.99905	P	0.36909	0.573	B	0.39217	0.294	T	0.23297	-1.0192	10	0.66056	D	0.02	-5.5677	5.0773	0.14638	0.512:0.0:0.3437:0.1443	.	101	Q8IYI0	CT196_HUMAN	S	101;101;101;148	ENSP00000305875:R101S;ENSP00000399331:R101S;ENSP00000410534:R148S	ENSP00000305875:R101S	R	+	3	2	C20orf196	5791794	0.010000	0.17322	0.775000	0.31657	0.120000	0.20174	-0.205000	0.09411	-0.129000	0.11620	-0.377000	0.06932	AGA		0.488	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504		T	5843794	A	T	5843794	3	4	111	1	0	0	0	0	1	0	0	0	2107	330	12	5	309	5	C20orf196	20	5843794	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3523273	5843794	57181726	999	30133										
CST5	1473	hgsc.bcm.edu	37	chr20	23860294	23860294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagtcagcagcagcagtgggGtgtgcatgggccacatcatg	15	10	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:23860294G>A	ENST00000304710.4	-	1	93	c.20C>T	c.(19-21)aCc>aTc	p.T7I		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	7					negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						CAGCAGTGGGGTGTGCATGGG	0.607																																																0			20											50	46	48					20																	23860294		2203	4300	6503	23808294	SO:0001583	missense	1473				CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.20C>T	20.37:g.23860294G>A	ENSP00000307132:p.Thr7Ile		23808294	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	37	CCDS13162.1	.	.	.	.	.	.	.	.	.	.	g	4.053	0.007452	0.07866	.	.	ENSG00000170367	ENST00000304710	T	0.09723	2.95	1.47	-0.667	0.11395	.	1.514020	0.03811	N	0.265914	T	0.05318	0.0141	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.36529	-0.9744	10	0.20519	T	0.43	.	4.0552	0.09813	0.429:0.0:0.571:0.0	.	7	P28325	CYTD_HUMAN	I	7	ENSP00000307132:T7I	ENSP00000307132:T7I	T	-	2	0	CST5	23808294	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.152000	0.10159	-0.188000	0.10499	0.443000	0.29094	ACC		0.607	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900		A	23860294	G	A	23860294	3	1	111	1	0	0	0	0	1	0	0	0	3981	1261	44	3	420	3	CST5	20	23860294	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	18016500	23860294	39165226	1000	30134										
C20orf70	140683	hgsc.bcm.edu	37	chr20	31757090	31757090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttcacgagggacttgagacaGttgacaatactcttaaaggt	10	7	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:31757090G>A	ENST00000253362.2	+	2	285	c.139G>A	c.(139-141)Gtt>Att	p.V47I	BPIFA2_ENST00000354932.5_Missense_Mutation_p.V47I			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	47						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										ACTTGAGACAGTTGACAATAC	0.463																																																0			20											131	109	117					20																	31757090		2203	4300	6503	31220751	SO:0001583	missense	140683			AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"BPI fold containing"	16203	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 70"	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.139G>A	20.37:g.31757090G>A	ENSP00000253362:p.Val47Ile		31220751	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	G	0.488	-0.876665	0.02550	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.14766	2.48;2.48	3.98	-2.99	0.05497	.	0.834058	0.10049	N	0.722475	T	0.04497	0.0123	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.43605	-0.9381	10	0.07175	T	0.84	-1.2677	4.5032	0.11874	0.3685:0.2977:0.3338:0.0	.	47	Q96DR5	BPIA2_HUMAN	I	47	ENSP00000253362:V47I;ENSP00000347012:V47I	ENSP00000253362:V47I	V	+	1	0	BPIFA2	31220751	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.012000	0.03649	-0.545000	0.06224	-0.137000	0.14449	GTT		0.463	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		A	31757090	G	A	31757090	3	1	111	1	0	0	0	0	1	0	0	0	2122	1029	36	3	141	3	C20orf70	20	31757090	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	7896796	31757090	31268430	1001	30135										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35422784	35422784	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcgctgcatctgcctccctGgggggtcctggcaggccagg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:35422784delG	ENST00000357779.3	-	14	3313	c.2987delC	c.(2986-2988)ccafs	p.P996fs	SOGA1_ENST00000237536.4_Frame_Shift_Del_p.P1234fs|SOGA1_ENST00000456801.2_Frame_Shift_Del_p.P837fs|SOGA1_ENST00000279034.6_Frame_Shift_Del_p.P996fs			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	996					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CTGCCTCCCTGGGGGGTCCTG	0.657																																																0			20											17	19	18					20																	35422784		1939	4128	6067	34856198	SO:0001589	frameshift_variant	140710			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2987delC	20.37:g.35422784delG	ENSP00000350424:p.Pro996fs		34856198	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Frame_Shift_Del	DEL	ENST00000357779.3	37																																																																																					0.657	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		-	35422784	G	-	35422784	7	5	111	1	0	1	0	1	0	0	0	0	2089	1348	47	0	1354	0	C20orf117	20	35422784	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	3665694	35422784	27602736	1002	30136										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35443677	35443677	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgcgtgaaggcattcagcTcctgctgcagcacgctcagg	12	14	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:35443677T>A	ENST00000357779.3	-	5	1780	c.1454A>T	c.(1453-1455)gAg>gTg	p.E485V	SOGA1_ENST00000237536.4_Missense_Mutation_p.E723V|SOGA1_ENST00000456801.2_Missense_Mutation_p.E326V|SOGA1_ENST00000279034.6_Missense_Mutation_p.E485V			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	485					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GGCATTCAGCTCCTGCTGCAG	0.642																																																0			20											53	61	58					20																	35443677		2200	4299	6499	34877091	SO:0001583	missense	140710			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1454A>T	20.37:g.35443677T>A	ENSP00000350424:p.Glu485Val		34877091	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	T	19.08	3.757153	0.69648	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.23950	1.93;1.88;1.91;1.93	5.04	5.04	0.67666	.	0.118537	0.56097	D	0.000025	T	0.49847	0.1581	M	0.69823	2.125	0.48975	D	0.999733	D	0.89917	1.0	D	0.85130	0.997	T	0.52704	-0.8540	10	0.66056	D	0.02	-37.2366	13.9024	0.63812	0.0:0.0:0.0:1.0	.	485	O94964-4	.	V	723;485;326;485	ENSP00000237536:E723V;ENSP00000279034:E485V;ENSP00000413886:E326V;ENSP00000350424:E485V	ENSP00000237536:E723V	E	-	2	0	KIAA0889	34877091	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	4.809000	0.62591	2.125000	0.65367	0.459000	0.35465	GAG		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		A	35443677	T	A	35443677	3	1	111	1	0	0	0	0	1	0	0	0	2089	1551	54	5	2923	5	C20orf117	20	35443677	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	20893	35443677	27581843	1003	30137										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36874451	36874451	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggaacacctgacccaggacGgtgggtgctgtggcctcgaa	15	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:36874451G>A	ENST00000279024.4	-	2	352	c.81C>T	c.(79-81)acC>acT	p.T27T		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	27										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GACCCAGGACGGTGGGTGCTG	0.642																																																0			20											61	54	57					20																	36874451		2203	4300	6503	36307865	SO:0001819	synonymous_variant	85449			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.81C>T	20.37:g.36874451G>A			36307865	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																				0.642	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36874451	G	A	36874451	2	1	111	1	0	0	0	0	0	0	0	1	8278	1103	39	1		1	KIAA1755	20	36874451	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1430774	36874451	26151069	1004	30138										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37146233	37146233	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagtgctgctgtcagtaccaCccccccacataaccggaggc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:37146233delC	ENST00000262879.6	+	8	1420	c.1136delC	c.(1135-1137)accfs	p.T379fs	RALGAPB_ENST00000397042.3_Frame_Shift_Del_p.T379fs|MIR548O2_ENST00000583129.1_RNA|RALGAPB_ENST00000397040.1_Frame_Shift_Del_p.T379fs|RALGAPB_ENST00000397038.1_Frame_Shift_Del_p.T157fs|RALGAPB_ENST00000537204.1_Frame_Shift_Del_p.T379fs			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	379					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.H382fs*2(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GTCAGTACCACCCCCCCACAT	0.448																																																1	Insertion - Frameshift(1)	lung(1)	20											134	123	126					20																	37146233		2203	4300	6503	36579647	SO:0001589	frameshift_variant	0			AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1136delC	20.37:g.37146233delC	ENSP00000262879:p.Thr379fs		36579647	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Frame_Shift_Del	DEL	ENST00000262879.6	37	CCDS13305.1																																																																																				0.448	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		-	37146233	C	-	37146233	7	5	111	1	0	1	0	1	0	0	0	0	13052	507	18	0	1162	0	RALGAPB	20	37146233	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	271782	37146233	25879287	1005	30139										
STK4	6789	hgsc.bcm.edu	37	chr20	43703740	43703740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcaggagattgaagagatcCggcagaagtaccagtccaag	13	8	0	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:43703740C>T	ENST00000372806.3	+	11	1482	c.1387C>T	c.(1387-1389)Cgg>Tgg	p.R463W	STK4_ENST00000372801.1_3'UTR|STK4_ENST00000499879.2_Missense_Mutation_p.R408W	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	463	SARAH. {ECO:0000255|PROSITE- ProRule:PRU00310}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				TGAAGAGATCCGGCAGAAGTA	0.552																																					GBM(187;1039 2137 11798 21916 33213)											0			20											55	53	54					20																	43703740		2203	4300	6503	43137154	SO:0001583	missense	6789				CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109			11408	protein-coding gene	gene with protein product	"mammalian sterile 20-like 1", "yeast Ste20-like", "kinase responsive to stress 2"	604965				8816758, 9545236, 11517310	Standard	NM_006282		Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.1387C>T	20.37:g.43703740C>T	ENSP00000361892:p.Arg463Trp		43137154	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	Missense_Mutation	SNP	ENST00000372806.3	37	CCDS13341.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732431	0.89482	.	.	ENSG00000101109	ENST00000372806;ENST00000499879	T;T	0.76448	-1.02;-0.07	5.99	5.05	0.67936	SARAH domain (1);SARAH (1);	0.063318	0.64402	D	0.000005	D	0.86777	0.6014	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.977	D	0.87504	0.2435	10	0.87932	D	0	.	14.6609	0.68870	0.0:0.9309:0.0:0.0691	.	408;463	F5H5B4;Q13043	.;STK4_HUMAN	W	463;408	ENSP00000361892:R463W;ENSP00000443514:R408W	ENSP00000361892:R463W	R	+	1	2	STK4	43137154	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.570000	0.60872	2.847000	0.97988	0.655000	0.94253	CGG		0.552	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080401.4	NM_006282		T	43703740	C	T	43703740	3	4	111	1	0	0	0	0	1	0	0	0	15345	643	23	1	1429	1	STK4	20	43703740	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6557507	43703740	19321780	1006	30140										
KCNS1	3787	hgsc.bcm.edu	37	chr20	43726379	43726379	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcggaagatgcgcatgaggCggaacacctgcaccaccttg	13	13	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:43726379C>T	ENST00000306117.1	-	4	1430	c.1034G>A	c.(1033-1035)cGc>cAc	p.R345H	KCNS1_ENST00000537075.1_Missense_Mutation_p.R345H	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	345					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GCGCATGAGGCGGAACACCTG	0.657																																																0			20											59	47	51					20																	43726379		2203	4299	6502	43159793	SO:0001583	missense	3787			AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.1034G>A	20.37:g.43726379C>T	ENSP00000307694:p.Arg345His		43159793	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	37	CCDS13342.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089941	0.94149	.	.	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.99239	-5.61;-5.61	5.31	5.31	0.75309	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99697	0.9885	H	0.97829	4.085	0.58432	D	0.999994	D	0.89917	1.0	D	0.85130	0.997	D	0.97270	0.9910	10	0.87932	D	0	.	18.9863	0.92771	0.0:1.0:0.0:0.0	.	345	Q96KK3	KCNS1_HUMAN	H	345	ENSP00000307694:R345H;ENSP00000445595:R345H	ENSP00000307694:R345H	R	-	2	0	KCNS1	43159793	0.994000	0.37717	1.000000	0.80357	0.994000	0.84299	5.867000	0.69597	2.490000	0.84030	0.561000	0.74099	CGC		0.657	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251		T	43726379	C	T	43726379	3	4	111	1	0	0	0	0	1	0	0	0	8109	768	27	1	554	1	KCNS1	20	43726379	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	22639	43726379	19299141	1007	30141										
PIGT	51604	hgsc.bcm.edu	37	chr20	44054454	44054454	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atccggcgcgcccgaggtgtCcccccactctgattcttgcc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:44054454delC	ENST00000279036.6	+	12	1805	c.1725delC	c.(1723-1725)gtcfs	p.V575fs	PIGT_ENST00000535404.1_Frame_Shift_Del_p.V420fs|PIGT_ENST00000545755.1_Frame_Shift_Del_p.V313fs|PIGT_ENST00000543458.2_Frame_Shift_Del_p.V519fs|PIGT_ENST00000341555.5_Frame_Shift_Del_p.V381fs|PIGT_ENST00000279035.9_Frame_Shift_Del_p.V473fs|PIGT_ENST00000372689.5_Frame_Shift_Del_p.V508fs	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	575					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				CCCGAGGTGTCCCCCCACTCT	0.627																																																0			20											22	25	24					20																	44054454		2203	4300	6503	43487868	SO:0001589	frameshift_variant	51604				CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"Phosphatidylinositol glycan anchor biosynthesis"	14938	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610272	"phosphatidylinositol glycan, class T"			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.1725delC	20.37:g.44054454delC	ENSP00000279036:p.Val575fs		43487868	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Frame_Shift_Del	DEL	ENST00000279036.6	37	CCDS13353.1																																																																																				0.627	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937		-	44054454	C	-	44054454	7	5	111	1	0	1	0	1	0	0	0	0	11930	842	30	0	1771	0	PIGT	20	44054454	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	328075	44054454	18971066	1008	30142										
NCOA5	57727	hgsc.bcm.edu	37	chr20	44698976	44698976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atccctcacgtcccgaacgtCgcgcacactcctgctgtctc	7	19	2	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:44698976C>T	ENST00000290231.6	-	3	402	c.238G>A	c.(238-240)Gac>Aac	p.D80N		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	80	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TCCCGAACGTCGCGCACACTC	0.537																																																0			20											137	130	132					20																	44698976		2203	4300	6503	44132383	SO:0001583	missense	57727				CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"coactivator independent of AF-2"					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.238G>A	20.37:g.44698976C>T	ENSP00000290231:p.Asp80Asn		44132383	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827018	0.50739	.	.	ENSG00000124160	ENST00000290231	T	0.59224	0.28	5.17	5.17	0.71159	.	0.100788	0.64402	D	0.000003	T	0.59445	0.2194	M	0.71036	2.16	0.36327	D	0.858623	P	0.34780	0.468	B	0.33295	0.161	T	0.70040	-0.4981	10	0.56958	D	0.05	-3.4659	17.8426	0.88719	0.0:1.0:0.0:0.0	.	80	Q9HCD5	NCOA5_HUMAN	N	80	ENSP00000290231:D80N	ENSP00000290231:D80N	D	-	1	0	NCOA5	44132383	0.998000	0.40836	0.945000	0.38365	0.027000	0.11550	5.837000	0.69381	2.684000	0.91462	0.650000	0.86243	GAC		0.537	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967		T	44698976	C	T	44698976	3	4	111	1	0	0	0	0	1	0	0	0	10263	884	31	1	1525	1	NCOA5	20	44698976	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	644522	44698976	18326544	1009	30143										
STAU1	6780	hgsc.bcm.edu	37	chr20	47741103	47741103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacaaagttcttcatgtgggGtgggccactctcccgggcca	12	13	3	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:47741103G>A	ENST00000371856.2	-	7	1041	c.631C>T	c.(631-633)Ccc>Tcc	p.P211S	STAU1_ENST00000347458.5_Missense_Mutation_p.P130S|STAU1_ENST00000371792.1_Missense_Mutation_p.P130S|STAU1_ENST00000371802.1_Missense_Mutation_p.P136S|STAU1_ENST00000360426.4_Missense_Mutation_p.P130S|STAU1_ENST00000340954.7_Missense_Mutation_p.P130S|STAU1_ENST00000371828.3_Missense_Mutation_p.P136S	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	211	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			TTCATGTGGGGTGGGCCACTC	0.507																																																0			20											73	79	77					20																	47741103		2203	4300	6503	47174510	SO:0001583	missense	6780				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.631C>T	20.37:g.47741103G>A	ENSP00000360922:p.Pro211Ser		47174510	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	37	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	G	34	5.330166	0.95733	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	T;T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.33	5.33	0.75918	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.83903	0.5355	L	0.50993	1.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.85305	0.1075	10	0.87932	D	0	-9.0618	19.0449	0.93015	0.0:0.0:1.0:0.0	.	211;136	O95793;Q5JW29	STAU1_HUMAN;.	S	136;130;211;130;130;130;136;130;136	ENSP00000360893:P136S;ENSP00000345425:P130S;ENSP00000360922:P211S;ENSP00000353604:P130S;ENSP00000323443:P130S;ENSP00000360867:P136S;ENSP00000360857:P130S;ENSP00000416779:P136S	ENSP00000345425:P130S	P	-	1	0	STAU1	47174510	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.964000	0.87933	2.492000	0.84095	0.650000	0.86243	CCC		0.507	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		A	47741103	G	A	47741103	3	1	111	1	0	0	0	0	1	0	0	0	15311	1261	44	3	1134	3	STAU1	20	47741103	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3042127	47741103	15284417	1010	30144										
KCNG1	3755	hgsc.bcm.edu	37	chr20	49620871	49620871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatggtgatgacagcccacCagtagcaggcagggatgctg	14	10	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:49620871C>A	ENST00000371571.4	-	3	1532	c.1247G>T	c.(1246-1248)tGg>tTg	p.W416L	KCNG1_ENST00000506387.1_5'UTR|RP5-955M13.4_ENST00000424566.1_RNA	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	416					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GACAGCCCACCAGTAGCAGGC	0.647																																																0			20											75	65	68					20																	49620871		2203	4300	6503	49054278	SO:0001583	missense	3755			AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.1247G>T	20.37:g.49620871C>A	ENSP00000360626:p.Trp416Leu		49054278	A8K3S4|O43528|Q5JXL5|Q9BRC1	Missense_Mutation	SNP	ENST00000371571.4	37	CCDS13436.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888432	0.91814	.	.	ENSG00000026559	ENST00000371571	D	0.97752	-4.52	5.49	5.49	0.81192	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99293	0.9753	H	0.97415	4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98718	1.0707	9	.	.	.	.	19.3567	0.94418	0.0:1.0:0.0:0.0	.	416	Q9UIX4	KCNG1_HUMAN	L	416	ENSP00000360626:W416L	.	W	-	2	0	KCNG1	49054278	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.773000	0.85462	2.578000	0.87016	0.462000	0.41574	TGG		0.647	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		A	49620871	C	A	49620871	3	1	111	1	0	0	0	0	1	0	0	0	8048	595	21	2	298	2	KCNG1	20	49620871	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1879768	49620871	13404649	1011	30145										
SALL4	57167	hgsc.bcm.edu	37	chr20	50400819	50400819	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcccttagctgaccgcaatCttgttttcttccaggaagtg	8	12	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:50400819C>A	ENST00000217086.4	-	4	3258	c.3147G>T	c.(3145-3147)aaG>aaT	p.K1049N	SALL4_ENST00000371539.3_Missense_Mutation_p.K272N|SALL4_ENST00000395997.3_Missense_Mutation_p.K612N	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	1049					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGACCGCAATCTTGTTTTCTT	0.478																																																0			20											97	87	90					20																	50400819		2203	4300	6503	49834226	SO:0001583	missense	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.3147G>T	20.37:g.50400819C>A	ENSP00000217086:p.Lys1049Asn		49834226	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550801	0.65311	.	.	ENSG00000101115	ENST00000217086;ENST00000395997;ENST00000371539	T;T;T	0.56776	0.44;0.44;0.44	4.69	3.73	0.42828	.	0.000000	0.42548	D	0.000699	T	0.67429	0.2892	M	0.83118	2.625	0.48696	D	0.999699	D;D;D	0.76494	0.964;0.999;0.999	P;D;D	0.78314	0.784;0.922;0.991	T	0.70605	-0.4826	10	0.87932	D	0	-33.9918	3.1299	0.06419	0.2458:0.5604:0.0:0.1938	.	612;272;1049	A2A2D8;Q6Y8G5;Q9UJQ4	.;.;SALL4_HUMAN	N	1049;612;272	ENSP00000217086:K1049N;ENSP00000379319:K612N;ENSP00000360594:K272N	ENSP00000217086:K1049N	K	-	3	2	SALL4	49834226	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	3.138000	0.50570	2.319000	0.78375	0.555000	0.69702	AAG		0.478	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50400819	C	A	50400819	3	1	111	1	0	0	0	0	1	0	0	0	13850	912	32	2	18	2	SALL4	20	50400819	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	779948	50400819	12624701	1012	30146										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52188288	52188288	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccctaattagtgaatcaagTttttttgtcatttggtcgat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:52188288delT	ENST00000371471.2	-	5	3567	c.3142delA	c.(3142-3144)actfs	p.T1048fs	ZNF217_ENST00000302342.3_Frame_Shift_Del_p.T1048fs|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	1048					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GTGAATCAAGTTTTTTTGTCA	0.413																																																0			20											179	166	170					20																	52188288		2202	4298	6500	51621695	SO:0001589	frameshift_variant	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.3142delA	20.37:g.52188288delT	ENSP00000360526:p.Thr1048fs		51621695	E1P5Y6|Q14DB8	Frame_Shift_Del	DEL	ENST00000371471.2	37	CCDS13443.1																																																																																				0.413	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		-	52188288	T	-	52188288	7	5	111	1	0	1	0	1	0	0	0	0	17811	1725	60	0	8	0	ZNF217	20	52188288	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	1787469	52188288	10837232	1013	30147										
ZBP1	81030	hgsc.bcm.edu	37	chr20	56185345	56185345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcatgtggattctctgggcgGcttccccctcagggtgagtt	13	11	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:56185345G>A	ENST00000371173.3	-	7	1130	c.953C>T	c.(952-954)gCc>gTc	p.A318V	ZBP1_ENST00000395822.3_Missense_Mutation_p.A243V|ZBP1_ENST00000340462.4_Missense_Mutation_p.A295V|ZBP1_ENST00000343535.4_Missense_Mutation_p.A318V	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	318					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TCTCTGGGCGGCTTCCCCCTC	0.577																																																0			20											197	212	207					20																	56185345		2203	4300	6503	55618751	SO:0001583	missense	81030			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.953C>T	20.37:g.56185345G>A	ENSP00000360215:p.Ala318Val		55618751	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	G	0.690	-0.794864	0.02862	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535	T;T;T;T	0.10960	3.18;2.82;3.18;3.14	3.79	-7.07	0.01563	.	1.647680	0.03506	N	0.218807	T	0.04137	0.0115	N	0.10874	0.06	0.09310	N	1	B;B;B	0.10296	0.002;0.003;0.003	B;B;B	0.11329	0.002;0.006;0.003	T	0.35847	-0.9772	10	0.11182	T	0.66	-0.575	3.2151	0.06696	0.2192:0.1215:0.5264:0.1329	.	318;243;318	A2RRL9;A2A2F7;Q9H171	.;.;ZBP1_HUMAN	V	318;243;295;318;318	ENSP00000360215:A318V;ENSP00000379167:A243V;ENSP00000344954:A295V;ENSP00000340584:A318V	ENSP00000344954:A295V	A	-	2	0	ZBP1	55618751	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.586000	0.02110	-1.459000	0.01914	0.491000	0.48974	GCC		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		A	56185345	G	A	56185345	3	1	111	1	0	0	0	0	1	0	0	0	17560	1203	42	3	344	3	ZBP1	20	56185345	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3997057	56185345	6840175	1014	30148										
GNAS	2778	hgsc.bcm.edu	37	chr20	57430215	57430215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccccagcccaaagcctcgcGctctctcaaggtcaagaagg	9	16	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:57430215G>A	ENST00000371100.4	+	1	2447	c.1895G>A	c.(1894-1896)cGc>cAc	p.R632H	GNAS_ENST00000371102.4_Missense_Mutation_p.R632H|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000306120.3_Missense_Mutation_p.A569T|GNAS_ENST00000371099.2_Missense_Mutation_p.R632H	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			AAAGCCTCGCGCTCTCTCAAG	0.622			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	0			20											24	28	26					20																	57430215		1988	4164	6152	56863610	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.1895G>A	20.37:g.57430215G>A	ENSP00000360141:p.Arg632His		56863610	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	37	CCDS46622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.003|0.003	-2.424394|-2.424394	0.00186|0.00186	.|.	.|.	ENSG00000087460|ENSG00000087460	ENST00000306120|ENST00000371099;ENST00000371100;ENST00000371102;ENST00000349036	.|D;D;D	.|0.90197	.|-2.46;-2.45;-2.63	2.77|2.77	-5.43|-5.43	0.02632|0.02632	.|.	.|3.372340	.|0.01189	.|N	.|0.007277	T|T	0.77054|0.77054	0.4074|0.4074	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.06405	.|0.002	T|T	0.65845|0.65845	-0.6069|-0.6069	6|10	0.23302|0.39692	T|T	0.38|0.17	.|.	1.8904|1.8904	0.03246|0.03246	0.393:0.1235:0.3496:0.1339|0.393:0.1235:0.3496:0.1339	.|.	.|632	.|Q5JWF2	.|GNAS1_HUMAN	T|H	569|632;632;632;5	.|ENSP00000360141:R632H;ENSP00000360143:R632H;ENSP00000265621:R5H	ENSP00000302237:A569T|ENSP00000265621:R5H	A|R	+|+	1|2	0|0	GNAS|GNAS	56863610|56863610	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.185000|-1.185000	0.03073|0.03073	-1.857000|-1.857000	0.01159|0.01159	-1.598000|-1.598000	0.00824|0.00824	GCT|CGC		0.622	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516		A	57430215	G	A	57430215	3	1	111	1	0	0	0	0	1	0	0	0	6530	1087	38	1	2639	1	GNAS	20	57430215	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1244870	57430215	5595305	1015	30149										
ADRM1	11047	hgsc.bcm.edu	37	chr20	60882875	60882875	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	taccagccgggccagcaggcGgccagcaaggtaacgtgtgc	15	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:60882875G>T	ENST00000253003.2	+	7	893	c.847G>T	c.(847-849)Ggc>Tgc	p.G283C	LAMA5_ENST00000492698.1_5'Flank|RP11-157P1.4_ENST00000414042.1_RNA	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	283					positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GCCAGCAGGCGGCCAGCAAGG	0.667																																																0			20											9	11	11					20																	60882875		2166	4262	6428	60316270	SO:0001583	missense	11047			D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.847G>T	20.37:g.60882875G>T	ENSP00000253003:p.Gly283Cys		60316270	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	G	8.389	0.839355	0.16891	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	5.4	-0.284	0.12870	.	0.160129	0.64402	D	0.000019	T	0.40909	0.1136	L	0.50919	1.6	0.38924	D	0.957806	P	0.39424	0.673	B	0.35607	0.206	T	0.29610	-1.0006	9	0.62326	D	0.03	-8.8758	9.1126	0.36737	0.4122:0.0:0.5878:0.0	.	283	Q16186	ADRM1_HUMAN	C	262;283	.	ENSP00000253003:G283C	G	+	1	0	ADRM1	60316270	0.700000	0.27796	0.032000	0.17829	0.166000	0.22503	-0.396000	0.07278	-0.301000	0.08882	0.561000	0.74099	GGC		0.667	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			T	60882875	G	T	60882875	3	4	111	1	0	0	0	0	1	0	0	0	345	1116	39	2	869	2	ADRM1	20	60882875	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3452660	60882875	2142645	1016	30150										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61513251	61513251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caacggaggtgccggcacccCgtcctctgctgtggttttgg	14	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:61513251C>T	ENST00000266070.4	-	16	4382	c.4057G>A	c.(4057-4059)Ggg>Agg	p.G1353R	DIDO1_ENST00000395343.1_Missense_Mutation_p.G1353R	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1353					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GCCGGCACCCCGTCCTCTGCT	0.577																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0			20											91	107	101					20																	61513251		2203	4300	6503	60983696	SO:0001583	missense	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.4057G>A	20.37:g.61513251C>T	ENSP00000266070:p.Gly1353Arg		60983696	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637238	0.47049	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.09073	3.02;3.02	5.4	3.04	0.35103	.	0.790616	0.10541	N	0.662729	T	0.11196	0.0273	M	0.75447	2.3	0.09310	N	0.999999	B	0.33841	0.428	B	0.24541	0.054	T	0.15093	-1.0449	10	0.62326	D	0.03	-24.5856	9.0535	0.36392	0.0:0.7258:0.0:0.2742	.	1353	Q9BTC0	DIDO1_HUMAN	R	1353	ENSP00000266070:G1353R;ENSP00000378752:G1353R	ENSP00000266070:G1353R	G	-	1	0	DIDO1	60983696	0.001000	0.12720	0.002000	0.10522	0.027000	0.11550	1.432000	0.34936	0.516000	0.28340	0.563000	0.77884	GGG		0.577	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61513251	C	T	61513251	3	4	111	1	0	0	0	0	1	0	0	0	4533	652	23	1	2669	1	DIDO1	20	61513251	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	630376	61513251	1512269	1017	30151										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61513713	61513713	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	actgtttgcgggacgtttgaTtttttggcagattactaacc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:61513713delT	ENST00000266070.4	-	16	3920	c.3595delA	c.(3595-3597)atcfs	p.I1199fs	DIDO1_ENST00000395343.1_Frame_Shift_Del_p.I1199fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1199					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGACGTTTGATTTTTTGGCAG	0.428																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0			20											90	97	94					20																	61513713		2203	4300	6503	60984158	SO:0001589	frameshift_variant	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3595delA	20.37:g.61513713delT	ENSP00000266070:p.Ile1199fs		60984158	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Frame_Shift_Del	DEL	ENST00000266070.4	37	CCDS33506.1																																																																																				0.428	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		-	61513713	T	-	61513713	7	5	111	1	0	1	0	1	0	0	0	0	4533	1493	52	0	3131	0	DIDO1	20	61513713	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	462	61513713	1511807	1018	30152										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981476	61981476	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccaggggctgctgaggaggGagctggtcggagggtgactt	20	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:61981476G>T	ENST00000370263.4	-	5	1508	c.1287C>A	c.(1285-1287)ctC>ctA	p.L429L	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	429					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCTGAGGAGGGAGCTGGTCGG	0.711																																																0			20											16	14	15					20																	61981476		2166	4263	6429	61451920	SO:0001819	synonymous_variant	1137				CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1287C>A	20.37:g.61981476G>T			61451920	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																				0.711	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			T	61981476	G	T	61981476	2	4	111	1	0	0	0	0	0	0	0	1	3391	1161	41	2		2	CHRNA4	20	61981476	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	467763	61981476	1044044	1019	30153										
STMN3	50861	hgsc.bcm.edu	37	chr20	62273466	62273466	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gccccgcccccgcaccttctCgcgcagccgctcgcgcagtg	11	22	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:62273466C>G	ENST00000370053.1	-	4	559	c.478G>C	c.(478-480)Gag>Cag	p.E160Q	STMN3_ENST00000540534.1_Missense_Mutation_p.E149Q	NM_001276310.1|NM_015894.2	NP_001263239.1|NP_056978.2	Q9NZ72	STMN3_HUMAN	stathmin-like 3	160	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cytoplasmic microtubule organization (GO:0031122)|negative regulation of Rac protein signal transduction (GO:0035021)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|regulation of cytoskeleton organization (GO:0051493)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of Rac GTPase activity (GO:0032314)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	protein domain specific binding (GO:0019904)	p.E160K(1)		kidney(1)|large_intestine(1)|lung(5)|prostate(1)	8	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			CGCACCTTCTCGCGCAGCCGC	0.756																																																1	Substitution - Missense(1)	lung(1)	20											13	13	13					20																	62273466		2181	4279	6460	61743910	SO:0001583	missense	50861			AF069709	CCDS13529.1, CCDS63330.1	20q13.3	2007-01-22			ENSG00000197457	ENSG00000197457			15926	protein-coding gene	gene with protein product		608362				9603203, 10655513	Standard	NM_001276310		Approved	SCLIP	uc002yfr.2	Q9NZ72	OTTHUMG00000032985	ENST00000370053.1:c.478G>C	20.37:g.62273466C>G	ENSP00000359070:p.Glu160Gln		61743910	B3KSQ5|B7WP52|B7Z5G4|O75527|Q969Y4	Missense_Mutation	SNP	ENST00000370053.1	37	CCDS13529.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.200670	0.79015	.	.	ENSG00000197457	ENST00000370053;ENST00000540534	.	.	.	5.27	5.27	0.74061	.	0.178523	0.34156	U	0.004207	D	0.83078	0.5176	M	0.82056	2.57	0.58432	D	0.999993	D	0.76494	0.999	D	0.81914	0.995	D	0.84481	0.0605	9	0.54805	T	0.06	-8.596	18.931	0.92566	0.0:1.0:0.0:0.0	.	160	Q9NZ72	STMN3_HUMAN	Q	160;149	.	ENSP00000359070:E160Q	E	-	1	0	STMN3	61743910	1.000000	0.71417	0.982000	0.44146	0.028000	0.11728	5.765000	0.68834	2.474000	0.83562	0.580000	0.79431	GAG		0.756	STMN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080163.1	NM_015894		G	62273466	C	G	62273466	3	3	111	1	0	0	0	0	1	0	0	0	15349	893	31	5	72	5	STMN3	20	62273466	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	291990	62273466	752054	1020	30154										
C20orf135	140701	hgsc.bcm.edu	37	chr20	62493445	62493445	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaaggcaacgcgggcttctaCgagatgggctgtctgtctgc	15	10	3	1	rs569049140	byFrequency	TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr20:62493445C>T	ENST00000369916.3	+	1	880	c.552C>T	c.(550-552)taC>taT	p.Y184Y	C20ORF135_ENST00000601296.1_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	184							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						CGGGCTTCTACGAGATGGGCT	0.677													C|||	2	0.000399361	0	0	5008	,	,		14205	0.002		0	False		,,,				2504	0															0			20											31	31	31					20																	62493445		2202	4300	6502	61963889	SO:0001819	synonymous_variant	0				CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"Abhydrolase domain containing"	16128	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 135"	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.552C>T	20.37:g.62493445C>T			61963889		Silent	SNP	ENST00000369916.3	37	CCDS13539.1																																																																																				0.677	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1			T	62493445	C	T	62493445	2	4	111	1	0	0	0	0	0	0	0	1	2094	547	19	1		1	C20orf135	20	62493445	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	219979	62493445	532075	1021	30155										
C21orf91	54149	hgsc.bcm.edu	37	chr21	19190537	19190537	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tttagctcaaaacaaatgtgGcagaaggagagtgtttcttt	10	5	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:19190537G>A	ENST00000400558.3	-	2	189	c.99C>T	c.(97-99)tgC>tgT	p.C33C	C21orf91_ENST00000493464.1_5'UTR|C21orf91_ENST00000400559.3_Silent_p.C33C|C21orf91_ENST00000284881.4_Silent_p.C33C	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91											endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		AACAAATGTGGCAGAAGGAGA	0.358																																																0			21											185	175	178					21																	19190537		1878	4124	6002	18112408	SO:0001819	synonymous_variant	54149			AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"cold sore susceptibility gene 1", "early undifferentiated retina and lens"		"chromosome 21 open reading frame 38"	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.99C>T	21.37:g.19190537G>A			18112408		Silent	SNP	ENST00000400558.3	37	CCDS42909.1																																																																																				0.358	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447		A	19190537	G	A	19190537	2	1	111	1	0	0	0	0	0	0	0	1	2140	1195	42	3		3	C21orf91	21	19190537	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10		19190537	28939358	1022	30156										
SON	6651	hgsc.bcm.edu	37	chr21	34945711	34945713	+	In_Frame_Del	DEL	AAG	AAG	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaaggattaggaaaaaacaAagaaggcaataaggaaccca							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	AAG	AAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:34945711_34945713delAAG	ENST00000356577.4	+	9	7458_7460	c.6983_6985delAAG	c.(6982-6987)aaagaa>aaa	p.E2329del	SON_ENST00000381692.2_In_Frame_Del_p.E357del|SON_ENST00000470533.1_3'UTR|SON_ENST00000290239.6_3'UTR	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2329	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GGAAAAAACAAAGAAGGCAATAA	0.399																																																0			21																																								33867583	SO:0001651	inframe_deletion	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6983_6985delAAG	21.37:g.34945714_34945716delAAG	ENSP00000348984:p.Glu2329del		33867581	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	In_Frame_Del	DEL	ENST00000356577.4	37	CCDS13629.1																																																																																				0.399	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		-	34945713	AAG	-	34945711	7	5	111	1	0	1	0	1	0	0	0	0	14963	14	1	0	7276	0	SON	21	34945711	In_Frame_Del	DEL	AAG	TCGA-EI-6507-01A-11D-1733-10	15755174	34945711	13184184	1023	30157										
TTC3	7267	hgsc.bcm.edu	37	chr21	38569962	38569962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atgaaattgtccaaagagtgAcagaacacattctagatgaa	8	6	1	6			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:38569962A>G	ENST00000399017.2	+	43	8418	c.5671A>G	c.(5671-5673)Aca>Gca	p.T1891A	TTC3_ENST00000355666.1_Missense_Mutation_p.T1891A|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.T1891A	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1891					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CCAAAGAGTGACAGAACACAT	0.308																																					Ovarian(38;194 1649 35661)											0			21											47	45	46					21																	38569962		2203	4300	6503	37491832	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5671A>G	21.37:g.38569962A>G	ENSP00000381981:p.Thr1891Ala		37491832	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.30|14.30	2.494624|2.494624	0.44352|0.44352	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000428693|ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T	.|0.08282	.|3.11;3.11;3.11	5.27|5.27	4.12|4.12	0.48240|0.48240	.|.	.|0.141349	.|0.44688	.|D	.|0.000431	T|T	0.08044|0.08044	0.0201|0.0201	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	.|P	.|0.38195	.|0.622	.|B	.|0.30179	.|0.112	T|T	0.26258|0.26258	-1.0108|-1.0108	5|10	.|0.29301	.|T	.|0.29	-4.4003|-4.4003	7.8788|7.8788	0.29610|0.29610	0.9059:0.0:0.0941:0.0|0.9059:0.0:0.0941:0.0	.|.	.|1891	.|P53804	.|TTC3_HUMAN	G|A	182|1891	.|ENSP00000347889:T1891A;ENSP00000381981:T1891A;ENSP00000346791:T1891A	.|ENSP00000346791:T1891A	D|T	+|+	2|1	0|0	TTC3|TTC3	37491832|37491832	0.947000|0.947000	0.32204|0.32204	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	2.429000|2.429000	0.44758|0.44758	0.853000|0.853000	0.35312|0.35312	0.528000|0.528000	0.53228|0.53228	GAC|ACA		0.308	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38569962	A	G	38569962	3	3	111	1	0	0	0	0	1	0	0	0	16737	275	10	4	5837	4	TTC3	21	38569962	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	3624251	38569962	9559933	1024	30158										
BACE2	25825	hgsc.bcm.edu	37	chr21	42540489	42540489	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cctggagatgctgatcgggaCccccccgcagaaggtaggga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:42540489delC	ENST00000330333.6	+	1	762	c.299delC	c.(298-300)accfs	p.T100fs	BACE2_ENST00000347667.5_Frame_Shift_Del_p.T100fs|MIR3197_ENST00000582241.1_RNA|BACE2_ENST00000328735.6_Frame_Shift_Del_p.T100fs	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	100					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				CTGATCGGGACCCCCCCGCAG	0.701																																																0			21							,,	16,3952		1,14,1969	7	8	8		,,	2.8	0.8	21		8	52,7696		0,52,3822	no	frameshift,frameshift,frameshift	BACE2	NM_138992.1,NM_138991.1,NM_012105.3	,,	1,66,5791	A1A1,A1R,RR		0.6711,0.4032,0.5804	,,	,,	42540489	68,11648	2131	4151	6282	41462359	SO:0001589	frameshift_variant	25825			AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.299delC	21.37:g.42540489delC	ENSP00000332979:p.Thr100fs		41462359	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Frame_Shift_Del	DEL	ENST00000330333.6	37	CCDS13668.1																																																																																				0.701	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			-	42540489	C	-	42540489	7	5	111	1	0	1	0	1	0	0	0	0	1283	507	18	0	301	0	BACE2	21	42540489	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	3970527	42540489	5589406	1025	30159										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43803247	43803247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggcctgccagggccactgcGagagcaaggacatgtttcca	13	12	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:43803247G>A	ENST00000291532.3	-	8	1632	c.677C>T	c.(676-678)tCg>tTg	p.S226L	TMPRSS3_ENST00000433957.2_Missense_Mutation_p.S226L|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.S226L|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.S310L|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.S224L	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GGGCCACTGCGAGAGCAAGGA	0.597																																																0			21											104	84	91					21																	43803247		2203	4300	6503	42676316	SO:0001583	missense	64699			AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.677C>T	21.37:g.43803247G>A	ENSP00000291532:p.Ser226Leu		42676316	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	G	9.869	1.198519	0.22037	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;D;D;T;D	0.81996	0.14;-1.56;-1.56;0.14;-1.56	5.38	1.62	0.23740	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.845761	0.10453	N	0.672809	T	0.61148	0.2324	N	0.11064	0.09	0.09310	N	1	B;B;B	0.12630	0.006;0.0;0.002	B;B;B	0.08055	0.003;0.001;0.003	T	0.45279	-0.9272	9	.	.	.	.	1.2875	0.02053	0.2114:0.3574:0.2331:0.1982	.	226;226;226	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	L	226;226;224;310;226	ENSP00000291532:S226L;ENSP00000411013:S226L;ENSP00000381442:S224L;ENSP00000369762:S310L;ENSP00000381434:S226L	.	S	-	2	0	TMPRSS3	42676316	0.000000	0.05858	0.000000	0.03702	0.227000	0.25037	0.905000	0.28504	0.473000	0.27368	0.591000	0.81541	TCG		0.597	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			A	43803247	G	A	43803247	3	1	111	1	0	0	0	0	1	0	0	0	16287	1059	37	1	794	1	TMPRSS3	21	43803247	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1262758	43803247	4326648	1026	30160										
HSF2BP	11077	hgsc.bcm.edu	37	chr21	45033773	45033773	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agctgcaatatggtgtccaaGagcacccggcttgaattaac	10	10	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:45033773G>T	ENST00000291560.2	-	7	961	c.630C>A	c.(628-630)ctC>ctA	p.L210L	HSF2BP_ENST00000542962.1_Silent_p.L135L	NM_007031.1	NP_008962.1	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding protein	210					spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)				kidney(2)|large_intestine(3)|prostate(1)|skin(1)	7				STAD - Stomach adenocarcinoma(101;0.18)		TGGTGTCCAAGAGCACCCGGC	0.393																																																0			21											90	85	87					21																	45033773		2203	4300	6503	43858201	SO:0001819	synonymous_variant	11077			AB007131	CCDS13697.1	21q22.3	2008-07-31			ENSG00000160207	ENSG00000160207			5226	protein-coding gene	gene with protein product	"heat shock factor 2 binding protein"	604554				9651507	Standard	XM_005261090		Approved		uc002zdi.3	O75031	OTTHUMG00000086863	ENST00000291560.2:c.630C>A	21.37:g.45033773G>T			43858201	B4DX36	Silent	SNP	ENST00000291560.2	37	CCDS13697.1																																																																																				0.393	HSF2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195620.1	NM_007031		T	45033773	G	T	45033773	2	4	111	1	0	0	0	0	0	0	0	1	7418	929	33	2		2	HSF2BP	21	45033773	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1230526	45033773	3096122	1027	30161										
AIRE	326	hgsc.bcm.edu	37	chr21	45705994	45705994	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgcacgcgctggctgaccaCgacgtggtccccgaggacaa	13	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:45705994C>T	ENST00000291582.5	+	1	232	c.105C>T	c.(103-105)caC>caT	p.H35H		NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	35	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		TGGCTGACCACGACGTGGTCC	0.716									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																																							0			21											6	6	6					21																	45705994		1878	3725	5603	44530422	SO:0001819	synonymous_variant	326	Familial Cancer Database	APECED	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"Zinc fingers, PHD-type"	360	protein-coding gene	gene with protein product	"autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"	607358	"autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.105C>T	21.37:g.45705994C>T			44530422	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																				0.716	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			T	45705994	C	T	45705994	2	4	111	1	0	0	0	0	0	0	0	1	437	535	19	1		1	AIRE	21	45705994	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	672221	45705994	2423901	1028	30162										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45773671	45773671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggtcactgacctggggatgGtctccaatctccggcgcagc	14	13	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:45773671G>A	ENST00000397928.1	+	1	533	c.88G>A	c.(88-90)Gtc>Atc	p.V30I	TRPM2_ENST00000397932.2_Missense_Mutation_p.V30I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V30I|TRPM2_ENST00000300482.5_Missense_Mutation_p.V30I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	30					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CCTGGGGATGGTCTCCAATCT	0.607																																																0			21											45	37	39					21																	45773671		2203	4300	6503	44598099	SO:0001583	missense	7226			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.88G>A	21.37:g.45773671G>A	ENSP00000381023:p.Val30Ile		44598099	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	9.765	1.171219	0.21621	.	.	ENSG00000142185	ENST00000300482;ENST00000431901;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T;T	0.55413	0.63;0.69;0.63;0.65;0.52	4.4	3.5	0.40072	.	0.791041	0.10517	N	0.665367	T	0.42337	0.1198	L	0.44542	1.39	0.37998	D	0.934139	P;P	0.39665	0.682;0.546	B;B	0.31547	0.132;0.132	T	0.37407	-0.9707	10	0.48119	T	0.1	-14.0406	11.2935	0.49265	0.0:0.185:0.815:0.0	.	30;30	E9PGK7;O94759	.;TRPM2_HUMAN	I	30	ENSP00000300482:V30I;ENSP00000393982:V30I;ENSP00000381023:V30I;ENSP00000300481:V30I;ENSP00000381026:V30I	ENSP00000300481:V30I	V	+	1	0	TRPM2	44598099	0.381000	0.25140	0.127000	0.21898	0.026000	0.11368	1.112000	0.31172	0.821000	0.34540	0.561000	0.74099	GTC		0.607	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45773671	G	A	45773671	3	1	111	1	0	0	0	0	1	0	0	0	16626	1261	44	3	90	3	TRPM2	21	45773671	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	67677	45773671	2356224	1029	30163										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45953746	45953746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cagctgggcaggtgacaaccGcaggccgagcagcagcaggt	16	12	0	1	rs146257403		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:45953746G>A	ENST00000323084.4	-	3	429	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	TSPEAR_ENST00000397916.1_Missense_Mutation_p.R54W	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	122	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GGTGACAACCGCAGGCCGAGC	0.687													G|||	1	0.000199681	8e-04	0	5008	,	,		10519	0		0	False		,,,				2504	0															0			21						G	TRP/ARG	5,4389	8.1+/-20.4	0,5,2192	35	34	34		364	3	0.8	21	dbSNP_134	34	0,8596		0,0,4298	yes	missense	TSPEAR	NM_144991.2	101	0,5,6490	AA,AG,GG		0.0,0.1138,0.0385	probably-damaging	122/670	45953746	5,12985	2197	4298	6495	44778174	SO:0001583	missense	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.364C>T	21.37:g.45953746G>A	ENSP00000321987:p.Arg122Trp		44778174		Missense_Mutation	SNP	ENST00000323084.4	37	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	g	15.77	2.932438	0.52866	0.001138	0.0	ENSG00000175894	ENST00000323084;ENST00000397918;ENST00000397916;ENST00000341581	T;T	0.49139	0.79;0.79	4.95	3.01	0.34805	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.060576	0.64402	D	0.000004	T	0.68495	0.3007	M	0.80183	2.485	0.53688	D	0.999975	D	0.89917	1.0	D	0.91635	0.999	T	0.71692	-0.4516	10	0.87932	D	0	-5.9092	13.241	0.59997	0.0:0.0:0.7101:0.2899	.	122	Q8WU66	TSEAR_HUMAN	W	122;122;54;122	ENSP00000321987:R122W;ENSP00000381012:R54W	ENSP00000321987:R122W	R	-	1	2	TSPEAR	44778174	0.181000	0.23161	0.848000	0.33437	0.062000	0.15995	0.729000	0.26028	0.414000	0.25790	0.555000	0.69702	CGG		0.687	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45953746	G	A	45953746	3	1	111	1	0	0	0	0	1	0	0	0	2130	1086	38	1	1685	1	C21orf29	21	45953746	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	180075	45953746	2176149	1030	30164										
KRTAP10-8	386681	hgsc.bcm.edu	37	chr21	46032347	46032347	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccagccggcttgctgcacCtcctccccctgccaacaggc	9	20	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:46032347C>T	ENST00000334662.2	+	1	352	c.330C>T	c.(328-330)acC>acT	p.T110T	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	110	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						CTTGCTGCACCTCCTCCCCCT	0.642																																																0			21											116	102	107					21																	46032347		2203	4300	6503	44856775	SO:0001819	synonymous_variant	386681			AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"Keratin associated proteins"	20525	protein-coding gene	gene with protein product			"keratin associated protein 18-8"	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.330C>T	21.37:g.46032347C>T			44856775	A0JNW4	Silent	SNP	ENST00000334662.2	37	CCDS13713.1																																																																																				0.642	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695		T	46032347	C	T	46032347	2	4	111	1	0	0	0	0	0	0	0	1	8536	668	24	3		3	KRTAP10-8	21	46032347	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	78601	46032347	2097548	1031	30165										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46931120	46931120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttctcctttgacggcaaggaCgtcctgaggcaccccacctg	10	15	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:46931120C>T	ENST00000359759.4	+	40	5055	c.5034C>T	c.(5032-5034)gaC>gaT	p.D1678D	COL18A1_ENST00000355480.5_Silent_p.D1443D|SLC19A1_ENST00000468508.1_5'Flank|SLC19A1_ENST00000567670.1_Intron|COL18A1_ENST00000400337.2_Silent_p.D1263D			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1678	Nonhelical region 11 (NC11).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		ACGGCAAGGACGTCCTGAGGC	0.647																																																0			21											36	38	38					21																	46931120		1980	4157	6137	45755548	SO:0001819	synonymous_variant	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.5034C>T	21.37:g.46931120C>T			45755548	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	6.670	0.492201	0.12702	.	.	ENSG00000182871	ENST00000423214	.	.	.	5.04	-1.31	0.09230	.	.	.	.	.	T	0.55577	0.1929	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49031	-0.8981	4	.	.	.	.	10.1087	0.42550	0.0:0.4602:0.0:0.5398	.	.	.	.	M	248	.	.	T	+	2	0	COL18A1	45755548	0.003000	0.15002	0.966000	0.40874	0.558000	0.35554	-1.442000	0.02407	-0.507000	0.06549	-0.140000	0.14226	ACG		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			T	46931120	C	T	46931120	2	4	111	1	0	0	0	0	0	0	0	1	3681	535	19	1		1	COL18A1	21	46931120	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	898773	46931120	1198775	1032	30166										
PCNT	5116	hgsc.bcm.edu	37	chr21	47836599	47836599	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agccctgagcctgtgcagtgCcgacacatccctgggggaca	13	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr21:47836599C>T	ENST00000359568.5	+	30	6874	c.6767C>T	c.(6766-6768)gCc>gTc	p.A2256V	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2256					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CTGTGCAGTGCCGACACATCC	0.692																																																0			21											24	28	27					21																	47836599		2190	4246	6436	46661027	SO:0001583	missense	5116			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.6767C>T	21.37:g.47836599C>T	ENSP00000352572:p.Ala2256Val		46661027	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	1.369	-0.586498	0.03827	.	.	ENSG00000160299	ENST00000359568	T	0.01414	4.92	4.92	-1.13	0.09775	.	0.946058	0.08569	N	0.926353	T	0.01189	0.0039	N	0.19112	0.55	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.12156	0.005;0.007	T	0.48043	-0.9069	10	0.25106	T	0.35	.	8.5361	0.33364	0.0:0.4858:0.0:0.5142	.	2138;2256	O95613-2;O95613	.;PCNT_HUMAN	V	2256	ENSP00000352572:A2256V	ENSP00000352572:A2256V	A	+	2	0	PCNT	46661027	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.427000	0.06999	-0.490000	0.06707	0.655000	0.94253	GCC		0.692	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47836599	C	T	47836599	3	4	111	1	0	0	0	0	1	0	0	0	11621	739	26	3	6885	3	PCNT	21	47836599	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	905479	47836599	293296	1033	30167										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25120966	25120966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atacacaataacagaatgtgGcatcgatgattcgtttttac	7	7	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:25120966G>A	ENST00000332271.5	-	18	2562	c.2146C>T	c.(2146-2148)Cca>Tca	p.P716S	PIWIL3_ENST00000527701.1_Missense_Mutation_p.P598S|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Missense_Mutation_p.P598S	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	716	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						ACAGAATGTGGCATCGATGAT	0.418																																																0			22											127	108	114					22																	25120966		2203	4300	6503	23450966	SO:0001583	missense	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.2146C>T	22.37:g.25120966G>A	ENSP00000330031:p.Pro716Ser		23450966		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.258484	0.59321	.	.	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.44881	0.91;0.91;0.91	3.11	3.11	0.35812	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.75034	0.3795	H	0.98155	4.16	0.50813	D	0.999896	D;D;D	0.89917	0.977;1.0;0.999	D;D;D	0.97110	0.919;1.0;0.994	D	0.83716	0.0190	10	0.87932	D	0	-6.5441	12.0505	0.53503	0.0:0.0:1.0:0.0	.	598;707;716	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	S	716;598;598	ENSP00000330031:P716S;ENSP00000431843:P598S;ENSP00000435718:P598S	ENSP00000330031:P716S	P	-	1	0	PIWIL3	23450966	1.000000	0.71417	0.014000	0.15608	0.018000	0.09664	4.458000	0.60095	1.760000	0.52011	0.555000	0.69702	CCA		0.418	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25120966	G	A	25120966	3	1	111	1	0	0	0	0	1	0	0	0	11990	1203	42	3	518	3	PIWIL3	22	25120966	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10		25120966	26183600	1034	30168										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26342201	26342201	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcgagctggagaacatgacGcggaacaagagcctggtacc	14	10	0	3			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:26342201G>A	ENST00000407587.2	+	35	5788	c.5619G>A	c.(5617-5619)acG>acA	p.T1873T	MYO18B_ENST00000335473.7_Silent_p.T1872T|MYO18B_ENST00000536101.1_Silent_p.T1872T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1872	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGAACATGACGCGGAACAAGA	0.607																																																0			22											45	54	51					22																	26342201		2104	4213	6317	24672201	SO:0001819	synonymous_variant	84700			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5619G>A	22.37:g.26342201G>A			24672201	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																					0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26342201	G	A	26342201	2	1	111	1	0	0	0	0	0	0	0	1	10096	1074	38	1		1	MYO18B	22	26342201	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1221235	26342201	24962365	1035	30169										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29674169	29674169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactcagcctgcttatccagCctatgggcagcagccagcag	10	15	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:29674169C>T	ENST00000397938.2	+	5	696	c.377C>T	c.(376-378)gCc>gTc	p.A126V	EWSR1_ENST00000406548.1_Missense_Mutation_p.A126V|EWSR1_ENST00000331029.7_Missense_Mutation_p.A126V|EWSR1_ENST00000332050.6_Missense_Mutation_p.A126V|EWSR1_ENST00000332035.6_Missense_Mutation_p.A126V|EWSR1_ENST00000333395.6_Missense_Mutation_p.A126V|EWSR1_ENST00000414183.2_Missense_Mutation_p.A132V	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	126	31 X approximate tandem repeats.|EAD (Gln/Pro/Thr-rich).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GCTTATCCAGCCTATGGGCAG	0.527			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	0			22											38	35	36					22																	29674169		2203	4300	6503	28004169	SO:0001583	missense	2130				CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.377C>T	22.37:g.29674169C>T	ENSP00000381031:p.Ala126Val		28004169	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	37	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587823	0.66105	.	.	ENSG00000182944	ENST00000332050;ENST00000397938;ENST00000436425;ENST00000447973;ENST00000406548;ENST00000437155;ENST00000415761;ENST00000331029;ENST00000414183;ENST00000333395;ENST00000455726;ENST00000332035	T;T;T;T;T;T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	5.07	5.07	0.68467	.	0.434432	0.21633	U	0.071454	D	0.82444	0.5038	L	0.43152	1.355	0.21802	N	0.99954	B;B;D;B;B	0.56521	0.004;0.004;0.976;0.004;0.005	B;B;P;B;B	0.57244	0.015;0.015;0.816;0.015;0.005	T	0.76542	-0.2921	10	0.66056	D	0.02	.	18.812	0.92061	0.0:1.0:0.0:0.0	.	126;126;132;126;126	Q96FE8;B0QYK1;Q96MX4;Q01844;Q9BWA2	.;.;.;EWS_HUMAN;.	V	126;126;133;132;126;127;51;126;132;126;126;126	ENSP00000330896:A126V;ENSP00000381031:A126V;ENSP00000406824:A133V;ENSP00000405947:A132V;ENSP00000385726:A126V;ENSP00000412670:A127V;ENSP00000330516:A126V;ENSP00000400142:A132V;ENSP00000327456:A126V;ENSP00000393637:A126V;ENSP00000331699:A126V	ENSP00000330516:A126V	A	+	2	0	EWSR1	28004169	0.234000	0.23783	0.984000	0.44739	0.999000	0.98932	3.479000	0.53165	2.494000	0.84150	0.650000	0.86243	GCC		0.527	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		T	29674169	C	T	29674169	3	4	111	1	0	0	0	0	1	0	0	0	5309	739	26	3	417	3	EWSR1	22	29674169	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	3331968	29674169	21630397	1036	30170										
NF2	4771	hgsc.bcm.edu	37	chr22	30054176	30054176	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgtcttccgttctccccacAgggatgaagctgaaatggaa	11	10	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:30054176A>G	ENST00000338641.4	+	7	1040		c.e7-1		NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000347330.5_Intron|NF2_ENST00000413209.2_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(6)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TTCTCCCCACAGGGATGAAGC	0.507			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																													yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	6	Unknown(6)	soft_tissue(2)|meninges(1)|large_intestine(1)|stomach(1)|central_nervous_system(1)	22	GRCh37	CS951486	NF2	S							136	104	115					22																	30054176		2203	4300	6503	28384176	SO:0001630	splice_region_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.600-1A>G	22.37:g.30054176A>G			28384176	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.557763	0.86231	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7916	0.78369	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28384176	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	9.244000	0.95423	2.123000	0.65237	0.374000	0.22700	.		0.507	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	G	30054176	A	G	30054176	5	3	111	1	0	0	0	0	0	0	1	0	10388	202	7	4	624	4	NF2	22	30054176	Splice_Site	SNP	A	TCGA-EI-6507-01A-11D-1733-10	380007	30054176	21250390	1037	30171										
SMTN	6525	hgsc.bcm.edu	37	chr22	31485922	31485922	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ttccaggcagcccagagccaCcccccagcccacccaagacc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:31485922delC	ENST00000347557.2	+	7	927	c.709delC	c.(709-711)cccfs	p.P238fs	SMTN_ENST00000358743.1_Frame_Shift_Del_p.P238fs|SMTN_ENST00000333137.7_Frame_Shift_Del_p.P238fs	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	238	Pro-rich.				muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CCCAGAGCCACCCCCCAGCCC	0.652																																																0			22											30	30	30					22																	31485922		2197	4298	6495	29815922	SO:0001589	frameshift_variant	6525			AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.709delC	22.37:g.31485922delC	ENSP00000328635:p.Pro238fs		29815922	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Frame_Shift_Del	DEL	ENST00000347557.2	37	CCDS13886.1																																																																																				0.652	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		-	31485922	C	-	31485922	7	5	111	1	0	1	0	1	0	0	0	0	14851	507	18	0	731	0	SMTN	22	31485922	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	1431746	31485922	19818644	1038	30172										
LIMK2	3985	hgsc.bcm.edu	37	chr22	31658225	31658225	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cgcacacttcgagtggaggaGgtagagtgtgtgtctaatct	14	7	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:31658225G>T	ENST00000331728.4	+	6	771	c.657G>T	c.(655-657)gaG>gaT	p.E219D	LIMK2_ENST00000340552.4_Splice_Site_p.E198D|LIMK2_ENST00000406516.1_Splice_Site_p.E141D|LIMK2_ENST00000444929.2_Intron|LIMK2_ENST00000333611.4_Splice_Site_p.E198D	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	219	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						GAGTGGAGGAGGTAGAGTGTG	0.552																																																0			22											104	101	102					22																	31658225		2203	4300	6503	29988225	SO:0001630	splice_region_variant	3985			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.657+1G>T	22.37:g.31658225G>T			29988225	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	37	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624364	0.96660	.	.	ENSG00000182541	ENST00000406516;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.62	5.62	0.85841	PDZ/DHR/GLGF (4);	0.050458	0.85682	D	0.000000	T	0.63010	0.2475	M	0.64997	1.995	0.80722	D	1	P;P;P;B	0.52463	0.888;0.953;0.908;0.314	P;D;D;B	0.65773	0.865;0.938;0.917;0.378	T	0.63033	-0.6727	10	0.62326	D	0.03	-40.3306	18.6466	0.91413	0.0:0.0:1.0:0.0	.	251;198;219;141	F5GY29;Q7L3H5;P53671;B5MC51	.;.;LIMK2_HUMAN;.	D	141;219;251;198;198	ENSP00000384602:E141D;ENSP00000332687:E219D;ENSP00000330470:E198D;ENSP00000339916:E198D	ENSP00000332687:E219D	E	+	3	2	LIMK2	29988225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.611000	0.82962	2.646000	0.89796	0.655000	0.94253	GAG		0.552	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733	Missense_Mutation	T	31658225	G	T	31658225	5	4	111	1	0	0	0	0	0	0	1	0	8825	1014	35	2	736	2	LIMK2	22	31658225	Splice_Site	SNP	G	TCGA-EI-6507-01A-11D-1733-10	172303	31658225	19646341	1039	30173										
C22orf42	150297	hgsc.bcm.edu	37	chr22	32547481	32547481	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaatacatcttacaatatctGacgttatattctcctccaca	2	11	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:32547481G>A	ENST00000382097.3	-	5	530	c.458C>T	c.(457-459)tCa>tTa	p.S153L	C22orf42_ENST00000490640.1_5'Flank	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	153										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						TACAATATCTGACGTTATATT	0.418																																																0			22											111	98	102					22																	32547481		2203	4300	6503	30877481	SO:0001583	missense	150297			BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.458C>T	22.37:g.32547481G>A	ENSP00000371529:p.Ser153Leu		30877481	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	.	.	.	.	.	.	.	.	.	.	G	4.608	0.112959	0.08831	.	.	ENSG00000205856	ENST00000382097	T	0.29397	1.57	0.81	-1.62	0.08372	.	.	.	.	.	T	0.17746	0.0426	N	0.08118	0	0.09310	N	1	P	0.37500	0.597	P	0.46110	0.504	T	0.21109	-1.0255	9	0.87932	D	0	.	1.6802	0.02830	0.2689:0.0:0.4058:0.3253	.	153	Q6IC83	CV042_HUMAN	L	153	ENSP00000371529:S153L	ENSP00000371529:S153L	S	-	2	0	C22orf42	30877481	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	0.248000	0.18198	-0.826000	0.04284	0.297000	0.19635	TCA		0.418	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		A	32547481	G	A	32547481	3	1	111	1	0	0	0	0	1	0	0	0	2155	1294	45	3	317	3	C22orf42	22	32547481	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	889256	32547481	18757085	1040	30174										
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32629009	32629009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtccttgccacacaggcagcGctgcacaatgacctgccggg	12	15	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:32629009G>A	ENST00000266086.4	-	9	909	c.898C>T	c.(898-900)Cgc>Tgc	p.R300C	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	300					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CACAGGCAGCGCTGCACAATG	0.532																																																0			22											101	69	80					22																	32629009		2203	4300	6503	30959009	SO:0001583	missense	6527			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.898C>T	22.37:g.32629009G>A	ENSP00000266086:p.Arg300Cys		30959009	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	.	15.19	2.759355	0.49468	.	.	ENSG00000100191	ENST00000266086	D	0.96200	-3.94	4.69	3.59	0.41128	.	0.000000	0.85682	D	0.000000	D	0.98362	0.9456	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98052	1.0388	10	0.87932	D	0	.	12.0383	0.53438	0.0:0.0:0.8271:0.1729	.	300	Q9NY91	SC5A4_HUMAN	C	300	ENSP00000266086:R300C	ENSP00000266086:R300C	R	-	1	0	SLC5A4	30959009	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	3.376000	0.52417	2.597000	0.87782	0.563000	0.77884	CGC		0.532	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		A	32629009	G	A	32629009	3	1	111	1	0	0	0	0	1	0	0	0	14704	1087	38	1	1109	1	SLC5A4	22	32629009	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	81528	32629009	18675557	1041	30175										
APOL1	8542	hgsc.bcm.edu	37	chr22	36661550	36661550	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacagccgctttgaccgggaTtaccagcagtaccatggact	10	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:36661550T>C	ENST00000397278.3	+	6	897	c.668T>C	c.(667-669)aTt>aCt	p.I223T	APOL1_ENST00000347595.7_Missense_Mutation_p.I102T|APOL1_ENST00000440669.2_3'UTR|APOL1_ENST00000426053.1_Missense_Mutation_p.I205T|APOL1_ENST00000319136.4_Missense_Mutation_p.I239T|APOL1_ENST00000422706.1_Missense_Mutation_p.I223T|APOL1_ENST00000397279.4_Missense_Mutation_p.I223T	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	223					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cholesterol metabolic process (GO:0008203)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|intrinsic component of membrane (GO:0031224)|very-low-density lipoprotein particle (GO:0034361)	chloride channel activity (GO:0005254)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	14						TTGACCGGGATTACCAGCAGT	0.557																																																0			22											99	96	97					22																	36661550		2203	4300	6503	34991496	SO:0001583	missense	8542			AF019225	CCDS13925.1, CCDS13926.1, CCDS46702.1	22q13.1	2014-09-17			ENSG00000100342	ENSG00000100342		"Apolipoproteins"	618	protein-coding gene	gene with protein product		603743		APOL		9325276, 11374903, 16020735	Standard	NM_003661		Approved		uc011amp.2	O14791	OTTHUMG00000030427	ENST00000397278.3:c.668T>C	22.37:g.36661550T>C	ENSP00000380448:p.Ile223Thr		34991496	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Missense_Mutation	SNP	ENST00000397278.3	37	CCDS13926.1	.	.	.	.	.	.	.	.	.	.	t	8.900	0.956196	0.18507	.	.	ENSG00000100342	ENST00000397278;ENST00000422706;ENST00000426053;ENST00000319136;ENST00000347595;ENST00000397279	T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4	3.42	1.16	0.20824	.	1.224690	0.05503	N	0.558711	T	0.06645	0.0170	L	0.41573	1.285	0.09310	N	1	B;B;B	0.33883	0.43;0.43;0.376	B;B;B	0.31869	0.137;0.137;0.084	T	0.39742	-0.9599	10	0.56958	D	0.05	.	5.3469	0.16014	0.0:0.2487:0.0:0.7513	.	205;223;239	E9PF24;O14791;O14791-2	.;APOL1_HUMAN;.	T	223;223;205;239;102;223	ENSP00000380448:I223T;ENSP00000411507:I223T;ENSP00000388477:I205T;ENSP00000317674:I239T;ENSP00000216178:I102T;ENSP00000380449:I223T	ENSP00000317674:I239T	I	+	2	0	APOL1	34991496	0.006000	0.16342	0.000000	0.03702	0.018000	0.09664	1.772000	0.38552	-0.022000	0.13986	0.172000	0.16884	ATT		0.557	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343		C	36661550	T	C	36661550	3	2	111	1	0	0	0	0	1	0	0	0	805	1493	52	4	738	4	APOL1	22	36661550	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	4032541	36661550	14643016	1042	30176										
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37328934	37328934	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atccagtacaggaaagacacGgccacgtggaaggtgagggc	15	9	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:37328934G>A	ENST00000403662.3	+	9	1362	c.1140G>A	c.(1138-1140)acG>acA	p.T380T	CSF2RB_ENST00000536485.1_Silent_p.T327T|CSF2RB_ENST00000406230.1_Silent_p.T386T|CSF2RB_ENST00000262825.5_Silent_p.T386T			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	380	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GGAAAGACACGGCCACGTGGA	0.557																																																0			22											105	79	87					22																	37328934		2203	4300	6503	35658880	SO:0001819	synonymous_variant	1439			M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1140G>A	22.37:g.37328934G>A			35658880	Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	37	CCDS13936.1																																																																																				0.557	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		A	37328934	G	A	37328934	2	1	111	1	0	0	0	0	0	0	0	1	3941	1103	39	1		1	CSF2RB	22	37328934	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	667384	37328934	13975632	1043	30177										
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37485808	37485808	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctggccctggcccacgtagcTgtagcggtaacaacctggag	13	13	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:37485808T>C	ENST00000346753.3	-	7	789	c.673A>G	c.(673-675)Agc>Ggc	p.S225G	TMPRSS6_ENST00000406856.1_Missense_Mutation_p.S216G|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.S225G|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.S216G|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.S216G	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	225	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CCCACGTAGCTGTAGCGGTAA	0.667																																																0			22											16	18	17					22																	37485808		2201	4297	6498	35815754	SO:0001583	missense	164656			AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.673A>G	22.37:g.37485808T>C	ENSP00000334962:p.Ser225Gly		35815754	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	T	12.23	1.874693	0.33069	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782	D;D;D;D;T	0.92099	-2.97;-2.97;-2.97;-2.97;-0.96	4.28	4.28	0.50868	CUB (1);	0.391895	0.28841	N	0.013973	D	0.87022	0.6074	L	0.34521	1.04	0.41203	D	0.986387	P;B;B	0.52316	0.952;0.4;0.278	B;B;B	0.40677	0.337;0.173;0.084	D	0.87780	0.2611	10	0.49607	T	0.09	.	13.6973	0.62587	0.0:0.0:0.0:1.0	.	225;216;225	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	G	216;225;216;216;225	ENSP00000371211:S216G;ENSP00000334962:S225G;ENSP00000385453:S216G;ENSP00000384964:S216G;ENSP00000397691:S225G	ENSP00000334962:S225G	S	-	1	0	TMPRSS6	35815754	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	2.040000	0.41203	1.691000	0.51100	0.374000	0.22700	AGC		0.667	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		C	37485808	T	C	37485808	3	2	111	1	0	0	0	0	1	0	0	0	16290	1580	55	4	1810	4	TMPRSS6	22	37485808	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	156874	37485808	13818758	1044	30178										
CYTH4	27128	hgsc.bcm.edu	37	chr22	37678616	37678616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccagaggcgtcggaatggaCctgtgccacccaggtaagca	13	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:37678616C>T	ENST00000248901.6	+	1	193	c.6C>T	c.(4-6)gaC>gaT	p.D2D	CYTH4_ENST00000405206.3_Silent_p.D2D|CYTH4_ENST00000402997.1_Silent_p.D2D|CYTH4_ENST00000439667.1_3'UTR	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	2					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						TCGGAATGGACctgtgccacc	0.607																																																0			22											73	61	65					22																	37678616		2203	4300	6503	36008562	SO:0001819	synonymous_variant	27128			AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"Pleckstrin homology (PH) domain containing"	9505	protein-coding gene	gene with protein product		606514	"pleckstrin homology, Sec7 and coiled/coil domains 4", "pleckstrin homology, Sec7 and coiled-coil domains 4"	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.6C>T	22.37:g.37678616C>T			36008562	Q5R3F9|Q9UGT6	Silent	SNP	ENST00000248901.6	37	CCDS13946.1																																																																																				0.607	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			T	37678616	C	T	37678616	2	4	111	1	0	0	0	0	0	0	0	1	4212	506	18	3		3	CYTH4	22	37678616	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	192808	37678616	13625950	1045	30179										
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39479830	39479830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	acctgtgttatgaggtggagCgcatgcacaatgacacctgg	13	9	0	2	rs552054727		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:39479830C>T	ENST00000407997.3	+	5	1033	c.676C>T	c.(676-678)Cgc>Tgc	p.R226C	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.R226C|APOBEC3G_ENST00000461827.1_3'UTR	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	226	Necessary for homooligomerization.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TGAGGTGGAGCGCATGCACAA	0.552													C|||	1	0.000199681	0	0	5008	,	,		16945	0.001		0	False		,,,				2504	0															0			22											120	98	106					22																	39479830		2203	4300	6503	37809776	SO:0001583	missense	60489			AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.676C>T	22.37:g.39479830C>T	ENSP00000385057:p.Arg226Cys		37809776	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	4.741	0.137852	0.09032	.	.	ENSG00000239713	ENST00000452957;ENST00000407997	D;D	0.85088	-1.94;-1.94	1.7	-0.804	0.10882	APOBEC-like, N-terminal (1);	.	.	.	.	T	0.82181	0.4981	M	0.77486	2.375	0.19300	N	0.999975	B	0.26195	0.144	B	0.23419	0.046	T	0.70766	-0.4783	9	0.46703	T	0.11	.	7.232	0.26049	0.4644:0.5355:0.0:0.0	.	226	Q9HC16	ABC3G_HUMAN	C	226	ENSP00000413376:R226C;ENSP00000385057:R226C	ENSP00000385057:R226C	R	+	1	0	APOBEC3G	37809776	0.536000	0.26378	0.009000	0.14445	0.001000	0.01503	1.117000	0.31234	-0.138000	0.11434	-0.282000	0.10007	CGC		0.552	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		T	39479830	C	T	39479830	3	4	111	1	0	0	0	0	1	0	0	0	794	768	27	1	694	1	APOBEC3G	22	39479830	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1801214	39479830	11824736	1046	30180										
ATF4	468	hgsc.bcm.edu	37	chr22	39918398	39918398	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agaaactggataagaagctgAaaaaaatggagcaaaacaag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:39918398delA	ENST00000337304.2	+	2	1729	c.847delA	c.(847-849)aaafs	p.K284fs	ATF4_ENST00000404241.2_Frame_Shift_Del_p.K284fs|ATF4_ENST00000396680.1_Frame_Shift_Del_p.K284fs	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	284	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.			K -> R (in Ref. 5; no nucleotide entry). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	TAAGAAGCTGAAAAAAATGGA	0.498																																																0			22											20	22	21					22																	39918398		2198	4279	6477	38248344	SO:0001589	frameshift_variant	468			D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.847delA	22.37:g.39918398delA	ENSP00000336790:p.Lys284fs		38248344	Q9UH31	Frame_Shift_Del	DEL	ENST00000337304.2	37	CCDS13996.1																																																																																				0.498	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		-	39918398	A	-	39918398	7	5	111	1	0	1	0	1	0	0	0	0	1083	247	9	0	853	0	ATF4	22	39918398	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	438568	39918398	11386168	1047	30181										
EP300	2033	hgsc.bcm.edu	37	chr22	41548251	41548251	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atggaatctaccgaaacagaAgagagaagcactgagttaaa	10	6	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:41548251A>G	ENST00000263253.7	+	16	4258	c.3039A>G	c.(3037-3039)gaA>gaG	p.E1013E		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1013			E -> G (in a breast cancer sample). {ECO:0000269|PubMed:10700188}.		apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CCGAAACAGAAGAGAGAAGCA	0.378			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											41	43	42					22																	41548251		2203	4300	6503	39878197	SO:0001819	synonymous_variant	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3039A>G	22.37:g.41548251A>G			39878197	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																				0.378	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41548251	A	G	41548251	2	3	111	1	0	0	0	0	0	0	0	1	5161	69	3	4		4	EP300	22	41548251	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	1629853	41548251	9756315	1048	30182										
EP300	2033	hgsc.bcm.edu	37	chr22	41574679	41574679	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctccacggccacagtcccagCccccccactccagtccttcc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:41574679delC	ENST00000263253.7	+	31	8183	c.6964delC	c.(6964-6966)cccfs	p.P2323fs	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2323					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACAGTCCCAGCCCCCCCACTC	0.612			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											87	91	90					22																	41574679		2203	4300	6503	39904625	SO:0001589	frameshift_variant	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6964delC	22.37:g.41574679delC	ENSP00000263253:p.Pro2323fs		39904625	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	37	CCDS14010.1																																																																																				0.612	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574679	C	-	41574679	7	5	111	1	0	1	0	1	0	0	0	0	5161	739	26	0	7086	0	EP300	22	41574679	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	26428	41574679	9729887	1049	30183										
CYB5R3	1727	hgsc.bcm.edu	37	chr22	43032804	43032804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggagcgctggaacagcttcaTgagcagactgtacaggaacc	13	10	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:43032804T>C	ENST00000352397.5	-	2	322	c.70A>G	c.(70-72)Atg>Gtg	p.M24V	CYB5R3_ENST00000361740.4_Missense_Mutation_p.M57V|CYB5R3_ENST00000407332.1_Start_Codon_SNP_p.M1V|CYB5R3_ENST00000396303.3_Start_Codon_SNP_p.M1V|CYB5R3_ENST00000407623.3_Start_Codon_SNP_p.M1V|CYB5R3_ENST00000402438.1_Start_Codon_SNP_p.M1V	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	24					blood circulation (GO:0008015)|cholesterol biosynthetic process (GO:0006695)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|hemoglobin complex (GO:0005833)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|FAD binding (GO:0071949)|flavin adenine dinucleotide binding (GO:0050660)|NAD binding (GO:0051287)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6					Flavin adenine dinucleotide(DB03147)	AACAGCTTCATGAGCAGACTG	0.632																																																0			22											77	67	70					22																	43032804		2203	4300	6503	41362748	SO:0001583	missense	1727			M16461	CCDS14040.1, CCDS33658.1, CCDS54535.1	22q13.2	2012-10-02		2005-07-13	ENSG00000100243	ENSG00000100243	1.6.2.2		2873	protein-coding gene	gene with protein product		613213	"diaphorase (NADH) (cytochrome b-5 reductase)"	DIA1		2479590, 3268037	Standard	NM_001129819		Approved		uc011aps.2	P00387	OTTHUMG00000150745	ENST00000352397.5:c.70A>G	22.37:g.43032804T>C	ENSP00000338461:p.Met24Val		41362748	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Missense_Mutation	SNP	ENST00000352397.5	37	CCDS33658.1	.	.	.	.	.	.	.	.	.	.	T	9.031	0.987393	0.18889	.	.	ENSG00000100243	ENST00000361740;ENST00000396303;ENST00000352397;ENST00000407623;ENST00000407332;ENST00000402438;ENST00000438270	D;D;D;D;D;D;T	0.86230	-2.09;-2.06;-2.05;-2.06;-2.06;-2.06;-1.4	4.82	4.82	0.62117	.	0.338170	0.32802	N	0.005625	T	0.78597	0.4308	L	0.36672	1.1	0.80722	D	1	B;B	0.18863	0.031;0.0	B;B	0.13407	0.009;0.001	T	0.71155	-0.4675	10	0.17369	T	0.5	-36.5269	8.9742	0.35926	0.0:0.0:0.1871:0.8129	.	57;24	B7Z7L3;P00387	.;NB5R3_HUMAN	V	57;1;24;1;1;1;1	ENSP00000354468:M57V;ENSP00000379597:M1V;ENSP00000338461:M24V;ENSP00000384834:M1V;ENSP00000384457:M1V;ENSP00000385679:M1V;ENSP00000403439:M1V	ENSP00000338461:M24V	M	-	1	0	CYB5R3	41362748	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	1.514000	0.35834	1.933000	0.56026	0.260000	0.18958	ATG		0.632	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1			C	43032804	T	C	43032804	3	2	111	1	0	0	0	0	1	0	0	0	4134	1464	51	4	867	4	CYB5R3	22	43032804	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1458125	43032804	8271762	1050	30184										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44285694	44285694	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctcacctcccctctgaactcGggggggatcagcccgcagta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:44285694delG	ENST00000597664.1	-	3	606	c.477delC	c.(475-477)cccfs	p.P159fs	PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000216177.4_Frame_Shift_Del_p.P159fs|PNPLA5_ENST00000593866.1_Intron			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	159	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)	p.E160fs*47(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CTCTGAACTCGGGGGGGATCA	0.572																																																1	Insertion - Frameshift(1)	ovary(1)	22																																								42617027	SO:0001589	frameshift_variant	150379			Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.477delC	22.37:g.44285694delG	ENSP00000471069:p.Pro159fs		42617027	B1AHL8|B3KPR1|Q6ZST0	Frame_Shift_Del	DEL	ENST00000597664.1	37																																																																																					0.572	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		-	44285694	G	-	44285694	7	5	111	1	0	1	0	1	0	0	0	0	12199	1103	39	0	840	0	PNPLA5	22	44285694	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	1252890	44285694	7018872	1051	30185										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44287046	44287046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ctgggaggccaggacgtgggCgtcggggggcagagcatcct	20	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:44287046C>T	ENST00000597664.1	-	2	451	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000216177.4_Missense_Mutation_p.A108T|PNPLA5_ENST00000593866.1_Intron			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	108	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AGGACGTGGGCGTCGGGGGGC	0.657																																																0			22											31	29	30					22																	44287046		2202	4298	6500	42618379	SO:0001583	missense	150379			Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.322G>A	22.37:g.44287046C>T	ENSP00000471069:p.Ala108Thr		42618379	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		.	.	.	.	.	.	.	.	.	.	C	15.67	2.901460	0.52227	.	.	ENSG00000100341	ENST00000216177;ENST00000438734	T;T	0.77098	-1.07;-0.87	4.92	-6.68	0.01778	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	1.831610	0.03000	N	0.148040	T	0.69088	0.3072	M	0.64404	1.975	0.19575	N	0.999964	P	0.39404	0.672	B	0.30943	0.122	T	0.64183	-0.6467	10	0.44086	T	0.13	-0.0787	9.7403	0.40413	0.2293:0.6002:0.0:0.1706	.	108	Q7Z6Z6	PLPL5_HUMAN	T	108	ENSP00000216177:A108T;ENSP00000405732:A108T	ENSP00000216177:A108T	A	-	1	0	PNPLA5	42618379	0.006000	0.16342	0.000000	0.03702	0.013000	0.08279	-0.083000	0.11286	-1.449000	0.01938	-0.367000	0.07326	GCC		0.657	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		T	44287046	C	T	44287046	3	4	111	1	0	0	0	0	1	0	0	0	12199	768	27	1	999	1	PNPLA5	22	44287046	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1352	44287046	7017520	1052	30186										
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50546632	50546632	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cggcctggcacgtggagcagCgaagccacctcagtgaagcc	14	14	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:50546632C>T	ENST00000262794.5	+	4	593	c.510C>T	c.(508-510)agC>agT	p.S170S	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.S170S|MOV10L1_ENST00000540615.1_Silent_p.S150S|MOV10L1_ENST00000545383.1_Silent_p.S170S	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	170					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CGTGGAGCAGCGAAGCCACCT	0.597																																																0			22											59	51	54					22																	50546632		2203	4300	6503	48888759	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.510C>T	22.37:g.50546632C>T			48888759	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.597	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50546632	C	T	50546632	2	4	111	1	0	0	0	0	0	0	0	1	9749	767	27	1		1	MOV10L1	22	50546632	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	6259586	50546632	757934	1053	30187										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50879410	50879410	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggggtcccggccgggaggCccccccgctgcccacagtgg							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:50879410delC	ENST00000216061.5	+	23	2925	c.2555delC	c.(2554-2556)gccfs	p.A852fs	PPP6R2_ENST00000359139.3_Frame_Shift_Del_p.A819fs|PPP6R2_ENST00000395744.3_Frame_Shift_Del_p.A818fs|PPP6R2_ENST00000395741.3_Frame_Shift_Del_p.A819fs			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	852						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GGCCGGGAGGCCCCCCCGCTG	0.721																																																0			22											16	19	18					22																	50879410		2198	4294	6492	49226276	SO:0001589	frameshift_variant	0			AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2555delC	22.37:g.50879410delC	ENSP00000216061:p.Ala852fs		49226276	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Frame_Shift_Del	DEL	ENST00000216061.5	37																																																																																					0.721	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		-	50879410	C	-	50879410	7	5	111	1	0	1	0	1	0	0	0	0	13874	739	26	0	2527	0	SAPS2	22	50879410	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	332778	50879410	425156	1054	30188										
ARSA	410	hgsc.bcm.edu	37	chr22	51064600	51064600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	accgggagcgatatgacctgGccagaaggccaaggcaggct	15	11	0	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chr22:51064600G>A	ENST00000547307.1	-	5	1360	c.955C>T	c.(955-957)Cca>Tca	p.P319S	ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000395621.3_Missense_Mutation_p.P321S|ARSA_ENST00000356098.5_Missense_Mutation_p.P321S|ARSA_ENST00000395619.3_Missense_Mutation_p.P321S|ARSA_ENST00000453344.2_Missense_Mutation_p.P235S|ARSA_ENST00000216124.5_Missense_Mutation_p.P321S|ARSA_ENST00000547805.1_Missense_Mutation_p.P319S			P15289	ARSA_HUMAN	arylsulfatase A	319					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	ATATGACCTGGCCAGAAGGCC	0.642																																																0			22											37	40	39					22																	51064600		2202	4298	6500	49411466	SO:0001583	missense	410			X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.955C>T	22.37:g.51064600G>A	ENSP00000448440:p.Pro319Ser		49411466	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.990322	0.74589	.	.	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63;-4.63;-4.63;-4.63	5.4	5.4	0.78164	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.264541	0.44097	D	0.000495	D	0.97480	0.9175	M	0.86028	2.79	0.58432	D	0.999998	P	0.45986	0.87	P	0.45071	0.468	D	0.97622	1.0136	10	0.72032	D	0.01	.	12.4102	0.55464	0.0:0.1692:0.8308:0.0	.	319	P15289	ARSA_HUMAN	S	321;321;319;319;321;235;321	ENSP00000348406:P321S;ENSP00000216124:P321S;ENSP00000448440:P319S;ENSP00000448932:P319S;ENSP00000378983:P321S;ENSP00000412542:P235S;ENSP00000378981:P321S	ENSP00000216124:P321S	P	-	1	0	ARSA	49411466	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.495000	0.81514	2.538000	0.85594	0.609000	0.83330	CCA		0.642	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		A	51064600	G	A	51064600	3	1	111	1	0	0	0	0	1	0	0	0	988	1203	42	3	584	3	ARSA	22	51064600	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	185190	51064600	239966	1055	30189										
SCML1	6322	hgsc.bcm.edu	37	chrX	17768146	17768146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccactttaccagtgtcaaggCgtgagaataattccccgagc	9	12	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:17768146C>T	ENST00000380041.3	+	6	764	c.436C>T	c.(436-438)Cgt>Tgt	p.R146C	SCML1_ENST00000380043.3_Missense_Mutation_p.R119C|SCML1_ENST00000380045.3_Missense_Mutation_p.R25C|SCML1_ENST00000398080.1_Missense_Mutation_p.R25C	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	146					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					AGTGTCAAGGCGTGAGAATAA	0.483																																																0			X											106	96	99					X																	17768146		2203	4300	6503	17678067	SO:0001583	missense	6322				CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"Sterile alpha motif (SAM) domain containing"	10580	protein-coding gene	gene with protein product		300227	"sex comb on midleg (Drosophila)-like 1"			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.436C>T	X.37:g.17768146C>T	ENSP00000369380:p.Arg146Cys		17678067	B0FZN6|B2RA08|Q5H968|Q5H969	Missense_Mutation	SNP	ENST00000380041.3	37	CCDS35210.1	.	.	.	.	.	.	.	.	.	.	C	8.122	0.781128	0.16120	.	.	ENSG00000047634	ENST00000380045;ENST00000380041;ENST00000380043;ENST00000398080;ENST00000419185	.	.	.	3.61	0.626	0.17670	.	1.186530	0.06384	N	0.715715	T	0.37404	0.1002	N	0.24115	0.695	0.09310	N	1	D;D	0.89917	1.0;0.999	P;P	0.59487	0.858;0.725	T	0.27088	-1.0084	9	0.37606	T	0.19	-0.4142	5.3535	0.16047	0.406:0.3983:0.1957:0.0	.	119;146	Q9UN30-2;Q9UN30	.;SCML1_HUMAN	C	25;146;119;25;119	.	ENSP00000369380:R146C	R	+	1	0	SCML1	17678067	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.453000	0.01005	0.013000	0.14918	0.600000	0.82982	CGT		0.483	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746		T	17768146	C	T	17768146	3	4	111	1	0	0	0	0	1	0	0	0	13946	768	27	1	457	1	SCML1	23	17768146	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10		17768146	137502414	1056	30190										
PHKA2	5256	hgsc.bcm.edu	37	chrX	18911701	18911701	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cccataagccccactcggagCgctgtcataaaagaagtggc	10	13	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:18911701C>T	ENST00000379942.4	-	33	4275	c.3610G>A	c.(3610-3612)Gct>Act	p.A1204T	PHKA2_ENST00000481718.1_5'UTR|PHKA2-AS1_ENST00000439295.1_RNA|PHKA2-AS1_ENST00000452900.1_RNA	NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1204					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CCACTCGGAGCGCTGTCATAA	0.522																																																0			X											190	184	186					X																	18911701		2203	4300	6503	18821622	SO:0001583	missense	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.3610G>A	X.37:g.18911701C>T	ENSP00000369274:p.Ala1204Thr		18821622	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574124	0.86542	.	.	ENSG00000044446	ENST00000379942	D	0.95137	-3.62	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.97829	0.9287	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98245	1.0490	10	0.87932	D	0	-15.9757	19.5561	0.95349	0.0:1.0:0.0:0.0	.	1204	P46019	KPB2_HUMAN	T	1204	ENSP00000369274:A1204T	ENSP00000369274:A1204T	A	-	1	0	PHKA2	18821622	1.000000	0.71417	0.680000	0.29994	0.251000	0.25915	7.400000	0.79949	2.574000	0.86865	0.600000	0.82982	GCT		0.522	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		T	18911701	C	T	18911701	3	4	111	1	0	0	0	0	1	0	0	0	11875	768	27	1	101	1	PHKA2	23	18911701	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1143555	18911701	136358859	1057	30191										
YY2	404281	hgsc.bcm.edu	37	chrX	21875100	21875100	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcagctccagcctgggcacGaggaagtgggagcagaagca	16	10	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:21875100G>A	ENST00000429584.2	+	1	996	c.498G>A	c.(496-498)acG>acA	p.T166T	MBTPS2_ENST00000465888.1_3'UTR|MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000365779.2_Intron	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	166					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						GCCTGGGCACGAGGAAGTGGG	0.587																																																0			X											78	78	78					X																	21875100		2203	4300	6503	21785021	SO:0001819	synonymous_variant	404281			AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.498G>A	X.37:g.21875100G>A			21785021	B2RP10|Q6Q1S4	Silent	SNP	ENST00000429584.2	37	CCDS14202.1																																																																																				0.587	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		A	21875100	G	A	21875100	2	1	111	1	0	0	0	0	0	0	0	1	17549	1045	37	1		1	YY2	23	21875100	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2963399	21875100	133395460	1058	30192										
DCAF8L1	139425	hgsc.bcm.edu	37	chrX	27998265	27998265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgccatcgtggctgtacacaAcgcaggtgatgtttgttggg	14	8	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:27998265A>G	ENST00000441525.1	-	1	1301	c.1187T>C	c.(1186-1188)gTt>gCt	p.V396A		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	396										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						GCTGTACACAACGCAGGTGAT	0.423																																																0			X											99	90	93					X																	27998265		2202	4300	6502	27908186	SO:0001583	missense	0				CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"WD repeat domain containing"	31810	protein-coding gene	gene with protein product			"WD repeat domain 42B"	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.1187T>C	X.37:g.27998265A>G	ENSP00000405222:p.Val396Ala		27908186	B3KXX1	Missense_Mutation	SNP	ENST00000441525.1	37	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	A	6.587	0.476739	0.12521	.	.	ENSG00000226372	ENST00000441525	D	0.83506	-1.73	1.08	-0.271	0.12922	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.177207	0.36932	N	0.002336	T	0.58495	0.2126	N	0.05383	-0.06	0.18873	N	0.999986	B	0.02656	0.0	B	0.04013	0.001	T	0.41998	-0.9477	10	0.21014	T	0.42	-2.0265	4.44	0.11570	0.772:0.0:0.228:0.0	.	396	A6NGE4	DC8L1_HUMAN	A	396	ENSP00000405222:V396A	ENSP00000405222:V396A	V	-	2	0	DCAF8L1	27908186	0.998000	0.40836	0.092000	0.20876	0.150000	0.21749	3.697000	0.54764	-0.145000	0.11294	-0.816000	0.03127	GTT		0.423	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		G	27998265	A	G	27998265	3	3	111	1	0	0	0	0	1	0	0	0	4283	43	2	4	619	4	DCAF8L1	23	27998265	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	6123165	27998265	127272295	1059	30193										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30236765	30236765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caaggcccgagatgagacccGgggtctcaatgttcctcagg	13	12	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:30236765G>A	ENST00000378988.4	+	2	169	c.68G>A	c.(67-69)cGg>cAg	p.R23Q		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	23										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						GATGAGACCCGGGGTCTCAAT	0.567																																																0			X											37	35	36					X																	30236765		2202	4300	6502	30146686	SO:0001583	missense	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.68G>A	X.37:g.30236765G>A	ENSP00000368273:p.Arg23Gln		30146686	O75860	Missense_Mutation	SNP	ENST00000378988.4	37	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	A	0.186	-1.057326	0.01965	.	.	ENSG00000099399	ENST00000378988	T	0.02974	4.09	3.43	0.959	0.19624	Melanoma associated antigen, MAGE, N-terminal (1);	0.653207	0.14428	N	0.320189	T	0.00468	0.0015	N	0.00036	-2.535	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	10	0.02654	T	1	.	3.0051	0.06026	0.5076:0.2281:0.2643:0.0	.	23	O15479	MAGB2_HUMAN	Q	23	ENSP00000368273:R23Q	ENSP00000368273:R23Q	R	+	2	0	MAGEB2	30146686	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.065000	0.11617	-0.166000	0.10890	-1.641000	0.00772	CGG		0.567	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		A	30236765	G	A	30236765	3	1	111	1	0	0	0	0	1	0	0	0	9206	1116	39	1	70	1	MAGEB2	23	30236765	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	2238500	30236765	125033795	1060	30194										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30237068	30237068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gttggtgcagttcctgttgtAcaagtataaaataaaaaagt	9	4	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:30237068A>G	ENST00000378988.4	+	2	472	c.371A>G	c.(370-372)tAc>tGc	p.Y124C		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	124	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						TTCCTGTTGTACAAGTATAAA	0.453																																																0			X											56	55	55					X																	30237068		2202	4300	6502	30146989	SO:0001583	missense	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.371A>G	X.37:g.30237068A>G	ENSP00000368273:p.Tyr124Cys		30146989	O75860	Missense_Mutation	SNP	ENST00000378988.4	37	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	A	1.547	-0.540170	0.04053	.	.	ENSG00000099399	ENST00000378988	T	0.04706	3.57	3.16	-6.32	0.01995	.	2.504050	0.02225	N	0.064345	T	0.04182	0.0116	L	0.38733	1.17	0.09310	N	1	B	0.17038	0.02	B	0.20577	0.03	T	0.28138	-1.0053	10	0.39692	T	0.17	.	2.3586	0.04301	0.1489:0.1177:0.3814:0.352	.	124	O15479	MAGB2_HUMAN	C	124	ENSP00000368273:Y124C	ENSP00000368273:Y124C	Y	+	2	0	MAGEB2	30146989	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.012000	0.01451	-3.386000	0.00174	-1.758000	0.00672	TAC		0.453	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		G	30237068	A	G	30237068	3	3	111	1	0	0	0	0	1	0	0	0	9206	391	14	4	373	4	MAGEB2	23	30237068	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	303	30237068	125033492	1061	30195										
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30261250	30261250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cactacagccatgactagtgCgtattccagggccacatcca	8	14	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:30261250C>T	ENST00000378982.2	+	1	1194	c.998C>T	c.(997-999)gCg>gTg	p.A333V	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	333										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						ATGACTAGTGCGTATTCCAGG	0.512																																																0			X											53	44	47					X																	30261250		2202	4300	6502	30171171	SO:0001583	missense	4115				CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.998C>T	X.37:g.30261250C>T	ENSP00000368266:p.Ala333Val		30171171	B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	37	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	C	9.414	1.081367	0.20309	.	.	ENSG00000120289	ENST00000378982	T	0.01821	4.62	2.9	-0.177	0.13307	.	.	.	.	.	T	0.02083	0.0065	L	0.55481	1.735	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.43702	-0.9375	9	0.33940	T	0.23	.	4.6422	0.12555	0.0:0.419:0.4374:0.1436	.	333	O15481	MAGB4_HUMAN	V	333	ENSP00000368266:A333V	ENSP00000368266:A333V	A	+	2	0	MAGEB4	30171171	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.791000	0.04599	-0.138000	0.11434	0.529000	0.55759	GCG		0.512	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		T	30261250	C	T	30261250	3	4	111	1	0	0	0	0	1	0	0	0	9208	768	27	1	1000	1	MAGEB4	23	30261250	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	24182	30261250	125009310	1062	30196										
DMD	1756	hgsc.bcm.edu	37	chrX	32361293	32361293	+	Frame_Shift_Del	DEL	T	T	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggctcaggtaggctggctaaTtttttttcaatgtcatccaa							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:32361293delT	ENST00000357033.4	-	40	5903	c.5697delA	c.(5695-5697)aaafs	p.K1899fs	DMD_ENST00000378677.2_Frame_Shift_Del_p.K1895fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1899	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		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)				GGCTGGCTAATTTTTTTTCAA	0.358																																																0			X	GRCh37	CD050845	DMD	D							101	93	96					X																	32361293		2202	4300	6502	32271214	SO:0001589	frameshift_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5697delA	X.37:g.32361293delT	ENSP00000354923:p.Lys1899fs		32271214	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	37	CCDS14233.1																																																																																				0.358	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		-	32361293	T	-	32361293	7	5	111	1	0	1	0	1	0	0	0	0	4591	1490	52	0	5668	0	DMD	23	32361293	Frame_Shift_Del	DEL	T	TCGA-EI-6507-01A-11D-1733-10	2100043	32361293	122909267	1063	30197										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820392	35820392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gtgagacccagagcctggagGttgcacaggtctccaaggct	14	11	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:35820392G>A	ENST00000399989.1	+	2	358	c.79G>A	c.(79-81)Gtt>Att	p.V27I	MAGEB16_ENST00000399988.1_Missense_Mutation_p.V27I|MAGEB16_ENST00000399987.1_Missense_Mutation_p.V27I|MAGEB16_ENST00000399992.1_Missense_Mutation_p.V59I|MAGEB16_ENST00000399985.1_Missense_Mutation_p.V27I	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	27										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGCCTGGAGGTTGCACAGGT	0.562																																																0			X											42	43	43					X																	35820392		2048	4181	6229	35730313	SO:0001583	missense	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.79G>A	X.37:g.35820392G>A	ENSP00000382871:p.Val27Ile		35730313	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	G	6.685	0.494971	0.12702	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04551	3.6;3.6;3.6;3.6;3.6	3.02	0.991	0.19813	Melanoma associated antigen, MAGE, N-terminal (1);	4.960410	0.00357	N	0.000022	T	0.08582	0.0213	M	0.63843	1.955	0.09310	N	1	B	0.28208	0.203	B	0.31614	0.133	T	0.35871	-0.9771	10	0.51188	T	0.08	.	4.8663	0.13609	0.3527:0.0:0.6473:0.0	.	27	A2A368	MAGBG_HUMAN	I	27;59;27;27;27	ENSP00000382870:V27I;ENSP00000382874:V59I;ENSP00000382869:V27I;ENSP00000382871:V27I;ENSP00000382867:V27I	ENSP00000382867:V27I	V	+	1	0	MAGEB16	35730313	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.024000	0.13555	0.129000	0.18514	-0.430000	0.05897	GTT		0.562	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			A	35820392	G	A	35820392	3	1	111	1	0	0	0	0	1	0	0	0	9204	1261	44	3	81	3	MAGEB16	23	35820392	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3459099	35820392	119450168	1064	30198										
KDM6A	7403	hgsc.bcm.edu	37	chrX	44929024	44929024	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	cacactgctacctcaggtggAcaacaaggcattaccttaac	7	13	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:44929024A>G	ENST00000377967.4	+	17	2165	c.2124A>G	c.(2122-2124)ggA>ggG	p.G708G	KDM6A_ENST00000382899.4_Silent_p.G715G|KDM6A_ENST00000536777.1_Silent_p.G663G|KDM6A_ENST00000543216.1_Silent_p.G629G	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	708	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						CCTCAGGTGGACAACAAGGCA	0.502			"D, N, F, S"		"renal, oesophageal SCC, MM"																																Colon(129;1273 1667 15230 27352 52914)		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	X											121	82	95					X																	44929024		2203	4300	6503	44813968	SO:0001819	synonymous_variant	7403			AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.2124A>G	X.37:g.44929024A>G			44813968	Q52LL9|Q5JVQ7	Silent	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	A	6.864	0.528837	0.13127	.	.	ENSG00000147050	ENST00000414389;ENST00000433797	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	T	0.69833	0.3155	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69355	-0.5167	4	.	.	.	-0.7565	13.8181	0.63303	1.0:0.0:0.0:0.0	.	.	.	.	A	306;351	.	.	T	+	1	0	KDM6A	44813968	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.317000	0.79018	1.707000	0.51288	0.486000	0.48141	ACA		0.502	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		G	44929024	A	G	44929024	2	3	111	1	0	0	0	0	0	0	0	1	8158	262	10	4		4	KDM6A	23	44929024	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	9108632	44929024	110341536	1065	30199										
UBA1	7317	hgsc.bcm.edu	37	chrX	47058303	47058303	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tccgtgttgtccgaagtgccCtcggtgccaaccaacgtgag	12	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:47058303C>A	ENST00000335972.6	+	2	285	c.102C>A	c.(100-102)ccC>ccA	p.P34P	UBA1_ENST00000377351.4_Silent_p.P34P	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	34					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCGAAGTGCCCTCGGTGCCAA	0.592																																																0			X											120	87	98					X																	47058303		2203	4300	6503	46943247	SO:0001819	synonymous_variant	7317			AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.102C>A	X.37:g.47058303C>A			46943247	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	37	CCDS14275.1																																																																																				0.592	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		A	47058303	C	A	47058303	2	1	111	1	0	0	0	0	0	0	0	1	16867	668	24	2		2	UBA1	23	47058303	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2129279	47058303	108212257	1066	30200										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48676708	48676708	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggtgccagcagccagatcggCcgggctgcgggcacaggctt	17	13	0	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:48676708C>A	ENST00000334136.5	+	22	2254	c.2076C>A	c.(2074-2076)ggC>ggA	p.G692G	HDAC6_ENST00000444343.2_Silent_p.G706G|HDAC6_ENST00000376619.2_Silent_p.G692G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	692	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GCCAGATCGGCCGGGCTGCGG	0.642																																					Pancreas(112;205 1675 2305 8976 15959)											0			X											38	29	32					X																	48676708		2200	4299	6499	48561652	SO:0001819	synonymous_variant	10013			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2076C>A	X.37:g.48676708C>A			48561652	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	37	CCDS14306.1																																																																																				0.642	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		A	48676708	C	A	48676708	2	1	111	1	0	0	0	0	0	0	0	1	7032	726	26	2		2	HDAC6	23	48676708	Silent	SNP	C	TCGA-EI-6507-01A-11D-1733-10	1618405	48676708	106593852	1067	30201										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49142836	49142836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tgcactatgcccggctggggCgtggcgtggagctcatcaag	16	11	2	0	rs199740337		TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:49142836C>T	ENST00000055335.6	+	4	1700	c.1684C>T	c.(1684-1686)Cgt>Tgt	p.R562C	PPP1R3F_ENST00000495799.1_Missense_Mutation_p.R216C|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.R233C|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.R216C|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.R216C	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	562					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CCGGCTGGGGCGTGGCGTGGA	0.647																																																0			X											23	21	22					X																	49142836		2203	4299	6502	49029780	SO:0001583	missense	89801				CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1684C>T	X.37:g.49142836C>T	ENSP00000055335:p.Arg562Cys		49029780	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501326	0.26861	.	.	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.56776	0.85;0.86;0.44;0.85;0.85	5.44	1.82	0.25136	.	0.493077	0.19360	N	0.116164	T	0.27063	0.0663	N	0.11560	0.145	0.32209	N	0.576735	B;B;B	0.14438	0.01;0.01;0.002	B;B;B	0.06405	0.002;0.002;0.001	T	0.10894	-1.0610	10	0.40728	T	0.16	0.5726	3.6526	0.08209	0.1775:0.5452:0.0:0.2773	.	233;247;562	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	C	216;233;562;216;216	ENSP00000420687:R216C;ENSP00000415548:R233C;ENSP00000055335:R562C;ENSP00000417535:R216C;ENSP00000365359:R216C	ENSP00000055335:R562C	R	+	1	0	PPP1R3F	49029780	0.968000	0.33430	0.973000	0.42090	0.871000	0.50021	0.531000	0.23052	-0.077000	0.12752	0.513000	0.50165	CGT		0.647	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		T	49142836	C	T	49142836	3	4	111	1	0	0	0	0	1	0	0	0	12409	768	27	1	1698	1	PPP1R3F	23	49142836	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	466128	49142836	106127724	1068	30202										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49851179	49851179	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	atatttggtggtctgtggggAgcactgtttatccgcacaaa	12	7	1	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:49851179A>G	ENST00000307367.2	+	8	1290	c.999A>G	c.(997-999)ggA>ggG	p.G333G	CLCN5_ENST00000376108.3_Silent_p.G333G|CLCN5_ENST00000376091.3_Silent_p.G403G|CLCN5_ENST00000376088.3_Silent_p.G403G			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	333					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					GTCTGTGGGGAGCACTGTTTA	0.507																																																0			X											103	79	87					X																	49851179		2203	4300	6503	49737919	SO:0001819	synonymous_variant	1184			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.999A>G	X.37:g.49851179A>G			49737919	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	37	CCDS14328.1																																																																																				0.507	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			G	49851179	A	G	49851179	2	3	111	1	0	0	0	0	0	0	0	1	3472	291	11	4		4	CLCN5	23	49851179	Silent	SNP	A	TCGA-EI-6507-01A-11D-1733-10	708343	49851179	105419381	1069	30203										
APEX2	27301	hgsc.bcm.edu	37	chrX	55029489	55029489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	agcggctagtctttaagatgCgcttctatcgtttgctgcaa	10	9	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:55029489C>T	ENST00000374987.3	+	4	583	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	APEX2_ENST00000471758.1_3'UTR	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	173					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CTTTAAGATGCGCTTCTATCG	0.577								Other BER factors																																								0			X											71	57	62					X																	55029489		2203	4300	6503	55046214	SO:0001583	missense	27301			AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.517C>T	X.37:g.55029489C>T	ENSP00000364126:p.Arg173Cys		55046214	Q9Y5X7	Missense_Mutation	SNP	ENST00000374987.3	37	CCDS14365.1	.	.	.	.	.	.	.	.	.	.	c	22.2	4.261477	0.80358	.	.	ENSG00000169188	ENST00000374987	T	0.80393	-1.37	5.15	3.33	0.38152	Endonuclease/exonuclease/phosphatase (2);	0.288543	0.40640	N	0.001056	T	0.79076	0.4385	M	0.84773	2.715	0.51767	D	0.999938	B	0.34372	0.451	B	0.29716	0.106	T	0.76119	-0.3076	10	0.62326	D	0.03	-7.9571	8.4913	0.33102	0.1531:0.762:0.0:0.0849	.	173	Q9UBZ4	APEX2_HUMAN	C	173	ENSP00000364126:R173C	ENSP00000364126:R173C	R	+	1	0	APEX2	55046214	1.000000	0.71417	0.985000	0.45067	0.953000	0.61014	2.882000	0.48546	0.470000	0.27294	0.597000	0.82753	CGC		0.577	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			T	55029489	C	T	55029489	3	4	111	1	0	0	0	0	1	0	0	0	770	768	27	1	531	1	APEX2	23	55029489	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	5178310	55029489	100241071	1070	30204										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64744047	64744047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gagcatcctctccaatagggCctgcgtgaagttctgggagt	13	10	2	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:64744047C>T	ENST00000374811.3	-	10	1229	c.1189G>A	c.(1189-1191)Gcc>Acc	p.A397T	LAS1L_ENST00000374804.5_Missense_Mutation_p.A338T|LAS1L_ENST00000312391.8_3'UTR|LAS1L_ENST00000374807.5_Missense_Mutation_p.A380T	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	397					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						TCCAATAGGGCCTGCGTGAAG	0.577																																																0			X											48	40	43					X																	64744047		2203	4300	6503	64660772	SO:0001583	missense	81887			BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.1189G>A	X.37:g.64744047C>T	ENSP00000363944:p.Ala397Thr		64660772	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	37	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	C	9.825	1.186880	0.21870	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804	.	.	.	4.55	3.68	0.42216	.	0.441226	0.24645	N	0.036761	T	0.50309	0.1608	L	0.40543	1.245	0.80722	D	1	B;B;D	0.58620	0.419;0.019;0.983	B;B;P	0.53401	0.118;0.019;0.725	T	0.35325	-0.9793	9	0.21540	T	0.41	.	9.2758	0.37698	0.2153:0.7847:0.0:0.0	.	338;380;397	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	T	380;397;338	.	ENSP00000363937:A338T	A	-	1	0	LAS1L	64660772	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	1.166000	0.31834	0.726000	0.32339	0.287000	0.19450	GCC		0.577	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		T	64744047	C	T	64744047	3	4	111	1	0	0	0	0	1	0	0	0	8658	739	26	3	1035	3	LAS1L	23	64744047	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	9714558	64744047	90526513	1071	30205										
AR	367	hgsc.bcm.edu	37	chrX	66765032	66765032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aagggtctaccctcggccgcCgtccaagacctaccgaggag	12	15	1	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:66765032C>T	ENST00000374690.3	+	1	568	c.44C>T	c.(43-45)cCg>cTg	p.P15L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.P15L|AR_ENST00000504326.1_Missense_Mutation_p.P15L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	15	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P15Q(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CCTCGGCCGCCGTCCAAGACC	0.617									Androgen Insensitivity Syndrome																																							1	Substitution - Missense(1)	lung(1)	X											62	48	52					X																	66765032		2203	4300	6503	66681757	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.44C>T	X.37:g.66765032C>T	ENSP00000363822:p.Pro15Leu		66681757	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	c	18.07	3.542759	0.65198	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	D;D;D	0.96136	-3.92;-3.92;-3.92	5.34	4.45	0.53987	.	0.151076	0.45606	D	0.000351	D	0.92463	0.7607	N	0.24115	0.695	0.44241	D	0.997087	D;D	0.58970	0.973;0.984	P;P	0.49597	0.616;0.616	D	0.92118	0.5701	10	0.72032	D	0.01	.	10.1568	0.42827	0.2116:0.7884:0.0:0.0	.	15;15	E7EVX6;D3YPQ2	.;.	L	15	ENSP00000363822:P15L;ENSP00000421155:P15L;ENSP00000379359:P15L	ENSP00000363822:P15L	P	+	2	0	AR	66681757	0.107000	0.21998	0.915000	0.36163	0.966000	0.64601	0.861000	0.27885	1.148000	0.42385	0.597000	0.82753	CCG		0.617	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765032	C	T	66765032	3	4	111	1	0	0	0	0	1	0	0	0	836	652	23	1	46	1	AR	23	66765032	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	2020985	66765032	88505528	1072	30206										
IL2RG	3561	hgsc.bcm.edu	37	chrX	70327614	70327614	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caggctttagggtgtaacatGggggggcccagtaggggcta							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:70327614delG	ENST00000374202.2	-	8	1173	c.1082delC	c.(1081-1083)ccafs	p.P361fs	CXorf65_ENST00000374251.5_5'Flank|IL2RG_ENST00000374188.3_Frame_Shift_Del_p.P90fs|IL2RG_ENST00000456850.2_Frame_Shift_Del_p.P171fs	NM_000206.2	NP_000197.1	P31785	IL2RG_HUMAN	interleukin 2 receptor, gamma	361					immune response (GO:0006955)|interleukin-2-mediated signaling pathway (GO:0038110)|interleukin-4-mediated signaling pathway (GO:0035771)|interleukin-7-mediated signaling pathway (GO:0038111)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|interleukin-2 binding (GO:0019976)			breast(1)|endometrium(3)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	15	Renal(35;0.156)				Aldesleukin(DB00041)|Denileukin diftitox(DB00004)	GGTGTAACATGGGGGGGCCCA	0.582									Severe Combined Immunodeficiency, X-linked																																							0			X											34	34	34					X																	70327614		2203	4293	6496	70244339	SO:0001589	frameshift_variant	3561	Familial Cancer Database	Agammaglobulinemia, Swiss Type	D11086	CCDS14406.1	Xq13	2014-09-17	2010-06-24		ENSG00000147168	ENSG00000147168		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6010	protein-coding gene	gene with protein product		308380	"severe combined immunodeficiency", "combined immunodeficiency, X-linked"	SCIDX1, IMD4, CIDX		1631559, 7883965	Standard	NM_000206		Approved	CD132	uc004dyw.2	P31785	OTTHUMG00000021787	ENST00000374202.2:c.1082delC	X.37:g.70327614delG	ENSP00000363318:p.Pro361fs		70244339	Q5FC12	Frame_Shift_Del	DEL	ENST00000374202.2	37	CCDS14406.1																																																																																				0.582	IL2RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057102.2			-	70327614	G	-	70327614	7	5	111	1	0	1	0	1	0	0	0	0	7709	1348	47	0	31	0	IL2RG	23	70327614	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	3562582	70327614	84942946	1073	30207										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71358928	71358928	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gactcaggcaccacagatgtGgactatgatgaggagcagaa	13	8	1	4			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:71358928G>T	ENST00000373677.1	+	2	1694	c.432G>T	c.(430-432)gtG>gtT	p.V144V	NHSL2_ENST00000540800.1_Silent_p.V510V|NHSL2_ENST00000535692.1_Silent_p.V144V|NHSL2_ENST00000510661.1_Silent_p.V279V			Q5HYW2	NHSL2_HUMAN	NHS-like 2	144										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCACAGATGTGGACTATGATG	0.597																																																0			X											29	20	23					X																	71358928		2172	4211	6383	71275653	SO:0001819	synonymous_variant	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.432G>T	X.37:g.71358928G>T			71275653	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																					0.597	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		T	71358928	G	T	71358928	2	4	111	1	0	0	0	0	0	0	0	1	10443	1335	47	2		2	NHSL2	23	71358928	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	1031314	71358928	83911632	1074	30208										
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71427620	71427620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gcttgactttttcttctgtaCgtcttctttagtcctcctga	6	11	4	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:71427620C>T	ENST00000334463.3	-	2	1132	c.997G>A	c.(997-999)Gta>Ata	p.V333I	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Missense_Mutation_p.V210I	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	333					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					TTCTTCTGTACGTCTTCTTTA	0.393																																																0			X											145	141	142					X																	71427620		2200	4299	6499	71344345	SO:0001583	missense	54821			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.997G>A	X.37:g.71427620C>T	ENSP00000334675:p.Val333Ile		71344345	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.357973	0.24598	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	D;D	0.94457	-3.43;-3.43	5.79	4.92	0.64577	SNF2-related (1);	.	.	.	.	D	0.92182	0.7521	M	0.67953	2.075	0.47778	D	0.999515	B	0.30824	0.296	B	0.23852	0.049	D	0.89471	0.3743	9	0.34782	T	0.22	-7.5099	12.912	0.58184	0.1633:0.8367:0.0:0.0	.	333	Q2NKX8	ERC6L_HUMAN	I	210;333	ENSP00000362761:V210I;ENSP00000334675:V333I	ENSP00000334675:V333I	V	-	1	0	ERCC6L	71344345	0.953000	0.32496	1.000000	0.80357	0.779000	0.44077	2.095000	0.41729	1.190000	0.43042	-0.237000	0.12165	GTA		0.393	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71427620	C	T	71427620	3	4	111	1	0	0	0	0	1	0	0	0	5231	536	19	1	2759	1	ERCC6L	23	71427620	Missense_Mutation	SNP	C	TCGA-EI-6507-01A-11D-1733-10	68692	71427620	83842940	1075	30209										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86877231	86877231	+	Frame_Shift_Del	DEL	A	A	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaacacttcattgaggtaatAaaaaaccaagaattcctcct							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:86877231delA	ENST00000373119.4	+	5	1090	c.945delA	c.(943-945)atafs	p.I315fs	KLHL4_ENST00000373114.4_Frame_Shift_Del_p.I315fs	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	315						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						TTGAGGTAATAAAAAACCAAG	0.333																																																0			X											65	57	60					X																	86877231		2203	4300	6503	86763887	SO:0001589	frameshift_variant	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.945delA	X.37:g.86877231delA	ENSP00000362211:p.Ile315fs		86763887	B2RTW2|Q9Y3J5	Frame_Shift_Del	DEL	ENST00000373119.4	37	CCDS14457.1																																																																																				0.333	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			-	86877231	A	-	86877231	7	5	111	1	0	1	0	1	0	0	0	0	8412	352	13	0	963	0	KLHL4	23	86877231	Frame_Shift_Del	DEL	A	TCGA-EI-6507-01A-11D-1733-10	15449611	86877231	68393329	1076	30210										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99662505	99662505	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ccaaggcgatcacgtagcccGggggggcgctctcgctgacc							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:99662505delG	ENST00000373034.4	-	1	2766	c.1091delC	c.(1090-1092)ccgfs	p.P364fs	PCDH19_ENST00000255531.7_Frame_Shift_Del_p.P364fs|PCDH19_ENST00000420881.2_Frame_Shift_Del_p.P364fs	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	364	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P364fs*4(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CACGTAGCCCGGGGGGGCGCT	0.607																																																1	Deletion - Frameshift(1)	large_intestine(1)	X											43	47	46					X																	99662505		2188	4265	6453	99549161	SO:0001589	frameshift_variant	57575			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1091delC	X.37:g.99662505delG	ENSP00000362125:p.Pro364fs		99549161	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Frame_Shift_Del	DEL	ENST00000373034.4	37	CCDS55462.1																																																																																				0.607	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		-	99662505	G	-	99662505	7	5	111	1	0	1	0	1	0	0	0	0	11545	1116	39	0	2379	0	PCDH19	23	99662505	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	12785274	99662505	55608055	1077	30211										
GLA	2717	hgsc.bcm.edu	37	chrX	100656741	100656741	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	aaactcccagggaagcctgcGcaggttttatttccaacatc	8	12	0	0			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:100656741G>A	ENST00000218516.3	-	3	447	c.426C>T	c.(424-426)tgC>tgT	p.C142C	RPL36A-HNRNPH2_ENST00000409170.3_Intron|GLA_ENST00000479445.1_5'UTR	NM_000169.2	NP_000160.1	P06280	AGAL_HUMAN	galactosidase, alpha	142			C -> R (in FD). {ECO:0000269|PubMed:10666480}.|C -> Y (in FD). {ECO:0000269|PubMed:7759078, ECO:0000269|PubMed:9105656}.		glycoside catabolic process (GO:0016139)|glycosphingolipid catabolic process (GO:0046479)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|oligosaccharide metabolic process (GO:0009311)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|catalytic activity (GO:0003824)|galactoside binding (GO:0016936)|hydrolase activity (GO:0016787)|protein homodimerization activity (GO:0042803)|raffinose alpha-galactosidase activity (GO:0052692)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GGAAGCCTGCGCAGGTTTTAT	0.448																																					Colon(193;776 2816 31189 44474)											0			X	GRCh37	CM051522|CM993654	GLA	M							144	133	137					X																	100656741		2203	4300	6503	100543397	SO:0001819	synonymous_variant	9027			X16889	CCDS14484.1	Xq21.3-q22	2014-09-17			ENSG00000102393	ENSG00000102393	3.2.1.22		4296	protein-coding gene	gene with protein product		300644					Standard	NM_000169		Approved	GALA	uc004ehl.1	P06280	OTTHUMG00000022026	ENST00000218516.3:c.426C>T	X.37:g.100656741G>A			100543397	Q6LER7	Silent	SNP	ENST00000218516.3	37	CCDS14484.1																																																																																				0.448	GLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057540.1			A	100656741	G	A	100656741	2	1	111	1	0	0	0	0	0	0	0	1	6446	1079	38	1		1	GLA	23	100656741	Silent	SNP	G	TCGA-EI-6507-01A-11D-1733-10	994236	100656741	54613819	1078	30212										
NXF3	56000	hgsc.bcm.edu	37	chrX	102337991	102337991	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gggagacatcacactgttggTtcatggccagctgcagagtt	13	9	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:102337991T>C	ENST00000395065.3	-	7	733	c.632A>G	c.(631-633)aAc>aGc	p.N211S	NXF3_ENST00000425463.2_Missense_Mutation_p.N122S|NXF3_ENST00000425644.1_5'UTR	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	211					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						ACACTGTTGGTTCATGGCCAG	0.502																																																0			X											194	186	189					X																	102337991		2203	4300	6503	102224647	SO:0001583	missense	56000			AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.632A>G	X.37:g.102337991T>C	ENSP00000378504:p.Asn211Ser		102224647	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	37	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	T	2.552	-0.303915	0.05495	.	.	ENSG00000147206	ENST00000395065;ENST00000425463	T;T	0.55588	0.51;0.51	3.64	3.64	0.41730	.	0.770328	0.12805	N	0.437710	T	0.24890	0.0604	N	0.13003	0.285	0.09310	N	1	P;P;B	0.41188	0.741;0.73;0.057	B;B;B	0.32533	0.147;0.135;0.034	T	0.12630	-1.0540	10	0.02654	T	1	0.0309	7.8687	0.29552	0.0:0.0:0.0:1.0	.	211;107;211	B4DYI1;E9PEY7;Q9H4D5	.;.;NXF3_HUMAN	S	211;122	ENSP00000378504:N211S;ENSP00000404347:N122S	ENSP00000378504:N211S	N	-	2	0	NXF3	102224647	0.050000	0.20438	0.002000	0.10522	0.004000	0.04260	0.411000	0.21115	1.672000	0.50884	0.486000	0.48141	AAC		0.502	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		C	102337991	T	C	102337991	3	2	111	1	0	0	0	0	1	0	0	0	10816	1725	60	4	1015	4	NXF3	23	102337991	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	1681250	102337991	52932569	1079	30213										
CXorf57	55086	hgsc.bcm.edu	37	chrX	105855767	105855767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	ggatcctgtgcatagataacGtccactgtggggagacttca	12	9	1	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:105855767G>A	ENST00000372548.4	+	1	566	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	CXorf57_ENST00000372544.2_Missense_Mutation_p.V153I	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	153							poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						CATAGATAACGTCCACTGTGG	0.438																																																0			X											108	115	113					X																	105855767		2203	4300	6503	105742423	SO:0001583	missense	55086			AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.457G>A	X.37:g.105855767G>A	ENSP00000361628:p.Val153Ile		105742423	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	G	8.071	0.770216	0.15983	.	.	ENSG00000147231	ENST00000372544;ENST00000372548	T;T	0.47177	0.86;0.85	4.0	-0.269	0.12930	Nucleic acid-binding, OB-fold-like (1);	0.606472	0.15830	N	0.242559	T	0.29256	0.0728	L	0.46157	1.445	0.24101	N	0.99587	B;B;B	0.34181	0.354;0.354;0.44	B;B;B	0.23275	0.045;0.045;0.025	T	0.10314	-1.0635	10	0.25106	T	0.35	-1.9872	5.1869	0.15189	0.2321:0.463:0.3049:0.0	.	153;153;153	A8K6R5;Q6NSI4;Q6NSI4-2	.;CX057_HUMAN;.	I	153	ENSP00000361623:V153I;ENSP00000361628:V153I	ENSP00000361623:V153I	V	+	1	0	CXorf57	105742423	0.008000	0.16893	0.394000	0.26270	0.957000	0.61999	-0.149000	0.10204	0.000000	0.14550	0.600000	0.82982	GTC		0.438	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015		A	105855767	G	A	105855767	3	1	111	1	0	0	0	0	1	0	0	0	4119	1145	40	1	459	1	CXorf57	23	105855767	Missense_Mutation	SNP	G	TCGA-EI-6507-01A-11D-1733-10	3517776	105855767	49414793	1080	30214										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118220567	118220567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tcagatttgggcctgctctgTtgcttatctgcaacgtaaga	10	9	3	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:118220567T>C	ENST00000402510.2	-	11	4625	c.4626A>G	c.(4624-4626)caA>caG	p.Q1542Q		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1542										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						GCCTGCTCTGTTGCTTATCTG	0.498																																																0			X											94	86	89					X																	118220567		1920	4107	6027	118104595	SO:0001819	synonymous_variant	57481			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4626A>G	X.37:g.118220567T>C			118104595	B7ZCI8|Q5JPN4	Silent	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	T	5.685	0.311039	0.10733	.	.	ENSG00000248857	ENST00000440399	.	.	.	4.95	1.04	0.20106	.	.	.	.	.	T	0.23133	0.0559	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23655	-1.0182	4	.	.	.	.	2.9139	0.05746	0.1873:0.2314:0.0:0.5813	.	.	.	.	A	949	.	.	T	-	1	0	KIAA1210	118104595	0.000000	0.05858	0.001000	0.08648	0.298000	0.27526	0.103000	0.15292	-0.022000	0.13986	0.412000	0.27726	ACA		0.498	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		C	118220567	T	C	118220567	2	2	111	1	0	0	0	0	0	0	0	1	8235	1722	60	4		4	KIAA1210	23	118220567	Silent	SNP	T	TCGA-EI-6507-01A-11D-1733-10	12364800	118220567	37049993	1081	30215										
SLC25A5	292	hgsc.bcm.edu	37	chrX	118603756	118603756	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggccaatgtcatcagatacTtccccacccaggctcttaac	6	15	3	1			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:118603756T>A	ENST00000317881.8	+	2	360	c.244T>A	c.(244-246)Ttc>Atc	p.F82I	SLC25A5-AS1_ENST00000446986.1_RNA|SLC25A5_ENST00000460013.1_3'UTR	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	82					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	CATCAGATACTTCCCCACCCA	0.493																																																0			X											122	118	120					X																	118603756		2203	4300	6503	118487784	SO:0001583	missense	292			BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.244T>A	X.37:g.118603756T>A	ENSP00000360671:p.Phe82Ile		118487784	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	37	CCDS14578.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.146439	0.77888	.	.	ENSG00000005022	ENST00000317881	T	0.78003	-1.14	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.81791	0.4897	M	0.83483	2.645	0.80722	D	1	P	0.47302	0.893	P	0.46718	0.525	D	0.84987	0.0892	10	0.87932	D	0	.	12.1849	0.54231	0.0:0.0:0.0:1.0	.	82	P05141	ADT2_HUMAN	I	82	ENSP00000360671:F82I	ENSP00000360671:F82I	F	+	1	0	SLC25A5	118487784	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.562000	0.82300	1.622000	0.50330	0.430000	0.28490	TTC		0.493	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		A	118603756	T	A	118603756	3	1	111	1	0	0	0	0	1	0	0	0	14549	1609	56	5	250	5	SLC25A5	23	118603756	Missense_Mutation	SNP	T	TCGA-EI-6507-01A-11D-1733-10	383189	118603756	36666804	1082	30216										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123870951	123870951	+	Frame_Shift_Del	DEL	G	G	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tctgaagagagtccgctgcaGggggtggcttcctggcacag							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:123870951delG	ENST00000371130.3	-	4	695	c.632delC	c.(631-633)cctfs	p.P211fs	TENM1_ENST00000422452.2_Frame_Shift_Del_p.P211fs	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	211	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTCCGCTGCAGGGGGTGGCTT	0.622																																																0			X											75	75	75					X																	123870951		2203	4300	6503	123698632	SO:0001589	frameshift_variant	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.632delC	X.37:g.123870951delG	ENSP00000360171:p.Pro211fs		123698632	B2RTR5|Q5JZ17	Frame_Shift_Del	DEL	ENST00000371130.3	37	CCDS14609.1																																																																																				0.622	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		-	123870951	G	-	123870951	7	5	111	1	0	1	0	1	0	0	0	0	10865	1000	35	0	7682	0	ODZ1	23	123870951	Frame_Shift_Del	DEL	G	TCGA-EI-6507-01A-11D-1733-10	5267195	123870951	31399609	1083	30217										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129190011	129190011	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	tggaggcttggacgacagatCccccccaggctcctctgaga							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:129190011delC	ENST00000218147.7	+	13	5233	c.5036delC	c.(5035-5037)tccfs	p.S1679fs	BCORL1_ENST00000359304.2_Frame_Shift_Del_p.S1549fs|BCORL1_ENST00000540052.1_Frame_Shift_Del_p.S1679fs|BCORL1_ENST00000303743.5_Frame_Shift_Del_p.S1753fs			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1679					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						GACGACAGATCCCCCCCAGGC	0.602																																																0			X																																								129017692	SO:0001589	frameshift_variant	63035			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.5036delC	X.37:g.129190011delC	ENSP00000218147:p.Ser1679fs		129017692	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Frame_Shift_Del	DEL	ENST00000218147.7	37	CCDS14616.1																																																																																				0.602	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		-	129190011	C	-	129190011	7	5	111	1	0	1	0	1	0	0	0	0	1388	855	30	0	5308	0	BCORL1	23	129190011	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	5319060	129190011	26080549	1084	30218										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904118	144904118	+	Frame_Shift_Del	DEL	C	C	-													0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	caacagttagcctgctccagCccccccagtatcgaatctat							TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:144904118delC	ENST00000370490.1	+	1	4430	c.175delC	c.(175-177)cccfs	p.P60fs	SLITRK2_ENST00000428560.2_Frame_Shift_Del_p.P60fs|SLITRK2_ENST00000434188.2_Frame_Shift_Del_p.P60fs|SLITRK2_ENST00000413937.2_Frame_Shift_Del_p.P60fs|SLITRK2_ENST00000447897.2_Frame_Shift_Del_p.P60fs			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	60					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CCTGCTCCAGCCCCCCCAGTA	0.428																																																0			X											94	84	87					X																	144904118		2203	4300	6503	144711810	SO:0001589	frameshift_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.175delC	X.37:g.144904118delC	ENSP00000359521:p.Pro60fs		144711810	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Frame_Shift_Del	DEL	ENST00000370490.1	37	CCDS14680.1																																																																																				0.428	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		-	144904118	C	-	144904118	7	5	111	1	0	1	0	1	0	0	0	0	14780	739	26	0	177	0	SLITRK2	23	144904118	Frame_Shift_Del	DEL	C	TCGA-EI-6507-01A-11D-1733-10	15714107	144904118	10366442	1085	30219										
MAGEA1	4100	hgsc.bcm.edu	37	chrX	152482569	152482569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0138121546961326	15	1	0.211731849054066	0.953577512776831	0.200585586994793	0.000183147697995668	0.0044688038310943	0	gaccagctgcaaggactcagAggctttgccgaagatctcag	12	11	2	2			TCGA-EI-6507-01A-11D-1733-10	TCGA-EI-6507-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	90b4f72f-2958-456b-8332-da30e09c110e	d8763e98-bd73-4505-83eb-9cb436a5a791	g.chrX:152482569A>G	ENST00000356661.5	-	3	660	c.442T>C	c.(442-444)Tct>Cct	p.S148P		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	148	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AAGGACTCAGAGGCTTTGCCG	0.512																																																0			X											134	129	131					X																	152482569		2203	4300	6503	152135763	SO:0001583	missense	4100				CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"melanoma-associated antigen 1", "melanoma-associated antigen MZ2-E", "melanoma antigen MAGE-1", "melanoma antigen family A 1", "cancer/testis antigen family 1, member 1"	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.442T>C	X.37:g.152482569A>G	ENSP00000349085:p.Ser148Pro		152135763	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	37	CCDS14720.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.777632	0.31502	.	.	ENSG00000198681	ENST00000356661	T	0.05717	3.4	1.28	1.28	0.21552	.	1.473130	0.03614	N	0.235249	T	0.15696	0.0378	M	0.89534	3.04	0.09310	N	1	P	0.34522	0.455	B	0.36922	0.236	T	0.37526	-0.9702	10	0.87932	D	0	.	4.336	0.11087	1.0:0.0:0.0:0.0	.	148	P43355	MAGA1_HUMAN	P	148	ENSP00000349085:S148P	ENSP00000349085:S148P	S	-	1	0	MAGEA1	152135763	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.282000	0.18829	0.758000	0.33059	0.158000	0.16466	TCT		0.512	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988		G	152482569	A	G	152482569	3	3	111	1	0	0	0	0	1	0	0	0	9193	304	11	4	491	4	MAGEA1	23	152482569	Missense_Mutation	SNP	A	TCGA-EI-6507-01A-11D-1733-10	7578451	152482569	2787991	1086	30220										
SPEN	23013	hgsc.bcm.edu	37	chr1	16257197	16257197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaaaggttgactctgctccaAgacctattccatcctggtac	7	12	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:16257197A>G	ENST00000375759.3	+	11	4666	c.4462A>G	c.(4462-4464)Aga>Gga	p.R1488G		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1488			R -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		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)		CTCTGCTCCAAGACCTATTCC	0.373																																																0			1											59	64	62					1																	16257197		2202	4300	6502	16129784	SO:0001583	missense	64783				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4462A>G	1.37:g.16257197A>G	ENSP00000364912:p.Arg1488Gly		16129784	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670413	0.29693	.	.	ENSG00000065526	ENST00000375759	T	0.17691	2.26	5.27	4.11	0.48088	.	.	.	.	.	T	0.27765	0.0683	L	0.34521	1.04	0.54753	D	0.999981	D	0.89917	1.0	D	0.66716	0.946	T	0.01121	-1.1445	9	0.46703	T	0.11	-20.8008	12.239	0.54532	0.8577:0.1423:0.0:0.0	.	1488	Q96T58	MINT_HUMAN	G	1488	ENSP00000364912:R1488G	ENSP00000364912:R1488G	R	+	1	2	SPEN	16129784	0.998000	0.40836	0.997000	0.53966	0.996000	0.88848	3.323000	0.52014	0.976000	0.38417	0.460000	0.39030	AGA		0.373	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16257197	A	G	16257197	3	3	112	1	0	0	0	0	1	0	0	0	15077	64	3	4	4504	4	SPEN	1	16257197	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10		16257197	232993424	1	30221										
CSF3R	1441	hgsc.bcm.edu	37	chr1	36937230	36937230	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccttggatccgtccgctgtcTtcctccaggggcactggctg	12	15	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:36937230T>C	ENST00000373106.1	-	10	1636	c.1089A>G	c.(1087-1089)gaA>gaG	p.E363E	CSF3R_ENST00000361632.4_Silent_p.E363E|CSF3R_ENST00000373104.1_Silent_p.E363E|CSF3R_ENST00000373103.1_Silent_p.E363E|CSF3R_ENST00000331941.5_Silent_p.E363E|CSF3R_ENST00000440588.2_Silent_p.E363E|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000418048.2_Silent_p.E363E|CSF3R_ENST00000338937.5_Silent_p.E363E	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	363	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.E363D(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GTCCGCTGTCTTCCTCCAGGG	0.592																																																1	Substitution - Missense(1)	ovary(1)	1											69	70	70					1																	36937230		2203	4300	6503	36709817	SO:0001819	synonymous_variant	1441			M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"CD molecules", "Fibronectin type III domain containing"	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1089A>G	1.37:g.36937230T>C			36709817		Silent	SNP	ENST00000373106.1	37	CCDS413.1																																																																																				0.592	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		C	36937230	T	C	36937230	2	2	112	1	0	0	0	0	0	0	0	1	3943	1606	56	4		4	CSF3R	1	36937230	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	20680033	36937230	212313391	2	30222										
TESK2	10420	hgsc.bcm.edu	37	chr1	45812692	45812692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cggatcggcctggatgcgggCgatgatctcgcagaggatga	17	9	1	3	rs374778347		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:45812692C>T	ENST00000372086.3	-	8	1151	c.751G>A	c.(751-753)Gcc>Acc	p.A251T	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.A251T|TESK2_ENST00000538496.1_Missense_Mutation_p.A168T|TESK2_ENST00000341771.6_Missense_Mutation_p.A251T	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					TGGATGCGGGCGATGATCTCG	0.537																																																0			1						C	THR/ALA	0,4038		0,0,2019	104	108	107		751	6	1	1		107	1,8343		0,1,4171	no	missense	TESK2	NM_007170.2	58	0,1,6190	TT,TC,CC		0.012,0.0,0.0081	probably-damaging	251/572	45812692	1,12381	2019	4172	6191	45585279	SO:0001583	missense	10420			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.751G>A	1.37:g.45812692C>T	ENSP00000361158:p.Ala251Thr		45585279	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	37	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	C	34	5.326504	0.95708	0.0	1.2E-4	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	D;T;D;T	0.86865	-2.18;0.35;-2.18;0.35	5.96	5.96	0.96718	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.180825	0.39341	N	0.001386	D	0.84488	0.5483	N	0.02275	-0.615	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72982	0.947;0.979	D	0.84395	0.0557	10	0.19590	T	0.45	-6.1614	20.4123	0.99019	0.0:1.0:0.0:0.0	.	251;251	Q96S53-3;Q96S53	.;TESK2_HUMAN	T	251;251;235;251;168	ENSP00000361156:A251T;ENSP00000361158:A251T;ENSP00000343940:A251T;ENSP00000441746:A168T	ENSP00000343940:A251T	A	-	1	0	TESK2	45585279	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.071000	0.71229	2.824000	0.97209	0.655000	0.94253	GCC		0.537	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		T	45812692	C	T	45812692	3	4	112	1	0	0	0	0	1	0	0	0	15807	768	27	1	980	1	TESK2	1	45812692	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	8875462	45812692	203437929	3	30223										
LRP8	7804	hgsc.bcm.edu	37	chr1	53727865	53727865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggagtctacccagtacaagcGctggctcagcagatcttggg	13	11	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:53727865G>A	ENST00000306052.6	-	12	1890	c.1789C>T	c.(1789-1791)Cgc>Tgc	p.R597C	LRP8_ENST00000465675.1_Missense_Mutation_p.R150C|LRP8_ENST00000371454.2_Missense_Mutation_p.R597C|LRP8_ENST00000347547.2_Missense_Mutation_p.R427C|LRP8_ENST00000354412.3_Missense_Mutation_p.R468C|LRP8_ENST00000460214.1_5'UTR	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	597					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						CAGTACAAGCGCTGGCTCAGC	0.537																																																0			1											104	103	104					1																	53727865		2203	4300	6503	53500453	SO:0001583	missense	7804			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.1789C>T	1.37:g.53727865G>A	ENSP00000303634:p.Arg597Cys		53500453	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318778	0.95682	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	D;D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16;-4.16	6.16	6.16	0.99307	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	.	.	.	.	D	0.98770	0.9586	M	0.93978	3.48	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;1.0;0.99	D	0.98886	1.0771	9	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	150;468;427;597;597;150	B3KU40;Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;.;LRP8_HUMAN;.	C	597;597;150;468;427	ENSP00000303634:R597C;ENSP00000360509:R597C;ENSP00000437009:R150C;ENSP00000346391:R468C;ENSP00000334522:R427C	ENSP00000303634:R597C	R	-	1	0	LRP8	53500453	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	CGC		0.537	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		A	53727865	G	A	53727865	3	1	112	1	0	0	0	0	1	0	0	0	8992	1087	38	1	1134	1	LRP8	1	53727865	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	7915173	53727865	195522756	4	30224										
ZZZ3	26009	hgsc.bcm.edu	37	chr1	78097673	78097673	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tattgagtcttgcctctgagGgtggtttacttactccttca	9	9	3	2	rs201029873		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:78097673G>T	ENST00000370801.3	-	5	1842	c.1367C>A	c.(1366-1368)cCc>cAc	p.P456H	ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	456			P -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						TGCCTCTGAGGGTGGTTTACT	0.393																																																0			1											181	166	171					1																	78097673		2203	4300	6503	77870261	SO:0001583	missense	26009			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"Zinc fingers, ZZ-type"	24523	protein-coding gene	gene with protein product	"ATAC component 1 homolog (Drosophila)"					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.1367C>A	1.37:g.78097673G>T	ENSP00000359837:p.Pro456His		77870261	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	37	CCDS677.1	.	.	.	.	.	.	.	.	.	.	G	3.684	-0.064909	0.07273	.	.	ENSG00000036549	ENST00000370801	.	.	.	5.74	5.74	0.90152	.	0.378995	0.30483	N	0.009523	T	0.41789	0.1174	L	0.43152	1.355	0.80722	D	1	P;B;B	0.52842	0.956;0.145;0.226	P;B;B	0.52267	0.694;0.189;0.348	T	0.34576	-0.9823	8	.	.	.	.	8.9209	0.35610	0.0794:0.0:0.7707:0.1499	.	456;456;456	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	H	456	.	.	P	-	2	0	ZZZ3	77870261	1.000000	0.71417	0.681000	0.30009	0.182000	0.23217	2.836000	0.48183	2.884000	0.98904	0.655000	0.94253	CCC		0.393	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		T	78097673	G	T	78097673	3	4	112	1	0	0	0	0	1	0	0	0	18295	1232	43	2	1388	2	ZZZ3	1	78097673	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	24369808	78097673	171152948	5	30225										
CDC14A	8556	hgsc.bcm.edu	37	chr1	100964777	100964777	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tccgaccctcctacaccgggCtttcttcttcttcagcgaga	7	16	4	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:100964777C>A	ENST00000336454.3	+	15	2069	c.1714C>A	c.(1714-1716)Ctt>Att	p.L572I	CDC14A_ENST00000544534.1_Missense_Mutation_p.L572I|CDC14A_ENST00000542213.1_Missense_Mutation_p.L514I|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000361544.6_Missense_Mutation_p.L572I	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	572					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		CTACACCGGGCTTTCTTCTTC	0.587																																																0			1											98	106	103					1																	100964777		2203	4300	6503	100737365	SO:0001583	missense	8556			AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.1714C>A	1.37:g.100964777C>A	ENSP00000336739:p.Leu572Ile		100737365	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	37	CCDS769.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103076	0.76983	.	.	ENSG00000079335	ENST00000542213;ENST00000361544;ENST00000336454;ENST00000544534	T;T;T;T	0.13089	2.71;2.8;3.02;2.62	5.66	5.66	0.87406	.	0.082541	0.51477	D	0.000081	T	0.22003	0.0530	L	0.32530	0.975	0.43936	D	0.996594	D;D;D;D	0.71674	0.998;0.997;0.997;0.998	D;D;D;D	0.83275	0.996;0.978;0.978;0.996	T	0.01162	-1.1432	10	0.52906	T	0.07	-6.0E-4	20.1253	0.97977	0.0:1.0:0.0:0.0	.	514;572;572;572	F5H7B3;A6MA65;Q9UNH5;Q9UNH5-2	.;.;CC14A_HUMAN;.	I	514;572;572;572	ENSP00000442640:L514I;ENSP00000354916:L572I;ENSP00000336739:L572I;ENSP00000442543:L572I	ENSP00000336739:L572I	L	+	1	0	CDC14A	100737365	0.996000	0.38824	0.991000	0.47740	0.914000	0.54420	2.322000	0.43814	2.832000	0.97577	0.655000	0.94253	CTT		0.587	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		A	100964777	C	A	100964777	3	1	112	1	0	0	0	0	1	0	0	0	3062	797	28	2	1787	2	CDC14A	1	100964777	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	22867104	100964777	148285844	6	30226										
IVL	3713	hgsc.bcm.edu	37	chr1	152882800	152882800	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggagggacagctgaagcaccCggagcagcaggaggggcagc	19	10	0	1	rs541736259		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:152882800C>A	ENST00000368764.3	+	2	591	c.527C>A	c.(526-528)cCg>cAg	p.P176Q	IVL_ENST00000392667.2_Missense_Mutation_p.P30Q			P07476	INVO_HUMAN	involucrin	176	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ctgaagcacccggagcagcag	0.642																																																0			1											19	21	20					1																	152882800		2203	4299	6502	151149424	SO:0001583	missense	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.527C>A	1.37:g.152882800C>A	ENSP00000357753:p.Pro176Gln		151149424	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	2.428	-0.331443	0.05314	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11712	2.99;2.75	2.13	-4.25	0.03766	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.21309	0.054	B	0.20384	0.029	T	0.48068	-0.9067	9	0.11485	T	0.65	.	5.3469	0.16014	0.3244:0.5011:0.1746:0.0	.	176	P07476	INVO_HUMAN	Q	176;30	ENSP00000357753:P176Q;ENSP00000376435:P30Q	ENSP00000357753:P176Q	P	+	2	0	IVL	151149424	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.509000	0.02264	-0.815000	0.04346	0.436000	0.28706	CCG		0.642	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152882800	C	A	152882800	3	1	112	1	0	0	0	0	1	0	0	0	7950	652	23	2	529	2	IVL	1	152882800	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	51918023	152882800	96367821	7	30227										
KCNH1	3756	hgsc.bcm.edu	37	chr1	210948826	210948826	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aggtcaaggccctaacattgGcacaggactgggcaagggtg	15	9	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:210948826G>T	ENST00000271751.4	-	10	2003	c.1976C>A	c.(1975-1977)gCc>gAc	p.A659D	KCNH1_ENST00000367007.4_Missense_Mutation_p.A632D			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	659					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.A659D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		CCTAACATTGGCACAGGACTG	0.522																																																1	Substitution - Missense(1)	large_intestine(1)	1											150	118	129					1																	210948826		2203	4300	6503	209015449	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1976C>A	1.37:g.210948826G>T	ENSP00000271751:p.Ala659Asp		209015449	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722640	0.89298	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.94793	-3.52;-3.52	5.47	5.47	0.80525	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.98030	0.9351	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.98834	1.0752	10	0.87932	D	0	.	19.3371	0.94324	0.0:0.0:1.0:0.0	.	632;659	Q14CL3;O95259	.;KCNH1_HUMAN	D	659;632	ENSP00000271751:A659D;ENSP00000355974:A632D	ENSP00000271751:A659D	A	-	2	0	KCNH1	209015449	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.507000	0.97996	2.567000	0.86603	0.561000	0.74099	GCC		0.522	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210948826	G	T	210948826	3	4	112	1	0	0	0	0	1	0	0	0	8052	1203	42	2	1001	2	KCNH1	1	210948826	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	58066026	210948826	38301795	8	30228										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233507792	233507792	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgcctccaacagatttccagCacaagataaccgtgcaggcc	8	14	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:233507792C>G	ENST00000366624.3	+	6	1822	c.1561C>G	c.(1561-1563)Cac>Gac	p.H521D	MLK4_ENST00000366623.3_Missense_Mutation_p.H521D	NM_032435.2	NP_115811.2																					AGATTTCCAGCACAAGATAAC	0.483																																																0			1											88	89	89					1																	233507792		2203	4300	6503	231574415	SO:0001583	missense	84451																														ENST00000366624.3:c.1561C>G	1.37:g.233507792C>G	ENSP00000355583:p.His521Asp		231574415		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791272	0.90367	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.79033	-0.89;-1.23	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.88819	0.6540	M	0.80508	2.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.993	D	0.90043	0.4143	10	0.87932	D	0	.	18.7231	0.91703	0.0:1.0:0.0:0.0	.	521;521	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	D	521	ENSP00000355582:H521D;ENSP00000355583:H521D	ENSP00000355582:H521D	H	+	1	0	RP5-862P8.2	231574415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.635000	0.83286	2.654000	0.90174	0.650000	0.86243	CAC		0.483	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			G	233507792	C	G	233507792	3	3	112	1	0	0	0	0	1	0	0	0	8280	710	25	5	1583	5	KIAA1804	1	233507792	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	22558966	233507792	15742829	9	30229										
ADSS	159	hgsc.bcm.edu	37	chr1	244587358	244587358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aatgcccttttttgttgtacCcaaacttaaaaacaaatcca	3	10	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:244587358C>T	ENST00000366535.3	-	6	794	c.478G>A	c.(478-480)Ggt>Agt	p.G160S	ADSS_ENST00000462358.1_5'UTR	NM_001126.3	NP_001117.2			adenylosuccinate synthase											endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			TTTGTTGTACCCAAACTTAAA	0.408																																																0			1											47	46	46					1																	244587358		2203	4300	6503	242653981	SO:0001583	missense	159			BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.478G>A	1.37:g.244587358C>T	ENSP00000355493:p.Gly160Ser		242653981		Missense_Mutation	SNP	ENST00000366535.3	37	CCDS1624.1	.	.	.	.	.	.	.	.	.	.	C	35	5.443181	0.96187	.	.	ENSG00000035687	ENST00000366535;ENST00000449326	D	0.83837	-1.77	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.94703	0.8291	H	0.97896	4.1	0.80722	D	1	D	0.67145	0.996	D	0.69824	0.966	D	0.96805	0.9592	10	0.87932	D	0	-14.8099	18.5791	0.91165	0.0:1.0:0.0:0.0	.	160	P30520	PURA2_HUMAN	S	160;139	ENSP00000355493:G160S	ENSP00000355493:G160S	G	-	1	0	ADSS	242653981	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.625000	0.83145	2.393000	0.81446	0.467000	0.42956	GGT		0.408	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		T	244587358	C	T	244587358	3	4	112	1	0	0	0	0	1	0	0	0	347	623	22	3	924	3	ADSS	1	244587358	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	11079566	244587358	4663263	10	30230										
OR2M4	26245	hgsc.bcm.edu	37	chr1	248402332	248402332	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttttctctggtcctgggcatCttctcactggcattgatgga	10	10	3	1	rs375886519		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr1:248402332C>A	ENST00000306687.1	+	1	102	c.102C>A	c.(100-102)atC>atA	p.I34I		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	34					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I34I(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCCTGGGCATCTTCTCACTGG	0.483																																																1	Substitution - coding silent(1)	breast(1)	1											154	153	154					1																	248402332		2203	4300	6503	246468955	SO:0001819	synonymous_variant	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.102C>A	1.37:g.248402332C>A			246468955	Q15611|Q8NG82	Silent	SNP	ENST00000306687.1	37	CCDS31108.1																																																																																				0.483	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		A	248402332	C	A	248402332	2	1	112	1	0	0	0	0	0	0	0	1	11043	903	32	2		2	OR2M4	1	248402332	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	3814974	248402332	848289	11	30231										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37230722	37230722	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tcttgcaaataatcctgagcAgctcttactatctgttgtac	6	10	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:37230722A>G	ENST00000233099.5	-	31	5108	c.5013T>C	c.(5011-5013)gcT>gcC	p.A1671A	HEATR5B_ENST00000354531.2_Silent_p.A1671A	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1671						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AATCCTGAGCAGCTCTTACTA	0.358																																																0			2											86	86	86					2																	37230722		2203	4300	6503	37084226	SO:0001819	synonymous_variant	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5013T>C	2.37:g.37230722A>G			37084226	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																				0.358	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		G	37230722	A	G	37230722	2	3	112	1	0	0	0	0	0	0	0	1	7053	175	7	4		4	HEATR5B	2	37230722	Silent	SNP	A	TCGA-EI-6508-01A-11D-1733-10		37230722	205968651	12	30232										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39494357	39494357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acacttctggcaccatttggTttcagggatttttgctgata	9	8	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:39494357T>C	ENST00000263881.3	-	27	2329	c.2005A>G	c.(2005-2007)Acc>Gcc	p.T669A	MAP4K3_ENST00000341681.5_Missense_Mutation_p.T648A|MAP4K3_ENST00000536018.1_Missense_Mutation_p.T222A|MAP4K3_ENST00000437545.1_Missense_Mutation_p.T585A	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	669	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.		T -> S (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.T669S(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CACCATTTGGTTTCAGGGATT	0.353																																																1	Substitution - Missense(1)	lung(1)	2											127	128	128					2																	39494357		2203	4300	6503	39347861	SO:0001583	missense	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.2005A>G	2.37:g.39494357T>C	ENSP00000263881:p.Thr669Ala		39347861	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.708638	0.89018	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000536018	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	5.42	5.42	0.78866	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.98;0.999	T	0.12993	-1.0526	10	0.87932	D	0	.	15.7745	0.78204	0.0:0.0:0.0:1.0	.	648;669	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	A	669;585;648;222	ENSP00000263881:T669A;ENSP00000416958:T585A;ENSP00000345434:T648A;ENSP00000440580:T222A	ENSP00000263881:T669A	T	-	1	0	MAP4K3	39347861	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.565000	0.82337	2.174000	0.68829	0.533000	0.62120	ACC		0.353	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		C	39494357	T	C	39494357	3	2	112	1	0	0	0	0	1	0	0	0	9291	1725	60	4	711	4	MAP4K3	2	39494357	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	2263635	39494357	203705016	13	30233										
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98154654	98154654	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttccagatttcccaccgcccGttattcttgtggcaatattc	6	13	1	1	rs369666439	byFrequency	TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:98154654G>A								AC159540.1 (63605 upstream) : ANKRD36B (9373 downstream)																							CCCACCGCCCGTTATTCTTGT	0.348													.|||	3	0.000599042	8e-04	0	5008	,	,		13444	0.002		0	False		,,,				2504	0															0			2						A	MET/THR	2,3008		1,0,1504	35	24	28		2066	-1.1	0	2		28	0,5340		0,0,2670	no	missense	ANKRD36B	NM_025190.3	81	1,0,4174	AA,AG,GG		0.0,0.0664,0.024	benign	689/1354	98154654	2,8348	1505	2670	4175	97521086	SO:0001628	intergenic_variant	57730																															2.37:g.98154654G>A			97521086		Missense_Mutation	SNP		37																																																																																				0	0.348									A	98154654	G	A	98154654	1	1	112	0	1	0	0	0	0	0	0	0	666	1145	40	1		1	ANKRD36B	2	98154654	IGR	SNP	G	TCGA-EI-6508-01A-11D-1733-10	58660297	98154654	145044719	14	30234										
TTN	7273	hgsc.bcm.edu	37	chr2	179476363	179476363	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aatggcaatgtgttttctccCagcatcagtcacatgtaggt	9	9	3	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:179476363C>A	ENST00000591111.1	-	219	45894	c.45670G>T	c.(45670-45672)Ggg>Tgg	p.G15224W	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G14297W|TTN_ENST00000460472.2_Missense_Mutation_p.G7800W|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G16865W|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G7925W|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G7992W			Q8WZ42	TITIN_HUMAN	titin	15224	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G14297W(2)|p.G7992W(1)|p.G7925W(1)|p.G7800W(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTTTTCTCCCAGCATCAGTC	0.438																																																5	Substitution - Missense(5)	lung(5)	2											98	93	94					2																	179476363		1901	4128	6029	179184608	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45670G>T	2.37:g.179476363C>A	ENSP00000465570:p.Gly15224Trp		179184608	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	8.925	0.961963	0.18583	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	6.17	6.17	0.99709	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67841	0.2936	L	0.46947	1.48	0.35457	D	0.796172	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.71870	0.975;0.975;0.975;0.975	T	0.75139	-0.3423	9	0.87932	D	0	.	11.0573	0.47927	0.0:0.8635:0.0:0.1365	.	7800;7925;7992;15224	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	W	14297;7800;7992;7925;7800	ENSP00000343764:G14297W;ENSP00000434586:G7800W;ENSP00000340554:G7992W;ENSP00000352154:G7925W	ENSP00000340554:G7992W	G	-	1	0	TTN	179184608	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.831000	0.55776	2.941000	0.99782	0.655000	0.94253	GGG		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179476363	C	A	179476363	3	1	112	1	0	0	0	0	1	0	0	0	16775	594	21	2	57476	2	TTN	2	179476363	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	81321709	179476363	63723010	15	30235										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189868844	189868844	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggccaaccaggagagaaggGatcgcctggtgcccagggcc	16	12	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:189868844G>T	ENST00000304636.3	+	39	2968	c.2798G>T	c.(2797-2799)gGa>gTa	p.G933V	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	933	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GGAGAGAAGGGATCGCCTGGT	0.493																																																0			2											32	38	36					2																	189868844		2203	4300	6503	189577089	SO:0001583	missense	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2798G>T	2.37:g.189868844G>T	ENSP00000304408:p.Gly933Val		189577089	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966030	0.74131	.	.	ENSG00000168542	ENST00000304636	D	0.99637	-6.29	5.63	5.63	0.86233	.	0.000000	0.50627	D	0.000108	D	0.99661	0.9874	H	0.95982	3.75	0.80722	D	1	P	0.50528	0.936	P	0.52189	0.692	D	0.97988	1.0353	10	0.87932	D	0	.	19.6914	0.96002	0.0:0.0:1.0:0.0	.	933	P02461	CO3A1_HUMAN	V	933	ENSP00000304408:G933V	ENSP00000304408:G933V	G	+	2	0	COL3A1	189577089	1.000000	0.71417	0.973000	0.42090	0.610000	0.37248	9.750000	0.98875	2.659000	0.90383	0.643000	0.83706	GGA		0.493	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189868844	G	T	189868844	3	4	112	1	0	0	0	0	1	0	0	0	3694	1174	41	2	2952	2	COL3A1	2	189868844	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10392481	189868844	53330529	16	30236										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713689	218713689	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtgtgttccacgtggttgggGgtggccgacagtgtaggacg	19	7	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr2:218713689G>A	ENST00000171887.4	-	17	1628	c.1176C>T	c.(1174-1176)acC>acT	p.T392T	TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Silent_p.T392T|TNS1_ENST00000419504.1_Silent_p.T392T	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	392					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		CGTGGTTGGGGGTGGCCGACA	0.612																																																0			2											156	148	150					2																	218713689		2203	4300	6503	218421934	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1176C>T	2.37:g.218713689G>A			218421934	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218713689	G	A	218713689	2	1	112	1	0	0	0	0	0	0	0	1	16382	1219	43	3		3	TNS1	2	218713689	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	28844845	218713689	24485684	17	30237										
TTLL3	26140	hgsc.bcm.edu	37	chr3	9871013	9871013	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtgcaagctgacaccctgcgCgtggtcattgaccggatgct	13	12	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:9871013C>T	ENST00000547186.1	+	10	1704	c.1488C>T	c.(1486-1488)cgC>cgT	p.R496R	TTLL3_ENST00000397241.1_Silent_p.R284R|ARPC4-TTLL3_ENST00000397256.1_Silent_p.R557R|TTLL3_ENST00000383827.1_Silent_p.R284R|TTLL3_ENST00000426895.4_Silent_p.R639R|TTLL3_ENST00000455274.1_Silent_p.R284R|TTLL3_ENST00000430793.1_Silent_p.R284R|TTLL3_ENST00000427853.3_Silent_p.R284R|TTLL3_ENST00000466245.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	496	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)	p.R496R(2)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					ACACCCTGCGCGTGGTCATTG	0.617																																																2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	3											68	68	68					3																	9871013		2203	4300	6503	9846013	SO:0001819	synonymous_variant	26140				CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"Tubulin tyrosine ligase-like family"	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1488C>T	3.37:g.9871013C>T			9846013	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37		.	.	.	.	.	.	.	.	.	.	C	8.216	0.801441	0.16397	.	.	ENSG00000214021	ENST00000310252	T	0.19806	2.12	5.03	-10.1	0.00402	.	0.070909	0.53938	U	0.000044	T	0.27313	0.0670	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63791	-0.6557	7	0.56958	D	0.05	.	12.6263	0.56632	0.0771:0.1524:0.0:0.7705	.	.	.	.	C	452	ENSP00000312148:R452C	ENSP00000312148:R452C	R	+	1	0	TTLL3	9846013	0.000000	0.05858	0.440000	0.26846	0.776000	0.43924	-3.582000	0.00424	-2.490000	0.00517	-1.138000	0.01928	CGT		0.617	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		T	9871013	C	T	9871013	2	4	112	1	0	0	0	0	0	0	0	1	16768	755	27	1		1	TTLL3	3	9871013	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10		9871013	188151417	18	30238										
VHL	7428	hgsc.bcm.edu	37	chr3	10188250	10188250	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cacgatgggcttctggttaaCcaaactgaattatttgtgcc	9	9	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:10188250C>T	ENST00000256474.2	+	2	1233	c.393C>T	c.(391-393)aaC>aaT	p.N131N	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	131	Involved in binding to CCT complex.		N -> K (in VHLD; type I). {ECO:0000269|PubMed:9829912}.|N -> T (in VHLD; type I). {ECO:0000269|PubMed:9829911}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.N131fs*27(2)|p.N131K(2)|p.Q132fs*27(1)|p.N131fs*10(1)|p.H125fs*27(1)|p.N131*(1)|p.N131fs*7(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTCTGGTTAACCAAACTGAAT	0.453		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	9	Deletion - Frameshift(6)|Substitution - Missense(2)|Complex - frameshift(1)	kidney(9)	3	GRCh37	CM042502|CX073799	VHL	M|X							207	191	197					3																	10188250		2203	4300	6503	10163250	SO:0001819	synonymous_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.393C>T	3.37:g.10188250C>T			10163250	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.453	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		T	10188250	C	T	10188250	2	4	112	1	0	0	0	0	0	0	0	1	17202	506	18	3		3	VHL	3	10188250	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	317237	10188250	187834180	19	30239										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39227196	39227196	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acaaaggcattatgggggtgCgggctggcacctgcagcttg	16	9	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:39227196C>T	ENST00000340369.3	-	2	3969	c.3741G>A	c.(3739-3741)ccG>ccA	p.P1247P	XIRP1_ENST00000396251.1_Intron|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1247	Pro-rich.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TATGGGGGTGCGGGCTGGCAC	0.637																																																0			3											28	34	32					3																	39227196		2203	4299	6502	39202200	SO:0001819	synonymous_variant	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3741G>A	3.37:g.39227196C>T			39202200	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																				0.637	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39227196	C	T	39227196	2	4	112	1	0	0	0	0	0	0	0	1	17469	755	27	1		1	XIRP1	3	39227196	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	29038946	39227196	158795234	20	30240										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39229116	39229116	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acctctgacccctgcttttcGgccaactcactcattgggca	7	16	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:39229116G>A	ENST00000340369.3	-	2	2049	c.1821C>T	c.(1819-1821)gcC>gcT	p.A607A	XIRP1_ENST00000396251.1_Silent_p.A607A|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	607	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCTGCTTTTCGGCCAACTCAC	0.602																																																0			3											82	71	74					3																	39229116		2203	4300	6503	39204120	SO:0001819	synonymous_variant	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1821C>T	3.37:g.39229116G>A			39204120	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																				0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39229116	G	A	39229116	2	1	112	1	0	0	0	0	0	0	0	1	17469	1103	39	1		1	XIRP1	3	39229116	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	1920	39229116	158793314	21	30241										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50197135	50197135	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccccacccaggaccacctccCggccacgccccgggtccggc	10	24	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:50197135C>A	ENST00000002829.3	+	2	564	c.80C>A	c.(79-81)cCg>cAg	p.P27Q	SEMA3F_ENST00000413852.1_5'UTR|SEMA3F_ENST00000434342.1_Missense_Mutation_p.P27Q	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	27					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		GACCACCTCCCGGCCACGCCC	0.607																																																0			3											47	49	48					3																	50197135		2203	4300	6503	50172139	SO:0001583	missense	6405			U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.80C>A	3.37:g.50197135C>A	ENSP00000002829:p.Pro27Gln		50172139	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	37	CCDS2811.1	.	.	.	.	.	.	.	.	.	.	C	6.742	0.505635	0.12822	.	.	ENSG00000001617	ENST00000414301;ENST00000450338;ENST00000002829;ENST00000426511;ENST00000434342	T;T;T;T	0.50277	2.03;1.84;0.75;0.81	5.6	-1.68	0.08212	Semaphorin/CD100 antigen (1);	0.542636	0.18802	N	0.130764	T	0.15478	0.0373	N	0.14661	0.345	0.09310	N	0.999996	P;B	0.38582	0.638;0.01	B;B	0.29663	0.105;0.003	T	0.39313	-0.9620	10	0.02654	T	1	.	3.6648	0.08252	0.3485:0.2424:0.0:0.4091	.	27;27	C9JQ85;Q13275	.;SEM3F_HUMAN	Q	27	ENSP00000392588:P27Q;ENSP00000398399:P27Q;ENSP00000002829:P27Q;ENSP00000409859:P27Q	ENSP00000002829:P27Q	P	+	2	0	SEMA3F	50172139	0.000000	0.05858	0.036000	0.18154	0.005000	0.04900	-0.785000	0.04628	-0.120000	0.11809	-0.140000	0.14226	CCG		0.607	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		A	50197135	C	A	50197135	3	1	112	1	0	0	0	0	1	0	0	0	14066	652	23	2	82	2	SEMA3F	3	50197135	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	10968019	50197135	147825295	22	30242										
CADM2	253559	hgsc.bcm.edu	37	chr3	85775653	85775653	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgtttgttctcttcttgtgcAacctttccttggtaccagcg	8	11	2	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:85775653A>G	ENST00000407528.2	+	2	123				CADM2_ENST00000405615.2_Missense_Mutation_p.N8D|CADM2_ENST00000383699.3_Intron	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2						adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTTCTTGTGCAACCTTTCCTT	0.348																																																0			3											159	159	159					3																	85775653		2203	4300	6503	85858343	SO:0001627	intron_variant	253559			AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.62-75544A>G	3.37:g.85775653A>G			85858343	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	A	4.558	0.103649	0.08731	.	.	ENSG00000175161	ENST00000405615	T	0.63096	-0.02	5.41	2.82	0.32997	.	0.761709	0.12124	N	0.497440	T	0.39759	0.1090	.	.	.	0.25603	N	0.986577	B	0.21905	0.062	B	0.18263	0.021	T	0.22836	-1.0205	9	0.13470	T	0.59	.	6.305	0.21133	0.5794:0.144:0.0:0.2766	.	8	Q8N3J6-3	.	D	8	ENSP00000384193:N8D	ENSP00000384193:N8D	N	+	1	0	CADM2	85858343	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	2.180000	0.42537	0.830000	0.34757	0.482000	0.46254	AAC		0.348	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		G	85775653	A	G	85775653	1	3	112	0	1	0	0	0	0	0	0	0	2573	130	5	4		4	CADM2	3	85775653	Intron	SNP	A	TCGA-EI-6508-01A-11D-1733-10	35578518	85775653	112246777	23	30243										
C3orf38	285237	hgsc.bcm.edu	37	chr3	88205255	88205255	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	attggttctttggacttcttAattctcagaatccttttcta	5	8	4	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:88205255A>C	ENST00000318887.3	+	3	770	c.460A>C	c.(460-462)Aat>Cat	p.N154H	C3orf38_ENST00000486971.1_Intron	NM_173824.3	NP_776185.2	Q5JPI3	CC038_HUMAN	chromosome 3 open reading frame 38	154					apoptotic process (GO:0006915)					breast(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	12		Lung NSC(201;0.17)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TGGACTTCTTAATTCTCAGAA	0.383																																																0			3											69	66	67					3																	88205255		2203	4300	6503	88287945	SO:0001583	missense	285237			AL832398	CCDS2921.1, CCDS2921.2	3p11.1	2011-01-25			ENSG00000179021	ENSG00000179021			28384	protein-coding gene	gene with protein product						12477932	Standard	NM_173824		Approved	MGC26717	uc003dqw.3	Q5JPI3	OTTHUMG00000155752	ENST00000318887.3:c.460A>C	3.37:g.88205255A>C	ENSP00000322469:p.Asn154His		88287945	B2R8X6|Q8TC85	Missense_Mutation	SNP	ENST00000318887.3	37	CCDS2921.2	.	.	.	.	.	.	.	.	.	.	A	21.4	4.143810	0.77888	.	.	ENSG00000179021	ENST00000318887	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.79764	-0.1666	9	0.87932	D	0	-18.5135	15.3164	0.74081	1.0:0.0:0.0:0.0	.	154	Q5JPI3	CC038_HUMAN	H	154	.	ENSP00000322469:N154H	N	+	1	0	C3orf38	88287945	1.000000	0.71417	0.990000	0.47175	0.930000	0.56654	8.497000	0.90488	2.261000	0.74972	0.460000	0.39030	AAT		0.383	C3orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341513.1	NM_173824		C	88205255	A	C	88205255	3	2	112	1	0	0	0	0	1	0	0	0	2234	362	13	4	470	4	C3orf38	3	88205255	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	2429602	88205255	109817175	24	30244										
IMPG2	50939	hgsc.bcm.edu	37	chr3	101038446	101038446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acctcggactttaaaatactTcacatgatttgccacagcct	5	12	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:101038446T>C	ENST00000193391.7	-	2	503	c.316A>G	c.(316-318)Aag>Gag	p.K106E		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	106					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TTAAAATACTTCACATGATTT	0.373																																																0			3											141	138	139					3																	101038446		2203	4300	6503	102521136	SO:0001583	missense	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.316A>G	3.37:g.101038446T>C	ENSP00000193391:p.Lys106Glu		102521136	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.314535	0.60524	.	.	ENSG00000081148	ENST00000193391	T	0.76186	-1.0	5.52	4.36	0.52297	.	0.131864	0.51477	D	0.000082	T	0.67335	0.2882	L	0.55834	1.745	0.29664	N	0.842967	B	0.27498	0.18	B	0.23150	0.044	T	0.65319	-0.6197	10	0.56958	D	0.05	-6.9647	10.001	0.41929	0.0:0.0767:0.0:0.9233	.	106	Q9BZV3	IMPG2_HUMAN	E	106	ENSP00000193391:K106E	ENSP00000193391:K106E	K	-	1	0	IMPG2	102521136	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	5.717000	0.68446	0.929000	0.37192	0.460000	0.39030	AAG		0.373	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			C	101038446	T	C	101038446	3	2	112	1	0	0	0	0	1	0	0	0	7750	1792	62	4	3481	4	IMPG2	3	101038446	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	12833191	101038446	96983984	25	30245										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113753852	113753852	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atctccctttgaatctcctcTtcctctttcttggcctccag	4	16	5	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:113753852T>C	ENST00000295878.3	-	6	884	c.738A>G	c.(736-738)gaA>gaG	p.E246E	KIAA1407_ENST00000545063.1_Silent_p.E77E	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	246										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GAATCTCCTCTTCCTCTTTCT	0.473																																																0			3											200	192	195					3																	113753852		2203	4300	6503	115236542	SO:0001819	synonymous_variant	57577			AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.738A>G	3.37:g.113753852T>C			115236542	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	37	CCDS2977.1																																																																																				0.473	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113753852	T	C	113753852	2	2	112	1	0	0	0	0	0	0	0	1	8250	1606	56	4		4	KIAA1407	3	113753852	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	12715406	113753852	84268578	26	30246										
FBXO40	51725	hgsc.bcm.edu	37	chr3	121340337	121340337	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	attgtgagggatgcttcaacCgccactgccacattcctgtg	10	12	1	1	rs572469869		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:121340337C>A	ENST00000338040.4	+	3	475	c.61C>A	c.(61-63)Cgc>Agc	p.R21S		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	21					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R21C(1)|p.R21S(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		ATGCTTCAACCGCCACTGCCA	0.567																																																2	Substitution - Missense(2)	lung(1)|breast(1)	3											99	91	94					3																	121340337		2203	4300	6503	122823027	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.61C>A	3.37:g.121340337C>A	ENSP00000337510:p.Arg21Ser		122823027	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.122759	0.56613	.	.	ENSG00000163833	ENST00000338040	T	0.13307	2.6	5.45	5.45	0.79879	.	0.177226	0.49916	D	0.000133	T	0.30885	0.0779	M	0.66939	2.045	0.44908	D	0.997923	D	0.61080	0.989	P	0.60789	0.879	T	0.01319	-1.1386	10	0.87932	D	0	-16.602	11.8089	0.52171	0.1752:0.8248:0.0:0.0	.	21	Q9UH90	FBX40_HUMAN	S	21	ENSP00000337510:R21S	ENSP00000337510:R21S	R	+	1	0	FBXO40	122823027	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	4.664000	0.61540	2.575000	0.86900	0.561000	0.74099	CGC		0.567	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		A	121340337	C	A	121340337	3	1	112	1	0	0	0	0	1	0	0	0	5768	652	23	2	67	2	FBXO40	3	121340337	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	7586485	121340337	76682093	27	30247										
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125271292	125271292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgctacctcgctttttggcaTcttccaggaacagtgaaatg	9	10	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:125271292T>C	ENST00000296220.5	-	9	1676	c.1387A>G	c.(1387-1389)Atg>Gtg	p.M463V		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	463					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)	p.M463V(1)		NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CTTTTTGGCATCTTCCAGGAA	0.458																																																1	Substitution - Missense(1)	ovary(1)	3											109	99	102					3																	125271292		2203	4300	6503	126753982	SO:0001583	missense	114885			AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1387A>G	3.37:g.125271292T>C	ENSP00000296220:p.Met463Val		126753982	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	37	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	T	0.350	-0.945368	0.02304	.	.	ENSG00000144909	ENST00000296220	T	0.27557	1.66	4.74	1.03	0.20045	.	0.293069	0.39759	N	0.001266	T	0.03477	0.0100	N	0.00036	-2.54	0.39674	D	0.970792	B	0.02656	0.0	B	0.01281	0.0	T	0.37430	-0.9706	10	0.02654	T	1	-21.0904	4.7671	0.13137	0.0:0.2324:0.1507:0.6169	.	463	Q9BXB4	OSB11_HUMAN	V	463	ENSP00000296220:M463V	ENSP00000296220:M463V	M	-	1	0	OSBPL11	126753982	0.292000	0.24362	0.916000	0.36221	0.954000	0.61252	0.339000	0.19875	0.033000	0.15463	0.482000	0.46254	ATG		0.458	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		C	125271292	T	C	125271292	3	2	112	1	0	0	0	0	1	0	0	0	11307	1435	50	4	876	4	OSBPL11	3	125271292	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	3930955	125271292	72751138	28	30248										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129290685	129290685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aggcgatgctggtatctgtgCgcctggggggagcagcaggt	19	8	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:129290685C>T	ENST00000324093.4	-	16	3258	c.3080G>A	c.(3079-3081)cGc>cAc	p.R1027H	PLXND1_ENST00000393239.1_Missense_Mutation_p.R1027H	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1027	IPT/TIG 2.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGTATCTGTGCGCCTGGGGGG	0.677																																					Ovarian(97;366 1484 3738 22084 39045)											0			3											17	17	17					3																	129290685		2193	4297	6490	130773375	SO:0001583	missense	23129			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3080G>A	3.37:g.129290685C>T	ENSP00000317128:p.Arg1027His		130773375	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390453	0.42410	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.76060	-0.99;-0.99	4.48	4.48	0.54585	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.072717	0.53938	D	0.000051	D	0.87732	0.6251	M	0.86651	2.83	0.49915	D	0.999836	D	0.89917	1.0	D	0.72982	0.979	D	0.90547	0.4506	10	0.87932	D	0	.	17.1864	0.86868	0.0:1.0:0.0:0.0	.	1027	Q9Y4D7	PLXD1_HUMAN	H	1027	ENSP00000317128:R1027H;ENSP00000376931:R1027H	ENSP00000317128:R1027H	R	-	2	0	PLXND1	130773375	0.903000	0.30736	0.992000	0.48379	0.095000	0.18619	1.685000	0.37659	2.057000	0.61298	0.555000	0.69702	CGC		0.677	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129290685	C	T	129290685	3	4	112	1	0	0	0	0	1	0	0	0	12158	768	27	1	2781	1	PLXND1	3	129290685	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	4019393	129290685	68731745	29	30249										
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172224435	172224435	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccatattctgcatctttagaCcaacaactatttctagcact	3	12	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr3:172224435C>T	ENST00000241261.2	-	5	815	c.693G>A	c.(691-693)tgG>tgA	p.W231*	TNFSF10_ENST00000420541.2_3'UTR	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	231					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)	p.W231*(1)		breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CATCTTTAGACCAACAACTAT	0.328																																																1	Substitution - Nonsense(1)	skin(1)	3											222	214	217					3																	172224435		2203	4300	6503	173707129	SO:0001587	stop_gained	8743			U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.693G>A	3.37:g.172224435C>T	ENSP00000241261:p.Trp231*		173707129	A1Y9B3	Nonsense_Mutation	SNP	ENST00000241261.2	37	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.776359	0.49786	.	.	ENSG00000121858	ENST00000241261	.	.	.	5.68	4.81	0.61882	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.9718	14.9323	0.70926	0.0:0.9312:0.0:0.0688	.	.	.	.	X	231	.	ENSP00000241261:W231X	W	-	3	0	TNFSF10	173707129	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	6.522000	0.73783	1.546000	0.49388	-0.229000	0.12294	TGG		0.328	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			T	172224435	C	T	172224435	4	4	112	1	0	0	0	0	0	1	0	0	16340	508	18	3	156	3	TNFSF10	3	172224435	Nonsense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	42933750	172224435	25797995	30	30250										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgcccgcctgctcacgtgccCatgtggagtgcccgcctgct	12	17	1	0	rs200849975	byFrequency	TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:1388631C>G	ENST00000324803.4	+	1	3292	c.332C>G	c.(331-333)cCa>cGa	p.P111R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	111					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P111R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCCATGTGGAGTG	0.667													N|||	218	0.0435304	0.0287	0.0548	5008	,	,		18151	0.006		0.0487	False		,,,				2504	0.089															1	Substitution - Missense(1)	skin(1)	4											193	146	162					4																	1388631		2203	4299	6502	1378631	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.332C>G	4.37:g.1388631C>G	ENSP00000323978:p.Pro111Arg		1378631	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.610	0.297336	0.10622	.	.	ENSG00000179979	ENST00000324803	T	0.22336	1.96	0.948	-0.0113	0.13993	Post-SET domain (1);	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	9	0.12103	T	0.63	.	2.6024	0.04869	0.0:0.4564:0.3174:0.2262	.	111	Q8N1N5	CRPAK_HUMAN	R	111	ENSP00000323978:P111R	ENSP00000323978:P111R	P	+	2	0	CRIPAK	1378631	0.005000	0.15991	0.001000	0.08648	0.013000	0.08279	-1.037000	0.03557	-0.011000	0.14247	-1.737000	0.00689	CCA		0.667	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		G	1388631	C	G	1388631	3	3	112	1	0	0	0	0	1	0	0	0	3883	594	21	5	334	5	CRIPAK	4	1388631	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		1388631	189765645	31	30251										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15517531	15517531	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cctgagaatgtacagcccagGttcctggaagatgaaggcct	12	10	0	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:15517531G>A	ENST00000503292.1	+	11	1101	c.921G>A	c.(919-921)agG>agA	p.R307R	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Silent_p.R307R|CC2D2A_ENST00000424120.1_Silent_p.R307R|CC2D2A_ENST00000389652.5_Silent_p.R258R	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	307					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						TACAGCCCAGGTTCCTGGAAG	0.428																																																0			4											43	41	42					4																	15517531		1870	4087	5957	15126629	SO:0001819	synonymous_variant	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.921G>A	4.37:g.15517531G>A			15126629	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																				0.428	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		A	15517531	G	A	15517531	2	1	112	1	0	0	0	0	0	0	0	1	2734	1252	44	3		3	CC2D2A	4	15517531	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	14128900	15517531	175636745	32	30252										
RHOH	399	hgsc.bcm.edu	37	chr4	40245229	40245229	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tccggcccctgtcctaccagCaggcagacgtggtgctgatg	13	14	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:40245229C>A	ENST00000381799.5	+	3	947	c.223C>A	c.(223-225)Cag>Aag	p.Q75K	RHOH_ENST00000505618.1_Missense_Mutation_p.Q75K	NM_001278363.1|NM_001278365.1|NM_001278366.1|NM_001278367.1|NM_001278369.1|NM_004310.4	NP_001265292.1|NP_001265294.1|NP_001265295.1|NP_001265296.1|NP_001265298.1|NP_004301.1	Q15669	RHOH_HUMAN	ras homolog family member H	75	Interaction with ZAP70. {ECO:0000250}.				mast cell activation (GO:0045576)|negative regulation of catalytic activity (GO:0043086)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of phosphorylation (GO:0042326)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase inhibitor activity (GO:0005095)|kinase inhibitor activity (GO:0019210)|Rho GTPase binding (GO:0017048)			kidney(1)|large_intestine(3)|lung(7)|ovary(1)	12						GTCCTACCAGCAGGCAGACGT	0.552																																																0			4											90	81	84					4																	40245229		2203	4300	6503	39921624	SO:0001583	missense	399			Z35227	CCDS3458.1	4p13	2014-09-17	2012-02-27	2004-03-24	ENSG00000168421	ENSG00000168421			686	protein-coding gene	gene with protein product		602037	"ras homolog gene family, member H"	ARHH		7784061	Standard	NM_001278359		Approved	RhoH, TTF	uc003guz.2	Q15669	OTTHUMG00000099373	ENST00000381799.5:c.223C>A	4.37:g.40245229C>A	ENSP00000371219:p.Gln75Lys		39921624		Missense_Mutation	SNP	ENST00000381799.5	37	CCDS3458.1	.	.	.	.	.	.	.	.	.	.	c	16.39	3.110796	0.56398	.	.	ENSG00000168421	ENST00000505618;ENST00000507851;ENST00000503941;ENST00000381799	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	5.74	5.74	0.90152	Small GTP-binding protein domain (1);	0.120752	0.64402	D	0.000018	T	0.69043	0.3067	L	0.51422	1.61	0.50171	D	0.999858	B	0.33000	0.393	B	0.28916	0.096	T	0.71520	-0.4568	10	0.87932	D	0	.	14.7331	0.69397	0.1447:0.8553:0.0:0.0	.	75	Q15669	RHOH_HUMAN	K	75	ENSP00000425010:Q75K;ENSP00000423384:Q75K;ENSP00000426439:Q75K;ENSP00000371219:Q75K	ENSP00000371219:Q75K	Q	+	1	0	RHOH	39921624	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.467000	0.60155	2.708000	0.92522	0.585000	0.79938	CAG		0.552	RHOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216820.3	NM_004310		A	40245229	C	A	40245229	3	1	112	1	0	0	0	0	1	0	0	0	13377	711	25	2	225	2	RHOH	4	40245229	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	24727698	40245229	150909047	33	30253										
KIT	3815	hgsc.bcm.edu	37	chr4	55599327	55599327	+	Missense_Mutation	SNP	A	A	G													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggtctagccagagacatcaAgaatgattctaattatgtgg							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:55599327A>G	ENST00000288135.5	+	17	2550	c.2453A>G	c.(2452-2454)aAg>aGg	p.K818R		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	818	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K818R(5)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGAGACATCAAGAATGATTCT	0.378		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	5	Substitution - Missense(5)	soft_tissue(4)|genital_tract(1)	4											145	147	147					4																	55599327		2203	4300	6503	55294084	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2453A>G	4.37:g.55599327A>G	ENSP00000288135:p.Lys818Arg		55294084	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	7.508	0.654128	0.14580	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.82893	-1.66;-1.66	5.62	4.45	0.53987	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.196826	0.35436	N	0.003206	T	0.64382	0.2593	N	0.16743	0.435	0.25514	N	0.98744	B;B	0.06786	0.0;0.001	B;B	0.13407	0.001;0.009	T	0.47923	-0.9079	10	0.07644	T	0.81	.	6.0185	0.19616	0.6796:0.0:0.3204:0.0	.	814;818	P10721-2;P10721	.;KIT_HUMAN	R	818;814	ENSP00000288135:K818R;ENSP00000390987:K814R	ENSP00000288135:K818R	K	+	2	0	KIT	55294084	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.953000	0.29162	0.983000	0.38602	0.477000	0.44152	AAG		0.378	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55599327	A	G	55599327	3	3	112	1	0	0	0	0	1	0	0	0	8350	72	3	4	2519	4	KIT	4	55599327	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	15354098	55599327	135554949	34	30254	53	2								
KIT	3815	hgsc.bcm.edu	37	chr4	55599334	55599334	+	Silent	SNP	T	T	C													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gccagagacatcaagaatgaTtctaattatgtggttaaagg							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:55599334T>C	ENST00000288135.5	+	17	2557	c.2460T>C	c.(2458-2460)gaT>gaC	p.D820D		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	820	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in mast cell disease; systemic). {ECO:0000269|PubMed:9029028}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D820E(3)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAAGAATGATTCTAATTATG	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	3	Substitution - Missense(3)	soft_tissue(2)|thymus(1)	4											147	149	149					4																	55599334		2203	4300	6503	55294091	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2460T>C	4.37:g.55599334T>C			55294091	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55599334	T	C	55599334	2	2	112	1	0	0	0	0	0	0	0	1	8350	1490	52	4		4	KIT	4	55599334	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	7	55599334	135554942	35	30255	53	2								
PARM1	25849	hgsc.bcm.edu	37	chr4	75937816	75937816	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acagcatcagccccaacatcTctgcttcctaagaacatttc	4	15	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:75937816T>G	ENST00000307428.7	+	2	437	c.225T>G	c.(223-225)tcT>tcG	p.S75S	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	75					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						CCCCAACATCTCTGCTTCCTA	0.527																																																0			4											143	137	139					4																	75937816		2074	4224	6298	76156840	SO:0001819	synonymous_variant	0			AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"Prostatic androgen-repressed message 1", "Castration-induced prostatic apoptosis-related protein 1", "WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.225T>G	4.37:g.75937816T>G			76156840	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	37	CCDS47077.1																																																																																				0.527	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393		G	75937816	T	G	75937816	2	3	112	1	0	0	0	0	0	0	0	1	11483	1538	54	4		4	PARM1	4	75937816	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	20338482	75937816	115216460	36	30256										
INTU	27152	hgsc.bcm.edu	37	chr4	128626827	128626827	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gccactattgcctgctgcctTtagcagcaaaacaaagaatt	7	11	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:128626827T>G	ENST00000335251.6	+	11	1751	c.1648T>G	c.(1648-1650)Tta>Gta	p.L550V	INTU_ENST00000512995.1_3'UTR	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	550					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						CCTGCTGCCTTTAGCAGCAAA	0.428																																																0			4											181	167	171					4																	128626827		2203	4300	6503	128846277	SO:0001583	missense	27152			BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.1648T>G	4.37:g.128626827T>G	ENSP00000334003:p.Leu550Val		128846277	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.069008	0.55539	.	.	ENSG00000164066	ENST00000335251;ENST00000506283	D;T	0.82619	-1.63;1.37	5.36	0.0314	0.14171	.	0.000000	0.64402	D	0.000005	D	0.87414	0.6171	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.85078	0.0944	10	0.46703	T	0.11	-6.9436	10.6194	0.45470	0.0:0.3815:0.0:0.6185	.	550	Q9ULD6	PDZD6_HUMAN	V	550;64	ENSP00000334003:L550V;ENSP00000426171:L64V	ENSP00000334003:L550V	L	+	1	2	INTU	128846277	0.989000	0.36119	0.998000	0.56505	0.689000	0.40095	1.985000	0.40668	0.251000	0.21505	0.383000	0.25322	TTA		0.428	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		G	128626827	T	G	128626827	3	3	112	1	0	0	0	0	1	0	0	0	7807	1838	64	4	1690	4	INTU	4	128626827	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	52689011	128626827	62527449	37	30257										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153251905	153251905	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttaggagatttgagttctccTcgcctccagttagtatcaat	8	9	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:153251905T>C	ENST00000281708.4	-	7	2330	c.1101A>G	c.(1099-1101)cgA>cgG	p.R367R	FBXW7_ENST00000603841.1_Silent_p.R367R|FBXW7_ENST00000393956.3_Silent_p.R191R|FBXW7_ENST00000263981.5_Silent_p.R287R|FBXW7_ENST00000603548.1_Silent_p.R367R|FBXW7_ENST00000296555.5_Silent_p.R249R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	367					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAGTTCTCCTCGCCTCCAGT	0.393			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											331	284	300					4																	153251905		2203	4300	6503	153471355	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1101A>G	4.37:g.153251905T>C			153471355	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.393	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153251905	T	C	153251905	2	2	112	1	0	0	0	0	0	0	0	1	5788	1538	54	4		4	FBXW7	4	153251905	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	24625078	153251905	37902371	38	30258										
GALNT7	51809	hgsc.bcm.edu	37	chr4	174169255	174169255	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agtagaagtggacttagagtCtattagaagaataaacaagg	11	3	1	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:174169255C>G	ENST00000265000.4	+	2	334	c.251C>G	c.(250-252)tCt>tGt	p.S84C	GALNT7_ENST00000512285.1_Missense_Mutation_p.S84C	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	84					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		GACTTAGAGTCTATTAGAAGA	0.468																																																0			4											76	69	71					4																	174169255		2203	4300	6503	174405830	SO:0001583	missense	117248			AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.251C>G	4.37:g.174169255C>G	ENSP00000265000:p.Ser84Cys		174405830	B3KQU3|Q7Z5W7|Q9UJ28	Missense_Mutation	SNP	ENST00000265000.4	37	CCDS3815.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.494908	0.85069	.	.	ENSG00000109586	ENST00000265000;ENST00000512285	T;T	0.59224	0.28;1.2	5.7	5.7	0.88788	.	0.382752	0.23084	U	0.052101	T	0.66567	0.2802	L	0.55481	1.735	0.80722	D	1	D	0.58620	0.983	P	0.51487	0.671	T	0.68907	-0.5285	10	0.72032	D	0.01	.	19.8411	0.96685	0.0:1.0:0.0:0.0	.	84	Q86SF2	GALT7_HUMAN	C	84	ENSP00000265000:S84C;ENSP00000427050:S84C	ENSP00000265000:S84C	S	+	2	0	GALNT7	174405830	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	2.683000	0.91414	0.655000	0.94253	TCT		0.468	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423		G	174169255	C	G	174169255	3	3	112	1	0	0	0	0	1	0	0	0	6238	913	32	5	257	5	GALNT7	4	174169255	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	20917350	174169255	16985021	39	30259										
TUBB4Q	56604	hgsc.bcm.edu	37	chr4	190905629	190905629	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtggtggtgcacgttgatgcGctccagctgcaggtggctgt	17	9	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr4:190905629G>A								FRG1 (21270 upstream) : RNA5SP174 (30663 downstream)																							ACGTTGATGCGCTCCAGCTGC	0.692																																																0			4											7	9	9					4																	190905629		1567	3407	4974	191142623	SO:0001628	intergenic_variant	56604																															4.37:g.190905629G>A			191142623		Missense_Mutation	SNP		37																																																																																				0	0.692									A	190905629	G	A	190905629	1	1	112	0	1	0	0	0	0	0	0	0	16799	1087	38	1		1	TUBB4Q	4	190905629	IGR	SNP	G	TCGA-EI-6508-01A-11D-1733-10	16736374	190905629	248647	40	30260										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13717480	13717480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gaactgcacagtggcattaaAgtccgcttggttaaattcgt	10	8	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:13717480A>T	ENST00000265104.4	-	73	12753	c.12649T>A	c.(12649-12651)Ttt>Att	p.F4217I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4217	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTGGCATTAAAGTCCGCTTGG	0.537									Kartagener syndrome																																							0			5											75	64	68					5																	13717480		2203	4300	6503	13770480	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12649T>A	5.37:g.13717480A>T	ENSP00000265104:p.Phe4217Ile		13770480	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	34	5.321564	0.95682	.	.	ENSG00000039139	ENST00000265104	T	0.08102	3.13	5.54	5.54	0.83059	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.31670	0.0804	M	0.91920	3.255	0.80722	D	1	P	0.43701	0.815	P	0.53035	0.716	T	0.21759	-1.0236	10	0.66056	D	0.02	.	15.6836	0.77391	1.0:0.0:0.0:0.0	.	4217	Q8TE73	DYH5_HUMAN	I	4217	ENSP00000265104:F4217I	ENSP00000265104:F4217I	F	-	1	0	DNAH5	13770480	1.000000	0.71417	0.996000	0.52242	0.826000	0.46750	9.315000	0.96313	2.105000	0.64084	0.533000	0.62120	TTT		0.537	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13717480	A	T	13717480	3	4	112	1	0	0	0	0	1	0	0	0	4615	72	3	5	1253	5	DNAH5	5	13717480	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10		13717480	167197780	41	30261										
TRIO	7204	hgsc.bcm.edu	37	chr5	14472722	14472722	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tacgttttgcaagaactagtGgagacagagcgtgactatgt	12	6	0	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:14472722G>A	ENST00000344204.4	+	39	5958	c.5934G>A	c.(5932-5934)gtG>gtA	p.V1978V	TRIO_ENST00000537187.1_Silent_p.V1978V	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1978	DH 2. {ECO:0000255|PROSITE- ProRule:PRU00062}.		V -> M (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					AAGAACTAGTGGAGACAGAGC	0.393																																																0			5											204	177	186					5																	14472722		2203	4300	6503	14525722	SO:0001819	synonymous_variant	7204			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.5934G>A	5.37:g.14472722G>A			14525722	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																				0.393	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14472722	G	A	14472722	2	1	112	1	0	0	0	0	0	0	0	1	16592	1335	47	3		3	TRIO	5	14472722	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	755242	14472722	166442538	42	30262										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67589612	67589612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ataacactcagtttcaagaaAaaagtcgagaatatgataga	7	5	2	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:67589612A>G	ENST00000521381.1	+	11	1991	c.1375A>G	c.(1375-1377)Aaa>Gaa	p.K459E	PIK3R1_ENST00000274335.5_Missense_Mutation_p.K459E|PIK3R1_ENST00000396611.1_Missense_Mutation_p.K459E|PIK3R1_ENST00000523872.1_Missense_Mutation_p.K96E|PIK3R1_ENST00000336483.5_Missense_Mutation_p.K189E|PIK3R1_ENST00000320694.8_Missense_Mutation_p.K159E|PIK3R1_ENST00000521657.1_Missense_Mutation_p.K459E	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	459					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)|p.K459E(1)|p.F456_R461>S(1)|p.F456_R461del(1)|p.Q457_R461del(1)|p.T454_D464del(1)|p.K459del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	GTTTCAAGAAAAAAGTCGAGA	0.274			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	8	Deletion - In frame(4)|Substitution - Missense(1)|Whole gene deletion(1)|Complex - deletion inframe(1)|Unknown(1)	endometrium(5)|large_intestine(1)|lung(1)|central_nervous_system(1)	5											45	49	47					5																	67589612		2186	4269	6455	67625368	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1375A>G	5.37:g.67589612A>G	ENSP00000428056:p.Lys459Glu		67625368	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.111229	0.77210	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	T;T;T;T;D;T;D;T;D	0.83335	-0.58;-0.58;-0.46;-0.58;-1.6;0.74;-1.62;0.3;-1.71	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.86569	0.5964	M	0.84846	2.72	0.80722	D	1	P;P;B;D	0.56746	0.603;0.711;0.413;0.977	B;P;B;P	0.46718	0.209;0.497;0.244;0.525	D	0.87415	0.2378	10	0.38643	T	0.18	-31.4976	15.3459	0.74337	1.0:0.0:0.0:0.0	.	129;189;159;459	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	E	459;459;459;459;159;96;189;132;96	ENSP00000428056:K459E;ENSP00000429277:K459E;ENSP00000379855:K459E;ENSP00000274335:K459E;ENSP00000323512:K159E;ENSP00000431058:K96E;ENSP00000338554:K189E;ENSP00000429156:K132E;ENSP00000430098:K96E	ENSP00000274335:K459E	K	+	1	0	PIK3R1	67625368	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.709000	0.91379	2.277000	0.76020	0.528000	0.53228	AAA		0.274	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67589612	A	G	67589612	3	3	112	1	0	0	0	0	1	0	0	0	11949	15	1	4	1543	4	PIK3R1	5	67589612	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	53116890	67589612	113325648	43	30263										
ATP6AP1L	92270	hgsc.bcm.edu	37	chr5	81613867	81613867	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tttaccaaagcccaagactgCgcctcctccttctcgccagc	6	18	1	1	rs371506768		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:81613867C>T	ENST00000380167.4	+	10	1748	c.423C>T	c.(421-423)tgC>tgT	p.C141C	ATP6AP1L_ENST00000439350.1_Silent_p.C141C|ATP6AP1L_ENST00000508366.1_Intron			Q52LC2	VAS1L_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1-like	141					ATP hydrolysis coupled proton transport (GO:0015991)	integral component of membrane (GO:0016021)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.C141C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	12						CCCAAGACTGCGCCTCCTCCT	0.547																																																1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	97	84	89		423	-6.3	0	5		89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP6AP1L	NM_001017971.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		141/225	81613867	1,13005	2203	4300	6503	81649623	SO:0001819	synonymous_variant	92270			AK022625	CCDS34196.1	5q14.2	2010-03-10				ENSG00000205464			28091	protein-coding gene	gene with protein product							Standard	XR_112744		Approved		uc003khw.3	Q52LC2		ENST00000380167.4:c.423C>T	5.37:g.81613867C>T			81649623		Silent	SNP	ENST00000380167.4	37	CCDS34196.1																																																																																				0.547	ATP6AP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369562.3	NM_001017971		T	81613867	C	T	81613867	2	4	112	1	0	0	0	0	0	0	0	1	1167	776	27	1		1	ATP6AP1L	5	81613867	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	14024255	81613867	99301393	44	30264										
GPR98	84059	hgsc.bcm.edu	37	chr5	90024539	90024539	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	catcaaaaactccctgtccgAggtgtgctgaccgtggcctt	10	13	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:90024539A>C	ENST00000405460.2	+	49	10311	c.10215A>C	c.(10213-10215)cgA>cgC	p.R3405R		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3405					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCCCTGTCCGAGGTGTGCTGA	0.463																																																0			5											167	164	165					5																	90024539		1987	4166	6153	90060295	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.10215A>C	5.37:g.90024539A>C			90060295	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	9.409	1.079988	0.20309	.	.	ENSG00000164199	ENST00000509621	.	.	.	5.46	-3.07	0.05363	.	.	.	.	.	T	0.17492	0.0420	.	.	.	0.24707	N	0.993227	.	.	.	.	.	.	T	0.27706	-1.0066	4	.	.	.	.	0.4076	0.00436	0.2024:0.1816:0.2256:0.3904	.	.	.	.	A	971	.	.	E	+	2	0	GPR98	90060295	0.036000	0.19791	0.947000	0.38551	0.889000	0.51656	0.029000	0.13666	-0.157000	0.11059	0.455000	0.32223	GAG		0.463	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90024539	A	C	90024539	2	2	112	1	0	0	0	0	0	0	0	1	6742	291	11	4		4	GPR98	5	90024539	Silent	SNP	A	TCGA-EI-6508-01A-11D-1733-10	8410672	90024539	90890721	45	30265										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94022409	94022409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtgtttcttctgagccactcTctcttcagaaaatggtaagt	8	9	5	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:94022409T>C	ENST00000265140.5	+	16	2526	c.2107T>C	c.(2107-2109)Tct>Cct	p.S703P		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	703						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TGAGCCACTCTCTCTTCAGAA	0.358																																																0			5											102	102	102					5																	94022409		2203	4300	6503	94048165	SO:0001583	missense	84250			AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2107T>C	5.37:g.94022409T>C	ENSP00000265140:p.Ser703Pro		94048165	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	37	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.984866	0.74474	.	.	ENSG00000133302	ENST00000265140	T	0.65549	-0.16	5.63	4.44	0.53790	.	0.077565	0.64402	D	0.000008	T	0.60958	0.2309	L	0.34521	1.04	0.36845	D	0.887613	D	0.54047	0.964	P	0.52267	0.694	T	0.69183	-0.5212	10	0.87932	D	0	.	11.8829	0.52586	0.131:0.0:0.0:0.869	.	703	Q9BQI6	ANR32_HUMAN	P	703	ENSP00000265140:S703P	ENSP00000265140:S703P	S	+	1	0	ANKRD32	94048165	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	6.338000	0.72963	1.019000	0.39547	0.533000	0.62120	TCT		0.358	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		C	94022409	T	C	94022409	3	2	112	1	0	0	0	0	1	0	0	0	660	1551	54	4	2165	4	ANKRD32	5	94022409	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	3997870	94022409	86892851	46	30266										
APC	324	hgsc.bcm.edu	37	chr5	112174225	112174225	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggttatggtaaaagaggtcaAatgaaaccctcgattgaatc	10	6	1	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:112174225A>G	ENST00000457016.1	+	16	3314	c.2934A>G	c.(2932-2934)caA>caG	p.Q978Q	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.Q978Q|APC_ENST00000508376.2_Silent_p.Q978Q			P25054	APC_HUMAN	adenomatous polyposis coli	978	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGAGGTCAAATGAAACCCT	0.363		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											79	74	76					5																	112174225		2202	4300	6502	112202124	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2934A>G	5.37:g.112174225A>G			112202124	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.363	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174225	A	G	112174225	2	3	112	1	0	0	0	0	0	0	0	1	763	11	1	4		4	APC	5	112174225	Silent	SNP	A	TCGA-EI-6508-01A-11D-1733-10	18151816	112174225	68741035	47	30267			1	33		4	4	1004	N	G_C_A	3.227456e-08
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	112	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	406	112174631	68740629	48	30268			1	33		4	4	1004	N	G_C_A	3.227456e-08
APC	324	hgsc.bcm.edu	37	chr5	112175216	112175216	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgcaaatagcagaaataaaaGaaaagattggaactaggtca	9	4	1	3	rs121913224		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:112175216G>T	ENST00000457016.1	+	16	4305	c.3925G>T	c.(3925-3927)Gaa>Taa	p.E1309*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.E1309*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1309*			P25054	APC_HUMAN	adenomatous polyposis coli	1309	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			E -> G (in Ref. 1; AAA60353/AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*4(42)|p.E1309*(25)|p.I1311fs*4(2)|p.?(1)|p.E1309fs*6(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.E1309K(1)|p.K1308fs*4(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAATAAAAGAAAAGATTGG	0.423		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	75	Deletion - Frameshift(45)|Substitution - Nonsense(25)|Insertion - Frameshift(3)|Unknown(1)|Substitution - Missense(1)	large_intestine(71)|upper_aerodigestive_tract(1)|stomach(1)|soft_tissue(1)|skin(1)	5	GRCh37	CD084022|CD941590|CM920052	APC	D|M							54	55	55					5																	112175216		2202	4300	6502	112203115	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3925G>T	5.37:g.112175216G>T	ENSP00000413133:p.Glu1309*		112203115	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	37	6.023820	0.97211	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	5.73	5.73	0.89815	.	0.365794	0.32503	N	0.006002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.1954	19.8705	0.96849	0.0:0.0:1.0:0.0	.	.	.	.	X	1309	.	.	E	+	1	0	APC	112203115	1.000000	0.71417	0.971000	0.41717	0.520000	0.34377	7.454000	0.80714	2.861000	0.98227	0.655000	0.94253	GAA		0.423	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175216	G	T	112175216	4	4	112	1	0	0	0	0	0	1	0	0	763	943	33	2	3983	2	APC	5	112175216	Nonsense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	585	112175216	68740044	49	30269			1	33		4	4	1004	N	G_C_A	3.227456e-08
APC	324	hgsc.bcm.edu	37	chr5	112175228	112175228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaataaaagaaaagattggaActaggtcagctgaagatcct	9	5	1	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:112175228A>G	ENST00000457016.1	+	16	4317	c.3937A>G	c.(3937-3939)Act>Gct	p.T1313A	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.T1313A|APC_ENST00000508376.2_Missense_Mutation_p.T1313A			P25054	APC_HUMAN	adenomatous polyposis coli	1313	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		T -> A (in FAP and colorectal tumor).		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.T1313A(1)|p.K1192fs*3(1)|p.T1313fs*8(1)|p.G1312fs*4(1)|p.G1312fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGATTGGAACTAGGTCAGC	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	6	Deletion - Frameshift(4)|Substitution - Missense(1)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											57	59	58					5																	112175228		2202	4300	6502	112203127	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3937A>G	5.37:g.112175228A>G	ENSP00000413133:p.Thr1313Ala		112203127	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.981073	0.00046	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88431	-2.38;-2.38;-2.38	6.03	-0.607	0.11615	.	0.686688	0.15487	N	0.259761	T	0.71451	0.3341	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57124	-0.7865	9	.	.	.	-2.9388	5.866	0.18775	0.3827:0.383:0.2343:0.0	.	1315;1313	Q4LE70;P25054	.;APC_HUMAN	A	1313	ENSP00000413133:T1313A;ENSP00000257430:T1313A;ENSP00000427089:T1313A	.	T	+	1	0	APC	112203127	0.000000	0.05858	0.009000	0.14445	0.007000	0.05969	-0.182000	0.09726	-0.080000	0.12685	-0.316000	0.08728	ACT		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175228	A	G	112175228	3	3	112	1	0	0	0	0	1	0	0	0	763	43	2	4	3995	4	APC	5	112175228	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	12	112175228	68740032	50	30270			1	33		4	4	1004	N	G_C_A	3.227456e-08
PRR16	51334	hgsc.bcm.edu	37	chr5	120022314	120022314	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ataagccacagtaacagcttCccccctatcagacctgcaac	5	16	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:120022314C>T	ENST00000407149.2	+	2	1034	c.825C>T	c.(823-825)ttC>ttT	p.F275F	PRR16_ENST00000505123.1_Silent_p.F205F|PRR16_ENST00000446965.1_Silent_p.F205F|PRR16_ENST00000379551.2_Silent_p.F252F			Q569H4	LARGN_HUMAN	proline rich 16	275	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		GTAACAGCTTCCCCCCTATCA	0.527																																																0			5											75	73	74					5																	120022314		2203	4300	6503	120050213	SO:0001819	synonymous_variant	51334			AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.825C>T	5.37:g.120022314C>T			120050213	D3DSZ0|Q8IXY1|Q9NYI5	Silent	SNP	ENST00000407149.2	37																																																																																					0.527	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		T	120022314	C	T	120022314	2	4	112	1	0	0	0	0	0	0	0	1	12623	854	30	3		3	PRR16	5	120022314	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	7847086	120022314	60892946	51	30271										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129521023	129521023	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tcagagaagattttctccaaCgatgtagagacaatacaatt	7	7	2	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:129521023C>A	ENST00000305031.4	+	3	2546	c.2188C>A	c.(2188-2190)Cga>Aga	p.R730R		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	730					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		TTTTCTCCAACGATGTAGAGA	0.433																																																0			5											115	109	111					5																	129521023		2203	4300	6503	129548922	SO:0001819	synonymous_variant	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.2188C>A	5.37:g.129521023C>A			129548922	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																				0.433	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		A	129521023	C	A	129521023	2	1	112	1	0	0	0	0	0	0	0	1	3419	528	19	2		2	CHSY3	5	129521023	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	9498709	129521023	51394237	52	30272										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140348597	140348597	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggaggcttctgtggagtaaGggaaaggtcccctgcagaac	15	8	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:140348597G>T	ENST00000289269.5	+	1	2778	c.2246G>T	c.(2245-2247)aGg>aTg	p.R749M	PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	749					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGGAGTAAGGGAAAGGTCC	0.453																																					Melanoma(190;638 2083 3390 11909 52360)											0			5											90	86	87					5																	140348597		2203	4300	6503	140328781	SO:0001583	missense	56134			AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.2246G>T	5.37:g.140348597G>T	ENSP00000289269:p.Arg749Met		140328781	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	37	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.458880	0.26248	.	.	ENSG00000243232	ENST00000289269	T	0.48836	0.8	5.53	4.67	0.58626	.	0.000000	0.45126	D	0.000396	T	0.47210	0.1433	N	0.08118	0	0.43000	D	0.994515	D;D	0.76494	0.999;0.996	D;P	0.69654	0.965;0.894	T	0.55598	-0.8116	10	0.46703	T	0.11	.	14.1215	0.65189	0.0721:0.0:0.9279:0.0	.	749;749	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	M	749	ENSP00000289269:R749M	ENSP00000289269:R749M	R	+	2	0	PCDHAC2	140328781	1.000000	0.71417	1.000000	0.80357	0.363000	0.29612	3.664000	0.54525	1.345000	0.45676	0.462000	0.41574	AGG		0.453	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		T	140348597	G	T	140348597	3	4	112	1	0	0	0	0	1	0	0	0	11564	1000	35	2	2248	2	PCDHAC2	5	140348597	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10827574	140348597	40566663	53	30273										
SLC25A2	83884	hgsc.bcm.edu	37	chr5	140683389	140683389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctgtcccccctgcggcccccGctgtgaggtcgatggcggct	14	17	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr5:140683389G>A	ENST00000239451.4	-	1	223	c.44C>T	c.(43-45)gCg>gTg	p.A15V		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	15					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.A15V(1)		breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	TGCGGCCCCCGCTGTGAGGTC	0.607																																																1	Substitution - Missense(1)	breast(1)	5											44	46	45					5																	140683389		2203	4300	6503	140663573	SO:0001583	missense	83884			AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"Solute carriers"	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.44C>T	5.37:g.140683389G>A	ENSP00000239451:p.Ala15Val		140663573	Q496C1|Q6XUI0|Q8NFZ2	Missense_Mutation	SNP	ENST00000239451.4	37	CCDS4258.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803561	0.50315	.	.	ENSG00000120329	ENST00000239451	D	0.82081	-1.57	4.27	3.39	0.38822	Mitochondrial carrier domain (2);	0.000000	0.85682	U	0.000000	D	0.91523	0.7323	M	0.92122	3.275	0.47308	D	0.999389	D	0.69078	0.997	D	0.65684	0.937	D	0.92302	0.5850	10	0.87932	D	0	-17.268	10.8236	0.46619	0.0984:0.0:0.9016:0.0	.	15	Q9BXI2	ORNT2_HUMAN	V	15	ENSP00000239451:A15V	ENSP00000239451:A15V	A	-	2	0	SLC25A2	140663573	0.197000	0.23362	0.712000	0.30502	0.319000	0.28217	3.134000	0.50538	1.099000	0.41499	0.484000	0.47621	GCG		0.607	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251799.2	NM_031947		A	140683389	G	A	140683389	3	1	112	1	0	0	0	0	1	0	0	0	14519	1087	38	1	865	1	SLC25A2	5	140683389	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	334792	140683389	40231871	54	30274										
RANBP9	10048	hgsc.bcm.edu	37	chr6	13625895	13625895	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctttacttacctaatattgcActgttaagagctgagcacac	6	10	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:13625895A>G	ENST00000011619.3	-	13	2107	c.2049T>C	c.(2047-2049)agT>agC	p.S683S	RANBP9_ENST00000539980.1_Silent_p.S454S|NOL7_ENST00000474485.1_Intron|RANBP9_ENST00000469916.1_5'UTR	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	683	Interaction with FMR1.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			CTAATATTGCACTGTTAAGAG	0.398																																																0			6											187	185	186					6																	13625895		2203	4300	6503	13733874	SO:0001819	synonymous_variant	10048			AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.2049T>C	6.37:g.13625895A>G			13733874	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Silent	SNP	ENST00000011619.3	37	CCDS4529.1																																																																																				0.398	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			G	13625895	A	G	13625895	2	3	112	1	0	0	0	0	0	0	0	1	13069	156	6	4		4	RANBP9	6	13625895	Silent	SNP	A	TCGA-EI-6508-01A-11D-1733-10		13625895	157489172	55	30275										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31860203	31860203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccttgctgtcggagtccacgCgctcatccacagagtaggaa	11	13	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:31860203C>T	ENST00000375537.4	-	7	851	c.845G>A	c.(844-846)cGc>cAc	p.R282H	EHMT2_ENST00000375528.4_Missense_Mutation_p.R339H|EHMT2_ENST00000395728.3_Missense_Mutation_p.R339H|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375530.4_Missense_Mutation_p.R282H	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	282					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)	p.R282H(1)		central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GGAGTCCACGCGCTCATCCAC	0.622																																																1	Substitution - Missense(1)	large_intestine(1)	6											89	69	76					6																	31860203		1511	2709	4220	31968182	SO:0001583	missense	10919			AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.845G>A	6.37:g.31860203C>T	ENSP00000364687:p.Arg282His		31968182	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735648	0.49045	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	T;T;T;T	0.73258	-0.46;-0.73;-0.65;-0.45	4.97	4.97	0.65823	.	0.084955	0.46145	D	0.000320	T	0.31606	0.0802	N	0.08118	0	0.43448	D	0.995635	B;B;B;B	0.14438	0.006;0.01;0.006;0.003	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.31475	-0.9942	10	0.42905	T	0.14	.	7.3862	0.26884	0.0:0.8216:0.0:0.1784	.	339;282;282;96	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	H	339;339;282;282;96	ENSP00000379078:R339H;ENSP00000364678:R339H;ENSP00000364680:R282H;ENSP00000364687:R282H	ENSP00000364678:R339H	R	-	2	0	EHMT2	31968182	0.971000	0.33674	1.000000	0.80357	0.996000	0.88848	2.174000	0.42482	2.582000	0.87167	0.491000	0.48974	CGC		0.622	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		T	31860203	C	T	31860203	3	4	112	1	0	0	0	0	1	0	0	0	4995	768	27	1	2875	1	EHMT2	6	31860203	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	18234308	31860203	139254864	56	30276										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33653286	33653286	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gccagccacatgaggaccgcGagccagtcgaccccaccacc	10	19	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:33653286G>T	ENST00000374316.5	+	41	6518	c.5458G>T	c.(5458-5460)Gag>Tag	p.E1820*	ITPR3_ENST00000605930.1_Nonsense_Mutation_p.E1820*			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1820					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.E1820K(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGAGGACCGCGAGCCAGTCGA	0.647																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											26	29	28					6																	33653286		2203	4300	6503	33761264	SO:0001587	stop_gained	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.5458G>T	6.37:g.33653286G>T	ENSP00000363435:p.Glu1820*		33761264	Q14649|Q5TAQ2	Nonsense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	50	16.851350	0.99873	.	.	ENSG00000096433	ENST00000374316	.	.	.	5.03	5.03	0.67393	.	0.505055	0.22392	N	0.060672	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-34.6547	14.0224	0.64563	0.0:0.1514:0.8485:0.0	.	.	.	.	X	1820	.	ENSP00000363435:E1820X	E	+	1	0	ITPR3	33761264	1.000000	0.71417	0.306000	0.25113	0.056000	0.15407	7.200000	0.77838	2.337000	0.79520	0.313000	0.20887	GAG		0.647	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33653286	G	T	33653286	4	4	112	1	0	0	0	0	0	1	0	0	7943	1059	37	2	5616	2	ITPR3	6	33653286	Nonsense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	1793083	33653286	137461781	57	30277										
PHIP	55023	hgsc.bcm.edu	37	chr6	79650763	79650763	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acgattctttttctgtaacaAatcttcctttacattattag	3	8	3	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:79650763A>C	ENST00000275034.4	-	40	5280	c.5113T>G	c.(5113-5115)Ttg>Gtg	p.L1705V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1705					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTCTGTAACAAATCTTCCTTT	0.363																																																0			6											136	129	132					6																	79650763		2202	4300	6502	79707482	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.5113T>G	6.37:g.79650763A>C	ENSP00000275034:p.Leu1705Val		79707482	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	A	3.425	-0.117415	0.06838	.	.	ENSG00000146247	ENST00000275034	T	0.39056	1.1	6.07	3.62	0.41486	.	0.400866	0.24426	N	0.038640	T	0.09291	0.0229	N	0.19112	0.55	0.30983	N	0.722254	B;B	0.20261	0.043;0.043	B;B	0.16722	0.016;0.016	T	0.26849	-1.0091	9	.	.	.	-3.2622	6.45	0.21898	0.7885:0.0:0.0732:0.1382	.	1705;1705	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	1705	ENSP00000275034:L1705V	.	L	-	1	2	PHIP	79707482	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	1.378000	0.34328	0.502000	0.28037	0.528000	0.53228	TTG		0.363	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79650763	A	C	79650763	3	2	112	1	0	0	0	0	1	0	0	0	11873	11	1	4	356	4	PHIP	6	79650763	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	45997477	79650763	91464304	58	30278										
PHIP	55023	hgsc.bcm.edu	37	chr6	79655100	79655100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttttacgtttgactggctttTccttttccatgttttctttt	5	8	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:79655100T>C	ENST00000275034.4	-	39	4912	c.4745A>G	c.(4744-4746)gAa>gGa	p.E1582G	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1582					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GACTGGCTTTTCCTTTTCCAT	0.393																																																0			6											224	210	214					6																	79655100		2203	4300	6503	79711819	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4745A>G	6.37:g.79655100T>C	ENSP00000275034:p.Glu1582Gly		79711819	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723865	0.48728	.	.	ENSG00000146247	ENST00000275034;ENST00000355098	T	0.41400	1.0	5.86	5.86	0.93980	.	0.064498	0.64402	D	0.000006	T	0.21718	0.0523	N	0.24115	0.695	0.47737	D	0.9995	P;P	0.47762	0.9;0.9	P;P	0.44518	0.452;0.452	T	0.02505	-1.1149	9	.	.	.	-24.1443	15.4264	0.75055	0.0:0.0:0.0:1.0	.	1582;1582	A7J992;Q8WWQ0	.;PHIP_HUMAN	G	1582;308	ENSP00000275034:E1582G	.	E	-	2	0	PHIP	79711819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.776000	0.55356	2.241000	0.73720	0.533000	0.62120	GAA		0.393	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79655100	T	C	79655100	3	2	112	1	0	0	0	0	1	0	0	0	11873	1783	62	4	728	4	PHIP	6	79655100	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	4337	79655100	91459967	59	30279										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119324732	119324732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccactttgagcttctcttctTctttcatggcagcaattgtt	6	11	4	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:119324732T>C	ENST00000338891.7	-	8	2314	c.1871A>G	c.(1870-1872)gAa>gGa	p.E624G	FAM184A_ENST00000352896.5_Missense_Mutation_p.E504G|FAM184A_ENST00000368475.4_Missense_Mutation_p.E504G|FAM184A_ENST00000521531.1_Missense_Mutation_p.E624G|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	624						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CTTCTCTTCTTCTTTCATGGC	0.333																																																0			6											102	94	97					6																	119324732		1829	4088	5917	119366431	SO:0001583	missense	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1871A>G	6.37:g.119324732T>C	ENSP00000342604:p.Glu624Gly		119366431	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085133	0.36758	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	6.07	3.69	0.42338	.	0.159662	0.53938	D	0.000053	T	0.15565	0.0375	L	0.51422	1.61	0.80722	D	1	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.06405	0.002;0.001;0.002	T	0.03608	-1.1020	10	0.31617	T	0.26	-13.5885	10.4991	0.44796	0.0:0.1302:0.0:0.8698	.	624;504;624	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	G	624;504;504;624	ENSP00000342604:E624G;ENSP00000326608:E504G;ENSP00000357460:E504G;ENSP00000430442:E624G	ENSP00000342604:E624G	E	-	2	0	FAM184A	119366431	1.000000	0.71417	0.955000	0.39395	0.404000	0.30871	2.228000	0.42981	0.544000	0.28883	0.528000	0.53228	GAA		0.333	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119324732	T	C	119324732	3	2	112	1	0	0	0	0	1	0	0	0	5527	1783	62	4	1595	4	FAM184A	6	119324732	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	39669632	119324732	51790335	60	30280										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121638681	121638681	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tatcagagcaattgtctgtgCggtaactatggcttttctcc	9	9	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:121638681C>T	ENST00000398212.2	-	3	504	c.455G>A	c.(454-456)cGc>cAc	p.R152H	TBC1D32_ENST00000275159.6_Missense_Mutation_p.R152H	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	152					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.R152H(2)									ATTGTCTGTGCGGTAACTATG	0.348																																																2	Substitution - Missense(2)	breast(2)	6											312	282	292					6																	121638681		1866	4095	5961	121680380	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.455G>A	6.37:g.121638681C>T	ENSP00000381270:p.Arg152His		121680380	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	8.651	0.898258	0.17686	.	.	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.16897	2.31;2.31;2.31	5.02	5.02	0.67125	.	0.166640	0.45606	D	0.000354	T	0.02533	0.0077	N	0.14661	0.345	0.19945	N	0.999944	B	0.33694	0.421	B	0.29524	0.103	T	0.34750	-0.9816	10	0.15066	T	0.55	-3.4063	6.8367	0.23941	0.0:0.7818:0.0:0.2182	.	152	Q96NH3	BROMI_HUMAN	H	152	ENSP00000275159:R152H;ENSP00000381270:R152H;ENSP00000397993:R152H	ENSP00000275159:R152H	R	-	2	0	C6orf170	121680380	1.000000	0.71417	0.996000	0.52242	0.351000	0.29236	3.044000	0.49830	2.485000	0.83878	0.655000	0.94253	CGC		0.348	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121638681	C	T	121638681	3	4	112	1	0	0	0	0	1	0	0	0	2350	768	27	1	3438	1	C6orf170	6	121638681	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	2313949	121638681	49476386	61	30281										
VNN1	8876	hgsc.bcm.edu	37	chr6	133004392	133004392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtccttctcatacaacctccCaaacagagttactgttaaga	5	12	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr6:133004392C>T	ENST00000367928.4	-	7	1442	c.1429G>A	c.(1429-1431)Ggg>Agg	p.G477R		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	477					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TACAACCTCCCAAACAGAGTT	0.423																																																0			6											129	118	122					6																	133004392		2203	4300	6503	133046085	SO:0001583	missense	8876			AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1429G>A	6.37:g.133004392C>T	ENSP00000356905:p.Gly477Arg		133046085	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993621	0.93167	.	.	ENSG00000112299	ENST00000367928	D	0.92495	-3.05	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.96197	0.8760	M	0.81341	2.54	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.95961	0.8962	10	0.87932	D	0	-28.9056	20.1823	0.98208	0.0:1.0:0.0:0.0	.	477	O95497	VNN1_HUMAN	R	477	ENSP00000356905:G477R	ENSP00000356905:G477R	G	-	1	0	VNN1	133046085	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.856000	0.62932	2.771000	0.95319	0.650000	0.86243	GGG		0.423	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			T	133004392	C	T	133004392	3	4	112	1	0	0	0	0	1	0	0	0	17222	594	21	3	116	3	VNN1	6	133004392	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	11365711	133004392	38110675	62	30282										
SDK1	221935	hgsc.bcm.edu	37	chr7	4089010	4089010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcccccgcagaacgtgcagaCggaagccgtgaactccacca	11	16	0	3	rs371559284		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:4089010C>T	ENST00000404826.2	+	18	2772	c.2633C>T	c.(2632-2634)aCg>aTg	p.T878M	SDK1_ENST00000389531.3_Missense_Mutation_p.T878M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	878	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AACGTGCAGACGGAAGCCGTG	0.577																																																0			7						C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	81	71	74		2633	3.2	0.2	7		74	0,8600		0,0,4300	no	missense	SDK1	NM_152744.3	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	878/2214	4089010	1,13005	2203	4300	6503	4055536	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2633C>T	7.37:g.4089010C>T	ENSP00000385899:p.Thr878Met		4055536	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	9.953	1.220720	0.22457	2.27E-4	0.0	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.56611	0.45;0.45	5.13	3.22	0.36961	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.062720	0.07344	N	0.881199	T	0.51075	0.1653	L	0.60455	1.87	0.09310	N	1	B;B	0.24651	0.108;0.102	B;B	0.22386	0.039;0.022	T	0.46020	-0.9221	10	0.66056	D	0.02	.	9.6155	0.39690	0.0:0.7415:0.0:0.2585	.	878;878	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	M	878	ENSP00000385899:T878M;ENSP00000374182:T878M	ENSP00000374182:T878M	T	+	2	0	SDK1	4055536	0.094000	0.21725	0.226000	0.23910	0.947000	0.59692	0.928000	0.28831	0.483000	0.27608	0.557000	0.71058	ACG		0.577	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4089010	C	T	4089010	3	4	112	1	0	0	0	0	1	0	0	0	14005	536	19	1	2703	1	SDK1	7	4089010	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		4089010	155049653	63	30283										
FKBP14	55033	hgsc.bcm.edu	37	chr7	30062407	30062407	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gatgcccagggtaaaccaaaTgggctgaccattgttatgtt	11	8	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:30062407T>A	ENST00000222803.5	-	2	398	c.223A>T	c.(223-225)Att>Ttt	p.I75F	AC007285.6_ENST00000422239.1_RNA|AC007285.6_ENST00000419103.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	75	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						GTAAACCAAATGGGCTGACCA	0.413																																																0			7											76	74	74					7																	30062407		2203	4300	6503	30028932	SO:0001583	missense	55033			AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"EF-hand domain containing"	18625	protein-coding gene	gene with protein product		614505	"FK506 binding protein 14 (22 kDa)"			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.223A>T	7.37:g.30062407T>A	ENSP00000222803:p.Ile75Phe		30028932		Missense_Mutation	SNP	ENST00000222803.5	37	CCDS5423.1	.	.	.	.	.	.	.	.	.	.	T	5.073	0.199139	0.09652	.	.	ENSG00000106080	ENST00000222803	D	0.84730	-1.89	5.81	2.14	0.27477	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.277481	0.41938	D	0.000787	T	0.55970	0.1954	N	0.00788	-1.185	0.40731	D	0.982749	B	0.21381	0.055	B	0.29598	0.104	T	0.54132	-0.8339	10	0.02654	T	1	-19.9282	8.1842	0.31328	0.0:0.3141:0.0:0.6859	.	75	Q9NWM8	FKB14_HUMAN	F	75	ENSP00000222803:I75F	ENSP00000222803:I75F	I	-	1	0	FKBP14	30028932	0.999000	0.42202	0.998000	0.56505	0.960000	0.62799	2.959000	0.49153	0.127000	0.18452	0.379000	0.24179	ATT		0.413	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946		A	30062407	T	A	30062407	3	1	112	1	0	0	0	0	1	0	0	0	5923	1464	51	5	424	5	FKBP14	7	30062407	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	25973397	30062407	129076256	64	30284										
VPS41	27072	hgsc.bcm.edu	37	chr7	38791872	38791872	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atctgtttttcatggtaacgCtgccccttatggtggtctct	9	10	3	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:38791872C>T	ENST00000310301.4	-	22	1884	c.1830G>A	c.(1828-1830)caG>caA	p.Q610Q	VPS41_ENST00000395969.2_Silent_p.Q585Q	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	610					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)	p.Q610Q(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CATGGTAACGCTGCCCCTTAT	0.403																																																1	Substitution - coding silent(1)	central_nervous_system(1)	7											176	167	170					7																	38791872		2203	4300	6503	38758397	SO:0001819	synonymous_variant	27072			U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1830G>A	7.37:g.38791872C>T			38758397	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																				0.403	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			T	38791872	C	T	38791872	2	4	112	1	0	0	0	0	0	0	0	1	17250	796	28	3		3	VPS41	7	38791872	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	8729465	38791872	120346791	65	30285										
HECW1	23072	hgsc.bcm.edu	37	chr7	43591930	43591930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcggaataacactgagtaccGgggaggtgagtgggcaggag	19	6	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:43591930G>A	ENST00000395891.2	+	28	5110	c.4505G>A	c.(4504-4506)cGg>cAg	p.R1502Q	HECW1_ENST00000453890.1_Missense_Mutation_p.R1468Q	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1502	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACTGAGTACCGGGGAGGTGAG	0.478																																																0			7											86	91	89					7																	43591930		2028	4174	6202	43558455	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4505G>A	7.37:g.43591930G>A	ENSP00000379228:p.Arg1502Gln		43558455	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	37	6.008838	0.97195	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.56941	0.43;0.43	5.81	5.81	0.92471	HECT (4);	0.058126	0.64402	D	0.000001	T	0.69333	0.3099	M	0.63428	1.95	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.60012	0.743;0.867	T	0.70741	-0.4789	10	0.87932	D	0	.	20.0628	0.97684	0.0:0.0:1.0:0.0	.	1468;1502	B4DH42;Q76N89	.;HECW1_HUMAN	Q	1502;1468;1502	ENSP00000379228:R1502Q;ENSP00000407774:R1468Q	ENSP00000265522:R1502Q	R	+	2	0	HECW1	43558455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.414000	0.97362	2.745000	0.94114	0.655000	0.94253	CGG		0.478	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43591930	G	A	43591930	3	1	112	1	0	0	0	0	1	0	0	0	7063	1116	39	1	4607	1	HECW1	7	43591930	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	4800058	43591930	115546733	66	30286										
EGFR	1956	hgsc.bcm.edu	37	chr7	55241637	55241637	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtggagcctcttacacccagTggagaagctcccaaccaagc	10	14	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:55241637T>C	ENST00000275493.2	+	18	2262	c.2085T>C	c.(2083-2085)agT>agC	p.S695S	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.S642S|EGFR_ENST00000455089.1_Silent_p.S650S	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	695	Important for dimerization, phosphorylation and activation.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TTACACCCAGTGGAGAAGCTC	0.542		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	0			7											102	105	104					7																	55241637		2203	4300	6503	55209131	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2085T>C	7.37:g.55241637T>C			55209131	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		C	55241637	T	C	55241637	2	2	112	1	0	0	0	0	0	0	0	1	4978	1693	59	4		4	EGFR	7	55241637	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	11649707	55241637	103897026	67	30287										
AZGP1	563	hgsc.bcm.edu	37	chr7	99566005	99566005	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tccagaatgctccgctgcttCtgttattctcgatctcacaa	6	13	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:99566005C>T	ENST00000292401.4	-	3	522	c.386G>A	c.(385-387)aGa>aAa	p.R129K	AZGP1_ENST00000483612.1_5'Flank|AZGP1_ENST00000411734.1_Missense_Mutation_p.R126K	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	129					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TCCGCTGCTTCTGTTATTCTC	0.488																																																0			7											213	229	224					7																	99566005		2203	4300	6503	99403941	SO:0001583	missense	563			BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"Immunoglobulin superfamily / C1-set domain containing"	910	protein-coding gene	gene with protein product		194460	"alpha-2-glycoprotein 1, zinc"			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.386G>A	7.37:g.99566005C>T	ENSP00000292401:p.Arg129Lys		99403941	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	37	CCDS5680.1	.	.	.	.	.	.	.	.	.	.	C	3.970	-0.008516	0.07727	.	.	ENSG00000160862	ENST00000292401;ENST00000411734	D;D	0.88818	-2.43;-2.43	2.76	-2.13	0.07144	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.268540	0.06134	N	0.671194	D	0.86372	0.5917	M	0.76328	2.33	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.71941	-0.4440	10	0.87932	D	0	.	4.6643	0.12657	0.0:0.4971:0.1858:0.3172	.	129	P25311	ZA2G_HUMAN	K	129;126	ENSP00000292401:R129K;ENSP00000396093:R126K	ENSP00000292401:R129K	R	-	2	0	AZGP1	99403941	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.147000	0.03188	-0.509000	0.06532	0.313000	0.20887	AGA		0.488	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185		T	99566005	C	T	99566005	3	4	112	1	0	0	0	0	1	0	0	0	1240	913	32	3	518	3	AZGP1	7	99566005	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	44324368	99566005	59572658	68	30288										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106508180	106508180	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aagagccccgaaacggcgctGctgcacgtggccggccacgg	15	15	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:106508180G>A	ENST00000359195.3	+	2	484	c.174G>A	c.(172-174)ctG>ctA	p.L58L	PIK3CG_ENST00000496166.1_Silent_p.L58L|PIK3CG_ENST00000440650.2_Silent_p.L58L	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	58	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L58L(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						AAACGGCGCTGCTGCACGTGG	0.682																																																1	Substitution - coding silent(1)	lung(1)	7											26	31	30					7																	106508180		2200	4296	6496	106295416	SO:0001819	synonymous_variant	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.174G>A	7.37:g.106508180G>A			106295416	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	CCDS5739.1																																																																																				0.682	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			A	106508180	G	A	106508180	2	1	112	1	0	0	0	0	0	0	0	1	11947	1306	46	3		3	PIK3CG	7	106508180	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	6942175	106508180	52630483	69	30289										
COG5	10466	hgsc.bcm.edu	37	chr7	106844055	106844055	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctctacttctcactgattgaAcataagcttccagggctccc	6	14	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:106844055A>C	ENST00000347053.3	-	21	2476	c.2426T>G	c.(2425-2427)gTt>gGt	p.V809G	COG5_ENST00000297135.3_Missense_Mutation_p.V830G	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	809					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						CACTGATTGAACATAAGCTTC	0.353																																																0			7											124	114	118					7																	106844055		2203	4300	6503	106631291	SO:0001583	missense	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.2426T>G	7.37:g.106844055A>C	ENSP00000334703:p.Val809Gly		106631291	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.374937	0.82573	.	.	ENSG00000164597	ENST00000347053;ENST00000297135	T;T	0.19394	2.18;2.15	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.44912	0.1316	M	0.72479	2.2	0.80722	D	1	D;D	0.64830	0.988;0.994	P;P	0.62184	0.779;0.899	T	0.37314	-0.9711	10	0.62326	D	0.03	-23.1603	16.5582	0.84512	1.0:0.0:0.0:0.0	.	809;830	Q9UP83;Q9UP83-2	COG5_HUMAN;.	G	809;830	ENSP00000334703:V809G;ENSP00000297135:V830G	ENSP00000297135:V830G	V	-	2	0	COG5	106631291	1.000000	0.71417	0.989000	0.46669	0.641000	0.38312	8.160000	0.89653	2.308000	0.77769	0.533000	0.62120	GTT		0.353	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			C	106844055	A	C	106844055	3	2	112	1	0	0	0	0	1	0	0	0	3667	43	2	4	97	4	COG5	7	106844055	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	335875	106844055	52294608	70	30290										
TSPAN33	340348	hgsc.bcm.edu	37	chr7	128806676	128806676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctcagaacatgtatttcaacTgctcagaagacaaccccagt	6	12	3	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:128806676T>C	ENST00000289407.4	+	6	626	c.517T>C	c.(517-519)Tgc>Cgc	p.C173R	RP11-286H14.6_ENST00000498745.1_RNA|Y_RNA_ENST00000363759.1_RNA	NM_178562.3	NP_848657.1	Q86UF1	TSN33_HUMAN	tetraspanin 33	173					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14						GTATTTCAACTGCTCAGAAGA	0.522																																																0			7											277	248	258					7																	128806676		2203	4300	6503	128593912	SO:0001583	missense	340348				CCDS5810.1	7q32.3	2013-02-14			ENSG00000158457	ENSG00000158457		"Tetraspanins"	28743	protein-coding gene	gene with protein product		610120				16213355, 16242907	Standard	XM_006715960		Approved	MGC50844, Penumbra	uc003vop.2	Q86UF1	OTTHUMG00000158420	ENST00000289407.4:c.517T>C	7.37:g.128806676T>C	ENSP00000289407:p.Cys173Arg		128593912		Missense_Mutation	SNP	ENST00000289407.4	37	CCDS5810.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327444	0.81690	.	.	ENSG00000158457	ENST00000289407	T	0.78707	-1.2	5.79	5.79	0.91817	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.90618	0.7058	H	0.94658	3.565	0.80722	D	1	D	0.61080	0.989	D	0.66716	0.946	D	0.92870	0.6313	10	0.72032	D	0.01	-26.7103	14.0849	0.64949	0.0:0.0:0.0:1.0	.	173	Q86UF1	TSN33_HUMAN	R	173	ENSP00000289407:C173R	ENSP00000289407:C173R	C	+	1	0	TSPAN33	128593912	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.560000	0.82277	2.208000	0.71279	0.533000	0.62120	TGC		0.522	TSPAN33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350983.1	NM_178562		C	128806676	T	C	128806676	3	2	112	1	0	0	0	0	1	0	0	0	16688	1580	55	4	539	4	TSPAN33	7	128806676	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	21962621	128806676	30331987	71	30291										
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139717476	139717476	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cacacggacctgcaggttcaCggctgaggcccggcagcagc	14	15	1	1	rs200831963		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:139717476C>T	ENST00000336425.5	+	16	1759	c.1370C>T	c.(1369-1371)aCg>aTg	p.T457M	TBXAS1_ENST00000425687.1_Missense_Mutation_p.T390M|TBXAS1_ENST00000411653.1_Intron|TBXAS1_ENST00000416849.2_Missense_Mutation_p.T504M|TBXAS1_ENST00000448866.1_Missense_Mutation_p.T457M|TBXAS1_ENST00000458722.1_Missense_Mutation_p.T503M|TBXAS1_ENST00000414508.2_Intron|TBXAS1_ENST00000263552.6_Missense_Mutation_p.T458M|TBXAS1_ENST00000436047.2_Missense_Mutation_p.T458M			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	457					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	TGCAGGTTCACGGCTGAGGCC	0.687													C|||	0	0	0	0	5008	,	,		16209	0		0	False		,,,				2504	0															0			7											28	32	31					7																	139717476		2203	4297	6500	139363945	SO:0001583	missense	6916			L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"Cytochrome P450s"	11609	protein-coding gene	gene with protein product	"cytochrome P450, family 5, subfamily A, polypeptide 1"	274180	"thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1370C>T	7.37:g.139717476C>T	ENSP00000338087:p.Thr457Met		139363945	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.10	1.837088	0.32513	.	.	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722	T;T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	4.69	0.411	0.16392	.	0.253618	0.38217	N	0.001766	T	0.71854	0.3389	L	0.49640	1.575	0.51233	D	0.99991	D;D;D;P;P	0.89917	0.997;0.999;1.0;0.948;0.948	P;D;D;P;P	0.70016	0.863;0.961;0.967;0.509;0.509	T	0.70992	-0.4721	10	0.87932	D	0	.	8.7726	0.34742	0.2438:0.4914:0.2647:0.0	.	438;504;390;458;457	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557	.;.;.;.;THAS_HUMAN	M	390;458;457;504;458;457;503	ENSP00000388736:T390M;ENSP00000263552:T458M;ENSP00000338087:T457M;ENSP00000389414:T504M;ENSP00000392361:T458M;ENSP00000402536:T457M;ENSP00000411274:T503M	ENSP00000263552:T458M	T	+	2	0	TBXAS1	139363945	0.795000	0.28851	0.420000	0.26596	0.066000	0.16364	1.479000	0.35453	0.373000	0.24621	0.561000	0.74099	ACG		0.687	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			T	139717476	C	T	139717476	3	4	112	1	0	0	0	0	1	0	0	0	15703	536	19	1	1561	1	TBXAS1	7	139717476	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	10910800	139717476	19421187	72	30292										
MKRN1	23608	hgsc.bcm.edu	37	chr7	140154929	140154929	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atgttcccactttctgtctcTgtggctcctctctacggcca	7	15	3	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:140154929T>C	ENST00000255977.2	-	7	1426	c.1202A>G	c.(1201-1203)cAg>cGg	p.Q401R	MKRN1_ENST00000474576.1_Missense_Mutation_p.Q337R|MKRN1_ENST00000437223.2_Missense_Mutation_p.Q135R	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	401					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					TTTCTGTCTCTGTGGCTCCTC	0.478																																																0			7											143	139	141					7																	140154929		2203	4300	6503	139801398	SO:0001583	missense	23608			AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"RING-type (C3HC4) zinc fingers"	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.1202A>G	7.37:g.140154929T>C	ENSP00000255977:p.Gln401Arg		139801398	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	37	CCDS5860.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.5|20.5	3.997269|3.997269	0.74818|0.74818	.|.	.|.	ENSG00000133606|ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000437223;ENST00000474576|ENST00000463142	T;T;T|.	0.41400|.	1.0;1.54;1.0|.	5.0|5.0	5.0|5.0	0.66597|0.66597	.|.	0.065987|.	0.64402|.	D|.	0.000009|.	T|T	0.64427|0.64427	0.2597|0.2597	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.68621|.	0.959|.	T|T	0.67902|0.67902	-0.5550|-0.5550	10|6	0.22109|0.72032	T|D	0.4|0.01	.|.	14.865|14.865	0.70406|0.70406	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	401|.	Q9UHC7|.	MKRN1_HUMAN|.	R|G	401;337;135;337|54	ENSP00000255977:Q401R;ENSP00000439823:Q135R;ENSP00000417863:Q337R|.	ENSP00000255977:Q401R|ENSP00000417346:R54G	Q|R	-|-	2|1	0|2	MKRN1|MKRN1	139801398|139801398	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.726000|5.726000	0.68515|0.68515	2.089000|2.089000	0.63090|0.63090	0.528000|0.528000	0.53228|0.53228	CAG|AGA		0.478	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446		C	140154929	T	C	140154929	3	2	112	1	0	0	0	0	1	0	0	0	9636	1580	55	4	254	4	MKRN1	7	140154929	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	437453	140154929	18983734	73	30293										
BRAF	673	hgsc.bcm.edu	37	chr7	140481402	140481402	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	actttcccttgtagactgttCcaaatgatccagatccaatt	5	11	0	3	rs121913358|rs397516890|rs121913355		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:140481402C>T	ENST00000288602.6	-	11	1466	c.1406G>A	c.(1405-1407)gGa>gAa	p.G469E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	469	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> A (in NHL; also in a lung adenocarcinoma sample; somatic mutation; elevated kinase activity; efficiently induces cell transformation). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:14612909, ECO:0000269|PubMed:17344846}.|G -> E (in CFC1 and colon cancer). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262, ECO:0000269|PubMed:19206169}.|G -> R (in NHL). {ECO:0000269|PubMed:14612909}.|G -> V (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G469A(19)|p.G469V(13)|p.G469S(5)|p.G469E(5)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	GTAGACTGTTCCAAATGATCC	0.373	G469A(NCIH1395_LUNG)|G469A(NCIH1755_LUNG)	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	42	Substitution - Missense(42)	lung(13)|large_intestine(9)|haematopoietic_and_lymphoid_tissue(6)|skin(6)|biliary_tract(2)|NS(2)|upper_aerodigestive_tract(1)|cervix(1)|small_intestine(1)|oesophagus(1)	7	GRCh37	CM060876	BRAF	M	rs121913355						174	149	158					7																	140481402		2203	4300	6503	140127871	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1406G>A	7.37:g.140481402C>T	ENSP00000288602:p.Gly469Glu		140127871	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.8|29.8	5.033024|5.033024	0.93575|0.93575	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.90324	.|-2.65	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97470|0.97470	0.9172|0.9172	H|H	0.98446|0.98446	4.235|4.235	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.91635	.|0.999	D|D	0.98855|0.98855	1.0760|1.0760	5|10	.|0.87932	.|D	.|0	.|.	17.8428|17.8428	0.88720|0.88720	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|469	.|P15056	.|BRAF_HUMAN	K|E	77|469	.|ENSP00000288602:G469E	.|ENSP00000288602:G469E	E|G	-|-	1|2	0|0	BRAF|BRAF	140127871|140127871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.818000|7.818000	0.86416|0.86416	2.637000|2.637000	0.89404|0.89404	0.585000|0.585000	0.79938|0.79938	GAA|GGA		0.373	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140481402	C	T	140481402	3	4	112	1	0	0	0	0	1	0	0	0	1499	855	30	3	926	3	BRAF	7	140481402	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	326473	140481402	18657261	74	30294										
NOS3	4846	hgsc.bcm.edu	37	chr7	150698506	150698506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tttcctgtccccggccttccGctaccaggtgcccaccctaa	7	19	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr7:150698506G>A	ENST00000484524.1	+	10	1421	c.1421G>A	c.(1420-1422)cGc>cAc	p.R474H	NOS3_ENST00000467517.1_Missense_Mutation_p.R474H|NOS3_ENST00000297494.3_Missense_Mutation_p.R474H|NOS3_ENST00000461406.1_Missense_Mutation_p.R268H	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGGCCTTCCGCTACCAGGTG	0.597																																																0			7											50	49	49					7																	150698506		2203	4300	6503	150329439	SO:0001583	missense	342977				CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1421G>A	7.37:g.150698506G>A	ENSP00000420215:p.Arg474His		150329439	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	37	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	G	9.338	1.062403	0.19987	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.22743	1.97;1.94;1.97;1.97	5.03	2.1	0.27182	Nitric oxide synthase, oxygenase domain (2);	0.442898	0.21205	N	0.078409	T	0.07143	0.0181	N	0.03324	-0.35	0.34677	D	0.724325	B;B;B;B;B	0.29590	0.006;0.006;0.25;0.001;0.005	B;B;B;B;B	0.28638	0.003;0.004;0.092;0.001;0.016	T	0.28106	-1.0054	10	0.26408	T	0.33	-16.2932	3.3773	0.07242	0.3227:0.0:0.4997:0.1775	rs61761728	474;474;474;268;474	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	H	474;268;474;474	ENSP00000297494:R474H;ENSP00000417143:R268H;ENSP00000420215:R474H;ENSP00000420551:R474H	ENSP00000297494:R474H	R	+	2	0	NOS3	150329439	0.619000	0.27059	1.000000	0.80357	0.905000	0.53344	0.320000	0.19540	0.108000	0.17862	0.561000	0.74099	CGC		0.597	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150698506	G	A	150698506	3	1	112	1	0	0	0	0	1	0	0	0	10575	1087	38	1	1459	1	NOS3	7	150698506	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10217104	150698506	8440157	75	30295										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24199173	24199173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	taatttgccctggaaaggacGgatagtgactttcctgacat	10	8	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr8:24199173G>A	ENST00000265769.4	+	16	1843	c.1733G>A	c.(1732-1734)cGg>cAg	p.R578Q	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.R325Q|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	578	Cys-rich.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R578L(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGGAAAGGACGGATAGTGACT	0.423																																					NSCLC(193;488 2149 22258 34798 40734)											1	Substitution - Missense(1)	lung(1)	8											258	242	248					8																	24199173		2203	4300	6503	24255118	SO:0001583	missense	10863			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1733G>A	8.37:g.24199173G>A	ENSP00000265769:p.Arg578Gln		24255118	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	G	4.866	0.160914	0.09287	.	.	ENSG00000042980	ENST00000265769;ENST00000397649	T;T	0.01613	4.83;4.73	5.84	0.567	0.17325	ADAM, cysteine-rich (1);	.	.	.	.	T	0.01558	0.0050	L	0.50919	1.6	0.09310	N	1	P;P	0.44816	0.844;0.844	B;B	0.35114	0.196;0.196	T	0.47235	-0.9133	9	0.15499	T	0.54	.	4.9572	0.14048	0.3117:0.0:0.5263:0.162	.	578;578	B2RMV5;Q9UKQ2	.;ADA28_HUMAN	Q	578;325	ENSP00000265769:R578Q;ENSP00000380770:R325Q	ENSP00000265769:R578Q	R	+	2	0	ADAM28	24255118	0.000000	0.05858	0.003000	0.11579	0.046000	0.14306	0.101000	0.15251	0.041000	0.15688	0.655000	0.94253	CGG		0.423	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		A	24199173	G	A	24199173	3	1	112	1	0	0	0	0	1	0	0	0	246	1116	39	1	1851	1	ADAM28	8	24199173	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10		24199173	122164849	76	30296										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77767926	77767926	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aatccctttaaatccaaaagTaatgatcggccgggtcacaa	7	10	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr8:77767926T>C	ENST00000521891.2	+	10	9217	c.8769T>C	c.(8767-8769)agT>agC	p.S2923S	ZFHX4_ENST00000050961.6_Silent_p.S2878S|ZFHX4_ENST00000455469.2_Silent_p.S2878S|ZFHX4_ENST00000518282.1_Silent_p.S2897S	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2878					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AATCCAAAAGTAATGATCGGC	0.512										HNSCC(33;0.089)																																						0			8											53	52	52					8																	77767926		1903	4114	6017	77930481	SO:0001819	synonymous_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8769T>C	8.37:g.77767926T>C			77930481	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																				0.512	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77767926	T	C	77767926	2	2	112	1	0	0	0	0	0	0	0	1	17674	1635	57	4		4	ZFHX4	8	77767926	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	53568753	77767926	68596096	77	30297										
PSKH2	85481	hgsc.bcm.edu	37	chr8	87076416	87076416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cagtcaccactttttttcccGgagtatgccaaaccaaaatc	5	13	1	0	rs376242267		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr8:87076416G>A	ENST00000276616.2	-	2	704	c.630C>T	c.(628-630)tcC>tcT	p.S210S	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			TTTTTTTCCCGGAGTATGCCA	0.423																																																0			8						G		1,4405	2.1+/-5.4	0,1,2202	72	76	75		630	-1.9	1	8		75	0,8600		0,0,4300	no	coding-synonymous	PSKH2	NM_033126.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		210/386	87076416	1,13005	2203	4300	6503	87145532	SO:0001819	synonymous_variant	85481			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.630C>T	8.37:g.87076416G>A			87145532	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																				0.423	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		A	87076416	G	A	87076416	2	1	112	1	0	0	0	0	0	0	0	1	12699	1103	39	1		1	PSKH2	8	87076416	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	9308490	87076416	59287606	78	30298										
GML	2765	hgsc.bcm.edu	37	chr8	143922589	143922589	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ataaatgacttcaactgtccCaacattagagtatgtccgta	6	9	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr8:143922589C>T	ENST00000220940.1	+	3	219	c.129C>T	c.(127-129)ccC>ccT	p.P43P		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	43	UPAR/Ly6.				apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCAACTGTCCCAACATTAGAG	0.458																																																0			8											225	182	196					8																	143922589		2203	4300	6503	143919591	SO:0001819	synonymous_variant	2765			D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"GPI anchored molecule like protein", "glycosylphosphatidylinositol anchored molecule like protein"			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.129C>T	8.37:g.143922589C>T			143919591	A0AVF6|O00686|O00731	Silent	SNP	ENST00000220940.1	37	CCDS6391.1																																																																																				0.458	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066		T	143922589	C	T	143922589	2	4	112	1	0	0	0	0	0	0	0	1	6512	581	21	3		3	GML	8	143922589	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	56846173	143922589	2441433	79	30299										
JAK2	3717	hgsc.bcm.edu	37	chr9	5070009	5070009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acagaggcctactcatatgaAccaaatggtgtttcacaaaa	7	9	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:5070009A>G	ENST00000381652.3	+	12	2092	c.1598A>G	c.(1597-1599)aAc>aGc	p.N533S	JAK2_ENST00000539801.1_Missense_Mutation_p.N533S|JAK2_ENST00000544510.1_Missense_Mutation_p.N384S	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	533					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ACTCATATGAACCAAATGGTG	0.313		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											86	81	83					9																	5070009		2203	4300	6503	5060009	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1598A>G	9.37:g.5070009A>G	ENSP00000371067:p.Asn533Ser		5060009	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	0.068	-1.207673	0.01568	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.32988	1.43;1.43;1.43	4.93	3.79	0.43588	Protein kinase-like domain (1);	0.174277	0.64402	N	0.000010	T	0.07908	0.0198	N	0.00841	-1.15	0.44555	D	0.99751	B	0.02656	0.0	B	0.06405	0.002	T	0.26018	-1.0115	10	0.02654	T	1	-15.4682	8.673	0.34163	0.8376:0.0:0.1624:0.0	.	533	O60674	JAK2_HUMAN	S	533;533;384	ENSP00000440387:N533S;ENSP00000371067:N533S;ENSP00000443103:N384S	ENSP00000371067:N533S	N	+	2	0	JAK2	5060009	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	3.770000	0.55310	0.724000	0.32296	-0.475000	0.04921	AAC		0.313	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5070009	A	G	5070009	3	3	112	1	0	0	0	0	1	0	0	0	7959	43	2	4	1636	4	JAK2	9	5070009	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10		5070009	136143422	80	30300										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8486143	8486143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tctggctgagagcctgaagaCgtatgatgctcccttgtgga	13	9	1	4	rs370631792	byFrequency	TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:8486143C>T	ENST00000381196.4	-	25	3217	c.2674G>A	c.(2674-2676)Gtc>Atc	p.V892I	PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000540109.1_Missense_Mutation_p.V892I|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.V879I|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000358503.5_Missense_Mutation_p.V870I|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000356435.5_Missense_Mutation_p.V892I	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	892	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		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)		AGCCTGAAGACGTATGATGCT	0.453										TSP Lung(15;0.13)			C|||	5	0.000998403	0	0	5008	,	,		20950	0		0.001	False		,,,				2504	0.0041															0			9						C	,,ILE/VAL,,,	2,4404	4.2+/-10.8	0,2,2201	103	97	99		,,2674,,,	-0.2	0	9		99	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,missense,intron,intron,intron	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,29,,,	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	,,benign,,,	,,892/1913,,,	8486143	4,13002	2203	4300	6503	8476143	SO:0001583	missense	5789			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2674G>A	9.37:g.8486143C>T	ENSP00000370593:p.Val892Ile		8476143	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.363739	0.01235	4.54E-4	2.33E-4	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38	5.68	-0.187	0.13268	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.341392	0.32852	N	0.005561	T	0.29620	0.0739	N	0.14661	0.345	0.29215	N	0.87431	B;B;B	0.20550	0.046;0.008;0.006	B;B;B	0.15870	0.013;0.003;0.014	T	0.17653	-1.0362	9	.	.	.	.	11.1214	0.48293	0.0:0.3346:0.0:0.6654	.	879;892;892	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	I	892;892;879;870;892	ENSP00000370593:V892I;ENSP00000348812:V892I;ENSP00000353187:V879I;ENSP00000351293:V870I;ENSP00000438164:V892I	.	V	-	1	0	PTPRD	8476143	0.001000	0.12720	0.032000	0.17829	0.364000	0.29643	-0.042000	0.12063	-0.245000	0.09625	-0.119000	0.15052	GTC		0.453	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8486143	C	T	8486143	3	4	112	1	0	0	0	0	1	0	0	0	12836	536	19	1	3208	1	PTPRD	9	8486143	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	3416134	8486143	132727288	81	30301										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32633293	32633293	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cacgaaaaaggttgttctcaAgtgcctgcagtaattggcca	10	9	1	0	rs113733449		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:32633293A>G	ENST00000242310.4	-	1	2374	c.2285T>C	c.(2284-2286)cTt>cCt	p.L762P	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	762			L -> I (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GTTGTTCTCAAGTGCCTGCAG	0.428																																																0			9											189	185	186					9																	32633293		2203	4300	6503	32623293	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2285T>C	9.37:g.32633293A>G	ENSP00000418379:p.Leu762Pro		32623293	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	5.458	0.269652	0.10349	.	.	ENSG00000122728	ENST00000242310	T	0.27104	1.69	1.19	1.19	0.21007	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.175861	0.64402	D	0.000012	T	0.44008	0.1273	M	0.87269	2.87	0.47698	D	0.999499	B	0.33171	0.4	P	0.49361	0.608	T	0.42682	-0.9437	10	0.87932	D	0	.	6.1457	0.20285	1.0:0.0:0.0:0.0	.	762	Q8IZX4	TAF1L_HUMAN	P	762	ENSP00000418379:L762P	ENSP00000418379:L762P	L	-	2	0	TAF1L	32623293	1.000000	0.71417	0.943000	0.38184	0.241000	0.25554	5.824000	0.69279	0.530000	0.28619	0.164000	0.16699	CTT		0.428	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32633293	A	G	32633293	3	3	112	1	0	0	0	0	1	0	0	0	15562	72	3	4	3199	4	TAF1L	9	32633293	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	24147150	32633293	108580138	82	30302										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72833433	72833433	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agaagacagtgaagagtcccTcttatggaggagaagaggtg	15	5	1	6			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:72833433T>A	ENST00000377182.4	+	12	2449	c.1832T>A	c.(1831-1833)cTc>cAc	p.L611H	SMC5-AS1_ENST00000594708.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	611	MAM 4. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GAAGAGTCCCTCTTATGGAGG	0.468																																																0			9											81	80	81					9																	72833433		2203	4300	6503	72023253	SO:0001583	missense	256691			BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.1832T>A	9.37:g.72833433T>A	ENSP00000366387:p.Leu611His		72023253	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	37	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657057	0.47467	.	.	ENSG00000165072	ENST00000377182	T	0.02369	4.32	5.21	4.07	0.47477	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.201385	0.41396	D	0.000897	T	0.11879	0.0289	M	0.75777	2.31	0.25358	N	0.988803	D	0.89917	1.0	D	0.79108	0.992	T	0.04153	-1.0973	10	0.42905	T	0.14	-7.4361	8.9237	0.35628	0.0:0.1655:0.0:0.8345	.	611	Q7Z304	MAMC2_HUMAN	H	611	ENSP00000366387:L611H	ENSP00000366387:L611H	L	+	2	0	MAMDC2	72023253	1.000000	0.71417	0.004000	0.12327	0.500000	0.33767	5.891000	0.69782	0.931000	0.37242	0.477000	0.44152	CTC		0.468	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		A	72833433	T	A	72833433	3	1	112	1	0	0	0	0	1	0	0	0	9233	1551	54	5	1878	5	MAMDC2	9	72833433	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	40200140	72833433	68379998	83	30303										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90500813	90500813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agaatgcacactctgtaccaCtggataaagcctccacttct	6	13	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:90500813C>T	ENST00000325643.5	+	4	1477	c.1411C>T	c.(1411-1413)Ctg>Ttg	p.L471L		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	471					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTCTGTACCACTGGATAAAGC	0.582																																																0			9											171	176	174					9																	90500813		2203	4300	6503	89690633	SO:0001819	synonymous_variant	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1411C>T	9.37:g.90500813C>T			89690633	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																				0.582	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90500813	C	T	90500813	2	4	112	1	0	0	0	0	0	0	0	1	2503	564	20	3		3	C9orf79	9	90500813	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	17667380	90500813	50712618	84	30304										
FAM120A	23196	hgsc.bcm.edu	37	chr9	96259756	96259756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tacgtttgttttctcaggtcCgggcccaccagctggtcttg	11	12	2	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:96259756C>T	ENST00000277165.6	+	4	1002	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W	FAM120A_ENST00000333936.5_Missense_Mutation_p.R270W|FAM120A_ENST00000375389.3_Missense_Mutation_p.R270W|FAM120A_ENST00000340893.4_Missense_Mutation_p.R270W	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	270						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTCTCAGGTCCGGGCCCACCA	0.507																																																0			9											153	132	139					9																	96259756		2203	4300	6503	95299577	SO:0001583	missense	23196			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.808C>T	9.37:g.96259756C>T	ENSP00000277165:p.Arg270Trp		95299577	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	C	31	5.095524	0.94197	.	.	ENSG00000048828	ENST00000375389;ENST00000277165;ENST00000333936;ENST00000340893	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	4.84	4.84	0.62591	.	0.112168	0.39083	N	0.001464	T	0.70971	0.3285	L	0.61218	1.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;0.994;0.996;1.0	T	0.74067	-0.3784	10	0.72032	D	0.01	-14.1653	18.1399	0.89636	0.0:1.0:0.0:0.0	.	270;270;270;270	Q9NZB2-6;Q9NZB2-5;Q9NZB2;Q9NZB2-2	.;.;F120A_HUMAN;.	W	270	ENSP00000364538:R270W;ENSP00000277165:R270W;ENSP00000334918:R270W;ENSP00000344698:R270W	ENSP00000277165:R270W	R	+	1	2	FAM120A	95299577	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.535000	0.82014	2.509000	0.84616	0.563000	0.77884	CGG		0.507	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		T	96259756	C	T	96259756	3	4	112	1	0	0	0	0	1	0	0	0	5431	643	23	1	822	1	FAM120A	9	96259756	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	5758943	96259756	44953675	85	30305										
ABL1	25	hgsc.bcm.edu	37	chr9	133748390	133748390	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccactcagatctcgtcagccAtggagtacctggagaagaaa	10	11	3	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:133748390A>G	ENST00000318560.5	+	6	1432	c.1051A>G	c.(1051-1053)Atg>Gtg	p.M351V		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	351	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CTCGTCAGCCATGGAGTACCT	0.602			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	0			9											62	50	54					9																	133748390		2203	4300	6503	132738211	SO:0001583	missense	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1051A>G	9.37:g.133748390A>G	ENSP00000323315:p.Met351Val		132738211	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.776868	0.90195	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.61859	0.07;0.07	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76765	0.4033	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79855	-0.1627	10	0.87932	D	0	.	15.5232	0.75881	1.0:0.0:0.0:0.0	.	351;388	P00519;Q59FK4	ABL1_HUMAN;.	V	166;370;351	ENSP00000361423:M370V;ENSP00000323315:M351V	ENSP00000323315:M351V	M	+	1	0	ABL1	132738211	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.317000	0.78254	0.460000	0.39030	ATG		0.602	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133748390	A	G	133748390	3	3	112	1	0	0	0	0	1	0	0	0	92	217	8	4	1213	4	ABL1	9	133748390	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	37488634	133748390	7465041	86	30306										
ABO	28	hgsc.bcm.edu	37	chr9	136131338	136131338	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cccaggtagtagaaatcgccCtcgtccttggggatgtaggc	13	11	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr9:136131338C>T	ENST00000453660.2	-	0	790				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		AGAAATCGCCCTCGTCCTTGG	0.677																																																0			9											18	21	20					9																	136131338		1963	4121	6084	135121159			28			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"Blood group antigens", "Glycosyltransferase family 6 domain containing"	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136131338C>T			135121159	B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	Missense_Mutation	SNP	ENST00000453660.2	37																																																																																					0.677	ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4	NM_020469		T	136131338	C	T	136131338	1	4	112	0	1	0	0	0	0	0	0	0	97	680	24	3		3	ABO	9	136131338	RNA	SNP	C	TCGA-EI-6508-01A-11D-1733-10	2382948	136131338	5082093	87	30307										
ADARB2	105	hgsc.bcm.edu	37	chr10	1262964	1262964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gccgtcccaggtctgcactgCgctggggccacgcacgggga	16	15	1	0	rs150320038		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:1262964C>T	ENST00000381312.1	-	7	1934	c.1609G>A	c.(1609-1611)Gca>Aca	p.A537T	ADARB2_ENST00000469464.1_5'UTR	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	537	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		GTCTGCACTGCGCTGGGGCCA	0.662																																																0			10						C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	50	43	45		1609	0.2	0	10	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADARB2	NM_018702.3	58	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	benign	537/740	1262964	3,13003	2203	4300	6503	1252964	SO:0001583	missense	105			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1609G>A	10.37:g.1262964C>T	ENSP00000370713:p.Ala537Thr		1252964	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	C	9.167	1.020170	0.19433	4.54E-4	1.16E-4	ENSG00000185736	ENST00000381312	D	0.93763	-3.28	5.41	0.166	0.14999	Adenosine deaminase/editase (3);	0.405255	0.29369	N	0.012348	D	0.83041	0.5168	N	0.19112	0.55	0.47308	D	0.999388	B	0.12013	0.005	B	0.19391	0.025	T	0.65393	-0.6179	10	0.12766	T	0.61	-3.2963	5.5037	0.16842	0.1796:0.5608:0.0:0.2596	.	537	Q9NS39	RED2_HUMAN	T	537	ENSP00000370713:A537T	ENSP00000370713:A537T	A	-	1	0	ADARB2	1252964	0.000000	0.05858	0.003000	0.11579	0.872000	0.50106	-0.332000	0.07904	-0.256000	0.09473	0.491000	0.48974	GCA		0.662	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		T	1262964	C	T	1262964	3	4	112	1	0	0	0	0	1	0	0	0	283	768	27	1	626	1	ADARB2	10	1262964	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		1262964	134271783	88	30308										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887864	25887864	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gagagggcaaaagaggagaaCggaggtcagcctcgtgcagc	17	8	1	3	rs149155339		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:25887864C>T	ENST00000376351.3	+	11	3668	c.3309C>T	c.(3307-3309)aaC>aaT	p.N1103N	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1103					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N1103N(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						AAGAGGAGAACGGAGGTCAGC	0.493													C|||	1	0.000199681	8e-04	0	5008	,	,		18272	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	10						C		1,4405		0,1,2202	79	84	82		3309	-11.8	0	10	dbSNP_134	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GPR158	NM_020752.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		1103/1216	25887864	3,13003	2203	4300	6503	25927870	SO:0001819	synonymous_variant	57512			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3309C>T	10.37:g.25887864C>T			25927870	Q6QR81|Q9ULT3	Silent	SNP	ENST00000376351.3	37	CCDS31166.1																																																																																				0.493	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25887864	C	T	25887864	2	4	112	1	0	0	0	0	0	0	0	1	6683	535	19	1		1	GPR158	10	25887864	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	24624900	25887864	109646883	89	30309										
ANK3	288	hgsc.bcm.edu	37	chr10	61832653	61832653	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agactgggtgccttctcctcGgccttggggaagccttgtcc	13	13	1	1	rs147625375		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:61832653G>A	ENST00000280772.2	-	37	8177	c.7986C>T	c.(7984-7986)gcC>gcT	p.A2662A	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2662					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CCTTCTCCTCGGCCTTGGGGA	0.547																																																0			10						G	,,,	1,4405	2.1+/-5.4	0,1,2202	91	76	81		,,,7986	-4.9	0.1	10	dbSNP_134	81	0,8600		0,0,4300	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	,,,2662/4378	61832653	1,13005	2203	4300	6503	61502659	SO:0001819	synonymous_variant	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.7986C>T	10.37:g.61832653G>A			61502659	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																				0.547	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61832653	G	A	61832653	2	1	112	1	0	0	0	0	0	0	0	1	622	1103	39	1		1	ANK3	10	61832653	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	35944789	61832653	73702094	90	30310										
LGI1	9211	hgsc.bcm.edu	37	chr10	95553061	95553061	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggaaaatgcattttccttgaAtgggaccatgtggaaaagac	11	6	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:95553061A>G	ENST00000371418.4	+	7	1052	c.792A>G	c.(790-792)gaA>gaG	p.E264E	LGI1_ENST00000371413.3_Silent_p.E264E|LGI1_ENST00000542308.1_Silent_p.E216E	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	264					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				TTTTCCTTGAATGGGACCATG	0.373																																																0			10											131	123	126					10																	95553061		2203	4300	6503	95543051	SO:0001819	synonymous_variant	9211			AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"epilepsy, partial"	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.792A>G	10.37:g.95553061A>G			95543051	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	37	CCDS7431.1																																																																																				0.373	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		G	95553061	A	G	95553061	2	3	112	1	0	0	0	0	0	0	0	1	8774	98	4	4		4	LGI1	10	95553061	Silent	SNP	A	TCGA-EI-6508-01A-11D-1733-10	33720408	95553061	39981686	91	30311										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101578640	101578640	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atcttctagatgaccccctgTctgcagtggatgctcatgta	9	11	4	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:101578640T>C	ENST00000370449.4	+	18	2478	c.2365T>C	c.(2365-2367)Tct>Cct	p.S789P		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	789	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		S -> F (in dbSNP:rs56220353). {ECO:0000269|PubMed:11266082}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TGACCCCCTGTCTGCAGTGGA	0.448																																																0			10											71	75	74					10																	101578640		2203	4300	6503	101568630	SO:0001583	missense	1244			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.2365T>C	10.37:g.101578640T>C	ENSP00000359478:p.Ser789Pro		101568630	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518621	0.64634	.	.	ENSG00000023839	ENST00000370449	D	0.93019	-3.15	6.08	6.08	0.98989	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.98324	0.9444	H	0.99182	4.46	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.99709	1.1006	10	0.87932	D	0	-9.0945	15.8241	0.78683	0.0:0.0:0.0:1.0	.	789	Q92887	MRP2_HUMAN	P	789	ENSP00000359478:S789P	ENSP00000359478:S789P	S	+	1	0	ABCC2	101568630	1.000000	0.71417	0.624000	0.29186	0.183000	0.23260	8.037000	0.88933	2.330000	0.79161	0.533000	0.62120	TCT		0.448	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		C	101578640	T	C	101578640	3	2	112	1	0	0	0	0	1	0	0	0	53	1667	58	4	2435	4	ABCC2	10	101578640	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	6025579	101578640	33956107	92	30312										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124402685	124402685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctactcctcgccatctcttcGcattgcccgcttccggttca	6	18	2	0	rs373485754		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:124402685G>A	ENST00000338354.3	+	53	7119	c.7013G>A	c.(7012-7014)cGc>cAc	p.R2338H	DMBT1_ENST00000368956.2_Missense_Mutation_p.R1710H|DMBT1_ENST00000368955.3_Missense_Mutation_p.R2328H|DMBT1_ENST00000344338.3_Missense_Mutation_p.R2328H|DMBT1_ENST00000330163.4_Missense_Mutation_p.R1710H|DMBT1_ENST00000368909.3_Missense_Mutation_p.R2338H|DMBT1_ENST00000359586.6_Missense_Mutation_p.R1058H			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2338	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCATCTCTTCGCATTGCCCGC	0.567																																					Ovarian(182;93 2026 18125 22222 38972)											0			10						G	HIS/ARG,HIS/ARG,HIS/ARG	0,4188		0,0,2094	122	133	129		5129,7013,6983	-2.3	0	10		129	2,8426		0,2,4212	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	29,29,29	0,2,6306	AA,AG,GG		0.0237,0.0,0.0159	probably-damaging,probably-damaging,probably-damaging	1710/1786,2338/2414,2328/2404	124402685	2,12614	2094	4214	6308	124392675	SO:0001583	missense	1755				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7013G>A	10.37:g.124402685G>A	ENSP00000342210:p.Arg2338His		124392675	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	G	15.87	2.960030	0.53400	0.0	2.37E-4	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	T;T;T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44;-1.44;-1.44	5.28	-2.3	0.06785	Zona pellucida sperm-binding protein (3);	0.647614	0.12372	U	0.474651	T	0.75686	0.3883	L	0.27053	0.805	0.09310	N	1	B;D;B;B;B;B;B	0.71674	0.054;0.998;0.011;0.043;0.011;0.043;0.054	B;P;B;B;B;B;B	0.53649	0.011;0.731;0.004;0.008;0.004;0.008;0.013	T	0.69548	-0.5116	10	0.40728	T	0.16	.	12.6859	0.56948	0.6711:0.0:0.3289:0.0	.	1058;2318;1587;2467;1710;2328;2338	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	H	2338;2467;2338;2338;2338;2337;1710;2328;1710;1710;2338;2328;1710;484;1058	ENSP00000342210:R2338H;ENSP00000343175:R2328H;ENSP00000327747:R1710H;ENSP00000357905:R2338H;ENSP00000357951:R2328H;ENSP00000357952:R1710H;ENSP00000352593:R1058H	ENSP00000331522:R1710H	R	+	2	0	DMBT1	124392675	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.426000	0.07008	-0.534000	0.06315	-0.136000	0.14681	CGC		0.567	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124402685	G	A	124402685	3	1	112	1	0	0	0	0	1	0	0	0	4588	1087	38	1	7223	1	DMBT1	10	124402685	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	22824045	124402685	11132062	93	30313										
MKI67	4288	hgsc.bcm.edu	37	chr10	129905236	129905236	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggagcttgctgggtttttgTctgggtctggttgtgaagat	16	4	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr10:129905236T>C	ENST00000368654.3	-	13	5243	c.4868A>G	c.(4867-4869)gAc>gGc	p.D1623G	MKI67_ENST00000368653.3_Missense_Mutation_p.D1263G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1623	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGGGTTTTTGTCTGGGTCTGG	0.498																																																0			10											212	212	212					10																	129905236		2203	4300	6503	129795226	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4868A>G	10.37:g.129905236T>C	ENSP00000357643:p.Asp1623Gly		129795226	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.810208	0.32053	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02121	4.44;4.44	2.75	0.203	0.15195	.	0.606583	0.12571	N	0.457287	T	0.02494	0.0076	N	0.22421	0.69	0.09310	N	1	P;D;P	0.63880	0.73;0.993;0.789	B;P;P	0.53062	0.181;0.717;0.504	T	0.47235	-0.9133	10	0.29301	T	0.29	.	2.595	0.04852	0.3999:0.0:0.1339:0.4663	.	1622;1263;1623	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	G	1623;1263;1622	ENSP00000357643:D1623G;ENSP00000357642:D1263G	ENSP00000357642:D1263G	D	-	2	0	MKI67	129795226	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-3.866000	0.00347	0.029000	0.15352	-0.624000	0.04008	GAC		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129905236	T	C	129905236	3	2	112	1	0	0	0	0	1	0	0	0	9628	1667	58	4	4914	4	MKI67	10	129905236	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	5502551	129905236	5629511	94	30314										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17126781	17126781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgcaagtggtttatctttaaAggatcctgtcacaccatatt	7	8	2	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:17126781A>G	ENST00000265970.7	-	22	3615	c.3616T>C	c.(3616-3618)Ttt>Ctt	p.F1206L	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.F826L	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1206	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.F1206L(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTATCTTTAAAGGATCCTGTC	0.383																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											104	99	101					11																	17126781		2200	4293	6493	17083357	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3616T>C	11.37:g.17126781A>G	ENSP00000265970:p.Phe1206Leu		17083357	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	35	5.430685	0.96150	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80566	-1.39;-1.39	5.64	5.64	0.86602	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.87410	0.6170	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.86555	0.1837	10	0.38643	T	0.18	-20.0574	15.8745	0.79151	1.0:0.0:0.0:0.0	.	1206	O00443	P3C2A_HUMAN	L	1206;826	ENSP00000265970:F1206L;ENSP00000438687:F826L	ENSP00000265970:F1206L	F	-	1	0	PIK3C2A	17083357	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.201000	0.95017	2.151000	0.67156	0.459000	0.35465	TTT		0.383	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17126781	A	G	17126781	3	3	112	1	0	0	0	0	1	0	0	0	11940	72	3	4	1488	4	PIK3C2A	11	17126781	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10		17126781	117879735	95	30315										
SAA2	6289	hgsc.bcm.edu	37	chr11	18267550	18267550	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atttgtctgagccgatgtaaTtggcttctctcatgtcagag	10	8	4	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:18267550T>G	ENST00000526900.1	-	3	320	c.137A>C	c.(136-138)aAt>aCt	p.N46T	SAA2_ENST00000528349.1_Missense_Mutation_p.N46T|SAA2_ENST00000256733.4_Missense_Mutation_p.N46T|SAA2_ENST00000529528.1_Missense_Mutation_p.N46T|SAA2_ENST00000414546.2_Missense_Mutation_p.N46T|SAA2-SAA4_ENST00000524555.1_RNA|RNA5SP333_ENST00000363466.1_RNA|SAA2_ENST00000530400.1_Missense_Mutation_p.N46T			P0DJI9	SAA2_HUMAN	serum amyloid A2	46					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						GCCGATGTAATTGGCTTCTCT	0.522																																																0			11											79	70	73					11																	18267550		2198	4273	6471	18224126	SO:0001583	missense	0			M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.137A>C	11.37:g.18267550T>G	ENSP00000436126:p.Asn46Thr		18224126	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Missense_Mutation	SNP	ENST00000526900.1	37	CCDS7833.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.614270	0.66672	.	.	ENSG00000134339	ENST00000414546;ENST00000530400;ENST00000528349;ENST00000256733;ENST00000529528;ENST00000526900	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25	5.19	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	.	.	.	0.36758	D	0.883159	D;D	0.60160	0.967;0.987	P;D	0.64506	0.676;0.926	T	0.44159	-0.9346	9	0.87932	D	0	.	9.2133	0.37331	0.0:0.0829:0.0:0.9171	.	46;46	G3XAK9;E9PR14	.;.	T	46	ENSP00000416716:N46T;ENSP00000432370:N46T;ENSP00000435659:N46T;ENSP00000256733:N46T;ENSP00000437162:N46T;ENSP00000436126:N46T	ENSP00000256733:N46T	N	-	2	0	SAA2	18224126	0.999000	0.42202	0.664000	0.29753	0.905000	0.53344	3.371000	0.52379	0.937000	0.37394	0.528000	0.53228	AAT		0.522	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754		G	18267550	T	G	18267550	3	3	112	1	0	0	0	0	1	0	0	0	13836	1493	52	4	265	4	SAA2	11	18267550	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	1140769	18267550	116738966	96	30316										
HPS5	11234	hgsc.bcm.edu	37	chr11	18305412	18305412	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaggcctctcttcttctctcCagctccaaacagagaattag	6	13	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:18305412C>T	ENST00000349215.3	-	21	3265	c.2988G>A	c.(2986-2988)ctG>ctA	p.L996L	HPS5_ENST00000438420.2_Silent_p.L882L|HPS5_ENST00000396253.3_Silent_p.L882L|HPS5_ENST00000352460.3_5'UTR|HPS5_ENST00000537258.1_Silent_p.L103L	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	996					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TTCTTCTCTCCAGCTCCAAAC	0.423									Hermansky-Pudlak syndrome																																							0			11											128	124	125					11																	18305412		2199	4293	6492	18261988	SO:0001819	synonymous_variant	11234	Familial Cancer Database	HPS, HPS1-8	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2988G>A	11.37:g.18305412C>T			18261988	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																				0.423	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		T	18305412	C	T	18305412	2	4	112	1	0	0	0	0	0	0	0	1	7363	581	21	3		3	HPS5	11	18305412	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	37862	18305412	116701104	97	30317										
OR4C12	283093	hgsc.bcm.edu	37	chr11	50003744	50003744	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaaatgtgttctgcataggcTtgagccatacacccattaaa	7	9	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:50003744T>A	ENST00000335238.4	-	1	327	c.294A>T	c.(292-294)caA>caT	p.Q98H		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						CTGCATAGGCTTGAGCCATAC	0.423																																																0			11											129	128	128					11																	50003744		2201	4296	6497	49960320	SO:0001583	missense	283093			BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"GPCR / Class A : Olfactory receptors"	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.294A>T	11.37:g.50003744T>A	ENSP00000334418:p.Gln98His		49960320	B2RNF0|Q6IF49	Missense_Mutation	SNP	ENST00000335238.4	37	CCDS31496.1	.	.	.	.	.	.	.	.	.	.	.	15.42	2.828055	0.50845	.	.	ENSG00000221954	ENST00000335238	T	0.00472	7.19	3.31	-0.498	0.12019	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	U	0.001169	T	0.02047	0.0064	H	0.98238	4.18	0.28323	N	0.922133	D	0.89917	1.0	D	0.91635	0.999	T	0.16928	-1.0386	10	0.87932	D	0	.	6.6433	0.22921	0.0:0.3485:0.0:0.6514	.	98	Q96R67	OR4CC_HUMAN	H	98	ENSP00000334418:Q98H	ENSP00000334418:Q98H	Q	-	3	2	OR4C12	49960320	0.002000	0.14202	0.922000	0.36590	0.937000	0.57800	-0.409000	0.07160	-0.194000	0.10399	-0.564000	0.04169	CAA		0.423	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1	NM_001005270		A	50003744	T	A	50003744	3	1	112	1	0	0	0	0	1	0	0	0	11077	1606	56	5	639	5	OR4C12	11	50003744	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	31698332	50003744	85002772	98	30318										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114150	56114150	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttgatcttctcaggctgtaaTttgctcttctccctctcaat	5	12	5	1	rs377093588		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:56114150T>A	ENST00000279783.2	+	1	730	c.636T>A	c.(634-636)aaT>aaA	p.N212K		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CAGGCTGTAATTTGCTCTTCT	0.373										HNSCC(65;0.19)																																						0			11											116	111	113					11																	56114150		2201	4296	6497	55870726	SO:0001583	missense	390157			AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.636T>A	11.37:g.56114150T>A	ENSP00000279783:p.Asn212Lys		55870726	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.501228	0.44455	.	.	ENSG00000150261	ENST00000279783	T	0.00099	8.73	5.0	1.39	0.22231	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000071	T	0.00384	0.0012	M	0.88906	2.99	0.25203	N	0.990036	D	0.54964	0.969	P	0.58130	0.833	T	0.35724	-0.9777	10	0.87932	D	0	-18.9539	6.9012	0.24283	0.0:0.3186:0.0:0.6814	.	212	Q8NGG5	OR8K1_HUMAN	K	212	ENSP00000279783:N212K	ENSP00000279783:N212K	N	+	3	2	OR8K1	55870726	0.000000	0.05858	0.371000	0.25978	0.423000	0.31445	-1.713000	0.01883	0.244000	0.21351	0.448000	0.29417	AAT		0.373	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		A	56114150	T	A	56114150	3	1	112	1	0	0	0	0	1	0	0	0	11274	1490	52	5	638	5	OR8K1	11	56114150	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	6110406	56114150	78892366	99	30319										
PC	5091	hgsc.bcm.edu	37	chr11	66639505	66639505	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggtgctcacctctgttggcCaccatgactttcttgatggg	11	11	3	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:66639505C>T	ENST00000393958.2	-	3	219	c.126G>A	c.(124-126)gtG>gtA	p.V42V	PC_ENST00000393955.2_Silent_p.V42V|PC_ENST00000524491.1_Silent_p.V2V|PC_ENST00000393960.1_Silent_p.V42V|PC_ENST00000355677.3_Silent_p.V42V	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	42	Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.V42V(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CTCTGTTGGCCACCATGACTT	0.657																																																1	Substitution - coding silent(1)	ovary(1)	11											26	20	22					11																	66639505		2175	4268	6443	66396081	SO:0001819	synonymous_variant	5624			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.126G>A	11.37:g.66639505C>T			66396081	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	37	CCDS8152.1																																																																																				0.657	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66639505	C	T	66639505	2	4	112	1	0	0	0	0	0	0	0	1	11528	581	21	3		3	PC	11	66639505	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	10525355	66639505	68367011	100	30320										
UVRAG	7405	hgsc.bcm.edu	37	chr11	75590981	75590981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agaccgtcttgatacatctgTgtcttgtttcgtggtgaaga	11	7	3	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:75590981T>C	ENST00000356136.3	+	4	570	c.329T>C	c.(328-330)gTg>gCg	p.V110A	UVRAG_ENST00000528420.1_Missense_Mutation_p.V9A	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	110	C2.				DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						GATACATCTGTGTCTTGTTTC	0.433																																																0			11											277	262	267					11																	75590981		2200	4293	6493	75268629	SO:0001583	missense	7405			X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.329T>C	11.37:g.75590981T>C	ENSP00000348455:p.Val110Ala		75268629	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.616580	0.46736	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000528264	T	0.45668	0.89	5.65	5.65	0.86999	C2 calcium-dependent membrane targeting (1);	0.054145	0.64402	D	0.000001	T	0.35913	0.0948	L	0.41236	1.265	0.80722	D	1	B	0.26935	0.164	B	0.26517	0.07	T	0.11251	-1.0595	10	0.28530	T	0.3	-12.7328	14.7229	0.69320	0.0:0.0:0.0:1.0	.	110	Q9P2Y5	UVRAG_HUMAN	A	110;9;9	ENSP00000348455:V110A	ENSP00000348455:V110A	V	+	2	0	UVRAG	75268629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.890000	0.69774	2.163000	0.67991	0.533000	0.62120	GTG		0.433	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		C	75590981	T	C	75590981	3	2	112	1	0	0	0	0	1	0	0	0	17148	1696	59	4	343	4	UVRAG	11	75590981	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	8951476	75590981	59415535	101	30321										
BIRC3	330	hgsc.bcm.edu	37	chr11	102195608	102195608	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agtaacaaattccacacactCattacttccgggtacagaaa	5	11	1	1	rs572690185		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:102195608C>T	ENST00000263464.3	+	2	3118	c.368C>T	c.(367-369)tCa>tTa	p.S123L	BIRC3_ENST00000532808.1_Missense_Mutation_p.S123L	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	123					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TCCACACACTCATTACTTCCG	0.408			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	0			11											171	179	176					11																	102195608		2203	4299	6502	101700818	SO:0001583	missense	330			L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.368C>T	11.37:g.102195608C>T	ENSP00000263464:p.Ser123Leu		101700818	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	C	3.937	-0.014949	0.07681	.	.	ENSG00000023445	ENST00000263464;ENST00000532808	T;T	0.21932	1.98;1.98	5.93	0.599	0.17519	.	0.417996	0.29046	N	0.013313	T	0.12944	0.0314	L	0.33485	1.01	0.09310	N	1	B	0.14012	0.009	B	0.15484	0.013	T	0.25047	-1.0143	10	0.25751	T	0.34	.	7.46	0.27289	0.0:0.6434:0.1113:0.2453	.	123	Q13489	BIRC3_HUMAN	L	123	ENSP00000263464:S123L;ENSP00000432907:S123L	ENSP00000263464:S123L	S	+	2	0	BIRC3	101700818	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.566000	0.23593	0.122000	0.18314	-0.229000	0.12294	TCA		0.408	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102195608	C	T	102195608	3	4	112	1	0	0	0	0	1	0	0	0	1437	838	29	3	370	3	BIRC3	11	102195608	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	26604627	102195608	32810908	102	30322										
ATM	472	hgsc.bcm.edu	37	chr11	108236081	108236081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccagagtttcaacaaagtagCtgaacgtgtcttaatgagac	9	8	2	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:108236081C>T	ENST00000452508.2	+	64	9206	c.9017C>T	c.(9016-9018)gCt>gTt	p.A3006V	ATM_ENST00000525178.1_3'UTR|ATM_ENST00000278616.4_Missense_Mutation_p.A3006V|C11orf65_ENST00000525729.1_Intron|C11orf65_ENST00000526725.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	3006			A -> P (in T-prolymphocytic leukemia). {ECO:0000269|PubMed:9334731}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.A3006V(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AACAAAGTAGCTGAACGTGTC	0.413			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											123	120	121					11																	108236081		2201	4298	6499	107741291	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.9017C>T	11.37:g.108236081C>T	ENSP00000388058:p.Ala3006Val		107741291	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067499	0.93898	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02579	4.24;4.24	5.22	5.22	0.72569	Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.108387	0.64402	D	0.000007	T	0.17577	0.0422	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.00096	-1.2074	10	0.66056	D	0.02	.	19.0354	0.92974	0.0:1.0:0.0:0.0	.	3006	Q13315	ATM_HUMAN	V	3006	ENSP00000278616:A3006V;ENSP00000388058:A3006V	ENSP00000278616:A3006V	A	+	2	0	ATM	107741291	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	7.458000	0.80787	2.726000	0.93360	0.650000	0.86243	GCT		0.413	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108236081	C	T	108236081	3	4	112	1	0	0	0	0	1	0	0	0	1110	797	28	3	9263	3	ATM	11	108236081	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	6040473	108236081	26770435	103	30323										
VWA5A	4013	hgsc.bcm.edu	37	chr11	123989725	123989725	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtttgatcgggacgtggaacTcctgatttactacaatgagg	12	7	0	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr11:123989725T>C	ENST00000456829.2	+	7	940	c.689T>C	c.(688-690)cTc>cCc	p.L230P	VWA5A_ENST00000392748.1_Missense_Mutation_p.L230P|VWA5A_ENST00000360334.4_Missense_Mutation_p.L230P|VWA5A_ENST00000449321.1_Missense_Mutation_p.L230P|VWA5A_ENST00000392744.4_Missense_Mutation_p.L246P|VWA5A_ENST00000361352.5_Missense_Mutation_p.L230P	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	230										autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						GACGTGGAACTCCTGATTTAC	0.478																																																0			11											149	118	129					11																	123989725		2201	4299	6500	123494935	SO:0001583	missense	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.689T>C	11.37:g.123989725T>C	ENSP00000407726:p.Leu230Pro		123494935	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901231	0.72754	.	.	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000524524;ENST00000530025;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.45668	2.95;0.89;2.95;1.26;1.26;1.23	5.73	5.73	0.89815	.	0.118802	0.64402	D	0.000017	T	0.65852	0.2731	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.977	T	0.70898	-0.4747	10	0.87932	D	0	-25.85	13.9569	0.64155	0.0:0.0:0.0:1.0	.	246;230	B4DHS6;O00534	.;VMA5A_HUMAN	P	230;230;230;230;230;230;230;246	ENSP00000407726:L230P;ENSP00000353485:L230P;ENSP00000376504:L230P;ENSP00000355070:L230P;ENSP00000404683:L230P;ENSP00000376501:L246P	ENSP00000353485:L230P	L	+	2	0	VWA5A	123494935	1.000000	0.71417	0.988000	0.46212	0.485000	0.33311	6.625000	0.74248	2.183000	0.69458	0.528000	0.53228	CTC		0.478	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		C	123989725	T	C	123989725	3	2	112	1	0	0	0	0	1	0	0	0	17282	1551	54	4	707	4	VWA5A	11	123989725	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	15753644	123989725	11016791	104	30324										
ACRBP	84519	hgsc.bcm.edu	37	chr12	6749646	6749646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	caaggagcagaagtcacagaGggcacaggtagacatgtgtc	14	8	1	3	rs369836113		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:6749646G>A	ENST00000229243.2	-	7	1213	c.1120C>T	c.(1120-1122)Ctc>Ttc	p.L374F	ACRBP_ENST00000414226.2_Missense_Mutation_p.L341F|ACRBP_ENST00000542357.1_5'UTR	NM_032489.2	NP_115878.2			acrosin binding protein											NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						AAGTCACAGAGGGCACAGGTA	0.612																																																0			12						G	PHE/LEU	0,4406		0,0,2203	52	54	53		1120	1.9	0.9	12		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACRBP	NM_032489.2	22	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	374/544	6749646	1,13005	2203	4300	6503	6619907	SO:0001583	missense	84519			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"proacrosin binding protein sp32", "cancer/testis antigen 23"	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.1120C>T	12.37:g.6749646G>A	ENSP00000229243:p.Leu374Phe		6619907		Missense_Mutation	SNP	ENST00000229243.2	37	CCDS8554.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.855324	0.32791	0.0	1.16E-4	ENSG00000111644	ENST00000229243;ENST00000414226	T;T	0.47528	0.84;0.84	5.22	1.93	0.25924	.	1.066800	0.07293	N	0.872865	T	0.41351	0.1155	L	0.50333	1.59	0.09310	N	0.999999	B;B	0.17465	0.022;0.022	B;B	0.12837	0.008;0.008	T	0.32241	-0.9914	10	0.37606	T	0.19	0.0207	7.2435	0.26109	0.2524:0.1639:0.5837:0.0	.	341;374	E7EP66;Q8NEB7	.;ACRBP_HUMAN	F	374;341	ENSP00000229243:L374F;ENSP00000402725:L341F	ENSP00000229243:L374F	L	-	1	0	ACRBP	6619907	0.815000	0.29118	0.938000	0.37757	0.974000	0.67602	1.125000	0.31332	0.594000	0.29761	0.561000	0.74099	CTC		0.612	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489		A	6749646	G	A	6749646	3	1	112	1	0	0	0	0	1	0	0	0	170	1000	35	3	527	3	ACRBP	12	6749646	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10		6749646	127102249	105	30325										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94543506	94543506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccctactacccctacaactaCacgagcggcgctgccaccgg	8	19	0	0	rs2230754	byFrequency	TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:94543506C>T	ENST00000258526.4	+	1	1008	c.759C>T	c.(757-759)taC>taT	p.Y253Y		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	253	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CCTACAACTACACGAGCGGCG	0.682													C|||	2261	0.451478	0.5204	0.4654	5008	,	,		15562	0.4831		0.34	False		,,,				2504	0.4305															0			12						C		1851,2441		433,985,728	31	36	34		759	4.1	1	12	dbSNP_98	34	3103,5439		592,1919,1760	no	coding-synonymous	PLXNC1	NM_005761.2		1025,2904,2488	TT,TC,CC		36.3264,43.1267,38.6006		253/1569	94543506	4954,7880	2146	4271	6417	93067637	SO:0001819	synonymous_variant	10154			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.759C>T	12.37:g.94543506C>T			93067637	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																				0.682	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94543506	C	T	94543506	2	4	112	1	0	0	0	0	0	0	0	1	12157	489	17	3		3	PLXNC1	12	94543506	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	87793860	94543506	39308389	106	30326										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100476887	100476887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aatactgaaggtgttctgcaTgtccctttcagagggtagtc	11	8	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:100476887T>C	ENST00000279907.7	-	11	1526	c.1314A>G	c.(1312-1314)acA>acG	p.T438T	UHRF1BP1L_ENST00000356828.3_Silent_p.T438T|UHRF1BP1L_ENST00000545232.2_Silent_p.T88T	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	438										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GTGTTCTGCATGTCCCTTTCA	0.348																																																0			12											156	141	146					12																	100476887		2203	4300	6503	99001018	SO:0001819	synonymous_variant	23074				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1314A>G	12.37:g.100476887T>C			99001018	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	37	CCDS31882.1																																																																																				0.348	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		C	100476887	T	C	100476887	2	2	112	1	0	0	0	0	0	0	0	1	17009	1451	51	4		4	UHRF1BP1L	12	100476887	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	5933381	100476887	33375008	107	30327										
NR1H4	9971	hgsc.bcm.edu	37	chr12	100930770	100930770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gaaaattttctcattttgacGgaaatggcaaccaatcatgt	7	7	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:100930770G>A	ENST00000551379.1	+	6	934	c.906G>A	c.(904-906)acG>acA	p.T302T	NR1H4_ENST00000549996.1_Silent_p.T241T|NR1H4_ENST00000548884.1_Silent_p.T288T|NR1H4_ENST00000392986.3_Silent_p.T292T|NR1H4_ENST00000188403.7_Silent_p.T298T			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	302	Ligand-binding.				bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TCATTTTGACGGAAATGGCAA	0.244																																																0			12											69	82	78					12																	100930770		2194	4281	6475	99454901	SO:0001819	synonymous_variant	9971			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.906G>A	12.37:g.100930770G>A			99454901	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Silent	SNP	ENST00000551379.1	37	CCDS55876.1																																																																																				0.244	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		A	100930770	G	A	100930770	2	1	112	1	0	0	0	0	0	0	0	1	10650	1103	39	1		1	NR1H4	12	100930770	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	453883	100930770	32921125	108	30328										
C12orf48	55010	hgsc.bcm.edu	37	chr12	102572530	102572530	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aatccatcatcatggaacgtCtattcttacactttttaggt	5	9	4	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:102572530C>T	ENST00000358383.5	+	8	1211	c.1166C>T	c.(1165-1167)tCt>tTt	p.S389F	PARPBP_ENST00000541394.1_Missense_Mutation_p.S466F|PARPBP_ENST00000392911.2_Missense_Mutation_p.S308F|PARPBP_ENST00000378128.3_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.S308F|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000543784.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	389					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						CATGGAACGTCTATTCTTACA	0.318																																																0			12											92	89	90					12																	102572530		2203	4300	6503	101096660	SO:0001583	missense	55010			AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"PARP-1 binding protein"	613687	"chromosome 12 open reading frame 48"	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.1166C>T	12.37:g.102572530C>T	ENSP00000351153:p.Ser389Phe		101096660	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	.	.	.	.	.	.	.	.	.	.	C	14.12	2.440598	0.43326	.	.	ENSG00000185480	ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911	T;T;T;T	0.53423	0.62;0.62;0.63;0.62	5.65	5.65	0.86999	.	0.143127	0.64402	D	0.000004	T	0.69602	0.3129	M	0.72894	2.215	0.45621	D	0.998557	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.961	T	0.71797	-0.4484	10	0.87932	D	0	-14.0851	19.3314	0.94291	0.0:1.0:0.0:0.0	.	466;389	B4DZ31;Q9NWS1	.;PR1BP_HUMAN	F	308;466;389;308	ENSP00000332915:S308F;ENSP00000440850:S466F;ENSP00000351153:S389F;ENSP00000376643:S308F	ENSP00000332915:S308F	S	+	2	0	C12orf48	101096660	1.000000	0.71417	0.476000	0.27291	0.251000	0.25915	3.978000	0.56881	2.652000	0.90054	0.650000	0.86243	TCT		0.318	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		T	102572530	C	T	102572530	3	4	112	1	0	0	0	0	1	0	0	0	1696	913	32	3	945	3	C12orf48	12	102572530	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	1641760	102572530	31279365	109	30329										
ACACB	32	hgsc.bcm.edu	37	chr12	109660682	109660682	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttttcctgtctgccattgacAtgtacggccaccagttctgc	8	13	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:109660682A>G	ENST00000338432.7	+	26	3876	c.3757A>G	c.(3757-3759)Atg>Gtg	p.M1253V	ACACB_ENST00000377854.5_Missense_Mutation_p.M1183V|ACACB_ENST00000377848.3_Missense_Mutation_p.M1253V			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1253					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TGCCATTGACATGTACGGCCA	0.612																																																0			12											93	66	75					12																	109660682		2203	4300	6503	108145065	SO:0001583	missense	32			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3757A>G	12.37:g.109660682A>G	ENSP00000341044:p.Met1253Val		108145065	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	8.115	0.779607	0.16120	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.36520	1.25;1.25;1.25	5.07	2.54	0.30619	Acetyl-CoA carboxylase, central domain (1);	0.125647	0.64402	D	0.000001	T	0.27169	0.0666	L	0.60455	1.87	0.80722	D	1	B	0.18741	0.03	B	0.25614	0.062	T	0.07385	-1.0775	10	0.17369	T	0.5	.	2.3134	0.04192	0.5618:0.1298:0.0768:0.2315	.	1253	O00763	ACACB_HUMAN	V	1253;1253;1183;484	ENSP00000341044:M1253V;ENSP00000367079:M1253V;ENSP00000367085:M1183V	ENSP00000341044:M1253V	M	+	1	0	ACACB	108145065	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.280000	0.43443	0.890000	0.36211	0.528000	0.53228	ATG		0.612	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109660682	A	G	109660682	3	3	112	1	0	0	0	0	1	0	0	0	107	217	8	4	3855	4	ACACB	12	109660682	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	7088152	109660682	24191213	110	30330										
HIP1R	9026	hgsc.bcm.edu	37	chr12	123344995	123344995	+	Missense_Mutation	SNP	A	A	T													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agccacgcagcaggaattttAcgccaagaactcgcgctgga							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:123344995A>T	ENST00000253083.4	+	27	2710	c.2585A>T	c.(2584-2586)tAc>tTc	p.Y862F		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	862	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CAGGAATTTTACGCCAAGAAC	0.647											OREG0022225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			12											57	64	62					12																	123344995		2203	4300	6503	121910948	SO:0001583	missense	9026			AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.2585A>T	12.37:g.123344995A>T	ENSP00000253083:p.Tyr862Phe	1526	121910948	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	A	34	5.367916	0.95900	.	.	ENSG00000130787	ENST00000253083	T	0.54675	0.56	5.33	5.33	0.75918	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.80025	0.4548	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86015	0.1503	10	0.87932	D	0	-25.7474	14.9737	0.71254	1.0:0.0:0.0:0.0	.	862	O75146	HIP1R_HUMAN	F	862	ENSP00000253083:Y862F	ENSP00000253083:Y862F	Y	+	2	0	HIP1R	121910948	1.000000	0.71417	0.989000	0.46669	0.936000	0.57629	9.237000	0.95368	2.013000	0.59113	0.533000	0.62120	TAC		0.647	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		T	123344995	A	T	123344995	3	4	112	1	0	0	0	0	1	0	0	0	7136	391	14	5	2691	5	HIP1R	12	123344995	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	13684313	123344995	10506900	111	30331	54	2								
HIP1R	9026	hgsc.bcm.edu	37	chr12	123344997	123344997	+	Missense_Mutation	SNP	G	G	T													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccacgcagcaggaattttacGccaagaactcgcgctggacc							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr12:123344997G>T	ENST00000253083.4	+	27	2712	c.2587G>T	c.(2587-2589)Gcc>Tcc	p.A863S		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	863	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GGAATTTTACGCCAAGAACTC	0.642											OREG0022225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			12											57	64	62					12																	123344997		2203	4300	6503	121910950	SO:0001583	missense	9026			AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.2587G>T	12.37:g.123344997G>T	ENSP00000253083:p.Ala863Ser	1526	121910950	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	G	34	5.409445	0.96072	.	.	ENSG00000130787	ENST00000253083	T	0.41758	0.99	5.33	5.33	0.75918	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.53674	0.1811	L	0.38692	1.165	0.80722	D	1	P	0.40578	0.722	P	0.60286	0.872	T	0.35101	-0.9802	10	0.17832	T	0.49	-26.4801	18.63	0.91357	0.0:0.0:1.0:0.0	.	863	O75146	HIP1R_HUMAN	S	863	ENSP00000253083:A863S	ENSP00000253083:A863S	A	+	1	0	HIP1R	121910950	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	9.760000	0.98935	2.486000	0.83907	0.655000	0.94253	GCC		0.642	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		T	123344997	G	T	123344997	3	4	112	1	0	0	0	0	1	0	0	0	7136	1087	38	2	2693	2	HIP1R	12	123344997	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	2	123344997	10506898	112	30332	54	2								
SACS	26278	hgsc.bcm.edu	37	chr13	23908582	23908582	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctcaacttcaatctcattttCttctgcatctttaaaacaat	1	11	6	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr13:23908582C>A	ENST00000382292.3	-	9	9706	c.9433G>T	c.(9433-9435)Gaa>Taa	p.E3145*	SACS_ENST00000382298.3_Nonsense_Mutation_p.E3145*|SACS_ENST00000402364.1_Nonsense_Mutation_p.E2395*			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3145					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATCTCATTTTCTTCTGCATCT	0.363																																																0			13											38	36	37					13																	23908582		2200	4298	6498	22806582	SO:0001587	stop_gained	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9433G>T	13.37:g.23908582C>A	ENSP00000371729:p.Glu3145*		22806582	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Nonsense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	58	30.201827	0.99977	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	.	.	.	5.75	5.75	0.90469	.	0.143577	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	19.9379	0.97147	0.0:1.0:0.0:0.0	.	.	.	.	X	3145;2395;3145	.	ENSP00000371729:E3145X	E	-	1	0	SACS	22806582	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.710000	0.92621	0.555000	0.69702	GAA		0.363	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23908582	C	A	23908582	4	1	112	1	0	0	0	0	0	1	0	0	13841	922	32	2	4310	2	SACS	13	23908582	Nonsense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		23908582	91261296	113	30333			2	34		3	3	392	C		2.545393e-06
SACS	26278	hgsc.bcm.edu	37	chr13	23908918	23908918	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tttaaggtgttgtaattcatCctgtagtaaattgtcaaaaa	7	4	2	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr13:23908918C>A	ENST00000382292.3	-	9	9370	c.9097G>T	c.(9097-9099)Gat>Tat	p.D3033Y	SACS_ENST00000382298.3_Missense_Mutation_p.D3033Y|SACS_ENST00000402364.1_Missense_Mutation_p.D2283Y			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3033					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGTAATTCATCCTGTAGTAAA	0.328																																																0			13											95	95	95					13																	23908918		2203	4299	6502	22806918	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9097G>T	13.37:g.23908918C>A	ENSP00000371729:p.Asp3033Tyr		22806918	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	19.79	3.892381	0.72524	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88124	-2.21;-2.34;-2.21	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.85039	0.5606	L	0.43152	1.355	0.54753	D	0.999989	P	0.42692	0.787	B	0.40134	0.32	D	0.86086	0.1547	10	0.56958	D	0.05	.	19.7024	0.96060	0.0:1.0:0.0:0.0	.	3033	Q9NZJ4	SACS_HUMAN	Y	3033;2283;3033	ENSP00000371729:D3033Y;ENSP00000385844:D2283Y;ENSP00000371735:D3033Y	ENSP00000371729:D3033Y	D	-	1	0	SACS	22806918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.653000	0.90120	0.555000	0.69702	GAT		0.328	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23908918	C	A	23908918	3	1	112	1	0	0	0	0	1	0	0	0	13841	855	30	2	4646	2	SACS	13	23908918	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	336	23908918	91260960	114	30334			2	34		3	3	392	C		2.545393e-06
SACS	26278	hgsc.bcm.edu	37	chr13	23908973	23908973	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttagaagtagacatattgatCcaagtaattataactgcaga	7	5	0	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr13:23908973C>T	ENST00000382292.3	-	9	9315	c.9042G>A	c.(9040-9042)tgG>tgA	p.W3014*	SACS_ENST00000382298.3_Nonsense_Mutation_p.W3014*|SACS_ENST00000402364.1_Nonsense_Mutation_p.W2264*			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3014					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ACATATTGATCCAAGTAATTA	0.343																																																0			13											83	86	85					13																	23908973		2203	4299	6502	22806973	SO:0001587	stop_gained	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9042G>A	13.37:g.23908973C>T	ENSP00000371729:p.Trp3014*		22806973	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Nonsense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	57	29.466346	0.99975	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.7024	0.96060	0.0:1.0:0.0:0.0	.	.	.	.	X	3014;2264;3014	.	ENSP00000371729:W3014X	W	-	3	0	SACS	22806973	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.487000	0.81328	2.653000	0.90120	0.555000	0.69702	TGG		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23908973	C	T	23908973	4	4	112	1	0	0	0	0	0	1	0	0	13841	856	30	3	4701	3	SACS	13	23908973	Nonsense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	55	23908973	91260905	115	30335			2	34		3	3	392	C		2.545393e-06
BRCA2	675	hgsc.bcm.edu	37	chr13	32937372	32937372	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tataaaaaagataatggaaaGggatgacacagctgcaaaaa	9	4	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr13:32937372G>T	ENST00000380152.3	+	18	8266	c.8033G>T	c.(8032-8034)aGg>aTg	p.R2678M	BRCA2_ENST00000544455.1_Missense_Mutation_p.R2678M			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2678					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATAATGGAAAGGGATGACACA	0.333			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	0			13	GRCh37	CI063649	BRCA2	I							80	76	77					13																	32937372		2203	4300	6503	31835372	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8033G>T	13.37:g.32937372G>T	ENSP00000369497:p.Arg2678Met		31835372	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405375	0.62288	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.81659	-1.52;-1.52	5.08	3.34	0.38264	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 1 (1);	0.094278	0.64402	D	0.000001	D	0.89801	0.6820	M	0.88105	2.93	0.49389	D	0.999785	D	0.89917	1.0	D	0.73708	0.981	D	0.90128	0.4204	10	0.87932	D	0	.	11.3906	0.49811	0.1476:0.0:0.8524:0.0	.	2678	P51587	BRCA2_HUMAN	M	2678	ENSP00000369497:R2678M;ENSP00000439902:R2678M	ENSP00000369497:R2678M	R	+	2	0	BRCA2	31835372	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.143000	0.50608	0.659000	0.30945	0.467000	0.42956	AGG		0.333	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32937372	G	T	32937372	3	4	112	1	0	0	0	0	1	0	0	0	1502	1000	35	2	8099	2	BRCA2	13	32937372	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	9028399	32937372	82232506	116	30336										
UBR7	55148	hgsc.bcm.edu	37	chr14	93678456	93678456	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcatttgcaagagaccttatCctgatcctgaagacgaggta	10	9	0	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr14:93678456C>G	ENST00000013070.6	+	4	660	c.424C>G	c.(424-426)Cct>Gct	p.P142A	RP11-371E8.4_ENST00000557574.1_Missense_Mutation_p.P161A|UBR7_ENST00000416753.1_Missense_Mutation_p.P66A|RP11-371E8.4_ENST00000557048.1_3'UTR	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	142							ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						GAGACCTTATCCTGATCCTGA	0.413																																																0			14											77	73	74					14																	93678456		2203	4300	6503	92748209	SO:0001583	missense	55148			AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963		"Ubiquitin protein ligase E3 component n-recognins"	20344	protein-coding gene	gene with protein product		613816	"chromosome 14 open reading frame 130"	C14orf130		18162545	Standard	NM_175748		Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.424C>G	14.37:g.93678456C>G	ENSP00000013070:p.Pro142Ala		92748209	Q86U21|Q86UA9|Q96BY0|Q9NVV6	Missense_Mutation	SNP	ENST00000013070.6	37	CCDS9909.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	27.7|27.7|27.7	4.855562|4.855562|4.855562	0.91355|0.91355|0.91355	.|.|.	.|.|.	ENSG00000012963|ENSG00000259066;ENSG00000012963;ENSG00000012963;ENSG00000012963|ENSG00000012963	ENST00000553857|ENST00000557574;ENST00000013070;ENST00000535646;ENST00000416753|ENST00000555113	.|T;T;T|.	.|0.76186|.	.|-1.0;-0.01;-0.01|.	5.89|5.89|5.89	5.89|5.89|5.89	0.94794|0.94794|0.94794	.|Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	D|D|D	0.84506|0.84506|0.84506	0.5487|0.5487|0.5487	M|M|M	0.87097|0.87097|0.87097	2.86|2.86|2.86	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.97110|.	.|1.0;1.0|.	D|D|D	0.85206|0.85206|0.85206	0.1018|0.1018|0.1018	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	-22.8126|-22.8126|-22.8126	20.2361|20.2361|20.2361	0.98357|0.98357|0.98357	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|66;142|.	.|E9PCJ7;Q8N806|.	.|.;UBR7_HUMAN|.	M|A|C	67|161;142;66;66|132	.|ENSP00000451369:P161A;ENSP00000013070:P142A;ENSP00000391706:P66A|.	.|ENSP00000013070:P142A|.	I|P|S	+|+|+	3|1|2	3|0|0	UBR7|RP11-371E8.4;UBR7|UBR7	92748209|92748209|92748209	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.561000|7.561000|7.561000	0.82288|0.82288|0.82288	2.791000|2.791000|2.791000	0.96007|0.96007|0.96007	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	ATC|CCT|TCC		0.413	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412693.1	NM_175748		G	93678456	C	G	93678456	3	3	112	1	0	0	0	0	1	0	0	0	16946	855	30	5	438	5	UBR7	14	93678456	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		93678456	13671084	117	30337										
EIF5	1983	hgsc.bcm.edu	37	chr14	103807329	103807329	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tcgaaggctgccagtgtaccGaaagttgagactgtaaagtc	12	8	0	1	rs140137312		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr14:103807329G>A	ENST00000216554.3	+	12	1912	c.1236G>A	c.(1234-1236)ccG>ccA	p.P412P	EIF5_ENST00000392715.2_Silent_p.P412P|EIF5_ENST00000558506.1_Silent_p.P412P	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	412					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(3)|kidney(2)|large_intestine(3)|lung(5)|pancreas(2)|skin(2)|upper_aerodigestive_tract(1)	18		Melanoma(154;0.155)	Epithelial(46;0.182)			CCAGTGTACCGAAAGTTGAGA	0.363																																																0			14						G	,	0,4406		0,0,2203	150	124	133		1236,1236	-4.1	0.9	14	dbSNP_134	133	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous	EIF5	NM_001969.3,NM_183004.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	412/432,412/432	103807329	2,13004	2203	4300	6503	102877082	SO:0001819	synonymous_variant	1983			U49436	CCDS9980.1	14q32.32	2006-05-11				ENSG00000100664			3299	protein-coding gene	gene with protein product		601710				8663286	Standard	NM_001969		Approved		uc001ymq.4	P55010		ENST00000216554.3:c.1236G>A	14.37:g.103807329G>A			102877082	Q53XB3|Q9H5N2|Q9UG48	Silent	SNP	ENST00000216554.3	37	CCDS9980.1																																																																																				0.363	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2	NM_001969		A	103807329	G	A	103807329	2	1	112	1	0	0	0	0	0	0	0	1	5053	1045	37	1		1	EIF5	14	103807329	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10128873	103807329	3542211	118	30338										
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382522	22382522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agaatttatcctccttggtcTgactcagtctcaagatattc	6	10	3	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:22382522T>C	ENST00000328795.4	+	1	141	c.50T>C	c.(49-51)cTg>cCg	p.L17P	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTCCTTGGTCTGACTCAGTCT	0.353																																																0			15											139	135	137					15																	22382522		2187	4260	6447	19883886	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.50T>C	15.37:g.22382522T>C	ENSP00000332500:p.Leu17Pro		19883886	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	8.244	0.807557	0.16467	.	.	ENSG00000183706	ENST00000328795	T	0.00344	8.02	3.24	3.24	0.37175	.	0.000000	0.37857	N	0.001901	T	0.01061	0.0035	H	0.94658	3.565	0.22412	N	0.999123	D	0.89917	1.0	D	0.83275	0.996	T	0.14420	-1.0473	10	0.87932	D	0	-8.0908	9.793	0.40717	0.0:0.0:0.0:1.0	.	17	Q8N0Y3	OR4N4_HUMAN	P	17	ENSP00000332500:L17P	ENSP00000332500:L17P	L	+	2	0	OR4N4	19883886	0.081000	0.21417	0.160000	0.22671	0.108000	0.19459	2.867000	0.48428	1.465000	0.48006	0.164000	0.16699	CTG		0.353	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382522	T	C	22382522	3	2	112	1	0	0	0	0	1	0	0	0	11109	1580	55	4	52	4	OR4N4	15	22382522	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10		22382522	80148870	119	30339										
RYR3	6263	hgsc.bcm.edu	37	chr15	33893658	33893658	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tccctctgtctctgcaatggGgttgcagtgagagccaacca	11	12	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:33893658G>T	ENST00000389232.4	+	17	1897	c.1827G>T	c.(1825-1827)ggG>ggT	p.G609G	RYR3_ENST00000415757.3_Silent_p.G609G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	609	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.G609G(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TCTGCAATGGGGTTGCAGTGA	0.547																																																1	Substitution - coding silent(1)	ovary(1)	15											118	110	113					15																	33893658		2064	4218	6282	31680950	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.1827G>T	15.37:g.33893658G>T			31680950	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.547	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33893658	G	T	33893658	2	4	112	1	0	0	0	0	0	0	0	1	13807	1219	43	2		2	RYR3	15	33893658	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	11511136	33893658	68637734	120	30340										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41813106	41813106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cggtgggcagcagcggctccGtaggcatgggcagtagcagg	19	10	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:41813106G>A	ENST00000304330.4	-	22	3394	c.3278C>T	c.(3277-3279)aCg>aTg	p.T1093M	RPAP1_ENST00000561603.1_Intron	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1093	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		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)		CAGCGGCTCCGTAGGCATGGG	0.657																																																0			15											57	48	51					15																	41813106		2203	4300	6503	39600398	SO:0001583	missense	26015			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3278C>T	15.37:g.41813106G>A	ENSP00000306123:p.Thr1093Met		39600398	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	g	9.843	1.191512	0.21954	.	.	ENSG00000103932	ENST00000304330	T	0.77098	-1.07	5.22	-3.22	0.05125	.	0.389240	0.28653	N	0.014593	T	0.50769	0.1635	N	0.19112	0.55	0.18873	N	0.999986	P	0.48350	0.909	B	0.40565	0.333	T	0.56444	-0.7978	10	0.26408	T	0.33	-1.322	1.5019	0.02478	0.2166:0.1288:0.3585:0.2961	.	1093	Q9BWH6	RPAP1_HUMAN	M	1093	ENSP00000306123:T1093M	ENSP00000306123:T1093M	T	-	2	0	RPAP1	39600398	0.990000	0.36364	0.937000	0.37676	0.150000	0.21749	0.119000	0.15626	-0.782000	0.04541	-3.043000	0.00070	ACG		0.657	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		A	41813106	G	A	41813106	3	1	112	1	0	0	0	0	1	0	0	0	13578	1145	40	1	919	1	RPAP1	15	41813106	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	7919448	41813106	60718286	121	30341										
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42132408	42132408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tcgtgtcctgcaggcccatcGcctaccctctaaggacctag	9	16	1	0	rs569293395		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:42132408G>A	ENST00000452633.1	+	3	414	c.62G>A	c.(61-63)cGc>cAc	p.R21H	JMJD7-PLA2G4B_ENST00000476036.1_3'UTR|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.R21H|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.R252H|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.R252H|PLA2G4B_ENST00000542534.2_Missense_Mutation_p.R252H			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	21	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		CAGGCCCATCGCCTACCCTCT	0.657													g|||	1	0.000199681	8e-04	0	5008	,	,		18979	0		0	False		,,,				2504	0															0			15											57	49	52					15																	42132408		2203	4300	6503	39919700	SO:0001583	missense	8681			AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.62G>A	15.37:g.42132408G>A	ENSP00000396045:p.Arg21His		39919700	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	.	.	.	.	.	.	.	.	.	.	.	13.19	2.163908	0.38217	.	.	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	5.17	1.19	0.21007	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.847376	0.10617	N	0.653837	T	0.07954	0.0199	N	0.05351	-0.065	0.09310	N	1	D;P;P	0.55605	0.972;0.825;0.954	P;B;B	0.48677	0.586;0.135;0.365	T	0.34925	-0.9809	10	0.56958	D	0.05	-11.3489	7.7261	0.28761	0.3511:0.0:0.6489:0.0	.	21;252;252	P0C869;P0C869-7;P0C869-6	PA24B_HUMAN;.;.	H	252;252;21;21	ENSP00000371886:R252H;ENSP00000342785:R252H;ENSP00000416610:R21H;ENSP00000396045:R21H	ENSP00000342785:R252H	R	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39919700	0.017000	0.18338	0.048000	0.18961	0.204000	0.24138	0.458000	0.21892	0.128000	0.18479	-0.140000	0.14226	CGC		0.657	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		A	42132408	G	A	42132408	3	1	112	1	0	0	0	0	1	0	0	0	7976	1087	38	1	781	1	JMJD7-PLA2G4B	15	42132408	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	319302	42132408	60398984	122	30342										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52497322	52497322	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccggaaatgccctgcaggctCtcatactccagcattcccgg	9	16	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:52497322C>G	ENST00000261839.7	-	38	4721	c.4560G>C	c.(4558-4560)gaG>gaC	p.E1520D	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1520	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		CCTGCAGGCTCTCATACTCCA	0.607																																																0			15											50	55	53					15																	52497322		2007	4149	6156	50284614	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4560G>C	15.37:g.52497322C>G	ENSP00000261839:p.Glu1520Asp		50284614	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485158	0.63962	.	.	ENSG00000128833	ENST00000261839	D	0.89746	-2.56	4.66	2.76	0.32466	Dilute (1);	0.000000	0.85682	D	0.000000	D	0.83760	0.5324	L	0.33792	1.035	0.80722	D	1	P	0.36753	0.568	P	0.45639	0.488	T	0.79296	-0.1862	10	0.39692	T	0.17	.	4.556	0.12136	0.0:0.574:0.0:0.426	.	1520	Q9NQX4	MYO5C_HUMAN	D	1520	ENSP00000261839:E1520D	ENSP00000261839:E1520D	E	-	3	2	MYO5C	50284614	1.000000	0.71417	0.999000	0.59377	0.724000	0.41520	2.549000	0.45803	1.311000	0.45024	0.462000	0.41574	GAG		0.607	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52497322	C	G	52497322	3	3	112	1	0	0	0	0	1	0	0	0	10110	912	32	5	684	5	MYO5C	15	52497322	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	10364914	52497322	50034070	123	30343										
TLN2	83660	hgsc.bcm.edu	37	chr15	62944241	62944241	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaagaaacagagacctcagaAaatccggatgctggatggat	11	7	1	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:62944241A>T	ENST00000561311.1	+	5	502	c.272A>T	c.(271-273)aAa>aTa	p.K91I	TLN2_ENST00000306829.6_Missense_Mutation_p.K91I			Q9Y4G6	TLN2_HUMAN	talin 2	91	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AGACCTCAGAAAATCCGGATG	0.408																																																0			15											88	91	90					15																	62944241		2203	4300	6503	60731533	SO:0001583	missense	83660			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.272A>T	15.37:g.62944241A>T	ENSP00000453508:p.Lys91Ile		60731533	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958714	0.92726	.	.	ENSG00000171914	ENST00000306829	T	0.79352	-1.26	5.92	5.92	0.95590	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	M	0.69823	2.125	0.80722	D	1	D	0.67145	0.996	P	0.62649	0.905	D	0.87728	0.2577	10	0.87932	D	0	-20.252	15.5338	0.75986	1.0:0.0:0.0:0.0	.	91	Q9Y4G6	TLN2_HUMAN	I	91	ENSP00000303476:K91I	ENSP00000303476:K91I	K	+	2	0	TLN2	60731533	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.237000	0.95368	2.268000	0.75426	0.482000	0.46254	AAA		0.408	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	62944241	A	T	62944241	3	4	112	1	0	0	0	0	1	0	0	0	15987	14	1	5	282	5	TLN2	15	62944241	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	10446919	62944241	39587151	124	30344										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83331452	83331452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaagcccttcgcaccaatttCgggaaattcttggatgctga	9	10	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:83331452C>T	ENST00000261722.3	-	22	2977	c.2770G>A	c.(2770-2772)Gaa>Aaa	p.E924K	AP3B2_ENST00000535359.1_Missense_Mutation_p.E943K|RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535348.1_Missense_Mutation_p.E892K	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	924					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			GCACCAATTTCGGGAAATTCT	0.577																																																0			15											31	34	33					15																	83331452		1941	4142	6083	81128507	SO:0001583	missense	8120			U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.2770G>A	15.37:g.83331452C>T	ENSP00000261722:p.Glu924Lys		81128507	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.863510	0.71949	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.57436	0.4;0.4;0.42	5.95	5.95	0.96441	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);	0.000000	0.85682	D	0.000000	T	0.72732	0.3497	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.981;0.981	T	0.65397	-0.6178	10	0.20046	T	0.44	-21.3809	20.3748	0.98911	0.0:1.0:0.0:0.0	.	892;943;924	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	K	924;892;943	ENSP00000261722:E924K;ENSP00000438721:E892K;ENSP00000440984:E943K	ENSP00000261722:E924K	E	-	1	0	AP3B2	81128507	1.000000	0.71417	0.999000	0.59377	0.787000	0.44495	7.697000	0.84279	2.817000	0.96982	0.563000	0.77884	GAA		0.577	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			T	83331452	C	T	83331452	3	4	112	1	0	0	0	0	1	0	0	0	745	893	31	1	498	1	AP3B2	15	83331452	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	20387211	83331452	19199940	125	30345										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88423538	88423538	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggaaccatggctgctttccaTaggtgaagatctcccagagg	12	10	1	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr15:88423538T>C	ENST00000360948.2	-	18	2458	c.2297A>G	c.(2296-2298)tAt>tGt	p.Y766C	NTRK3_ENST00000357724.2_Missense_Mutation_p.Y758C|NTRK3_ENST00000394480.2_Missense_Mutation_p.Y752C|NTRK3_ENST00000557856.1_Missense_Mutation_p.Y744C|NTRK3_ENST00000355254.2_Missense_Mutation_p.Y752C	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	766	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Y -> F (in a lung carcinoma sample; somatic mutation). {ECO:0000269|PubMed:18293376}.		activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y752F(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTGCTTTCCATAGGTGAAGAT	0.517			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	1	Substitution - Missense(1)	lung(1)	15											133	122	126					15																	88423538		2201	4299	6500	86224542	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.2297A>G	15.37:g.88423538T>C	ENSP00000354207:p.Tyr766Cys		86224542	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.773612	0.69992	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254	D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92176	0.7519	L	0.48642	1.525	0.80722	D	1	P;D;D	0.89917	0.883;1.0;0.964	D;D;P	0.87578	0.928;0.998;0.901	D	0.92989	0.6413	10	0.87932	D	0	.	14.1307	0.65253	0.0:0.0:0.0:1.0	.	744;752;766	B7Z4C5;Q16288-3;Q16288	.;.;NTRK3_HUMAN	C	752;766;758;752	ENSP00000377990:Y752C;ENSP00000354207:Y766C;ENSP00000350356:Y758C;ENSP00000347397:Y752C	ENSP00000347397:Y752C	Y	-	2	0	NTRK3	86224542	1.000000	0.71417	0.971000	0.41717	0.998000	0.95712	5.893000	0.69798	2.007000	0.58848	0.533000	0.62120	TAT		0.517	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88423538	T	C	88423538	3	2	112	1	0	0	0	0	1	0	0	0	10739	1406	49	4	230	4	NTRK3	15	88423538	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	5092086	88423538	14107854	126	30346										
MSLNL	401827	hgsc.bcm.edu	37	chr16	830433	830433	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtgtaagtgacagtgtgcacGggtaggtgacagtatgcaca	15	6	0	2	rs202228997		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr16:830433G>T	ENST00000442466.1	-	2	37				MSLNL_ENST00000293892.3_Missense_Mutation_p.R190S			Q96KJ4	MSLNL_HUMAN	mesothelin-like						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.R190S(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(15)|ovary(2)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	36						CAGTGTGCACGGGTAGGTGAC	0.567																																																1	Substitution - Missense(1)	ovary(1)	16											213	189	197					16																	830433		2178	4274	6452	770434	SO:0001627	intron_variant	401827					16p13.3	2008-08-06	2008-07-04	2008-07-04	ENSG00000162006	ENSG00000162006			14170	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 37"	C16orf37			Standard	NG_032123		Approved	MPFL		Q96KJ4		ENST00000442466.1:c.38-271C>A	16.37:g.830433G>T			770434		Missense_Mutation	SNP	ENST00000442466.1	37		.	.	.	.	.	.	.	.	.	.	G	7.806	0.714594	0.15306	.	.	ENSG00000162006	ENST00000293892	T	0.18338	2.22	1.33	0.33	0.15929	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35351	-0.9792	5	.	.	.	.	3.4078	0.07347	0.2778:0.0:0.7222:0.0	.	.	.	.	S	190	ENSP00000293892:R190S	.	R	-	1	0	MSLNL	770434	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.195000	0.00276	0.125000	0.18397	0.411000	0.27672	CGT		0.567	MSLNL-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001025190		T	830433	G	T	830433	1	4	112	0	1	0	0	0	0	0	0	0	9912	1116	39	2		2	MSLNL	16	830433	Intron	SNP	G	TCGA-EI-6508-01A-11D-1733-10		830433	89524320	127	30347										
MYH11	4629	hgsc.bcm.edu	37	chr16	15854404	15854404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agtacatcattacctgttctTttgtctgagctttctgtacc	6	10	4	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr16:15854404T>C	ENST00000300036.5	-	11	1350	c.1241A>G	c.(1240-1242)aAa>aGa	p.K414R	MYH11_ENST00000396324.3_Missense_Mutation_p.K421R|MYH11_ENST00000576790.2_Missense_Mutation_p.K414R|MYH11_ENST00000452625.2_Missense_Mutation_p.K421R	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	414	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TACCTGTTCTTTTGTCTGAGC	0.433			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	0			16											435	337	370					16																	15854404		2197	4300	6497	15761905	SO:0001583	missense	4629			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1241A>G	16.37:g.15854404T>C	ENSP00000300036:p.Lys414Arg		15761905	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.214305	0.58452	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.0	5.0	0.66597	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.79429	0.4444	M	0.62016	1.91	0.80722	D	1	P;P;P;P;P;P	0.48640	0.645;0.913;0.913;0.913;0.913;0.913	P;P;P;P;P;P	0.58577	0.841;0.841;0.841;0.841;0.841;0.841	T	0.81324	-0.0984	10	0.62326	D	0.03	.	13.9242	0.63952	0.0:0.0:0.0:1.0	.	421;414;414;421;414;421	B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;.;MYH11_HUMAN;.;.;.	R	414;414;421;421;421	ENSP00000300036:K414R;ENSP00000345136:K414R;ENSP00000379616:K421R;ENSP00000407821:K421R	ENSP00000300036:K414R	K	-	2	0	MYH11	15761905	1.000000	0.71417	0.999000	0.59377	0.818000	0.46254	8.016000	0.88706	1.891000	0.54761	0.254000	0.18369	AAA		0.433	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		C	15854404	T	C	15854404	3	2	112	1	0	0	0	0	1	0	0	0	10061	1841	64	4	4836	4	MYH11	16	15854404	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	15023971	15854404	74500349	128	30348										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22151533	22151533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gctgaaatctctgaaatggcGtccactcagtagcagagttg	11	9	2	3	rs564353975		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr16:22151533G>A	ENST00000389398.5	+	23	2447	c.2351G>A	c.(2350-2352)cGt>cAt	p.R784H	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	784						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CTGAAATGGCGTCCACTCAGT	0.527													G|||	1	0.000199681	8e-04	0	5008	,	,		19421	0		0	False		,,,				2504	0															0			16											53	52	53					16																	22151533		2008	4175	6183	22059034	SO:0001583	missense	146177			AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2351G>A	16.37:g.22151533G>A	ENSP00000374049:p.Arg784His		22059034	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.684645	0.29872	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.15139	2.45	5.42	-4.28	0.03732	.	1.046580	0.07461	N	0.900632	T	0.10294	0.0252	L	0.28192	0.835	0.20196	N	0.999928	B	0.16396	0.017	B	0.06405	0.002	T	0.37150	-0.9718	10	0.31617	T	0.26	.	8.0116	0.30357	0.5036:0.1079:0.3884:0.0	.	784	A6NCI4	VWA3A_HUMAN	H	784;407	ENSP00000374049:R784H	ENSP00000299840:R407H	R	+	2	0	VWA3A	22059034	0.659000	0.27411	0.000000	0.03702	0.082000	0.17680	-0.238000	0.08977	-0.733000	0.04850	-0.140000	0.14226	CGT		0.527	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22151533	G	A	22151533	3	1	112	1	0	0	0	0	1	0	0	0	17280	1145	40	1	2441	1	VWA3A	16	22151533	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	6297129	22151533	68203220	129	30349										
MYLK3	91807	hgsc.bcm.edu	37	chr16	46755054	46755054	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccttctggccagcccaaagtCaatgatcttaatttgatgtc	7	11	3	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr16:46755054C>T	ENST00000394809.4	-	9	2081	c.1966G>A	c.(1966-1968)Gac>Aac	p.D656N	MYLK3_ENST00000536476.1_Missense_Mutation_p.D315N	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	656	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AGCCCAAAGTCAATGATCTTA	0.458																																																0			16											139	141	141					16																	46755054		2203	4300	6503	45312555	SO:0001583	missense	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1966G>A	16.37:g.46755054C>T	ENSP00000378288:p.Asp656Asn		45312555	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	33	5.210759	0.95069	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	D;D	0.92965	-3.14;-3.14	5.09	5.09	0.68999	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.37857	N	0.001917	D	0.97996	0.9340	H	0.99074	4.42	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	D	0.99143	1.0856	10	0.56958	D	0.05	.	18.8594	0.92266	0.0:1.0:0.0:0.0	.	656	Q32MK0	MYLK3_HUMAN	N	656;315	ENSP00000378288:D656N;ENSP00000439297:D315N	ENSP00000378288:D656N	D	-	1	0	MYLK3	45312555	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.591000	0.82666	2.517000	0.84864	0.557000	0.71058	GAC		0.458	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46755054	C	T	46755054	3	4	112	1	0	0	0	0	1	0	0	0	10088	826	29	3	513	3	MYLK3	16	46755054	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	24603521	46755054	43599699	130	30350										
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89920751	89920751	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agacgcctcgggcagagctgGacagcctgggtcacacagac	14	13	1	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr16:89920751G>T	ENST00000378247.3	+	4	746	c.703G>T	c.(703-705)Gac>Tac	p.D235Y	SPIRE2_ENST00000393062.2_Missense_Mutation_p.D235Y	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	235					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		GGCAGAGCTGGACAGCCTGGG	0.657																																																0			16											43	38	40					16																	89920751		2188	4290	6478	88448252	SO:0001583	missense	84501			AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"spire homolog 2 (Drosophila)", "spire family actin nucleation factor 2"			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.703G>T	16.37:g.89920751G>T	ENSP00000367494:p.Asp235Tyr		88448252	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	37	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118248	0.37339	.	.	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.51071	0.72;0.72	5.67	4.61	0.57282	.	0.146294	0.64402	D	0.000009	T	0.66819	0.2828	M	0.80847	2.515	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.993;0.999	D;D;D;D	0.65874	0.912;0.939;0.911;0.939	T	0.70876	-0.4753	10	0.72032	D	0.01	-9.7734	11.4581	0.50193	0.0915:0.0:0.9085:0.0	.	104;235;187;235	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	Y	235	ENSP00000367494:D235Y;ENSP00000376782:D235Y	ENSP00000367494:D235Y	D	+	1	0	SPIRE2	88448252	1.000000	0.71417	0.047000	0.18901	0.007000	0.05969	5.492000	0.66893	1.223000	0.43536	0.563000	0.77884	GAC		0.657	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		T	89920751	G	T	89920751	3	4	112	1	0	0	0	0	1	0	0	0	15111	1174	41	2	717	2	SPIRE2	16	89920751	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	43165697	89920751	434002	131	30351										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7399374	7399374	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gggtgattgagcggactggcCgctgccaaacatgtgcaggt	16	9	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:7399374C>T	ENST00000322644.6	+	2	607	c.208C>T	c.(208-210)Cgc>Tgc	p.R70C	POLR2A_ENST00000572844.1_Missense_Mutation_p.R70C	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	70					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCGGACTGGCCGCTGCCAAAC	0.632																																																0			17											32	37	35					17																	7399374		2199	4296	6495	7340098	SO:0001583	missense	5430					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.208C>T	17.37:g.7399374C>T	ENSP00000314949:p.Arg70Cys		7340098	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662662	0.47572	.	.	ENSG00000181222	ENST00000322644	T	0.68181	-0.31	5.33	5.33	0.75918	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.73048	0.3537	M	0.92317	3.295	0.80722	D	1	B;B	0.33964	0.434;0.154	B;B	0.31614	0.133;0.12	T	0.78398	-0.2219	10	0.72032	D	0.01	.	12.8388	0.57788	0.1634:0.8365:0.0:0.0	.	70;70	P24928;Q6NX41	RPB1_HUMAN;.	C	70	ENSP00000314949:R70C	ENSP00000314949:R70C	R	+	1	0	SLC35G6	7340098	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.468000	0.60162	2.499000	0.84300	0.467000	0.42956	CGC		0.632	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7399374	C	T	7399374	3	4	112	1	0	0	0	0	1	0	0	0	12245	652	23	1	214	1	POLR2A	17	7399374	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10		7399374	73795836	132	30352										
TP53	7157	hgsc.bcm.edu	37	chr17	7578370	7578370	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tctccagccccagctgctcaCcatcgctatctgagcagcgc	8	18	3	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:7578370C>T	ENST00000269305.4	-	5	749		c.e5+1		TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(54)|p.0?(8)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGCTGCTCACCATCGCTATC	0.632		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	68	Unknown(54)|Whole gene deletion(8)|Deletion - Frameshift(3)|Deletion - In frame(2)|Insertion - Frameshift(1)	lung(12)|breast(9)|oesophagus(7)|ovary(7)|liver(7)|urinary_tract(5)|NS(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(2)|stomach(1)|soft_tissue(1)	17											48	46	47					17																	7578370		2203	4300	6503	7519095	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.559+1G>A	17.37:g.7578370C>T			7519095	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.774230	0.31411	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	4.7	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0738	0.59075	0.0:0.8363:0.1637:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519095	1.000000	0.71417	0.967000	0.41034	0.201000	0.24016	3.085000	0.50151	1.248000	0.43934	0.655000	0.94253	.		0.632	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7578370	C	T	7578370	5	4	112	1	0	0	0	0	0	0	1	0	16421	521	18	3	738	3	TP53	17	7578370	Splice_Site	SNP	C	TCGA-EI-6508-01A-11D-1733-10	178996	7578370	73616840	133	30353										
TP53	7157	hgsc.bcm.edu	37	chr17	7579329	7579329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gaccgtgcaagtcacagactTggctgtcccagaatgcaaga	11	11	1	3	rs121912658		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:7579329T>C	ENST00000269305.4	-	4	547	c.358A>G	c.(358-360)Aag>Gag	p.K120E	TP53_ENST00000413465.2_Missense_Mutation_p.K120E|TP53_ENST00000455263.2_Missense_Mutation_p.K120E|TP53_ENST00000420246.2_Missense_Mutation_p.K120E|TP53_ENST00000359597.4_Missense_Mutation_p.K120E|TP53_ENST00000445888.2_Missense_Mutation_p.K120E|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	120	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.	Interaction with DNA.	K -> E (in sporadic cancers; somatic mutation).|K -> M (in sporadic cancers; somatic mutation).|K -> Q (in a sporadic cancer; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.K120E(3)|p.G59fs*23(3)|p.K120*(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.T118fs*27(1)|p.H115fs*27(1)|p.Y107fs*44(1)|p.K120Q(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.K120fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCACAGACTTGGCTGTCCCA	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	26	Deletion - Frameshift(10)|Whole gene deletion(8)|Substitution - Missense(4)|Deletion - In frame(2)|Substitution - Nonsense(2)	upper_aerodigestive_tract(5)|lung(4)|bone(4)|breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|stomach(1)|liver(1)|ovary(1)	17	GRCh37	CM921039	TP53	M	rs121912658						66	61	63					17																	7579329		2203	4300	6503	7520054	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.358A>G	17.37:g.7579329T>C	ENSP00000269305:p.Lys120Glu		7520054	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.565227	0.86439	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99854	-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99862	0.9935	M	0.90759	3.145	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.993;1.0;0.999;0.999	D;D;D;D;D;D;D	0.97110	0.995;0.998;1.0;0.979;1.0;1.0;0.993	D	0.96452	0.9335	10	0.87932	D	0	-37.4061	12.5363	0.56144	0.0:0.0:0.0:1.0	.	81;120;120;120;120;120;120	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	E	120	ENSP00000410739:K120E;ENSP00000352610:K120E;ENSP00000269305:K120E;ENSP00000398846:K120E;ENSP00000391127:K120E;ENSP00000391478:K120E;ENSP00000424104:K120E;ENSP00000426252:K120E	ENSP00000269305:K120E	K	-	1	0	TP53	7520054	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.383000	0.73172	2.125000	0.65367	0.533000	0.62120	AAG		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7579329	T	C	7579329	3	2	112	1	0	0	0	0	1	0	0	0	16421	1821	63	4	944	4	TP53	17	7579329	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	959	7579329	73615881	134	30354										
PIGS	94005	hgsc.bcm.edu	37	chr17	26897872	26897872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgatccccagtaactcacatTtcagaggaatctctctttca	5	12	5	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:26897872T>C	ENST00000308360.7	-	3	659	c.284A>G	c.(283-285)aAa>aGa	p.K95R	RP11-192H23.5_ENST00000585189.1_RNA|PIGS_ENST00000395346.2_Missense_Mutation_p.K87R|PIGS_ENST00000543734.1_Missense_Mutation_p.K34R	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	95					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					TAACTCACATTTCAGAGGAAT	0.542																																																0			17											88	84	85					17																	26897872		2203	4300	6503	23921999	SO:0001583	missense	94005				CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.284A>G	17.37:g.26897872T>C	ENSP00000309430:p.Lys95Arg		23921999	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480988	0.63849	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.46063	0.89;0.89;0.88	4.64	4.64	0.57946	.	0.209983	0.48767	D	0.000171	T	0.36963	0.0986	L	0.44542	1.39	0.53005	D	0.999962	P;P	0.44521	0.837;0.804	P;B	0.45794	0.493;0.292	T	0.08659	-1.0711	10	0.23302	T	0.38	-0.5764	8.7337	0.34514	0.0:0.0927:0.0:0.9073	.	95;87	Q96S52;Q96S52-2	PIGS_HUMAN;.	R	87;95;34	ENSP00000378755:K87R;ENSP00000309430:K95R;ENSP00000438447:K34R	ENSP00000309430:K95R	K	-	2	0	PIGS	23921999	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	6.172000	0.71932	1.860000	0.53959	0.254000	0.18369	AAA		0.542	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		C	26897872	T	C	26897872	3	2	112	1	0	0	0	0	1	0	0	0	11929	1841	64	4	1423	4	PIGS	17	26897872	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	19318543	26897872	54297338	135	30355										
FNDC8	54752	hgsc.bcm.edu	37	chr17	33454242	33454242	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccccaatggccaagaatgcaGaaaatgaggacctggcgctc	11	12	0	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:33454242G>A	ENST00000158009.5	+	2	506	c.391G>A	c.(391-393)Gaa>Aaa	p.E131K		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	131						nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		CAAGAATGCAGAAAATGAGGA	0.577																																																0			17											121	127	125					17																	33454242		2203	4300	6503	30478355	SO:0001583	missense	54752			BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"Fibronectin type III domain containing"	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.391G>A	17.37:g.33454242G>A	ENSP00000158009:p.Glu131Lys		30478355	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	37	CCDS11290.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295366	0.23564	.	.	ENSG00000073598	ENST00000158009	T	0.34072	1.38	5.38	4.41	0.53225	.	0.540328	0.16991	N	0.191309	T	0.24928	0.0605	L	0.27053	0.805	0.09310	N	1	P	0.43094	0.799	B	0.35931	0.214	T	0.11397	-1.0589	10	0.72032	D	0.01	-1.028	12.065	0.53583	0.0:0.1725:0.8275:0.0	.	131	Q8TC99	FNDC8_HUMAN	K	131	ENSP00000158009:E131K	ENSP00000158009:E131K	E	+	1	0	FNDC8	30478355	0.381000	0.25140	0.167000	0.22817	0.033000	0.12548	2.701000	0.47094	1.485000	0.48380	0.655000	0.94253	GAA		0.577	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		A	33454242	G	A	33454242	3	1	112	1	0	0	0	0	1	0	0	0	5993	943	33	3	397	3	FNDC8	17	33454242	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	6556370	33454242	47740968	136	30356										
ASB16	92591	hgsc.bcm.edu	37	chr17	42255595	42255595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcacgaagccttctacagctCggccctgtgcatggtgaacc	11	14	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:42255595C>T	ENST00000293414.1	+	5	1283	c.1199C>T	c.(1198-1200)tCg>tTg	p.S400L	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	400	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TTCTACAGCTCGGCCCTGTGC	0.657																																																0			17											48	39	42					17																	42255595		2203	4300	6503	39611121	SO:0001583	missense	92591			AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"Ankyrin repeat domain containing"	19768	protein-coding gene	gene with protein product		615056	"ankyrin repeat and SOCS box-containing 16"			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1199C>T	17.37:g.42255595C>T	ENSP00000293414:p.Ser400Leu		39611121	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	37	CCDS11478.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603460	0.66445	.	.	ENSG00000161664	ENST00000293414	T	0.65549	-0.16	5.27	5.27	0.74061	.	0.394804	0.25189	N	0.032474	T	0.52256	0.1723	L	0.49571	1.57	0.39008	D	0.959482	P	0.43231	0.801	B	0.24701	0.055	T	0.64597	-0.6370	10	0.59425	D	0.04	-12.9981	17.8117	0.88619	0.0:1.0:0.0:0.0	.	400	Q96NS5	ASB16_HUMAN	L	400	ENSP00000293414:S400L	ENSP00000293414:S400L	S	+	2	0	ASB16	39611121	0.992000	0.36948	0.963000	0.40424	0.625000	0.37756	4.259000	0.58828	2.736000	0.93811	0.561000	0.74099	TCG		0.657	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			T	42255595	C	T	42255595	3	4	112	1	0	0	0	0	1	0	0	0	1021	893	31	1	1217	1	ASB16	17	42255595	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	8801353	42255595	38939615	137	30357										
RNF213	57674	hgsc.bcm.edu	37	chr17	78360567	78360567	+	Frame_Shift_Del	DEL	T	T	-													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcgggacctgactccactgaTtctctccaactgccagtacc							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:78360567delT	ENST00000582970.1	+	63	14941	c.14798delT	c.(14797-14799)attfs	p.I4933fs	RNF213_ENST00000336301.6_Frame_Shift_Del_p.I3006fs|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Frame_Shift_Del_p.I4982fs|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA|RNF213_ENST00000427003.3_3'UTR	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4933					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ACTCCACTGATTCTCTCCAAC	0.572																																																0			17											76	68	71					17																	78360567		2203	4300	6503	75975162	SO:0001589	frameshift_variant	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.14798delT	17.37:g.78360567delT	ENSP00000464087:p.Ile4933fs		75975162	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Frame_Shift_Del	DEL	ENST00000582970.1	37	CCDS58606.1																																																																																				0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		-	78360567	T	-	78360567	7	5	112	1	0	1	0	1	0	0	0	0	13514	1493	52	0	15363	0	RNF213	17	78360567	Frame_Shift_Del	DEL	T	TCGA-EI-6508-01A-11D-1733-10	36104972	78360567	2834643	138	30358										
THOC4	10189	hgsc.bcm.edu	37	chr17	79846185	79846185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctgctgctttgaattcctgcCggcacctctgcctcttccac	7	17	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr17:79846185C>T	ENST00000331204.4	-	5	717	c.691G>A	c.(691-693)Ggc>Agc	p.G231S	ALYREF_ENST00000512673.1_5'Flank|ALYREF_ENST00000505490.2_Missense_Mutation_p.G238S|ANAPC11_ENST00000571570.1_5'Flank	NM_005782.3	NP_005773.3	Q86V81	THOC4_HUMAN	Aly/REF export factor	231	Ala/Arg/Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|replication fork processing (GO:0031297)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral mRNA export from host cell nucleus (GO:0046784)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|transcription export complex (GO:0000346)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)										GAATTCCTGCCGGCACCTCTG	0.652																																																0			17											27	29	29					17																	79846185		2203	4300	6503	77439481	SO:0001583	missense	10189			AF047002	CCDS32768.1, CCDS32768.2	17q25.3	2013-02-12	2011-12-12	2011-12-12	ENSG00000183684	ENSG00000183684		"THO complex subunits", "RNA binding motif (RRM) containing"	19071	protein-coding gene	gene with protein product		604171	"THO complex 4"	THOC4		11032328	Standard	NM_005782		Approved	ALY, BEF, ALY/REF, REF	uc002kbu.2	Q86V81	OTTHUMG00000160470	ENST00000331204.4:c.691G>A	17.37:g.79846185C>T	ENSP00000331817:p.Gly231Ser		77439481	O43672	Missense_Mutation	SNP	ENST00000331204.4	37		.	.	.	.	.	.	.	.	.	.	C	15.48	2.844941	0.51164	.	.	ENSG00000183684	ENST00000331204;ENST00000505490	D;D	0.92299	-3.01;-3.01	5.43	4.47	0.54385	.	0.059051	0.64402	D	0.000002	D	0.88966	0.6581	L	0.37850	1.14	0.46011	D	0.998816	D	0.55172	0.97	P	0.48400	0.576	D	0.86076	0.1541	10	0.11182	T	0.66	.	14.3803	0.66907	0.0:0.9292:0.0:0.0708	.	238	E9PB61	.	S	231;238	ENSP00000331817:G231S;ENSP00000421592:G238S	ENSP00000331817:G231S	G	-	1	0	THOC4	77439481	1.000000	0.71417	0.924000	0.36721	0.463000	0.32649	3.362000	0.52314	1.539000	0.49286	0.655000	0.94253	GGC		0.652	ALYREF-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005782		T	79846185	C	T	79846185	3	4	112	1	0	0	0	0	1	0	0	0	15906	652	23	1	90	1	THOC4	17	79846185	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	1485618	79846185	1349025	139	30359										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3879898	3879898	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gggtcgctgaaggggcccacGcactcagcctggaaggagtt	16	11	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr18:3879898G>A	ENST00000315677.3	-	4	766	c.171C>T	c.(169-171)tgC>tgT	p.C57C	DLGAP1_ENST00000581527.1_Silent_p.C57C|DLGAP1-AS3_ENST00000577649.1_RNA|DLGAP1_ENST00000515196.2_Silent_p.C57C|DLGAP1_ENST00000584874.1_Silent_p.C57C	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	57					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				AGGGGCCCACGCACTCAGCCT	0.672																																																0			18											52	53	53					18																	3879898		2203	4300	6503	3869898	SO:0001819	synonymous_variant	9229			AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.171C>T	18.37:g.3879898G>A			3869898	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Silent	SNP	ENST00000315677.3	37	CCDS11836.1																																																																																				0.672	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			A	3879898	G	A	3879898	2	1	112	1	0	0	0	0	0	0	0	1	4570	1079	38	1		1	DLGAP1	18	3879898	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10		3879898	74197350	140	30360										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8825456	8825456	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cagaccaatgggtcccggacGatggggacccagactgttca	13	12	1	2	rs147203549	byFrequency	TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr18:8825456G>A	ENST00000306329.11	+	13	4905	c.4905G>A	c.(4903-4905)acG>acA	p.T1635T	SOGA2_ENST00000306285.7_Silent_p.T641T|SOGA2_ENST00000359865.3_Silent_p.T1316T|SOGA2_ENST00000518815.1_Silent_p.T641T|SOGA2_ENST00000400050.3_Silent_p.T1275T|SOGA2_ENST00000517570.1_Silent_p.T1275T																							GGTCCCGGACGATGGGGACCC	0.607													G|||	2	0.000399361	0	0.0014	5008	,	,		19426	0		0.001	False		,,,				2504	0															0			18						G		1,4405	2.1+/-5.4	0,1,2202	34	34	34		3948	-10.8	0	18	dbSNP_134	34	0,8598		0,0,4299	no	coding-synonymous	CCDC165	NM_015210.3		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		1316/1587	8825456	1,13003	2203	4299	6502	8815456	SO:0001819	synonymous_variant	23255																														ENST00000306329.11:c.4905G>A	18.37:g.8825456G>A			8815456		Silent	SNP	ENST00000306329.11	37																																																																																					0.607	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			A	8825456	G	A	8825456	2	1	112	1	0	0	0	0	0	0	0	1	8215	1045	37	1		1	KIAA0802	18	8825456	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	4945558	8825456	69251792	141	30361										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14752564	14752564	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aaagtcctctcactctcgtaGgactgctctacactgggcct	8	14	3	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr18:14752564G>A	ENST00000358984.4	+	2	401		c.e2-1		ANKRD30B_ENST00000447268.2_Splice_Site|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B											breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						CACTCTCGTAGGACTGCTCTA	0.433																																																0			18											57	48	51					18																	14752564		692	1591	2283	14742564	SO:0001630	splice_region_variant	374860			BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.222-1G>A	18.37:g.14752564G>A			14742564	B4DGP1|F8WAG3|Q4G175	Splice_Site	SNP	ENST00000358984.4	37	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	G	4.544	0.101069	0.08731	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	.	.	.	1.63	1.63	0.23807	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.6992	0.23215	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKRD30B	14742564	1.000000	0.71417	0.843000	0.33291	0.091000	0.18340	5.172000	0.65003	1.218000	0.43458	0.290000	0.19541	.		0.433	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	Intron	A	14752564	G	A	14752564	5	1	112	1	0	0	0	0	0	0	1	0	659	1014	35	3	227	3	ANKRD30B	18	14752564	Splice_Site	SNP	G	TCGA-EI-6508-01A-11D-1733-10	5927108	14752564	63324684	142	30362										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48604662	48604662	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggaattggtgttgatgaccTtcgtcgcttatgcatactca	10	8	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr18:48604662T>G	ENST00000342988.3	+	12	2022	c.1484T>G	c.(1483-1485)cTt>cGt	p.L495R	SMAD4_ENST00000588745.1_Missense_Mutation_p.L399R|SMAD4_ENST00000398417.2_Missense_Mutation_p.L495R|SMAD4_ENST00000586253.1_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	495	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GTTGATGACCTTCGTCGCTTA	0.468																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											124	106	112					18																	48604662		2203	4300	6503	46858660	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1484T>G	18.37:g.48604662T>G	ENSP00000341551:p.Leu495Arg		46858660	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.791064	0.70452	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98633	-5.04;-5.04	5.99	5.99	0.97316	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.061993	0.64402	D	0.000003	D	0.99333	0.9766	M	0.93720	3.45	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	D	0.98842	1.0755	10	0.87932	D	0	.	15.4471	0.75238	0.0:0.0:0.0:1.0	.	495	Q13485	SMAD4_HUMAN	R	495	ENSP00000341551:L495R;ENSP00000381452:L495R	ENSP00000341551:L495R	L	+	2	0	SMAD4	46858660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.819000	0.86621	2.292000	0.77174	0.533000	0.62120	CTT		0.468	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48604662	T	G	48604662	3	3	112	1	0	0	0	0	1	0	0	0	14797	1609	56	4	1526	4	SMAD4	18	48604662	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	33852098	48604662	29472586	143	30363										
PLIN5	440503	hgsc.bcm.edu	37	chr19	4531793	4531793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tcgcagaccgcggtgcacgtGgccctgaccaggggcagagc	16	14	0	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:4531793G>A	ENST00000381848.3	-	3	182	c.102C>T	c.(100-102)gcC>gcT	p.A34A	CTB-50L17.14_ENST00000586020.1_Missense_Mutation_p.P52L	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	34	Essential for lipid droplet targeting. {ECO:0000250}.|Interaction with LIPE. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						CGGTGCACGTGGCCCTGACCA	0.687																																																0			19											10	13	12					19																	4531793		2038	4160	6198	4482793	SO:0001819	synonymous_variant	0			DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"Perilipins"	33196	protein-coding gene	gene with protein product	"lipid storage droplet protein 5"	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.102C>T	19.37:g.4531793G>A			4482793	A2RRC1|Q6ZS68	Silent	SNP	ENST00000381848.3	37	CCDS42473.1																																																																																				0.687	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706		A	4531793	G	A	4531793	2	1	112	1	0	0	0	0	0	0	0	1	12124	1335	47	3		3	PLIN5	19	4531793	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10		4531793	54597190	144	30364										
MUC16	94025	hgsc.bcm.edu	37	chr19	9076366	9076366	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgtactactgggagtccaacTtgtacttaaaatgtcaggaa	9	7	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:9076366T>G	ENST00000397910.4	-	3	11283	c.11080A>C	c.(11080-11082)Agt>Cgt	p.S3694R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3695	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAGTCCAACTTGTACTTAAA	0.443																																																0			19											98	94	95					19																	9076366		1955	4152	6107	8937366	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11080A>C	19.37:g.9076366T>G	ENSP00000381008:p.Ser3694Arg		8937366	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	5.307	0.242014	0.10077	.	.	ENSG00000181143	ENST00000397910	T	0.02656	4.21	2.03	2.03	0.26663	.	.	.	.	.	T	0.02494	0.0076	N	0.08118	0	.	.	.	P	0.35208	0.49	B	0.43728	0.429	T	0.33599	-0.9862	8	0.87932	D	0	.	6.0601	0.19832	0.0:0.0:0.0:1.0	.	3694	B5ME49	.	R	3694	ENSP00000381008:S3694R	ENSP00000381008:S3694R	S	-	1	0	MUC16	8937366	0.016000	0.18221	0.016000	0.15963	0.085000	0.17905	1.839000	0.39220	1.173000	0.42796	0.260000	0.18958	AGT		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9076366	T	G	9076366	3	3	112	1	0	0	0	0	1	0	0	0	10003	1609	56	4	32771	4	MUC16	19	9076366	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	4544573	9076366	50052617	145	30365										
HAPLN4	404037	hgsc.bcm.edu	37	chr19	19371743	19371743	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agggaggcatccccaggcccGtcgccctgcagctcagcccg	13	18	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:19371743G>A	ENST00000291481.7	-	3	426	c.363C>T	c.(361-363)gaC>gaT	p.D121D	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	121	Ig-like C2-type.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	CCCCAGGCCCGTCGCCCTGCA	0.662																																																0			19											55	53	54					19																	19371743		2203	4300	6503	19232743	SO:0001819	synonymous_variant	404037			AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.363C>T	19.37:g.19371743G>A			19232743	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	37	CCDS12398.1																																																																																				0.662	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		A	19371743	G	A	19371743	2	1	112	1	0	0	0	0	0	0	0	1	6978	1136	40	1		1	HAPLN4	19	19371743	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10295377	19371743	39757240	146	30366										
ZNF90	7643	hgsc.bcm.edu	37	chr19	20228743	20228743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggatgagggtaaagtacacaAaagaggttataatggactta	12	3	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:20228743A>G	ENST00000418063.2	+	4	492	c.380A>G	c.(379-381)aAa>aGa	p.K127R	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	127					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						AAAGTACACAAAAGAGGTTAT	0.328																																																0			19											119	110	112					19																	20228743		692	1591	2283	20089743	SO:0001583	missense	7643			M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"Zinc fingers, C2H2-type", "-"	13165	protein-coding gene	gene with protein product		603973	"zinc finger protein 90 (HTF9)"			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.380A>G	19.37:g.20228743A>G	ENSP00000410466:p.Lys127Arg		20089743	B9EH87	Missense_Mutation	SNP	ENST00000418063.2	37	CCDS46028.1	.	.	.	.	.	.	.	.	.	.	a	6.655	0.489375	0.12641	.	.	ENSG00000213988	ENST00000418063	T	0.04970	3.52	0.81	-1.62	0.08372	.	.	.	.	.	T	0.09024	0.0223	M	0.90082	3.085	0.09310	N	1	P	0.44195	0.828	B	0.35859	0.212	T	0.09930	-1.0652	9	0.31617	T	0.26	.	4.1737	0.10341	0.7415:0.0:0.2585:0.0	.	127	Q03938	ZNF90_HUMAN	R	127	ENSP00000410466:K127R	ENSP00000410466:K127R	K	+	2	0	ZNF90	20089743	0.000000	0.05858	0.036000	0.18154	0.036000	0.12997	-1.636000	0.02016	-1.367000	0.02152	-1.412000	0.01120	AAA		0.328	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138		G	20228743	A	G	20228743	3	3	112	1	0	0	0	0	1	0	0	0	18238	14	1	4	394	4	ZNF90	19	20228743	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	857000	20228743	38900240	147	30367										
EIF3K	11184	hgsc.bcm.edu	37	chr19	39111066	39111074	+	5'Flank	DEL	TCCTGAAGC	TCCTGAAGC	-													0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tctggaagccaacctggctgTcctgaagctgtaagtgtcta							TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	TCCTGAAGC	TCCTGAAGC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:39111066_39111074delTCCTGAAGC	ENST00000591517.1	-	0	0				MAP4K1_ENST00000589130.1_5'Flank|EIF3K_ENST00000592558.1_Splice_Site_p.LKL51del|EIF3K_ENST00000593149.1_5'UTR|EIF3K_ENST00000593062.1_3'UTR|EIF3K_ENST00000538434.1_Intron|EIF3K_ENST00000588934.1_Splice_Site_p.LKL51del|MAP4K1_ENST00000396857.2_5'Flank|EIF3K_ENST00000248342.4_Splice_Site_p.LKL51del|MAP4K1_ENST00000586296.1_5'Flank|EIF3K_ENST00000545173.2_Splice_Site_p.LKL51del	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1						activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AACCTGGCTGTCCTGAAGCTGTAAGTGTC	0.531																																																0			19																																								43802914	SO:0001631	upstream_gene_variant	27335			U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918			19.37:g.39111066_39111074delTCCTGAAGC	Exception_encountered		43802906		In_Frame_Del	DEL	ENST00000591517.1	37	CCDS59385.1																																																																																				0.531	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		-	39111074	TCCTGAAGC	-	39111066	6	5	112	0	1	1	0	1	0	0	0	0	5034	1667	58	0		0	EIF3K	19	39111066	5'Flank	DEL	TCCTGAAGC	TCGA-EI-6508-01A-11D-1733-10	18882323	39111066	20017917	148	30368										
DYRK1B	9149	hgsc.bcm.edu	37	chr19	40320645	40320645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tggccacaagctcctgggtcTgatgatcataggctttcacc	10	12	3	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr19:40320645T>C	ENST00000593685.1	-	5	863	c.395A>G	c.(394-396)cAg>cGg	p.Q132R	DYRK1B_ENST00000430012.2_Missense_Mutation_p.Q132R|DYRK1B_ENST00000597639.1_Missense_Mutation_p.Q132R|DYRK1B_ENST00000348817.3_Missense_Mutation_p.Q132R|DYRK1B_ENST00000323039.5_Missense_Mutation_p.Q132R			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			CTCCTGGGTCTGATGATCATA	0.552																																																0			19											109	97	101					19																	40320645		2203	4300	6503	45012485	SO:0001583	missense	9149			Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"minibrain-related kinase"	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.395A>G	19.37:g.40320645T>C	ENSP00000469863:p.Gln132Arg		45012485	O75258|O75788|O75789	Missense_Mutation	SNP	ENST00000593685.1	37	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653275	0.47362	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	T;T;T	0.64991	-0.13;-0.13;-0.13	4.19	4.19	0.49359	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.127014	0.53938	D	0.000047	T	0.41903	0.1179	N	0.10645	0.015	0.46078	D	0.998854	B;B;B	0.22146	0.032;0.04;0.065	B;B;B	0.25987	0.039;0.065;0.039	T	0.37291	-0.9712	10	0.44086	T	0.13	.	11.2397	0.48962	0.0:0.0:0.0:1.0	.	132;132;132	Q9Y463-2;Q9Y463;Q9Y463-3	.;DYR1B_HUMAN;.	R	132	ENSP00000312789:Q132R;ENSP00000221803:Q132R;ENSP00000403182:Q132R	ENSP00000312789:Q132R	Q	-	2	0	DYRK1B	45012485	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.047000	0.57383	1.761000	0.52028	0.459000	0.35465	CAG		0.552	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714		C	40320645	T	C	40320645	3	2	112	1	0	0	0	0	1	0	0	0	4866	1580	55	4	1522	4	DYRK1B	19	40320645	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	1209579	40320645	18808338	149	30369										
RNF24	11237	hgsc.bcm.edu	37	chr20	3944554	3944554	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	caacagaagagtaaactaagGatgaagacaaatatagcagt	9	5	0	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:3944554G>C	ENST00000336095.6	-	2	362	c.111C>G	c.(109-111)atC>atG	p.I37M	RNF24_ENST00000432261.2_Missense_Mutation_p.I58M|RNF24_ENST00000545616.2_Missense_Mutation_p.I58M|RNF24_ENST00000358395.6_Missense_Mutation_p.I37M	NM_007219.3	NP_009150.1	Q9Y225	RNF24_HUMAN	ring finger protein 24	37						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			large_intestine(1)|upper_aerodigestive_tract(1)	2						GTAAACTAAGGATGAAGACAA	0.318																																																0			20											80	75	77					20																	3944554		2203	4300	6503	3892554	SO:0001583	missense	11237			AF151081	CCDS13074.1, CCDS46577.1	20p13	2013-01-09			ENSG00000101236	ENSG00000101236		"RING-type (C3HC4) zinc fingers"	13779	protein-coding gene	gene with protein product		612489					Standard	NM_007219		Approved	G1L	uc002wki.2	Q9Y225	OTTHUMG00000031770	ENST00000336095.6:c.111C>G	20.37:g.3944554G>C	ENSP00000336753:p.Ile37Met		3892554	D3DVZ2|D3DVZ3|Q9UMH1	Missense_Mutation	SNP	ENST00000336095.6	37	CCDS13074.1	.	.	.	.	.	.	.	.	.	.	G	2.982	-0.210027	0.06140	.	.	ENSG00000101236	ENST00000336095;ENST00000358395;ENST00000545616;ENST00000432261	T;T;T;T	0.25085	1.84;1.84;1.82;1.82	6.02	0.611	0.17586	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	N	0.01168	-0.975	0.49915	D	0.999835	B;B	0.31680	0.335;0.141	B;B	0.31751	0.135;0.032	T	0.23476	-1.0187	10	0.19147	T	0.46	-15.9977	2.9581	0.05883	0.2084:0.1214:0.5449:0.1253	.	58;37	Q9Y225-2;Q9Y225	.;RNF24_HUMAN	M	37;37;58;58	ENSP00000336753:I37M;ENSP00000351166:I37M;ENSP00000444711:I58M;ENSP00000388550:I58M	ENSP00000336753:I37M	I	-	3	3	RNF24	3892554	1.000000	0.71417	0.999000	0.59377	0.377000	0.30045	1.575000	0.36493	0.154000	0.19237	-0.903000	0.02851	ATC		0.318	RNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077795.2			C	3944554	G	C	3944554	3	2	112	1	0	0	0	0	1	0	0	0	13521	1164	41	5	355	5	RNF24	20	3944554	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10		3944554	59080966	150	30370										
PAK7	57144	hgsc.bcm.edu	37	chr20	9561556	9561556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gatggaggtttccttgcaggGtttgtttcctctaacgattg	12	7	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:9561556G>A	ENST00000378429.3	-	5	772	c.226C>T	c.(226-228)Ccc>Tcc	p.P76S	PAK7_ENST00000353224.5_Missense_Mutation_p.P76S|PAK7_ENST00000378423.1_Missense_Mutation_p.P76S	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	76	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P76T(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TCCTTGCAGGGTTTGTTTCCT	0.458																																																1	Substitution - Missense(1)	lung(1)	20											93	95	94					20																	9561556		2203	4300	6503	9509556	SO:0001583	missense	57144			AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.226C>T	20.37:g.9561556G>A	ENSP00000367686:p.Pro76Ser		9509556	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	G	5.764	0.325416	0.10900	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.47177	0.85;0.85;0.85	5.82	4.63	0.57726	.	0.140389	0.64402	N	0.000003	T	0.33731	0.0873	N	0.25647	0.755	0.48185	D	0.999605	B;B	0.06786	0.0;0.001	B;B	0.15870	0.001;0.014	T	0.07888	-1.0749	9	.	.	.	.	12.4512	0.55679	0.0996:0.0:0.9004:0.0	.	76;76	B0AZM9;Q9P286	.;PAK7_HUMAN	S	76;76;76;24	ENSP00000367686:P76S;ENSP00000322957:P76S;ENSP00000367679:P76S	.	P	-	1	0	PAK7	9509556	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	4.678000	0.61641	1.098000	0.41479	0.655000	0.94253	CCC		0.458	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9561556	G	A	9561556	3	1	112	1	0	0	0	0	1	0	0	0	11436	1261	44	3	1961	3	PAK7	20	9561556	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	5617002	9561556	53463964	151	30371										
DTD1	92675	hgsc.bcm.edu	37	chr20	18576856	18576856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cagcttcctggagcagctgcGtaaaacatacaggccggagc	12	12	0	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:18576856G>A	ENST00000377452.3	+	3	521	c.341G>A	c.(340-342)cGt>cAt	p.R114H	DTD1_ENST00000494921.1_3'UTR	NM_080820.4	NP_543010.3	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1	114					D-amino acid catabolic process (GO:0019478)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			large_intestine(4)|lung(1)|ovary(2)	7						GAGCAGCTGCGTAAAACATAC	0.532																																																0			20											53	50	51					20																	18576856		2203	4300	6503	18524856	SO:0001583	missense	92675			AF332356	CCDS13138.1	20p11.23	2012-09-25	2012-09-25	2007-02-23	ENSG00000125821	ENSG00000125821			16219	protein-coding gene	gene with protein product		610996	"chromosome 20 open reading frame 88", "D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae)"	C20orf88, HARS2			Standard	NM_080820		Approved	DUEB, MGC119131, MGC41905, bA379J5.3, bA555E18.1, pqn-68	uc002wrf.4	Q8TEA8	OTTHUMG00000031980	ENST00000377452.3:c.341G>A	20.37:g.18576856G>A	ENSP00000366672:p.Arg114His		18524856	A8K5X5|D3DW37|Q496D1|Q5W184|Q8WXU8|Q9BW67|Q9H464|Q9H474	Missense_Mutation	SNP	ENST00000377452.3	37	CCDS13138.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577167	0.86645	.	.	ENSG00000125821	ENST00000377452	.	.	.	5.83	5.83	0.93111	D-Tyr tRNAtyr deacylase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.84124	0.5403	M	0.92970	3.365	0.80722	D	1	D	0.67145	0.996	P	0.56960	0.81	D	0.87242	0.2267	9	0.62326	D	0.03	-7.2791	19.0992	0.93266	0.0:0.0:1.0:0.0	.	114	Q8TEA8	DTD1_HUMAN	H	114	.	ENSP00000366672:R114H	R	+	2	0	DTD1	18524856	1.000000	0.71417	0.971000	0.41717	0.359000	0.29487	7.950000	0.87804	2.741000	0.93983	0.655000	0.94253	CGT		0.532	DTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078189.3	NM_080820		A	18576856	G	A	18576856	3	1	112	1	0	0	0	0	1	0	0	0	4797	1145	40	1	351	1	DTD1	20	18576856	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	9015300	18576856	44448664	152	30372										
C20orf71	128861	hgsc.bcm.edu	37	chr20	31805446	31805446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cctggcccaagcccacagagAcaacaaatccaccctggcaa	7	17	0	1	rs564972529		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:31805446A>G	ENST00000375454.3	+	1	314	c.104A>G	c.(103-105)gAc>gGc	p.D35G	RP11-49G10.3_ENST00000419613.1_RNA|BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Missense_Mutation_p.D35G	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	35						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GCCCACAGAGACAACAAATCC	0.622													A|||	1	0.000199681	0	0	5008	,	,		18879	0		0	False		,,,				2504	0.001															0			20											86	79	81					20																	31805446		2203	4300	6503	31269107	SO:0001583	missense	128861				CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"BPI fold containing"	16204	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 71"	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.104A>G	20.37:g.31805446A>G	ENSP00000364603:p.Asp35Gly		31269107	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	.	.	.	.	.	.	.	.	.	.	A	7.233	0.599747	0.13939	.	.	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.44083	0.93;1.09	4.36	2.13	0.27403	.	0.494508	0.17292	N	0.179589	T	0.27278	0.0669	L	0.29908	0.895	0.09310	N	1	B;P	0.40970	0.004;0.734	B;B	0.37731	0.006;0.257	T	0.13202	-1.0518	10	0.87932	D	0	-8.8923	5.8413	0.18635	0.789:0.0:0.211:0.0	.	35;35	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	G	35	ENSP00000364603:D35G;ENSP00000364601:D35G	ENSP00000364601:D35G	D	+	2	0	BPIFA3	31269107	0.528000	0.26314	0.010000	0.14722	0.060000	0.15804	1.269000	0.33074	0.458000	0.26988	0.533000	0.62120	GAC		0.622	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		G	31805446	A	G	31805446	3	3	112	1	0	0	0	0	1	0	0	0	2123	275	10	4	106	4	C20orf71	20	31805446	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	13228590	31805446	31220074	153	30373										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33328653	33328653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcttcgccggttgccagaggAccctggactattggtcaaaa	12	11	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:33328653A>G	ENST00000374796.2	-	12	7977	c.5407T>C	c.(5407-5409)Tcc>Ccc	p.S1803P	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1803P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1803	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TTGCCAGAGGACCCTGGACTA	0.488																																																0			20											79	78	78					20																	33328653		2203	4300	6503	32792314	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5407T>C	20.37:g.33328653A>G	ENSP00000363929:p.Ser1803Pro		32792314	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211721	0.58452	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25085	1.82;1.82	5.65	5.65	0.86999	.	0.280434	0.31531	N	0.007485	T	0.14657	0.0354	N	0.12182	0.205	0.31858	N	0.621315	P	0.44090	0.826	B	0.41860	0.368	T	0.08146	-1.0736	10	0.25751	T	0.34	-7.4797	9.077	0.36527	0.8369:0.0:0.0:0.1631	.	1803	Q14686	NCOA6_HUMAN	P	1803	ENSP00000363929:S1803P;ENSP00000351894:S1803P	ENSP00000351894:S1803P	S	-	1	0	NCOA6	32792314	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.196000	0.51020	2.371000	0.80710	0.533000	0.62120	TCC		0.488	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		G	33328653	A	G	33328653	3	3	112	1	0	0	0	0	1	0	0	0	10264	275	10	4	804	4	NCOA6	20	33328653	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	1523207	33328653	29696867	154	30374										
RBM12	10137	hgsc.bcm.edu	37	chr20	34242181	34242181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gtttcaaagcttcaaatgtaTcttgaggggagagaaactta	10	5	3	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:34242181T>C	ENST00000374114.3	-	3	1327	c.1064A>G	c.(1063-1065)gAt>gGt	p.D355G	CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397443.1_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.D355G|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397446.1_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.D355G|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397442.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	355	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TTCAAATGTATCTTGAGGGGA	0.433											OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0			20											152	148	149					20																	34242181		2203	4300	6503	33705595	SO:0001583	missense	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1064A>G	20.37:g.34242181T>C	ENSP00000363228:p.Asp355Gly	846	33705595	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	T	16.63	3.177462	0.57692	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.35421	1.31;1.31;1.31	4.92	4.92	0.64577	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.068850	0.56097	D	0.000029	T	0.55986	0.1955	L	0.61036	1.89	0.80722	D	1	P	0.52842	0.956	D	0.66196	0.942	T	0.59679	-0.7409	10	0.72032	D	0.01	-11.4275	14.8093	0.69982	0.0:0.0:0.0:1.0	.	355	Q9NTZ6	RBM12_HUMAN	G	355;355;355;154	ENSP00000363228:D355G;ENSP00000352668:D355G;ENSP00000363217:D355G	ENSP00000339879:D154G	D	-	2	0	RBM12	33705595	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.525000	0.81892	2.083000	0.62718	0.449000	0.29647	GAT		0.433	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		C	34242181	T	C	34242181	3	2	112	1	0	0	0	0	1	0	0	0	13150	1435	50	4	1738	4	RBM12	20	34242181	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	913528	34242181	28783339	155	30375										
PREX1	57580	hgsc.bcm.edu	37	chr20	47305234	47305234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggacagtgctcagctttctcCggcggtccttgatgaggttc	13	11	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:47305234C>T	ENST00000371941.3	-	10	1317	c.1295G>A	c.(1294-1296)cGg>cAg	p.R432Q	PREX1_ENST00000396220.1_Missense_Mutation_p.R432Q	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	432	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R432Q(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAGCTTTCTCCGGCGGTCCTT	0.562																																																1	Substitution - Missense(1)	ovary(1)	20											167	119	136					20																	47305234		2203	4300	6503	46738641	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1295G>A	20.37:g.47305234C>T	ENSP00000361009:p.Arg432Gln		46738641	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.795891	0.90453	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.28895	1.59;1.59	5.29	4.35	0.52113	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.56097	U	0.000034	T	0.45034	0.1322	M	0.75884	2.315	0.51767	D	0.999934	D	0.56287	0.975	P	0.50791	0.65	T	0.51934	-0.8642	10	0.72032	D	0.01	.	13.8488	0.63483	0.0:0.9265:0.0:0.0735	.	432	Q8TCU6	PREX1_HUMAN	Q	432	ENSP00000361009:R432Q;ENSP00000379522:R432Q	ENSP00000361009:R432Q	R	-	2	0	PREX1	46738641	0.965000	0.33210	0.619000	0.29118	0.996000	0.88848	3.822000	0.55708	1.229000	0.43630	0.563000	0.77884	CGG		0.562	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47305234	C	T	47305234	3	4	112	1	0	0	0	0	1	0	0	0	12510	652	23	1	3808	1	PREX1	20	47305234	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	13063053	47305234	15720286	156	30376										
STAU1	6780	hgsc.bcm.edu	37	chr20	47741010	47741010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ctcctcaagaacagctatggCggcatttttctttgaaatct	7	10	3	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:47741010C>T	ENST00000371856.2	-	7	1134	c.724G>A	c.(724-726)Gcc>Acc	p.A242T	STAU1_ENST00000340954.7_Missense_Mutation_p.A161T|STAU1_ENST00000371828.3_Missense_Mutation_p.A167T|STAU1_ENST00000347458.5_Missense_Mutation_p.A161T|STAU1_ENST00000371792.1_Missense_Mutation_p.A161T|STAU1_ENST00000371802.1_Missense_Mutation_p.A167T|STAU1_ENST00000360426.4_Missense_Mutation_p.A161T	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	242	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.A242T(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			ACAGCTATGGCGGCATTTTTC	0.468																																																1	Substitution - Missense(1)	ovary(1)	20											163	181	175					20																	47741010		2203	4300	6503	47174417	SO:0001583	missense	6780				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.724G>A	20.37:g.47741010C>T	ENSP00000360922:p.Ala242Thr		47174417	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	37	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	C	34	5.337601	0.95758	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	D;D;D;D;D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46;-3.46;-3.46;-3.46;-3.46	5.33	5.33	0.75918	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.98795	0.9594	H	0.99650	4.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99461	1.0943	10	0.87932	D	0	-10.4462	19.0449	0.93015	0.0:1.0:0.0:0.0	.	242;167	O95793;Q5JW29	STAU1_HUMAN;.	T	167;161;242;161;161;161;167;161;167	ENSP00000360893:A167T;ENSP00000345425:A161T;ENSP00000360922:A242T;ENSP00000353604:A161T;ENSP00000323443:A161T;ENSP00000360867:A167T;ENSP00000360857:A161T;ENSP00000416779:A167T	ENSP00000345425:A161T	A	-	1	0	STAU1	47174417	1.000000	0.71417	0.376000	0.26042	0.702000	0.40608	7.814000	0.86154	2.492000	0.84095	0.650000	0.86243	GCC		0.468	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		T	47741010	C	T	47741010	3	4	112	1	0	0	0	0	1	0	0	0	15311	768	27	1	1041	1	STAU1	20	47741010	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	435776	47741010	15284510	157	30377										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50292694	50292694	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	acttcggggatttgaggtatTcatgacactccggagttctc	11	9	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:50292694T>A	ENST00000338821.5	-	10	1117	c.853A>T	c.(853-855)Aat>Tat	p.N285Y	ATP9A_ENST00000402822.1_Missense_Mutation_p.N164Y|ATP9A_ENST00000311637.5_Missense_Mutation_p.N149Y	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	285					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTTGAGGTATTCATGACACTC	0.413																																																0			20											96	87	90					20																	50292694		2203	4300	6503	49726101	SO:0001583	missense	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.853A>T	20.37:g.50292694T>A	ENSP00000342481:p.Asn285Tyr		49726101	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741611	0.89573	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.90844	-1.52;-2.74;-1.53	5.61	5.61	0.85477	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.96800	0.8955	H	0.95574	3.69	0.80722	D	1	P;D	0.89917	0.566;1.0	B;D	0.83275	0.175;0.996	D	0.97992	1.0355	10	0.87932	D	0	-28.9316	15.7941	0.78394	0.0:0.0:0.0:1.0	.	164;285	O75110-2;O75110	.;ATP9A_HUMAN	Y	149;285;164	ENSP00000309086:N149Y;ENSP00000342481:N285Y;ENSP00000385875:N164Y	ENSP00000309086:N149Y	N	-	1	0	ATP9A	49726101	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.638000	0.83328	2.123000	0.65237	0.533000	0.62120	AAT		0.413	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50292694	T	A	50292694	3	1	112	1	0	0	0	0	1	0	0	0	1199	1783	62	5	2366	5	ATP9A	20	50292694	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10	2551684	50292694	12732826	158	30378										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51873043	51873043	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	taaaactccacctaagcaaaAcgcacagcaagtcacccgaa	5	14	1	0			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr20:51873043A>G	ENST00000371497.5	+	2	3933	c.3046A>G	c.(3046-3048)Acg>Gcg	p.T1016A	TSHZ2_ENST00000329613.6_Missense_Mutation_p.T1013A|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.T1013A	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	1016					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CCTAAGCAAAACGCACAGCAA	0.463																																																0			20											131	117	122					20																	51873043		2203	4300	6503	51306450	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.3046A>G	20.37:g.51873043A>G	ENSP00000360552:p.Thr1016Ala		51306450	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729010	0.69074	.	.	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.24908	1.84;1.83	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.53626	0.1808	M	0.77616	2.38	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.58284	-0.7663	10	0.72032	D	0.01	-1.6328	15.957	0.79893	1.0:0.0:0.0:0.0	.	1016	Q9NRE2	TSH2_HUMAN	A	1016;1013	ENSP00000360552:T1016A;ENSP00000333114:T1013A	ENSP00000333114:T1013A	T	+	1	0	TSHZ2	51306450	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.956000	0.93066	2.168000	0.68352	0.523000	0.50628	ACG		0.463	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		G	51873043	A	G	51873043	3	3	112	1	0	0	0	0	1	0	0	0	16664	43	2	4	3052	4	TSHZ2	20	51873043	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	1580349	51873043	11152477	159	30379										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15889220	15889220	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agagaatatttaccttttccTcagaaagggctttgatgtac	8	7	1	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr21:15889220T>C	ENST00000400566.1	-	3	353	c.272A>G	c.(271-273)gAg>gGg	p.E91G	SAMSN1_ENST00000400564.1_Intron|SAMSN1_ENST00000285670.2_Missense_Mutation_p.E159G	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	91					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TACCTTTTCCTCAGAAAGGGC	0.313																																																0			21											95	84	87					21																	15889220		1793	4062	5855	14811091	SO:0001583	missense	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.272A>G	21.37:g.15889220T>C	ENSP00000383411:p.Glu91Gly		14811091	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317443	0.81469	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.61392	0.11;0.11	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.78666	0.4319	M	0.87682	2.9	0.58432	D	0.999997	D;D	0.71674	0.997;0.998	D;D	0.71656	0.913;0.974	T	0.83172	-0.0093	10	0.87932	D	0	-29.7102	15.3481	0.74359	0.0:0.0:0.0:1.0	.	159;91	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	G	159;91	ENSP00000285670:E159G;ENSP00000383411:E91G	ENSP00000285670:E159G	E	-	2	0	SAMSN1	14811091	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.637000	0.74304	2.033000	0.60031	0.533000	0.62120	GAG		0.313	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			C	15889220	T	C	15889220	3	2	112	1	0	0	0	0	1	0	0	0	13867	1551	54	4	873	4	SAMSN1	21	15889220	Missense_Mutation	SNP	T	TCGA-EI-6508-01A-11D-1733-10		15889220	32240675	160	30380										
C21orf63	59271	hgsc.bcm.edu	37	chr21	33887402	33887402	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccatagaagctgcagagctcGcagaaaggattgagcgcagg	14	9	0	4	rs146340457		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr21:33887402G>A	ENST00000300255.2	+	8	1701	c.1228G>A	c.(1228-1230)Gca>Aca	p.A410T	EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000401402.3_Missense_Mutation_p.A362T|EVA1C_ENST00000382699.3_Missense_Mutation_p.A407T	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	410						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										TGCAGAGCTCGCAGAAAGGAT	0.493																																																0			21						G	THR/ALA	0,4406		0,0,2203	101	111	107		1228	5.9	1	21	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	missense	C21orf63	NM_058187.3	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	410/442	33887402	1,13005	2203	4300	6503	32809273	SO:0001583	missense	59271			AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.1228G>A	21.37:g.33887402G>A	ENSP00000300255:p.Ala410Thr		32809273	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	.	.	.	.	.	.	.	.	.	.	G	35	5.525646	0.96431	0.0	1.16E-4	ENSG00000166979	ENST00000300255;ENST00000401402;ENST00000382699	T;T;T	0.61980	0.06;0.06;0.06	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.83445	0.5256	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.83593	0.0124	10	0.46703	T	0.11	-17.5624	20.2963	0.98556	0.0:0.0:1.0:0.0	.	407;410	A6ND58;P58658	.;CU063_HUMAN	T	410;362;407	ENSP00000300255:A410T;ENSP00000384594:A362T;ENSP00000372146:A407T	ENSP00000300255:A410T	A	+	1	0	C21orf63	32809273	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	8.929000	0.92859	2.813000	0.96785	0.655000	0.94253	GCA		0.493	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		A	33887402	G	A	33887402	3	1	112	1	0	0	0	0	1	0	0	0	2137	1087	38	1	1258	1	C21orf63	21	33887402	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	17998182	33887402	14242493	161	30381										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47545812	47545812	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	aggaggctgtcaagaacctcGagtggattgcgggcggcacc	16	10	1	1	rs377376395		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr21:47545812G>T	ENST00000300527.4	+	26	2187	c.2083G>T	c.(2083-2085)Gag>Tag	p.E695*	COL6A2_ENST00000357838.4_Nonsense_Mutation_p.E695*|COL6A2_ENST00000409416.1_Nonsense_Mutation_p.E695*|COL6A2_ENST00000397763.1_Nonsense_Mutation_p.E695*|COL6A2_ENST00000310645.5_Nonsense_Mutation_p.E695*	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	695	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)		p.E695Q(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CAAGAACCTCGAGTGGATTGC	0.607																																																1	Substitution - Missense(1)	ovary(1)	21											74	67	70					21																	47545812		2203	4300	6503	46370240	SO:0001587	stop_gained	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2083G>T	21.37:g.47545812G>T	ENSP00000300527:p.Glu695*		46370240	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Nonsense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	36	5.659939	0.96734	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	.	.	.	4.21	4.21	0.49690	.	0.052830	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-24.9483	16.5536	0.84479	0.0:0.0:1.0:0.0	.	.	.	.	X	695	.	ENSP00000300527:E695X	E	+	1	0	COL6A2	46370240	1.000000	0.71417	0.994000	0.49952	0.776000	0.43924	7.742000	0.85008	1.889000	0.54706	0.491000	0.48974	GAG		0.607	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			T	47545812	G	T	47545812	4	4	112	1	0	0	0	0	0	1	0	0	3706	1059	37	2	2181	2	COL6A2	21	47545812	Nonsense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	13658410	47545812	584083	162	30382										
CECR2	27443	hgsc.bcm.edu	37	chr22	18028280	18028280	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ggacagaacgcagcgacaccGcccagcacagaccccggttt	11	16	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr22:18028280G>A	ENST00000400585.2	+	17	3249	c.2811G>A	c.(2809-2811)ccG>ccA	p.P937P	CECR2_ENST00000400573.5_Silent_p.P1079P|CECR2_ENST00000262608.8_Silent_p.P1080P			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1121					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.P1079P(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		CAGCGACACCGCCCAGCACAG	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	22											27	32	31					22																	18028280		2172	4263	6435	16408280	SO:0001819	synonymous_variant	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.2811G>A	22.37:g.18028280G>A			16408280	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37																																																																																					0.597	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		A	18028280	G	A	18028280	2	1	112	1	0	0	0	0	0	0	0	1	3212	1074	38	1		1	CECR2	22	18028280	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10		18028280	33276286	163	30383										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26747060	26747060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agaggtggatcactcgacccGcttaatttcggatcctgtgc	11	11	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr22:26747060G>A	ENST00000248933.6	+	12	2545	c.2450G>A	c.(2449-2451)cGc>cAc	p.R817H	SEZ6L_ENST00000404234.3_Missense_Mutation_p.R817H|SEZ6L_ENST00000529632.2_Missense_Mutation_p.R817H|SEZ6L_ENST00000343706.4_Missense_Mutation_p.R817H|SEZ6L_ENST00000411842.2_Missense_Mutation_p.R14H|SEZ6L_ENST00000402979.1_Missense_Mutation_p.R590H|SEZ6L_ENST00000403121.1_Missense_Mutation_p.R590H|SEZ6L_ENST00000360929.3_Intron			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	817	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CACTCGACCCGCTTAATTTCG	0.547																																																0			22											117	102	107					22																	26747060		2203	4300	6503	25077060	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2450G>A	22.37:g.26747060G>A	ENSP00000248933:p.Arg817His		25077060	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	g	28.4	4.913610	0.92178	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979;ENST00000411842	T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	4.54	4.54	0.55810	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.56097	D	0.000035	T	0.76183	0.3952	M	0.72118	2.19	0.54753	D	0.99998	D;D;D;D;D;D	0.59357	0.961;0.985;0.977;0.978;0.968;0.985	P;P;P;P;P;P	0.62298	0.757;0.9;0.833;0.79;0.828;0.9	T	0.79548	-0.1758	10	0.66056	D	0.02	.	16.5015	0.84257	0.0:0.0:1.0:0.0	.	817;817;590;817;817;817	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	H	817;817;817;817;590;590;14	ENSP00000384772:R817H;ENSP00000437037:R817H;ENSP00000248933:R817H;ENSP00000342661:R817H;ENSP00000384838:R590H;ENSP00000384733:R590H;ENSP00000397274:R14H	ENSP00000248933:R817H	R	+	2	0	SEZ6L	25077060	1.000000	0.71417	0.995000	0.50966	0.697000	0.40408	8.815000	0.91973	2.381000	0.81170	0.539000	0.68188	CGC		0.547	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26747060	G	A	26747060	3	1	112	1	0	0	0	0	1	0	0	0	14180	1087	38	1	2496	1	SEZ6L	22	26747060	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	8718780	26747060	24557506	164	30384										
CSDC2	27254	hgsc.bcm.edu	37	chr22	41970768	41970768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agtacgtgccagtggagggcGacgaggtgacctacaagatg	16	8	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr22:41970768G>A	ENST00000306149.7	+	4	875	c.331G>A	c.(331-333)Gac>Aac	p.D111N		NM_014460.3	NP_055275.1	Q9Y534	CSDC2_HUMAN	cold shock domain containing C2, RNA binding	111	CSD.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			prostate(2)|upper_aerodigestive_tract(1)	3						AGTGGAGGGCGACGAGGTGAC	0.642																																					NSCLC(181;294 2110 12667 14717 31090)											0			22											93	69	77					22																	41970768		2203	4300	6503	40300714	SO:0001583	missense	27254			AL834417	CCDS14019.1	22q13.2	2006-02-24			ENSG00000172346	ENSG00000172346			30359	protein-coding gene	gene with protein product						8573167, 12767259	Standard	NM_014460		Approved	PIPPin	uc003bak.1	Q9Y534	OTTHUMG00000150967	ENST00000306149.7:c.331G>A	22.37:g.41970768G>A	ENSP00000302485:p.Asp111Asn		40300714	Q8ND37	Missense_Mutation	SNP	ENST00000306149.7	37	CCDS14019.1	.	.	.	.	.	.	.	.	.	.	g	24.2	4.506827	0.85282	.	.	ENSG00000172346	ENST00000306149	.	.	.	5.02	4.0	0.46444	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.052250	0.85682	D	0.000000	T	0.77758	0.4178	H	0.95224	3.64	0.80722	D	1	B	0.34255	0.445	B	0.35813	0.211	D	0.83379	0.0011	9	0.87932	D	0	.	15.6339	0.76933	0.0:0.1376:0.8624:0.0	.	111	Q9Y534	CSDC2_HUMAN	N	111	.	ENSP00000302485:D111N	D	+	1	0	CSDC2	40300714	1.000000	0.71417	0.736000	0.30914	0.598000	0.36846	7.797000	0.85911	1.323000	0.45263	0.651000	0.88453	GAC		0.642	CSDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320689.1	NM_014460		A	41970768	G	A	41970768	3	1	112	1	0	0	0	0	1	0	0	0	3934	1058	37	1	341	1	CSDC2	22	41970768	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	15223708	41970768	9333798	165	30385										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50657130	50657130	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cgcggccagggctgctgctgAccttgtacctgagctccagg	14	14	0	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chr22:50657130A>G	ENST00000248846.5	-	21	4926		c.e21+1		TUBGCP6_ENST00000439308.2_Splice_Site|TUBGCP6_ENST00000491449.1_Splice_Site			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6						G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.?(1)		breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		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)		GCTGCTGCTGACCTTGTACCT	0.672																																																1	Unknown(1)	central_nervous_system(1)	22											41	39	40					22																	50657130		2203	4300	6503	48999257	SO:0001630	splice_region_variant	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4821+1T>C	22.37:g.50657130A>G			48999257	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Splice_Site	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.180931	0.78677	.	.	ENSG00000128159	ENST00000248846;ENST00000425018	.	.	.	4.63	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8622	0.63569	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TUBGCP6	48999257	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.859000	0.92264	1.945000	0.56424	0.482000	0.46254	.		0.672	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	Intron	G	50657130	A	G	50657130	5	3	112	1	0	0	0	0	0	0	1	0	16810	289	10	4	656	4	TUBGCP6	22	50657130	Splice_Site	SNP	A	TCGA-EI-6508-01A-11D-1733-10	8686362	50657130	647436	166	30386										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3227826	3227826	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tttgccatgcacttgtagaaGccggcatctctctgtgtggc	11	11	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:3227826G>T	ENST00000217939.6	-	7	8572	c.8418C>A	c.(8416-8418)ggC>ggA	p.G2806G		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2806	Ig-like C2-type 12.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				ACTTGTAGAAGCCGGCATCTC	0.488																																																0			X											82	76	78					X																	3227826		2203	4300	6503	3237826	SO:0001819	synonymous_variant	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.8418C>A	X.37:g.3227826G>T			3237826	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3227826	G	T	3227826	2	4	112	1	0	0	0	0	0	0	0	1	10033	958	34	2		2	MXRA5	23	3227826	Silent	SNP	G	TCGA-EI-6508-01A-11D-1733-10		3227826	152042734	167	30387										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3240724	3240724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	agatggtgggggttggagtaAggtgtgcaaaggtgtcttct	18	3	2	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:3240724A>G	ENST00000217939.6	-	5	3156	c.3002T>C	c.(3001-3003)cTt>cCt	p.L1001P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1001						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGTTGGAGTAAGGTGTGCAAA	0.463																																																0			X											191	146	161					X																	3240724		2203	4300	6503	3250724	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3002T>C	X.37:g.3240724A>G	ENSP00000217939:p.Leu1001Pro		3250724	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	a	7.998	0.754690	0.15778	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.66460	-0.21	3.33	0.607	0.17564	.	1.608970	0.04378	U	0.360350	T	0.42720	0.1215	N	0.14661	0.345	0.09310	N	1	P	0.46277	0.875	B	0.35240	0.198	T	0.41142	-0.9525	10	0.72032	D	0.01	.	1.2723	0.02023	0.5262:0.1856:0.1054:0.1828	.	1001	Q9NR99	MXRA5_HUMAN	P	1001	ENSP00000217939:L1001P	ENSP00000217939:L1001P	L	-	2	0	MXRA5	3250724	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.668000	0.25127	-0.163000	0.10946	0.430000	0.28490	CTT		0.463	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		G	3240724	A	G	3240724	3	3	112	1	0	0	0	0	1	0	0	0	10033	72	3	4	5496	4	MXRA5	23	3240724	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	12898	3240724	152029836	168	30388										
MID1	4281	hgsc.bcm.edu	37	chrX	10417466	10417466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tagggagcccagtgataatcGtcagacacttgttccacacg	10	11	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:10417466G>A	ENST00000317552.4	-	10	2346	c.1946C>T	c.(1945-1947)aCg>aTg	p.T649M	MID1_ENST00000479925.1_5'Flank|MID1_ENST00000380787.1_Missense_Mutation_p.T649M|MID1_ENST00000453318.2_Missense_Mutation_p.T649M|MID1_ENST00000380785.1_Missense_Mutation_p.T649M|MID1_ENST00000380782.2_3'UTR|MID1_ENST00000380779.1_Missense_Mutation_p.T649M|MID1_ENST00000380780.1_Missense_Mutation_p.T649M	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	649	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						AGTGATAATCGTCAGACACTT	0.542																																																0			X											89	71	77					X																	10417466		2203	4300	6503	10377466	SO:0001583	missense	4281			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1946C>T	X.37:g.10417466G>A	ENSP00000312678:p.Thr649Met		10377466	B2RCG2|O75361|Q9BZX5	Missense_Mutation	SNP	ENST00000317552.4	37	CCDS14138.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789279	0.49997	.	.	ENSG00000101871	ENST00000453318;ENST00000317552;ENST00000380785;ENST00000380779;ENST00000380787;ENST00000380780;ENST00000454373	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.74412	0.3713	L	0.59912	1.85	0.58432	D	0.999999	P;D;P	0.60160	0.926;0.987;0.789	P;P;B	0.53593	0.507;0.73;0.407	T	0.73940	-0.3824	10	0.37606	T	0.19	.	11.9983	0.53216	0.0809:0.0:0.9191:0.0	.	649;649;599	A8K5A0;O15344;B4DLX8	.;TRI18_HUMAN;.	M	649;649;649;649;649;649;599	ENSP00000414521:T649M;ENSP00000312678:T649M;ENSP00000370162:T649M;ENSP00000370156:T649M;ENSP00000370164:T649M;ENSP00000370157:T649M	ENSP00000312678:T649M	T	-	2	0	MID1	10377466	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.438000	0.80431	2.322000	0.78497	0.422000	0.28245	ACG		0.542	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10417466	G	A	10417466	3	1	112	1	0	0	0	0	1	0	0	0	9606	1145	40	1	61	1	MID1	23	10417466	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	7176742	10417466	144853094	169	30389										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35971785	35971785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tctttttgagatttgagtccGtaggaagtaaagatggattt	11	3	1	3	rs145395039		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:35971785G>A	ENST00000297866.5	+	7	1189	c.1123G>A	c.(1123-1125)Gta>Ata	p.V375I		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	375										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						ATTTGAGTCCGTAGGAAGTAA	0.328																																																0			X						G	ILE/VAL	0,3833		0,0,1631,571	90	83	85		1123	0.1	0	X	dbSNP_134	85	1,6725		0,1,2427,1870	no	missense	CXorf22	NM_152632.3	29	0,1,4058,2441	AA,AG,GG,G		0.0149,0.0,0.0095	benign	375/977	35971785	1,10558	2202	4298	6500	35881706	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1123G>A	X.37:g.35971785G>A	ENSP00000297866:p.Val375Ile		35881706	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	G	2.785	-0.252702	0.05829	0.0	1.49E-4	ENSG00000165164	ENST00000297866	T	0.56776	0.44	5.69	0.0515	0.14298	.	0.459833	0.24657	N	0.036675	T	0.34716	0.0907	L	0.55481	1.735	0.09310	N	1	P	0.36171	0.541	B	0.25291	0.059	T	0.16424	-1.0403	10	0.22706	T	0.39	-22.9848	5.9897	0.19454	0.4034:0.0:0.4705:0.1261	.	375	Q6ZTR5	CX022_HUMAN	I	375	ENSP00000297866:V375I	ENSP00000297866:V375I	V	+	1	0	CXorf22	35881706	0.853000	0.29707	0.003000	0.11579	0.001000	0.01503	1.073000	0.30691	-0.063000	0.13065	-0.296000	0.09543	GTA		0.328	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		A	35971785	G	A	35971785	3	1	112	1	0	0	0	0	1	0	0	0	4108	1145	40	1	1149	1	CXorf22	23	35971785	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	25554319	35971785	119298775	170	30390										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028941	37028941	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gcccggagcctaccaagaccGgagcgtcccatctaaaagaa	10	14	1	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:37028941G>T	ENST00000358047.3	+	1	2510	c.2458G>T	c.(2458-2460)Gga>Tga	p.G820*		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	820								p.G820R(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TACCAAGACCGGAGCGTCCCA	0.552																																																1	Substitution - Missense(1)	ovary(1)	X											62	61	61					X																	37028941		2202	4300	6502	36938862	SO:0001587	stop_gained	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2458G>T	X.37:g.37028941G>T	ENSP00000367913:p.Gly820*		36938862	Q6ZU46	Nonsense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741785	0.69304	.	.	ENSG00000198173	ENST00000358047	.	.	.	0.14	0.14	0.14804	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	.	.	.	.	.	.	.	X	820	.	ENSP00000367913:G820X	G	+	1	0	FAM47C	36938862	0.019000	0.18553	0.005000	0.12908	0.005000	0.04900	-0.349000	0.07731	0.168000	0.19655	0.169000	0.16792	GGA		0.552	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37028941	G	T	37028941	4	4	112	1	0	0	0	0	0	1	0	0	5590	1117	39	2	2460	2	FAM47C	23	37028941	Nonsense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	1057156	37028941	118241619	171	30391										
ERAS	3266	hgsc.bcm.edu	37	chrX	48688028	48688028	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	gctggagatgctcatgccgcTgctgcagccctcgcacacag	12	15	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:48688028T>C	ENST00000338270.1	+	1	746	c.495T>C	c.(493-495)gcT>gcC	p.A165A	PCSK1N_ENST00000478242.1_5'Flank	NM_181532.2	NP_853510.1	Q7Z444	RASE_HUMAN	ES cell expressed Ras	165					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(2)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	14						CTCATGCCGCTGCTGCAGCCC	0.642																																																0			X											29	25	26					X																	48688028		2203	4300	6503	48572972	SO:0001819	synonymous_variant	3266			X00419	CCDS35246.1	Xp11.23	2014-05-09	2003-07-14	2003-07-16	ENSG00000187682	ENSG00000187682			5174	protein-coding gene	gene with protein product		300437	"v-Ha-ras Harvey rat sarcoma viral oncogene homolog pseudogene"	HRAS2, HRASP		12774123	Standard	NM_181532		Approved		uc031tjl.1	Q7Z444	OTTHUMG00000059533	ENST00000338270.1:c.495T>C	X.37:g.48688028T>C			48572972		Silent	SNP	ENST00000338270.1	37	CCDS35246.1																																																																																				0.642	ERAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132402.1	NM_181532		C	48688028	T	C	48688028	2	2	112	1	0	0	0	0	0	0	0	1	5218	1567	55	4		4	ERAS	23	48688028	Silent	SNP	T	TCGA-EI-6508-01A-11D-1733-10	11659087	48688028	106582532	172	30392										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75649145	75649145	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccgagcacctccgtgctgccCgccgcctctgacggacaaag	11	18	1	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:75649145C>T	ENST00000361470.2	+	1	1100	c.822C>T	c.(820-822)ccC>ccT	p.P274P		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	274	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCGTGCTGCCCGCCGCCTCTG	0.701																																																0			X											28	26	27					X																	75649145		2198	4297	6495	75565549	SO:0001819	synonymous_variant	728239			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.822C>T	X.37:g.75649145C>T			75565549	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																				0.701	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		T	75649145	C	T	75649145	2	4	112	1	0	0	0	0	0	0	0	1	9215	639	23	1		1	MAGEE1	23	75649145	Silent	SNP	C	TCGA-EI-6508-01A-11D-1733-10	26961117	75649145	79621415	173	30393										
ARMCX1	51309	hgsc.bcm.edu	37	chrX	100808743	100808743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ccttaataacttgagtgtgaAcgcagaaaatcagggcaaga	10	7	1	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:100808743A>G	ENST00000372829.3	+	4	1201	c.830A>G	c.(829-831)aAc>aGc	p.N277S		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	277						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						TTGAGTGTGAACGCAGAAAAT	0.433																																																0			X											111	88	96					X																	100808743		2203	4300	6503	100695399	SO:0001583	missense	51309			AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.830A>G	X.37:g.100808743A>G	ENSP00000361917:p.Asn277Ser		100695399	Q53HK2|Q9H2Q0	Missense_Mutation	SNP	ENST00000372829.3	37	CCDS14487.1	.	.	.	.	.	.	.	.	.	.	a	14.35	2.510680	0.44660	.	.	ENSG00000126947	ENST00000372829	T	0.35048	1.33	3.54	2.34	0.29019	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35307	0.0927	N	0.22421	0.69	0.39904	D	0.973949	D	0.60160	0.987	D	0.66351	0.943	T	0.16837	-1.0389	10	0.27785	T	0.31	-5.8605	5.1583	0.15046	0.7162:0.0:0.0:0.2838	.	277	Q9P291	ARMX1_HUMAN	S	277	ENSP00000361917:N277S	ENSP00000361917:N277S	N	+	2	0	ARMCX1	100695399	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	2.688000	0.46984	0.528000	0.28580	0.441000	0.28932	AAC		0.433	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		G	100808743	A	G	100808743	3	3	112	1	0	0	0	0	1	0	0	0	960	43	2	4	832	4	ARMCX1	23	100808743	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	25159598	100808743	54461817	174	30394										
NRK	203447	hgsc.bcm.edu	37	chrX	105153287	105153287	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tgcctgaacaagagctggagCagaaccaggcacctgaacag	12	11	0	4			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:105153287C>T	ENST00000243300.9	+	13	1957	c.1654C>T	c.(1654-1656)Cag>Tag	p.Q552*	NRK_ENST00000428173.2_Nonsense_Mutation_p.Q553*	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	552	Gln-rich.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						AGAGCTGGAGCAGAACCAGGC	0.562										HNSCC(51;0.14)																																						0			X											38	38	38					X																	105153287		2015	4150	6165	105039943	SO:0001587	stop_gained	203447			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.1654C>T	X.37:g.105153287C>T	ENSP00000434830:p.Gln552*		105039943	Q32ND6|Q5H9K2|Q6ZMP2	Nonsense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	C	36	5.623787	0.96660	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	.	.	.	4.49	3.6	0.41247	.	0.480497	0.17763	N	0.162823	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	11.3444	0.49552	0.0:0.8131:0.1869:0.0	.	.	.	.	X	552;553	.	ENSP00000434830:Q552X	Q	+	1	0	NRK	105039943	0.979000	0.34478	0.037000	0.18230	0.017000	0.09413	1.705000	0.37867	1.208000	0.43306	0.600000	0.82982	CAG		0.562	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105153287	C	T	105153287	4	4	112	1	0	0	0	0	0	1	0	0	10686	711	25	3	1704	3	NRK	23	105153287	Nonsense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	4344544	105153287	50117273	175	30395										
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106064218	106064218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	tactaattttgtacaaggaaAaataagagtaagtggcacgg	10	4	0	1			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:106064218A>G	ENST00000357242.5	+	3	527	c.353A>G	c.(352-354)aAa>aGa	p.K118R	TBC1D8B_ENST00000310452.2_Missense_Mutation_p.K118R|TBC1D8B_ENST00000276175.3_Missense_Mutation_p.K118R|TBC1D8B_ENST00000481617.2_Missense_Mutation_p.K118R	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	118							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTACAAGGAAAAATAAGAGTA	0.338																																																0			X											60	58	58					X																	106064218		2203	4297	6500	105950874	SO:0001583	missense	54885			AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"EF-hand domain containing"	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.353A>G	X.37:g.106064218A>G	ENSP00000349781:p.Lys118Arg		105950874	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	37	CCDS14522.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.078625	0.55753	.	.	ENSG00000133138	ENST00000357242;ENST00000310452;ENST00000481617;ENST00000276175;ENST00000460545	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.52980	0.1768	M	0.87269	2.87	0.80722	D	1	P;D;D	0.59357	0.685;0.985;0.961	B;P;B	0.62649	0.436;0.905;0.393	T	0.61589	-0.7032	10	0.72032	D	0.01	-16.6277	12.9925	0.58627	1.0:0.0:0.0:0.0	.	118;118;118	Q0IIM8;B9A6K6;D6RFZ2	TBC8B_HUMAN;.;.	R	118;118;118;118;20	ENSP00000349781:K118R;ENSP00000310675:K118R;ENSP00000421375:K118R;ENSP00000276175:K118R	ENSP00000276175:K118R	K	+	2	0	TBC1D8B	105950874	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	9.284000	0.95882	1.813000	0.52934	0.339000	0.21740	AAA		0.338	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		G	106064218	A	G	106064218	3	3	112	1	0	0	0	0	1	0	0	0	15665	14	1	4	363	4	TBC1D8B	23	106064218	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	910931	106064218	49206342	176	30396										
ZCCHC16	340595	hgsc.bcm.edu	37	chrX	111698393	111698393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cacaaaacaggaaatcaatcCtctgatgaatgctaagtttg	7	8	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:111698393C>A	ENST00000340433.2	+	1	667	c.437C>A	c.(436-438)cCt>cAt	p.P146H		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	146							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.P146L(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						GAAATCAATCCTCTGATGAAT	0.418																																																1	Substitution - Missense(1)	ovary(1)	X											83	79	81					X																	111698393		2203	4300	6503	111585049	SO:0001583	missense	340595			AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"Zinc fingers, CCHC domain containing"	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.437C>A	X.37:g.111698393C>A	ENSP00000340590:p.Pro146His		111585049	B2RPG1	Missense_Mutation	SNP	ENST00000340433.2	37	CCDS35369.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.496101	0.01009	.	.	ENSG00000187823	ENST00000340433	T	0.30714	1.52	4.12	1.3	0.21679	.	1.081410	0.07229	N	0.862202	T	0.27241	0.0668	L	0.27053	0.805	0.09310	N	1	P	0.43431	0.807	P	0.47673	0.554	T	0.19386	-1.0307	10	0.59425	D	0.04	-0.3401	4.1987	0.10455	0.1566:0.5941:0.1507:0.0986	.	146	Q6ZR62	ZCH16_HUMAN	H	146	ENSP00000340590:P146H	ENSP00000340590:P146H	P	+	2	0	ZCCHC16	111585049	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.066000	0.03454	-0.073000	0.12842	-1.225000	0.01585	CCT		0.418	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308		A	111698393	C	A	111698393	3	1	112	1	0	0	0	0	1	0	0	0	17623	681	24	2	439	2	ZCCHC16	23	111698393	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	5634175	111698393	43572167	177	30397										
GPR112	139378	hgsc.bcm.edu	37	chrX	135427393	135427393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cagtccattcattgactctcCcaactaggcttattgagacc	6	13	2	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:135427393C>T	ENST00000394143.1	+	6	1819	c.1528C>T	c.(1528-1530)Cca>Tca	p.P510S	GPR112_ENST00000394141.1_Missense_Mutation_p.P305S|GPR112_ENST00000412101.1_Missense_Mutation_p.P305S|GPR112_ENST00000370652.1_Missense_Mutation_p.P510S|GPR112_ENST00000287534.4_Missense_Mutation_p.P447S	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	510					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ATTGACTCTCCCAACTAGGCT	0.423																																																0			X											74	63	67					X																	135427393		2203	4300	6503	135255059	SO:0001583	missense	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1528C>T	X.37:g.135427393C>T	ENSP00000377699:p.Pro510Ser		135255059	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	2.111	-0.403825	0.04832	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.52057	0.72;0.72;0.68;0.76;0.68	2.3	1.41	0.22369	.	.	.	.	.	T	0.22898	0.0553	N	0.12182	0.205	0.09310	N	1	B;B;B	0.19935	0.012;0.04;0.024	B;B;B	0.15484	0.013;0.01;0.004	T	0.25152	-1.0140	9	0.10377	T	0.69	.	5.4176	0.16382	0.0:0.807:0.0:0.193	.	447;305;510	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	S	510;510;305;447;305	ENSP00000377699:P510S;ENSP00000359686:P510S;ENSP00000416526:P305S;ENSP00000287534:P447S;ENSP00000377697:P305S	ENSP00000287534:P447S	P	+	1	0	GPR112	135255059	0.033000	0.19621	0.015000	0.15790	0.006000	0.05464	-0.049000	0.11924	0.188000	0.20168	-0.537000	0.04273	CCA		0.423	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135427393	C	T	135427393	3	4	112	1	0	0	0	0	1	0	0	0	6649	623	22	3	1538	3	GPR112	23	135427393	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	23729000	135427393	19843167	178	30398										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141290856	141290856	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	ttcttcttgatgctttctgaAtgggctctcggaccccacag	9	12	4	2			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:141290856A>T	ENST00000247452.3	-	3	1265	c.918T>A	c.(916-918)caT>caA	p.H306Q		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	306	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					TGCTTTCTGAATGGGCTCTCG	0.463										HNSCC(46;0.14)																																						0			X											91	89	90					X																	141290856		2203	4300	6503	141118522	SO:0001583	missense	51438			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.918T>A	X.37:g.141290856A>T	ENSP00000354660:p.His306Gln		141118522	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	37	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	14.02	2.410788	0.42817	.	.	ENSG00000046774	ENST00000247452	T	0.04317	3.65	0.988	0.988	0.19796	.	0.915653	0.09130	U	0.844511	T	0.15696	0.0378	M	0.75150	2.29	0.19300	N	0.999977	P	0.47962	0.903	D	0.64042	0.921	T	0.16335	-1.0406	10	0.72032	D	0.01	.	3.916	0.09224	1.0:0.0:0.0:0.0	.	306	Q9UBF1	MAGC2_HUMAN	Q	306	ENSP00000354660:H306Q	ENSP00000354660:H306Q	H	-	3	2	MAGEC2	141118522	0.028000	0.19301	0.506000	0.27664	0.245000	0.25701	0.066000	0.14489	0.635000	0.30488	0.235000	0.17854	CAT		0.463	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		T	141290856	A	T	141290856	3	4	112	1	0	0	0	0	1	0	0	0	9211	98	4	5	207	5	MAGEC2	23	141290856	Missense_Mutation	SNP	A	TCGA-EI-6508-01A-11D-1733-10	5863463	141290856	13979704	179	30399										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718309	142718309	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	atcttccagttgcaattcaaCgacacggccaatgtgttcca	7	12	2	0	rs143575705		TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:142718309C>T	ENST00000381779.4	-	2	841	c.616G>A	c.(616-618)Gtt>Att	p.V206I	SLITRK4_ENST00000338017.4_Missense_Mutation_p.V206I|SLITRK4_ENST00000356928.1_Missense_Mutation_p.V206I	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	206			V -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			integral component of membrane (GO:0016021)		p.V206I(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TGCAATTCAACGACACGGCCA	0.428													c|||	1	0.000264901	0	0	3775	,	,		14413	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	X							ILE/VAL,ILE/VAL,ILE/VAL	0,3835		0,0,0,1632,571	89	85	86		616,616,616	3.9	0	X	dbSNP_134	86	3,6725		0,2,1,2426,1871	yes	missense,missense,missense	SLITRK4	NM_001184749.1,NM_001184750.1,NM_173078.3	29,29,29	0,2,1,4058,2442	TT,TC,T,CC,C		0.0446,0.0,0.0284	possibly-damaging,possibly-damaging,possibly-damaging	206/838,206/838,206/838	142718309	3,10560	2203	4300	6503	142545975	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.616G>A	X.37:g.142718309C>T	ENSP00000371198:p.Val206Ile		142545975	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	c	11.05	1.523895	0.27299	0.0	4.46E-4	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.52295	0.67;0.67;0.67	5.73	3.93	0.45458	.	0.000000	0.85682	U	0.000000	T	0.46328	0.1387	N	0.20685	0.6	0.46336	D	0.998993	D	0.71674	0.998	P	0.62560	0.904	T	0.32798	-0.9893	10	0.37606	T	0.19	-5.3159	8.7621	0.34680	0.1503:0.7692:0.0:0.0805	.	206	Q8IW52	SLIK4_HUMAN	I	206	ENSP00000371198:V206I;ENSP00000349400:V206I;ENSP00000336627:V206I	ENSP00000336627:V206I	V	-	1	0	SLITRK4	142545975	0.995000	0.38212	0.005000	0.12908	0.217000	0.24651	3.349000	0.52217	0.549000	0.28973	0.597000	0.82753	GTT		0.428	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		T	142718309	C	T	142718309	3	4	112	1	0	0	0	0	1	0	0	0	14782	536	19	1	1901	1	SLITRK4	23	142718309	Missense_Mutation	SNP	C	TCGA-EI-6508-01A-11D-1733-10	1427453	142718309	12552251	180	30400										
EMD	2010	hgsc.bcm.edu	37	chrX	153608713	153608713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0391061452513966	7	1	0.56229712303793	2.30274059910771	0.431763862332696	0.34984520123839	1	0	cttcattcccagatgctgacGctttccatcaccaggtgagc	8	14	2	3			TCGA-EI-6508-01A-11D-1733-10	TCGA-EI-6508-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	de5b9d77-af36-4d87-9a59-2cf76efd9e46	c6f9d0e7-8806-4088-ada0-b1ae85374e7f	g.chrX:153608713G>A	ENST00000369842.4	+	4	673	c.385G>A	c.(385-387)Gct>Act	p.A129T	EMD_ENST00000369835.3_Missense_Mutation_p.A94T|EMD_ENST00000492448.1_3'UTR	NM_000117.2	NP_000108.1	P50402	EMD_HUMAN	emerin	129	Interaction with F-actin. {ECO:0000305}.				cellular response to growth factor stimulus (GO:0071363)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of protein export from nucleus (GO:0046827)|regulation of canonical Wnt signaling pathway (GO:0060828)|skeletal muscle cell differentiation (GO:0035914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	actin binding (GO:0003779)|beta-tubulin binding (GO:0048487)			lung(5)	5	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AGATGCTGACGCTTTCCATCA	0.592																																																0			X											51	47	49					X																	153608713		2203	4299	6502	153261907	SO:0001583	missense	2010			X82434	CCDS14745.1	Xq27.3-q28	2014-09-17	2008-07-29		ENSG00000102119	ENSG00000102119			3331	protein-coding gene	gene with protein product	"LEM domain containing 5"	300384	"Emery-Dreifuss muscular dystrophy"				Standard	NM_000117		Approved	STA, LEMD5	uc004fkl.3	P50402	OTTHUMG00000033186	ENST00000369842.4:c.385G>A	X.37:g.153608713G>A	ENSP00000358857:p.Ala129Thr		153261907	Q6FI02	Missense_Mutation	SNP	ENST00000369842.4	37	CCDS14745.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.985501	0.00443	.	.	ENSG00000102119	ENST00000369842;ENST00000369835	D;D	0.85702	-1.59;-2.02	4.01	0.223	0.15292	.	0.609355	0.15514	N	0.258388	T	0.54759	0.1878	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50996	-0.8761	10	0.02654	T	1	-25.3034	2.9076	0.05726	0.5014:0.2348:0.2638:0.0	.	129	P50402	EMD_HUMAN	T	129;94	ENSP00000358857:A129T;ENSP00000358850:A94T	ENSP00000358850:A94T	A	+	1	0	EMD	153261907	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	0.170000	0.16663	0.077000	0.16863	-0.536000	0.04276	GCT		0.592	EMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080921.1			A	153608713	G	A	153608713	3	1	112	1	0	0	0	0	1	0	0	0	5100	1087	38	1	399	1	EMD	23	153608713	Missense_Mutation	SNP	G	TCGA-EI-6508-01A-11D-1733-10	10890404	153608713	1661847	181	30401										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20470056	20470056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctactgtgggctggggggccGtggccagcccaaggatgagg	19	10	0	1	rs145617803	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:20470056G>A	ENST00000375102.3	+	3	389	c.287G>A	c.(286-288)cGt>cAt	p.R96H		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	53					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CTGGGGGGCCGTGGCCAGCCC	0.642													G|||	9	0.00179712	0.0068	0	5008	,	,		18629	0		0	False		,,,				2504	0															0			1						G	HIS/ARG	14,4392	20.2+/-43.8	0,14,2189	74	66	69		287	-0.7	0	1	dbSNP_134	69	0,8600		0,0,4300	yes	missense	PLA2G2F	NM_022819.3	29	0,14,6489	AA,AG,GG		0.0,0.3177,0.1076	benign	96/212	20470056	14,12992	2203	4300	6503	20342643	SO:0001583	missense	64600			AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.287G>A	1.37:g.20470056G>A	ENSP00000364243:p.Arg96His		20342643	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	37	CCDS204.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.66	2.004584	0.35320	0.003177	0.0	ENSG00000158786	ENST00000375102	T	0.28069	1.63	5.25	-0.689	0.11313	.	1.201530	0.05971	N	0.642339	T	0.25382	0.0617	L	0.45581	1.43	0.09310	N	1	B	0.21309	0.054	B	0.17098	0.017	T	0.29243	-1.0018	10	0.48119	T	0.1	-11.9822	4.5605	0.12158	0.2948:0.0:0.5703:0.135	.	96	Q9BZM2-2	.	H	96	ENSP00000364243:R96H	ENSP00000364243:R96H	R	+	2	0	PLA2G2F	20342643	0.000000	0.05858	0.037000	0.18230	0.935000	0.57460	0.013000	0.13310	-0.459000	0.07013	-0.309000	0.09137	CGT		0.642	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		A	20470056	G	A	20470056	3	1	113	1	0	0	0	0	1	0	0	0	12030	1145	40	1	297	1	PLA2G2F	1	20470056	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10		20470056	228780565	1	30402										
SYTL1	84958	hgsc.bcm.edu	37	chr1	27674052	27674052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtctatgcgcaggaagaagaGcaccaggggtgagaggagat	17	6	1	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:27674052G>T	ENST00000543823.1	+	2	794	c.332G>T	c.(331-333)aGc>aTc	p.S111I	SYTL1_ENST00000490170.1_3'UTR|SYTL1_ENST00000318074.5_Missense_Mutation_p.S111I			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	111				S -> N (in Ref. 1; AAK67636). {ECO:0000305}.	exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGGAAGAAGAGCACCAGGGGT	0.627																																																0			1											52	50	51					1																	27674052		2203	4300	6503	27546639	SO:0001583	missense	84958			AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.332G>T	1.37:g.27674052G>T	ENSP00000440704:p.Ser111Ile		27546639	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Missense_Mutation	SNP	ENST00000543823.1	37	CCDS53286.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361611	0.61403	.	.	ENSG00000142765	ENST00000318074;ENST00000543823	T;T	0.25912	1.77;1.79	4.54	4.54	0.55810	.	1.646450	0.03200	N	0.174586	T	0.45276	0.1334	L	0.60455	1.87	0.29116	N	0.880545	P;D;P;P	0.71674	0.832;0.998;0.832;0.895	B;D;B;B	0.65010	0.352;0.931;0.248;0.431	T	0.12268	-1.0554	10	0.29301	T	0.29	-2.7078	6.7561	0.23514	0.1923:0.0:0.8077:0.0	.	111;111;111;111	A8KAH3;G3V181;Q8IYJ3;Q8IYJ3-2	.;.;SYTL1_HUMAN;.	I	111	ENSP00000316464:S111I;ENSP00000440704:S111I	ENSP00000316464:S111I	S	+	2	0	SYTL1	27546639	0.571000	0.26659	0.930000	0.37139	0.854000	0.48673	0.616000	0.24344	2.340000	0.79590	0.561000	0.74099	AGC		0.627	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872		T	27674052	G	T	27674052	3	4	113	1	0	0	0	0	1	0	0	0	15521	971	34	2	338	2	SYTL1	1	27674052	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	7203996	27674052	221576569	2	30403										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35881235	35881235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctttgcccatgtgatgagacGgaccaggactctgaagtaca	11	10	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:35881235G>A	ENST00000314607.6	+	28	4309	c.4229G>A	c.(4228-4230)cGg>cAg	p.R1410Q	ZMYM4_ENST00000373297.2_Missense_Mutation_p.R1321Q	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1410			R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTGATGAGACGGACCAGGACT	0.433																																																0			1											147	130	136					1																	35881235		2203	4300	6503	35653822	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4229G>A	1.37:g.35881235G>A	ENSP00000322915:p.Arg1410Gln		35653822	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.754998	0.69648	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.21031	2.03;2.06	5.63	5.63	0.86233	.	0.052234	0.85682	D	0.000000	T	0.13030	0.0316	N	0.12887	0.27	0.54753	D	0.999985	P	0.38148	0.62	B	0.35312	0.2	T	0.10917	-1.0609	10	0.09843	T	0.71	-8.5764	20.0401	0.97581	0.0:0.0:1.0:0.0	.	1410	Q5VZL5	ZMYM4_HUMAN	Q	1410;1321	ENSP00000322915:R1410Q;ENSP00000362394:R1321Q	ENSP00000322915:R1410Q	R	+	2	0	ZMYM4	35653822	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.496000	0.81526	2.805000	0.96524	0.655000	0.94253	CGG		0.433	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35881235	G	A	35881235	3	1	113	1	0	0	0	0	1	0	0	0	17741	1116	39	1	4339	1	ZMYM4	1	35881235	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	8207183	35881235	213369386	3	30404										
MAST2	23139	hgsc.bcm.edu	37	chr1	46489483	46489483	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cacaagtccacccggcagcgCtttgccatgaagaagatcaa	9	13	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:46489483C>A	ENST00000361297.2	+	15	1894	c.1611C>A	c.(1609-1611)cgC>cgA	p.R537R	MAST2_ENST00000372009.2_Silent_p.R467R	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCCGGCAGCGCTTTGCCATGA	0.572																																																0			1											77	77	77					1																	46489483		2203	4300	6503	46262070	SO:0001819	synonymous_variant	23139			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1611C>A	1.37:g.46489483C>A			46262070		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																				0.572	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46489483	C	A	46489483	2	1	113	1	0	0	0	0	0	0	0	1	9355	784	28	2		2	MAST2	1	46489483	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	10608248	46489483	202761138	4	30405										
USP24	23358	hgsc.bcm.edu	37	chr1	55612632	55612632	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aattcacaaacatcctggccAgttacaagacactcccagat	5	13	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:55612632A>G	ENST00000294383.6	-	19	2219	c.2220T>C	c.(2218-2220)acT>acC	p.T740T	USP24_ENST00000407756.1_Silent_p.T580T	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	740					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.T657T(1)		breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CATCCTGGCCAGTTACAAGAC	0.388																																																1	Substitution - coding silent(1)	ovary(1)	1											115	110	112					1																	55612632		1862	4105	5967	55385220	SO:0001819	synonymous_variant	23358			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2220T>C	1.37:g.55612632A>G			55385220	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																				0.388	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55612632	A	G	55612632	2	3	113	1	0	0	0	0	0	0	0	1	17095	175	7	4		4	USP24	1	55612632	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	9123149	55612632	193637989	5	30406										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66834501	66834501	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catggtacactgtgcagaccTgagcaaccccaccaagtcct	8	15	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:66834501T>A	ENST00000329654.4	+	16	1881	c.1694T>A	c.(1693-1695)cTg>cAg	p.L565Q	PDE4B_ENST00000480109.2_Missense_Mutation_p.L332Q|PDE4B_ENST00000423207.2_Missense_Mutation_p.L550Q|PDE4B_ENST00000371049.3_Missense_Mutation_p.L565Q|PDE4B_ENST00000371045.5_Missense_Mutation_p.L393Q	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	565					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	TGTGCAGACCTGAGCAACCCC	0.473																																																0			1											108	100	103					1																	66834501		2203	4300	6503	66607089	SO:0001583	missense	5142			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.1694T>A	1.37:g.66834501T>A	ENSP00000332116:p.Leu565Gln		66607089	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	37	CCDS632.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979798	0.74360	.	.	ENSG00000184588	ENST00000329654;ENST00000341517;ENST00000371049;ENST00000423207;ENST00000371045;ENST00000480109	D;D;D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15;-2.15;-2.15	4.44	4.44	0.53790	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.64402	D	0.000001	D	0.94801	0.8321	H	0.96269	3.795	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	D	0.96175	0.9126	10	0.87932	D	0	.	13.8025	0.63208	0.0:0.0:0.0:1.0	.	332;550;435;555;565	A5YW33;Q07343-3;Q13945;Q59GM8;Q07343	.;.;.;.;PDE4B_HUMAN	Q	565;565;565;550;393;332	ENSP00000332116:L565Q;ENSP00000342637:L565Q;ENSP00000360088:L565Q;ENSP00000392947:L550Q;ENSP00000360084:L393Q;ENSP00000432592:L332Q	ENSP00000332116:L565Q	L	+	2	0	PDE4B	66607089	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.776000	0.85560	1.984000	0.57885	0.460000	0.39030	CTG		0.473	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		A	66834501	T	A	66834501	3	1	113	1	0	0	0	0	1	0	0	0	11671	1580	55	5	2110	5	PDE4B	1	66834501	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	11221869	66834501	182416120	6	30407										
GTF2B	2959	hgsc.bcm.edu	37	chr1	89325834	89325834	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agaacttacaactatatttcGaggtagattgattctgtctg	8	6	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:89325834G>T	ENST00000370500.5	-	4	512	c.394C>A	c.(394-396)Cga>Aga	p.R132R	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	132			R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		ACTATATTTCGAGGTAGATTG	0.363																																																0			1											148	135	140					1																	89325834		2203	4300	6503	89098422	SO:0001819	synonymous_variant	2959			M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.394C>A	1.37:g.89325834G>T			89098422	A8K1A7|Q5JS30	Silent	SNP	ENST00000370500.5	37	CCDS715.1																																																																																				0.363	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		T	89325834	G	T	89325834	2	4	113	1	0	0	0	0	0	0	0	1	6876	1066	37	2		2	GTF2B	1	89325834	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	22491333	89325834	159924787	7	30408										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91406753	91406753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttggcttatgaactccgctcTctttgtctgagataaaattg	8	8	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:91406753T>C	ENST00000370440.1	-	3	375	c.158A>G	c.(157-159)gAg>gGg	p.E53G	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.E53G|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000467231.1_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	53			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		AACTCCGCTCTCTTTGTCTGA	0.373																																																0			1											156	159	158					1																	91406753		2203	4300	6503	91179341	SO:0001583	missense	84146			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.158A>G	1.37:g.91406753T>C	ENSP00000359469:p.Glu53Gly		91179341	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	12.08	1.829797	0.32329	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000541557	T;T	0.00603	6.28;6.28	5.9	5.9	0.94986	.	0.160556	0.43919	D	0.000514	T	0.00300	0.0009	N	0.24115	0.695	0.34389	D	0.69401	B	0.23377	0.084	B	0.19148	0.024	T	0.63148	-0.6702	10	0.66056	D	0.02	-4.1234	16.3291	0.83001	0.0:0.0:0.0:1.0	.	53	Q9H582	ZN644_HUMAN	G	53	ENSP00000359469:E53G;ENSP00000337008:E53G	ENSP00000337008:E53G	E	-	2	0	ZNF644	91179341	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	4.130000	0.57964	2.257000	0.74773	0.528000	0.53228	GAG		0.373	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		C	91406753	T	C	91406753	3	2	113	1	0	0	0	0	1	0	0	0	18099	1551	54	4	3841	4	ZNF644	1	91406753	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2080919	91406753	157843868	8	30409										
EVI5	7813	hgsc.bcm.edu	37	chr1	93070951	93070951	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agcctcacagccatcacttcTtccttattctagtgtggtaa	6	12	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:93070951T>C	ENST00000370331.1	-	16	1944	c.1935A>G	c.(1933-1935)gaA>gaG	p.E645E	EVI5_ENST00000543509.1_Silent_p.E656E|EVI5_ENST00000540033.1_Silent_p.E645E|EVI5_ENST00000491940.1_5'UTR	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	645	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		CCATCACTTCTTCCTTATTCT	0.403																																																0			1											115	110	112					1																	93070951		2203	4300	6503	92843539	SO:0001819	synonymous_variant	7813			AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1935A>G	1.37:g.93070951T>C			92843539	A6NKX8|B9A6J0|Q9H1Y9	Silent	SNP	ENST00000370331.1	37	CCDS30774.1																																																																																				0.403	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		C	93070951	T	C	93070951	2	2	113	1	0	0	0	0	0	0	0	1	5302	1606	56	4		4	EVI5	1	93070951	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1664198	93070951	156179670	9	30410										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93680445	93680445	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gatttgaaggttaacatggcTcacagaactagtcagtttca	9	7	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:93680445T>C	ENST00000343253.7	+	12	2140	c.1638T>C	c.(1636-1638)gcT>gcC	p.A546A	CCDC18_ENST00000401026.3_Silent_p.A547A|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000557479.1_Silent_p.A665A|CCDC18_ENST00000338949.4_Silent_p.A346A			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	546										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TTAACATGGCTCACAGAACTA	0.388																																																0			1											50	48	48					1																	93680445		1842	4098	5940	93453033	SO:0001819	synonymous_variant	343099					1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1638T>C	1.37:g.93680445T>C			93453033	Q6ZU17	Silent	SNP	ENST00000343253.7	37		.	.	.	.	.	.	.	.	.	.	T	10.58	1.391220	0.25118	.	.	ENSG00000122483	ENST00000370276	.	.	.	5.16	-3.14	0.05250	.	.	.	.	.	T	0.32466	0.0830	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39143	-0.9628	4	.	.	.	.	6.1446	0.20278	0.2055:0.2453:0.0:0.5491	.	.	.	.	P	600	.	.	L	+	2	0	CCDC18	93453033	0.673000	0.27539	0.990000	0.47175	0.999000	0.98932	-0.434000	0.06939	-0.480000	0.06803	0.533000	0.62120	CTC		0.388	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		C	93680445	T	C	93680445	2	2	113	1	0	0	0	0	0	0	0	1	2800	1538	54	4		4	CCDC18	1	93680445	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	609494	93680445	155570176	10	30411										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94645386	94645386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcggtttatttctatacacAtatttggccattttttgtct	5	7	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:94645386A>G	ENST00000260526.6	-	20	2557	c.2375T>C	c.(2374-2376)aTg>aCg	p.M792T	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	792	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TTCTATACACATATTTGGCCA	0.308																																																0			1											154	150	152					1																	94645386		2203	4295	6498	94417974	SO:0001583	missense	9411				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.2375T>C	1.37:g.94645386A>G	ENSP00000260526:p.Met792Thr		94417974	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	A	3.019	-0.202144	0.06219	.	.	ENSG00000137962	ENST00000260526	T	0.19669	2.13	5.8	-1.35	0.09114	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.873453	0.09480	N	0.796497	T	0.01320	0.0043	N	0.01168	-0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48281	-0.9049	10	0.07813	T	0.8	0.0157	6.1709	0.20416	0.5417:0.0:0.338:0.1203	.	792;792	F8VWZ8;Q52LW3	.;RHG29_HUMAN	T	792	ENSP00000260526:M792T	ENSP00000260526:M792T	M	-	2	0	ARHGAP29	94417974	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.803000	0.27083	-0.019000	0.14055	0.528000	0.53228	ATG		0.308	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94645386	A	G	94645386	3	3	113	1	0	0	0	0	1	0	0	0	878	217	8	4	1426	4	ARHGAP29	1	94645386	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	964941	94645386	154605235	11	30412										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256539	115256539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtactcttcttgtccagctgTatccagtatgtccaacaaac	6	12	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:115256539T>C	ENST00000369535.4	-	3	425	c.172A>G	c.(172-174)Aca>Gca	p.T58A		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	58					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		TGTCCAGCTGTATCCAGTATG	0.478		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	0			1											178	156	163					1																	115256539		2203	4300	6503	115058062	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.172A>G	1.37:g.115256539T>C	ENSP00000358548:p.Thr58Ala		115058062	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.823958	0.90873	.	.	ENSG00000213281	ENST00000369535	D	0.87491	-2.26	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	D	0.94476	0.8222	H	0.94620	3.56	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.95798	0.8830	10	0.72032	D	0.01	.	15.0132	0.71565	0.0:0.0:0.0:1.0	.	58	P01111	RASN_HUMAN	A	58	ENSP00000358548:T58A	ENSP00000358548:T58A	T	-	1	0	NRAS	115058062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	ACA		0.478	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		C	115256539	T	C	115256539	3	2	113	1	0	0	0	0	1	0	0	0	10671	1638	57	4	409	4	NRAS	1	115256539	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	20611153	115256539	133994082	12	30413										
NRAS	4893	hgsc.bcm.edu	37	chr1	115258728	115258728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggattagctggattgtcagTgcgcttttcccaacaccacc	9	12	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:115258728T>C	ENST00000369535.4	-	2	307	c.54A>G	c.(52-54)gcA>gcG	p.A18A	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	18					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		GGATTGTCAGTGCGCTTTTCC	0.493		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	0			1											214	188	197					1																	115258728		2203	4300	6503	115060251	SO:0001819	synonymous_variant	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.54A>G	1.37:g.115258728T>C			115060251	Q14971|Q15104|Q15282	Silent	SNP	ENST00000369535.4	37	CCDS877.1																																																																																				0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		C	115258728	T	C	115258728	2	2	113	1	0	0	0	0	0	0	0	1	10671	1683	59	4		4	NRAS	1	115258728	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2189	115258728	133991893	13	30414										
FLG	2312	hgsc.bcm.edu	37	chr1	152282661	152282661	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagtgtctagagctgccggcCcgagtggaaggttcatggtg	17	8	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:152282661C>A	ENST00000368799.1	-	3	4736	c.4701G>T	c.(4699-4701)cgG>cgT	p.R1567R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1567	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTGCCGGCCCGAGTGGAAG	0.582									Ichthyosis																																							0			1											188	198	195					1																	152282661		2203	4300	6503	150549285	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4701G>T	1.37:g.152282661C>A			150549285	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152282661	C	A	152282661	2	1	113	1	0	0	0	0	0	0	0	1	5941	610	22	2		2	FLG	1	152282661	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	37023933	152282661	96967960	14	30415										
HSD17B7	51478	hgsc.bcm.edu	37	chr1	162773313	162773313	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atatggacgctgttgatgccGgcaatattgctagtaagtga	12	6	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:162773313G>A	ENST00000254521.3	+	6	790	c.735G>A	c.(733-735)ccG>ccA	p.P245P	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Intron	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	245					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)	p.P245P(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					TGTTGATGCCGGCAATATTGC	0.388																																																1	Substitution - coding silent(1)	ovary(1)	1											122	107	112					1																	162773313		2203	4300	6503	161039937	SO:0001819	synonymous_variant	158160			AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5215	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 37C, member 1"	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.735G>A	1.37:g.162773313G>A			161039937	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	37	CCDS1242.1																																																																																				0.388	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371		A	162773313	G	A	162773313	2	1	113	1	0	0	0	0	0	0	0	1	7409	1103	39	1		1	HSD17B7	1	162773313	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	10490652	162773313	86477308	15	30416										
NME7	29922	hgsc.bcm.edu	37	chr1	169267823	169267823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agaagcaaaagaatcagggcCatgcgctgcatttcttatgc	10	9	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:169267823C>T	ENST00000367811.3	-	6	875	c.619G>A	c.(619-621)Ggc>Agc	p.G207S	NME7_ENST00000472647.1_Missense_Mutation_p.G171S|NME7_ENST00000469474.1_5'UTR	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	207					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					GAATCAGGGCCATGCGCTGCA	0.418																																																0			1											99	104	102					1																	169267823		2203	4300	6503	167534447	SO:0001583	missense	29922			AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.619G>A	1.37:g.169267823C>T	ENSP00000356785:p.Gly207Ser		167534447	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Missense_Mutation	SNP	ENST00000367811.3	37	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	C	32	5.142795	0.94560	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	T;T	0.58940	0.3;0.3	5.74	5.74	0.90152	.	0.046015	0.85682	D	0.000000	T	0.75989	0.3925	M	0.90369	3.11	0.48452	D	0.999659	P;P	0.46142	0.873;0.616	P;P	0.58577	0.841;0.83	T	0.78130	-0.2324	9	0.52906	T	0.07	-12.2602	19.5303	0.95226	0.0:1.0:0.0:0.0	.	211;207	Q59GR0;Q9Y5B8	.;NDK7_HUMAN	S	171;207	ENSP00000433341:G171S;ENSP00000356785:G207S	ENSP00000356785:G207S	G	-	1	0	NME7	167534447	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	6.670000	0.74467	2.703000	0.92315	0.643000	0.83706	GGC		0.418	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		T	169267823	C	T	169267823	3	4	113	1	0	0	0	0	1	0	0	0	10527	594	21	3	539	3	NME7	1	169267823	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	6494510	169267823	79982798	16	30417										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176668548	176668548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggatgggaaggtgtcgggggTgaaagtctacacctttgatg	17	5	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:176668548T>C	ENST00000367662.3	+	8	4223	c.3059T>C	c.(3058-3060)gTg>gCg	p.V1020A		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1020					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GTGTCGGGGGTGAAAGTCTAC	0.537																																																0			1											139	145	143					1																	176668548		2108	4239	6347	174935171	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.3059T>C	1.37:g.176668548T>C	ENSP00000356634:p.Val1020Ala		174935171	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316417	0.40996	.	.	ENSG00000116183	ENST00000367662	T	0.47869	0.83	5.38	1.81	0.25067	Fibronectin, type III (2);	0.320145	0.33875	N	0.004479	T	0.36358	0.0964	L	0.46157	1.445	0.80722	D	1	B	0.21309	0.054	B	0.24394	0.053	T	0.10132	-1.0643	10	0.41790	T	0.15	-7.2083	6.0406	0.19732	0.0:0.1478:0.1381:0.714	.	1020	Q9BXP8	PAPP2_HUMAN	A	1020	ENSP00000356634:V1020A	ENSP00000356634:V1020A	V	+	2	0	PAPPA2	174935171	1.000000	0.71417	0.970000	0.41538	0.723000	0.41478	3.626000	0.54245	0.143000	0.18926	0.533000	0.62120	GTG		0.537	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176668548	T	C	176668548	3	2	113	1	0	0	0	0	1	0	0	0	11464	1696	59	4	3138	4	PAPPA2	1	176668548	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	7400725	176668548	72582073	17	30418										
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179887078	179887078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	accgctttgagtcatttcccGcaggctctactttgatcttc	7	13	3	2	rs138345857		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:179887078G>A	ENST00000606911.2	+	10	1647	c.1456G>A	c.(1456-1458)Gca>Aca	p.A486T	TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.A365T|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.A502T|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.A487T			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	486	Interaction with TOR1A.				positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						GTCATTTCCCGCAGGCTCTAC	0.443													G|||	1	0.000199681	8e-04	0	5008	,	,		20120	0		0	False		,,,				2504	0															0			1						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	88	92	91		1456	4.1	0.1	1	dbSNP_134	91	1,8599		0,1,4299	no	missense	TOR1AIP1	NM_015602.2	58	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	486/584	179887078	2,13004	2203	4300	6503	178153701	SO:0001583	missense	26092				CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"lamina associated polypeptide 1B"	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1456G>A	1.37:g.179887078G>A	ENSP00000476687:p.Ala486Thr		178153701	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.32|19.32	3.805398|3.805398	0.70682|0.70682	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000143337|ENSG00000143337	ENST00000325993|ENST00000271583;ENST00000435319	.|T;T	.|0.35789	.|1.29;1.29	5.96|5.96	4.09|4.09	0.47781|0.47781	.|.	.|0.107189	.|0.64402	.|D	.|0.000004	.|T	.|0.57932	.|0.2087	M|M	0.78049|0.78049	2.395|2.395	0.37695|0.37695	D|D	0.923987|0.923987	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	.|T	.|0.63444	.|-0.6636	.|9	.|.	.|.	.|.	.|-18.6137	10.2687|10.2687	0.43470|0.43470	0.0677:0.2546:0.6776:0.0|0.0677:0.2546:0.6776:0.0	.|.	.|486	.|Q5JTV8	.|TOIP1_HUMAN	.|T	-1|502;486	.|ENSP00000271583:A502T;ENSP00000393292:A486T	.|.	.|A	+|+	.|1	.|0	TOR1AIP1|TOR1AIP1	178153701|178153701	1.000000|1.000000	0.71417|0.71417	0.120000|0.120000	0.21714|0.21714	0.840000|0.840000	0.47671|0.47671	6.660000|6.660000	0.74417|0.74417	0.854000|0.854000	0.35336|0.35336	-0.150000|-0.150000	0.13652|0.13652	.|GCA		0.443	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		A	179887078	G	A	179887078	3	1	113	1	0	0	0	0	1	0	0	0	16412	1087	38	1	1494	1	TOR1AIP1	1	179887078	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	3218530	179887078	69363543	18	30419										
PRG4	10216	hgsc.bcm.edu	37	chr1	186276728	186276728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cacccccaagaagctcacgcCcaccacccccgagaagctcg	7	21	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:186276728C>T	ENST00000445192.2	+	7	1922	c.1877C>T	c.(1876-1878)cCc>cTc	p.P626L	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.P533L|PRG4_ENST00000367486.3_Missense_Mutation_p.P583L|PRG4_ENST00000367483.4_Missense_Mutation_p.P585L	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	626	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AAGCTCACGCCCACCACCCCC	0.677																																																0			1											43	42	43					1																	186276728		2203	4294	6497	184543351	SO:0001583	missense	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1877C>T	1.37:g.186276728C>T	ENSP00000399679:p.Pro626Leu		184543351	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	C	7.471	0.646746	0.14516	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.09350	2.99;3.07;3.02;3.12	3.23	1.28	0.21552	.	0.000000	0.38058	U	0.001835	T	0.08313	0.0207	L	0.34521	1.04	0.25633	N	0.986286	P;P;P;P	0.42908	0.793;0.793;0.689;0.793	B;B;B;B	0.42163	0.378;0.378;0.21;0.378	T	0.24154	-1.0168	9	.	.	.	.	7.3579	0.26729	0.0:0.7627:0.0:0.2373	.	492;533;626;585	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	L	583;492;585;533;626	ENSP00000356456:P583L;ENSP00000356453:P585L;ENSP00000356455:P533L;ENSP00000399679:P626L	.	P	+	2	0	PRG4	184543351	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.611000	0.24268	0.059000	0.16252	-0.480000	0.04831	CCC		0.677	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		T	186276728	C	T	186276728	3	4	113	1	0	0	0	0	1	0	0	0	12515	623	22	3	1899	3	PRG4	1	186276728	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	6389650	186276728	62973893	19	30420										
NR5A2	2494	hgsc.bcm.edu	37	chr1	200012984	200012984	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtggagataaagtgtctggGtaccattatgggctcctcac	12	8	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:200012984G>A	ENST00000367362.3	+	3	531	c.285G>A	c.(283-285)ggG>ggA	p.G95G	NR5A2_ENST00000236914.3_Silent_p.G49G|NR5A2_ENST00000544748.1_Silent_p.G23G	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	95					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AAGTGTCTGGGTACCATTATG	0.398																																					Melanoma(179;1138 2773 15678 26136)											0			1											108	100	103					1																	200012984		2203	4300	6503	198279607	SO:0001819	synonymous_variant	2494			U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"Nuclear hormone receptors"	7984	protein-coding gene	gene with protein product	"liver receptor homolog-1"	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.285G>A	1.37:g.200012984G>A			198279607	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1	.	.	.	.	.	.	.	.	.	.	G	9.987	1.229863	0.22542	.	.	ENSG00000116833	ENST00000367357	D	0.98701	-5.08	5.91	0.552	0.17230	.	0.000000	0.85682	D	0.000000	D	0.97291	0.9114	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.93356	0.6722	6	.	.	.	.	6.1296	0.20197	0.2639:0.3482:0.3879:0.0	.	.	.	.	D	16	ENSP00000356326:G16D	.	G	+	2	0	NR5A2	198279607	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	0.899000	0.28417	-0.136000	0.11475	-0.172000	0.13284	GGT		0.398	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			A	200012984	G	A	200012984	2	1	113	1	0	0	0	0	0	0	0	1	10667	1248	44	3		3	NR5A2	1	200012984	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	13736256	200012984	49237637	20	30421										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212538603	212538603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcttcttttaaggtatctcTttctaattttgatcatccat	3	9	5	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:212538603T>C	ENST00000261455.4	-	8	1144	c.1007A>G	c.(1006-1008)aAg>aGg	p.K336R	TMEM206_ENST00000535273.1_Missense_Mutation_p.K397R	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	336			K -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		AAGGTATCTCTTTCTAATTTT	0.428																																																0			1											222	213	216					1																	212538603		2203	4300	6503	210605226	SO:0001583	missense	55248			AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.1007A>G	1.37:g.212538603T>C	ENSP00000261455:p.Lys336Arg		210605226	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.090053	0.36855	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.91	1.08	0.20341	.	0.175979	0.64402	N	0.000010	T	0.35248	0.0925	N	0.20986	0.625	0.35576	D	0.805866	B;B	0.14805	0.011;0.0	B;B	0.16722	0.016;0.004	T	0.22836	-1.0205	9	0.33940	T	0.23	-27.1738	10.6969	0.45905	0.0:0.3769:0.0:0.6231	.	397;336	B7Z4D6;Q9H813	.;TM206_HUMAN	R	336;397	.	ENSP00000261455:K336R	K	-	2	0	TMEM206	210605226	1.000000	0.71417	0.023000	0.16930	0.994000	0.84299	1.695000	0.37763	-0.054000	0.13266	0.528000	0.53228	AAG		0.428	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		C	212538603	T	C	212538603	3	2	113	1	0	0	0	0	1	0	0	0	16170	1609	56	4	49	4	TMEM206	1	212538603	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	12525619	212538603	36712018	21	30422										
USH2A	7399	hgsc.bcm.edu	37	chr1	216256828	216256828	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcaggtccatctttgttataAacgaaaagaagcaatccatt	6	8	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:216256828A>G	ENST00000307340.3	-	26	5654	c.5268T>C	c.(5266-5268)gtT>gtC	p.V1756V	RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Silent_p.V1756V|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1756	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTTGTTATAAACGAAAAGAA	0.303										HNSCC(13;0.011)																																						0			1											96	100	98					1																	216256828		2202	4299	6501	214323451	SO:0001819	synonymous_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5268T>C	1.37:g.216256828A>G			214323451	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.303	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216256828	A	G	216256828	2	3	113	1	0	0	0	0	0	0	0	1	17076	1	1	4		4	USH2A	1	216256828	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	3718225	216256828	32993793	22	30423										
ACTN2	88	hgsc.bcm.edu	37	chr1	236918421	236918421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcaactataagaacaacatcGacaagctggagggagaccat	9	9	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr1:236918421G>A	ENST00000366578.4	+	17	2243	c.2077G>A	c.(2077-2079)Gac>Aac	p.D693N	ACTN2_ENST00000542672.1_Missense_Mutation_p.D693N|ACTN2_ENST00000546208.1_Missense_Mutation_p.D187N	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	693					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)	p.D693N(1)		endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	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)			GAACAACATCGACAAGCTGGA	0.527																																																1	Substitution - Missense(1)	ovary(1)	1											201	192	195					1																	236918421		2203	4300	6503	234985044	SO:0001583	missense	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2077G>A	1.37:g.236918421G>A	ENSP00000355537:p.Asp693Asn		234985044	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.574577	0.65878	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000546208;ENST00000545611	T;T;T	0.51574	0.7;0.7;0.7	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.62429	0.2427	L	0.47716	1.5	0.80722	D	1	D;B;D;D	0.76494	0.999;0.028;0.999;0.995	D;B;D;D	0.87578	0.998;0.057;0.998;0.987	T	0.61168	-0.7117	10	0.36615	T	0.2	.	17.4718	0.87648	0.0:0.0:1.0:0.0	.	478;693;463;693	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	N	693;693;187;462	ENSP00000443495:D693N;ENSP00000355537:D693N;ENSP00000438384:D187N	ENSP00000355537:D693N	D	+	1	0	ACTN2	234985044	1.000000	0.71417	0.986000	0.45419	0.968000	0.65278	9.835000	0.99442	2.100000	0.63781	0.557000	0.71058	GAC		0.527	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236918421	G	A	236918421	3	1	113	1	0	0	0	0	1	0	0	0	205	1058	37	1	2143	1	ACTN2	1	236918421	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	20661593	236918421	12332200	23	30424										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11355647	11355647	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	accacaaaccatcattttccAaatttcgttttttgtctgct							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:11355647delA	ENST00000315872.6	-	14	2034	c.1586delT	c.(1585-1587)ttgfs	p.L529fs	ROCK2_ENST00000401753.1_Frame_Shift_Del_p.L286fs	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	529	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		ATCATTTTCCAAATTTCGTTT	0.343																																																0			2											115	112	113					2																	11355647		1817	4087	5904	11273098	SO:0001589	frameshift_variant	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1586delT	2.37:g.11355647delA	ENSP00000317985:p.Leu529fs		11273098	Q53QZ0|Q53SJ7|Q9UQN5	Frame_Shift_Del	DEL	ENST00000315872.6	37	CCDS42654.1																																																																																				0.343	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			-	11355647	A	-	11355647	7	5	113	1	0	1	0	1	0	0	0	0	13555	131	5	0	2660	0	ROCK2	2	11355647	Frame_Shift_Del	DEL	A	TCGA-EI-6510-01A-11D-1733-10		11355647	231843726	24	30425										
GREB1	9687	hgsc.bcm.edu	37	chr2	11777956	11777956	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggagaagttcctgcagcacCacagccacctcttcttcccg	8	16	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:11777956C>A	ENST00000381486.2	+	31	5761	c.5461C>A	c.(5461-5463)Cac>Aac	p.H1821N	GREB1_ENST00000234142.5_Missense_Mutation_p.H1821N|GREB1_ENST00000396123.1_Missense_Mutation_p.H819N	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1821						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCTGCAGCACCACAGCCACCT	0.617																																					Ovarian(39;850 945 2785 23371 33093)											0			2											74	81	79					2																	11777956		2151	4258	6409	11695407	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5461C>A	2.37:g.11777956C>A	ENSP00000370896:p.His1821Asn		11695407	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351241	0.24512	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.47177	0.85;0.85;0.85	4.75	4.75	0.60458	.	0.109140	0.64402	D	0.000008	T	0.42268	0.1195	L	0.43152	1.355	0.37995	D	0.934045	B	0.13145	0.007	B	0.16722	0.016	T	0.37934	-0.9684	10	0.21014	T	0.42	-28.2448	17.7654	0.88476	0.0:1.0:0.0:0.0	.	1821	Q4ZG55	GREB1_HUMAN	N	1821;1821;819	ENSP00000370896:H1821N;ENSP00000234142:H1821N;ENSP00000379429:H819N	ENSP00000234142:H1821N	H	+	1	0	GREB1	11695407	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.169000	0.42434	2.186000	0.69663	0.557000	0.71058	CAC		0.617	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11777956	C	A	11777956	3	1	113	1	0	0	0	0	1	0	0	0	6781	594	21	2	5687	2	GREB1	2	11777956	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	422309	11777956	231421417	25	30426										
MYCN	4613	hgsc.bcm.edu	37	chr2	16085898	16085898	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agcgaggcgtccccacgtccGctcaagagtgtcatcccccc	10	18	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:16085898G>A	ENST00000281043.3	+	3	1371	c.1074G>A	c.(1072-1074)ccG>ccA	p.P358P		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	358					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			CCCCACGTCCGCTCAAGAGTG	0.597			A		neuroblastoma																																		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	0			2											43	43	43					2																	16085898		2203	4300	6503	16003349	SO:0001819	synonymous_variant	4613			BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.1074G>A	2.37:g.16085898G>A			16003349	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	37	CCDS1687.1																																																																																				0.597	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		A	16085898	G	A	16085898	2	1	113	1	0	0	0	0	0	0	0	1	10051	1074	38	1		1	MYCN	2	16085898	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4307942	16085898	227113475	26	30427										
APOB	338	hgsc.bcm.edu	37	chr2	21231334	21231334	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgaaaatcaaaattgagaacTtctaatttggactctccttt	5	7	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:21231334T>C	ENST00000233242.1	-	26	8533	c.8406A>G	c.(8404-8406)gaA>gaG	p.E2802E		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2802					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATTGAGAACTTCTAATTTGG	0.438																																																0			2											104	106	105					2																	21231334		2203	4300	6503	21084839	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8406A>G	2.37:g.21231334T>C			21084839	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21231334	T	C	21231334	2	2	113	1	0	0	0	0	0	0	0	1	785	1606	56	4		4	APOB	2	21231334	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	5145436	21231334	221968039	27	30428										
APOB	338	hgsc.bcm.edu	37	chr2	21235160	21235160	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttatctggttggtgccttggAggtaggaggagttaaacctc	14	6	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:21235160A>G	ENST00000233242.1	-	26	4707	c.4580T>C	c.(4579-4581)cTc>cCc	p.L1527P		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1527					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.L1527H(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTGCCTTGGAGGTAGGAGGA	0.488																																																1	Substitution - Missense(1)	ovary(1)	2											121	123	123					2																	21235160		2203	4300	6503	21088665	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4580T>C	2.37:g.21235160A>G	ENSP00000233242:p.Leu1527Pro		21088665	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286495	0.80803	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01076	5.37	5.88	5.88	0.94601	.	1.077840	0.07220	N	0.860701	T	0.01661	0.0053	L	0.29908	0.895	0.80722	D	1	B	0.34372	0.451	B	0.26517	0.07	T	0.65751	-0.6092	10	0.87932	D	0	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	1527	P04114	APOB_HUMAN	P	1527	ENSP00000233242:L1527P	ENSP00000233242:L1527P	L	-	2	0	APOB	21088665	1.000000	0.71417	0.908000	0.35775	0.994000	0.84299	8.842000	0.92136	2.246000	0.74042	0.533000	0.62120	CTC		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21235160	A	G	21235160	3	3	113	1	0	0	0	0	1	0	0	0	785	304	11	4	9127	4	APOB	2	21235160	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	3826	21235160	221964213	28	30429										
PLB1	151056	hgsc.bcm.edu	37	chr2	28821613	28821613	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcctcaatcaagctgttccCggagcaaaggctgagtatgg	11	10	2	1	rs35746006	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:28821613C>T	ENST00000327757.5	+	35	2504	c.2460C>T	c.(2458-2460)ccC>ccT	p.P820P	PLB1_ENST00000422425.2_Silent_p.P809P	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	820	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					AAGCTGTTCCCGGAGCAAAGG	0.537													C|||	187	0.0373403	0.0061	0.062	5008	,	,		23140	0		0.1034	False		,,,				2504	0.0327															0			2						C	,	90,4316	74.1+/-112.3	1,88,2114	126	117	120		2427,2460	-3	1	2	dbSNP_126	120	912,7688	203.4+/-246.4	44,824,3432	no	coding-synonymous,coding-synonymous	PLB1	NM_001170585.1,NM_153021.4	,	45,912,5546	TT,TC,CC		10.6047,2.0427,7.7041	,	809/1448,820/1459	28821613	1002,12004	2203	4300	6503	28675117	SO:0001819	synonymous_variant	151056				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.2460C>T	2.37:g.28821613C>T			28675117	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	125	0.05723443223443223	7	0.014227642276422764	32	0.08839779005524862	0	0.0	86	0.11345646437994723	C	6.397	0.441408	0.12164	0.020427	0.106047	ENSG00000163803	ENST00000404858	T	0.23147	1.92	5.84	-3.04	0.05412	.	0.176611	0.40908	D	0.000982	T	0.00328	0.0010	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.07501	-1.0769	6	0.54805	T	0.06	-7.3789	1.0688	0.01616	0.1433:0.2178:0.1962:0.4428	rs35746006;rs61745135	.	.	.	L	808	ENSP00000384187:P808L	ENSP00000384187:P808L	P	+	2	0	PLB1	28675117	0.014000	0.17966	0.980000	0.43619	0.589000	0.36550	-1.888000	0.01616	-0.131000	0.11578	-1.434000	0.01081	CCG		0.537	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			T	28821613	C	T	28821613	2	4	113	1	0	0	0	0	0	0	0	1	12055	639	23	1		1	PLB1	2	28821613	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	7586453	28821613	214377760	29	30430										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48873704	48873704	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cagcttggccagccttcagtAatacaaactagtgttccaca	7	12	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:48873704A>G	ENST00000403751.3	+	6	538	c.501A>G	c.(499-501)gtA>gtG	p.V167V	STON1-GTF2A1L_ENST00000309827.2_Silent_p.V871V|LHCGR_ENST00000420913.3_5'UTR|STON1-GTF2A1L_ENST00000394754.1_Silent_p.V871V|STON1-GTF2A1L_ENST00000394751.3_Silent_p.V824V|GTF2A1L_ENST00000430487.2_Silent_p.V133V|STON1-GTF2A1L_ENST00000402114.2_Silent_p.V871V|STON1-GTF2A1L_ENST00000405008.1_Silent_p.V871V	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	167					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.V871V(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCCTTCAGTAATACAAACTA	0.413																																																1	Substitution - coding silent(1)	ovary(1)	2											99	98	98					2																	48873704		2203	4300	6503	48727208	SO:0001819	synonymous_variant	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.501A>G	2.37:g.48873704A>G			48727208	B4DY14|Q53FD9|Q5D050	Silent	SNP	ENST00000403751.3	37	CCDS46281.1																																																																																				0.413	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		G	48873704	A	G	48873704	2	3	113	1	0	0	0	0	0	0	0	1	6874	349	13	4		4	GTF2A1L	2	48873704	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	20052091	48873704	194325669	30	30431										
USP34	9736	hgsc.bcm.edu	37	chr2	61577702	61577702	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atcatgttttgaatgtattaCctgttcagtatgaacacttg	7	6	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:61577702C>T	ENST00000398571.2	-	11	1454		c.e11+1			NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34						positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GAATGTATTACCTGTTCAGTA	0.338																																																0			2											95	88	90					2																	61577702		1833	4080	5913	61431206	SO:0001630	splice_region_variant	9736			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.1377+1G>A	2.37:g.61577702C>T			61431206	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Splice_Site	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118166	0.94385	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9697	0.97280	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP34	61431206	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.818000	0.86416	2.807000	0.96579	0.591000	0.81541	.		0.338	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		Intron	T	61577702	C	T	61577702	5	4	113	1	0	0	0	0	0	0	1	0	17105	521	18	3	9542	3	USP34	2	61577702	Splice_Site	SNP	C	TCGA-EI-6510-01A-11D-1733-10	12703998	61577702	181621671	31	30432										
CCT4	10575	hgsc.bcm.edu	37	chr2	62099331	62099331	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gctagtgtagatggaatgacCtccatagcatctgcaaaagc	10	9	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:62099331C>T	ENST00000394440.3	-	12	1673	c.1377G>A	c.(1375-1377)gaG>gaA	p.E459E	CCT4_ENST00000544185.1_Silent_p.E309E|CCT4_ENST00000544079.1_Silent_p.E429E|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000461540.2_Intron|CCT4_ENST00000538252.1_Silent_p.E403E	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	459					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.E459D(1)		breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	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)			ATGGAATGACCTCCATAGCAT	0.463																																																1	Substitution - Missense(1)	ovary(1)	2											108	101	103					2																	62099331		2203	4300	6503	61952835	SO:0001819	synonymous_variant	10575				CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.1377G>A	2.37:g.62099331C>T			61952835	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Silent	SNP	ENST00000394440.3	37	CCDS33206.1																																																																																				0.463	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			T	62099331	C	T	62099331	2	4	113	1	0	0	0	0	0	0	0	1	2961	680	24	3		3	CCT4	2	62099331	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	521629	62099331	181100042	32	30433										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125521565	125521565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catttgcaggacgcttctggAacgccgtctcattttataca	8	11	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:125521565A>G	ENST00000431078.1	+	16	2735	c.2371A>G	c.(2371-2373)Aac>Gac	p.N791D		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	791	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		ACGCTTCTGGAACGCCGTCTC	0.423																																																0			2											123	117	119					2																	125521565		1883	4094	5977	125238035	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2371A>G	2.37:g.125521565A>G	ENSP00000399013:p.Asn791Asp		125238035	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.939680	0.92526	.	.	ENSG00000155052	ENST00000431078	T	0.44881	0.91	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.000000	0.53938	D	0.000049	T	0.62282	0.2415	M	0.73372	2.23	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.59172	-0.7504	10	0.26408	T	0.33	.	15.5035	0.75719	1.0:0.0:0.0:0.0	.	791	Q8WYK1	CNTP5_HUMAN	D	791	ENSP00000399013:N791D	ENSP00000399013:N791D	N	+	1	0	CNTNAP5	125238035	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.205000	0.95048	2.263000	0.75096	0.533000	0.62120	AAC		0.423	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125521565	A	G	125521565	3	3	113	1	0	0	0	0	1	0	0	0	3656	246	9	4	2433	4	CNTNAP5	2	125521565	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	63422234	125521565	117677808	33	30434										
YSK4	80122	hgsc.bcm.edu	37	chr2	135744386	135744386	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggagccgaacatatctcacGgtaatacgtgttttcatccc	8	11	2	0	rs148647253		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:135744386G>C	ENST00000375845.3	-	7	2086	c.2056C>G	c.(2056-2058)Cgt>Ggt	p.R686G	MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392915.1_Missense_Mutation_p.R703G|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.R573G|MAP3K19_ENST00000392918.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	686							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										CATATCTCACGGTAATACGTG	0.418																																																0			2											191	174	180					2																	135744386		2203	4300	6503	135460856	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2056C>G	2.37:g.135744386G>C	ENSP00000365005:p.Arg686Gly		135460856	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	G	3.989	-0.004861	0.07773	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.77750	-1.01;-0.98;1.35;-1.12	4.94	3.99	0.46301	.	0.918070	0.09061	N	0.854365	T	0.81049	0.4742	L	0.43923	1.385	0.21627	N	0.999618	P;D;P	0.58620	0.841;0.983;0.753	B;P;B	0.57548	0.401;0.823;0.226	T	0.69292	-0.5183	10	0.87932	D	0	.	10.6429	0.45602	0.0:0.0:0.6214:0.3786	.	573;703;686	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	G	686;573;703;76	ENSP00000365005:R686G;ENSP00000351140:R573G;ENSP00000376647:R703G;ENSP00000392827:R76G	ENSP00000351140:R573G	R	-	1	0	YSK4	135460856	0.134000	0.22483	0.079000	0.20413	0.039000	0.13416	1.413000	0.34725	2.557000	0.86248	0.561000	0.74099	CGT		0.418	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		C	135744386	G	C	135744386	3	2	113	1	0	0	0	0	1	0	0	0	17535	1116	39	5	1946	5	YSK4	2	135744386	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	10222821	135744386	107454987	34	30435										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289481	160289481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gctaactgctttttccttccCttgactatgcaggatgggag	10	10	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:160289481C>A	ENST00000392783.2	-	9	2182	c.1687G>T	c.(1687-1689)Ggg>Tgg	p.G563W	BAZ2B_ENST00000392782.1_Missense_Mutation_p.G561W|BAZ2B_ENST00000343439.5_Missense_Mutation_p.G561W|BAZ2B_ENST00000355831.2_Missense_Mutation_p.G563W	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G563R(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTTTCCTTCCCTTGACTATGC	0.448																																																1	Substitution - Missense(1)	ovary(1)	2											196	182	187					2																	160289481		1909	4126	6035	159997727	SO:0001583	missense	29994			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.1687G>T	2.37:g.160289481C>A	ENSP00000376534:p.Gly563Trp		159997727	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	13.30	2.196863	0.38806	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.92	5.92	0.95590	.	0.000000	0.37669	U	0.001981	T	0.71247	0.3317	L	0.51422	1.61	0.45390	D	0.998376	D;D;D;D;D	0.89917	1.0;0.997;0.993;0.993;0.988	D;D;P;P;P	0.87578	0.998;0.924;0.724;0.852;0.715	T	0.72265	-0.4344	10	0.87932	D	0	-8.9802	15.0866	0.72158	0.1417:0.8583:0.0:0.0	.	563;367;561;561;563	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	W	561;563;563;561;500	ENSP00000376533:G561W;ENSP00000376534:G563W;ENSP00000348087:G563W;ENSP00000339670:G561W	ENSP00000339670:G561W	G	-	1	0	BAZ2B	159997727	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.112000	0.50368	2.818000	0.97014	0.655000	0.94253	GGG		0.448	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160289481	C	A	160289481	3	1	113	1	0	0	0	0	1	0	0	0	1333	681	24	2	4935	2	BAZ2B	2	160289481	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	24545095	160289481	82909892	35	30436										
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170417202	170417202	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttgacctcagaagaatctatGgtgtcaaaaagaagttctgt	9	6	4	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:170417202G>A	ENST00000453153.2	-	5	1012	c.666C>T	c.(664-666)acC>acT	p.T222T	FASTKD1_ENST00000453929.2_Silent_p.T222T	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	222					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AAGAATCTATGGTGTCAAAAA	0.333																																																0			2											51	50	50					2																	170417202		2203	4298	6501	170125448	SO:0001819	synonymous_variant	79675			AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.666C>T	2.37:g.170417202G>A			170125448	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																				0.333	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170417202	G	A	170417202	2	1	113	1	0	0	0	0	0	0	0	1	5704	1335	47	3		3	FASTKD1	2	170417202	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	10127721	170417202	72782171	36	30437										
ZAK	51776	hgsc.bcm.edu	37	chr2	174055832	174055832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catgtccttggttggaacttTcccatggatggctccagaag	11	10	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:174055832T>C	ENST00000375213.3	+	7	587	c.509T>C	c.(508-510)tTc>tCc	p.F170S	MLTK_ENST00000431503.2_Missense_Mutation_p.F69S|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000480606.1_3'UTR|MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000338983.3_Missense_Mutation_p.F170S|MLTK_ENST00000409176.2_Missense_Mutation_p.F170S|MLTK_ENST00000539448.1_Missense_Mutation_p.F170S	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										GTTGGAACTTTCCCATGGATG	0.423																																																0			2											168	158	161					2																	174055832		2203	4300	6503	173764078	SO:0001583	missense	51776																														ENST00000375213.3:c.509T>C	2.37:g.174055832T>C	ENSP00000364361:p.Phe170Ser		173764078	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	T	33	5.214533	0.95104	.	.	ENSG00000091436	ENST00000539448;ENST00000409176;ENST00000338983;ENST00000431503;ENST00000375213	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.9	5.9	0.94986	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	N	0.13098	0.295	0.80722	D	1	D;P;D;D;D	0.76494	0.964;0.955;0.999;0.964;0.999	P;P;D;P;D	0.80764	0.761;0.648;0.98;0.761;0.994	D	0.86880	0.2041	10	0.59425	D	0.04	.	16.3318	0.83023	0.0:0.0:0.0:1.0	.	170;170;170;170;170	A8K710;Q9NYL2-2;Q9NYL2;D4Q8H0;Q9NYL2-3	.;.;MLTK_HUMAN;.;.	S	170;170;170;69;170	ENSP00000439414:F170S;ENSP00000387259:F170S;ENSP00000340257:F170S;ENSP00000399787:F69S;ENSP00000364361:F170S	ENSP00000340257:F170S	F	+	2	0	AC013461.1	173764078	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.966000	0.87956	2.248000	0.74166	0.460000	0.39030	TTC		0.423	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			C	174055832	T	C	174055832	3	2	113	1	0	0	0	0	1	0	0	0	17552	1783	62	4	531	4	ZAK	2	174055832	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	3638630	174055832	69143541	37	30438										
TTN	7273	hgsc.bcm.edu	37	chr2	179440587	179440587	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctgacgttcacaaagccactTttcttcccagccgggttttc	7	14	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179440587T>C	ENST00000591111.1	-	276	65573	c.65349A>G	c.(65347-65349)aaA>aaG	p.K21783K	TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.K20856K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.K14484K|TTN_ENST00000460472.2_Silent_p.K14359K|TTN_ENST00000589042.1_Silent_p.K23424K|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Silent_p.K14551K			Q8WZ42	TITIN_HUMAN	titin	21783	Ig-like 114.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAAGCCACTTTTCTTCCCAG	0.473																																																0			2											104	115	111					2																	179440587		2024	4200	6224	179148833	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65349A>G	2.37:g.179440587T>C			179148833	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179440587	T	C	179440587	2	2	113	1	0	0	0	0	0	0	0	1	16775	1838	64	4		4	TTN	2	179440587	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	5384755	179440587	63758786	38	30439										
TTN	7273	hgsc.bcm.edu	37	chr2	179452773	179452773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcgtacaagctgtgctgcagCattacaccgtttccagcctt	9	13	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179452773C>T	ENST00000591111.1	-	255	58662	c.58438G>A	c.(58438-58440)Gct>Act	p.A19480T	TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A18553T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A12181T|TTN_ENST00000460472.2_Missense_Mutation_p.A12056T|TTN_ENST00000589042.1_Missense_Mutation_p.A21121T|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A12248T			Q8WZ42	TITIN_HUMAN	titin	19480	Fibronectin type-III 41. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> S (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A12056S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTGCTGCAGCATTACACCGT	0.463																																																1	Substitution - Missense(1)	stomach(1)	2											99	95	96					2																	179452773		1974	4168	6142	179161019	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58438G>A	2.37:g.179452773C>T	ENSP00000465570:p.Ala19480Thr		179161019	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.49	1.655221	0.29425	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.78	5.78	0.91487	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.27278	0.0669	N	0.00473	-1.45	0.37235	D	0.905862	B;B;B;B	0.17465	0.022;0.022;0.022;0.022	B;B;B;B	0.16289	0.008;0.008;0.008;0.015	T	0.40308	-0.9570	9	0.87932	D	0	.	20.0204	0.97499	0.0:1.0:0.0:0.0	.	12056;12181;12248;19480	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	18553;12056;12248;12181;12054	ENSP00000343764:A18553T;ENSP00000434586:A12056T;ENSP00000340554:A12248T;ENSP00000352154:A12181T	ENSP00000340554:A12248T	A	-	1	0	TTN	179161019	1.000000	0.71417	0.994000	0.49952	0.534000	0.34807	5.893000	0.69798	2.729000	0.93468	0.650000	0.86243	GCT		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179452773	C	T	179452773	3	4	113	1	0	0	0	0	1	0	0	0	16775	710	25	3	44850	3	TTN	2	179452773	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	12186	179452773	63746600	39	30440										
TTN	7273	hgsc.bcm.edu	37	chr2	179474015	179474015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tatacagaccatggtcaggtCggagagaatctcggacgcgt	13	9	2	2	rs370390570	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179474015C>T	ENST00000591111.1	-	223	47323	c.47099G>A	c.(47098-47100)cGa>cAa	p.R15700Q	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R14773Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R8401Q|TTN_ENST00000460472.2_Missense_Mutation_p.R8276Q|TTN_ENST00000589042.1_Missense_Mutation_p.R17341Q|TTN_ENST00000342175.6_Missense_Mutation_p.R8468Q			Q8WZ42	TITIN_HUMAN	titin	15700	Ig-like 98.		R -> Q. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGGTCAGGTCGGAGAGAATC	0.438													C|||	2	0.000399361	0.0015	0	5008	,	,		19855	0		0	False		,,,				2504	0															0			2						C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2,3820		0,2,1909	95	91	92		24827,44318,25202,25403	5.7	1	2		92	1,8245		0,1,4122	no	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	43,43,43,43	0,3,6031	TT,TC,CC		0.0121,0.0523,0.0249	probably-damaging,probably-damaging,probably-damaging,probably-damaging	8276/26927,14773/33424,8401/27052,8468/27119	179474015	3,12065	1911	4123	6034	179182260	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.47099G>A	2.37:g.179474015C>T	ENSP00000465570:p.Arg15700Gln		179182260	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	18.46	3.629500	0.67015	5.23E-4	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.68	5.68	0.88126	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71434	0.3339	M	0.88241	2.94	0.58432	D	0.999991	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.68943	0.961;0.961;0.961;0.961	T	0.76664	-0.2876	9	0.87932	D	0	.	19.8608	0.96783	0.0:1.0:0.0:0.0	.	8276;8401;8468;15700	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	14773;8276;8468;8401;8276	ENSP00000343764:R14773Q;ENSP00000434586:R8276Q;ENSP00000340554:R8468Q;ENSP00000352154:R8401Q	ENSP00000340554:R8468Q	R	-	2	0	TTN	179182260	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	7.514000	0.81750	2.680000	0.91292	0.558000	0.71614	CGA		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179474015	C	T	179474015	3	4	113	1	0	0	0	0	1	0	0	0	16775	884	31	1	56031	1	TTN	2	179474015	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	21242	179474015	63725358	40	30441										
TTN	7273	hgsc.bcm.edu	37	chr2	179605985	179605985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgacaatgaaagttccagagCcattagggttatgaatgata	10	5	0	5	rs72648919		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179605985C>A	ENST00000591111.1	-	46	11248	c.11024G>T	c.(11023-11025)gGc>gTc	p.G3675V	TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G3754V|TTN_ENST00000460472.2_Missense_Mutation_p.G3629V|TTN_ENST00000589042.1_Missense_Mutation_p.G3992V|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G3821V			Q8WZ42	TITIN_HUMAN	titin	13978	Ig-like 22.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTTCCAGAGCCATTAGGGTT	0.453																																																0			2											83	82	82					2																	179605985		1907	4126	6033	179314230	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11024G>T	2.37:g.179605985C>A	ENSP00000465570:p.Gly3675Val		179314230	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	10.58	1.391175	0.25118	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.68479	-0.33;-0.33;-0.33	5.87	5.87	0.94306	.	.	.	.	.	D	0.86306	0.5901	M	0.90425	3.115	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87623	0.2511	9	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	3629;3754;3821	D3DPF9;E7EQE6;E7ET18	.;.;.	V	3629;3821;3754;3629	ENSP00000434586:G3629V;ENSP00000340554:G3821V;ENSP00000352154:G3754V	ENSP00000340554:G3821V	G	-	2	0	TTN	179314230	1.000000	0.71417	0.958000	0.39756	0.083000	0.17756	7.360000	0.79487	2.941000	0.99782	0.655000	0.94253	GGC		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179605985	C	A	179605985	3	1	113	1	0	0	0	0	1	0	0	0	16775	739	26	2	92814	2	TTN	2	179605985	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	131970	179605985	63593388	41	30442										
TTN	7273	hgsc.bcm.edu	37	chr2	179611219	179611219	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tttcttgaggagaaggtgttCttgatgatgtggtgtgttcc	14	4	2	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179611219C>A	ENST00000591111.1	-	46	10585				TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.R5303I|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGAAGGTGTTCTTGATGATGT	0.413																																																0			2											95	90	92					2																	179611219		2203	4299	6502	179319464	SO:0001627	intron_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-4571G>T	2.37:g.179611219C>A			179319464	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	19.32	3.804401	0.70682	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.59083	0.29	5.88	5.88	0.94601	.	.	.	.	.	T	0.75019	0.3793	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70403	-0.4881	9	0.35671	T	0.21	.	20.2422	0.98381	0.0:1.0:0.0:0.0	.	5303	Q8WZ42-6	.	I	5303;584	ENSP00000354117:R5303I	ENSP00000304714:R584I	R	-	2	0	TTN	179319464	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.070000	0.71220	2.782000	0.95742	0.655000	0.94253	AGA		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179611219	C	A	179611219	1	1	113	0	1	0	0	0	0	0	0	0	16775	913	32	2		2	TTN	2	179611219	Intron	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5234	179611219	63588154	42	30443										
TTN	7273	hgsc.bcm.edu	37	chr2	179648840	179648840	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cttcaaagcgctcttcacggAcggtggtgccagtgatgctc	12	12	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:179648840A>G	ENST00000591111.1	-	16	2956	c.2732T>C	c.(2731-2733)gTc>gCc	p.V911A	TTN_ENST00000342992.6_Missense_Mutation_p.V911A|TTN_ENST00000360870.5_Missense_Mutation_p.V911A|TTN_ENST00000359218.5_Missense_Mutation_p.V865A|TTN_ENST00000460472.2_Missense_Mutation_p.V865A|TTN_ENST00000589042.1_Missense_Mutation_p.V911A|TTN_ENST00000342175.6_Missense_Mutation_p.V865A			Q8WZ42	TITIN_HUMAN	titin	33948					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTTCACGGACGGTGGTGCC	0.552																																																0			2											150	120	131					2																	179648840		2203	4300	6503	179357085	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2732T>C	2.37:g.179648840A>G	ENSP00000465570:p.Val911Ala		179357085	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	12.98	2.098943	0.37048	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.63744	-0.06;0.18;0.16;0.15;0.29	5.52	4.36	0.52297	Ribonuclease H-like (1);	.	.	.	.	T	0.47746	0.1462	N	0.20986	0.625	0.09310	N	0.999993	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.001	B;B;B;B;B	0.09377	0.0;0.0;0.001;0.002;0.004	T	0.43909	-0.9362	9	0.87932	D	0	.	9.0211	0.36200	0.8571:0.0:0.1429:0.0	.	865;865;865;911;911	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	911;865;865;865;865;911	ENSP00000343764:V911A;ENSP00000434586:V865A;ENSP00000340554:V865A;ENSP00000352154:V865A;ENSP00000354117:V911A	ENSP00000340554:V865A	V	-	2	0	TTN	179357085	0.097000	0.21791	0.597000	0.28824	0.228000	0.25075	3.488000	0.53229	1.033000	0.39918	0.533000	0.62120	GTC		0.552	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179648840	A	G	179648840	3	3	113	1	0	0	0	0	1	0	0	0	16775	275	10	4	108644	4	TTN	2	179648840	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	37621	179648840	63550533	43	30444										
DUSP19	142679	hgsc.bcm.edu	37	chr2	183960271	183960271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	taccagtgctttttctttggTgaaaaatgcaagaccttcca	7	9	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:183960271T>C	ENST00000354221.4	+	4	714	c.539T>C	c.(538-540)gTg>gCg	p.V180A	AC064871.3_ENST00000413954.1_RNA|DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Missense_Mutation_p.V129A|AC064871.3_ENST00000444562.1_RNA	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	180	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						TTTTCTTTGGTGAAAAATGCA	0.408																																																0			2											133	135	134					2																	183960271		2203	4300	6503	183668516	SO:0001583	missense	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.539T>C	2.37:g.183960271T>C	ENSP00000346160:p.Val180Ala		183668516	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.647117	0.67358	.	.	ENSG00000162999	ENST00000342619;ENST00000354221	D;D	0.89270	-2.49;-2.49	5.74	5.74	0.90152	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.107189	0.64402	D	0.000005	D	0.93533	0.7936	M	0.83118	2.625	0.80722	D	1	P;P	0.46578	0.778;0.88	B;P	0.55087	0.399;0.768	D	0.94081	0.7344	10	0.62326	D	0.03	.	16.0247	0.80536	0.0:0.0:0.0:1.0	.	129;180	Q8WTR2-2;Q8WTR2	.;DUS19_HUMAN	A	129;180	ENSP00000343905:V129A;ENSP00000346160:V180A	ENSP00000343905:V129A	V	+	2	0	DUSP19	183668516	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.193000	0.77780	2.189000	0.69895	0.482000	0.46254	GTG		0.408	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			C	183960271	T	C	183960271	3	2	113	1	0	0	0	0	1	0	0	0	4829	1696	59	4	553	4	DUSP19	2	183960271	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	4311431	183960271	59239102	44	30445										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187615954	187615954	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggtcaatggctctattcaagTttctcttcctcttctacgtc	6	12	6	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:187615954T>C	ENST00000304698.5	+	5	1021	c.818T>C	c.(817-819)gTt>gCt	p.V273A		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	273						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TCTATTCAAGTTTCTCTTCCT	0.368																																																0			2											108	114	112					2																	187615954		2203	4300	6503	187324199	SO:0001583	missense	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.818T>C	2.37:g.187615954T>C	ENSP00000304108:p.Val273Ala		187324199	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967552	0.53507	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.42513	0.97	5.34	5.34	0.76211	.	0.550372	0.20261	N	0.095865	T	0.37571	0.1008	L	0.38175	1.15	0.21473	N	0.999674	B;B	0.21147	0.052;0.052	B;B	0.27715	0.082;0.082	T	0.35325	-0.9793	10	0.54805	T	0.06	-0.8584	13.897	0.63778	0.0:0.0:0.0:1.0	.	273;274	Q6P995;A8K122	F171B_HUMAN;.	A	273	ENSP00000304108:V273A	ENSP00000272804:V273A	V	+	2	0	FAM171B	187324199	1.000000	0.71417	0.485000	0.27403	0.689000	0.40095	6.318000	0.72866	2.029000	0.59856	0.496000	0.49642	GTT		0.368	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		C	187615954	T	C	187615954	3	2	113	1	0	0	0	0	1	0	0	0	5507	1725	60	4	836	4	FAM171B	2	187615954	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	3655683	187615954	55583419	45	30446										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189875583	189875583	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaggctgaaggaaatagcaaAttcacctacacagttctgga	9	8	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:189875583A>G	ENST00000304636.3	+	50	4391	c.4221A>G	c.(4219-4221)aaA>aaG	p.K1407K	COL3A1_ENST00000317840.5_Silent_p.K1104K	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1407	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GAAATAGCAAATTCACCTACA	0.398																																																0			2											100	92	95					2																	189875583		2203	4300	6503	189583828	SO:0001819	synonymous_variant	1281			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.4221A>G	2.37:g.189875583A>G			189583828	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																				0.398	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		G	189875583	A	G	189875583	2	3	113	1	0	0	0	0	0	0	0	1	3694	98	4	4		4	COL3A1	2	189875583	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	2259629	189875583	53323790	46	30447										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212286805	212286805	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccagttccttaaatttaggtCtactgtcagcatcaatcatc	5	11	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:212286805C>T	ENST00000342788.4	-	24	3201	c.2891G>A	c.(2890-2892)aGa>aAa	p.R964K	ERBB4_ENST00000402597.1_Missense_Mutation_p.R954K|ERBB4_ENST00000436443.1_Missense_Mutation_p.R964K	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	964	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AAATTTAGGTCTACTGTCAGC	0.353										TSP Lung(8;0.080)																																						0			2											109	102	105					2																	212286805		2203	4300	6503	211995050	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2891G>A	2.37:g.212286805C>T	ENSP00000342235:p.Arg964Lys		211995050	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	36	5.633688	0.96682	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	D;D;D	0.87029	-2.2;-2.2;-2.2	5.71	5.71	0.89125	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97087	0.9048	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.993;1.0;0.993;0.994	P;D;P;D	0.91635	0.87;0.999;0.87;0.921	D	0.98626	1.0669	10	0.87932	D	0	.	19.8494	0.96733	0.0:1.0:0.0:0.0	.	954;954;964;964	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	K	964;964;954	ENSP00000342235:R964K;ENSP00000403204:R964K;ENSP00000385565:R954K	ENSP00000342235:R964K	R	-	2	0	ERBB4	211995050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.800000	0.85949	2.705000	0.92388	0.585000	0.79938	AGA		0.353	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212286805	C	T	212286805	3	4	113	1	0	0	0	0	1	0	0	0	5222	913	32	3	1055	3	ERBB4	2	212286805	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	22411222	212286805	30912568	47	30448										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215862429	215862429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcaacatacctcatgaagcCggaggtctttctcatagaca	7	11	4	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:215862429C>T	ENST00000272895.7	-	23	3503	c.3284G>A	c.(3283-3285)cGg>cAg	p.R1095Q	ABCA12_ENST00000389661.4_Missense_Mutation_p.R777Q	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1095					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.R1095P(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		CTCATGAAGCCGGAGGTCTTT	0.358																																					Ovarian(66;664 1488 5121 34295)											1	Substitution - Missense(1)	ovary(1)	2											79	76	77					2																	215862429		2203	4300	6503	215570674	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3284G>A	2.37:g.215862429C>T	ENSP00000272895:p.Arg1095Gln		215570674	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769713	0.69992	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.83992	-1.79;-1.79	5.88	5.88	0.94601	.	0.000000	0.64402	D	0.000019	D	0.87237	0.6127	M	0.64997	1.995	0.80722	D	1	D;P	0.65815	0.995;0.882	P;B	0.53722	0.733;0.292	D	0.84146	0.0420	10	0.27785	T	0.31	.	20.2187	0.98312	0.0:1.0:0.0:0.0	.	1095;777	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	Q	1095;777	ENSP00000272895:R1095Q;ENSP00000374312:R777Q	ENSP00000272895:R1095Q	R	-	2	0	ABCA12	215570674	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.283000	0.78640	2.780000	0.95670	0.655000	0.94253	CGG		0.358	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215862429	C	T	215862429	3	4	113	1	0	0	0	0	1	0	0	0	30	652	23	1	4627	1	ABCA12	2	215862429	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	3575624	215862429	27336944	48	30449										
SP100	6672	hgsc.bcm.edu	37	chr2	231309028	231309028	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcaacatgcaggaataccccGatttaattcacatttataaa	4	9	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:231309028G>A	ENST00000264052.5	+	4	761	c.406G>A	c.(406-408)Gat>Aat	p.D136N	SP100_ENST00000409112.1_Missense_Mutation_p.D136N|SP100_ENST00000409824.1_Missense_Mutation_p.D111N|SP100_ENST00000341950.4_Missense_Mutation_p.D136N|SP100_ENST00000409341.1_Missense_Mutation_p.D136N|SP100_ENST00000340126.4_Missense_Mutation_p.D136N|SP100_ENST00000409897.1_Missense_Mutation_p.D101N|SP100_ENST00000427101.2_Missense_Mutation_p.D111N	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	136	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.D136N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GGAATACCCCGATTTAATTCA	0.358																																																1	Substitution - Missense(1)	ovary(1)	2											119	122	121					2																	231309028		2203	4300	6503	231017272	SO:0001583	missense	6672			AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"Zinc fingers, PHD-type"	11206	protein-coding gene	gene with protein product		604585	"nuclear antigen Sp100"			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.406G>A	2.37:g.231309028G>A	ENSP00000264052:p.Asp136Asn		231017272	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124922	0.56613	.	.	ENSG00000067066	ENST00000264052;ENST00000427101;ENST00000432979;ENST00000409824;ENST00000409341;ENST00000409112;ENST00000340126;ENST00000341950;ENST00000409897	D;D;D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	3.89	3.01	0.34805	Sp100 (2);	.	.	.	.	D	0.95300	0.8475	L	0.56124	1.755	0.09310	N	1	D;D;D;D;D;D;P;D	0.89917	0.992;1.0;0.997;0.999;0.996;1.0;0.897;0.996	P;D;P;P;P;D;P;P	0.72982	0.803;0.979;0.876;0.905;0.885;0.932;0.447;0.803	D	0.87584	0.2486	9	0.48119	T	0.1	.	7.4744	0.27368	0.1177:0.0:0.8823:0.0	.	111;136;101;136;136;136;111;136	F8WFE2;B4E2B9;B8ZZD8;P23497-4;P23497;E7EUA7;E9PHV6;P23497-2	.;.;.;.;SP100_HUMAN;.;.;.	N	136;111;111;111;136;136;136;136;101	ENSP00000264052:D136N;ENSP00000399389:D111N;ENSP00000391616:D111N;ENSP00000387311:D111N;ENSP00000386404:D136N;ENSP00000386427:D136N;ENSP00000343023:D136N;ENSP00000342729:D136N;ENSP00000386998:D101N	ENSP00000264052:D136N	D	+	1	0	SP100	231017272	0.001000	0.12720	0.002000	0.10522	0.060000	0.15804	0.865000	0.27940	1.218000	0.43458	0.557000	0.71058	GAT		0.358	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		A	231309028	G	A	231309028	3	1	113	1	0	0	0	0	1	0	0	0	14997	1058	37	1	420	1	SP100	2	231309028	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	15446599	231309028	11890345	49	30450										
ESPNL	339768	hgsc.bcm.edu	37	chr2	239013475	239013475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtggccactactccctcgtcGtctggctggtaagtgggtgc	14	12	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr2:239013475G>A	ENST00000343063.3	+	3	927	c.664G>A	c.(664-666)Gtc>Atc	p.V222I	ESPNL_ENST00000409169.1_Missense_Mutation_p.V222I	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	222										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CTCCCTCGTCGTCTGGCTGGT	0.667																																																0			2											17	16	17					2																	239013475		2183	4270	6453	238678214	SO:0001583	missense	339768			AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"Ankyrin repeat domain containing"	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.664G>A	2.37:g.239013475G>A	ENSP00000339115:p.Val222Ile		238678214	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015904	0.35606	.	.	ENSG00000144488	ENST00000343063;ENST00000409169	T;T	0.64085	-0.08;-0.08	4.84	4.84	0.62591	Ankyrin repeat-containing domain (3);	0.209205	0.30177	N	0.010237	T	0.42381	0.1200	N	0.12961	0.28	0.80722	D	1	B	0.29115	0.233	B	0.24394	0.053	T	0.39251	-0.9623	10	0.37606	T	0.19	-42.6716	11.0879	0.48097	0.0921:0.0:0.9079:0.0	.	222	Q6ZVH7	ESPNL_HUMAN	I	222	ENSP00000339115:V222I;ENSP00000386577:V222I	ENSP00000339115:V222I	V	+	1	0	ESPNL	238678214	1.000000	0.71417	0.987000	0.45799	0.154000	0.21943	4.115000	0.57865	2.246000	0.74042	0.462000	0.41574	GTC		0.667	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		A	239013475	G	A	239013475	3	1	113	1	0	0	0	0	1	0	0	0	5268	1145	40	1	674	1	ESPNL	2	239013475	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	7704447	239013475	4185898	50	30451										
VHL	7428	hgsc.bcm.edu	37	chr3	10183677	10183677	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtccggcccggaggaactggGcgccgaggaggagatggagg	21	9	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:10183677G>A	ENST00000256474.2	+	1	986	c.146G>A	c.(145-147)gGc>gAc	p.G49D	VHL_ENST00000345392.2_Missense_Mutation_p.G49D|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	49	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.G49D(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAGGAACTGGGCGCCGAGGAG	0.721		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	1	Substitution - Missense(1)	kidney(1)	3											5	9	8					3																	10183677		2069	4085	6154	10158677	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.146G>A	3.37:g.10183677G>A	ENSP00000256474:p.Gly49Asp		10158677	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.937583	0.52972	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.85556	-2.0;-2.0	4.58	1.56	0.23342	.	0.384464	0.22182	N	0.063498	T	0.70116	0.3187	N	0.19112	0.55	0.09310	N	1	B;B	0.14438	0.01;0.005	B;B	0.15052	0.012;0.004	T	0.58775	-0.7577	10	0.46703	T	0.11	-6.8546	4.7288	0.12954	0.0893:0.1491:0.6087:0.1528	.	49;49	P40337-2;P40337	.;VHL_HUMAN	D	49	ENSP00000256474:G49D;ENSP00000344757:G49D	ENSP00000256474:G49D	G	+	2	0	VHL	10158677	0.227000	0.23707	0.037000	0.18230	0.029000	0.11900	1.680000	0.37607	0.652000	0.30806	0.550000	0.68814	GGC		0.721	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10183677	G	A	10183677	3	1	113	1	0	0	0	0	1	0	0	0	17202	1203	42	3	148	3	VHL	3	10183677	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10		10183677	187838753	51	30452										
VHL	7428	hgsc.bcm.edu	37	chr3	10188219	10188219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcacctttggctcttcagagAtgcagggacacacgatgggc	12	11	3	1	rs5030832		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:10188219A>G	ENST00000256474.2	+	2	1202	c.362A>G	c.(361-363)gAt>gGt	p.D121G	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	121	Involved in binding to CCT complex.		D -> G (in VHLD; type I; dbSNP:rs5030832). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.D121G(3)|p.D121_A122del(1)|p.?(1)|p.R120fs*34(1)|p.R120fs*10(1)|p.L118_G123>P(1)|p.W117fs*1(1)|p.A122fs*7(1)|p.D121fs*11(1)|p.D121fs*35(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CTCTTCAGAGATGCAGGGACA	0.502		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	12	Deletion - Frameshift(5)|Substitution - Missense(3)|Deletion - In frame(1)|Insertion - Frameshift(1)|Unknown(1)|Complex - deletion inframe(1)	kidney(12)	3	GRCh37	CM941374	VHL	M	rs5030832						186	173	177					3																	10188219		2203	4300	6503	10163219	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.362A>G	3.37:g.10188219A>G	ENSP00000256474:p.Asp121Gly		10163219	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.856490	0.51376	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99836	-7.05	5.07	3.89	0.44902	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.050790	0.85682	D	0.000000	D	0.99704	0.9887	M	0.79011	2.435	0.80722	D	1	D	0.63880	0.993	D	0.69654	0.965	D	0.97903	1.0304	10	0.72032	D	0.01	-24.4217	10.4626	0.44590	0.8361:0.1639:0.0:0.0	rs5030832	121	P40337	VHL_HUMAN	G	121;39	ENSP00000256474:D121G	ENSP00000256474:D121G	D	+	2	0	VHL	10163219	1.000000	0.71417	0.998000	0.56505	0.249000	0.25844	5.209000	0.65208	0.869000	0.35703	-0.460000	0.05396	GAT		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10188219	A	G	10188219	3	3	113	1	0	0	0	0	1	0	0	0	17202	333	12	4	368	4	VHL	3	10188219	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	4542	10188219	187834211	52	30453										
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15311315	15311315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcggccagggagatggtctCcttggcggcacggagcacct	15	13	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:15311315C>T	ENST00000383791.3	-	4	620	c.400G>A	c.(400-402)Gag>Aag	p.E134K	SH3BP5_ENST00000253688.5_5'UTR|SH3BP5_ENST00000465894.2_5'Flank|SH3BP5_ENST00000408919.3_5'UTR|SH3BP5_ENST00000426925.1_5'UTR	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	134					intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						GAGATGGTCTCCTTGGCGGCA	0.607																																																0			3											111	114	113					3																	15311315		2203	4300	6503	15286319	SO:0001583	missense	9467			AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"SH3 binding protein"	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.400G>A	3.37:g.15311315C>T	ENSP00000373301:p.Glu134Lys		15286319	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	C	34	5.318577	0.95682	.	.	ENSG00000131370	ENST00000383791	.	.	.	5.62	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.79701	0.4491	M	0.87900	2.915	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.81304	-0.0993	9	0.87932	D	0	-22.5735	10.9615	0.47387	0.0:0.7989:0.1305:0.0706	.	134	O60239	3BP5_HUMAN	K	134	.	ENSP00000373301:E134K	E	-	1	0	SH3BP5	15286319	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	7.710000	0.84655	0.731000	0.32448	0.555000	0.69702	GAG		0.607	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		T	15311315	C	T	15311315	3	4	113	1	0	0	0	0	1	0	0	0	14284	864	30	3	991	3	SH3BP5	3	15311315	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5123096	15311315	182711115	53	30454										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15776985	15776985	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cattaatattggcacctctaGacaagagtagtttgaccatc	7	9	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:15776985G>A	ENST00000399451.2	-	6	849	c.482C>T	c.(481-483)tCt>tTt	p.S161F	RP11-44D5.1_ENST00000605733.1_RNA|ANKRD28_ENST00000383777.1_Missense_Mutation_p.S194F|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	161						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						GGCACCTCTAGACAAGAGTAG	0.338																																																0			3											61	58	59					3																	15776985		1846	4074	5920	15751989	SO:0001583	missense	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.482C>T	3.37:g.15776985G>A	ENSP00000382379:p.Ser161Phe		15751989	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650205	0.87958	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.67523	-0.27;-0.27;-0.27	5.38	4.49	0.54785	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	L	0.58925	1.835	0.80722	D	1	D;D;P	0.57257	0.979;0.978;0.952	P;P;P	0.62740	0.906;0.62;0.905	T	0.80538	-0.1338	10	0.87932	D	0	.	16.1167	0.81309	0.0:0.134:0.866:0.0	.	194;191;161	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	F	161;194;161	ENSP00000382379:S161F;ENSP00000373287:S194F;ENSP00000397341:S161F	ENSP00000373287:S194F	S	-	2	0	ANKRD28	15751989	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.943000	0.87716	1.250000	0.43966	0.484000	0.47621	TCT		0.338	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		A	15776985	G	A	15776985	3	1	113	1	0	0	0	0	1	0	0	0	656	942	33	3	2771	3	ANKRD28	3	15776985	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	465670	15776985	182245445	54	30455										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25675409	25675409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgagacaaacatcccatcTttcatttgcaagctcatgaa	6	10	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:25675409T>C	ENST00000264331.4	-	8	948	c.949A>G	c.(949-951)Aga>Gga	p.R317G	TOP2B_ENST00000435706.2_Missense_Mutation_p.R312G	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	317					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.R312G(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	ACATCCCATCTTTCATTTGCA	0.343																																																1	Substitution - Missense(1)	lung(1)	3											142	137	138					3																	25675409		1849	4085	5934	25650413	SO:0001583	missense	7155			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.949A>G	3.37:g.25675409T>C	ENSP00000264331:p.Arg317Gly		25650413	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	T	22.4	4.281582	0.80692	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.50001	0.76;0.76	5.49	4.27	0.50696	.	0.046152	0.85682	D	0.000000	T	0.72882	0.3516	M	0.92880	3.355	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.79697	-0.1695	10	0.87932	D	0	-6.27	11.7693	0.51949	0.0:0.0:0.28:0.72	.	312	Q02880-2	.	G	312;317;312	ENSP00000396704:R312G;ENSP00000264331:R317G	ENSP00000264331:R317G	R	-	1	2	TOP2B	25650413	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.308000	0.51896	2.092000	0.63282	0.528000	0.53228	AGA		0.343	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25675409	T	C	25675409	3	2	113	1	0	0	0	0	1	0	0	0	16406	1617	56	4	4047	4	TOP2B	3	25675409	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	9898424	25675409	172347021	55	30456										
MLH1	4292	hgsc.bcm.edu	37	chr3	37053589	37053589	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tctttggaaatgctgttagtCggtatgtcgataacctatat	9	6	1	0	rs267607774|rs587779032|rs63751615|rs267607779		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:37053589C>A	ENST00000231790.2	+	8	892	c.676C>A	c.(676-678)Cga>Aga	p.R226R	MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000435176.1_Splice_Site_p.R128R|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000536378.1_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	226			Missing (in HNPCC2).|R -> L (in HNPCC2). {ECO:0000269|PubMed:8566964}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.R226*(2)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TGCTGTTAGTCGGTATGTCGA	0.353		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	3	Substitution - Nonsense(2)|Whole gene deletion(1)	ovary(1)|stomach(1)|large_intestine(1)	3	GRCh37	CM960967	MLH1	M	rs121912958						116	105	109					3																	37053589		2203	4300	6503	37028593	SO:0001630	splice_region_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.677+1C>A	3.37:g.37053589C>A			37028593	B4DI13|B4DQ11|E9PCU2	Silent	SNP	ENST00000231790.2	37	CCDS2663.1																																																																																				0.353	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	Silent	A	37053589	C	A	37053589	5	1	113	1	0	0	0	0	0	0	1	0	9647	898	31	2	706	2	MLH1	3	37053589	Splice_Site	SNP	C	TCGA-EI-6510-01A-11D-1733-10	11378180	37053589	160968841	56	30457										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266134	41266134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggtgccactaccacagctcCttctctgagtggtaaaggca	10	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:41266134C>T	ENST00000349496.5	+	3	411	c.131C>T	c.(130-132)cCt>cTt	p.P44L	CTNNB1_ENST00000396185.3_Missense_Mutation_p.P44L|CTNNB1_ENST00000396183.3_Missense_Mutation_p.P44L|CTNNB1_ENST00000453024.1_Missense_Mutation_p.P37L|CTNNB1_ENST00000405570.1_Missense_Mutation_p.P44L	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	44					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.P44L(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_S45insAP(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S45del(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.P44del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACCACAGCTCCTTCTCTGAGT	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	126	Deletion - In frame(98)|Complex - deletion inframe(18)|Unknown(7)|Substitution - Missense(2)|Insertion - In frame(1)	liver(88)|large_intestine(17)|stomach(7)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|skin(2)|kidney(2)|thyroid(1)	3											85	75	79					3																	41266134		2203	4300	6503	41241138	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.131C>T	3.37:g.41266134C>T	ENSP00000344456:p.Pro44Leu		41241138	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779708	0.90195	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.82116	0.4967	M	0.64997	1.995	0.80722	D	1	D	0.67145	0.996	P	0.61477	0.889	T	0.82655	-0.0350	10	0.87932	D	0	-5.5494	20.2983	0.98569	0.0:1.0:0.0:0.0	.	44	P35222	CTNB1_HUMAN	L	37;44;44;44;44;37;44;44;44	ENSP00000400508:P37L;ENSP00000385604:P44L;ENSP00000412219:P44L;ENSP00000379486:P44L;ENSP00000344456:P44L;ENSP00000411226:P37L;ENSP00000379488:P44L;ENSP00000409302:P44L;ENSP00000401599:P44L	ENSP00000344456:P44L	P	+	2	0	CTNNB1	41241138	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	CCT		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266134	C	T	41266134	3	4	113	1	0	0	0	0	1	0	0	0	4022	681	24	3	137	3	CTNNB1	3	41266134	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	4212545	41266134	156756296	57	30458										
KLHL18	23276	hgsc.bcm.edu	37	chr3	47385056	47385056	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccactgcaggtggaacactaCaaccaccacacagccacctg	7	17	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:47385056C>T	ENST00000232766.5	+	10	1370	c.1350C>T	c.(1348-1350)taC>taT	p.Y450Y	KLHL18_ENST00000455924.2_Silent_p.Y338Y	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	450										endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		TGGAACACTACAACCACCACA	0.632																																																0			3											41	43	42					3																	47385056		2203	4300	6503	47360060	SO:0001819	synonymous_variant	23276			AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"Kelch-like", "BTB/POZ domain containing"	29120	protein-coding gene	gene with protein product			"kelch-like 18 (Drosophila)"			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.1350C>T	3.37:g.47385056C>T			47360060	A8K612|Q7Z3E8|Q8N125	Silent	SNP	ENST00000232766.5	37	CCDS33749.1																																																																																				0.632	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		T	47385056	C	T	47385056	2	4	113	1	0	0	0	0	0	0	0	1	8394	489	17	3		3	KLHL18	3	47385056	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	6118922	47385056	150637374	58	30459										
USP4	7375	hgsc.bcm.edu	37	chr3	49337909	49337909	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gattctgtcacctgagtaggTctgcagtgagggtcagcagg	15	8	4	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:49337909T>C	ENST00000265560.4	-	11	1549	c.1503A>G	c.(1501-1503)agA>agG	p.R501R	USP4_ENST00000351842.4_Silent_p.R454R|USP4_ENST00000488520.1_5'Flank	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	501	USP.|Ubiquitin-like 2.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		CCTGAGTAGGTCTGCAGTGAG	0.532																																																0			3											116	114	114					3																	49337909		2203	4300	6503	49312913	SO:0001819	synonymous_variant	7375			U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1503A>G	3.37:g.49337909T>C			49312913	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.280966	0.23392	.	.	ENSG00000114316	ENST00000431357	.	.	.	5.83	0.917	0.19380	.	.	.	.	.	T	0.55800	0.1943	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47394	-0.9121	4	.	.	.	-18.5278	8.833	0.35096	0.0:0.2953:0.0:0.7047	.	.	.	.	A	240	.	.	T	-	1	0	USP4	49312913	0.996000	0.38824	0.997000	0.53966	0.991000	0.79684	0.344000	0.19962	0.141000	0.18875	0.459000	0.35465	ACC		0.532	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49337909	T	C	49337909	2	2	113	1	0	0	0	0	0	0	0	1	17111	1664	58	4		4	USP4	3	49337909	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1952853	49337909	148684521	59	30460										
IQCF1	132141	hgsc.bcm.edu	37	chr3	51930880	51930880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcattggcattgtccactgTctgtgtctcaaccagaactg	8	12	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:51930880T>C	ENST00000310914.5	-	3	201	c.139A>G	c.(139-141)Aca>Gca	p.T47A		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	47										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TTGTCCACTGTCTGTGTCTCA	0.473																																																0			3											172	163	166					3																	51930880		2203	4300	6503	51905920	SO:0001583	missense	132141			BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.139A>G	3.37:g.51930880T>C	ENSP00000307958:p.Thr47Ala		51905920	Q8N711	Missense_Mutation	SNP	ENST00000310914.5	37	CCDS2836.1	.	.	.	.	.	.	.	.	.	.	T	0.395	-0.921453	0.02396	.	.	ENSG00000173389	ENST00000535733;ENST00000310914	T	0.29142	1.58	2.96	0.587	0.17439	.	4.031320	0.00397	N	0.000049	T	0.16727	0.0402	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13764	-1.0497	10	0.09084	T	0.74	.	4.4529	0.11630	0.0:0.3283:0.0:0.6717	.	47	Q8N6M8	IQCF1_HUMAN	A	47	ENSP00000307958:T47A	ENSP00000307958:T47A	T	-	1	0	IQCF1	51905920	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.074000	0.11450	0.118000	0.18165	0.448000	0.29417	ACA		0.473	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397		C	51930880	T	C	51930880	3	2	113	1	0	0	0	0	1	0	0	0	7828	1667	58	4	486	4	IQCF1	3	51930880	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2592971	51930880	146091550	60	30461										
TKT	7086	hgsc.bcm.edu	37	chr3	53260781	53260781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggcctccttaccttcataatAatggtcctccacggtgagga	9	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:53260781A>G	ENST00000462138.1	-	13	1775	c.1687T>C	c.(1687-1689)Tat>Cat	p.Y563H	TKT_ENST00000461139.1_5'UTR|TKT_ENST00000423525.2_Missense_Mutation_p.Y563H|TKT_ENST00000423516.1_Missense_Mutation_p.Y571H|TKT_ENST00000296289.6_Missense_Mutation_p.Y516H			P29401	TKT_HUMAN	transketolase	563					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)	p.Y563D(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		CCTTCATAATAATGGTCCTCC	0.617																																					Colon(133;1506 2347 35238 42177)											1	Substitution - Missense(1)	ovary(1)	3											112	102	106					3																	53260781		2203	4300	6503	53235821	SO:0001583	missense	7086				CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1687T>C	3.37:g.53260781A>G	ENSP00000417773:p.Tyr563His		53235821	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	37	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.275613	0.59649	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289;ENST00000414014	D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63	5.14	5.14	0.70334	Transketolase, C-terminal (1);Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93413	0.7899	L	0.52823	1.66	0.80722	D	1	D;P;P	0.89917	1.0;0.93;0.886	D;P;P	0.97110	1.0;0.864;0.69	D	0.92156	0.5732	10	0.29301	T	0.29	-17.4573	14.9669	0.71201	1.0:0.0:0.0:0.0	.	571;480;563	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	H	563;563;571;516;397	ENSP00000417773:Y563H;ENSP00000405455:Y563H;ENSP00000391481:Y571H;ENSP00000296289:Y516H	ENSP00000296289:Y516H	Y	-	1	0	TKT	53235821	1.000000	0.71417	0.936000	0.37596	0.298000	0.27526	9.253000	0.95501	1.953000	0.56701	0.533000	0.62120	TAT		0.617	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			G	53260781	A	G	53260781	3	3	113	1	0	0	0	0	1	0	0	0	15973	362	13	4	192	4	TKT	3	53260781	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	1329901	53260781	144761649	61	30462										
PSMD6	9861	hgsc.bcm.edu	37	chr3	64008049	64008049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccatcattgcatcgcgaattTcgctctctcctagattcttc	5	14	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:64008049T>C	ENST00000295901.4	-	2	436	c.296A>G	c.(295-297)gAa>gGa	p.E99G	PSMD6_ENST00000492933.1_Missense_Mutation_p.E152G|PSMD6_ENST00000482510.1_Missense_Mutation_p.E60G|PSMD6_ENST00000394431.2_Missense_Mutation_p.E61G|RP11-245J9.6_ENST00000605919.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	99					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		ATCGCGAATTTCGCTCTCTCC	0.453																																																0			3											177	169	172					3																	64008049		2203	4300	6503	63983089	SO:0001583	missense	9861			AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.296A>G	3.37:g.64008049T>C	ENSP00000295901:p.Glu99Gly		63983089	A8K2E0|E9PHI9|Q6UV22	Missense_Mutation	SNP	ENST00000295901.4	37	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	T	30	5.049784	0.93740	.	.	ENSG00000163636	ENST00000295901;ENST00000492933;ENST00000394431;ENST00000482510;ENST00000497323;ENST00000478185	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.19	5.19	0.71726	.	0.090629	0.85682	D	0.000000	D	0.91307	0.7259	H	0.95328	3.655	0.80722	D	1	D;D;D;D	0.71674	0.992;0.998;0.998;0.975	D;D;D;D	0.81914	0.938;0.981;0.995;0.936	D	0.93742	0.7051	10	0.72032	D	0.01	.	15.2232	0.73330	0.0:0.0:0.0:1.0	.	61;60;152;99	Q6UV22;E9PHI9;C9IZE4;Q15008	.;.;.;PSMD6_HUMAN	G	99;152;61;60;113;120	ENSP00000295901:E99G;ENSP00000418695:E152G;ENSP00000377952:E61G;ENSP00000419227:E60G;ENSP00000418887:E113G	ENSP00000295901:E99G	E	-	2	0	PSMD6	63983089	1.000000	0.71417	0.980000	0.43619	0.970000	0.65996	7.786000	0.85741	2.184000	0.69523	0.533000	0.62120	GAA		0.453	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814		C	64008049	T	C	64008049	3	2	113	1	0	0	0	0	1	0	0	0	12736	1783	62	4	901	4	PSMD6	3	64008049	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	10747268	64008049	134014381	62	30463										
FAM19A1	407738	hgsc.bcm.edu	37	chr3	68466553	68466553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggctggaacaacaagaaaccGgccttcttgcgtcgatggta	12	10	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:68466553G>A	ENST00000478136.1	+	3	732	c.242G>A	c.(241-243)cGg>cAg	p.R81Q	FAM19A1_ENST00000491017.1_3'UTR|FAM19A1_ENST00000496687.1_Missense_Mutation_p.R81Q	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	81						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.R81Q(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	7		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		ACAAGAAACCGGCCTTCTTGC	0.418																																																2	Substitution - Missense(2)	central_nervous_system(2)	3											146	147	147					3																	68466553		1899	4118	6017	68549243	SO:0001583	missense	407738			AY325114	CCDS54606.1	3p14.1	2005-01-20			ENSG00000183662	ENSG00000183662			21587	protein-coding gene	gene with protein product						15028294	Standard	NM_213609		Approved	TAFA-1	uc003dnd.3	Q7Z5A9	OTTHUMG00000158745	ENST00000478136.1:c.242G>A	3.37:g.68466553G>A	ENSP00000418575:p.Arg81Gln		68549243	A8K0V3|Q8TCL8	Missense_Mutation	SNP	ENST00000478136.1	37	CCDS54606.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565394	0.27915	.	.	ENSG00000183662	ENST00000478136;ENST00000496687	.	.	.	5.55	4.68	0.58851	.	0.112355	0.64402	D	0.000019	T	0.25158	0.0611	L	0.27053	0.805	0.27313	N	0.95725	P	0.52061	0.95	B	0.40702	0.338	T	0.09443	-1.0674	9	0.16420	T	0.52	.	14.678	0.68996	0.0701:0.0:0.9299:0.0	.	81	Q7Z5A9	F19A1_HUMAN	Q	81	.	ENSP00000418575:R81Q	R	+	2	0	FAM19A1	68549243	1.000000	0.71417	0.928000	0.36995	0.141000	0.21300	5.961000	0.70356	1.482000	0.48325	0.591000	0.81541	CGG		0.418	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609		A	68466553	G	A	68466553	3	1	113	1	0	0	0	0	1	0	0	0	5547	1116	39	1	248	1	FAM19A1	3	68466553	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4458504	68466553	129555877	63	30464										
SHQ1	55164	hgsc.bcm.edu	37	chr3	72866503	72866503	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agatttattgacaaattttcGtagctgatacttctcttctt	5	7	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:72866503G>A	ENST00000325599.8	-	7	899	c.760C>T	c.(760-762)Cga>Tga	p.R254*	SHQ1_ENST00000463369.1_Nonsense_Mutation_p.R226*	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	254					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		ACAAATTTTCGTAGCTGATAC	0.363																																																0			3											88	84	86					3																	72866503		2203	4299	6502	72949193	SO:0001587	stop_gained	55164			BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.760C>T	3.37:g.72866503G>A	ENSP00000315182:p.Arg254*		72949193	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Nonsense_Mutation	SNP	ENST00000325599.8	37	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	G	39	7.304644	0.98200	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	.	.	.	5.79	2.86	0.33363	.	0.068718	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6998	13.7329	0.62799	0.0:0.0:0.3849:0.6151	.	.	.	.	X	254;226	.	ENSP00000315182:R254X	R	-	1	2	SHQ1	72949193	1.000000	0.71417	0.913000	0.36048	0.898000	0.52572	3.274000	0.51631	0.772000	0.33382	-1.338000	0.01255	CGA		0.363	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		A	72866503	G	A	72866503	4	1	113	1	0	0	0	0	0	1	0	0	14329	1153	40	1	993	1	SHQ1	3	72866503	Nonsense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4399950	72866503	125155927	64	30465										
OR5AC2	81050	hgsc.bcm.edu	37	chr3	97806804	97806804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tctgatcttcatgtatgtgcGtcctgcatctggcttagctg	10	10	4	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:97806804G>A	ENST00000358642.2	+	1	788	c.788G>A	c.(787-789)cGt>cAt	p.R263H		NM_054106.1	NP_473447.1	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC, member 2	263					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R263H(1)		endometrium(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	28						ATGTATGTGCGTCCTGCATCT	0.428																																																1	Substitution - Missense(1)	urinary_tract(1)	3											104	94	97					3																	97806804		2203	4300	6503	99289494	SO:0001583	missense	81050			AF179759	CCDS33796.1	3q11.2	2013-09-23			ENSG00000196578	ENSG00000196578		"GPCR / Class A : Olfactory receptors"	15431	protein-coding gene	gene with protein product							Standard	NM_054106		Approved	HSA1	uc011bgs.2	Q9NZP5	OTTHUMG00000160083	ENST00000358642.2:c.788G>A	3.37:g.97806804G>A	ENSP00000351466:p.Arg263His		99289494		Missense_Mutation	SNP	ENST00000358642.2	37	CCDS33796.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484251	0.44147	.	.	ENSG00000196578	ENST00000358642	T	0.37752	1.18	4.51	0.388	0.16264	GPCR, rhodopsin-like superfamily (1);	0.431404	0.17055	N	0.188790	T	0.31979	0.0814	M	0.70903	2.155	0.09310	N	1	B	0.18166	0.026	B	0.18263	0.021	T	0.28267	-1.0049	10	0.49607	T	0.09	-0.8097	4.9953	0.14235	0.1694:0.0:0.5431:0.2875	.	263	Q9NZP5	O5AC2_HUMAN	H	263	ENSP00000351466:R263H	ENSP00000351466:R263H	R	+	2	0	OR5AC2	99289494	0.000000	0.05858	0.001000	0.08648	0.548000	0.35241	-0.623000	0.05546	0.180000	0.19960	0.590000	0.80494	CGT		0.428	OR5AC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359116.1			A	97806804	G	A	97806804	3	1	113	1	0	0	0	0	1	0	0	0	11172	1145	40	1	790	1	OR5AC2	3	97806804	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	24940301	97806804	100215626	65	30466										
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100489784	100489784	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtcaggcttttggatgtatCgcacatgaggtcctacgaga	12	8	1	2	rs376662738		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:100489784C>A	ENST00000284322.5	-	29	2520	c.2411G>T	c.(2410-2412)cGa>cTa	p.R804L	ABI3BP_ENST00000471714.1_Missense_Mutation_p.R1506L|ABI3BP_ENST00000383691.4_Missense_Mutation_p.R758L	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	804					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.R805Q(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						TTGGATGTATCGCACATGAGG	0.458																																																1	Substitution - Missense(1)	large_intestine(1)	3											156	155	155					3																	100489784		1952	4165	6117	101972474	SO:0001583	missense	25890			AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.2411G>T	3.37:g.100489784C>A	ENSP00000284322:p.Arg804Leu		101972474	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.72|18.72	3.684299|3.684299	0.68157|0.68157	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000495591|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691;ENST00000486770	.|T;T;T	.|0.24350	.|2.19;1.89;1.86	5.88|5.88	3.77|3.77	0.43336|0.43336	.|.	.|0.391146	.|0.24869	.|N	.|0.034944	T|T	0.31734|0.31734	0.0806|0.0806	L|L	0.36672|0.36672	1.1|1.1	0.24994|0.24994	N|N	0.991519|0.991519	.|D;P;D;D	.|0.71674	.|0.998;0.799;0.98;0.995	.|P;B;P;D	.|0.64144	.|0.871;0.343;0.822;0.922	T|T	0.06267|0.06267	-1.0836|-1.0836	5|10	.|0.51188	.|T	.|0.08	-7.3535|-7.3535	4.9128|4.9128	0.13831|0.13831	0.0:0.5686:0.181:0.2504|0.0:0.5686:0.181:0.2504	.|.	.|758;804;1506;513	.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.|.;TARSH_HUMAN;.;.	Y|L	860|1506;804;513;215;758;216	.|ENSP00000420524:R1506L;ENSP00000284322:R804L;ENSP00000373189:R758L	.|ENSP00000284322:R804L	D|R	-|-	1|2	0|0	ABI3BP|ABI3BP	101972474|101972474	0.024000|0.024000	0.19004|0.19004	1.000000|1.000000	0.80357|0.80357	0.849000|0.849000	0.48306|0.48306	1.363000|1.363000	0.34159|0.34159	1.489000|1.489000	0.48450|0.48450	0.591000|0.591000	0.81541|0.81541	GAT|CGA		0.458	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			A	100489784	C	A	100489784	3	1	113	1	0	0	0	0	1	0	0	0	91	884	31	2	844	2	ABI3BP	3	100489784	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2682980	100489784	97532646	66	30467										
ZPLD1	131368	hgsc.bcm.edu	37	chr3	102187823	102187823	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tttagctgtgacaaggacccTcagaccaccgtcattgagaa	9	11	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:102187823T>C	ENST00000491959.1	+	15	1659	c.777T>C	c.(775-777)ccT>ccC	p.P259P	ZPLD1_ENST00000466937.1_Silent_p.P259P|ZPLD1_ENST00000306176.1_Silent_p.P275P			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	259	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						ACAAGGACCCTCAGACCACCG	0.438																																																0			3											64	64	64					3																	102187823		2203	4300	6503	103670513	SO:0001819	synonymous_variant	131368			AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.777T>C	3.37:g.102187823T>C			103670513	Q49AS1|Q8WU36	Silent	SNP	ENST00000491959.1	37																																																																																					0.438	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		C	102187823	T	C	102187823	2	2	113	1	0	0	0	0	0	0	0	1	18260	1538	54	4		4	ZPLD1	3	102187823	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1698039	102187823	95834607	67	30468										
KLF15	28999	hgsc.bcm.edu	37	chr3	126071520	126071520	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccactgcccagcgtggcctgGgacaataggaagtccaagat	12	12	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:126071520G>T	ENST00000296233.3	-	2	476	c.246C>A	c.(244-246)tcC>tcA	p.S82S	KLF15_ENST00000509675.1_5'UTR	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	82					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		GCGTGGCCTGGGACAATAGGA	0.682																																																0			3											10	10	10					3																	126071520		2192	4286	6478	127554210	SO:0001819	synonymous_variant	28999			AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.246C>A	3.37:g.126071520G>T			127554210		Silent	SNP	ENST00000296233.3	37	CCDS3036.1																																																																																				0.682	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		T	126071520	G	T	126071520	2	4	113	1	0	0	0	0	0	0	0	1	8364	1219	43	2		2	KLF15	3	126071520	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	23883697	126071520	71950910	68	30469										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130300562	130300562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgaggtgggcacagagacTcaggtcagtgtggcttttca	15	7	3	2	rs373427912		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:130300562T>C	ENST00000358511.6	+	8	3736	c.3705T>C	c.(3703-3705)acT>acC	p.T1235T	COL6A6_ENST00000453409.2_Silent_p.T1235T	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1235	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.T1235T(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GCACAGAGACTCAGGTCAGTG	0.443																																																1	Substitution - coding silent(1)	ovary(1)	3											97	96	96					3																	130300562		2016	4174	6190	131783252	SO:0001819	synonymous_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3705T>C	3.37:g.130300562T>C			131783252	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.443	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130300562	T	C	130300562	2	2	113	1	0	0	0	0	0	0	0	1	3709	1538	54	4		4	COL6A6	3	130300562	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	4229042	130300562	67721868	69	30470										
UBA5	79876	hgsc.bcm.edu	37	chr3	132389866	132389866	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gttcttagctgtgtggacaaTtttgaagctcgaatgacaat	10	6	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:132389866T>C	ENST00000356232.4	+	6	1624	c.552T>C	c.(550-552)aaT>aaC	p.N184N	UBA5_ENST00000473651.1_Silent_p.N184N|UBA5_ENST00000264991.4_Silent_p.N128N|UBA5_ENST00000494238.2_Silent_p.N128N|UBA5_ENST00000493720.2_Silent_p.N184N	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	184					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)			breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						GTGTGGACAATTTTGAAGCTC	0.328																																																0			3											188	183	185					3																	132389866		2203	4300	6503	133872556	SO:0001819	synonymous_variant	79876			AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"Ubiquitin-like modifier activating enzymes"	23230	protein-coding gene	gene with protein product	"UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"	610552	"ubiquitin-activating enzyme E1-domain containing 1"	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.552T>C	3.37:g.132389866T>C			133872556	A6NJL3|D3DNC8|Q96ST1	Silent	SNP	ENST00000356232.4	37	CCDS3076.1																																																																																				0.328	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818		C	132389866	T	C	132389866	2	2	113	1	0	0	0	0	0	0	0	1	16870	1490	52	4		4	UBA5	3	132389866	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2089304	132389866	65632564	70	30471										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164908337	164908337	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcaaatgaagaaaactgttGgtatataatttcctcataga	6	5	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:164908337G>T	ENST00000475390.1	-	2	725	c.282C>A	c.(280-282)acC>acA	p.T94T	SLITRK3_ENST00000241274.3_Silent_p.T94T			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	94					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.T94T(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GAAAACTGTTGGTATATAATT	0.343										HNSCC(40;0.11)																																						1	Substitution - coding silent(1)	ovary(1)	3											53	57	56					3																	164908337		2203	4299	6502	166391031	SO:0001819	synonymous_variant	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.282C>A	3.37:g.164908337G>T			166391031	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																				0.343	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164908337	G	T	164908337	2	4	113	1	0	0	0	0	0	0	0	1	14781	1335	47	2		2	SLITRK3	3	164908337	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	32518471	164908337	33114093	71	30472										
TNIK	23043	hgsc.bcm.edu	37	chr3	170846571	170846571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tccactaatgctgaaggactCcgaccttgggggcaggttgg	14	10	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:170846571C>T	ENST00000436636.2	-	16	2049	c.1705G>A	c.(1705-1707)Gag>Aag	p.E569K	TNIK_ENST00000470834.1_Missense_Mutation_p.E540K|TNIK_ENST00000538048.1_Intron|TNIK_ENST00000341852.6_Intron|TNIK_ENST00000460047.1_Intron|TNIK_ENST00000488470.1_Intron|TNIK_ENST00000284483.8_Missense_Mutation_p.E569K|TNIK_ENST00000369326.5_Missense_Mutation_p.E540K|TNIK_ENST00000475336.1_Intron|TNIK_ENST00000357327.5_Missense_Mutation_p.E540K	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	569	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CTGAAGGACTCCGACCTTGGG	0.567																																																0			3											57	61	60					3																	170846571		1978	4163	6141	172329265	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.1705G>A	3.37:g.170846571C>T	ENSP00000399511:p.Glu569Lys		172329265	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	C	31	5.060846	0.93846	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000284483;ENST00000357327;ENST00000470834	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.11	5.11	0.69529	.	0.116276	0.64402	D	0.000018	T	0.64046	0.2563	L	0.35854	1.095	0.80722	D	1	D;D;D;D	0.58970	0.984;0.984;0.984;0.973	P;P;P;P	0.59115	0.79;0.852;0.79;0.829	T	0.58120	-0.7692	10	0.25751	T	0.34	.	18.7271	0.91718	0.0:1.0:0.0:0.0	.	540;569;540;569	Q9UKE5-6;Q9UKE5-4;Q9UKE5-2;Q9UKE5	.;.;.;TNIK_HUMAN	K	569;540;569;540;540	ENSP00000399511:E569K;ENSP00000358332:E540K;ENSP00000284483:E569K;ENSP00000349880:E540K;ENSP00000419990:E540K	ENSP00000284483:E569K	E	-	1	0	TNIK	172329265	1.000000	0.71417	0.978000	0.43139	0.991000	0.79684	7.320000	0.79064	2.652000	0.90054	0.561000	0.74099	GAG		0.567	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		T	170846571	C	T	170846571	3	4	113	1	0	0	0	0	1	0	0	0	16352	864	30	3	2449	3	TNIK	3	170846571	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5938234	170846571	27175859	72	30473										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178922326	178922326	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggtatctaccatggaggagaAcccttatgtgacaatgtgaa	11	7	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:178922326A>G	ENST00000263967.3	+	6	1252	c.1095A>G	c.(1093-1095)gaA>gaG	p.E365E		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	365	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		E -> K (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGGAGGAGAACCCTTATGTG	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											225	184	197					3																	178922326		1845	4096	5941	180405020	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1095A>G	3.37:g.178922326A>G			180405020	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178922326	A	G	178922326	2	3	113	1	0	0	0	0	0	0	0	1	11944	40	2	4		4	PIK3CA	3	178922326	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	8075755	178922326	19100104	73	30474										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952035	178952035	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aagaccctagccttagataaAactgagcaagaggctttgga	10	8	0	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:178952035A>G	ENST00000263967.3	+	21	3247	c.3090A>G	c.(3088-3090)aaA>aaG	p.K1030K	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1030	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CCTTAGATAAAACTGAGCAAG	0.378		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											93	82	85					3																	178952035		1871	4117	5988	180434729	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3090A>G	3.37:g.178952035A>G			180434729	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952035	A	G	178952035	2	3	113	1	0	0	0	0	0	0	0	1	11944	11	1	4		4	PIK3CA	3	178952035	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	29709	178952035	19070395	74	30475										
FXR1	8087	hgsc.bcm.edu	37	chr3	180669153	180669153	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agaagatttaatgggcctggCaataggaacacatggtagta	12	5	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:180669153C>T	ENST00000357559.4	+	8	1082	c.698C>T	c.(697-699)gCa>gTa	p.A233V	FXR1_ENST00000491062.1_Missense_Mutation_p.A184V|FXR1_ENST00000480918.1_Missense_Mutation_p.A220V|FXR1_ENST00000468861.1_Missense_Mutation_p.A148V|FXR1_ENST00000445140.2_Missense_Mutation_p.A233V|FXR1_ENST00000305586.7_Missense_Mutation_p.A148V	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	233	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.		A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			ATGGGCCTGGCAATAGGAACA	0.388																																																0			3											102	98	100					3																	180669153		2203	4300	6503	182151847	SO:0001583	missense	8087			M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.698C>T	3.37:g.180669153C>T	ENSP00000350170:p.Ala233Val		182151847	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	37	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	C	34	5.338588	0.95783	.	.	ENSG00000114416	ENST00000357559;ENST00000305586;ENST00000491062;ENST00000468861;ENST00000445140;ENST00000480918	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	5.35	5.35	0.76521	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.52484	0.1737	M	0.82716	2.605	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D	0.78314	0.984;0.991;0.988;0.932;0.985;0.987	T	0.58864	-0.7561	10	0.87932	D	0	-10.3035	19.0696	0.93127	0.0:1.0:0.0:0.0	.	220;184;148;148;233;233	B4DXZ6;E9PFF5;E7EU85;E7ERF5;P51114-2;P51114	.;.;.;.;.;FXR1_HUMAN	V	233;148;184;148;233;220	ENSP00000350170:A233V;ENSP00000307633:A148V;ENSP00000420643:A184V;ENSP00000420515:A148V;ENSP00000388828:A233V;ENSP00000418097:A220V	ENSP00000307633:A148V	A	+	2	0	FXR1	182151847	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.788000	0.85771	2.485000	0.83878	0.563000	0.77884	GCA		0.388	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			T	180669153	C	T	180669153	3	4	113	1	0	0	0	0	1	0	0	0	6134	710	25	3	728	3	FXR1	3	180669153	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	1717118	180669153	17353277	75	30476										
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185542704	185542705	+	Missense_Mutation	DNP	GG	GG	CT													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agctgccggaggtcgtcggcGgtgacggcggggctcaggtt							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:185542704_185542705GG>CT	ENST00000382199.2	-	1	139_140	c.44_45CC>AG	c.(43-45)aCC>aAG	p.T15K	IGF2BP2_ENST00000457616.2_Missense_Mutation_p.T15K|IGF2BP2_ENST00000346192.3_Missense_Mutation_p.T15K	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	15	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GGTCGTCGGCGGTGACGGCGGG	0.683																																																0			3																																								187025398|187025399	SO:0001583	missense	10644			BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"RNA binding motif (RRM) containing"	28867	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 2"	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.44_45delinsCT	3.37:g.185542704_185542705delinsCT	ENSP00000371634:p.Thr15Lys		187025398|187025399	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent|Missense_Mutation	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																				0.683	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		CT	185542705	GG	CT	185542704	3	2	113	1	0	0	0	0	1	0	0	0	7595	1103	39	5	1818	5	IGF2BP2	3	185542704	Missense_Mutation	DNP	GG	TCGA-EI-6510-01A-11D-1733-10	4873551	185542704	12479726	76	30477										
TRA2B	6434	hgsc.bcm.edu	37	chr3	185639878	185639878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gaaatcaactctgatcctacGcccatcaagctccattccat	4	15	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:185639878G>A	ENST00000453386.2	-	5	834	c.559C>T	c.(559-561)Cgt>Tgt	p.R187C	TRA2B_ENST00000382191.4_Missense_Mutation_p.R87C	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	187	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R187C(1)		breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						CTGATCCTACGCCCATCAAGC	0.378																																																1	Substitution - Missense(1)	large_intestine(1)	3											142	134	137					3																	185639878		2203	4300	6503	187122572	SO:0001583	missense	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"RNA binding motif (RRM) containing"	10781	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 156"	602719	"splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.559C>T	3.37:g.185639878G>A	ENSP00000416959:p.Arg187Cys		187122572	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Missense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365073	0.82463	.	.	ENSG00000136527	ENST00000453386;ENST00000382191	D;D	0.92699	-3.09;-3.09	6.03	5.15	0.70609	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.94847	0.8335	M	0.92412	3.305	0.80722	D	1	P;P	0.47484	0.896;0.896	P;P	0.48571	0.582;0.582	D	0.95190	0.8307	10	0.87932	D	0	-4.8752	11.7683	0.51943	0.0:0.1335:0.7279:0.1385	.	187;187	B2RDQ3;P62995	.;TRA2B_HUMAN	C	187;87	ENSP00000416959:R187C;ENSP00000371626:R87C	ENSP00000371626:R87C	R	-	1	0	TRA2B	187122572	1.000000	0.71417	0.997000	0.53966	0.960000	0.62799	7.573000	0.82421	1.539000	0.49286	-0.176000	0.13171	CGT		0.378	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		A	185639878	G	A	185639878	3	1	113	1	0	0	0	0	1	0	0	0	16474	1087	38	1	327	1	TRA2B	3	185639878	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	97174	185639878	12382552	77	30478										
RTP1	132112	hgsc.bcm.edu	37	chr3	186917438	186917438	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cagcgggcgggctcggtgcgCatgcgcgtcttcaagcagct	16	13	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr3:186917438C>T	ENST00000312295.4	+	2	402	c.372C>T	c.(370-372)cgC>cgT	p.R124R	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	124			R -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GCTCGGTGCGCATGCGCGTCT	0.652																																																0			3											41	40	40					3																	186917438		2203	4296	6499	188400132	SO:0001819	synonymous_variant	132112			BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.372C>T	3.37:g.186917438C>T			188400132		Silent	SNP	ENST00000312295.4	37	CCDS3287.2																																																																																				0.652	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		T	186917438	C	T	186917438	2	4	113	1	0	0	0	0	0	0	0	1	13770	697	25	3		3	RTP1	3	186917438	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	1277560	186917438	11104992	78	30479										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55133833	55133833	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cccacctcccaggatatcctGgctgaaaaacaatctgactc	6	15	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:55133833G>A	ENST00000257290.5	+	7	1377	c.1046G>A	c.(1045-1047)tGg>tAg	p.W349*	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	349	Ig-like C2-type 4.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	AGGATATCCTGGCTGAAAAAC	0.443			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	0			4											56	54	55					4																	55133833		2203	4300	6503	54828590	SO:0001587	stop_gained	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1046G>A	4.37:g.55133833G>A	ENSP00000257290:p.Trp349*		54828590	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Nonsense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	41	8.637975	0.98895	.	.	ENSG00000134853	ENST00000257290	.	.	.	5.79	5.79	0.91817	.	0.000000	0.30538	U	0.009404	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0361	0.97558	0.0:0.0:1.0:0.0	.	.	.	.	X	349	.	ENSP00000257290:W349X	W	+	2	0	PDGFRA	54828590	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.401000	0.90202	2.745000	0.94114	0.462000	0.41574	TGG		0.443	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55133833	G	A	55133833	4	1	113	1	0	0	0	0	0	1	0	0	11692	1357	47	3	1068	3	PDGFRA	4	55133833	Nonsense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10		55133833	136020443	79	30480										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55144138	55144138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcacctggggccacatttgaAcattgtaaacttgctgggag	11	9	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:55144138A>G	ENST00000257290.5	+	14	2298	c.1967A>G	c.(1966-1968)aAc>aGc	p.N656S	FIP1L1_ENST00000507166.1_Missense_Mutation_p.N416S	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	656	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CCACATTTGAACATTGTAAAC	0.458			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	0			4											82	82	82					4																	55144138		2203	4300	6503	54838895	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1967A>G	4.37:g.55144138A>G	ENSP00000257290:p.Asn656Ser		54838895	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.840613	0.91197	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.92545	-3.06;-3.06	5.83	5.83	0.93111	Serine-threonine/tyrosine-protein kinase (1);Tyrosine-protein kinase, receptor class III, conserved site (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.34484	U	0.003926	D	0.95965	0.8686	M	0.79011	2.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96409	0.9303	10	0.87932	D	0	.	16.2025	0.82095	1.0:0.0:0.0:0.0	.	656;656	P16234-3;P16234	.;PGFRA_HUMAN	S	416;656	ENSP00000423325:N416S;ENSP00000257290:N656S	ENSP00000423325:N416S	N	+	2	0	FIP1L1;PDGFRA	54838895	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	9.201000	0.95017	2.231000	0.72958	0.459000	0.35465	AAC		0.458	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		G	55144138	A	G	55144138	3	3	113	1	0	0	0	0	1	0	0	0	11692	43	2	4	2017	4	PDGFRA	4	55144138	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	10305	55144138	136010138	80	30481										
KIT	3815	hgsc.bcm.edu	37	chr4	55602695	55602695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgaagtggatggcacctgAaagcattttcaactgtgtat	11	6	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:55602695A>G	ENST00000288135.5	+	18	2613	c.2516A>G	c.(2515-2517)gAa>gGa	p.E839G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	839	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in mastocytosis; somatic mutation; dominant negative mutation; loss of autophosphorylation). {ECO:0000269|PubMed:9990072}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATGGCACCTGAAAGCATTTTC	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4											147	144	145					4																	55602695		2203	4300	6503	55297452	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2516A>G	4.37:g.55602695A>G	ENSP00000288135:p.Glu839Gly		55297452	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.83	3.708041	0.68615	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.97575	-4.44;-4.44	5.7	5.7	0.88788	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000016	D	0.98982	0.9653	H	0.96301	3.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99501	1.0953	10	0.87932	D	0	.	15.9745	0.80049	1.0:0.0:0.0:0.0	.	835;839	P10721-2;P10721	.;KIT_HUMAN	G	839;835	ENSP00000288135:E839G;ENSP00000390987:E835G	ENSP00000288135:E839G	E	+	2	0	KIT	55297452	1.000000	0.71417	0.486000	0.27416	0.245000	0.25701	9.190000	0.94934	2.168000	0.68352	0.533000	0.62120	GAA		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55602695	A	G	55602695	3	3	113	1	0	0	0	0	1	0	0	0	8350	246	9	4	2586	4	KIT	4	55602695	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	458557	55602695	135551581	81	30482										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181854	57181854	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcctgcctggcagaaattttCcgatggtggcacggagacct	13	11	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:57181854C>T	ENST00000504228.1	+	6	2291	c.2186C>T	c.(2185-2187)tCc>tTc	p.S729F	KIAA1211_ENST00000264229.6_Missense_Mutation_p.S729F|KIAA1211_ENST00000541073.1_Missense_Mutation_p.S722F			Q6ZU35	K1211_HUMAN	KIAA1211	729										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CAGAAATTTTCCGATGGTGGC	0.572																																																0			4											67	77	74					4																	57181854		1964	4153	6117	56876611	SO:0001583	missense	57482			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2186C>T	4.37:g.57181854C>T	ENSP00000423366:p.Ser729Phe		56876611	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.095332	0.56075	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.02787	4.16;4.16;4.16	4.49	4.49	0.54785	.	.	.	.	.	T	0.14056	0.0340	M	0.66939	2.045	0.41687	D	0.98932	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.987;0.987;0.994	T	0.00710	-1.1599	9	0.87932	D	0	-6.4779	17.3612	0.87350	0.0:1.0:0.0:0.0	.	722;722;729	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	F	729;729;722;639	ENSP00000264229:S729F;ENSP00000423366:S729F;ENSP00000444006:S722F	ENSP00000264229:S729F	S	+	2	0	KIAA1211	56876611	1.000000	0.71417	0.724000	0.30704	0.382000	0.30200	5.587000	0.67510	2.317000	0.78254	0.484000	0.47621	TCC		0.572	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57181854	C	T	57181854	3	4	113	1	0	0	0	0	1	0	0	0	8236	855	30	3	2204	3	KIAA1211	4	57181854	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	1579159	57181854	133972422	82	30483										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346819	71346819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctgtgactttcccatcagctTccaccaaaattactaccctt	3	15	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:71346819T>C	ENST00000304887.5	+	3	548	c.358T>C	c.(358-360)Tcc>Ccc	p.S120P	MUC7_ENST00000456088.1_Missense_Mutation_p.S120P|MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000413702.1_Missense_Mutation_p.S120P	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	120	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			CCCATCAGCTTCCACCAAAAT	0.433																																																0			4											126	119	121					4																	71346819		2203	4300	6503	71381408	SO:0001583	missense	4589			BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.358T>C	4.37:g.71346819T>C	ENSP00000302021:p.Ser120Pro		71381408	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	9.389	1.075013	0.20227	.	.	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.54866	0.56;0.55;0.56;0.56	2.82	-5.46	0.02608	.	.	.	.	.	T	0.30324	0.0761	N	0.24115	0.695	0.09310	N	1	P	0.39157	0.662	B	0.43225	0.412	T	0.24621	-1.0155	9	0.15499	T	0.54	-0.6797	0.9092	0.01291	0.1475:0.2068:0.3008:0.345	.	120	Q8TAX7	MUC7_HUMAN	P	120	ENSP00000407422:S120P;ENSP00000427594:S120P;ENSP00000400585:S120P;ENSP00000302021:S120P	ENSP00000302021:S120P	S	+	1	0	MUC7	71381408	0.004000	0.15560	0.000000	0.03702	0.006000	0.05464	-0.234000	0.09028	-1.196000	0.02676	-0.316000	0.08728	TCC		0.433	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		C	71346819	T	C	71346819	3	2	113	1	0	0	0	0	1	0	0	0	10011	1783	62	4	364	4	MUC7	4	71346819	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	14164965	71346819	119807457	83	30484										
HERC5	51191	hgsc.bcm.edu	37	chr4	89425522	89425522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	accccgaagaactgaaggatGtgattgttggaaatacagat	11	6	0	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:89425522G>T	ENST00000264350.3	+	21	2875	c.2722G>T	c.(2722-2724)Gtg>Ttg	p.V908L	HERC5_ENST00000508159.1_Missense_Mutation_p.V546L	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	908	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ACTGAAGGATGTGATTGTTGG	0.343																																					Esophageal Squamous(39;887 1012 34045 50514)											0			4											78	80	79					4																	89425522		2203	4300	6503	89644545	SO:0001583	missense	51191			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.2722G>T	4.37:g.89425522G>T	ENSP00000264350:p.Val908Leu		89644545	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	G	5.388	0.256790	0.10185	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	T;T	0.46063	0.88;0.88	4.62	3.78	0.43462	HECT (4);	0.371554	0.18438	N	0.141213	T	0.20700	0.0498	N	0.04959	-0.14	0.22266	N	0.999241	B	0.10296	0.003	B	0.28305	0.088	T	0.24693	-1.0153	10	0.18276	T	0.48	.	6.3947	0.21605	0.0987:0.1853:0.716:0.0	.	908	Q9UII4	HERC5_HUMAN	L	908;546	ENSP00000264350:V908L;ENSP00000424129:V546L	ENSP00000264350:V908L	V	+	1	0	HERC5	89644545	0.002000	0.14202	0.945000	0.38365	0.262000	0.26303	0.586000	0.23894	1.173000	0.42796	0.655000	0.94253	GTG		0.343	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		T	89425522	G	T	89425522	3	4	113	1	0	0	0	0	1	0	0	0	7082	1377	48	2	2804	2	HERC5	4	89425522	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	18078703	89425522	101728754	84	30485										
ADH1B	125	hgsc.bcm.edu	37	chr4	100235226	100235226	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gccaaacacagcacaggtagAgcctggggtgacctgtgttt	13	10	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:100235226A>G	ENST00000305046.8	-	6	647	c.580T>C	c.(580-582)Tct>Cct	p.S194P	ADH1B_ENST00000394887.3_Missense_Mutation_p.S154P			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	194					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCACAGGTAGAGCCTGGGGTG	0.468																																																0			4											107	116	113					4																	100235226		2203	4300	6503	100454249	SO:0001583	missense	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.580T>C	4.37:g.100235226A>G	ENSP00000306606:p.Ser194Pro		100454249	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Missense_Mutation	SNP	ENST00000305046.8	37	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683449	0.47991	.	.	ENSG00000196616	ENST00000305046;ENST00000394887;ENST00000412614	T;T	0.32272	1.46;1.46	3.81	3.81	0.43845	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.70482	0.3229	H	0.98996	4.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.82030	-0.0659	10	0.87932	D	0	-12.0051	12.5708	0.56337	1.0:0.0:0.0:0.0	.	181;154;194	F5HB16;A8MYN5;P00325	.;.;ADH1B_HUMAN	P	194;154;181	ENSP00000306606:S194P;ENSP00000378351:S154P	ENSP00000306606:S194P	S	-	1	0	ADH1B	100454249	1.000000	0.71417	0.981000	0.43875	0.050000	0.14768	8.453000	0.90349	1.343000	0.45638	0.459000	0.35465	TCT		0.468	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		G	100235226	A	G	100235226	3	3	113	1	0	0	0	0	1	0	0	0	308	304	11	4	563	4	ADH1B	4	100235226	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	10809704	100235226	90919050	85	30486										
TBCK	93627	hgsc.bcm.edu	37	chr4	107154748	107154748	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gaaaacctaaatcatacttgTctatctgtaggaattggagt	8	6	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:107154748T>C	ENST00000273980.5	-	17	1956	c.1509A>G	c.(1507-1509)agA>agG	p.R503R	TBCK_ENST00000432496.2_Silent_p.R503R|TBCK_ENST00000361687.4_Silent_p.R440R|TBCK_ENST00000394708.2_Silent_p.R503R|TBCK_ENST00000394706.3_Silent_p.R464R					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						ATCATACTTGTCTATCTGTAG	0.318																																																0			4											58	55	56					4																	107154748		2202	4297	6499	107374197	SO:0001819	synonymous_variant	0				CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1509A>G	4.37:g.107154748T>C			107374197		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																				0.318	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		C	107154748	T	C	107154748	2	2	113	1	0	0	0	0	0	0	0	1	15675	1664	58	4		4	TBCK	4	107154748	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	6919522	107154748	83999528	86	30487										
MFSD8	256471	hgsc.bcm.edu	37	chr4	128863276	128863276	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gttctttcctgaagggaagtAgcaccagcagtatatgatct	10	8	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:128863276A>G	ENST00000296468.3	-	6	604	c.477T>C	c.(475-477)gcT>gcC	p.A159A	MFSD8_ENST00000515130.1_5'UTR|MFSD8_ENST00000513559.1_Silent_p.A114A|MFSD8_ENST00000541133.1_Silent_p.A114A	NM_152778.2	NP_689991.1	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing 8	159					cell death (GO:0008219)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				cervix(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)	23						GAAGGGAAGTAGCACCAGCAG	0.348																																																0			4											189	168	175					4																	128863276		2203	4300	6503	129082726	SO:0001819	synonymous_variant	256471			AK074564	CCDS3736.1	4q28.2	2014-09-17			ENSG00000164073	ENSG00000164073			28486	protein-coding gene	gene with protein product		611124	"ceroid-lipofuscinosis, neuronal 7, late infantile, variant"	CLN7		17564970	Standard	NM_152778		Approved	MGC33302	uc003ifp.3	Q8NHS3	OTTHUMG00000133303	ENST00000296468.3:c.477T>C	4.37:g.128863276A>G			129082726	B2RDM1|B7Z205|Q8N2P3	Silent	SNP	ENST00000296468.3	37	CCDS3736.1																																																																																				0.348	MFSD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257097.1	NM_152778		G	128863276	A	G	128863276	2	3	113	1	0	0	0	0	0	0	0	1	9568	407	15	4		4	MFSD8	4	128863276	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	21708528	128863276	62291000	87	30488										
TLR2	7097	hgsc.bcm.edu	37	chr4	154626007	154626007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catttgtttcttacagtgagCgggatgcctactgggtggag	14	7	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:154626007C>T	ENST00000260010.6	+	1	3356	c.1948C>T	c.(1948-1950)Cgg>Tgg	p.R650W		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	650	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	TTACAGTGAGCGGGATGCCTA	0.502																																																0			4											42	41	42					4																	154626007		2203	4300	6503	154845457	SO:0001583	missense	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.1948C>T	4.37:g.154626007C>T	ENSP00000260010:p.Arg650Trp		154845457	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608959	0.46527	.	.	ENSG00000137462	ENST00000260010	T	0.28895	1.59	5.65	3.77	0.43336	Toll/interleukin-1 receptor homology (TIR) domain (4);	1.767260	0.02534	N	0.093961	T	0.47710	0.1460	M	0.61703	1.905	0.09310	N	1	D	0.64830	0.994	P	0.53518	0.728	T	0.16630	-1.0396	10	0.87932	D	0	.	8.5546	0.33474	0.3748:0.4886:0.1366:0.0	.	650	O60603	TLR2_HUMAN	W	650	ENSP00000260010:R650W	ENSP00000260010:R650W	R	+	1	2	TLR2	154845457	0.000000	0.05858	0.005000	0.12908	0.720000	0.41350	0.763000	0.26517	1.293000	0.44690	0.655000	0.94253	CGG		0.502	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			T	154626007	C	T	154626007	3	4	113	1	0	0	0	0	1	0	0	0	15990	759	27	1	1950	1	TLR2	4	154626007	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	25762731	154626007	36528269	88	30489										
FAT1	2195	hgsc.bcm.edu	37	chr4	187560893	187560893	+	Frame_Shift_Del	DEL	C	C	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tacctctaatatgtgttcatCttgctgttctcggtctagct							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:187560893delC	ENST00000441802.2	-	4	3834	c.3625delG	c.(3625-3627)gatfs	p.D1209fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1209	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATGTGTTCATCTTGCTGTTCT	0.323										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4											144	143	143					4																	187560893		1838	4097	5935	187797887	SO:0001589	frameshift_variant	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.3625delG	4.37:g.187560893delC	ENSP00000406229:p.Asp1209fs		187797887		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																				0.323	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187560893	C	-	187560893	7	5	113	1	0	1	0	1	0	0	0	0	5708	913	32	0	10237	0	FAT1	4	187560893	Frame_Shift_Del	DEL	C	TCGA-EI-6510-01A-11D-1733-10	32934886	187560893	3593383	89	30490										
FAT1	2195	hgsc.bcm.edu	37	chr4	187628149	187628149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggcttctaaccacatgatgaCggttccttctggaagatcct	9	11	2	3	rs377150532		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr4:187628149C>T	ENST00000441802.2	-	2	3042	c.2833G>A	c.(2833-2835)Gtc>Atc	p.V945I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	945	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CACATGATGACGGTTCCTTCT	0.448										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0			4						C	ILE/VAL	0,3856		0,0,1928	232	222	225		2833	-1.4	0.7	4		225	1,8283		0,1,4141	no	missense	FAT1	NM_005245.3	29	0,1,6069	TT,TC,CC		0.0121,0.0,0.0082	benign	945/4589	187628149	1,12139	1928	4142	6070	187865143	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2833G>A	4.37:g.187628149C>T	ENSP00000406229:p.Val945Ile		187865143		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	5.535	0.283562	0.10458	0.0	1.21E-4	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.51817	0.69	4.67	-1.35	0.09114	Cadherin (3);Cadherin-like (1);	0.299519	0.35495	N	0.003161	T	0.31734	0.0806	L	0.41415	1.275	0.43688	D	0.996131	B	0.15141	0.012	B	0.15484	0.013	T	0.13124	-1.0521	10	0.15499	T	0.54	.	10.5338	0.44992	0.0:0.4501:0.0:0.5499	.	945	Q14517	FAT1_HUMAN	I	945	ENSP00000406229:V945I	ENSP00000260147:V945I	V	-	1	0	FAT1	187865143	0.965000	0.33210	0.713000	0.30519	0.124000	0.20399	1.462000	0.35266	-0.135000	0.11495	-0.339000	0.08088	GTC		0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187628149	C	T	187628149	3	4	113	1	0	0	0	0	1	0	0	0	5708	536	19	1	11037	1	FAT1	4	187628149	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	67256	187628149	3526127	90	30491										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599862	3599862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcttgcccgggaccaaggctCgccgctggcagcagccgacg	14	16	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:3599862C>T	ENST00000302006.3	+	2	852	c.800C>T	c.(799-801)tCg>tTg	p.S267L	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	267					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GACCAAGGCTCGCCGCTGGCA	0.711																																																0			5											11	14	13					5																	3599862		2185	4283	6468	3652862	SO:0001583	missense	79192			U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.800C>T	5.37:g.3599862C>T	ENSP00000305244:p.Ser267Leu		3652862	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	37	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	3.892	-0.023880	0.07634	.	.	ENSG00000170549	ENST00000302006	T	0.59364	0.27	3.98	3.0	0.34707	.	1.005700	0.07985	N	0.986191	T	0.23727	0.0574	N	0.00926	-1.1	0.26542	N	0.974068	B	0.09022	0.002	B	0.04013	0.001	T	0.22977	-1.0201	10	0.21014	T	0.42	.	3.2582	0.06839	0.0:0.5933:0.0:0.4067	.	267	P78414	IRX1_HUMAN	L	267	ENSP00000305244:S267L	ENSP00000305244:S267L	S	+	2	0	IRX1	3652862	0.994000	0.37717	0.962000	0.40283	0.371000	0.29859	1.874000	0.39568	2.012000	0.59069	0.655000	0.94253	TCG		0.711	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		T	3599862	C	T	3599862	3	4	113	1	0	0	0	0	1	0	0	0	7864	893	31	1	806	1	IRX1	5	3599862	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10		3599862	177315398	91	30492										
LIX1	167410	hgsc.bcm.edu	37	chr5	96430636	96430636	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gggccattcgtagctcttgaGagacaattcctggtgagtcc	12	10	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:96430636G>A	ENST00000274382.4	-	6	960	c.665C>T	c.(664-666)tCt>tTt	p.S222F	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	222										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		TAGCTCTTGAGAGACAATTCC	0.473																																																0			5											101	106	104					5																	96430636		2203	4300	6503	96456392	SO:0001583	missense	167410				CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.665C>T	5.37:g.96430636G>A	ENSP00000274382:p.Ser222Phe		96456392	A8K4R9|Q8N7I2	Missense_Mutation	SNP	ENST00000274382.4	37	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.230003	0.79688	.	.	ENSG00000145721	ENST00000274382	T	0.48201	0.82	5.82	5.82	0.92795	.	0.101987	0.64402	D	0.000002	T	0.55000	0.1893	L	0.58101	1.795	0.53005	D	0.999963	P	0.39883	0.693	B	0.43783	0.431	T	0.57130	-0.7864	10	0.72032	D	0.01	-10.0461	19.6941	0.96016	0.0:0.0:1.0:0.0	.	222	Q8N485	LIX1_HUMAN	F	222	ENSP00000274382:S222F	ENSP00000274382:S222F	S	-	2	0	LIX1	96456392	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	3.459000	0.53021	2.752000	0.94435	0.655000	0.94253	TCT		0.473	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96430636	G	A	96430636	3	1	113	1	0	0	0	0	1	0	0	0	8855	942	33	3	187	3	LIX1	5	96430636	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	92830774	96430636	84484624	92	30493										
APC	324	hgsc.bcm.edu	37	chr5	112128184	112128188	+	Frame_Shift_Del	DEL	TCGTA	TCGTA	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	caaatcgaaaaggacatactTcgtatacgacagcttttaca					rs587779805|rs587780545		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	TCGTA	TCGTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:112128184_112128188delTCGTA	ENST00000457016.1	+	7	1067_1071	c.687_691delTCGTA	c.(685-693)cttcgtatafs	p.RI230fs	APC_ENST00000508376.2_Frame_Shift_Del_p.RI230fs|APC_ENST00000257430.4_Frame_Shift_Del_p.RI230fs			P25054	APC_HUMAN	adenomatous polyposis coli	230	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGGACATACTTCGTATACGACAGCT	0.302		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	0			5	GRCh37	CD023229	APC	D																																				112156087	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.687_691delTCGTA	5.37:g.112128184_112128188delTCGTA	ENSP00000413133:p.Arg230fs		112156083	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.302	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112128188	TCGTA	-	112128184	7	5	113	1	0	1	0	1	0	0	0	0	763	1770	62	0	709	0	APC	5	112128184	Frame_Shift_Del	DEL	TCGTA	TCGA-EI-6510-01A-11D-1733-10	15697548	112128184	68787076	93	30494										
APC	324	hgsc.bcm.edu	37	chr5	112173497	112173497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcatggcaaataggcctgcgAagtacaaggatgccaatatt	10	8	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:112173497A>G	ENST00000457016.1	+	16	2586	c.2206A>G	c.(2206-2208)Aag>Gag	p.K736E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.K736E|APC_ENST00000257430.4_Missense_Mutation_p.K736E			P25054	APC_HUMAN	adenomatous polyposis coli	736	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K736*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGGCCTGCGAAGTACAAGGA	0.433		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											75	66	69					5																	112173497		2202	4300	6502	112201396	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2206A>G	5.37:g.112173497A>G	ENSP00000413133:p.Lys736Glu		112201396	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.676730	0.47886	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	T;T;T;T;T	0.62639	0.01;0.97;0.01;0.01;0.97	6.17	5.0	0.66597	Armadillo-like helical (1);Armadillo-type fold (1);	0.150088	0.56097	D	0.000025	T	0.68183	0.2973	M	0.74881	2.28	0.48087	D	0.999588	P;P	0.47545	0.897;0.897	P;P	0.47075	0.536;0.536	T	0.70532	-0.4846	10	0.51188	T	0.08	-18.4837	13.612	0.62086	0.8705:0.1295:0.0:0.0	.	738;736	Q4LE70;P25054	.;APC_HUMAN	E	736;718;736;736;736	ENSP00000413133:K736E;ENSP00000423224:K718E;ENSP00000257430:K736E;ENSP00000427089:K736E;ENSP00000423828:K736E	ENSP00000257430:K736E	K	+	1	0	APC	112201396	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.576000	0.67437	1.123000	0.41961	0.533000	0.62120	AAG		0.433	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112173497	A	G	112173497	3	3	113	1	0	0	0	0	1	0	0	0	763	247	9	4	2264	4	APC	5	112173497	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	45313	112173497	68741763	94	30495										
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136328277	136328277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aggcaaggttccgcaactccTtgtctgtgcaggctagagaa	12	10	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:136328277T>C	ENST00000394945.1	-	7	771	c.602A>G	c.(601-603)aAg>aGg	p.K201R	SPOCK1_ENST00000282223.7_Missense_Mutation_p.K201R	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	201					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCGCAACTCCTTGTCTGTGCA	0.552																																																0			5											107	100	102					5																	136328277		2203	4300	6503	136356176	SO:0001583	missense	6695			AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.602A>G	5.37:g.136328277T>C	ENSP00000378401:p.Lys201Arg		136356176	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.255156	0.39896	.	.	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000510689	T;T;T	0.45668	0.89;0.89;0.92	5.89	5.89	0.94794	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.266401	0.37304	N	0.002153	T	0.22975	0.0555	N	0.12182	0.205	0.36891	D	0.889882	B	0.30634	0.288	B	0.26416	0.069	T	0.27938	-1.0059	10	0.24483	T	0.36	.	9.9004	0.41344	0.0:0.0754:0.0:0.9246	.	201	Q08629	TICN1_HUMAN	R	201;201;56	ENSP00000378401:K201R;ENSP00000282223:K201R;ENSP00000421677:K56R	ENSP00000282223:K201R	K	-	2	0	SPOCK1	136356176	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.901000	0.56303	2.254000	0.74563	0.533000	0.62120	AAG		0.552	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		C	136328277	T	C	136328277	3	2	113	1	0	0	0	0	1	0	0	0	15118	1609	56	4	737	4	SPOCK1	5	136328277	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	24154780	136328277	44586983	95	30496										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137726985	137726985	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgatgattcttctagtcgggActcattcaaacaaagccttg							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:137726985delA	ENST00000314358.5	+	8	1864	c.1664delA	c.(1663-1665)gacfs	p.D555fs	KDM3B_ENST00000394866.1_Frame_Shift_Del_p.D211fs|KDM3B_ENST00000542866.1_Intron	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	555					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						TCTAGTCGGGACTCATTCAAA	0.453																																																0			5											76	75	75					5																	137726985		2203	4300	6503	137754884	SO:0001589	frameshift_variant	51780			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.1664delA	5.37:g.137726985delA	ENSP00000326563:p.Asp555fs		137754884	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Frame_Shift_Del	DEL	ENST00000314358.5	37	CCDS34242.1																																																																																				0.453	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		-	137726985	A	-	137726985	7	5	113	1	0	1	0	1	0	0	0	0	8148	275	10	0	1694	0	KDM3B	5	137726985	Frame_Shift_Del	DEL	A	TCGA-EI-6510-01A-11D-1733-10	1398708	137726985	43188275	96	30497										
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138718225	138718225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtaccaaggtggcacgtcctCgatcttgtacaacatgtcaa	9	11	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:138718225C>T	ENST00000348729.3	-	2	152	c.106G>A	c.(106-108)Gag>Aag	p.E36K	SLC23A1_ENST00000503919.1_5'UTR|SLC23A1_ENST00000353963.3_Missense_Mutation_p.E36K	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	36					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	GGCACGTCCTCGATCTTGTAC	0.612																																																0			5											140	115	124					5																	138718225		2203	4300	6503	138746124	SO:0001583	missense	9963			AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.106G>A	5.37:g.138718225C>T	ENSP00000302701:p.Glu36Lys		138746124	O95191|Q8WWB6|Q9UGH4|Q9UI39	Missense_Mutation	SNP	ENST00000348729.3	37	CCDS4212.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223886	0.95139	.	.	ENSG00000170482	ENST00000353963;ENST00000348729;ENST00000339881;ENST00000453898;ENST00000508270	T;T	0.18657	2.21;2.2	4.68	4.68	0.58851	.	0.050461	0.85682	D	0.000000	T	0.24198	0.0586	N	0.08118	0	0.80722	D	1	D;D	0.61697	0.99;0.971	P;P	0.59761	0.863;0.576	T	0.29119	-1.0022	10	0.87932	D	0	-0.0446	16.5757	0.84637	0.0:1.0:0.0:0.0	.	36;36	Q9UHI7;Q9UHI7-2	S23A1_HUMAN;.	K	36;36;36;36;110	ENSP00000302851:E36K;ENSP00000302701:E36K	ENSP00000343584:E36K	E	-	1	0	SLC23A1	138746124	1.000000	0.71417	0.941000	0.38009	0.834000	0.47266	7.459000	0.80802	2.437000	0.82529	0.456000	0.33151	GAG		0.612	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		T	138718225	C	T	138718225	3	4	113	1	0	0	0	0	1	0	0	0	14499	893	31	1	1754	1	SLC23A1	5	138718225	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	991240	138718225	42197035	97	30498										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209489	140209489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acgccgactcaggctacaacGcgtggctttcgtatgagctg	12	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:140209489G>A	ENST00000529310.1	+	1	1927	c.1813G>A	c.(1813-1815)Gcg>Acg	p.A605T	PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	605	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCTACAACGCGTGGCTTTC	0.652																																																0			5											83	84	84					5																	140209489		2203	4300	6503	140189673	SO:0001583	missense	56142			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1813G>A	5.37:g.140209489G>A	ENSP00000433378:p.Ala605Thr		140189673	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.073736	0.55646	.	.	ENSG00000081842	ENST00000529310	T	0.40225	1.04	3.87	3.87	0.44632	Cadherin (4);Cadherin-like (1);	0.000000	0.36444	U	0.002584	T	0.72843	0.3511	H	0.95504	3.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.991;0.996	T	0.81590	-0.0863	10	0.87932	D	0	.	13.1052	0.59244	0.0:0.0:0.8393:0.1607	.	605;605	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	T	605	ENSP00000433378:A605T	ENSP00000433378:A605T	A	+	1	0	PCDHA6	140189673	0.999000	0.42202	1.000000	0.80357	0.194000	0.23727	5.654000	0.67974	2.158000	0.67659	0.306000	0.20318	GCG		0.652	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140209489	G	A	140209489	3	1	113	1	0	0	0	0	1	0	0	0	11559	1087	38	1	1815	1	PCDHA6	5	140209489	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	1491264	140209489	40705771	98	30499										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250875	140250875	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcggcaacgcccactgagggCgcgtgcgcgccggggaagcc	17	15	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:140250875C>T	ENST00000398640.2	+	1	2187	c.2187C>T	c.(2185-2187)ggC>ggT	p.G729G	PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	729					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACTGAGGGCGCGTGCGCGC	0.677																																																0			5											31	32	32					5																	140250875		2203	4299	6502	140231059	SO:0001819	synonymous_variant	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2187C>T	5.37:g.140250875C>T			140231059	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																				0.677	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140250875	C	T	140250875	2	4	113	1	0	0	0	0	0	0	0	1	11552	755	27	1		1	PCDHA11	5	140250875	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	41386	140250875	40664385	99	30500										
CCDC69	26112	hgsc.bcm.edu	37	chr5	150585026	150585026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtggctgttctggttctggtTcttggcgcttctggaagaaa	14	7	4	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:150585026T>C	ENST00000355417.2	-	2	233	c.59A>G	c.(58-60)gAa>gGa	p.E20G	CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	20										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTTCTGGTTCTTGGCGCTT	0.572																																																0			5											169	152	158					5																	150585026		2203	4300	6503	150565219	SO:0001583	missense	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.59A>G	5.37:g.150585026T>C	ENSP00000347586:p.Glu20Gly		150565219	A8K9X6	Missense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326242	0.41197	.	.	ENSG00000198624	ENST00000355417	T	0.24151	1.87	4.32	3.16	0.36331	.	1.077990	0.07209	N	0.858869	T	0.14013	0.0339	N	0.08118	0	0.21256	N	0.999746	B	0.34290	0.447	B	0.33254	0.16	T	0.24621	-1.0155	10	0.52906	T	0.07	-1.8048	6.2558	0.20874	0.0:0.1135:0.0:0.8865	.	20	A6NI79	CCD69_HUMAN	G	20	ENSP00000347586:E20G	ENSP00000347586:E20G	E	-	2	0	CCDC69	150565219	0.931000	0.31567	0.883000	0.34634	0.804000	0.45430	0.858000	0.27845	0.705000	0.31890	0.454000	0.30748	GAA		0.572	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		C	150585026	T	C	150585026	3	2	113	1	0	0	0	0	1	0	0	0	2847	1783	62	4	863	4	CCDC69	5	150585026	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	10334151	150585026	30330234	100	30501										
FAT2	2196	hgsc.bcm.edu	37	chr5	150921910	150921910	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcatccagggtctttagagtCgccaccagttcgccaggctc	11	14	1	1	rs374640362		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:150921910C>T	ENST00000261800.5	-	9	8790	c.8778G>A	c.(8776-8778)gcG>gcA	p.A2926A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2926	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A2926A(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTTTAGAGTCGCCACCAGTT	0.502																																																1	Substitution - coding silent(1)	lung(1)	5						C		0,4406		0,0,2203	149	145	146		8778	-1.5	0	5		146	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAT2	NM_001447.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		2926/4350	150921910	1,13005	2203	4300	6503	150902103	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.8778G>A	5.37:g.150921910C>T			150902103	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150921910	C	T	150921910	2	4	113	1	0	0	0	0	0	0	0	1	5709	871	31	1		1	FAT2	5	150921910	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	336884	150921910	29993350	101	30502										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590186	156590186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gctgtcttgggagagactggCggcccccgccatcgaggtgg	17	12	1	1	rs148867837		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:156590186C>T	ENST00000302938.4	-	2	1185	c.1090G>A	c.(1090-1092)Gcc>Acc	p.A364T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	364						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAGAGACTGGCGGCCCCCGCC	0.582																																																0			5											32	36	35					5																	156590186		2203	4300	6503	156522764	SO:0001583	missense	153745				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1090G>A	5.37:g.156590186C>T	ENSP00000305596:p.Ala364Thr		156522764	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.560909	0.00910	.	.	ENSG00000170613	ENST00000302938	T	0.03801	3.8	3.83	-7.65	0.01281	.	1.936930	0.02643	N	0.105505	T	0.02970	0.0088	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38866	-0.9641	10	0.15499	T	0.54	-0.1102	4.9439	0.13980	0.314:0.245:0.0:0.441	.	364	Q8TC56	FA71B_HUMAN	T	364	ENSP00000305596:A364T	ENSP00000305596:A364T	A	-	1	0	FAM71B	156522764	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.675000	0.01947	-2.565000	0.00471	-2.630000	0.00154	GCC		0.582	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156590186	C	T	156590186	3	4	113	1	0	0	0	0	1	0	0	0	5627	768	27	1	731	1	FAM71B	5	156590186	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5668276	156590186	24325074	102	30503										
DBN1	1627	hgsc.bcm.edu	37	chr5	176884466	176884466	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcgaagccctcctcctcttCtggaactgggtctgcatccc	8	17	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr5:176884466C>T	ENST00000309007.5	-	14	2137	c.1918G>A	c.(1918-1920)Gaa>Aaa	p.E640K	DBN1_ENST00000393563.4_Missense_Mutation_p.E372K|DBN1_ENST00000393565.1_Missense_Mutation_p.E686K|DBN1_ENST00000292385.5_Missense_Mutation_p.E642K|DBN1_ENST00000512501.1_3'UTR	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	640			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.E640Q(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			TCCTCCTCTTCTGGAACTGGG	0.617											OREG0016462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	breast(1)	5											141	123	129					5																	176884466		2203	4300	6503	176817072	SO:0001583	missense	1627				CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1918G>A	5.37:g.176884466C>T	ENSP00000308532:p.Glu640Lys	1934	176817072	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170877	0.57584	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000393563	D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57	4.75	3.88	0.44766	.	0.108327	0.64402	N	0.000009	D	0.89508	0.6735	L	0.27053	0.805	0.42732	D	0.993717	B;B;B	0.23891	0.093;0.006;0.01	B;B;B	0.23018	0.043;0.007;0.016	D	0.86838	0.2015	10	0.66056	D	0.02	-13.0301	11.8685	0.52507	0.0:0.9129:0.0:0.0871	.	590;640;642	B3KSQ7;Q16643;Q16643-2	.;DREB_HUMAN;.	K	640;642;686;372	ENSP00000308532:E640K;ENSP00000292385:E642K;ENSP00000377195:E686K;ENSP00000377193:E372K	ENSP00000292385:E642K	E	-	1	0	DBN1	176817072	0.991000	0.36638	0.789000	0.31954	0.961000	0.63080	3.003000	0.49505	1.216000	0.43427	0.561000	0.74099	GAA		0.617	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		T	176884466	C	T	176884466	3	4	113	1	0	0	0	0	1	0	0	0	4258	922	32	3	35	3	DBN1	5	176884466	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	20294280	176884466	4030794	103	30504										
SOX4	6659	hgsc.bcm.edu	37	chr6	21595968	21595968	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcgtcctccgacgacgagttCgaagacgacctgctcgacct	10	15	0	1	rs145209759	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:21595968C>T	ENST00000244745.1	+	1	1997	c.1203C>T	c.(1201-1203)ttC>ttT	p.F401F	SOX4_ENST00000543472.1_Silent_p.F401F	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	401					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.F401L(1)		kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			ACGACGAGTTCGAAGACGACC	0.657																																																1	Substitution - Missense(1)	lung(1)	6											24	20	21					6																	21595968		2202	4297	6499	21703947	SO:0001819	synonymous_variant	6659			AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"SRY (sex determining region Y)-boxes"	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.1203C>T	6.37:g.21595968C>T			21703947		Silent	SNP	ENST00000244745.1	37	CCDS4547.1																																																																																				0.657	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		T	21595968	C	T	21595968	2	4	113	1	0	0	0	0	0	0	0	1	14990	883	31	1		1	SOX4	6	21595968	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10		21595968	149519099	104	30505										
GPLD1	2822	hgsc.bcm.edu	37	chr6	24454269	24454269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gccttcaaggatcctgtgggCctccttgtccaggtccaggt	12	13	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:24454269C>T	ENST00000230036.1	-	14	1419	c.1309G>A	c.(1309-1311)Gcc>Acc	p.A437T		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	437					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						ATCCTGTGGGCCTCCTTGTCC	0.562																																																0			6											108	99	102					6																	24454269		2203	4300	6503	24562248	SO:0001583	missense	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1309G>A	6.37:g.24454269C>T	ENSP00000230036:p.Ala437Thr		24562248	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474024	0.63737	.	.	ENSG00000112293	ENST00000230036	T	0.71934	-0.61	5.44	4.55	0.56014	.	0.075012	0.56097	D	0.000037	T	0.77432	0.4129	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79512	-0.1773	10	0.49607	T	0.09	-19.5248	14.6277	0.68635	0.147:0.853:0.0:0.0	.	437	P80108	PHLD_HUMAN	T	437	ENSP00000230036:A437T	ENSP00000230036:A437T	A	-	1	0	GPLD1	24562248	1.000000	0.71417	0.995000	0.50966	0.446000	0.32137	3.241000	0.51376	1.371000	0.46172	0.655000	0.94253	GCC		0.562	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24454269	C	T	24454269	3	4	113	1	0	0	0	0	1	0	0	0	6634	739	26	3	1261	3	GPLD1	6	24454269	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2858301	24454269	146660798	105	30506										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28333754	28333754	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgtggcaaagcctttaggCgaagttcacatctcctgaga	11	9	2	1	rs149951499		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:28333754C>T	ENST00000377255.3	+	7	1606	c.1309C>T	c.(1309-1311)Cga>Tga	p.R437*	ZKSCAN3_ENST00000341464.5_Nonsense_Mutation_p.R289*|ZKSCAN3_ENST00000252211.2_Nonsense_Mutation_p.R437*	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	437				R -> D (in Ref. 6; AAB16813). {ECO:0000305}.	autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						AGCCTTTAGGCGAAGTTCACA	0.507													C|||	1	0.000199681	0	0.0014	5008	,	,		20755	0		0	False		,,,				2504	0															0			6						C	stop/ARG,stop/ARG,stop/ARG	1,4405		0,1,2202	75	76	76		1309,865,1309	3.1	1	6	dbSNP_134	76	0,8600		0,0,4300	yes	stop-gained,stop-gained,stop-gained	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	437/539,289/391,437/539	28333754	1,13005	2203	4300	6503	28441733	SO:0001587	stop_gained	80317			U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1309C>T	6.37:g.28333754C>T	ENSP00000366465:p.Arg437*		28441733	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Nonsense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	35	5.538910	0.96474	2.27E-4	0.0	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	.	.	.	3.97	3.1	0.35709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9458	0.29985	0.0:0.7978:0.0:0.2022	.	.	.	.	X	437;289;437	.	ENSP00000252211:R437X	R	+	1	2	ZKSCAN3	28441733	0.000000	0.05858	0.999000	0.59377	0.984000	0.73092	-0.076000	0.11412	0.883000	0.36040	0.655000	0.94253	CGA		0.507	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		T	28333754	C	T	28333754	4	4	113	1	0	0	0	0	0	1	0	0	17727	760	27	1	1327	1	ZKSCAN3	6	28333754	Nonsense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	3879485	28333754	142781313	106	30507										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29589553	29589553	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	caaaaaactttccgggcttcAgtctcatagaaaagtcccac	6	12	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:29589553A>G	ENST00000377034.4	-	10	1442	c.1107T>C	c.(1105-1107)acT>acC	p.T369T	GABBR1_ENST00000377016.4_Silent_p.T307T|GABBR1_ENST00000355973.3_Silent_p.T252T|GABBR1_ENST00000377012.4_Silent_p.T252T|GABBR1_ENST00000376977.3_Silent_p.T369T	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	369					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.T369T(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	TCCGGGCTTCAGTCTCATAGA	0.547																																																1	Substitution - coding silent(1)	ovary(1)	6											62	66	65					6																	29589553		2203	4300	6503	29697532	SO:0001819	synonymous_variant	10537			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1107T>C	6.37:g.29589553A>G			29697532	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																				0.547	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			G	29589553	A	G	29589553	2	3	113	1	0	0	0	0	0	0	0	1	6174	175	7	4		4	GABBR1	6	29589553	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	1255799	29589553	141525514	107	30508										
STK38	11329	hgsc.bcm.edu	37	chr6	36466221	36466221	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctttccagttcatcaccttcTtatatgtctcttgaggggtc	7	11	4	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:36466221T>A	ENST00000229812.7	-	11	1280	c.995A>T	c.(994-996)aAg>aTg	p.K332M		NM_007271.2	NP_009202.1			serine/threonine kinase 38									p.K332T(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CATCACCTTCTTATATGTCTC	0.418																																					Colon(180;997 3561 16158)											1	Substitution - Missense(1)	ovary(1)	6											104	105	104					6																	36466221		2203	4300	6503	36574199	SO:0001583	missense	11329				CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.995A>T	6.37:g.36466221T>A	ENSP00000229812:p.Lys332Met		36574199		Missense_Mutation	SNP	ENST00000229812.7	37	CCDS4822.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.070721	0.76301	.	.	ENSG00000112079	ENST00000229812	T	0.46063	0.88	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042888	0.85682	D	0.000000	T	0.42877	0.1222	L	0.41632	1.29	0.53005	D	0.99996	D	0.58970	0.984	P	0.57548	0.823	T	0.44467	-0.9326	10	0.87932	D	0	.	16.3469	0.83138	0.0:0.0:0.0:1.0	.	332	Q15208	STK38_HUMAN	M	332	ENSP00000229812:K332M	ENSP00000229812:K332M	K	-	2	0	STK38	36574199	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.663000	0.68038	2.263000	0.75096	0.528000	0.53228	AAG		0.418	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		A	36466221	T	A	36466221	3	1	113	1	0	0	0	0	1	0	0	0	15342	1609	56	5	418	5	STK38	6	36466221	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	6876668	36466221	134648846	108	30509										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38702322	38702322	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtatatagacaatgcagcccCggataaactaaaaggactgt	9	8	0	1	rs370991185		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:38702322C>T	ENST00000359357.3	+	3	286	c.32C>T	c.(31-33)cCg>cTg	p.P11L	DNAH8_ENST00000449981.2_Missense_Mutation_p.P228L|DNAH8_ENST00000441566.1_Missense_Mutation_p.P11L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	11					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AATGCAGCCCCGGATAAACTA	0.353																																																0			6						C	LEU/PRO	0,4406		0,0,2203	145	153	150		683	5	0.9	6		150	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH8	NM_001206927.1	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	228/4708	38702322	1,13005	2203	4300	6503	38810300	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.32C>T	6.37:g.38702322C>T	ENSP00000352312:p.Pro11Leu		38810300	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	C	12.56	1.973461	0.34848	0.0	1.16E-4	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.24350	1.89;1.89;1.86	5.86	5.0	0.66597	.	0.065949	0.64402	D	0.000007	T	0.12008	0.0292	L	0.39898	1.24	0.53005	D	0.999962	B	0.12630	0.006	B	0.10450	0.005	T	0.03335	-1.1047	10	0.56958	D	0.05	.	13.501	0.61454	0.0:0.9277:0.0:0.0723	.	11	Q96JB1	DYH8_HUMAN	L	216;216;11;11	ENSP00000333363:P216L;ENSP00000352312:P11L;ENSP00000402294:P11L	ENSP00000333363:P216L	P	+	2	0	DNAH8	38810300	0.456000	0.25744	0.885000	0.34714	0.594000	0.36715	3.984000	0.56923	1.488000	0.48433	0.585000	0.79938	CCG		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38702322	C	T	38702322	3	4	113	1	0	0	0	0	1	0	0	0	4618	652	23	1	34	1	DNAH8	6	38702322	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2236101	38702322	132412745	109	30510										
PRPH2	5961	hgsc.bcm.edu	37	chr6	42689612	42689612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tctgcagcatgtcgatggtcTtcttcatgaaacacctgcca	8	12	4	1	rs61755786		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:42689612T>C	ENST00000230381.5	-	1	700	c.461A>G	c.(460-462)aAg>aGg	p.K154R		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	154					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			GTCGATGGTCTTCTTCATGAA	0.542																																																0			6											119	105	110					6																	42689612		2203	4300	6503	42797590	SO:0001583	missense	5961				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.461A>G	6.37:g.42689612T>C	ENSP00000230381:p.Lys154Arg		42797590	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	T	8.112	0.779109	0.16120	.	.	ENSG00000112619	ENST00000230381	T	0.78816	-1.21	5.78	5.78	0.91487	Tetraspanin, EC2 domain (1);	0.042558	0.85682	D	0.000000	T	0.41166	0.1147	N	0.04686	-0.185	0.43874	D	0.996483	B	0.02656	0.0	B	0.11329	0.006	T	0.47195	-0.9136	10	0.09084	T	0.74	.	16.3979	0.83621	0.0:0.0:0.0:1.0	.	154	P23942	PRPH2_HUMAN	R	154	ENSP00000230381:K154R	ENSP00000230381:K154R	K	-	2	0	PRPH2	42797590	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.331000	0.52075	2.333000	0.79357	0.533000	0.62120	AAG		0.542	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		C	42689612	T	C	42689612	3	2	113	1	0	0	0	0	1	0	0	0	12611	1609	56	4	591	4	PRPH2	6	42689612	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	3987290	42689612	128425455	110	30511										
GPR116	221395	hgsc.bcm.edu	37	chr6	46832857	46832857	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaagtgacaacacacatcaaCagtttttgaacaccaggaaa	6	9	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:46832857C>A	ENST00000283296.7	-	14	2200	c.1912G>T	c.(1912-1914)Gtt>Ttt	p.V638F	GPR116_ENST00000545669.1_Missense_Mutation_p.V67F|GPR116_ENST00000265417.7_Missense_Mutation_p.V638F|GPR116_ENST00000456426.2_Missense_Mutation_p.V496F|GPR116_ENST00000362015.4_Missense_Mutation_p.V638F	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	638					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CACACATCAACAGTTTTTGAA	0.358																																					NSCLC(59;410 1274 8751 36715 50546)											0			6											214	187	196					6																	46832857		2203	4300	6503	46940816	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1912G>T	6.37:g.46832857C>A	ENSP00000283296:p.Val638Phe		46940816	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	2.135	-0.398189	0.04865	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417;ENST00000545669	T;T;T;T;T	0.27256	1.71;2.08;1.72;1.71;1.68	5.91	-2.83	0.05769	.	1.301620	0.05099	N	0.486766	T	0.08358	0.0208	L	0.50333	1.59	0.09310	N	1	B;B;B;B;B	0.26081	0.113;0.009;0.009;0.141;0.009	B;B;B;B;B	0.23716	0.027;0.005;0.004;0.048;0.004	T	0.38478	-0.9659	10	0.40728	T	0.16	-0.9488	6.9102	0.24331	0.0:0.1862:0.3592:0.4546	.	67;193;638;496;638	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	F	638;638;638;496;638;67	ENSP00000283296:V638F;ENSP00000354563:V638F;ENSP00000412866:V496F;ENSP00000265417:V638F;ENSP00000441581:V67F	ENSP00000265417:V638F	V	-	1	0	GPR116	46940816	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.902000	0.04088	-0.629000	0.05575	-0.163000	0.13421	GTT		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46832857	C	A	46832857	3	1	113	1	0	0	0	0	1	0	0	0	6653	478	17	2	2160	2	GPR116	6	46832857	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	4143245	46832857	124282210	111	30512										
EYS	346007	hgsc.bcm.edu	37	chr6	65612337	65612337	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcacagtcaccataatcctGgcaggaaaggaagaggcagt	11	9	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:65612337G>A	ENST00000370621.3	-	17	3224	c.2698C>T	c.(2698-2700)Cag>Tag	p.Q900*	EYS_ENST00000503581.1_Nonsense_Mutation_p.Q900*|EYS_ENST00000370616.2_Nonsense_Mutation_p.Q900*			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	900	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCATAATCCTGGCAGGAAAGG	0.353																																																0			6											157	129	138					6																	65612337		692	1590	2282	65669058	SO:0001587	stop_gained	346007				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2698C>T	6.37:g.65612337G>A	ENSP00000359655:p.Gln900*		65669058	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Nonsense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	G	38	6.731848	0.97796	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	.	.	.	4.36	3.47	0.39725	.	0.931884	0.08711	N	0.904966	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	10.739	0.46141	0.0:0.0:0.6562:0.3438	.	.	.	.	X	900	.	ENSP00000359650:Q900X	Q	-	1	0	EYS	65669058	1.000000	0.71417	0.754000	0.31244	0.467000	0.32768	2.087000	0.41653	0.924000	0.37069	0.591000	0.81541	CAG		0.353	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65612337	G	A	65612337	4	1	113	1	0	0	0	0	0	1	0	0	5345	1357	47	3	6689	3	EYS	6	65612337	Nonsense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	18779480	65612337	105502730	112	30513										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102124516	102124516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aggtctcattcgtttgcaagAgctcatcaaagctccatcaa	7	11	4	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:102124516A>G	ENST00000421544.1	+	4	1050	c.560A>G	c.(559-561)gAg>gGg	p.E187G	GRIK2_ENST00000413795.1_Missense_Mutation_p.E187G|GRIK2_ENST00000369138.1_Missense_Mutation_p.E187G|GRIK2_ENST00000358361.3_Missense_Mutation_p.E187G|GRIK2_ENST00000369137.3_Missense_Mutation_p.E187G|GRIK2_ENST00000369134.4_Missense_Mutation_p.E138G|GRIK2_ENST00000318991.6_Missense_Mutation_p.E187G	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	187			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CGTTTGCAAGAGCTCATCAAA	0.318																																																0			6											50	49	49					6																	102124516		2203	4299	6502	102231209	SO:0001583	missense	2901				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.560A>G	6.37:g.102124516A>G	ENSP00000397026:p.Glu187Gly		102231209	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820196	0.71028	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076	D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.64	5.64	0.86602	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.86623	0.5977	M	0.72894	2.215	0.58432	D	0.999992	B;B;B	0.25272	0.1;0.122;0.1	B;B;B	0.43916	0.309;0.436;0.309	D	0.86517	0.1813	10	0.59425	D	0.04	.	15.9105	0.79470	1.0:0.0:0.0:0.0	.	187;187;187	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	G	187;187;187;187;187;187;187;138;149	ENSP00000397026:E187G;ENSP00000405596:E187G;ENSP00000358134:E187G;ENSP00000351128:E187G;ENSP00000358133:E187G;ENSP00000313276:E187G;ENSP00000358130:E138G	ENSP00000313276:E187G	E	+	2	0	GRIK2	102231209	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.334000	0.96470	2.175000	0.68902	0.473000	0.43528	GAG		0.318	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102124516	A	G	102124516	3	3	113	1	0	0	0	0	1	0	0	0	6795	304	11	4	574	4	GRIK2	6	102124516	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	36512179	102124516	68990551	113	30514										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112443320	112443320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tctagggctgttggaaaggtGgcaatgagagtttcttggag	16	4	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:112443320G>A	ENST00000230538.7	-	32	4769	c.4372C>T	c.(4372-4374)Cac>Tac	p.H1458Y	LAMA4_ENST00000424408.2_Missense_Mutation_p.H1451Y|LAMA4_ENST00000522006.1_Missense_Mutation_p.H1451Y|LAMA4_ENST00000389463.4_Missense_Mutation_p.H1451Y	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1458					blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		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)		TTGGAAAGGTGGCAATGAGAG	0.458																																																0			6											163	153	156					6																	112443320		2203	4300	6503	112550013	SO:0001583	missense	3910				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.4372C>T	6.37:g.112443320G>A	ENSP00000230538:p.His1458Tyr		112550013	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	G	8.278	0.815002	0.16607	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.16897	2.31;2.31;2.31;2.31	5.62	5.62	0.85841	.	0.482261	0.25388	N	0.031038	T	0.03136	0.0092	N	0.12182	0.205	0.80722	D	1	B;B	0.29766	0.167;0.256	B;B	0.30855	0.057;0.121	T	0.12889	-1.0530	10	0.02654	T	1	.	12.6205	0.56600	0.0762:0.0:0.9238:0.0	.	1458;1451	Q16363;Q16363-2	LAMA4_HUMAN;.	Y	1458;1451;1451;1451	ENSP00000230538:H1458Y;ENSP00000429488:H1451Y;ENSP00000374114:H1451Y;ENSP00000416470:H1451Y	ENSP00000230538:H1458Y	H	-	1	0	LAMA4	112550013	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.737000	0.55060	2.644000	0.89710	0.561000	0.74099	CAC		0.458	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112443320	G	A	112443320	3	1	113	1	0	0	0	0	1	0	0	0	8630	1348	47	3	1131	3	LAMA4	6	112443320	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	10318804	112443320	58671747	114	30515										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129802422	129802422	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcacagaatgtttacacagtTagctttcctaagcctggttt	7	9	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:129802422T>C	ENST00000421865.2	+	55	7636	c.7587T>C	c.(7585-7587)gtT>gtC	p.V2529V	RP1-69D17.3_ENST00000442449.1_RNA	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2529	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTTACACAGTTAGCTTTCCTA	0.413																																																0			6											129	121	124					6																	129802422		2203	4300	6503	129844115	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7587T>C	6.37:g.129802422T>C			129844115	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.413	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129802422	T	C	129802422	2	2	113	1	0	0	0	0	0	0	0	1	8628	1741	61	4		4	LAMA2	6	129802422	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	17359102	129802422	41312645	115	30516										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152708320	152708320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctggacttcgcaattagacGgtgaagggctctcgtgtgat	13	9	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr6:152708320G>A	ENST00000367255.5	-	54	8975	c.8374C>T	c.(8374-8376)Cgt>Tgt	p.R2792C	SYNE1_ENST00000423061.1_Missense_Mutation_p.R2799C|SYNE1_ENST00000448038.1_Missense_Mutation_p.R2799C|SYNE1_ENST00000341594.5_Missense_Mutation_p.R2831C|SYNE1_ENST00000265368.4_Missense_Mutation_p.R2792C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2792					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R2792S(2)|p.R2799S(1)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCAATTAGACGGTGAAGGGCT	0.483										HNSCC(10;0.0054)																																						3	Substitution - Missense(3)	lung(3)	6											208	183	191					6																	152708320		2203	4300	6503	152750013	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.8374C>T	6.37:g.152708320G>A	ENSP00000356224:p.Arg2792Cys		152750013	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	2.642	-0.283986	0.05642	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.58	1.23	0.21249	.	0.979395	0.08364	N	0.957153	T	0.11836	0.0288	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.14805	0.004;0.004;0.004;0.011	B;B;B;B	0.09377	0.002;0.001;0.001;0.004	T	0.35025	-0.9805	10	0.40728	T	0.16	.	7.5023	0.27524	0.0641:0.1014:0.6079:0.2265	.	2775;2792;2792;2799	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	C	2792;2799;2792;2799;2831	ENSP00000356224:R2792C;ENSP00000396024:R2799C;ENSP00000265368:R2792C;ENSP00000390975:R2799C;ENSP00000341887:R2831C	ENSP00000265368:R2792C	R	-	1	0	SYNE1	152750013	0.019000	0.18553	0.001000	0.08648	0.016000	0.09150	1.681000	0.37618	0.292000	0.22492	-0.140000	0.14226	CGT		0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152708320	G	A	152708320	3	1	113	1	0	0	0	0	1	0	0	0	15484	1116	39	1	18464	1	SYNE1	6	152708320	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	22905898	152708320	18406747	116	30517										
CYTH3	9265	hgsc.bcm.edu	37	chr7	6230096	6230096	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttacctcaatgtcatcaataAgttccttttttcttcgacga	4	10	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:6230096A>C	ENST00000350796.3	-	2	237	c.101T>G	c.(100-102)cTt>cGt	p.L34R		NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	34					establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						GTCATCAATAAGTTCCTTTTT	0.299																																																0			7											35	26	29					7																	6230096		2131	4133	6264	6196621	SO:0001583	missense	9265			AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"Pleckstrin homology (PH) domain containing"	9504	protein-coding gene	gene with protein product		605081	"pleckstrin homology, Sec7 and coiled-coil domains 3"	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.101T>G	7.37:g.6230096A>C	ENSP00000297044:p.Leu34Arg		6196621	A4D2N8	Missense_Mutation	SNP	ENST00000350796.3	37	CCDS5346.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400879	0.83120	.	.	ENSG00000008256	ENST00000350796	T	0.18810	2.19	5.64	5.64	0.86602	.	0.056820	0.64402	N	0.000001	T	0.47340	0.1440	M	0.74467	2.265	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.49854	-0.8895	10	0.87932	D	0	.	14.8465	0.70264	1.0:0.0:0.0:0.0	.	34	O43739-2	.	R	34	ENSP00000297044:L34R	ENSP00000297044:L34R	L	-	2	0	CYTH3	6196621	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.980000	0.88113	2.162000	0.67917	0.455000	0.32223	CTT		0.299	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227		C	6230096	A	C	6230096	3	2	113	1	0	0	0	0	1	0	0	0	4211	72	3	4	1146	4	CYTH3	7	6230096	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10		6230096	152908567	117	30518										
GPR141	353345	hgsc.bcm.edu	37	chr7	37780910	37780910	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggaattgtgttttgtgccgTtagccacaaactacagtatt	9	7	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:37780910T>C	ENST00000447769.1	+	4	1204	c.915T>C	c.(913-915)cgT>cgC	p.R305R	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Silent_p.R305R			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTTGTGCCGTTAGCCACAAA	0.358																																																0			7											58	56	57					7																	37780910		2203	4300	6503	37747435	SO:0001819	synonymous_variant	353345			AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"GPCR / Class A : Orphans"	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.915T>C	7.37:g.37780910T>C			37747435	A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	37	CCDS5451.1																																																																																				0.358	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		C	37780910	T	C	37780910	2	2	113	1	0	0	0	0	0	0	0	1	6669	1712	60	4		4	GPR141	7	37780910	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	31550814	37780910	121357753	118	30519										
HECW1	23072	hgsc.bcm.edu	37	chr7	43581521	43581521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgaggaattccaccagagttTgcagtggatgaaggacaaca	12	7	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:43581521T>C	ENST00000395891.2	+	26	4777	c.4172T>C	c.(4171-4173)tTg>tCg	p.L1391S	HECW1_ENST00000453890.1_Missense_Mutation_p.L1357S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1391	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CACCAGAGTTTGCAGTGGATG	0.438																																																0			7											172	155	160					7																	43581521		1886	4137	6023	43548046	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4172T>C	7.37:g.43581521T>C	ENSP00000379228:p.Leu1391Ser		43548046	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.0|27.0	4.793619|4.793619	0.90453|0.90453	.|.	.|.	ENSG00000002746|ENSG00000002746	ENST00000429529|ENST00000395891;ENST00000453890;ENST00000265522	.|T;T	.|0.69040	.|-0.37;-0.37	5.95|5.95	5.95|5.95	0.96441|0.96441	.|HECT (4);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88202|0.88202	0.6373|0.6373	H|H	0.97077|0.97077	3.935|3.935	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.92040|0.92040	0.5640|0.5640	5|10	.|0.87932	.|D	.|0	.|.	16.4069|16.4069	0.83677|0.83677	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1357;1391	.|B4DH42;Q76N89	.|.;HECW1_HUMAN	R|S	115|1391;1357;1391	.|ENSP00000379228:L1391S;ENSP00000407774:L1357S	.|ENSP00000265522:L1391S	C|L	+|+	1|2	0|0	HECW1|HECW1	43548046|43548046	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	7.691000|7.691000	0.84191|0.84191	2.272000|2.272000	0.75746|0.75746	0.460000|0.460000	0.39030|0.39030	TGC|TTG		0.438	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		C	43581521	T	C	43581521	3	2	113	1	0	0	0	0	1	0	0	0	7063	1821	63	4	4266	4	HECW1	7	43581521	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	5800611	43581521	115557142	119	30520										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70597883	70597883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggccaagtgccggcccatcgCggtgcgcagcggagacgcct	16	15	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:70597883C>T	ENST00000333538.5	+	1	729	c.95C>T	c.(94-96)gCg>gTg	p.A32V		NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	32					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CGGCCCATCGCGGTGCGCAGC	0.637																																																0			7											47	43	44					7																	70597883		2203	4297	6500	70235819	SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.95C>T	7.37:g.70597883C>T	ENSP00000329654:p.Ala32Val		70235819	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720381	0.48728	.	.	ENSG00000185274	ENST00000333538	T	0.55413	0.52	4.85	4.85	0.62838	.	0.689293	0.12343	N	0.477303	T	0.35913	0.0948	N	0.08118	0	0.33768	D	0.622742	B	0.22003	0.063	B	0.14578	0.011	T	0.37502	-0.9703	10	0.30854	T	0.27	.	17.1215	0.86702	0.0:1.0:0.0:0.0	.	32	Q6IS24	GLTL3_HUMAN	V	32	ENSP00000329654:A32V	ENSP00000329654:A32V	A	+	2	0	WBSCR17	70235819	0.987000	0.35691	0.998000	0.56505	0.981000	0.71138	4.290000	0.59019	2.512000	0.84698	0.563000	0.77884	GCG		0.637	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	70597883	C	T	70597883	3	4	113	1	0	0	0	0	1	0	0	0	17304	768	27	1	97	1	WBSCR17	7	70597883	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	27016362	70597883	88540780	120	30521										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72891396	72891396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atttttggcttccatttcttTccgtttctgtttctctgctc	5	11	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:72891396T>C	ENST00000339594.4	-	7	2733	c.2395A>G	c.(2395-2397)Aaa>Gaa	p.K799E	BAZ1B_ENST00000404251.1_Missense_Mutation_p.K799E	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	799					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				tccatttctttccgtttctgt	0.403																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											0			7											85	79	81					7																	72891396		2203	4300	6503	72529332	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2395A>G	7.37:g.72891396T>C	ENSP00000342434:p.Lys799Glu		72529332	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.002956	0.54254	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.63096	-0.02;-0.02	5.7	4.48	0.54585	.	0.042265	0.85682	D	0.000000	T	0.53400	0.1794	M	0.66939	2.045	0.40587	D	0.981459	P	0.42871	0.792	B	0.35182	0.197	T	0.59768	-0.7392	10	0.46703	T	0.11	-25.6355	7.7886	0.29106	0.0:0.0746:0.1402:0.7852	.	799	Q9UIG0	BAZ1B_HUMAN	E	799	ENSP00000342434:K799E;ENSP00000385442:K799E	ENSP00000342434:K799E	K	-	1	0	BAZ1B	72529332	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.863000	0.69568	2.182000	0.69389	0.402000	0.26972	AAA		0.403	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72891396	T	C	72891396	3	2	113	1	0	0	0	0	1	0	0	0	1331	1792	62	4	2108	4	BAZ1B	7	72891396	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2293513	72891396	86247267	121	30522										
BCL7B	9275	hgsc.bcm.edu	37	chr7	72966511	72966511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acttacctccttgctgtctgTcacaggaacccacttaaata	5	13	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:72966511T>C	ENST00000223368.2	-	2	577	c.154A>G	c.(154-156)Aca>Gca	p.T52A	BCL7B_ENST00000482231.1_5'UTR|BCL7B_ENST00000411832.1_Missense_Mutation_p.T52A	NM_001707.3	NP_001698.2	Q9BQE9	BCL7B_HUMAN	B-cell CLL/lymphoma 7B	52							actin binding (GO:0003779)	p.T52S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	9		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTGCTGTCTGTCACAGGAACC	0.388																																																1	Substitution - Missense(1)	ovary(1)	7											112	110	110					7																	72966511		2203	4300	6503	72604447	SO:0001583	missense	9275			X89985	CCDS5550.1, CCDS56489.1, CCDS75613.1	7q11.23	2008-07-18			ENSG00000106635	ENSG00000106635			1005	protein-coding gene	gene with protein product		605846				8605326, 9806765	Standard	NM_001707		Approved		uc003tyf.2	Q9BQE9	OTTHUMG00000023412	ENST00000223368.2:c.154A>G	7.37:g.72966511T>C	ENSP00000223368:p.Thr52Ala		72604447	A8K226|C9JWD3|D3DXF0|O43769|Q13845|Q6ZW75	Missense_Mutation	SNP	ENST00000223368.2	37	CCDS5550.1	.	.	.	.	.	.	.	.	.	.	t	13.65	2.299541	0.40694	.	.	ENSG00000106635	ENST00000223368;ENST00000411832	T	0.44881	0.91	4.83	3.65	0.41850	.	0.234553	0.41294	D	0.000914	T	0.24470	0.0593	N	0.14661	0.345	0.29734	N	0.83767	B;B	0.14805	0.011;0.0	B;B	0.18561	0.022;0.003	T	0.11299	-1.0593	10	0.39692	T	0.17	.	9.1027	0.36678	0.0:0.0947:0.0:0.9053	.	52;52	C9JWD3;Q9BQE9	.;BCL7B_HUMAN	A	52	ENSP00000223368:T52A	ENSP00000223368:T52A	T	-	1	0	BCL7B	72604447	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	1.691000	0.37721	1.925000	0.55765	0.378000	0.23410	ACA		0.388	BCL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252194.1	NM_001707		C	72966511	T	C	72966511	3	2	113	1	0	0	0	0	1	0	0	0	1380	1667	58	4	474	4	BCL7B	7	72966511	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	75115	72966511	86172152	122	30523										
GTF2IRD1	9569	hgsc.bcm.edu	37	chr7	73944105	73944105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acatggtccccgtgccctacCggaagattgcctgtgacccg	11	15	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:73944105C>T	ENST00000265755.3	+	9	1525	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.R410W|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.R378W	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	378				R -> Q (in Ref. 5; AAF21796). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R378W(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGTGCCCTACCGGAAGATTGC	0.607																																																1	Substitution - Missense(1)	ovary(1)	7											69	59	62					7																	73944105		2203	4300	6503	73582041	SO:0001583	missense	9569			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1132C>T	7.37:g.73944105C>T	ENSP00000265755:p.Arg378Trp		73582041	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	c	19.69	3.873889	0.72180	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.46	-2.05	0.07321	.	0.000000	0.85682	D	0.000000	T	0.46927	0.1418	N	0.19112	0.55	0.52501	D	0.999952	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.993;0.957;0.996;0.974	T	0.52245	-0.8601	10	0.87932	D	0	-25.9307	17.2233	0.86963	0.259:0.7409:0.0:0.0	.	410;378;378;378	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	W	378;410;378;378	ENSP00000265755:R378W;ENSP00000397566:R410W;ENSP00000408477:R378W;ENSP00000418383:R378W	ENSP00000265755:R378W	R	+	1	2	GTF2IRD1	73582041	1.000000	0.71417	0.996000	0.52242	0.862000	0.49288	2.453000	0.44970	-0.142000	0.11354	-0.535000	0.04281	CGG		0.607	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		T	73944105	C	T	73944105	3	4	113	1	0	0	0	0	1	0	0	0	6889	643	23	1	1162	1	GTF2IRD1	7	73944105	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	977594	73944105	85194558	123	30524										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81596485	81596485	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	attttaaatagttttcttacGtcactgtttcttttgcagtc	5	7	3	0	rs142390338	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:81596485G>A	ENST00000356253.5	-	31	2793	c.2538C>T	c.(2536-2538)gaC>gaT	p.D846D	CACNA2D1_ENST00000356860.3_Splice_Site_p.D834D|CACNA2D1_ENST00000535308.1_Splice_Site_p.D46D			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	846					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTTTTCTTACGTCACTGTTTC	0.294													g|||	9	0.00179712	0	0	5008	,	,		13957	0.0089		0	False		,,,				2504	0															0			7						G		0,4402		0,0,2201	73	71	72		2502	1.3	1	7	dbSNP_134	72	1,8589	1.2+/-3.3	0,1,4294	yes	coding-synonymous-near-splice	CACNA2D1	NM_000722.2		0,1,6495	AA,AG,GG		0.0116,0.0,0.0077		834/1092	81596485	1,12991	2201	4295	6496	81434421	SO:0001630	splice_region_variant	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2538+1C>T	7.37:g.81596485G>A			81434421	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																					0.294	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			Silent	A	81596485	G	A	81596485	5	1	113	1	0	0	0	0	0	0	1	0	2554	1159	40	1	809	1	CACNA2D1	7	81596485	Splice_Site	SNP	G	TCGA-EI-6510-01A-11D-1733-10	7652380	81596485	77542178	124	30525										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87092143	87092143	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tccaaatactatcatcatgaGggggagacctgatccgtgag	11	9	2	4	rs8187788	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:87092143G>A	ENST00000265723.4	-	4	328	c.217C>T	c.(217-219)Ctc>Ttc	p.L73F	ABCB4_ENST00000545634.1_Missense_Mutation_p.L73F|ABCB4_ENST00000453593.1_Missense_Mutation_p.L73F|ABCB4_ENST00000358400.3_Missense_Mutation_p.L73F|ABCB4_ENST00000359206.3_Missense_Mutation_p.L73F	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	73	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	ATCATCATGAGGGGGAGACCT	0.388																																																0			7											97	88	91					7																	87092143		2203	4300	6503	86930079	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.217C>T	7.37:g.87092143G>A	ENSP00000265723:p.Leu73Phe		86930079	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706364	0.48412	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72	5.45	3.65	0.41850	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.073720	0.64402	D	0.000009	D	0.92303	0.7558	M	0.64080	1.96	0.58432	D	0.999999	B;B;D;D	0.54397	0.211;0.226;0.958;0.966	B;B;P;P	0.61132	0.079;0.117;0.816;0.884	D	0.90709	0.4626	10	0.54805	T	0.06	-11.3351	8.4984	0.33144	0.1353:0.0:0.7388:0.1259	.	73;73;73;73	Q6PJ81;A4D1D5;P21439-2;P21439	.;.;.;MDR3_HUMAN	F	73	ENSP00000352135:L73F;ENSP00000351172:L73F;ENSP00000265723:L73F;ENSP00000392983:L73F;ENSP00000437465:L73F	ENSP00000265723:L73F	L	-	1	0	ABCB4	86930079	0.072000	0.21174	0.997000	0.53966	0.591000	0.36615	0.047000	0.14056	0.687000	0.31509	-0.824000	0.03097	CTC		0.388	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		A	87092143	G	A	87092143	3	1	113	1	0	0	0	0	1	0	0	0	43	1000	35	3	3743	3	ABCB4	7	87092143	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5495658	87092143	72046520	125	30526										
BAIAP2L1	55971	hgsc.bcm.edu	37	chr7	97933535	97933552	+	In_Frame_Del	DEL	TGGGGCCTTAAAGGTGGA	TGGGGCCTTAAAGGTGGA	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcggtctcgggcttggacgcTggggccttaaaggtggatgt					rs2269966|rs528998595	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	TGGGGCCTTAAAGGTGGA	TGGGGCCTTAAAGGTGGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:97933535_97933552delTGGGGCCTTAAAGGTGGA	ENST00000005260.8	-	12	1593_1610	c.1378_1395delTCCACCTTTAAGGCCCCA	c.(1378-1395)tccacctttaaggccccadel	p.STFKAP460del		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	460			S -> T (in dbSNP:rs2269966).	S -> F (in Ref. 6; BAB15671). {ECO:0000305}.	filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			GCTTGGACGCTGGGGCCTTAAAGGTGGATGTCGTCCTG	0.633																																																0			7																																								97771488	SO:0001651	inframe_deletion	55971			AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1378_1395delTCCACCTTTAAGGCCCCA	7.37:g.97933535_97933552delTGGGGCCTTAAAGGTGGA	ENSP00000005260:p.Ser460_Pro465del		97771471	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	In_Frame_Del	DEL	ENST00000005260.8	37	CCDS34687.1																																																																																				0.633	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		-	97933552	TGGGGCCTTAAAGGTGGA	-	97933535	7	5	113	1	0	1	0	1	0	0	0	0	1303	1567	55	0	152	0	BAIAP2L1	7	97933535	In_Frame_Del	DEL	TGGGGCCTTAAAGGTGGA	TCGA-EI-6510-01A-11D-1733-10	10841392	97933535	61205128	126	30527										
STAG3	10734	hgsc.bcm.edu	37	chr7	99786620	99786620	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcacaagtccgcgccttccgTcacactagcaccctggctgg	9	17	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:99786620T>C	ENST00000426455.1	+	7	1103	c.696T>C	c.(694-696)cgT>cgC	p.R232R	STAG3_ENST00000317296.5_Silent_p.R232R|STAG3_ENST00000394018.2_Silent_p.R174R	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	232					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCGCCTTCCGTCACACTAGCA	0.512																																																0			7											88	86	87					7																	99786620		2203	4300	6503	99624556	SO:0001819	synonymous_variant	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.696T>C	7.37:g.99786620T>C			99624556	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																				0.512	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		C	99786620	T	C	99786620	2	2	113	1	0	0	0	0	0	0	0	1	15283	1654	58	4		4	STAG3	7	99786620	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1853085	99786620	59352043	127	30528										
MUC17	140453	hgsc.bcm.edu	37	chr7	100680242	100680242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctacagcagtcagttcatctCctacacctgctgaaggtacc	7	14	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:100680242C>T	ENST00000306151.4	+	3	5609	c.5545C>T	c.(5545-5547)Cct>Tct	p.P1849S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1849	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.P1849A(1)|p.P1849S(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CAGTTCATCTCCTACACCTGC	0.507																																																2	Substitution - Missense(2)	ovary(1)|endometrium(1)	7											187	195	192					7																	100680242		2203	4300	6503	100466962	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5545C>T	7.37:g.100680242C>T	ENSP00000302716:p.Pro1849Ser		100466962	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.593	-0.832073	0.02713	.	.	ENSG00000169876	ENST00000306151	T	0.03152	4.03	0.824	-0.342	0.12635	.	.	.	.	.	T	0.01421	0.0046	N	0.04880	-0.145	0.09310	N	1	B	0.20459	0.045	B	0.08055	0.003	T	0.47774	-0.9091	9	0.08381	T	0.77	.	1.9183	0.03302	0.3058:0.4521:0.0:0.2421	.	1849	Q685J3	MUC17_HUMAN	S	1849	ENSP00000302716:P1849S	ENSP00000302716:P1849S	P	+	1	0	MUC17	100466962	0.000000	0.05858	0.005000	0.12908	0.041000	0.13682	-5.003000	0.00161	-0.081000	0.12662	0.134000	0.15878	CCT		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100680242	C	T	100680242	3	4	113	1	0	0	0	0	1	0	0	0	10004	855	30	3	5555	3	MUC17	7	100680242	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	893622	100680242	58458421	128	30529										
RINT1	60561	hgsc.bcm.edu	37	chr7	105183037	105183037	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggaaccatgattagccagatTgaagagatcgaacgtcatct	10	8	2	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:105183037T>C	ENST00000257700.2	+	4	687	c.456T>C	c.(454-456)atT>atC	p.I152I		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	152					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TTAGCCAGATTGAAGAGATCG	0.413																																																0			7											130	115	120					7																	105183037		2203	4300	6503	104970273	SO:0001819	synonymous_variant	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.456T>C	7.37:g.105183037T>C			104970273	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Silent	SNP	ENST00000257700.2	37	CCDS34726.1																																																																																				0.413	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		C	105183037	T	C	105183037	2	2	113	1	0	0	0	0	0	0	0	1	13413	1800	63	4		4	RINT1	7	105183037	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	4502795	105183037	53955626	129	30530										
RINT1	60561	hgsc.bcm.edu	37	chr7	105187418	105187418	+	Missense_Mutation	SNP	T	T	C													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aggcagcctccactctagtgTctatggcagaacttgacatt							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:105187418T>C	ENST00000257700.2	+	5	808	c.577T>C	c.(577-579)Tct>Cct	p.S193P		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	193					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CACTCTAGTGTCTATGGCAGA	0.363																																																0			7											115	98	104					7																	105187418		2203	4300	6503	104974654	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.577T>C	7.37:g.105187418T>C	ENSP00000257700:p.Ser193Pro		104974654	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.587494	0.46110	.	.	ENSG00000135249	ENST00000257700	T	0.24723	1.84	5.26	2.81	0.32909	.	0.628834	0.17024	N	0.189993	T	0.23249	0.0562	L	0.50333	1.59	0.36262	D	0.854619	B	0.23540	0.087	B	0.28553	0.091	T	0.10451	-1.0629	10	0.34782	T	0.22	-0.4982	8.1289	0.31016	0.1334:0.0:0.1397:0.7269	.	193	Q6NUQ1	RINT1_HUMAN	P	193	ENSP00000257700:S193P	ENSP00000257700:S193P	S	+	1	0	RINT1	104974654	0.672000	0.27530	0.925000	0.36789	0.997000	0.91878	2.153000	0.42282	0.288000	0.22398	0.460000	0.39030	TCT		0.363	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		C	105187418	T	C	105187418	3	2	113	1	0	0	0	0	1	0	0	0	13413	1667	58	4	595	4	RINT1	7	105187418	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	4381	105187418	53951245	130	30531	55	2								
RINT1	60561	hgsc.bcm.edu	37	chr7	105187424	105187424	+	Missense_Mutation	SNP	G	G	A													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctccactctagtgtctatgGcagaacttgacattaaactt							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:105187424G>A	ENST00000257700.2	+	5	814	c.583G>A	c.(583-585)Gca>Aca	p.A195T		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	195					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.A195S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AGTGTCTATGGCAGAACTTGA	0.368																																																1	Substitution - Missense(1)	ovary(1)	7											117	100	106					7																	105187424		2203	4300	6503	104974660	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.583G>A	7.37:g.105187424G>A	ENSP00000257700:p.Ala195Thr		104974660	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	G	9.977	1.227155	0.22542	.	.	ENSG00000135249	ENST00000257700	T	0.22743	1.94	5.26	4.13	0.48395	.	0.115584	0.64402	N	0.000012	T	0.10981	0.0268	N	0.12471	0.22	0.51767	D	0.999939	B	0.06786	0.001	B	0.09377	0.004	T	0.11891	-1.0569	10	0.13108	T	0.6	-8.3789	11.3866	0.49789	0.1166:0.0:0.8834:0.0	.	195	Q6NUQ1	RINT1_HUMAN	T	195	ENSP00000257700:A195T	ENSP00000257700:A195T	A	+	1	0	RINT1	104974660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.291000	0.72719	0.887000	0.36136	0.563000	0.77884	GCA		0.368	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		A	105187424	G	A	105187424	3	1	113	1	0	0	0	0	1	0	0	0	13413	1203	42	3	601	3	RINT1	7	105187424	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	6	105187424	53951239	131	30532	55	2								
TRIM24	8805	hgsc.bcm.edu	37	chr7	138268672	138268672	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agactacaagaagattattcCatgtactcaaaacctgaaga	6	8	1	5			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:138268672C>T	ENST00000343526.4	+	18	3086	c.2871C>T	c.(2869-2871)tcC>tcT	p.S957S	TRIM24_ENST00000415680.2_Silent_p.S923S			O15164	TIF1A_HUMAN	tripartite motif containing 24	957	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S923S(2)|p.S957S(1)		breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						AAGATTATTCCATGTACTCAA	0.348																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)											3	Substitution - coding silent(3)	breast(3)	7											69	77	74					7																	138268672		2203	4300	6503	137919212	SO:0001819	synonymous_variant	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.2871C>T	7.37:g.138268672C>T			137919212	A4D1R7|A4D1R8|O95854	Silent	SNP	ENST00000343526.4	37	CCDS5847.1																																																																																				0.348	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		T	138268672	C	T	138268672	2	4	113	1	0	0	0	0	0	0	0	1	16538	581	21	3		3	TRIM24	7	138268672	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	33081248	138268672	20869991	132	30533										
BRAF	673	hgsc.bcm.edu	37	chr7	140453085	140453085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	caattcttaccatccacaaaAtggatccagacaactgttca	4	12	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:140453085A>G	ENST00000288602.6	-	15	1910	c.1850T>C	c.(1849-1851)aTt>aCt	p.I617T		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	617	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I617T(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CATCCACAAAATGGATCCAGA	0.398		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	1	Substitution - Missense(1)	skin(1)	7											89	82	84					7																	140453085		2203	4300	6503	140099554	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1850T>C	7.37:g.140453085A>G	ENSP00000288602:p.Ile617Thr		140099554	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.56|17.56	3.419458|3.419458	0.62622|0.62622	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.84223	.|-1.82	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81814|0.81814	0.4902|0.4902	L|L	0.35644|0.35644	1.08|1.08	0.80722|0.80722	D|D	1|1	.|B	.|0.20368	.|0.044	.|B	.|0.28784	.|0.094	T|T	0.78957|0.78957	-0.1999|-0.1999	5|10	.|0.72032	.|D	.|0.01	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|617	.|P15056	.|BRAF_HUMAN	L|T	225|617	.|ENSP00000288602:I617T	.|ENSP00000288602:I617T	F|I	-|-	1|2	0|0	BRAF|BRAF	140099554|140099554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	TTT|ATT		0.398	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		G	140453085	A	G	140453085	3	3	113	1	0	0	0	0	1	0	0	0	1499	101	4	4	466	4	BRAF	7	140453085	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	2184413	140453085	18685578	133	30534										
TPK1	27010	hgsc.bcm.edu	37	chr7	144320303	144320303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cttttggagcattttaaggcActtagtaaagtcagtgtggt	11	5	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:144320303A>G	ENST00000360057.3	-	6	412	c.310T>C	c.(310-312)Tgc>Cgc	p.C104R	TPK1_ENST00000378099.3_Missense_Mutation_p.C104R|TPK1_ENST00000549981.1_5'UTR|TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Missense_Mutation_p.C99R	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	104					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	ATTTTAAGGCACTTAGTAAAG	0.318																																					Ovarian(45;88 1034 2073 5829 28455)											0			7											202	218	213					7																	144320303		2203	4300	6503	143951236	SO:0001583	missense	27010			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.310T>C	7.37:g.144320303A>G	ENSP00000353165:p.Cys104Arg		143951236	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	A	19.67	3.871570	0.72065	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099;ENST00000552881	D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74	6.02	6.02	0.97574	Thiamin pyrophosphokinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.93220	0.7840	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.997	D	0.94618	0.7810	10	0.87932	D	0	-15.1097	12.9364	0.58316	1.0:0.0:0.0:0.0	.	104;104;99	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	R	104;99;104;104	ENSP00000353165:C104R;ENSP00000438813:C99R;ENSP00000367339:C104R;ENSP00000448655:C104R	ENSP00000353165:C104R	C	-	1	0	TPK1	143951236	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.979000	0.56888	2.311000	0.77944	0.533000	0.62120	TGC		0.318	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		G	144320303	A	G	144320303	3	3	113	1	0	0	0	0	1	0	0	0	16444	159	6	4	437	4	TPK1	7	144320303	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	3867218	144320303	14818360	134	30535										
WDR60	55112	hgsc.bcm.edu	37	chr7	158672483	158672483	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cagatcgagacaacaaacacCgagaaaaaagcagcacaagg	9	10	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr7:158672483C>A	ENST00000407559.3	+	5	840	c.682C>A	c.(682-684)Cga>Aga	p.R228R		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	228					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	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)		CAACAAACACCGAGAAAAAAG	0.433																																																0			7											69	76	74					7																	158672483		1859	4099	5958	158365244	SO:0001819	synonymous_variant	55112				CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.682C>A	7.37:g.158672483C>A			158365244	Q9NW58	Silent	SNP	ENST00000407559.3	37	CCDS47757.1																																																																																				0.433	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		A	158672483	C	A	158672483	2	1	113	1	0	0	0	0	0	0	0	1	17351	644	23	2		2	WDR60	7	158672483	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	14352180	158672483	466180	135	30536										
PPP3CC	5533	hgsc.bcm.edu	37	chr8	22398232	22398232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cccgaaaggatagcatacacGctggtgggccaatgaaatct	11	10	1	1	rs558233561		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:22398232G>A	ENST00000240139.5	+	14	1783	c.1456G>A	c.(1456-1458)Gct>Act	p.A486T	PPP3CC_ENST00000397775.3_Missense_Mutation_p.A495T|PPP3CC_ENST00000289963.8_Missense_Mutation_p.A476T|RP11-582J16.4_ENST00000514980.1_RNA	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	486				HA -> YP (in Ref. 1; AAB23769). {ECO:0000305}.	apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		TAGCATACACGCTGGTGGGCC	0.532													G|||	1	0.000199681	0	0	5008	,	,		16806	0.001		0	False		,,,				2504	0															0			8											85	81	82					8																	22398232		2203	4300	6503	22454177	SO:0001583	missense	5533				CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9316	protein-coding gene	gene with protein product	"calcineurin A gamma", "protein phosphatase 2B, catalytic subunit, gamma isoform"	114107	"protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)", "protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.1456G>A	8.37:g.22398232G>A	ENSP00000240139:p.Ala486Thr		22454177	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	.	.	.	.	.	.	.	.	.	.	G	6.906	0.536712	0.13188	.	.	ENSG00000120910	ENST00000240139;ENST00000289963;ENST00000397775	T;T;T	0.14022	2.55;2.54;2.55	5.29	-8.59	0.00893	.	2.814430	0.01025	N	0.004053	T	0.04998	0.0134	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.28490	-1.0042	10	0.19590	T	0.45	10.3949	2.5077	0.04649	0.0948:0.3114:0.2883:0.3055	.	495;476;486	B4DRT5;P48454-2;P48454	.;.;PP2BC_HUMAN	T	486;476;495	ENSP00000240139:A486T;ENSP00000289963:A476T;ENSP00000380878:A495T	ENSP00000240139:A486T	A	+	1	0	PPP3CC	22454177	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.530000	0.02221	-1.809000	0.01232	-1.744000	0.00683	GCT		0.532	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605		A	22398232	G	A	22398232	3	1	113	1	0	0	0	0	1	0	0	0	12433	1087	38	1	1510	1	PPP3CC	8	22398232	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10		22398232	123965790	136	30537										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36788611	36788611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gctcttgtctggaagaaaccGgtgtaagctggggcttctgt	14	8	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:36788611G>A	ENST00000399881.3	+	25	2916	c.2879G>A	c.(2878-2880)cGg>cAg	p.R960Q	KCNU1_ENST00000518904.1_3'UTR	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	960					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GGAAGAAACCGGTGTAAGCTG	0.433																																																0			8											139	134	136					8																	36788611		1902	4118	6020	36907769	SO:0001583	missense	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2879G>A	8.37:g.36788611G>A	ENSP00000382770:p.Arg960Gln		36907769		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.936626	0.52972	.	.	ENSG00000215262	ENST00000399881	T	0.50548	0.74	5.41	4.54	0.55810	.	0.000000	0.34555	U	0.003866	T	0.44030	0.1274	M	0.70595	2.14	0.80722	D	1	P	0.35872	0.525	B	0.28638	0.092	T	0.49934	-0.8886	10	0.87932	D	0	-8.7265	11.1602	0.48512	0.0858:0.0:0.9142:0.0	.	960	A8MYU2	KCNU1_HUMAN	Q	960	ENSP00000382770:R960Q	ENSP00000382770:R960Q	R	+	2	0	KCNU1	36907769	1.000000	0.71417	0.935000	0.37517	0.011000	0.07611	4.824000	0.62701	1.287000	0.44583	-0.142000	0.14014	CGG		0.433	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36788611	G	A	36788611	3	1	113	1	0	0	0	0	1	0	0	0	8114	1116	39	1	2977	1	KCNU1	8	36788611	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	14390379	36788611	109575411	137	30538										
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42587321	42587321	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaatcatcccatcgtcttccAaagtcattcctctcattgga							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:42587321delA	ENST00000289957.2	+	5	999	c.871delA	c.(871-873)aaafs	p.K291fs		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	291					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	ATCGTCTTCCAAAGTCATTCC	0.408																																																0			8											260	238	245					8																	42587321		2203	4300	6503	42706478	SO:0001589	frameshift_variant	1142			U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.871delA	8.37:g.42587321delA	ENSP00000289957:p.Lys291fs		42706478	Q15827	Frame_Shift_Del	DEL	ENST00000289957.2	37	CCDS6134.1																																																																																				0.408	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			-	42587321	A	-	42587321	7	5	113	1	0	1	0	1	0	0	0	0	3398	131	5	0	889	0	CHRNB3	8	42587321	Frame_Shift_Del	DEL	A	TCGA-EI-6510-01A-11D-1733-10	5798710	42587321	103776701	138	30539										
FABP12	646486	hgsc.bcm.edu	37	chr8	82439312	82439312	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtggtttctttgccatcccaGtcctgaacttgaatcaggga	10	10	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:82439312G>T	ENST00000360464.4	-	3	353	c.291C>A	c.(289-291)gaC>gaA	p.D97E	RP11-257P3.3_ENST00000518637.1_RNA|RP11-257P3.3_ENST00000523380.1_RNA	NM_001105281.1	NP_001098751.1	A6NFH5	FBP12_HUMAN	fatty acid binding protein 12	97							lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(3)	4						TGCCATCCCAGTCCTGAACTT	0.413																																																0			8											98	88	92					8																	82439312		1903	4135	6038	82601867	SO:0001583	missense	646486				CCDS47882.1	8q21.13	2013-03-01			ENSG00000197416	ENSG00000197416		"Fatty acid binding protein family"	34524	protein-coding gene	gene with protein product						18786628	Standard	NM_001105281		Approved		uc011lfp.2	A6NFH5	OTTHUMG00000164679	ENST00000360464.4:c.291C>A	8.37:g.82439312G>T	ENSP00000353650:p.Asp97Glu		82601867	B7SUN0	Missense_Mutation	SNP	ENST00000360464.4	37	CCDS47882.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.556156	0.27827	.	.	ENSG00000197416	ENST00000360464	T	0.06294	3.32	5.18	1.02	0.19986	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.364009	0.31134	N	0.008193	T	0.02610	0.0079	N	0.08118	0	0.26649	N	0.972148	B	0.14012	0.009	B	0.19946	0.027	T	0.37526	-0.9702	10	0.39692	T	0.17	.	1.325	0.02123	0.2365:0.1267:0.4045:0.2324	.	97	A6NFH5	FBP12_HUMAN	E	97	ENSP00000353650:D97E	ENSP00000353650:D97E	D	-	3	2	FABP12	82601867	0.711000	0.27906	0.986000	0.45419	0.582000	0.36321	-0.162000	0.10012	0.313000	0.23062	0.655000	0.94253	GAC		0.413	FABP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379720.1	NM_001105281		T	82439312	G	T	82439312	3	4	113	1	0	0	0	0	1	0	0	0	5372	1020	36	2	137	2	FABP12	8	82439312	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	39851991	82439312	63924710	139	30540										
PDP1	54704	hgsc.bcm.edu	37	chr8	94934356	94934356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctgagcaggatctatggcacTgcatgttactgccaccacaa	9	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:94934356T>C	ENST00000297598.4	+	2	338	c.69T>C	c.(67-69)acT>acC	p.T23T	PDP1_ENST00000517764.1_Silent_p.T23T|PDP1_ENST00000396200.3_Silent_p.T48T|PDP1_ENST00000520728.1_Silent_p.T23T	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	23					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TCTATGGCACTGCATGTTACT	0.478																																																0			8											176	155	162					8																	94934356		2203	4300	6503	95003532	SO:0001819	synonymous_variant	54704			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.69T>C	8.37:g.94934356T>C			95003532	B3KX71|J3KPU0|Q5U5K1	Silent	SNP	ENST00000297598.4	37	CCDS6259.1																																																																																				0.478	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		C	94934356	T	C	94934356	2	2	113	1	0	0	0	0	0	0	0	1	11716	1567	55	4		4	PDP1	8	94934356	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	12495044	94934356	51429666	140	30541										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100832314	100832314	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagaaaattgttctacaggtTcctgctggcaaaattattat	8	6	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:100832314T>C	ENST00000358544.2	+	49	9144	c.9033T>C	c.(9031-9033)gtT>gtC	p.V3011V	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Silent_p.V2986V	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3011					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTCTACAGGTTCCTGCTGGCA	0.348																																					Colon(161;2205 2542 7338 31318)											0			8											93	101	98					8																	100832314		2203	4300	6503	100901490	SO:0001819	synonymous_variant	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.9033T>C	8.37:g.100832314T>C			100901490	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.348	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100832314	T	C	100832314	2	2	113	1	0	0	0	0	0	0	0	1	17230	1770	62	4		4	VPS13B	8	100832314	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	5897958	100832314	45531708	141	30542										
KLF10	7071	hgsc.bcm.edu	37	chr8	103663555	103663555	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagagtctggtgccattcggGctcaccaccggaggctttga	14	11	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:103663555G>A	ENST00000285407.6	-	3	1305	c.1005C>T	c.(1003-1005)agC>agT	p.S335S	KLF10_ENST00000395884.3_Silent_p.S324S	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	335					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGCCATTCGGGCTCACCACCG	0.557																																					Esophageal Squamous(16;495 519 2144 16528 44005)											0			8											82	92	88					8																	103663555		2203	4300	6503	103732731	SO:0001819	synonymous_variant	7071			U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11810	protein-coding gene	gene with protein product		601878	"TGFB inducible early growth response"	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.1005C>T	8.37:g.103663555G>A			103732731	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Silent	SNP	ENST00000285407.6	37	CCDS6294.1																																																																																				0.557	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			A	103663555	G	A	103663555	2	1	113	1	0	0	0	0	0	0	0	1	8359	1194	42	3		3	KLF10	8	103663555	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	2831241	103663555	42700467	142	30543										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113529390	113529390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acagtgtccccaggttctctTccatccccatttcgagtccc	6	17	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:113529390T>C	ENST00000297405.5	-	28	4873	c.4629A>G	c.(4627-4629)ggA>ggG	p.G1543G	CSMD3_ENST00000455883.2_Silent_p.G1439G|CSMD3_ENST00000343508.3_Silent_p.G1503G|CSMD3_ENST00000352409.3_Silent_p.G1543G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1543	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAGGTTCTCTTCCATCCCCAT	0.443										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											94	84	88					8																	113529390		2203	4300	6503	113598566	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4629A>G	8.37:g.113529390T>C			113598566	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.443	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113529390	T	C	113529390	2	2	113	1	0	0	0	0	0	0	0	1	3952	1770	62	4		4	CSMD3	8	113529390	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	9865835	113529390	32834632	143	30544										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118165303	118165303	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atcgaagcctccctctaagcGgctgacatttggatggcacc	10	13	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:118165303G>A	ENST00000456015.2	+	3	392	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	SLC30A8_ENST00000519688.1_Missense_Mutation_p.R82Q|SLC30A8_ENST00000521243.1_Missense_Mutation_p.R82Q|SLC30A8_ENST00000427715.2_Missense_Mutation_p.R82Q	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	131					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			CCCTCTAAGCGGCTGACATTT	0.512																																					Ovarian(162;1202 1922 6011 16223 52092)											0			8											112	82	92					8																	118165303		2203	4300	6503	118234484	SO:0001583	missense	169026				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.392G>A	8.37:g.118165303G>A	ENSP00000415011:p.Arg131Gln		118234484	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	G	8.995	0.978758	0.18812	.	.	ENSG00000164756	ENST00000521243;ENST00000524274;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	5.37	-5.26	0.02772	.	0.812377	0.11451	N	0.562795	T	0.44307	0.1287	L	0.35542	1.07	0.09310	N	1	B	0.26120	0.142	B	0.28232	0.087	T	0.32268	-0.9913	10	0.24483	T	0.36	-1.0271	9.8645	0.41134	0.6541:0.2107:0.1352:0.0	.	131	Q8IWU4	ZNT8_HUMAN	Q	82;82;82;82;131	ENSP00000428545:R82Q;ENSP00000427760:R82Q;ENSP00000407505:R82Q;ENSP00000431069:R82Q;ENSP00000415011:R131Q	ENSP00000407505:R82Q	R	+	2	0	SLC30A8	118234484	0.001000	0.12720	0.003000	0.11579	0.324000	0.28378	-0.173000	0.09854	-1.007000	0.03408	-0.768000	0.03414	CGG		0.512	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118165303	G	A	118165303	3	1	113	1	0	0	0	0	1	0	0	0	14598	1116	39	1	402	1	SLC30A8	8	118165303	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4635913	118165303	28198719	144	30545										
EFR3A	23167	hgsc.bcm.edu	37	chr8	132958829	132958829	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agctttcttcatatggtggcAaagctgctggaatcggggga	14	7	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:132958829A>G	ENST00000254624.5	+	4	540	c.315A>G	c.(313-315)gcA>gcG	p.A105A	EFR3A_ENST00000519656.1_Silent_p.A69A|EFR3A_ENST00000334503.4_Silent_p.A105A	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	105						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATATGGTGGCAAAGCTGCTGG	0.393																																																0			8											69	66	67					8																	132958829		2203	4300	6503	133028011	SO:0001819	synonymous_variant	23167			D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.315A>G	8.37:g.132958829A>G			133028011	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																				0.393	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		G	132958829	A	G	132958829	2	3	113	1	0	0	0	0	0	0	0	1	4969	117	5	4		4	EFR3A	8	132958829	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	14793526	132958829	13405193	145	30546										
TG	7038	hgsc.bcm.edu	37	chr8	133913707	133913707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggcttttccccagtgcaatgTgaccaggcccagggcagctg	13	13	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:133913707T>C	ENST00000220616.4	+	16	3583	c.3543T>C	c.(3541-3543)tgT>tgC	p.C1181C	TG_ENST00000377869.1_Silent_p.C1181C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1181	Thyroglobulin type-1 10. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		CAGTGCAATGTGACCAGGCCC	0.627																																																0			8											53	56	55					8																	133913707		2203	4300	6503	133982889	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3543T>C	8.37:g.133913707T>C			133982889	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	T	0.722	-0.783165	0.02907	.	.	ENSG00000042832	ENST00000518505	.	.	.	5.12	-8.47	0.00939	.	.	.	.	.	T	0.59998	0.2235	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67169	-0.5738	4	.	.	.	.	14.7477	0.69501	0.0:0.5674:0.0:0.4326	.	.	.	.	A	125	.	.	V	+	2	0	TG	133982889	0.005000	0.15991	0.009000	0.14445	0.010000	0.07245	-1.768000	0.01794	-1.836000	0.01190	-0.836000	0.03065	GTG		0.627	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133913707	T	C	133913707	2	2	113	1	0	0	0	0	0	0	0	1	15852	1702	59	4		4	TG	8	133913707	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	954878	133913707	12450315	146	30547										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144668984	144668984	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atttgaacttgtcgaaccagAtcttctcatgtgctaggaag	9	8	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr8:144668984A>G	ENST00000529272.1	-	2	432	c.32T>C	c.(31-33)aTc>aCc	p.I11T	EEF1D_ENST00000532741.1_Missense_Mutation_p.I427T|EEF1D_ENST00000423316.2_Missense_Mutation_p.I377T|EEF1D_ENST00000531621.1_Missense_Mutation_p.I11T|EEF1D_ENST00000532400.1_Missense_Mutation_p.I11T|EEF1D_ENST00000395119.3_Missense_Mutation_p.I11T|EEF1D_ENST00000317198.6_Missense_Mutation_p.I11T|EEF1D_ENST00000526838.1_Missense_Mutation_p.I11T|EEF1D_ENST00000524624.1_Missense_Mutation_p.I11T|EEF1D_ENST00000528610.1_Missense_Mutation_p.I11T|EEF1D_ENST00000442189.2_Missense_Mutation_p.I377T|EEF1D_ENST00000419152.2_Missense_Mutation_p.I11T			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	11					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			GTCGAACCAGATCTTCTCATG	0.547																																																0			8											130	129	129					8																	144668984		2203	4300	6503	144740127	SO:0001583	missense	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.32T>C	8.37:g.144668984A>G	ENSP00000434872:p.Ile11Thr		144740127	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.897767	0.72639	.	.	ENSG00000104529	ENST00000419152;ENST00000532400;ENST00000532741;ENST00000526838;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000337369;ENST00000531621;ENST00000524624;ENST00000534380;ENST00000534377;ENST00000533204;ENST00000530191;ENST00000531218;ENST00000533494;ENST00000530445;ENST00000529516;ENST00000533749;ENST00000526340;ENST00000525223;ENST00000532543;ENST00000531931	.	.	.	4.81	3.61	0.41365	.	0.218494	0.46442	D	0.000296	T	0.78310	0.4263	M	0.83953	2.67	0.45366	D	0.998357	B;D;D;B;D;D	0.89917	0.275;0.986;1.0;0.398;0.999;0.996	B;P;D;B;D;D	0.80764	0.158;0.82;0.994;0.21;0.986;0.912	T	0.79624	-0.1726	9	0.72032	D	0.01	.	11.0019	0.47611	0.8434:0.1566:0.0:0.0	.	11;377;329;11;427;377	E9PBQ9;D3DWK1;F8W934;P29692;E9PRY8;P29692-2	.;.;.;EF1D_HUMAN;.;.	T	11;11;427;11;377;11;11;11;377;329;11;377;11;11;11;11;11;11;11;11;11;11;27;11;11;11;11	.	ENSP00000317399:I11T	I	-	2	0	EEF1D	144740127	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.428000	0.90278	0.746000	0.32786	0.459000	0.35465	ATC		0.547	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		G	144668984	A	G	144668984	3	3	113	1	0	0	0	0	1	0	0	0	4937	333	12	4	841	4	EEF1D	8	144668984	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	10755277	144668984	1695038	147	30548										
C9orf66	157983	hgsc.bcm.edu	37	chr9	214864	214864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cggaagtttccagcgccgacCgacagacgaggtttgcgctt	13	12	0	1	rs2236547	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:214864C>T	ENST00000382387.2	-	1	1029	c.533G>A	c.(532-534)cGg>cAg	p.R178Q	DOCK8_ENST00000432829.2_5'Flank|DOCK8_ENST00000453981.1_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	178			R -> Q (in dbSNP:rs2236547).							central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	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)		CAGCGCCGACCGACAGACGAG	0.692													T|||	1630	0.325479	0.326	0.3213	5008	,	,		11784	0.4117		0.2048	False		,,,				2504	0.363															0			9						T	GLN/ARG	1030,2672		136,758,957	20	17	18		533	3.5	0.4	9	dbSNP_98	18	1388,6106		127,1134,2486	yes	missense	C9orf66	NM_152569.2	43	263,1892,3443	TT,TC,CC		18.5215,27.8228,21.597	benign	178/296	214864	2418,8778	1851	3747	5598	204864	SO:0001583	missense	157983			AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.533G>A	9.37:g.214864C>T	ENSP00000371824:p.Arg178Gln		204864	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	646	0.2957875457875458	174	0.35365853658536583	101	0.27900552486187846	211	0.3688811188811189	160	0.21108179419525067	.	9.102	1.004339	0.19199	0.278228	0.185215	ENSG00000183784	ENST00000382387	T	0.21031	2.03	4.63	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999999980934	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	8	0.87932	D	0	.	4.0571	0.09821	0.18:0.1005:0.0:0.7195	rs2236547;rs2236547	178	Q5T8R8	CI066_HUMAN	Q	178	ENSP00000371824:R178Q	ENSP00000371824:R178Q	R	-	2	0	C9orf66	204864	0.139000	0.22563	0.407000	0.26434	0.054000	0.15201	0.094000	0.15107	0.146000	0.19002	-0.524000	0.04348	CGG		0.692	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569		T	214864	C	T	214864	3	4	113	1	0	0	0	0	1	0	0	0	2496	652	23	1	358	1	C9orf66	9	214864	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10		214864	140998567	148	30549										
MOBKL2B	79817	hgsc.bcm.edu	37	chr9	27455163	27455163	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gaaatatttcctcgttgttgAtctgaacctcaatccaatcc	5	11	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:27455163A>G	ENST00000262244.5	-	2	810	c.386T>C	c.(385-387)aTc>aCc	p.I129T		NM_024761.4	NP_079037.3	Q86TA1	MOB3B_HUMAN	MOB kinase activator 3B	129							metal ion binding (GO:0046872)										CTCGTTGTTGATCTGAACCTC	0.428																																																0			9											107	98	101					9																	27455163		2203	4300	6503	27445163	SO:0001583	missense	79817			AK023266	CCDS6520.1	9p21.1	2012-07-05	2011-09-28	2011-09-28	ENSG00000120162	ENSG00000120162		"MOB kinase activators"	23825	protein-coding gene	gene with protein product	"monopolar spindle 1 binding, MOB1, domain containing"		"MOB1, Mps One Binder kinase activator-like 2B (yeast)", "chromosome 9 open reading frame 35"	MOBKL2B, C9orf35		12477932	Standard	NM_024761		Approved	MOB1D, FLJ13204	uc003zqn.3	Q86TA1	OTTHUMG00000019717	ENST00000262244.5:c.386T>C	9.37:g.27455163A>G	ENSP00000262244:p.Ile129Thr		27445163	Q8NEB4|Q9H8V4	Missense_Mutation	SNP	ENST00000262244.5	37	CCDS6520.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113865	0.77210	.	.	ENSG00000120162	ENST00000262244	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.86091	0.5850	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.89636	0.3859	9	0.87932	D	0	-31.062	15.0387	0.71770	1.0:0.0:0.0:0.0	.	129	Q86TA1	MOB3B_HUMAN	T	129	.	ENSP00000262244:I129T	I	-	2	0	MOBKL2B	27445163	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.231000	0.72958	0.460000	0.39030	ATC		0.428	MOB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051974.2	NM_024761		G	27455163	A	G	27455163	3	3	113	1	0	0	0	0	1	0	0	0	9715	333	12	4	276	4	MOBKL2B	9	27455163	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	27240299	27455163	113758268	149	30550										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32635359	32635359	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agttcagtgattaggctgccCagccccaaagcccccaagcc	9	16	1	1	rs267602212		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:32635359C>A	ENST00000242310.4	-	1	308	c.219G>T	c.(217-219)ctG>ctT	p.L73L	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	73					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.L73L(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTAGGCTGCCCAGCCCCAAAG	0.537																																																2	Substitution - coding silent(2)	skin(2)	9											129	125	127					9																	32635359		2203	4300	6503	32625359	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.219G>T	9.37:g.32635359C>A			32625359	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.537	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32635359	C	A	32635359	2	1	113	1	0	0	0	0	0	0	0	1	15562	581	21	2		2	TAF1L	9	32635359	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5180196	32635359	108578072	150	30551										
SPINK4	27290	hgsc.bcm.edu	37	chr9	33240219	33240219	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggatcagcatggccgtccgcCagtgggtaatcgccctggcc	14	14	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:33240219C>T	ENST00000379721.3	+	1	58	c.13C>T	c.(13-15)Cag>Tag	p.Q5*	SPINK4_ENST00000379725.1_Intron|SPINK4_ENST00000379723.1_Intron	NM_014471.1	NP_055286.1	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	5					response to drug (GO:0042493)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			GGCCGTCCGCCAGTGGGTAAT	0.592																																																0			9											66	57	60					9																	33240219		2203	4300	6503	33230219	SO:0001587	stop_gained	27290			AF048700	CCDS6536.1	9p13.3	2011-08-31	2005-08-17		ENSG00000122711	ENSG00000122711		"Serine peptidase inhibitors, Kazal type"	16646	protein-coding gene	gene with protein product		613929	"serine protease inhibitor, Kazal type 4"			1400298, 17333166	Standard	NM_014471		Approved	PEC-60, MGC133107	uc003zsh.3	O60575	OTTHUMG00000019762	ENST00000379721.3:c.13C>T	9.37:g.33240219C>T	ENSP00000369045:p.Gln5*		33230219	Q2YDT7	Nonsense_Mutation	SNP	ENST00000379721.3	37	CCDS6536.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365448	0.41902	.	.	ENSG00000122711	ENST00000379721	.	.	.	4.26	3.36	0.38483	.	.	.	.	.	.	.	.	.	.	.	0.25991	N	0.982243	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	8.1905	0.31366	0.0:0.8923:0.0:0.1077	.	.	.	.	X	5	.	ENSP00000369045:Q5X	Q	+	1	0	SPINK4	33230219	0.313000	0.24554	0.075000	0.20258	0.006000	0.05464	1.563000	0.36364	1.394000	0.46624	0.462000	0.41574	CAG		0.592	SPINK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052035.1	NM_014471		T	33240219	C	T	33240219	4	4	113	1	0	0	0	0	0	1	0	0	15100	595	21	3	15	3	SPINK4	9	33240219	Nonsense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	604860	33240219	107973212	151	30552										
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39086820	39086820	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atcaggattttgatgtctatCtagcttgtacctaatctgca	7	8	4	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:39086820C>A	ENST00000297668.6	-	20	3320	c.3247G>T	c.(3247-3249)Gat>Tat	p.D1083Y	CNTNAP3_ENST00000377656.2_Missense_Mutation_p.D1002Y|CNTNAP3_ENST00000358144.2_Missense_Mutation_p.D995Y	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	1083	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D1083H(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGATGTCTATCTAGCTTGTAC	0.328																																																1	Substitution - Missense(1)	ovary(1)	9											4	4	4					9																	39086820		1728	3625	5353	39076820	SO:0001583	missense	79937			AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.3247G>T	9.37:g.39086820C>A	ENSP00000297668:p.Asp1083Tyr		39076820	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.713666	0.30413	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144	T;T;T	0.79940	-1.32;-1.32;-1.32	2.73	1.82	0.25136	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.82861	0.5129	L	0.56769	1.78	0.80722	D	1	P;D;P	0.53462	0.947;0.96;0.828	P;P;P	0.57425	0.8;0.742;0.82	T	0.81531	-0.0890	9	0.87932	D	0	.	8.5714	0.33572	0.0:0.8769:0.0:0.1231	.	1083;1002;1083	Q9BZ76-2;A6NC89;Q9BZ76	.;.;CNTP3_HUMAN	Y	1083;1002;995	ENSP00000297668:D1083Y;ENSP00000366884:D1002Y;ENSP00000350863:D995Y	ENSP00000297668:D1083Y	D	-	1	0	CNTNAP3	39076820	1.000000	0.71417	0.304000	0.25085	0.724000	0.41520	1.167000	0.31847	0.486000	0.27676	0.306000	0.20318	GAT		0.328	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39086820	C	A	39086820	3	1	113	1	0	0	0	0	1	0	0	0	3654	913	32	2	639	2	CNTNAP3	9	39086820	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5846601	39086820	102126611	152	30553										
RNF20	56254	hgsc.bcm.edu	37	chr9	104309423	104309423	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tttgtgttctctgtaggtgaAttccaaaggttataaggtgt	11	4	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:104309423A>T	ENST00000389120.3	+	8	989	c.899A>T	c.(898-900)aAt>aTt	p.N300I	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	300					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		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)		CTGTAGGTGAATTCCAAAGGT	0.403																																																0			9											108	104	106					9																	104309423		2203	4300	6503	103349244	SO:0001583	missense	56254			AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.899A>T	9.37:g.104309423A>T	ENSP00000373772:p.Asn300Ile		103349244	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.282935	0.40394	.	.	ENSG00000155827	ENST00000389120	T	0.29142	1.58	5.84	5.84	0.93424	.	0.087718	0.85682	D	0.000000	T	0.50497	0.1619	L	0.49126	1.545	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.47341	-0.9125	10	0.52906	T	0.07	-28.4988	15.8917	0.79303	1.0:0.0:0.0:0.0	.	300	Q5VTR2	BRE1A_HUMAN	I	300	ENSP00000373772:N300I	ENSP00000373772:N300I	N	+	2	0	RNF20	103349244	1.000000	0.71417	1.000000	0.80357	0.097000	0.18754	8.927000	0.92846	2.228000	0.72767	0.533000	0.62120	AAT		0.403	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		T	104309423	A	T	104309423	3	4	113	1	0	0	0	0	1	0	0	0	13510	101	4	5	925	5	RNF20	9	104309423	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	65222603	104309423	36904008	153	30554										
FKTN	2218	hgsc.bcm.edu	37	chr9	108370126	108370126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gttacagcaagttactgttgAtggactggaagttctcattc	10	7	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:108370126A>G	ENST00000223528.2	+	6	798	c.674A>G	c.(673-675)gAt>gGt	p.D225G	FKTN_ENST00000357998.5_Missense_Mutation_p.D225G|FKTN_ENST00000602661.1_Missense_Mutation_p.D225G|FKTN_ENST00000448551.2_Missense_Mutation_p.D225G|FKTN_ENST00000540160.1_Missense_Mutation_p.D225G	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	225			D -> E (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|D -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						GTTACTGTTGATGGACTGGAA	0.408																																																0			9											122	120	121					9																	108370126		2203	4300	6503	107409947	SO:0001583	missense	2218				CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"Fukuyama type congenital muscular dystrophy (fukutin)"	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.674A>G	9.37:g.108370126A>G	ENSP00000223528:p.Asp225Gly		107409947	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	37	CCDS6766.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518417	0.85495	.	.	ENSG00000106692	ENST00000223528;ENST00000540160;ENST00000357998;ENST00000374705	D;D;D;D	0.94650	-3.11;-3.24;-3.48;-3.17	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.992	D	0.97340	0.9956	10	0.87932	D	0	.	14.9908	0.71387	1.0:0.0:0.0:0.0	.	225;225;225	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	G	225;225;225;202	ENSP00000223528:D225G;ENSP00000439423:D225G;ENSP00000350687:D225G;ENSP00000363837:D202G	ENSP00000223528:D225G	D	+	2	0	FKTN	107409947	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.734000	0.84928	2.132000	0.65825	0.533000	0.62120	GAT		0.408	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731		G	108370126	A	G	108370126	3	3	113	1	0	0	0	0	1	0	0	0	5938	333	12	4	692	4	FKTN	9	108370126	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	4060703	108370126	32843305	154	30555										
C9orf43	257169	hgsc.bcm.edu	37	chr9	116185755	116185755	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctctgggctcaatccgaagcGttacctcaggatctactgaa	9	12	4	1	rs141883275		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:116185755G>A	ENST00000288462.4	+	7	1079	c.633G>A	c.(631-633)gcG>gcA	p.A211A	C9orf43_ENST00000374165.1_Silent_p.A211A	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	211										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						AATCCGAAGCGTTACCTCAGG	0.502													G|||	1	0.000199681	0	0	5008	,	,		21052	0		0.001	False		,,,				2504	0															0			9						G		4,4402	8.1+/-20.4	0,4,2199	103	92	96		633	0.1	0	9	dbSNP_134	96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C9orf43	NM_152786.1		0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384		211/462	116185755	5,13001	2203	4300	6503	115225576	SO:0001819	synonymous_variant	257169			BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.633G>A	9.37:g.116185755G>A			115225576		Silent	SNP	ENST00000288462.4	37	CCDS6796.1																																																																																				0.502	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786		A	116185755	G	A	116185755	2	1	113	1	0	0	0	0	0	0	0	1	2489	1132	40	1		1	C9orf43	9	116185755	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	7815629	116185755	25027676	155	30556										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140952516	140952516	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cccagggtgctgaaacactcCgtggatgccacctatgagga	12	12	0	2	rs140374106	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr9:140952516C>T	ENST00000371372.1	+	28	4267	c.4122C>T	c.(4120-4122)tcC>tcT	p.S1374S	CACNA1B_ENST00000277549.5_Silent_p.S570S|CACNA1B_ENST00000277551.2_Silent_p.S1374S|CACNA1B_ENST00000371357.1_Silent_p.S1375S|CACNA1B_ENST00000371355.4_Silent_p.S1375S|CACNA1B_ENST00000371363.1_Silent_p.S1374S	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1374					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGAAACACTCCGTGGATGCCA	0.562													C|||	8	0.00159744	0	0	5008	,	,		22283	0.0079		0	False		,,,				2504	0															0			9											141	131	134					9																	140952516		2006	4190	6196	140072337	SO:0001819	synonymous_variant	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4122C>T	9.37:g.140952516C>T			140072337	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																				0.562	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140952516	C	T	140952516	2	4	113	1	0	0	0	0	0	0	0	1	2545	639	23	1		1	CACNA1B	9	140952516	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	24766761	140952516	260915	156	30557										
BEND7	222389	hgsc.bcm.edu	37	chr10	13481451	13481451	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctctgcaagactagggtcacCgctgcactcccacccggcag	10	17	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:13481451C>T	ENST00000396900.2	-	9	1280	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	BEND7_ENST00000341083.3_Silent_p.A376A|BEND7_ENST00000486542.1_5'UTR			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	427						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CTAGGGTCACCGCTGCACTCC	0.532																																																0			10											78	67	71					10																	13481451		2203	4300	6503	13521457	SO:0001819	synonymous_variant	222389			BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"BEN domain containing"	23514	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 30"	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1281G>A	10.37:g.13481451C>T			13521457	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																					0.532	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		T	13481451	C	T	13481451	2	4	113	1	0	0	0	0	0	0	0	1	1404	639	23	1		1	BEND7	10	13481451	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10		13481451	122053296	157	30558										
CUBN	8029	hgsc.bcm.edu	37	chr10	17145126	17145126	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aagagttactacatttacctTtcccatttcagttttgataa	4	8	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:17145126T>C	ENST00000377833.4	-	13	1593	c.1528A>G	c.(1528-1530)Aag>Gag	p.K510E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	510	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACATTTACCTTTCCCATTTCA	0.333																																																0			10											88	85	86					10																	17145126		2203	4300	6503	17185132	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1528A>G	10.37:g.17145126T>C	ENSP00000367064:p.Lys510Glu		17185132	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.904797	0.52333	.	.	ENSG00000107611	ENST00000377833	T	0.59364	0.27	5.65	4.5	0.54988	CUB (5);	0.000000	0.46758	D	0.000263	T	0.71417	0.3337	M	0.62088	1.915	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.70945	-0.4734	10	0.45353	T	0.12	.	12.8579	0.57897	0.0:0.0:0.1363:0.8637	.	510	O60494	CUBN_HUMAN	E	510	ENSP00000367064:K510E	ENSP00000367064:K510E	K	-	1	0	CUBN	17185132	1.000000	0.71417	0.993000	0.49108	0.186000	0.23388	4.417000	0.59822	0.955000	0.37878	0.528000	0.53228	AAG		0.333	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17145126	T	C	17145126	3	2	113	1	0	0	0	0	1	0	0	0	4057	1850	64	4	9563	4	CUBN	10	17145126	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	3663675	17145126	118389621	158	30559										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27303581	27303581	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctgagttccatctgacttttCattgaagcaaaattattctc	5	9	3	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:27303581C>T	ENST00000376087.4	-	31	4731	c.4566G>A	c.(4564-4566)atG>atA	p.M1522I	ANKRD26_ENST00000376070.3_Missense_Mutation_p.M1079I|ANKRD26_ENST00000436985.2_Missense_Mutation_p.M1538I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1521				NNFASMK -> KQDLPDS (in Ref. 3; BAC87508). {ECO:0000305}.	glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCTGACTTTTCATTGAAGCAA	0.294																																																0			10											59	53	55					10																	27303581		1796	4067	5863	27343587	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4566G>A	10.37:g.27303581C>T	ENSP00000365255:p.Met1522Ile		27343587	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.730|0.730	-0.780231|-0.780231	0.02929|0.02929	.|.	.|.	ENSG00000107890|ENSG00000107890	ENST00000445828|ENST00000376070;ENST00000376087;ENST00000436985	.|T;T;T	.|0.29397	.|1.57;1.57;1.57	5.27|5.27	-6.17|-6.17	0.02091|0.02091	.|.	.|0.918054	.|0.09030	.|N	.|0.858881	T|T	0.07279|0.07279	0.0184|0.0184	N|N	0.01228|0.01228	-0.945|-0.945	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.06405	.|0.0;0.001;0.002	T|T	0.32481|0.32481	-0.9905|-0.9905	5|10	.|0.16420	.|T	.|0.52	.|.	4.1005|4.1005	0.10012|0.10012	0.124:0.4662:0.1197:0.2901|0.124:0.4662:0.1197:0.2901	.|.	.|1522;1521;1538	.|Q9UPS8-3;Q9UPS8;A1L497	.|.;ANR26_HUMAN;.	K|I	10|1079;1522;1538	.|ENSP00000365238:M1079I;ENSP00000365255:M1522I;ENSP00000405112:M1538I	.|ENSP00000365238:M1079I	E|M	-|-	1|3	0|0	ANKRD26|ANKRD26	27343587|27343587	0.068000|0.068000	0.21057|0.21057	0.026000|0.026000	0.17262|0.17262	0.877000|0.877000	0.50540|0.50540	-0.789000|-0.789000	0.04609|0.04609	-1.072000|-1.072000	0.03141|0.03141	0.313000|0.313000	0.20887|0.20887	GAA|ATG		0.294	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			T	27303581	C	T	27303581	3	4	113	1	0	0	0	0	1	0	0	0	654	826	29	3	582	3	ANKRD26	10	27303581	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	10158455	27303581	108231166	159	30560										
KIF5B	3799	hgsc.bcm.edu	37	chr10	32306152	32306152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atctacttcttgctgatagcGtttgcgatcacgagatgcat	9	9	3	2	rs141491660	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:32306152G>A	ENST00000302418.4	-	24	3137	c.2680C>T	c.(2680-2682)Cgc>Tgc	p.R894C	KIF5B_ENST00000493889.1_5'UTR	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	894					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TGCTGATAGCGTTTGCGATCA	0.428			T	"RET, ALK"	NSCLC																																		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	0			10						G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	309	271	284		2680	5.6	1	10	dbSNP_134	284	0,8600		0,0,4300	no	missense	KIF5B	NM_004521.2	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	894/964	32306152	2,13004	2203	4300	6503	32346158	SO:0001583	missense	3799			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2680C>T	10.37:g.32306152G>A	ENSP00000307078:p.Arg894Cys		32346158	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.319353	0.95682	4.54E-4	0.0	ENSG00000170759	ENST00000302418	T	0.78003	-1.14	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.89448	0.6718	M	0.82923	2.615	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.90432	0.4425	10	0.87932	D	0	.	19.5519	0.95324	0.0:0.0:1.0:0.0	.	894	P33176	KINH_HUMAN	C	894	ENSP00000307078:R894C	ENSP00000307078:R894C	R	-	1	0	KIF5B	32346158	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.776000	0.99001	2.623000	0.88846	0.467000	0.42956	CGC		0.428	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32306152	G	A	32306152	3	1	113	1	0	0	0	0	1	0	0	0	8327	1145	40	1	219	1	KIF5B	10	32306152	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5002571	32306152	103228595	160	30561										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75506596	75506596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gggaatgctttcataatgaaCgtcaaccagtcagttccacc	8	11	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:75506596C>T	ENST00000339365.2	+	3	168	c.6C>T	c.(4-6)aaC>aaT	p.N2N	SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000411652.2_5'UTR|SEC24C_ENST00000345254.4_Silent_p.N2N	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	2					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCATAATGAACGTCAACCAGT	0.483																																																0			10											101	94	96					10																	75506596		2203	4300	6503	75176602	SO:0001819	synonymous_variant	9632			D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.6C>T	10.37:g.75506596C>T			75176602	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																				0.483	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			T	75506596	C	T	75506596	2	4	113	1	0	0	0	0	0	0	0	1	14033	535	19	1		1	SEC24C	10	75506596	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	43200444	75506596	60028151	161	30562										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717733	89717733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gttacctgtgtgtggtgataTcaaagtagagttcttccaca	10	7	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:89717733T>C	ENST00000371953.3	+	7	2115	c.758T>C	c.(757-759)aTc>aCc	p.I253T	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	253	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.I253N(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.D252_K263>AKE(1)|p.I253fs*3(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TGTGGTGATATCAAAGTAGAG	0.388		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(9)|Substitution - Missense(2)|Deletion - In frame(1)|Complex - frameshift(1)|Complex - deletion inframe(1)|Unknown(1)	prostate(16)|central_nervous_system(11)|skin(7)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	10											117	103	108					10																	89717733		2203	4300	6503	89707713	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.758T>C	10.37:g.89717733T>C	ENSP00000361021:p.Ile253Thr		89707713	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.520932	0.85495	.	.	ENSG00000171862	ENST00000371953	D	0.89123	-2.47	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.93314	0.7869	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93157	0.6554	9	.	.	.	-2.4401	14.9657	0.71193	0.0:0.0:0.0:1.0	.	253	P60484	PTEN_HUMAN	T	253	ENSP00000361021:I253T	.	I	+	2	0	PTEN	89707713	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.661000	0.83786	1.928000	0.55862	0.477000	0.44152	ATC		0.388	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89717733	T	C	89717733	3	2	113	1	0	0	0	0	1	0	0	0	12772	1435	50	4	784	4	PTEN	10	89717733	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	14211137	89717733	45817014	162	30563										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720722	89720722	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gaaacctcagaaaaagtagaAaatggaagtctatgtgatca	9	5	3	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:89720722A>G	ENST00000371953.3	+	8	2230	c.873A>G	c.(871-873)gaA>gaG	p.E291E	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	291	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AAAAAGTAGAAAATGGAAGTC	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											68	70	69					10																	89720722		2203	4297	6500	89710702	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.873A>G	10.37:g.89720722A>G			89710702	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720722	A	G	89720722	2	3	113	1	0	0	0	0	0	0	0	1	12772	11	1	4		4	PTEN	10	89720722	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	2989	89720722	45814025	163	30564										
NFKB2	4791	hgsc.bcm.edu	37	chr10	104161814	104161814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtcttctcagctggctggcGgggacctggcaggtctactg	15	11	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:104161814G>A	ENST00000369966.3	+	22	2726	c.2476G>A	c.(2476-2478)Ggg>Agg	p.G826R	NFKB2_ENST00000428099.1_Missense_Mutation_p.G826R|NFKB2_ENST00000189444.6_Missense_Mutation_p.G826R	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	826	Death.		Missing (in truncated form EB308).|Missing (in truncated form LB40).|Missing (in truncated form p80HT).		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	GCTGGCTGGCGGGGACCTGGC	0.627			T	IGH@	B-NHL																																		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	0			10																																								104151804	SO:0001583	missense	4791			X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.2476G>A	10.37:g.104161814G>A	ENSP00000358983:p.Gly826Arg		104151804	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	16.94	3.260785	0.59431	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	D;D;D	0.86230	-2.09;-2.09;-2.09	3.79	3.79	0.43588	Death (2);DEATH-like (2);	0.065685	0.64402	D	0.000016	D	0.92502	0.7619	M	0.70595	2.14	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93555	0.6890	10	0.72032	D	0.01	.	15.832	0.78760	0.0:0.0:1.0:0.0	.	826;826	Q00653;A8K9D9	NFKB2_HUMAN;.	R	826	ENSP00000410256:G826R;ENSP00000358983:G826R;ENSP00000189444:G826R	ENSP00000189444:G826R	G	+	1	0	NFKB2	104151804	1.000000	0.71417	0.997000	0.53966	0.039000	0.13416	8.489000	0.90461	2.105000	0.64084	0.556000	0.70494	GGG		0.627	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104161814	G	A	104161814	3	1	113	1	0	0	0	0	1	0	0	0	10407	1116	39	1	2558	1	NFKB2	10	104161814	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	14441092	104161814	31372933	164	30565										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129209180	129209180	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagagaaaaacccagacaatGaatttgcggtaaaaaacaaa	8	6	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr10:129209180G>C	ENST00000280333.6	+	43	4466	c.4357G>C	c.(4357-4359)Gaa>Caa	p.E1453Q		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1453	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CCCAGACAATGAATTTGCGGT	0.448																																																0			10											50	50	50					10																	129209180		1885	4108	5993	129099170	SO:0001583	missense	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4357G>C	10.37:g.129209180G>C	ENSP00000280333:p.Glu1453Gln		129099170	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	29.3	4.997365	0.93227	.	.	ENSG00000150760	ENST00000280333	T	0.19105	2.17	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	M	0.88031	2.925	0.80722	D	1	D;D;P	0.69078	0.96;0.997;0.954	P;D;P	0.75484	0.812;0.986;0.812	T	0.64512	-0.6390	10	0.87932	D	0	.	18.3037	0.90172	0.0:0.0:1.0:0.0	.	1453;1519;1453	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	Q	1453	ENSP00000280333:E1453Q	ENSP00000280333:E1453Q	E	+	1	0	DOCK1	129099170	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.314000	0.96306	2.546000	0.85860	0.655000	0.94253	GAA		0.448	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		C	129209180	G	C	129209180	3	2	113	1	0	0	0	0	1	0	0	0	4695	1291	45	5	4527	5	DOCK1	10	129209180	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	25047366	129209180	6325567	165	30566										
RIC3	79608	hgsc.bcm.edu	37	chr11	8132395	8132395	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tagctatctgcactgaatccAgcattctctgccaagacagc	7	13	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:8132395A>G	ENST00000309737.6	-	6	959	c.960T>C	c.(958-960)gcT>gcC	p.A320A	RIC3_ENST00000425599.2_Silent_p.A239A|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000539720.1_Silent_p.A271A|RIC3_ENST00000343202.4_Silent_p.A319A|RIC3_ENST00000335425.7_Silent_p.A138A|RIC3_ENST00000396677.2_Silent_p.A158A			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	320					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		CACTGAATCCAGCATTCTCTG	0.473																																																0			11											139	128	132					11																	8132395		2201	4296	6497	8088971	SO:0001819	synonymous_variant	79608				CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.960T>C	11.37:g.8132395A>G			8088971	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Silent	SNP	ENST00000309737.6	37	CCDS55742.1																																																																																				0.473	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557		G	8132395	A	G	8132395	2	3	113	1	0	0	0	0	0	0	0	1	13391	175	7	4		4	RIC3	11	8132395	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10		8132395	126874121	166	30567										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17126781	17126781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgcaagtggtttatctttaaAggatcctgtcacaccatatt	7	8	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:17126781A>G	ENST00000265970.7	-	22	3615	c.3616T>C	c.(3616-3618)Ttt>Ctt	p.F1206L	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.F826L	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1206	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.F1206L(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTATCTTTAAAGGATCCTGTC	0.383																																																1	Substitution - Missense(1)	central_nervous_system(1)	11											104	99	101					11																	17126781		2200	4293	6493	17083357	SO:0001583	missense	5286			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3616T>C	11.37:g.17126781A>G	ENSP00000265970:p.Phe1206Leu		17083357	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	35	5.430685	0.96150	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80566	-1.39;-1.39	5.64	5.64	0.86602	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.87410	0.6170	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.86555	0.1837	10	0.38643	T	0.18	-20.0574	15.8745	0.79151	1.0:0.0:0.0:0.0	.	1206	O00443	P3C2A_HUMAN	L	1206;826	ENSP00000265970:F1206L;ENSP00000438687:F826L	ENSP00000265970:F1206L	F	-	1	0	PIK3C2A	17083357	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.201000	0.95017	2.151000	0.67156	0.459000	0.35465	TTT		0.383	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17126781	A	G	17126781	3	3	113	1	0	0	0	0	1	0	0	0	11940	72	3	4	1488	4	PIK3C2A	11	17126781	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	8994386	17126781	117879735	167	30568										
LGR4	55366	hgsc.bcm.edu	37	chr11	27390274	27390274	+	Frame_Shift_Del	DEL	C	C	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acctaggaaagccaaaagggCagcaacccggaactgtttga							TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:27390274delC	ENST00000379214.4	-	18	2439	c.1996delG	c.(1996-1998)gccfs	p.A666fs	LGR4_ENST00000389858.4_Frame_Shift_Del_p.A642fs	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	666					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						GCCAAAAGGGCAGCAACCCGG	0.418																																																0			11											91	86	88					11																	27390274		2202	4299	6501	27346850	SO:0001589	frameshift_variant	55366			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1996delG	11.37:g.27390274delC	ENSP00000368516:p.Ala666fs		27346850	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Frame_Shift_Del	DEL	ENST00000379214.4	37	CCDS31449.1																																																																																				0.418	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		-	27390274	C	-	27390274	7	5	113	1	0	1	0	1	0	0	0	0	8779	710	25	0	863	0	LGR4	11	27390274	Frame_Shift_Del	DEL	C	TCGA-EI-6510-01A-11D-1733-10	10263493	27390274	107616242	168	30569										
KIF18A	81930	hgsc.bcm.edu	37	chr11	28058013	28058013	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttaaggttactgtagacggaTtttgaaaagcttttctacag	9	5	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:28058013T>C	ENST00000263181.6	-	14	2437	c.2147A>G	c.(2146-2148)aAt>aGt	p.N716S		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	716					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TGTAGACGGATTTTGAAAAGC	0.358																																																0			11											117	119	118					11																	28058013		2202	4298	6500	28014589	SO:0001583	missense	81930			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2147A>G	11.37:g.28058013T>C	ENSP00000263181:p.Asn716Ser		28014589	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	T	7.188	0.590943	0.13812	.	.	ENSG00000121621	ENST00000263181	T	0.71103	-0.54	5.87	2.29	0.28610	.	0.282420	0.34932	N	0.003561	T	0.49864	0.1582	L	0.47716	1.5	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.34204	-0.9838	10	0.02654	T	1	.	1.0649	0.01608	0.1392:0.192:0.1795:0.4893	.	716	Q8NI77	KI18A_HUMAN	S	716	ENSP00000263181:N716S	ENSP00000263181:N716S	N	-	2	0	KIF18A	28014589	0.081000	0.21417	0.001000	0.08648	0.314000	0.28054	0.301000	0.19174	0.201000	0.20466	0.533000	0.62120	AAT		0.358	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		C	28058013	T	C	28058013	3	2	113	1	0	0	0	0	1	0	0	0	8301	1493	52	4	565	4	KIF18A	11	28058013	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	667739	28058013	106948503	169	30570										
OR4A16	81327	hgsc.bcm.edu	37	chr11	55110866	55110866	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtacttcttccttgcctacTtgtcacttatggatgccata	6	11	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:55110866T>C	ENST00000314721.2	+	1	240	c.190T>C	c.(190-192)Ttg>Ctg	p.L64L		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L64L(1)		NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						CCTTGCCTACTTGTCACTTAT	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)	11											179	166	171					11																	55110866		2201	4296	6497	54867442	SO:0001819	synonymous_variant	81327			AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.190T>C	11.37:g.55110866T>C			54867442	Q6IFL3	Silent	SNP	ENST00000314721.2	37	CCDS31499.1																																																																																				0.443	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		C	55110866	T	C	55110866	2	2	113	1	0	0	0	0	0	0	0	1	11072	1606	56	4		4	OR4A16	11	55110866	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	27052853	55110866	79895650	170	30571										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563737	55563737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaatccgttctgttagtgggCgccacaaagccttctccacc	8	14	2	0	rs145440752	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:55563737C>T	ENST00000335605.1	+	1	706	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TGTTAGTGGGCGCCACAAAGC	0.463													c|||	5	0.000998403	0.003	0.0014	5008	,	,		18723	0		0	False		,,,				2504	0															0			11						C	CYS/ARG	2,4398	4.2+/-10.8	0,2,2198	131	122	125		706	0.6	0	11	dbSNP_134	125	12,8580	8.4+/-32.0	0,12,4284	yes	missense	OR5D14	NM_001004735.1	180	0,14,6482	TT,TC,CC		0.1397,0.0455,0.1078	benign	236/315	55563737	14,12978	2200	4296	6496	55320313	SO:0001583	missense	219436			AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.706C>T	11.37:g.55563737C>T	ENSP00000334456:p.Arg236Cys		55320313	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	c	4.361	0.066473	0.08388	4.55E-4	0.001397	ENSG00000186113	ENST00000335605	T	0.00337	8.05	5.08	0.556	0.17253	GPCR, rhodopsin-like superfamily (1);	0.172823	0.25774	N	0.028382	T	0.00271	0.0008	M	0.90759	3.145	0.09310	N	1	B	0.26512	0.151	B	0.29524	0.103	T	0.43702	-0.9375	10	0.66056	D	0.02	-3.9031	4.8553	0.13555	0.4904:0.3237:0.0:0.1859	.	236	Q8NGL3	OR5DE_HUMAN	C	236	ENSP00000334456:R236C	ENSP00000334456:R236C	R	+	1	0	OR5D14	55320313	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.501000	0.06398	0.180000	0.19960	-0.195000	0.12781	CGC		0.463	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		T	55563737	C	T	55563737	3	4	113	1	0	0	0	0	1	0	0	0	11186	768	27	1	708	1	OR5D14	11	55563737	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	452871	55563737	79442779	171	30572										
OR8H3	390152	hgsc.bcm.edu	37	chr11	55890336	55890336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctttgtcaatgtggtttccaTgagcagattgcatttctgtg	10	7	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:55890336T>C	ENST00000313472.3	+	1	488	c.488T>C	c.(487-489)aTg>aCg	p.M163T		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	163						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					GTGGTTTCCATGAGCAGATTG	0.433																																																0			11											240	213	222					11																	55890336		2201	4296	6497	55646912	SO:0001583	missense	390152			AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.488T>C	11.37:g.55890336T>C	ENSP00000323928:p.Met163Thr		55646912	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.374414	0.00015	.	.	ENSG00000181761	ENST00000313472	T	0.00016	9.11	3.62	2.46	0.29980	GPCR, rhodopsin-like superfamily (1);	0.090906	0.49305	D	0.000150	T	0.00039	0.0001	N	0.04297	-0.235	0.09310	N	1	B	0.27068	0.167	B	0.30572	0.117	T	0.20974	-1.0259	10	0.02654	T	1	.	4.9378	0.13950	0.0:0.1752:0.165:0.6598	.	163	Q8N146	OR8H3_HUMAN	T	163	ENSP00000323928:M163T	ENSP00000323928:M163T	M	+	2	0	OR8H3	55646912	0.000000	0.05858	0.016000	0.15963	0.076000	0.17211	-0.308000	0.08156	1.415000	0.47037	0.145000	0.16022	ATG		0.433	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		C	55890336	T	C	55890336	3	2	113	1	0	0	0	0	1	0	0	0	11270	1464	51	4	490	4	OR8H3	11	55890336	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	326599	55890336	79116180	172	30573										
MEN1	4221	hgsc.bcm.edu	37	chr11	64571899	64571899	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atctgcacttgcgactgtgcCgtgagttgcagcttgatggc	13	10	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:64571899C>T	ENST00000337652.1	-	10	2258	c.1755G>A	c.(1753-1755)acG>acA	p.T585T	MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000377313.1_Silent_p.T585T|MEN1_ENST00000394376.1_Silent_p.T585T|MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000443283.1_Silent_p.T585T|MEN1_ENST00000377316.2_Silent_p.T525T|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000315422.4_Silent_p.T580T|MEN1_ENST00000394374.2_Silent_p.T585T|MEN1_ENST00000312049.6_Silent_p.T580T|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377321.1_Silent_p.T545T|MEN1_ENST00000377326.3_Silent_p.T580T	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	585					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GCGACTGTGCCGTGAGTTGCA	0.542			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	0			11											241	215	224					11																	64571899		2201	4297	6498	64328475	SO:0001819	synonymous_variant	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1755G>A	11.37:g.64571899C>T			64328475	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000337652.1	37	CCDS8083.1																																																																																				0.542	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			T	64571899	C	T	64571899	2	4	113	1	0	0	0	0	0	0	0	1	9502	639	23	1		1	MEN1	11	64571899	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	8681563	64571899	70434617	173	30574										
TYR	7299	hgsc.bcm.edu	37	chr11	89028403	89028403	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gggcggcgatggtaggggccGtcctcactgccctgctggca	17	13	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:89028403G>T	ENST00000263321.5	+	5	1961	c.1459G>T	c.(1459-1461)Gtc>Ttc	p.V487F		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	487					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GGTAGGGGCCGTCCTCACTGC	0.527																																																0			11											51	53	53					11																	89028403		2201	4299	6500	88668051	SO:0001583	missense	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1459G>T	11.37:g.89028403G>T	ENSP00000263321:p.Val487Phe		88668051	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	9.339	1.062450	0.19987	.	.	ENSG00000077498	ENST00000263321	D	0.99226	-5.59	5.02	4.1	0.47936	.	0.622492	0.16746	N	0.201244	D	0.96315	0.8798	L	0.28344	0.845	0.09310	N	1	P	0.48764	0.915	B	0.37601	0.254	D	0.92603	0.6093	9	.	.	.	.	8.4361	0.32789	0.0851:0.1555:0.7594:0.0	.	487	P14679	TYRO_HUMAN	F	487	ENSP00000263321:V487F	.	V	+	1	0	TYR	88668051	0.003000	0.15002	0.033000	0.17914	0.034000	0.12701	0.787000	0.26858	1.230000	0.43646	0.455000	0.32223	GTC		0.527	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		T	89028403	G	T	89028403	3	4	113	1	0	0	0	0	1	0	0	0	16853	1145	40	2	1477	2	TYR	11	89028403	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	24456504	89028403	45978113	174	30575										
PDGFD	80310	hgsc.bcm.edu	37	chr11	103866948	103866948	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aatggtactggtttcggataTatcttcaacttccacaaaat	6	8	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:103866948T>G	ENST00000393158.2	-	3	534	c.355A>C	c.(355-357)Ata>Cta	p.I119L	PDGFD_ENST00000302251.5_Missense_Mutation_p.I113L			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	119	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		GTTTCGGATATATCTTCAACT	0.323																																																0			11											117	107	110					11																	103866948		2202	4299	6501	103372158	SO:0001583	missense	80310			AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.355A>C	11.37:g.103866948T>G	ENSP00000376865:p.Ile119Leu		103372158	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	37	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	T	2.141	-0.396806	0.04899	.	.	ENSG00000170962	ENST00000393158;ENST00000302251;ENST00000529268	T;T;T	0.17370	2.28;2.28;2.28	5.67	-5.23	0.02798	CUB (5);	0.665176	0.15761	N	0.245905	T	0.05456	0.0144	N	0.02286	-0.61	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.003	T	0.37267	-0.9713	10	0.15952	T	0.53	-4.8026	14.1461	0.65351	0.0953:0.6161:0.0:0.2886	.	119;113	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	L	119;113;142	ENSP00000376865:I119L;ENSP00000302193:I113L;ENSP00000432909:I142L	ENSP00000302193:I113L	I	-	1	0	PDGFD	103372158	0.000000	0.05858	0.014000	0.15608	0.331000	0.28603	-0.781000	0.04648	-0.935000	0.03728	-0.263000	0.10527	ATA		0.323	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		G	103866948	T	G	103866948	3	3	113	1	0	0	0	0	1	0	0	0	11691	1406	49	4	777	4	PDGFD	11	103866948	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	14838545	103866948	31139568	175	30576										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125514021	125514021	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtactccagttctcagccagAaccccgcacaggtctttcct	7	16	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:125514021A>G	ENST00000534070.1	+	10	1214	c.959A>G	c.(958-960)gAa>gGa	p.E320G	CHEK1_ENST00000438015.1_Missense_Mutation_p.E320G|CHEK1_ENST00000427383.2_Missense_Mutation_p.E336G|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000428830.2_Missense_Mutation_p.E320G|CHEK1_ENST00000524737.1_Missense_Mutation_p.E320G|CHEK1_ENST00000544373.1_Missense_Mutation_p.E320G|CHEK1_ENST00000278916.3_Missense_Mutation_p.E320G	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	320					cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		TCTCAGCCAGAACCCCGCACA	0.403								Other conserved DNA damage response genes																																								0			11											107	105	106					11																	125514021		2201	4299	6500	125019231	SO:0001583	missense	1111			AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.959A>G	11.37:g.125514021A>G	ENSP00000435371:p.Glu320Gly		125019231	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	37	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149788	0.57151	.	.	ENSG00000149554	ENST00000438015;ENST00000427383;ENST00000428830;ENST00000544373;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T	0.74106	-0.81;-0.52;-0.81;-0.77;-0.81;-0.81;-0.75	5.58	5.58	0.84498	Protein kinase-like domain (1);	0.053038	0.64402	D	0.000001	T	0.70842	0.3270	L	0.60455	1.87	0.80722	D	1	B;B;B;B	0.21147	0.02;0.052;0.014;0.014	B;B;B;B	0.23419	0.025;0.046;0.015;0.015	T	0.66035	-0.6023	10	0.23302	T	0.38	-23.2131	14.7386	0.69437	1.0:0.0:0.0:0.0	.	320;336;320;320	F5H7S4;E7EPP6;B5BTY6;O14757	.;.;.;CHK1_HUMAN	G	320;336;320;320;320;320;320	ENSP00000388648:E320G;ENSP00000391090:E336G;ENSP00000412504:E320G;ENSP00000442317:E320G;ENSP00000435371:E320G;ENSP00000432890:E320G;ENSP00000278916:E320G	ENSP00000278916:E320G	E	+	2	0	CHEK1	125019231	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.328000	0.90014	2.131000	0.65755	0.533000	0.62120	GAA		0.403	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		G	125514021	A	G	125514021	3	3	113	1	0	0	0	0	1	0	0	0	3340	246	9	4	993	4	CHEK1	11	125514021	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	21647073	125514021	9492495	176	30577										
FLI1	2313	hgsc.bcm.edu	37	chr11	128680652	128680652	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cagccacatccgaccgagtcGtccatgtacaagtacccttc	7	16	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr11:128680652G>A	ENST00000527786.2	+	9	1617	c.1128G>A	c.(1126-1128)tcG>tcA	p.S376S	FLI1_ENST00000344954.6_Silent_p.S343S|FLI1_ENST00000534087.2_Silent_p.S343S|FLI1_ENST00000525560.1_Silent_p.S183S|FLI1_ENST00000281428.8_Silent_p.S310S	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	376					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		CGACCGAGTCGTCCATGTACA	0.498			T	EWSR1	Ewing sarcoma																																		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	0			11											94	97	96					11																	128680652		2138	4255	6393	128185862	SO:0001819	synonymous_variant	2313			M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"Friend leukemia virus integration 1"			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.1128G>A	11.37:g.128680652G>A			128185862	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Silent	SNP	ENST00000527786.2	37	CCDS44768.1																																																																																				0.498	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017		A	128680652	G	A	128680652	2	1	113	1	0	0	0	0	0	0	0	1	5943	1132	40	1		1	FLI1	11	128680652	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	3166631	128680652	6325864	177	30578										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10532376	10532376	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctacagcgatgaagcagcagAaaaaaaatggagatgctgtc	11	7	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:10532376A>G	ENST00000240618.6	-	4	304	c.164T>C	c.(163-165)tTc>tCc	p.F55S	RP11-277P12.20_ENST00000500682.1_RNA|KLRK1_ENST00000540818.1_Missense_Mutation_p.F55S|KLRC4-KLRK1_ENST00000539300.1_3'UTR	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	55					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						GAAGCAGCAGAAAAAAAATGG	0.338																																																0			12											51	48	49					12																	10532376		2203	4300	6503	10423643	SO:0001583	missense	22914			AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.164T>C	12.37:g.10532376A>G	ENSP00000240618:p.Phe55Ser		10423643	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	37	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079598	0.55753	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01379	4.96;4.96	5.64	4.49	0.54785	.	1.007090	0.07995	N	0.987835	T	0.01976	0.0062	L	0.40543	1.245	0.09310	N	1	B;P;P	0.38335	0.119;0.468;0.627	B;B;B	0.35607	0.069;0.206;0.096	T	0.51371	-0.8714	10	0.72032	D	0.01	.	8.4475	0.32852	0.9114:0.0:0.0886:0.0	.	55;36;55	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	S	55	ENSP00000240618:F55S;ENSP00000446003:F55S	ENSP00000240618:F55S	F	-	2	0	KLRK1	10423643	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.573000	0.23699	0.968000	0.38212	0.528000	0.53228	TTC		0.338	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		G	10532376	A	G	10532376	3	3	113	1	0	0	0	0	1	0	0	0	8444	246	9	4	506	4	KLRK1	12	10532376	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10		10532376	123319519	178	30579										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18836249	18836249	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttctggaaaacagaggaataCgacgataacctgcaaaagga	10	7	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:18836249C>A	ENST00000538330.1	-	11	1478	c.1097G>T	c.(1096-1098)cGt>cTt	p.R366L	PLCZ1_ENST00000435379.1_Missense_Mutation_p.R389L|PLCZ1_ENST00000447925.2_Missense_Mutation_p.R582L|PLCZ1_ENST00000266505.7_Missense_Mutation_p.R584L|PLCZ1_ENST00000541695.1_3'UTR|PLCZ1_ENST00000534932.1_Missense_Mutation_p.R65L|PLCZ1_ENST00000539875.1_Missense_Mutation_p.R391L					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CAGAGGAATACGACGATAACC	0.378																																																0			12											111	101	105					12																	18836249		2203	4300	6503	18727516	SO:0001583	missense	89869			AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.1097G>T	12.37:g.18836249C>A	ENSP00000445880:p.Arg366Leu		18727516		Missense_Mutation	SNP	ENST00000538330.1	37		.	.	.	.	.	.	.	.	.	.	C	11.49	1.653803	0.29425	.	.	ENSG00000139151	ENST00000534932;ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000539875	T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64	5.34	2.43	0.29744	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.308722	0.33515	N	0.004826	T	0.08403	0.0209	L	0.40543	1.245	0.32695	N	0.513698	B;P	0.40794	0.304;0.729	B;B	0.31290	0.069;0.127	T	0.18587	-1.0332	10	0.87932	D	0	.	5.0721	0.14611	0.0:0.6269:0.1849:0.1882	.	584;366	Q86YW0;Q8N7S5	PLCZ1_HUMAN;.	L	65;366;584;582;389;391	ENSP00000438826:R65L;ENSP00000445880:R366L;ENSP00000266505:R584L;ENSP00000402358:R582L;ENSP00000400504:R389L;ENSP00000445026:R391L	ENSP00000266505:R584L	R	-	2	0	PLCZ1	18727516	0.074000	0.21230	0.948000	0.38648	0.367000	0.29736	0.376000	0.20535	0.828000	0.34709	-0.140000	0.14226	CGT		0.378	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		A	18836249	C	A	18836249	3	1	113	1	0	0	0	0	1	0	0	0	12075	536	19	2	79	2	PLCZ1	12	18836249	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	8303873	18836249	115015646	179	30580										
KRAS	3845	hgsc.bcm.edu	37	chr12	25362804	25362804	+	3'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcatcttttctttatgtttTcgaatttctcgaactaatgt	4	8	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:25362804T>A	ENST00000256078.4	-	0	679				KRAS_ENST00000557334.1_Silent_p.R51R|KRAS_ENST00000311936.3_Silent_p.R164R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CTTTATGTTTTCGAATTTCTC	0.289		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											63	61	62					12																	25362804		2201	4289	6490	25254071	SO:0001624	3_prime_UTR_variant	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.*46A>T	12.37:g.25362804T>A			25254071	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.289	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25362804	T	A	25362804	1	1	113	0	1	0	0	0	0	0	0	0	8459	1770	62	5		5	KRAS	12	25362804	3'UTR	SNP	T	TCGA-EI-6510-01A-11D-1733-10	6526555	25362804	108489091	180	30581										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	113	1	0	0	0	0	1	0	0	0	8459	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	35480	25398284	108453611	181	30582										
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759698	55759698	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gccagagaaagggtgactttAagcaaaggagtagctgtgct	14	6	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:55759698A>T	ENST00000343399.3	+	1	804	c.804A>T	c.(802-804)ttA>ttT	p.L268F		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						GGGTGACTTTAAGCAAAGGAG	0.433																																																0			12											91	79	83					12																	55759698		2203	4300	6503	54045965	SO:0001583	missense	390323				CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"GPCR / Class A : Olfactory receptors"	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.804A>T	12.37:g.55759698A>T	ENSP00000368987:p.Leu268Phe		54045965		Missense_Mutation	SNP	ENST00000343399.3	37	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	a	13.43	2.234221	0.39498	.	.	ENSG00000187857	ENST00000343399	T	0.00237	8.47	5.22	0.244	0.15507	GPCR, rhodopsin-like superfamily (1);	0.196773	0.24745	N	0.035941	T	0.00271	0.0008	L	0.41632	1.29	0.09310	N	1	D	0.60575	0.988	D	0.67548	0.952	T	0.53927	-0.8369	10	0.27785	T	0.31	.	6.0294	0.19671	0.418:0.3425:0.2394:0.0	.	268	A6NL08	O6C75_HUMAN	F	268	ENSP00000368987:L268F	ENSP00000368987:L268F	L	+	3	2	OR6C75	54045965	0.000000	0.05858	0.798000	0.32154	0.956000	0.61745	-0.545000	0.06069	-0.097000	0.12307	-1.686000	0.00732	TTA		0.433	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			T	55759698	A	T	55759698	3	4	113	1	0	0	0	0	1	0	0	0	11230	359	13	5	806	5	OR6C75	12	55759698	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	30361414	55759698	78092197	182	30583										
XPOT	11260	hgsc.bcm.edu	37	chr12	64827255	64827255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcttcatgcaatttttgaagTgctgctccggccagcagaag	11	10	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:64827255T>C	ENST00000332707.5	+	19	2853	c.2324T>C	c.(2323-2325)gTg>gCg	p.V775A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	775	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		ATTTTTGAAGTGCTGCTCCGG	0.428																																																0			12											133	131	132					12																	64827255		2203	4300	6503	63113522	SO:0001583	missense	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2324T>C	12.37:g.64827255T>C	ENSP00000327821:p.Val775Ala		63113522	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	T	9.444	1.088905	0.20390	.	.	ENSG00000184575	ENST00000332707	T	0.31247	1.5	4.99	4.99	0.66335	Armadillo-type fold (1);	0.059852	0.64402	D	0.000003	T	0.15219	0.0367	N	0.04203	-0.255	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09840	-1.0656	9	.	.	.	.	14.9893	0.71374	0.0:0.0:0.0:1.0	.	775	O43592	XPOT_HUMAN	A	775	ENSP00000327821:V775A	.	V	+	2	0	XPOT	63113522	1.000000	0.71417	0.991000	0.47740	0.096000	0.18686	7.873000	0.87193	2.004000	0.58718	0.528000	0.53228	GTG		0.428	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		C	64827255	T	C	64827255	3	2	113	1	0	0	0	0	1	0	0	0	17490	1696	59	4	2394	4	XPOT	12	64827255	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	9067557	64827255	69024640	183	30584										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83379735	83379735	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atgcgtttaagcaaactcccCgaagcagagcattggtatat	9	9	0	1	rs148211417		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:83379735C>T	ENST00000321196.3	+	8	2687	c.1980C>T	c.(1978-1980)ccC>ccT	p.P660P	TMTC2_ENST00000549919.1_Silent_p.P654P	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	660					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						GCAAACTCCCCGAAGCAGAGC	0.443																																																0			12											191	173	179					12																	83379735		2203	4300	6503	81903866	SO:0001819	synonymous_variant	160335			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1980C>T	12.37:g.83379735C>T			81903866	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	37	CCDS9025.1																																																																																				0.443	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83379735	C	T	83379735	2	4	113	1	0	0	0	0	0	0	0	1	16300	639	23	1		1	TMTC2	12	83379735	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	18552480	83379735	50472160	184	30585										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85438525	85438525	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atggagcagtttctaataatCatatgcatttaagaacagga	8	5	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:85438525C>A	ENST00000393217.2	+	4	335	c.274C>A	c.(274-276)Cat>Aat	p.H92N		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	92										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTCTAATAATCATATGCATTT	0.269																																																0			12											57	62	60					12																	85438525		2192	4250	6442	83962656	SO:0001583	missense	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.274C>A	12.37:g.85438525C>A	ENSP00000376910:p.His92Asn		83962656	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	C	1.816	-0.473399	0.04445	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393212;ENST00000393217	T;T	0.52057	1.5;0.68	4.79	2.96	0.34315	.	0.287844	0.24737	N	0.036005	T	0.39572	0.1083	L	0.53249	1.67	0.20489	N	0.999895	B;B	0.21688	0.041;0.059	B;B	0.24155	0.051;0.05	T	0.30736	-0.9968	10	0.41790	T	0.15	.	6.8087	0.23792	0.0:0.7274:0.1772:0.0953	.	92;92	Q96JM4;C9JI57	LRIQ1_HUMAN;.	N	92	ENSP00000376906:H92N;ENSP00000376910:H92N	ENSP00000256007:H92N	H	+	1	0	LRRIQ1	83962656	0.867000	0.29959	0.468000	0.27192	0.021000	0.10359	0.849000	0.27723	0.729000	0.32403	-0.384000	0.06662	CAT		0.269	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85438525	C	A	85438525	3	1	113	1	0	0	0	0	1	0	0	0	9058	826	29	2	284	2	LRRIQ1	12	85438525	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2058790	85438525	48413370	185	30586										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85521777	85521777	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agaaaatattgtgaatatccGaaaacagagggagaaggctg	12	4	0	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:85521777G>A	ENST00000393217.2	+	18	4236	c.4175G>A	c.(4174-4176)cGa>cAa	p.R1392Q		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1392										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTGAATATCCGAAAACAGAGG	0.328																																																0			12											111	112	112					12																	85521777		1817	4085	5902	84045908	SO:0001583	missense	84125			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4175G>A	12.37:g.85521777G>A	ENSP00000376910:p.Arg1392Gln		84045908	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.463437	0.01062	.	.	ENSG00000133640	ENST00000393217	T	0.50277	0.75	5.21	2.8	0.32819	.	.	.	.	.	T	0.18257	0.0438	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	9	0.02654	T	1	.	0.6727	0.00861	0.4515:0.1361:0.1501:0.2623	.	1392	Q96JM4	LRIQ1_HUMAN	Q	1392	ENSP00000376910:R1392Q	ENSP00000376910:R1392Q	R	+	2	0	LRRIQ1	84045908	0.006000	0.16342	0.970000	0.41538	0.385000	0.30292	0.500000	0.22562	0.361000	0.24292	-0.383000	0.06682	CGA		0.328	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85521777	G	A	85521777	3	1	113	1	0	0	0	0	1	0	0	0	9058	1058	37	1	4245	1	LRRIQ1	12	85521777	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	83252	85521777	48330118	186	30587										
CEP290	80184	hgsc.bcm.edu	37	chr12	88474160	88474160	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tttttcacttcatcttcatgGttttcttgaagcctgatgta	6	8	5	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:88474160G>A	ENST00000552810.1	-	38	5368	c.5025C>T	c.(5023-5025)aaC>aaT	p.N1675N	CEP290_ENST00000397838.3_Silent_p.N735N|CEP290_ENST00000547691.2_Silent_p.N735N|CEP290_ENST00000309041.7_Silent_p.N1677N	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.N1677N(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CATCTTCATGGTTTTCTTGAA	0.363																																																1	Substitution - coding silent(1)	breast(1)	12											111	99	102					12																	88474160		1818	4077	5895	86998291	SO:0001819	synonymous_variant	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5025C>T	12.37:g.88474160G>A			86998291	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1																																																																																				0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88474160	G	A	88474160	2	1	113	1	0	0	0	0	0	0	0	1	3259	1252	44	3		3	CEP290	12	88474160	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	2952383	88474160	45377735	187	30588										
OAS2	4939	hgsc.bcm.edu	37	chr12	113442751	113442751	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttccttagggaggatcaaccGccaaaggcacagctctgaag	11	11	2	1	rs143746502		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:113442751G>A	ENST00000342315.4	+	7	1406	c.1192G>A	c.(1192-1194)Gcc>Acc	p.A398T	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.A398T	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	398	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AGGATCAACCGCCAAAGGCAC	0.517													G|||	1	0.000199681	0	0	5008	,	,		19896	0.001		0	False		,,,				2504	0				Pancreas(199;709 2232 18410 33584 35052)											0			12											62	62	62					12																	113442751		2203	4300	6503	111927134	SO:0001583	missense	4939			M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1192G>A	12.37:g.113442751G>A	ENSP00000342278:p.Ala398Thr		111927134	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	37	CCDS31906.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	.	13.86	2.364157	0.41902	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.10099	2.91;2.91	4.17	3.27	0.37495	2-5-oligoadenylate synthetase, N-terminal (1);Nucleotidyl transferase domain (1);2-5-oligoadenylate synthetase, conserved site (1);	0.768093	0.10875	N	0.624472	T	0.26666	0.0652	M	0.72894	2.215	0.24669	N	0.993428	D;D	0.76494	0.999;0.999	P;P	0.61477	0.889;0.823	T	0.06338	-1.0832	10	0.72032	D	0.01	-3.8504	7.9747	0.30149	0.1147:0.0:0.8853:0.0	.	398;398	P29728;P29728-2	OAS2_HUMAN;.	T	398	ENSP00000342278:A398T;ENSP00000376362:A398T	ENSP00000342278:A398T	A	+	1	0	OAS2	111927134	0.898000	0.30612	0.137000	0.22149	0.045000	0.14185	2.538000	0.45710	1.106000	0.41623	0.591000	0.81541	GCC		0.517	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			A	113442751	G	A	113442751	3	1	113	1	0	0	0	0	1	0	0	0	10831	1087	38	1	1289	1	OAS2	12	113442751	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	24968591	113442751	20409144	188	30589										
KSR2	283455	hgsc.bcm.edu	37	chr12	117923480	117923480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctcacaacggaatagagcgTccgtcccttacagaggctga	10	13	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:117923480T>C	ENST00000339824.5	-	15	2963	c.2236A>G	c.(2236-2238)Acg>Gcg	p.T746A	KSR2_ENST00000302438.5_3'UTR|KSR2_ENST00000425217.1_Missense_Mutation_p.T717A			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	746	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAATAGAGCGTCCGTCCCTTA	0.448																																																0			12											105	98	100					12																	117923480		1916	4134	6050	116407863	SO:0001583	missense	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2236A>G	12.37:g.117923480T>C	ENSP00000339952:p.Thr746Ala		116407863	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	37		.	.	.	.	.	.	.	.	.	.	T	14.81	2.645720	0.47258	.	.	ENSG00000171435	ENST00000425217;ENST00000339824	D;D	0.89552	-2.53;-2.53	5.75	5.75	0.90469	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87888	0.6291	M	0.71871	2.18	0.58432	D	0.999999	B	0.21606	0.058	B	0.24541	0.054	D	0.85360	0.1107	10	0.62326	D	0.03	.	11.1531	0.48471	0.0:0.0712:0.0:0.9288	.	746	Q6VAB6	KSR2_HUMAN	A	717;746	ENSP00000389715:T717A;ENSP00000339952:T746A	ENSP00000339952:T746A	T	-	1	0	KSR2	116407863	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	6.236000	0.72339	2.194000	0.70268	0.533000	0.62120	ACG		0.448	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		C	117923480	T	C	117923480	3	2	113	1	0	0	0	0	1	0	0	0	8604	1667	58	4	640	4	KSR2	12	117923480	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	4480729	117923480	15928415	189	30590										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130884319	130884319	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atcaggcacttcttccaagaAgtttgagggcacaaggcctt	10	10	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:130884319A>G	ENST00000261655.4	-	18	3200	c.3037T>C	c.(3037-3039)Ttc>Ctc	p.F1013L		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	1013	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCTTCCAAGAAGTTTGAGGGC	0.463																																																0			12											114	103	106					12																	130884319		2203	4300	6503	129450272	SO:0001583	missense	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.3037T>C	12.37:g.130884319A>G	ENSP00000261655:p.Phe1013Leu		129450272	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.005962	0.93287	.	.	ENSG00000060709	ENST00000261655;ENST00000536632	T;T	0.54479	0.57;0.57	5.32	5.32	0.75619	Src homology-3 domain (4);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.66577	0.2803	L	0.52573	1.65	0.80722	D	1	D	0.65815	0.995	D	0.80764	0.994	T	0.65253	-0.6213	10	0.38643	T	0.18	-33.4778	15.3201	0.74115	1.0:0.0:0.0:0.0	.	1013	O15034	RIMB2_HUMAN	L	1013;150	ENSP00000261655:F1013L;ENSP00000439030:F150L	ENSP00000261655:F1013L	F	-	1	0	RIMBP2	129450272	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.898000	0.92538	2.028000	0.59812	0.392000	0.25879	TTC		0.463	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		G	130884319	A	G	130884319	3	3	113	1	0	0	0	0	1	0	0	0	13400	72	3	4	129	4	RIMBP2	12	130884319	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	12960839	130884319	2967576	190	30591										
GALNT9	50614	hgsc.bcm.edu	37	chr12	132685760	132685760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgcgacacttcagcctctgaCgcagggccagcctctcagac	10	16	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr12:132685760C>T	ENST00000328957.8	-	8	1309	c.1310G>A	c.(1309-1311)cGt>cAt	p.R437H	GALNT9_ENST00000541995.1_Missense_Mutation_p.R71H|GALNT9_ENST00000535228.1_Missense_Mutation_p.R188H|GALNT9_ENST00000397325.2_Missense_Mutation_p.R71H	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	437					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		CAGCCTCTGACGCAGGGCCAG	0.587																																					Colon(186;2147 2752 13553 41466)											0			12											59	73	68					12																	132685760		2126	4226	6352	131251713	SO:0001583	missense	50614			AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4131	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 9"	606251	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1310G>A	12.37:g.132685760C>T	ENSP00000329846:p.Arg437His		131251713	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	37		.	.	.	.	.	.	.	.	.	.	c	32	5.150128	0.94645	.	.	ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995;ENST00000538356	T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	D	0.83566	0.5282	H	0.96142	3.775	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89833	0.3997	10	0.87932	D	0	.	16.9295	0.86186	0.0:1.0:0.0:0.0	.	188;437;294	B3KNR7;Q9HCQ5;B3KP58	.;GALT9_HUMAN;.	H	71;437;188;71;71	ENSP00000380488:R71H;ENSP00000329846:R437H;ENSP00000439745:R188H;ENSP00000440544:R71H;ENSP00000444709:R71H	ENSP00000329846:R437H	R	-	2	0	GALNT9	131251713	1.000000	0.71417	0.975000	0.42487	0.981000	0.71138	7.571000	0.82399	1.967000	0.57214	0.462000	0.41574	CGT		0.587	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		T	132685760	C	T	132685760	3	4	113	1	0	0	0	0	1	0	0	0	6240	536	19	1	517	1	GALNT9	12	132685760	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	1801441	132685760	1166135	191	30592										
RB1	5925	hgsc.bcm.edu	37	chr13	49037904	49037904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtatggcatatgcaaagtgaAgaatatagaccttaaattca	8	5	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr13:49037904A>G	ENST00000267163.4	+	21	2282	c.2144A>G	c.(2143-2145)aAg>aGg	p.K715R		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	715	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TGCAAAGTGAAGAATATAGAC	0.289		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											108	114	112					13																	49037904		2203	4293	6496	47935905	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2144A>G	13.37:g.49037904A>G	ENSP00000267163:p.Lys715Arg		47935905	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326729	0.81690	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.91237	-2.81	6.07	6.07	0.98685	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.92319	0.7563	M	0.62723	1.935	0.54753	D	0.999986	P	0.48911	0.917	P	0.54706	0.759	D	0.91611	0.5303	10	0.41790	T	0.15	-18.13	12.4026	0.55422	0.9333:0.0:0.0667:0.0	.	715	P06400	RB_HUMAN	R	694;715	ENSP00000267163:K715R	ENSP00000267163:K715R	K	+	2	0	RB1	47935905	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.161000	0.77505	2.326000	0.78906	0.533000	0.62120	AAG		0.289	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	49037904	A	G	49037904	3	3	113	1	0	0	0	0	1	0	0	0	13135	72	3	4	2226	4	RB1	13	49037904	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10		49037904	66131974	192	30593										
CARKD	55739	hgsc.bcm.edu	37	chr13	111287085	111287085	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	accggaaggctgtgctcactCccaaccacgtggagttcagc	11	14	2	0	rs267603758		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr13:111287085C>A	ENST00000309957.2	+	7	627	c.613C>A	c.(613-615)Ccc>Acc	p.P205T	CARKD_ENST00000458711.2_Missense_Mutation_p.P74T|CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000424185.2_Missense_Mutation_p.P95T|CARKD_ENST00000397191.4_3'UTR	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing									p.P205S(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						TGTGCTCACTCCCAACCACGT	0.607																																																1	Substitution - Missense(1)	skin(1)	13											73	60	64					13																	111287085		2203	4300	6503	110085086	SO:0001583	missense	55739			AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.613C>A	13.37:g.111287085C>A	ENSP00000311984:p.Pro205Thr		110085086		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.631804	0.67015	.	.	ENSG00000213995	ENST00000458711;ENST00000424185;ENST00000439607;ENST00000309957	T;T;T	0.75050	-0.9;-0.9;-0.9	5.12	5.12	0.69794	Uncharacterised domain, carbohydrate kinase-related (3);	0.000000	0.85682	D	0.000000	D	0.91334	0.7267	H	0.97440	4.005	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.998;0.999;0.998	D	0.94445	0.7662	10	0.87932	D	0	-34.7158	17.3438	0.87305	0.0:1.0:0.0:0.0	.	74;95;187;205;205	B4DQR1;Q8IW45-4;B4DKX7;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	T	74;95;187;205	ENSP00000412789:P74T;ENSP00000413191:P95T;ENSP00000311984:P205T	ENSP00000311984:P205T	P	+	1	0	CARKD	110085086	1.000000	0.71417	0.942000	0.38095	0.199000	0.23934	7.093000	0.76937	2.360000	0.80028	0.655000	0.94253	CCC		0.607	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210		A	111287085	C	A	111287085	3	1	113	1	0	0	0	0	1	0	0	0	2660	855	30	2	639	2	CARKD	13	111287085	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	62249181	111287085	3882793	193	30594										
ZNF828	283489	hgsc.bcm.edu	37	chr13	115090658	115090658	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaaccctcagggtcaccagaTctttggaagctttctcctga	8	12	4	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr13:115090658T>C	ENST00000361283.1	+	3	1650	c.1341T>C	c.(1339-1341)gaT>gaC	p.D447D		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	447	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.D447D(1)									GGTCACCAGATCTTTGGAAGC	0.532																																																1	Substitution - coding silent(1)	ovary(1)	13											112	129	123					13																	115090658		2203	4300	6503	114108760	SO:0001819	synonymous_variant	283489			AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.1341T>C	13.37:g.115090658T>C			114108760	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	37	CCDS9545.1																																																																																				0.532	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		C	115090658	T	C	115090658	2	2	113	1	0	0	0	0	0	0	0	1	18220	1432	50	4		4	ZNF828	13	115090658	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	3803573	115090658	79220	194	30595										
SPTB	6710	hgsc.bcm.edu	37	chr14	65216156	65216156	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctctgggactcgttgatggcGgtgctcacgccctgcagcca	13	14	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:65216156G>A	ENST00000556626.1	-	36	6997	c.6855C>T	c.(6853-6855)acC>acT	p.T2285T	SPTB_ENST00000342835.4_5'UTR|SPTB_ENST00000389722.3_Silent_p.T2285T			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	0					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CGTTGATGGCGGTGCTCACGC	0.692																																																0			14											47	44	45					14																	65216156		2203	4300	6503	64285909	SO:0001819	synonymous_variant	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000556626.1:c.6855C>T	14.37:g.65216156G>A			64285909	Q15510|Q15519	Silent	SNP	ENST00000556626.1	37	CCDS32099.1																																																																																				0.692	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414076.1			A	65216156	G	A	65216156	2	1	113	1	0	0	0	0	0	0	0	1	15157	1103	39	1		1	SPTB	14	65216156	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10		65216156	42133384	195	30596										
SPTB	6710	hgsc.bcm.edu	37	chr14	65253730	65253730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gatgatacctgccaggtcccGccccaggtcttttgtggact	11	13	1	1	rs371628390	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:65253730G>A	ENST00000389721.5	-	15	2985	c.2953C>T	c.(2953-2955)Cgg>Tgg	p.R985W	SPTB_ENST00000389720.3_Missense_Mutation_p.R985W|SPTB_ENST00000542895.1_Missense_Mutation_p.R985W|SPTB_ENST00000389722.3_Missense_Mutation_p.R985W|SPTB_ENST00000556626.1_Missense_Mutation_p.R985W	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	985					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCCAGGTCCCGCCCCAGGTCT	0.602													g|||	2	0.000399361	8e-04	0	5008	,	,		18467	0		0	False		,,,				2504	0.001															0			14							TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	81	76	78		2953,2953	4.2	1	14		78	0,8600		0,0,4300	no	missense,missense	SPTB	NM_000347.5,NM_001024858.2	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	985/2138,985/2329	65253730	1,13005	2203	4300	6503	64323483	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.2953C>T	14.37:g.65253730G>A	ENSP00000374371:p.Arg985Trp		64323483	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028681	0.75390	2.27E-4	0.0	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	5.06	4.16	0.48862	.	0.443348	0.24463	N	0.038311	T	0.55194	0.1905	M	0.68952	2.095	0.20074	N	0.999935	D;D	0.60160	0.987;0.977	P;P	0.51453	0.67;0.67	T	0.52902	-0.8513	10	0.72032	D	0.01	.	11.6703	0.51396	0.0:0.0:0.5623:0.4377	.	985;989	P11277;Q59FP5	SPTB1_HUMAN;.	W	989;985;985;985;985;985	ENSP00000374372:R985W;ENSP00000451752:R985W;ENSP00000374371:R985W;ENSP00000443882:R985W;ENSP00000374370:R985W	ENSP00000374370:R985W	R	-	1	2	SPTB	64323483	0.000000	0.05858	0.992000	0.48379	0.992000	0.81027	0.862000	0.27899	1.253000	0.44018	0.549000	0.68633	CGG		0.602	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			A	65253730	G	A	65253730	3	1	113	1	0	0	0	0	1	0	0	0	15157	1086	38	1	4186	1	SPTB	14	65253730	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	37574	65253730	42095810	196	30597										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92480701	92480701	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aatttcaagttttcacattcTtccattatttgtctcttttc	2	9	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:92480701T>C	ENST00000267622.4	-	7	1417	c.1044A>G	c.(1042-1044)gaA>gaG	p.E348E		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	348					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTTCACATTCTTCCATTATTT	0.328			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											151	127	135					14																	92480701		2203	4299	6502	91550454	SO:0001819	synonymous_variant	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.1044A>G	14.37:g.92480701T>C			91550454	B2RUT2|O14689|O15154|O95949	Silent	SNP	ENST00000267622.4	37	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	T	8.182	0.794013	0.16327	.	.	ENSG00000100815	ENST00000554357	.	.	.	5.43	1.61	0.23674	.	.	.	.	.	T	0.45756	0.1358	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23904	-1.0175	4	.	.	.	.	3.406	0.07341	0.2765:0.1949:0.0:0.5286	.	.	.	.	G	93	.	.	R	-	1	2	TRIP11	91550454	0.998000	0.40836	0.186000	0.23195	0.981000	0.71138	0.289000	0.18957	0.082000	0.17018	-0.496000	0.04628	AGA		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92480701	T	C	92480701	2	2	113	1	0	0	0	0	0	0	0	1	16595	1606	56	4		4	TRIP11	14	92480701	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	27226971	92480701	14868839	197	30598										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94060163	94060163	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	caatttcaacagcaaagactGgaagatgaggtttgaagcag	11	6	1	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:94060163G>A	ENST00000393151.2	+	23	3170	c.3170G>A	c.(3169-3171)tGg>tAg	p.W1057*	UNC79_ENST00000555664.1_Nonsense_Mutation_p.W1057*|UNC79_ENST00000553484.1_Nonsense_Mutation_p.W1057*|UNC79_ENST00000256339.4_Nonsense_Mutation_p.W880*			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1057					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.W880*(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGCAAAGACTGGAAGATGAGG	0.483																																																1	Substitution - Nonsense(1)	ovary(1)	14											156	136	143					14																	94060163		2203	4300	6503	93129916	SO:0001587	stop_gained	57578			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.3170G>A	14.37:g.94060163G>A	ENSP00000376858:p.Trp1057*		93129916	B5MDL6|Q6ZUT7	Nonsense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	G	42	9.368463	0.99150	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.1738	19.978	0.97315	0.0:0.0:1.0:0.0	.	.	.	.	X	880;1057;1057;1057;1057	.	ENSP00000256339:W880X	W	+	2	0	KIAA1409	93129916	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.733000	0.93635	0.557000	0.71058	TGG		0.483	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94060163	G	A	94060163	4	1	113	1	0	0	0	0	0	1	0	0	8251	1357	47	3	2717	3	KIAA1409	14	94060163	Nonsense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	1579462	94060163	13289377	198	30599										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95899734	95899734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atgctgaccttctggcacccGagcctccagctcctggggga	12	15	1	1	rs542033506		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:95899734G>A	ENST00000334258.5	-	15	2565	c.2551C>T	c.(2551-2553)Cgg>Tgg	p.R851W	SYNE3_ENST00000557275.1_Missense_Mutation_p.R846W|SYNE3_ENST00000554873.1_Missense_Mutation_p.R608W	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	851					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						TCTGGCACCCGAGCCTCCAGC	0.582																																																0			14											63	64	64					14																	95899734		2203	4300	6503	94969487	SO:0001583	missense	161176			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2551C>T	14.37:g.95899734G>A	ENSP00000334308:p.Arg851Trp		94969487	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192208	0.58017	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.16743	3.35;2.32;3.36	5.55	3.46	0.39613	.	0.257321	0.20260	N	0.095889	T	0.39489	0.1080	M	0.71581	2.175	0.09310	N	0.999998	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.958	T	0.15780	-1.0425	10	0.72032	D	0.01	-30.7355	13.3618	0.60661	0.0:0.0:0.7036:0.2964	.	846;851	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	W	851;608;846	ENSP00000334308:R851W;ENSP00000452154:R608W;ENSP00000450562:R846W	ENSP00000334308:R851W	R	-	1	2	C14orf49	94969487	0.298000	0.24417	0.130000	0.21974	0.997000	0.91878	3.052000	0.49893	1.290000	0.44636	0.655000	0.94253	CGG		0.582	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95899734	G	A	95899734	3	1	113	1	0	0	0	0	1	0	0	0	1780	1057	37	1	388	1	C14orf49	14	95899734	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	1839571	95899734	11449806	199	30600										
BDKRB2	624	hgsc.bcm.edu	37	chr14	96707252	96707252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctcacccatgctggtgttccGgaccatgaaggagtacagcg	12	12	1	1	rs201760673		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr14:96707252G>A	ENST00000306005.3	+	3	783	c.587G>A	c.(586-588)cGg>cAg	p.R196Q	BDKRB2_ENST00000542454.2_Missense_Mutation_p.R169Q|RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000539359.1_Missense_Mutation_p.R169Q|BDKRB2_ENST00000554311.1_Missense_Mutation_p.R196Q	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	196					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)	p.R196Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	CTGGTGTTCCGGACCATGAAG	0.587																																																1	Substitution - Missense(1)	ovary(1)	14											111	93	99					14																	96707252		2203	4300	6503	95777005	SO:0001583	missense	624			S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.587G>A	14.37:g.96707252G>A	ENSP00000307713:p.Arg196Gln		95777005		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	G	32	5.167607	0.94768	.	.	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	4.72	4.72	0.59763	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61776	0.2374	M	0.75264	2.295	0.51767	D	0.999931	D	0.89917	1.0	D	0.97110	1.0	T	0.65829	-0.6073	10	0.56958	D	0.05	-39.987	18.0446	0.89328	0.0:0.0:1.0:0.0	.	196	P30411	BKRB2_HUMAN	Q	169;196;196;169	ENSP00000439459:R169Q;ENSP00000450482:R196Q;ENSP00000307713:R196Q;ENSP00000438376:R169Q	ENSP00000307713:R196Q	R	+	2	0	BDKRB2	95777005	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.695000	0.98691	2.332000	0.79248	0.561000	0.74099	CGG		0.587	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			A	96707252	G	A	96707252	3	1	113	1	0	0	0	0	1	0	0	0	1394	1116	39	1	593	1	BDKRB2	14	96707252	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	807518	96707252	10642288	200	30601										
CHRM5	1133	hgsc.bcm.edu	37	chr15	34356328	34356328	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtttctaccttctgtgacaaGtgtgtcccagtcaccctgtg	9	12	3	1	rs547672974		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:34356328G>A	ENST00000383263.5	+	3	2080	c.1410G>A	c.(1408-1410)aaG>aaA	p.K470K	CHRM5_ENST00000557872.1_Silent_p.K470K	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	470					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	TCTGTGACAAGTGTGTCCCAG	0.512																																																0			15											189	165	173					15																	34356328		2201	4298	6499	32143620	SO:0001819	synonymous_variant	1133				CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.1410G>A	15.37:g.34356328G>A			32143620	Q96RG7	Silent	SNP	ENST00000383263.5	37	CCDS10031.1																																																																																				0.512	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			A	34356328	G	A	34356328	2	1	113	1	0	0	0	0	0	0	0	1	3386	1020	36	3		3	CHRM5	15	34356328	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10		34356328	68175064	201	30602										
MFAP1	4236	hgsc.bcm.edu	37	chr15	44097661	44097661	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttgtatacttcttcatcctcAtcctgtataaaaaaaatctt	2	9	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:44097661A>G	ENST00000267812.3	-	8	1282	c.1050T>C	c.(1048-1050)gaT>gaC	p.D350D		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	350					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		CTTCATCCTCATCCTGTATAA	0.353																																																0			15											97	95	96					15																	44097661		2198	4298	6496	41884953	SO:0001819	synonymous_variant	4236				CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.1050T>C	15.37:g.44097661A>G			41884953	Q86TG6	Silent	SNP	ENST00000267812.3	37	CCDS10105.1																																																																																				0.353	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		G	44097661	A	G	44097661	2	3	113	1	0	0	0	0	0	0	0	1	9543	214	8	4		4	MFAP1	15	44097661	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10	9741333	44097661	58433731	202	30603										
SGK269	79834	hgsc.bcm.edu	37	chr15	77425989	77425989	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggtgtaggttgggaagcattGggtgcttcttggtctgtttt	16	4	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:77425989G>T	ENST00000560626.2	-	6	3910	c.3435C>A	c.(3433-3435)ccC>ccA	p.P1145P	PEAK1_ENST00000312493.4_Silent_p.P1145P			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1145			P -> L (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGGAAGCATTGGGTGCTTCTT	0.512																																																0			15											115	108	110					15																	77425989		1970	4143	6113	75213044	SO:0001819	synonymous_variant	0				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3435C>A	15.37:g.77425989G>T			75213044	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																				0.512	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			T	77425989	G	T	77425989	2	4	113	1	0	0	0	0	0	0	0	1	14248	1335	47	2		2	SGK269	15	77425989	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	33328328	77425989	25105403	203	30604										
FSD2	123722	hgsc.bcm.edu	37	chr15	83455685	83455685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctcgctggcacggccgtgtGtgtacctataggcttcccgc	12	15	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:83455685G>A	ENST00000334574.8	-	2	639	c.458C>T	c.(457-459)aCa>aTa	p.T153I	FSD2_ENST00000541889.1_Missense_Mutation_p.T153I			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	153										breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						ACGGCCGTGTGTGTACCTATA	0.577																																																0			15											71	75	74					15																	83455685		2070	4210	6280	81252739	SO:0001583	missense	123722			AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.458C>T	15.37:g.83455685G>A	ENSP00000335651:p.Thr153Ile		81252739	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.313378	0.23908	.	.	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.46063	0.88;0.88	5.27	1.17	0.20885	.	1.190140	0.05920	N	0.633266	T	0.37679	0.1012	L	0.51422	1.61	0.09310	N	1	B;B	0.28713	0.22;0.138	B;B	0.27380	0.058;0.079	T	0.34079	-0.9843	10	0.49607	T	0.09	-0.1755	7.2875	0.26348	0.1459:0.2614:0.5927:0.0	.	153;153	B7ZM02;A1L4K1	.;FSD2_HUMAN	I	153	ENSP00000335651:T153I;ENSP00000444078:T153I	ENSP00000335651:T153I	T	-	2	0	FSD2	81252739	0.015000	0.18098	0.000000	0.03702	0.287000	0.27160	1.047000	0.30367	0.202000	0.20498	0.655000	0.94253	ACA		0.577	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		A	83455685	G	A	83455685	3	1	113	1	0	0	0	0	1	0	0	0	6090	1377	48	3	1839	3	FSD2	15	83455685	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	6029696	83455685	19075707	204	30605										
BTBD1	53339	hgsc.bcm.edu	37	chr15	83718827	83718827	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	acttcatagcgaacttacctAtatcaatatcagtaaaccct	3	11	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:83718827A>G	ENST00000261721.4	-	3	864	c.662T>C	c.(661-663)aTa>aCa	p.I221T	RP11-382A20.7_ENST00000570202.1_RNA|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.6_ENST00000568441.1_RNA|BTBD1_ENST00000379403.2_Missense_Mutation_p.I221T	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	221					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		GAACTTACCTATATCAATATC	0.358																																																0			15											122	113	116					15																	83718827		2202	4299	6501	81509831	SO:0001583	missense	53339			AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.662T>C	15.37:g.83718827A>G	ENSP00000261721:p.Ile221Thr		81509831	A6NMI8|Q9BX71|Q9NWN4	Missense_Mutation	SNP	ENST00000261721.4	37	CCDS10322.1	.	.	.	.	.	.	.	.	.	.	A	16.27	3.074558	0.55646	.	.	ENSG00000064726	ENST00000261721;ENST00000379403	T;T	0.68624	-0.34;-0.34	5.51	4.35	0.52113	BTB/Kelch-associated (2);	0.100357	0.64402	D	0.000002	T	0.58652	0.2137	L	0.29908	0.895	0.47584	D	0.999462	P;B	0.36633	0.562;0.452	B;B	0.41135	0.348;0.266	T	0.58994	-0.7537	10	0.49607	T	0.09	-27.3197	12.6224	0.56610	0.8614:0.1386:0.0:0.0	.	221;221	A6NMI8;Q9H0C5	.;BTBD1_HUMAN	T	221	ENSP00000261721:I221T;ENSP00000368713:I221T	ENSP00000261721:I221T	I	-	2	0	BTBD1	81509831	1.000000	0.71417	0.942000	0.38095	0.993000	0.82548	5.856000	0.69518	0.970000	0.38263	0.533000	0.62120	ATA		0.358	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			G	83718827	A	G	83718827	3	3	113	1	0	0	0	0	1	0	0	0	1540	449	16	4	810	4	BTBD1	15	83718827	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	263142	83718827	18812565	205	30606										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84659942	84659942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aggcagcccttggagcaaacGtgacaatccgatgtcctgta	11	11	0	1	rs77086705		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:84659942G>A	ENST00000286744.5	+	23	4173	c.3949G>A	c.(3949-3951)Gtg>Atg	p.V1317M	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.V1317M|AC027807.1_ENST00000408557.1_RNA	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1317	Ig-like C2-type 3.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V1317M(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGGAGCAAACGTGACAATCCG	0.498																																																1	Substitution - Missense(1)	lung(1)	15						G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	243	220	228		3949	1.9	0.6	15	dbSNP_131	228	0,8598		0,0,4299	no	missense	ADAMTSL3	NM_207517.2	21	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	1317/1692	84659942	1,13003	2203	4299	6502	82450946	SO:0001583	missense	57188			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.3949G>A	15.37:g.84659942G>A	ENSP00000286744:p.Val1317Met		82450946	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.363487	0.24684	2.27E-4	0.0	ENSG00000156218	ENST00000286744	T	0.37235	1.21	5.21	1.94	0.25998	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.32802	N	0.005634	T	0.34687	0.0906	M	0.66939	2.045	0.32056	N	0.596305	B;B	0.25235	0.121;0.101	B;B	0.30401	0.115;0.05	T	0.42241	-0.9463	10	0.62326	D	0.03	.	6.7034	0.23236	0.4378:0.0:0.5622:0.0	.	1317;1317	P82987-2;P82987	.;ATL3_HUMAN	M	1317	ENSP00000286744:V1317M	ENSP00000286744:V1317M	V	+	1	0	ADAMTSL3	82450946	0.481000	0.25941	0.592000	0.28758	0.653000	0.38743	0.495000	0.22483	0.599000	0.29845	-0.995000	0.02519	GTG		0.498	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		A	84659942	G	A	84659942	3	1	113	1	0	0	0	0	1	0	0	0	276	1145	40	1	4035	1	ADAMTSL3	15	84659942	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	941115	84659942	17871450	206	30607										
DET1	55070	hgsc.bcm.edu	37	chr15	89070831	89070831	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtctggtggaacagcttaccGgcgctggatctgccttgcaa	13	11	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:89070831G>A	ENST00000268148.8	-	3	1415	c.1270C>T	c.(1270-1272)Cgg>Tgg	p.R424W	DET1_ENST00000444300.1_Splice_Site_p.R435W|DET1_ENST00000564406.1_Splice_Site_p.R435W	NM_001144074.1	NP_001137546.1	Q7L5Y6	DET1_HUMAN	de-etiolated homolog 1 (Arabidopsis)	424						nucleus (GO:0005634)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			ACAGCTTACCGGCGCTGGATC	0.448																																																0			15											65	62	63					15																	89070831		1870	4108	5978	86871835	SO:0001630	splice_region_variant	55070			BC001242	CCDS45343.1, CCDS45344.1	15q25.3	2004-12-13				ENSG00000140543			25477	protein-coding gene	gene with protein product		608727				14739464	Standard	NM_001144074		Approved	FLJ10103	uc002bmq.2	Q7L5Y6		ENST00000268148.8:c.1271+1C>T	15.37:g.89070831G>A			86871835	B3KNN6|Q2VPC0|Q9NWD5	Missense_Mutation	SNP	ENST00000268148.8	37	CCDS45344.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798334	0.70567	.	.	ENSG00000140543	ENST00000444300;ENST00000268148	.	.	.	5.7	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.79953	0.4535	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.83273	-0.0042	9	0.87932	D	0	-20.376	15.1781	0.72931	0.0:0.0:0.858:0.142	.	424;435	Q7L5Y6;B3KNN6	DET1_HUMAN;.	W	435;424	.	ENSP00000268148:R424W	R	-	1	2	DET1	86871835	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.652000	0.67959	1.394000	0.46624	0.655000	0.94253	CGG		0.448	DET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415442.2	NM_017996	Missense_Mutation	A	89070831	G	A	89070831	5	1	113	1	0	0	0	0	0	0	1	0	4461	1130	39	1	394	1	DET1	15	89070831	Splice_Site	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4410889	89070831	13460561	207	30608										
IDH2	3418	hgsc.bcm.edu	37	chr15	90631880	90631880	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tccagccagggactaggcgtGggatgtttttgcagatgatg	15	7	0	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:90631880G>T	ENST00000330062.3	-	4	586	c.473C>A	c.(472-474)cCa>cAa	p.P158Q	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.P106Q|IDH2_ENST00000539790.1_Missense_Mutation_p.P28Q	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	158					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			GACTAGGCGTGGGATGTTTTT	0.587			M		GBM																																		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	0			15											115	111	112					15																	90631880		2200	4298	6498	88432884	SO:0001583	missense	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.473C>A	15.37:g.90631880G>T	ENSP00000331897:p.Pro158Gln		88432884	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.426768	0.62733	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	T;T;T	0.68903	-0.36;-0.36;-0.36	5.93	5.01	0.66863	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.80869	0.4706	M	0.93594	3.435	0.58432	D	0.999999	D	0.56746	0.977	P	0.50659	0.647	D	0.86313	0.1687	10	0.87932	D	0	.	14.2254	0.65855	0.0:0.0:0.8496:0.1504	.	158	P48735	IDHP_HUMAN	Q	158;28;106	ENSP00000331897:P158Q;ENSP00000438457:P28Q;ENSP00000446147:P106Q	ENSP00000331897:P158Q	P	-	2	0	IDH2	88432884	1.000000	0.71417	0.899000	0.35326	0.249000	0.25844	9.842000	0.99487	1.494000	0.48533	0.561000	0.74099	CCA		0.587	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			T	90631880	G	T	90631880	3	4	113	1	0	0	0	0	1	0	0	0	7516	1348	47	2	917	2	IDH2	15	90631880	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	1561049	90631880	11899512	208	30609										
MCTP2	55784	hgsc.bcm.edu	37	chr15	95020006	95020006	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agacttcctctctagggtacCgtctgatgttcaaaaggtat	9	9	3	2	rs372254409		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr15:95020006C>A	ENST00000357742.4	+	21	2552	c.2552C>A	c.(2551-2553)cCg>cAg	p.P851Q	MCTP2_ENST00000449432.3_3'UTR|MCTP2_ENST00000451018.3_Missense_Mutation_p.P796Q	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	851					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TCTAGGGTACCGTCTGATGTT	0.438																																																0			15											101	103	103					15																	95020006		2197	4298	6495	92821010	SO:0001583	missense	55784			AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.2552C>A	15.37:g.95020006C>A	ENSP00000350377:p.Pro851Gln		92821010	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562474	0.65538	.	.	ENSG00000140563	ENST00000451018;ENST00000357742	D;D	0.94537	-3.27;-3.45	5.77	5.77	0.91146	Phosphoribosyltransferase C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97914	0.9314	M	0.89534	3.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98310	1.0523	10	0.87932	D	0	.	19.9944	0.97379	0.0:1.0:0.0:0.0	.	796;851	Q6DN12-2;Q6DN12	.;MCTP2_HUMAN	Q	796;851	ENSP00000395109:P796Q;ENSP00000350377:P851Q	ENSP00000350377:P851Q	P	+	2	0	MCTP2	92821010	1.000000	0.71417	0.250000	0.24296	0.750000	0.42670	7.818000	0.86416	2.720000	0.93068	0.557000	0.71058	CCG		0.438	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		A	95020006	C	A	95020006	3	1	113	1	0	0	0	0	1	0	0	0	9431	652	23	2	2710	2	MCTP2	15	95020006	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	4388126	95020006	7511386	209	30610										
SOX8	30812	hgsc.bcm.edu	37	chr16	1033737	1033737	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ctgtgctgcagcttgctgagCgagagcgagaagcggccctt	15	11	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:1033737C>T	ENST00000293894.3	+	2	547	c.432C>T	c.(430-432)agC>agT	p.S144S	RP11-161M6.2_ENST00000565467.1_lincRNA	NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	144					adipose tissue development (GO:0060612)|astrocyte fate commitment (GO:0060018)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|enteric nervous system development (GO:0048484)|fat cell differentiation (GO:0045444)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of gliogenesis (GO:0014015)|positive regulation of kidney development (GO:0090184)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone levels (GO:0010817)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|ureter morphogenesis (GO:0072197)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				GCTTGCTGAGCGAGAGCGAGA	0.677																																																0			16											39	35	36					16																	1033737		2198	4299	6497	973738	SO:0001819	synonymous_variant	30812			AF164104	CCDS10428.1	16p13.3	2008-05-23			ENSG00000005513	ENSG00000005513		"SRY (sex determining region Y)-boxes"	11203	protein-coding gene	gene with protein product		605923				10662550, 10684944	Standard	NM_014587		Approved		uc002ckn.3	P57073	OTTHUMG00000122101	ENST00000293894.3:c.432C>T	16.37:g.1033737C>T			973738	Q9NZW2	Silent	SNP	ENST00000293894.3	37	CCDS10428.1																																																																																				0.677	SOX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242867.1			T	1033737	C	T	1033737	2	4	113	1	0	0	0	0	0	0	0	1	14994	767	27	1		1	SOX8	16	1033737	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10		1033737	89321016	210	30611										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3790511	3790511	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gccgcaaaaatttgttcactCggtcttccaagtggtttccc	8	12	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:3790511C>A	ENST00000262367.5	-	24	4831	c.4022G>T	c.(4021-4023)cGa>cTa	p.R1341L	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1303L	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1341	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1341Q(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTTGTTCACTCGGTCTTCCAA	0.567			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	16											70	73	72					16																	3790511		2197	4300	6497	3730512	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4022G>T	16.37:g.3790511C>A	ENSP00000262367:p.Arg1341Leu		3730512	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.544403	0.86022	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.87179	-2.22;-2.14	5.05	5.05	0.67936	.	0.094335	0.44483	D	0.000453	D	0.92557	0.7636	M	0.90650	3.135	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.50659	0.647;0.647	D	0.94255	0.7497	10	0.87932	D	0	-10.5698	18.784	0.91946	0.0:1.0:0.0:0.0	.	1371;1341	Q4LE28;Q92793	.;CBP_HUMAN	L	1341;1371;1303	ENSP00000262367:R1341L;ENSP00000371502:R1303L	ENSP00000262367:R1341L	R	-	2	0	CREBBP	3730512	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.713000	0.84693	2.503000	0.84419	0.555000	0.69702	CGA		0.567	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3790511	C	A	3790511	3	1	113	1	0	0	0	0	1	0	0	0	3867	884	31	2	3338	2	CREBBP	16	3790511	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2756774	3790511	86564242	211	30612										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3817735	3817735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gcctactttttttgcgcggcTgcgaaggagatgttgactga	13	8	0	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:3817735T>C	ENST00000262367.5	-	16	4045	c.3236A>G	c.(3235-3237)cAg>cGg	p.Q1079R	CREBBP_ENST00000382070.3_Missense_Mutation_p.Q1041R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1079					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTTGCGCGGCTGCGAAGGAGA	0.418			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											185	170	175					16																	3817735		2197	4300	6497	3757736	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3236A>G	16.37:g.3817735T>C	ENSP00000262367:p.Gln1079Arg		3757736	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375527	0.24857	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.16597	2.33;2.33	5.61	5.61	0.85477	Bromodomain (1);	0.000000	0.64402	D	0.000001	T	0.37404	0.1002	M	0.62723	1.935	0.80722	D	1	D;D	0.54601	0.967;0.967	D;D	0.65140	0.932;0.932	T	0.02774	-1.1112	10	0.31617	T	0.26	-12.9594	16.1054	0.81216	0.0:0.0:0.0:1.0	.	1109;1079	Q4LE28;Q92793	.;CBP_HUMAN	R	1079;1109;1041	ENSP00000262367:Q1079R;ENSP00000371502:Q1041R	ENSP00000262367:Q1079R	Q	-	2	0	CREBBP	3757736	1.000000	0.71417	0.997000	0.53966	0.031000	0.12232	7.158000	0.77470	2.266000	0.75297	0.533000	0.62120	CAG		0.418	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3817735	T	C	3817735	3	2	113	1	0	0	0	0	1	0	0	0	3867	1580	55	4	4156	4	CREBBP	16	3817735	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	27224	3817735	86537018	212	30613										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10524822	10524822	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttggaacaagttgtttgttcGtaccaaaagccaagtagaac	9	7	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:10524822G>A	ENST00000396560.2	+	3	572	c.345G>A	c.(343-345)tcG>tcA	p.S115S	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.S115S|ATF7IP2_ENST00000324570.5_Silent_p.S115S|ATF7IP2_ENST00000356427.2_Silent_p.S115S	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TTGTTTGTTCGTACCAAAAGC	0.363																																																0			16											59	61	60					16																	10524822		2197	4300	6497	10432323	SO:0001819	synonymous_variant	80063			AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.345G>A	16.37:g.10524822G>A			10432323	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																				0.363	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		A	10524822	G	A	10524822	2	1	113	1	0	0	0	0	0	0	0	1	1089	1132	40	1		1	ATF7IP2	16	10524822	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	6707087	10524822	79829931	213	30614										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14041760	14041760	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctagcaagcctttctctctCacttcccgaggtgccttgtt	7	15	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:14041760C>T	ENST00000311895.7	+	11	2316	c.2307C>T	c.(2305-2307)ctC>ctT	p.L769L		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	769	Nuclease.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						CTTTCTCTCTCACTTCCCGAG	0.498			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	0			16											121	116	117					16																	14041760		2197	4300	6497	13949261	SO:0001819	synonymous_variant	2072	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.2307C>T	16.37:g.14041760C>T			13949261	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																				0.498	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		T	14041760	C	T	14041760	2	4	113	1	0	0	0	0	0	0	0	1	5228	813	29	3		3	ERCC4	16	14041760	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	3516938	14041760	76312993	214	30615										
SLC5A2	6524	hgsc.bcm.edu	37	chr16	31499714	31499714	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tctctggcagacgaggtggcGtgcgtggtgcctgaggtgtg	19	8	1	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:31499714G>A	ENST00000330498.3	+	9	1051	c.1032G>A	c.(1030-1032)gcG>gcA	p.A344A	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	344					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	ACGAGGTGGCGTGCGTGGTGC	0.672																																																0			16											34	34	34					16																	31499714		2196	4299	6495	31407215	SO:0001819	synonymous_variant	6524				CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"Solute carriers"	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1032G>A	16.37:g.31499714G>A			31407215	A2RRD2	Silent	SNP	ENST00000330498.3	37	CCDS10714.1																																																																																				0.672	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2			A	31499714	G	A	31499714	2	1	113	1	0	0	0	0	0	0	0	1	14702	1132	40	1		1	SLC5A2	16	31499714	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	17457954	31499714	58855039	215	30616										
CDH11	1009	hgsc.bcm.edu	37	chr16	65005939	65005939	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcaaggaccctaatggccacTgggactttggcttcctgatg	11	11	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:65005939T>A	ENST00000268603.4	-	10	2034	c.1419A>T	c.(1417-1419)ccA>ccT	p.P473P	CDH11_ENST00000566827.1_Silent_p.P347P|CDH11_ENST00000394156.3_Silent_p.P473P	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	473	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TAATGGCCACTGGGACTTTGG	0.478			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																													Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	0			16											102	88	93					16																	65005939		2203	4300	6503	63563440	SO:0001819	synonymous_variant	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1419A>T	16.37:g.65005939T>A			63563440	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.478	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		A	65005939	T	A	65005939	2	1	113	1	0	0	0	0	0	0	0	1	3103	1567	55	5		5	CDH11	16	65005939	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	33506225	65005939	25348814	216	30617										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70937809	70937809	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgtccacatgaccgtaccTgcttctcattgggtttcagg	10	11	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:70937809T>A	ENST00000393567.2	-	51	8825	c.8675A>T	c.(8674-8676)cAg>cTg	p.Q2892L		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2892					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGACCGTACCTGCTTCTCATT	0.453																																																0			16											5	5	5					16																	70937809		1541	3854	5395	69495310	SO:0001630	splice_region_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8676+1A>T	16.37:g.70937809T>A			69495310	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586827	0.86851	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01043	5.41	4.73	4.73	0.59995	.	0.000000	0.31872	U	0.006930	T	0.03434	0.0099	M	0.76002	2.32	0.80722	D	1	P	0.52170	0.951	P	0.52454	0.699	T	0.61441	-0.7062	10	0.10636	T	0.68	.	14.0232	0.64571	0.0:0.0:0.0:1.0	.	2891	F8WD23	.	L	2892;2891	ENSP00000377197:Q2892L	ENSP00000313052:Q2891L	Q	-	2	0	HYDIN	69495310	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.548000	0.82154	1.970000	0.57323	0.491000	0.48974	CAG		0.453	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		Missense_Mutation	A	70937809	T	A	70937809	5	1	113	1	0	0	0	0	0	0	1	0	7488	1594	55	5	6834	5	HYDIN	16	70937809	Splice_Site	SNP	T	TCGA-EI-6510-01A-11D-1733-10	5931870	70937809	19416944	217	30618										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81922794	81922794	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	aaggagcattgggctcaggaTctgaacaaagtccgtgagcg	14	8	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:81922794T>C	ENST00000359376.3	+	10	997	c.783T>C	c.(781-783)gaT>gaC	p.D261D		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	261					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GGGCTCAGGATCTGAACAAAG	0.458																																																0			16											150	138	142					16																	81922794		1976	4154	6130	80480295	SO:0001819	synonymous_variant	5336				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.783T>C	16.37:g.81922794T>C			80480295	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																				0.458	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			C	81922794	T	C	81922794	2	2	113	1	0	0	0	0	0	0	0	1	12067	1432	50	4		4	PLCG2	16	81922794	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	10984985	81922794	8431959	218	30619										
JPH3	57338	hgsc.bcm.edu	37	chr16	87723385	87723385	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccctccgacctgacccccgaCgacagccccctgcagagctt	8	21	0	2	rs539750381		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr16:87723385C>T	ENST00000284262.2	+	4	1661	c.1419C>T	c.(1417-1419)gaC>gaT	p.D473D	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	473					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		TGACCCCCGACGACAGCCCCC	0.721													C|||	1	0.000199681	8e-04	0	5008	,	,		10405	0		0	False		,,,				2504	0															0			16											25	22	23					16																	87723385		2183	4291	6474	86280886	SO:0001819	synonymous_variant	57338			AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"trinucleotide repeat containing 22"	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1419C>T	16.37:g.87723385C>T			86280886	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																				0.721	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			T	87723385	C	T	87723385	2	4	113	1	0	0	0	0	0	0	0	1	7983	535	19	1		1	JPH3	16	87723385	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	5800591	87723385	2631368	219	30620										
NXN	64359	hgsc.bcm.edu	37	chr17	722689	722689	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagcgcctaccttggattccGtacagccggttgaggcgcga	14	12	0	1	rs72810286	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:722689G>A	ENST00000336868.3	-	5	901	c.810C>T	c.(808-810)taC>taT	p.Y270Y	NXN_ENST00000537628.2_Silent_p.Y21Y|NXN_ENST00000575801.1_Silent_p.Y162Y|NXN_ENST00000538650.1_Silent_p.Y21Y	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	270	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		CTTGGATTCCGTACAGCCGGT	0.607													G|||	2	0.000399361	0	0	5008	,	,		14647	0		0.002	False		,,,				2504	0															0			17						G	,	2,4404	4.2+/-10.8	0,2,2201	45	48	47		486,810	-1.5	1	17	dbSNP_130	47	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous,coding-synonymous	NXN	NM_001205319.1,NM_022463.4	,	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	,	162/328,270/436	722689	19,12987	2203	4300	6503	669439	SO:0001819	synonymous_variant	64359				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.810C>T	17.37:g.722689G>A			669439	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Silent	SNP	ENST00000336868.3	37	CCDS10998.1																																																																																				0.607	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1			A	722689	G	A	722689	2	1	113	1	0	0	0	0	0	0	0	1	10818	1140	40	1		1	NXN	17	722689	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10		722689	80472521	220	30621										
TP53	7157	hgsc.bcm.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	113	1	0	0	0	0	1	0	0	0	16421	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	6854850	7577539	73617671	221	30622										
NEK8	284086	hgsc.bcm.edu	37	chr17	27064865	27064865	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cggggacctgtgaggccagcCatcccaccaccactgtcgtc	11	17	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:27064865C>T	ENST00000268766.6	+	7	952	c.918C>T	c.(916-918)gcC>gcT	p.A306A	AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	306					organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					TGAGGCCAGCCATCCCACCAC	0.627																																					NSCLC(6;19 293 14866 25253 49845)											0			17											67	76	73					17																	27064865		2203	4300	6503	24088992	SO:0001819	synonymous_variant	284086			AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.918C>T	17.37:g.27064865C>T			24088992	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Silent	SNP	ENST00000268766.6	37	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	C	2.469	-0.322260	0.05350	.	.	ENSG00000160602	ENST00000543014	T	0.71461	-0.57	5.54	1.18	0.20946	.	.	.	.	.	T	0.69860	0.3158	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65030	-0.6267	6	0.59425	D	0.04	.	4.3785	0.11283	0.2434:0.483:0.0:0.2736	.	.	.	.	Y	360	ENSP00000465859:H360Y	ENSP00000446066:H360Y	H	+	1	0	NEK8	24088992	0.981000	0.34729	0.861000	0.33841	0.069000	0.16628	0.449000	0.21744	0.022000	0.15160	0.591000	0.81541	CAT		0.627	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			T	27064865	C	T	27064865	2	4	113	1	0	0	0	0	0	0	0	1	10361	581	21	3		3	NEK8	17	27064865	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	19487326	27064865	54130345	222	30623										
NF1	4763	hgsc.bcm.edu	37	chr17	29562692	29562692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atttactctaccaactgctcTggaacatgttttctaaagaa	5	9	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:29562692T>C	ENST00000358273.4	+	28	4155	c.3772T>C	c.(3772-3774)Tgg>Cgg	p.W1258R	NF1_ENST00000356175.3_Missense_Mutation_p.W1258R	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1258	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCAACTGCTCTGGAACATGTT	0.413			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17											210	207	208					17																	29562692		2203	4300	6503	26586818	SO:0001583	missense	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3772T>C	17.37:g.29562692T>C	ENSP00000351015:p.Trp1258Arg		26586818	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.058368	0.55325	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.78246	-1.16;-1.16;-1.16	5.92	5.92	0.95590	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (3);	0.059684	0.64402	D	0.000001	D	0.86239	0.5885	M	0.67397	2.05	0.80722	D	1	D;B;D;B	0.64830	0.965;0.002;0.994;0.216	P;B;D;B	0.78314	0.863;0.004;0.991;0.151	D	0.83900	0.0289	10	0.25751	T	0.34	.	16.3782	0.83418	0.0:0.0:0.0:1.0	.	1258;308;1258;1258	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	R	1258;1258;924	ENSP00000351015:W1258R;ENSP00000348498:W1258R;ENSP00000389907:W924R	ENSP00000348498:W1258R	W	+	1	0	NF1	26586818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.542000	0.82095	2.277000	0.76020	0.528000	0.53228	TGG		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29562692	T	C	29562692	3	2	113	1	0	0	0	0	1	0	0	0	10387	1580	55	4	3943	4	NF1	17	29562692	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2497827	29562692	51632518	223	30624										
GPR179	440435	hgsc.bcm.edu	37	chr17	36495367	36495367	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggccacttgcacactgattgAtgtccacactctggagatct	9	12	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:36495367A>G	ENST00000342292.4	-	2	856	c.836T>C	c.(835-837)aTc>aCc	p.I279T		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	279					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				ACACTGATTGATGTCCACACT	0.542																																																0			17											126	127	126					17																	36495367		2133	4229	6362	33748893	SO:0001583	missense	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.836T>C	17.37:g.36495367A>G	ENSP00000345060:p.Ile279Thr		33748893		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981804	0.74474	.	.	ENSG00000188888	ENST00000342292	T	0.68479	-0.33	4.32	4.32	0.51571	.	0.239629	0.30920	N	0.008615	T	0.82190	0.4983	M	0.87269	2.87	0.43021	D	0.994574	D	0.89917	1.0	D	0.69307	0.963	D	0.85938	0.1456	10	0.87932	D	0	-17.1579	12.899	0.58115	1.0:0.0:0.0:0.0	.	279	Q6PRD1	GP179_HUMAN	T	279	ENSP00000345060:I279T	ENSP00000345060:I279T	I	-	2	0	GPR179	33748893	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.271000	0.89883	1.942000	0.56320	0.379000	0.24179	ATC		0.542	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			G	36495367	A	G	36495367	3	3	113	1	0	0	0	0	1	0	0	0	6694	333	12	4	6307	4	GPR179	17	36495367	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	6932675	36495367	44699843	224	30625										
PLCD3	113026	hgsc.bcm.edu	37	chr17	43195850	43195850	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catccagtgtcatcagctcaTgctgcttggctgcaggggtg	13	11	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:43195850T>A	ENST00000322765.5	-	6	1036	c.923A>T	c.(922-924)cAt>cTt	p.H308L	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	308					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						CATCAGCTCATGCTGCTTGGC	0.582																																																0			17											81	86	84					17																	43195850		2126	4256	6382	40551376	SO:0001583	missense	113026			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.923A>T	17.37:g.43195850T>A	ENSP00000313731:p.His308Leu		40551376	Q8TEC1|Q8TF37|Q96FL6	Missense_Mutation	SNP	ENST00000322765.5	37		.	.	.	.	.	.	.	.	.	.	T	13.35	2.211717	0.39102	.	.	ENSG00000161714	ENST00000322765	T	0.41065	1.01	4.26	4.26	0.50523	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.053678	0.64402	D	0.000001	T	0.56485	0.1988	.	.	.	0.43988	D	0.996682	D	0.57257	0.979	P	0.60236	0.871	T	0.57154	-0.7860	9	0.40728	T	0.16	.	12.7687	0.57408	0.0:0.0:0.0:1.0	.	308	Q8N3E9	PLCD3_HUMAN	L	308	ENSP00000313731:H308L	ENSP00000313731:H308L	H	-	2	0	PLCD3	40551376	0.986000	0.35501	0.954000	0.39281	0.862000	0.49288	2.038000	0.41184	1.905000	0.55150	0.374000	0.22700	CAT		0.582	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_133373		A	43195850	T	A	43195850	3	1	113	1	0	0	0	0	1	0	0	0	12063	1464	51	5	1485	5	PLCD3	17	43195850	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	6700483	43195850	37999360	225	30626										
EPN3	55040	hgsc.bcm.edu	37	chr17	48614238	48614238	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tacaccatccagacactcaaGgacttccagtacatcgaccg	6	15	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:48614238G>A	ENST00000268933.3	+	2	900	c.321G>A	c.(319-321)aaG>aaA	p.K107K	EPN3_ENST00000537145.1_Silent_p.K162K|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Silent_p.K51K	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	107	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.					clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			AGACACTCAAGGACTTCCAGT	0.607																																																0			17											116	100	106					17																	48614238		2203	4300	6503	45969237	SO:0001819	synonymous_variant	55040			AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.321G>A	17.37:g.48614238G>A			45969237	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																				0.607	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		A	48614238	G	A	48614238	2	1	113	1	0	0	0	0	0	0	0	1	5200	991	35	3		3	EPN3	17	48614238	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5418388	48614238	32580972	226	30627										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67149484	67149484	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tcggggtccatcccggtgaaCggctcatctagaagcaccac	11	14	2	2	rs78875590	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:67149484C>T	ENST00000269081.4	-	35	5007	c.4098G>A	c.(4096-4098)ccG>ccA	p.P1366P	ABCA10_ENST00000519732.1_5'UTR|ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1366	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TCCCGGTGAACGGCTCATCTA	0.522													c|||	80	0.0159744	0.0582	0.0014	5008	,	,		17314	0.001		0.001	False		,,,				2504	0															0			17						T		275,4131	154.0+/-187.5	10,255,1938	98	100	99		4098	-6.7	0	17	dbSNP_132	99	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ABCA10	NM_080282.3		10,260,6233	TT,TC,CC		0.0581,6.2415,2.1529		1366/1544	67149484	280,12726	2203	4300	6503	64661079	SO:0001819	synonymous_variant	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.4098G>A	17.37:g.67149484C>T			64661079	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																				0.522	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67149484	C	T	67149484	2	4	113	1	0	0	0	0	0	0	0	1	29	523	19	1		1	ABCA10	17	67149484	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10	18535246	67149484	14045726	227	30628										
FADS6	283985	hgsc.bcm.edu	37	chr17	72889693	72889701	+	Start_Codon_Del	DEL	TGGACTCTG	TGGACTCTG	-													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	catgggctccgtgggttccaTggactctgtgggctcgggcc					rs112996472|rs2683273	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	TGGACTCTG	TGGACTCTG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr17:72889693_72889701delTGGACTCTG	ENST00000310226.6	-	0	7_15					NM_178128.3	NP_835229.2	Q8N9I5	FADS6_HUMAN	fatty acid desaturase 6						fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|lung(4)	8	all_lung(278;0.172)|Lung NSC(278;0.207)					GTGGGTTCCATGGACTCTGTGGGCTCGGG	0.746																																																0			17																																								70401296	SO:0001582	initiator_codon_variant	283985			AK094411	CCDS54163.1	17q25.1	2014-07-17	2013-01-25			ENSG00000172782		"Fatty acid desaturases"	30459	protein-coding gene	gene with protein product			"fatty acid desaturase domain family, member 6"				Standard	XM_005257224		Approved		uc002jmd.1	Q8N9I5			17.37:g.72889693_72889701delTGGACTCTG			70401288	Q17RQ7|Q6XYE1	Frame_Shift_Del	DEL	ENST00000310226.6	37	CCDS54163.1																																																																																				0.746	FADS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445219.1			-	72889701	TGGACTCTG	-	72889693	7	5	113	1	0	1	0	1	0	0	0	0	5384	1464	51	0	1075	0	FADS6	17	72889693	Start_Codon_Del	DEL	TGGACTCTG	TCGA-EI-6510-01A-11D-1733-10	5740209	72889693	8305517	228	30629										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7042167	7042167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtgtaagtcagaatggaggTcatccttaatacagacagaa	10	6	2	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr18:7042167T>C	ENST00000389658.3	-	9	1331	c.1238A>G	c.(1237-1239)gAc>gGc	p.D413G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	413	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGAATGGAGGTCATCCTTAAT	0.448																																																0			18											75	61	65					18																	7042167		2203	4300	6503	7032167	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1238A>G	18.37:g.7042167T>C	ENSP00000374309:p.Asp413Gly		7032167		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.960946	0.74016	.	.	ENSG00000101680	ENST00000389658	T	0.20200	2.09	5.81	5.81	0.92471	EGF-like, laminin (3);	0.110185	0.64402	D	0.000019	T	0.44371	0.1290	M	0.76727	2.345	0.54753	D	0.999987	D	0.58970	0.984	P	0.62382	0.901	T	0.35549	-0.9784	10	0.49607	T	0.09	.	14.7212	0.69308	0.0:0.0:0.0:1.0	.	413	P25391	LAMA1_HUMAN	G	413	ENSP00000374309:D413G	ENSP00000374309:D413G	D	-	2	0	LAMA1	7032167	1.000000	0.71417	0.928000	0.36995	0.556000	0.35491	5.004000	0.63966	2.219000	0.72066	0.533000	0.62120	GAC		0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7042167	T	C	7042167	3	2	113	1	0	0	0	0	1	0	0	0	8627	1667	58	4	8209	4	LAMA1	18	7042167	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10		7042167	71035081	229	30630										
CDH2	1000	hgsc.bcm.edu	37	chr18	25565524	25565524	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgatggtccaatttctcttaAtagtcactggagataaagga	9	6	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr18:25565524A>G	ENST00000269141.3	-	12	2366	c.1943T>C	c.(1942-1944)aTt>aCt	p.I648T	CDH2_ENST00000399380.3_Missense_Mutation_p.I617T	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	648	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ATTTCTCTTAATAGTCACTGG	0.358																																																0			18											69	68	68					18																	25565524		2203	4300	6503	23819522	SO:0001583	missense	1000			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1943T>C	18.37:g.25565524A>G	ENSP00000269141:p.Ile648Thr		23819522	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425302	0.62733	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.60672	0.17;0.17	5.96	5.96	0.96718	Cadherin (3);Cadherin-like (1);	0.110120	0.64402	D	0.000005	T	0.72260	0.3438	M	0.70842	2.15	0.80722	D	1	P;P	0.47545	0.833;0.897	P;P	0.57846	0.828;0.706	T	0.72164	-0.4373	10	0.44086	T	0.13	.	16.4221	0.83766	1.0:0.0:0.0:0.0	.	617;648	A8MWK3;P19022	.;CADH2_HUMAN	T	648;617	ENSP00000269141:I648T;ENSP00000382312:I617T	ENSP00000269141:I648T	I	-	2	0	CDH2	23819522	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.904000	0.92590	2.283000	0.76528	0.477000	0.44152	ATT		0.358	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		G	25565524	A	G	25565524	3	3	113	1	0	0	0	0	1	0	0	0	3111	101	4	4	797	4	CDH2	18	25565524	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	18523357	25565524	52511724	230	30631										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29493394	29493394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atctggtatctgttcatctgAtgctcgattagatgttcgag	10	7	4	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr18:29493394A>G	ENST00000283351.4	-	5	1044	c.709T>C	c.(709-711)Tca>Cca	p.S237P	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.S183P|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.S237P	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	237					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGTTCATCTGATGCTCGATTA	0.323																																																0			18											91	92	92					18																	29493394		2203	4300	6503	27747392	SO:0001583	missense	0			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.709T>C	18.37:g.29493394A>G	ENSP00000283351:p.Ser237Pro		27747392	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.800933	0.31869	.	.	ENSG00000153339	ENST00000283351	T	0.18338	2.22	5.65	4.42	0.53409	.	0.425407	0.24200	N	0.040622	T	0.10680	0.0261	N	0.25890	0.77	0.28954	N	0.890253	B;B	0.22414	0.002;0.069	B;B	0.23018	0.011;0.043	T	0.08722	-1.0708	10	0.30078	T	0.28	.	6.0861	0.19968	0.4766:0.3057:0.0:0.2176	.	237;237	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	P	237	ENSP00000283351:S237P	ENSP00000283351:S237P	S	-	1	0	TRAPPC8	27747392	0.915000	0.31059	1.000000	0.80357	0.998000	0.95712	1.193000	0.32162	2.276000	0.75962	0.528000	0.53228	TCA		0.323	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29493394	A	G	29493394	3	3	113	1	0	0	0	0	1	0	0	0	8225	333	12	4	3698	4	KIAA1012	18	29493394	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	3927870	29493394	48583854	231	30632										
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61585319	61585319	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atgcgatatatggagagaaaAcgtatgcatttcacaatgta	9	5	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr18:61585319A>G	ENST00000238508.3	+	4	414	c.355A>G	c.(355-357)Acg>Gcg	p.T119A		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	119					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				TGGAGAGAAAACGTATGCATT	0.348																																																0			18											103	94	97					18																	61585319		2202	4300	6502	59736299	SO:0001583	missense	5273			U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.355A>G	18.37:g.61585319A>G	ENSP00000238508:p.Thr119Ala		59736299	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	A	7.543	0.661148	0.14645	.	.	ENSG00000242550	ENST00000238508	D	0.83075	-1.68	5.83	2.04	0.26737	Serpin domain (3);	0.242512	0.41500	N	0.000877	T	0.76118	0.3943	M	0.64676	1.99	0.31591	N	0.653924	B	0.17038	0.02	B	0.20184	0.028	T	0.70077	-0.4971	10	0.59425	D	0.04	.	3.1416	0.06457	0.5332:0.0:0.1731:0.2937	.	119	P48595	SPB10_HUMAN	A	119	ENSP00000238508:T119A	ENSP00000238508:T119A	T	+	1	0	SERPINB10	59736299	0.488000	0.25996	0.185000	0.23176	0.089000	0.18198	1.061000	0.30542	0.107000	0.17824	0.533000	0.62120	ACG		0.348	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		G	61585319	A	G	61585319	3	3	113	1	0	0	0	0	1	0	0	0	14134	43	2	4	365	4	SERPINB10	18	61585319	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	32091925	61585319	16491929	232	30633										
DAPK3	1613	hgsc.bcm.edu	37	chr19	3959259	3959259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggccgctggtccccagcagcGcgcccttggcctcctcctgc	12	20	0	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:3959259G>A	ENST00000545797.2	-	9	1448	c.1205C>T	c.(1204-1206)gCg>gTg	p.A402V	MIR637_ENST00000385000.1_RNA|DAPK3_ENST00000301264.3_Missense_Mutation_p.A402V			O43293	DAPK3_HUMAN	death-associated protein kinase 3	402					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCAGCAGCGCGCCCTTGGC	0.697																																																0			19											12	13	12					19																	3959259		2191	4277	6468	3910259	SO:0001583	missense	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.1205C>T	19.37:g.3959259G>A	ENSP00000442973:p.Ala402Val		3910259	A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	37	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	G	4.566	0.105216	0.08731	.	.	ENSG00000167657	ENST00000301264;ENST00000545797	T;T	0.68624	-0.34;-0.34	4.91	4.91	0.64330	.	0.061542	0.64402	D	0.000004	T	0.48804	0.1520	L	0.27053	0.805	0.37948	D	0.932569	B	0.19706	0.038	B	0.06405	0.002	T	0.47774	-0.9091	10	0.13853	T	0.58	.	10.6525	0.45657	0.0996:0.0:0.9004:0.0	.	402	O43293	DAPK3_HUMAN	V	402	ENSP00000301264:A402V;ENSP00000442973:A402V	ENSP00000301264:A402V	A	-	2	0	DAPK3	3910259	0.957000	0.32711	0.452000	0.26994	0.130000	0.20726	5.591000	0.67536	2.279000	0.76181	0.561000	0.74099	GCG		0.697	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		A	3959259	G	A	3959259	3	1	113	1	0	0	0	0	1	0	0	0	4243	1087	38	1	163	1	DAPK3	19	3959259	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10		3959259	55169724	233	30634										
SAFB	6294	hgsc.bcm.edu	37	chr19	5641842	5641842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agaaattgataatggaagcgTtgcagattgtgtcgaagacg	13	4	0	4			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:5641842T>C	ENST00000292123.5	+	4	538	c.431T>C	c.(430-432)gTt>gCt	p.V144A	SAFB_ENST00000588852.1_Missense_Mutation_p.V144A|SAFB_ENST00000538656.1_Intron|SAFB_ENST00000454510.1_Intron|SAFB_ENST00000592224.1_Missense_Mutation_p.V144A|SAFB_ENST00000586934.1_3'UTR|SAFB_ENST00000433404.1_5'UTR	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	144					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		AATGGAAGCGTTGCAGATTGT	0.488																																					Colon(88;338 1345 6184 8214 20897)											0			19											157	154	155					19																	5641842		2203	4300	6503	5592842	SO:0001583	missense	6294			L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.431T>C	19.37:g.5641842T>C	ENSP00000292123:p.Val144Ala		5592842	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	37	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	T	0.956	-0.704974	0.03255	.	.	ENSG00000160633	ENST00000292123	T	0.09445	2.98	5.7	4.63	0.57726	.	0.122641	0.36303	N	0.002678	T	0.02494	0.0076	N	0.01209	-0.955	0.80722	D	1	B;B;B;B;B	0.15719	0.014;0.0;0.014;0.008;0.014	B;B;B;B;B	0.18871	0.023;0.001;0.023;0.023;0.023	T	0.38650	-0.9651	10	0.02654	T	1	-17.463	3.5602	0.07880	0.0:0.2369:0.0:0.7631	.	144;144;144;144;144	B7ZLP5;B7Z2H3;A0AV56;Q15424;B7ZLP6	.;.;.;SAFB1_HUMAN;.	A	144	ENSP00000292123:V144A	ENSP00000292123:V144A	V	+	2	0	SAFB	5592842	0.830000	0.29337	0.074000	0.20217	0.227000	0.25037	3.019000	0.49635	2.165000	0.68154	0.455000	0.32223	GTT		0.488	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			C	5641842	T	C	5641842	3	2	113	1	0	0	0	0	1	0	0	0	13843	1725	60	4	445	4	SAFB	19	5641842	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1682583	5641842	53487141	234	30635										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10248608	10248608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgtaggagatctccagtgccGaggctccattccgcacctcc	10	15	1	1	rs375225009		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:10248608G>A	ENST00000340748.4	-	35	4380	c.4145C>T	c.(4144-4146)tCg>tTg	p.S1382L	DNMT1_ENST00000540357.1_Missense_Mutation_p.S1382L|DNMT1_ENST00000589538.1_5'Flank|DNMT1_ENST00000359526.4_Missense_Mutation_p.S1398L			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1382	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S1382L(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTCCAGTGCCGAGGCTCCATT	0.622																																																1	Substitution - Missense(1)	ovary(1)	19						G	LEU/SER,LEU/SER	0,4406		0,0,2203	65	49	54		4193,4145	4.3	0	19		54	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DNMT1	NM_001130823.1,NM_001379.2	145,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	1398/1633,1382/1617	10248608	1,13005	2203	4300	6503	10109608	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4145C>T	19.37:g.10248608G>A	ENSP00000345739:p.Ser1382Leu		10109608	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405251	0.62288	0.0	1.16E-4	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	D;D;D	0.84223	-1.82;-1.82;-1.82	5.38	4.34	0.51931	.	0.121936	0.56097	D	0.000027	D	0.86703	0.5996	M	0.64630	1.985	0.48185	D	0.999608	P;P;D	0.53619	0.952;0.952;0.961	P;P;P	0.50537	0.51;0.51;0.643	D	0.87259	0.2278	10	0.59425	D	0.04	.	13.1521	0.59494	0.0795:0.0:0.9205:0.0	.	1382;1398;1382	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	L	1398;1382;1382;1250	ENSP00000352516:S1398L;ENSP00000440457:S1382L;ENSP00000345739:S1382L	ENSP00000345739:S1382L	S	-	2	0	DNMT1	10109608	1.000000	0.71417	0.015000	0.15790	0.008000	0.06430	9.416000	0.97383	1.255000	0.44051	0.655000	0.94253	TCG		0.622	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		A	10248608	G	A	10248608	3	1	113	1	0	0	0	0	1	0	0	0	4686	1059	37	1	729	1	DNMT1	19	10248608	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	4606766	10248608	48880375	235	30636										
LPPR2	64748	hgsc.bcm.edu	37	chr19	11471965	11471965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggtggtgaccggcaatcccaCgccacacttcctgtccgtgt	11	15	0	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:11471965C>T	ENST00000251473.5	+	6	840	c.464C>T	c.(463-465)aCg>aTg	p.T155M	DKFZP761J1410_ENST00000591608.1_Missense_Mutation_p.T130M	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2												p.T155M(1)									GGCAATCCCACGCCACACTTC	0.647																																																1	Substitution - Missense(1)	large_intestine(1)	19											81	59	66					19																	11471965		2203	4300	6503	11332965	SO:0001583	missense	64748																														ENST00000251473.5:c.464C>T	19.37:g.11471965C>T	ENSP00000251473:p.Thr155Met		11332965		Missense_Mutation	SNP	ENST00000251473.5	37	CCDS12258.1	.	.	.	.	.	.	.	.	.	.	c	25.4	4.638352	0.87760	.	.	ENSG00000105520	ENST00000251473	T	0.74737	-0.87	5.18	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.84356	0.5454	M	0.71581	2.175	0.58432	D	0.999996	D;D	0.76494	0.999;0.998	D;D	0.71870	0.975;0.953	D	0.86199	0.1617	10	0.72032	D	0.01	-5.2274	14.7355	0.69412	0.0:0.854:0.146:0.0	.	130;155	Q96GM1-2;Q96GM1	.;LPPR2_HUMAN	M	155	ENSP00000251473:T155M	ENSP00000251473:T155M	T	+	2	0	AC024575.1	11332965	1.000000	0.71417	0.860000	0.33809	0.946000	0.59487	7.123000	0.77176	1.174000	0.42811	0.450000	0.29827	ACG		0.647	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1			T	11471965	C	T	11471965	3	4	113	1	0	0	0	0	1	0	0	0	8954	536	19	1	478	1	LPPR2	19	11471965	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	1223357	11471965	47657018	236	30637										
RHPN2	85415	hgsc.bcm.edu	37	chr19	33493200	33493201	+	Missense_Mutation	DNP	GC	GC	AT													0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgaagtagtgggccagggccGcgtagtggtgggccttcacg					rs200623446|rs201601538	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:33493200_33493201GC>AT	ENST00000254260.3	-	9	1092_1093	c.1057_1058GC>AT	c.(1057-1059)GCg>ATg	p.A353M	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202M	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.A353T(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					GGCCAGGGCCGCGTAGTGGTGG	0.639																																																2	Substitution - Missense(2)	central_nervous_system(2)	19																																								38185040|38185041	SO:0001583	missense	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1057_1058delinsAT	19.37:g.33493200_33493201delinsAT	ENSP00000254260:p.Ala353Met		38185040|38185041	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																				0.639	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		AT	33493201	GC	AT	33493200	3	1	113	1	0	0	0	0	1	0	0	0	13388	1087	38	1	1030	1	RHPN2	19	33493200	Missense_Mutation	DNP	GC	TCGA-EI-6510-01A-11D-1733-10	22021235	33493200	25635783	237	30638										
ZNF599	148103	hgsc.bcm.edu	37	chr19	35250005	35250005	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tggctgaaggtctttccacaTtcattgcattcaaagggttt	9	8	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:35250005T>C	ENST00000329285.8	-	4	2074	c.1701A>G	c.(1699-1701)gaA>gaG	p.E567E		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TCTTTCCACATTCATTGCATT	0.403																																																0			19											154	143	147					19																	35250005		2203	4300	6503	39941845	SO:0001819	synonymous_variant	148103			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1701A>G	19.37:g.35250005T>C			39941845	Q569K0|Q5PRG1	Silent	SNP	ENST00000329285.8	37	CCDS32991.1																																																																																				0.403	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		C	35250005	T	C	35250005	2	2	113	1	0	0	0	0	0	0	0	1	18068	1490	52	4		4	ZNF599	19	35250005	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	1756805	35250005	23878978	238	30639										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40485749	40485749	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcatccgggtcgtgggctcGgagtttgtacagaagtatct	13	8	2	1	rs11542837		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:40485749G>A	ENST00000157812.2	+	7	897	c.699G>A	c.(697-699)tcG>tcA	p.S233S	PSMC4_ENST00000455878.2_Silent_p.S202S	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	233					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S233S(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TCGTGGGCTCGGAGTTTGTAC	0.557																																					Colon(105;1478 1543 4034 6132 38638)											1	Substitution - coding silent(1)	ovary(1)	19						G	,	0,4406		0,0,2203	97	103	101		699,606	-12.1	0	19	dbSNP_120	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PSMC4	NM_006503.2,NM_153001.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	233/419,202/388	40485749	1,13005	2203	4300	6503	45177589	SO:0001819	synonymous_variant	5704			U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.699G>A	19.37:g.40485749G>A			45177589	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																				0.557	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		A	40485749	G	A	40485749	2	1	113	1	0	0	0	0	0	0	0	1	12723	1103	39	1		1	PSMC4	19	40485749	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5235744	40485749	18643234	239	30640										
CKM	1158	hgsc.bcm.edu	37	chr19	45815033	45815033	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccacgggcgtcgggccagtcGcgggccatgcctgaggccag	17	15	0	1	rs17875616	byFrequency	TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:45815033G>A	ENST00000221476.3	-	5	801	c.627C>T	c.(625-627)cgC>cgT	p.R209R		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	209	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	CGGGCCAGTCGCGGGCCATGC	0.672																																																0			19											30	24	26					19																	45815033		2202	4299	6501	50506873	SO:0001819	synonymous_variant	1158			M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.627C>T	19.37:g.45815033G>A			50506873	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																				0.672	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			A	45815033	G	A	45815033	2	1	113	1	0	0	0	0	0	0	0	1	3454	1074	38	1		1	CKM	19	45815033	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5329284	45815033	13313950	240	30641										
LIG1	3978	hgsc.bcm.edu	37	chr19	48657140	48657140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggggctcaccttcctcctccTtcttcctcttggcttctctg	7	17	4	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:48657140T>C	ENST00000263274.7	-	6	874	c.455A>G	c.(454-456)aAg>aGg	p.K152R	LIG1_ENST00000536218.1_Intron|LIG1_ENST00000427526.2_Missense_Mutation_p.K122R|LIG1_ENST00000599165.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	152			K -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ttcctcctccttcttcctctt	0.577								Nucleotide excision repair (NER)																																								0			19											196	113	141					19																	48657140		2203	4300	6503	53348952	SO:0001583	missense	26018				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.455A>G	19.37:g.48657140T>C	ENSP00000263274:p.Lys152Arg		53348952	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	6.386	0.439422	0.12104	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526	T;T	0.58506	0.44;0.33	3.99	2.94	0.34122	.	0.866238	0.10215	N	0.701604	T	0.48714	0.1515	L	0.54323	1.7	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.28839	-1.0031	10	0.18710	T	0.47	-18.4584	7.3918	0.26913	0.0:0.0:0.2229:0.7771	.	122;152	B4DTU4;P18858	.;DNLI1_HUMAN	R	152;184;122	ENSP00000263274:K152R;ENSP00000442841:K122R	ENSP00000263274:K152R	K	-	2	0	LIG1	53348952	0.292000	0.24362	0.892000	0.35008	0.244000	0.25665	1.067000	0.30616	0.837000	0.34925	0.496000	0.49642	AAG		0.577	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48657140	T	C	48657140	3	2	113	1	0	0	0	0	1	0	0	0	8804	1609	56	4	2396	4	LIG1	19	48657140	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2842107	48657140	10471843	241	30642										
ZNF544	27300	hgsc.bcm.edu	37	chr19	58773800	58773800	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctatgaatgtaacgagtgtGgaaaagccttcaatcgaagc	10	8	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr19:58773800G>A	ENST00000596652.1	+	6	2062	c.1828G>A	c.(1828-1830)Gga>Aga	p.G610R	ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000415203.2_Missense_Mutation_p.G582R|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000269829.4_Missense_Mutation_p.G610R|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000600044.1_Missense_Mutation_p.G582R|ZNF544_ENST00000600220.1_Missense_Mutation_p.G582R|ZNF544_ENST00000599953.1_Missense_Mutation_p.G468R			Q6NX49	ZN544_HUMAN	zinc finger protein 544	610					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TAACGAGTGTGGAAAAGCCTT	0.448																																																0			19											104	92	96					19																	58773800		2203	4300	6503	63465612	SO:0001583	missense	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1828G>A	19.37:g.58773800G>A	ENSP00000469635:p.Gly610Arg		63465612	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.999695	0.54147	.	.	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.01484	4.84;4.84	3.68	2.63	0.31362	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06645	0.0170	M	0.75777	2.31	0.80722	D	1	D;D;D	0.69078	0.988;0.997;0.997	P;P;P	0.56865	0.791;0.808;0.808	T	0.10730	-1.0617	9	0.87932	D	0	.	11.3464	0.49563	0.0:0.3542:0.6458:0.0	.	582;582;610	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	R	610;582;162	ENSP00000269829:G610R;ENSP00000394341:G582R	ENSP00000269829:G610R	G	+	1	0	ZNF544	63465612	1.000000	0.71417	0.026000	0.17262	0.033000	0.12548	3.347000	0.52200	0.901000	0.36495	-0.257000	0.10917	GGA		0.448	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58773800	G	A	58773800	3	1	113	1	0	0	0	0	1	0	0	0	18016	1349	47	3	1842	3	ZNF544	19	58773800	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	10116660	58773800	355183	242	30643										
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23966529	23966529	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gccatggtgatctgcgtgccCccggcagctcccaccaccat	10	18	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr20:23966529C>A	ENST00000335694.4	-	4	591	c.387G>T	c.(385-387)ggG>ggT	p.G129G	GGTLC1_ENST00000278765.4_Silent_p.G129G|GGTLC1_ENST00000286890.4_Silent_p.G129G	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	129	Glutamate binding. {ECO:0000250}.				glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						TCTGCGTGCCCCCGGCAGCTC	0.647																																																0			20											110	120	116					20																	23966529		1511	2709	4220	23914529	SO:0001819	synonymous_variant	92086			AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"Gamma-glutamyltransferases"	16437	protein-coding gene	gene with protein product		612338	"gamma-glutamyltransferase-like activity 4", "gamma-glutamyltransferase-like activity 3"	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.387G>T	20.37:g.23966529C>A			23914529	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	37	CCDS13163.1																																																																																				0.647	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		A	23966529	C	A	23966529	2	1	113	1	0	0	0	0	0	0	0	1	6385	610	22	2		2	GGTLC1	20	23966529	Silent	SNP	C	TCGA-EI-6510-01A-11D-1733-10		23966529	39058991	243	30644										
KRTAP20-1	337975	hgsc.bcm.edu	37	chr21	31988928	31988928	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttgctatggaagatattggtCatatggtttctactgaacaa	9	5	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr21:31988928C>T	ENST00000334664.2	+	1	179	c.155C>T	c.(154-156)tCa>tTa	p.S52L	KRTAP6-1_ENST00000329122.2_5'Flank	NM_181615.1	NP_853646.1	Q3LI63	KR201_HUMAN	keratin associated protein 20-1	52			S -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			intermediate filament (GO:0005882)		p.S52L(1)		breast(1)|endometrium(3)|lung(1)|pancreas(1)|skin(1)	7						AGATATTGGTCATATGGTTTC	0.448																																																1	Substitution - Missense(1)	breast(1)	21											239	213	221					21																	31988928		2203	4300	6503	30910799	SO:0001583	missense	337975			AP001708	CCDS13603.1	21q22.1	2011-02-10			ENSG00000244624	ENSG00000244624		"Keratin associated proteins"	18943	protein-coding gene	gene with protein product						12359730	Standard	NM_181615		Approved	KAP20.1	uc011ade.2	Q3LI63	OTTHUMG00000057801	ENST00000334664.2:c.155C>T	21.37:g.31988928C>T	ENSP00000335503:p.Ser52Leu		30910799		Missense_Mutation	SNP	ENST00000334664.2	37	CCDS13603.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533663	0.27387	.	.	ENSG00000244624	ENST00000334664	T	0.30981	1.51	4.1	3.21	0.36854	.	0.655352	0.11666	U	0.541317	T	0.22166	0.0534	.	.	.	0.09310	N	1	B	0.30179	0.271	B	0.25405	0.06	T	0.17745	-1.0359	9	0.87932	D	0	.	7.582	0.27970	0.0:0.8864:0.0:0.1136	.	52	Q3LI63	KR201_HUMAN	L	52	ENSP00000335503:S52L	ENSP00000335503:S52L	S	+	2	0	KRTAP20-1	30910799	0.003000	0.15002	0.034000	0.17996	0.416000	0.31233	0.554000	0.23407	1.301000	0.44836	0.643000	0.83706	TCA		0.448	KRTAP20-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128253.3			T	31988928	C	T	31988928	3	4	113	1	0	0	0	0	1	0	0	0	8557	838	29	3	157	3	KRTAP20-1	21	31988928	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10		31988928	16140967	244	30645										
GCFC1	94104	hgsc.bcm.edu	37	chr21	34117133	34117133	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttattttctgcattcactacTgaaggatatccattgattaa	5	7	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr21:34117133T>C	ENST00000331923.4	-	13	2349	c.2160A>G	c.(2158-2160)tcA>tcG	p.S720S	PAXBP1-AS1_ENST00000440052.1_RNA|PAXBP1_ENST00000290178.4_Silent_p.S720S	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	720					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CATTCACTACTGAAGGATATC	0.318																																																0			21											110	122	118					21																	34117133		2203	4296	6499	33039004	SO:0001819	synonymous_variant	0			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.2160A>G	21.37:g.34117133T>C			33039004	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																				0.318	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		C	34117133	T	C	34117133	2	2	113	1	0	0	0	0	0	0	0	1	6309	1567	55	4		4	GCFC1	21	34117133	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	2128205	34117133	14012762	245	30646										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46320234	46320234	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtgcctggggtggggacttaCgaattcgttgctcctcttgt	14	9	1	0	rs201752283		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr21:46320234C>T	ENST00000397850.2	-	8	1350		c.e8+1		ITGB2_ENST00000397857.1_Splice_Site|ITGB2_ENST00000397854.3_Splice_Site|ITGB2_ENST00000397852.1_Splice_Site|ITGB2_ENST00000355153.4_Splice_Site|ITGB2_ENST00000302347.5_Splice_Site			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)						apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.?(1)		breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	TGGGGACTTACGAATTCGTTG	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		16834	0		0	False		,,,				2504	0															1	Unknown(1)	central_nervous_system(1)	21	GRCh37	CS920765	ITGB2	S							116	92	100					21																	46320234		2203	4300	6503	45144662	SO:0001630	splice_region_variant	3689			AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.897+1G>A	21.37:g.46320234C>T			45144662	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Splice_Site	SNP	ENST00000397850.2	37	CCDS13716.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.19	1.864750	0.32977	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5843	0.76470	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGB2	45144662	1.000000	0.71417	0.779000	0.31741	0.008000	0.06430	7.108000	0.77055	2.546000	0.85860	0.591000	0.81541	.		0.632	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	Intron	T	46320234	C	T	46320234	5	4	113	1	0	0	0	0	0	0	1	0	7915	550	19	1	1451	1	ITGB2	21	46320234	Splice_Site	SNP	C	TCGA-EI-6510-01A-11D-1733-10	12203101	46320234	1809661	246	30647										
EP300	2033	hgsc.bcm.edu	37	chr22	41572350	41572350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cctgcgatctgatggatggtCgggatgcgtttctcacgctg	14	10	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr22:41572350C>T	ENST00000263253.7	+	30	6098	c.4879C>T	c.(4879-4881)Cgg>Tgg	p.R1627W	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1627	Binding region for E1A adenovirus.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.R1627W(3)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GATGGATGGTCGGGATGCGTT	0.577			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	3	Substitution - Missense(3)	urinary_tract(1)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	22											119	102	108					22																	41572350		2203	4300	6503	39902296	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4879C>T	22.37:g.41572350C>T	ENSP00000263253:p.Arg1627Trp		39902296	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861386	0.51482	.	.	ENSG00000100393	ENST00000263253	D	0.93076	-3.16	5.03	3.99	0.46301	.	0.000000	0.46758	D	0.000274	D	0.96935	0.8999	H	0.94620	3.56	0.52099	D	0.99994	D	0.76494	0.999	P	0.57846	0.828	D	0.97750	1.0214	10	0.87932	D	0	-15.4519	14.5885	0.68344	0.1518:0.8482:0.0:0.0	.	1627	Q09472	EP300_HUMAN	W	1627	ENSP00000263253:R1627W	ENSP00000263253:R1627W	R	+	1	2	EP300	39902296	1.000000	0.71417	0.998000	0.56505	0.698000	0.40448	4.864000	0.62990	1.184000	0.42957	0.650000	0.86243	CGG		0.577	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41572350	C	T	41572350	3	4	113	1	0	0	0	0	1	0	0	0	5161	875	31	1	4997	1	EP300	22	41572350	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10		41572350	9732216	247	30648										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	43933328	43933328	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	tgcattctttcaggagctggCgccagcagccctggattctc	11	13	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr22:43933328C>T	ENST00000262726.7	-	29	4230	c.3977G>A	c.(3976-3978)cGc>cAc	p.R1326H	EFCAB6_ENST00000396231.2_Missense_Mutation_p.R1174H|EFCAB6-AS1_ENST00000431327.3_RNA|EFCAB6_ENST00000461800.1_5'UTR	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1326	Interaction with PARK7.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				CAGGAGCTGGCGCCAGCAGCC	0.567																																																0			22											94	95	95					22																	43933328		2203	4300	6503	42264661	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3977G>A	22.37:g.43933328C>T	ENSP00000262726:p.Arg1326His		42264661	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997616	0.54147	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.08546	3.08;3.08	4.71	3.6	0.41247	EF-hand calcium-binding domain-containing protein 6 (1);	0.164835	0.37136	N	0.002232	T	0.22085	0.0532	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.00304	-1.1832	10	0.45353	T	0.12	-11.9951	9.1685	0.37065	0.0:0.8508:0.0:0.1492	.	1326	Q5THR3	EFCB6_HUMAN	H	1174;1326	ENSP00000379533:R1174H;ENSP00000262726:R1326H	ENSP00000262726:R1326H	R	-	2	0	EFCAB6	42264661	0.685000	0.27652	0.919000	0.36401	0.427000	0.31564	0.998000	0.29744	2.155000	0.67459	0.655000	0.94253	CGC		0.567	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43933328	C	T	43933328	3	4	113	1	0	0	0	0	1	0	0	0	4950	768	27	1	544	1	EFCAB6	22	43933328	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	2360978	43933328	7371238	248	30649										
PANX2	56666	hgsc.bcm.edu	37	chr22	50617527	50617527	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	agcccctcaccatcctgagcCgaaacgccacacacccgctg	7	20	1	1	rs377448993		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chr22:50617527C>T	ENST00000395842.2	+	3	1855	c.1855C>T	c.(1855-1857)Cga>Tga	p.R619*	PANX2_ENST00000159647.5_Nonsense_Mutation_p.R619*	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	619					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CATCCTGAGCCGAAACGCCAC	0.721																																																0			22						C	stop/ARG,stop/ARG	1,4395	2.1+/-5.4	0,1,2197	38	36	37		1855,1855	3.7	1	22		37	0,8588		0,0,4294	no	stop-gained,stop-gained	PANX2	NM_001160300.1,NM_052839.3	,	0,1,6491	TT,TC,CC		0.0,0.0227,0.0077	,	619/644,619/678	50617527	1,12983	2198	4294	6492	48959654	SO:0001587	stop_gained	56666				CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"Ion channels / Pannexins"	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.1855C>T	22.37:g.50617527C>T	ENSP00000379183:p.Arg619*		48959654	B7Z684|Q96RD5|Q9UGX8	Nonsense_Mutation	SNP	ENST00000395842.2	37	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	C	35	5.466906	0.96257	2.27E-4	0.0	ENSG00000073150	ENST00000159647;ENST00000395842;ENST00000401643	.	.	.	3.72	3.72	0.42706	.	0.355511	0.21888	N	0.067626	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.8294	7.7374	0.28823	0.0:0.8322:0.0:0.1678	.	.	.	.	X	619;619;296	.	ENSP00000159647:R619X	R	+	1	2	PANX2	48959654	1.000000	0.71417	0.998000	0.56505	0.838000	0.47535	2.138000	0.42140	2.081000	0.62600	0.313000	0.20887	CGA		0.721	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		T	50617527	C	T	50617527	4	4	113	1	0	0	0	0	0	1	0	0	11452	644	23	1	1865	1	PANX2	22	50617527	Nonsense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	6684199	50617527	687039	249	30650										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241266	3241266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gggggagaaatagcaggaaaAggtggtgtgacttctagact	16	4	1	3			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:3241266A>G	ENST00000217939.6	-	5	2614	c.2460T>C	c.(2458-2460)ccT>ccC	p.P820P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	820						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TAGCAGGAAAAGGTGGTGTGA	0.488																																																0			X											141	139	140					X																	3241266		2203	4300	6503	3251266	SO:0001819	synonymous_variant	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2460T>C	X.37:g.3241266A>G			3251266	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		G	3241266	A	G	3241266	2	3	113	1	0	0	0	0	0	0	0	1	10033	59	3	4		4	MXRA5	23	3241266	Silent	SNP	A	TCGA-EI-6510-01A-11D-1733-10		3241266	152029294	250	30651										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24608202	24608202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	atctctgataacttcgtctaCgtagcgacagtgtctgagag	10	9	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:24608202C>T	ENST00000379144.2	-	4	554	c.424G>A	c.(424-426)Gta>Ata	p.V142I	PCYT1B_ENST00000356768.4_Missense_Mutation_p.V142I|PCYT1B_ENST00000379145.1_Missense_Mutation_p.V124I	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	142					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	ACTTCGTCTACGTAGCGACAG	0.453																																																0			X											173	132	146					X																	24608202		2203	4300	6503	24518123	SO:0001583	missense	9468			AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.424G>A	X.37:g.24608202C>T	ENSP00000368439:p.Val142Ile		24518123	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	37	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774288	0.90108	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	D;D;D	0.97089	-4.24;-4.24;-4.24	5.44	5.44	0.79542	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1);	0.000000	0.85682	D	0.000000	D	0.98403	0.9469	M	0.87269	2.87	0.80722	D	1	D;D;D	0.76494	0.996;0.996;0.999	P;P;P	0.60949	0.7;0.881;0.881	D	0.99316	1.0905	10	0.72032	D	0.01	-26.3929	18.3331	0.90277	0.0:1.0:0.0:0.0	.	142;124;142	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	I	124;142;142	ENSP00000368440:V124I;ENSP00000368439:V142I;ENSP00000349211:V142I	ENSP00000349211:V142I	V	-	1	0	PCYT1B	24518123	1.000000	0.71417	0.998000	0.56505	0.738000	0.42128	7.320000	0.79064	2.524000	0.85096	0.600000	0.82982	GTA		0.453	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		T	24608202	C	T	24608202	3	4	113	1	0	0	0	0	1	0	0	0	11642	536	19	1	742	1	PCYT1B	23	24608202	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	21366936	24608202	130662358	251	30652										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30236765	30236765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	caaggcccgagatgagacccGgggtctcaatgttcctcagg	13	12	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:30236765G>A	ENST00000378988.4	+	2	169	c.68G>A	c.(67-69)cGg>cAg	p.R23Q		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	23										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						GATGAGACCCGGGGTCTCAAT	0.567																																																0			X											37	35	36					X																	30236765		2202	4300	6502	30146686	SO:0001583	missense	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.68G>A	X.37:g.30236765G>A	ENSP00000368273:p.Arg23Gln		30146686	O75860	Missense_Mutation	SNP	ENST00000378988.4	37	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	A	0.186	-1.057326	0.01965	.	.	ENSG00000099399	ENST00000378988	T	0.02974	4.09	3.43	0.959	0.19624	Melanoma associated antigen, MAGE, N-terminal (1);	0.653207	0.14428	N	0.320189	T	0.00468	0.0015	N	0.00036	-2.535	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	10	0.02654	T	1	.	3.0051	0.06026	0.5076:0.2281:0.2643:0.0	.	23	O15479	MAGB2_HUMAN	Q	23	ENSP00000368273:R23Q	ENSP00000368273:R23Q	R	+	2	0	MAGEB2	30146686	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.065000	0.11617	-0.166000	0.10890	-1.641000	0.00772	CGG		0.567	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		A	30236765	G	A	30236765	3	1	113	1	0	0	0	0	1	0	0	0	9206	1116	39	1	70	1	MAGEB2	23	30236765	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	5628563	30236765	125033795	252	30653										
RBM10	8241	hgsc.bcm.edu	37	chrX	47040620	47040620	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cacctgcccttcaggcctccCaaggtggggagggtacctgg	14	14	1	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:47040620C>T	ENST00000377604.3	+	13	1997	c.1255C>T	c.(1255-1257)Caa>Taa	p.Q419*	RBM10_ENST00000329236.7_Nonsense_Mutation_p.Q341*|RBM10_ENST00000478410.1_3'UTR|RBM10_ENST00000345781.6_Nonsense_Mutation_p.Q342*	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	419					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TCAGGCCTCCCAAGGTGGGGA	0.632																																					Melanoma(171;120 2705 19495 39241)											0			X											13	9	11					X																	47040620		2128	4155	6283	46925564	SO:0001587	stop_gained	8241			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1255C>T	X.37:g.47040620C>T	ENSP00000366829:p.Gln419*		46925564	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Nonsense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	39	7.805038	0.98498	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	.	.	.	4.46	4.46	0.54185	.	0.532223	0.19082	N	0.123208	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-19.703	11.6041	0.51022	0.0:1.0:0.0:0.0	.	.	.	.	X	419;341;342	.	ENSP00000328848:Q341X	Q	+	1	0	RBM10	46925564	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.122000	0.57910	2.219000	0.72066	0.597000	0.82753	CAA		0.632	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47040620	C	T	47040620	4	4	113	1	0	0	0	0	0	1	0	0	13148	595	21	3	1301	3	RBM10	23	47040620	Nonsense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	16803855	47040620	108229940	253	30654										
ZNF182	7569	hgsc.bcm.edu	37	chrX	47836341	47836341	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gagttgacttatcactgaaaGttttcttacactcattacat	5	8	3	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:47836341G>C	ENST00000396965.1	-	7	1495	c.1145C>G	c.(1144-1146)aCt>aGt	p.T382S	ZNF182_ENST00000376943.3_Missense_Mutation_p.T363S|ZNF182_ENST00000305127.6_Missense_Mutation_p.T382S	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						ATCACTGAAAGTTTTCTTACA	0.358																																																0			X											113	108	109					X																	47836341		2203	4300	6503	47721285	SO:0001583	missense	7988			AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"Zinc fingers, C2H2-type", "-"	13001	protein-coding gene	gene with protein product		314993	"zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)"	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.1145C>G	X.37:g.47836341G>C	ENSP00000380165:p.Thr382Ser		47721285	A2IDD7|Q3KP67|Q96QH7	Missense_Mutation	SNP	ENST00000396965.1	37	CCDS35236.1	.	.	.	.	.	.	.	.	.	.	G	9.450	1.090366	0.20471	.	.	ENSG00000147118	ENST00000376943;ENST00000396965;ENST00000305127	T;T;T	0.00801	5.68;5.68;5.68	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00967	0.0032	N	0.01631	-0.79	0.23192	N	0.99814	D;B;P	0.56035	0.974;0.115;0.889	P;B;P	0.57548	0.823;0.173;0.581	T	0.64892	-0.6300	9	0.40728	T	0.16	.	9.446	0.38697	0.0:0.2119:0.7881:0.0	.	362;363;382	B4DRM0;Q96QH7;P17025	.;.;ZN182_HUMAN	S	363;382;382	ENSP00000366142:T363S;ENSP00000380165:T382S;ENSP00000306351:T382S	ENSP00000306351:T382S	T	-	2	0	ZNF182	47721285	0.001000	0.12720	0.985000	0.45067	0.923000	0.55619	1.099000	0.31013	2.128000	0.65567	0.422000	0.28245	ACT		0.358	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962		C	47836341	G	C	47836341	3	2	113	1	0	0	0	0	1	0	0	0	17789	1029	36	5	778	5	ZNF182	23	47836341	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	795721	47836341	107434219	254	30655										
FOXO4	4303	hgsc.bcm.edu	37	chrX	70320926	70320926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccagagtctgaggtgctggcGgaggaaataccagcttcagt	14	9	2	2			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:70320926G>A	ENST00000374259.3	+	2	1178	c.846G>A	c.(844-846)gcG>gcA	p.A282A	FOXO4_ENST00000341558.3_Silent_p.A227A	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	282					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					AGGTGCTGGCGGAGGAAATAC	0.567											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			X											42	45	44					X																	70320926		2101	4204	6305	70237651	SO:0001819	synonymous_variant	4303				CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.846G>A	X.37:g.70320926G>A		1121	70237651	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Silent	SNP	ENST00000374259.3	37	CCDS43969.1																																																																																				0.567	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		A	70320926	G	A	70320926	2	1	113	1	0	0	0	0	0	0	0	1	6044	1103	39	1		1	FOXO4	23	70320926	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	22484585	70320926	84949634	255	30656										
OGT	8473	hgsc.bcm.edu	37	chrX	70757811	70757811	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	cattatcgacatgcattgcgTctcaaacctgatttcatcga	6	11	2	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:70757811T>C	ENST00000373719.3	+	3	568	c.351T>C	c.(349-351)cgT>cgC	p.R117R	OGT_ENST00000373701.3_Silent_p.R107R|OGT_ENST00000498566.1_3'UTR	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	117					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					ATGCATTGCGTCTCAAACCTG	0.493																																																0			X											159	127	138					X																	70757811		2203	4300	6503	70674536	SO:0001819	synonymous_variant	8473			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.351T>C	X.37:g.70757811T>C			70674536	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Silent	SNP	ENST00000373719.3	37	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	t	10.71	1.425947	0.25726	.	.	ENSG00000147162	ENST00000455587	.	.	.	4.86	1.11	0.20524	.	.	.	.	.	T	0.46054	0.1373	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25222	-1.0138	4	.	.	.	-19.0221	4.1695	0.10322	0.0:0.3196:0.4266:0.2538	.	.	.	.	A	77	.	.	V	+	2	0	OGT	70674536	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.411000	0.21115	0.213000	0.20722	0.427000	0.28365	GTC		0.493	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		C	70757811	T	C	70757811	2	2	113	1	0	0	0	0	0	0	0	1	10878	1654	58	4		4	OGT	23	70757811	Silent	SNP	T	TCGA-EI-6510-01A-11D-1733-10	436885	70757811	84512749	256	30657										
TCEAL8	90843	hgsc.bcm.edu	37	chrX	102508779	102508779	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gggtttccttctgcttcctgGcttacgccttcttcggaagg	11	12	2	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:102508779G>T	ENST00000372685.3	-	3	365	c.129C>A	c.(127-129)agC>agA	p.S43R	TCEAL8_ENST00000360000.4_Missense_Mutation_p.S43R	NM_153333.2	NP_699164.1	Q8IYN2	TCAL8_HUMAN	transcription elongation factor A (SII)-like 8	43					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.S43S(1)		kidney(2)|lung(1)|ovary(1)	4						CTGCTTCCTGGCTTACGCCTT	0.522																																																1	Substitution - coding silent(1)	ovary(1)	X											156	136	143					X																	102508779		2203	4300	6503	102395435	SO:0001583	missense	90843			AL833632	CCDS14504.1	Xq22.1	2014-03-21			ENSG00000180964	ENSG00000180964			28683	protein-coding gene	gene with protein product						16221301	Standard	NM_001006684		Approved	MGC45400, WEX3	uc004ejy.3	Q8IYN2	OTTHUMG00000022094	ENST00000372685.3:c.129C>A	X.37:g.102508779G>T	ENSP00000361770:p.Ser43Arg		102395435		Missense_Mutation	SNP	ENST00000372685.3	37	CCDS14504.1	.	.	.	.	.	.	.	.	.	.	G	5.684	0.310732	0.10733	.	.	ENSG00000180964	ENST00000360000;ENST00000372685	T;T	0.09255	3.0;3.0	4.52	1.76	0.24704	.	0.339341	0.25968	N	0.027155	T	0.07818	0.0196	L	0.53249	1.67	0.21290	N	0.999739	B	0.06786	0.001	B	0.08055	0.003	T	0.39333	-0.9619	10	0.13108	T	0.6	-3.1427	2.439	0.04490	0.1077:0.185:0.5127:0.1947	.	43	Q8IYN2	TCAL8_HUMAN	R	43	ENSP00000353093:S43R;ENSP00000361770:S43R	ENSP00000353093:S43R	S	-	3	2	TCEAL8	102395435	0.546000	0.26457	0.785000	0.31869	0.536000	0.34869	-0.012000	0.12699	0.242000	0.21303	0.600000	0.82982	AGC		0.522	TCEAL8-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057698.1	NM_153333		T	102508779	G	T	102508779	3	4	113	1	0	0	0	0	1	0	0	0	15716	1194	42	2	228	2	TCEAL8	23	102508779	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	31750968	102508779	52761781	257	30658										
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106108792	106108792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttttaatctttttaaagttgCgtgttgtatcacaagatgtg	8	4	2	1	rs372432035		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:106108792C>T	ENST00000357242.5	+	15	2530	c.2356C>T	c.(2356-2358)Cgt>Tgt	p.R786C	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.R780C	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	786							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TTTAAAGTTGCGTGTTGTATC	0.303																																																0			X						C	CYS/ARG	1,3830		0,1,1629,571	90	82	85		2356	5.5	1	X		85	0,6711		0,0,2424,1863	no	missense	TBC1D8B	NM_017752.2	180	0,1,4053,2434	TT,TC,CC,C		0.0,0.0261,0.0095	probably-damaging	786/1121	106108792	1,10541	2201	4287	6488	105995448	SO:0001583	missense	54885			AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"EF-hand domain containing"	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.2356C>T	X.37:g.106108792C>T	ENSP00000349781:p.Arg786Cys		105995448	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	37	CCDS14522.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.548861|4.548861	0.86127|0.86127	2.61E-4|2.61E-4	0.0|0.0	ENSG00000133138|ENSG00000133138	ENST00000431860|ENST00000357242;ENST00000276175;ENST00000394972	.|T;T	.|0.33865	.|1.39;1.39	5.49|5.49	5.49|5.49	0.81192|0.81192	.|EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64713|0.64713	0.2623|0.2623	M|M	0.84219|0.84219	2.685|2.685	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	T|T	0.70502|0.70502	-0.4854|-0.4854	5|10	.|0.87932	.|D	.|0	-11.5945|-11.5945	16.804|16.804	0.85621|0.85621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|786	.|Q0IIM8	.|TBC8B_HUMAN	V|C	48|786;780;48	.|ENSP00000349781:R786C;ENSP00000276175:R780C	.|ENSP00000276175:R780C	A|R	+|+	2|1	0|0	TBC1D8B|TBC1D8B	105995448|105995448	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	4.081000|4.081000	0.57627|0.57627	2.279000|2.279000	0.76181|0.76181	0.506000|0.506000	0.49869|0.49869	GCG|CGT		0.303	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		T	106108792	C	T	106108792	3	4	113	1	0	0	0	0	1	0	0	0	15665	768	27	1	2480	1	TBC1D8B	23	106108792	Missense_Mutation	SNP	C	TCGA-EI-6510-01A-11D-1733-10	3600013	106108792	49161768	258	30659										
TSC22D3	392517	hgsc.bcm.edu	37	chrX	107018441	107018441	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ccggctctagcgaatcctgcCgcattatgctgttgagcttg	11	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:107018441C>T	ENST00000509000.2	+	0	0				TSC22D3_ENST00000506081.1_Missense_Mutation_p.R70Q|TSC22D3_ENST00000514426.1_Missense_Mutation_p.R2Q|TSC22D3_ENST00000372384.2_Missense_Mutation_p.R70Q|TSC22D3_ENST00000372383.4_Missense_Mutation_p.R70Q|TSC22D3_ENST00000315660.4_Missense_Mutation_p.R70Q			A6PVI3	NCB2L_HUMAN	nuclear cap binding protein subunit 2-like						mRNA cis splicing, via spliceosome (GO:0045292)	nuclear cap binding complex (GO:0005846)	nucleotide binding (GO:0000166)|RNA cap binding (GO:0000339)			large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	5						CGAATCCTGCCGCATTATGCT	0.562																																																0			X											131	100	110					X																	107018441		2203	4300	6503	106905097	SO:0001631	upstream_gene_variant	1831					Xq22.3	2013-02-12			ENSG00000170935	ENSG00000170935		"RNA binding motif (RRM) containing"	31795	protein-coding gene	gene with protein product							Standard	NG_011409		Approved			A6PVI3	OTTHUMG00000022169		X.37:g.107018441C>T	Exception_encountered		106905097		Missense_Mutation	SNP	ENST00000509000.2	37		.	.	.	.	.	.	.	.	.	.	C	34	5.371236	0.95923	.	.	ENSG00000157514	ENST00000315660;ENST00000372383;ENST00000372384;ENST00000506081;ENST00000514426;ENST00000514897;ENST00000480691;ENST00000510887;ENST00000502650;ENST00000506724;ENST00000505965	.	.	.	5.22	5.22	0.72569	.	0.301954	0.38326	N	0.001727	T	0.59074	0.2167	N	0.14661	0.345	0.50313	D	0.999866	D	0.71674	0.998	D	0.72982	0.979	T	0.57985	-0.7716	9	0.25106	T	0.35	-16.8342	15.3861	0.74703	0.0:1.0:0.0:0.0	.	70	Q99576-3	.	Q	70;70;70;70;2;70;70;70;70;70;70	.	ENSP00000314655:R70Q	R	-	2	0	TSC22D3	106905097	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.514000	0.67043	2.313000	0.78055	0.600000	0.82982	CGG		0.562	NCBP2L-001	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000057850.2	XM_373362		T	107018441	C	T	107018441	1	4	113	0	1	0	0	0	0	0	0	0	16649	652	23	1		1	TSC22D3	23	107018441	5'Flank	SNP	C	TCGA-EI-6510-01A-11D-1733-10	909649	107018441	48252119	259	30660										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114239799	114239799	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ggcttacgcaaaagcagaccGgttacaaatataactaatat	7	8	0	1	rs191854615		TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:114239799G>A	ENST00000371936.1	-	10	1326	c.1077C>T	c.(1075-1077)acC>acT	p.T359T	IL13RA2_ENST00000243213.1_Silent_p.T359T			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	359					cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						AAAGCAGACCGGTTACAAATA	0.358																																																0			X											73	68	70					X																	114239799		2203	4300	6503	114146055	SO:0001819	synonymous_variant	3598			X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.1077C>T	X.37:g.114239799G>A			114146055	A8K7E2|O00667	Silent	SNP	ENST00000371936.1	37	CCDS14565.1																																																																																				0.358	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		A	114239799	G	A	114239799	2	1	113	1	0	0	0	0	0	0	0	1	7651	1103	39	1		1	IL13RA2	23	114239799	Silent	SNP	G	TCGA-EI-6510-01A-11D-1733-10	7221358	114239799	41030761	260	30661										
MST4	51765	hgsc.bcm.edu	37	chrX	131202442	131202442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttctttttttcctcctagctGccaatgtcttgctctcagaa	5	12	3	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:131202442G>A	ENST00000354719.6	+	6	658	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	MST4_ENST00000394335.2_Missense_Mutation_p.A71T|MST4_ENST00000496850.1_Missense_Mutation_p.A148T|MST4_ENST00000481105.1_Missense_Mutation_p.A170T|MST4_ENST00000394334.2_Missense_Mutation_p.A148T																endometrium(2)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(192;0.000127)					CCTCCTAGCTGCCAATGTCTT	0.368																																																0			X											61	64	63					X																	131202442		2202	4299	6501	131030123	SO:0001583	missense	51765																														ENST00000354719.6:c.442G>A	X.37:g.131202442G>A	ENSP00000346755:p.Ala148Thr		131030123		Missense_Mutation	SNP	ENST00000354719.6	37		.	.	.	.	.	.	.	.	.	.	G	27.1	4.801157	0.90538	.	.	ENSG00000134602	ENST00000394334;ENST00000481105;ENST00000354719;ENST00000394335;ENST00000496850	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.54481	0.1861	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.986;0.995;0.974;0.99	T	0.57613	-0.7781	10	0.87932	D	0	.	18.9063	0.92462	0.0:0.0:1.0:0.0	.	170;148;148;71;148	B4E0Y9;Q8NBY1;Q9P289-3;Q9P289-2;Q9P289	.;.;.;.;MST4_HUMAN	T	148;170;148;71;148	ENSP00000377867:A148T;ENSP00000418753:A170T;ENSP00000346755:A148T;ENSP00000377868:A71T;ENSP00000419702:A148T	ENSP00000346755:A148T	A	+	1	0	AL109749.1	131030123	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.413000	0.81919	0.600000	0.82982	GCC		0.368	MST4-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000058308.2			A	131202442	G	A	131202442	3	1	113	1	0	0	0	0	1	0	0	0	9922	1319	46	3	460	3	MST4	23	131202442	Missense_Mutation	SNP	G	TCGA-EI-6510-01A-11D-1733-10	16962643	131202442	24068118	261	30662										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138864756	138864756	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	ttcatgtttgtctcaatatcAtcgaaaactttttccatttt	3	8	3	0			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:138864756A>C	ENST00000327569.3	-	18	2009	c.1911T>G	c.(1909-1911)gaT>gaG	p.D637E	ATP11C_ENST00000361648.2_Missense_Mutation_p.D637E|ATP11C_ENST00000359686.2_Missense_Mutation_p.D637E|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000370557.1_Missense_Mutation_p.D634E|ATP11C_ENST00000370543.1_Missense_Mutation_p.D637E	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	637					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TCTCAATATCATCGAAAACTT	0.333																																																0			X											129	102	111					X																	138864756		2203	4300	6503	138692422	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1911T>G	X.37:g.138864756A>C	ENSP00000332756:p.Asp637Glu		138692422	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.265|7.265	0.606007|0.606007	0.14002|0.14002	.|.	.|.	ENSG00000101974|ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686|ENST00000422228	T;T;T;T;T|.	0.69306|.	-0.39;-0.39;-0.39;-0.39;-0.39|.	5.68|5.68	5.68|5.68	0.88126|0.88126	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);|.	0.098435|.	0.64402|.	D|.	0.000002|.	T|T	0.25568|0.25568	0.0622|0.0622	N|N	0.03071|0.03071	-0.42|-0.42	0.36569|0.36569	D|D	0.872866|0.872866	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.14578|.	0.011;0.011|.	T|T	0.37150|0.37150	-0.9718|-0.9718	10|5	0.02654|.	T|.	1|.	.|.	10.5621|10.5621	0.45152|0.45152	0.854:0.0:0.0:0.146|0.854:0.0:0.0:0.146	.|.	637;637|.	Q8NB49-3;Q8NB49|.	.;AT11C_HUMAN|.	E|R	634;637;637;637;637|189	ENSP00000359588:D634E;ENSP00000355165:D637E;ENSP00000332756:D637E;ENSP00000359574:D637E;ENSP00000352715:D637E|.	ENSP00000332756:D637E|.	D|M	-|-	3|2	2|0	ATP11C|ATP11C	138692422|138692422	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	2.910000|2.910000	0.48766|0.48766	1.906000|1.906000	0.55180|0.55180	0.481000|0.481000	0.45027|0.45027	GAT|ATG		0.333	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		C	138864756	A	C	138864756	3	2	113	1	0	0	0	0	1	0	0	0	1122	214	8	4	1602	4	ATP11C	23	138864756	Missense_Mutation	SNP	A	TCGA-EI-6510-01A-11D-1733-10	7662314	138864756	16405804	262	30663										
ATP6AP1	537	hgsc.bcm.edu	37	chrX	153662732	153662732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	8	1	0.452375372459741	2.24302788844621	0.406065393598022	0.0237358101135191	0.180985552115583	0	gtgggaggacctgactccccTcacctttggggtgcaggaac	14	12	1	1			TCGA-EI-6510-01A-11D-1733-10	TCGA-EI-6510-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e6b7c001-ada2-46df-abc3-ff65c313fe5d	b9e5ae43-f76a-4003-8819-58155f6d1ebc	g.chrX:153662732T>C	ENST00000369762.2	+	7	924	c.863T>C	c.(862-864)cTc>cCc	p.L288P	GDI1_ENST00000447750.2_5'Flank	NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	288					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)	p.L288R(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGACTCCCCTCACCTTTGGG	0.582																																																1	Substitution - Missense(1)	ovary(1)	X											123	103	110					X																	153662732		2203	4300	6503	153315926	SO:0001583	missense	537			D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.863T>C	X.37:g.153662732T>C	ENSP00000358777:p.Leu288Pro		153315926	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	37	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289882	0.40494	.	.	ENSG00000071553	ENST00000369762;ENST00000422890;ENST00000445849	.	.	.	5.49	-1.74	0.08056	.	1.228710	0.05262	N	0.515940	T	0.34687	0.0906	L	0.55481	1.735	0.25678	N	0.98583	P;P	0.51791	0.703;0.948	P;P	0.48114	0.567;0.567	T	0.19712	-1.0297	9	0.29301	T	0.29	-1.9916	2.0956	0.03667	0.1311:0.1595:0.3985:0.3109	.	248;288	B3KR70;Q15904	.;VAS1_HUMAN	P	288;218;112	.	ENSP00000358777:L288P	L	+	2	0	ATP6AP1	153315926	0.000000	0.05858	0.005000	0.12908	0.847000	0.48162	-0.480000	0.06559	-0.726000	0.04895	0.430000	0.28490	CTC		0.582	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183		C	153662732	T	C	153662732	3	2	113	1	0	0	0	0	1	0	0	0	1166	1551	54	4	889	4	ATP6AP1	23	153662732	Missense_Mutation	SNP	T	TCGA-EI-6510-01A-11D-1733-10	14797976	153662732	1607828	263	30664										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22151218	22151218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcctggagaagacatggccaGggaaggcgaggaagccatca	15	9	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:22151218G>A	ENST00000374695.3	-	92	12723	c.12644C>T	c.(12643-12645)cCt>cTt	p.P4215L	HSPG2_ENST00000486901.1_5'UTR|LDLRAD2_ENST00000344642.2_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	4215	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GACATGGCCAGGGAAGGCGAG	0.597																																																0			1											88	73	78					1																	22151218		2202	4300	6502	22023805	SO:0001583	missense	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.12644C>T	1.37:g.22151218G>A	ENSP00000363827:p.Pro4215Leu		22023805	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588727	0.86851	.	.	ENSG00000142798	ENST00000374695	T	0.71341	-0.56	4.74	4.74	0.60224	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.39146	N	0.001460	D	0.84719	0.5534	M	0.84156	2.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.87145	0.2205	10	0.66056	D	0.02	.	15.2396	0.73458	0.0:0.0:1.0:0.0	.	2155;4215	Q59EG0;P98160	.;PGBM_HUMAN	L	4215	ENSP00000363827:P4215L	ENSP00000363827:P4215L	P	-	2	0	HSPG2	22023805	1.000000	0.71417	0.083000	0.20561	0.011000	0.07611	8.789000	0.91839	2.194000	0.70268	0.462000	0.41574	CCT		0.597	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22151218	G	A	22151218	3	1	114	1	0	0	0	0	1	0	0	0	7451	1000	35	3	555	3	HSPG2	1	22151218	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		22151218	227099403	1	30665										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114401688	114401688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ttatcagggatagttctaccCggctataatcatctataata	6	8	4	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:114401688C>T	ENST00000359785.5	-	3	344	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	PTPN22_ENST00000538253.1_5'UTR|PTPN22_ENST00000420377.2_Missense_Mutation_p.R70Q|PTPN22_ENST00000534519.1_5'UTR|AP4B1-AS1_ENST00000419536.1_RNA|PTPN22_ENST00000528414.1_Missense_Mutation_p.R70Q|PTPN22_ENST00000460620.1_Missense_Mutation_p.R70Q|PTPN22_ENST00000525799.1_Missense_Mutation_p.R70Q	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	70	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)	p.R70P(1)		NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		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)		TAGTTCTACCCGGCTATAATC	0.368																																																1	Substitution - Missense(1)	kidney(1)	1											62	62	62					1																	114401688		2203	4300	6503	114203211	SO:0001583	missense	26191			AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.209G>A	1.37:g.114401688C>T	ENSP00000352833:p.Arg70Gln		114203211	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	37	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595614	0.86953	.	.	ENSG00000134242	ENST00000460620;ENST00000359785;ENST00000528414;ENST00000420377;ENST00000525799;ENST00000354605	T;D;T;D;T	0.88509	1.59;-2.39;1.59;-2.39;1.51	5.28	-0.805	0.10879	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.386006	0.24059	N	0.041937	D	0.94709	0.8293	H	0.95043	3.615	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.997;1.0	D;D;D;D;P;D	0.77004	0.957;0.935;0.968;0.981;0.9;0.989	D	0.95489	0.8567	10	0.72032	D	0.01	.	15.9978	0.80265	0.6366:0.3634:0.0:0.0	.	70;70;70;70;70;70	E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2-5;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	Q	70	ENSP00000433141:R70Q;ENSP00000352833:R70Q;ENSP00000435176:R70Q;ENSP00000388229:R70Q;ENSP00000432674:R70Q	ENSP00000346621:R70Q	R	-	2	0	PTPN22	114203211	0.906000	0.30813	0.937000	0.37676	0.832000	0.47134	0.723000	0.25939	-0.338000	0.08413	0.563000	0.77884	CGG		0.368	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		T	114401688	C	T	114401688	3	4	114	1	0	0	0	0	1	0	0	0	12824	652	23	1	2313	1	PTPN22	1	114401688	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	92250470	114401688	134848933	2	30666										
CGN	57530	hgsc.bcm.edu	37	chr1	151509309	151509309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggcccagcgtgaggtggaggAgcagcatgaggtcaatgaac	17	8	1	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:151509309A>G	ENST00000271636.7	+	20	3543	c.3410A>G	c.(3409-3411)gAg>gGg	p.E1137G		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	1131					transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GAGGTGGAGGAGCAGCATGAG	0.562																																																0			1											143	147	146					1																	151509309		2203	4300	6503	149775933	SO:0001583	missense	57530			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.3410A>G	1.37:g.151509309A>G	ENSP00000271636:p.Glu1137Gly		149775933	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.843265	0.91197	.	.	ENSG00000143375	ENST00000271636	T	0.80909	-1.43	5.41	5.41	0.78517	Myosin tail (1);	0.099528	0.64402	D	0.000002	D	0.88633	0.6489	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90747	0.4654	10	0.87932	D	0	-26.8742	14.2703	0.66147	1.0:0.0:0.0:0.0	.	1131	Q9P2M7	CING_HUMAN	G	1137	ENSP00000271636:E1137G	ENSP00000271636:E1137G	E	+	2	0	CGN	149775933	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.138000	0.94501	2.055000	0.61198	0.533000	0.62120	GAG		0.562	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		G	151509309	A	G	151509309	3	3	114	1	0	0	0	0	1	0	0	0	3309	304	11	4	3484	4	CGN	1	151509309	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	37107621	151509309	97741312	3	30667										
RPTN	126638	hgsc.bcm.edu	37	chr1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cttgtctctcaggctgactgTggtgggaatctctgtcttgt					rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152129101	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	152129066	7	5	114	1	0	1	0	1	0	0	0	0	13701	1696	59	0	1849	0	RPTN	1	152129066	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TCGA-F5-6464-01A-11D-1733-10	619757	152129066	97121555	4	30668										
CRNN	49860	hgsc.bcm.edu	37	chr1	152383391	152383391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	catccagcagacgcaggaccTcatccacagttgctggatcg	10	14	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:152383391T>C	ENST00000271835.3	-	3	229	c.167A>G	c.(166-168)gAg>gGg	p.E56G	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	56	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGCAGGACCTCATCCACAGT	0.532																																																0			1											40	40	40					1																	152383391		2186	4276	6462	150650015	SO:0001583	missense	49860			AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.167A>G	1.37:g.152383391T>C	ENSP00000271835:p.Glu56Gly		150650015	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637784	0.47049	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.15256	2.44	4.73	4.73	0.59995	EF-hand-like domain (1);	0.298666	0.23803	N	0.044401	T	0.16727	0.0402	L	0.60067	1.865	0.32174	N	0.581301	D	0.63880	0.993	P	0.53954	0.738	T	0.02805	-1.1108	10	0.56958	D	0.05	.	10.5413	0.45035	0.0:0.0:0.0:1.0	.	56	Q9UBG3	CRNN_HUMAN	G	56	ENSP00000271835:E56G	ENSP00000271835:E56G	E	-	2	0	CRNN	150650015	0.983000	0.35010	0.998000	0.56505	0.133000	0.20885	2.432000	0.44784	1.983000	0.57843	0.254000	0.18369	GAG		0.532	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		C	152383391	T	C	152383391	3	2	114	1	0	0	0	0	1	0	0	0	3898	1551	54	4	1324	4	CRNN	1	152383391	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	254325	152383391	96867230	5	30669										
S100A7	6278	hgsc.bcm.edu	37	chr1	153430384	153430384	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aactcagaaaaatcaatcttCttatcctcattcttgtcctt	2	11	6	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:153430384C>A	ENST00000368723.3	-	3	314	c.204G>T	c.(202-204)aaG>aaT	p.K68N	S100A7_ENST00000368722.1_Missense_Mutation_p.K68N	NM_002963.3	NP_002954.2	P31151	S10A7_HUMAN	S100 calcium binding protein A7	68	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				angiogenesis (GO:0001525)|defense response to Gram-negative bacterium (GO:0050829)|epidermis development (GO:0008544)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of granulocyte chemotaxis (GO:0071624)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of T cell chemotaxis (GO:0010820)|response to lipopolysaccharide (GO:0032496)|response to reactive oxygen species (GO:0000302)|sequestering of metal ion (GO:0051238)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(5)|skin(2)	10	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			AATCAATCTTCTTATCCTCAT	0.443																																																0			1											105	94	97					1																	153430384		2203	4300	6503	151697008	SO:0001583	missense	6278			BC034687	CCDS1039.1	1q21	2013-01-10	2006-09-11		ENSG00000143556	ENSG00000143556		"S100 calcium binding proteins", "EF-hand domain containing"	10497	protein-coding gene	gene with protein product		600353	"S100 calcium-binding protein A7 (psoriasin 1)", "S100 calcium binding protein A7 (psoriasin 1)"	PSOR1		1940442	Standard	NM_002963		Approved	S100A7c	uc001fbv.1	P31151	OTTHUMG00000013123	ENST00000368723.3:c.204G>T	1.37:g.153430384C>A	ENSP00000357712:p.Lys68Asn		151697008	Q5SY67|Q6FGE3|Q9H1E2	Missense_Mutation	SNP	ENST00000368723.3	37	CCDS1039.1	.	.	.	.	.	.	.	.	.	.	.	11.00	1.510539	0.27036	.	.	ENSG00000143556	ENST00000368723;ENST00000368722	T;T	0.06142	3.34;3.34	1.77	1.77	0.24775	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	.	.	.	.	T	0.03348	0.0097	L	0.33792	1.035	0.09310	N	1	D	0.63880	0.993	P	0.57468	0.821	T	0.42481	-0.9449	9	0.15066	T	0.55	.	7.0818	0.25235	0.0:1.0:0.0:0.0	.	68	P31151	S10A7_HUMAN	N	68	ENSP00000357712:K68N;ENSP00000357711:K68N	ENSP00000357711:K68N	K	-	3	2	S100A7	151697008	0.001000	0.12720	0.051000	0.19133	0.173000	0.22820	-0.033000	0.12246	1.321000	0.45227	0.194000	0.17425	AAG		0.443	S100A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036789.1	NM_002963		A	153430384	C	A	153430384	3	1	114	1	0	0	0	0	1	0	0	0	13820	912	32	2	105	2	S100A7	1	153430384	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	1046993	153430384	95820237	6	30670										
PKP1	5317	hgsc.bcm.edu	37	chr1	201286871	201286871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aggcagtcagcctcctgaggAgaaccgggaacgccgagatc	14	12	1	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:201286871A>G	ENST00000352845.3	+	5	1018	c.1018A>G	c.(1018-1020)Aga>Gga	p.R340G	PKP1_ENST00000367324.3_Missense_Mutation_p.R340G|PKP1_ENST00000475988.1_3'UTR|PKP1_ENST00000263946.3_Missense_Mutation_p.R340G			Q13835	PKP1_HUMAN	plakophilin 1	340					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						CCTCCTGAGGAGAACCGGGAA	0.652																																																0			1											32	34	33					1																	201286871		2203	4300	6503	199553494	SO:0001583	missense	5317			X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.1018A>G	1.37:g.201286871A>G	ENSP00000295597:p.Arg340Gly		199553494	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.619577	0.46736	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.48836	0.8;0.8;0.8	5.24	4.09	0.47781	Armadillo-like helical (1);Armadillo-type fold (1);	0.297519	0.42172	D	0.000749	T	0.46619	0.1402	M	0.69358	2.11	0.28386	N	0.919327	B;B	0.26258	0.019;0.145	B;B	0.23419	0.033;0.046	T	0.48222	-0.9054	10	0.62326	D	0.03	-11.3622	12.402	0.55418	0.8596:0.1404:0.0:0.0	.	340;340	Q13835-2;Q13835	.;PKP1_HUMAN	G	340	ENSP00000356293:R340G;ENSP00000263946:R340G;ENSP00000295597:R340G	ENSP00000263946:R340G	R	+	1	2	PKP1	199553494	1.000000	0.71417	0.939000	0.37840	0.791000	0.44710	4.213000	0.58520	0.809000	0.34255	0.451000	0.29950	AGA		0.652	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		G	201286871	A	G	201286871	3	3	114	1	0	0	0	0	1	0	0	0	12015	296	11	4	1036	4	PKP1	1	201286871	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	47856487	201286871	47963750	7	30671										
ATP2B4	493	hgsc.bcm.edu	37	chr1	203708819	203708819	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	accactcctggatgaggaagAggaggaaaatcctgacaagg	13	8	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:203708819A>G	ENST00000357681.5	+	21	4578	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	ATP2B4_ENST00000367219.3_3'UTR|ATP2B4_ENST00000391954.2_3'UTR|ATP2B4_ENST00000367218.3_3'UTR|ATP2B4_ENST00000341360.2_3'UTR	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	1188					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.E1152V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GATGAGGAAGAGGAGGAAAAT	0.498																																																1	Substitution - Missense(1)	ovary(1)	1											123	110	114					1																	203708819		2203	4300	6503	201975442	SO:0001583	missense	493			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.3455A>G	1.37:g.203708819A>G	ENSP00000350310:p.Glu1152Gly		201975442	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	37	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012101	0.54468	.	.	ENSG00000058668	ENST00000357681	T	0.79554	-1.28	5.46	5.46	0.80206	.	1.166840	0.06393	N	0.717426	T	0.77558	0.4148	L	0.38175	1.15	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.57717	-0.7763	10	0.51188	T	0.08	-11.0127	15.1947	0.73078	1.0:0.0:0.0:0.0	.	1152	P23634-6	.	G	1152	ENSP00000350310:E1152G	ENSP00000350310:E1152G	E	+	2	0	ATP2B4	201975442	1.000000	0.71417	0.966000	0.40874	0.400000	0.30750	2.550000	0.45811	2.077000	0.62373	0.533000	0.62120	GAG		0.498	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		G	203708819	A	G	203708819	3	3	114	1	0	0	0	0	1	0	0	0	1143	304	11	4	3715	4	ATP2B4	1	203708819	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	2421948	203708819	45541802	8	30672										
LYST	1130	hgsc.bcm.edu	37	chr1	235969926	235969926	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgtctatcccatcaatatctGgaactgaggcatctttctgt	7	10	5	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:235969926G>T	ENST00000389794.3	-	6	2684	c.2510C>A	c.(2509-2511)cCa>cAa	p.P837Q	LYST_ENST00000536965.1_Missense_Mutation_p.P837Q|LYST_ENST00000389793.2_Missense_Mutation_p.P837Q			Q99698	LYST_HUMAN	lysosomal trafficking regulator	837					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATCAATATCTGGAACTGAGGC	0.388																																																0			1											225	215	218					1																	235969926		2203	4300	6503	234036549	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.2510C>A	1.37:g.235969926G>T	ENSP00000374444:p.Pro837Gln		234036549	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.469893	0.26423	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.61040	0.14;0.14;1.28	5.48	3.58	0.41010	.	0.407398	0.28140	N	0.016444	T	0.54255	0.1847	L	0.43152	1.355	0.24121	N	0.995807	B;B	0.31680	0.335;0.033	B;B	0.40901	0.343;0.012	T	0.48186	-0.9057	10	0.35671	T	0.21	.	11.9722	0.53069	0.1441:0.0:0.8559:0.0	.	837;837	Q99698-3;Q99698	.;LYST_HUMAN	Q	837	ENSP00000374444:P837Q;ENSP00000374443:P837Q;ENSP00000438315:P837Q	ENSP00000374443:P837Q	P	-	2	0	LYST	234036549	0.997000	0.39634	0.006000	0.13384	0.953000	0.61014	2.433000	0.44793	0.673000	0.31224	0.655000	0.94253	CCA		0.388	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235969926	G	T	235969926	3	4	114	1	0	0	0	0	1	0	0	0	9158	1348	47	2	9087	2	LYST	1	235969926	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	32261107	235969926	13280695	9	30673										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751751	247751751	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cctcagttacagaaggttctAtttgtgctcatattgattct	7	8	4	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr1:247751751A>G	ENST00000320065.1	+	1	90	c.90A>G	c.(88-90)ctA>ctG	p.L30L	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	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;0.017)			AGAAGGTTCTATTTGTGCTCA	0.393																																																0			1											213	205	208					1																	247751751		2203	4300	6503	245818374	SO:0001819	synonymous_variant	81470			BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.90A>G	1.37:g.247751751A>G			245818374	Q5JQT2|Q6IEZ0	Silent	SNP	ENST00000320065.1	37	CCDS31092.1																																																																																				0.393	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			G	247751751	A	G	247751751	2	3	114	1	0	0	0	0	0	0	0	1	11029	436	16	4		4	OR2G2	1	247751751	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	11781825	247751751	1498870	10	30674										
PPP3R1	5534	hgsc.bcm.edu	37	chr2	68415795	68415795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	caagcttcttaaatctctttCctagccttttaatttcatcc	2	12	3	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:68415795C>T	ENST00000234310.3	-	3	474	c.71G>A	c.(70-72)gGa>gAa	p.G24E	RP11-474G23.1_ENST00000406334.3_Missense_Mutation_p.G14E|PPP3R1_ENST00000409752.1_Missense_Mutation_p.G43E|PPP3R1_ENST00000409377.1_Missense_Mutation_p.G14E	NM_000945.3	NP_000936.1	P63098	CANB1_HUMAN	protein phosphatase 3, regulatory subunit B, alpha	24	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				apoptotic process (GO:0006915)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lung epithelial cell differentiation (GO:0060487)|NFAT protein import into nucleus (GO:0051531)|patterning of blood vessels (GO:0001569)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein dephosphorylation (GO:0006470)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|protein domain specific binding (GO:0019904)			large_intestine(1)	1						AAATCTCTTTCCTAGCCTTTT	0.363																																																0			2											50	47	48					2																	68415795		1810	4073	5883	68269299	SO:0001583	missense	5534			M30773	CCDS46310.1	2p14	2013-01-10	2010-04-14		ENSG00000221823	ENSG00000221823	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 3, regulatory subunits", "EF-hand domain containing"	9317	protein-coding gene	gene with protein product	"calcineurin B, type I (19kDa)", "protein phosphatase 2B regulatory subunit B alpha"	601302	"protein phosphatase 3 (formerly 2B), regulatory subunit B (19kD), alpha isoform (calcineurin B, type I)", "protein phosphatase 3 (formerly 2B), regulatory subunit B, 19kDa, alpha isoform (calcineurin B, type I)", "protein phosphatase 3 (formerly 2B), regulatory subunit B, alpha isoform"			8978785, 2558868	Standard	NM_000945		Approved	CALNB1, CNB, CNB1	uc002sei.1	P63098	OTTHUMG00000129561	ENST00000234310.3:c.71G>A	2.37:g.68415795C>T	ENSP00000234310:p.Gly24Glu		68269299	B2RC10|B5MDU4|P06705|P15117|Q08044|Q53SL0	Missense_Mutation	SNP	ENST00000234310.3	37	CCDS46310.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934955	0.92458	.	.	ENSG00000221823	ENST00000234310;ENST00000409752;ENST00000409377	T;T;T	0.70749	-0.51;-0.51;-0.51	5.93	5.93	0.95920	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.64800	0.2631	L	0.33753	1.03	0.58432	D	0.999995	B	0.20988	0.05	B	0.18263	0.021	T	0.57917	-0.7728	10	0.45353	T	0.12	.	20.3409	0.98764	0.0:1.0:0.0:0.0	.	24	P63098	CANB1_HUMAN	E	24;43;14	ENSP00000234310:G24E;ENSP00000387216:G43E;ENSP00000387148:G14E	ENSP00000234310:G24E	G	-	2	0	PPP3R1	68269299	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.738000	0.84966	2.814000	0.96858	0.655000	0.94253	GGA		0.363	PPP3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326765.4	NM_000945		T	68415795	C	T	68415795	3	4	114	1	0	0	0	0	1	0	0	0	12434	855	30	3	457	3	PPP3R1	2	68415795	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		68415795	174783578	11	30675										
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746015	77746015	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccttatttcctttgaaattcTtaagccaataaaataaagga	4	7	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:77746015T>G	ENST00000409093.1	-	3	1316	c.980A>C	c.(979-981)aAg>aCg	p.K327T	LRRTM4_ENST00000409911.1_Missense_Mutation_p.K328T|LRRTM4_ENST00000409884.1_Missense_Mutation_p.K327T|LRRTM4_ENST00000409282.1_Missense_Mutation_p.K328T|LRRTM4_ENST00000409088.3_Missense_Mutation_p.K327T			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	327	LRRCT.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		TTTGAAATTCTTAAGCCAATA	0.388																																																0			2											40	36	37					2																	77746015		1860	4084	5944	77599523	SO:0001583	missense	80059			AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.980A>C	2.37:g.77746015T>G	ENSP00000386357:p.Lys327Thr		77599523	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.893777	0.33442	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.04758	3.56;3.56;3.56;3.56;3.56	5.73	5.73	0.89815	.	0.179666	0.51477	D	0.000084	T	0.08714	0.0216	L	0.40543	1.245	0.40661	D	0.982128	P;P;P	0.47910	0.902;0.848;0.902	P;P;P	0.51229	0.448;0.65;0.663	T	0.46020	-0.9221	10	0.13470	T	0.59	.	14.8361	0.70183	0.0:0.0:0.0:1.0	.	328;327;327	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	T	328;327;327;327;328	ENSP00000387228:K328T;ENSP00000387297:K327T;ENSP00000386357:K327T;ENSP00000386236:K327T;ENSP00000386286:K328T	ENSP00000386236:K327T	K	-	2	0	LRRTM4	77599523	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.475000	0.45162	2.175000	0.68902	0.533000	0.62120	AAG		0.388	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		G	77746015	T	G	77746015	3	3	114	1	0	0	0	0	1	0	0	0	9071	1609	56	4	806	4	LRRTM4	2	77746015	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	9330220	77746015	165453358	12	30676										
SFTPB	6439	hgsc.bcm.edu	37	chr2	85895300	85895300	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccactgcagcaggtgtgactCagccatggcacctctgcagc	11	15	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:85895300C>T	ENST00000519937.2	-	1	26	c.7G>A	c.(7-9)Gag>Aag	p.E3K	SFTPB_ENST00000409383.1_Missense_Mutation_p.E15K|SFTPB_ENST00000393822.3_Missense_Mutation_p.E15K|SFTPB_ENST00000342375.3_Missense_Mutation_p.E3K			P07988	PSPB_HUMAN	surfactant protein B	3					organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						AGGTGTGACTCAGCCATGGCA	0.667																																																0			2											38	24	29					2																	85895300		2024	3918	5942	85748811	SO:0001583	missense	6439			J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"surfactant, pulmonary-associated protein B"	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.7G>A	2.37:g.85895300C>T	ENSP00000428719:p.Glu3Lys		85748811	Q96R04	Missense_Mutation	SNP	ENST00000519937.2	37		.	.	.	.	.	.	.	.	.	.	C	0.091	-1.167713	0.01660	.	.	ENSG00000168878	ENST00000519937;ENST00000393822;ENST00000342375;ENST00000409383;ENST00000441838	T;T;T;T	0.67345	0.78;-0.07;-0.26;-0.07	4.0	1.56	0.23342	.	3.353680	0.01511	N	0.017948	T	0.33294	0.0858	N	0.00926	-1.1	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50516	-0.8819	10	0.02654	T	1	-9.4914	5.7426	0.18102	0.0:0.2253:0.0:0.7747	.	15;3	D6W5L6;P07988	.;PSPB_HUMAN	K	5;15;3;15;3	ENSP00000428719:E5K;ENSP00000377409:E15K;ENSP00000345161:E3K;ENSP00000386346:E15K	ENSP00000345161:E3K	E	-	1	0	SFTPB	85748811	0.177000	0.23109	0.998000	0.56505	0.017000	0.09413	-0.026000	0.12392	0.217000	0.20800	-1.004000	0.02495	GAG		0.667	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843		T	85895300	C	T	85895300	3	4	114	1	0	0	0	0	1	0	0	0	14228	835	29	3	1178	3	SFTPB	2	85895300	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	8149285	85895300	157304073	13	30677										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163256866	163256866	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggcaacctttacttgcccccCgaaaggctttgcagttttgc	9	13	0	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:163256866C>A	ENST00000332142.5	-	10	2339	c.2240G>T	c.(2239-2241)cGg>cTg	p.R747L		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	747					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	ACTTGCCCCCCGAAAGGCTTT	0.478																																					GBM(196;1492 2208 17507 24132 45496)											0			2											127	130	129					2																	163256866		2203	4300	6503	162965112	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2240G>T	2.37:g.163256866C>A	ENSP00000331727:p.Arg747Leu		162965112	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064853	0.55432	.	.	ENSG00000184611	ENST00000332142	D	0.96885	-4.16	5.47	5.47	0.80525	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.226045	0.46145	D	0.000318	D	0.93592	0.7954	L	0.45352	1.415	0.80722	D	1	P	0.38745	0.645	B	0.36885	0.235	D	0.93795	0.7096	10	0.66056	D	0.02	.	13.6126	0.62088	0.0:0.9256:0.0:0.0744	.	747	Q9NS40	KCNH7_HUMAN	L	747	ENSP00000331727:R747L	ENSP00000331727:R747L	R	-	2	0	KCNH7	162965112	0.938000	0.31826	1.000000	0.80357	0.997000	0.91878	1.929000	0.40114	2.571000	0.86741	0.591000	0.81541	CGG		0.478	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163256866	C	A	163256866	3	1	114	1	0	0	0	0	1	0	0	0	8058	652	23	2	1378	2	KCNH7	2	163256866	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	77361566	163256866	79942507	14	30678										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165952157	165952157	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	catatacaggctgaagtttaAcctaaatgatattgaaaata	6	5	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:165952157A>G	ENST00000360093.3	-	25	4786	c.4295T>C	c.(4294-4296)gTt>gCt	p.V1432A	SCN3A_ENST00000540861.1_5'Flank|SCN3A_ENST00000409101.3_Splice_Site_p.V1383A|SCN3A_ENST00000283254.7_Splice_Site_p.V1432A|SCN3A_ENST00000465043.1_5'Flank	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1432					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAGTTTAACCTAAATGAT	0.264																																																0			2											37	36	37					2																	165952157		2197	4294	6491	165660403	SO:0001630	splice_region_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4294-1T>C	2.37:g.165952157A>G			165660403	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	10.23	1.293585	0.23564	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101	D;D;D	0.96522	-4.04;-4.04;-3.99	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000003	D	0.95739	0.8614	M	0.85542	2.76	0.80722	D	1	B;B;B	0.25272	0.122;0.122;0.01	B;B;B	0.25291	0.059;0.059;0.042	D	0.94256	0.7498	10	0.66056	D	0.02	.	10.8051	0.46514	0.8589:0.0:0.0:0.1411	.	1383;1383;1432	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	A	1432;1432;1383	ENSP00000353206:V1432A;ENSP00000283254:V1432A;ENSP00000386726:V1383A	ENSP00000283254:V1432A	V	-	2	0	SCN3A	165660403	1.000000	0.71417	1.000000	0.80357	0.074000	0.17049	3.968000	0.56809	2.333000	0.79357	0.482000	0.46254	GTT		0.264	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	Missense_Mutation	G	165952157	A	G	165952157	5	3	114	1	0	0	0	0	0	0	1	0	13955	57	2	4	1723	4	SCN3A	2	165952157	Splice_Site	SNP	A	TCGA-F5-6464-01A-11D-1733-10	2695291	165952157	77247216	15	30679										
TTN	7273	hgsc.bcm.edu	37	chr2	179584867	179584867	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ttttcactctctctgatgacTtcacctctatctttcagcca	3	14	7	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:179584867T>G	ENST00000591111.1	-	79	22775	c.22551A>C	c.(22549-22551)gaA>gaC	p.E7517D	TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E7834D|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.E6590D			Q8WZ42	TITIN_HUMAN	titin	13071	Ig-like 57.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTGATGACTTCACCTCTAT	0.438																																																0			2											107	100	102					2																	179584867		1859	4093	5952	179293112	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22551A>C	2.37:g.179584867T>G	ENSP00000465570:p.Glu7517Asp		179293112	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	11.09	1.536819	0.27475	.	.	ENSG00000155657	ENST00000342992	T	0.68624	-0.34	5.9	0.796	0.18648	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61375	0.2342	M	0.63208	1.945	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57573	-0.7788	9	0.87932	D	0	.	11.0092	0.47652	0.1042:0.0:0.535:0.3608	.	7517	Q8WZ42	TITIN_HUMAN	D	6590	ENSP00000343764:E6590D	ENSP00000343764:E6590D	E	-	3	2	TTN	179293112	0.000000	0.05858	0.996000	0.52242	0.973000	0.67179	-1.906000	0.01590	-0.083000	0.12618	-0.340000	0.08031	GAA		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179584867	T	G	179584867	3	3	114	1	0	0	0	0	1	0	0	0	16775	1606	56	4	81155	4	TTN	2	179584867	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	13632710	179584867	63614506	16	30680										
MDH1B	130752	hgsc.bcm.edu	37	chr2	207620125	207620125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggcttttgagatgttcttccGcctgcttgttgtcaaataga	10	8	2	2	rs112729308	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:207620125G>A	ENST00000374412.3	-	5	793	c.518C>T	c.(517-519)gCg>gTg	p.A173V	MDH1B_ENST00000449792.1_Missense_Mutation_p.A75V|MDH1B_ENST00000454776.2_Missense_Mutation_p.A173V|MDH1B_ENST00000392214.2_Intron	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	173					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		ATGTTCTTCCGCCTGCTTGTT	0.517													G|||	2	0.000399361	0.0015	0	5008	,	,		20572	0		0	False		,,,				2504	0				Pancreas(76;29 1355 28675 37177 51207)											0			2						G	VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	95	85	88		518	-2.8	0	2	dbSNP_132	88	0,8600		0,0,4300	yes	missense	MDH1B	NM_001039845.1	64	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	173/519	207620125	3,13003	2203	4300	6503	207328370	SO:0001583	missense	130752				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.518C>T	2.37:g.207620125G>A	ENSP00000363533:p.Ala173Val		207328370	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	8.794	0.931370	0.18131	6.81E-4	0.0	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.44881	0.91;0.91;0.91	5.54	-2.8	0.05823	NAD(P)-binding domain (1);	2.209980	0.01250	N	0.008861	T	0.34745	0.0908	M	0.65975	2.015	0.09310	N	0.999999	B;B	0.18461	0.028;0.017	B;B	0.14023	0.01;0.004	T	0.03922	-1.0992	10	0.16420	T	0.52	4.2796	0.9914	0.01458	0.3888:0.1132:0.2964:0.2016	.	173;173	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	V	173;75;173	ENSP00000363533:A173V;ENSP00000416577:A75V;ENSP00000389916:A173V	ENSP00000363533:A173V	A	-	2	0	MDH1B	207328370	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.675000	0.05227	-0.339000	0.08401	0.650000	0.86243	GCG		0.517	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		A	207620125	G	A	207620125	3	1	114	1	0	0	0	0	1	0	0	0	9439	1087	38	1	1070	1	MDH1B	2	207620125	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	28035258	207620125	35579248	17	30681										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cttgatccccataagcatgaCgacctatgatgataggtttt	8	9	0	4	rs121913500		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	2											79	73	75					2																	209113112		2203	4300	6503	208821357	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		208821357	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			T	209113112	C	T	209113112	3	4	114	1	0	0	0	0	1	0	0	0	7515	536	19	1	877	1	IDH1	2	209113112	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	1492987	209113112	34086261	18	30682										
MAP2	4133	hgsc.bcm.edu	37	chr2	210560896	210560896	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gaagaagagtttgaagtagaAgaggcagctgaagcccaggc	15	6	0	6			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:210560896A>C	ENST00000360351.4	+	7	4508	c.4002A>C	c.(4000-4002)gaA>gaC	p.E1334D	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.E1330D	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1334					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		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)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TTGAAGTAGAAGAGGCAGCTG	0.522																																					Pancreas(27;423 979 28787 29963)											0			2											77	84	81					2																	210560896		2203	4300	6503	210269141	SO:0001583	missense	10988				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4002A>C	2.37:g.210560896A>C	ENSP00000353508:p.Glu1334Asp		210269141	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	9.258	1.042471	0.19748	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.18810	2.19;2.19	5.73	0.798	0.18660	MAP2/Tau projection (1);	0.307617	0.27549	N	0.018872	T	0.11750	0.0286	N	0.25647	0.755	0.40662	D	0.982131	B;B	0.15719	0.011;0.014	B;B	0.20184	0.016;0.028	T	0.11817	-1.0572	10	0.40728	T	0.16	-7.7148	3.8872	0.09103	0.418:0.0:0.3232:0.2588	.	1330;1334	P11137-3;P11137	.;MAP2_HUMAN	D	1334;1330	ENSP00000353508:E1334D;ENSP00000392164:E1330D	ENSP00000353508:E1334D	E	+	3	2	MAP2	210269141	0.995000	0.38212	0.895000	0.35142	0.740000	0.42216	0.355000	0.20163	0.118000	0.18165	0.528000	0.53228	GAA		0.522	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		C	210560896	A	C	210560896	3	2	114	1	0	0	0	0	1	0	0	0	9265	69	3	4	4016	4	MAP2	2	210560896	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	1447784	210560896	32638477	19	30683										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215843133	215843133	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cccaattttcttttgtgttaAgtgctcaagactcatagcac	6	10	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:215843133A>C	ENST00000272895.7	-	33	5254	c.5035T>G	c.(5035-5037)Tta>Gta	p.L1679V	ABCA12_ENST00000389661.4_Missense_Mutation_p.L1361V	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1679					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		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)		TTTTGTGTTAAGTGCTCAAGA	0.388																																					Ovarian(66;664 1488 5121 34295)											0			2											182	164	170					2																	215843133		2203	4300	6503	215551378	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5035T>G	2.37:g.215843133A>C	ENSP00000272895:p.Leu1679Val		215551378	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	9.132	1.011712	0.19277	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.86297	-2.1;-2.1	5.31	4.16	0.48862	.	0.574535	0.14559	N	0.312173	D	0.85544	0.5721	M	0.76170	2.325	0.80722	D	1	B;B	0.21147	0.031;0.052	B;B	0.26969	0.034;0.075	T	0.77787	-0.2457	10	0.21014	T	0.42	.	9.4834	0.38915	0.9155:0.0:0.0845:0.0	.	1679;1361	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	V	1679;1361	ENSP00000272895:L1679V;ENSP00000374312:L1361V	ENSP00000272895:L1679V	L	-	1	2	ABCA12	215551378	0.979000	0.34478	0.996000	0.52242	0.302000	0.27658	1.541000	0.36126	0.961000	0.38030	0.533000	0.62120	TTA		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215843133	A	C	215843133	3	2	114	1	0	0	0	0	1	0	0	0	30	69	3	4	2836	4	ABCA12	2	215843133	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	5282237	215843133	27356240	20	30684										
NGEF	25791	hgsc.bcm.edu	37	chr2	233834941	233834941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tacctcatttcctgggctccTgggtctgtctgcattgctgt	10	12	3	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:233834941T>C	ENST00000264051.3	-	3	644	c.366A>G	c.(364-366)ccA>ccG	p.P122P		NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	122	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		CCTGGGCTCCTGGGTCTGTCT	0.493																																																0			2											166	132	144					2																	233834941		2203	4300	6503	233543185	SO:0001819	synonymous_variant	25791			AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"Rho guanine nucleotide exchange factors"	7807	protein-coding gene	gene with protein product	"ephexin"	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.366A>G	2.37:g.233834941T>C			233543185	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	T	4.105	0.017603	0.07959	.	.	ENSG00000066248	ENST00000414326	.	.	.	4.29	0.11	0.14611	.	.	.	.	.	T	0.23094	0.0558	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-0.5332	3.6971	0.08368	0.0:0.2509:0.1904:0.5587	.	.	.	.	R	91	.	.	Q	-	2	0	NGEF	233543185	0.001000	0.12720	0.016000	0.15963	0.065000	0.16274	-0.324000	0.07986	-0.071000	0.12886	-0.487000	0.04747	CAG		0.493	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		C	233834941	T	C	233834941	2	2	114	1	0	0	0	0	0	0	0	1	10425	1567	55	4		4	NGEF	2	233834941	Silent	SNP	T	TCGA-F5-6464-01A-11D-1733-10	17991808	233834941	9364432	21	30685										
USP40	55230	hgsc.bcm.edu	37	chr2	234399874	234399874	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctatgtctcccaagtagaggAgagaaacttgcgcaggctcg	12	10	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr2:234399874A>C	ENST00000427112.2	-	25	2983	c.2948T>G	c.(2947-2949)cTc>cGc	p.L983R	USP40_ENST00000251722.6_Missense_Mutation_p.L983R|USP40_ENST00000450966.1_Missense_Mutation_p.L995R|USP40_ENST00000496298.1_5'Flank			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	983					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CAAGTAGAGGAGAGAAACTTG	0.463																																																0			2											46	46	46					2																	234399874		1894	4127	6021	234064613	SO:0001583	missense	55230			AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2948T>G	2.37:g.234399874A>C	ENSP00000387898:p.Leu983Arg		234064613	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.13|13.13	2.145463|2.145463	0.37825|0.37825	.|.	.|.	ENSG00000085982|ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112|ENST00000430158	T;T;T|.	0.10477|.	2.87;2.88;2.88|.	4.95|4.95	3.78|3.78	0.43462|0.43462	.|.	3.808960|.	0.00520|.	N|.	0.000196|.	T|T	0.47967|0.47967	0.1474|0.1474	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	D;D|.	0.71674|.	0.997;0.998|.	D;D|.	0.65874|.	0.939;0.93|.	T|T	0.35276|0.35276	-0.9795|-0.9795	10|5	0.87932|.	D|.	0|.	.|.	9.9826|9.9826	0.41821|0.41821	0.9184:0.0:0.0816:0.0|0.9184:0.0:0.0816:0.0	.|.	995;643|.	Q9NVE5-3;B4DN96|.	.;.|.	R|A	995;983;983|159	ENSP00000415434:L995R;ENSP00000251722:L983R;ENSP00000387898:L983R|.	ENSP00000251722:L983R|.	L|S	-|-	2|1	0|0	USP40|USP40	234064613|234064613	0.998000|0.998000	0.40836|0.40836	0.166000|0.166000	0.22797|0.22797	0.124000|0.124000	0.20399|0.20399	5.759000|5.759000	0.68785|0.68785	1.988000|1.988000	0.58038|0.58038	0.533000|0.533000	0.62120|0.62120	CTC|TCC		0.463	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		C	234399874	A	C	234399874	3	2	114	1	0	0	0	0	1	0	0	0	17112	304	11	4	787	4	USP40	2	234399874	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	564933	234399874	8799499	22	30686										
ULK4	54986	hgsc.bcm.edu	37	chr3	41497079	41497079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggtcctctcctgagccagacTtctgggcctggaacagagag	13	12	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr3:41497079T>G	ENST00000301831.4	-	34	3863	c.3401A>C	c.(3400-3402)aAg>aCg	p.K1134T		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	1134					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGAGCCAGACTTCTGGGCCTG	0.537																																																0			3											73	75	75					3																	41497079		1922	4140	6062	41472083	SO:0001583	missense	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.3401A>C	3.37:g.41497079T>G	ENSP00000301831:p.Lys1134Thr		41472083	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.553827	0.45487	.	.	ENSG00000168038	ENST00000301831	T	0.55588	0.51	5.37	5.37	0.77165	Armadillo-like helical (1);Armadillo-type fold (1);	0.627480	0.12056	U	0.503659	T	0.52125	0.1715	L	0.38175	1.15	0.80722	D	1	P	0.52842	0.956	P	0.50082	0.63	T	0.51387	-0.8712	10	0.72032	D	0.01	.	9.8325	0.40950	0.0:0.0765:0.0:0.9235	.	1134	Q96C45	ULK4_HUMAN	T	1134	ENSP00000301831:K1134T	ENSP00000301831:K1134T	K	-	2	0	ULK4	41472083	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	4.181000	0.58303	2.050000	0.60909	0.533000	0.62120	AAG		0.537	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41497079	T	G	41497079	3	3	114	1	0	0	0	0	1	0	0	0	17018	1609	56	4	442	4	ULK4	3	41497079	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10		41497079	156525351	23	30687										
THOC7	80145	hgsc.bcm.edu	37	chr3	63824089	63824089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cataattttccatttctctgAgattcatatcatatactagt	3	8	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr3:63824089A>G	ENST00000295899.5	-	3	336	c.224T>C	c.(223-225)cTc>cCc	p.L75P	C3orf49_ENST00000295896.8_Intron|THOC7_ENST00000498422.1_5'UTR	NM_025075.2	NP_079351.2	Q6I9Y2	THOC7_HUMAN	THO complex 7 homolog (Drosophila)	75	Interaction with THOC5.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4				BRCA - Breast invasive adenocarcinoma(55;0.000439)|Kidney(15;0.00194)|KIRC - Kidney renal clear cell carcinoma(15;0.00218)		CATTTCTCTGAGATTCATATC	0.289																																					Colon(48;665 1127 6720 18651)											0			3											43	45	44					3																	63824089		2202	4297	6499	63799129	SO:0001583	missense	80145			BC020599	CCDS2900.1, CCDS74957.1	3p14.1	2013-02-11			ENSG00000163634	ENSG00000163634		"THO complex subunits"	29874	protein-coding gene	gene with protein product	"Ngg1 interacting factor 3 like 1 binding protein 1", "functional spliceosome-associated protein 24"	611965				12951069	Standard	NM_001285404		Approved	NIF3L1BP1, FLJ23445, fSAP24	uc003dlt.4	Q6I9Y2	OTTHUMG00000158767	ENST00000295899.5:c.224T>C	3.37:g.63824089A>G	ENSP00000295899:p.Leu75Pro		63799129	Q6P1L3|Q8WUF2|Q9H5H0	Missense_Mutation	SNP	ENST00000295899.5	37	CCDS2900.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.118794	0.77323	.	.	ENSG00000163634	ENST00000295899	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.68732	0.3033	L	0.53249	1.67	0.80722	D	1	D	0.67145	0.996	P	0.60609	0.877	T	0.65776	-0.6086	9	0.31617	T	0.26	-29.5076	16.4534	0.84003	1.0:0.0:0.0:0.0	.	75	Q6I9Y2	THOC7_HUMAN	P	75	.	ENSP00000295899:L75P	L	-	2	0	THOC7	63799129	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.296000	0.96104	2.285000	0.76669	0.477000	0.44152	CTC		0.289	THOC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352096.1	NM_025075		G	63824089	A	G	63824089	3	3	114	1	0	0	0	0	1	0	0	0	15909	304	11	4	414	4	THOC7	3	63824089	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	22327010	63824089	134198341	24	30688										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410505	121410505	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tagcatatttattttccagcTccttattttgctgaagttga	6	7	0	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr3:121410505T>C	ENST00000340645.5	-	14	7816	c.7691A>G	c.(7690-7692)gAg>gGg	p.E2564G	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2569G	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2564					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		ATTTTCCAGCTCCTTATTTTG	0.388																																																0			3											111	116	114					3																	121410505		2203	4300	6503	122893195	SO:0001583	missense	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7691A>G	3.37:g.121410505T>C	ENSP00000341848:p.Glu2564Gly		122893195	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	2.678	-0.275967	0.05679	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.15017	2.46;2.46	5.25	2.83	0.33086	.	0.310848	0.28317	N	0.015796	T	0.15003	0.0362	L	0.55481	1.735	0.21915	N	0.999479	P;B;B	0.41978	0.767;0.005;0.016	B;B;B	0.41510	0.359;0.004;0.022	T	0.11275	-1.0594	10	0.30854	T	0.27	.	4.4329	0.11536	0.0:0.1705:0.1684:0.6611	.	2569;2569;2564	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	G	2564;2569	ENSP00000341848:E2564G;ENSP00000377275:E2569G	ENSP00000341848:E2564G	E	-	2	0	GOLGB1	122893195	0.026000	0.19158	0.995000	0.50966	0.369000	0.29798	1.640000	0.37186	0.430000	0.26230	0.533000	0.62120	GAG		0.388	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121410505	T	C	121410505	3	2	114	1	0	0	0	0	1	0	0	0	6585	1551	54	4	2124	4	GOLGB1	3	121410505	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	57586416	121410505	76611925	25	30689										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840829	142840829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcggccccgcagactaccacGctctgggcgctatggaggtc	14	15	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr3:142840829G>T	ENST00000309575.3	+	2	2555	c.1171G>T	c.(1171-1173)Gct>Tct	p.A391S		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	391					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						AGACTACCACGCTCTGGGCGC	0.667																																																0			3											44	53	50					3																	142840829		2203	4300	6503	144323519	SO:0001583	missense	9435			BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.1171G>T	3.37:g.142840829G>T	ENSP00000307911:p.Ala391Ser		144323519	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	G	8.578	0.881619	0.17467	.	.	ENSG00000175040	ENST00000309575	D	0.81996	-1.56	4.47	4.47	0.54385	Sulfotransferase domain (1);	0.236707	0.35320	N	0.003291	T	0.61912	0.2385	N	0.02011	-0.69	0.50039	D	0.999846	P	0.44006	0.824	B	0.40285	0.325	T	0.67051	-0.5768	10	0.09338	T	0.73	-1.1166	17.3237	0.87242	0.0:0.0:1.0:0.0	.	391	Q9Y4C5	CHST2_HUMAN	S	391	ENSP00000307911:A391S	ENSP00000307911:A391S	A	+	1	0	CHST2	144323519	1.000000	0.71417	0.638000	0.29380	0.845000	0.48019	5.663000	0.68038	2.322000	0.78497	0.407000	0.27541	GCT		0.667	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		T	142840829	G	T	142840829	3	4	114	1	0	0	0	0	1	0	0	0	3410	1087	38	2	1173	2	CHST2	3	142840829	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	21430324	142840829	55181601	26	30690										
TP63	8626	hgsc.bcm.edu	37	chr3	189526170	189526170	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cgcgcagaacagcgtcacggCgccctcgccctacgcacagc	11	19	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr3:189526170C>T	ENST00000264731.3	+	4	523	c.434C>T	c.(433-435)gCg>gTg	p.A145V	TP63_ENST00000456148.1_Missense_Mutation_p.A51V|TP63_ENST00000382063.4_Intron|TP63_ENST00000392463.2_Missense_Mutation_p.A51V|TP63_ENST00000354600.5_Missense_Mutation_p.A51V|TP63_ENST00000320472.5_Missense_Mutation_p.A145V|TP63_ENST00000440651.2_Missense_Mutation_p.A145V|TP63_ENST00000437221.1_Missense_Mutation_p.A51V|TP63_ENST00000449992.1_Intron|TP63_ENST00000418709.2_Missense_Mutation_p.A145V|TP63_ENST00000392460.3_Missense_Mutation_p.A145V|TP63_ENST00000392461.3_Missense_Mutation_p.A51V	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	145					apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		AGCGTCACGGCGCCCTCGCCC	0.622										HNSCC(45;0.13)																																						0			3											204	146	166					3																	189526170		2203	4300	6503	191008864	SO:0001583	missense	8626			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.434C>T	3.37:g.189526170C>T	ENSP00000264731:p.Ala145Val		191008864	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	31	5.064122	0.93898	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000354600;ENST00000434928;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000456148	D;D;D;D;D;D;T;D;D;D;D	0.99709	-6.2;-6.48;-6.45;-6.46;-6.2;-6.18;-0.96;-6.45;-6.43;-6.41;-6.18	5.83	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.98921	0.9634	N	0.19112	0.55	0.80722	D	1	D;D;D;D;D;P;D;P;D	0.69078	0.986;0.986;0.972;0.972;0.972;0.908;0.997;0.955;0.986	P;P;P;P;P;B;P;P;P	0.56648	0.674;0.746;0.526;0.526;0.606;0.277;0.803;0.562;0.746	D	0.98977	1.0803	9	.	.	.	-4.842	14.2277	0.65871	0.0:0.9286:0.0:0.0714	.	145;145;51;51;51;51;145;145;145	Q9H3D4-7;Q9H3D4-11;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;.;.;.;.;.;P63_HUMAN;.	V	145;145;145;145;145;51;51;51;51;51;51	ENSP00000264731:A145V;ENSP00000407144:A145V;ENSP00000317510:A145V;ENSP00000376253:A145V;ENSP00000394337:A145V;ENSP00000346614:A51V;ENSP00000401661:A51V;ENSP00000392488:A51V;ENSP00000376256:A51V;ENSP00000376254:A51V;ENSP00000389485:A51V	.	A	+	2	0	TP63	191008864	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	7.487000	0.81328	1.480000	0.48289	0.655000	0.94253	GCG		0.622	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189526170	C	T	189526170	3	4	114	1	0	0	0	0	1	0	0	0	16432	768	27	1	494	1	TP63	3	189526170	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	46685341	189526170	8496260	27	30691										
TLR6	10333	hgsc.bcm.edu	37	chr4	38829758	38829758	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgatcctgggaggtaaacatCtgaaaacagagtcagtaagc	11	7	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:38829758C>T	ENST00000381950.1	-	1	1402	c.1337G>A	c.(1336-1338)aGa>aAa	p.R446K	TLR6_ENST00000436693.2_Missense_Mutation_p.R446K			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	446					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R446T(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGTAAACATCTGAAAACAGA	0.363																																																1	Substitution - Missense(1)	ovary(1)	4											119	128	125					4																	38829758		2203	4300	6503	38506153	SO:0001583	missense	10333				CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1337G>A	4.37:g.38829758C>T	ENSP00000371376:p.Arg446Lys		38506153	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.139053	0.37728	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.51071	0.72;0.72	5.14	5.14	0.70334	.	0.229670	0.39020	N	0.001495	T	0.36853	0.0982	L	0.37630	1.12	0.27531	N	0.951097	B	0.11235	0.004	B	0.09377	0.004	T	0.22836	-1.0205	10	0.45353	T	0.12	.	10.2453	0.43336	0.0:0.8708:0.0:0.1292	.	446	Q9Y2C9	TLR6_HUMAN	K	446	ENSP00000389600:R446K;ENSP00000371376:R446K	ENSP00000371376:R446K	R	-	2	0	TLR6	38506153	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.521000	0.45563	2.392000	0.81423	0.484000	0.47621	AGA		0.363	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			T	38829758	C	T	38829758	3	4	114	1	0	0	0	0	1	0	0	0	15994	913	32	3	1057	3	TLR6	4	38829758	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		38829758	152324518	28	30692										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66217173	66217173	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agtccaaagtcagacactttGcacacaaggttactgttgat	8	9	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:66217173G>T	ENST00000273854.3	-	14	3042	c.2442C>A	c.(2440-2442)tgC>tgA	p.C814*	EPHA5_ENST00000511294.1_Nonsense_Mutation_p.C815*|EPHA5_ENST00000432638.2_Nonsense_Mutation_p.C651*|EPHA5_ENST00000354839.4_Nonsense_Mutation_p.C792*	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	814	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CAGACACTTTGCACACAAGGT	0.453										TSP Lung(17;0.13)																																						0			4											139	120	126					4																	66217173		2203	4300	6503	65899768	SO:0001587	stop_gained	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2442C>A	4.37:g.66217173G>T	ENSP00000273854:p.Cys814*		65899768	Q7Z3F2	Nonsense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	45	11.947361	0.99620	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	.	.	.	5.98	5.14	0.70334	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3185	0.49407	0.1386:0.0:0.8614:0.0	.	.	.	.	X	814;651;792;815	.	ENSP00000273854:C814X	C	-	3	2	EPHA5	65899768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.209000	0.42806	1.551000	0.49450	0.585000	0.79938	TGC		0.453	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66217173	G	T	66217173	4	4	114	1	0	0	0	0	0	1	0	0	5183	1311	46	2	691	2	EPHA5	4	66217173	Nonsense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	27387415	66217173	124937103	29	30693										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125592462	125592462	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcaaattcagtacaatatccTcgtgtcctccccatgctgct	6	14	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:125592462T>A	ENST00000504087.1	-	4	3007	c.1970A>T	c.(1969-1971)gAg>gTg	p.E657V	ANKRD50_ENST00000515641.1_Missense_Mutation_p.E478V	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	657										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TACAATATCCTCGTGTCCTCC	0.453																																																0			4											183	155	165					4																	125592462		2203	4300	6503	125811912	SO:0001583	missense	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1970A>T	4.37:g.125592462T>A	ENSP00000425658:p.Glu657Val		125811912	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	10.33	1.321515	0.23994	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.62105	0.05;0.05	5.43	5.43	0.79202	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.49133	0.1539	N	0.16790	0.44	0.80722	D	1	P	0.36577	0.558	B	0.39068	0.289	T	0.48019	-0.9071	10	0.26408	T	0.33	.	15.6398	0.76989	0.0:0.0:0.0:1.0	.	657	Q9ULJ7	ANR50_HUMAN	V	657;478	ENSP00000425658:E657V;ENSP00000425355:E478V	ENSP00000425658:E657V	E	-	2	0	ANKRD50	125811912	1.000000	0.71417	0.998000	0.56505	0.023000	0.10783	7.365000	0.79537	2.283000	0.76528	0.477000	0.44152	GAG		0.453	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		A	125592462	T	A	125592462	3	1	114	1	0	0	0	0	1	0	0	0	677	1551	54	5	2323	5	ANKRD50	4	125592462	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	59375289	125592462	65561814	30	30694										
TRIM60	166655	hgsc.bcm.edu	37	chr4	165962036	165962036	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccctgaactcttttcatttaGattaacaaaatatggtttca	4	8	3	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:165962036G>T	ENST00000512596.1	+	3	1028	c.812G>T	c.(811-813)aGa>aTa	p.R271I	TRIM60_ENST00000341062.5_Missense_Mutation_p.R271I|TRIM60_ENST00000508504.1_Missense_Mutation_p.R271I	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	271						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R271T(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		TTTTCATTTAGATTAACAAAA	0.388																																																1	Substitution - Missense(1)	skin(1)	4											59	64	62					4																	165962036		2203	4300	6503	166181486	SO:0001583	missense	166655			AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.812G>T	4.37:g.165962036G>T	ENSP00000421142:p.Arg271Ile		166181486	Q8NA35	Missense_Mutation	SNP	ENST00000512596.1	37	CCDS3808.1	.	.	.	.	.	.	.	.	.	.	g	8.888	0.953305	0.18431	.	.	ENSG00000176979	ENST00000512596;ENST00000508504;ENST00000341062	T;T;T	0.05258	3.47;3.47;3.47	2.49	-3.75	0.04372	.	1.773430	0.04021	U	0.299770	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	B	0.26744	0.158	B	0.27262	0.078	T	0.41288	-0.9517	10	0.59425	D	0.04	.	4.9054	0.13795	0.5702:0.174:0.2557:0.0	.	271	Q495X7	TRI60_HUMAN	I	271	ENSP00000421142:R271I;ENSP00000426496:R271I;ENSP00000343765:R271I	ENSP00000343765:R271I	R	+	2	0	TRIM60	166181486	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-1.208000	0.03005	-1.207000	0.02637	-0.751000	0.03497	AGA		0.388	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		T	165962036	G	T	165962036	3	4	114	1	0	0	0	0	1	0	0	0	16575	942	33	2	814	2	TRIM60	4	165962036	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	40369574	165962036	25192240	31	30695										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167675850	167675850	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acatccagccaagtgagtccTtgcaaattggcaagatgctg	10	10	0	2	rs555736304		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:167675850T>G	ENST00000357154.3	-	9	886	c.749A>C	c.(748-750)aAg>aCg	p.K250T	SPOCK3_ENST00000534949.1_Missense_Mutation_p.K154T|SPOCK3_ENST00000506886.1_Missense_Mutation_p.K250T|SPOCK3_ENST00000510741.1_Missense_Mutation_p.K207T|SPOCK3_ENST00000541637.1_Missense_Mutation_p.K152T|SPOCK3_ENST00000357545.4_Missense_Mutation_p.K247T|SPOCK3_ENST00000512648.1_Missense_Mutation_p.K247T|SPOCK3_ENST00000535728.1_Missense_Mutation_p.K118T|SPOCK3_ENST00000511531.1_Missense_Mutation_p.K250T|SPOCK3_ENST00000512681.1_Missense_Mutation_p.K152T|SPOCK3_ENST00000541354.1_Missense_Mutation_p.K130T|SPOCK3_ENST00000504953.1_Missense_Mutation_p.K247T|SPOCK3_ENST00000502330.1_Missense_Mutation_p.K250T|SPOCK3_ENST00000421836.2_Missense_Mutation_p.K199T|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000511269.1_Missense_Mutation_p.K247T	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	250					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		AAGTGAGTCCTTGCAAATTGG	0.368																																																0			4											135	124	128					4																	167675850		2203	4300	6503	167912425	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.749A>C	4.37:g.167675850T>G	ENSP00000349677:p.Lys250Thr		167912425	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176075	0.78564	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949;ENST00000512648;ENST00000510403	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.53640	1.22;1.2;1.2;1.22;1.22;1.22;1.37;1.14;0.61;1.2;1.35;1.01;0.61;0.91;1.98	5.64	5.64	0.86602	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70029	0.3177	M	0.86651	2.83	0.58432	D	0.999997	D;D;D;D;D;D;D;D	0.76494	0.997;0.999;0.998;0.993;0.993;0.995;0.989;0.993	D;D;D;P;P;P;P;P	0.77557	0.935;0.947;0.99;0.855;0.855;0.897;0.691;0.843	T	0.74012	-0.3801	10	0.52906	T	0.07	0.9931	10.5042	0.44823	0.0:0.0725:0.0:0.9275	.	152;154;199;259;207;250;247;250	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;.;TICN3_HUMAN	T	250;247;247;250;250;250;207;130;152;247;118;199;152;154;247;129	ENSP00000349677:K250T;ENSP00000350153:K247T;ENSP00000425570:K247T;ENSP00000420920:K250T;ENSP00000423421:K250T;ENSP00000423606:K250T;ENSP00000426716:K207T;ENSP00000444789:K130T;ENSP00000426318:K152T;ENSP00000425502:K247T;ENSP00000441396:K118T;ENSP00000411344:K199T;ENSP00000445430:K152T;ENSP00000438142:K154T;ENSP00000426177:K247T	ENSP00000349677:K250T	K	-	2	0	SPOCK3	167912425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.041000	0.64196	2.274000	0.75844	0.528000	0.53228	AAG		0.368	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			G	167675850	T	G	167675850	3	3	114	1	0	0	0	0	1	0	0	0	15120	1609	56	4	577	4	SPOCK3	4	167675850	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	1713814	167675850	23478426	32	30696										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170608810	170608810	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	taaacatttctaatttcagaTcaacagcaaaaagaaagaat	4	6	3	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr4:170608810T>C	ENST00000513761.1	+	4	879	c.320T>C	c.(319-321)aTc>aCc	p.I107T	CLCN3_ENST00000504131.2_Splice_Site_p.I90T|CLCN3_ENST00000360642.3_Splice_Site_p.I107T|CLCN3_ENST00000347613.4_Splice_Site_p.I107T	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	107					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		TAATTTCAGATCAACAGCAAA	0.353																																																0			4											97	92	94					4																	170608810		2203	4300	6503	170845385	SO:0001630	splice_region_variant	1182			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.319-1T>C	4.37:g.170608810T>C			170845385	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.680351	0.88542	.	.	ENSG00000109572	ENST00000511092;ENST00000513761;ENST00000347613;ENST00000360642;ENST00000512813;ENST00000538301;ENST00000504131;ENST00000507875	D;D;D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93;-2.93;-2.93	5.29	5.29	0.74685	Chloride channel, core (1);	0.000000	0.85682	D	0.000000	D	0.93693	0.7985	L	0.48260	1.515	0.80722	D	1	D;P;P;D;D	0.61080	0.981;0.95;0.95;0.981;0.989	P;P;P;P;P	0.61201	0.844;0.77;0.77;0.844;0.885	D	0.94436	0.7654	10	0.87932	D	0	-7.2237	15.2291	0.73372	0.0:0.0:0.0:1.0	.	107;90;80;107;107	B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.;.;.;CLCN3_HUMAN;.	T	107;107;107;107;107;107;90;80	ENSP00000425160:I107T;ENSP00000424603:I107T;ENSP00000261514:I107T;ENSP00000353857:I107T;ENSP00000425823:I107T;ENSP00000424540:I90T;ENSP00000425323:I80T	ENSP00000261514:I107T	I	+	2	0	CLCN3	170845385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	1.998000	0.58463	0.455000	0.32223	ATC		0.353	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		Missense_Mutation	C	170608810	T	C	170608810	5	2	114	1	0	0	0	0	0	0	1	0	3470	1449	50	4	330	4	CLCN3	4	170608810	Splice_Site	SNP	T	TCGA-F5-6464-01A-11D-1733-10	2932960	170608810	20545466	33	30697										
FAM105B	90268	hgsc.bcm.edu	37	chr5	14687711	14687711	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ttgatgggaagaatgaggacCtggttgataaaattaaagag	13	2	0	5			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:14687711C>A	ENST00000284274.4	+	5	628	c.550C>A	c.(550-552)Ctg>Atg	p.L184M		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		184	OTU.				canonical Wnt signaling pathway (GO:0060070)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|protein linear deubiquitination (GO:1990108)|sprouting angiogenesis (GO:0002040)	cytoplasm (GO:0005737)|LUBAC complex (GO:0071797)	cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	14	Lung NSC(4;0.00696)					GAATGAGGACCTGGTTGATAA	0.413																																																0			5											140	144	143					5																	14687711		1835	4089	5924	14740711	SO:0001583	missense	90268																														ENST00000284274.4:c.550C>A	5.37:g.14687711C>A	ENSP00000284274:p.Leu184Met		14740711	D3DTD3|Q8NAS0|Q96IA3	Missense_Mutation	SNP	ENST00000284274.4	37	CCDS43302.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.732146	0.69189	.	.	ENSG00000154124	ENST00000284274	T	0.17370	2.28	6.17	6.17	0.99709	.	0.214339	0.41194	D	0.000933	T	0.31199	0.0789	L	0.36672	1.1	0.34688	D	0.725434	D	0.76494	0.999	D	0.72075	0.976	T	0.20638	-1.0269	10	0.52906	T	0.07	-20.5998	13.3717	0.60717	0.1668:0.8332:0.0:0.0	.	184	Q96BN8	F105B_HUMAN	M	184	ENSP00000284274:L184M	ENSP00000284274:L184M	L	+	1	2	FAM105B	14740711	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.513000	0.45494	2.941000	0.99782	0.655000	0.94253	CTG		0.413	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1			A	14687711	C	A	14687711	3	1	114	1	0	0	0	0	1	0	0	0	5404	680	24	2	568	2	FAM105B	5	14687711	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		14687711	166227549	34	30698										
CDH10	1008	hgsc.bcm.edu	37	chr5	24487992	24487992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gatcatgctcttttagccttTcattaatgaaatcccggacg	7	10	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:24487992T>C	ENST00000264463.4	-	12	2654	c.2147A>G	c.(2146-2148)gAa>gGa	p.E716G	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	716					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TTTTAGCCTTTCATTAATGAA	0.458										HNSCC(23;0.051)																																						0			5											93	98	97					5																	24487992		2203	4300	6503	24523749	SO:0001583	missense	1008			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.2147A>G	5.37:g.24487992T>C	ENSP00000264463:p.Glu716Gly		24523749	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.645906	0.29246	.	.	ENSG00000040731	ENST00000264463	T	0.79454	-1.27	5.68	5.68	0.88126	Cadherin, cytoplasmic domain (1);	0.277720	0.42294	D	0.000729	T	0.67822	0.2934	L	0.28192	0.835	0.32239	N	0.572965	B	0.02656	0.0	B	0.08055	0.003	T	0.69756	-0.5059	10	0.44086	T	0.13	.	15.1134	0.72380	0.0:0.0:0.0:1.0	.	716	Q9Y6N8	CAD10_HUMAN	G	716	ENSP00000264463:E716G	ENSP00000264463:E716G	E	-	2	0	CDH10	24523749	1.000000	0.71417	0.471000	0.27229	0.996000	0.88848	3.602000	0.54066	2.175000	0.68902	0.533000	0.62120	GAA		0.458	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		C	24487992	T	C	24487992	3	2	114	1	0	0	0	0	1	0	0	0	3102	1783	62	4	223	4	CDH10	5	24487992	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	9800281	24487992	156427268	35	30699										
APC	324	hgsc.bcm.edu	37	chr5	112174424	112174424	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctggaaggcaaagtccttcaCagaatgaaagatgggcaaga	12	7	1	4			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:112174424C>T	ENST00000457016.1	+	16	3513	c.3133C>T	c.(3133-3135)Cag>Tag	p.Q1045*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1045*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1045*			P25054	APC_HUMAN	adenomatous polyposis coli	1045	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1045*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGTCCTTCACAGAATGAAAG	0.333		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5	GRCh37	CM940070	APC	M							64	64	64					5																	112174424		2202	4300	6502	112202323	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3133C>T	5.37:g.112174424C>T	ENSP00000413133:p.Gln1045*		112202323	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.850017	0.97885	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	5.76	0.90799	.	0.058024	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-7.9916	15.141	0.72609	0.0:0.9305:0.0:0.0695	.	.	.	.	X	1045;1027;1045;1045;1045	.	ENSP00000257430:Q1045X	Q	+	1	0	APC	112202323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.465000	0.73538	2.726000	0.93360	0.655000	0.94253	CAG		0.333	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174424	C	T	112174424	4	4	114	1	0	0	0	0	0	1	0	0	763	479	17	3	3191	3	APC	5	112174424	Nonsense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	87686432	112174424	68740836	36	30700										
APC	324	hgsc.bcm.edu	37	chr5	112175951	112175952	+	Frame_Shift_Ins	INS	-	-	A													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aaaccaagagaaagaggcagINSaaaaaactattgattctgaa					rs587783031		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:112175951_112175952insA	ENST00000457016.1	+	16	5040_5041	c.4660_4661insA	c.(4660-4662)gaafs	p.E1554fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Ins_p.E1554fs|APC_ENST00000257430.4_Frame_Shift_Ins_p.E1554fs			P25054	APC_HUMAN	adenomatous polyposis coli	1554	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1556fs*3(42)|p.E1554fs*5(2)|p.E1554fs*3(1)|p.?(1)|p.T1556fs*9(1)|p.?fs(1)|p.K1192fs*3(1)|p.E1554*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAGAGGCAGAAAAAACTATT	0.342		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	50	Insertion - Frameshift(45)|Deletion - Frameshift(3)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(45)|stomach(3)|soft_tissue(1)|skin(1)	5																																								112203851	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4666dupA	5.37:g.112175957_112175957dupA	ENSP00000413133:p.Glu1554fs		112203850	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.342	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175952	-	A	112175951	7	5	114	1	0	1	1	0	0	0	0	0	763	943	33	0	4718	0	APC	5	112175951	Frame_Shift_Ins	INS	-	TCGA-F5-6464-01A-11D-1733-10	1527	112175951	68739309	37	30701										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250830	140250830	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agcctcctggtactcacgctGctgctgtatacggcgctgtg	12	13	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:140250830G>T	ENST00000398640.2	+	1	2142	c.2142G>T	c.(2140-2142)ctG>ctT	p.L714L	PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	714					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTCACGCTGCTGCTGTATA	0.687																																																0			5											39	40	40					5																	140250830		2203	4300	6503	140231014	SO:0001819	synonymous_variant	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2142G>T	5.37:g.140250830G>T			140231014	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																				0.687	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140250830	G	T	140250830	2	4	114	1	0	0	0	0	0	0	0	1	11552	1306	46	2		2	PCDHA11	5	140250830	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	28074879	140250830	40664430	38	30702										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161119061	161119061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agctgtttgctttgcattcgTcttctctgcgcttatcgagt	9	10	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:161119061T>C	ENST00000274545.5	+	8	1374	c.941T>C	c.(940-942)gTc>gCc	p.V314A	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.V304A			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	314					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TTTGCATTCGTCTTCTCTGCG	0.483										TCGA Ovarian(5;0.080)																																						0			5											176	145	155					5																	161119061		2203	4300	6503	161051639	SO:0001583	missense	2559				CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.941T>C	5.37:g.161119061T>C	ENSP00000274545:p.Val314Ala		161051639	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.810009	0.90707	.	.	ENSG00000145863	ENST00000274545;ENST00000523217	D;D	0.88818	-2.43;-2.43	5.32	5.32	0.75619	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.96144	0.8743	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97401	0.9996	10	0.87932	D	0	.	15.2799	0.73773	0.0:0.0:0.0:1.0	.	314	Q16445	GBRA6_HUMAN	A	314;304	ENSP00000274545:V314A;ENSP00000430527:V304A	ENSP00000274545:V314A	V	+	2	0	GABRA6	161051639	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	7.946000	0.87746	1.997000	0.58415	0.528000	0.53228	GTC		0.483	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			C	161119061	T	C	161119061	3	2	114	1	0	0	0	0	1	0	0	0	6184	1667	58	4	971	4	GABRA6	5	161119061	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	20868231	161119061	19796199	39	30703										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161300147	161300147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	atacaatagatgtatttttcCgtcaaagctggaaggatgaa	9	5	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr5:161300147C>T	ENST00000428797.2	+	6	635	c.280C>T	c.(280-282)Cgt>Tgt	p.R94C	GABRA1_ENST00000420560.1_Missense_Mutation_p.R94C|GABRA1_ENST00000444819.1_Missense_Mutation_p.R94C|GABRA1_ENST00000437025.2_Missense_Mutation_p.R94C|GABRA1_ENST00000023897.6_Missense_Mutation_p.R94C|GABRA1_ENST00000393943.4_Missense_Mutation_p.R94C	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	94					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R94C(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	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;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	TGTATTTTTCCGTCAAAGCTG	0.373																																																1	Substitution - Missense(1)	prostate(1)	5											91	97	95					5																	161300147		2203	4300	6503	161232725	SO:0001583	missense	2554				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.280C>T	5.37:g.161300147C>T	ENSP00000393097:p.Arg94Cys		161232725	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.257033	0.80246	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819;ENST00000519621	T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.107484	0.64402	D	0.000008	D	0.92727	0.7688	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.93907	0.7193	10	0.87932	D	0	.	19.9462	0.97183	0.0:1.0:0.0:0.0	.	94	P14867	GBRA1_HUMAN	C	94	ENSP00000023897:R94C;ENSP00000393097:R94C;ENSP00000377517:R94C;ENSP00000415441:R94C;ENSP00000408041:R94C;ENSP00000414232:R94C;ENSP00000430435:R94C	ENSP00000023897:R94C	R	+	1	0	GABRA1	161232725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.008000	0.57103	2.717000	0.92951	0.585000	0.79938	CGT		0.373	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		T	161300147	C	T	161300147	3	4	114	1	0	0	0	0	1	0	0	0	6179	652	23	1	294	1	GABRA1	5	161300147	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	181086	161300147	19615113	40	30704										
BAI3	577	hgsc.bcm.edu	37	chr6	70071241	70071241	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tccccctgtaatggaccagtTcaatatgaacttagagcaac	7	11	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:70071241T>C	ENST00000370598.1	+	29	4897	c.4076T>C	c.(4075-4077)tTc>tCc	p.F1359S	BAI3_ENST00000546190.1_Missense_Mutation_p.F323S|BAI3_ENST00000238918.8_Missense_Mutation_p.F565S	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1359					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				ATGGACCAGTTCAATATGAAC	0.433																																																0			6											108	111	110					6																	70071241		2203	4300	6503	70127962	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4076T>C	6.37:g.70071241T>C	ENSP00000359630:p.Phe1359Ser		70127962	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207705	0.39003	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.05717	3.4;3.4;3.4	5.8	5.8	0.92144	.	0.091421	0.85682	D	0.000000	T	0.01905	0.0060	N	0.19112	0.55	0.44409	D	0.997327	P;B	0.37466	0.596;0.097	B;B	0.32864	0.154;0.031	T	0.58629	-0.7603	10	0.19147	T	0.46	.	16.1965	0.82029	0.0:0.0:0.0:1.0	.	565;1359	B7Z356;O60242	.;BAI3_HUMAN	S	1359;565;323	ENSP00000359630:F1359S;ENSP00000238918:F565S;ENSP00000441821:F323S	ENSP00000238918:F565S	F	+	2	0	BAI3	70127962	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.474000	0.81024	2.232000	0.73038	0.529000	0.55759	TTC		0.433	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70071241	T	C	70071241	3	2	114	1	0	0	0	0	1	0	0	0	1301	1783	62	4	4182	4	BAI3	6	70071241	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10		70071241	101043826	41	30705										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76023146	76023146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cagtttggactccagttgacGtcacaggaacatccaccatt	8	12	1	1	rs78566620		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:76023146G>A	ENST00000237172.7	-	5	2732	c.2402C>T	c.(2401-2403)aCg>aTg	p.T801M	FILIP1_ENST00000393004.2_Missense_Mutation_p.T801M|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Missense_Mutation_p.T702M	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	801										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TCCAGTTGACGTCACAGGAAC	0.478													G|||	1	0.000199681	0	0	5008	,	,		18354	0.001		0	False		,,,				2504	0															0			6						G	MET/THR	0,4406		0,0,2203	132	137	135		2402	5.3	0.7	6	dbSNP_131	135	1,8599	1.2+/-3.3	0,1,4299	yes	missense	FILIP1	NM_015687.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	801/1214	76023146	1,13005	2203	4300	6503	76079866	SO:0001583	missense	27145			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2402C>T	6.37:g.76023146G>A	ENSP00000237172:p.Thr801Met		76079866	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.68	2.010634	0.35511	0.0	1.16E-4	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.19938	2.12;2.11;2.12	5.28	5.28	0.74379	.	0.158221	0.56097	D	0.000034	T	0.26048	0.0635	L	0.54323	1.7	0.54753	D	0.999988	D;P;P	0.69078	0.997;0.884;0.783	P;P;P	0.54312	0.655;0.564;0.748	T	0.00366	-1.1786	10	0.34782	T	0.22	-6.9156	19.1041	0.93285	0.0:0.0:1.0:0.0	.	801;801;801	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	M	801;801;702	ENSP00000376728:T801M;ENSP00000237172:T801M;ENSP00000359037:T702M	ENSP00000237172:T801M	T	-	2	0	FILIP1	76079866	1.000000	0.71417	0.737000	0.30932	0.033000	0.12548	5.481000	0.66826	2.758000	0.94735	0.563000	0.77884	ACG		0.478	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023146	G	A	76023146	3	1	114	1	0	0	0	0	1	0	0	0	5913	1145	40	1	1247	1	FILIP1	6	76023146	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	5951905	76023146	95091921	42	30706										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854560	88854560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aaggcctgcagcggaggctgCgggagtggaggatgacgcac	19	9	0	1	rs143463104		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:88854560C>T	ENST00000537554.1	-	2	3996	c.434G>A	c.(433-435)cGc>cAc	p.R145H	CNR1_ENST00000369499.2_Missense_Mutation_p.R145H|CNR1_ENST00000369501.2_Missense_Mutation_p.R145H|CNR1_ENST00000549890.1_Missense_Mutation_p.R145H|CNR1_ENST00000549716.1_Missense_Mutation_p.R84H|CNR1_ENST00000535130.1_Missense_Mutation_p.R145H|CNR1_ENST00000468898.1_Missense_Mutation_p.R112H|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000428600.2_Missense_Mutation_p.R145H	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	145					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		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)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	GCGGAGGCTGCGGGAGTGGAG	0.612																																																0			6						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	41	38	39		434,434,434,434,335	5.8	1	6	dbSNP_134	39	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	CNR1	NM_001160226.1,NM_001160258.1,NM_001160259.1,NM_016083.4,NM_033181.3	29,29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	145/473,145/473,145/473,145/473,112/440	88854560	1,13005	2203	4300	6503	88911279	SO:0001583	missense	56144			AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.434G>A	6.37:g.88854560C>T	ENSP00000441046:p.Arg145His		88911279	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	37	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662778	0.47572	2.27E-4	0.0	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.77	5.77	0.91146	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.26702	0.0653	L	0.43152	1.355	0.80722	D	1	B;B	0.21688	0.059;0.056	B;B	0.20184	0.02;0.028	T	0.03443	-1.1036	10	0.30854	T	0.27	.	20.0015	0.97412	0.0:1.0:0.0:0.0	.	112;145	P21554-3;P21554	.;CNR1_HUMAN	H	145;145;145;145;145;112;145;84	ENSP00000358513:R145H;ENSP00000442689:R145H;ENSP00000441046:R145H;ENSP00000358511:R145H;ENSP00000446819:R145H;ENSP00000420188:R112H;ENSP00000412192:R145H;ENSP00000449549:R84H	ENSP00000358511:R145H	R	-	2	0	CNR1	88911279	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	7.818000	0.86416	2.732000	0.93576	0.563000	0.77884	CGC		0.612	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			T	88854560	C	T	88854560	3	4	114	1	0	0	0	0	1	0	0	0	3637	768	27	1	988	1	CNR1	6	88854560	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	12831414	88854560	82260507	43	30707										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102124561	102124561	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	taatcttcgactcaaaattcGtcagttacctgctgatacaa	5	10	3	1	rs192827644		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:102124561G>T	ENST00000421544.1	+	4	1095	c.605G>T	c.(604-606)cGt>cTt	p.R202L	GRIK2_ENST00000358361.3_Missense_Mutation_p.R202L|GRIK2_ENST00000369138.1_Missense_Mutation_p.R202L|GRIK2_ENST00000318991.6_Missense_Mutation_p.R202L|GRIK2_ENST00000413795.1_Missense_Mutation_p.R202L|GRIK2_ENST00000369134.4_Missense_Mutation_p.R153L|GRIK2_ENST00000369137.3_Missense_Mutation_p.R202L	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	202					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CTCAAAATTCGTCAGTTACCT	0.338																																																0			6											65	65	65					6																	102124561		2203	4300	6503	102231254	SO:0001583	missense	2901				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.605G>T	6.37:g.102124561G>T	ENSP00000397026:p.Arg202Leu		102231254	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	33	5.248238	0.95305	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.64	5.64	0.86602	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.51210	0.1661	M	0.90309	3.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.992	T	0.60924	-0.7166	10	0.87932	D	0	.	19.766	0.96342	0.0:0.0:1.0:0.0	.	202;202;202	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	L	202;202;202;202;202;202;202;153;164	ENSP00000397026:R202L;ENSP00000405596:R202L;ENSP00000358134:R202L;ENSP00000351128:R202L;ENSP00000358133:R202L;ENSP00000313276:R202L;ENSP00000358130:R153L	ENSP00000313276:R202L	R	+	2	0	GRIK2	102231254	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.864000	0.99589	2.694000	0.91930	0.580000	0.79431	CGT		0.338	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			T	102124561	G	T	102124561	3	4	114	1	0	0	0	0	1	0	0	0	6795	1145	40	2	619	2	GRIK2	6	102124561	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	13270001	102124561	68990506	44	30708										
DCBLD1	285761	hgsc.bcm.edu	37	chr6	117853525	117853525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aagggatcagtcgatatgaaGggattctggccaatggtgtt	14	5	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:117853525G>T	ENST00000338728.5	+	6	808	c.688G>T	c.(688-690)Ggg>Tgg	p.G230W	DCBLD1_ENST00000296955.8_Missense_Mutation_p.G230W|GOPC_ENST00000467125.1_Intron|DCBLD1_ENST00000368503.4_Missense_Mutation_p.G230W			Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1	230	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)		TCGATATGAAGGGATTCTGGC	0.433																																																0			6											236	193	207					6																	117853525		2203	4300	6503	117960218	SO:0001583	missense	285761			AK055462	CCDS34522.1	6q22.31	2003-06-20			ENSG00000164465	ENSG00000164465			21479	protein-coding gene	gene with protein product							Standard	NM_173674		Approved	MGC46341, dJ94G16.1	uc003pxs.3	Q8N8Z6	OTTHUMG00000015455	ENST00000338728.5:c.688G>T	6.37:g.117853525G>T	ENSP00000342422:p.Gly230Trp		117960218	Q5H992|Q8IYK5|Q8N7L9|Q96NH2	Missense_Mutation	SNP	ENST00000338728.5	37		.	.	.	.	.	.	.	.	.	.	G	24.0	4.483383	0.84854	.	.	ENSG00000164465	ENST00000296955;ENST00000368503;ENST00000338728	D;D;D	0.91068	-2.78;-2.78;-2.78	5.53	5.53	0.82687	LCCL (4);	0.247096	0.40302	N	0.001128	D	0.96191	0.8758	M	0.90082	3.085	0.40498	D	0.98061	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96656	0.9485	10	0.87932	D	0	-9.397	19.4633	0.94927	0.0:0.0:1.0:0.0	.	230;230	Q8N8Z6-2;Q8N8Z6	.;DCBD1_HUMAN	W	230	ENSP00000296955:G230W;ENSP00000357489:G230W;ENSP00000342422:G230W	ENSP00000296955:G230W	G	+	1	0	DCBLD1	117960218	1.000000	0.71417	0.996000	0.52242	0.921000	0.55340	5.407000	0.66363	2.608000	0.88229	0.467000	0.42956	GGG		0.433	DCBLD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000041979.2	NM_173674		T	117853525	G	T	117853525	3	4	114	1	0	0	0	0	1	0	0	0	4286	1000	35	2	710	2	DCBLD1	6	117853525	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	15728964	117853525	53261542	45	30709										
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938807	132938807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	atctgcataggcctctgagaAgaccaccccgaaggcaaatg	10	12	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:132938807A>G	ENST00000367931.1	-	2	537	c.538T>C	c.(538-540)Ttc>Ctc	p.F180L	TAAR2_ENST00000275191.2_Missense_Mutation_p.F135L|TAAR2_ENST00000537809.1_Missense_Mutation_p.F135L			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	180					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		GCCTCTGAGAAGACCACCCCG	0.458																																																0			6											67	61	63					6																	132938807		2203	4300	6503	132980500	SO:0001583	missense	9288			AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"GPCR / Class A : Trace amine associated receptors"	4514	protein-coding gene	gene with protein product		604849	"G protein-coupled receptor 58"	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.538T>C	6.37:g.132938807A>G	ENSP00000356908:p.Phe180Leu		132980500	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	37	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	A	13.80	2.345557	0.41498	.	.	ENSG00000146378	ENST00000275191;ENST00000367931;ENST00000537809	T;T;T	0.36340	1.26;1.26;1.26	6.0	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.124650	0.56097	D	0.000035	T	0.13841	0.0335	L	0.33624	1.015	0.38002	D	0.934251	B	0.10296	0.003	B	0.14023	0.01	T	0.05321	-1.0892	10	0.26408	T	0.33	-35.5707	11.5719	0.50839	0.9309:0.0:0.0691:0.0	.	180	Q9P1P5	TAAR2_HUMAN	L	135;180;135	ENSP00000275191:F135L;ENSP00000356908:F180L;ENSP00000441263:F135L	ENSP00000275191:F135L	F	-	1	0	TAAR2	132980500	0.990000	0.36364	1.000000	0.80357	0.986000	0.74619	2.639000	0.46570	2.295000	0.77249	0.528000	0.53228	TTC		0.458	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		G	132938807	A	G	132938807	3	3	114	1	0	0	0	0	1	0	0	0	15529	72	3	4	521	4	TAAR2	6	132938807	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	15085282	132938807	38176260	46	30710										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152577846	152577846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agatttatcttgggttggcaCgtcccctttgtacagtggca	11	9	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr6:152577846C>T	ENST00000367255.5	-	102	19628	c.19027G>A	c.(19027-19029)Gtg>Atg	p.V6343M	SYNE1_ENST00000341594.5_Missense_Mutation_p.V5955M|SYNE1_ENST00000423061.1_Missense_Mutation_p.V6272M|SYNE1_ENST00000356820.4_Missense_Mutation_p.V867M|SYNE1_ENST00000265368.4_Missense_Mutation_p.V6343M|SYNE1_ENST00000448038.1_Missense_Mutation_p.V6272M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6343					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V6343L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGGGTTGGCACGTCCCCTTTG	0.468										HNSCC(10;0.0054)																																						2	Substitution - Missense(2)	prostate(2)	6											179	149	159					6																	152577846		2203	4300	6503	152619539	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.19027G>A	6.37:g.152577846C>T	ENSP00000356224:p.Val6343Met		152619539	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	5.689	0.311623	0.10789	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.53857	0.7;0.69;0.6;0.69;0.79;2.65	5.29	4.43	0.53597	.	0.206659	0.33854	N	0.004500	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P;P;P	0.44578	0.75;0.75;0.838	B;B;B	0.40565	0.115;0.115;0.333	T	0.02721	-1.1119	10	0.44086	T	0.13	.	9.6366	0.39811	0.0:0.7808:0.0:0.2192	.	6343;6343;6272	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	M	6343;6272;6343;6272;5955;867	ENSP00000356224:V6343M;ENSP00000396024:V6272M;ENSP00000265368:V6343M;ENSP00000390975:V6272M;ENSP00000341887:V5955M;ENSP00000349276:V867M	ENSP00000265368:V6343M	V	-	1	0	SYNE1	152619539	0.005000	0.15991	0.013000	0.15412	0.233000	0.25261	1.384000	0.34396	1.373000	0.46208	-0.142000	0.14014	GTG		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152577846	C	T	152577846	3	4	114	1	0	0	0	0	1	0	0	0	15484	536	19	1	7619	1	SYNE1	6	152577846	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	19639039	152577846	18537221	47	30711										
OGDH	4967	hgsc.bcm.edu	37	chr7	44747240	44747240	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cagaagtaccccaatgctgaGctggcctggtgccaggagga	14	11	0	2	rs373124686		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr7:44747240G>T	ENST00000222673.5	+	22	2898	c.2856G>T	c.(2854-2856)gaG>gaT	p.E952D	OGDH_ENST00000444676.1_Missense_Mutation_p.E967D|OGDH_ENST00000439616.2_Missense_Mutation_p.E802D|OGDH_ENST00000543843.1_Missense_Mutation_p.E903D|OGDH_ENST00000447398.1_Missense_Mutation_p.E963D|OGDH_ENST00000449767.1_Missense_Mutation_p.E948D	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	952					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CCAATGCTGAGCTGGCCTGGT	0.562																																																0			7											127	112	117					7																	44747240		2203	4300	6503	44713765	SO:0001583	missense	4967			D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2856G>T	7.37:g.44747240G>T	ENSP00000222673:p.Glu952Asp		44713765	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738034	0.30774	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68;2.68	5.24	3.34	0.38264	.	0.154508	0.56097	N	0.000026	T	0.08313	0.0207	N	0.25890	0.77	0.46222	D	0.998936	B;B;B;B;B	0.12013	0.003;0.005;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.003;0.005;0.005;0.003;0.003	T	0.26395	-1.0104	10	0.31617	T	0.26	-23.3543	4.8279	0.13425	0.0769:0.2832:0.4937:0.1462	.	747;802;948;963;952	B4E3E9;E9PFG7;E9PBM1;E9PDF2;Q02218	.;.;.;.;ODO1_HUMAN	D	802;948;963;967;952;903	ENSP00000398576:E802D;ENSP00000392878:E948D;ENSP00000388183:E963D;ENSP00000414662:E967D;ENSP00000222673:E952D;ENSP00000443821:E903D	ENSP00000222673:E952D	E	+	3	2	OGDH	44713765	0.979000	0.34478	0.998000	0.56505	0.987000	0.75469	0.198000	0.17217	0.519000	0.28406	0.491000	0.48974	GAG		0.562	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44747240	G	T	44747240	3	4	114	1	0	0	0	0	1	0	0	0	10870	962	34	2	3111	2	OGDH	7	44747240	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		44747240	114391423	48	30712										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92940486	92940486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ttccatatcaagtgtttctcGggaaactctaaaaagcagga	8	8	3	0	rs537217820		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr7:92940486G>A	ENST00000305866.5	+	20	1885	c.1757G>A	c.(1756-1758)cGg>cAg	p.R586Q	CCDC132_ENST00000535481.1_Missense_Mutation_p.R306Q|CCDC132_ENST00000541136.1_Missense_Mutation_p.R397Q|CCDC132_ENST00000317751.6_Missense_Mutation_p.R317Q|CCDC132_ENST00000544910.1_Missense_Mutation_p.R556Q	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	586						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.R586L(1)		endometrium(1)|large_intestine(2)|lung(5)	8	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)			AGTGTTTCTCGGGAAACTCTA	0.333													G|||	1	0.000199681	8e-04	0	5008	,	,		15552	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	7											115	114	114					7																	92940486		1813	4062	5875	92778422	SO:0001583	missense	55610			AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1757G>A	7.37:g.92940486G>A	ENSP00000307666:p.Arg586Gln		92778422	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.384108|4.384108	0.82792|0.82792	.|.	.|.	ENSG00000004766|ENSG00000004766	ENST00000458707|ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	.|T	.|0.43688	.|0.94	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.58991|0.58991	0.2161|0.2161	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.994;0.997;0.994	.|D;D;D	.|0.69479	.|0.921;0.964;0.921	T|T	0.53301|0.53301	-0.8458|-0.8458	5|10	.|0.40728	.|T	.|0.16	-14.5355|-14.5355	19.7839|19.7839	0.96430|0.96430	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|306;556;586	.|B4DS55;F5H5U7;Q96JG6	.|.;.;CC132_HUMAN	R|Q	373|586;556;397;306;317	.|ENSP00000325582:R317Q	.|ENSP00000307666:R586Q	G|R	+|+	1|2	0|0	CCDC132|CCDC132	92778422|92778422	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	9.521000|9.521000	0.98029|0.98029	2.756000|2.756000	0.94617|0.94617	0.655000|0.655000	0.94253|0.94253	GGG|CGG		0.333	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		A	92940486	G	A	92940486	3	1	114	1	0	0	0	0	1	0	0	0	2773	1116	39	1	1877	1	CCDC132	7	92940486	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	48193246	92940486	66198177	49	30713										
MET	4233	hgsc.bcm.edu	37	chr7	116436144	116436144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	taacgctgatgatgaggtggAcacacgaccagcctccttct	10	12	1	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr7:116436144A>G	ENST00000318493.6	+	21	4380	c.4193A>G	c.(4192-4194)gAc>gGc	p.D1398G	MET_ENST00000539704.1_Missense_Mutation_p.D250G|MET_ENST00000397752.3_Missense_Mutation_p.D1380G			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GATGAGGTGGACACACGACCA	0.453			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											196	180	185					7																	116436144		2020	4196	6216	116223380	SO:0001583	missense	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.4193A>G	7.37:g.116436144A>G	ENSP00000317272:p.Asp1398Gly		116223380	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.068806	0.76301	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.77750	-0.83;-0.85;-1.12	4.43	4.43	0.53597	.	0.231206	0.52532	D	0.000078	T	0.77651	0.4162	L	0.60455	1.87	0.37957	D	0.932844	P;P	0.40534	0.72;0.598	B;B	0.43838	0.433;0.171	T	0.82579	-0.0387	10	0.66056	D	0.02	.	13.6968	0.62585	1.0:0.0:0.0:0.0	.	1398;1380	P08581-2;P08581	.;MET_HUMAN	G	1380;1398;250	ENSP00000380860:D1380G;ENSP00000317272:D1398G;ENSP00000445020:D250G	ENSP00000317272:D1398G	D	+	2	0	MET	116223380	1.000000	0.71417	0.996000	0.52242	0.599000	0.36880	3.336000	0.52113	1.615000	0.50252	0.533000	0.62120	GAC		0.453	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116436144	A	G	116436144	3	3	114	1	0	0	0	0	1	0	0	0	9515	275	10	4	4271	4	MET	7	116436144	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	23495658	116436144	42702519	50	30714										
OR2F2	135948	hgsc.bcm.edu	37	chr7	143632421	143632421	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tccctgttttccctgttcttGgtcacatacctcatgacagt	6	13	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr7:143632421G>T	ENST00000408955.2	+	1	163	c.96G>T	c.(94-96)ttG>ttT	p.L32F		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CCCTGTTCTTGGTCACATACC	0.458																																																0			7											198	192	194					7																	143632421		2203	4300	6503	143263354	SO:0001583	missense	135948				CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"GPCR / Class A : Olfactory receptors"	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.96G>T	7.37:g.143632421G>T	ENSP00000386222:p.Leu32Phe		143263354	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686039	0.29962	.	.	ENSG00000221910	ENST00000408955	T	0.01804	4.63	3.26	2.36	0.29203	.	0.617739	0.13493	N	0.383824	T	0.04907	0.0132	M	0.67569	2.06	0.23700	N	0.997079	D	0.53462	0.96	P	0.54312	0.748	T	0.33059	-0.9883	10	0.51188	T	0.08	-1.3192	5.9562	0.19275	0.0:0.2145:0.565:0.2205	.	32	O95006	OR2F2_HUMAN	F	32	ENSP00000386222:L32F	ENSP00000386222:L32F	L	+	3	2	OR2F2	143263354	0.000000	0.05858	0.607000	0.28956	0.575000	0.36095	-1.148000	0.03185	0.687000	0.31509	0.491000	0.48974	TTG		0.458	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1			T	143632421	G	T	143632421	3	4	114	1	0	0	0	0	1	0	0	0	11028	1339	47	2	98	2	OR2F2	7	143632421	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	27196277	143632421	15506242	51	30715										
MCM4	4173	hgsc.bcm.edu	37	chr8	48883167	48883167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcaacatcttgctgtgtggcGaccctggtaccagcaagtcc	10	13	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:48883167G>A	ENST00000262105.2	+	11	1740	c.1531G>A	c.(1531-1533)Gac>Aac	p.D511N	MCM4_ENST00000523944.1_Missense_Mutation_p.D511N|MCM4_ENST00000518680.1_3'UTR	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	511	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.D511N(1)		biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GCTGTGTGGCGACCCTGGTAC	0.552																																																1	Substitution - Missense(1)	ovary(1)	8											112	98	102					8																	48883167		2203	4300	6503	49045720	SO:0001583	missense	4173				CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1531G>A	8.37:g.48883167G>A	ENSP00000262105:p.Asp511Asn		49045720	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	G	35	5.416122	0.96092	.	.	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229;ENST00000520637	T;T;T	0.15139	2.45;2.45;2.45	6.17	6.17	0.99709	ATPase, AAA+ type, core (1);	0.082144	0.85682	D	0.000000	T	0.67230	0.2871	H	0.99682	4.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82037	-0.0656	10	0.87932	D	0	-39.4048	20.8794	0.99867	0.0:0.0:1.0:0.0	.	511;511	B3KMX0;P33991	.;MCM4_HUMAN	N	511;511;498;471;229	ENSP00000430194:D511N;ENSP00000262105:D511N;ENSP00000427875:D229N	ENSP00000262105:D511N	D	+	1	0	MCM4	49045720	1.000000	0.71417	0.995000	0.50966	0.708000	0.40852	9.790000	0.99075	2.941000	0.99782	0.655000	0.94253	GAC		0.552	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		A	48883167	G	A	48883167	3	1	114	1	0	0	0	0	1	0	0	0	9419	1058	37	1	1573	1	MCM4	8	48883167	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		48883167	97480855	52	30716										
PDE7A	5150	hgsc.bcm.edu	37	chr8	66691991	66691991	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	atcaatatatgggtgagaacCtcttctttctgattcaaatc	6	8	5	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:66691991C>T	ENST00000401827.3	-	3	690	c.247G>A	c.(247-249)Ggt>Agt	p.G83S	PDE7A_ENST00000379419.4_Missense_Mutation_p.G57S|PDE7A_ENST00000396642.3_Missense_Mutation_p.G83S	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	83					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	GGGTGAGAACCTCTTCTTTCT	0.358																																																0			8											123	128	127					8																	66691991		2203	4300	6503	66854545	SO:0001583	missense	5150			L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"Phosphodiesterases"	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.247G>A	8.37:g.66691991C>T	ENSP00000385632:p.Gly83Ser		66854545	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Missense_Mutation	SNP	ENST00000401827.3	37	CCDS56538.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801104	0.70567	.	.	ENSG00000205268	ENST00000401827;ENST00000379419;ENST00000396642;ENST00000523253	T;T;T;T	0.70045	-0.45;-0.42;-0.45;0.73	5.87	5.87	0.94306	.	0.397956	0.27388	N	0.019582	T	0.56470	0.1987	L	0.31065	0.9	0.43372	D	0.995465	B;B;B	0.23891	0.093;0.092;0.002	B;B;B	0.27715	0.047;0.082;0.005	T	0.52041	-0.8628	10	0.09084	T	0.74	.	18.9794	0.92749	0.0:1.0:0.0:0.0	.	83;83;57	Q13946-3;Q13946;Q13946-2	.;PDE7A_HUMAN;.	S	83;57;83;57	ENSP00000385632:G83S;ENSP00000368730:G57S;ENSP00000379881:G83S;ENSP00000430262:G57S	ENSP00000368730:G57S	G	-	1	0	PDE7A	66854545	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.654000	0.61469	2.781000	0.95711	0.655000	0.94253	GGT		0.358	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1			T	66691991	C	T	66691991	3	4	114	1	0	0	0	0	1	0	0	0	11682	681	24	3	1277	3	PDE7A	8	66691991	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	17808824	66691991	79672031	53	30717										
MMP16	4325	hgsc.bcm.edu	37	chr8	89198818	89198818	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggtacaccgcatcggggcttCttcatccagctgcaaaaaaa	9	12	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:89198818C>A	ENST00000286614.6	-	3	572	c.291G>T	c.(289-291)aaG>aaT	p.K97N	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	97					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	ATCGGGGCTTCTTCATCCAGC	0.363																																																0			8											125	113	117					8																	89198818		2203	4300	6503	89267934	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.291G>T	8.37:g.89198818C>A	ENSP00000286614:p.Lys97Asn		89267934	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787989	0.49997	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	T;T	0.39406	1.08;1.08	5.72	4.85	0.62838	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	0.093928	0.64402	D	0.000001	T	0.39436	0.1078	L	0.54863	1.705	0.51012	D	0.999903	B;B	0.19445	0.036;0.023	B;B	0.23419	0.042;0.046	T	0.28681	-1.0036	10	0.54805	T	0.06	.	10.7208	0.46040	0.0:0.8546:0.0:0.1454	.	97;97	P51512-2;P51512	.;MMP16_HUMAN	N	97;114	ENSP00000286614:K97N;ENSP00000429147:K114N	ENSP00000286614:K97N	K	-	3	2	MMP16	89267934	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.910000	0.48766	1.428000	0.47296	0.585000	0.79938	AAG		0.363	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89198818	C	A	89198818	3	1	114	1	0	0	0	0	1	0	0	0	9685	912	32	2	1720	2	MMP16	8	89198818	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	22506827	89198818	57165204	54	30718										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104973341	104973341	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctctgactatgactgtgatgAtggaattggtgtagtatcag	12	5	2	4			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:104973341A>G	ENST00000436393.2	+	13	2325	c.2084A>G	c.(2083-2085)gAt>gGt	p.D695G	RIMS2_ENST00000406091.3_Missense_Mutation_p.D917G|RIMS2_ENST00000262231.10_Missense_Mutation_p.D756G|RIMS2_ENST00000507740.1_Missense_Mutation_p.D709G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	979	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GACTGTGATGATGGAATTGGT	0.274										HNSCC(12;0.0054)																																						0			8											104	112	110					8																	104973341		1800	4056	5856	105042517	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.2084A>G	8.37:g.104973341A>G	ENSP00000390665:p.Asp695Gly		105042517	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	A	21.5	4.162935	0.78226	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T	0.36157	1.27;1.81;1.58;1.55;1.54;1.77	5.71	5.71	0.89125	.	.	.	.	.	T	0.59742	0.2216	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.984;0.997;0.999;0.999;0.999	D;D;D;D;D;D	0.79784	0.984;0.966;0.993;0.989;0.986;0.991	T	0.63541	-0.6614	9	0.66056	D	0.02	.	13.5005	0.61452	1.0:0.0:0.0:0.0	.	979;979;695;756;709;917	Q9UQ26;Q9UQ26-2;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.;.	G	917;932;917;979;756;709;709;695	ENSP00000427018:D917G;ENSP00000384892:D917G;ENSP00000262231:D756G;ENSP00000423559:D709G;ENSP00000386228:D709G;ENSP00000390665:D695G	ENSP00000262231:D756G	D	+	2	0	RIMS2	105042517	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.042000	0.76565	2.189000	0.69895	0.402000	0.26972	GAT		0.274	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104973341	A	G	104973341	3	3	114	1	0	0	0	0	1	0	0	0	13405	333	12	4	2934	4	RIMS2	8	104973341	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	15774523	104973341	41390681	55	30719										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361283	105361283	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgatgaccttgtttcttggaAccagaccctggcagtctctc	9	12	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:105361283A>C	ENST00000297581.2	+	2	552	c.503A>C	c.(502-504)aAc>aCc	p.N168T	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.N168T	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	168					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GTTTCTTGGAACCAGACCCTG	0.453																																																0			8											94	94	94					8																	105361283		2203	4300	6503	105430459	SO:0001583	missense	81501			AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.503A>C	8.37:g.105361283A>C	ENSP00000297581:p.Asn168Thr		105430459	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993745	0.35131	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.30448	1.53	5.7	5.7	0.88788	.	0.747051	0.13908	N	0.354434	T	0.32406	0.0828	L	0.60455	1.87	0.37234	D	0.905811	B	0.22346	0.068	B	0.15870	0.014	T	0.16247	-1.0409	9	.	.	.	-10.6139	14.541	0.67995	1.0:0.0:0.0:0.0	.	168	Q9H295	TM7S4_HUMAN	T	168	ENSP00000297581:N168T	.	N	+	2	0	TM7SF4	105430459	0.843000	0.29541	0.999000	0.59377	0.998000	0.95712	1.604000	0.36804	2.189000	0.69895	0.459000	0.35465	AAC		0.453	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		C	105361283	A	C	105361283	3	2	114	1	0	0	0	0	1	0	0	0	16015	43	2	4	505	4	TM7SF4	8	105361283	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	387942	105361283	41002739	56	30720										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106814187	106814187	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acttcttcaaacatcttgcaTcaattcttccactgtcttag	3	12	6	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:106814187T>A	ENST00000407775.2	+	8	2127	c.1877T>A	c.(1876-1878)aTc>aAc	p.I626N	RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.I494N|ZFPM2_ENST00000517361.1_Missense_Mutation_p.I494N|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000378472.4_Missense_Mutation_p.I357N|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000518932.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	626					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.I626S(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ACATCTTGCATCAATTCTTCC	0.448																																																1	Substitution - Missense(1)	kidney(1)	8											87	82	84					8																	106814187		1900	4143	6043	106883363	SO:0001583	missense	23414			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1877T>A	8.37:g.106814187T>A	ENSP00000384179:p.Ile626Asn		106883363	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.053056	0.55218	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.20463	2.07;2.52;2.52;3.78	5.86	5.86	0.93980	.	0.219510	0.46758	D	0.000279	T	0.17450	0.0419	L	0.27053	0.805	0.51233	D	0.999919	B	0.31790	0.34	B	0.33890	0.172	T	0.08186	-1.0734	10	0.19590	T	0.45	.	16.2479	0.82454	0.0:0.0:0.0:1.0	.	626	Q8WW38	FOG2_HUMAN	N	626;494;494;357	ENSP00000384179:I626N;ENSP00000430757:I494N;ENSP00000428720:I494N;ENSP00000367733:I357N	ENSP00000367733:I357N	I	+	2	0	ZFPM2	106883363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.241000	0.73720	0.533000	0.62120	ATC		0.448	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106814187	T	A	106814187	3	1	114	1	0	0	0	0	1	0	0	0	17697	1435	50	5	1907	5	ZFPM2	8	106814187	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	1452904	106814187	39549835	57	30721										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113871405	113871405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcactgctgtgatgacccagAcacattgtgcattgctgtca	9	11	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:113871405A>G	ENST00000297405.5	-	11	1968	c.1724T>C	c.(1723-1725)gTc>gCc	p.V575A	CSMD3_ENST00000455883.2_Missense_Mutation_p.V471A|CSMD3_ENST00000343508.3_Missense_Mutation_p.V535A|CSMD3_ENST00000352409.3_Missense_Mutation_p.V575A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	575	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GATGACCCAGACACATTGTGC	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											148	133	138					8																	113871405		2203	4299	6502	113940581	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1724T>C	8.37:g.113871405A>G	ENSP00000297405:p.Val575Ala		113940581	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322555	0.81580	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.67	5.67	0.87782	CUB (5);	0.000000	0.64402	D	0.000007	T	0.50360	0.1611	M	0.70595	2.14	0.42474	D	0.992835	D;D;P	0.69078	0.997;0.996;0.814	D;D;P	0.85130	0.967;0.997;0.9	T	0.51694	-0.8673	10	0.05620	T	0.96	.	15.9132	0.79488	1.0:0.0:0.0:0.0	.	471;575;535	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	535;575;471;575	ENSP00000345799:V535A;ENSP00000297405:V575A;ENSP00000412263:V471A;ENSP00000343124:V575A	ENSP00000297405:V575A	V	-	2	0	CSMD3	113940581	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	9.251000	0.95483	2.154000	0.67381	0.482000	0.46254	GTC		0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113871405	A	G	113871405	3	3	114	1	0	0	0	0	1	0	0	0	3952	275	10	4	9643	4	CSMD3	8	113871405	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	7057218	113871405	32492617	58	30722										
TG	7038	hgsc.bcm.edu	37	chr8	133900728	133900728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ttcagcactcctttggcacaTtttgatcttcggaactgctg	8	11	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:133900728T>C	ENST00000220616.4	+	10	2716	c.2676T>C	c.(2674-2676)caT>caC	p.H892H	TG_ENST00000377869.1_Silent_p.H892H	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	892	Thyroglobulin type-1 7. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.H892H(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	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)		CTTTGGCACATTTTGATCTTC	0.517																																																1	Substitution - coding silent(1)	ovary(1)	8											38	37	37					8																	133900728		2203	4300	6503	133969910	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2676T>C	8.37:g.133900728T>C			133969910	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																				0.517	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133900728	T	C	133900728	2	2	114	1	0	0	0	0	0	0	0	1	15852	1490	52	4		4	TG	8	133900728	Silent	SNP	T	TCGA-F5-6464-01A-11D-1733-10	20029323	133900728	12463294	59	30723										
BAI1	575	hgsc.bcm.edu	37	chr8	143614743	143614743	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gccgtcaccgaccgccgctcCgccctcttccagatcctctt	7	21	3	1	rs374683811	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr8:143614743C>T	ENST00000517894.1	+	25	4380	c.3486C>T	c.(3484-3486)tcC>tcT	p.S1162S	BAI1_ENST00000323289.5_Silent_p.S1162S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1162					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					ACCGCCGCTCCGCCCTCTTCC	0.657																																																0			8											25	33	31					8																	143614743		2198	4296	6494	143611745	SO:0001819	synonymous_variant	575			AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3486C>T	8.37:g.143614743C>T			143611745		Silent	SNP	ENST00000517894.1	37																																																																																					0.657	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143614743	C	T	143614743	2	4	114	1	0	0	0	0	0	0	0	1	1299	639	23	1		1	BAI1	8	143614743	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10	9714015	143614743	2749279	60	30724										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6013873	6013873	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgcatcttgcataaatttttCcttcccaacagcaagaccaa	4	12	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr9:6013873C>T	ENST00000259569.5	-	1	1745	c.1735G>A	c.(1735-1737)Gaa>Aaa	p.E579K	RANBP6_ENST00000485372.1_5'UTR	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	579					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E579K(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		ATAAATTTTTCCTTCCCAACA	0.393																																																1	Substitution - Missense(1)	ovary(1)	9											159	152	154					9																	6013873		2203	4300	6503	6003873	SO:0001583	missense	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.1735G>A	9.37:g.6013873C>T	ENSP00000259569:p.Glu579Lys		6003873	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	37	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951946	0.53293	.	.	ENSG00000137040	ENST00000259569	T	0.68765	-0.35	3.76	2.86	0.33363	Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	T	0.79470	0.4451	M	0.85859	2.78	0.80722	D	1	D;D	0.71674	0.998;0.987	D;P	0.64506	0.926;0.78	T	0.80808	-0.1217	10	0.62326	D	0.03	-11.9682	9.4465	0.38701	0.0:0.8934:0.0:0.1066	.	167;579	B4DTX6;O60518	.;RNBP6_HUMAN	K	579	ENSP00000259569:E579K	ENSP00000259569:E579K	E	-	1	0	RANBP6	6003873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.662000	0.61525	1.162000	0.42619	0.650000	0.86243	GAA		0.393	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		T	6013873	C	T	6013873	3	4	114	1	0	0	0	0	1	0	0	0	13068	864	30	3	1586	3	RANBP6	9	6013873	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		6013873	135199558	61	30725										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35310725	35310725	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aaagaagatgccacaacccaCcctcccccagatctggtgct	7	16	1	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr9:35310725C>G	ENST00000378495.3	+	9	1245	c.1023C>G	c.(1021-1023)caC>caG	p.H341Q	UNC13B_ENST00000378496.4_Missense_Mutation_p.H341Q|UNC13B_ENST00000396787.1_Missense_Mutation_p.H353Q	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	341					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CCACAACCCACCCTCCCCCAG	0.537																																																0			9											107	98	101					9																	35310725		2203	4300	6503	35300725	SO:0001583	missense	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.1023C>G	9.37:g.35310725C>G	ENSP00000367756:p.His341Gln		35300725	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	C	0.108	-1.142115	0.01728	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496	D;T;D	0.83075	-1.56;-1.49;-1.68	5.81	-3.19	0.05171	.	1.179490	0.05832	N	0.617769	T	0.54240	0.1846	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.13407	0.001;0.009;0.001	T	0.40534	-0.9558	10	0.20519	T	0.43	0.5164	0.2385	0.00189	0.3024:0.2469:0.2322:0.2185	.	341;341;341	Q2NKJ5;F8W8M9;O14795	.;.;UN13B_HUMAN	Q	353;341;341	ENSP00000380006:H353Q;ENSP00000367756:H341Q;ENSP00000367757:H341Q	ENSP00000367756:H341Q	H	+	3	2	UNC13B	35300725	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-0.032000	0.12266	-0.445000	0.07159	-0.857000	0.03018	CAC		0.537	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35310725	C	G	35310725	3	3	114	1	0	0	0	0	1	0	0	0	17025	506	18	5	1057	5	UNC13B	9	35310725	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	29296852	35310725	105902706	62	30726										
OR13C8	138802	hgsc.bcm.edu	37	chr9	107332184	107332184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccacctgctcagcccacctgAcagtggtgattatattctat	7	13	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr9:107332184A>G	ENST00000335040.1	+	1	736	c.736A>G	c.(736-738)Aca>Gca	p.T246A		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						AGCCCACCTGACAGTGGTGAT	0.423																																																0			9											122	113	116					9																	107332184		2203	4300	6503	106372005	SO:0001583	missense	138802				CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"GPCR / Class A : Olfactory receptors"	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.736A>G	9.37:g.107332184A>G	ENSP00000334068:p.Thr246Ala		106372005	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.390914	0.25118	.	.	ENSG00000186943	ENST00000335040	T	0.37235	1.21	4.9	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.34279	0.0892	L	0.56340	1.77	0.09310	N	1	B	0.25486	0.127	B	0.33620	0.167	T	0.24119	-1.0169	10	0.38643	T	0.18	.	7.4015	0.26967	0.9042:0.0:0.0958:0.0	.	246	Q8NGS7	O13C8_HUMAN	A	246	ENSP00000334068:T246A	ENSP00000334068:T246A	T	+	1	0	OR13C8	106372005	0.000000	0.05858	0.989000	0.46669	0.993000	0.82548	0.646000	0.24797	2.181000	0.69327	0.459000	0.35465	ACA		0.423	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1			G	107332184	A	G	107332184	3	3	114	1	0	0	0	0	1	0	0	0	10969	275	10	4	738	4	OR13C8	9	107332184	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	72021459	107332184	33881247	63	30727										
ZNF618	114991	hgsc.bcm.edu	37	chr9	116779063	116779063	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gtggccttacacgcccccatCagtgagtacctcctcccggt	9	17	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr9:116779063C>A	ENST00000374126.5	+	10	942	c.843C>A	c.(841-843)atC>atA	p.I281I	ZNF618_ENST00000288466.7_Splice_Site_p.I269I			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ACGCCCCCATCAGTGAGTACC	0.577																																																0			9											55	54	54					9																	116779063		1891	4114	6005	115818884	SO:0001630	splice_region_variant	114991			BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.844+1C>A	9.37:g.116779063C>A			115818884	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																					0.577	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	Silent	A	116779063	C	A	116779063	5	1	114	1	0	0	0	0	0	0	1	0	18081	840	29	2	845	2	ZNF618	9	116779063	Splice_Site	SNP	C	TCGA-F5-6464-01A-11D-1733-10	9446879	116779063	24434368	64	30728										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692903	89692903	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cactgtaaagctggaaagggAcgaactggtgtaatgatatg	13	5	0	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr10:89692903A>G	ENST00000371953.3	+	5	1744	c.387A>G	c.(385-387)ggA>ggG	p.G129G		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	129	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		G -> E (in CWS1; no lipid phosphatase activity but retains protein phosphatase activity; retains ability to inhibit focal adhesion formation). {ECO:0000269|PubMed:9140396}.|G -> R (in glioblastoma; severely reduced protein phosphatase activity; loss of phosphatase activity towards Ins(1,3,4,5)P4). {ECO:0000269|PubMed:9072974, ECO:0000269|PubMed:9331071}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.K128_R130del(3)|p.Y27fs*1(2)|p.A121_F145del(1)|p.G129fs*5(1)|p.G129fs*51(1)|p.F56fs*2(1)|p.G129fs*50(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CTGGAAAGGGACGAACTGGTG	0.408		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	58	Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(2)	prostate(16)|central_nervous_system(12)|skin(6)|haematopoietic_and_lymphoid_tissue(5)|lung(5)|ovary(5)|endometrium(4)|breast(3)|soft_tissue(1)|urinary_tract(1)	10											142	131	135					10																	89692903		2203	4300	6503	89682883	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.387A>G	10.37:g.89692903A>G			89682883	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.408	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692903	A	G	89692903	2	3	114	1	0	0	0	0	0	0	0	1	12772	262	10	4		4	PTEN	10	89692903	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10		89692903	45841844	65	30729										
BLNK	29760	hgsc.bcm.edu	37	chr10	97983657	97983657	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gtcagggccggcagggtggaGgtgagccttgctttctctga	17	9	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr10:97983657G>T	ENST00000224337.5	-	6	591	c.450C>A	c.(448-450)acC>acA	p.T150T	BLNK_ENST00000427367.2_Silent_p.T150T|BLNK_ENST00000371176.2_Silent_p.T150T|BLNK_ENST00000413476.2_Silent_p.T150T	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	150	Pro-rich.				B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		GCAGGGTGGAGGTGAGCCTTG	0.537																																																0			10											134	127	129					10																	97983657		2203	4300	6503	97973647	SO:0001819	synonymous_variant	29760			AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"SH2 domain containing"	14211	protein-coding gene	gene with protein product	"B-cell adapter containing a SH2 domain protein", "B-cell activation", "Src homology [SH2] domain-containing leukocyte protein of 65 kD", "B cell adaptor containing SH2 domain"	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.450C>A	10.37:g.97983657G>T			97973647	O75498|O75499|Q2MD49	Silent	SNP	ENST00000224337.5	37	CCDS7446.1																																																																																				0.537	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314		T	97983657	G	T	97983657	2	4	114	1	0	0	0	0	0	0	0	1	1448	987	35	2		2	BLNK	10	97983657	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	8290754	97983657	37551090	66	30730										
TLX1NB	100038246	hgsc.bcm.edu	37	chr10	102849625	102849625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gctgacttgcccatgcccccCgccttccccagggatggagc	11	18	0	1	rs151326673	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr10:102849625C>T	ENST00000445873.1	-	3	1314	c.38G>A	c.(37-39)cGg>cAg	p.R13Q	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	13																	CCATGCCCCCCGCCTTCCCCA	0.622													C|||	21	0.00419329	0.0159	0	5008	,	,		15532	0		0	False		,,,				2504	0															0			10						C	GLN/ARG	44,3794		0,44,1875	16	18	17		38	0.1	0	10	dbSNP_134	17	1,8201		0,1,4100	yes	missense	TLX1NB	NM_001085398.1	43	0,45,5975	TT,TC,CC		0.0122,1.1464,0.3738	possibly-damaging	13/123	102849625	45,11995	1919	4101	6020	102839615	SO:0001583	missense	0			BC019674	CCDS60615.1	10q24	2014-04-01			ENSG00000236311	ENSG00000236311			37183	protein-coding gene	gene with protein product		612734				17303350	Standard	NM_001085398		Approved	TD1, TDI, APT-B7	uc001ksv.3	P0CAT3	OTTHUMG00000018925	ENST00000445873.1:c.38G>A	10.37:g.102849625C>T	ENSP00000475001:p.Arg13Gln		102839615		Missense_Mutation	SNP	ENST00000445873.1	37																																																																																					0.622	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398		T	102849625	C	T	102849625	3	4	114	1	0	0	0	0	1	0	0	0	15999	652	23	1	334	1	TLX1NB	10	102849625	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	4865968	102849625	32685122	67	30731										
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159317	18159317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggctggtttttttatgtgtgGttctctgtgggtccagcctg	14	7	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:18159317G>A	ENST00000396275.2	+	3	929	c.568G>A	c.(568-570)Gtt>Att	p.V190I		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V190F(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTTATGTGTGGTTCTCTGTGG	0.507																																																1	Substitution - Missense(1)	ovary(1)	11											142	132	135					11																	18159317		2200	4293	6493	18115893	SO:0001583	missense	117195				CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.568G>A	11.37:g.18159317G>A	ENSP00000379571:p.Val190Ile		18115893	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	.	.	.	.	.	.	.	.	.	.	G	9.109	1.006023	0.19199	.	.	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.72394	-0.65;-0.65	1.46	-2.82	0.05787	GPCR, rhodopsin-like superfamily (1);	1.016490	0.07876	N	0.968818	T	0.71108	0.3301	M	0.80422	2.495	0.21184	N	0.999766	P	0.35107	0.484	B	0.42245	0.381	T	0.63994	-0.6511	10	0.59425	D	0.04	.	3.679	0.08304	0.3211:0.2105:0.4685:0.0	.	190	Q96LB0	MRGX3_HUMAN	I	190	ENSP00000379571:V190I;ENSP00000436242:V190I	ENSP00000379571:V190I	V	+	1	0	MRGPRX3	18115893	0.420000	0.25457	0.030000	0.17652	0.017000	0.09413	-0.327000	0.07955	-0.873000	0.04032	0.430000	0.28490	GTT		0.507	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		A	18159317	G	A	18159317	3	1	114	1	0	0	0	0	1	0	0	0	9798	1261	44	3	570	3	MRGPRX3	11	18159317	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		18159317	116847199	68	30732										
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974035	49974035	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggcttacagagaatccaaaaAtgcagaaaatcatatttgtt	7	6	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:49974035A>C	ENST00000555099.1	+	1	93	c.61A>C	c.(61-63)Atg>Ctg	p.M21L		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						GAATCCAAAAATGCAGAAAAT	0.373																																																0			11											128	124	125					11																	49974035		2201	4296	6497	49930611	SO:0001583	missense	283092			AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.61A>C	11.37:g.49974035A>C	ENSP00000452277:p.Met21Leu		49930611	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.530380	0.00145	.	.	ENSG00000258817	ENST00000555099	T	0.02656	4.21	2.95	-1.24	0.09435	.	0.000000	0.43579	U	0.000551	T	0.00875	0.0029	N	0.01228	-0.945	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.47824	-0.9087	9	.	.	.	.	4.7536	0.13073	0.5191:0.3617:0.1192:0.0	.	21	Q8NGP0	OR4CD_HUMAN	L	21	ENSP00000452277:M21L	.	M	+	1	0	OR4C13	49930611	0.002000	0.14202	0.498000	0.27564	0.115000	0.19883	0.049000	0.14099	-0.017000	0.14103	-1.331000	0.01271	ATG		0.373	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		C	49974035	A	C	49974035	3	2	114	1	0	0	0	0	1	0	0	0	11078	101	4	4	63	4	OR4C13	11	49974035	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	31814718	49974035	85032481	69	30733										
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974351	49974351	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccactatgtggccatctgcaAgcccttgcactataccaccg	7	16	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:49974351A>C	ENST00000555099.1	+	1	409	c.377A>C	c.(376-378)aAg>aCg	p.K126T		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						GCCATCTGCAAGCCCTTGCAC	0.463																																																0			11											115	103	107					11																	49974351		2201	4296	6497	49930927	SO:0001583	missense	283092			AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.377A>C	11.37:g.49974351A>C	ENSP00000452277:p.Lys126Thr		49930927	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	7.049	0.564051	0.13498	.	.	ENSG00000258817	ENST00000555099	T	0.00382	7.61	2.95	2.95	0.34219	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000157	T	0.00637	0.0021	M	0.92649	3.33	0.25951	N	0.982744	B	0.32573	0.376	B	0.39935	0.314	T	0.05750	-1.0866	9	.	.	.	.	9.2896	0.37778	1.0:0.0:0.0:0.0	.	126	Q8NGP0	OR4CD_HUMAN	T	126	ENSP00000452277:K126T	.	K	+	2	0	OR4C13	49930927	0.068000	0.21057	0.998000	0.56505	0.031000	0.12232	2.483000	0.45233	1.346000	0.45694	0.164000	0.16699	AAG		0.463	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		C	49974351	A	C	49974351	3	2	114	1	0	0	0	0	1	0	0	0	11078	72	3	4	379	4	OR4C13	11	49974351	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	316	49974351	85032165	70	30734										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135463	55135463	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agaacacatgaaaaataagaAcaatgtgactgaatttatcc	6	6	0	5			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:55135463A>G	ENST00000314706.3	+	1	104	c.104A>G	c.(103-105)aAc>aGc	p.N35S		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						AAAAATAAGAACAATGTGACT	0.393																																																0			11											67	63	64					11																	55135463		2201	4296	6497	54892039	SO:0001583	missense	81328			AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.104A>G	11.37:g.55135463A>G	ENSP00000325065:p.Asn35Ser		54892039	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	37	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	a	9.535	1.111784	0.20714	.	.	ENSG00000181958	ENST00000314706	T	0.01221	5.15	3.48	0.961	0.19638	.	0.000000	0.43110	U	0.000620	T	0.00496	0.0016	N	0.00652	-1.29	0.09310	N	1	B	0.25904	0.137	B	0.25506	0.061	T	0.47355	-0.9124	10	0.28530	T	0.3	.	3.6922	0.08350	0.6476:0.2245:0.1279:0.0	.	35	Q8NGL6	O4A15_HUMAN	S	35	ENSP00000325065:N35S	ENSP00000325065:N35S	N	+	2	0	OR4A15	54892039	0.285000	0.24296	0.409000	0.26459	0.191000	0.23601	1.336000	0.33850	0.410000	0.25675	0.403000	0.27427	AAC		0.393	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		G	55135463	A	G	55135463	3	3	114	1	0	0	0	0	1	0	0	0	11071	43	2	4	106	4	OR4A15	11	55135463	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	5161112	55135463	79871053	71	30735										
INCENP	3619	hgsc.bcm.edu	37	chr11	61897543	61897543	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agcgccagaatgctgagcagCatgtcacccagctcatgtcc	10	14	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:61897543C>G	ENST00000394818.3	+	4	746	c.544C>G	c.(544-546)Cat>Gat	p.H182D	INCENP_ENST00000278849.4_Missense_Mutation_p.H182D	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	182					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTGAGCAGCATGTCACCCA	0.612																																																0			11											65	57	60					11																	61897543		2202	4299	6501	61654119	SO:0001583	missense	3619			AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.544C>G	11.37:g.61897543C>G	ENSP00000378295:p.His182Asp		61654119	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	C	9.542	1.113530	0.20795	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.14144	2.53;2.53	4.73	0.0484	0.14285	.	1.332830	0.04781	N	0.429911	T	0.16642	0.0400	L	0.57536	1.79	0.09310	N	1	D;B;B	0.54601	0.967;0.358;0.244	B;B;B	0.44044	0.439;0.117;0.055	T	0.31223	-0.9951	10	0.39692	T	0.17	.	6.3473	0.21357	0.0:0.4671:0.0:0.5329	.	182;182;182	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	D	182	ENSP00000378295:H182D;ENSP00000278849:H182D	ENSP00000278849:H182D	H	+	1	0	INCENP	61654119	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.593000	0.05740	0.088000	0.17205	-0.258000	0.10820	CAT		0.612	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		G	61897543	C	G	61897543	3	3	114	1	0	0	0	0	1	0	0	0	7754	710	25	5	554	5	INCENP	11	61897543	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	6762080	61897543	73108973	72	30736										
GANAB	23193	hgsc.bcm.edu	37	chr11	62407103	62407103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cccagaaatatcatacttgcAgaaagaactctcttcacagg	6	11	3	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:62407103A>G	ENST00000356638.3	-	2	155	c.139T>C	c.(139-141)Tgc>Cgc	p.C47R	GANAB_ENST00000346178.4_Missense_Mutation_p.C47R|GANAB_ENST00000534422.1_5'Flank|GANAB_ENST00000540933.1_5'UTR|GANAB_ENST00000534779.1_Intron	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	47					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	TCATACTTGCAGAAAGAACTC	0.488																																					Melanoma(23;1005 1074 15747 18937)											0			11											80	77	78					11																	62407103		2202	4299	6501	62163679	SO:0001583	missense	23193			AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.139T>C	11.37:g.62407103A>G	ENSP00000349053:p.Cys47Arg		62163679	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058667	0.55325	.	.	ENSG00000089597	ENST00000346178;ENST00000356638	D;D	0.94931	-3.56;-3.41	5.31	5.31	0.75309	Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	D	0.97207	0.9087	M	0.87547	2.89	0.80722	D	1	D;D	0.65815	0.981;0.995	P;D	0.68192	0.904;0.956	D	0.97850	1.0274	10	0.87932	D	0	.	13.2706	0.60159	1.0:0.0:0.0:0.0	.	47;47	Q14697;Q14697-2	GANAB_HUMAN;.	R	47	ENSP00000340466:C47R;ENSP00000349053:C47R	ENSP00000340466:C47R	C	-	1	0	GANAB	62163679	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	9.037000	0.93765	2.020000	0.59435	0.454000	0.30748	TGC		0.488	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		G	62407103	A	G	62407103	3	3	114	1	0	0	0	0	1	0	0	0	6253	188	7	4	2857	4	GANAB	11	62407103	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	509560	62407103	72599413	73	30737										
DLG2	1740	hgsc.bcm.edu	37	chr11	84245625	84245625	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	taactgaccttcagaggagaAatatgagactgcaagacata	9	7	1	5			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:84245625A>C	ENST00000532653.1	-	2	494	c.192T>G	c.(190-192)atT>atG	p.I64M	DLG2_ENST00000398309.2_Missense_Mutation_p.I64M|DLG2_ENST00000376104.2_Missense_Mutation_p.I169M|DLG2_ENST00000524982.1_Missense_Mutation_p.I64M|DLG2_ENST00000543673.1_Missense_Mutation_p.I169M			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TCAGAGGAGAAATATGAGACT	0.413																																																0			11											159	151	153					11																	84245625		1880	4099	5979	83923273	SO:0001583	missense	4355			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.192T>G	11.37:g.84245625A>C	ENSP00000435849:p.Ile64Met		83923273	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	A	18.11	3.551319	0.65311	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000543673;ENST00000524982;ENST00000532653;ENST00000546021	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.88	1.27	0.21489	Membrane-associated guanylate kinase (MAGUK), PEST domain, N-terminal (1);PDZ/DHR/GLGF (1);	0.000000	0.52532	D	0.000080	T	0.63850	0.2546	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.62365	0.991;0.985;0.988;0.991	D;D;D;D	0.75484	0.986;0.924;0.977;0.986	T	0.60707	-0.7210	9	.	.	.	.	5.6365	0.17540	0.3973:0.0:0.4582:0.1446	.	64;64;169;64	B7Z2T4;E9PN83;Q15700-2;Q15700	.;.;.;DLG2_HUMAN	M	64;169;169;64;64;169	ENSP00000381355:I64M;ENSP00000365272:I169M;ENSP00000441994:I169M;ENSP00000432894:I64M;ENSP00000435849:I64M	.	I	-	3	3	DLG2	83923273	0.995000	0.38212	1.000000	0.80357	0.985000	0.73830	0.417000	0.21214	0.554000	0.29061	0.533000	0.62120	ATT		0.413	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		C	84245625	A	C	84245625	3	2	114	1	0	0	0	0	1	0	0	0	4566	10	1	4	2667	4	DLG2	11	84245625	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	21838522	84245625	50760891	74	30738										
C2CD2L	1798	hgsc.bcm.edu	37	chr11	118981273	118981274	+	5'Flank	DNP	GC	GC	TT													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccacctcgccggtctcaggtGctgcgttgccagctctctgc							TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:118981273_118981274GC>TT	ENST00000409993.2	-	0	0				C2CD2L_ENST00000528586.1_5'Flank|C2CD2L_ENST00000336702.3_Silent_p.151_152VL>VL			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)						cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GGTCTCAGGTGCTGCGTTGCCA	0.609																																																0			11																																								118486483|118486484	SO:0001631	upstream_gene_variant	9854			Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.1_1delinsTT	11.37:g.118981273_118981274delinsTT	Exception_encountered		118486483|118486484	O15216|Q86WV9|Q9BWE6	Silent	SNP	ENST00000409993.2	37	CCDS8411.1																																																																																				0.609	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		TT	118981274	GC	TT	118981273	1	4	114	0	1	0	0	0	0	0	0	0	2159	1306	46	2		2	C2CD2L	11	118981273	5'Flank	DNP	GC	TCGA-F5-6464-01A-11D-1733-10	34735648	118981273	16025243	75	30739										
TMEM136	219902	hgsc.bcm.edu	37	chr11	120198134	120198134	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcctttgtttttctggttttGgtcttttcatcacaggatgg	9	7	4	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr11:120198134G>T	ENST00000375095.2	+	2	240				TMEM136_ENST00000529187.1_Missense_Mutation_p.W17L|TMEM136_ENST00000531346.1_Intron|TMEM136_ENST00000314475.2_Missense_Mutation_p.W17L	NM_001198671.1|NM_001198672.1|NM_001198673.1|NM_001198674.1|NM_001198675.1	NP_001185600.1|NP_001185601.1|NP_001185602.1|NP_001185603.1|NP_001185604.1	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral component of membrane (GO:0016021)		p.W17*(1)		endometrium(1)|lung(2)|ovary(1)	4		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		TTCTGGTTTTGGTCTTTTCAT	0.413																																																1	Substitution - Nonsense(1)	ovary(1)	11											178	165	169					11																	120198134		2203	4299	6502	119703344	SO:0001627	intron_variant	219902			BC015232	CCDS8432.1, CCDS55792.1, CCDS55793.1	11q23.3	2006-11-24				ENSG00000181264			28280	protein-coding gene	gene with protein product						12477932	Standard	NM_174926		Approved	MGC17839	uc001pxj.3	Q6ZRR5		ENST00000375095.2:c.-1-16G>T	11.37:g.120198134G>T			119703344	B4DGQ4|B4E230|Q8IZ79	Missense_Mutation	SNP	ENST00000375095.2	37	CCDS55793.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.787243	0.31593	.	.	ENSG00000181264	ENST00000314475;ENST00000529187	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.27663	0.0680	.	.	.	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07927	-1.0747	7	0.27082	T	0.32	.	7.7709	0.29008	0.0808:0.0:0.7133:0.2059	.	17;17	Q6ZRR5-3;Q6ZRR5-4	.;.	L	17	.	ENSP00000312672:W17L	W	+	2	0	TMEM136	119703344	0.999000	0.42202	0.998000	0.56505	0.994000	0.84299	2.756000	0.47549	2.629000	0.89072	0.655000	0.94253	TGG		0.413	TMEM136-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388045.1	NM_174926		T	120198134	G	T	120198134	1	4	114	0	1	0	0	0	0	0	0	0	16091	1357	47	2		2	TMEM136	11	120198134	Intron	SNP	G	TCGA-F5-6464-01A-11D-1733-10	1216861	120198134	14808382	76	30740										
KIAA1467	57613	hgsc.bcm.edu	37	chr12	13208558	13208558	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gatgagagcgaagacgatctGgtgcttaacctgcagaagaa	13	7	1	4			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:13208558G>A	ENST00000197268.8	+	2	231	c.111G>A	c.(109-111)ctG>ctA	p.L37L		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	37						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		AAGACGATCTGGTGCTTAACC	0.507																																																0			12											80	80	80					12																	13208558		2203	4300	6503	13099825	SO:0001819	synonymous_variant	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.111G>A	12.37:g.13208558G>A			13099825	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Silent	SNP	ENST00000197268.8	37	CCDS31750.1																																																																																				0.507	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		A	13208558	G	A	13208558	2	1	114	1	0	0	0	0	0	0	0	1	8256	1335	47	3		3	KIAA1467	12	13208558	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10		13208558	120643337	77	30741										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20766576	20766576	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cgtcacttcgctcagtgaaaActatacctgttctgactctg	7	12	4	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:20766576A>C	ENST00000359062.3	+	3	1251	c.1211A>C	c.(1210-1212)aAc>aCc	p.N404T	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	404					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CTCAGTGAAAACTATACCTGT	0.458																																																0			12											80	79	80					12																	20766576		2203	4300	6503	20657843	SO:0001583	missense	5139				CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1211A>C	12.37:g.20766576A>C	ENSP00000351957:p.Asn404Thr		20657843	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542687	0.27563	.	.	ENSG00000172572	ENST00000359062	T	0.49432	0.78	5.87	3.48	0.39840	.	2.068590	0.03653	U	0.241337	T	0.40909	0.1136	L	0.46157	1.445	0.30053	N	0.811557	B	0.27882	0.192	B	0.19391	0.025	T	0.30060	-0.9991	10	0.17832	T	0.49	.	7.5819	0.27970	0.6039:0.326:0.0701:0.0	.	404	Q14432	PDE3A_HUMAN	T	404	ENSP00000351957:N404T	ENSP00000351957:N404T	N	+	2	0	PDE3A	20657843	0.357000	0.24938	0.990000	0.47175	0.706000	0.40770	1.405000	0.34635	1.090000	0.41315	0.533000	0.62120	AAC		0.458	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			C	20766576	A	C	20766576	3	2	114	1	0	0	0	0	1	0	0	0	11668	43	2	4	1221	4	PDE3A	12	20766576	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	7558018	20766576	113085319	78	30742										
ABCD2	225	hgsc.bcm.edu	37	chr12	39979967	39979967	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	actttacctccttctctttgAactatgtgatagagatggac	7	9	1	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:39979967A>G	ENST00000308666.3	-	7	1914	c.1779T>C	c.(1777-1779)gtT>gtC	p.V593V		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	593	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CTTCTCTTTGAACTATGTGAT	0.333																																																0			12											163	139	147					12																	39979967		2203	4300	6503	38266234	SO:0001819	synonymous_variant	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1779T>C	12.37:g.39979967A>G			38266234	B2RAM3|Q13210|Q2M3H9	Silent	SNP	ENST00000308666.3	37	CCDS8734.1																																																																																				0.333	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		G	39979967	A	G	39979967	2	3	114	1	0	0	0	0	0	0	0	1	61	233	9	4		4	ABCD2	12	39979967	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	19213391	39979967	93871928	79	30743										
ABCD2	225	hgsc.bcm.edu	37	chr12	39980006	39980006	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acattgtgtaggatacgttcCagatcttggtctgtataacc	9	8	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:39980006C>T	ENST00000308666.3	-	7	1875	c.1740G>A	c.(1738-1740)ctG>ctA	p.L580L		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	580	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						GGATACGTTCCAGATCTTGGT	0.353																																																0			12											192	160	171					12																	39980006		2203	4300	6503	38266273	SO:0001819	synonymous_variant	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1740G>A	12.37:g.39980006C>T			38266273	B2RAM3|Q13210|Q2M3H9	Silent	SNP	ENST00000308666.3	37	CCDS8734.1																																																																																				0.353	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		T	39980006	C	T	39980006	2	4	114	1	0	0	0	0	0	0	0	1	61	581	21	3		3	ABCD2	12	39980006	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10	39	39980006	93871889	80	30744										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43822123	43822123	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tttcattatcttcaagttttTgagttaatggcaaattcgtg	7	5	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:43822123T>G	ENST00000389420.3	-	26	3865	c.3866A>C	c.(3865-3867)cAa>cCa	p.Q1289P	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.Q407P|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.Q1289P	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1289					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	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)		TTCAAGTTTTTGAGTTAATGG	0.473																																																0			12											99	95	96					12																	43822123		2203	4300	6503	42108390	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3866A>C	12.37:g.43822123T>G	ENSP00000374071:p.Gln1289Pro		42108390	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	8.119	0.780511	0.16120	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.62105	0.24;0.09;0.1;0.05	5.35	5.35	0.76521	.	0.120609	0.36932	N	0.002325	T	0.35740	0.0942	N	0.08118	0	0.24712	N	0.993192	B;P	0.38863	0.0;0.65	B;B	0.31101	0.0;0.124	T	0.24225	-1.0166	10	0.27082	T	0.32	.	10.8978	0.47034	0.1405:0.0:0.0:0.8595	.	1289;407	P59510;E9PBD5	ATS20_HUMAN;.	P	1289;419;407;1289;1289	ENSP00000374071:Q1289P;ENSP00000447427:Q419P;ENSP00000378911:Q407P;ENSP00000448341:Q1289P	ENSP00000374068:Q1289P	Q	-	2	0	ADAMTS20	42108390	1.000000	0.71417	1.000000	0.80357	0.250000	0.25880	2.509000	0.45459	2.330000	0.79161	0.477000	0.44152	CAA		0.473	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43822123	T	G	43822123	3	3	114	1	0	0	0	0	1	0	0	0	266	1812	63	4	1921	4	ADAMTS20	12	43822123	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	3842117	43822123	90029772	81	30745										
OR6C1	390321	hgsc.bcm.edu	37	chr12	55714821	55714821	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acactgcttgtttttacttcTtggctggtttcattcttaat	6	8	3	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:55714821T>C	ENST00000379668.2	+	1	476	c.438T>C	c.(436-438)tcT>tcC	p.S146S		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S146S(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						TTTTTACTTCTTGGCTGGTTT	0.403																																																1	Substitution - coding silent(1)	ovary(1)	12											45	42	43					12																	55714821		2203	4299	6502	54001088	SO:0001819	synonymous_variant	390321			AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.438T>C	12.37:g.55714821T>C			54001088	B2RNM0	Silent	SNP	ENST00000379668.2	37	CCDS31818.1																																																																																				0.403	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		C	55714821	T	C	55714821	2	2	114	1	0	0	0	0	0	0	0	1	11221	1596	56	4		4	OR6C1	12	55714821	Silent	SNP	T	TCGA-F5-6464-01A-11D-1733-10	11892698	55714821	78137074	82	30746										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56478794	56478794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cacagtggattcgagaagtgAcaggctatgtcctcgtggcc	13	10	0	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:56478794A>G	ENST00000267101.3	+	3	690	c.250A>G	c.(250-252)Aca>Gca	p.T84A	ERBB3_ENST00000411731.2_Missense_Mutation_p.T84A|ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Missense_Mutation_p.T25A	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	84					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TCGAGAAGTGACAGGCTATGT	0.483																																																0			12											142	118	127					12																	56478794		2203	4300	6503	54765061	SO:0001583	missense	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.250A>G	12.37:g.56478794A>G	ENSP00000267101:p.Thr84Ala		54765061	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.841500	0.51057	.	.	ENSG00000065361	ENST00000549282;ENST00000549061;ENST00000267101;ENST00000394099;ENST00000411731;ENST00000549672;ENST00000415288	T;D;D;T;D;D	0.84730	-1.44;-1.89;-1.89;-1.44;-1.89;-1.89	5.82	5.82	0.92795	EGF receptor, L domain (1);	0.000000	0.64402	D	0.000002	D	0.88789	0.6532	L	0.43598	1.365	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.975;0.998	D	0.86327	0.1696	10	0.23302	T	0.38	.	15.1658	0.72825	1.0:0.0:0.0:0.0	.	84;84	P21860;P21860-2	ERBB3_HUMAN;.	A	84;25;84;84;84;25;25	ENSP00000448636:T84A;ENSP00000449138:T25A;ENSP00000267101:T84A;ENSP00000415753:T84A;ENSP00000449713:T25A;ENSP00000408340:T25A	ENSP00000267101:T84A	T	+	1	0	ERBB3	54765061	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.618000	0.67722	2.218000	0.71995	0.533000	0.62120	ACA		0.483	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			G	56478794	A	G	56478794	3	3	114	1	0	0	0	0	1	0	0	0	5221	275	10	4	260	4	ERBB3	12	56478794	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	763973	56478794	77373101	83	30747										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56561900	56561900	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctcaaagtgccgaagtttgaTctccaactttttcatctggg	8	10	4	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:56561900T>C	ENST00000267064.4	-	25	2787	c.2701A>G	c.(2701-2703)Atc>Gtc	p.I901V	SMARCC2_ENST00000550164.1_Missense_Mutation_p.I932V|SMARCC2_ENST00000347471.4_Missense_Mutation_p.I932V|SMARCC2_ENST00000394023.3_Missense_Mutation_p.I932V|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	901					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CGAAGTTTGATCTCCAACTTT	0.552																																																0			12											127	120	123					12																	56561900		2203	4300	6503	54848167	SO:0001583	missense	6601			U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.2701A>G	12.37:g.56561900T>C	ENSP00000267064:p.Ile901Val		54848167	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429400	0.62844	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.51071	1.2;0.72;0.74;0.74	4.19	4.19	0.49359	.	0.000000	0.64402	D	0.000002	T	0.56470	0.1987	L	0.45470	1.425	0.50813	D	0.999899	P;P;P;P;P	0.43750	0.816;0.61;0.816;0.476;0.61	P;B;P;B;B	0.56648	0.803;0.399;0.803;0.224;0.399	T	0.60115	-0.7326	10	0.72032	D	0.01	-13.0106	12.6932	0.56988	0.0:0.0:0.0:1.0	.	821;932;936;901;932	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	V	932;932;932;901	ENSP00000377591:I932V;ENSP00000449396:I932V;ENSP00000302919:I932V;ENSP00000267064:I901V	ENSP00000267064:I901V	I	-	1	0	SMARCC2	54848167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.638000	0.83328	1.906000	0.55180	0.533000	0.62120	ATC		0.552	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			C	56561900	T	C	56561900	3	2	114	1	0	0	0	0	1	0	0	0	14813	1435	50	4	959	4	SMARCC2	12	56561900	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	83106	56561900	77289995	84	30748										
TMPO	7112	hgsc.bcm.edu	37	chr12	98927830	98927830	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctatgcaggcagacattagtCaagctgcacagattcttagc	9	10	2	2	rs17459334	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:98927830C>A	ENST00000556029.1	+	3	921				TMPO_ENST00000343315.5_Intron|TMPO_ENST00000266732.4_Missense_Mutation_p.Q599K|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000261210.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AGACATTAGTCAAGCTGCACA	0.468																																																0			12											99	79	86					12																	98927830		2203	4300	6503	97451961	SO:0001627	intron_variant	7112				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.565+2214C>A	12.37:g.98927830C>A			97451961	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.698977	0.48307	.	.	ENSG00000120802	ENST00000266732	T	0.59502	0.26	5.96	5.96	0.96718	.	0.461649	0.22945	N	0.053734	T	0.48241	0.1489	N	0.24115	0.695	0.80722	D	1	P	0.44877	0.845	B	0.41764	0.366	T	0.52208	-0.8606	10	0.59425	D	0.04	.	15.9221	0.79583	0.0:1.0:0.0:0.0	.	599	P42166	LAP2A_HUMAN	K	599	ENSP00000266732:Q599K	ENSP00000266732:Q599K	Q	+	1	0	TMPO	97451961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.147000	0.42226	2.832000	0.97577	0.655000	0.94253	CAA		0.468	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		A	98927830	C	A	98927830	1	1	114	0	1	0	0	0	0	0	0	0	16276	827	29	2		2	TMPO	12	98927830	Intron	SNP	C	TCGA-F5-6464-01A-11D-1733-10	42365930	98927830	34924065	85	30749										
TCTN1	79600	hgsc.bcm.edu	37	chr12	111057657	111057657	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcagttgctgttctctgtgtCtgtgacttatccccagcaca	9	12	2	1	rs374598052		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:111057657C>T	ENST00000551590.1	+	2	393	c.237C>T	c.(235-237)gtC>gtT	p.V79V	TCTN1_ENST00000550703.2_Silent_p.V79V|TCTN1_ENST00000551555.2_3'UTR|TCTN1_ENST00000471804.2_Silent_p.V79V|TCTN1_ENST00000377654.3_5'UTR|TCTN1_ENST00000397655.3_Silent_p.V79V|TCTN1_ENST00000397659.4_Silent_p.V79V			Q2MV58	TECT1_HUMAN	tectonic family member 1	79	Cys-rich.				central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						TTCTCTGTGTCTGTGACTTAT	0.522																																																0			12											194	184	188					12																	111057657		1993	4171	6164	109542040	SO:0001819	synonymous_variant	79600			AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.237C>T	12.37:g.111057657C>T			109542040	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Silent	SNP	ENST00000551590.1	37	CCDS41835.1																																																																																				0.522	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		T	111057657	C	T	111057657	2	4	114	1	0	0	0	0	0	0	0	1	15761	900	32	3		3	TCTN1	12	111057657	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10	12129827	111057657	22794238	86	30750										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926886	112926886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	atggtgcggtctcagaggtcAgggatggtccagacagaagc	16	8	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr12:112926886A>G	ENST00000351677.2	+	13	1704	c.1506A>G	c.(1504-1506)tcA>tcG	p.S502S		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	506	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		R -> L (in LEOPARD1). {ECO:0000269|PubMed:15121796}.|R -> W (in LEOPARD1; reduced phosphatase activity). {ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:24891296}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CTCAGAGGTCAGGGATGGTCC	0.463			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	0			12											180	168	172					12																	112926886		2203	4300	6503	111411269	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1506A>G	12.37:g.112926886A>G			111411269	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.463	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112926886	A	G	112926886	2	3	114	1	0	0	0	0	0	0	0	1	12815	175	7	4		4	PTPN11	12	112926886	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	1869229	112926886	20925009	87	30751										
NBEA	26960	hgsc.bcm.edu	37	chr13	35615220	35615220	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccattctacgaaaaagtgttCggaatttacagactagcaca	7	9	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr13:35615220C>A	ENST00000400445.3	+	2	979	c.445C>A	c.(445-447)Cgg>Agg	p.R149R	NBEA_ENST00000379939.2_Silent_p.R149R|NBEA_ENST00000540320.1_Silent_p.R149R|NBEA_ENST00000310336.4_Silent_p.R149R	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	149					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R149W(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AAAAAGTGTTCGGAATTTACA	0.403																																																1	Substitution - Missense(1)	ovary(1)	13											92	85	87					13																	35615220		1890	4150	6040	34513220	SO:0001819	synonymous_variant	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.445C>A	13.37:g.35615220C>A			34513220	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	37	CCDS45026.1																																																																																				0.403	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35615220	C	A	35615220	2	1	114	1	0	0	0	0	0	0	0	1	10217	875	31	2		2	NBEA	13	35615220	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10		35615220	79554658	88	30752										
RB1	5925	hgsc.bcm.edu	37	chr13	48947576	48947576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tatccaacaattaatgatgaTtttaaattcagcaagtgatc	5	6	1	3	rs373623059		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr13:48947576T>C	ENST00000267163.4	+	12	1301	c.1163T>C	c.(1162-1164)aTt>aCt	p.I388T		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	388	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.I388S(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTAATGATGATTTTAAATTCA	0.284		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	24	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(1)	bone(11)|breast(6)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											106	114	112					13																	48947576		2202	4288	6490	47845577	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1163T>C	13.37:g.48947576T>C	ENSP00000267163:p.Ile388Thr		47845577	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	12.08	1.830563	0.32329	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.88124	-2.34	5.54	4.37	0.52481	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.219298	0.47093	N	0.000248	T	0.74779	0.3761	N	0.26042	0.785	0.42957	D	0.994391	B	0.33637	0.42	B	0.28553	0.091	T	0.67791	-0.5579	10	0.16420	T	0.52	.	8.5803	0.33623	0.0:0.1482:0.0:0.8518	.	388	P06400	RB_HUMAN	T	367;388	ENSP00000267163:I388T	ENSP00000267163:I388T	I	+	2	0	RB1	47845577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.401000	0.44513	0.946000	0.37632	0.460000	0.39030	ATT		0.284	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	48947576	T	C	48947576	3	2	114	1	0	0	0	0	1	0	0	0	13135	1493	52	4	1209	4	RB1	13	48947576	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	13332356	48947576	66222302	89	30753										
RAB2B	84932	hgsc.bcm.edu	37	chr14	21931835	21931835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctcttcaacattgcaggctgTtttggctgaagtttccatga	9	9	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr14:21931835T>C	ENST00000397762.1	-	6	554	c.454A>G	c.(454-456)Aca>Gca	p.T152A	RAB2B_ENST00000461909.1_5'UTR	NM_001163380.1|NM_032846.3	NP_001156852.1|NP_116235.2	Q8WUD1	RAB2B_HUMAN	RAB2B, member RAS oncogene family	152					positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)		TTGCAGGCTGTTTTGGCTGAA	0.438																																					Melanoma(131;1007 1750 28652 34486 42672)											0			14											143	132	136					14																	21931835		2203	4300	6503	21001675	SO:0001583	missense	84932			AK027730	CCDS9570.1	14q11.1	2006-12-18			ENSG00000129472	ENSG00000129472		"RAB, member RAS oncogene"	20246	protein-coding gene	gene with protein product		607466				12376746	Standard	NM_032846		Approved	FLJ14824	uc010tlt.2	Q8WUD1	OTTHUMG00000029693	ENST00000397762.1:c.454A>G	14.37:g.21931835T>C	ENSP00000380869:p.Thr152Ala		21001675	B2RD03|D3DS24|Q6NZ33	Missense_Mutation	SNP	ENST00000397762.1	37	CCDS9570.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.261608	0.80358	.	.	ENSG00000129472	ENST00000397762;ENST00000304034	D	0.81739	-1.53	6.01	6.01	0.97437	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.84106	0.5399	M	0.83774	2.66	0.58432	D	0.999999	B;B;B	0.23377	0.004;0.053;0.084	B;B;B	0.31337	0.037;0.128;0.073	T	0.82561	-0.0396	10	0.66056	D	0.02	.	15.5031	0.75716	0.0:0.0:0.0:1.0	.	152;106;87	Q8WUD1;B4DUD4;Q6NZ33	RAB2B_HUMAN;.;.	A	152	ENSP00000380869:T152A	ENSP00000302005:T152A	T	-	1	0	RAB2B	21001675	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.676000	0.68131	2.299000	0.77371	0.533000	0.62120	ACA		0.438	RAB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074053.4			C	21931835	T	C	21931835	3	2	114	1	0	0	0	0	1	0	0	0	12955	1725	60	4	208	4	RAB2B	14	21931835	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10		21931835	85417705	90	30754										
C14orf28	122525	hgsc.bcm.edu	37	chr14	45373648	45373648	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aattttctgccatggggcacCcccttttgttgtcttaaata	7	10	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr14:45373648C>A	ENST00000325192.3	+	4	940	c.665C>A	c.(664-666)cCc>cAc	p.P222H	C14orf28_ENST00000553841.1_3'UTR|RP11-857B24.5_ENST00000555157.1_RNA|C14orf28_ENST00000557112.1_Missense_Mutation_p.P192H	NM_001017923.1	NP_001017923.1	Q4W4Y0	CN028_HUMAN	chromosome 14 open reading frame 28	222										endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(2)	11						CATGGGGCACCCCCTTTTGTT	0.403																																																0			14											184	179	181					14																	45373648		2203	4300	6503	44443398	SO:0001583	missense	122525			AA496212	CCDS32069.1	14q21.2	2012-08-16			ENSG00000179476	ENSG00000179476			19834	protein-coding gene	gene with protein product	"dopamine receptor interacting protein 1"						Standard	XM_005267316		Approved	DRIP-1	uc001wvo.3	Q4W4Y0	OTTHUMG00000170722	ENST00000325192.3:c.665C>A	14.37:g.45373648C>A	ENSP00000326846:p.Pro222His		44443398		Missense_Mutation	SNP	ENST00000325192.3	37	CCDS32069.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552591	0.65425	.	.	ENSG00000179476	ENST00000325192;ENST00000557112	T;T	0.65732	-0.17;-0.17	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.69033	0.3066	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72541	-0.4262	10	0.87932	D	0	.	17.9074	0.88923	0.0:1.0:0.0:0.0	.	222	Q4W4Y0	CN028_HUMAN	H	222;192	ENSP00000326846:P222H;ENSP00000451791:P192H	ENSP00000326846:P222H	P	+	2	0	C14orf28	44443398	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.119000	0.71590	2.835000	0.97688	0.591000	0.81541	CCC		0.403	C14orf28-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410086.1	NM_001017923		A	45373648	C	A	45373648	3	1	114	1	0	0	0	0	1	0	0	0	1774	623	22	2	675	2	C14orf28	14	45373648	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	23441813	45373648	61975892	91	30755										
FBXO34	55030	hgsc.bcm.edu	37	chr14	55818419	55818419	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gctgttgattgtatgagcagAgagcttgtgtcccttactag	12	7	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr14:55818419A>G	ENST00000313833.4	+	2	1556	c.1311A>G	c.(1309-1311)agA>agG	p.R437R	FBXO34_ENST00000440021.1_Silent_p.R437R	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	437										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GTATGAGCAGAGAGCTTGTGT	0.428																																																0			14											136	128	131					14																	55818419		2203	4300	6503	54888172	SO:0001819	synonymous_variant	55030			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1311A>G	14.37:g.55818419A>G			54888172	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																				0.428	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			G	55818419	A	G	55818419	2	3	114	1	0	0	0	0	0	0	0	1	5763	301	11	4		4	FBXO34	14	55818419	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	10444771	55818419	51531121	92	30756										
ATP10A	57194	hgsc.bcm.edu	37	chr15	26026187	26026187	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agctccgagaagccgcggacCacctgccgccgcttcaggtt	12	16	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr15:26026187C>A	ENST00000356865.6	-	2	744	c.633G>T	c.(631-633)gtG>gtT	p.V211V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	211					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V211V(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGCCGCGGACCACCTGCCGCC	0.617																																																1	Substitution - coding silent(1)	large_intestine(1)	15											65	68	67					15																	26026187		2203	4300	6503	23577280	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.633G>T	15.37:g.26026187C>A			23577280	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.617	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	26026187	C	A	26026187	2	1	114	1	0	0	0	0	0	0	0	1	1117	581	21	2		2	ATP10A	15	26026187	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10		26026187	76505205	93	30757										
HDGFRP3	50810	hgsc.bcm.edu	37	chr15	83826709	83826709	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tctatttcccacaatccttcGttaaatcctttccgtttgtt	3	12	1	0	rs145113533		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr15:83826709G>A	ENST00000299633.4	-	3	849	c.246C>T	c.(244-246)aaC>aaT	p.N82N		NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		82					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						ACAATCCTTCGTTAAATCCTT	0.373																																																0			15						G		1,4405	2.1+/-5.4	0,1,2202	153	137	142		246	1.7	1	15	dbSNP_134	142	0,8600		0,0,4300	no	coding-synonymous	HDGFRP3	NM_016073.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		82/204	83826709	1,13005	2203	4300	6503	81617713	SO:0001819	synonymous_variant	50810																														ENST00000299633.4:c.246C>T	15.37:g.83826709G>A			81617713		Silent	SNP	ENST00000299633.4	37	CCDS32314.1																																																																																				0.373	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419898.1			A	83826709	G	A	83826709	2	1	114	1	0	0	0	0	0	0	0	1	7042	1136	40	1		1	HDGFRP3	15	83826709	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	57800522	83826709	18704683	94	30758										
GDE1	51573	hgsc.bcm.edu	37	chr16	19514867	19514867	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agatgggattcgtagtaactCttttcatcaaaggtattaac	8	6	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr16:19514867C>G	ENST00000353258.3	-	6	1101	c.921G>C	c.(919-921)aaG>aaC	p.K307N	CTA-363E6.7_ENST00000569345.1_RNA	NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	307	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						CGTAGTAACTCTTTTCATCAA	0.463											OREG0023659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			16											163	143	150					16																	19514867		2197	4300	6497	19422368	SO:0001583	missense	51573				CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"membrane interacting protein of RGS16"	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.921G>C	16.37:g.19514867C>G	ENSP00000261386:p.Lys307Asn	733	19422368	O43334|Q6PKF7|Q7KYR4	Missense_Mutation	SNP	ENST00000353258.3	37	CCDS10578.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586872	0.66105	.	.	ENSG00000006007	ENST00000353258	T	0.28069	1.63	6.08	0.0954	0.14485	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.041958	0.85682	D	0.000000	T	0.46756	0.1409	M	0.69358	2.11	0.44330	D	0.997218	D	0.89917	1.0	D	0.85130	0.997	T	0.23726	-1.0180	10	0.27785	T	0.31	-19.3987	10.6732	0.45770	0.0:0.5008:0.0:0.4992	.	307	Q9NZC3	GDE1_HUMAN	N	307	ENSP00000261386:K307N	ENSP00000261386:K307N	K	-	3	2	GDE1	19422368	0.613000	0.27009	0.971000	0.41717	0.964000	0.63967	0.462000	0.21956	-0.232000	0.09811	-0.302000	0.09304	AAG		0.463	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641		G	19514867	C	G	19514867	3	3	114	1	0	0	0	0	1	0	0	0	6330	912	32	5	78	5	GDE1	16	19514867	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		19514867	70839886	95	30759										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50109493	50109493	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcctcgtagcatattgtttgCagacagtgactgaggataac	11	8	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr16:50109493C>T	ENST00000299192.7	+	6	825	c.634C>T	c.(634-636)Cag>Tag	p.Q212*	HEATR3_ENST00000285767.4_Nonsense_Mutation_p.Q126*	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	212										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						ATATTGTTTGCAGACAGTGAC	0.383																																																0			16											105	92	97					16																	50109493		2198	4300	6498	48666994	SO:0001587	stop_gained	55027			BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.634C>T	16.37:g.50109493C>T	ENSP00000299192:p.Gln212*		48666994	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Nonsense_Mutation	SNP	ENST00000299192.7	37	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	C	38	7.154938	0.98099	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	4.94	4.94	0.65067	.	0.104699	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	18.5556	0.91083	0.0:1.0:0.0:0.0	.	.	.	.	X	126;212	.	ENSP00000285767:Q126X	Q	+	1	0	HEATR3	48666994	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.631000	0.74277	2.441000	0.82636	0.650000	0.86243	CAG		0.383	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		T	50109493	C	T	50109493	4	4	114	1	0	0	0	0	0	1	0	0	7050	711	25	3	656	3	HEATR3	16	50109493	Nonsense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	30594626	50109493	40245260	96	30760										
SALL1	6299	hgsc.bcm.edu	37	chr16	51175403	51175403	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aatctgttcgatcaattgcaGctggtggatctgctgctgct	11	9	3	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr16:51175403G>A	ENST00000251020.4	-	2	763	c.730C>T	c.(730-732)Ctg>Ttg	p.L244L	SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.L147L	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	244					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ATCAATTGCAGCTGGTGGATC	0.547																																					GBM(103;1352 1446 1855 4775 8890)											0			16											82	85	84					16																	51175403		2198	4300	6498	49732904	SO:0001819	synonymous_variant	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.730C>T	16.37:g.51175403G>A			49732904	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																				0.547	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51175403	G	A	51175403	2	1	114	1	0	0	0	0	0	0	0	1	13847	962	34	3		3	SALL1	16	51175403	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	1065910	51175403	39179350	97	30761										
PDPR	55066	hgsc.bcm.edu	37	chr16	70177447	70177447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggcattagaagttctacagtAcctcttctccaatgacctgg	8	11	3	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr16:70177447A>G	ENST00000288050.4	+	14	2597	c.1640A>G	c.(1639-1641)tAc>tGc	p.Y547C	PDPR_ENST00000398122.3_Missense_Mutation_p.Y447C|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000567046.1_5'Flank|PDPR_ENST00000568530.1_Missense_Mutation_p.Y547C|PDPR_ENST00000542659.1_5'Flank	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	547					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.Y547F(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GTTCTACAGTACCTCTTCTCC	0.542																																																1	Substitution - Missense(1)	breast(1)	16											73	76	75					16																	70177447		2014	4200	6214	68734948	SO:0001583	missense	55066				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1640A>G	16.37:g.70177447A>G	ENSP00000288050:p.Tyr547Cys		68734948	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254674	0.59212	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	T;T	0.75938	-0.98;-0.98	4.8	2.4	0.29515	Glycine cleavage T-protein, N-terminal (1);	0.115330	0.64402	D	0.000010	T	0.81631	0.4863	M	0.76574	2.34	0.80722	D	1	D;P	0.71674	0.998;0.885	P;P	0.62813	0.907;0.755	T	0.79127	-0.1931	10	0.49607	T	0.09	.	9.387	0.38349	0.7292:0.0:0.0:0.2708	.	275;547	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	C	547;447;275	ENSP00000288050:Y547C;ENSP00000381190:Y447C	ENSP00000205055:Y275C	Y	+	2	0	PDPR	68734948	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	3.119000	0.50422	0.227000	0.20999	0.459000	0.35465	TAC		0.542	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		G	70177447	A	G	70177447	3	3	114	1	0	0	0	0	1	0	0	0	11720	391	14	4	1686	4	PDPR	16	70177447	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	19002044	70177447	20177306	98	30762										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70894711	70894711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgatggccacttatgtagtcCgagtctttcagatcaaaatg	9	8	3	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr16:70894711C>T	ENST00000393567.2	-	70	12021	c.11871G>A	c.(11869-11871)tcG>tcA	p.S3957S		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3957					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TTATGTAGTCCGAGTCTTTCA	0.577																																																0			16											2	2	2					16																	70894711		1290	2918	4208	69452212	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11871G>A	16.37:g.70894711C>T			69452212	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.577	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70894711	C	T	70894711	2	4	114	1	0	0	0	0	0	0	0	1	7488	639	23	1		1	HYDIN	16	70894711	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10	717264	70894711	19460042	99	30763										
TEKT1	83659	hgsc.bcm.edu	37	chr17	6704171	6704171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gtgtcctggtctccaagcgcGtatgagccaccttggctggc	13	13	1	1	rs139532367		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:6704171G>A	ENST00000338694.2	-	7	1073	c.944C>T	c.(943-945)aCg>aTg	p.T315M	TEKT1_ENST00000535086.1_Missense_Mutation_p.T169M	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	315						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				CTCCAAGCGCGTATGAGCCAC	0.498											OREG0024124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		21176	0.001		0	False		,,,				2504	0															0			17						G	MET/THR	2,4404	4.2+/-10.8	0,2,2201	204	194	197		944	5.8	0.7	17	dbSNP_134	197	0,8600		0,0,4300	yes	missense	TEKT1	NM_053285.1	81	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	315/419	6704171	2,13004	2203	4300	6503	6644895	SO:0001583	missense	83659				CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.944C>T	17.37:g.6704171G>A	ENSP00000341346:p.Thr315Met	636	6644895	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021128	0.75275	4.54E-4	0.0	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.05447	3.44;3.44	5.85	5.85	0.93711	.	0.049041	0.85682	D	0.000000	T	0.36991	0.0987	M	0.94063	3.49	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.41484	-0.9506	10	0.87932	D	0	.	18.0364	0.89305	0.0:0.0:1.0:0.0	.	315	Q969V4	TEKT1_HUMAN	M	315;169	ENSP00000341346:T315M;ENSP00000444142:T169M	ENSP00000341346:T315M	T	-	2	0	TEKT1	6644895	1.000000	0.71417	0.728000	0.30774	0.600000	0.36913	6.955000	0.76007	2.941000	0.99782	0.655000	0.94253	ACG		0.498	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		A	6704171	G	A	6704171	3	1	114	1	0	0	0	0	1	0	0	0	15791	1145	40	1	320	1	TEKT1	17	6704171	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		6704171	74491039	100	30764										
TP53	7157	hgsc.bcm.edu	37	chr17	7577114	7577114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggtctctcccaggacaggcaCaaacacgcacctcaaagctg	9	15	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:7577114C>T	ENST00000269305.4	-	8	1013	c.824G>A	c.(823-825)tGt>tAt	p.C275Y	TP53_ENST00000420246.2_Missense_Mutation_p.C275Y|TP53_ENST00000359597.4_Missense_Mutation_p.C275Y|TP53_ENST00000445888.2_Missense_Mutation_p.C275Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.C275Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	275	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7887414}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGACAGGCACAAACACGCAC	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	115	Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	lung(14)|large_intestine(13)|breast(13)|upper_aerodigestive_tract(12)|central_nervous_system(10)|haematopoietic_and_lymphoid_tissue(10)|ovary(7)|urinary_tract(6)|stomach(5)|oesophagus(5)|bone(5)|liver(5)|skin(3)|pancreas(2)|NS(2)|prostate(2)|biliary_tract(1)	17	GRCh37	CM076568|CM951234	TP53	M							71	61	64					17																	7577114		2203	4300	6503	7517839	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.824G>A	17.37:g.7577114C>T	ENSP00000269305:p.Cys275Tyr		7517839	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605675	0.87157	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.997;0.997	D	0.96317	0.9233	10	0.87932	D	0	-17.2181	15.662	0.77193	0.0:1.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	Y	275;275;275;275;275;264;143	ENSP00000352610:C275Y;ENSP00000269305:C275Y;ENSP00000398846:C275Y;ENSP00000391127:C275Y;ENSP00000391478:C275Y;ENSP00000425104:C143Y	ENSP00000269305:C275Y	C	-	2	0	TP53	7517839	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	TGT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577114	C	T	7577114	3	4	114	1	0	0	0	0	1	0	0	0	16421	478	17	3	462	3	TP53	17	7577114	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	872943	7577114	73618096	101	30765										
FBXW10	10517	hgsc.bcm.edu	37	chr17	18673283	18673283	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcttcctccgggtcatcagcGcctgtgcagatggcaagatc	11	13	3	2	rs371753550		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:18673283G>C	ENST00000395665.4	+	11	2112	c.1891G>C	c.(1891-1893)Gcc>Ccc	p.A631P	FBXW10_ENST00000308799.4_Missense_Mutation_p.A660P|FBXW10_ENST00000301938.4_Intron|FBXW10_ENST00000395667.1_Missense_Mutation_p.A631P|FBXW10_ENST00000573605.1_3'UTR			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	631										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GGTCATCAGCGCCTGTGCAGA	0.517																																																0			17											207	203	205					17																	18673283		2203	4300	6503	18614008	SO:0001583	missense	10517			BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.1891G>C	17.37:g.18673283G>C	ENSP00000379025:p.Ala631Pro		18614008	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	G	16.31	3.088128	0.55968	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000395665	T;T;T	0.20738	2.05;2.05;2.05	3.4	3.4	0.38934	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.982297	0.08228	U	0.978034	T	0.46425	0.1392	M	0.67953	2.075	0.36920	D	0.891343	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.996;0.997;0.996	T	0.45352	-0.9267	10	0.72032	D	0.01	.	12.7048	0.57054	0.0:0.0:1.0:0.0	.	660;631;631	Q5XX13-2;Q5XX13;Q5XX13-4	.;FBW10_HUMAN;.	P	631;660;631	ENSP00000379026:A631P;ENSP00000310382:A660P;ENSP00000379025:A631P	ENSP00000310382:A660P	A	+	1	0	FBXW10	18614008	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	5.362000	0.66098	1.888000	0.54679	0.194000	0.17425	GCC		0.517	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		C	18673283	G	C	18673283	3	2	114	1	0	0	0	0	1	0	0	0	5782	1087	38	5	1933	5	FBXW10	17	18673283	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	11096169	18673283	62521927	102	30766										
CCL11	6356	hgsc.bcm.edu	37	chr17	32612830	32612832	+	Start_Codon_Del	DEL	GAA	GAA	-													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acaccttcagcctccaacatGaaggtctccgcagcacttct					rs549369948		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:32612830_32612832delGAA	ENST00000305869.3	+	0	144_146					NM_002986.2	NP_002977.1	P51671	CCL11_HUMAN	chemokine (C-C motif) ligand 11						actin filament organization (GO:0007015)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|chronic inflammatory response (GO:0002544)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary duct terminal end bud growth (GO:0060763)|mast cell chemotaxis (GO:0002551)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of Rac GTPase activity (GO:0032855)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|response to interleukin-4 (GO:0070670)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			breast(1)|lung(1)|prostate(1)	3	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		CCTCCAACATGAAGGTCTCCGCA	0.591																																																0			17																																								29636945	SO:0001582	initiator_codon_variant	6356			AB063614	CCDS11279.1	17q21.1-q21.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000172156	ENSG00000172156		"Chemokine ligands", "Endogenous ligands"	10610	protein-coding gene	gene with protein product	"eotaxin-1"	601156	"small inducible cytokine subfamily A (Cys-Cys), member 11 (eotaxin)"	SCYA11		9169149	Standard	NM_002986		Approved	eotaxin, MGC22554	uc002hia.1	P51671	OTTHUMG00000132884		17.37:g.32612830_32612832delGAA			29636943	P50877|Q92490|Q92491	In_Frame_Del	DEL	ENST00000305869.3	37	CCDS11279.1																																																																																				0.591	CCL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256377.2	NM_002986		-	32612832	GAA	-	32612830	7	5	114	1	0	1	0	1	0	0	0	0	2889	1290	45	0	5	0	CCL11	17	32612830	Start_Codon_Del	DEL	GAA	TCGA-F5-6464-01A-11D-1733-10	13939547	32612830	48582380	103	30767										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37868207	37868207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acctttctacggacgtgggaTcctgcaccctcgtctgcccc	9	17	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:37868207T>C	ENST00000269571.5	+	8	1087	c.928T>C	c.(928-930)Tcc>Ccc	p.S310P	ERBB2_ENST00000406381.2_Missense_Mutation_p.S280P|ERBB2_ENST00000540147.1_Missense_Mutation_p.S280P|ERBB2_ENST00000541774.1_Missense_Mutation_p.S295P|ERBB2_ENST00000584450.1_Missense_Mutation_p.S310P|ERBB2_ENST00000540042.1_Missense_Mutation_p.S280P|ERBB2_ENST00000584601.1_Missense_Mutation_p.S280P|ERBB2_ENST00000445658.2_Missense_Mutation_p.S34P|ERBB2_ENST00000578199.1_Missense_Mutation_p.S280P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	310					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GGACGTGGGATCCTGCACCCT	0.577		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																													Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	0			17											253	205	221					17																	37868207		2203	4300	6503	35121733	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.928T>C	17.37:g.37868207T>C	ENSP00000269571:p.Ser310Pro		35121733	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480057	0.44044	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.83	5.83	0.93111	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.	.	.	.	T	0.81158	0.4764	M	0.84511	2.7	0.49798	D	0.999827	D;D;D;D;D	0.89917	0.999;1.0;0.997;1.0;1.0	D;D;P;D;D	0.78314	0.921;0.955;0.875;0.986;0.991	D	0.84349	0.0531	9	0.87932	D	0	.	15.1749	0.72903	0.0:0.0:0.0:1.0	.	34;280;295;310;310	B4DTR1;F5H1T4;P04626-4;P04626;Q9UK79	.;.;.;ERBB2_HUMAN;.	P	280;295;34;310;280;280	ENSP00000385185:S280P;ENSP00000446466:S295P;ENSP00000404047:S34P;ENSP00000269571:S310P;ENSP00000443562:S280P;ENSP00000446382:S280P	ENSP00000269571:S310P	S	+	1	0	ERBB2	35121733	1.000000	0.71417	0.996000	0.52242	0.745000	0.42441	5.449000	0.66619	2.232000	0.73038	0.402000	0.26972	TCC		0.577	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			C	37868207	T	C	37868207	3	2	114	1	0	0	0	0	1	0	0	0	5219	1435	50	4	958	4	ERBB2	17	37868207	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	5255377	37868207	43327003	104	30768										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37944519	37944519	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcgtgaactcaccagtgtccCctgggtcagtgctctgaaga	12	12	3	3	rs112301322	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:37944519C>G	ENST00000346872.3	-	6	762	c.701G>C	c.(700-702)gGg>gCg	p.G234A	IKZF3_ENST00000377958.2_Missense_Mutation_p.G147A|IKZF3_ENST00000377944.3_Missense_Mutation_p.G91A|IKZF3_ENST00000535189.1_Missense_Mutation_p.G200A|IKZF3_ENST00000467757.1_Missense_Mutation_p.G178A|IKZF3_ENST00000350532.3_Missense_Mutation_p.G234A|IKZF3_ENST00000439016.2_Intron|IKZF3_ENST00000377945.3_Intron|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000439167.2_Intron|IKZF3_ENST00000346243.3_Intron|IKZF3_ENST00000351680.3_Intron|IKZF3_ENST00000377952.2_Intron	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	234					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACCAGTGTCCCCTGGGTCAGT	0.463													C|||	70	0.0139776	0.003	0.0274	5008	,	,		19399	0		0.0308	False		,,,				2504	0.0164															0			17						C	ALA/GLY,ALA/GLY,,ALA/GLY,,	32,4374	37.6+/-69.7	1,30,2172	132	101	111		701,533,,701,,	2.9	0	17	dbSNP_132	111	273,8327	104.0+/-165.0	3,267,4030	yes	missense,missense,intron,missense,intron,intron	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	60,60,,60,,	4,297,6202	GG,GC,CC		3.1744,0.7263,2.3451	benign,benign,,benign,,	234/510,178/454,,234/471,,	37944519	305,12701	2203	4300	6503	35198045	SO:0001583	missense	22806			AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.701G>C	17.37:g.37944519C>G	ENSP00000344544:p.Gly234Ala		35198045	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	36|36	0.016483516483516484|0.016483516483516484	2|2	0.0040650406504065045|0.0040650406504065045	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	25|25	0.032981530343007916|0.032981530343007916	C|C	1.864|1.864	-0.461818|-0.461818	0.04508|0.04508	0.007263|0.007263	0.031744|0.031744	ENSG00000161405|ENSG00000161405	ENST00000488188;ENST00000377944;ENST00000377958;ENST00000535189;ENST00000350532;ENST00000467757|ENST00000439016	T;T;T;T;T|.	0.08896|.	3.25;3.04;3.3;3.24;4.29|.	6.04|6.04	2.93|2.93	0.34026|0.34026	.|.	0.232813|0.232813	0.30575|0.30575	N|N	0.009333|0.009333	T|T	0.04952|0.04952	0.0133|0.0133	N|N	0.08118|0.08118	0|0	0.18873|0.18873	N|N	0.999984|0.999984	B;B;B;B;B;B|.	0.33171|.	0.4;0.041;0.007;0.002;0.004;0.006|.	B;B;B;B;B;B|.	0.28011|.	0.085;0.026;0.009;0.007;0.007;0.008|.	T|T	0.16867|0.16867	-1.0388|-1.0388	10|7	0.18710|0.18276	T|T	0.47|0.48	-8.0392|-8.0392	4.9351|4.9351	0.13937|0.13937	0.1251:0.6226:0.1207:0.1316|0.1251:0.6226:0.1207:0.1316	.|.	147;91;200;234;178;234|.	Q9UKT9-9;Q9UKT9-10;Q9UKT9-7;Q9UKT9-4;Q9UKT9-2;Q9UKT9|.	.;.;.;.;.;IKZF3_HUMAN|.	A|R	234;91;147;200;234;178|188	ENSP00000367179:G91A;ENSP00000367194:G147A;ENSP00000438972:G200A;ENSP00000344471:G234A;ENSP00000420463:G178A|.	ENSP00000344471:G234A|ENSP00000403027:G188R	G|G	-|-	2|1	0|0	IKZF3|IKZF3	35198045|35198045	0.751000|0.751000	0.28327|0.28327	0.011000|0.011000	0.14972|0.14972	0.055000|0.055000	0.15305|0.15305	2.583000|2.583000	0.46094|0.46094	0.418000|0.418000	0.25898|0.25898	0.563000|0.563000	0.77884|0.77884	GGG|GGG		0.463	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		G	37944519	C	G	37944519	3	3	114	1	0	0	0	0	1	0	0	0	7637	623	22	5	840	5	IKZF3	17	37944519	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	76312	37944519	43250691	105	30769										
KRTAP9-8	83901	hgsc.bcm.edu	37	chr17	39394650	39394650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gactgtctgcctgcctggttGcctaaaccagagctgtggct	12	12	1	1	rs556439657	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:39394650G>A	ENST00000254072.6	+	1	354	c.347G>A	c.(346-348)tGc>tAc	p.C116Y		NM_031963.2	NP_114169.2	Q9BYQ0	KRA98_HUMAN	keratin associated protein 9-8	116	15 X 5 AA repeats of C-C-[RQVSGE]- [SPSNQ]-[TASPI].					keratin filament (GO:0045095)		p.C116S(1)		lung(8)|ovary(1)|prostate(1)	10		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCTGGTTGCCTAAACCAG	0.617													.|||	2	0.000399361	0	0	5008	,	,		17603	0.002		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	17											92	112	106					17																	39394650		2105	4300	6405	36648176	SO:0001583	missense	83901			AJ406950	CCDS42334.1	17q21.2	2013-06-25			ENSG00000187272	ENSG00000187272		"Keratin associated proteins"	17231	protein-coding gene	gene with protein product						11279113	Standard	NM_031963		Approved	KAP9.8	uc002hwh.4	Q9BYQ0	OTTHUMG00000133604	ENST00000254072.6:c.347G>A	17.37:g.39394650G>A	ENSP00000254072:p.Cys116Tyr		36648176		Missense_Mutation	SNP	ENST00000254072.6	37	CCDS42334.1	.	.	.	.	.	.	.	.	.	.	.	12.26	1.885234	0.33255	.	.	ENSG00000187272	ENST00000254072	T	0.01295	5.04	2.1	1.09	0.20402	.	.	.	.	.	T	0.05044	0.0135	M	0.68317	2.08	0.09310	N	1	D	0.62365	0.991	D	0.77557	0.99	T	0.37056	-0.9722	9	0.66056	D	0.02	.	3.4405	0.07461	0.399:0.0:0.601:0.0	.	116	Q9BYQ0	KRA98_HUMAN	Y	116	ENSP00000254072:C116Y	ENSP00000254072:C116Y	C	+	2	0	KRTAP9-8	36648176	0.107000	0.21998	0.009000	0.14445	0.164000	0.22412	0.315000	0.19451	1.105000	0.41606	0.508000	0.49915	TGC		0.617	KRTAP9-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257712.1			A	39394650	G	A	39394650	3	1	114	1	0	0	0	0	1	0	0	0	8598	1319	46	3	349	3	KRTAP9-8	17	39394650	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	1450131	39394650	41800560	106	30770										
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74901330	74901330	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cctgatcttcatgaagaagcGgaccaagaggctcacagccc	10	13	3	4	rs62080221		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:74901330G>A	ENST00000569840.2	+	7	1344	c.770G>A	c.(769-771)cGg>cAg	p.R257Q	MGAT5B_ENST00000428789.2_Missense_Mutation_p.R268Q|MGAT5B_ENST00000301618.4_Missense_Mutation_p.R257Q|MGAT5B_ENST00000374998.3_3'UTR	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	257					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATGAAGAAGCGGACCAAGAGG	0.647																																																0			17											35	39	38					17																	74901330		2203	4300	6503	72412925	SO:0001583	missense	146664			AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.770G>A	17.37:g.74901330G>A	ENSP00000456037:p.Arg257Gln		72412925	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	37	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261410	0.80358	.	.	ENSG00000167889	ENST00000374998;ENST00000301618;ENST00000428789	T;T	0.62232	0.06;0.04	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.80686	0.4670	M	0.81341	2.54	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.83565	0.0109	10	0.87932	D	0	-42.6426	17.3425	0.87301	0.0:0.0:1.0:0.0	rs62080221	268;257	Q3V5L5-2;Q3V5L5-5	.;.	Q	257;257;268	ENSP00000301618:R257Q;ENSP00000391227:R268Q	ENSP00000301618:R257Q	R	+	2	0	MGAT5B	72412925	1.000000	0.71417	0.993000	0.49108	0.919000	0.55068	8.927000	0.92846	2.416000	0.81992	0.514000	0.50259	CGG		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		A	74901330	G	A	74901330	3	1	114	1	0	0	0	0	1	0	0	0	9579	1116	39	1	897	1	MGAT5B	17	74901330	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	35506680	74901330	6293880	107	30771										
C1QTNF1	114897	hgsc.bcm.edu	37	chr17	77043751	77043751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cccctggggagcggtgcaagAgccactacgccgccttttcg	13	15	0	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr17:77043751A>G	ENST00000339142.2	+	5	982	c.427A>G	c.(427-429)Agc>Ggc	p.S143G	C1QTNF1_ENST00000580454.1_Missense_Mutation_p.S143G|C1QTNF1_ENST00000581774.1_Missense_Mutation_p.S143G|C1QTNF1_ENST00000579760.1_Missense_Mutation_p.S143G|C1QTNF1_ENST00000578229.1_Missense_Mutation_p.S61G|C1QTNF1_ENST00000582625.1_3'UTR|C1QTNF1_ENST00000583904.1_Missense_Mutation_p.S143G|C1QTNF1_ENST00000580474.1_Missense_Mutation_p.S143G|C1QTNF1_ENST00000311661.4_Missense_Mutation_p.S61G|C1QTNF1_ENST00000354124.3_Missense_Mutation_p.S153G|C1QTNF1_ENST00000392445.2_Missense_Mutation_p.S143G	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	143	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			GCGGTGCAAGAGCCACTACGC	0.612																																																0			17											60	60	60					17																	77043751		2203	4300	6503	74555346	SO:0001583	missense	114897			AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"G protein coupled receptor interacting protein"	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.427A>G	17.37:g.77043751A>G	ENSP00000340864:p.Ser143Gly		74555346	Q6ZMH6|Q96NF2|Q9GZR4	Missense_Mutation	SNP	ENST00000339142.2	37	CCDS11761.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082539	0.36758	.	.	ENSG00000173918	ENST00000339142;ENST00000311661;ENST00000354124;ENST00000392444;ENST00000392445	T;D;T	0.81821	-1.02;-1.54;-1.02	5.33	4.25	0.50352	Tumour necrosis factor-like (1);Complement C1q protein (2);	0.459560	0.23724	N	0.045183	T	0.76357	0.3976	L	0.54323	1.7	0.34340	D	0.688712	B;B;B	0.26708	0.157;0.034;0.095	B;B;B	0.33121	0.158;0.044;0.158	T	0.75271	-0.3376	10	0.23891	T	0.37	.	10.9119	0.47114	0.9259:0.0:0.0741:0.0	.	153;153;143	A8K7L9;Q6ZMH6;Q9BXJ1	.;.;C1QT1_HUMAN	G	143;61;153;143;153	ENSP00000340864:S143G;ENSP00000311265:S61G;ENSP00000343230:S153G	ENSP00000311265:S61G	S	+	1	0	C1QTNF1	74555346	0.960000	0.32886	1.000000	0.80357	0.740000	0.42216	2.343000	0.44001	0.861000	0.35504	0.459000	0.35465	AGC		0.612	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968		G	77043751	A	G	77043751	3	3	114	1	0	0	0	0	1	0	0	0	1968	304	11	4	437	4	C1QTNF1	17	77043751	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	2142421	77043751	4151459	108	30772										
NPC1	4864	hgsc.bcm.edu	37	chr18	21121352	21121352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	caatgaagactgccaatcccGcaaagagagagaaggtgtgc	12	9	0	4			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr18:21121352G>A	ENST00000269228.5	-	15	2845	c.2291C>T	c.(2290-2292)gCg>gTg	p.A764V	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.A446V	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	764	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGCCAATCCCGCAAAGAGAGA	0.522																																																0			18											92	84	87					18																	21121352		2203	4300	6503	19375350	SO:0001583	missense	257641			AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2291C>T	18.37:g.21121352G>A	ENSP00000269228:p.Ala764Val		19375350	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755210	0.89843	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.90900	-2.75;-2.75	5.89	5.89	0.94794	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.96738	0.9544	10	0.87932	D	0	-31.3387	20.2566	0.98424	0.0:0.0:1.0:0.0	.	775;764	Q59GR1;O15118	.;NPC1_HUMAN	V	764;446;609	ENSP00000269228:A764V;ENSP00000408606:A446V	ENSP00000269228:A764V	A	-	2	0	NPC1	19375350	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	9.787000	0.99055	2.793000	0.96121	0.561000	0.74099	GCG		0.522	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		A	21121352	G	A	21121352	3	1	114	1	0	0	0	0	1	0	0	0	10601	1087	38	1	1589	1	NPC1	18	21121352	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		21121352	56955896	109	30773										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805807	22805807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aactctcacagatgtaatacGttgaagtgatcataaagtga	8	6	2	4	rs114072043		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr18:22805807G>A	ENST00000361524.3	-	4	2223	c.2075C>T	c.(2074-2076)aCg>aTg	p.T692M	ZNF521_ENST00000538137.2_Missense_Mutation_p.T692M|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.T472M	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	692					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GATGTAATACGTTGAAGTGAT	0.443			T	PAX5	ALL								G|||	1	0.000199681	0	0	5008	,	,		24012	0.001		0	False		,,,				2504	0						Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0			18											160	149	153					18																	22805807		2203	4300	6503	21059805	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2075C>T	18.37:g.22805807G>A	ENSP00000354794:p.Thr692Met		21059805	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	7.823	0.718244	0.15372	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.09911	2.93;2.95	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.26882	0.0658	L	0.35288	1.05	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.00330	-1.1812	10	0.87932	D	0	-23.2526	20.5827	0.99408	0.0:0.0:1.0:0.0	.	692	Q96K83	ZN521_HUMAN	M	692;726;692	ENSP00000354794:T692M;ENSP00000382352:T692M	ENSP00000354794:T692M	T	-	2	0	ZNF521	21059805	1.000000	0.71417	0.277000	0.24703	0.693000	0.40251	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	ACG		0.443	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22805807	G	A	22805807	3	1	114	1	0	0	0	0	1	0	0	0	18004	1145	40	1	1880	1	ZNF521	18	22805807	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	1684455	22805807	55271441	110	30774										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591923	48591925	+	In_Frame_Del	DEL	TTG	TTG	-													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccttctggaggagatcgcttTtgtttgggtcaactctccaa					rs377767348|rs377767349|rs1801250	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	TTG	TTG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr18:48591923_48591925delTTG	ENST00000342988.3	+	9	1624_1626	c.1086_1088delTTG	c.(1084-1089)ttttgt>ttt	p.C363del	SMAD4_ENST00000398417.2_In_Frame_Del_p.C363del|SMAD4_ENST00000588745.1_In_Frame_Del_p.C267del	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	363	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.C363R(1)|p.C363S(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GAGATCGCTTTTGTTTGGGTCAA	0.414																																																40	Whole gene deletion(36)|Substitution - Missense(2)|Unknown(2)	pancreas(27)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18	GRCh37	CD064635|CM075017	SMAD4	D|M																																				46845923	SO:0001651	inframe_deletion	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1086_1088delTTG	18.37:g.48591923_48591925delTTG	ENSP00000341551:p.Cys363del		46845921	A8K405	In_Frame_Del	DEL	ENST00000342988.3	37	CCDS11950.1																																																																																				0.414	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		-	48591925	TTG	-	48591923	7	5	114	1	0	1	0	1	0	0	0	0	14797	1838	64	0	1116	0	SMAD4	18	48591923	In_Frame_Del	DEL	TTG	TCGA-F5-6464-01A-11D-1733-10	25786116	48591923	29485325	111	30775										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5151356	5151356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tctcccgcagtcactgagcaCgggggcaccgcaggagcccg	14	16	2	1	rs200961372		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:5151356C>T	ENST00000159111.4	+	23	3343	c.3125C>T	c.(3124-3126)aCg>aTg	p.T1042M	KDM4B_ENST00000536461.1_Missense_Mutation_p.T1076M	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	1042					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TCACTGAGCACGGGGGCACCG	0.701													C|||	1	0.000199681	0	0	5008	,	,		13726	0		0.001	False		,,,				2504	0															0			19											7	9	9					19																	5151356		2047	4085	6132	5102356	SO:0001583	missense	23030			AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.3125C>T	19.37:g.5151356C>T	ENSP00000159111:p.Thr1042Met		5102356	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	37	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289273	0.40494	.	.	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.78246	-1.16;-1.16	5.0	5.0	0.66597	.	0.615885	0.16421	N	0.215178	D	0.86285	0.5896	M	0.71581	2.175	0.36510	D	0.869549	D;D	0.89917	0.999;1.0	P;D	0.68621	0.83;0.959	D	0.89270	0.3604	10	0.87932	D	0	-26.0473	13.1242	0.59344	0.0:0.8395:0.1605:0.0	.	1076;1042	F5GX28;O94953	.;KDM4B_HUMAN	M	1042;1076	ENSP00000159111:T1042M;ENSP00000440495:T1076M	ENSP00000159111:T1042M	T	+	2	0	KDM4B	5102356	0.990000	0.36364	0.961000	0.40146	0.328000	0.28507	2.973000	0.49264	2.304000	0.77564	0.549000	0.68633	ACG		0.701	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		T	5151356	C	T	5151356	3	4	114	1	0	0	0	0	1	0	0	0	8150	536	19	1	3207	1	KDM4B	19	5151356	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		5151356	53977627	112	30776										
ZNF559	84527	hgsc.bcm.edu	37	chr19	9453118	9453118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cgtatgagtgcaacaaatgtGggaaagccttcactgattca	10	8	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:9453118G>A	ENST00000393883.2	+	6	1639	c.991G>A	c.(991-993)Ggg>Agg	p.G331R	ZNF559_ENST00000538743.1_Missense_Mutation_p.G251R|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000586255.1_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.G331R|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF559_ENST00000587557.1_Missense_Mutation_p.G395R|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000592896.1_3'UTR	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						CAACAAATGTGGGAAAGCCTT	0.383																																																0			19											67	65	65					19																	9453118		2203	4300	6503	9314118	SO:0001583	missense	84527			AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.991G>A	19.37:g.9453118G>A	ENSP00000377461:p.Gly331Arg		9314118	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.225446	0.58668	.	.	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	T;T	0.22743	1.94;1.94	2.14	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46014	0.1371	M	0.85542	2.76	0.28564	N	0.910999	D;D;D	0.89917	0.998;1.0;0.997	D;D;P	0.80764	0.94;0.994;0.698	T	0.31641	-0.9936	9	0.72032	D	0.01	.	8.6304	0.33915	0.0:0.239:0.761:0.0	.	331;331;251	B3KPL8;Q9BR84;B4DP29	.;ZN559_HUMAN;.	R	331;251;331	ENSP00000442832:G251R;ENSP00000377461:G331R	ENSP00000325393:G331R	G	+	1	0	ZNF559	9314118	1.000000	0.71417	0.179000	0.23059	0.220000	0.24768	4.029000	0.57253	0.441000	0.26529	0.462000	0.41574	GGG		0.383	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		A	9453118	G	A	9453118	3	1	114	1	0	0	0	0	1	0	0	0	18029	1348	47	3	1005	3	ZNF559	19	9453118	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	4301762	9453118	49675865	113	30777										
KRI1	84971	hgsc.bcm.edu	37	chr19	10664680	10664680	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccgctgccggcccagctggcGgaagtgcagccgtttggggt	17	13	0	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:10664680G>A	ENST00000309469.4	+	0	1949				KRI1_ENST00000361821.5_Missense_Mutation_p.R689C|MIR1238_ENST00000408483.1_RNA|RNU7-140P_ENST00000459546.1_RNA|KRI1_ENST00000312962.6_Missense_Mutation_p.R693C	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase						apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CCCAGCTGGCGGAAGTGCAGC	0.642																																																0			19											28	29	29					19																	10664680		2203	4300	6503	10525680	SO:0001628	intergenic_variant	65095			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582		19.37:g.10664680G>A			10525680	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401300	0.83120	.	.	ENSG00000129347	ENST00000312962;ENST00000361821	T;T	0.23147	2.26;1.92	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.50429	0.1615	M	0.68952	2.095	0.51482	D	0.999925	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.54139	-0.8338	10	0.87932	D	0	-22.302	16.9839	0.86335	0.0:0.0:1.0:0.0	.	693;689	Q8N9T8;D3YTE0	KRI1_HUMAN;.	C	693;689	ENSP00000320917:R693C;ENSP00000355366:R689C	ENSP00000320917:R693C	R	-	1	0	KRI1	10525680	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.319000	0.65835	2.310000	0.77875	0.655000	0.94253	CGC		0.642	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		A	10664680	G	A	10664680	1	1	114	0	1	0	0	0	0	0	0	0	8465	1116	39	1		1	KRI1	19	10664680	IGR	SNP	G	TCGA-F5-6464-01A-11D-1733-10	1211562	10664680	48464303	114	30778										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17038952	17038952	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tcacccatggagccccagccGgtggaaaagccaatgaactg	11	13	1	1	rs193127821		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:17038952G>A	ENST00000443236.1	-	25	3409	c.3378C>T	c.(3376-3378)acC>acT	p.T1126T		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1079						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						AGCCCCAGCCGGTGGAAAAGC	0.602													G|||	1	0.000199681	0	0	5008	,	,		19279	0.001		0	False		,,,				2504	0															0			19						G		0,3820		0,0,1910	49	55	53		3378	-6.1	1	19		53	2,8242		0,2,4120	no	coding-synonymous	CPAMD8	NM_015692.2		0,2,6030	AA,AG,GG		0.0243,0.0,0.0166		1126/1933	17038952	2,12062	1910	4122	6032	16899952	SO:0001819	synonymous_variant	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3378C>T	19.37:g.17038952G>A			16899952	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	8.017	0.758796	0.15846	0.0	2.43E-4	ENSG00000160111	ENST00000443236	.	.	.	3.02	-6.05	0.02172	.	.	.	.	.	T	0.33876	0.0878	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42666	-0.9438	4	.	.	.	.	0.0392	0.00008	0.3168:0.1919:0.2217:0.2696	.	.	.	.	L	1137	.	.	P	-	2	0	CPAMD8	16899952	0.829000	0.29322	0.992000	0.48379	0.829000	0.46940	-0.260000	0.08708	-0.806000	0.04398	-1.581000	0.00855	CCG		0.602	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17038952	G	A	17038952	2	1	114	1	0	0	0	0	0	0	0	1	3801	1103	39	1		1	CPAMD8	19	17038952	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	6374272	17038952	42090031	115	30779										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543952	23543952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gggttgaggaccatagaaatGctttgccacattcttcacac	9	10	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:23543952G>A	ENST00000300619.7	-	4	2034	c.1829C>T	c.(1828-1830)gCa>gTa	p.A610V	ZNF91_ENST00000397082.2_Missense_Mutation_p.A578V|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	610					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CCATAGAAATGCTTTGCCACA	0.383																																																0			19											59	62	61					19																	23543952		2181	4285	6466	23335792	SO:0001583	missense	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1829C>T	19.37:g.23543952G>A	ENSP00000300619:p.Ala610Val		23335792	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	8.991	0.977635	0.18812	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.19105	2.17;2.17	1.78	1.78	0.24846	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19446	0.0467	N	0.16602	0.42	0.18873	N	0.999987	D;P	0.58268	0.982;0.884	P;P	0.56751	0.805;0.482	T	0.08953	-1.0697	9	0.49607	T	0.09	.	3.8829	0.09086	0.3754:0.0:0.6246:0.0	.	578;610	Q05481-2;Q05481	.;ZNF91_HUMAN	V	610;578	ENSP00000300619:A610V;ENSP00000380272:A578V	ENSP00000300619:A610V	A	-	2	0	ZNF91	23335792	0.007000	0.16637	0.190000	0.23270	0.059000	0.15707	0.872000	0.28037	0.962000	0.38057	0.313000	0.20887	GCA		0.383	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23543952	G	A	23543952	3	1	114	1	0	0	0	0	1	0	0	0	18239	1319	46	3	1750	3	ZNF91	19	23543952	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	6505000	23543952	35585031	116	30780										
PDCD5	9141	hgsc.bcm.edu	37	chr19	33076809	33076809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aagatatggacaactaagtgAgaaggtaagcttagacagcc	11	6	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:33076809A>G	ENST00000590247.2	+	4	448	c.254A>G	c.(253-255)gAg>gGg	p.E85G	PDCD5_ENST00000586035.1_Missense_Mutation_p.E47G|PDCD5_ENST00000592786.1_Intron|PDCD5_ENST00000419343.3_Missense_Mutation_p.E85G|PDCD5_ENST00000379316.3_Intron	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	85					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					CAACTAAGTGAGAAGGTAAGC	0.363																																																0			19											103	108	106					19																	33076809		2203	4300	6503	37768649	SO:0001583	missense	9141			AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"TFAR19 novel apoptosis-related", "TF1 cell apoptosis-related gene 19"	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.254A>G	19.37:g.33076809A>G	ENSP00000466214:p.Glu85Gly		37768649	B4DE64|Q53YC9|Q6IB70	Missense_Mutation	SNP	ENST00000590247.2	37	CCDS12423.1	.	.	.	.	.	.	.	.	.	.	A	5.109	0.205798	0.09704	.	.	ENSG00000105185	ENST00000419343;ENST00000221784	.	.	.	5.6	4.57	0.56435	.	0.148836	0.64402	N	0.000011	T	0.15262	0.0368	N	0.00690	-1.25	0.37085	D	0.899182	B;B	0.09022	0.0;0.002	B;B	0.09377	0.004;0.004	T	0.29058	-1.0024	9	0.02654	T	1	-14.8081	12.4858	0.55872	0.083:0.0:0.917:0.0	.	85;85	O14737;B4DE64	PDCD5_HUMAN;.	G	85	.	ENSP00000221784:E85G	E	+	2	0	PDCD5	37768649	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	6.533000	0.73829	1.325000	0.45301	-0.468000	0.05107	GAG		0.363	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708		G	33076809	A	G	33076809	3	3	114	1	0	0	0	0	1	0	0	0	11653	304	11	4	268	4	PDCD5	19	33076809	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	9532857	33076809	26052174	117	30781										
RYR1	6261	hgsc.bcm.edu	37	chr19	39070725	39070725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	catcgccatgggggtcaagaCgctgcgcaccatcctgtcct	11	15	1	1	rs148540135		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:39070725C>T	ENST00000359596.3	+	100	14468	c.14468C>T	c.(14467-14469)aCg>aTg	p.T4823M	RYR1_ENST00000355481.4_Missense_Mutation_p.T4818M|RYR1_ENST00000360985.3_Missense_Mutation_p.T4818M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4823					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGGTCAAGACGCTGCGCACC	0.597																																																0			19	GRCh37	CM083554	RYR1	M	rs148540135	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	122	85	98		14468,14453	4.6	1	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	4823/5039,4818/5034	39070725	1,13005	2203	4300	6503	43762565	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14468C>T	19.37:g.39070725C>T	ENSP00000352608:p.Thr4823Met		43762565	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.746556	0.49257	2.27E-4	0.0	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98617	-5.03;-5.03;-5.03	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000001	D	0.99026	0.9667	M	0.80422	2.495	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99342	1.0912	10	0.36615	T	0.2	.	17.129	0.86722	0.0:1.0:0.0:0.0	.	4818;4823	P21817-2;P21817	.;RYR1_HUMAN	M	4823;4818;4818	ENSP00000352608:T4823M;ENSP00000347667:T4818M;ENSP00000354254:T4818M	ENSP00000347667:T4818M	T	+	2	0	RYR1	43762565	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.617000	0.83032	2.357000	0.79964	0.462000	0.41574	ACG		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39070725	C	T	39070725	3	4	114	1	0	0	0	0	1	0	0	0	13805	536	19	1	14866	1	RYR1	19	39070725	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	5993916	39070725	20058258	118	30782										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44831844	44831844	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	catttgtatggtttctctccTgtgtggactctgtgatgggc	12	8	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:44831844T>A	ENST00000337401.4	-	5	2572	c.2484A>T	c.(2482-2484)acA>acT	p.T828T	ZNF112_ENST00000536500.1_Silent_p.T845T|ZNF112_ENST00000354340.4_Silent_p.T822T	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	828					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T822T(1)									GTTTCTCTCCTGTGTGGACTC	0.463																																																1	Substitution - coding silent(1)	ovary(1)	19											148	146	147					19																	44831844		2203	4300	6503	49523684	SO:0001819	synonymous_variant	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2484A>T	19.37:g.44831844T>A			49523684	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																				0.463	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		A	44831844	T	A	44831844	2	1	114	1	0	0	0	0	0	0	0	1	17677	1567	55	5		5	ZFP112	19	44831844	Silent	SNP	T	TCGA-F5-6464-01A-11D-1733-10	5761119	44831844	14297139	119	30783										
POLD1	5424	hgsc.bcm.edu	37	chr19	50918762	50918762	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgctgtgcaaccgcatcgatAtctcccagctggtcatcacc	8	15	3	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:50918762A>G	ENST00000440232.2	+	21	2685	c.2632A>G	c.(2632-2634)Atc>Gtc	p.I878V	POLD1_ENST00000595904.1_Missense_Mutation_p.I904V|CTD-2545M3.6_ENST00000599632.1_5'Flank|POLD1_ENST00000599857.1_Missense_Mutation_p.I878V	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	878					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CCGCATCGATATCTCCCAGCT	0.672								DNA polymerases (catalytic subunits)																																								0			19											44	34	38					19																	50918762		2203	4299	6502	55610574	SO:0001583	missense	5424				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2632A>G	19.37:g.50918762A>G	ENSP00000406046:p.Ile878Val		55610574	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.427946	0.62733	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.15718	2.4	4.25	4.25	0.50352	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.85682	D	0.000000	T	0.27832	0.0685	M	0.73962	2.25	0.80722	D	1	P;B	0.35575	0.51;0.201	B;B	0.42245	0.381;0.291	T	0.09751	-1.0660	10	0.72032	D	0.01	-29.3221	12.6607	0.56811	1.0:0.0:0.0:0.0	.	904;878	E7EVW0;P28340	.;DPOD1_HUMAN	V	878;879	ENSP00000406046:I878V	ENSP00000366129:I879V	I	+	1	0	POLD1	55610574	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	3.739000	0.55075	1.717000	0.51406	0.370000	0.22315	ATC		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			G	50918762	A	G	50918762	3	3	114	1	0	0	0	0	1	0	0	0	12221	449	16	4	2710	4	POLD1	19	50918762	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	6086918	50918762	8210221	120	30784										
ZNF160	90338	hgsc.bcm.edu	37	chr19	53573480	53573480	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgtactgctcttctcttttgGtagcaaatccttgattgtac	7	9	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:53573480G>C	ENST00000429604.1	-	7	722	c.307C>G	c.(307-309)Cca>Gca	p.P103A	ZNF160_ENST00000599056.1_Missense_Mutation_p.P103A|ZNF160_ENST00000601421.1_Missense_Mutation_p.P67A|ZNF160_ENST00000418871.1_Missense_Mutation_p.P103A	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	103					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TTCTCTTTTGGTAGCAAATCC	0.353																																																0			19											78	76	76					19																	53573480		2202	4300	6502	58265292	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.307C>G	19.37:g.53573480G>C	ENSP00000406201:p.Pro103Ala		58265292	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	G	7.492	0.650859	0.14516	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.07021	3.23;3.23	2.39	-1.76	0.08006	.	.	.	.	.	T	0.04003	0.0112	L	0.27053	0.805	0.09310	N	1	B	0.25667	0.131	B	0.19666	0.026	T	0.44982	-0.9292	9	0.18276	T	0.48	.	0.4628	0.00519	0.2685:0.1932:0.3424:0.1959	.	103	Q9HCG1	ZN160_HUMAN	A	103	ENSP00000406201:P103A;ENSP00000409597:P103A	ENSP00000409597:P103A	P	-	1	0	ZNF160	58265292	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.494000	0.06451	-0.444000	0.07170	-0.258000	0.10820	CCA		0.353	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53573480	G	C	53573480	3	2	114	1	0	0	0	0	1	0	0	0	17778	1261	44	5	2153	5	ZNF160	19	53573480	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	2654718	53573480	5555503	121	30785										
PEG3	5178	hgsc.bcm.edu	37	chr19	57328632	57328632	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	catctgtgtcaaaatgatagCgcctctttctttcaagaact	6	10	5	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr19:57328632C>A	ENST00000326441.9	-	10	1541	c.1178G>T	c.(1177-1179)cGc>cTc	p.R393L	PEG3_ENST00000593695.1_Missense_Mutation_p.R267L|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R393L|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.R269L|ZIM2_ENST00000391708.3_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	393					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AAAATGATAGCGCCTCTTTCT	0.453																																																0			19											107	112	110					19																	57328632		2203	4300	6503	62020444	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.1178G>T	19.37:g.57328632C>A	ENSP00000326581:p.Arg393Leu		62020444	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411927	0.62511	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02345	4.33;4.33	4.35	2.18	0.27775	.	0.000000	0.45361	D	0.000378	T	0.04137	0.0115	L	0.34521	1.04	.	.	.	P;P;D	0.61697	0.956;0.915;0.99	P;P;P	0.54629	0.682;0.535;0.757	T	0.44081	-0.9351	9	0.22109	T	0.4	-26.0019	6.4559	0.21930	0.0:0.5439:0.3586:0.0975	.	269;393;328	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	L	393;393;363	ENSP00000326581:R393L;ENSP00000403051:R393L	ENSP00000292074:R363L	R	-	2	0	ZIM2	62020444	0.196000	0.23350	0.996000	0.52242	0.935000	0.57460	0.300000	0.19156	0.748000	0.32831	0.655000	0.94253	CGC		0.453	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57328632	C	A	57328632	3	1	114	1	0	0	0	0	1	0	0	0	11751	768	27	2	3592	2	PEG3	19	57328632	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	3755152	57328632	1800351	122	30786										
TGM3	7053	hgsc.bcm.edu	37	chr20	2320521	2320521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tgctgaacgaggctcgtgtgCggaagcctgtgaacgtgcag	16	9	0	2	rs370607077	byFrequency	TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr20:2320521C>T	ENST00000381458.5	+	12	1885	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	608					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	GGCTCGTGTGCGGAAGCCTGT	0.632													C|||	2	0.000399361	8e-04	0	5008	,	,		13698	0		0	False		,,,				2504	0.001															0			20						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	89	73	78		1822	0.3	0.1	20		78	0,8600		0,0,4300	no	missense	TGM3	NM_003245.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	608/694	2320521	1,13005	2203	4300	6503	2268521	SO:0001583	missense	7053			L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.1822C>T	20.37:g.2320521C>T	ENSP00000370867:p.Arg608Trp		2268521	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.366131	0.61513	2.27E-4	0.0	ENSG00000125780	ENST00000381458	T	0.69040	-0.37	5.26	0.351	0.16042	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	1.405290	0.04301	N	0.347352	T	0.59878	0.2226	L	0.27053	0.805	0.09310	N	1	D	0.76494	0.999	P	0.47864	0.559	T	0.55730	-0.8095	10	0.72032	D	0.01	-8.4543	7.9084	0.29776	0.5464:0.3121:0.1415:0.0	.	608	Q08188	TGM3_HUMAN	W	608	ENSP00000370867:R608W	ENSP00000370867:R608W	R	+	1	2	TGM3	2268521	0.000000	0.05858	0.130000	0.21974	0.035000	0.12851	-0.450000	0.06803	0.553000	0.29044	0.561000	0.74099	CGG		0.632	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2320521	C	T	2320521	3	4	114	1	0	0	0	0	1	0	0	0	15870	759	27	1	1868	1	TGM3	20	2320521	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10		2320521	60704999	123	30787										
AHCY	191	hgsc.bcm.edu	37	chr20	32868877	32868877	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ccggcttgaaggggccatcaCaggacatgcccaggtactgg	14	12	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr20:32868877C>T	ENST00000217426.2	-	10	1339	c.1262G>A	c.(1261-1263)tGt>tAt	p.C421Y	CTD-3216D2.5_ENST00000609218.1_RNA|AHCY_ENST00000538132.1_Missense_Mutation_p.C393Y|RP4-785G19.5_ENST00000512005.1_RNA	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	421					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GGGGCCATCACAGGACATGCC	0.597																																																0			20											69	56	60					20																	32868877		2203	4300	6503	32332538	SO:0001583	missense	191			M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1262G>A	20.37:g.32868877C>T	ENSP00000217426:p.Cys421Tyr		32332538	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	37	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.521188	0.27211	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.75938	-0.98;-0.98	4.79	0.0596	0.14333	.	1.155360	0.06152	N	0.674434	T	0.56877	0.2015	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.48937	-0.8990	10	0.72032	D	0.01	.	1.4322	0.02336	0.262:0.3216:0.2681:0.1483	.	421	P23526	SAHH_HUMAN	Y	421;393	ENSP00000217426:C421Y;ENSP00000442820:C393Y	ENSP00000217426:C421Y	C	-	2	0	AHCY	32332538	0.000000	0.05858	0.002000	0.10522	0.978000	0.69477	-0.978000	0.03778	0.265000	0.21872	0.650000	0.86243	TGT		0.597	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32868877	C	T	32868877	3	4	114	1	0	0	0	0	1	0	0	0	409	478	17	3	40	3	AHCY	20	32868877	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	30548356	32868877	30156643	124	30788										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43567344	43567344	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcagtggccgtgctgcaggcAcaccaggctatggagcagcc	15	13	0	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr20:43567344A>T	ENST00000217073.2	+	14	1806	c.1806A>T	c.(1804-1806)gcA>gcT	p.A602A	PABPC1L_ENST00000255136.3_Silent_p.A602A|PABPC1L_ENST00000372824.1_Silent_p.A156A|PABPC1L_ENST00000490798.1_Intron|PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000372819.1_Intron|PABPC1L_ENST00000217075.2_Intron			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	602	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TGCTGCAGGCACACCAGGCTA	0.572																																																0			20											40	38	39					20																	43567344		1568	3581	5149	43000758	SO:0001819	synonymous_variant	80336			AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1806A>T	20.37:g.43567344A>T			43000758	Q4VY17	Silent	SNP	ENST00000217073.2	37	CCDS42878.1																																																																																				0.572	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			T	43567344	A	T	43567344	2	4	114	1	0	0	0	0	0	0	0	1	11395	146	6	5		5	PABPC1L	20	43567344	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	10698467	43567344	19458176	125	30789										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15873051	15873051	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	caaataatgtctatgatgtcTcctttctaagggcaaagaaa	7	7	3	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr21:15873051T>C	ENST00000400566.1	-	6	648	c.567A>G	c.(565-567)ggA>ggG	p.G189G	SAMSN1_ENST00000285670.2_Silent_p.G257G|SAMSN1_ENST00000463807.1_5'Flank|SAMSN1_ENST00000400564.1_Silent_p.G21G	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	189	SH3.				negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		CTATGATGTCTCCTTTCTAAG	0.343																																																0			21											159	140	145					21																	15873051		1848	4102	5950	14794922	SO:0001819	synonymous_variant	64092			AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.567A>G	21.37:g.15873051T>C			14794922	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Silent	SNP	ENST00000400566.1	37	CCDS42906.1																																																																																				0.343	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			C	15873051	T	C	15873051	2	2	114	1	0	0	0	0	0	0	0	1	13867	1538	54	4		4	SAMSN1	21	15873051	Silent	SNP	T	TCGA-F5-6464-01A-11D-1733-10		15873051	32256844	126	30790										
CXADR	1525	hgsc.bcm.edu	37	chr21	18924199	18924199	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cgaatttacaactgtcagatAttggcacatatcagtgcaaa	7	8	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr21:18924199A>G	ENST00000284878.7	+	3	1091	c.343A>G	c.(343-345)Att>Gtt	p.I115V	CXADR_ENST00000356275.6_Intron|CXADR_ENST00000306618.10_Missense_Mutation_p.I115V|CXADR_ENST00000400166.1_Missense_Mutation_p.I115V|CXADR_ENST00000400169.1_Missense_Mutation_p.I115V|CXADR_ENST00000400165.1_Missense_Mutation_p.I115V	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	115	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		ACTGTCAGATATTGGCACATA	0.358																																																0			21											90	91	90					21																	18924199		2203	4300	6503	17846070	SO:0001583	missense	1525			Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.343A>G	21.37:g.18924199A>G	ENSP00000284878:p.Ile115Val		17846070	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	37	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	A	5.130	0.209542	0.09757	.	.	ENSG00000154639	ENST00000284878;ENST00000400166;ENST00000400169;ENST00000400165;ENST00000306618	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.04	3.88	0.44766	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.331011	0.36134	N	0.002763	T	0.42720	0.1215	N	0.12182	0.205	0.27664	N	0.946989	B;B;B;B	0.17465	0.022;0.008;0.002;0.011	B;B;B;B	0.14578	0.011;0.01;0.006;0.008	T	0.41197	-0.9522	10	0.62326	D	0.03	.	10.4371	0.44441	0.9219:0.0:0.0781:0.0	.	115;115;115;115	P78310-4;B7WPI3;P78310;P78310-5	.;.;CXAR_HUMAN;.	V	115	ENSP00000284878:I115V;ENSP00000383030:I115V;ENSP00000383033:I115V;ENSP00000383029:I115V;ENSP00000303395:I115V	ENSP00000284878:I115V	I	+	1	0	CXADR	17846070	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	4.563000	0.60823	0.999000	0.39023	0.533000	0.62120	ATT		0.358	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			G	18924199	A	G	18924199	3	3	114	1	0	0	0	0	1	0	0	0	4082	449	16	4	353	4	CXADR	21	18924199	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	3051148	18924199	29205696	127	30791										
TTC3	7267	hgsc.bcm.edu	37	chr21	38538382	38538382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctctgaggatgcaaattacaAgcgagtctcctgtaattccc	8	11	2	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr21:38538382A>G	ENST00000399017.2	+	33	6613	c.3866A>G	c.(3865-3867)aAg>aGg	p.K1289R	TTC3_ENST00000355666.1_Missense_Mutation_p.K1289R|TTC3_ENST00000354749.2_Missense_Mutation_p.K1289R|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1289			K -> M (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K1289M(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCAAATTACAAGCGAGTCTCC	0.458																																					Ovarian(38;194 1649 35661)											1	Substitution - Missense(1)	breast(1)	21											81	87	85					21																	38538382		2203	4300	6503	37460252	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3866A>G	21.37:g.38538382A>G	ENSP00000381981:p.Lys1289Arg		37460252	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	a	12.12	1.843523	0.32606	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.09630	2.96;2.96;2.96	3.87	-1.87	0.07737	.	2.008250	0.02470	N	0.087400	T	0.08626	0.0214	L	0.44542	1.39	0.09310	N	1	B;B	0.28636	0.218;0.08	B;B	0.25405	0.06;0.012	T	0.23547	-1.0185	9	.	.	.	-7.0E-4	0.7966	0.01067	0.3977:0.17:0.1023:0.33	.	347;1289	Q5GIT6;P53804	.;TTC3_HUMAN	R	1289	ENSP00000347889:K1289R;ENSP00000381981:K1289R;ENSP00000346791:K1289R	.	K	+	2	0	TTC3	37460252	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.031000	0.13710	-0.403000	0.07622	-0.253000	0.11424	AAG		0.458	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38538382	A	G	38538382	3	3	114	1	0	0	0	0	1	0	0	0	16737	72	3	4	3992	4	TTC3	21	38538382	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	19614183	38538382	9591513	128	30792										
PRMT2	3275	hgsc.bcm.edu	37	chr21	48083335	48083335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cgctgttcatgatggacgacCcagtccctgtccatacagga	10	13	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chr21:48083335C>T	ENST00000397637.1	+	10	2092	c.1138C>T	c.(1138-1140)Cca>Tca	p.P380S	PRMT2_ENST00000458387.2_Missense_Mutation_p.P232L|PRMT2_ENST00000291705.6_Intron|PRMT2_ENST00000397638.2_Missense_Mutation_p.P380S|PRMT2_ENST00000355680.3_Missense_Mutation_p.P380S|PRMT2_ENST00000451211.2_Intron|PRMT2_ENST00000440086.1_Missense_Mutation_p.P278S			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	380	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		GATGGACGACCCAGTCCCTGT	0.582																																																0			21											185	140	155					21																	48083335		2203	4300	6503	46907763	SO:0001583	missense	3275			U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"Protein arginine methyltransferases"	5186	protein-coding gene	gene with protein product		601961	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1", "HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.1138C>T	21.37:g.48083335C>T	ENSP00000380759:p.Pro380Ser		46907763	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	28.6|28.6	4.937337|4.937337	0.92458|0.92458	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000458387|ENST00000355680;ENST00000397638;ENST00000397637;ENST00000440086	T|D;D;D;D	0.63580|0.88354	-0.05|-2.37;-2.37;-2.37;-2.37	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.055858|0.055858	0.64402|0.64402	D|N	0.000001|0.000001	D|D	0.93989|0.93989	0.8075|0.8075	M|M	0.74546|0.74546	2.27|2.27	0.80722|0.80722	D|D	1|1	B|D;D	0.31680|0.89917	0.335|1.0;0.999	B|D;D	0.25140|0.85130	0.058|0.997;0.974	D|D	0.93523|0.93523	0.6863|0.6863	9|9	.|.	.|.	.|.	-17.8136|-17.8136	16.8042|16.8042	0.85621|0.85621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	232|278;380	B7U631|Q498Y5;P55345	.|.;ANM2_HUMAN	L|S	232|380;380;380;278	ENSP00000407463:P232L|ENSP00000347906:P380S;ENSP00000380760:P380S;ENSP00000380759:P380S;ENSP00000397266:P278S	.|.	P|P	+|+	2|1	0|0	PRMT2|PRMT2	46907763|46907763	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.574000|0.574000	0.36063|0.36063	5.413000|5.413000	0.66399|0.66399	2.652000|2.652000	0.90054|0.90054	0.655000|0.655000	0.94253|0.94253	CCC|CCA		0.582	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535		T	48083335	C	T	48083335	3	4	114	1	0	0	0	0	1	0	0	0	12571	623	22	3	1172	3	PRMT2	21	48083335	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	9544953	48083335	46560	129	30793										
WWC3	55841	hgsc.bcm.edu	37	chrX	10058885	10058885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggctatcatgagtgagctccGgaccatcaagaaggccattt	11	10	2	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:10058885G>A	ENST00000380861.4	+	6	843	c.452G>A	c.(451-453)cGg>cAg	p.R151Q	WWC3_ENST00000454666.1_Missense_Mutation_p.R151Q	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	151					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						AGTGAGCTCCGGACCATCAAG	0.458																																																0			X											108	90	96					X																	10058885		2203	4300	6503	10018885	SO:0001583	missense	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.452G>A	X.37:g.10058885G>A	ENSP00000370242:p.Arg151Gln		10018885	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.156318	0.57259	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000398613	T;T	0.05258	3.47;3.47	5.05	4.18	0.49190	.	0.119886	0.53938	D	0.000049	T	0.12987	0.0315	L	0.52364	1.645	0.37893	D	0.930788	D	0.63880	0.993	P	0.53549	0.729	T	0.05716	-1.0868	10	0.40728	T	0.16	-23.4289	12.877	0.57996	0.082:0.0:0.918:0.0	.	151	Q9ULE0	WWC3_HUMAN	Q	151	ENSP00000370242:R151Q;ENSP00000399584:R151Q	ENSP00000370242:R151Q	R	+	2	0	WWC3	10018885	1.000000	0.71417	0.606000	0.28943	0.017000	0.09413	6.387000	0.73191	1.012000	0.39366	0.506000	0.49869	CGG		0.458	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10058885	G	A	10058885	3	1	114	1	0	0	0	0	1	0	0	0	17453	1116	39	1	470	1	WWC3	23	10058885	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10		10058885	145211675	130	30794										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23397858	23397858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	agaatgctcgggccaccaatCggaccaattttgctatcaca	8	12	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:23397858C>T	ENST00000379361.4	+	2	1362	c.502C>T	c.(502-504)Cgg>Tgg	p.R168W		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	168					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)	p.R63R(1)		NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GGCCACCAATCGGACCAATTT	0.488																																																1	Substitution - coding silent(1)	ovary(1)	X											100	86	90					X																	23397858		2203	4300	6503	23307779	SO:0001583	missense	139411			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.502C>T	X.37:g.23397858C>T	ENSP00000368666:p.Arg168Trp		23307779	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	37	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	C	15.28	2.788193	0.49997	.	.	ENSG00000165186	ENST00000379361	D	0.89415	-2.51	5.06	4.2	0.49525	.	0.199272	0.43919	D	0.000512	D	0.87811	0.6271	L	0.29908	0.895	0.33407	D	0.578101	D;P	0.76494	0.999;0.953	P;P	0.55303	0.711;0.773	D	0.90871	0.4746	10	0.59425	D	0.04	0.0188	12.3099	0.54922	0.306:0.694:0.0:0.0	.	63;168	Q96NR3-3;Q96NR3	.;PTHD1_HUMAN	W	168	ENSP00000368666:R168W	ENSP00000368666:R168W	R	+	1	2	PTCHD1	23307779	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.074000	0.41529	1.233000	0.43693	0.600000	0.82982	CGG		0.488	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		T	23397858	C	T	23397858	3	4	114	1	0	0	0	0	1	0	0	0	12766	875	31	1	508	1	PTCHD1	23	23397858	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	13338973	23397858	131872702	131	30795										
OTC	5009	hgsc.bcm.edu	37	chrX	38211986	38211986	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ggatcctgttaaacaatgcaGcttttagaaatggtcacaac	8	8	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:38211986G>C	ENST00000039007.4	+	1	189	c.37G>C	c.(37-39)Gct>Cct	p.A13P	OTC_ENST00000488812.1_3'UTR|TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	13					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	AAACAATGCAGCTTTTAGAAA	0.383																																																0			X											153	126	136					X																	38211986		2202	4300	6502	38096930	SO:0001583	missense	5009			K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.37G>C	X.37:g.38211986G>C	ENSP00000039007:p.Ala13Pro		38096930	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	G	7.762	0.705517	0.15172	.	.	ENSG00000036473	ENST00000039007	D	0.99150	-5.49	5.77	3.05	0.35203	.	0.748493	0.13045	N	0.418218	D	0.94479	0.8223	N	0.08118	0	0.27955	N	0.936998	B	0.02656	0.0	B	0.01281	0.0	D	0.89509	0.3770	10	0.27082	T	0.32	.	4.8057	0.13319	0.1823:0.0:0.647:0.1707	.	13	P00480	OTC_HUMAN	P	13	ENSP00000039007:A13P	ENSP00000039007:A13P	A	+	1	0	OTC	38096930	0.995000	0.38212	0.447000	0.26932	0.641000	0.38312	0.706000	0.25690	0.216000	0.20781	-0.192000	0.12808	GCT		0.383	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			C	38211986	G	C	38211986	3	2	114	1	0	0	0	0	1	0	0	0	11332	971	34	5	39	5	OTC	23	38211986	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	14814128	38211986	117058574	132	30796										
EBP	10682	hgsc.bcm.edu	37	chrX	48382321	48382321	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	ctgttgtcaggtcgtgctgcGgttgtcccattggggacttg	15	9	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:48382321G>T	ENST00000495186.1	+	2	985	c.162G>T	c.(160-162)gcG>gcT	p.A54A	EBP_ENST00000276096.6_3'UTR	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	54					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	GTCGTGCTGCGGTTGTCCCAT	0.567																																					Ovarian(41;550 1000 33077 33474 52335)											0			X											200	167	178					X																	48382321		2203	4300	6503	48267265	SO:0001819	synonymous_variant	152503			Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"3-beta-hydroxysteroid-delta-8,delta-7-isomerase", "Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)", "sterol 8-isomerase"	300205	"emopamil-binding protein (sterol isomerase)"	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.162G>T	X.37:g.48382321G>T			48267265	Q6FGL3|Q6IBI9	Silent	SNP	ENST00000495186.1	37	CCDS14300.1																																																																																				0.567	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579		T	48382321	G	T	48382321	2	4	114	1	0	0	0	0	0	0	0	1	4897	1103	39	2		2	EBP	23	48382321	Silent	SNP	G	TCGA-F5-6464-01A-11D-1733-10	10170335	48382321	106888239	133	30797										
WNK3	65267	hgsc.bcm.edu	37	chrX	54259351	54259351	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	gcaggtggcaaaggaatctcAgtagattgggttttgctatc	13	6	1	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:54259351A>C	ENST00000375159.2	-	20	4730	c.4731T>G	c.(4729-4731)acT>acG	p.T1577T	WNK3_ENST00000375169.3_Silent_p.T1530T|WNK3_ENST00000354646.2_Silent_p.T1577T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1577					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AAGGAATCTCAGTAGATTGGG	0.473																																																0			X											160	143	149					X																	54259351		2203	4300	6503	54276076	SO:0001819	synonymous_variant	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4731T>G	X.37:g.54259351A>C			54276076	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	37	CCDS14357.1																																																																																				0.473	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		C	54259351	A	C	54259351	2	2	114	1	0	0	0	0	0	0	0	1	17419	175	7	4		4	WNK3	23	54259351	Silent	SNP	A	TCGA-F5-6464-01A-11D-1733-10	5877030	54259351	101011209	134	30798										
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56591723	56591724	+	Frame_Shift_Ins	INS	-	-	T													0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cactgaagcacctggcctgaINSttccgagcttcactccaggt							TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:56591723_56591724insT	ENST00000338222.5	+	1	1698_1699	c.1417_1418insT	c.(1417-1419)attfs	p.I473fs		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	473					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						ACCTGGCCTGATTCCGAGCTTC	0.574																																					Esophageal Squamous(104;218 1492 6022 10838 28884)											0			X																																								56608449	SO:0001589	frameshift_variant	29978			AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"Ubiquilin family"	12509	protein-coding gene	gene with protein product	"NEDD4 binding protein 4"	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1419dupT	X.37:g.56591725_56591725dupT	ENSP00000345195:p.Ile473fs		56608448	O94798|Q5D027|Q9H3W6|Q9HAZ4	Frame_Shift_Ins	INS	ENST00000338222.5	37	CCDS14374.1																																																																																				0.574	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		T	56591724	-	T	56591723	7	5	114	1	0	1	1	0	0	0	0	0	16937	333	12	0	1419	0	UBQLN2	23	56591723	Frame_Shift_Ins	INS	-	TCGA-F5-6464-01A-11D-1733-10	2332372	56591723	98678837	135	30799										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63564991	63564991	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	aatgcccatgaatctgaagcGaatgttggcatagttgtctt	10	7	2	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:63564991G>A	ENST00000374852.3	-	7	866	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	MTMR8_ENST00000453546.1_Missense_Mutation_p.R267C|MTMR8_ENST00000478487.1_5'UTR	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	267	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						AATCTGAAGCGAATGTTGGCA	0.488																																																1	Whole gene deletion(1)	ovary(1)	X											236	179	198					X																	63564991		2203	4300	6503	63481716	SO:0001583	missense	66036			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.799C>T	X.37:g.63564991G>A	ENSP00000363985:p.Arg267Cys		63481716	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.17|17.17	3.321849|3.321849	0.60634|0.60634	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400|ENST00000442913	D;D|.	0.90676|.	-2.71;-2.71|.	3.23|3.23	3.23|3.23	0.37069|0.37069	Myotubularin phosphatase domain (1);Myotubularin-related (1);|.	0.000000|.	0.44285|.	U|.	0.000476|.	T|T	0.79317|0.79317	0.4425|0.4425	M|M	0.89715|0.89715	3.055|3.055	0.58432|0.58432	D|D	0.999994|0.999994	D;D|.	0.89917|.	0.999;1.0|.	P;D|.	0.70716|.	0.765;0.97|.	D|D	0.83551|0.83551	0.0101|0.0101	10|5	0.87932|.	D|.	0|.	.|.	12.8898|12.8898	0.58066|0.58066	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	267;267|.	B4DQL0;Q96EF0|.	.;MTMR8_HUMAN|.	C|L	267;267;153|70	ENSP00000394003:R267C;ENSP00000363985:R267C|.	ENSP00000247400:R153C|.	R|S	-|-	1|2	0|0	MTMR8|MTMR8	63481716|63481716	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.995000|0.995000	0.86356|0.86356	2.793000|2.793000	0.47845|0.47845	1.638000|1.638000	0.50547|0.50547	0.513000|0.513000	0.50165|0.50165	CGC|TCG		0.488	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		A	63564991	G	A	63564991	3	1	114	1	0	0	0	0	1	0	0	0	9979	1058	37	1	1347	1	MTMR8	23	63564991	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	6973268	63564991	91705569	136	30800										
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92928039	92928039	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	atttgttcccaacggggcccGccgcgcccttctggaaggct	12	15	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:92928039G>A	ENST00000373079.3	-	1	528	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W	NAP1L3_ENST00000475430.2_Missense_Mutation_p.R82W|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	89					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						AACGGGGCCCGCCGCGCCCTT	0.567																																																0			X											19	21	20					X																	92928039		2185	4244	6429	92814695	SO:0001583	missense	4675				CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.265C>T	X.37:g.92928039G>A	ENSP00000362171:p.Arg89Trp		92814695	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	G	1.558	-0.537543	0.04082	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.30981	1.51	3.33	0.197	0.15164	.	0.431559	0.26373	N	0.024757	T	0.14570	0.0352	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.14364	-1.0475	10	0.40728	T	0.16	-10.8327	6.2714	0.20956	0.1371:0.5442:0.3187:0.0	.	89	Q99457	NP1L3_HUMAN	W	89;82	ENSP00000362171:R89W	ENSP00000362171:R89W	R	-	1	2	NAP1L3	92814695	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.053000	0.11846	-0.073000	0.12842	0.529000	0.55759	CGG		0.567	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92928039	G	A	92928039	3	1	114	1	0	0	0	0	1	0	0	0	10188	1086	38	1	1259	1	NAP1L3	23	92928039	Missense_Mutation	SNP	G	TCGA-F5-6464-01A-11D-1733-10	29363048	92928039	62342521	137	30801										
XKRX	402415	hgsc.bcm.edu	37	chrX	100177923	100177923	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cagggtccggatggagtggcCcacctcccattctatcagca	11	14	2	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:100177923C>G	ENST00000372956.2	-	2	1067	c.463G>C	c.(463-465)Ggc>Cgc	p.G155R	XKRX_ENST00000468904.1_Intron|XKRX_ENST00000328526.5_Missense_Mutation_p.G168R			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						ATGGAGTGGCCCACCTCCCAT	0.557																																																0			X											203	167	179					X																	100177923		2203	4300	6503	100064579	SO:0001583	missense	402415			AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"X Kell blood group precursor-related, X-linked"				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.463G>C	X.37:g.100177923C>G	ENSP00000362047:p.Gly155Arg		100064579	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	37	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785355	0.90282	.	.	ENSG00000182489	ENST00000328526;ENST00000372956	T;T	0.72505	-0.66;-0.64	5.9	5.04	0.67666	.	0.045117	0.85682	D	0.000000	T	0.80778	0.4688	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.80747	-0.1244	10	0.48119	T	0.1	-7.2368	13.5075	0.61491	0.0:0.9223:0.0:0.0777	.	155	Q6PP77	XKR2_HUMAN	R	168;155	ENSP00000327570:G168R;ENSP00000362047:G155R	ENSP00000327570:G168R	G	-	1	0	XKRX	100064579	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.740000	0.68629	2.493000	0.84123	0.600000	0.82982	GGC		0.557	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559		G	100177923	C	G	100177923	3	3	114	1	0	0	0	0	1	0	0	0	17479	623	22	5	894	5	XKRX	23	100177923	Missense_Mutation	SNP	C	TCGA-F5-6464-01A-11D-1733-10	7249884	100177923	55092637	138	30802										
TAF7L	54457	hgsc.bcm.edu	37	chrX	100532686	100532686	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tttctatttccttggttccaTcttcagcaatgacttcccaa	4	12	3	1			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:100532686T>C	ENST00000372907.3	-	9	868	c.857A>G	c.(856-858)gAt>gGt	p.D286G	TAF7L_ENST00000356784.1_Missense_Mutation_p.D200G|TAF7L_ENST00000324762.6_Missense_Mutation_p.D200G|TAF7L_ENST00000372905.2_Missense_Mutation_p.D200G	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	286					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CTTGGTTCCATCTTCAGCAAT	0.468																																					Ovarian(104;431 1530 3210 15406 18594)											0			X											141	128	132					X																	100532686		2203	4300	6503	100419342	SO:0001583	missense	54457			AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"cancer/testis antigen 40"	300314	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.857A>G	X.37:g.100532686T>C	ENSP00000361998:p.Asp286Gly		100419342	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	t	7.922	0.738864	0.15642	.	.	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	T;T;T;T	0.33438	3.59;1.41;1.41;3.03	5.29	-5.55	0.02536	.	0.768919	0.11491	N	0.558748	T	0.27349	0.0671	L	0.60067	1.865	0.34232	D	0.676612	B;B	0.24043	0.069;0.096	B;B	0.24155	0.029;0.051	T	0.09250	-1.0683	10	0.62326	D	0.03	-0.545	12.2589	0.54638	0.0:0.3696:0.0:0.6304	.	286;200	Q5H9L4;Q5H9L4-3	TAF7L_HUMAN;.	G	286;200;200;200	ENSP00000361998:D286G;ENSP00000361996:D200G;ENSP00000320283:D200G;ENSP00000349235:D200G	ENSP00000320283:D200G	D	-	2	0	TAF7L	100419342	1.000000	0.71417	0.002000	0.10522	0.065000	0.16274	1.178000	0.31981	-1.429000	0.01987	-0.327000	0.08410	GAT		0.468	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			C	100532686	T	C	100532686	3	2	114	1	0	0	0	0	1	0	0	0	15572	1435	50	4	551	4	TAF7L	23	100532686	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	354763	100532686	54737874	139	30803										
KLHL13	90293	hgsc.bcm.edu	37	chrX	117043321	117043321	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	cagatatcctttgagggcacTtaggtggaagaaggtgcgct	14	7	0	3			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:117043321T>G	ENST00000262820.3	-	5	2218	c.1309A>C	c.(1309-1311)Agt>Cgt	p.S437R	KLHL13_ENST00000540167.1_Missense_Mutation_p.S421R|KLHL13_ENST00000371882.1_Missense_Mutation_p.S386R|KLHL13_ENST00000371876.1_Missense_Mutation_p.S386R|KLHL13_ENST00000469946.1_Missense_Mutation_p.S386R|KLHL13_ENST00000539496.1_Missense_Mutation_p.S440R|KLHL13_ENST00000541812.1_Missense_Mutation_p.S421R|KLHL13_ENST00000545703.1_Missense_Mutation_p.S395R|KLHL13_ENST00000371878.1_Missense_Mutation_p.S386R	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	437					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TTGAGGGCACTTAGGTGGAAG	0.408																																																0			X											52	45	47					X																	117043321		2203	4300	6503	116927349	SO:0001583	missense	90293			AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.1309A>C	X.37:g.117043321T>G	ENSP00000262820:p.Ser437Arg		116927349	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	37	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196908	0.79015	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946	T;T;T;T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.02	5.02	0.67125	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.88175	0.6366	M	0.82323	2.585	0.80722	D	1	D;D;P;P	0.89917	0.989;1.0;0.94;0.952	P;D;P;P	0.80764	0.78;0.994;0.749;0.837	D	0.89979	0.4099	10	0.87932	D	0	.	13.8251	0.63346	0.0:0.0:0.0:1.0	.	421;440;431;437	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	R	386;386;386;386;421;421;440;437;395;386	ENSP00000360949:S386R;ENSP00000360943:S386R;ENSP00000360945:S386R;ENSP00000412640:S386R;ENSP00000444450:S421R;ENSP00000441029:S421R;ENSP00000443191:S440R;ENSP00000262820:S437R;ENSP00000440707:S395R;ENSP00000419803:S386R	ENSP00000262820:S437R	S	-	1	0	KLHL13	116927349	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	1.838000	0.53458	0.481000	0.45027	AGT		0.408	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		G	117043321	T	G	117043321	3	3	114	1	0	0	0	0	1	0	0	0	8390	1609	56	4	670	4	KLHL13	23	117043321	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	16510635	117043321	38227239	140	30804										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135313098	135313098	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	acgcttcttggcaatagggaTtaaggcctgtttgtccattt	10	8	1	0			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:135313098T>G	ENST00000316077.9	-	9	1661	c.1441A>C	c.(1441-1443)Atc>Ctc	p.I481L	MAP7D3_ENST00000370661.1_Missense_Mutation_p.I446L|MAP7D3_ENST00000370663.5_Missense_Mutation_p.I463L|MAP7D3_ENST00000495432.1_5'Flank	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	481					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					GCAATAGGGATTAAGGCCTGT	0.373																																																0			X											158	135	142					X																	135313098		1925	4118	6043	135140764	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1441A>C	X.37:g.135313098T>G	ENSP00000318086:p.Ile481Leu		135140764	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	t	10.10	1.258793	0.23051	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.04015	4.36;3.88;3.88;3.73	5.71	-1.74	0.08056	.	.	.	.	.	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.002;0.004;0.002;0.004	T	0.46289	-0.9202	9	0.29301	T	0.29	-0.5017	3.6148	0.08073	0.443:0.168:0.0:0.389	.	463;440;481;446	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	L	446;481;463;440	ENSP00000359695:I446L;ENSP00000318086:I481L;ENSP00000359697:I463L;ENSP00000359694:I440L	ENSP00000318086:I481L	I	-	1	0	MAP7D3	135140764	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.118000	0.10692	-0.302000	0.08869	-0.340000	0.08031	ATC		0.373	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			G	135313098	T	G	135313098	3	3	114	1	0	0	0	0	1	0	0	0	9299	1493	52	4	1229	4	MAP7D3	23	135313098	Missense_Mutation	SNP	T	TCGA-F5-6464-01A-11D-1733-10	18269777	135313098	19957462	141	30805										
CDR1	1038	hgsc.bcm.edu	37	chrX	139866322	139866322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tccctcaaatccatagcttcCgaaaaatccaggtcttccag	5	14	2	0	rs191541717		TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:139866322C>T	ENST00000370532.2	-	1	401	c.210G>A	c.(208-210)tcG>tcA	p.S70S		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	70	23 X 6 AA approximate repeats.							p.S70S(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CCATAGCTTCCGAAAAATCCA	0.458													C|||	1	0.000264901	0	0	3775	,	,		15685	0		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	endometrium(1)	X											82	80	80					X																	139866322		2203	4300	6503	139693988	SO:0001819	synonymous_variant	1038				CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.210G>A	X.37:g.139866322C>T			139693988	Q5JXH6	Silent	SNP	ENST00000370532.2	37	CCDS14670.1																																																																																				0.458	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		T	139866322	C	T	139866322	2	4	114	1	0	0	0	0	0	0	0	1	3177	639	23	1		1	CDR1	23	139866322	Silent	SNP	C	TCGA-F5-6464-01A-11D-1733-10	4553224	139866322	15404238	142	30806										
F8	2157	hgsc.bcm.edu	37	chrX	154157707	154157707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027972027972028	4	1	0.426603699330972	0.733225108225108	0.374412821221332	0.576470588235294	1	0	tttttttggctccttgtaagAaatgactgctttcttggacc	8	8	1	2			TCGA-F5-6464-01A-11D-1733-10	TCGA-F5-6464-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	c56b4512-6203-4be1-bcd4-c57301c901c0	1ade85ad-e4ad-450e-9b4a-ab37dd6fdf28	g.chrX:154157707A>G	ENST00000360256.4	-	14	4558	c.4358T>C	c.(4357-4359)tTc>tCc	p.F1453S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1453	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCCTTGTAAGAAATGACTGCT	0.433																																																0			X											101	99	100					X																	154157707		2203	4300	6503	153810901	SO:0001583	missense	2157			M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4358T>C	X.37:g.154157707A>G	ENSP00000353393:p.Phe1453Ser		153810901	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	a	5.468	0.271412	0.10349	.	.	ENSG00000185010	ENST00000360256	D	0.99304	-5.72	5.56	4.19	0.49359	.	0.787548	0.11967	N	0.512145	D	0.97707	0.9248	L	0.59436	1.845	0.09310	N	1	B	0.32245	0.361	B	0.29440	0.102	D	0.96549	0.9406	10	0.72032	D	0.01	-2.1606	7.009	0.24851	0.8797:0.0:0.1203:0.0	.	1453	P00451	FA8_HUMAN	S	1453	ENSP00000353393:F1453S	ENSP00000353393:F1453S	F	-	2	0	F8	153810901	0.527000	0.26306	0.029000	0.17559	0.005000	0.04900	1.911000	0.39937	1.876000	0.54355	0.483000	0.47432	TTC		0.433	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			G	154157707	A	G	154157707	3	3	114	1	0	0	0	0	1	0	0	0	5363	246	9	4	2777	4	F8	23	154157707	Missense_Mutation	SNP	A	TCGA-F5-6464-01A-11D-1733-10	14291385	154157707	1112853	143	30807										
ZBTB48	3104	hgsc.bcm.edu	37	chr1	6648899	6648899	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agtgtggctacaagtttaccCgacaggtaggccagggcctg	14	10	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:6648899C>T	ENST00000377674.4	+	10	1923	c.1765C>T	c.(1765-1767)Cga>Tga	p.R589*		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	589					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		CAAGTTTACCCGACAGGTAGG	0.627																																					Esophageal Squamous(125;1449 1657 4031 29866 49542)											0			1											80	87	85					1																	6648899		2203	4300	6503	6571486	SO:0001587	stop_gained	3104			BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4930	protein-coding gene	gene with protein product		165270	"GLI-Kruppel family member HKR3"	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.1765C>T	1.37:g.6648899C>T	ENSP00000366902:p.Arg589*		6571486	Q5SY19	Nonsense_Mutation	SNP	ENST00000377674.4	37	CCDS84.1	.	.	.	.	.	.	.	.	.	.	C	36	5.806574	0.96967	.	.	ENSG00000204859	ENST00000377674	.	.	.	5.52	4.6	0.57074	.	0.109170	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-16.5962	13.1713	0.59599	0.0:0.9222:0.0:0.0778	.	.	.	.	X	589	.	ENSP00000366902:R589X	R	+	1	2	ZBTB48	6571486	0.983000	0.35010	0.909000	0.35828	0.123000	0.20343	2.632000	0.46511	1.479000	0.48272	0.655000	0.94253	CGA		0.627	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341		T	6648899	C	T	6648899	4	4	115	1	0	0	0	0	0	1	0	0	17588	644	23	1	1799	1	ZBTB48	1	6648899	Nonsense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		6648899	242601722	1	30808										
YBX1	4904	hgsc.bcm.edu	37	chr1	43162403	43162403	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtaaccattatagacgctatCcacgtcgtaggggtcctcca	9	12	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:43162403C>A	ENST00000321358.7	+	5	584	c.445C>A	c.(445-447)Cca>Aca	p.P149T	YBX1_ENST00000467957.1_3'UTR	NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	149					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TAGACGCTATCCACGTCGTAG	0.517																																																0			1											76	78	77					1																	43162403		2203	4300	6503	42934990	SO:0001583	missense	4904			BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.445C>A	1.37:g.43162403C>A	ENSP00000361626:p.Pro149Thr		42934990	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218003	0.79352	.	.	ENSG00000065978	ENST00000321358;ENST00000332220;ENST00000318612	T;T	0.34859	1.34;1.34	5.24	5.24	0.73138	.	0.094233	0.85682	D	0.000000	T	0.41627	0.1167	M	0.79011	2.435	0.58432	D	0.999998	P	0.37781	0.608	B	0.36534	0.227	T	0.33701	-0.9858	10	0.23891	T	0.37	-0.5043	16.6713	0.85267	0.0:1.0:0.0:0.0	.	149	P67809	YBOX1_HUMAN	T	149;119;145	ENSP00000361626:P149T;ENSP00000405937:P119T	ENSP00000361621:P145T	P	+	1	0	YBX1	42934990	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.256000	0.78350	2.600000	0.87896	0.563000	0.77884	CCA		0.517	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		A	43162403	C	A	43162403	3	1	115	1	0	0	0	0	1	0	0	0	17509	855	30	2	463	2	YBX1	1	43162403	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	36513504	43162403	206088218	2	30809										
C1orf177	163747	hgsc.bcm.edu	37	chr1	55277491	55277491	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	actatccaggccctggaaatTatggggagaagggtaaccca	12	9	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:55277491T>A	ENST00000371273.3	+	5	520	c.505T>A	c.(505-507)Tat>Aat	p.Y169N	C1orf177_ENST00000358193.3_Missense_Mutation_p.Y169N	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	169										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						CCCTGGAAATTATGGGGAGAA	0.577																																																0			1											54	52	53					1																	55277491		2203	4300	6503	55050079	SO:0001583	missense	163747			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.505T>A	1.37:g.55277491T>A	ENSP00000360320:p.Tyr169Asn		55050079	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781851	0.70222	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26957	1.7;1.7	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000013	T	0.48624	0.1510	M	0.71581	2.175	0.50632	D	0.999882	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.51364	-0.8715	10	0.87932	D	0	-1.3074	11.5217	0.50555	0.0:0.0:0.0:1.0	.	169;169	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	N	169	ENSP00000350924:Y169N;ENSP00000360320:Y169N	ENSP00000350924:Y169N	Y	+	1	0	C1orf177	55050079	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.131000	0.57970	2.033000	0.60031	0.454000	0.30748	TAT		0.577	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		A	55277491	T	A	55277491	3	1	115	1	0	0	0	0	1	0	0	0	2023	1754	61	5	523	5	C1orf177	1	55277491	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	12115088	55277491	193973130	3	30810										
PRKAA2	5563	hgsc.bcm.edu	37	chr1	57173243	57173243	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gatcaagttttgattccacaActgcagagagccattcactt	7	10	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:57173243A>G	ENST00000371244.4	+	9	1582	c.1516A>G	c.(1516-1518)Act>Gct	p.T506A		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	506					autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.T506A(2)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TGATTCCACAACTGCAGAGAG	0.493																																																2	Substitution - Missense(2)	ovary(2)	1											164	154	157					1																	57173243		2203	4300	6503	56945831	SO:0001583	missense	5563			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.1516A>G	1.37:g.57173243A>G	ENSP00000360290:p.Thr506Ala		56945831	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	A	0.839	-0.742599	0.03088	.	.	ENSG00000162409	ENST00000371244	T	0.08807	3.05	5.99	0.865	0.19074	.	0.281293	0.40554	N	0.001066	T	0.02649	0.0080	N	0.08118	0	0.25119	N	0.990655	B	0.02656	0.0	B	0.01281	0.0	T	0.42172	-0.9467	10	0.08179	T	0.78	-11.4974	2.157	0.03814	0.4817:0.1211:0.2802:0.117	.	506	P54646	AAPK2_HUMAN	A	506	ENSP00000360290:T506A	ENSP00000360290:T506A	T	+	1	0	PRKAA2	56945831	0.004000	0.15560	0.005000	0.12908	0.506000	0.33950	0.640000	0.24705	0.159000	0.19401	-1.054000	0.02325	ACT		0.493	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252		G	57173243	A	G	57173243	3	3	115	1	0	0	0	0	1	0	0	0	12528	43	2	4	1550	4	PRKAA2	1	57173243	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	1895752	57173243	192077378	4	30811										
USP33	23032	hgsc.bcm.edu	37	chr1	78207427	78207427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cccaagactttcaaaatgagGtaacacctataagaaaagta	6	8	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:78207427G>A	ENST00000370793.1	-	3	395	c.49C>T	c.(49-51)Cct>Tct	p.P17S	USP33_ENST00000370794.3_5'UTR|USP33_ENST00000357428.1_Missense_Mutation_p.P17S|USP33_ENST00000370792.3_Missense_Mutation_p.P17S|USP33_ENST00000528150.1_5'UTR	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	17					axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						TCAAAATGAGGTAACACCTAT	0.279																																					Melanoma(152;72 1870 11110 26780 42647)											0			1											30	32	31					1																	78207427		2203	4290	6493	77980015	SO:0001583	missense	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.49C>T	1.37:g.78207427G>A	ENSP00000359829:p.Pro17Ser		77980015	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060308	0.36373	.	.	ENSG00000077254	ENST00000370793;ENST00000357428;ENST00000370792;ENST00000524536;ENST00000530709	T;T;T;T	0.28255	3.05;3.05;3.05;1.62	5.61	4.68	0.58851	.	.	.	.	.	T	0.06234	0.0161	N	0.08118	0	0.22050	N	0.999395	B;B	0.10296	0.003;0.002	B;B	0.10450	0.005;0.001	T	0.24621	-1.0155	9	0.23302	T	0.38	.	9.6012	0.39605	0.1226:0.1261:0.7513:0.0	.	17;17	Q8TEY7-3;Q8TEY7	.;UBP33_HUMAN	S	17	ENSP00000359829:P17S;ENSP00000350009:P17S;ENSP00000359828:P17S;ENSP00000434441:P17S	ENSP00000350009:P17S	P	-	1	0	USP33	77980015	0.592000	0.26832	0.988000	0.46212	0.787000	0.44495	1.178000	0.31981	2.812000	0.96745	0.557000	0.71058	CCT		0.279	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		A	78207427	G	A	78207427	3	1	115	1	0	0	0	0	1	0	0	0	17104	1261	44	3	2883	3	USP33	1	78207427	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	21034184	78207427	171043194	5	30812										
NRAS	4893	hgsc.bcm.edu	37	chr1	115258747	115258747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtgcgcttttcccaacaccaCctgctccaaccaccaccagt	5	19	0	0	rs121913237		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:115258747C>T	ENST00000369535.4	-	2	288	c.35G>A	c.(34-36)gGt>gAt	p.G12D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	12			G -> C (in leukemia). {ECO:0000269|PubMed:2998510}.|G -> D (in KNEN). {ECO:0000269|PubMed:22499344}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(375)|p.G12V(59)|p.G12A(42)|p.G12N(2)|p.G12E(1)|p.G12P(1)|p.G12Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		CCCAACACCACCTGCTCCAAC	0.493	G12D(697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(HEC151_ENDOMETRIUM)|G12D(KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	481	Substitution - Missense(481)	haematopoietic_and_lymphoid_tissue(375)|skin(59)|large_intestine(21)|testis(5)|thyroid(4)|central_nervous_system(3)|endometrium(3)|biliary_tract(3)|ovary(3)|soft_tissue(2)|lung(2)|prostate(1)	1						C	ASP/GLY	0,4406		0,0,2203	206	184	191	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	35	5.6	1	1	dbSNP_133	191	1,8599	1.2+/-3.3	0,1,4299	no	missense	NRAS	NM_002524.4	94	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	12/190	115258747	1,13005	2203	4300	6503	115060270	SO:0001583	missense	4893	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.35G>A	1.37:g.115258747C>T	ENSP00000358548:p.Gly12Asp		115060270	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	35	5.524414	0.96431	0.0	1.16E-4	ENSG00000213281	ENST00000369535	T	0.78595	-1.19	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000025	D	0.85252	0.5654	M	0.92604	3.325	0.80722	D	1	B	0.32467	0.372	B	0.42827	0.399	D	0.86173	0.1601	10	0.87932	D	0	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	12	P01111	RASN_HUMAN	D	12	ENSP00000358548:G12D	ENSP00000358548:G12D	G	-	2	0	NRAS	115060270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT		0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115258747	C	T	115258747	3	4	115	1	0	0	0	0	1	0	0	0	10671	507	18	3	550	3	NRAS	1	115258747	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	37051320	115258747	133991874	6	30813										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206712	116206712	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggtccgcattttggactctcGggaccggaattaccagggca	13	11	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:116206712G>A	ENST00000355485.2	+	4	906	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	VANGL1_ENST00000369509.1_Missense_Mutation_p.R212Q|VANGL1_ENST00000369510.4_Missense_Mutation_p.R210Q|VANGL1_ENST00000310260.3_Missense_Mutation_p.R212Q	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	212					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGGACTCTCGGGACCGGAAT	0.517																																																0			1											195	197	196					1																	116206712		2203	4300	6503	116008235	SO:0001583	missense	81839			AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.635G>A	1.37:g.116206712G>A	ENSP00000347672:p.Arg212Gln		116008235	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274091	0.40194	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.73	4.82	0.62117	.	0.120688	0.64402	D	0.000018	T	0.51449	0.1675	N	0.25890	0.77	0.39974	D	0.974838	B;B	0.15930	0.012;0.015	B;B	0.15052	0.007;0.012	T	0.50939	-0.8768	10	0.21014	T	0.42	2.8345	9.7263	0.40333	0.197:0.0:0.803:0.0	.	210;212	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	Q	212;210;212;212	ENSP00000347672:R212Q;ENSP00000358523:R210Q;ENSP00000310800:R212Q;ENSP00000358522:R212Q	ENSP00000310800:R212Q	R	+	2	0	VANGL1	116008235	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.819000	0.62664	1.582000	0.49881	-0.142000	0.14014	CGG		0.517	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116206712	G	A	116206712	3	1	115	1	0	0	0	0	1	0	0	0	17159	1116	39	1	645	1	VANGL1	1	116206712	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	947965	116206712	133043909	7	30814										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120438740	120438740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttgggccacaaatggaggaCgtgcttcttgccttttaact	10	10	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:120438740C>T	ENST00000369400.1	-	1	378	c.220G>A	c.(220-222)Gtc>Atc	p.V74I		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	74					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	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)		AAATGGAGGACGTGCTTCTTG	0.532																																																0			1											86	78	80					1																	120438740		2203	4300	6503	120240263	SO:0001583	missense	11085			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.220G>A	1.37:g.120438740C>T	ENSP00000358407:p.Val74Ile		120240263	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.211325	0.39102	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.06528	3.29	4.75	1.75	0.24633	Peptidase M12B, propeptide (1);	0.204212	0.24211	N	0.040530	T	0.01222	0.0040	L	0.28504	0.86	0.09310	N	1	P	0.42375	0.778	B	0.38921	0.285	T	0.47535	-0.9110	10	0.18710	T	0.47	.	4.984	0.14180	0.0:0.6301:0.1749:0.1951	.	74	Q9UKF2	ADA30_HUMAN	I	74	ENSP00000358407:V74I	ENSP00000358407:V74I	V	-	1	0	ADAM30	120240263	0.000000	0.05858	0.004000	0.12327	0.681000	0.39784	-0.505000	0.06367	0.597000	0.29811	0.455000	0.32223	GTC		0.532	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		T	120438740	C	T	120438740	3	4	115	1	0	0	0	0	1	0	0	0	248	536	19	1	2156	1	ADAM30	1	120438740	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	4232028	120438740	128811881	8	30815										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120466369	120466369	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtacaccatgagttccccctGggagtcccgcttaatgcgca	10	14	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:120466369G>T	ENST00000256646.2	-	26	4969	c.4750C>A	c.(4750-4752)Cag>Aag	p.Q1584K	NOTCH2_ENST00000493703.1_5'UTR	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1584	Negative regulatory region (NRR).				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.Q1584*(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGTTCCCCCTGGGAGTCCCGC	0.542			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Nonsense(1)	lung(1)	1											86	84	85					1																	120466369		2203	4300	6503	120267892	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4750C>A	1.37:g.120466369G>T	ENSP00000256646:p.Gln1584Lys		120267892	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	0.248	-1.008605	0.02112	.	.	ENSG00000134250	ENST00000256646	D	0.85171	-1.95	5.94	4.08	0.47627	Notch, NOD domain (1);	0.000000	0.35903	U	0.002913	T	0.48677	0.1513	N	0.24115	0.695	0.31239	N	0.695464	B	0.33777	0.425	B	0.31812	0.136	T	0.44726	-0.9309	10	0.06236	T	0.91	.	6.2596	0.20893	0.0701:0.1331:0.6586:0.1382	.	1584	Q04721	NOTC2_HUMAN	K	1584	ENSP00000256646:Q1584K	ENSP00000256646:Q1584K	Q	-	1	0	NOTCH2	120267892	0.980000	0.34600	0.814000	0.32528	0.266000	0.26442	1.880000	0.39628	0.863000	0.35553	-0.268000	0.10319	CAG		0.542	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120466369	G	T	120466369	3	4	115	1	0	0	0	0	1	0	0	0	10579	1357	47	2	2701	2	NOTCH2	1	120466369	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	27629	120466369	128784252	9	30816										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155491264	155491264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gactctttcttgaaaaacctTcggaatcagaacccaatcct	5	12	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:155491264T>C	ENST00000368346.3	-	2	686	c.47A>G	c.(46-48)gAa>gGa	p.E16G	ASH1L_ENST00000548830.1_Missense_Mutation_p.E16G|ASH1L_ENST00000392403.3_Missense_Mutation_p.E16G			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	16					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGAAAAACCTTCGGAATCAGA	0.398																																																0			1											169	165	166					1																	155491264		2203	4300	6503	153757888	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.47A>G	1.37:g.155491264T>C	ENSP00000357330:p.Glu16Gly		153757888	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	T	24.9	4.579297	0.86645	.	.	ENSG00000116539	ENST00000368346;ENST00000392403;ENST00000548830	D;D	0.91521	-2.86;-2.86	6.03	6.03	0.97812	.	0.064498	0.64402	D	0.000017	T	0.75874	0.3909	N	0.08118	0	0.43569	D	0.995899	P;P	0.37330	0.455;0.59	B;B	0.37239	0.123;0.244	T	0.83257	-0.0050	10	0.87932	D	0	.	14.8022	0.69924	0.0:0.0:0.0:1.0	.	16;16	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	16	ENSP00000357330:E16G;ENSP00000376204:E16G	ENSP00000357330:E16G	E	-	2	0	ASH1L	153757888	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.721000	0.68477	2.313000	0.78055	0.455000	0.32223	GAA		0.398	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155491264	T	C	155491264	3	2	115	1	0	0	0	0	1	0	0	0	1042	1783	62	4	8955	4	ASH1L	1	155491264	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	35024895	155491264	93759357	10	30817										
FCRL4	83417	hgsc.bcm.edu	37	chr1	157559005	157559005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctttctcacctgaagaaaagAgcaagcgcacagggttactt	9	10	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:157559005A>G	ENST00000271532.1	-	3	431	c.296T>C	c.(295-297)cTc>cCc	p.L99P	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	99					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L99R(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TGAAGAAAAGAGCAAGCGCAC	0.493																																																1	Substitution - Missense(1)	ovary(1)	1											63	68	66					1																	157559005		2203	4300	6503	155825629	SO:0001583	missense	83417			AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.296T>C	1.37:g.157559005A>G	ENSP00000271532:p.Leu99Pro		155825629	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	A	8.570	0.879827	0.17467	.	.	ENSG00000163518	ENST00000271532	T	0.19394	2.15	4.2	-8.41	0.00961	Immunoglobulin subtype (1);	4.121640	0.01047	N	0.004417	T	0.03305	0.0096	L	0.31664	0.95	0.09310	N	1	B	0.22800	0.075	B	0.25759	0.063	T	0.21415	-1.0246	10	0.30078	T	0.28	.	1.5384	0.02550	0.1751:0.115:0.3146:0.3954	.	99	Q96PJ5	FCRL4_HUMAN	P	99	ENSP00000271532:L99P	ENSP00000271532:L99P	L	-	2	0	FCRL4	155825629	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.190000	0.01247	-1.651000	0.01504	-0.410000	0.06199	CTC		0.493	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		G	157559005	A	G	157559005	3	3	115	1	0	0	0	0	1	0	0	0	5816	304	11	4	1291	4	FCRL4	1	157559005	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	2067741	157559005	91691616	11	30818										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158609792	158609792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgttccttcagctgttccagTtgctcctaacccaaggagag	9	12	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:158609792T>C	ENST00000368147.4	-	34	4923	c.4743A>G	c.(4741-4743)caA>caG	p.Q1581Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1581					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.Q1581H(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GCTGTTCCAGTTGCTCCTAAC	0.473																																																1	Substitution - Missense(1)	breast(1)	1											165	147	153					1																	158609792		1936	4144	6080	156876416	SO:0001819	synonymous_variant	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4743A>G	1.37:g.158609792T>C			156876416	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158609792	T	C	158609792	2	2	115	1	0	0	0	0	0	0	0	1	15155	1722	60	4		4	SPTA1	1	158609792	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1050787	158609792	90640829	12	30819										
FCRL6	343413	hgsc.bcm.edu	37	chr1	159783322	159783322	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cccacagctccaggtggagaGcagtgcccactatatgccaa	10	14	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:159783322G>T	ENST00000368106.3	+	7	1054	c.1053G>T	c.(1051-1053)gaG>gaT	p.E351D	FCRL6_ENST00000321935.6_Missense_Mutation_p.E358D|FCRL6_ENST00000339348.5_Missense_Mutation_p.E351D|FCRL6_ENST00000392235.3_Missense_Mutation_p.E256D	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	351						external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					CAGGTGGAGAGCAGTGCCCAC	0.557																																																0			1											113	101	105					1																	159783322		2203	4300	6503	158049946	SO:0001583	missense	343413			AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.1053G>T	1.37:g.159783322G>T	ENSP00000357086:p.Glu351Asp		158049946	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Missense_Mutation	SNP	ENST00000368106.3	37	CCDS30912.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007244	0.35415	.	.	ENSG00000181036	ENST00000321935;ENST00000339348;ENST00000392235;ENST00000368106	T;T;T;T	0.01126	5.37;5.31;5.68;5.3	3.94	2.05	0.26809	.	.	.	.	.	T	0.00552	0.0018	L	0.27053	0.805	0.09310	N	1	D;D;P;D	0.54207	0.965;0.965;0.9;0.965	P;P;B;P	0.50352	0.558;0.638;0.227;0.558	T	0.54057	-0.8350	9	0.27785	T	0.31	.	6.2205	0.20679	0.2323:0.0:0.7677:0.0	.	351;256;351;358	Q6DN72-3;Q6DN72-4;Q6DN72;Q6DN72-2	.;.;FCRL6_HUMAN;.	D	358;351;256;351	ENSP00000320625:E358D;ENSP00000340949:E351D;ENSP00000376068:E256D;ENSP00000357086:E351D	ENSP00000320625:E358D	E	+	3	2	FCRL6	158049946	0.077000	0.21312	0.060000	0.19600	0.005000	0.04900	1.255000	0.32909	0.451000	0.26802	-0.258000	0.10820	GAG		0.557	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310		T	159783322	G	T	159783322	3	4	115	1	0	0	0	0	1	0	0	0	5818	962	34	2	1079	2	FCRL6	1	159783322	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	1173530	159783322	89467299	13	30820										
DCAF6	55827	hgsc.bcm.edu	37	chr1	168032997	168032997	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	catcgcaactccaggacaatGgtaccaaatgttcatggcat	8	11	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:168032997G>A	ENST00000312263.6	+	15	2370	c.2166G>A	c.(2164-2166)atG>atA	p.M722I	DCAF6_ENST00000367840.3_Splice_Site_p.M813I|DCAF6_ENST00000432587.2_Splice_Site_p.M782I|DCAF6_ENST00000367843.3_Splice_Site_p.M742I	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	722					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						CCAGGACAATGGTACCAAATG	0.363																																																0			1											93	92	92					1																	168032997		2203	4300	6503	166299621	SO:0001630	splice_region_variant	0			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2166+1G>A	1.37:g.168032997G>A			166299621	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953377	0.73902	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.084494	0.85682	D	0.000000	D	0.84165	0.5412	L	0.58101	1.795	.	.	.	B;B;B;B;D	0.56968	0.005;0.402;0.028;0.264;0.978	B;B;B;B;D	0.65684	0.035;0.17;0.159;0.235;0.937	T	0.79067	-0.1955	9	0.20046	T	0.44	.	19.7122	0.96100	0.0:0.0:1.0:0.0	.	782;395;813;722;742	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	I	742;782;722;813	ENSP00000356817:M742I;ENSP00000396238:M782I;ENSP00000311949:M722I;ENSP00000356814:M813I	ENSP00000311949:M722I	M	+	3	0	DCAF6	166299621	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.296000	0.96104	2.681000	0.91329	0.561000	0.74099	ATG		0.363	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	Missense_Mutation	A	168032997	G	A	168032997	5	1	115	1	0	0	0	0	0	0	1	0	4280	1362	47	3	2288	3	DCAF6	1	168032997	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10	8249675	168032997	81217624	14	30821										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181727109	181727109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgcatcgacttcgccatcagCgccaaacctctcacccgcta	6	18	2	0	rs571237279		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:181727109C>T	ENST00000367573.2	+	31	4356	c.4356C>T	c.(4354-4356)agC>agT	p.S1452S	CACNA1E_ENST00000526775.1_Silent_p.S1433S|CACNA1E_ENST00000357570.5_Silent_p.S1403S|CACNA1E_ENST00000367570.1_Silent_p.S1452S|CACNA1E_ENST00000360108.3_Silent_p.S1433S|CACNA1E_ENST00000358338.5_Silent_p.S1384S|CACNA1E_ENST00000367567.4_Silent_p.S1059S	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1452					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TCGCCATCAGCGCCAAACCTC	0.522													C|||	1	0.000199681	8e-04	0	5008	,	,		19615	0		0	False		,,,				2504	0															0			1											147	153	151					1																	181727109		2139	4233	6372	179993732	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4356C>T	1.37:g.181727109C>T			179993732	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.522	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181727109	C	T	181727109	2	4	115	1	0	0	0	0	0	0	0	1	2548	767	27	1		1	CACNA1E	1	181727109	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	13694112	181727109	67523512	15	30822										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186059939	186059939	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccaagtgatgtcagtgtcctTctaggagaaaatgttgagct	11	7	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:186059939T>C	ENST00000271588.4	+	64	10006	c.9777T>C	c.(9775-9777)ctT>ctC	p.L3259L	HMCN1_ENST00000367492.2_Silent_p.L3259L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3259	Ig-like C2-type 31.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.L3259L(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TCAGTGTCCTTCTAGGAGAAA	0.398																																																1	Substitution - coding silent(1)	ovary(1)	1											131	126	128					1																	186059939		2203	4300	6503	184326562	SO:0001819	synonymous_variant	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9777T>C	1.37:g.186059939T>C			184326562	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186059939	T	C	186059939	2	2	115	1	0	0	0	0	0	0	0	1	7241	1770	62	4		4	HMCN1	1	186059939	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	4332830	186059939	63190682	16	30823										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121955	186121955	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttgctgctagatatcgttgtGagtggctatgtcctacagct	11	8	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:186121955G>A	ENST00000271588.4	+	96	15199	c.14970G>A	c.(14968-14970)gtG>gtA	p.V4990V	HMCN1_ENST00000367492.2_Silent_p.V4990V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4990	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATATCGTTGTGAGTGGCTATG	0.428																																																0			1											237	206	216					1																	186121955		2203	4300	6503	184388578	SO:0001819	synonymous_variant	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14970G>A	1.37:g.186121955G>A			184388578	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186121955	G	A	186121955	2	1	115	1	0	0	0	0	0	0	0	1	7241	1277	45	3		3	HMCN1	1	186121955	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	62016	186121955	63128666	17	30824										
CRB1	23418	hgsc.bcm.edu	37	chr1	197397061	197397061	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggaattctttccaaatccaaCaaacaatgcatctctcaatc	3	12	3	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:197397061C>A	ENST00000367400.3	+	7	2741	c.2606C>A	c.(2605-2607)aCa>aAa	p.T869K	CRB1_ENST00000538660.1_Intron|CRB1_ENST00000535699.1_Missense_Mutation_p.T800K|CRB1_ENST00000367399.2_Missense_Mutation_p.T757K|CRB1_ENST00000367397.1_Missense_Mutation_p.T250K|CRB1_ENST00000544212.1_Missense_Mutation_p.T350K	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	869	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CCAAATCCAACAAACAATGCA	0.393																																																0			1											88	82	84					1																	197397061		2203	4300	6503	195663684	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2606C>A	1.37:g.197397061C>A	ENSP00000356370:p.Thr869Lys		195663684	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	2.081	-0.410741	0.04799	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T	0.79247	-1.25;-0.96;-0.96;-0.96;-0.96	4.98	-0.891	0.10573	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.60483	0.2272	L	0.43701	1.375	0.09310	N	1	B;B;B;B	0.12630	0.006;0.003;0.001;0.001	B;B;B;B	0.11329	0.006;0.004;0.003;0.002	T	0.44452	-0.9327	9	0.05959	T	0.93	.	4.4955	0.11835	0.3113:0.3603:0.0:0.3284	.	800;757;518;869	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	K	800;869;757;350;250;518	ENSP00000438786:T800K;ENSP00000356370:T869K;ENSP00000356369:T757K;ENSP00000444556:T350K;ENSP00000356367:T250K	ENSP00000356367:T250K	T	+	2	0	CRB1	195663684	0.000000	0.05858	0.102000	0.21198	0.032000	0.12392	-0.901000	0.04093	-0.045000	0.13468	0.555000	0.69702	ACA		0.393	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197397061	C	A	197397061	3	1	115	1	0	0	0	0	1	0	0	0	3854	478	17	2	2632	2	CRB1	1	197397061	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	11275106	197397061	51853560	18	30825										
DDX59	83479	hgsc.bcm.edu	37	chr1	200619724	200619724	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggaattgtggctgaaaccaaAatggtctgacaatcattagg	11	6	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:200619724A>G	ENST00000331314.6	-	5	1356	c.1143T>C	c.(1141-1143)atT>atC	p.I381I	DDX59_ENST00000447706.2_Silent_p.I381I|DDX59_ENST00000367348.3_Silent_p.I381I	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	381	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						CTGAAACCAAAATGGTCTGAC	0.368																																																0			1											99	91	93					1																	200619724		2203	4300	6503	198886347	SO:0001819	synonymous_variant	83479			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.1143T>C	1.37:g.200619724A>G			198886347	Q6PJL2|Q8IVW3|Q9H0W3	Silent	SNP	ENST00000331314.6	37	CCDS30964.1																																																																																				0.368	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		G	200619724	A	G	200619724	2	3	115	1	0	0	0	0	0	0	0	1	4382	10	1	4		4	DDX59	1	200619724	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	3222663	200619724	48630897	19	30826										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211486113	211486113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tattgcagatgtaattggcaAcaagactgttggccaagtga	11	6	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:211486113A>G	ENST00000367005.4	+	10	1094	c.953A>G	c.(952-954)aAc>aGc	p.N318S	RCOR3_ENST00000452621.2_Missense_Mutation_p.N376S|RCOR3_ENST00000526255.1_3'UTR|RCOR3_ENST00000367006.4_Intron|RCOR3_ENST00000419091.2_Missense_Mutation_p.N376S	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	318	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.N318S(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		GTAATTGGCAACAAGACTGTT	0.428																																																1	Substitution - Missense(1)	ovary(1)	1											116	116	116					1																	211486113		2203	4300	6503	209552736	SO:0001583	missense	55758			AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.953A>G	1.37:g.211486113A>G	ENSP00000355972:p.Asn318Ser		209552736	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	37	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.718337	0.30503	.	.	ENSG00000117625	ENST00000452621;ENST00000419091;ENST00000367005;ENST00000529763	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.22	4.07	0.47477	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.080945	0.85682	D	0.000000	T	0.44726	0.1307	N	0.20986	0.625	0.40443	D	0.980068	P;D;P	0.57571	0.882;0.98;0.931	B;P;P	0.59948	0.414;0.866;0.55	T	0.38067	-0.9678	10	0.41790	T	0.15	-9.4574	12.4824	0.55852	0.8599:0.1401:0.0:0.0	.	376;318;376	Q9P2K3-3;Q9P2K3;Q9P2K3-4	.;RCOR3_HUMAN;.	S	376;376;318;136	ENSP00000398558:N376S;ENSP00000413929:N376S;ENSP00000355972:N318S;ENSP00000437048:N136S	ENSP00000355972:N318S	N	+	2	0	RCOR3	209552736	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.141000	0.77330	0.908000	0.36671	0.528000	0.53228	AAC		0.428	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		G	211486113	A	G	211486113	3	3	115	1	0	0	0	0	1	0	0	0	13221	43	2	4	1169	4	RCOR3	1	211486113	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	10866389	211486113	37764508	20	30827										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494622	228494622	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgcgcctgtgcggttcctcCgagagctgcagcaccaggag	14	14	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:228494622C>T	ENST00000422127.1	+	45	11991	c.11947C>T	c.(11947-11949)Cga>Tga	p.R3983*	OBSCN_ENST00000570156.2_Nonsense_Mutation_p.R4940*|OBSCN_ENST00000366709.4_Nonsense_Mutation_p.R1102*|OBSCN_ENST00000366707.4_Nonsense_Mutation_p.R1617*|OBSCN_ENST00000284548.11_Nonsense_Mutation_p.R3983*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3983	Ig-like 41.		R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGGTTCCTCCGAGAGCTGCA	0.652																																																0			1											11	13	13					1																	228494622		2076	4198	6274	226561245	SO:0001587	stop_gained	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11947C>T	1.37:g.228494622C>T	ENSP00000409493:p.Arg3983*		226561245	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	62	71.054468	0.99992	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.	.	.	5.75	2.5	0.30297	.	0.744078	0.12001	N	0.508834	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	9.7265	0.40335	0.611:0.2855:0.1035:0.0	.	.	.	.	X	3983;3983;1617;1102	.	ENSP00000284548:R3983X	R	+	1	2	OBSCN	226561245	0.000000	0.05858	0.034000	0.17996	0.011000	0.07611	-1.013000	0.03645	0.730000	0.32425	0.462000	0.41574	CGA		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228494622	C	T	228494622	4	4	115	1	0	0	0	0	0	1	0	0	10843	644	23	1	12121	1	OBSCN	1	228494622	Nonsense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	17008509	228494622	20755999	21	30828										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650410	232650410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttcagggaacccaaaagggaCcattgctttgtggtcataat	10	8	2	0	rs201202325		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:232650410C>T	ENST00000366630.1	-	2	1034	c.676G>A	c.(676-678)Gtc>Atc	p.V226I	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.V226I			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	226					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CCAAAAGGGACCATTGCTTTG	0.468																																																0			1						C	ILE/VAL	0,3762		0,0,1881	101	100	100		676	1.2	0	1		100	1,8215		0,1,4107	no	missense	SIPA1L2	NM_020808.3	29	0,1,5988	TT,TC,CC		0.0122,0.0,0.0083	benign	226/1723	232650410	1,11977	1881	4108	5989	230717033	SO:0001583	missense	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.676G>A	1.37:g.232650410C>T	ENSP00000355589:p.Val226Ile		230717033	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	9.976	1.226787	0.22542	0.0	1.22E-4	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78364	-1.17;-1.17	5.19	1.24	0.21308	.	0.514786	0.21155	N	0.079253	T	0.55369	0.1916	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45411	-0.9263	10	0.41790	T	0.15	-2.0194	8.9806	0.35964	0.0:0.5661:0.0:0.4339	.	226	Q9P2F8	SI1L2_HUMAN	I	226	ENSP00000355589:V226I;ENSP00000262861:V226I	ENSP00000262861:V226I	V	-	1	0	SIPA1L2	230717033	0.884000	0.30299	0.001000	0.08648	0.971000	0.66376	1.518000	0.35877	0.076000	0.16826	-0.142000	0.14014	GTC		0.468	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232650410	C	T	232650410	3	4	115	1	0	0	0	0	1	0	0	0	14367	507	18	3	4576	3	SIPA1L2	1	232650410	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	4155788	232650410	16600211	22	30829										
OR14I1	401994	hgsc.bcm.edu	37	chr1	248844879	248844879	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaagagcatgatgacaatgaGctggggggagcaggtggaga	18	4	0	5			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr1:248844879G>T	ENST00000342623.3	-	1	750	c.727C>A	c.(727-729)Ctc>Atc	p.L243I		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						ATGACAATGAGCTGGGGGGAG	0.463																																																0			1											96	92	93					1																	248844879		2203	4300	6503	246911502	SO:0001583	missense	401994				CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"GPCR / Class A : Olfactory receptors"	19575	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BU, member 1"	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.727C>A	1.37:g.248844879G>T	ENSP00000339726:p.Leu243Ile		246911502		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	.	.	.	.	.	.	.	.	.	.	.	14.60	2.583125	0.46006	.	.	ENSG00000189181	ENST00000342623	T	0.43294	0.95	3.36	-1.29	0.09288	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36200	N	0.002722	T	0.52805	0.1757	M	0.80183	2.485	0.09310	N	1	P	0.45827	0.867	P	0.60415	0.874	T	0.44112	-0.9349	10	0.51188	T	0.08	.	3.4928	0.07644	0.4484:0.0:0.3723:0.1792	.	243	A6ND48	O14I1_HUMAN	I	243	ENSP00000339726:L243I	ENSP00000339726:L243I	L	-	1	0	OR14I1	246911502	0.071000	0.21146	0.000000	0.03702	0.183000	0.23260	0.181000	0.16880	-0.186000	0.10533	0.543000	0.68304	CTC		0.463	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734		T	248844879	G	T	248844879	3	4	115	1	0	0	0	0	1	0	0	0	10978	971	34	2	212	2	OR14I1	1	248844879	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	16194469	248844879	405742	23	30830										
PPM1G	5496	hgsc.bcm.edu	37	chr2	27605446	27605446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgttcctcaggtggcaggtTcttgtttctcttatagaagt	10	8	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:27605446T>C	ENST00000344034.4	-	8	1492	c.1228A>G	c.(1228-1230)Aac>Gac	p.N410D	ZNF513_ENST00000323703.6_5'Flank|PPM1G_ENST00000350803.4_Missense_Mutation_p.N410D|ZNF513_ENST00000407879.1_5'Flank	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G	410					cell cycle arrest (GO:0007050)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GGTGGCAGGTTCTTGTTTCTC	0.473																																																0			2											307	294	298					2																	27605446		2203	4300	6503	27458950	SO:0001583	missense	5496			Y13936	CCDS1752.1	2p23.3	2012-04-17	2010-03-05		ENSG00000115241	ENSG00000115241	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9278	protein-coding gene	gene with protein product	"PP2C, gamma", "protein phosphatase 2C, gamma isoform"	605119	"protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform"			9276438	Standard	NM_177983		Approved	PP2CG, PP2Cgamma	uc002rkl.4	O15355	OTTHUMG00000097788	ENST00000344034.4:c.1228A>G	2.37:g.27605446T>C	ENSP00000342778:p.Asn410Asp		27458950		Missense_Mutation	SNP	ENST00000344034.4	37	CCDS1752.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.140351	0.37825	.	.	ENSG00000115241	ENST00000344034;ENST00000350803;ENST00000544412;ENST00000395543	T;T	0.09350	2.99;2.99	5.63	4.46	0.54185	Protein phosphatase 2C-like (5);	0.094910	0.64402	D	0.000001	T	0.05547	0.0146	N	0.13043	0.29	0.37711	D	0.924582	B;P	0.37176	0.018;0.586	B;B	0.33846	0.055;0.171	T	0.32268	-0.9913	10	0.07813	T	0.8	-11.7167	11.8211	0.52238	0.0:0.0:0.147:0.853	.	211;410	Q59GB2;O15355	.;PPM1G_HUMAN	D	410;410;393;211	ENSP00000342778:N410D;ENSP00000264714:N410D	ENSP00000342778:N410D	N	-	1	0	PPM1G	27458950	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.380000	0.44327	0.955000	0.37878	-0.313000	0.08912	AAC		0.473	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	NM_002707		C	27605446	T	C	27605446	3	2	115	1	0	0	0	0	1	0	0	0	12374	1783	62	4	424	4	PPM1G	2	27605446	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10		27605446	215593927	24	30831										
GCKR	2646	hgsc.bcm.edu	37	chr2	27730108	27730108	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttaaacttcccagatttccGagatgtccgtggctttctca	7	12	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:27730108G>T	ENST00000264717.2	+	13	1136	c.1073G>T	c.(1072-1074)cGa>cTa	p.R358L	GCKR_ENST00000424318.2_Missense_Mutation_p.R168L	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	358	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					CCAGATTTCCGAGATGTCCGT	0.488																																																0			2											242	252	249					2																	27730108		2203	4300	6503	27583612	SO:0001583	missense	11183			Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"glucokinase (hexokinase 4) regulatory protein"			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1073G>T	2.37:g.27730108G>T	ENSP00000264717:p.Arg358Leu		27583612	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.24|11.24	1.581850|1.581850	0.28180|0.28180	.|.	.|.	ENSG00000084734|ENSG00000084734	ENST00000411584|ENST00000264717;ENST00000424318	.|D;D	.|0.82893	.|-1.66;-1.66	4.8|4.8	-4.02|-4.02	0.04034|0.04034	.|Sugar isomerase (SIS) (1);	.|1.347880	.|0.04756	.|N	.|0.425533	.|T	.|0.69504	.|0.3118	N|N	0.13098|0.13098	0.295|0.295	0.28353|0.28353	N|N	0.920795|0.920795	.|B;B;B	.|0.14438	.|0.01;0.002;0.002	.|B;B;B	.|0.14023	.|0.01;0.004;0.004	.|T	.|0.56135	.|-0.8029	.|10	.|0.41790	.|T	.|0.15	3.6618|3.6618	10.9419|10.9419	0.47278|0.47278	0.6396:0.0:0.3604:0.0|0.6396:0.0:0.3604:0.0	.|.	.|168;356;358	.|F5H1P6;A8K731;Q14397	.|.;.;GCKR_HUMAN	X|L	59|358;168	.|ENSP00000264717:R358L;ENSP00000409109:R168L	.|ENSP00000264717:R358L	E|R	+|+	1|2	0|0	GCKR|GCKR	27583612|27583612	0.000000|0.000000	0.05858|0.05858	0.317000|0.317000	0.25265|0.25265	0.659000|0.659000	0.38960|0.38960	-1.682000|-1.682000	0.01935|0.01935	-0.701000|-0.701000	0.05063|0.05063	-0.137000|-0.137000	0.14449|0.14449	GAG|CGA		0.488	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486		T	27730108	G	T	27730108	3	4	115	1	0	0	0	0	1	0	0	0	6314	1058	37	2	1123	2	GCKR	2	27730108	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	124662	27730108	215469265	25	30832										
ALK	238	hgsc.bcm.edu	37	chr2	29443586	29443586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	actcaccgggcgagggcgggTctctcggaggaaggacttga	17	10	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:29443586T>C	ENST00000389048.3	-	23	4537	c.3631A>G	c.(3631-3633)Acc>Gcc	p.T1211A	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CGAGGGCGGGTCTCTCGGAGG	0.607			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	0			2											46	45	46					2																	29443586		2203	4300	6503	29297090	SO:0001583	missense	238	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3631A>G	2.37:g.29443586T>C	ENSP00000373700:p.Thr1211Ala		29297090	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	t	15.32	2.797373	0.50208	.	.	ENSG00000171094	ENST00000389048	D	0.82255	-1.59	5.59	5.59	0.84812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49305	U	0.000150	T	0.73659	0.3615	N	0.21324	0.655	0.80722	D	1	B	0.12630	0.006	B	0.19946	0.027	T	0.67879	-0.5556	9	.	.	.	.	16.0904	0.81088	0.0:0.0:0.0:1.0	.	1211	Q9UM73	ALK_HUMAN	A	1211	ENSP00000373700:T1211A	.	T	-	1	0	ALK	29297090	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.238000	0.72350	2.256000	0.74724	0.524000	0.50904	ACC		0.607	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	29443586	T	C	29443586	3	2	115	1	0	0	0	0	1	0	0	0	525	1667	58	4	1259	4	ALK	2	29443586	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1713478	29443586	213755787	26	30833										
LCLAT1	253558	hgsc.bcm.edu	37	chr2	30682500	30682500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgcattccaggggaagggaaAttgtggtgcttctgaaccca	13	8	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:30682500A>G	ENST00000309052.4	+	2	231	c.22A>G	c.(22-24)Att>Gtt	p.I8V	LCLAT1_ENST00000540623.1_5'UTR|LCLAT1_ENST00000319406.4_Missense_Mutation_p.I8V|LCLAT1_ENST00000359433.1_Missense_Mutation_p.I8V|LCLAT1_ENST00000491680.2_Intron|LCLAT1_ENST00000379509.3_Intron	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	8					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						GGGAAGGGAAATTGTGGTGCT	0.443																																																0			2											284	274	277					2																	30682500		2203	4300	6503	30536004	SO:0001583	missense	253558			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.22A>G	2.37:g.30682500A>G	ENSP00000310551:p.Ile8Val		30536004	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	.	.	.	.	.	.	.	.	.	.	A	2.998	-0.206618	0.06180	.	.	ENSG00000172954	ENST00000319406;ENST00000309052;ENST00000359433;ENST00000497423	T;T;T	0.49720	0.77;1.5;0.77	3.28	-1.88	0.07713	.	24.407300	0.00664	N	0.000601	T	0.29256	0.0728	N	0.08118	0	0.09310	N	0.999998	B;B	0.14012	0.009;0.0	B;B	0.08055	0.003;0.0	T	0.35051	-0.9804	10	0.87932	D	0	0.1381	7.4991	0.27507	0.4713:0.0:0.5287:0.0	.	8;8	Q6UWP7-2;Q6UWP7	.;LCLT1_HUMAN	V	8	ENSP00000368826:I8V;ENSP00000310551:I8V;ENSP00000352406:I8V	ENSP00000310551:I8V	I	+	1	0	LCLAT1	30536004	0.134000	0.22483	0.000000	0.03702	0.005000	0.04900	0.183000	0.16919	-0.388000	0.07797	0.533000	0.62120	ATT		0.443	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		G	30682500	A	G	30682500	3	3	115	1	0	0	0	0	1	0	0	0	8699	101	4	4	24	4	LCLAT1	2	30682500	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	1238914	30682500	212516873	27	30834										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70064744	70064744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttgaatggtgaaaacagtgAcattaagatttgtgctctag	10	4	1	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:70064744A>G	ENST00000282570.3	+	2	577	c.326A>G	c.(325-327)gAc>gGc	p.D109G	GMCL1_ENST00000468386.2_3'UTR	NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	109	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)		p.D109G(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						GAAAACAGTGACATTAAGATT	0.259																																																1	Substitution - Missense(1)	ovary(1)	2											42	44	44					2																	70064744		2192	4291	6483	69918248	SO:0001583	missense	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.326A>G	2.37:g.70064744A>G	ENSP00000282570:p.Asp109Gly		69918248	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	37	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281341	0.80692	.	.	ENSG00000087338	ENST00000282570	D	0.91351	-2.83	4.92	4.92	0.64577	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.96750	0.8939	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97655	1.0157	10	0.87932	D	0	-32.076	12.832	0.57750	1.0:0.0:0.0:0.0	.	109	Q96IK5	GMCL1_HUMAN	G	109	ENSP00000282570:D109G	ENSP00000282570:D109G	D	+	2	0	GMCL1	69918248	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.131000	0.89601	2.181000	0.69327	0.455000	0.32223	GAC		0.259	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70064744	A	G	70064744	3	3	115	1	0	0	0	0	1	0	0	0	6505	275	10	4	332	4	GMCL1	2	70064744	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	39382244	70064744	173134629	28	30835										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315174	70315174	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cagcaggcccccggtcacccTgaggctggtggtgccggcca	15	16	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:70315174T>A	ENST00000303577.5	+	1	590	c.299T>A	c.(298-300)cTg>cAg	p.L100Q	PCBP1-AS1_ENST00000458698.2_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	100	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L100P(1)|p.L100Q(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						CCGGTCACCCTGAGGCTGGTG	0.602																																					Colon(85;1146 1307 3484 18706 25380)											2	Substitution - Missense(2)	large_intestine(2)	2											59	73	68					2																	70315174		2201	4300	6501	70168678	SO:0001583	missense	5093				CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.299T>A	2.37:g.70315174T>A	ENSP00000305556:p.Leu100Gln		70168678	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	37	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551119	0.65311	.	.	ENSG00000169564	ENST00000303577	T	0.30714	1.52	4.16	4.16	0.48862	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.168590	0.40469	U	0.001094	T	0.60573	0.2279	M	0.91459	3.21	0.54753	D	0.999986	D	0.71674	0.998	D	0.70487	0.969	T	0.69781	-0.5052	10	0.87932	D	0	.	11.8577	0.52449	0.0:0.0:0.0:1.0	.	100	Q15365	PCBP1_HUMAN	Q	100	ENSP00000305556:L100Q	ENSP00000305556:L100Q	L	+	2	0	PCBP1	70168678	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.884000	0.69729	2.120000	0.65058	0.477000	0.44152	CTG		0.602	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70315174	T	A	70315174	3	1	115	1	0	0	0	0	1	0	0	0	11531	1580	55	5	301	5	PCBP1	2	70315174	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	250430	70315174	172884199	29	30836										
INO80B	83444	hgsc.bcm.edu	37	chr2	74684548	74684548	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gcccacctcccgccctcacaGaggagatgctgctgaagcgc	11	17	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:74684548G>T	ENST00000233331.7	+	5	722	c.628G>T	c.(628-630)Gag>Tag	p.E210*	INO80B_ENST00000409917.1_Splice_Site|WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000393972.3_5'Flank|INO80B_ENST00000469849.1_3'UTR|WBP1_ENST00000409737.1_5'Flank	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	210					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						CGCCCTCACAGAGGAGATGCT	0.672																																																0			2											9	10	10					2																	74684548		2184	4280	6464	74538056	SO:0001587	stop_gained	83444			AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"Zinc fingers, HIT-type", "INO80 complex subunits"	13324	protein-coding gene	gene with protein product	"PAP-1 binding protein", "IES2 homolog (S. cerevisiae)"		"high mobility group AT-hook 1-like 4", "zinc finger, HIT type 4"	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.628G>T	2.37:g.74684548G>T	ENSP00000233331:p.Glu210*		74538056		Nonsense_Mutation	SNP	ENST00000233331.7	37	CCDS1942.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.74|12.74	2.029564|2.029564	0.35797|0.35797	.|.	.|.	ENSG00000115274|ENSG00000115274	ENST00000409917|ENST00000233331	.|.	.|.	.|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.115830	.|0.56097	.|D	.|0.000026	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|0.59425	.|D	.|0.04	.|-26.1777	15.0094|15.0094	0.71539|0.71539	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|X	-1|210	.|.	.|ENSP00000233331:E210X	.|E	+|+	.|1	.|0	INO80B|INO80B	74538056|74538056	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.078000|0.078000	0.17371|0.17371	7.176000|7.176000	0.77643|0.77643	2.418000|2.418000	0.82041|0.82041	0.462000|0.462000	0.41574|0.41574	.|GAG		0.672	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288		T	74684548	G	T	74684548	4	4	115	1	0	0	0	0	0	1	0	0	7768	943	33	2	646	2	INO80B	2	74684548	Nonsense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	4369374	74684548	168514825	30	30837										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99013312	99013312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gaacatcaaggggagcaagtCggggaaccgcaggacggcca	16	10	1	0	rs370911601		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:99013312C>T	ENST00000272602.2	+	7	1718	c.1679C>T	c.(1678-1680)tCg>tTg	p.S560L	CNGA3_ENST00000436404.2_Missense_Mutation_p.S542L|CNGA3_ENST00000409937.1_Missense_Mutation_p.S564L|CNGA3_ENST00000393504.1_Missense_Mutation_p.S560L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	560					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GGGAGCAAGTCGGGGAACCGC	0.592																																																0			2						C	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	135	131	132		1625,1679	5.4	0.9	2		132	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	145,145	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	possibly-damaging,possibly-damaging	542/677,560/695	99013312	4,13002	2203	4300	6503	98379744	SO:0001583	missense	1261			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1679C>T	2.37:g.99013312C>T	ENSP00000272602:p.Ser560Leu		98379744	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	37	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706853	0.48412	2.27E-4	3.49E-4	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.97831	-4.46;-4.37;-4.46;-4.56	5.42	5.42	0.78866	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.172665	0.52532	D	0.000075	D	0.95326	0.8483	L	0.41236	1.265	0.46185	D	0.998915	B;B;B	0.32717	0.069;0.112;0.381	B;B;B	0.25884	0.019;0.041;0.064	D	0.94452	0.7668	10	0.72032	D	0.01	.	18.154	0.89686	0.0:1.0:0.0:0.0	.	564;542;560	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	L	560;542;560;564	ENSP00000377140:S560L;ENSP00000410070:S542L;ENSP00000272602:S560L;ENSP00000386761:S564L	ENSP00000272602:S560L	S	+	2	0	CNGA3	98379744	0.000000	0.05858	0.858000	0.33744	0.890000	0.51754	0.666000	0.25097	2.826000	0.97356	0.563000	0.77884	TCG		0.592	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	99013312	C	T	99013312	3	4	115	1	0	0	0	0	1	0	0	0	3604	893	31	1	1705	1	CNGA3	2	99013312	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	24328764	99013312	144186061	31	30838										
AFF3	3899	hgsc.bcm.edu	37	chr2	100210211	100210211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggaggagcgcagctccttgcGgtggctcgctctgttgttgc	16	11	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:100210211G>A	ENST00000409236.2	-	13	2024	c.1912C>T	c.(1912-1914)Cgc>Tgc	p.R638C	AFF3_ENST00000409579.1_Missense_Mutation_p.R663C|AFF3_ENST00000356421.2_Missense_Mutation_p.R663C|AFF3_ENST00000317233.4_Missense_Mutation_p.R638C			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	638					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						AGCTCCTTGCGGTGGCTCGCT	0.682																																																0			2											41	46	44					2																	100210211		2203	4300	6503	99576643	SO:0001583	missense	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1912C>T	2.37:g.100210211G>A	ENSP00000387207:p.Arg638Cys		99576643	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.918514	0.52546	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	4.58	2.57	0.30868	.	0.266767	0.25481	N	0.030361	T	0.77391	0.4123	M	0.74647	2.275	0.49389	D	0.999783	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.984;0.971;0.911	T	0.77327	-0.2629	10	0.66056	D	0.02	.	8.2833	0.31913	0.0:0.1507:0.5394:0.3099	.	791;638;663	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	C	638;663;663;638;638;791;663	ENSP00000317421:R638C;ENSP00000348793:R663C;ENSP00000386834:R663C;ENSP00000387207:R638C	ENSP00000317421:R638C	R	-	1	0	AFF3	99576643	0.975000	0.34042	1.000000	0.80357	0.698000	0.40448	0.399000	0.20916	1.041000	0.40125	0.462000	0.41574	CGC		0.682	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		A	100210211	G	A	100210211	3	1	115	1	0	0	0	0	1	0	0	0	358	1116	39	1	1812	1	AFF3	2	100210211	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	1196899	100210211	142989162	32	30839										
RIF1	55183	hgsc.bcm.edu	37	chr2	152322493	152322493	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaactaagggaacttgatccTtcacttgtgtcagcaaatga	8	8	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:152322493T>C	ENST00000243326.5	+	29	6942	c.6459T>C	c.(6457-6459)ccT>ccC	p.P2153P	RIF1_ENST00000430328.2_Silent_p.P2153P|RIF1_ENST00000428287.2_Silent_p.P2153P|RIF1_ENST00000453091.2_Silent_p.P2153P|RIF1_ENST00000444746.2_Silent_p.P2153P			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		AACTTGATCCTTCACTTGTGT	0.448																																																0			2											112	105	107					2																	152322493		2203	4300	6503	152030739	SO:0001819	synonymous_variant	55791			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.6459T>C	2.37:g.152322493T>C			152030739	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																				0.448	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			C	152322493	T	C	152322493	2	2	115	1	0	0	0	0	0	0	0	1	13396	1596	56	4		4	RIF1	2	152322493	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	52112282	152322493	90876880	33	30840										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163279946	163279946	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttggtgaaagcgaatgaacTcttttactcgcagcatctgc	9	9	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:163279946T>A	ENST00000332142.5	-	9	2153	c.2054A>T	c.(2053-2055)gAg>gTg	p.E685V	KCNH7_ENST00000328032.4_Missense_Mutation_p.E678V	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	685					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.E685G(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GCGAATGAACTCTTTTACTCG	0.443																																					GBM(196;1492 2208 17507 24132 45496)											1	Substitution - Missense(1)	ovary(1)	2											241	224	229					2																	163279946		2203	4300	6503	162988192	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2054A>T	2.37:g.163279946T>A	ENSP00000331727:p.Glu685Val		162988192	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935053	0.92458	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.96940	-4.18;-4.18	5.95	5.95	0.96441	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.98419	0.9474	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.96	D	0.99490	1.0950	10	0.87932	D	0	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	678;685	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	V	685;678	ENSP00000331727:E685V;ENSP00000333781:E678V	ENSP00000333781:E678V	E	-	2	0	KCNH7	162988192	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.279000	0.76181	0.533000	0.62120	GAG		0.443	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		A	163279946	T	A	163279946	3	1	115	1	0	0	0	0	1	0	0	0	8058	1551	54	5	1634	5	KCNH7	2	163279946	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	10957453	163279946	79919427	34	30841										
DLX2	1746	hgsc.bcm.edu	37	chr2	172966865	172966865	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttgacttcagcgttatgcatAccaggctcgttgttggctgg	12	9	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:172966865A>G	ENST00000234198.4	-	1	762		c.e1+1		DLX2_ENST00000466293.2_Splice_Site|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2						brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)	p.?(1)		endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			CGTTATGCATACCAGGCTCGT	0.562																																					GBM(188;775 2993 11256 23072)											1	Unknown(1)	ovary(1)	2											124	117	120					2																	172966865		2203	4300	6503	172675111	SO:0001630	splice_region_variant	9856			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"Homeoboxes / ANTP class : NKL subclass"	2915	protein-coding gene	gene with protein product		126255	"distal-less homeo box 2"			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.400+1T>C	2.37:g.172966865A>G			172675111	B4DMK4|B7ZA14	Splice_Site	SNP	ENST00000234198.4	37	CCDS2248.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894395	0.72639	.	.	ENSG00000115844	ENST00000234198;ENST00000466293	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0935	0.65006	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLX2	172675111	1.000000	0.71417	0.866000	0.34008	0.891000	0.51852	6.618000	0.74214	1.799000	0.52666	0.454000	0.30748	.		0.562	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3		Intron	G	172966865	A	G	172966865	5	3	115	1	0	0	0	0	0	0	1	0	4582	405	14	4	596	4	DLX2	2	172966865	Splice_Site	SNP	A	TCGA-F5-6465-01A-11D-1733-10	9686919	172966865	70232508	35	30842										
ITGA6	3655	hgsc.bcm.edu	37	chr2	173349833	173349856	+	Splice_Site	DEL	CATGCTTTTCATGCAGGATAATAT	CATGCTTTTCATGCAGGATAATAT	-													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	accccacttaactctgactgCatgcttttcatgcaggataa							TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	CATGCTTTTCATGCAGGATAATAT	CATGCTTTTCATGCAGGATAATAT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:173349833_173349856delCATGCTTTTCATGCAGGATAATAT	ENST00000264106.6	+	14	2030_2038	c.1827_1835delCATGCTTTTCATGCAGGATAATAT	c.(1825-1836)cacatgcttttc>cac	p.MLF610del	ITGA6_ENST00000409532.1_Splice_Site_p.MLF452del|ITGA6_ENST00000343713.4_Splice_Site_p.MLF566del|ITGA6_ENST00000375221.2_Splice_Site_p.MLF610del|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Splice_Site_p.MLF571del|ITGA6_ENST00000409080.1_Splice_Site_p.MLF571del			P23229	ITA6_HUMAN	integrin, alpha 6	610					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			ACTCTGACTGCATGCTTTTCATGCAGGATAATATCAGAGATAAA	0.406																																																0			2																																								173058102	SO:0001630	splice_region_variant	3655				CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1828-1CATGCTTTTCATGCAGGATAATAT>-	2.37:g.173349833_173349856delCATGCTTTTCATGCAGGATAATAT			173058079	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	37																																																																																					0.406	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			In_Frame_Del	-	173349856	CATGCTTTTCATGCAGGATAATAT	-	173349833	8	5	115	1	0	1	0	1	0	0	1	0	7901	725	25	0		0	ITGA6	2	173349833	Splice_Site	DEL	CATGCTTTTCATGCAGGATAATAT	TCGA-F5-6465-01A-11D-1733-10	382968	173349833	69849540	36	30843										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178562149	178562149	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttggaggacaggttagcaaaGatattgtgaccctgtaatga	12	5	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:178562149G>C	ENST00000286063.6	-	15	2573	c.2256C>G	c.(2254-2256)atC>atG	p.I752M	AC012499.1_ENST00000412133.1_RNA|AC012499.1_ENST00000450227.1_RNA|PDE11A_ENST00000358450.4_Missense_Mutation_p.I502M|PDE11A_ENST00000389683.3_Missense_Mutation_p.I308M|PDE11A_ENST00000449286.2_Missense_Mutation_p.I394M|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000409504.1_Missense_Mutation_p.I394M	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	752	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GGTTAGCAAAGATATTGTGAC	0.368									Primary Pigmented Nodular Adrenocortical Disease, Familial																																							0			2											109	93	98					2																	178562149		2203	4300	6503	178270395	SO:0001583	missense	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2256C>G	2.37:g.178562149G>C	ENSP00000286063:p.Ile752Met		178270395	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.21|18.21	3.572706|3.572706	0.65765|0.65765	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000433879	D;D;D;D;D|.	0.81908|.	-1.55;-1.55;-1.55;-1.55;-1.55|.	5.57|5.57	4.67|4.67	0.58626|0.58626	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77638|0.77638	0.4160|0.4160	M|M	0.90425|0.90425	3.115|3.115	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.79988|0.79988	-0.1571|-0.1571	10|5	0.87932|.	D|.	0|.	.|.	8.7982|8.7982	0.34892|0.34892	0.0744:0.0:0.7629:0.1627|0.0744:0.0:0.7629:0.1627	.|.	502;752|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	M|C	752;502;394;308;394|360	ENSP00000286063:I752M;ENSP00000351232:I502M;ENSP00000386539:I394M;ENSP00000374333:I308M;ENSP00000390599:I394M|.	ENSP00000286063:I752M|.	I|S	-|-	3|2	3|0	PDE11A|PDE11A	178270395|178270395	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	3.784000|3.784000	0.55416|0.55416	1.288000|1.288000	0.44600|0.44600	0.650000|0.650000	0.86243|0.86243	ATC|TCT		0.368	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			C	178562149	G	C	178562149	3	2	115	1	0	0	0	0	1	0	0	0	11662	932	33	5	569	5	PDE11A	2	178562149	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	5212316	178562149	64637224	37	30844										
TTN	7273	hgsc.bcm.edu	37	chr2	179579734	179579734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttgagagcgatggaaccaaCgcaagtgtcgcttcccacat	10	11	0	1	rs544958705		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:179579734C>T	ENST00000591111.1	-	88	25452	c.25228G>A	c.(25228-25230)Gtt>Att	p.V8410I	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V7483I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V8727I|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12582	Ig-like 66.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGGAACCAACGCAAGTGTCG	0.478													C|||	1	0.000199681	0	0	5008	,	,		21242	0		0	False		,,,				2504	0.001															0			2											210	205	207					2																	179579734		2042	4198	6240	179287979	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25228G>A	2.37:g.179579734C>T	ENSP00000465570:p.Val8410Ile		179287979	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	6.529	0.465908	0.12402	.	.	ENSG00000155657	ENST00000342992	T	0.41065	1.01	5.91	0.841	0.18918	Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.22205	0.0535	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24657	-1.0154	9	0.87932	D	0	.	1.2802	0.02039	0.1486:0.282:0.1453:0.424	.	8410	Q8WZ42	TITIN_HUMAN	I	7483	ENSP00000343764:V7483I	ENSP00000343764:V7483I	V	-	1	0	TTN	179287979	0.004000	0.15560	0.004000	0.12327	0.031000	0.12232	-0.148000	0.10219	0.091000	0.17302	0.655000	0.94253	GTT		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179579734	C	T	179579734	3	4	115	1	0	0	0	0	1	0	0	0	16775	536	19	1	78442	1	TTN	2	179579734	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	1017585	179579734	63619639	38	30845										
TUBA4A	7277	hgsc.bcm.edu	37	chr2	220116426	220116426	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctgtcggtatgggccatttCggatctcatctggaagggca	14	9	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:220116426C>A	ENST00000248437.4	-	3	409	c.236G>T	c.(235-237)cGa>cTa	p.R79L	TUBA4A_ENST00000498660.1_5'UTR|TUBA4A_ENST00000392088.2_Missense_Mutation_p.R64L|TUBA4B_ENST00000490341.1_RNA	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	79					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R79Q(2)|p.R64Q(2)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	TGGGCCATTTCGGATCTCATC	0.547																																																4	Substitution - Missense(4)	ovary(2)|large_intestine(2)	2											81	74	76					2																	220116426		2203	4300	6503	219824670	SO:0001583	missense	7277			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.236G>T	2.37:g.220116426C>A	ENSP00000248437:p.Arg79Leu		219824670	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001505	0.54254	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000427737;ENST00000456818;ENST00000447205;ENST00000425551	T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.06	5.06	0.68205	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000002	T	0.76026	0.3930	M	0.88310	2.945	0.80722	D	1	B	0.20368	0.044	B	0.28849	0.095	T	0.77127	-0.2702	10	0.87932	D	0	.	18.6248	0.91333	0.0:1.0:0.0:0.0	.	79	P68366	TBA4A_HUMAN	L	79;64;64;102;64;81	ENSP00000248437:R79L;ENSP00000375938:R64L;ENSP00000408194:R64L;ENSP00000416992:R102L;ENSP00000396061:R64L;ENSP00000404740:R81L	ENSP00000248437:R79L	R	-	2	0	TUBA4A	219824670	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.564000	0.82326	2.639000	0.89480	0.655000	0.94253	CGA		0.547	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		A	220116426	C	A	220116426	3	1	115	1	0	0	0	0	1	0	0	0	16789	884	31	2	1118	2	TUBA4A	2	220116426	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	40536692	220116426	23082947	39	30846										
C2orf85	285093	hgsc.bcm.edu	37	chr2	242814002	242814002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agcggtgcaggctgtgccccGcacccggggactgccaggtg	17	14	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr2:242814002G>A	ENST00000343216.3	+	2	323	c.295G>A	c.(295-297)Gca>Aca	p.A99T		NM_173821.2	NP_776182.2																					GCTGTGCCCCGCACCCGGGGA	0.711																																																0			2											7	10	9					2																	242814002		1877	4066	5943	242462675	SO:0001583	missense	285093																														ENST00000343216.3:c.295G>A	2.37:g.242814002G>A	ENSP00000345374:p.Ala99Thr		242462675		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.514723	0.00975	.	.	ENSG00000188011	ENST00000343216	T	0.21191	2.02	2.67	-5.35	0.02697	.	.	.	.	.	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	P	0.34522	0.455	B	0.24155	0.051	T	0.25847	-1.0120	9	0.18710	T	0.47	.	1.4037	0.02276	0.3992:0.2898:0.1808:0.1301	.	99	Q14D33	CB085_HUMAN	T	99	ENSP00000345374:A99T	ENSP00000345374:A99T	A	+	1	0	C2orf85	242462675	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.352000	0.01091	-2.233000	0.00716	-0.532000	0.04303	GCA		0.711	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			A	242814002	G	A	242814002	3	1	115	1	0	0	0	0	1	0	0	0	2206	1087	38	1	301	1	C2orf85	2	242814002	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	22697576	242814002	385371	40	30847										
EOMES	8320	hgsc.bcm.edu	37	chr3	27758785	27758785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tatccaagaagagccaatttCctctttcactttctccttgg	5	12	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:27758785C>T	ENST00000295743.4	-	6	2040	c.1837G>A	c.(1837-1839)Gaa>Aaa	p.E613K	EOMES_ENST00000461503.1_5'Flank|EOMES_ENST00000537516.1_Missense_Mutation_p.E337K|EOMES_ENST00000449599.1_Missense_Mutation_p.E632K			O95936	EOMES_HUMAN	eomesodermin	613	Required for transcription activation. {ECO:0000250}.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E613*(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						GAGCCAATTTCCTCTTTCACT	0.483																																																1	Substitution - Nonsense(1)	ovary(1)	3											106	110	108					3																	27758785		2203	4300	6503	27733789	SO:0001583	missense	8320			BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1837G>A	3.37:g.27758785C>T	ENSP00000295743:p.Glu613Lys		27733789	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	37	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	C	9.813	1.183657	0.21870	.	.	ENSG00000163508	ENST00000295743;ENST00000449599;ENST00000537516;ENST00000535713	D;D;D	0.85556	-2.0;-2.0;-1.69	5.05	5.05	0.67936	.	1.966750	0.02853	N	0.129301	D	0.88948	0.6576	L	0.47716	1.5	0.80722	D	1	B;P;D	0.58268	0.01;0.935;0.982	B;P;P	0.51266	0.023;0.604;0.664	T	0.77935	-0.2401	10	0.28530	T	0.3	.	19.3091	0.94177	0.0:1.0:0.0:0.0	.	346;632;613	B7Z4I2;G3XAI5;O95936	.;.;EOMES_HUMAN	K	613;632;337;497	ENSP00000295743:E613K;ENSP00000388620:E632K;ENSP00000442097:E337K	ENSP00000295743:E613K	E	-	1	0	EOMES	27733789	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.665000	0.68052	2.724000	0.93272	0.563000	0.77884	GAA		0.483	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		T	27758785	C	T	27758785	3	4	115	1	0	0	0	0	1	0	0	0	5160	864	30	3	227	3	EOMES	3	27758785	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		27758785	170263645	41	30848										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266170	41266170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aggcaatcctgaggaagaggAtgtggatacctcccaagtcc	12	10	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:41266170A>G	ENST00000349496.5	+	3	447	c.167A>G	c.(166-168)gAt>gGt	p.D56G	CTNNB1_ENST00000405570.1_Missense_Mutation_p.D56G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D56G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D49G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D56G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	56					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GAGGAAGAGGATGTGGATACC	0.468		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	109	Deletion - In frame(87)|Complex - deletion inframe(15)|Unknown(7)	liver(80)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											72	67	69					3																	41266170		2203	4300	6503	41241174	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.167A>G	3.37:g.41266170A>G	ENSP00000344456:p.Asp56Gly		41241174	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838765	0.51057	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.91	5.91	0.95273	.	0.089868	0.85682	D	0.000000	T	0.24699	0.0599	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.06789	-1.0807	10	0.44086	T	0.13	-31.3631	16.3453	0.83126	1.0:0.0:0.0:0.0	.	56	P35222	CTNB1_HUMAN	G	49;56;56;56;56;49;56;56;56	ENSP00000400508:D49G;ENSP00000385604:D56G;ENSP00000412219:D56G;ENSP00000379486:D56G;ENSP00000344456:D56G;ENSP00000411226:D49G;ENSP00000379488:D56G;ENSP00000409302:D56G;ENSP00000401599:D56G	ENSP00000344456:D56G	D	+	2	0	CTNNB1	41241174	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	GAT		0.468	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266170	A	G	41266170	3	3	115	1	0	0	0	0	1	0	0	0	4022	333	12	4	173	4	CTNNB1	3	41266170	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	13507385	41266170	156756260	42	30849										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266860	41266860	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctgcagttatggtccatcaGctttctaaaaaggaagcttc	9	9	2	0	rs267599822		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:41266860G>T	ENST00000349496.5	+	5	811	c.531G>T	c.(529-531)caG>caT	p.Q177H	CTNNB1_ENST00000405570.1_Missense_Mutation_p.Q177H|CTNNB1_ENST00000396183.3_Missense_Mutation_p.Q177H|CTNNB1_ENST00000453024.1_Missense_Mutation_p.Q170H|CTNNB1_ENST00000396185.3_Missense_Mutation_p.Q177H	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	177	Interaction with BCL9.				adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTCCATCAGCTTTCTAAAA	0.408		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	0			3											65	68	67					3																	41266860		2203	4299	6502	41241864	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.531G>T	3.37:g.41266860G>T	ENSP00000344456:p.Gln177His		41241864	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138746	0.37728	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	5.7	4.82	0.62117	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55449	0.1921	L	0.37561	1.115	0.80722	D	1	B;B	0.16802	0.009;0.019	B;B	0.15870	0.009;0.014	T	0.54323	-0.8311	10	0.51188	T	0.08	-2.7834	11.2741	0.49157	0.1403:0.0:0.8597:0.0	.	105;177	B4DSW9;P35222	.;CTNB1_HUMAN	H	177;177;177;170;177	ENSP00000385604:Q177H;ENSP00000379486:Q177H;ENSP00000344456:Q177H;ENSP00000411226:Q170H;ENSP00000379488:Q177H	ENSP00000344456:Q177H	Q	+	3	2	CTNNB1	41241864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.560000	0.67332	2.692000	0.91855	0.655000	0.94253	CAG		0.408	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266860	G	T	41266860	3	4	115	1	0	0	0	0	1	0	0	0	4022	962	34	2	545	2	CTNNB1	3	41266860	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	690	41266860	156755570	43	30850										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48696750	48696750	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcagggatgttcccctccacGatctggtacattatatgggc	10	11	2	0	rs149132560	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:48696750G>T	ENST00000164024.4	-	1	3598	c.3318C>A	c.(3316-3318)atC>atA	p.I1106I	CELSR3_ENST00000544264.1_Silent_p.I1106I	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1106	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.I1106I(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCCCCTCCACGATCTGGTACA	0.522																																																1	Substitution - coding silent(1)	skin(1)	3											91	87	89					3																	48696750		2203	4300	6503	48671754	SO:0001819	synonymous_variant	1951			AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.3318C>A	3.37:g.48696750G>T			48671754	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																				0.522	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		T	48696750	G	T	48696750	2	4	115	1	0	0	0	0	0	0	0	1	3229	1048	37	2		2	CELSR3	3	48696750	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	7429890	48696750	149325680	44	30851										
WDR6	11180	hgsc.bcm.edu	37	chr3	49050135	49050135	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agctgctagaggataaacatTtccagtcctactgcctgctg	9	11	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:49050135T>C	ENST00000608424.1	+	2	1207	c.1168T>C	c.(1168-1170)Ttc>Ctc	p.F390L	WDR6_ENST00000489684.1_3'UTR|WDR6_ENST00000395474.3_Missense_Mutation_p.F420L|WDR6_ENST00000415265.2_Intron|WDR6_ENST00000448293.1_Missense_Mutation_p.F339L			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	390					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		GGATAAACATTTCCAGTCCTA	0.572																																																0			3											53	52	53					3																	49050135		2203	4300	6503	49025139	SO:0001583	missense	11180			AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"WD repeat domain containing"	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.1168T>C	3.37:g.49050135T>C	ENSP00000477389:p.Phe390Leu		49025139	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		.	.	.	.	.	.	.	.	.	.	T	19.70	3.875950	0.72180	.	.	ENSG00000178252	ENST00000395474;ENST00000448293	T;T	0.64803	-0.12;2.34	5.28	5.28	0.74379	WD40 repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	0.123171	0.56097	D	0.000025	T	0.52677	0.1749	N	0.19112	0.55	0.47584	D	0.999466	D;D;D	0.56521	0.958;0.976;0.976	P;P;P	0.49922	0.501;0.626;0.626	T	0.48080	-0.9066	10	0.11485	T	0.65	-23.5207	14.1816	0.65578	0.0:0.0:0.0:1.0	.	261;390;339	B4DK45;Q9NNW5;E9PDU5	.;WDR6_HUMAN;.	L	420;339	ENSP00000378857:F420L;ENSP00000413432:F339L	ENSP00000378857:F420L	F	+	1	0	WDR6	49025139	1.000000	0.71417	0.869000	0.34112	0.927000	0.56198	5.413000	0.66399	2.005000	0.58758	0.459000	0.35465	TTC		0.572	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			C	49050135	T	C	49050135	3	2	115	1	0	0	0	0	1	0	0	0	17350	1841	64	4	1264	4	WDR6	3	49050135	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	353385	49050135	148972295	45	30852										
SHQ1	55164	hgsc.bcm.edu	37	chr3	72881525	72881525	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aatctcattactcacagataAtgatcaggatcaaacttggc	6	9	4	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:72881525A>G	ENST00000325599.8	-	5	733	c.594T>C	c.(592-594)caT>caC	p.H198H	SHQ1_ENST00000463369.1_Silent_p.H170H	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	198					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		CTCACAGATAATGATCAGGAT	0.378																																																0			3											64	71	69					3																	72881525		2203	4300	6503	72964215	SO:0001819	synonymous_variant	55164			BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.594T>C	3.37:g.72881525A>G			72964215	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Silent	SNP	ENST00000325599.8	37	CCDS33788.1																																																																																				0.378	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		G	72881525	A	G	72881525	2	3	115	1	0	0	0	0	0	0	0	1	14329	98	4	4		4	SHQ1	3	72881525	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	23831390	72881525	125140905	46	30853										
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133674025	133674025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggcagagctcggcctgcaagCggctgttgttccctgcaacg	14	13	0	1	rs202244173		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:133674025C>T	ENST00000310926.4	-	4	683	c.410G>A	c.(409-411)cGc>cAc	p.R137H	SLCO2A1_ENST00000478651.1_5'Flank|SLCO2A1_ENST00000493729.1_Intron	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	137					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	GGCCTGCAAGCGGCTGTTGTT	0.637																																																0			3											44	44	44					3																	133674025		2203	4300	6503	135156715	SO:0001583	missense	6578				CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.410G>A	3.37:g.133674025C>T	ENSP00000311291:p.Arg137His		135156715	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	37	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	C	0.415	-0.911160	0.02434	.	.	ENSG00000174640	ENST00000310926	T	0.39406	1.08	5.5	-11.0	0.00169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.303740	0.01346	N	0.011720	T	0.17916	0.0430	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36529	-0.9744	10	0.37606	T	0.19	.	8.7006	0.34323	0.2149:0.1949:0.0:0.5901	.	137	Q92959	SO2A1_HUMAN	H	137	ENSP00000311291:R137H	ENSP00000311291:R137H	R	-	2	0	SLCO2A1	135156715	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.320000	0.02700	-4.546000	0.00043	-2.754000	0.00123	CGC		0.637	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		T	133674025	C	T	133674025	3	4	115	1	0	0	0	0	1	0	0	0	14763	768	27	1	1565	1	SLCO2A1	3	133674025	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	60792500	133674025	64348405	47	30854										
TFDP2	7029	hgsc.bcm.edu	37	chr3	141692893	141692893	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cagattttctcacttacctcCagattctgacattcctgagc	5	13	2	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:141692893C>A	ENST00000489671.1	-	8	1090	c.660G>T	c.(658-660)ctG>ctT	p.L220L	TFDP2_ENST00000486111.1_Silent_p.L160L|TFDP2_ENST00000479040.1_Silent_p.L159L|TFDP2_ENST00000397991.4_Silent_p.L192L|TFDP2_ENST00000310282.6_Silent_p.L160L|TFDP2_ENST00000477292.1_Silent_p.L84L|TFDP2_ENST00000317104.7_Silent_p.L144L|TFDP2_ENST00000467072.1_Silent_p.L160L|TFDP2_ENST00000499676.2_Silent_p.L160L|TFDP2_ENST00000495310.1_Silent_p.L123L			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	220	Dimerization. {ECO:0000255}.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						CACTTACCTCCAGATTCTGAC	0.303																																																0			3											86	80	82					3																	141692893		1843	4118	5961	143175583	SO:0001819	synonymous_variant	7029			U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.660G>T	3.37:g.141692893C>A			143175583	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1																																																																																				0.303	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		A	141692893	C	A	141692893	2	1	115	1	0	0	0	0	0	0	0	1	15837	581	21	2		2	TFDP2	3	141692893	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	8018868	141692893	56329537	48	30855										
OPA1	4976	hgsc.bcm.edu	37	chr3	193332592	193332592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaaactacatctggtttcacGaagcatttatcattcacatc	4	10	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr3:193332592G>A	ENST00000392438.3	+	2	347	c.113G>A	c.(112-114)cGa>cAa	p.R38Q	OPA1_ENST00000361510.2_Missense_Mutation_p.R38Q|OPA1_ENST00000361828.2_Missense_Mutation_p.R38Q|OPA1_ENST00000361150.2_Missense_Mutation_p.R38Q|OPA1_ENST00000361715.2_Missense_Mutation_p.R38Q|OPA1_ENST00000361908.3_Missense_Mutation_p.R38Q|OPA1_ENST00000487986.1_3'UTR	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	38			Missing (in OPA1). {ECO:0000269|PubMed:12036970}.		apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)	p.R38Q(1)		breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		CTGGTTTCACGAAGCATTTAT	0.388																																																1	Substitution - Missense(1)	large_intestine(1)	3	GRCh37	CD014021	OPA1	D							117	103	108					3																	193332592		2203	4300	6503	194815286	SO:0001583	missense	9968			AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.113G>A	3.37:g.193332592G>A	ENSP00000376233:p.Arg38Gln		194815286	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183823	0.94885	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150;ENST00000392437;ENST00000392436	D;D;D;D;D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15	5.98	5.98	0.97165	.	0.064498	0.64402	D	0.000004	D	0.84647	0.5518	L	0.59436	1.845	0.58432	D	0.999997	P;B;P;P;P;P;P;D	0.52996	0.553;0.052;0.688;0.824;0.85;0.804;0.804;0.957	B;B;B;B;B;B;B;B	0.41440	0.116;0.005;0.079;0.203;0.163;0.079;0.116;0.357	D	0.85907	0.1438	10	0.59425	D	0.04	-10.1713	12.7122	0.57096	0.0742:0.0:0.9258:0.0	.	38;38;38;38;38;38;38;38	E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.;OPA1_HUMAN;.;.;.;.;.;.	Q	38	ENSP00000354681:R38Q;ENSP00000376233:R38Q;ENSP00000355324:R38Q;ENSP00000355311:R38Q;ENSP00000354429:R38Q;ENSP00000354781:R38Q;ENSP00000376232:R38Q;ENSP00000376231:R38Q	ENSP00000354781:R38Q	R	+	2	0	OPA1	194815286	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.662000	0.74426	2.835000	0.97688	0.650000	0.86243	CGA		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		A	193332592	G	A	193332592	3	1	115	1	0	0	0	0	1	0	0	0	10902	1058	37	1	119	1	OPA1	3	193332592	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	51639699	193332592	4689838	49	30856										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tggagtgccacctgctcacaCacgtgcccatgtggagtgcc					rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																																1	Substitution - Missense(1)	pancreas(1)	4																																								1378622	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs		1378594	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388622	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	1388594	7	5	115	1	0	1	0	1	0	0	0	0	3883	478	17	0	297	0	CRIPAK	4	1388594	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	TCGA-F5-6465-01A-11D-1733-10		1388594	189765682	50	30857										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6086640	6086640	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tccgtatcactgaattcagtTcagcaatttttagttgaaat	6	7	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:6086640T>C	ENST00000282924.5	-	5	1372	c.887A>G	c.(886-888)gAa>gGa	p.E296G	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.E296G|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.E296G|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.E131G|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.E131G|JAKMIP1_ENST00000457227.2_5'UTR	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	296	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGAATTCAGTTCAGCAATTTT	0.393																																																0			4											236	228	231					4																	6086640		2203	4300	6503	6137541	SO:0001583	missense	152789			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.887A>G	4.37:g.6086640T>C	ENSP00000282924:p.Glu296Gly		6137541	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526568	0.85706	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.47528	1.32;0.9;1.31;1.31;0.84	4.79	4.79	0.61399	.	0.216872	0.32640	N	0.005823	T	0.67552	0.2905	M	0.78049	2.395	0.49483	D	0.999793	D;P;D;D;P	0.76494	0.999;0.573;0.999;0.999;0.728	D;B;D;D;B	0.78314	0.986;0.23;0.991;0.991;0.23	T	0.72181	-0.4368	10	0.87932	D	0	.	12.1034	0.53798	0.0:0.0:0.0:1.0	.	131;296;131;296;296	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	G	296;131;296;296;188;296;296;131	ENSP00000386711:E296G;ENSP00000387042:E131G;ENSP00000282924:E296G;ENSP00000386925:E296G;ENSP00000386745:E131G	ENSP00000282924:E296G	E	-	2	0	JAKMIP1	6137541	1.000000	0.71417	0.982000	0.44146	0.979000	0.70002	7.605000	0.82844	1.789000	0.52484	0.482000	0.46254	GAA		0.393	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		C	6086640	T	C	6086640	3	2	115	1	0	0	0	0	1	0	0	0	7961	1783	62	4	1751	4	JAKMIP1	4	6086640	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	4698046	6086640	185067636	51	30858										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6598966	6598966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctacctgtggccggccccccGtgggcatctggaccccacct	11	19	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:6598966G>A	ENST00000285599.3	+	8	1220	c.1184G>A	c.(1183-1185)cGt>cAt	p.R395H	MAN2B2_ENST00000504248.1_Missense_Mutation_p.R344H	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	395					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCGGCCCCCCGTGGGCATCTG	0.652																																																0			4											48	57	54					4																	6598966		2203	4299	6502	6649867	SO:0001583	missense	23324			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1184G>A	4.37:g.6598966G>A	ENSP00000285599:p.Arg395His		6649867	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.055|0.055	-1.239696|-1.239696	0.01493|0.01493	.|.	.|.	ENSG00000013288|ENSG00000013288	ENST00000285599;ENST00000504248|ENST00000505907	T;D|.	0.84800|.	-1.45;-1.9|.	5.27|5.27	-10.5|-10.5	0.00291|0.00291	Glycoside hydrolase, family 38, central domain (2);|.	2.300860|.	0.01436|.	N|.	0.014904|.	T|T	0.10852|0.10852	0.0265|0.0265	N|N	0.04148|0.04148	-0.265|-0.265	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.06405|.	0.002;0.002;0.001|.	T|T	0.10941|0.10941	-1.0608|-1.0608	10|5	0.40728|.	T|.	0.16|.	-2.5013|-2.5013	4.2207|4.2207	0.10556|0.10556	0.1084:0.3125:0.3679:0.2113|0.1084:0.3125:0.3679:0.2113	.|.	344;395;395|.	E9PCD7;Q9Y2E5;Q9Y2E5-2|.	.;MA2B2_HUMAN;.|.	H|M	395;344|394	ENSP00000285599:R395H;ENSP00000423129:R344H|.	ENSP00000285599:R395H|.	R|V	+|+	2|1	0|0	MAN2B2|MAN2B2	6649867|6649867	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.049000|0.049000	0.14656|0.14656	-3.125000|-3.125000	0.00593|0.00593	-3.620000|-3.620000	0.00131|0.00131	-2.243000|-2.243000	0.00286|0.00286	CGT|GTG		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6598966	G	A	6598966	3	1	115	1	0	0	0	0	1	0	0	0	9247	1145	40	1	1214	1	MAN2B2	4	6598966	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	512326	6598966	184555310	52	30859										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13605821	13605821	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agtttctcttctaacaagctCtttgttcgtcgtttctcctt	5	11	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:13605821C>G	ENST00000040738.5	-	10	2838	c.2703G>C	c.(2701-2703)aaG>aaC	p.K901N		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	901	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)										CTAACAAGCTCTTTGTTCGTC	0.368																																																0			4											123	122	122					4																	13605821		2203	4300	6503	13214919	SO:0001583	missense	259282			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.2703G>C	4.37:g.13605821C>G	ENSP00000040738:p.Lys901Asn		13214919	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	15.88	2.963501	0.53507	.	.	ENSG00000038219	ENST00000040738	T	0.15603	2.41	5.53	5.53	0.82687	.	0.000000	0.52532	D	0.000069	T	0.38931	0.1059	M	0.63843	1.955	0.34089	D	0.660534	D	0.89917	1.0	D	0.79784	0.993	T	0.50849	-0.8779	10	0.59425	D	0.04	-7.4526	14.3136	0.66432	0.1485:0.8515:0.0:0.0	.	901	Q8NFC6	BOD1L_HUMAN	N	901	ENSP00000040738:K901N	ENSP00000040738:K901N	K	-	3	2	BOD1L	13214919	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	2.023000	0.41040	2.603000	0.88011	0.650000	0.86243	AAG		0.368	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13605821	C	G	13605821	3	3	115	1	0	0	0	0	1	0	0	0	1484	912	32	5	6520	5	BOD1L	4	13605821	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	7006855	13605821	177548455	53	30860										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25160601	25160601	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgacgacgagcaaccagtgcGgatgccactctcccttccct	9	16	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:25160601G>A	ENST00000382103.2	-	2	315	c.243C>T	c.(241-243)tcC>tcT	p.S81S	PI4K2B_ENST00000512921.1_5'Flank|SEPSECS_ENST00000302922.3_Intron	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	81					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				CAACCAGTGCGGATGCCACTC	0.383																																																0			4											170	169	170					4																	25160601		1924	4135	6059	24769699	SO:0001819	synonymous_variant	51091			AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.243C>T	4.37:g.25160601G>A			24769699	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Silent	SNP	ENST00000382103.2	37	CCDS3432.2																																																																																				0.383	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		A	25160601	G	A	25160601	2	1	115	1	0	0	0	0	0	0	0	1	14095	1103	39	1		1	SEPSECS	4	25160601	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	11554780	25160601	165993675	54	30861										
TLR6	10333	hgsc.bcm.edu	37	chr4	38830422	38830422	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	attcaatttaatattagtcaGttgtaagcaccctaaagtat	5	6	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:38830422G>T	ENST00000381950.1	-	1	738	c.673C>A	c.(673-675)Ctg>Atg	p.L225M	TLR6_ENST00000436693.2_Missense_Mutation_p.L225M			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	225					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ATATTAGTCAGTTGTAAGCAC	0.333																																																0			4											48	53	51					4																	38830422		2202	4300	6502	38506817	SO:0001583	missense	10333				CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.673C>A	4.37:g.38830422G>T	ENSP00000371376:p.Leu225Met		38506817	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	G	5.584	0.292625	0.10567	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.10382	2.88;2.88	5.6	1.45	0.22620	.	0.338259	0.23400	N	0.048593	T	0.06508	0.0167	L	0.28740	0.885	0.24435	N	0.994557	B	0.22146	0.065	B	0.25405	0.06	T	0.31194	-0.9952	10	0.27082	T	0.32	.	3.7178	0.08445	0.0912:0.1273:0.267:0.5145	.	225	Q9Y2C9	TLR6_HUMAN	M	225	ENSP00000389600:L225M;ENSP00000371376:L225M	ENSP00000371376:L225M	L	-	1	2	TLR6	38506817	0.988000	0.35896	1.000000	0.80357	0.907000	0.53573	0.259000	0.18405	0.689000	0.31550	0.491000	0.48974	CTG		0.333	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			T	38830422	G	T	38830422	3	4	115	1	0	0	0	0	1	0	0	0	15994	1020	36	2	1721	2	TLR6	4	38830422	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	13669821	38830422	152323854	55	30862										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060510	46060510	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tattctttttaccagagatcGtgtgagtgatttcagttgag	10	5	2	4	rs369652618		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:46060510G>A	ENST00000295452.4	-	6	922	c.755C>T	c.(754-756)aCg>aTg	p.T252M		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	252					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.T252M(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACCAGAGATCGTGTGAGTGAT	0.328																																																1	Substitution - Missense(1)	large_intestine(1)	4						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	89	86	87		755	5.8	1	4		87	0,8600		0,0,4300	no	missense	GABRG1	NM_173536.3	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	252/466	46060510	1,13005	2203	4300	6503	45755267	SO:0001583	missense	2565			BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.755C>T	4.37:g.46060510G>A	ENSP00000295452:p.Thr252Met		45755267	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	37	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.602615	0.87157	2.27E-4	0.0	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.78003	-1.14	5.83	5.83	0.93111	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.89543	0.6745	M	0.85710	2.77	0.47862	D	0.999532	D	0.89917	1.0	D	0.74023	0.982	D	0.89753	0.3941	10	0.56958	D	0.05	.	19.1642	0.93548	0.0:0.0:1.0:0.0	.	252	Q8N1C3	GBRG1_HUMAN	M	252	ENSP00000295452:T252M	ENSP00000295452:T252M	T	-	2	0	GABRG1	45755267	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.974000	0.88039	2.775000	0.95449	0.650000	0.86243	ACG		0.328	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46060510	G	A	46060510	3	1	115	1	0	0	0	0	1	0	0	0	6190	1145	40	1	658	1	GABRG1	4	46060510	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	7230088	46060510	145093766	56	30863										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55152032	55152032	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tccaccgtgatctggctgctCgcaacgtcctcctggcacaa	9	16	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:55152032C>A	ENST00000257290.5	+	18	2795	c.2464C>A	c.(2464-2466)Cgc>Agc	p.R822S	FIP1L1_ENST00000507166.1_Missense_Mutation_p.R582S	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	822	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.R822S(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TCTGGCTGCTCGCAACGTCCT	0.498			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	1	Substitution - Missense(1)	soft_tissue(1)	4											174	158	163					4																	55152032		2203	4300	6503	54846789	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2464C>A	4.37:g.55152032C>A	ENSP00000257290:p.Arg822Ser		54846789	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.591674	0.86953	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.87491	-2.26;-2.26	6.17	6.17	0.99709	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.32386	U	0.006179	D	0.91700	0.7376	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91699	0.5372	10	0.87932	D	0	.	16.376	0.83392	0.1323:0.8677:0.0:0.0	.	822	P16234	PGFRA_HUMAN	S	582;822	ENSP00000423325:R582S;ENSP00000257290:R822S	ENSP00000423325:R582S	R	+	1	0	FIP1L1;PDGFRA	54846789	0.998000	0.40836	0.998000	0.56505	0.891000	0.51852	1.878000	0.39608	2.941000	0.99782	0.655000	0.94253	CGC		0.498	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55152032	C	A	55152032	3	1	115	1	0	0	0	0	1	0	0	0	11692	884	31	2	2530	2	PDGFRA	4	55152032	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	9091522	55152032	136002244	57	30864										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110415905	110415905	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaatggctaagccttttggcTatggctatccaacacttcag	8	10	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:110415905T>C	ENST00000265175.5	+	6	1436	c.1381T>C	c.(1381-1383)Tat>Cat	p.Y461H	SEC24B_ENST00000399100.2_Missense_Mutation_p.Y426H|SEC24B_ENST00000504968.2_Missense_Mutation_p.Y492H	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	461					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		GCCTTTTGGCTATGGCTATCC	0.512																																																0			4											110	114	112					4																	110415905		2122	4280	6402	110635354	SO:0001583	missense	10427			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.1381T>C	4.37:g.110415905T>C	ENSP00000265175:p.Tyr461His		110635354	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.460017	0.43736	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.23754	1.89;1.89;1.89	5.47	4.3	0.51218	.	.	.	.	.	T	0.22003	0.0530	L	0.49126	1.545	0.46654	D	0.999142	B;B;B;B;B	0.12630	0.003;0.001;0.006;0.001;0.001	B;B;B;B;B	0.17433	0.005;0.007;0.008;0.018;0.008	T	0.04593	-1.0940	9	0.19147	T	0.46	4.5137	9.5013	0.39019	0.0:0.0807:0.0:0.9193	.	376;60;492;426;461	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	H	492;426;461	ENSP00000428564:Y492H;ENSP00000382051:Y426H;ENSP00000265175:Y461H	ENSP00000265175:Y461H	Y	+	1	0	SEC24B	110635354	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.249000	0.43169	0.914000	0.36822	0.533000	0.62120	TAT		0.512	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			C	110415905	T	C	110415905	3	2	115	1	0	0	0	0	1	0	0	0	14032	1522	53	4	1403	4	SEC24B	4	110415905	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	55263873	110415905	80738371	58	30865										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153258971	153258971	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tacctctttagggagcaatgAaatgaagtctcgttgaaact	9	7	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:153258971A>T	ENST00000281708.4	-	5	2073	c.844T>A	c.(844-846)Tca>Aca	p.S282T	FBXW7_ENST00000296555.5_Missense_Mutation_p.S164T|FBXW7_ENST00000263981.5_Missense_Mutation_p.S202T|FBXW7_ENST00000603548.1_Missense_Mutation_p.S282T|RP11-461L13.2_ENST00000605147.1_RNA|FBXW7_ENST00000393956.3_Missense_Mutation_p.S106T|FBXW7_ENST00000603841.1_Missense_Mutation_p.S282T	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	282	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GGGAGCAATGAAATGAAGTCT	0.343			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											174	169	170					4																	153258971		2203	4300	6503	153478421	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.844T>A	4.37:g.153258971A>T	ENSP00000281708:p.Ser282Thr		153478421	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.162661	0.78226	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.63	5.63	0.86233	F-box domain, cyclin-like (1);F-box domain, Skp2-like (1);	0.105513	0.64402	D	0.000002	T	0.59959	0.2232	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.71674	0.995;0.998;0.993;0.993	D;D;D;D	0.70227	0.953;0.968;0.922;0.922	T	0.55823	-0.8080	10	0.24483	T	0.36	-7.1899	15.8279	0.78727	1.0:0.0:0.0:0.0	.	106;282;164;202	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	T	282;164;202;106	ENSP00000281708:S282T;ENSP00000296555:S164T;ENSP00000263981:S202T;ENSP00000377528:S106T	ENSP00000263981:S202T	S	-	1	0	FBXW7	153478421	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	9.268000	0.95675	2.133000	0.65898	0.528000	0.53228	TCA		0.343	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153258971	A	T	153258971	3	4	115	1	0	0	0	0	1	0	0	0	5788	246	9	5	1311	5	FBXW7	4	153258971	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	42843066	153258971	37895305	59	30866										
MAP9	79884	hgsc.bcm.edu	37	chr4	156269037	156269037	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttctgttttcgttcaattctTtcttgtttttccttattttc	3	8	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:156269037T>G	ENST00000311277.4	-	14	2105	c.1842A>C	c.(1840-1842)gaA>gaC	p.E614D	MAP9_ENST00000515654.1_Missense_Mutation_p.E590D|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000512269.1_RNA|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000595760.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000597955.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000593486.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000608762.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	614					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		GTTCAATTCTTTCTTGTTTTT	0.343																																																0			4											83	80	81					4																	156269037		2202	4300	6502	156488487	SO:0001583	missense	79884			AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1842A>C	4.37:g.156269037T>G	ENSP00000310593:p.Glu614Asp		156488487	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735313	0.69189	.	.	ENSG00000164114	ENST00000311277;ENST00000515654	T;T	0.19938	2.11;2.13	5.72	0.531	0.17108	.	0.178457	0.49305	D	0.000160	T	0.32436	0.0829	M	0.64997	1.995	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.59056	0.851;0.851	T	0.02751	-1.1115	10	0.54805	T	0.06	-27.1077	8.3821	0.32477	0.0:0.3046:0.0:0.6954	.	589;614	B4DVG9;Q49MG5	.;MAP9_HUMAN	D	614;590	ENSP00000310593:E614D;ENSP00000427402:E590D	ENSP00000310593:E614D	E	-	3	2	MAP9	156488487	1.000000	0.71417	0.997000	0.53966	0.757000	0.42996	0.378000	0.20569	-0.044000	0.13491	-0.256000	0.11100	GAA		0.343	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		G	156269037	T	G	156269037	3	3	115	1	0	0	0	0	1	0	0	0	9300	1838	64	4	105	4	MAP9	4	156269037	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	3010066	156269037	34885239	60	30867										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170634427	170634427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gaaagctgggactgaggcagTgccttgtaactcacaatggg	14	8	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr4:170634427T>C	ENST00000513761.1	+	12	2906	c.2347T>C	c.(2347-2349)Tgc>Cgc	p.C783R	CLCN3_ENST00000347613.4_Missense_Mutation_p.C783R|CLCN3_ENST00000504131.2_Missense_Mutation_p.C766R|CLCN3_ENST00000360642.3_Missense_Mutation_p.C756R	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	783	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		ACTGAGGCAGTGCCTTGTAAC	0.443																																																0			4											92	83	86					4																	170634427		2203	4300	6503	170871002	SO:0001583	missense	1182			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2347T>C	4.37:g.170634427T>C	ENSP00000424603:p.Cys783Arg		170871002	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295495	0.81025	.	.	ENSG00000109572	ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131	D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2	5.2	5.2	0.72013	Cystathionine beta-synthase, core (3);	0.042013	0.85682	D	0.000000	D	0.94932	0.8361	L	0.43152	1.355	0.80722	D	1	D;D;D;P	0.76494	0.998;0.999;0.998;0.799	D;D;D;P	0.73708	0.975;0.981;0.975;0.625	D	0.95597	0.8659	10	0.87932	D	0	-2.5636	15.209	0.73202	0.0:0.0:0.0:1.0	.	756;766;783;783	B7Z932;B9EGJ9;P51790;P51790-2	.;.;CLCN3_HUMAN;.	R	783;783;756;766	ENSP00000424603:C783R;ENSP00000261514:C783R;ENSP00000353857:C756R;ENSP00000424540:C766R	ENSP00000261514:C783R	C	+	1	0	CLCN3	170871002	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.037000	0.88933	1.985000	0.57927	0.519000	0.50382	TGC		0.443	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			C	170634427	T	C	170634427	3	2	115	1	0	0	0	0	1	0	0	0	3470	1696	59	4	2389	4	CLCN3	4	170634427	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	14365390	170634427	20519849	61	30868										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11565132	11565132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggctacgatctgccgttcagCctccagctctcgggtcagcc	11	16	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:11565132C>T	ENST00000304623.8	-	3	400	c.211G>A	c.(211-213)Gct>Act	p.A71T	CTNND2_ENST00000511377.1_5'UTR|CTNND2_ENST00000359640.2_Missense_Mutation_p.A71T|CTNND2_ENST00000503622.1_5'UTR|CTNND2_ENST00000458100.2_5'UTR	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	71					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						TGCCGTTCAGCCTCCAGCTCT	0.502																																																0			5											87	70	76					5																	11565132		2203	4300	6503	11618132	SO:0001583	missense	1501			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.211G>A	5.37:g.11565132C>T	ENSP00000307134:p.Ala71Thr		11618132	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468860	0.84533	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000502551;ENST00000508761	T;T	0.77750	-1.05;-1.12	5.77	4.9	0.64082	.	0.000000	0.64402	D	0.000012	T	0.66790	0.2825	L	0.29908	0.895	0.80722	D	1	P	0.38922	0.651	B	0.35859	0.212	T	0.66590	-0.5885	10	0.33940	T	0.23	-9.119	14.7597	0.69596	0.0:0.845:0.155:0.0	.	71	Q9UQB3	CTND2_HUMAN	T	71;71;57;57	ENSP00000307134:A71T;ENSP00000352661:A71T	ENSP00000307134:A71T	A	-	1	0	CTNND2	11618132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.389000	0.79806	1.563000	0.49615	0.655000	0.94253	GCT		0.502	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11565132	C	T	11565132	3	4	115	1	0	0	0	0	1	0	0	0	4026	739	26	3	3546	3	CTNND2	5	11565132	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		11565132	169350128	62	30869										
FST	10468	hgsc.bcm.edu	37	chr5	52779467	52779467	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtctgcgggctggatgggaaAacctaccgcaatgaatgtgc	14	9	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:52779467A>G	ENST00000256759.3	+	3	794	c.411A>G	c.(409-411)aaA>aaG	p.K137K	FST_ENST00000396947.3_Silent_p.K137K	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	137	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				TGGATGGGAAAACCTACCGCA	0.512																																																0			5											74	72	72					5																	52779467		2203	4300	6503	52815224	SO:0001819	synonymous_variant	10468			M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.411A>G	5.37:g.52779467A>G			52815224	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1																																																																																				0.512	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		G	52779467	A	G	52779467	2	3	115	1	0	0	0	0	0	0	0	1	6095	11	1	4		4	FST	5	52779467	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	41214335	52779467	128135793	63	30870										
DDX4	54514	hgsc.bcm.edu	37	chr5	55111252	55111252	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	catcagttgataccagaaagGttagtagaaaggaaaacttg	10	5	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:55111252G>T	ENST00000505374.1	+	21	2189		c.e21+1		DDX4_ENST00000514278.2_Splice_Site|DDX4_ENST00000511853.1_Splice_Site|DDX4_ENST00000354991.5_Splice_Site|DDX4_ENST00000353507.5_Splice_Site	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4						male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TACCAGAAAGGTTAGTAGAAA	0.348																																																0			5											104	100	102					5																	55111252		2203	4300	6503	55147009	SO:0001630	splice_region_variant	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.2097+1G>T	5.37:g.55111252G>T			55147009	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Splice_Site	SNP	ENST00000505374.1	37	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588780	0.46110	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000354991;ENST00000511853	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5171	0.61547	0.0:0.1567:0.8433:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DDX4	55147009	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	4.991000	0.63883	2.513000	0.84729	0.563000	0.77884	.		0.348	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	Intron	T	55111252	G	T	55111252	5	4	115	1	0	0	0	0	0	0	1	0	4366	1275	44	2	2217	2	DDX4	5	55111252	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10	2331785	55111252	125804008	64	30871										
APC	324	hgsc.bcm.edu	37	chr5	112174784	112174784	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gaccaacaaattatagcataAaatataatgaagagaaacgt	6	5	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:112174784A>T	ENST00000457016.1	+	16	3873	c.3493A>T	c.(3493-3495)Aaa>Taa	p.K1165*	APC_ENST00000257430.4_Nonsense_Mutation_p.K1165*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.K1165*			P25054	APC_HUMAN	adenomatous polyposis coli	1165	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1165*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTATAGCATAAAATATAATGA	0.333		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	5											58	61	60					5																	112174784		2202	4299	6501	112202683	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3493A>T	5.37:g.112174784A>T	ENSP00000413133:p.Lys1165*		112202683	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	38	7.110393	0.98070	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.3002	16.0796	0.80995	1.0:0.0:0.0:0.0	.	.	.	.	X	1165	.	.	K	+	1	0	APC	112202683	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	3.954000	0.56708	2.206000	0.71126	0.533000	0.62120	AAA		0.333	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174784	A	T	112174784	4	4	115	1	0	0	0	0	0	1	0	0	763	15	1	5	3551	5	APC	5	112174784	Nonsense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	57063532	112174784	68740476	65	30872										
APC	324	hgsc.bcm.edu	37	chr5	112175207	112175207	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctaataccctgcaaatagcaGaaataaaagaaaagattgga	7	6	0	3	rs121913462		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:112175207G>T	ENST00000457016.1	+	16	4296	c.3916G>T	c.(3916-3918)Gaa>Taa	p.E1306*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1306*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1306*			P25054	APC_HUMAN	adenomatous polyposis coli	1306	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1306*(25)|p.E1306K(2)|p.K1192fs*3(1)|p.?(1)|p.E1306fs*8(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCAAATAGCAGAAATAAAAGA	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Substitution - Nonsense(25)|Substitution - Missense(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(26)|pancreas(1)|soft_tissue(1)|liver(1)|skin(1)	5	GRCh37	CM077502	APC	M	rs121913462						53	55	54					5																	112175207		2202	4300	6502	112203106	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3916G>T	5.37:g.112175207G>T	ENSP00000413133:p.Glu1306*		112203106	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	37	6.245438	0.97408	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	5.73	5.73	0.89815	.	0.179091	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.6779	14.1203	0.65182	0.0727:0.0:0.9273:0.0	.	.	.	.	X	1306	.	.	E	+	1	0	APC	112203106	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.734000	0.62043	2.861000	0.98227	0.655000	0.94253	GAA		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175207	G	T	112175207	4	4	115	1	0	0	0	0	0	1	0	0	763	943	33	2	3974	2	APC	5	112175207	Nonsense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	423	112175207	68740053	66	30873										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139903763	139903763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	acaggaagaagatgaagaaaAcaaacctaaggagaattcgg	11	5	0	5	rs369260709		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:139903763A>G	ENST00000360839.2	+	25	4584	c.4430A>G	c.(4429-4431)aAc>aGc	p.N1477S	ANKHD1_ENST00000544120.1_5'Flank|ANKHD1_ENST00000297183.6_Missense_Mutation_p.N1477S|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.N1477S	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1477						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGAAGAAAACAAACCTAAG	0.358																																																0			5						A	SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	130	123	126		4430,4430	5	1	5		126	0,8600		0,0,4300	no	missense,missense	ANKHD1,ANKHD1-EIF4EBP3	NM_020690.5,NM_017747.2	46,46	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign,benign	1477/2618,1477/2543	139903763	1,13005	2203	4300	6503	139883947	SO:0001583	missense	54882			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4430A>G	5.37:g.139903763A>G	ENSP00000354085:p.Asn1477Ser		139883947	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.206503	0.39003	2.27E-4	0.0	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000421134;ENST00000431508;ENST00000532219	T;T;T;T;T	0.64803	-0.08;-0.12;-0.02;1.96;-0.12	5.0	5.0	0.66597	.	0.354425	0.32640	N	0.005836	T	0.34629	0.0904	N	0.04959	-0.14	0.25404	N	0.988411	B;B;B;B;B	0.10296	0.003;0.001;0.0;0.001;0.001	B;B;B;B;B	0.08055	0.002;0.002;0.0;0.003;0.001	T	0.16778	-1.0391	10	0.08179	T	0.78	.	9.2719	0.37677	0.9178:0.0:0.0822:0.0	.	1477;1477;1496;1477;1477	E9PF56;Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3	.;.;.;.;ANKH1_HUMAN	S	1477;1477;1477;1496;133;1477	ENSP00000354085:N1477S;ENSP00000297183:N1477S;ENSP00000394489:N1496S;ENSP00000393204:N133S;ENSP00000432016:N1477S	ENSP00000432016:N1477S	N	+	2	0	ANKHD1-EIF4EBP3;ANKHD1	139883947	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.539000	0.45718	2.006000	0.58801	0.528000	0.53228	AAC		0.358	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139903763	A	G	139903763	3	3	115	1	0	0	0	0	1	0	0	0	628	43	2	4	4634	4	ANKHD1	5	139903763	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	27728556	139903763	41011497	67	30874										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140221294	140221294	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgaaggatgttaatgacaacCcgccagtgttccgggtaaaa	11	8	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:140221294C>G	ENST00000531613.1	+	1	388	c.388C>G	c.(388-390)Ccg>Gcg	p.P130A	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.P130A|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	130	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.P130A(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATGACAACCCGCCAGTGTT	0.567																																																2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	5											103	115	111					5																	140221294		2203	4299	6502	140201478	SO:0001583	missense	56140			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.388C>G	5.37:g.140221294C>G	ENSP00000434655:p.Pro130Ala		140201478	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	0.734	-0.778747	0.02929	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.18657	2.2;2.2	3.72	1.67	0.24075	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.213089	0.23185	N	0.050974	T	0.05640	0.0148	N	0.01188	-0.97	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.22601	0.04;0.01	T	0.42599	-0.9442	10	0.08179	T	0.78	.	7.0592	0.25115	0.0:0.3721:0.4471:0.1808	.	130;130	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	A	130	ENSP00000434655:P130A;ENSP00000367363:P130A	ENSP00000367363:P130A	P	+	1	0	PCDHA8	140201478	0.000000	0.05858	0.783000	0.31826	0.460000	0.32559	-1.589000	0.02104	0.652000	0.30806	0.552000	0.68991	CCG		0.567	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		G	140221294	C	G	140221294	3	3	115	1	0	0	0	0	1	0	0	0	11561	623	22	5	390	5	PCDHA8	5	140221294	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	317531	140221294	40693966	68	30875										
RNF145	153830	hgsc.bcm.edu	37	chr5	158595954	158595954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agactgtaggatagaagctaCgacaatgaaaaggataatac	10	5	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:158595954C>T	ENST00000424310.2	-	8	1407	c.1048G>A	c.(1048-1050)Gta>Ata	p.V350I	RNF145_ENST00000518802.1_Missense_Mutation_p.V380I|RNF145_ENST00000520638.1_Missense_Mutation_p.V364I|RNF145_ENST00000274542.2_Missense_Mutation_p.V378I|RNF145_ENST00000521606.2_Missense_Mutation_p.V367I|RNF145_ENST00000519865.1_Missense_Mutation_p.V350I	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	350						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATAGAAGCTACGACAATGAAA	0.408																																																0			5											118	117	117					5																	158595954		2203	4300	6503	158528532	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1048G>A	5.37:g.158595954C>T	ENSP00000409064:p.Val350Ile		158528532	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.115532	0.56505	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.77877	-1.13;-1.12;-1.12;-1.13;-1.13;-1.13;-1.13	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.71550	0.3353	L	0.43152	1.355	0.80722	D	1	P;P;P;P;P	0.50369	0.922;0.922;0.922;0.934;0.904	B;B;B;B;B	0.40782	0.234;0.234;0.34;0.28;0.23	T	0.70085	-0.4969	10	0.21014	T	0.42	-14.435	18.836	0.92162	0.0:1.0:0.0:0.0	.	367;364;380;350;378	B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;RN145_HUMAN;.	I	378;350;350;366;367;380;350;364	ENSP00000274542:V378I;ENSP00000430397:V350I;ENSP00000409064:V350I;ENSP00000430753:V366I;ENSP00000445115:V367I;ENSP00000430955:V380I;ENSP00000429071:V364I	ENSP00000274542:V378I	V	-	1	0	RNF145	158528532	1.000000	0.71417	0.114000	0.21550	0.681000	0.39784	7.776000	0.85560	2.516000	0.84829	0.585000	0.79938	GTA		0.408	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		T	158595954	C	T	158595954	3	4	115	1	0	0	0	0	1	0	0	0	13484	536	19	1	959	1	RNF145	5	158595954	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	18374660	158595954	22319306	69	30876										
WWC1	23286	hgsc.bcm.edu	37	chr5	167887746	167887746	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	acgcagcgtccggatgaagcGggtaagagagtcacctcaaa	13	10	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:167887746G>A	ENST00000265293.4	+	20	3417	c.2915G>A	c.(2914-2916)cGg>cAg	p.R972Q	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Splice_Site_p.R972Q	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	972	Interaction with PRKCZ.|Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CGGATGAAGCGGGTAAGAGAG	0.532																																																0			5											73	72	73					5																	167887746		2203	4300	6503	167820324	SO:0001630	splice_region_variant	23286			AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2916+1G>A	5.37:g.167887746G>A			167820324	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.042729	0.75732	.	.	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.59364	0.27;0.27;0.27	5.62	5.62	0.85841	.	0.064020	0.64402	D	0.000011	T	0.66674	0.2813	L	0.39397	1.21	0.53688	D	0.999974	D;D	0.76494	0.999;0.997	P;P	0.61940	0.896;0.736	T	0.59747	-0.7396	10	0.23302	T	0.38	.	19.665	0.95890	0.0:0.0:1.0:0.0	.	972;972	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	Q	972;972;298	ENSP00000265293:R972Q;ENSP00000427772:R972Q;ENSP00000428084:R298Q	ENSP00000265293:R972Q	R	+	2	0	WWC1	167820324	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.417000	0.59822	2.640000	0.89533	0.650000	0.86243	CGG		0.532	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	Missense_Mutation	A	167887746	G	A	167887746	5	1	115	1	0	0	0	0	0	0	1	0	17451	1130	39	1	2993	1	WWC1	5	167887746	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10	9291792	167887746	13027514	70	30877										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178505825	178505825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgaagaagctgtggaatttgAgagcgagatagaagaagagc	15	3	0	7			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr5:178505825A>G	ENST00000315475.6	+	5	698	c.392A>G	c.(391-393)gAg>gGg	p.E131G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GTGGAATTTGAGAGCGAGATA	0.378																																																0			5											88	94	92					5																	178505825		2203	4300	6503	178438431	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.392A>G	5.37:g.178505825A>G	ENSP00000324064:p.Glu131Gly		178438431	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	11.86	1.765119	0.31228	.	.	ENSG00000177932	ENST00000315475	T	0.05925	3.37	3.87	2.66	0.31614	.	.	.	.	.	T	0.04998	0.0134	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.38499	-0.9658	9	0.39692	T	0.17	-4.6231	7.2189	0.25975	0.7724:0.2276:0.0:0.0	.	131	Q86Y25	Z354C_HUMAN	G	131	ENSP00000324064:E131G	ENSP00000324064:E131G	E	+	2	0	ZNF354C	178438431	0.057000	0.20700	0.003000	0.11579	0.019000	0.09904	1.850000	0.39328	0.610000	0.30035	0.482000	0.46254	GAG		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178505825	A	G	178505825	3	3	115	1	0	0	0	0	1	0	0	0	17905	304	11	4	406	4	ZNF354C	5	178505825	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	10618079	178505825	2409435	71	30878										
TBC1D7	51256	hgsc.bcm.edu	37	chr6	13321191	13321191	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccagactccagctgatacatGcggagatagacttcagcctg	10	12	1	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:13321191G>T	ENST00000379300.3	-	4	573	c.330C>A	c.(328-330)cgC>cgA	p.R110R	TBC1D7_ENST00000607658.1_Silent_p.R83R|TBC1D7_ENST00000356436.4_Silent_p.R110R|TBC1D7_ENST00000343141.4_Silent_p.R110R|TBC1D7_ENST00000379307.2_Silent_p.R83R|TBC1D7_ENST00000607532.1_5'UTR	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	110	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			GCTGATACATGCGGAGATAGA	0.483																																																0			6											249	214	226					6																	13321191		2203	4300	6503	13429170	SO:0001819	synonymous_variant	51256			AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.330C>A	6.37:g.13321191G>T			13429170	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Silent	SNP	ENST00000379300.3	37	CCDS4523.1																																																																																				0.483	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		T	13321191	G	T	13321191	2	4	115	1	0	0	0	0	0	0	0	1	15663	1306	46	2		2	TBC1D7	6	13321191	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10		13321191	157793876	72	30879										
HIST1H2BG	8339	hgsc.bcm.edu	37	chr6	26216614	26216614	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctggaggtaatggtcgagcgCttgttgtagtgggccagacg	17	7	0	1	rs202170052		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:26216614C>G	ENST00000244601.3	-	1	258	c.258G>C	c.(256-258)aaG>aaC	p.K86N	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	86					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				TGGTCGAGCGCTTGTTGTAGT	0.587																																																0			6											112	108	109					6																	26216614		2203	4300	6503	26324593	SO:0001583	missense	8339			M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"Histones / Replication-dependent"	4746	protein-coding gene	gene with protein product		602798	"H2B histone family, member A", "histone 1, H2bg"	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.258G>C	6.37:g.26216614C>G	ENSP00000244601:p.Lys86Asn		26324593	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000244601.3	37	CCDS4594.1	.	.	.	.	.	.	.	.	.	.	.	15.89	2.966306	0.53507	.	.	ENSG00000187990	ENST00000244601	T	0.75050	-0.9	3.89	3.89	0.44902	.	0.000000	0.34531	U	0.003887	T	0.77870	0.4195	.	.	.	0.34749	D	0.731539	.	.	.	.	.	.	T	0.82192	-0.0579	7	0.87932	D	0	.	15.3699	0.74554	0.0:1.0:0.0:0.0	.	.	.	.	N	86	ENSP00000244601:K86N	ENSP00000244601:K86N	K	-	3	2	HIST1H2BG	26324593	1.000000	0.71417	1.000000	0.80357	0.143000	0.21401	3.777000	0.55364	2.172000	0.68678	0.561000	0.74099	AAG		0.587	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518		G	26216614	C	G	26216614	3	3	115	1	0	0	0	0	1	0	0	0	7167	796	28	5	126	5	HIST1H2BG	6	26216614	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	12895423	26216614	144898453	73	30880										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323086	29323086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttttgacagcttctttgatgTccttattcctcaatgtgtaa	6	8	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:29323086T>C	ENST00000377154.1	-	4	1186	c.887A>G	c.(886-888)gAc>gGc	p.D296G	OR5V1_ENST00000543825.1_Missense_Mutation_p.D296G			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	296						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D296G(1)		breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTCTTTGATGTCCTTATTCCT	0.378																																					Ovarian(32;43 883 21137 32120 42650)											1	Substitution - Missense(1)	ovary(1)	6											113	110	111					6																	29323086		2203	4300	6503	29431065	SO:0001583	missense	81696				CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.887A>G	6.37:g.29323086T>C	ENSP00000366359:p.Asp296Gly		29431065	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.714295	0.68730	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.39592	1.07;1.07	4.53	4.53	0.55603	.	0.000000	0.34580	N	0.003844	T	0.46425	0.1392	L	0.49126	1.545	0.46458	D	0.999056	D	0.69078	0.997	P	0.62885	0.908	T	0.51710	-0.8671	10	0.87932	D	0	-25.7631	13.9454	0.64082	0.0:0.0:0.0:1.0	.	296	Q9UGF6	OR5V1_HUMAN	G	296	ENSP00000366359:D296G;ENSP00000443309:D296G	ENSP00000366356:D296G	D	-	2	0	OR5V1	29431065	1.000000	0.71417	0.932000	0.37286	0.634000	0.38068	6.942000	0.75928	2.021000	0.59480	0.443000	0.29094	GAC		0.378	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			C	29323086	T	C	29323086	3	2	115	1	0	0	0	0	1	0	0	0	11215	1667	58	4	81	4	OR5V1	6	29323086	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	3106472	29323086	141791981	74	30881										
CUL9	23113	hgsc.bcm.edu	37	chr6	43180950	43180950	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gcagtggacgtggctgggccGggctgagctgcagtttggga	20	8	0	1	rs531967221		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:43180950G>A	ENST00000252050.4	+	27	5360	c.5276G>A	c.(5275-5277)cGg>cAg	p.R1759Q	CUL9_ENST00000502937.1_3'UTR|CUL9_ENST00000372647.2_Missense_Mutation_p.R1759Q|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Missense_Mutation_p.R1649Q	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1759					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TGGCTGGGCCGGGCTGAGCTG	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		18584	0		0	False		,,,				2504	0															0			6											97	85	89					6																	43180950		2203	4300	6503	43288928	SO:0001583	missense	23113			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5276G>A	6.37:g.43180950G>A	ENSP00000252050:p.Arg1759Gln		43288928	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260415	0.80246	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.74106	-0.81;-0.81;-0.81	4.97	4.11	0.48088	Cullin, N-terminal (1);Cullin homology (2);	0.369213	0.27754	N	0.017981	T	0.54095	0.1837	L	0.55481	1.735	0.29114	N	0.880709	P;P;P	0.52061	0.942;0.95;0.95	P;P;B	0.45037	0.455;0.467;0.293	T	0.53215	-0.8470	10	0.45353	T	0.12	-23.9725	6.186	0.20498	0.3325:0.0:0.6674:0.0	.	1649;1759;1759	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	Q	1759;1649;1759	ENSP00000252050:R1759Q;ENSP00000346490:R1649Q;ENSP00000361730:R1759Q	ENSP00000252050:R1759Q	R	+	2	0	CUL9	43288928	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.678000	0.46900	1.087000	0.41251	0.655000	0.94253	CGG		0.567	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43180950	G	A	43180950	3	1	115	1	0	0	0	0	1	0	0	0	4067	1116	39	1	5378	1	CUL9	6	43180950	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	13857864	43180950	127934117	75	30882										
TMEM63B	55362	hgsc.bcm.edu	37	chr6	44107234	44107234	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atccgggacaaatgtgggggCgatgccgtgcactacctgtc	14	11	0	0	rs199984650		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:44107234C>T	ENST00000259746.9	+	7	621	c.438C>T	c.(436-438)ggC>ggT	p.G146G	TMEM63B_ENST00000323267.6_Silent_p.G146G|TMEM63B_ENST00000527188.1_3'UTR			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	146					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			AATGTGGGGGCGATGCCGTGC	0.582																																																0			6						C		0,4406		0,0,2203	133	110	118		438	-1.9	0.8	6		118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM63B	NM_018426.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		146/833	44107234	1,13005	2203	4300	6503	44215212	SO:0001819	synonymous_variant	55362			BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.438C>T	6.37:g.44107234C>T			44215212	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	C	2.105	-0.405067	0.04832	0.0	1.16E-4	ENSG00000137216	ENST00000371893	.	.	.	4.53	-1.87	0.07737	.	.	.	.	.	T	0.22898	0.0553	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28808	-1.0032	4	.	.	.	.	2.0558	0.03581	0.1439:0.1929:0.1424:0.5208	.	.	.	.	V	75	.	.	A	+	2	0	TMEM63B	44215212	0.023000	0.18921	0.801000	0.32222	0.134000	0.20937	-0.786000	0.04623	-0.370000	0.08016	-0.305000	0.09177	GCG		0.582	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		T	44107234	C	T	44107234	2	4	115	1	0	0	0	0	0	0	0	1	16230	755	27	1		1	TMEM63B	6	44107234	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	926284	44107234	127007833	76	30883										
DST	667	hgsc.bcm.edu	37	chr6	56504783	56504783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttcttcaatagctctatgaaCatttttatgattttctaaat	3	6	4	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:56504783C>T	ENST00000361203.3	-	15	1937	c.1930G>A	c.(1930-1932)Gtt>Att	p.V644I	DST_ENST00000421834.2_Missense_Mutation_p.V644I|DST_ENST00000370765.6_Missense_Mutation_p.V318I|DST_ENST00000446842.2_Missense_Mutation_p.V318I|DST_ENST00000312431.6_Missense_Mutation_p.V644I|DST_ENST00000370769.4_Missense_Mutation_p.V644I|DST_ENST00000518935.1_Missense_Mutation_p.V318I|DST_ENST00000370754.5_Missense_Mutation_p.V822I|DST_ENST00000370788.2_Missense_Mutation_p.V644I|DST_ENST00000244364.6_Missense_Mutation_p.V318I			Q03001	DYST_HUMAN	dystonin	644					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCTCTATGAACATTTTTATGA	0.318																																																0			6											55	60	58					6																	56504783		2203	4300	6503	56612742	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1930G>A	6.37:g.56504783C>T	ENSP00000354508:p.Val644Ile		56612742	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	12.71	2.019880	0.35606	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	D;D;D;D;D;D;D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	5.45	4.58	0.56647	.	0.000000	0.44688	D	0.000440	D	0.84866	0.5567	N	0.17474	0.49	0.28342	N	0.921302	B;B;D;B;B;B;B;B;B;B	0.55385	0.002;0.0;0.971;0.0;0.008;0.002;0.016;0.109;0.0;0.004	B;B;D;B;B;B;B;B;B;B	0.68353	0.003;0.002;0.957;0.002;0.028;0.003;0.086;0.246;0.002;0.011	T	0.81693	-0.0817	9	0.08837	T	0.75	.	9.1727	0.37093	0.1454:0.7817:0.0:0.0729	.	673;644;644;822;760;318;318;318;644;318	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	I	318;822;644;644;318;644;644;644;318;684;318;318	ENSP00000244364:V318I;ENSP00000359790:V822I;ENSP00000359805:V644I;ENSP00000400883:V644I;ENSP00000393645:V318I;ENSP00000307959:V644I;ENSP00000359824:V644I;ENSP00000354508:V644I;ENSP00000404924:V318I;ENSP00000431030:V684I;ENSP00000359801:V318I;ENSP00000431003:V318I	ENSP00000244364:V318I	V	-	1	0	DST	56612742	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.726000	0.38085	1.525000	0.49052	0.655000	0.94253	GTT		0.318	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56504783	C	T	56504783	3	4	115	1	0	0	0	0	1	0	0	0	4794	478	17	3	19523	3	DST	6	56504783	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	12397549	56504783	114610284	77	30884										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76728499	76728499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gggagtcagcgagctctgccTtgaacttctggtttaccaga	12	10	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:76728499T>C	ENST00000369950.3	-	7	932	c.743A>G	c.(742-744)aAg>aGg	p.K248R	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GAGCTCTGCCTTGAACTTCTG	0.498																																					Pancreas(37;839 1141 2599 26037)											0			6											123	114	117					6																	76728499		2203	4300	6503	76785219	SO:0001583	missense	3617			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.743A>G	6.37:g.76728499T>C	ENSP00000358966:p.Lys248Arg		76785219		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306861	0.23821	.	.	ENSG00000112706	ENST00000369950	T	0.38560	1.13	6.17	2.3	0.28687	SEA (3);	0.480009	0.21210	N	0.078333	T	0.17534	0.0421	L	0.43923	1.385	0.80722	D	1	B	0.32968	0.392	B	0.33960	0.173	T	0.04178	-1.0971	10	0.51188	T	0.08	.	6.9835	0.24715	0.0:0.0783:0.3998:0.5219	.	248	Q17R60	IMPG1_HUMAN	R	248	ENSP00000358966:K248R	ENSP00000358966:K248R	K	-	2	0	IMPG1	76785219	0.953000	0.32496	0.805000	0.32314	0.553000	0.35397	1.542000	0.36137	0.555000	0.29079	0.533000	0.62120	AAG		0.498	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		C	76728499	T	C	76728499	3	2	115	1	0	0	0	0	1	0	0	0	7749	1609	56	4	1694	4	IMPG1	6	76728499	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	20223716	76728499	94386568	78	30885										
UST	10090	hgsc.bcm.edu	37	chr6	149285593	149285593	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	caacatcattagagaccccgTcaaccggttcttatccaact	5	14	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:149285593T>C	ENST00000367463.4	+	5	678	c.575T>C	c.(574-576)gTc>gCc	p.V192A	RP11-162J8.2_ENST00000413845.1_RNA	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	192					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		AGAGACCCCGTCAACCGGTTC	0.502																																																0			6											104	95	98					6																	149285593		2203	4300	6503	149327286	SO:0001583	missense	10090			AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.575T>C	6.37:g.149285593T>C	ENSP00000356433:p.Val192Ala		149327286	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.805897	0.90623	.	.	ENSG00000111962	ENST00000367463	T	0.75704	-0.96	5.87	5.87	0.94306	.	0.110649	0.64402	D	0.000008	T	0.66458	0.2791	L	0.48218	1.51	0.49483	D	0.999795	P	0.38250	0.624	B	0.43623	0.425	T	0.71048	-0.4705	10	0.52906	T	0.07	-19.6816	16.3322	0.83039	0.0:0.0:0.0:1.0	.	192	Q9Y2C2	UST_HUMAN	A	192	ENSP00000356433:V192A	ENSP00000356433:V192A	V	+	2	0	UST	149327286	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.999000	0.88496	2.251000	0.74343	0.529000	0.55759	GTC		0.502	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		C	149285593	T	C	149285593	3	2	115	1	0	0	0	0	1	0	0	0	17133	1667	58	4	593	4	UST	6	149285593	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	72557094	149285593	21829474	79	30886										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152461139	152461139	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atgtcagtgctgagttccagAcgctggagctgttccaactc	11	11	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:152461139A>G	ENST00000367255.5	-	140	26005	c.25404T>C	c.(25402-25404)cgT>cgC	p.R8468R	SYNE1_ENST00000448038.1_Silent_p.R8420R|SYNE1_ENST00000423061.1_Silent_p.R8420R|SYNE1_ENST00000356820.4_Silent_p.R2992R|SYNE1_ENST00000539504.1_Silent_p.R623R|SYNE1_ENST00000265368.4_Silent_p.R8468R|SYNE1_ENST00000354674.4_Silent_p.R646R|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000341594.5_Silent_p.R8080R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8468			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGAGTTCCAGACGCTGGAGCT	0.562										HNSCC(10;0.0054)																																						0			6											118	96	104					6																	152461139		2203	4300	6503	152502832	SO:0001819	synonymous_variant	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25404T>C	6.37:g.152461139A>G			152502832	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.562	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152461139	A	G	152461139	2	3	115	1	0	0	0	0	0	0	0	1	15484	262	10	4		4	SYNE1	6	152461139	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	3175546	152461139	18653928	80	30887										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168352576	168352576	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agcaaagaggagctttcctcGggggacagtctgtcccccga	13	12	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr6:168352576G>A	ENST00000447894.2	+	29	4521	c.4521G>A	c.(4519-4521)tcG>tcA	p.S1507S	MLLT4_ENST00000392112.1_Silent_p.S1490S|MLLT4_ENST00000351017.4_Silent_p.S1514S|MLLT4_ENST00000400822.3_Silent_p.S1506S|MLLT4_ENST00000392108.3_Silent_p.S1507S|MLLT4_ENST00000344191.4_Silent_p.S1507S|MLLT4_ENST00000366806.2_Silent_p.S1507S			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1507					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.S1507S(1)|p.S1491S(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		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)		AGCTTTCCTCGGGGGACAGTC	0.592			T	MLL	AL																																		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	2	Substitution - coding silent(2)	kidney(2)	6											33	41	38					6																	168352576		2202	4298	6500	168095425	SO:0001819	synonymous_variant	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.4521G>A	6.37:g.168352576G>A			168095425	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																					0.592	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		A	168352576	G	A	168352576	2	1	115	1	0	0	0	0	0	0	0	1	9659	1103	39	1		1	MLLT4	6	168352576	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	15891437	168352576	2762491	81	30888										
RBAK	57786	hgsc.bcm.edu	37	chr7	5097321	5097321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttcccattaacaggatatgAtaccaccaagccaaacgtca	5	12	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:5097321A>G	ENST00000353796.3	+	5	473	c.149A>G	c.(148-150)gAt>gGt	p.D50G	RBAK-RBAKDN_ENST00000407184.1_Missense_Mutation_p.D50G|RBAK-RBAKDN_ENST00000396904.2_Missense_Mutation_p.D50G|RBAK_ENST00000396912.1_Missense_Mutation_p.D50G	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	50	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		ACAGGATATGATACCACCAAG	0.453																																																0			7											130	114	119					7																	5097321		2203	4300	6503	5063847	SO:0001583	missense	57786			AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.149A>G	7.37:g.5097321A>G	ENSP00000275423:p.Asp50Gly		5063847	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	37	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.862177	0.32884	.	.	ENSG00000146587	ENST00000407184;ENST00000353796;ENST00000396904;ENST00000396912	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	3.3	3.3	0.37823	Krueppel-associated box (3);	0.141960	0.32459	N	0.006063	T	0.34395	0.0896	N	0.04746	-0.17	0.30448	N	0.775556	D	0.63880	0.993	D	0.72338	0.977	T	0.37663	-0.9696	9	0.20046	T	0.44	.	6.725	0.23350	0.7574:0.2426:0.0:0.0	.	50	Q9NYW8	RBAK_HUMAN	G	50	ENSP00000385560:D50G;ENSP00000275423:D50G;ENSP00000380112:D50G;ENSP00000380120:D50G	ENSP00000275423:D50G	D	+	2	0	RBAK	5063847	0.093000	0.21703	0.025000	0.17156	0.073000	0.16967	1.763000	0.38461	1.724000	0.51502	0.379000	0.24179	GAT		0.453	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		G	5097321	A	G	5097321	3	3	115	1	0	0	0	0	1	0	0	0	13137	333	12	4	159	4	RBAK	7	5097321	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10		5097321	154041342	82	30889										
GLI3	2737	hgsc.bcm.edu	37	chr7	42006129	42006129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gatggtgctggcgctgctgtCccttctgttgagcatgttca	13	10	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:42006129C>T	ENST00000395925.3	-	15	2626	c.2542G>A	c.(2542-2544)Gac>Aac	p.D848N	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	848					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCGCTGCTGTCCCTTCTGTTG	0.642									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																							0			7											57	58	57					7																	42006129		2203	4300	6503	41972654	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2542G>A	7.37:g.42006129C>T	ENSP00000379258:p.Asp848Asn		41972654	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.305867	0.40795	.	.	ENSG00000106571	ENST00000395925	D	0.92348	-3.02	4.98	4.98	0.66077	.	0.198643	0.52532	D	0.000065	D	0.94879	0.8345	M	0.71036	2.16	0.80722	D	1	D	0.56035	0.974	P	0.58577	0.841	D	0.94807	0.7975	10	0.49607	T	0.09	.	18.268	0.90057	0.0:1.0:0.0:0.0	.	848	P10071	GLI3_HUMAN	N	848	ENSP00000379258:D848N	ENSP00000379258:D848N	D	-	1	0	GLI3	41972654	1.000000	0.71417	1.000000	0.80357	0.163000	0.22366	5.958000	0.70330	2.284000	0.76573	0.561000	0.74099	GAC		0.642	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42006129	C	T	42006129	3	4	115	1	0	0	0	0	1	0	0	0	6459	855	30	3	2204	3	GLI3	7	42006129	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	36908808	42006129	117132534	83	30890										
EGFR	1956	hgsc.bcm.edu	37	chr7	55241660	55241660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agaagctcccaaccaagctcTcttgaggatcttgaaggaaa	9	10	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:55241660T>C	ENST00000275493.2	+	18	2285	c.2108T>C	c.(2107-2109)cTc>cCc	p.L703P	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.L658P|EGFR_ENST00000454757.2_Missense_Mutation_p.L650P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	703	Important for dimerization, phosphorylation and activation.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.L703P(4)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AACCAAGCTCTCTTGAGGATC	0.547		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	4	Substitution - Missense(4)	ovary(3)|lung(1)	7											93	96	95					7																	55241660		2203	4300	6503	55209154	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2108T>C	7.37:g.55241660T>C	ENSP00000275493:p.Leu703Pro		55209154	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.349012	0.61183	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.76578	-1.03;-1.03;-1.02	5.83	4.65	0.58169	Protein kinase-like domain (1);	0.116895	0.64402	D	0.000017	T	0.71945	0.3400	L	0.40543	1.245	0.58432	D	0.999999	P;P	0.49358	0.923;0.825	B;P	0.46110	0.386;0.504	T	0.70945	-0.4734	10	0.48119	T	0.1	.	9.7366	0.40392	0.2841:0.0:0.0:0.7159	.	658;703	Q504U8;P00533	.;EGFR_HUMAN	P	658;573;703;650	ENSP00000415559:L658P;ENSP00000275493:L703P;ENSP00000395243:L650P	ENSP00000275493:L703P	L	+	2	0	EGFR	55209154	1.000000	0.71417	0.986000	0.45419	0.959000	0.62525	3.250000	0.51445	0.981000	0.38548	0.460000	0.39030	CTC		0.547	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		C	55241660	T	C	55241660	3	2	115	1	0	0	0	0	1	0	0	0	4978	1551	54	4	2442	4	EGFR	7	55241660	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	13235531	55241660	103897003	84	30891										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82997234	82997234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tacctccaaggtgattttacGgaccgtatggacaaagctat	9	9	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:82997234G>A	ENST00000307792.3	-	17	2463	c.1996C>T	c.(1996-1998)Cgt>Tgt	p.R666C	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R606C	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	666	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GTGATTTTACGGACCGTATGG	0.463																																																0			7											131	115	120					7																	82997234		2203	4300	6503	82835170	SO:0001583	missense	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1996C>T	7.37:g.82997234G>A	ENSP00000303212:p.Arg666Cys		82835170	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222734	0.58668	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.01613	4.73;4.73	5.77	5.77	0.91146	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.066187	0.64402	D	0.000012	T	0.05318	0.0141	L	0.59436	1.845	0.37516	D	0.917325	D	0.63880	0.993	P	0.53649	0.731	T	0.38993	-0.9635	10	0.42905	T	0.14	.	12.9659	0.58483	0.0:0.0:0.7318:0.2682	.	666	O15041	SEM3E_HUMAN	C	666;606;666	ENSP00000303212:R666C;ENSP00000405052:R606C	ENSP00000303212:R666C	R	-	1	0	SEMA3E	82835170	0.138000	0.22547	0.370000	0.25965	0.978000	0.69477	1.280000	0.33202	2.727000	0.93392	0.585000	0.79938	CGT		0.463	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	82997234	G	A	82997234	3	1	115	1	0	0	0	0	1	0	0	0	14065	1116	39	1	335	1	SEMA3E	7	82997234	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	27755574	82997234	76141429	85	30892										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83592543	83592543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttcttttcgctcttcatttCgcctctggaattgccaatag	6	12	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:83592543C>T	ENST00000265362.4	-	16	2152	c.1838G>A	c.(1837-1839)cGa>cAa	p.R613Q	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R613Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	613	Ig-like C2-type.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.R613Q(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTCTTCATTTCGCCTCTGGAA	0.403																																																1	Substitution - Missense(1)	large_intestine(1)	7											187	187	187					7																	83592543		2203	4300	6503	83430479	SO:0001583	missense	10371			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1838G>A	7.37:g.83592543C>T	ENSP00000265362:p.Arg613Gln		83430479		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740001	0.30865	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.01527	4.8;4.8	5.9	4.91	0.64330	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.355176	0.32624	N	0.005858	T	0.00724	0.0024	N	0.01705	-0.755	0.31357	N	0.681812	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.14252	T	0.57	.	3.4603	0.07531	0.0:0.5419:0.2844:0.1737	.	613	Q14563	SEM3A_HUMAN	Q	613	ENSP00000265362:R613Q;ENSP00000415260:R613Q	ENSP00000265362:R613Q	R	-	2	0	SEMA3A	83430479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.637000	0.46553	2.802000	0.96397	0.650000	0.86243	CGA		0.403	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83592543	C	T	83592543	3	4	115	1	0	0	0	0	1	0	0	0	14061	884	31	1	485	1	SEMA3A	7	83592543	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	595309	83592543	75546120	86	30893										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964351	88964351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agtaaccacatcagcatgacCagcaaggtttccggatgtgg	11	10	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:88964351C>T	ENST00000333190.4	+	4	2664	c.2055C>T	c.(2053-2055)acC>acT	p.T685T		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	685							metal ion binding (GO:0046872)	p.T685T(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TCAGCATGACCAGCAAGGTTT	0.448										HNSCC(36;0.09)																																						1	Substitution - coding silent(1)	ovary(1)	7											80	77	78					7																	88964351		2203	4300	6503	88802287	SO:0001819	synonymous_variant	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2055C>T	7.37:g.88964351C>T			88802287	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																				0.448	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88964351	C	T	88964351	2	4	115	1	0	0	0	0	0	0	0	1	18210	581	21	3		3	ZNF804B	7	88964351	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	5371808	88964351	70174312	87	30894										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107342418	107342418	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttccagtcaaagtgaacgtTcccaaagtgccaatccatag	7	12	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:107342418T>C	ENST00000265715.3	+	17	2174	c.1950T>C	c.(1948-1950)gtT>gtC	p.V650V	SLC26A4_ENST00000541474.1_Silent_p.V211V|SLC26A4_ENST00000543100.1_Silent_p.V219V|SLC26A4_ENST00000544569.1_Silent_p.V237V	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	650	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.V650V(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AAGTGAACGTTCCCAAAGTGC	0.453									Pendred syndrome																																							1	Substitution - coding silent(1)	ovary(1)	7											130	109	116					7																	107342418		2203	4300	6503	107129654	SO:0001819	synonymous_variant	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1950T>C	7.37:g.107342418T>C			107129654	B7Z266|O43170	Silent	SNP	ENST00000265715.3	37	CCDS5746.1																																																																																				0.453	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		C	107342418	T	C	107342418	2	2	115	1	0	0	0	0	0	0	0	1	14556	1770	62	4		4	SLC26A4	7	107342418	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	18378067	107342418	51796245	88	30895										
ASZ1	136991	hgsc.bcm.edu	37	chr7	117008723	117008723	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgtacagctgttattaaatgGccacactgtttatttaattt	6	6	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:117008723G>A	ENST00000284629.2	-	11	1166	c.1104C>T	c.(1102-1104)ggC>ggT	p.G368G		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1									p.G368G(2)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			TTATTAAATGGCCACACTGTT	0.308																																																2	Substitution - coding silent(2)	central_nervous_system(2)	7											103	111	108					7																	117008723		2202	4288	6490	116795959	SO:0001819	synonymous_variant	136991			AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	1350	protein-coding gene	gene with protein product		605797	"ankyrin-like 1"	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.1104C>T	7.37:g.117008723G>A			116795959		Silent	SNP	ENST00000284629.2	37	CCDS5772.1																																																																																				0.308	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768		A	117008723	G	A	117008723	2	1	115	1	0	0	0	0	0	0	0	1	1070	1190	42	3		3	ASZ1	7	117008723	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	9666305	117008723	42129940	89	30896										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123599953	123599953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttctacaatgcttcaccctCcacactatctgccacaatgt	3	15	3	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:123599953C>T	ENST00000439500.1	+	6	2073	c.1460C>T	c.(1459-1461)tCc>tTc	p.S487F	SPAM1_ENST00000460182.1_Missense_Mutation_p.S487F|SPAM1_ENST00000223028.7_Missense_Mutation_p.S487F|SPAM1_ENST00000340011.5_Missense_Mutation_p.S487F|SPAM1_ENST00000402183.2_Missense_Mutation_p.S487F	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	487					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCTTCACCCTCCACACTATCT	0.383																																																0			7											127	118	121					7																	123599953		2203	4300	6503	123387189	SO:0001583	missense	6677			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1460C>T	7.37:g.123599953C>T	ENSP00000402123:p.Ser487Phe		123387189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	C	8.418	0.845787	0.16963	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.25	-0.999	0.10208	.	2.367520	0.01853	N	0.036020	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.32693	-0.9897	10	0.41790	T	0.15	3.7967	6.4218	0.21748	0.0:0.4434:0.0:0.5566	.	487;487	Q8TC30;P38567	.;HYALP_HUMAN	F	487	ENSP00000386028:S487F;ENSP00000417934:S487F;ENSP00000345849:S487F;ENSP00000402123:S487F;ENSP00000223028:S487F	ENSP00000223028:S487F	S	+	2	0	SPAM1	123387189	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.291000	0.18994	-0.235000	0.09767	-0.157000	0.13467	TCC		0.383	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			T	123599953	C	T	123599953	3	4	115	1	0	0	0	0	1	0	0	0	15025	855	30	3	1470	3	SPAM1	7	123599953	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	6591230	123599953	35538710	90	30897										
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150325095	150325095	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgtgccctgttgttgaagccGcaatggcgccgtgcaagggt	15	10	0	1	rs561097678		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:150325095G>A	ENST00000328902.5	-	3	807	c.591C>T	c.(589-591)tgC>tgT	p.C197C	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	197	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)	p.C197C(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGTTGAAGCCGCAATGGCGCC	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		18922	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	large_intestine(1)	7											115	121	119					7																	150325095		2203	4300	6503	149956028	SO:0001819	synonymous_variant	474344			AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.591C>T	7.37:g.150325095G>A			149956028	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Silent	SNP	ENST00000328902.5	37	CCDS34778.1																																																																																				0.572	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		A	150325095	G	A	150325095	2	1	115	1	0	0	0	0	0	0	0	1	6403	1079	38	1		1	GIMAP6	7	150325095	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	26725142	150325095	8813568	91	30898										
MLL3	58508	hgsc.bcm.edu	37	chr7	151962266	151962266	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aagaggtctcccgggctgtcGcacactgcacagtttgcatc	11	13	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr7:151962266G>A	ENST00000262189.6	-	8	1259	c.1041C>T	c.(1039-1041)tgC>tgT	p.C347C	KMT2C_ENST00000355193.2_Silent_p.C347C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	347			C -> G (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CCGGGCTGTCGCACACTGCAC	0.378																																																0			7											108	98	101					7																	151962266		2203	4296	6499	151593199	SO:0001819	synonymous_variant	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1041C>T	7.37:g.151962266G>A			151593199	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																				0.378	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151962266	G	A	151962266	2	1	115	1	0	0	0	0	0	0	0	1	9652	1079	38	1		1	MLL3	7	151962266	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	1637171	151962266	7176397	92	30899										
MSR1	4481	hgsc.bcm.edu	37	chr8	16007743	16007743	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	acacattattgtaatacctgGccttccggcatatcctggga	8	11	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr8:16007743G>A	ENST00000262101.5	-	7	1097	c.976C>T	c.(976-978)Cca>Tca	p.P326S	MSR1_ENST00000355282.2_Missense_Mutation_p.P326S|MSR1_ENST00000445506.2_Missense_Mutation_p.P344S|MSR1_ENST00000381998.4_Missense_Mutation_p.P326S|MSR1_ENST00000536385.1_Missense_Mutation_p.P100S|MSR1_ENST00000350896.3_Missense_Mutation_p.P326S			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	326	Collagen-like.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)			haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		GTAATACCTGGCCTTCCGGCA	0.343																																																0			8											32	33	33					8																	16007743		2203	4298	6501	16052114	SO:0001583	missense	4481			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.976C>T	8.37:g.16007743G>A	ENSP00000262101:p.Pro326Ser		16052114	D3DSP3|O60505|P21759|Q45F10	Missense_Mutation	SNP	ENST00000262101.5	37	CCDS5995.1	.	.	.	.	.	.	.	.	.	.	G	8.290	0.817432	0.16607	.	.	ENSG00000038945	ENST00000350896;ENST00000262101;ENST00000445506;ENST00000355282;ENST00000522672;ENST00000381998;ENST00000536385	D;T;T;D;D;D;D	0.96587	-4.06;2.39;2.39;-4.06;-2.65;-4.06;-4.06	4.38	-0.613	0.11594	.	0.672540	0.13592	N	0.376552	D	0.92446	0.7602	M	0.62209	1.925	0.20074	N	0.999931	B;B;B;B;B	0.17465	0.001;0.022;0.001;0.01;0.012	B;B;B;B;B	0.15052	0.002;0.012;0.003;0.011;0.006	T	0.79822	-0.1641	10	0.12103	T	0.63	.	6.3327	0.21279	0.0979:0.0:0.3137:0.5884	.	100;344;326;326;326	F5GZJ2;B4DDJ5;P21757-2;P21757-3;P21757	.;.;.;.;MSRE_HUMAN	S	326;326;344;326;116;326;100	ENSP00000262100:P326S;ENSP00000262101:P326S;ENSP00000405453:P344S;ENSP00000347430:P326S;ENSP00000430536:P116S;ENSP00000371428:P326S;ENSP00000444414:P100S	ENSP00000262101:P326S	P	-	1	0	MSR1	16052114	0.010000	0.17322	0.062000	0.19696	0.386000	0.30323	-0.279000	0.08479	-0.277000	0.09193	0.650000	0.86243	CCA		0.343	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			A	16007743	G	A	16007743	3	1	115	1	0	0	0	0	1	0	0	0	9916	1203	42	3	443	3	MSR1	8	16007743	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10		16007743	130356279	93	30900										
ASH2L	9070	hgsc.bcm.edu	37	chr8	37985835	37985835	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agttaaagatctcagatgacCggctgactgtggttggagag	14	6	1	5			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr8:37985835C>T	ENST00000343823.6	+	11	1501	c.1192C>T	c.(1192-1194)Cgg>Tgg	p.R398W	ASH2L_ENST00000428278.2_Missense_Mutation_p.R304W|ASH2L_ENST00000545394.1_Missense_Mutation_p.R259W|ASH2L_ENST00000521652.1_Missense_Mutation_p.R304W|ASH2L_ENST00000250635.7_Missense_Mutation_p.R304W	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	398	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				cellular response to DNA damage stimulus (GO:0006974)|hemopoiesis (GO:0030097)|histone H3-K4 methylation (GO:0051568)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				CTCAGATGACCGGCTGACTGT	0.478																																																0			8											60	55	57					8																	37985835		2203	4300	6503	38104992	SO:0001583	missense	9070			AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691		"Zinc fingers, PHD-type"	744	protein-coding gene	gene with protein product		604782	"ash2 (absent, small, or homeotic, Drosophila, homolog)-like"	ASH2L1		10393421	Standard	NM_004674		Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.1192C>T	8.37:g.37985835C>T	ENSP00000340896:p.Arg398Trp		38104992	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Missense_Mutation	SNP	ENST00000343823.6	37	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813348	0.90707	.	.	ENSG00000129691	ENST00000343823;ENST00000250635;ENST00000545394;ENST00000428278;ENST00000521652	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.58	5.58	0.84498	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	D	0.88522	0.6459	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.99	D	0.90571	0.4522	10	0.87932	D	0	.	14.3123	0.66424	0.1845:0.8155:0.0:0.0	.	304;398	Q9UBL3-2;Q9UBL3	.;ASH2L_HUMAN	W	398;304;259;304;304	ENSP00000340896:R398W;ENSP00000250635:R304W;ENSP00000443606:R259W;ENSP00000395310:R304W;ENSP00000430259:R304W	ENSP00000250635:R304W	R	+	1	2	ASH2L	38104992	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.924000	0.63418	2.640000	0.89533	0.561000	0.74099	CGG		0.478	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		T	37985835	C	T	37985835	3	4	115	1	0	0	0	0	1	0	0	0	1043	643	23	1	1234	1	ASH2L	8	37985835	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	21978092	37985835	108378187	94	30901										
UBR5	51366	hgsc.bcm.edu	37	chr8	103284867	103284867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aacttcgtgctacaccactgCcctctcctggctcatcctta	5	17	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr8:103284867C>T	ENST00000520539.1	-	48	7469	c.6863G>A	c.(6862-6864)gGc>gAc	p.G2288D	UBR5_ENST00000518205.1_Missense_Mutation_p.G17D|UBR5_ENST00000521922.1_Missense_Mutation_p.G2282D|UBR5_ENST00000220959.4_Missense_Mutation_p.G2288D	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2288					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.G2288D(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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)			TACACCACTGCCCTCTCCTGG	0.408																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	central_nervous_system(1)	8											145	124	131					8																	103284867		2203	4300	6503	103354043	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.6863G>A	8.37:g.103284867C>T	ENSP00000429084:p.Gly2288Asp		103354043	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	33	5.209857	0.95069	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922;ENST00000521566	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.44	5.44	0.79542	HECT (1);	0.000000	0.85682	D	0.000000	T	0.54398	0.1856	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.57522	-0.7797	10	0.87932	D	0	.	19.2658	0.93984	0.0:1.0:0.0:0.0	.	2282;2288	E7EMW7;O95071	.;UBR5_HUMAN	D	2288;2288;17;2282;113	ENSP00000429084:G2288D;ENSP00000220959:G2288D;ENSP00000428693:G17D;ENSP00000427819:G2282D	ENSP00000220959:G2288D	G	-	2	0	UBR5	103354043	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.570000	0.86706	0.585000	0.79938	GGC		0.408	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103284867	C	T	103284867	3	4	115	1	0	0	0	0	1	0	0	0	16945	739	26	3	1584	3	UBR5	8	103284867	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	65299032	103284867	43079155	95	30902										
DPYS	1807	hgsc.bcm.edu	37	chr8	105459696	105459696	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atcttgaaagagttaacaccTttatcttgcacaaggatttt	6	7	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr8:105459696T>C	ENST00000351513.2	-	3	591	c.459A>G	c.(457-459)aaA>aaG	p.K153K		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	153					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AGTTAACACCTTTATCTTGCA	0.368																																																0			8											123	112	116					8																	105459696		2203	4300	6503	105528872	SO:0001819	synonymous_variant	1807			D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.459A>G	8.37:g.105459696T>C			105528872		Silent	SNP	ENST00000351513.2	37	CCDS6302.1																																																																																				0.368	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		C	105459696	T	C	105459696	2	2	115	1	0	0	0	0	0	0	0	1	4757	1606	56	4		4	DPYS	8	105459696	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	2174829	105459696	40904326	96	30903										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616327	116616327	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tggcactgatgtttgactcgCgagcttccagccgccccagg	12	14	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr8:116616327C>T	ENST00000220888.5	-	3	1989	c.1830G>A	c.(1828-1830)tcG>tcA	p.S610S	TRPS1_ENST00000519674.1_Silent_p.S610S|TRPS1_ENST00000520276.1_Silent_p.S614S|TRPS1_ENST00000395715.3_Silent_p.S623S|TRPS1_ENST00000519076.1_Intron			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	610					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	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)			GTTTGACTCGCGAGCTTCCAG	0.478									Langer-Giedion syndrome																																							0			8											67	68	68					8																	116616327		2024	4184	6208	116685502	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1830G>A	8.37:g.116616327C>T			116685502	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.478	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116616327	C	T	116616327	2	4	115	1	0	0	0	0	0	0	0	1	16633	755	27	1		1	TRPS1	8	116616327	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	11156631	116616327	29747695	97	30904										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5743014	5743014	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	acacttggaggagattttgcGtaagtcaaaaaagacaattt	9	5	1	2	rs370606357		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:5743014G>A	ENST00000414202.2	+	9	1237		c.e9+1		KIAA1432_ENST00000449720.2_Splice_Site|KIAA1432_ENST00000418622.3_Splice_Site|KIAA1432_ENST00000381532.2_Splice_Site|KIAA1432_ENST00000251879.6_Splice_Site	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GAGATTTTGCGTAAGTCAAAA	0.373																																																0			9											133	131	132					9																	5743014		2203	4300	6503	5733014	SO:0001630	splice_region_variant	57589																														ENST00000414202.2:c.1046+1G>A	9.37:g.5743014G>A			5733014		Splice_Site	SNP	ENST00000414202.2	37	CCDS34982.2	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714597	0.89112	.	.	ENSG00000107036	ENST00000251879;ENST00000414202;ENST00000381532;ENST00000418622;ENST00000545641;ENST00000449720	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1432	5733014	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.342000	0.97044	2.941000	0.99782	0.655000	0.94253	.		0.373	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		Intron	A	5743014	G	A	5743014	5	1	115	1	0	0	0	0	0	0	1	0	8254	1159	40	1	840	1	KIAA1432	9	5743014	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10		5743014	135470417	98	30905										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19063007	19063007	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cattacagtcttttctcaccTcttctaccagatgatcttgc	4	13	5	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:19063007T>C	ENST00000380502.3	-	14	2095	c.1628A>G	c.(1627-1629)gAg>gGg	p.E543G	HAUS6_ENST00000380496.1_Splice_Site_p.E407G|SCARNA8_ENST00000515924.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	543					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TTTTCTCACCTCTTCTACCAG	0.413																																																0			9											163	148	153					9																	19063007		2203	4300	6503	19053007	SO:0001630	splice_region_variant	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1629+1A>G	9.37:g.19063007T>C			19053007	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	T	19.91	3.914091	0.72983	.	.	ENSG00000147874	ENST00000380502;ENST00000380496;ENST00000415524	T;T;T	0.54675	1.58;1.57;0.56	5.54	5.54	0.83059	.	0.101103	0.64402	D	0.000002	T	0.70640	0.3247	M	0.72479	2.2	0.39215	D	0.963381	D;D;D;D	0.89917	0.992;0.992;1.0;0.992	P;P;D;P	0.87578	0.813;0.801;0.998;0.813	T	0.76000	-0.3119	10	0.87932	D	0	-7.6635	13.061	0.59008	0.0:0.0:0.0:1.0	.	508;543;407;543	Q7Z4H7-3;Q7Z4H7-2;Q5VY60;Q7Z4H7	.;.;.;HAUS6_HUMAN	G	543;407;59	ENSP00000369871:E543G;ENSP00000369865:E407G;ENSP00000409615:E59G	ENSP00000369865:E407G	E	-	2	0	HAUS6	19053007	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	4.628000	0.61282	2.106000	0.64143	0.460000	0.39030	GAG		0.413	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	Missense_Mutation	C	19063007	T	C	19063007	5	2	115	1	0	0	0	0	0	0	1	0	6991	1565	54	4	1255	4	HAUS6	9	19063007	Splice_Site	SNP	T	TCGA-F5-6465-01A-11D-1733-10	13319993	19063007	122150424	99	30906										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20885121	20885121	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttaaaggtggtatgttattTtgctatgatgtttccatgta	9	3	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:20885121T>C	ENST00000380249.1	+	23	2881	c.2517T>C	c.(2515-2517)ttT>ttC	p.F839F	FOCAD_ENST00000338382.6_Silent_p.F839F|FOCAD_ENST00000605086.1_Silent_p.F275F	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	839						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											GTATGTTATTTTGCTATGATG	0.353																																																0			9											100	91	94					9																	20885121		2203	4300	6503	20875121	SO:0001819	synonymous_variant	54914			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2517T>C	9.37:g.20885121T>C			20875121	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																				0.353	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		C	20885121	T	C	20885121	2	2	115	1	0	0	0	0	0	0	0	1	8279	1838	64	4		4	KIAA1797	9	20885121	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1822114	20885121	120328310	100	30907										
IFNB1	3456	hgsc.bcm.edu	37	chr9	21077536	21077536	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tggtttatctgatgatagacAttagccaggaggttctcaac	10	7	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:21077536A>G	ENST00000380232.2	-	1	407	c.333T>C	c.(331-333)aaT>aaC	p.N111N		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	111					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.N111K(1)		breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		GATGATAGACATTAGCCAGGA	0.418																																																1	Substitution - Missense(1)	ovary(1)	9											174	173	174					9																	21077536		2203	4300	6503	21067536	SO:0001819	synonymous_variant	3456				CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"Interferons"	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.333T>C	9.37:g.21077536A>G			21067536	Q5VWC9	Silent	SNP	ENST00000380232.2	37	CCDS6495.1																																																																																				0.418	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176		G	21077536	A	G	21077536	2	3	115	1	0	0	0	0	0	0	0	1	7567	214	8	4		4	IFNB1	9	21077536	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	192415	21077536	120135895	101	30908										
MOBKL2B	79817	hgsc.bcm.edu	37	chr9	27455164	27455164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaatatttcctcgttgttgaTctgaacctcaatccaatcca	4	11	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:27455164T>C	ENST00000262244.5	-	2	809	c.385A>G	c.(385-387)Atc>Gtc	p.I129V		NM_024761.4	NP_079037.3	Q86TA1	MOB3B_HUMAN	MOB kinase activator 3B	129							metal ion binding (GO:0046872)										TCGTTGTTGATCTGAACCTCA	0.428																																																0			9											107	98	101					9																	27455164		2203	4300	6503	27445164	SO:0001583	missense	79817			AK023266	CCDS6520.1	9p21.1	2012-07-05	2011-09-28	2011-09-28	ENSG00000120162	ENSG00000120162		"MOB kinase activators"	23825	protein-coding gene	gene with protein product	"monopolar spindle 1 binding, MOB1, domain containing"		"MOB1, Mps One Binder kinase activator-like 2B (yeast)", "chromosome 9 open reading frame 35"	MOBKL2B, C9orf35		12477932	Standard	NM_024761		Approved	MOB1D, FLJ13204	uc003zqn.3	Q86TA1	OTTHUMG00000019717	ENST00000262244.5:c.385A>G	9.37:g.27455164T>C	ENSP00000262244:p.Ile129Val		27445164	Q8NEB4|Q9H8V4	Missense_Mutation	SNP	ENST00000262244.5	37	CCDS6520.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816944	0.70912	.	.	ENSG00000120162	ENST00000262244	.	.	.	5.83	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.64182	0.2575	L	0.58354	1.805	0.53688	D	0.999977	D	0.55605	0.972	P	0.55303	0.773	T	0.61821	-0.6984	9	0.34782	T	0.22	-31.062	11.4228	0.49991	0.1352:0.0:0.0:0.8648	.	129	Q86TA1	MOB3B_HUMAN	V	129	.	ENSP00000262244:I129V	I	-	1	0	MOBKL2B	27445164	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	1.018000	0.39521	0.460000	0.39030	ATC		0.428	MOB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051974.2	NM_024761		C	27455164	T	C	27455164	3	2	115	1	0	0	0	0	1	0	0	0	9715	1435	50	4	277	4	MOBKL2B	9	27455164	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	6377628	27455164	113758267	102	30909										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32635359	32635359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agttcagtgattaggctgccCagccccaaagcccccaagcc	9	16	1	1	rs267602212		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:32635359C>T	ENST00000242310.4	-	1	308	c.219G>A	c.(217-219)ctG>ctA	p.L73L	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	73					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.L73L(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTAGGCTGCCCAGCCCCAAAG	0.537																																																2	Substitution - coding silent(2)	skin(2)	9											129	125	127					9																	32635359		2203	4300	6503	32625359	SO:0001819	synonymous_variant	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.219G>A	9.37:g.32635359C>T			32625359	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.537	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			T	32635359	C	T	32635359	2	4	115	1	0	0	0	0	0	0	0	1	15562	581	21	3		3	TAF1L	9	32635359	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	5180195	32635359	108578072	103	30910										
CTSL1	1514	hgsc.bcm.edu	37	chr9	90343679	90343679	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctttccagtatgttcaggaTaatggaggcctggactctga	12	8	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:90343679T>C	ENST00000343150.5	+	5	1466	c.576T>C	c.(574-576)gaT>gaC	p.D192D	CTSL_ENST00000495822.1_3'UTR|CTSL_ENST00000342020.5_Silent_p.D192D|CTSL_ENST00000340342.6_Silent_p.D192D			P07711	CATL1_HUMAN	cathepsin L	192					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										ATGTTCAGGATAATGGAGGCC	0.483																																																0			9											103	93	96					9																	90343679		2203	4300	6503	89533499	SO:0001819	synonymous_variant	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.576T>C	9.37:g.90343679T>C			89533499	Q6IAV1|Q96QJ0	Silent	SNP	ENST00000343150.5	37	CCDS6675.1																																																																																				0.483	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		C	90343679	T	C	90343679	2	2	115	1	0	0	0	0	0	0	0	1	4044	1403	49	4		4	CTSL1	9	90343679	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	57708320	90343679	50869752	104	30911										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98229650	98229650	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtccagcccgtctctcactcGggtggtgccataaaggctga	12	13	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:98229650G>A	ENST00000331920.6	-	15	2607	c.2308C>T	c.(2308-2310)Cga>Tga	p.R770*	PTCH1_ENST00000418258.1_Nonsense_Mutation_p.R619*|PTCH1_ENST00000421141.1_Nonsense_Mutation_p.R619*|PTCH1_ENST00000429896.2_Nonsense_Mutation_p.R619*|PTCH1_ENST00000430669.2_Nonsense_Mutation_p.R704*|PTCH1_ENST00000375274.2_Nonsense_Mutation_p.R769*|PTCH1_ENST00000437951.1_Nonsense_Mutation_p.R704*	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	770					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.R770*(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TCTCTCACTCGGGTGGTGCCA	0.498																																																1	Substitution - Nonsense(1)	skin(1)	9	GRCh37	CD054985	PTCH1	D							70	71	71					9																	98229650		2203	4300	6503	97269471	SO:0001587	stop_gained	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2308C>T	9.37:g.98229650G>A	ENSP00000332353:p.Arg770*		97269471	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Nonsense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	41	8.896394	0.98994	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	.	.	.	5.82	5.82	0.92795	.	0.061164	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3775	20.1013	0.97878	0.0:0.0:1.0:0.0	.	.	.	.	X	770;704;619;619;206;704;619;769	.	ENSP00000332353:R770X	R	-	1	2	PTCH1	97269471	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.485000	0.60279	2.748000	0.94277	0.655000	0.94253	CGA		0.498	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98229650	G	A	98229650	4	1	115	1	0	0	0	0	0	1	0	0	12764	1124	39	1	2071	1	PTCH1	9	98229650	Nonsense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	7885971	98229650	42983781	105	30912										
OR13C5	138799	hgsc.bcm.edu	37	chr9	107361264	107361264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgatccaggacccagctgccAtgggtacataggcatcctta	10	12	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:107361264A>G	ENST00000374779.2	-	1	524	c.431T>C	c.(430-432)aTg>aCg	p.M144T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CCCAGCTGCCATGGGTACATA	0.473																																																0			9											102	102	102					9																	107361264		2203	4298	6501	106401085	SO:0001583	missense	138799				CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"GPCR / Class A : Olfactory receptors"	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.431T>C	9.37:g.107361264A>G	ENSP00000363911:p.Met144Thr		106401085	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.398574	0.42512	.	.	ENSG00000255800	ENST00000374779	T	0.38240	1.15	4.17	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	U	0.000405	T	0.60261	0.2255	M	0.88775	2.98	0.09310	N	1	D	0.71674	0.998	D	0.75020	0.985	T	0.53415	-0.8442	10	0.87932	D	0	.	7.5593	0.27843	0.8952:0.0:0.1048:0.0	.	144	Q8NGS8	O13C5_HUMAN	T	144	ENSP00000363911:M144T	ENSP00000363911:M144T	M	-	2	0	OR13C5	106401085	0.172000	0.23043	0.046000	0.18839	0.178000	0.23041	4.303000	0.59098	0.671000	0.31185	0.433000	0.28618	ATG		0.473	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		G	107361264	A	G	107361264	3	3	115	1	0	0	0	0	1	0	0	0	10968	217	8	4	527	4	OR13C5	9	107361264	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	9131614	107361264	33852167	106	30913										
OR13C2	392376	hgsc.bcm.edu	37	chr9	107367287	107367287	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gattaataacaaaggtgtcaAtatgaacaatgttgtggcca	9	5	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr9:107367287A>C	ENST00000542196.1	-	1	664	c.622T>G	c.(622-624)Ttg>Gtg	p.L208V		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AAAGGTGTCAATATGAACAAT	0.413																																																0			9											138	132	134					9																	107367287		2201	4300	6501	106407108	SO:0001583	missense	392376				CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"GPCR / Class A : Olfactory receptors"	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.622T>G	9.37:g.107367287A>C	ENSP00000438815:p.Leu208Val		106407108	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-2.011825	0.00422	.	.	ENSG00000257019	ENST00000542196	T	0.39056	1.1	3.53	-4.49	0.03504	GPCR, rhodopsin-like superfamily (1);	0.352991	0.14602	U	0.309548	T	0.13543	0.0328	N	0.05554	-0.025	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.24119	-1.0169	10	0.10902	T	0.67	.	2.0211	0.03509	0.4772:0.1249:0.2751:0.1228	.	208	Q8NGS9	O13C2_HUMAN	V	208	ENSP00000438815:L208V	ENSP00000438815:L208V	L	-	1	2	OR13C2	106407108	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-6.778000	0.00054	-1.155000	0.02822	-1.777000	0.00654	TTG		0.413	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481		C	107367287	A	C	107367287	3	2	115	1	0	0	0	0	1	0	0	0	10965	98	4	4	337	4	OR13C2	9	107367287	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	6023	107367287	33846144	107	30914										
MINPP1	9562	hgsc.bcm.edu	37	chr10	89311877	89311877	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tccagtcatcctccagtttgGtcatgcagagactcttcttc	7	13	4	1	rs369261111		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:89311877G>C	ENST00000371996.4	+	5	1147	c.1106G>C	c.(1105-1107)gGt>gCt	p.G369A	MINPP1_ENST00000536010.1_Missense_Mutation_p.G168A|MINPP1_ENST00000371994.4_Missense_Mutation_p.V292L|MINPP1_ENST00000472891.1_3'UTR	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	369					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		CTCCAGTTTGGTCATGCAGAG	0.368																																																0			10											93	90	91					10																	89311877		2203	4300	6503	89301857	SO:0001583	missense	9562			AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"multiple inositol polyphosphate histidine phosphatase, 1"			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1106G>C	10.37:g.89311877G>C	ENSP00000361064:p.Gly369Ala		89301857	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	37	CCDS7384.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.092095|4.092095	0.76756|0.76756	.|.	.|.	ENSG00000107789|ENSG00000107789	ENST00000371996;ENST00000546140;ENST00000536010|ENST00000371994	T;T|T	0.26067|0.77620	1.76;1.76|-1.11	6.08|6.08	5.17|5.17	0.71159|0.71159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61776|0.61776	0.2374|0.2374	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	P|B	0.47191|0.29988	0.891|0.264	P|B	0.58577|0.24269	0.841|0.052	T|T	0.59627|0.59627	-0.7419|-0.7419	9|8	0.07990|0.08599	T|T	0.79|0.76	-9.1256|-9.1256	16.0026|16.0026	0.80306|0.80306	0.0:0.0:0.8646:0.1353|0.0:0.0:0.8646:0.1353	.|.	369|292	Q9UNW1|Q9UNW1-2	MINP1_HUMAN|.	A|L	369;228;168|292	ENSP00000361064:G369A;ENSP00000437823:G168A|ENSP00000361062:V292L	ENSP00000361064:G369A|ENSP00000361062:V292L	G|V	+|+	2|1	0|0	MINPP1|MINPP1	89301857|89301857	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.988000|0.988000	0.76386|0.76386	9.325000|9.325000	0.96381|0.96381	1.574000|1.574000	0.49760|0.49760	0.591000|0.591000	0.81541|0.81541	GGT|GTC		0.368	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			C	89311877	G	C	89311877	3	2	115	1	0	0	0	0	1	0	0	0	9618	1261	44	5	1162	5	MINPP1	10	89311877	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10		89311877	46222870	108	30915										
PTEN	5728	hgsc.bcm.edu	37	chr10	89653816	89653816	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	attattgctatgggatttccTgcagaaagacttgaaggcgt	11	6	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:89653816T>C	ENST00000371953.3	+	2	1471	c.114T>C	c.(112-114)ccT>ccC	p.P38P		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	38	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(2)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TGGGATTTCCTGCAGAAAGAC	0.289		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	47	Whole gene deletion(37)|Unknown(8)|Deletion - Frameshift(2)	prostate(14)|central_nervous_system(8)|skin(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|ovary(3)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	10											112	111	112					10																	89653816		2203	4296	6499	89643796	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.114T>C	10.37:g.89653816T>C			89643796	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.289	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89653816	T	C	89653816	2	2	115	1	0	0	0	0	0	0	0	1	12772	1567	55	4		4	PTEN	10	89653816	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	341939	89653816	45880931	109	30916										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720728	89720728	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcagaaaaagtagaaaatggAagtctatgtgatcaagaaat	9	3	3	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:89720728A>G	ENST00000371953.3	+	8	2236	c.879A>G	c.(877-879)ggA>ggG	p.G293G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	293	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.G293G(1)|p.W274_F341del(1)|p.G293fs*4(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TAGAAAATGGAAGTCTATGTG	0.318		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	52	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(2)|Unknown(2)|Substitution - coding silent(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|stomach(1)|soft_tissue(1)|endometrium(1)	10											75	76	75					10																	89720728		2203	4298	6501	89710708	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.879A>G	10.37:g.89720728A>G			89710708	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.318	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720728	A	G	89720728	2	3	115	1	0	0	0	0	0	0	0	1	12772	233	9	4		4	PTEN	10	89720728	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	66912	89720728	45814019	110	30917			1	35		2	2	15	A		9.722796e-05
PTEN	5728	hgsc.bcm.edu	37	chr10	89720742	89720742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaatggaagtctatgtgatcAagaaatcgatagcatttgca	9	5	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:89720742A>G	ENST00000371953.3	+	8	2250	c.893A>G	c.(892-894)cAa>cGa	p.Q298R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	298	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CTATGTGATCAAGAAATCGAT	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											91	90	90					10																	89720742		2203	4299	6502	89710722	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.893A>G	10.37:g.89720742A>G	ENSP00000361021:p.Gln298Arg		89710722	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.257615	0.22965	.	.	ENSG00000171862	ENST00000371953	D	0.94457	-3.43	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.221302	0.47093	D	0.000259	D	0.87180	0.6113	N	0.13098	0.295	0.39166	D	0.96249	B	0.02656	0.0	B	0.06405	0.002	T	0.83062	-0.0147	9	.	.	.	-10.289	11.5808	0.50889	0.8508:0.1492:0.0:0.0	.	298	P60484	PTEN_HUMAN	R	298	ENSP00000361021:Q298R	.	Q	+	2	0	PTEN	89710722	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.359000	0.66074	1.942000	0.56320	0.482000	0.46254	CAA		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720742	A	G	89720742	3	3	115	1	0	0	0	0	1	0	0	0	12772	130	5	4	923	4	PTEN	10	89720742	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	14	89720742	45814005	111	30918			1	35		2	2	15	A		9.722796e-05
ANKRD22	118932	hgsc.bcm.edu	37	chr10	90582737	90582737	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	attaattcaatctgggaaaaTtttaatctccgtgcaatatc	5	7	3	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:90582737T>C	ENST00000371930.4	-	6	747	c.537A>G	c.(535-537)aaA>aaG	p.K179K	ANKRD22_ENST00000476963.1_5'UTR	NM_144590.2	NP_653191.2	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	179										NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		TCTGGGAAAATTTTAATCTCC	0.393																																																0			10											113	121	118					10																	90582737		2203	4300	6503	90572717	SO:0001819	synonymous_variant	118932			BC021671	CCDS7390.1	10q23.31	2013-09-20			ENSG00000152766	ENSG00000152766		"Ankyrin repeat domain containing"	28321	protein-coding gene	gene with protein product						12477932	Standard	NM_144590		Approved	MGC22805	uc001kfj.4	Q5VYY1	OTTHUMG00000018699	ENST00000371930.4:c.537A>G	10.37:g.90582737T>C			90572717	B2R9Y7|Q8WU06	Silent	SNP	ENST00000371930.4	37	CCDS7390.1																																																																																				0.393	ANKRD22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049262.1	NM_144590		C	90582737	T	C	90582737	2	2	115	1	0	0	0	0	0	0	0	1	651	1490	52	4		4	ANKRD22	10	90582737	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	861995	90582737	44952010	112	30919										
PDCD4	27250	hgsc.bcm.edu	37	chr10	112641175	112641175	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gactctggcagaggcgattcGgtcagcgacagtgggagtga	17	8	2	2	rs372715017	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:112641175G>A	ENST00000280154.7	+	3	502	c.228G>A	c.(226-228)tcG>tcA	p.S76S	PDCD4_ENST00000393104.2_Silent_p.S65S	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	76					apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.S76S(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GAGGCGATTCGGTCAGCGACA	0.498													G|||	3	0.000599042	0.0023	0	5008	,	,		17068	0		0	False		,,,				2504	0				Ovarian(115;1498 1603 9363 40056 40885)											1	Substitution - coding silent(1)	ovary(1)	10						G	,,	2,4404	4.2+/-10.8	0,2,2201	92	99	97		186,228,195	-11.4	0.1	10		97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	,,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	,,	62/456,76/470,65/459	112641175	3,13003	2203	4300	6503	112631165	SO:0001819	synonymous_variant	27250			U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"nuclear antigen H731"	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.228G>A	10.37:g.112641175G>A			112631165	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																				0.498	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		A	112641175	G	A	112641175	2	1	115	1	0	0	0	0	0	0	0	1	11652	1103	39	1		1	PDCD4	10	112641175	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	22058438	112641175	22893572	113	30920										
PNLIP	5406	hgsc.bcm.edu	37	chr10	118318795	118318795	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtgatgccagtaattttgcaCgtaagtttctgttttctgta	9	6	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:118318795C>A	ENST00000369221.2	+	10	1088	c.1060C>A	c.(1060-1062)Cgt>Agt	p.R354S		NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	354					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)	p.R354C(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	TAATTTTGCACGTAAGTTTCT	0.343																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											97	94	95					10																	118318795		2203	4300	6503	118308785	SO:0001630	splice_region_variant	5406			BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.1060+1C>A	10.37:g.118318795C>A			118308785	Q5VSQ2	Missense_Mutation	SNP	ENST00000369221.2	37	CCDS7594.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486103	0.44147	.	.	ENSG00000175535	ENST00000369221	T	0.44881	0.91	6.16	6.16	0.99307	Lipase/lipooxygenase, PLAT/LH2 (1);	0.082771	0.51477	D	0.000091	T	0.49830	0.1580	M	0.71581	2.175	0.50171	D	0.999857	D	0.58620	0.983	P	0.51516	0.672	T	0.40421	-0.9564	10	0.10636	T	0.68	.	13.5646	0.61810	0.0:0.9261:0.0:0.0739	.	354	P16233	LIPP_HUMAN	S	354	ENSP00000358223:R354S	ENSP00000358223:R354S	R	+	1	0	PNLIP	118308785	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	2.541000	0.45735	2.937000	0.99478	0.650000	0.86243	CGT		0.343	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936	Missense_Mutation	A	118318795	C	A	118318795	5	1	115	1	0	0	0	0	0	0	1	0	12180	550	19	2	1094	2	PNLIP	10	118318795	Splice_Site	SNP	C	TCGA-F5-6465-01A-11D-1733-10	5677620	118318795	17215952	114	30921										
VAX1	11023	hgsc.bcm.edu	37	chr10	118891808	118891808	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tccttttcttcttttgttttTttatccttcaaatataagac	2	8	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr10:118891808T>G	ENST00000369206.5	-	0	1723				VAX1_ENST00000277905.2_Missense_Mutation_p.K158T	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1						axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		CTTTTGTTTTTTTATCCTTCA	0.408																																																0			10											45	53	51					10																	118891808		2203	4300	6503	118881798	SO:0001628	intergenic_variant	11023			AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117		10.37:g.118891808T>G			118881798	B1AVW5|Q6ZSX0	Missense_Mutation	SNP	ENST00000369206.5	37	CCDS44483.1	.	.	.	.	.	.	.	.	.	.	T	0.218	-1.030623	0.02045	.	.	ENSG00000148704	ENST00000277905	D	0.89123	-2.47	4.07	0.253	0.15551	.	.	.	.	.	T	0.77844	0.4191	.	.	.	0.09310	N	1	P	0.40476	0.718	B	0.35353	0.201	T	0.65994	-0.6033	8	0.32370	T	0.25	.	3.8503	0.08953	0.3277:0.0942:0.0:0.578	.	158	Q5SQQ9-2	.	T	158	ENSP00000277905:K158T	ENSP00000277905:K158T	K	-	2	0	VAX1	118881798	0.998000	0.40836	0.001000	0.08648	0.099000	0.18886	2.130000	0.42064	0.027000	0.15297	0.533000	0.62120	AAA		0.408	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		G	118891808	T	G	118891808	1	3	115	0	1	0	0	0	0	0	0	0	17174	1841	64	4		4	VAX1	10	118891808	IGR	SNP	T	TCGA-F5-6465-01A-11D-1733-10	573013	118891808	16642939	115	30922										
TRIM68	55128	hgsc.bcm.edu	37	chr11	4622019	4622019	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgtcctcagacacgatgagAcgggagtaagcagtatctgg	13	9	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:4622019A>G	ENST00000300747.5	-	7	1234	c.945T>C	c.(943-945)cgT>cgC	p.R315R		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	315	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		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)		ACACGATGAGACGGGAGTAAG	0.498																																																0			11											78	73	75					11																	4622019		2201	4298	6499	4578595	SO:0001819	synonymous_variant	55128			AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21161	protein-coding gene	gene with protein product		613184	"ring finger protein 137", "tripartite motif-containing 68"	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.945T>C	11.37:g.4622019A>G			4578595	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Silent	SNP	ENST00000300747.5	37	CCDS31356.1																																																																																				0.498	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073		G	4622019	A	G	4622019	2	3	115	1	0	0	0	0	0	0	0	1	16581	262	10	4		4	TRIM68	11	4622019	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10		4622019	130384497	116	30923										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17429962	17429962	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctccagctcttggtcctgtcGgttcatgagggtcttccagt	11	12	3	1	rs570388861		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:17429962G>A	ENST00000389817.3	-	23	2865	c.2797C>T	c.(2797-2799)Cga>Tga	p.R933*	ABCC8_ENST00000302539.4_Nonsense_Mutation_p.R934*			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	933					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TGGTCCTGTCGGTTCATGAGG	0.537																																																0			11	GRCh37	CM060771	ABCC8	M							101	93	95					11																	17429962		2200	4293	6493	17386538	SO:0001587	stop_gained	6833			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.2797C>T	11.37:g.17429962G>A	ENSP00000374467:p.Arg933*		17386538	A6NMX8|E3UYX6|O75948|Q16583	Nonsense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	G	41	8.687084	0.98914	.	.	ENSG00000006071	ENST00000389817;ENST00000302539;ENST00000379493	.	.	.	6.04	3.09	0.35607	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	14.4014	0.67050	0.0:0.0:0.6316:0.3684	.	.	.	.	X	933;934;937	.	ENSP00000303960:R934X	R	-	1	2	ABCC8	17386538	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.094000	0.41719	0.396000	0.25283	0.563000	0.77884	CGA		0.537	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17429962	G	A	17429962	4	1	115	1	0	0	0	0	0	1	0	0	58	1124	39	1	2016	1	ABCC8	11	17429962	Nonsense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	12807943	17429962	117576554	117	30924										
ANO5	203859	hgsc.bcm.edu	37	chr11	22294385	22294385	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcttttcctttggctcctctTcttgctctcataaataatat	3	11	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:22294385T>C	ENST00000324559.8	+	19	2402	c.2085T>C	c.(2083-2085)ctT>ctC	p.L695L	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	695					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)	p.L695L(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGCTCCTCTTCTTGCTCTCA	0.383																																																1	Substitution - coding silent(1)	ovary(1)	11											141	125	130					11																	22294385		2203	4300	6503	22250961	SO:0001819	synonymous_variant	203859			AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2085T>C	11.37:g.22294385T>C			22250961		Silent	SNP	ENST00000324559.8	37	CCDS31444.1																																																																																				0.383	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		C	22294385	T	C	22294385	2	2	115	1	0	0	0	0	0	0	0	1	700	1770	62	4		4	ANO5	11	22294385	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	4864423	22294385	112712131	118	30925										
MPPED2	744	hgsc.bcm.edu	37	chr11	30516995	30516995	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tagtcctgtttaacaaggtcTgccatgaattccttatcaaa	6	9	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:30516995T>G	ENST00000358117.5	-	3	506	c.384A>C	c.(382-384)gcA>gcC	p.A128A	MPPED2_ENST00000448418.2_Silent_p.A128A	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	128					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						TAACAAGGTCTGCCATGAATT	0.383																																																0			11											152	141	144					11																	30516995		2202	4299	6501	30473571	SO:0001819	synonymous_variant	744			U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"chromosome 11 open reading frame 8"	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.384A>C	11.37:g.30516995T>G			30473571	D3DQZ5|E9PB10|Q59GE6	Silent	SNP	ENST00000358117.5	37	CCDS7870.1																																																																																				0.383	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584		G	30516995	T	G	30516995	2	3	115	1	0	0	0	0	0	0	0	1	9772	1567	55	4		4	MPPED2	11	30516995	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	8222610	30516995	104489521	119	30926										
ACCS	84680	hgsc.bcm.edu	37	chr11	44104786	44104786	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctgcccacacctatgtctcAgaagagcttagggcattggg	12	11	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:44104786A>T	ENST00000263776.8	+	13	1613	c.1179A>T	c.(1177-1179)tcA>tcT	p.S393S		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	393			S -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CCTATGTCTCAGAAGAGCTTA	0.542																																					Esophageal Squamous(158;148 1889 8077 23160 41213)											0			11											114	110	111					11																	44104786		2203	4300	6503	44061362	SO:0001819	synonymous_variant	84680			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.1179A>T	11.37:g.44104786A>T			44061362	B4E219|Q8WUL4|Q96LX5	Silent	SNP	ENST00000263776.8	37	CCDS7907.1																																																																																				0.542	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		T	44104786	A	T	44104786	2	4	115	1	0	0	0	0	0	0	0	1	133	175	7	5		5	ACCS	11	44104786	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	13587791	44104786	90901730	120	30927										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48149353	48149353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgctattcaggtttttgacgTcaccgctgtgaacatcagtg	10	9	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:48149353T>C	ENST00000418331.2	+	7	1467	c.1115T>C	c.(1114-1116)gTc>gCc	p.V372A	PTPRJ_ENST00000440289.2_Missense_Mutation_p.V372A	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	372	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs2229703).		contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GTTTTTGACGTCACCGCTGTG	0.502																																																0			11											108	96	100					11																	48149353		2201	4298	6499	48105929	SO:0001583	missense	5795			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1115T>C	11.37:g.48149353T>C	ENSP00000400010:p.Val372Ala		48105929	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.996182	0.74703	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.60797	0.16;0.16	5.75	5.75	0.90469	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66896	0.2836	L	0.43152	1.355	0.09310	N	1	P;D	0.54964	0.587;0.969	P;P	0.62298	0.489;0.9	T	0.60850	-0.7181	9	0.72032	D	0.01	.	12.4582	0.55716	0.0:0.0:0.0:1.0	.	372;372	Q12913;Q6P4H4	PTPRJ_HUMAN;.	A	372	ENSP00000400010:V372A;ENSP00000409733:V372A	ENSP00000278456:V372A	V	+	2	0	PTPRJ	48105929	0.054000	0.20591	0.003000	0.11579	0.186000	0.23388	3.834000	0.55798	2.201000	0.70794	0.533000	0.62120	GTC		0.502	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			C	48149353	T	C	48149353	3	2	115	1	0	0	0	0	1	0	0	0	12841	1667	58	4	1141	4	PTPRJ	11	48149353	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	4044567	48149353	86857163	121	30928										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587291	55587291	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgcatacccccatgtacttTttcctcagccaactctcctt	3	17	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:55587291T>C	ENST00000333976.4	+	1	206	c.186T>C	c.(184-186)ttT>ttC	p.F62F		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F62L(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				CCATGTACTTTTTCCTCAGCC	0.423																																																1	Substitution - Missense(1)	ovary(1)	11											257	237	244					11																	55587291		2200	4296	6496	55343867	SO:0001819	synonymous_variant	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.186T>C	11.37:g.55587291T>C			55343867	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	37	CCDS31510.1																																																																																				0.423	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		C	55587291	T	C	55587291	2	2	115	1	0	0	0	0	0	0	0	1	11188	1838	64	4		4	OR5D18	11	55587291	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	7437938	55587291	79419225	122	30929										
OR5M9	390162	hgsc.bcm.edu	37	chr11	56230864	56230864	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gagtaaattctgtcacatccGtgaaattaggcattgcctta	8	8	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:56230864G>A	ENST00000279791.1	-	1	13	c.14C>T	c.(13-15)aCg>aTg	p.T5M		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					TGTCACATCCGTGAAATTAGG	0.408																																																0			11											23	24	24					11																	56230864		2201	4296	6497	55987440	SO:0001583	missense	390162			AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"GPCR / Class A : Olfactory receptors"	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.14C>T	11.37:g.56230864G>A	ENSP00000279791:p.Thr5Met		55987440	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	CCDS31531.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920239	0.52653	.	.	ENSG00000150269	ENST00000279791	T	0.04809	3.55	4.79	3.81	0.43845	.	0.000000	0.42821	D	0.000641	T	0.24470	0.0593	M	0.89601	3.045	0.19575	N	0.999962	D	0.89917	1.0	D	0.79784	0.993	T	0.03673	-1.1014	10	0.87932	D	0	-1.3461	11.7726	0.51967	0.0:0.0:0.8234:0.1765	.	5	Q8NGP3	OR5M9_HUMAN	M	5	ENSP00000279791:T5M	ENSP00000279791:T5M	T	-	2	0	OR5M9	55987440	0.143000	0.22626	0.946000	0.38457	0.813000	0.45954	0.515000	0.22801	2.349000	0.79799	0.549000	0.68633	ACG		0.408	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743		A	56230864	G	A	56230864	3	1	115	1	0	0	0	0	1	0	0	0	11208	1145	40	1	920	1	OR5M9	11	56230864	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	643573	56230864	78775652	123	30930										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190126	58190126	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agaagaacaaaaaagatattAaagcttgacataaaaaccag	6	5	0	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:58190126A>G	ENST00000302581.2	-	1	660	c.609T>C	c.(607-609)ttT>ttC	p.F203F		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AAAAGATATTAAAGCTTGACA	0.368																																																0			11											57	56	57					11																	58190126		2201	4295	6496	57946702	SO:0001819	synonymous_variant	390190			AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.609T>C	11.37:g.58190126A>G			57946702	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Silent	SNP	ENST00000302581.2	37	CCDS31550.1																																																																																				0.368	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		G	58190126	A	G	58190126	2	3	115	1	0	0	0	0	0	0	0	1	11181	359	13	4		4	OR5B2	11	58190126	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	1959262	58190126	76816390	124	30931										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71725052	71725053	+	Missense_Mutation	DNP	GT	GT	AG													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cctctaactggccctgcagaGtctccagagcactgtcccgc							TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G|T	G|T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:71725052_71725053GT>AG	ENST00000393695.3	-	15	3827_3828	c.3496_3497AC>CT	c.(3496-3498)ACt>CTt	p.T1166L	NUMA1_ENST00000358965.6_Missense_Mutation_p.T1166L|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GCCCTGCAGAGTCTCCAGAGCA	0.644			T	RARA	APL																																		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	0			11																																								71402700|71402701	SO:0001583	missense	4926			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3496_3497delinsAG	11.37:g.71725052_71725053delinsAG	ENSP00000377298:p.Thr1166Leu		71402700|71402701		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																				0.644	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			AG	71725053	GT	AG	71725052	3	1	115	1	0	0	0	0	1	0	0	0	10781	1029	36	3	2902	3	NUMA1	11	71725052	Missense_Mutation	DNP	GT	TCGA-F5-6465-01A-11D-1733-10	13534926	71725052	63281464	125	30932										
P2RY2	5029	hgsc.bcm.edu	37	chr11	72945451	72945451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgtgtctgatgcactgtatGcggcctccctgccgctgctg	12	14	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:72945451G>A	ENST00000311131.2	+	3	714	c.247G>A	c.(247-249)Gcg>Acg	p.A83T	P2RY2_ENST00000393597.2_Missense_Mutation_p.A83T|P2RY2_ENST00000393596.2_Missense_Mutation_p.A83T	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	83					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	TGCACTGTATGCGGCCTCCCT	0.587																																																0			11											129	107	114					11																	72945451		2200	4293	6493	72623099	SO:0001583	missense	5029			U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.247G>A	11.37:g.72945451G>A	ENSP00000310305:p.Ala83Thr		72623099	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658908	0.67586	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.36699	1.24;1.24;1.24	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.201227	0.43260	D	0.000600	T	0.34861	0.0912	N	0.13272	0.32	0.30952	N	0.724591	P	0.38729	0.644	P	0.46758	0.526	T	0.41734	-0.9492	10	0.59425	D	0.04	.	17.8515	0.88748	0.0:0.0:1.0:0.0	.	83	P41231	P2RY2_HUMAN	T	83	ENSP00000377222:A83T;ENSP00000310305:A83T;ENSP00000377221:A83T	ENSP00000310305:A83T	A	+	1	0	P2RY2	72623099	1.000000	0.71417	0.921000	0.36526	0.922000	0.55478	3.276000	0.51646	2.460000	0.83146	0.650000	0.86243	GCG		0.587	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		A	72945451	G	A	72945451	3	1	115	1	0	0	0	0	1	0	0	0	11383	1319	46	3	249	3	P2RY2	11	72945451	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	1220399	72945451	62061065	126	30933										
SORL1	6653	hgsc.bcm.edu	37	chr11	121461797	121461797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cagtgggacctgcgtgatggAcacctgggtgtgcgacgggt	18	9	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr11:121461797A>G	ENST00000260197.7	+	31	4430	c.4301A>G	c.(4300-4302)gAc>gGc	p.D1434G	SORL1_ENST00000525532.1_Missense_Mutation_p.D378G|SORL1_ENST00000534286.1_Missense_Mutation_p.D344G|SORL1_ENST00000527934.1_Missense_Mutation_p.D49G|SORL1_ENST00000532694.1_Missense_Mutation_p.D280G	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1434	LDL-receptor class A 9. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TGCGTGATGGACACCTGGGTG	0.572											OREG0021431	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			11											216	192	200					11																	121461797		2203	4299	6502	120967007	SO:0001583	missense	6653			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4301A>G	11.37:g.121461797A>G	ENSP00000260197:p.Asp1434Gly	1511	120967007	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559940	0.45590	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7	5.55	4.43	0.53597	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.169309	0.50627	N	0.000103	D	0.87947	0.6306	N	0.16743	0.435	0.33258	D	0.559396	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.82350	-0.0501	10	0.19590	T	0.45	.	5.9527	0.19255	0.775:0.0:0.0799:0.1451	.	49;1434	E9PKB0;Q92673	.;SORL_HUMAN	G	1434;378;280;344;49	ENSP00000260197:D1434G;ENSP00000434634:D378G;ENSP00000432131:D280G;ENSP00000436447:D344G;ENSP00000435405:D49G	ENSP00000260197:D1434G	D	+	2	0	SORL1	120967007	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.686000	0.61700	0.954000	0.37851	0.533000	0.62120	GAC		0.572	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		G	121461797	A	G	121461797	3	3	115	1	0	0	0	0	1	0	0	0	14971	275	10	4	4423	4	SORL1	11	121461797	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	48516346	121461797	13544719	127	30934										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21069013	21069013	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	attgttttcatttttgctatGaagaaaaaatttcaaggaaa	6	3	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:21069013G>A	ENST00000381545.3	+	16	2160	c.1941G>A	c.(1939-1941)atG>atA	p.M647I	SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.M647I|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	647			M -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTTTTGCTATGAAGAAAAAAT	0.318																																																0			12											68	69	69					12																	21069013		2202	4299	6501	20960280	SO:0001583	missense	28234				CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1941G>A	12.37:g.21069013G>A	ENSP00000370956:p.Met647Ile		20960280	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	.	3.946	-0.013198	0.07727	.	.	ENSG00000111700	ENST00000261196;ENST00000381545	T;T	0.57436	0.4;0.4	3.6	0.538	0.17150	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.880700	0.09921	N	0.738419	T	0.28300	0.0699	N	0.15975	0.35	0.32383	N	0.554246	B	0.02656	0.0	B	0.04013	0.001	T	0.36841	-0.9731	10	0.13108	T	0.6	.	4.3515	0.11158	0.2284:0.186:0.5856:0.0	.	647	Q9NPD5	SO1B3_HUMAN	I	647	ENSP00000261196:M647I;ENSP00000370956:M647I	ENSP00000261196:M647I	M	+	3	0	SLCO1B3	20960280	0.991000	0.36638	0.025000	0.17156	0.002000	0.02628	0.673000	0.25203	-0.142000	0.11354	-1.211000	0.01629	ATG		0.318	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		A	21069013	G	A	21069013	3	1	115	1	0	0	0	0	1	0	0	0	14761	1290	45	3	1995	3	SLCO1B3	12	21069013	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10		21069013	112782882	128	30935										
STK38L	23012	hgsc.bcm.edu	37	chr12	27467506	27467506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aacacagttctacatttcagAgactgttctggcaatagatg	8	8	3	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:27467506A>G	ENST00000389032.3	+	7	756	c.587A>G	c.(586-588)gAg>gGg	p.E196G	STK38L_ENST00000539577.1_Missense_Mutation_p.E103G	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TACATTTCAGAGACTGTTCTG	0.378																																																0			12											121	108	112					12																	27467506		2203	4300	6503	27358773	SO:0001583	missense	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.587A>G	12.37:g.27467506A>G	ENSP00000373684:p.Glu196Gly		27358773		Missense_Mutation	SNP	ENST00000389032.3	37	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.778203	0.90195	.	.	ENSG00000211455	ENST00000389032;ENST00000545470;ENST00000539577	T;T;T	0.24908	3.12;1.83;1.83	4.74	4.74	0.60224	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115109	0.64402	D	0.000017	T	0.50905	0.1643	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.994	T	0.56414	-0.7983	10	0.87932	D	0	.	14.6964	0.69124	1.0:0.0:0.0:0.0	.	103;196	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	G	196;155;103	ENSP00000373684:E196G;ENSP00000439457:E155G;ENSP00000446386:E103G	ENSP00000373684:E196G	E	+	2	0	STK38L	27358773	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.123000	0.94387	2.121000	0.65114	0.460000	0.39030	GAG		0.378	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		G	27467506	A	G	27467506	3	3	115	1	0	0	0	0	1	0	0	0	15343	304	11	4	609	4	STK38L	12	27467506	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	6398493	27467506	106384389	129	30936										
SYT10	341359	hgsc.bcm.edu	37	chr12	33532789	33532789	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccagcaatgggtgccagtgcGttattggttttcgatgatag	13	7	0	1	rs545012156		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:33532789G>A	ENST00000228567.3	-	6	1774	c.1478C>T	c.(1477-1479)aCg>aTg	p.T493M	SYT10_ENST00000535526.1_Missense_Mutation_p.T312M	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	493					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.T493M(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GTGCCAGTGCGTTATTGGTTT	0.443																																																1	Substitution - Missense(1)	prostate(1)	12											239	204	216					12																	33532789		2203	4300	6503	33424056	SO:0001583	missense	341359			AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.1478C>T	12.37:g.33532789G>A	ENSP00000228567:p.Thr493Met		33424056	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.558694	0.86231	.	.	ENSG00000110975	ENST00000228567;ENST00000535526	T;T	0.72051	-0.62;-0.62	4.21	4.21	0.49690	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.42548	U	0.000681	T	0.68860	0.3047	L	0.48642	1.525	0.58432	D	0.999999	P	0.46020	0.871	P	0.44597	0.454	T	0.75224	-0.3393	10	0.87932	D	0	.	16.8349	0.85954	0.0:0.0:1.0:0.0	.	493	Q6XYQ8	SYT10_HUMAN	M	493;312	ENSP00000228567:T493M;ENSP00000438691:T312M	ENSP00000228567:T493M	T	-	2	0	SYT10	33424056	1.000000	0.71417	0.958000	0.39756	0.889000	0.51656	9.044000	0.93805	2.631000	0.89168	0.585000	0.79938	ACG		0.443	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		A	33532789	G	A	33532789	3	1	115	1	0	0	0	0	1	0	0	0	15505	1145	40	1	101	1	SYT10	12	33532789	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	6065283	33532789	100319106	130	30937										
TUBA1C	84790	hgsc.bcm.edu	37	chr12	49663698	49663698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgctgccaataactatgcccGagggcactacaccattggca	9	13	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:49663698G>A	ENST00000301072.6	+	3	589	c.314G>A	c.(313-315)cGa>cAa	p.R105Q	TUBA1C_ENST00000549183.1_Missense_Mutation_p.R105Q|RP11-161H23.5_ENST00000550468.2_RNA|TUBA1C_ENST00000541364.1_Missense_Mutation_p.R175Q	NM_032704.3	NP_116093.1	Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	105					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						AACTATGCCCGAGGGCACTAC	0.483																																																0			12											163	153	157					12																	49663698		2203	4300	6503	47949965	SO:0001583	missense	84790			BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553		"Tubulins"	20768	protein-coding gene	gene with protein product			"tubulin, alpha 6"	TUBA6		7821789	Standard	NM_032704		Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000301072.6:c.314G>A	12.37:g.49663698G>A	ENSP00000301072:p.Arg105Gln		47949965		Missense_Mutation	SNP	ENST00000301072.6	37	CCDS8782.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.341431	0.81911	.	.	ENSG00000167553	ENST00000541364;ENST00000301072;ENST00000549183;ENST00000321665	T;T;T	0.70282	-0.47;-0.47;-0.47	3.99	3.99	0.46301	Tubulin/FtsZ, GTPase domain (4);	0.130230	0.51477	D	0.000084	D	0.85961	0.5819	M	0.93638	3.44	0.51767	D	0.999932	P;B	0.51351	0.944;0.17	P;B	0.58331	0.837;0.107	D	0.90081	0.4170	10	0.87932	D	0	.	16.0532	0.80777	0.0:0.0:1.0:0.0	.	175;105	F5H5D3;Q9BQE3	.;TBA1C_HUMAN	Q	175;105;105;105	ENSP00000443475:R175Q;ENSP00000301072:R105Q;ENSP00000448211:R105Q	ENSP00000301072:R105Q	R	+	2	0	TUBA1C	47949965	1.000000	0.71417	0.970000	0.41538	0.992000	0.81027	9.391000	0.97249	2.504000	0.84457	0.455000	0.32223	CGA		0.483	TUBA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404424.1	NM_032704		A	49663698	G	A	49663698	3	1	115	1	0	0	0	0	1	0	0	0	16785	1058	37	1	324	1	TUBA1C	12	49663698	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	16130909	49663698	84188197	131	30938										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53877728	53877728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcctcctcatcaccagttccTcttctaggcggtgcagacag	8	15	4	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:53877728T>C	ENST00000267079.2	-	9	1451	c.1226A>G	c.(1225-1227)gAg>gGg	p.E409G	MAP3K12_ENST00000547035.1_Missense_Mutation_p.E442G|MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547488.1_Missense_Mutation_p.E442G	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	409	Leucine-zipper 1.		E -> K (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.E409G(1)		NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						CACCAGTTCCTCTTCTAGGCG	0.512																																																1	Substitution - Missense(1)	large_intestine(1)	12											192	185	187					12																	53877728		2203	4300	6503	52163995	SO:0001583	missense	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1226A>G	12.37:g.53877728T>C	ENSP00000267079:p.Glu409Gly		52163995	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.910583	0.92107	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	T;T;T	0.79247	-1.23;-1.25;-1.25	4.85	4.85	0.62838	Protein kinase-like domain (1);	0.149661	0.31268	N	0.007941	D	0.84800	0.5552	M	0.66939	2.045	0.80722	D	1	D;D	0.58970	0.984;0.972	P;P	0.61201	0.885;0.771	D	0.86699	0.1928	10	0.87932	D	0	.	13.8578	0.63540	0.0:0.0:0.0:1.0	.	442;409	G3V1Y2;Q12852	.;M3K12_HUMAN	G	409;442;442	ENSP00000267079:E409G;ENSP00000449038:E442G;ENSP00000448689:E442G	ENSP00000267079:E409G	E	-	2	0	MAP3K12	52163995	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.636000	0.83301	2.180000	0.69256	0.379000	0.24179	GAG		0.512	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		C	53877728	T	C	53877728	3	2	115	1	0	0	0	0	1	0	0	0	9276	1551	54	4	1381	4	MAP3K12	12	53877728	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	4214030	53877728	79974167	132	30939										
TPH2	121278	hgsc.bcm.edu	37	chr12	72335393	72335393	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cctaactctggcaaaaatgaCgacaaaggcaacaagggaag	10	9	1	1	rs74510566		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:72335393C>T	ENST00000333850.3	+	2	276	c.135C>T	c.(133-135)gaC>gaT	p.D45D	TPH2_ENST00000546576.1_3'UTR	NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	45					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.D45D(2)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	GCAAAAATGACGACAAAGGCA	0.393													C|||	1	0.000199681	0	0	5008	,	,		6803	0		0.001	False		,,,				2504	0															2	Substitution - coding silent(2)	ovary(1)|lung(1)	12											82	76	78					12																	72335393		2203	4300	6503	70621660	SO:0001819	synonymous_variant	121278			AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.135C>T	12.37:g.72335393C>T			70621660	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	37	CCDS31859.1																																																																																				0.393	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		T	72335393	C	T	72335393	2	4	115	1	0	0	0	0	0	0	0	1	16442	535	19	1		1	TPH2	12	72335393	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	18457665	72335393	61516502	133	30940										
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76425433	76425433	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atcttccccacccccgagtgAcacccagcggaaaaggcggc	10	17	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:76425433A>T	ENST00000266671.5	-	1	2279	c.89T>A	c.(88-90)gTc>gAc	p.V30D	RP11-290L1.2_ENST00000547721.1_RNA|RP11-290L1.3_ENST00000552367.1_RNA|PHLDA1_ENST00000602540.1_5'Flank			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	30					apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				CCCCCGAGTGACACCCAGCGG	0.706																																																0			12											4	5	5					12																	76425433		1904	4016	5920	74711700	SO:0001583	missense	22822			Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.89T>A	12.37:g.76425433A>T	ENSP00000266671:p.Val30Asp		74711700	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	ENST00000266671.5	37	CCDS31861.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436775	0.83885	.	.	ENSG00000139289	ENST00000266671	T	0.58210	0.35	4.71	4.71	0.59529	.	.	.	.	.	T	0.59715	0.2214	L	0.29908	0.895	0.51767	D	0.999933	D	0.76494	0.999	D	0.85130	0.997	T	0.63620	-0.6596	9	0.87932	D	0	-7.1392	11.66	0.51341	1.0:0.0:0.0:0.0	.	30	Q8WV24	PHLA1_HUMAN	D	30	ENSP00000266671:V30D	ENSP00000266671:V30D	V	-	2	0	PHLDA1	74711700	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.444000	0.35068	1.973000	0.57446	0.402000	0.26972	GTC		0.706	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		T	76425433	A	T	76425433	3	4	115	1	0	0	0	0	1	0	0	0	11879	275	10	5	1120	5	PHLDA1	12	76425433	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	4090040	76425433	57426462	134	30941										
CUX2	23316	hgsc.bcm.edu	37	chr12	111701582	111701582	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aaggtggtggcccttagtaaGagaagtcaggaggcggaggc	18	6	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:111701582G>C	ENST00000261726.6	+	4	394	c.240G>C	c.(238-240)aaG>aaC	p.K80N	CUX2_ENST00000551604.2_3'UTR	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	80					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCCTTAGTAAGAGAAGTCAGG	0.423																																																0			12											184	187	186					12																	111701582		1909	4132	6041	110185965	SO:0001583	missense	23316			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.240G>C	12.37:g.111701582G>C	ENSP00000261726:p.Lys80Asn		110185965	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	37	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118947	0.56505	.	.	ENSG00000111249	ENST00000261726;ENST00000397643;ENST00000552889	T	0.59638	0.25	5.92	0.693	0.18056	.	0.000000	0.85682	D	0.000000	T	0.67933	0.2946	M	0.64170	1.965	0.37060	D	0.89801	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.67898	-0.5551	10	0.40728	T	0.16	-30.474	10.0522	0.42223	0.5019:0.0:0.4981:0.0	.	140;80	F5GWR6;O14529	.;CUX2_HUMAN	N	80;140;18	ENSP00000261726:K80N	ENSP00000261726:K80N	K	+	3	2	CUX2	110185965	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.881000	0.39638	0.060000	0.16281	-0.258000	0.10820	AAG		0.423	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		C	111701582	G	C	111701582	3	2	115	1	0	0	0	0	1	0	0	0	4071	933	33	5	254	5	CUX2	12	111701582	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	35276149	111701582	22150313	135	30942										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126138807	126138807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cctggaaatacagacacaaaAggtttgctgtgagtgagcag	12	7	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:126138807A>G	ENST00000299308.3	+	9	2796	c.2788A>G	c.(2788-2790)Agg>Ggg	p.R930G	TMEM132B_ENST00000535886.1_Missense_Mutation_p.R442G	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	930						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	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)		CAGACACAAAAGGTTTGCTGT	0.502																																																0			12											106	105	105					12																	126138807		2031	4202	6233	124704760	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2788A>G	12.37:g.126138807A>G	ENSP00000299308:p.Arg930Gly		124704760	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338885	0.60963	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.10960	3.61;2.82	5.54	4.38	0.52667	.	0.000000	0.64402	D	0.000001	T	0.12987	0.0315	L	0.56199	1.76	0.44289	D	0.997156	P	0.41848	0.763	B	0.39027	0.288	T	0.01596	-1.1316	10	0.56958	D	0.05	.	12.7078	0.57070	0.8623:0.1377:0.0:0.0	.	930	Q14DG7	T132B_HUMAN	G	930;442	ENSP00000299308:R930G;ENSP00000440436:R442G	ENSP00000299308:R930G	R	+	1	2	TMEM132B	124704760	1.000000	0.71417	0.957000	0.39632	0.980000	0.70556	4.422000	0.59854	0.905000	0.36596	0.533000	0.62120	AGG		0.502	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		G	126138807	A	G	126138807	3	3	115	1	0	0	0	0	1	0	0	0	16085	63	3	4	2822	4	TMEM132B	12	126138807	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	14437225	126138807	7713088	136	30943										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184522	130184522	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgataaaggaagatgctcccGatcctctgcaaggggggccc	13	11	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:130184522G>A	ENST00000422113.2	-	2	1127	c.801C>T	c.(799-801)atC>atT	p.I267I	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	267					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.I267I(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	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)		AGATGCTCCCGATCCTCTGCA	0.572																																																1	Substitution - coding silent(1)	ovary(1)	12											92	82	86					12																	130184522		2203	4300	6503	128750475	SO:0001819	synonymous_variant	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.801C>T	12.37:g.130184522G>A			128750475	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.572	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130184522	G	A	130184522	2	1	115	1	0	0	0	0	0	0	0	1	16086	1048	37	1		1	TMEM132D	12	130184522	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	4045715	130184522	3667373	137	30944										
EP400	57634	hgsc.bcm.edu	37	chr12	132446294	132446294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctatcattaccaggagatgcAggctctgaaggaggtcttca	11	9	4	2	rs200853343		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr12:132446294A>G	ENST00000333577.4	+	2	1239	c.1130A>G	c.(1129-1131)cAg>cGg	p.Q377R	EP400_ENST00000332482.4_Missense_Mutation_p.Q377R|EP400_ENST00000389561.2_Missense_Mutation_p.Q377R|EP400_ENST00000330386.6_Missense_Mutation_p.Q377R|EP400_ENST00000389562.2_Missense_Mutation_p.Q377R			Q96L91	EP400_HUMAN	E1A binding protein p400	377					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	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)		CAGGAGATGCAGGCTCTGAAG	0.448																																																0			12						A	ARG/GLN	0,4406		0,0,2203	127	107	114		1130	5.5	1	12		114	1,8599	1.2+/-3.3	0,1,4299	no	missense	EP400	NM_015409.4	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	377/3124	132446294	1,13005	2203	4300	6503	131012247	SO:0001583	missense	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.1130A>G	12.37:g.132446294A>G	ENSP00000333602:p.Gln377Arg		131012247	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	A	11.31	1.602270	0.28534	0.0	1.16E-4	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.88975	-2.39;-2.45;-2.45;-2.45;-2.45	5.48	5.48	0.80851	.	0.213241	0.48286	D	0.000193	T	0.77343	0.4116	N	0.08118	0	0.30361	N	0.783792	B;B;B;B;B	0.26547	0.152;0.152;0.152;0.019;0.152	B;B;B;B;B	0.25614	0.036;0.036;0.036;0.062;0.036	T	0.67875	-0.5557	10	0.11182	T	0.66	.	15.5655	0.76287	1.0:0.0:0.0:0.0	.	377;377;377;377;377	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	R	377	ENSP00000333602:Q377R;ENSP00000374212:Q377R;ENSP00000374213:Q377R;ENSP00000331737:Q377R;ENSP00000330620:Q377R	ENSP00000330620:Q377R	Q	+	2	0	EP400	131012247	1.000000	0.71417	0.977000	0.42913	0.684000	0.39900	8.962000	0.93254	2.090000	0.63153	0.459000	0.35465	CAG		0.448	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		G	132446294	A	G	132446294	3	3	115	1	0	0	0	0	1	0	0	0	5162	188	7	4	1132	4	EP400	12	132446294	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	2261772	132446294	1405601	138	30945										
TUBA3C	7278	hgsc.bcm.edu	37	chr13	19751234	19751234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gaccatctgattggctggctCgaagcaggcattggtgatct	13	9	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:19751234C>T	ENST00000400113.3	-	4	993	c.889G>A	c.(889-891)Gag>Aag	p.E297K		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	297					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TTGGCTGGCTCGAAGCAGGCA	0.607																																																0			13											160	138	146					13																	19751234		2203	4300	6503	18649234	SO:0001583	missense	7278			AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"Tubulins"	12408	protein-coding gene	gene with protein product		602528	"tubulin, alpha 2"	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.889G>A	13.37:g.19751234C>T	ENSP00000382982:p.Glu297Lys		18649234	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	37	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	c	14.89	2.670081	0.47677	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	D	0.84730	-1.89	1.19	1.19	0.21007	.	0.000000	0.47455	U	0.000229	D	0.86539	0.5957	.	.	.	0.43238	D	0.995142	.	.	.	.	.	.	D	0.85825	0.1388	7	0.87932	D	0	.	8.3297	0.32178	0.0:1.0:0.0:0.0	.	.	.	.	K	297	ENSP00000382982:E297K	ENSP00000354037:E297K	E	-	1	0	TUBA3C	18649234	0.999000	0.42202	0.999000	0.59377	0.694000	0.40290	4.652000	0.61454	0.972000	0.38314	0.175000	0.17021	GAG		0.607	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001		T	19751234	C	T	19751234	3	4	115	1	0	0	0	0	1	0	0	0	16786	893	31	1	471	1	TUBA3C	13	19751234	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		19751234	95418644	139	30946										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36744745	36744745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gagaagctttgagaccggggGcatggctgaaggtaaatgaa	16	5	0	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:36744745G>A	ENST00000379881.3	-	10	1268	c.1180C>T	c.(1180-1182)Ccc>Tcc	p.P394S	CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.P471S|SOHLH2_ENST00000554962.1_Missense_Mutation_p.P471S	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	394					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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)		GAGACCGGGGGCATGGCTGAA	0.483																																																0			13											111	98	102					13																	36744745		2203	4300	6503	35642745	SO:0001583	missense	54937			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1180C>T	13.37:g.36744745G>A	ENSP00000369210:p.Pro394Ser		35642745	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	37	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	G	4.629	0.116976	0.08881	.	.	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	T;T;T	0.58210	0.36;0.35;0.35	5.14	2.44	0.29823	.	0.242039	0.29410	N	0.012224	T	0.47229	0.1434	M	0.61703	1.905	0.20873	N	0.999835	B;B	0.11235	0.004;0.004	B;B	0.16722	0.016;0.016	T	0.39623	-0.9605	10	0.38643	T	0.18	0.0287	9.7139	0.40263	0.0862:0.1423:0.7715:0.0	.	471;394	B4DX90;Q9NX45	.;SOLH2_HUMAN	S	394;471;471	ENSP00000369210:P394S;ENSP00000451542:P471S;ENSP00000421868:P471S	ENSP00000421868:P471S	P	-	1	0	CCDC169-SOHLH2;SOHLH2	35642745	0.073000	0.21202	0.060000	0.19600	0.141000	0.21300	0.097000	0.15168	0.185000	0.20105	-0.907000	0.02831	CCC		0.483	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		A	36744745	G	A	36744745	3	1	115	1	0	0	0	0	1	0	0	0	14961	1203	42	3	105	3	SOHLH2	13	36744745	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	16993511	36744745	78425133	140	30947										
SPG20	23111	hgsc.bcm.edu	37	chr13	36909193	36909193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aggacggtttagaaccgtatCgagagaattatccaaaaacc	9	8	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:36909193C>T	ENST00000451493.1	-	2	992	c.775G>A	c.(775-777)Gat>Aat	p.D259N	SPG20_ENST00000495510.1_5'UTR|SPG20_ENST00000438666.2_Missense_Mutation_p.D259N|SPG20_ENST00000355182.4_Missense_Mutation_p.D259N|SPG20_ENST00000494062.2_Missense_Mutation_p.D259N	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	259					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)	p.D259N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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)		AGAACCGTATCGAGAGAATTA	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	13											92	98	96					13																	36909193		2203	4300	6503	35807193	SO:0001583	missense	23111			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.775G>A	13.37:g.36909193C>T	ENSP00000414147:p.Asp259Asn		35807193	O60349|Q86Y67|Q9H1T2|Q9H1T3	Missense_Mutation	SNP	ENST00000451493.1	37	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485019	0.84854	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	D;D;D	0.89875	-2.58;-2.58;-2.58	5.82	5.82	0.92795	.	0.148772	0.64402	D	0.000013	D	0.90349	0.6980	L	0.54323	1.7	0.46222	D	0.99893	D;D;D	0.69078	0.997;0.984;0.997	P;B;P	0.51701	0.677;0.413;0.677	D	0.87214	0.2249	10	0.21014	T	0.42	-36.2299	20.1064	0.97896	0.0:1.0:0.0:0.0	.	259;259;259	A8K6Q9;B3KMI3;Q8N0X7	.;.;SPG20_HUMAN	N	259	ENSP00000406061:D259N;ENSP00000347314:D259N;ENSP00000414147:D259N	ENSP00000347314:D259N	D	-	1	0	SPG20	35807193	1.000000	0.71417	0.994000	0.49952	0.864000	0.49448	5.356000	0.66052	2.745000	0.94114	0.650000	0.86243	GAT		0.383	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			T	36909193	C	T	36909193	3	4	115	1	0	0	0	0	1	0	0	0	15081	884	31	1	1257	1	SPG20	13	36909193	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	164448	36909193	78260685	141	30948										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37599457	37599457	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtaacattaatgaaacacacAtctgtttctttccctggaga	6	9	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:37599457A>T	ENST00000350612.6	-	17	1549	c.1329T>A	c.(1327-1329)gaT>gaA	p.D443E	SUPT20H_ENST00000464744.1_Splice_Site_p.D444E|SUPT20H_ENST00000356185.3_Splice_Site_p.D444E|SUPT20H_ENST00000360252.4_Splice_Site_p.D444E|SUPT20H_ENST00000542180.1_Splice_Site_p.D407E|SUPT20H_ENST00000475892.1_Splice_Site_p.D443E	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	443					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TGAAACACACATCTGTTTCTT	0.433																																																0			13											110	104	106					13																	37599457		2203	4300	6503	36497457	SO:0001630	splice_region_variant	55578			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1329+1T>A	13.37:g.37599457A>T			36497457	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	3.790|3.790	-0.043852|-0.043852	0.07452|0.07452	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180|ENST00000469488	T;T;T;T;T;T|.	0.37752|.	1.2;1.18;1.8;1.2;1.2;1.31|.	5.33|5.33	4.15|4.15	0.48705|0.48705	.|.	0.169634|.	0.53938|.	N|.	0.000052|.	T|T	0.04137|0.04137	0.0115|0.0115	N|N	0.00053|0.00053	-2.39|-2.39	0.20196|0.20196	N|N	0.999925|0.999925	B;B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	T|T	0.32375|0.32375	-0.9909|-0.9909	10|5	0.02654|.	T|.	1|.	-14.0226|-14.0226	6.5754|6.5754	0.22562|0.22562	0.1385:0.0722:0.0:0.7893|0.1385:0.0722:0.0:0.7893	.|.	407;443;443;444;444;443;443|.	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7;F5GX46|.	.;.;.;.;.;FA48A_HUMAN;.|.	E|N	444;443;443;444;443;444;407|51	ENSP00000353388:D444E;ENSP00000417510:D443E;ENSP00000218894:D443E;ENSP00000348512:D444E;ENSP00000419754:D444E;ENSP00000439000:D407E|.	ENSP00000218894:D443E|.	D|I	-|-	3|2	2|0	FAM48A|FAM48A	36497457|36497457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.773000|0.773000	0.43773|0.43773	2.535000|2.535000	0.45685|0.45685	0.972000|0.972000	0.38314|0.38314	-0.343000|-0.343000	0.07986|0.07986	GAT|ATC		0.433	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	Missense_Mutation	T	37599457	A	T	37599457	5	4	115	1	0	0	0	0	0	0	1	0	5591	231	8	5	1050	5	FAM48A	13	37599457	Splice_Site	SNP	A	TCGA-F5-6465-01A-11D-1733-10	690264	37599457	77570421	142	30949										
FREM2	341640	hgsc.bcm.edu	37	chr13	39438545	39438545	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtgaagactcattatggtttCttgactgatgctaccaaaaa	8	7	2	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:39438545C>A	ENST00000280481.7	+	16	8001	c.7785C>A	c.(7783-7785)ttC>ttA	p.F2595L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2595					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ATTATGGTTTCTTGACTGATG	0.458																																																0			13											145	134	138					13																	39438545		2203	4300	6503	38336545	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.7785C>A	13.37:g.39438545C>A	ENSP00000280481:p.Phe2595Leu		38336545	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361014	0.82353	.	.	ENSG00000150893	ENST00000280481	T	0.28454	1.61	5.81	4.91	0.64330	.	0.053822	0.85682	D	0.000000	T	0.58906	0.2155	M	0.89287	3.02	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.85130	0.997;0.997	T	0.64795	-0.6323	10	0.87932	D	0	.	9.4515	0.38729	0.0:0.7655:0.0:0.2345	.	2595;2595	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	L	2595	ENSP00000280481:F2595L	ENSP00000280481:F2595L	F	+	3	2	FREM2	38336545	0.999000	0.42202	0.953000	0.39169	0.965000	0.64279	2.703000	0.47110	1.333000	0.45449	0.650000	0.86243	TTC		0.458	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39438545	C	A	39438545	3	1	115	1	0	0	0	0	1	0	0	0	6064	912	32	2	7847	2	FREM2	13	39438545	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	1839088	39438545	75731333	143	30950										
KBTBD7	84078	hgsc.bcm.edu	37	chr13	41767120	41767120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atgccacatccatgccctcaCgacacagcaagcgatctgca	7	16	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:41767120C>T	ENST00000379483.3	-	1	1582	c.1274G>A	c.(1273-1275)cGt>cAt	p.R425H		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	425										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		CATGCCCTCACGACACAGCAA	0.483																																																0			13											121	110	114					13																	41767120		2203	4300	6503	40665120	SO:0001583	missense	84078			AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1274G>A	13.37:g.41767120C>T	ENSP00000368797:p.Arg425His		40665120	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	37	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.534351	0.45073	.	.	ENSG00000120696	ENST00000379483;ENST00000501885	T	0.79554	-1.28	5.05	5.05	0.67936	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.83344	0.5234	M	0.88181	2.935	0.49687	D	0.999814	B	0.29886	0.26	B	0.24974	0.057	D	0.85003	0.0901	10	0.87932	D	0	.	15.9128	0.79485	0.0:1.0:0.0:0.0	.	425	Q8WVZ9	KBTB7_HUMAN	H	425;327	ENSP00000368797:R425H	ENSP00000368797:R425H	R	-	2	0	KBTBD7	40665120	1.000000	0.71417	0.750000	0.31169	0.922000	0.55478	5.132000	0.64758	2.328000	0.79073	0.557000	0.71058	CGT		0.483	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		T	41767120	C	T	41767120	3	4	115	1	0	0	0	0	1	0	0	0	8019	536	19	1	784	1	KBTBD7	13	41767120	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	2328575	41767120	73402758	144	30951										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58299162	58299162	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctgaagcaagcagtcagtacTtgcccactgacagtcaatat	8	11	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr13:58299162T>C	ENST00000377918.3	+	4	3240	c.3214T>C	c.(3214-3216)Ttg>Ctg	p.L1072L		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1072					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1072V(2)|p.L1072L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CAGTCAGTACTTGCCCACTGA	0.532																																					Melanoma(72;952 1291 1619 12849 33676)											3	Substitution - Missense(2)|Substitution - coding silent(1)	prostate(1)|large_intestine(1)|lung(1)	13											107	103	104					13																	58299162		2203	4300	6503	57197163	SO:0001819	synonymous_variant	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3214T>C	13.37:g.58299162T>C			57197163	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.532	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		C	58299162	T	C	58299162	2	2	115	1	0	0	0	0	0	0	0	1	11543	1606	56	4		4	PCDH17	13	58299162	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	16532042	58299162	56870716	145	30952										
PYGL	5836	hgsc.bcm.edu	37	chr14	51378483	51378483	+	Frame_Shift_Del	DEL	A	A	-													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atactctgtagttctccaagAagatgactttcaacttgctt							TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:51378483delA	ENST00000216392.7	-	16	2266	c.1934delT	c.(1933-1935)ttcfs	p.F645fs	RP11-218E20.5_ENST00000557343.1_RNA|PYGL_ENST00000544180.2_Frame_Shift_Del_p.F611fs|PYGL_ENST00000532462.1_Frame_Shift_Del_p.F645fs	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	645					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	GTTCTCCAAGAAGATGACTTT	0.428																																																0			14											94	85	88					14																	51378483		2203	4300	6503	50448233	SO:0001589	frameshift_variant	5836				CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"Glycogen phosphorylases"	9725	protein-coding gene	gene with protein product	"Hers disease", "glycogen storage disease type VI", "glycogen phosphorylase, liver form"	613741	"phosphorylase, glycogen; liver"			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.1934delT	14.37:g.51378483delA	ENSP00000216392:p.Phe645fs		50448233	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Frame_Shift_Del	DEL	ENST00000216392.7	37	CCDS32080.1																																																																																				0.428	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		-	51378483	A	-	51378483	7	5	115	1	0	1	0	1	0	0	0	0	12898	246	9	0	629	0	PYGL	14	51378483	Frame_Shift_Del	DEL	A	TCGA-F5-6465-01A-11D-1733-10		51378483	55971057	146	30953										
PNMA1	9240	hgsc.bcm.edu	37	chr14	74179954	74179954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gcatctctgggcccggggtcGgagtagggttctgaaaccca	15	11	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:74179954G>A	ENST00000316836.3	-	1	1174	c.389C>T	c.(388-390)cCg>cTg	p.P130L		NM_006029.4	NP_006020.4	Q8ND90	PNMA1_HUMAN	paraneoplastic Ma antigen 1	130					inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|urinary_tract(2)	13				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)		gcccggggtcggagtagggtt	0.478																																																0			14											75	81	79					14																	74179954		2203	4300	6503	73249707	SO:0001583	missense	9240			AF037364	CCDS9818.1	14q24.3	2012-02-09	2012-02-09		ENSG00000176903	ENSG00000176903		"Paraneoplastic Ma antigens"	9158	protein-coding gene	gene with protein product		604010	"paraneoplastic antigen MA1"			10050892	Standard	NM_006029		Approved	MA1	uc001xor.1	Q8ND90	OTTHUMG00000169183	ENST00000316836.3:c.389C>T	14.37:g.74179954G>A	ENSP00000318914:p.Pro130Leu		73249707	A8K4L5|O95144|Q8NG07	Missense_Mutation	SNP	ENST00000316836.3	37	CCDS9818.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.361643	0.41801	.	.	ENSG00000176903	ENST00000316836	T	0.08458	3.09	4.06	4.06	0.47325	.	0.159057	0.30168	N	0.010249	T	0.03564	0.0102	N	0.02697	-0.525	0.23381	N	0.997795	B	0.18013	0.025	B	0.14578	0.011	T	0.43572	-0.9383	10	0.19147	T	0.46	0.0	12.0532	0.53518	0.0:0.0:1.0:0.0	.	130	Q8ND90	PNMA1_HUMAN	L	130	ENSP00000318914:P130L	ENSP00000318914:P130L	P	-	2	0	PNMA1	73249707	0.268000	0.24133	0.104000	0.21259	0.826000	0.46750	2.352000	0.44080	2.551000	0.86045	0.655000	0.94253	CCG		0.478	PNMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402774.1	NM_006029		A	74179954	G	A	74179954	3	1	115	1	0	0	0	0	1	0	0	0	12184	1116	39	1	676	1	PNMA1	14	74179954	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	22801471	74179954	33169586	147	30954										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81329141	81329141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgagtcccagttgatcctggCgtctttccaccagctccctt	8	15	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:81329141C>T	ENST00000555265.1	-	9	1097	c.722G>A	c.(721-723)cGc>cAc	p.R241H	CEP128_ENST00000281129.3_Missense_Mutation_p.R241H|CEP128_ENST00000216517.6_Missense_Mutation_p.R241H			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	241						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TTGATCCTGGCGTCTTTCCAC	0.463																																																0			14											136	117	124					14																	81329141		2203	4300	6503	80398894	SO:0001583	missense	145508			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.722G>A	14.37:g.81329141C>T	ENSP00000451162:p.Arg241His		80398894	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.96|14.96	2.692058|2.692058	0.48097|0.48097	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000554827|ENST00000281129;ENST00000555265;ENST00000393619;ENST00000216517	.|T;T;T	.|0.55930	.|1.13;1.13;0.49	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	.|0.155258	.|0.45606	.|D	.|0.000341	T|T	0.59252|0.59252	0.2180|0.2180	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.67145	.|0.925;0.988;0.996	.|B;P;P	.|0.57371	.|0.271;0.737;0.819	T|T	0.53913|0.53913	-0.8371|-0.8371	5|10	.|0.33940	.|T	.|0.23	.|.	12.7223|12.7223	0.57149|0.57149	0.0:0.9243:0.0:0.0757|0.0:0.9243:0.0:0.0757	.|.	.|241;122;241	.|Q6ZU80-3;Q8N3Z7;Q6ZU80	.|.;.;CE128_HUMAN	T|H	120|241	.|ENSP00000281129:R241H;ENSP00000451162:R241H;ENSP00000216517:R241H	.|ENSP00000216517:R241H	A|R	-|-	1|2	0|0	CEP128|CEP128	80398894|80398894	0.924000|0.924000	0.31332|0.31332	0.947000|0.947000	0.38551|0.38551	0.019000|0.019000	0.09904|0.09904	1.774000|1.774000	0.38573|0.38573	2.894000|2.894000	0.99253|0.99253	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.463	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		T	81329141	C	T	81329141	3	4	115	1	0	0	0	0	1	0	0	0	1753	768	27	1	2630	1	C14orf145	14	81329141	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	7149187	81329141	26020399	148	30955										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610258	81610258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gtacaacccaggggacaaagAtaccaaaattgccaagagga	10	9	0	2	rs121908859		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:81610258A>G	ENST00000541158.2	+	11	2178	c.1856A>G	c.(1855-1857)gAt>gGt	p.D619G	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Missense_Mutation_p.D619G			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	619			D -> G (in hyperthyroidism and TTNs; associated with hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:11434721, ECO:0000269|PubMed:8413627, ECO:0000269|PubMed:9253356}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.D619G(10)|p.D619del(1)|p.Y613_K621del(1)|p.D619_T620>S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	GGGGACAAAGATACCAAAATT	0.468			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	13	Substitution - Missense(10)|Deletion - In frame(2)|Complex - deletion inframe(1)	thyroid(13)	14											210	188	196					14																	81610258		2203	4300	6503	80680011	SO:0001583	missense	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1856A>G	14.37:g.81610258A>G	ENSP00000441235:p.Asp619Gly		80680011	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.762392	0.69763	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.72051	-0.62;-0.62	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.89619	0.6767	H	0.97214	3.96	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.93270	0.6651	10	0.87932	D	0	.	15.3712	0.74568	1.0:0.0:0.0:0.0	.	619	F5GYU5	.	G	619;266;619	ENSP00000441235:D619G;ENSP00000298171:D619G	ENSP00000298171:D619G	D	+	2	0	TSHR	80680011	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	9.339000	0.96797	2.042000	0.60477	0.459000	0.35465	GAT		0.468	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		G	81610258	A	G	81610258	3	3	115	1	0	0	0	0	1	0	0	0	16662	333	12	4	2031	4	TSHR	14	81610258	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	281117	81610258	25739282	149	30956										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610295	81610295	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aggatggctgtgttgatcttCaccgacttcatatgcatggc	11	9	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:81610295C>T	ENST00000541158.2	+	11	2215	c.1893C>T	c.(1891-1893)ttC>ttT	p.F631F	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Silent_p.F631F			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	631			F -> C (in hyperthyroidism; associated with hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:8045989}.|F -> L (in HTNA; gain of function; found in toxic thyroid nodules and hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:11434721, ECO:0000269|PubMed:7800007, ECO:0000269|PubMed:9253356}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.F631L(3)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGTTGATCTTCACCGACTTCA	0.458			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	3	Substitution - Missense(3)	thyroid(3)	14											211	187	195					14																	81610295		2203	4300	6503	80680048	SO:0001819	synonymous_variant	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1893C>T	14.37:g.81610295C>T			80680048	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	CCDS9872.1																																																																																				0.458	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		T	81610295	C	T	81610295	2	4	115	1	0	0	0	0	0	0	0	1	16662	825	29	3		3	TSHR	14	81610295	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	37	81610295	25739245	150	30957										
FBLN5	10516	hgsc.bcm.edu	37	chr14	92403488	92403488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ataaatacccgccattttggTtaacacacatcatgtctcct	4	12	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:92403488T>C	ENST00000342058.4	-	4	775	c.182A>G	c.(181-183)aAc>aGc	p.N61S	FBLN5_ENST00000267620.10_Missense_Mutation_p.N102S|FBLN5_ENST00000556154.1_Missense_Mutation_p.N66S	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	61	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				GCCATTTTGGTTAACACACAT	0.547																																																0			14											91	83	85					14																	92403488		2203	4300	6503	91473241	SO:0001583	missense	10516			AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.182A>G	14.37:g.92403488T>C	ENSP00000345008:p.Asn61Ser		91473241	O75966|Q6IAL4|Q6UWA3	Missense_Mutation	SNP	ENST00000342058.4	37	CCDS9898.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601655	0.87055	.	.	ENSG00000140092	ENST00000267620;ENST00000342058;ENST00000556154;ENST00000554468	D;D;D;D	0.98777	-5.13;-5.13;-5.13;-5.13	5.58	5.58	0.84498	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99396	0.9787	H	0.95224	3.64	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.974;0.997	D;D;D	0.81914	0.995;0.953;0.983	D	0.98530	1.0627	10	0.87932	D	0	.	15.7499	0.77976	0.0:0.0:0.0:1.0	.	102;66;61	G3XA98;G3V4U0;Q9UBX5	.;.;FBLN5_HUMAN	S	102;61;66;61	ENSP00000267620:N102S;ENSP00000345008:N61S;ENSP00000451982:N66S;ENSP00000451486:N61S	ENSP00000267620:N158S	N	-	2	0	FBLN5	91473241	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.155000	0.71833	2.134000	0.65973	0.459000	0.35465	AAC		0.547	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			C	92403488	T	C	92403488	3	2	115	1	0	0	0	0	1	0	0	0	5719	1725	60	4	1196	4	FBLN5	14	92403488	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	10793193	92403488	14946052	151	30958										
UBR7	55148	hgsc.bcm.edu	37	chr14	93681298	93681298	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccagatgagatgatccagtgCgtagtctgtgaagactggtt	13	7	1	5	rs567093314		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:93681298C>T	ENST00000013070.6	+	5	701	c.465C>T	c.(463-465)tgC>tgT	p.C155C	UBR7_ENST00000416753.1_Silent_p.C79C|RP11-371E8.4_ENST00000557048.1_3'UTR	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	155							ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						TGATCCAGTGCGTAGTCTGTG	0.358													C|||	1	0.000199681	0	0	5008	,	,		18733	0.001		0	False		,,,				2504	0															0			14											100	93	95					14																	93681298		2203	4300	6503	92751051	SO:0001819	synonymous_variant	55148			AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963		"Ubiquitin protein ligase E3 component n-recognins"	20344	protein-coding gene	gene with protein product		613816	"chromosome 14 open reading frame 130"	C14orf130		18162545	Standard	NM_175748		Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.465C>T	14.37:g.93681298C>T			92751051	Q86U21|Q86UA9|Q96BY0|Q9NVV6	Silent	SNP	ENST00000013070.6	37	CCDS9909.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.87|13.87	2.364625|2.364625	0.41902|0.41902	.|.	.|.	ENSG00000012963|ENSG00000012963	ENST00000553857|ENST00000555113	.|.	.|.	.|.	5.91|5.91	-1.64|-1.64	0.08318|0.08318	.|.	.|.	.|.	.|.	.|.	T|T	0.57799|0.57799	0.2078|0.2078	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.56372|0.56372	-0.7990|-0.7990	4|4	.|.	.|.	.|.	-19.5629|-19.5629	11.4942|11.4942	0.50398|0.50398	0.0:0.5184:0.0:0.4816|0.0:0.5184:0.0:0.4816	.|.	.|.	.|.	.|.	V|C	81|146	.|.	.|.	A|R	+|+	2|1	0|0	UBR7|UBR7	92751051|92751051	0.889000|0.889000	0.30405|0.30405	0.935000|0.935000	0.37517|0.37517	0.953000|0.953000	0.61014|0.61014	0.064000|0.064000	0.14437|0.14437	-0.049000|-0.049000	0.13379|0.13379	-0.247000|-0.247000	0.11927|0.11927	GCG|CGT		0.358	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412693.1	NM_175748		T	93681298	C	T	93681298	2	4	115	1	0	0	0	0	0	0	0	1	16946	776	27	1		1	UBR7	14	93681298	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	1277810	93681298	13668242	152	30959										
RAGE	5891	hgsc.bcm.edu	37	chr14	102698924	102698924	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctggtgggcggcgattctctCatcgggatcataggccacca	13	12	3	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr14:102698924C>T	ENST00000361847.2	-	9	1045	c.814G>A	c.(814-816)Gag>Aag	p.E272K	MOK_ENST00000522867.1_Missense_Mutation_p.M4I|MOK_ENST00000193029.6_Missense_Mutation_p.E38K|MOK_ENST00000519058.1_Missense_Mutation_p.M4I|MOK_ENST00000522874.1_Missense_Mutation_p.E271K|MOK_ENST00000524370.1_Missense_Mutation_p.M4I|MOK_ENST00000524214.1_Missense_Mutation_p.E242K|MOK_ENST00000523231.1_Missense_Mutation_p.M4I|MOK_ENST00000520266.1_Intron|MOK_ENST00000561150.1_Missense_Mutation_p.M4I|MOK_ENST00000517966.1_Missense_Mutation_p.M4I|MOK_ENST00000522534.1_Missense_Mutation_p.M4I	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										GCGATTCTCTCATCGGGATCA	0.537																																																0			14											149	151	151					14																	102698924		2203	4300	6503	101768677	SO:0001583	missense	5891			AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"renal tumor antigen"	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.814G>A	14.37:g.102698924C>T	ENSP00000355304:p.Glu272Lys		101768677	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.96|13.96	2.392085|2.392085	0.42410|0.42410	.|.	.|.	ENSG00000080823|ENSG00000080823	ENST00000193029;ENST00000522874;ENST00000361847;ENST00000524214|ENST00000519058	T;T;T;T|.	0.62788|.	1.08;-0.0;-0.0;-0.0|.	5.5|5.5	4.57|4.57	0.56435|0.56435	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.308209|.	0.34178|.	N|.	0.004183|.	T|T	0.33206|0.33206	0.0855|0.0855	N|N	0.01779|0.01779	-0.725|-0.725	0.44275|0.44275	D|D	0.997135|0.997135	B;B|.	0.25169|.	0.119;0.07|.	B;B|.	0.29267|.	0.1;0.1|.	T|T	0.48364|0.48364	-0.9042|-0.9042	10|6	0.37606|0.87932	T|D	0.19|0	-1.6855|-1.6855	12.8612|12.8612	0.57913|0.57913	0.0:0.9168:0.0:0.0832|0.0:0.9168:0.0:0.0832	.|.	242;272|.	E7ERR8;Q9UQ07|.	.;MOK_HUMAN|.	K|I	38;271;272;242|4	ENSP00000193029:E38K;ENSP00000429469:E271K;ENSP00000355304:E272K;ENSP00000428942:E242K|.	ENSP00000193029:E38K|ENSP00000429672:M4I	E|M	-|-	1|3	0|0	RAGE|RAGE	101768677|101768677	1.000000|1.000000	0.71417|0.71417	0.049000|0.049000	0.19019|0.19019	0.940000|0.940000	0.58332|0.58332	4.346000|4.346000	0.59367|0.59367	1.244000|1.244000	0.43870|0.43870	0.462000|0.462000	0.41574|0.41574	GAG|ATG		0.537	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3			T	102698924	C	T	102698924	3	4	115	1	0	0	0	0	1	0	0	0	13043	835	29	3	461	3	RAGE	14	102698924	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	9017626	102698924	4650616	153	30960										
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382522	22382522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agaatttatcctccttggtcTgactcagtctcaagatattc	6	10	3	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:22382522T>C	ENST00000328795.4	+	1	141	c.50T>C	c.(49-51)cTg>cCg	p.L17P	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTCCTTGGTCTGACTCAGTCT	0.353																																																0			15											139	135	137					15																	22382522		2187	4260	6447	19883886	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.50T>C	15.37:g.22382522T>C	ENSP00000332500:p.Leu17Pro		19883886	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	8.244	0.807557	0.16467	.	.	ENSG00000183706	ENST00000328795	T	0.00344	8.02	3.24	3.24	0.37175	.	0.000000	0.37857	N	0.001901	T	0.01061	0.0035	H	0.94658	3.565	0.22412	N	0.999123	D	0.89917	1.0	D	0.83275	0.996	T	0.14420	-1.0473	10	0.87932	D	0	-8.0908	9.793	0.40717	0.0:0.0:0.0:1.0	.	17	Q8N0Y3	OR4N4_HUMAN	P	17	ENSP00000332500:L17P	ENSP00000332500:L17P	L	+	2	0	OR4N4	19883886	0.081000	0.21417	0.160000	0.22671	0.108000	0.19459	2.867000	0.48428	1.465000	0.48006	0.164000	0.16699	CTG		0.353	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382522	T	C	22382522	3	2	115	1	0	0	0	0	1	0	0	0	11109	1580	55	4	52	4	OR4N4	15	22382522	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10		22382522	80148870	154	30961										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959224	25959224	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agcctgagaagcatgccgtcGctggacggggtggacgggaa	18	9	0	1	rs116609652	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:25959224G>A	ENST00000356865.6	-	10	2052	c.1941C>T	c.(1939-1941)agC>agT	p.S647S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	647					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCATGCCGTCGCTGGACGGGG	0.682													G|||	10	0.00199681	0	0	5008	,	,		16683	0.0099		0	False		,,,				2504	0															0			15											41	45	44					15																	25959224		2203	4300	6503	23510317	SO:0001819	synonymous_variant	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1941C>T	15.37:g.25959224G>A			23510317	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																				0.682	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25959224	G	A	25959224	2	1	115	1	0	0	0	0	0	0	0	1	1117	1078	38	1		1	ATP10A	15	25959224	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	3576702	25959224	76572168	155	30962										
ZNF280D	54816	hgsc.bcm.edu	37	chr15	56950659	56950659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttcttaaaaatacaaaaccTtttgcttggacggttactat	5	8	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:56950659T>C	ENST00000267807.7	-	17	2236	c.2020A>G	c.(2020-2022)Agg>Ggg	p.R674G	ZNF280D_ENST00000559237.1_Missense_Mutation_p.R661G|ZNF280D_ENST00000396245.1_Missense_Mutation_p.R378G|ZNF280D_ENST00000559000.1_Missense_Mutation_p.R661G	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	674					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R674R(1)		endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		ATACAAAACCTTTTGCTTGGA	0.254																																																1	Substitution - coding silent(1)	large_intestine(1)	15											53	58	56					15																	56950659		2191	4287	6478	54737951	SO:0001583	missense	54816			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2020A>G	15.37:g.56950659T>C	ENSP00000267807:p.Arg674Gly		54737951	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.166536	0.78339	.	.	ENSG00000137871	ENST00000267807;ENST00000455329;ENST00000396245	T;T	0.03663	3.85;4.21	5.31	5.31	0.75309	.	2.874010	0.00718	N	0.000873	T	0.20129	0.0484	M	0.66939	2.045	0.35827	D	0.825048	D;D	0.67145	0.996;0.996	D;D	0.65987	0.94;0.94	T	0.00015	-1.2392	10	0.87932	D	0	-14.8862	12.9963	0.58648	0.0:0.0:0.0:1.0	.	737;674	B4DHL1;Q6N043	.;Z280D_HUMAN	G	674;661;378	ENSP00000267807:R674G;ENSP00000379545:R378G	ENSP00000267807:R674G	R	-	1	2	ZNF280D	54737951	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.055000	0.64282	2.010000	0.58986	0.416000	0.27883	AGG		0.254	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		C	56950659	T	C	56950659	3	2	115	1	0	0	0	0	1	0	0	0	17856	1608	56	4	943	4	ZNF280D	15	56950659	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	30991435	56950659	45580733	156	30963										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59455418	59455418	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcgtaacgctttgctaagagGcttaggaattcagttttgaa	10	6	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:59455418G>A	ENST00000288235.4	-	23	2964	c.2565C>T	c.(2563-2565)agC>agT	p.S855S		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	855	Myosin tail. {ECO:0000255}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.S855S(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TTGCTAAGAGGCTTAGGAATT	0.433																																																1	Substitution - coding silent(1)	central_nervous_system(1)	15											114	101	105					15																	59455418		2191	4291	6482	57242710	SO:0001819	synonymous_variant	4643			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2565C>T	15.37:g.59455418G>A			57242710	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																				0.433	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59455418	G	A	59455418	2	1	115	1	0	0	0	0	0	0	0	1	10102	1194	42	3		3	MYO1E	15	59455418	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	2504759	59455418	43075974	157	30964										
HERC1	8925	hgsc.bcm.edu	37	chr15	63952073	63952073	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	accaagcggtccagcaagtaAttcaaattcttcttcaccag	6	12	4	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:63952073A>G	ENST00000443617.2	-	47	9373	c.9286T>C	c.(9286-9288)Tta>Cta	p.L3096L		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3096					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCAGCAAGTAATTCAAATTCT	0.408																																																0			15											78	73	75					15																	63952073		1888	4114	6002	61739126	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.9286T>C	15.37:g.63952073A>G			61739126	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.408	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63952073	A	G	63952073	2	3	115	1	0	0	0	0	0	0	0	1	7078	98	4	4		4	HERC1	15	63952073	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	4496655	63952073	38579319	158	30965										
WDR61	80349	hgsc.bcm.edu	37	chr15	78581978	78581978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	taccttccagggtatgcagaAgttttccagttgcaatatca	8	9	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr15:78581978A>G	ENST00000267973.2	-	7	816	c.545T>C	c.(544-546)cTt>cCt	p.L182P	WDR61_ENST00000558311.1_Missense_Mutation_p.L182P|WDR61_ENST00000558459.1_Missense_Mutation_p.L89P			Q9GZS3	WDR61_HUMAN	WD repeat domain 61	182					histone H3-K4 trimethylation (GO:0080182)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						GGTATGCAGAAGTTTTCCAGT	0.348																																																0			15											78	76	77					15																	78581978		2196	4293	6489	76369033	SO:0001583	missense	80349				CCDS10300.1	15q25.1	2013-01-09			ENSG00000140395	ENSG00000140395		"WD repeat domain containing"	30300	protein-coding gene	gene with protein product		609540				12477932	Standard	NM_025234		Approved	REC14	uc002bdn.3	Q9GZS3	OTTHUMG00000143735	ENST00000267973.2:c.545T>C	15.37:g.78581978A>G	ENSP00000267973:p.Leu182Pro		76369033	D3DW84|Q6IA22|Q7Z4X4	Missense_Mutation	SNP	ENST00000267973.2	37	CCDS10300.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.481188	0.84747	.	.	ENSG00000140395	ENST00000267973	T	0.59502	0.26	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056292	0.64402	D	0.000001	T	0.71126	0.3303	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69139	-0.5224	10	0.34782	T	0.22	-8.0166	15.197	0.73100	1.0:0.0:0.0:0.0	.	182	Q9GZS3	WDR61_HUMAN	P	182	ENSP00000267973:L182P	ENSP00000267973:L182P	L	-	2	0	WDR61	76369033	1.000000	0.71417	0.985000	0.45067	0.983000	0.72400	9.116000	0.94341	2.195000	0.70347	0.482000	0.46254	CTT		0.348	WDR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289803.3	NM_025234		G	78581978	A	G	78581978	3	3	115	1	0	0	0	0	1	0	0	0	17352	72	3	4	392	4	WDR61	15	78581978	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	14629905	78581978	23949414	159	30966										
TMEM8A	58986	hgsc.bcm.edu	37	chr16	425221	425221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gaggttggccctgcgagaccAggcgctcagagacaaagggt	16	10	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr16:425221A>G	ENST00000431232.2	-	8	1511	c.1351T>C	c.(1351-1353)Tgg>Cgg	p.W451R	TMEM8A_ENST00000250930.3_Missense_Mutation_p.W258R|TMEM8A_ENST00000476735.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	451					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						CTGCGAGACCAGGCGCTCAGA	0.637																																																0			16											77	70	73					16																	425221		2202	4300	6502	365222	SO:0001583	missense	58986			AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1351T>C	16.37:g.425221A>G	ENSP00000401338:p.Trp451Arg		365222	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	A	7.082	0.570459	0.13560	.	.	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.28069	2.04;1.63	4.31	-2.56	0.06268	.	1.168690	0.06285	N	0.698184	T	0.17450	0.0419	N	0.22421	0.69	0.09310	N	1	B	0.16166	0.016	B	0.06405	0.002	T	0.27905	-1.0060	10	0.72032	D	0.01	-9.4489	2.2774	0.04105	0.2983:0.3667:0.0762:0.2588	.	451	Q9HCN3	TMM8A_HUMAN	R	451;258	ENSP00000401338:W451R;ENSP00000250930:W258R	ENSP00000250930:W258R	W	-	1	0	TMEM8A	365222	0.000000	0.05858	0.000000	0.03702	0.677000	0.39632	0.725000	0.25970	-0.781000	0.04548	0.459000	0.35465	TGG		0.637	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		G	425221	A	G	425221	3	3	115	1	0	0	0	0	1	0	0	0	16253	188	7	4	988	4	TMEM8A	16	425221	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10		425221	89929532	160	30967										
PDILT	204474	hgsc.bcm.edu	37	chr16	20396059	20396059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	actcctgctgaagctccttcTctatggtaatgtccactttg	7	12	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr16:20396059T>C	ENST00000302451.4	-	3	565	c.317A>G	c.(316-318)gAg>gGg	p.E106G	RP11-429K17.1_ENST00000577173.1_RNA	NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	106			E -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						AAGCTCCTTCTCTATGGTAAT	0.512																																																0			16											268	264	265					16																	20396059		2203	4300	6503	20303560	SO:0001583	missense	204474				CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.317A>G	16.37:g.20396059T>C	ENSP00000305465:p.Glu106Gly		20303560	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	T	15.30	2.794170	0.50102	.	.	ENSG00000169340	ENST00000302451	T	0.03524	3.9	5.43	4.32	0.51571	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.116359	0.56097	D	0.000021	T	0.15869	0.0382	M	0.79926	2.475	0.36722	D	0.881239	D	0.89917	1.0	D	0.79784	0.993	T	0.02691	-1.1123	10	0.52906	T	0.07	.	8.5088	0.33204	0.172:0.0:0.0:0.828	.	106	Q8N807	PDILT_HUMAN	G	106	ENSP00000305465:E106G	ENSP00000305465:E106G	E	-	2	0	PDILT	20303560	1.000000	0.71417	0.987000	0.45799	0.332000	0.28634	3.732000	0.55021	1.050000	0.40346	0.533000	0.62120	GAG		0.512	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		C	20396059	T	C	20396059	3	2	115	1	0	0	0	0	1	0	0	0	11705	1551	54	4	1477	4	PDILT	16	20396059	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	19970838	20396059	69958694	161	30968										
CES3	23491	hgsc.bcm.edu	37	chr16	66995285	66995285	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctcctggcatgccctgccacAgccactggtaagacacacct	8	17	0	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr16:66995285A>G	ENST00000303334.4	+	1	146	c.75A>G	c.(73-75)acA>acG	p.T25T	CES3_ENST00000394037.1_Silent_p.T25T|RP11-361L15.4_ENST00000566869.1_RNA	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	25						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GCCCTGCCACAGCCACTGGTA	0.602											OREG0023869	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			16											63	53	57					16																	66995285		2200	4300	6500	65552786	SO:0001819	synonymous_variant	23491			AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"Carboxylesterases"	1865	protein-coding gene	gene with protein product	"esterase 31", "brain carboxylesterase BR3"	605279	"carboxylesterase 3 (brain)"			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.75A>G	16.37:g.66995285A>G		1096	65552786	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Silent	SNP	ENST00000303334.4	37	CCDS10826.1																																																																																				0.602	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		G	66995285	A	G	66995285	2	3	115	1	0	0	0	0	0	0	0	1	3277	175	7	4		4	CES3	16	66995285	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	46599226	66995285	23359468	162	30969										
CDH1	999	hgsc.bcm.edu	37	chr16	68857497	68857497	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	attgcaaattcctgccattcTggggattcttggaggaattc	10	8	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr16:68857497T>A	ENST00000261769.5	+	13	2323	c.2132T>A	c.(2131-2133)cTg>cAg	p.L711Q	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.L650Q|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	711			L -> V (detected in an endometrial cancer sample). {ECO:0000269|PubMed:8075649}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCTGCCATTCTGGGGATTCTT	0.493			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	0			16											66	70	68					16																	68857497		2198	4300	6498	67414998	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2132T>A	16.37:g.68857497T>A	ENSP00000261769:p.Leu711Gln		67414998	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962849	0.74016	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	T;T	0.57436	0.41;0.4	6.04	4.96	0.65561	.	0.180883	0.26586	N	0.023550	T	0.74450	0.3718	M	0.86343	2.81	0.51482	D	0.99992	D;D	0.89917	0.996;1.0	D;D	0.76071	0.943;0.987	T	0.78201	-0.2296	10	0.87932	D	0	.	11.8028	0.52137	0.0:0.0686:0.0:0.9314	.	650;711	Q9UII8;P12830	.;CADH1_HUMAN	Q	711;729;650	ENSP00000261769:L711Q;ENSP00000414946:L650Q	ENSP00000261769:L711Q	L	+	2	0	CDH1	67414998	1.000000	0.71417	0.806000	0.32338	0.980000	0.70556	5.211000	0.65219	1.118000	0.41863	0.460000	0.39030	CTG		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68857497	T	A	68857497	3	1	115	1	0	0	0	0	1	0	0	0	3101	1580	55	5	2182	5	CDH1	16	68857497	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1862212	68857497	21497256	163	30970										
TBC1D28	254272	hgsc.bcm.edu	37	chr17	18541684	18541684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tatctagcaaaagtgacaacGcccggccccgcaccgccagg	10	16	1	1	rs574074719		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:18541684G>A	ENST00000345096.4	-	7	1028	c.329C>T	c.(328-330)gCg>gTg	p.A110V	TBC1D28_ENST00000405044.1_Missense_Mutation_p.A110V			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	110	Rab-GAP TBC.						Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						AAGTGACAACGCCCGGCCCCG	0.512													.|||	1	0.000199681	0	0	5008	,	,		20578	0.001		0	False		,,,				2504	0															0			17											120	122	121					17																	18541684		1928	4120	6048	18482409	SO:0001583	missense	254272				CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.329C>T	17.37:g.18541684G>A	ENSP00000339973:p.Ala110Val		18482409	Q2M2E1	Missense_Mutation	SNP	ENST00000345096.4	37	CCDS42273.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.027225	0.00410	.	.	ENSG00000189375	ENST00000345096;ENST00000405044	T;T	0.07021	3.23;3.23	0.185	0.185	0.15096	Rab-GAP/TBC domain (2);	0.416873	0.22654	N	0.057281	T	0.03827	0.0108	L	0.33093	0.98	0.09310	N	1	P	0.40578	0.722	B	0.34038	0.174	T	0.36383	-0.9750	9	0.02654	T	1	.	.	.	.	.	110	Q2M2D7	TBC28_HUMAN	V	110	ENSP00000339973:A110V;ENSP00000385821:A110V	ENSP00000339973:A110V	A	-	2	0	TBC1D28	18482409	0.724000	0.28038	0.001000	0.08648	0.001000	0.01503	0.235000	0.17948	0.293000	0.22520	0.298000	0.19748	GCG		0.512	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397		A	18541684	G	A	18541684	3	1	115	1	0	0	0	0	1	0	0	0	15656	1087	38	1	315	1	TBC1D28	17	18541684	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10		18541684	62653526	164	30971										
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36719669	36719669	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttctgcgggaacatgtgcgcGatgagtgcgtgcagcgtgtc	16	9	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:36719669G>C	ENST00000264659.7	-	5	854	c.630C>G	c.(628-630)atC>atG	p.I210M	SRCIN1_ENST00000578925.1_Missense_Mutation_p.I244M|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	82					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						ACATGTGCGCGATGAGTGCGT	0.607																																																0			17											46	50	49					17																	36719669		2187	4271	6458	33973195	SO:0001583	missense	0				CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.630C>G	17.37:g.36719669G>C	ENSP00000264659:p.Ile210Met		33973195	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	37	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337936	0.81911	.	.	ENSG00000017373	ENST00000264659;ENST00000398579	T	0.58060	0.36	5.0	4.01	0.46588	.	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	L	0.58101	1.795	0.46298	D	0.99897	D;D;D;D	0.89917	0.982;1.0;1.0;1.0	P;D;D;D	0.91635	0.884;0.998;0.998;0.999	T	0.67268	-0.5713	10	0.87932	D	0	-16.6874	9.767	0.40567	0.1673:0.0:0.8327:0.0	.	64;82;82;210	B4DHC2;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	M	210;64	ENSP00000264659:I210M	ENSP00000264659:I210M	I	-	3	3	SRCIN1	33973195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.353000	0.52247	2.477000	0.83638	0.650000	0.86243	ATC		0.607	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		C	36719669	G	C	36719669	3	2	115	1	0	0	0	0	1	0	0	0	15175	1048	37	5	2981	5	SRCIN1	17	36719669	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	18177985	36719669	44475541	165	30972										
SLC25A39	51629	hgsc.bcm.edu	37	chr17	42397597	42397597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cttggtgcccgactcggcccGgatcctccgcagcagcagcc	12	18	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:42397597G>A	ENST00000377095.5	-	11	1050	c.931C>T	c.(931-933)Cgg>Tgg	p.R311W	SLC25A39_ENST00000225308.8_Missense_Mutation_p.R303W|SLC25A39_ENST00000586016.1_Missense_Mutation_p.R179W|SLC25A39_ENST00000590194.1_Missense_Mutation_p.R303W|SLC25A39_ENST00000537904.2_Missense_Mutation_p.R288W	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	311					heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GACTCGGCCCGGATCCTCCGC	0.677																																																0			17											50	54	53					17																	42397597		2203	4300	6503	39753123	SO:0001583	missense	51629			BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"Solute carriers"	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.931C>T	17.37:g.42397597G>A	ENSP00000366299:p.Arg311Trp		39753123	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Missense_Mutation	SNP	ENST00000377095.5	37	CCDS45700.1	.	.	.	.	.	.	.	.	.	.	G	7.531	0.658711	0.14645	.	.	ENSG00000013306	ENST00000225308;ENST00000377095;ENST00000537904	T;T;T	0.78364	-1.17;-1.17;-1.17	5.38	2.31	0.28768	Mitochondrial carrier domain (2);	0.498482	0.21711	N	0.070272	T	0.54287	0.1849	N	0.05351	-0.065	0.22940	N	0.99853	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.35151	-0.9800	9	.	.	.	-0.5848	9.3464	0.38111	0.0676:0.0:0.6741:0.2584	.	288;311;303	B4DFG5;Q9BZJ4;Q9BZJ4-2	.;S2539_HUMAN;.	W	303;311;288	ENSP00000225308:R303W;ENSP00000366299:R311W;ENSP00000444540:R288W	.	R	-	1	2	SLC25A39	39753123	0.913000	0.31002	0.347000	0.25668	0.007000	0.05969	1.522000	0.35921	0.395000	0.25257	-0.169000	0.13324	CGG		0.677	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016		A	42397597	G	A	42397597	3	1	115	1	0	0	0	0	1	0	0	0	14540	1115	39	1	156	1	SLC25A39	17	42397597	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	5677928	42397597	38797613	166	30973										
CLTC	1213	hgsc.bcm.edu	37	chr17	57746254	57746254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aagaagtagaaagaatctgtAgagaaagcaactgctacgat	10	5	1	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:57746254A>G	ENST00000269122.3	+	14	2519	c.2245A>G	c.(2245-2247)Aga>Gga	p.R749G	CLTC_ENST00000393043.1_Missense_Mutation_p.R749G|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	749	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					AAGAATCTGTAGAGAAAGCAA	0.408			T	"ALK, TFE3"	"ALCL, renal "																																		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	0			17											114	116	115					17																	57746254		2203	4300	6503	55101036	SO:0001583	missense	1213			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2245A>G	17.37:g.57746254A>G	ENSP00000269122:p.Arg749Gly		55101036	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.615894	0.66672	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.20200	2.09;2.09	5.42	3.02	0.34903	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.52645	0.1747	M	0.91663	3.23	0.80722	D	1	D;P	0.62365	0.991;0.947	D;D	0.81914	0.995;0.957	T	0.64457	-0.6403	10	0.87932	D	0	.	13.0929	0.59176	0.6403:0.3597:0.0:0.0	.	749;749	Q00610;Q00610-2	CLH1_HUMAN;.	G	749	ENSP00000269122:R749G;ENSP00000376763:R749G	ENSP00000269122:R749G	R	+	1	2	CLTC	55101036	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	0.812000	0.27211	0.970000	0.38263	0.383000	0.25322	AGA		0.408	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57746254	A	G	57746254	3	3	115	1	0	0	0	0	1	0	0	0	3572	412	15	4	2299	4	CLTC	17	57746254	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	15348657	57746254	23448956	167	30974										
USP32	84669	hgsc.bcm.edu	37	chr17	58365981	58365981	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gatagaagccatcgagagaaAgtaaaagcatctttgtttag	10	5	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:58365981A>C	ENST00000300896.4	-	5	668	c.474T>G	c.(472-474)acT>acG	p.T158T	USP32_ENST00000393003.3_Silent_p.T158T	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	158					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ATCGAGAGAAAGTAAAAGCAT	0.343																																																0			17											87	83	85					17																	58365981		2203	4300	6503	55720763	SO:0001819	synonymous_variant	84669			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.474T>G	17.37:g.58365981A>C			55720763	Q7Z5T3|Q9BX85|Q9Y591	Silent	SNP	ENST00000300896.4	37	CCDS32697.1																																																																																				0.343	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		C	58365981	A	C	58365981	2	2	115	1	0	0	0	0	0	0	0	1	17103	59	3	4		4	USP32	17	58365981	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	619727	58365981	22829229	168	30975										
SOX9	6662	hgsc.bcm.edu	37	chr17	70119038	70119039	+	In_Frame_Ins	INS	-	-	AAG													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	catctcccccaacgccatctINStcaaggcgctgcaggccgac							TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:70119038_70119039insAAG	ENST00000245479.2	+	2	982_983	c.610_611insAAG	c.(610-612)ttc>tAAGtc	p.204_204F>*V		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	204					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CAACGCCATCTTCAAGGCGCTG	0.678																																					Pancreas(42;83 1041 2320 35205 39456)											0			17																																								67630634	SO:0001652	inframe_insertion	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	Exception_encountered	17.37:g.70119038_70119039insAAG	ENSP00000245479:p.Phe204delins*Val		67630633	Q53Y80	In_Frame_Del	INS	ENST00000245479.2	37	CCDS11689.1																																																																																				0.678	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		AAG	70119039	-	AAG	70119038	7	5	115	1	0	1	1	0	0	0	0	0	14995	1609	56	0	616	0	SOX9	17	70119038	In_Frame_Ins	INS	-	TCGA-F5-6465-01A-11D-1733-10	11753057	70119038	11076172	169	30976	56	2								
SOX9	6662	hgsc.bcm.edu	37	chr17	70119039	70119039	+	Missense_Mutation	SNP	T	T	A													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	catctcccccaacgccatctTcaaggcgctgcaggccgact							TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:70119039T>A	ENST00000245479.2	+	2	983	c.611T>A	c.(610-612)tTc>tAc	p.F204Y		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	204					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			AACGCCATCTTCAAGGCGCTG	0.677																																					Pancreas(42;83 1041 2320 35205 39456)											0			17											70	77	75					17																	70119039		2203	4300	6503	67630634	SO:0001583	missense	6662			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.611T>A	17.37:g.70119039T>A	ENSP00000245479:p.Phe204Tyr		67630634	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	37	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.786499	0.49997	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	D	0.82167	-1.58	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.65760	0.2722	L	0.31752	0.955	0.53688	D	0.999975	P	0.43094	0.799	B	0.30179	0.112	T	0.70156	-0.4949	10	0.02654	T	1	.	14.0059	0.64463	0.0:0.0:0.0:1.0	.	204	P48436	SOX9_HUMAN	Y	204	ENSP00000245479:F204Y	ENSP00000245479:F204Y	F	+	2	0	SOX9	67630634	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.962000	0.70364	1.716000	0.51395	0.402000	0.26972	TTC		0.677	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		A	70119039	T	A	70119039	3	1	115	1	0	0	0	0	1	0	0	0	14995	1783	62	5	617	5	SOX9	17	70119039	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1	70119039	11076171	170	30977	56	2								
KIF19	124602	hgsc.bcm.edu	37	chr17	72350578	72350578	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cgggcagtcggacatcatggGgacggccccaggccctggct	16	14	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:72350578G>T	ENST00000389916.4	+	18	2724	c.2586G>T	c.(2584-2586)ggG>ggT	p.G862G	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	862					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GACATCATGGGGACGGCCCCA	0.662																																																0			17											12	15	14					17																	72350578		1915	4079	5994	69862173	SO:0001819	synonymous_variant	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2586G>T	17.37:g.72350578G>T			69862173	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																				0.662	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72350578	G	T	72350578	2	4	115	1	0	0	0	0	0	0	0	1	8303	1219	43	2		2	KIF19	17	72350578	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	2231539	72350578	8844632	171	30978										
RNF213	57674	hgsc.bcm.edu	37	chr17	78321010	78321010	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggcttcgtgactactacagcCtcatcaaaatggtctttgct	8	11	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr17:78321010C>G	ENST00000582970.1	+	29	9018	c.8875C>G	c.(8875-8877)Ctc>Gtc	p.L2959V	RNF213_ENST00000508628.2_Missense_Mutation_p.L3008V|RNF213_ENST00000336301.6_Missense_Mutation_p.L1032V	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2959					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTACTACAGCCTCATCAAAAT	0.507																																																0			17											40	33	36					17																	78321010		2203	4300	6503	75935605	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.8875C>G	17.37:g.78321010C>G	ENSP00000464087:p.Leu2959Val		75935605	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801083	0.31869	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.34275	1.37;1.39	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000006	T	0.57651	0.2068	M	0.79475	2.455	0.34043	D	0.655189	P	0.46457	0.878	P	0.59056	0.851	T	0.70901	-0.4746	10	0.72032	D	0.01	.	13.3182	0.60419	0.0:0.9278:0.0:0.0722	.	1032	Q63HN8	RN213_HUMAN	V	2959;3008;1032	ENSP00000425956:L2959V;ENSP00000338218:L1032V	ENSP00000338218:L1032V	L	+	1	0	RNF213	75935605	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.652000	0.54439	2.751000	0.94390	0.563000	0.77884	CTC		0.507	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78321010	C	G	78321010	3	3	115	1	0	0	0	0	1	0	0	0	13514	681	24	5	9304	5	RNF213	17	78321010	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	5970432	78321010	2874200	172	30979										
MIB1	57534	hgsc.bcm.edu	37	chr18	19378063	19378063	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agactttaggtaaagttggcCgagtacaacagatttattca	9	6	1	2	rs141236852		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr18:19378063C>T	ENST00000261537.6	+	8	1375	c.1111C>T	c.(1111-1113)Cga>Tga	p.R371*	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	371					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			TAAAGTTGGCCGAGTACAACA	0.368																																																0			18						C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	117	118	117		1111	2.4	1	18	dbSNP_134	117	3,8595	3.0+/-9.4	0,3,4296	yes	stop-gained	MIB1	NM_020774.2		0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308		371/1007	19378063	4,13000	2203	4299	6502	17632061	SO:0001587	stop_gained	57534			AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.1111C>T	18.37:g.19378063C>T	ENSP00000261537:p.Arg371*		17632061	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Nonsense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	C	41	8.812577	0.98964	2.27E-4	3.49E-4	ENSG00000101752	ENST00000261537	.	.	.	5.2	2.39	0.29439	.	0.063642	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-9.7576	10.7384	0.46139	0.4891:0.392:0.119:0.0	.	.	.	.	X	371	.	ENSP00000261537:R371X	R	+	1	2	MIB1	17632061	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.905000	0.39878	0.269000	0.21961	-0.182000	0.12963	CGA		0.368	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		T	19378063	C	T	19378063	4	4	115	1	0	0	0	0	0	1	0	0	9596	644	23	1	1141	1	MIB1	18	19378063	Nonsense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		19378063	58699185	173	30980										
SMAD2	4087	hgsc.bcm.edu	37	chr18	45391501	45391501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgatatatccaggaggtggcGtttctacaaaagtttaaaac	9	6	1	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr18:45391501G>A	ENST00000402690.2	-	6	1053	c.659C>T	c.(658-660)aCg>aTg	p.T220M	SMAD2_ENST00000262160.6_Missense_Mutation_p.T220M|SMAD2_ENST00000356825.4_Missense_Mutation_p.T190M|SMAD2_ENST00000586040.1_Missense_Mutation_p.T190M|SMAD2_ENST00000591214.1_Missense_Mutation_p.T190M	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	220					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.T220M(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						AGGAGGTGGCGTTTCTACAAA	0.368																																																1	Substitution - Missense(1)	central_nervous_system(1)	18											88	74	79					18																	45391501		2203	4300	6503	43645499	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.659C>T	18.37:g.45391501G>A	ENSP00000384449:p.Thr220Met		43645499		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918373	0.92249	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.97209	-4.29;-4.29;-4.29	5.82	5.82	0.92795	SMAD/FHA domain (1);	0.046520	0.85682	D	0.000000	D	0.98052	0.9358	M	0.84948	2.725	0.80722	D	1	D;B;D	0.59357	0.985;0.318;0.985	P;B;P	0.53224	0.721;0.084;0.613	D	0.98254	1.0495	10	0.56958	D	0.05	.	19.7014	0.96054	0.0:0.0:1.0:0.0	.	190;190;220	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	M	220;190;220	ENSP00000262160:T220M;ENSP00000349282:T190M;ENSP00000384449:T220M	ENSP00000262160:T220M	T	-	2	0	SMAD2	43645499	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	9.747000	0.98863	2.755000	0.94549	0.591000	0.81541	ACG		0.368	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		A	45391501	G	A	45391501	3	1	115	1	0	0	0	0	1	0	0	0	14795	1145	40	1	768	1	SMAD2	18	45391501	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	26013438	45391501	32685747	174	30981										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575671	48575671	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttaaacaattaagatctctCaggattaacactgcagagta	6	7	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr18:48575671C>A	ENST00000342988.3	+	4	969	c.431C>A	c.(430-432)tCa>tAa	p.S144*	SMAD4_ENST00000588745.1_Nonsense_Mutation_p.S144*|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_Nonsense_Mutation_p.S144*|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.S144*	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	144					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.S144*(5)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TAAGATCTCTCAGGATTAACA	0.294																																																45	Whole gene deletion(36)|Substitution - Nonsense(5)|Unknown(4)	pancreas(26)|lung(4)|breast(4)|large_intestine(3)|stomach(3)|upper_aerodigestive_tract(2)|skin(1)|oesophagus(1)|NS(1)	18											182	163	169					18																	48575671		2202	4298	6500	46829669	SO:0001587	stop_gained	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.431C>A	18.37:g.48575671C>A	ENSP00000341551:p.Ser144*		46829669	A8K405	Nonsense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	42	9.580243	0.99210	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	19.1014	0.93275	0.0:1.0:0.0:0.0	.	.	.	.	X	144	.	ENSP00000341551:S144X	S	+	2	0	SMAD4	46829669	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.885000	0.63142	2.810000	0.96702	0.585000	0.79938	TCA		0.294	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48575671	C	A	48575671	4	1	115	1	0	0	0	0	0	1	0	0	14797	838	29	2	441	2	SMAD4	18	48575671	Nonsense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	3184170	48575671	29501577	175	30982										
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5455583	5455583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tcactgcctctgagccacgcGgtcattccaactcaactgcc	7	17	4	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:5455583G>A	ENST00000222033.4	+	1	158	c.81G>A	c.(79-81)gcG>gcA	p.A27A		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	27						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		TGAGCCACGCGGTCATTCCAA	0.657																																																0			19											42	49	46					19																	5455583		2104	4208	6312	5406583	SO:0001819	synonymous_variant	148066			AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"RING-type (C3HC4) zinc fingers"	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.81G>A	19.37:g.5455583G>A			5406583	A8K886|O75866	Silent	SNP	ENST00000222033.4	37	CCDS42475.1																																																																																				0.657	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		A	5455583	G	A	5455583	2	1	115	1	0	0	0	0	0	0	0	1	18253	1103	39	1		1	ZNRF4	19	5455583	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10		5455583	53673400	176	30983										
FBN3	84467	hgsc.bcm.edu	37	chr19	8174153	8174153	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctcacagggattgccccaagCccggcccagggagcaacagc	12	16	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:8174153C>A	ENST00000600128.1	-	36	4990	c.4576G>T	c.(4576-4578)Gct>Tct	p.A1526S	FBN3_ENST00000270509.2_Missense_Mutation_p.A1526S|FBN3_ENST00000601739.1_Missense_Mutation_p.A1526S			Q75N90	FBN3_HUMAN	fibrillin 3	1526	TB 6.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TTGCCCCAAGCCCGGCCCAGG	0.627																																																0			19											64	58	60					19																	8174153		2203	4300	6503	8080153	SO:0001583	missense	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4576G>T	19.37:g.8174153C>A	ENSP00000470498:p.Ala1526Ser		8080153	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.581611	0.65992	.	.	ENSG00000142449	ENST00000270509	D	0.95518	-3.73	4.23	4.23	0.50019	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	U	0.000000	D	0.97663	0.9234	M	0.82630	2.6	0.80722	D	1	D	0.62365	0.991	D	0.83275	0.996	D	0.98268	1.0502	10	0.56958	D	0.05	.	16.5549	0.84482	0.0:1.0:0.0:0.0	.	1526	Q75N90	FBN3_HUMAN	S	1526	ENSP00000270509:A1526S	ENSP00000270509:A1526S	A	-	1	0	FBN3	8080153	1.000000	0.71417	0.999000	0.59377	0.160000	0.22226	7.351000	0.79395	2.068000	0.61886	0.313000	0.20887	GCT		0.627	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8174153	C	A	8174153	3	1	115	1	0	0	0	0	1	0	0	0	5723	739	26	2	3969	2	FBN3	19	8174153	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	2718570	8174153	50954830	177	30984										
ATG4D	84971	hgsc.bcm.edu	37	chr19	10659630	10659630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccaggccagaccccacagccGagtggaagtctgtggtcatc	12	14	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:10659630G>A	ENST00000309469.4	+	6	1059	c.886G>A	c.(886-888)Gag>Aag	p.E296K	ATG4D_ENST00000540862.1_Intron|RNU7-140P_ENST00000459546.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	296					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CCCCACAGCCGAGTGGAAGTC	0.617																																																0			19											105	82	90					19																	10659630		2203	4300	6503	10520630	SO:0001583	missense	84971			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.886G>A	19.37:g.10659630G>A	ENSP00000311318:p.Glu296Lys		10520630	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.433596	0.43224	.	.	ENSG00000130734	ENST00000309469	T	0.42900	0.96	5.56	5.56	0.83823	.	0.359311	0.30820	N	0.008816	T	0.29914	0.0748	L	0.31664	0.95	0.80722	D	1	B;P	0.34837	0.307;0.472	B;B	0.30855	0.069;0.121	T	0.09185	-1.0686	10	0.07644	T	0.81	-5.0892	18.2767	0.90085	0.0:0.0:1.0:0.0	.	233;296	B4DGM8;Q86TL0	.;ATG4D_HUMAN	K	296	ENSP00000311318:E296K	ENSP00000311318:E296K	E	+	1	0	ATG4D	10520630	0.792000	0.28813	0.967000	0.41034	0.934000	0.57294	2.421000	0.44688	2.626000	0.88956	0.549000	0.68633	GAG		0.617	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		A	10659630	G	A	10659630	3	1	115	1	0	0	0	0	1	0	0	0	1100	1059	37	1	908	1	ATG4D	19	10659630	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	2485477	10659630	48469353	178	30985										
ZNF493	284443	hgsc.bcm.edu	37	chr19	21587986	21587986	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctctctggaggagtggcaatGcctggacactgctcagcagg	14	11	2	0	rs181874152		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:21587986G>A	ENST00000355504.4	+	1	135				ZNF493_ENST00000339914.6_Missense_Mutation_p.C29Y|ZNF493_ENST00000596302.1_Missense_Mutation_p.C29Y|ZNF493_ENST00000594390.1_Missense_Mutation_p.C29Y|CTD-2561J22.3_ENST00000600810.1_Missense_Mutation_p.C9Y|ZNF493_ENST00000392288.2_Missense_Mutation_p.C29Y	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GAGTGGCAATGCCTGGACACT	0.433																																																0			19											103	109	107					19																	21587986		2203	4300	6503	21379826	SO:0001627	intron_variant	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.-132+7917G>A	19.37:g.21587986G>A			21379826	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	6.345	0.431675	0.12045	.	.	ENSG00000196268	ENST00000392288;ENST00000339914	T;T	0.01767	4.65;4.65	1.14	-2.28	0.06826	.	.	.	.	.	T	0.02047	0.0064	L	0.52206	1.635	0.09310	N	1	B;P	0.39601	0.379;0.68	B;B	0.40982	0.031;0.345	T	0.37150	-0.9718	9	0.66056	D	0.02	.	1.9101	0.03285	0.2387:0.0:0.4533:0.308	.	29;29	Q6ZR52-2;G5E974	.;.	Y	29	ENSP00000376110:C29Y;ENSP00000340651:C29Y	ENSP00000340651:C29Y	C	+	2	0	ZNF493	21379826	0.006000	0.16342	0.110000	0.21437	0.022000	0.10575	-0.401000	0.07232	-0.546000	0.06216	-0.474000	0.04947	TGC		0.433	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		A	21587986	G	A	21587986	1	1	115	0	1	0	0	0	0	0	0	0	17983	1319	46	3		3	ZNF493	19	21587986	Intron	SNP	G	TCGA-F5-6465-01A-11D-1733-10	10928356	21587986	37540997	179	30986										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792390	33792390	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cagctccagcaccttctgctGcgtctccacgttgcgctgct	9	17	2	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:33792390G>A	ENST00000498907.2	-	1	1080	c.931C>T	c.(931-933)Cag>Tag	p.Q311*	CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	311	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R306fs*48(3)|p.T310_Q311insS(2)|p.T310_Q311insT(2)|p.T310_Q311insV(2)|p.T310_Q311insET(2)|p.Q311*(1)|p.H200_K352>Q(1)|p.?(1)|p.T310_Q312>K(1)|p.Q311>PQ(1)|p.T310_Q311insGGQT(1)|p.N307_Q312del(1)|p.Q311del(1)|p.T310_Q311del(1)|p.T310_Q311insKQ(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					ACCTTCTGCTGCGTCTCCACG	0.647			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																														Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	21	Insertion - In frame(10)|Complex - deletion inframe(5)|Deletion - In frame(3)|Substitution - Nonsense(1)|Unknown(1)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(21)	19											53	54	54					19																	33792390		2203	4300	6503	38484230	SO:0001587	stop_gained	1050	Familial Cancer Database	Familial AML	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.931C>T	19.37:g.33792390G>A	ENSP00000427514:p.Gln311*		38484230	A7LNP2|P78319|Q05CA4	Nonsense_Mutation	SNP	ENST00000498907.2	37	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	38	7.103821	0.98066	.	.	ENSG00000245848	ENST00000498907	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.6187	0.84924	0.0:0.0:1.0:0.0	.	.	.	.	X	311	.	ENSP00000427514:Q311X	Q	-	1	0	CEBPA	38484230	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.914000	0.87478	2.133000	0.65898	0.462000	0.41574	CAG		0.647	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		A	33792390	G	A	33792390	4	1	115	1	0	0	0	0	0	1	0	0	3205	1328	46	3	149	3	CEBPA	19	33792390	Nonsense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	12204404	33792390	25336593	180	30987										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351228	36351228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aggtgactctgtctgcttcgCcacacactgtgcaggaggga	13	11	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:36351228C>T	ENST00000360202.5	+	6	901	c.703C>T	c.(703-705)Cca>Tca	p.P235S	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.P235S|KIRREL2_ENST00000262625.7_Missense_Mutation_p.P235S|KIRREL2_ENST00000347900.6_Missense_Mutation_p.P185S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	235	Ig-like C2-type 3.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTCTGCTTCGCCACACACTGT	0.602																																																0			19											76	61	66					19																	36351228		2203	4300	6503	41043068	SO:0001583	missense	84063			AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.703C>T	19.37:g.36351228C>T	ENSP00000353331:p.Pro235Ser		41043068	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733144	0.69189	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.15256	2.44;2.44;2.44	3.86	3.86	0.44501	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41605	D	0.000848	T	0.43590	0.1254	M	0.85630	2.765	0.45097	D	0.998114	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.995;0.992;0.999;0.998;0.998	T	0.47129	-0.9141	10	0.62326	D	0.03	-10.0435	11.5369	0.50643	0.0:1.0:0.0:0.0	.	235;215;235;185;235	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	S	235;185;235;215	ENSP00000262625:P235S;ENSP00000345067:P185S;ENSP00000353331:P235S	ENSP00000262625:P235S	P	+	1	0	KIRREL2	41043068	1.000000	0.71417	0.999000	0.59377	0.502000	0.33828	6.514000	0.73746	2.182000	0.69389	0.449000	0.29647	CCA		0.602	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		T	36351228	C	T	36351228	3	4	115	1	0	0	0	0	1	0	0	0	8346	739	26	3	725	3	KIRREL2	19	36351228	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	2558838	36351228	22777755	181	30988										
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37678049	37678049	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttccaaattcagcacactcAtaggatttttccccagaata	4	11	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:37678049A>G	ENST00000532828.2	-	5	641	c.390T>C	c.(388-390)taT>taC	p.Y130Y	ZNF585B_ENST00000527838.1_Silent_p.Y130Y|ZNF585B_ENST00000531805.1_Silent_p.Y75Y|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000312908.5_5'Flank	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGCACACTCATAGGATTTTT	0.368																																					Melanoma(93;882 1454 18863 28917 48427)											0			19											67	71	69					19																	37678049		2202	4300	6502	42369889	SO:0001819	synonymous_variant	92285			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.390T>C	19.37:g.37678049A>G			42369889	Q8IZD3|Q96JW6	Silent	SNP	ENST00000532828.2	37	CCDS12500.1																																																																																				0.368	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		G	37678049	A	G	37678049	2	3	115	1	0	0	0	0	0	0	0	1	18057	224	8	4		4	ZNF585B	19	37678049	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	1326821	37678049	21450934	182	30989										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44536079	44536079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agtgacttaaccaggtctcaAgataccaccataagtaactc	6	11	1	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:44536079A>G	ENST00000187879.8	+	4	414	c.252A>G	c.(250-252)caA>caG	p.Q84Q	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Silent_p.Q124Q	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	84	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q84H(1)		endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				CCAGGTCTCAAGATACCACCA	0.403																																																1	Substitution - Missense(1)	ovary(1)	19											105	103	104					19																	44536079		2203	4300	6503	49227919	SO:0001819	synonymous_variant	7673			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.252A>G	19.37:g.44536079A>G			49227919	G5E9B9|Q8N6G7|Q9P1U5	Silent	SNP	ENST00000187879.8	37	CCDS33045.1																																																																																				0.403	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			G	44536079	A	G	44536079	2	3	115	1	0	0	0	0	0	0	0	1	17815	69	3	4		4	ZNF222	19	44536079	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	6858030	44536079	14592904	183	30990										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51769113	51769113	+	Frame_Shift_Del	DEL	C	C	-													0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggaattgtaattgcgctgctCttcctctgcctcctccctct					rs149317024		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:51769113delC	ENST00000316401.7	+	4	768	c.387delC	c.(385-387)ctcfs	p.L129fs	SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Frame_Shift_Del_p.L35fs|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	491	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										TTGCGCTGCTCTTCCTCTGCC	0.562																																																0			19											225	207	213					19																	51769113		2203	4300	6503	56460925	SO:0001589	frameshift_variant	0			AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.387delC	19.37:g.51769113delC	ENSP00000321249:p.Leu129fs		56460925	Q8IYH7	Frame_Shift_Del	DEL	ENST00000316401.7	37	CCDS12827.1																																																																																				0.562	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		-	51769113	C	-	51769113	7	5	115	1	0	1	0	1	0	0	0	0	1955	900	32	0	397	0	C19orf75	19	51769113	Frame_Shift_Del	DEL	C	TCGA-F5-6465-01A-11D-1733-10	7233034	51769113	7359870	184	30991										
USP29	57663	hgsc.bcm.edu	37	chr19	57642200	57642200	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aatggcttttatgactgtaaAgaaaacaggattccagaagg	10	5	0	3	rs562830906		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr19:57642200A>G	ENST00000254181.4	+	4	2611	c.2157A>G	c.(2155-2157)aaA>aaG	p.K719K	USP29_ENST00000598197.1_Silent_p.K719K	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	719	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATGACTGTAAAGAAAACAGGA	0.423																																																0			19											73	71	72					19																	57642200		2203	4300	6503	62334012	SO:0001819	synonymous_variant	57663				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.2157A>G	19.37:g.57642200A>G			62334012		Silent	SNP	ENST00000254181.4	37	CCDS33124.1																																																																																				0.423	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			G	57642200	A	G	57642200	2	3	115	1	0	0	0	0	0	0	0	1	17099	69	3	4		4	USP29	19	57642200	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	5873087	57642200	1486783	185	30992										
PCNA	5111	hgsc.bcm.edu	37	chr20	5099471	5099471	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tatcttcggcccttagtgtaAtgatatcttcattgccggcg	9	10	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:5099471A>G	ENST00000379160.3	-	3	505	c.263T>C	c.(262-264)aTt>aCt	p.I88T	SNORA26_ENST00000391215.1_RNA|PCNA_ENST00000379143.5_Missense_Mutation_p.I88T	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	88	Interaction with NUDT15.				base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CCTTAGTGTAATGATATCTTC	0.433								DNA polymerases (catalytic subunits)																																								0			20											224	217	219					20																	5099471		2203	4300	6503	5047471	SO:0001583	missense	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.263T>C	20.37:g.5099471A>G	ENSP00000368458:p.Ile88Thr		5047471	B2R897|D3DW02	Missense_Mutation	SNP	ENST00000379160.3	37	CCDS13087.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.100166	0.76983	.	.	ENSG00000132646	ENST00000379143;ENST00000379160	.	.	.	4.57	4.57	0.56435	Proliferating cell nuclear antigen, PCNA, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75989	0.3925	M	0.67569	2.06	0.80722	D	1	P;B	0.51057	0.941;0.328	D;D	0.74023	0.982;0.938	T	0.77960	-0.2391	9	0.59425	D	0.04	-13.1607	12.9032	0.58137	1.0:0.0:0.0:0.0	.	88;88	B4DUA2;P12004	.;PCNA_HUMAN	T	88	.	ENSP00000368438:I88T	I	-	2	0	PCNA	5047471	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.739000	0.91574	1.908000	0.55244	0.460000	0.39030	ATT		0.433	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			G	5099471	A	G	5099471	3	3	115	1	0	0	0	0	1	0	0	0	11619	101	4	4	542	4	PCNA	20	5099471	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10		5099471	57926049	186	30993										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10035156	10035156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	accaaccacatcagagggaaAgaaagtacagaagggtaatg	11	7	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:10035156A>G	ENST00000378380.3	+	9	2410	c.2081A>G	c.(2080-2082)aAg>aGg	p.K694R	ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Missense_Mutation_p.K694R|SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|AL109754.1_ENST00000408554.2_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	694			K -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				calcium ion binding (GO:0005509)										TCAGAGGGAAAGAAAGTACAG	0.343																																																0			20											108	98	101					20																	10035156		2203	4300	6503	9983156	SO:0001583	missense	63926			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.2081A>G	20.37:g.10035156A>G	ENSP00000367631:p.Lys694Arg		9983156	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	A	11.89	1.774029	0.31411	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.68331	-0.32;-0.32	4.94	4.94	0.65067	.	0.539360	0.20727	N	0.086786	T	0.53318	0.1789	L	0.42245	1.32	0.36039	D	0.839981	P	0.40000	0.698	B	0.28553	0.091	T	0.65138	-0.6241	10	0.40728	T	0.16	-17.8875	13.1369	0.59413	1.0:0.0:0.0:0.0	.	694	Q9NU02	ANKR5_HUMAN	R	694	ENSP00000367644:K694R;ENSP00000367631:K694R	ENSP00000367631:K694R	K	+	2	0	ANKRD5	9983156	1.000000	0.71417	0.622000	0.29159	0.310000	0.27922	4.076000	0.57591	1.976000	0.57569	0.459000	0.35465	AAG		0.343	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		G	10035156	A	G	10035156	3	3	115	1	0	0	0	0	1	0	0	0	676	72	3	4	2111	4	ANKRD5	20	10035156	Missense_Mutation	SNP	A	TCGA-F5-6465-01A-11D-1733-10	4935685	10035156	52990364	187	30994										
FLRT3	23767	hgsc.bcm.edu	37	chr20	14307499	14307499	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	actaggttgaagaaaactttGtcacctaaaccatgattgtt	7	7	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:14307499G>C	ENST00000378053.3	-	2	910	c.654C>G	c.(652-654)gaC>gaG	p.D218E	FLRT3_ENST00000341420.4_Missense_Mutation_p.D218E|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	218					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		AGAAAACTTTGTCACCTAAAC	0.448																																																0			20											61	60	60					20																	14307499		2203	4300	6503	14255499	SO:0001583	missense	23767			AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"Fibronectin type III domain containing"	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.654C>G	20.37:g.14307499G>C	ENSP00000367292:p.Asp218Glu		14255499	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	37	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	G	3.159	-0.172481	0.06421	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.56941	0.43;0.43	6.16	1.69	0.24217	.	0.063932	0.64402	D	0.000004	T	0.25121	0.0610	N	0.10618	0.005	0.42957	D	0.994396	B	0.11235	0.004	B	0.23574	0.047	T	0.03555	-1.1025	10	0.12766	T	0.61	-16.2879	4.9528	0.14023	0.2754:0.0:0.4564:0.2682	.	218	Q9NZU0	FLRT3_HUMAN	E	218	ENSP00000367292:D218E;ENSP00000339912:D218E	ENSP00000339912:D218E	D	-	3	2	FLRT3	14255499	0.974000	0.33945	1.000000	0.80357	0.997000	0.91878	0.164000	0.16542	0.835000	0.34877	0.650000	0.86243	GAC		0.448	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281		C	14307499	G	C	14307499	3	2	115	1	0	0	0	0	1	0	0	0	5959	1368	48	5	1299	5	FLRT3	20	14307499	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	4272343	14307499	48718021	188	30995										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20501609	20501609	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ttctgctgatgaatgatactGgactggctcagagctcttca	10	9	4	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:20501609G>T	ENST00000202677.7	-	31	4043	c.4036C>A	c.(4036-4038)Cag>Aag	p.Q1346K		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1346					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						GAATGATACTGGACTGGCTCA	0.468																																																0			20											95	93	94					20																	20501609		1927	4131	6058	20449609	SO:0001583	missense	0			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4036C>A	20.37:g.20501609G>T	ENSP00000202677:p.Gln1346Lys		20449609	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.757749	0.31137	.	.	ENSG00000188559	ENST00000202677	T	0.28666	1.6	6.17	6.17	0.99709	.	0.261032	0.41001	D	0.000972	T	0.33876	0.0878	M	0.63428	1.95	0.51012	D	0.999902	B;B;B	0.26902	0.002;0.163;0.002	B;B;B	0.29440	0.003;0.102;0.007	T	0.29458	-1.0011	10	0.05721	T	0.95	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1184;1346;1346	A8MSM5;Q2PPJ7-2;Q2PPJ7	.;.;RGPA2_HUMAN	K	1346	ENSP00000202677:Q1346K	ENSP00000202677:Q1346K	Q	-	1	0	RALGAPA2	20449609	1.000000	0.71417	0.959000	0.39883	0.727000	0.41649	6.669000	0.74462	2.941000	0.99782	0.655000	0.94253	CAG		0.468	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20501609	G	T	20501609	3	4	115	1	0	0	0	0	1	0	0	0	13051	1357	47	2	1621	2	RALGAPA2	20	20501609	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	6194110	20501609	42523911	189	30996										
ZNF337	26152	hgsc.bcm.edu	37	chr20	25666698	25666698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cagggccctctgagcagggcTcagcagcctccattccttct	10	16	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:25666698T>C	ENST00000376436.1	-	2	627	c.88A>G	c.(88-90)Agc>Ggc	p.S30G	ZNF337_ENST00000538750.1_Missense_Mutation_p.S30G|ZNF337_ENST00000481610.1_5'UTR|ZNF337_ENST00000252979.5_Missense_Mutation_p.S30G			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGAGCAGGGCTCAGCAGCCTC	0.552																																																0			20											108	108	108					20																	25666698		2203	4300	6503	25614698	SO:0001583	missense	26152				CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.88A>G	20.37:g.25666698T>C	ENSP00000365619:p.Ser30Gly		25614698	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	37	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	7.569	0.666378	0.14710	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.01613	4.73;4.73;4.73	2.02	0.879	0.19155	Krueppel-associated box (4);	.	.	.	.	T	0.02649	0.0080	N	0.17564	0.495	0.09310	N	1	P;P	0.51057	0.941;0.941	P;P	0.60415	0.874;0.874	T	0.50939	-0.8768	9	0.37606	T	0.19	.	4.9012	0.13775	0.0:0.1762:0.0:0.8238	.	30;30	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	G	30	ENSP00000365619:S30G;ENSP00000252979:S30G;ENSP00000442181:S30G	ENSP00000252979:S30G	S	-	1	0	ZNF337	25614698	0.013000	0.17824	0.001000	0.08648	0.201000	0.24016	-0.352000	0.07701	-0.016000	0.14127	0.378000	0.23410	AGC		0.552	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			C	25666698	T	C	25666698	3	2	115	1	0	0	0	0	1	0	0	0	17892	1551	54	4	2179	4	ZNF337	20	25666698	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	5165089	25666698	37358822	190	30997										
LBP	3929	hgsc.bcm.edu	37	chr20	36982805	36982805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccagctgcagcagtgacatcGctgacgtggaggtggacatg	15	10	0	2	rs139250125	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:36982805G>A	ENST00000217407.2	+	4	651	c.490G>A	c.(490-492)Gct>Act	p.A164T		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	164					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CAGTGACATCGCTGACGTGGA	0.617													G|||	3	0.000599042	0	0	5008	,	,		17210	0		0.002	False		,,,				2504	0.001															0			20						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	57	48	51		490	-5.3	0	20	dbSNP_134	51	7,8593	5.7+/-21.5	0,7,4293	yes	missense	LBP	NM_004139.2	58	0,8,6495	AA,AG,GG		0.0814,0.0227,0.0615	benign	164/482	36982805	8,12998	2203	4300	6503	36416219	SO:0001583	missense	3929				CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.490G>A	20.37:g.36982805G>A	ENSP00000217407:p.Ala164Thr		36416219	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.958	0.969977	0.18659	2.27E-4	8.14E-4	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.04454	3.62	4.77	-5.27	0.02763	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	2.755460	0.00894	N	0.002269	T	0.03783	0.0107	N	0.22421	0.69	0.09310	N	1	B	0.21753	0.06	B	0.26416	0.069	T	0.40720	-0.9548	10	0.22706	T	0.39	16.9367	6.3072	0.21145	0.0:0.2195:0.375:0.4055	.	164	P18428	LBP_HUMAN	T	164	ENSP00000217407:A164T	ENSP00000217407:A164T	A	+	1	0	LBP	36416219	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.395000	0.01053	-0.738000	0.04817	-0.311000	0.09066	GCT		0.617	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		A	36982805	G	A	36982805	3	1	115	1	0	0	0	0	1	0	0	0	8673	1087	38	1	504	1	LBP	20	36982805	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	11316107	36982805	26042715	191	30998										
TUBB1	81027	hgsc.bcm.edu	37	chr20	57598986	57598986	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	cggatcatgaattccttcagCgtcatgccttctcccaaggt	8	13	4	1	rs375902986		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:57598986C>T	ENST00000217133.1	+	4	773	c.504C>T	c.(502-504)agC>agT	p.S168S		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	168					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	ATTCCTTCAGCGTCATGCCTT	0.567																																																0			20											128	129	129					20																	57598986		2203	4300	6503	57032381	SO:0001819	synonymous_variant	203068			AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.504C>T	20.37:g.57598986C>T			57032381		Silent	SNP	ENST00000217133.1	37	CCDS13475.1																																																																																				0.567	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		T	57598986	C	T	57598986	2	4	115	1	0	0	0	0	0	0	0	1	16793	767	27	1		1	TUBB1	20	57598986	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	20616181	57598986	5426534	192	30999										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58467262	58467262	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tagtttcagattcaacaggcCaatcactctgcttggcattt	7	10	4	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr20:58467262C>G	ENST00000357552.3	-	24	2372	c.2147G>C	c.(2146-2148)tGg>tCg	p.W716S	SYCP2_ENST00000371001.2_Missense_Mutation_p.W716S			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	716					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TTCAACAGGCCAATCACTCTG	0.338																																																0			20											154	159	157					20																	58467262		2203	4298	6501	57900657	SO:0001583	missense	10388			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.2147G>C	20.37:g.58467262C>G	ENSP00000350162:p.Trp716Ser		57900657	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812606	0.50527	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.24350	2.07;2.07;1.86	5.17	4.15	0.48705	.	0.099997	0.45606	D	0.000359	T	0.44498	0.1296	M	0.64997	1.995	0.51012	D	0.999909	D	0.76494	0.999	D	0.74023	0.982	T	0.36311	-0.9753	10	0.87932	D	0	-5.5717	10.4546	0.44542	0.1941:0.8059:0.0:0.0	.	716	Q9BX26	SYCP2_HUMAN	S	716	ENSP00000360040:W716S;ENSP00000350162:W716S;ENSP00000402456:W716S	ENSP00000350162:W716S	W	-	2	0	SYCP2	57900657	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	2.017000	0.40981	2.575000	0.86900	0.491000	0.48974	TGG		0.338	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		G	58467262	C	G	58467262	3	3	115	1	0	0	0	0	1	0	0	0	15471	595	21	5	2533	5	SYCP2	20	58467262	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	868276	58467262	4558258	193	31000										
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31691839	31691839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	caacgtgaagactttgaggaCgataggccaagcaactcgag	12	9	0	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr21:31691839C>T	ENST00000360542.3	-	1	768	c.515G>A	c.(514-516)cGt>cAt	p.R172H		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	172						intermediate filament (GO:0005882)		p.R172H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						ACTTTGAGGACGATAGGCCAA	0.562																																																1	Substitution - Missense(1)	ovary(1)	21											192	193	193					21																	31691839		2203	4300	6503	30613710	SO:0001583	missense	388818			AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"Keratin associated proteins"	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.515G>A	21.37:g.31691839C>T	ENSP00000353742:p.Arg172His		30613710	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.379383	0.42207	.	.	ENSG00000197683	ENST00000360542	T	0.16897	2.31	5.06	2.27	0.28462	.	1.468220	0.04336	N	0.353191	T	0.12092	0.0294	L	0.27053	0.805	0.09310	N	1	P	0.47350	0.894	B	0.39068	0.289	T	0.22487	-1.0215	10	0.24483	T	0.36	1.0E-4	6.4572	0.21936	0.0:0.7061:0.0:0.2939	.	172	Q6PEX3	KR261_HUMAN	H	172	ENSP00000353742:R172H	ENSP00000353742:R172H	R	-	2	0	KRTAP26-1	30613710	0.000000	0.05858	0.020000	0.16555	0.006000	0.05464	0.114000	0.15520	0.782000	0.33613	0.650000	0.86243	CGT		0.562	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31691839	C	T	31691839	3	4	115	1	0	0	0	0	1	0	0	0	8565	536	19	1	121	1	KRTAP26-1	21	31691839	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		31691839	16438056	194	31001										
KLHL22	84861	hgsc.bcm.edu	37	chr22	20800900	20800900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tgtctctttcaggtaatcctCccctctgcggccgcaggtga	10	14	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr22:20800900C>T	ENST00000328879.4	-	6	1525	c.1369G>A	c.(1369-1371)Gag>Aag	p.E457K	KLHL22_ENST00000440659.2_Missense_Mutation_p.E314K	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	457					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	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)			AGGTAATCCTCCCCTCTGCGG	0.622																																																0			22											239	188	205					22																	20800900		2203	4300	6503	19130900	SO:0001583	missense	84861				CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1369G>A	22.37:g.20800900C>T	ENSP00000331682:p.Glu457Lys		19130900	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Missense_Mutation	SNP	ENST00000328879.4	37	CCDS13780.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169310	0.57584	.	.	ENSG00000099910	ENST00000328879;ENST00000440659	T;T	0.41065	1.01;1.01	5.67	5.67	0.87782	Kelch-type beta propeller (1);	0.311451	0.36234	N	0.002710	T	0.30792	0.0776	L	0.40543	1.245	0.36901	D	0.890402	B	0.28820	0.224	B	0.28916	0.096	T	0.17561	-1.0365	10	0.08837	T	0.75	.	10.6721	0.45764	0.0:0.9133:0.0:0.0867	.	457	Q53GT1	KLH22_HUMAN	K	457;314	ENSP00000331682:E457K;ENSP00000405521:E314K	ENSP00000331682:E457K	E	-	1	0	KLHL22	19130900	0.882000	0.30256	1.000000	0.80357	0.996000	0.88848	1.709000	0.37909	2.687000	0.91594	0.563000	0.77884	GAG		0.622	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		T	20800900	C	T	20800900	3	4	115	1	0	0	0	0	1	0	0	0	8398	864	30	3	543	3	KLHL22	22	20800900	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		20800900	30503666	195	31002										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656620	46656620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctggttgataccccactttTcaactttcttgacatacatg	6	11	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chr22:46656620T>C	ENST00000253255.5	-	1	2599	c.2600A>G	c.(2599-2601)gAa>gGa	p.E867G		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	867	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACCCCACTTTTCAACTTTCTT	0.398																																																0			22											66	66	66					22																	46656620		2203	4300	6503	45035284	SO:0001583	missense	10343			AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2600A>G	22.37:g.46656620T>C	ENSP00000253255:p.Glu867Gly		45035284	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317425	0.60524	.	.	ENSG00000130943	ENST00000253255	T	0.42131	0.98	5.16	2.99	0.34606	Egg jelly receptor, REJ-like (1);	0.000000	0.64402	D	0.000009	T	0.35278	0.0926	M	0.68952	2.095	0.09310	N	1	B	0.34372	0.451	B	0.31101	0.124	T	0.34453	-0.9828	10	0.59425	D	0.04	-13.2984	5.2622	0.15580	0.1565:0.0835:0.0:0.76	.	867	Q9NTG1	PKDRE_HUMAN	G	867	ENSP00000253255:E867G	ENSP00000253255:E867G	E	-	2	0	PKDREJ	45035284	0.781000	0.28676	0.005000	0.12908	0.322000	0.28314	1.723000	0.38053	0.367000	0.24454	0.533000	0.62120	GAA		0.398	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		C	46656620	T	C	46656620	3	2	115	1	0	0	0	0	1	0	0	0	12001	1783	62	4	4165	4	PKDREJ	22	46656620	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	25855720	46656620	4647946	196	31003										
MSL3	10943	hgsc.bcm.edu	37	chrX	11783633	11783633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gcctttgttgaatccatccaCgccacagtccacagagagtc	8	14	0	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:11783633C>T	ENST00000312196.4	+	9	1061	c.956C>T	c.(955-957)aCg>aTg	p.T319M	MSL3_ENST00000398527.2_Missense_Mutation_p.T307M|MSL3_ENST00000337339.2_Missense_Mutation_p.T319M|MSL3_ENST00000380693.3_Missense_Mutation_p.T153M|MSL3_ENST00000361672.2_Missense_Mutation_p.T170M	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	319	MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.|Required for the histone acetyltransferase activity of the MSL complex.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						AATCCATCCACGCCACAGTCC	0.577																																																0			X											113	104	107					X																	11783633		2203	4300	6503	11693554	SO:0001583	missense	10943			AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"male-specific lethal-3 (Drosophila)-like 1", "male-specific lethal 3-like 1 (Drosophila)"	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.956C>T	X.37:g.11783633C>T	ENSP00000312244:p.Thr319Met		11693554	A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Missense_Mutation	SNP	ENST00000312196.4	37	CCDS14147.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315976	0.81469	.	.	ENSG00000005302	ENST00000312196;ENST00000337339;ENST00000361672;ENST00000398527;ENST00000380693;ENST00000380692	T;T;T;T;T;T	0.13196	3.07;3.09;2.71;2.88;2.72;2.61	4.61	4.61	0.57282	.	0.157660	0.56097	D	0.000035	T	0.38161	0.1030	M	0.76574	2.34	0.54753	D	0.999989	D;D;D;D;D	0.89917	0.999;0.983;0.998;0.999;1.0	P;P;P;D;D	0.73380	0.903;0.595;0.674;0.95;0.98	T	0.27640	-1.0068	10	0.52906	T	0.07	.	17.0067	0.86395	0.0:1.0:0.0:0.0	.	307;170;260;319;319	B4DUV8;B7Z227;Q8N5Y2-2;Q8N5Y2;A6NHW8	.;.;.;MS3L1_HUMAN;.	M	319;319;170;307;153;153	ENSP00000312244:T319M;ENSP00000338078:T319M;ENSP00000354562:T170M;ENSP00000381538:T307M;ENSP00000370069:T153M;ENSP00000370068:T153M	ENSP00000312244:T319M	T	+	2	0	MSL3	11693554	1.000000	0.71417	0.995000	0.50966	0.928000	0.56348	6.436000	0.73417	2.021000	0.59480	0.600000	0.82982	ACG		0.577	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800		T	11783633	C	T	11783633	3	4	115	1	0	0	0	0	1	0	0	0	9909	536	19	1	990	1	MSL3	23	11783633	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10		11783633	143486927	197	31004										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12701706	12701706	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atcatcaacggccaagtgtcGgtgagtttacagtcacctgc	10	11	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:12701706G>A	ENST00000380682.1	+	6	1079	c.573G>A	c.(571-573)tcG>tcA	p.S191S		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	191					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.S191S(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GCCAAGTGTCGGTGAGTTTAC	0.448																																																1	Substitution - coding silent(1)	central_nervous_system(1)	X											96	73	81					X																	12701706		2203	4300	6503	12611627	SO:0001630	splice_region_variant	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.573+1G>A	X.37:g.12701706G>A			12611627	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																				0.448	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	Silent	A	12701706	G	A	12701706	5	1	115	1	0	0	0	0	0	0	1	0	6078	1130	39	1	595	1	FRMPD4	23	12701706	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10	918073	12701706	142568854	198	31005										
ATXN3L	92552	hgsc.bcm.edu	37	chrX	13337617	13337617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ccaagaaatttgcaaggcatGtatctgatattaattctgga	8	6	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:13337617G>A	ENST00000380622.2	-	1	901	c.437C>T	c.(436-438)aCa>aTa	p.T146I	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	146	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.				protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TGCAAGGCATGTATCTGATAT	0.373																																																0			X											64	61	62					X																	13337617		1568	3582	5150	13247538	SO:0001583	missense	92552				CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.437C>T	X.37:g.13337617G>A	ENSP00000369996:p.Thr146Ile		13247538	B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.257742	0.22965	.	.	ENSG00000123594	ENST00000380622	T	0.45668	0.89	0.661	-1.32	0.09201	.	0.000000	0.85682	D	0.000000	T	0.57577	0.2063	M	0.84585	2.705	0.52501	D	0.99995	D	0.58268	0.982	D	0.72338	0.977	T	0.52909	-0.8512	10	0.87932	D	0	.	2.9331	0.05805	0.211:0.0:0.5345:0.2545	.	146	Q9H3M9	ATX3L_HUMAN	I	146	ENSP00000369996:T146I	ENSP00000369996:T146I	T	-	2	0	ATXN3L	13247538	1.000000	0.71417	0.001000	0.08648	0.003000	0.03518	2.426000	0.44731	-1.311000	0.02309	-1.788000	0.00630	ACA		0.373	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		A	13337617	G	A	13337617	3	1	115	1	0	0	0	0	1	0	0	0	1215	1377	48	3	634	3	ATXN3L	23	13337617	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	635911	13337617	141932943	199	31006										
PDHA1	5160	hgsc.bcm.edu	37	chrX	19373556	19373556	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aatcgctatggaatgggaacGtctgttgagagagcggcagc	15	7	1	2	rs138237215	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:19373556G>A	ENST00000422285.2	+	7	798	c.693G>A	c.(691-693)acG>acA	p.T231T	PDHA1_ENST00000379804.1_5'Flank|PDHA1_ENST00000540249.1_Silent_p.T200T|PDHA1_ENST00000545074.1_Silent_p.T238T|PDHA1_ENST00000379806.5_Silent_p.T269T			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	231			T -> A (in PDHAD). {ECO:0000269|PubMed:8504306}.		acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)	18	Hepatocellular(33;0.183)					GAATGGGAACGTCTGTTGAGA	0.498													G|||	2	0.000529801	0	0	3775	,	,		13578	0		0	False		,,,				2504	0.002															0			X						G	,,,	0,3835		0,0,0,1632,571	126	121	123		693,807,714,600	-11.5	0.2	X	dbSNP_134	123	6,6722		0,3,3,2425,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDHA1	NM_000284.3,NM_001173454.1,NM_001173455.1,NM_001173456.1	,,,	0,3,3,4057,2440	AA,AG,A,GG,G		0.0892,0.0,0.0568	,,,	231/391,269/429,238/398,200/360	19373556	6,10557	2203	4300	6503	19283477	SO:0001819	synonymous_variant	5160				CCDS14192.1, CCDS55380.1, CCDS55381.1, CCDS55382.1	Xp22.1	2008-02-05			ENSG00000131828	ENSG00000131828	1.2.4.1		8806	protein-coding gene	gene with protein product		300502		PDHA			Standard	NM_001173454		Approved		uc004czh.4	P08559	OTTHUMG00000021224	ENST00000422285.2:c.693G>A	X.37:g.19373556G>A			19283477	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Silent	SNP	ENST00000422285.2	37	CCDS14192.1																																																																																				0.498	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			A	19373556	G	A	19373556	2	1	115	1	0	0	0	0	0	0	0	1	11695	1132	40	1		1	PDHA1	23	19373556	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	6035939	19373556	135897004	200	31007										
CXorf23	256643	hgsc.bcm.edu	37	chrX	19971168	19971168	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggccaaagacatatctattcTcctaaaataataaaggcata	5	8	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:19971168T>C	ENST00000379682.4	-	6	1600	c.1567A>G	c.(1567-1569)Aga>Gga	p.R523G	CXorf23_ENST00000356980.3_Splice_Site_p.R523G|CXorf23_ENST00000379687.3_Splice_Site_p.R523G			A2AJT9	CX023_HUMAN	chromosome X open reading frame 23	523						mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(6)|skin(1)|urinary_tract(1)	11						ATATCTATTCTCCTAAAATAA	0.303																																																0			X											57	57	57					X																	19971168		2203	4300	6503	19881089	SO:0001630	splice_region_variant	256643			AL833278	CCDS14194.2	Xp22.13	2012-11-27			ENSG00000173681	ENSG00000173681			27413	protein-coding gene	gene with protein product						14702039	Standard	NM_198279		Approved		uc004czp.3	A2AJT9	OTTHUMG00000021226	ENST00000379682.4:c.1566-1A>G	X.37:g.19971168T>C			19881089	A1A4E8|Q5VSM7|Q5VSN1|Q6ZS60|Q8N1W7	Missense_Mutation	SNP	ENST00000379682.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.56|16.56	3.157788|3.157788	0.57368|0.57368	.|.	.|.	ENSG00000173681|ENSG00000173681	ENST00000340625|ENST00000379687;ENST00000379682;ENST00000356980;ENST00000539038	.|T;T;T	.|0.28454	.|1.61;1.61;1.61	5.97|5.97	4.8|4.8	0.61643|0.61643	.|.	.|.	.|.	.|.	.|.	T|T	0.52853|0.52853	0.1760|0.1760	M|M	0.78049|0.78049	2.395|2.395	0.32874|0.32874	D|D	0.509621|0.509621	.|D;D;D	.|0.69078	.|0.997;0.997;0.997	.|D;D;D	.|0.65443	.|0.935;0.913;0.913	T|T	0.66139|0.66139	-0.5998|-0.5998	5|8	.|.	.|.	.|.	.|.	11.0422|11.0422	0.47838|0.47838	0.0:0.0:0.1575:0.8425|0.0:0.0:0.1575:0.8425	.|.	.|234;523;523	.|B7ZLM9;A2AJT9-2;A2AJT9	.|.;.;CX023_HUMAN	G|G	131|523;523;523;411	.|ENSP00000369009:R523G;ENSP00000369004:R523G;ENSP00000349470:R523G	.|.	E|R	-|-	2|1	0|2	CXorf23|CXorf23	19881089|19881089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	2.148000|2.148000	0.42235|0.42235	0.850000|0.850000	0.35239|0.35239	0.486000|0.486000	0.48141|0.48141	GAG|AGA		0.303	CXorf23-006	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000055991.2	NM_198279	Missense_Mutation	C	19971168	T	C	19971168	5	2	115	1	0	0	0	0	0	0	1	0	4109	1565	54	4	505	4	CXorf23	23	19971168	Splice_Site	SNP	T	TCGA-F5-6465-01A-11D-1733-10	597612	19971168	135299392	201	31008										
PDK3	5165	hgsc.bcm.edu	37	chrX	24537111	24537111	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ctggtagctccagagctggaAgttgaagaattcaatggtaa	12	6	1	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:24537111A>G	ENST00000379162.4	+	6	892	c.657A>G	c.(655-657)gaA>gaG	p.E219E	PDK3_ENST00000441463.2_Silent_p.E219E|AC004656.1_ENST00000580722.1_RNA	NM_005391.4	NP_005382.1	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase, isozyme 3	219	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.		E -> A (in a head & neck squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell death (GO:0008219)|cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|peptidyl-serine phosphorylation (GO:0018105)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|regulation of reactive oxygen species metabolic process (GO:2000377)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			NS(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CAGAGCTGGAAGTTGAAGAAT	0.363																																																0			X											80	71	74					X																	24537111		2203	4300	6503	24447032	SO:0001819	synonymous_variant	5165			L42452	CCDS14212.1, CCDS48088.1	Xp22.12	2008-02-05	2005-11-16		ENSG00000067992	ENSG00000067992			8811	protein-coding gene	gene with protein product		300906	"pyruvate dehydrogenase kinase, isoenzyme 3"			7499431	Standard	NM_001142386		Approved		uc004dbh.3	Q15120	OTTHUMG00000021269	ENST00000379162.4:c.657A>G	X.37:g.24537111A>G			24447032	B4DXG6	Silent	SNP	ENST00000379162.4	37	CCDS14212.1																																																																																				0.363	PDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056097.1	NM_005391		G	24537111	A	G	24537111	2	3	115	1	0	0	0	0	0	0	0	1	11708	69	3	4		4	PDK3	23	24537111	Silent	SNP	A	TCGA-F5-6465-01A-11D-1733-10	4565943	24537111	130733449	202	31009										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34150181	34150181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggagtaaaaactcgtcacggCgacaaacgagagtatcttcg	11	9	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:34150181C>T	ENST00000346193.3	-	1	266	c.215G>A	c.(214-216)cGc>cAc	p.R72H		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	72								p.R72H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CTCGTCACGGCGACAAACGAG	0.537																																																1	Substitution - Missense(1)	ovary(1)	X											89	84	86					X																	34150181		2202	4300	6502	34060102	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.215G>A	X.37:g.34150181C>T	ENSP00000345029:p.Arg72His		34060102	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	C	3.358	-0.131099	0.06753	.	.	ENSG00000185448	ENST00000346193	T	0.21191	2.02	1.17	1.17	0.20885	.	.	.	.	.	T	0.13415	0.0325	L	0.57536	1.79	0.09310	N	1	P	0.38280	0.625	B	0.24974	0.057	T	0.18023	-1.0350	9	0.14252	T	0.57	.	5.3637	0.16101	0.0:1.0:0.0:0.0	.	72	Q5JRC9	FA47A_HUMAN	H	72	ENSP00000345029:R72H	ENSP00000345029:R72H	R	-	2	0	FAM47A	34060102	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.184000	0.09698	0.880000	0.35969	0.544000	0.68410	CGC		0.537	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34150181	C	T	34150181	3	4	115	1	0	0	0	0	1	0	0	0	5588	768	27	1	2164	1	FAM47A	23	34150181	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	9613070	34150181	121120379	203	31010										
EBP	10682	hgsc.bcm.edu	37	chrX	48382320	48382320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gctgttgtcaggtcgtgctgCggttgtcccattggggactt	15	9	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:48382320C>T	ENST00000495186.1	+	2	984	c.161C>T	c.(160-162)gCg>gTg	p.A54V	EBP_ENST00000276096.6_3'UTR	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	54					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)	p.A54V(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	GGTCGTGCTGCGGTTGTCCCA	0.562																																					Ovarian(41;550 1000 33077 33474 52335)											1	Substitution - Missense(1)	ovary(1)	X											196	163	175					X																	48382320		2203	4300	6503	48267264	SO:0001583	missense	152503			Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"3-beta-hydroxysteroid-delta-8,delta-7-isomerase", "Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)", "sterol 8-isomerase"	300205	"emopamil-binding protein (sterol isomerase)"	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.161C>T	X.37:g.48382320C>T	ENSP00000417052:p.Ala54Val		48267264	Q6FGL3|Q6IBI9	Missense_Mutation	SNP	ENST00000495186.1	37	CCDS14300.1	.	.	.	.	.	.	.	.	.	.	C	5.660	0.306331	0.10733	.	.	ENSG00000147155	ENST00000495186;ENST00000446158;ENST00000414061	D;D;D	0.97772	-4.53;-4.53;-4.53	5.72	2.86	0.33363	.	0.593501	0.17274	N	0.180272	D	0.91513	0.7320	N	0.16790	0.44	0.09310	N	1	B	0.23185	0.081	B	0.17722	0.019	T	0.82362	-0.0495	10	0.16420	T	0.52	-4.3153	4.5869	0.12287	0.1512:0.6114:0.1457:0.0917	.	54	Q15125	EBP_HUMAN	V	54	ENSP00000417052:A54V;ENSP00000390031:A54V;ENSP00000405832:A54V	ENSP00000405832:A54V	A	+	2	0	EBP	48267264	0.022000	0.18835	0.581000	0.28614	0.112000	0.19704	1.428000	0.34892	1.190000	0.43042	0.536000	0.68110	GCG		0.562	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579		T	48382320	C	T	48382320	3	4	115	1	0	0	0	0	1	0	0	0	4897	768	27	1	163	1	EBP	23	48382320	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	14232139	48382320	106888240	204	31011										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50053208	50053208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	ggaactattttcattgcatgTtaagcataccaacaaaagtg	7	7	1	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:50053208T>C	ENST00000376042.1	+	6	2337	c.2039T>C	c.(2038-2040)gTt>gCt	p.V680A	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.V680A			Q8WWL7	CCNB3_HUMAN	cyclin B3	680					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TCATTGCATGTTAAGCATACC	0.468																																																0			X											35	29	31					X																	50053208		2203	4300	6503	50069948	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2039T>C	X.37:g.50053208T>C	ENSP00000365210:p.Val680Ala		50069948	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953633	0.34471	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.37058	1.22;1.22	4.19	-1.46	0.08800	.	.	.	.	.	T	0.16514	0.0397	N	0.16478	0.41	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.24225	-1.0166	8	.	.	.	.	2.7077	0.05166	0.4249:0.2538:0.0:0.3213	.	680	Q8WWL7	CCNB3_HUMAN	A	680	ENSP00000365210:V680A;ENSP00000276014:V680A	.	V	+	2	0	CCNB3	50069948	0.000000	0.05858	0.000000	0.03702	0.545000	0.35147	-0.905000	0.04075	-0.374000	0.07967	0.486000	0.48141	GTT		0.468	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			C	50053208	T	C	50053208	3	2	115	1	0	0	0	0	1	0	0	0	2920	1725	60	4	2053	4	CCNB3	23	50053208	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	1670888	50053208	105217352	205	31012										
FAAH2	158584	hgsc.bcm.edu	37	chrX	57319015	57319015	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	atggaattgtcaagtacaggTgagcatttccactctctcaa	8	9	3	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:57319015T>C	ENST00000374900.4	+	2	395		c.e2+2			NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)	p.?(1)		endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						CAAGTACAGGTGAGCATTTCC	0.383										HNSCC(52;0.14)																																						1	Unknown(1)	ovary(1)	X											155	139	144					X																	57319015		2203	4300	6503	57335740	SO:0001630	splice_region_variant	158584			AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"amidase domain containing"	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.275+2T>C	X.37:g.57319015T>C			57335740	Q86VT2|Q96N98	Splice_Site	SNP	ENST00000374900.4	37	CCDS14375.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.286112	0.40394	.	.	ENSG00000165591	ENST00000374900	.	.	.	2.95	2.95	0.34219	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2418	0.26100	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAAH2	57335740	1.000000	0.71417	0.559000	0.28332	0.812000	0.45895	2.731000	0.47343	0.991000	0.38814	0.481000	0.45027	.		0.383	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912	Intron	C	57319015	T	C	57319015	5	2	115	1	0	0	0	0	0	0	1	0	5370	1710	59	4	283	4	FAAH2	23	57319015	Splice_Site	SNP	T	TCGA-F5-6465-01A-11D-1733-10	7265807	57319015	97951545	206	31013										
LPAR4	2846	hgsc.bcm.edu	37	chrX	78010951	78010951	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttgaaggcttctccaaacgTgtctggaagacttatttatc	8	8	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:78010951T>C	ENST00000435339.3	+	2	971	c.585T>C	c.(583-585)cgT>cgC	p.R195R		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	195					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						TCTCCAAACGTGTCTGGAAGA	0.413																																																0			X											87	78	81					X																	78010951		2202	4299	6501	77897607	SO:0001819	synonymous_variant	2846			U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.585T>C	X.37:g.78010951T>C			77897607	B2RAC7|O15132|Q502U9|Q6NSP5	Silent	SNP	ENST00000435339.3	37	CCDS14441.1																																																																																				0.413	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		C	78010951	T	C	78010951	2	2	115	1	0	0	0	0	0	0	0	1	8936	1683	59	4		4	LPAR4	23	78010951	Silent	SNP	T	TCGA-F5-6465-01A-11D-1733-10	20691936	78010951	77259609	207	31014										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128419	83128419	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agactagtaatgatcccataTcagagatttgctcagaaaat	7	7	2	4			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:83128419T>C	ENST00000329312.4	+	4	740	c.703T>C	c.(703-705)Tca>Cca	p.S235P		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	235					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TGATCCCATATCAGAGATTTG	0.328																																																0			X											33	30	31					X																	83128419		2192	4289	6481	83015075	SO:0001583	missense	1538			Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.703T>C	X.37:g.83128419T>C	ENSP00000331556:p.Ser235Pro		83015075	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	t	9.537	1.112407	0.20795	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.60548	0.18	4.13	2.97	0.34412	.	.	.	.	.	T	0.62720	0.2451	L	0.46157	1.445	0.09310	N	1	D;D	0.69078	0.997;0.997	D;D	0.64410	0.925;0.925	T	0.48779	-0.9005	9	0.42905	T	0.14	-0.5689	5.5601	0.17140	0.0:0.1253:0.0:0.8747	.	235;235	P35663;F5H4V5	CYLC1_HUMAN;.	P	235	ENSP00000331556:S235P	ENSP00000331556:S235P	S	+	1	0	CYLC1	83015075	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.354000	0.20146	0.716000	0.32124	-0.466000	0.05196	TCA		0.328	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		C	83128419	T	C	83128419	3	2	115	1	0	0	0	0	1	0	0	0	4147	1435	50	4	717	4	CYLC1	23	83128419	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	5117468	83128419	72142141	208	31015										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101138644	101138644	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttcctgaactgaccttgacTctatcctcctctcttttcct	3	15	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:101138644T>A	ENST00000372782.3	-	7	1802	c.1755A>T	c.(1753-1755)agA>agT	p.R585S	ZMAT1_ENST00000540921.1_Missense_Mutation_p.R585S|ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Missense_Mutation_p.R414S	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	585						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						TGACCTTGACTCTATCCTCCT	0.388																																																0			X											232	194	207					X																	101138644		2203	4300	6503	101025300	SO:0001583	missense	84460			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1755A>T	X.37:g.101138644T>A	ENSP00000361868:p.Arg585Ser		101025300	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	T	8.106	0.777737	0.16120	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	T;T;T	0.21543	2.59;2.59;2.0	4.27	3.08	0.35506	.	1.576670	0.03473	N	0.213973	T	0.13372	0.0324	N	0.08118	0	0.09310	N	0.999999	B	0.19445	0.036	B	0.12156	0.007	T	0.22765	-1.0207	10	0.48119	T	0.1	-4.693	7.8355	0.29368	0.0:0.0:0.4184:0.5816	.	585	Q5H9K5	ZMAT1_HUMAN	S	585;585;414	ENSP00000361868:R585S;ENSP00000437529:R585S;ENSP00000413044:R414S	ENSP00000361868:R585S	R	-	3	2	ZMAT1	101025300	0.011000	0.17503	0.542000	0.28115	0.377000	0.30045	1.635000	0.37134	0.743000	0.32719	0.486000	0.48141	AGA		0.388	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			A	101138644	T	A	101138644	3	1	115	1	0	0	0	0	1	0	0	0	17730	1548	54	5	165	5	ZMAT1	23	101138644	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	18010225	101138644	54131916	209	31016										
MCART6	401612	hgsc.bcm.edu	37	chrX	103349157	103349157	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	caggagcagctttcggccccGagtgttccatacatcctggg	12	13	0	0	rs12863544		TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:103349157G>A	ENST00000357421.4	-	2	964	c.784C>T	c.(784-786)Cgg>Tgg	p.R262W		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	262					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											TTTCGGCCCCGAGTGTTCCAT	0.542																																																0			X											56	46	50					X																	103349157		2203	4300	6503	103235813	SO:0001583	missense	401612				CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"Solute carriers"	31894	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 6"	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.784C>T	X.37:g.103349157G>A	ENSP00000361681:p.Arg262Trp		103235813	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	37	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	g	7.824	0.718495	0.15372	.	.	ENSG00000176274	ENST00000357421	T	0.78816	-1.21	4.23	2.35	0.29111	Mitochondrial carrier domain (2);	0.069586	0.56097	D	0.000031	T	0.71256	0.3318	M	0.64170	1.965	0.37753	D	0.926046	B	0.19445	0.036	B	0.06405	0.002	T	0.67829	-0.5569	10	0.66056	D	0.02	-23.1756	8.475	0.33007	0.0:0.0:0.5823:0.4177	rs12863544	262	Q5H9E4	MCAR6_HUMAN	W	262	ENSP00000361681:R262W	ENSP00000361681:R262W	R	-	1	2	MCART6	103235813	0.898000	0.30612	1.000000	0.80357	0.300000	0.27592	1.130000	0.31393	0.315000	0.23110	0.594000	0.82650	CGG		0.542	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755		A	103349157	G	A	103349157	3	1	115	1	0	0	0	0	1	0	0	0	9401	1057	37	1	143	1	MCART6	23	103349157	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	2210513	103349157	51921403	210	31017										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107898654	107898654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	gattaccaggaacccctggaGcaaaaggacaaccaggcctt	10	12	0	0			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:107898654G>A	ENST00000361603.2	+	37	3584	c.3340G>A	c.(3340-3342)Gca>Aca	p.A1114T	COL4A5_ENST00000328300.6_Missense_Mutation_p.A1114T	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1114	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						AACCCCTGGAGCAAAAGGACA	0.498									Alport syndrome with Diffuse Leiomyomatosis																																							0			X											71	68	69					X																	107898654		2203	4300	6503	107785310	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.3340G>A	X.37:g.107898654G>A	ENSP00000354505:p.Ala1114Thr		107785310	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.004819	0.35320	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.93366	-3.21;-3.21	5.41	2.42	0.29668	.	0.364418	0.26903	N	0.021918	D	0.83926	0.5360	N	0.17564	0.495	0.32876	D	0.509916	B;B	0.21606	0.058;0.058	B;B	0.16289	0.015;0.015	T	0.76841	-0.2810	10	0.14252	T	0.57	.	9.3272	0.37999	0.0792:0.3941:0.5267:0.0	.	1114;1114	E7EVY4;P29400	.;CO4A5_HUMAN	T	1114	ENSP00000331902:A1114T;ENSP00000354505:A1114T	ENSP00000331902:A1114T	A	+	1	0	COL4A5	107785310	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.409000	0.34680	0.547000	0.28938	0.594000	0.82650	GCA		0.498	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107898654	G	A	107898654	3	1	115	1	0	0	0	0	1	0	0	0	3700	971	34	3	3486	3	COL4A5	23	107898654	Missense_Mutation	SNP	G	TCGA-F5-6465-01A-11D-1733-10	4549497	107898654	47371906	211	31018										
AGTR2	186	hgsc.bcm.edu	37	chrX	115304583	115304583	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agagagagtatgtcttgccgGaaaagcagttctcttagaga	12	6	2	3			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:115304583G>A	ENST00000371906.4	+	3	1240	c.1050G>A	c.(1048-1050)cgG>cgA	p.R350R		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	350					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TGTCTTGCCGGAAAAGCAGTT	0.433																																																0			X											90	85	87					X																	115304583		2203	4300	6503	115218611	SO:0001819	synonymous_variant	186			AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.1050G>A	X.37:g.115304583G>A			115218611	B2R9V1|Q13016|Q6FGY7	Silent	SNP	ENST00000371906.4	37	CCDS14569.1																																																																																				0.433	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		A	115304583	G	A	115304583	2	1	115	1	0	0	0	0	0	0	0	1	402	1161	41	3		3	AGTR2	23	115304583	Silent	SNP	G	TCGA-F5-6465-01A-11D-1733-10	7405929	115304583	39965977	212	31019										
GPR112	139378	hgsc.bcm.edu	37	chrX	135427479	135427479	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttcaggatgtctctttaccCagagtggaagatgccatgtc	10	9	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:135427479C>T	ENST00000394143.1	+	6	1905	c.1614C>T	c.(1612-1614)ccC>ccT	p.P538P	GPR112_ENST00000394141.1_Silent_p.P333P|GPR112_ENST00000370652.1_Silent_p.P538P|GPR112_ENST00000287534.4_Silent_p.P475P|GPR112_ENST00000412101.1_Silent_p.P333P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	538					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TCTCTTTACCCAGAGTGGAAG	0.428																																																0			X											61	56	58					X																	135427479		2202	4300	6502	135255145	SO:0001819	synonymous_variant	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1614C>T	X.37:g.135427479C>T			135255145	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																				0.428	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135427479	C	T	135427479	2	4	115	1	0	0	0	0	0	0	0	1	6649	581	21	3		3	GPR112	23	135427479	Silent	SNP	C	TCGA-F5-6465-01A-11D-1733-10	20122896	135427479	19843081	213	31020										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140996359	140996359	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	aggaacattacctagagtacCgggaggtgcccaactcttct	10	11	2	1	rs141172739	byFrequency	TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:140996359C>T	ENST00000285879.4	+	4	3455	c.3169C>T	c.(3169-3171)Cgg>Tgg	p.R1057W	MAGEC1_ENST00000406005.2_Missense_Mutation_p.R124W	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	1057	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.R1057G(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCTAGAGTACCGGGAGGTGCC	0.522										HNSCC(15;0.026)			C|||	20	0.00529801	0.0136	0.0029	3775	,	,		13558	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	X						C	TRP/ARG	58,3777		0,53,5,1579,566	104	101	102		3169	0.8	0	X	dbSNP_134	102	1,6727		0,1,0,2427,1872	yes	missense	MAGEC1	NM_005462.4	101	0,54,5,4006,2438	TT,TC,T,CC,C		0.0149,1.5124,0.5586	probably-damaging	1057/1143	140996359	59,10504	2203	4300	6503	140824025	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.3169C>T	X.37:g.140996359C>T	ENSP00000285879:p.Arg1057Trp		140824025	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	8	0.004822182037371911	7	0.014285714285714285	0	0.0	0	0.0	0	0.0	c	9.304	1.053853	0.19907	0.015124	1.49E-4	ENSG00000155495	ENST00000285879;ENST00000406005	T;T	0.06449	3.3;3.3	0.837	0.837	0.18896	.	.	.	.	.	T	0.08846	0.0219	M	0.75615	2.305	0.09310	N	1	D	0.76494	0.999	P	0.60286	0.872	T	0.03922	-1.0992	8	0.66056	D	0.02	.	.	.	.	.	1057	O60732	MAGC1_HUMAN	W	1057;124	ENSP00000285879:R1057W;ENSP00000385500:R124W	ENSP00000285879:R1057W	R	+	1	2	MAGEC1	140824025	0.001000	0.12720	0.002000	0.10522	0.190000	0.23558	0.267000	0.18552	0.696000	0.31696	0.279000	0.19357	CGG		0.522	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140996359	C	T	140996359	3	4	115	1	0	0	0	0	1	0	0	0	9210	643	23	1	3175	1	MAGEC1	23	140996359	Missense_Mutation	SNP	C	TCGA-F5-6465-01A-11D-1733-10	5568880	140996359	14274201	214	31021										
PASD1	139135	hgsc.bcm.edu	37	chrX	150842515	150842515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	agtttcccataacttcagacTcaaccataagcaccctggag	6	13	2	1			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:150842515T>C	ENST00000370357.4	+	15	2277	c.2032T>C	c.(2032-2034)Tca>Cca	p.S678P		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	678						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					AACTTCAGACTCAACCATAAG	0.493																																																0			X											127	114	118					X																	150842515		2203	4300	6503	150593171	SO:0001583	missense	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2032T>C	X.37:g.150842515T>C	ENSP00000359382:p.Ser678Pro		150593171	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.191955	0.38707	.	.	ENSG00000166049	ENST00000370357	T	0.47528	0.84	3.15	-0.63	0.11530	.	.	.	.	.	T	0.28167	0.0695	L	0.27053	0.805	0.09310	N	1	B	0.17465	0.022	B	0.18871	0.023	T	0.30736	-0.9968	9	0.87932	D	0	-8.3229	0.4415	0.00487	0.2181:0.1349:0.2212:0.4257	.	678	Q8IV76	PASD1_HUMAN	P	678	ENSP00000359382:S678P	ENSP00000359382:S678P	S	+	1	0	PASD1	150593171	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.420000	0.07062	-0.228000	0.09869	-1.227000	0.01581	TCA		0.493	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		C	150842515	T	C	150842515	3	2	115	1	0	0	0	0	1	0	0	0	11502	1551	54	4	2086	4	PASD1	23	150842515	Missense_Mutation	SNP	T	TCGA-F5-6465-01A-11D-1733-10	9846156	150842515	4428045	215	31022										
VBP1	7411	hgsc.bcm.edu	37	chrX	154467052	154467052	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0372093023255814	8	1	0.539224349533628	2.37748917748918	0.304097452934662	1	1	0	tttctttgacaattcttgcaGatatggccagggtttataat	8	6	2	2			TCGA-F5-6465-01A-11D-1733-10	TCGA-F5-6465-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	9f79e099-5b22-4299-a3fb-94de8acdaedb	405707a2-f7e0-45b2-8215-fe3cbecb56fd	g.chrX:154467052G>C	ENST00000286428.5	+	6	640		c.e6-1		VBP1_ENST00000535916.1_Splice_Site|VBP1_ENST00000459836.1_Splice_Site	NM_003372.5	NP_003363.1	P61758	PFD3_HUMAN	von Hippel-Lindau binding protein 1						'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)				NS(1)|endometrium(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AATTCTTGCAGATATGGCCAG	0.338																																																0			X											150	148	148					X																	154467052		2203	4298	6501	154120246	SO:0001630	splice_region_variant	7411			U56833	CCDS14765.1	Xq28	2008-07-07			ENSG00000155959	ENSG00000155959			12662	protein-coding gene	gene with protein product	"prefoldin 3"	300133				8674032, 9339366	Standard	NM_003372		Approved	PFD3, PFDN3	uc004fnc.3	P61758	OTTHUMG00000022666	ENST00000286428.5:c.524-1G>C	X.37:g.154467052G>C			154120246	B2R8L5|O55228|Q15765|Q5JT81|Q86X96	Splice_Site	SNP	ENST00000286428.5	37	CCDS14765.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.232152	0.58777	.	.	ENSG00000155959	ENST00000535916;ENST00000286428	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0552	0.71908	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VBP1	154120246	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.781000	0.85668	2.359000	0.80004	0.594000	0.82650	.		0.338	VBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058806.1		Intron	C	154467052	G	C	154467052	5	2	115	1	0	0	0	0	0	0	1	0	17176	956	33	5	545	5	VBP1	23	154467052	Splice_Site	SNP	G	TCGA-F5-6465-01A-11D-1733-10	3624537	154467052	803508	216	31023										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	6885166	6885166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttgtagatgatcatgggaacAgcaatagtagtcatgtaaaa	10	4	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:6885166A>G	ENST00000303635.7	+	3	337	c.130A>G	c.(130-132)Agc>Ggc	p.S44G	CAMTA1_ENST00000476163.1_3'UTR|CAMTA1_ENST00000473578.1_Missense_Mutation_p.S44G|CAMTA1_ENST00000467404.2_Missense_Mutation_p.S56G|CAMTA1_ENST00000557126.1_Missense_Mutation_p.S44G|CAMTA1_ENST00000439411.2_Missense_Mutation_p.S44G	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	44					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCATGGGAACAGCAATAGTAG	0.343			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0			1											63	67	65					1																	6885166		2203	4300	6503	6807753	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.130A>G	1.37:g.6885166A>G	ENSP00000306522:p.Ser44Gly		6807753	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.290398	0.80914	.	.	ENSG00000171735	ENST00000303635;ENST00000473578;ENST00000557126;ENST00000467404;ENST00000439411	T;T	0.20598	2.06;2.06	6.05	6.05	0.98169	.	0.208076	0.33916	N	0.004433	T	0.15609	0.0376	N	0.08118	0	0.33173	D	0.548574	P	0.43788	0.817	B	0.44224	0.444	T	0.14896	-1.0456	10	0.44086	T	0.13	-15.5163	15.7743	0.78198	1.0:0.0:0.0:0.0	.	44	Q9Y6Y1	CMTA1_HUMAN	G	44;44;44;56;44	ENSP00000306522:S44G;ENSP00000402561:S44G	ENSP00000306522:S44G	S	+	1	0	CAMTA1	6807753	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.757000	0.74924	2.320000	0.78422	0.528000	0.53228	AGC		0.343	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	6885166	A	G	6885166	3	3	116	1	0	0	0	0	1	0	0	0	2619	188	7	4	140	4	CAMTA1	1	6885166	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10		6885166	242365455	1	31024										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29630428	29630428	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctggggggctccccgaggcgTccctgtggccggaagggctc	18	14	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:29630428T>C	ENST00000345512.3	+	17	2697	c.2568T>C	c.(2566-2568)cgT>cgC	p.R856R	PTPRU_ENST00000428026.2_Silent_p.R846R|PTPRU_ENST00000460170.2_Silent_p.R846R|PTPRU_ENST00000373779.3_Silent_p.R846R|PTPRU_ENST00000323874.8_Silent_p.R846R|PTPRU_ENST00000356870.3_Silent_p.R846R|PTPRU_ENST00000415600.2_3'UTR	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	856	Mediates interaction with CTNNB1. {ECO:0000250}.		R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CCCCGAGGCGTCCCTGTGGCC	0.642																																																0			1											39	44	42					1																	29630428		2203	4299	6502	29503015	SO:0001819	synonymous_variant	10076			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2568T>C	1.37:g.29630428T>C			29503015	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Silent	SNP	ENST00000345512.3	37	CCDS334.1																																																																																				0.642	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			C	29630428	T	C	29630428	2	2	116	1	0	0	0	0	0	0	0	1	12850	1654	58	4		4	PTPRU	1	29630428	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	22745262	29630428	219620193	2	31025										
TSPAN1	10103	hgsc.bcm.edu	37	chr1	46650757	46650757	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acagccaatgaaacctgcacCaagcaaaaggctcacgacca	7	14	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:46650757C>A	ENST00000372003.1	+	7	1028	c.564C>A	c.(562-564)acC>acA	p.T188T	TSPAN1_ENST00000498443.1_3'UTR	NM_005727.3	NP_005718.2	O60635	TSN1_HUMAN	tetraspanin 1	188					cell migration (GO:0016477)|cell proliferation (GO:0008283)|positive regulation of endocytosis (GO:0045807)|protein stabilization (GO:0050821)|thiamine transmembrane transport (GO:0071934)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.T188T(1)		kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)	Medulloblastoma(700;0.00498)|all_neural(321;0.0212)				AAACCTGCACCAAGCAAAAGG	0.512																																																1	Substitution - coding silent(1)	ovary(1)	1											122	128	126					1																	46650757		2203	4300	6503	46423344	SO:0001819	synonymous_variant	10103			BC013404	CCDS530.1	1p33	2013-02-14			ENSG00000117472	ENSG00000117472		"Tetraspanins"	20657	protein-coding gene	gene with protein product		613170				9714763, 10719184	Standard	NM_005727		Approved	TSPAN-1, NET-1	uc001cpd.3	O60635	OTTHUMG00000007602	ENST00000372003.1:c.564C>A	1.37:g.46650757C>A			46423344	D3DQ14|O60745|Q5VST0	Silent	SNP	ENST00000372003.1	37	CCDS530.1																																																																																				0.512	TSPAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020135.1	NM_005727		A	46650757	C	A	46650757	2	1	116	1	0	0	0	0	0	0	0	1	16673	581	21	2		2	TSPAN1	1	46650757	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	17020329	46650757	202599864	3	31026										
CYP4Z1	199974	hgsc.bcm.edu	37	chr1	47582359	47582359	+	Frame_Shift_Del	DEL	A	A	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	attctccagggaaaattctgAaaaaatacatccctatgcct							TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:47582359delA	ENST00000334194.3	+	11	1307	c.1304delA	c.(1303-1305)gaafs	p.E435fs	CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4Z1_ENST00000471598.1_3'UTR	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	435						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						GAAAATTCTGAAAAAATACAT	0.423																																																0			1											77	78	78					1																	47582359		2203	4300	6503	47354946	SO:0001589	frameshift_variant	199974			AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"Cytochrome P450s"	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1304delA	1.37:g.47582359delA	ENSP00000334246:p.Glu435fs		47354946	Q5VVE4	Frame_Shift_Del	DEL	ENST00000334194.3	37	CCDS545.1																																																																																				0.423	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		-	47582359	A	-	47582359	7	5	116	1	0	1	0	1	0	0	0	0	4200	246	9	0	1346	0	CYP4Z1	1	47582359	Frame_Shift_Del	DEL	A	TCGA-F5-6571-01A-12D-1826-10	931602	47582359	201668262	4	31027										
FGGY	55277	hgsc.bcm.edu	37	chr1	60228197	60228197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	actatgataagaaataccaaGtattcctgaagctggttgaa	8	6	0	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:60228197G>A	ENST00000303721.7	+	16	1771	c.1597G>A	c.(1597-1599)Gta>Ata	p.V533I	FGGY_ENST00000371212.1_Missense_Mutation_p.V445I|FGGY_ENST00000371210.1_Missense_Mutation_p.V234I|RP4-782L23.2_ENST00000443012.1_RNA|FGGY_ENST00000371218.4_Missense_Mutation_p.V557I	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	533					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					GAAATACCAAGTATTCCTGAA	0.418																																																0			1											69	66	67					1																	60228197		2203	4300	6503	60000785	SO:0001583	missense	55277				CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1597G>A	1.37:g.60228197G>A	ENSP00000305922:p.Val533Ile		60000785	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	17.65	3.443070	0.63067	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59	5.26	4.35	0.52113	.	0.074188	0.52532	D	0.000067	D	0.90501	0.7024	L	0.52905	1.665	0.49389	D	0.999785	D;D;P	0.60160	0.987;0.972;0.923	P;P;P	0.58454	0.839;0.545;0.545	D	0.89438	0.3721	9	.	.	.	-9.9171	11.4353	0.50064	0.0827:0.0:0.9173:0.0	.	557;445;533	Q96C11-3;B1AK94;Q96C11	.;.;FGGY_HUMAN	I	557;533;445;234	ENSP00000360262:V557I;ENSP00000305922:V533I;ENSP00000360256:V445I;ENSP00000360254:V234I	.	V	+	1	0	FGGY	60000785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.416000	0.66417	1.468000	0.48064	0.557000	0.71058	GTA		0.418	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		A	60228197	G	A	60228197	3	1	116	1	0	0	0	0	1	0	0	0	5890	1029	36	3	1731	3	FGGY	1	60228197	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	12645838	60228197	189022424	5	31028										
DPYD	1806	hgsc.bcm.edu	37	chr1	97547897	97547897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gattcttacctggtagccagAatcattacaggtcatgtagc	9	9	3	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:97547897A>G	ENST00000370192.3	-	22	2996	c.2896T>C	c.(2896-2898)Tct>Cct	p.S966P		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	966	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TGGTAGCCAGAATCATTACAG	0.383																																																0			1											216	199	205					1																	97547897		2203	4300	6503	97320485	SO:0001583	missense	1806			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2896T>C	1.37:g.97547897A>G	ENSP00000359211:p.Ser966Pro		97320485	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392669	0.83011	.	.	ENSG00000188641	ENST00000370192	D	0.90444	-2.67	5.82	5.82	0.92795	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95522	0.8545	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.96318	0.9234	10	0.87932	D	0	-23.809	16.1779	0.81874	1.0:0.0:0.0:0.0	.	966	Q12882	DPYD_HUMAN	P	966	ENSP00000359211:S966P	ENSP00000359211:S966P	S	-	1	0	DPYD	97320485	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	7.114000	0.77103	2.216000	0.71823	0.533000	0.62120	TCT		0.383	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		G	97547897	A	G	97547897	3	3	116	1	0	0	0	0	1	0	0	0	4756	246	9	4	189	4	DPYD	1	97547897	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	37319700	97547897	151702724	6	31029										
RBM15	64783	hgsc.bcm.edu	37	chr1	110888224	110888224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	agaaaacttggcgctgacccTgttatagtggttatagtggt	12	6	0	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:110888224T>C	ENST00000369784.3	+	2	3827	c.2927T>C	c.(2926-2928)cTg>cCg	p.L976P	RBM15_ENST00000487146.2_Intron	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	976					negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			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)		GCGCTGACCCTGTTATAGTGG	0.378			T	MKL1	acute megakaryocytic leukemia																																		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	0			1											215	238	230					1																	110888224		2203	4300	6503	110689747	SO:0001583	missense	64783			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2927T>C	1.37:g.110888224T>C	ENSP00000358799:p.Leu976Pro		110689747	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	T	5.732	0.319451	0.10845	.	.	ENSG00000162775	ENST00000369784	T	0.20881	2.04	5.57	2.01	0.26516	.	.	.	.	.	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42816	-0.9429	9	0.87932	D	0	53.3357	7.0412	0.25021	0.0:0.2655:0.0:0.7345	.	976	Q96T37	RBM15_HUMAN	P	976	ENSP00000358799:L976P	ENSP00000358799:L976P	L	+	2	0	RBM15	110689747	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.479000	0.22228	0.091000	0.17302	0.482000	0.46254	CTG		0.378	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		C	110888224	T	C	110888224	3	2	116	1	0	0	0	0	1	0	0	0	13153	1580	55	4	2933	4	RBM15	1	110888224	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	13340327	110888224	138362397	7	31030										
FAM71A	149647	hgsc.bcm.edu	37	chr1	212799671	212799671	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tgtggcaacccggggagcagCaggcacagggactcgcataa	15	11	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:212799671C>T	ENST00000294829.3	+	1	1883	c.1452C>T	c.(1450-1452)agC>agT	p.S484S	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	484						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		CGGGGAGCAGCAGGCACAGGG	0.547																																																0			1											80	80	80					1																	212799671		2203	4300	6503	210866294	SO:0001819	synonymous_variant	149647				CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1452C>T	1.37:g.212799671C>T			210866294	Q5VTZ1	Silent	SNP	ENST00000294829.3	37	CCDS1507.1																																																																																				0.547	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		T	212799671	C	T	212799671	2	4	116	1	0	0	0	0	0	0	0	1	5626	709	25	3		3	FAM71A	1	212799671	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	101911447	212799671	36450950	8	31031										
WNT9A	7483	hgsc.bcm.edu	37	chr1	228112049	228112049	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctgcacgccttggccagtgcGtgcgtcaggccagccgagga	15	14	1	0	rs147711960	byFrequency	TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr1:228112049G>A	ENST00000272164.5	-	3	415	c.405C>T	c.(403-405)caC>caT	p.H135H		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	135					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.H135H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				TGGCCAGTGCGTGCGTCAGGC	0.677													G|||	2	0.000399361	0	0	5008	,	,		12282	0.001		0.001	False		,,,				2504	0															1	Substitution - coding silent(1)	endometrium(1)	1						G		0,4406		0,0,2203	61	63	62		405	-6.3	0	1	dbSNP_134	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WNT9A	NM_003395.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		135/366	228112049	2,13004	2203	4300	6503	226178672	SO:0001819	synonymous_variant	7483			AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"Wingless-type MMTV integration sites"	12778	protein-coding gene	gene with protein product		602863	"wingless-type MMTV integration site family, member 14"	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.405C>T	1.37:g.228112049G>A			226178672	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																				0.677	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395		A	228112049	G	A	228112049	2	1	116	1	0	0	0	0	0	0	0	1	17438	1136	40	1		1	WNT9A	1	228112049	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	15312378	228112049	21138572	9	31032										
SOX11	6664	hgsc.bcm.edu	37	chr2	5834045	5834045	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ccctgtcgctggtggataagGatttggattcgttcagcgag	14	8	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:5834045G>T	ENST00000322002.3	+	1	1247	c.1192G>T	c.(1192-1194)Gat>Tat	p.D398Y	AC010729.1_ENST00000455579.2_RNA|AC108025.2_ENST00000453678.1_RNA|AC108025.2_ENST00000420221.1_RNA|AC107057.2_ENST00000458264.1_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	398					cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)			central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		GGTGGATAAGGATTTGGATTC	0.652																																																0			2											17	13	14					2																	5834045		1902	3645	5547	5751496	SO:0001583	missense	6664				CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.1192G>T	2.37:g.5834045G>T	ENSP00000322568:p.Asp398Tyr		5751496	Q4ZFV8	Missense_Mutation	SNP	ENST00000322002.3	37	CCDS1654.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.992915	0.74703	.	.	ENSG00000176887	ENST00000322002	D	0.99382	-5.8	4.91	4.91	0.64330	.	0.000000	0.64402	U	0.000001	D	0.99387	0.9784	M	0.84683	2.71	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	D	0.98832	1.0751	10	0.87932	D	0	.	18.0824	0.89445	0.0:0.0:1.0:0.0	.	398	P35716	SOX11_HUMAN	Y	398	ENSP00000322568:D398Y	ENSP00000322568:D398Y	D	+	1	0	SOX11	5751496	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.514000	0.98013	2.276000	0.75962	0.561000	0.74099	GAT		0.652	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		T	5834045	G	T	5834045	3	4	116	1	0	0	0	0	1	0	0	0	14979	1174	41	2	1194	2	SOX11	2	5834045	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		5834045	237365328	10	31033										
OXER1	165140	hgsc.bcm.edu	37	chr2	42990512	42990512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cccaatgctcacaatagcaaAgaggatgagcgccagtggca	11	11	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:42990512A>G	ENST00000378661.2	-	1	889	c.808T>C	c.(808-810)Ttt>Ctt	p.F270L		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	270					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						ACAATAGCAAAGAGGATGAGC	0.657																																																0			2											17	18	18					2																	42990512		2202	4299	6501	42844016	SO:0001583	missense	165140			AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"GPCR / Class A : Leukotriene receptors"	24884	protein-coding gene	gene with protein product	"5-oxo-ETE acid G-protein-coupled receptor 1"					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.808T>C	2.37:g.42990512A>G	ENSP00000367930:p.Phe270Leu		42844016	Q86WP7|Q8NGW4	Missense_Mutation	SNP	ENST00000378661.2	37	CCDS1810.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.746994	0.69418	.	.	ENSG00000162881	ENST00000378661	T	0.37584	1.19	4.32	3.12	0.35913	GPCR, rhodopsin-like superfamily (1);	0.090176	0.44285	U	0.000464	T	0.47135	0.1429	L	0.52011	1.625	0.32714	N	0.511164	D	0.71674	0.998	D	0.70227	0.968	T	0.53704	-0.8401	10	0.25751	T	0.34	.	9.0718	0.36497	0.814:0.186:0.0:0.0	.	270	Q8TDS5	OXER1_HUMAN	L	270	ENSP00000367930:F270L	ENSP00000367930:F270L	F	-	1	0	OXER1	42844016	0.000000	0.05858	0.130000	0.21974	0.005000	0.04900	0.567000	0.23608	0.504000	0.28082	0.454000	0.30748	TTT		0.657	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962		G	42990512	A	G	42990512	3	3	116	1	0	0	0	0	1	0	0	0	11362	72	3	4	467	4	OXER1	2	42990512	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	37156467	42990512	200208861	11	31034										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103274046	103274046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tccatctgtatcacaagttgCccacaatagtgcctgagagc	8	12	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:103274046C>T	ENST00000233969.2	+	2	455	c.313C>T	c.(313-315)Ccc>Tcc	p.P105S		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	105					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TCACAAGTTGCCCACAATAGT	0.423																																																0			2											76	72	74					2																	103274046		2203	4300	6503	102640478	SO:0001583	missense	6549				CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.313C>T	2.37:g.103274046C>T	ENSP00000233969:p.Pro105Ser		102640478	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	37	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878250	0.33162	.	.	ENSG00000115616	ENST00000233969	T	0.14391	2.51	5.73	5.73	0.89815	Cation/H+ exchanger (1);	0.049070	0.85682	D	0.000000	T	0.11367	0.0277	N	0.17800	0.525	0.49483	D	0.999793	P	0.36086	0.536	B	0.39660	0.306	T	0.02417	-1.1162	10	0.02654	T	1	.	20.27	0.98469	0.0:1.0:0.0:0.0	.	105	Q9UBY0	SL9A2_HUMAN	S	105	ENSP00000233969:P105S	ENSP00000233969:P105S	P	+	1	0	SLC9A2	102640478	1.000000	0.71417	0.994000	0.49952	0.962000	0.63368	3.403000	0.52615	2.854000	0.98071	0.655000	0.94253	CCC		0.423	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			T	103274046	C	T	103274046	3	4	116	1	0	0	0	0	1	0	0	0	14749	739	26	3	319	3	SLC9A2	2	103274046	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	60283534	103274046	139925327	12	31035										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145161614	145161614	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtacttgatgtgctccttcaGtgatgtcaagcgcttgtagc	11	9	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:145161614G>A	ENST00000558170.2	-	6	1860	c.676C>T	c.(676-678)Ctg>Ttg	p.L226L	ZEB2_ENST00000409487.3_Silent_p.L226L|ZEB2_ENST00000539609.3_Silent_p.L202L|ZEB2_ENST00000303660.4_Silent_p.L226L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	226					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		TGCTCCTTCAGTGATGTCAAG	0.567																																					Melanoma(33;1235 1264 5755 16332)											0			2											196	180	185					2																	145161614		2203	4300	6503	144878084	SO:0001819	synonymous_variant	9839			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.676C>T	2.37:g.145161614G>A			144878084	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	37	CCDS2186.1																																																																																				0.567	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145161614	G	A	145161614	2	1	116	1	0	0	0	0	0	0	0	1	17663	1020	36	3		3	ZEB2	2	145161614	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	41887568	145161614	98037759	13	31036										
TTN	7273	hgsc.bcm.edu	37	chr2	179429590	179429590	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctggctcatgccattgcacaAgcatctgatcttttgagatt	8	10	3	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:179429590A>G	ENST00000591111.1	-	276	76570	c.76346T>C	c.(76345-76347)cTt>cCt	p.L25449P	TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L18217P|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L27090P|TTN_ENST00000342992.6_Missense_Mutation_p.L24522P|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L18150P|TTN_ENST00000460472.2_Missense_Mutation_p.L18025P|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25449	Fibronectin type-III 85. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATTGCACAAGCATCTGATC	0.398																																																0			2											67	63	64					2																	179429590		1879	4115	5994	179137836	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76346T>C	2.37:g.179429590A>G	ENSP00000465570:p.Leu25449Pro		179137836	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	9.641	1.139091	0.21205	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	6.02	6.02	0.97574	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60353	0.2262	L	0.46157	1.445	0.58432	D	0.999996	P;P;P;P	0.36599	0.484;0.484;0.484;0.56	B;B;P;P	0.47786	0.22;0.22;0.557;0.447	T	0.62515	-0.6838	9	0.87932	D	0	.	16.542	0.84395	1.0:0.0:0.0:0.0	.	18025;18150;18217;25449	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	24522;18025;18217;18150;18023	ENSP00000343764:L24522P;ENSP00000434586:L18025P;ENSP00000340554:L18217P;ENSP00000352154:L18150P	ENSP00000340554:L18217P	L	-	2	0	TTN	179137836	1.000000	0.71417	0.976000	0.42696	0.952000	0.60782	5.302000	0.65733	2.304000	0.77564	0.528000	0.53228	CTT		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179429590	A	G	179429590	3	3	116	1	0	0	0	0	1	0	0	0	16775	72	3	4	26858	4	TTN	2	179429590	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	34267976	179429590	63769783	14	31037										
TTN	7273	hgsc.bcm.edu	37	chr2	179452695	179452695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aataccaacttggttttgggCacacaccctgaactcatatt	6	11	1	1	rs72646853	byFrequency	TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:179452695C>T	ENST00000591111.1	-	255	58740	c.58516G>A	c.(58516-58518)Gcc>Acc	p.A19506T	TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A12274T|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A21147T|TTN_ENST00000342992.6_Missense_Mutation_p.A18579T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A12207T|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A12082T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19506	Fibronectin type-III 41. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGTTTTGGGCACACACCCTG	0.458													C|||	4	0.000798722	0	0	5008	,	,		20578	0		0	False		,,,				2504	0.0041															0			2						C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,3834		0,0,1917	58	56	57		36244,55735,36619,36820	5.8	1	2	dbSNP_130	57	1,8233		0,1,4116	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	58,58,58,58	0,1,6033	TT,TC,CC		0.0121,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging	12082/26927,18579/33424,12207/27052,12274/27119	179452695	1,12067	1917	4117	6034	179160941	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58516G>A	2.37:g.179452695C>T	ENSP00000465570:p.Ala19506Thr		179160941	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.17	3.047746	0.55110	0.0	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44	5.78	5.78	0.91487	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.88890	0.6560	H	0.96833	3.89	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.91913	0.5541	9	0.87932	D	0	.	20.0204	0.97499	0.0:1.0:0.0:0.0	.	12082;12207;12274;19506	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	18579;12082;12274;12207;12080	ENSP00000343764:A18579T;ENSP00000434586:A12082T;ENSP00000340554:A12274T;ENSP00000352154:A12207T	ENSP00000340554:A12274T	A	-	1	0	TTN	179160941	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.770000	0.85390	2.729000	0.93468	0.650000	0.86243	GCC		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179452695	C	T	179452695	3	4	116	1	0	0	0	0	1	0	0	0	16775	710	25	3	44772	3	TTN	2	179452695	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	23105	179452695	63746678	15	31038										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185803696	185803696	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ccatctttaccccatgcactCtttccttcactgctttcccc	2	19	3	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:185803696C>A	ENST00000302277.6	+	4	4167	c.3573C>A	c.(3571-3573)ctC>ctA	p.L1191L		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1191							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CCCATGCACTCTTTCCTTCAC	0.458																																																0			2											290	253	266					2																	185803696		2203	4300	6503	185511941	SO:0001819	synonymous_variant	91752			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3573C>A	2.37:g.185803696C>A			185511941	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																				0.458	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185803696	C	A	185803696	2	1	116	1	0	0	0	0	0	0	0	1	18209	900	32	2		2	ZNF804A	2	185803696	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	6351001	185803696	57395677	16	31039										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209163420	209163420	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctggttctcctatggtacctTcatatgagacatctgtcagt	8	10	4	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr2:209163420T>C	ENST00000264380.4	+	8	1125	c.967T>C	c.(967-969)Tca>Cca	p.S323P	PIKFYVE_ENST00000308862.6_Missense_Mutation_p.S237P|PIKFYVE_ENST00000407449.1_Missense_Mutation_p.S323P|PIKFYVE_ENST00000392202.3_Missense_Mutation_p.S226P	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	323					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TATGGTACCTTCATATGAGAC	0.423																																																0			2											139	118	125					2																	209163420		2203	4300	6503	208871665	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.967T>C	2.37:g.209163420T>C	ENSP00000264380:p.Ser323Pro		208871665	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471816	0.43942	.	.	ENSG00000115020	ENST00000392202;ENST00000264380;ENST00000407449;ENST00000308862;ENST00000452564	T;T;T	0.70516	1.26;-0.49;1.39	5.53	3.14	0.36123	.	0.075049	0.56097	D	0.000038	T	0.40171	0.1106	N	0.03608	-0.345	0.44927	D	0.997945	B;B;B;B;B	0.12630	0.006;0.002;0.002;0.0;0.005	B;B;B;B;B	0.12156	0.006;0.004;0.005;0.0;0.007	T	0.17806	-1.0357	10	0.37606	T	0.19	-12.0254	2.2328	0.04001	0.1306:0.1338:0.1361:0.5995	.	323;323;237;323;226	Q9Y2I7;E9PDH4;Q9Y2I7-3;Q08AR7;Q9Y2I7-2	FYV1_HUMAN;.;.;.;.	P	226;323;323;237;323	ENSP00000264380:S323P;ENSP00000384356:S323P;ENSP00000405736:S323P	ENSP00000264380:S323P	S	+	1	0	PIKFYVE	208871665	0.995000	0.38212	0.994000	0.49952	0.991000	0.79684	0.512000	0.22755	1.013000	0.39391	-0.309000	0.09137	TCA		0.423	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		C	209163420	T	C	209163420	3	2	116	1	0	0	0	0	1	0	0	0	11955	1783	62	4	993	4	PIKFYVE	2	209163420	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	23359724	209163420	34035953	17	31040										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38968293	38968293	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaacatctttaatattcttaCgctattccaatgacaatgga	4	8	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:38968293C>T	ENST00000302328.3	-	4	816		c.e4+1		SCN11A_ENST00000450244.1_Splice_Site|SCN11A_ENST00000444237.2_Splice_Site|SCN11A_ENST00000456224.3_Splice_Site	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit						cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AATATTCTTACGCTATTCCAA	0.413																																																0			3											113	123	120					3																	38968293		2203	4300	6503	38943297	SO:0001630	splice_region_variant	11280			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.617+1G>A	3.37:g.38968293C>T			38943297	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Splice_Site	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818147	0.90790	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1906	0.86878	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCN11A	38943297	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.468000	0.80943	2.658000	0.90341	0.563000	0.77884	.		0.413	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	Intron	T	38968293	C	T	38968293	5	4	116	1	0	0	0	0	0	0	1	0	13950	550	19	1	4849	1	SCN11A	3	38968293	Splice_Site	SNP	C	TCGA-F5-6571-01A-12D-1826-10		38968293	159054137	18	31041										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acagtcttacctggactctgGaatccattctggtgccacta	8	12	3	0	rs28931589|rs121913416		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	3											93	78	83					3																	41266104		2203	4300	6503	41241108	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	3.37:g.41266104G>T	ENSP00000344456:p.Gly34Val		41241108	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266104	G	T	41266104	3	4	116	1	0	0	0	0	1	0	0	0	4022	1174	41	2	107	2	CTNNB1	3	41266104	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	2297811	41266104	156756326	19	31042										
BSN	8927	hgsc.bcm.edu	37	chr3	49690386	49690386	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	actcaccctcaccctcccttGactctgaggctgaggccttg	8	17	3	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:49690386G>A	ENST00000296452.4	+	5	3511	c.3397G>A	c.(3397-3399)Gac>Aac	p.D1133N		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1133					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACCCTCCCTTGACTCTGAGGC	0.612																																																0			3											57	57	57					3																	49690386		2203	4300	6503	49665390	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3397G>A	3.37:g.49690386G>A	ENSP00000296452:p.Asp1133Asn		49665390	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347889	0.61183	.	.	ENSG00000164061	ENST00000296452	T	0.22945	1.93	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.74674	0.984	T	0.55915	-0.8065	10	0.72032	D	0.01	.	18.4911	0.90848	0.0:0.0:1.0:0.0	.	1133	Q9UPA5	BSN_HUMAN	N	1133	ENSP00000296452:D1133N	ENSP00000296452:D1133N	D	+	1	0	BSN	49665390	1.000000	0.71417	0.884000	0.34674	0.938000	0.57974	9.835000	0.99442	2.390000	0.81377	0.561000	0.74099	GAC		0.612	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49690386	G	A	49690386	3	1	116	1	0	0	0	0	1	0	0	0	1533	1290	45	3	3415	3	BSN	3	49690386	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	8424282	49690386	148332044	20	31043										
OR5H15	403274	hgsc.bcm.edu	37	chr3	97888307	97888307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctgtttatactatggcccccTtctcttaatgtatgtgggcc	8	11	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:97888307T>C	ENST00000356526.2	+	1	764	c.764T>C	c.(763-765)cTt>cCt	p.L255P		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						TATGGCCCCCTTCTCTTAATG	0.438																																																0			3											94	97	96					3																	97888307		2203	4300	6503	99370997	SO:0001583	missense	403274				CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.764T>C	3.37:g.97888307T>C	ENSP00000373195:p.Leu255Pro		99370997		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	11.36	1.616582	0.28801	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.00183	8.6	2.48	2.48	0.30137	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42548	D	0.000696	T	0.00552	0.0018	M	0.86343	2.81	0.09310	N	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.29971	-0.9994	10	0.72032	D	0.01	.	8.4982	0.33141	0.0:0.0:0.0:1.0	.	255	A6NDH6	O5H15_HUMAN	P	255	ENSP00000373195:L255P	ENSP00000373195:L255P	L	+	2	0	OR5H15	99370997	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.140000	0.10342	1.138000	0.42230	0.155000	0.16302	CTT		0.438	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			C	97888307	T	C	97888307	3	2	116	1	0	0	0	0	1	0	0	0	11192	1609	56	4	766	4	OR5H15	3	97888307	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	48197921	97888307	100134123	21	31044										
TF	7018	hgsc.bcm.edu	37	chr3	133473445	133473445	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cacacgggtctaggcaggtcCgctgggtggaacatccccat	13	13	1	0	rs41298987	byFrequency	TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:133473445C>T	ENST00000402696.3	+	4	917	c.432C>T	c.(430-432)tcC>tcT	p.S144S	TF_ENST00000475382.1_3'UTR|TF_ENST00000264998.3_Silent_p.S17S|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	144	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TAGGCAGGTCCGCTGGGTGGA	0.522													C|||	64	0.0127796	0.0446	0.0043	5008	,	,		20464	0.002		0	False		,,,				2504	0															0			3						C		151,4255	103.8+/-142.4	1,149,2053	182	178	179		432	-10.5	0.1	3	dbSNP_127	179	0,8600		0,0,4300	no	coding-synonymous	TF	NM_001063.3		1,149,6353	TT,TC,CC		0.0,3.4271,1.161		144/699	133473445	151,12855	2203	4300	6503	134956135	SO:0001819	synonymous_variant	7018				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.432C>T	3.37:g.133473445C>T			134956135	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																				0.522	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133473445	C	T	133473445	2	4	116	1	0	0	0	0	0	0	0	1	15824	639	23	1		1	TF	3	133473445	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	35585138	133473445	64548985	22	31045										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952001	178952001	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	actacaatcttttgatgacaTtgcatacattcgaaagaccc	5	10	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:178952001T>C	ENST00000263967.3	+	21	3213	c.3056T>C	c.(3055-3057)aTt>aCt	p.I1019T	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1019	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTTGATGACATTGCATACATT	0.398		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											108	95	99					3																	178952001		1881	4115	5996	180434695	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3056T>C	3.37:g.178952001T>C	ENSP00000263967:p.Ile1019Thr		180434695	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.521955	0.44866	.	.	ENSG00000121879	ENST00000263967	D	0.82526	-1.62	5.81	5.81	0.92471	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.110998	0.64402	D	0.000010	D	0.83732	0.5318	M	0.73753	2.245	0.80722	D	1	P	0.37688	0.605	B	0.37091	0.241	D	0.85646	0.1279	10	0.87932	D	0	-18.4609	16.1773	0.81862	0.0:0.0:0.0:1.0	.	1019	P42336	PK3CA_HUMAN	T	1019	ENSP00000263967:I1019T	ENSP00000263967:I1019T	I	+	2	0	PIK3CA	180434695	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.560000	0.82277	2.217000	0.71921	0.482000	0.46254	ATT		0.398	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178952001	T	C	178952001	3	2	116	1	0	0	0	0	1	0	0	0	11944	1493	52	4	3134	4	PIK3CA	3	178952001	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	45478556	178952001	19070429	23	31046										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197559134	197559134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctaaagaacaaagactacgaAgagaaagccagtaccaagag	9	8	0	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr3:197559134A>G	ENST00000425562.2	+	8	1048	c.1048A>G	c.(1048-1050)Aga>Gga	p.R350G	LRCH3_ENST00000536618.1_5'UTR|LRCH3_ENST00000334859.4_Missense_Mutation_p.R350G|LRCH3_ENST00000414675.2_Missense_Mutation_p.R350G|LRCH3_ENST00000441090.2_Missense_Mutation_p.R224G|LRCH3_ENST00000438796.2_Missense_Mutation_p.R350G|AC055764.1_ENST00000454526.1_RNA			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	350						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AAGACTACGAAGAGAAAGCCA	0.398																																																0			3											85	80	82					3																	197559134		2203	4300	6503	199043531	SO:0001583	missense	84859			AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1048A>G	3.37:g.197559134A>G	ENSP00000393579:p.Arg350Gly		199043531	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	A	15.34	2.804548	0.50315	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562	T;T;T;T;T	0.33438	2.01;1.41;2.03;2.25;2.03	5.51	5.51	0.81932	.	0.051413	0.85682	D	0.000000	T	0.45013	0.1321	L	0.34521	1.04	0.80722	D	1	B;D;B;P	0.69078	0.131;0.997;0.037;0.841	B;D;B;P	0.77004	0.07;0.989;0.029;0.693	T	0.33979	-0.9847	10	0.45353	T	0.12	-14.7564	15.6494	0.77078	1.0:0.0:0.0:0.0	.	224;350;350;350	E9PD99;B4E0T7;Q96II8-2;Q96II8-3	.;.;.;.	G	350;224;350;350;350	ENSP00000399751:R350G;ENSP00000394609:R224G;ENSP00000394965:R350G;ENSP00000334375:R350G;ENSP00000393579:R350G	ENSP00000334375:R350G	R	+	1	2	LRCH3	199043531	1.000000	0.71417	0.978000	0.43139	0.972000	0.66771	3.838000	0.55828	2.101000	0.63845	0.477000	0.44152	AGA		0.398	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		G	197559134	A	G	197559134	3	3	116	1	0	0	0	0	1	0	0	0	8963	64	3	4	1078	4	LRCH3	3	197559134	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	18607133	197559134	463296	24	31047										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15560806	15560806	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aggactatgagaaacggttaCgagacagaaatgtaatagaa	11	4	0	4	rs118204053		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:15560806C>T	ENST00000503292.1	+	23	3028	c.2848C>T	c.(2848-2850)Cga>Tga	p.R950*	CC2D2A_ENST00000413206.1_Nonsense_Mutation_p.R950*|CC2D2A_ENST00000424120.1_Nonsense_Mutation_p.R950*|CC2D2A_ENST00000389652.5_Nonsense_Mutation_p.R901*	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	950					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GAAACGGTTACGAGACAGAAA	0.353																																																0			4	GRCh37	CM085305	CC2D2A	M	rs118204053	C	stop/ARG	1,3601		0,1,1800	60	56	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2848	5.4	1	4	dbSNP_132	57	0,8056		0,0,4028	no	stop-gained	CC2D2A	NM_001080522.2		0,1,5828	TT,TC,CC		0.0,0.0278,0.0086		950/1621	15560806	1,11657	1801	4028	5829	15169904	SO:0001587	stop_gained	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.2848C>T	4.37:g.15560806C>T	ENSP00000421809:p.Arg950*		15169904	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Nonsense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	C	37	6.634735	0.97722	2.78E-4	0.0	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000503292;ENST00000389652	.	.	.	5.37	5.37	0.77165	.	0.324747	0.29486	N	0.012013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	19.1238	0.93374	0.0:1.0:0.0:0.0	.	.	.	.	X	950;950;901;901;950;901	.	ENSP00000374303:R901X	R	+	1	2	CC2D2A	15169904	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.021000	0.64072	2.522000	0.85027	0.650000	0.86243	CGA		0.353	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		T	15560806	C	T	15560806	4	4	116	1	0	0	0	0	0	1	0	0	2734	528	19	1	3133	1	CC2D2A	4	15560806	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10		15560806	175593470	25	31048										
DKK2	27123	hgsc.bcm.edu	37	chr4	107845227	107845227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaaaatttccagcccatgagAacccttcttgcgttgtttgg	9	10	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:107845227A>G	ENST00000285311.3	-	4	1369	c.664T>C	c.(664-666)Tct>Cct	p.S222P	DKK2_ENST00000510463.1_Missense_Mutation_p.S176P|DKK2_ENST00000513208.1_Missense_Mutation_p.S122P	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	222	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		AGCCCATGAGAACCCTTCTTG	0.502																																																0			4											169	154	159					4																	107845227		2203	4300	6503	108064676	SO:0001583	missense	27123			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.664T>C	4.37:g.107845227A>G	ENSP00000285311:p.Ser222Pro		108064676	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.042941	0.75732	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.48522	0.81;0.86;0.83	5.64	4.43	0.53597	.	0.107163	0.64402	D	0.000004	T	0.42988	0.1227	L	0.59436	1.845	0.49213	D	0.999763	P	0.45348	0.856	B	0.37346	0.247	T	0.45011	-0.9290	10	0.66056	D	0.02	-15.1533	12.7558	0.57335	0.8626:0.1374:0.0:0.0	.	222	Q9UBU2	DKK2_HUMAN	P	222;122;176	ENSP00000285311:S222P;ENSP00000421255:S122P;ENSP00000423797:S176P	ENSP00000285311:S222P	S	-	1	0	DKK2	108064676	1.000000	0.71417	0.878000	0.34440	0.994000	0.84299	2.066000	0.41452	0.937000	0.37394	0.477000	0.44152	TCT		0.502	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			G	107845227	A	G	107845227	3	3	116	1	0	0	0	0	1	0	0	0	4556	246	9	4	119	4	DKK2	4	107845227	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	92284421	107845227	83309049	26	31049										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123118413	123118413	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttagaaattaatattccaatGacagttgaagaaaatggtaa	7	3	0	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:123118413G>A	ENST00000264501.4	+	13	1645	c.1272G>A	c.(1270-1272)atG>atA	p.M424I	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.M424I|KIAA1109_ENST00000388738.3_Missense_Mutation_p.M424I			Q2LD37	K1109_HUMAN	KIAA1109	424					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATATTCCAATGACAGTTGAAG	0.249																																																0			4											40	42	41					4																	123118413		1784	4015	5799	123337863	SO:0001583	missense	84162			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1272G>A	4.37:g.123118413G>A	ENSP00000264501:p.Met424Ile		123337863	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.0|21.0	4.078497|4.078497	0.76528|0.76528	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|D;D;D	.|0.93906	.|-3.31;-3.31;-3.31	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|1592.350000	.|0.00166	.|N	.|0.000000	D|D	0.96275|0.96275	0.8785|0.8785	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999999|0.999999	.|P	.|0.50528	.|0.936	.|P	.|0.61201	.|0.885	D|D	0.85531|0.85531	0.1209|0.1209	5|10	.|0.54805	.|T	.|0.06	.|.	19.7617|19.7617	0.96321|0.96321	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|424	.|Q2LD37	.|K1109_HUMAN	N|I	257|424	.|ENSP00000264501:M424I;ENSP00000373390:M424I;ENSP00000389925:M424I	.|ENSP00000264501:M424I	D|M	+|+	1|3	0|0	KIAA1109|KIAA1109	123337863|123337863	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.591000|7.591000	0.82666|0.82666	2.671000|2.671000	0.90904|0.90904	0.655000|0.655000	0.94253|0.94253	GAC|ATG		0.249	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123118413	G	A	123118413	3	1	116	1	0	0	0	0	1	0	0	0	8229	1290	45	3	1314	3	KIAA1109	4	123118413	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	15273186	123118413	68035863	27	31050										
INTU	27152	hgsc.bcm.edu	37	chr4	128565122	128565122	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaccaagtggagctggagaaGaaccggaaagcagggtgatg	17	6	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:128565122G>T	ENST00000335251.6	+	2	696	c.593G>T	c.(592-594)aGa>aTa	p.R198I	INTU_ENST00000296461.5_Missense_Mutation_p.R198I	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	198	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						AGCTGGAGAAGAACCGGAAAG	0.498																																																0			4											140	135	137					4																	128565122		2203	4300	6503	128784572	SO:0001583	missense	27152			BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.593G>T	4.37:g.128565122G>T	ENSP00000334003:p.Arg198Ile		128784572	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601199	0.46423	.	.	ENSG00000164066	ENST00000504491;ENST00000335251;ENST00000296461	T	0.47528	0.84	4.8	3.01	0.34805	PDZ/DHR/GLGF (2);	0.319549	0.34156	N	0.004218	T	0.40546	0.1121	L	0.47716	1.5	0.51767	D	0.99993	B	0.33919	0.432	B	0.35550	0.205	T	0.34104	-0.9842	10	0.66056	D	0.02	-13.1171	9.7754	0.40616	0.1729:0.0:0.8271:0.0	.	198	Q9ULD6	PDZD6_HUMAN	I	179;198;198	ENSP00000296461:R198I	ENSP00000296461:R198I	R	+	2	0	INTU	128784572	1.000000	0.71417	0.766000	0.31476	0.893000	0.52053	2.309000	0.43699	0.685000	0.31468	0.655000	0.94253	AGA		0.498	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		T	128565122	G	T	128565122	3	4	116	1	0	0	0	0	1	0	0	0	7807	942	33	2	599	2	INTU	4	128565122	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	5446709	128565122	62589154	28	31051										
SCLT1	132320	hgsc.bcm.edu	37	chr4	129960213	129960213	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tacctttcattttccttgatGacattttcaagttgtaattt	4	7	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:129960213G>A	ENST00000281142.5	-	5	776	c.273C>T	c.(271-273)gtC>gtT	p.V91V	SCLT1_ENST00000506368.1_Silent_p.V91V|SCLT1_ENST00000434680.1_Silent_p.V91V|SCLT1_ENST00000439369.2_Silent_p.V91V|SCLT1_ENST00000503215.1_Silent_p.V68V	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	91					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TTTCCTTGATGACATTTTCAA	0.279																																																0			4											54	52	53					4																	129960213		2199	4297	6496	130179663	SO:0001819	synonymous_variant	132320			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.273C>T	4.37:g.129960213G>A			130179663	A4QN04|Q0VAH2|Q6P2M4	Silent	SNP	ENST00000281142.5	37	CCDS3740.1																																																																																				0.279	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		A	129960213	G	A	129960213	2	1	116	1	0	0	0	0	0	0	0	1	13943	1277	45	3		3	SCLT1	4	129960213	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	1395091	129960213	61194063	29	31052										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177608450	177608450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gggttgatttctggggcaggTtcttttacatacacactggc	12	8	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr4:177608450T>C	ENST00000280193.2	-	6	1451	c.1036A>G	c.(1036-1038)Acc>Gcc	p.T346A	RP11-313E19.2_ENST00000504017.1_RNA|RP11-313E19.2_ENST00000509194.1_RNA|VEGFC_ENST00000507638.1_5'Flank	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	346	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.T346P(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		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)		CTGGGGCAGGTTCTTTTACAT	0.433																																																1	Substitution - Missense(1)	lung(1)	4											263	234	243					4																	177608450		1848	4101	5949	177845444	SO:0001583	missense	7424			BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.1036A>G	4.37:g.177608450T>C	ENSP00000280193:p.Thr346Ala		177845444	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.433771	0.25813	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.61	3.22	0.36961	.	0.184991	0.46442	N	0.000282	T	0.32406	0.0828	N	0.25647	0.755	0.36387	D	0.862262	B	0.12630	0.006	B	0.09377	0.004	T	0.18053	-1.0349	9	0.23302	T	0.38	-6.1851	4.8551	0.13555	0.1375:0.1458:0.0:0.7168	.	346	P49767	VEGFC_HUMAN	A	346	.	ENSP00000280193:T346A	T	-	1	0	VEGFC	177845444	0.920000	0.31207	0.996000	0.52242	0.924000	0.55760	1.379000	0.34340	0.954000	0.37851	0.528000	0.53228	ACC		0.433	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		C	177608450	T	C	177608450	3	2	116	1	0	0	0	0	1	0	0	0	17192	1725	60	4	234	4	VEGFC	4	177608450	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	47648237	177608450	13545826	30	31053										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37198855	37198855	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tgcaatatataccactgtgcTacaggaaaagaacactgagc	8	9	0	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:37198855T>C	ENST00000508244.1	-	19	3714	c.3621A>G	c.(3619-3621)gtA>gtG	p.V1207V	C5orf42_ENST00000425232.2_Silent_p.V1207V|C5orf42_ENST00000274258.7_Silent_p.V88V			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1207						integral component of membrane (GO:0016021)		p.V88V(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ACCACTGTGCTACAGGAAAAG	0.403																																																1	Substitution - coding silent(1)	ovary(1)	5											94	96	95					5																	37198855		2203	4300	6503	37234612	SO:0001819	synonymous_variant	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3621A>G	5.37:g.37198855T>C			37234612	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																				0.403	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37198855	T	C	37198855	2	2	116	1	0	0	0	0	0	0	0	1	2307	1509	53	4		4	C5orf42	5	37198855	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10		37198855	143716405	31	31054										
MAST4	375449	hgsc.bcm.edu	37	chr5	66438283	66438283	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tatcatcatatggaaacggaGgaagaagatgacacaaatga	10	5	2	4	rs544939743		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:66438283G>T	ENST00000403625.2	+	21	2947	c.2652G>T	c.(2650-2652)gaG>gaT	p.E884D	MAST4_ENST00000261569.7_Missense_Mutation_p.E690D|MAST4_ENST00000405643.1_Missense_Mutation_p.E705D|MAST4_ENST00000403666.1_Missense_Mutation_p.E695D|MAST4_ENST00000404260.3_Missense_Mutation_p.E887D	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	887	AGC-kinase C-terminal.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TGGAAACGGAGGAAGAAGATG	0.348																																																0			5											63	62	62					5																	66438283		1906	4118	6024	66474039	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2652G>T	5.37:g.66438283G>T	ENSP00000385727:p.Glu884Asp		66474039	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.39|12.39	1.923377|1.923377	0.33908|0.33908	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399|ENST00000443808	T;T;T;T;T|.	0.25085|.	1.82;1.82;1.82;1.82;1.82|.	5.71|5.71	-1.03|-1.03	0.10102|0.10102	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.50000|.	0.1590|.	L|L	0.32530|0.32530	0.975|0.975	0.41011|0.41011	D|D	0.985008|0.985008	B;B;B;B|.	0.23185|.	0.014;0.014;0.081;0.023|.	B;B;B;B|.	0.22601|.	0.028;0.018;0.04;0.021|.	T|.	0.39881|.	-0.9592|.	10|.	0.37606|.	T|.	0.19|.	-31.9782|-31.9782	12.333|12.333	0.55049|0.55049	0.5287:0.0:0.4713:0.0|0.5287:0.0:0.4713:0.0	.|.	705;887;690;695|.	E7EWQ5;O15021;O15021-2;O15021-3|.	.;MAST4_HUMAN;.;.|.	D|X	887;884;695;705;705;690;690|8	ENSP00000385048:E887D;ENSP00000385727:E884D;ENSP00000384313:E695D;ENSP00000384099:E705D;ENSP00000261569:E690D|.	ENSP00000261569:E690D|.	E|G	+|+	3|1	2|0	MAST4|MAST4	66474039|66474039	1.000000|1.000000	0.71417|0.71417	0.949000|0.949000	0.38748|0.38748	0.743000|0.743000	0.42351|0.42351	1.779000|1.779000	0.38624|0.38624	-0.117000|-0.117000	0.11872|0.11872	-0.192000|-0.192000	0.12808|0.12808	GAG|GGA		0.348	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66438283	G	T	66438283	3	4	116	1	0	0	0	0	1	0	0	0	9357	991	35	2	2864	2	MAST4	5	66438283	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	29239428	66438283	114476977	32	31055										
THBS4	7060	hgsc.bcm.edu	37	chr5	79336091	79336091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttgaatttactgtgatgggaCgcttaaacaaaggtaagcaa	10	5	0	2	rs200373343		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:79336091C>T	ENST00000350881.2	+	2	470	c.280C>T	c.(280-282)Cgc>Tgc	p.R94C	THBS4_ENST00000511733.1_Missense_Mutation_p.R3C	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	94	Laminin G-like.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TGTGATGGGACGCTTAAACAA	0.358																																																0			5						C	CYS/ARG	0,4406		0,0,2203	32	33	32		280	5.5	1	5		32	1,8599	1.2+/-3.3	0,1,4299	yes	missense	THBS4	NM_003248.4	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	94/962	79336091	1,13005	2203	4300	6503	79371847	SO:0001583	missense	7060				CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.280C>T	5.37:g.79336091C>T	ENSP00000339730:p.Arg94Cys		79371847	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944247	0.73672	0.0	1.16E-4	ENSG00000113296	ENST00000350881;ENST00000511733	T;D	0.87729	4.38;-2.29	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.055762	0.64402	D	0.000001	D	0.92341	0.7570	L	0.57536	1.79	0.54753	D	0.999986	D	0.89917	1.0	D	0.79784	0.993	D	0.92874	0.6317	10	0.87932	D	0	-22.2117	18.167	0.89731	0.0:1.0:0.0:0.0	.	94	P35443	TSP4_HUMAN	C	94;3	ENSP00000339730:R94C;ENSP00000422298:R3C	ENSP00000339730:R94C	R	+	1	0	THBS4	79371847	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.285000	0.58989	2.573000	0.86826	0.544000	0.68410	CGC		0.358	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			T	79336091	C	T	79336091	3	4	116	1	0	0	0	0	1	0	0	0	15895	536	19	1	286	1	THBS4	5	79336091	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	12897808	79336091	101579169	33	31056										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101748744	101748744	+	Frame_Shift_Del	DEL	A	A	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acaccctgcaaagcagggagAaaaatattcaatatcatctc							TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:101748744delA	ENST00000506729.1	-	9	1747	c.1576delT	c.(1576-1578)tctfs	p.S526fs	SLCO6A1_ENST00000513675.1_Frame_Shift_Del_p.S273fs|SLCO6A1_ENST00000379810.1_Frame_Shift_Del_p.S273fs|SLCO6A1_ENST00000379807.3_Frame_Shift_Del_p.S526fs|SLCO6A1_ENST00000389019.3_Frame_Shift_Del_p.S464fs			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	526	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		AAGCAGGGAGAAAAATATTCA	0.299																																																0			5											30	31	30					5																	101748744		2199	4296	6495	101776643	SO:0001589	frameshift_variant	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1576delT	5.37:g.101748744delA	ENSP00000421339:p.Ser526fs		101776643	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Del	DEL	ENST00000506729.1	37	CCDS34206.1																																																																																				0.299	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		-	101748744	A	-	101748744	7	5	116	1	0	1	0	1	0	0	0	0	14769	246	9	0	603	0	SLCO6A1	5	101748744	Frame_Shift_Del	DEL	A	TCGA-F5-6571-01A-12D-1826-10	22412653	101748744	79166516	34	31057										
APC	324	hgsc.bcm.edu	37	chr5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atccaggaacttcttcaaagCgaggtttgcagatctccacc	8	12	3	1	rs121913333		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R876*|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*			P25054	APC_HUMAN	adenomatous polyposis coli	876	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R876*(38)|p.S874_R876>*(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCTTCAAAGCGAGGTTTGCA	0.463		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	5	GRCh37	CM942020	APC	M	rs121913333						70	72	71					5																	112173917		2202	4300	6502	112201816	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*		112201816	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173917	C	T	112173917	4	4	116	1	0	0	0	0	0	1	0	0	763	760	27	1	2684	1	APC	5	112173917	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	10425173	112173917	68741343	35	31058			1	36		3	3	1856	N	C_A	3.960076e-05
APC	324	hgsc.bcm.edu	37	chr5	112175594	112175594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gacaaaccatgccaccaagcAgaagtaaaacacctccacca	5	15	0	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:112175594A>G	ENST00000457016.1	+	16	4683	c.4303A>G	c.(4303-4305)Aga>Gga	p.R1435G	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.R1435G|APC_ENST00000508376.2_Missense_Mutation_p.R1435G			P25054	APC_HUMAN	adenomatous polyposis coli	1435	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1435*(3)|p.R1435fs*38(1)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.P1432fs*35(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCCACCAAGCAGAAGTAAAAC	0.478		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	8	Deletion - Frameshift(4)|Substitution - Nonsense(3)|Unknown(1)	large_intestine(6)|soft_tissue(1)|skin(1)	5											114	102	106					5																	112175594		2202	4300	6502	112203493	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4303A>G	5.37:g.112175594A>G	ENSP00000413133:p.Arg1435Gly		112203493	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675982	0.67928	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91631	-2.88;-2.88;-2.88	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.95204	0.8445	M	0.64404	1.975	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	D	0.94696	0.7878	9	.	.	.	-26.4321	16.6288	0.85011	1.0:0.0:0.0:0.0	.	1437;1435	Q4LE70;P25054	.;APC_HUMAN	G	1435	ENSP00000413133:R1435G;ENSP00000257430:R1435G;ENSP00000427089:R1435G	.	R	+	1	2	APC	112203493	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.608000	0.74168	2.326000	0.78906	0.533000	0.62120	AGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175594	A	G	112175594	3	3	116	1	0	0	0	0	1	0	0	0	763	180	7	4	4361	4	APC	5	112175594	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	1677	112175594	68739666	36	31059			1	36		3	3	1856	N	C_A	3.960076e-05
APC	324	hgsc.bcm.edu	37	chr5	112175772	112175772	+	Frame_Shift_Del	DEL	A	A	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tttattacattttgccacggAaagtactccagatggatttt							TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:112175772delA	ENST00000457016.1	+	16	4861	c.4481delA	c.(4480-4482)gaafs	p.E1494fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.E1494fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1494fs			P25054	APC_HUMAN	adenomatous polyposis coli	1494	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.K1454fs*3(1)|p.T1493fs*17(1)|p.S1495fs*19(1)|p.K1192fs*3(1)|p.E1494fs*12(1)|p.E1494fs*11(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTGCCACGGAAAGTACTCCA	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Deletion - Frameshift(3)|Complex - frameshift(2)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(4)|thyroid(1)|soft_tissue(1)|skin(1)	5											70	72	71					5																	112175772		2201	4300	6501	112203671	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4481delA	5.37:g.112175772delA	ENSP00000413133:p.Glu1494fs		112203671	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175772	A	-	112175772	7	5	116	1	0	1	0	1	0	0	0	0	763	246	9	0	4539	0	APC	5	112175772	Frame_Shift_Del	DEL	A	TCGA-F5-6571-01A-12D-1826-10	178	112175772	68739488	37	31060			1	36		3	3	1856	N	C_A	3.960076e-05
TGFBI	7045	hgsc.bcm.edu	37	chr5	135383085	135383085	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atccagcagatcattgagatCgaggacacctttgagaccct	9	11	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:135383085C>T	ENST00000442011.2	+	6	908	c.747C>T	c.(745-747)atC>atT	p.I249I	TGFBI_ENST00000305126.8_Silent_p.I249I	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	249	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCATTGAGATCGAGGACACCT	0.572																																																0			5											240	236	238					5																	135383085		2108	4214	6322	135410984	SO:0001819	synonymous_variant	7045			M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.747C>T	5.37:g.135383085C>T			135410984	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	C	9.305	1.054134	0.19907	.	.	ENSG00000120708	ENST00000508767	.	.	.	6.0	-5.07	0.02938	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-30.0916	10.9106	0.47106	0.0905:0.2391:0.0:0.6704	.	.	.	.	X	25	.	.	R	+	1	2	TGFBI	135410984	0.000000	0.05858	0.811000	0.32455	0.894000	0.52154	-2.839000	0.00738	-0.987000	0.03494	-1.060000	0.02296	CGA		0.572	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			T	135383085	C	T	135383085	2	4	116	1	0	0	0	0	0	0	0	1	15859	874	31	1		1	TGFBI	5	135383085	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	23207313	135383085	45532175	38	31061										
DNAJC18	202052	hgsc.bcm.edu	37	chr5	138760697	138760697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cctccctccctaggtacctgAggtttctcttcttcctcctc	5	18	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:138760697A>G	ENST00000302060.5	-	5	746	c.666T>C	c.(664-666)ccT>ccC	p.P222P		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	222						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TAGGTACCTGAGGTTTCTCTT	0.458																																																0			5											257	220	233					5																	138760697		2203	4300	6503	138788596	SO:0001819	synonymous_variant	202052			AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.666T>C	5.37:g.138760697A>G			138788596		Silent	SNP	ENST00000302060.5	37	CCDS4214.1	.	.	.	.	.	.	.	.	.	.	A	9.821	1.185669	0.21870	.	.	ENSG00000170464	ENST00000514052	.	.	.	5.72	3.28	0.37604	.	.	.	.	.	T	0.53012	0.1770	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43605	-0.9381	4	.	.	.	-4.4335	4.5204	0.11956	0.6181:0.0:0.0817:0.3001	.	.	.	.	P	14	.	.	L	-	2	0	DNAJC18	138788596	0.999000	0.42202	1.000000	0.80357	0.797000	0.45037	0.555000	0.23422	0.413000	0.25759	0.460000	0.39030	CTC		0.458	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		G	138760697	A	G	138760697	2	3	116	1	0	0	0	0	0	0	0	1	4648	291	11	4		4	DNAJC18	5	138760697	Silent	SNP	A	TCGA-F5-6571-01A-12D-1826-10	3377612	138760697	42154563	39	31062										
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140594465	140594465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gcagatctctgaggacagtcCggtaggcttcctggttgtga	14	9	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:140594465C>T	ENST00000341948.4	+	1	957	c.770C>T	c.(769-771)cCg>cTg	p.P257L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	257	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGGACAGTCCGGTAGGCTTC	0.493																																																0			5											176	174	175					5																	140594465		2203	4300	6503	140574649	SO:0001583	missense	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.770C>T	5.37:g.140594465C>T	ENSP00000345491:p.Pro257Leu		140574649	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	c	16.56	3.158181	0.57368	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.01685	4.69	3.51	3.51	0.40186	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06005	0.0156	M	0.66297	2.02	0.20307	N	0.999919	P	0.42375	0.778	P	0.49012	0.598	T	0.09100	-1.0690	9	0.66056	D	0.02	.	15.0392	0.71774	0.0:1.0:0.0:0.0	.	257	Q9Y5F0	PCDBD_HUMAN	L	257	ENSP00000345491:P257L	ENSP00000345491:P257L	P	+	2	0	PCDHB13	140574649	0.000000	0.05858	0.014000	0.15608	0.727000	0.41649	0.906000	0.28517	1.675000	0.50919	0.306000	0.20318	CCG		0.493	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		T	140594465	C	T	140594465	3	4	116	1	0	0	0	0	1	0	0	0	11569	652	23	1	772	1	PCDHB13	5	140594465	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1833768	140594465	40320795	40	31063										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142661473	142661473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtcacttttgatgaaacagaAgttttttgatatttccattt	6	5	1	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:142661473A>G	ENST00000343796.2	-	9	3308	c.2315T>C	c.(2314-2316)cTt>cCt	p.L772P	NR3C1_ENST00000415690.2_Intron|NR3C1_ENST00000394464.2_Missense_Mutation_p.L772P|NR3C1_ENST00000504572.1_Missense_Mutation_p.L773P|NR3C1_ENST00000394466.2_Missense_Mutation_p.L773P|NR3C1_ENST00000231509.3_Missense_Mutation_p.L773P|NR3C1_ENST00000503201.1_Missense_Mutation_p.L772P|NR3C1_ENST00000416954.2_Missense_Mutation_p.L375P|NR3C1_ENST00000424646.2_Missense_Mutation_p.L746P	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	772	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)	p.L773P(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	ATGAAACAGAAGTTTTTTGAT	0.318																																																1	Substitution - Missense(1)	ovary(1)	5											87	90	89					5																	142661473		2202	4300	6502	142641666	SO:0001583	missense	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2315T>C	5.37:g.142661473A>G	ENSP00000343205:p.Leu772Pro		142641666	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593056	0.66219	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	5.93	5.93	0.95920	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.97300	0.9117	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97948	1.0330	10	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	772;773	P04150;E5KQF6	GCR_HUMAN;.	P	772;772;588;746;773;773;773;375;772	ENSP00000377977:L772P;ENSP00000343205:L772P;ENSP00000405282:L746P;ENSP00000422518:L773P;ENSP00000377979:L773P;ENSP00000231509:L773P;ENSP00000404218:L375P;ENSP00000427672:L772P	ENSP00000231509:L773P	L	-	2	0	NR3C1	142641666	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.281000	0.76405	0.533000	0.62120	CTT		0.318	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			G	142661473	A	G	142661473	3	3	116	1	0	0	0	0	1	0	0	0	10661	72	3	4	74	4	NR3C1	5	142661473	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	2067008	142661473	38253787	41	31064										
HK3	3101	hgsc.bcm.edu	37	chr5	176308808	176308808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atgtaaaaggatgtggcggaCgatctcccccaggtacatgc	12	10	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:176308808C>T	ENST00000292432.5	-	17	2369	c.2278G>A	c.(2278-2280)Gtc>Atc	p.V760I		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	760	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	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)			ATGTGGCGGACGATCTCCCCC	0.562																																																0			5											109	113	112					5																	176308808		2203	4300	6503	176241414	SO:0001583	missense	84376				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2278G>A	5.37:g.176308808C>T	ENSP00000292432:p.Val760Ile		176241414	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	33	5.206114	0.95033	.	.	ENSG00000160883	ENST00000292432	D	0.97016	-4.21	4.82	4.82	0.62117	Hexokinase, C-terminal (1);	0.000000	0.48286	D	0.000194	D	0.98264	0.9425	M	0.91459	3.21	0.80722	D	1	D	0.63880	0.993	P	0.60949	0.881	D	0.99239	1.0884	10	0.87932	D	0	.	18.0642	0.89386	0.0:1.0:0.0:0.0	.	760	P52790	HXK3_HUMAN	I	760	ENSP00000292432:V760I	ENSP00000292432:V760I	V	-	1	0	HK3	176241414	1.000000	0.71417	0.977000	0.42913	0.780000	0.44128	7.651000	0.83577	2.657000	0.90304	0.561000	0.74099	GTC		0.562	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			T	176308808	C	T	176308808	3	4	116	1	0	0	0	0	1	0	0	0	7213	536	19	1	505	1	HK3	5	176308808	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	33647335	176308808	4606452	42	31065										
RNF130	55819	hgsc.bcm.edu	37	chr5	179405233	179405233	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaattcggacgacatcattcTgcttatagctctctatgcag	8	10	3	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr5:179405233T>A	ENST00000261947.4	-	5	1216	c.818A>T	c.(817-819)cAg>cTg	p.Q273L	RNF130_ENST00000522208.2_Missense_Mutation_p.Q273L|RNF130_ENST00000521389.1_Missense_Mutation_p.Q273L	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACATCATTCTGCTTATAGCT	0.393																																					GBM(24;432 554 38471 39699 51728)											0			5											140	123	129					5																	179405233		2203	4300	6503	179337839	SO:0001583	missense	55819			AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"RING-type (C3HC4) zinc fingers"	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.818A>T	5.37:g.179405233T>A	ENSP00000261947:p.Gln273Leu		179337839		Missense_Mutation	SNP	ENST00000261947.4	37		.	.	.	.	.	.	.	.	.	.	T	13.41	2.229025	0.39399	.	.	ENSG00000113269	ENST00000522208;ENST00000521389;ENST00000261947	T;T;T	0.42900	0.96;0.96;0.96	5.65	4.45	0.53987	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.064398	0.64402	D	0.000005	T	0.24624	0.0597	N	0.05592	-0.015	0.44424	D	0.997341	B;B	0.06786	0.001;0.001	B;B	0.14023	0.01;0.001	T	0.03221	-1.1059	10	0.40728	T	0.16	.	12.7151	0.57111	0.0:0.0:0.1377:0.8623	.	290;273	Q59EL1;Q86XS8	.;GOLI_HUMAN	L	273	ENSP00000429509:Q273L;ENSP00000430237:Q273L;ENSP00000261947:Q273L	ENSP00000261947:Q273L	Q	-	2	0	RNF130	179337839	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.681000	0.46926	1.030000	0.39839	0.459000	0.35465	CAG		0.393	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434		A	179405233	T	A	179405233	3	1	116	1	0	0	0	0	1	0	0	0	13475	1580	55	5	461	5	RNF130	5	179405233	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	3096425	179405233	1510027	43	31066										
DUSP22	56940	hgsc.bcm.edu	37	chr6	348156	348156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gatcgcatacatcatgaccgTcactgactttggctgggagg	12	10	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:348156T>C	ENST00000344450.5	+	6	760	c.317T>C	c.(316-318)gTc>gCc	p.V106A	DUSP22_ENST00000605035.1_Missense_Mutation_p.V3A|DUSP22_ENST00000605863.1_Missense_Mutation_p.V3A|DUSP22_ENST00000605315.1_Missense_Mutation_p.V3A|DUSP22_ENST00000419235.2_Missense_Mutation_p.V106A|DUSP22_ENST00000603453.1_Missense_Mutation_p.V3A|DUSP22_ENST00000604971.1_Missense_Mutation_p.V3A	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	106	Tyrosine-protein phosphatase.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		ATCATGACCGTCACTGACTTT	0.602																																																0			6											193	175	181					6																	348156		2203	4300	6503	293156	SO:0001583	missense	56940			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.317T>C	6.37:g.348156T>C	ENSP00000345281:p.Val106Ala		293156	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Missense_Mutation	SNP	ENST00000344450.5	37	CCDS4468.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.499891	0.85176	.	.	ENSG00000112679	ENST00000344450	D	0.85484	-1.99	5.82	5.82	0.92795	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.259964	0.34200	N	0.004176	D	0.83431	0.5253	L	0.55213	1.73	0.52501	D	0.999958	B;P;P	0.51147	0.04;0.942;0.942	B;P;P	0.57468	0.108;0.821;0.766	T	0.81699	-0.0814	10	0.10377	T	0.69	.	16.1697	0.81793	0.0:0.0:0.0:1.0	.	106;63;106	Q9NRW4-2;B3KSA8;Q9NRW4	.;.;DUS22_HUMAN	A	106	ENSP00000345281:V106A	ENSP00000345281:V106A	V	+	2	0	DUSP22	293156	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	6.229000	0.72294	2.221000	0.72209	0.533000	0.62120	GTC		0.602	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185		C	348156	T	C	348156	3	2	116	1	0	0	0	0	1	0	0	0	4832	1667	58	4	339	4	DUSP22	6	348156	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10		348156	170766911	44	31067										
ZNF184	7738	hgsc.bcm.edu	37	chr6	27420014	27420014	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acaatcatagggtttctcccCagtatgagttttttgatgct	8	8	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:27420014C>A	ENST00000211936.6	-	6	1608	c.1324G>T	c.(1324-1326)Ggg>Tgg	p.G442W	ZNF184_ENST00000377419.1_Missense_Mutation_p.G442W	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						GGTTTCTCCCCAGTATGAGTT	0.403																																																0			6											85	85	85					6																	27420014		2203	4300	6503	27527993	SO:0001583	missense	7738			U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1324G>T	6.37:g.27420014C>A	ENSP00000211936:p.Gly442Trp		27527993	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198781	0.58126	.	.	ENSG00000096654	ENST00000211936;ENST00000377419	T;T	0.26810	1.71;1.71	5.27	4.38	0.52667	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000117	T	0.53786	0.1818	H	0.94808	3.585	0.44061	D	0.996807	D	0.89917	1.0	D	0.91635	0.999	T	0.64101	-0.6486	10	0.87932	D	0	.	12.0054	0.53257	0.0:0.9139:0.0:0.0861	.	442	Q99676	ZN184_HUMAN	W	442	ENSP00000211936:G442W;ENSP00000366636:G442W	ENSP00000211936:G442W	G	-	1	0	ZNF184	27527993	0.225000	0.23685	0.975000	0.42487	0.999000	0.98932	2.424000	0.44714	2.744000	0.94065	0.655000	0.94253	GGG		0.403	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		A	27420014	C	A	27420014	3	1	116	1	0	0	0	0	1	0	0	0	17790	594	21	2	935	2	ZNF184	6	27420014	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	27071858	27420014	143695053	45	31068										
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408114	29408114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcttcttcctcttctttggcGccacggagtgctgcctcctg	9	15	4	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:29408114G>A	ENST00000444197.2	+	1	1032	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CTTCTTTGGCGCCACGGAGTG	0.607																																																0			6											77	79	79					6																	29408114		1510	2709	4219	29516093	SO:0001583	missense	442194				CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.322G>A	6.37:g.29408114G>A	ENSP00000419119:p.Ala108Thr		29516093	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	5.706	0.314869	0.10789	.	.	ENSG00000206474	ENST00000444197	T	0.02050	4.48	3.1	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38897	N	0.001525	T	0.00496	0.0016	N	0.21545	0.675	0.09310	N	1	P	0.39352	0.669	B	0.27380	0.079	T	0.52593	-0.8555	10	0.35671	T	0.21	.	7.1879	0.25809	0.2339:0.0:0.7661:0.0	.	108	Q96KK4	O10C1_HUMAN	T	108	ENSP00000419119:A108T	ENSP00000419119:A108T	A	+	1	0	OR10C1	29516093	0.000000	0.05858	0.019000	0.16419	0.650000	0.38633	0.281000	0.18810	0.632000	0.30432	0.186000	0.17326	GCC		0.607	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			A	29408114	G	A	29408114	3	1	116	1	0	0	0	0	1	0	0	0	10929	1087	38	1	324	1	OR10C1	6	29408114	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	1988100	29408114	141706953	46	31069										
CDC5L	988	hgsc.bcm.edu	37	chr6	44387288	44387288	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tctcaggtgtaactccacagCgacaagttgtacagactcca	8	12	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:44387288C>T	ENST00000371477.3	+	9	1494	c.1195C>T	c.(1195-1197)Cga>Tga	p.R399*		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	399	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AACTCCACAGCGACAAGTTGT	0.428																																																0			6											160	142	148					6																	44387288		2203	4300	6503	44495266	SO:0001587	stop_gained	988			D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1195C>T	6.37:g.44387288C>T	ENSP00000360532:p.Arg399*		44495266	Q76N46|Q99974	Nonsense_Mutation	SNP	ENST00000371477.3	37	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	C	40	8.209698	0.98706	.	.	ENSG00000096401	ENST00000371477	.	.	.	5.57	3.7	0.42460	.	0.050209	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.512	9.7057	0.40214	0.4075:0.4828:0.1097:0.0	.	.	.	.	X	399	.	ENSP00000360532:R399X	R	+	1	2	CDC5L	44495266	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.027000	0.41078	1.312000	0.45043	0.563000	0.77884	CGA		0.428	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			T	44387288	C	T	44387288	4	4	116	1	0	0	0	0	0	1	0	0	3088	760	27	1	1229	1	CDC5L	6	44387288	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	14979174	44387288	126727779	47	31070										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52317601	52317601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tgtcaccccatcagactttgAtcaactcaagcaatttctca	4	13	5	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:52317601A>G	ENST00000371068.5	+	4	792	c.689A>G	c.(688-690)gAt>gGt	p.D230G	EFHC1_ENST00000433625.2_Missense_Mutation_p.D139G|EFHC1_ENST00000538167.1_Missense_Mutation_p.D211G	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	230						axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TCAGACTTTGATCAACTCAAG	0.398																																																0			6											155	148	150					6																	52317601		2203	4300	6503	52425560	SO:0001583	missense	114327			AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.689A>G	6.37:g.52317601A>G	ENSP00000360107:p.Asp230Gly		52425560	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.573303	0.86542	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.70631	-0.28;-0.5;-0.49	6.01	6.01	0.97437	.	0.084947	0.85682	D	0.000000	D	0.82825	0.5121	M	0.83774	2.66	0.49483	D	0.999796	D;P;P	0.89917	1.0;0.928;0.803	D;P;B	0.77557	0.99;0.609;0.41	D	0.85557	0.1225	10	0.72032	D	0.01	-13.4637	16.5205	0.84312	1.0:0.0:0.0:0.0	.	211;139;230	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	G	230;139;211	ENSP00000360107:D230G;ENSP00000416492:D139G;ENSP00000444521:D211G	ENSP00000360107:D230G	D	+	2	0	EFHC1	52425560	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.246000	0.78247	2.299000	0.77371	0.533000	0.62120	GAT		0.398	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		G	52317601	A	G	52317601	3	3	116	1	0	0	0	0	1	0	0	0	4957	333	12	4	713	4	EFHC1	6	52317601	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	7930313	52317601	118797466	48	31071										
LGSN	51557	hgsc.bcm.edu	37	chr6	63995630	63995630	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaagagagttgaggtggggtCaaaatttgactgctgtccct	14	6	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:63995630C>T	ENST00000370657.4	-	3	225	c.192G>A	c.(190-192)ttG>ttA	p.L64L	LGSN_ENST00000370658.5_Silent_p.L64L			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	64					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)	p.L64L(1)		NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GAGGTGGGGTCAAAATTTGAC	0.438																																																1	Substitution - coding silent(1)	skin(1)	6											103	95	97					6																	63995630		2203	4300	6503	64053589	SO:0001819	synonymous_variant	51557			AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.192G>A	6.37:g.63995630C>T			64053589	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Silent	SNP	ENST00000370657.4	37	CCDS4964.1																																																																																				0.438	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		T	63995630	C	T	63995630	2	4	116	1	0	0	0	0	0	0	0	1	8782	825	29	3		3	LGSN	6	63995630	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	11678029	63995630	107119437	49	31072										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76751711	76751711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaaatgcggatctttttgttCgatgctttgccaaatcgaat	8	7	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:76751711C>T	ENST00000369950.3	-	2	389	c.200G>A	c.(199-201)cGa>cAa	p.R67Q	IMPG1_ENST00000369963.3_Intron	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TCTTTTTGTTCGATGCTTTGC	0.363																																					Pancreas(37;839 1141 2599 26037)											0			6											162	154	156					6																	76751711		2203	4300	6503	76808431	SO:0001583	missense	3617			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.200G>A	6.37:g.76751711C>T	ENSP00000358966:p.Arg67Gln		76808431		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	32	5.115017	0.94339	.	.	ENSG00000112706	ENST00000369950	T	0.79554	-1.28	6.07	5.21	0.72293	.	0.125602	0.36591	N	0.002519	D	0.88012	0.6323	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89237	0.3581	9	.	.	.	.	15.5075	0.75753	0.0:0.9339:0.0:0.0661	.	67	Q17R60	IMPG1_HUMAN	Q	67	ENSP00000358966:R67Q	.	R	-	2	0	IMPG1	76808431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.573000	0.53856	1.581000	0.49865	0.655000	0.94253	CGA		0.363	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		T	76751711	C	T	76751711	3	4	116	1	0	0	0	0	1	0	0	0	7749	884	31	1	2257	1	IMPG1	6	76751711	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	12756081	76751711	94363356	50	31073										
IBTK	25998	hgsc.bcm.edu	37	chr6	82922424	82922424	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atcttcctttccttacttacCattttttctgacttagcttc	2	12	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:82922424C>T	ENST00000306270.7	-	13	2840	c.2291G>A	c.(2290-2292)tGt>tAt	p.C764Y	IBTK_ENST00000503631.1_Splice_Site_p.C563Y|IBTK_ENST00000510291.1_Splice_Site_p.C764Y|RNU6-130P_ENST00000411112.1_RNA	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	764					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.C764S(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CCTTACTTACCATTTTTTCTG	0.333																																																1	Substitution - Missense(1)	central_nervous_system(1)	6											180	160	167					6																	82922424		2203	4299	6502	82979143	SO:0001630	splice_region_variant	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2291+1G>A	6.37:g.82922424C>T			82979143	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967938	0.53507	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.70399	-0.48;-0.48;-0.48	5.66	5.66	0.87406	BTB/POZ (1);BTB/POZ fold (2);	0.050926	0.85682	D	0.000000	T	0.72153	0.3425	L	0.28608	0.87	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.998;1.0	D;D;D;D	0.77557	0.987;0.99;0.943;0.99	T	0.68296	-0.5446	9	.	.	.	-14.684	19.6923	0.96007	0.0:1.0:0.0:0.0	.	563;764;764;764	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	Y	764;563;764	ENSP00000305721:C764Y;ENSP00000422762:C563Y;ENSP00000426405:C764Y	.	C	-	2	0	IBTK	82979143	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	6.465000	0.73538	2.830000	0.97506	0.585000	0.79938	TGT		0.333	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	Missense_Mutation	T	82922424	C	T	82922424	5	4	116	1	0	0	0	0	0	0	1	0	7497	608	21	3	1838	3	IBTK	6	82922424	Splice_Site	SNP	C	TCGA-F5-6571-01A-12D-1826-10	6170713	82922424	88192643	51	31074										
UST	10090	hgsc.bcm.edu	37	chr6	149342612	149342612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cgtgctcagtatctacaaagAcccaggtaacttcatttgta	7	10	3	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:149342612A>G	ENST00000367463.4	+	7	1035	c.932A>G	c.(931-933)gAc>gGc	p.D311G		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	311					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		ATCTACAAAGACCCAGGTAAC	0.448																																																0			6											102	96	98					6																	149342612		2203	4300	6503	149384305	SO:0001583	missense	10090			AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.932A>G	6.37:g.149342612A>G	ENSP00000356433:p.Asp311Gly		149384305	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.649963	0.47362	.	.	ENSG00000111962	ENST00000367463	T	0.73575	-0.76	5.64	5.64	0.86602	.	0.208451	0.49916	D	0.000133	T	0.54029	0.1833	L	0.29908	0.895	0.39173	D	0.962632	B	0.19445	0.036	B	0.32393	0.145	T	0.53767	-0.8392	10	0.22706	T	0.39	-19.0774	16.1617	0.81721	1.0:0.0:0.0:0.0	.	311	Q9Y2C2	UST_HUMAN	G	311	ENSP00000356433:D311G	ENSP00000356433:D311G	D	+	2	0	UST	149384305	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.020000	0.64066	2.275000	0.75901	0.528000	0.53228	GAC		0.448	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		G	149342612	A	G	149342612	3	3	116	1	0	0	0	0	1	0	0	0	17133	275	10	4	958	4	UST	6	149342612	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	66420188	149342612	21772455	52	31075										
TAB2	23118	hgsc.bcm.edu	37	chr6	149699662	149699662	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acatggtgtacctccacctgTacttaacagtccacagggaa	8	12	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:149699662T>A	ENST00000367456.1	+	4	1188	c.611T>A	c.(610-612)gTa>gAa	p.V204E	TAB2_ENST00000392282.1_Missense_Mutation_p.V204E|TAB2_ENST00000286332.5_Missense_Mutation_p.V204E|TAB2_ENST00000538427.1_Missense_Mutation_p.V204E|TAB2_ENST00000536230.1_Missense_Mutation_p.V172E			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	204					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						CCTCCACCTGTACTTAACAGT	0.428																																																0			6											123	121	122					6																	149699662		2203	4300	6503	149741355	SO:0001583	missense	23118			AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"mitogen-activated protein kinase kinase kinase 7 interacting protein 2"	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.611T>A	6.37:g.149699662T>A	ENSP00000356426:p.Val204Glu		149741355	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Missense_Mutation	SNP	ENST00000367456.1	37	CCDS5214.1	.	.	.	.	.	.	.	.	.	.	T	0.248	-1.008327	0.02112	.	.	ENSG00000055208	ENST00000536230;ENST00000392282;ENST00000538427;ENST00000367456;ENST00000286332	T;T;T;T;T	0.72835	-0.69;-0.69;-0.68;-0.68;-0.68	5.96	3.58	0.41010	.	0.440056	0.25631	N	0.029342	T	0.28267	0.0698	N	0.08118	0	0.39616	D	0.969967	B;B	0.22604	0.072;0.01	B;B	0.15870	0.008;0.014	T	0.15723	-1.0427	10	0.20519	T	0.43	-10.0088	8.7023	0.34334	0.0:0.0736:0.1406:0.7857	.	172;204	B4DIR9;Q9NYJ8	.;TAB2_HUMAN	E	172;204;204;204;204	ENSP00000443206:V172E;ENSP00000376106:V204E;ENSP00000445752:V204E;ENSP00000356426:V204E;ENSP00000286332:V204E	ENSP00000286332:V204E	V	+	2	0	TAB2	149741355	1.000000	0.71417	1.000000	0.80357	0.069000	0.16628	2.937000	0.48979	2.284000	0.76573	0.528000	0.53228	GTA		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3			A	149699662	T	A	149699662	3	1	116	1	0	0	0	0	1	0	0	0	15535	1638	57	5	617	5	TAB2	6	149699662	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	357050	149699662	21415405	53	31076										
PARK2	5071	hgsc.bcm.edu	37	chr6	161990435	161990435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggagctctttaatcaaggaGttgggacagccagctgttgg	14	7	2	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr6:161990435G>T	ENST00000366898.1	-	8	987	c.885C>A	c.(883-885)aaC>aaA	p.N295K	PARK2_ENST00000338468.3_Missense_Mutation_p.N104K|PARK2_ENST00000366897.1_Missense_Mutation_p.N267K|PARK2_ENST00000366892.1_Missense_Mutation_p.N295K|PARK2_ENST00000366894.1_Missense_Mutation_p.N104K|PARK2_ENST00000366896.1_Missense_Mutation_p.N146K	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	295					adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TAATCAAGGAGTTGGGACAGC	0.428																																																0			6											116	111	113					6																	161990435		2203	4300	6503	161910425	SO:0001583	missense	5071				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.885C>A	6.37:g.161990435G>T	ENSP00000355865:p.Asn295Lys		161910425	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465662	0.43839	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892	D;D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31;-2.31	5.11	4.24	0.50183	.	0.208574	0.40818	N	0.001020	T	0.75369	0.3840	M	0.62723	1.935	0.38422	D	0.946217	P;B;P;P;P	0.47762	0.9;0.012;0.611;0.611;0.856	B;B;B;B;B	0.39840	0.311;0.01;0.221;0.221;0.282	T	0.74269	-0.3720	10	0.33141	T	0.24	.	9.2289	0.37425	0.1665:0.0:0.8335:0.0	.	314;146;267;295;104	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	K	295;267;146;104;104;104;295	ENSP00000355865:N295K;ENSP00000355863:N267K;ENSP00000355862:N146K;ENSP00000355860:N104K;ENSP00000343589:N104K;ENSP00000355858:N295K	ENSP00000343589:N104K	N	-	3	2	PARK2	161910425	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.306000	0.33505	1.162000	0.42619	-0.148000	0.13756	AAC		0.428	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			T	161990435	G	T	161990435	3	4	116	1	0	0	0	0	1	0	0	0	11480	1020	36	2	532	2	PARK2	6	161990435	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	12290773	161990435	9124632	54	31077										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72883967	72883967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	taatcctggaacttcatctgAgaagagccagtatctacaaa	7	9	3	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:72883967A>G	ENST00000339594.4	-	9	3084	c.2746T>C	c.(2746-2748)Tca>Cca	p.S916P	BAZ1B_ENST00000404251.1_Missense_Mutation_p.S916P	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	916					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ACTTCATCTGAGAAGAGCCAG	0.398																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)											0			7											150	132	138					7																	72883967		2203	4300	6503	72521903	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2746T>C	7.37:g.72883967A>G	ENSP00000342434:p.Ser916Pro		72521903	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.421080	0.62622	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.57273	0.41;0.41	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.58538	0.2129	L	0.27053	0.805	0.58432	D	0.999999	D	0.76494	0.999	D	0.80764	0.994	T	0.54111	-0.8342	10	0.20519	T	0.43	-13.4297	14.9817	0.71316	1.0:0.0:0.0:0.0	.	916	Q9UIG0	BAZ1B_HUMAN	P	916	ENSP00000342434:S916P;ENSP00000385442:S916P	ENSP00000342434:S916P	S	-	1	0	BAZ1B	72521903	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.754000	0.91642	2.144000	0.66660	0.460000	0.39030	TCA		0.398	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		G	72883967	A	G	72883967	3	3	116	1	0	0	0	0	1	0	0	0	1331	304	11	4	1749	4	BAZ1B	7	72883967	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10		72883967	86254696	55	31078										
PCLO	27445	hgsc.bcm.edu	37	chr7	82584540	82584540	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tctcctcagcactttttaacGccttttggctaccttctttc	4	14	3	0	rs375287995		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:82584540G>A	ENST00000333891.9	-	5	6066	c.5729C>T	c.(5728-5730)gCg>gTg	p.A1910V	PCLO_ENST00000423517.2_Missense_Mutation_p.A1910V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ACTTTTTAACGCCTTTTGGCT	0.343													G|||	1	0.000199681	0	0	5008	,	,		19185	0		0.001	False		,,,				2504	0															0			7						G	VAL/ALA,VAL/ALA	0,3748		0,0,1874	57	56	56		5729,5729	4.3	0.6	7		56	3,8193		0,3,4095	no	missense,missense	PCLO	NM_033026.5,NM_014510.2	64,64	0,3,5969	AA,AG,GG		0.0366,0.0,0.0251	benign,benign	1910/5143,1910/4936	82584540	3,11941	1874	4098	5972	82422476	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5729C>T	7.37:g.82584540G>A	ENSP00000334319:p.Ala1910Val		82422476		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	4.492	0.091311	0.08632	0.0	3.66E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16073	2.38;2.37	5.38	4.3	0.51218	.	.	.	.	.	T	0.15565	0.0375	L	0.44542	1.39	0.09310	N	1	B;B	0.14805	0.011;0.011	B;B	0.09377	0.004;0.004	T	0.06552	-1.0820	9	0.87932	D	0	.	8.3819	0.32477	0.136:0.1465:0.7175:0.0	.	1910;1910	Q9Y6V0-5;Q9Y6V0-6	.;.	V	1841;1910;1910	ENSP00000334319:A1910V;ENSP00000388393:A1910V	ENSP00000334319:A1910V	A	-	2	0	PCLO	82422476	0.076000	0.21285	0.623000	0.29173	0.733000	0.41908	2.027000	0.41078	2.517000	0.84864	0.655000	0.94253	GCG		0.343	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82584540	G	A	82584540	3	1	116	1	0	0	0	0	1	0	0	0	11614	1087	38	1	9800	1	PCLO	7	82584540	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	9700573	82584540	76554123	56	31079										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98515222	98515222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggtcagccaaggcctcaggAcgctggagctgtgtgtggac	16	10	2	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:98515222A>G	ENST00000359863.4	+	20	2751	c.2542A>G	c.(2542-2544)Acg>Gcg	p.T848A	TRRAP_ENST00000446306.3_Missense_Mutation_p.T847A|TRRAP_ENST00000355540.3_Missense_Mutation_p.T848A	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	848					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGGCCTCAGGACGCTGGAGCT	0.577																																																0			7											114	92	100					7																	98515222		2203	4300	6503	98353158	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.2542A>G	7.37:g.98515222A>G	ENSP00000352925:p.Thr848Ala		98353158	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.878176	0.91664	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.60171	0.21;0.21	5.6	5.6	0.85130	Armadillo-like helical (1);Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	T	0.82190	0.4983	M	0.93978	3.48	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.99;0.996	D	0.87140	0.2202	10	0.87932	D	0	.	15.7903	0.78350	1.0:0.0:0.0:0.0	.	848;562;848	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	A	848;848;846	ENSP00000352925:T848A;ENSP00000347733:T848A	ENSP00000347733:T848A	T	+	1	0	TRRAP	98353158	1.000000	0.71417	0.996000	0.52242	0.882000	0.50991	9.339000	0.96797	2.139000	0.66308	0.379000	0.24179	ACG		0.577	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98515222	A	G	98515222	3	3	116	1	0	0	0	0	1	0	0	0	16641	275	10	4	2616	4	TRRAP	7	98515222	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	15930682	98515222	60623441	57	31080										
BRAF	673	hgsc.bcm.edu	37	chr7	140482872	140482872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gacttcctttctcgctgaggTcctggagatttctgtaaggc	11	10	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:140482872T>C	ENST00000288602.6	-	10	1323	c.1263A>G	c.(1261-1263)ggA>ggG	p.G421G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	421					activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CTCGCTGAGGTCCTGGAGATT	0.413		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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											83	77	79					7																	140482872		2203	4300	6503	140129341	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1263A>G	7.37:g.140482872T>C			140129341	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454849	0.26161	.	.	ENSG00000157764	ENST00000496384	.	.	.	5.83	2.1	0.27182	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22556	-1.0213	4	.	.	.	.	1.8921	0.03250	0.1205:0.2654:0.1251:0.489	.	.	.	.	G	29	.	.	D	-	2	0	BRAF	140129341	0.441000	0.25626	1.000000	0.80357	0.998000	0.95712	-0.363000	0.07593	0.115000	0.18071	0.533000	0.62120	GAC		0.413	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140482872	T	C	140482872	2	2	116	1	0	0	0	0	0	0	0	1	1499	1654	58	4		4	BRAF	7	140482872	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	41967650	140482872	18655791	58	31081										
ZNF425	155054	hgsc.bcm.edu	37	chr7	148801353	148801353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gctctgtgagatgcgcgcgtCggcggaaactgcggccgcac	16	13	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:148801353C>T	ENST00000378061.2	-	4	1742	c.1610G>A	c.(1609-1611)cGa>cAa	p.R537Q		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	537					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ATGCGCGCGTCGGCGGAAACT	0.612																																																0			7											36	34	35					7																	148801353		2203	4300	6503	148432286	SO:0001583	missense	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1610G>A	7.37:g.148801353C>T	ENSP00000367300:p.Arg537Gln		148432286	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	8.543	0.873758	0.17322	.	.	ENSG00000204947	ENST00000378061	T	0.15017	2.46	3.02	-0.383	0.12477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06872	0.0175	N	0.17345	0.48	0.09310	N	1	B	0.27791	0.189	B	0.12837	0.008	T	0.39840	-0.9594	9	0.10111	T	0.7	.	4.1062	0.10038	0.5432:0.3244:0.0:0.1324	.	537	Q6IV72	ZN425_HUMAN	Q	537	ENSP00000367300:R537Q	ENSP00000367300:R537Q	R	-	2	0	ZNF425	148432286	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-3.430000	0.00473	0.124000	0.18369	0.655000	0.94253	CGA		0.612	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148801353	C	T	148801353	3	4	116	1	0	0	0	0	1	0	0	0	17938	884	31	1	652	1	ZNF425	7	148801353	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	8318481	148801353	10337310	59	31082										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154760440	154760440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cagggcatgctgctgctgaaAgggctggagctgctgctgag	17	9	0	2	rs550122265	byFrequency	TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr7:154760440A>G	ENST00000404141.1	-	7	1625	c.1471T>C	c.(1471-1473)Ttt>Ctt	p.F491L	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.F491L			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	491	Gln-rich.			Missing (in Ref. 4; AAB91434). {ECO:0000305}.	adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		tgctgctgaaagggctggagc	0.597																																																0			7											31	37	35					7																	154760440		1807	3276	5083	154391373	SO:0001583	missense	22976			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1471T>C	7.37:g.154760440A>G	ENSP00000384048:p.Phe491Leu		154391373	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	A	3.265	-0.150294	0.06585	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000323199	D;D	0.89485	-2.52;-2.52	4.66	3.51	0.40186	.	0.000000	0.36066	U	0.002815	T	0.73024	0.3534	N	0.11201	0.11	0.24176	N	0.9956	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.55780	-0.8087	10	0.10377	T	0.69	-5.7397	6.5946	0.22666	0.7961:0.0:0.2039:0.0	.	444;400;457;491	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	L	491;491;444	ENSP00000384048:F491L;ENSP00000380376:F491L	ENSP00000319149:F444L	F	-	1	0	PAXIP1	154391373	0.974000	0.33945	0.106000	0.21319	0.868000	0.49771	2.004000	0.40854	0.645000	0.30675	0.528000	0.53228	TTT		0.597	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		G	154760440	A	G	154760440	3	3	116	1	0	0	0	0	1	0	0	0	11518	72	3	4	1798	4	PAXIP1	7	154760440	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	5959087	154760440	4378223	60	31083										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2026918	2026918	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaggaaggtcttacatattcCgagtgagggcagtgaacagt	13	6	1	2	rs143448287		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:2026918C>T	ENST00000262113.4	+	12	1507	c.1366C>T	c.(1366-1368)Cga>Tga	p.R456*	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	456	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R456*(2)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TTACATATTCCGAGTGAGGGC	0.517													C|||	1	0.000199681	0	0	5008	,	,		17025	0.001		0	False		,,,				2504	0															2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	8						C	stop/ARG	0,4406		0,0,2203	160	173	169		1366	4.7	1	8	dbSNP_134	169	3,8597	3.0+/-9.4	0,3,4297	yes	stop-gained	MYOM2	NM_003970.2		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		456/1466	2026918	3,13003	2203	4300	6503	2014325	SO:0001587	stop_gained	9172				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.1366C>T	8.37:g.2026918C>T	ENSP00000262113:p.Arg456*		2014325	Q7Z3Y2	Nonsense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	38	7.154352	0.98099	0.0	3.49E-4	ENSG00000036448	ENST00000262113	.	.	.	4.71	4.71	0.59529	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.0367	0.89305	0.0:1.0:0.0:0.0	.	.	.	.	X	456	.	ENSP00000262113:R456X	R	+	1	2	MYOM2	2014325	1.000000	0.71417	1.000000	0.80357	0.341000	0.28922	4.548000	0.60718	2.308000	0.77769	0.561000	0.74099	CGA		0.517	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2026918	C	T	2026918	4	4	116	1	0	0	0	0	0	1	0	0	10122	644	23	1	1408	1	MYOM2	8	2026918	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10		2026918	144337104	61	31084										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68102916	68102916	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gagacatatcctgccattgaAgatgacgtcctccctccacc	7	15	0	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:68102916A>G	ENST00000262210.5	+	27	3268	c.3237A>G	c.(3235-3237)gaA>gaG	p.E1079E	CSPP1_ENST00000521168.1_3'UTR|CSPP1_ENST00000412460.1_Silent_p.E734E|ARFGEF1_ENST00000520381.1_Intron	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1114					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CTGCCATTGAAGATGACGTCC	0.488																																																0			8											119	115	116					8																	68102916		1948	4138	6086	68265470	SO:0001819	synonymous_variant	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3237A>G	8.37:g.68102916A>G			68265470	A6ND63|Q70F00|Q8TBC1	Silent	SNP	ENST00000262210.5	37	CCDS43744.1																																																																																				0.488	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68102916	A	G	68102916	2	3	116	1	0	0	0	0	0	0	0	1	3968	69	3	4		4	CSPP1	8	68102916	Silent	SNP	A	TCGA-F5-6571-01A-12D-1826-10	66075998	68102916	78261106	62	31085										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70978520	70978520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gctctgtgacctgaaggctcAcaggaatatccagaaatttc	9	10	2	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:70978520A>G	ENST00000276594.2	-	5	1334	c.1133T>C	c.(1132-1134)gTg>gCg	p.V378A		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	378					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			CTGAAGGCTCACAGGAATATC	0.517																																					NSCLC(129;99 1813 5906 40656 46114)											0			8											70	73	72					8																	70978520		2203	4300	6503	71141074	SO:0001583	missense	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1133T>C	8.37:g.70978520A>G	ENSP00000276594:p.Val378Ala		71141074	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959459	0.74016	.	.	ENSG00000147596	ENST00000276594	T	0.11604	2.76	5.46	5.46	0.80206	.	0.432075	0.24796	N	0.035534	T	0.06872	0.0175	N	0.19112	0.55	0.31667	N	0.644845	P	0.39665	0.682	B	0.27380	0.079	T	0.09684	-1.0663	10	0.34782	T	0.22	-2.0433	15.5356	0.76001	1.0:0.0:0.0:0.0	.	378	Q9GZV8	PRD14_HUMAN	A	378	ENSP00000276594:V378A	ENSP00000276594:V378A	V	-	2	0	PRDM14	71141074	0.999000	0.42202	0.528000	0.27938	0.486000	0.33341	4.758000	0.62220	2.070000	0.61991	0.459000	0.35465	GTG		0.517	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			G	70978520	A	G	70978520	3	3	116	1	0	0	0	0	1	0	0	0	12489	159	6	4	598	4	PRDM14	8	70978520	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	2875604	70978520	75385502	63	31086										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101299932	101299932	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cttaaatattgtcgtaagcaAtccacacaagatctgtgatg	7	8	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:101299932A>G	ENST00000519449.1	-	3	787	c.471T>C	c.(469-471)gaT>gaC	p.D157D	RNF19A_ENST00000341084.2_Silent_p.D157D	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	157					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	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)			GTCGTAAGCAATCCACACAAG	0.378																																																0			8											107	109	108					8																	101299932		2203	4300	6503	101369108	SO:0001819	synonymous_variant	25897			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.471T>C	8.37:g.101299932A>G			101369108	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Silent	SNP	ENST00000519449.1	37	CCDS6286.1																																																																																				0.378	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		G	101299932	A	G	101299932	2	3	116	1	0	0	0	0	0	0	0	1	13507	98	4	4		4	RNF19A	8	101299932	Silent	SNP	A	TCGA-F5-6571-01A-12D-1826-10	30321412	101299932	45064090	64	31087										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110474073	110474073	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aagtgaccaatttggaggctGcgttatgtttcatgctcctg	11	8	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:110474073G>T	ENST00000378402.5	+	48	7423	c.7319G>T	c.(7318-7320)tGc>tTc	p.C2440F		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2440					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.C2442S(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTTGGAGGCTGCGTTATGTTT	0.398										HNSCC(38;0.096)																																						1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	8											71	75	74					8																	110474073		2059	4214	6273	110543249	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.7319G>T	8.37:g.110474073G>T	ENSP00000367655:p.Cys2440Phe		110543249	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194877	0.78902	.	.	ENSG00000205038	ENST00000378402	D	0.85484	-1.99	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.89543	0.6745	M	0.72479	2.2	0.50467	D	0.999874	P	0.49961	0.93	P	0.54026	0.74	D	0.88760	0.3256	10	0.41790	T	0.15	.	17.2064	0.86920	0.0:0.0:1.0:0.0	.	2440	Q86WI1	PKHL1_HUMAN	F	2440	ENSP00000367655:C2440F	ENSP00000367655:C2440F	C	+	2	0	PKHD1L1	110543249	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	8.378000	0.90144	2.664000	0.90586	0.650000	0.86243	TGC		0.398	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110474073	G	T	110474073	3	4	116	1	0	0	0	0	1	0	0	0	12003	1319	46	2	7509	2	PKHD1L1	8	110474073	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	9174141	110474073	35889949	65	31088										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126079939	126079939	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggtccttgatttgacgaagGcgtttgttgtttgggtcaca	13	6	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:126079939G>T	ENST00000318410.7	-	10	1522	c.1173C>A	c.(1171-1173)cgC>cgA	p.R391R	KIAA0196_ENST00000517845.1_Silent_p.R243R	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	391					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTTGACGAAGGCGTTTGTTGT	0.363																																																0			8											197	182	187					8																	126079939		2203	4300	6503	126149121	SO:0001819	synonymous_variant	9897				CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.1173C>A	8.37:g.126079939G>T			126149121	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	G	7.354	0.623408	0.14193	.	.	ENSG00000164961	ENST00000523273	.	.	.	5.61	3.72	0.42706	.	.	.	.	.	T	0.48466	0.1501	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42982	-0.9419	4	.	.	.	-10.1884	4.7219	0.12922	0.2083:0.3313:0.4604:0.0	.	.	.	.	D	8	.	.	A	-	2	0	KIAA0196	126149121	0.397000	0.25270	1.000000	0.80357	0.680000	0.39746	-0.244000	0.08903	1.382000	0.46385	-0.339000	0.08088	GCC		0.363	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		T	126079939	G	T	126079939	2	4	116	1	0	0	0	0	0	0	0	1	8182	1190	42	2		2	KIAA0196	8	126079939	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	15605866	126079939	20284083	66	31089										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139675948	139675948	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttatttaaagcatactgtacCggggatcctttgtctcctgg	9	9	1	0	rs371517268		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr8:139675948C>T	ENST00000303045.6	-	42	3632	c.3186G>A	c.(3184-3186)ccG>ccA	p.P1062P	COL22A1_ENST00000435777.1_Splice_Site_p.P1042P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1062	Collagen-like 9.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CATACTGTACCGGGGATCCTT	0.423										HNSCC(7;0.00092)																																						0			8						C		0,4406		0,0,2203	127	127	127		3186	4.5	1	8		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	COL22A1	NM_152888.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1062/1627	139675948	1,13005	2203	4300	6503	139745130	SO:0001630	splice_region_variant	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3186+1G>A	8.37:g.139675948C>T			139745130	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																				0.423	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Silent	T	139675948	C	T	139675948	5	4	116	1	0	0	0	0	0	0	1	0	3687	666	23	1	1790	1	COL22A1	8	139675948	Splice_Site	SNP	C	TCGA-F5-6571-01A-12D-1826-10	13596009	139675948	6688074	67	31090										
GDA	9615	hgsc.bcm.edu	37	chr9	74860096	74860096	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atggtgagattggaaactttGaagtgggcaaggaatttgat	14	2	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:74860096G>T	ENST00000358399.3	+	12	1261	c.1168G>T	c.(1168-1170)Gaa>Taa	p.E390*	GDA_ENST00000376986.1_Nonsense_Mutation_p.E312*|GDA_ENST00000376989.3_Nonsense_Mutation_p.E329*|GDA_ENST00000545168.1_Nonsense_Mutation_p.E316*|GDA_ENST00000238018.4_Nonsense_Mutation_p.E390*	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	390					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)	p.E390K(1)		central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		TGGAAACTTTGAAGTGGGCAA	0.448																																																1	Substitution - Missense(1)	ovary(1)	9											208	203	205					9																	74860096		2203	4300	6503	74049916	SO:0001587	stop_gained	9615			AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.1168G>T	9.37:g.74860096G>T	ENSP00000351170:p.Glu390*		74049916	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Nonsense_Mutation	SNP	ENST00000358399.3	37	CCDS6641.1	.	.	.	.	.	.	.	.	.	.	G	39	7.774242	0.98483	.	.	ENSG00000119125	ENST00000545168;ENST00000238018;ENST00000376989;ENST00000376986;ENST00000358399;ENST00000436438	.	.	.	5.3	5.3	0.74995	.	0.046040	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-13.9582	16.2414	0.82409	0.0:0.0:1.0:0.0	.	.	.	.	X	316;390;329;312;390;98	.	ENSP00000238018:E390X	E	+	1	0	GDA	74049916	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.831000	0.69330	2.633000	0.89246	0.650000	0.86243	GAA		0.448	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			T	74860096	G	T	74860096	4	4	116	1	0	0	0	0	0	1	0	0	6326	1291	45	2	1214	2	GDA	9	74860096	Nonsense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		74860096	66353335	68	31091										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88937965	88937965	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcttcatacttagcagcttcGcctaactcatcatcctcttc	3	15	5	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:88937965G>T	ENST00000375963.3	-	13	2872	c.2700C>A	c.(2698-2700)ggC>ggA	p.G900G	ZCCHC6_ENST00000375961.2_Silent_p.G900G|ZCCHC6_ENST00000277141.6_Silent_p.G189G|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375960.2_Silent_p.G777G	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	900	Glu-rich.			G -> V (in Ref. 1; CAI45944). {ECO:0000305}.	RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.G900G(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						TAGCAGCTTCGCCTAACTCAT	0.423																																																2	Substitution - coding silent(2)	ovary(1)|endometrium(1)	9											173	147	156					9																	88937965		2203	4300	6503	88127785	SO:0001819	synonymous_variant	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2700C>A	9.37:g.88937965G>T			88127785	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Silent	SNP	ENST00000375963.3	37	CCDS35057.1																																																																																				0.423	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		T	88937965	G	T	88937965	2	4	116	1	0	0	0	0	0	0	0	1	17631	1074	38	2		2	ZCCHC6	9	88937965	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	14077869	88937965	52275466	69	31092										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90499929	90499929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gcctgctaaggcccaccagcCgcatgggaaatgcatgcaag	12	13	0	0	rs577973609		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:90499929C>T	ENST00000325643.5	+	4	593	c.527C>T	c.(526-528)cCg>cTg	p.P176L		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	176	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCCCACCAGCCGCATGGGAAA	0.642													.|||	1	0.000199681	8e-04	0	5008	,	,		17324	0		0	False		,,,				2504	0															0			9											65	68	67					9																	90499929		2203	4300	6503	89689749	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.527C>T	9.37:g.90499929C>T	ENSP00000322640:p.Pro176Leu		89689749	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	.	4.199	0.035719	0.08148	.	.	ENSG00000177992	ENST00000325643	T	0.03889	3.77	2.35	-1.17	0.09648	.	0.943104	0.08694	N	0.907424	T	0.02304	0.0071	N	0.19112	0.55	0.09310	N	1	P	0.38420	0.63	B	0.31946	0.138	T	0.43426	-0.9392	10	0.11794	T	0.64	.	3.8908	0.09117	0.2082:0.5116:0.0:0.2803	.	176	Q6ZUB1	CI079_HUMAN	L	176	ENSP00000322640:P176L	ENSP00000322640:P176L	P	+	2	0	C9orf79	89689749	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.704000	0.05058	-0.627000	0.05589	-1.338000	0.01255	CCG		0.642	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90499929	C	T	90499929	3	4	116	1	0	0	0	0	1	0	0	0	2503	652	23	1	541	1	C9orf79	9	90499929	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1561964	90499929	50713502	70	31093										
TEX10	54881	hgsc.bcm.edu	37	chr9	103082640	103082640	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggatgacatgaggaactccTcgaaggctctgaagccaagt	12	9	1	3	rs557947404		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:103082640T>C	ENST00000374902.4	-	11	2285	c.2109A>G	c.(2107-2109)cgA>cgG	p.R703R	TEX10_ENST00000535814.1_Silent_p.R706R	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	703						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GAGGAACTCCTCGAAGGCTCT	0.388													T|||	1	0.000199681	0	0	5008	,	,		16260	0		0.001	False		,,,				2504	0															0			9											63	56	59					9																	103082640		2203	4300	6503	102122461	SO:0001819	synonymous_variant	54881			AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.2109A>G	9.37:g.103082640T>C			102122461	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	37	CCDS6748.1																																																																																				0.388	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		C	103082640	T	C	103082640	2	2	116	1	0	0	0	0	0	0	0	1	15811	1538	54	4		4	TEX10	9	103082640	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	12582711	103082640	38130791	71	31094										
GOLGA1	2800	hgsc.bcm.edu	37	chr9	127644214	127644214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tctcccggacttcgaagagcTcattatcgggtctgattttc	9	11	3	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:127644214T>C	ENST00000373555.4	-	21	2318	c.1985A>G	c.(1984-1986)gAg>gGg	p.E662G		NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	662					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)		p.E662G(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						TTCGAAGAGCTCATTATCGGG	0.507																																																1	Substitution - Missense(1)	ovary(1)	9											110	107	108					9																	127644214		2203	4300	6503	126684035	SO:0001583	missense	2800			U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"golgi autoantigen, golgin subfamily a, 1"			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.1985A>G	9.37:g.127644214T>C	ENSP00000362656:p.Glu662Gly		126684035	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	37	CCDS6860.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937736	0.73557	.	.	ENSG00000136935	ENST00000373555	T	0.27104	1.69	5.81	5.81	0.92471	.	0.142200	0.31747	N	0.007140	T	0.29190	0.0726	L	0.46157	1.445	0.58432	D	0.999997	P	0.46395	0.877	B	0.43360	0.417	T	0.03473	-1.1033	10	0.66056	D	0.02	-19.6737	15.333	0.74229	0.0:0.0:0.0:1.0	.	662	Q92805	GOGA1_HUMAN	G	662	ENSP00000362656:E662G	ENSP00000362656:E662G	E	-	2	0	GOLGA1	126684035	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.476000	0.66793	2.216000	0.71823	0.533000	0.62120	GAG		0.507	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077		C	127644214	T	C	127644214	3	2	116	1	0	0	0	0	1	0	0	0	6571	1551	54	4	330	4	GOLGA1	9	127644214	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	24561574	127644214	13569217	72	31095										
NUP214	8021	hgsc.bcm.edu	37	chr9	134073620	134073620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ggtccctgatgccaggacggAggcagtaccacctgcttcct	12	14	0	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr9:134073620A>G	ENST00000359428.5	+	29	4883	c.4739A>G	c.(4738-4740)gAg>gGg	p.E1580G	NUP214_ENST00000483497.2_Missense_Mutation_p.E406G|NUP214_ENST00000411637.2_Missense_Mutation_p.E1570G|NUP214_ENST00000451030.1_Missense_Mutation_p.E1581G			P35658	NU214_HUMAN	nucleoporin 214kDa	1580	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GCCAGGACGGAGGCAGTACCA	0.577			T	"DEK, SET, ABL1"	"AML, T-ALL"																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0			9											75	78	77					9																	134073620		2203	4300	6503	133063441	SO:0001583	missense	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4739A>G	9.37:g.134073620A>G	ENSP00000352400:p.Glu1580Gly		133063441	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.719663	0.68844	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.54279	1.33;1.61;1.61;1.61;0.58	5.44	5.44	0.79542	.	0.000000	0.45126	D	0.000398	T	0.51126	0.1656	N	0.08118	0	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.997;0.994;0.994;0.994;0.994	T	0.48592	-0.9022	10	0.48119	T	0.1	-16.5007	11.0644	0.47966	0.8448:0.1552:0.0:0.0	.	406;1009;1174;1570;1580	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	G	1580;1570;1581;1559;1174;1009;406;357;357	ENSP00000352400:E1580G;ENSP00000396576:E1570G;ENSP00000405014:E1581G;ENSP00000436793:E406G;ENSP00000435364:E357G	ENSP00000352400:E1580G	E	+	2	0	NUP214	133063441	0.660000	0.27420	0.100000	0.21137	0.155000	0.21991	2.377000	0.44300	2.070000	0.61991	0.379000	0.24179	GAG		0.577	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134073620	A	G	134073620	3	3	116	1	0	0	0	0	1	0	0	0	10793	304	11	4	4853	4	NUP214	9	134073620	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	6429406	134073620	7139811	73	31096										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3202103	3202103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gatctgtagcaaatgaatccGggccacatgttatctggaat	10	8	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:3202103G>A	ENST00000224949.4	-	9	978	c.944C>T	c.(943-945)cCg>cTg	p.P315L	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.P315L|PITRM1_ENST00000380994.1_5'Flank|PITRM1_ENST00000451104.2_Missense_Mutation_p.P283L|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	315					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AAATGAATCCGGGCCACATGT	0.433																																																0			10											169	165	166					10																	3202103		1055	2149	3204	3192103	SO:0001583	missense	10531			AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.944C>T	10.37:g.3202103G>A	ENSP00000224949:p.Pro315Leu		3192103	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	g	6.279	0.419594	0.11928	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.08807	3.05;3.05;3.05	6.17	5.27	0.74061	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.104471	0.64402	D	0.000003	T	0.05181	0.0138	N	0.17379	0.485	0.52099	D	0.99994	B;B;B;B;B;B	0.28258	0.002;0.01;0.205;0.123;0.123;0.123	B;B;B;B;B;B	0.30029	0.001;0.009;0.105;0.11;0.11;0.11	T	0.41998	-0.9477	10	0.11485	T	0.65	-31.4691	8.966	0.35877	0.0966:0.149:0.7544:0.0	.	308;283;315;315;315;308	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	L	315;308;315;283	ENSP00000224949:P315L;ENSP00000370377:P315L;ENSP00000401201:P283L	ENSP00000224949:P315L	P	-	2	0	PITRM1	3192103	1.000000	0.71417	0.913000	0.36048	0.194000	0.23727	3.817000	0.55668	1.615000	0.50252	0.655000	0.94253	CCG		0.433	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			A	3202103	G	A	3202103	3	1	116	1	0	0	0	0	1	0	0	0	11984	1116	39	1	2245	1	PITRM1	10	3202103	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		3202103	132332644	74	31097										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31791299	31791299	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aagatgatgaatgcgagtcaGatgcagaaaatgagcaaaac	11	5	1	6			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:31791299G>T	ENST00000320985.10	+	4	453	c.343G>T	c.(343-345)Gat>Tat	p.D115Y	ZEB1_ENST00000446923.2_Missense_Mutation_p.D99Y|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Missense_Mutation_p.D48Y|ZEB1_ENST00000560721.2_Missense_Mutation_p.D95Y|ZEB1_ENST00000361642.5_Missense_Mutation_p.D116Y			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	115					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				ATGCGAGTCAGATGCAGAAAA	0.348																																					Ovarian(40;423 959 14296 36701 49589)											0			10											107	98	101					10																	31791299		2203	4300	6503	31831305	SO:0001583	missense	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.343G>T	10.37:g.31791299G>T	ENSP00000319248:p.Asp115Tyr		31831305	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.464381|4.464381	0.84425|0.84425	.|.	.|.	ENSG00000148516|ENSG00000148516	ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000424869;ENST00000446923|ENST00000543514	D;D;D;D;D|.	0.82526|.	-1.62;-1.62;-1.62;-1.62;-1.62|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.099877|.	0.44285|.	D|.	0.000462|.	T|T	0.78091|0.78091	0.4229|0.4229	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.999;1.0;1.0;0.999;1.0;1.0|.	D;D;D;D;D;D|.	0.80764|.	0.993;0.994;0.994;0.971;0.994;0.994|.	T|T	0.78768|0.78768	-0.2075|-0.2075	10|6	0.66056|0.87932	D|D	0.02|0	-26.901|-26.901	20.3129|20.3129	0.98645|0.98645	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	48;99;115;95;116;115|.	F5H4I8;E9PCM7;B2RBI8;Q5VZ84;Q2KJ05;P37275|.	.;.;.;.;.;ZEB1_HUMAN|.	Y|H	115;116;115;48;115;95;116;99|6	ENSP00000354487:D116Y;ENSP00000444891:D48Y;ENSP00000319248:D115Y;ENSP00000415961:D116Y;ENSP00000391612:D99Y|.	ENSP00000319248:D115Y|ENSP00000443742:Q6H	D|Q	+|+	1|3	0|2	ZEB1|ZEB1	31831305|31831305	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.404000|7.404000	0.79996|0.79996	2.800000|2.800000	0.96347|0.96347	0.650000|0.650000	0.86243|0.86243	GAT|CAG		0.348	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31791299	G	T	31791299	3	4	116	1	0	0	0	0	1	0	0	0	17662	942	33	2	371	2	ZEB1	10	31791299	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	28589196	31791299	103743448	75	31098										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37431116	37431116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cacctgtaaagactggatgcGtggcaagagtaacatctaat	10	8	1	2	rs373496322		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:37431116G>A	ENST00000602533.1	+	7	1222	c.1123G>A	c.(1123-1125)Gtg>Atg	p.V375M	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.V375M|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.V375M			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	431					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						GACTGGATGCGTGGCAAGAGT	0.388																																																0			10						G	MET/VAL	1,3737		0,1,1868	75	75	75		1123	0.1	0	10		75	0,8230		0,0,4115	no	missense	ANKRD30A	NM_052997.2	21	0,1,5983	AA,AG,GG		0.0,0.0268,0.0084	benign	375/1342	37431116	1,11967	1869	4115	5984	37471122	SO:0001583	missense	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1123G>A	10.37:g.37431116G>A	ENSP00000473551:p.Val375Met		37471122	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	6.416	0.444848	0.12164	2.68E-4	0.0	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.50813	0.8;0.73	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.30008	0.0751	L	0.40543	1.245	0.09310	N	1	P	0.47841	0.901	B	0.34779	0.189	T	0.15492	-1.0435	8	0.51188	T	0.08	.	.	.	.	.	431	Q9BXX3	AN30A_HUMAN	M	375	ENSP00000354432:V375M;ENSP00000363792:V375M	ENSP00000354432:V375M	V	+	1	0	ANKRD30A	37471122	0.003000	0.15002	0.013000	0.15412	0.013000	0.08279	-0.895000	0.04118	0.132000	0.18615	0.134000	0.15878	GTG		0.388	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37431116	G	A	37431116	3	1	116	1	0	0	0	0	1	0	0	0	658	1145	40	1	1149	1	ANKRD30A	10	37431116	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	5639817	37431116	98103631	76	31099										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49395321	49395321	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aggcactcttcagctgctccCggccagtgcaggggctgccg	14	15	2	0	rs142488456		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:49395321C>A	ENST00000374201.3	-	17	2482	c.2180G>T	c.(2179-2181)cGg>cTg	p.R727L	FRMPD2_ENST00000407470.4_Missense_Mutation_p.R695L|FRMPD2_ENST00000305531.3_Missense_Mutation_p.R702L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	727			R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CAGCTGCTCCCGGCCAGTGCA	0.572																																																0			10											59	54	56					10																	49395321		2203	4300	6503	49065327	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2180G>T	10.37:g.49395321C>A	ENSP00000363317:p.Arg727Leu		49065327	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	C	8.958	0.969834	0.18659	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.64438	-0.05;-0.09;-0.1	4.06	-8.12	0.01078	.	.	.	.	.	T	0.41236	0.1150	L	0.27053	0.805	0.09310	N	1	B;B;B	0.26318	0.146;0.007;0.146	B;B;B	0.22601	0.04;0.003;0.04	T	0.24584	-1.0156	9	0.30078	T	0.28	.	10.3274	0.43801	0.0:0.1389:0.186:0.6751	.	702;727;695	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	L	727;702;695	ENSP00000363317:R727L;ENSP00000307079:R702L;ENSP00000384339:R695L	ENSP00000307079:R702L	R	-	2	0	FRMPD2	49065327	0.000000	0.05858	0.000000	0.03702	0.855000	0.48748	-4.405000	0.00239	-3.053000	0.00259	-0.123000	0.14984	CGG		0.572	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		A	49395321	C	A	49395321	3	1	116	1	0	0	0	0	1	0	0	0	6077	652	23	2	1801	2	FRMPD2	10	49395321	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	11964205	49395321	86139426	77	31100										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61029686	61029686	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	actgctgagtgctgggtggaGatggggctgactcggggtct	19	7	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:61029686G>A	ENST00000373868.2	-	7	863	c.776C>T	c.(775-777)tCt>tTt	p.S259F	FAM13C_ENST00000442566.3_Missense_Mutation_p.S280F|FAM13C_ENST00000373867.3_Missense_Mutation_p.S176F|FAM13C_ENST00000435852.2_Missense_Mutation_p.S259F|FAM13C_ENST00000419214.2_Missense_Mutation_p.S259F|FAM13C_ENST00000422313.2_Missense_Mutation_p.S259F|FAM13C_ENST00000277705.6_Missense_Mutation_p.S280F|FAM13C_ENST00000468840.2_Missense_Mutation_p.S176F	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	259										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCTGGGTGGAGATGGGGCTGA	0.428																																																0			10											77	71	73					10																	61029686		2203	4300	6503	60699692	SO:0001583	missense	220965			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.776C>T	10.37:g.61029686G>A	ENSP00000362975:p.Ser259Phe		60699692	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.777731	0.90195	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000468696	T;T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;0.09;-1.2;-1.2;-1.2;-1.2	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	D	0.88160	0.6362	M	0.71581	2.175	0.53688	D	0.999975	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.999	D	0.88255	0.2919	10	0.62326	D	0.03	-14.0136	19.7156	0.96119	0.0:0.0:1.0:0.0	.	259;176;259;259;259	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	F	176;259;280;280;259;176;259;259;37	ENSP00000362974:S176F;ENSP00000362975:S259F;ENSP00000395661:S280F;ENSP00000277705:S280F;ENSP00000391993:S259F;ENSP00000423896:S176F;ENSP00000392302:S259F;ENSP00000400241:S259F;ENSP00000445068:S37F	ENSP00000277705:S280F	S	-	2	0	FAM13C	60699692	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.954000	0.93051	2.658000	0.90341	0.655000	0.94253	TCT		0.428	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			A	61029686	G	A	61029686	3	1	116	1	0	0	0	0	1	0	0	0	5470	942	33	3	1013	3	FAM13C	10	61029686	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	11634365	61029686	74505061	78	31101										
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74103215	74103215	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gccttcttcaggtcctcatcCgaggcccctctgctcacccc	7	20	5	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:74103215C>T	ENST00000444643.2	-	3	698	c.366G>A	c.(364-366)tcG>tcA	p.S122S	DNAJB12_ENST00000461919.1_5'UTR|DNAJB12_ENST00000394903.2_Silent_p.S156S|DNAJB12_ENST00000338820.3_Silent_p.S156S			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	122	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GGTCCTCATCCGAGGCCCCTC	0.562																																																0			10											133	114	121					10																	74103215		2203	4300	6503	73773221	SO:0001819	synonymous_variant	54788			AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.366G>A	10.37:g.74103215C>T			73773221	B7Z7I3|Q9H6H0	Silent	SNP	ENST00000444643.2	37																																																																																					0.562	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			T	74103215	C	T	74103215	2	4	116	1	0	0	0	0	0	0	0	1	4628	639	23	1		1	DNAJB12	10	74103215	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	13073529	74103215	61431532	79	31102										
PTEN	5728	hgsc.bcm.edu	37	chr10	89690836	89690836	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cattatgacaccgccaaattTaattgcagaggtaggtatga	9	7	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:89690836T>A	ENST00000371953.3	+	4	1600	c.243T>A	c.(241-243)ttT>ttA	p.F81L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	81	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CCGCCAAATTTAATTGCAGAG	0.303		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	56	Whole gene deletion(37)|Deletion - Frameshift(14)|Unknown(5)	prostate(16)|central_nervous_system(14)|skin(6)|lung(5)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10	GRCh37	CI984161	PTEN	I							80	75	77					10																	89690836		2202	4294	6496	89680816	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.243T>A	10.37:g.89690836T>A	ENSP00000361021:p.Phe81Leu		89680816	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	36	5.606492	0.96626	.	.	ENSG00000171862	ENST00000371953	D	0.83992	-1.79	5.62	5.62	0.85841	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90494	0.7022	M	0.75264	2.295	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.90568	0.4520	9	.	.	.	-9.5547	16.1135	0.81278	0.0:0.0:0.0:1.0	.	81	P60484	PTEN_HUMAN	L	81	ENSP00000361021:F81L	.	F	+	3	2	PTEN	89680816	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.586000	0.82596	2.267000	0.75376	0.383000	0.25322	TTT		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89690836	T	A	89690836	3	1	116	1	0	0	0	0	1	0	0	0	12772	1751	61	5	257	5	PTEN	10	89690836	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	15587621	89690836	45843911	80	31103										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692899	89692899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aattcactgtaaagctggaaAgggacgaactggtgtaatga	12	5	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:89692899A>G	ENST00000371953.3	+	5	1740	c.383A>G	c.(382-384)aAg>aGg	p.K128R		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	128	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.K128_R130del(3)|p.Y27fs*1(2)|p.A121_F145del(1)|p.G127fs*5(1)|p.F56fs*2(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		AAAGCTGGAAAGGGACGAACT	0.413		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	56	Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(5)|Deletion - In frame(4)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|breast(3)|cervix(1)|soft_tissue(1)|urinary_tract(1)	10											141	130	134					10																	89692899		2203	4300	6503	89682879	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.383A>G	10.37:g.89692899A>G	ENSP00000361021:p.Lys128Arg		89682879	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.960666	0.92791	.	.	ENSG00000171862	ENST00000371953	D	0.85171	-1.95	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92205	0.7528	M	0.79693	2.465	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.92647	0.6129	9	.	.	.	-9.6267	15.1019	0.72284	1.0:0.0:0.0:0.0	.	128	P60484	PTEN_HUMAN	R	128	ENSP00000361021:K128R	.	K	+	2	0	PTEN	89682879	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.918000	0.92759	1.953000	0.56701	0.533000	0.62120	AAG		0.413	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89692899	A	G	89692899	3	3	116	1	0	0	0	0	1	0	0	0	12772	72	3	4	401	4	PTEN	10	89692899	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	2063	89692899	45841848	81	31104										
PTEN	5728	hgsc.bcm.edu	37	chr10	89725051	89725051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tttctttctctaggtgaagcTgtacttcacaaaaacagtag	7	8	3	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:89725051T>C	ENST00000371953.3	+	9	2391	c.1034T>C	c.(1033-1035)cTg>cCg	p.L345P		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	345	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.		L -> Q (in glioblastoma; reduced tumor suppressor activity; loss of phosphatase activity towards Ins(1,3,4,5)P4; reduced ability to inactivate AKT/PKB; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9331071}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.L345Q(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		TAGGTGAAGCTGTACTTCACA	0.323		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Substitution - Missense(1)|Deletion - In frame(1)	prostate(16)|central_nervous_system(11)|skin(5)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											39	37	37					10																	89725051		2203	4300	6503	89715031	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1034T>C	10.37:g.89725051T>C	ENSP00000361021:p.Leu345Pro		89715031	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.728670	0.30593	.	.	ENSG00000171862	ENST00000371953	D	0.89196	-2.48	5.11	5.11	0.69529	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.068871	0.64402	D	0.000020	D	0.89291	0.6673	M	0.80332	2.49	0.80722	D	1	B	0.18968	0.032	B	0.23716	0.048	D	0.86345	0.1707	9	.	.	.	-2.7052	15.2038	0.73162	0.0:0.0:0.0:1.0	.	345	P60484	PTEN_HUMAN	P	345	ENSP00000361021:L345P	.	L	+	2	0	PTEN	89715031	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.661000	0.83786	2.055000	0.61198	0.482000	0.46254	CTG		0.323	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		C	89725051	T	C	89725051	3	2	116	1	0	0	0	0	1	0	0	0	12772	1580	55	4	1068	4	PTEN	10	89725051	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	32152	89725051	45809696	82	31105										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105202056	105202056	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaggaggcgctgatggatccTgggcggcagccagagtccgc	18	11	0	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:105202056T>C	ENST00000369797.3	+	32	4888	c.4794T>C	c.(4792-4794)ccT>ccC	p.P1598P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1598					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TGATGGATCCTGGGCGGCAGC	0.547																																																0			10											97	98	97					10																	105202056		2203	4300	6503	105192046	SO:0001819	synonymous_variant	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.4794T>C	10.37:g.105202056T>C			105192046	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																				0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			C	105202056	T	C	105202056	2	2	116	1	0	0	0	0	0	0	0	1	11648	1567	55	4		4	PDCD11	10	105202056	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	15477005	105202056	30332691	83	31106										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105203740	105203740	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaagctgtgtggatcaaataCggcgccttccttctgcggag	12	10	2	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr10:105203740C>T	ENST00000369797.3	+	34	5287	c.5193C>T	c.(5191-5193)taC>taT	p.Y1731Y		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1731					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GGATCAAATACGGCGCCTTCC	0.602																																																0			10											71	70	70					10																	105203740		2203	4300	6503	105193730	SO:0001819	synonymous_variant	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5193C>T	10.37:g.105203740C>T			105193730	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																				0.602	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105203740	C	T	105203740	2	4	116	1	0	0	0	0	0	0	0	1	11648	547	19	1		1	PDCD11	10	105203740	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1684	105203740	30331007	84	31107										
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20623125	20623125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atacccctgttgtgggctggGtgaacatgagccagagcacc	13	11	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:20623125G>A	ENST00000525748.1	+	2	727	c.454G>A	c.(454-456)Gtg>Atg	p.V152M		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	152					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	TGTGGGCTGGGTGAACATGAG	0.632																																																0			11											102	89	93					11																	20623125		2203	4300	6503	20579701	SO:0001583	missense	9152			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.454G>A	11.37:g.20623125G>A	ENSP00000434364:p.Val152Met		20579701	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628565	0.67015	.	.	ENSG00000165970	ENST00000525748	T	0.74632	-0.86	5.69	3.46	0.39613	.	1.073890	0.07162	N	0.850944	T	0.64249	0.2581	L	0.27053	0.805	0.42866	D	0.994126	P	0.43477	0.808	B	0.38712	0.28	T	0.60622	-0.7227	10	0.87932	D	0	.	10.7536	0.46223	0.0809:0.0:0.7841:0.135	.	152	Q9Y345	SC6A5_HUMAN	M	152	ENSP00000434364:V152M	ENSP00000298923:V152M	V	+	1	0	SLC6A5	20579701	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.808000	0.47963	1.380000	0.46344	0.455000	0.32223	GTG		0.632	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		A	20623125	G	A	20623125	3	1	116	1	0	0	0	0	1	0	0	0	14724	1261	44	3	460	3	SLC6A5	11	20623125	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		20623125	114383391	85	31108										
MAPK8IP1	9479	hgsc.bcm.edu	37	chr11	45924235	45924235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cctgccgcccactgagagccGgatgtcagtcagctccgatc	11	16	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:45924235G>A	ENST00000241014.2	+	5	1087	c.917G>A	c.(916-918)cGg>cAg	p.R306Q	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.R296Q	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	306	Interaction with MAP3K7.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)	p.R306L(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		ACTGAGAGCCGGATGTCAGTC	0.667																																																2	Substitution - Missense(2)	lung(2)	11											19	23	21					11																	45924235		2203	4299	6502	45880811	SO:0001583	missense	9479				CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.917G>A	11.37:g.45924235G>A	ENSP00000241014:p.Arg306Gln		45880811	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110548	0.77210	.	.	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.39787	1.06;1.08	4.58	4.58	0.56647	.	0.058859	0.64402	D	0.000002	T	0.50820	0.1638	N	0.19112	0.55	0.58432	D	0.99999	D	0.89917	1.0	D	0.79108	0.992	T	0.57260	-0.7842	10	0.62326	D	0.03	-27.4477	17.9065	0.88919	0.0:0.0:1.0:0.0	.	306	Q9UQF2	JIP1_HUMAN	Q	306;296	ENSP00000241014:R306Q;ENSP00000378991:R296Q	ENSP00000241014:R306Q	R	+	2	0	MAPK8IP1	45880811	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.907000	0.75724	2.541000	0.85698	0.561000	0.74099	CGG		0.667	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		A	45924235	G	A	45924235	3	1	116	1	0	0	0	0	1	0	0	0	9314	1116	39	1	935	1	MAPK8IP1	11	45924235	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	25301110	45924235	89082281	86	31109										
ANKRD42	338699	hgsc.bcm.edu	37	chr11	82936044	82936044	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gttcttcaagcagaacatttTacagtttatccagggggctg	10	8	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:82936044T>A	ENST00000393392.2	+	6	812	c.650T>A	c.(649-651)tTa>tAa	p.L217*	ANKRD42_ENST00000531895.1_Nonsense_Mutation_p.L245*|ANKRD42_ENST00000533342.1_Nonsense_Mutation_p.L245*|ANKRD42_ENST00000260047.6_Nonsense_Mutation_p.L244*	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42	217					positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						CAGAACATTTTACAGTTTATC	0.378																																																0			11											95	101	99					11																	82936044		2203	4300	6503	82613692	SO:0001587	stop_gained	338699			AK095193	CCDS8265.1, CCDS73355.1, CCDS73356.1	11q14.1	2014-06-12			ENSG00000137494	ENSG00000137494		"Ankyrin repeat domain containing"	26752	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 79"						Standard	XM_005273971		Approved	FLJ37874, SARP, PPP1R79	uc001ozz.1	Q8N9B4	OTTHUMG00000167075	ENST00000393392.2:c.650T>A	11.37:g.82936044T>A	ENSP00000377051:p.Leu217*		82613692	Q49A49	Nonsense_Mutation	SNP	ENST00000393392.2	37	CCDS8265.1	.	.	.	.	.	.	.	.	.	.	T	41	9.058389	0.99051	.	.	ENSG00000137494	ENST00000545672;ENST00000260047;ENST00000531895;ENST00000393392;ENST00000533342	.	.	.	5.43	5.43	0.79202	.	0.705612	0.12326	N	0.478847	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.1351	14.4561	0.67418	0.0:0.0:0.0:1.0	.	.	.	.	X	564;244;245;217;245	.	.	L	+	2	0	ANKRD42	82613692	0.809000	0.29036	0.995000	0.50966	0.198000	0.23893	3.696000	0.54757	2.043000	0.60533	0.460000	0.39030	TTA		0.378	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392934.1	NM_182603		A	82936044	T	A	82936044	4	1	116	1	0	0	0	0	0	1	0	0	670	1764	61	5	672	5	ANKRD42	11	82936044	Nonsense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	37011809	82936044	52070472	87	31110										
PICALM	8301	hgsc.bcm.edu	37	chr11	85685794	85685794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aggggtttggaggtctcatgAcaggctggctgtatattaag	15	5	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:85685794A>G	ENST00000393346.3	-	19	2049	c.1901T>C	c.(1900-1902)gTc>gCc	p.V634A	PICALM_ENST00000356360.5_Missense_Mutation_p.V614A|PICALM_ENST00000526033.1_Missense_Mutation_p.V627A|PICALM_ENST00000532317.1_Missense_Mutation_p.V592A|PICALM_ENST00000528398.1_Missense_Mutation_p.V533A			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	634					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				AGGTCTCATGACAGGCTGGCT	0.408			T	"MLLT10, MLL"	"TALL, AML, "																																		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	0			11											240	201	214					11																	85685794		2203	4299	6502	85363442	SO:0001583	missense	8301			BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1901T>C	11.37:g.85685794A>G	ENSP00000377015:p.Val634Ala		85363442	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	37	CCDS8272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.15|15.15	2.748759|2.748759	0.49257|0.49257	.|.	.|.	ENSG00000073921|ENSG00000073921	ENST00000530692|ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	.|T;T;T;T;T	.|0.54479	.|0.57;0.57;0.57;0.57;0.57	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.196377	.|0.43416	.|D	.|0.000577	T|T	0.64327|0.64327	0.2588|0.2588	L|L	0.40543|0.40543	1.245|1.245	0.49299|0.49299	D|D	0.999777|0.999777	.|B;D;B;B;B;B	.|0.58268	.|0.002;0.982;0.005;0.009;0.004;0.016	.|B;D;B;B;B;B	.|0.70227	.|0.006;0.968;0.012;0.017;0.012;0.009	T|T	0.61113|0.61113	-0.7128|-0.7128	5|9	.|.	.|.	.|.	-7.3254|-7.3254	16.5764|16.5764	0.84681|0.84681	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|533;219;642;627;634;592	.|E9PN05;B4DLM1;A8MX97;F8VPG7;Q13492;Q13492-3	.|.;.;.;.;PICAL_HUMAN;.	P|A	171|592;627;634;634;533;614	.|ENSP00000436958:V592A;ENSP00000433846:V627A;ENSP00000377015:V634A;ENSP00000434884:V533A;ENSP00000348718:V614A	.|.	S|V	-|-	1|2	0|0	PICALM|PICALM	85363442|85363442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.444000|6.444000	0.73452|0.73452	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TCA|GTC		0.408	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85685794	A	G	85685794	3	3	116	1	0	0	0	0	1	0	0	0	11911	275	10	4	65	4	PICALM	11	85685794	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	2749750	85685794	49320722	88	31111										
RDX	5962	hgsc.bcm.edu	37	chr11	110124794	110124794	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ccatacataaggccaaaatcCgcttattgattctcagacga	6	11	1	2	rs150863373		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:110124794C>T	ENST00000343115.4	-	9	1155	c.836G>A	c.(835-837)cGg>cAg	p.R279Q	RDX_ENST00000530301.1_Intron|RDX_ENST00000405097.1_Missense_Mutation_p.R279Q|RDX_ENST00000544551.1_Missense_Mutation_p.R143Q|RDX_ENST00000528900.1_Intron|RDX_ENST00000528498.1_Missense_Mutation_p.R279Q	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	279	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)	p.R279Q(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GGCCAAAATCCGCTTATTGAT	0.383																																					Esophageal Squamous(55;25 1062 11040 28755 44273)											1	Substitution - Missense(1)	kidney(1)	11						C	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	102	90	94		836	5.7	1	11	dbSNP_134	94	0,8596		0,0,4298	yes	missense	RDX	NM_002906.3	43	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	279/584	110124794	1,12997	2201	4298	6499	109630004	SO:0001583	missense	5962			BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.836G>A	11.37:g.110124794C>T	ENSP00000342830:p.Arg279Gln		109630004	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	37	CCDS8343.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.014321	0.93404	2.27E-4	0.0	ENSG00000137710	ENST00000528498;ENST00000429481;ENST00000405097;ENST00000343115;ENST00000544551	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.72	5.72	0.89469	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.89787	0.6816	M	0.81239	2.535	0.80722	D	1	D;D;P	0.69078	0.967;0.997;0.6	B;P;B	0.55112	0.438;0.769;0.194	D	0.89757	0.3944	10	0.51188	T	0.08	.	19.8831	0.96905	0.0:1.0:0.0:0.0	.	143;279;279	F5H1A7;A7YIJ8;P35241	.;.;RADI_HUMAN	Q	279;279;279;279;143	ENSP00000432112:R279Q;ENSP00000384136:R279Q;ENSP00000342830:R279Q;ENSP00000445826:R143Q	ENSP00000342830:R279Q	R	-	2	0	RDX	109630004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.765000	0.85310	2.705000	0.92388	0.655000	0.94253	CGG		0.383	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		T	110124794	C	T	110124794	3	4	116	1	0	0	0	0	1	0	0	0	13235	652	23	1	939	1	RDX	11	110124794	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	24439000	110124794	24881722	89	31112										
MLL	4297	hgsc.bcm.edu	37	chr11	118368707	118368707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggacacatgtaaattgtgcTttgtggtcagcggaagtgtt	13	5	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:118368707T>C	ENST00000389506.5	+	21	5712	c.5712T>C	c.(5710-5712)gcT>gcC	p.A1904A	KMT2A_ENST00000354520.4_Silent_p.A1866A|KMT2A_ENST00000534358.1_Silent_p.A1907A			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1904					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TAAATTGTGCTTTGTGGTCAG	0.388																																																0			11											160	151	154					11																	118368707		2200	4296	6496	117873917	SO:0001819	synonymous_variant	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.5712T>C	11.37:g.118368707T>C			117873917	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.388	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		C	118368707	T	C	118368707	2	2	116	1	0	0	0	0	0	0	0	1	9650	1596	56	4		4	MLL	11	118368707	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	8243913	118368707	16637809	90	31113										
MFRP	83552	hgsc.bcm.edu	37	chr11	119213328	119213328	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gggggtgggaacaaggggccGctgcagttgtcatcgctgcc	18	10	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr11:119213328G>A	ENST00000530681.1	-	11	1509	c.1365C>T	c.(1363-1365)agC>agT	p.S455S	MFRP_ENST00000360167.4_Missense_Mutation_p.A380V|C1QTNF5_ENST00000525657.1_5'Flank|C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000555262.1_Silent_p.S455S|MFRP_ENST00000529147.1_5'Flank|C1QTNF5_ENST00000528368.1_5'Flank|MFRP_ENST00000449574.2_Silent_p.S455S	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	455	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		ACAAGGGGCCGCTGCAGTTGT	0.632																																																0			11											80	79	79					11																	119213328		2199	4295	6494	118718538	SO:0001819	synonymous_variant	83552			AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"membrane-type frizzled-related protein", "complement C1q tumor necrosis factor-related protein 5 precursor variant 1"	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.1365C>T	11.37:g.119213328G>A			118718538	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1	.	.	.	.	.	.	.	.	.	.	G	9.097	1.003243	0.19121	.	.	ENSG00000235718	ENST00000360167	T	0.76186	-1.0	5.3	5.3	0.74995	.	.	.	.	.	T	0.65760	0.2722	.	.	.	0.80722	D	1	P	0.48016	0.904	B	0.41374	0.355	T	0.63580	-0.6605	8	0.15952	T	0.53	-12.1788	17.534	0.87822	0.0:0.0:1.0:0.0	.	380	B4DHN8	.	V	380	ENSP00000353291:A380V	ENSP00000353291:A380V	A	-	2	0	MFRP	118718538	0.135000	0.22499	0.849000	0.33467	0.534000	0.34807	0.937000	0.28951	2.469000	0.83416	0.561000	0.74099	GCG		0.632	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433		A	119213328	G	A	119213328	2	1	116	1	0	0	0	0	0	0	0	1	9556	1078	38	1		1	MFRP	11	119213328	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	844621	119213328	15793188	91	31114										
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7970607	7970607	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aagatagccccaatacagacAaagctcatcccattatagtg	6	11	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr12:7970607A>G	ENST00000543909.1	-	15	1923	c.1164T>C	c.(1162-1164)ttT>ttC	p.F388F	SLC2A14_ENST00000340749.5_Silent_p.F365F|SLC2A14_ENST00000539924.1_Silent_p.F403F|SLC2A14_ENST00000431042.2_Silent_p.F365F|SLC2A14_ENST00000535295.1_Silent_p.F279F|SLC2A14_ENST00000396589.2_Silent_p.F388F|SLC2A14_ENST00000542505.1_Silent_p.F29F|SLC2A14_ENST00000542546.1_Silent_p.F279F			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	388					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		CAATACAGACAAAGCTCATCC	0.463																																																0			12											40	41	41					12																	7970607		2203	4300	6503	7861874	SO:0001819	synonymous_variant	144195			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1164T>C	12.37:g.7970607A>G			7861874	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																				0.463	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		G	7970607	A	G	7970607	2	3	116	1	0	0	0	0	0	0	0	1	14580	127	5	4		4	SLC2A14	12	7970607	Silent	SNP	A	TCGA-F5-6571-01A-12D-1826-10		7970607	125881288	92	31115										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	116	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	17427674	25398281	108453614	93	31116										
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30882099	30882099	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gcttaccagaagcctcccagGacttaaaggactcctgtttc	8	13	0	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr12:30882099G>T	ENST00000395805.2	-	8	1812	c.1265C>A	c.(1264-1266)tCc>tAc	p.S422Y	CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.S422Y|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.S89Y|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.S422Y|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.S422Y	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					AGCCTCCCAGGACTTAAAGGA	0.468																																																0			12											109	104	106					12																	30882099		2203	4300	6503	30773366	SO:0001583	missense	65981			AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.1265C>A	12.37:g.30882099G>T	ENSP00000379150:p.Ser422Tyr		30773366		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932146	0.73442	.	.	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000308433;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T;T	0.75938	2.37;-0.7;2.78;-0.67;-0.98;2.77;2.4	4.94	4.94	0.65067	.	0.393919	0.19479	N	0.113277	T	0.76126	0.3944	N	0.14661	0.345	0.38710	D	0.953209	D;D;D;D;D;D;D	0.76494	0.995;0.999;0.991;0.995;0.976;0.986;0.976	P;D;P;P;P;P;P	0.68943	0.885;0.961;0.77;0.885;0.656;0.742;0.556	T	0.81634	-0.0844	10	0.72032	D	0.01	-7.1896	16.7176	0.85400	0.0:0.0:1.0:0.0	.	422;148;422;422;422;422;422	Q6IMN6-6;E9PAU5;Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;.;.;CAPR2_HUMAN;.;.	Y	168;422;422;422;89;422;148;341	ENSP00000415407:S168Y;ENSP00000298892:S422Y;ENSP00000379150:S422Y;ENSP00000251071:S422Y;ENSP00000309785:S89Y;ENSP00000391479:S422Y;ENSP00000438010:S341Y	ENSP00000251071:S422Y	S	-	2	0	CAPRIN2	30773366	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.054000	0.57434	2.443000	0.82685	0.655000	0.94253	TCC		0.468	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		T	30882099	G	T	30882099	3	4	116	1	0	0	0	0	1	0	0	0	2642	1174	41	2	2162	2	CAPRIN2	12	30882099	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	5483818	30882099	102969796	94	31117										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40668475	40668475	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cattagagatgttatccctgGaaggtgctatggattcagtg	12	6	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr12:40668475G>T	ENST00000298910.7	+	15	1805	c.1747G>T	c.(1747-1749)Gaa>Taa	p.E583*	LRRK2_ENST00000343742.2_Nonsense_Mutation_p.E583*	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	583					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GTTATCCCTGGAAGGTGCTAT	0.363																																																0			12											150	148	148					12																	40668475		2203	4300	6503	38954742	SO:0001587	stop_gained	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1747G>T	12.37:g.40668475G>T	ENSP00000298910:p.Glu583*		38954742	A6NJU2|Q6ZS50|Q8NCX9	Nonsense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	37	6.550654	0.97658	.	.	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	.	.	.	5.97	4.08	0.47627	.	0.163970	0.56097	D	0.000036	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	14.8938	0.70627	0.0:0.5845:0.4155:0.0	.	.	.	.	X	331;583;583	.	ENSP00000298910:E583X	E	+	1	0	LRRK2	38954742	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	2.721000	0.47260	1.492000	0.48499	0.585000	0.79938	GAA		0.363	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40668475	G	T	40668475	4	4	116	1	0	0	0	0	0	1	0	0	9062	1175	41	2	1805	2	LRRK2	12	40668475	Nonsense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	9786376	40668475	93183420	95	31118										
WASF3	10810	hgsc.bcm.edu	37	chr13	27259961	27259961	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gacgacgactcagagttcgaCgagaacgactggtccgactg	13	11	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:27259961C>T	ENST00000335327.5	+	10	1666	c.1488C>T	c.(1486-1488)gaC>gaT	p.D496D	WASF3_ENST00000361042.4_Silent_p.D493D	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	496					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CAGAGTTCGACGAGAACGACT	0.587																																																0			13											79	64	69					13																	27259961		2203	4300	6503	26157961	SO:0001819	synonymous_variant	10810			AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.1488C>T	13.37:g.27259961C>T			26157961	O94974|Q86VQ2	Silent	SNP	ENST00000335327.5	37	CCDS9318.1																																																																																				0.587	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			T	27259961	C	T	27259961	2	4	116	1	0	0	0	0	0	0	0	1	17294	535	19	1		1	WASF3	13	27259961	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10		27259961	87909917	96	31119										
FLT3	2322	hgsc.bcm.edu	37	chr13	28608472	28608472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gacaaattagcagggttaaaAcgacaatgaagaggagacaa	11	5	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:28608472A>G	ENST00000241453.7	-	13	1751	c.1670T>C	c.(1669-1671)gTt>gCt	p.V557A	FLT3_ENST00000380982.4_Missense_Mutation_p.V557A|FLT3_ENST00000537084.1_Missense_Mutation_p.V557A	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	557			V -> I (in dbSNP:rs35958982). {ECO:0000269|PubMed:17344846}.		B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGGGTTAAAACGACAATGAA	0.393			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13											96	89	92					13																	28608472		2203	4300	6503	27506472	SO:0001583	missense	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1670T>C	13.37:g.28608472A>G	ENSP00000241453:p.Val557Ala		27506472	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.466433	0.26335	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.78595	-1.12;-1.19;-0.93	5.83	5.83	0.93111	.	0.552763	0.17442	N	0.174076	T	0.72748	0.3499	L	0.50333	1.59	0.09310	N	1	B;B	0.16802	0.019;0.004	B;B	0.12156	0.007;0.005	T	0.65919	-0.6051	10	0.72032	D	0.01	.	11.2703	0.49136	0.9292:0.0:0.0708:0.0	.	557;557	P36888-2;P36888	.;FLT3_HUMAN	A	557	ENSP00000241453:V557A;ENSP00000370369:V557A;ENSP00000438139:V557A	ENSP00000241453:V557A	V	-	2	0	FLT3	27506472	0.567000	0.26626	0.005000	0.12908	0.516000	0.34256	5.917000	0.69989	2.226000	0.72624	0.533000	0.62120	GTT		0.393	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			G	28608472	A	G	28608472	3	3	116	1	0	0	0	0	1	0	0	0	5961	43	2	4	1359	4	FLT3	13	28608472	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	1348511	28608472	86561406	97	31120										
FLT1	2321	hgsc.bcm.edu	37	chr13	28895699	28895699	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcagataaaagaatgtttctCgctgccaggtcccgatgaat	9	9	2	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:28895699C>A	ENST00000282397.4	-	23	3326	c.3075G>T	c.(3073-3075)gcG>gcT	p.A1025A	FLT1_ENST00000543394.1_Silent_p.A48A|FLT1_ENST00000540678.1_Silent_p.A243A	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1025	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAATGTTTCTCGCTGCCAGGT	0.393																																																0			13											117	103	108					13																	28895699		2203	4300	6503	27793699	SO:0001819	synonymous_variant	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3075G>T	13.37:g.28895699C>A			27793699	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																				0.393	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28895699	C	A	28895699	2	1	116	1	0	0	0	0	0	0	0	1	5960	871	31	2		2	FLT1	13	28895699	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	287227	28895699	86274179	98	31121										
RB1	5925	hgsc.bcm.edu	37	chr13	48881500	48881500	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gatcatgtcagagagagagcTtggttaacttgggagaaagt	14	4	2	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:48881500T>C	ENST00000267163.4	+	2	360	c.222T>C	c.(220-222)gcT>gcC	p.A74A		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	74					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GAGAGAGAGCTTGGTTAACTT	0.318		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	18	Whole gene deletion(15)|Unknown(3)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|stomach(1)	13											138	141	140					13																	48881500		2203	4299	6502	47779501	SO:0001819	synonymous_variant	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.222T>C	13.37:g.48881500T>C			47779501	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																				0.318	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	48881500	T	C	48881500	2	2	116	1	0	0	0	0	0	0	0	1	13135	1596	56	4		4	RB1	13	48881500	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	19985801	48881500	66288378	99	31122										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208514	58208514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atctggtgagcactgtgcgcGccctagacagcgacttcggc	13	13	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:58208514G>A	ENST00000377918.3	+	1	1860	c.1834G>A	c.(1834-1836)Gcc>Acc	p.A612T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	612	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CACTGTGCGCGCCCTAGACAG	0.657																																					Melanoma(72;952 1291 1619 12849 33676)											0			13											35	35	35					13																	58208514		2201	4296	6497	57106515	SO:0001583	missense	27253			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1834G>A	13.37:g.58208514G>A	ENSP00000367151:p.Ala612Thr		57106515	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.406418	0.83230	.	.	ENSG00000118946	ENST00000377918	T	0.61392	0.11	5.36	5.36	0.76844	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.85401	0.5688	H	0.97340	3.985	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90677	0.4602	9	.	.	.	.	19.0883	0.93215	0.0:0.0:1.0:0.0	.	612;612	O14917-2;O14917	.;PCD17_HUMAN	T	612	ENSP00000367151:A612T	.	A	+	1	0	PCDH17	57106515	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	9.869000	0.99810	2.500000	0.84329	0.561000	0.74099	GCC		0.657	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58208514	G	A	58208514	3	1	116	1	0	0	0	0	1	0	0	0	11543	1087	38	1	1836	1	PCDH17	13	58208514	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	9327014	58208514	56961364	100	31123										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78474696	78474696	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gggatcattctgattataaaGagtgagcttcagaatcctgc	10	7	3	4			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:78474696G>C	ENST00000334286.5	-	5	1281	c.1045C>G	c.(1045-1047)Ctt>Gtt	p.L349V	EDNRB_ENST00000377211.4_Missense_Mutation_p.L439V|EDNRB_ENST00000446573.1_Missense_Mutation_p.L349V	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	349					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.L349I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGATTATAAAGAGTGAGCTTC	0.433																																																1	Substitution - Missense(1)	large_intestine(1)	13											83	87	86					13																	78474696		2203	4300	6503	77372697	SO:0001583	missense	1910			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1045C>G	13.37:g.78474696G>C	ENSP00000335311:p.Leu349Val		77372697	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	G	7.342	0.621060	0.14193	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.71698	-0.59;-0.59;-0.59	5.62	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.217810	0.45867	D	0.000326	T	0.36524	0.0970	N	0.01188	-0.97	0.32728	N	0.509345	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.14023	0.009;0.007;0.01	T	0.36089	-0.9762	10	0.12430	T	0.62	-6.993	9.0855	0.36579	0.0694:0.0:0.4439:0.4867	.	349;439;349	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	V	439;349;349	ENSP00000366416:L439V;ENSP00000403401:L349V;ENSP00000335311:L349V	ENSP00000335311:L349V	L	-	1	0	EDNRB	77372697	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.495000	0.35627	0.823000	0.34589	0.650000	0.86243	CTT		0.433	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78474696	G	C	78474696	3	2	116	1	0	0	0	0	1	0	0	0	4931	942	33	5	416	5	EDNRB	13	78474696	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	20266182	78474696	36695182	101	31124										
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454756	84454756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	accctggtgtggcatgatccTcttgcccatttgtcttgaaa	9	11	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr13:84454756T>C	ENST00000377084.2	-	1	1772	c.887A>G	c.(886-888)gAg>gGg	p.E296G		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	296					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGCATGATCCTCTTGCCCATT	0.552																																																0			13											77	76	76					13																	84454756		2203	4300	6503	83352757	SO:0001583	missense	114798			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.887A>G	13.37:g.84454756T>C	ENSP00000366288:p.Glu296Gly		83352757	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	5.870	0.344633	0.11126	.	.	ENSG00000178235	ENST00000377084	T	0.58940	0.3	4.85	4.85	0.62838	.	0.209202	0.45126	D	0.000386	T	0.36166	0.0957	N	0.08118	0	0.40981	D	0.984771	B	0.09022	0.002	B	0.06405	0.002	T	0.20672	-1.0268	10	0.23302	T	0.38	-7.8753	13.4025	0.60891	0.0:0.0:0.0:1.0	.	296	Q96PX8	SLIK1_HUMAN	G	296	ENSP00000366288:E296G	ENSP00000366288:E296G	E	-	2	0	SLITRK1	83352757	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	3.963000	0.56773	2.042000	0.60477	0.454000	0.30748	GAG		0.552	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		C	84454756	T	C	84454756	3	2	116	1	0	0	0	0	1	0	0	0	14779	1551	54	4	1207	4	SLITRK1	13	84454756	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	5980060	84454756	30715122	102	31125										
SERPINA12	145264	hgsc.bcm.edu	37	chr14	94964309	94964309	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttacgctgtggctgcagcctCtggtcaatgaacagcgtgtt	12	10	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr14:94964309C>T	ENST00000341228.2	-	3	1221	c.426G>A	c.(424-426)caG>caA	p.Q142Q	SERPINA12_ENST00000556881.1_Silent_p.Q142Q	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	142			Q -> K (in dbSNP:rs17090972).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		GCTGCAGCCTCTGGTCAATGA	0.468																																																0			14											128	125	126					14																	94964309		2203	4300	6503	94034062	SO:0001819	synonymous_variant	145264			AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.426G>A	14.37:g.94964309C>T			94034062		Silent	SNP	ENST00000341228.2	37	CCDS9926.1																																																																																				0.468	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		T	94964309	C	T	94964309	2	4	116	1	0	0	0	0	0	0	0	1	14126	912	32	3		3	SERPINA12	14	94964309	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10		94964309	12385231	103	31126										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75499747	75499747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gaaagagaagctccagccccGgctcagtgagcactctgggc	13	13	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr15:75499747G>A	ENST00000360639.2	+	2	1678	c.1358G>A	c.(1357-1359)cGg>cAg	p.R453Q	C15orf39_ENST00000394987.4_Missense_Mutation_p.R453Q|C15orf39_ENST00000567617.1_Missense_Mutation_p.R453Q			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	453						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CTCCAGCCCCGGCTCAGTGAG	0.652																																																0			15											33	41	38					15																	75499747		2197	4295	6492	73286800	SO:0001583	missense	56905			AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1358G>A	15.37:g.75499747G>A	ENSP00000353854:p.Arg453Gln		73286800	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.253716	0.22965	.	.	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.63913	-0.07;-0.07	4.86	-7.13	0.01532	.	1.216240	0.06401	N	0.718743	T	0.30198	0.0757	N	0.05510	-0.035	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.10941	-1.0608	10	0.21540	T	0.41	-2.4066	1.8518	0.03171	0.3427:0.2178:0.33:0.1095	.	453	Q6ZRI6	CO039_HUMAN	Q	453	ENSP00000353854:R453Q;ENSP00000378438:R453Q	ENSP00000353854:R453Q	R	+	2	0	C15orf39	73286800	0.000000	0.05858	0.001000	0.08648	0.301000	0.27625	-0.809000	0.04510	-1.513000	0.01789	0.462000	0.41574	CGG		0.652	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		A	75499747	G	A	75499747	3	1	116	1	0	0	0	0	1	0	0	0	1797	1116	39	1	1360	1	C15orf39	15	75499747	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		75499747	27031645	104	31127										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14029410	14029410	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttgatgtaaatttgtcatcgGatgctgctttcggaatcctg	10	7	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:14029410G>A	ENST00000311895.7	+	8	1630	c.1621G>A	c.(1621-1623)Gat>Aat	p.D541N	CTD-2135D7.2_ENST00000570663.1_RNA|CTD-2135D7.2_ENST00000575137.1_RNA	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	541					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						TTTGTCATCGGATGCTGCTTT	0.468			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	0			16											63	65	64					16																	14029410		2197	4300	6497	13936911	SO:0001583	missense	2072	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.1621G>A	16.37:g.14029410G>A	ENSP00000310520:p.Asp541Asn		13936911	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	37	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200575	0.79015	.	.	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.61742	0.08	5.12	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.51346	0.1669	M	0.64997	1.995	0.80722	D	1	P	0.40660	0.726	B	0.36567	0.228	T	0.53788	-0.8389	10	0.33940	T	0.23	-36.7844	12.459	0.55721	0.0811:0.0:0.9189:0.0	.	541	Q92889	XPF_HUMAN	N	541;530	ENSP00000310520:D541N	ENSP00000310520:D541N	D	+	1	0	ERCC4	13936911	1.000000	0.71417	0.638000	0.29380	0.658000	0.38924	7.597000	0.82733	2.533000	0.85409	0.591000	0.81541	GAT		0.468	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		A	14029410	G	A	14029410	3	1	116	1	0	0	0	0	1	0	0	0	5228	1174	41	3	1651	3	ERCC4	16	14029410	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		14029410	76325343	105	31128										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20976234	20976234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	caccagtcagattagtatagCggatccccagctgtcgggca	11	12	1	1	rs368894340		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:20976234C>T	ENST00000261383.3	-	53	8971	c.8972G>A	c.(8971-8973)cGc>cAc	p.R2991H	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2991					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATTAGTATAGCGGATCCCCAG	0.537													C|||	1	0.000199681	0	0	5008	,	,		19838	0.001		0	False		,,,				2504	0															0			16						C	HIS/ARG	0,4402		0,0,2201	104	104	104		8972	1.8	0	16		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH3	NM_017539.1	29	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	2991/4117	20976234	1,13001	2201	4300	6501	20883735	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8972G>A	16.37:g.20976234C>T	ENSP00000261383:p.Arg2991His		20883735	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	1.964	-0.438138	0.04636	0.0	1.16E-4	ENSG00000158486	ENST00000261383	T	0.74737	-0.87	6.17	1.82	0.25136	Dynein heavy chain, coiled coil stalk (1);	0.200037	0.41396	D	0.000897	T	0.67562	0.2906	M	0.75085	2.285	0.09310	N	0.999999	B	0.29270	0.24	B	0.22601	0.04	T	0.58629	-0.7603	10	0.46703	T	0.11	.	6.7691	0.23585	0.3303:0.504:0.1065:0.0591	.	2991	Q8TD57	DYH3_HUMAN	H	2991	ENSP00000261383:R2991H	ENSP00000261383:R2991H	R	-	2	0	DNAH3	20883735	0.997000	0.39634	0.000000	0.03702	0.002000	0.02628	2.564000	0.45931	0.116000	0.18110	-0.175000	0.13238	CGC		0.537	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	20976234	C	T	20976234	3	4	116	1	0	0	0	0	1	0	0	0	4614	768	27	1	3417	1	DNAH3	16	20976234	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	6946824	20976234	69378519	106	31129										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24135244	24135244	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	caacaatggcaacagagaccGgatgaaactgaccgatttta	9	9	0	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:24135244G>A	ENST00000321728.7	+	9	1182	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	PRKCB_ENST00000303531.7_Missense_Mutation_p.R336Q	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	336					apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	AACAGAGACCGGATGAAACTG	0.483																																																0			16											188	178	182					16																	24135244		2197	4300	6497	24042745	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1007G>A	16.37:g.24135244G>A	ENSP00000318315:p.Arg336Gln		24042745	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.858992	0.71834	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.71341	-0.56;-0.56	4.92	4.92	0.64577	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71702	0.3371	M	0.76328	2.33	0.80722	D	1	B;B	0.17268	0.021;0.012	B;B	0.06405	0.001;0.002	T	0.70506	-0.4853	10	0.51188	T	0.08	.	17.2875	0.87146	0.0:0.0:1.0:0.0	.	336;336	P05771-2;P05771	.;KPCB_HUMAN	Q	336	ENSP00000318315:R336Q;ENSP00000305355:R336Q	ENSP00000305355:R336Q	R	+	2	0	PRKCB	24042745	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.040000	0.93783	2.562000	0.86427	0.563000	0.77884	CGG		0.483	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		A	24135244	G	A	24135244	3	1	116	1	0	0	0	0	1	0	0	0	12542	1116	39	1	1041	1	PRKCB	16	24135244	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	3159010	24135244	66219509	107	31130										
HS3ST4	9951	hgsc.bcm.edu	37	chr16	25704190	25704190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ggcccccagcgagatgatcaCggctcagagcgcgctgccgg	15	15	2	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:25704190C>T	ENST00000331351.5	+	1	844	c.452C>T	c.(451-453)aCg>aTg	p.T151M		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	151					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GAGATGATCACGGCTCAGAGC	0.761																																																0			16											4	7	6					16																	25704190		1875	3959	5834	25611691	SO:0001583	missense	9951			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.452C>T	16.37:g.25704190C>T	ENSP00000330606:p.Thr151Met		25611691	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	.	18.09	3.546342	0.65198	.	.	ENSG00000182601	ENST00000331351	T	0.47869	0.83	3.08	3.08	0.35506	.	1.392810	0.05603	U	0.576652	T	0.35740	0.0942	N	0.19112	0.55	0.25686	N	0.985743	D	0.61080	0.989	B	0.42087	0.375	T	0.30909	-0.9962	10	0.66056	D	0.02	.	8.5892	0.33677	0.2299:0.7701:0.0:0.0	.	151	Q9Y661	HS3S4_HUMAN	M	151	ENSP00000330606:T151M	ENSP00000330606:T151M	T	+	2	0	HS3ST4	25611691	1.000000	0.71417	0.900000	0.35374	0.972000	0.66771	6.476000	0.73587	1.533000	0.49186	0.514000	0.50259	ACG		0.761	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		T	25704190	C	T	25704190	3	4	116	1	0	0	0	0	1	0	0	0	7388	536	19	1	454	1	HS3ST4	16	25704190	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1568946	25704190	64650563	108	31131										
C16orf92	146378	hgsc.bcm.edu	37	chr16	30035138	30035138	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cttcttcgattatccggactCagaccaagccaggctgctgg	10	13	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:30035138C>G	ENST00000300575.2	+	2	242	c.221C>G	c.(220-222)tCa>tGa	p.S74*	DOC2A_ENST00000567824.1_5'Flank	NM_001109659.1|NM_001109660.1	NP_001103129.1|NP_001103130.1	Q96LL3	CP092_HUMAN	chromosome 16 open reading frame 92	74						integral component of membrane (GO:0016021)				breast(3)|lung(3)	6						TATCCGGACTCAGACCAAGCC	0.567																																																0			16											38	39	39					16																	30035138		1960	4130	6090	29942639	SO:0001587	stop_gained	146378			AK058133	CCDS42146.1	16p11.2	2012-05-30			ENSG00000167194	ENSG00000167194			26346	protein-coding gene	gene with protein product							Standard	NM_001109659		Approved	FLJ25404	uc002dvs.2	Q96LL3	OTTHUMG00000177107	ENST00000300575.2:c.221C>G	16.37:g.30035138C>G	ENSP00000300575:p.Ser74*		29942639	Q494R8	Nonsense_Mutation	SNP	ENST00000300575.2	37	CCDS42146.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037618	0.75617	.	.	ENSG00000167194	ENST00000300575	.	.	.	5.4	4.45	0.53987	.	0.200419	0.25164	N	0.032648	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.3027	11.3838	0.49773	0.0:0.915:0.0:0.085	.	.	.	.	X	74	.	ENSP00000300575:S74X	S	+	2	0	C16orf92	29942639	0.309000	0.24518	0.977000	0.42913	0.894000	0.52154	1.052000	0.30429	1.285000	0.44548	0.655000	0.94253	TCA		0.567	C16orf92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435351.1	NM_001109659		G	30035138	C	G	30035138	4	3	116	1	0	0	0	0	0	1	0	0	1849	838	29	5	241	5	C16orf92	16	30035138	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	4330948	30035138	60319615	109	31132										
CYLD	1540	hgsc.bcm.edu	37	chr16	50826539	50826539	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tctgattattcagatgcctcGatttggaaaagactttaaac	7	7	2	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:50826539G>T	ENST00000427738.3	+	15	2478	c.2273G>T	c.(2272-2274)cGa>cTa	p.R758L	RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000540145.1_Missense_Mutation_p.R758L|CYLD_ENST00000566206.1_Missense_Mutation_p.R755L|CYLD_ENST00000311559.9_Missense_Mutation_p.R758L|CYLD_ENST00000398568.2_Missense_Mutation_p.R755L|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000569418.1_Missense_Mutation_p.R755L|CYLD_ENST00000568704.2_Missense_Mutation_p.R573L|CYLD_ENST00000564326.1_Missense_Mutation_p.R755L			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	758	USP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CAGATGCCTCGATTTGGAAAA	0.264			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											39	36	37					16																	50826539		1780	4049	5829	49384040	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.2273G>T	16.37:g.50826539G>T	ENSP00000392025:p.Arg758Leu		49384040	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994567	0.74703	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D	0.91843	-2.92;-2.92;-2.92	5.69	5.69	0.88448	.	0.061256	0.64402	D	0.000002	D	0.92247	0.7541	M	0.72479	2.2	0.80722	D	1	B;B	0.24651	0.108;0.088	B;B	0.26310	0.068;0.04	D	0.89763	0.3948	10	0.87932	D	0	-8.1553	19.4071	0.94651	0.0:0.0:1.0:0.0	.	755;755	A8KAB0;Q9NQC7-2	.;.	L	758;758;755;755	ENSP00000445447:R758L;ENSP00000308928:R758L;ENSP00000381574:R755L	ENSP00000308928:R758L	R	+	2	0	CYLD	49384040	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.399000	0.97285	2.683000	0.91414	0.557000	0.71058	CGA		0.264	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			T	50826539	G	T	50826539	3	4	116	1	0	0	0	0	1	0	0	0	4149	1058	37	2	2327	2	CYLD	16	50826539	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	20791401	50826539	39528214	110	31133										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70862201	70862201	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttcagccagttggtgattggCagaagctcagtgtagggggt	16	6	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:70862201C>A	ENST00000393567.2	-	82	14394	c.14244G>T	c.(14242-14244)ctG>ctT	p.L4748L		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4748					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGTGATTGGCAGAAGCTCAG	0.567																																																0			16											1	1	1					16																	70862201		31	62	93	69419702	SO:0001819	synonymous_variant	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14244G>T	16.37:g.70862201C>A			69419702	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.567	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70862201	C	A	70862201	2	1	116	1	0	0	0	0	0	0	0	1	7488	697	25	2		2	HYDIN	16	70862201	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	20035662	70862201	19492552	111	31134										
GLG1	2734	hgsc.bcm.edu	37	chr16	74499630	74499630	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtctagctctgggtccatcaTctctgtctcctgcagcttaa	8	13	5	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:74499630T>C	ENST00000422840.2	-	19	2610	c.2611A>G	c.(2611-2613)Atg>Gtg	p.M871V	GLG1_ENST00000447066.2_Missense_Mutation_p.M860V|Y_RNA_ENST00000384794.1_RNA|GLG1_ENST00000205061.5_Missense_Mutation_p.M871V	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	871					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						GGGTCCATCATCTCTGTCTCC	0.458																																																0			16											212	201	205					16																	74499630		2198	4300	6498	73057131	SO:0001583	missense	2734				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2611A>G	16.37:g.74499630T>C	ENSP00000405984:p.Met871Val		73057131	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.644363	0.47258	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.59514	0.2199	L	0.48362	1.52	0.80722	D	1	P;B;B;B	0.38677	0.642;0.078;0.335;0.387	P;B;B;B	0.46144	0.505;0.055;0.208;0.219	T	0.53697	-0.8402	9	0.19147	T	0.46	-16.7589	16.4101	0.83708	0.0:0.0:0.0:1.0	.	1;871;871;860	Q6ZMF1;Q92896;Q92896-2;B7Z8Y4	.;GSLG1_HUMAN;.;.	V	871;860;871	.	ENSP00000205061:M871V	M	-	1	0	GLG1	73057131	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.747000	0.85070	2.280000	0.76307	0.460000	0.39030	ATG		0.458	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		C	74499630	T	C	74499630	3	2	116	1	0	0	0	0	1	0	0	0	6456	1435	50	4	1040	4	GLG1	16	74499630	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	3637429	74499630	15855123	112	31135										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81145838	81145838	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaatgtcgccccaggcacggCgtagggctgccgtgatcatg	14	12	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr16:81145838C>T	ENST00000534142.1	-	0	1301				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000533478.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCAGGCACGGCGTAGGGCTGC	0.512																																																0			16											164	154	157					16																	81145838		2007	4183	6190	79703339			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81145838C>T			79703339	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000534142.1	37																																																																																					0.512	PKD1L2-009	PUTATIVE	basic|exp_conf	processed_transcript	polymorphic_pseudogene	OTTHUMT00000387969.1			T	81145838	C	T	81145838	1	4	116	0	1	0	0	0	0	0	0	0	11996	768	27	1		1	PKD1L2	16	81145838	RNA	SNP	C	TCGA-F5-6571-01A-12D-1826-10	6646208	81145838	9208915	113	31136										
TP53	7157	hgsc.bcm.edu	37	chr17	7578263	7578263	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acgcaaatttccttccactcGgataagatgctgaggagggg	12	9	0	2	rs397516435		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:7578263G>A	ENST00000269305.4	-	6	775	c.586C>T	c.(586-588)Cga>Tga	p.R196*	TP53_ENST00000413465.2_Nonsense_Mutation_p.R196*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R196*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R196*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R196*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.R196*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	196	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R196*(167)|p.R64*(14)|p.R103*(14)|p.0?(8)|p.R196fs*51(7)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.R196R(2)|p.I195fs*50(1)|p.R64fs*>27(1)|p.R103fs*51(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I195fs*12(1)|p.P59_E66>Q(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCTTCCACTCGGATAAGATGC	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	232	Substitution - Nonsense(195)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(5)|Complex - deletion inframe(5)|Unknown(5)|Substitution - coding silent(2)|Complex - frameshift(1)	large_intestine(54)|breast(29)|upper_aerodigestive_tract(22)|lung(22)|haematopoietic_and_lymphoid_tissue(17)|skin(17)|biliary_tract(11)|central_nervous_system(11)|oesophagus(11)|ovary(11)|stomach(8)|urinary_tract(7)|bone(4)|liver(3)|pancreas(3)|eye(1)|kidney(1)	17	GRCh37	CM941329	TP53	M							102	91	94					17																	7578263		2203	4300	6503	7518988	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.586C>T	17.37:g.7578263G>A	ENSP00000269305:p.Arg196*		7518988	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409843	0.42715	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	4.44	0.53790	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.9531	12.3046	0.54895	0.0827:0.0:0.9173:0.0	.	.	.	.	X	196;196;196;196;196;196;185;103;64;103;64	.	ENSP00000269305:R196X	R	-	1	2	TP53	7518988	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	2.166000	0.42406	1.427000	0.47276	-0.140000	0.14226	CGA		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578263	G	A	7578263	4	1	116	1	0	0	0	0	0	1	0	0	16421	1124	39	1	708	1	TP53	17	7578263	Nonsense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10		7578263	73616947	114	31137										
NF1	4763	hgsc.bcm.edu	37	chr17	29496967	29496967	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atgttcatgatatagaattgTtacagtatatcaatgtggat	8	3	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:29496967T>C	ENST00000358273.4	+	5	921	c.538T>C	c.(538-540)Tta>Cta	p.L180L	NF1_ENST00000431387.4_Silent_p.L180L|NF1_ENST00000356175.3_Silent_p.L180L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	180					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.E178_D186del(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TATAGAATTGTTACAGTATAT	0.274			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(4)|Deletion - In frame(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(2)	17											91	91	91					17																	29496967		2203	4299	6502	26521093	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.538T>C	17.37:g.29496967T>C			26521093	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.274	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29496967	T	C	29496967	2	2	116	1	0	0	0	0	0	0	0	1	10387	1722	60	4		4	NF1	17	29496967	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	21918704	29496967	51698243	115	31138										
CDK12	51755	hgsc.bcm.edu	37	chr17	37650863	37650863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttcgtgaaatcaaaatccttCgtcagttaatccaccgaagt	6	10	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:37650863C>T	ENST00000447079.4	+	5	2368	c.2335C>T	c.(2335-2337)Cgt>Tgt	p.R779C	CDK12_ENST00000430627.2_Missense_Mutation_p.R779C	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	779	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CAAAATCCTTCGTCAGTTAat	0.408			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0			17											75	66	69					17																	37650863		2203	4300	6503	34904389	SO:0001583	missense	0			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2335C>T	17.37:g.37650863C>T	ENSP00000398880:p.Arg779Cys		34904389	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	19.77	3.889860	0.72524	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.67698	-0.28;-0.28	5.23	5.23	0.72850	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000162	T	0.81978	0.4937	M	0.72353	2.195	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.83707	0.0185	10	0.87932	D	0	-8.3296	19.1644	0.93548	0.0:1.0:0.0:0.0	.	778;779;779	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	C	779	ENSP00000407720:R779C;ENSP00000398880:R779C	ENSP00000407720:R779C	R	+	1	0	CDK12	34904389	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.720000	0.54933	2.601000	0.87937	0.561000	0.74099	CGT		0.408	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37650863	C	T	37650863	3	4	116	1	0	0	0	0	1	0	0	0	3134	884	31	1	2353	1	CDK12	17	37650863	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	8153896	37650863	43544347	116	31139										
CCDC40	55036	hgsc.bcm.edu	37	chr17	78014023	78014023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ccacggagtcttaggcccgtCggagcaaatgggccaggtca	14	12	2	0	rs369066468		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:78014023C>T	ENST00000397545.4	+	3	533	c.506C>T	c.(505-507)tCg>tTg	p.S169L	CCDC40_ENST00000374877.3_Missense_Mutation_p.S169L|CCDC40_ENST00000374876.4_Missense_Mutation_p.S169L|CCDC40_ENST00000269318.5_Missense_Mutation_p.S169L	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	169					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TTAGGCCCGTCGGAGCAAATG	0.617																																																0			17						C	LEU/SER	0,3942		0,0,1971	30	34	33		506	0.2	0	17		33	1,8319		0,1,4159	no	missense	CCDC40	NM_017950.3	145	0,1,6130	TT,TC,CC		0.012,0.0,0.0082	benign	169/1143	78014023	1,12261	1971	4160	6131	75628618	SO:0001583	missense	55036			AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.506C>T	17.37:g.78014023C>T	ENSP00000380679:p.Ser169Leu		75628618	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.242838	0.39598	0.0	1.2E-4	ENSG00000141519	ENST00000374877;ENST00000269318;ENST00000374876;ENST00000397545	T;T;T;T	0.59502	0.3;0.26;0.29;0.38	2.22	0.194	0.15143	.	.	.	.	.	T	0.39226	0.1070	L	0.27053	0.805	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.12156	0.007;0.001	T	0.29458	-1.0011	9	0.54805	T	0.06	.	4.5223	0.11964	0.0:0.6662:0.0:0.3338	.	169;169	Q4G0X9-5;Q4G0X9	.;CCD40_HUMAN	L	169	ENSP00000364011:S169L;ENSP00000269318:S169L;ENSP00000364010:S169L;ENSP00000380679:S169L	ENSP00000269318:S169L	S	+	2	0	CCDC40	75628618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.221000	0.17680	0.093000	0.17368	-0.123000	0.14984	TCG		0.617	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78014023	C	T	78014023	3	4	116	1	0	0	0	0	1	0	0	0	2818	893	31	1	516	1	CCDC40	17	78014023	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	40363160	78014023	3181187	117	31140										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78882647	78882647	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tgtttacactcagatttggaGagtcctgctgcacctggctg	11	10	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:78882647G>T	ENST00000306801.3	+	21	2800	c.2438G>T	c.(2437-2439)aGa>aTa	p.R813I	RPTOR_ENST00000544334.2_Missense_Mutation_p.R655I|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	813					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R813K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CAGATTTGGAGAGTCCTGCTG	0.527																																																1	Substitution - Missense(1)	urinary_tract(1)	17											177	186	183					17																	78882647		2203	4300	6503	76497242	SO:0001583	missense	57521				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.2438G>T	17.37:g.78882647G>T	ENSP00000307272:p.Arg813Ile		76497242	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474794	0.84640	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.35236	1.32;1.32	4.77	4.77	0.60923	Armadillo-like helical (1);Armadillo-type fold (1);	0.117924	0.56097	D	0.000034	T	0.46658	0.1404	N	0.22421	0.69	0.80722	D	1	D;P	0.64830	0.994;0.704	D;B	0.74348	0.983;0.065	T	0.44329	-0.9335	10	0.40728	T	0.16	.	17.7606	0.88463	0.0:0.0:1.0:0.0	.	655;813	F5H7J5;Q8N122	.;RPTOR_HUMAN	I	813;655	ENSP00000307272:R813I;ENSP00000442479:R655I	ENSP00000307272:R813I	R	+	2	0	RPTOR	76497242	1.000000	0.71417	0.991000	0.47740	0.720000	0.41350	8.992000	0.93519	2.363000	0.80096	0.585000	0.79938	AGA		0.527	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78882647	G	T	78882647	3	4	116	1	0	0	0	0	1	0	0	0	13702	942	33	2	2520	2	RPTOR	17	78882647	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	868624	78882647	2312563	118	31141										
C17orf70	80233	hgsc.bcm.edu	37	chr17	79514034	79514034	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ggcccgcagggaggcgggtcCtgctggctggctgccaggct	19	13	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr17:79514034C>A	ENST00000327787.8	-	5	2120	c.2074G>T	c.(2074-2076)Gga>Tga	p.G692*	C17orf70_ENST00000537152.1_Nonsense_Mutation_p.G541*|C17orf70_ENST00000425898.2_Nonsense_Mutation_p.G341*			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	692					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GAGGCGGGTCCTGCTGGCTGG	0.687																																																0			17											8	10	9					17																	79514034		2169	4255	6424	77124487	SO:0001587	stop_gained	80233			BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.2074G>T	17.37:g.79514034C>A	ENSP00000333283:p.Gly692*		77124487	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Nonsense_Mutation	SNP	ENST00000327787.8	37	CCDS32765.2	.	.	.	.	.	.	.	.	.	.	C	40	8.116053	0.98662	.	.	ENSG00000185504	ENST00000327787;ENST00000425898;ENST00000361039;ENST00000537152	.	.	.	4.52	4.52	0.55395	.	0.361104	0.25695	N	0.028905	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.1177	0.53873	0.0:0.8264:0.1735:0.0	.	.	.	.	X	692;341;65;541	.	ENSP00000333283:G692X	G	-	1	0	C17orf70	77124487	0.002000	0.14202	0.010000	0.14722	0.002000	0.02628	1.203000	0.32284	2.343000	0.79666	0.655000	0.94253	GGA		0.687	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		A	79514034	C	A	79514034	4	1	116	1	0	0	0	0	0	1	0	0	1882	690	24	2	591	2	C17orf70	17	79514034	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	631387	79514034	1681176	119	31142										
YES1	7525	hgsc.bcm.edu	37	chr18	746048	746048	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctccccattttgccaaaataCcatctggaaaaaaattaagt	4	10	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr18:746048C>T	ENST00000584307.1	-	5	644	c.474G>A	c.(472-474)tgG>tgA	p.W158*	YES1_ENST00000577961.1_Nonsense_Mutation_p.W163*|YES1_ENST00000314574.4_Nonsense_Mutation_p.W158*			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	158	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	TGCCAAAATACCATCTGGAAA	0.343																																																0			18											39	40	40					18																	746048		2191	4287	6478	736048	SO:0001587	stop_gained	7525			M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"SH2 domain containing"	12841	protein-coding gene	gene with protein product		164880	"v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.474G>A	18.37:g.746048C>T	ENSP00000462468:p.Trp158*		736048	A6NLB3|D3DUH1	Nonsense_Mutation	SNP	ENST00000584307.1	37	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	C	37	6.492415	0.97612	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.8338	0.96646	0.0:1.0:0.0:0.0	.	.	.	.	X	158	.	ENSP00000324740:W158X	W	-	3	0	YES1	736048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.717000	0.84732	2.692000	0.91855	0.591000	0.81541	TGG		0.343	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		T	746048	C	T	746048	4	4	116	1	0	0	0	0	0	1	0	0	17514	508	18	3	1189	3	YES1	18	746048	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10		746048	77331200	120	31143										
PRSSL1	400668	hgsc.bcm.edu	37	chr19	691933	691933	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtgagagcatcgatgccaaaCacctgctgggtgggctccgc	14	12	0	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:691933C>T	ENST00000329267.7	-	3	335	c.306G>A	c.(304-306)gtG>gtA	p.V102V		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	102	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						CGATGCCAAACACCTGCTGGG	0.672																																																0			19											90	59	69					19																	691933		2203	4300	6503	642933	SO:0001819	synonymous_variant	400668			AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"Serine peptidases / Serine peptidases"	31397	protein-coding gene	gene with protein product			"protease, serine-like 1"	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.306G>A	19.37:g.691933C>T			642933	B2RNW8	Silent	SNP	ENST00000329267.7	37	CCDS12041.1																																																																																				0.672	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710		T	691933	C	T	691933	2	4	116	1	0	0	0	0	0	0	0	1	12670	465	17	3		3	PRSSL1	19	691933	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10		691933	58437050	121	31144										
MUC16	94025	hgsc.bcm.edu	37	chr19	9049229	9049229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tagttgtacttgtctttgccGccaaactggtgaccattgag	10	9	1	2	rs370847991		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:9049229G>A	ENST00000397910.4	-	5	32605	c.32402C>T	c.(32401-32403)gCg>gTg	p.A10801V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10803	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTCTTTGCCGCCAAACTGGT	0.502																																																0			19							VAL/ALA	0,3956		0,0,1978	174	159	164		32402	-5	0	19		164	1,8333		0,1,4166	no	missense	MUC16	NM_024690.2	64	0,1,6144	AA,AG,GG		0.012,0.0,0.0081	benign	10801/14508	9049229	1,12289	1978	4167	6145	8910229	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32402C>T	19.37:g.9049229G>A	ENSP00000381008:p.Ala10801Val		8910229	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	8.348	0.830163	0.16749	0.0	1.2E-4	ENSG00000181143	ENST00000397910	T	0.02709	4.19	2.86	-4.99	0.03010	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	.	.	.	B	0.25521	0.128	B	0.14578	0.011	T	0.47018	-0.9149	8	0.87932	D	0	.	1.0837	0.01648	0.1634:0.2854:0.3273:0.2239	.	10801	B5ME49	.	V	10801	ENSP00000381008:A10801V	ENSP00000381008:A10801V	A	-	2	0	MUC16	8910229	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.244000	0.02902	-0.758000	0.04690	-0.629000	0.03991	GCG		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9049229	G	A	9049229	3	1	116	1	0	0	0	0	1	0	0	0	10003	1087	38	1	11441	1	MUC16	19	9049229	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	8357296	9049229	50079754	122	31145										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10250808	10250808	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ccgctgaagccctggcagggCggcccgccgcacagcatctc	13	18	1	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:10250808C>G	ENST00000340748.4	-	32	3907	c.3672G>C	c.(3670-3672)ccG>ccC	p.P1224P	DNMT1_ENST00000540357.1_Silent_p.P1224P|DNMT1_ENST00000589538.1_Intron|DNMT1_ENST00000359526.4_Silent_p.P1240P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1224	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CCTGGCAGGGCGGCCCGCCGC	0.607																																																0			19											41	44	43					19																	10250808		2203	4300	6503	10111808	SO:0001819	synonymous_variant	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.3672G>C	19.37:g.10250808C>G			10111808	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																				0.607	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		G	10250808	C	G	10250808	2	3	116	1	0	0	0	0	0	0	0	1	4686	755	27	5		5	DNMT1	19	10250808	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1201579	10250808	48878175	123	31146										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10406046	10406046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gccagtggtggccgaacttgCtgcctcgccccctggaggcg	15	15	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:10406046C>T	ENST00000221980.4	+	10	2318	c.2255C>T	c.(2254-2256)gCt>gTt	p.A752V		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	752	Ig-like C2-type 9.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			GCCGAACTTGCTGCCTCGCCC	0.692																																																0			19											12	14	13					19																	10406046		2138	4261	6399	10267046	SO:0001583	missense	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2255C>T	19.37:g.10406046C>T	ENSP00000221980:p.Ala752Val		10267046	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.250123	0.39797	.	.	ENSG00000105376	ENST00000221980	T	0.33438	1.41	4.72	3.63	0.41609	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.131104	0.35067	N	0.003477	T	0.09642	0.0237	N	0.01576	-0.805	0.31812	N	0.627062	B	0.32409	0.37	B	0.30316	0.114	T	0.06075	-1.0847	10	0.28530	T	0.3	-22.1816	7.0059	0.24836	0.0:0.8736:0.0:0.1264	.	752	Q9UMF0	ICAM5_HUMAN	V	752	ENSP00000221980:A752V	ENSP00000221980:A752V	A	+	2	0	ICAM5	10267046	0.883000	0.30277	0.956000	0.39512	0.360000	0.29518	1.519000	0.35888	2.469000	0.83416	0.549000	0.68633	GCT		0.692	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		T	10406046	C	T	10406046	3	4	116	1	0	0	0	0	1	0	0	0	7504	797	28	3	2293	3	ICAM5	19	10406046	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	155238	10406046	48722937	124	31147										
MED26	9441	hgsc.bcm.edu	37	chr19	16687285	16687285	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	agctctgtcctggactgctgCtccatgtgcacagggctgtc	12	13	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:16687285C>T	ENST00000263390.3	-	3	1618	c.1356G>A	c.(1354-1356)gaG>gaA	p.E452E	CTC-429P9.4_ENST00000593962.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Intron	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	452					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						TGGACTGCTGCTCCATGTGCA	0.577																																																0			19											85	73	77					19																	16687285		2203	4300	6503	16548285	SO:0001819	synonymous_variant	9441			AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.1356G>A	19.37:g.16687285C>T			16548285	A1A4S3|Q0VGB6	Silent	SNP	ENST00000263390.3	37	CCDS12347.1																																																																																				0.577	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		T	16687285	C	T	16687285	2	4	116	1	0	0	0	0	0	0	0	1	9474	796	28	3		3	MED26	19	16687285	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	6281239	16687285	42441698	125	31148										
FKBP8	23770	hgsc.bcm.edu	37	chr19	18652666	18652677	+	In_Frame_Del	DEL	CTTCCTCCTCAC	CTTCCTCCTCAC	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttcctcctcttcctcctcctCttcctcctcaccctctgcat					rs371561631		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	CTTCCTCCTCAC	CTTCCTCCTCAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:18652666_18652677delCTTCCTCCTCAC	ENST00000596558.2	-	2	213_224	c.104_115delGTGAGGAGGAAG	c.(103-117)ggtgaggaggaagag>gag	p.GEEE35del	FKBP8_ENST00000453489.2_In_Frame_Del_p.GEEE64del|FKBP8_ENST00000222308.4_In_Frame_Del_p.GEEE35del|FKBP8_ENST00000608443.1_In_Frame_Del_p.GEEE35del|FKBP8_ENST00000597960.3_In_Frame_Del_p.GEEE35del|FKBP8_ENST00000610101.1_In_Frame_Del_p.GEEE35del			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	35	Glu-rich.				apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						tcctcctcctcttcctcctcACCCTCTGCATC	0.656																																																0			19																																								18513677	SO:0001651	inframe_deletion	23770			L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"Tetratricopeptide (TTC) repeat domain containing"	3724	protein-coding gene	gene with protein product	"FK506-binding protein 8 (38kD)"	604840	"FK506-binding protein 8 (38kD)"			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.104_115delGTGAGGAGGAAG	19.37:g.18652666_18652677delCTTCCTCCTCAC	ENSP00000472302:p.Gly35_Glu38del		18513666	C8C9T5|Q53GU3|Q7Z349|Q86YK6	In_Frame_Del	DEL	ENST00000596558.2	37																																																																																					0.656	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		-	18652677	CTTCCTCCTCAC	-	18652666	7	5	116	1	0	1	0	1	0	0	0	0	5933	922	32	0	1158	0	FKBP8	19	18652666	In_Frame_Del	DEL	CTTCCTCCTCAC	TCGA-F5-6571-01A-12D-1826-10	1965381	18652666	40476317	126	31149			2	37		2	2	12	N	CTTCCTCCTCAC_C	5.294352e-05
FKBP8	23770	hgsc.bcm.edu	37	chr19	18652677	18652677	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cctcctcctcttcctcctcaCcctctgcatcctcaacccca	1	24	4	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:18652677C>T	ENST00000596558.2	-	2	213	c.104G>A	c.(103-105)gGt>gAt	p.G35D	FKBP8_ENST00000453489.2_Missense_Mutation_p.G64D|FKBP8_ENST00000222308.4_Missense_Mutation_p.G35D|FKBP8_ENST00000608443.1_Missense_Mutation_p.G35D|FKBP8_ENST00000597960.3_Missense_Mutation_p.G35D|FKBP8_ENST00000610101.1_Missense_Mutation_p.G35D			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	35	Glu-rich.				apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						ttcctcctcACCCTCTGCATC	0.647																																																0			19											36	29	31					19																	18652677		2203	4300	6503	18513677	SO:0001583	missense	23770			L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"Tetratricopeptide (TTC) repeat domain containing"	3724	protein-coding gene	gene with protein product	"FK506-binding protein 8 (38kD)"	604840	"FK506-binding protein 8 (38kD)"			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.104G>A	19.37:g.18652677C>T	ENSP00000472302:p.Gly35Asp		18513677	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	37		.	.	.	.	.	.	.	.	.	.	C	8.429	0.848183	0.17034	.	.	ENSG00000105701	ENST00000222308;ENST00000544835;ENST00000453489	T;T;T	0.34667	1.35;1.51;1.59	3.69	-2.81	0.05805	.	1.277580	0.06064	N	0.658782	T	0.14570	0.0352	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19289	-1.0310	10	0.32370	T	0.25	-4.5216	0.3233	0.00306	0.2558:0.2493:0.1383:0.3565	.	64;35;35	B7Z6M0;Q14318;Q14318-2	.;FKBP8_HUMAN;.	D	35;35;64	ENSP00000222308:G35D;ENSP00000441267:G35D;ENSP00000388891:G64D	ENSP00000222308:G35D	G	-	2	0	FKBP8	18513677	0.000000	0.05858	0.012000	0.15200	0.145000	0.21501	-0.289000	0.08365	-0.093000	0.12396	0.491000	0.48974	GGT		0.647	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		T	18652677	C	T	18652677	3	4	116	1	0	0	0	0	1	0	0	0	5933	507	18	3	1169	3	FKBP8	19	18652677	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	11	18652677	40476306	127	31150			2	37		2	2	12	N	CTTCCTCCTCAC_C	5.294352e-05
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55603861	55603861	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tctggctcaggttctgggttGaggtcccgctgccaccgctg	14	13	3	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr19:55603861G>A	ENST00000263433.3	-	18	2019	c.2004C>T	c.(2002-2004)ctC>ctT	p.L668L	PPP1R12C_ENST00000435544.2_Silent_p.L593L|PPP1R12C_ENST00000376393.2_Silent_p.L605L	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GTTCTGGGTTGAGGTCCCGCT	0.726																																																0			19											19	22	21					19																	55603861		2188	4292	6480	60295673	SO:0001819	synonymous_variant	54776			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14947	protein-coding gene	gene with protein product	"myosin-binding subunit 85"	613245	"leukocyte receptor cluster (LRC) member 3", "protein phosphatase 1, regulatory (inhibitor) subunit 12C"	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.2004C>T	19.37:g.55603861G>A			60295673		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																				0.726	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		A	55603861	G	A	55603861	2	1	116	1	0	0	0	0	0	0	0	1	12390	1277	45	3		3	PPP1R12C	19	55603861	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	36951184	55603861	3525122	128	31151										
ANGPT4	51378	hgsc.bcm.edu	37	chr20	853640	853640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtatcatcatgcgagaggcaCgcagtgagtagctggggccc	15	10	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr20:853640C>T	ENST00000381922.3	-	9	1577	c.1475G>A	c.(1474-1476)cGt>cAt	p.R492H	ANGPT4_ENST00000546022.1_3'UTR	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	492	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GCGAGAGGCACGCAGTGAGTA	0.572																																					Pancreas(181;481 2077 3259 31286 49856)											0			20											134	118	123					20																	853640		2203	4300	6503	801640	SO:0001583	missense	51378			AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1475G>A	20.37:g.853640C>T	ENSP00000371347:p.Arg492His		801640	B4E3J9|Q5TFF4|Q9H4Z4	Missense_Mutation	SNP	ENST00000381922.3	37	CCDS13009.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089882	0.36855	.	.	ENSG00000101280	ENST00000381922	T	0.21543	2.0	4.25	3.29	0.37713	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.074260	0.53938	N	0.000050	T	0.17619	0.0423	L	0.56769	1.78	0.80722	D	1	P	0.47962	0.903	B	0.39027	0.288	T	0.02728	-1.1118	10	0.59425	D	0.04	.	5.1263	0.14886	0.0:0.6414:0.0:0.3586	.	492	Q9Y264	ANGP4_HUMAN	H	492	ENSP00000371347:R492H	ENSP00000371347:R492H	R	-	2	0	ANGPT4	801640	0.967000	0.33354	0.771000	0.31576	0.622000	0.37654	2.153000	0.42282	0.979000	0.38497	0.491000	0.48974	CGT		0.572	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		T	853640	C	T	853640	3	4	116	1	0	0	0	0	1	0	0	0	612	536	19	1	40	1	ANGPT4	20	853640	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10		853640	62171880	129	31152										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31019464	31019464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cccatgcggctcagagctggCgggagcgcctggctgatggt	17	12	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr20:31019464C>T	ENST00000375687.4	+	10	1385	c.961C>T	c.(961-963)Cgg>Tgg	p.R321W	ASXL1_ENST00000306058.5_Missense_Mutation_p.R316W	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	321	Interaction with KDM1A. {ECO:0000250}.|Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TCAGAGCTGGCGGGAGCGCCT	0.542			"F, N, Mis"		"MDS, CMML"																																		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0			20											54	55	54					20																	31019464		2203	4300	6503	30483125	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.961C>T	20.37:g.31019464C>T	ENSP00000364839:p.Arg321Trp		30483125	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.664004	0.67700	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058;ENST00000553345	T;T	0.20200	2.09;2.09	5.27	1.98	0.26296	.	0.053822	0.64402	D	0.000001	T	0.41719	0.1171	M	0.64404	1.975	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.43147	-0.9409	10	0.87932	D	0	-15.6676	13.7913	0.63143	0.4889:0.5111:0.0:0.0	.	316;321	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	W	321;321;321;260;316;93	ENSP00000364839:R321W;ENSP00000305119:R316W	ENSP00000305119:R316W	R	+	1	2	ASXL1	30483125	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.953000	0.40352	0.755000	0.32990	0.650000	0.86243	CGG		0.542	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31019464	C	T	31019464	3	4	116	1	0	0	0	0	1	0	0	0	1067	759	27	1	1005	1	ASXL1	20	31019464	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	30165824	31019464	32006056	130	31153										
GDF5	8200	hgsc.bcm.edu	37	chr20	34025243	34025243	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	aaacggctccttgggctctcGtgggggcccgggctccctgg	16	14	1	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr20:34025243G>A	ENST00000374372.1	-	3	969	c.466C>T	c.(466-468)Cga>Tga	p.R156*	GDF5_ENST00000374369.3_Nonsense_Mutation_p.R156*			P43026	GDF5_HUMAN	growth differentiation factor 5	156					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			TTGGGCTCTCGTGGGGGCCCG	0.632																																																0			20											49	55	53					20																	34025243		2203	4300	6503	33488657	SO:0001587	stop_gained	8200			X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.466C>T	20.37:g.34025243G>A	ENSP00000363492:p.Arg156*		33488657	E1P5Q2|Q96SB1	Nonsense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787004	0.90367	.	.	ENSG00000125965	ENST00000374369;ENST00000374372	.	.	.	4.48	3.46	0.39613	.	0.355112	0.22460	N	0.059777	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9315	0.41525	0.0:0.0:0.5838:0.4162	.	.	.	.	X	156	.	ENSP00000363489:R156X	R	-	1	2	GDF5	33488657	1.000000	0.71417	0.998000	0.56505	0.087000	0.18053	4.338000	0.59316	2.304000	0.77564	0.313000	0.20887	CGA		0.632	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			A	34025243	G	A	34025243	4	1	116	1	0	0	0	0	0	1	0	0	6336	1153	40	1	1047	1	GDF5	20	34025243	Nonsense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	3005779	34025243	29000277	131	31154										
KCNB1	3745	hgsc.bcm.edu	37	chr20	48098748	48098748	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttgaggatggaggtgaaggcGcccgggtggcggtcaaagaa	19	6	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr20:48098748G>A	ENST00000371741.4	-	1	436	c.270C>T	c.(268-270)ggC>ggT	p.G90G		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	90					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)	p.G90G(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	AGGTGAAGGCGCCCGGGTGGC	0.607																																																1	Substitution - coding silent(1)	lung(1)	20											48	38	42					20																	48098748		2203	4300	6503	47532155	SO:0001819	synonymous_variant	3745			AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.270C>T	20.37:g.48098748G>A			47532155	Q14193	Silent	SNP	ENST00000371741.4	37	CCDS13418.1																																																																																				0.607	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		A	48098748	G	A	48098748	2	1	116	1	0	0	0	0	0	0	0	1	8033	1074	38	1		1	KCNB1	20	48098748	Silent	SNP	G	TCGA-F5-6571-01A-12D-1826-10	14073505	48098748	14926772	132	31155										
SNAI1	6615	hgsc.bcm.edu	37	chr20	48604411	48604411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctggcgttctctccccaggcGagaagcccttctcctgtccc	9	18	2	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr20:48604411G>A	ENST00000244050.2	+	3	674	c.613G>A	c.(613-615)Gag>Aag	p.E205K		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	205	Required for nuclear localization and interaction with KPNB1, NOTCH1 and PARP1.				cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	p.E205*(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CTCCCCAGGCGAGAAGCCCTT	0.622																																																1	Substitution - Nonsense(1)	lung(1)	20											75	67	69					20																	48604411		2203	4300	6503	48037818	SO:0001583	missense	6615			AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"Snail homologs", "Zinc fingers, C2H2-type"	11128	protein-coding gene	gene with protein product		604238	"snail 1 (drosophila homolog), zinc finger protein", "snail homolog 1 (Drosophila)"			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.613G>A	20.37:g.48604411G>A	ENSP00000244050:p.Glu205Lys		48037818	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	.	.	.	.	.	.	.	.	.	.	G	35	5.420325	0.96111	.	.	ENSG00000124216	ENST00000244050	T	0.24350	1.86	4.96	4.96	0.65561	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.52645	0.1747	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.56980	-0.7889	10	0.87932	D	0	-28.8275	18.5926	0.91218	0.0:0.0:1.0:0.0	.	205	O95863	SNAI1_HUMAN	K	205	ENSP00000244050:E205K	ENSP00000244050:E205K	E	+	1	0	SNAI1	48037818	1.000000	0.71417	0.964000	0.40570	0.805000	0.45488	9.420000	0.97426	2.462000	0.83206	0.455000	0.32223	GAG		0.622	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1			A	48604411	G	A	48604411	3	1	116	1	0	0	0	0	1	0	0	0	14863	1059	37	1	623	1	SNAI1	20	48604411	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	505663	48604411	14421109	133	31156										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19701534	19701534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	atctcttatttcaactacatCgttaatattttctaagtcaa	2	8	4	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr21:19701534C>T	ENST00000284885.3	-	15	1765	c.1732G>A	c.(1732-1734)Gat>Aat	p.D578N		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	578	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.D578N(2)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCAACTACATCGTTAATATTT	0.308																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	21											91	88	89					21																	19701534		2203	4298	6501	18623405	SO:0001583	missense	0				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1732G>A	21.37:g.19701534C>T	ENSP00000284885:p.Asp578Asn		18623405	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.758031	0.69648	.	.	ENSG00000154646	ENST00000284885	T	0.33865	1.39	5.53	5.53	0.82687	CUB (5);	0.000000	0.85682	D	0.000000	T	0.71443	0.3340	H	0.94345	3.525	0.53005	D	0.999961	D	0.89917	1.0	D	0.97110	1.0	T	0.79598	-0.1737	9	.	.	.	.	17.3132	0.87215	0.0:1.0:0.0:0.0	.	578	P98073	ENTK_HUMAN	N	578	ENSP00000284885:D578N	.	D	-	1	0	TMPRSS15	18623405	1.000000	0.71417	0.983000	0.44433	0.332000	0.28634	5.609000	0.67661	2.758000	0.94735	0.655000	0.94253	GAT		0.308	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19701534	C	T	19701534	3	4	116	1	0	0	0	0	1	0	0	0	16285	884	31	1	1371	1	TMPRSS15	21	19701534	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10		19701534	28428361	134	31157										
GGT1	2678	hgsc.bcm.edu	37	chr22	25017037	25017037	+	Splice_Site	DEL	G	G	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tgaaggacatccaggcggccGgtgagtgggtaacctcaggg					rs74210474		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr22:25017037delG	ENST00000400382.1	+	9	1488	c.733delG	c.(733-735)ggg>gg	p.G246fs	GGT1_ENST00000406383.2_Splice_Site_p.G246fs|GGT1_ENST00000400380.1_Splice_Site_p.G246fs|GGT1_ENST00000466310.1_Intron|GGT1_ENST00000400383.1_Splice_Site_p.G246fs|GGT1_ENST00000248923.4_Splice_Site_p.G246fs			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	246					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	CCAGGCGGCCGGTGAGTGGGT	0.632																																																0			22											8	8	8					22																	25017037		1894	4096	5990	23347037	SO:0001630	splice_region_variant	2678			M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"CD molecules", "Gamma-glutamyltransferases"	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.733+1G>-	22.37:g.25017037delG			23347037	Q08247|Q14404|Q8TBS1|Q9UMK1	Frame_Shift_Del	DEL	ENST00000400382.1	37	CCDS42992.1																																																																																				0.632	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	Frame_Shift_Del	-	25017037	G	-	25017037	8	5	116	1	0	1	0	1	0	0	1	0	6381	1130	39	0	751	0	GGT1	22	25017037	Splice_Site	DEL	G	TCGA-F5-6571-01A-12D-1826-10		25017037	26287529	135	31158										
TFIP11	24144	hgsc.bcm.edu	37	chr22	26894921	26894921	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cttttccacttagagatgatCtcggtgccataagtgcagtc	9	10	1	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr22:26894921C>T	ENST00000407690.1	-	10	1633	c.1350G>A	c.(1348-1350)gaG>gaA	p.E450E	TFIP11_ENST00000405938.1_Silent_p.E450E|TFIP11_ENST00000407431.1_Silent_p.E450E|TFIP11_ENST00000496523.1_5'Flank|TFIP11_ENST00000407148.1_Silent_p.E450E	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	450					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						TAGAGATGATCTCGGTGCCAT	0.557																																																0			22											159	152	155					22																	26894921		2203	4300	6503	25224921	SO:0001819	synonymous_variant	24144			AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"G patch domain containing"	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.1350G>A	22.37:g.26894921C>T			25224921	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1																																																																																				0.557	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697		T	26894921	C	T	26894921	2	4	116	1	0	0	0	0	0	0	0	1	15846	912	32	3		3	TFIP11	22	26894921	Silent	SNP	C	TCGA-F5-6571-01A-12D-1826-10	1877884	26894921	24409645	136	31159										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	43950910	43950910	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gcgagccaggatgtctctgtCggctgtggccttgggagagg	18	9	1	1	rs376390055		TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chr22:43950910C>T	ENST00000262726.7	-	27	3740	c.3487G>A	c.(3487-3489)Gac>Aac	p.D1163N	EFCAB6_ENST00000461800.1_5'UTR|EFCAB6_ENST00000396231.2_Missense_Mutation_p.D1011N	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1163					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATGTCTCTGTCGGCTGTGGCC	0.507																																																0			22						C	ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	96	88	91		3487,3031	-9.8	0	22		91	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	23,23	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign	1163/1502,1011/1350	43950910	2,13004	2203	4300	6503	42282243	SO:0001583	missense	64800			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3487G>A	22.37:g.43950910C>T	ENSP00000262726:p.Asp1163Asn		42282243	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	2.699	-0.271462	0.05716	2.27E-4	1.16E-4	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.13901	2.55;2.56	4.88	-9.75	0.00506	.	3.661370	0.00447	N	0.000090	T	0.02571	0.0078	N	0.00538	-1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38478	-0.9659	10	0.17832	T	0.49	0.6795	2.2884	0.04132	0.325:0.3146:0.2467:0.1137	.	1011;1163	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	N	1011;1163	ENSP00000379533:D1011N;ENSP00000262726:D1163N	ENSP00000262726:D1163N	D	-	1	0	EFCAB6	42282243	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.741000	0.04855	-2.857000	0.00329	-1.021000	0.02439	GAC		0.507	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	43950910	C	T	43950910	3	4	116	1	0	0	0	0	1	0	0	0	4950	884	31	1	1042	1	EFCAB6	22	43950910	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	17055989	43950910	7353656	137	31160										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3239201	3239201	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	actgggaagtgctggcttagTggtggtggtttgtcccaaag	16	6	0	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:3239201T>C	ENST00000217939.6	-	5	4679	c.4525A>G	c.(4525-4527)Act>Gct	p.T1509A		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1509						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GCTGGCTTAGTGGTGGTGGTT	0.473																																																0			X											151	132	138					X																	3239201		2203	4300	6503	3249201	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4525A>G	X.37:g.3239201T>C	ENSP00000217939:p.Thr1509Ala		3249201	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	t	0.041	-1.285341	0.01387	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62788	0.0	2.87	-3.72	0.04411	.	0.837651	0.09848	N	0.747936	T	0.30727	0.0774	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24154	-1.0168	10	0.09590	T	0.72	.	5.0762	0.14632	0.0:0.3822:0.309:0.3088	.	1509	Q9NR99	MXRA5_HUMAN	A	1509	ENSP00000217939:T1509A	ENSP00000217939:T1509A	T	-	1	0	MXRA5	3249201	0.011000	0.17503	0.000000	0.03702	0.009000	0.06853	0.292000	0.19011	-0.862000	0.04089	0.225000	0.17782	ACT		0.473	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3239201	T	C	3239201	3	2	116	1	0	0	0	0	1	0	0	0	10033	1696	59	4	3973	4	MXRA5	23	3239201	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10		3239201	152031359	138	31161										
NHS	4810	hgsc.bcm.edu	37	chrX	17750558	17750558	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ctgacgggagcccacatgacGaccgttcctcccagagttca	10	15	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:17750558G>T	ENST00000380060.3	+	8	5205	c.4867G>T	c.(4867-4869)Gac>Tac	p.D1623Y	NHS_ENST00000398097.3_Missense_Mutation_p.D1467Y	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1644					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					CCCACATGACGACCGTTCCTC	0.567																																																0			X											74	76	75					X																	17750558		2203	4300	6503	17660479	SO:0001583	missense	4810				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.4867G>T	X.37:g.17750558G>T	ENSP00000369400:p.Asp1623Tyr		17660479	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248520	0.80024	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.57907	0.37;0.38	5.87	5.87	0.94306	.	0.095474	0.64402	D	0.000001	T	0.72953	0.3525	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.74172	-0.3751	10	0.72032	D	0.01	-23.1882	19.3889	0.94570	0.0:0.0:1.0:0.0	.	1644;1465;1467;1623	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	Y	1623;1467;1465	ENSP00000369400:D1623Y;ENSP00000381170:D1467Y	ENSP00000369397:D1465Y	D	+	1	0	NHS	17660479	1.000000	0.71417	0.955000	0.39395	0.678000	0.39670	9.226000	0.95229	2.618000	0.88619	0.600000	0.82982	GAC		0.567	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		T	17750558	G	T	17750558	3	4	116	1	0	0	0	0	1	0	0	0	10442	1058	37	2	5002	2	NHS	23	17750558	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	14511357	17750558	137520002	139	31162										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49851219	49851219	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	acattgcctggtgtcggaagCgaaagaccacccagttgggc	13	11	0	1			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:49851219C>T	ENST00000307367.2	+	8	1330	c.1039C>T	c.(1039-1041)Cga>Tga	p.R347*	CLCN5_ENST00000376088.3_Nonsense_Mutation_p.R417*|CLCN5_ENST00000376108.3_Nonsense_Mutation_p.R347*|CLCN5_ENST00000376091.3_Nonsense_Mutation_p.R417*			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	347					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					GTGTCGGAAGCGAAAGACCAC	0.512																																																0			X	GRCh37	CM983859	CLCN5	M							110	86	94					X																	49851219		2203	4300	6503	49737959	SO:0001587	stop_gained	1184			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1039C>T	X.37:g.49851219C>T	ENSP00000304257:p.Arg347*		49737959	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Nonsense_Mutation	SNP	ENST00000307367.2	37	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	C	40	8.131018	0.98670	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.7086	17.5228	0.87792	0.0:1.0:0.0:0.0	.	.	.	.	X	417;249;417;347;347	.	ENSP00000304257:R347X	R	+	1	2	CLCN5	49737959	1.000000	0.71417	0.995000	0.50966	0.803000	0.45373	3.995000	0.57001	2.408000	0.81797	0.436000	0.28706	CGA		0.512	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			T	49851219	C	T	49851219	4	4	116	1	0	0	0	0	0	1	0	0	3472	760	27	1	1283	1	CLCN5	23	49851219	Nonsense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	32100661	49851219	105419341	140	31163										
TAF1	6872	hgsc.bcm.edu	37	chrX	70603938	70603938	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gtgaggaaaatggacccttaAtgatgcaggttggcatggca	14	6	0	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:70603938A>G	ENST00000373790.4	+	13	2122	c.2071A>G	c.(2071-2073)Atg>Gtg	p.M691V	TAF1_ENST00000276072.3_Missense_Mutation_p.M712V|TAF1_ENST00000449580.1_Missense_Mutation_p.M691V|TAF1_ENST00000423759.1_Missense_Mutation_p.M712V	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	691	Histone acetyltransferase (HAT).		M -> I (in a lung bronchoalveolar carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TGGACCCTTAATGATGCAGGT	0.408																																																0			X											129	107	115					X																	70603938		2203	4298	6501	70520663	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2071A>G	X.37:g.70603938A>G	ENSP00000362895:p.Met691Val		70520663	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	12.72	2.021232	0.35701	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.88	5.88	0.94601	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.176391	0.64402	D	0.000011	T	0.13372	0.0324	L	0.28740	0.885	0.35957	D	0.834345	B;B	0.14012	0.009;0.007	B;B	0.22880	0.042;0.012	T	0.07809	-1.0753	10	0.52906	T	0.07	.	15.2112	0.73225	1.0:0.0:0.0:0.0	.	691;712	P21675;P21675-2	TAF1_HUMAN;.	V	691;691;712;712	ENSP00000362895:M691V;ENSP00000389000:M691V;ENSP00000406549:M712V;ENSP00000276072:M712V	ENSP00000276072:M712V	M	+	1	0	TAF1	70520663	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.495000	0.60353	1.976000	0.57569	0.486000	0.48141	ATG		0.408	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70603938	A	G	70603938	3	3	116	1	0	0	0	0	1	0	0	0	15552	101	4	4	2184	4	TAF1	23	70603938	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	20752719	70603938	84666622	141	31164										
HMGN5	79366	hgsc.bcm.edu	37	chrX	80370223	80370223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcctcttttccttcttcctcTtcttttaaatcttctttctc	0	14	7	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:80370223T>C	ENST00000358130.2	-	7	1102	c.774A>G	c.(772-774)gaA>gaG	p.E258E	HMGN5_ENST00000491275.1_5'Flank	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	258					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						cttcttcctcttcttttaaat	0.343																																																0			X											240	213	222					X																	80370223		1620	2844	4464	80256879	SO:0001819	synonymous_variant	0			AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"High-mobility group / Canonical"	8013	protein-coding gene	gene with protein product		300385	"nucleosomal binding protein 1", "high-mobility group nucleosome binding domain 5"	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.774A>G	X.37:g.80370223T>C			80256879	Q5JSL1	Silent	SNP	ENST00000358130.2	37	CCDS14448.1																																																																																				0.343	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763		C	80370223	T	C	80370223	2	2	116	1	0	0	0	0	0	0	0	1	7259	1606	56	4		4	HMGN5	23	80370223	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	9766285	80370223	74900337	142	31165										
CXorf57	55086	hgsc.bcm.edu	37	chrX	105868476	105868476	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	cattcagaatacagcctgtcCccgtggatccacagatcaaa	7	13	2	2			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:105868476C>T	ENST00000372548.4	+	3	1052	c.943C>T	c.(943-945)Ccc>Tcc	p.P315S	CXorf57_ENST00000372544.2_Missense_Mutation_p.P315S	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	315							poly(A) RNA binding (GO:0044822)	p.P315S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						ACAGCCTGTCCCCGTGGATCC	0.368																																																1	Substitution - Missense(1)	ovary(1)	X											125	110	115					X																	105868476		2203	4300	6503	105755132	SO:0001583	missense	55086			AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.943C>T	X.37:g.105868476C>T	ENSP00000361628:p.Pro315Ser		105755132	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388357	0.25118	.	.	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.46063	0.89;0.88;0.92	3.89	3.02	0.34903	Nucleic acid-binding, OB-fold-like (1);	0.238642	0.42172	D	0.000750	T	0.48484	0.1502	L	0.41236	1.265	0.35581	D	0.806287	B;B;D	0.76494	0.297;0.297;0.999	B;B;D	0.85130	0.134;0.134;0.997	T	0.51092	-0.8749	10	0.13108	T	0.6	-9.1425	10.2285	0.43241	0.0:0.8931:0.0:0.1069	.	315;315;315	A8K6R5;Q6NSI4;Q6NSI4-2	.;CX057_HUMAN;.	S	315;315;123	ENSP00000361623:P315S;ENSP00000361628:P315S;ENSP00000405866:P123S	ENSP00000361623:P315S	P	+	1	0	CXorf57	105755132	0.350000	0.24878	0.389000	0.26208	0.162000	0.22319	2.922000	0.48860	0.755000	0.32990	-0.192000	0.12808	CCC		0.368	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015		T	105868476	C	T	105868476	3	4	116	1	0	0	0	0	1	0	0	0	4119	623	22	3	953	3	CXorf57	23	105868476	Missense_Mutation	SNP	C	TCGA-F5-6571-01A-12D-1826-10	25498253	105868476	49402084	143	31166										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109694989	109694989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ggtcaacacaaaatgtagacTctgaaatgatgtctaatccg	8	8	3	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:109694989T>C	ENST00000465301.2	+	3	1390	c.1144T>C	c.(1144-1146)Tct>Cct	p.S382P	RGAG1_ENST00000540313.1_Missense_Mutation_p.S382P	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	382										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						AAATGTAGACTCTGAAATGAT	0.542																																																0			X											174	179	177					X																	109694989		2203	4300	6503	109581645	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1144T>C	X.37:g.109694989T>C	ENSP00000419786:p.Ser382Pro		109581645	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.807497	0.31961	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.57595	0.39;0.39	4.28	0.404	0.16355	.	0.679439	0.12217	N	0.488771	T	0.29423	0.0733	N	0.19112	0.55	0.09310	N	1	B	0.17268	0.021	B	0.19946	0.027	T	0.16719	-1.0393	9	.	.	.	-0.6536	1.8684	0.03203	0.1636:0.0978:0.1662:0.5724	.	382	Q8NET4	RGAG1_HUMAN	P	382	ENSP00000419786:S382P;ENSP00000441452:S382P	.	S	+	1	0	RGAG1	109581645	0.100000	0.21855	0.002000	0.10522	0.263000	0.26337	-0.694000	0.05115	-0.030000	0.13804	0.486000	0.48141	TCT		0.542	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		C	109694989	T	C	109694989	3	2	116	1	0	0	0	0	1	0	0	0	13311	1551	54	4	1146	4	RGAG1	23	109694989	Missense_Mutation	SNP	T	TCGA-F5-6571-01A-12D-1826-10	3826513	109694989	45575571	144	31167										
CAPN6	827	hgsc.bcm.edu	37	chrX	110494229	110494229	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcatcatccacagtccagcaTcccaacaccgattccagctc	4	18	2	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:110494229T>C	ENST00000324068.1	-	8	1241	c.1074A>G	c.(1072-1074)ggA>ggG	p.G358G	CAPN6_ENST00000541758.1_Silent_p.G103G	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	358	Domain III.		G -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						CAGTCCAGCATCCCAACACCG	0.493																																																0			X											330	288	302					X																	110494229		2203	4300	6503	110380885	SO:0001819	synonymous_variant	827			AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1074A>G	X.37:g.110494229T>C			110380885	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	37	CCDS14555.1																																																																																				0.493	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			C	110494229	T	C	110494229	2	2	116	1	0	0	0	0	0	0	0	1	2636	1422	50	4		4	CAPN6	23	110494229	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	799240	110494229	44776331	145	31168										
NKAP	79576	hgsc.bcm.edu	37	chrX	119064064	119064064	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	ttcacctcttcgtgggatacGttttccagcttttacatatt	6	10	2	0			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:119064064G>A	ENST00000371410.3	-	8	1154	c.988C>T	c.(988-990)Cgt>Tgt	p.R330C	NKAP_ENST00000477789.1_5'UTR	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	330	Necessary for interaction with HDAC3 and transcriptional repression.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						CGTGGGATACGTTTTCCAGCT	0.408																																																0			X											154	132	139					X																	119064064		2203	4300	6503	118948092	SO:0001583	missense	79576			BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"NF kappaB activating protein"	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.988C>T	X.37:g.119064064G>A	ENSP00000360464:p.Arg330Cys		118948092	Q6IPW6|Q96BQ2|Q9H638	Missense_Mutation	SNP	ENST00000371410.3	37	CCDS14592.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222179	0.79464	.	.	ENSG00000101882	ENST00000371410	T	0.57436	0.4	5.27	5.27	0.74061	.	0.053550	0.64402	D	0.000001	T	0.76572	0.4006	M	0.92507	3.315	0.80722	D	1	D	0.69078	0.997	P	0.59643	0.861	D	0.83381	0.0012	10	0.87932	D	0	-9.6259	16.9007	0.86113	0.0:0.0:1.0:0.0	.	330	Q8N5F7	NKAP_HUMAN	C	330	ENSP00000360464:R330C	ENSP00000360464:R330C	R	-	1	0	NKAP	118948092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.211000	0.65219	2.457000	0.83068	0.600000	0.82982	CGT		0.408	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528		A	119064064	G	A	119064064	3	1	116	1	0	0	0	0	1	0	0	0	10470	1145	40	1	267	1	NKAP	23	119064064	Missense_Mutation	SNP	G	TCGA-F5-6571-01A-12D-1826-10	8569835	119064064	36206496	146	31169										
CT47B1	643311	hgsc.bcm.edu	37	chrX	120009232	120009234	+	In_Frame_Del	DEL	TCC	TCC	-													0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tggccgcctcgttcccctctTcctcctcctcctcttcctcc							TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	TCC	TCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:120009232_120009234delTCC	ENST00000371311.3	-	1	545_547	c.291_293delGGA	c.(289-294)gaggaa>gaa	p.97_98EE>E		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	97	Poly-Glu.									breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						gttcccctcttcctcctcctcct	0.69														11	0.00291391	0	0	3775	,	,		12235	0		0.0099	False		,,,				2504	0.001															0			X								33,3157		4,18,7,1330,479						0.2	0			60	187,5428		14,105,54,1882,1559	no	coding	CT47B1	NM_001145718.1		18,123,61,3212,2038	A1A1,A1R,A1,RR,R		3.3304,1.0345,2.4986				220,8585				119893262	SO:0001651	inframe_deletion	643311				CCDS48161.1	Xq24	2014-05-06	2011-03-24		ENSG00000236446	ENSG00000236446			33293	protein-coding gene	gene with protein product	"cancer/testis CT47 family, member 13"	300790				16382448	Standard	NM_001145718		Approved	CT47.13	uc011muc.2	P0C2W7	OTTHUMG00000187483	ENST00000371311.3:c.291_293delGGA	X.37:g.120009241_120009243delTCC	ENSP00000360360:p.Glu99del		119893260	A6NM97	In_Frame_Del	DEL	ENST00000371311.3	37	CCDS48161.1																																																																																				0.69	CT47B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058121.1	NM_001145718		-	120009234	TCC	-	120009232	7	5	116	1	0	1	0	1	0	0	0	0	3995	1783	62	0	614	0	CT47B1	23	120009232	In_Frame_Del	DEL	TCC	TCGA-F5-6571-01A-12D-1826-10	945168	120009232	35261328	147	31170										
ZNF449	203523	hgsc.bcm.edu	37	chrX	134493889	134493889	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	gccatgggtgaaggaattacAggattctaaagaaatgaaac	11	5	1	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:134493889A>G	ENST00000339249.4	+	4	772	c.632A>G	c.(631-633)cAg>cGg	p.Q211R		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	211					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					AAGGAATTACAGGATTCTAAA	0.328																																																0			X											100	97	98					X																	134493889		2203	4299	6502	134321555	SO:0001583	missense	203523			AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.632A>G	X.37:g.134493889A>G	ENSP00000339585:p.Gln211Arg		134321555	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	37	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096944	0.37048	.	.	ENSG00000173275	ENST00000339249	T	0.05925	3.37	4.85	4.85	0.62838	.	0.161421	0.29572	N	0.011763	T	0.04770	0.0129	N	0.24115	0.695	0.80722	D	1	B	0.26635	0.155	B	0.25759	0.063	T	0.45556	-0.9253	10	0.14252	T	0.57	.	11.5598	0.50769	1.0:0.0:0.0:0.0	.	211	Q6P9G9	ZN449_HUMAN	R	211	ENSP00000339585:Q211R	ENSP00000339585:Q211R	Q	+	2	0	ZNF449	134321555	0.020000	0.18652	0.963000	0.40424	0.973000	0.67179	1.028000	0.30128	1.932000	0.55993	0.425000	0.28330	CAG		0.328	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		G	134493889	A	G	134493889	3	3	116	1	0	0	0	0	1	0	0	0	17959	188	7	4	642	4	ZNF449	23	134493889	Missense_Mutation	SNP	A	TCGA-F5-6571-01A-12D-1826-10	14484657	134493889	20776671	148	31171										
SPANXN3	139067	hgsc.bcm.edu	37	chrX	142596797	142596797	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0671140939597315	10	1	0.969646981194325	4.52501924557352	0.810451208162421	0.0501749125437281	0.291492349063563	0	tcatttgaagatccttcagaTaagtctacgccttcgtcctc	6	12	3	3			TCGA-F5-6571-01A-12D-1826-10	TCGA-F5-6571-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	4fb0e46c-9df3-4919-bfe3-602073f6e5de	90feaed4-7945-4669-b191-39ec2bf89bc1	g.chrX:142596797T>C	ENST00000370503.2	-	2	356	c.273A>G	c.(271-273)ttA>ttG	p.L91L	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	91										endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					ATCCTTCAGATAAGTCTACGC	0.443																																																0			X											216	178	191					X																	142596797		2203	4300	6503	142424463	SO:0001819	synonymous_variant	139067				CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 8"	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.273A>G	X.37:g.142596797T>C			142424463	Q0ZNK4	Silent	SNP	ENST00000370503.2	37	CCDS35418.1																																																																																				0.443	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609		C	142596797	T	C	142596797	2	2	116	1	0	0	0	0	0	0	0	1	15031	1403	49	4		4	SPANXN3	23	142596797	Silent	SNP	T	TCGA-F5-6571-01A-12D-1826-10	8102908	142596797	12673763	149	31172										
NPHP4	261734	hgsc.bcm.edu	37	chr1	5935031	5935031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctcggcgacccccagcgtggCgtggagcgtgtgctccgtgg	17	14	0	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:5935031C>T	ENST00000378156.4	-	21	3212	c.2947G>A	c.(2947-2949)Gcc>Acc	p.A983T	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	983					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CCCAGCGTGGCGTGGAGCGTG	0.632																																																0			1											74	93	87					1																	5935031		2185	4269	6454	5857618	SO:0001583	missense	261734			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2947G>A	1.37:g.5935031C>T	ENSP00000367398:p.Ala983Thr		5857618	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	c	17.58	3.424073	0.62733	.	.	ENSG00000131697	ENST00000378156	D	0.88124	-2.34	4.95	3.97	0.46021	.	0.327731	0.27088	N	0.020992	D	0.88280	0.6394	M	0.63843	1.955	0.40586	D	0.981446	D	0.64830	0.994	P	0.51055	0.657	D	0.88677	0.3199	10	0.44086	T	0.13	.	13.8589	0.63548	0.0:0.8464:0.1536:0.0	.	983	O75161	NPHP4_HUMAN	T	983	ENSP00000367398:A983T	ENSP00000367398:A983T	A	-	1	0	NPHP4	5857618	0.998000	0.40836	0.008000	0.14137	0.023000	0.10783	3.849000	0.55910	2.306000	0.77630	0.550000	0.68814	GCC		0.632	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			T	5935031	C	T	5935031	3	4	117	1	0	0	0	0	1	0	0	0	10612	768	27	1	1373	1	NPHP4	1	5935031	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		5935031	243315590	1	31173										
NECAP2	55707	hgsc.bcm.edu	37	chr1	16778357	16778357	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgaagaagaaggaaggagcaGctgggaatccccgagtccgg	16	8	0	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:16778357G>T	ENST00000337132.5	+	6	604	c.514G>T	c.(514-516)Gct>Tct	p.A172S	NECAP2_ENST00000443980.2_Missense_Mutation_p.A172S|NECAP2_ENST00000406746.1_Missense_Mutation_p.A172S|NECAP2_ENST00000457722.2_Missense_Mutation_p.A146S|NECAP2_ENST00000504551.2_Missense_Mutation_p.A111S	NM_001145278.1|NM_018090.4	NP_001138750.1|NP_060560.1	Q9NVZ3	NECP2_HUMAN	NECAP endocytosis associated 2	172					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|Kidney(64;0.000181)|KIRC - Kidney renal clear cell carcinoma(64;0.00268)|STAD - Stomach adenocarcinoma(196;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GGAAGGAGCAGCTGGGAATCC	0.602																																																0			1											65	75	71					1																	16778357		2203	4300	6503	16650944	SO:0001583	missense	55707			AK021938	CCDS173.1, CCDS44066.1, CCDS44067.1	1p36.13	2008-02-05			ENSG00000157191	ENSG00000157191			25528	protein-coding gene	gene with protein product		611624				14555962, 15494011	Standard	NM_001145277		Approved	FLJ10420	uc001ayq.3	Q9NVZ3	OTTHUMG00000002313	ENST00000337132.5:c.514G>T	1.37:g.16778357G>T	ENSP00000338746:p.Ala172Ser		16650944	B4DY19|E9PGQ8|Q5VSU4|Q5VSU5|Q9H7L1|Q9H8L1	Missense_Mutation	SNP	ENST00000337132.5	37	CCDS173.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.596230	0.28445	.	.	ENSG00000157191	ENST00000337132;ENST00000504551;ENST00000457722;ENST00000406746;ENST00000443980;ENST00000492095	T;T;T;T;T;T	0.40476	1.6;1.54;1.59;1.6;1.03;1.6	5.68	1.58	0.23477	.	0.514295	0.20526	N	0.090603	T	0.22166	0.0534	L	0.34521	1.04	0.09310	N	1	B;B;B	0.20988	0.01;0.05;0.015	B;B;B	0.19391	0.025;0.022;0.018	T	0.27706	-1.0066	10	0.05959	T	0.93	-1.0793	3.6119	0.08063	0.1509:0.1329:0.579:0.1373	.	146;172;172	Q9NVZ3-4;Q9NVZ3-2;Q9NVZ3	.;.;NECP2_HUMAN	S	172;111;146;172;172;172	ENSP00000338746:A172S;ENSP00000424509:A111S;ENSP00000407091:A146S;ENSP00000383925:A172S;ENSP00000391942:A172S;ENSP00000427620:A172S	ENSP00000338746:A172S	A	+	1	0	NECAP2	16650944	0.006000	0.16342	0.028000	0.17463	0.961000	0.63080	0.306000	0.19279	0.044000	0.15775	0.561000	0.74099	GCT		0.602	NECAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006680.2	NM_018090		T	16778357	G	T	16778357	3	4	117	1	0	0	0	0	1	0	0	0	10339	971	34	2	536	2	NECAP2	1	16778357	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	10843326	16778357	232472264	2	31174										
TAL1	6886	hgsc.bcm.edu	37	chr1	47685631	47685631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtccttgccagtcttggcccGctgggtgccctcctcctcct	10	18	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:47685631G>A	ENST00000294339.3	-	4	1333	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	TAL1_ENST00000371883.3_Missense_Mutation_p.R255W|TAL1_ENST00000371884.2_Missense_Mutation_p.R253W|TAL1_ENST00000459729.1_5'UTR	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	253					angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						GTCTTGGCCCGCTGGGTGCCC	0.627			T	"TRD@, SIL"	lymphoblastic leukemia/biphasic																																		Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	0			1											19	19	19					1																	47685631		2203	4300	6503	47458218	SO:0001583	missense	6886			M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367		"Basic helix-loop-helix proteins"	11556	protein-coding gene	gene with protein product		187040		TCL5		2740341	Standard	NM_001287347		Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.757C>T	1.37:g.47685631G>A	ENSP00000294339:p.Arg253Trp		47458218	D3DQ24	Missense_Mutation	SNP	ENST00000294339.3	37	CCDS547.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609011	0.66558	.	.	ENSG00000162367	ENST00000371884;ENST00000371883;ENST00000294339	D;D;D	0.97850	-4.57;-4.57;-4.57	5.53	3.61	0.41365	Helix-loop-helix DNA-binding (1);	0.135229	0.46442	D	0.000296	D	0.97077	0.9045	L	0.27053	0.805	0.41023	D	0.985097	D	0.89917	1.0	D	0.66979	0.948	D	0.97102	0.9798	10	0.72032	D	0.01	.	13.6831	0.62499	0.0:0.0:0.4225:0.5775	.	253	P17542	TAL1_HUMAN	W	253;255;253	ENSP00000360951:R253W;ENSP00000360950:R255W;ENSP00000294339:R253W	ENSP00000294339:R253W	R	-	1	2	TAL1	47458218	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.269000	0.43346	0.661000	0.30985	-0.313000	0.08912	CGG		0.627	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021640.1	NM_003189		A	47685631	G	A	47685631	3	1	117	1	0	0	0	0	1	0	0	0	15580	1086	38	1	242	1	TAL1	1	47685631	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	30907274	47685631	201564990	3	31175										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99753654	99753654	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cattgaaccaacccaggaggCaattccattcctcatgttgc	7	13	1	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:99753654C>A	ENST00000370185.3	+	2	853	c.356C>A	c.(355-357)gCa>gAa	p.A119E	LPPR4_ENST00000457765.1_Missense_Mutation_p.A119E	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		119					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ACCCAGGAGGCAATTCCATTC	0.438																																																0			1											159	150	153					1																	99753654		2203	4300	6503	99526242	SO:0001583	missense	9890																														ENST00000370185.3:c.356C>A	1.37:g.99753654C>A	ENSP00000359204:p.Ala119Glu		99526242	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.007518	0.54361	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178	T;T	0.14766	2.48;2.5	5.79	5.79	0.91817	.	0.577013	0.19675	N	0.108655	T	0.05777	0.0151	L	0.29908	0.895	0.36230	D	0.852593	P;B	0.37276	0.589;0.01	B;B	0.31101	0.124;0.028	T	0.36016	-0.9765	10	0.29301	T	0.29	-11.639	20.0243	0.97517	0.0:1.0:0.0:0.0	.	119;119	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	E	119	ENSP00000359204:A119E;ENSP00000394913:A119E	ENSP00000263178:A119E	A	+	2	0	RP4-788L13.1	99526242	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.857000	0.55972	2.727000	0.93392	0.557000	0.71058	GCA		0.438	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			A	99753654	C	A	99753654	3	1	117	1	0	0	0	0	1	0	0	0	8956	710	25	2	362	2	LPPR4	1	99753654	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	52068023	99753654	149496967	4	31176										
FLG	2312	hgsc.bcm.edu	37	chr1	152280001	152280001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgtcctgaccctcttgggacGttgagtgcctggagctgtct	13	11	2	2	rs553191250		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:152280001G>A	ENST00000368799.1	-	3	7396	c.7361C>T	c.(7360-7362)aCg>aTg	p.T2454M	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2454	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTTGGGACGTTGAGTGCCT	0.582									Ichthyosis				g|||	1	0.000199681	0	0.0014	5008	,	,		21498	0		0	False		,,,				2504	0															0			1											342	313	323					1																	152280001		2203	4300	6503	150546625	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7361C>T	1.37:g.152280001G>A	ENSP00000357789:p.Thr2454Met		150546625	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.362603	0.00212	.	.	ENSG00000143631	ENST00000368799	T	0.01787	4.64	2.63	-5.27	0.02763	.	.	.	.	.	T	0.00300	0.0009	N	0.22421	0.69	0.09310	N	1	B	0.22541	0.071	B	0.08055	0.003	T	0.46331	-0.9199	9	0.48119	T	0.1	.	1.5569	0.02586	0.1958:0.152:0.4016:0.2506	.	2454	P20930	FILA_HUMAN	M	2454	ENSP00000357789:T2454M	ENSP00000357789:T2454M	T	-	2	0	FLG	150546625	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.777000	0.00054	-5.537000	0.00013	-3.523000	0.00032	ACG		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280001	G	A	152280001	3	1	117	1	0	0	0	0	1	0	0	0	5941	1145	40	1	4828	1	FLG	1	152280001	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	52526347	152280001	96970620	5	31177										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158612225	158612225	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	atggcctcttcattgccatcAcaagcgctacactcaatcag	6	14	5	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:158612225A>C	ENST00000368147.4	-	33	4893	c.4713T>G	c.(4711-4713)tgT>tgG	p.C1571W		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1571					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CATTGCCATCACAAGCGCTAC	0.448																																																0			1											107	107	107					1																	158612225		1963	4169	6132	156878849	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4713T>G	1.37:g.158612225A>C	ENSP00000357129:p.Cys1571Trp		156878849	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894413	0.33442	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.34667	1.35;1.36	5.26	-0.882	0.10604	.	0.000000	0.34750	N	0.003705	T	0.43986	0.1272	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.46400	-0.9194	10	0.39692	T	0.17	.	10.6321	0.45543	0.564:0.0:0.436:0.0	.	1571	P02549	SPTA1_HUMAN	W	1571	ENSP00000357130:C1571W;ENSP00000357129:C1571W	ENSP00000357129:C1571W	C	-	3	2	SPTA1	156878849	0.995000	0.38212	0.922000	0.36590	0.005000	0.04900	0.379000	0.20585	-0.318000	0.08665	-0.256000	0.11100	TGT		0.448	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158612225	A	C	158612225	3	2	117	1	0	0	0	0	1	0	0	0	15155	157	6	4	2626	4	SPTA1	1	158612225	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	6332224	158612225	90638396	6	31178										
HSD17B7	51478	hgsc.bcm.edu	37	chr1	162773313	162773313	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	atatggacgctgttgatgccGgcaatattgctagtaagtga	12	6	0	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:162773313G>T	ENST00000254521.3	+	6	790	c.735G>T	c.(733-735)ccG>ccT	p.P245P	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Intron	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	245					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)	p.P245P(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					TGTTGATGCCGGCAATATTGC	0.388																																																1	Substitution - coding silent(1)	ovary(1)	1											122	107	112					1																	162773313		2203	4300	6503	161039937	SO:0001819	synonymous_variant	158160			AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5215	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 37C, member 1"	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.735G>T	1.37:g.162773313G>T			161039937	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	37	CCDS1242.1																																																																																				0.388	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371		T	162773313	G	T	162773313	2	4	117	1	0	0	0	0	0	0	0	1	7409	1103	39	2		2	HSD17B7	1	162773313	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10	4161088	162773313	86477308	7	31179										
MAEL	84944	hgsc.bcm.edu	37	chr1	166991080	166991080	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gatggatacaaatctttctcTtccttatcttaatgatggta	6	7	3	1	rs559496772		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:166991080T>C	ENST00000367872.4	+	12	1537	c.1293T>C	c.(1291-1293)tcT>tcC	p.S431S	MAEL_ENST00000367870.2_Silent_p.S400S|MAEL_ENST00000491055.1_3'UTR	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	431					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						AATCTTTCTCTTCCTTATCTT	0.363													T|||	1	0.000199681	8e-04	0	5008	,	,		17657	0		0	False		,,,				2504	0															0			1											118	121	120					1																	166991080		2203	4300	6503	165257704	SO:0001819	synonymous_variant	84944			AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.1293T>C	1.37:g.166991080T>C			165257704	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Silent	SNP	ENST00000367872.4	37	CCDS1257.1																																																																																				0.363	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		C	166991080	T	C	166991080	2	2	117	1	0	0	0	0	0	0	0	1	9184	1596	56	4		4	MAEL	1	166991080	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	4217767	166991080	82259541	8	31180										
ASTN1	460	hgsc.bcm.edu	37	chr1	176838106	176838106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggagggtgttgtaggcggtcTgctgctccttcccactagtg	15	10	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:176838106T>C	ENST00000367654.3	-	22	3756	c.3545A>G	c.(3544-3546)cAg>cGg	p.Q1182R	ASTN1_ENST00000361833.2_Missense_Mutation_p.Q1174R|ASTN1_ENST00000424564.2_Missense_Mutation_p.Q1174R|ASTN1_ENST00000367657.3_Missense_Mutation_p.Q1174R	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1182					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GTAGGCGGTCTGCTGCTCCTT	0.458																																																0			1											149	136	140					1																	176838106		2203	4300	6503	175104729	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3545A>G	1.37:g.176838106T>C	ENSP00000356626:p.Gln1182Arg		175104729	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	T	19.18	3.777789	0.70107	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.18016	2.24;2.66;2.65;2.24	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.31199	0.0789	L	0.58101	1.795	0.80722	D	1	D;D	0.62365	0.991;0.978	P;P	0.53401	0.725;0.641	T	0.02789	-1.1110	10	0.87932	D	0	-25.3466	15.6389	0.76981	0.0:0.0:0.0:1.0	.	1174;1174	O14525-2;B1AJS1	.;.	R	1174;1174;1182;1174;1174	ENSP00000356629:Q1174R;ENSP00000354536:Q1174R;ENSP00000356626:Q1182R;ENSP00000395041:Q1174R	ENSP00000354536:Q1174R	Q	-	2	0	ASTN1	175104729	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	6.005000	0.70716	2.179000	0.69175	0.533000	0.62120	CAG		0.458	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		C	176838106	T	C	176838106	3	2	117	1	0	0	0	0	1	0	0	0	1065	1580	55	4	375	4	ASTN1	1	176838106	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	9847026	176838106	72412515	9	31181										
LYST	1130	hgsc.bcm.edu	37	chr1	235840882	235840882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ttatctcttctgtgtgaccaTagagatgtatttgagtctcc	8	8	3	3	rs151167023		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:235840882T>C	ENST00000389794.3	-	49	11012	c.10838A>G	c.(10837-10839)tAt>tGt	p.Y3613C	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.Y3613C			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3613					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.Y3613C(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TGTGTGACCATAGAGATGTAT	0.338																																																1	Substitution - Missense(1)	ovary(1)	1						T	CYS/TYR	0,4406		0,0,2203	147	130	136		10838	5.7	1	1	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	missense	LYST	NM_000081.2	194	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	3613/3802	235840882	1,13005	2203	4300	6503	233907505	SO:0001583	missense	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10838A>G	1.37:g.235840882T>C	ENSP00000374444:p.Tyr3613Cys		233907505	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388862	0.82902	0.0	1.16E-4	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.28895	1.59;1.59	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.46328	0.1387	L	0.33245	0.995	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.46373	-0.9196	10	0.87932	D	0	.	15.9462	0.79796	0.0:0.0:0.0:1.0	.	3613	Q99698	LYST_HUMAN	C	3613	ENSP00000374444:Y3613C;ENSP00000374443:Y3613C	ENSP00000374443:Y3613C	Y	-	2	0	LYST	233907505	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.950000	0.87804	2.168000	0.68352	0.533000	0.62120	TAT		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235840882	T	C	235840882	3	2	117	1	0	0	0	0	1	0	0	0	9158	1406	49	4	587	4	LYST	1	235840882	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	59002776	235840882	13409739	10	31182										
NID1	4811	hgsc.bcm.edu	37	chr1	236144926	236144926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gataccctctcacggaatccGttacaatgcctctgggattc	8	13	2	0	rs533832624		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr1:236144926G>A	ENST00000264187.6	-	16	3294	c.3212C>T	c.(3211-3213)aCg>aTg	p.T1071M	NID1_ENST00000366595.3_Missense_Mutation_p.T938M	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1071					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CACGGAATCCGTTACAATGCC	0.483													G|||	1	0.000199681	0	0.0014	5008	,	,		19657	0		0	False		,,,				2504	0															0			1											90	90	90					1																	236144926		2203	4300	6503	234211549	SO:0001583	missense	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3212C>T	1.37:g.236144926G>A	ENSP00000264187:p.Thr1071Met		234211549	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.097157	0.37048	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.29655	1.56;1.56	5.87	4.01	0.46588	Six-bladed beta-propeller, TolB-like (1);	0.410931	0.32041	N	0.006677	T	0.40196	0.1107	L	0.31664	0.95	0.09310	N	1	D;D	0.89917	0.998;1.0	P;D	0.73708	0.877;0.981	T	0.16247	-1.0409	10	0.72032	D	0.01	.	10.2347	0.43275	0.2266:0.0:0.7734:0.0	.	938;1071	P14543-2;P14543	.;NID1_HUMAN	M	1071;938	ENSP00000264187:T1071M;ENSP00000355554:T938M	ENSP00000264187:T1071M	T	-	2	0	NID1	234211549	0.731000	0.28111	0.089000	0.20774	0.091000	0.18340	4.120000	0.57897	0.821000	0.34540	0.650000	0.86243	ACG		0.483	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236144926	G	A	236144926	3	1	117	1	0	0	0	0	1	0	0	0	10445	1145	40	1	551	1	NID1	1	236144926	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	304044	236144926	13105695	11	31183										
GLI2	2736	hgsc.bcm.edu	37	chr2	121746706	121746706	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtggtgcagtacatcaaggcGcacgccagtggcgctctgga	15	11	2	0	rs557121635		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:121746706G>A	ENST00000452319.1	+	14	3276	c.3216G>A	c.(3214-3216)gcG>gcA	p.A1072A	GLI2_ENST00000314490.11_Silent_p.A744A|GLI2_ENST00000361492.4_Silent_p.A1072A					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				ACATCAAGGCGCACGCCAGTG	0.697													G|||	1	0.000199681	8e-04	0	5008	,	,		11685	0		0	False		,,,				2504	0															0			2											48	52	51					2																	121746706		2203	4300	6503	121463176	SO:0001819	synonymous_variant	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3216G>A	2.37:g.121746706G>A			121463176		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																				0.697	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121746706	G	A	121746706	2	1	117	1	0	0	0	0	0	0	0	1	6458	1074	38	1		1	GLI2	2	121746706	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10		121746706	121452667	12	31184										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141202224	141202224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtccagtcccacactgaaatCggcctggctgacatctaaat	8	13	1	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:141202224C>T	ENST00000389484.3	-	64	11053	c.10082G>A	c.(10081-10083)cGa>cAa	p.R3361Q		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3361	LDL-receptor class A 22. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		ACACTGAAATCGGCCTGGCTG	0.428										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											89	83	85					2																	141202224		2203	4300	6503	140918694	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10082G>A	2.37:g.141202224C>T	ENSP00000374135:p.Arg3361Gln		140918694	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.226530	0.39300	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94966	-3.57	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000002	T	0.71476	0.3344	N	0.00074	-2.255	0.45837	D	0.998705	B	0.33000	0.393	B	0.22601	0.04	T	0.82196	-0.0577	10	0.02654	T	1	.	13.3636	0.60669	0.0:0.9283:0.0:0.0717	.	3361	Q9NZR2	LRP1B_HUMAN	Q	3361;3299	ENSP00000374135:R3361Q	ENSP00000374135:R3361Q	R	-	2	0	LRP1B	140918694	0.996000	0.38824	0.997000	0.53966	0.998000	0.95712	3.352000	0.52239	2.767000	0.95098	0.563000	0.77884	CGA		0.428	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141202224	C	T	141202224	3	4	117	1	0	0	0	0	1	0	0	0	8984	884	31	1	3829	1	LRP1B	2	141202224	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	19455518	141202224	101997149	13	31185										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171264305	171264305	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gttgtggtcctgagaacgtcAgaaaacaagcttcttcagca	10	9	3	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:171264305A>G	ENST00000408978.4	+	22	2744	c.2601A>G	c.(2599-2601)tcA>tcG	p.S867S	MYO3B_ENST00000334231.6_Silent_p.S876S|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.S867S	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	867	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGAGAACGTCAGAAAACAAGC	0.453																																																0			2											197	190	192					2																	171264305		1921	4131	6052	170972551	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2601A>G	2.37:g.171264305A>G			170972551	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																				0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			G	171264305	A	G	171264305	2	3	117	1	0	0	0	0	0	0	0	1	10107	175	7	4		4	MYO3B	2	171264305	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10	30062081	171264305	71935068	14	31186										
TTN	7273	hgsc.bcm.edu	37	chr2	179437535	179437535	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aagtctcagggtgcagcaggCccttatagtaacaactttgc	10	10	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:179437535C>T	ENST00000591111.1	-	276	68625	c.68401G>A	c.(68401-68403)Gcc>Acc	p.A22801T	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A15569T|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A21874T|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A15502T|TTN_ENST00000460472.2_Missense_Mutation_p.A15377T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A24442T			Q8WZ42	TITIN_HUMAN	titin	22801	Ig-like 117.		A -> T (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A15377T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTGCAGCAGGCCCTTATAGTA	0.507																																																1	Substitution - Missense(1)	skin(1)	2											93	96	95					2																	179437535		1954	4141	6095	179145781	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.68401G>A	2.37:g.179437535C>T	ENSP00000465570:p.Ala22801Thr		179145781	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.52	3.145286	0.57044	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.91	5.91	0.95273	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.62600	0.2441	M	0.77820	2.39	0.80722	D	1	D;D;D;D	0.56746	0.977;0.977;0.977;0.958	P;P;P;P	0.54889	0.763;0.763;0.763;0.686	T	0.65586	-0.6132	9	0.87932	D	0	.	20.2963	0.98556	0.0:1.0:0.0:0.0	.	15377;15502;15569;22801	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	21874;15377;15569;15502;15375	ENSP00000343764:A21874T;ENSP00000434586:A15377T;ENSP00000340554:A15569T;ENSP00000352154:A15502T	ENSP00000340554:A15569T	A	-	1	0	TTN	179145781	1.000000	0.71417	0.996000	0.52242	0.972000	0.66771	7.818000	0.86416	2.813000	0.96785	0.655000	0.94253	GCC		0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179437535	C	T	179437535	3	4	117	1	0	0	0	0	1	0	0	0	16775	739	26	3	34803	3	TTN	2	179437535	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	8173230	179437535	63761838	15	31187										
CERKL	375298	hgsc.bcm.edu	37	chr2	182468789	182468789	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aaattcttctttacatagcaAgtcatacttagaatcacctg	4	9	4	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:182468789A>C	ENST00000339098.5	-	2	255	c.256T>G	c.(256-258)Ttg>Gtg	p.L86V	CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000409440.3_Missense_Mutation_p.L86V|CERKL_ENST00000410087.3_Missense_Mutation_p.L86V|CERKL_ENST00000374970.2_Missense_Mutation_p.L86V|CERKL_ENST00000374969.2_Missense_Mutation_p.L86V			Q49MI3	CERKL_HUMAN	ceramide kinase-like	86					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			TTACATAGCAAGTCATACTTA	0.353																																																0			2											43	42	42					2																	182468789		2202	4294	6496	182177034	SO:0001583	missense	375298			BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.256T>G	2.37:g.182468789A>C	ENSP00000341159:p.Leu86Val		182177034	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Missense_Mutation	SNP	ENST00000339098.5	37	CCDS42789.1	.	.	.	.	.	.	.	.	.	.	A	8.372	0.835533	0.16820	.	.	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	T;T;T;T;T	0.31247	2.28;2.49;1.5;2.55;1.54	5.4	-1.22	0.09494	.	1.176470	0.06361	N	0.711671	T	0.13157	0.0319	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.10296	0.002;0.003;0.003;0.001;0.002	B;B;B;B;B	0.09377	0.004;0.004;0.004;0.003;0.003	T	0.25293	-1.0136	10	0.20519	T	0.43	.	0.3674	0.00374	0.3821:0.127:0.2192:0.2717	.	86;86;86;86;86	B4DEY1;Q49MI3-4;Q49MI3-3;Q49MI3-2;Q49MI3	.;.;.;.;CERKL_HUMAN	V	86	ENSP00000386725:L86V;ENSP00000387080:L86V;ENSP00000364108:L86V;ENSP00000341159:L86V;ENSP00000364109:L86V	ENSP00000341159:L86V	L	-	1	2	CERKL	182177034	0.000000	0.05858	0.000000	0.03702	0.797000	0.45037	0.484000	0.22308	-0.207000	0.10187	-0.451000	0.05528	TTG		0.353	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			C	182468789	A	C	182468789	3	2	117	1	0	0	0	0	1	0	0	0	3274	69	3	4	1472	4	CERKL	2	182468789	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	3031254	182468789	60730584	16	31188										
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207652842	207652842	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctgggaggtgaaggacacttCtcaaaggatgtgcacttgcc	13	9	1	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:207652842C>T	ENST00000236980.6	+	9	2124	c.1776C>T	c.(1774-1776)ttC>ttT	p.F592F	FASTKD2_ENST00000402774.3_Silent_p.F592F|FASTKD2_ENST00000403094.3_Silent_p.F592F	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	592					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		AAGGACACTTCTCAAAGGATG	0.443																																																0			2											56	52	53					2																	207652842		2203	4300	6503	207361087	SO:0001819	synonymous_variant	22868			BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1776C>T	2.37:g.207652842C>T			207361087	Q9NVX6|Q9Y2H7	Silent	SNP	ENST00000236980.6	37	CCDS2371.1																																																																																				0.443	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207652842	C	T	207652842	2	4	117	1	0	0	0	0	0	0	0	1	5705	912	32	3		3	FASTKD2	2	207652842	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	25184053	207652842	35546531	17	31189										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113210	209113210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtgccacccagaatatttcgTatggtgccatttggtgattt	10	8	0	2	rs142883642		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr2:209113210T>C	ENST00000415913.1	-	4	678	c.297A>G	c.(295-297)atA>atG	p.I99M	IDH1_ENST00000446179.1_Missense_Mutation_p.I99M|IDH1_ENST00000345146.2_Missense_Mutation_p.I99M	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	99	Substrate binding.				2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I99M(4)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		GAATATTTCGTATGGTGCCAT	0.448			Mis		gliobastoma								T|||	1	0.000199681	0	0	5008	,	,		18804	0.001		0	False		,,,				2504	0				Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	4	Substitution - Missense(4)	haematopoietic_and_lymphoid_tissue(3)|biliary_tract(1)	2											137	120	126					2																	209113210		2203	4300	6503	208821455	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.297A>G	2.37:g.209113210T>C	ENSP00000390265:p.Ile99Met		208821455	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	20.5	3.995213	0.74703	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	5.57	3.75	0.43078	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.84543	0.5495	H	0.95328	3.655	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	D	0.84428	0.0575	10	0.87932	D	0	-4.7522	7.4619	0.27300	0.1544:0.0:0.7048:0.1408	.	99	O75874	IDHC_HUMAN	M	99	ENSP00000260985:I99M;ENSP00000410513:I99M;ENSP00000390265:I99M;ENSP00000391075:I99M	ENSP00000260985:I99M	I	-	3	3	IDH1	208821455	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.768000	0.62293	0.691000	0.31592	-0.406000	0.06334	ATA		0.448	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			C	209113210	T	C	209113210	3	2	117	1	0	0	0	0	1	0	0	0	7515	1628	57	4	975	4	IDH1	2	209113210	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	1460368	209113210	34086163	18	31190										
GRM7	2917	hgsc.bcm.edu	37	chr3	7188223	7188223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tctctcgcgtggtgccacccGattccttccaagcccaggcc	9	18	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:7188223G>A	ENST00000357716.4	+	2	878	c.604G>A	c.(604-606)Gat>Aat	p.D202N	GRM7_ENST00000403881.1_Missense_Mutation_p.D202N|GRM7_ENST00000402647.2_Missense_Mutation_p.D202N|GRM7_ENST00000389336.4_Missense_Mutation_p.D202N|GRM7_ENST00000486284.1_Missense_Mutation_p.D202N	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	202					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						GGTGCCACCCGATTCCTTCCA	0.512																																																0			3											126	114	118					3																	7188223		2203	4300	6503	7163223	SO:0001583	missense	2917			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.604G>A	3.37:g.7188223G>A	ENSP00000350348:p.Asp202Asn		7163223	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111641	0.94339	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492	D;D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73;-2.73	5.87	5.87	0.94306	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.96414	0.8830	M	0.89534	3.04	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.994;0.994;1.0	D	0.96472	0.9349	10	0.87932	D	0	.	19.1458	0.93467	0.0:0.0:1.0:0.0	.	202;202;202	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	N	202	ENSP00000350348:D202N;ENSP00000417536:D202N;ENSP00000373987:D202N;ENSP00000385664:D202N;ENSP00000384585:D202N	ENSP00000350348:D202N	D	+	1	0	GRM7	7163223	1.000000	0.71417	0.981000	0.43875	0.514000	0.34195	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	GAT		0.512	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		A	7188223	G	A	7188223	3	1	117	1	0	0	0	0	1	0	0	0	6823	1058	37	1	610	1	GRM7	3	7188223	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10		7188223	190834207	19	31191										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52859928	52859928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggagcccccggagatggcccGgtccacatcatagcggataa	13	13	1	1	rs550860646		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:52859928G>A	ENST00000266041.4	-	6	829	c.733C>T	c.(733-735)Cgg>Tgg	p.R245W	RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000485816.1_Missense_Mutation_p.R245W|ITIH4_ENST00000346281.5_Missense_Mutation_p.R245W|ITIH4_ENST00000434759.3_Missense_Mutation_p.R157W|ITIH4-AS1_ENST00000478366.1_RNA|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000406595.1_Missense_Mutation_p.R245W	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	245					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				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)		GAGATGGCCCGGTCCACATCA	0.562													G|||	1	0.000199681	0	0	5008	,	,		17585	0.001		0	False		,,,				2504	0															0			3											126	108	114					3																	52859928		2203	4300	6503	52834968	SO:0001583	missense	3700			D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.733C>T	3.37:g.52859928G>A	ENSP00000266041:p.Arg245Trp		52834968	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	37	CCDS2865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.72|14.72	2.619610|2.619610	0.46736|0.46736	.|.	.|.	ENSG00000055955|ENSG00000055955	ENST00000441637|ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421;ENST00000434759	.|T;T;T;T;T	.|0.78481	.|-1.18;-1.18;-1.18;-1.18;-1.18	4.98|4.98	4.1|4.1	0.47936|0.47936	.|.	.|0.218832	.|0.30109	.|N	.|0.010388	D|D	0.89008|0.89008	0.6593|0.6593	M|M	0.89968|0.89968	3.075|3.075	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.993;0.993;0.993;1.0	D|D	0.90014|0.90014	0.4123|0.4123	5|10	.|0.87932	.|D	.|0	-21.941|-21.941	11.2529|11.2529	0.49037|0.49037	0.0:0.0:0.5437:0.4563|0.0:0.0:0.5437:0.4563	.|.	.|245;245;245;245	.|E9PGN5;B7ZKJ8;Q14624;Q14624-2	.|.;.;ITIH4_HUMAN;.	L|W	102|245;245;245;245;233;157	.|ENSP00000266041:R245W;ENSP00000340520:R245W;ENSP00000417824:R245W;ENSP00000384425:R245W;ENSP00000440036:R157W	.|ENSP00000266041:R245W	P|R	-|-	2|1	0|2	ITIH4|ITIH4	52834968|52834968	0.926000|0.926000	0.31397|0.31397	0.982000|0.982000	0.44146|0.44146	0.291000|0.291000	0.27294|0.27294	1.293000|1.293000	0.33353|0.33353	1.086000|1.086000	0.41228|0.41228	0.561000|0.561000	0.74099|0.74099	CCG|CGG		0.562	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		A	52859928	G	A	52859928	3	1	117	1	0	0	0	0	1	0	0	0	7927	1115	39	1	2135	1	ITIH4	3	52859928	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	45671705	52859928	145162502	20	31192										
NFKBIZ	64332	hgsc.bcm.edu	37	chr3	101574636	101574636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctgtggtccatgaactccagAgaaatcaacagcctcattca	7	12	3	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:101574636A>G	ENST00000326172.5	+	9	1829	c.1714A>G	c.(1714-1716)Aga>Gga	p.R572G	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.R472G|NFKBIZ_ENST00000326151.5_Missense_Mutation_p.R450G	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	572	Interaction with NFKB1/p50. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TGAACTCCAGAGAAATCAACA	0.453																																																0			3											116	108	110					3																	101574636		2203	4300	6503	103057326	SO:0001583	missense	64332			AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"Ankyrin repeat domain containing"	29805	protein-coding gene	gene with protein product	"IL-1 inducible nuclear ankyrin-repeat protein"	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1714A>G	3.37:g.101574636A>G	ENSP00000325663:p.Arg572Gly		103057326	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.355704	0.41700	.	.	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172	T;T;T;T	0.56444	0.5;0.46;0.52;0.54	5.92	4.73	0.59995	Ankyrin repeat-containing domain (3);	0.416158	0.27577	N	0.018747	T	0.36220	0.0959	L	0.28344	0.845	0.28350	N	0.92095	B;B	0.19445	0.002;0.036	B;B	0.21151	0.005;0.033	T	0.22661	-1.0210	10	0.19590	T	0.45	-11.058	8.889	0.35420	0.7426:0.1317:0.0:0.1257	.	450;572	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	G	472;472;450;572	ENSP00000419800:R472G;ENSP00000377618:R472G;ENSP00000325593:R450G;ENSP00000325663:R572G	ENSP00000325593:R450G	R	+	1	2	NFKBIZ	103057326	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	1.684000	0.37649	1.017000	0.39495	0.528000	0.53228	AGA		0.453	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		G	101574636	A	G	101574636	3	3	117	1	0	0	0	0	1	0	0	0	10414	296	11	4	1748	4	NFKBIZ	3	101574636	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	48714708	101574636	96447794	21	31193										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120628436	120628436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	agtgtttaaaatgaagaagtTtaatttccgaaaagttttgg	9	2	0	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:120628436T>C	ENST00000273666.6	+	2	282	c.11T>C	c.(10-12)tTt>tCt	p.F4S	STXBP5L_ENST00000492541.1_Missense_Mutation_p.F4S|STXBP5L_ENST00000497029.1_Missense_Mutation_p.F4S|STXBP5L_ENST00000471454.1_Missense_Mutation_p.F4S|STXBP5L_ENST00000472879.1_Missense_Mutation_p.F4S	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	4					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		ATGAAGAAGTTTAATTTCCGA	0.433																																																0			3											45	48	47					3																	120628436		1872	4106	5978	122111126	SO:0001583	missense	9515			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.11T>C	3.37:g.120628436T>C	ENSP00000273666:p.Phe4Ser		122111126	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.720293	0.68959	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000495504;ENST00000471262	T;T;T;T;T;T;T	0.58358	1.55;1.53;1.31;0.82;1.3;0.34;1.58	5.0	5.0	0.66597	.	0.291678	0.28983	N	0.013502	T	0.72326	0.3446	M	0.85099	2.735	0.58432	D	0.999992	D;P	0.54601	0.967;0.717	D;P	0.63033	0.91;0.693	T	0.77408	-0.2599	10	0.87932	D	0	-15.0876	12.8654	0.57936	0.0:0.0:0.0:1.0	.	4;4	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	S	4	ENSP00000273666:F4S;ENSP00000420019:F4S;ENSP00000419627:F4S;ENSP00000420287:F4S;ENSP00000420666:F4S;ENSP00000419404:F4S;ENSP00000420167:F4S	ENSP00000273666:F4S	F	+	2	0	STXBP5L	122111126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.242000	0.65389	2.228000	0.72767	0.528000	0.53228	TTT		0.433	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			C	120628436	T	C	120628436	3	2	117	1	0	0	0	0	1	0	0	0	15396	1841	64	4	13	4	STXBP5L	3	120628436	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	19053800	120628436	77393994	22	31194										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281734	140281734	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tccggcttcccttgaggcccGgcgtttccggattaagtgct	12	13	0	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:140281734G>T	ENST00000458420.3	+	14	2484	c.2294G>T	c.(2293-2295)cGg>cTg	p.R765L		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	765			R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.R765Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CTTGAGGCCCGGCGTTTCCGG	0.572										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)	large_intestine(1)	3											54	52	53					3																	140281734		2203	4300	6503	141764424	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2294G>T	3.37:g.140281734G>T	ENSP00000402460:p.Arg765Leu		141764424	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.885702	0.91814	.	.	ENSG00000158258	ENST00000458420	T	0.24350	1.86	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.55194	0.1905	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.61397	-0.7071	9	.	.	.	-25.2099	15.766	0.78126	0.0:0.0:1.0:0.0	.	765	Q9H4D0	CSTN2_HUMAN	L	765	ENSP00000402460:R765L	.	R	+	2	0	CLSTN2	141764424	1.000000	0.71417	0.727000	0.30756	0.871000	0.50021	9.813000	0.99286	2.377000	0.81083	0.563000	0.77884	CGG		0.572	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140281734	G	T	140281734	3	4	117	1	0	0	0	0	1	0	0	0	3568	1116	39	2	2348	2	CLSTN2	3	140281734	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	19653298	140281734	57740696	23	31195										
GPR87	53836	hgsc.bcm.edu	37	chr3	151012461	151012461	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggacttttaagttttgagcaGtcatggatattgtcctctgt	10	6	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:151012461G>A	ENST00000260843.4	-	3	1037	c.573C>T	c.(571-573)gaC>gaT	p.D191D	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	191			D -> Y (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTTTTGAGCAGTCATGGATAT	0.448																																																0			3											121	117	118					3																	151012461		2203	4300	6503	152495151	SO:0001819	synonymous_variant	53836			AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"GPCR / Class A : Orphans"	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.573C>T	3.37:g.151012461G>A			152495151	Q5KU35|Q96JZ8|Q9BXC2	Silent	SNP	ENST00000260843.4	37	CCDS3157.1																																																																																				0.448	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			A	151012461	G	A	151012461	2	1	117	1	0	0	0	0	0	0	0	1	6736	1020	36	3		3	GPR87	3	151012461	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10	10730727	151012461	47009969	24	31196										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906123	164906123	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgagggtgatggtgattcacCgtcactatggtgttaagctg	14	6	2	3	rs377111636		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:164906123C>A	ENST00000475390.1	-	2	2939	c.2496G>T	c.(2494-2496)acG>acT	p.T832T	SLITRK3_ENST00000241274.3_Silent_p.T832T			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	832					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GGTGATTCACCGTCACTATGG	0.547										HNSCC(40;0.11)																																						0			3											106	104	105					3																	164906123		2203	4300	6503	166388817	SO:0001819	synonymous_variant	22865			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.2496G>T	3.37:g.164906123C>A			166388817	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																				0.547	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		A	164906123	C	A	164906123	2	1	117	1	0	0	0	0	0	0	0	1	14781	639	23	2		2	SLITRK3	3	164906123	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	13893662	164906123	33116307	25	31197										
PRKCI	5584	hgsc.bcm.edu	37	chr3	170013720	170013720	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tattttggaaaaacaaattcGcataccacgttctctgtctg	6	9	2	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr3:170013720G>T	ENST00000295797.4	+	15	1744	c.1439G>T	c.(1438-1440)cGc>cTc	p.R480L		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	480	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	AAACAAATTCGCATACCACGT	0.274																																																0			3											64	68	67					3																	170013720		2202	4299	6501	171496414	SO:0001583	missense	5584				CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1439G>T	3.37:g.170013720G>T	ENSP00000295797:p.Arg480Leu		171496414	D3DNQ4|Q8WW06	Missense_Mutation	SNP	ENST00000295797.4	37	CCDS3212.2	.	.	.	.	.	.	.	.	.	.	G	11.36	1.616046	0.28801	.	.	ENSG00000163558	ENST00000295797	T	0.48201	0.82	5.29	5.29	0.74685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.099543	0.64402	D	0.000002	T	0.52517	0.1739	L	0.45581	1.43	0.80722	D	1	P	0.46064	0.872	P	0.48571	0.582	T	0.45293	-0.9271	9	.	.	.	.	19.2927	0.94108	0.0:0.0:1.0:0.0	.	480	P41743	KPCI_HUMAN	L	480	ENSP00000295797:R480L	.	R	+	2	0	PRKCI	171496414	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	9.471000	0.97696	2.621000	0.88768	0.655000	0.94253	CGC		0.274	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		T	170013720	G	T	170013720	3	4	117	1	0	0	0	0	1	0	0	0	12548	1087	38	2	1497	2	PRKCI	3	170013720	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	5107597	170013720	28008710	26	31198										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66230763	66230763	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	accacaccttctaaatggatGatgttaggatgatcaaactg	8	8	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr4:66230763G>A	ENST00000273854.3	-	12	2808	c.2208C>T	c.(2206-2208)atC>atT	p.I736I	EPHA5_ENST00000354839.4_Silent_p.I714I|EPHA5_ENST00000511294.1_Silent_p.I737I|EPHA5_ENST00000432638.2_Silent_p.I573I	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	736	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CTAAATGGATGATGTTAGGAT	0.373										TSP Lung(17;0.13)																																						0			4											209	199	202					4																	66230763		2203	4300	6503	65913358	SO:0001819	synonymous_variant	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2208C>T	4.37:g.66230763G>A			65913358	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																				0.373	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66230763	G	A	66230763	2	1	117	1	0	0	0	0	0	0	0	1	5183	1280	45	3		3	EPHA5	4	66230763	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10		66230763	124923513	27	31199										
LARP7	51574	hgsc.bcm.edu	37	chr4	113571625	113571625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ttttctaatcagcagccaacAgggaagagtgtcgcacccag	10	11	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr4:113571625A>G	ENST00000344442.5	+	10	1581	c.1303A>G	c.(1303-1305)Agg>Ggg	p.R435G	MIR367_ENST00000362299.1_RNA|MIR302C_ENST00000362232.1_RNA|LARP7_ENST00000324052.6_Missense_Mutation_p.R435G|MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000510655.1_RNA|MIR302D_ENST00000362275.1_RNA|LARP7_ENST00000509061.1_Missense_Mutation_p.R442G|MIR302B_ENST00000362188.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302B_ENST00000505215.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	435					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		AGCAGCCAACAGGGAAGAGTG	0.433																																																0			4											105	97	100					4																	113571625		2203	4300	6503	113791074	SO:0001583	missense	51574			AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.1303A>G	4.37:g.113571625A>G	ENSP00000344950:p.Arg435Gly		113791074	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	37	CCDS3701.2	.	.	.	.	.	.	.	.	.	.	A	0.248	-1.008398	0.02112	.	.	ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000513553;ENST00000324052	T;T;T	0.17854	2.26;2.25;2.26	5.4	-1.16	0.09678	.	0.839390	0.11169	N	0.592242	T	0.04318	0.0119	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43065	-0.9414	10	0.16896	T	0.51	-1.209	4.4394	0.11566	0.5483:0.0:0.3114:0.1404	.	435	Q4G0J3	LARP7_HUMAN	G	435;442;103;435	ENSP00000344950:R435G;ENSP00000422626:R442G;ENSP00000314311:R435G	ENSP00000314311:R435G	R	+	1	2	LARP7	113791074	0.008000	0.16893	0.001000	0.08648	0.057000	0.15508	0.388000	0.20735	-0.177000	0.10690	0.482000	0.46254	AGG		0.433	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		G	113571625	A	G	113571625	3	3	117	1	0	0	0	0	1	0	0	0	8655	179	7	4	1337	4	LARP7	4	113571625	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	47340862	113571625	77582651	28	31200										
MAP9	79884	hgsc.bcm.edu	37	chr4	156281396	156281396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtggatcaactgttctgtcaTcatccataatcagttccgct	7	11	5	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr4:156281396T>C	ENST00000311277.4	-	7	1237	c.974A>G	c.(973-975)gAt>gGt	p.D325G	AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000594492.1_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000594666.1_RNA|AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000609254.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.D301G|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000596754.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	325					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TGTTCTGTCATCATCCATAAT	0.378																																																0			4											158	143	148					4																	156281396		2203	4300	6503	156500846	SO:0001583	missense	79884			AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.974A>G	4.37:g.156281396T>C	ENSP00000310593:p.Asp325Gly		156500846	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	T	7.978	0.750635	0.15778	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836	T;T;T	0.32753	2.16;2.15;1.44	5.3	-0.0751	0.13728	.	0.465598	0.21348	N	0.076010	T	0.22936	0.0554	M	0.63428	1.95	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32134	-0.9918	10	0.15066	T	0.55	-4.7399	5.3695	0.16132	0.1239:0.2269:0.0:0.6492	.	300;325;325	B4DVG9;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	G	325;301;324;325	ENSP00000310593:D325G;ENSP00000427402:D301G;ENSP00000394048:D324G	ENSP00000310593:D325G	D	-	2	0	MAP9	156500846	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.595000	0.24029	-0.419000	0.07439	-2.945000	0.00085	GAT		0.378	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		C	156281396	T	C	156281396	3	2	117	1	0	0	0	0	1	0	0	0	9300	1435	50	4	1001	4	MAP9	4	156281396	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	42709771	156281396	34872880	29	31201										
TLR3	7098	hgsc.bcm.edu	37	chr4	187004246	187004246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tctttcctacaacaagtaccTgcagctgactaggaactcct	6	13	1	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr4:187004246T>C	ENST00000296795.3	+	4	1510	c.1406T>C	c.(1405-1407)cTg>cCg	p.L469P	TLR3_ENST00000504367.1_Missense_Mutation_p.L192P	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	469					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		AACAAGTACCTGCAGCTGACT	0.468																																																0			4											70	71	71					4																	187004246		2203	4300	6503	187241240	SO:0001583	missense	7098			U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1406T>C	4.37:g.187004246T>C	ENSP00000296795:p.Leu469Pro		187241240	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	T	7.951	0.744946	0.15710	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.25085	1.82;1.82	5.57	5.57	0.84162	.	0.372655	0.27437	N	0.019379	T	0.22399	0.0540	L	0.28649	0.875	0.37136	D	0.901473	B	0.26744	0.158	B	0.26416	0.069	T	0.10497	-1.0627	10	0.51188	T	0.08	.	15.7394	0.77876	0.0:0.0:0.0:1.0	.	469	O15455	TLR3_HUMAN	P	469;469;192	ENSP00000296795:L469P;ENSP00000423684:L192P	ENSP00000296795:L469P	L	+	2	0	TLR3	187241240	0.983000	0.35010	0.175000	0.22980	0.009000	0.06853	8.008000	0.88588	2.122000	0.65172	0.455000	0.32223	CTG		0.468	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	187004246	T	C	187004246	3	2	117	1	0	0	0	0	1	0	0	0	15991	1580	55	4	1416	4	TLR3	4	187004246	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	30722850	187004246	4150030	30	31202										
APC	324	hgsc.bcm.edu	37	chr5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctcaaacagctcaaaccaagCgagaagtacctaaaaataaa	5	10	2	1	rs121913332		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CM930030	APC	M	rs121913332						102	90	94					5																	112175639		2202	4300	6502	112203538	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*		112203538	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175639	C	T	112175639	4	4	117	1	0	0	0	0	0	1	0	0	763	760	27	1	4406	1	APC	5	112175639	Nonsense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		112175639	68739621	31	31203										
FAT2	2196	hgsc.bcm.edu	37	chr5	150901015	150901015	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gaccgcatctgaacccccacTgaatgctccatctccttggc	7	17	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr5:150901015T>G	ENST00000261800.5	-	18	11151	c.11139A>C	c.(11137-11139)tcA>tcC	p.S3713S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3713					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAACCCCCACTGAATGCTCCA	0.557																																																0			5											79	78	79					5																	150901015		2203	4300	6503	150881208	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.11139A>C	5.37:g.150901015T>G			150881208	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	7.674	0.687604	0.14973	.	.	ENSG00000086570	ENST00000520200	T	0.70986	-0.53	5.89	-11.8	0.00035	.	0.694941	0.13025	N	0.419755	T	0.47544	0.1451	.	.	.	0.32553	N	0.532061	.	.	.	.	.	.	T	0.44574	-0.9319	7	0.15499	T	0.54	.	8.6555	0.34060	0.0574:0.1772:0.1794:0.5861	.	.	.	.	R	572	ENSP00000429678:S572R	ENSP00000429678:S572R	S	-	1	0	FAT2	150881208	0.000000	0.05858	0.059000	0.19551	0.951000	0.60555	-5.987000	0.00087	-2.541000	0.00485	-0.313000	0.08912	AGT		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150901015	T	G	150901015	2	3	117	1	0	0	0	0	0	0	0	1	5709	1567	55	4		4	FAT2	5	150901015	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	38725376	150901015	30014245	32	31204										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10894116	10894116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ccagcttcaatcacttattaCggatgcattccatgataaag	6	10	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr6:10894116C>T	ENST00000283141.6	+	3	391	c.95C>T	c.(94-96)aCg>aTg	p.T32M	SYCP2L_ENST00000543878.1_5'UTR|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	32						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TCACTTATTACGGATGCATTC	0.294																																																0			6											34	32	33					6																	10894116		1796	4059	5855	11002102	SO:0001583	missense	221711			AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.95C>T	6.37:g.10894116C>T	ENSP00000283141:p.Thr32Met		11002102	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	37	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	C	2.059	-0.415829	0.04766	.	.	ENSG00000153157	ENST00000283141	T	0.18960	2.18	5.59	-3.13	0.05266	.	0.452216	0.22644	N	0.057407	T	0.03434	0.0099	N	0.25144	0.715	0.19300	N	0.99998	B	0.33379	0.41	B	0.24701	0.055	T	0.28902	-1.0029	10	0.49607	T	0.09	-3.583	9.5604	0.39366	0.0:0.3851:0.0949:0.5199	.	32	Q5T4T6	SYC2L_HUMAN	M	32	ENSP00000283141:T32M	ENSP00000283141:T32M	T	+	2	0	SYCP2L	11002102	0.049000	0.20398	0.000000	0.03702	0.009000	0.06853	-0.932000	0.03963	-0.702000	0.05056	-1.321000	0.01291	ACG		0.294	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		T	10894116	C	T	10894116	3	4	117	1	0	0	0	0	1	0	0	0	15472	536	19	1	105	1	SYCP2L	6	10894116	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		10894116	160220951	33	31205										
DAXX	1616	hgsc.bcm.edu	37	chr6	33287497	33287497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gggggccaggggttcttctgAcagtaacgatggtgacacta	15	8	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr6:33287497A>G	ENST00000374542.5	-	6	1804	c.1600T>C	c.(1600-1602)Tca>Cca	p.S534P	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000414083.2_Missense_Mutation_p.S459P|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Missense_Mutation_p.S534P	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	534	Asp/Glu-rich (acidic).|Interaction with MAP3K5.|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GGTTCTTCTGACAGTAACGAT	0.512			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	0			6											109	97	101					6																	33287497		2203	4300	6503	33395475	SO:0001583	missense	1616			AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1600T>C	6.37:g.33287497A>G	ENSP00000363668:p.Ser534Pro		33395475	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	37	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	A	6.703	0.498432	0.12762	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083	.	.	.	4.69	-3.83	0.04269	.	1.603610	0.04160	N	0.322905	T	0.08447	0.0210	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.18903	-1.0322	9	0.23891	T	0.37	1.2301	6.1894	0.20516	0.2394:0.4727:0.2878:0.0	.	546;534	B4E1C1;Q9UER7	.;DAXX_HUMAN	P	534;534;459	.	ENSP00000266000:S534P	S	-	1	0	DAXX	33395475	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.044000	0.12023	-0.240000	0.09696	0.448000	0.29417	TCA		0.512	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			G	33287497	A	G	33287497	3	3	117	1	0	0	0	0	1	0	0	0	4249	275	10	4	634	4	DAXX	6	33287497	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	22393381	33287497	137827570	34	31206										
GSTA2	2939	hgsc.bcm.edu	37	chr6	52616423	52616423	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctagagtcaagctcttccacGtagtagagaagttccaccag	9	11	2	2	rs112390337	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr6:52616423G>A	ENST00000493422.1	-	6	653	c.498C>T	c.(496-498)taC>taT	p.Y166Y		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	166	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	GCTCTTCCACGTAGTAGAGAA	0.517													.|||	15	0.00299521	0.0091	0	5008	,	,		19775	0.003		0	False		,,,				2504	0															0			6						G		39,4367	46.7+/-81.2	0,39,2164	165	143	150		498	-5	0	6	dbSNP_132	150	0,8600		0,0,4300	no	coding-synonymous	GSTA2	NM_000846.4		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		166/223	52616423	39,12967	2203	4300	6503	52724382	SO:0001819	synonymous_variant	2939			AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"Glutathione S-transferases / Soluble"	4627	protein-coding gene	gene with protein product		138360	"glutathione S-transferase A2"	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.498C>T	6.37:g.52616423G>A			52724382	Q12759|Q16491|Q9NTY6	Silent	SNP	ENST00000493422.1	37	CCDS4944.1																																																																																				0.517	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846		A	52616423	G	A	52616423	2	1	117	1	0	0	0	0	0	0	0	1	6852	1140	40	1		1	GSTA2	6	52616423	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10	19328926	52616423	118498644	35	31207										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70410701	70410701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aatatttcgaattcctgccaTtgaagtaaaaataaagtaca	5	6	0	1	rs561540830	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr6:70410701T>C	ENST00000370577.3	-	12	1373	c.1144A>G	c.(1144-1146)Atg>Gtg	p.M382V	LMBRD1_ENST00000370570.1_Missense_Mutation_p.M309V	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	382					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						ATTCCTGCCATTGAAGTAAAA	0.239													T|||	2	0.000399361	0	0	5008	,	,		14703	0.002		0	False		,,,				2504	0															0			6											14	15	15					6																	70410701		2137	4220	6357	70467422	SO:0001583	missense	55788			AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1144A>G	6.37:g.70410701T>C	ENSP00000359609:p.Met382Val		70467422	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930362	0.52866	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.15834	2.39;2.39	5.23	5.23	0.72850	.	.	.	.	.	T	0.06096	0.0158	N	0.25332	0.735	0.80722	D	1	P	0.38020	0.615	B	0.40134	0.32	T	0.16630	-1.0396	9	0.09843	T	0.71	-17.5341	15.1467	0.72657	0.0:0.0:0.0:1.0	.	382	Q9NUN5	LMBD1_HUMAN	V	382;309	ENSP00000359609:M382V;ENSP00000359602:M309V	ENSP00000359602:M309V	M	-	1	0	LMBRD1	70467422	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.021000	0.88750	1.982000	0.57802	0.482000	0.46254	ATG		0.239	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		C	70410701	T	C	70410701	3	2	117	1	0	0	0	0	1	0	0	0	8866	1493	52	4	498	4	LMBRD1	6	70410701	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	17794278	70410701	100704366	36	31208										
MDN1	23195	hgsc.bcm.edu	37	chr6	90383052	90383052	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	acatattccagactttcaacTagtgccatttgtgagtctct	6	10	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr6:90383052T>C	ENST00000369393.3	-	80	13492	c.13377A>G	c.(13375-13377)ctA>ctG	p.L4459L	MDN1_ENST00000468568.1_5'Flank|MDN1_ENST00000428876.1_Silent_p.L4459L|RP1-122O8.7_ENST00000438877.1_RNA			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4459					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GACTTTCAACTAGTGCCATTT	0.453																																																0			6											106	100	102					6																	90383052		2203	4300	6503	90439773	SO:0001819	synonymous_variant	23195			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13377A>G	6.37:g.90383052T>C			90439773	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																				0.453	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90383052	T	C	90383052	2	2	117	1	0	0	0	0	0	0	0	1	9445	1509	53	4		4	MDN1	6	90383052	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	19972351	90383052	80732015	37	31209										
ADAM22	53616	hgsc.bcm.edu	37	chr7	87810862	87810862	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tggagtgaaaggattccagaCacaaaacatatttcagacat	8	7	1	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr7:87810862C>T	ENST00000265727.7	+	28	2530	c.2451C>T	c.(2449-2451)gaC>gaT	p.D817D	ADAM22_ENST00000398209.3_Silent_p.D781D|ADAM22_ENST00000398201.4_Silent_p.D817D|ADAM22_ENST00000315984.7_Silent_p.D781D|ADAM22_ENST00000398204.4_Silent_p.D781D			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	817					adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			GGATTCCAGACACAAAACATA	0.378																																																0			7											101	90	93					7																	87810862		1842	4099	5941	87648798	SO:0001819	synonymous_variant	53616			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.2451C>T	7.37:g.87810862C>T			87648798	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Silent	SNP	ENST00000265727.7	37	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	C	5.881	0.346716	0.11126	.	.	ENSG00000008277	ENST00000413139	.	.	.	5.79	3.66	0.41972	.	.	.	.	.	T	0.62792	0.2457	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61608	-0.7028	4	.	.	.	.	12.0107	0.53286	0.0:0.7906:0.0:0.2094	.	.	.	.	Y	146	.	.	H	+	1	0	ADAM22	87648798	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.952000	0.29149	1.441000	0.47550	0.655000	0.94253	CAC		0.378	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87810862	C	T	87810862	2	4	117	1	0	0	0	0	0	0	0	1	244	477	17	3		3	ADAM22	7	87810862	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10		87810862	71327801	38	31210										
CALCR	799	hgsc.bcm.edu	37	chr7	93055794	93055794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	attgggatgtcgccagcctcCgcagcagcggctgcagcgcg	15	14	0	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr7:93055794C>T	ENST00000394441.1	-	13	1614	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	CALCR_ENST00000360249.4_Silent_p.A449A|CALCR_ENST00000359558.2_Silent_p.A467A|CALCR_ENST00000426151.1_Silent_p.A433A|CALCR_ENST00000421592.1_Silent_p.A449A	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	467					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.A433A(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CGCCAGCCTCCGCAGCAGCGG	0.582																																																1	Substitution - coding silent(1)	pancreas(1)	7											96	97	97					7																	93055794		2203	4300	6503	92893730	SO:0001819	synonymous_variant	799			L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1299G>A	7.37:g.93055794C>T			92893730	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	37	CCDS5631.1																																																																																				0.582	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		T	93055794	C	T	93055794	2	4	117	1	0	0	0	0	0	0	0	1	2585	639	23	1		1	CALCR	7	93055794	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	5244932	93055794	66082869	39	31211										
HOOK3	84376	hgsc.bcm.edu	37	chr8	42819500	42819500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tagtttgttggcagagaatcAggtattaatggaaagactca	11	4	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr8:42819500A>G	ENST00000307602.4	+	9	862	c.662A>G	c.(661-663)cAg>cGg	p.Q221R		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	221			Q -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)	p.Q221R(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			GCAGAGAATCAGGTATTAATG	0.433			T	RET	papillary thyroid																																		Dom	yes		8	8p11.21	84376	hook homolog 3		E	1	Substitution - Missense(1)	breast(1)	8											127	123	125					8																	42819500		2203	4300	6503	42938657	SO:0001583	missense	84376			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.662A>G	8.37:g.42819500A>G	ENSP00000305699:p.Gln221Arg		42938657	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	37	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235972	0.39498	.	.	ENSG00000168172	ENST00000307602	T	0.16897	2.31	5.93	5.93	0.95920	.	0.056213	0.64402	D	0.000001	T	0.29423	0.0733	L	0.40543	1.245	0.47698	D	0.999493	D;P	0.58268	0.982;0.889	P;P	0.59595	0.86;0.636	T	0.00970	-1.1496	10	0.27785	T	0.31	-4.8245	16.418	0.83748	1.0:0.0:0.0:0.0	.	221;221	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	R	221	ENSP00000305699:Q221R	ENSP00000305699:Q221R	Q	+	2	0	HOOK3	42938657	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	8.899000	0.92544	2.281000	0.76405	0.524000	0.50904	CAG		0.433	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		G	42819500	A	G	42819500	3	3	117	1	0	0	0	0	1	0	0	0	7305	188	7	4	696	4	HOOK3	8	42819500	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10		42819500	103544522	40	31212										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113299452	113299452	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	atggccgggagtacctggatCgccacatgtcccagtagcat	12	12	0	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr8:113299452C>A	ENST00000297405.5	-	58	9416	c.9172G>T	c.(9172-9174)Gat>Tat	p.D3058Y	CSMD3_ENST00000352409.3_Missense_Mutation_p.D2988Y|CSMD3_ENST00000455883.2_Missense_Mutation_p.D2889Y|CSMD3_ENST00000343508.3_Missense_Mutation_p.D3018Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3058	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D3058N(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTACCTGGATCGCCACATGTC	0.443										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	skin(1)	8											113	103	106					8																	113299452		2203	4300	6503	113368628	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9172G>T	8.37:g.113299452C>A	ENSP00000297405:p.Asp3058Tyr		113368628	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188402	0.78789	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.22	5.22	0.72569	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.81484	0.4832	M	0.82923	2.615	0.58432	D	0.999999	D;P;D	0.89917	0.993;0.95;1.0	D;P;D	0.77004	0.92;0.858;0.989	D	0.83377	0.0010	10	0.59425	D	0.04	.	19.2093	0.93747	0.0:1.0:0.0:0.0	.	2889;3058;3018	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	3018;3058;2328;2889;2988	ENSP00000345799:D3018Y;ENSP00000297405:D3058Y;ENSP00000341558:D2328Y;ENSP00000412263:D2889Y;ENSP00000343124:D2988Y	ENSP00000297405:D3058Y	D	-	1	0	CSMD3	113368628	1.000000	0.71417	0.996000	0.52242	0.642000	0.38348	7.583000	0.82559	2.614000	0.88457	0.644000	0.83932	GAT		0.443	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113299452	C	A	113299452	3	1	117	1	0	0	0	0	1	0	0	0	3952	884	31	2	2007	2	CSMD3	8	113299452	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	70479952	113299452	33064570	41	31213										
BAI1	575	hgsc.bcm.edu	37	chr8	143614774	143614774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	agatcctcttcgctgtcttcGactcgctggagggcttcgtc	11	13	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr8:143614774G>A	ENST00000517894.1	+	25	4411	c.3517G>A	c.(3517-3519)Gac>Aac	p.D1173N	BAI1_ENST00000323289.5_Missense_Mutation_p.D1173N			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1173					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.D1173N(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CGCTGTCTTCGACTCGCTGGA	0.672																																																1	Substitution - Missense(1)	cervix(1)	8											35	44	41					8																	143614774		2196	4290	6486	143611776	SO:0001583	missense	575			AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3517G>A	8.37:g.143614774G>A	ENSP00000430945:p.Asp1173Asn		143611776		Missense_Mutation	SNP	ENST00000517894.1	37		.	.	.	.	.	.	.	.	.	.	G	17.97	3.517841	0.64634	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.39406	1.08;1.08	4.56	3.65	0.41850	.	0.064020	0.64402	U	0.000011	T	0.21227	0.0511	N	0.00102	-2.13	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	T	0.44360	-0.9333	10	0.06494	T	0.89	.	13.6407	0.62249	0.0:0.1567:0.8433:0.0	.	1173	E9PBK0	.	N	1173	ENSP00000430945:D1173N;ENSP00000313046:D1173N	ENSP00000313046:D1173N	D	+	1	0	BAI1	143611776	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	4.566000	0.60843	0.980000	0.38523	0.655000	0.94253	GAC		0.672	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143614774	G	A	143614774	3	1	117	1	0	0	0	0	1	0	0	0	1299	1058	37	1	3611	1	BAI1	8	143614774	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	30315322	143614774	2749248	42	31214										
PAX5	5079	hgsc.bcm.edu	37	chr9	37020739	37020739	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cactatcctctggcggactaCatccgggagtggccgtccat	11	14	1	0	rs570062385		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr9:37020739C>A	ENST00000358127.4	-	2	180	c.106G>T	c.(106-108)Gta>Tta	p.V36L	PAX5_ENST00000522003.1_Intron|PAX5_ENST00000523241.1_Missense_Mutation_p.V36L|PAX5_ENST00000523145.1_Intron|PAX5_ENST00000446742.1_Missense_Mutation_p.V36L|PAX5_ENST00000520281.1_Missense_Mutation_p.V36L|PAX5_ENST00000414447.1_Missense_Mutation_p.V36L|PAX5_ENST00000377852.2_Missense_Mutation_p.V36L|PAX5_ENST00000377847.2_Missense_Mutation_p.V36L|PAX5_ENST00000520154.1_Missense_Mutation_p.V36L|PAX5_ENST00000377853.2_Missense_Mutation_p.V36L	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	36	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(41)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		TGGCGGACTACATCCGGGAGT	0.517			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	41	Unknown(41)	haematopoietic_and_lymphoid_tissue(41)	9											116	107	110					9																	37020739		2203	4300	6503	37010739	SO:0001583	missense	5079				CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"Paired boxes", "Homeoboxes / PRD class"	8619	protein-coding gene	gene with protein product	"B-cell lineage specific activator"	167414	"paired box gene 5 (B-cell lineage specific activator protein)", "paired box gene 5 (B-cell lineage specific activator)"			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.106G>T	9.37:g.37020739C>A	ENSP00000350844:p.Val36Leu		37010739	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491559	0.84962	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.99329	-5.73;-5.73;-5.73;-5.73;-5.73;-5.73;-5.75;-5.73;-5.73	5.59	5.59	0.84812	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98701	0.9564	N	0.16790	0.44	0.80722	D	1	B;P;D;B;P;B;B;P;P;P	0.53462	0.025;0.624;0.96;0.21;0.624;0.035;0.049;0.624;0.624;0.624	B;B;D;B;B;B;B;B;B;B	0.70487	0.066;0.272;0.969;0.246;0.357;0.124;0.059;0.36;0.272;0.357	D	0.99931	1.1321	10	0.49607	T	0.09	.	19.5898	0.95506	0.0:1.0:0.0:0.0	.	35;36;36;36;36;36;36;36;36;36	C0KTF2;C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;.;PAX5_HUMAN	L	36	ENSP00000350844:V36L;ENSP00000367084:V36L;ENSP00000367083:V36L;ENSP00000429637:V36L;ENSP00000429291:V36L;ENSP00000430773:V36L;ENSP00000404687:V36L;ENSP00000412188:V36L;ENSP00000367078:V36L	ENSP00000350844:V36L	V	-	1	0	PAX5	37010739	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.976000	0.70484	2.624000	0.88883	0.655000	0.94253	GTA		0.517	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			A	37020739	C	A	37020739	3	1	117	1	0	0	0	0	1	0	0	0	11513	478	17	2	1105	2	PAX5	9	37020739	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		37020739	104192692	43	31215										
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139277716	139277716	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gcagacctcgggacagggccGtgggccctggcagggacctg	18	13	0	1	rs61731237	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr9:139277716G>A	ENST00000298532.2	-	15	2273	c.1905C>T	c.(1903-1905)caC>caT	p.H635H		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GGACAGGGCCGTGGGCCCTGG	0.716													G|||	77	0.0153754	0.0567	0.0029	5008	,	,		14587	0		0	False		,,,				2504	0															0			9						A		205,4187		1,203,1992	20	26	24		1905	-5.1	0	9	dbSNP_129	24	8,8574		0,8,4283	no	coding-synonymous	SNAPC4	NM_003086.2		1,211,6275	AA,AG,GG		0.0932,4.6676,1.6417		635/1470	139277716	213,12761	2196	4291	6487	138397537	SO:0001819	synonymous_variant	6621			AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.1905C>T	9.37:g.139277716G>A			138397537		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																				0.716	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		A	139277716	G	A	139277716	2	1	117	1	0	0	0	0	0	0	0	1	14874	1136	40	1		1	SNAPC4	9	139277716	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10	102256977	139277716	1935715	44	31216										
OR51B4	79339	hgsc.bcm.edu	37	chr11	5322500	5322500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tagcttcctcttgtccagacGcaatgcccatcactgtcttg	7	14	3	1	rs116026654	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:5322500G>A	ENST00000380224.1	-	1	726	c.677C>T	c.(676-678)gCg>gTg	p.A226V	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	226					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A226V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGTCCAGACGCAATGCCCAT	0.383													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		21374	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	11						G	VAL/ALA	41,4361	44.6+/-78.6	1,39,2161	88	81	83		677	2.6	1	11	dbSNP_132	83	0,8594		0,0,4297	yes	missense	OR51B4	NM_033179.2	64	1,39,6458	AA,AG,GG		0.0,0.9314,0.3155	benign	226/311	5322500	41,12955	2201	4297	6498	5279076	SO:0001583	missense	79339			BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.677C>T	11.37:g.5322500G>A	ENSP00000369573:p.Ala226Val		5279076	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	10.69	1.420861	0.25639	0.009314	0.0	ENSG00000183251	ENST00000380224	T	0.38722	1.12	4.41	2.56	0.30785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000160	T	0.28267	0.0698	M	0.77486	2.375	0.23581	N	0.997363	P	0.43578	0.811	B	0.41466	0.358	T	0.30736	-0.9968	10	0.72032	D	0.01	.	10.1836	0.42984	0.1508:0.0:0.8492:0.0	.	226	Q9Y5P0	O51B4_HUMAN	V	226	ENSP00000369573:A226V	ENSP00000369573:A226V	A	-	2	0	OR51B4	5279076	0.006000	0.16342	1.000000	0.80357	0.004000	0.04260	1.578000	0.36525	0.510000	0.28216	-0.732000	0.03574	GCG		0.383	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		A	5322500	G	A	5322500	3	1	117	1	0	0	0	0	1	0	0	0	11121	1087	38	1	258	1	OR51B4	11	5322500	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10		5322500	129684016	45	31217										
SYT9	143425	hgsc.bcm.edu	37	chr11	7334966	7334966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	agactaaagttcacagaaagAccctgaaccctgtgtttgat	8	9	1	5			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:7334966A>G	ENST00000318881.6	+	3	1075	c.838A>G	c.(838-840)Acc>Gcc	p.T280A	SYT9_ENST00000396716.2_Missense_Mutation_p.T248A	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	280	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TCACAGAAAGACCCTGAACCC	0.433																																																0			11											199	198	199					11																	7334966		2201	4296	6497	7291542	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.838A>G	11.37:g.7334966A>G	ENSP00000324419:p.Thr280Ala		7291542		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.496461	0.85069	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.11495	2.77;2.77	6.17	6.17	0.99709	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000001	T	0.41604	0.1166	M	0.92784	3.345	0.80722	D	1	D	0.58620	0.983	D	0.64506	0.926	T	0.51849	-0.8653	9	.	.	.	.	14.7743	0.69713	1.0:0.0:0.0:0.0	.	280	Q86SS6	SYT9_HUMAN	A	248;280	ENSP00000379944:T248A;ENSP00000324419:T280A	.	T	+	1	0	SYT9	7291542	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	ACC		0.433	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		G	7334966	A	G	7334966	3	3	117	1	0	0	0	0	1	0	0	0	15520	275	10	4	848	4	SYT9	11	7334966	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	2012466	7334966	127671550	46	31218										
MADD	4607	hgsc.bcm.edu	37	chr11	47350617	47350617	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gcccacgaaatctgctactcCgtattatgtctcttctcgta	6	13	3	0	rs181428672	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:47350617C>A	ENST00000545968.1	-	0	4217				MADD_ENST00000349238.3_Silent_p.S1581S|MADD_ENST00000395336.3_3'UTR|MADD_ENST00000311027.5_Silent_p.S1620S|MADD_ENST00000342922.4_Silent_p.S1561S|MADD_ENST00000402192.2_Silent_p.S1560S|MADD_ENST00000406482.1_3'UTR|MADD_ENST00000395344.3_Silent_p.S1514S|MADD_ENST00000402799.1_Silent_p.S1518S|MADD_ENST00000407859.3_Silent_p.S1538S	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac						cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.S1620S(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		TCTGCTACTCCGTATTATGTC	0.537																																																1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	11											197	168	178					11																	47350617		2201	4298	6499	47307193	SO:0001628	intergenic_variant	8567			X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7551	protein-coding gene	gene with protein product		600958	"myosin-binding protein C, cardiac"	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896			11.37:g.47350617C>A			47307193	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	37	CCDS53621.1																																																																																				0.537	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			A	47350617	C	A	47350617	1	1	117	0	1	0	0	0	0	0	0	0	9182	639	23	2		2	MADD	11	47350617	IGR	SNP	C	TCGA-F5-6702-01A-11D-1826-10	40015651	47350617	87655899	47	31219										
OR4S1	256148	hgsc.bcm.edu	37	chr11	48328640	48328640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tttgatctatacactaaggaAcaacgatgtgaaaaatgcca	7	7	1	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:48328640A>G	ENST00000319988.1	+	1	866	c.866A>G	c.(865-867)aAc>aGc	p.N289S		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N289I(1)		endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						ACACTAAGGAACAACGATGTG	0.453																																																1	Substitution - Missense(1)	ovary(1)	11											96	88	91					11																	48328640		2201	4298	6499	48285216	SO:0001583	missense	256148			AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"GPCR / Class A : Olfactory receptors"	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.866A>G	11.37:g.48328640A>G	ENSP00000321447:p.Asn289Ser		48285216	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.818961	0.32145	.	.	ENSG00000176555	ENST00000319988	T	0.39997	1.05	5.02	5.02	0.67125	.	.	.	.	.	T	0.58264	0.2110	M	0.80847	2.515	0.27740	N	0.944509	D	0.61080	0.989	P	0.53401	0.725	T	0.58725	-0.7586	9	0.66056	D	0.02	.	12.9764	0.58540	1.0:0.0:0.0:0.0	.	289	Q8NGB4	OR4S1_HUMAN	S	289	ENSP00000321447:N289S	ENSP00000321447:N289S	N	+	2	0	OR4S1	48285216	0.970000	0.33590	0.379000	0.26080	0.079000	0.17450	2.445000	0.44899	2.020000	0.59435	0.533000	0.62120	AAC		0.453	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		G	48328640	A	G	48328640	3	3	117	1	0	0	0	0	1	0	0	0	11113	43	2	4	868	4	OR4S1	11	48328640	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	978023	48328640	86677876	48	31220										
SF1	7536	hgsc.bcm.edu	37	chr11	64544046	64544046	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cctggaatcactgtcttctgTtccattgtgtcttggttcca	8	11	4	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:64544046T>C	ENST00000377390.3	-	2	421	c.84A>G	c.(82-84)gaA>gaG	p.E28E	SF1_ENST00000433274.2_Silent_p.E2E|SF1_ENST00000377387.1_Silent_p.E153E|SF1_ENST00000377394.3_Silent_p.E28E|SF1_ENST00000422298.2_5'UTR|SF1_ENST00000227503.9_Silent_p.E28E|AP001462.6_ENST00000594089.1_lincRNA|SF1_ENST00000334944.5_Silent_p.E28E	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	28					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.E28E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						CTGTCTTCTGTTCCATTGTGT	0.423																																																1	Substitution - coding silent(1)	breast(1)	11											157	147	150					11																	64544046		2201	4297	6498	64300622	SO:0001819	synonymous_variant	7536			D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.84A>G	11.37:g.64544046T>C			64300622	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Silent	SNP	ENST00000377390.3	37	CCDS31599.1																																																																																				0.423	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		C	64544046	T	C	64544046	2	2	117	1	0	0	0	0	0	0	0	1	14182	1722	60	4		4	SF1	11	64544046	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	16215406	64544046	70462470	49	31221										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76174958	76174958	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgttctaaaggaagttccaaAggccgttgttccagtctcaa	9	9	2	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:76174958A>G	ENST00000529032.1	+	6	665	c.665A>G	c.(664-666)aAg>aGg	p.K222R	C11orf30_ENST00000533248.1_Missense_Mutation_p.K236R|C11orf30_ENST00000524767.1_Missense_Mutation_p.K237R|C11orf30_ENST00000334736.3_Missense_Mutation_p.K222R|C11orf30_ENST00000524490.1_Missense_Mutation_p.K223R|C11orf30_ENST00000525038.1_Missense_Mutation_p.K237R|C11orf30_ENST00000343878.3_Missense_Mutation_p.K222R|C11orf30_ENST00000525919.1_Missense_Mutation_p.K223R			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	222	Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.K222M(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						GAAGTTCCAAAGGCCGTTGTT	0.483																																																1	Substitution - Missense(1)	ovary(1)	11											184	182	183					11																	76174958		2200	4292	6492	75852606	SO:0001583	missense	56946			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.665A>G	11.37:g.76174958A>G	ENSP00000432327:p.Lys222Arg		75852606	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.436807	0.62955	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.62	4.5	0.54988	.	0.044831	0.85682	N	0.000000	T	0.47655	0.1457	L	0.29908	0.895	0.58432	D	0.999997	B;B;B;D;B;D;B;D	0.67145	0.009;0.024;0.024;0.996;0.099;0.993;0.024;0.993	B;B;B;D;B;D;B;D	0.72982	0.007;0.012;0.012;0.979;0.041;0.953;0.012;0.953	T	0.29212	-1.0019	10	0.20519	T	0.43	-4.0501	11.2765	0.49170	0.929:0.0:0.071:0.0	.	236;237;237;222;172;223;223;222	B7ZKT8;B7ZKU2;B7ZKU0;Q7Z589-2;F5H2F0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;.;EMSY_HUMAN	R	223;222;222;172;237;236;223;237;222	ENSP00000431166:K223R;ENSP00000334130:K222R;ENSP00000344688:K222R;ENSP00000433205:K237R;ENSP00000433634:K236R;ENSP00000432010:K223R;ENSP00000436968:K237R;ENSP00000432327:K222R	ENSP00000334130:K222R	K	+	2	0	C11orf30	75852606	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.173000	0.77612	0.972000	0.38314	0.460000	0.39030	AAG		0.483	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		G	76174958	A	G	76174958	3	3	117	1	0	0	0	0	1	0	0	0	1640	72	3	4	687	4	C11orf30	11	76174958	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	11630912	76174958	58831558	50	31222										
PICALM	8301	hgsc.bcm.edu	37	chr11	85733487	85733487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tttaaatatctactataccgCctaataaatgtagacatgtc	4	8	1	1	rs200363412		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:85733487C>T	ENST00000393346.3	-	4	523	c.375G>A	c.(373-375)agG>agA	p.R125R	PICALM_ENST00000528398.1_Silent_p.R74R|PICALM_ENST00000528411.1_5'UTR|PICALM_ENST00000532317.1_Silent_p.R125R|PICALM_ENST00000356360.5_Silent_p.R125R|PICALM_ENST00000526033.1_Silent_p.R125R			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	125	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				TACTATACCGCCTAATAAATG	0.299			T	"MLLT10, MLL"	"TALL, AML, "																																		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	0			11											87	91	89					11																	85733487		2202	4292	6494	85411135	SO:0001819	synonymous_variant	8301			BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.375G>A	11.37:g.85733487C>T			85411135	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	37	CCDS8272.1																																																																																				0.299	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		T	85733487	C	T	85733487	2	4	117	1	0	0	0	0	0	0	0	1	11911	738	26	3		3	PICALM	11	85733487	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	9558529	85733487	49273029	51	31223										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105797501	105797501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gaattgttggaggtgtttggTggttctttacactcatcatt	11	5	3	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr11:105797501T>C	ENST00000530497.1	+	12	1882	c.1882T>C	c.(1882-1884)Tgg>Cgg	p.W628R	GRIA4_ENST00000525187.1_Missense_Mutation_p.W628R|GRIA4_ENST00000282499.5_Missense_Mutation_p.W628R|GRIA4_ENST00000393127.2_Missense_Mutation_p.W628R			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	628					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AGGTGTTTGGTGGTTCTTTAC	0.393																																																0			11											139	139	139					11																	105797501		2202	4298	6500	105302711	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1882T>C	11.37:g.105797501T>C	ENSP00000435775:p.Trp628Arg		105302711	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.579226	0.86645	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.6	5.6	0.85130	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000003	T	0.82033	0.4949	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.88285	0.2939	10	0.87932	D	0	.	16.0858	0.81049	0.0:0.0:0.0:1.0	.	628;628	P48058;G3V164	GRIA4_HUMAN;.	R	628	ENSP00000282499:W628R;ENSP00000376835:W628R;ENSP00000435775:W628R;ENSP00000432180:W628R	ENSP00000282499:W628R	W	+	1	0	GRIA4	105302711	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.997000	0.88414	2.264000	0.75181	0.533000	0.62120	TGG		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			C	105797501	T	C	105797501	3	2	117	1	0	0	0	0	1	0	0	0	6791	1696	59	4	1965	4	GRIA4	11	105797501	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	20064014	105797501	29209015	52	31224										
DCP1B	196513	hgsc.bcm.edu	37	chr12	2102455	2102455	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gcatttctgtagagaaggaaAgggtcctggagttggaaatc	14	5	1	1	rs150415068	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr12:2102455A>G	ENST00000280665.6	-	3	373	c.294T>C	c.(292-294)ccT>ccC	p.P98P	DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_5'UTR	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	98					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			AGAGAAGGAAAGGGTCCTGGA	0.403																																																0			12											148	156	153					12																	2102455		2203	4300	6503	1972716	SO:0001819	synonymous_variant	196513			AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.294T>C	12.37:g.2102455A>G			1972716	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	37	CCDS31727.1																																																																																				0.403	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		G	2102455	A	G	2102455	2	3	117	1	0	0	0	0	0	0	0	1	4305	59	3	4		4	DCP1B	12	2102455	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10		2102455	131749440	53	31225										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2719800	2719800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aagtgtggtacgtggtcaacTccacctacttcgagtacctg	10	11	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr12:2719800T>C	ENST00000347598.4	+	29	3712	c.3712T>C	c.(3712-3714)Tcc>Ccc	p.S1238P	CACNA1C_ENST00000399649.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399601.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399597.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000402845.3_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399591.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000480911.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399634.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000344100.3_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399655.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000406454.3_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399637.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399595.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399603.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399621.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399641.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399644.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399629.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399606.1_Missense_Mutation_p.S1238P|CACNA1C_ENST00000335762.5_Missense_Mutation_p.S1243P|CACNA1C_ENST00000399638.1_Missense_Mutation_p.S1218P|CACNA1C_ENST00000327702.7_Missense_Mutation_p.S1218P|CACNA1C_ENST00000399617.1_Missense_Mutation_p.S1218P	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1238					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGTGGTCAACTCCACCTACTT	0.592																																																0			12											114	121	119					12																	2719800		2199	4300	6499	2590061	SO:0001583	missense	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3712T>C	12.37:g.2719800T>C	ENSP00000266376:p.Ser1238Pro		2590061	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.885085	0.91814	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97710	-4.5;-4.5;-4.19;-4.5;-4.5;-4.5;-4.24;-4.14;-4.21;-4.5;-4.5;-4.16;-4.5;-4.26;-4.5;-4.07;-4.5;-4.25;-4.5;-4.26;-4.2;-4.28;-4.32	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.99127	0.9699	H	0.95917	3.74	0.80722	D	1	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.99;0.999;1.0;0.995;0.997;0.999;0.999;1.0;0.887;0.997;0.999;1.0;0.999;0.998;0.996;0.992;1.0;0.999;1.0;0.998;0.999;0.999;0.999;0.981;0.999	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.991;0.996;0.999;0.991;0.996;0.996;0.998;1.0;0.816;0.997;0.996;0.996;0.997;0.986;0.993;0.981;1.0;0.997;0.998;0.993;0.997;0.997;0.996;0.972;0.996	D	0.99204	1.0874	10	0.87932	D	0	.	15.1042	0.72306	0.0:0.0:0.0:1.0	.	1218;1215;1238;1218;1218;1218;1218;1218;1218;1238;1218;1189;1238;1218;1218;1218;1218;1218;1218;1218;1218;1218;1218;1218;1218	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	P	1243;1218;1218;1218;1218;1218;1218;1218;1218;1218;1238;1238;1218;1218;1218;1218;1218;1218;1218;1218;1218;1218;1218;1059	ENSP00000336982:S1243P;ENSP00000382563:S1218P;ENSP00000437936:S1218P;ENSP00000382552:S1218P;ENSP00000382547:S1218P;ENSP00000382506:S1218P;ENSP00000382530:S1218P;ENSP00000382546:S1218P;ENSP00000382500:S1218P;ENSP00000382549:S1218P;ENSP00000266376:S1238P;ENSP00000382515:S1238P;ENSP00000382510:S1218P;ENSP00000341092:S1218P;ENSP00000382537:S1218P;ENSP00000329877:S1218P;ENSP00000382557:S1218P;ENSP00000385724:S1218P;ENSP00000382512:S1218P;ENSP00000382542:S1218P;ENSP00000382526:S1218P;ENSP00000385896:S1218P;ENSP00000382504:S1218P	ENSP00000323129:S1059P	S	+	1	0	CACNA1C	2590061	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.980000	0.88113	2.029000	0.59856	0.533000	0.62120	TCC		0.592	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		C	2719800	T	C	2719800	3	2	117	1	0	0	0	0	1	0	0	0	2546	1551	54	4	3934	4	CACNA1C	12	2719800	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	617345	2719800	131132095	54	31226										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398294	25398294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gcctacgccaccagctccaaCtaccacaagtttatattcag	5	15	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr12:25398294C>T	ENST00000256078.4	-	2	88	c.25G>A	c.(25-27)Gtt>Att	p.V9I	KRAS_ENST00000556131.1_Missense_Mutation_p.V9I|KRAS_ENST00000311936.3_Missense_Mutation_p.V9I|KRAS_ENST00000557334.1_Missense_Mutation_p.V9I	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	9					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			CCAGCTCCAACTACCACAAGT	0.348		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	0			12											90	80	83					12																	25398294		2203	4300	6503	25289561	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.25G>A	12.37:g.25398294C>T	ENSP00000256078:p.Val9Ile		25289561	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.964152	0.92791	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.68	4.77	0.60923	Small GTP-binding protein domain (1);	0.057339	0.64402	D	0.000002	T	0.79822	0.4512	N	0.25825	0.765	0.80722	D	1	D;D	0.59767	0.969;0.986	P;D	0.63283	0.859;0.913	T	0.82339	-0.0506	10	0.72032	D	0.01	.	14.5201	0.67844	0.1479:0.8521:0.0:0.0	.	9;9	P01116-2;P01116	.;RASK_HUMAN	I	9	ENSP00000308495:V9I;ENSP00000452512:V9I;ENSP00000256078:V9I;ENSP00000451856:V9I	ENSP00000256078:V9I	V	-	1	0	KRAS	25289561	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	1.349000	0.45751	0.563000	0.77884	GTT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398294	C	T	25398294	3	4	117	1	0	0	0	0	1	0	0	0	8459	565	20	3	681	3	KRAS	12	25398294	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	22678494	25398294	108453601	55	31227										
OR6C68	403284	hgsc.bcm.edu	37	chr12	55886497	55886497	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggggtaactgaattttttctTttggctaccatgtcatatga	9	6	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr12:55886497T>A	ENST00000548615.1	+	1	336	c.336T>A	c.(334-336)ctT>ctA	p.L112L	RP11-110A12.2_ENST00000555138.1_RNA|OR6C68_ENST00000379662.1_Silent_p.L117L|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						AATTTTTTCTTTTGGCTACCA	0.363																																																0			12											156	147	150					12																	55886497		2203	4300	6503	54172764	SO:0001819	synonymous_variant	403284				CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"GPCR / Class A : Olfactory receptors"	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.336T>A	12.37:g.55886497T>A			54172764		Silent	SNP	ENST00000548615.1	37	CCDS31826.2																																																																																				0.363	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1			A	55886497	T	A	55886497	2	1	117	1	0	0	0	0	0	0	0	1	11227	1828	64	5		5	OR6C68	12	55886497	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	30488203	55886497	77965398	56	31228										
CDK8	1024	hgsc.bcm.edu	37	chr13	26970427	26970427	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	caatgtatttcacagataaaGattgggaagatataaaaaag	8	3	1	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr13:26970427G>T	ENST00000381527.3	+	8	1299	c.796G>T	c.(796-798)Gat>Tat	p.D266Y	CDK8_ENST00000536792.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		CACAGATAAAGATTGGGAAGA	0.284																																																0			13											37	41	40					13																	26970427		2200	4286	6486	25868427	SO:0001583	missense	1024			X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.796G>T	13.37:g.26970427G>T	ENSP00000370938:p.Asp266Tyr		25868427	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	37	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850294	0.71719	.	.	ENSG00000132964	ENST00000381527	T	0.68025	-0.3	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.087078	0.85682	D	0.000000	T	0.69223	0.3087	L	0.46819	1.47	0.80722	D	1	B;B	0.27700	0.154;0.186	B;B	0.37387	0.16;0.248	T	0.66941	-0.5796	10	0.62326	D	0.03	-15.4702	20.1896	0.98226	0.0:0.0:1.0:0.0	.	266;266	P49336-2;P49336	.;CDK8_HUMAN	Y	266	ENSP00000370938:D266Y	ENSP00000370938:D266Y	D	+	1	0	CDK8	25868427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.772000	0.95346	0.650000	0.86243	GAT		0.284	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			T	26970427	G	T	26970427	3	4	117	1	0	0	0	0	1	0	0	0	3156	942	33	2	826	2	CDK8	13	26970427	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10		26970427	88199451	57	31229			1	38		2	2	21	G		5.879001e-05
CDK8	1024	hgsc.bcm.edu	37	chr13	26970447	26970447	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gattgggaagatataaaaaaGatgcctgaacattcaacatt	8	5	1	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr13:26970447G>C	ENST00000381527.3	+	8	1319	c.816G>C	c.(814-816)aaG>aaC	p.K272N	CDK8_ENST00000536792.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		ATATAAAAAAGATGCCTGAAC	0.289																																																0			13											41	45	44					13																	26970447		2199	4283	6482	25868447	SO:0001583	missense	1024			X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.816G>C	13.37:g.26970447G>C	ENSP00000370938:p.Lys272Asn		25868447	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	37	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.105563	0.77096	.	.	ENSG00000132964	ENST00000381527	T	0.66099	-0.19	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.041014	0.85682	D	0.000000	T	0.60508	0.2274	N	0.14661	0.345	0.80722	D	1	D;D	0.57571	0.975;0.98	P;P	0.60541	0.804;0.876	T	0.59674	-0.7410	10	0.33940	T	0.23	-12.0291	13.404	0.60900	0.0719:0.0:0.9281:0.0	.	272;272	P49336-2;P49336	.;CDK8_HUMAN	N	272	ENSP00000370938:K272N	ENSP00000370938:K272N	K	+	3	2	CDK8	25868447	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.628000	0.83189	2.772000	0.95346	0.650000	0.86243	AAG		0.289	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			C	26970447	G	C	26970447	3	2	117	1	0	0	0	0	1	0	0	0	3156	933	33	5	846	5	CDK8	13	26970447	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	20	26970447	88199431	58	31230			1	38		2	2	21	G		5.879001e-05
FRY	10129	hgsc.bcm.edu	37	chr13	32808806	32808806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtcggtccttccagatattcCgggccctcaagcaacctctg	9	15	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr13:32808806C>T	ENST00000380250.3	+	42	6119	c.5623C>T	c.(5623-5625)Cgg>Tgg	p.R1875W		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1875						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CCAGATATTCCGGGCCCTCAA	0.512																																																0			13											113	109	111					13																	32808806		1967	4141	6108	31706806	SO:0001583	missense	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5623C>T	13.37:g.32808806C>T	ENSP00000369600:p.Arg1875Trp		31706806	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747081	0.69418	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.53206	0.63	5.91	1.13	0.20643	.	0.000000	0.85682	D	0.000000	T	0.72622	0.3483	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.81634	-0.0844	10	0.87932	D	0	.	17.889	0.88865	0.3528:0.6472:0.0:0.0	.	1875	Q5TBA9	FRY_HUMAN	W	1875;712	ENSP00000369600:R1875W	ENSP00000369600:R1875W	R	+	1	2	FRY	31706806	0.965000	0.33210	0.999000	0.59377	0.992000	0.81027	0.691000	0.25467	0.370000	0.24538	-0.188000	0.12872	CGG		0.512	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32808806	C	T	32808806	3	4	117	1	0	0	0	0	1	0	0	0	6082	643	23	1	5789	1	FRY	13	32808806	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	5838359	32808806	82361072	59	31231										
LHFP	10186	hgsc.bcm.edu	37	chr13	40175189	40175189	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	atcatctgccgactctcatcAtgcacaggatatgagcacct	7	13	4	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr13:40175189A>G	ENST00000379589.3	-	2	627	c.165T>C	c.(163-165)caT>caC	p.H55H	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	55						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		GACTCTCATCATGCACAGGAT	0.572			T	HMGA2	lipoma																																		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	0			13											214	192	199					13																	40175189		2203	4300	6503	39073189	SO:0001819	synonymous_variant	10186			AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.165T>C	13.37:g.40175189A>G			39073189	B2R7M2|Q53FC0|Q96SH5	Silent	SNP	ENST00000379589.3	37	CCDS9369.1																																																																																				0.572	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780		G	40175189	A	G	40175189	2	3	117	1	0	0	0	0	0	0	0	1	8786	214	8	4		4	LHFP	13	40175189	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10	7366383	40175189	74994689	60	31232										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88329446	88329446	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cccaaaaaattcgctgagacCgacatgcgctccattaagtc	7	13	0	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr13:88329446C>A	ENST00000325089.6	+	2	2022	c.1803C>A	c.(1801-1803)acC>acA	p.T601T	SLITRK5_ENST00000400028.3_Silent_p.T360T	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	601	LRRCT 2.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TCGCTGAGACCGACATGCGCT	0.557																																																0			13											168	152	157					13																	88329446		2203	4300	6503	87127447	SO:0001819	synonymous_variant	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1803C>A	13.37:g.88329446C>A			87127447	B3KNB8|B4DSH5|Q5VT81	Silent	SNP	ENST00000325089.6	37	CCDS9465.1																																																																																				0.557	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88329446	C	A	88329446	2	1	117	1	0	0	0	0	0	0	0	1	14783	639	23	2		2	SLITRK5	13	88329446	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	48154257	88329446	26840432	61	31233										
RTN1	6252	hgsc.bcm.edu	37	chr14	60212780	60212780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	agtgtctttattcttaaagtCcaagtctttatcttccagct	5	9	4	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr14:60212780C>T	ENST00000267484.5	-	2	996	c.661G>A	c.(661-663)Gac>Aac	p.D221N		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	221					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TTCTTAAAGTCCAAGTCTTTA	0.443																																																0			14											235	232	233					14																	60212780		2203	4300	6503	59282533	SO:0001583	missense	6252			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.661G>A	14.37:g.60212780C>T	ENSP00000267484:p.Asp221Asn		59282533	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	37	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.953151	0.53293	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.24151	1.87	5.7	4.81	0.61882	.	0.680304	0.14701	N	0.303554	T	0.31451	0.0797	M	0.67953	2.075	0.24045	N	0.996065	D	0.53151	0.958	P	0.45343	0.477	T	0.20940	-1.0260	10	0.12430	T	0.62	.	14.5442	0.68017	0.0:0.9293:0.0:0.0707	.	221	Q16799	RTN1_HUMAN	N	221;147	ENSP00000267484:D221N	ENSP00000267484:D221N	D	-	1	0	RTN1	59282533	0.486000	0.25980	0.995000	0.50966	0.857000	0.48899	2.274000	0.43390	1.400000	0.46741	0.557000	0.71058	GAC		0.443	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			T	60212780	C	T	60212780	3	4	117	1	0	0	0	0	1	0	0	0	13762	855	30	3	1766	3	RTN1	14	60212780	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		60212780	47136760	62	31234										
TSHR	7253	hgsc.bcm.edu	37	chr14	81609338	81609338	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	atgcagagcttgcgccagagAaaatctgtgaatgccttgaa	11	8	1	4			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr14:81609338A>G	ENST00000541158.2	+	11	1258	c.936A>G	c.(934-936)agA>agG	p.R312R	TSHR_ENST00000298171.2_Silent_p.R312R|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	312					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGCGCCAGAGAAAATCTGTGA	0.493			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	0			14											128	124	125					14																	81609338		2203	4300	6503	80679091	SO:0001819	synonymous_variant	7253			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.936A>G	14.37:g.81609338A>G			80679091	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	CCDS9872.1																																																																																				0.493	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		G	81609338	A	G	81609338	2	3	117	1	0	0	0	0	0	0	0	1	16662	243	9	4		4	TSHR	14	81609338	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10	21396558	81609338	25740202	63	31235										
RYR3	6263	hgsc.bcm.edu	37	chr15	33855175	33855175	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gtgacctacaaagcacaagaCgccaaaacttcccgcctggg	9	14	0	2	rs16972317	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr15:33855175C>T	ENST00000389232.4	+	11	1180	c.1110C>T	c.(1108-1110)gaC>gaT	p.D370D	RYR3_ENST00000415757.3_Silent_p.D370D	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	370	MIR 5. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAGCACAAGACGCCAAAACTT	0.448													C|||	138	0.0275559	0.0915	0.013	5008	,	,		19427	0.0069		0	False		,,,				2504	0.001															0			15						C		313,3453		6,301,1576	128	128	128		1110	0.3	1	15	dbSNP_123	128	14,8196		0,14,4091	yes	coding-synonymous	RYR3	NM_001036.3		6,315,5667	TT,TC,CC		0.1705,8.3112,2.7305		370/4871	33855175	327,11649	1883	4105	5988	31642467	SO:0001819	synonymous_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.1110C>T	15.37:g.33855175C>T			31642467	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.448	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33855175	C	T	33855175	2	4	117	1	0	0	0	0	0	0	0	1	13807	535	19	1		1	RYR3	15	33855175	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10		33855175	68676217	64	31236										
ADCY9	115	hgsc.bcm.edu	37	chr16	4015909	4015909	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgacgggctccttccacggtCtcttgggggacaggtgggca	16	11	1	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr16:4015909C>T	ENST00000294016.3	-	11	4467	c.3929G>A	c.(3928-3930)aGa>aAa	p.R1310K		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1310					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTTCCACGGTCTCTTGGGGGA	0.537																																																0			16											100	97	98					16																	4015909		2197	4300	6497	3955910	SO:0001583	missense	115			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.3929G>A	16.37:g.4015909C>T	ENSP00000294016:p.Arg1310Lys		3955910	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	7.433	0.639085	0.14386	.	.	ENSG00000162104	ENST00000294016	D	0.81499	-1.5	5.66	3.67	0.42095	.	0.250430	0.41500	D	0.000869	T	0.60130	0.2245	N	0.11560	0.145	0.25816	N	0.984334	B	0.06786	0.001	B	0.06405	0.002	T	0.42632	-0.9440	10	0.14252	T	0.57	.	10.2356	0.43282	0.0:0.782:0.0:0.218	.	1310	O60503	ADCY9_HUMAN	K	1310	ENSP00000294016:R1310K	ENSP00000294016:R1310K	R	-	2	0	ADCY9	3955910	0.955000	0.32602	0.996000	0.52242	0.342000	0.28953	1.379000	0.34340	1.524000	0.49035	0.650000	0.86243	AGA		0.537	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			T	4015909	C	T	4015909	3	4	117	1	0	0	0	0	1	0	0	0	301	913	32	3	136	3	ADCY9	16	4015909	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		4015909	86338844	65	31237										
SMG1	23049	hgsc.bcm.edu	37	chr16	18882777	18882777	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ttcttcattaaaacagctgcTtccaaagcccaagtcattaa	4	11	3	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr16:18882777T>C	ENST00000446231.2	-	16	2623	c.2211A>G	c.(2209-2211)gaA>gaG	p.E737E	snoU13_ENST00000459248.1_RNA|SMG1_ENST00000389467.3_Silent_p.E737E			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	737	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AAACAGCTGCTTCCAAAGCCC	0.343																																																0			16											57	53	54					16																	18882777		1813	4081	5894	18790278	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2211A>G	16.37:g.18882777T>C			18790278	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.343	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18882777	T	C	18882777	2	2	117	1	0	0	0	0	0	0	0	1	14832	1606	56	4		4	SMG1	16	18882777	Silent	SNP	T	TCGA-F5-6702-01A-11D-1826-10	14866868	18882777	71471976	66	31238										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27499589	27499589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tcttcccagggtccttcttcAgccgcttccgcttctggctt	8	16	4	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr16:27499589A>G	ENST00000356183.4	-	23	3674	c.3659T>C	c.(3658-3660)cTg>cCg	p.L1220P	GTF3C1_ENST00000561623.1_Missense_Mutation_p.L1220P	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1220	Arg/Lys-rich (basic).				5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GTCCTTCTTCAGCCGCTTCCG	0.522																																																0			16											158	170	166					16																	27499589		2197	4300	6497	27407090	SO:0001583	missense	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3659T>C	16.37:g.27499589A>G	ENSP00000348510:p.Leu1220Pro		27407090	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.147887	0.37923	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.26660	1.72	4.71	4.71	0.59529	.	0.433107	0.21168	N	0.079030	T	0.25938	0.0632	M	0.67953	2.075	0.58432	D	0.999998	B;B	0.18166	0.009;0.026	B;B	0.18561	0.01;0.022	T	0.05767	-1.0865	10	0.30078	T	0.28	-7.305	8.5244	0.33296	0.9077:0.0:0.0923:0.0	.	1220;1220	Q12789;Q12789-3	TF3C1_HUMAN;.	P	1220;1216	ENSP00000348510:L1220P	ENSP00000348510:L1220P	L	-	2	0	GTF3C1	27407090	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.426000	0.52778	1.763000	0.52060	0.459000	0.35465	CTG		0.522	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		G	27499589	A	G	27499589	3	3	117	1	0	0	0	0	1	0	0	0	6893	188	7	4	2730	4	GTF3C1	16	27499589	Missense_Mutation	SNP	A	TCGA-F5-6702-01A-11D-1826-10	8616812	27499589	62855164	67	31239										
TP53	7157	hgsc.bcm.edu	37	chr17	7577141	7577141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gcacctcaaagctgttccgtCccagtagattaccactactc	6	15	1	1	rs193920774		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:7577141C>A	ENST00000269305.4	-	8	986	c.797G>T	c.(796-798)gGa>gTa	p.G266V	TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.G266V|TP53_ENST00000420246.2_Missense_Mutation_p.G266V|TP53_ENST00000359597.4_Missense_Mutation_p.G266V|TP53_ENST00000445888.2_Missense_Mutation_p.G266V|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266E(50)|p.G266V(42)|p.0?(8)|p.?(3)|p.G266fs*79(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTGTTCCGTCCCAGTAGATT	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	121	Substitution - Missense(95)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(3)	lung(23)|oesophagus(10)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(9)|breast(9)|upper_aerodigestive_tract(8)|ovary(8)|urinary_tract(7)|pancreas(6)|skin(5)|central_nervous_system(4)|stomach(4)|bone(4)|liver(4)|endometrium(3)|vulva(1)|kidney(1)|thyroid(1)|cervix(1)|eye(1)|genital_tract(1)|biliary_tract(1)	17											50	44	46					17																	7577141		2203	4300	6503	7517866	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.797G>T	17.37:g.7577141C>A	ENSP00000269305:p.Gly266Val		7517866	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388215	0.82902	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99900	-7.62;-7.62;-7.62;-7.62;-7.62;-7.62	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	266;266;266;266;266;255;134	ENSP00000352610:G266V;ENSP00000269305:G266V;ENSP00000398846:G266V;ENSP00000391127:G266V;ENSP00000391478:G266V;ENSP00000425104:G134V	ENSP00000269305:G266V	G	-	2	0	TP53	7517866	1.000000	0.71417	0.996000	0.52242	0.744000	0.42396	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577141	C	A	7577141	3	1	117	1	0	0	0	0	1	0	0	0	16421	855	30	2	489	2	TP53	17	7577141	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		7577141	73618069	68	31240										
MYH2	4620	hgsc.bcm.edu	37	chr17	10443999	10443999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggtaatcatatgggttcgtgGtaatcagaagcatttctaag	11	5	3	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:10443999G>A	ENST00000245503.5	-	11	1304	c.920C>T	c.(919-921)aCc>aTc	p.T307I	MYH2_ENST00000532183.2_Missense_Mutation_p.T307I|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.T307I|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	307	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TGGGTTCGTGGTAATCAGAAG	0.383																																																0			17											94	86	89					17																	10443999		2203	4300	6503	10384724	SO:0001583	missense	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.920C>T	17.37:g.10443999G>A	ENSP00000245503:p.Thr307Ile		10384724	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839338	0.91117	.	.	ENSG00000125414	ENST00000532183;ENST00000245503;ENST00000397183	D;D;D	0.87887	-2.31;-2.31;-2.31	5.25	5.25	0.73442	Myosin head, motor domain (2);	0.000000	0.40385	U	0.001102	D	0.95828	0.8642	H	0.96365	3.81	0.80722	D	1	D;P	0.71674	0.998;0.901	D;D	0.83275	0.996;0.909	D	0.96890	0.9652	10	0.87932	D	0	.	18.0234	0.89261	0.0:0.0:1.0:0.0	.	307;307	Q567P6;Q9UKX2	.;MYH2_HUMAN	I	307	ENSP00000433944:T307I;ENSP00000245503:T307I;ENSP00000380367:T307I	ENSP00000245503:T307I	T	-	2	0	MYH2	10384724	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.643000	0.98464	2.742000	0.94016	0.650000	0.86243	ACC		0.383	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10443999	G	A	10443999	3	1	117	1	0	0	0	0	1	0	0	0	10065	1261	44	3	5025	3	MYH2	17	10443999	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	2866858	10443999	70751211	69	31241										
AP2B1	163	hgsc.bcm.edu	37	chr17	33951544	33951544	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aatgaatgcactgaatggggCcagattttcatcctggactg	11	8	1	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:33951544C>T	ENST00000262325.7	+	6	1207	c.654C>T	c.(652-654)ggC>ggT	p.G218G	AP2B1_ENST00000592545.1_Silent_p.G180G|AP2B1_ENST00000537622.2_Silent_p.G218G|AP2B1_ENST00000589344.1_Silent_p.G218G|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000312678.8_Silent_p.G218G|AP2B1_ENST00000538556.1_Silent_p.G161G	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	218					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CTGAATGGGGCCAGATTTTCA	0.463																																																0			17											104	92	96					17																	33951544		2203	4300	6503	30975657	SO:0001819	synonymous_variant	163			M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.654C>T	17.37:g.33951544C>T			30975657	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	37	CCDS32622.1																																																																																				0.463	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			T	33951544	C	T	33951544	2	4	117	1	0	0	0	0	0	0	0	1	741	726	26	3		3	AP2B1	17	33951544	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	23507545	33951544	47243666	70	31242										
MLLT6	4302	hgsc.bcm.edu	37	chr17	36864101	36864107	+	Frame_Shift_Del	DEL	CGTGCCT	CGTGCCT	-													0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gagcccatcgtgctgcagtaCgtgcctcatgatcgcttcaa							TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	CGTGCCT	CGTGCCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:36864101_36864107delCGTGCCT	ENST00000325718.7	+	4	421_427	c.330_336delCGTGCCT	c.(328-336)tacgtgcctfs	p.YVP110fs	MLLT6_ENST00000378137.5_Frame_Shift_Del_p.YVP110fs|CTB-58E17.3_ENST00000583409.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	110					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TGCTGCAGTACGTGCCTCATGATCGCT	0.599			T	MLL	AL																																		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	0			17																																								34117633	SO:0001589	frameshift_variant	4302				CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.330_336delCGTGCCT	17.37:g.36864101_36864107delCGTGCCT	ENSP00000316426:p.Tyr110fs		34117627	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Frame_Shift_Del	DEL	ENST00000325718.7	37	CCDS11327.1																																																																																				0.599	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		-	36864107	CGTGCCT	-	36864101	7	5	117	1	0	1	0	1	0	0	0	0	9660	547	19	0	344	0	MLLT6	17	36864101	Frame_Shift_Del	DEL	CGTGCCT	TCGA-F5-6702-01A-11D-1826-10	2912557	36864101	44331109	71	31243										
STH	246744	hgsc.bcm.edu	37	chr17	44076664	44076664	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ccatgagtgagggtggaggcCaagtctcatgcatttttgca	13	8	1	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:44076664C>T	ENST00000537309.1	+	1	49	c.19C>T	c.(19-21)Caa>Taa	p.Q7*	MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000576518.1_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	7			Q -> R (in dbSNP:rs62063857). {ECO:0000269|PubMed:12032355, ECO:0000269|PubMed:12402275, ECO:0000269|PubMed:12913211}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						gggtggaggccaagtctcatg	0.537																																																0			17											50	48	49					17																	44076664		1974	4170	6144	41432501	SO:0001587	stop_gained	246744			AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"microtubule-associated protein tau (MAPT) intronic transcript"	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.19C>T	17.37:g.44076664C>T	ENSP00000443168:p.Gln7*		41432501	A1L3X7	Nonsense_Mutation	SNP	ENST00000537309.1	37	CCDS54136.1	.	.	.	.	.	.	.	.	.	.	C	9.513	1.106210	0.20632	.	.	ENSG00000256762	ENST00000537309	.	.	.	1.27	-1.89	0.07689	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	1.9899	0.03444	0.3728:0.3918:0.0:0.2353	.	.	.	.	X	7	.	ENSP00000443168:Q7X	Q	+	1	0	STH	41432501	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.334000	0.02665	-0.505000	0.06568	0.491000	0.48974	CAA		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1			T	44076664	C	T	44076664	4	4	117	1	0	0	0	0	0	1	0	0	15320	595	21	3	21	3	STH	17	44076664	Nonsense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	7212563	44076664	37118546	72	31244										
SNF8	11267	hgsc.bcm.edu	37	chr17	47018360	47018360	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	actcaggattcttccggatcTcctgcttgtgtttgctggca	10	11	3	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr17:47018360T>A	ENST00000502492.1	-	3	552	c.170A>T	c.(169-171)gAg>gTg	p.E57V	SNF8_ENST00000290330.3_Missense_Mutation_p.E57V			Q96H20	SNF8_HUMAN	SNF8, ESCRT-II complex subunit	57					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|lung(1)	3						CTTCCGGATCTCCTGCTTGTG	0.532																																																0			17											160	138	145					17																	47018360		2203	4300	6503	44373359	SO:0001583	missense	11267			AF156102	CCDS11541.1	17q21.32	2013-06-05	2013-06-05		ENSG00000159210	ENSG00000159210			17028	protein-coding gene	gene with protein product		610904	"SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)"			10419521, 15329733	Standard	NM_007241		Approved	EAP30, VPS22, Dot3	uc002ioj.3	Q96H20	OTTHUMG00000160569	ENST00000502492.1:c.170A>T	17.37:g.47018360T>A	ENSP00000421380:p.Glu57Val		44373359	Q8IXY3|Q9UN50	Missense_Mutation	SNP	ENST00000502492.1	37	CCDS11541.1	.	.	.	.	.	.	.	.	.	.	t	20.8	4.056050	0.76074	.	.	ENSG00000159210	ENST00000502492;ENST00000290330;ENST00000510558	.	.	.	5.24	5.24	0.73138	.	0.110758	0.64402	D	0.000011	T	0.65863	0.2732	M	0.80508	2.5	0.80722	D	1	P;P	0.40144	0.655;0.704	B;B	0.38428	0.178;0.273	T	0.73279	-0.4033	9	0.87932	D	0	-15.3207	14.9547	0.71104	0.0:0.0:0.0:1.0	.	57;57	Q96H20-2;Q96H20	.;SNF8_HUMAN	V	57	.	ENSP00000290330:E57V	E	-	2	0	SNF8	44373359	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.542000	0.82095	2.201000	0.70794	0.529000	0.55759	GAG		0.532	SNF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361172.1	NM_007241		A	47018360	T	A	47018360	3	1	117	1	0	0	0	0	1	0	0	0	14883	1551	54	5	630	5	SNF8	17	47018360	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	2941696	47018360	34176850	73	31245										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21897128	21897128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cctaccgtgcatactgcttgAgtcaggtgtttgcatccctg	10	12	1	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr18:21897128A>G	ENST00000319481.3	-	11	1061	c.855T>C	c.(853-855)acT>acC	p.T285T		NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	285	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ATACTGCTTGAGTCAGGTGTT	0.373																																																0			18											107	104	105					18																	21897128		2203	4300	6503	20151126	SO:0001819	synonymous_variant	114876			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.855T>C	18.37:g.21897128A>G			20151126	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																				0.373	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		G	21897128	A	G	21897128	2	3	117	1	0	0	0	0	0	0	0	1	11308	291	11	4		4	OSBPL1A	18	21897128	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10		21897128	56180120	74	31246										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1053334	1053334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctttgtccacacaggcactcCtcagctgctggccctggtac	9	16	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:1053334C>T	ENST00000263094.6	+	24	3458	c.3227C>T	c.(3226-3228)cCt>cTt	p.P1076L	ABCA7_ENST00000435683.2_Missense_Mutation_p.P938L|ABCA7_ENST00000433129.1_Missense_Mutation_p.P1076L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1076					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		ACAGGCACTCCTCAGCTGCTG	0.672																																																0			19											18	17	17					19																	1053334		2196	4285	6481	1004334	SO:0001583	missense	10347			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3227C>T	19.37:g.1053334C>T	ENSP00000263094:p.Pro1076Leu		1004334	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	C	9.263	1.043762	0.19748	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86366	-2.11;-2.11	4.36	1.7	0.24286	.	.	.	.	.	T	0.77805	0.4185	L	0.38838	1.175	0.09310	N	1	B;B	0.16396	0.0;0.017	B;B	0.14578	0.001;0.011	T	0.61950	-0.6957	9	0.25751	T	0.34	.	5.486	0.16749	0.0:0.6441:0.1991:0.1568	.	938;1076	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	L	1076	ENSP00000263094:P1076L;ENSP00000414062:P1076L	ENSP00000263094:P1076L	P	+	2	0	ABCA7	1004334	0.000000	0.05858	0.011000	0.14972	0.008000	0.06430	0.265000	0.18515	0.922000	0.37019	0.491000	0.48974	CCT		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1053334	C	T	1053334	3	4	117	1	0	0	0	0	1	0	0	0	37	681	24	3	3317	3	ABCA7	19	1053334	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		1053334	58075649	75	31247										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5244269	5244269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cccctggccgatggagttgaCggccgacacccagatctcgt	12	15	1	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:5244269C>T	ENST00000587303.1	-	10	1312	c.1213G>A	c.(1213-1215)Gtc>Atc	p.V405I	PTPRS_ENST00000262963.6_Missense_Mutation_p.V401I|PTPRS_ENST00000588012.1_Missense_Mutation_p.V392I|PTPRS_ENST00000592099.1_Missense_Mutation_p.V392I|PTPRS_ENST00000372412.4_Missense_Mutation_p.V406I|PTPRS_ENST00000348075.2_Missense_Mutation_p.V392I|PTPRS_ENST00000353284.2_Missense_Mutation_p.V392I|PTPRS_ENST00000357368.4_Missense_Mutation_p.V405I|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	405	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ATGGAGTTGACGGCCGACACC	0.667																																																0			19											53	47	49					19																	5244269		2203	4300	6503	5195269	SO:0001583	missense	5802			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.1213G>A	19.37:g.5244269C>T	ENSP00000467537:p.Val405Ile		5195269	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.774337	0.31411	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09	3.93	3.93	0.45458	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.095040	0.41938	U	0.000784	T	0.67277	0.2876	M	0.77616	2.38	0.22591	N	0.998958	P;P;P;D;P;P	0.58970	0.56;0.723;0.588;0.984;0.939;0.92	B;B;B;P;P;B	0.50708	0.216;0.216;0.172;0.648;0.603;0.265	T	0.64037	-0.6501	10	0.42905	T	0.14	.	16.1378	0.81497	0.0:1.0:0.0:0.0	.	405;392;396;392;405;418	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	I	418;406;405;405;405;401;392;405;396;392	ENSP00000361489:V406I;ENSP00000349932:V405I;ENSP00000262963:V401I;ENSP00000269907:V392I;ENSP00000327313:V392I	ENSP00000262963:V401I	V	-	1	0	PTPRS	5195269	0.989000	0.36119	0.858000	0.33744	0.269000	0.26545	2.834000	0.48167	2.052000	0.61016	0.462000	0.41574	GTC		0.667	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			T	5244269	C	T	5244269	3	4	117	1	0	0	0	0	1	0	0	0	12848	536	19	1	4745	1	PTPRS	19	5244269	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	4190935	5244269	53884714	76	31248										
OR7C1	26664	hgsc.bcm.edu	37	chr19	14910584	14910584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ggtgacagacggccacgaagCggtcataggccatcacggtc	14	12	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:14910584C>T	ENST00000248073.2	-	1	439	c.365G>A	c.(364-366)cGc>cAc	p.R122H	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	122					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122H(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						GGCCACGAAGCGGTCATAGGC	0.493																																																1	Substitution - Missense(1)	endometrium(1)	19											85	81	82					19																	14910584		2203	4300	6503	14771584	SO:0001583	missense	26664			X89676	CCDS12317.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.365G>A	19.37:g.14910584C>T	ENSP00000248073:p.Arg122His		14771584	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	.	.	.	.	.	.	.	.	.	.	c	12.41	1.929879	0.34096	.	.	ENSG00000127530	ENST00000248073	T	0.77489	-1.1	3.64	-3.48	0.04739	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37669	U	0.001985	D	0.86493	0.5946	M	0.93507	3.425	0.20764	N	0.999856	D	0.89917	1.0	D	0.91635	0.999	T	0.76924	-0.2779	10	0.72032	D	0.01	.	4.6135	0.12415	0.1423:0.4912:0.0:0.3664	.	122	O76099	OR7C1_HUMAN	H	122	ENSP00000248073:R122H	ENSP00000248073:R122H	R	-	2	0	OR7C1	14771584	0.351000	0.24887	0.008000	0.14137	0.006000	0.05464	1.562000	0.36353	-0.620000	0.05641	-0.324000	0.08512	CGC		0.493	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			T	14910584	C	T	14910584	3	4	117	1	0	0	0	0	1	0	0	0	11248	768	27	1	599	1	OR7C1	19	14910584	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	9666315	14910584	44218399	77	31249										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40368553	40368553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tccaaccggtcctcagggcaCgttgggcaggacccccgaca	12	16	1	0	rs554943335		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:40368553C>T	ENST00000221347.6	-	28	12802	c.12795G>A	c.(12793-12795)acG>acA	p.T4265T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4265	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	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)			CCTCAGGGCACGTTGGGCAGG	0.662													C|||	1	0.000199681	0	0	5008	,	,		18375	0		0	False		,,,				2504	0.001															0			19											21	24	23					19																	40368553		2195	4257	6452	45060393	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12795G>A	19.37:g.40368553C>T			45060393	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40368553	C	T	40368553	2	4	117	1	0	0	0	0	0	0	0	1	5797	523	19	1		1	FCGBP	19	40368553	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	25457969	40368553	18760430	78	31250										
CCDC114	93233	hgsc.bcm.edu	37	chr19	48815355	48815355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cttactgtgggtaaagatccGcgtctcccactcctggatct	9	13	2	1			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:48815355G>A	ENST00000315396.7	-	4	950	c.268C>T	c.(268-270)Cgg>Tgg	p.R90W		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	90					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		GTAAAGATCCGCGTCTCCCAC	0.488																																																0			19											119	100	106					19																	48815355		692	1591	2283	53507167	SO:0001583	missense	93233			BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.268C>T	19.37:g.48815355G>A	ENSP00000318429:p.Arg90Trp		53507167	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	.	.	.	.	.	.	.	.	.	.	g	14.02	2.410386	0.42715	.	.	ENSG00000105479	ENST00000315396	T	0.30981	1.51	4.1	0.542	0.17174	.	.	.	.	.	T	0.35537	0.0935	N	0.24115	0.695	0.09310	N	1	D;D	0.76494	0.999;0.999	D;P	0.63488	0.915;0.859	T	0.28038	-1.0056	9	0.72032	D	0.01	-13.4719	10.0181	0.42027	0.0:0.0:0.4649:0.5351	.	90;90	Q96M63;Q96M63-5	CC114_HUMAN;.	W	90	ENSP00000318429:R90W	ENSP00000318429:R90W	R	-	1	2	CCDC114	53507167	0.020000	0.18652	0.001000	0.08648	0.063000	0.16089	1.530000	0.36007	0.001000	0.14605	-1.085000	0.02201	CGG		0.488	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		A	48815355	G	A	48815355	3	1	117	1	0	0	0	0	1	0	0	0	2757	1086	38	1	1788	1	CCDC114	19	48815355	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	8446802	48815355	10313628	79	31251										
TSKS	60385	hgsc.bcm.edu	37	chr19	50251426	50251426	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctcagcacagaacactcgctCtggagcatggaaggaggaga	13	10	2	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:50251426C>A	ENST00000246801.3	-	4	578		c.e4-1		TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate						negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		AACACTCGCTCTGGAGCATGG	0.552																																																0			19											118	99	105					19																	50251426		2203	4300	6503	54943238	SO:0001630	splice_region_variant	60385			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.496-1G>T	19.37:g.50251426C>A			54943238	Q8WXJ0	Splice_Site	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421846	0.25639	.	.	ENSG00000126467	ENST00000246801	.	.	.	5.6	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6184	0.51102	0.1778:0.8222:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TSKS	54943238	1.000000	0.71417	0.929000	0.37066	0.265000	0.26407	3.972000	0.56838	1.306000	0.44926	0.462000	0.41574	.		0.552	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	Intron	A	50251426	C	A	50251426	5	1	117	1	0	0	0	0	0	0	1	0	16666	927	32	2	1315	2	TSKS	19	50251426	Splice_Site	SNP	C	TCGA-F5-6702-01A-11D-1826-10	1436071	50251426	8877557	80	31252										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54394940	54394940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ccgtttagttggcgaggcccGtaacctaattcctatggacc	10	12	0	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr19:54394940G>A	ENST00000263431.3	+	6	824	c.542G>A	c.(541-543)cGt>cAt	p.R181H	PRKCG_ENST00000536044.1_Missense_Mutation_p.R181H|PRKCG_ENST00000542049.1_Missense_Mutation_p.R68H|PRKCG_ENST00000540413.1_Missense_Mutation_p.R181H	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	181	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	GGCGAGGCCCGTAACCTAATT	0.542																																																0			19											135	129	131					19																	54394940		2203	4300	6503	59086752	SO:0001583	missense	5582			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.542G>A	19.37:g.54394940G>A	ENSP00000263431:p.Arg181His		59086752	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.811604	0.70797	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.34	4.3	0.51218	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.73024	0.3534	L	0.46885	1.475	0.49915	D	0.99983	D;P;B;P;P	0.69078	0.997;0.47;0.433;0.526;0.563	P;B;B;B;B	0.55055	0.767;0.027;0.056;0.046;0.101	T	0.73471	-0.3972	9	0.45353	T	0.12	.	12.3369	0.55073	0.083:0.0:0.917:0.0	.	68;181;181;181;181	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	H	181;181;181;68	ENSP00000440541:R181H;ENSP00000443493:R181H;ENSP00000263431:R181H;ENSP00000438090:R68H	ENSP00000263431:R181H	R	+	2	0	PRKCG	59086752	0.750000	0.28316	0.870000	0.34147	0.647000	0.38526	3.353000	0.52247	1.399000	0.46721	0.561000	0.74099	CGT		0.542	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54394940	G	A	54394940	3	1	117	1	0	0	0	0	1	0	0	0	12546	1145	40	1	564	1	PRKCG	19	54394940	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	4143514	54394940	4734043	81	31253										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35422061	35422061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tgtcccgcgtggtggtggagCgggcccaggccgagccgttc	18	13	0	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr20:35422061C>T	ENST00000357779.3	-	14	4036	c.3710G>A	c.(3709-3711)cGc>cAc	p.R1237H	SOGA1_ENST00000456801.2_Missense_Mutation_p.R1078H|SOGA1_ENST00000279034.6_Intron|SOGA1_ENST00000237536.4_Missense_Mutation_p.R1475H			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1237					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GGTGGTGGAGCGGGCCCAGGC	0.622																																																0			20											15	20	19					20																	35422061		692	1591	2283	34855475	SO:0001583	missense	140710			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.3710G>A	20.37:g.35422061C>T	ENSP00000350424:p.Arg1237His		34855475	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.200067	0.79015	.	.	ENSG00000149639	ENST00000237536;ENST00000456801;ENST00000357779	T;T;T	0.36520	1.25;1.38;1.32	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.57213	0.2038	M	0.73962	2.25	0.58432	D	0.999998	.	.	.	.	.	.	T	0.62789	-0.6780	8	0.87932	D	0	-23.1653	16.6544	0.85224	0.0:1.0:0.0:0.0	.	.	.	.	H	1475;1078;1237	ENSP00000237536:R1475H;ENSP00000413886:R1078H;ENSP00000350424:R1237H	ENSP00000237536:R1475H	R	-	2	0	KIAA0889	34855475	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	5.874000	0.69652	2.472000	0.83506	0.561000	0.74099	CGC		0.622	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35422061	C	T	35422061	3	4	117	1	0	0	0	0	1	0	0	0	2089	768	27	1	631	1	C20orf117	20	35422061	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		35422061	27603459	82	31254										
BPI	671	hgsc.bcm.edu	37	chr20	36965562	36965562	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ccctagaacttcctgctgttCggtgcagacgttgtctataa	9	11	1	2	rs145842777		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr20:36965562C>T	ENST00000262865.4	+	15	1529	c.1440C>T	c.(1438-1440)ttC>ttT	p.F480F		NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	480					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.F480F(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				TCCTGCTGTTCGGTGCAGACG	0.542																																																1	Substitution - coding silent(1)	large_intestine(1)	20						C		0,4406		0,0,2203	129	118	121		1440	-7.8	0	20	dbSNP_134	121	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	BPI	NM_001725.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		480/488	36965562	4,13002	2203	4300	6503	36398976	SO:0001819	synonymous_variant	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1440C>T	20.37:g.36965562C>T			36398976	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1	.	.	.	.	.	.	.	.	.	.	C	3.452	-0.111742	0.06881	0.0	4.65E-4	ENSG00000101425	ENST00000417318	.	.	.	4.26	-7.8	0.01214	.	.	.	.	.	T	0.16811	0.0404	.	.	.	0.22366	N	0.999168	.	.	.	.	.	.	T	0.20405	-1.0276	4	.	.	.	-9.7201	2.825	0.05483	0.1145:0.1489:0.227:0.5096	.	.	.	.	L	306	.	.	S	+	2	0	BPI	36398976	0.033000	0.19621	0.009000	0.14445	0.063000	0.16089	-2.098000	0.01347	-1.741000	0.01344	-0.137000	0.14449	TCG		0.542	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		T	36965562	C	T	36965562	2	4	117	1	0	0	0	0	0	0	0	1	1493	883	31	1		1	BPI	20	36965562	Silent	SNP	C	TCGA-F5-6702-01A-11D-1826-10	1543501	36965562	26059958	83	31255										
C2CD2	25966	hgsc.bcm.edu	37	chr21	43327136	43327136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	acgccctccccacgtcgacgCgaggcttggtcttcacagca	10	17	2	0	rs571197268		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr21:43327136C>T	ENST00000380486.3	-	10	1524	c.1283G>A	c.(1282-1284)cGc>cAc	p.R428H	C2CD2_ENST00000329623.7_Missense_Mutation_p.R273H	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	428						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						CACGTCGACGCGAGGCTTGGT	0.592																																																0			21											86	73	78					21																	43327136		2203	4300	6503	42200205	SO:0001583	missense	25966			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1283G>A	21.37:g.43327136C>T	ENSP00000369853:p.Arg428His		42200205	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.256072	0.59321	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.29917	1.55;1.55	4.9	4.0	0.46444	.	0.182021	0.49916	D	0.000136	T	0.44244	0.1284	M	0.71581	2.175	0.31137	N	0.707058	D;D	0.76494	0.996;0.999	P;P	0.59221	0.642;0.854	T	0.52442	-0.8575	10	0.66056	D	0.02	-22.7842	6.385	0.21556	0.1567:0.6864:0.0:0.1568	.	273;428	Q6P6D1;Q9Y426	.;CU025_HUMAN	H	273;428	ENSP00000329302:R273H;ENSP00000369853:R428H	ENSP00000329302:R273H	R	-	2	0	C2CD2	42200205	0.979000	0.34478	0.931000	0.37212	0.443000	0.32047	2.502000	0.45398	2.413000	0.81919	0.655000	0.94253	CGC		0.592	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		T	43327136	C	T	43327136	3	4	117	1	0	0	0	0	1	0	0	0	2158	768	27	1	827	1	C2CD2	21	43327136	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10		43327136	4802759	84	31256										
SIK1	150094	hgsc.bcm.edu	37	chr21	44838331	44838331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ccggggtgccactgagccccGcggggcttttgctcgcagag	16	14	0	2	rs142171557		TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr21:44838331G>A	ENST00000270162.6	-	12	1685	c.1553C>T	c.(1552-1554)gCg>gTg	p.A518V		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	518					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	ACTGAGCCCCGCGGGGCTTTT	0.687													G|||	1	0.000199681	0	0	5008	,	,		16850	0		0	False		,,,				2504	0.001															0			21						G	VAL/ALA	0,4400		0,0,2200	22	25	24		1553	-9.6	0	21	dbSNP_134	24	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SIK1	NM_173354.3	64	0,4,6496	AA,AG,GG		0.0465,0.0,0.0308	benign	518/784	44838331	4,12996	2200	4300	6500	43662759	SO:0001583	missense	150094			BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1553C>T	21.37:g.44838331G>A	ENSP00000270162:p.Ala518Val		43662759	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	G	1.091	-0.663992	0.03428	0.0	4.65E-4	ENSG00000142178	ENST00000270162	T	0.71222	-0.55	4.79	-9.58	0.00559	.	1.353990	0.05053	N	0.478487	T	0.39200	0.1069	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.24012	-1.0172	10	0.22706	T	0.39	.	0.951	0.01376	0.3899:0.1771:0.2284:0.2046	.	518	P57059	SIK1_HUMAN	V	518	ENSP00000270162:A518V	ENSP00000270162:A518V	A	-	2	0	SIK1	43662759	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.074000	0.03427	-2.476000	0.00526	-0.940000	0.02684	GCG		0.687	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		A	44838331	G	A	44838331	3	1	117	1	0	0	0	0	1	0	0	0	14354	1087	38	1	810	1	SIK1	21	44838331	Missense_Mutation	SNP	G	TCGA-F5-6702-01A-11D-1826-10	1511195	44838331	3291564	85	31257										
MAPK1	5594	hgsc.bcm.edu	37	chr22	22160202	22160202	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aggtcacggtgcagaacgttAgctgaatggatatattttaa	11	5	1	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr22:22160202A>G	ENST00000215832.6	-	3	617	c.429T>C	c.(427-429)gcT>gcC	p.A143A	MAPK1_ENST00000398822.3_Silent_p.A143A|MAPK1_ENST00000544786.1_Silent_p.A143A	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.A143A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	GCAGAACGTTAGCTGAATGGA	0.423																																																1	Substitution - coding silent(1)	ovary(1)	22											204	184	191					22																	22160202		2203	4300	6503	20490202	SO:0001819	synonymous_variant	5594			M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.429T>C	22.37:g.22160202A>G			20490202	A8CZ64	Silent	SNP	ENST00000215832.6	37	CCDS13795.1																																																																																				0.423	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2			G	22160202	A	G	22160202	2	3	117	1	0	0	0	0	0	0	0	1	9301	407	15	4		4	MAPK1	22	22160202	Silent	SNP	A	TCGA-F5-6702-01A-11D-1826-10		22160202	29144364	86	31258										
KREMEN1	83999	hgsc.bcm.edu	37	chr22	29494867	29494867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	cagaaatccagatggagacgTgagcccctggtgctatgtgg	14	9	0	4			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chr22:29494867T>C	ENST00000407188.1	+	3	272	c.272T>C	c.(271-273)gTg>gCg	p.V91A	CTA-747E2.10_ENST00000456740.1_RNA|KREMEN1_ENST00000400335.4_Missense_Mutation_p.V93A|KREMEN1_ENST00000327813.5_Missense_Mutation_p.V93A|KREMEN1_ENST00000400338.2_Missense_Mutation_p.V93A			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	91	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						GATGGAGACGTGAGCCCCTGG	0.438																																																0			22											121	118	119					22																	29494867		1965	4147	6112	27824867	SO:0001583	missense	83999			AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"kringle containing transmembrane protein"	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.272T>C	22.37:g.29494867T>C	ENSP00000385431:p.Val91Ala		27824867	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	.	.	.	.	.	.	.	.	.	.	T	24.4	4.532910	0.85812	.	.	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	4.97	4.97	0.65823	.	0.000000	0.53938	D	0.000058	T	0.66406	0.2786	L	0.28344	0.845	0.58432	D	0.999996	D;P	0.71674	0.998;0.849	D;B	0.77557	0.99;0.343	T	0.65364	-0.6186	10	0.34782	T	0.22	.	12.902	0.58130	0.0:0.0:0.0:1.0	.	93;93	Q96MU8-2;Q96MU8-3	.;.	A	93;93;93;91	ENSP00000383189:V93A;ENSP00000383192:V93A;ENSP00000331242:V93A;ENSP00000385431:V91A	ENSP00000331242:V93A	V	+	2	0	KREMEN1	27824867	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.122000	0.77169	2.010000	0.58986	0.528000	0.53228	GTG		0.438	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1			C	29494867	T	C	29494867	3	2	117	1	0	0	0	0	1	0	0	0	8463	1696	59	4	288	4	KREMEN1	22	29494867	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	7334665	29494867	21809699	87	31259										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-													0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	ctgactcagtggttcttccaCctcgctctcctgactcaggg					rs1058237|rs144469326	byFrequency	TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs		8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				0.642	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138168	CCTC	-	8138165	7	5	117	1	0	1	0	1	0	0	0	0	17183	507	18	0	95	0	VCX2	23	8138165	Frame_Shift_Del	DEL	CCTC	TCGA-F5-6702-01A-11D-1826-10		8138165	147132395	88	31260										
CXorf38	159013	hgsc.bcm.edu	37	chrX	40496389	40496389	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	tctctgaagagtgcatgatcTcattacgacatttaattacc	6	9	2	3			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chrX:40496389T>C	ENST00000327877.5	-	4	517	c.491A>G	c.(490-492)gAg>gGg	p.E164G	CXorf38_ENST00000378421.1_Missense_Mutation_p.E45G|CXorf38_ENST00000378426.1_Missense_Mutation_p.E45G|CXorf38_ENST00000440784.2_Missense_Mutation_p.E79G	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	164										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						GTGCATGATCTCATTACGACA	0.348																																																0			X											45	40	42					X																	40496389		2203	4298	6501	40381333	SO:0001583	missense	159013			AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.491A>G	X.37:g.40496389T>C	ENSP00000330488:p.Glu164Gly		40381333	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.593093	0.46214	.	.	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	4.84	4.84	0.62591	.	0.227884	0.35151	N	0.003411	T	0.51244	0.1663	L	0.57536	1.79	0.80722	D	1	D;P	0.53619	0.961;0.827	P;P	0.48654	0.585;0.526	T	0.55360	-0.8153	10	0.54805	T	0.06	-20.0439	12.4877	0.55883	0.0:0.0:0.0:1.0	.	79;164	E7EN46;Q8TB03	.;CX038_HUMAN	G	45;164;45;79	ENSP00000367683:E45G;ENSP00000330488:E164G;ENSP00000367677:E45G;ENSP00000400019:E79G	ENSP00000330488:E164G	E	-	2	0	CXorf38	40381333	1.000000	0.71417	0.996000	0.52242	0.743000	0.42351	5.070000	0.64376	1.792000	0.52537	0.345000	0.21793	GAG		0.348	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		C	40496389	T	C	40496389	3	2	117	1	0	0	0	0	1	0	0	0	4113	1551	54	4	480	4	CXorf38	23	40496389	Missense_Mutation	SNP	T	TCGA-F5-6702-01A-11D-1826-10	32358224	40496389	114774171	89	31261										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71360137	71360137	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	aggagctcaattcaacatgcGagaccactccctcaagacag	8	13	3	2			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chrX:71360137G>A	ENST00000373677.1	+	2	2903	c.1641G>A	c.(1639-1641)gcG>gcA	p.A547A	NHSL2_ENST00000540800.1_Silent_p.A913A|NHSL2_ENST00000510661.1_Silent_p.A682A|NHSL2_ENST00000535692.1_Silent_p.A547A			Q5HYW2	NHSL2_HUMAN	NHS-like 2	547										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TTCAACATGCGAGACCACTCC	0.562																																																0			X											97	74	82					X																	71360137		2203	4300	6503	71276862	SO:0001819	synonymous_variant	340527					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1641G>A	X.37:g.71360137G>A			71276862	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																					0.562	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71360137	G	A	71360137	2	1	117	1	0	0	0	0	0	0	0	1	10443	1045	37	1		1	NHSL2	23	71360137	Silent	SNP	G	TCGA-F5-6702-01A-11D-1826-10	30863748	71360137	83910423	90	31262										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151818310	151818310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043956043956044	4	1	0.686696900982615	7.21031746031746	0.527584204413473	0.545454545454546	1	0	gttcactttcctgggaaggaCgattactagcaaggaggtgt	13	7	1	0			TCGA-F5-6702-01A-11D-1826-10	TCGA-F5-6702-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	7e34a04a-ec52-44dc-857c-6ffa656387f4	9c18fd3a-c6b4-4981-9398-e06c753e5b43	g.chrX:151818310C>T	ENST00000370306.2	+	6	736	c.716C>T	c.(715-717)aCg>aTg	p.T239M		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	239					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGGGAAGGACGATTACTAGC	0.498																																																0			X											200	148	165					X																	151818310		2203	4300	6503	151568966	SO:0001583	missense	55879			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.716C>T	X.37:g.151818310C>T	ENSP00000359329:p.Thr239Met		151568966	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376608	0.24857	.	.	ENSG00000147402	ENST00000370306	T	0.79141	-1.24	5.82	-1.22	0.09494	Neurotransmitter-gated ion-channel ligand-binding (3);	0.436678	0.19876	N	0.104089	T	0.67221	0.2870	M	0.75264	2.295	0.09310	N	1	P	0.50066	0.931	B	0.39706	0.307	T	0.62803	-0.6777	10	0.62326	D	0.03	.	0.8197	0.01109	0.1648:0.3607:0.206:0.2684	.	239	Q9UN88	GBRT_HUMAN	M	239	ENSP00000359329:T239M	ENSP00000359329:T239M	T	+	2	0	GABRQ	151568966	0.006000	0.16342	0.001000	0.08648	0.061000	0.15899	0.323000	0.19593	-0.084000	0.12595	-0.191000	0.12829	ACG		0.498	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		T	151818310	C	T	151818310	3	4	117	1	0	0	0	0	1	0	0	0	6194	536	19	1	738	1	GABRQ	23	151818310	Missense_Mutation	SNP	C	TCGA-F5-6702-01A-11D-1826-10	80458173	151818310	3452250	91	31263										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2077532	2077532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggacgccgaccttccttccGaggagacagatggaagtagg	14	10	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:2077532G>A	ENST00000400921.2	+	4	753	c.70G>A	c.(70-72)Gag>Aag	p.E24K	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Missense_Mutation_p.E24K|RP5-892K4.1_ENST00000606533.1_RNA	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	207	OPR.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	CCTTCCTTCCGAGGAGACAGA	0.582																																																0			1											94	71	79					1																	2077532		2203	4300	6503	2067392	SO:0001583	missense	5590			BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.70G>A	1.37:g.2077532G>A	ENSP00000383712:p.Glu24Lys		2067392	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Missense_Mutation	SNP	ENST00000400921.2	37	CCDS41229.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706115	0.48412	.	.	ENSG00000067606	ENST00000378567;ENST00000468310;ENST00000400921;ENST00000461106;ENST00000470596;ENST00000496325;ENST00000482686;ENST00000400920;ENST00000486681;ENST00000470986;ENST00000470511;ENST00000471018;ENST00000466352;ENST00000497183	T;D;T;T;T;T;T;T;T	0.88664	-0.3;-2.41;-0.2;-0.32;1.42;-0.2;0.26;0.85;0.86	5.04	5.04	0.67666	.	0.056301	0.64402	D	0.000002	T	0.73249	0.3563	N	0.08118	0	0.80722	D	1	P;P;P	0.46578	0.88;0.856;0.851	B;B;B	0.31869	0.114;0.06;0.137	T	0.76572	-0.2910	10	0.09843	T	0.71	.	17.3593	0.87345	0.0:0.0:1.0:0.0	.	103;31;207	E9PCW2;B3KUN5;Q05513	.;.;KPCZ_HUMAN	K	207;177;24;103;24;24;24;24;20;24;24;24;24;20	ENSP00000367830:E207K;ENSP00000424945:E177K;ENSP00000383712:E24K;ENSP00000426412:E103K;ENSP00000424228:E24K;ENSP00000383711:E24K;ENSP00000424763:E20K;ENSP00000421219:E24K;ENSP00000422764:E20K	ENSP00000367830:E207K	E	+	1	0	PRKCZ	2067392	1.000000	0.71417	0.871000	0.34182	0.884000	0.51177	8.484000	0.90445	2.348000	0.79779	0.462000	0.41574	GAG		0.582	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		A	2077532	G	A	2077532	3	1	118	1	0	0	0	0	1	0	0	0	12551	1059	37	1	645	1	PRKCZ	1	2077532	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10		2077532	247173089	1	31264										
UBR4	23352	hgsc.bcm.edu	37	chr1	19480385	19480385	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aagccagggtggttcatcacCtcagaccactggcaaagagc	11	12	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:19480385C>A	ENST00000375254.3	-	45	6534	c.6507G>T	c.(6505-6507)gaG>gaT	p.E2169D	UBR4_ENST00000375267.2_Missense_Mutation_p.E2169D|UBR4_ENST00000375217.2_Missense_Mutation_p.E2169D|UBR4_ENST00000375226.2_Missense_Mutation_p.E2169D	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2169					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGTTCATCACCTCAGACCACT	0.483																																																0			1											101	94	96					1																	19480385		2203	4300	6503	19352972	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6507G>T	1.37:g.19480385C>A	ENSP00000364403:p.Glu2169Asp		19352972	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972364	0.74246	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.35048	1.36;1.36;1.36;1.33	5.31	2.4	0.29515	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.65975	2.015	0.51767	D	0.99993	D;P	0.89917	1.0;0.956	D;D	0.83275	0.996;0.931	T	0.51387	-0.8712	10	0.54805	T	0.06	.	8.7709	0.34731	0.0:0.6294:0.0:0.3706	.	2170;2169	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	D	2169;2169;2169;2169;879;1386	ENSP00000364403:E2169D;ENSP00000364416:E2169D;ENSP00000364365:E2169D;ENSP00000364374:E2169D	ENSP00000364365:E2169D	E	-	3	2	UBR4	19352972	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.975000	0.29449	0.827000	0.34685	-0.229000	0.12294	GAG		0.483	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19480385	C	A	19480385	3	1	118	1	0	0	0	0	1	0	0	0	16944	680	24	2	9292	2	UBR4	1	19480385	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	17402853	19480385	229770236	2	31265										
PPCS	79717	hgsc.bcm.edu	37	chr1	42922602	42922602	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctgagcctggaggccgaggaGaatgcacttccgggttttgc	15	10	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:42922602G>A	ENST00000372561.3	+	1	373	c.366G>A	c.(364-366)gaG>gaA	p.E122E	ZMYND12_ENST00000372565.3_5'Flank|PPCS_ENST00000372560.3_Silent_p.E122E|PPCS_ENST00000472013.1_3'UTR|PPCS_ENST00000455780.1_Intron|ZMYND12_ENST00000433602.2_5'Flank|PPCS_ENST00000372562.1_Intron|PPCS_ENST00000372556.3_Intron	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	122					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGGCCGAGGAGAATGCACTTC	0.632																																																0			1											52	57	55					1																	42922602		1942	4118	6060	42695189	SO:0001819	synonymous_variant	79717			AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.366G>A	1.37:g.42922602G>A			42695189	Q3KQT2|Q5VVM0	Silent	SNP	ENST00000372561.3	37	CCDS41311.1																																																																																				0.632	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		A	42922602	G	A	42922602	2	1	118	1	0	0	0	0	0	0	0	1	12336	933	33	3		3	PPCS	1	42922602	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	23442217	42922602	206328019	3	31266										
TTLL7	79739	hgsc.bcm.edu	37	chr1	84417546	84417546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	accaatttcaaactttgtccCggcaacatttgctgtaatgg	7	10	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:84417546C>T	ENST00000260505.8	-	3	516	c.139G>A	c.(139-141)Ggg>Agg	p.G47R	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	47	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		AACTTTGTCCCGGCAACATTT	0.363																																																0			1											80	83	82					1																	84417546		2203	4300	6503	84190134	SO:0001583	missense	79739			AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.139G>A	1.37:g.84417546C>T	ENSP00000260505:p.Gly47Arg		84190134	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	37	CCDS690.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682395	0.88542	.	.	ENSG00000137941	ENST00000260505;ENST00000370703	T	0.03745	3.82	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.06371	0.0164	L	0.33710	1.025	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.56798	-0.7919	10	0.25106	T	0.35	.	19.0987	0.93265	0.0:1.0:0.0:0.0	.	47	Q6ZT98	TTLL7_HUMAN	R	47	ENSP00000260505:G47R	ENSP00000260505:G47R	G	-	1	0	TTLL7	84190134	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.473000	0.73572	2.595000	0.87683	0.650000	0.86243	GGG		0.363	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		T	84417546	C	T	84417546	3	4	118	1	0	0	0	0	1	0	0	0	16772	652	23	1	2600	1	TTLL7	1	84417546	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	41494944	84417546	164833075	4	31267										
SARS	6301	hgsc.bcm.edu	37	chr1	109780387	109780387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atcccctttgtgaagcctgcGcccattgagcaggagccatc	10	14	0	2	rs374920184		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:109780387G>A	ENST00000234677.2	+	11	1497	c.1422G>A	c.(1420-1422)gcG>gcA	p.A474A	SARS_ENST00000468588.1_3'UTR|SARS_ENST00000369923.4_Silent_p.A496A	NM_006513.3	NP_006504.2	P49591	SYSC_HUMAN	seryl-tRNA synthetase	474					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|RNA binding (GO:0003723)|serine-tRNA ligase activity (GO:0004828)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	17		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	TGAAGCCTGCGCCCATTGAGC	0.512													G|||	1	0.000199681	0	0	5008	,	,		19662	0		0	False		,,,				2504	0.001															0			1						G		0,4406		0,0,2203	132	119	123		1422	-12.1	0.1	1		123	1,8599		0,1,4299	no	coding-synonymous	SARS	NM_006513.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		474/515	109780387	1,13005	2203	4300	6503	109581910	SO:0001819	synonymous_variant	54938			BC009390	CCDS795.1	1p13.3	2011-07-01			ENSG00000031698	ENSG00000031698	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	10537	protein-coding gene	gene with protein product	"serine tRNA ligase 1, cytoplasmic"	607529				9431993	Standard	NM_006513		Approved	SERS	uc001dwu.2	P49591	OTTHUMG00000011726	ENST00000234677.2:c.1422G>A	1.37:g.109780387G>A			109581910	B2R6Y9|Q5T5C8|Q9NSE3	Silent	SNP	ENST00000234677.2	37	CCDS795.1																																																																																				0.512	SARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032394.2	NM_006513		A	109780387	G	A	109780387	2	1	118	1	0	0	0	0	0	0	0	1	13881	1074	38	1		1	SARS	1	109780387	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	25362841	109780387	139470234	5	31268										
POGZ	23126	hgsc.bcm.edu	37	chr1	151400754	151400754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggacggtgcttcgaatggtaAgagtggccgggatgacggtg	19	6	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:151400754A>G	ENST00000271715.2	-	6	1018	c.704T>C	c.(703-705)cTt>cCt	p.L235P	POGZ_ENST00000361398.3_Missense_Mutation_p.L182P|POGZ_ENST00000531094.1_Missense_Mutation_p.L182P|POGZ_ENST00000368863.2_Missense_Mutation_p.L140P|POGZ_ENST00000392723.1_Missense_Mutation_p.L182P|POGZ_ENST00000409503.1_Missense_Mutation_p.L235P|POGZ_ENST00000491586.1_Missense_Mutation_p.L182P|POGZ_ENST00000540984.1_Intron	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	235					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCGAATGGTAAGAGTGGCCGG	0.602																																																0			1											293	280	284					1																	151400754		2203	4300	6503	149667378	SO:0001583	missense	23126			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.704T>C	1.37:g.151400754A>G	ENSP00000271715:p.Leu235Pro		149667378	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810187	0.70797	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000437847	D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000011	T	0.80899	0.4712	N	0.19112	0.55	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.995;1.0;0.999;0.999;0.997;0.999	D;D;D;D;D;D;D	0.91635	0.997;0.986;0.999;0.997;0.996;0.994;0.997	D	0.84970	0.0882	10	0.62326	D	0.03	-15.8125	13.97	0.64233	1.0:0.0:0.0:0.0	.	182;235;140;235;182;182;235	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-4;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;.;POGZ_HUMAN	P	182;235;182;140;235;182;182;235	ENSP00000376484:L182P;ENSP00000271715:L235P;ENSP00000354467:L182P;ENSP00000357856:L140P;ENSP00000386836:L235P;ENSP00000431259:L182P;ENSP00000418408:L182P	ENSP00000271715:L235P	L	-	2	0	POGZ	149667378	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.516000	0.73755	2.164000	0.68074	0.460000	0.39030	CTT		0.602	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		G	151400754	A	G	151400754	3	3	118	1	0	0	0	0	1	0	0	0	12217	72	3	4	3598	4	POGZ	1	151400754	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	41620367	151400754	97849867	6	31269										
MNDA	4332	hgsc.bcm.edu	37	chr1	158815633	158815633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgattactctgaatgtaaagGagtaatggaaataaaggaag	11	2	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:158815633G>A	ENST00000368141.4	+	5	1088	c.827G>A	c.(826-828)gGa>gAa	p.G276E		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	276	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					GAATGTAAAGGAGTAATGGAA	0.333																																																0			1											75	77	77					1																	158815633		2203	4300	6503	157082257	SO:0001583	missense	4332			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.827G>A	1.37:g.158815633G>A	ENSP00000357123:p.Gly276Glu		157082257		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215950	0.39201	.	.	ENSG00000163563	ENST00000368141	T	0.17213	2.29	4.28	1.25	0.21368	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	0.203127	0.24557	N	0.037511	T	0.15089	0.0364	M	0.80183	2.485	0.09310	N	1	P	0.51537	0.946	P	0.51945	0.685	T	0.04537	-1.0944	10	0.56958	D	0.05	-14.5925	7.0429	0.25031	0.3013:0.0:0.6987:0.0	.	276	P41218	MNDA_HUMAN	E	276	ENSP00000357123:G276E	ENSP00000357123:G276E	G	+	2	0	MNDA	157082257	0.002000	0.14202	0.000000	0.03702	0.025000	0.11179	0.258000	0.18387	0.150000	0.19136	0.655000	0.94253	GGA		0.333	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		A	158815633	G	A	158815633	3	1	118	1	0	0	0	0	1	0	0	0	9706	1174	41	3	841	3	MNDA	1	158815633	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	7414879	158815633	90434988	7	31270										
CENPL	91687	hgsc.bcm.edu	37	chr1	173772350	173772350	+	Frame_Shift_Del	DEL	T	T	-													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cagggtacagaccaaagaaaTtcagtagtagccacataatg							TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:173772350delT	ENST00000345664.6	-	4	927	c.714delA	c.(712-714)gaafs	p.E238fs	CENPL_ENST00000356198.2_Frame_Shift_Del_p.E284fs|CENPL_ENST00000367710.3_Frame_Shift_Del_p.E238fs	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	238					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						ACCAAAGAAATTCAGTAGTAG	0.428																																																0			1											99	100	100					1																	173772350		2203	4300	6503	172038973	SO:0001589	frameshift_variant	91687			BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.714delA	1.37:g.173772350delT	ENSP00000323543:p.Glu238fs		172038973	Q5TEL5|Q96ND4	Frame_Shift_Del	DEL	ENST00000345664.6	37	CCDS30938.1																																																																																				0.428	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		-	173772350	T	-	173772350	7	5	118	1	0	1	0	1	0	0	0	0	3242	1490	52	0	328	0	CENPL	1	173772350	Frame_Shift_Del	DEL	T	TCGA-F5-6811-01A-11D-1826-10	14956717	173772350	75478271	8	31271										
TNN	63923	hgsc.bcm.edu	37	chr1	175066670	175066670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggtgcgctacacctctgctgAcgaccaagagaccagagagg	13	12	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:175066670A>G	ENST00000239462.4	+	8	1819	c.1706A>G	c.(1705-1707)gAc>gGc	p.D569G		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	569	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ACCTCTGCTGACGACCAAGAG	0.597																																																0			1											84	71	76					1																	175066670		2203	4300	6503	173333293	SO:0001583	missense	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1706A>G	1.37:g.175066670A>G	ENSP00000239462:p.Asp569Gly		173333293	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.990309	0.35131	.	.	ENSG00000120332	ENST00000239462	T	0.55930	0.49	5.63	5.63	0.86233	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.234670	0.37530	N	0.002046	T	0.63414	0.2509	M	0.74881	2.28	0.40726	D	0.982708	P	0.52692	0.955	P	0.54100	0.742	T	0.62709	-0.6797	10	0.11794	T	0.64	.	15.5013	0.75700	1.0:0.0:0.0:0.0	.	569	Q9UQP3	TENN_HUMAN	G	569	ENSP00000239462:D569G	ENSP00000239462:D569G	D	+	2	0	TNN	173333293	.	.	0.012000	0.15200	0.004000	0.04260	.	.	2.126000	0.65437	0.533000	0.62120	GAC		0.597	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		G	175066670	A	G	175066670	3	3	118	1	0	0	0	0	1	0	0	0	16362	275	10	4	1732	4	TNN	1	175066670	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	1294320	175066670	74183951	9	31272										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564627	176564627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cgcagggatgggctctgtcaCgtggagtgtaacaacatgct	14	9	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:176564627C>T	ENST00000367662.3	+	3	3051	c.1887C>T	c.(1885-1887)caC>caT	p.H629H	PAPPA2_ENST00000367661.3_Silent_p.H629H	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	629	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GGCTCTGTCACGTGGAGTGTA	0.612																																																0			1											75	79	78					1																	176564627		2149	4257	6406	174831250	SO:0001819	synonymous_variant	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1887C>T	1.37:g.176564627C>T			174831250	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																				0.612	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176564627	C	T	176564627	2	4	118	1	0	0	0	0	0	0	0	1	11464	535	19	1		1	PAPPA2	1	176564627	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	1497957	176564627	72685994	10	31273										
IPO9	55705	hgsc.bcm.edu	37	chr1	201821292	201821292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgctcctgtcattctcccagAgatgtataagatcttcacca	6	12	4	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:201821292A>G	ENST00000361565.4	+	5	644	c.575A>G	c.(574-576)gAg>gGg	p.E192G	IPO9_ENST00000464348.1_3'UTR	NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	192					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						ATTCTCCCAGAGATGTATAAG	0.418																																																0			1											97	95	96					1																	201821292		2203	4300	6503	200087915	SO:0001583	missense	55705			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.575A>G	1.37:g.201821292A>G	ENSP00000354742:p.Glu192Gly		200087915	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	A	32	5.178500	0.94846	.	.	ENSG00000198700	ENST00000361565	T	0.66460	-0.21	5.93	5.93	0.95920	Armadillo-like helical (1);Armadillo-type fold (1);	0.044602	0.85682	D	0.000000	T	0.76983	0.4064	M	0.72353	2.195	0.80722	D	1	D	0.63046	0.992	P	0.60415	0.874	T	0.74509	-0.3642	10	0.23891	T	0.37	-5.0673	14.331	0.66556	1.0:0.0:0.0:0.0	.	192	Q96P70	IPO9_HUMAN	G	192	ENSP00000354742:E192G	ENSP00000354742:E192G	E	+	2	0	IPO9	200087915	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.192000	0.94947	2.268000	0.75426	0.455000	0.32223	GAG		0.418	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		G	201821292	A	G	201821292	3	3	118	1	0	0	0	0	1	0	0	0	7820	304	11	4	593	4	IPO9	1	201821292	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	25256665	201821292	47429329	11	31274										
TMCC2	9911	hgsc.bcm.edu	37	chr1	205238518	205238518	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aacgtgcgcgcaggcatcagCggctttgggggcggcgtggt	19	10	1	0	rs558212864		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:205238518C>T	ENST00000358024.3	+	3	1577	c.1188C>T	c.(1186-1188)agC>agT	p.S396S	TMCC2_ENST00000330675.7_Silent_p.S171S|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000329800.7_Silent_p.S156S|TMCC2_ENST00000545499.1_Silent_p.S318S	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	396						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CAGGCATCAGCGGCTTTGGGG	0.692																																																0			1											27	29	28					1																	205238518		2199	4297	6496	203505141	SO:0001819	synonymous_variant	9911			AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"Transmembrane and coiled-coil domain containing"	24239	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 2"			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.1188C>T	1.37:g.205238518C>T			203505141	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																				0.692	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		T	205238518	C	T	205238518	2	4	118	1	0	0	0	0	0	0	0	1	16032	767	27	1		1	TMCC2	1	205238518	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	3417226	205238518	44012103	12	31275										
C4BPA	722	hgsc.bcm.edu	37	chr1	207314546	207314546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttatatatgaatgtgataaaGgctacattctggtcggacag	10	5	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:207314546G>A	ENST00000367070.3	+	10	1563	c.1369G>A	c.(1369-1371)Ggc>Agc	p.G457S		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	457	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						ATGTGATAAAGGCTACATTCT	0.408																																																0			1											93	95	94					1																	207314546		2203	4300	6503	205381169	SO:0001583	missense	722			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1369G>A	1.37:g.207314546G>A	ENSP00000356037:p.Gly457Ser		205381169	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286835	0.80803	.	.	ENSG00000123838	ENST00000367070	T	0.76448	-1.02	5.36	5.36	0.76844	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.51477	D	0.000096	D	0.88119	0.6351	M	0.82716	2.605	0.36133	D	0.846256	D	0.76494	0.999	D	0.70016	0.967	D	0.91505	0.5222	10	0.62326	D	0.03	.	14.9497	0.71064	0.0:0.0:1.0:0.0	.	457	P04003	C4BPA_HUMAN	S	457	ENSP00000356037:G457S	ENSP00000356037:G457S	G	+	1	0	C4BPA	205381169	0.997000	0.39634	0.621000	0.29145	0.169000	0.22640	4.010000	0.57117	2.665000	0.90641	0.655000	0.94253	GGC		0.408	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			A	207314546	G	A	207314546	3	1	118	1	0	0	0	0	1	0	0	0	2255	1000	35	3	1403	3	C4BPA	1	207314546	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	2076028	207314546	41936075	13	31276										
LPGAT1	9926	hgsc.bcm.edu	37	chr1	211956633	211956633	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gttgtgctacaagtgcattcAaaataatttttgttgcccca	7	8	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:211956633A>T	ENST00000366997.4	-	5	891	c.665T>A	c.(664-666)tTg>tAg	p.L222*	LPGAT1_ENST00000366996.1_Nonsense_Mutation_p.L222*	NM_014873.2	NP_055688.1	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1	222					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)		AAGTGCATTCAAAATAATTTT	0.383																																																0			1											70	70	70					1																	211956633		2203	4300	6503	210023256	SO:0001587	stop_gained	9926			D86960	CCDS31018.1	1q32.3	2008-05-14	2004-11-25	2004-11-26	ENSG00000123684	ENSG00000123684			28985	protein-coding gene	gene with protein product		610473	"family with sequence similarity 34, member A"	FAM34A		9039502, 15485873	Standard	NM_014873		Approved	KIAA0205, FAM34A1, NET8	uc001hiv.3	Q92604	OTTHUMG00000037120	ENST00000366997.4:c.665T>A	1.37:g.211956633A>T	ENSP00000355964:p.Leu222*		210023256	Q53YL2	Nonsense_Mutation	SNP	ENST00000366997.4	37	CCDS31018.1	.	.	.	.	.	.	.	.	.	.	A	44	11.268734	0.99539	.	.	ENSG00000123684	ENST00000366997;ENST00000366996	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.068	16.3766	0.83401	1.0:0.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000355963:L222X	L	-	2	0	LPGAT1	210023256	1.000000	0.71417	0.594000	0.28785	0.901000	0.52897	8.369000	0.90118	2.263000	0.75096	0.533000	0.62120	TTG		0.383	LPGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090150.1	NM_014873		T	211956633	A	T	211956633	4	4	118	1	0	0	0	0	0	1	0	0	8943	131	5	5	463	5	LPGAT1	1	211956633	Nonsense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	4642087	211956633	37293988	14	31277										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218607468	218607468	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tctccaacccagcgctacatCgacagcaaagttgtgaaaac	7	13	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:218607468C>T	ENST00000366930.4	+	3	1022	c.555C>T	c.(553-555)atC>atT	p.I185I	TGFB2_ENST00000479322.1_3'UTR|TGFB2_ENST00000366929.4_Silent_p.I213I	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	185					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		AGCGCTACATCGACAGCAAAG	0.453																																																0			1											195	190	191					1																	218607468		2203	4300	6503	216674091	SO:0001819	synonymous_variant	7042			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.555C>T	1.37:g.218607468C>T			216674091	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Silent	SNP	ENST00000366930.4	37	CCDS1521.1																																																																																				0.453	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		T	218607468	C	T	218607468	2	4	118	1	0	0	0	0	0	0	0	1	15857	874	31	1		1	TGFB2	1	218607468	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	6650835	218607468	30643153	15	31278										
TLR5	7100	hgsc.bcm.edu	37	chr1	223285573	223285573	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atgttatggaagccaaacccGgcacccatgatgtggtgggc	13	10	0	1	rs200513847		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:223285573G>A	ENST00000540964.1	-	4	1262	c.801C>T	c.(799-801)gcC>gcT	p.A267A	TLR5_ENST00000342210.6_Silent_p.A267A			O60602	TLR5_HUMAN	toll-like receptor 5	267					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AGCCAAACCCGGCACCCATGA	0.493																																																0			1											96	86	90					1																	223285573		2203	4300	6503	221352196	SO:0001819	synonymous_variant	7100				CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.801C>T	1.37:g.223285573G>A			221352196	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	37	CCDS31033.1																																																																																				0.493	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223285573	G	A	223285573	2	1	118	1	0	0	0	0	0	0	0	1	15993	1103	39	1		1	TLR5	1	223285573	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	4678105	223285573	25965048	16	31279										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223986087	223986087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggtgtctttggaaggctggGgagtaaagggccggacggca	19	6	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:223986087G>A	ENST00000343537.7	-	12	2069	c.1778C>T	c.(1777-1779)cCc>cTc	p.P593L	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.P464L|TP53BP2_ENST00000391879.2_Intron	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	587					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GGAAGGCTGGGGAGTAAAGGG	0.537																																																0			1											128	138	135					1																	223986087		2203	4300	6503	222052710	SO:0001583	missense	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.1778C>T	1.37:g.223986087G>A	ENSP00000341957:p.Pro593Leu		222052710	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142793	0.94560	.	.	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.53423	0.62;0.8	5.88	5.88	0.94601	.	0.048575	0.85682	D	0.000000	T	0.70684	0.3252	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.971	T	0.67496	-0.5656	10	0.40728	T	0.16	.	20.2422	0.98381	0.0:0.0:1.0:0.0	.	593;587	B4DG66;Q13625	.;ASPP2_HUMAN	L	464;593	ENSP00000375750:P464L;ENSP00000341957:P593L	ENSP00000341957:P593L	P	-	2	0	TP53BP2	222052710	1.000000	0.71417	0.230000	0.23976	0.992000	0.81027	9.461000	0.97646	2.782000	0.95742	0.655000	0.94253	CCC		0.537	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223986087	G	A	223986087	3	1	118	1	0	0	0	0	1	0	0	0	16424	1232	43	3	1654	3	TP53BP2	1	223986087	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	700514	223986087	25264534	17	31280										
OR2L13	284521	hgsc.bcm.edu	37	chr1	248263455	248263455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cttttgtctacacctatcttCggcccaggaatctccgctca	6	15	4	0	rs202188433		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:248263455C>T	ENST00000358120.2	+	2	923	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W	OR2L13_ENST00000366478.2_Missense_Mutation_p.R260W			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			CACCTATCTTCGGCCCAGGAA	0.463													C|||	1	0.000199681	0	0.0014	5008	,	,		16895	0		0	False		,,,				2504	0															0			1											123	121	122					1																	248263455		2203	4300	6503	246330078	SO:0001583	missense	284521			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.778C>T	1.37:g.248263455C>T	ENSP00000350836:p.Arg260Trp		246330078	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	10.12	1.264307	0.23136	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.37915	1.17;1.17	4.08	-0.65	0.11457	GPCR, rhodopsin-like superfamily (1);	0.177126	0.26058	N	0.026584	T	0.31040	0.0784	M	0.70903	2.155	0.09310	N	1	B	0.27932	0.194	B	0.24541	0.054	T	0.21280	-1.0250	10	0.45353	T	0.12	.	7.4108	0.27016	0.5178:0.3969:0.0:0.0854	.	260	Q8N349	OR2LD_HUMAN	W	260	ENSP00000355434:R260W;ENSP00000350836:R260W	ENSP00000350836:R260W	R	+	1	2	OR2L13	246330078	0.000000	0.05858	0.012000	0.15200	0.509000	0.34042	-1.495000	0.02294	0.001000	0.14605	0.555000	0.69702	CGG		0.463	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		T	248263455	C	T	248263455	3	4	118	1	0	0	0	0	1	0	0	0	11037	875	31	1	780	1	OR2L13	1	248263455	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	24277368	248263455	987166	18	31281										
OR2T33	391195	hgsc.bcm.edu	37	chr1	248436585	248436585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	acgcaccagcacgggggtctCgcagaagaagtgatcgatct	13	11	2	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr1:248436585C>T	ENST00000318021.2	-	1	553	c.532G>A	c.(532-534)Gag>Aag	p.E178K		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E178K(1)		NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ACGGGGGTCTCGCAGAAGAAG	0.552																																																1	Substitution - Missense(1)	large_intestine(1)	1											37	41	40					1																	248436585		2200	4289	6489	246503208	SO:0001583	missense	391195				CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.532G>A	1.37:g.248436585C>T	ENSP00000324687:p.Glu178Lys		246503208	B2RNN0	Missense_Mutation	SNP	ENST00000318021.2	37	CCDS31109.1	.	.	.	.	.	.	.	.	.	.	-	14.51	2.556107	0.45487	.	.	ENSG00000177212	ENST00000318021	T	0.00202	8.56	1.86	1.86	0.25419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35495	U	0.003180	T	0.00695	0.0023	H	0.94925	3.6	0.39781	D	0.972299	D	0.89917	1.0	D	0.65874	0.939	T	0.61312	-0.7088	10	0.87932	D	0	.	12.3733	0.55265	0.0:1.0:0.0:0.0	.	178	Q8NG76	O2T33_HUMAN	K	178	ENSP00000324687:E178K	ENSP00000324687:E178K	E	-	1	0	OR2T33	246503208	1.000000	0.71417	0.961000	0.40146	0.163000	0.22366	2.197000	0.42696	1.338000	0.45544	0.494000	0.49563	GAG		0.552	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		T	248436585	C	T	248436585	3	4	118	1	0	0	0	0	1	0	0	0	11055	893	31	1	433	1	OR2T33	1	248436585	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	173130	248436585	814036	19	31282										
E2F6	1876	hgsc.bcm.edu	37	chr2	11587813	11587813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggtcccgacaccttcagaccTtttgttactggtctgaccct	8	14	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:11587813T>C	ENST00000381525.3	-	6	1008	c.739A>G	c.(739-741)Agg>Ggg	p.R247G	E2F6_ENST00000542100.1_Missense_Mutation_p.R172G|E2F6_ENST00000546212.1_Missense_Mutation_p.R172G|E2F6_ENST00000307236.4_Missense_Mutation_p.R215G|E2F6_ENST00000362009.4_3'UTR	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6	247	Transcription repression.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		CCTTCAGACCTTTTGTTACTG	0.458																																																0			2											102	93	96					2																	11587813		1880	4105	5985	11505264	SO:0001583	missense	1876			AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.739A>G	2.37:g.11587813T>C	ENSP00000370936:p.Arg247Gly		11505264	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Missense_Mutation	SNP	ENST00000381525.3	37	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	T	9.749	1.167010	0.21621	.	.	ENSG00000169016	ENST00000381525;ENST00000307236;ENST00000542100;ENST00000546212	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	4.88	-7.31	0.01441	.	3.278190	0.00654	N	0.000577	T	0.04048	0.0113	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34925	-0.9809	10	0.48119	T	0.1	17.3777	3.0861	0.06278	0.1853:0.1219:0.0931:0.5996	.	247;215	O75461;G5E936	E2F6_HUMAN;.	G	247;215;172;172	ENSP00000370936:R247G;ENSP00000302159:R215G;ENSP00000446315:R172G;ENSP00000438864:R172G	ENSP00000302159:R215G	R	-	1	2	E2F6	11505264	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.524000	0.06222	-1.305000	0.02327	0.533000	0.62120	AGG		0.458	E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952		C	11587813	T	C	11587813	3	2	118	1	0	0	0	0	1	0	0	0	4882	1608	56	4	114	4	E2F6	2	11587813	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10		11587813	231611560	20	31283										
SOS1	6654	hgsc.bcm.edu	37	chr2	39250271	39250271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	actgtccaatgtcttttcccTcccaaccatcaatattcttc	2	15	3	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:39250271T>C	ENST00000426016.1	-	11	1384	c.1298A>G	c.(1297-1299)gAg>gGg	p.E433G	SOS1_ENST00000402219.2_Missense_Mutation_p.E433G|SOS1_ENST00000472480.1_5'UTR|SOS1_ENST00000395038.2_Missense_Mutation_p.E433G			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	433			E -> K (in NS4). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:19953625, ECO:0000269|PubMed:21387466}.|Missing (in NS4). {ECO:0000269|PubMed:21387466}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				GTCTTTTCCCTCCCAACCATC	0.393									Noonan syndrome																																							0			2											114	102	106					2																	39250271		2203	4300	6503	39103775	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1298A>G	2.37:g.39250271T>C	ENSP00000387784:p.Glu433Gly		39103775	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179725	0.78564	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	D;D;D	0.89875	-2.58;-2.58;-2.58	5.52	5.52	0.82312	Dbl homology (DH) domain (1);	0.000000	0.85682	D	0.000000	D	0.93523	0.7933	M	0.70275	2.135	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.67231	0.947;0.95	D	0.94141	0.7397	10	0.72032	D	0.01	.	15.932	0.79668	0.0:0.0:0.0:1.0	.	165;433	F5GX06;Q07889	.;SOS1_HUMAN	G	433;433;165;433;433	ENSP00000387784:E433G;ENSP00000384675:E433G;ENSP00000378479:E433G	ENSP00000263879:E433G	E	-	2	0	SOS1	39103775	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.884000	0.87274	2.222000	0.72286	0.455000	0.32223	GAG		0.393	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		C	39250271	T	C	39250271	3	2	118	1	0	0	0	0	1	0	0	0	14973	1551	54	4	2759	4	SOS1	2	39250271	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	27662458	39250271	203949102	21	31284										
CCT7	10574	hgsc.bcm.edu	37	chr2	73475050	73475050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgagataagagtccacacagTtgaggtaggtgggttcacca	13	7	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:73475050T>C	ENST00000258091.5	+	7	920	c.779T>C	c.(778-780)gTt>gCt	p.V260A	CCT7_ENST00000538797.1_Missense_Mutation_p.V132A|CCT7_ENST00000540468.1_Missense_Mutation_p.V173A|CCT7_ENST00000398422.2_Missense_Mutation_p.V56A|CCT7_ENST00000539919.1_Missense_Mutation_p.V216A|CCT7_ENST00000537131.1_Missense_Mutation_p.V160A|CCT7_ENST00000473786.1_3'UTR	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	260					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						GTCCACACAGTTGAGGTAGGT	0.502																																																0			2											67	64	65					2																	73475050		1939	4137	6076	73328558	SO:0001583	missense	10574			AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.779T>C	2.37:g.73475050T>C	ENSP00000258091:p.Val260Ala		73328558	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Missense_Mutation	SNP	ENST00000258091.5	37	CCDS46336.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.130500	0.77549	.	.	ENSG00000135624	ENST00000540468;ENST00000539919;ENST00000258091;ENST00000398422;ENST00000537131;ENST00000538797;ENST00000409081	T;T;T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01;-1.01;-1.01	4.9	4.9	0.64082	.	0.057965	0.64402	D	0.000001	D	0.82907	0.5139	M	0.63428	1.95	0.80722	D	1	B;B;B;B;B;P	0.41910	0.274;0.038;0.03;0.304;0.091;0.764	B;B;B;P;B;P	0.53490	0.162;0.079;0.029;0.458;0.15;0.727	T	0.83334	-0.0011	10	0.48119	T	0.1	-29.0466	13.7901	0.63135	0.0:0.0:0.0:1.0	.	173;132;160;218;56;260	B7Z4Z7;B7Z1C9;F5GZK5;B8ZZC9;A8MWI8;Q99832	.;.;.;.;.;TCPH_HUMAN	A	173;216;260;56;160;132;218	ENSP00000442058:V173A;ENSP00000437824:V216A;ENSP00000258091:V260A;ENSP00000381456:V56A;ENSP00000444379:V160A;ENSP00000438462:V132A	ENSP00000258091:V260A	V	+	2	0	CCT7	73328558	1.000000	0.71417	0.989000	0.46669	0.981000	0.71138	7.843000	0.86859	2.196000	0.70406	0.533000	0.62120	GTT		0.502	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			C	73475050	T	C	73475050	3	2	118	1	0	0	0	0	1	0	0	0	2965	1725	60	4	805	4	CCT7	2	73475050	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	34224779	73475050	169724323	22	31285										
C2orf65	130951	hgsc.bcm.edu	37	chr2	74789458	74789458	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	agcagtgtgagggagtgtgaCggcatgatcacatagaaggt	16	5	1	4	rs186424282	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:74789458C>T	ENST00000290536.5	-	8	1283	c.1167G>A	c.(1165-1167)ccG>ccA	p.P389P	M1AP_ENST00000464686.1_5'UTR|M1AP_ENST00000409585.1_Silent_p.P389P|M1AP_ENST00000536235.1_Silent_p.P389P|M1AP_ENST00000358434.2_Intron	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	389					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGGAGTGTGACGGCATGATCA	0.582													T|||	3	0.000599042	0	0.0029	5008	,	,		22185	0.001		0	False		,,,				2504	0															0			2											226	186	199					2																	74789458		2203	4300	6503	74642966	SO:0001819	synonymous_variant	130951				CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.1167G>A	2.37:g.74789458C>T			74642966	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Silent	SNP	ENST00000290536.5	37	CCDS33229.1																																																																																				0.582	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		T	74789458	C	T	74789458	2	4	118	1	0	0	0	0	0	0	0	1	2190	523	19	1		1	C2orf65	2	74789458	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	1314408	74789458	168409915	23	31286										
SFTPB	6439	hgsc.bcm.edu	37	chr2	85890543	85890543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggcctgctcgctgctgttccCggcctgggtggtcacggaca	15	14	1	0	rs201986026	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:85890543C>T	ENST00000519937.2	-	8	947	c.928G>A	c.(928-930)Ggg>Agg	p.G310R	SFTPB_ENST00000342375.3_Missense_Mutation_p.G310R|SFTPB_ENST00000393822.3_Missense_Mutation_p.G322R|SFTPB_ENST00000409383.1_Missense_Mutation_p.G322R			P07988	PSPB_HUMAN	surfactant protein B	310	Saposin B-type 3. {ECO:0000255|PROSITE- ProRule:PRU00415}.				organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						CTGCTGTTCCCGGCCTGGGTG	0.617													C|||	2	0.000399361	0	0.0029	5008	,	,		19561	0		0	False		,,,				2504	0															0			2						C	ARG/GLY,ARG/GLY	0,4406		0,0,2203	50	48	49		964,964	-9.5	0	2		49	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	SFTPB	NM_000542.3,NM_198843.2	125,125	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	322/394,322/394	85890543	2,13004	2203	4300	6503	85744054	SO:0001583	missense	6439			J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"surfactant, pulmonary-associated protein B"	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.928G>A	2.37:g.85890543C>T	ENSP00000428719:p.Gly310Arg		85744054	Q96R04	Missense_Mutation	SNP	ENST00000519937.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.044|0.044	-1.271601|-1.271601	0.01421|0.01421	0.0|0.0	2.33E-4|2.33E-4	ENSG00000168878|ENSG00000168878	ENST00000519937;ENST00000393822;ENST00000342375;ENST00000409383;ENST00000441838|ENST00000428225	D;D;D;D|.	0.84660|.	-1.88;-1.88;-1.88;-1.88|.	5.15|5.15	-9.47|-9.47	0.00594|0.00594	Saposin-like (2);Saposin B (2);|.	1.425570|.	0.04536|.	N|.	0.387230|.	T|T	0.21509|0.21509	0.0518|0.0518	N|N	0.20401|0.20401	0.57|0.57	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.005;0.001|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.19976|0.19976	-1.0289|-1.0289	10|5	0.17369|.	T|.	0.5|.	-0.9383|-0.9383	7.5266|7.5266	0.27658|0.27658	0.1987:0.5307:0.0:0.2705|0.1987:0.5307:0.0:0.2705	.|.	322;310|.	D6W5L6;P07988|.	.;PSPB_HUMAN|.	R|Q	312;322;310;322;278|302	ENSP00000428719:G312R;ENSP00000377409:G322R;ENSP00000345161:G310R;ENSP00000386346:G322R|.	ENSP00000345161:G310R|.	G|R	-|-	1|2	0|0	SFTPB|SFTPB	85744054|85744054	0.000000|0.000000	0.05858|0.05858	0.022000|0.022000	0.16811|0.16811	0.084000|0.084000	0.17831|0.17831	-1.154000|-1.154000	0.03166|0.03166	-2.249000|-2.249000	0.00702|0.00702	-2.677000|-2.677000	0.00143|0.00143	GGG|CGG		0.617	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843		T	85890543	C	T	85890543	3	4	118	1	0	0	0	0	1	0	0	0	14228	652	23	1	229	1	SFTPB	2	85890543	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	11101085	85890543	157308830	24	31287										
MFSD9	84804	hgsc.bcm.edu	37	chr2	103348857	103348857	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aaaggcacaaccatgctgacAccaaacaaatcctaaaacaa	4	12	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:103348857A>G	ENST00000258436.5	-	2	220	c.177T>C	c.(175-177)ggT>ggC	p.G59G		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	59			G -> A (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CCATGCTGACACCAAACAAAT	0.338																																																0			2											117	110	112					2																	103348857		2203	4300	6503	102715289	SO:0001819	synonymous_variant	84804				CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.177T>C	2.37:g.103348857A>G			102715289	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																				0.338	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		G	103348857	A	G	103348857	2	3	118	1	0	0	0	0	0	0	0	1	9569	146	6	4		4	MFSD9	2	103348857	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	17458314	103348857	139850516	25	31288										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110259191	110259191	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gacggctggtacaaggggacCctgcagcggaacggccgcac	16	13	0	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:110259191C>G	ENST00000309415.6	+	10	2592	c.2592C>G	c.(2590-2592)acC>acG	p.T864T		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	864	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						ACAAGGGGACCCTGCAGCGGA	0.637																																																0			2											53	55	54					2																	110259191		2097	4210	6307	109616473	SO:0001819	synonymous_variant	344558			AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.2592C>G	2.37:g.110259191C>G			109616473	A0SDZ7|A8MPR1|Q8NDU1	Silent	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	C	9.527	1.109892	0.20714	.	.	ENSG00000172985	ENST00000444352	.	.	.	5.07	-4.88	0.03113	.	.	.	.	.	T	0.36524	0.0970	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39981	-0.9587	4	.	.	.	-39.8473	1.6743	0.02818	0.3357:0.1364:0.3453:0.1826	.	.	.	.	A	38	.	.	P	+	1	0	SH3RF3	109616473	0.019000	0.18553	0.961000	0.40146	0.912000	0.54170	-0.958000	0.03857	-0.499000	0.06623	-0.521000	0.04368	CCT		0.637	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		G	110259191	C	G	110259191	2	3	118	1	0	0	0	0	0	0	0	1	14297	610	22	5		5	SH3RF3	2	110259191	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	6910334	110259191	132940182	26	31289										
BUB1	699	hgsc.bcm.edu	37	chr2	111415139	111415139	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttacccataattttctttgtTtccatcttcaaacacatgaa	2	10	3	1	rs36109304	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:111415139T>C	ENST00000302759.6	-	14	1718	c.1600A>G	c.(1600-1602)Aac>Gac	p.N534D	BUB1_ENST00000409311.1_Missense_Mutation_p.N534D|BUB1_ENST00000535254.1_Missense_Mutation_p.N514D	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	534			N -> D (in dbSNP:rs36109304). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TTTTCTTTGTTTCCATCTTCA	0.408													T|||	4	0.000798722	0	0	5008	,	,		16570	0.004		0	False		,,,				2504	0															0			2											71	68	69					2																	111415139		2203	4300	6503	111131612	SO:0001583	missense	699			AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.1600A>G	2.37:g.111415139T>C	ENSP00000302530:p.Asn534Asp		111131612	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	T	13.63	2.295291	0.40594	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.30981	2.24;1.51;2.5	5.89	5.89	0.94794	.	0.306470	0.38897	N	0.001522	T	0.20740	0.0499	L	0.54323	1.7	0.36391	D	0.862538	P;B;P	0.42871	0.792;0.366;0.737	B;B;B	0.38264	0.269;0.032;0.138	T	0.22347	-1.0219	10	0.12103	T	0.63	-23.2649	14.2677	0.66129	0.0:0.0:0.0:1.0	rs36109304	514;534;534	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	D	514;534;534;534	ENSP00000441013:N514D;ENSP00000386701:N534D;ENSP00000302530:N534D	ENSP00000302530:N534D	N	-	1	0	BUB1	111131612	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.722000	0.47269	2.245000	0.73994	0.455000	0.32223	AAC		0.408	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		C	111415139	T	C	111415139	3	2	118	1	0	0	0	0	1	0	0	0	1573	1841	64	4	1705	4	BUB1	2	111415139	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	1155948	111415139	131784234	27	31290										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113089706	113089706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cagcttcttcaggagaaaacTcaaagaaccagaaaaaaagt	7	8	3	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:113089706T>C	ENST00000409871.1	+	12	3612	c.3211T>C	c.(3211-3213)Tca>Cca	p.S1071P	ZC3H6_ENST00000343936.4_Missense_Mutation_p.S1071P|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1071							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AGGAGAAAACTCAAAGAACCA	0.433																																																0			2											45	43	44					2																	113089706		1868	4108	5976	112806177	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3211T>C	2.37:g.113089706T>C	ENSP00000386764:p.Ser1071Pro		112806177	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	T	1.372	-0.585714	0.03827	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.14640	2.49;2.49	5.33	-2.67	0.06059	.	2.194330	0.01585	N	0.021297	T	0.05547	0.0146	N	0.08118	0	0.09310	N	1	B	0.24533	0.105	B	0.20384	0.029	T	0.25082	-1.0142	10	0.02654	T	1	0.0299	4.6257	0.12477	0.3175:0.0:0.4339:0.2486	.	1071	P61129	ZC3H6_HUMAN	P	1071	ENSP00000386764:S1071P;ENSP00000340298:S1071P	ENSP00000340298:S1071P	S	+	1	0	ZC3H6	112806177	0.619000	0.27059	0.325000	0.25375	0.820000	0.46376	0.785000	0.26830	-1.051000	0.03226	-0.435000	0.05868	TCA		0.433	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		C	113089706	T	C	113089706	3	2	118	1	0	0	0	0	1	0	0	0	17610	1551	54	4	3257	4	ZC3H6	2	113089706	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	1674567	113089706	130109667	28	31291										
MARCO	8685	hgsc.bcm.edu	37	chr2	119750754	119750754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tagtaaccgaggccgggctgAagtttactacagtggtacct	12	9	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:119750754A>G	ENST00000327097.4	+	16	1442	c.1307A>G	c.(1306-1308)gAa>gGa	p.E436G	MARCO_ENST00000541757.1_Missense_Mutation_p.E358G	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	436	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						GGCCGGGCTGAAGTTTACTAC	0.532																																					GBM(8;18 374 7467 11269 32796)											0			2											152	143	146					2																	119750754		2203	4300	6503	119467224	SO:0001583	missense	8685			AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.1307A>G	2.37:g.119750754A>G	ENSP00000318916:p.Glu436Gly		119467224	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.173692	0.57584	.	.	ENSG00000019169	ENST00000327097;ENST00000541757	T;T	0.49139	0.79;0.79	6.07	6.07	0.98685	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.070848	0.53938	D	0.000044	T	0.81009	0.4734	H	0.98818	4.34	0.51767	D	0.999934	D	0.89917	1.0	D	0.97110	1.0	D	0.87897	0.2688	9	.	.	.	.	13.0206	0.58784	1.0:0.0:0.0:0.0	.	436	Q9UEW3	MARCO_HUMAN	G	436;358	ENSP00000318916:E436G;ENSP00000441769:E358G	.	E	+	2	0	MARCO	119467224	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	6.572000	0.74005	2.326000	0.78906	0.533000	0.62120	GAA		0.532	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		G	119750754	A	G	119750754	3	3	118	1	0	0	0	0	1	0	0	0	9341	246	9	4	1369	4	MARCO	2	119750754	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	6661048	119750754	123448619	29	31292										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125521566	125521566	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atttgcaggacgcttctggaAcgccgtctcattttatacag	9	10	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:125521566A>G	ENST00000431078.1	+	16	2736	c.2372A>G	c.(2371-2373)aAc>aGc	p.N791S		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	791	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CGCTTCTGGAACGCCGTCTCA	0.418																																																0			2											124	118	120					2																	125521566		1883	4093	5976	125238036	SO:0001583	missense	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2372A>G	2.37:g.125521566A>G	ENSP00000399013:p.Asn791Ser		125238036	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442691	0.83993	.	.	ENSG00000155052	ENST00000431078	T	0.45668	0.89	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.000000	0.53938	D	0.000049	T	0.71467	0.3343	M	0.91406	3.205	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.78137	-0.2321	10	0.62326	D	0.03	.	15.5035	0.75719	1.0:0.0:0.0:0.0	.	791	Q8WYK1	CNTP5_HUMAN	S	791	ENSP00000399013:N791S	ENSP00000399013:N791S	N	+	2	0	CNTNAP5	125238036	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	9.205000	0.95048	2.263000	0.75096	0.533000	0.62120	AAC		0.418	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125521566	A	G	125521566	3	3	118	1	0	0	0	0	1	0	0	0	3656	43	2	4	2434	4	CNTNAP5	2	125521566	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	5770812	125521566	117677807	30	31293										
LCT	3938	hgsc.bcm.edu	37	chr2	136567004	136567004	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atagagaagcggtaggccttCaccttcaaagctcggagcat	11	10	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:136567004C>T	ENST00000264162.2	-	8	2923	c.2913G>A	c.(2911-2913)gtG>gtA	p.V971V	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	971	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGTAGGCCTTCACCTTCAAAG	0.498																																																0			2											88	90	89					2																	136567004		2203	4300	6503	136283474	SO:0001819	synonymous_variant	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2913G>A	2.37:g.136567004C>T			136283474	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.498	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136567004	C	T	136567004	2	4	118	1	0	0	0	0	0	0	0	1	8715	813	29	3		3	LCT	2	136567004	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	11045438	136567004	106632369	31	31294										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141459741	141459741	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtagatgtaagccccaaagaCtgcaactgaaaacatatcca	7	10	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:141459741C>G	ENST00000389484.3	-	39	7242	c.6271G>C	c.(6271-6273)Gtc>Ctc	p.V2091L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2091					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		GCCCCAAAGACTGCAACTGAA	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											185	157	167					2																	141459741		2203	4300	6503	141176211	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6271G>C	2.37:g.141459741C>G	ENSP00000374135:p.Val2091Leu		141176211	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.269931	0.59540	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91792	-2.91	5.5	5.5	0.81552	Six-bladed beta-propeller, TolB-like (1);	0.091610	0.44285	U	0.000465	D	0.93061	0.7791	L	0.39147	1.195	0.58432	D	0.999999	D	0.64830	0.994	D	0.72625	0.978	D	0.88237	0.2907	10	0.02654	T	1	.	19.388	0.94565	0.0:1.0:0.0:0.0	.	2091	Q9NZR2	LRP1B_HUMAN	L	2091;2029	ENSP00000374135:V2091L	ENSP00000374135:V2091L	V	-	1	0	LRP1B	141176211	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.710000	0.84655	2.586000	0.87340	0.563000	0.77884	GTC		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141459741	C	G	141459741	3	3	118	1	0	0	0	0	1	0	0	0	8984	565	20	5	7740	5	LRP1B	2	141459741	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	4892737	141459741	101739632	32	31295										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166165282	166165282	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gggatccatggaattggttgGatttcacagtcattactttt	10	6	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:166165282G>T	ENST00000375437.2	+	5	873	c.583G>T	c.(583-585)Gat>Tat	p.D195Y	SCN2A_ENST00000375427.2_Missense_Mutation_p.D195Y|SCN2A_ENST00000283256.6_Missense_Mutation_p.D195Y|SCN2A_ENST00000357398.3_Missense_Mutation_p.D195Y	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	195					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAATTGGTTGGATTTCACAGT	0.343																																																0			2											114	115	114					2																	166165282		2200	4299	6499	165873528	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.583G>T	2.37:g.166165282G>T	ENSP00000364586:p.Asp195Tyr		165873528	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.606199	0.66445	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.99399	-5.83;-5.83;-5.83;-5.83;-5.83	5.57	5.57	0.84162	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.99825	0.9922	H	0.99590	4.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96671	0.9496	10	0.87932	D	0	.	19.9065	0.97010	0.0:0.0:1.0:0.0	.	195;195	Q99250-2;Q99250	.;SCN2A_HUMAN	Y	195	ENSP00000406454:D195Y;ENSP00000364586:D195Y;ENSP00000349973:D195Y;ENSP00000283256:D195Y;ENSP00000364576:D195Y	ENSP00000283256:D195Y	D	+	1	0	SCN2A	165873528	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.938000	0.87678	2.785000	0.95823	0.650000	0.86243	GAT		0.343	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166165282	G	T	166165282	3	4	118	1	0	0	0	0	1	0	0	0	13953	1174	41	2	597	2	SCN2A	2	166165282	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	24705541	166165282	77034091	33	31296										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171264305	171264305	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gttgtggtcctgagaacgtcAgaaaacaagcttcttcagca	10	9	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:171264305A>G	ENST00000408978.4	+	22	2744	c.2601A>G	c.(2599-2601)tcA>tcG	p.S867S	MYO3B_ENST00000409044.3_Silent_p.S867S|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.S876S	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	867	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGAGAACGTCAGAAAACAAGC	0.453																																																0			2											197	190	192					2																	171264305		1921	4131	6052	170972551	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2601A>G	2.37:g.171264305A>G			170972551	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																				0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			G	171264305	A	G	171264305	2	3	118	1	0	0	0	0	0	0	0	1	10107	175	7	4		4	MYO3B	2	171264305	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	5099023	171264305	71935068	34	31297										
EVX2	344191	hgsc.bcm.edu	37	chr2	176948352	176948352	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggggggcagacggcaggcgCgggcttaggcgagccgggtg	23	9	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:176948352C>T	ENST00000308618.4	-	1	289	c.153G>A	c.(151-153)ccG>ccA	p.P51P		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	51					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		ACGGCAGGCGCGGGCTTAGGC	0.617																																																0			2											37	44	42					2																	176948352		2203	4300	6503	176656598	SO:0001819	synonymous_variant	344191				CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"Homeoboxes / ANTP class : HOXL subclass"	3507	protein-coding gene	gene with protein product		142991	"eve, even-skipped homeobox homolog 2 (Drosophila)"			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.153G>A	2.37:g.176948352C>T			176656598		Silent	SNP	ENST00000308618.4	37	CCDS33333.1																																																																																				0.617	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1			T	176948352	C	T	176948352	2	4	118	1	0	0	0	0	0	0	0	1	5308	755	27	1		1	EVX2	2	176948352	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	5684047	176948352	66251021	35	31298										
TTN	7273	hgsc.bcm.edu	37	chr2	179437468	179437468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctaaagattctccatggtccCgggcccacttcacctcaggt	8	15	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:179437468C>T	ENST00000591111.1	-	276	68692	c.68468G>A	c.(68467-68469)cGg>cAg	p.R22823Q	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R15399Q|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R15591Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R15524Q|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R24464Q|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R21896Q			Q8WZ42	TITIN_HUMAN	titin	22823	Ig-like 117.		R -> W (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCATGGTCCCGGGCCCACTT	0.468																																																0			2											80	82	81					2																	179437468		1909	4108	6017	179145714	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.68468G>A	2.37:g.179437468C>T	ENSP00000465570:p.Arg22823Gln		179145714	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	14.87	2.665630	0.47677	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.9	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65026	0.2652	M	0.80847	2.515	0.50632	D	0.999885	D;D;D;D	0.69078	0.997;0.997;0.997;0.994	P;P;P;P	0.55545	0.778;0.778;0.778;0.704	T	0.72050	-0.4407	9	0.87932	D	0	.	15.4432	0.75204	0.0:0.9328:0.0:0.0672	.	15399;15524;15591;22823	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	21896;15399;15591;15524;15397	ENSP00000343764:R21896Q;ENSP00000434586:R15399Q;ENSP00000340554:R15591Q;ENSP00000352154:R15524Q	ENSP00000340554:R15591Q	R	-	2	0	TTN	179145714	1.000000	0.71417	0.936000	0.37596	0.958000	0.62258	6.008000	0.70739	1.484000	0.48361	0.650000	0.86243	CGG		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179437468	C	T	179437468	3	4	118	1	0	0	0	0	1	0	0	0	16775	652	23	1	34736	1	TTN	2	179437468	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	2489116	179437468	63761905	36	31299										
TTN	7273	hgsc.bcm.edu	37	chr2	179437533	179437533	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aaaagtctcagggtgcagcaGgcccttatagtaacaacttt	9	9	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:179437533G>A	ENST00000591111.1	-	276	68627	c.68403C>T	c.(68401-68403)gcC>gcT	p.A22801A	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Silent_p.A15377A|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Silent_p.A15569A|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.A15502A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.A24442A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Silent_p.A21874A			Q8WZ42	TITIN_HUMAN	titin	22801	Ig-like 117.		A -> T (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGTGCAGCAGGCCCTTATAG	0.507																																																0			2											94	97	96					2																	179437533		1955	4139	6094	179145779	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.68403C>T	2.37:g.179437533G>A			179145779	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37																																																																																					0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179437533	G	A	179437533	2	1	118	1	0	0	0	0	0	0	0	1	16775	987	35	3		3	TTN	2	179437533	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	65	179437533	63761840	37	31300										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197639859	197639859	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccttttgcatcacaatttgcTgactcttggtcattgctgtc	7	11	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:197639859T>C	ENST00000263956.3	-	13	1901	c.1812A>G	c.(1810-1812)tcA>tcG	p.S604S		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	604					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CACAATTTGCTGACTCTTGGT	0.348																																																0			2											123	112	116					2																	197639859		2203	4300	6503	197348104	SO:0001819	synonymous_variant	9330			AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1812A>G	2.37:g.197639859T>C			197348104	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Silent	SNP	ENST00000263956.3	37	CCDS2316.1																																																																																				0.348	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			C	197639859	T	C	197639859	2	2	118	1	0	0	0	0	0	0	0	1	6895	1567	55	4		4	GTF3C3	2	197639859	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	18202326	197639859	45559514	38	31301										
STK36	27148	hgsc.bcm.edu	37	chr2	219563892	219563892	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gagatcctcaggctggtatcCggcgcaatgttgcatcagct	12	11	2	1	rs142956585		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:219563892C>T	ENST00000295709.3	+	26	3904	c.3625C>T	c.(3625-3627)Cgg>Tgg	p.R1209W	STK36_ENST00000392106.2_Missense_Mutation_p.R1188W|STK36_ENST00000440309.1_Missense_Mutation_p.R1209W|STK36_ENST00000392105.3_Missense_Mutation_p.R1188W	NM_015690.4	NP_056505.2			serine/threonine kinase 36									p.R1209W(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		GGCTGGTATCCGGCGCAATGT	0.592																																																1	Substitution - Missense(1)	lung(1)	2						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	49	46	47		3625	5	1	2	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	no	missense	STK36	NM_015690.4	101	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	1209/1316	219563892	3,13003	2203	4300	6503	219272136	SO:0001583	missense	27148			AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3625C>T	2.37:g.219563892C>T	ENSP00000295709:p.Arg1209Trp		219272136		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.978917	0.74360	2.27E-4	2.33E-4	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	5.91	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.41194	D	0.000938	T	0.61800	0.2376	M	0.85041	2.73	0.51012	D	0.999903	P;D;D	0.89917	0.952;1.0;1.0	P;D;D	0.91635	0.563;0.999;0.999	T	0.66101	-0.6007	10	0.87932	D	0	-23.2499	11.0941	0.48134	0.0:0.8618:0.0:0.1382	.	1188;1188;1209	A8MU99;Q9NRP7-2;Q9NRP7	.;.;STK36_HUMAN	W	1209;1188;1188;1209	ENSP00000295709:R1209W;ENSP00000375955:R1188W;ENSP00000375954:R1188W;ENSP00000394095:R1209W	ENSP00000295709:R1209W	R	+	1	2	STK36	219272136	0.998000	0.40836	1.000000	0.80357	0.961000	0.63080	1.310000	0.33551	2.793000	0.96121	0.655000	0.94253	CGG		0.592	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			T	219563892	C	T	219563892	3	4	118	1	0	0	0	0	1	0	0	0	15341	643	23	1	3723	1	STK36	2	219563892	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	21924033	219563892	23635481	39	31302										
NCL	4691	hgsc.bcm.edu	37	chr2	232320319	232320319	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggcatcctcctcactgttgaAgtctacaaaaccaaacctag	6	13	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr2:232320319A>G	ENST00000322723.4	-	13	2089	c.1849T>C	c.(1849-1851)Ttc>Ctc	p.F617L	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	617	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TCACTGTTGAAGTCTACAAAA	0.453																																																0			2											148	158	155					2																	232320319		2203	4300	6503	232028563	SO:0001583	missense	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1849T>C	2.37:g.232320319A>G	ENSP00000318195:p.Phe617Leu		232028563	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	37	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.278048	0.80692	.	.	ENSG00000115053	ENST00000322723;ENST00000392033;ENST00000322732;ENST00000356936	D;D	0.86164	-2.08;-2.08	5.91	4.76	0.60689	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.043558	0.85682	N	0.000000	D	0.92087	0.7492	M	0.83953	2.67	0.58432	D	0.999999	P	0.45569	0.861	P	0.57502	0.822	D	0.92196	0.5764	10	0.87932	D	0	-8.7321	11.0211	0.47718	0.9277:0.0:0.0723:0.0	.	617	P19338	NUCL_HUMAN	L	617;509;389;242	ENSP00000318195:F617L;ENSP00000349410:F242L	ENSP00000318195:F617L	F	-	1	0	NCL	232028563	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	8.755000	0.91646	1.078000	0.41014	0.524000	0.50904	TTC		0.453	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		G	232320319	A	G	232320319	3	3	118	1	0	0	0	0	1	0	0	0	10257	72	3	4	291	4	NCL	2	232320319	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	12756427	232320319	10879054	40	31303										
VHL	7428	hgsc.bcm.edu	37	chr3	10188210	10188210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccgataggtcacctttggcTcttcagagatgcagggacac	11	12	3	1	rs5030830		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:10188210T>C	ENST00000256474.2	+	2	1193	c.353T>C	c.(352-354)cTc>cCc	p.L118P	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	118	Involved in binding to CCT complex.		L -> P (in VHLD; type I; dbSNP:rs5030830). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.|L -> R (in VHLD). {ECO:0000269|PubMed:8730290}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L118P(5)|p.?(1)|p.L118H(1)|p.W117fs*40(1)|p.L118_G123>P(1)|p.W117fs*1(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CACCTTTGGCTCTTCAGAGAT	0.512		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	10	Substitution - Missense(6)|Deletion - Frameshift(2)|Unknown(1)|Complex - deletion inframe(1)	kidney(9)|large_intestine(1)	3	GRCh37	CM941373|CM961426	VHL	M	rs5030830						180	167	171					3																	10188210		2203	4300	6503	10163210	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.353T>C	3.37:g.10188210T>C	ENSP00000256474:p.Leu118Pro		10163210	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152050	0.57259	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.119674	0.56097	D	0.000037	D	0.99674	0.9878	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97192	0.9858	10	0.87932	D	0	0.0466	13.0887	0.59156	0.0:0.0:0.0:1.0	rs5030830	118	P40337	VHL_HUMAN	P	118;36	ENSP00000256474:L118P	ENSP00000256474:L118P	L	+	2	0	VHL	10163210	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	5.968000	0.70413	2.047000	0.60756	0.460000	0.39030	CTC		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188210	T	C	10188210	3	2	118	1	0	0	0	0	1	0	0	0	17202	1551	54	4	359	4	VHL	3	10188210	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10		10188210	187834220	41	31304										
EOMES	8320	hgsc.bcm.edu	37	chr3	27760315	27760315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gggctcattcaagtcctccaCgccatcctctgtaacttcaa	6	15	4	0	rs371656694		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:27760315C>T	ENST00000295743.4	-	4	1431	c.1228G>A	c.(1228-1230)Gtg>Atg	p.V410M	EOMES_ENST00000461503.1_5'Flank|EOMES_ENST00000449599.1_Missense_Mutation_p.V410M|EOMES_ENST00000537516.1_Missense_Mutation_p.V115M			O95936	EOMES_HUMAN	eomesodermin	410					brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						AAGTCCTCCACGCCATCCTCT	0.428																																																0			3						C	MET/VAL	0,4406		0,0,2203	115	112	113		1228	5.3	1	3		113	1,8599	1.2+/-3.3	0,1,4299	no	missense	EOMES	NM_005442.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	410/687	27760315	1,13005	2203	4300	6503	27735319	SO:0001583	missense	8320			BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1228G>A	3.37:g.27760315C>T	ENSP00000295743:p.Val410Met		27735319	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	37	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530460	0.85706	0.0	1.16E-4	ENSG00000163508	ENST00000295743;ENST00000449599;ENST00000537516;ENST00000535713	D;D;D	0.87729	-2.29;-2.29;-2.29	5.34	5.34	0.76211	p53-like transcription factor, DNA-binding (1);	0.061993	0.64402	D	0.000004	D	0.90314	0.6970	L	0.38649	1.16	0.80722	D	1	D;D;D	0.71674	0.973;0.998;0.998	P;D;D	0.66716	0.671;0.91;0.946	D	0.90065	0.4159	10	0.48119	T	0.1	.	19.4408	0.94820	0.0:1.0:0.0:0.0	.	124;410;410	B7Z4I2;G3XAI5;O95936	.;.;EOMES_HUMAN	M	410;410;115;275	ENSP00000295743:V410M;ENSP00000388620:V410M;ENSP00000442097:V115M	ENSP00000295743:V410M	V	-	1	0	EOMES	27735319	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	4.967000	0.63722	2.677000	0.91161	0.655000	0.94253	GTG		0.428	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		T	27760315	C	T	27760315	3	4	118	1	0	0	0	0	1	0	0	0	5160	536	19	1	844	1	EOMES	3	27760315	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	17572105	27760315	170262115	42	31305										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	3											84	74	78					3																	41266136		2203	4300	6503	41241140	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	3.37:g.41266136T>C	ENSP00000344456:p.Ser45Pro		41241140	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	118	1	0	0	0	0	1	0	0	0	4022	1783	62	4	139	4	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	13505821	41266136	156756294	43	31306										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266181	41266181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggaagaggatgtggataccTcccaagtcctgtatgagtgg	14	7	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:41266181T>C	ENST00000349496.5	+	3	458	c.178T>C	c.(178-180)Tcc>Ccc	p.S60P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S60P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S53P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S60P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S60P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	60					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGTGGATACCTCCCAAGTCCT	0.458		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	108	Deletion - In frame(86)|Complex - deletion inframe(15)|Unknown(7)	liver(79)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											65	62	63					3																	41266181		2203	4300	6503	41241185	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.178T>C	3.37:g.41266181T>C	ENSP00000344456:p.Ser60Pro		41241185	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.871453	0.33069	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.91	3.48	0.39840	.	0.154766	0.56097	D	0.000040	T	0.28466	0.0704	L	0.35854	1.095	0.29701	N	0.840169	B	0.02656	0.0	B	0.04013	0.001	T	0.17107	-1.0380	10	0.29301	T	0.29	-3.6161	6.1112	0.20102	0.71:0.0:0.0846:0.2053	.	60	P35222	CTNB1_HUMAN	P	53;60;60;60;60;53;60;60;60	ENSP00000400508:S53P;ENSP00000385604:S60P;ENSP00000412219:S60P;ENSP00000379486:S60P;ENSP00000344456:S60P;ENSP00000411226:S53P;ENSP00000379488:S60P;ENSP00000409302:S60P;ENSP00000401599:S60P	ENSP00000344456:S60P	S	+	1	0	CTNNB1	41241185	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.318000	0.79029	0.464000	0.27142	0.533000	0.62120	TCC		0.458	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266181	T	C	41266181	3	2	118	1	0	0	0	0	1	0	0	0	4022	1551	54	4	184	4	CTNNB1	3	41266181	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	45	41266181	156756249	44	31307										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64085170	64085170	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttcgctggccaggtggagggCgttgtcggagcgagagcgtc	19	9	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:64085170C>T	ENST00000295902.6	-	8	2677	c.2092G>A	c.(2092-2094)Gcc>Acc	p.A698T	PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2_ENST00000564377.1_Missense_Mutation_p.A754T	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	698	Arg-rich.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		AGGTGGAGGGCGTTGTCGGAG	0.617																																																0			3											44	47	46					3																	64085170		2203	4300	6503	64060210	SO:0001583	missense	166336			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.2092G>A	3.37:g.64085170C>T	ENSP00000295902:p.Ala698Thr		64060210	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	C	30	5.057797	0.93846	.	.	ENSG00000163637	ENST00000295902	D	0.90676	-2.71	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000001	D	0.94955	0.8368	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95139	0.8262	10	0.87932	D	0	-28.0869	19.3767	0.94512	0.0:1.0:0.0:0.0	.	698	Q7Z3G6	PRIC2_HUMAN	T	698	ENSP00000295902:A698T	ENSP00000295902:A698T	A	-	1	0	PRICKLE2	64060210	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.209000	0.77916	2.651000	0.90000	0.591000	0.81541	GCC		0.617	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64085170	C	T	64085170	3	4	118	1	0	0	0	0	1	0	0	0	12521	768	27	1	446	1	PRICKLE2	3	64085170	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	22818989	64085170	133937260	45	31308										
VGLL3	389136	hgsc.bcm.edu	37	chr3	87027942	87027942	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cctgcatcttgctgaataccGctaacttcttctgggatgga	9	11	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:87027942G>A	ENST00000398399.2	-	2	500	c.137C>T	c.(136-138)gCg>gTg	p.A46V	VGLL3_ENST00000383698.3_Missense_Mutation_p.A46V	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GCTGAATACCGCTAACTTCTT	0.428																																																0			3											57	54	55					3																	87027942		1942	4165	6107	87110632	SO:0001583	missense	389136			AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"vestigial like 3 (Drosophila)"			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.137C>T	3.37:g.87027942G>A	ENSP00000381436:p.Ala46Val		87110632		Missense_Mutation	SNP	ENST00000398399.2	37	CCDS43110.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471695	0.43942	.	.	ENSG00000206538	ENST00000398399;ENST00000383698	T;T	0.55234	0.57;0.53	5.14	5.14	0.70334	.	0.353082	0.30193	N	0.010196	T	0.35653	0.0939	L	0.32530	0.975	0.34741	D	0.730782	P	0.49961	0.93	B	0.30943	0.122	T	0.58521	-0.7622	10	0.66056	D	0.02	-7.3039	12.9789	0.58552	0.0777:0.0:0.9223:0.0	.	46	A8MV65	VGLL3_HUMAN	V	46	ENSP00000381436:A46V;ENSP00000373199:A46V	ENSP00000373199:A46V	A	-	2	0	VGLL3	87110632	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.733000	0.38156	2.391000	0.81399	0.655000	0.94253	GCG		0.428	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206		A	87027942	G	A	87027942	3	1	118	1	0	0	0	0	1	0	0	0	17200	1087	38	1	855	1	VGLL3	3	87027942	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	22942772	87027942	110994488	46	31309										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142525010	142525010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccaagatctgtcaaaattccGaaatgaaataagggatttac	7	7	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:142525010G>A	ENST00000476941.1	+	13	2801	c.2315G>A	c.(2314-2316)cGa>cAa	p.R772Q	TRPC1_ENST00000273482.6_Missense_Mutation_p.R738Q	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	772					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						TCAAAATTCCGAAATGAAATA	0.363																																																0			3											80	79	80					3																	142525010		2203	4300	6503	144007700	SO:0001583	missense	7220			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2315G>A	3.37:g.142525010G>A	ENSP00000419313:p.Arg772Gln		144007700	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	37	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516550	0.85495	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	D;D	0.89343	-2.5;-2.5	5.59	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.92545	0.7632	L	0.54965	1.715	0.80722	D	1	B;D	0.89917	0.029;1.0	B;D	0.85130	0.003;0.997	D	0.92513	0.6018	10	0.51188	T	0.08	-12.5995	14.4326	0.67261	0.0708:0.0:0.9292:0.0	.	772;738	P48995;P48995-2	TRPC1_HUMAN;.	Q	772;738	ENSP00000419313:R772Q;ENSP00000273482:R738Q	ENSP00000273482:R738Q	R	+	2	0	TRPC1	144007700	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.455000	0.97625	1.378000	0.46305	0.563000	0.77884	CGA		0.363	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		A	142525010	G	A	142525010	3	1	118	1	0	0	0	0	1	0	0	0	16618	1058	37	1	2259	1	TRPC1	3	142525010	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	55497068	142525010	55497420	47	31310										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916875	178916875	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aattttttgatgaaacaagaCgactttgtgaccttcggctt	8	7	0	4			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:178916875C>T	ENST00000263967.3	+	2	419	c.262C>T	c.(262-264)Cga>Tga	p.R88*		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	88	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.		R -> Q (in MCAP; also found in a glioblastoma multiforme sample; may disrupt the interaction between the PI3K- ABD domain and the N-terminal lobe of PI3K/PI4K kinase domain possibly affecting the conformation of the kinase domain). {ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAACAAGACGACTTTGTGA	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											108	102	104					3																	178916875		1821	4079	5900	180399569	SO:0001587	stop_gained	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.262C>T	3.37:g.178916875C>T	ENSP00000263967:p.Arg88*		180399569	Q14CW1|Q99762	Nonsense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.350936	0.82132	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	.	.	.	5.44	3.6	0.41247	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8194	14.1999	0.65696	0.408:0.592:0.0:0.0	.	.	.	.	X	88	.	.	R	+	1	2	PIK3CA	180399569	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.500000	0.35682	0.622000	0.30249	0.555000	0.69702	CGA		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916875	C	T	178916875	4	4	118	1	0	0	0	0	0	1	0	0	11944	528	19	1	264	1	PIK3CA	3	178916875	Nonsense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	36391865	178916875	19105555	48	31311										
KLHL24	54800	hgsc.bcm.edu	37	chr3	183368865	183368865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgcgttgggtctatcgtgccGttgatctgagaagaccactg	13	9	2	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:183368865G>A	ENST00000454652.2	+	4	1107	c.721G>A	c.(721-723)Gtt>Att	p.V241I	KLHL24_ENST00000242810.6_Missense_Mutation_p.V241I|KLHL24_ENST00000476808.1_Missense_Mutation_p.V241I	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	241	BACK.					cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			CTATCGTGCCGTTGATCTGAG	0.418																																																0			3											140	133	136					3																	183368865		2203	4300	6503	184851559	SO:0001583	missense	54800				CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"Kelch-like", "BTB/POZ domain containing"	25947	protein-coding gene	gene with protein product		611295	"kelch-like 24 (Drosophila)"				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.721G>A	3.37:g.183368865G>A	ENSP00000395012:p.Val241Ile		184851559	A5PLN8|Q9H620|Q9NXT9	Missense_Mutation	SNP	ENST00000454652.2	37	CCDS3246.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273662	0.80580	.	.	ENSG00000114796	ENST00000242810;ENST00000454652;ENST00000476808	T;T;T	0.69306	-0.39;-0.39;-0.39	5.09	5.09	0.68999	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.61135	0.2323	L	0.42686	1.345	0.80722	D	1	D;P	0.55605	0.972;0.635	B;B	0.41723	0.365;0.274	T	0.63283	-0.6672	10	0.35671	T	0.21	.	18.5002	0.90878	0.0:0.0:1.0:0.0	.	241;241	Q6TFL4-2;Q6TFL4	.;KLH24_HUMAN	I	241	ENSP00000242810:V241I;ENSP00000395012:V241I;ENSP00000419010:V241I	ENSP00000242810:V241I	V	+	1	0	KLHL24	184851559	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	7.540000	0.82074	2.361000	0.80049	0.460000	0.39030	GTT		0.418	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644		A	183368865	G	A	183368865	3	1	118	1	0	0	0	0	1	0	0	0	8400	1145	40	1	723	1	KLHL24	3	183368865	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	4451990	183368865	14653565	49	31312										
ALG3	10195	hgsc.bcm.edu	37	chr3	183963060	183963060	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggaagagcagcaccatggcCactgggtcattgaagagccg	14	10	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:183963060C>T	ENST00000397676.3	-	4	561	c.531G>A	c.(529-531)gtG>gtA	p.V177V	ALG3_ENST00000418734.2_Silent_p.V121V|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000445626.2_Silent_p.V129V|ALG3_ENST00000455059.1_Silent_p.V137V	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	177					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCACCATGGCCACTGGGTCAT	0.547																																																0			3											34	38	37					3																	183963060		2017	4186	6203	185445754	SO:0001819	synonymous_variant	10195			BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	23056	protein-coding gene	gene with protein product	"carbohydrate deficient glycoprotein syndrome type IV", "dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase", "dol-P-Man dependent alpha-1,3- mannosyltransferase"	608750	"asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)", "asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.531G>A	3.37:g.183963060C>T			185445754	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	CCDS46968.1	.	.	.	.	.	.	.	.	.	.	C	9.659	1.143611	0.21205	.	.	ENSG00000214160	ENST00000446569	.	.	.	5.14	3.32	0.38043	.	.	.	.	.	T	0.59211	0.2177	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53222	-0.8469	4	.	.	.	-9.6794	9.6045	0.39626	0.0:0.8288:0.0:0.1712	.	.	.	.	S	81	.	.	G	-	1	0	ALG3	185445754	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	0.910000	0.28571	0.535000	0.28714	0.462000	0.41574	GGC		0.547	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787		T	183963060	C	T	183963060	2	4	118	1	0	0	0	0	0	0	0	1	520	581	21	3		3	ALG3	3	183963060	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	594195	183963060	14059370	50	31313										
CHRD	8646	hgsc.bcm.edu	37	chr3	184102473	184102473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctactgtgggcatagcgcccGccatgacagtgagtgtcctt	12	12	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:184102473G>A	ENST00000204604.1	+	13	1835	c.1589G>A	c.(1588-1590)cGc>cAc	p.R530H	CHRD_ENST00000545352.1_Missense_Mutation_p.R160H|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000348986.3_Missense_Mutation_p.R490H|CHRD_ENST00000450923.1_Missense_Mutation_p.R530H	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	530	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CATAGCGCCCGCCATGACAGT	0.587																																																0			3											43	38	40					3																	184102473		2202	4300	6502	185585167	SO:0001583	missense	8646			AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1589G>A	3.37:g.184102473G>A	ENSP00000204604:p.Arg530His		185585167	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.023180	0.35701	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.50813	2.53;2.31;2.32;0.73	5.23	4.34	0.51931	CHRD (1);	0.239700	0.39909	N	0.001227	T	0.40448	0.1117	L	0.51422	1.61	0.48696	D	0.999695	B;P;B;P	0.38440	0.362;0.631;0.163;0.498	B;B;B;B	0.31751	0.117;0.135;0.05;0.064	T	0.44559	-0.9320	10	0.59425	D	0.04	-9.8221	13.7096	0.62661	0.0775:0.0:0.9225:0.0	.	160;490;530;530	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	H	530;530;490;160;243	ENSP00000204604:R530H;ENSP00000408972:R530H;ENSP00000334036:R490H;ENSP00000442948:R160H	ENSP00000204604:R530H	R	+	2	0	CHRD	185585167	0.997000	0.39634	1.000000	0.80357	0.230000	0.25150	1.000000	0.29770	1.498000	0.48600	0.655000	0.94253	CGC		0.587	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		A	184102473	G	A	184102473	3	1	118	1	0	0	0	0	1	0	0	0	3378	1087	38	1	1639	1	CHRD	3	184102473	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	139413	184102473	13919957	51	31314										
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186503978	186503978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aaatggatcaaaatgtttgtTttggatgaagcagatgaaat	10	2	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr3:186503978T>C	ENST00000323963.5	+	6	607	c.543T>C	c.(541-543)gtT>gtC	p.V181V	SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA|EIF4A2_ENST00000356531.5_Silent_p.V86V|SNORA63_ENST00000363548.1_RNA|RP11-573D15.9_ENST00000577781.1_RNA|EIF4A2_ENST00000440191.2_Silent_p.V182V|SNORD2_ENST00000459163.1_RNA|SNORA81_ENST00000408493.2_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	181	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		V -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		AAATGTTTGTTTTGGATGAAG	0.328			T	BCL6	NHL																																		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	0			3											79	78	79					3																	186503978		2203	4300	6503	187986672	SO:0001819	synonymous_variant	1974			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.543T>C	3.37:g.186503978T>C			187986672	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Silent	SNP	ENST00000323963.5	37	CCDS3282.1																																																																																				0.328	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		C	186503978	T	C	186503978	2	2	118	1	0	0	0	0	0	0	0	1	5038	1828	64	4		4	EIF4A2	3	186503978	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	2401505	186503978	11518452	52	31315										
POLN	353497	hgsc.bcm.edu	37	chr4	2209835	2209836	+	Frame_Shift_Ins	INS	-	-	A													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atccaaatgcctaatatcacINSaaaaatgttttttcaatgct							TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:2209835_2209836insA	ENST00000511885.2	-	5	945_946	c.592_593insT	c.(592-594)tgtfs	p.C198fs	POLN_ENST00000515357.1_5'UTR|POLN_ENST00000382865.1_Frame_Shift_Ins_p.C198fs			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	198					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			CCTAATATCACAAAAATGTTTT	0.416								DNA polymerases (catalytic subunits)																																								0			4																																								2179634	SO:0001589	frameshift_variant	353497			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"DNA polymerases"	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.593dupT	4.37:g.2209840_2209840dupA	ENSP00000435506:p.Cys198fs		2179633	A2A336|B4E158|Q4TTW4|Q6ZNF4	Frame_Shift_Ins	INS	ENST00000511885.2	37	CCDS3360.1																																																																																				0.416	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		A	2209836	-	A	2209835	7	5	118	1	0	1	1	0	0	0	0	0	12238	478	17	0	2197	0	POLN	4	2209835	Frame_Shift_Ins	INS	-	TCGA-F5-6811-01A-11D-1826-10		2209835	188944441	53	31316										
APBB2	323	hgsc.bcm.edu	37	chr4	40892392	40892392	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gggactcaccggccattgtcGcggcccacgccccacacgcg	12	19	1	0	rs377258984		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:40892392G>A	ENST00000295974.8	-	12	2144	c.1515C>T	c.(1513-1515)cgC>cgT	p.R505R	APBB2_ENST00000508593.1_Silent_p.R506R|APBB2_ENST00000513140.1_Silent_p.R484R|APBB2_ENST00000506352.1_Silent_p.R484R	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	505	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GGCCATTGTCGCGGCCCACGC	0.642																																					Ovarian(3;20 75 16686 49997)											0			4						G	,,	0,4278		0,0,2139	40	45	44		1515,1518,1452	1.8	1	4		44	1,8525		0,1,4262	no	coding-synonymous,coding-synonymous,coding-synonymous	APBB2	NM_001166050.1,NM_004307.1,NM_173075.4	,,	0,1,6401	AA,AG,GG		0.0117,0.0,0.0078	,,	505/759,506/760,484/737	40892392	1,12803	2139	4263	6402	40587149	SO:0001819	synonymous_variant	323			U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.1515C>T	4.37:g.40892392G>A			40587149	B4DSL4|E9PG87|Q8IUI6	Silent	SNP	ENST00000295974.8	37	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.46|11.46	1.645098|1.645098	0.29246|0.29246	0.0|0.0	1.17E-4|1.17E-4	ENSG00000163697|ENSG00000163697	ENST00000513493|ENST00000513611	.|.	.|.	.|.	5.98|5.98	1.81|1.81	0.25067|0.25067	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.18130|.	0.0435|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.19192|.	-1.0313|.	4|.	.|0.02654	.|T	.|1	-18.0896|-18.0896	2.4299|2.4299	0.04469|0.04469	0.235:0.0966:0.4436:0.2248|0.235:0.0966:0.4436:0.2248	.|.	.|.	.|.	.|.	V|X	42|475	.|.	.|ENSP00000427307:R475X	A|R	-|-	2|1	0|2	APBB2|APBB2	40587149|40587149	0.161000|0.161000	0.22892|0.22892	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	-0.418000|-0.418000	0.07080|0.07080	0.395000|0.395000	0.25257|0.25257	0.591000|0.591000	0.81541|0.81541	GCG|CGA		0.642	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	40892392	G	A	40892392	2	1	118	1	0	0	0	0	0	0	0	1	761	1074	38	1		1	APBB2	4	40892392	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	38682557	40892392	150261884	54	31317										
SLC30A9	10463	hgsc.bcm.edu	37	chr4	41992692	41992692	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttacccggcttggccgccgcCgcggcccacagatgtagctg	13	16	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:41992692C>T	ENST00000264451.7	+	1	204	c.24C>T	c.(22-24)gcC>gcT	p.A8A	RP11-814H16.2_ENST00000608029.1_lincRNA	NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	8					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TGGCCGCCGCCGCGGCCCACA	0.697																																																0			4											20	21	20					4																	41992692		2183	4274	6457	41687449	SO:0001819	synonymous_variant	10463			AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.24C>T	4.37:g.41992692C>T			41687449	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																				0.697	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			T	41992692	C	T	41992692	2	4	118	1	0	0	0	0	0	0	0	1	14599	639	23	1		1	SLC30A9	4	41992692	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	1100300	41992692	149161584	55	31318										
KIT	3815	hgsc.bcm.edu	37	chr4	55594223	55594223	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gccctcatgtctgaactcaaAgtcctgagttaccttggtaa	8	11	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:55594223A>G	ENST00000288135.5	+	13	2023	c.1926A>G	c.(1924-1926)aaA>aaG	p.K642K		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	642	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAACTCAAAGTCCTGAGTT	0.438		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	0			4											126	115	119					4																	55594223		2203	4300	6503	55288980	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1926A>G	4.37:g.55594223A>G			55288980	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.438	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55594223	A	G	55594223	2	3	118	1	0	0	0	0	0	0	0	1	8350	69	3	4		4	KIT	4	55594223	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	13601531	55594223	135560053	56	31319										
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154533465	154533465	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtgaaaatttgaagaaggtGgacacaaagccttcttcaga	10	6	2	4			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:154533465G>A	ENST00000409663.3	+	26	3529	c.3477G>A	c.(3475-3477)gtG>gtA	p.V1159V	KIAA0922_ENST00000409959.3_Silent_p.V1160V|KIAA0922_ENST00000440693.1_Silent_p.V1076V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1159						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TGAAGAAGGTGGACACAAAGC	0.333																																																0			4											72	74	73					4																	154533465		2203	4299	6502	154752915	SO:0001819	synonymous_variant	23240			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3477G>A	4.37:g.154533465G>A			154752915	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																				0.333	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154533465	G	A	154533465	2	1	118	1	0	0	0	0	0	0	0	1	8222	1335	47	3		3	KIAA0922	4	154533465	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	98939242	154533465	36620811	57	31320										
C4orf27	54969	hgsc.bcm.edu	37	chr4	170663135	170663135	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tctctctgtttcatcttcacGgttctctgttcaagcgagta	7	11	7	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr4:170663135G>A	ENST00000393381.2	-	5	696	c.621C>T	c.(619-621)acC>acT	p.T207T		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	207						nucleus (GO:0005634)		p.T207T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		TCATCTTCACGGTTCTCTGTT	0.373																																																1	Substitution - coding silent(1)	ovary(1)	4											143	134	137					4																	170663135		2203	4300	6503	170899710	SO:0001819	synonymous_variant	54969			BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.621C>T	4.37:g.170663135G>A			170899710		Silent	SNP	ENST00000393381.2	37	CCDS3813.1																																																																																				0.373	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867		A	170663135	G	A	170663135	2	1	118	1	0	0	0	0	0	0	0	1	2264	1103	39	1		1	C4orf27	4	170663135	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	16129670	170663135	20491141	58	31321										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33534957	33534957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccggcacttttcttgcaggcCtgctggttgcattttttgaa	10	10	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:33534957C>A	ENST00000504830.1	-	23	4922	c.4587G>T	c.(4585-4587)caG>caT	p.Q1529H	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q1444H	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1529	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCTTGCAGGCCTGCTGGTTGC	0.453										HNSCC(64;0.19)																																						0			5											138	132	134					5																	33534957		2203	4300	6503	33570714	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4587G>T	5.37:g.33534957C>A	ENSP00000422554:p.Gln1529His		33570714	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.194399	0.58017	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.55052	0.54;0.54	5.13	0.915	0.19366	.	0.253016	0.39834	N	0.001251	T	0.60392	0.2265	M	0.62088	1.915	0.80722	D	1	D;D	0.59767	0.983;0.986	P;P	0.62649	0.847;0.905	T	0.56195	-0.8019	10	0.44086	T	0.13	.	7.3731	0.26813	0.0:0.5161:0.0:0.4839	.	1444;1529	P58397-3;P58397	.;ATS12_HUMAN	H	1529;1444	ENSP00000422554:Q1529H;ENSP00000344847:Q1444H	ENSP00000344847:Q1444H	Q	-	3	2	ADAMTS12	33570714	0.998000	0.40836	0.998000	0.56505	0.951000	0.60555	0.230000	0.17852	0.184000	0.20083	0.563000	0.77884	CAG		0.453	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33534957	C	A	33534957	3	1	118	1	0	0	0	0	1	0	0	0	257	680	24	2	205	2	ADAMTS12	5	33534957	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		33534957	147380303	59	31322										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54693248	54693248	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aactttttggtcataggttgTcccagttttggtgcatctcc	9	9	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:54693248T>C	ENST00000230640.5	+	20	2440	c.2186T>C	c.(2185-2187)gTc>gCc	p.V729A	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.V628A	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	729					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TCATAGGTTGTCCCAGTTTTG	0.383																																					Melanoma(2;92 134 23744 29976 33782)											0			5											154	145	148					5																	54693248		2203	4300	6503	54729005	SO:0001583	missense	23517			D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.2186T>C	5.37:g.54693248T>C	ENSP00000230640:p.Val729Ala		54729005	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824980	0.90955	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.35973	1.28;1.33	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.68696	0.3029	M	0.93898	3.47	0.80722	D	1	P;D	0.76494	0.95;0.999	P;D	0.68621	0.641;0.959	T	0.78170	-0.2308	10	0.66056	D	0.02	-18.3469	15.5101	0.75772	0.0:0.0:0.0:1.0	.	628;729	F5H7E2;P42285	.;SK2L2_HUMAN	A	729;628	ENSP00000230640:V729A;ENSP00000442583:V628A	ENSP00000230640:V729A	V	+	2	0	SKIV2L2	54729005	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.562000	0.82300	2.131000	0.65755	0.533000	0.62120	GTC		0.383	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			C	54693248	T	C	54693248	3	2	118	1	0	0	0	0	1	0	0	0	14397	1667	58	4	2264	4	SKIV2L2	5	54693248	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	21158291	54693248	126222012	60	31323										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65288660	65288660	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgcagcttagaacaagttccGaaagagatttttacttttga	8	6	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:65288660G>A	ENST00000284037.5	+	3	503	c.114G>A	c.(112-114)ccG>ccA	p.P38P	ERBB2IP_ENST00000506030.1_Silent_p.P38P|ERBB2IP_ENST00000508515.1_Silent_p.P38P|ERBB2IP_ENST00000380943.2_Silent_p.P38P|ERBB2IP_ENST00000380939.2_Silent_p.P38P|ERBB2IP_ENST00000380935.1_Silent_p.P38P|ERBB2IP_ENST00000380938.2_Silent_p.P38P|ERBB2IP_ENST00000511297.1_Silent_p.P38P|ERBB2IP_ENST00000380936.1_Silent_p.P38P|ERBB2IP_ENST00000416865.2_Silent_p.P38P	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	38					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		AACAAGTTCCGAAAGAGATTT	0.388																																																0			5											80	80	80					5																	65288660		2203	4300	6503	65324416	SO:0001819	synonymous_variant	55914				CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.114G>A	5.37:g.65288660G>A			65324416	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																				0.388	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65288660	G	A	65288660	2	1	118	1	0	0	0	0	0	0	0	1	5220	1045	37	1		1	ERBB2IP	5	65288660	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	10595412	65288660	115626600	61	31324										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83433096	83433096	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccataaattcgcctgggcaCtcacaggaatagttagcaac	8	12	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:83433096C>T	ENST00000296591.5	-	5	850	c.432G>A	c.(430-432)gaG>gaA	p.E144E	EDIL3_ENST00000380138.3_Silent_p.E134E	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	144	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		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)		CGCCTGGGCACTCACAGGAAT	0.393																																																0			5											188	164	172					5																	83433096		2203	4300	6503	83468852	SO:0001819	synonymous_variant	10085			U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.432G>A	5.37:g.83433096C>T			83468852	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	37	CCDS4062.1																																																																																				0.393	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		T	83433096	C	T	83433096	2	4	118	1	0	0	0	0	0	0	0	1	4926	564	20	3		3	EDIL3	5	83433096	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	18144436	83433096	97482164	62	31325										
APC	324	hgsc.bcm.edu	37	chr5	112175217	112175217	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcaaatagcagaaataaaagAaaagattggaactaggtcag	10	4	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:112175217A>G	ENST00000457016.1	+	16	4306	c.3926A>G	c.(3925-3927)gAa>gGa	p.E1309G	APC_ENST00000508376.2_Missense_Mutation_p.E1309G|APC_ENST00000257430.4_Missense_Mutation_p.E1309G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1309	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.			E -> G (in Ref. 1; AAA60353/AAA60354). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*4(22)|p.I1311fs*4(2)|p.K1310fs*4(2)|p.?(1)|p.E1309fs*6(1)|p.K1192fs*3(1)|p.K1308fs*4(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAATAAAAGAAAAGATTGGA	0.423		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	30	Deletion - Frameshift(26)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(28)|soft_tissue(1)|skin(1)	5	GRCh37	CD995194|CM973705	APC	D|M							53	55	55					5																	112175217		2202	4300	6502	112203116	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3926A>G	5.37:g.112175217A>G	ENSP00000413133:p.Glu1309Gly		112203116	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	8.395	0.840561	0.16891	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90676	-2.71;-2.71;-2.71	6.03	6.03	0.97812	.	0.365794	0.32503	N	0.006002	D	0.85301	0.5665	L	0.29908	0.895	0.31972	N	0.607027	B;B	0.12630	0.0;0.006	B;B	0.11329	0.0;0.006	T	0.81185	-0.1048	9	.	.	.	-11.1954	16.2316	0.82347	1.0:0.0:0.0:0.0	.	1311;1309	Q4LE70;P25054	.;APC_HUMAN	G	1309	ENSP00000413133:E1309G;ENSP00000257430:E1309G;ENSP00000427089:E1309G	.	E	+	2	0	APC	112203116	1.000000	0.71417	0.946000	0.38457	0.365000	0.29674	8.900000	0.92551	2.308000	0.77769	0.533000	0.62120	GAA		0.423	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175217	A	G	112175217	3	3	118	1	0	0	0	0	1	0	0	0	763	246	9	4	3984	4	APC	5	112175217	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	28742121	112175217	68740043	63	31326			1	39		3	3	505	N	A_-	4.324786e-06
APC	324	hgsc.bcm.edu	37	chr5	112175258	112175259	+	Frame_Shift_Ins	INS	-	-	T													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgaagatcctgtgagcgaagINSttccagcagtgtcacagcac							TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:112175258_112175259insT	ENST00000457016.1	+	16	4347_4348	c.3967_3968insT	c.(3967-3969)gttfs	p.V1323fs	APC_ENST00000508376.2_Frame_Shift_Ins_p.V1323fs|APC_ENST00000257430.4_Frame_Shift_Ins_p.V1323fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1323	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.P1324fs*8(3)|p.V1320fs*8(1)|p.K1192fs*3(1)|p.?(1)|p.E1322fs*8(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGTGAGCGAAGTTCCAGCAGTG	0.436		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	7	Insertion - Frameshift(3)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(5)|soft_tissue(1)|skin(1)	5																																								112203158	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3969dupT	5.37:g.112175260_112175260dupT	ENSP00000413133:p.Val1323fs		112203157	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				0.436	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175259	-	T	112175258	7	5	118	1	0	1	1	0	0	0	0	0	763	1029	36	0	4025	0	APC	5	112175258	Frame_Shift_Ins	INS	-	TCGA-F5-6811-01A-11D-1826-10	41	112175258	68740002	64	31327			1	39		3	3	505	N	A_-	4.324786e-06
APC	324	hgsc.bcm.edu	37	chr5	112175721	112175721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgcagtaaatgctgcagttcAgagggtccaggttcttccag	12	9	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:112175721A>G	ENST00000457016.1	+	16	4810	c.4430A>G	c.(4429-4431)cAg>cGg	p.Q1477R	APC_ENST00000508376.2_Missense_Mutation_p.Q1477R|APC_ENST00000257430.4_Missense_Mutation_p.Q1477R|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1477	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCTGCAGTTCAGAGGGTCCAG	0.448		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Unknown(1)|Complex - frameshift(1)|Deletion - Frameshift(1)	thyroid(1)|soft_tissue(1)|skin(1)	5											74	73	74					5																	112175721		2202	4300	6502	112203620	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4430A>G	5.37:g.112175721A>G	ENSP00000413133:p.Gln1477Arg		112203620	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.816728	0.50633	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89270	-2.49;-2.49;-2.49	6.16	6.16	0.99307	.	0.058617	0.64402	D	0.000002	D	0.92090	0.7493	L	0.47716	1.5	0.58432	D	0.999995	D;D	0.60160	0.987;0.967	D;D	0.67725	0.953;0.932	D	0.91230	0.5013	9	.	.	.	-8.5287	16.8061	0.85666	1.0:0.0:0.0:0.0	.	1479;1477	Q4LE70;P25054	.;APC_HUMAN	R	1477	ENSP00000413133:Q1477R;ENSP00000257430:Q1477R;ENSP00000427089:Q1477R	.	Q	+	2	0	APC	112203620	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	3.349000	0.52217	2.367000	0.80283	0.528000	0.53228	CAG		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175721	A	G	112175721	3	3	118	1	0	0	0	0	1	0	0	0	763	188	7	4	4488	4	APC	5	112175721	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	463	112175721	68739539	65	31328			1	39		3	3	505	N	A_-	4.324786e-06
FBN2	2201	hgsc.bcm.edu	37	chr5	127710340	127710340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccaacacacacacgtccatcCatgcccacagccaggcctgg	7	19	0	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:127710340C>T	ENST00000508053.1	-	21	3050	c.2076G>A	c.(2074-2076)atG>atA	p.M692I	FBN2_ENST00000262464.4_Missense_Mutation_p.M692I|FBN2_ENST00000511489.1_5'UTR|FBN2_ENST00000508989.1_Missense_Mutation_p.M659I			P35556	FBN2_HUMAN	fibrillin 2	692	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CACGTCCATCCATGCCCACAG	0.478																																																0			5											113	101	105					5																	127710340		2203	4300	6503	127738239	SO:0001583	missense	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2076G>A	5.37:g.127710340C>T	ENSP00000424571:p.Met692Ile		127738239	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.707512	0.30322	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.91894	-2.93;-2.93;-2.93	4.45	-0.684	0.11331	Matrix fibril-associated (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.189541	0.34362	N	0.004032	T	0.74809	0.3765	N	0.04959	-0.14	0.30737	N	0.746545	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.62105	-0.6924	10	0.14656	T	0.56	.	2.702	0.05152	0.3946:0.3574:0.1017:0.1463	.	659;692	D6RJI3;P35556	.;FBN2_HUMAN	I	692;692;659	ENSP00000262464:M692I;ENSP00000424571:M692I;ENSP00000425596:M659I	ENSP00000262464:M692I	M	-	3	0	FBN2	127738239	0.157000	0.22836	0.982000	0.44146	0.996000	0.88848	-0.466000	0.06672	-0.136000	0.11475	0.655000	0.94253	ATG		0.478	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127710340	C	T	127710340	3	4	118	1	0	0	0	0	1	0	0	0	5722	594	21	3	6866	3	FBN2	5	127710340	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	15534619	127710340	53204920	66	31329										
AFF4	27125	hgsc.bcm.edu	37	chr5	132232707	132232707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccacgcccactttctgatcCcttttggatggttttggagt	9	12	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:132232707C>T	ENST00000265343.5	-	11	1994	c.1615G>A	c.(1615-1617)Gga>Aga	p.G539R	AFF4_ENST00000378595.3_Missense_Mutation_p.G539R	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	539					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTTTCTGATCCCTTTTGGATG	0.502																																					Ovarian(126;889 1733 2942 10745 11605)											0			5											137	127	130					5																	132232707		2203	4300	6503	132260606	SO:0001583	missense	27125			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.1615G>A	5.37:g.132232707C>T	ENSP00000265343:p.Gly539Arg		132260606	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.932753	0.73442	.	.	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.66280	-0.2;-0.2	5.36	5.36	0.76844	.	0.047599	0.85682	D	0.000000	T	0.77791	0.4183	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.985	T	0.71928	-0.4444	10	0.17369	T	0.5	-11.9944	19.4427	0.94827	0.0:1.0:0.0:0.0	.	539;539	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	R	539	ENSP00000265343:G539R;ENSP00000367858:G539R	ENSP00000265343:G539R	G	-	1	0	AFF4	132260606	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.488000	0.66869	2.649000	0.89929	0.563000	0.77884	GGA		0.502	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		T	132232707	C	T	132232707	3	4	118	1	0	0	0	0	1	0	0	0	359	632	22	3	1920	3	AFF4	5	132232707	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	4522367	132232707	48682553	67	31330										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202971	140202971	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cagttccaggtgagcgcgcgCgacgcgggcgtgccgcctct	16	15	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:140202971C>T	ENST00000529859.1	+	1	1611	c.1611C>T	c.(1609-1611)cgC>cgT	p.R537R	PCDHA5_ENST00000529619.1_Silent_p.R537R|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Silent_p.R537R|PCDHA4_ENST00000512229.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGCGCGCGCGACGCGGGCG	0.682																																																0			5											46	53	51					5																	140202971		2202	4298	6500	140183155	SO:0001819	synonymous_variant	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1611C>T	5.37:g.140202971C>T			140183155	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																				0.682	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140202971	C	T	140202971	2	4	118	1	0	0	0	0	0	0	0	1	11558	755	27	1		1	PCDHA5	5	140202971	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	7970264	140202971	40712289	68	31331										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140307377	140307377	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caagtagctgcttcactaggTccgcctgaaacgctcttgga	10	12	2	1	rs12522306	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:140307377T>C	ENST00000253807.2	+	1	900	c.900T>C	c.(898-900)ggT>ggC	p.G300G	PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.G300G|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000409494.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	300	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCACTAGGTCCGCCTGAAA	0.547													t|||	64	0.0127796	0.0015	0.0893	5008	,	,		22611	0		0	False		,,,				2504	0															0			5						T	,,,,,,,,,,,,,,,,,	6,4400	12.9+/-30.5	0,6,2197	131	116	121		900,,,,,,,,,,,,,,,,,900	0.4	0.2	5	dbSNP_120	121	0,8600		0,0,4300	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,,,,,,,,,,,,,,,,,	300/964,,,,,,,,,,,,,,,,,300/819	140307377	6,13000	2203	4300	6503	140287561	SO:0001819	synonymous_variant	56135			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.900T>C	5.37:g.140307377T>C			140287561	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																				0.547	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		C	140307377	T	C	140307377	2	2	118	1	0	0	0	0	0	0	0	1	11563	1654	58	4		4	PCDHAC1	5	140307377	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	104406	140307377	40607883	69	31332										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140553098	140553098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caagatcagggaccgccctcGtgcgcattctggttctagac	11	13	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:140553098G>A	ENST00000231137.3	+	1	856	c.682G>A	c.(682-684)Gtg>Atg	p.V228M		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	228	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V228M(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACCGCCCTCGTGCGCATTCT	0.547																																																1	Substitution - Missense(1)	endometrium(1)	5											58	60	59					5																	140553098		2203	4300	6503	140533282	SO:0001583	missense	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.682G>A	5.37:g.140553098G>A	ENSP00000231137:p.Val228Met		140533282	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	8.236	0.805796	0.16467	.	.	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.33216	1.42	4.61	1.67	0.24075	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.52191	0.1719	M	0.88512	2.96	0.09310	N	1	D	0.67145	0.996	D	0.63033	0.91	T	0.41251	-0.9519	9	0.72032	D	0.01	.	4.1948	0.10438	0.3445:0.0:0.5046:0.1508	.	228	Q9Y5E2	PCDB7_HUMAN	M	228;11	ENSP00000231137:V228M	ENSP00000231137:V228M	V	+	1	0	PCDHB7	140533282	0.015000	0.18098	0.001000	0.08648	0.003000	0.03518	0.333000	0.19768	0.078000	0.16900	0.655000	0.94253	GTG		0.547	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140553098	G	A	140553098	3	1	118	1	0	0	0	0	1	0	0	0	11578	1145	40	1	684	1	PCDHB7	5	140553098	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	245721	140553098	40362162	70	31333										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563764	140563764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gctccccggctttgagcagcGaggcgctggtgcgcgtgctg	17	13	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:140563764G>A	ENST00000361016.2	+	1	2785	c.1630G>A	c.(1630-1632)Gag>Aag	p.E544K		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	544	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTTGAGCAGCGAGGCGCTGGT	0.697																																																0			5											17	19	18					5																	140563764		1822	3391	5213	140543948	SO:0001583	missense	57717			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1630G>A	5.37:g.140563764G>A	ENSP00000354293:p.Glu544Lys		140543948	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	15.92	2.975092	0.53720	.	.	ENSG00000196963	ENST00000361016	T	0.01705	4.68	4.12	1.13	0.20643	Cadherin (5);Cadherin-like (1);	0.702237	0.11206	N	0.588250	T	0.01156	0.0038	N	0.05259	-0.085	0.24366	N	0.994857	P	0.35242	0.492	B	0.32090	0.14	T	0.51332	-0.8719	10	0.72032	D	0.01	.	9.0876	0.36590	0.2032:0.323:0.4739:0.0	.	544	Q9NRJ7	PCDBG_HUMAN	K	544	ENSP00000354293:E544K	ENSP00000354293:E544K	E	+	1	0	PCDHB16	140543948	0.223000	0.23663	1.000000	0.80357	0.920000	0.55202	0.821000	0.27338	0.202000	0.20498	0.479000	0.44913	GAG		0.697	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563764	G	A	140563764	3	1	118	1	0	0	0	0	1	0	0	0	11572	1059	37	1	1632	1	PCDHB16	5	140563764	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	10666	140563764	40351496	71	31334										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140744083	140744083	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccccaggagctggcggagcgCggagtccgcatcgtctccag	15	15	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:140744083C>T	ENST00000518069.1	+	1	186	c.186C>T	c.(184-186)cgC>cgT	p.R62R	PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCGGAGCGCGGAGTCCGCA	0.647																																																0			5											48	59	55					5																	140744083		2201	4298	6499	140724267	SO:0001819	synonymous_variant	56110			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.186C>T	5.37:g.140744083C>T			140724267	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	37	CCDS54925.1																																																																																				0.647	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140744083	C	T	140744083	2	4	118	1	0	0	0	0	0	0	0	1	11588	755	27	1		1	PCDHGA5	5	140744083	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	180319	140744083	40171177	72	31335										
DUSP1	1843	hgsc.bcm.edu	37	chr5	172196694	172196694	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggttgggacaattggctgagAcgttgatcaaggcagtgatg	16	5	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:172196694A>G	ENST00000239223.3	-	3	859	c.617T>C	c.(616-618)gTc>gCc	p.V206A	RP11-779O18.3_ENST00000523005.1_RNA	NM_004417.3	NP_004408.1	P28562	DUS1_HUMAN	dual specificity phosphatase 1	206	Tyrosine-protein phosphatase.				cellular response to hormone stimulus (GO:0032870)|endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of meiotic cell cycle (GO:0051447)|peptidyl-threonine dephosphorylation (GO:0035970)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|protein dephosphorylation (GO:0006470)|regulation of apoptotic process (GO:0042981)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to light stimulus (GO:0009416)|response to oxidative stress (GO:0006979)|response to retinoic acid (GO:0032526)|response to testosterone (GO:0033574)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|liver(1)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00431)|all_lung(126;0.00729)	all_hematologic(541;4.11e-18)|Breast(839;0.00637)|Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.15)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	GBM - Glioblastoma multiforme(465;0.0103)		ATTGGCTGAGACGTTGATCAA	0.552																																																0			5											216	182	193					5																	172196694		2203	4300	6503	172129300	SO:0001583	missense	11266			X68277	CCDS4380.1	5q35.1	2011-06-09			ENSG00000120129	ENSG00000120129		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3064	protein-coding gene	gene with protein product		600714		PTPN10		1406996, 7806236	Standard	NM_004417		Approved	HVH1, CL100, MKP-1	uc003mbv.2	P28562	OTTHUMG00000130523	ENST00000239223.3:c.617T>C	5.37:g.172196694A>G	ENSP00000239223:p.Val206Ala		172129300	D3DQL9|Q2V508	Missense_Mutation	SNP	ENST00000239223.3	37	CCDS4380.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.640510	0.87859	.	.	ENSG00000120129	ENST00000239223;ENST00000457103;ENST00000434080	T	0.62498	0.02	5.32	5.32	0.75619	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	T	0.74152	0.3679	L	0.49513	1.565	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;1.0	T	0.74688	-0.3581	10	0.46703	T	0.11	.	15.3007	0.73949	1.0:0.0:0.0:0.0	.	206;163	P28562;B4DNT2	DUS1_HUMAN;.	A	206;179;141	ENSP00000239223:V206A	ENSP00000239223:V206A	V	-	2	0	DUSP1	172129300	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.296000	0.96104	2.023000	0.59567	0.459000	0.35465	GTC		0.552	DUSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252943.3	NM_004417		G	172196694	A	G	172196694	3	3	118	1	0	0	0	0	1	0	0	0	4820	275	10	4	494	4	DUSP1	5	172196694	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	31452611	172196694	8718566	73	31336										
BOD1	91272	hgsc.bcm.edu	37	chr5	173036350	173036350	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggaactcatgaattgctcgTtctatttgtggcctgaagat	10	7	2	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:173036350T>C	ENST00000311086.4	-	3	673	c.450A>G	c.(448-450)gaA>gaG	p.E150E	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000471339.1_5'Flank|BOD1_ENST00000480951.1_Intron	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	150					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GAATTGCTCGTTCTATTTGTG	0.527																																																0			5											145	128	134					5																	173036350		2203	4300	6503	172968956	SO:0001819	synonymous_variant	91272			AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"biorientation defective 1"		"family with sequence similarity 44, member B"	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.450A>G	5.37:g.173036350T>C			172968956	B4DXH8|Q9BTW1	Silent	SNP	ENST00000311086.4	37	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.425778	0.25639	.	.	ENSG00000145919	ENST00000477985	.	.	.	5.65	-1.03	0.10102	.	.	.	.	.	T	0.58061	0.2096	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54925	-0.8220	4	.	.	.	-39.1734	11.5227	0.50560	0.0:0.6527:0.0:0.3473	.	.	.	.	A	83	.	.	T	-	1	0	BOD1	172968956	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	0.804000	0.27098	-0.122000	0.11766	-0.256000	0.11100	ACG		0.527	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369		C	173036350	T	C	173036350	2	2	118	1	0	0	0	0	0	0	0	1	1483	1722	60	4		4	BOD1	5	173036350	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	839656	173036350	7878910	74	31337										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176026123	176026123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	acacaggatccacctttctcAaagacccaggatcctccttc	5	16	1	1	rs142779818|rs550332435|rs371149640|rs386695335	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr5:176026123A>G	ENST00000303991.4	-	2	890	c.713T>C	c.(712-714)tTg>tCg	p.L238S		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	238				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACCTTTCTCAAAGACCCAGG	0.488																																																0			5											91	95	94					5																	176026123		2116	4165	6281	175958729	SO:0001583	missense	114787			AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.713T>C	5.37:g.176026123A>G	ENSP00000305839:p.Leu238Ser		175958729	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	37	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	A	0.426	-0.905972	0.02453	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08458	3.09	4.02	0.308	0.15815	.	.	.	.	.	T	0.05686	0.0149	L	0.45698	1.435	0.09310	N	1	B	0.32573	0.376	B	0.30401	0.115	T	0.38351	-0.9665	9	0.09338	T	0.73	-0.2075	3.0934	0.06301	0.4377:0.0:0.3657:0.1966	.	238	Q7Z2K8	GRIN1_HUMAN	S	238	ENSP00000305839:L238S	ENSP00000305839:L238S	L	-	2	0	GPRIN1	175958729	0.000000	0.05858	0.009000	0.14445	0.480000	0.33159	0.211000	0.17474	0.402000	0.25451	0.260000	0.18958	TTG		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		G	176026123	A	G	176026123	3	3	118	1	0	0	0	0	1	0	0	0	6750	131	5	4	2317	4	GPRIN1	5	176026123	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	2989773	176026123	4889137	75	31338										
DUSP22	56940	hgsc.bcm.edu	37	chr6	348819	348819	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gagagccctttgcaggatgcAgaagaagccaaaaacattct	10	9	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:348819A>G	ENST00000344450.5	+	7	929	c.486A>G	c.(484-486)gcA>gcG	p.A162A	DUSP22_ENST00000419235.2_Silent_p.A162A|DUSP22_ENST00000605035.1_3'UTR|DUSP22_ENST00000605315.1_Silent_p.A59A|DUSP22_ENST00000603453.1_Silent_p.A59A|DUSP22_ENST00000604971.1_Silent_p.A59A	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	162					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGCAGGATGCAGAAGAAGCCA	0.557																																																0			6											131	119	123					6																	348819		2203	4300	6503	293819	SO:0001819	synonymous_variant	56940			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.486A>G	6.37:g.348819A>G			293819	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Silent	SNP	ENST00000344450.5	37	CCDS4468.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.767114	0.31320	.	.	ENSG00000112679	ENST00000419235	.	.	.	4.8	-5.38	0.02673	.	.	.	.	.	T	0.17789	0.0427	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40887	-0.9539	4	.	.	.	.	0.3071	0.00282	0.3623:0.219:0.2058:0.2129	.	.	.	.	G	100	.	.	R	+	1	2	DUSP22	293819	0.033000	0.19621	0.935000	0.37517	0.981000	0.71138	-0.791000	0.04599	-1.177000	0.02744	0.533000	0.62120	AGA		0.557	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185		G	348819	A	G	348819	2	3	118	1	0	0	0	0	0	0	0	1	4832	175	7	4		4	DUSP22	6	348819	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10		348819	170766248	76	31339										
TRIM31	11074	hgsc.bcm.edu	37	chr6	30078241	30078241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tcacctccagcagctgcctgGgtggcatgttctgcttggtc	12	13	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:30078241G>A	ENST00000376734.3	-	4	853	c.728C>T	c.(727-729)cCc>cTc	p.P243L	TRIM31_ENST00000540829.1_Missense_Mutation_p.P243L|TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	243					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CAGCTGCCTGGGTGGCATGTT	0.557																																																0			6											147	134	139					6																	30078241		2203	4300	6503	30186220	SO:0001583	missense	11074			AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16289	protein-coding gene	gene with protein product		609316	"tripartite motif-containing 31"			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.728C>T	6.37:g.30078241G>A	ENSP00000365924:p.Pro243Leu		30186220	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.088606	0.55968	.	.	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.65732	-0.17;-0.17	3.49	3.49	0.39957	.	.	.	.	.	T	0.29716	0.0742	N	0.24115	0.695	0.09310	N	1	B	0.30439	0.279	B	0.30943	0.122	T	0.15009	-1.0452	9	0.41790	T	0.15	.	10.6926	0.45879	0.0:0.0:1.0:0.0	.	243	Q9BZY9	TRI31_HUMAN	L	243	ENSP00000365924:P243L;ENSP00000444311:P243L	ENSP00000365918:P243L	P	-	2	0	TRIM31	30186220	0.039000	0.19947	0.006000	0.13384	0.348000	0.29142	2.515000	0.45512	1.940000	0.56252	0.453000	0.30009	CCC		0.557	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2			A	30078241	G	A	30078241	3	1	118	1	0	0	0	0	1	0	0	0	16545	1232	43	3	573	3	TRIM31	6	30078241	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	29729422	30078241	141036826	77	31340										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524434	51524434	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggagctcatggtagaatacaGccaagagaagcttggaggta	14	6	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:51524434G>T	ENST00000371117.3	-	61	10765	c.10490C>A	c.(10489-10491)gCt>gAt	p.A3497D		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3497					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GTAGAATACAGCCAAGAGAAG	0.453																																																0			6											64	65	65					6																	51524434		2203	4300	6503	51632393	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10490C>A	6.37:g.51524434G>T	ENSP00000360158:p.Ala3497Asp		51632393	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257965	0.80246	.	.	ENSG00000170927	ENST00000371117	D	0.86562	-2.14	5.72	5.72	0.89469	.	0.158779	0.42821	D	0.000641	D	0.88070	0.6338	L	0.32530	0.975	0.80722	D	1	D	0.65815	0.995	D	0.64144	0.922	D	0.88654	0.3184	10	0.56958	D	0.05	.	18.8671	0.92296	0.0:0.0:1.0:0.0	.	3497	P08F94	PKHD1_HUMAN	D	3497	ENSP00000360158:A3497D	ENSP00000360158:A3497D	A	-	2	0	PKHD1	51632393	0.901000	0.30685	0.966000	0.40874	0.945000	0.59286	3.822000	0.55708	2.695000	0.91970	0.655000	0.94253	GCT		0.453	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51524434	G	T	51524434	3	4	118	1	0	0	0	0	1	0	0	0	12002	971	34	2	1762	2	PKHD1	6	51524434	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	21446193	51524434	119590633	78	31341										
DST	667	hgsc.bcm.edu	37	chr6	56505333	56505333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtctgttctgttgtcagtaTgcgtcctttgctgtacacag	10	9	3	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:56505333T>C	ENST00000361203.3	-	14	1472	c.1465A>G	c.(1465-1467)Ata>Gta	p.I489V	DST_ENST00000244364.6_Missense_Mutation_p.I163V|DST_ENST00000370765.6_Missense_Mutation_p.I163V|DST_ENST00000370754.5_Missense_Mutation_p.I667V|DST_ENST00000421834.2_Missense_Mutation_p.I489V|DST_ENST00000446842.2_Missense_Mutation_p.I163V|DST_ENST00000370769.4_Missense_Mutation_p.I489V|DST_ENST00000312431.6_Missense_Mutation_p.I489V|DST_ENST00000518935.1_Missense_Mutation_p.I163V|DST_ENST00000370788.2_Missense_Mutation_p.I489V			Q03001	DYST_HUMAN	dystonin	489					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GTTGTCAGTATGCGTCCTTTG	0.428																																																0			6											111	109	110					6																	56505333		2203	4300	6503	56613292	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1465A>G	6.37:g.56505333T>C	ENSP00000354508:p.Ile489Val		56613292	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	T	8.379	0.837149	0.16891	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935;ENST00000449297	D;D;D;D;D;D;D;D;D;D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07;-3.07	5.65	-4.89	0.03103	.	1.540830	0.03921	N	0.283513	T	0.58133	0.2101	N	0.03608	-0.345	0.09310	N	0.999992	B;B;B;B;B;B;B;B;B;B	0.15473	0.0;0.0;0.0;0.0;0.013;0.0;0.0;0.0;0.0;0.003	B;B;B;B;B;B;B;B;B;B	0.09377	0.001;0.0;0.0;0.0;0.004;0.0;0.0;0.0;0.0;0.002	T	0.60078	-0.7333	9	0.25106	T	0.35	.	2.8844	0.05657	0.0928:0.2964:0.2901:0.3207	.	518;489;489;667;605;163;163;163;489;163	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	V	163;667;489;489;163;489;489;489;163;529;163;163;667	ENSP00000244364:I163V;ENSP00000359790:I667V;ENSP00000359805:I489V;ENSP00000400883:I489V;ENSP00000393645:I163V;ENSP00000307959:I489V;ENSP00000359824:I489V;ENSP00000354508:I489V;ENSP00000404924:I163V;ENSP00000431030:I529V;ENSP00000359801:I163V;ENSP00000431003:I163V;ENSP00000393082:I667V	ENSP00000244364:I163V	I	-	1	0	DST	56613292	1.000000	0.71417	0.808000	0.32385	0.935000	0.57460	1.183000	0.32041	-0.536000	0.06298	-0.313000	0.08912	ATA		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56505333	T	C	56505333	3	2	118	1	0	0	0	0	1	0	0	0	4794	1464	51	4	19992	4	DST	6	56505333	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	4980899	56505333	114609734	79	31342										
SIM1	6492	hgsc.bcm.edu	37	chr6	100838889	100838889	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tactttgatactgctcagtaCgatatcggtcacctgattca	7	10	3	2	rs137870558		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:100838889C>T	ENST00000369208.3	-	12	2431	c.1649G>A	c.(1648-1650)cGt>cAt	p.R550H	SIM1_ENST00000262901.4_Missense_Mutation_p.R550H			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	550	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		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)		CTGCTCAGTACGATATCGGTC	0.428													C|||	1	0.000199681	0	0	5008	,	,		16431	0		0	False		,,,				2504	0.001															0			6						C	HIS/ARG	0,4406		0,0,2203	87	91	89		1649	5.9	1	6	dbSNP_134	89	2,8598	2.2+/-6.3	0,2,4298	no	missense	SIM1	NM_005068.2	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	550/767	100838889	2,13004	2203	4300	6503	100945610	SO:0001583	missense	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1649G>A	6.37:g.100838889C>T	ENSP00000358210:p.Arg550His		100945610	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.632217	0.29068	0.0	2.33E-4	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.32515	1.45;1.45	5.9	5.9	0.94986	Single-minded, C-terminal (2);	0.092906	0.85682	D	0.000000	T	0.09862	0.0242	N	0.12182	0.205	0.58432	D	0.999997	B	0.09022	0.002	B	0.08055	0.003	T	0.06770	-1.0808	10	0.36615	T	0.2	.	14.4259	0.67215	0.0:0.9302:0.0:0.0698	.	550	P81133	SIM1_HUMAN	H	550	ENSP00000358210:R550H;ENSP00000262901:R550H	ENSP00000262901:R550H	R	-	2	0	SIM1	100945610	0.920000	0.31207	0.993000	0.49108	0.990000	0.78478	1.881000	0.39638	2.788000	0.95919	0.650000	0.86243	CGT		0.428	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		T	100838889	C	T	100838889	3	4	118	1	0	0	0	0	1	0	0	0	14360	536	19	1	655	1	SIM1	6	100838889	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	44333556	100838889	70276178	80	31343										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119399306	119399306	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccgtcgctgccccccttacCttggtgagctgggcgatttt	11	15	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:119399306C>T	ENST00000338891.7	-	1	602	c.159G>A	c.(157-159)aaG>aaA	p.K53K	FAM184A_ENST00000521531.1_Splice_Site_p.K53K|FAM184A_ENST00000352896.5_Intron|FAM184A_ENST00000368475.4_Intron|FAM184A_ENST00000522284.1_Intron	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	53						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CCCCCCTTACCTTGGTGAGCT	0.701																																																0			6											20	22	21					6																	119399306		1986	4159	6145	119441005	SO:0001630	splice_region_variant	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.159+1G>A	6.37:g.119399306C>T			119441005	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																				0.701	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	Silent	T	119399306	C	T	119399306	5	4	118	1	0	0	0	0	0	0	1	0	5527	695	24	3	3335	3	FAM184A	6	119399306	Splice_Site	SNP	C	TCGA-F5-6811-01A-11D-1826-10	18560417	119399306	51715761	81	31344										
MRPL18	29074	hgsc.bcm.edu	37	chr6	160211646	160211648	+	In_Frame_Del	DEL	GTT	GTT	-													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cttcggtcgcggttttggggGttgttctcggtttgcaggaa					rs58504486|rs79336325	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	GTT	GTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr6:160211646_160211648delGTT	ENST00000367034.4	+	1	149_151	c.27_29delGTT	c.(25-30)gggttg>ggg	p.L10del	TCP1_ENST00000420894.2_5'Flank|TCP1_ENST00000546023.1_5'Flank|TCP1_ENST00000544255.1_5'Flank|MRPL18_ENST00000480842.1_3'UTR|TCP1_ENST00000321394.7_5'Flank|TCP1_ENST00000392168.2_5'Flank	NM_014161.3	NP_054880.2	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18	10				Missing (in Ref. 2; AAF29043). {ECO:0000305}.	rRNA import into mitochondrion (GO:0035928)|translation (GO:0006412)	extracellular space (GO:0005615)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	11		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		GGTTTTGGGGGTTGTTCTCGGTT	0.571														3331	0.665136	0.4818	0.8285	5008	,	,		17145	0.5883		0.7575	False		,,,				2504	0.7812															0			6								2244,2020		587,1070,475						2.9	0		dbSNP_130	101	6166,2086		2314,1538,274	no	coding	MRPL18	NM_014161.3		2901,2608,749	A1A1,A1R,RR		25.2787,47.3734,32.806				8410,4106				160131638	SO:0001651	inframe_deletion	29074			AF161556	CCDS5270.1	6q25.3	2012-09-13			ENSG00000112110	ENSG00000112110		"Mitochondrial ribosomal proteins / large subunits"	14477	protein-coding gene	gene with protein product		611831				11042152, 11551941	Standard	NM_014161		Approved	HSPC071	uc003qsw.4	Q9H0U6	OTTHUMG00000015942	ENST00000367034.4:c.27_29delGTT	6.37:g.160211649_160211651delGTT	ENSP00000356001:p.Leu10del		160131636	Q5TAP9|Q9NZW8	In_Frame_Del	DEL	ENST00000367034.4	37	CCDS5270.1																																																																																				0.571	MRPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042925.1			-	160211648	GTT	-	160211646	7	5	118	1	0	1	0	1	0	0	0	0	9813	1248	44	0	29	0	MRPL18	6	160211646	In_Frame_Del	DEL	GTT	TCGA-F5-6811-01A-11D-1826-10	40812340	160211646	10903421	82	31345										
CARD11	84433	hgsc.bcm.edu	37	chr7	2958154	2958154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccgcagggtgtggtgggtgcCgtctacctcctcccggctgc	15	15	1	0	rs368181734	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:2958154C>T	ENST00000396946.4	-	19	2981	c.2578G>A	c.(2578-2580)Ggc>Agc	p.G860S		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	860					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TGGTGGGTGCCGTCTACCTCC	0.667			Mis		DLBCL								C|||	5	0.000998403	0	0	5008	,	,		15292	0		0	False		,,,				2504	0.0051						Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	0			7						C	SER/GLY	0,4130		0,0,2065	22	19	20		2578	-7.1	0	7		20	1,8037		0,1,4018	no	missense	CARD11	NM_032415.4	56	0,1,6083	TT,TC,CC		0.0124,0.0,0.0082	benign	860/1155	2958154	1,12167	2065	4019	6084	2924680	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2578G>A	7.37:g.2958154C>T	ENSP00000380150:p.Gly860Ser		2924680	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.466329	0.01053	0.0	1.24E-4	ENSG00000198286	ENST00000396946	T	0.28454	1.61	4.67	-7.13	0.01532	.	2.683750	0.02112	N	0.054864	T	0.12263	0.0298	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21759	-1.0236	10	0.08837	T	0.75	-0.805	6.3159	0.21190	0.0:0.3758:0.2542:0.37	.	860	Q9BXL7	CAR11_HUMAN	S	860	ENSP00000380150:G860S	ENSP00000380150:G860S	G	-	1	0	CARD11	2924680	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.519000	0.22862	-1.822000	0.01211	-0.479000	0.04858	GGC		0.667	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2958154	C	T	2958154	3	4	118	1	0	0	0	0	1	0	0	0	2651	652	23	1	914	1	CARD11	7	2958154	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		2958154	156180509	83	31346										
CARD11	84433	hgsc.bcm.edu	37	chr7	2983959	2983959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caccttgaccagctcgtcatTgtagctgtcccgctcttcct	7	16	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:2983959T>C	ENST00000396946.4	-	5	974	c.571A>G	c.(571-573)Aat>Gat	p.N191D	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	191					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		AGCTCGTCATTGTAGCTGTCC	0.552			Mis		DLBCL																																		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	0			7											262	159	194					7																	2983959		2203	4300	6503	2950485	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.571A>G	7.37:g.2983959T>C	ENSP00000380150:p.Asn191Asp		2950485	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.15	3.559359	0.65538	.	.	ENSG00000198286	ENST00000396946	T	0.33865	1.39	4.36	4.36	0.52297	.	0.053045	0.85682	D	0.000000	T	0.28995	0.0720	L	0.40543	1.245	0.46478	D	0.999068	B	0.29378	0.243	B	0.23275	0.045	T	0.07616	-1.0763	10	0.35671	T	0.21	-30.901	13.8596	0.63552	0.0:0.0:0.0:1.0	.	191	Q9BXL7	CAR11_HUMAN	D	191	ENSP00000380150:N191D	ENSP00000380150:N191D	N	-	1	0	CARD11	2950485	1.000000	0.71417	0.987000	0.45799	0.991000	0.79684	7.484000	0.81180	1.736000	0.51660	0.459000	0.35465	AAT		0.552	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2983959	T	C	2983959	3	2	118	1	0	0	0	0	1	0	0	0	2651	1812	63	4	2977	4	CARD11	7	2983959	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	25805	2983959	156154704	84	31347										
PMS2	5395	hgsc.bcm.edu	37	chr7	6038886	6038886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atacagtatgcatgtaagacCtggaccattttggcatactc	8	9	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:6038886C>T	ENST00000265849.7	-	6	663	c.558G>A	c.(556-558)caG>caA	p.Q186Q	PMS2_ENST00000406569.3_Silent_p.Q186Q|PMS2_ENST00000441476.2_Silent_p.Q80Q|PMS2_ENST00000382321.4_Silent_p.Q186Q|PMS2_ENST00000469652.1_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	186					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		CATGTAAGACCTGGACCATTT	0.393			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	0			7											135	123	127					7																	6038886		2203	4300	6503	6005412	SO:0001819	synonymous_variant	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.558G>A	7.37:g.6038886C>T			6005412	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.393	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		T	6038886	C	T	6038886	2	4	118	1	0	0	0	0	0	0	0	1	12174	680	24	3		3	PMS2	7	6038886	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	3054927	6038886	153099777	85	31348										
MIOS	54468	hgsc.bcm.edu	37	chr7	7646629	7646629	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tttgacctatttttttagggAccatgcagagtgccctgtgt	10	8	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:7646629A>T	ENST00000340080.4	+	13	2955	c.2534A>T	c.(2533-2535)gAc>gTc	p.D845V	MIOS_ENST00000405785.1_Missense_Mutation_p.D845V	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	845						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTTTTAGGGACCATGCAGAG	0.368																																																0			7											81	77	78					7																	7646629		1848	4096	5944	7613154	SO:0001583	missense	54468				CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.2534A>T	7.37:g.7646629A>T	ENSP00000339881:p.Asp845Val		7613154	B2RTV6|O75216|Q7L551|Q9H092	Missense_Mutation	SNP	ENST00000340080.4	37	CCDS43554.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726169	0.48833	.	.	ENSG00000164654	ENST00000340080;ENST00000405785	T;T	0.45668	0.89;0.89	5.11	5.11	0.69529	.	0.091916	0.85682	D	0.000000	T	0.38719	0.1051	L	0.55990	1.75	0.80722	D	1	B;B	0.19706	0.038;0.038	B;B	0.25614	0.062;0.062	T	0.28522	-1.0041	10	0.46703	T	0.11	-18.2541	9.8198	0.40876	0.9234:0.0:0.0766:0.0	.	845;845	B4DGE7;Q9NXC5	.;MIO_HUMAN	V	845	ENSP00000339881:D845V;ENSP00000384088:D845V	ENSP00000339881:D845V	D	+	2	0	MIOS	7613154	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.902000	0.75699	2.270000	0.75569	0.533000	0.62120	GAC		0.368	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		T	7646629	A	T	7646629	3	4	118	1	0	0	0	0	1	0	0	0	9619	275	10	5	2572	5	MIOS	7	7646629	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	1607743	7646629	151492034	86	31349										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21847577	21847577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtggagatgttcttctcacGgcggcatttgtgtcttacgt	12	8	3	1	rs559218045	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:21847577G>A	ENST00000409508.3	+	63	10273	c.10242G>A	c.(10240-10242)acG>acA	p.T3414T	DNAH11_ENST00000328843.6_Silent_p.T3421T	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3421					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTCTTCTCACGGCGGCATTTG	0.478									Kartagener syndrome				G|||	2	0.000399361	0	0	5008	,	,		18307	0		0	False		,,,				2504	0.002															0			7											63	63	63					7																	21847577		1918	4127	6045	21814102	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10242G>A	7.37:g.21847577G>A			21814102	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37																																																																																					0.478	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21847577	G	A	21847577	2	1	118	1	0	0	0	0	0	0	0	1	4610	1103	39	1		1	DNAH11	7	21847577	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	14200948	21847577	137291086	87	31350										
GHRHR	2692	hgsc.bcm.edu	37	chr7	31008526	31008526	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	agtgcctgtctacaagcagcAgaggagatgcccaacaccac	10	13	1	2	rs201978703		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:31008526A>G	ENST00000326139.2	+	2	181	c.135A>G	c.(133-135)gcA>gcG	p.A45A	GHRHR_ENST00000409316.1_5'Flank|GHRHR_ENST00000409904.3_5'Flank	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	45			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	TACAAGCAGCAGAGGAGATGC	0.542																																																0			7											120	98	106					7																	31008526		2203	4300	6503	30975051	SO:0001819	synonymous_variant	2692				CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"GPCR / Class B : Glucagon receptors"	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.135A>G	7.37:g.31008526A>G			30975051	Q99863	Silent	SNP	ENST00000326139.2	37	CCDS5432.1																																																																																				0.542	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2			G	31008526	A	G	31008526	2	3	118	1	0	0	0	0	0	0	0	1	6393	175	7	4		4	GHRHR	7	31008526	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	9160949	31008526	128130137	88	31351										
STARD3NL	83930	hgsc.bcm.edu	37	chr7	38256633	38256633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atgtgtcttgcagttgacaaCggcagtgaccagtgcctttt	11	9	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:38256633C>T	ENST00000009041.7	+	5	646	c.389C>T	c.(388-390)aCg>aTg	p.T130M	STARD3NL_ENST00000544203.1_Missense_Mutation_p.T123M|STARD3NL_ENST00000434197.1_Intron|STARD3NL_ENST00000396013.1_Missense_Mutation_p.T130M	NM_032016.3	NP_114405.1	O95772	MENTO_HUMAN	STARD3 N-terminal like	130	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.					endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.T130M(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10						CAGTTGACAACGGCAGTGACC	0.478																																																1	Substitution - Missense(1)	ovary(1)	7											298	259	272					7																	38256633		2203	4300	6503	38223158	SO:0001583	missense	83930			AJ492267	CCDS5455.1	7p14-p13	2003-02-06			ENSG00000010270	ENSG00000010270			19169	protein-coding gene	gene with protein product		611759				12393907	Standard	NM_032016		Approved	MENTHO, MGC3251	uc003tfr.3	O95772	OTTHUMG00000023659	ENST00000009041.7:c.389C>T	7.37:g.38256633C>T	ENSP00000009041:p.Thr130Met		38223158	A4D1X0	Missense_Mutation	SNP	ENST00000009041.7	37	CCDS5455.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.884854	0.91814	.	.	ENSG00000010270	ENST00000009041;ENST00000544203;ENST00000396013;ENST00000440144;ENST00000453225;ENST00000429075	T;T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16;0.16	5.79	5.79	0.91817	MENTAL domain (2);	0.000000	0.85682	D	0.000000	T	0.81029	0.4738	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83524	0.0087	10	0.66056	D	0.02	-19.5212	18.8126	0.92064	0.0:1.0:0.0:0.0	.	130	O95772	MENTO_HUMAN	M	130;123;130;130;130;130	ENSP00000009041:T130M;ENSP00000439436:T123M;ENSP00000379334:T130M;ENSP00000411933:T130M;ENSP00000395455:T130M;ENSP00000402028:T130M	ENSP00000009041:T130M	T	+	2	0	STARD3NL	38223158	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.202000	0.77856	2.739000	0.93911	0.655000	0.94253	ACG		0.478	STARD3NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226929.2			T	38256633	C	T	38256633	3	4	118	1	0	0	0	0	1	0	0	0	15297	536	19	1	403	1	STARD3NL	7	38256633	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	7248107	38256633	120882030	89	31352										
GCK	2645	hgsc.bcm.edu	37	chr7	44184850	44184850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cgcagctgggcgtcagcctgCgcacgctggcatggaaccgc	15	15	1	0	rs193922275|rs193922274		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:44184850C>T	ENST00000403799.3	-	10	1752	c.1283G>A	c.(1282-1284)cGc>cAc	p.R428H	GCK_ENST00000345378.2_Missense_Mutation_p.R429H|GCK_ENST00000437084.1_Missense_Mutation_p.R411H|GCK_ENST00000395796.3_Missense_Mutation_p.R427H	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	428	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						CGTCAGCCTGCGCACGCTGGC	0.662																																																0			7											26	29	28					7																	44184850		2203	4300	6503	44151375	SO:0001583	missense	5871			AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.1283G>A	7.37:g.44184850C>T	ENSP00000384247:p.Arg428His		44151375	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	37	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.814880	0.70912	.	.	ENSG00000106633	ENST00000336642;ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D;D	0.96967	-4.19;-4.19;-4.19;-4.19;-4.19	5.83	5.83	0.93111	Hexokinase, C-terminal (1);	0.186889	0.47093	D	0.000256	D	0.94076	0.8101	L	0.55213	1.73	0.49582	D	0.999804	B;B;B;B;B	0.24920	0.065;0.082;0.024;0.1;0.114	B;B;B;B;B	0.17722	0.007;0.007;0.002;0.019;0.01	D	0.90990	0.4834	10	0.48119	T	0.1	-43.1941	13.0101	0.58727	0.0:0.9257:0.0:0.0743	.	428;429;427;411;428	P35557;P35557-2;P35557-3;C9JQD1;A7LFL1	HXK4_HUMAN;.;.;.;.	H	112;428;427;429;411	ENSP00000338009:R112H;ENSP00000384247:R428H;ENSP00000379142:R427H;ENSP00000223366:R429H;ENSP00000402840:R411H	ENSP00000338009:R112H	R	-	2	0	GCK	44151375	0.605000	0.26941	1.000000	0.80357	0.847000	0.48162	3.381000	0.52455	2.756000	0.94617	0.561000	0.74099	CGC		0.662	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			T	44184850	C	T	44184850	3	4	118	1	0	0	0	0	1	0	0	0	6313	768	27	1	118	1	GCK	7	44184850	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	5928217	44184850	114953813	90	31353										
HUS1	3364	hgsc.bcm.edu	37	chr7	48007443	48007443	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tttacttgttgtccagcaagAaactgtaggagcttcctaat	8	8	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:48007443A>G	ENST00000258774.5	-	7	743	c.720T>C	c.(718-720)ttT>ttC	p.F240F	HUS1_ENST00000432325.1_Silent_p.F219F	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	240					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				GTCCAGCAAGAAACTGTAGGA	0.398								Direct reversal of damage;Other conserved DNA damage response genes																													Ovarian(103;466 1517 21788 34610 43890)											0			7											176	156	163					7																	48007443		2203	4300	6503	47973968	SO:0001819	synonymous_variant	3364			Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"hus1+-like protein"	603760	"HUS1 (S. pombe) checkpoint homolog"			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.720T>C	7.37:g.48007443A>G			47973968	B4DFI9	Silent	SNP	ENST00000258774.5	37	CCDS34635.1																																																																																				0.398	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507		G	48007443	A	G	48007443	2	3	118	1	0	0	0	0	0	0	0	1	7480	243	9	4		4	HUS1	7	48007443	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	3822593	48007443	111131220	91	31354										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63721253	63721253	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	acttgatcacctgtctggagCaaaataaagagccttggaat	9	8	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:63721253C>T	ENST00000421025.1	+	4	477	c.208C>T	c.(208-210)Caa>Taa	p.Q70*	ZNF679_ENST00000255746.4_Nonsense_Mutation_p.Q70*	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	70	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						CTGTCTGGAGCAAAATAAAGA	0.378																																																0			7											119	105	109					7																	63721253		692	1591	2283	63358688	SO:0001587	stop_gained	168417			BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.208C>T	7.37:g.63721253C>T	ENSP00000416809:p.Gln70*		63358688		Nonsense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	C	6.117	0.389913	0.11581	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	.	.	.	0.235	-0.47	0.12131	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	.	.	.	.	.	.	.	X	70	.	ENSP00000255746:Q70X	Q	+	1	0	ZNF679	63358688	0.115000	0.22152	0.030000	0.17652	0.032000	0.12392	-0.068000	0.11561	-0.808000	0.04387	-0.802000	0.03209	CAA		0.378	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		T	63721253	C	T	63721253	4	4	118	1	0	0	0	0	0	1	0	0	18125	711	25	3	218	3	ZNF679	7	63721253	Nonsense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	15713810	63721253	95417410	92	31355										
CDK14	5218	hgsc.bcm.edu	37	chr7	90741856	90741856	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cttttttgctcatgtttttaGgctcagctatgtgaaccatg	8	8	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:90741856G>T	ENST00000380050.3	+	13	1285		c.e13-1		CDK14_ENST00000436577.2_Splice_Site|CDK14_ENST00000265741.3_Splice_Site|CDK14_ENST00000406263.1_Splice_Site			O94921	CDK14_HUMAN	cyclin-dependent kinase 14						cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						CATGTTTTTAGGCTCAGCTAT	0.433																																					GBM(83;1228 1256 8311 16577 31299)											0			7											132	144	140					7																	90741856		2203	4300	6503	90579792	SO:0001630	splice_region_variant	0				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.1155-1G>T	7.37:g.90741856G>T			90579792	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Splice_Site	SNP	ENST00000380050.3	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.184567	0.78677	.	.	ENSG00000058091	ENST00000380050;ENST00000265741;ENST00000406263;ENST00000436577	.	.	.	5.97	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.19	0.86877	0.0:0.1261:0.8739:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDK14	90579792	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	8.819000	0.91997	1.507000	0.48752	0.655000	0.94253	.		0.433	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395	Intron	T	90741856	G	T	90741856	5	4	118	1	0	0	0	0	0	0	1	0	3136	1014	35	2	1146	2	CDK14	7	90741856	Splice_Site	SNP	G	TCGA-F5-6811-01A-11D-1826-10	27020603	90741856	68396807	93	31356										
MEPCE	56257	hgsc.bcm.edu	37	chr7	100028938	100028938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atccttcctgtgaggatgggCgccttcgggtgttgaagcct	14	10	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:100028938C>T	ENST00000310512.2	+	1	1685	c.1297C>T	c.(1297-1299)Cgc>Tgc	p.R433C	MEPCE_ENST00000414441.1_5'UTR|ZCWPW1_ENST00000324725.6_5'Flank|ZCWPW1_ENST00000360951.4_5'Flank|ZCWPW1_ENST00000398027.2_5'Flank	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	433	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGAGGATGGGCGCCTTCGGGT	0.562																																																0			7											79	71	73					7																	100028938		2203	4300	6503	99866874	SO:0001583	missense	56257			AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"bin3, bicoid-interacting 3, homolog (Drosophila)"	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.1297C>T	7.37:g.100028938C>T	ENSP00000308546:p.Arg433Cys		99866874	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	37	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306845	0.60305	.	.	ENSG00000146834	ENST00000310512	T	0.24723	1.84	4.83	2.87	0.33458	Bin3-type S-adenosyl-L-methionine binding domain (1);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	M	0.70108	2.13	0.80722	D	1	D	0.89917	1.0	P	0.61722	0.893	T	0.34129	-0.9841	10	0.87932	D	0	-15.1851	7.6137	0.28145	0.173:0.7329:0.0:0.0942	.	433	Q7L2J0	MEPCE_HUMAN	C	433	ENSP00000308546:R433C	ENSP00000308546:R433C	R	+	1	0	MEPCE	99866874	0.988000	0.35896	1.000000	0.80357	0.993000	0.82548	2.711000	0.47177	1.267000	0.44247	0.462000	0.41574	CGC		0.562	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			T	100028938	C	T	100028938	3	4	118	1	0	0	0	0	1	0	0	0	9507	768	27	1	1299	1	MEPCE	7	100028938	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	9287082	100028938	59109725	94	31357										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100160265	100160266	+	In_Frame_Ins	INS	-	-	GGC													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cgctccagtctgtcacgatgINSggcggcggcggcggcagcag							TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:100160265_100160266insGGC	ENST00000300176.4	+	8	1169_1170	c.1047_1048insGGC	c.(1048-1050)ggc>GGCggc	p.350_350G>GG	AGFG2_ENST00000474713.1_3'UTR|AGFG2_ENST00000262935.4_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	350					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTGTCACGATGGGCGGCGGCGG	0.649																																																0			7								0,4248		0,0,2124						-9.6	0			31	8,8230		0,8,4111	no	coding	AGFG2	NM_006076.4		0,8,6235	A1A1,A1R,RR		0.0971,0.0,0.0641				8,12478				99998202	SO:0001652	inframe_insertion	3268			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1060_1062dupGGC	7.37:g.100160272_100160274dupGGC	ENSP00000300176:p.Gly354dup		99998201	O75429|Q96AB9|Q96GL4	In_Frame_Ins	INS	ENST00000300176.4	37	CCDS5697.1																																																																																				0.649	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		GGC	100160266	-	GGC	100160265	7	5	118	1	0	1	1	0	0	0	0	0	381	1348	47	0	1077	0	AGFG2	7	100160265	In_Frame_Ins	INS	-	TCGA-F5-6811-01A-11D-1826-10	131327	100160265	58978398	95	31358										
ZNF277	11179	hgsc.bcm.edu	37	chr7	111936291	111936291	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aatctctcaacagaagaacaAgagaattattttttgttatg	6	5	2	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:111936291A>G	ENST00000361822.3	+	4	519	c.390A>G	c.(388-390)caA>caG	p.Q130Q	ZNF277_ENST00000450657.1_Silent_p.Q130Q	NM_021994.2	NP_068834.2	Q9NRM2	ZN277_HUMAN	zinc finger protein 277	130					cellular response to hydrogen peroxide (GO:0070301)|regulation of cellular senescence (GO:2000772)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			breast(4)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	15						CAGAAGAACAAGAGAATTATT	0.308																																																0			7											57	62	60					7																	111936291		2198	4283	6481	111723527	SO:0001819	synonymous_variant	11179			AF209198	CCDS5755.2	7q31.1	2012-10-05	2007-10-23	2007-10-23	ENSG00000198839	ENSG00000198839			13070	protein-coding gene	gene with protein product		605465	"zinc finger protein (C2H2 type) 277", "zinc finger protein 277 pseudogene"	ZNF277P		10860669, 16213364, 16395595	Standard	NM_021994		Approved	NRIF4	uc003vge.2	Q9NRM2	OTTHUMG00000150209	ENST00000361822.3:c.390A>G	7.37:g.111936291A>G			111723527	Q75MZ2|Q75MZ3|Q8WY14	Silent	SNP	ENST00000361822.3	37	CCDS5755.2																																																																																				0.308	ZNF277-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316843.2	NM_021994		G	111936291	A	G	111936291	2	3	118	1	0	0	0	0	0	0	0	1	17851	69	3	4		4	ZNF277	7	111936291	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	11776026	111936291	47202372	96	31359										
KCND2	3751	hgsc.bcm.edu	37	chr7	120373037	120373037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gagtggggtcttggtcattgCtctacctgttccggtgattg	14	8	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:120373037C>T	ENST00000331113.4	+	2	2161	c.1196C>T	c.(1195-1197)gCt>gTt	p.A399V		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	399					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TTGGTCATTGCTCTACCTGTT	0.448																																																0			7											185	158	168					7																	120373037		2203	4300	6503	120160273	SO:0001583	missense	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1196C>T	7.37:g.120373037C>T	ENSP00000333496:p.Ala399Val		120160273	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	36	5.645957	0.96704	.	.	ENSG00000184408	ENST00000331113	D	0.98862	-5.19	5.41	5.41	0.78517	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99236	0.9734	M	0.90198	3.095	0.58432	D	0.999995	P	0.51351	0.944	D	0.62955	0.909	D	0.99204	1.0874	9	.	.	.	.	18.807	0.92041	0.0:1.0:0.0:0.0	.	399	Q9NZV8	KCND2_HUMAN	V	399	ENSP00000333496:A399V	.	A	+	2	0	KCND2	120160273	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	7.783000	0.85696	2.530000	0.85305	0.655000	0.94253	GCT		0.448	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	120373037	C	T	120373037	3	4	118	1	0	0	0	0	1	0	0	0	8040	797	28	3	1202	3	KCND2	7	120373037	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	8436746	120373037	38765626	97	31360										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140287514	140287514	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtcagccccagcttagtctgCgcgtaccagtccaccctgct	9	17	2	0	rs201968906		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:140287514C>T	ENST00000275884.6	-	3	1479	c.1062G>A	c.(1060-1062)gcG>gcA	p.A354A	DENND2A_ENST00000496613.1_Silent_p.A354A|DENND2A_ENST00000492720.1_Silent_p.A354A|DENND2A_ENST00000537639.1_Silent_p.A354A			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	354					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					GCTTAGTCTGCGCGTACCAGT	0.493																																																0			7						C		1,4055		0,1,2027	85	89	87		1062	-6.2	1	7		87	0,8360		0,0,4180	no	coding-synonymous	DENND2A	NM_015689.3		0,1,6207	TT,TC,CC		0.0,0.0247,0.0081		354/1010	140287514	1,12415	2028	4180	6208	139933983	SO:0001819	synonymous_variant	27147			AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1062G>A	7.37:g.140287514C>T			139933983	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																				0.493	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		T	140287514	C	T	140287514	2	4	118	1	0	0	0	0	0	0	0	1	4440	755	27	1		1	DENND2A	7	140287514	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	19914477	140287514	18851149	98	31361										
BRAF	673	hgsc.bcm.edu	37	chr7	140481402	140481402	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	actttcccttgtagactgttCcaaatgatccagatccaatt	5	11	0	3	rs121913358|rs397516890|rs121913355		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:140481402C>G	ENST00000288602.6	-	11	1466	c.1406G>C	c.(1405-1407)gGa>gCa	p.G469A		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	469	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> A (in NHL; also in a lung adenocarcinoma sample; somatic mutation; elevated kinase activity; efficiently induces cell transformation). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:14612909, ECO:0000269|PubMed:17344846}.|G -> E (in CFC1 and colon cancer). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262, ECO:0000269|PubMed:19206169}.|G -> R (in NHL). {ECO:0000269|PubMed:14612909}.|G -> V (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G469A(19)|p.G469V(13)|p.G469S(5)|p.G469E(5)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	GTAGACTGTTCCAAATGATCC	0.373	G469A(NCIH1395_LUNG)|G469A(NCIH1755_LUNG)	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																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	42	Substitution - Missense(42)	lung(13)|large_intestine(9)|haematopoietic_and_lymphoid_tissue(6)|skin(6)|biliary_tract(2)|NS(2)|upper_aerodigestive_tract(1)|cervix(1)|small_intestine(1)|oesophagus(1)	7	GRCh37	CM060876	BRAF	M	rs121913355						174	149	158					7																	140481402		2203	4300	6503	140127871	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1406G>C	7.37:g.140481402C>G	ENSP00000288602:p.Gly469Ala		140127871	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.088365|5.088365	0.94100|0.94100	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.89415	.|-2.51	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92008|0.92008	0.7468|0.7468	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|D	.|0.59357	.|0.985	.|P	.|0.58210	.|0.835	D|D	0.92595|0.92595	0.6086|0.6086	5|10	.|0.87932	.|D	.|0	.|.	17.8428|17.8428	0.88720|0.88720	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|469	.|P15056	.|BRAF_HUMAN	Q|A	77|469	.|ENSP00000288602:G469A	.|ENSP00000288602:G469A	E|G	-|-	1|2	0|0	BRAF|BRAF	140127871|140127871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.818000|7.818000	0.86416|0.86416	2.637000|2.637000	0.89404|0.89404	0.585000|0.585000	0.79938|0.79938	GAA|GGA		0.373	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		G	140481402	C	G	140481402	3	3	118	1	0	0	0	0	1	0	0	0	1499	855	30	5	926	5	BRAF	7	140481402	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	193888	140481402	18657261	99	31362										
OR2A25	392138	hgsc.bcm.edu	37	chr7	143771517	143771517	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tctcacacctggcggtcgtcGacatcgcctgtgcttgcagc	11	15	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr7:143771517G>A	ENST00000408898.2	+	1	243	c.205G>A	c.(205-207)Gac>Aac	p.D69N		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					GGCGGTCGTCGACATCGCCTG	0.577																																																0			7											80	81	80					7																	143771517		2203	4300	6503	143402450	SO:0001583	missense	392138				CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"GPCR / Class A : Olfactory receptors"	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.205G>A	7.37:g.143771517G>A	ENSP00000386167:p.Asp69Asn		143402450	B2RNC9	Missense_Mutation	SNP	ENST00000408898.2	37	CCDS43669.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.515090	0.64634	.	.	ENSG00000221933	ENST00000408898	T	0.01165	5.24	4.88	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.10680	0.0261	M	0.93939	3.475	0.51482	D	0.999927	D	0.89917	1.0	D	0.85130	0.997	T	0.00465	-1.1723	9	0.87932	D	0	-9.9501	15.5662	0.76294	0.0:0.0:1.0:0.0	.	69	A4D2G3	O2A25_HUMAN	N	69	ENSP00000386167:D69N	ENSP00000386167:D69N	D	+	1	0	OR2A25	143402450	1.000000	0.71417	0.886000	0.34754	0.057000	0.15508	9.417000	0.97391	2.531000	0.85337	0.563000	0.77884	GAC		0.577	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1			A	143771517	G	A	143771517	3	1	118	1	0	0	0	0	1	0	0	0	11009	1058	37	1	207	1	OR2A25	7	143771517	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	3290115	143771517	15367146	100	31363										
FBXO25	26260	hgsc.bcm.edu	37	chr8	401363	401363	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	attagaggagtagggaagtcTgtattagtgggaaacatcaa	13	3	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr8:401363T>C	ENST00000276326.5	+	7	689	c.570T>C	c.(568-570)tcT>tcC	p.S190S	FBXO25_ENST00000382824.1_Silent_p.S123S|FBXO25_ENST00000352684.2_Silent_p.S123S|RP11-91J19.3_ENST00000607549.1_RNA|FBXO25_ENST00000350302.3_Silent_p.S190S	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	190					protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.S190S(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		TAGGGAAGTCTGTATTAGTGG	0.403																																																1	Substitution - coding silent(1)	lung(1)	8											122	119	120					8																	401363		2203	4300	6503	391363	SO:0001819	synonymous_variant	26260			AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"F-boxes /  "other""	13596	protein-coding gene	gene with protein product		609098	"F-box only protein 25"			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.570T>C	8.37:g.401363T>C			391363	Q6PJ83|Q7Z4V4|Q9UKB8	Silent	SNP	ENST00000276326.5	37	CCDS5953.1																																																																																				0.403	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173		C	401363	T	C	401363	2	2	118	1	0	0	0	0	0	0	0	1	5755	1567	55	4		4	FBXO25	8	401363	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10		401363	145962659	101	31364										
IMPAD1	54928	hgsc.bcm.edu	37	chr8	57878751	57878751	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cacaggaagaggaacataccAgcaccaccagctgggataat	10	11	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr8:57878751A>T	ENST00000262644.4	-	4	1065	c.807T>A	c.(805-807)gcT>gcA	p.A269A		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	269					chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				GGAACATACCAGCACCACCAG	0.498																																																0			8											132	108	116					8																	57878751		2203	4300	6503	58041305	SO:0001630	splice_region_variant	54928				CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331			26019	protein-coding gene	gene with protein product		614010				21549340	Standard	NM_017813		Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.808+1T>A	8.37:g.57878751A>T			58041305	Q6NVY7	Silent	SNP	ENST00000262644.4	37	CCDS6169.1																																																																																				0.498	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813	Silent	T	57878751	A	T	57878751	5	4	118	1	0	0	0	0	0	0	1	0	7746	202	7	5	280	5	IMPAD1	8	57878751	Splice_Site	SNP	A	TCGA-F5-6811-01A-11D-1826-10	57477388	57878751	88485271	102	31365										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68087633	68087633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cctgctaagagagcagcagaAgaggctgaacagaataaaaa	11	7	0	5			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr8:68087633A>G	ENST00000262210.5	+	24	3087	c.3056A>G	c.(3055-3057)aAg>aGg	p.K1019R	CSPP1_ENST00000412460.1_Missense_Mutation_p.K674R|CSPP1_ENST00000521168.1_3'UTR|ARFGEF1_ENST00000520381.1_3'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1054					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GAGCAGCAGAAGAGGCTGAAC	0.428																																																0			8											56	55	55					8																	68087633		1907	4120	6027	68250187	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3056A>G	8.37:g.68087633A>G	ENSP00000262210:p.Lys1019Arg		68250187	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.060839	0.36373	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.33438	1.41;1.44;1.44	4.8	2.1	0.27182	.	0.232657	0.35291	N	0.003310	T	0.17959	0.0431	N	0.25380	0.74	0.80722	D	1	B;B;B;B	0.14805	0.011;0.008;0.011;0.004	B;B;B;B	0.16722	0.016;0.009;0.016;0.011	T	0.08513	-1.0718	10	0.20046	T	0.44	-13.3239	7.5124	0.27581	0.7184:0.0:0.2816:0.0	.	177;674;1019;1054	Q9H688;Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;.;CSPP1_HUMAN	R	1019;1054;674;674	ENSP00000262210:K1019R;ENSP00000415782:K674R;ENSP00000430092:K674R	ENSP00000262210:K1019R	K	+	2	0	CSPP1	68250187	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	1.380000	0.34351	0.203000	0.20529	0.482000	0.46254	AAG		0.428	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68087633	A	G	68087633	3	3	118	1	0	0	0	0	1	0	0	0	3968	72	3	4	3263	4	CSPP1	8	68087633	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	10208882	68087633	78276389	103	31366										
FZD6	8323	hgsc.bcm.edu	37	chr8	104340565	104340565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgatgacattaattgttggcAtctctgctgtcttctgggtt	10	7	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr8:104340565A>G	ENST00000358755.4	+	5	1779	c.1462A>G	c.(1462-1464)Atc>Gtc	p.I488V	FZD6_ENST00000522566.1_Missense_Mutation_p.I488V|FZD6_ENST00000523739.1_Missense_Mutation_p.I456V|FZD6_ENST00000540287.1_Missense_Mutation_p.I183V	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	488					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			AATTGTTGGCATCTCTGCTGT	0.348																																																0			8											107	112	110					8																	104340565		2203	4300	6503	104409741	SO:0001583	missense	8323			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.1462A>G	8.37:g.104340565A>G	ENSP00000351605:p.Ile488Val		104409741	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.658957	0.88154	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000540287;ENST00000539487	D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89	5.45	5.45	0.79879	GPCR, family 2-like (1);	0.169147	0.53938	D	0.000046	D	0.91768	0.7396	M	0.76328	2.33	0.50171	D	0.99985	P;D;D;P	0.69078	0.891;0.996;0.997;0.938	P;D;D;P	0.80764	0.773;0.99;0.994;0.773	D	0.92209	0.5774	10	0.54805	T	0.06	.	15.8118	0.78571	1.0:0.0:0.0:0.0	.	433;183;488;488	B4E236;F5H831;B2R9H9;O60353	.;.;.;FZD6_HUMAN	V	488;488;456;183;433	ENSP00000429055:I488V;ENSP00000351605:I488V;ENSP00000429528:I456V;ENSP00000443757:I183V	ENSP00000351605:I488V	I	+	1	0	FZD6	104409741	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.056000	0.93881	2.194000	0.70268	0.383000	0.25322	ATC		0.348	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		G	104340565	A	G	104340565	3	3	118	1	0	0	0	0	1	0	0	0	6153	217	8	4	1476	4	FZD6	8	104340565	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	36252932	104340565	42023457	104	31367										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13205997	13205997	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atgagctcggcttcctgcttCattcctctcctcattagtgt	7	13	3	1	rs560846483		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr9:13205997C>A	ENST00000319217.7	-	11	1639	c.1392G>T	c.(1390-1392)atG>atT	p.M464I	MPDZ_ENST00000541718.1_Missense_Mutation_p.M464I|MPDZ_ENST00000381022.2_Missense_Mutation_p.M464I|MPDZ_ENST00000381015.4_Missense_Mutation_p.M464I|MPDZ_ENST00000536827.1_Missense_Mutation_p.M464I|MPDZ_ENST00000447879.1_Missense_Mutation_p.M464I|MPDZ_ENST00000546205.1_Missense_Mutation_p.M464I	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	464					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CTTCCTGCTTCATTCCTCTCC	0.433																																																0			9											181	172	175					9																	13205997		1941	4140	6081	13195997	SO:0001583	missense	84708			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1392G>T	9.37:g.13205997C>A	ENSP00000320006:p.Met464Ile		13195997	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	7.623	0.677144	0.14841	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16	6.17	-10.8	0.00216	.	1.641340	0.03802	N	0.264705	T	0.12475	0.0303	N	0.08118	0	0.53688	D	0.999977	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.0;0.0;0.001	T	0.12451	-1.0547	10	0.17832	T	0.49	.	2.9272	0.05788	0.179:0.1114:0.2181:0.4916	.	464;464;464	B7ZMI4;O75970-3;O75970-2	.;.;.	I	464	ENSP00000320006:M464I;ENSP00000439807:M464I;ENSP00000370410:M464I;ENSP00000444151:M464I;ENSP00000415208:M464I;ENSP00000370403:M464I;ENSP00000446358:M464I	ENSP00000320006:M464I	M	-	3	0	MPDZ	13195997	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.836000	0.00740	-1.826000	0.01205	-0.793000	0.03317	ATG		0.433	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13205997	C	A	13205997	3	1	118	1	0	0	0	0	1	0	0	0	9752	826	29	2	4877	2	MPDZ	9	13205997	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		13205997	128007434	105	31368										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632339	32632339	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gctgacattcctctttgtaaCgctcttgatgctcagccaca	7	13	3	2	rs201241616		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr9:32632339C>T	ENST00000242310.4	-	1	3328	c.3239G>A	c.(3238-3240)cGt>cAt	p.R1080H	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1080					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.R1080H(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTCTTTGTAACGCTCTTGATG	0.473													c|||	1	0.000199681	0	0	5008	,	,		23067	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	9						T	HIS/ARG	0,4406		0,0,2203	178	167	171		3239	-0.9	1	9	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TAF1L	NM_153809.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1080/1827	32632339	1,13005	2203	4300	6503	32622339	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3239G>A	9.37:g.32632339C>T	ENSP00000418379:p.Arg1080His		32622339	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	c	13.21	2.167696	0.38315	0.0	1.16E-4	ENSG00000122728	ENST00000242310	T	0.18174	2.23	0.479	-0.924	0.10462	.	0.047970	0.85682	D	0.000000	T	0.13286	0.0322	L	0.55481	1.735	0.51767	D	0.999931	B	0.18741	0.03	B	0.14578	0.011	T	0.05920	-1.0856	10	0.66056	D	0.02	.	4.8372	0.13471	0.0:0.7251:0.0:0.2749	.	1080	Q8IZX4	TAF1L_HUMAN	H	1080	ENSP00000418379:R1080H	ENSP00000418379:R1080H	R	-	2	0	TAF1L	32622339	0.998000	0.40836	0.981000	0.43875	0.686000	0.39977	2.492000	0.45311	-0.377000	0.07930	-1.051000	0.02340	CGT		0.473	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			T	32632339	C	T	32632339	3	4	118	1	0	0	0	0	1	0	0	0	15562	536	19	1	2245	1	TAF1L	9	32632339	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	19426342	32632339	108581092	106	31369										
PAX5	5079	hgsc.bcm.edu	37	chr9	36846903	36846903	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggaatactgagggtggctgtAgggactcccggaaaactcac	14	9	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr9:36846903A>G	ENST00000358127.4	-	9	1110	c.1036T>C	c.(1036-1038)Tac>Cac	p.Y346H	PAX5_ENST00000520154.1_Intron|PAX5_ENST00000377847.2_Intron|PAX5_ENST00000414447.1_Missense_Mutation_p.Y303H|PAX5_ENST00000522003.1_Missense_Mutation_p.Y238H|PAX5_ENST00000377852.2_Missense_Mutation_p.Y312H|PAX5_ENST00000523241.1_Silent_p.P268P|PAX5_ENST00000520281.1_Intron|PAX5_ENST00000377853.2_Intron|PAX5_ENST00000523145.1_Intron|PAX5_ENST00000446742.1_Missense_Mutation_p.Y246H	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	346					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(11)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GGGTGGCTGTAGGGACTCCCG	0.602			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	11	Unknown(11)	haematopoietic_and_lymphoid_tissue(11)	9											68	65	66					9																	36846903		2203	4300	6503	36836903	SO:0001583	missense	5079				CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"Paired boxes", "Homeoboxes / PRD class"	8619	protein-coding gene	gene with protein product	"B-cell lineage specific activator"	167414	"paired box gene 5 (B-cell lineage specific activator protein)", "paired box gene 5 (B-cell lineage specific activator)"			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.1036T>C	9.37:g.36846903A>G	ENSP00000350844:p.Tyr346His		36836903	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.369685	0.82573	.	.	ENSG00000196092	ENST00000358127;ENST00000377849;ENST00000377852;ENST00000446742;ENST00000522003;ENST00000414447;ENST00000524340	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.52	5.52	0.82312	.	0.201442	0.43747	D	0.000540	T	0.66127	0.2758	M	0.73217	2.22	0.80722	D	1	B;D;D;D;D	0.76494	0.151;0.999;0.999;0.997;0.997	B;D;D;D;D	0.87578	0.066;0.996;0.998;0.992;0.992	T	0.63756	-0.6565	10	0.25751	T	0.34	.	14.6275	0.68632	1.0:0.0:0.0:0.0	.	303;246;173;312;346	C0KTF7;C0KTF9;C0KTE2;Q6S731;Q02548	.;.;.;.;PAX5_HUMAN	H	346;257;312;246;238;303;173	ENSP00000350844:Y346H;ENSP00000367083:Y312H;ENSP00000404687:Y246H;ENSP00000429359:Y238H;ENSP00000412188:Y303H;ENSP00000429404:Y173H	ENSP00000350844:Y346H	Y	-	1	0	PAX5	36836903	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.732000	0.84908	2.091000	0.63221	0.459000	0.35465	TAC		0.602	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			G	36846903	A	G	36846903	3	3	118	1	0	0	0	0	1	0	0	0	11513	420	15	4	147	4	PAX5	9	36846903	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	4214564	36846903	104366528	107	31370										
OR13C8	138802	hgsc.bcm.edu	37	chr9	107332185	107332185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cacctgctcagcccacctgaCagtggtgattatattctatg	8	12	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr9:107332185C>T	ENST00000335040.1	+	1	737	c.737C>T	c.(736-738)aCa>aTa	p.T246I		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						GCCCACCTGACAGTGGTGATT	0.428																																																0			9											122	113	116					9																	107332185		2203	4300	6503	106372006	SO:0001583	missense	138802				CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"GPCR / Class A : Olfactory receptors"	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.737C>T	9.37:g.107332185C>T	ENSP00000334068:p.Thr246Ile		106372006	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.646723	0.29246	.	.	ENSG00000186943	ENST00000335040	T	0.36157	1.27	4.9	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.36744	0.0978	M	0.64260	1.97	0.09310	N	1	B	0.29590	0.25	B	0.37346	0.247	T	0.25710	-1.0124	10	0.33141	T	0.24	.	7.6298	0.28232	0.0:0.8115:0.0:0.1885	.	246	Q8NGS7	O13C8_HUMAN	I	246	ENSP00000334068:T246I	ENSP00000334068:T246I	T	+	2	0	OR13C8	106372006	0.000000	0.05858	0.989000	0.46669	0.994000	0.84299	0.421000	0.21280	1.421000	0.47157	0.561000	0.74099	ACA		0.428	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1			T	107332185	C	T	107332185	3	4	118	1	0	0	0	0	1	0	0	0	10969	478	17	3	739	3	OR13C8	9	107332185	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	70485282	107332185	33881246	108	31371										
NUP188	23511	hgsc.bcm.edu	37	chr9	131745577	131745577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttgttctccaaccaggttaaCgacagtgatctccccacctg	7	14	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr9:131745577C>T	ENST00000372577.2	+	18	1823	c.1802C>T	c.(1801-1803)aCg>aTg	p.T601M		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	601					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						ACCAGGTTAACGACAGTGATC	0.453																																																0			9											194	183	186					9																	131745577		2203	4300	6503	130785398	SO:0001583	missense	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1802C>T	9.37:g.131745577C>T	ENSP00000361658:p.Thr601Met		130785398	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.778464	0.70107	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.64991	-0.13	5.43	5.43	0.79202	.	0.046875	0.85682	D	0.000000	T	0.66906	0.2837	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.69939	-0.5009	10	0.46703	T	0.11	-6.0591	18.5867	0.91192	0.0:1.0:0.0:0.0	.	601	Q5SRE5	NU188_HUMAN	M	490;601	ENSP00000361658:T601M	ENSP00000349125:T490M	T	+	2	0	NUP188	130785398	1.000000	0.71417	0.947000	0.38551	0.752000	0.42762	7.256000	0.78350	2.708000	0.92522	0.563000	0.77884	ACG		0.453	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131745577	C	T	131745577	3	4	118	1	0	0	0	0	1	0	0	0	10789	536	19	1	1872	1	NUP188	9	131745577	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	24413392	131745577	9467854	109	31372										
CUBN	8029	hgsc.bcm.edu	37	chr10	17153023	17153023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctcacattcattgatatcttCgcaaatatatccattgcctt	3	11	3	1	rs78201384	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:17153023C>T	ENST00000377833.4	-	9	975	c.910G>A	c.(910-912)Gaa>Aaa	p.E304K		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	304	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.E304K(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTGATATCTTCGCAAATATAT	0.438													C|||	46	0.0091853	0	0.0058	5008	,	,		17195	0.0327		0	False		,,,				2504	0.0092															1	Substitution - Missense(1)	urinary_tract(1)	10						C	LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	100	97	98		910	-4.2	0	10	dbSNP_131	98	0,8600		0,0,4300	yes	missense	CUBN	NM_001081.3	56	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	304/3624	17153023	3,13003	2203	4300	6503	17193029	SO:0001583	missense	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.910G>A	10.37:g.17153023C>T	ENSP00000367064:p.Glu304Lys		17193029	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	16	0.027972027972027972	0	0.0	C	13.79	2.342338	0.41498	6.81E-4	0.0	ENSG00000107611	ENST00000377833	D	0.95622	-3.76	5.83	-4.25	0.03766	Growth factor, receptor (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.882805	0.09536	N	0.788951	D	0.84451	0.5475	L	0.45744	1.44	0.80722	D	1	B	0.33120	0.398	B	0.22152	0.038	T	0.73260	-0.4039	10	0.29301	T	0.29	.	26.5331	0.99996	0.0:0.7354:0.2646:0.0	.	304	O60494	CUBN_HUMAN	K	304	ENSP00000367064:E304K	ENSP00000367064:E304K	E	-	1	0	CUBN	17193029	0.551000	0.26497	0.028000	0.17463	0.584000	0.36387	0.706000	0.25690	-0.507000	0.06549	0.650000	0.86243	GAA		0.438	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17153023	C	T	17153023	3	4	118	1	0	0	0	0	1	0	0	0	4057	893	31	1	10197	1	CUBN	10	17153023	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		17153023	118381724	110	31373										
FAM35A	54537	hgsc.bcm.edu	37	chr10	88911655	88911655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cagctgtgttggatttggttTgtagtactgaaaaaattaat	10	3	0	1	rs148112938		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:88911655T>C	ENST00000298784.1	+	3	658	c.544T>C	c.(544-546)Tgt>Cgt	p.C182R	FAM35A_ENST00000298786.4_Missense_Mutation_p.C182R|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	182										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						GGATTTGGTTTGTAGTACTGA	0.363																																					Ovarian(175;703 2004 25460 32514 43441)											0			10						T	ARG/CYS	0,3982		0,0,1991	23	25	25		544	3.1	0	10	dbSNP_134	25	1,7881		0,1,3940	no	missense	FAM35A	NM_019054.2	180	0,1,5931	CC,CT,TT		0.0127,0.0,0.0084	benign	182/836	88911655	1,11863	1991	3941	5932	88901635	SO:0001583	missense	54537			BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.544T>C	10.37:g.88911655T>C	ENSP00000298784:p.Cys182Arg		88901635	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	t	13.94	2.388321	0.42308	0.0	1.27E-4	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.24538	1.85;1.85;1.85	4.23	3.07	0.35406	.	0.510762	0.16503	N	0.211575	T	0.25005	0.0607	L	0.50333	1.59	0.09310	N	0.999991	P	0.39157	0.662	B	0.42422	0.387	T	0.13602	-1.0503	10	0.56958	D	0.05	-0.1512	5.3425	0.15990	0.0:0.0975:0.3939:0.5086	.	182	Q86V20	FA35A_HUMAN	R	182	ENSP00000298786:C182R;ENSP00000298784:C182R;ENSP00000351064:C182R	ENSP00000298784:C182R	C	+	1	0	FAM35A	88901635	0.000000	0.05858	0.001000	0.08648	0.513000	0.34164	0.401000	0.20948	0.652000	0.30806	0.438000	0.28831	TGT		0.363	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		C	88911655	T	C	88911655	3	2	118	1	0	0	0	0	1	0	0	0	5572	1812	63	4	546	4	FAM35A	10	88911655	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	71758632	88911655	46623092	111	31374										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624302	89624302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	atggattcgacttagacttgAcctgtatccatttctgcggc	9	10	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:89624302A>G	ENST00000371953.3	+	1	1433	c.76A>G	c.(76-78)Acc>Gcc	p.T26A	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	26	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.T26P(2)|p.L25fs*28(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		CTTAGACTTGACCTGTATCCA	0.458		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Unknown(13)|Substitution - Missense(2)|Deletion - Frameshift(1)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|endometrium(3)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	10											159	152	154					10																	89624302		2203	4300	6503	89614282	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.76A>G	10.37:g.89624302A>G	ENSP00000361021:p.Thr26Ala		89614282	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.442635	0.63067	.	.	ENSG00000171862	ENST00000371953	D	0.98617	-5.03	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.054781	0.64402	D	0.000001	D	0.97417	0.9155	M	0.72479	2.2	0.80722	D	1	B	0.20368	0.044	B	0.18561	0.022	D	0.96696	0.9514	9	.	.	.	-0.0938	14.1807	0.65572	1.0:0.0:0.0:0.0	.	26	P60484	PTEN_HUMAN	A	26	ENSP00000361021:T26A	.	T	+	1	0	PTEN	89614282	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.379000	0.90146	1.996000	0.58369	0.459000	0.35465	ACC		0.458	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89624302	A	G	89624302	3	3	118	1	0	0	0	0	1	0	0	0	12772	275	10	4	78	4	PTEN	10	89624302	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	712647	89624302	45910445	112	31375										
PTEN	5728	hgsc.bcm.edu	37	chr10	89725211	89725211	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tttgatgaagatcagcatacAcaaattacaaaagtctgaat	6	6	2	4			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:89725211A>G	ENST00000371953.3	+	9	2551	c.1194A>G	c.(1192-1194)acA>acG	p.T398T		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	398					activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		ATCAGCATACACAAATTACAA	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	47	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)	prostate(16)|central_nervous_system(10)|skin(5)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											16	17	16					10																	89725211		2161	4272	6433	89715191	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1194A>G	10.37:g.89725211A>G			89715191	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89725211	A	G	89725211	2	3	118	1	0	0	0	0	0	0	0	1	12772	146	6	4		4	PTEN	10	89725211	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	100909	89725211	45809536	113	31376										
POLL	27343	hgsc.bcm.edu	37	chr10	103345880	103345880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gggctcgtccaatgccagtgCgcacaacatgggcccgaagg	14	13	0	0	rs548269958	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:103345880C>T	ENST00000370162.3	-	3	643	c.149G>A	c.(148-150)cGc>cAc	p.R50H	POLL_ENST00000436284.2_5'UTR|POLL_ENST00000456836.2_Intron|POLL_ENST00000339310.3_Intron|DPCD_ENST00000370148.2_5'Flank|POLL_ENST00000370172.1_5'UTR|DPCD_ENST00000370151.4_5'Flank|DPCD_ENST00000370147.1_5'Flank|POLL_ENST00000299206.4_Missense_Mutation_p.R50H|DPCD_ENST00000416979.2_Intron|DPCD_ENST00000470165.1_Intron|POLL_ENST00000370169.1_Missense_Mutation_p.R50H|POLL_ENST00000370168.3_5'Flank|POLL_ENST00000370158.3_Intron	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	50	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		AATGCCAGTGCGCACAACATG	0.547								DNA polymerases (catalytic subunits)					C|||	2	0.000399361	0	0	5008	,	,		18635	0		0	False		,,,				2504	0.002															0			10											37	36	37					10																	103345880		2203	4300	6503	103335870	SO:0001583	missense	27343			AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"DNA polymerases"	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.149G>A	10.37:g.103345880C>T	ENSP00000359181:p.Arg50His		103335870	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Missense_Mutation	SNP	ENST00000370162.3	37	CCDS7513.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032181	0.54790	.	.	ENSG00000166169	ENST00000299206;ENST00000370174;ENST00000370169;ENST00000370162;ENST00000370157;ENST00000415897;ENST00000426919;ENST00000413344;ENST00000430045	T;T;T;T;T;T;T	0.79554	2.76;2.76;2.76;2.28;1.54;0.96;-1.28	5.59	4.68	0.58851	BRCT (2);	0.107348	0.64402	D	0.000004	T	0.56292	0.1975	N	0.08118	0	0.80722	D	1	B;P	0.40000	0.015;0.698	B;B	0.28638	0.002;0.092	T	0.59440	-0.7454	10	0.37606	T	0.19	-24.8613	9.0845	0.36572	0.0:0.1231:0.6056:0.2712	.	50;50	Q9UGP5;A8K860	DPOLL_HUMAN;.	H	50;50;50;50;50;50;61;50;50	ENSP00000299206:R50H;ENSP00000359188:R50H;ENSP00000359181:R50H;ENSP00000400676:R50H;ENSP00000411678:R61H;ENSP00000400517:R50H;ENSP00000414293:R50H	ENSP00000299206:R50H	R	-	2	0	POLL	103335870	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.794000	0.47853	1.373000	0.46208	-0.311000	0.09066	CGC		0.547	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274		T	103345880	C	T	103345880	3	4	118	1	0	0	0	0	1	0	0	0	12236	768	27	1	1606	1	POLL	10	103345880	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	13620669	103345880	32188867	114	31377										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123258041	123258041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aggctccaagaagatttatgAtattcttgtgtttcccaatc	7	8	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr10:123258041A>G	ENST00000358487.5	-	12	1912	c.1640T>C	c.(1639-1641)aTc>aCc	p.I547T	FGFR2_ENST00000356226.4_Missense_Mutation_p.I430T|FGFR2_ENST00000369061.4_Missense_Mutation_p.I435T|FGFR2_ENST00000478859.1_Missense_Mutation_p.I319T|FGFR2_ENST00000346997.2_Missense_Mutation_p.I545T|FGFR2_ENST00000457416.2_Missense_Mutation_p.I548T|FGFR2_ENST00000369060.4_Missense_Mutation_p.I431T|FGFR2_ENST00000360144.3_Missense_Mutation_p.I459T|FGFR2_ENST00000351936.6_Missense_Mutation_p.I545T|FGFR2_ENST00000369056.1_Missense_Mutation_p.I548T|FGFR2_ENST00000369059.1_Missense_Mutation_p.I433T|FGFR2_ENST00000357555.5_Missense_Mutation_p.I458T	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	547	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	AAGATTTATGATATTCTTGTG	0.408		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											171	153	159					10																	123258041		2203	4300	6503	123248031	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1640T>C	10.37:g.123258041A>G	ENSP00000351276:p.Ile547Thr		123248031	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361038	0.82353	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51	5.02	5.02	0.67125	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97688	0.9242	M	0.91196	3.185	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.998;0.999;1.0;0.996;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D	0.97110	0.996;0.996;1.0;0.967;0.998;0.995;0.996;0.992	D	0.98720	1.0708	10	0.87932	D	0	.	14.7307	0.69379	1.0:0.0:0.0:0.0	.	564;546;458;430;547;459;548;450	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	T	458;548;435;547;430;431;433;139;545;548;545;459;548;548;456	ENSP00000350166:I458T;ENSP00000358057:I435T;ENSP00000351276:I547T;ENSP00000348559:I430T;ENSP00000358056:I431T;ENSP00000358055:I433T;ENSP00000404219:I139T;ENSP00000263451:I545T;ENSP00000410294:I548T;ENSP00000309878:I545T;ENSP00000353262:I459T;ENSP00000358052:I548T;ENSP00000358054:I548T;ENSP00000337665:I456T	ENSP00000337665:I456T	I	-	2	0	FGFR2	123248031	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.273000	0.95719	1.883000	0.54544	0.482000	0.46254	ATC		0.408	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		G	123258041	A	G	123258041	3	3	118	1	0	0	0	0	1	0	0	0	5885	333	12	4	957	4	FGFR2	10	123258041	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	19912161	123258041	12276706	115	31378										
OR56A1	120796	hgsc.bcm.edu	37	chr11	6048216	6048216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgctcagggccttcactgccGccccctctgctttgaatcta	8	16	4	1	rs139301829		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:6048216G>A	ENST00000316650.5	-	1	755	c.719C>T	c.(718-720)gCg>gTg	p.A240V		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTTCACTGCCGCCCCCTCTGC	0.498													.|||	1	0.000199681	8e-04	0	5008	,	,		21498	0		0	False		,,,				2504	0															0			11						G	VAL/ALA	1,4401	2.1+/-5.4	0,1,2200	49	48	48		719	3.3	0.6	11	dbSNP_134	48	0,8592		0,0,4296	yes	missense	OR56A1	NM_001001917.2	64	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	240/319	6048216	1,12993	2201	4296	6497	6004792	SO:0001583	missense	120796			AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"GPCR / Class A : Olfactory receptors"	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.719C>T	11.37:g.6048216G>A	ENSP00000321246:p.Ala240Val		6004792	B2RNI2|Q6IFL0	Missense_Mutation	SNP	ENST00000316650.5	37	CCDS31405.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424014	0.25639	2.27E-4	0.0	ENSG00000180934	ENST00000316650	T	0.00145	8.67	4.27	3.35	0.38373	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42294	D	0.000729	T	0.00552	0.0018	M	0.92317	3.295	0.20196	N	0.999923	D	0.69078	0.997	D	0.68353	0.957	T	0.15636	-1.0430	10	0.72032	D	0.01	.	11.1515	0.48462	0.0917:0.0:0.9083:0.0	.	240	Q8NGH5	O56A1_HUMAN	V	240	ENSP00000321246:A240V	ENSP00000321246:A240V	A	-	2	0	OR56A1	6004792	0.074000	0.21230	0.623000	0.29173	0.003000	0.03518	2.503000	0.45407	1.145000	0.42336	-0.136000	0.14681	GCG		0.498	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		A	6048216	G	A	6048216	3	1	118	1	0	0	0	0	1	0	0	0	11164	1087	38	1	241	1	OR56A1	11	6048216	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10		6048216	128958300	116	31379										
OR5B21	219968	hgsc.bcm.edu	37	chr11	58275031	58275031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtcagagcatgagagagccAggagtgggggaatgtcacag	17	6	2	3	rs531148002		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:58275031A>G	ENST00000360374.2	-	1	547	c.548T>C	c.(547-549)cTg>cCg	p.L183P		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGAGAGAGCCAGGAGTGGGGG	0.483																																																0			11											53	50	51					11																	58275031		2201	4295	6496	58031607	SO:0001583	missense	219968				CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.548T>C	11.37:g.58275031A>G	ENSP00000353537:p.Leu183Pro		58031607		Missense_Mutation	SNP	ENST00000360374.2	37	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.213543	0.39102	.	.	ENSG00000198283	ENST00000360374	T	0.00340	8.04	5.22	5.22	0.72569	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29335	U	0.012450	T	0.00967	0.0032	M	0.89715	3.055	0.36201	D	0.850714	D	0.56968	0.978	P	0.62649	0.905	T	0.56517	-0.7966	10	0.87932	D	0	-4.8057	14.0674	0.64839	1.0:0.0:0.0:0.0	.	183	A6NL26	OR5BL_HUMAN	P	183	ENSP00000353537:L183P	ENSP00000353537:L183P	L	-	2	0	OR5B21	58031607	0.002000	0.14202	0.162000	0.22713	0.532000	0.34746	1.927000	0.40094	2.194000	0.70268	0.460000	0.39030	CTG		0.483	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		G	58275031	A	G	58275031	3	3	118	1	0	0	0	0	1	0	0	0	11182	188	7	4	383	4	OR5B21	11	58275031	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	52226815	58275031	76731485	117	31380										
OR5A1	219982	hgsc.bcm.edu	37	chr11	59211350	59211350	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	agatcccttcagcagagggcCgatggaaagcctgcaacacg	12	12	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:59211350C>T	ENST00000302030.2	+	1	734	c.709C>T	c.(709-711)Cga>Tga	p.R237*		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R237*(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						AGCAGAGGGCCGATGGAAAGC	0.547																																																1	Substitution - Nonsense(1)	ovary(1)	11											257	215	229					11																	59211350		2201	4295	6496	58967926	SO:0001587	stop_gained	219982			AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"GPCR / Class A : Olfactory receptors"	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.709C>T	11.37:g.59211350C>T	ENSP00000303096:p.Arg237*		58967926	B9EH58|Q6IFF2|Q96RB1	Nonsense_Mutation	SNP	ENST00000302030.2	37	CCDS31561.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.278495	0.23307	.	.	ENSG00000172320	ENST00000302030	.	.	.	5.98	0.101	0.14517	.	0.291504	0.23922	N	0.043237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.7219	10.2104	0.43136	0.5557:0.3744:0.0:0.0699	.	.	.	.	X	237	.	ENSP00000303096:R237X	R	+	1	2	OR5A1	58967926	0.000000	0.05858	0.018000	0.16275	0.011000	0.07611	-0.261000	0.08694	0.113000	0.18004	-0.912000	0.02778	CGA		0.547	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728		T	59211350	C	T	59211350	4	4	118	1	0	0	0	0	0	1	0	0	11170	644	23	1	711	1	OR5A1	11	59211350	Nonsense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	936319	59211350	75795166	118	31381										
MTL5	9633	hgsc.bcm.edu	37	chr11	68512558	68512558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tatacatagcatttgtgtgcCccctttcaattggcatatca	6	10	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:68512558C>T	ENST00000255087.5	-	4	835	c.652G>A	c.(652-654)Ggc>Agc	p.G218S	MTL5_ENST00000540869.1_Intron|MTL5_ENST00000443940.2_Missense_Mutation_p.G218S|MTL5_ENST00000544963.1_Missense_Mutation_p.G218S	NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	218					cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			ATTTGTGTGCCCCCTTTCAAT	0.318																																																0			11											135	130	132					11																	68512558		2200	4293	6493	68269134	SO:0001583	missense	9633			U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"CXC domain containing 2"	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.652G>A	11.37:g.68512558C>T	ENSP00000255087:p.Gly218Ser		68269134	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Missense_Mutation	SNP	ENST00000255087.5	37	CCDS8184.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827114	0.90955	.	.	ENSG00000132749	ENST00000255087;ENST00000443940;ENST00000544963	T;T;T	0.70869	0.54;-0.52;0.07	5.35	5.35	0.76521	.	0.000000	0.52532	D	0.000063	T	0.77805	0.4185	L	0.34521	1.04	0.38848	D	0.956212	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80211	-0.1476	10	0.54805	T	0.06	-16.753	16.8394	0.85964	0.0:1.0:0.0:0.0	.	218;218	Q9Y4I5-3;Q9Y4I5	.;MTL5_HUMAN	S	218	ENSP00000255087:G218S;ENSP00000403086:G218S;ENSP00000440968:G218S	ENSP00000255087:G218S	G	-	1	0	MTL5	68269134	0.993000	0.37304	0.998000	0.56505	0.989000	0.77384	2.793000	0.47845	2.479000	0.83701	0.655000	0.94253	GGC		0.318	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923		T	68512558	C	T	68512558	3	4	118	1	0	0	0	0	1	0	0	0	9966	623	22	3	906	3	MTL5	11	68512558	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	9301208	68512558	66493958	119	31382										
FAT3	120114	hgsc.bcm.edu	37	chr11	92532069	92532069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtctgatggaaagttctacAgtacctccatggtcaccatc	8	11	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:92532069A>G	ENST00000298047.6	+	9	5907	c.5890A>G	c.(5890-5892)Agt>Ggt	p.S1964G	FAT3_ENST00000409404.2_Missense_Mutation_p.S1964G|FAT3_ENST00000525166.1_Missense_Mutation_p.S1814G			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1964	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAAGTTCTACAGTACCTCCAT	0.413										TCGA Ovarian(4;0.039)																																						0			11											125	121	122					11																	92532069		1930	4130	6060	92171717	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.5890A>G	11.37:g.92532069A>G	ENSP00000298047:p.Ser1964Gly		92171717	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	A	6.772	0.511369	0.12944	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01804	4.63;4.63;4.63	6.02	4.71	0.59529	.	.	.	.	.	T	0.02494	0.0076	L	0.46157	1.445	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.52403	-0.8580	9	0.36615	T	0.2	.	12.7228	0.57152	0.9266:0.0:0.0734:0.0	.	1964	Q8TDW7-3	.	G	1964;1964;1814	ENSP00000298047:S1964G;ENSP00000387040:S1964G;ENSP00000432586:S1814G	ENSP00000298047:S1964G	S	+	1	0	FAT3	92171717	1.000000	0.71417	0.997000	0.53966	0.821000	0.46438	6.229000	0.72294	2.311000	0.77944	0.533000	0.62120	AGT		0.413	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92532069	A	G	92532069	3	3	118	1	0	0	0	0	1	0	0	0	5710	188	7	4	5924	4	FAT3	11	92532069	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	24019511	92532069	42474447	120	31383										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92703048	92703048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgctcatcgtcaccaccgccGtggacgtcgtgggcaacctc	11	16	2	0	rs541167036		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:92703048G>A	ENST00000257068.2	+	1	163	c.157G>A	c.(157-159)Gtg>Atg	p.V53M		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	53					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CACCACCGCCGTGGACGTCGT	0.697																																																0			11											34	27	30					11																	92703048		2199	4291	6490	92342696	SO:0001583	missense	4544			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.157G>A	11.37:g.92703048G>A	ENSP00000257068:p.Val53Met		92342696		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	G	6.680	0.494052	0.12702	.	.	ENSG00000134640	ENST00000257068	T	0.44083	0.93	4.72	0.645	0.17782	.	0.089710	0.44285	D	0.000469	T	0.30070	0.0753	L	0.52905	1.665	0.32383	N	0.554341	P	0.46621	0.881	B	0.38616	0.277	T	0.38415	-0.9662	10	0.51188	T	0.08	-0.8729	4.6583	0.12630	0.165:0.0:0.5302:0.3048	.	53	P49286	MTR1B_HUMAN	M	53	ENSP00000257068:V53M	ENSP00000257068:V53M	V	+	1	0	MTNR1B	92342696	1.000000	0.71417	0.039000	0.18376	0.006000	0.05464	4.598000	0.61069	0.078000	0.16900	-0.840000	0.03056	GTG		0.697	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92703048	G	A	92703048	3	1	118	1	0	0	0	0	1	0	0	0	9982	1145	40	1	159	1	MTNR1B	11	92703048	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	170979	92703048	42303468	121	31384										
CCDC82	79780	hgsc.bcm.edu	37	chr11	96117863	96117863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tcgagatttctgctcaggcaCgtgactcttagaatttctcc	8	11	4	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr11:96117863C>T	ENST00000278520.5	-	3	477	c.49G>A	c.(49-51)Gtg>Atg	p.V17M	CCDC82_ENST00000525786.1_5'Flank|CCDC82_ENST00000423339.2_Missense_Mutation_p.V17M|CCDC82_ENST00000542662.1_Missense_Mutation_p.V17M			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	17								p.V17M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		TGCTCAGGCACGTGACTCTTA	0.338																																																1	Substitution - Missense(1)	ovary(1)	11											74	71	72					11																	96117863		2200	4296	6496	95757511	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.49G>A	11.37:g.96117863C>T	ENSP00000278520:p.Val17Met		95757511	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874879	0.33069	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339;ENST00000538597;ENST00000530203	T;T;T;T	0.32515	1.83;1.83;1.83;1.45	5.77	1.77	0.24775	.	0.983418	0.08295	N	0.967843	T	0.20170	0.0485	L	0.36672	1.1	0.09310	N	0.999995	P;B	0.42757	0.789;0.226	B;B	0.27500	0.08;0.025	T	0.10847	-1.0612	10	0.52906	T	0.07	1.4465	9.947	0.41616	0.0:0.728:0.0:0.272	.	17;17	Q8N4S0-2;Q8N4S0	.;CCD82_HUMAN	M	17	ENSP00000278520:V17M;ENSP00000444010:V17M;ENSP00000397156:V17M;ENSP00000442723:V17M	ENSP00000278520:V17M	V	-	1	0	CCDC82	95757511	0.000000	0.05858	0.612000	0.29024	0.957000	0.61999	-0.767000	0.04720	0.141000	0.18875	0.655000	0.94253	GTG		0.338	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		T	96117863	C	T	96117863	3	4	118	1	0	0	0	0	1	0	0	0	2862	536	19	1	1613	1	CCDC82	11	96117863	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	3414815	96117863	38888653	122	31385										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7531632	7531632	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcagtctgtttccactcccaTcgtatacaatcccagagaga	7	13	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:7531632T>C	ENST00000313599.3	-	9	2370	c.2313A>G	c.(2311-2313)cgA>cgG	p.R771R	CD163L1_ENST00000396630.1_Silent_p.R771R|CD163L1_ENST00000544331.1_5'UTR|CD163L1_ENST00000416109.2_Silent_p.R781R			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	771	SRCR 7. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TCCACTCCCATCGTATACAAT	0.403																																																0			12											71	72	71					12																	7531632		2203	4300	6503	7422899	SO:0001819	synonymous_variant	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.2313A>G	12.37:g.7531632T>C			7422899	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																				0.403	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7531632	T	C	7531632	2	2	118	1	0	0	0	0	0	0	0	1	2974	1422	50	4		4	CD163L1	12	7531632	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10		7531632	126320263	123	31386										
FGD4	121512	hgsc.bcm.edu	37	chr12	32778645	32778645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gagataatgaagtgacaatgTgtatgaaatgtaaagaacct	10	3	0	5			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:32778645T>C	ENST00000427716.2	+	14	2117	c.1693T>C	c.(1693-1695)Tgt>Cgt	p.C565R	FGD4_ENST00000266482.3_Missense_Mutation_p.C317R|FGD4_ENST00000546442.1_Missense_Mutation_p.C472R|FGD4_ENST00000531134.1_Missense_Mutation_p.C650R|FGD4_ENST00000525053.1_Missense_Mutation_p.C677R|FGD4_ENST00000534526.2_Missense_Mutation_p.C702R	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	565					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AGTGACAATGTGTATGAAATG	0.373																																																0			12											120	116	117					12																	32778645		2203	4300	6503	32669912	SO:0001583	missense	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1693T>C	12.37:g.32778645T>C	ENSP00000394487:p.Cys565Arg		32669912	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.328530	0.81690	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000266482;ENST00000546442;ENST00000525053	D;D;D;D;D;D	0.97831	-3.32;-3.32;-3.32;-4.56;-3.32;-3.32	5.39	5.39	0.77823	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.358411	0.23900	N	0.043445	D	0.99318	0.9761	H	0.98918	4.37	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.995;0.994	D	0.98552	1.0637	10	0.87932	D	0	-10.9357	15.3974	0.74808	0.0:0.0:0.0:1.0	.	677;650;565;317	E9PJX4;B7Z493;Q96M96;G3XA97	.;.;FGD4_HUMAN;.	R	702;650;565;317;472;677	ENSP00000449273:C702R;ENSP00000431323:C650R;ENSP00000394487:C565R;ENSP00000266482:C317R;ENSP00000446695:C472R;ENSP00000433666:C677R	ENSP00000266482:C317R	C	+	1	0	FGD4	32669912	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.380000	0.79704	2.030000	0.59900	0.454000	0.30748	TGT		0.373	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		C	32778645	T	C	32778645	3	2	118	1	0	0	0	0	1	0	0	0	5854	1696	59	4	1739	4	FGD4	12	32778645	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	25247013	32778645	101073250	124	31387										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51512474	51512474	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtagcagcacaaagcacataTtgaaaaggcaggattttatt	9	6	0	1	rs146119086		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:51512474T>C	ENST00000257915.5	-	2	662	c.204A>G	c.(202-204)caA>caG	p.Q68Q	TFCP2_ENST00000307660.4_Silent_p.Q68Q|TFCP2_ENST00000548115.1_Silent_p.Q68Q|TFCP2_ENST00000549867.1_Silent_p.Q68Q	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	68					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q68H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AAAGCACATATTGAAAAGGCA	0.383																																																1	Substitution - Missense(1)	ovary(1)	12											185	175	179					12																	51512474		2203	4300	6503	49798741	SO:0001819	synonymous_variant	7024			U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.204A>G	12.37:g.51512474T>C			49798741	A8K5E9|Q12801|Q9UD75|Q9UD77	Silent	SNP	ENST00000257915.5	37	CCDS8808.1																																																																																				0.383	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		C	51512474	T	C	51512474	2	2	118	1	0	0	0	0	0	0	0	1	15834	1490	52	4		4	TFCP2	12	51512474	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	18733829	51512474	82339421	125	31388										
TARBP2	8620	hgsc.bcm.edu	37	chr12	53899461	53899461	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctcccgcctggatggtcttcGaaaccggggcccaggttgca	13	14	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:53899461G>A	ENST00000267017.3	-	0	592				TARBP2_ENST00000552857.1_Silent_p.S123S|TARBP2_ENST00000266987.2_Missense_Mutation_p.R257Q|TARBP2_ENST00000456234.2_Missense_Mutation_p.R236Q|TARBP2_ENST00000394357.2_Missense_Mutation_p.R236Q	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GATGGTCTTCGAAACCGGGGC	0.577																																																0			12											117	121	120					12																	53899461		2203	4300	6503	52185728	SO:0001628	intergenic_variant	6895			AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		12.37:g.53899461G>A			52185728	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.552843	0.65425	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000394357	T;T;T	0.63255	-0.03;-0.03;-0.03	4.98	4.98	0.66077	.	0.300777	0.32624	N	0.005857	T	0.32376	0.0827	N	0.14661	0.345	0.40274	D	0.978324	P	0.43352	0.804	B	0.25140	0.058	T	0.29792	-1.0000	10	0.13470	T	0.59	-8.6472	9.5313	0.39196	0.0939:0.0:0.9061:0.0	.	257	Q15633	TRBP2_HUMAN	Q	257;236;236	ENSP00000266987:R257Q;ENSP00000416077:R236Q;ENSP00000377885:R236Q	ENSP00000266987:R257Q	R	+	2	0	TARBP2	52185728	1.000000	0.71417	0.995000	0.50966	0.951000	0.60555	3.058000	0.49939	2.759000	0.94783	0.561000	0.74099	CGA		0.577	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		A	53899461	G	A	53899461	1	1	118	0	1	0	0	0	0	0	0	0	15595	1058	37	1		1	TARBP2	12	53899461	IGR	SNP	G	TCGA-F5-6811-01A-11D-1826-10	2386987	53899461	79952434	126	31389										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100708281	100708281	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttttagattcccttctttgaTgatgttggtgcagtaacact	8	7	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:100708281T>G	ENST00000360820.2	+	8	1421	c.984T>G	c.(982-984)gaT>gaG	p.D328E		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	328					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						CCTTCTTTGATGATGTTGGTG	0.299																																																0			12											59	57	58					12																	100708281		2203	4295	6498	99232412	SO:0001583	missense	55681			AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.984T>G	12.37:g.100708281T>G	ENSP00000354061:p.Asp328Glu		99232412	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.498521	0.44455	.	.	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.73258	-0.73;-0.73	5.6	5.6	0.85130	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53012	0.1770	N	0.12887	0.27	0.80722	D	1	B	0.15719	0.014	B	0.15052	0.012	T	0.49854	-0.8895	10	0.16896	T	0.51	.	15.7992	0.78439	0.0:0.0:0.0:1.0	.	328	Q6P3W7	SCYL2_HUMAN	E	328;155;328	ENSP00000448366:D328E;ENSP00000354061:D328E	ENSP00000258506:D155E	D	+	3	2	SCYL2	99232412	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.977000	0.70492	2.143000	0.66587	0.460000	0.39030	GAT		0.299	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		G	100708281	T	G	100708281	3	3	118	1	0	0	0	0	1	0	0	0	13985	1461	51	4	1010	4	SCYL2	12	100708281	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	46808820	100708281	33143614	127	31390										
PAH	5053	hgsc.bcm.edu	37	chr12	103249074	103249074	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtgccccatgttttcttttcTtcctccatgtattccactcg	5	14	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:103249074T>C	ENST00000553106.1	-	6	1018	c.546A>G	c.(544-546)gaA>gaG	p.E182E	PAH_ENST00000551988.1_5'UTR|PAH_ENST00000307000.2_Silent_p.E177E	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	182					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	TTTTCTTTTCTTCCTCCATGT	0.463																																																0			12											99	93	95					12																	103249074		2203	4300	6503	101773204	SO:0001819	synonymous_variant	5053			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.546A>G	12.37:g.103249074T>C			101773204	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	37	CCDS9092.1																																																																																				0.463	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			C	103249074	T	C	103249074	2	2	118	1	0	0	0	0	0	0	0	1	11425	1606	56	4		4	PAH	12	103249074	Silent	SNP	T	TCGA-F5-6811-01A-11D-1826-10	2540793	103249074	30602821	128	31391										
STAB2	55576	hgsc.bcm.edu	37	chr12	104031890	104031890	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tacatgccaagaaggctaccGtggggatggccaagtgtgct	14	9	0	1	rs374968745		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:104031890G>A	ENST00000388887.2	+	8	1010	c.806G>A	c.(805-807)cGt>cAt	p.R269H		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GAAGGCTACCGTGGGGATGGC	0.498																																																0			12						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	177	151	160		806	-10.7	0	12		160	1,8599		0,1,4299	no	missense	STAB2	NM_017564.9	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	269/2552	104031890	2,13004	2203	4300	6503	102556020	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.806G>A	12.37:g.104031890G>A	ENSP00000373539:p.Arg269His		102556020		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	0.287	-0.982590	0.02180	2.27E-4	1.16E-4	ENSG00000136011	ENST00000388887	T	0.04970	3.52	5.34	-10.7	0.00240	EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.796511	0.11661	N	0.541825	T	0.03348	0.0097	N	0.20986	0.625	0.09310	N	0.999999	B	0.14438	0.01	B	0.09377	0.004	T	0.32508	-0.9904	10	0.26408	T	0.33	.	12.2094	0.54371	0.3687:0.0:0.539:0.0924	.	269	Q8WWQ8	STAB2_HUMAN	H	269	ENSP00000373539:R269H	ENSP00000373539:R269H	R	+	2	0	STAB2	102556020	0.000000	0.05858	0.000000	0.03702	0.453000	0.32348	-1.459000	0.02370	-2.678000	0.00410	-1.036000	0.02392	CGT		0.498	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104031890	G	A	104031890	3	1	118	1	0	0	0	0	1	0	0	0	15277	1145	40	1	836	1	STAB2	12	104031890	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	782816	104031890	29820005	129	31392										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123057756	123057756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccagagcttattccctccaTcttagagaagtttataagag	7	10	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:123057756T>C	ENST00000333479.7	+	26	2384	c.2207T>C	c.(2206-2208)aTc>aCc	p.I736T	KNTC1_ENST00000450485.2_Missense_Mutation_p.I699T	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	736					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	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)		ATTCCCTCCATCTTAGAGAAG	0.393																																																0			12											145	143	143					12																	123057756		1832	4085	5917	121623709	SO:0001583	missense	9735				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2207T>C	12.37:g.123057756T>C	ENSP00000328236:p.Ile736Thr		121623709	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	T	2.236	-0.374941	0.05034	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.21191	2.02;2.61	5.66	3.23	0.37069	.	0.592037	0.18102	N	0.151644	T	0.08626	0.0214	N	0.04043	-0.29	0.19575	N	0.999962	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.33111	-0.9881	10	0.21014	T	0.42	-0.4593	7.635	0.28261	0.0:0.3316:0.0:0.6684	.	699;736	E7ES84;P50748	.;KNTC1_HUMAN	T	699;736	ENSP00000397992:I699T;ENSP00000328236:I736T	ENSP00000328236:I736T	I	+	2	0	KNTC1	121623709	0.003000	0.15002	0.047000	0.18901	0.008000	0.06430	1.644000	0.37228	0.951000	0.37770	0.533000	0.62120	ATC		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			C	123057756	T	C	123057756	3	2	118	1	0	0	0	0	1	0	0	0	8449	1435	50	4	2305	4	KNTC1	12	123057756	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	19025866	123057756	10794139	130	31393										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130927134	130927134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccccagcgtgcttgccaaccGcgactcgttgtcctgcacaa	9	17	0	0	rs549158714		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr12:130927134G>A	ENST00000261655.4	-	8	875	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	RIMBP2_ENST00000535703.1_Missense_Mutation_p.R146W|RIMBP2_ENST00000536002.1_Missense_Mutation_p.R146W	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	238					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTTGCCAACCGCGACTCGTTG	0.587													G|||	1	0.000199681	0	0	5008	,	,		18516	0		0	False		,,,				2504	0.001															0			12											130	129	129					12																	130927134		2203	4300	6503	129493087	SO:0001583	missense	23504			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.712C>T	12.37:g.130927134G>A	ENSP00000261655:p.Arg238Trp		129493087	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885658	0.51908	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.30448	1.53;1.53;1.53	4.53	3.61	0.41365	Src homology-3 domain (1);	0.538961	0.20115	N	0.098937	T	0.52837	0.1759	M	0.68317	2.08	0.42057	D	0.991146	D;D	0.89917	0.998;1.0	D;D	0.83275	0.928;0.996	T	0.55611	-0.8114	10	0.66056	D	0.02	-24.1815	13.5684	0.61832	0.0:0.0:0.8432:0.1568	.	146;238	O15034-2;O15034	.;RIMB2_HUMAN	W	238;146;146;146	ENSP00000261655:R238W;ENSP00000440347:R146W;ENSP00000439159:R146W	ENSP00000261655:R238W	R	-	1	2	RIMBP2	129493087	1.000000	0.71417	0.020000	0.16555	0.317000	0.28152	5.216000	0.65246	0.840000	0.34995	0.561000	0.74099	CGG		0.587	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130927134	G	A	130927134	3	1	118	1	0	0	0	0	1	0	0	0	13400	1086	38	1	2494	1	RIMBP2	12	130927134	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	7869378	130927134	2924761	131	31394										
FLT3	2322	hgsc.bcm.edu	37	chr13	28592645	28592645	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggaatcactcatgatatctcGagccaatccaaagtcacata	6	11	4	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr13:28592645G>A	ENST00000241453.7	-	20	2581	c.2500C>T	c.(2500-2502)Cga>Tga	p.R834*	FLT3_ENST00000537084.1_Intron|FLT3_ENST00000380982.4_Nonsense_Mutation_p.R834*	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	834	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.R834_D835del(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATGATATCTCGAGCCAATCCA	0.453			"Mis, O"		"AML, ALL"																																		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	13											189	142	158					13																	28592645		2203	4300	6503	27490645	SO:0001587	stop_gained	2322			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2500C>T	13.37:g.28592645G>A	ENSP00000241453:p.Arg834*		27490645	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Nonsense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	40	8.517642	0.98845	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	.	.	.	5.84	4.92	0.64577	.	0.000000	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5869	0.50923	0.0:0.0:0.6168:0.3832	.	.	.	.	X	834	.	ENSP00000241453:R834X	R	-	1	2	FLT3	27490645	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.082000	0.41605	2.792000	0.96026	0.556000	0.70494	CGA		0.453	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			A	28592645	G	A	28592645	4	1	118	1	0	0	0	0	0	1	0	0	5961	1066	37	1	501	1	FLT3	13	28592645	Nonsense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10		28592645	86577233	132	31395										
C13orf15	28984	hgsc.bcm.edu	37	chr13	42032565	42032565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcgcatgaagcggcgcagcaGcgccagtgtcagcgacagca	15	13	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr13:42032565G>A	ENST00000379359.3	+	2	343	c.194G>A	c.(193-195)aGc>aAc	p.S65N		NM_014059.2	NP_054778.2	Q9H4X1	RGCC_HUMAN	regulator of cell cycle	65	Ser/Thr-rich.				cellular response to hypoxia (GO:0071456)|complement activation (GO:0006956)|fibroblast activation (GO:0072537)|mitotic cell cycle arrest (GO:0071850)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of exit from mitosis (GO:0001100)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mitotic cell cycle phase transition (GO:1901991)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of mitosis (GO:0045840)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stress fiber assembly (GO:0051496)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)										CGGCGCAGCAGCGCCAGTGTC	0.682																																																0			13											8	9	9					13																	42032565		1907	4107	6014	40930565	SO:0001583	missense	28984			AF036549	CCDS41880.1	13q14.11	2012-02-20	2012-02-20	2012-02-20	ENSG00000102760	ENSG00000102760			20369	protein-coding gene	gene with protein product	"response gene to complement 32"	610077	"chromosome 13 open reading frame 15"	C13orf15		17146433, 19158077, 19652095	Standard	NM_014059		Approved	bA157L14.2, RGC-32, RGC32	uc001uyi.2	Q9H4X1	OTTHUMG00000016796	ENST00000379359.3:c.194G>A	13.37:g.42032565G>A	ENSP00000368664:p.Ser65Asn		40930565	Q6NZ48|Q9UL69	Missense_Mutation	SNP	ENST00000379359.3	37	CCDS41880.1	.	.	.	.	.	.	.	.	.	.	G	33	5.251360	0.95305	.	.	ENSG00000102760	ENST00000379359	.	.	.	5.32	5.32	0.75619	.	0.042149	0.85682	D	0.000000	T	0.73458	0.3589	M	0.69823	2.125	0.46028	D	0.998829	D	0.55605	0.972	P	0.56398	0.797	T	0.76162	-0.3060	9	0.59425	D	0.04	-25.1517	14.5723	0.68220	0.0:0.1461:0.8539:0.0	.	65	Q9H4X1	RGC32_HUMAN	N	65	.	ENSP00000368664:S65N	S	+	2	0	C13orf15	40930565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.643000	0.74334	2.473000	0.83533	0.561000	0.74099	AGC		0.682	RGCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044684.1	NM_014059		A	42032565	G	A	42032565	3	1	118	1	0	0	0	0	1	0	0	0	1722	971	34	3	200	3	C13orf15	13	42032565	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	13439920	42032565	73137313	133	31396										
SYT16	83851	hgsc.bcm.edu	37	chr14	62547981	62547981	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctctggttctggagccaagaAgtaatataagcgtgagtatg	12	6	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr14:62547981A>G	ENST00000430451.2	+	4	1620	c.1423A>G	c.(1423-1425)Agt>Ggt	p.S475G	RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	475					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GGAGCCAAGAAGTAATATAAG	0.453																																																0			14											24	25	25					14																	62547981		2069	4217	6286	61617734	SO:0001583	missense	83851			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1423A>G	14.37:g.62547981A>G	ENSP00000394700:p.Ser475Gly		61617734	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729276	0.48833	.	.	ENSG00000139973	ENST00000430451	T	0.78246	-1.16	4.88	4.88	0.63580	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.77294	0.4109	M	0.69823	2.125	0.80722	D	1	B	0.33212	0.402	B	0.34590	0.186	T	0.77472	-0.2575	10	0.40728	T	0.16	-8.2862	14.9411	0.70994	1.0:0.0:0.0:0.0	.	475	Q17RD7	SYT16_HUMAN	G	475	ENSP00000394700:S475G	ENSP00000394700:S475G	S	+	1	0	SYT16	61617734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.725000	0.54970	2.164000	0.68074	0.533000	0.62120	AGT		0.453	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		G	62547981	A	G	62547981	3	3	118	1	0	0	0	0	1	0	0	0	15511	72	3	4	1437	4	SYT16	14	62547981	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10		62547981	44801559	134	31397										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27182398	27182398	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caccaagtcggtggtggtggCggaagatggctccagactga	16	9	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:27182398C>T	ENST00000335625.5	+	8	1535	c.647C>T	c.(646-648)gCg>gTg	p.A216V	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Missense_Mutation_p.A216V|GABRA5_ENST00000400081.3_Missense_Mutation_p.A216V	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	216					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	GTGGTGGTGGCGGAAGATGGC	0.572																																																0			15											97	101	100					15																	27182398		2084	4208	6292	24765144	SO:0001583	missense	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.647C>T	15.37:g.27182398C>T	ENSP00000335592:p.Ala216Val		24765144	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	35	5.489540	0.96323	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	T;T;T	0.79247	-1.25;-1.25;-1.25	5.13	5.13	0.70059	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.77631	0.4159	L	0.48642	1.525	0.80722	D	1	P	0.51933	0.949	P	0.48425	0.577	T	0.75280	-0.3373	10	0.27785	T	0.31	.	17.9326	0.89002	0.0:1.0:0.0:0.0	.	216	P31644	GBRA5_HUMAN	V	216	ENSP00000335592:A216V;ENSP00000347557:A216V;ENSP00000382953:A216V	ENSP00000335592:A216V	A	+	2	0	GABRA5	24765144	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.610000	0.82949	2.539000	0.85634	0.462000	0.41574	GCG		0.572	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27182398	C	T	27182398	3	4	118	1	0	0	0	0	1	0	0	0	6183	768	27	1	669	1	GABRA5	15	27182398	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		27182398	75348994	135	31398										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34547528	34547528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtggtaccaagataaaagcAgaggccaacagccccaccaa	9	12	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:34547528A>G	ENST00000354181.3	-	8	1303	c.811T>C	c.(811-813)Tgc>Cgc	p.C271R	SLC12A6_ENST00000451844.2_Missense_Mutation_p.C83R|SLC12A6_ENST00000397707.2_Missense_Mutation_p.C256R|SLC12A6_ENST00000397702.2_Missense_Mutation_p.C212R|SLC12A6_ENST00000290209.5_Missense_Mutation_p.C220R|SLC12A6_ENST00000458406.2_Missense_Mutation_p.C212R|SLC12A6_ENST00000560164.1_Missense_Mutation_p.C83R|SLC12A6_ENST00000558667.1_Missense_Mutation_p.C271R|SLC12A6_ENST00000560611.1_Missense_Mutation_p.C271R|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000558589.1_Missense_Mutation_p.C262R			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	271					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	AGATAAAAGCAGAGGCCAACA	0.438																																																0			15											86	88	87					15																	34547528		2201	4298	6499	32334820	SO:0001583	missense	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.811T>C	15.37:g.34547528A>G	ENSP00000346112:p.Cys271Arg		32334820	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.433281	0.83776	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05	5.43	5.43	0.79202	Amino acid permease domain (1);	0.053820	0.85682	D	0.000000	D	0.99187	0.9718	M	0.90082	3.085	0.80722	D	1	D;D;D;D	0.69078	0.982;0.997;0.997;0.997	P;D;D;D	0.68943	0.831;0.926;0.917;0.961	D	0.99289	1.0898	10	0.87932	D	0	.	14.5986	0.68424	1.0:0.0:0.0:0.0	.	256;271;220;83	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	R	220;256;262;212;212;83	ENSP00000290209:C220R;ENSP00000380819:C256R;ENSP00000380814:C212R;ENSP00000387725:C212R;ENSP00000390199:C83R	ENSP00000290209:C220R	C	-	1	0	SLC12A6	32334820	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.139000	0.94554	2.279000	0.76181	0.533000	0.62120	TGC		0.438	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		G	34547528	A	G	34547528	3	3	118	1	0	0	0	0	1	0	0	0	14424	188	7	4	2717	4	SLC12A6	15	34547528	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	7365130	34547528	67983864	136	31399										
MGA	23269	hgsc.bcm.edu	37	chr15	42041563	42041563	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caagtaaaacaggctctgaaAccaaaataacttatagctca	5	9	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:42041563A>G	ENST00000570161.1	+	16	5758	c.5758A>G	c.(5758-5760)Acc>Gcc	p.T1920A	MGA_ENST00000389936.4_Missense_Mutation_p.T1881A|MGA_ENST00000545763.1_Missense_Mutation_p.T1711A|MGA_ENST00000566586.1_Missense_Mutation_p.T1711A|MGA_ENST00000219905.7_Missense_Mutation_p.T1920A			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.T1969A(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGGCTCTGAAACCAAAATAAC	0.463																																																1	Substitution - Missense(1)	ovary(1)	15											60	55	57					15																	42041563		1874	4103	5977	39828855	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5758A>G	15.37:g.42041563A>G	ENSP00000457035:p.Thr1920Ala		39828855	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.194424	0.38806	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.24350	1.86;1.86;1.86	5.72	4.56	0.56223	.	0.385199	0.22241	N	0.062697	T	0.11153	0.0272	N	0.08118	0	0.19945	N	0.999945	B;B;B;B	0.34372	0.451;0.433;0.048;0.048	B;B;B;B	0.33454	0.079;0.164;0.05;0.05	T	0.09058	-1.0692	10	0.38643	T	0.18	.	4.625	0.12474	0.624:0.0:0.0946:0.2814	.	536;1711;1920;1881	B4DVS1;F5H7K2;E7ENI0;Q8IWI9	.;.;.;MGAP_HUMAN	A	1920;1881;1711	ENSP00000219905:T1920A;ENSP00000374586:T1881A;ENSP00000442467:T1711A	ENSP00000219905:T1920A	T	+	1	0	MGA	39828855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.062000	0.41413	2.184000	0.69523	0.460000	0.39030	ACC		0.463	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42041563	A	G	42041563	3	3	118	1	0	0	0	0	1	0	0	0	9570	43	2	4	5820	4	MGA	15	42041563	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	7494035	42041563	60489829	137	31400										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54556406	54556406	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aaacatggtgccgaagacaaGactcagaccattattacagc	8	10	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:54556406G>A	ENST00000260323.11	+	8	3489	c.3489G>A	c.(3487-3489)aaG>aaA	p.K1163K	UNC13C_ENST00000537900.1_Silent_p.K1161K|UNC13C_ENST00000545554.1_Silent_p.K1163K	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1163					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CCGAAGACAAGACTCAGACCA	0.378																																																0			15											58	52	54					15																	54556406		1867	4089	5956	52343698	SO:0001819	synonymous_variant	440279			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3489G>A	15.37:g.54556406G>A			52343698	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																				0.378	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54556406	G	A	54556406	2	1	118	1	0	0	0	0	0	0	0	1	17026	933	33	3		3	UNC13C	15	54556406	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	12514843	54556406	47974986	138	31401										
CLPX	10845	hgsc.bcm.edu	37	chr15	65450131	65450131	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tggcatcttggagtagttttGcaatcacagattcaatatct	8	7	4	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:65450131G>T	ENST00000300107.3	-	8	1198	c.1010C>A	c.(1009-1011)gCa>gAa	p.A337E		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	337					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						GAGTAGTTTTGCAATCACAGA	0.403																																																0			15											188	167	174					15																	65450131		2202	4299	6501	63237184	SO:0001583	missense	10845			AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"ATPases / AAA-type"	2088	protein-coding gene	gene with protein product		615611	"ClpX (caseinolytic protease X, E. coli) homolog", "ClpX caseinolytic protease X homolog (E. coli)", "ClpX caseinolytic peptidase X homolog (E. coli)"			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1010C>A	15.37:g.65450131G>T	ENSP00000300107:p.Ala337Glu		63237184	A1L428|A8K8F1|B9EGI8|Q9H4D9	Missense_Mutation	SNP	ENST00000300107.3	37	CCDS10202.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857376	0.91433	.	.	ENSG00000166855	ENST00000300107;ENST00000546194	T	0.42513	0.97	6.07	5.13	0.70059	ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.55689	0.1936	L	0.37697	1.125	0.80722	D	1	D;P	0.89917	1.0;0.899	D;P	0.87578	0.998;0.826	T	0.54423	-0.8296	10	0.56958	D	0.05	.	16.8594	0.86014	0.0:0.0:0.8712:0.1288	.	337;337	Q9H072;O76031	.;CLPX_HUMAN	E	337	ENSP00000300107:A337E	ENSP00000300107:A337E	A	-	2	0	CLPX	63237184	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	GCA		0.403	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660		T	65450131	G	T	65450131	3	4	118	1	0	0	0	0	1	0	0	0	3562	1319	46	2	919	2	CLPX	15	65450131	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	10893725	65450131	37081261	139	31402										
TMEM202	338949	hgsc.bcm.edu	37	chr15	72691086	72691086	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcacacatctacatccgaacGctctgtggcagcctctgtag	9	14	3	0	rs148667101		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr15:72691086G>A	ENST00000341689.3	+	2	228	c.174G>A	c.(172-174)acG>acA	p.T58T	TMEM202_ENST00000567679.1_Intron	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	58						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						ACATCCGAACGCTCTGTGGCA	0.522													G|||	1	0.000199681	0	0	5008	,	,		19245	0		0.001	False		,,,				2504	0															0			15						G		0,4398		0,0,2199	155	110	125		174	1.4	1	15	dbSNP_134	125	9,8585	6.4+/-24.3	0,9,4288	no	coding-synonymous	TMEM202	NM_001080462.1		0,9,6487	AA,AG,GG		0.1047,0.0,0.0693		58/274	72691086	9,12983	2199	4297	6496	70478140	SO:0001819	synonymous_variant	338949				CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.174G>A	15.37:g.72691086G>A			70478140		Silent	SNP	ENST00000341689.3	37	CCDS32287.1																																																																																				0.522	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		A	72691086	G	A	72691086	2	1	118	1	0	0	0	0	0	0	0	1	16166	1074	38	1		1	TMEM202	15	72691086	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	7240955	72691086	29840306	140	31403										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16162034	16162034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tggccttgtgcacatttgccGtctacgtgaccattgacgag	11	11	1	2	rs545772203		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr16:16162034G>A	ENST00000399410.3	+	13	1874	c.1699G>A	c.(1699-1701)Gtc>Atc	p.V567I	ABCC1_ENST00000349029.5_Missense_Mutation_p.V567I|ABCC1_ENST00000399408.2_Missense_Mutation_p.V567I|ABCC1_ENST00000345148.5_Missense_Mutation_p.V567I|ABCC1_ENST00000346370.5_Missense_Mutation_p.V567I|ABCC1_ENST00000351154.5_Missense_Mutation_p.V567I	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	567	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CACATTTGCCGTCTACGTGAC	0.562													G|||	1	0.000199681	0	0.0014	5008	,	,		19450	0		0	False		,,,				2504	0															0			16											176	172	173					16																	16162034		2127	4239	6366	16069535	SO:0001583	missense	4363			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1699G>A	16.37:g.16162034G>A	ENSP00000382342:p.Val567Ile		16069535	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.751466	0.69533	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	4.46	4.46	0.54185	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93762	0.8006	L	0.56124	1.755	0.54753	D	0.99998	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.989;1.0;1.0	D;D;D;P;D;D	0.91635	0.991;0.991;0.997;0.85;0.999;0.998	D	0.94497	0.7706	10	0.72032	D	0.01	-40.2625	15.6775	0.77338	0.0:0.0:1.0:0.0	.	567;567;567;567;567;567	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	I	567;567;567;567;567;567;241	ENSP00000382342:V567I;ENSP00000382340:V567I;ENSP00000263019:V567I;ENSP00000263017:V567I;ENSP00000263014:V567I;ENSP00000263016:V567I	ENSP00000263014:V567I	V	+	1	0	ABCC1	16069535	1.000000	0.71417	0.988000	0.46212	0.173000	0.22820	9.551000	0.98112	2.030000	0.59900	0.462000	0.41574	GTC		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16162034	G	A	16162034	3	1	118	1	0	0	0	0	1	0	0	0	49	1145	40	1	1749	1	ABCC1	16	16162034	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10		16162034	74192719	141	31404										
SMG1	23049	hgsc.bcm.edu	37	chr16	18861437	18861437	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgcagcctagggtcatcctcAtctaaaggaatctaagagtg	10	9	4	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr16:18861437A>G	ENST00000446231.2	-	35	5707	c.5295T>C	c.(5293-5295)gaT>gaC	p.D1765D	SMG1_ENST00000389467.3_Silent_p.D1765D			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1765	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GGTCATCCTCATCTAAAGGAA	0.393																																																0			16											64	62	62					16																	18861437		1958	4155	6113	18768938	SO:0001819	synonymous_variant	23049			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5295T>C	16.37:g.18861437A>G			18768938	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																				0.393	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18861437	A	G	18861437	2	3	118	1	0	0	0	0	0	0	0	1	14832	214	8	4		4	SMG1	16	18861437	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	2699403	18861437	71493316	142	31405										
DCUN1D3	123879	hgsc.bcm.edu	37	chr16	20871560	20871560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cttcagagtccaggccaaacTgaaatgtaaaccggtagaga	10	9	1	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr16:20871560T>C	ENST00000324344.4	-	3	848	c.563A>G	c.(562-564)cAg>cGg	p.Q188R	ERI2_ENST00000564349.1_Intron|DCUN1D3_ENST00000563934.1_Missense_Mutation_p.Q188R	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	188	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.				negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		CAGGCCAAACTGAAATGTAAA	0.483																																																0			16											149	152	151					16																	20871560		2201	4300	6501	20779061	SO:0001583	missense	123879			BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.563A>G	16.37:g.20871560T>C	ENSP00000319482:p.Gln188Arg		20779061	B3KVY4	Missense_Mutation	SNP	ENST00000324344.4	37	CCDS10592.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.157952	0.38119	.	.	ENSG00000188215	ENST00000324344	.	.	.	5.92	5.92	0.95590	Domain of unknown function DUF298 (2);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	N	0.02960	-0.455	0.80722	D	1	B	0.23377	0.084	B	0.22880	0.042	T	0.25152	-1.0140	9	0.08599	T	0.76	.	16.3662	0.83325	0.0:0.0:0.0:1.0	.	188	Q8IWE4	DCNL3_HUMAN	R	188	.	ENSP00000319482:Q188R	Q	-	2	0	DCUN1D3	20779061	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.980000	0.88113	2.274000	0.75844	0.533000	0.62120	CAG		0.483	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475		C	20871560	T	C	20871560	3	2	118	1	0	0	0	0	1	0	0	0	4321	1580	55	4	355	4	DCUN1D3	16	20871560	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	2010123	20871560	69483193	143	31406										
CDH1	999	hgsc.bcm.edu	37	chr16	68835727	68835727	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtctacgcctgggactccacCtacagaaagttttccaccaa	7	14	1	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr16:68835727C>T	ENST00000261769.5	+	3	509	c.318C>T	c.(316-318)acC>acT	p.T106T	CDH1_ENST00000422392.2_Silent_p.T106T|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	106					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GGGACTCCACCTACAGAAAGT	0.517			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	2	Unknown(2)	breast(2)	16											121	111	115					16																	68835727		2198	4300	6498	67393228	SO:0001819	synonymous_variant	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.318C>T	16.37:g.68835727C>T			67393228	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																				0.517	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68835727	C	T	68835727	2	4	118	1	0	0	0	0	0	0	0	1	3101	668	24	3		3	CDH1	16	68835727	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	47964167	68835727	21519026	144	31407										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	118	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10		7578406	73616804	145	31408										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27000472	27000472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtcagaggaagaatacaatgAtgaaggcgaggtggtacccc	14	7	1	4			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:27000472A>G	ENST00000314616.6	+	2	336	c.53A>G	c.(52-54)gAt>gGt	p.D18G	SUPT6H_ENST00000347486.4_Missense_Mutation_p.D18G|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	18	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					GAATACAATGATGAAGGCGAG	0.498																																																0			17											89	84	86					17																	27000472		2203	4300	6503	24024599	SO:0001583	missense	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.53A>G	17.37:g.27000472A>G	ENSP00000319104:p.Asp18Gly		24024599	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.408933	0.42715	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.75	5.75	0.90469	.	0.149195	0.64402	D	0.000018	T	0.39358	0.1075	N	0.08118	0	0.39561	D	0.969121	B	0.17667	0.023	B	0.13407	0.009	T	0.27054	-1.0085	9	0.31617	T	0.26	-14.4731	16.0518	0.80769	1.0:0.0:0.0:0.0	.	18	Q7KZ85	SPT6H_HUMAN	G	18	.	ENSP00000319104:D18G	D	+	2	0	SUPT6H	24024599	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.848000	0.92172	2.191000	0.70037	0.533000	0.62120	GAT		0.498	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27000472	A	G	27000472	3	3	118	1	0	0	0	0	1	0	0	0	15439	333	12	4	55	4	SUPT6H	17	27000472	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	19422066	27000472	54194738	146	31409										
CDC6	990	hgsc.bcm.edu	37	chr17	38447589	38447589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgtgagactattcaagcaagAaggtttgttcttacatggca	10	6	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:38447589A>G	ENST00000209728.4	+	3	929	c.458A>G	c.(457-459)gAa>gGa	p.E153G		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	153					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						TTCAAGCAAGAAGGTTTGTTC	0.408																																																0			17											84	87	86					17																	38447589		2203	4300	6503	35701115	SO:0001583	missense	990			U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.458A>G	17.37:g.38447589A>G	ENSP00000209728:p.Glu153Gly		35701115	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712008	0.48517	.	.	ENSG00000094804	ENST00000209728	T	0.53640	0.61	5.86	4.76	0.60689	.	0.253355	0.45126	D	0.000395	T	0.43366	0.1244	L	0.59436	1.845	0.45464	D	0.998435	B	0.19073	0.033	B	0.13407	0.009	T	0.25572	-1.0128	10	0.26408	T	0.33	-2.1609	12.3968	0.55389	0.8592:0.1408:0.0:0.0	.	153	Q99741	CDC6_HUMAN	G	153	ENSP00000209728:E153G	ENSP00000209728:E153G	E	+	2	0	CDC6	35701115	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.682000	0.54656	1.101000	0.41535	0.528000	0.53228	GAA		0.408	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			G	38447589	A	G	38447589	3	3	118	1	0	0	0	0	1	0	0	0	3089	246	9	4	464	4	CDC6	17	38447589	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	11447117	38447589	42747621	147	31410										
C17orf64	124773	hgsc.bcm.edu	37	chr17	58506840	58506840	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	acatcagcggcatgaaggagCggctgtccaacatgcagacc	12	12	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:58506840C>T	ENST00000269127.4	+	5	631	c.547C>T	c.(547-549)Cgg>Tgg	p.R183W		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	183										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CATGAAGGAGCGGCTGTCCAA	0.612																																																0			17											53	52	52					17																	58506840		2203	4300	6503	55861622	SO:0001583	missense	124773			BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.547C>T	17.37:g.58506840C>T	ENSP00000269127:p.Arg183Trp		55861622	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	37	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	C	13.94	2.386648	0.42308	.	.	ENSG00000141371	ENST00000269127	.	.	.	4.89	2.68	0.31781	.	0.223009	0.31859	N	0.006944	T	0.57257	0.2041	M	0.70595	2.14	0.31036	N	0.71687	D	0.76494	0.999	P	0.61722	0.893	T	0.60571	-0.7237	9	0.87932	D	0	-33.3571	4.4176	0.11465	0.6756:0.2186:0.1058:0.0	.	183	Q86WR6	CQ064_HUMAN	W	183	.	ENSP00000269127:R183W	R	+	1	2	C17orf64	55861622	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	0.863000	0.27913	0.724000	0.32296	-0.397000	0.06425	CGG		0.612	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		T	58506840	C	T	58506840	3	4	118	1	0	0	0	0	1	0	0	0	1877	759	27	1	565	1	C17orf64	17	58506840	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	20059251	58506840	22688370	148	31411										
OTOP3	347741	hgsc.bcm.edu	37	chr17	72945464	72945464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tgcctctgggggtcttctacCgcatgcactctgtgggaggc	14	12	4	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:72945464C>T	ENST00000328801.4	+	7	1744	c.1744C>T	c.(1744-1746)Cgc>Tgc	p.R582C		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	582						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					GGTCTTCTACCGCATGCACTC	0.597																																																0			17											63	58	60					17																	72945464		2203	4300	6503	70457059	SO:0001583	missense	347741			BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1744C>T	17.37:g.72945464C>T	ENSP00000328090:p.Arg582Cys		70457059		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.639199	0.67244	.	.	ENSG00000182938	ENST00000328801	T	0.54866	0.55	4.28	4.28	0.50868	.	0.000000	0.64402	D	0.000002	T	0.72045	0.3412	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76345	-0.2993	10	0.87932	D	0	-24.9005	10.9265	0.47193	0.3293:0.6707:0.0:0.0	.	582	Q7RTS5	OTOP3_HUMAN	C	582	ENSP00000328090:R582C	ENSP00000328090:R582C	R	+	1	0	OTOP3	70457059	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	0.933000	0.28897	1.946000	0.56461	0.313000	0.20887	CGC		0.597	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		T	72945464	C	T	72945464	3	4	118	1	0	0	0	0	1	0	0	0	11338	652	23	1	1770	1	OTOP3	17	72945464	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	14438624	72945464	8249746	149	31412										
NUP85	79902	hgsc.bcm.edu	37	chr17	73231686	73231686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tttgcaggatgatgacatagAgaccaccaaggtggaaatgc	12	7	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:73231686A>G	ENST00000245544.4	+	19	1954	c.1883A>G	c.(1882-1884)gAg>gGg	p.E628G	NUP85_ENST00000579324.1_Missense_Mutation_p.E516G|NUP85_ENST00000579298.1_Missense_Mutation_p.E583G|NUP85_ENST00000540768.1_Missense_Mutation_p.E231G|NUP85_ENST00000447371.2_3'UTR|NUP85_ENST00000541827.1_Missense_Mutation_p.E582G	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	628					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			GATGACATAGAGACCACCAAG	0.498																																																0			17											81	76	78					17																	73231686		2203	4300	6503	70743281	SO:0001583	missense	79902			AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.1883A>G	17.37:g.73231686A>G	ENSP00000245544:p.Glu628Gly		70743281	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	37	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.944389	0.73672	.	.	ENSG00000125450	ENST00000245544;ENST00000541827;ENST00000540768	.	.	.	5.91	4.83	0.62350	.	0.046847	0.85682	D	0.000000	T	0.35038	0.0918	N	0.08118	0	0.80722	D	1	B;B	0.17465	0.022;0.022	B;B	0.14578	0.011;0.011	T	0.17806	-1.0357	9	0.25106	T	0.35	-23.556	11.4297	0.50032	0.9304:0.0:0.0696:0.0	.	582;628	B4DMQ3;Q9BW27	.;NUP85_HUMAN	G	628;582;231	.	ENSP00000245544:E628G	E	+	2	0	NUP85	70743281	1.000000	0.71417	0.998000	0.56505	0.609000	0.37215	6.657000	0.74402	2.254000	0.74563	0.533000	0.62120	GAG		0.498	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844		G	73231686	A	G	73231686	3	3	118	1	0	0	0	0	1	0	0	0	10801	304	11	4	1957	4	NUP85	17	73231686	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	286222	73231686	7963524	150	31413										
RNF213	57674	hgsc.bcm.edu	37	chr17	78317685	78317685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tggaatttgggtgtttctttTcaagctcctcattttacaat	7	7	3	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr17:78317685T>C	ENST00000582970.1	+	28	6355	c.6212T>C	c.(6211-6213)tTc>tCc	p.F2071S	RNF213_ENST00000336301.6_Missense_Mutation_p.F144S|RNF213_ENST00000508628.2_Missense_Mutation_p.F2120S	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2071					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GTGTTTCTTTTCAAGCTCCTC	0.443																																																0			17											177	159	165					17																	78317685		2203	4300	6503	75932280	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.6212T>C	17.37:g.78317685T>C	ENSP00000464087:p.Phe2071Ser		75932280	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.941927	0.53079	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.60672	0.17	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.68824	0.3043	L	0.36672	1.1	0.41884	D	0.990333	D	0.89917	1.0	D	0.97110	1.0	T	0.72187	-0.4366	10	0.87932	D	0	.	16.3544	0.83230	0.0:0.0:0.0:1.0	.	144	Q63HN8	RN213_HUMAN	S	2071;2120;144	ENSP00000338218:F144S	ENSP00000338218:F144S	F	+	2	0	RNF213	75932280	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	7.232000	0.78116	2.265000	0.75225	0.459000	0.35465	TTC		0.443	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78317685	T	C	78317685	3	2	118	1	0	0	0	0	1	0	0	0	13514	1783	62	4	6637	4	RNF213	17	78317685	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	5085999	78317685	2877525	151	31414										
FBXO15	201456	hgsc.bcm.edu	37	chr18	71790624	71790624	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tctcttggtgaagagattgcGaaatgtaccacataggtaga	11	6	1	3	rs144253482		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr18:71790624G>A	ENST00000419743.2	-	8	1196	c.1117C>T	c.(1117-1119)Cgc>Tgc	p.R373C	FBXO15_ENST00000269500.5_Missense_Mutation_p.R297C	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	373						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		AAGAGATTGCGAAATGTACCA	0.428													G|||	1	0.000199681	0	0	5008	,	,		15347	0		0	False		,,,				2504	0.001															0			18						G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	76	76	76		1117,889	4.6	0	18	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FBXO15	NM_001142958.1,NM_152676.2	180,180	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	373/511,297/435	71790624	2,13004	2203	4300	6503	69941604	SO:0001583	missense	201456			AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1117C>T	18.37:g.71790624G>A	ENSP00000393154:p.Arg373Cys		69941604	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.822669	0.32237	2.27E-4	1.16E-4	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.46063	0.88;0.88	5.45	4.58	0.56647	.	0.718217	0.13850	N	0.358421	T	0.50837	0.1639	L	0.59436	1.845	0.09310	N	0.999999	D;D	0.76494	0.999;0.998	P;P	0.50490	0.642;0.549	T	0.46775	-0.9167	10	0.87932	D	0	-24.4827	14.1359	0.65287	0.0:0.1514:0.8486:0.0	.	373;297	B3KST3;Q8NCQ5	.;FBX15_HUMAN	C	297;373	ENSP00000269500:R297C;ENSP00000393154:R373C	ENSP00000269500:R297C	R	-	1	0	FBXO15	69941604	0.793000	0.28825	0.007000	0.13788	0.007000	0.05969	1.823000	0.39062	1.290000	0.44636	0.655000	0.94253	CGC		0.428	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		A	71790624	G	A	71790624	3	1	118	1	0	0	0	0	1	0	0	0	5747	1058	37	1	427	1	FBXO15	18	71790624	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10		71790624	6286624	152	31415										
MADCAM1	8174	hgsc.bcm.edu	37	chr19	501801	501801	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctccccggagcctcccgacaAgacctccccggagcccgccc	9	23	0	1	rs76476234		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:501801A>C	ENST00000215637.3	+	4	846	c.800A>C	c.(799-801)aAg>aCg	p.K267T	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.K48T	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	267	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|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)		CCTCCCGACAAGACCTCCCCG	0.726																																																0			19											12	14	13					19																	501801		2117	4144	6261	452801	SO:0001583	missense	8174			U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6765	protein-coding gene	gene with protein product	"mucosal addressin cell adhesion molecule-1"	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.800A>C	19.37:g.501801A>C	ENSP00000215637:p.Lys267Thr		452801	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	N	1.280	-0.610573	0.03690	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09538	2.97	2.48	-2.54	0.06307	.	2.146880	0.03414	N	0.205240	T	0.03739	0.0106	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30387	-0.9980	10	0.13108	T	0.6	.	1.2163	0.01915	0.159:0.2278:0.1571:0.4562	.	267	Q13477	MADCA_HUMAN	T	291;283;275;267	ENSP00000215637:K267T	ENSP00000215637:K267T	K	+	2	0	MADCAM1	452801	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.457000	0.06745	-0.940000	0.03705	-1.725000	0.00704	AAG		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760		C	501801	A	C	501801	3	2	118	1	0	0	0	0	1	0	0	0	9181	72	3	4	814	4	MADCAM1	19	501801	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10		501801	58627182	153	31416										
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975192	7975192	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gagaacttgggcgagatgggCagcggcacctgcggccaggt	18	10	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:7975192C>G	ENST00000397979.3	+	4	435	c.381C>G	c.(379-381)ggC>ggG	p.G127G	CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397981.3_Silent_p.G127G|MAP2K7_ENST00000397983.3_Silent_p.G143G|MAP2K7_ENST00000545011.1_Silent_p.G169G	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	127	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						GCGAGATGGGCAGCGGCACCT	0.672																																																0			19											33	39	37					19																	7975192		2040	4177	6217	7881192	SO:0001819	synonymous_variant	5609			AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.381C>G	19.37:g.7975192C>G			7881192	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Silent	SNP	ENST00000397979.3	37	CCDS42491.1																																																																																				0.672	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			G	7975192	C	G	7975192	2	3	118	1	0	0	0	0	0	0	0	1	9272	697	25	5		5	MAP2K7	19	7975192	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	7473391	7975192	51153791	154	31417										
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43098027	43098027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtgagctgagcagtggtgggCgggttccagaaggtgaaaag	19	5	0	4	rs369527473		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:43098027C>T	ENST00000244336.5	-	2	191	c.90G>A	c.(88-90)ccG>ccA	p.P30P	CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	30					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				CAGTGGTGGGCGGGTTCCAGA	0.512																																																0			19						C		0,4406		0,0,2203	111	103	106		90	-3.3	0	19		106	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEACAM8	NM_001816.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		30/350	43098027	1,13005	2203	4300	6503	47789867	SO:0001819	synonymous_variant	1088			D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.90G>A	19.37:g.43098027C>T			47789867	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																				0.512	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			T	43098027	C	T	43098027	2	4	118	1	0	0	0	0	0	0	0	1	3204	755	27	1		1	CEACAM8	19	43098027	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	35122835	43098027	16030956	155	31418										
CCDC114	93233	hgsc.bcm.edu	37	chr19	48800266	48800266	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tctttgctggtggaggagccCgggccagtgctggaggcagg	19	9	1	0	rs572589870		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:48800266C>T	ENST00000315396.7	-	14	2662	c.1980G>A	c.(1978-1980)ccG>ccA	p.P660P		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	660	Ser-rich.				outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		TGGAGGAGCCCGGGCCAGTGC	0.657													C|||	1	0.000199681	0	0	5008	,	,		15065	0		0	False		,,,				2504	0.001															0			19											28	30	30					19																	48800266		2203	4299	6502	53492078	SO:0001819	synonymous_variant	93233			BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1980G>A	19.37:g.48800266C>T			53492078	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																				0.657	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		T	48800266	C	T	48800266	2	4	118	1	0	0	0	0	0	0	0	1	2757	639	23	1		1	CCDC114	19	48800266	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	5702239	48800266	10328717	156	31419										
CPT1C	126129	hgsc.bcm.edu	37	chr19	50208286	50208286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cttcctgtatgtcacacccaCgcctctgcaggcagctcgcg	9	17	2	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:50208286C>T	ENST00000392518.4	+	9	1166	c.794C>T	c.(793-795)aCg>aTg	p.T265M	CPT1C_ENST00000405931.2_Intron|CPT1C_ENST00000598293.1_Missense_Mutation_p.T265M|CPT1C_ENST00000323446.5_Missense_Mutation_p.T265M|CPT1C_ENST00000354199.5_Missense_Mutation_p.T265M	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	265					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GTCACACCCACGCCTCTGCAG	0.642																																																0			19											59	66	64					19																	50208286		2203	4300	6503	54900098	SO:0001583	missense	126129			AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.794C>T	19.37:g.50208286C>T	ENSP00000376303:p.Thr265Met		54900098	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	37	CCDS12779.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636252	0.87760	.	.	ENSG00000169169	ENST00000392518;ENST00000354199;ENST00000323446;ENST00000295404	D;D;D	0.89810	-2.57;-2.57;-2.57	4.34	4.34	0.51931	.	0.000000	0.48767	D	0.000161	D	0.95079	0.8406	M	0.88979	2.995	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.99;0.999;0.99	D	0.96018	0.9007	10	0.87932	D	0	-16.6048	15.7686	0.78146	0.0:1.0:0.0:0.0	.	103;265;265	C9IY45;Q8TCG5-3;Q8TCG5	.;.;CPT1C_HUMAN	M	265;265;265;103	ENSP00000376303:T265M;ENSP00000346138:T265M;ENSP00000319343:T265M	ENSP00000295404:T103M	T	+	2	0	CPT1C	54900098	0.999000	0.42202	0.927000	0.36925	0.973000	0.67179	4.185000	0.58330	2.260000	0.74910	0.561000	0.74099	ACG		0.642	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		T	50208286	C	T	50208286	3	4	118	1	0	0	0	0	1	0	0	0	3839	536	19	1	820	1	CPT1C	19	50208286	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	1408020	50208286	8920697	157	31420										
MYH14	79784	hgsc.bcm.edu	37	chr19	50775819	50775819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ccccacccctgcctccagacCgcctacggaaggaggagaag	11	17	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:50775819C>T	ENST00000596571.1	+	24	3175	c.3175C>T	c.(3175-3177)Cgc>Tgc	p.R1059C	MYH14_ENST00000440075.2_Missense_Mutation_p.R1100C|MYH14_ENST00000262269.8_Missense_Mutation_p.R1100C|MYH14_ENST00000425460.1_Missense_Mutation_p.R1067C|MYH14_ENST00000376970.2_Missense_Mutation_p.R1092C|MYH14_ENST00000601313.1_Missense_Mutation_p.R1100C|MYH14_ENST00000598205.1_Missense_Mutation_p.R1067C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1059					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R1059C(1)|p.R1100C(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCCTCCAGACCGCCTACGGAA	0.627																																																2	Substitution - Missense(2)	large_intestine(2)	19											8	10	9					19																	50775819		2082	4203	6285	55467631	SO:0001583	missense	79784			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3175C>T	19.37:g.50775819C>T	ENSP00000472819:p.Arg1059Cys		55467631	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999873	0.54147	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66	3.06	3.06	0.35304	.	.	.	.	.	D	0.96420	0.8832	M	0.82517	2.595	0.58432	D	0.999999	D;P;D	0.89917	0.977;0.923;1.0	P;B;D	0.72075	0.514;0.198;0.976	D	0.95647	0.8703	9	0.66056	D	0.02	.	7.6324	0.28247	0.253:0.747:0.0:0.0	.	1100;1059;1067	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	1059;1100;1092;1067;1059;1100	ENSP00000406273:R1100C;ENSP00000366169:R1092C;ENSP00000407879:R1067C;ENSP00000262269:R1100C	ENSP00000262269:R1100C	R	+	1	0	MYH14	55467631	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.445000	0.52921	2.040000	0.60383	0.491000	0.48974	CGC		0.627	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50775819	C	T	50775819	3	4	118	1	0	0	0	0	1	0	0	0	10063	652	23	1	3400	1	MYH14	19	50775819	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	567533	50775819	8353164	158	31421										
VN1R4	317703	hgsc.bcm.edu	37	chr19	53770852	53770852	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ataatggagaagaacagagaAgctccccaggactcccacca	9	12	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:53770852A>G	ENST00000311170.4	-	1	120	c.67T>C	c.(67-69)Ttc>Ctc	p.F23L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	23					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		AGAACAGAGAAGCTCCCCAGG	0.483										HNSCC(26;0.072)																																						0			19											58	64	62					19																	53770852		2203	4300	6503	58462664	SO:0001583	missense	317703			AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.67T>C	19.37:g.53770852A>G	ENSP00000310856:p.Phe23Leu		58462664	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	.	.	.	.	.	.	.	.	.	.	A	8.026	0.760669	0.15914	.	.	ENSG00000228567	ENST00000311170	T	0.31510	1.49	2.28	1.21	0.21127	GPCR, rhodopsin-like superfamily (1);	1.476590	0.04844	N	0.440975	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	B	0.18166	0.026	B	0.21151	0.033	T	0.24368	-1.0162	10	0.40728	T	0.16	.	3.1173	0.06379	0.5035:0.2515:0.0:0.245	.	23	Q7Z5H5	VN1R4_HUMAN	L	23	ENSP00000310856:F23L	ENSP00000310856:F23L	F	-	1	0	VN1R4	58462664	0.037000	0.19845	0.001000	0.08648	0.004000	0.04260	0.587000	0.23909	0.302000	0.22762	-0.510000	0.04470	TTC		0.483	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857		G	53770852	A	G	53770852	3	3	118	1	0	0	0	0	1	0	0	0	17220	72	3	4	841	4	VN1R4	19	53770852	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	2995033	53770852	5358131	159	31422										
KIR3DL1	3811	hgsc.bcm.edu	37	chr19	55329797	55329797	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ggacaaacccttcctgtctgCctggcccagcgctgtggtgc	12	15	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr19:55329797C>A	ENST00000391728.4	+	3	131	c.98C>A	c.(97-99)gCc>gAc	p.A33D	KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.A33D|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.A33D|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.A33D|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.A33D	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	33					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TTCCTGTCTGCCTGGCCCAGC	0.547																																																0			19											55	75	68					19																	55329797		2170	4118	6288	60021609	SO:0001583	missense	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.98C>A	19.37:g.55329797C>A	ENSP00000375608:p.Ala33Asp		60021609	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.816003	0.32145	.	.	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.00922	5.54;5.54;5.54;5.54;5.54	1.41	0.314	0.15847	Immunoglobulin-like fold (1);	0.551703	0.13505	U	0.382927	T	0.06096	0.0158	H	0.94306	3.52	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.15896	-1.0421	10	0.72032	D	0.01	.	3.7747	0.08656	0.0:0.7471:0.0:0.2529	.	33;33	F6QF33;P43629	.;KI3L1_HUMAN	D	33;33;33;11;33;33	ENSP00000384528:A33D;ENSP00000443350:A33D;ENSP00000442355:A33D;ENSP00000375608:A33D;ENSP00000326868:A33D	ENSP00000326868:A33D	A	+	2	0	KIR3DL1	60021609	0.068000	0.21057	0.003000	0.11579	0.031000	0.12232	0.499000	0.22546	0.173000	0.19788	0.184000	0.17185	GCC		0.547	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		A	55329797	C	A	55329797	3	1	118	1	0	0	0	0	1	0	0	0	8341	739	26	2	108	2	KIR3DL1	19	55329797	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	1558945	55329797	3799186	160	31423										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39793963	39793963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctgagaacgacatcagcaacTctatcaagaatggcatcctc	7	12	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr20:39793963T>C	ENST00000373271.1	+	14	1870	c.1465T>C	c.(1465-1467)Tct>Cct	p.S489P	PLCG1_ENST00000244007.3_Missense_Mutation_p.S489P|PLCG1_ENST00000373272.2_Missense_Mutation_p.S489P	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	489	PH 2; first part. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				CATCAGCAACTCTATCAAGAA	0.582																																																0			20											107	97	100					20																	39793963		2203	4300	6503	39227377	SO:0001583	missense	5335			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.1465T>C	20.37:g.39793963T>C	ENSP00000362368:p.Ser489Pro		39227377	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287719	0.80803	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.68181	-0.31;-0.31;-0.31	5.13	4.04	0.47022	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.102825	0.64402	D	0.000001	T	0.74442	0.3717	M	0.70275	2.135	0.80722	D	1	D;D;D	0.62365	0.991;0.985;0.985	P;P;P	0.58721	0.844;0.781;0.703	T	0.72276	-0.4341	10	0.31617	T	0.26	.	10.7166	0.46015	0.0:0.0744:0.0:0.9256	.	489;489;489	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	P	489	ENSP00000244007:S489P;ENSP00000362368:S489P;ENSP00000362369:S489P	ENSP00000244007:S489P	S	+	1	0	PLCG1	39227377	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.331000	0.79192	0.990000	0.38787	0.533000	0.62120	TCT		0.582	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		C	39793963	T	C	39793963	3	2	118	1	0	0	0	0	1	0	0	0	12066	1551	54	4	1519	4	PLCG1	20	39793963	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10		39793963	23231557	161	31424										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766734	57766734	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctggaggaaggggacaaggcCggagagccccccagaccaga	16	12	0	3			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr20:57766734C>T	ENST00000371030.2	+	1	660	c.660C>T	c.(658-660)gcC>gcT	p.A220A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	220							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GGGACAAGGCCGGAGAGCCCC	0.701																																																0			20											24	31	29					20																	57766734		1870	4098	5968	57200129	SO:0001819	synonymous_variant	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.660C>T	20.37:g.57766734C>T			57200129	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																				0.701	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57766734	C	T	57766734	2	4	118	1	0	0	0	0	0	0	0	1	18224	639	23	1		1	ZNF831	20	57766734	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	17972771	57766734	5258786	162	31425										
CDH4	1002	hgsc.bcm.edu	37	chr20	60504710	60504710	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cgcatcctgtacctggaggcCgggatgtatgacgtccccat	12	13	0	1	rs201703403		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr20:60504710C>T	ENST00000360469.5	+	13	2137	c.2049C>T	c.(2047-2049)gcC>gcT	p.A683A	CDH4_ENST00000543233.1_Silent_p.A609A	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	683	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A683A(2)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ACCTGGAGGCCGGGATGTATG	0.547																																																2	Substitution - coding silent(2)	breast(2)	20											140	105	117					20																	60504710		2203	4300	6503	59938105	SO:0001819	synonymous_variant	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2049C>T	20.37:g.60504710C>T			59938105	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																				0.547	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60504710	C	T	60504710	2	4	118	1	0	0	0	0	0	0	0	1	3118	639	23	1		1	CDH4	20	60504710	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	2737976	60504710	2520810	163	31426										
TMEM50B	757	hgsc.bcm.edu	37	chr21	34828045	34828045	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcaacttacctaaaaaatatAagtgcattttgaaaaaacac	4	7	0	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr21:34828045A>G	ENST00000542230.2	-	6	634	c.420T>C	c.(418-420)ctT>ctC	p.L140L		NM_006134.6	NP_006125.2	P56557	TM50B_HUMAN	transmembrane protein 50B	140						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L140L(1)		breast(1)|kidney(1)|ovary(1)|skin(1)	4						TAAAAAATATAAGTGCATTTT	0.318																																																1	Substitution - coding silent(1)	ovary(1)	21											98	97	97					21																	34828045		2202	4298	6500	33749915	SO:0001819	synonymous_variant	757			AF045606	CCDS13625.1	21q22.1	2008-07-29	2005-06-02	2005-06-02	ENSG00000142188	ENSG00000142188			1280	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 4"	C21orf4			Standard	NR_040016		Approved		uc002yrs.2	P56557	OTTHUMG00000065286	ENST00000542230.2:c.420T>C	21.37:g.34828045A>G			33749915	B2R4L4|D3DSF1|O60537|Q5PY47	Silent	SNP	ENST00000542230.2	37	CCDS13625.1																																																																																				0.318	TMEM50B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140080.5			G	34828045	A	G	34828045	2	3	118	1	0	0	0	0	0	0	0	1	16215	349	13	4		4	TMEM50B	21	34828045	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10		34828045	13301850	164	31427										
RUNX1	861	hgsc.bcm.edu	37	chr21	36252867	36252867	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aacgtacctcttccacttcgAccgacaaacctgaggtcatt	6	14	2	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr21:36252867A>G	ENST00000344691.4	-	2	1991	c.414T>C	c.(412-414)ggT>ggC	p.G138G	RUNX1_ENST00000399240.1_Silent_p.G138G|RUNX1_ENST00000358356.5_Silent_p.G138G|RUNX1_ENST00000486278.2_Silent_p.G141G|RUNX1_ENST00000325074.5_Silent_p.G153G|RUNX1_ENST00000300305.3_Silent_p.G165G|RUNX1_ENST00000437180.1_Silent_p.G165G	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	138	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.G165_R166insGG(1)|p.R166fs*47(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TTCCACTTCGACCGACAAACC	0.428			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	2	Insertion - In frame(1)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	21											122	108	113					21																	36252867		2203	4300	6503	35174737	SO:0001819	synonymous_variant	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.414T>C	21.37:g.36252867A>G			35174737	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Silent	SNP	ENST00000344691.4	37	CCDS42922.1																																																																																				0.428	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			G	36252867	A	G	36252867	2	3	118	1	0	0	0	0	0	0	0	1	13783	262	10	4		4	RUNX1	21	36252867	Silent	SNP	A	TCGA-F5-6811-01A-11D-1826-10	1424822	36252867	11877028	165	31428										
MORC3	23515	hgsc.bcm.edu	37	chr21	37744778	37744778	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tcaacagacggcaacagatgTttcaacatcaagtaacattg	7	9	3	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr21:37744778T>C	ENST00000400485.1	+	16	2691	c.2615T>C	c.(2614-2616)gTt>gCt	p.V872A	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	872					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						GCAACAGATGTTTCAACATCA	0.368																																																0			21											143	131	134					21																	37744778		1848	4103	5951	36666648	SO:0001583	missense	23515			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.2615T>C	21.37:g.37744778T>C	ENSP00000383333:p.Val872Ala		36666648	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	T	7.677	0.688221	0.14973	.	.	ENSG00000159256	ENST00000400485	D	0.88046	-2.33	5.6	3.05	0.35203	.	0.639196	0.16071	N	0.231017	T	0.77370	0.4120	L	0.47716	1.5	0.25346	N	0.988907	B	0.20887	0.049	B	0.14023	0.01	T	0.58457	-0.7633	10	0.07482	T	0.82	-9.8741	4.8885	0.13715	0.2503:0.0:0.2538:0.4958	.	872	Q14149	MORC3_HUMAN	A	872	ENSP00000383333:V872A	ENSP00000383333:V872A	V	+	2	0	MORC3	36666648	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	1.927000	0.40094	0.911000	0.36747	0.402000	0.26972	GTT		0.368	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		C	37744778	T	C	37744778	3	2	118	1	0	0	0	0	1	0	0	0	9733	1725	60	4	2677	4	MORC3	21	37744778	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	1491911	37744778	10385117	166	31429										
ZDHHC8	29801	hgsc.bcm.edu	37	chr22	20132830	20132830	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcccggctgggacctgccacCggccccccagggccctctgc	13	21	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr22:20132830C>T	ENST00000334554.7	+	11	2346	c.2205C>T	c.(2203-2205)acC>acT	p.T735T	ZDHHC8_ENST00000405930.3_Intron|ZDHHC8_ENST00000320602.7_Silent_p.T643T	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	735					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GACCTGCCACCGGCCCCCCAG	0.637																																																0			22											59	68	65					22																	20132830		2202	4300	6502	18512830	SO:0001819	synonymous_variant	29801			AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.2205C>T	22.37:g.20132830C>T			18512830	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																				0.637	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20132830	C	T	20132830	2	4	118	1	0	0	0	0	0	0	0	1	17660	639	23	1		1	ZDHHC8	22	20132830	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10		20132830	31171736	167	31430										
CSDC2	27254	hgsc.bcm.edu	37	chr22	41969714	41969714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcgtctgtaagcagttctcaCgctcacagggccatggcttc	11	13	3	0	rs373284212		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr22:41969714C>T	ENST00000306149.7	+	3	776	c.232C>T	c.(232-234)Cgc>Tgc	p.R78C		NM_014460.3	NP_055275.1	Q9Y534	CSDC2_HUMAN	cold shock domain containing C2, RNA binding	78	CSD.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			prostate(2)|upper_aerodigestive_tract(1)	3						GCAGTTCTCACGCTCACAGGG	0.612																																					NSCLC(181;294 2110 12667 14717 31090)											0			22											131	109	117					22																	41969714		2203	4300	6503	40299660	SO:0001583	missense	27254			AL834417	CCDS14019.1	22q13.2	2006-02-24			ENSG00000172346	ENSG00000172346			30359	protein-coding gene	gene with protein product						8573167, 12767259	Standard	NM_014460		Approved	PIPPin	uc003bak.1	Q9Y534	OTTHUMG00000150967	ENST00000306149.7:c.232C>T	22.37:g.41969714C>T	ENSP00000302485:p.Arg78Cys		40299660	Q8ND37	Missense_Mutation	SNP	ENST00000306149.7	37	CCDS14019.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701763	0.88924	.	.	ENSG00000172346	ENST00000306149;ENST00000460790	.	.	.	5.41	5.41	0.78517	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.85221	0.5647	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87432	0.2389	9	0.62326	D	0.03	.	18.8152	0.92075	0.0:1.0:0.0:0.0	.	78	Q9Y534	CSDC2_HUMAN	C	78;61	.	ENSP00000302485:R78C	R	+	1	0	CSDC2	40299660	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	4.689000	0.61723	2.534000	0.85438	0.555000	0.69702	CGC		0.612	CSDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320689.1	NM_014460		T	41969714	C	T	41969714	3	4	118	1	0	0	0	0	1	0	0	0	3934	536	19	1	238	1	CSDC2	22	41969714	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	21836884	41969714	9334852	168	31431										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50279382	50279382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gcttgaatacttgaaacctcAgtactccctccccgcccctt	5	17	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr22:50279382A>G	ENST00000216268.5	+	2	2549	c.2072A>G	c.(2071-2073)cAg>cGg	p.Q691R		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	691						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		TTGAAACCTCAGTACTCCCTC	0.448																																																0			22											110	115	114					22																	50279382		2203	4300	6503	48665386	SO:0001583	missense	9889			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2072A>G	22.37:g.50279382A>G	ENSP00000216268:p.Gln691Arg		48665386	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	A	13.99	2.401414	0.42613	.	.	ENSG00000100426	ENST00000216268	T	0.39406	1.08	5.36	4.32	0.51571	.	0.065867	0.64402	D	0.000006	T	0.31136	0.0787	L	0.37561	1.115	0.58432	D	0.999996	B	0.27656	0.184	B	0.26310	0.068	T	0.09530	-1.0670	10	0.27785	T	0.31	-28.2004	10.5939	0.45325	0.9247:0.0:0.0753:0.0	.	691	O75132	ZBED4_HUMAN	R	691	ENSP00000216268:Q691R	ENSP00000216268:Q691R	Q	+	2	0	ZBED4	48665386	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.028000	0.76470	2.017000	0.59298	0.533000	0.62120	CAG		0.448	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		G	50279382	A	G	50279382	3	3	118	1	0	0	0	0	1	0	0	0	17559	188	7	4	2074	4	ZBED4	22	50279382	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	8309668	50279382	1025184	169	31432										
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50555769	50555769	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aaaactacagttgttgtgacCgcacagaaaaggtaccataa	8	8	0	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chr22:50555769C>T	ENST00000262794.5	+	9	1526	c.1443C>T	c.(1441-1443)acC>acT	p.T481T	MOV10L1_ENST00000545383.1_Silent_p.T481T|MOV10L1_ENST00000395858.3_Silent_p.T481T|MOV10L1_ENST00000540615.1_Silent_p.T461T|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	481					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TTGTTGTGACCGCACAGAAAA	0.473																																																0			22											47	44	45					22																	50555769		2203	4300	6503	48897896	SO:0001819	synonymous_variant	54456			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1443C>T	22.37:g.50555769C>T			48897896	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.473	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50555769	C	T	50555769	2	4	118	1	0	0	0	0	0	0	0	1	9749	639	23	1		1	MOV10L1	22	50555769	Silent	SNP	C	TCGA-F5-6811-01A-11D-1826-10	276387	50555769	748797	170	31433										
XG	7499	hgsc.bcm.edu	37	chrX	2729383	2729383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ctccactcctgcaggcaataTggtagcaaaaatcgtgtctc	8	12	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:2729383T>C	ENST00000381174.5	+	9	641	c.416T>C	c.(415-417)aTg>aCg	p.M139T	XG_ENST00000419513.2_Missense_Mutation_p.M154T|XG_ENST00000426774.1_Missense_Mutation_p.M140T|snoU13_ENST00000516039.1_RNA			P55808	XG_HUMAN	Xg blood group	139						integral component of plasma membrane (GO:0005887)		p.M139T(1)		endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GCAGGCAATATGGTAGCAAAA	0.438																																																1	Substitution - Missense(1)	ovary(1)	X											51	48	49					X																	2729383		2203	4298	6501	2739383	SO:0001583	missense	100132596			AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"Blood group antigens", "Pseudoautosomal regions / PAR1"	12806	protein-coding gene	gene with protein product		300879	"Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.416T>C	X.37:g.2729383T>C	ENSP00000370566:p.Met139Thr		2739383	E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Missense_Mutation	SNP	ENST00000381174.5	37	CCDS14120.1	.	.	.	.	.	.	.	.	.	.	T	1.900	-0.453427	0.04540	.	.	ENSG00000124343	ENST00000381174;ENST00000419513;ENST00000426774;ENST00000509484;ENST00000533923	T;T;T;T	0.20598	2.06;2.06;2.06;2.06	3.58	1.43	0.22495	.	2.178760	0.02607	N	0.101685	T	0.05914	0.0154	N	0.00707	-1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34576	-0.9823	10	0.07325	T	0.83	.	4.0654	0.09857	0.0:0.6032:0.2202:0.1766	.	139;154	P55808;P55808-3	XG_HUMAN;.	T	139;154;140;117;1	ENSP00000370566:M139T;ENSP00000411004:M154T;ENSP00000398503:M140T;ENSP00000430005:M117T	ENSP00000370566:M139T	M	+	2	0	XG	2739383	0.000000	0.05858	0.002000	0.10522	0.161000	0.22273	-1.013000	0.03645	-0.027000	0.13873	0.303000	0.19852	ATG		0.438	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		C	2729383	T	C	2729383	3	2	118	1	0	0	0	0	1	0	0	0	17467	1464	51	4	502	4	XG	23	2729383	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10		2729383	152541177	171	31434										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241453	3241453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	acactctgcgaccttctgcaAcattggtctctggttctttt	7	12	4	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:3241453A>G	ENST00000217939.6	-	5	2427	c.2273T>C	c.(2272-2274)gTt>gCt	p.V758A		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	758						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				ACCTTCTGCAACATTGGTCTC	0.433																																																0			X											112	98	103					X																	3241453		2203	4300	6503	3251453	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2273T>C	X.37:g.3241453A>G	ENSP00000217939:p.Val758Ala		3251453	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	a	10.79	1.449434	0.26074	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.68624	-0.34	3.63	3.63	0.41609	.	0.755193	0.10598	U	0.656033	T	0.56746	0.2006	L	0.29908	0.895	0.09310	N	1	B	0.28082	0.2	B	0.28385	0.089	T	0.52881	-0.8516	10	0.66056	D	0.02	.	11.977	0.53098	1.0:0.0:0.0:0.0	.	758	Q9NR99	MXRA5_HUMAN	A	758	ENSP00000217939:V758A	ENSP00000217939:V758A	V	-	2	0	MXRA5	3251453	0.004000	0.15560	0.001000	0.08648	0.102000	0.19082	1.978000	0.40598	1.174000	0.42811	0.430000	0.28490	GTT		0.433	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		G	3241453	A	G	3241453	3	3	118	1	0	0	0	0	1	0	0	0	10033	43	2	4	6225	4	MXRA5	23	3241453	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	512070	3241453	152029107	172	31435										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241640	3241640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cgagcccccttcatcctccaCgatgtcttctctgactctgg	7	17	4	1	rs143552209	byFrequency	TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:3241640C>T	ENST00000217939.6	-	5	2240	c.2086G>A	c.(2086-2088)Gtg>Atg	p.V696M		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	696						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCATCCTCCACGATGTCTTCT	0.517																																																0			X											76	72	73					X																	3241640		2203	4300	6503	3251640	SO:0001583	missense	25878			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2086G>A	X.37:g.3241640C>T	ENSP00000217939:p.Val696Met		3251640	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	10.46	1.355138	0.24512	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64260	-0.09	3.49	-0.208	0.13185	.	0.847121	0.09497	U	0.794126	T	0.36744	0.0978	N	0.08118	0	0.09310	N	1	B	0.26081	0.141	B	0.19666	0.026	T	0.18023	-1.0350	10	0.33141	T	0.24	.	7.1395	0.25548	0.0:0.2197:0.0:0.7803	.	696	Q9NR99	MXRA5_HUMAN	M	696	ENSP00000217939:V696M	ENSP00000217939:V696M	V	-	1	0	MXRA5	3251640	0.000000	0.05858	0.002000	0.10522	0.076000	0.17211	0.114000	0.15520	-0.032000	0.13758	0.529000	0.55759	GTG		0.517	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3241640	C	T	3241640	3	4	118	1	0	0	0	0	1	0	0	0	10033	536	19	1	6412	1	MXRA5	23	3241640	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	187	3241640	152028920	173	31436										
GPR64	10149	hgsc.bcm.edu	37	chrX	19032031	19032031	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cccctattggagagggaacaTtgtgggtcacaggtgaataa	13	7	1	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:19032031T>G	ENST00000379869.3	-	16	1035	c.872A>C	c.(871-873)aAt>aCt	p.N291T	GPR64_ENST00000379878.3_Missense_Mutation_p.N275T|GPR64_ENST00000379873.2_Missense_Mutation_p.N291T|GPR64_ENST00000357991.3_Missense_Mutation_p.N288T|GPR64_ENST00000360279.4_Missense_Mutation_p.N269T|GPR64_ENST00000379876.1_Missense_Mutation_p.N267T|GPR64_ENST00000340581.3_Missense_Mutation_p.N261T|GPR64_ENST00000357544.3_Missense_Mutation_p.N261T|GPR64_ENST00000356606.4_Missense_Mutation_p.N277T|GPR64_ENST00000354791.3_Missense_Mutation_p.N275T	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	291					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					AGAGGGAACATTGTGGGTCAC	0.557																																																0			X											126	121	123					X																	19032031		2203	4300	6503	18941952	SO:0001583	missense	10149			X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.872A>C	X.37:g.19032031T>G	ENSP00000369198:p.Asn291Thr		18941952	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Missense_Mutation	SNP	ENST00000379869.3	37	CCDS43923.1	.	.	.	.	.	.	.	.	.	.	T	9.418	1.082283	0.20309	.	.	ENSG00000173698	ENST00000379873;ENST00000379878;ENST00000354791;ENST00000379876;ENST00000357544;ENST00000379869;ENST00000360279;ENST00000357991;ENST00000356606;ENST00000340581	T;T;T;T;T;T;T;T;T;T	0.32272	1.5;1.61;1.61;1.61;1.6;1.65;1.61;1.65;1.65;1.46	5.36	-0.0717	0.13742	.	1.840750	0.02435	N	0.084012	T	0.14270	0.0345	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B;B;B;B;B	0.22909	0.012;0.001;0.071;0.002;0.002;0.077;0.071;0.071;0.071;0.001;0.025	B;B;B;B;B;B;B;B;B;B;B	0.25614	0.007;0.009;0.062;0.009;0.009;0.062;0.062;0.062;0.062;0.004;0.028	T	0.14643	-1.0465	10	0.09084	T	0.74	.	3.0389	0.06132	0.2477:0.3419:0.0:0.4104	.	261;253;261;267;275;291;269;277;288;291;275	Q14CE0;Q8IZP9-8;Q8IZP9-7;Q8IZP9-5;Q8IZP9-3;Q8IZP9-9;Q8IZP9-6;Q8IZP9-4;Q8IZP9-2;Q8IZP9;Q14CE1	.;.;.;.;.;.;.;.;.;GPR64_HUMAN;.	T	291;275;275;267;261;291;269;288;277;261	ENSP00000369202:N291T;ENSP00000369207:N275T;ENSP00000346845:N275T;ENSP00000369205:N267T;ENSP00000350152:N261T;ENSP00000369198:N291T;ENSP00000353421:N269T;ENSP00000350680:N288T;ENSP00000349015:N277T;ENSP00000344972:N261T	ENSP00000344972:N261T	N	-	2	0	GPR64	18941952	0.003000	0.15002	0.000000	0.03702	0.035000	0.12851	-0.039000	0.12124	0.066000	0.16515	0.356000	0.21956	AAT		0.557	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2			G	19032031	T	G	19032031	3	3	118	1	0	0	0	0	1	0	0	0	6725	1493	52	4	2237	4	GPR64	23	19032031	Missense_Mutation	SNP	T	TCGA-F5-6811-01A-11D-1826-10	15790391	19032031	136238529	174	31437										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83374910	83374910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	taccataagaacaccatatgAccaccaatcagcactctggg	6	13	2	2			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:83374910A>G	ENST00000262752.2	-	9	779	c.772T>C	c.(772-774)Tca>Cca	p.S258P	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.S258P	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	258	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S258T(2)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						ACACCATATGACCACCAATCA	0.333																																																2	Substitution - Missense(2)	lung(2)	X											81	71	75					X																	83374910		2203	4300	6503	83261566	SO:0001583	missense	27330			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.772T>C	X.37:g.83374910A>G	ENSP00000262752:p.Ser258Pro		83261566	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	37	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018095	0.75275	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.52754	0.65;0.65	5.42	5.42	0.78866	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73869	0.3642	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	T	0.80374	-0.1409	10	0.87932	D	0	.	14.4766	0.67551	1.0:0.0:0.0:0.0	.	258;258	B7ZL90;Q9UK32	.;KS6A6_HUMAN	P	258	ENSP00000262752:S258P;ENSP00000440830:S258P	ENSP00000262752:S258P	S	-	1	0	RPS6KA6	83261566	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	9.126000	0.94411	1.798000	0.52647	0.486000	0.48141	TCA		0.333	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		G	83374910	A	G	83374910	3	3	118	1	0	0	0	0	1	0	0	0	13692	275	10	4	1521	4	RPS6KA6	23	83374910	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	64342879	83374910	71895650	175	31438										
SLC25A5	292	hgsc.bcm.edu	37	chrX	118603706	118603707	+	Frame_Shift_Ins	INS	-	-	G													0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	gtccgtattcccaaggagcaINSgggagttctgtccttctggc					rs113356560		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:118603706_118603707insG	ENST00000317881.8	+	2	310_311	c.194_195insG	c.(193-198)cagggafs	p.QG65fs	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	65					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	CCCAAGGAGCAGGGAGTTCTGT	0.49																																																0			X																																								118487735	SO:0001589	frameshift_variant	292			BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.197dupG	X.37:g.118603709_118603709dupG	ENSP00000360671:p.Gln65fs		118487734	B2RCV1|O43350	Frame_Shift_Ins	INS	ENST00000317881.8	37	CCDS14578.1																																																																																				0.49	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		G	118603707	-	G	118603706	7	5	118	1	0	1	1	0	0	0	0	0	14549	188	7	0	200	0	SLC25A5	23	118603706	Frame_Shift_Ins	INS	-	TCGA-F5-6811-01A-11D-1826-10	35228796	118603706	36666854	176	31439										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123514421	123514421	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	ttcgctctgtctcataaagtGaatattattggcactgtcag	8	8	3	1			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:123514421G>A	ENST00000371130.3	-	31	8206	c.8143C>T	c.(8143-8145)Cac>Tac	p.H2715Y	TENM1_ENST00000422452.2_Missense_Mutation_p.H2722Y|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2715					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CTCATAAAGTGAATATTATTG	0.398																																																0			X											98	94	95					X																	123514421		2203	4300	6503	123342102	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.8143C>T	X.37:g.123514421G>A	ENSP00000360171:p.His2715Tyr		123342102	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835340	0.71373	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85702	-2.02;-1.99	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.91442	0.7299	M	0.61703	1.905	0.80722	D	1	D;D;D	0.63880	0.993;0.985;0.988	D;P;P	0.70227	0.968;0.838;0.841	D	0.91812	0.5460	10	0.66056	D	0.02	.	18.9144	0.92499	0.0:0.0:1.0:0.0	.	2721;2722;2715	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	Y	2715;2722	ENSP00000360171:H2715Y;ENSP00000403954:H2722Y	ENSP00000360171:H2715Y	H	-	1	0	ODZ1	123342102	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.414000	0.81942	0.538000	0.68166	CAC		0.398	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123514421	G	A	123514421	3	1	118	1	0	0	0	0	1	0	0	0	10865	1290	45	3	38	3	ODZ1	23	123514421	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	4910715	123514421	31756139	177	31440										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517633	123517633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	cagcaacaacatcataatccCtttgccccaggtgcactaat	5	14	1	0			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:123517633C>T	ENST00000371130.3	-	29	7190	c.7127G>A	c.(7126-7128)aGg>aAg	p.R2376K	TENM1_ENST00000422452.2_Missense_Mutation_p.R2383K|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2376					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R2378K(1)									ATCATAATCCCTTTGCCCCAG	0.418																																																1	Substitution - Missense(1)	ovary(1)	X											138	130	132					X																	123517633		2203	4300	6503	123345314	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7127G>A	X.37:g.123517633C>T	ENSP00000360171:p.Arg2376Lys		123345314	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043921	0.75732	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.92149	-2.98;-2.94	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.95965	0.8686	M	0.79011	2.435	0.58432	D	0.999997	D;D;B	0.64830	0.982;0.994;0.287	D;D;B	0.70716	0.952;0.97;0.085	D	0.95608	0.8669	10	0.49607	T	0.09	.	18.7972	0.91999	0.0:1.0:0.0:0.0	.	2382;2383;2376	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	K	2376;2383	ENSP00000360171:R2376K;ENSP00000403954:R2383K	ENSP00000360171:R2376K	R	-	2	0	ODZ1	123345314	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.050000	0.71063	2.471000	0.83476	0.600000	0.82982	AGG		0.418	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123517633	C	T	123517633	3	4	118	1	0	0	0	0	1	0	0	0	10865	681	24	3	1062	3	ODZ1	23	123517633	Missense_Mutation	SNP	C	TCGA-F5-6811-01A-11D-1826-10	3212	123517633	31752927	178	31441										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123787615	123787615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	caacttctccagtgtctatcGcccgtcccttctgaaacact	5	16	3	1	rs146613496		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:123787615G>A	ENST00000371130.3	-	7	1250	c.1187C>T	c.(1186-1188)gCg>gTg	p.A396V	TENM1_ENST00000422452.2_Missense_Mutation_p.A396V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	396					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGTGTCTATCGCCCGTCCCTT	0.383																																																0			X						G	VAL/ALA,VAL/ALA,VAL/ALA	0,3835		0,0,1632,571	102	87	92		1187,1184,1187	5.6	1	X	dbSNP_134	92	1,6727		0,1,2427,1872	no	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	64,64,64	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	benign,benign,benign	396/2733,395/2732,396/2726	123787615	1,10562	2203	4300	6503	123615296	SO:0001583	missense	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.1187C>T	X.37:g.123787615G>A	ENSP00000360171:p.Ala396Val		123615296	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.042620	0.75732	0.0	1.49E-4	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.26810	1.71;1.71	5.6	5.6	0.85130	.	0.062449	0.64402	D	0.000005	T	0.15132	0.0365	N	0.22421	0.69	0.58432	D	0.999999	P;P;B	0.37688	0.605;0.462;0.339	B;B;B	0.18871	0.019;0.023;0.013	T	0.08889	-1.0700	10	0.15066	T	0.55	.	18.6615	0.91473	0.0:0.0:1.0:0.0	.	395;396;396	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	396	ENSP00000360171:A396V;ENSP00000403954:A396V	ENSP00000360171:A396V	A	-	2	0	ODZ1	123615296	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	4.443000	0.59994	2.351000	0.79841	0.529000	0.55759	GCG		0.383	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123787615	G	A	123787615	3	1	118	1	0	0	0	0	1	0	0	0	10865	1087	38	1	7115	1	ODZ1	23	123787615	Missense_Mutation	SNP	G	TCGA-F5-6811-01A-11D-1826-10	269982	123787615	31482945	179	31442										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129271123	129271123	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	tttcccatatttcctttctcGgggaagagttgaatcacttc	7	10	2	2	rs371944474		TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:129271123G>T	ENST00000287295.3	-	10	1235	c.1005C>A	c.(1003-1005)ccC>ccA	p.P335P	AIFM1_ENST00000319908.3_Silent_p.P331P|AIFM1_ENST00000460436.2_5'UTR|AIFM1_ENST00000440263.1_5'UTR|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000346424.2_Silent_p.P48P	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	335	FAD-dependent oxidoreductase. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.P331P(1)|p.P335P(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	TTCCTTTCTCGGGGAAGAGTT	0.468																																																2	Substitution - coding silent(2)	ovary(2)	X											161	134	143					X																	129271123		2203	4300	6503	129098804	SO:0001819	synonymous_variant	9131			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1005C>A	X.37:g.129271123G>T			129098804	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	37	CCDS14618.1																																																																																				0.468	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			T	129271123	G	T	129271123	2	4	118	1	0	0	0	0	0	0	0	1	426	1103	39	2		2	AIFM1	23	129271123	Silent	SNP	G	TCGA-F5-6811-01A-11D-1826-10	5483508	129271123	25999437	180	31443										
GABRE	2564	hgsc.bcm.edu	37	chrX	151129761	151129761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0220994475138122	4	1	0.299018003273322	0	0.312307692307692	0.0476190476190476	0.29047619047619	0	aagaaggtactcacagctagAgaaagatagagggcaagagt	13	5	1	5			TCGA-F5-6811-01A-11D-1826-10	TCGA-F5-6811-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	f13f0ad4-f356-4674-ac6f-8a50bce4ad7c	236e43a6-590b-4f52-9d90-4cc8d139bdfa	g.chrX:151129761A>G	ENST00000370328.3	-	5	693	c.640T>C	c.(640-642)Tct>Cct	p.S214P	MIR224_ENST00000384889.1_RNA|GABRE_ENST00000370325.1_Missense_Mutation_p.S214P|GABRE_ENST00000393914.3_Intron|MIR452_ENST00000385020.1_RNA	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	214					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S101P(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCACAGCTAGAGAAAGATAGA	0.468																																																1	Substitution - Missense(1)	ovary(1)	X											119	110	113					X																	151129761		2203	4300	6503	150880417	SO:0001583	missense	2564			Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4085	protein-coding gene	gene with protein product	"GABA(A) receptor, epsilon"	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.640T>C	X.37:g.151129761A>G	ENSP00000359353:p.Ser214Pro		150880417	E7ET93|O15345|O15346|Q6PCD2|Q99520	Missense_Mutation	SNP	ENST00000370328.3	37	CCDS14703.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.620304	0.87460	.	.	ENSG00000102287	ENST00000370328;ENST00000370325	T;T	0.79940	-1.32;-1.32	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.252575	0.28219	N	0.016154	D	0.86657	0.5985	L	0.58583	1.82	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85075	0.0942	10	0.31617	T	0.26	.	12.79	0.57528	1.0:0.0:0.0:0.0	.	214	P78334	GBRE_HUMAN	P	214	ENSP00000359353:S214P;ENSP00000359350:S214P	ENSP00000359350:S214P	S	-	1	0	GABRE	150880417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.379000	0.66196	1.928000	0.55862	0.486000	0.48141	TCT		0.468	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984		G	151129761	A	G	151129761	3	3	118	1	0	0	0	0	1	0	0	0	6189	304	11	4	900	4	GABRE	23	151129761	Missense_Mutation	SNP	A	TCGA-F5-6811-01A-11D-1826-10	21858638	151129761	4140799	181	31444										
CDK11A	728642	hgsc.bcm.edu	37	chr1	1653140	1653140	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gggaatcccgcttggaatccCggtcatcagactaagaagca	11	11	2	2	rs200953503		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:1653140C>A	ENST00000378633.1	-	3	201	c.122G>T	c.(121-123)cGg>cTg	p.R41L	CDK11A_ENST00000356200.3_Missense_Mutation_p.R7L|CDK11A_ENST00000378635.3_Missense_Mutation_p.R41L|CDK11A_ENST00000357760.2_Missense_Mutation_p.R41L|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000358779.5_Missense_Mutation_p.R41L|CDK11A_ENST00000404249.3_Missense_Mutation_p.R41L|RP1-283E3.4_ENST00000417099.1_RNA|CDK11A_ENST00000378638.2_Missense_Mutation_p.R7L			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	41	Glu-rich.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						cttggaatcccggtcatcaga	0.388																																					Pancreas(186;965 2119 30274 40311 50569)											0			1											55	47	49					1																	1653140		1803	4053	5856	1643000	SO:0001583	missense	0			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"Cyclin-dependent kinases"	1730	protein-coding gene	gene with protein product		116951	"cell division cycle 2-like 2", "cell division cycle 2-like 2 (PITSLRE proteins)"	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.122G>T	1.37:g.1653140C>A	ENSP00000367900:p.Arg41Leu		1643000	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Missense_Mutation	SNP	ENST00000378633.1	37		.	.	.	.	.	.	.	.	.	.	c	17.18	3.324699	0.60634	.	.	ENSG00000008128	ENST00000356200;ENST00000404249;ENST00000357760;ENST00000358779;ENST00000378633;ENST00000378638;ENST00000378630;ENST00000378635;ENST00000479362	T;T;T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54	3.09	3.09	0.35607	.	0.072136	0.53938	D	0.000041	T	0.23926	0.0579	L	0.32530	0.975	0.42889	D	0.994192	P;D;P;D;D;D;D;D;D;D;D	0.71674	0.911;0.982;0.952;0.969;0.982;0.992;0.987;0.998;0.998;0.992;0.997	B;P;P;P;P;D;D;D;P;D;P	0.70487	0.392;0.598;0.74;0.682;0.831;0.969;0.931;0.943;0.875;0.969;0.834	T	0.02526	-1.1146	10	0.46703	T	0.11	.	13.3368	0.60522	0.0:1.0:0.0:0.0	.	41;41;41;41;41;41;7;41;41;7;41	B4E0M9;B4E0N4;E7ESP2;Q5QPR3;Q9UQ88-2;Q9UQ88-4;Q5QPR4;P21127-3;Q9UQ88;P21127-6;P21127-2	.;.;.;.;.;.;.;.;CD11A_HUMAN;.;.	L	7;41;41;41;41;7;7;41;41	ENSP00000348529:R7L;ENSP00000384442:R41L;ENSP00000350403:R41L;ENSP00000351629:R41L;ENSP00000367900:R41L;ENSP00000367905:R7L;ENSP00000367902:R41L;ENSP00000423900:R41L	ENSP00000348529:R7L	R	-	2	0	CDK11A	1643000	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	4.760000	0.62235	1.567000	0.49668	0.398000	0.26397	CGG		0.388	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		A	1653140	C	A	1653140	3	1	119	1	0	0	0	0	1	0	0	0	3132	652	23	2	2292	2	CDK11A	1	1653140	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10		1653140	247597481	1	31445										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11579845	11579845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tctgcagccagcctccaacaCgggcagccgcggccatctca	10	18	2	0	rs370213637		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:11579845C>T	ENST00000294484.6	+	9	2246	c.2108C>T	c.(2107-2109)aCg>aTg	p.T703M	PTCHD2_ENST00000389575.3_Missense_Mutation_p.T703M	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	703					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCCTCCAACACGGGCAGCCGC	0.657																																																0			1											60	72	68					1																	11579845		2109	4223	6332	11502432	SO:0001583	missense	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.2108C>T	1.37:g.11579845C>T	ENSP00000294484:p.Thr703Met		11502432	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	5.791	0.330187	0.10956	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.89810	-2.57;-2.57	5.27	-2.4	0.06583	.	0.818608	0.11675	N	0.540422	T	0.74749	0.3757	N	0.08118	0	0.09310	N	1	B	0.32939	0.391	B	0.34991	0.193	T	0.65323	-0.6196	10	0.48119	T	0.1	-0.2748	7.5277	0.27664	0.0876:0.545:0.2603:0.1071	.	703	Q9P2K9	PTHD2_HUMAN	M	703	ENSP00000294484:T703M;ENSP00000374226:T703M	ENSP00000294484:T703M	T	+	2	0	PTCHD2	11502432	0.025000	0.19082	0.000000	0.03702	0.011000	0.07611	0.181000	0.16880	-0.309000	0.08779	-1.157000	0.01802	ACG		0.657	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11579845	C	T	11579845	3	4	119	1	0	0	0	0	1	0	0	0	12767	536	19	1	2138	1	PTCHD2	1	11579845	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	9926705	11579845	237670776	2	31446										
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12835687	12835687	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcttctcttttacccacaggCggtggaaacttcaagtgttg	9	10	3	0	rs375662448	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:12835687C>T	ENST00000357726.4	+	2	316	c.289C>T	c.(289-291)Cgg>Tgg	p.R97W		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	97					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TACCCACAGGCGGTGGAAACT	0.517													C|||	3	0.000599042	0.0015	0	5008	,	,		20101	0.001		0	False		,,,				2504	0															0			1						C	TRP/ARG	0,4312		0,0,2156	140	160	153		289	-3	0	1		153	1,8569		0,1,4284	no	missense-near-splice	PRAMEF12	NM_001080830.1	101	0,1,6440	TT,TC,CC		0.0117,0.0,0.0078	benign	97/484	12835687	1,12881	2156	4285	6441	12758274	SO:0001630	splice_region_variant	390999				CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.288-1C>T	1.37:g.12835687C>T			12758274		Missense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	9.429	1.084967	0.20390	0.0	1.17E-4	ENSG00000116726	ENST00000357726	T	0.05081	3.5	2.8	-2.99	0.05497	.	0.177429	0.46442	D	0.000282	T	0.09335	0.0230	M	0.87547	2.89	0.09310	N	1	B	0.21606	0.058	B	0.21546	0.035	T	0.21042	-1.0257	10	0.87932	D	0	.	5.8088	0.18454	0.271:0.5608:0.0:0.1683	.	97	O95522	PRA12_HUMAN	W	97	ENSP00000350358:R97W	ENSP00000350358:R97W	R	+	1	2	PRAMEF12	12758274	0.007000	0.16637	0.001000	0.08648	0.060000	0.15804	0.046000	0.14035	-0.674000	0.05253	0.313000	0.20887	CGG		0.517	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	Missense_Mutation	T	12835687	C	T	12835687	5	4	119	1	0	0	0	0	0	0	1	0	12462	782	27	1	295	1	PRAMEF12	1	12835687	Splice_Site	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1255842	12835687	236414934	3	31447										
RPL11	6135	hgsc.bcm.edu	37	chr1	24021271	24021271	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cattggtatctacggcctggActtctatgtggtatgaatat	10	7	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:24021271A>T	ENST00000374550.3	+	4	431	c.386A>T	c.(385-387)gAc>gTc	p.D129V	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	129					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		TACGGCCTGGACTTCTATGTG	0.413																																																0			1											141	134	137					1																	24021271		2203	4300	6503	23893858	SO:0001583	missense	6135			L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.386A>T	1.37:g.24021271A>T	ENSP00000363676:p.Asp129Val		23893858	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	37	CCDS238.1	.	.	.	.	.	.	.	.	.	.	a	31	5.074392	0.94000	.	.	ENSG00000142676	ENST00000374550;ENST00000443624;ENST00000458455	T;T;T	0.80994	-1.44;-1.44;-1.44	5.94	5.94	0.96194	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.94272	0.8160	H	0.98996	4.395	0.80722	D	1	D;D	0.64830	0.993;0.994	D;D	0.85130	0.995;0.997	D	0.96517	0.9383	10	0.87932	D	0	-14.9648	16.4114	0.83713	1.0:0.0:0.0:0.0	.	128;129	P62913-2;P62913	.;RL11_HUMAN	V	129;127;127	ENSP00000363676:D129V;ENSP00000390839:D127V;ENSP00000398888:D127V	ENSP00000363676:D129V	D	+	2	0	RPL11	23893858	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.143000	0.94623	2.276000	0.75962	0.529000	0.55759	GAC		0.413	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		T	24021271	A	T	24021271	3	4	119	1	0	0	0	0	1	0	0	0	13594	275	10	5	400	5	RPL11	1	24021271	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	11185584	24021271	225229350	4	31448										
MACF1	23499	hgsc.bcm.edu	37	chr1	39905072	39905072	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gttctggtatgacatggcagCtctcctgaccaccatcaaag	9	12	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:39905072C>T	ENST00000372915.3	+	71	18131	c.18044C>T	c.(18043-18045)gCt>gTt	p.A6015V	MACF1_ENST00000289893.4_Missense_Mutation_p.A4559V|MACF1_ENST00000545844.1_Missense_Mutation_p.A4057V|MACF1_ENST00000317713.7_Missense_Mutation_p.A4057V|MACF1_ENST00000539005.1_Missense_Mutation_p.A3927V|MACF1_ENST00000567887.1_Missense_Mutation_p.A6153V|MACF1_ENST00000564288.1_Missense_Mutation_p.A6116V|MACF1_ENST00000361689.2_Missense_Mutation_p.A4057V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6015					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.A4057G(1)|p.A4559G(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	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)			GACATGGCAGCTCTCCTGACC	0.458																																																2	Substitution - Missense(2)	ovary(2)	1											86	81	83					1																	39905072		2203	4300	6503	39677659	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18044C>T	1.37:g.39905072C>T	ENSP00000362006:p.Ala6015Val		39677659	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	36	5.644298	0.96704	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000007	T	0.67277	0.2876	M	0.64997	1.995	0.80722	D	1	D;D	0.69078	0.997;0.991	D;D	0.65773	0.913;0.938	T	0.67616	-0.5625	10	0.66056	D	0.02	.	19.9826	0.97334	0.0:1.0:0.0:0.0	.	6015;4057	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	V	4057;6015;4057;4057;3927;4559	ENSP00000439537:A4057V;ENSP00000362006:A6015V;ENSP00000354573:A4057V;ENSP00000313438:A4057V;ENSP00000444364:A3927V;ENSP00000289893:A4559V	ENSP00000289893:A4559V	A	+	2	0	MACF1	39677659	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.814000	0.86154	2.734000	0.93682	0.650000	0.86243	GCT		0.458	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39905072	C	T	39905072	3	4	119	1	0	0	0	0	1	0	0	0	9174	797	28	3	18591	3	MACF1	1	39905072	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	15883801	39905072	209345549	5	31449										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45475351	45475351	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcaggcaggacacgttgaacTcctcctggggaggggcagag	16	10	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:45475351T>G	ENST00000372172.4	-	5	835	c.764A>C	c.(763-765)gAg>gCg	p.E255A	UROD_ENST00000246337.4_5'Flank|HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	255	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CACGTTGAACTCCTCCTGGGG	0.582																																																0			1											55	54	55					1																	45475351		2118	4213	6331	45247938	SO:0001583	missense	79654			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.764A>C	1.37:g.45475351T>G	ENSP00000361245:p.Glu255Ala		45247938	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	37	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	T	13.36	2.213400	0.39102	.	.	ENSG00000126107	ENST00000372172	T	0.70516	-0.49	4.9	4.9	0.64082	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	1.043500	0.07480	N	0.903639	T	0.74045	0.3665	M	0.65975	2.015	0.80722	D	1	B	0.29481	0.245	B	0.32090	0.14	T	0.66372	-0.5940	10	0.72032	D	0.01	.	14.8076	0.69968	0.0:0.0:0.0:1.0	.	255	Q5T447	HECD3_HUMAN	A	255	ENSP00000361245:E255A	ENSP00000361245:E255A	E	-	2	0	HECTD3	45247938	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	6.700000	0.74619	1.965000	0.57142	0.460000	0.39030	GAG		0.582	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		G	45475351	T	G	45475351	3	3	119	1	0	0	0	0	1	0	0	0	7062	1551	54	4	1889	4	HECTD3	1	45475351	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	5570279	45475351	203775270	6	31450										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93680443	93680443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctgatttgaaggttaacatgGctcacagaactagtcagttt	9	7	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:93680443G>T	ENST00000343253.7	+	12	2138	c.1636G>T	c.(1636-1638)Gct>Tct	p.A546S	CCDC18_ENST00000401026.3_Missense_Mutation_p.A547S|CCDC18_ENST00000338949.4_Missense_Mutation_p.A346S|CCDC18_ENST00000557479.1_Missense_Mutation_p.A665S|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	546								p.A665T(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		GGTTAACATGGCTCACAGAAC	0.383																																																1	Substitution - Missense(1)	ovary(1)	1											51	49	50					1																	93680443		1844	4098	5942	93453031	SO:0001583	missense	343099					1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1636G>T	1.37:g.93680443G>T	ENSP00000343377:p.Ala546Ser		93453031	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.60|14.60	2.585289|2.585289	0.46110|0.46110	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267|ENST00000370276	T;T;T;T;T|.	0.18810|.	2.19;2.19;2.19;2.19;2.19|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	0.196285|.	0.42548|.	D|.	0.000694|.	T|T	0.55257|0.55257	0.1909|0.1909	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	P;D|.	0.59767|.	0.932;0.986|.	P;P|.	0.53593|.	0.647;0.73|.	T|T	0.55354|0.55354	-0.8154|-0.8154	10|5	0.18276|.	T|.	0.48|.	.|.	13.0106|13.0106	0.58729|0.58729	0.0777:0.0:0.9223:0.0|0.0777:0.0:0.9223:0.0	.|.	546;665|.	Q5T9S5;G3V388|.	CCD18_HUMAN;.|.	S|C	546;547;665;346;266|599	ENSP00000343377:A546S;ENSP00000383808:A547S;ENSP00000451099:A665S;ENSP00000344380:A346S;ENSP00000391151:A266S|.	ENSP00000344380:A346S|.	A|W	+|+	1|3	0|0	CCDC18|CCDC18	93453031|93453031	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.057000|3.057000	0.49931|0.49931	2.373000|2.373000	0.80994|0.80994	0.655000|0.655000	0.94253|0.94253	GCT|TGG		0.383	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		T	93680443	G	T	93680443	3	4	119	1	0	0	0	0	1	0	0	0	2800	1203	42	2	2039	2	CCDC18	1	93680443	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	48205092	93680443	155570178	7	31451										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858598	149858598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctcgtcccgcgctggcctccAgttcccggtagggcgagtgc	14	16	0	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:149858598A>G	ENST00000331380.2	+	1	74	c.74A>G	c.(73-75)cAg>cGg	p.Q25R	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	25						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GCTGGCCTCCAGTTCCCGGTA	0.652																																																0			1											68	75	72					1																	149858598		2203	4299	6502	148125222	SO:0001583	missense	8338			AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.74A>G	1.37:g.149858598A>G	ENSP00000332194:p.Gln25Arg		148125222	Q6DRA7|Q8IUE5	Missense_Mutation	SNP	ENST00000331380.2	37	CCDS937.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.213734	0.58452	.	.	ENSG00000184260	ENST00000331380	T	0.66995	-0.24	5.81	4.66	0.58398	Histone-fold (2);Histone core (1);Histone H2A (3);	0.000000	0.42053	D	0.000761	T	0.78848	0.4348	H	0.95470	3.675	0.41055	D	0.985331	P	0.35793	0.521	P	0.50405	0.64	T	0.82303	-0.0524	10	0.87932	D	0	.	12.0124	0.53295	0.855:0.145:0.0:0.0	.	25	Q16777	H2A2C_HUMAN	R	25	ENSP00000332194:Q25R	ENSP00000332194:Q25R	Q	+	2	0	HIST2H2AC	148125222	1.000000	0.71417	0.989000	0.46669	0.940000	0.58332	6.119000	0.71590	0.995000	0.38917	0.533000	0.62120	CAG		0.652	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		G	149858598	A	G	149858598	3	3	119	1	0	0	0	0	1	0	0	0	7199	188	7	4	76	4	HIST2H2AC	1	149858598	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	56178155	149858598	99392023	8	31452										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182025552	182025552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gccgcagtcctcacactggtAgggcctctctccgttgtgca	11	15	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:182025552A>G	ENST00000339948.3	-	2	1801	c.1594T>C	c.(1594-1596)Tac>Cac	p.Y532H		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						TCACACTGGTAGGGCCTCTCT	0.622																																					NSCLC(71;908 1374 5429 20458 35642)											0			1											168	133	145					1																	182025552		2203	4300	6503	180292175	SO:0001583	missense	127665			AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.1594T>C	1.37:g.182025552A>G	ENSP00000344129:p.Tyr532His		180292175	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.802173	0.50315	.	.	ENSG00000179930	ENST00000339948	T	0.21734	1.99	2.77	1.58	0.23477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26231	0.0640	L	0.33137	0.985	0.29422	N	0.860488	P	0.52061	0.95	P	0.57468	0.821	T	0.11203	-1.0597	9	0.72032	D	0.01	.	7.2646	0.26222	0.7746:0.2254:0.0:0.0	.	532	Q5T619	ZN648_HUMAN	H	532	ENSP00000344129:Y532H	ENSP00000344129:Y532H	Y	-	1	0	ZNF648	180292175	0.506000	0.26139	0.991000	0.47740	0.971000	0.66376	3.612000	0.54142	0.430000	0.26230	0.533000	0.62120	TAC		0.622	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		G	182025552	A	G	182025552	3	3	119	1	0	0	0	0	1	0	0	0	18102	420	15	4	116	4	ZNF648	1	182025552	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	32166954	182025552	67225069	9	31453										
CDC73	79577	hgsc.bcm.edu	37	chr1	193094270	193094270	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aggaaggccaacccagagagTactacacattggattccatt	9	10	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:193094270T>C	ENST00000367435.3	+	2	344	c.160T>C	c.(160-162)Tac>Cac	p.Y54H		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	54					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						ACCCAGAGAGTACTACACATT	0.353																																																0			1											144	143	143					1																	193094270		2203	4300	6503	191360893	SO:0001583	missense	79577			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.160T>C	1.37:g.193094270T>C	ENSP00000356405:p.Tyr54His		191360893	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.790854	0.90367	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.86497	-2.13	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.93585	0.7952	M	0.83483	2.645	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	D	0.94210	0.7458	10	0.66056	D	0.02	-8.6067	16.3009	0.82811	0.0:0.0:0.0:1.0	.	54	Q6P1J9	CDC73_HUMAN	H	54	ENSP00000356405:Y54H	ENSP00000356405:Y54H	Y	+	1	0	CDC73	191360893	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.768000	0.85345	2.246000	0.74042	0.533000	0.62120	TAC		0.353	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		C	193094270	T	C	193094270	3	2	119	1	0	0	0	0	1	0	0	0	3091	1638	57	4	166	4	CDC73	1	193094270	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	11068718	193094270	56156351	10	31454										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198668819	198668819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	actcaaccctaccccaggcaGcaatgctatctcaggtttgc	7	15	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:198668819G>A	ENST00000367376.2	+	5	590	c.419G>A	c.(418-420)aGc>aAc	p.S140N	PTPRC_ENST00000352140.3_Missense_Mutation_p.S140N|PTPRC_ENST00000594404.1_Intron|PTPRC_ENST00000391970.3_3'UTR|PTPRC_ENST00000348564.6_Intron|PTPRC_ENST00000442510.2_Missense_Mutation_p.S142N	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	140					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						ACCCCAGGCAGCAATGCTATC	0.512											OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			1											111	115	113					1																	198668819		2203	4300	6503	196935442	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.419G>A	1.37:g.198668819G>A	ENSP00000356346:p.Ser140Asn	2100	196935442	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	10.67	1.416047	0.25552	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000271610;ENST00000530727;ENST00000442510;ENST00000367367	T	0.02606	4.23	5.33	-0.533	0.11887	.	1.774010	0.02493	N	0.089646	T	0.03520	0.0101	L	0.47716	1.5	0.09310	N	1	P;P;P;P;B;B	0.47302	0.893;0.828;0.61;0.61;0.255;0.255	B;B;B;B;B;B	0.40134	0.32;0.17;0.145;0.127;0.045;0.071	T	0.38243	-0.9670	10	0.42905	T	0.14	.	3.2344	0.06760	0.1618:0.2573:0.4621:0.1188	.	76;76;76;181;140;140	F5GXZ3;B4DSZ5;Q5T9M4;Q6Q1P2;E9PC28;P08575	.;.;.;.;.;PTPRC_HUMAN	N	142;76;140;140;181;74;140;74	ENSP00000193532:S140N	ENSP00000271610:S181N	S	+	2	0	PTPRC	196935442	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.033000	0.12246	0.191000	0.20236	0.555000	0.69702	AGC		0.512	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198668819	G	A	198668819	3	1	119	1	0	0	0	0	1	0	0	0	12834	971	34	3	444	3	PTPRC	1	198668819	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	5574549	198668819	50581802	11	31455										
GREM2	64388	hgsc.bcm.edu	37	chr1	240656552	240656552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccgtctgccgcagcggctgcGtcttgcaccagtcactcttg	11	16	4	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:240656552G>A	ENST00000318160.4	-	2	490	c.224C>T	c.(223-225)aCg>aTg	p.T75M		NM_022469.3	NP_071914.3	Q9H772	GREM2_HUMAN	gremlin 2, DAN family BMP antagonist	75	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				BMP signaling pathway (GO:0030509)|cytokine-mediated signaling pathway (GO:0019221)|determination of dorsal identity (GO:0048263)|embryonic body morphogenesis (GO:0010172)|regulation of cytokine activity (GO:0060300)|sequestering of BMP from receptor via BMP binding (GO:0038098)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	10		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			CAGCGGCTGCGTCTTGCACCA	0.647																																																0			1											51	51	51					1																	240656552		2203	4300	6503	238723175	SO:0001583	missense	64388			AK024848	CCDS31070.1	1q43	2013-02-26	2013-02-26		ENSG00000180875	ENSG00000180875			17655	protein-coding gene	gene with protein product	"protein related to DAN and cerberus"	608832	"gremlin 2, cysteine knot superfamily, homolog (Xenopus laevis)", "gremlin 2"			15039429	Standard	XM_005273226		Approved	Prdc, FLJ21195, CKTSF1B2, DAND3	uc001hys.3	Q9H772	OTTHUMG00000039909	ENST00000318160.4:c.224C>T	1.37:g.240656552G>A	ENSP00000318650:p.Thr75Met		238723175	Q86UD9	Missense_Mutation	SNP	ENST00000318160.4	37	CCDS31070.1	.	.	.	.	.	.	.	.	.	.	G	32	5.126793	0.94429	.	.	ENSG00000180875	ENST00000318160	T	0.35421	1.31	5.03	5.03	0.67393	DAN (1);Cystine knot, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.63426	0.2510	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68872	-0.5294	10	0.87932	D	0	-24.8534	18.3609	0.90374	0.0:0.0:1.0:0.0	.	75	Q9H772	GREM2_HUMAN	M	75	ENSP00000318650:T75M	ENSP00000318650:T75M	T	-	2	0	GREM2	238723175	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.635000	0.98437	2.327000	0.79052	0.557000	0.71058	ACG		0.647	GREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096286.1	NM_022469		A	240656552	G	A	240656552	3	1	119	1	0	0	0	0	1	0	0	0	6783	1145	40	1	286	1	GREM2	1	240656552	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	41987733	240656552	8594069	12	31456										
KMO	8564	hgsc.bcm.edu	37	chr1	241753350	241753350	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	actcaagctggttcatttttCagaagaacatggagagattt	9	6	3	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:241753350C>G	ENST00000366559.4	+	13	1446	c.1135C>G	c.(1135-1137)Cag>Gag	p.Q379E	KMO_ENST00000366558.3_Intron|KMO_ENST00000366557.4_Intron	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			GTTCATTTTTCAGAAGAACAT	0.393																																																0			1											146	140	142					1																	241753350		2203	4300	6503	239819973	SO:0001583	missense	8564			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.1135C>G	1.37:g.241753350C>G	ENSP00000355517:p.Gln379Glu		239819973		Missense_Mutation	SNP	ENST00000366559.4	37	CCDS1618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.57|12.57	1.977307|1.977307	0.34848|0.34848	.|.	.|.	ENSG00000117009|ENSG00000117009	ENST00000366559|ENST00000366555	T|.	0.41758|.	0.99|.	5.71|5.71	4.8|4.8	0.61643|0.61643	.|.	0.346172|.	0.30446|.	N|.	0.009620|.	T|.	0.62085|.	0.2399|.	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	B;B|.	0.17038|.	0.02;0.02|.	B;B|.	0.10450|.	0.005;0.005|.	T|.	0.60464|.	-0.7258|.	10|.	0.87932|.	D|.	0|.	.|.	10.4131|10.4131	0.44305|0.44305	0.0:0.9107:0.0:0.0893|0.0:0.9107:0.0:0.0893	.|.	379;379|.	O15229;A8K693|.	KMO_HUMAN;.|.	E|X	379|64	ENSP00000355517:Q379E|.	ENSP00000355517:Q379E|.	Q|S	+|+	1|2	0|0	KMO|KMO	239819973|239819973	1.000000|1.000000	0.71417|0.71417	0.735000|0.735000	0.30896|0.30896	0.509000|0.509000	0.34042|0.34042	2.987000|2.987000	0.49378|0.49378	1.413000|1.413000	0.46997|0.46997	0.655000|0.655000	0.94253|0.94253	CAG|TCA		0.393	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679		G	241753350	C	G	241753350	3	3	119	1	0	0	0	0	1	0	0	0	8445	827	29	5	1185	5	KMO	1	241753350	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1096798	241753350	7497271	13	31457										
CHML	1122	hgsc.bcm.edu	37	chr1	241797528	241797528	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cttctcttgctgttttagaaGatgaacatgtcaaatgtacc	7	8	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:241797528G>T	ENST00000366553.1	-	1	1704	c.1541C>A	c.(1540-1542)tCt>tAt	p.S514Y	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000331838.5_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	514					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.S514C(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TGTTTTAGAAGATGAACATGT	0.408																																																1	Substitution - Missense(1)	ovary(1)	1											83	78	80					1																	241797528		2203	4299	6502	239864151	SO:0001583	missense	1122			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1541C>A	1.37:g.241797528G>T	ENSP00000355511:p.Ser514Tyr		239864151	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.448002	0.63178	.	.	ENSG00000203668	ENST00000366553	D	0.84370	-1.84	5.08	5.08	0.68730	.	0.000000	0.85682	U	0.000000	D	0.92388	0.7584	.	.	.	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	D	0.92741	0.6208	9	0.66056	D	0.02	-13.9275	16.3808	0.83460	0.0:0.0:1.0:0.0	.	514	P26374	RAE2_HUMAN	Y	514	ENSP00000355511:S514Y	ENSP00000355511:S514Y	S	-	2	0	CHML	239864151	1.000000	0.71417	0.986000	0.45419	0.976000	0.68499	2.468000	0.45102	2.826000	0.97356	0.655000	0.94253	TCT		0.408	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		T	241797528	G	T	241797528	3	4	119	1	0	0	0	0	1	0	0	0	3357	942	33	2	433	2	CHML	1	241797528	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	44178	241797528	7453093	14	31458										
WDR64	128025	hgsc.bcm.edu	37	chr1	241834420	241834420	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gaagatcctattgcttcccaGttggatgaagaaaatttggt	10	6	0	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:241834420G>A	ENST00000366552.2	+	3	528	c.321G>A	c.(319-321)caG>caA	p.Q107Q	WDR64_ENST00000461971.1_3'UTR|WDR64_ENST00000437684.2_Silent_p.Q107Q	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	107										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TTGCTTCCCAGTTGGATGAAG	0.328																																																0			1											204	166	178					1																	241834420		692	1591	2283	239901043	SO:0001819	synonymous_variant	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.321G>A	1.37:g.241834420G>A			239901043	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	37																																																																																					0.328	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241834420	G	A	241834420	2	1	119	1	0	0	0	0	0	0	0	1	17355	1020	36	3		3	WDR64	1	241834420	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10	36892	241834420	7416201	15	31459										
OR2M4	26245	hgsc.bcm.edu	37	chr1	248403030	248403030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gagaccagcttctaaacataCgccagaccaggacaagatgg	10	11	1	3	rs144697226	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr1:248403030C>T	ENST00000306687.1	+	1	800	c.800C>T	c.(799-801)aCg>aTg	p.T267M		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	267					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T267M(2)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCTAAACATACGCCAGACCAG	0.517													t|||	11	0.00219649	0.0045	0.0014	5008	,	,		18038	0		0	False		,,,				2504	0.0041															2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	1						T	MET/THR	29,4377	823.6+/-416.5	0,29,2174	131	113	119		800	1.4	0	1	dbSNP_134	119	1,8599	819.2+/-406.8	0,1,4299	yes	missense	OR2M4	NM_017504.1	81	0,30,6473	TT,TC,CC		0.0116,0.6582,0.2307	probably-damaging	267/312	248403030	30,12976	2203	4300	6503	246469653	SO:0001583	missense	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.800C>T	1.37:g.248403030C>T	ENSP00000306688:p.Thr267Met		246469653	Q15611|Q8NG82	Missense_Mutation	SNP	ENST00000306687.1	37	CCDS31108.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	t	7.287	0.610196	0.14066	0.006582	1.16E-4	ENSG00000171180	ENST00000306687	T	0.00130	8.69	3.34	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	2.248960	0.02593	N	0.100179	T	0.00210	0.0006	L	0.45228	1.405	0.09310	N	1	D	0.71674	0.998	D	0.65140	0.932	T	0.50742	-0.8792	10	0.72032	D	0.01	.	3.4528	0.07505	0.298:0.4908:0.0:0.2112	.	267	Q96R27	OR2M4_HUMAN	M	267	ENSP00000306688:T267M	ENSP00000306688:T267M	T	+	2	0	OR2M4	246469653	0.000000	0.05858	0.002000	0.10522	0.027000	0.11550	-0.096000	0.11059	0.238000	0.21222	-1.215000	0.01618	ACG		0.517	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		T	248403030	C	T	248403030	3	4	119	1	0	0	0	0	1	0	0	0	11043	536	19	1	802	1	OR2M4	1	248403030	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	6568610	248403030	847591	16	31460										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50850690	50850690	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cactgctgctttgaatggggTtttgagacaagtcgtagcag	13	7	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:50850690T>A	ENST00000406316.2	-	6	2372	c.896A>T	c.(895-897)aAc>aTc	p.N299I	NRXN1_ENST00000401669.2_Missense_Mutation_p.N299I|NRXN1_ENST00000402717.3_Missense_Mutation_p.N299I|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Missense_Mutation_p.N299I|NRXN1_ENST00000404971.1_Missense_Mutation_p.N332I|NRXN1_ENST00000406859.3_Missense_Mutation_p.N299I	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	299	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TTGAATGGGGTTTTGAGACAA	0.378																																																0			2											137	127	130					2																	50850690		1871	4097	5968	50704194	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.896A>T	2.37:g.50850690T>A	ENSP00000384311:p.Asn299Ile		50704194	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006383	0.74932	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.24;-1.36;-1.24;-1.36	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.86058	0.5842	L	0.43923	1.385	0.47949	D	0.999556	D;D	0.76494	0.967;0.999	D;D	0.85130	0.928;0.997	D	0.87256	0.2276	10	0.66056	D	0.02	.	15.4704	0.75437	0.0:0.0:0.0:1.0	.	332;299	Q9ULB1-3;F8WB18	.;.	I	332;299;299;299;333;299;299	ENSP00000385142:N332I;ENSP00000384311:N299I;ENSP00000434015:N299I;ENSP00000385017:N299I;ENSP00000385434:N299I;ENSP00000385681:N299I	ENSP00000385017:N299I	N	-	2	0	NRXN1	50704194	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.868000	0.87116	2.240000	0.73641	0.528000	0.53228	AAC		0.378	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50850690	T	A	50850690	3	1	119	1	0	0	0	0	1	0	0	0	10696	1725	60	5	3983	5	NRXN1	2	50850690	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10		50850690	192348683	17	31461										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55536107	55536107	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctggcgttcccgattaatatCtttcttagactttatcaatt	5	9	3	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:55536107C>A	ENST00000436346.1	-	25	5066	c.4225G>T	c.(4225-4227)Gat>Tat	p.D1409Y	CCDC88A_ENST00000413716.2_Missense_Mutation_p.D1408Y|AC012358.8_ENST00000366287.4_RNA|CCDC88A_ENST00000422883.2_Missense_Mutation_p.D32Y|CCDC88A_ENST00000336838.6_Missense_Mutation_p.D1408Y|CCDC88A_ENST00000263630.8_Missense_Mutation_p.D1409Y	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1409					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CGATTAATATCTTTCTTAGAC	0.353																																																0			2											90	88	89					2																	55536107		2203	4300	6503	55389611	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4225G>T	2.37:g.55536107C>A	ENSP00000410608:p.Asp1409Tyr		55389611	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	21.7|21.7|21.7	4.182161|4.182161|4.182161	0.78677|0.78677|0.78677	.|.|.	.|.|.	ENSG00000115355|ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000444458|ENST00000456975	T;T;T;T;T;T|.|.	0.46451|.|.	2.43;2.66;2.65;0.87;2.44;1.4|.|.	4.75|4.75|4.75	4.75|4.75|4.75	0.60458|0.60458|0.60458	.|.|.	0.000000|.|.	0.49305|.|.	U|.|.	0.000143|.|.	T|T|T	0.62998|0.62998|0.62998	0.2474|0.2474|0.2474	L|L|L	0.44542|0.44542|0.44542	1.39|1.39|1.39	0.38295|0.38295|0.38295	D|D|D	0.942825|0.942825|0.942825	P;P;P;D;P;P;P|.|.	0.69078|.|.	0.913;0.955;0.924;0.997;0.823;0.955;0.955|.|.	P;P;P;P;P;P;P|.|.	0.60345|.|.	0.786;0.748;0.564;0.873;0.707;0.748;0.748|.|.	T|T|T	0.63528|0.63528|0.63528	-0.6617|-0.6617|-0.6617	10|6|5	0.87932|0.54805|.	D|T|.	0|0.06|.	-12.3101|-12.3101|-12.3101	18.1082|18.1082|18.1082	0.89527|0.89527|0.89527	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	1408;1409;1354;32;1409;1408;1408|.|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.|.	.;.;.;.;GRDN_HUMAN;.;.|.|.	Y|N|I	1408;1409;1409;32;454;1408;584|33|389	ENSP00000338728:D1408Y;ENSP00000263630:D1409Y;ENSP00000410608:D1409Y;ENSP00000390012:D454Y;ENSP00000404431:D1408Y;ENSP00000405080:D584Y|.|.	ENSP00000263630:D1409Y|ENSP00000413401:K33N|.	D|K|R	-|-|-	1|3|2	0|2|0	CCDC88A|CCDC88A|CCDC88A	55389611|55389611|55389611	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	5.671000|5.671000|5.671000	0.68095|0.68095|0.68095	2.332000|2.332000|2.332000	0.79248|0.79248|0.79248	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAT|AAG|AGA		0.353	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		A	55536107	C	A	55536107	3	1	119	1	0	0	0	0	1	0	0	0	2869	913	32	2	1422	2	CCDC88A	2	55536107	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	4685417	55536107	187663266	18	31462										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74900823	74900823	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gccccagcctttgtcgcagcCgtggccttgagcccagccga	12	17	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:74900823C>T	ENST00000357877.2	+	7	839	c.690C>T	c.(688-690)gcC>gcT	p.A230A	SEMA4F_ENST00000339773.5_Intron	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	230	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TTGTCGCAGCCGTGGCCTTGA	0.567																																																0			2											64	63	63					2																	74900823		2203	4300	6503	74754331	SO:0001819	synonymous_variant	10505			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.690C>T	2.37:g.74900823C>T			74754331	Q542Y7|Q9NS35	Silent	SNP	ENST00000357877.2	37	CCDS1955.1																																																																																				0.567	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		T	74900823	C	T	74900823	2	4	119	1	0	0	0	0	0	0	0	1	14072	639	23	1		1	SEMA4F	2	74900823	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10	19364716	74900823	168298550	19	31463										
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102805702	102805702	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	atacagtctagaattcaccaGgacgagacttggattttgtt	9	7	2	2	rs200302961		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:102805702G>T	ENST00000264257.2	+	3	351	c.225G>T	c.(223-225)caG>caT	p.Q75H	IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.Q75H	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	75	Ig-like C2-type 1.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						GAATTCACCAGGACGAGACTT	0.398																																																0			2											70	69	69					2																	102805702		2203	4300	6503	102172134	SO:0001583	missense	8808			U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.225G>T	2.37:g.102805702G>T	ENSP00000264257:p.Gln75His		102172134	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.653647	0.67472	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.35605	4.07;1.3;4.07	5.86	4.04	0.47022	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.306760	0.33161	N	0.005207	T	0.56321	0.1977	M	0.77103	2.36	0.41935	D	0.990582	D	0.89917	1.0	D	0.91635	0.999	T	0.57015	-0.7883	10	0.37606	T	0.19	.	9.2879	0.37769	0.172:0.0:0.828:0.0	.	75	Q9HB29	ILRL2_HUMAN	H	75	ENSP00000264257:Q75H;ENSP00000387611:Q75H;ENSP00000442184:Q75H	ENSP00000264257:Q75H	Q	+	3	2	IL1RL2	102172134	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.601000	0.46249	1.626000	0.50381	0.650000	0.86243	CAG		0.398	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		T	102805702	G	T	102805702	3	4	119	1	0	0	0	0	1	0	0	0	7685	991	35	2	231	2	IL1RL2	2	102805702	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	27904879	102805702	140393671	20	31464										
MERTK	10461	hgsc.bcm.edu	37	chr2	112740567	112740567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gtgtggcagagtgcagggatTtccgtaagtctaaaccctag	13	8	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:112740567T>C	ENST00000295408.4	+	8	1550	c.1293T>C	c.(1291-1293)atT>atC	p.I431I	MERTK_ENST00000409780.1_Silent_p.I255I|MERTK_ENST00000421804.2_Silent_p.I431I			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	431	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GTGCAGGGATTTCCGTAAGTC	0.458																																																0			2											107	102	104					2																	112740567		2203	4300	6503	112457038	SO:0001819	synonymous_variant	10461			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1293T>C	2.37:g.112740567T>C			112457038	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																				0.458	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			C	112740567	T	C	112740567	2	2	119	1	0	0	0	0	0	0	0	1	9509	1829	64	4		4	MERTK	2	112740567	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10	9934865	112740567	130458806	21	31465										
WDR33	55339	hgsc.bcm.edu	37	chr2	128482644	128482644	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cagccactgacctgtggcttCtttcttatgacctcggaaga	9	12	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:128482644C>T	ENST00000322313.4	-	9	1155	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	333					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CCTGTGGCTTCTTTCTTATGA	0.403																																																0			2											85	82	83					2																	128482644		2203	4300	6503	128199114	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.997G>A	2.37:g.128482644C>T	ENSP00000325377:p.Glu333Lys		128199114	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757683	0.89843	.	.	ENSG00000136709	ENST00000322313	T	0.60040	0.22	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72930	0.3522	L	0.49640	1.575	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.74337	-0.3698	10	0.72032	D	0.01	-16.59	19.4772	0.94994	0.0:1.0:0.0:0.0	.	333	Q9C0J8	WDR33_HUMAN	K	333	ENSP00000325377:E333K	ENSP00000325377:E333K	E	-	1	0	WDR33	128199114	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.629000	0.83207	2.602000	0.87976	0.563000	0.77884	GAA		0.403	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128482644	C	T	128482644	3	4	119	1	0	0	0	0	1	0	0	0	17327	922	32	3	3069	3	WDR33	2	128482644	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	15742077	128482644	114716729	22	31466										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100204	168100204	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	acgttgaaaagggagatgtaAgaacagcacggtggatgttt	14	4	0	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:168100204A>C	ENST00000409195.1	+	9	2391	c.2302A>C	c.(2302-2304)Aga>Cga	p.R768R	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Silent_p.R768R|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Silent_p.R546R	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	593					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GGGAGATGTAAGAACAGCACG	0.378																																																0			2											73	67	69					2																	168100204		1860	4093	5953	167808450	SO:0001819	synonymous_variant	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2302A>C	2.37:g.168100204A>C			167808450	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																				0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168100204	A	C	168100204	2	2	119	1	0	0	0	0	0	0	0	1	17470	64	3	4		4	XIRP2	2	168100204	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10	39617560	168100204	75099169	23	31467										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105245	168105245	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccccaaagttgaactggcaaCctccctgtcagatatggaat	8	12	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:168105245C>A	ENST00000409195.1	+	9	7432	c.7343C>A	c.(7342-7344)aCc>aAc	p.T2448N	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.T2448N|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.T2226N	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2273					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAACTGGCAACCTCCCTGTCA	0.423																																																0			2											88	87	87					2																	168105245		1848	4113	5961	167813491	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7343C>A	2.37:g.168105245C>A	ENSP00000386840:p.Thr2448Asn		167813491	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.564110	0.00134	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02446	4.29;4.29;4.3	5.85	-3.23	0.05109	.	0.853088	0.10558	N	0.660562	T	0.00608	0.0020	N	0.00347	-1.61	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48103	-0.9064	10	0.09084	T	0.74	-7.3652	1.1806	0.01844	0.1621:0.3492:0.1824:0.3063	.	2273;2273;2226	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2448;2448;2226	ENSP00000386840:T2448N;ENSP00000295237:T2448N;ENSP00000387255:T2226N	ENSP00000295237:T2448N	T	+	2	0	XIRP2	167813491	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.282000	0.08445	-0.131000	0.11578	-0.280000	0.10049	ACC		0.423	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168105245	C	A	168105245	3	1	119	1	0	0	0	0	1	0	0	0	17470	507	18	2	7373	2	XIRP2	2	168105245	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	5041	168105245	75094128	24	31468										
PRKRA	8575	hgsc.bcm.edu	37	chr2	179296906	179296906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cattgccacaggagataccgGagccatgacagactgtgatg	12	10	0	4			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:179296906G>A	ENST00000325748.4	-	8	1060	c.860C>T	c.(859-861)tCc>tTc	p.S287F	PRKRA_ENST00000438687.3_Missense_Mutation_p.S174F|AC009948.5_ENST00000415236.1_RNA|AC009948.5_ENST00000436616.2_RNA|AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000453026.2_RNA|AC009948.5_ENST00000420672.1_RNA|PRKRA_ENST00000487082.1_Missense_Mutation_p.S262F|PRKRA_ENST00000432031.2_Missense_Mutation_p.S276F|AC009948.5_ENST00000450044.1_RNA	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	287	DRBM 3. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			GGAGATACCGGAGCCATGACA	0.428																																					Melanoma(200;68 3001 23825 48764)											0			2											149	129	136					2																	179296906		2203	4300	6503	179005152	SO:0001583	missense	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.860C>T	2.37:g.179296906G>A	ENSP00000318176:p.Ser287Phe		179005152	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720677	0.30503	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.12	2.3	0.28687	Double-stranded RNA-binding (2);	0.318671	0.26711	N	0.022895	T	0.81394	0.4813	L	0.45137	1.4	0.21802	N	0.999538	B;D	0.54601	0.103;0.967	B;P	0.55303	0.029;0.773	T	0.70586	-0.4831	10	0.36615	T	0.2	.	7.4038	0.26979	0.1603:0.1466:0.6931:0.0	.	287;276	O75569;O75569-2	PRKRA_HUMAN;.	F	287;174;262;276	ENSP00000318176:S287F;ENSP00000398980:S174F;ENSP00000430604:S262F;ENSP00000393883:S276F	ENSP00000318176:S287F	S	-	2	0	PRKRA	179005152	1.000000	0.71417	0.497000	0.27552	0.978000	0.69477	3.142000	0.50601	0.185000	0.20105	0.467000	0.42956	TCC		0.428	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690		A	179296906	G	A	179296906	3	1	119	1	0	0	0	0	1	0	0	0	12558	1174	41	3	85	3	PRKRA	2	179296906	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	11191661	179296906	63902467	25	31469										
TTN	7273	hgsc.bcm.edu	37	chr2	179472247	179472247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttagttcagatttggttccaAcgttgtctattacaacacgg	8	8	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:179472247A>G	ENST00000591111.1	-	227	48469	c.48245T>C	c.(48244-48246)gTt>gCt	p.V16082A	TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V8850A|TTN_ENST00000460472.2_Missense_Mutation_p.V8658A|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V15155A|TTN_ENST00000589042.1_Missense_Mutation_p.V17723A|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V8783A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16082	Ig-like 99.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTGGTTCCAACGTTGTCTAT	0.433																																																0			2											426	400	408					2																	179472247		1903	4128	6031	179180492	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48245T>C	2.37:g.179472247A>G	ENSP00000465570:p.Val16082Ala		179180492	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	9.990	1.230469	0.22542	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.99	5.99	0.97316	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.52419	0.1733	N	0.11724	0.165	0.38706	D	0.953097	B;B;B;B	0.21821	0.061;0.061;0.061;0.061	B;B;B;B	0.20767	0.031;0.031;0.031;0.031	T	0.55173	-0.8182	9	0.87932	D	0	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	8658;8783;8850;16082	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	15155;8658;8850;8783;8658	ENSP00000343764:V15155A;ENSP00000434586:V8658A;ENSP00000340554:V8850A;ENSP00000352154:V8783A	ENSP00000340554:V8850A	V	-	2	0	TTN	179180492	1.000000	0.71417	0.995000	0.50966	0.904000	0.53231	5.463000	0.66712	2.291000	0.77112	0.533000	0.62120	GTT		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179472247	A	G	179472247	3	3	119	1	0	0	0	0	1	0	0	0	16775	43	2	4	54869	4	TTN	2	179472247	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	175341	179472247	63727126	26	31470										
CALCRL	10203	hgsc.bcm.edu	37	chr2	188217025	188217025	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cttttaacttggtgatgagaAcgcgtacaatatttaacaag	8	6	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:188217025A>G	ENST00000409998.1	-	14	1725	c.944T>C	c.(943-945)gTt>gCt	p.V315A	CALCRL_ENST00000392370.3_Missense_Mutation_p.V315A|AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000410068.1_Missense_Mutation_p.V315A|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	315					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)	p.V315A(1)		endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			GGTGATGAGAACGCGTACAAT	0.333																																																1	Substitution - Missense(1)	large_intestine(1)	2											52	50	51					2																	188217025		2203	4299	6502	187925270	SO:0001583	missense	10203			U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"GPCR / Class B : Calcitonin receptors"	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.944T>C	2.37:g.188217025A>G	ENSP00000386972:p.Val315Ala		187925270	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.809543	0.90707	.	.	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.49432	0.78;0.78;0.78	5.82	5.82	0.92795	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000021	T	0.78188	0.4244	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85015	0.0908	10	0.87932	D	0	.	15.3496	0.74373	1.0:0.0:0.0:0.0	.	315	Q16602	CALRL_HUMAN	A	315	ENSP00000376177:V315A;ENSP00000386972:V315A;ENSP00000387190:V315A	ENSP00000376177:V315A	V	-	2	0	CALCRL	187925270	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	9.326000	0.96389	2.225000	0.72522	0.528000	0.53228	GTT		0.333	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		G	188217025	A	G	188217025	3	3	119	1	0	0	0	0	1	0	0	0	2586	43	2	4	453	4	CALCRL	2	188217025	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	8744778	188217025	54982348	27	31471										
FN1	2335	hgsc.bcm.edu	37	chr2	216298121	216298121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agatcatggagtctttaggaCgctcataagtgtcacccact	9	10	4	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:216298121C>T	ENST00000359671.1	-	3	606	c.341G>A	c.(340-342)cGt>cAt	p.R114H	FN1_ENST00000346544.3_Missense_Mutation_p.R114H|FN1_ENST00000421182.1_Missense_Mutation_p.R114H|FN1_ENST00000345488.5_Missense_Mutation_p.R114H|FN1_ENST00000357867.4_Missense_Mutation_p.R114H|FN1_ENST00000446046.1_Missense_Mutation_p.R114H|FN1_ENST00000443816.1_Missense_Mutation_p.R114H|FN1_ENST00000354785.4_Missense_Mutation_p.R114H|FN1_ENST00000323926.6_Missense_Mutation_p.R114H|FN1_ENST00000336916.4_Missense_Mutation_p.R114H|FN1_ENST00000356005.4_Missense_Mutation_p.R114H|FN1_ENST00000432072.2_Missense_Mutation_p.R114H|FN1_ENST00000357009.2_Missense_Mutation_p.R114H|FN1_ENST00000426059.1_Missense_Mutation_p.R114H|AC012462.1_ENST00000412951.1_RNA			P02751	FINC_HUMAN	fibronectin 1	114	Fibrin- and heparin-binding 1.|Fibronectin type-I 2. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		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)	Ocriplasmin(DB08888)	GTCTTTAGGACGCTCATAAGT	0.483																																																0			2											153	131	138					2																	216298121		2203	4300	6503	216006366	SO:0001583	missense	2335				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.341G>A	2.37:g.216298121C>T	ENSP00000352696:p.Arg114His		216006366	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.933140	0.97116	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000001	T	0.79251	0.4414	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;0.999	D;D;D;D;D;D;D;P;D;D;D	0.97110	1.0;0.997;0.972;0.981;0.998;0.999;1.0;0.895;0.998;0.998;0.997	T	0.78846	-0.2043	10	0.87932	D	0	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	114;114;114;114;114;114;114;114;114;114;114	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	H	114	ENSP00000394423:R114H;ENSP00000323534:R114H;ENSP00000338200:R114H;ENSP00000350534:R114H;ENSP00000346839:R114H;ENSP00000352696:R114H;ENSP00000265312:R114H;ENSP00000273049:R114H;ENSP00000349509:R114H;ENSP00000410422:R114H;ENSP00000415018:R114H;ENSP00000399538:R114H;ENSP00000348285:R114H;ENSP00000398907:R114H	ENSP00000265313:R114H	R	-	2	0	FN1	216006366	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.715000	0.68430	2.885000	0.99019	0.655000	0.94253	CGT		0.483	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216298121	C	T	216298121	3	4	119	1	0	0	0	0	1	0	0	0	5981	536	19	1	7301	1	FN1	2	216298121	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	28081096	216298121	26901252	28	31472										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713452	218713452	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cgtccagaggagggcacagcCgagccccctgctgggcggga	17	14	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:218713452C>T	ENST00000171887.4	-	17	1865	c.1413G>A	c.(1411-1413)tcG>tcA	p.S471S	TNS1_ENST00000419504.1_Silent_p.S471S|TNS1_ENST00000430930.1_Silent_p.S471S|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	471					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		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)		AGGGCACAGCCGAGCCCCCTG	0.627																																																0			2											66	68	67					2																	218713452		2203	4300	6503	218421697	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1413G>A	2.37:g.218713452C>T			218421697	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.627	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218713452	C	T	218713452	2	4	119	1	0	0	0	0	0	0	0	1	16382	639	23	1		1	TNS1	2	218713452	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10	2415331	218713452	24485921	29	31473										
SCG2	7857	hgsc.bcm.edu	37	chr2	224462614	224462614	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	accataagggagccttggcaGaactttctcctggttatatg	10	9	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:224462614G>C	ENST00000305409.2	-	2	1619	c.1387C>G	c.(1387-1389)Ctg>Gtg	p.L463V		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		AGCCTTGGCAGAACTTTCTCC	0.438																																																0			2											114	114	114					2																	224462614		2203	4300	6503	224170858	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1387C>G	2.37:g.224462614G>C	ENSP00000304133:p.Leu463Val		224170858	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.963006	0.34659	.	.	ENSG00000171951	ENST00000305409;ENST00000450330	T	0.02050	4.48	5.86	5.86	0.93980	.	0.092407	0.45606	D	0.000360	T	0.07728	0.0194	M	0.64997	1.995	0.44728	D	0.997725	P	0.49783	0.928	P	0.59171	0.853	T	0.11084	-1.0602	10	0.35671	T	0.21	.	10.2408	0.43310	0.1506:0.0:0.8494:0.0	.	463	P13521	SCG2_HUMAN	V	463;323	ENSP00000304133:L463V	ENSP00000304133:L463V	L	-	1	2	SCG2	224170858	0.739000	0.28196	0.285000	0.24819	0.707000	0.40811	1.264000	0.33015	2.781000	0.95711	0.650000	0.86243	CTG		0.438	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		C	224462614	G	C	224462614	3	2	119	1	0	0	0	0	1	0	0	0	13928	933	33	5	470	5	SCG2	2	224462614	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	5749162	224462614	18736759	30	31474										
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235950065	235950065	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	atagcactggcaacatcttcGatgagcttccagtcacaaac	7	12	2	1	rs532208992		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:235950065G>T	ENST00000409212.1	+	4	1159	c.652G>T	c.(652-654)Gat>Tat	p.D218Y	SH3BP4_ENST00000344528.4_Missense_Mutation_p.D218Y|SH3BP4_ENST00000392011.2_Missense_Mutation_p.D218Y			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	218					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CAACATCTTCGATGAGCTTCC	0.542																																																0			2											92	99	96					2																	235950065		2203	4300	6503	235614804	SO:0001583	missense	23677			AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.652G>T	2.37:g.235950065G>T	ENSP00000386862:p.Asp218Tyr		235614804	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030458	0.35797	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.13089	2.62;2.62;2.62	5.58	5.58	0.84498	.	0.370625	0.31648	N	0.007285	T	0.15392	0.0371	L	0.27053	0.805	0.58432	D	0.999997	P;P	0.49447	0.924;0.8	P;B	0.44990	0.466;0.279	T	0.00842	-1.1544	10	0.87932	D	0	-4.0656	18.1499	0.89671	0.0:0.0:1.0:0.0	.	218;218	A8K594;Q9P0V3	.;SH3B4_HUMAN	Y	218	ENSP00000375867:D218Y;ENSP00000386862:D218Y;ENSP00000340237:D218Y	ENSP00000340237:D218Y	D	+	1	0	SH3BP4	235614804	1.000000	0.71417	0.263000	0.24496	0.691000	0.40173	4.980000	0.63812	2.621000	0.88768	0.650000	0.86243	GAT		0.542	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235950065	G	T	235950065	3	4	119	1	0	0	0	0	1	0	0	0	14283	1058	37	2	658	2	SH3BP4	2	235950065	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	11487451	235950065	7249308	31	31475										
ILKAP	80895	hgsc.bcm.edu	37	chr2	239090820	239090820	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tctcctcattataacgacacAagattgcctgggaagatgga	9	9	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr2:239090820A>G	ENST00000254654.3	-	9	897	c.722T>C	c.(721-723)tTg>tCg	p.L241S		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	241	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		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)		ATAACGACACAAGATTGCCTG	0.413																																																0			2											196	175	182					2																	239090820		2203	4300	6503	238755559	SO:0001583	missense	80895			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.722T>C	2.37:g.239090820A>G	ENSP00000254654:p.Leu241Ser		238755559	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.577584	0.65878	.	.	ENSG00000132323	ENST00000254654;ENST00000450411	T;T	0.39406	1.08;1.08	5.37	5.37	0.77165	Protein phosphatase 2C-like (5);	0.072044	0.56097	D	0.000036	T	0.74869	0.3773	H	0.96208	3.785	0.58432	D	0.999991	D	0.89917	1.0	D	0.81914	0.995	D	0.83593	0.0124	10	0.87932	D	0	1.4726	14.3541	0.66724	1.0:0.0:0.0:0.0	.	241	Q9H0C8	ILKAP_HUMAN	S	241;58	ENSP00000254654:L241S;ENSP00000406254:L58S	ENSP00000254654:L241S	L	-	2	0	ILKAP	238755559	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	6.066000	0.71185	2.024000	0.59613	0.533000	0.62120	TTG		0.413	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		G	239090820	A	G	239090820	3	3	119	1	0	0	0	0	1	0	0	0	7735	131	5	4	472	4	ILKAP	2	239090820	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	3140755	239090820	4108553	32	31476										
VHL	7428	hgsc.bcm.edu	37	chr3	10188212	10188212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cgataggtcacctttggctcTtcagagatgcagggacacac	11	11	3	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr3:10188212T>C	ENST00000256474.2	+	2	1195	c.355T>C	c.(355-357)Ttc>Ctc	p.F119L	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	119	Involved in binding to CCT complex.		F -> L (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816}.|F -> S (in VHLD; type II). {ECO:0000269|PubMed:8825918}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L118_G123>P(1)|p.W117fs*1(1)|p.?(1)|p.F119fs*11(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCTTTGGCTCTTCAGAGATGC	0.507		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	4	Deletion - Frameshift(2)|Unknown(1)|Complex - deletion inframe(1)	kidney(4)	3	GRCh37	CM056725	VHL	M							178	166	170					3																	10188212		2203	4300	6503	10163212	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.355T>C	3.37:g.10188212T>C	ENSP00000256474:p.Phe119Leu		10163212	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936672	0.73442	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99677	-6.37	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99474	0.9813	L	0.56340	1.77	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.98220	1.0477	10	0.66056	D	0.02	-6.0328	13.0887	0.59156	0.0:0.0:0.0:1.0	.	119	P40337	VHL_HUMAN	L	119;37	ENSP00000256474:F119L	ENSP00000256474:F119L	F	+	1	0	VHL	10163212	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	5.965000	0.70387	2.047000	0.60756	0.460000	0.39030	TTC		0.507	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		C	10188212	T	C	10188212	3	2	119	1	0	0	0	0	1	0	0	0	17202	1609	56	4	361	4	VHL	3	10188212	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10		10188212	187834218	33	31477										
ZNF197	10168	hgsc.bcm.edu	37	chr3	44670728	44670728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	atgatacctggaaatggggaAccagcttccaaggaagtagc	12	8	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr3:44670728A>G	ENST00000396058.1	+	1	249	c.82A>G	c.(82-84)Acc>Gcc	p.T28A	RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383745.2_Missense_Mutation_p.T28A|ZNF197_ENST00000344387.4_Missense_Mutation_p.T28A|ZNF197_ENST00000383744.4_Missense_Mutation_p.T28A			O14709	ZN197_HUMAN	zinc finger protein 197	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		GAAATGGGGAACCAGCTTCCA	0.478																																																0			3											113	125	121					3																	44670728		2203	4300	6503	44645732	SO:0001583	missense	10168			AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.82A>G	3.37:g.44670728A>G	ENSP00000379370:p.Thr28Ala		44645732	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	37	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516394	0.44763	.	.	ENSG00000186448	ENST00000412641;ENST00000383744;ENST00000536299;ENST00000344387;ENST00000383745;ENST00000396058	T;T;T;T;T	0.09445	2.98;5.72;3.39;5.72;3.39	4.88	0.841	0.18918	.	0.201697	0.24745	N	0.035950	T	0.03959	0.0111	N	0.08118	0	0.21878	N	0.999493	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.42120	-0.9470	10	0.17832	T	0.49	.	4.4814	0.11769	0.6127:0.0:0.0879:0.2994	.	28;28	Q86VG0;O14709	.;ZN197_HUMAN	A	28	ENSP00000394713:T28A;ENSP00000373250:T28A;ENSP00000345809:T28A;ENSP00000373251:T28A;ENSP00000379370:T28A	ENSP00000334616:T28A	T	+	1	0	ZNF197	44645732	0.794000	0.28838	0.994000	0.49952	0.993000	0.82548	0.459000	0.21908	0.410000	0.25675	0.533000	0.62120	ACC		0.478	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		G	44670728	A	G	44670728	3	3	119	1	0	0	0	0	1	0	0	0	17798	43	2	4	84	4	ZNF197	3	44670728	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	34482516	44670728	153351702	34	31478										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129304808	129304808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gactcactgggtactcctggCgcacatcgatctcggaaggc	12	13	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr3:129304808C>T	ENST00000324093.4	-	5	2016	c.1838G>A	c.(1837-1839)cGc>cAc	p.R613H	PLXND1_ENST00000393239.1_Missense_Mutation_p.R613H	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	613					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GTACTCCTGGCGCACATCGAT	0.657																																					Ovarian(97;366 1484 3738 22084 39045)											0			3											110	117	114					3																	129304808		2203	4300	6503	130787498	SO:0001583	missense	23129			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.1838G>A	3.37:g.129304808C>T	ENSP00000317128:p.Arg613His		130787498	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	8.257	0.810323	0.16537	.	.	ENSG00000004399	ENST00000324093;ENST00000393239;ENST00000505237	T;T;T	0.37235	1.26;1.21;2.97	4.98	-8.03	0.01114	.	1.397370	0.03961	N	0.290045	T	0.18676	0.0448	N	0.03154	-0.405	0.20489	N	0.999897	B	0.02656	0.0	B	0.01281	0.0	T	0.19128	-1.0315	10	0.33940	T	0.23	.	17.6896	0.88266	0.0:0.1177:0.0:0.8823	.	613	Q9Y4D7	PLXD1_HUMAN	H	613;613;165	ENSP00000317128:R613H;ENSP00000376931:R613H;ENSP00000426241:R165H	ENSP00000317128:R613H	R	-	2	0	PLXND1	130787498	0.001000	0.12720	0.314000	0.25224	0.027000	0.11550	-3.019000	0.00643	-1.764000	0.01305	-1.036000	0.02392	CGC		0.657	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129304808	C	T	129304808	3	4	119	1	0	0	0	0	1	0	0	0	12158	768	27	1	4067	1	PLXND1	3	129304808	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	84634080	129304808	68717622	35	31479										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130110086	130110086	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cattcaggtagcataaaaaaAcaatatcaagatcacatgat	5	7	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr3:130110086A>C	ENST00000432398.2	+	7	2975	c.2481A>C	c.(2479-2481)aaA>aaC	p.K827N	COL6A5_ENST00000265379.6_Missense_Mutation_p.K827N	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	827	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GCATAAAAAAACAATATCAAG	0.388																																																0			3											98	78	84					3																	130110086		692	1591	2283	131592776	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.2481A>C	3.37:g.130110086A>C	ENSP00000390895:p.Lys827Asn		131592776	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	A	9.524	1.108990	0.20714	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.83591	-1.74;-1.74	5.72	-9.22	0.00675	.	.	.	.	.	T	0.57636	0.2067	N	0.12637	0.245	0.09310	N	1	B	0.19200	0.034	B	0.25614	0.062	T	0.48163	-0.9059	9	0.17369	T	0.5	.	2.0105	0.03486	0.282:0.2621:0.3118:0.1441	.	827	A8TX70-2	.	N	827	ENSP00000390895:K827N;ENSP00000265379:K827N	ENSP00000265379:K827N	K	+	3	2	COL6A5	131592776	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.767000	0.01795	-1.071000	0.03145	-1.117000	0.02048	AAA		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		C	130110086	A	C	130110086	3	2	119	1	0	0	0	0	1	0	0	0	3708	40	2	4	2503	4	COL6A5	3	130110086	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	805278	130110086	67912344	36	31480										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178922365	178922365	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aacactcaaagagtaccttgTtccaatcccaggtaaggaag	8	10	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr3:178922365T>C	ENST00000263967.3	+	6	1291	c.1134T>C	c.(1132-1134)tgT>tgC	p.C378C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	378	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		C -> Y (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAGTACCTTGTTCCAATCCCA	0.333		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	0			3											188	149	161					3																	178922365		1836	4093	5929	180405059	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1134T>C	3.37:g.178922365T>C			180405059	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178922365	T	C	178922365	2	2	119	1	0	0	0	0	0	0	0	1	11944	1731	60	4		4	PIK3CA	3	178922365	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10	48812279	178922365	19100065	37	31481										
ZBTB49	166793	hgsc.bcm.edu	37	chr4	4303787	4303787	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgttaaaaatgtcagtggcaTagggcagatcctggacttca	11	7	2	1	rs145711052		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:4303787T>C	ENST00000337872.4	+	3	345	c.224T>C	c.(223-225)aTa>aCa	p.I75T	ZBTB49_ENST00000355834.3_Missense_Mutation_p.I75T|ZBTB49_ENST00000538529.1_5'UTR	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	75	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						GTCAGTGGCATAGGGCAGATC	0.383																																																0			4						T	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	118	108	111		224	5.4	1	4	dbSNP_134	111	0,8600		0,0,4300	no	missense	ZBTB49	NM_145291.3	89	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	75/766	4303787	1,13005	2203	4300	6503	4354688	SO:0001583	missense	0			AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19883	protein-coding gene	gene with protein product			"zinc finger protein 509"	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.224T>C	4.37:g.4303787T>C	ENSP00000338807:p.Ile75Thr		4354688	Q59FJ4|Q5EBN0|Q8TB80	Missense_Mutation	SNP	ENST00000337872.4	37	CCDS3375.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.525127	0.85600	2.27E-4	0.0	ENSG00000168826	ENST00000355834;ENST00000337872;ENST00000502918	T;T;T	0.67865	-0.29;-0.29;-0.29	5.38	5.38	0.77491	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	D	0.000006	T	0.79913	0.4528	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82125	-0.0612	10	0.87932	D	0	.	15.6808	0.77367	0.0:0.0:0.0:1.0	.	75	Q6ZSB9	ZBT49_HUMAN	T	75	ENSP00000348091:I75T;ENSP00000338807:I75T;ENSP00000425747:I75T	ENSP00000338807:I75T	I	+	2	0	ZBTB49	4354688	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.806000	0.86020	2.179000	0.69175	0.477000	0.44152	ATA		0.383	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		C	4303787	T	C	4303787	3	2	119	1	0	0	0	0	1	0	0	0	17589	1406	49	4	230	4	ZBTB49	4	4303787	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10		4303787	186850489	38	31482										
PROM1	8842	hgsc.bcm.edu	37	chr4	15993986	15993986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	taagatttaccttcagacttTccaattcactgcttatgctt	4	10	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:15993986T>C	ENST00000510224.1	-	17	2044	c.1796A>G	c.(1795-1797)gAa>gGa	p.E599G	PROM1_ENST00000447510.2_Missense_Mutation_p.E599G|PROM1_ENST00000540805.1_Missense_Mutation_p.E599G|PROM1_ENST00000508167.1_Missense_Mutation_p.E590G|PROM1_ENST00000539194.1_Missense_Mutation_p.E599G|PROM1_ENST00000505450.1_Missense_Mutation_p.E590G|PROM1_ENST00000543373.1_Missense_Mutation_p.E590G			O43490	PROM1_HUMAN	prominin 1	599					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						CTTCAGACTTTCCAATTCACT	0.373																																																0			4											78	77	77					4																	15993986		1844	4102	5946	15603084	SO:0001583	missense	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1796A>G	4.37:g.15993986T>C	ENSP00000426809:p.Glu599Gly		15603084	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.171998	0.57584	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.29	4.09	0.47781	.	0.353403	0.34652	N	0.003797	T	0.58466	0.2124	M	0.73962	2.25	0.09310	N	0.999997	D;D;D;D;P;P	0.54964	0.969;0.969;0.969;0.969;0.952;0.949	P;P;P;P;P;P	0.54544	0.755;0.755;0.755;0.755;0.575;0.733	T	0.52697	-0.8541	10	0.42905	T	0.14	-6.2559	10.2054	0.43109	0.0:0.0:0.1672:0.8328	.	590;599;590;599;590;599	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	G	599;599;599;590;590;599;590	ENSP00000415481:E599G;ENSP00000438045:E599G;ENSP00000443620:E599G;ENSP00000426090:E590G;ENSP00000427346:E590G;ENSP00000426809:E599G;ENSP00000445526:E590G	ENSP00000415481:E599G	E	-	2	0	PROM1	15603084	0.012000	0.17670	0.002000	0.10522	0.007000	0.05969	1.671000	0.37513	0.826000	0.34661	0.533000	0.62120	GAA		0.373	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		C	15993986	T	C	15993986	3	2	119	1	0	0	0	0	1	0	0	0	12589	1783	62	4	845	4	PROM1	4	15993986	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	11690199	15993986	175160290	39	31483										
ANAPC4	29945	hgsc.bcm.edu	37	chr4	25392591	25392591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tttgaaatcattatcagtggTcacagaagtctctaccaatg	7	8	4	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:25392591T>C	ENST00000315368.3	+	9	801	c.659T>C	c.(658-660)gTc>gCc	p.V220A	ANAPC4_ENST00000510092.1_Missense_Mutation_p.V220A	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	220					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				TTATCAGTGGTCACAGAAGTC	0.348																																																0			4											183	180	181					4																	25392591		2203	4299	6502	25001689	SO:0001583	missense	29945			AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.659T>C	4.37:g.25392591T>C	ENSP00000318775:p.Val220Ala		25001689	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.254810	0.59212	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.25579	1.79;1.79	5.74	5.74	0.90152	WD40 repeat-like-containing domain (1);	0.099806	0.64402	D	0.000002	T	0.23532	0.0569	L	0.42245	1.32	0.41711	D	0.989456	P;B;P	0.42692	0.787;0.435;0.622	B;B;B	0.38264	0.269;0.078;0.152	T	0.02917	-1.1094	10	0.24483	T	0.36	-17.3294	16.0363	0.80631	0.0:0.0:0.0:1.0	.	220;220;220	Q9UJX5-2;E9PCR4;Q9UJX5	.;.;APC4_HUMAN	A	220	ENSP00000318775:V220A;ENSP00000426654:V220A	ENSP00000318775:V220A	V	+	2	0	ANAPC4	25001689	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.579000	0.74036	2.200000	0.70718	0.477000	0.44152	GTC		0.348	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		C	25392591	T	C	25392591	3	2	119	1	0	0	0	0	1	0	0	0	604	1667	58	4	689	4	ANAPC4	4	25392591	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	9398605	25392591	165761685	40	31484										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39839791	39839791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttttctttcctcggtcactgCtgatgttgccctgggtagcc	10	12	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:39839791C>T	ENST00000303538.8	-	32	4234	c.3695G>A	c.(3694-3696)aGc>aAc	p.S1232N		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)									p.S1232N(1)		breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TCGGTCACTGCTGATGTTGCC	0.388																																																1	Substitution - Missense(1)	lung(1)	4											77	73	74					4																	39839791		1895	4119	6014	39516186	SO:0001583	missense	23244			AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.3695G>A	4.37:g.39839791C>T	ENSP00000303427:p.Ser1232Asn		39516186		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.988033	0.53934	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.34	5.34	0.76211	.	0.371511	0.32719	N	0.005738	T	0.38931	0.1059	N	0.08118	0	0.80722	D	1	B	0.23990	0.095	B	0.20955	0.032	T	0.23691	-1.0181	8	.	.	.	-9.5515	19.0327	0.92963	0.0:1.0:0.0:0.0	.	1232	Q29RF7	PDS5A_HUMAN	N	1232	.	.	S	-	2	0	PDS5A	39516186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.114000	0.64648	2.502000	0.84385	0.655000	0.94253	AGC		0.388	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		T	39839791	C	T	39839791	3	4	119	1	0	0	0	0	1	0	0	0	11722	797	28	3	326	3	PDS5A	4	39839791	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	14447200	39839791	151314485	41	31485										
CDS1	1040	hgsc.bcm.edu	37	chr4	85560117	85560117	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggaaggattcattggtggttTcttttccacagttgtgtttg	12	5	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:85560117T>G	ENST00000295887.5	+	9	1274	c.851T>G	c.(850-852)tTc>tGc	p.F284C		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		ATTGGTGGTTTCTTTTCCACA	0.299																																																0			4											110	106	107					4																	85560117		2202	4297	6499	85779141	SO:0001583	missense	11200			U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.851T>G	4.37:g.85560117T>G	ENSP00000295887:p.Phe284Cys		85779141	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	37	CCDS3608.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.991687	0.35131	.	.	ENSG00000163624	ENST00000295887	T	0.49720	0.77	4.63	4.63	0.57726	.	0.300242	0.41712	D	0.000826	T	0.42517	0.1206	L	0.52759	1.655	0.54753	D	0.99998	B	0.18013	0.025	B	0.24394	0.053	T	0.33854	-0.9852	10	0.38643	T	0.18	-10.3076	11.5397	0.50659	0.0:0.0:0.1489:0.851	.	284	Q92903	CDS1_HUMAN	C	284	ENSP00000295887:F284C	ENSP00000295887:F284C	F	+	2	0	CDS1	85779141	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.062000	0.71155	1.950000	0.56595	0.455000	0.32223	TTC		0.299	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			G	85560117	T	G	85560117	3	3	119	1	0	0	0	0	1	0	0	0	3183	1783	62	4	885	4	CDS1	4	85560117	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	45720326	85560117	105594159	42	31486										
EMCN	51705	hgsc.bcm.edu	37	chr4	101401184	101401184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caacaagtgaattattagctGcctctaaaacacctgaaaaa	5	9	1	2	rs199976013		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr4:101401184G>A	ENST00000296420.4	-	2	255	c.77C>T	c.(76-78)gCa>gTa	p.A26V	EMCN_ENST00000502327.1_5'UTR|EMCN_ENST00000305864.3_Missense_Mutation_p.A26V|EMCN_ENST00000511970.1_Missense_Mutation_p.A26V	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	26						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		ATTATTAGCTGCCTCTAAAAC	0.313																																																0			4						T	VAL/ALA,VAL/ALA	1,4401	2.1+/-5.4	0,1,2200	117	107	110		77,77	-7.8	0	4		110	0,8592		0,0,4296	no	missense,missense	EMCN	NM_001159694.1,NM_016242.3	64,64	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	26/249,26/262	101401184	1,12993	2201	4296	6497	101620207	SO:0001583	missense	51705			AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"Mucins"	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.77C>T	4.37:g.101401184G>A	ENSP00000296420:p.Ala26Val		101620207	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	37	CCDS3655.1	.	.	.	.	.	.	.	.	.	.	g	8.620	0.891133	0.17613	2.27E-4	0.0	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000511970;ENST00000502569	.	.	.	3.9	-7.81	0.01210	.	6.403370	0.00481	U	0.000127	T	0.16727	0.0402	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18968	0.025;0.032;0.032	B;B;B	0.19666	0.015;0.026;0.026	T	0.10753	-1.0616	9	0.28530	T	0.3	.	1.1016	0.01685	0.2962:0.1074:0.164:0.4324	.	26;26;26	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	V	26	.	ENSP00000296420:A26V	A	-	2	0	EMCN	101620207	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.007000	0.00160	-2.160000	0.00786	-1.094000	0.02160	GCA		0.313	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242		A	101401184	G	A	101401184	3	1	119	1	0	0	0	0	1	0	0	0	5099	1319	46	3	748	3	EMCN	4	101401184	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	15841067	101401184	89753092	43	31487										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5464067	5464067	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	attgttgcgtctgatcacacAtattataactcaaaactaga	5	8	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr5:5464067A>G	ENST00000296564.7	+	13	4842	c.4620A>G	c.(4618-4620)acA>acG	p.T1540T		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1540					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CTGATCACACATATTATAACT	0.363																																																0			5											45	41	42					5																	5464067		1834	4093	5927	5517067	SO:0001819	synonymous_variant	23379																														ENST00000296564.7:c.4620A>G	5.37:g.5464067A>G			5517067	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																				0.363	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5464067	A	G	5464067	2	3	119	1	0	0	0	0	0	0	0	1	8223	204	8	4		4	KIAA0947	5	5464067	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10		5464067	175451193	44	31488										
CAMK4	814	hgsc.bcm.edu	37	chr5	110730470	110730470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgccgttaaacaaatcctggAggcagttgctgtaagtatga	11	7	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr5:110730470A>G	ENST00000282356.4	+	5	847	c.449A>G	c.(448-450)gAg>gGg	p.E150G	CAMK4_ENST00000512453.1_Missense_Mutation_p.E150G	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> G (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.E150G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		CAAATCCTGGAGGCAGTTGCT	0.403																																																1	Substitution - Missense(1)	lung(1)	5											127	127	127					5																	110730470		2202	4300	6502	110758369	SO:0001583	missense	814			D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.449A>G	5.37:g.110730470A>G	ENSP00000282356:p.Glu150Gly		110758369	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898550	0.72639	.	.	ENSG00000152495	ENST00000512453;ENST00000282356	T;T	0.67698	-0.28;-0.28	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72961	0.3526	L	0.35593	1.075	0.58432	D	0.999996	D	0.89917	1.0	D	0.77004	0.989	T	0.71738	-0.4502	9	.	.	.	.	14.8633	0.70397	1.0:0.0:0.0:0.0	.	150	Q16566	KCC4_HUMAN	G	150	ENSP00000422634:E150G;ENSP00000282356:E150G	.	E	+	2	0	CAMK4	110758369	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.227000	0.78070	2.165000	0.68154	0.383000	0.25322	GAG		0.403	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		G	110730470	A	G	110730470	3	3	119	1	0	0	0	0	1	0	0	0	2611	304	11	4	467	4	CAMK4	5	110730470	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	105266403	110730470	70184790	45	31489										
APC	324	hgsc.bcm.edu	37	chr5	112175303	112175303	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gaaccaaatccagcagactgCagggttctagtttatcttca	8	10	3	1	rs121913327		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr5:112175303C>T	ENST00000457016.1	+	16	4392	c.4012C>T	c.(4012-4014)Cag>Tag	p.Q1338*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1338*|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1338*			P25054	APC_HUMAN	adenomatous polyposis coli	1338	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1338*(30)|p.L1337fs*76(4)|p.?(1)|p.K1192fs*3(1)|p.V1326fs*3(1)|p.S1335fs*70(1)|p.L1337>?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGCAGACTGCAGGGTTCTAG	0.458	Q1338*(SW480_LARGE_INTESTINE)|Q1338*(SW620_LARGE_INTESTINE)	12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	39	Substitution - Nonsense(30)|Deletion - Frameshift(7)|Unknown(1)|Complex(1)	large_intestine(34)|thyroid(1)|biliary_tract(1)|stomach(1)|soft_tissue(1)|skin(1)	5	GRCh37	CM930029	APC	M	rs121913327						57	60	59					5																	112175303		2202	4300	6502	112203202	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4012C>T	5.37:g.112175303C>T	ENSP00000413133:p.Gln1338*		112203202	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.909540	0.98557	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.226724	0.46145	D	0.000316	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.6325	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1338	.	.	Q	+	1	0	APC	112203202	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	4.607000	0.61133	2.861000	0.98227	0.655000	0.94253	CAG		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175303	C	T	112175303	4	4	119	1	0	0	0	0	0	1	0	0	763	711	25	3	4070	3	APC	5	112175303	Nonsense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1444833	112175303	68739957	46	31490										
MCC	4163	hgsc.bcm.edu	37	chr5	112487091	112487091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	taagttccactatatctcccTttagtgatgccagggctgct	8	11	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr5:112487091T>C	ENST00000302475.4	-	2	649	c.86A>G	c.(85-87)aAg>aGg	p.K29R	MCC_ENST00000515367.2_5'UTR|MCC_ENST00000408903.3_Missense_Mutation_p.K219R|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	29					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.K29M(1)|p.K219M(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TATATCTCCCTTTAGTGATGC	0.468																																																2	Substitution - Missense(2)	ovary(2)	5											90	81	84					5																	112487091		2202	4300	6502	112514990	SO:0001583	missense	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.86A>G	5.37:g.112487091T>C	ENSP00000305617:p.Lys29Arg		112514990	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	T	8.353	0.831304	0.16820	.	.	ENSG00000171444	ENST00000302475;ENST00000408903	T;T	0.78595	-1.19;1.32	5.25	4.1	0.47936	.	0.132653	0.52532	N	0.000067	T	0.53254	0.1785	N	0.04203	-0.255	0.36772	D	0.883845	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.11329	0.001;0.006;0.001	T	0.50039	-0.8874	10	0.22109	T	0.4	-38.5269	8.1987	0.31411	0.0:0.1523:0.0:0.8477	.	29;219;29	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	R	29;219	ENSP00000305617:K29R;ENSP00000386227:K219R	ENSP00000305617:K29R	K	-	2	0	MCC	112514990	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	2.637000	0.46553	1.034000	0.39945	0.459000	0.35465	AAG		0.468	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		C	112487091	T	C	112487091	3	2	119	1	0	0	0	0	1	0	0	0	9403	1609	56	4	2467	4	MCC	5	112487091	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	311788	112487091	68428169	47	31491										
MGAT4B	11282	hgsc.bcm.edu	37	chr5	179226572	179226572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aggagccagtcgatgggcttGtcccggtagaacatgagaat	14	8	0	2	rs141460358		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr5:179226572G>T	ENST00000292591.7	-	9	1325	c.975C>A	c.(973-975)gaC>gaA	p.D325E	MGAT4B_ENST00000521305.1_5'Flank|MIR1229_ENST00000408467.1_RNA|MGAT4B_ENST00000337755.5_Missense_Mutation_p.D340E	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B	325					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGATGGGCTTGTCCCGGTAGA	0.582																																					GBM(13;414 434 4098 22176 23230)											0			5						G	GLU/ASP,GLU/ASP	0,4406		0,0,2203	102	102	102		975,1020	4.4	1	5	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	MGAT4B	NM_014275.4,NM_054013.3	45,45	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	325/549,340/564	179226572	1,13005	2203	4300	6503	179159178	SO:0001583	missense	11282			AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7048	protein-coding gene	gene with protein product		604561	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.975C>A	5.37:g.179226572G>T	ENSP00000292591:p.Asp325Glu		179159178	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Missense_Mutation	SNP	ENST00000292591.7	37	CCDS4448.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	13.19|13.19|13.19	2.164392|2.164392|2.164392	0.38217|0.38217|0.38217	0.0|0.0|0.0	1.16E-4|1.16E-4|1.16E-4	ENSG00000161013|ENSG00000161013|ENSG00000161013	ENST00000337755;ENST00000292591;ENST00000523108|ENST00000518778;ENST00000520875;ENST00000518867|ENST00000520969	T;T;T|.|.	0.43688|.|.	0.94;0.94;0.94|.|.	4.37|4.37|4.37	4.37|4.37|4.37	0.52481|0.52481|0.52481	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.47838|0.47838|0.47838	0.1467|0.1467|0.1467	N|N|N	0.12527|0.12527|0.12527	0.23|0.23|0.23	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;P;D|.|.	0.61697|.|.	0.788;0.767;0.99|.|.	P;B;D|.|.	0.75484|.|.	0.548;0.394;0.986|.|.	T|T|T	0.44112|0.44112|0.44112	-0.9349|-0.9349|-0.9349	10|5|5	0.23891|.|.	T|.|.	0.37|.|.	-41.3493|-41.3493|-41.3493	17.1369|17.1369|17.1369	0.86743|0.86743|0.86743	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	325;340;325|.|.	Q9UQ53;A8MPR0;Q9UQ53-2|.|.	MGT4B_HUMAN;.;.|.|.	E|K|K	340;325;180|151;124;137|22	ENSP00000338487:D340E;ENSP00000292591:D325E;ENSP00000427995:D180E|.|.	ENSP00000292591:D325E|.|.	D|Q|T	-|-|-	3|1|2	2|0|0	MGAT4B|MGAT4B|MGAT4B	179159178|179159178|179159178	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	3.612000|3.612000|3.612000	0.54142|0.54142|0.54142	2.269000|2.269000|2.269000	0.75478|0.75478|0.75478	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAC|CAA|ACA		0.582	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275		T	179226572	G	T	179226572	3	4	119	1	0	0	0	0	1	0	0	0	9576	1368	48	2	699	2	MGAT4B	5	179226572	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	66739481	179226572	1688688	48	31492										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38840416	38840416	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	atgaaggcgcaaacagaatgCggaaggcctcatagagaaat	12	7	1	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:38840416C>T	ENST00000359357.3	+	48	6698	c.6444C>T	c.(6442-6444)tgC>tgT	p.C2148C	DNAH8_ENST00000441566.1_Silent_p.C2112C|DNAH8_ENST00000449981.2_Silent_p.C2365C			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2148	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AAACAGAATGCGGAAGGCCTC	0.483																																																0			6											112	106	108					6																	38840416		2203	4300	6503	38948394	SO:0001819	synonymous_variant	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6444C>T	6.37:g.38840416C>T			38948394	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																					0.483	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38840416	C	T	38840416	2	4	119	1	0	0	0	0	0	0	0	1	4618	776	27	1		1	DNAH8	6	38840416	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10		38840416	132274651	49	31493										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38851758	38851758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tattaatatgcctgtgattaAtgagtggggagatcaggtat	12	3	1	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:38851758A>G	ENST00000359357.3	+	54	7846	c.7592A>G	c.(7591-7593)aAt>aGt	p.N2531S	DNAH8_ENST00000441566.1_Missense_Mutation_p.N2495S|DNAH8_ENST00000449981.2_Missense_Mutation_p.N2748S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2531	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.N2531I(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CCTGTGATTAATGAGTGGGGA	0.318																																																1	Substitution - Missense(1)	ovary(1)	6											99	102	101					6																	38851758		2203	4300	6503	38959736	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7592A>G	6.37:g.38851758A>G	ENSP00000352312:p.Asn2531Ser		38959736	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	22.5	4.302909	0.81136	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.16897	2.31;2.31;2.31	5.07	5.07	0.68467	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.41143	0.1146	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51379	-0.8713	10	0.52906	T	0.07	.	15.1103	0.72351	1.0:0.0:0.0:0.0	.	2531	Q96JB1	DYH8_HUMAN	S	2736;2736;2531;2495	ENSP00000333363:N2736S;ENSP00000352312:N2531S;ENSP00000402294:N2495S	ENSP00000333363:N2736S	N	+	2	0	DNAH8	38959736	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.277000	0.95755	2.030000	0.59900	0.454000	0.30748	AAT		0.318	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38851758	A	G	38851758	3	3	119	1	0	0	0	0	1	0	0	0	4618	101	4	4	7798	4	DNAH8	6	38851758	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	11342	38851758	132263309	50	31494										
DST	667	hgsc.bcm.edu	37	chr6	56357224	56357224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gatgagaatttacttcattgGcaaaaacctttcccagaaaa	6	8	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:56357224G>A	ENST00000361203.3	-	80	19605	c.19598C>T	c.(19597-19599)gCc>gTc	p.A6533V	DST_ENST00000244364.6_Missense_Mutation_p.A4230V|DST_ENST00000446842.2_Missense_Mutation_p.A6318V|DST_ENST00000340834.4_5'Flank|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Missense_Mutation_p.A4447V|DST_ENST00000421834.2_Missense_Mutation_p.A4556V|DST_ENST00000370769.4_Missense_Mutation_p.A6644V|DST_ENST00000370754.5_Missense_Mutation_p.A6822V			Q03001	DYST_HUMAN	dystonin	6533					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACTTCATTGGCAAAAACCTT	0.313																																																0			6											73	70	71					6																	56357224		1802	4064	5866	56465183	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.19598C>T	6.37:g.56357224G>A	ENSP00000354508:p.Ala6533Val		56465183	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	16.84	3.232729	0.58777	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.11	5.11	0.69529	.	0.000000	0.48286	D	0.000195	T	0.19927	0.0479	N	0.02368	-0.58	0.33387	D	0.575589	B;P;P;B;B	0.40032	0.153;0.699;0.518;0.019;0.035	B;P;B;B;B	0.51806	0.095;0.68;0.349;0.015;0.034	T	0.16129	-1.0413	9	0.19147	T	0.46	.	12.2938	0.54833	0.0781:0.0:0.9219:0.0	.	4556;6644;6822;6642;4230	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	V	4230;6822;6644;4556;6318;4447;6533	ENSP00000244364:A4230V;ENSP00000359790:A6822V;ENSP00000359805:A6644V;ENSP00000400883:A4556V;ENSP00000393645:A6318V;ENSP00000359824:A4447V;ENSP00000354508:A6533V	ENSP00000244364:A4230V	A	-	2	0	DST	56465183	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.888000	0.69758	2.540000	0.85666	0.591000	0.81541	GCC		0.313	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56357224	G	A	56357224	3	1	119	1	0	0	0	0	1	0	0	0	4794	1203	42	3	2902	3	DST	6	56357224	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	17505466	56357224	114757843	51	31495										
FYN	2534	hgsc.bcm.edu	37	chr6	112041168	112041168	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggggtggggtctgtgccataGcggtacccagagctctggtt	17	9	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:112041168G>T	ENST00000354650.3	-	4	693	c.87C>A	c.(85-87)cgC>cgA	p.R29R	FYN_ENST00000229471.4_Silent_p.R29R|FYN_ENST00000538466.1_Silent_p.R29R|FYN_ENST00000368667.2_Silent_p.R29R|FYN_ENST00000229470.5_Silent_p.R29R|FYN_ENST00000356013.2_Silent_p.R29R|FYN_ENST00000368682.3_Silent_p.R29R|FYN_ENST00000368678.4_Silent_p.R29R	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	29					activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	CTGTGCCATAGCGGTACCCAG	0.562																																																0			6											145	106	119					6																	112041168		2203	4300	6503	112147861	SO:0001819	synonymous_variant	2534			AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"SH2 domain containing"	4037	protein-coding gene	gene with protein product		137025	"FYN oncogene related to SRC, FGR, YES"			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.87C>A	6.37:g.112041168G>T			112147861	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Silent	SNP	ENST00000354650.3	37	CCDS5094.1																																																																																				0.562	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			T	112041168	G	T	112041168	2	4	119	1	0	0	0	0	0	0	0	1	6145	958	34	2		2	FYN	6	112041168	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10	55683944	112041168	59073899	52	31496										
ROS1	6098	hgsc.bcm.edu	37	chr6	117665427	117665427	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agagacagaaacgctttatcTaaaataagaagaaaccaaaa	6	6	1	4			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:117665427T>C	ENST00000368508.3	-	27	4520		c.e27-2		ROS1_ENST00000368507.3_Splice_Site|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase						cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.?(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ACGCTTTATCTAAAATAAGAA	0.323			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	1	Unknown(1)	central_nervous_system(1)	6											109	108	108					6																	117665427		2203	4300	6503	117772120	SO:0001630	splice_region_variant	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4322-2A>G	6.37:g.117665427T>C			117772120	Q15368|Q5TDB5	Splice_Site	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020239	0.35606	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	.	.	.	5.16	3.91	0.45181	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6017	0.33749	0.1712:0.0:0.0:0.8288	.	.	.	.	.	-1	.	.	.	-	.	.	ROS1	117772120	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	3.397000	0.52572	2.077000	0.62373	0.459000	0.35465	.		0.323	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		Intron	C	117665427	T	C	117665427	5	2	119	1	0	0	0	0	0	0	1	0	13568	1536	53	4	2791	4	ROS1	6	117665427	Splice_Site	SNP	T	TCGA-F5-6812-01A-11D-1826-10	5624259	117665427	53449640	53	31497										
LPA	4018	hgsc.bcm.edu	37	chr6	160977188	160977188	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccattaccatggtagcactgCcggaccacaggggtttgctc	11	13	0	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:160977188C>T	ENST00000316300.5	-	30	4886	c.4842G>A	c.(4840-4842)cgG>cgA	p.R1614R	LPA_ENST00000447678.1_Silent_p.R1614R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4122	Kringle 15. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGTAGCACTGCCGGACCACAG	0.468																																																0			6											111	115	114					6																	160977188		2168	4297	6465	160897178	SO:0001819	synonymous_variant	4018			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4842G>A	6.37:g.160977188C>T			160897178	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																				0.468	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	160977188	C	T	160977188	2	4	119	1	0	0	0	0	0	0	0	1	8932	726	26	3		3	LPA	6	160977188	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10	43311761	160977188	10137879	54	31498										
DLL1	28514	hgsc.bcm.edu	37	chr6	170592670	170592670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gcctcagccggacgcagaccAccacagcggcacagcccagc	11	19	1	1	rs531005727	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr6:170592670A>G	ENST00000366756.3	-	9	2030	c.1697T>C	c.(1696-1698)gTg>gCg	p.V566A		NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	566					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		GACGCAGACCACCACAGCGGC	0.687																																																0			6											37	37	37					6																	170592670		2202	4298	6500	170434595	SO:0001583	missense	28514			AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.1697T>C	6.37:g.170592670A>G	ENSP00000355718:p.Val566Ala		170434595	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	37	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	A	6.686	0.495192	0.12762	.	.	ENSG00000198719	ENST00000366756	D	0.86562	-2.14	5.11	-0.421	0.12332	.	0.174666	0.49916	D	0.000130	T	0.81250	0.4783	M	0.80847	2.515	0.41963	D	0.990717	B	0.30021	0.265	B	0.32211	0.142	T	0.76629	-0.2889	10	0.54805	T	0.06	.	14.7823	0.69776	0.4533:0.5467:0.0:0.0	.	566	O00548	DLL1_HUMAN	A	566	ENSP00000355718:V566A	ENSP00000355718:V566A	V	-	2	0	DLL1	170434595	0.995000	0.38212	0.017000	0.16124	0.035000	0.12851	4.217000	0.58547	-0.229000	0.09854	-0.331000	0.08364	GTG		0.687	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			G	170592670	A	G	170592670	3	3	119	1	0	0	0	0	1	0	0	0	4577	159	6	4	486	4	DLL1	6	170592670	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	9615482	170592670	522397	55	31499										
STK31	56164	hgsc.bcm.edu	37	chr7	23802527	23802527	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gagtcatctcttaataaacgCttaaaaacattgcaggttgg	8	7	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:23802527C>G	ENST00000355870.3	+	11	1520	c.1401C>G	c.(1399-1401)cgC>cgG	p.R467R	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Silent_p.R444R|STK31_ENST00000433467.2_Silent_p.R467R|STK31_ENST00000354639.3_Silent_p.R444R	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	467						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTAATAAACGCTTAAAAACAT	0.284																																																0			7											60	61	61					7																	23802527		2203	4299	6502	23769052	SO:0001819	synonymous_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1401C>G	7.37:g.23802527C>G			23769052	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				0.284	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		G	23802527	C	G	23802527	2	3	119	1	0	0	0	0	0	0	0	1	15335	784	28	5		5	STK31	7	23802527	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10		23802527	135336136	56	31500										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963642	88963642	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttttctccacgttcaaagcaAggatggccacaccactcttc	6	14	3	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:88963642A>G	ENST00000333190.4	+	4	1955	c.1346A>G	c.(1345-1347)aAg>aGg	p.K449R		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	449							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GTTCAAAGCAAGGATGGCCAC	0.398										HNSCC(36;0.09)																																						0			7											73	71	72					7																	88963642		2201	4295	6496	88801578	SO:0001583	missense	219578			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1346A>G	7.37:g.88963642A>G	ENSP00000329638:p.Lys449Arg		88801578	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.640877	0.67244	.	.	ENSG00000182348	ENST00000333190	T	0.15372	2.43	5.49	4.35	0.52113	.	0.079395	0.53938	N	0.000052	T	0.21509	0.0518	M	0.81942	2.565	0.39819	D	0.97281	P	0.38110	0.618	B	0.32211	0.142	T	0.09143	-1.0688	10	0.87932	D	0	-13.1028	11.2704	0.49136	0.9294:0.0:0.0706:0.0	.	449	A4D1E1	Z804B_HUMAN	R	449	ENSP00000329638:K449R	ENSP00000329638:K449R	K	+	2	0	ZNF804B	88801578	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	5.822000	0.69265	1.116000	0.41820	0.533000	0.62120	AAG		0.398	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88963642	A	G	88963642	3	3	119	1	0	0	0	0	1	0	0	0	18210	72	3	4	1360	4	ZNF804B	7	88963642	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	65161115	88963642	70175021	57	31501										
CDK14	5218	hgsc.bcm.edu	37	chr7	90585055	90585055	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cctagccacacatactccaaCgaagtggttaccttgtggta	8	12	0	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:90585055C>T	ENST00000380050.3	+	9	1001	c.870C>T	c.(868-870)aaC>aaT	p.N290N	CDK14_ENST00000436577.2_Silent_p.N161N|CDK14_ENST00000406263.1_Silent_p.N244N|CDK14_ENST00000265741.3_Silent_p.N272N			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						CATACTCCAACGAAGTGGTTA	0.433																																					GBM(83;1228 1256 8311 16577 31299)											0			7											186	161	169					7																	90585055		2203	4300	6503	90422991	SO:0001819	synonymous_variant	0				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.870C>T	7.37:g.90585055C>T			90422991	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Silent	SNP	ENST00000380050.3	37																																																																																					0.433	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		T	90585055	C	T	90585055	2	4	119	1	0	0	0	0	0	0	0	1	3136	535	19	1		1	CDK14	7	90585055	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1621413	90585055	68553608	58	31502										
SRPK2	6733	hgsc.bcm.edu	37	chr7	104783609	104783609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cacctctgggcagtattcgcCatcctggtcattggaaggtg	12	11	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:104783609C>T	ENST00000393651.3	-	10	1069	c.982G>A	c.(982-984)Ggc>Agc	p.G328S	SRPK2_ENST00000489828.1_Missense_Mutation_p.G317S|SRPK2_ENST00000357311.3_Missense_Mutation_p.G317S	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						CAGTATTCGCCATCCTGGTCA	0.502																																																0			7											139	125	130					7																	104783609		2203	4300	6503	104570845	SO:0001583	missense	6733			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.982G>A	7.37:g.104783609C>T	ENSP00000377262:p.Gly328Ser		104570845		Missense_Mutation	SNP	ENST00000393651.3	37	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	C	3.944	-0.013704	0.07681	.	.	ENSG00000135250	ENST00000393651;ENST00000357311;ENST00000489828	T;T;T	0.20738	2.05;2.05;2.05	5.57	3.74	0.42951	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.813348	0.11592	N	0.548646	T	0.07188	0.0182	N	0.02539	-0.55	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.16289	0.015;0.004	T	0.40232	-0.9574	10	0.07325	T	0.83	0.1734	6.3588	0.21417	0.1366:0.6616:0.1317:0.0701	.	328;317	P78362-2;P78362	.;SRPK2_HUMAN	S	328;317;317	ENSP00000377262:G328S;ENSP00000349863:G317S;ENSP00000419791:G317S	ENSP00000349863:G317S	G	-	1	0	SRPK2	104570845	0.672000	0.27530	0.085000	0.20634	0.793000	0.44817	2.631000	0.46502	0.691000	0.31592	-0.263000	0.10527	GGC		0.502	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		T	104783609	C	T	104783609	3	4	119	1	0	0	0	0	1	0	0	0	15199	594	21	3	1145	3	SRPK2	7	104783609	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	14198554	104783609	54355054	59	31503										
RINT1	60561	hgsc.bcm.edu	37	chr7	105182974	105182974	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	actcatctcttcagcgccatTaacagccatttgctgactgc	6	14	3	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:105182974T>G	ENST00000257700.2	+	4	624	c.393T>G	c.(391-393)atT>atG	p.I131M	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	131					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TCAGCGCCATTAACAGCCATT	0.403																																																0			7											115	110	111					7																	105182974		2203	4300	6503	104970210	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.393T>G	7.37:g.105182974T>G	ENSP00000257700:p.Ile131Met		104970210	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	T	7.513	0.655091	0.14580	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.25749	1.78	4.95	-0.402	0.12404	.	0.056804	0.64402	D	0.000001	T	0.33440	0.0863	L	0.58101	1.795	0.42570	D	0.993179	D	0.57899	0.981	P	0.55455	0.776	T	0.06588	-1.0818	10	0.41790	T	0.15	-20.074	9.5795	0.39479	0.0:0.4655:0.0:0.5345	.	131	Q6NUQ1	RINT1_HUMAN	M	131;100	ENSP00000257700:I131M	ENSP00000257700:I131M	I	+	3	3	RINT1	104970210	0.702000	0.27816	0.725000	0.30721	0.309000	0.27889	0.024000	0.13555	-0.048000	0.13401	0.379000	0.24179	ATT		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		G	105182974	T	G	105182974	3	3	119	1	0	0	0	0	1	0	0	0	13413	1742	61	4	407	4	RINT1	7	105182974	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	399365	105182974	53955689	60	31504										
MET	4233	hgsc.bcm.edu	37	chr7	116417482	116417482	+	De_novo_Start_OutOfFrame	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcatgggactttgttggacaAtgatggcaagaaaattcact	10	6	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:116417482A>T	ENST00000539704.1	+	0	110				MET_ENST00000318493.6_Missense_Mutation_p.N1118I|MET_ENST00000397752.3_Missense_Mutation_p.N1100I			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase						apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTGTTGGACAATGATGGCAAG	0.333			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	0			7											202	189	193					7																	116417482		1842	4088	5930	116204718			8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000539704.1:c.-92A>T	7.37:g.116417482A>T			116204718	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000539704.1	37		.	.	.	.	.	.	.	.	.	.	A	11.73	1.725268	0.30593	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	D;D	0.82893	-1.66;-1.66	5.29	-1.64	0.08318	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.454051	0.26394	N	0.024625	T	0.67363	0.2885	L	0.28556	0.865	0.27831	N	0.941447	B;B	0.32573	0.001;0.376	B;B	0.35770	0.002;0.21	T	0.57499	-0.7801	10	0.40728	T	0.16	.	2.7718	0.05336	0.4374:0.1162:0.3337:0.1127	.	1118;1100	P08581-2;P08581	.;MET_HUMAN	I	1100;1118	ENSP00000380860:N1100I;ENSP00000317272:N1118I	ENSP00000317272:N1118I	N	+	2	0	MET	116204718	0.002000	0.14202	0.380000	0.26093	0.997000	0.91878	-0.002000	0.12924	-0.450000	0.07107	0.533000	0.62120	AAT		0.333	MET-202	KNOWN	basic	protein_coding	protein_coding				T	116417482	A	T	116417482	1	4	119	1	0	1	0	0	0	0	0	0	9515	101	4	5		5	MET	7	116417482	De_novo_Start_OutOfFrame	SNP	A	TCGA-F5-6812-01A-11D-1826-10	11234508	116417482	42721181	61	31505										
CPA1	1357	hgsc.bcm.edu	37	chr7	130021652	130021652	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gatgttcgccttccggtcccGggcgcgctccaccgacactt	11	17	0	0	rs537076438		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:130021652G>A	ENST00000011292.3	+	3	479	c.329G>A	c.(328-330)cGg>cAg	p.R110Q	CPA1_ENST00000484324.1_Missense_Mutation_p.R22Q	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	110					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					TTCCGGTCCCGGGCGCGCTCC	0.627											OREG0018314	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		17262	0.001		0	False		,,,				2504	0															0			7											46	47	46					7																	130021652		2203	4300	6503	129808888	SO:0001583	missense	1357				CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase A"	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.329G>A	7.37:g.130021652G>A	ENSP00000011292:p.Arg110Gln	1576	129808888	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Missense_Mutation	SNP	ENST00000011292.3	37	CCDS5820.1	.	.	.	.	.	.	.	.	.	.	G	0.947	-0.707737	0.03230	.	.	ENSG00000091704	ENST00000481342;ENST00000011292;ENST00000476062;ENST00000484324	T;T;T;T	0.16324	2.72;2.78;2.35;2.44	5.06	-1.34	0.09143	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (1);	0.719730	0.13956	N	0.351190	T	0.08313	0.0207	L	0.37466	1.105	0.09310	N	1	B;B	0.21688	0.059;0.001	B;B	0.11329	0.006;0.001	T	0.39231	-0.9624	10	0.11485	T	0.65	.	0.5851	0.00718	0.2824:0.1124:0.262:0.3432	.	22;110	B4DDW9;P15085	.;CBPA1_HUMAN	Q	22;110;22;22	ENSP00000420218:R22Q;ENSP00000011292:R110Q;ENSP00000419408:R22Q;ENSP00000419497:R22Q	ENSP00000011292:R110Q	R	+	2	0	CPA1	129808888	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.304000	0.08199	-0.680000	0.05211	-1.516000	0.00938	CGG		0.627	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868		A	130021652	G	A	130021652	3	1	119	1	0	0	0	0	1	0	0	0	3795	1116	39	1	339	1	CPA1	7	130021652	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	13604170	130021652	29117011	62	31506										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146536869	146536869	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcaggttgactttggcaatcGgaagcagatcagtgccattg	12	8	2	2	rs138924087		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr7:146536869G>A	ENST00000361727.3	+	3	791	c.275G>A	c.(274-276)cGg>cAg	p.R92Q		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	92	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.R92Q(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TTTGGCAATCGGAAGCAGATC	0.502										HNSCC(39;0.1)			G|||	1	0.000199681	8e-04	0	5008	,	,		17468	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	7						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	95	82	86		275	5.8	1	7	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTNAP2	NM_014141.5	43	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	92/1332	146536869	2,13004	2203	4300	6503	146167802	SO:0001583	missense	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.275G>A	7.37:g.146536869G>A	ENSP00000354778:p.Arg92Gln		146167802	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	36	5.636114	0.96693	2.27E-4	1.16E-4	ENSG00000174469	ENST00000361727	D	0.98150	-4.75	5.83	5.83	0.93111	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.000000	0.51477	D	0.000081	D	0.97343	0.9131	L	0.52011	1.625	0.80722	D	1	P	0.51933	0.949	P	0.50754	0.649	D	0.97724	1.0198	10	0.66056	D	0.02	.	18.6885	0.91574	0.0:0.0:1.0:0.0	.	92	Q9UHC6	CNTP2_HUMAN	Q	92	ENSP00000354778:R92Q	ENSP00000354778:R92Q	R	+	2	0	CNTNAP2	146167802	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.760000	0.94817	0.650000	0.86243	CGG		0.502	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	146536869	G	A	146536869	3	1	119	1	0	0	0	0	1	0	0	0	3653	1116	39	1	285	1	CNTNAP2	7	146536869	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	16515217	146536869	12601794	63	31507										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27634264	27634264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cacagaagagtttaactgctAagtatcaaccaaagtataga	7	7	1	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr8:27634264A>G	ENST00000305188.8	+	3	677	c.439A>G	c.(439-441)Aag>Gag	p.K147E	ESCO2_ENST00000523910.1_3'UTR|RNU6-1276P_ENST00000365372.1_RNA|ESCO2_ENST00000397418.2_5'UTR	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	147					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		TTTAACTGCTAAGTATCAACC	0.358									SC Phocomelia syndrome																																							0			8											54	51	52					8																	27634264		2203	4300	6503	27690183	SO:0001583	missense	157570	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.439A>G	8.37:g.27634264A>G	ENSP00000306999:p.Lys147Glu		27690183	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	37	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.117277	0.56505	.	.	ENSG00000171320	ENST00000523566;ENST00000305188	T;T	0.67171	0.66;-0.25	5.93	5.93	0.95920	.	0.487974	0.23070	N	0.052278	T	0.78629	0.4313	M	0.67953	2.075	0.80722	D	1	D;P	0.65815	0.995;0.952	D;B	0.66196	0.942;0.339	T	0.79983	-0.1573	10	0.62326	D	0.03	-10.7085	12.7654	0.57388	1.0:0.0:0.0:0.0	.	147;147	E5RFE4;Q56NI9	.;ESCO2_HUMAN	E	147	ENSP00000428435:K147E;ENSP00000306999:K147E	ENSP00000306999:K147E	K	+	1	0	ESCO2	27690183	1.000000	0.71417	0.990000	0.47175	0.878000	0.50629	4.546000	0.60705	2.273000	0.75805	0.482000	0.46254	AAG		0.358	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		G	27634264	A	G	27634264	3	3	119	1	0	0	0	0	1	0	0	0	5262	363	13	4	445	4	ESCO2	8	27634264	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10		27634264	118729758	64	31508										
CNGB3	54714	hgsc.bcm.edu	37	chr8	87738778	87738778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cctgtttggaccttctttccCggggtccatttccttctgct	8	14	2	0	rs146688972	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr8:87738778C>T	ENST00000320005.5	-	3	366	c.319G>A	c.(319-321)Ggg>Agg	p.G107R	RP11-386D6.1_ENST00000519041.1_RNA|CNGB3_ENST00000519777.1_5'UTR	NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	107			G -> R (in ACHM3; unknown pathological significance; dbSNP:rs146688972). {ECO:0000269|PubMed:15712225}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.G107R(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CCTTCTTTCCCGGGGTCCATT	0.458													C|||	4	0.000798722	0	0.0043	5008	,	,		17451	0		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	8						C	ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	285	267	273		319	1.8	0	8	dbSNP_134	273	8,8592	6.4+/-24.3	0,8,4292	yes	missense	CNGB3	NM_019098.4	125	0,11,6492	TT,TC,CC		0.093,0.0681,0.0846	benign	107/810	87738778	11,12995	2203	4300	6503	87807894	SO:0001583	missense	54714			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.319G>A	8.37:g.87738778C>T	ENSP00000316605:p.Gly107Arg		87807894	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	C	7.794	0.712236	0.15306	6.81E-4	9.3E-4	ENSG00000170289	ENST00000320005	T	0.61510	0.1	5.71	1.76	0.24704	.	0.985643	0.08227	N	0.978212	T	0.34048	0.0884	L	0.38838	1.175	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.22068	-1.0227	10	0.19590	T	0.45	.	4.8138	0.13356	0.1478:0.6098:0.0:0.2424	.	107	Q9NQW8	CNGB3_HUMAN	R	107	ENSP00000316605:G107R	ENSP00000316605:G107R	G	-	1	0	CNGB3	87807894	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.118000	0.15605	0.338000	0.23692	-0.140000	0.14226	GGG		0.458	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87738778	C	T	87738778	3	4	119	1	0	0	0	0	1	0	0	0	3607	652	23	1	2174	1	CNGB3	8	87738778	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	60104514	87738778	58625244	65	31509										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92301370	92301370	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agtcttcttcacaggattggCctttgctgttctctcatctg	8	11	6	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr8:92301370C>A	ENST00000276609.3	+	3	439	c.200C>A	c.(199-201)gCc>gAc	p.A67D	SLC26A7_ENST00000523719.1_Missense_Mutation_p.A67D|SLC26A7_ENST00000309536.2_Missense_Mutation_p.A67D	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			ACAGGATTGGCCTTTGCTGTT	0.398																																																0			8											238	214	222					8																	92301370		2203	4300	6503	92370546	SO:0001583	missense	115111			AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.200C>A	8.37:g.92301370C>A	ENSP00000276609:p.Ala67Asp		92370546		Missense_Mutation	SNP	ENST00000276609.3	37	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506888	0.85282	.	.	ENSG00000147606	ENST00000522862;ENST00000523719;ENST00000276609;ENST00000309536	D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66	6.17	5.28	0.74379	.	0.338048	0.28198	N	0.016238	D	0.96846	0.8970	H	0.97023	3.925	0.31631	N	0.649018	P;P	0.51147	0.879;0.942	B;P	0.45276	0.295;0.475	D	0.97365	0.9972	10	0.87932	D	0	.	16.4093	0.83701	0.0:0.8681:0.1319:0.0	.	67;67	Q8TE54-2;Q8TE54	.;S26A7_HUMAN	D	67	ENSP00000428881:A67D;ENSP00000428849:A67D;ENSP00000276609:A67D;ENSP00000309504:A67D	ENSP00000276609:A67D	A	+	2	0	SLC26A7	92370546	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.748000	0.62148	1.578000	0.49821	0.655000	0.94253	GCC		0.398	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			A	92301370	C	A	92301370	3	1	119	1	0	0	0	0	1	0	0	0	14559	739	26	2	206	2	SLC26A7	8	92301370	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	4562592	92301370	54062652	66	31510										
JAK2	3717	hgsc.bcm.edu	37	chr9	5022143	5022143	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcccttgggaaatctgaggcAgattatctgacctttccatc	8	11	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:5022143A>T	ENST00000381652.3	+	3	650	c.156A>T	c.(154-156)gcA>gcT	p.A52A	JAK2_ENST00000539801.1_Silent_p.A52A	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	52	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	AATCTGAGGCAGATTATCTGA	0.368		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											142	138	139					9																	5022143		2203	4300	6503	5012143	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.156A>T	9.37:g.5022143A>T			5012143	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.368	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5022143	A	T	5022143	2	4	119	1	0	0	0	0	0	0	0	1	7959	175	7	5		5	JAK2	9	5022143	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10		5022143	136191288	67	31511										
PLAA	9373	hgsc.bcm.edu	37	chr9	26906045	26906045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggggtgtttaattgacaaccGaagaatgtcaagtgcaggaa	13	5	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:26906045G>A	ENST00000397292.3	-	14	2269	c.1852C>T	c.(1852-1854)Cgg>Tgg	p.R618W		NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	618	PUL. {ECO:0000255|PROSITE- ProRule:PRU00729}.				inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		ATTGACAACCGAAGAATGTCA	0.348																																					Melanoma(175;2670 2735 14091 35526)											0			9											37	40	39					9																	26906045		2191	4295	6486	26896045	SO:0001583	missense	9373			AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.1852C>T	9.37:g.26906045G>A	ENSP00000380460:p.Arg618Trp		26896045	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Missense_Mutation	SNP	ENST00000397292.3	37	CCDS35000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.03|17.03	3.285386|3.285386	0.59867|0.59867	.|.	.|.	ENSG00000137055|ENSG00000137055	ENST00000397292|ENST00000517642	T|.	0.50001|.	0.76|.	6.07|6.07	6.07|6.07	0.98685|0.98685	PUL (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74891|0.74891	0.3776|0.3776	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.72887|0.72887	-0.4156|-0.4156	10|5	0.87932|.	D|.	0|.	-11.7749|-11.7749	16.2596|16.2596	0.82533|0.82533	0.0:0.0:0.8596:0.1404|0.0:0.0:0.8596:0.1404	.|.	618|.	Q9Y263|.	PLAP_HUMAN|.	W|L	618|235	ENSP00000380460:R618W|.	ENSP00000380460:R618W|.	R|S	-|-	1|2	2|0	PLAA|PLAA	26896045|26896045	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.642000|5.642000	0.67888|0.67888	2.885000|2.885000	0.99019|0.99019	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.348	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		A	26906045	G	A	26906045	3	1	119	1	0	0	0	0	1	0	0	0	12042	1057	37	1	539	1	PLAA	9	26906045	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	21883902	26906045	114307386	68	31512										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33927851	33927851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tggatgcactcgcgggggtcCcacccagacagaggctgttc	14	13	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:33927851C>T	ENST00000379238.1	-	20	2432	c.2315G>A	c.(2314-2316)gGg>gAg	p.G772E	UBAP2_ENST00000379239.4_Missense_Mutation_p.G505E|UBAP2_ENST00000379235.1_Missense_Mutation_p.G11E|UBAP2_ENST00000449054.1_Missense_Mutation_p.G772E|UBAP2_ENST00000418786.2_3'UTR|UBAP2_ENST00000360802.1_Missense_Mutation_p.G772E|UBAP2_ENST00000539807.1_Missense_Mutation_p.G527E					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CGCGGGGGTCCCACCCAGACA	0.647																																																0			9											86	86	86					9																	33927851		2203	4300	6503	33917851	SO:0001583	missense	55833			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2315G>A	9.37:g.33927851C>T	ENSP00000368540:p.Gly772Glu		33917851		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	C	6.546	0.468932	0.12461	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6	5.92	1.67	0.24075	.	0.483078	0.24495	N	0.038021	T	0.18923	0.0454	L	0.43152	1.355	0.34905	D	0.746912	B;B;B;B;B	0.15930	0.015;0.015;0.015;0.007;0.009	B;B;B;B;B	0.18561	0.022;0.022;0.013;0.011;0.01	T	0.12268	-1.0554	10	0.29301	T	0.29	-0.9383	0.6284	0.00790	0.1957:0.3533:0.209:0.242	.	697;527;505;681;772	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;.;UBAP2_HUMAN	E	772;772;772;681;11;505;527;208	ENSP00000368540:G772E;ENSP00000416932:G772E;ENSP00000354039:G772E;ENSP00000368537:G11E;ENSP00000368541:G505E;ENSP00000439329:G527E	ENSP00000259602:G208E	G	-	2	0	UBAP2	33917851	0.001000	0.12720	0.011000	0.14972	0.014000	0.08584	0.618000	0.24373	0.412000	0.25729	0.655000	0.94253	GGG		0.647	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		T	33927851	C	T	33927851	3	4	119	1	0	0	0	0	1	0	0	0	16877	623	22	3	1084	3	UBAP2	9	33927851	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	7021806	33927851	107285580	69	31513										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100105779	100105779	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agccatgttcatcaacgacaCttccagtgccaagttcatag	7	12	3	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:100105779C>T	ENST00000357054.1	+	33	3916	c.2981C>T	c.(2980-2982)aCt>aTt	p.T994I	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.T855I|CCDC180_ENST00000411667.2_Missense_Mutation_p.T852I|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.T855I|CCDC180_ENST00000460482.2_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	994						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T994I(1)									ATCAACGACACTTCCAGTGCC	0.383																																																1	Substitution - Missense(1)	large_intestine(1)	9											104	97	100					9																	100105779		2203	4300	6503	99145600	SO:0001583	missense	0			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2981C>T	9.37:g.100105779C>T	ENSP00000349562:p.Thr994Ile		99145600	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	C	7.616	0.675831	0.14841	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.13089	3.02;3.06;2.62;3.06	5.39	-2.07	0.07276	.	2.428630	0.01127	N	0.005901	T	0.09335	0.0230	N	0.12182	0.205	0.09310	N	1	B;B;B	0.13145	0.007;0.001;0.003	B;B;B	0.10450	0.005;0.003;0.005	T	0.35450	-0.9788	10	0.35671	T	0.21	10.0467	10.4242	0.44367	0.0:0.4286:0.0:0.5714	.	878;994;994	Q86Y65;B7ZMG3;Q9P1Z9	.;.;CI174_HUMAN	I	994;855;852;878;855	ENSP00000349562:T994I;ENSP00000364348:T855I;ENSP00000414000:T852I;ENSP00000434727:T855I	ENSP00000349562:T994I	T	+	2	0	C9orf174	99145600	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.253000	0.08794	-0.350000	0.08262	0.655000	0.94253	ACT		0.383	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100105779	C	T	100105779	3	4	119	1	0	0	0	0	1	0	0	0	8261	565	20	3	3067	3	KIAA1529	9	100105779	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	66177928	100105779	41107652	70	31514										
MUSK	4593	hgsc.bcm.edu	37	chr9	113563218	113563218	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccagtttcaccagtattcacCgaattctggaacgcatgtgt	8	11	3	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:113563218C>T	ENST00000374448.4	+	15	2694	c.2560C>T	c.(2560-2562)Cga>Tga	p.R854*	MUSK_ENST00000416899.2_Nonsense_Mutation_p.R846*|MUSK_ENST00000189978.5_Nonsense_Mutation_p.R854*	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	854	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						CAGTATTCACCGAATTCTGGA	0.507																																																0			9											37	36	36					9																	113563218		2017	4188	6205	112603039	SO:0001587	stop_gained	4593			AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.2560C>T	9.37:g.113563218C>T	ENSP00000363571:p.Arg854*		112603039	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Nonsense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	C	38	7.179488	0.98118	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	.	.	.	5.62	3.72	0.42706	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4478	0.67364	0.2673:0.7327:0.0:0.0	.	.	.	.	X	860;854;854;768;768;852	.	ENSP00000189978:R860X	R	+	1	2	MUSK	112603039	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.228000	0.51270	0.790000	0.33803	0.557000	0.71058	CGA		0.507	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	113563218	C	T	113563218	4	4	119	1	0	0	0	0	0	1	0	0	10019	644	23	1	2650	1	MUSK	9	113563218	Nonsense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	13457439	113563218	27650213	71	31515										
ATP6V1G1	9550	hgsc.bcm.edu	37	chr9	117354865	117354865	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gctgaagcaggccaaagaagAagctcaggctgaaattgaac	12	8	1	5	rs72752535	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:117354865A>C	ENST00000374050.3	+	2	209	c.116A>C	c.(115-117)gAa>gCa	p.E39A	ATP6V1G1_ENST00000473413.1_3'UTR	NM_004888.3	NP_004879.1	O75348	VATG1_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1	39					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5						GCCAAAGAAGAAGCTCAGGCT	0.463													A|||	6	0.00119808	0	0.0014	5008	,	,		18424	0.001		0.003	False		,,,				2504	0.001															0			9						A	ALA/GLU	4,4390		0,4,2193	55	54	55		116	4.5	1	9	dbSNP_130	55	31,8559		0,31,4264	yes	missense	ATP6V1G1	NM_004888.3	107	0,35,6457	CC,CA,AA		0.3609,0.091,0.2696	benign	39/119	117354865	35,12949	2197	4295	6492	116394686	SO:0001583	missense	9550			AF038954	CCDS6807.1	9q33.1	2010-04-21	2006-01-13	2002-05-10	ENSG00000136888	ENSG00000136888		"ATPases / V-type"	864	protein-coding gene	gene with protein product		607296	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), member J", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 1"	ATP6J, ATP6G1		9653160	Standard	NM_004888		Approved	ATP6GL, Vma10, ATP6G, DKFZp547P234	uc004bjc.3	O75348	OTTHUMG00000021023	ENST00000374050.3:c.116A>C	9.37:g.117354865A>C	ENSP00000363162:p.Glu39Ala		116394686	Q6IB33	Missense_Mutation	SNP	ENST00000374050.3	37	CCDS6807.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	16.00	2.998943	0.54147	9.1E-4	0.003609	ENSG00000136888	ENST00000374050	T	0.55930	0.49	5.68	4.54	0.55810	.	0.148106	0.64402	N	0.000010	T	0.51568	0.1682	M	0.75085	2.285	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.50668	-0.8801	10	0.49607	T	0.09	.	10.1267	0.42654	0.9236:0.0:0.0764:0.0	.	39	O75348	VATG1_HUMAN	A	39	ENSP00000363162:E39A	ENSP00000363162:E39A	E	+	2	0	ATP6V1G1	116394686	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.709000	0.91379	1.091000	0.41335	0.528000	0.53228	GAA		0.463	ATP6V1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055454.1	NM_004888		C	117354865	A	C	117354865	3	2	119	1	0	0	0	0	1	0	0	0	1187	246	9	4	122	4	ATP6V1G1	9	117354865	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	3791647	117354865	23858566	72	31516										
DBC1	1620	hgsc.bcm.edu	37	chr9	121929963	121929963	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cgctaaaggggttgacatagAcaaagaacatggggtccagg	14	7	0	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:121929963A>G	ENST00000265922.3	-	8	2146	c.1685T>C	c.(1684-1686)gTc>gCc	p.V562A	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	562					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											GTTGACATAGACAAAGAACAT	0.552																																																0			9											42	41	42					9																	121929963		2203	4300	6503	120969784	SO:0001583	missense	57805			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1685T>C	9.37:g.121929963A>G	ENSP00000265922:p.Val562Ala		120969784	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.029009	0.54790	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.18810	2.19	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.37073	0.0990	L	0.50333	1.59	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	T	0.02391	-1.1166	10	0.29301	T	0.29	-29.7714	15.8802	0.79197	1.0:0.0:0.0:0.0	.	562	O60477	DBC1_HUMAN	A	562	ENSP00000265922:V562A	ENSP00000265922:V562A	V	-	2	0	DBC1	120969784	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.243000	0.95416	2.145000	0.66743	0.533000	0.62120	GTC		0.552	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		G	121929963	A	G	121929963	3	3	119	1	0	0	0	0	1	0	0	0	4253	275	10	4	604	4	DBC1	9	121929963	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	4575098	121929963	19283468	73	31517										
TRAF1	7185	hgsc.bcm.edu	37	chr9	123667348	123667348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gaacattgtgtcgtccttcaCgtaggcgtgcttgggtgact	13	9	1	1	rs371039591		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr9:123667348C>T	ENST00000373887.3	-	8	3646	c.1201G>A	c.(1201-1203)Gtg>Atg	p.V401M	TRAF1_ENST00000546084.1_Missense_Mutation_p.V279M|TRAF1_ENST00000540010.1_Missense_Mutation_p.V401M	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	401	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						TCGTCCTTCACGTAGGCGTGC	0.587																																																0			9						C	MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	133	85	102		1201,835,1201	5.6	1	9		102	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TRAF1	NM_001190945.1,NM_001190947.1,NM_005658.4	21,21,21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	401/417,279/295,401/417	123667348	1,13005	2203	4300	6503	122707169	SO:0001583	missense	7185			AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.1201G>A	9.37:g.123667348C>T	ENSP00000362994:p.Val401Met		122707169	B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	37	CCDS6825.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.645332	0.67358	0.0	1.16E-4	ENSG00000056558	ENST00000373887;ENST00000540010;ENST00000546084	T;T;T	0.49139	0.79;0.79;0.79	5.58	5.58	0.84498	TRAF-type (1);TRAF-like (1);MATH (2);	0.242364	0.35936	N	0.002894	T	0.60431	0.2268	M	0.77712	2.385	0.33206	D	0.552796	D	0.62365	0.991	P	0.53146	0.719	T	0.74213	-0.3738	10	0.66056	D	0.02	-33.7156	12.2726	0.54714	0.0:0.9222:0.0:0.0778	.	401	Q13077	TRAF1_HUMAN	M	401;401;279	ENSP00000362994:V401M;ENSP00000443183:V401M;ENSP00000438583:V279M	ENSP00000362994:V401M	V	-	1	0	TRAF1	122707169	1.000000	0.71417	0.993000	0.49108	0.640000	0.38277	2.373000	0.44266	2.786000	0.95864	0.655000	0.94253	GTG		0.587	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658		T	123667348	C	T	123667348	3	4	119	1	0	0	0	0	1	0	0	0	16477	536	19	1	53	1	TRAF1	9	123667348	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1737385	123667348	17546083	74	31518										
ATP5C1	509	hgsc.bcm.edu	37	chr10	7844757	7844757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	attgacattgacattcaaccGtacccgccaagctgtcatca	6	13	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:7844757G>A	ENST00000356708.7	+	8	909	c.830G>A	c.(829-831)cGt>cAt	p.R277H	ATP5C1_ENST00000335698.4_Missense_Mutation_p.R277H|ATP5C1_ENST00000541227.1_Missense_Mutation_p.R230H|ATP5C1_ENST00000493053.1_3'UTR	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	277					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						ACATTCAACCGTACCCGCCAA	0.348																																					Melanoma(143;1012 1820 16249 30920 33158)											0			10											92	90	91					10																	7844757		2203	4300	6503	7884763	SO:0001583	missense	509			D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.830G>A	10.37:g.7844757G>A	ENSP00000349142:p.Arg277His		7884763	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	37	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.635646	0.87760	.	.	ENSG00000165629	ENST00000356708;ENST00000335698;ENST00000541227	.	.	.	5.5	5.5	0.81552	ATPase, F1 complex, gamma subunit domain (1);	0.000000	0.85682	D	0.000000	T	0.72187	0.3429	M	0.91354	3.2	0.80722	D	1	P	0.47302	0.893	B	0.39935	0.314	T	0.81289	-0.1000	9	0.87932	D	0	-6.9791	19.3767	0.94512	0.0:0.0:1.0:0.0	.	277	P36542	ATPG_HUMAN	H	277;277;230	.	ENSP00000338568:R277H	R	+	2	0	ATP5C1	7884763	1.000000	0.71417	0.995000	0.50966	0.959000	0.62525	9.681000	0.98653	2.735000	0.93741	0.655000	0.94253	CGT		0.348	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		A	7844757	G	A	7844757	3	1	119	1	0	0	0	0	1	0	0	0	1150	1145	40	1	860	1	ATP5C1	10	7844757	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10		7844757	127689990	75	31519										
UPF2	26019	hgsc.bcm.edu	37	chr10	12021100	12021100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	catggaacaaagatcctctgCtacatcagacatgcagggat	9	10	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:12021100C>T	ENST00000356352.2	-	8	2382	c.1909G>A	c.(1909-1911)Gca>Aca	p.A637T	UPF2_ENST00000397053.2_Missense_Mutation_p.A637T|UPF2_ENST00000357604.5_Missense_Mutation_p.A637T			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	637	MIF4G 2.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.A637S(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				AGATCCTCTGCTACATCAGAC	0.358																																																1	Substitution - Missense(1)	central_nervous_system(1)	10											92	82	85					10																	12021100		2203	4300	6503	12061106	SO:0001583	missense	26019			AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1909G>A	10.37:g.12021100C>T	ENSP00000348708:p.Ala637Thr		12061106	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	C	34	5.327949	0.95733	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.21361	2.01;2.01;2.01	5.94	5.94	0.96194	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	M	0.61703	1.905	0.80722	D	1	D	0.55800	0.973	D	0.63283	0.913	T	0.04178	-1.0971	10	0.40728	T	0.16	.	20.352	0.98815	0.0:1.0:0.0:0.0	.	637	Q9HAU5	RENT2_HUMAN	T	637	ENSP00000348708:A637T;ENSP00000350221:A637T;ENSP00000380244:A637T	ENSP00000348708:A637T	A	-	1	0	UPF2	12061106	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.803000	0.96430	0.655000	0.94253	GCA		0.358	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			T	12021100	C	T	12021100	3	4	119	1	0	0	0	0	1	0	0	0	17044	797	28	3	1965	3	UPF2	10	12021100	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	4176343	12021100	123513647	76	31520										
MLLT10	8028	hgsc.bcm.edu	37	chr10	22016857	22016857	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccgaggaagtctctcgccacGgtaagcgctatttacactgc	10	13	1	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:22016857G>T	ENST00000307729.7	+	16	2241	c.2063G>T	c.(2062-2064)cGa>cTa	p.R688L	MLLT10_ENST00000377072.3_Splice_Site_p.R704L|MLLT10_ENST00000446906.2_Splice_Site_p.R688L|MLLT10_ENST00000377059.3_Splice_Site_p.R688L			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	688					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CTCTCGCCACGGTAAGCGCTA	0.423			T	"MLL, PICALM, CDK6"	AL																																		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	0			10											58	55	56					10																	22016857		2203	4300	6503	22056863	SO:0001630	splice_region_variant	8028			U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.2063+1G>T	10.37:g.22016857G>T			22056863	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269744	0.80469	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66	5.82	5.82	0.92795	.	0.061993	0.64402	D	0.000006	D	0.96716	0.8928	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.63880	0.99;0.992;0.993;0.992	P;P;D;P	0.74023	0.839;0.694;0.982;0.694	D	0.96558	0.9413	10	0.62326	D	0.03	.	20.1064	0.97896	0.0:0.0:1.0:0.0	.	383;688;688;704	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	L	704;688;688;523;688;347;346	ENSP00000366272:R704L;ENSP00000401406:R688L;ENSP00000307411:R688L;ENSP00000366258:R688L	ENSP00000307411:R688L	R	+	2	0	MLLT10	22056863	1.000000	0.71417	0.993000	0.49108	0.966000	0.64601	5.817000	0.69229	2.745000	0.94114	0.650000	0.86243	CGA		0.423	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		Missense_Mutation	T	22016857	G	T	22016857	5	4	119	1	0	0	0	0	0	0	1	0	9656	1130	39	2	2173	2	MLLT10	10	22016857	Splice_Site	SNP	G	TCGA-F5-6812-01A-11D-1826-10	9995757	22016857	113517890	77	31521										
REEP3	221035	hgsc.bcm.edu	37	chr10	65357872	65357872	+	Frame_Shift_Del	DEL	T	T	-													0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caagtttaatatatagaaaaTtccttcatccacttctttct							TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:65357872delT	ENST00000373758.4	+	4	454	c.271delT	c.(271-273)ttcfs	p.F91fs	REEP3_ENST00000298249.4_Frame_Shift_Del_p.F76fs	NM_001001330.2	NP_001001330.1	Q6NUK4	REEP3_HUMAN	receptor accessory protein 3	91					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)				endometrium(1)|large_intestine(2)|lung(3)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					ATATAGAAAATTCCTTCATCC	0.363																																																0			10											51	49	50					10																	65357872		1791	4073	5864	65027878	SO:0001589	frameshift_variant	221035			BC057832	CCDS44411.1	10q21.3	2011-01-05	2006-02-07	2006-02-07	ENSG00000165476	ENSG00000165476		"Receptor accessory proteins"	23711	protein-coding gene	gene with protein product		609348	"chromosome 10 open reading frame 74"	C10orf74		16271481, 15550249	Standard	NM_001001330		Approved		uc001jmt.3	Q6NUK4	OTTHUMG00000018318	ENST00000373758.4:c.271delT	10.37:g.65357872delT	ENSP00000362863:p.Phe91fs		65027878	Q5JQR5|Q5QGT2|Q6PEW8|Q6PJY4	Frame_Shift_Del	DEL	ENST00000373758.4	37	CCDS44411.1																																																																																				0.363	REEP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001001330		-	65357872	T	-	65357872	7	5	119	1	0	1	0	1	0	0	0	0	13243	1493	52	0	285	0	REEP3	10	65357872	Frame_Shift_Del	DEL	T	TCGA-F5-6812-01A-11D-1826-10	43341015	65357872	70176875	78	31522										
PTEN	5728	hgsc.bcm.edu	37	chr10	89653819	89653819	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	attgctatgggatttcctgcAgaaagacttgaaggcgtata	11	6	0	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:89653819A>G	ENST00000371953.3	+	2	1474	c.117A>G	c.(115-117)gcA>gcG	p.A39A		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	39	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(2)|p.A39fs*5(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		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)		GATTTCCTGCAGAAAGACTTG	0.294		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	48	Whole gene deletion(37)|Unknown(8)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	prostate(14)|central_nervous_system(9)|skin(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|ovary(3)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	10											111	111	111					10																	89653819		2203	4296	6499	89643799	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.117A>G	10.37:g.89653819A>G			89643799	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.294	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89653819	A	G	89653819	2	3	119	1	0	0	0	0	0	0	0	1	12772	175	7	4		4	PTEN	10	89653819	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10	24295947	89653819	45880928	79	31523										
GBF1	8729	hgsc.bcm.edu	37	chr10	104139152	104139152	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agaagattgaagctgattctCgcaccctctgggcccactgc	10	13	2	4			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr10:104139152C>T	ENST00000369983.3	+	34	4863	c.4603C>T	c.(4603-4605)Cgc>Tgc	p.R1535C		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1535					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		AGCTGATTCTCGCACCCTCTG	0.597																																																0			10											58	52	54					10																	104139152		2203	4300	6503	104129142	SO:0001583	missense	80142			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4603C>T	10.37:g.104139152C>T	ENSP00000359000:p.Arg1535Cys		104129142	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.772729	0.49680	.	.	ENSG00000107862	ENST00000369983	T	0.10192	2.9	5.03	3.17	0.36434	.	0.171968	0.51477	N	0.000095	T	0.07999	0.0200	N	0.24115	0.695	0.53005	D	0.999961	D;D;B	0.64830	0.994;0.987;0.001	B;B;B	0.44163	0.443;0.361;0.0	T	0.19516	-1.0303	10	0.62326	D	0.03	-3.5028	7.5939	0.28037	0.2941:0.631:0.0:0.0749	.	1531;1531;1535	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	C	1535	ENSP00000359000:R1535C	ENSP00000359000:R1535C	R	+	1	0	GBF1	104129142	0.957000	0.32711	0.989000	0.46669	0.773000	0.43773	2.347000	0.44036	0.697000	0.31718	0.561000	0.74099	CGC		0.597	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104139152	C	T	104139152	3	4	119	1	0	0	0	0	1	0	0	0	6291	884	31	1	4733	1	GBF1	10	104139152	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	14485333	104139152	31395595	80	31524										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092816	1092818	+	In_Frame_Del	DEL	GGT	GGT	-													0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cccatcaccaccaccaccacGgtgaccccaaccccaacacc					rs540845725	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	GGT	GGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:1092816_1092818delGGT	ENST00000441003.2	+	30	4662_4664	c.4635_4637delGGT	c.(4633-4638)acggtg>acg	p.V1546del	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_In_Frame_Del_p.V1547del	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccacGGTGACCCCAACC	0.635																																																0			11																																								1082818	SO:0001651	inframe_deletion	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4635_4637delGGT	11.37:g.1092816_1092818delGGT	ENSP00000415183:p.Val1546del		1082816	Q14878	In_Frame_Del	DEL	ENST00000441003.2	37																																																																																					0.635	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		-	1092818	GGT	-	1092816	7	5	119	1	0	1	0	1	0	0	0	0	10005	1103	39	0	4753	0	MUC2	11	1092816	In_Frame_Del	DEL	GGT	TCGA-F5-6812-01A-11D-1826-10		1092816	133913700	81	31525										
OR10A5	144124	hgsc.bcm.edu	37	chr11	6867549	6867549	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctggtggtcatgatcccctgCttgctgatcttgtgttccta	10	11	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:6867549C>T	ENST00000299454.4	+	1	667	c.636C>T	c.(634-636)tgC>tgT	p.C212C	OR10A5_ENST00000379831.2_Silent_p.C216C			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	212					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGATCCCCTGCTTGCTGATCT	0.522																																					Pancreas(44;21 1072 25662 28041 45559)											0			11											307	245	266					11																	6867549		2201	4296	6497	6824125	SO:0001819	synonymous_variant	144124			AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"GPCR / Class A : Olfactory receptors"	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.636C>T	11.37:g.6867549C>T			6824125	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																				0.522	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		T	6867549	C	T	6867549	2	4	119	1	0	0	0	0	0	0	0	1	10924	805	28	3		3	OR10A5	11	6867549	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10	5774733	6867549	128138967	82	31526										
ANO5	203859	hgsc.bcm.edu	37	chr11	22294384	22294384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctcttttcctttggctcctcTtcttgctctcataaataata	3	12	4	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:22294384T>C	ENST00000324559.8	+	19	2401	c.2084T>C	c.(2083-2085)cTt>cCt	p.L695P	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	695					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTGGCTCCTCTTCTTGCTCTC	0.378																																																0			11											143	126	132					11																	22294384		2203	4300	6503	22250960	SO:0001583	missense	203859			AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2084T>C	11.37:g.22294384T>C	ENSP00000315371:p.Leu695Pro		22250960		Missense_Mutation	SNP	ENST00000324559.8	37	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	t	24.4	4.532381	0.85812	.	.	ENSG00000171714	ENST00000324559	T	0.69806	-0.43	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.87621	0.6223	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91549	0.5255	10	0.87932	D	0	.	16.0211	0.80493	0.0:0.0:0.0:1.0	.	695	Q75V66	ANO5_HUMAN	P	695	ENSP00000315371:L695P	ENSP00000315371:L695P	L	+	2	0	ANO5	22250960	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.988000	0.88194	2.240000	0.73641	0.529000	0.55759	CTT		0.378	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		C	22294384	T	C	22294384	3	2	119	1	0	0	0	0	1	0	0	0	700	1609	56	4	2158	4	ANO5	11	22294384	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	15426835	22294384	112712132	83	31527										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190047	58190047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caatgctttttggtgtccctTagctgaatgcatcttcaaga	8	9	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:58190047T>C	ENST00000302581.2	-	1	739	c.688A>G	c.(688-690)Aag>Gag	p.K230E		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGGTGTCCCTTAGCTGAATGC	0.408																																																0			11											101	95	97					11																	58190047		2201	4295	6496	57946623	SO:0001583	missense	390190			AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.688A>G	11.37:g.58190047T>C	ENSP00000303076:p.Lys230Glu		57946623	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-2.912680	0.00056	.	.	ENSG00000172365	ENST00000302581	T	0.00034	8.87	3.73	-7.46	0.01369	GPCR, rhodopsin-like superfamily (1);	1.194340	0.06592	U	0.752284	T	0.00039	0.0001	N	0.00405	-1.535	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.34428	-0.9829	10	0.02654	T	1	-0.0272	10.5667	0.45177	0.0:0.4635:0.357:0.1795	.	230	Q96R09	OR5B2_HUMAN	E	230	ENSP00000303076:K230E	ENSP00000303076:K230E	K	-	1	0	OR5B2	57946623	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.989000	0.01480	-1.700000	0.01414	-1.227000	0.01581	AAG		0.408	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		C	58190047	T	C	58190047	3	2	119	1	0	0	0	0	1	0	0	0	11181	1763	61	4	245	4	OR5B2	11	58190047	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	35895663	58190047	76816469	84	31528										
LGALS12	85329	hgsc.bcm.edu	37	chr11	63279284	63279284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctgggcaggtcatcatagtaCggggactggtcttgcaagag	15	8	3	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:63279284C>T	ENST00000394618.3	+	7	976	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	LGALS12_ENST00000425950.2_Missense_Mutation_p.R159W|LGALS12_ENST00000340246.5_Missense_Mutation_p.R230W|LGALS12_ENST00000255684.5_Missense_Mutation_p.R220W|LGALS12_ENST00000415491.2_Missense_Mutation_p.R168W	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	229	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						CATCATAGTACGGGGACTGGT	0.532																																																0			11											107	89	95					11																	63279284		2201	4298	6499	63035860	SO:0001583	missense	85329			AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.685C>T	11.37:g.63279284C>T	ENSP00000378116:p.Arg229Trp		63035860	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000394618.3	37	CCDS8045.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653394	0.47362	.	.	ENSG00000133317	ENST00000255684;ENST00000394618;ENST00000340246;ENST00000415491;ENST00000425950	T;T;T;T;T	0.05996	3.36;3.36;3.36;3.36;3.36	4.89	3.97	0.46021	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (3);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.47852	D	0.000210	T	0.18882	0.0453	L	0.60455	1.87	0.40490	D	0.980538	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.938;0.998	T	0.00655	-1.1624	10	0.46703	T	0.11	-34.8376	10.979	0.47483	0.1867:0.8133:0.0:0.0	.	189;230;220;229	Q9NZ03;G5E970;Q96DT0-3;Q96DT0	.;.;.;LEG12_HUMAN	W	220;229;230;168;159	ENSP00000255684:R220W;ENSP00000378116:R229W;ENSP00000339374:R230W;ENSP00000394659:R168W;ENSP00000399093:R159W	ENSP00000255684:R220W	R	+	1	2	LGALS12	63035860	0.939000	0.31865	0.998000	0.56505	0.151000	0.21798	0.203000	0.17315	1.183000	0.42943	0.462000	0.41574	CGG		0.532	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		T	63279284	C	T	63279284	3	4	119	1	0	0	0	0	1	0	0	0	8761	527	19	1	714	1	LGALS12	11	63279284	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	5089237	63279284	71727232	85	31529										
FAT3	120114	hgsc.bcm.edu	37	chr11	92495184	92495185	+	Missense_Mutation	DNP	GC	GC	TT													0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gaggagaaccgatttacaggGcttttgcatttgatagagat							TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:92495184_92495185GC>TT	ENST00000298047.6	+	4	3849_3850	c.3832_3833GC>TT	c.(3832-3834)GCt>TTt	p.A1278F	FAT3_ENST00000409404.2_Missense_Mutation_p.A1278F|FAT3_ENST00000525166.1_Missense_Mutation_p.A1128F|RP11-203F8.1_ENST00000529884.1_RNA			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1278	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GATTTACAGGGCTTTTGCATTT	0.46										TCGA Ovarian(4;0.039)																																						0			11																																								92134832|92134833	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	Exception_encountered	11.37:g.92495184_92495185delinsTT	ENSP00000298047:p.Ala1278Phe		92134832|92134833	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37																																																																																					0.46	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		TT	92495185	GC	TT	92495184	3	4	119	1	0	0	0	0	1	0	0	0	5710	1203	42	2	3846	2	FAT3	11	92495184	Missense_Mutation	DNP	GC	TCGA-F5-6812-01A-11D-1826-10	29215900	92495184	42511332	86	31530										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99786793	99786793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	attatgttgacagatctgggAaattttagtggccggacaag	12	5	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr11:99786793A>G	ENST00000524871.1	+	7	875	c.585A>G	c.(583-585)ggA>ggG	p.G195G	CNTN5_ENST00000418526.2_Silent_p.G121G|CNTN5_ENST00000279463.3_Silent_p.G195G|CNTN5_ENST00000527185.1_Silent_p.G195G|CNTN5_ENST00000528682.1_Silent_p.G195G	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	195					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		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)		CAGATCTGGGAAATTTTAGTG	0.418																																																0			11											114	112	113					11																	99786793		1918	4139	6057	99292003	SO:0001819	synonymous_variant	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.585A>G	11.37:g.99786793A>G			99292003	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																				0.418	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		G	99786793	A	G	99786793	2	3	119	1	0	0	0	0	0	0	0	1	3650	233	9	4		4	CNTN5	11	99786793	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10	7291609	99786793	35219723	87	31531										
MAGOHB	55110	hgsc.bcm.edu	37	chr12	10758964	10758964	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tagtaaaatactcgaaggccTtcaggatccctaaaatttaa	6	8	1	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:10758964T>C	ENST00000320756.2	-	5	447	c.357A>G	c.(355-357)gaA>gaG	p.E119E	MAGOHB_ENST00000539554.1_Silent_p.E73E|MAGOHB_ENST00000381881.2_Silent_p.E82E	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	119			E -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|large_intestine(2)	4						CTCGAAGGCCTTCAGGATCCC	0.274																																																0			12											27	27	27					12																	10758964		2192	4275	6467	10650231	SO:0001819	synonymous_variant	55110				CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.357A>G	12.37:g.10758964T>C			10650231		Silent	SNP	ENST00000320756.2	37	CCDS8628.1																																																																																				0.274	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		C	10758964	T	C	10758964	2	2	119	1	0	0	0	0	0	0	0	1	9225	1606	56	4		4	MAGOHB	12	10758964	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10		10758964	123092931	88	31532										
SOX5	6660	hgsc.bcm.edu	37	chr12	23999034	23999034	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggctgtactagacaaggactCgccactctgtcgcccacctt	9	15	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:23999034C>T	ENST00000451604.2	-	3	465	c.364G>A	c.(364-366)Gag>Aag	p.E122K	SOX5_ENST00000541847.1_Missense_Mutation_p.E112K|SOX5_ENST00000441133.2_Missense_Mutation_p.E87K|SOX5_ENST00000545921.1_Missense_Mutation_p.E112K|SOX5_ENST00000546136.1_Missense_Mutation_p.E109K|SOX5_ENST00000537393.1_Missense_Mutation_p.E87K|SOX5_ENST00000309359.1_Missense_Mutation_p.E109K|SOX5_ENST00000541536.1_Missense_Mutation_p.E109K|SOX5_ENST00000381381.2_Missense_Mutation_p.E109K			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	122					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						GACAAGGACTCGCCACTCTGT	0.493																																																0			12											135	121	126					12																	23999034		2203	4300	6503	23890301	SO:0001583	missense	6660			AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.364G>A	12.37:g.23999034C>T	ENSP00000398273:p.Glu122Lys		23890301	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221560	0.79464	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	D;D;D;D;D;D;D	0.97731	-4.5;-4.5;-4.51;-4.5;-4.27;-4.51;-4.5	5.79	5.79	0.91817	.	0.237331	0.43919	D	0.000508	D	0.96374	0.8817	L	0.48642	1.525	0.48511	D	0.999667	D;P;P;P	0.54047	0.964;0.898;0.953;0.915	B;B;B;B	0.42738	0.364;0.396;0.182;0.283	D	0.96334	0.9246	10	0.54805	T	0.06	.	20.0349	0.97554	0.0:1.0:0.0:0.0	.	87;87;109;122	G3V0H1;F5H0I3;P35711-4;P35711	.;.;.;SOX5_HUMAN	K	109;109;109;122;74;87;109;112;112;87;109	ENSP00000437487:E109K;ENSP00000308927:E109K;ENSP00000370788:E109K;ENSP00000398273:E122K;ENSP00000439832:E87K;ENSP00000441973:E109K;ENSP00000443520:E112K	ENSP00000308927:E109K	E	-	1	0	SOX5	23890301	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.737000	0.55060	2.744000	0.94065	0.650000	0.86243	GAG		0.493	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		T	23999034	C	T	23999034	3	4	119	1	0	0	0	0	1	0	0	0	14991	893	31	1	1989	1	SOX5	12	23999034	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	13240070	23999034	109852861	89	31533										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:25398284C>G	ENST00000256078.4	-	2	98	c.35G>C	c.(34-36)gGt>gCt	p.G12A	KRAS_ENST00000311936.3_Missense_Mutation_p.G12A|KRAS_ENST00000557334.1_Missense_Mutation_p.G12A|KRAS_ENST00000556131.1_Missense_Mutation_p.G12A	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91	81	85					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>C	12.37:g.25398284C>G	ENSP00000256078:p.Gly12Ala		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996285	0.93167	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85643	0.5744	M	0.74546	2.27	0.80722	D	1	P;P	0.52842	0.898;0.956	P;P	0.55303	0.658;0.773	D	0.87064	0.2155	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	A	12	ENSP00000308495:G12A;ENSP00000452512:G12A;ENSP00000256078:G12A;ENSP00000451856:G12A	ENSP00000256078:G12A	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		G	25398284	C	G	25398284	3	3	119	1	0	0	0	0	1	0	0	0	8459	507	18	5	671	5	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	1399250	25398284	108453611	90	31534										
DIP2B	57609	hgsc.bcm.edu	37	chr12	51117078	51117078	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgctcagaacctcacggccaCgctgcccactgtccgaatga	9	16	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:51117078C>T	ENST00000301180.5	+	27	3294	c.3260C>T	c.(3259-3261)aCg>aTg	p.T1087M		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1087						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						CTCACGGCCACGCTGCCCACT	0.502																																																0			12											196	143	161					12																	51117078		2203	4300	6503	49403345	SO:0001583	missense	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.3260C>T	12.37:g.51117078C>T	ENSP00000301180:p.Thr1087Met		49403345	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.340367	0.81911	.	.	ENSG00000066084	ENST00000301180	T	0.46063	0.88	4.95	4.95	0.65309	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.67088	0.2856	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69262	-0.5191	10	0.56958	D	0.05	-13.2213	18.7686	0.91882	0.0:1.0:0.0:0.0	.	1087	Q9P265	DIP2B_HUMAN	M	1087	ENSP00000301180:T1087M	ENSP00000301180:T1087M	T	+	2	0	DIP2B	49403345	1.000000	0.71417	0.795000	0.32087	0.584000	0.36387	7.651000	0.83577	2.758000	0.94735	0.563000	0.77884	ACG		0.502	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		T	51117078	C	T	51117078	3	4	119	1	0	0	0	0	1	0	0	0	4539	536	19	1	3366	1	DIP2B	12	51117078	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	25718794	51117078	82734817	91	31535										
NACA	4666	hgsc.bcm.edu	37	chr12	57111520	57111588	+	In_Frame_Del	DEL	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	-													0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gaggagttgcagctgggggaGtgggggcccctttggggggt					rs200567357|rs200125059|rs546033694|rs200929777|rs201766056|rs201949086|rs200070725|rs368778367|rs201249962	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:57111520_57111588delGTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	ENST00000454682.1	-	3	4007_4075	c.3726_3794delAACCCCAGCTGCAACTCCTCCCTCCCCAAAAGGAGGCCCAGCTACCCCACCCCCCAAAGGGGCCCCCAC	c.(3724-3795)acaaccccagctgcaactcctccctccccaaaaggaggcccagctaccccaccccccaaaggggcccccact>act	p.1242_1265TTPAATPPSPKGGPATPPPKGAPT>T	NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000393891.4_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1242	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AGCTGGGGGAGTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTTGTGGGGGCCC	0.639			T	BCL6	NHL																																		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0			12							,,,	330,1842		66,198,822					,,,	-6.7	0			53	175,4659		36,103,2278	no	intron,intron,intron,intron	NACA	NM_005594.4,NM_001113203.2,NM_001113202.1,NM_001113201.1	,,,	102,301,3100	A1A1,A1R,RR		3.6202,15.1934,7.2081	,,,	,,,		505,6501				55397855	SO:0001651	inframe_deletion	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3726_3794delAACCCCAGCTGCAACTCCTCCCTCCCCAAAAGGAGGCCCAGCTACCCCACCCCCCAAAGGGGCCCCCAC	12.37:g.57111520_57111588delGTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	ENSP00000403817:p.Thr1242_Pro1264del		55397787		In_Frame_Del	DEL	ENST00000454682.1	37																																																																																					0.639	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		-	57111588	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	-	57111520	7	5	119	1	0	1	0	1	0	0	0	0	10163	1029	36	0	2470	0	NACA	12	57111520	In_Frame_Del	DEL	GTGGGGGCCCCTTTGGGGGGTGGGGTAGCTGGGCCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGTT	TCGA-F5-6812-01A-11D-1826-10	5994442	57111520	76740375	92	31536										
C12orf26	84190	hgsc.bcm.edu	37	chr12	82796894	82796894	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	acctcttatctgaagaatttGaaaaccagcataaaggtaca	6	8	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:82796894G>C	ENST00000248306.3	+	5	1333	c.1264G>C	c.(1264-1266)Gaa>Caa	p.E422Q	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	422							methyltransferase activity (GO:0008168)										TGAAGAATTTGAAAACCAGCA	0.358																																																0			12											82	78	80					12																	82796894		2203	4300	6503	81321025	SO:0001583	missense	84190			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1264G>C	12.37:g.82796894G>C	ENSP00000248306:p.Glu422Gln		81321025	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998346	0.74818	.	.	ENSG00000127720	ENST00000248306;ENST00000550298	T	0.33216	1.42	5.49	5.49	0.81192	.	0.106321	0.64402	D	0.000006	T	0.39200	0.1069	L	0.51422	1.61	0.58432	D	0.999995	P	0.50710	0.938	P	0.49528	0.614	T	0.04153	-1.0973	10	0.19590	T	0.45	-19.95	19.3599	0.94432	0.0:0.0:1.0:0.0	.	422	Q8N6Q8	CL026_HUMAN	Q	422;57	ENSP00000248306:E422Q	ENSP00000248306:E422Q	E	+	1	0	C12orf26	81321025	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.027000	0.93706	2.569000	0.86673	0.591000	0.81541	GAA		0.358	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		C	82796894	G	C	82796894	3	2	119	1	0	0	0	0	1	0	0	0	1683	1291	45	5	1282	5	C12orf26	12	82796894	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	25685374	82796894	51055001	93	31537										
NAA25	80018	hgsc.bcm.edu	37	chr12	112516503	112516503	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cattctctcagcaaggggcaGaaacattgtttttgagaggt	11	7	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:112516503G>T	ENST00000261745.4	-	6	768	c.520C>A	c.(520-522)Ctg>Atg	p.L174M		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	174						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						GCAAGGGGCAGAAACATTGTT	0.368																																																0			12											168	152	158					12																	112516503		2203	4300	6503	111000886	SO:0001583	missense	0			AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.520C>A	12.37:g.112516503G>T	ENSP00000261745:p.Leu174Met		111000886	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.40|19.40	3.819749|3.819749	0.71028|0.71028	.|.	.|.	ENSG00000111300|ENSG00000111300	ENST00000261745|ENST00000547133	T|.	0.35973|.	1.28|.	6.05|6.05	4.02|4.02	0.46733|0.46733	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.67730|0.67730	0.2924|0.2924	M|M	0.85630|0.85630	2.765|2.765	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.998|.	T|T	0.69734|0.69734	-0.5065|-0.5065	10|5	0.39692|.	T|.	0.17|.	-7.5836|-7.5836	4.3651|4.3651	0.11220|0.11220	0.4245:0.0:0.5755:0.0|0.4245:0.0:0.5755:0.0	.|.	174;174|.	A8K8X0;Q14CX7|.	.;NAA25_HUMAN|.	M|Y	174|135	ENSP00000261745:L174M|.	ENSP00000261745:L174M|.	L|S	-|-	1|2	2|0	NAA25|NAA25	111000886|111000886	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.161000|3.161000	0.50747|0.50747	1.577000|1.577000	0.49804|0.49804	0.650000|0.650000	0.86243|0.86243	CTG|TCT		0.368	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112516503	G	T	112516503	3	4	119	1	0	0	0	0	1	0	0	0	10151	933	33	2	2474	2	NAA25	12	112516503	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	29719609	112516503	21335392	94	31538										
UBC	7316	hgsc.bcm.edu	37	chr12	125397696	125397696	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctggatgttgtagtcagacaGggtacgaccatcttccagct	11	10	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr12:125397696G>T	ENST00000536769.1	-	1	2198	c.622C>A	c.(622-624)Ctg>Atg	p.L208M	UBC_ENST00000538617.1_Intron|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Missense_Mutation_p.L132M|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Missense_Mutation_p.L208M			P0CG48	UBC_HUMAN	ubiquitin C	208	Ubiquitin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)	p.L208V(1)		breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TAGTCAGACAGGGTACGACCA	0.488																																																1	Substitution - Missense(1)	ovary(1)	12											174	158	163					12																	125397696		2203	4296	6499	123963649	SO:0001583	missense	7316				CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.622C>A	12.37:g.125397696G>T	ENSP00000441543:p.Leu208Met		123963649	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000536769.1	37	CCDS9260.1	.	.	.	.	.	.	.	.	.	.	-	14.99	2.699094	0.48307	.	.	ENSG00000150991	ENST00000536769;ENST00000535460;ENST00000541046;ENST00000339647;ENST00000546120;ENST00000541272	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	2.42	2.42	0.29668	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.41294	U	0.000918	D	0.86598	0.5971	M	0.70842	2.15	0.46823	D	0.999216	P;D;P	0.63046	0.855;0.992;0.855	P;D;P	0.68353	0.893;0.957;0.893	D	0.87623	0.2511	10	0.87932	D	0	.	11.1259	0.48317	0.0:0.0:1.0:0.0	.	297;208;208	Q66K58;F5H7K6;P0CG48	.;.;UBC_HUMAN	M	208;208;132;208;132;132	ENSP00000441543:L208M;ENSP00000344818:L208M;ENSP00000438394:L132M;ENSP00000440205:L132M	ENSP00000344818:L208M	L	-	1	2	UBC	123963649	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.827000	0.62723	1.696000	0.51158	0.543000	0.68304	CTG		0.488	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009		T	125397696	G	T	125397696	3	4	119	1	0	0	0	0	1	0	0	0	16882	991	35	2	1439	2	UBC	12	125397696	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	12881193	125397696	8454199	95	31539										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587390	39587390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgaaccatttaaaggagtacTcaagctggagagacctgaca	10	8	1	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr13:39587390T>C	ENST00000352251.3	-	11	2832	c.1999A>G	c.(1999-2001)Agt>Ggt	p.S667G	PROSER1_ENST00000350125.3_Missense_Mutation_p.S645G|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	667	Ser-rich.							p.S667G(1)									AAAGGAGTACTCAAGCTGGAG	0.463																																																1	Substitution - Missense(1)	ovary(1)	13											122	114	116					13																	39587390		2203	4300	6503	38485390	SO:0001583	missense	80209			AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1999A>G	13.37:g.39587390T>C	ENSP00000332034:p.Ser667Gly		38485390	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	T	15.91	2.971030	0.53614	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.56611	0.45;0.45	5.27	5.27	0.74061	.	.	.	.	.	T	0.38665	0.1049	L	0.29908	0.895	0.37949	D	0.932604	P;P	0.39480	0.675;0.461	B;B	0.34093	0.175;0.145	T	0.40813	-0.9543	8	.	.	.	-13.1738	14.659	0.68855	0.0:0.0:0.0:1.0	.	645;667	A6NJ97;Q86XN7	.;PRSR1_HUMAN	G	667;645	ENSP00000332034:S667G;ENSP00000339123:S645G	.	S	-	1	0	PROSER1	38485390	0.999000	0.42202	0.856000	0.33681	0.659000	0.38960	3.386000	0.52492	2.116000	0.64780	0.459000	0.35465	AGT		0.463	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		C	39587390	T	C	39587390	3	2	119	1	0	0	0	0	1	0	0	0	1725	1551	54	4	847	4	C13orf23	13	39587390	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10		39587390	75582488	96	31540										
RB1	5925	hgsc.bcm.edu	37	chr13	48881511	48881511	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agagagagcttggttaacttGggagaaagtttcatctgtgg	14	4	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr13:48881511G>A	ENST00000267163.4	+	2	371	c.233G>A	c.(232-234)tGg>tAg	p.W78*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	78					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TGGTTAACTTGGGAGAAAGTT	0.328		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	18	Whole gene deletion(15)|Unknown(3)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|stomach(1)	13											134	136	135					13																	48881511		2203	4299	6502	47779512	SO:0001587	stop_gained	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.233G>A	13.37:g.48881511G>A	ENSP00000267163:p.Trp78*		47779512	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	37	5.984466	0.97173	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	4.86	4.86	0.63082	.	0.135639	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2922	13.8493	0.63487	0.0:0.0:1.0:0.0	.	.	.	.	X	57;78	.	ENSP00000267163:W78X	W	+	2	0	RB1	47779512	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.055000	0.49916	2.401000	0.81631	0.650000	0.86243	TGG		0.328	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48881511	G	A	48881511	4	1	119	1	0	0	0	0	0	1	0	0	13135	1357	47	3	239	3	RB1	13	48881511	Nonsense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	9294121	48881511	66288367	97	31541										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96536927	96536927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttctggttccagaacaaaacGgtaaaagctgttaataaaac	7	7	1	1	rs200610064		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr13:96536927G>A	ENST00000376747.3	-	27	3116	c.3046C>T	c.(3046-3048)Cgt>Tgt	p.R1016C		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1016					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AGAACAAAACGGTAAAAGCTG	0.328													G|||	1	0.000199681	0	0	5008	,	,		17544	0		0.001	False		,,,				2504	0															0			13											56	54	55					13																	96536927		2203	4300	6503	95334928	SO:0001583	missense	0			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3046C>T	13.37:g.96536927G>A	ENSP00000365938:p.Arg1016Cys		95334928	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.4	4.411260	0.83340	.	.	ENSG00000102595	ENST00000376747	T	0.45276	0.9	5.97	5.97	0.96955	.	0.055638	0.85682	D	0.000000	T	0.74099	0.3672	H	0.94423	3.535	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.80763	-0.1237	10	0.87932	D	0	-13.6687	15.1877	0.73016	0.0:0.0:0.8592:0.1408	.	1016;1016	Q9NV86;Q9NYU1	.;UGGG2_HUMAN	C	1016	ENSP00000365938:R1016C	ENSP00000365938:R1016C	R	-	1	0	UGGT2	95334928	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.217000	0.72218	2.836000	0.97738	0.655000	0.94253	CGT		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96536927	G	A	96536927	3	1	119	1	0	0	0	0	1	0	0	0	16982	1116	39	1	1556	1	UGGT2	13	96536927	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	47655416	96536927	18632951	98	31542										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36104682	36104682	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aagtttaccttataaatgcaAttgagaacagatttttctgt	6	5	1	2	rs146883356	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr14:36104682A>G	ENST00000389698.3	-	31	4671	c.4281T>C	c.(4279-4281)aaT>aaC	p.N1427N	RALGAPA1_ENST00000307138.6_Silent_p.N1427N|RALGAPA1_ENST00000382366.3_Silent_p.N1440N|RALGAPA1_ENST00000258840.6_Silent_p.N1474N	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1427	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TATAAATGCAATTGAGAACAG	0.348																																																0			14						A	,	6,4400	11.4+/-27.6	0,6,2197	42	41	41		4281,4281	-3	1	14	dbSNP_134	41	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RALGAPA1	NM_014990.1,NM_194301.2	,	0,6,6497	GG,GA,AA		0.0,0.1362,0.0461	,	1427/2037,1427/2084	36104682	6,13000	2203	4300	6503	35174433	SO:0001819	synonymous_variant	0			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4281T>C	14.37:g.36104682A>G			35174433	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Silent	SNP	ENST00000389698.3	37	CCDS32065.1																																																																																				0.348	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		G	36104682	A	G	36104682	2	3	119	1	0	0	0	0	0	0	0	1	13050	98	4	4		4	RALGAPA1	14	36104682	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10		36104682	71244858	99	31543										
PTGDR	5729	hgsc.bcm.edu	37	chr14	52734788	52734788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	taagcccggtggtgctggctGcctacgctcagaaccggagt	14	12	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr14:52734788G>A	ENST00000306051.2	+	1	358	c.256G>A	c.(256-258)Gcc>Acc	p.A86T	PTGDR_ENST00000553372.1_Missense_Mutation_p.A86T	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	86					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	GGTGCTGGCTGCCTACGCTCA	0.622																																																0			14											78	84	82					14																	52734788		2203	4300	6503	51804538	SO:0001583	missense	5729			U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"GPCR / Class A : Prostanoid receptors"	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	ENST00000306051.2:c.256G>A	14.37:g.52734788G>A	ENSP00000303424:p.Ala86Thr		51804538	G3V5L3|Q13250|Q13251|Q1ZZ52	Missense_Mutation	SNP	ENST00000306051.2	37	CCDS9707.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681316	0.68042	.	.	ENSG00000168229	ENST00000306051;ENST00000553372	T;T	0.36699	1.24;1.24	4.83	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.142736	0.32836	N	0.005595	T	0.27798	0.0684	L	0.27053	0.805	0.34015	D	0.651999	P	0.44344	0.833	P	0.49085	0.6	T	0.25779	-1.0122	10	0.13470	T	0.59	-15.4235	7.0568	0.25104	0.0932:0.0:0.7307:0.176	.	86	Q13258	PD2R_HUMAN	T	86	ENSP00000303424:A86T;ENSP00000452408:A86T	ENSP00000303424:A86T	A	+	1	0	PTGDR	51804538	0.038000	0.19896	0.996000	0.52242	0.951000	0.60555	0.292000	0.19011	1.288000	0.44600	0.563000	0.77884	GCC		0.622	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953		A	52734788	G	A	52734788	3	1	119	1	0	0	0	0	1	0	0	0	12775	1319	46	3	258	3	PTGDR	14	52734788	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	16630106	52734788	54614752	100	31544										
NEDD4	4734	hgsc.bcm.edu	37	chr15	56207629	56207629	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgcttaaggctggatagacaGgaaatatttggataagctcc	11	6	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr15:56207629G>A	ENST00000508342.1	-	1	1700	c.1401C>T	c.(1399-1401)tcC>tcT	p.S467S	NEDD4_ENST00000338963.2_Silent_p.S467S|NEDD4_ENST00000506154.1_Silent_p.S467S|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	467					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TGGATAGACAGGAAATATTTG	0.358																																																0			15											137	140	139					15																	56207629		2193	4291	6484	53994921	SO:0001819	synonymous_variant	4734			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.1401C>T	15.37:g.56207629G>A			53994921	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	37		.	.	.	.	.	.	.	.	.	.	G	8.501	0.864313	0.17250	.	.	ENSG00000069869	ENST00000508871	.	.	.	5.46	4.44	0.53790	.	.	.	.	.	T	0.62134	0.2403	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59129	-0.7512	4	.	.	.	.	11.6164	0.51092	0.1178:0.0:0.8822:0.0	.	.	.	.	L	75	.	.	P	-	2	0	NEDD4	53994921	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.391000	0.34475	2.580000	0.87095	0.460000	0.39030	CCT		0.358	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56207629	G	A	56207629	2	1	119	1	0	0	0	0	0	0	0	1	10341	987	35	3		3	NEDD4	15	56207629	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10		56207629	46323763	101	31545										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99472877	99472877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggtgattatgctgtacgtctTccatagaaagaggtcagtga	12	6	2	4			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr15:99472877T>C	ENST00000268035.6	+	14	3484	c.2873T>C	c.(2872-2874)tTc>tCc	p.F958S	IGF1R_ENST00000558762.1_Missense_Mutation_p.F957S	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	958					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CTGTACGTCTTCCATAGAAAG	0.438																																																0			15											188	163	172					15																	99472877		2197	4297	6494	97290400	SO:0001583	missense	3480			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2873T>C	15.37:g.99472877T>C	ENSP00000268035:p.Phe958Ser		97290400	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.819275	0.50633	.	.	ENSG00000140443	ENST00000268035	T	0.76316	-1.01	5.67	1.76	0.24704	.	0.211795	0.32578	N	0.005905	T	0.67674	0.2918	L	0.54323	1.7	0.34186	D	0.671474	B;B	0.30511	0.282;0.013	B;B	0.26614	0.048;0.071	T	0.68907	-0.5285	10	0.62326	D	0.03	.	6.4952	0.22138	0.356:0.0:0.2457:0.3983	.	957;958	C9J5X1;P08069	.;IGF1R_HUMAN	S	958	ENSP00000268035:F958S	ENSP00000268035:F958S	F	+	2	0	IGF1R	97290400	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	0.892000	0.28322	0.371000	0.24564	0.533000	0.62120	TTC		0.438	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		C	99472877	T	C	99472877	3	2	119	1	0	0	0	0	1	0	0	0	7592	1783	62	4	2927	4	IGF1R	15	99472877	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	43265248	99472877	3058515	102	31546										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786763	3786763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caggtgggtggcaatggaagAtgtaatcatctccttcactt	11	8	3	1	rs201719835		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr16:3786763A>G	ENST00000262367.5	-	27	5257	c.4448T>C	c.(4447-4449)aTc>aCc	p.I1483T	CREBBP_ENST00000382070.3_Missense_Mutation_p.I1445T	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1483	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.I1483S(2)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GCAATGGAAGATGTAATCATC	0.512			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																																Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	16											227	193	204					16																	3786763		2197	4300	6497	3726764	SO:0001583	missense	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4448T>C	16.37:g.3786763A>G	ENSP00000262367:p.Ile1483Thr		3726764	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	a	18.70	3.680249	0.68042	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94862	-3.54;-3.54	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.98036	0.9353	H	0.95645	3.7	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.97110	1.0;1.0	D	0.99293	1.0899	10	0.87932	D	0	-22.4571	14.6308	0.68655	1.0:0.0:0.0:0.0	.	1513;1483	Q4LE28;Q92793	.;CBP_HUMAN	T	1483;1513;1445;72	ENSP00000262367:I1483T;ENSP00000371502:I1445T	ENSP00000262367:I1483T	I	-	2	0	CREBBP	3726764	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.287000	0.95975	2.107000	0.64212	0.459000	0.35465	ATC		0.512	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3786763	A	G	3786763	3	3	119	1	0	0	0	0	1	0	0	0	3867	333	12	4	2900	4	CREBBP	16	3786763	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10		3786763	86567990	103	31547										
ACSM1	116285	hgsc.bcm.edu	37	chr16	20702394	20702394	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggtacttcatagtcattccaTcttggggctccaaattctga	8	10	4	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr16:20702394T>C	ENST00000307493.4	-	1	184	c.117A>G	c.(115-117)agA>agG	p.R39R	ACSM1_ENST00000520010.1_Silent_p.R39R|ACSM1_ENST00000219151.4_5'UTR	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	39					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						AGTCATTCCATCTTGGGGCTC	0.507																																																0			16											132	138	136					16																	20702394		2201	4300	6501	20609895	SO:0001819	synonymous_variant	116285			AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.117A>G	16.37:g.20702394T>C			20609895	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1																																																																																				0.507	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		C	20702394	T	C	20702394	2	2	119	1	0	0	0	0	0	0	0	1	182	1432	50	4		4	ACSM1	16	20702394	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10	16915631	20702394	69652359	104	31548										
CHD9	80205	hgsc.bcm.edu	37	chr16	53301838	53301838	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aactataccttttttaaccaGgtggggccgatggagagaga	12	7	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr16:53301838G>T	ENST00000398510.3	+	21	4604		c.e21-1		CHD9_ENST00000564845.1_Splice_Site|CHD9_ENST00000447540.1_Splice_Site|CHD9_ENST00000566029.1_Splice_Site			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9						cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TTTTTAACCAGGTGGGGCCGA	0.348																																																0			16											74	68	70					16																	53301838		1812	4067	5879	51859339	SO:0001630	splice_region_variant	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.4518-1G>T	16.37:g.53301838G>T			51859339	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Splice_Site	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	G	24.9	4.580582	0.86645	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7167	0.96124	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CHD9	51859339	1.000000	0.71417	0.989000	0.46669	0.902000	0.53008	9.807000	0.99171	2.673000	0.90976	0.650000	0.86243	.		0.348	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	Intron	T	53301838	G	T	53301838	5	4	119	1	0	0	0	0	0	0	1	0	3338	1014	35	2	4599	2	CHD9	16	53301838	Splice_Site	SNP	G	TCGA-F5-6812-01A-11D-1826-10	32599444	53301838	37052915	105	31549										
NAE1	8883	hgsc.bcm.edu	37	chr16	66842916	66842916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttcatccttgttaattgtatCcaaaccatattcttcagcta	3	10	3	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr16:66842916C>T	ENST00000290810.3	-	16	1310	c.1213G>A	c.(1213-1215)Gat>Aat	p.D405N	NAE1_ENST00000394074.2_Missense_Mutation_p.D316N|NAE1_ENST00000379463.2_Missense_Mutation_p.D399N|NAE1_ENST00000359087.4_Missense_Mutation_p.D408N			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	405					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	TTAATTGTATCCAAACCATAT	0.313																																																0			16											89	84	86					16																	66842916		2200	4300	6500	65400417	SO:0001583	missense	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.1213G>A	16.37:g.66842916C>T	ENSP00000290810:p.Asp405Asn		65400417	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Missense_Mutation	SNP	ENST00000290810.3	37	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992147	0.35131	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463;ENST00000394074	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.14	-0.305	0.12784	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.217835	0.45361	N	0.000361	T	0.19644	0.0472	N	0.16478	0.41	0.52501	D	0.999956	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.08411	-1.0723	10	0.17832	T	0.49	-12.7033	5.634	0.17526	0.0:0.4388:0.2376:0.3236	.	408;405;399	A6NCK0;Q13564;A6NFN4	.;ULA1_HUMAN;.	N	408;405;399;316	ENSP00000351990:D408N;ENSP00000290810:D405N;ENSP00000368776:D399N;ENSP00000377637:D316N	ENSP00000290810:D405N	D	-	1	0	NAE1	65400417	0.997000	0.39634	0.964000	0.40570	0.889000	0.51656	0.823000	0.27366	-0.288000	0.09051	-0.145000	0.13849	GAT		0.313	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905		T	66842916	C	T	66842916	3	4	119	1	0	0	0	0	1	0	0	0	10169	855	30	3	411	3	NAE1	16	66842916	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	13541078	66842916	23511837	106	31550										
TXNL4B	54957	hgsc.bcm.edu	37	chr16	72120643	72120643	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tcgatagattacttcaatcaAatctatgaagtcttgtttgg	7	6	4	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr16:72120643A>G	ENST00000268483.3	-	4	664	c.343T>C	c.(343-345)Ttg>Ctg	p.L115L	TXNL4B_ENST00000426362.2_Silent_p.L115L|TXNL4B_ENST00000423037.1_Silent_p.L115L|RP11-384M15.3_ENST00000561827.1_RNA	NM_001142318.1|NM_017853.2	NP_001135790.1|NP_060323.1	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	115					mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)				cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)	8						ACTTCAATCAAATCTATGAAG	0.383																																																0			16											104	98	100					16																	72120643		2198	4300	6498	70678144	SO:0001819	synonymous_variant	54957			BC009646	CCDS10906.1	16q22.2	2012-11-19			ENSG00000140830	ENSG00000140830			26041	protein-coding gene	gene with protein product						15161931	Standard	NM_017853		Approved	FLJ20511, DLP, Dim2	uc010vmn.2	Q9NX01	OTTHUMG00000173453	ENST00000268483.3:c.343T>C	16.37:g.72120643A>G			70678144	D3DWS6	Silent	SNP	ENST00000268483.3	37	CCDS10906.1																																																																																				0.383	TXNL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269007.2	NM_017853		G	72120643	A	G	72120643	2	3	119	1	0	0	0	0	0	0	0	1	16846	11	1	4		4	TXNL4B	16	72120643	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10	5277727	72120643	18234110	107	31551										
TP53	7157	hgsc.bcm.edu	37	chr17	7577106	7577106	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgtgcgccggtctctcccagGacaggcacaaacacgcacct	10	16	1	0	rs17849781		TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:7577106G>T	ENST00000269305.4	-	8	1021	c.832C>A	c.(832-834)Cct>Act	p.P278T	TP53_ENST00000359597.4_Missense_Mutation_p.P278T|TP53_ENST00000445888.2_Missense_Mutation_p.P278T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.P278T|TP53_ENST00000420246.2_Missense_Mutation_p.P278T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	278	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation; dbSNP:rs17849781). {ECO:0000269|PubMed:15489334}.|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:9450901}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P278S(55)|p.P278A(24)|p.P278T(23)|p.0?(8)|p.P278F(3)|p.P278fs*67(3)|p.?(2)|p.P278fs*28(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.F270_D281del12(1)|p.C275fs*67(1)|p.V274_P278del(1)|p.S269fs*21(1)|p.C277_P278insXXXXXXX(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTCTCCCAGGACAGGCACAA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	131	Substitution - Missense(105)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Insertion - Frameshift(2)|Unknown(2)|Insertion - In frame(1)	upper_aerodigestive_tract(19)|breast(18)|skin(16)|large_intestine(14)|oesophagus(11)|lung(11)|central_nervous_system(7)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|ovary(4)|bone(4)|kidney(3)|endometrium(3)|urinary_tract(3)|soft_tissue(2)|pancreas(2)|eye(1)|biliary_tract(1)|liver(1)|prostate(1)	17	GRCh37	CM011015|CM052927	TP53	M	rs17849781						72	62	65					17																	7577106		2203	4300	6503	7517831	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.832C>A	17.37:g.7577106G>T	ENSP00000269305:p.Pro278Thr		7517831	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.953650	0.92660	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99884	-7.49;-7.49;-7.49;-7.49;-7.49;-7.49	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.050655	0.85682	D	0.000000	D	0.99894	0.9949	M	0.88570	2.965	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.997	D	0.96194	0.9140	10	0.87932	D	0	-13.7877	16.1198	0.81342	0.0:0.0:1.0:0.0	.	278;278;278;278	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	T	278;278;278;278;278;267;146	ENSP00000352610:P278T;ENSP00000269305:P278T;ENSP00000398846:P278T;ENSP00000391127:P278T;ENSP00000391478:P278T;ENSP00000425104:P146T	ENSP00000269305:P278T	P	-	1	0	TP53	7517831	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.573000	0.98181	2.667000	0.90743	0.462000	0.41574	CCT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577106	G	T	7577106	3	4	119	1	0	0	0	0	1	0	0	0	16421	1174	41	2	454	2	TP53	17	7577106	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10		7577106	73618104	108	31552			1	40		3	3	402	N	T_G_A	1.568891e-06
TP53	7157	hgsc.bcm.edu	37	chr17	7577123	7577123	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caggacaggcacaaacacgcAcctcaaagctgttccgtccc	8	16	1	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:7577123A>C	ENST00000269305.4	-	8	1004	c.815T>G	c.(814-816)gTg>gGg	p.V272G	TP53_ENST00000359597.4_Missense_Mutation_p.V272G|TP53_ENST00000445888.2_Missense_Mutation_p.V272G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.V272G|TP53_ENST00000420246.2_Missense_Mutation_p.V272G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	272	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		V -> A (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1737852}.|V -> M (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.V272E(8)|p.V272A(7)|p.V272G(6)|p.?(2)|p.F270fs*72(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.E271fs*73(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACAAACACGCACCTCAAAGCT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	39	Substitution - Missense(21)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Unknown(2)	haematopoietic_and_lymphoid_tissue(6)|upper_aerodigestive_tract(5)|lung(4)|bone(4)|stomach(3)|central_nervous_system(3)|breast(3)|skin(3)|endometrium(2)|large_intestine(1)|soft_tissue(1)|liver(1)|urinary_tract(1)|ovary(1)|pancreas(1)	17	GRCh37	CM942122	TP53	M							63	55	57					17																	7577123		2203	4300	6503	7517848	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.815T>G	17.37:g.7577123A>C	ENSP00000269305:p.Val272Gly		7517848	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708162	0.48412	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99824	-6.96;-6.96;-6.96;-6.96;-6.96;-6.96	5.13	2.87	0.33458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.057604	0.64402	N	0.000002	D	0.99648	0.9870	M	0.78456	2.415	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99087	1.0839	10	0.33141	T	0.24	-27.8222	6.511	0.22222	0.7602:0.1564:0.0833:0.0	.	272;272;272;272	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	G	272;272;272;272;272;261;140	ENSP00000352610:V272G;ENSP00000269305:V272G;ENSP00000398846:V272G;ENSP00000391127:V272G;ENSP00000391478:V272G;ENSP00000425104:V140G	ENSP00000269305:V272G	V	-	2	0	TP53	7517848	0.032000	0.19561	0.353000	0.25747	0.798000	0.45092	0.523000	0.22925	0.396000	0.25283	0.379000	0.24179	GTG		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577123	A	C	7577123	3	2	119	1	0	0	0	0	1	0	0	0	16421	159	6	4	471	4	TP53	17	7577123	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	17	7577123	73618087	109	31553			1	40		3	3	402	N	T_G_A	1.568891e-06
TP53	7157	hgsc.bcm.edu	37	chr17	7577507	7577507	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gtggctcctgacctggagtcTtccagtgtgatgatggtgag	15	8	1	4			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:7577507T>C	ENST00000269305.4	-	7	963	c.774A>G	c.(772-774)gaA>gaG	p.E258E	TP53_ENST00000359597.4_Silent_p.E258E|TP53_ENST00000445888.2_Silent_p.E258E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Silent_p.E258E|TP53_ENST00000455263.2_Silent_p.E258E|TP53_ENST00000420246.2_Silent_p.E258E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E258D(9)|p.0?(8)|p.D259fs*5(1)|p.?(1)|p.E258fs*85(1)|p.E258fs*71(1)|p.D259fs*86(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACCTGGAGTCTTCCAGTGTGA	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	25	Substitution - Missense(9)|Whole gene deletion(8)|Deletion - Frameshift(4)|Deletion - In frame(2)|Insertion - Frameshift(1)|Unknown(1)	large_intestine(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(2)|oesophagus(2)|lung(2)|ovary(2)|stomach(1)|breast(1)	17											136	96	110					17																	7577507		2203	4300	6503	7518232	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.774A>G	17.37:g.7577507T>C			7518232	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577507	T	C	7577507	2	2	119	1	0	0	0	0	0	0	0	1	16421	1606	56	4		4	TP53	17	7577507	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10	384	7577507	73617703	110	31554			1	40		3	3	402	N	T_G_A	1.568891e-06
MYH8	4626	hgsc.bcm.edu	37	chr17	10302911	10302911	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgtgaggtcattgatcagccGctgctgctcctcttccttgg	11	12	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:10302911G>T	ENST00000403437.2	-	28	3905	c.3811C>A	c.(3811-3813)Cgg>Agg	p.R1271R	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1271					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TTGATCAGCCGCTGCTGCTCC	0.483									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																																							0			17											142	130	134					17																	10302911		2203	4300	6503	10243636	SO:0001819	synonymous_variant	4626	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3811C>A	17.37:g.10302911G>T			10243636	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																				0.483	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10302911	G	T	10302911	2	4	119	1	0	0	0	0	0	0	0	1	10071	1086	38	2		2	MYH8	17	10302911	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10	2725404	10302911	70892299	111	31555										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12032493	12032493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccgatttccttatccaaagtGgaatagtgtatttgatcaac	7	8	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:12032493G>T	ENST00000353533.5	+	9	992	c.929G>T	c.(928-930)tGg>tTg	p.W310L	MAP2K4_ENST00000415385.3_Missense_Mutation_p.W321L	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	310	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.W310*(1)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TATCCAAAGTGGAATAGTGTA	0.428			"D, Mis, N"		"pancreatic, breast, colorectal"																																		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	12	Whole gene deletion(10)|Substitution - Nonsense(1)|Unknown(1)	breast(4)|ovary(4)|biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	17											76	70	72					17																	12032493		2203	4300	6503	11973218	SO:0001583	missense	6416			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.929G>T	17.37:g.12032493G>T	ENSP00000262445:p.Trp310Leu		11973218	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.045499	0.93685	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.63913	-0.07;-0.07	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65176	0.2666	N	0.12831	0.26	0.80722	D	1	D;P;P	0.76494	0.999;0.923;0.862	D;P;P	0.70716	0.97;0.703;0.749	T	0.71856	-0.4466	10	0.87932	D	0	.	17.8069	0.88604	0.0:0.0:1.0:0.0	.	182;321;310	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	L	310;321;287;182	ENSP00000262445:W310L;ENSP00000410402:W321L	ENSP00000262445:W310L	W	+	2	0	MAP2K4	11973218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.586000	0.98226	2.805000	0.96524	0.655000	0.94253	TGG		0.428	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	12032493	G	T	12032493	3	4	119	1	0	0	0	0	1	0	0	0	9269	1357	47	2	963	2	MAP2K4	17	12032493	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	1729582	12032493	69162717	112	31556										
NF1	4763	hgsc.bcm.edu	37	chr17	29556399	29556399	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aatgttaaggatctggtgggTctagaattgagtcctgctct	12	6	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:29556399T>C	ENST00000358273.4	+	21	3149	c.2766T>C	c.(2764-2766)ggT>ggC	p.G922G	NF1_ENST00000356175.3_Silent_p.G922G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	922					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ATCTGGTGGGTCTAGAATTGA	0.408			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17											113	113	113					17																	29556399		2203	4300	6503	26580525	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2766T>C	17.37:g.29556399T>C			26580525	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29556399	T	C	29556399	2	2	119	1	0	0	0	0	0	0	0	1	10387	1654	58	4		4	NF1	17	29556399	Silent	SNP	T	TCGA-F5-6812-01A-11D-1826-10	17523906	29556399	51638811	113	31557										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37922534	37922534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gtttgacatctcagcccgggTgagggctatgggatacatgc	14	9	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:37922534T>C	ENST00000346872.3	-	8	1100	c.1039A>G	c.(1039-1041)Acc>Gcc	p.T347A	RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000350532.3_Missense_Mutation_p.T308A|IKZF3_ENST00000377958.2_Missense_Mutation_p.T260A|IKZF3_ENST00000377945.3_Missense_Mutation_p.T213A|IKZF3_ENST00000377944.3_Missense_Mutation_p.T204A|IKZF3_ENST00000439167.2_Missense_Mutation_p.T274A|IKZF3_ENST00000351680.3_Missense_Mutation_p.T308A|IKZF3_ENST00000346243.3_Missense_Mutation_p.T269A|IKZF3_ENST00000439016.2_Missense_Mutation_p.T252A|IKZF3_ENST00000467757.1_Missense_Mutation_p.T291A|IKZF3_ENST00000377952.2_Missense_Mutation_p.T126A|IKZF3_ENST00000394189.2_Missense_Mutation_p.T165A|IKZF3_ENST00000583368.1_Missense_Mutation_p.T100A|IKZF3_ENST00000535189.1_Missense_Mutation_p.T313A	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	347					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCAGCCCGGGTGAGGGCTATG	0.582																																																0			17											97	89	92					17																	37922534		2203	4300	6503	35176060	SO:0001583	missense	22806			AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1039A>G	17.37:g.37922534T>C	ENSP00000344544:p.Thr347Ala		35176060	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.626044	0.28978	.	.	ENSG00000161405	ENST00000488188;ENST00000346872;ENST00000377945;ENST00000394189;ENST00000377944;ENST00000377958;ENST00000377952;ENST00000535189;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	T;T;T;T;T;T;T;T;T;T	0.08546	3.51;3.56;3.29;3.08;3.76;3.35;3.42;3.43;3.31;4.37	5.91	4.84	0.62591	.	0.000000	0.64402	D	0.000009	T	0.12178	0.0296	L	0.43152	1.355	0.31627	N	0.649505	P;B;B;B;D;B;P;B;B;B;P;P;B	0.63880	0.888;0.001;0.004;0.001;0.993;0.041;0.812;0.002;0.036;0.094;0.888;0.888;0.011	P;B;B;B;P;B;P;B;B;B;P;P;B	0.53518	0.539;0.003;0.004;0.003;0.728;0.036;0.539;0.004;0.036;0.171;0.539;0.539;0.024	T	0.07520	-1.0768	10	0.18276	T	0.48	-10.9571	8.8102	0.34963	0.0:0.0687:0.136:0.7953	.	260;126;165;213;204;313;269;252;308;291;308;274;347	Q9UKT9-9;Q9UKT9-12;Q9UKT9-11;Q9UKT9-13;Q9UKT9-10;Q9UKT9-7;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9-8;Q9UKT9	.;.;.;.;.;.;.;.;.;.;.;.;IKZF3_HUMAN	A	347;252;213;165;204;260;126;313;308;269;308;291	ENSP00000367180:T213A;ENSP00000377741:T165A;ENSP00000367179:T204A;ENSP00000367194:T260A;ENSP00000367188:T126A;ENSP00000438972:T313A;ENSP00000345622:T308A;ENSP00000341977:T269A;ENSP00000344471:T308A;ENSP00000420463:T291A	ENSP00000341977:T269A	T	-	1	0	IKZF3	35176060	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.737000	0.38197	1.057000	0.40506	0.533000	0.62120	ACC		0.582	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		C	37922534	T	C	37922534	3	2	119	1	0	0	0	0	1	0	0	0	7637	1696	59	4	494	4	IKZF3	17	37922534	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	8366135	37922534	43272676	114	31558										
KLHL10	317719	hgsc.bcm.edu	37	chr17	39998265	39998265	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	tgggtatcgtcaggggttgcTgcgagttcctcaagtcagag	15	8	3	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:39998265T>C	ENST00000293303.4	+	2	538	c.385T>C	c.(385-387)Tgc>Cgc	p.C129R	KLHL10_ENST00000485613.1_3'UTR	NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	129					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				CAGGGGTTGCTGCGAGTTCCT	0.507																																																0			17											122	114	116					17																	39998265		1994	4174	6168	37251791	SO:0001583	missense	317719			AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.385T>C	17.37:g.39998265T>C	ENSP00000293303:p.Cys129Arg		37251791	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	37	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	T	19.24	3.789451	0.70337	.	.	ENSG00000161594	ENST00000293303;ENST00000438813	T;T	0.66099	-0.19;-0.19	5.73	5.73	0.89815	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.135639	0.64402	D	0.000001	T	0.73233	0.3561	M	0.67700	2.07	0.80722	D	1	P;D	0.54772	0.942;0.968	P;P	0.61940	0.811;0.896	T	0.74041	-0.3792	9	.	.	.	.	10.9335	0.47233	0.0:0.0:0.1568:0.8432	.	123;129	B4DXV2;Q6JEL2	.;KLH10_HUMAN	R	129;123	ENSP00000293303:C129R;ENSP00000416221:C123R	.	C	+	1	0	KLHL10	37251791	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.840000	0.62817	2.177000	0.69029	0.533000	0.62120	TGC		0.507	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		C	39998265	T	C	39998265	3	2	119	1	0	0	0	0	1	0	0	0	8387	1580	55	4	391	4	KLHL10	17	39998265	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	2075731	39998265	41196945	115	31559										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76486905	76486905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ggtgcggttcagggggatccGctcgttgctggccagggtga	19	9	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr17:76486905G>A	ENST00000585328.1	-	44	6803	c.6679C>T	c.(6679-6681)Cgg>Tgg	p.R2227W	DNAH17_ENST00000586052.1_5'UTR|RP11-559N14.5_ENST00000585969.1_RNA|DNAH17_ENST00000389840.5_Missense_Mutation_p.R2218W|RP11-559N14.5_ENST00000588565.1_RNA|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2218	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AGGGGGATCCGCTCGTTGCTG	0.632																																																0			17											22	28	26					17																	76486905		2022	4163	6185	73998500	SO:0001583	missense	8632			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6679C>T	17.37:g.76486905G>A	ENSP00000465516:p.Arg2227Trp		73998500	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	G	15.29	2.790818	0.50102	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	D	0.89343	-2.5	4.45	4.45	0.53987	.	.	.	.	.	D	0.96790	0.8952	H	0.99600	4.65	0.42210	D	0.991804	.	.	.	.	.	.	D	0.97415	1.0005	7	0.87932	D	0	.	11.4839	0.50342	0.0:0.0:0.6855:0.3145	.	.	.	.	W	2227;2218	ENSP00000374490:R2218W	ENSP00000300671:R2227W	R	-	1	2	DNAH17	73998500	1.000000	0.71417	0.981000	0.43875	0.246000	0.25737	4.347000	0.59373	2.187000	0.69744	0.561000	0.74099	CGG		0.632	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76486905	G	A	76486905	3	1	119	1	0	0	0	0	1	0	0	0	4612	1086	38	1	6846	1	DNAH17	17	76486905	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	36488640	76486905	4708305	116	31560										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591838	48591838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttactttgaaatggatgttcAggtaggagagacatttaagg	12	3	1	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr18:48591838A>G	ENST00000342988.3	+	9	1539	c.1001A>G	c.(1000-1002)cAg>cGg	p.Q334R	SMAD4_ENST00000588745.1_Missense_Mutation_p.Q238R|SMAD4_ENST00000398417.2_Missense_Mutation_p.Q334R	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	334	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ATGGATGTTCAGGTAGGAGAG	0.423																																																38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											266	230	242					18																	48591838		2203	4300	6503	46845836	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1001A>G	18.37:g.48591838A>G	ENSP00000341551:p.Gln334Arg		46845836	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.134922	0.56828	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.95588	-3.75;-3.75	5.99	5.99	0.97316	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.90693	0.7080	N	0.25094	0.71	0.80722	D	1	B	0.18013	0.025	B	0.20955	0.032	D	0.87120	0.2190	10	0.13108	T	0.6	.	15.4768	0.75489	1.0:0.0:0.0:0.0	.	334	Q13485	SMAD4_HUMAN	R	334	ENSP00000341551:Q334R;ENSP00000381452:Q334R	ENSP00000341551:Q334R	Q	+	2	0	SMAD4	46845836	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.159000	0.94728	2.291000	0.77112	0.533000	0.62120	CAG		0.423	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48591838	A	G	48591838	3	3	119	1	0	0	0	0	1	0	0	0	14797	188	7	4	1031	4	SMAD4	18	48591838	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10		48591838	29485410	117	31561										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55338741	55338741	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttgcttagtaggattcattcGatgtaaccgttcataaataa	7	6	2	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr18:55338741G>A	ENST00000283684.4	-	16	1890	c.1891C>T	c.(1891-1893)Cga>Tga	p.R631*	RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA|ATP8B1_ENST00000536015.1_Nonsense_Mutation_p.R631*|RP11-35G9.5_ENST00000588925.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	631					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				GGATTCATTCGATGTAACCGT	0.383																																																0			18											172	148	156					18																	55338741		2203	4300	6503	53489739	SO:0001587	stop_gained	5205			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.1891C>T	18.37:g.55338741G>A	ENSP00000283684:p.Arg631*		53489739	Q9BTP8	Nonsense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	G	38	7.067276	0.98040	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	.	.	.	5.87	5.87	0.94306	.	0.448811	0.25397	N	0.030970	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	19.8132	0.96556	0.0:0.0:1.0:0.0	.	.	.	.	X	631	.	ENSP00000283684:R631X	R	-	1	2	ATP8B1	53489739	1.000000	0.71417	0.938000	0.37757	0.805000	0.45488	4.468000	0.60162	2.785000	0.95823	0.655000	0.94253	CGA		0.383	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		A	55338741	G	A	55338741	4	1	119	1	0	0	0	0	0	1	0	0	1195	1066	37	1	1912	1	ATP8B1	18	55338741	Nonsense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	6746903	55338741	22738507	118	31562										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171675	4171675	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttctccagaactttgcacaaCgatgctgcctcccgcgtggc	9	15	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr19:4171675C>T	ENST00000078445.2	+	10	1242	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	CREB3L3_ENST00000595923.1_Silent_p.N364N|CREB3L3_ENST00000602257.1_Silent_p.N363N|CREB3L3_ENST00000252587.3_Missense_Mutation_p.T254M|CREB3L3_ENST00000602147.1_Nonsense_Mutation_p.R330*	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	365					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTTGCACAACGATGCTGCCT	0.642																																																0			19											66	79	74					19																	4171675		2198	4288	6486	4122675	SO:0001819	synonymous_variant	84699				CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1095C>T	19.37:g.4171675C>T			4122675	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	c	0.543	-0.852716	0.02630	.	.	ENSG00000060566	ENST00000252587	T	0.79554	-1.28	3.53	-1.01	0.10169	.	.	.	.	.	T	0.64238	0.2580	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.51317	-0.8721	6	0.18276	T	0.48	-4.1442	6.0877	0.19976	0.0:0.507:0.0:0.493	.	.	.	.	M	254	ENSP00000252587:T254M	ENSP00000252587:T254M	T	+	2	0	CREB3L3	4122675	0.001000	0.12720	0.433000	0.26760	0.870000	0.49936	-0.758000	0.04766	0.020000	0.15106	-0.993000	0.02533	ACG		0.642	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4171675	C	T	4171675	2	4	119	1	0	0	0	0	0	0	0	1	3864	535	19	1		1	CREB3L3	19	4171675	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10		4171675	54957308	119	31563										
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938248	14938248	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ctgaggctgttgcacttgagTgtgagttgcgggtggcagca	17	7	0	3	rs112284734	byFrequency	TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr19:14938248T>A	ENST00000322301.3	-	2	893	c.806A>T	c.(805-807)cAc>cTc	p.H269L	OR7A5_ENST00000594432.1_Missense_Mutation_p.H269L|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	269					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TGCACTTGAGTGTGAGTTGCG	0.483																																																0			19											94	81	86					19																	14938248		2203	4300	6503	14799248	SO:0001583	missense	26659			X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.806A>T	19.37:g.14938248T>A	ENSP00000316955:p.His269Leu		14799248	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	37	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	t	11.34	1.609869	0.28712	.	.	ENSG00000188269	ENST00000322301	T	0.00069	8.77	3.12	-0.173	0.13322	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.20445	0.575	0.09310	N	1	B	0.23990	0.095	B	0.33254	0.16	T	0.04976	-1.0914	9	0.48119	T	0.1	.	6.5609	0.22485	0.0:0.5426:0.0:0.4574	.	269	Q15622	OR7A5_HUMAN	L	269	ENSP00000316955:H269L	ENSP00000316955:H269L	H	-	2	0	OR7A5	14799248	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-0.053000	0.11846	0.050000	0.15949	0.102000	0.15555	CAC		0.483	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		A	14938248	T	A	14938248	3	1	119	1	0	0	0	0	1	0	0	0	11247	1696	59	5	157	5	OR7A5	19	14938248	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	10766573	14938248	44190735	120	31564										
CEACAM1	634	hgsc.bcm.edu	37	chr19	43025479	43025479	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agtgactgagttattggcgtGgcaggtataggatccactat	13	6	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr19:43025479G>T	ENST00000161559.6	-	4	1032	c.898C>A	c.(898-900)Cac>Aac	p.H300N	CEACAM1_ENST00000351134.3_Intron|CEACAM1_ENST00000403461.1_Missense_Mutation_p.H300N|CEACAM1_ENST00000403444.3_Missense_Mutation_p.H300N|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000308072.4_Missense_Mutation_p.H260N|CEACAM1_ENST00000358394.3_Missense_Mutation_p.H300N|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000352591.5_Missense_Mutation_p.H300N|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000599389.1_Missense_Mutation_p.H300N	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	300	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	TTATTGGCGTGGCAGGTATAG	0.453																																																0			19											182	164	170					19																	43025479		2203	4300	6503	47717319	SO:0001583	missense	634			M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.898C>A	19.37:g.43025479G>T	ENSP00000161559:p.His300Asn		47717319	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	g	9.921	1.212162	0.22289	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73;2.73	4.9	-3.21	0.05140	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08891	0.0220	N	0.26042	0.785	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.33073	0.228;0.332;0.228;0.228;0.228;0.11;0.01;0.11;0.396	B;B;B;B;B;B;B;B;B	0.41135	0.236;0.076;0.133;0.185;0.185;0.236;0.017;0.185;0.348	T	0.40515	-0.9559	9	0.27785	T	0.31	.	1.4872	0.02449	0.2517:0.2385:0.3811:0.1287	.	300;300;300;300;300;300;300;300;300	P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;CEAM1_HUMAN	N	300;300;327;260;300;300;300;260;300;300;300	ENSP00000161559:H300N;ENSP00000351165:H300N;ENSP00000244291:H300N;ENSP00000384709:H300N;ENSP00000384083:H300N;ENSP00000312184:H260N	ENSP00000161559:H300N	H	-	1	0	CEACAM1	47717319	0.004000	0.15560	0.024000	0.17045	0.086000	0.17979	-0.611000	0.05622	-0.201000	0.10284	-0.280000	0.10049	CAC		0.453	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		T	43025479	G	T	43025479	3	4	119	1	0	0	0	0	1	0	0	0	3193	1348	47	2	803	2	CEACAM1	19	43025479	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	28087231	43025479	16103504	121	31565										
SALL4	57167	hgsc.bcm.edu	37	chr20	50418828	50418828	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ccccactcacccagctccccCgccgcgggcgccgctggggc	12	23	1	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr20:50418828C>T	ENST00000217086.4	-	1	231	c.120G>A	c.(118-120)gcG>gcA	p.A40A	SALL4_ENST00000395997.3_Silent_p.A40A|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Silent_p.A40A	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	40					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCAGCTcccccgccgcgggcg	0.751																																																0			20											6	9	8					20																	50418828		1894	3857	5751	49852235	SO:0001819	synonymous_variant	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.120G>A	20.37:g.50418828C>T			49852235	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.751	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			T	50418828	C	T	50418828	2	4	119	1	0	0	0	0	0	0	0	1	13850	639	23	1		1	SALL4	20	50418828	Silent	SNP	C	TCGA-F5-6812-01A-11D-1826-10		50418828	12606692	122	31566										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50701144	50701144	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gcctcgagctgccccacggaGaccagggtgctgagctgtcc	14	15	0	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr20:50701144G>A	ENST00000361387.2	-	9	1950	c.1890C>T	c.(1888-1890)gtC>gtT	p.V630V	ZFP64_ENST00000371523.4_Silent_p.V411V|ZFP64_ENST00000371518.2_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GCCCCACGGAGACCAGGGTGC	0.602																																																0			20											43	43	43					20																	50701144		2203	4300	6503	50134551	SO:0001819	synonymous_variant	55734			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1890C>T	20.37:g.50701144G>A			50134551	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000361387.2	37	CCDS13439.1																																																																																				0.602	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		A	50701144	G	A	50701144	2	1	119	1	0	0	0	0	0	0	0	1	17691	929	33	3		3	ZFP64	20	50701144	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10	282316	50701144	12324376	123	31567										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52199015	52199015	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttgcaattcttttccttgggAggttctgttcgcacttgact	9	9	2	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr20:52199015A>G	ENST00000371471.2	-	2	776	c.351T>C	c.(349-351)ccT>ccC	p.P117P	ZNF217_ENST00000302342.3_Silent_p.P117P|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	117					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TTTCCTTGGGAGGTTCTGTTC	0.448																																																0			20											140	123	129					20																	52199015		2203	4300	6503	51632422	SO:0001819	synonymous_variant	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.351T>C	20.37:g.52199015A>G			51632422	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																				0.448	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		G	52199015	A	G	52199015	2	3	119	1	0	0	0	0	0	0	0	1	17811	291	11	4		4	ZNF217	20	52199015	Silent	SNP	A	TCGA-F5-6812-01A-11D-1826-10	1497871	52199015	10826505	124	31568										
CABLES2	81928	hgsc.bcm.edu	37	chr20	60967489	60967489	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	ttgacatgggggaacttctcCctgaaggtctcgttcatgtc	11	10	3	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr20:60967489C>A	ENST00000279101.5	-	8	1055	c.1047G>T	c.(1045-1047)agG>agT	p.R349S		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	349					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGAACTTCTCCCTGAAGGTCT	0.572																																																0			20											235	207	217					20																	60967489		2203	4300	6503	60400884	SO:0001583	missense	81928			BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.1047G>T	20.37:g.60967489C>A	ENSP00000279101:p.Arg349Ser		60400884	Q5JWL0|Q9BYK0	Missense_Mutation	SNP	ENST00000279101.5	37	CCDS33503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.71|19.71	3.877590|3.877590	0.72294|0.72294	.|.	.|.	ENSG00000149679|ENSG00000149679	ENST00000453274|ENST00000370560;ENST00000279101	.|T	.|0.18502	.|2.21	5.53|5.53	-2.25|-2.25	0.06888|0.06888	.|Cyclin-like (2);	.|0.251002	.|0.47852	.|D	.|0.000214	T|T	0.18676|0.18676	0.0448|0.0448	L|L	0.53729|0.53729	1.69|1.69	0.50813|0.50813	D|D	0.999897|0.999897	.|P	.|0.45768	.|0.866	.|P	.|0.46208	.|0.507	T|T	0.05784|0.05784	-1.0864|-1.0864	5|10	.|0.66056	.|D	.|0.02	-23.6675|-23.6675	10.8826|10.8826	0.46948|0.46948	0.0:0.332:0.0:0.668|0.0:0.332:0.0:0.668	.|.	.|349	.|Q9BTV7	.|CABL2_HUMAN	V|S	143|137;349	.|ENSP00000279101:R349S	.|ENSP00000279101:R349S	G|R	-|-	2|3	0|2	CABLES2|CABLES2	60400884|60400884	0.749000|0.749000	0.28305|0.28305	0.988000|0.988000	0.46212|0.46212	0.976000|0.976000	0.68499|0.68499	-0.096000|-0.096000	0.11059|0.11059	-0.211000|-0.211000	0.10124|0.10124	-0.345000|-0.345000	0.07892|0.07892	GGG|AGG		0.572	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		A	60967489	C	A	60967489	3	1	119	1	0	0	0	0	1	0	0	0	2536	622	22	2	401	2	CABLES2	20	60967489	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	8768474	60967489	2058031	125	31569										
RBM11	54033	hgsc.bcm.edu	37	chr21	15599508	15599508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cctttatcagatgaataaacGaaagagacaaaagcaaacaa	6	7	1	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr21:15599508G>A	ENST00000400577.3	+	5	749	c.740G>A	c.(739-741)cGa>cAa	p.R247Q	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	247					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)	p.R247Q(1)		endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		ATGAATAAACGAAAGAGACAA	0.408																																																1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	21											211	203	206					21																	15599508		1947	4150	6097	14521379	SO:0001583	missense	54033			AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"RNA binding motif (RRM) containing"	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.740G>A	21.37:g.15599508G>A	ENSP00000383421:p.Arg247Gln		14521379	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.041604	0.75732	.	.	ENSG00000185272	ENST00000400577	T	0.10477	2.87	4.99	4.07	0.47477	.	.	.	.	.	T	0.13329	0.0323	M	0.66939	2.045	0.27241	N	0.959134	B	0.24533	0.105	B	0.16722	0.016	T	0.09037	-1.0693	9	0.49607	T	0.09	-10.1345	8.7994	0.34898	0.1862:0.0:0.8138:0.0	.	247	P57052	RBM11_HUMAN	Q	247	ENSP00000383421:R247Q	ENSP00000383421:R247Q	R	+	2	0	RBM11	14521379	1.000000	0.71417	0.967000	0.41034	0.776000	0.43924	1.464000	0.35288	1.352000	0.45808	0.650000	0.86243	CGA		0.408	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		A	15599508	G	A	15599508	3	1	119	1	0	0	0	0	1	0	0	0	13149	1058	37	1	758	1	RBM11	21	15599508	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10		15599508	32530387	126	31570										
GAB4	128954	hgsc.bcm.edu	37	chr22	17445730	17445730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cgtggagatggggtgttgggAggagctggagtcaaaggtgt	21	3	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr22:17445730A>G	ENST00000400588.1	-	8	1509	c.1402T>C	c.(1402-1404)Tcc>Ccc	p.S468P	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	468								p.S468T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GGGTGTTGGGAGGAGCTGGAG	0.587																																																1	Substitution - Missense(1)	ovary(1)	22											138	148	145					22																	17445730		2187	4293	6480	15825730	SO:0001583	missense	128954			AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1402T>C	22.37:g.17445730A>G	ENSP00000383431:p.Ser468Pro		15825730		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.014036	0.35511	.	.	ENSG00000215568	ENST00000400588	T	0.20332	2.08	1.96	1.96	0.26148	.	0.254391	0.40302	N	0.001138	T	0.28863	0.0716	L	0.46157	1.445	0.46437	D	0.999042	D	0.71674	0.998	D	0.76071	0.987	T	0.22312	-1.0220	10	0.08179	T	0.78	.	7.8586	0.29497	1.0:0.0:0.0:0.0	.	468	Q2WGN9	GAB4_HUMAN	P	468	ENSP00000383431:S468P	ENSP00000383431:S468P	S	-	1	0	GAB4	15825730	1.000000	0.71417	0.988000	0.46212	0.047000	0.14425	3.516000	0.53436	1.144000	0.42321	0.332000	0.21555	TCC		0.587	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		G	17445730	A	G	17445730	3	3	119	1	0	0	0	0	1	0	0	0	6170	304	11	4	334	4	GAB4	22	17445730	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10		17445730	33858836	127	31571										
CRYBB1	1414	hgsc.bcm.edu	37	chr22	27008120	27008120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cccccgagaattctgctcgaCggccctggaagttttccagt	10	14	1	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chr22:27008120C>T	ENST00000215939.2	-	3	345	c.215G>A	c.(214-216)cGt>cAt	p.R72H		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	72	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						TTCTGCTCGACGGCCCTGGAA	0.577																																																0			22											74	66	69					22																	27008120		2203	4300	6503	25338120	SO:0001583	missense	1414				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.215G>A	22.37:g.27008120C>T	ENSP00000215939:p.Arg72His		25338120		Missense_Mutation	SNP	ENST00000215939.2	37	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.586190	0.46110	.	.	ENSG00000100122	ENST00000215939	T	0.78003	-1.14	4.02	2.97	0.34412	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.056916	0.64402	D	0.000017	T	0.72851	0.3512	M	0.70787	2.145	0.58432	D	0.999996	B	0.33073	0.396	B	0.25759	0.063	T	0.72636	-0.4233	10	0.48119	T	0.1	.	12.6108	0.56549	0.0:0.8314:0.1686:0.0	.	72	P53674	CRBB1_HUMAN	H	72	ENSP00000215939:R72H	ENSP00000215939:R72H	R	-	2	0	CRYBB1	25338120	0.819000	0.29175	0.743000	0.31040	0.668000	0.39293	1.553000	0.36255	0.861000	0.35504	0.491000	0.48974	CGT		0.577	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887		T	27008120	C	T	27008120	3	4	119	1	0	0	0	0	1	0	0	0	3916	536	19	1	559	1	CRYBB1	22	27008120	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	9562390	27008120	24296446	128	31572										
TLR7	51284	hgsc.bcm.edu	37	chrX	12904056	12904056	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aaccagctactagagataccGcagggcctcccgcctagctt	9	15	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:12904056G>A	ENST00000380659.3	+	3	568	c.429G>A	c.(427-429)ccG>ccA	p.P143P		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	143					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	TAGAGATACCGCAGGGCCTCC	0.448																																																0			X											57	58	58					X																	12904056		2203	4299	6502	12813977	SO:0001819	synonymous_variant	51284			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.429G>A	X.37:g.12904056G>A			12813977	D1CS69|Q9NR98	Silent	SNP	ENST00000380659.3	37	CCDS14151.1																																																																																				0.448	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12904056	G	A	12904056	2	1	119	1	0	0	0	0	0	0	0	1	15995	1074	38	1		1	TLR7	23	12904056	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10		12904056	142366504	129	31573										
YY2	404281	hgsc.bcm.edu	37	chrX	21874910	21874910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gctaggcaacgacttggaggAccagttggccctcccggata	13	12	0	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:21874910A>G	ENST00000429584.2	+	1	806	c.308A>G	c.(307-309)gAc>gGc	p.D103G	MBTPS2_ENST00000365779.2_Intron|MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000465888.1_3'UTR	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	103			D -> N (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						GACTTGGAGGACCAGTTGGCC	0.562																																																0			X											99	79	86					X																	21874910		2203	4300	6503	21784831	SO:0001583	missense	404281			AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.308A>G	X.37:g.21874910A>G	ENSP00000389381:p.Asp103Gly		21784831	B2RP10|Q6Q1S4	Missense_Mutation	SNP	ENST00000429584.2	37	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.086854	0.55861	.	.	ENSG00000230797	ENST00000429584	T	0.14144	2.53	3.99	-0.82	0.10826	.	0.578618	0.16301	U	0.220444	T	0.11965	0.0291	L	0.52573	1.65	0.09310	N	1	B	0.19200	0.034	B	0.16722	0.016	T	0.21075	-1.0256	10	0.72032	D	0.01	.	7.8239	0.29303	0.5718:0.0:0.4282:0.0	.	103	O15391	TYY2_HUMAN	G	103	ENSP00000389381:D103G	ENSP00000389381:D103G	D	+	2	0	YY2	21784831	0.716000	0.27956	0.000000	0.03702	0.006000	0.05464	2.264000	0.43302	-0.279000	0.09167	0.486000	0.48141	GAC		0.562	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		G	21874910	A	G	21874910	3	3	119	1	0	0	0	0	1	0	0	0	17549	275	10	4	310	4	YY2	23	21874910	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	8970854	21874910	133395650	130	31574										
ZNF41	7592	hgsc.bcm.edu	37	chrX	47315383	47315383	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cccctctccttgctccaactTgaaggcagcctctgacttgg	8	16	2	2			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:47315383T>G	ENST00000377065.4	-	4	871	c.232A>C	c.(232-234)Aag>Cag	p.K78Q	ZNF41_ENST00000397050.2_Missense_Mutation_p.K88Q|ZNF41_ENST00000313116.7_Missense_Mutation_p.K78Q|ZNF41_ENST00000465311.1_5'UTR	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	120	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				TGCTCCAACTTGAAGGCAGCC	0.537																																																0			X											100	84	89					X																	47315383		2203	4300	6503	47200327	SO:0001583	missense	7592			X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.232A>C	X.37:g.47315383T>G	ENSP00000366265:p.Lys78Gln		47200327	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	1.078	-0.667768	0.03428	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050;ENST00000432977	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	2.32	1.08	0.20341	Krueppel-associated box (3);	0.682383	0.12047	N	0.504429	T	0.23846	0.0577	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B	0.34015	0.002;0.002;0.435;0.003;0.002	B;B;B;B;B	0.28139	0.008;0.008;0.086;0.008;0.004	T	0.15065	-1.0450	10	0.15066	T	0.55	.	6.2632	0.20912	0.0:0.0:0.2532:0.7468	.	78;80;88;112;120	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	Q	78;78;88;88	ENSP00000315173:K78Q;ENSP00000366265:K78Q;ENSP00000380243:K88Q;ENSP00000390385:K88Q	ENSP00000315173:K78Q	K	-	1	0	ZNF41	47200327	0.153000	0.22777	0.156000	0.22583	0.214000	0.24535	0.211000	0.17474	0.212000	0.20703	0.242000	0.17961	AAG		0.537	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		G	47315383	T	G	47315383	3	3	119	1	0	0	0	0	1	0	0	0	17928	1821	63	4	2115	4	ZNF41	23	47315383	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	25440473	47315383	107955177	131	31575										
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100911496	100911496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gtcttcttcccctccctctgCgctgggtctcgggctcagag	11	16	5	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:100911496C>T	ENST00000328766.5	-	5	1532	c.1079G>A	c.(1078-1080)cGc>cAc	p.R360H	ARMCX2_ENST00000356824.4_Missense_Mutation_p.R360H|ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Missense_Mutation_p.R360H	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	360						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						CCTCCCTCTGCGCTGGGTCTC	0.582													C|||	1	0.000264901	0	0	3775	,	,		12834	0		0	False		,,,				2504	0.001															0			X											73	63	66					X																	100911496		2203	4300	6503	100798152	SO:0001583	missense	9823			AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"Armadillo repeat containing"	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1079G>A	X.37:g.100911496C>T	ENSP00000331662:p.Arg360His		100798152	O60267|Q5H9D9	Missense_Mutation	SNP	ENST00000328766.5	37	CCDS14490.1	.	.	.	.	.	.	.	.	.	.	C	0.464	-0.887682	0.02511	.	.	ENSG00000184867	ENST00000328766;ENST00000330154;ENST00000356824	T;T;T	0.30981	1.51;1.51;1.51	3.66	-1.98	0.07480	.	2.250750	0.01580	N	0.021058	T	0.18759	0.0450	N	0.08118	0	0.19945	N	0.999942	B	0.13145	0.007	B	0.08055	0.003	T	0.31475	-0.9942	10	0.48119	T	0.1	2.551	10.7037	0.45942	0.0:0.1576:0.0:0.8424	.	360	Q7L311	ARMX2_HUMAN	H	360	ENSP00000331662:R360H;ENSP00000328631:R360H;ENSP00000349281:R360H	ENSP00000331662:R360H	R	-	2	0	ARMCX2	100798152	0.185000	0.23213	0.288000	0.24862	0.128000	0.20619	-0.408000	0.07169	-0.543000	0.06240	-0.508000	0.04489	CGC		0.582	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		T	100911496	C	T	100911496	3	4	119	1	0	0	0	0	1	0	0	0	961	768	27	1	823	1	ARMCX2	23	100911496	Missense_Mutation	SNP	C	TCGA-F5-6812-01A-11D-1826-10	53596113	100911496	54359064	132	31576										
PLP1	5354	hgsc.bcm.edu	37	chrX	103041613	103041613	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	caagctcattctttggagcgGgtgtgtcattgtttgggaaa	13	6	3	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:103041613G>A	ENST00000303958.2	+	3	557	c.411G>A	c.(409-411)cgG>cgA	p.R137R	PLP1_ENST00000418604.1_Silent_p.R137R|PLP1_ENST00000361621.2_Intron	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	137			Missing (in HLD1).|R -> W (in SPG2). {ECO:0000269|PubMed:17438221}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						CTTTGGAGCGGGTGTGTCATT	0.552																																																0			X											148	126	133					X																	103041613		2203	4300	6503	102928269	SO:0001819	synonymous_variant	5354			M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.411G>A	X.37:g.103041613G>A			102928269	P04400|P06905|Q502Y1|Q6FHZ6	Silent	SNP	ENST00000303958.2	37	CCDS14513.1																																																																																				0.552	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			A	103041613	G	A	103041613	2	1	119	1	0	0	0	0	0	0	0	1	12135	1219	43	3		3	PLP1	23	103041613	Silent	SNP	G	TCGA-F5-6812-01A-11D-1826-10	2130117	103041613	52228947	133	31577										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122616762	122616762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	agaattctgttacaaatcacGggcagagtccaaacgcatga	9	9	2	3			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:122616762G>A	ENST00000371251.1	+	15	2604	c.2552G>A	c.(2551-2553)cGg>cAg	p.R851Q	GRIA3_ENST00000542149.1_3'UTR|GRIA3_ENST00000264357.5_Missense_Mutation_p.R851Q|GRIA3_ENST00000371256.5_Missense_Mutation_p.R851Q			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	851					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TACAAATCACGGGCAGAGTCC	0.478																																																0			X											121	100	108					X																	122616762		2203	4300	6503	122444443	SO:0001583	missense	2892			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.2552G>A	X.37:g.122616762G>A	ENSP00000360297:p.Arg851Gln		122444443	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139663	0.94560	.	.	ENSG00000125675	ENST00000264357;ENST00000371256;ENST00000371251	T;T;T	0.15718	2.41;2.4;2.41	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.28001	0.0690	M	0.85041	2.73	0.80722	D	1	P;P	0.39624	0.553;0.681	B;B	0.34385	0.088;0.181	T	0.22836	-1.0205	10	0.87932	D	0	.	17.8613	0.88781	0.0:0.0:1.0:0.0	.	851;851	P42263;P42263-2	GRIA3_HUMAN;.	Q	851	ENSP00000264357:R851Q;ENSP00000360302:R851Q;ENSP00000360297:R851Q	ENSP00000264357:R851Q	R	+	2	0	GRIA3	122444443	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.436000	0.82500	0.600000	0.82982	CGG		0.478	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		A	122616762	G	A	122616762	3	1	119	1	0	0	0	0	1	0	0	0	6790	1116	39	1	2729	1	GRIA3	23	122616762	Missense_Mutation	SNP	G	TCGA-F5-6812-01A-11D-1826-10	19575149	122616762	32653798	134	31578										
ACTRT1	139741	hgsc.bcm.edu	37	chrX	127185564	127185564	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	gttatttaccacggccttgtTgagtatgcaagggaagttaa	11	6	0	1			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:127185564T>A	ENST00000371124.3	-	1	818	c.622A>T	c.(622-624)Aac>Tac	p.N208Y		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	208						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						ACGGCCTTGTTGAGTATGCAA	0.537																																																0			X											113	109	110					X																	127185564		2203	4300	6503	127013245	SO:0001583	missense	139741			AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.622A>T	X.37:g.127185564T>A	ENSP00000360165:p.Asn208Tyr		127013245	Q6X7C1|Q96L10	Missense_Mutation	SNP	ENST00000371124.3	37	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	T	8.139	0.784736	0.16189	.	.	ENSG00000123165	ENST00000371124	T	0.31769	1.48	3.48	1.02	0.19986	.	0.275955	0.29438	N	0.012143	T	0.24431	0.0592	L	0.59436	1.845	0.20926	N	0.999821	B	0.19445	0.036	B	0.19391	0.025	T	0.27123	-1.0083	10	0.87932	D	0	.	2.9158	0.05752	0.0:0.2576:0.2331:0.5094	.	208	Q8TDG2	ACTT1_HUMAN	Y	208	ENSP00000360165:N208Y	ENSP00000360165:N208Y	N	-	1	0	ACTRT1	127013245	0.946000	0.32159	0.007000	0.13788	0.001000	0.01503	1.980000	0.40618	0.105000	0.17753	-0.507000	0.04495	AAC		0.537	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289		A	127185564	T	A	127185564	3	1	119	1	0	0	0	0	1	0	0	0	218	1812	63	5	512	5	ACTRT1	23	127185564	Missense_Mutation	SNP	T	TCGA-F5-6812-01A-11D-1826-10	4568802	127185564	28084996	135	31579										
GPR101	83550	hgsc.bcm.edu	37	chrX	136113068	136113068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	aaactcactctcatcctggaActcctccttcttctctgctc	3	17	4	0			TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:136113068A>G	ENST00000298110.1	-	1	765	c.766T>C	c.(766-768)Ttc>Ctc	p.F256L		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.F256I(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					TCATCCTGGAACTCCTCCTTC	0.547																																																1	Substitution - Missense(1)	ovary(1)	X											158	132	141					X																	136113068		2203	4300	6503	135940734	SO:0001583	missense	83550			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.766T>C	X.37:g.136113068A>G	ENSP00000298110:p.Phe256Leu		135940734	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.952496	0.00470	.	.	ENSG00000165370	ENST00000298110	T	0.62639	0.01	4.46	-2.34	0.06704	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.37019	0.0988	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.23297	-1.0192	9	0.09843	T	0.71	-3.9407	4.3692	0.11239	0.337:0.3493:0.3137:0.0	.	256	Q96P66	GP101_HUMAN	L	256	ENSP00000298110:F256L	ENSP00000298110:F256L	F	-	1	0	GPR101	135940734	0.009000	0.17119	0.000000	0.03702	0.017000	0.09413	0.827000	0.27421	-0.401000	0.07644	-0.369000	0.07265	TTC		0.547	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			G	136113068	A	G	136113068	3	3	119	1	0	0	0	0	1	0	0	0	6642	43	2	4	763	4	GPR101	23	136113068	Missense_Mutation	SNP	A	TCGA-F5-6812-01A-11D-1826-10	8927504	136113068	19157492	136	31580										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904649	144904655	+	Frame_Shift_Del	DEL	GTTTTTG	GTTTTTG	-													0.0364963503649635	5	1	0.561871912791688	3.84320388349515	0.246359223300971	1	1	0	cctggctagacaccataactGtttttgtgggagagattgtc							TCGA-F5-6812-01A-11D-1826-10	TCGA-F5-6812-10A-01D-1826-10	GTTTTTG	GTTTTTG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	5e34fd1b-3d8a-4c61-afaf-3889c5004655	480fe73e-fe48-4e8d-81f2-b557b2373278	g.chrX:144904649_144904655delGTTTTTG	ENST00000370490.1	+	1	4961_4967	c.706_712delGTTTTTG	c.(706-714)gtttttgtgfs	p.VFV236fs	SLITRK2_ENST00000428560.2_Frame_Shift_Del_p.VFV236fs|SLITRK2_ENST00000413937.2_Frame_Shift_Del_p.VFV236fs|SLITRK2_ENST00000447897.2_Frame_Shift_Del_p.VFV236fs|SLITRK2_ENST00000434188.2_Frame_Shift_Del_p.VFV236fs			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	236	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.F237C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CACCATAACTGTTTTTGTGGGAGAGAT	0.478																																																1	Substitution - Missense(1)	large_intestine(1)	X																																								144712347	SO:0001589	frameshift_variant	84631			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.706_712delGTTTTTG	X.37:g.144904649_144904655delGTTTTTG	ENSP00000359521:p.Val236fs		144712341	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Frame_Shift_Del	DEL	ENST00000370490.1	37	CCDS14680.1																																																																																				0.478	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		-	144904655	GTTTTTG	-	144904649	7	5	119	1	0	1	0	1	0	0	0	0	14780	1377	48	0	708	0	SLITRK2	23	144904649	Frame_Shift_Del	DEL	GTTTTTG	TCGA-F5-6812-01A-11D-1826-10	8791581	144904649	10365911	137	31581										
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43636446	43636446	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccttctgcatctgcagatcaGatttggccatttccgcaaaa	7	12	3	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:43636446G>T	ENST00000236051.2	-	4	569	c.428C>A	c.(427-429)tCt>tAt	p.S143Y	WDR65_ENST00000372492.4_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000431635.2_Missense_Mutation_p.S198Y|WDR65_ENST00000528956.1_5'Flank	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	143					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTGCAGATCAGATTTGGCCAT	0.468																																																0			1											158	157	157					1																	43636446		2203	4300	6503	43409033	SO:0001583	missense	10969			U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"EBNA1-binding protein 2"			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.428C>A	1.37:g.43636446G>T	ENSP00000236051:p.Ser143Tyr		43409033	Q96A66	Missense_Mutation	SNP	ENST00000236051.2	37	CCDS478.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.670576	0.88348	.	.	ENSG00000117395	ENST00000431635;ENST00000236051	T;T	0.57436	0.4;0.4	5.47	5.47	0.80525	.	0.108671	0.64402	D	0.000004	T	0.79155	0.4398	M	0.90870	3.155	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69142	0.962;0.962	D	0.83480	0.0064	10	0.87932	D	0	-6.2641	19.6961	0.96026	0.0:0.0:1.0:0.0	.	143;143	Q6IB29;Q99848	.;EBP2_HUMAN	Y	198;143	ENSP00000407323:S198Y;ENSP00000236051:S143Y	ENSP00000236051:S143Y	S	-	2	0	EBNA1BP2	43409033	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.271000	0.95698	2.745000	0.94114	0.650000	0.86243	TCT		0.468	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			T	43636446	G	T	43636446	3	4	120	1	0	0	0	0	1	0	0	0	4896	942	33	2	516	2	EBNA1BP2	1	43636446	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		43636446	205614175	1	31582										
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47183671	47183671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gaggctcagtgcgaagcaggCggtgactgcttgggcctttc	16	10	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:47183671C>T	ENST00000371933.3	-	1	1065	c.89G>A	c.(88-90)cGc>cAc	p.R30H	EFCAB14_ENST00000544071.1_Missense_Mutation_p.R30H	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	30							calcium ion binding (GO:0005509)										GCGAAGCAGGCGGTGACTGCT	0.532																																																0			1											86	82	83					1																	47183671		2203	4300	6503	46956258	SO:0001583	missense	100130197			AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.89G>A	1.37:g.47183671C>T	ENSP00000361001:p.Arg30His		46956258	D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	37	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.193975	0.78902	.	.	ENSG00000159658	ENST00000544071;ENST00000371933	T;T	0.50813	0.73;1.67	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	L	0.44542	1.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65084	-0.6254	10	0.87932	D	0	-2.7117	19.1736	0.93590	0.0:1.0:0.0:0.0	.	30;30;30	F5H7K3;B7Z444;O75071	.;.;K0494_HUMAN	H	30	ENSP00000442465:R30H;ENSP00000361001:R30H	ENSP00000361001:R30H	R	-	2	0	KIAA0494	46956258	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.619000	0.61218	2.836000	0.97738	0.655000	0.94253	CGC		0.532	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		T	47183671	C	T	47183671	3	4	120	1	0	0	0	0	1	0	0	0	8200	768	27	1	1442	1	KIAA0494	1	47183671	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3547225	47183671	202066950	2	31583										
SLC16A1	6566	hgsc.bcm.edu	37	chr1	113464681	113464681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agaagctgcaatcaagccacAgcctgacaagcagccaccaa	8	14	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:113464681A>G	ENST00000538576.1	-	3	1123	c.292T>C	c.(292-294)Tgt>Cgt	p.C98R	SLC16A1_ENST00000369626.3_Missense_Mutation_p.C98R|SLC16A1_ENST00000433570.4_Missense_Mutation_p.C98R	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	98					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.C98S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	ATCAAGCCACAGCCTGACAAG	0.408																																																1	Substitution - Missense(1)	central_nervous_system(1)	1											123	102	109					1																	113464681		2203	4300	6503	113266204	SO:0001583	missense	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.292T>C	1.37:g.113464681A>G	ENSP00000441065:p.Cys98Arg		113266204	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381368	0.24944	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570;ENST00000443580;ENST00000429288	T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.9	-7.71	0.01254	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.844771	0.11205	N	0.588376	T	0.63861	0.2547	L	0.57536	1.79	0.34684	D	0.725073	B;B	0.27882	0.192;0.192	B;B	0.35770	0.21;0.139	T	0.53634	-0.8411	10	0.59425	D	0.04	.	13.0852	0.59135	0.1864:0.0924:0.0:0.7212	.	98;98	Q49A45;P53985	.;MOT1_HUMAN	R	98	ENSP00000358640:C98R;ENSP00000441065:C98R;ENSP00000416167:C98R;ENSP00000445061:C98R;ENSP00000399104:C98R;ENSP00000397106:C98R	ENSP00000358640:C98R	C	-	1	0	SLC16A1	113266204	0.000000	0.05858	0.343000	0.25615	0.356000	0.29392	-1.838000	0.01687	-1.862000	0.01151	-0.468000	0.05107	TGT		0.408	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		G	113464681	A	G	113464681	3	3	120	1	0	0	0	0	1	0	0	0	14439	188	7	4	1222	4	SLC16A1	1	113464681	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	66281010	113464681	135785940	3	31584										
TCHH	7062	hgsc.bcm.edu	37	chr1	152085426	152085426	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccagtcccgtggcctggccGagagcatagtaacaagcttg	12	12	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:152085426G>A	ENST00000368804.1	-	2	266	c.267C>T	c.(265-267)ctC>ctT	p.L89L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	89	S-100-like.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.L89L(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGCCTGGCCGAGAGCATAGT	0.498																																																1	Substitution - coding silent(1)	central_nervous_system(1)	1											86	85	85					1																	152085426		1914	4122	6036	150352050	SO:0001819	synonymous_variant	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.267C>T	1.37:g.152085426G>A			150352050	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																				0.498	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152085426	G	A	152085426	2	1	120	1	0	0	0	0	0	0	0	1	15739	1045	37	1		1	TCHH	1	152085426	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	38620745	152085426	97165195	4	31585										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157771887	157771887	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	accagtacaggatcggaggaGagcctctcagggcctcacag	13	12	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:157771887G>T	ENST00000368176.3	-	5	771	c.704C>A	c.(703-705)tCt>tAt	p.S235Y	FCRL1_ENST00000358292.3_Missense_Mutation_p.S235Y|FCRL1_ENST00000491942.1_Missense_Mutation_p.S235Y|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	235	Ig-like C2-type 3.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GATCGGAGGAGAGCCTCTCAG	0.607																																					GBM(54;482 1003 11223 30131 35730)											0			1											42	43	43					1																	157771887		2203	4300	6503	156038511	SO:0001583	missense	115350			BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.704C>A	1.37:g.157771887G>T	ENSP00000357158:p.Ser235Tyr		156038511	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	37	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409648	0.42715	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.03124	4.04;4.04;4.04	4.96	4.96	0.65561	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.205916	0.35466	N	0.003189	T	0.17450	0.0419	M	0.92784	3.345	0.37549	D	0.91863	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.994;0.996;0.989	T	0.01367	-1.1373	9	.	.	.	.	13.9028	0.63815	0.0:0.0:1.0:0.0	.	235;235;235	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	Y	235	ENSP00000351039:S235Y;ENSP00000357158:S235Y;ENSP00000418130:S235Y	.	S	-	2	0	FCRL1	156038511	1.000000	0.71417	0.964000	0.40570	0.029000	0.11900	4.446000	0.60014	2.716000	0.92895	0.655000	0.94253	TCT		0.607	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		T	157771887	G	T	157771887	3	4	120	1	0	0	0	0	1	0	0	0	5813	942	33	2	679	2	FCRL1	1	157771887	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	5686461	157771887	91478734	5	31586										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158623119	158623119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcctggctcttctcgtcgccGctgtgggagcatcgggaact	13	13	2	0	rs373548086		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:158623119G>A	ENST00000368147.4	-	22	3313	c.3133C>T	c.(3133-3135)Cgg>Tgg	p.R1045W		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1045					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTCGTCGCCGCTGTGGGAGC	0.542																																																0			1						G	TRP/ARG	1,4003		0,1,2001	107	109	109		3133	1.4	0	1		109	0,8378		0,0,4189	no	missense	SPTA1	NM_003126.2	101	0,1,6190	AA,AG,GG		0.0,0.025,0.0081	probably-damaging	1045/2420	158623119	1,12381	2002	4189	6191	156889743	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3133C>T	1.37:g.158623119G>A	ENSP00000357129:p.Arg1045Trp		156889743	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.452910	0.43531	2.5E-4	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.67865	-0.29;-0.29	5.15	1.36	0.22044	Src homology-3 domain (1);	0.648067	0.11865	N	0.521990	T	0.46718	0.1407	L	0.44542	1.39	0.09310	N	1	D	0.61080	0.989	P	0.48677	0.586	T	0.31586	-0.9938	10	0.72032	D	0.01	.	8.349	0.32290	0.0774:0.0:0.3119:0.6107	.	1045	P02549	SPTA1_HUMAN	W	1045	ENSP00000357130:R1045W;ENSP00000357129:R1045W	ENSP00000357129:R1045W	R	-	1	2	SPTA1	156889743	1.000000	0.71417	0.000000	0.03702	0.268000	0.26511	2.676000	0.46883	0.183000	0.20059	0.655000	0.94253	CGG		0.542	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158623119	G	A	158623119	3	1	120	1	0	0	0	0	1	0	0	0	15155	1086	38	1	4250	1	SPTA1	1	158623119	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	851232	158623119	90627502	6	31587										
NCF2	4688	hgsc.bcm.edu	37	chr1	183532626	183532626	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tagacaccatgtcccggaccTggctgtaggggagcccgggc	15	13	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:183532626T>A	ENST00000367535.3	-	12	1372	c.1121A>T	c.(1120-1122)cAg>cTg	p.Q374L	NCF2_ENST00000367536.1_Missense_Mutation_p.Q374L|NCF2_ENST00000413720.1_Missense_Mutation_p.Q329L|NCF2_ENST00000418089.1_Missense_Mutation_p.Q293L|NCF2_ENST00000469280.1_5'UTR	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	374	OPR.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	GTCCCGGACCTGGCTGTAGGG	0.562																																																0			1											112	111	112					1																	183532626		2203	4300	6503	181799249	SO:0001583	missense	4688			BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"Tetratricopeptide (TTC) repeat domain containing"	7661	protein-coding gene	gene with protein product	"NADPH oxidase activator 2", "chronic granulomatous disease, autosomal 2"	608515	"neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.1121A>T	1.37:g.183532626T>A	ENSP00000356505:p.Gln374Leu		181799249	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455009	0.43634	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535;ENST00000420553;ENST00000419402	T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96	5.47	4.34	0.51931	Phox/Bem1p (2);	0.431941	0.26003	N	0.026923	T	0.26919	0.0659	M	0.75447	2.3	0.26347	N	0.977273	B;P;B	0.37781	0.029;0.608;0.024	B;B;B	0.42343	0.037;0.384;0.034	T	0.11518	-1.0584	10	0.27785	T	0.31	-55.7358	8.1156	0.30942	0.0:0.1569:0.0:0.8431	.	293;329;374	E9PHJ2;E9PHX3;P19878	.;.;NCF2_HUMAN	L	374;446;329;293;374;25;113	ENSP00000356506:Q374L;ENSP00000399294:Q329L;ENSP00000407217:Q293L;ENSP00000356505:Q374L;ENSP00000397228:Q25L;ENSP00000406198:Q113L	ENSP00000356505:Q374L	Q	-	2	0	NCF2	181799249	1.000000	0.71417	0.976000	0.42696	0.876000	0.50452	1.975000	0.40569	0.923000	0.37045	0.529000	0.55759	CAG		0.562	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433		A	183532626	T	A	183532626	3	1	120	1	0	0	0	0	1	0	0	0	10248	1580	55	5	475	5	NCF2	1	183532626	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	24909507	183532626	65717995	7	31588										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185171787	185171787	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cccaacctcccaaccttaggGatgatagaaacttaagaaac	6	12	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:185171787G>T	ENST00000367500.4	+	11	1690	c.1525G>T	c.(1525-1527)Gat>Tat	p.D509Y	SWT1_ENST00000367501.3_Splice_Site_p.D509Y	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	509	PINc.									breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CAACCTTAGGGATGATAGAAA	0.373																																																0			1											67	68	67					1																	185171787		2203	4300	6503	183438410	SO:0001630	splice_region_variant	54823			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1524-1G>T	1.37:g.185171787G>T			183438410	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.815025	0.32053	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.20598	2.06;2.06	5.09	4.17	0.49024	Nucleotide binding protein, PINc (1);	0.049555	0.85682	D	0.000000	T	0.16599	0.0399	L	0.28504	0.86	0.43647	D	0.996058	B	0.30281	0.275	B	0.35607	0.206	T	0.06409	-1.0828	10	0.72032	D	0.01	.	6.8989	0.24271	0.089:0.0:0.7351:0.1759	.	509	Q5T5J6	SWT1_HUMAN	Y	509	ENSP00000356471:D509Y;ENSP00000356470:D509Y	ENSP00000356470:D509Y	D	+	1	0	SWT1	183438410	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.925000	0.40074	1.277000	0.44412	0.650000	0.86243	GAT		0.373	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	Missense_Mutation	T	185171787	G	T	185171787	5	4	120	1	0	0	0	0	0	0	1	0	2041	1188	41	2	1563	2	C1orf26	1	185171787	Splice_Site	SNP	G	TCGA-F5-6813-01A-11D-1826-10	1639161	185171787	64078834	8	31589										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201017737	201017737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cttgatcttgagtgccgtgcGgaccagggcaaagagtgtgg	16	8	1	3	rs201257304		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:201017737G>A	ENST00000362061.3	-	36	4640	c.4414C>T	c.(4414-4416)Cgc>Tgc	p.R1472C	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R1453C	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1472				R -> G (in Ref. 2; AAB37235). {ECO:0000305}.	axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGTGCCGTGCGGACCAGGGCA	0.582																																																0			1						G	CYS/ARG	0,4406		0,0,2203	132	104	113		4414	5.2	1	1		113	3,8597		0,3,4297	no	missense	CACNA1S	NM_000069.2	180	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	1472/1874	201017737	3,13003	2203	4300	6503	199284360	SO:0001583	missense	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4414C>T	1.37:g.201017737G>A	ENSP00000355192:p.Arg1472Cys		199284360	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	21.4	4.140970	0.77775	0.0	3.49E-4	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97352	-4.35;-4.22	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.98689	0.9560	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99204	1.0874	10	0.87932	D	0	.	12.2213	0.54435	0.0:0.0:0.7137:0.2863	.	1472	Q13698	CAC1S_HUMAN	C	1472;1453	ENSP00000355192:R1472C;ENSP00000356307:R1453C	ENSP00000355192:R1472C	R	-	1	0	CACNA1S	199284360	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.243000	0.51392	2.549000	0.85964	0.557000	0.71058	CGC		0.582	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201017737	G	A	201017737	3	1	120	1	0	0	0	0	1	0	0	0	2553	1116	39	1	1243	1	CACNA1S	1	201017737	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	15845950	201017737	48232884	9	31590										
VASH2	79805	hgsc.bcm.edu	37	chr1	213125037	213125037	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggcggggtgctgttccacgtCaacaagagcggcttccccat	13	13	1	1	rs572856204		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:213125037C>A	ENST00000517399.1	+	1	153	c.153C>A	c.(151-153)gtC>gtA	p.V51V	VASH2_ENST00000366964.3_5'UTR|VASH2_ENST00000271776.4_Intron|VASH2_ENST00000366966.2_5'UTR|VASH2_ENST00000366965.2_Silent_p.V51V|VASH2_ENST00000366968.4_5'UTR|VASH2_ENST00000366967.2_Intron			Q86V25	VASH2_HUMAN	vasohibin 2	51					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		TGTTCCACGTCAACAAGAGCG	0.672																																																0			1											44	39	40					1																	213125037		2200	4297	6497	211191660	SO:0001819	synonymous_variant	79805			AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.153C>A	1.37:g.213125037C>A			211191660	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Silent	SNP	ENST00000517399.1	37	CCDS1511.1																																																																																				0.672	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749		A	213125037	C	A	213125037	2	1	120	1	0	0	0	0	0	0	0	1	17166	813	29	2		2	VASH2	1	213125037	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	12107300	213125037	36125584	10	31591										
ZNF678	339500	hgsc.bcm.edu	37	chr1	227842536	227842536	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtttttaattggtggtcacaActaactagccataagaaaat	7	6	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:227842536A>G	ENST00000343776.5	+	4	930	c.585A>G	c.(583-585)caA>caG	p.Q195Q	ZNF678_ENST00000397097.3_Silent_p.Q250Q|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				GGTGGTCACAACTAACTAGCC	0.363																																																0			1											90	105	100					1																	227842536		2203	4298	6501	225909159	SO:0001819	synonymous_variant	339500			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.585A>G	1.37:g.227842536A>G			225909159	Q8IVQ9	Silent	SNP	ENST00000343776.5	37																																																																																					0.363	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		G	227842536	A	G	227842536	2	3	120	1	0	0	0	0	0	0	0	1	18124	40	2	4		4	ZNF678	1	227842536	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	14717499	227842536	21408085	11	31592										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228525710	228525710	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gctgagcaggatgccatcacGctgcgggaaggccagtatgt	15	10	1	1	rs375507173		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:228525710G>A	ENST00000422127.1	+	67	16910	c.16866G>A	c.(16864-16866)acG>acA	p.T5622T	OBSCN_ENST00000366707.4_Silent_p.T3256T|OBSCN_ENST00000570156.2_Silent_p.T6579T|OBSCN_ENST00000284548.11_Silent_p.T5622T|OBSCN_ENST00000366709.4_Silent_p.T2741T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5622	SH3.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ATGCCATCACGCTGCGGGAAG	0.627													G|||	1	0.000199681	8e-04	0	5008	,	,		17724	0		0	False		,,,				2504	0															0			1						G	,	3,4393		0,3,2195	43	43	43		16866,16866	-8.7	0	1		43	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,3,6489	AA,AG,GG		0.0,0.0682,0.0231	,	5622/7969,5622/6621	228525710	3,12981	2198	4294	6492	226592333	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16866G>A	1.37:g.228525710G>A			226592333	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	6.226	0.409755	0.11812	6.82E-4	0.0	ENSG00000154358	ENST00000441106	.	.	.	4.35	-8.7	0.00851	.	.	.	.	.	T	0.48607	0.1509	.	.	.	0.37238	D	0.905976	.	.	.	.	.	.	T	0.60177	-0.7314	4	.	.	.	.	9.6739	0.40028	0.095:0.2036:0.5607:0.1407	.	.	.	.	T	238	.	.	A	+	1	0	OBSCN	226592333	0.000000	0.05858	0.000000	0.03702	0.245000	0.25701	-1.443000	0.02405	-3.412000	0.00168	-1.579000	0.00862	GCT		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228525710	G	A	228525710	2	1	120	1	0	0	0	0	0	0	0	1	10843	1074	38	1		1	OBSCN	1	228525710	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	683174	228525710	20724911	12	31593										
TRIM58	25893	hgsc.bcm.edu	37	chr1	248031152	248031152	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttctttccttttcagggtgtGagaggagtcctgagcaggta	13	7	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:248031152G>C	ENST00000366481.3	+	4	801	c.753G>C	c.(751-753)gtG>gtC	p.V251V	OR2W3_ENST00000537741.1_5'Flank	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	251						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	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)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TTCAGGGTGTGAGAGGAGTCC	0.468																																																0			1											129	122	125					1																	248031152		2203	4300	6503	246097775	SO:0001819	synonymous_variant	25893			AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.753G>C	1.37:g.248031152G>C			246097775	Q6B0H9	Silent	SNP	ENST00000366481.3	37	CCDS1636.1																																																																																				0.468	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		C	248031152	G	C	248031152	2	2	120	1	0	0	0	0	0	0	0	1	16571	1277	45	5		5	TRIM58	1	248031152	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	19505442	248031152	1219469	13	31594										
OR2M4	26245	hgsc.bcm.edu	37	chr1	248402566	248402566	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccctgcttggagctgaatgTttcttgttggctgtcatggc	12	9	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr1:248402566T>C	ENST00000306687.1	+	1	336	c.336T>C	c.(334-336)tgT>tgC	p.C112C		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	112					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C112*(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GAGCTGAATGTTTCTTGTTGG	0.453																																																1	Substitution - Nonsense(1)	breast(1)	1											155	125	135					1																	248402566		2203	4300	6503	246469189	SO:0001819	synonymous_variant	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.336T>C	1.37:g.248402566T>C			246469189	Q15611|Q8NG82	Silent	SNP	ENST00000306687.1	37	CCDS31108.1																																																																																				0.453	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		C	248402566	T	C	248402566	2	2	120	1	0	0	0	0	0	0	0	1	11043	1731	60	4		4	OR2M4	1	248402566	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	371414	248402566	848055	14	31595										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9633048	9633048	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	acacaatggacaagaatgctGaaaggaatccaaaatatcaa	7	7	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:9633048G>A	ENST00000310823.3	-	17	2243	c.2061C>T	c.(2059-2061)ttC>ttT	p.F687F	IAH1_ENST00000545602.1_Intron	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	687					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CAAGAATGCTGAAAGGAATCC	0.343																																																0			2											115	103	107					2																	9633048		2203	4300	6503	9550499	SO:0001819	synonymous_variant	6868			U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.2061C>T	2.37:g.9633048G>A			9550499	O60226	Silent	SNP	ENST00000310823.3	37	CCDS1665.1																																																																																				0.343	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			A	9633048	G	A	9633048	2	1	120	1	0	0	0	0	0	0	0	1	238	1281	45	3		3	ADAM17	2	9633048	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10		9633048	233566325	15	31596										
RBKS	64080	hgsc.bcm.edu	37	chr2	28050540	28050540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctaaggtaatgattaccaccTggcagccccttttcaagagc	8	12	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:28050540T>C	ENST00000302188.3	-	7	1441	c.689A>G	c.(688-690)cAg>cGg	p.Q230R	RBKS_ENST00000444339.2_Missense_Mutation_p.Q230R	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	230					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					GATTACCACCTGGCAGCCCCT	0.517																																																0			2											102	93	96					2																	28050540		2203	4300	6503	27904044	SO:0001583	missense	64080			BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.689A>G	2.37:g.28050540T>C	ENSP00000306817:p.Gln230Arg		27904044	A9UK04|B4DV96	Missense_Mutation	SNP	ENST00000302188.3	37	CCDS1762.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746891	0.30955	.	.	ENSG00000171174	ENST00000302188;ENST00000444339	T;T	0.75589	-0.95;-0.95	5.63	0.73	0.18271	Carbohydrate/purine kinase (1);	0.756003	0.13642	N	0.372884	T	0.51346	0.1669	N	0.08118	0	0.23150	N	0.998218	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.37753	-0.9692	10	0.36615	T	0.2	1.1854	9.0212	0.36202	0.0:0.2809:0.0:0.7191	.	230;230	B4DV96;Q9H477	.;RBSK_HUMAN	R	230	ENSP00000306817:Q230R;ENSP00000413232:Q230R	ENSP00000306817:Q230R	Q	-	2	0	RBKS	27904044	0.381000	0.25140	0.656000	0.29637	0.979000	0.70002	0.604000	0.24164	0.108000	0.17862	0.402000	0.26972	CAG		0.517	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128		C	28050540	T	C	28050540	3	2	120	1	0	0	0	0	1	0	0	0	13145	1580	55	4	287	4	RBKS	2	28050540	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	18417492	28050540	215148833	16	31597										
RTKN	84058	hgsc.bcm.edu	37	chr2	74653570	74653570	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggctggggccactgaggcagGcgagcaggggttaggcaggg	22	8	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:74653570G>A	ENST00000348227.4	+	0	1147				RTKN_ENST00000305557.5_Missense_Mutation_p.P485S|RTKN_ENST00000233330.6_Missense_Mutation_p.P448S|RTKN_ENST00000272430.5_Missense_Mutation_p.P498S	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54											breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						ACTGAGGCAGGCGAGCAGGGG	0.672																																																0			2											22	27	26					2																	74653570		2188	4271	6459	74507078	SO:0001628	intergenic_variant	6242			AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"WD repeat domain containing"	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951		2.37:g.74653570G>A			74507078	D6W5I3|Q53H85|Q86V45	Missense_Mutation	SNP	ENST00000348227.4	37	CCDS1940.1	.	.	.	.	.	.	.	.	.	.	G	8.234	0.805365	0.16467	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.28895	1.59;1.59;1.61	5.17	1.24	0.21308	.	0.130371	0.52532	D	0.000077	T	0.14313	0.0346	N	0.17082	0.46	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.21724	-1.0237	10	0.19590	T	0.45	.	5.8782	0.18840	0.175:0.3279:0.4971:0.0	.	498;485	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	S	485;498;448	ENSP00000305298:P485S;ENSP00000272430:P498S;ENSP00000233330:P448S	ENSP00000233330:P448S	P	-	1	0	RTKN	74507078	0.573000	0.26676	0.412000	0.26496	0.954000	0.61252	0.677000	0.25262	0.331000	0.23511	-0.257000	0.10917	CCT		0.672	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118		A	74653570	G	A	74653570	1	1	120	0	1	0	0	0	0	0	0	0	13759	1203	42	3		3	RTKN	2	74653570	IGR	SNP	G	TCGA-F5-6813-01A-11D-1826-10	46603030	74653570	168545803	17	31598										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109368375	109368375	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctagttcagcatgaaataaaCactctaagagcccaggaaaa	7	9	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:109368375C>T	ENST00000283195.6	+	12	1806	c.1680C>T	c.(1678-1680)aaC>aaT	p.N560N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	560					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATGAAATAAACACTCTAAGAG	0.368																																																0			2											110	133	125					2																	109368375		1508	2709	4217	108734807	SO:0001819	synonymous_variant	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1680C>T	2.37:g.109368375C>T			108734807	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																				0.368	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109368375	C	T	109368375	2	4	120	1	0	0	0	0	0	0	0	1	13065	477	17	3		3	RANBP2	2	109368375	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	34714805	109368375	133830998	18	31599										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141267507	141267507	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtgttcataccgcagcctgcTgtggaaagctcatcgcttcc	10	13	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:141267507T>C	ENST00000389484.3	-	52	9359	c.8388A>G	c.(8386-8388)acA>acG	p.T2796T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2796	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		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)		CGCAGCCTGCTGTGGAAAGCT	0.507										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)											0			2											130	112	118					2																	141267507		2203	4300	6503	140983977	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8388A>G	2.37:g.141267507T>C			140983977	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.507	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141267507	T	C	141267507	2	2	120	1	0	0	0	0	0	0	0	1	8984	1567	55	4		4	LRP1B	2	141267507	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	31899132	141267507	101931866	19	31600										
ASNSD1	54529	hgsc.bcm.edu	37	chr2	190532026	190532026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aagaattctctaaagatgttGctgctgctgctgctgacagt	10	8	1	3	rs140770284		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:190532026G>T	ENST00000260952.4	+	4	1581	c.1168G>T	c.(1168-1170)Gct>Tct	p.A390S	ASNSD1_ENST00000607062.1_Intron	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	390	Asparagine synthetase.				asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			TAAAGATGTTGCTGCTGCTGC	0.423																																																0			2											48	46	47					2																	190532026		2203	4300	6503	190240271	SO:0001583	missense	54529			AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.1168G>T	2.37:g.190532026G>T	ENSP00000260952:p.Ala390Ser		190240271	D3DPH6|Q3LIC3|Q4ZG45	Missense_Mutation	SNP	ENST00000260952.4	37	CCDS2300.1	.	.	.	.	.	.	.	.	.	.	G	1.030	-0.682182	0.03353	.	.	ENSG00000138381	ENST00000260952;ENST00000420250	T;T	0.41400	1.0;1.0	5.13	0.361	0.16107	Rossmann-like alpha/beta/alpha sandwich fold (1);Asparagine synthase (1);	0.697413	0.14112	N	0.340663	T	0.36386	0.0965	M	0.63428	1.95	0.09310	N	1	B	0.31125	0.309	B	0.31946	0.138	T	0.27297	-1.0078	10	0.16420	T	0.52	-1.5679	10.5187	0.44905	0.3441:0.0:0.6559:0.0	.	390	Q9NWL6	ASND1_HUMAN	S	390	ENSP00000260952:A390S;ENSP00000406790:A390S	ENSP00000260952:A390S	A	+	1	0	ASNSD1	190240271	0.000000	0.05858	0.003000	0.11579	0.198000	0.23893	0.298000	0.19120	-0.121000	0.11787	0.655000	0.94253	GCT		0.423	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048		T	190532026	G	T	190532026	3	4	120	1	0	0	0	0	1	0	0	0	1050	1319	46	2	1170	2	ASNSD1	2	190532026	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	49264519	190532026	52667347	20	31601										
KLF7	8609	hgsc.bcm.edu	37	chr2	207988559	207988559	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtataaactttccggcacccGttaaactgacagcggtgaac	9	11	0	2	rs201005804		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:207988559G>A	ENST00000309446.6	-	2	1048	c.672C>T	c.(670-672)aaC>aaT	p.N224N	KLF7_ENST00000458272.1_Intron|KLF7-IT1_ENST00000428777.1_RNA|KLF7_ENST00000412414.2_Silent_p.N196N|KLF7_ENST00000421199.1_Silent_p.N191N|KLF7_ENST00000423015.1_Intron|KLF7_ENST00000467833.1_Intron	NM_003709.3	NP_003700.1	O75840	KLF7_HUMAN	Kruppel-like factor 7 (ubiquitous)	224					axon guidance (GO:0007411)|dendrite morphogenesis (GO:0048813)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|large_intestine(3)|liver(1)|lung(4)|skin(1)	11				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)		TCCGGCACCCGTTAAACTGAC	0.542													G|||	1	0.000199681	0	0.0014	5008	,	,		19533	0		0	False		,,,				2504	0															0			2											84	85	85					2																	207988559		2203	4300	6503	207696804	SO:0001819	synonymous_variant	8609			AB015132	CCDS2373.1, CCDS59438.1, CCDS59439.1, CCDS59440.1	2q32	2013-01-08			ENSG00000118263	ENSG00000118263		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6350	protein-coding gene	gene with protein product		604865				9774444	Standard	NM_003709		Approved	UKLF	uc010zix.2	O75840	OTTHUMG00000132935	ENST00000309446.6:c.672C>T	2.37:g.207988559G>A			207696804	B2RB03|B7Z4F7|C9JF04|E7EWH1|L0R4P2|Q7Z3H8|Q96E51	Silent	SNP	ENST00000309446.6	37	CCDS2373.1																																																																																				0.542	KLF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256466.2	NM_003709		A	207988559	G	A	207988559	2	1	120	1	0	0	0	0	0	0	0	1	8372	1136	40	1		1	KLF7	2	207988559	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	17456533	207988559	35210814	21	31602										
IDH1	3417	hgsc.bcm.edu	37	chr2	209103949	209103949	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	taaccctctggtccaggcaaAaatggaagctaaaagagggg	12	8	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:209103949A>T	ENST00000415913.1	-	9	1381	c.1000T>A	c.(1000-1002)Ttt>Att	p.F334I	IDH1_ENST00000345146.2_Missense_Mutation_p.F334I|IDH1_ENST00000446179.1_Missense_Mutation_p.F334I	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	334					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		GTCCAGGCAAAAATGGAAGCT	0.388			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	0			2											55	54	54					2																	209103949		2203	4300	6503	208812194	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.1000T>A	2.37:g.209103949A>T	ENSP00000390265:p.Phe334Ile		208812194	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	A	32	5.190759	0.94923	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.68624	-0.34;-0.34;-0.34	5.53	5.53	0.82687	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.89378	0.6698	H	0.98980	4.39	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93636	0.6960	10	0.87932	D	0	-1.6806	15.9613	0.79933	1.0:0.0:0.0:0.0	.	334	O75874	IDHC_HUMAN	I	334	ENSP00000260985:F334I;ENSP00000410513:F334I;ENSP00000390265:F334I	ENSP00000260985:F334I	F	-	1	0	IDH1	208812194	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.230000	0.95299	2.240000	0.73641	0.477000	0.44152	TTT		0.388	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			T	209103949	A	T	209103949	3	4	120	1	0	0	0	0	1	0	0	0	7515	14	1	5	252	5	IDH1	2	209103949	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	1115390	209103949	34095424	22	31603										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220161201	220161201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tatgggacagcgggccctgcGtggctatgtaggctggcatc	16	10	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:220161201G>A	ENST00000295718.2	-	17	2588	c.2348C>T	c.(2347-2349)aCg>aTg	p.T783M	PTPRN_ENST00000497977.1_5'UTR|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.T754M|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.T693M	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	783	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T783M(1)		breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGGGCCCTGCGTGGCTATGTA	0.607																																																1	Substitution - Missense(1)	large_intestine(1)	2											80	74	76					2																	220161201		2203	4300	6503	219869445	SO:0001583	missense	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2348C>T	2.37:g.220161201G>A	ENSP00000295718:p.Thr783Met		219869445	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615140	0.66672	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	D;D;D	0.88046	-2.33;-2.33;-2.33	4.56	4.56	0.56223	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	D	0.95862	0.8653	H	0.96720	3.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97614	1.0131	10	0.87932	D	0	.	17.3328	0.87271	0.0:0.0:1.0:0.0	.	754;783	Q6NSL1;Q16849	.;PTPRN_HUMAN	M	754;783;754;693	ENSP00000386638:T754M;ENSP00000295718:T783M;ENSP00000444244:T693M	ENSP00000295718:T783M	T	-	2	0	PTPRN	219869445	1.000000	0.71417	0.944000	0.38274	0.526000	0.34562	9.734000	0.98822	2.245000	0.73994	0.655000	0.94253	ACG		0.607	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220161201	G	A	220161201	3	1	120	1	0	0	0	0	1	0	0	0	12844	1145	40	1	619	1	PTPRN	2	220161201	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	11057252	220161201	23038172	23	31604										
SGPP2	130367	hgsc.bcm.edu	37	chr2	223423167	223423167	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcggccagccccctcttcccCgtgtgtgtcatagttgtgcc	10	16	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr2:223423167C>T	ENST00000321276.7	+	5	836	c.750C>T	c.(748-750)ccC>ccT	p.P250P		NM_152386.2	NP_689599.2	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphatase 2	250					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	18		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		CCCTCTTCCCCGTGTGTGTCA	0.582																																																0			2											149	134	139					2																	223423167		2203	4300	6503	223131411	SO:0001819	synonymous_variant	130367			AF542512	CCDS2453.1	2q36.3	2010-05-26	2010-05-26		ENSG00000163082	ENSG00000163082			19953	protein-coding gene	gene with protein product		612827				12411432	Standard	NM_152386		Approved	SPP2, FLJ39004	uc010zlo.2	Q8IWX5	OTTHUMG00000133156	ENST00000321276.7:c.750C>T	2.37:g.223423167C>T			223131411	A3KPB4|Q8N8Q6	Silent	SNP	ENST00000321276.7	37	CCDS2453.1																																																																																				0.582	SGPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256856.2			T	223423167	C	T	223423167	2	4	120	1	0	0	0	0	0	0	0	1	14257	639	23	1		1	SGPP2	2	223423167	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3261966	223423167	19776206	24	31605										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9034656	9034656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gggactggaggtcgtttttgGaagaggccttgtcatccagc	15	8	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:9034656G>A	ENST00000383836.3	-	20	2919	c.2492C>T	c.(2491-2493)tCc>tTc	p.S831F	SRGAP3_ENST00000360413.3_Missense_Mutation_p.S807F	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	831					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GTCGTTTTTGGAAGAGGCCTT	0.582			T	RAF1	pilocytic astrocytoma																																		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	0			3											83	71	75					3																	9034656		2203	4300	6503	9009656	SO:0001583	missense	9901			AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2492C>T	3.37:g.9034656G>A	ENSP00000373347:p.Ser831Phe		9009656	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212068	0.58452	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.27402	1.67;2.08	5.41	5.41	0.78517	Src homology-3 domain (1);	0.117770	0.64402	D	0.000014	T	0.32675	0.0837	L	0.46157	1.445	0.54753	D	0.999983	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.08472	-1.0720	10	0.72032	D	0.01	.	18.7906	0.91973	0.0:0.0:1.0:0.0	.	807;831	O43295-2;O43295	.;SRGP2_HUMAN	F	831;807	ENSP00000373347:S831F;ENSP00000353587:S807F	ENSP00000353587:S807F	S	-	2	0	SRGAP3	9009656	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.513000	0.73742	2.526000	0.85167	0.591000	0.81541	TCC		0.582	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			A	9034656	G	A	9034656	3	1	120	1	0	0	0	0	1	0	0	0	15186	1174	41	3	819	3	SRGAP3	3	9034656	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		9034656	188987774	25	31606										
MLH1	4292	hgsc.bcm.edu	37	chr3	37050324	37050324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggtggaggaccttttttacaAcatagccacgaggagaaaag	12	7	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:37050324A>G	ENST00000231790.2	+	6	689	c.473A>G	c.(472-474)aAc>aGc	p.N158S	MLH1_ENST00000492474.1_3'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000539477.1_Intron|MLH1_ENST00000435176.1_Missense_Mutation_p.N60S|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	158					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CTTTTTTACAACATAGCCACG	0.383		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	1	Whole gene deletion(1)	ovary(1)	3											93	94	94					3																	37050324		2203	4300	6503	37025328	SO:0001583	missense	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.473A>G	3.37:g.37050324A>G	ENSP00000231790:p.Asn158Ser		37025328	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.1|27.1	4.804810|4.804810	0.90623|0.90623	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176;ENST00000429117|ENST00000456676	D;D;T|.	0.90955|.	-2.76;-2.76;-0.92|.	6.17|6.17	6.17|6.17	0.99709|0.99709	DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (3);|.	0.088124|.	0.85682|.	D|.	0.000000|.	D|D	0.84465|0.84465	0.5478|0.5478	M|M	0.90542|0.90542	3.125|3.125	0.80722|0.80722	D|D	1|1	D;D;D|.	0.60160|.	0.987;0.97;0.987|.	P;P;P|.	0.56278|.	0.718;0.718;0.795|.	D|D	0.87176|0.87176	0.2224|0.2224	10|5	0.66056|.	D|.	0.02|.	-27.2727|-27.2727	16.4837|16.4837	0.84171|0.84171	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	60;158;158|.	E9PCU2;Q53GX1;P40692|.	.;.;MLH1_HUMAN|.	S|A	158;124;124;22;60;60|150	ENSP00000231790:N158S;ENSP00000402564:N60S;ENSP00000407019:N60S|.	ENSP00000231790:N158S|.	N|T	+|+	2|1	0|0	MLH1|MLH1	37025328|37025328	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.783000|7.783000	0.85696|0.85696	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	AAC|ACA		0.383	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37050324	A	G	37050324	3	3	120	1	0	0	0	0	1	0	0	0	9647	43	2	4	495	4	MLH1	3	37050324	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	28015668	37050324	160972106	26	31607										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266197	41266197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tacctcccaagtcctgtatgAgtgggaacagggattttctc	10	10	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:41266197A>G	ENST00000349496.5	+	3	474	c.194A>G	c.(193-195)gAg>gGg	p.E65G	CTNNB1_ENST00000405570.1_Missense_Mutation_p.E65G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.E58G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.E65G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.E65G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	65					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.P16_K133del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A21_A80del(1)|p.V22_S71>A(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCCTGTATGAGTGGGAACAG	0.448		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	105	Deletion - In frame(83)|Complex - deletion inframe(15)|Unknown(7)	liver(76)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											55	54	54					3																	41266197		2203	4300	6503	41241201	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.194A>G	3.37:g.41266197A>G	ENSP00000344456:p.Glu65Gly		41241201	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287510	0.59976	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.55052	0.54;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.91	5.91	0.95273	.	0.091563	0.85682	D	0.000000	T	0.50069	0.1594	L	0.46157	1.445	0.80722	D	1	B	0.18968	0.032	B	0.20184	0.028	T	0.46596	-0.9180	10	0.66056	D	0.02	-11.2622	16.3453	0.83126	1.0:0.0:0.0:0.0	.	65	P35222	CTNB1_HUMAN	G	58;65;65;65;65;58;65;65;65	ENSP00000400508:E58G;ENSP00000385604:E65G;ENSP00000412219:E65G;ENSP00000379486:E65G;ENSP00000344456:E65G;ENSP00000411226:E58G;ENSP00000379488:E65G;ENSP00000409302:E65G;ENSP00000401599:E65G	ENSP00000344456:E65G	E	+	2	0	CTNNB1	41241201	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.519000	0.81809	2.261000	0.74972	0.533000	0.62120	GAG		0.448	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266197	A	G	41266197	3	3	120	1	0	0	0	0	1	0	0	0	4022	304	11	4	200	4	CTNNB1	3	41266197	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	4215873	41266197	156756233	27	31608										
SETD2	29072	hgsc.bcm.edu	37	chr3	47144860	47144860	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgggtttcacaatttggttcAcagctgtgattcatgaaacg	10	7	3	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:47144860A>G	ENST00000409792.3	-	7	4935	c.4893T>C	c.(4891-4893)tgT>tgC	p.C1631C		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1631	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AATTTGGTTCACAGCTGTGAT	0.333			"N, F, S, Mis"		clear cell renal carcinoma																																		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0			3											170	155	160					3																	47144860		2203	4300	6503	47119864	SO:0001819	synonymous_variant	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4893T>C	3.37:g.47144860A>G			47119864	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.333	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47144860	A	G	47144860	2	3	120	1	0	0	0	0	0	0	0	1	14168	157	6	4		4	SETD2	3	47144860	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	5878663	47144860	150877570	28	31609										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48697378	48697378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	actggggcaggttgtcctccAggagataggtgatacgagca	15	8	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:48697378A>G	ENST00000164024.4	-	1	2970	c.2690T>C	c.(2689-2691)cTg>cCg	p.L897P	CELSR3_ENST00000544264.1_Missense_Mutation_p.L897P	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	897	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTTGTCCTCCAGGAGATAGGT	0.522																																																0			3											101	89	93					3																	48697378		2203	4300	6503	48672382	SO:0001583	missense	1951			AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.2690T>C	3.37:g.48697378A>G	ENSP00000164024:p.Leu897Pro		48672382	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295968	0.60086	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.02085	4.46;4.46	5.65	5.65	0.86999	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.20251	0.0487	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.992;0.998	T	0.08534	-1.0717	9	0.87932	D	0	.	15.8723	0.79129	1.0:0.0:0.0:0.0	.	897;967	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	P	897	ENSP00000164024:L897P;ENSP00000445694:L897P	ENSP00000164024:L897P	L	-	2	0	CELSR3	48672382	1.000000	0.71417	0.996000	0.52242	0.949000	0.60115	9.331000	0.96430	2.154000	0.67381	0.448000	0.29417	CTG		0.522	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		G	48697378	A	G	48697378	3	3	120	1	0	0	0	0	1	0	0	0	3229	188	7	4	7388	4	CELSR3	3	48697378	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	1552518	48697378	149325052	29	31610										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52828867	52828867	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atcttggctctgctctccagCttggcagcctctggcttccc	9	16	4	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:52828867C>T	ENST00000449956.2	+	1	54	c.48C>T	c.(46-48)agC>agT	p.S16S	ITIH3_ENST00000416872.2_Silent_p.S16S	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	16					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		TGCTCTCCAGCTTGGCAGCCT	0.582																																																0			3											120	131	127					3																	52828867		2063	4213	6276	52803907	SO:0001819	synonymous_variant	3699				CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.48C>T	3.37:g.52828867C>T			52803907	Q3B7H5|Q53F06|Q6LAM2|Q99085	Silent	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	0.735	-0.778465	0.02929	.	.	ENSG00000162267	ENST00000273291	.	.	.	4.89	3.1	0.35709	.	0.751653	0.12829	N	0.435799	T	0.31544	0.0800	.	.	.	0.32284	N	0.567219	.	.	.	.	.	.	T	0.35724	-0.9777	6	0.12430	T	0.62	0.0215	7.4049	0.26985	0.0:0.8036:0.0:0.1964	.	.	.	.	F	13	.	ENSP00000273291:L13F	L	+	1	0	ITIH3	52803907	0.566000	0.26618	0.139000	0.22197	0.109000	0.19521	1.746000	0.38288	0.778000	0.33520	-0.218000	0.12543	CTT		0.582	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52828867	C	T	52828867	2	4	120	1	0	0	0	0	0	0	0	1	7926	796	28	3		3	ITIH3	3	52828867	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4131489	52828867	145193563	30	31611										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78667156	78667156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aggtatgtggaggggagatcGgccgtggtggtggaggagga	23	3	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:78667156G>A	ENST00000464233.1	-	27	4024	c.3911C>T	c.(3910-3912)cCg>cTg	p.P1304L	ROBO1_ENST00000495273.1_Missense_Mutation_p.P1259L|ROBO1_ENST00000467549.1_Missense_Mutation_p.P1204L|ROBO1_ENST00000436010.2_Missense_Mutation_p.P1265L	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1304					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AGGGGAGATCGGCCGTGGTGG	0.493																																																0			3											48	49	49					3																	78667156		1965	4160	6125	78749846	SO:0001583	missense	6091			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3911C>T	3.37:g.78667156G>A	ENSP00000420321:p.Pro1304Leu		78749846	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429465	0.62844	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.71934	-0.26;-0.3;-0.27;-0.61	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.78329	0.4266	L	0.32530	0.975	0.80722	D	1	D;B;D;D;D	0.89917	1.0;0.297;1.0;0.997;0.976	D;B;D;P;P	0.87578	0.998;0.026;0.998;0.668;0.668	T	0.75110	-0.3433	9	.	.	.	.	19.7984	0.96495	0.0:0.0:1.0:0.0	.	1268;1304;1259;1204;1265	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	L	1265;1259;1304;1259;1204;1308	ENSP00000406043:P1265L;ENSP00000420321:P1304L;ENSP00000420637:P1259L;ENSP00000417992:P1204L	.	P	-	2	0	ROBO1	78749846	1.000000	0.71417	0.831000	0.32960	0.014000	0.08584	9.813000	0.99286	2.753000	0.94483	0.467000	0.42956	CCG		0.493	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78667156	G	A	78667156	3	1	120	1	0	0	0	0	1	0	0	0	13550	1116	39	1	1064	1	ROBO1	3	78667156	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	25838289	78667156	119355274	31	31612										
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125295149	125295149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttgacttggtctcctctgcgAtataggagaattactactag	9	8	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:125295149A>G	ENST00000296220.5	-	5	839	c.550T>C	c.(550-552)Tcg>Ccg	p.S184P		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	184			S -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CTCCTCTGCGATATAGGAGAA	0.368																																																0			3											92	95	94					3																	125295149		2203	4300	6503	126777839	SO:0001583	missense	114885			AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.550T>C	3.37:g.125295149A>G	ENSP00000296220:p.Ser184Pro		126777839	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	37	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.287271	0.40494	.	.	ENSG00000144909	ENST00000296220	T	0.44083	0.93	5.06	3.88	0.44766	.	0.419093	0.25114	N	0.033038	T	0.32941	0.0846	M	0.62723	1.935	0.42291	D	0.992136	P	0.34909	0.475	B	0.31614	0.133	T	0.18871	-1.0323	10	0.38643	T	0.18	-1.471	3.15	0.06484	0.5794:0.2178:0.0764:0.1265	.	184	Q9BXB4	OSB11_HUMAN	P	184	ENSP00000296220:S184P	ENSP00000296220:S184P	S	-	1	0	OSBPL11	126777839	0.889000	0.30405	1.000000	0.80357	0.991000	0.79684	2.530000	0.45641	0.923000	0.37045	0.451000	0.29950	TCG		0.368	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		G	125295149	A	G	125295149	3	3	120	1	0	0	0	0	1	0	0	0	11307	333	12	4	1729	4	OSBPL11	3	125295149	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	46627993	125295149	72727281	32	31613										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130300560	130300560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gctgtgaggtgggcacagagActcaggtcagtgtggctttt	16	7	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:130300560A>G	ENST00000358511.6	+	8	3734	c.3703A>G	c.(3703-3705)Act>Gct	p.T1235A	COL6A6_ENST00000453409.2_Missense_Mutation_p.T1235A	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1235	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGGCACAGAGACTCAGGTCAG	0.448																																																0			3											98	96	97					3																	130300560		2018	4175	6193	131783250	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3703A>G	3.37:g.130300560A>G	ENSP00000351310:p.Thr1235Ala		131783250	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.666675	0.47677	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.38887	1.11;1.11	6.06	6.06	0.98353	von Willebrand factor, type A (2);	.	.	.	.	T	0.32556	0.0833	N	0.24115	0.695	0.28237	N	0.925854	P	0.52463	0.953	P	0.47603	0.551	T	0.07233	-1.0783	9	0.08179	T	0.78	.	11.5702	0.50829	0.8509:0.1491:0.0:0.0	.	1235	A6NMZ7	CO6A6_HUMAN	A	1235	ENSP00000351310:T1235A;ENSP00000399236:T1235A	ENSP00000351310:T1235A	T	+	1	0	COL6A6	131783250	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.558000	0.45879	2.324000	0.78689	0.533000	0.62120	ACT		0.448	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130300560	A	G	130300560	3	3	120	1	0	0	0	0	1	0	0	0	3709	275	10	4	3733	4	COL6A6	3	130300560	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	5005411	130300560	67721870	33	31614										
TNIK	23043	hgsc.bcm.edu	37	chr3	170885009	170885009	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gttctgttgctggtcgctggCtgtgattctttaccaagcag	12	9	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:170885009C>A	ENST00000436636.2	-	10	1168	c.824G>T	c.(823-825)aGc>aTc	p.S275I	TNIK_ENST00000475336.1_Missense_Mutation_p.S275I|TNIK_ENST00000460047.1_Missense_Mutation_p.S275I|TNIK_ENST00000488470.1_Missense_Mutation_p.S275I|TNIK_ENST00000284483.8_Missense_Mutation_p.S275I|TNIK_ENST00000369326.5_Missense_Mutation_p.S275I|TNIK_ENST00000357327.5_Missense_Mutation_p.S275I|TNIK_ENST00000470834.1_Missense_Mutation_p.S275I|TNIK_ENST00000538048.1_Missense_Mutation_p.S275I|TNIK_ENST00000341852.6_Missense_Mutation_p.S275I	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TGGTCGCTGGCTGTGATTCTT	0.408																																																0			3											136	119	125					3																	170885009		1910	4136	6046	172367703	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.824G>T	3.37:g.170885009C>A	ENSP00000399511:p.Ser275Ile		172367703	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.605352	0.46423	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834;ENST00000468757	D;D;D;D;D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.33	4.45	0.53987	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.125985	0.64402	D	0.000001	D	0.84629	0.5514	M	0.66378	2.025	0.54753	D	0.999983	B;B;B;P;B;B;B;B	0.47484	0.013;0.042;0.337;0.896;0.042;0.042;0.337;0.052	B;B;B;P;B;B;B;B	0.45753	0.024;0.015;0.392;0.492;0.015;0.015;0.392;0.025	T	0.82186	-0.0582	10	0.19147	T	0.46	.	14.2107	0.65762	0.0:0.9275:0.0:0.0725	.	275;275;275;275;275;275;275;275	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	I	275;275;275;275;275;275;275;275;275;275;249	ENSP00000399511:S275I;ENSP00000358332:S275I;ENSP00000443278:S275I;ENSP00000345352:S275I;ENSP00000284483:S275I;ENSP00000418156:S275I;ENSP00000349880:S275I;ENSP00000418916:S275I;ENSP00000418378:S275I;ENSP00000419990:S275I;ENSP00000417338:S249I	ENSP00000284483:S275I	S	-	2	0	TNIK	172367703	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.977000	0.40589	1.366000	0.46076	0.655000	0.94253	AGC		0.408	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170885009	C	A	170885009	3	1	120	1	0	0	0	0	1	0	0	0	16352	797	28	2	3354	2	TNIK	3	170885009	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	40584449	170885009	27137421	34	31615										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178947850	178947850	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctggatactgtgtagctaccTtcattttgggaattggagat	11	6	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:178947850T>C	ENST00000263967.3	+	19	2882	c.2725T>C	c.(2725-2727)Ttc>Ctc	p.F909L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	909	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.F909L(4)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGTAGCTACCTTCATTTTGGG	0.363		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	3											200	188	192					3																	178947850		1899	4124	6023	180430544	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2725T>C	3.37:g.178947850T>C	ENSP00000263967:p.Phe909Leu		180430544	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.802275	0.90538	.	.	ENSG00000121879	ENST00000263967	T	0.75477	-0.94	5.61	5.61	0.85477	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.74419	0.3714	L	0.49455	1.56	0.80722	D	1	P	0.37612	0.602	B	0.42245	0.381	T	0.77405	-0.2600	10	0.87932	D	0	-12.9985	15.802	0.78458	0.0:0.0:0.0:1.0	.	909	P42336	PK3CA_HUMAN	L	909	ENSP00000263967:F909L	ENSP00000263967:F909L	F	+	1	0	PIK3CA	180430544	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	7.611000	0.82962	2.139000	0.66308	0.477000	0.44152	TTC		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178947850	T	C	178947850	3	2	120	1	0	0	0	0	1	0	0	0	11944	1609	56	4	2795	4	PIK3CA	3	178947850	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	8062841	178947850	19074580	35	31616										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197553751	197553751	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cattttaccttcttgcagagCtggcggagttgcctttgata	10	9	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr3:197553751C>T	ENST00000425562.2	+	5	643	c.643C>T	c.(643-645)Ctg>Ttg	p.L215L	LRCH3_ENST00000438796.2_Silent_p.L215L|LRCH3_ENST00000334859.4_Silent_p.L215L|LRCH3_ENST00000414675.2_Silent_p.L215L|LRCH3_ENST00000536618.1_5'Flank|LRCH3_ENST00000441090.2_Silent_p.L89L			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	215						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		TCTTGCAGAGCTGGCGGAGTT	0.363																																																0			3											125	118	121					3																	197553751		2203	4300	6503	199038148	SO:0001819	synonymous_variant	84859			AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.643C>T	3.37:g.197553751C>T			199038148	B4E0T7|Q96FP9|Q9NT52	Silent	SNP	ENST00000425562.2	37																																																																																					0.363	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		T	197553751	C	T	197553751	2	4	120	1	0	0	0	0	0	0	0	1	8963	796	28	3		3	LRCH3	3	197553751	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	18605901	197553751	468679	36	31617										
CCKAR	886	hgsc.bcm.edu	37	chr4	26483598	26483598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gaagaagaggaccacgatgaCgatgagcatgcggatcaccc	13	10	1	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:26483598C>T	ENST00000295589.3	-	5	1143	c.949G>A	c.(949-951)Gtc>Atc	p.V317I		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	317					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	ACCACGATGACGATGAGCATG	0.637																																																0			4											135	116	123					4																	26483598		2203	4300	6503	26092696	SO:0001583	missense	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.949G>A	4.37:g.26483598C>T	ENSP00000295589:p.Val317Ile		26092696	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887200	0.91814	.	.	ENSG00000163394	ENST00000295589	T	0.39056	1.1	5.16	5.16	0.70880	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49949	0.1587	L	0.35593	1.075	0.49130	D	0.99975	D	0.76494	0.999	D	0.67900	0.954	T	0.31280	-0.9949	10	0.07813	T	0.8	.	18.622	0.91324	0.0:1.0:0.0:0.0	.	317	P32238	CCKAR_HUMAN	I	317	ENSP00000295589:V317I	ENSP00000295589:V317I	V	-	1	0	CCKAR	26092696	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	6.085000	0.71343	2.404000	0.81709	0.462000	0.41574	GTC		0.637	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			T	26483598	C	T	26483598	3	4	120	1	0	0	0	0	1	0	0	0	2886	536	19	1	341	1	CCKAR	4	26483598	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		26483598	164670678	37	31618										
AASDH	132949	hgsc.bcm.edu	37	chr4	57215996	57215996	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tttcctttttgtggcacaacTcttcctgaatgtcacatctt	5	11	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:57215996T>C	ENST00000205214.6	-	11	2101	c.1921A>G	c.(1921-1923)Agt>Ggt	p.S641G	AASDH_ENST00000513376.1_Missense_Mutation_p.S541G|AASDH_ENST00000502617.1_Missense_Mutation_p.S641G|AASDH_ENST00000451613.1_Missense_Mutation_p.S641G|AASDH_ENST00000434343.2_Missense_Mutation_p.S156G|AASDH_ENST00000602986.1_Missense_Mutation_p.S488G	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	641					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.S641G(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GTGGCACAACTCTTCCTGAAT	0.403																																																1	Substitution - Missense(1)	lung(1)	4											190	163	172					4																	57215996		2203	4300	6503	56910753	SO:0001583	missense	132949			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1921A>G	4.37:g.57215996T>C	ENSP00000205214:p.Ser641Gly		56910753	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	T	10.01	1.233405	0.22626	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	6.06	2.02	0.26589	.	0.805159	0.12194	N	0.490902	T	0.07999	0.0200	N	0.24115	0.695	0.09310	N	1	P;B;B;B	0.38078	0.617;0.383;0.383;0.049	B;B;B;B	0.36719	0.121;0.115;0.231;0.016	T	0.32877	-0.9890	10	0.18710	T	0.47	-2.6864	6.3835	0.21548	0.0:0.1395:0.2467:0.6138	.	488;641;641;641	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	G	641;541;156;641;488;641	ENSP00000205214:S641G;ENSP00000423760:S541G;ENSP00000392158:S156G;ENSP00000409656:S641G;ENSP00000421171:S641G	ENSP00000205214:S641G	S	-	1	0	AASDH	56910753	0.005000	0.15991	0.027000	0.17364	0.822000	0.46500	1.251000	0.32862	0.493000	0.27837	0.533000	0.62120	AGT		0.403	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		C	57215996	T	C	57215996	3	2	120	1	0	0	0	0	1	0	0	0	22	1551	54	4	1395	4	AASDH	4	57215996	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	30732398	57215996	133938280	38	31619										
UGT2A3	79799	hgsc.bcm.edu	37	chr4	69817093	69817093	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcataagcgtctgattgtagAtaaagctctcacacatcatt	6	9	4	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:69817093A>G	ENST00000251566.4	-	1	416	c.386T>C	c.(385-387)aTc>aCc	p.I129T	UGT2A3_ENST00000420231.2_5'Flank	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	129					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGATTGTAGATAAAGCTCTC	0.373																																																0			4											63	65	64					4																	69817093		2203	4300	6503	69851682	SO:0001583	missense	79799				CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.386T>C	4.37:g.69817093A>G	ENSP00000251566:p.Ile129Thr		69851682	Q9H6S4	Missense_Mutation	SNP	ENST00000251566.4	37	CCDS3525.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284671	0.59867	.	.	ENSG00000135220	ENST00000251566	T	0.61980	0.06	4.74	4.74	0.60224	.	0.351072	0.25587	N	0.029647	T	0.57110	0.2031	L	0.32530	0.975	0.80722	D	1	P	0.37688	0.605	B	0.43445	0.42	T	0.62803	-0.6777	10	0.87932	D	0	.	12.2413	0.54544	1.0:0.0:0.0:0.0	.	129	Q6UWM9	UD2A3_HUMAN	T	129	ENSP00000251566:I129T	ENSP00000251566:I129T	I	-	2	0	UGT2A3	69851682	0.107000	0.21998	0.003000	0.11579	0.566000	0.35808	5.132000	0.64758	1.996000	0.58369	0.482000	0.46254	ATC		0.373	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		G	69817093	A	G	69817093	3	3	120	1	0	0	0	0	1	0	0	0	16995	333	12	4	1221	4	UGT2A3	4	69817093	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	12601097	69817093	121337183	39	31620										
UGT2B28	54490	hgsc.bcm.edu	37	chr4	70156530	70156530	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	acagtaattaatgatccttcGtgagtagaacagtatttttc	7	6	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:70156530G>A	ENST00000335568.5	+	5	1312		c.e5+1		UGT2B28_ENST00000511240.1_Intron	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28						metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						ATGATCCTTCGTGAGTAGAAC	0.398																																																0			4											109	118	115					4																	70156530		2043	4237	6280	70191119	SO:0001630	splice_region_variant	54490			AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"UDP glucuronosyltransferases"	13479	protein-coding gene	gene with protein product		606497	"UDP glycosyltransferase 2 family, polypeptide B28"			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1310+1G>A	4.37:g.70156530G>A			70191119	B5BUM0|Q9BY62|Q9BY63	Splice_Site	SNP	ENST00000335568.5	37	CCDS3528.1	.	.	.	.	.	.	.	.	.	.	.	10.50	1.366935	0.24771	.	.	ENSG00000135226	ENST00000335568	.	.	.	1.85	1.85	0.25348	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3109	0.37903	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UGT2B28	70191119	1.000000	0.71417	0.860000	0.33809	0.110000	0.19582	3.081000	0.50120	1.023000	0.39654	0.184000	0.17185	.		0.398	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	Intron	A	70156530	G	A	70156530	5	1	120	1	0	0	0	0	0	0	1	0	17000	1159	40	1	1329	1	UGT2B28	4	70156530	Splice_Site	SNP	G	TCGA-F5-6813-01A-11D-1826-10	339437	70156530	120997746	40	31621										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79400650	79400650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gagggatgtctgccgcgagtCgtgtgatattcgggcctggt	17	8	1	1	rs184784250		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:79400650C>T	ENST00000264895.6	+	56	8661	c.8221C>T	c.(8221-8223)Cgt>Tgt	p.R2741C		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2737	Calx-beta 2.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TGCCGCGAGTCGTGTGATATT	0.473													C|||	1	0.000199681	0	0	5008	,	,		21541	0		0.001	False		,,,				2504	0															0			4											99	98	99					4																	79400650		2101	4221	6322	79619674	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.8221C>T	4.37:g.79400650C>T	ENSP00000264895:p.Arg2741Cys		79619674	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	15.02|15.02	2.709791|2.709791	0.48517|0.48517	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|T	0.27557|0.27557	1.66|1.66	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	0.056303|.	0.64402|.	D|.	0.000001|.	T|T	0.60650|0.60650	0.2285|0.2285	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.72075|.	0.976|.	T|T	0.62760|0.62760	-0.6786|-0.6786	10|7	0.59425|0.62326	D|D	0.04|0.03	.|.	20.308|20.308	0.98638|0.98638	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2741|.	E9PHH6|.	.|.	C|L	2741|969	ENSP00000264895:R2741C|ENSP00000422834:S969L	ENSP00000264895:R2741C|ENSP00000422834:S969L	R|S	+|+	1|2	0|0	FRAS1|FRAS1	79619674|79619674	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.016000|0.016000	0.09150|0.09150	5.499000|5.499000	0.66937|0.66937	2.875000|2.875000	0.98604|0.98604	0.644000|0.644000	0.83932|0.83932	CGT|TCG		0.473	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79400650	C	T	79400650	3	4	120	1	0	0	0	0	1	0	0	0	6061	884	31	1	8518	1	FRAS1	4	79400650	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	9244120	79400650	111753626	41	31622										
NKX6-1	4825	hgsc.bcm.edu	37	chr4	85418774	85418774	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcatcactccgggccagaagAtgggcgtccggccaggcagc	15	14	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:85418774A>C	ENST00000295886.4	-	1	829	c.608T>G	c.(607-609)aTc>aGc	p.I203S	NKX6-1_ENST00000515820.2_5'Flank	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	203	Repressor domain. {ECO:0000250}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		GGGCCAGAAGATGGGCGTCCG	0.751																																																0			4											8	9	9					4																	85418774		2003	3987	5990	85637798	SO:0001583	missense	4825			AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"Homeoboxes / ANTP class : NKL subclass"	7839	protein-coding gene	gene with protein product		602563	"NK homeobox (Drosophila), family 6, A", "NK6 transcription factor related, locus 1 (Drosophila)"	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.608T>G	4.37:g.85418774A>C	ENSP00000295886:p.Ile203Ser		85637798		Missense_Mutation	SNP	ENST00000295886.4	37	CCDS3607.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.234315	0.58886	.	.	ENSG00000163623	ENST00000295886	D	0.90844	-2.74	3.86	3.86	0.44501	.	0.000000	0.64402	D	0.000001	D	0.89763	0.6809	L	0.49126	1.545	0.80722	D	1	D	0.65815	0.995	P	0.53185	0.72	D	0.86662	0.1905	10	0.17832	T	0.49	-12.6967	11.7815	0.52018	1.0:0.0:0.0:0.0	.	203	P78426	NKX61_HUMAN	S	203	ENSP00000295886:I203S	ENSP00000295886:I203S	I	-	2	0	NKX6-1	85637798	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.233000	0.72320	1.624000	0.50355	0.397000	0.26171	ATC		0.751	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168		C	85418774	A	C	85418774	3	2	120	1	0	0	0	0	1	0	0	0	10488	333	12	4	507	4	NKX6-1	4	85418774	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	6018124	85418774	105735502	42	31623										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113462250	113462250	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aacattaatgtcatttacctGttctagtcctttaacattat	3	8	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:113462250G>A	ENST00000505019.1	-	25	5898	c.5773C>T	c.(5773-5775)Cag>Tag	p.Q1925*	RP11-402J6.1_ENST00000504009.1_RNA	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		1925						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TCATTTACCTGTTCTAGTCCT	0.363																																																0			4											41	42	42					4																	113462250		2203	4298	6501	113681699	SO:0001587	stop_gained	55345																														ENST00000505019.1:c.5773C>T	4.37:g.113462250G>A	ENSP00000424737:p.Gln1925*		113681699	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Nonsense_Mutation	SNP	ENST00000505019.1	37		.	.	.	.	.	.	.	.	.	.	G	46	12.616402	0.99682	.	.	ENSG00000138658	ENST00000505019	.	.	.	5.78	5.78	0.91487	.	0.078653	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-15.3936	20.0137	0.97470	0.0:0.0:1.0:0.0	.	.	.	.	X	1925	.	ENSP00000424737:Q1925X	Q	-	1	0	C4orf21	113681699	1.000000	0.71417	0.968000	0.41197	0.947000	0.59692	6.716000	0.74702	2.734000	0.93682	0.563000	0.77884	CAG		0.363	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113462250	G	A	113462250	4	1	120	1	0	0	0	0	0	1	0	0	2260	1386	48	3	557	3	C4orf21	4	113462250	Nonsense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	28043476	113462250	77692026	43	31624										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247363	153247363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cccaaaccctaagagtggcaTctcgagaaccgctaacaact	7	14	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr4:153247363T>C	ENST00000281708.4	-	10	2668	c.1439A>G	c.(1438-1440)gAt>gGt	p.D480G	FBXW7_ENST00000603548.1_Missense_Mutation_p.D480G|FBXW7_ENST00000393956.3_Missense_Mutation_p.D304G|FBXW7_ENST00000603841.1_Missense_Mutation_p.D480G|FBXW7_ENST00000263981.5_Missense_Mutation_p.D400G|FBXW7_ENST00000296555.5_Missense_Mutation_p.D362G	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	480					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AAGAGTGGCATCTCGAGAACC	0.408			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											93	87	89					4																	153247363		2203	4299	6502	153466813	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1439A>G	4.37:g.153247363T>C	ENSP00000281708:p.Asp480Gly		153466813	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775990	0.90195	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.96531	0.8868	H	0.96970	3.915	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97877	1.0289	10	0.87932	D	0	-23.0277	16.2962	0.82776	0.0:0.0:0.0:1.0	.	304;480;362;400	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	G	480;362;400;304	ENSP00000281708:D480G;ENSP00000296555:D362G;ENSP00000263981:D400G;ENSP00000377528:D304G	ENSP00000263981:D400G	D	-	2	0	FBXW7	153466813	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.934000	0.87649	2.304000	0.77564	0.528000	0.53228	GAT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153247363	T	C	153247363	3	2	120	1	0	0	0	0	1	0	0	0	5788	1435	50	4	696	4	FBXW7	4	153247363	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	39785113	153247363	37906913	44	31625										
C5orf49	134121	hgsc.bcm.edu	37	chr5	7835501	7835501	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgtcttaatattacctcttcGttaacatgaagtcccaggct	6	10	2	1	rs116024658	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:7835501G>A	ENST00000399810.2	-	2	726	c.258C>T	c.(256-258)aaC>aaT	p.N86N	C5orf49_ENST00000509627.1_Silent_p.N86N	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	86										large_intestine(3)|lung(5)|skin(1)	9						TTACCTCTTCGTTAACATGAA	0.343													G|||	192	0.0383387	0.1399	0.0086	5008	,	,		19430	0		0.001	False		,,,				2504	0															0			5						G		399,3251		17,365,1443	135	133	133		258	-5	0.1	5	dbSNP_132	133	4,8190		0,4,4093	no	coding-synonymous	C5orf49	NM_001089584.1		17,369,5536	AA,AG,GG		0.0488,10.9315,3.4026		86/148	7835501	403,11441	1825	4097	5922	7888501	SO:0001819	synonymous_variant	134121				CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.258C>T	5.37:g.7835501G>A			7888501		Silent	SNP	ENST00000399810.2	37	CCDS43300.1																																																																																				0.343	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584		A	7835501	G	A	7835501	2	1	120	1	0	0	0	0	0	0	0	1	2313	1136	40	1		1	C5orf49	5	7835501	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10		7835501	173079759	45	31626										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71490158	71490158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gaataaacagcatgttacagCggaaaattgcagagctcgag	11	7	0	1	rs200457818		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:71490158C>T	ENST00000296755.7	+	5	1274	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	326			R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		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)		CATGTTACAGCGGAAAATTGC	0.488																																					Melanoma(17;367 822 11631 31730 47712)											0			5											65	62	63					5																	71490158		2203	4300	6503	71525914	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.976C>T	5.37:g.71490158C>T	ENSP00000296755:p.Arg326Trp		71525914	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.214346	0.58452	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	T;T;T	0.26067	1.76;1.76;1.76	6.17	5.23	0.72850	.	0.000000	0.64402	D	0.000016	T	0.55337	0.1914	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.58929	-0.7549	10	0.87932	D	0	-9.6741	16.3651	0.83317	0.2155:0.7845:0.0:0.0	.	200;326	A2BDK6;P46821	.;MAP1B_HUMAN	W	326;343;200	ENSP00000296755:R326W;ENSP00000423444:R343W;ENSP00000423416:R200W	ENSP00000296755:R326W	R	+	1	2	MAP1B	71525914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.220000	0.32491	2.941000	0.99782	0.655000	0.94253	CGG		0.488	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71490158	C	T	71490158	3	4	120	1	0	0	0	0	1	0	0	0	9258	759	27	1	994	1	MAP1B	5	71490158	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	63654657	71490158	109425102	46	31627										
APC	324	hgsc.bcm.edu	37	chr5	112174596	112174596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcaggaatgtgtttctccatAcaggtcacggggagccaatg	13	9	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:112174596A>G	ENST00000457016.1	+	16	3685	c.3305A>G	c.(3304-3306)tAc>tGc	p.Y1102C	APC_ENST00000257430.4_Missense_Mutation_p.Y1102C|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.Y1102C			P25054	APC_HUMAN	adenomatous polyposis coli	1102	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTTTCTCCATACAGGTCACGG	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	1	Unknown(1)	skin(1)	5											91	85	87					5																	112174596		2202	4300	6502	112202495	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3305A>G	5.37:g.112174596A>G	ENSP00000413133:p.Tyr1102Cys		112202495	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	9.141	1.013775	0.19277	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94897	-2.8;-3.55;-2.8;-2.8;-2.97	5.76	4.57	0.56435	.	0.227965	0.39615	N	0.001309	D	0.89083	0.6614	N	0.24115	0.695	0.34643	D	0.720894	P;P	0.46327	0.876;0.464	B;B	0.43360	0.417;0.219	D	0.89905	0.4047	10	0.51188	T	0.08	-10.0347	7.1184	0.25429	0.566:0.1195:0.0:0.3145	.	1104;1102	Q4LE70;P25054	.;APC_HUMAN	C	1102;1084;1102;1102;1102	ENSP00000413133:Y1102C;ENSP00000423224:Y1084C;ENSP00000257430:Y1102C;ENSP00000427089:Y1102C;ENSP00000423828:Y1102C	ENSP00000257430:Y1102C	Y	+	2	0	APC	112202495	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	1.878000	0.39608	0.977000	0.38444	0.533000	0.62120	TAC		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112174596	A	G	112174596	3	3	120	1	0	0	0	0	1	0	0	0	763	391	14	4	3363	4	APC	5	112174596	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	40684438	112174596	68740664	47	31628										
APC	324	hgsc.bcm.edu	37	chr5	112175423	112175423	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtccacctgaacactatgttCaggagaccccactcatgttt	7	13	2	2	rs121913329		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:112175423C>T	ENST00000457016.1	+	16	4512	c.4132C>T	c.(4132-4134)Cag>Tag	p.Q1378*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q1378*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1378*			P25054	APC_HUMAN	adenomatous polyposis coli	1378	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1378*(47)|p.Q1378fs*7(2)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.Q1378fs*8(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)|p.Y1376fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACACTATGTTCAGGAGACCCC	0.468		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	56	Substitution - Nonsense(47)|Deletion - Frameshift(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(49)|stomach(5)|soft_tissue(1)|skin(1)	5											91	87	88					5																	112175423		2202	4300	6502	112203322	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4132C>T	5.37:g.112175423C>T	ENSP00000413133:p.Gln1378*		112203322	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.764727	0.98945	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1139	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1378	.	.	Q	+	1	0	APC	112203322	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	5.761000	0.68801	2.941000	0.99782	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175423	C	T	112175423	4	4	120	1	0	0	0	0	0	1	0	0	763	827	29	3	4190	3	APC	5	112175423	Nonsense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	827	112175423	68739837	48	31629										
SMAD5	4090	hgsc.bcm.edu	37	chr5	135489805	135489805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccttttggatctaagcaaaAagaagtttgtatcaacccat	6	8	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:135489805A>G	ENST00000545279.1	+	3	716	c.356A>G	c.(355-357)aAa>aGa	p.K119R	SMAD5_ENST00000545620.1_Missense_Mutation_p.K119R|SMAD5_ENST00000514641.2_3'UTR	NM_001001419.1|NM_005903.5	NP_001001419.1|NP_005894.3	Q99717	SMAD5_HUMAN	SMAD family member 5	119	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle contraction (GO:0060048)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|embryonic pattern specification (GO:0009880)|erythrocyte differentiation (GO:0030218)|germ cell development (GO:0007281)|intracellular signal transduction (GO:0035556)|Mullerian duct regression (GO:0001880)|osteoblast fate commitment (GO:0002051)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|large_intestine(4)|lung(3)	8			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCTAAGCAAAAAGAAGTTTGT	0.388																																																0			5											48	44	46					5																	135489805		1843	4103	5946	135517704	SO:0001583	missense	4090			U59913	CCDS75308.1	5q31	2008-02-05	2006-11-06	2004-05-26		ENSG00000113658		"SMADs"	6771	protein-coding gene	gene with protein product		603110	"MAD, mothers against decapentaplegic homolog 5 (Drosophila)", "SMAD, mothers against DPP homolog 5 (Drosophila)"	MADH5		8673135	Standard	NM_005903		Approved	Dwfc, JV5-1	uc003lbl.1	Q99717		ENST00000545279.1:c.356A>G	5.37:g.135489805A>G	ENSP00000441954:p.Lys119Arg		135517704	O14688|Q15798|Q9UQA1	Missense_Mutation	SNP	ENST00000545279.1	37		.	.	.	.	.	.	.	.	.	.	A	27.9	4.875622	0.91664	.	.	ENSG00000113658	ENST00000507118;ENST00000511116;ENST00000545279;ENST00000545620	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.87277	0.6137	M	0.83852	2.665	0.80722	D	1	D	0.56035	0.974	P	0.58928	0.848	D	0.89301	0.3626	10	0.87932	D	0	.	15.8063	0.78513	1.0:0.0:0.0:0.0	.	119	F5GWU7	.	R	119	ENSP00000425749:K119R;ENSP00000424279:K119R;ENSP00000441954:K119R;ENSP00000446474:K119R	ENSP00000425749:K119R	K	+	2	0	SMAD5	135517704	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.135000	0.66039	0.528000	0.53228	AAA		0.388	SMAD5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005903		G	135489805	A	G	135489805	3	3	120	1	0	0	0	0	1	0	0	0	14798	14	1	4	358	4	SMAD5	5	135489805	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	23314382	135489805	45425455	49	31630										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203498	140203498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtccagcctgctggtgctcaCgctgctgctgtacaccgcgc	12	16	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:140203498C>T	ENST00000529859.1	+	1	2138	c.2138C>T	c.(2137-2139)aCg>aTg	p.T713M	PCDHA5_ENST00000529619.1_Missense_Mutation_p.T713M|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T713M|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	713					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGCTCACGCTGCTGCTG	0.697																																																0			5											61	58	59					5																	140203498		2203	4299	6502	140183682	SO:0001583	missense	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2138C>T	5.37:g.140203498C>T	ENSP00000436557:p.Thr713Met		140183682	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207693	0.39003	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.14516	2.5;2.5;2.5	4.17	3.23	0.37069	.	.	.	.	.	T	0.25606	0.0623	M	0.79011	2.435	0.09310	N	1	P;D;D	0.58268	0.904;0.982;0.982	B;P;P	0.51582	0.246;0.674;0.674	T	0.08576	-1.0715	9	0.66056	D	0.02	.	8.0924	0.30807	0.0:0.7137:0.1468:0.1396	.	713;713;713	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	M	713	ENSP00000433416:T713M;ENSP00000436557:T713M;ENSP00000367366:T713M	ENSP00000367366:T713M	T	+	2	0	PCDHA5	140183682	0.002000	0.14202	0.993000	0.49108	0.302000	0.27658	1.228000	0.32588	2.046000	0.60703	0.491000	0.48974	ACG		0.697	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140203498	C	T	140203498	3	4	120	1	0	0	0	0	1	0	0	0	11558	536	19	1	2140	1	PCDHA5	5	140203498	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4713693	140203498	40711762	50	31631										
SCGB3A2	117156	hgsc.bcm.edu	37	chr5	147261095	147261095	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	acattcttccctttatggatCcattaaagcttcttctgaaa	4	10	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:147261095C>A	ENST00000296694.4	+	2	235	c.142C>A	c.(142-144)Cca>Aca	p.P48T	SCGB3A2_ENST00000504320.1_Missense_Mutation_p.P3T|C5orf46_ENST00000510432.1_Intron|SCGB3A2_ENST00000514688.1_3'UTR	NM_054023.4	NP_473364.1	Q96PL1	SG3A2_HUMAN	secretoglobin, family 3A, member 2	48						endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTATGGATCCATTAAAGCT	0.473																																																0			5											173	171	172					5																	147261095		2203	4300	6503	147241288	SO:0001583	missense	117156			AF313455	CCDS4287.1	5q32	2011-12-14			ENSG00000164265	ENSG00000164265		"Secretoglobins"	18391	protein-coding gene	gene with protein product	"uteroglobin-related protein 1", "pneumo secretory protein 1", "uteroglobin related protein 1"	606531				11682631, 22155607	Standard	NM_054023		Approved	UGRP1, LU103, PNSP1	uc003lot.2	Q96PL1	OTTHUMG00000129729	ENST00000296694.4:c.142C>A	5.37:g.147261095C>A	ENSP00000296694:p.Pro48Thr		147241288		Missense_Mutation	SNP	ENST00000296694.4	37	CCDS4287.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723909	0.68959	.	.	ENSG00000164265	ENST00000504320;ENST00000296694	T;T	0.14022	2.54;2.54	5.5	5.5	0.81552	.	0.090124	0.49305	D	0.000144	T	0.31918	0.0812	.	.	.	0.80722	D	1	D	0.63046	0.992	P	0.60415	0.874	T	0.00449	-1.1732	9	0.45353	T	0.12	-4.5118	15.2625	0.73634	0.0:1.0:0.0:0.0	.	48	Q96PL1	SG3A2_HUMAN	T	3;48	ENSP00000423930:P3T;ENSP00000296694:P48T	ENSP00000296694:P48T	P	+	1	0	SCGB3A2	147241288	0.972000	0.33761	0.672000	0.29872	0.151000	0.21798	3.542000	0.53625	2.755000	0.94549	0.555000	0.69702	CCA		0.473	SCGB3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251939.1	NM_054023		A	147261095	C	A	147261095	3	1	120	1	0	0	0	0	1	0	0	0	13938	855	30	2	148	2	SCGB3A2	5	147261095	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	7057597	147261095	33654165	51	31632										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178505825	178505825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgaagaagctgtggaatttgAgagcgagatagaagaagagc	15	3	0	7			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr5:178505825A>G	ENST00000315475.6	+	5	698	c.392A>G	c.(391-393)gAg>gGg	p.E131G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GTGGAATTTGAGAGCGAGATA	0.378																																																0			5											88	94	92					5																	178505825		2203	4300	6503	178438431	SO:0001583	missense	30832				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.392A>G	5.37:g.178505825A>G	ENSP00000324064:p.Glu131Gly		178438431	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	11.86	1.765119	0.31228	.	.	ENSG00000177932	ENST00000315475	T	0.05925	3.37	3.87	2.66	0.31614	.	.	.	.	.	T	0.04998	0.0134	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.38499	-0.9658	9	0.39692	T	0.17	-4.6231	7.2189	0.25975	0.7724:0.2276:0.0:0.0	.	131	Q86Y25	Z354C_HUMAN	G	131	ENSP00000324064:E131G	ENSP00000324064:E131G	E	+	2	0	ZNF354C	178438431	0.057000	0.20700	0.003000	0.11579	0.019000	0.09904	1.850000	0.39328	0.610000	0.30035	0.482000	0.46254	GAG		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178505825	A	G	178505825	3	3	120	1	0	0	0	0	1	0	0	0	17905	304	11	4	406	4	ZNF354C	5	178505825	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	31244730	178505825	2409435	52	31633										
TPMT	7172	hgsc.bcm.edu	37	chr6	18149270	18149270	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgccgttcacccacttgtctTgccattcttccagagttagt	7	13	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:18149270T>C	ENST00000309983.4	-	2	174	c.89A>G	c.(88-90)cAa>cGa	p.Q30R		NM_000367.2	NP_000358.1	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	30	S-adenosyl-L-methionine binding.				methylation (GO:0032259)|nucleobase-containing compound metabolic process (GO:0006139)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	thiopurine S-methyltransferase activity (GO:0008119)			large_intestine(2)|lung(1)	3	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Azathioprine(DB00993)|Bendroflumethiazide(DB00436)|Cefazolin(DB01327)|Mercaptopurine(DB01033)|Olsalazine(DB01250)|Trichlormethiazide(DB01021)	CCACTTGTCTTGCCATTCTTC	0.388																																					Colon(190;1381 2791 16728 32493)											0			6											277	246	257					6																	18149270		2203	4300	6503	18257249	SO:0001583	missense	7172				CCDS4543.1	6p22.3	2014-09-17			ENSG00000137364	ENSG00000137364	2.1.1.67		12014	protein-coding gene	gene with protein product		187680				8316220	Standard	NM_000367		Approved		uc003ncm.3	P51580	OTTHUMG00000014317	ENST00000309983.4:c.89A>G	6.37:g.18149270T>C	ENSP00000312304:p.Gln30Arg		18257249	O14806|O15423|O15424|O15425|O15426|O15515|O15548|O43213|Q5VUK6|Q9UBE6|Q9UBT8|Q9UE62	Missense_Mutation	SNP	ENST00000309983.4	37	CCDS4543.1	.	.	.	.	.	.	.	.	.	.	T	12.11	1.838576	0.32513	.	.	ENSG00000137364	ENST00000309983	T	0.63913	-0.07	5.75	0.367	0.16140	.	0.464195	0.25839	N	0.027962	T	0.23289	0.0563	L	0.49640	1.575	0.09310	N	0.999999	B;B	0.10296	0.0;0.003	B;B	0.12837	0.003;0.008	T	0.22765	-1.0207	10	0.11485	T	0.65	-11.9799	4.4231	0.11490	0.2106:0.2354:0.0:0.5541	.	30;30	Q9BS45;P51580	.;TPMT_HUMAN	R	30	ENSP00000312304:Q30R	ENSP00000312304:Q30R	Q	-	2	0	TPMT	18257249	0.465000	0.25815	0.957000	0.39632	0.998000	0.95712	0.577000	0.23758	0.180000	0.19960	0.528000	0.53228	CAA		0.388	TPMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039960.1			C	18149270	T	C	18149270	3	2	120	1	0	0	0	0	1	0	0	0	16449	1812	63	4	680	4	TPMT	6	18149270	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10		18149270	152965797	53	31634										
PSORS1C2	170680	hgsc.bcm.edu	37	chr6	31105792	31105792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gaggtcggttgtccacctcaGgggcaggaggccaggggttt	18	9	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:31105792G>A	ENST00000259845.4	-	2	670	c.347C>T	c.(346-348)cCt>cTt	p.P116L	PSORS1C1_ENST00000259881.9_Intron|PSORS1C1_ENST00000481450.2_5'Flank|PSORS1C1_ENST00000547221.1_Intron	NM_014069.2	NP_054788.2	Q9UIG4	PS1C2_HUMAN	psoriasis susceptibility 1 candidate 2	116						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						GTCCACCTCAGGGGCAGGAGG	0.642																																																0			6											28	30	29					6																	31105792		1503	2689	4192	31213771	SO:0001583	missense	170680			AB031480	CCDS4694.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204538	ENSG00000204538			17199	protein-coding gene	gene with protein product		613526	"chromosome 6 open reading frame 17"	C6orf17			Standard	NM_014069		Approved	SPR1	uc003nso.4	Q9UIG4	OTTHUMG00000031081	ENST00000259845.4:c.347C>T	6.37:g.31105792G>A	ENSP00000259845:p.Pro116Leu		31213771	Q5STD0	Missense_Mutation	SNP	ENST00000259845.4	37	CCDS4694.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075243	0.76415	.	.	ENSG00000204538	ENST00000259845	T	0.25414	1.8	4.82	4.82	0.62117	.	0.000000	0.45606	D	0.000346	T	0.22003	0.0530	L	0.34521	1.04	0.49915	D	0.999837	D	0.57257	0.979	P	0.54270	0.747	T	0.01409	-1.1362	10	0.87932	D	0	-0.7565	13.2517	0.60055	0.0:0.0:1.0:0.0	.	116	Q9UIG4	PS1C2_HUMAN	L	116	ENSP00000259845:P116L	ENSP00000259845:P116L	P	-	2	0	PSORS1C2	31213771	0.999000	0.42202	0.998000	0.56505	0.887000	0.51463	2.724000	0.47285	2.511000	0.84671	0.579000	0.79373	CCT		0.642	PSORS1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076115.3			A	31105792	G	A	31105792	3	1	120	1	0	0	0	0	1	0	0	0	12749	1000	35	3	67	3	PSORS1C2	6	31105792	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	12956522	31105792	140009275	54	31635										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778963	31778963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcaggcggtgcgcagccgccTcacggctcgcttgttctggc	15	15	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:31778963T>C	ENST00000375654.4	-	2	976	c.787A>G	c.(787-789)Agg>Ggg	p.R263G	HSPA1L_ENST00000417199.3_Missense_Mutation_p.R263G	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	263					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CGCAGCCGCCTCACGGCTCGC	0.552																																																0			6											59	64	62					6																	31778963		2203	4300	6503	31886942	SO:0001583	missense	3305			D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.787A>G	6.37:g.31778963T>C	ENSP00000364805:p.Arg263Gly		31886942	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	37	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877175	0.51801	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653;ENST00000424494	T;T	0.01051	5.4;5.4	5.26	-0.22	0.13130	.	0.000000	0.36444	N	0.002598	T	0.02418	0.0074	M	0.67625	2.065	0.54753	D	0.999983	D	0.76494	0.999	D	0.87578	0.998	T	0.32161	-0.9917	10	0.87932	D	0	-10.4254	13.6097	0.62071	0.0:0.0:0.5926:0.4074	.	263	P34931	HS71L_HUMAN	G	263;263;208;153	ENSP00000364805:R263G;ENSP00000387691:R263G	ENSP00000364804:R208G	R	-	1	2	HSPA1L	31886942	0.934000	0.31675	0.994000	0.49952	0.791000	0.44710	-0.027000	0.12371	-0.155000	0.11098	0.397000	0.26171	AGG		0.552	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			C	31778963	T	C	31778963	3	2	120	1	0	0	0	0	1	0	0	0	7431	1550	54	4	1142	4	HSPA1L	6	31778963	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	673171	31778963	139336104	55	31636										
HLA-DPA1	3113	hgsc.bcm.edu	37	chr6	33037508	33037508	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agccagcccgccctgagcctCaaaggaaaaggcttggccaa	11	14	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:33037508C>A	ENST00000419277.1	-	3	385	c.256G>T	c.(256-258)Gag>Tag	p.E86*	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Nonsense_Mutation_p.E86*	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	86	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CCCTGAGCCTCAAAGGAAAAG	0.478																																																0			6											90	96	94					6																	33037508		1511	2709	4220	33145486	SO:0001587	stop_gained	3113			X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.256G>T	6.37:g.33037508C>A	ENSP00000393566:p.Glu86*		33145486	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Nonsense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629286	0.87560	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	.	.	.	3.08	3.08	0.35506	.	1.174860	0.06490	U	0.734532	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.3887	0.55347	0.0:1.0:0.0:0.0	.	.	.	.	X	86	.	ENSP00000393566:E86X	E	-	1	0	HLA-DPA1	33145486	0.898000	0.30612	0.839000	0.33178	0.987000	0.75469	0.995000	0.29706	1.647000	0.50633	0.643000	0.83706	GAG		0.478	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554		A	33037508	C	A	33037508	4	1	120	1	0	0	0	0	0	1	0	0	7223	835	29	2	538	2	HLA-DPA1	6	33037508	Nonsense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	1258545	33037508	138077559	56	31637										
STK38	11329	hgsc.bcm.edu	37	chr6	36507927	36507927	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctttggtcattgtcacccttTcctttgtgtggttactcatg	8	10	3	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:36507927T>C	ENST00000229812.7	-	2	338	c.53A>G	c.(52-54)gAa>gGa	p.E18G		NM_007271.2	NP_009202.1			serine/threonine kinase 38											NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGTCACCCTTTCCTTTGTGTG	0.388																																					Colon(180;997 3561 16158)											0			6											274	258	264					6																	36507927		2203	4300	6503	36615905	SO:0001583	missense	11329				CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.53A>G	6.37:g.36507927T>C	ENSP00000229812:p.Glu18Gly		36615905		Missense_Mutation	SNP	ENST00000229812.7	37	CCDS4822.1	.	.	.	.	.	.	.	.	.	.	T	31	5.090105	0.94149	.	.	ENSG00000112079	ENST00000229812	T	0.52295	0.67	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.56804	0.2010	M	0.81341	2.54	0.80722	D	1	D	0.56287	0.975	P	0.55161	0.77	T	0.63686	-0.6581	10	0.56958	D	0.05	.	15.5485	0.76129	0.0:0.0:0.0:1.0	.	18	Q15208	STK38_HUMAN	G	18	ENSP00000229812:E18G	ENSP00000229812:E18G	E	-	2	0	STK38	36615905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.154000	0.67381	0.477000	0.44152	GAA		0.388	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		C	36507927	T	C	36507927	3	2	120	1	0	0	0	0	1	0	0	0	15342	1783	62	4	1396	4	STK38	6	36507927	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	3470419	36507927	134607140	57	31638										
UBR2	23304	hgsc.bcm.edu	37	chr6	42647492	42647492	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aagccattttgaacatttatGtagctatctttccctaccaa	4	10	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:42647492G>C	ENST00000372899.1	+	42	4898	c.4640G>C	c.(4639-4641)tGt>tCt	p.C1547S	UBR2_ENST00000372901.1_Missense_Mutation_p.C1547S|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1547					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GAACATTTATGTAGCTATCTT	0.328																																																0			6											124	107	113					6																	42647492		2202	4299	6501	42755470	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.4640G>C	6.37:g.42647492G>C	ENSP00000361990:p.Cys1547Ser		42755470	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813636	0.90790	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.59906	0.23;0.23	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.71508	0.3348	M	0.73319	2.225	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.973	T	0.64575	-0.6375	10	0.30854	T	0.27	-9.0789	20.4777	0.99188	0.0:0.0:1.0:0.0	.	1547;1547	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	S	1547	ENSP00000361990:C1547S;ENSP00000361992:C1547S	ENSP00000361990:C1547S	C	+	2	0	UBR2	42755470	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.364000	0.90105	2.840000	0.97914	0.655000	0.94253	TGT		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		C	42647492	G	C	42647492	3	2	120	1	0	0	0	0	1	0	0	0	16942	1377	48	5	4952	5	UBR2	6	42647492	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	6139565	42647492	128467575	58	31639										
PHF3	23469	hgsc.bcm.edu	37	chr6	64423171	64423171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cattcggaggccagaaaggcGccatagtgacccttggggta	14	10	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:64423171G>A	ENST00000262043.3	+	16	6027	c.5687G>A	c.(5686-5688)cGc>cAc	p.R1896H	PHF3_ENST00000393387.1_Missense_Mutation_p.R1896H			Q92576	PHF3_HUMAN	PHD finger protein 3	1896					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			CCAGAAAGGCGCCATAGTGAC	0.493																																					GBM(135;136 1820 29512 34071 46235)											0			6											74	83	80					6																	64423171		2203	4300	6503	64481130	SO:0001583	missense	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.5687G>A	6.37:g.64423171G>A	ENSP00000262043:p.Arg1896His		64481130	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319786	0.41096	.	.	ENSG00000118482	ENST00000262043;ENST00000393387	T;T	0.39229	1.09;1.09	5.97	5.11	0.69529	.	0.000000	0.40144	N	0.001176	T	0.14399	0.0348	L	0.29908	0.895	0.47862	D	0.999539	P	0.39022	0.655	B	0.27076	0.076	T	0.03374	-1.1043	9	.	.	.	-1.9023	15.3109	0.74031	0.0669:0.0:0.9331:0.0	.	1896	Q92576	PHF3_HUMAN	H	1896	ENSP00000262043:R1896H;ENSP00000377048:R1896H	.	R	+	2	0	PHF3	64481130	1.000000	0.71417	0.979000	0.43373	0.996000	0.88848	4.810000	0.62598	1.539000	0.49286	0.655000	0.94253	CGC		0.493	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			A	64423171	G	A	64423171	3	1	120	1	0	0	0	0	1	0	0	0	11867	1087	38	1	5745	1	PHF3	6	64423171	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	21775679	64423171	106691896	59	31640										
MYO6	4646	hgsc.bcm.edu	37	chr6	76566848	76566848	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tggagcaagcaaacaatgctCgtgatgccctggcaaagaca	11	10	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:76566848C>G	ENST00000369977.3	+	13	1397	c.1258C>G	c.(1258-1260)Cgt>Ggt	p.R420G	MYO6_ENST00000369981.3_Missense_Mutation_p.R420G|MYO6_ENST00000369985.4_Missense_Mutation_p.R420G|MYO6_ENST00000369975.1_Missense_Mutation_p.R420G	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	420	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AAACAATGCTCGTGATGCCCT	0.368																																																0			6											150	134	140					6																	76566848		2203	4300	6503	76623568	SO:0001583	missense	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1258C>G	6.37:g.76566848C>G	ENSP00000358994:p.Arg420Gly		76623568	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.439281	0.63067	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.92766	0.7700	H	0.99565	4.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95427	0.8513	10	0.87932	D	0	.	19.9764	0.97312	0.0:1.0:0.0:0.0	.	420;420	Q9UM54-2;Q9UM54-1	.;.	G	420	ENSP00000358998:R420G;ENSP00000359002:R420G;ENSP00000358994:R420G;ENSP00000358992:R420G	ENSP00000358992:R420G	R	+	1	0	MYO6	76623568	1.000000	0.71417	0.809000	0.32408	0.048000	0.14542	5.740000	0.68629	2.727000	0.93392	0.585000	0.79938	CGT		0.368	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76566848	C	G	76566848	3	3	120	1	0	0	0	0	1	0	0	0	10111	884	31	5	1304	5	MYO6	6	76566848	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	12143677	76566848	94548219	60	31641										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94066483	94066483	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agcaaagagcctctgggatcGgcttaagtcagaaactccat	10	10	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:94066483G>T	ENST00000369303.4	-	5	1460	c.1276C>A	c.(1276-1278)Cga>Aga	p.R426R		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	426	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.R426*(1)|p.R426R(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CTCTGGGATCGGCTTAAGTCA	0.418																																																2	Substitution - Nonsense(1)|Substitution - coding silent(1)	lung(2)	6											112	112	112					6																	94066483		2203	4300	6503	94123204	SO:0001819	synonymous_variant	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1276C>A	6.37:g.94066483G>T			94123204	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																				0.418	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	94066483	G	T	94066483	2	4	120	1	0	0	0	0	0	0	0	1	5185	1124	39	2		2	EPHA7	6	94066483	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	17499635	94066483	77048584	61	31642										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102516287	102516287	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aagtgccagcgtcggttaaaAcataagccacaggccccagt	10	12	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:102516287A>G	ENST00000421544.1	+	16	3118	c.2628A>G	c.(2626-2628)aaA>aaG	p.K876K	GRIK2_ENST00000369138.1_3'UTR|GRIK2_ENST00000369134.4_Silent_p.K827K|GRIK2_ENST00000369137.3_Silent_p.K800K|GRIK2_ENST00000413795.1_3'UTR	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	876					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GTCGGTTAAAACATAAGCCAC	0.408																																																0			6											113	103	106					6																	102516287		2203	4300	6503	102622980	SO:0001819	synonymous_variant	2901				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2628A>G	6.37:g.102516287A>G			102622980	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																				0.408	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102516287	A	G	102516287	2	3	120	1	0	0	0	0	0	0	0	1	6795	40	2	4		4	GRIK2	6	102516287	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	8449804	102516287	68598780	62	31643										
TRAF3IP2	10758	hgsc.bcm.edu	37	chr6	111884188	111884188	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cttcttagcatttgggaagaGcacagggatgaatctgaaat	11	6	2	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:111884188G>C	ENST00000340026.6	-	9	2152	c.1558C>G	c.(1558-1560)Ctc>Gtc	p.L520V	TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2-AS1_ENST00000606892.1_RNA|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.L510V|TRAF3IP2-AS1_ENST00000442928.2_RNA|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.L511V|TRAF3IP2-AS1_ENST00000438298.2_RNA|TRAF3IP2_ENST00000368731.2_5'UTR|TRAF3IP2_ENST00000392556.4_Missense_Mutation_p.L99V|TRAF3IP2-AS1_ENST00000456352.2_RNA|TRAF3IP2-AS1_ENST00000440395.1_RNA|TRAF3IP2-AS1_ENST00000449449.2_RNA|TRAF3IP2_ENST00000368735.1_Missense_Mutation_p.L55V			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	520	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		TTTGGGAAGAGCACAGGGATG	0.348																																																0			6											90	76	81					6																	111884188		2203	4300	6503	111990881	SO:0001583	missense	10758			AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.1558C>G	6.37:g.111884188G>C	ENSP00000345984:p.Leu520Val		111990881	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	G	25.1	4.600292	0.87055	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000392556;ENST00000340026;ENST00000359831;ENST00000368735	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.43669	-0.9377	10	0.54805	T	0.06	-27.8804	20.3437	0.98782	0.0:0.0:1.0:0.0	.	510	Q7Z6Q1	.	V	520;511;99;520;510;55	ENSP00000357750:L511V;ENSP00000376339:L99V;ENSP00000345984:L520V;ENSP00000352889:L510V;ENSP00000357724:L55V	ENSP00000345984:L520V	L	-	1	0	TRAF3IP2	111990881	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.735000	0.74806	2.815000	0.96918	0.561000	0.74099	CTC		0.348	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			C	111884188	G	C	111884188	3	2	120	1	0	0	0	0	1	0	0	0	16481	971	34	5	174	5	TRAF3IP2	6	111884188	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	9367901	111884188	59230879	63	31644										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119301420	119301420	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcttcaagctcttgcgtaagCcgctgtcgttcttgcgtaaa	9	11	4	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:119301420C>A	ENST00000338891.7	-	10	2627	c.2184G>T	c.(2182-2184)cgG>cgT	p.R728R	FAM184A_ENST00000521531.1_Silent_p.R728R|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Silent_p.R608R|FAM184A_ENST00000352896.5_Silent_p.R608R	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	728						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CTTGCGTAAGCCGCTGTCGTT	0.423																																																0			6											123	116	118					6																	119301420		1907	4127	6034	119343119	SO:0001819	synonymous_variant	79632			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2184G>T	6.37:g.119301420C>A			119343119	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																				0.423	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119301420	C	A	119301420	2	1	120	1	0	0	0	0	0	0	0	1	5527	726	26	2		2	FAM184A	6	119301420	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	7417232	119301420	51813647	64	31645										
UST	10090	hgsc.bcm.edu	37	chr6	149262525	149262525	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aagcacggatttaatttggtCacatcagacattcacaacaa	6	9	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:149262525C>T	ENST00000367463.4	+	3	505	c.402C>T	c.(400-402)gtC>gtT	p.V134V		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	134					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		TTAATTTGGTCACATCAGACA	0.423																																																0			6											182	169	173					6																	149262525		2203	4300	6503	149304218	SO:0001819	synonymous_variant	10090			AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.402C>T	6.37:g.149262525C>T			149304218	B2RCX6	Silent	SNP	ENST00000367463.4	37	CCDS5213.1																																																																																				0.423	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		T	149262525	C	T	149262525	2	4	120	1	0	0	0	0	0	0	0	1	17133	813	29	3		3	UST	6	149262525	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	29961105	149262525	21852542	65	31646										
QKI	9444	hgsc.bcm.edu	37	chr6	163987757	163987757	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	attgcaatttaactaggtgcGgtggctactaaagttcgaag	11	6	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr6:163987757G>A	ENST00000361752.3	+	7	1490	c.939G>A	c.(937-939)gcG>gcA	p.A313A	QKI_ENST00000275262.7_3'UTR|QKI_ENST00000361195.2_Silent_p.A305A|QKI_ENST00000392127.2_3'UTR|QKI_ENST00000453779.2_3'UTR	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	313					long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		AACTAGGTGCGGTGGCTACTA	0.398																																																0			6											113	97	102					6																	163987757		2203	4300	6503	163907747	SO:0001819	synonymous_variant	9444			AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531			21100	protein-coding gene	gene with protein product		609590	"quaking homolog, KH domain RNA binding (mouse)"			10535969	Standard	NM_006775		Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.939G>A	6.37:g.163987757G>A			163907747	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	Silent	SNP	ENST00000361752.3	37	CCDS5285.1	.	.	.	.	.	.	.	.	.	.	G	4.512	0.094926	0.08681	.	.	ENSG00000112531	ENST00000537883;ENST00000544361	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	T	0.71921	0.3397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68599	-0.5366	4	.	.	.	-1.6504	20.1358	0.98028	0.0:0.0:1.0:0.0	.	.	.	.	S	210;147	.	.	G	+	1	0	QKI	163907747	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.151000	0.77411	2.833000	0.97629	0.585000	0.79938	GGT		0.398	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043016.2	NM_006775		A	163987757	G	A	163987757	2	1	120	1	0	0	0	0	0	0	0	1	12910	1103	39	1		1	QKI	6	163987757	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	14725232	163987757	7127310	66	31647										
PHF14	9678	hgsc.bcm.edu	37	chr7	11076698	11076698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tagagaatgaacaagaaaagCttcatgtagaatataataag	8	3	1	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:11076698C>T	ENST00000403050.3	+	10	2412	c.1960C>T	c.(1960-1962)Ctt>Ttt	p.L654F	PHF14_ENST00000445996.2_Missense_Mutation_p.L369F	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	654					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		ACAAGAAAAGCTTCATGTAGA	0.269																																																0			7											33	31	31					7																	11076698		1772	4035	5807	11043223	SO:0001583	missense	9678			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1960C>T	7.37:g.11076698C>T	ENSP00000385795:p.Leu654Phe		11043223	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646317	0.67358	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	T;T	0.72725	-0.4;-0.68	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.78761	0.4334	L	0.29908	0.895	0.80722	D	1	D;D;D;P	0.71674	0.997;0.995;0.998;0.493	D;D;D;B	0.78314	0.991;0.969;0.991;0.066	T	0.80139	-0.1507	10	0.87932	D	0	.	20.2192	0.98319	0.0:1.0:0.0:0.0	.	369;369;654;654	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	F	654;369	ENSP00000385795:L654F;ENSP00000403907:L369F	ENSP00000385795:L654F	L	+	1	0	PHF14	11043223	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.469000	0.80959	2.780000	0.95670	0.655000	0.94253	CTT		0.269	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		T	11076698	C	T	11076698	3	4	120	1	0	0	0	0	1	0	0	0	11856	797	28	3	1998	3	PHF14	7	11076698	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		11076698	148061965	67	31648										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21906230	21906230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gaagaaaagtttaatacagaAgctgattcttctgagagcaa	9	5	2	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:21906230A>G	ENST00000409508.3	+	71	11670	c.11639A>G	c.(11638-11640)aAg>aGg	p.K3880R	DNAH11_ENST00000328843.6_Missense_Mutation_p.K3887R	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3887					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTAATACAGAAGCTGATTCTT	0.428									Kartagener syndrome																																							0			7											79	79	79					7																	21906230		1853	4094	5947	21872755	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.11639A>G	7.37:g.21906230A>G	ENSP00000475939:p.Lys3880Arg		21872755	Q9UJ82	Silent	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	A	12.97	2.097580	0.37048	.	.	ENSG00000105877	ENST00000328843	T	0.10382	2.88	5.81	5.81	0.92471	Dynein heavy chain (1);	0.086087	0.85682	D	0.000000	T	0.08403	0.0209	.	.	.	0.54753	D	0.999982	P	0.35628	0.513	B	0.35510	0.204	T	0.33523	-0.9865	9	0.10902	T	0.67	.	15.8235	0.78678	1.0:0.0:0.0:0.0	.	3887	Q96DT5	DYH11_HUMAN	R	3887	ENSP00000330671:K3887R	ENSP00000330671:K3887R	K	+	2	0	DNAH11	21872755	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.322000	0.65852	2.224000	0.72417	0.533000	0.62120	AAG		0.428	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21906230	A	G	21906230	3	3	120	1	0	0	0	0	1	0	0	0	4610	72	3	4	11943	4	DNAH11	7	21906230	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	10829532	21906230	137232433	68	31649										
WIPF3	644150	hgsc.bcm.edu	37	chr7	29928974	29928974	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtggaagactttccccctccGgatgaatataaaccatgcca	8	12	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:29928974G>A	ENST00000409290.1	+	6	1302	c.1302G>A	c.(1300-1302)ccG>ccA	p.P434P	WIPF3_ENST00000242140.5_Silent_p.P434P|WIPF3_ENST00000409123.1_Silent_p.P434P	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	434					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						TTCCCCCTCCGGATGAATATA	0.448																																																0			7											120	110	113					7																	29928974		1886	4115	6001	29895499	SO:0001819	synonymous_variant	644150			AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.1302G>A	7.37:g.29928974G>A			29895499	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																				0.448	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			A	29928974	G	A	29928974	2	1	120	1	0	0	0	0	0	0	0	1	17409	1103	39	1		1	WIPF3	7	29928974	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	8022744	29928974	129209689	69	31650										
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35674831	35674831	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atgctaaggagaatcgcagcTcgtgagaacgtgtacatcca	11	9	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:35674831T>C	ENST00000396081.1	-	6	1659	c.855A>G	c.(853-855)cgA>cgG	p.R285R	HERPUD2_ENST00000426180.1_5'UTR|HERPUD2_ENST00000311350.3_Silent_p.R285R	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	285					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						GAATCGCAGCTCGTGAGAACG	0.413																																																0			7											184	165	171					7																	35674831		2203	4300	6503	35641356	SO:0001819	synonymous_variant	64224			BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.855A>G	7.37:g.35674831T>C			35641356	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	37	CCDS5446.1																																																																																				0.413	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		C	35674831	T	C	35674831	2	2	120	1	0	0	0	0	0	0	0	1	7085	1538	54	4		4	HERPUD2	7	35674831	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	5745857	35674831	123463832	70	31651										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50514774	50514774	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cagattcaacattgtcagaaTcaataattgcagaatatttc	5	7	3	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:50514774T>C	ENST00000419119.1	-	2	1765	c.212A>G	c.(211-213)gAt>gGt	p.D71G	FIGNL1_ENST00000435566.1_Intron|FIGNL1_ENST00000356889.4_Missense_Mutation_p.D71G|FIGNL1_ENST00000433017.1_Missense_Mutation_p.D71G|FIGNL1_ENST00000395556.2_Missense_Mutation_p.D71G			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	71					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				ATTGTCAGAATCAATAATTGC	0.368																																																0			7											87	83	84					7																	50514774		2203	4300	6503	50482268	SO:0001583	missense	63979			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.212A>G	7.37:g.50514774T>C	ENSP00000410811:p.Asp71Gly		50482268	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939096	0.73557	.	.	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119;ENST00000436590;ENST00000422854;ENST00000440350	T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.46946	0.1419	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48843	-0.8999	10	0.87932	D	0	-23.2158	15.6587	0.77165	0.0:0.0:0.0:1.0	.	71	Q6PIW4	FIGL1_HUMAN	G	71	ENSP00000349356:D71G;ENSP00000378924:D71G;ENSP00000399997:D71G;ENSP00000410811:D71G;ENSP00000394070:D71G;ENSP00000403012:D71G;ENSP00000388471:D71G	ENSP00000349356:D71G	D	-	2	0	FIGNL1	50482268	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.563000	0.82314	2.164000	0.68074	0.460000	0.39030	GAT		0.368	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		C	50514774	T	C	50514774	3	2	120	1	0	0	0	0	1	0	0	0	5911	1435	50	4	1816	4	FIGNL1	7	50514774	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	14839943	50514774	108623889	71	31652										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98493411	98493411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atcattttctggattttgtgAaacagatttacaaggagctt	8	5	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:98493411A>G	ENST00000359863.4	+	7	684	c.475A>G	c.(475-477)Aaa>Gaa	p.K159E	TRRAP_ENST00000446306.3_Missense_Mutation_p.K159E|TRRAP_ENST00000355540.3_Missense_Mutation_p.K159E	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	159					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGATTTTGTGAAACAGATTTA	0.274																																																0			7											82	79	80					7																	98493411		2199	4298	6497	98331347	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.475A>G	7.37:g.98493411A>G	ENSP00000352925:p.Lys159Glu		98331347	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091903	0.76756	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.63913	3.6;-0.07	5.63	5.63	0.86233	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	M	0.68317	2.08	0.80722	D	1	B;B	0.16603	0.018;0.01	B;B	0.20767	0.031;0.014	T	0.57435	-0.7812	10	0.21540	T	0.41	.	16.1358	0.81487	1.0:0.0:0.0:0.0	.	159;159	Q9Y4A5-2;Q9Y4A5	.;TRRAP_HUMAN	E	159	ENSP00000352925:K159E;ENSP00000347733:K159E	ENSP00000347733:K159E	K	+	1	0	TRRAP	98331347	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.014000	0.93635	2.261000	0.74972	0.460000	0.39030	AAA		0.274	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98493411	A	G	98493411	3	3	120	1	0	0	0	0	1	0	0	0	16641	247	9	4	497	4	TRRAP	7	98493411	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	47978637	98493411	60645252	72	31653										
RBM28	55131	hgsc.bcm.edu	37	chr7	127953300	127953300	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tttggctttttgggatggacGggcttcactttgcctttgtc	12	8	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:127953300G>A	ENST00000223073.2	-	18	2187	c.2073C>T	c.(2071-2073)ccC>ccT	p.P691P	RBM28_ENST00000481788.1_5'UTR|RBM28_ENST00000415472.2_Silent_p.P550P	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	691					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						TGGGATGGACG